diff --git a/cl-base.owl b/cl-base.owl index 0d594722c..83cd211fd 100644 --- a/cl-base.owl +++ b/cl-base.owl @@ -8,16 +8,12 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" - xmlns:core="http://purl.obolibrary.org/obo/uberon/core#" xmlns:foaf="http://xmlns.com/foaf/0.1/" - xmlns:pato="http://purl.obolibrary.org/obo/pato#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:terms="http://purl.org/dc/terms/" - xmlns:uberon="http://purl.obolibrary.org/obo/uberon#" - xmlns:ubprop="http://purl.obolibrary.org/obo/ubprop#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + An ontology of cell types. Cell Ontology @@ -33,7 +29,7 @@ See PMID:15693950, PMID:12799354, PMID:20123131, PMID:21208450; Contact Alexander Diehl, addiehl@buffalo.edu, University at Buffalo. - 2024-02-13 + 2024-04-05 @@ -51,17 +47,13 @@ - - symbol - + - - definition - + @@ -85,25 +77,19 @@ - - expand expression to - + - - preferred_root - + - - term replaced by - + @@ -127,17 +113,13 @@ - - - + - - - + @@ -147,7 +129,6 @@ 2023-03-31T09:17:34Z a subset of general classes related to blood and the immune system, primarily of hematopoietic origin blood_and_immune_upper_slim - @@ -157,7 +138,6 @@ a subset of general classes related to specific cell types in the eye. eye_upper_slim - @@ -167,7 +147,6 @@ a subset of general classes of cell types in the cell ontology. general_cell_types_upper_slim - @@ -178,75 +157,10 @@ 2023-11-22T11:18:57Z a subset of general classes related to specific cell types in the kidney kidney_upper_slim - - - - - - - - - - - - - - - - - preferred term when talking about an instance of this class in Homo sapiens - - - - - - - - - latin term - - - - - - - - - plural term - - - - - - - - - - - - - - - - - abstract upper-level terms not directly useful for analysis - - - - - - - - - - - - - @@ -259,12 +173,6 @@ - - - - - - @@ -295,27 +203,15 @@ - - - - subset_property - - - - - - synonym_type_property - + - - consider - + @@ -333,41 +229,31 @@ - - has_alternative_id - + - - has_broad_synonym - + - - database_cross_reference - + - - has_exact_synonym - + - - has_narrow_synonym - + @@ -379,17 +265,13 @@ - - has_related_synonym - + - - has_synonym_type - + @@ -401,9 +283,7 @@ - - in_subset - + @@ -419,48 +299,12 @@ - - - - shorthand - - - - - - - - - - - - - - - - - - - - http://www.w3.org/2000/01/rdf-schema#seeAlso - seeAlso - see also - - - - - - - - - - @@ -777,6 +621,9 @@ + + + A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. CALOHA:TS-2035 FMA:68646 @@ -908,13 +755,14 @@ Covers cells actively being cultured or stored in a quiescent state for future u - Any fibroblast that is deriived from the neural crest. - fibroblast neural crest derived + Any fibroblast that is derived from the neural crest. + fibroblast neural crest derived + neural crest derived fibroblast - Any fibroblast that is deriived from the neural crest. + Any fibroblast that is derived from the neural crest. https://orcid.org/0000-0001-5208-3432 @@ -935,6 +783,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + neuronal receptor cell (sensu Animalia) @@ -1068,6 +917,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + A stem cell that is the precursor of gametes. FBbt:00004861 germline stem cell @@ -1155,12 +1005,19 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A male germ cell that develops from spermatogonia. The euploid primary spermatocytes undergo meiosis and give rise to the haploid secondary spermatocytes which in turn give rise to spermatids. BTO:0001275 CALOHA:TS-0951 @@ -1206,12 +1063,32 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + + + + + + + + + + + + + A male germ cell that develops from the haploid secondary spermatocytes. Without further division, spermatids undergo structural changes and give rise to spermatozoa. BTO:0001274 CALOHA:TS-0950 @@ -1288,6 +1165,19 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + + + + + + An euploid male germ cell of an early stage of spermatogenesis. BTO:0000958 CALOHA:TS-2193 @@ -1322,6 +1212,12 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + Female germ cell is a germ cell that supports female gamete production. MA:0000388 VHOG:0001530 @@ -1391,6 +1287,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -1451,6 +1348,12 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + An undifferentiated germ cell that proliferates rapidly and gives rise to oocytes. FMA:83673 @@ -1656,6 +1559,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -1737,6 +1641,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -1746,7 +1651,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells. @@ -1789,6 +1694,12 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + A stem cell that self-renews as well as give rise to a single mature cell type. FMA:70569 unipotent stem cell @@ -1883,14 +1794,93 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A stem cell from which all cells of the lymphoid and myeloid lineages develop, including blood cells and cells of the immune system. Hematopoietic stem cells lack cell markers of effector cells (lin-negative). Lin-negative is defined by lacking one or more of the following cell surface markers: CD2, CD3 epsilon, CD4, CD5 ,CD8 alpha chain, CD11b, CD14, CD19, CD20, CD56, ly6G, ter119. BTO:0000725 @@ -1908,12 +1898,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u Markers differ between species, and two sets of markers have been described for mice. HSCs are reportedly CD34-positive, CD45-positive, CD48-negative, CD150-positive, CD133-positive, and CD244-negative. hematopoietic stem cell - - - - - true - @@ -2040,7 +2024,33 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -2145,13 +2155,90 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A fully differentiated eosinophil, a granular leukocyte with a nucleus that usually has two lobes connected by one or more slender threads, and cytoplasm containing coarse, round granules that are uniform in size and which can be stained by the dye eosin. Cells are also differentiated from other granulocytes by a small nuclear-to-cytoplasm ratio (1:3). This cell type is CD49d-positive. The status of eosinophils as true professional antigen presenting cells is unclear, despite their ability to present exogenous peptides and peptides processed from exogenous proteins (in certain studies) via MHC Class II and activate T cells. Per the equivalence axioms, 'eosinophil' is reasoned to be a subclass of 'professional antigen presenting cell', though the role of eosinophils as such in the body may be limited. @@ -2217,7 +2304,38 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -2301,12 +2419,64 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A fully differentiated basophil, a granular leukocyte with an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation. polymorphonuclear leucocyte polymorphonuclear leukocyte @@ -2423,6 +2593,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A stem cell that can give rise to multiple lineages of cells. FMA:84789 multi-fate stem cell @@ -2543,11 +2720,19 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + - - + + + + + + + + @@ -2601,6 +2786,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A oligopotent progenitor cell committed to the lymphoid lineage. common lymphocyte precursor @@ -2690,13 +2882,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - - - - - - + A precursor cell with a limited number of potential fates. BTO:0000125 FMA:84782 @@ -2810,6 +2996,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -2863,8 +3050,9 @@ Covers cells actively being cultured or stored in a quiescent state for future u + - + @@ -2946,6 +3134,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -3011,6 +3200,14 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + A cell that has a filiform extrusion of the cell surface. VHOG:0001532 XAO:0000031 @@ -3029,13 +3226,8 @@ Covers cells actively being cultured or stored in a quiescent state for future u + - - - - - - A neurectoderm derived cell that lines the neural lumen. BTO:0001724 @@ -3107,6 +3299,8 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + An epithelial cell that has a cilia. FMA:70605 @@ -3136,6 +3330,12 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + An epithelial cell that is part of a duct. duct epithelial cell @@ -3183,6 +3383,12 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + @@ -3215,12 +3421,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - - - - - + non-branched duct epithelial cell @@ -3291,12 +3492,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - - - - - + A flattened epithelial cell of mesenchymal origin that lines the serous cavity. FMA:66773 @@ -3354,6 +3550,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A cell which moves among different tissues of the body, via blood, lymph, or other medium. circulating cell @@ -3381,6 +3584,12 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + A cell found predominately in the blood. FMA:62844 MESH:D001773 @@ -3418,6 +3627,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -3453,6 +3663,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + @@ -3495,6 +3712,12 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex. @@ -3637,6 +3860,43 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A tissue-resident macrophage of the reticuloendothelial system found on the luminal surface of the hepatic sinusoids involved in erythrocyte clearance. Markers include F4/80+, CD11b-low, CD68-positive, sialoadhesin-positive, CD163/SRCR-positive. Irregular, with long processes including lamellipodia extending into the sinusoid lumen, have flattened nucleus with cytoplasm containing characteristic invaginations of the plasma membrane (vermiform bodies); lie within the sinusoid lumen attached to the endothelial surface; derived from the bone marrow, form a major part of the body's mononuclear phagocyte system. BTO:0000685 @@ -3722,12 +3982,61 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue, which typically differentiates from monocytes. This cell has the following markers: tartrate-resistant acid phosphatase type 5-positive, PU.1-positive, c-fos-positive, nuclear factor NF-kappa-B p100 subunit-positive, tumor necrosis factor receptor superfamily member 11A-positive and macrophage colony-stimulating factor 1 receptor-positive. BTO:0000968 CALOHA:TS-0721 @@ -3822,7 +4131,57 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A leukocyte with abundant granules in the cytoplasm. BTO:0000539 @@ -3958,7 +4317,108 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A fully differentiated neutrophil, a granular leukocyte having a nucleus with three to five lobes connected by slender threads, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes. They are produced in bone marrow at a rate of 5e10-10e10/day and have a half-life of 6-8 hours. Neutrophils are CD15-positive, CD16-positive, CD32-positive, CD43-positive, CD181-positive, and CD182-positive. poly @@ -4060,12 +4520,85 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. Progenitors leave bone marrow and mature in connective and mucosal tissue. Mature mast cells are found in all tissues, except the bloodstream. Their phenotype is CD117-high, CD123-negative, CD193-positive, CD200R3-positive, and FceRI-high. Stem-cell factor (KIT-ligand; SCF) is the main controlling signal of their survival and development. BTO:0000830 @@ -4139,6 +4672,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + A specialized epithelial cell involved in sensory perception. Restricted to special sense organs of the olfactory, gustatory, and vestibulocochlear receptor systems; contain sensory cells surrounded by supportive, non-receptive cells. neuroepithelial cell @@ -4221,6 +4755,12 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + Any neuron having a sensory function; an afferent neuron conveying sensory impulses. BTO:0001037 FMA:84649 @@ -4261,6 +4801,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A type of interneuron that has two neurites, usually an axon and a dendrite, extending from opposite poles of an ovoid cell body. FMA:67282 @@ -4291,6 +4838,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A neuron with three or more neurites, usually an axon and multiple dendrites. FMA:67287 @@ -4357,7 +4911,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + + + + + + + A neuron whose cell body is within an autonomic ganglion. FMA:80121 autonomic neuron @@ -4385,6 +4945,14 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + A neuron that uses acetylcholine as a vesicular neurotransmitter. BTO:0004902 FMA:84796 @@ -4405,7 +4973,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - MESH:D059331 adrenergic neuron @@ -4607,6 +5174,14 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + Basket cells are inhibitory GABAergic interneurons of the brain. In general, dendrites of basket cells are free branching and contain smooth spines. Axons are highly branched. The branched axonal arborizations give rise to basket-like structures that surround the soma of the target cell. Basket cells form axo-somatic synapses, meaning their synapses target somas of other cells. @@ -4624,13 +5199,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - - - - - - + Large intrinsic neuron located in the granule layer of the cerebellar cortex that extends its dendrites into the molecular layer where they receive contact from parallel fibers. The axon of the Golgi cell ramifies densely in the granule layer and enters into a complex arrangement with mossy fiber terminals and granule cell dendrites to form the cerebellar glomerulus. Llinas, Walton and Lang. In The Synaptic Organization of the Brain. 5th ed. 2004. MESH:D000080906 Golgi cell @@ -4672,6 +5241,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -4712,6 +5282,14 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + A neuron that has dendritic processes radiating from the cell body forming a star-like shape. BTO:0002316 @@ -4731,6 +5309,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -4856,18 +5435,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + - - - - - - @@ -4938,7 +5512,27 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + + + + + + + + + + + + + @@ -4961,6 +5555,12 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + A central nervous system macrophage found in the parenchyma of the central nervous system. Marker include CD11b-positive, F4/80-positive, and CD68-positive. brain macrophage @@ -5027,6 +5627,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -5058,6 +5659,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -5229,6 +5831,18 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + + + + + An inactive fibroblast; cytoplasm is sparse, endoplasmic reticulum is scanty with flattened nucleus. Term used by some histologists; when fibroblasts become relatively inactive in fiber formation. However, this cell has the potential for fibrogenesis in quiescent connective tissue of the adult, as well as during development, other histologists prefer to use the term fibroblast in all circumstances. These cells represent ~0.5% of peripheral blood leukocytes. FMA:63879 @@ -5296,6 +5910,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -5332,7 +5947,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - @@ -5501,6 +6115,12 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + A cell capable of processing and presenting lipid and protein antigens to T cells in order to initiate an immune response. APC @@ -5572,6 +6192,19 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + + + + + + A pigment cell derived from the neural crest. Contains melanin-filled pigment granules, which gives a brown to black appearance. BTO:0000847 @@ -5644,6 +6277,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A cell that specializes in controlled release of one or more substances. BTO:0003659 FMA:86916 @@ -5675,6 +6315,12 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + A cell of an exocrine gland; i.e. a gland that discharges its secretion via a duct. FMA:16014 @@ -5722,6 +6368,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + protein secreting cell @@ -5731,7 +6384,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - A cell that is usually basal in position, cuboidal with round nucleus, short microvilli, secretes pepsinogen. FMA:62902 @@ -5777,6 +6429,12 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + A cell that specializes in secretion of surfactant in the alveoli of the lung. surfactant secreting cell @@ -5799,6 +6457,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -5807,18 +6466,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - - - - - - - - - - - A non-mucous, epithelial secretory cell that is part of the tracheobronchial tree. A club cell has short microvilli but no cilia. A club cell is able to multiply and differentiate into ciliated cells to regenerate the bronchiolar epithelium and it also protects the tracheobronchial epithelium. BTO:0004811 @@ -5855,12 +6502,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - - - - - + A cell of the epithelial lining that produce and secrete mucins. BTO:0001540 FMA:13148 @@ -5892,9 +6534,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - - + @@ -5942,12 +6582,29 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + + + + + + + + + + A cell of an endocrine gland, ductless glands that secrete substances which are released directly into the circulation and which influence metabolism and other body functions. FMA:83809 @@ -6003,7 +6660,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - A neuron that is capable of some hormone secretion in response to neuronal signals. @@ -6041,13 +6697,8 @@ The modern definition of neurosecretion has evolved to include the release of an + - - - - - - A cell that stores epinephrine secretory vesicles. During times of stress, the nervous system signals the vesicles to secrete their hormonal content. Their name derives from their ability to stain a brownish color with chromic salts. Characteristically, they are located in the adrenal medulla and paraganglia of the sympathetic nervous system. BTO:0000259 FMA:69263 @@ -6078,6 +6729,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + peptide hormone secreting cell @@ -6097,6 +6755,14 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + + BTO:0000783 insulin secreting cell @@ -6121,8 +6787,14 @@ The modern definition of neurosecretion has evolved to include the release of an - + + + + + + + @@ -6151,12 +6823,6 @@ The modern definition of neurosecretion has evolved to include the release of an Pancreatic beta cells are also reportedly CD284-positive. Upon activation, they upregulate their CD14 expression. type B pancreatic cell - - - - - true - @@ -6242,6 +6908,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + A cell that secretes glucagon. FMA:84045 glucagon-secreting cell @@ -6271,6 +6944,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -6283,12 +6957,6 @@ The modern definition of neurosecretion has evolved to include the release of an - - - - - - A type of enteocrine cell found in the periphery of the islets of Langerhans that secretes glucagon. BTO:0000990 @@ -6324,6 +6992,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + somatostatin secreting cell @@ -6344,6 +7019,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -6394,6 +7070,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + steroid hormone secreting cell @@ -6402,7 +7085,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -6410,12 +7093,6 @@ The modern definition of neurosecretion has evolved to include the release of an - - - - - - A progesterone secreting cell in the corpus luteum. The large luteal cells develop from the granulosa cells. The small luteal cells develop from the theca cells. BTO:0003939 @@ -6454,6 +7131,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + ecdysteroid secreting cell @@ -6473,6 +7157,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + testosterone secreting cell @@ -6482,6 +7173,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -6530,6 +7222,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + progesterone secreting cell @@ -6549,6 +7248,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + A steroid hormone secreting cell that secretes estradiol. estradiol secreting cell @@ -6602,12 +7308,6 @@ The modern definition of neurosecretion has evolved to include the release of an - - - - - - @@ -6669,12 +7369,7 @@ The modern definition of neurosecretion has evolved to include the release of an - - - - - - + Contractile cells resembling smooth muscle cells that are present in glands, notably the mammary gland, and aid in secretion. This cell has long weaving dendritic processes containing myofilament. BTO:0002309 CALOHA:TS-2379 @@ -6698,12 +7393,7 @@ The modern definition of neurosecretion has evolved to include the release of an - - - - - - + An animal cell that has characteristics of both a fibroblast cell and a smooth muscle cell. MFB @@ -6779,6 +7469,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + A somatic cell located in skeletal muscle. BTO:0004392 @@ -6927,6 +7624,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + A striated muscle cell of an arthropod heart that participates in heart contraction. cardiac muscle cell (sensu Arthopoda) @@ -6961,25 +7665,7 @@ The modern definition of neurosecretion has evolved to include the release of an - - - - - - - - - - - - - - - - - - - + A muscle cell that is involved in the mechanism of insect flight. This encompasses both, cells that power flight and cells that control flight. FBbt:00003360 insect flight muscle cell @@ -7011,6 +7697,19 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + + + + + + + A cell that is capable of detection of a stimulus involved in sensory perception. MESH:D011984 receptor cell @@ -7064,6 +7763,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + A cell specialized to transduce mechanical stimuli and relay that information centrally in the nervous system. mechanoreceptor mechanoreceptor cell @@ -7097,6 +7803,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + touch receptor cell @@ -7151,6 +7864,14 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + + gravity sensitive cell @@ -7179,6 +7900,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + A cellular receptor which mediates the sense of temperature. Thermoreceptor cells in vertebrates are mostly located under the skin. In mammals there are separate types of thermoreceptors for cold and for warmth and pain receptor cells which detect cold or heat extreme enough to cause pain. thermoreceptor cell @@ -7207,6 +7935,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + A cell specialized to detect chemical substances and relay that information centrally in the nervous system. Chemoreceptors may monitor external stimuli, as in taste and olfaction, or internal stimuli, such as the concentrations of oxygen and carbon dioxide in the blood. chemoreceptor cell @@ -7233,12 +7968,20 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + + BTO:0004185 FMA:67860 MESH:D018034 @@ -7276,7 +8019,14 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + A specialized cell involved in gustatory sensory perception. FMA:67910 taste bud cell @@ -7308,6 +8058,12 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + A cell specialized to detect and transduce light. BTO:0001060 CALOHA:TS-0868 @@ -7437,7 +8193,6 @@ The modern definition of neurosecretion has evolved to include the release of an - @@ -7478,12 +8233,7 @@ The modern definition of neurosecretion has evolved to include the release of an - - - - - - + @@ -7523,6 +8273,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + A cell that moves by its own activities. motile cell @@ -7657,6 +8414,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + A cell that lacks a nucleus. FMA:68647 @@ -7686,6 +8450,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + A cell with a single nucleus. single nucleate cell @@ -7713,6 +8484,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + binucleate cell @@ -7732,6 +8510,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + A cell with more than one nucleus. AEO:0000203 WBbt:0008074 @@ -7812,7 +8597,27 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + + + + + + + + + + + + + + @@ -7851,13 +8656,9 @@ The modern definition of neurosecretion has evolved to include the release of an + + - - - - - - @@ -7870,12 +8671,6 @@ The modern definition of neurosecretion has evolved to include the release of an - - - - - - @@ -7937,6 +8732,12 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + Any cell capable of ingesting particulate matter via phagocytosis. BTO:0001044 FMA:83806 @@ -7977,6 +8778,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -7984,6 +8786,12 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells. BTO:0000801 @@ -8035,8 +8843,8 @@ The modern definition of neurosecretion has evolved to include the release of an - - + + A lymphocyte of B lineage that is capable of B cell mediated immunity. @@ -8078,6 +8886,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -8101,13 +8910,8 @@ The modern definition of neurosecretion has evolved to include the release of an + - - - - - - brush border epithelial cell @@ -8142,6 +8946,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -8238,6 +9043,7 @@ The modern definition of neurosecretion has evolved to include the release of an + Type of neuron that is a primary mechanosensory cell, with peripheral neurites innervating the skin with free nerve endings. @@ -8384,6 +9190,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + MESH:D005057 @@ -8416,6 +9229,12 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + Eumycetozoan cell @@ -8834,6 +9653,12 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + @@ -8961,6 +9786,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + A peptide hormone secreting cell that produces growth hormone, somatotropin. growth hormone secreting cell somatotrophin secreting cell @@ -9063,7 +9895,14 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + A mature sexual reproductive cell having a single set of unpaired chromosomes. CALOHA:TS-0395 FMA:18649 @@ -9175,6 +10014,12 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + @@ -9255,6 +10100,12 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + @@ -9345,7 +10196,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -9396,19 +10247,14 @@ The modern definition of neurosecretion has evolved to include the release of an - + + A cell secreting sebun, an oily substance secreted by sebaceous glands, composed of keratin, fat, and cellular debris. sebocyte sebum secreting cell - - - - - true - @@ -9422,7 +10268,6 @@ The modern definition of neurosecretion has evolved to include the release of an - A cell secreting sweat, the fluid excreted by the sweat glands of mammals. It consists of water containing sodium chloride, phosphate, urea, ammonia, and other waste products. sweat secreting cell @@ -9498,7 +10343,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -9609,6 +10454,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + oxygen accumulating cell @@ -9669,9 +10521,9 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -9734,9 +10586,14 @@ The modern definition of neurosecretion has evolved to include the release of an - - + + + + + + + @@ -9748,18 +10605,6 @@ The modern definition of neurosecretion has evolved to include the release of an medullary chromaffin cell of adrenal gland adrenal medulla chromaffin cell - - - - - true - - - - - - true - @@ -9790,6 +10635,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -9815,12 +10661,7 @@ The modern definition of neurosecretion has evolved to include the release of an - - - - - - + An early neural cell developing from the early ependymal cell of the neural tube. FMA:70564 spongioblast @@ -9868,6 +10709,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -9903,6 +10745,12 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + A pigment cell that is capable of detecting light stimulus that is involved in visual perception. FMA:63846 visual pigment cell (sensu Vertebrata) @@ -9976,6 +10824,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + @@ -10016,6 +10871,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + @@ -10049,6 +10911,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + @@ -10082,6 +10951,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + extraembryonic cell @@ -10102,6 +10978,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + amnioserosal cell @@ -10200,6 +11083,7 @@ The modern definition of neurosecretion has evolved to include the release of an + A multifate stem cell found in skeletal muscle than can differentiate into many different cell types, including muscle. Distinct cell type from satellite cell. FMA:86767 Multi-potency demonstrated ex vivo. At the time of writing, it is unclear whether the endogenous population differentiates into multiple cell types in vivo. @@ -10253,6 +11137,12 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + A smooth muscle cell that is part of a sphincter. A sphincter is a typically circular muscle that normally maintains constriction of a natural body passage or orifice and which relaxes as required by normal physiological functioning. sphincter associated smooth muscle cell @@ -10287,6 +11177,12 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + A smooth muscle cell associated with the vasculature. VSMC @@ -10370,6 +11266,12 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + An epithelial cell of the integument (the outer layer of an organism). BTO:0001470 CALOHA:TS-0283 @@ -10450,7 +11352,14 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + Diploid cell produced by the fusion of sperm cell nucleus and egg cell. zygote BTO:0000854 @@ -10587,6 +11496,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -10739,6 +11649,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -10789,6 +11700,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -10831,6 +11743,12 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + An elongated fibrocyte that is part of a tendon. The cytoplasm is stretched between the collagen fibres of the tendon. They have a central cell nucleus with a prominent nucleolus. Tendon cells have a well-developed rough endoplasmic reticulum and they are responsible for synthesis and turnover of tendon fibres and ground substance. muscle attachment cell tenocyte @@ -10998,6 +11916,12 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + ganglion interneuron @@ -11082,6 +12006,8 @@ The modern definition of neurosecretion has evolved to include the release of an + + An interneuron that has its cell body in a central nervous system. @@ -11267,6 +12193,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + A cell that contains more than two haploid sets of chromosomes. polyploid cell @@ -11295,6 +12228,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + A cell whose nucleus contains a single haploid genome. haploid cell @@ -11538,6 +12478,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -11735,6 +12676,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + A peptide hormone secreting cell pituitary that produces luteinizing hormone. luteinizing hormone secreting cell @@ -11761,6 +12709,14 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + + A peptide hormone cell that secretes prolactin. prolactin secreting cell @@ -11788,6 +12744,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + A cell of the intermediate pituitary that produces melanocyte stimulating hormone. BTO:0002277 melanotrope @@ -11807,20 +12770,21 @@ The modern definition of neurosecretion has evolved to include the release of an - + + A stem cell that gives rise to the follicle cells that surround the oocyte in female arthropods. somatic stem cell FBbt:00004903 follicle stem cell (sensu Arthropoda) - + - + https://github.com/obophenotype/cell-ontology/issues/1943 @@ -11877,6 +12841,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + calcitonin secreting cell @@ -11900,6 +12871,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + A muscle cell in which the fibers are organised into sarcomeres but in which adjacent myofibrils are offset from each other, producing an oblique banding pattern. Examples include the somatic muscles of nemotodes and cephalopods. obliquely striated muscle cell @@ -12088,7 +13066,56 @@ The modern definition of neurosecretion has evolved to include the release of an - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative). @@ -12103,12 +13130,6 @@ The modern definition of neurosecretion has evolved to include the release of an dendritic cell - - - - - true - @@ -12146,13 +13167,26 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + + + + + + + Langerhans cell is a conventional dendritic cell that has plasma membrane part CD207. A Langerhans cell is a stellate dendritic cell of myeloid origin, that appears clear on light microscopy and has a dark-staining, indented nucleus and characteristic inclusions (Birbeck granules) in the cytoplasm; Langerhans cells are found principally in the stratum spinosum of the epidermis, but they also occur in other stratified epithelia and have been identified in the lung, lymph nodes, spleen, and thymus. BTO:0000705 @@ -12201,6 +13235,12 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + A cell capable of producing epinephrine. Epiniphrine is synthesized from norepiniphrine by the actions of the phenylethanolamine N-methyltransferase enzyme, which is expressed in the adrenal glands, androgenic neurons, and in other cell types. adrenaline secreting cell epinephrin secreting cell @@ -12253,6 +13293,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + mineralocorticoid secreting cell @@ -12282,6 +13329,12 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + A cell type that secretes 5-Hydroxytryptamine (serotonin). 5-HT secreting cell 5-Hydroxytryptamine secreting cell @@ -12312,6 +13365,12 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + A cell capable of producting norepiniphrine. Norepiniphrine is a catecholamine with multiple roles including as a hormone and a neurotransmitter. In addition, epiniphrine is synthesized from norepiniphrine by the actions of the phenylethanolamine N-methyltransferase enzyme. noradrenaline secreting cell norepinephrin secreting cell @@ -12342,6 +13401,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + glucocorticoid secreting cell @@ -12360,6 +13426,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -12383,7 +13450,9 @@ The modern definition of neurosecretion has evolved to include the release of an + + @@ -12439,6 +13508,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -12483,6 +13553,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + A peptide hormone secreting cell that produces adrenocorticotropin, or corticotropin. ACTH secreting cell adrenocorticotrophic hormone secreting cell @@ -12517,6 +13594,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -12684,14 +13762,10 @@ The modern definition of neurosecretion has evolved to include the release of an + - - - - - - - + + @@ -12704,14 +13778,14 @@ The modern definition of neurosecretion has evolved to include the release of an FBbt:00004904 follicle cell of egg chamber - + - + @@ -12795,6 +13869,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + An endocrine cell that secretes juvenile hormone. FBbt:00058020 juvenile hormone secreting cell @@ -12840,6 +13921,7 @@ The modern definition of neurosecretion has evolved to include the release of an + Mast cell subtype whose granules contain both the serine proteases tryptase and chymase. These cells are primarily found in connective tissue, such as the peritoneal cavity, skin, and intestinal submucosa. Their development is T-cell independent. MC(TC) @@ -12887,6 +13969,18 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + + + + + + Mast cell subtype that contains only the serine protease trypase in its granules. These cells are primarily found in mucosal tissue, such as intestinal mucosa and alveoli. They depend upon T-cells for development of phenotype. MC(T) @@ -12947,6 +14041,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -12993,6 +14088,12 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + A photoreceptor cell that detects visible light. visible light photoreceptor cell @@ -13055,6 +14156,12 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + @@ -13119,6 +14226,12 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + A photoreceptor cell that detects ultraviolet light. UV sensitive photoreceptor cell @@ -13263,12 +14376,7 @@ The modern definition of neurosecretion has evolved to include the release of an - - - - - - + A cell found throughout the gastrointestinal tract and in the pancreas. They secrete somatostatin in both an endocrine and paracrine manner. Somatostatin inhibits gastrin, cholecystokinin, insulin, glucagon, pancreatic enzymes, and gastric hydrochloric acid. A variety of substances which inhibit gastric acid secretion (vasoactive intestinal peptide, calcitonin gene-related peptide, cholecystokinin, beta-adrenergic agonists, and gastric inhibitory peptide) are thought to act by releasing somatostatin. FMA:62935 D cell @@ -13287,8 +14395,8 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -13386,6 +14494,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -13433,12 +14542,7 @@ The modern definition of neurosecretion has evolved to include the release of an - - - - - - + @@ -13521,7 +14625,14 @@ The modern definition of neurosecretion has evolved to include the release of an - + + + + + + + + A precursor cell destined to differentiate into cardiac muscle cell. FMA:84797 cardiac muscle progenitor cell @@ -13529,12 +14640,6 @@ The modern definition of neurosecretion has evolved to include the release of an cardiac muscle myoblast - - - - - true - @@ -13559,6 +14664,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + A precursor cell destined to differentiate into smooth muscle myocytes. FMA:84798 myoblast, smooth muscle @@ -13596,12 +14708,20 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + + A myoblast that differentiates into skeletal muscle fibers. FMA:84799 skeletal myoblast @@ -13671,6 +14791,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -13732,6 +14853,12 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + fungal cell @@ -13804,6 +14931,8 @@ The modern definition of neurosecretion has evolved to include the release of an + + @@ -13912,19 +15041,20 @@ The modern definition of neurosecretion has evolved to include the release of an + - + A neuron that develops during the early segmentation stages in teleosts, before the neural tube is formed. primary neuron (sensu Teleostei) - + - + https://github.com/obophenotype/cell-ontology/pull/1950 @@ -13948,6 +15078,8 @@ The modern definition of neurosecretion has evolved to include the release of an + + A primary neuron (sensu Teleostei) that has a sensory function. primary sensory neuron (sensu Teleostei) @@ -14007,19 +15139,20 @@ The modern definition of neurosecretion has evolved to include the release of an + - + A neuron of teleosts that develops later than a primary neuron, typically during the larval stages. secondary neuron (sensu Teleostei) - + - + https://github.com/obophenotype/cell-ontology/pull/1950 @@ -14043,6 +15176,8 @@ The modern definition of neurosecretion has evolved to include the release of an + + A secondary neuron (sensu Teleostei) that has a motor function. secondary motor neuron (sensu Teleostei) @@ -14147,6 +15282,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -14195,7 +15331,26 @@ The modern definition of neurosecretion has evolved to include the release of an - + + + + + + + + + + + + + + + + + + + + @@ -14215,12 +15370,6 @@ The modern definition of neurosecretion has evolved to include the release of an Editors note: consider adding taxon constraint to vertebrata (PMID:18025161) lymphocyte - - - - - true - @@ -14288,8 +15437,26 @@ The modern definition of neurosecretion has evolved to include the release of an - - + + + + + + + + + + + + + + + + + + + + A CD4-positive, alpha-beta T cell that has the phenotype T-bet-positive, CXCR3-positive, CCR6-negative, and is capable of producing interferon-gamma. @@ -14370,10 +15537,17 @@ The modern definition of neurosecretion has evolved to include the release of an + - - + + + + + + + + A CD4-positive, alpha-beta T cell that has the phenotype GATA-3-positive, CXCR3-negative, CCR6-negative, and is capable of producing interleukin-4. @@ -14496,6 +15670,98 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -14571,10 +15837,23 @@ The modern definition of neurosecretion has evolved to include the release of an + - - + + + + + + + + + + + + + + A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers. @@ -14648,6 +15927,25 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + + + + + + + + + + + + + @@ -14743,6 +16041,18 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + + + + + + @@ -14863,13 +16173,98 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The earliest cytologically identifiable precursor in the thrombocytic series. This cell is capable of endomitosis and lacks expression of hematopoieitic lineage markers (lin-negative). BTO:0001164 @@ -15050,11 +16445,51 @@ The modern definition of neurosecretion has evolved to include the release of an - + + + + + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A hematopoietic progenitor cell that is committed to the granulocyte and monocyte lineages. These cells are CD123-positive, and do not express Gata1 or Gata2 but do express C/EBPa, and Pu.1. @@ -15071,12 +16506,6 @@ The modern definition of neurosecretion has evolved to include the release of an Originally described in the dendritic cell ontology (DC_CL:0000042)(PMID:19243617). GMPs are reportedly CD16-positive, CD32-positive, CD34-positive, CD38-positive, CD45RA-positive, CD110-negative, CD117-positive, CD123-positive, and SCA1-negative. granulocyte monocyte progenitor cell - - - - - true - @@ -15200,12 +16629,91 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds. BTO:0001173 CALOHA:TS-0864 @@ -15254,7 +16762,21 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + + + + + + + + @@ -15341,6 +16863,54 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -15382,6 +16952,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -15453,6 +17024,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -15537,7 +17109,44 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -15610,6 +17219,26 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + + + + + + + + + + + + + + @@ -15683,7 +17312,14 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + A mesenchymal cell found in the developing heart and that develops into some part of the heart. These cells derive from intra- and extra-cardiac sources, including the endocardium, epicardium, neural crest, and second heart field. cardiac mesenchymal cell @@ -15724,19 +17360,33 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + + + + + + + + A neuroepithelial cells that occurs singly or in small groups, close to the outer follicular borders but within the follicular basement membrane of the thyroid. Expresses a form of the neural cell adhesion molecule (N-CAM) on their surface. Secretes calcitonin, 5-hydroxytryptamine and dopamine. FMA:68653 SCTID:176770005 @@ -15896,7 +17546,14 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + An epithelial cell of the cornea. BTO:0004298 @@ -15951,12 +17608,31 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + + + + + + + + + + + + + Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells. BTO:0000876 @@ -15992,6 +17668,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -16125,11 +17802,90 @@ The modern definition of neurosecretion has evolved to include the release of an + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A neutrophil precursor in the granulocytic series, being a cell intermediate in development between a promyelocyte and a metamyelocyte; in this stage, production of primary granules is complete and neutrophil-specific granules has started. No nucleolus is present. This cell type is CD13-positive, CD16-negative, integrin alpha-M-positive, CD15-positive, CD33-positive, CD24-positive, C/EBP-a-positive, C/EBPe-positive, PU.1-positive, lactotransferrin-positive, myeloperoxidase-positive and NGAL-positive. @@ -16207,6 +17963,61 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A macrophage resident in the peritoneum under non-inflammatory conditions. Markers include F4/80-high, CD11b-high, CD68-positive, SIGNR1-positive, CD115-high, MHC-II-negative, and Dectin-1-positive. BTO:0001034 FMA:83025 @@ -16314,6 +18125,108 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -16400,6 +18313,61 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A tissue-resident macrophage found in the alveoli of the lungs. Ingests small inhaled particles resulting in degradation and presentation of the antigen to immunocompetent cells. Markers include F4/80-positive, CD11b-/low, CD11c-positive, CD68-positive, sialoadhesin-positive, dectin-1-positive, MR-positive, CX3CR1-negative. BTO:0000802 @@ -16546,6 +18514,12 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + A specialized osteoclast associated with the absorption and removal of cementum. BTO:0002516 FMA:83027 @@ -16589,7 +18563,6 @@ The modern definition of neurosecretion has evolved to include the release of an - @@ -16671,6 +18644,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + A steroid hormone secreting cell that secretes androgen. androgen secreting cell @@ -16686,13 +18666,8 @@ The modern definition of neurosecretion has evolved to include the release of an + - - - - - - An elongated, spindle-shaped, cell that is located between the basal lamina and the plasmalemma of a muscle fiber. These cells are mostly quiescent, but upon activation they divide to produce cells that generate new muscle fibers. Skeletal muscle satellite cells are not traditionally referred to as myoblasts. They are a heterogeneous population whose division, following activiation, contributes to the formation of skeletal muscle fibers and to maintenance of the skeletal muscle statelite cell population. @@ -16724,6 +18699,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -16813,6 +18789,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + Pyramidal neurons have a pyramid-shaped soma with a single axon, a large apical dendrite and multiple basal dendrites. The apex and an apical dendrite typically point toward the pial surface and other dendrites and an axon emerging from the base. The axons may have local collaterals but also project outside their region. Pyramidal neurons are found in the cerebral cortex, the hippocampus, and the amygdala. BTO:0003102 FMA:67310 @@ -16875,13 +18858,7 @@ The modern definition of neurosecretion has evolved to include the release of an - - - - - - - + A mechanoreceptor in the organ of Corti. In mammals the outer hair cells are arranged in three rows which are further from the modiolus than the single row of inner hair cells. The motile properties of the outer hair cells may contribute actively to tuning the sensitivity and frequency selectivity of the cochlea. BTO:0003666 FMA:62366 @@ -17166,13 +19143,141 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + CFU-Eo EoP colony forming unit eosinophil @@ -17246,7 +19351,50 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a promyelocyte and a metamyelocyte;in this stage, production of primary granules is complete and eosinophil-specific granules has started. No nucleolus is present. These cells are integrin alpha-M-positive, CD13-positive, CD15-positive, CD16-negative, CD24-positive, and CD33-positive. BTO:0003454 FMA:83542 @@ -17357,13 +19505,129 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A progenitor cell committed to the basophil lineage. This cell lacks hematopoietic lineage markers (lin-negative) and is CD34-positive, T1/ST2-low, CD117-negative, and FceRIa-high. This cell also expresses Gata-1, Gata-2 and C/EBPa. BaP CFU-Bas @@ -17437,10 +19701,53 @@ The modern definition of neurosecretion has evolved to include the release of an + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A basophil precursor in the granulocytic series, being a cell intermediate in development between a promyelocyte and a metamyelocyte; in this stage, production of primary granules is complete and basophil-specific granules has started. No nucleolus is present. Markers are being integrin alpha-M-positive, fucosyltransferase FUT4-positive, CD33-positive, CD24-positive, aminopeptidase N-positive. @@ -17517,7 +19824,14 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + A neuron that uses GABA as a vesicular neurotransmitter FMA:84788 MESH:D059330 @@ -17575,13 +19889,7 @@ The modern definition of neurosecretion has evolved to include the release of an - - - - - - - + A myoblast that is committed to a myotube-specific program of differentiation but not yet fused. It undergoes very limited additional proliferation. After fusion, it will take on a muscle identity specified by a `muscle founder cell` (CL:0008006). fusion competent myoblast @@ -17657,12 +19965,37 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + + + + + + + + + + + + + + + + + + + A lymphocyte that can spontaneously kill a variety of target cells without prior antigenic activation via germline encoded activation receptors and also regulate immune responses via cytokine release and direct contact with other cells. large granular lymphocyte @@ -17710,6 +20043,18 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + + + + + + A mature alpha-beta T cell that expresses an alpha-beta T cell receptor and the CD4 coreceptor. @@ -17755,6 +20100,18 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + + + + + + A T cell expressing an alpha-beta T cell receptor and the CD8 coreceptor. CD8-positive, alpha-beta T lymphocyte @@ -17795,7 +20152,15 @@ The modern definition of neurosecretion has evolved to include the release of an - + + + + + + + + + @@ -17964,7 +20329,19 @@ The modern definition of neurosecretion has evolved to include the release of an - + + + + + + + + + + + + + A cell that is found in the perisinusoidal space of the liver that is capable of multiple roles including storage of retinol, presentation of antigen to T cells (including CD1d-restricted NKT cells), and upon activation, production of extracellular matrix components that can contribute to liver fibrosis. This activated state has a myofibroblast-like phenotype, though it's not clear in the literature if this is terminally differentiated. This cell type comprises approximately 8-15% of total cells in the liver. BTO:0002741 @@ -17981,12 +20358,6 @@ The modern definition of neurosecretion has evolved to include the release of an Hepatic stellate cells are CD271-positive, desmin-positive, DDR-2-positive, GFAP-positive, synamin-positive, synaptophysin-positive, vimentin-positive, They are capable of producing angiotensin II, fibronectin, laminin, MMP-1, MMP-2, MMP-3, MMP-9, MMP-11, TGF-beta1, TIMP-1, TIMP-2, type I collagen, type III collagen, type IV collagen, and type VI collagen. hepatic stellate cell - - - - - true - @@ -18124,10 +20495,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + - - + + A cell that stains readily in the anterior pituitary gland. @@ -18224,6 +20598,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -18328,7 +20703,8 @@ The modern definition of neurosecretion has evolved to include the release of an - + + @@ -18396,7 +20772,20 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + + + + + + + @@ -18487,11 +20876,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + - - + + A smooth muscle cell that synthesizes, stores, and secretes the enzyme renin. This cell type are located in the wall of the afferent arteriole at the entrance to the glomerulus. While having a different origin than other kidney smooth muscle cells, this cell type expresses smooth muscle actin upon maturation. @@ -18577,12 +20968,7 @@ The modern definition of neurosecretion has evolved to include the release of an - - - - - - + A mucus-secreting cell, with numerous apical secretory vesicles containing mucins; nucleus are basally displaced; numerous at the neck of mucus secreting glands neck cell @@ -18602,6 +20988,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -18646,6 +21033,13 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + A specialized kidney epithelial cell, contained within a glomerulus, that contains "feet" that interdigitate with the "feet" of other podocytes. epithelial cell of visceral layer of glomerular capsule @@ -18697,6 +21091,12 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + @@ -18742,6 +21142,12 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + @@ -18788,6 +21194,19 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + + + + + + + A diploid cell that has derived from a spermatogonium and can subsequently begin meiosis and divide into two haploid secondary spermatocytes. BTO:0001115 CALOHA:TS-2194 @@ -18822,12 +21241,20 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + + One of the two haploid cells into which a primary spermatocyte divides, and which in turn gives origin to spermatids. BTO:0000709 CALOHA:TS-2195 @@ -19057,6 +21484,12 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + A primordial germ cell is a diploid germ cell precursors that transiently exist in the embryo before they enter into close association with the somatic cells of the gonad and become irreversibly committed as germ cells. FMA:70567 gonocyte @@ -19244,7 +21677,14 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + A neuron that is capable of some neurotansmission by glutamate secretion. WBbt:0006829 @@ -19277,6 +21717,12 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + A non-terminally differentiated cell that is capable of developing into a muscle cell. muscle precursor cell @@ -19319,9 +21765,9 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -19415,14 +21861,20 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + A columnar/cuboidal epithelial cell that secretes cerebrospinal fluid. cerebrospinal fluid secreting cell @@ -19445,6 +21897,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -19494,6 +21947,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -19520,6 +21974,14 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + stellate interneuron @@ -19559,6 +22021,14 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + An interneuron that has spider-like appearance with a small round soma, a large number (7-10) of short, smooth, or slightly beaded primary dendrites that give rise to only a few secondary branches, and a branched axon that establishes a dense axonal mesh with thin shafts. NGF cell neuroglioform cell @@ -19592,6 +22062,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -19608,6 +22079,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -19683,6 +22155,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -19734,8 +22207,13 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + A neuron that releases dopamine as a neurotransmitter. BTO:0004032 FMA:84787 @@ -19775,6 +22253,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -19825,6 +22304,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -19851,7 +22331,15 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + Specialized ependymal cell that produces the cerebrospinal fluid from the blood and secretes it into the lumen of the brain and spinal chord. 2023-08-04T08:48:30Z @@ -19906,7 +22394,13 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + Stromal cell that forms the internal covering of the vertebrate brain and produces ECM for this and the choroid plexus. leptomemingeal cell @@ -19918,12 +22412,6 @@ radial glial cells acting as neural progenitors throughout life. true - - - - - true - @@ -19937,6 +22425,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -19964,6 +22453,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + Epithelial cells derived from neural plate and neural crest. neuroepithelial cell BTO:0004301 @@ -20026,7 +22522,7 @@ radial glial cells acting as neural progenitors throughout life. - + stratum granulosum cell @@ -20099,6 +22595,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -20158,6 +22655,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -20184,6 +22682,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A stem cell that can give rise to cell types of the body other than those of the germ-line. CALOHA:TS-2086 MESH:D053687 @@ -20230,6 +22735,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + nitrogen fixing cell @@ -20316,6 +22828,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A cell of a layer of transitional epithelium in the wall of the proximal urethra, bladder, ureter or renal pelvis, external to the lamina propria. FMA:84127 urinary tract transitional epithelial cell @@ -20411,6 +22930,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + Muscle cell which has as its direct parts myofilaments organized into sarcomeres. BTO:0002916 @@ -20446,7 +22977,10 @@ radial glial cells acting as neural progenitors throughout life. + + + @@ -20465,6 +22999,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue. BTO:0000751 @@ -20574,22 +23114,10 @@ radial glial cells acting as neural progenitors throughout life. - - - - - - - + A round chondrocyte that first differentiates in the late embryonic growth plate of bone. periarticular chondrocyte - - - - - true - @@ -20706,6 +23234,20 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + @@ -20786,7 +23328,16 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + @@ -20803,12 +23354,6 @@ radial glial cells acting as neural progenitors throughout life. - - - - - - A bipolar neuron found in the retina and having connections with photoreceptors cells and neurons in the inner plexiform layer. BC @@ -20892,6 +23437,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -20949,6 +23495,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A bipolar neuron found in the retina and having connections with cone photoreceptor cells and neurons in the inner plexiform layer. cone retinal bipolar cell @@ -20964,19 +23516,13 @@ radial glial cells acting as neural progenitors throughout life. - + - - - - - - An OFF-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the outer half of the inner plexiform layer. The cell body of these cells is in the middle of the inner plexiform layer. The dendritic tree is stout and the axon terminates in sublamina 1. The axonal terminal is wide and has only a few varicosities. DB1 cone bipolar cell type 1 cone bipolar cell (sensu Mus) @@ -20993,8 +23539,8 @@ radial glial cells acting as neural progenitors throughout life. - - + + @@ -21003,15 +23549,27 @@ radial glial cells acting as neural progenitors throughout life. - - + + + + + + + + + + + + + + An OFF-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the outer half of the inner plexiform layer. The dendritic tree is not well filled and the dendrites are more delicate than in type 1 cells. The axon terminal is bushier and exhibits a dense plexus of varicosities in the inner part of sublamina 1 (Ghosh et al., 2004). It can be differentiated from other retinal bipolar neurons by its expression of marker genes: Neto1, Lhx3 and Irx-6 (Shekhar, 2016). FMB cone bipolar cell type 2 cone bipolar cell (sensu Mus) - + @@ -21031,7 +23589,7 @@ radial glial cells acting as neural progenitors throughout life. - + PMID:27565351 @@ -21047,19 +23605,13 @@ radial glial cells acting as neural progenitors throughout life. - + - - - - - - @@ -21082,7 +23634,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -21095,12 +23647,6 @@ radial glial cells acting as neural progenitors throughout life. - - - - - - @@ -21123,19 +23669,13 @@ radial glial cells acting as neural progenitors throughout life. - + - - - - - - An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The axon terminal is restricted to sublamina 3 of the inner plexiform layer. It is narrowly stratified and branched. The dendritic tree has many delicate branches. DB4 cone bipolar cell type 5 cone bipolar cell (sensu Mus) @@ -21152,19 +23692,13 @@ radial glial cells acting as neural progenitors throughout life. - + - - - - - - An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The cell has a loose, delicate axon terminal that opens in sublamina 3 of the inner plexiform layer and descends into sublamina 4. DB5 cone bipolar cell type 6 cone bipolar cell (sensu Mus) @@ -21181,19 +23715,13 @@ radial glial cells acting as neural progenitors throughout life. - + - - - - - - An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The axon terminal is narrowly stratified and are found just below a calretinin-expressing band in sublamina 4 of the inner plexiform layer. IMB cone bipolar cell type 7 cone bipolar cell (sensu Mus) @@ -21210,7 +23738,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -21223,12 +23751,6 @@ radial glial cells acting as neural progenitors throughout life. - - - - - - An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. This cell has the widest dendritic field and the widest axon terminal of all retinal bipolar cells. The axon terminal is delicate and stratified through sublaminae 4 and 5 of the inner plexiform layer. DB6 cone bipolar cell type 8 cone bipolar cell (sensu Mus) @@ -21245,19 +23767,13 @@ radial glial cells acting as neural progenitors throughout life. - + - - - - - - An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The dendritic tree is wide and the dendritic convergence indicates cone selectivity. The axon terminal is sparsely branched and terminates in sublamina 5 of the inner plexiform layer. BB cone bipolar cell type 9 cone bipolar cell (sensu Mus) @@ -21289,6 +23805,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -21296,6 +23813,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A nucleated blood cell involved in coagulation, typically seen in birds and other non-mammalian vertebrates. Note that this is a non-mammalian cell type. Use platelet ; CL:0000233 for thrombocytes (platelets) in mammals. @@ -21333,6 +23856,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage. BTO:0001441 CALOHA:TS-0647 @@ -21447,12 +23976,97 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers. BTO:0001571 CALOHA:TS-0289 @@ -21495,6 +24109,7 @@ radial glial cells acting as neural progenitors throughout life. + A cell of the monocyte, granulocyte, or mast cell lineage. myeloid leukocyte @@ -21545,6 +24160,36 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any of the immature or mature forms of a granular leukocyte that in its mature form has an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse, bluish-black granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation. A basophil is CD123-positive, CD193-positive, CD203c-positive, and FceRIa-positive. polymorphonuclear leucocyte @@ -21600,6 +24245,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + @@ -21679,6 +24330,60 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -21721,6 +24426,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + @@ -21779,6 +24490,36 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Any of the immature or mature forms of a granular leukocyte with a nucleus that usually has two lobes connected by one or more slender threads of chromatin, and cytoplasm containing coarse, round granules that are uniform in size and which can be stained by the dye eosin. Eosinophils are CD9-positive, CD191-positive, and CD193-positive. polymorphonuclear leucocyte @@ -21834,6 +24575,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + @@ -21918,6 +24665,66 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -21960,6 +24767,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + @@ -22007,6 +24820,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes. PMN @@ -22063,6 +24888,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + @@ -22117,6 +24948,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A tissue-resident macrophage of the renal glomerular mesangium involved in the disposal and degradation of filtration residues, presentation of antigen to T cells and in tissue remodeling. mesangial cell mesangial phagocyte @@ -22156,6 +24999,7 @@ radial glial cells acting as neural progenitors throughout life. + A specialized mononuclear osteoclast associated with the absorption and removal of bone, precursor of multinuclear osteoclasts. Morphology: mononuclear, highly vesicular. mononuclear osteoclast @@ -22195,6 +25039,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -22238,6 +25083,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -22325,7 +25171,20 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + A dendritic cell of the myeloid lineage. interdigitating cell veiled cell @@ -22368,6 +25227,7 @@ radial glial cells acting as neural progenitors throughout life. + A phagocyte formed by the fusion of mononuclear phagocytes. multinucleated phagocyte @@ -22405,8 +25265,8 @@ radial glial cells acting as neural progenitors throughout life. - - + + A dendritic cell type of distinct morphology, localization, and surface marker expression (CD123-positive) from other dendritic cell types and associated with early stage immune responses, particularly the release of physiologically abundant amounts of type I interferons in response to infection. @@ -22470,6 +25330,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -22477,6 +25338,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + @@ -22540,6 +25413,42 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -22614,6 +25523,30 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + A memory B cell is a mature B cell that is long-lived, readily activated upon re-encounter of its antigenic determinant, and has been selected for expression of higher affinity immunoglobulin. This cell type has the phenotype CD19-positive, CD20-positive, MHC Class II-positive, and CD138-negative. memory B lymphocyte @@ -22679,8 +25612,32 @@ radial glial cells acting as neural progenitors throughout life. - - + + + + + + + + + + + + + + + + + + + + + + + + + + A naive B cell is a mature B cell that has the phenotype surface IgD-positive, surface IgM-positive, CD20-positive, CD27-negative and that has not yet been activated by antigen in the periphery. @@ -22732,6 +25689,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A T cell that expresses an alpha-beta T cell receptor complex. alpha-beta T lymphocyte @@ -22773,6 +25736,7 @@ radial glial cells acting as neural progenitors throughout life. + An alpha-beta T cell that has an immature phenotype and has not completed T cell selection. immature alpha-beta T lymphocyte immature alpha-beta T-cell @@ -22812,6 +25776,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -22865,6 +25830,19 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + A CD4-positive, CD25-positive, alpha-beta T cell that regulates overall immune responses as well as the responses of other T cell subsets through direct cell-cell contact and cytokine release. Treg suppressor T cell @@ -22922,6 +25900,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -22986,12 +25965,42 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A CD8-positive, alpha-beta T cell that is capable of killing target cells in an antigen specific manner with the phenotype perforin-positive and granzyme B-positive. cytotoxic T cell @@ -23045,6 +26054,7 @@ radial glial cells acting as neural progenitors throughout life. + A CD8-positive, alpha-beta T cell that regulates overall immune responses as well as the responses of other T cell subsets through direct cell-cell contact and cytokine release. suppressor T cell suppressor T lymphocyte @@ -23093,6 +26103,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A alpha-beta intraepithelial T cell found in the columnar epithelium of the gastrointestinal tract. Intraepithelial T cells often have distinct developmental pathways and activation requirements. IEL @@ -23139,6 +26155,7 @@ radial glial cells acting as neural progenitors throughout life. + A mature alpha-beta T cell of the columnar epithelium of the gastrointestinal tract. Intraepithelial T cells often have distinct developmental pathways and activation requirements. IEL intraepithelial lymphocyte @@ -23179,6 +26196,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A T cell that expresses a gamma-delta T cell receptor complex. gamma-delta T lymphocyte @@ -23234,6 +26257,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + @@ -23278,6 +26308,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -23327,6 +26358,7 @@ radial glial cells acting as neural progenitors throughout life. + A mature gamma-delta T cell that is found in the columnar epithelium of the gastrointestinal tract. These cells participate in mucosal immune responses. IEL intraepithelial lymphocyte @@ -23367,6 +26399,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A gamma-delta intraepithelial T cell that has the phenotype CD8-alpha alpha-positive. IEL @@ -23414,6 +26452,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A gamma-delta intraepithelial T cell that has the phenotype CD4-negative and CD8-negative. IEL intraepithelial lymphocyte @@ -23484,12 +26534,48 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A thymocyte that has the phenotype CD4-negative, CD8-positive, CD44-negative, CD25-negative, and pre-TCR-positive. ISP T.ISP.th @@ -23544,6 +26630,19 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + @@ -23605,6 +26704,25 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + @@ -23668,6 +26786,25 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + @@ -23722,6 +26859,19 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + @@ -23780,6 +26930,19 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + @@ -23835,6 +26998,19 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + @@ -23901,6 +27077,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A long-lived, antigen-experienced T cell that has acquired a memory phenotype including distinct surface markers and the ability to differentiate into an effector T cell upon antigen reexposure. BTO:0003435 @@ -23956,12 +27144,36 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + A mature alpha-beta T cell of a distinct lineage that bears natural killer markers and a T cell receptor specific for a limited set of ligands. NK T cells have activation and regulatory roles particularly early in an immune response. mature NK T lymphocyte @@ -24007,6 +27219,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A T cell which regulates overall immune responses as well as the responses of other T cell subsets through direct cell-cell contact and cytokine release. suppressor T cell @@ -24068,6 +27286,30 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + @@ -24127,6 +27369,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A precursor B cell is a B cell with the phenotype CD10-positive. @@ -24185,12 +27439,42 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An immature B cell of an intermediate stage between the pre-B cell stage and the mature naive stage with the phenotype surface IgM-positive and CD19-positive, and are subject to the process of B cell selection. A transitional B cell migrates from the bone marrow into the peripheral circulation, and then to the spleen. transitional B cell @@ -24261,6 +27545,36 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A B cell of distinct lineage and surface marker expression. B-1 B cells are thought to be the primary source of natural IgM immunoglobulin, that is, IgM produced in large quantities without prior antigenic stimulation and generally reactive against various microorganisms, as well as the source of T-independent IgA immunoglobulin in the mucosal areas. These cells are CD43-positive. B-1 B lymphocyte B-1 B-cell @@ -24311,6 +27625,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A B-1 B cell that has the phenotype CD5-positive. B-1a B lymphocyte B-1a B-cell @@ -24357,6 +27677,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A B-1 B cell that has the phenotype CD5-negative, but having other phenotypic attributes of a B-1 B cell. B-1b B lymphocyte B-1b B-cell @@ -24404,6 +27730,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A conventional B cell subject to antigenic stimulation and dependent on T cell help and with a distinct surface marker expression pattern from B-1 B cells. These cells are CD43-negative. B-2 B lymphocyte B-2 B-cell @@ -24452,6 +27790,8 @@ radial glial cells acting as neural progenitors throughout life. + + @@ -24562,6 +27902,43 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -24641,6 +28018,25 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + @@ -24717,6 +28113,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A lymphoid progenitor cell of the T cell lineage, with some lineage specific marker expression, but not yet fully committed to the T cell lineage. pro-T lymphocyte progenitor T cell @@ -24760,6 +28162,8 @@ radial glial cells acting as neural progenitors throughout life. + + @@ -24767,6 +28171,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A progenitor cell of the thrombocyte, a nucleated blood cell involved in coagulation typically seen in birds and other non-mammalian vertebrates. Note that this is a non-mammalian cell type. thromboblast @@ -24809,6 +28219,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A myeloblast committed to the basophil lineage. basophilic myeloblast @@ -24849,6 +28265,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A promyelocyte committed to the basophil lineage. FMA:84208 basophilic promyelocyte @@ -24975,13 +28397,159 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A progenitor cell of the mast cell lineage. Markers for this cell are FceRIa-low, CD117-positive, CD9-positive, T1/ST2-positive, SCA1-negative, and lineage-negative. MCP CFU-MC @@ -25032,6 +28600,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A myeloblast committed to the eosinophil lineage. eosinophilic myeloblast @@ -25072,6 +28646,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A promyelocyte committed to the eosinophil lineage. FMA:84199 eosinophilic promyelocyte @@ -25106,6 +28686,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -25113,6 +28694,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A progenitor cell of the neutrophil lineage. neutrophil stem cell @@ -25161,7 +28748,33 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -25237,7 +28850,63 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -25335,8 +29004,98 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -25356,12 +29115,6 @@ radial glial cells acting as neural progenitors throughout life. Markers differ between mouse and human. hematopoietic multipotent progenitor cell - - - - - true - @@ -25388,6 +29141,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A progenitor cell restricted to the lymphoid lineage. lymphoid progenitor cell @@ -25429,6 +29189,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A progenitor cell restricted to the myeloid lineage. myeloid progenitor cell @@ -25479,6 +29246,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -25486,6 +29254,24 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + An immature cell of the conventional dendritic cell lineage, characterized by high levels of antigen uptake via endocytosis, macropinocytosis, and phagocytosis, and typically found resident in the tissues. Markers for this cell are CD80-low, CD86-low, and MHC-II-low. immature myeloid dendritic cell @@ -25535,13 +29321,38 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + A mature cell of the conventional dendritic cell lineage, characterized by a high capacity for antigen presentation and typically found in a lymph node. mature dendritic cell FMA:83038 @@ -25586,6 +29397,7 @@ radial glial cells acting as neural progenitors throughout life. + A leukocyte with a single non-segmented nucleus in the mature form. BTO:0000878 @@ -25654,7 +29466,43 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A resting mature B cell that has the phenotype IgM-positive, IgD-positive, CD23-positive and CD21-positive, and found in the B cell follicles of the white pulp of the spleen or the corticol areas of the peripheral lymph nodes. This cell type is also described as being CD19-positive, B220-positive, AA4-negative, CD43-negative, and CD5-negative. Fo B cell Fo B-cell @@ -25665,12 +29513,6 @@ radial glial cells acting as neural progenitors throughout life. Follicular B cells are also reportedly CD48-positive, CD84-positive, CD229-positive, and CD352-positive. follicular B cell - - - - - true - @@ -25704,6 +29546,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + @@ -25783,6 +29637,49 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A mature B cell that is located in the marginal zone of the spleen with the phenotype CD23-negative and CD21-positive and expressing a B cell receptor usually reactive to bacterial cell wall components or senescent self components such as oxidized-LDL. This cell type is also described as being CD19-positive, B220-positive, IgM-high, AA4-negative, CD35-high. MZ B cell @@ -25849,6 +29746,8 @@ radial glial cells acting as neural progenitors throughout life. + + An olfactory receptor cell in which the apical ending of the dendrite is a pronounced ciliated olfactory knob. ciliated olfactory sensory neuron ciliated sensory neuron @@ -25914,7 +29813,14 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A neuron that releases serotonin as a neurotransmitter. MESH:D059326 WBbt:0006837 @@ -25995,7 +29901,7 @@ radial glial cells acting as neural progenitors throughout life. - + Olfactory epithelial support cell is a columnar cell that extends from the epithelial free margin to the basement membrane of the olfactory epithelium. This cell type has a large, vertically, elongate, euchromatic nucleus, along with other nuclei, forms a layer superficial to the cell body of the receptor cell; sends long somewhat irregular microvilli into the mucus layer; at the base, with expanded end-feet containing numerous lamellated dense bodies resembling lipofuscin of neurons. FMA:62302 olfactory epithelial support cell @@ -26069,7 +29975,14 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + Neuromast hair cell is a hair cell that acts as a sensory receptor of the neuromast; it is morphologically polarized as a result of the relative position of the single kinocilium and the clusters of stereocilia on its apical surface. neuromast hair cell @@ -26096,6 +30009,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A skeletal muscle myoblast that differentiates into slow muscle fibers. slow muscle myoblast @@ -26122,6 +30042,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A skeletal muscle myoblast that differentiates into fast muscle fibers. fast muscle myoblast @@ -26183,6 +30110,43 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A monocyte that responds rapidly to microbial stimuli by secreting cytokines and antimicrobial factors and which is characterized by high expression of CCR2 in both rodents and humans, negative for the lineage markers CD3, CD19, and CD20, and of larger size than non-classical monocytes. inflammatory monocyte @@ -26238,6 +30202,31 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + @@ -26287,6 +30276,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A macrophage that suppresses immune responses. Markers: May express: IL10, TGFbeta. suppressor macrophage @@ -26343,6 +30338,42 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An elicited macrophage that is recruited into the tissues in response to injury and infection as part of an inflammatory response, expresses high levels of pro-inflammatory cytokines, ROS and NO, and shows potent microbicidal activity. classically activated macrophage M1 macrophage @@ -26388,6 +30419,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A macrophage constitutively resident in a particular tissue under non-inflammatory conditions, and capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells. FMA:84642 @@ -26429,6 +30466,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A gut-associated lymphoid tissue macrophage found in lamina propria of the gut. gastrointestinal system (lamina propria) macrophage macrophage of gastrointestinal system (lamina propria) @@ -26466,6 +30510,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A tissue-resident macrophage resident found in the thymus, involved in the clearance of apoptotic thymocytes. @@ -26535,6 +30591,31 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + A secondary lymphoid organ macrophage found in a lymph node. This cell is CD169-high. MF.LN Marker was observed on rat cells. @@ -26576,16 +30657,22 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + + + + + + + A gut-associated lymphoid tissue macrophage found in tonsils. tonsillar macrophage - - - - - true - @@ -26612,6 +30699,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A gut-associated lymphoid tissue macrophage found in the Peyer's patches. Peyer's patch macrophage @@ -26651,6 +30744,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A secondary lymphoid organ macrophage found in the spleen. FMA:83026 Role or process: immune, clearance of apoptotic and senescent cells. @@ -26708,6 +30808,43 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A splenic macrophage found in the marginal zone of the spleen, involved in recognition and clearance of particulate material from the splenic circulation. Markers include F4/80-negative, MARCO-positive, SR-A-positive, SIGN-R1-positive, and Dectin2-positive. @@ -26762,6 +30899,37 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A splenic macrophage found in the areas surrounding the white pulp of the spleen, adjacent to the marginal sinus. Markers include F4/80-negative, Dectin2-low, sialoadhesin-positive. Markers: Mouse: F4/80-, Dectin2-low, sialoadhesin+. splenic metallophillic macrophage @@ -26834,6 +31002,61 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A splenic macrophage found in the red-pulp of the spleen, and involved in immune responses to blood-borne pathogens and in the clearance of senescent erythrocytes. Markers include F4/80-positive, CD68-positive, MR-positive, Dectin2-positive, macrosialin-positive, and sialoadhesin-low. @@ -26896,12 +31119,55 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A type of monocyte characterized by low expression of CCR2, low responsiveness to monocyte chemoattractant CCL2/MCP1, low phagocytic activity, and decrease size relative to classical monocytes, but increased co-stimulatory activity. May also play a role in tissue repair. patrolling monocyte @@ -26954,6 +31220,25 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + A splenic macrophage found in the white pulp of the spleen. Markers include F4/80-negative, CD68-positive, and macrosialin-positive. @@ -27000,6 +31285,24 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + A splenic white pulp macrophage found in and around the germinal centers of the white pulp of the spleen that participates in phagocytosis of apoptotic B cells from the germinal centers. A marker for a cell of this type is Mertk-positive. @@ -27038,6 +31341,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A tissue-resident macrophage found in the central nervous system. CNS macrophage @@ -27065,7 +31375,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -27077,23 +31387,69 @@ radial glial cells acting as neural progenitors throughout life. - - A central nervous system macrophage found in the meninges (the three membranes that surround the brain). This macrophage types is highly phagocytic and expresses scavenger receptors. + + + + + + + + + + + + + + A border associated macrophage that is part of a meninx. This macrophage type is elongated and amoeboid spindle-shaped with limited mobility. This macrophage is highly phagocytic, expresses scavenger receptors, has dynamic protrusions and extends its processes during inflammation. + subdural leptomeningeal macrophage + subdural meningeal macrophage + MM + MnMΦ + sdΜΦ meningeal macrophage - - - - - true - - A central nervous system macrophage found in the meninges (the three membranes that surround the brain). This macrophage types is highly phagocytic and expresses scavenger receptors. + A border associated macrophage that is part of a meninx. This macrophage type is elongated and amoeboid spindle-shaped with limited mobility. This macrophage is highly phagocytic, expresses scavenger receptors, has dynamic protrusions and extends its processes during inflammation. GOC:ana GO_REF:0000031 PMID:11591794 + PMID:24078900 + PMID:37232741 + + + + + subdural leptomeningeal macrophage + PMID:33556248 + + + + + subdural meningeal macrophage + PMID:28323268 + + + + + MM + PMID:33556248 + + + + + + MnMΦ + PMID:38347231 + + + + + + sdΜΦ + PMID:37232741 + @@ -27104,9 +31460,9 @@ radial glial cells acting as neural progenitors throughout life. - + - + @@ -27116,24 +31472,39 @@ radial glial cells acting as neural progenitors throughout life. - - A central nervous system macrophage found at the interface between the blood and the cerebrospinal fluid in the brain. This cell expresses scavenger receptors. - choroid-plexus macrophage + + + + + + + + + + + + + + A border associated macrophage found at the interface between the blood and the cerebrospinal fluid in the brain. This central nervous system macrophage has a star-like shaped body and expresses scavenger receptors. + cpMΦ + choroid plexus macrophage - - - - - true - - A central nervous system macrophage found at the interface between the blood and the cerebrospinal fluid in the brain. This cell expresses scavenger receptors. + A border associated macrophage found at the interface between the blood and the cerebrospinal fluid in the brain. This central nervous system macrophage has a star-like shaped body and expresses scavenger receptors. GOC:ana GO_REF:0000031 + PMID:37232741 PMID:9550136 + + + + cpMΦ + PMID:37232741 + + @@ -27143,7 +31514,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -27163,25 +31534,58 @@ radial glial cells acting as neural progenitors throughout life. - - A central nervous system macrophage found in small blood vessels in the brain. Markers include CD14+CD16+CD163+. - Markers: Human/monkey, mice: CD163. Human: CD14+CD16+CD163+. + + + + + + + + + + + + + + + + + + + + + + + + + + + A border associated macrophage that is adjacent to a small blood vessel of a brain. A perivascular macrophage expresses the markers CD14, CD16 and CD163. In homeostatic conditions, this central nervous system macrophage has a non-motile cell body with extending and retracting projections through the blood vessel wall. + pvMΦ perivascular macrophage - + true - A central nervous system macrophage found in small blood vessels in the brain. Markers include CD14+CD16+CD163+. + A border associated macrophage that is adjacent to a small blood vessel of a brain. A perivascular macrophage expresses the markers CD14, CD16 and CD163. In homeostatic conditions, this central nervous system macrophage has a non-motile cell body with extending and retracting projections through the blood vessel wall. GOC:tfm GO_REF:0000031 PMID:16507898 + PMID:37232741 + + + + + pvMΦ + PMID:37232741 + @@ -27201,6 +31605,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A thymic macrophage found in the thymic medulla. @@ -27238,6 +31648,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A thymic macrophage found in the thymic cortex. @@ -27276,6 +31692,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A tissue-resident macrophage found in the mucosa associated lymphoid tissue. mucosa-associated lymphoid tissue macrophage @@ -27316,6 +31738,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A mucosa-associated lymphoid tissue macrophage found in the mucosa-associated lymphoid tissues of the gut. gut-associated lymphoid tissue macrophage @@ -27355,6 +31789,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A mucosa-associated lymphoid tissue macrophage found in the nasal and bronchial mucosa-associated lymphoid tissues. nasal and broncial associated lymphoid tissue macrophage @@ -27398,6 +31844,24 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + A lymph node macrophage found in the subcapsular sinus of lymph nodes that participates in sensing, clearance, and antigen presentation of lymph-borne particulate antigens. This macrophage is capable of activating invaraint NKT cells and is CD169-positive. @@ -27445,6 +31909,24 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + A lymph node macrophage found in the cortex of lymph nodes, in particular in and around the germinal centers, and that participates in phagocytosis of apoptotic B cells from the germinal centers. @@ -27495,6 +31977,31 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + An immature myeloid leukocyte of heterogeneous phenotype found particularly in cancer and sepsis patients that is capable of suppressing activity of T cells in ex vivo assays. This cell type is CD45-positive, CD11b-positive. Markers: Mouse: CD11b+GR1+CD31+; Human: CD34+ CD33+CD15-CD13+. (According to some reports in humans these cells are iNOS+ARG1+IL13+IFNg+); location: In cancerous tissue; in the blood and lymphoid organs in sepsis. @@ -27539,6 +32046,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + An elicited macrophage characterized by low production of pro-inflammatory and Th1 polarizing cytokines and high expression of arginase-1, and associated with tissue remodelling. M2 macrophage @@ -27630,6 +32149,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + An immature T cell located in the thymus. immature T cell immature T lymphocyte @@ -27693,6 +32218,37 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -27762,6 +32318,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + @@ -27840,6 +32403,30 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + @@ -27893,6 +32480,7 @@ radial glial cells acting as neural progenitors throughout life. + A CD4-positive, alpha-beta T cell that has differentiated into a memory T cell. @@ -27950,6 +32538,36 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Mature T cell not yet exposed to antigen with the phenotype CCR7-positive, CD45RA-positive, and CD127-positive. This cell type is also described as being CD25-negative, CD62L-high and CD44-low. naive T lymphocyte naive T-cell @@ -28005,8 +32623,26 @@ radial glial cells acting as neural progenitors throughout life. - - + + + + + + + + + + + + + + + + + + + + CD4-positive, alpha-beta T cell with the phenotype RORgamma-t-positive, CXCR3-negative, CCR6-positive, and capable of producing IL-17. @@ -28088,6 +32724,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + @@ -28150,11 +32793,12 @@ radial glial cells acting as neural progenitors throughout life. - + + - - + + CD4-positive alpha-beta T cell with regulatory function that produces IL-10. @@ -28166,12 +32810,6 @@ radial glial cells acting as neural progenitors throughout life. These cells are reportedly induced by IL-10 and are capable of producing IFN-gamma, IL-5, IL-10, and TGF-beta.) Tr1 cell - - - - - true - @@ -28207,6 +32845,24 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + CD4-positive alpha-beta T cell with the phenotype CD25-positive, CTLA-4-positive, and FoxP3-positive with regulatory function. iTreg induced Treg @@ -28264,6 +32920,30 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + CD4-positive alpha-beta T cell with the phenotype FoxP3-positive, CD25-positive, CD62L-positive, and CTLA-4 positive with regulatory function. nTreg natural Treg @@ -28316,6 +32996,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + CD4-positive, alpha-beta memory T cell with the phenotype CCR7-positive, CD127-positive, CD45RA-negative, CD45RO-positive, and CD25-negative. central memory CD4+ T cell central CD4-positive, alpha-beta memory T cell @@ -28376,6 +33068,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + CD4-positive, alpha-beta memory T cell with the phenotype CCR7-negative, CD127-positive, CD45RA-negative, CD45RO-positive, and CD25-negative. effector memory CD4+ T cell @@ -28447,6 +33151,36 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -28501,6 +33235,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + CD8-positive, alpha-beta memory T cell with the phenotype CCR7-positive, CD127-positive, CD45RA-negative, CD45RO-positive, and CD25-negative. central memory CD8+ T cell central CD8-positive, alpha-beta memory T cell @@ -28575,12 +33321,48 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A CD8-positive, alpha-beta T cell with the phenotype CD69-positive, CD62L-negative, CD127-negative, and CD25-positive, that secretes cytokines. CD8-positive, alpha-beta cytokine secreting effector T lymphocyte CD8-positive, alpha-beta cytokine secreting effector T-cell @@ -28629,6 +33411,8 @@ radial glial cells acting as neural progenitors throughout life. + + A CD8-positive, alpha-beta T cell that has differentiated into a memory T cell. @@ -28665,6 +33449,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A mature T cell that differentiated and acquired cytotoxic function with the phenotype perforin-positive and granzyme-B positive. BTO:0000289 @@ -28719,6 +33509,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A differentiated T cell with ability to traffic to peripheral tissues and is capable of mounting a specific immune response. effector T lymphocyte effector T-cell @@ -28758,6 +33560,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A effector T cell that provides help in the form of secreted cytokines to other immune cells. BTO:0002417 MESH:D006377 @@ -28810,6 +33618,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + CD8-positive, alpha-beta memory T cell with the phenotype CCR7-negative, CD127-positive, CD45RA-negative, CD45RO-positive, and CD25-negative. effector memory CD8+ T cell @@ -28865,6 +33685,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + @@ -28924,6 +33750,24 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + @@ -28976,12 +33820,24 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A mature gamma-delta T cell located in the epidermis that regulates wound healing. DETC dendritic epidermal T lymphocyte @@ -29040,6 +33896,36 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A CD8-positive, alpha-beta positive T cell that has the phenotype T-bet-positive, eomesodermin-positive, CXCR3-positive, CCR6-negative, and is capable of producing interferon-gamma. BTO:0004793 BTO:0004888 @@ -29108,6 +33994,19 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + A CD8-positive, alpha-beta positive T cell expressing GATA-3 and secreting IL-4. BTO:0004794 FMA:84794 @@ -29160,6 +34059,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + @@ -29217,6 +34128,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + @@ -29271,6 +34194,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + An alpha-beta T cell expressing NK cell markers that is CD1d restricted and expresses specific V-alpha chains. NK T cells of this type recognize the glycolipid alpha-galactosylceramide in the context of CD1d. classical NK T cell @@ -29318,6 +34247,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + An alpha-beta T cell expressing NK call markers that is CD1d restricted and expresses a diverse TCR repertoire. Type II NKT cells do not become activated by alpha-galactosylceramide when presented by CD1d. type II NK T lymphocyte type II NK T-cell @@ -29360,6 +34295,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A type I NK T cell that has the phenotype CD4-positive. CD4-positive type I NK T lymphocyte CD4-positive type I NK T-cell @@ -29406,6 +34347,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A type I NK T cell that has the phenotype CD4-negative and CD8-negative. CD4-negative, CD8-negative type I NK T lymphocyte CD4-negative, CD8-negative type I NK T-cell @@ -29459,13 +34412,31 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + + + + + + + + + + + + + A type I NK T cell that has been recently activated, secretes interferon-gamma and IL-4, and has the phenotype CD4-positive, CD69-positive, and downregulated NK markers. activated CD4-positive type I NK T lymphocyte activated CD4-positive type I NK T-cell @@ -29473,12 +34444,6 @@ radial glial cells acting as neural progenitors throughout life. activated CD4-positive type I NKT cell activated CD4-positive type I NK T cell - - - - - true - @@ -29514,13 +34479,25 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + + + + + + + A mature NK T cell that secretes interferon-gamma and enhances type 1 immune responses. CD4-positive type I NK T cell secreting IFN-gamma CD4-positive type I NK T lymphocyte secreting interferon-gamma @@ -29529,12 +34506,6 @@ radial glial cells acting as neural progenitors throughout life. CD4-positive type I NKT cell secreting interferon-gamma CD4-positive type I NK T cell secreting interferon-gamma - - - - - true - @@ -29574,13 +34545,31 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + + + + + + + + + + + + + A mature NK T cell that predominantly secretes type 2 cytokines such as interleukin-4 and interleukin-13 and enhances type 2 immune responses. CD4-positive type I NK T cell secreting IL-4 CD4-positive type I NK T lymphocyte secreting interleukin-4 @@ -29589,12 +34578,6 @@ radial glial cells acting as neural progenitors throughout life. CD4-positive type I NKT cell secreting interleukin-4 CD4-positive type I NK T cell secreting interleukin-4 - - - - - true - @@ -29633,13 +34616,25 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + + + + + + + A type I NK T cell that has been recently activated, secretes interferon-gamma and interleukin-4, and has phenotype CD4-negative, CD8-negative, CD69-positive, and downregulated NK markers. activated CD4-negative, CD8-negative type I NK T lymphocyte activated CD4-negative, CD8-negative type I NK T-cell @@ -29647,12 +34642,6 @@ radial glial cells acting as neural progenitors throughout life. activated CD4-negative, CD8-negative type I NKT cell activated CD4-negative, CD8-negative type I NK T cell - - - - - true - @@ -29692,13 +34681,25 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + + + + + + + A mature NK T cell that secretes interferon-gamma and enhances Th1 immune responses. CD4-negative, CD8-negative type I NK T cell secreting IFN-gamma CD4-negative, CD8-negative type I NK T lymphocyte secreting interferon-gamma @@ -29707,12 +34708,6 @@ radial glial cells acting as neural progenitors throughout life. CD4-negative, CD8-negative type I NKT cell secreting interferon-gamma CD4-negative, CD8-negative type I NK T cell secreting interferon-gamma - - - - - true - @@ -29752,13 +34747,25 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + + + + + + + A mature NK T cell that secretes interleukin-4 and enhances Th2 immune responses. CD4-negative, CD8-negative type I NK T cell secreting IL-4 CD4-negative, CD8-negative type I NK T lymphocyte secreting interleukin-4 @@ -29767,12 +34774,6 @@ radial glial cells acting as neural progenitors throughout life. CD4-negative, CD8-negative type I NKT cell secreting interleukin-4 CD4-negative, CD8-negative type I NK T cell secreting interleukin-4 - - - - - true - @@ -29805,6 +34806,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A type II NK T cell that has been recently activated, secretes interferon-gamma and interleukin-4, and has the phenotype CD69-positive and downregulated NK markers. activated type II NK T lymphocyte activated type II NK T-cell @@ -29851,12 +34864,24 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A type II NK T cell that has been recently activated, secretes interferon-gamma, and has the phenotype CD69-positive and downregulated NK markers. type II NK T cell secreting IFN-gamma type II NK T lymphocyte secreting interferon-gamma @@ -29902,12 +34927,24 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A type II NK T cell that has been recently activated, secretes interleukin-4, and has the phenotype CD69-positive and downregulated NK markers. type II NK T cell secreting IL-4 type II NK T lymphocyte secreting interleukin-4 @@ -29960,6 +34997,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A CD4-positive, alpha-beta T cell that has cytotoxic function. CD4-positive, alpha-beta cytotoxic T lymphocyte @@ -30007,6 +35056,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A CD4-negative, CD8-negative, alpha-beta intraepithelial T cell that is found in the columnar epithelium of the gastrointestinal tract. CD4-negative, CD8-negative, alpha-beta intraepithelial T lymphocyte @@ -30068,12 +35129,43 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A lymphoid progenitor cell that is found in bone marrow, gives rise to B cells, T cells, natural killer cells and dendritic cells, and has the phenotype Lin-negative, Kit-positive, Sca-1-positive, FLT3-positive, CD34-positive, CD150 negative, and GlyA-negative. lymphoid-primed multipotent progenitor @@ -30146,6 +35238,25 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + Cell committed to natural killer cell lineage that has the phenotype CD122-positive, CD34-positive, and CD117-positive. This cell type lacks expression of natural killer receptor proteins. pre-NK cell @@ -30201,6 +35312,37 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + NK cell that has the phenotype CD56-bright, CD16-negative, and CD84-positive with the function to secrete interferon-gamma but is not cytotoxic. CD16-CD56bright NK cell @@ -30266,6 +35408,37 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A mature natural killer cell that has the phenotype CD56-low, CD16-positive and which is capable of cytotoxicity and cytokine production. CD16+CD56+ NK cell CD16-positive, CD56-dim NK cell @@ -30321,6 +35494,24 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + An alpha-beta T cell that is found in the lamina propria of mucosal tissues and is restricted by the MR-1 molecule. mucosal invariant T lymphocyte @@ -30376,6 +35567,30 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + @@ -30427,6 +35642,24 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + @@ -30484,6 +35717,30 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + A Be cell that facilitates development of T-helper 1 (Th1) phenotype in CD4-positive T cells, and secretes high levels of interleukin-2, tumor necrosis factor-alpha and interferon-gamma. B effector 1 cell B effector cell type 1 @@ -30548,6 +35805,36 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A Be cell that facilitates development of T-helper 2 (Th2) phenotype T cells, and secretes high levels of interleukin-2, interleukin-10, interleukin-4, and interleukin-6. B effector 2 cell B effector cell type 2 @@ -30631,6 +35918,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A lymphocyte of B lineage that is devoted to secreting large amounts of immunoglobulin. antibody secreting cell @@ -30668,6 +35961,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A long lived plasma cell that secretes IgE. IgE plasma cell @@ -30703,6 +36002,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A class switched memory B cell that expresses IgE on the cell surface. IgE memory B lymphocyte IgE memory B-cell @@ -30745,6 +36050,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A plasmablast that secretes IgD, and which occur in a small proportion of B cells in the adult. IgD plasmablast @@ -30779,6 +36090,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A plasmablast that secretes IgE. IgE plasmablast @@ -30813,6 +36130,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A short lived plasma cell that secretes IgE. IgE short lived plasma cell @@ -30860,6 +36183,30 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + An preBRC-positive large pre-B-II cell is a large pre-B-II cell that is pre-B cell receptor-positive, composed of surrogate light chain protein (SL), which is composed of VpreB , Lambda 5/14.1, in complex with immunoglobulin mu heavy chain (IgHmu) on the cell surface. preBCR-positive large pre-B-II cell @@ -30908,6 +36255,30 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + A pre-BCR-negative large pre-B-II cell is a large pre-B-II cell that is pre-B cell receptor-negative, composed of surrogate light chain protein (SL), which is composed of VpreB and Lambda 5/14.1, in complex with immunoglobulin mu heavy chain (IgHmu), on the cell surface, and lack a DNA rearrangement of immunoglobulin light chain genes. preBCR-negative large pre-B-II cell @@ -30960,6 +36331,36 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A small pre-B-II cell is a pre-B-II cell that is Rag1-positive, Rag2-positive, pre-BCR-negative, and BCR-negative, is not proliferating, and carries a DNA rearrangement of one or more immunoglobulin light chain genes. small pre-BII cell @@ -31012,8 +36413,20 @@ radial glial cells acting as neural progenitors throughout life. - - + + + + + + + + + + + + + + @@ -31085,8 +36498,44 @@ radial glial cells acting as neural progenitors throughout life. - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A pre-B-I cell is a precursor B cell that expresses CD34 and surrogate immunoglobulin light chain (VpreB , Lambda 5 (mouse)/14.1 (human)) on the cell surface, and TdT, Rag1,and Rag2 intracellularly. Cell type carries a D-JH DNA rearrangement, and lacks expression of immunglobulin heavy chain protein. @@ -31147,6 +36596,24 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + A large pre-B-II cell is a pre-B-II cell that is proliferating and is Rag1-negative and Rag2-negative. large pre-B cell large pre-BII cell @@ -31211,6 +36678,36 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A transitional stage B cell that migrates from the bone marrow into the peripheral circulation, and finally to the spleen. This cell type has the phenotype surface IgM-positive, surface IgD-negative, CD21-negative, CD23-negative, and CD62L-negative, and CD93-positive. This cell type has also been described as IgM-high, CD19-positive, B220-positive, AA4-positive, and CD23-negative. T1 B lymphocyte T1 B-cell @@ -31274,6 +36771,36 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -31343,6 +36870,36 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -31406,10 +36963,11 @@ radial glial cells acting as neural progenitors throughout life. + - - + + A follicular B cell that is IgD-positive, CD23-negative, and CD38-negative. This naive cell type is activated in the extrafollicular areas through interaction with interdigitating dendritic cells and antigen-specific CD4-positive T cells. @@ -31462,6 +37020,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + @@ -31518,6 +37088,24 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + @@ -31576,12 +37164,36 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + A germinal center B cell that founds a germinal center, and has the phenotype IgD-positive, CD38-positive, and CD23-negative. Bm2' B lymphocyte Bm2' B-cell @@ -31639,12 +37251,36 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + A germinal center B cell that is rapidly dividing and has the phenotype IgD-negative, CD38-positive, and CD77-positive. Somatic hypermutation of the immunoglobulin V gene region can occur during proliferation of this cell type. Bm3 B lymphocyte Bm3 B-cell @@ -31705,12 +37341,36 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + A germinal center B cell that has the phenotype CD77-negative, IgD-negative, and CD38-positive. These cells have undergone somatic mutation of the B cell receptor. Bm4 B lymphocyte Bm4 B-cell @@ -31766,13 +37426,25 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + + + + + + + A memory B cell arising in the germinal center that is IgD-negative and has undergone somatic mutation of the variable region of the immunoglobulin heavy and light chain genes. Bm5 B lymphocyte Bm5 B-cell @@ -31780,12 +37452,6 @@ radial glial cells acting as neural progenitors throughout life. Bm5 B cells are also reportedly CD10-positive, CD23-negative, CD38-negative, CD39-positive, CD44-positive, CD71-positive, and CD77-negative. Bm5 B cell - - - - - true - @@ -31823,6 +37489,24 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + A mature B cell that produces cytokines that can influence CD4 T cell differentiation. B effector cell effector B cell @@ -31877,6 +37561,30 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + A mature B cell that has the phenotype CD1d-positive and expresses interleukin-10. This cell type has been associated with suppression of chronic inflammatory responses and T cell responses. B(reg) B10 cell @@ -31949,6 +37657,42 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -32018,7 +37762,13 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + An IgM memory B cell is an unswitched memory B cell with the phenotype IgM-positive and IgD-negative. IgM memory B lymphocyte IgM memory B-cell @@ -32066,12 +37816,30 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + A class switched memory B cell is a memory B cell that has undergone Ig class switching and therefore is IgM-negative on the cell surface. These cells are CD27-positive and have either IgG, IgE, or IgA on the cell surface. class switched memory B lymphocyte @@ -32118,6 +37886,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A class switched memory B cell that expresses IgA. IgA memory B lymphocyte IgA memory B-cell @@ -32186,12 +37960,36 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + A fully differentiated plasma cell that lives for years, as opposed to months, secretes immunoglobulin, and has the phenotype weakly CD19-positive, CD20-negative, CD38-negative, strongly CD138-positive, MHC Class II-negative, surface immunoglobulin-negative, IgD-negative, and strongly CXCR4-positive. The majority of these cells of this type reside in the bone marrow. long lived plasma cell @@ -32231,8 +38029,8 @@ radial glial cells acting as neural progenitors throughout life. - - + + A fully differentiated plasma cell that lives for months. @@ -32270,6 +38068,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A short lived plasma cell that secretes IgA. These cells may be found in the bone marrow as well as in the mucosal immune system. IgA short lived plasma cell @@ -32305,6 +38109,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A short lived plasma cell that secretes IgG. IgG short lived plasma cell @@ -32340,6 +38150,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A short lived plasma cell that secretes IgM. IgM short lived plasma cell @@ -32375,6 +38191,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + An IgG memory B cell is a class switched memory B cell that is class switched and expresses IgG on the cell surface. IgG memory B lymphocyte IgG memory B-cell @@ -32434,12 +38256,37 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + An activated mature (naive or memory) B cell that is secreting immunoglobulin, typified by being CD27-positive, CD38-positive, CD138-negative. CD20-negative B cell @@ -32487,7 +38334,13 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + A memory B cell with the phenotype IgD-negative and CD27-negative. dn memory B cell dn memory B lymphocyte @@ -32498,12 +38351,6 @@ radial glial cells acting as neural progenitors throughout life. double negative memory B-lymphocyte double negative memory B cell - - - - - true - @@ -32530,6 +38377,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A plasmablast that secretes IgG. IgG plasmablast @@ -32565,6 +38418,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A plasmablast that secretes IgM. IgM plasmablast @@ -32599,6 +38458,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A plasmablast that secretes IgA. IgA plasmablast @@ -32634,6 +38499,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A fully differentiated plasma cell that secretes IgG. IgG plasma cell @@ -32670,6 +38541,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A fully differentiated plasma cell that secretes IgM. IgM plasma cell @@ -32706,6 +38583,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A fully differentiated plasma cell that secretes IgA. IgA plasma cell @@ -32779,6 +38662,30 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + CD11c-low plasmacytoid dendritic cell is a leukocyte that is CD11c-low, CD45R-positive, GR1-positive and CD11b-negative. Originally described in the dendritic cell ontology (DC_CL:0000001)(PMID:19243617). These cells are CD281-positive (TLR1), CD282-positive (TLR2), CD285-positive (TLR5), CD286-positive (TLR6), and CD288-positive (TLR8). CD11c-low plasmacytoid dendritic cell @@ -32817,6 +38724,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + Conventional dendritic cell is a dendritic cell that is CD11c-high. interdigitating cell @@ -32884,6 +38797,30 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + CD11c-negative plasmacytoid dendritic cell is a leukocyte is CD11c-negative, CD45RA-positive, CD85g-positive(ILT7), CD123-positive, CD303-positive. CD303-positive dendritic cell Originally described in the dendritic cell ontology (DC_CL:0000004)(PMID:19243617). These cells are CD281-positive (TLR1), CD286-positive (TLR6), and CD290-positive (TLR10). @@ -32925,6 +38862,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -32932,6 +38870,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + Immature CD11c-low plasmacytoid dendritic cell is a CD11c-low plasmacytoid dendritic cell that is CD80-low and CD86-low. Originally described in the dendritic cell ontology (DC_CL:0000006)(PMID:19243617). immature CD11c-low plasmacytoid dendritic cell @@ -32980,13 +38930,38 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + Mature CD11c-low plasmacytoid dendritic cell is a CD11c-low plasmacytoid dendritic cell that is CD83-high and is CD80-positive, CD86-positive, and MHCII-positive. Originally described in the dendritic cell ontology (DC_CL:0000007)(PMID:19243617). mature CD11c-low plasmacytoid dendritic cell @@ -33036,12 +39011,30 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + Immature CD11c-negative plasmacytoid dendritic cell is a CD11c-negative plasmacytoid dendritic cell is CD80-negative, CD86-low and MHCII-low. Originally described in the dendritic cell ontology (DC_CL:0000008)(PMID:19243617). immature CD11c-negative plasmacytoid dendritic cell @@ -33110,12 +39103,36 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + Mature CD11c-negative plasmacytoid dendritic cell is a CD11c-negative plasmacytoid dendritic cell is CD80-high, CD86-high, MHCII-high and is CD83-positive. Originally described in the dendritic cell ontology (DC_CL:0000009)(PMID:19243617). mature CD11c-negative plasmacytoid dendritic cell @@ -33160,13 +39177,8 @@ radial glial cells acting as neural progenitors throughout life. + - - - - - - Immature CD8_alpha-negative CD11b-positive dendritic cell is a CD8_alpha-negative CD11b-positive dendritic cell that is CD80-low, CD86-low, and MHCII-low. Originally described in the dendritic cell ontology (DC_CL:0000010)(PMID:19243617). immature CD8_alpha-negative CD11b-positive dendritic cell @@ -33219,13 +39231,44 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + CD8_alpha-negative CD11b-negative dendritic cell is a conventional dendritic cell that is CD11b-negative, CD4-negative CD8_alpha-negative and is CD205-positive. This cell is able to cross- present antigen to CD8-alpha-positive T cells. DC.8-4-11b- triple negative dendritic cell @@ -33280,13 +39323,38 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + CD8_alpha-negative CD11b-positive dendritic cell is a conventional dendritic cell that is CD11b-positive, CD4-positive and is CD205-negative and CD8_alpha-negative. DC.4+ Defined as having a disposition to secreting anti-inflammatory cytokines. These markers are associated with mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000012)(PMID:19243617). @@ -33342,13 +39410,50 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + CD8_alpha-positive CD11b-negative dendritic cell is a conventional dendritic cell that is CD11b-negative, CD4-negative and is CD205-positive and CD8_alpha-positive. DC.8+ Cells are defined as having a disposition to secreting inflammatory cytokines. Originally described in the dendritic cell ontology (DC_CL:0000013)(PMID:19243617). @@ -33394,13 +39499,8 @@ radial glial cells acting as neural progenitors throughout life. + - - - - - - Immature CD8_alpha-negative CD11b-negative dendritic cell is a CD8_alpha-negative CD11b-negative dendritic cell that is CD80-low, CD86-low, and MHCII-low. These markers are associated with mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000014)(PMID:19243617). immature CD8_alpha-negative CD11b-negative dendritic cell @@ -33452,6 +39552,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -33507,6 +39608,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -33558,13 +39660,8 @@ radial glial cells acting as neural progenitors throughout life. + - - - - - - Immature CD8_alpha-positive CD11b-negative dendritic cell is a CD8_alpha-positive CD11b-negative dendritic cell that is CD80-low, CD86-low, and MHCII-low. Originally described in the dendritic cell ontology (DC_CL:0000017)(PMID:19243617). immature CD8_alpha-positive CD11b-negative dendritic cell @@ -33613,6 +39710,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -33667,7 +39765,25 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + + + + + + + + + + + + + Dermal dendritic cell is a conventional dendritic cell that is CD11b-positive, CD205-positive and CD8 alpha-negative. BTO:0004812 @@ -33675,12 +39791,6 @@ radial glial cells acting as neural progenitors throughout life. Originally described in the dendritic cell ontology (DC_CL:0000019)(PMID:19243617). These cells are also CD281-positive (TLR1), CD282-positive (TLR2), CD283-positive (TLR3), CD284-positive (TLR4), CD285-positive (TLR5), CD288-positive (TLR8), and CD289-positive (TLR9). dermal dendritic cell - - - - - true - @@ -33722,17 +39832,35 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + + + + + + + + + + + + + + + + + + + Interstitial dendritic cell is a conventional dendritic cell that is CD11b-positive, CD1a-positive, CD206-positive, CD209-positive, and CD36-positive. Originally described in the dendritic cell ontology (DC_CL:0000020)(PMID:19243617). These cells are also CD281-positive (TLR1), CD282-positive (TLR2), CD283-positive (TLR3), CD284-positive (TLR4), CD286-positive (TLR6), CD288-positive (TLR8), and CD290-positive (TLR10). interstitial dendritic cell - - - - - true - @@ -33799,6 +39927,55 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A hematopoietic stem cell that has plasma membrane part Kit-positive, SCA-1-positive, CD150-positive and CD34-negative. LSK stem cell @@ -33848,13 +40025,8 @@ radial glial cells acting as neural progenitors throughout life. + - - - - - - Immature dermal dendritic cell is a dermal dendritic cell that is CD80-low, CD86-low, and MHCII-low. Originally described in the dendritic cell ontology (DC_CL:0000022)(PMID:19243617). immature dermal dendritic cell @@ -33902,6 +40074,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -33952,13 +40125,8 @@ radial glial cells acting as neural progenitors throughout life. + - - - - - - Immature interstitial dendritic cell is a interstitial dendritic cell that is CD80-low, CD86-low, and MHCII-low. Originally described in the dendritic cell ontology (DC_CL:0000024)(PMID:19243617). immature interstitial dendritic cell @@ -34025,6 +40193,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -34073,6 +40242,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + CD1a-positive Langerhans cell is a Langerhans_cell that is CD1a-positive and CD324-positive. CD1a-LC These markers are associated with human cells. Originally described in the dendritic cell ontology (DC_CL:0000026)(PMID:19243617). These cells are also CD281-positive (TLR1), CD282-positive (TLR2), CD284-positive (TLR4), CD286-positive (TLR6), CD287-positive (TLR7), and CD290-positive (TLR10). When activated, these cells are capable of producing IL-6, IL-8, and IL-15. @@ -34114,6 +40295,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + CD8_alpha-low Langerhans cell is a Langerhans cell that is CD205-high and is CD8_alpha-low. These markers are associated with mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000027)(PMID:19243617). They are also CD205-high, CD281-positive (TLR1), CD282-positive (TLR2), CD283-positive (TLR3), CD285-positive (TLR5), CD286-positive (TLR6), and CD289-positive (TLR9). CD8_alpha-low Langerhans cell @@ -34157,6 +40350,7 @@ radial glial cells acting as neural progenitors throughout life. + Immature CD1a-positive Langerhans cell is a CD1a-positive Langerhans cell that is CD80-low, CD86-low, and MHCII-low. Originally described in the dendritic cell ontology (DC_CL:0000028)(PMID:19243617). @@ -34206,6 +40400,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -34257,13 +40452,8 @@ radial glial cells acting as neural progenitors throughout life. + - - - - - - Immature CD8_alpha-low Langerhans cell is a CD8_alpha-low Langerhans cell that is CD80-low, CD86-low, and MHCII-low. These markers are associated with mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000030)(PMID:19243617). immature CD8_alpha-low Langerhans cell @@ -34330,6 +40520,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -34385,6 +40576,32 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -34438,6 +40655,21 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + @@ -34496,13 +40728,44 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A common myeloid progenitor that is Kit-positive and CD34-positive, Il7ra-negative, and is SCA1-low and Fcgr2-low and Fcgr3-low. CD117-positive common myeloid precursor @@ -34577,6 +40840,55 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + CD133-positive hematopoietic stem cell is a hematopoietic stem cell that is CD34-positive, CD90-positive, and CD133-positive. CALOHA:TS-0448 CD133-positive hematopoietic stem cell @@ -34652,12 +40964,56 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A common lymphoid progenitor that is Kit-low, FLT3-positive, IL7ralpha-positive, and SCA1-low. CD217-positive common lymphocyte precursor CD217-positive common lymphocyte progenitor @@ -34719,13 +41075,50 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A common myeloid progenitor that is CD34-positive, CD38-positive, IL3ra-low, CD10-negative, CD7-negative, CD45RA-negative, and IL-5Ralpha-negative. CD71-positive common myeloid precursor Markers are associated with human cell type. Originally described in the dendritic cell ontology (DC_CL:0000038)(PMID:19243617). @@ -34767,6 +41160,26 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + @@ -34818,6 +41231,25 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + @@ -34918,13 +41350,105 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Common dendritic precursor is a hematopoietic progenitor cell that is CD117-low, CD135-positive, CD115-positive and lacks plasma membrane parts for hematopoietic lineage markers. CDP common dendritic precursor @@ -34933,12 +41457,6 @@ radial glial cells acting as neural progenitors throughout life. Surface markers are for mouse cells. Originally described in the dendritic cell ontology (DC_CL:0000041) CDP are reportedly CD2-negative, CD3-negative, CD4-negative, CD5-negative, CD8a-negative, CD11c-positive, CD14-negative, CD19-negative, CD20-negative, CD56-negative, B220-negative, Ly6g-negative, MHCII-positive, and Ter119-negative. (PMID:19243617). common dendritic progenitor - - - - - true - @@ -34997,7 +41515,9 @@ radial glial cells acting as neural progenitors throughout life. - + + + @@ -35048,6 +41568,9 @@ radial glial cells acting as neural progenitors throughout life. + + + Granule cell that is part of the cerebral cortex. cortical granule cell @@ -35074,6 +41597,8 @@ radial glial cells acting as neural progenitors throughout life. + + Granule cell with a soma found in the hippocampus. hippocampal granule cell @@ -35119,6 +41644,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A connective tissue cell found in bone. @@ -35158,6 +41690,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -35205,6 +41738,30 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + A CD8-positive alpha-beta-positive T cell with the phenotype CXCR3-positive and having suppressor function. They are capable of producing IL-10, suppressing proliferation, and suppressing IFN-gamma production. CD8+CXCR3+ T cell CD8+CXCR3+ T lymphocyte @@ -35252,8 +41809,8 @@ radial glial cells acting as neural progenitors throughout life. - - + + CD4-positive, alpha-beta T cell that produces IL-22. @@ -35304,6 +41861,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A recently activated CD4-positive, alpha-beta T cell with the phenotype HLA-DRA-positive, CD38-positive, CD69-positive, CD62L-negative, CD127-negative, and CD25-positive. activated CD4+ T cell activated CD4-positive, alpha-beta T lymphocyte, human @@ -35359,7 +41928,20 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + A CD4-positive, alpha-beta T cell with the phenotype CCR7-negative, CD45RA-positive. effector CD4+ T cell effector CD4-positive, alpha-beta T lymphocyte @@ -35403,7 +41985,14 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A naive regulatory T cell with the phenotype CD4-positive, CD25-positive, CD127lo, CCR4-positive, and CD45RO-negative. naive CCR4+ Treg naive CCR4-positive regulatory T lymphocyte @@ -35450,7 +42039,20 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + A memory regulatory T cell with phenotype CD4-positive, CD25-positive, CD127lo, CCR4-positive, and CD45RO-positive. memory CCR4+ Treg memory CCR4-positive regulatory T lymphocyte @@ -35490,6 +42092,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A CD4-positive, CD25-positive, alpha-beta regulatory T cell with the additional phenotype CCR4-positive. CCR+ Treg CD4-positive, CD25-positive, CCR4-positive, alpha-beta regulatory T lymphocyte @@ -35529,6 +42137,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A CD4-positive, CD25-positive, CCR4-positive, alpha-beta T regulatory cell with the phenotype HLA-DRA-positive, indicating recent activation. activated CCR4+ Treg activated CD4-positive, CD25-positive, CCR4-positive, alpha-beta regulatory T lymphocyte @@ -35572,6 +42186,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A recently activated CD8-positive, alpha-beta T cell with the phenotype HLA-DRA-positive, CD38-positive, CD69-positive, CD62L-negative, CD127-negative, CCR7-negative, and CD25-positive. activated CD8+ T cell activated CD8-positive, alpha-beta T lymphocyte, human @@ -35627,7 +42253,20 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + A CD8-positive, alpha-beta T cell with the phenotype CCR7-negative, CD45RA-positive. effector CD8+ T cell @@ -35674,6 +42313,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A CD4-positive, alpha-beta T cell that has the phenotype CXCR3-negative, CCR6-negative. non-Th1/Th17 CD4+ T cell CD4-positive, CXCR3-negative, CCR6-negative, alpha-beta T lymphocyte @@ -35717,6 +42368,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A CD8-positive, alpha-beta T cell that has the phenotype CXCR3-negative, CCR6-negative. non-Tc1/Tc17 CD8+ T cell CD8-positive, CXCR3-negative, CCR6-negative, alpha-beta T lymphocyte @@ -35756,6 +42419,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A memory B cell that lacks expression of surface IgD. IgD- memory B cell This cell type is compatible with the HIPC Lyoplate markers for 'IgD- memory B cell'. The majority of these cells are class-switched, though some are IgM-positive. @@ -35804,6 +42473,31 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + A monocyte that expresses CD14 and is negative for the lineage markers CD3, CD19, and CD20. monocyte @@ -35847,6 +42541,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + An intermediate monocyte that is CD14-positive and with low amounts of CD16. intermediate monocyte, human @@ -35879,6 +42580,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A dendritic cell with the phenotype HLA-DRA-positive. dendritic cell @@ -35918,6 +42625,7 @@ radial glial cells acting as neural progenitors throughout life. + A myeloid dendritic cell with the phenotype HLA-DRA-positive. myeloid dendritic cell @@ -35963,6 +42671,19 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + A plasmacytoid dendritic cell with the phenotype HLA-DRA-positive, CD123-positive, and CD11c-negative. plasmacytoid dendritic cell @@ -36026,6 +42747,44 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages. These cells are CD34-positive, and express Gata1, Gata2, C/EBPa, and Pu.1. common myeloid precursor, CD34-positive CFU-GEMM @@ -36162,11 +42921,76 @@ radial glial cells acting as neural progenitors throughout life. - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers. @@ -36199,6 +43023,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A cell found in an organism or derived from an organism exhibiting a phenotype that deviates from the expected phenotype of any native cell type of that organism. Abnormal cells are typically found in disease states or disease models. 2017-01-30T18:53:32Z @@ -36250,6 +43080,30 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + @@ -36312,6 +43166,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + An abnormal cell exhibiting dysregulation of cell proliferation or programmed cell death and capable of forming a neoplasm, an aggregate of cells in the form of a tumor mass or an excess number of abnormal cells (liquid tumor) within an organism. 2017-01-30T19:16:26Z @@ -36348,6 +43208,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A neoplastic cell that is capable of entering a surrounding tissue 2017-01-30T19:39:12Z @@ -36394,6 +43260,31 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + A lymphocyte that lacks characteristic T cell, B cell, myeloid cell, and dendritic cell markers, that functions as part of the innate immune response to produce cytokines and other effector responses. @@ -36478,6 +43369,85 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A progenitor cell committed to the erythroid lineage. This cell is ter119-positive but lacks expression of other hematopoietic lineage markers (lin-negative). BTO:0004911 BFU-E @@ -36525,6 +43495,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + An innate lymphoid cell that is capable of producing the type 1 cytokine IFN-gamma, but not Th2 or Th17 cell-associated cytokines. @@ -36578,6 +43555,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + An innate lymphoid cell that is capable of producing T-helper 2-cell associated cytokines upon stimulation. @@ -36650,6 +43634,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + An innate lymphoid cell that constituitively expresses RORgt and is capable of expressing IL17A and/or IL-22. @@ -36697,6 +43688,25 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + @@ -36742,6 +43752,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + An innate lymphoid cell in the human with the phenotype CD34-negative, CD56-positive, CD117-positive.Thie cell type may include precusors to NK cells and ILC3 cells. CD34-negative, CD56-positive, CD117-positive ILC CD34-negative, CD56-positive, CD117-positive ILCP @@ -36789,6 +43806,31 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + An innate lymphoid cell precursor in the human with the phenotype CD34-positive, CD56-positive, CD117-positive.Thie cell type may include precusors to NK cells and ILC3 cells. CD34-positive, CD56-positive, CD117-positive CILP @@ -36822,6 +43864,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + An innate lymphoid cell in the human with the phenotype KLRG1-positive that is a precusor for ILC2 cells. KLRG1-positive ILC KLRG1-positive innate lymphoid cell, human @@ -36854,6 +43903,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + An innate lymphoid cell in the human with the phenotype NKp46-positive that is a precusor for NK cells and ILC3 cells. NKp46-positive ILC @@ -36892,6 +43948,25 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + An ILC1 cell in the human with the phenotype CD56-negative, IL-7Ralpha-positive, T-bet-positive. innate lymphoid cell 1, human @@ -36925,6 +44000,19 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + A group 3 innate lymphoid cell in the human with the phenotype IL-7Ralpha-positive. ILC3, human @@ -36964,6 +44052,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A group 3 innate lymphoid cell in the human with the phenotype IL-7Ralpha-positive, and NKp44-positive. NKp44-positive group 3 innate lymphoid cell, human @@ -37001,6 +44096,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A group 3 innate lymphoid cell in the human with the phenotype IL-7Ralpha-positive, and NKp44-negative. NKp44-negative group 3 innate lymphoid cell, human @@ -37050,6 +44152,43 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A group 2 innate lymphoid cell in the human with the phenotype CD25-positive, CD127-positive, CD161-positive, and GATA-3-positive. ILC2, human @@ -37080,6 +44219,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + An innate lyphoid cell with an immature phenotype. immature ILC @@ -37126,6 +44272,30 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + @@ -37197,6 +44367,24 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + A lymphocyte of B lineage that is CD19-positive. Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells). Lymphocytes of B cell lineage can be distinguished from those of T cell lineage by their lack of CD3e (as part of the T cell receptor complex). @@ -37234,6 +44422,7 @@ radial glial cells acting as neural progenitors throughout life. + A B cell that is CD19-positive. B lymphocyte, CD19-positive @@ -37267,6 +44456,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A plasmablast that is CD86-positive. CD86-positive, CD20-negative plasmablast @@ -37321,84 +44516,156 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A CD8-positive, alpha-beta T cell with memory phenotype indicated by being CD45RO and CD127-positive. This cell type is also described as being CD25-negative, CD44-high, and CD122-high. + + CD8-positive, alpha-beta memory T lymphocyte, CD45RO-positive + CD8-positive, alpha-beta memory T-cell, CD45RO-positive + CD8-positive, alpha-beta memory T-lymphocyte, CD45RO-positive + + + CD8-positive, alpha-beta memory T cell, CD45RO-positive + + + + + + true + + + + + A CD8-positive, alpha-beta T cell with memory phenotype indicated by being CD45RO and CD127-positive. This cell type is also described as being CD25-negative, CD44-high, and CD122-high. + GOC:tfm + GO_REF:0000031 + PMID:20146720 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + + + + + + + + + + + + + + + + + + + - A CD8-positive, alpha-beta T cell with memory phenotype indicated by being CD45RO and CD127-positive. This cell type is also described as being CD25-negative, CD44-high, and CD122-high. - - CD8-positive, alpha-beta memory T lymphocyte, CD45RO-positive - CD8-positive, alpha-beta memory T-cell, CD45RO-positive - CD8-positive, alpha-beta memory T-lymphocyte, CD45RO-positive - - - CD8-positive, alpha-beta memory T cell, CD45RO-positive - - - - - - true - - - - - A CD8-positive, alpha-beta T cell with memory phenotype indicated by being CD45RO and CD127-positive. This cell type is also described as being CD25-negative, CD44-high, and CD122-high. - GOC:tfm - GO_REF:0000031 - PMID:20146720 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + CD4-positive, alpha-beta long-lived T cell with the phenotype CD45RO-positive and CD127-positive. This cell type is also described as being CD25-negative, CD44-high, and CD122-high. CD4-positive, alpha-beta memory T lymphocyte, CD45RO-positive CD4-positive, alpha-beta memory T-cell, CD45RO-positive @@ -37478,6 +44745,54 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -37532,6 +44847,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + @@ -37604,12 +44931,60 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A granulocyte monocyte progenitor that is Kit-positive, CD34-positive, Fc-gamma receptor II/II-positive, and is Sca-1-negative, Il7ra-negative, Cxc3r1-negative, and CD90-negative. 2010-01-13T03:19:28Z @@ -37655,6 +45030,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + @@ -37704,6 +45091,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + @@ -37760,6 +45159,31 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + A megakaryocyte erythroid progenitor cell is CD34-positive, CD38-positive and is IL3-receptor alpha-negative and CD45RA-negative. 2010-01-13T03:43:10Z @@ -37822,6 +45246,49 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A megakaryocyte erythroid progenitor cell that is Kit-positive and is Sca1-negative, CD34-negative, CD90-negative, IL7r-alpha-negative and Fcgr II/III-low. 2010-01-13T03:43:12Z @@ -37873,12 +45340,24 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A lineage marker-negative, CD34-positive, IL5r-alpha-positive, and Sca1-negative eosinophil progenitor cell. 2010-01-14T03:25:15Z @@ -37924,6 +45403,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + @@ -37970,13 +45455,27 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + A progenitor cell that can give rise to plasmacytoid and myeloid dendritic cells, and to monocytes and macrophages. 2010-01-19T02:51:58Z @@ -38074,7 +45573,105 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -38128,12 +45725,37 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + A progenitor cell that can give rise to plasmacytoid and myeloid dendritic cells, and to monocytes and macrophages. Marker for this cell is Kit-high, CD115-positive, CD135-positive, Cx3cr1-positive, and is Il7ra-negative. 2010-01-26T02:43:40Z @@ -38188,12 +45810,42 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A proerythoblast that is Kit-low, Lyg76-positive, and CD71-positive. 2010-04-26T10:31:56Z @@ -38236,6 +45888,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + @@ -38292,12 +45956,36 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + A basophilic erythroblast that is Lyg 76-high and is Kit-negative. 2010-04-26T10:41:22Z @@ -38348,12 +46036,36 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + A polychromatophilic erythroblast that is Lyg 76-high and is Kit-negative. 2010-04-26T10:53:11Z @@ -38396,12 +46108,24 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A polychromatiic erythroblast that is Gly-A-positive and CD71-low. 2010-04-26T10:53:16Z @@ -38456,12 +46180,43 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An orthochromatophilic erythroblast that is ter119-high, CD71-low, and Kit-negative. 2010-04-26T11:04:15Z @@ -38504,6 +46259,19 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + @@ -38554,6 +46322,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A reticulocyte that is Ly76-high and is Kit-negative. 2010-04-26T11:37:00Z @@ -38592,6 +46366,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + @@ -38636,6 +46416,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + @@ -38680,12 +46467,19 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + An enucleate erythrocyte that is Lyg-76-high. 2010-04-26T11:51:27Z @@ -38732,6 +46526,25 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + @@ -38800,12 +46613,55 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A megakaryocyte progenitor cell that is Kit-positive, CD41-positive, CD9-positive, Sca-1-negative, IL7ralpha-negative, CD150-negative, and Fcgamma receptor II/III-low. 2010-04-26T02:39:15Z @@ -38852,6 +46708,25 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + @@ -38904,6 +46779,25 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + @@ -38952,6 +46846,19 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + @@ -39021,13 +46928,63 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A cell type that can give rise to basophil and mast cells. This cell is CD34-positive, CD117-positive, CD125-positive, FceRIa-negative, and T1/ST2-negative, and expresses Gata-1, Gata-2, C/EBPa 2010-04-27T12:46:33Z @@ -39036,12 +46993,6 @@ radial glial cells acting as neural progenitors throughout life. There may be an intermediate cell type. These cells also CD13-positive, CD16-positive, CD32-positive, and integrin beta 7-positive. Transcription factors: GATA1-positive, MCP-1-positive, mitf-positive, PU.1-positive, and CEBP/a-low. basophil mast progenitor cell - - - - - true - @@ -39085,6 +47036,24 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + @@ -39139,6 +47108,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + @@ -39181,8 +47162,13 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + @@ -39196,12 +47182,6 @@ radial glial cells acting as neural progenitors throughout life. hematopoietic lineage restricted progenitor cell - - - - - true - @@ -39226,8 +47206,13 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + @@ -39241,12 +47226,6 @@ radial glial cells acting as neural progenitors throughout life. This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). hematopoietic oligopotent progenitor cell - - - - - true - @@ -39281,6 +47260,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + @@ -39339,6 +47330,24 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + A hematopoietic stem cell with long term self renewal capability. This cell is Kit-positive, Sca1-positive, CD150-positive, CD90-low, CD34-negative and Flt3-negative. 2010-01-08T09:19:28Z @@ -39391,6 +47400,30 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + @@ -39442,6 +47475,24 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + @@ -39495,6 +47546,24 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + Intraepithelial T cells with a memory phenotype of CD2-positive, CD5-positive, and CD44-positive. 2009-10-20T02:20:43Z @@ -39564,8 +47633,44 @@ radial glial cells acting as neural progenitors throughout life. - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A CD4-positive, CXCR5-positive, CCR7-negative alpha-beta T cell located in follicles of secondary lymph nodes that is BCL6-high, ICOS-high and PD1-high, and stimulates follicular B cells to undergo class-switching and antibody production. @@ -39679,8 +47784,32 @@ radial glial cells acting as neural progenitors throughout life. - - + + + + + + + + + + + + + + + + + + + + + + + + + + A CD24-high, CD4-low, CD8-low, CD44-negative, NK1.1-negative NK T cell. @@ -39727,12 +47856,30 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + A CD24-low, CD44-negative, NK1.1-negative NK T cell. 2009-10-29T04:13:43Z @@ -39784,12 +47931,36 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + A CD24-low, CD44-positive, DX5-low, NK1.1-negative NK T cell. 2009-10-29T04:14:48Z @@ -39838,12 +48009,36 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + A CD24-low, CD44-positive, DX5-high, NK1.1-negative NK T cell. @@ -39896,6 +48091,24 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + @@ -39956,6 +48169,36 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A basophil mast progenitor cell that is Beta-7 integrin-high, Kit-positive FcRgammaII/III-positive and Sca1-negative. 2010-04-27T01:22:38Z @@ -40017,6 +48260,48 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A pro-B cell that is CD45R/B220-positive, CD43-positive, HSA-low, BP-1-negative and Ly6c-negative. This cell type is also described as being lin-negative, AA4-positive, Kit-positive, IL7Ra-positive and CD45R-positive. 2010-04-28T10:50:07Z @@ -40092,6 +48377,60 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A pro-B cell that is CD22-positive, CD34-positive, CD38-positive and TdT-positive (has TdT activity). Pre-BCR is expressed on the cell surface. Cell is CD19-negative, CD20-negative, complement receptor type 2-negative and CD10-low. D-to-J recombination of the heavy chain occurs at this stage. 2010-04-28T11:19:11Z @@ -40139,6 +48478,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + @@ -40197,12 +48548,36 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + A pre-B cell precursor is CD19-low, CD22-positive , CD34-positive, CD38-positive. 2010-04-28T12:06:06Z @@ -40270,6 +48645,48 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -40333,12 +48750,48 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A pre-BCR-positive precursor B cell that is CD24-high, CD25-positive, CD43-positive, CD45R-positive and BP-positive. 2010-04-28T02:13:46Z @@ -40381,12 +48834,24 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A pre-BCR positive B cell that is CD38-high. 2010-04-28T02:27:47Z @@ -40456,13 +48921,49 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A pre-B cell that is pre-BCR-negative, and the kappa- and lambda- light immunoglobulin light chain-negative, CD43-low, and is BP-1-positive, CD45R-positive and CD25-positive. This cell type is also described as being AA4-positive, IgM-negative, CD19-positive, CD43-low/negative, and HSA-positive. 2010-04-28T02:55:16Z @@ -40471,12 +48972,6 @@ radial glial cells acting as neural progenitors throughout life. Fraction D precursor B cells are also reportedly CD24-positive and sIgD-negative. fraction D precursor B cell - - - - - true - @@ -40516,12 +49011,24 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A small pre-B cell that is CD22-positive and CD38-low. 2010-04-28T03:04:48Z @@ -40580,12 +49087,42 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An immature B cell that is IgM-positive, CD45R-positive, CD43-low, CD25-negative, and CD127-negative. This cell type has also been described as being AA4-positive, IgM-positive, CD19-positive, CD43-low/negative, and HSA-positive. 2010-04-28T03:13:47Z @@ -40638,12 +49175,36 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + An immature B cell that is CD38-negative, CD10-low, CD21-low, and CD22-high. 2010-04-28T03:19:14Z @@ -40708,7 +49269,43 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -40720,12 +49317,6 @@ radial glial cells acting as neural progenitors throughout life. 2010-04-30T03:01:48Z fraction F mature B cell - - - - - true - @@ -40763,6 +49354,25 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + A classical monocyte that is CD14-positive, CD16-negative, CD64-positive, CD163-positive. 2010-06-05T08:25:41Z @@ -40837,12 +49447,37 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + A resident monocyte that is Gr-1 low, CD43-positive, and CX3CR1-positive. 2010-06-05T08:25:44Z @@ -40880,6 +49515,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A conventional thymic dendritic cell that is CD8alpha-positive. @@ -40961,6 +49602,24 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + A T-helper cell that is characterized by secreting interleukin 9 and responding to helminth infections. This cell-type can derives from Th2 cells in the presence of TGF-beta and IL-4. Th2 cytokine production is surpressed. 2010-06-22T11:18:44Z @@ -41007,6 +49666,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A type I pneumocyte is a flattened, branched pneumocyte that covers more than 98% of the alveolar surface. This large cell has thin (50-100 nm) cytoplasmic extensions to form the air-blood barrier essential for normal gas exchange. @@ -41058,6 +49724,9 @@ radial glial cells acting as neural progenitors throughout life. + + + @@ -41114,8 +49783,14 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + @@ -41134,12 +49809,6 @@ radial glial cells acting as neural progenitors throughout life. pancreatic acinar cell - - - - - true - @@ -41213,6 +49882,8 @@ radial glial cells acting as neural progenitors throughout life. + + An enteroendocrine cell that produces glucagon. 2010-09-10T10:48:54Z @@ -41316,7 +49987,14 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + Columnar cell which populate the epithelium of large intestine and absorb water. This cell is the most numerous of the epithelial cell types in the large intestine; bear apical microvilli, contain secretory granules in their apical cytoplasm; secretion appears to be largely mucins, but is also rich in antibodies of the IgA type. @@ -41433,6 +50111,8 @@ radial glial cells acting as neural progenitors throughout life. + + Infrequent type of columnar epithelial cell. This cell is characterized by the presence of a tuft of blunt, squat microvilli (approximately 120-140/cell) on the cell surface. The microvilli contain filaments that stretch into the underlying cytoplasm. They have a distinctive pear shape with a wide base and a narrow microvillous apex. Function not known. 2010-06-29T03:22:46Z @@ -41491,6 +50171,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + An epithelial cell derived from ectoderm. 2010-06-29T03:38:22Z @@ -41521,6 +50208,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + Epithelial cell derived from mesoderm or mesenchyme. 2010-06-29T03:49:14Z @@ -41557,7 +50251,19 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + + + + + + + Epithelial cell found in the ducts of the pancreas. This cell type contributes to the high luminal pH. @@ -41567,12 +50273,6 @@ radial glial cells acting as neural progenitors throughout life. pancreatic ductal cell - - - - - true - @@ -41602,7 +50302,19 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + + + + + + + A cubodial epithelial cell that is continuous with the lining of intercalated ducts that drain the acinus. This cell type secretes a high pH solution to aid in activation of zymogens, and can differentiate into endocrine and exocrine pancreatic cell types. @@ -41613,12 +50325,6 @@ radial glial cells acting as neural progenitors throughout life. pancreatic centro-acinar cell - - - - - true - @@ -41673,6 +50379,7 @@ radial glial cells acting as neural progenitors throughout life. + A chromaffin cell of the adrenal medulla that produces epinephrine. 2010-07-14T09:41:42Z @@ -41716,6 +50423,7 @@ radial glial cells acting as neural progenitors throughout life. + A chromaffin cell of the adrenal medulla that produces norepinephrine. 2010-07-14T10:12:24Z @@ -41819,6 +50527,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A leukocyte that lacks granules. 2010-07-22T11:30:33Z @@ -41857,6 +50571,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + This is a cell found in the gastrointestinal tract of mammals and serves as a pacemaker that triggers gut contraction. ICCs mediate inputs from the enteric nervous system to smooth muscle cells and are thought to be the cells from which gastrointestinal stromal tumors (GISTs) arise. @@ -41975,6 +50695,103 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A group 2 innate lymphoid cell in the mouse capable of secreting IL-13 in response to a helminth infection. This cell is lineage-negative, ICOS-positive, IL1RL1-positive, IL7Ralpha-positive, and IL17Br-positive. 2010-08-12T02:22:19Z @@ -42069,6 +50886,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A cell found in the bone marrow. This can include fibroblasts, macrophages, adipocytes, osteoblasts, osteoclasts, endothelial cells and hematopoietic cells. 2010-07-22T04:48:15Z @@ -42191,6 +51014,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A specialised myocyte that lies between the sinoatrial node and the atrioventricular node and is involved in the conduction of electrical signals. 2010-08-23T11:24:11Z @@ -42221,9 +51051,9 @@ radial glial cells acting as neural progenitors throughout life. - + A cell of the adrenal cortex. Cell types include those that synthesize and secrete chemical derivatives (steroids) of cholesterol. 2010-08-24T01:37:44Z @@ -42285,6 +51115,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A small, polyhedral, cell found in rounded groups or curved columns with deeply staining nuclei, scanty basophilic cytoplasm and a few lipid droplets. This cell in the zona glomerulosa produces mineralocorticoids. 2010-08-24T01:42:02Z @@ -42342,6 +51178,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A CD38-positive naive B cell is a mature B cell that has the phenotype CD38-positive, surface IgD-positive, surface IgM-positive, and CD27-negative, and that has not yet been activated by antigen in the periphery. CD38+ naive B cell CD38+ naive B lymphocyte @@ -42385,6 +51227,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A CD38-negative naive B cell is a mature B cell that has the phenotype CD38-negative, surface IgD-positive, surface IgM-positive, and CD27-negative, that has not yet been activated by antigen in the periphery. CD38- naive B cell CD38- naive B lymphocyte @@ -42428,6 +51276,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + An IgG-positive double negative memory B cell is a double negative memory B cell with the phenotype IgG-positive, IgD-negative, and CD27-negative. IgG+ dn memory B cell IgG+ dn memory B lymphocyte @@ -42479,6 +51333,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + An IgG-negative double negative memory B cell is a double negative memory B cell with the phenotype IgG-negative, IgD-negative, and CD27-negative. IgG- dn memory B cell IgG- dn memory B lymphocyte @@ -42530,6 +51390,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A CD38-positive IgG memory B cell is a class switched memory B cell that expresses IgG on the cell surface with the phenotype CD38-positive and IgG-positive. CD38+ IgG memory B cell CD38+ IgG memory B lymphocyte @@ -42573,6 +51439,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + An IgD-positive CD38-positive IgG memory B cell is a CD38-positive IgG-positive class switched memory B cell that has class switched and expresses IgD on the cell surface with the phenotype IgD-positive, CD38-positive, and IgG-positive. IgD-positive CD38-positive IgG memory B cell @@ -42608,6 +51480,7 @@ radial glial cells acting as neural progenitors throughout life. + An IgD-negative CD38-positive IgG memory B cell is a CD38-positive IgG-positive that has class switched and lacks expression of IgD on the cell surface with the phenotype IgD-negative, CD38-positive, and IgG-positive. IgD-negative CD38-positive IgG memory B cell @@ -42649,6 +51522,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A CD38-negative IgG memory B cell is a IgG-positive class switched memory B cell that has class switched and expresses IgG on the cell surface with the phenotype CD38-negative, IgD-negative, and IgG-positive. CD38-negative IgG memory B cell @@ -42685,6 +51565,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A B220-positive CD38-positive naive B cell is a CD38-positive naive B cell that has the phenotype B220-positive, CD38-positive, surface IgD-positive, surface IgM-positive, and CD27-negative, and that has not yet been activated by antigen in the periphery. B220+CD38+ naive B cell B220+CD38+ naive B lymphocyte @@ -42731,16 +51617,16 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + A B220-low CD38-positive naive B cell is a CD38-positive naive B cell that has the phenotype B220-low, CD38-positive, surface IgD-positive, surface IgM-positive, and CD27-negative, that has not yet been activated by antigen in the periphery. B220-low CD38-positive naive B cell - - - - - true - @@ -42768,6 +51654,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + An CD38-negative unswitched memory B cell is an unswitched memory B cell that has the phenotype CD38-negative, IgD-positive, CD138-negative, and IgG-negative. CD38- unswitched memory B cell CD38- unswitched memory B lymphocyte @@ -42811,6 +51703,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A B220-positive CD38-negative unswitched memory B cell is a CD38-negative unswitched memory B cell that has the phenotype B220-positive, CD38-negative, IgD-positive, CD138-negative, and IgG-negative. B220-positive CD38-negative unswitched memory B cell @@ -42846,16 +51744,16 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + A B220-low CD38-negative unswitched memory B cell is a CD38-negative unswitched memory B cell that has the phenotype B220-low, CD38-negative, IgD-positive, CD138-negative, and IgG-negative. B220-low CD38-negative unswitched memory B cell - - - - - true - @@ -42883,6 +51781,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A CD38-positive unswitched memory B cell is an unswitched memory B cell that has the phenotype CD38-positive, IgD-positive, CD138-negative, and IgG-negative. CD38+ unswitched memory B cell CD38+ unswitched memory B lymphocyte @@ -42926,6 +51830,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A B220-positive CD38-positive unswitched memory B cell is a CD38-positive unswitched memory B cell that has the phenotype B220-positive, CD38-positive, IgD-positive, CD138-negative, and IgG-negative. B220-positive CD38-positive unswitched memory B cell @@ -42961,16 +51871,16 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + A B220-low CD38-positive unswitched memory B cell is a CD38-positive unswitched memory B cell that has the phenotype B220-low, CD38-positive, IgD-positive, CD138-negative, and IgG-negative. B220-low CD38-positive unswitched memory B cell - - - - - true - @@ -42998,6 +51908,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A class switched memory B cell that lacks IgG on the cell surface. IgG- class switched memory B cell IgG- class switched memory B lymphocyte @@ -43042,6 +51958,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A CD38-negative IgG-negative memory B cell is a IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype CD38-negative and IgG-negative. CD38-negative IgG-negative class switched memory B cell @@ -43078,6 +52000,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A CD38-positive IgG-negative memory B cell is an IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype CD38-positive and IgG-negative. CD38-positive IgG-negative class switched memory B cell @@ -43114,6 +52042,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + An CD24-positive CD38-negative IgG-negative memory B cell is a CD38-negative IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype CD24-positive, CD38-negative, and IgG-negative. CD24-positive CD38-negative IgG-negative class switched memory B cell @@ -43150,6 +52084,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A CD24-negative CD38-negative IgG-negative memory B cell is a CD38-negative IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype CD24-negative, CD38-negative, and IgG-negative. CD24-negative CD38-negative IgG-negative class switched memory B cell @@ -43186,6 +52126,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A B220-positive CD38-positive IgG-negative memory B cell is a CD38-positive IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype B220-positive, CD38-positive, and IgG-negative. B220-positive CD38-positive IgG-negative class switched memory B cell @@ -43221,16 +52167,16 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + A B220-low CD38-positive IgG-negative memory B cell is a CD38-positive IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype B220-low, CD38-positive, and IgG-positive. B220-low CD38-positive IgG-negative class switched memory B cell - - - - - true - @@ -43266,12 +52212,30 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + A circulating gamma-delta T cell that is CD27-positive and capable of producing IFN-gamma. 2010-08-18T09:57:19Z @@ -43323,12 +52287,36 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + A circulating gamma-delta T cell that expresses RORgamma(t), is CD27-negative and is capable of IL-17 secretion. 2010-08-18T09:57:29Z @@ -43401,6 +52389,49 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A CD25-positive, CD27-positive immature gamma-delta T cell found in the thymus that has an immature phenotype (i.e. CD24-high, CD25-high, CD62L-high, CD44-high, CD2-low, CD5-low). 2010-08-18T10:35:37Z @@ -43437,6 +52468,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A T cell with a receptor of limited diversity that is capable of immediate effector functions upon stimulation. 2010-08-20T02:14:25Z @@ -43485,6 +52522,30 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + A CD8-positive, alpha-beta T cell that has the phenotype CXCR3-negative, CCR6-positive, CCR5-high, CD45RA-negative, and capable of producing IL-17 and some IFNg. CD8-positive Th17 cell Tc17 CD8+ T cell @@ -43615,6 +52676,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A stomal cell of the ovary 2010-08-23T12:10:31Z @@ -43672,6 +52740,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A stromal cell of the ovarian medulla. 2010-08-23T12:12:17Z @@ -43781,6 +52855,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A endothelial cell of a lymphatic vessel. The border of the oak leaf-shaped endothelial cell of initial lymphatics are joined by specialized buttons. The discontinuous feature of buttons distinguishes them from zippers in collecting lymphatics, but both types of junctions are composed of proteins typical of adherens junctions and tight junctions found in the endothelium of blood vessels. Buttons seal the sides of flaps of the oak leaf-shaped endothelial cell, leaving open the tips of flaps as routes for fluid entry without disassembly and reformation of intercellular junctions. @@ -43853,6 +52939,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A sebum secreting cell of the skin that secretes sebum into the hair follicles. 2010-08-24T09:27:52Z @@ -43899,8 +52991,10 @@ radial glial cells acting as neural progenitors throughout life. + + @@ -43956,7 +53050,13 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + An endothelial cell found in capillaries. @@ -43968,12 +53068,6 @@ radial glial cells acting as neural progenitors throughout life. capillary endothelial cell - - - - - true - @@ -44017,8 +53111,10 @@ radial glial cells acting as neural progenitors throughout life. + + @@ -44076,6 +53172,14 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + A cell found within the dental pulp. 2010-08-24T02:52:09Z @@ -44108,6 +53212,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + An epithelial cell of the uterus. 2010-08-24T10:45:54Z @@ -44302,6 +53412,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -44491,6 +53602,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -44537,7 +53649,14 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A specialized cell involved in sensory perception of smell. 2010-08-26T01:47:13Z @@ -44589,6 +53708,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + An epithelial cell located on the basal lamina of the olfactory epithelium. 2010-08-26T01:58:54Z @@ -44627,6 +53753,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -44713,8 +53840,14 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + A cell that is a specialized type of pericyte providing structural support for the capillary loops of kidney. A flat, elongated cell with extensive fine cytoplasmic processes found outside the kidney glomerulus near the macula densa and bound laterally by afferent and efferent arterioles. Being phagocytic, this cell participates in the continuous turnover of the basal lamina by removing its outer portion containing residues of filtration, while the lamina is renewed on its inner surface by the endothelial cells. 2010-08-25T02:20:55Z @@ -44725,12 +53858,6 @@ radial glial cells acting as neural progenitors throughout life. lacis cell extraglomerular mesangial cell - - - - - true - @@ -44830,6 +53957,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A supporting cell of the anterior pituitary gland involved in trophic and catabolic processes; expresses a broad spectrum of cytokeratins indicative of their epithelial nature. 2010-08-25T03:10:10Z @@ -44867,6 +54000,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + An epithelial cell found in the lining of the stomach. 2010-08-25T03:22:08Z @@ -44923,20 +54062,19 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + A mucous cell in the epithelium of the stomach. 2010-08-25T03:38:51Z FMA:63464 mucous cell of stomach - - - - - true - @@ -44960,8 +54098,15 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A neck cell that secretes mucus within the stomach. Its products are distinct histochemically from those of the surface mucous cells of stomach. 2010-08-25T03:41:30Z @@ -44994,13 +54139,8 @@ radial glial cells acting as neural progenitors throughout life. + - - - - - - A simple columnar cell that populates the entire luminal surface including the gastric pits. This cell types secrete mucus to form a thick protective, lubricant layer over the gastric wall. 2010-08-25T03:45:10Z @@ -45032,7 +54172,14 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + + A stomach epithelial cell that is olumnar in form with a few short apical microvilli; relatively undifferentiated mitotic cell from which other types of gland are derived; few in number, situated in the isthmus region of the gland and base of the gastric pit. 2010-08-25T03:57:08Z @@ -45113,6 +54260,8 @@ radial glial cells acting as neural progenitors throughout life. + + A basally situated, mitotically active, columnar-shaped keratinocyte attached to the basement membrane. 2010-08-26T03:12:49Z @@ -45152,6 +54301,7 @@ radial glial cells acting as neural progenitors throughout life. + An endothelial cell found in the glomerulus of the kidney. This cell is flattened, highly fenestrated, and plays a vital role in the formation of glomerular ultrafiltrate. 2010-08-26T10:59:44Z @@ -45232,6 +54382,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A cell involved in the formation of a granulocyte. 2010-08-30T12:54:27Z @@ -45257,6 +54413,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -45284,6 +54441,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -45327,6 +54485,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A cell involved in the formation of a monocyte (monopoiesis). 2010-08-30T01:27:48Z @@ -45363,6 +54527,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A stem cell that can give rise to the cells of the liver. The term usually refers to the self-renewing pool of hepatocyte precursors in the adult liver (differently from 'hepatoblast', often used for fetal precursors of hepatocytes). 2010-08-30T02:00:42Z @@ -45522,6 +54692,8 @@ radial glial cells acting as neural progenitors throughout life. + + An oncocyte located in the thyroid. 2010-09-02T11:33:26Z @@ -45592,6 +54764,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + An epithelial cell of the tracheobronchial tree. 2010-09-02T02:09:14Z @@ -45621,8 +54799,8 @@ radial glial cells acting as neural progenitors throughout life. - + Brush cell found in the epithelial layer of the colon. 2010-09-02T02:20:50Z @@ -45701,6 +54879,14 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + A brush cell found in the epithelium of lobular bronchiole. 2010-09-02T02:38:34Z @@ -45730,6 +54916,14 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + A brush cell of the epithelium in the terminal bronchiole. 2010-09-02T02:38:36Z @@ -45761,6 +54955,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + Brush cell of the epithelium in the trachea. @@ -45805,6 +55005,8 @@ radial glial cells acting as neural progenitors throughout life. + + A brush cell found in the epithelium of bronchus. @@ -46195,6 +55397,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A cell of the cuboidal epithelium that covers the lens. The cells of the lens epithelium regulate most of the homeostatic functions of the lens. As ions, nutrients, and liquid enter the lens from the aqueous humor, Na+/K+ ATPase pumps in the lens epithelial cells pump ions out of the lens to maintain appropriate lens osmolarity and volume, with equatorially positioned lens epithelium cells contributing most to this current. The activity of the Na+/K+ ATPases keeps water and current flowing through the lens from the poles and exiting through the equatorial regions. The cells of the lens epithelium also serve as the progenitors for new lens fibers. It constantly lays down fibers in the embryo, fetus, infant, and adult, and continues to lay down fibers for lifelong growth. @@ -46370,6 +55578,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + An epithelial cell of the prostate. 2010-09-07T01:49:29Z @@ -46410,6 +55624,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + An epithelial cell of prostatic duct. 2010-09-07T01:55:51Z @@ -46453,6 +55673,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + An epithelial cell of the prostatic acinus. 2010-09-07T01:55:53Z @@ -46496,6 +55722,8 @@ radial glial cells acting as neural progenitors throughout life. + + A cell of the basal layer of the epithelium in the prostatic acinus. 2010-09-07T01:59:08Z @@ -46532,6 +55760,8 @@ radial glial cells acting as neural progenitors throughout life. + + A cell of the luminal layer of the epithelium in the prostatic acinus. 2010-09-07T01:59:10Z @@ -46561,6 +55791,14 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + A cell that constitutes the basal layer of epithelium in the prostatic duct. 2010-09-07T01:59:12Z @@ -46592,6 +55830,14 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + A cell that constitutes the luminal layer of epithelium of prostatic duct. 2010-09-07T01:59:16Z @@ -46701,6 +55947,7 @@ radial glial cells acting as neural progenitors throughout life. + A fibroblast in the bone marrow. 2010-09-07T02:25:18Z @@ -46735,6 +55982,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A fibroblasts found in interstitial spaces in the pulmonary tract. Greater numbers of these cells are found in idiopathic pulmonary fibrosis. 2010-09-07T02:29:38Z @@ -46773,6 +56027,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A cell containing at least one nucleus. 2010-09-07T03:32:33Z @@ -46803,6 +56064,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + @@ -46892,6 +56159,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A hematopoeitic stem cell found in the blood. Normally found in very limited numbers in the peripheral circulation (less than 0.1% of all nucleated cells). 2010-09-07T03:57:09Z @@ -46993,6 +56267,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A cell that is found in a zone occupying the bottom region of the crypt; provide the source of most of the cell types of the intestinal epithelium; proliferate by mitotic division; differentiates into columnar or goblet cells. 2010-09-08T09:21:22Z @@ -47026,6 +56306,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + An epithelial cell of the musculomembranous digestive tube extending from the mouth to the anus. 2010-09-08T09:26:53Z @@ -47056,6 +56342,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + An epithelial cell of the esophagus. 2010-09-08T09:28:20Z @@ -47093,6 +56385,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + An epithelial cell of the large intestine. 2010-09-08T09:28:22Z @@ -47132,6 +56430,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + An epithelial cell of the small intestine. 2010-09-08T09:41:46Z @@ -47256,6 +56560,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + An epithelial cell of thyroid gland. 2010-09-08T01:46:51Z @@ -47340,8 +56650,8 @@ radial glial cells acting as neural progenitors throughout life. - + An epithelial cell of the parathyroid gland. 2010-09-08T02:29:38Z @@ -47397,6 +56707,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + An endothelial cell that lines any of the venous cavities through which blood passes in various glands and organs such as the spleen and liver. @@ -47451,6 +56768,7 @@ radial glial cells acting as neural progenitors throughout life. + A type of enteroendocrine cell found in the stomach that secretes glucagon. 2010-09-10T10:54:42Z @@ -47481,7 +56799,7 @@ radial glial cells acting as neural progenitors throughout life. - + A D cell located in the colon. 2010-09-10T11:37:35Z @@ -47515,7 +56833,7 @@ radial glial cells acting as neural progenitors throughout life. - + A type D cell of the small intestine. 2010-09-10T01:34:22Z @@ -47572,7 +56890,6 @@ radial glial cells acting as neural progenitors throughout life. - An enteroendocrine cell that stores and secretes Ghrelin. @@ -47613,7 +56930,6 @@ radial glial cells acting as neural progenitors throughout life. - A type EC enteroendocrine cell in the duodenum and jejunum that stores and secretes motilin and 5-hydroxytryptamine. @@ -47677,7 +56993,6 @@ radial glial cells acting as neural progenitors throughout life. - A type EC enteroendocrine cell type that is numerous in the fundus of the stomach; stores 5-hydroxytryptamine and histamine. @@ -47712,6 +57027,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A cell type that secretes histamine. 2010-09-10T03:04:42Z @@ -47744,6 +57065,14 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + A PP cell located in the islets of the pancreas. @@ -47813,14 +57142,8 @@ radial glial cells acting as neural progenitors throughout life. - - - - - - - + An enteroendocrine cell of duodenum and jejunum that produces gastric inhibitory peptide. 2010-09-10T03:51:47Z @@ -48167,6 +57490,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + An epithelial cell of the thymus. Epithelial reticular cells are pleomorphic, stellate, non-phagocytic cells which seem to be supportive in function and are held together by desmosomes. They replace the fibroblastoid reticular cells found in other lymphoid organs. Other epithelial cells in the medulla have the ultrastructure of secretory cells. Although different epithelial cells throughout the thymus appear alike by light microscopy their ultrastructure and function varies. 2010-09-13T02:34:22Z @@ -48374,6 +57703,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + @@ -48426,19 +57761,14 @@ radial glial cells acting as neural progenitors throughout life. + - - - - - - - + A synovial cell that is macrophage-like, characterized by surface ruffles or lamellipodia, plasma membrane invaginations and associated micropinocytotic vesicles, Golgi apparatus and little granular endoplasmic reticulum. 2010-09-13T03:39:17Z @@ -48447,14 +57777,14 @@ radial glial cells acting as neural progenitors throughout life. Type A cells are usually round and located in the upper part of the synovial intima. type A synovial cell - + - + PMID:10770586 @@ -48630,6 +57960,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -48665,7 +57996,6 @@ radial glial cells acting as neural progenitors throughout life. - A brush border epithelial cell located in the proximal tubule of the kidney that detects fluid flow. @@ -48697,6 +58027,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + An epithelial cell of a skin gland. 2010-09-14T12:00:07Z @@ -48827,6 +58163,19 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + An ecto-epithelial cell of the prostate gland that secretes hormones. 2010-09-14T03:01:58Z @@ -48880,6 +58229,14 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + An epithelial supporting cell located in the cochlea. 2010-09-14T03:31:38Z @@ -48909,6 +58266,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A supporting cell of the vestibular epithelium. 2010-09-14T03:31:44Z @@ -48984,6 +58348,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A cell that is part of the nervous system. 2010-09-15T01:34:57Z @@ -49016,6 +58387,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone. 2010-09-15T03:01:54Z @@ -49100,6 +58478,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A cell of a fetus which is suspended in the amniotic fluid. Amniocytes are considered to arise from several tissues including fetal skin, the fetal urinary tract, umbilical cord, and the inner amniotic surface. 2010-09-20T10:13:37Z @@ -49138,30 +58522,85 @@ radial glial cells acting as neural progenitors throughout life. - A myoepithelial cell that surrounds milk-secreting luminal epithelial cells. This cell type contracts under the stimulation of oxytocin and is attached to the basement membrane by hemidesmosomes and to the adjacent luminal cells by desmosomes. This cell type expresses high level of keratin-14 and is estrogen receptor alpha negative. + + A myoepithelial cell that is part of a mammary gland and is located in the basal layer. During lactation, a basal-myoepithelial cell of mammary gland contracts under the stimulation of oxytocin. In humans, a basal-myoepithelial cell of mammary gland can be identified by high levels of CD49f and low levels of EpCAM. + + 2010-09-20T11:42:14Z + basal myoepithelial cell + basal-myoepithelial cell CALOHA:TS-2378 FMA:67800 - basal cell of lactiferous duct - myoepithelial cell of lactiferous gland + myoepithelial cell of mammary gland + basal cell of lactiferous duct + myoepithelial cell of lactiferous gland + B-Myo cell + BM + basal - myoepithelial cell of mammary gland + Due inconsistencies in naming this and other mammary gland epithelial cell types, several mammary gland experts gathered for a breast atlas annotation jamboree organized by Chan-Zuckerberg initiative. They agreed to label this cell type as basal-myoepithelial cell (and abbreviated: B-Myo cell). + basal-myoepithelial cell of mammary gland - A myoepithelial cell that surrounds milk-secreting luminal epithelial cells. This cell type contracts under the stimulation of oxytocin and is attached to the basement membrane by hemidesmosomes and to the adjacent luminal cells by desmosomes. This cell type expresses high level of keratin-14 and is estrogen receptor alpha negative. + A myoepithelial cell that is part of a mammary gland and is located in the basal layer. During lactation, a basal-myoepithelial cell of mammary gland contracts under the stimulation of oxytocin. In humans, a basal-myoepithelial cell of mammary gland can be identified by high levels of CD49f and low levels of EpCAM. GOC:tfm PMID:11250738 PMID:19022771 + PMID:38059556 + + + + + basal myoepithelial cell + PMID:37694522 + + + + + basal-myoepithelial cell + PMID:37380767 + myoepithelial cell of mammary gland + PMID:11250738 + + + + basal cell of lactiferous duct FMA:67800 + + + + B-Myo cell + + + + + + BM + PMID:38059556 + + + + + + basal + PMID:37380767 + + + + + + Due inconsistencies in naming this and other mammary gland epithelial cell types, several mammary gland experts gathered for a breast atlas annotation jamboree organized by Chan-Zuckerberg initiative. They agreed to label this cell type as basal-myoepithelial cell (and abbreviated: B-Myo cell). + PMID:38059556 + @@ -49181,6 +58620,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + @@ -49299,6 +58745,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + An epithelial cell of the mammary gland. 2010-09-20T01:49:37Z @@ -49332,6 +58785,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -49419,6 +58873,7 @@ radial glial cells acting as neural progenitors throughout life. + A ciliated cell of the bronchus. @@ -49451,6 +58906,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -49535,6 +58991,7 @@ radial glial cells acting as neural progenitors throughout life. + A stem cell located in the bulge of the hair follicle that can give rise to regenerate the new follicle with each hair cycle and to reepithelialize the epidermis during wound repair. @@ -49587,6 +59044,43 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -49739,6 +59233,31 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + A natural killer cell subset that is found in the decidual of the uterus and is CD56-high, Galectin-1-positive and CD16-negative. This cell type represents the most abundant immune cell type in the decidual during the first trimester of pregnancy. @@ -49793,6 +59312,43 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A natural killer cell that is developmentally immature, has the phenotype CD34-negative, CD56-negative, CD117-positive, CD122-positive,and CD161-positive. 2010-09-20T04:33:11Z @@ -49852,12 +59408,49 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An immature natural killer cell that is NK1.1-positive, DX5-positive, Ly49-positive, CD27-low and CD11b-low. This cell type is found in high numbers in the liver. 2010-09-20T04:41:01Z @@ -49898,6 +59491,25 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + An immature natural killer cell that is NK1.1-positive and DX-5 negative. 2010-09-21T10:11:44Z @@ -49939,12 +59551,31 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + A mature natural killer cell that is CD27-high and CD11b-high. This cell type is capable of interferon-gamma secretion. 2010-09-21T10:19:49Z @@ -49982,12 +59613,31 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + A CD27-low, CD11b-high natural killer cell that has a higher threshold of activation due to higher expression of inhibitory receptors. 2010-09-21T10:19:54Z @@ -50025,12 +59675,31 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + A natural killer cell that is CD27-high and CD11b-low. 2010-09-21T10:20:00Z @@ -50060,7 +59729,13 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + An endothelial cell that lines the intracavitary lumen of the heart, separating the circulating blood from the underlying myocardium. This cell type releases a number of vasoactive substances including prostacyclin, nitrous oxide and endothelin. @@ -50072,12 +59747,6 @@ radial glial cells acting as neural progenitors throughout life. endocardial cell - - - - - true - @@ -50133,6 +59802,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A hematopoietic stem cell that exists during embryogenesis. 2010-09-22T09:05:13Z @@ -50191,12 +59866,61 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A hematopoietic stem cell that resides in the fetal liver. In mice, this cell type is first observed at E10.5. This cell type is MHC-positive, HSA-positive, AA4.1-positive, CD45-positive, Sca-1 positive, CD150-positive, CD48-negative and CD244-negative. 2010-09-22T09:08:32Z @@ -50254,12 +59978,49 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A hematopoietic stem found in the yolk sac. In mice, this cell type is Sca-1-negative, CD45-negative, MHC-negative, HSA-positive, AA4.1-positive, CD44-positive. 2010-09-22T09:08:34Z @@ -50309,6 +60070,31 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + @@ -50360,6 +60146,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A primitive erythrocyte that has undergone enucleation. This cell type is 3-6 fold bigger than the fetal derived erythrocytes that they co-circulate with during fetal development. Expresses epsilon-gamma hemoglobin chains. 2010-09-22T09:35:16Z @@ -50402,6 +60200,19 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + @@ -50449,6 +60260,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + Derived from the Greek word pyren (the pit of a stone fruit), this is a transient nucleated cell type that results from exclusion of the nucleus from the primitive erythrocyte. 2010-09-22T10:02:37Z @@ -50484,6 +60307,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A hematopoietic stem cell of the placenta. This cell type is first observed E10.5 This cell type may give rise to fetal liver hematopoietic stem cells. 2010-09-22T10:30:02Z @@ -50533,6 +60362,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + @@ -50567,6 +60403,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -50624,11 +60461,11 @@ radial glial cells acting as neural progenitors throughout life. - + - - + + A keratocyte is a specialized fibroblast residing in the cornea stroma that has a flattened, dendritic morphology; located between the lamellae with a large flattened nucleus, and lengthy processes which communicate with neighboring cells. This corneal layer, representing about 85-90% of corneal thickness, is built up from highly regular collagenous lamellae and extracellular matrix components. Keratocytes play the major role in keeping it transparent, healing its wounds, and synthesizing its components. This cell type secretes collagen I, V, VI, and keratan sulfate. @@ -50642,12 +60479,6 @@ radial glial cells acting as neural progenitors throughout life. keratocyte - - - - - true - @@ -50673,6 +60504,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + An epithelial cell of the cortical portion of the thymus. Epithelial cells in this region are required for positive selection of CD8-positive T cells. @@ -50708,6 +60545,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + An epithelial cell of the medullary thymus. This cell type expresses a diverse range of tissue-specific antigens. This promiscuous gene expression is a cell-autonomous property of medullary epithelial cells and is maintained during the entire period of thymic T cell output. 2010-09-23T03:17:14Z @@ -50740,6 +60583,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A smooth muscle cell of the myometrium that enlarges and stretches during pregnancy, and contracts in response to oxytocin. 2010-09-23T03:46:34Z @@ -50773,6 +60623,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A cell that lines the trabecular meshwork, which is an area of tissue in the eye located around the base of the cornea, near the ciliary body, and is responsible for draining the aqueous humor from the eye via the anterior chamber (the chamber on the front of the eye covered by the cornea). This cell may play a role in regulating intraocular pressure. 2010-09-23T04:18:50Z @@ -50810,6 +60666,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + An endo-epithelial cell of the respiratory tract. 2010-09-23T04:38:49Z @@ -50867,6 +60729,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -50944,6 +60807,14 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + A transversely striated, synctial muscle cell, formed by the fusion of myoblasts. 2010-09-24T01:13:01Z @@ -50999,6 +60870,14 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + A hair cell of the ear that contains the organs of balance and hearing. 2010-09-24T01:49:31Z @@ -51020,6 +60899,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -51424,6 +61304,36 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -51474,6 +61384,25 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + A myeloid dendritic cell found in the blood, lymph nodes, tonsil, bone marrow, and spleen that is CD141-positive (BDCA-3), XCR1-positive, and Clec9A-positive. This cell-type can cross-present antigen to CD8-positive T cells and can produce inteferon-beta. @@ -51538,6 +61467,31 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + A resident monocyte that is Gr-1 high, CD43-negative, CX3CR1-negative, CD115-positive, and B220-negative. 2010-10-04T11:26:18Z @@ -51581,12 +61535,25 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + A patrolling monocyte that is CD14-low and CD16-positive. @@ -51632,6 +61599,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A CD14-positive monocyte that is also CD16-positive and CCR2-negative. 2010-10-04T12:49:47Z @@ -51684,7 +61663,20 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + @@ -51725,6 +61717,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A myeloid dendritic cell found in the blood that is CD1c-positive. @@ -51783,6 +61787,24 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + A precursor B cell that is AA4-positive, IgM-negative, CD19-positive, CD43-positive and HSA-positive. 2010-10-05T10:11:38Z @@ -51874,19 +61896,44 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A resting mature B cell within the Peyer's patch that is CD19-positive, B220-positive, IgM-positive, AA4-negative, CD23-positive, CD43-negative, and CD5-negative. 2010-10-05T11:18:03Z Peyers patch B cell Peyer's patch B cell - - - - - true - @@ -51964,7 +62011,8 @@ radial glial cells acting as neural progenitors throughout life. - + + A post-natal thymocyte expressing components of the gamma-delta T cell receptor. This cell type is always double-negative (i.e. CD4-negative, CD8-negative). 2010-10-07T02:33:39Z @@ -51972,12 +62020,6 @@ radial glial cells acting as neural progenitors throughout life. gd thymocyte gamma-delta thymocyte - - - - - true - @@ -52300,6 +62342,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A T cell that expresses a T cell receptor complex and has completed T cell selection. 2010-10-12T01:56:15Z @@ -52339,6 +62393,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A T cell that has not completed T cell selection. 2010-10-12T01:56:17Z @@ -52379,6 +62439,7 @@ radial glial cells acting as neural progenitors throughout life. + A reticulocyte that retains the nucleus and other organelles. Found in birds, fish, amphibians and reptiles. 2010-10-15T09:24:05Z @@ -52420,7 +62481,14 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A reticulocyte lacking a nucleus and showing a basophilic reticulum under vital staining due to the presence of ribosomes. 2010-10-15T09:24:08Z @@ -52461,6 +62529,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A DN2 thymocyte that is Kit-hi. 2010-10-21T10:12:05Z @@ -52504,6 +62578,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A DN2 thymocyte that is Kit-low. 2010-10-21T10:12:08Z @@ -52553,6 +62633,31 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + A pro-T cell that is lin-negative, CD25-negative, CD127-negative, CD44-positive and kit-positive. @@ -52604,6 +62709,19 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + A mature natural killer cell that is CD11b-positive and CD27-positive. 2010-10-25T03:07:59Z @@ -52635,6 +62753,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A double-positive, alpha-beta thymocyte that is small and not proliferating. 2010-10-21T01:59:06Z @@ -52676,6 +62800,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + @@ -52728,12 +62864,30 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + A double-positive thymocyte that is CD69-positive and has begun positive selection. 2010-10-21T02:11:52Z @@ -52783,12 +62937,36 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + A double-positive thymocyte that is undergoing positive selection, has high expression of the alpha-beta T cell receptor, is CD69-positive, and is in the process of down regulating the CD4 co-receptor. 2010-10-21T02:29:19Z @@ -52839,12 +63017,36 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + A double-positive thymocyte that is undergoing positive selection, has high expression of the alpha-beta T cell receptor, is CD69-positive, and is in the process of down regulating the CD8 co-receptor. 2010-10-21T02:29:23Z @@ -52887,12 +63089,24 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A CD4-positive, CD8-negative thymocyte that is CD24-positive and expresses high levels of the alpha-beta T cell receptor. 2010-10-21T02:43:52Z @@ -52936,12 +63150,24 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A CD4-positive, CD8-negative thymocyte that expresses high levels of the alpha-beta T cell receptor and is CD69-positive. 2010-10-21T02:46:02Z @@ -52984,12 +63210,24 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A CD8-positive, CD4-negative thymocyte that is CD24-positive and expresses high levels of the alpha-beta T cell receptor. 2010-10-21T02:59:10Z @@ -53033,12 +63271,24 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A CD8-positive, CD4-negative thymocyte that expresses high levels of the alpha-beta T cell receptor and is CD69-positive. 2010-10-21T02:59:14Z @@ -53088,6 +63338,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A mature CD4-positive, CD8-negative alpha-beta T cell found in the thymus that is CD24-low and has high expression of the T cell receptor. @@ -53143,6 +63405,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A mature CD8-positive, CD4-negative alpha-beta T cell found in the thymus that is CD24-low and has high expression of the T cell receptor. @@ -53185,6 +63459,19 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + A mature NK cell that is NK1.1-positive. 2010-10-25T03:18:04Z @@ -53220,6 +63507,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A NK1.1-positive T cell that is NKGA2-positive. 2010-10-25T03:31:09Z @@ -53254,6 +63548,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A NK1.1-positive T cell that is Ly49D-positive. 2010-10-25T03:36:19Z @@ -53288,6 +63589,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A NK1.1-positive T cell that is CD94-positive. 2010-10-25T03:36:28Z @@ -53326,6 +63634,25 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + A NK1.1-positive T cell that is CD94-negative and Ly49Cl-negative. 2010-10-25T03:56:21Z @@ -53361,6 +63688,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A NK1.1-positive T cell that is Ly49Cl-positive. 2010-10-25T03:36:38Z @@ -53396,6 +63730,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A NK1.1-positive T cell that is Ly49H-positive. 2010-10-25T03:36:43Z @@ -53430,6 +63771,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A NK1.1-positive T cell that is Ly49D-negative. 2010-10-25T03:39:02Z @@ -53464,6 +63812,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A NK1.1-positive T cell that is Ly49Cl-negative. 2010-10-25T03:52:04Z @@ -53499,6 +63854,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A NK1.1-positive T cell that is CD94-negative. 2010-10-25T03:54:18Z @@ -53533,6 +63895,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A NK1.1-positive T cell that is Ly49H-negative. 2010-10-25T03:42:42Z @@ -53571,6 +63940,8 @@ radial glial cells acting as neural progenitors throughout life. + + A NK1.1-positive T cell that is CD94-positive and Ly49Cl-positive. 2010-10-25T03:56:27Z @@ -53642,6 +64013,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -53659,12 +64031,6 @@ radial glial cells acting as neural progenitors throughout life. - - - - - - A progenitor cell of the central nervous system that can differentiate into oligodendrocytes or type-2 astrocytes. This cell originates from multiple structures within the developing brain including the medial ganglion eminence and the lateral ganglionic eminence. These cells migrate throughout the central nervous system and persist into adulthood where they play an important role in remyelination of injured neurons. @@ -53748,6 +64114,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic cell is a conventional dendritic cell that is CD11b-positive, CD4-negative, CD8_alpha-negative and is CD205-positive. 2010-11-22T01:10:28Z @@ -53790,6 +64168,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A CD11c-low plasmacytoid dendritic cell that is CD8alpha-negative and CD4-positive. 2010-11-22T01:27:37Z @@ -53831,6 +64221,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A CD11c-low plasmacytoid dendritic cell that is CD8alpha-positive and CD4-positive. 2010-11-22T01:23:07Z @@ -53880,6 +64282,25 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + A Langerhans cell that is in the epidermis and is CD45-positive, MHCII-positive, and CD11b-positive. @@ -53919,6 +64340,7 @@ radial glial cells acting as neural progenitors throughout life. + A dermal dendritic cell that is langerin-positive and CD103-positive. 2010-11-22T04:06:22Z @@ -53959,6 +64381,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A dermal dendritic cell that is langerin-negative, CD103-negative, and CD11b-positive. 2010-11-22T04:09:44Z @@ -53995,6 +64423,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A conventional thymic dendritic cell that is CD8alpha-negative. @@ -54034,7 +64468,14 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + @@ -54080,7 +64521,21 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + @@ -54123,6 +64578,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + An adipose dendritic cell that is SIRPa-positive. 2010-11-23T01:40:44Z @@ -54154,6 +64615,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + An adipose dendritic cell that is SIRPa-negative. 2010-11-23T01:40:46Z @@ -54185,6 +64652,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A conventional dendritic cell that expresses CD11b (ITGAM). 2010-11-23T01:50:05Z @@ -54233,6 +64706,30 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + A CD11b-positive dendritic cell located in the serosal portion of the small intestine epithelium. This cell type is CD45-positive, MHC-II-positive, CD11c-low, CD103-negative. 2010-11-23T02:00:21Z @@ -54274,6 +64771,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A myeloid suppressor cell that is Gr1-high and CD11c-negative. 2010-11-23T02:15:12Z @@ -54315,6 +64824,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A myeloid suppressor cell that is Gr1-low and CD11c-positive. 2010-11-23T02:19:43Z @@ -54352,6 +64873,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + Gr1-high monocyte that lacks MHC-II receptor complex. 2010-11-23T03:27:12Z @@ -54389,6 +64916,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + Gr1-high monocyte that has a MHC-II receptor complex. 2010-11-23T03:30:21Z @@ -54427,6 +64960,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + Gr1-low non-classical monocyte that lacks expression of a MHC-II complex. 2010-11-23T03:38:15Z @@ -54464,6 +65003,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + Gr1-low non-classical monocyte that has low to intermediate expression of the MHC-II complex. 2010-11-23T03:47:53Z @@ -54501,6 +65046,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + Gr1-low non-classical monocyte that has high surface expression of a MHC-II complex. 2010-11-23T03:47:55Z @@ -54546,6 +65097,24 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + A MHC-II-negative classical monocyte located in lymphoid tissue that is F4/80-positive, CD11c-negative, and CD11b-high. 2010-11-23T04:00:52Z @@ -54590,6 +65159,24 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + A MHC-II-negative classical monocyte located in lymphoid tissue that is F4/80-positive, CD11c-intermediate, and CD11b-high. 2010-11-23T04:09:09Z @@ -54636,10 +65223,36 @@ radial glial cells acting as neural progenitors throughout life. + + - - + + + + + + + + + + + + + + + + + + + + + + + + + + A tissue-resident macrophage located in the bone marrow. This cell type is B220-negative, CD3e-negative, Ly-6C-negative, CD115-positive, F4/80-positive. @@ -54694,6 +65307,25 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + A macrophage located in adipose tissue that is CD45-positive, CD11c-positive, and SIRPa-positive. 2010-11-23T04:31:28Z @@ -54733,6 +65365,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + An adipose macrophage that does not express F4/80but is MHC-II-positive. This cell type exhibits autofluorescence under typical flow cyometry conditions. 2010-11-23T04:40:50Z @@ -54774,6 +65418,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + An adipose macrophage that does not express MHC-II but is F4/80-positive. 2010-11-23T04:35:53Z @@ -54810,6 +65466,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -54848,6 +65505,7 @@ radial glial cells acting as neural progenitors throughout life. + The flattened smooth myoepithelial cells of mesodermal origin that lie just outside the basal lamina of the seminiferous tubule. 2010-12-03T03:11:48Z @@ -54884,6 +65542,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A melanocyte that produces pigment in the dermis. 2010-12-03T03:17:05Z @@ -54914,18 +65579,13 @@ radial glial cells acting as neural progenitors throughout life. - + + A melanocyte that produces pigment within the hair follicle. 2010-12-03T03:17:09Z hair follicle melanocyte - - - - - true - @@ -54951,6 +65611,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A melanocyte that produces pigment in the epithelium. 2010-12-03T03:17:14Z @@ -54987,6 +65653,14 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + A melanocyte of the retina. This cell type is distinct from pigmented retinal epithelium. 2010-12-03T03:25:32Z @@ -55017,19 +65691,20 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + + A melanocyte located between the epithelial marginal cell layer and the mesodermal basal cell layer within the intrastrial space; the predominant cellular component of the electrogenic machinery that generates an endocochlear potential (80-100 mV) . 2010-12-03T03:29:15Z strial intermediate cell - - - - - true - @@ -55078,6 +65753,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A trophoblast cell that has a large volume of cytoplasm, is polyploid and is usually mononuclear but is also occasionally multi-nucleate. This cell type is important in establishing maternal physiology and remodeling of the vasculature of the placenta. 2010-12-06T02:55:24Z @@ -55120,6 +65807,19 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + A thymocyte that lacks expression of CD4 and CD8. 2010-12-06T03:03:38Z @@ -55160,6 +65860,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A supporting cell of the organ of Corti. 2010-12-06T03:09:01Z @@ -55190,6 +65896,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A specialized cell involved in auditory sensory perception. 2010-12-06T03:18:43Z @@ -55263,6 +65975,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A cell located in the heart, including both muscle and non muscle cells. 2010-12-07T09:37:22Z @@ -55324,6 +66043,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A T cell that is located in the intestinal epithelium and is capable of a mucosal immune response. 2010-12-07T09:54:50Z @@ -55457,14 +66188,8 @@ radial glial cells acting as neural progenitors throughout life. - - - - - - - + An enteroendocrine cell of the small intestine that secretes motilin. 2010-12-07T03:55:49Z @@ -55498,6 +66223,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A cell of the adventitial layer of ductal structures such as the uterer, defent duct, biliary duct, etc 2010-12-07T04:03:56Z @@ -55530,6 +66261,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A smooth muscle cell of the intestine. 2011-01-17T03:39:38Z @@ -55583,6 +66320,36 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A CD11b-positive dendritic cell that is CD11b-high, CD45-positive, MHC-II-positive and CD103-negative. 2011-01-21T01:27:41Z @@ -55636,6 +66403,31 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + A CD11b-positive dendritic cell that is CD11b-low, CD45-positive, MHC-II-high and CD103-positive that is located in the liver. 2011-01-21T01:27:45Z @@ -55685,6 +66477,30 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + A dermal dendritic cell isolated from skin draining lymph nodes that is langerin-positive, MHC-II-positive, and CD4-negative and CD8a-negative. 2011-01-21T01:57:00Z @@ -55737,6 +66553,36 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A dermal dendritic cell isolated from skin draining lymph nodes that is langerin-negative, MHC-II-positive, and CD4-negative and CD8a-negative. 2011-01-21T02:13:58Z @@ -55776,7 +66622,15 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + A langerin-positive lymph node dendritic cell that is CD103-positive and CD11b-low. 2011-01-21T02:07:54Z @@ -55816,7 +66670,20 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + A langerin-positive lymph node dendritic cell that is CD103-negative and CD11b-high. 2011-01-21T02:11:14Z @@ -55852,7 +66719,14 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A langerin-negative lymph node dendritic cell that is CD103-negative and CD11b-low. 2011-01-21T02:22:15Z @@ -55888,7 +66762,14 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A langerin-negative lymph node dendritic cell that is CD103-negative and CD11b-high. 2011-01-21T02:16:21Z @@ -56030,6 +66911,7 @@ radial glial cells acting as neural progenitors throughout life. + An epithelial cell of the kidney. @@ -56077,6 +66959,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -56115,6 +66998,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + An adipocyte that is part of subcutaneous adipose tissue. @@ -56178,6 +67067,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A specialized epithelial cell that contains "feet" that interdigitate with the "feet" of other glomerular epithelial cells in the mesonephros. 2011-02-08T01:58:30Z @@ -56234,6 +67129,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A specialized epithelial cell that contains "feet" that interdigitate with the "feet" of other glomerular epithelial cells in the metanephros. 2011-02-08T02:02:13Z @@ -56278,6 +67179,24 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + A dermal dendritic cell that is CD1a-negative and CD14-positive. CD14+ dermal DC They are also CD11c-positive, CD40-positive, CD85j-positive (ILT-2), CD163-positive, CD205-positive (DEC205), CD207-negative (langerin), CD209-positive (DC-SIGN), CD274-positive (PD-L1), CD324-negative (E-cadherin), Factor XIIIa-positive, LOX-I-positive, CLEC6-positive, Dectin-1-positive, and DCIR-positive. Upon stimulation, these cells are capable of producing IL1-beta, IL6, IL8, IL10, IL12p40, IL19, IL20, IL24, TGF-beta, TNF-alpha, GM-CSF, and MCP1. They reside in the dermis. @@ -56322,6 +67241,7 @@ radial glial cells acting as neural progenitors throughout life. + An immature CD14-positive dermal dendritic cell is CD80-low, CD86-low, and MHCII-low. immature CD14-positive dermal dendritic cell @@ -56367,6 +67287,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -56407,6 +67328,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A dermal dendritic cell that is CD1a-positive and CD14-negative. CD1a+ dermal DC Reside in the dermis. They are also CD11c-positive, CD40-positive, CD207-negative (langerin), CD209-negative (DC-SIGN), and CD324-negative (E-cadherin). When activated, they are capable of producing CXCL8 (IL-8) and IL-15. Possibly a precursor of Langerhans cells or equivalent of langerin-positive dermal DCs in the mouse. @@ -56450,6 +67377,7 @@ radial glial cells acting as neural progenitors throughout life. + An immature CD1a-positive dermal dendritic cell is CD80-low, CD86-low, and MHCII-low. immature CD1a-positive dermal dendritic cell @@ -56495,6 +67423,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -56539,6 +67468,18 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + A myeloid dendritic cell found in the blood that is CD16-positive. CD16+ mDC CD16-mDC @@ -56583,6 +67524,7 @@ radial glial cells acting as neural progenitors throughout life. + An immature CD16-positive myeloid dendritic cell is CD80-low, CD86-low, and MHCII-low. immature CD16-positive myeloid dendritic cell @@ -56628,6 +67570,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -56667,6 +67610,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -56778,6 +67722,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + An epithelial cell that is part of the amnion. @@ -56809,6 +67760,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A mesenchymal stem cell of the amnion membrane. 2011-02-28T12:44:24Z @@ -56841,6 +67799,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + An epithelial cell of the intrahepatic portion of the bile duct. These cells are flattened or cuboidal in shape, and have a small nuclear-to-cytoplasmic ratio relative to large/extrahepatic cholangiocytes. 2011-02-28T01:20:20Z @@ -56884,7 +67848,13 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + A smooth muscle cell of the aorta. 2011-02-28T01:42:12Z @@ -56892,12 +67862,6 @@ radial glial cells acting as neural progenitors throughout life. aortic smooth muscle cell - - - - - true - @@ -56921,6 +67885,8 @@ radial glial cells acting as neural progenitors throughout life. + + A mesenchymal stem cell that is part of the bone marrow. 2011-02-28T01:47:47Z @@ -56949,6 +67915,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A mesenchymal stem cell of the chorionic membrane. @@ -56990,6 +67963,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + An endothelial cell that is part of the vein. @@ -57053,6 +68032,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + An endothelial cell that is part of the thoracic endothelium. 2011-02-28T03:59:09Z @@ -57107,6 +68092,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A fibroblast of the aortic adventitia. 2011-02-28T04:43:41Z @@ -57143,6 +68134,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A fibroblast that is part of the heart. 2011-02-28T04:57:44Z @@ -57186,6 +68183,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A fibroblast that is part of the choroid plexus. 2011-02-28T05:01:39Z @@ -57221,6 +68225,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A fibroblast that is part of the conjuctiva of the eye. 2011-02-28T05:03:44Z @@ -57250,6 +68260,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + 2011-02-28T05:05:33Z fibroblast of dermis @@ -57278,6 +68294,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + 2011-02-28T05:09:12Z fibroblast of gingiva @@ -57306,6 +68328,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A fibroblast that is part of lung. 2011-02-28T05:11:03Z @@ -57344,6 +68372,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A fibroblast of the lymphatic system. 2011-02-28T05:16:18Z @@ -57379,6 +68413,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A fibroblast that is part of the mammary gland. 2011-02-28T05:18:38Z @@ -57415,6 +68455,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A fibroblast of the periodontium. 2011-02-28T05:19:48Z @@ -57450,6 +68496,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A fibroblast of pulmonary artery. @@ -57512,6 +68564,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + An animal cell that is part of a hair follicle. 2011-03-01T04:11:01Z @@ -57540,8 +68599,14 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + An epithelial cell that resides in the inner root sheath of the hair follicle. 2011-03-01T04:27:51Z @@ -57576,7 +68641,14 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + An epithelial cell that is part of the outer root sheath. 2011-03-01T04:29:47Z @@ -57612,6 +68684,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + An epidermal cell that is part of the germinal matrix. 2011-03-01T04:31:06Z @@ -57647,6 +68726,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -57683,6 +68763,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A connective tissue cell of the nucleus pulposus cell of intervertebral disc. 2011-03-02T02:12:23Z @@ -57713,6 +68799,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A pigment cell located in the epithelium of the iris. @@ -57834,6 +68926,14 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + A mesenchymal stem cell of the umbilical cord. 2011-03-01T09:55:12Z @@ -57862,6 +68962,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A mesenchymal stem cell of adipose tissue. 2011-03-01T09:57:17Z @@ -57893,6 +69000,7 @@ radial glial cells acting as neural progenitors throughout life. + A mesenchymal stem cell of liver. 2011-03-01T09:58:51Z @@ -57928,6 +69036,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A mesenchymal stem cell of the vertebrae. 2011-03-01T10:40:27Z @@ -58001,6 +69116,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A stromal cell of the pancreas. @@ -58038,6 +69159,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A pericyte of the central nervous system. 2011-03-02T02:54:18Z @@ -58062,6 +69190,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -58116,7 +69245,14 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + An epithelial cell of the placenta. 2011-03-02T03:21:30Z @@ -58152,6 +69288,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A preadipocyte found in mesenteric tissue. 2011-03-03T04:19:40Z @@ -58187,6 +69329,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A preadipocyte that is part of an omentum. 2011-03-03T04:19:42Z omentum preadipocyte @@ -58197,6 +69346,12 @@ radial glial cells acting as neural progenitors throughout life. true + + + + A preadipocyte that is part of an omentum. + PMID:21484051 + @@ -58215,6 +69370,7 @@ radial glial cells acting as neural progenitors throughout life. + A preadipocyte that is part of the breast. 2011-03-03T04:19:46Z @@ -58250,6 +69406,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A preadipocyte that is part of a perirenal fat tissue. 2011-03-03T04:20:04Z perirenal preadipocyte @@ -58260,6 +69423,13 @@ radial glial cells acting as neural progenitors throughout life. true + + + + A preadipocyte that is part of a perirenal fat tissue. + PMID:20106964 + PMID:31079959 + @@ -58296,6 +69466,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A preadipocyte that is part of subcutaneous tissue. 2011-03-03T04:33:01Z @@ -58372,6 +69548,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A blood vessel endothelial cell that is part of the retina. @@ -58410,7 +69593,15 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + @@ -58461,18 +69652,18 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + A smooth muscle cell of the umbilical vein. 2011-03-06T05:00:51Z smooth muscle cell of the umbilical vein - - - - - true - @@ -58496,18 +69687,18 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + A smooth muscle cell of the bachiocephalic vasculature. 2011-03-06T05:00:58Z smooth muscle cell of the brachiocephalic vasculature - - - - - true - @@ -58532,6 +69723,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A vascular associated smooth muscle cell of the brain vasculature. 2011-03-06T05:01:20Z @@ -58566,7 +69764,13 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + A smooth muscle of the pulmonary artery. @@ -58576,12 +69780,6 @@ radial glial cells acting as neural progenitors throughout life. smooth muscle cell of the pulmonary artery - - - - - true - @@ -58605,7 +69803,14 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + + A smooth muscle cell of the coronary artery. @@ -58613,12 +69818,6 @@ radial glial cells acting as neural progenitors throughout life. smooth muscle cell of the coronary artery - - - - - true - @@ -58642,18 +69841,18 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + A smooth muscle of the internal thoracic artery. 2011-03-06T05:01:41Z smooth muscle cell of the internal thoracic artery - - - - - true - @@ -58677,18 +69876,18 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + A smooth muscle cell of the umbilical artery. 2011-03-06T05:01:48Z smooth muscle cell of the umbilical artery - - - - - true - @@ -58712,18 +69911,18 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + A smooth muscle cell of the subclavian artery. 2011-03-06T05:01:52Z smooth muscle cell of the subclavian artery - - - - - true - @@ -58747,18 +69946,18 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + Smooth muscle cell of the carotid artery. 2011-03-06T05:01:56Z smooth muscle cell of the carotid artery - - - - - true - @@ -58783,6 +69982,7 @@ radial glial cells acting as neural progenitors throughout life. + A smooth muscle cell of the bladder. @@ -58820,7 +70020,13 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + 2011-03-06T05:46:39Z @@ -58829,12 +70035,6 @@ radial glial cells acting as neural progenitors throughout life. bronchial smooth muscle cell - - - - - true - @@ -58853,6 +70053,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A smooth muscle cell of the esophagus. 2011-03-06T05:48:17Z @@ -58887,19 +70093,19 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + A smooth muscle cell of the trachea. 2011-03-06T05:50:28Z smooth muscle cell of trachea - - - - - true - @@ -58924,6 +70130,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A smooth muscle cell of the uterus. 2011-03-06T05:53:28Z @@ -58960,6 +70172,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + 2011-03-06T06:50:53Z anulus pulposus cell @@ -58989,6 +70207,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + An astrocyte of the cerebellum. 2011-03-06T06:57:27Z @@ -59024,7 +70249,8 @@ radial glial cells acting as neural progenitors throughout life. - + + An astrocyte that is part of the hippocampus. @@ -59034,12 +70260,6 @@ radial glial cells acting as neural progenitors throughout life. hippocampal astrocyte - - - - - true - @@ -59063,7 +70283,8 @@ radial glial cells acting as neural progenitors throughout life. - + + An astrocyte of the cerebral cortex. @@ -59072,12 +70293,6 @@ radial glial cells acting as neural progenitors throughout life. astrocyte of the cerebral cortex - - - - - true - @@ -59102,6 +70317,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + An astrocyte of the spinal cord. 2011-03-06T07:11:26Z @@ -59155,6 +70376,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A neuron with a soma found in the hippocampus. 2011-03-06T07:31:49Z @@ -59208,6 +70436,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A neuron of the raphe nuclei. 2011-03-06T07:42:06Z @@ -59243,6 +70478,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A CNS neuron of the dorsal spinal cord. 2011-03-06T07:43:34Z @@ -59278,6 +70520,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A neuron of the ventral spinal cord. 2011-03-06T07:46:03Z @@ -59312,18 +70561,18 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + A neuron of the striatum. 2011-03-06T07:47:12Z striatum neuron - - - - - true - @@ -59348,6 +70597,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A neuron of the substantia nigra. 2011-03-06T07:48:42Z @@ -59383,6 +70639,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + An adipocyte that is part of omentum tissue. 2011-03-14T10:17:00Z @@ -59420,6 +70682,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + An adipocyte of perirenal fat tissue. 2011-03-14T10:17:05Z @@ -59457,6 +70725,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + An adipocyte that is part of the breast. 2011-03-14T10:17:07Z @@ -59497,6 +70771,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + An endothelial cell of the umbilical vein. 2011-03-14T11:36:51Z @@ -59554,6 +70834,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A fibroblast of skin. @@ -59593,6 +70879,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + 2011-03-14T12:46:28Z gingival epithelial cell @@ -59615,6 +70908,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A stromal cell of the prostate. 2011-03-14T02:11:10Z @@ -59652,6 +70951,7 @@ radial glial cells acting as neural progenitors throughout life. + An acinar cell of salivary gland. 2011-03-14T02:22:22Z @@ -59688,6 +70988,7 @@ radial glial cells acting as neural progenitors throughout life. + A paneth cell of the appendix. 2011-03-15T09:38:18Z @@ -59722,6 +71023,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -59853,6 +71155,24 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + A mature microglial cell that has changed shape to an amoeboid morphology and is capable of cytokine production and antigen presentation. activated microglia mature microglia @@ -59928,6 +71248,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + 2011-06-21T12:28:55Z epithelial cell of upper respiratory tract @@ -59956,6 +71282,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + 2011-06-21T12:29:31Z @@ -60007,6 +71339,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + An epithelial cell of the anal column. 2011-07-08T12:11:38Z @@ -60076,6 +71415,7 @@ radial glial cells acting as neural progenitors throughout life. + An epithelial cell of the anal canal that is keratinized. This cell type is found towards the lower, rectal end of the anal canal. 2011-07-08T02:08:40Z @@ -60108,7 +71448,8 @@ radial glial cells acting as neural progenitors throughout life. - + + A respiratory stem cell found at the junction of the terminal (conductive) bronchiole and the respiratory bronchiole. This cell types gives rise to alveolar cell types and club cells in response to lung injury. This cell type expresses markers Scgb1a1 and Sftpc. @@ -60117,12 +71458,6 @@ radial glial cells acting as neural progenitors throughout life. basal epithelial cell of bronchioalveolar duct junction bronchioalveolar stem cell - - - - - true - @@ -60407,6 +71742,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A venule endothelial cell that is cubodial, expresses leukocyte-specific receptors, and allows for passage of lymphocytes into bloodstream. @@ -60499,7 +71840,13 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + A glandular epithelial cell of the endometrium. 2011-07-08T03:54:08Z @@ -60574,6 +71921,7 @@ radial glial cells acting as neural progenitors throughout life. + A glandular epithelial cell of the large intestine. 2011-07-08T04:03:01Z @@ -60610,6 +71958,7 @@ radial glial cells acting as neural progenitors throughout life. + A glandular epithelial cell that is part of the stomach. 2011-07-11T01:20:35Z @@ -60706,6 +72055,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A myocardial endocrine cell that is part of the atrium. 2011-07-11T02:45:39Z @@ -60977,6 +72332,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A skeletal muscle cell that is part of the tongue. 2011-08-16T03:10:02Z @@ -61046,6 +72408,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -61108,7 +72471,7 @@ radial glial cells acting as neural progenitors throughout life. - + A CD4-positive, CD25-positive alpha-beta regulatory T cell that has encountered antigen. 2011-08-25T03:17:34Z @@ -61177,6 +72540,66 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A lymphocyte found in adipose tissue that lacks lineage markers of other lymphocytes but is capable of mediating TH2 cytokine responses. This cell type is found in fat associated lymphoid clusters, proliferates in response to IL2 and produce large amounts of TH2 cytokines such as IL5, IL6 and IL13 2011-08-29T10:08:02Z @@ -61214,6 +72637,7 @@ radial glial cells acting as neural progenitors throughout life. + A PP cell found in intestine. 2011-09-27T11:59:01Z @@ -61250,6 +72674,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A cell that is part of a cortex of kidney. 2011-10-25T03:49:41Z @@ -61272,6 +72703,8 @@ radial glial cells acting as neural progenitors throughout life. + + A retinal ganglion cell that has dendrites stratified in two layers of the inner-plexiform layer. https://orcid.org/0000-0001-7258-9596 https://orcid.org/0000-0002-5260-9315 @@ -61344,13 +72777,7 @@ radial glial cells acting as neural progenitors throughout life. - - - - - - - + @@ -61541,13 +72968,7 @@ radial glial cells acting as neural progenitors throughout life. - - - - - - - + @@ -61950,13 +73371,7 @@ radial glial cells acting as neural progenitors throughout life. - - - - - - - + @@ -61988,13 +73403,7 @@ radial glial cells acting as neural progenitors throughout life. - - - - - - - + @@ -62486,13 +73895,7 @@ radial glial cells acting as neural progenitors throughout life. - - - - - - - + @@ -62524,13 +73927,7 @@ radial glial cells acting as neural progenitors throughout life. - - - - - - - + @@ -62562,13 +73959,7 @@ radial glial cells acting as neural progenitors throughout life. - - - - - - - + @@ -62600,13 +73991,7 @@ radial glial cells acting as neural progenitors throughout life. - - - - - - - + @@ -62639,6 +74024,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -62699,6 +74085,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -63407,14 +74794,9 @@ radial glial cells acting as neural progenitors throughout life. + - - - - - - @@ -63671,6 +75053,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + @@ -63702,14 +75091,9 @@ radial glial cells acting as neural progenitors throughout life. + - - - - - - @@ -63786,13 +75170,8 @@ radial glial cells acting as neural progenitors throughout life. + - - - - - - @@ -63824,13 +75203,8 @@ radial glial cells acting as neural progenitors throughout life. + - - - - - - @@ -63912,14 +75286,8 @@ radial glial cells acting as neural progenitors throughout life. - + - - - - - - @@ -63949,14 +75317,9 @@ radial glial cells acting as neural progenitors throughout life. + - - - - - - @@ -64140,13 +75503,8 @@ radial glial cells acting as neural progenitors throughout life. + - - - - - - @@ -64178,13 +75536,8 @@ radial glial cells acting as neural progenitors throughout life. + - - - - - - @@ -64352,14 +75705,9 @@ radial glial cells acting as neural progenitors throughout life. + - - - - - - @@ -64401,6 +75749,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A central nervous system neuron that stratifies at one and only one location. https://orcid.org/0000-0001-7258-9596 https://orcid.org/0000-0002-5260-9315 @@ -64431,6 +75786,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A neuron that stratifies dendrites at two and only two locations. https://orcid.org/0000-0001-7258-9596 cell @@ -64461,6 +75823,8 @@ radial glial cells acting as neural progenitors throughout life. + + An amicrine that stratifies dendrites at two and only two locations. https://orcid.org/0000-0001-7258-9596 https://orcid.org/0000-0002-5260-9315 @@ -64556,6 +75920,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + A CNS interneuron located in the spinal cord. Is_a interneuron, part_of UBERON:0002240. spinal cord interneuron @@ -64579,6 +75949,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -64602,6 +75973,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -64624,6 +75996,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -64646,6 +76019,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -64668,6 +76042,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -64709,8 +76084,8 @@ radial glial cells acting as neural progenitors throughout life. - + Kolmer-Agduhr neurons are ciliated GABAergic neurons that contact the central canal of the spinal cord and have ipsilateral ascending axons. KA cell KA interneuron @@ -64754,6 +76129,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + An auditory hair cell located in the macula that is sensitive to auditory stimuli. macular hair cell @@ -64789,13 +76171,7 @@ radial glial cells acting as neural progenitors throughout life. - - - - - - - + A cuboidal epithelial cell of the kidney that regulates acid/base balance. FMA:86560 intercalated cell @@ -64865,13 +76241,7 @@ radial glial cells acting as neural progenitors throughout life. - - - - - - - + A ciliated epithelial cell with many cilia. multi-ciliated cell multiciliated cell @@ -64898,13 +76268,7 @@ radial glial cells acting as neural progenitors throughout life. - - - - - - - + A ciliated epithelial cell with a single cilium. single ciliated epithelial cell @@ -65002,6 +76366,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A cell that secretes ghrelin, the peptide hormone that stimulates hunger. ghrelin secreting cell @@ -65029,6 +76400,7 @@ radial glial cells acting as neural progenitors throughout life. + Ghrelin secreting cells found in the endocrine pancreas. pancreatic E cell @@ -65061,6 +76433,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + Lymphatic progenitor cells. 2012-01-12T04:44:34Z @@ -65118,6 +76497,12 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + Lymphatic progenitor cells, derived from the veins, that give rise to lymphatic endothelial cells. 2012-01-12T05:21:09Z @@ -65154,6 +76539,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + Cranial motor neuron which innervates muscles derived from the branchial (pharyngeal) arches. PMID:14699587 branchi motor neuron @@ -65183,10 +76575,12 @@ radial glial cells acting as neural progenitors throughout life. + + - - + + A motor neuron that innervates a skeletal muscle. These motor neurons are all excitatory and cholinergic. @@ -65341,6 +76735,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -65525,6 +76920,9 @@ radial glial cells acting as neural progenitors throughout life. + + + @@ -65573,13 +76971,20 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + + + @@ -65739,6 +77144,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -65746,12 +77152,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - - - - - Ciliated cell of the embryonic epidermis and functions in embryonic movements. Taxon specificity not clear -present in embryonic anurans. @@ -65797,6 +77197,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -65804,12 +77205,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - - - - - Secretory cell that produces a chemical mixture that triggers antipredator behavior. The substance is released only upon disruption of the epidermis. [Behavior of teleost fishes, second edition, edited by Pitcher, 1992] alarm substance secreting cell @@ -65946,6 +77341,8 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + @@ -65989,6 +77386,8 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + A myotube that is part of some somatic muscle. Examples include arthropod somatic muscle cells. somatic muscle myotube @@ -66041,6 +77440,8 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + A somatic muscle cell that is oblquely striated. Examples include the somatic muscles of nematodes. obliquely striated somatic muscle cell @@ -66057,13 +77458,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - - - - - - + A myoblast that detemines the properties (size, shape and attachment to the epidermis) of a `somatic muscle myotube` (CL:0008003) . It develops into a somatic muscle myotube via fusion with `fusion component myoblasts` (CL:0000621). muscle founder cell @@ -66090,6 +77485,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A muscle cell that is part of some visceral muscle. FBbt:00005070 visceral muscle cell @@ -66125,6 +77527,8 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + A visceral muscle cell that is striated. Examples include the visceral muscle cells of arhtropods. striated visceral muscle cell @@ -66159,6 +77563,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A visceral muscle that is transversely striated. Examples include the visceral muscle cells of arthropods. transversely striated visceral muscle cell @@ -66185,6 +77596,8 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + A cranial motor neuron whose soma is located in the midbrain andor hindbrain and which innervates the skeletal muscles of the eye or tongue. cranial somatomotor neuron @@ -66215,6 +77628,8 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + A skeletal muscle satellite cell that divides by stem cell division. A proportion of this population undergoes symmetric stem cell division, producing two skeletal muscle satellite stem cells. The rest undergo asymmetric stem cell division - retaining their identity while budding off a daughter cell that differentiates into an adult skeletal muscle myoblast. @@ -66260,7 +77675,15 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + A visceromotor motor neuron whose soma is located in the hindbrain, and which synapses to parasympathetic neurons that innervate tear glands, sweat glands, and the smooth muscles of the head. cranial visceromotor neuron @@ -66301,18 +77724,18 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + A skeletal muscle satellite cell that has become mitotically active - typically following muscle damage. activated skeletal muscle satellite cell - + - + More accurately - transformation_of ? @@ -66343,6 +77766,8 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + A skeletal muscle myoblast that is part of a skeletal mucle. These cells are formed following acivation and division of skeletal muscle satellite cells. They form a transient population that is lost when they fuse to form skeletal muscle fibers. myogenic precursor cell The vast majority of these cells develop from skeletal muscle satellite cells, although there are some reports of other origins. @@ -66377,6 +77802,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A myoblast that is commited to developing into a somatic muscle. somatic muscle myoblast @@ -66386,7 +77818,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + @@ -66446,6 +77878,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + anterior lateral line ganglion neuron @@ -66465,6 +77904,14 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + A mesenchymal cell of the endocardial cushion. These cells develop via an epithelial to mesenchymal transition when endocardial cells break cell-to-cell contacts and migrate into the cardiac jelly. Cells from this population form the heart septa and valves. endocardial cushion cell @@ -66502,7 +77949,8 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + + An endocrine cell that is part of the pancreas. @@ -66532,6 +77980,14 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + A neuron that release noradrenaline (noriphinephrine) as a neurotransmitter. noradrenergic neuron @@ -66558,6 +78014,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + An epithelial cell that is part of the epithelium of a tracheal tube in an open tracheal system, such as that found in insects. FBbt:00005038 open tracheal system tracheocyte @@ -66597,6 +78060,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + 2017-07-09T19:12:36Z visual system neuron @@ -66644,6 +78114,8 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + An interneuron that has its soma located in the cerebral cortex. cerebral cortex interneuron @@ -66655,7 +78127,8 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + + @@ -66682,12 +78155,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - - - - - @@ -66727,7 +78194,14 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + + + + + + + + A pericyte of the decidual vasculature. 2020-02-29T11:45:57Z @@ -66780,7 +78254,14 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + 2020-02-29T17:37:00Z microcirculation associated smooth muscle cell @@ -66880,13 +78361,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - - - - - - + @@ -66950,6 +78425,14 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + A skeletal muscle fiber that is part of a muscle spindle. These are specialized muscle fibers that serve as proprioceptors, detecting the amount and rate of change in length of a muscle. They are innervated by both sensory neurons and motor neurons (gamma and beta motorneurons, collectively referred to as fusimotor neurons). 2020-09-26T21:07:01Z @@ -66971,6 +78454,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -66983,12 +78467,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - - - - - A glutamatergic motor neuron with a soma in the brainstem or cerebral cortex. They do not synapse directly to muscles but rather to lower motor neurons, which do. They are the main controllers of voluntary movement. 2020-09-28T09:41:48Z @@ -67006,6 +78484,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -67057,17 +78536,17 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + + + + + + + A sensory neuron of the spinal nerve that senses body position and sends information about how much the muscle is stretched to the spinal cord. spinal sensory neuron sensory neuron of spinal nerve - - - - - true - @@ -67102,6 +78581,23 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + + + + + + + + + + Any cell in the compound eye, a light sensing organ composed of ommatidia. GOC:pr PMID:12021768 @@ -67175,6 +78671,12 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + Any cell in the retina, the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. PMID:10702418 @@ -67222,6 +78724,8 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + An enteroendocrine cell that is located in the small intestine. small intestine enteroendocrine cell @@ -67252,6 +78756,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A macrophage which is resident in the lamina propria of the small intestine. macrophage of small intestine @@ -67282,6 +78793,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A macrophage which is resident in the lamina propria of the large intestine. macrophage of large intestine @@ -67312,7 +78830,8 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + + A paneth cell that is located in the epithelium of the colon. @@ -67385,6 +78904,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + @@ -67429,6 +78955,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + @@ -67503,6 +79036,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A lymphocyte that is part of a Peyer's patch. These cells have a major role in driving the immune response to antigens sampled from the intestinal lumen, and in regulating the formation of follicle-associated epithelium and M cells in Peyer's patches by converting intestitial enterocytes into M cells. Peyer's patch resident lymphocyte @@ -67535,6 +79075,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A follicular dendritic cell located in the Peyer's patch. These cells from a meshwork in which Peyer's patch B cells reside. @@ -67564,6 +79111,14 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + An intestinal stem cell that is located in the large intestine crypt of Liberkuhn. These stem cells reside at the bottom of crypts in the large intestine and are highly proliferative. They either differentiate into transit amplifying cells or self-renew to form new stem cells. @@ -67598,6 +79153,14 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + An intestinal stem cell that is located in the small intestine crypt of Liberkuhn. These stem cells reside at the bottom of crypts in the small intestine and are highly proliferative. They either differentiate into transit amplifying cells or self-renew to form new stem cells. crypt stem cell of small intestine @@ -67630,6 +79193,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A lymphocyte that resides in the lamina propria of the large intestine. @@ -67662,6 +79232,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A kidney cortical cell that is part of the nephrogenic zone. cortical nephrogenic niche cell @@ -67693,6 +79270,8 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + An intestinal tuft cell that is a part of a vermiform appendix. appendix tuft cell @@ -67724,6 +79303,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A stromal cell found in the lamina propria of the large intestine. @@ -67752,6 +79338,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A stromal cell found in the lamina propria of the small intestine. @@ -67781,6 +79374,14 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + A T cell which resides in the Peyer's patch of the small intestine. T cell of Peyer's patch of small intestine @@ -67811,6 +79412,8 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + A mesothelial cell that is part of the small intestine. @@ -67839,6 +79442,8 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + A mesothelial cell that is part of the colon. mesothelial cell of large intestine @@ -67869,6 +79474,8 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + An enterocyte that is a part of a vermiform appendix. appendix enterocyte @@ -67900,6 +79507,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + @@ -67937,6 +79551,14 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + An intestinal crypt stem cell that is located in the vermiform appendix. These stem cells reside at the bottom of crypts in the appendix and are highly proliferative. They either differentiate into transit amplifying cells or self-renew to form new stem cells. appendix intestinal crypt stem cell @@ -67971,6 +79593,8 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + A mesothelial cell that is located in a vermiform appendix. appendix mesothelial cell @@ -68002,6 +79626,8 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + An intestinal enteroendocrine cell that is located in a vermiform appendix. appendix enteroendocrine cell @@ -68033,6 +79659,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A T cell that is located in a vermiform appendix. T cell of appendix vermiformis @@ -68065,6 +79698,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A B cell that is located in a vermiform appendix. B cell of appendix vermiformis @@ -68097,6 +79737,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A plasma cell that is located in a vermiform appendix. appendix plasma cell @@ -68129,6 +79776,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A dendritic cell that is located in a vermiform appendix. appendix dendritic cell @@ -68165,6 +79819,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A stromal cell found in the lamina propria of the vermiform appendix. stromal cell of appendix lamina propria @@ -68195,6 +79856,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A macrophage located in the vermiform appendix. macrophage of appendix @@ -68227,6 +79895,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A B lymphocyte that resides in the mantle zone of the lymph node germinal center. These are generally IgM and IgD positive activated B cells that form a 'corona' around the germinal center and are part of the establishment of a secondary lymphatic follicule. mantle zone B cell @@ -68260,6 +79935,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A macrophage that is located in the colon. macrophage of colon @@ -68291,6 +79973,8 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + A goblet cell that is located in the colon. goblet cell of colon @@ -68321,6 +80005,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A stromal cell found in the lamina propria of the colon. stromal cell of colon lamina propria @@ -68350,6 +80041,8 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + A tuft cell that is a part of the colon. colon tuft cell @@ -68380,6 +80073,8 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + An enteroendocrine cell that is located in the colon. colon enteroendocrine cell @@ -68410,6 +80105,8 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + An intestinal crypt stem cell that is located in the colon. @@ -68439,6 +80136,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A lymphocyte that resides in the lamina propria of the small intestine. Lamina propria leukocytes and intraepithelial lymphocytes are the effector compartments of the gut mucosal immune system. Lymphocytes circulate through gut associated lymphoid tissues until recruitment by intestinal antigens. They are involved in the gut immune response. gastrointestinal tract small intestine (lamina propria) leukocyte @@ -68475,6 +80179,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A B cell found in the lymph node medullary sinus. @@ -68504,6 +80215,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A T cell found in the lymph node medullary sinus. @@ -68533,6 +80251,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A macrophage found in the medullary sinus of the lymph node. medullary sinus macrophage @@ -68564,6 +80289,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A macrophage that is located in the anorectum. macrophage of anorectum @@ -68594,6 +80326,14 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + A layer of smooth muscle cells that forms the outer layer of the high endothelial venule of lymph node and pumps to allow flow of lymph fluid carrying lymphocytes. high endothelial venule smooth muscle cell @@ -68625,6 +80365,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A B cell that is located in the anorectum. @@ -68654,6 +80401,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A T cell that is located in the anorectum. @@ -68683,6 +80437,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A smooth muscle cell that is located in the anorectum. anorectum smooth muscle cell @@ -68716,6 +80477,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A stromal cell found in the lamina propria of the anorectum. @@ -68744,6 +80512,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A microfold cell (M cell) that is part of the anorectum. M cell of anorectum @@ -68773,6 +80548,14 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + A paneth cell that is located in the anorectum. anorectum paneth cell @@ -68802,6 +80585,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A transit amplifying cell that is located in the anorectum. anorectum transit amplifying cell @@ -68831,6 +80621,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A goblet cell that is located in the anorectum. goblet cell of anorectum @@ -68860,6 +80657,14 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + An enterocyte that is located in the anorectum. anorectum enterocyte @@ -68889,6 +80694,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A plasma cell that is located in the medullary sinus of the lymph node. medullary plasma cell @@ -68921,6 +80733,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A mature B cell located in the marginal zone of the lymph node. marginal zone B cell @@ -68952,6 +80771,14 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + An intestinal crypt stem cell that is located in the anorectum. anorectum intestinal crypt stem cell @@ -68981,6 +80808,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A specialized type of CD4 positive T cell, the follicular helper T cell (TFH cell), that upregulates CXCR5 expression to enable its follicular localization. These specialised T cells reside in the germinal center of the lymph node. T follicular helper cell of germinal center of lymph node @@ -69013,6 +80847,14 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + An enteroendocrine cell that is located in the anorectum. anorectum enteroendocrine cell @@ -69042,6 +80884,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A T cell located in the lymph node paracortex, where macrophages and dendritic cells present antigenic peptides to these naïve T cells, stimulating them to become activated helper T cells or cytotoxic T lymphocytes. paracortex T cell @@ -69073,6 +80922,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + An intestinal tuft cell that is located in the anorectum. anorectum tuft cell @@ -69102,6 +80958,14 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + A stratified squamous epithelial cell that is part of the anal canal. anal canal stratified squamous epithelial cell @@ -69122,12 +80986,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - - - - - + @@ -69496,6 +81355,8 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + A tuft cell located in the small intestine. @@ -69593,6 +81454,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + An epithelial cell that is part of an endometrial gland. @@ -69646,6 +81514,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -69724,6 +81593,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A pericyte cell that is part of a lung. @@ -69777,6 +81653,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -69813,6 +81690,8 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + An endothelial cell that is part of a placenta. 2021-12-13T13:53:01Z @@ -69846,6 +81725,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A smooth muscle cell that is part of a placenta. 2021-12-13T13:56:42Z @@ -69878,6 +81764,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + An endothelial cell that is part of a hepatic portal vein. 2021-12-13T14:01:05Z @@ -69911,6 +81804,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + An endothelial cell that is part of a uterus. 2021-12-13T14:39:25Z @@ -69944,6 +81844,14 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + Any cell that is part of the esophageal non-keratinized stratified squamous epithelium. In humans, the esophagus, which requires flexibility to accommodate swallowing of a bolus, is covered with a non-keratinized epithelium. @@ -69982,6 +81890,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A skeletal muscle fiber found in an embryo. In mammalian embryos, skeletal muscle expresses myosin heavy chain-embryonic (MyHC-emb, encoded by the MYH3 gene), which regulates skeletal muscle development. 2022-02-21T15:39:10Z @@ -70016,6 +81931,19 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + + + + + + A skeletal muscle fiber found at the fetal and neonatal stages. In mammalian fetuses and neonates, skeletal muscle expresses myosin heavy chain-neonatal (MyHC-neo, encoded by the MYH8 gene). This expression disappears shortly after birth and is replaced by expression of adult heavy chain myosins. 2022-02-21T15:43:16Z @@ -70069,6 +81997,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A fibroblast located in the portal triad. Hepatic portal fibroblast are a non-parenchymal cell population located adjacent to bile duct epithelia in liver and are distinct from stellate cells. They differentiate into fibrogenic myofibroblasts during chronic injury states producing high levels of collagen. @@ -70116,6 +82051,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A specialized, fibroblastic reticular cell of mesenchymal origin found in lymph nodes. In human, it expresses several markers common to myofibroblasts (desmin, vimentin, CD73, CD90, α-smooth muscle actin (αSMA)), and can be differentiated from endothelial cells by its lack of CD31 expression. These cells are critical for the overall organization and function of the lymph node. Lymph node fibroblastic reticular cells (FRCs) can be further classified based on their location, function, and unique marker expression. @@ -70298,6 +82240,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -70327,6 +82270,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -70356,6 +82300,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -70386,6 +82331,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -70547,6 +82493,19 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + + + + + + An endothelial cell located in a lymph node lymphatic vessel. @@ -70628,6 +82587,8 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + A stromal cell that is part_of a bone marrow. bone marrow stromal cell @@ -70650,6 +82611,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + An epithelial cell that is part_of a umbilical artery. umbilical artery epithelial cell @@ -70672,6 +82640,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + An epithelial cell that is part_of a alveolus of lung. MESH:D056809 @@ -70697,6 +82672,8 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + A mononuclear cell that is part_of a bone marrow. bone marrow mononuclear cell @@ -70719,6 +82696,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A specialized cardiomyocyte that transmit signals from the AV node to the cardiac Purkinje fibers. AV bundle cell atrioventricular bundle cell @@ -70746,6 +82730,8 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + cardiac blood vessel endothelial cell @@ -70765,6 +82751,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + His-Purkinje system cell @@ -70784,6 +82777,14 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + @@ -70806,9 +82807,22 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + camera type eye photoreceptor cell camera-type eye photoreceptor cell + + + + + + + + + https://github.com/obophenotype/cell-ontology/issues/2245 + @@ -70826,6 +82840,8 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + cerebellar stellate cell @@ -70845,6 +82861,8 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + A GABAergic interneuron whose soma is located in the cerebral cortex. cerebral cortex GABAergic interneuron @@ -70872,6 +82890,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A CNS neuron of the cerebral cortex. @@ -70934,13 +82959,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - - - - - - + A cell with a flagellum surrounded by a collar of microvilli. The motion of the flagellum draws water past the microvilli, serving either a feeding or sensory function. Collar cells are found in multiple animals, including sponges, echinoderms, and cnidarians. They are also found outside animals in the choanoflagellates. Although collar cells are superficially similar, their cytoskeletal structure and functional biology are different in different groups of organisms. collar cell @@ -70979,6 +82998,14 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + cardiac glial cell @@ -70998,6 +83025,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + MESH:D032386 cardiac myoblast @@ -71018,6 +83052,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A neuron that has its soma in the heart. This term is used in 3 GO terms that were created as part of the heart development focus project. @@ -71049,6 +83090,12 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + A CNS interneuron located in the dorsal horn of the spinal cord. dorsal spinal cord interneuron dorsal horn interneuron @@ -71083,6 +83130,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A motor neuron that passes from the spinal cord toward or to a muscle and conducts an impulse that causes movement. spinal cord motor neuron @@ -71122,18 +83176,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - - - - - - - - - - - + @@ -71193,6 +83236,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + An interneuron that uses GABA as a vesicular neurotransmitter. These interneurons are inhibitory GABAergic inhibitory interneuron @@ -71214,13 +83258,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - - - - - - + An inhibitory GABAergic interneuron found in the cerebellar cortex. Lugaro cell @@ -71248,6 +83286,12 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + A cell in the area of mesoderm in the neurulating embryo that flanks and forms simultaneously with the neural tube. The cells of this region give rise to somites. paraxial mesoderm cell somitic mesoderm cell @@ -71366,6 +83410,14 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + A sperm cell that is cabaple of motion (motility). motile sperm cell @@ -71428,6 +83480,12 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + A motile sperm cell that contains a slender threadlike microscopic appendage that enables motion. flagellated sperm cell @@ -71504,6 +83562,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + A mesothelial cell that is part of the epicardium. @@ -71545,6 +83610,12 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + A fibroblast that is part of upper back skin. fibroblast of upper back skin @@ -71566,7 +83637,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + + + + + + + A fibroblast that is part of skin of back. fibroblast of skin of back @@ -71593,6 +83670,19 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + + + + + + A mast cell that is CD25+. CD25+ neoplastic mast cell @@ -71617,6 +83707,12 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + A double negative thymocyte that is CD3-positive, CD4-negative, CD8-negative, that that are present in the periphery in very low numbers and predominantly produce INF-gamma, TNF-alpha, and a low amount of TGF-beta, but not IL-2, IL-4, IL-10 or IL-13 upon activation. CD4-negative, CD8-negative, alpha-beta regulatory T cells @@ -71668,6 +83764,12 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses. @@ -71697,7 +83799,8 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + + Any fibroblast that is part of skeletal muscle tissue. skeleton muscle fibroblast @@ -71779,6 +83882,8 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + Any microvascular endothelial cell that is part of the dermis. DMEC cell @@ -71894,6 +83999,12 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + Cells of the uterine chorion that acquire specialized structural and/or functional features that characterize chorionic trophoblasts. These cells will migrate towards the spongiotrophoblast layer and give rise to syncytiotrophoblasts of the labyrinthine layer. chorionic trophoblast cell @@ -71948,6 +84059,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -71987,6 +84099,8 @@ plexiform layer. + + A type of interneuron in the retinal inner nuclear layer which carries information from the inner plexiform layer and the outer plexiform layer, using dopamine. @@ -72019,6 +84133,8 @@ plexiform layer, using dopamine. + + A type of interneuron in the retinal inner nuclear layer which carries information from the inner plexiform layer and the outer plexiform layer using GABA. @@ -72072,6 +84188,7 @@ plexiform layer using GABA. + @@ -72106,7 +84223,14 @@ plexiform layer using GABA. + + + + + + + A neuron that releases hypocretin as a neurotransmitter. orexin hypocretin-secreting neuron @@ -72136,6 +84260,13 @@ plexiform layer using GABA. + + + + + + + Neuron that secretes histamine. FBbt:00007367 histaminergic neuron @@ -72209,6 +84340,12 @@ plexiform layer using GABA. + + + + + + Neuron found in the spiral ganglion. spiral ganglion neuron @@ -72225,24 +84362,7 @@ plexiform layer using GABA. - - - - - - - - - - - - - - - - - - + A segmented neutrophilic cell of the bone marrow reserve pool that expresses CD11b (integrin alpha-M) and high levels of CD16 (low affinity immunoglobulin gamma Fc region receptor III) on its cell surface. segmented neutrophil of bone marrow @@ -72270,6 +84390,13 @@ plexiform layer using GABA. + + + + + + + A cell that, by division or terminal differentiation, can give rise to other cell types. Work is needed on GO 'cell differentiation' before it is clear whether the equivalent class definition 'native cell' that capable_of some 'cell differentiation' works. Also, may want to consider merging this with non-terminally differentiated cell. @@ -72299,6 +84426,13 @@ plexiform layer using GABA. + + + + + + + An astrocyte of the forebrain. @@ -72330,6 +84464,13 @@ plexiform layer using GABA. + + + + + + + A CNS neuron of the forebrain. @@ -72361,6 +84502,12 @@ plexiform layer using GABA. + + + + + + forebrain radial glial cell @@ -72438,6 +84585,13 @@ plexiform layer using GABA. + + + + + + + A neuroendocrine cell that is part of the prostate epithelium. @@ -72470,6 +84624,13 @@ plexiform layer using GABA. + + + + + + + An epithelial cell that is part of the prostatic urethra. epithelial cell of prostatic urethra @@ -72646,6 +84807,8 @@ plexiform layer using GABA. + + A hillock cell that is part of the urethra. 2022-10-13T13:51:35Z @@ -72676,6 +84839,8 @@ plexiform layer using GABA. + + A hillock cell that is part of the prostatic urethra. @@ -72708,6 +84873,13 @@ plexiform layer using GABA. + + + + + + + Cytoplasm that exhibits a characteristic staining and color, pale-pink, with Wright-Giemsa stain. 2010-05-25T01:36:34Z @@ -72757,6 +84929,13 @@ plexiform layer using GABA. + + + + + + + Cytoplasm that exhibits a characteristic staining and color, red or pink, with Eosin stain. 2009-12-22T04:23:25Z @@ -72787,6 +84966,12 @@ plexiform layer using GABA. + + + + + + Cytoplasm that exhibits molecular interaction for basic dyes under specific pH conditions. 2009-12-22T04:24:54Z @@ -72815,6 +85000,13 @@ plexiform layer using GABA. + + + + + + + Cytoplasm that exhibits affinity for both basic and acid stains under specific pH conditions. 2009-12-28T04:25:23Z @@ -72883,6 +85075,12 @@ plexiform layer using GABA. + + + + + + A concave nucleus shape where the indentation is smaller than half of the distance to the farthest nuclear margin. 2009-12-23T02:31:25Z @@ -72930,6 +85128,12 @@ plexiform layer using GABA. + + + + + + alobate nucleus @@ -72949,6 +85153,13 @@ plexiform layer using GABA. + + + + + + + Any serous secreting cell that is part of the tracheobronchial epithelium. 2020-05-07T16:03:27Z @@ -72974,6 +85185,13 @@ plexiform layer using GABA. + + + + + + + Any chondrocyte that is part of the tracheobronchial tree. @@ -73000,6 +85218,8 @@ plexiform layer using GABA. + + Any goblet cell that is part of the tracheobronchial epithelium. @@ -73027,6 +85247,13 @@ plexiform layer using GABA. + + + + + + + An eosinophil with a ring-shaped nucleus that is resident in the lung parenchyma. In mouse, lung parenchyma resident eosinophils are IL-5-independent Siglec-F(intermediate) CD62L+ CD101(low). In human, they are Siglec-8+ CD62L+ IL-3R(low). @@ -73071,6 +85298,13 @@ plexiform layer using GABA. + + + + + + + A smooth muscle cell that is part of any lymphatic vessel. @@ -73102,6 +85336,13 @@ plexiform layer using GABA. + + + + + + + A smooth muscle cell that is part of any blood vessel. @@ -73133,6 +85374,13 @@ plexiform layer using GABA. + + + + + + + A smooth muscle cell that is part of the tracheobronchial tree. @@ -73165,6 +85413,13 @@ plexiform layer using GABA. + + + + + + + An epithelial cell of the extrahepatic bile ducts, including the left and right hepatic duct, common hepatic duct, and common bile duct. They are columnar in shape, and have a large nuclear-to-cytoplasmic ratio relative to small/intrahepatic cholangiocytes. 2020-09-03T12:24:24Z @@ -73200,6 +85455,13 @@ plexiform layer using GABA. + + + + + + + An endothelial cell found in the periportal region hepatic sinusoid, near the portal triad. The fenestrae of these cells are larger but fewer in number compared with those of endothelial cells near the centrilobular region of the hepatic sinusoid. 2020-09-09T13:56:47Z @@ -73244,6 +85506,13 @@ plexiform layer using GABA. + + + + + + + An endothelial cell found in the centrilobular region hepatic sinusoid, near the central vein. The fenestrae of these cells are smaller but more numerous compared with those of endothelial cells near the periportal region of the hepatic sinusoid. 2020-09-10T12:38:29Z @@ -73288,6 +85557,13 @@ plexiform layer using GABA. + + + + + + + Any hepatocyte that is part of the liver lobule periportal region. These cells are primarily involved in oxidative energy metabolism. @@ -73326,6 +85602,13 @@ plexiform layer using GABA. + + + + + + + Any hepatocyte that is part of the liver lobule midzonal region. These cells have mixed functionality in comparison with those in the other two regions of the liver lobule. @@ -73364,6 +85647,13 @@ plexiform layer using GABA. + + + + + + + Any hepatocyte that is part of the liver lobule centrilobular region. These cells are the primary location for the biotransformation of drugs. @@ -73402,6 +85692,8 @@ plexiform layer using GABA. + + Goblet cells reside throughout the length of the small and large intestine and are responsible for the production and maintenance of the protective mucus blanket by synthesizing and secreting high-molecular-weight glycoproteins known as mucins. Human intestinal goblet cells secrete the MUC2 mucin, as well as a number of typical mucus components: CLCA1, FCGBP, AGR2, ZG16, and TFF3. 2020-10-14T14:59:07Z @@ -73439,6 +85731,8 @@ plexiform layer using GABA. + + Any brush cell that is part of the intestinal epithelium. @@ -73512,6 +85806,13 @@ plexiform layer using GABA. + + + + + + + retrotrapezoid nucleus neuron @@ -73531,6 +85832,14 @@ plexiform layer using GABA. + + + + + + + + mesonephric nephron tubule epithelial cell @@ -73560,6 +85869,14 @@ plexiform layer using GABA. + + + + + + + + forebrain neuroblast @@ -73579,6 +85896,13 @@ plexiform layer using GABA. + + + + + + + lateral line nerve glial cell @@ -73598,6 +85922,13 @@ plexiform layer using GABA. + + + + + + + spinal cord radial glial cell @@ -73644,6 +85975,14 @@ plexiform layer using GABA. + + + + + + + + pronephric nephron tubule epithelial cell @@ -73663,6 +86002,14 @@ plexiform layer using GABA. + + + + + + + + metanephric nephron tubule epithelial cell @@ -73682,6 +86029,9 @@ plexiform layer using GABA. + + + lung goblet cell @@ -73702,6 +86052,13 @@ plexiform layer using GABA. + + + + + + + A cell that is part of a cardiac valve. heart valve cell @@ -73766,6 +86123,13 @@ plexiform layer using GABA. + + + + + + + malpighian tubule tip cell @@ -73807,6 +86171,13 @@ plexiform layer using GABA. + + + + + + + growth plate cartilage chondrocyte @@ -73826,6 +86197,9 @@ plexiform layer using GABA. + + + stomach neuroendocrine cell @@ -73845,19 +86219,19 @@ plexiform layer using GABA. + + + + + + - - - - - - @@ -73910,6 +86284,13 @@ plexiform layer using GABA. + + + + + + + posterior lateral line nerve glial cell @@ -73929,6 +86310,13 @@ plexiform layer using GABA. + + + + + + + anterior lateral line nerve glial cell @@ -73948,6 +86336,13 @@ plexiform layer using GABA. + + + + + + + posterior lateral line ganglion neuron @@ -73968,6 +86363,12 @@ plexiform layer using GABA. + + + + + + @@ -73990,6 +86391,13 @@ plexiform layer using GABA. + + + + + + + lung secretory cell @@ -74021,6 +86429,12 @@ plexiform layer using GABA. + + + + + + A smooth muscle cell that is part of the small intestine. FMA:15050 non-striated muscle fiber of small intestine @@ -74063,6 +86477,12 @@ plexiform layer using GABA. + + + + + + A smooth muscle cell that is part of the duodenum. FMA:15058 non-striated muscle fiber of duodenum @@ -74104,6 +86524,12 @@ plexiform layer using GABA. + + + + + + A smooth muscle cell that is part of the jejunum. FMA:15062 non-striated muscle fiber of jejunum @@ -74145,6 +86571,12 @@ plexiform layer using GABA. + + + + + + A smooth muscle cell that is part of the ileum. FMA:15066 non-striated muscle fiber of ileum @@ -74187,6 +86619,12 @@ plexiform layer using GABA. + + + + + + A smooth muscle cell that is part of the large intestine. FMA:15653 @@ -74230,18 +86668,18 @@ plexiform layer using GABA. - + + + + + + + A smooth muscle cell that is part of the colon. FMA:15663 non-striated muscle fiber of colon smooth muscle cell of colon - - - - - true - @@ -74271,19 +86709,19 @@ plexiform layer using GABA. - + + + + + + + A smooth muscle cell that is part of the cecum. FMA:15681 non-striated muscle fiber of cecum smooth muscle fiber of cecum smooth muscle cell of cecum - - - - - true - @@ -74314,6 +86752,12 @@ plexiform layer using GABA. + + + + + + A smooth muscle cell that is part of the ascending colon. FMA:17518 non-striated muscle fiber of ascending colon @@ -74355,6 +86799,12 @@ plexiform layer using GABA. + + + + + + A smooth muscle cell that is part of the transverse colon. FMA:17519 non-striated muscle fiber of transverse colon @@ -74396,6 +86846,12 @@ plexiform layer using GABA. + + + + + + A smooth muscle cell that is part of the descending colon. FMA:17520 non-striated muscle fiber of descending colon @@ -74437,6 +86893,12 @@ plexiform layer using GABA. + + + + + + A smooth muscle cell that is part of the sigmoid colon. FMA:17521 non-striated muscle fiber of sigmoid colon @@ -74477,19 +86939,19 @@ plexiform layer using GABA. - + + + + + + + A smooth muscle cell that is part of the rectum. FMA:17522 non-striated muscle fiber of rectum smooth muscle fiber of rectum smooth muscle cell of rectum - - - - - true - @@ -74644,6 +87106,8 @@ plexiform layer using GABA. + + An epithelial cell that is part of the urethra. FMA:256165 @@ -74682,6 +87146,14 @@ plexiform layer using GABA. + + + + + + + + A mesothelial cell that is part of the dura mater. FMA:256516 squamous mesothelial cell of dura mater @@ -74791,6 +87263,12 @@ plexiform layer using GABA. + + + + + + A fibroblast that is part of the papillary layer of dermis. FMA:261277 fibroblast of papillary layer of dermis @@ -74913,6 +87391,13 @@ plexiform layer using GABA. + + + + + + + A fibroblast that is part of the tunica adventitia of artery. FMA:261285 fibroblast of tunica adventitia of artery @@ -74953,6 +87438,12 @@ plexiform layer using GABA. + + + + + + A fibroblast that is part of the dense regular elastic tissue. FMA:261287 fibroblast of dense regular elastic tissue @@ -74981,6 +87472,7 @@ plexiform layer using GABA. + A fibrocyte that is part of the adventitia of ureter. FMA:261289 @@ -75006,6 +87498,7 @@ plexiform layer using GABA. + @@ -75056,7 +87549,7 @@ plexiform layer using GABA. - + @@ -75069,12 +87562,6 @@ plexiform layer using GABA. epicardial fat cell of right ventricle adipocyte of epicardial fat of right ventricle - - - - - true - @@ -75110,7 +87597,7 @@ plexiform layer using GABA. - + @@ -75124,12 +87611,6 @@ plexiform layer using GABA. adipocyte of epicardial fat of left ventricle - - - - - true - @@ -75165,12 +87646,8 @@ plexiform layer using GABA. - - - - - - + + A goblet cell that is part of the epithelium of bronchus. FMA:263032 goblet cell of epithelium of bronchus @@ -75206,6 +87683,8 @@ plexiform layer using GABA. + + @@ -75246,6 +87725,8 @@ plexiform layer using GABA. + + @@ -75290,7 +87771,14 @@ plexiform layer using GABA. + + + + + + + A goblet cell that is part of the epithelium of principal gastric gland. FMA:263040 goblet cell of epithelium of principal gastric gland @@ -75337,6 +87825,7 @@ plexiform layer using GABA. + @@ -75405,6 +87894,8 @@ plexiform layer using GABA. + + @@ -75450,6 +87941,7 @@ plexiform layer using GABA. + @@ -75506,6 +87998,8 @@ plexiform layer using GABA. + + @@ -75548,6 +88042,8 @@ plexiform layer using GABA. + + @@ -75592,12 +88088,8 @@ plexiform layer using GABA. - - - - - - + + A goblet cell that is part of the epithelium proper of duodenum. FMA:263063 @@ -75628,6 +88120,7 @@ plexiform layer using GABA. + @@ -75674,6 +88167,7 @@ plexiform layer using GABA. + @@ -75719,22 +88213,8 @@ plexiform layer using GABA. - - - - - - - - - - - - - - - - + + A goblet cell that is part of the epithelium proper of appendix. FMA:263069 goblet cell of epithelium proper of appendix @@ -75780,6 +88260,8 @@ plexiform layer using GABA. + + @@ -75823,6 +88305,13 @@ plexiform layer using GABA. + + + + + + + A serous secreting cell that is part of the epithelium of trachea. FMA:263078 @@ -75853,6 +88342,13 @@ plexiform layer using GABA. + + + + + + + A serous secreting cell that is part of the epithelium of bronchus. FMA:263080 @@ -75883,6 +88379,14 @@ plexiform layer using GABA. + + + + + + + + A serous secreting cell that is part of the epithelium of terminal bronchiole. FMA:263082 serous cell of epithelium of terminal bronchiole @@ -75910,6 +88414,14 @@ plexiform layer using GABA. + + + + + + + + A serous secreting cell that is part of the epithelium of bronchiole. FMA:263084 serous cell of epithelium of lobular bronchiole @@ -75938,6 +88450,13 @@ plexiform layer using GABA. + + + + + + + An enterocyte that is part of the epithelium of small intestine. FMA:263086 @@ -75972,23 +88491,17 @@ plexiform layer using GABA. - + - + An enterocyte that is part of the epithelium of intestinal villus. FMA:263088 enterocyte of epithelium of intestinal villus - - - - - true - @@ -76022,6 +88535,14 @@ plexiform layer using GABA. + + + + + + + + An enterocyte that is part of the epithelium of duodenal gland. FMA:263092 enterocyte of epithelium of duodenal gland @@ -76148,7 +88669,7 @@ plexiform layer using GABA. - + A paneth cell that is part of the epithelium of small intestine. FMA:263104 @@ -76160,12 +88681,6 @@ plexiform layer using GABA. true - - - - - true - @@ -76198,12 +88713,6 @@ plexiform layer using GABA. - - - - - - A paneth cell that is part of the epithelium of crypt of Lieberkuhn of small intestine. FMA:263108 paneth cell of epithelium of crypt of Lieberkuhn of small intestine @@ -76251,6 +88760,7 @@ plexiform layer using GABA. + A columnar cell of the colon that is part of the colonic epithelium. FMA:263114 vacuolar absorptive cell of epithelium of colon @@ -76286,7 +88796,14 @@ plexiform layer using GABA. + + + + + + + A basal cell that is part of the epithelium of trachea. FMA:263118 @@ -76323,7 +88840,9 @@ plexiform layer using GABA. + + A basal cell found in the bronchus epithelium. FMA:263120 @@ -76354,7 +88873,15 @@ plexiform layer using GABA. + + + + + + + + A basal cell that is part of the epithelium of terminal bronchiole. FMA:263122 @@ -76390,7 +88917,15 @@ plexiform layer using GABA. + + + + + + + + A basal cell that is part of the epithelium of respiratory bronchiole. FMA:263124 @@ -76426,7 +88961,15 @@ plexiform layer using GABA. + + + + + + + + A basal cell that is part of the epithelium of bronchiole. FMA:263126 @@ -76463,6 +89006,7 @@ plexiform layer using GABA. + @@ -76503,7 +89047,7 @@ plexiform layer using GABA. - + @@ -76554,7 +89098,7 @@ plexiform layer using GABA. - + @@ -76588,7 +89132,13 @@ plexiform layer using GABA. - + + + + + + + A M cell that is part of the epithelium proper of jejunum. FMA:263136 microfold cell of epithelium proper of jejunum @@ -76616,7 +89166,13 @@ plexiform layer using GABA. - + + + + + + + A M cell that is part of the epithelium proper of ileum. FMA:263138 microfold cell of epithelium proper of ileum @@ -76644,7 +89200,8 @@ plexiform layer using GABA. - + + @@ -76708,6 +89265,13 @@ plexiform layer using GABA. + + + + + + + A transitional myocyte that is part of the interatrial septum. FMA:263152 transitional myocyte of interatrial septum @@ -76742,6 +89306,13 @@ plexiform layer using GABA. + + + + + + + A transitional myocyte that is part of the interventricular septum. FMA:263154 transitional myocyte of interventricular septum @@ -76849,13 +89420,7 @@ plexiform layer using GABA. - - - - - - - + A transitional myocyte that is part of the anterior division of left branch of atrioventricular bundle. FMA:263166 transitional myocyte of anterior division of left branch of atrioventricular bundle @@ -76872,13 +89437,7 @@ plexiform layer using GABA. - - - - - - - + A transitional myocyte that is part of the septal division of left branch of atrioventricular bundle. FMA:263168 transitional myocyte of septal division of left branch of atrioventricular bundle @@ -76997,13 +89556,7 @@ plexiform layer using GABA. - - - - - - - + A transitional myocyte that is part of the posterior division of left branch of atrioventricular bundle. FMA:263178 transitional myocyte of posterior division of left branch of atrioventricular bundle @@ -77021,6 +89574,9 @@ plexiform layer using GABA. + + + @@ -77055,6 +89611,13 @@ plexiform layer using GABA. + + + + + + + A Purkinje myocyte that is part of the interventricular septum. FMA:263182 Purkinje myocyte of interventricular septum @@ -77090,6 +89653,12 @@ plexiform layer using GABA. + + + + + + A Feyrter cell that is part of the epithelium of trachea. FMA:263184 dense-core granulated cell of epithelium of trachea @@ -77129,6 +89698,13 @@ plexiform layer using GABA. + + + + + + + A type I vestibular sensory cell that is part of the stato-acoustic epithelium. FMA:263186 type 1 vestibular sensory cell of stato-acoustic epithelium @@ -77156,6 +89732,7 @@ plexiform layer using GABA. + @@ -77189,6 +89766,13 @@ plexiform layer using GABA. + + + + + + + @@ -77222,6 +89806,13 @@ plexiform layer using GABA. + + + + + + + A type I vestibular sensory cell that is part of the epithelium of crista of ampulla of semicircular duct of membranous labyrinth. FMA:263192 type 1 vestibular sensory cell of epithelium of crista of ampulla of semicircular duct of membranous labyrinth @@ -77249,6 +89840,13 @@ plexiform layer using GABA. + + + + + + + A type II vestibular sensory cell that is part of the stato-acoustic epithelium. FMA:263194 type 2 vestibular sensory cell of stato-acoustic epithelium @@ -77276,6 +89874,7 @@ plexiform layer using GABA. + @@ -77309,6 +89908,13 @@ plexiform layer using GABA. + + + + + + + @@ -77342,6 +89948,13 @@ plexiform layer using GABA. + + + + + + + A type II vestibular sensory cell that is part of the epithelium of crista of ampulla of semicircular duct of membranous labyrinth. FMA:263200 type 2 vestibular sensory cell of epithelium of crista of ampulla of semicircular duct of membranous labyrinth @@ -77420,6 +90033,12 @@ plexiform layer using GABA. + + + + + + A melanocyte that is part of the eyelid. FMA:59175 eyelid melanocyte @@ -77515,6 +90134,13 @@ plexiform layer using GABA. + + + + + + + An endothelial cell that is part of the venous sinus of red pulp of spleen. FMA:62817 todo - add logical definition to UBERON:0009967 @@ -77543,6 +90169,13 @@ plexiform layer using GABA. + + + + + + + An endothelial cell that is part of the hepatic sinusoid. These cells possess flattened areas containing perforations about 0.1 micrometers in diameter, known as fenestrae. The fenestrae are arranged in groups known as sieve plates. BTO:000125 @@ -77656,6 +90289,13 @@ plexiform layer using GABA. + + + + + + + An epithelial cell that is part of the appendix. FMA:63602 columnar epitheliocyte of appendix @@ -77728,6 +90368,13 @@ plexiform layer using GABA. + + + + + + + A muscle cell that is part of the sinoatrial node. FMA:67102 SA nodal myocyte @@ -77786,6 +90433,14 @@ plexiform layer using GABA. + + + + + + + + A muscle cell that is part of the atrioventricular node. FMA:67106 AV nodal myocyte @@ -77850,6 +90505,13 @@ plexiform layer using GABA. + + + + + + + An endothelial cell that is part of the small intestine Peyer's patch. FMA:67757 endothelial cell of Peyer's patch @@ -77884,6 +90546,12 @@ plexiform layer using GABA. + + + + + + An endothelial cell that is part of the arteriole. FMA:67760 @@ -77961,6 +90629,12 @@ plexiform layer using GABA. + + + + + + An endothelial cell that is part of the venule. FMA:67762 @@ -77997,6 +90671,13 @@ plexiform layer using GABA. + + + + + + + An epithelial cell that is part of the gallbladder. FMA:67780 epithelial cell of gallbladder @@ -78043,6 +90724,7 @@ plexiform layer using GABA. + A myoepithelial cell that is part of the sweat gland. FMA:67801 @@ -78078,19 +90760,19 @@ plexiform layer using GABA. - + + + + + + + A myoepithelial cell that is part of the mammary gland alveolus. FMA:67802 basal cell of alveolus of lactiferous gland myoepithelial cell of mammary alveolus myoepithelial cell of lactiferous alveolus - - - - - true - @@ -78126,17 +90808,18 @@ plexiform layer using GABA. - + + + + + + + + A myoepithelial cell that is part of the lactiferous duct. FMA:67803 myoepithelial cell of lactiferous duct - - - - - true - @@ -78207,18 +90890,18 @@ plexiform layer using GABA. - + + + + + + + A chromaffin cell that is part of the paraaortic body. FMA:69328 chromaffin cell of para-aortic body chromaffin cell of paraaortic body - - - - - true - @@ -78249,6 +90932,12 @@ plexiform layer using GABA. + + + + + + A chromaffin cell that is part of the paraganglion. FMA:69335 chromaffin cell of paraganglion @@ -78284,6 +90973,12 @@ plexiform layer using GABA. + + + + + + A chromaffin cell that is part of the adrenal gland. FMA:69794 adrenal chromaffin cell @@ -78324,19 +91019,14 @@ plexiform layer using GABA. - + + A chromaffin cell that is part of the adrenal cortex. FMA:69795 chromaffin cell of adrenal cortex Not clear this cell type exists. Can't call it a cortical adrenal cell because of different germ layer origin. adrenal cortex chromaffin cell - - - - - true - @@ -78361,6 +91051,12 @@ plexiform layer using GABA. + + + + + + A somatic stem cell that is part of the epidermis. FMA:70541 epidermal stem cell @@ -78433,6 +91129,12 @@ plexiform layer using GABA. + + + + + + An epithelial cell that is part of the conjunctiva. FMA:70552 epithelial cell of conjunctiva @@ -78475,6 +91177,13 @@ plexiform layer using GABA. + + + + + + + An epithelial cell that is part of the lacrimal canaliculus. FMA:70553 epithelial cell of lacrimal canaliculus @@ -78502,6 +91211,13 @@ plexiform layer using GABA. + + + + + + + An epithelial cell that is part of the external acoustic meatus. FMA:70555 epithelial cell of external acoustic meatus @@ -78530,6 +91246,12 @@ plexiform layer using GABA. + + + + + + An epithelial cell that is part of the lacrimal drainage system. FMA:70559 epithelial cell of lacrimal duct @@ -78565,6 +91287,13 @@ plexiform layer using GABA. + + + + + + + An epithelial cell that is part of the lacrimal sac. FMA:70560 @@ -78593,17 +91322,17 @@ plexiform layer using GABA. - + + + + + + + An epithelial cell that is part of the nasolacrimal duct. FMA:70561 epithelial cell of nasolacrimal duct - - - - - true - @@ -78691,6 +91420,23 @@ plexiform layer using GABA. + + + + + + + + + + + + + + + + + An urothelial cell that is part of the trigone of urinary bladder. FMA:70598 epithelial cell of vesical trigone @@ -78726,6 +91472,12 @@ plexiform layer using GABA. + + + + + + A smooth muscle cell that is part of the ciliary body. FMA:70610 smooth muscle cell of ciliary body @@ -78768,6 +91520,13 @@ plexiform layer using GABA. + + + + + + + A mesothelial cell that is part of the anterior chamber of eyeball. FMA:70615 mesothelial cell of anterior chamber of eye @@ -78796,6 +91555,12 @@ plexiform layer using GABA. + + + + + + A myoepithelial cell that is part of the dilatator pupillae. FMA:70619 myoepithelial cell of dilator pupillae @@ -78840,6 +91605,12 @@ plexiform layer using GABA. + + + + + + A basal cell that is part of the epithelium of esophagus. FMA:70731 basal cell of esophageal epithelium @@ -78881,6 +91652,14 @@ plexiform layer using GABA. + + + + + + + + An epithelial cell that is part of the sweat gland. FMA:70952 @@ -78909,6 +91688,13 @@ plexiform layer using GABA. + + + + + + + An epithelial cell that is part of the nephron. FMA:70965 @@ -78938,7 +91724,12 @@ plexiform layer using GABA. - + + + + + + An epithelial cell that is part of the glomerular capsule. FMA:70966 KUPO:0001034 @@ -78948,12 +91739,6 @@ plexiform layer using GABA. epithelial cell of glomerular capsule - - - - - true - @@ -78993,7 +91778,13 @@ plexiform layer using GABA. - + + + + + + + An epithelial cell that is part of the glomerular parietal epithelium. FMA:70968 @@ -79003,12 +91794,6 @@ plexiform layer using GABA. parietal epithelial cell - - - - - true - @@ -79038,6 +91823,13 @@ plexiform layer using GABA. + + + + + + + An epithelial cell that is part of the intermediate tubule. FMA:70980 epithelial cell of intermediate tubule @@ -79066,7 +91858,7 @@ plexiform layer using GABA. - + An epithelial cell that is part of the collecting duct of renal tubule. @@ -79084,12 +91876,6 @@ plexiform layer using GABA. true - - - - - true - @@ -79125,6 +91911,13 @@ plexiform layer using GABA. + + + + + + + A mesothelial cell that is part of the parietal peritoneum. FMA:72142 mesothelial cell of parietal peritoneum @@ -79152,6 +91945,13 @@ plexiform layer using GABA. + + + + + + + A mesothelial cell that is part of the visceral peritoneum. FMA:72143 @@ -79182,6 +91982,12 @@ plexiform layer using GABA. + + + + + + A melanocyte that is part of the skin of body. CALOHA:TS-2374 @@ -79277,6 +92083,7 @@ plexiform layer using GABA. + A chromaffin cell that is part of the ovary. FMA:74319 chromaffin cell of ovary @@ -79310,17 +92117,17 @@ plexiform layer using GABA. - + + + + + + + A chromaffin cell that is part of the right ovary. FMA:74320 chromaffin cell of right ovary - - - - - true - @@ -79344,17 +92151,17 @@ plexiform layer using GABA. - + + + + + + + A chromaffin cell that is part of the left ovary. FMA:74321 chromaffin cell of left ovary - - - - - true - @@ -79367,7 +92174,7 @@ plexiform layer using GABA. - + @@ -79513,12 +92320,6 @@ plexiform layer using GABA. - - - - - - A nodal myocyte that is part of the sinoatrial node. FMA:83383 @@ -79552,6 +92353,7 @@ plexiform layer using GABA. + A transitional myocyte that is part of the sinoatrial node. FMA:83384 transitinal myocyte of sinuatrial node @@ -79587,6 +92389,7 @@ plexiform layer using GABA. + A Purkinje myocyte that is part of the atrioventricular node. FMA:83386 Purkinje myocyte of atrioventricular node @@ -79621,6 +92424,7 @@ plexiform layer using GABA. + A transitional myocyte that is part of the internodal tract. FMA:83387 transitional myocyte of internodal tract @@ -79655,6 +92459,9 @@ plexiform layer using GABA. + + + A transitional myocyte that is part of the atrioventricular bundle. FMA:83388 transitional myocyte of atrioventricular bundle @@ -79689,6 +92496,13 @@ plexiform layer using GABA. + + + + + + + A myocardial endocrine cell that is part of the interventricular septum. FMA:83390 myocardial endocrine cell of interventricular septum @@ -79723,6 +92537,7 @@ plexiform layer using GABA. + A Purkinje myocyte that is part of the internodal tract. FMA:83392 Purkinje myocyte of internodal tract @@ -79757,6 +92572,9 @@ plexiform layer using GABA. + + + A Purkinje myocyte that is part of the atrioventricular bundle. FMA:83393 Purkinje myocyte of atrioventricular bundle @@ -79844,6 +92662,12 @@ plexiform layer using GABA. + + + + + + A smooth muscle cell that is part of the prostate gland. FMA:84583 @@ -79892,6 +92716,12 @@ plexiform layer using GABA. + + + + + + @@ -79952,6 +92782,13 @@ plexiform layer using GABA. + + + + + + + A reticular cell that is part of the splenic cord. FMA:86497 @@ -79987,6 +92824,13 @@ plexiform layer using GABA. + + + + + + + A mesothelial cell that is part of the peritoneum. FMA:86736 peritoneal mesothelial cell @@ -80021,6 +92865,13 @@ plexiform layer using GABA. + + + + + + + A mesothelial cell that is part of the pleura. FMA:86737 pleural mesothelial cell @@ -80056,6 +92907,13 @@ plexiform layer using GABA. + + + + + + + A mesothelial cell that is part of the parietal pleura. FMA:86738 mesothelial cell of parietal pleura @@ -80083,6 +92941,14 @@ plexiform layer using GABA. + + + + + + + + A mesothelial cell that is part of the visceral pleura. FMA:86739 @@ -80113,6 +92979,14 @@ plexiform layer using GABA. + + + + + + + + An epithelial cell that is part of a nephron tubule. FMA:86785 KUPO:0001022 @@ -80144,12 +93018,8 @@ plexiform layer using GABA. - - - - - - + + A goblet cell that is part of the small intestine. FMA:86929 goblet cell of epithelium of small intestine @@ -80187,6 +93057,13 @@ plexiform layer using GABA. + + + + + + + A cell that is part of a kidney. KUPO:0001010 @@ -80209,6 +93086,14 @@ plexiform layer using GABA. + + + + + + + + A cell that is part of kidney interstitium. KUPO:0001013 @@ -80232,10 +93117,23 @@ plexiform layer using GABA. + + + + + + + A cell that is part of a renal medulla. KUPO:0001017 kidney medulla cell + + + + A cell that is part of a renal medulla. + PMID:22343825 + @@ -80253,6 +93151,13 @@ plexiform layer using GABA. + + + + + + + A cell that is part of a renal pelvis. KUPO:0001018 @@ -80275,6 +93180,13 @@ plexiform layer using GABA. + + + + + + + A cell that is part of a nephron tubule. KUPO:0001020 @@ -80297,7 +93209,7 @@ plexiform layer using GABA. - + @@ -80308,12 +93220,6 @@ plexiform layer using GABA. kidney glomerular epithelial cell - - - - - true - @@ -80331,6 +93237,14 @@ plexiform layer using GABA. + + + + + + + + An epithelial cell that is part of a renal medulla collecting duct. KUPO:0001060 @@ -80354,6 +93268,13 @@ plexiform layer using GABA. + + + + + + + An epithelial cell that is part of some inner medullary collecting duct. KUPO:0001061 kidney inner medulla collecting duct epithelial cell @@ -80376,6 +93297,13 @@ plexiform layer using GABA. + + + + + + + An epithelial cell that is part of an outer medullary collecting duct. KUPO:0001062 kidney outer medulla collecting duct epithelial cell @@ -80397,6 +93325,14 @@ plexiform layer using GABA. + + + + + + + + An epithelial cell that is part of a cortical collecting duct. KUPO:0001063 kidney cortex collecting duct epithelial cell @@ -80418,7 +93354,7 @@ plexiform layer using GABA. - + @@ -80429,12 +93365,6 @@ plexiform layer using GABA. kidney papillary duct principal epithelial cell - - - - - true - @@ -80452,7 +93382,7 @@ plexiform layer using GABA. - + @@ -80462,12 +93392,6 @@ plexiform layer using GABA. KUPO:0001111 inner renal cortex cell - - - - - true - @@ -80485,7 +93409,8 @@ plexiform layer using GABA. - + + @@ -80499,12 +93424,6 @@ plexiform layer using GABA. papillary tips cell - - - - - true - @@ -80522,6 +93441,7 @@ plexiform layer using GABA. + @@ -80548,6 +93468,7 @@ plexiform layer using GABA. + @@ -80576,6 +93497,12 @@ plexiform layer using GABA. + + + + + + KUPO:0001015 kidney nerve cell @@ -80597,6 +93524,7 @@ plexiform layer using GABA. + @@ -80631,6 +93559,7 @@ plexiform layer using GABA. + @@ -80780,6 +93709,7 @@ plexiform layer using GABA. + A cell that is part of an interstitial compartment of a renal cortex. KUPO:0001091 kidney cortex interstitial cell @@ -80789,6 +93719,12 @@ plexiform layer using GABA. true + + + + A cell that is part of an interstitial compartment of a renal cortex. + PMID:18575881 + @@ -80814,6 +93750,7 @@ plexiform layer using GABA. + A cell that is part of an interstitum of a renal medulla. KUPO:0001092 kidney medulla interstitial cell @@ -80829,6 +93766,12 @@ plexiform layer using GABA. true + + + + A cell that is part of an interstitum of a renal medulla. + PMID:21359760 + @@ -80859,12 +93802,21 @@ plexiform layer using GABA. + + + A fibroblast that is part of an interstitial compartment of a kidney. KUPO:0001102 kidney interstitial fibroblast + + + + A fibroblast that is part of an interstitial compartment of a kidney. + PMID:10559635 + @@ -80932,9 +93884,16 @@ plexiform layer using GABA. + A resident-dendritic cell that is part of a kidney. KUPO:0001110 kidney resident dendritic cell + + + + A resident-dendritic cell that is part of a kidney. + PMID:25266210 + @@ -81111,25 +94070,13 @@ plexiform layer using GABA. - - - - - - - + KUPO:0001130 kidney cortex collecting duct principal cell - - - - - true - @@ -81153,25 +94100,13 @@ plexiform layer using GABA. - - - - - - - + KUPO:0001131 kidney cortex collecting duct intercalated cell - - - - - true - @@ -81195,26 +94130,14 @@ plexiform layer using GABA. - - - - - - - + Principal cell that is part of some outer medullary collecting duct. It is known in some mammalian species that this cell may express the epithelial sodium channel (ENaC). KUPO:0001132 kidney outer medulla collecting duct principal cell - - - - - true - @@ -81244,26 +94167,14 @@ plexiform layer using GABA. - - - - - - - + Intercalated cell that is part of some outer medullary collecting duct. It is known in some mammalian species that this cell may contribute in the maintenance of acid/base homeostasis. KUPO:0001133 kidney outer medulla collecting duct intercalated cell - - - - - true - @@ -81293,25 +94204,13 @@ plexiform layer using GABA. - - - - - - - + KUPO:0001134 kidney inner medulla collecting duct principal cell - - - - - true - @@ -81335,23 +94234,11 @@ plexiform layer using GABA. - - - - - - - + KUPO:0001135 kidney inner medulla collecting duct intercalated cell - - - - - true - @@ -81375,23 +94262,11 @@ plexiform layer using GABA. - - - - - - - + KUPO:0001136 kidney papillary duct intercalated cell - - - - - true - @@ -81415,23 +94290,11 @@ plexiform layer using GABA. - - - - - - - + KUPO:0001137 kidney papillary duct principal cell - - - - - true - @@ -81444,20 +94307,16 @@ plexiform layer using GABA. + - + + - - - - - - @@ -81472,12 +94331,6 @@ plexiform layer using GABA. Like smooth muscle, a glomerular mesangial cell is contractile and possesses the filaments actin and myosin. The contractile mechanism is also similar to that of smooth muscle, with Ca2+/calmodulin-activated myosin light-chain kinase instigating myosin-actin cross-bridge cycling. Mesangial cell phagocytosis of apoptotic neutrophils involves a novel CD36-independent, alpha(v)beta3/TSP-mediated mechanism that is uncoupled from chemokine secretion, emphasizing the injury-limiting potential of mesangial cell phagocytosis of apoptotic cells. glomerular mesangial cell - - - - - true - @@ -81515,7 +94368,6 @@ plexiform layer using GABA. - @@ -81526,12 +94378,6 @@ plexiform layer using GABA. KUPO:0001036 glomerular cell - - - - - true - @@ -81601,6 +94447,7 @@ plexiform layer using GABA. + A cell that is part of an interstitial compartment of an inner renal medulla. KUPO:0001093 kidney inner medulla interstitial cell @@ -81616,6 +94463,12 @@ plexiform layer using GABA. true + + + + A cell that is part of an interstitial compartment of an inner renal medulla. + PMID:21359760 + @@ -81641,6 +94494,7 @@ plexiform layer using GABA. + A kidney cell that is part of an interstitial compartment of an outer renal medulla. KUPO:0001094 kidney outer medulla interstitial cell @@ -81656,6 +94510,12 @@ plexiform layer using GABA. true + + + + A kidney cell that is part of an interstitial compartment of an outer renal medulla. + PMID:8694267 + @@ -81674,7 +94534,6 @@ plexiform layer using GABA. - @@ -81691,12 +94550,6 @@ plexiform layer using GABA. true - - - - - true - @@ -81715,8 +94568,8 @@ plexiform layer using GABA. - + @@ -81733,12 +94586,6 @@ plexiform layer using GABA. true - - - - - true - @@ -81800,7 +94647,6 @@ plexiform layer using GABA. - @@ -81820,12 +94666,6 @@ plexiform layer using GABA. true - - - - - true - @@ -81841,7 +94681,7 @@ plexiform layer using GABA. - + @@ -81863,6 +94703,7 @@ plexiform layer using GABA. + A blood vessel cell that is part of a kidney. KUPO:0001014 kidney blood vessel cell @@ -81872,6 +94713,12 @@ plexiform layer using GABA. true + + + + A blood vessel cell that is part of a kidney. + PMID:34843404 + @@ -81925,6 +94772,12 @@ plexiform layer using GABA. + + + + + + KUPO:0001030 @@ -82065,7 +94918,9 @@ plexiform layer using GABA. - + + + @@ -82079,12 +94934,6 @@ plexiform layer using GABA. glomerular capillary endothelial cell - - - - - true - @@ -82108,7 +94957,7 @@ plexiform layer using GABA. - + @@ -82119,12 +94968,6 @@ plexiform layer using GABA. KUPO:0001038 kidney afferent arteriole cell - - - - - true - @@ -82148,7 +94991,7 @@ plexiform layer using GABA. - + @@ -82159,12 +95002,6 @@ plexiform layer using GABA. KUPO:0001041 kidney efferent arteriole cell - - - - - true - @@ -82188,6 +95025,7 @@ plexiform layer using GABA. + @@ -82257,13 +95095,8 @@ plexiform layer using GABA. + - - - - - - @@ -82300,28 +95133,31 @@ plexiform layer using GABA. - + + + A cell that is part of a vasa recta. KUPO:0001068 vasa recta cell - + true - - - true + + A cell that is part of a vasa recta. + PMID:12529271 + PMID:24381184 @@ -82340,7 +95176,6 @@ plexiform layer using GABA. - @@ -82352,12 +95187,6 @@ plexiform layer using GABA. kidney cortex artery cell - - - - - true - @@ -82381,7 +95210,6 @@ plexiform layer using GABA. - @@ -82392,12 +95220,6 @@ plexiform layer using GABA. KUPO:0001084 kidney cortex vein cell - - - - - true - @@ -82410,7 +95232,8 @@ plexiform layer using GABA. - + + KUPO:0001096 Note that the source of this term is KUPO:0001096 (artery smooth muscle cell), which we believe actually denotes the kidney specific structure. @@ -82422,7 +95245,8 @@ plexiform layer using GABA. - + + KUPO:0001098 Note that the source of this term is KUPO:0001098 (arteriole smooth muscle cell), which we believe actually denotes the kidney specific structure. @@ -82434,7 +95258,8 @@ plexiform layer using GABA. - + + KUPO:0001100 Note that the source of this term is KUPO:0001068 (venous system smooth muscle cell), which we believe actually denotes the kidney specific structure. @@ -82457,8 +95282,8 @@ plexiform layer using GABA. - + KUPO:0001039 @@ -82466,12 +95291,6 @@ plexiform layer using GABA. kidney afferent arteriole endothelial cell - - - - - true - @@ -82495,18 +95314,12 @@ plexiform layer using GABA. - + KUPO:0001040 kidney afferent arteriole smooth muscle cell - - - - - true - @@ -82524,7 +95337,6 @@ plexiform layer using GABA. - @@ -82533,12 +95345,6 @@ plexiform layer using GABA. kidney efferent arteriole endothelial cell - - - - - true - @@ -82562,18 +95368,12 @@ plexiform layer using GABA. - + KUPO:0001043 kidney efferent arteriole smooth muscle cell - - - - - true - @@ -82592,7 +95392,6 @@ plexiform layer using GABA. - @@ -82607,12 +95406,6 @@ plexiform layer using GABA. kidney loop of Henle thick ascending limb epithelial cell - - - - - true - @@ -82642,6 +95435,7 @@ plexiform layer using GABA. + @@ -82680,7 +95474,7 @@ plexiform layer using GABA. - + @@ -82700,12 +95494,6 @@ plexiform layer using GABA. true - - - - - true - @@ -82723,8 +95511,7 @@ plexiform layer using GABA. - - + @@ -82738,18 +95525,6 @@ plexiform layer using GABA. kidney loop of Henle cortical thick ascending limb epithelial cell - - - - - true - - - - - - true - @@ -82767,6 +95542,7 @@ plexiform layer using GABA. + @@ -82845,7 +95621,6 @@ plexiform layer using GABA. - @@ -82856,12 +95631,6 @@ plexiform layer using GABA. KUPO:0001067 kidney cortex peritubular capillary cell - - - - - true - @@ -83223,18 +95992,11 @@ plexiform layer using GABA. - KUPO:0001079 arcuate artery endothelial cell - - - - - true - @@ -83258,18 +96020,11 @@ plexiform layer using GABA. - KUPO:0001080 arcuate artery smooth muscle cell - - - - - true - @@ -83287,7 +96042,6 @@ plexiform layer using GABA. - KUPO:0001082 @@ -83310,18 +96064,11 @@ plexiform layer using GABA. - KUPO:0001083 interlobulary artery smooth muscle cell - - - - - true - @@ -83339,7 +96086,6 @@ plexiform layer using GABA. - KUPO:0001086 @@ -83362,18 +96108,11 @@ plexiform layer using GABA. - KUPO:0001087 arcuate vein smooth muscle cell - - - - - true - @@ -83391,7 +96130,6 @@ plexiform layer using GABA. - KUPO:0001089 @@ -83414,18 +96152,11 @@ plexiform layer using GABA. - KUPO:0001090 interlobulary vein smooth muscle cell - - - - - true - @@ -83443,6 +96174,13 @@ plexiform layer using GABA. + + + + + + + A cell that is part of a collecting duct of renal tubule. KUPO:0001012 Wikipedia:Kidney_collecting_duct_cell @@ -83593,6 +96331,7 @@ plexiform layer using GABA. + A pericyte cell located in the kidney interstitium. KUPO:0001104 @@ -83623,6 +96362,7 @@ plexiform layer using GABA. + @@ -83652,6 +96392,7 @@ plexiform layer using GABA. + @@ -83678,6 +96419,14 @@ plexiform layer using GABA. + + + + + + + + A urothelial cell that is part of the urothelium of the urinary bladder. KUPO:0001121 @@ -83712,7 +96461,7 @@ plexiform layer using GABA. - + @@ -83729,12 +96478,6 @@ plexiform layer using GABA. true - - - - - true - @@ -83754,12 +96497,6 @@ plexiform layer using GABA. - - - - - - KUPO:0001128 @@ -83791,12 +96528,6 @@ plexiform layer using GABA. - - - - - - KUPO:0001129 http://en.wikipedia.org/wiki/Collecting_duct_system#Intercalated_cells @@ -83827,6 +96558,13 @@ plexiform layer using GABA. + + + + + + + An epithelial cell of the exocrine pancreas. FMA:70986 @@ -83859,12 +96597,19 @@ plexiform layer using GABA. + + + + + + + A neuron residing in the olfactory bulb that serve to process and refine signals arising from olfactory sensory neurons olfactory bulb interneuron @@ -83976,6 +96721,7 @@ plexiform layer using GABA. + @@ -83983,6 +96729,12 @@ plexiform layer using GABA. + + + + + + A sensory neuron of the dorsal root ganglia that senses body position and sends information about how much the muscle is stretched to the spinal cord. proprioceptive neuron sensory neuron of dorsal root ganglion @@ -84005,19 +96757,14 @@ plexiform layer using GABA. - + + - - - - - - An inhibitory, GABAergic projection neuron in the striatum that integrates glutamatergic signals arising from the cerebral cortex and thalamus. BTO:0004778 @@ -84110,7 +96857,9 @@ plexiform layer using GABA. - + + + @@ -84151,7 +96900,14 @@ plexiform layer using GABA. + + + + + + + The neurons that utilize glycine as a neurotransmitter. FBbt:00048032 glycinergic neuron @@ -84179,6 +96935,8 @@ plexiform layer using GABA. + + The various hormone- or neurotransmitter-secreting cells present throughout the mucosa of the intestinal tract. intestinal enteroendocrine cell @@ -84206,6 +96964,14 @@ plexiform layer using GABA. + + + + + + + + The various hormone- or neurotransmitter-secreting cells present throughout the mucosa of the stomach. stomach enteroendocrine cell @@ -84236,6 +97002,19 @@ plexiform layer using GABA. + + + + + + + + + + + + + Chemosensitive cells that innervate the vomernasal organ epithelium and are responsible for receiving and transmitting pheromone signals. vomeronasal sensory neuron @@ -84281,6 +97060,8 @@ plexiform layer using GABA. + + @@ -84308,6 +97089,7 @@ plexiform layer using GABA. + @@ -84344,6 +97126,8 @@ plexiform layer using GABA. + + An interneuron with a soma found in the hippocampus. FMA:84777 hippocampal interneuron @@ -84371,6 +97155,8 @@ plexiform layer using GABA. + + @@ -84420,6 +97206,8 @@ plexiform layer using GABA. + + @@ -84469,7 +97257,8 @@ plexiform layer using GABA. - + + @@ -84510,12 +97299,8 @@ plexiform layer using GABA. - - - - - - + + Squamous cell of uterine cervix epithelium. CALOHA:TS-1251 cervix squamous cell @@ -84578,6 +97363,14 @@ plexiform layer using GABA. + + + + + + + + Squamous cell of oral epithelium. CALOHA:TS-1252 oral cavity mucosa squamous cell @@ -84633,6 +97426,8 @@ plexiform layer using GABA. + + @@ -84696,6 +97491,7 @@ plexiform layer using GABA. + @@ -84757,6 +97553,13 @@ plexiform layer using GABA. + + + + + + + Glial cell of cerebral cortex. CALOHA:TS-1256 brain cortex glial cell @@ -84805,6 +97608,13 @@ plexiform layer using GABA. + + + + + + + A glial cell that is part of the hippocampus. CALOHA:TS-1257 hippocampus glial cell @@ -84846,6 +97656,13 @@ plexiform layer using GABA. + + + + + + + Glial cell of lateral ventricle. CALOHA:TS-1258 lateral ventricle glial cells @@ -84880,6 +97697,13 @@ plexiform layer using GABA. + + + + + + + Neuron of lateral ventricle. CALOHA:TS-1261 lateral ventricle neural cell @@ -84952,6 +97776,8 @@ plexiform layer using GABA. + + @@ -85013,6 +97839,9 @@ plexiform layer using GABA. + + + @@ -85068,12 +97897,8 @@ plexiform layer using GABA. - - - - - - + + Glandular cell of uterine cervix epithelium. CALOHA:TS-1273 cervix glandular cell @@ -85122,12 +97947,8 @@ plexiform layer using GABA. - - - - - - + + Glandular cell of colon epithelium. Example: Goblet cells; enterocytes or absorptive cells; enteroendocrine and M cells. CALOHA:TS-1274 colon glandular cells @@ -85162,6 +97983,7 @@ plexiform layer using GABA. + @@ -85203,6 +98025,8 @@ plexiform layer using GABA. + + @@ -85250,6 +98074,7 @@ plexiform layer using GABA. + @@ -85305,6 +98130,8 @@ plexiform layer using GABA. + + @@ -85359,6 +98186,7 @@ plexiform layer using GABA. + @@ -85407,6 +98235,7 @@ plexiform layer using GABA. + @@ -85454,6 +98283,9 @@ plexiform layer using GABA. + + + @@ -85495,6 +98327,8 @@ plexiform layer using GABA. + + @@ -85536,6 +98370,8 @@ plexiform layer using GABA. + + @@ -85592,6 +98428,9 @@ plexiform layer using GABA. + + + @@ -85643,6 +98482,13 @@ plexiform layer using GABA. + + + + + + + Hormone secreting cell located in the cortex of adrenal gland. Glandular cells in the adrenal cortex secrete mineralocorticoids, glucocorticoids and androgens. CALOHA:TS-2177 adrenal gland glandular cells @@ -85691,6 +98537,14 @@ plexiform layer using GABA. + + + + + + + + @@ -85739,6 +98593,13 @@ plexiform layer using GABA. + + + + + + + Circulating macrophages and tissue macrophages (alveolar macrophages) of lung. CALOHA:TS-0576 lung macrophages @@ -85775,6 +98636,13 @@ plexiform layer using GABA. + + + + + + + Keratinocyte from foreskin. CALOHA:TS-0385 foreskin keratinocyte @@ -85802,6 +98670,13 @@ plexiform layer using GABA. + + + + + + + Chondrocyte forming the hyaline cartilage found in joints. CALOHA:TS-0056 @@ -85831,6 +98706,13 @@ plexiform layer using GABA. + + + + + + + Fibroblast from foreskin. CALOHA:TS-0384 BJ fibroblast @@ -85859,6 +98741,13 @@ plexiform layer using GABA. + + + + + + + Fibroblast from muscle organ. CALOHA:TS-0643 muscle fibroblast @@ -85886,6 +98775,8 @@ plexiform layer using GABA. + + @@ -85933,6 +98824,13 @@ plexiform layer using GABA. + + + + + + + Neuron of the cerebellum. CALOHA:TS-2359 FMA:84665 @@ -85968,6 +98866,14 @@ plexiform layer using GABA. + + + + + + + + Any melanocyte that is part of a epidermis. 2014-02-03T23:03:09Z @@ -85998,6 +98904,14 @@ plexiform layer using GABA. + + + + + + + + A leukocyte with a single non-segmented nucleus in the mature form found in the circulatory pool of blood. 2014-02-11T17:29:04Z @@ -86017,6 +98931,7 @@ plexiform layer using GABA. + @@ -86083,6 +98998,13 @@ plexiform layer using GABA. + + + + + + + Any cell that is part of a pituitary gland. 2014-03-26T22:14:56Z @@ -86113,6 +99035,13 @@ plexiform layer using GABA. + + + + + + + Any macroglial cell that is part of a brain. 2014-03-28T21:35:27Z @@ -86142,6 +99071,13 @@ plexiform layer using GABA. + + + + + + + Any germinal center B cell that is part of a tonsil. 2014-03-28T21:35:33Z @@ -86172,6 +99108,13 @@ plexiform layer using GABA. + + + + + + + Chondrocyte forming the hyaline cartilage found in the knee joint. 2014-06-04T14:40:11Z @@ -86201,6 +99144,13 @@ plexiform layer using GABA. + + + + + + + Any blood vessel endothelial cell that is part of a microvascular endothelium. 2014-06-04T15:07:42Z @@ -86250,6 +99200,13 @@ plexiform layer using GABA. + + + + + + + Any blood vessel endothelial cell that is part of a dermis. 2014-06-04T15:12:06Z @@ -86279,6 +99236,13 @@ plexiform layer using GABA. + + + + + + + Any endothelial cell of lymphatic vessel that is part of a dermis. 2014-06-04T15:15:08Z @@ -86308,6 +99272,13 @@ plexiform layer using GABA. + + + + + + + Any skin fibroblast that is part of a pedal digit skin. 2014-06-04T15:16:44Z @@ -86337,6 +99308,13 @@ plexiform layer using GABA. + + + + + + + Any skin fibroblast that is part of a skin of abdomen. 2014-06-04T15:18:16Z @@ -86366,6 +99344,13 @@ plexiform layer using GABA. + + + + + + + Any skin fibroblast that is part of a upper leg skin. 2014-06-04T15:19:44Z @@ -86395,6 +99380,13 @@ plexiform layer using GABA. + + + + + + + Any skin fibroblast that is part of a arm. 2014-06-04T15:29:06Z @@ -86424,6 +99416,7 @@ plexiform layer using GABA. + Any lung endothelial cell that is part of a microvascular endothelium. @@ -86455,6 +99448,13 @@ plexiform layer using GABA. + + + + + + + Any fibroblast that is part of a periodontal ligament. 2014-06-04T16:50:33Z @@ -86484,6 +99484,14 @@ plexiform layer using GABA. + + + + + + + + Any endothelial cell of artery that is part of a coronary artery. 2014-06-04T17:08:47Z @@ -86514,6 +99522,13 @@ plexiform layer using GABA. + + + + + + + Any photoreceptor cell that is part of a compound eye. 2014-06-24T23:16:45Z @@ -86544,6 +99559,13 @@ plexiform layer using GABA. + + + + + + + Any native cell that is part of a inner cell mass. 2014-06-24T23:16:53Z @@ -86573,6 +99595,13 @@ plexiform layer using GABA. + + + + + + + Any native cell that is part of a sebaceous gland. 2014-06-24T23:17:00Z @@ -86603,6 +99632,13 @@ plexiform layer using GABA. + + + + + + + Any native cell that is part of a cardiac septum. 2014-06-24T23:17:07Z @@ -86632,6 +99668,13 @@ plexiform layer using GABA. + + + + + + + Any interneuron that is part of a spinal cord ventral column. 2014-06-25T00:23:36Z @@ -86661,6 +99704,13 @@ plexiform layer using GABA. + + + + + + + Any neuron that is part of a spinal cord medial motor column. 2014-06-25T00:23:43Z @@ -86690,6 +99740,13 @@ plexiform layer using GABA. + + + + + + + Any oligodendrocyte that is part of a spinal cord. 2014-06-25T00:23:50Z @@ -86738,6 +99795,9 @@ plexiform layer using GABA. + + + Any basket cell that is part of a cerebellum. 2014-06-25T00:24:03Z @@ -86767,6 +99827,8 @@ plexiform layer using GABA. + + Any glutamatergic neuron that is part of a cerebellum. 2014-06-25T00:24:10Z @@ -86796,6 +99858,13 @@ plexiform layer using GABA. + + + + + + + Any neuron that is part of a central nervous system. 2014-06-25T01:17:43Z @@ -86825,6 +99894,13 @@ plexiform layer using GABA. + + + + + + + Any native cell that is part of a hypothalamus. 2014-06-25T01:17:50Z @@ -86854,6 +99930,13 @@ plexiform layer using GABA. + + + + + + + Any neuron that is part of a lateral line ganglion. 2014-06-25T01:17:57Z @@ -86883,6 +99966,13 @@ plexiform layer using GABA. + + + + + + + A neuron that is part of a peripheral nervous system. 2014-06-25T02:28:17Z @@ -86917,6 +100007,13 @@ plexiform layer using GABA. + + + + + + + Any basal cell of epidermis that is part of a limb. 2014-06-25T02:28:25Z @@ -86946,6 +100043,13 @@ plexiform layer using GABA. + + + + + + + Any neuromast hair cell that is part of a anterior lateral line. 2014-06-25T03:44:37Z @@ -86975,6 +100079,13 @@ plexiform layer using GABA. + + + + + + + Any neuromast mantle cell that is part of an anterior lateral line. 2014-06-25T03:44:44Z @@ -87004,6 +100115,13 @@ plexiform layer using GABA. + + + + + + + Any neuromast support cell that is part of a anterior lateral line. 2014-06-25T03:44:51Z @@ -87034,6 +100152,13 @@ plexiform layer using GABA. + + + + + + + Any neuromast hair cell that is part of a posterior lateral line. 2014-06-25T03:44:57Z @@ -87063,6 +100188,13 @@ plexiform layer using GABA. + + + + + + + Any neuromast mantle cell that is part of a posterior lateral line. 2014-06-25T03:45:04Z @@ -87092,6 +100224,13 @@ plexiform layer using GABA. + + + + + + + Any neuromast support cell that is part of a posterior lateral line. 2014-06-25T03:45:11Z @@ -87122,6 +100261,8 @@ plexiform layer using GABA. + + Any microvascular endothelial cell that is part of a urinary bladder. @@ -87153,6 +100294,13 @@ plexiform layer using GABA. + + + + + + + Any dermis lymphatic vessel endothelial cell that is part of a microvascular endothelium. 2014-07-09T00:09:54Z @@ -87183,6 +100331,13 @@ plexiform layer using GABA. + + + + + + + Any fibroblast that is part of a embryo. 2014-07-09T00:12:00Z @@ -87213,6 +100368,13 @@ plexiform layer using GABA. + + + + + + + Any pericyte cell that is part of a brain. 2014-07-09T00:18:22Z @@ -87243,6 +100405,14 @@ plexiform layer using GABA. + + + + + + + + Any microvascular endothelial cell that is part of a brain. 2014-07-09T00:24:53Z @@ -87272,6 +100442,13 @@ plexiform layer using GABA. + + + + + + + Any melanocyte that is part of a prepuce of penis. 2014-07-09T00:45:07Z @@ -87301,6 +100478,13 @@ plexiform layer using GABA. + + + + + + + Any cardiac muscle cell that is part of a cardiac ventricle. 2014-08-12T20:50:28Z @@ -87331,6 +100515,14 @@ plexiform layer using GABA. + + + + + + + + Any motor neuron that is part of a brainstem. 2014-10-02T23:52:53Z @@ -87350,6 +100542,7 @@ plexiform layer using GABA. + @@ -87389,6 +100582,13 @@ plexiform layer using GABA. + + + + + + + Any pyramidal cell that is part of a primary motor cortex. 2014-10-06T17:39:04Z @@ -87439,6 +100639,13 @@ plexiform layer using GABA. + + + + + + + Any fibroblast that is part of a spleen. 2014-10-06T18:58:47Z @@ -87468,6 +100675,14 @@ plexiform layer using GABA. + + + + + + + + Any endothelial cell of artery that is part of a umbilical cord. 2014-10-06T19:01:48Z @@ -87498,6 +100713,13 @@ plexiform layer using GABA. + + + + + + + Any endothelial cell that is part of a spleen. @@ -87556,6 +100778,13 @@ plexiform layer using GABA. + + + + + + + Any dendritic cell that is part of a liver. 2014-10-06T19:16:11Z @@ -87577,13 +100806,7 @@ plexiform layer using GABA. - - - - - - - + Any pyramidal cell that is part of a regional part of cerebral cortex. 2014-10-06T19:20:41Z @@ -87613,6 +100836,14 @@ plexiform layer using GABA. + + + + + + + + Any osteoblast that is part of a femur. 2014-10-06T19:29:45Z @@ -87643,6 +100874,13 @@ plexiform layer using GABA. + + + + + + + Any osteoblast that is part of a skull. 2014-10-06T19:48:30Z @@ -87673,6 +100911,13 @@ plexiform layer using GABA. + + + + + + + Any microvascular endothelial cell that is part of a prostate gland. 2014-10-07T17:46:27Z @@ -87704,6 +100949,13 @@ plexiform layer using GABA. + + + + + + + A trophoblast of placental villi. These cells fuse to form synctial trophoplast - the placental side of the interface between the placenta and maternal blood sinusoids in the decidua. 2014-10-07T17:48:27Z @@ -87746,6 +100998,13 @@ plexiform layer using GABA. + + + + + + + Any mesenchymal stem cell that is part of a placenta. @@ -87778,6 +101037,14 @@ plexiform layer using GABA. + + + + + + + + Any capillary endothelial cell that is part of a placenta. 2014-10-07T17:55:56Z @@ -87808,6 +101075,13 @@ plexiform layer using GABA. + + + + + + + Any fibroblast that is part of a female gonad. 2014-10-07T17:57:42Z @@ -87838,6 +101112,13 @@ plexiform layer using GABA. + + + + + + + Any epithelial cell that is part of a female gonad. 2014-10-07T17:59:13Z @@ -87869,6 +101150,14 @@ plexiform layer using GABA. + + + + + + + + Any microvascular endothelial cell that is part of a female urethra. 2014-10-07T18:18:01Z @@ -87899,6 +101188,13 @@ plexiform layer using GABA. + + + + + + + Any fibroblast that is part of a cardiac ventricle. @@ -87931,6 +101227,13 @@ plexiform layer using GABA. + + + + + + + Any fibroblast that is part of a cardiac atrium. @@ -87963,6 +101266,13 @@ plexiform layer using GABA. + + + + + + + Any fibroblast that is part of a pericardium. 2014-10-07T18:38:06Z @@ -87993,6 +101303,13 @@ plexiform layer using GABA. + + + + + + + Any fibroblast that is part of a gallbladder. 2014-10-07T18:41:43Z @@ -88023,6 +101340,13 @@ plexiform layer using GABA. + + + + + + + Any fibroblast that is part of a optic choroid. 2014-10-07T18:50:43Z @@ -88053,6 +101377,13 @@ plexiform layer using GABA. + + + + + + + Any microvascular endothelial cell that is part of a breast. 2014-10-07T19:55:30Z @@ -88083,6 +101414,14 @@ plexiform layer using GABA. + + + + + + + + Any microvascular endothelial cell that is part of a adipose tissue. 2014-10-07T22:13:45Z @@ -88113,6 +101452,13 @@ plexiform layer using GABA. + + + + + + + Any migratory neural crest cell that is part of a cardiac neural crest. 2014-11-05T01:18:43Z @@ -88149,6 +101495,13 @@ plexiform layer using GABA. + + + + + + + Any leukocyte that is part of a spleen. 2014-11-05T01:26:50Z @@ -88179,6 +101532,13 @@ plexiform layer using GABA. + + + + + + + Any endodermal cell that is part of a anterior visceral endoderm. 2014-11-05T01:34:13Z @@ -88208,6 +101568,13 @@ plexiform layer using GABA. + + + + + + + Any vein endothelial cell that is part of a hindlimb stylopod. 2014-12-02T18:40:47Z @@ -88237,6 +101604,14 @@ plexiform layer using GABA. + + + + + + + + Any striated muscle cell that is part of a skeletal muscle tissue of pectoralis major. 2014-12-02T18:48:17Z @@ -88266,6 +101641,13 @@ plexiform layer using GABA. + + + + + + + Any pericyte cell that is part of a placenta. 2014-12-02T18:51:03Z @@ -88295,6 +101677,13 @@ plexiform layer using GABA. + + + + + + + Any mesenchymal stem cell of the bone marrow that is part of a femur. 2014-12-02T19:07:31Z @@ -88324,6 +101713,13 @@ plexiform layer using GABA. + + + + + + + Any mesenchymal stem cell of adipose tissue that is part of an abdomen. 2014-12-02T19:10:34Z @@ -88354,6 +101750,13 @@ plexiform layer using GABA. + + + + + + + Any melanocyte of skin that is part of a skin of face. 2014-12-02T19:10:40Z @@ -88383,6 +101786,14 @@ plexiform layer using GABA. + + + + + + + + Any melanocyte of skin that is part of a skin of prepuce of penis. 2014-12-02T19:10:45Z @@ -88412,6 +101823,13 @@ plexiform layer using GABA. + + + + + + + Any hair follicle dermal papilla cell that is part of a scalp. 2014-12-02T19:10:50Z @@ -88441,6 +101859,8 @@ plexiform layer using GABA. + + Any goblet cell that is part of a conjunctiva. 2014-12-02T19:28:38Z @@ -88470,6 +101890,14 @@ plexiform layer using GABA. + + + + + + + + Any mononuclear cell that is part of a umbilical cord. 2014-12-02T20:14:16Z @@ -88499,6 +101927,14 @@ plexiform layer using GABA. + + + + + + + + Any basket cell that is part of a neocortex. 2014-12-24T00:37:19Z @@ -88528,6 +101964,10 @@ plexiform layer using GABA. + + + + Any basket cell that is part of a dentate gyrus of hippocampal formation. 2014-12-24T00:37:24Z @@ -88557,6 +101997,15 @@ plexiform layer using GABA. + + + + + + + + + Any basket cell that is part of a Ammon's horn. 2014-12-24T00:37:30Z @@ -88586,6 +102035,14 @@ plexiform layer using GABA. + + + + + + + + A granule cell that has soma location in the dentate gyrus cell layer of the hippocampal formation and has an elliptical cell body and characteristic cone-shaped tree of spiny apical dendrites. The branches extend throughout the molecular layer and the distal tips of the dendritic tree end just at the hippocampal fissure or at the ventricular surface. The dentate gyrus granule cell is the principal cell type of the dentate gyrus. 2015-02-23T05:48:23Z @@ -88624,6 +102081,9 @@ plexiform layer using GABA. + + + Any stellate cell that is part of a dentate gyrus of hippocampal formation. 2015-02-23T05:48:40Z @@ -88653,6 +102113,14 @@ plexiform layer using GABA. + + + + + + + + Any microvascular endothelial cell that is part of a endometrial blood vessel. @@ -88684,6 +102152,8 @@ plexiform layer using GABA. + + Any keratinocyte that is part of a hair follicle. 2015-03-31T21:07:02Z @@ -88714,6 +102184,13 @@ plexiform layer using GABA. + + + + + + + Any fibroblast of lung that is part of a bronchus. 2015-03-31T21:16:22Z @@ -88744,6 +102221,13 @@ plexiform layer using GABA. + + + + + + + Any epithelial cell of viscerocranial mucosa that is part of a nasal cavity respiratory epithelium. 2015-03-31T22:25:17Z @@ -88773,6 +102257,14 @@ plexiform layer using GABA. + + + + + + + + Any hematopoietic stem cell that is part of a umbilical cord blood. 2015-05-26T18:58:34Z @@ -88803,6 +102295,13 @@ plexiform layer using GABA. + + + + + + + Any fibroblast that is part of a reticular layer of dermis. 2015-08-11T16:28:16Z @@ -88832,6 +102331,14 @@ plexiform layer using GABA. + + + + + + + + Any dopaminergic neuron that is part of a midbrain. 2015-12-03T16:42:40Z @@ -88861,6 +102368,14 @@ plexiform layer using GABA. + + + + + + + + A ciliated epithelial cell of the esophagus. 2019-02-09T16:40:30Z @@ -88936,6 +102451,8 @@ plexiform layer using GABA. + + Sympathetic noradrenergic neuron. @@ -88968,6 +102485,8 @@ plexiform layer using GABA. + + Sympathetic cholinergic neuron. 2019-02-25T19:32:20Z @@ -88998,6 +102517,8 @@ plexiform layer using GABA. + + Peripheral sensory neuron. 2019-02-25T19:34:33Z @@ -89029,6 +102550,12 @@ plexiform layer using GABA. + + + + + + A fibroblast that is part of the breast. breast fibroblast @@ -89052,7 +102579,13 @@ plexiform layer using GABA. - + + + + + + + A fibroblast that is part of the skin of scalp. skin of scalp fibroblast @@ -89201,19 +102734,8 @@ plexiform layer using GABA. - - - - - - - - - - - - - + + @@ -89226,12 +102748,6 @@ plexiform layer using GABA. - - - - - - @@ -89272,6 +102788,14 @@ plexiform layer using GABA. + + + + + + + + IT glut A glutamatergic neuron located in the cerebral cortex that projects to structures of telencephalic origins. @@ -89309,6 +102833,14 @@ plexiform layer using GABA. + + + + + + + + ET glut A glutamatergic neuron located in the cerebral cortex that projects to structures not derived from telencephalon. @@ -89331,25 +102863,13 @@ plexiform layer using GABA. - - - - - - - + - - - - - - @@ -89404,6 +102924,13 @@ plexiform layer using GABA. + + + + + + + Lamp5 cortical interneuron A GABAergic neuron located in the cerebral cortex that expresses Lamp5 @@ -89439,6 +102966,14 @@ plexiform layer using GABA. + + + + + + + + NP glut neuron A glutamatergic neuron located in the cerebral cortex that projects axons locally rather than distantly. @@ -89477,6 +103012,14 @@ plexiform layer using GABA. + + + + + + + + CT glut A glutamatergic neuron located in the cerebral cortex that projects to the thalamus. @@ -89499,7 +103042,7 @@ plexiform layer using GABA. - + @@ -89512,12 +103055,6 @@ plexiform layer using GABA. - - - - - - @@ -89563,6 +103100,13 @@ plexiform layer using GABA. + + + + + + + sncg cortical interneuron A GABAergic neuron located in the cerebral cortex that expresses Gamma-synuclein @@ -89602,6 +103146,13 @@ plexiform layer using GABA. + + + + + + + vip cortical interneuron A GABAergic neuron located in the cerebral cortex that expresses vasoactive intestinal polypeptide @@ -89641,6 +103192,13 @@ plexiform layer using GABA. + + + + + + + sst cortical interneuron A GABAergic neuron located in the cerebral cortex that expresses somatostatin (sst) @@ -89680,6 +103238,13 @@ plexiform layer using GABA. + + + + + + + pvalb cortical interneuron A GABAergic interneuron located in the cerebral cortex that expresses Parvalbumin. @@ -89711,6 +103276,14 @@ plexiform layer using GABA. + + + + + + + + A vip GABAergic cortical interneuron that expresses cck. L5/6 cck cells have soma found mainly in L5 and L6 and have large axonal arborization. L5/6 CCK Vip (Mus musculus) @@ -89779,25 +103352,13 @@ plexiform layer using GABA. - - - - - - - + - - - - - - @@ -89822,31 +103383,14 @@ plexiform layer using GABA. - - - - - - - - - - - - - + + - - - - - - @@ -89872,31 +103416,14 @@ plexiform layer using GABA. - - - - - - - - - - - - - + + - - - - - - @@ -89923,24 +103450,12 @@ plexiform layer using GABA. - - - - - - - - - - - - @@ -90012,19 +103527,8 @@ plexiform layer using GABA. - - - - - - - - - - - - - + + @@ -90037,12 +103541,6 @@ plexiform layer using GABA. - - - - - - @@ -90069,7 +103567,7 @@ plexiform layer using GABA. - + @@ -90082,12 +103580,6 @@ plexiform layer using GABA. - - - - - - @@ -90161,31 +103653,14 @@ plexiform layer using GABA. - - - - - - - - - - - - - + + - - - - - - @@ -90221,13 +103696,8 @@ plexiform layer using GABA. - - - - - - - + + @@ -90240,12 +103710,6 @@ plexiform layer using GABA. - - - - - - @@ -90339,6 +103803,13 @@ plexiform layer using GABA. + + + + + + + A neuron that is derived from a precursor cell in the lateral ganglion eminence. https://orcid.org/0000-0001-7258-9596 https://orcid.org/0000-0002-7073-9172 @@ -90363,31 +103834,8 @@ plexiform layer using GABA. - - - - - - - - - - - - - - - - - - - - - - - - - + + chandelier PV interneuron A pvalb GABAergic cortical interneuron that is recognizable by the straight terminal axonal 'cartridges' of vertically oriented strings of synaptic boutons. Chandelier PV cells' boutons target exclusively the axon initial segment (AIS) of pyramidal cells, with a single cell innervating hundreds of pyramidal cells in a clustered manner. @@ -90427,6 +103875,14 @@ plexiform layer using GABA. + + + + + + + + L6b glut A glutamatergic neuron with a soma found in cortical layer 6b. They are transcriptomically related to corticothalamic-projecting neurons but have differential projections to the thalamus or anterior cingulate. @@ -90463,6 +103919,14 @@ plexiform layer using GABA. + + + + + + + + @@ -90513,10 +103977,12 @@ plexiform layer using GABA. + + - - + + L5 ET glut @@ -90593,6 +104059,13 @@ plexiform layer using GABA. + + + + + + + @@ -90630,6 +104103,13 @@ plexiform layer using GABA. + + + + + + + L5/6 NP glut MOp A near-projecting glutamatergic neuron with a soma found in layer 5/6 of the primary motor cortex. @@ -90653,13 +104133,8 @@ plexiform layer using GABA. + - - - - - - non-MY ET glut MOp An extratelencephalic-projecting glutamatergic neuron located in layer 5b of the primary motor cortex that does not project to the medulla. Non-MY ET cells are large, big-tufted cells with the apical dendrite often bifurcating close to the soma, suggesting they are corticospinal cells. Non-MY ET cells have bigger hyperpolarization sag, lower input resistance, and smaller AP width, compared to L5 IT neurons. @@ -90682,6 +104157,7 @@ plexiform layer using GABA. + @@ -90689,12 +104165,6 @@ plexiform layer using GABA. - - - - - - @@ -90761,6 +104231,13 @@ plexiform layer using GABA. + + + + + + + L2/3 IT glut MOp An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 2/3 of the primary motor cortex. @@ -90793,6 +104270,13 @@ plexiform layer using GABA. + + + + + + + L4/5 IT glut MOp An intratelencephalic-projecting glutamatergic with a soma located in upper L5 of the primary motor cortex. These cells have thin untufted apical dendrites. @@ -90826,6 +104310,13 @@ plexiform layer using GABA. + + + + + + + L5 IT glut MOp An intratelencephalic-projecting glutamatergic neuron with a soma found in L5 of the primary motor cortex. @@ -90858,6 +104349,8 @@ plexiform layer using GABA. + + @@ -90886,13 +104379,7 @@ plexiform layer using GABA. - - - - - - - + @@ -90997,6 +104484,7 @@ plexiform layer using GABA. + @@ -91004,12 +104492,6 @@ plexiform layer using GABA. - - - - - - CT VAL/VM glut MOp A corticothalamic-projecting glutamatergic neuron that is located in L6 and lower L5 of the primary motor cortex, with a pyramidal morphology and mostly untufted apical dendrites terminating in midcortical layers. CT VAL/VM (ventroanterior-ventrolateral complex/ventromedial nucleus) cells have a near tonic firing pattern and are distinguished from L6 IT neurons by a lower inter-spike interval adaptation index. @@ -91039,9 +104521,9 @@ plexiform layer using GABA. - - - + + + A type of mouse mesothelial fibroblast that is derived from the neural crest, is localized on blood vessels, and is a key component of the pia and arachnoid membranes surrounding the brain. VLMC (Mus musculus) @@ -91049,34 +104531,34 @@ plexiform layer using GABA. vascular leptomeningeal cell (Mmus) - + - + - + - + PMID:30096314 - + PMID:30096314 - + PMID:30096314 @@ -91102,6 +104584,15 @@ plexiform layer using GABA. + + + + + + + + + @@ -91131,6 +104622,14 @@ plexiform layer using GABA. + + + + + + + + A mesothelial fibroblast found in the leptomeninx. mesothelial fibroblast of the leptomeninx @@ -91182,7 +104681,7 @@ plexiform layer using GABA. - + @@ -91238,6 +104737,13 @@ plexiform layer using GABA. + + + + + + + A neuron with its soma located in the dentate gyrus of the hippocampus. @@ -91261,6 +104767,13 @@ plexiform layer using GABA. + + + + + + + MGE interneuron An interneuron that is derived from the medial ganglionic eminence. @@ -91292,6 +104805,13 @@ plexiform layer using GABA. + + + + + + + CGE interneuron An interneuron that is derived from the caudal ganglionic eminence. @@ -91313,12 +104833,7 @@ plexiform layer using GABA. - - - - - - + @@ -91355,6 +104870,14 @@ plexiform layer using GABA. + + + + + + + + A pyramidal neuron which has an apical tree which is oriented parallel to the pia. This is unlike typical pyramidal neurons which have its apical dendrite aligned vertically. @@ -91408,6 +104931,14 @@ plexiform layer using GABA. + + + + + + + + An excitatory neuron that has its soma located in the thalamic complex. @@ -91445,6 +104976,8 @@ plexiform layer using GABA. + + MGE cortical gaba interneuron A GABAergic cortical interneuron that develops from the medial ganglionic eminence and has migrated to the cerebral cortex. @@ -91482,6 +105015,8 @@ plexiform layer using GABA. + + CGE gaba cortical interneuron A GABAergic cortical interneuron that develops from the caudal ganglionic eminence and has migrated to the cerebral cortex. @@ -91501,7 +105036,7 @@ plexiform layer using GABA. - + @@ -91514,12 +105049,6 @@ plexiform layer using GABA. - - - - - - @@ -91556,6 +105085,13 @@ plexiform layer using GABA. + + + + + + + A cell that is part of the brain vasculature. @@ -91604,6 +105140,13 @@ plexiform layer using GABA. + + + + + + + A neuron that has its soma located in the mammillary body. @@ -91622,7 +105165,7 @@ plexiform layer using GABA. - + @@ -91635,12 +105178,6 @@ plexiform layer using GABA. - - - - - - @@ -91688,6 +105225,14 @@ plexiform layer using GABA. + + + + + + + + An interneuron that has Martinotti morphology. These interneurons are scattered throughout various layers of the cerebral cortex, sending their axons up to the cortical layer I where they form axonal arborization. ILX:0107375 @@ -91718,6 +105263,13 @@ plexiform layer using GABA. + + + + + + + A type of interneuron that has two clusters of dendritic branches that originate directly from the soma and extend in opposite directions and axons that form a plexus which spreads widely. Compared to bipolar neurons, bitufted neurons have branching that occur close to the soma. ILX:0777212 @@ -91774,6 +105326,14 @@ plexiform layer using GABA. + + + + + + + + A GABAergic inhibitory neuron that is derived from the midbrain. @@ -91855,6 +105415,13 @@ plexiform layer using GABA. + + + + + + + A GABAergic interneuron that selectively innervates the axon initial segment of pyramidal cells. Their local axonal clusters are formed by high-frequency branching at shallow angles, often ramifying around, above or below their somata with a high bouton density. The characteristic terminal portions of the axon form short vertical rows of boutons, resembling the candlesticks and candles of a chandelier. Chandelier cells can be multipolar or bitufted. axo-axonic cell @@ -91911,6 +105478,13 @@ plexiform layer using GABA. + + + + + + + A Martinotti neuron that has axons that form a horizontal ramification, making it T-shaped. T-shaped Martinotti neuron @@ -91944,6 +105518,13 @@ plexiform layer using GABA. + + + + + + + A Martinotti neuron that has axons that form a fan-like plexus. fanning-out Martinotti neuron @@ -91981,6 +105562,13 @@ plexiform layer using GABA. + + + + + + + A basket cell that is large, and typically ascends to give rise to many long horizontally and vertically projecting axon collaterals that traverse neighboring columns and can extend through all cortical layers. @@ -92017,6 +105605,13 @@ plexiform layer using GABA. + + + + + + + A basket cell which has simpler dendritic arbors (compared to small or large basket cells), and an axonal plexus of intermediate density, composed of a few long, smooth axonal branches. @@ -92053,6 +105648,13 @@ plexiform layer using GABA. + + + + + + + A basket cell with axonal arbors composed of frequent, short, curvy axonal branches that tend to be near their somata and within the same layer. @@ -92081,6 +105683,14 @@ plexiform layer using GABA. + + + + + + + + A pyramidal neuron which has an apical tree which is oriented towards the white matter. @@ -92109,6 +105719,14 @@ plexiform layer using GABA. + + + + + + + + A pyramidal neuron which lacks a tuft formation but extends small radial distances forming a star-like shape. @@ -92137,6 +105755,14 @@ plexiform layer using GABA. + + + + + + + + A pyramidal neuron which has a distinctive tuft formation, distal from the soma. @@ -92165,6 +105791,14 @@ plexiform layer using GABA. + + + + + + + + A pyramidal neuron which lacks a clear tuft formation but extends to large radial distances. @@ -92182,7 +105816,7 @@ plexiform layer using GABA. - + @@ -92423,6 +106057,19 @@ plexiform layer using GABA. + + + + + + + + + + + + + A neuron with soma location in the reticular formation with axons that extend into the spinal cord such. Reticulospinal neuron activity can lead to a variety of motor behaviors. RSN @@ -92457,6 +106104,13 @@ plexiform layer using GABA. + + + + + + + A magnocellular neurosecretory cell that is capable of producing and secreting oxytocin. oxytocin-secreting magnocellular cell @@ -92484,6 +106138,14 @@ plexiform layer using GABA. + + + + + + + + A magnocellular neurosecretory cell that is capable of producing and secreting vasopressin. vasopressin-secreting magnocellular cell @@ -92511,6 +106173,14 @@ plexiform layer using GABA. + + + + + + + + A pyramidal neuron with soma located in the amygdala. amygdala pyramidal neuron @@ -92538,6 +106208,8 @@ plexiform layer using GABA. + + A pyramidal neuron with soma located in the cerebral cortex. cerebral cortex pyramidal neuron @@ -92646,12 +106318,20 @@ plexiform layer using GABA. + + + + + + + + A spiral ganglion neuron that innervates inner hair cells. Type 1 spiral ganglion neurons are myelinated and bipolar. type I spiral ganglion cell @@ -92687,12 +106367,20 @@ plexiform layer using GABA. + + + + + + + + A spiral ganglion neuron that innervates outer hair cells. Type 1 spiral ganglion neurons are unmyelinated and unipolar. type II spiral ganglion cell @@ -92717,7 +106405,7 @@ plexiform layer using GABA. - + @@ -92730,12 +106418,6 @@ plexiform layer using GABA. - - - - - - @@ -92813,6 +106495,14 @@ plexiform layer using GABA. + + + + + + + + An auditory hair cell found in the cochlea. FMA:62364 @@ -92831,31 +106521,13 @@ plexiform layer using GABA. - - - - - - - - - - - - - + - - - - - - sst chodl cortical interneuron A sst GABAergic cortical interneuron that also expresses Chodl. These neurons are rare and correspond to the only known cortical interneurons with long-range projection. @@ -92877,31 +106549,13 @@ plexiform layer using GABA. - - - - - - - - - - - - - + - - - - - - An interneuron located in the cerebral cortex that expresses the oxytocin receptor. These interneurons also express somatostatin. @@ -92951,6 +106605,14 @@ plexiform layer using GABA. + + + + + + + + A kisspeptin neuron that is located in the hypothalamus. These neurons project to and activate gonadotrophin-releasing hormone neurons (acting via the kisspeptin receptor) in the hypothalamus and stimulate the secretion of gonadotrophin-releasing hormone. @@ -92979,6 +106641,8 @@ plexiform layer using GABA. + + A kisspeptin neuron that is located in the dentate gyrus of the hippocampus. @@ -93011,6 +106675,19 @@ plexiform layer using GABA. + + + + + + + + + + + + + A hypothalamus kisspeptin neuron that coexpresses kisspeptin, neurokinin B and dynorphin. @@ -93047,6 +106724,13 @@ plexiform layer using GABA. + + + + + + + a KNDy neuron that is located in the arcuate nucleus of the hypothalamus. @@ -93075,6 +106759,13 @@ plexiform layer using GABA. + + + + + + + a KNDy neuron that is located in the rostral periventricular region of the third ventricle. In rats and mice, the anteroventral periventricular nucleus plus the periventricular nucleus make up the rostral periventricular region of the third ventricle (RP3V). @@ -93144,6 +106835,13 @@ plexiform layer using GABA. + + + + + + + A neuron that expresses kisspeptin. These neurons are predominantly located in the hypothalamus, but also found in other parts of the brain including the hippocampal dentate gyrus. @@ -93179,6 +106877,13 @@ plexiform layer using GABA. + + + + + + + A glial cell that myelinates axonal processes. myelinating glial cell @@ -93195,7 +106900,7 @@ plexiform layer using GABA. - + @@ -93244,6 +106949,13 @@ plexiform layer using GABA. + + + + + + + An interneuron that has double bouquet morphology. double bouquet cell @@ -93260,7 +106972,9 @@ plexiform layer using GABA. - + + + @@ -93273,18 +106987,6 @@ plexiform layer using GABA. - - - - - - - - - - - - A neuron of the dorsal cochlear nucleus with spiny dendrites that receive input from the axons of granule cells and with axons that release GABA and glycine onto cartwheel, pyramidal and giant cell targets. ILX:0102311 @@ -93310,7 +107012,8 @@ plexiform layer using GABA. - + + @@ -93323,12 +107026,6 @@ plexiform layer using GABA. - - - - - - An excitatory glutamatergic interneuron found in the granular layer of the cerebellar cortex and also in the granule cell domain of the cochlear nucleus. Unipolar brush cells have a round or oval cell body with usually a single short dendrite that ends in a brush-like tuft of short dendrites unique to them known as dendrioles. unipolar brush cell @@ -93346,7 +107043,7 @@ plexiform layer using GABA. - + @@ -93438,6 +107135,13 @@ plexiform layer using GABA. + + + + + + + A neuron that is part of the somatic sensory system. Somatosensory neurons innervate the skin or integument to detect different types of thermal, chemical, and mechanical touch stimuli. somatosensory neuron @@ -93483,12 +107187,9 @@ plexiform layer using GABA. - - - - - - + + + A trigeminal neuron that is responsible for sensation in the face. trigeminal sensory neuron @@ -93513,6 +107214,8 @@ plexiform layer using GABA. + + A trigeminal neuron that is responsible for motor functions such as biting and chewing. trigeminal motor neuron @@ -93530,6 +107233,7 @@ plexiform layer using GABA. + @@ -93572,6 +107276,13 @@ plexiform layer using GABA. + + + + + + + A neuron with a small cell body that is located in a koniocellular layer of the lateral geniculate nucleus (LGN). NIFEXT:44 @@ -93673,6 +107384,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + @@ -93692,13 +107404,8 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + - - - - - - An alveolar capillary endothelial cell that is located distally to alveolar capillary type 2 endothelial cells. @@ -93746,13 +107453,8 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + - - - - - - An alveolar capillary endothelial cell that is located proximally to alveolar capillary type 1 endothelial cells and in close apposition to alveolar type 1 epithelial cells (also known as type I pneumocytes). @@ -93795,6 +107497,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + @@ -93845,6 +107548,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + @@ -93979,6 +107683,13 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + A melanocyte located in the vascular uvea and involved in photoprotection, regulation of oxidative damage and immune responses. 2022-01-20T12:59:06Z uveal melanocyte @@ -94016,6 +107727,13 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + A stromal cell that is part of the thymus. 2022-07-08T11:39:38Z thymic stromal cell @@ -94132,6 +107850,8 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + A renal beta-intercalated cell that is part of the cortical collecting duct. The medullary collecting duct does not contain the renal beta-intercalated cell type. 2022-09-14T16:19:11Z B-IC @@ -94165,12 +107885,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - - - - - An epithelial cell that is part of the fallopian tube epithelium that secretes mucous fluid and oviduct-specific products through the stimulation of estrogen and luteinizing hormone. The fallopian tube secretory cell has approximately the same height as the ciliated cell and is usually a more narrow columnar cell. The nucleus is ovoid and perpendicular to the long axis of the cell. The chromatin is more dense and the nucleolus smaller than that seen in the ciliated cell. 2022-03-03T10:39:31Z @@ -94203,12 +107917,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - - - - - @@ -94248,6 +107956,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + A specialized epithelial cell that contains "feet" that interdigitate with the "feet" of other glomerular epithelial cells in the pronephros. 2022-03-11T14:38:32Z pronephric glomerular visceral epithelial cell @@ -94346,6 +108060,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + Epithelial cell of the descending thin limb of the short loop (cortical) nephron limited to the outer medulla (mainly inner strip). It is known in some mammalian species that the short descending limb of the loop of Henle selectively expresses the serine protease Corin, the homeobox TF Uncx, and the urea channel Slc14a2. 2022-05-13T11:00:29Z @@ -94432,6 +108152,8 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + A renal alpha-intercalated cell that is part of the collecting duct of the renal tubule. 2022-05-31T11:15:10Z @@ -94470,6 +108192,13 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + An epithelial cell located in the early distal convoluted tubule. 2022-06-21T12:47:48Z @@ -94507,6 +108236,13 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + An epithelial cell located in the late distal convoluted tubule. 2022-06-21T13:51:46Z @@ -94551,6 +108287,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + A renal principal cell located in the connecting tubule. @@ -94584,6 +108321,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + A renal intercalated cell that is part of the renal connecting tubule. @@ -94614,6 +108352,8 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + A renal alpha-intercalated cell that is part of the renal connecting tubule. 2022-06-29T12:48:43Z @@ -94659,6 +108399,8 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + A renal beta-intercalated cell that is part of the renal connecting tubule. 2022-06-29T14:31:18Z @@ -94703,6 +108445,8 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + A fibroblast that is located in the renal medulla interstitium. 2022-07-05T12:13:40Z @@ -94742,6 +108486,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + A hillock cell that is located in respiratory epithelium. In some mammalian species, this cell type has been noted to express KRT13 and KRT4 and is postulated to play a role in squamous barrier function and immunomodulation. 2022-06-06T08:31:09Z hillock cell of respiratory tract @@ -94791,6 +108536,8 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + A fibroblast that is located in the renal cortical interstitium. 2022-07-05T15:50:17Z kidney cortical fibroblast @@ -94815,6 +108562,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + @@ -94858,6 +108606,8 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + An amacrine cell that uses GABA as a neurotransmitter. 2022-10-17T12:35:11Z amacrine cell, GABAergic @@ -94887,6 +108637,8 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + An amacrine cell that uses glycine as a neurotransmitter. 2022-10-17T12:40:06Z @@ -94918,6 +108670,8 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + A lymphocyte located in blood. 2022-11-04T14:40:00Z @@ -94979,6 +108733,13 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + Any cell that is located within the interstitium between the cells most prominent in defining a given tissue. "Interstitial cell" is a morphological term and refers to a variety of cells with differing origins and phenotypes. 2022-11-30T14:35:08Z interstitial cell @@ -95006,6 +108767,9 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + @@ -95070,6 +108834,8 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + An endothelial cell that lines a surface of a cardiac valve leaflet. Along with valve interstitial cells, a valve endothelial cell maintains tissue homeostasis for the function of cardiac valves through secreting biochemical signals, matrix proteins and matrix remodeling enzymes. 2022-12-09T11:58:49Z VEC @@ -95120,10 +108886,11 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + - + A ciliated cell of the respiratory system. Ciliated cells are present in airway epithelium. @@ -95155,6 +108922,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + A dental pulp cell that possesses stem-cell-like qualities, including self-renewal capability and multi-lineage differentiation. 2023-01-10T14:02:02Z @@ -95380,6 +109148,13 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + A ciliated cell of the endometrial epithelium. The cilia of this cell type help move mucus from glandular tissue of the endometrium. 2023-02-09T11:25:14Z ciliated cell of the uterus @@ -95925,6 +109700,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + @@ -96176,6 +109952,14 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + + A macrophage that expresses the T cell receptor complex at the cell surface. 2023-09-26T12:27:14Z @@ -96227,6 +110011,13 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 2/3. 2023-10-10T14:10:21Z @@ -96264,6 +110055,13 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 2. 2023-10-10T14:10:36Z @@ -96300,6 +110098,13 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 3. 2023-10-10T14:10:47Z @@ -96336,6 +110141,13 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + An intratelencephalic-projecting glutamatergic with a soma located in cortical layer 4/5. 2023-10-10T14:11:04Z @@ -96372,6 +110184,13 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 4. 2023-10-10T14:11:25Z @@ -96408,6 +110227,13 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 5. 2023-10-10T14:11:59Z @@ -96445,6 +110271,13 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 6. 2023-10-10T14:12:23Z @@ -96482,21 +110315,29 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - + + + + + + + + + An epithelial cell that is part of a ureteric bud. A ureteric bud cell has the potential to induce metanephric mesenchymal cells to proliferate and convert to epithelia that form renal tubules via: (1) the secretion of multiple diffusible growth factors that rescue renal progenitors from apoptosis and stimulate them to proliferate and (2) contact-dependent mechanisms that induce mesenchymal-epithelial conversion. https://orcid.org/0000-0002-1425-877X 2023-10-13T11:22:42Z UB cell ureteric bud cell - + - + PMID:9374839 @@ -96531,6 +110372,13 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + A near-projecting glutamatergic neuron with a soma found in cortical layer 5/6. 2023-11-17T11:35:06Z @@ -96572,6 +110420,13 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 6 that expresses Car3. 2023-11-23T09:16:14Z @@ -96699,6 +110554,13 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + A GABAergic interneuron located in the cerebral cortex that expresses reelin (rln). http://orcid.org/0000-0001-5501-853X @@ -96735,6 +110597,13 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + A(n) endothelial cell that is part of a(n) venule of lymph node. endothelial cell of venule of lymph node @@ -96762,6 +110631,13 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + A(n) endothelial cell that is part of a(n) arteriole of lymph node. endothelial cell of arteriole of lymph node @@ -96789,6 +110665,14 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + + A(n) neuroendocrine cell that is part of a(n) epithelium of crypt of Lieberkuhn. neuroendocrine cell of epithelium of crypt of Lieberkuhn @@ -96816,6 +110700,14 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + + A(n) myoepithelial cell that is part of a(n) bronchus submucosal gland. @@ -96846,6 +110738,13 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + A(n) smooth muscle cell that is part of a(n) taenia coli. smooth muscle cell of taenia coli @@ -96874,6 +110773,14 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + + A(n) serous secreting cell that is part of a(n) bronchus submucosal gland. @@ -96904,6 +110811,13 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + A(n) endothelial cell that is part of a(n) efferent lymphatic vessel. endothelial cell of efferent lymphatic vessel @@ -96931,6 +110845,14 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + + A(n) brush cell that is part of a(n) epithelium of lobar bronchus. @@ -96960,6 +110882,13 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + A(n) vein endothelial cell that is part of a(n) respiratory system. @@ -96989,6 +110918,14 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + + A(n) goblet cell that is part of a(n) epithelium of lobar bronchus. @@ -97018,6 +110955,14 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + + A(n) neuroendocrine cell that is part of a(n) epithelium of lobar bronchus. @@ -97048,6 +110993,13 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + A(n) smooth muscle cell that is part of a(n) large intestine smooth muscle circular layer. smooth muscle cell of large intestine smooth muscle circular layer @@ -97075,6 +111027,13 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + A(n) smooth muscle cell that is part of a(n) large intestine smooth muscle longitudinal layer. smooth muscle cell of large intestine smooth muscle longitudinal layer @@ -97102,6 +111061,13 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + A keratinocyte of the epidermis suprabasal layer. This cell may express the differentiation markers keratin 10 and keratin 1. 2023-02-02T11:17:04Z @@ -97196,6 +111162,14 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + + A star-shaped glial cell that is part of some retina. This cell links neurons to blood vessels and may provide structural and physiological support to optic nerve head axons. 2023-03-02T14:38:32Z @@ -97307,6 +111281,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + @@ -97346,6 +111321,13 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + A megakaryocyte that is resident in the lung connective tissue. @@ -97443,6 +111425,14 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + + A mucus secreting cell that is part of a submucosal gland of the trachea. @@ -97482,6 +111472,14 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + + A myoepithelial cell that is part of a submucosal gland of the trachea. @@ -97513,6 +111511,14 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + + A mucus secreting cell of a submucosal gland of the bronchus. @@ -97607,6 +111613,13 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + A fibroblast that is part of the fibrous layer of the perichondrium. This cell is responsible for collagen fiber production. @@ -97638,6 +111651,8 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + A perichondrial fibroblast that is part of the lung. @@ -98039,7 +112054,15 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + + A mucus secreting cell of a submucosal gland of the tracheobronchial tree. 2023-04-20T10:55:50Z @@ -98154,6 +112177,13 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + A lung resident memory CD8-positive, alpha-beta T cell that is CD103-positive. @@ -98262,7 +112292,9 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - + + + @@ -98384,6 +112416,8 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + A midget ganglion cell that depolarizes in response to increased light intensity in the center of its receptive field. The majority of input that this cell receives comes from invaginating midget bipolar cells. 2023-08-08T09:40:08Z @@ -98430,6 +112464,8 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + A midget ganglion cell that depolarizes in response to decreased light intensity in the center of its receptive field. The majority of input that this cell receives comes from flat midget bipolar cells. 2023-08-08T11:05:37Z @@ -98535,6 +112571,15 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + + + A taste receptor cell that is part of a taste bud of a tongue. 2023-05-03T07:59:58Z @@ -98573,6 +112618,14 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + + A neuron that releases catecholamine as a neurotransmitter. 2023-05-18T12:07:45Z @@ -98609,6 +112662,8 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + A parasol ganglion cell that depolarizes in response to decreased light intensity in the center of its receptive field. The majority of input that this cell receives comes from DB3a bipolar cells. 2023-08-08T12:34:57Z @@ -98655,6 +112710,8 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + A parasol ganglion cell that depolarizes in response to increased light intensity in the center of its receptive field. The majority of input that this cell receives comes from DB4 bipolar cells. 2023-08-08T12:39:35Z @@ -98765,6 +112822,13 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + A cell that is adjacent to a vessel. A perivascular cell plays a crucial role in maintaining vascular function and tissue homeostasis. This cell type regulates vessel integrity and flow dynamics. 2023-08-22T13:40:28Z @@ -98798,6 +112862,19 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + + + + + + + A ciliated cell that is part of a ciliated duct of an airway submucosal gland. @@ -98846,7 +112923,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - + A luminal epithelial cell of the mammary gland that can proliferate and has the potential to differentiate into a lactocyte during pregnancy. In humans, a luminal adaptive secretory precursor cell can be identified by high levels of the markers EpCAM and CD49f, and in mice it can be identified by low levels of CD29 and high levels of CD14, Kit, CD61, and Tspan8. @@ -98950,8 +113027,10 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + @@ -99159,6 +113238,13 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + An endothelial cell that is part of a central vein of liver. endothelial cell of central vein @@ -99301,6 +113387,13 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + A tissue-resident macrophage that is part of the uterus. 2024-01-08T16:05:09Z @@ -99333,7 +113426,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - + A glial precursor cell that generates oligodendrocytes and type-1 and type-2 astrocytes. It has been shown in some mammals that this cell type may express A2B5, nestin, FGFR-1, FGFR-2, FGFR-3, PLP, and DM-20 antigens. Unlike oligodendrocyte precursor cell, it does not initially express PDGFR-alpha and can differentiate into both type-1 and type-2 astrocytes. 2023-04-03T14:54:32Z @@ -99373,13 +113466,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - - - - - - + A horse-specific, highly invasive trophoblast cell that invades the endometrium where it forms endometrial cups. @@ -99424,6 +113511,13 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + @@ -99516,6 +113610,13 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + Any mesenchymal stem cell of adipose tissue that is part of an orbital region. 2023-09-18T10:43:00Z @@ -99608,6 +113709,297 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + + + + + A chromatophore that is part of the dermis. + + 2024-03-07T09:37:14Z + dermal chromatophore + + + + + A chromatophore that is part of the dermis. + PMID:28553007 + + + + + + + + + + + + + + + + + + + + + + + A GABAergic interneuron that has its soma located in the striatum and that has an enriched expression of the gene TAC3. + + 2024-03-05T14:29:32Z + TAC3 interneuron + TAC3-positive striatal interneuron + + + + + A GABAergic interneuron that has its soma located in the striatum and that has an enriched expression of the gene TAC3. + PMID:32999462 + PMID:34727523 + + + + + TAC3 interneuron + PMID:34727523 + + + + + + + + + + + + + + + + A nucleus accumbens shell and olfactory tubercle D1 medium spiny neuron that co-expresses TAC3 and the DRD1 receptor. + + 2024-03-05T13:36:54Z + D1Sh TAC3 archetype + TAC3-positive D1Sh-MSN + TAC3-positive MSN + A TAC3-positive medium spiny neuron has its soma in a cluster in the medial shell region of the nucleus accumbens. In Rhesus Macaque, this medium spiny neuron has an enriched expression of the genes MPPED1, HPCAL1, MEIS3. + TAC3-positive medium spiny neuron + + + + + A nucleus accumbens shell and olfactory tubercle D1 medium spiny neuron that co-expresses TAC3 and the DRD1 receptor. + PMID:34727523 + + + + + D1Sh TAC3 archetype + PMID:34727523 + + + + + + TAC3-positive D1Sh-MSN + PMID:34727523 + + + + + + TAC3-positive MSN + PMID:34727523 + + + + + + A TAC3-positive medium spiny neuron has its soma in a cluster in the medial shell region of the nucleus accumbens. In Rhesus Macaque, this medium spiny neuron has an enriched expression of the genes MPPED1, HPCAL1, MEIS3. + PMID:34727523 + + + + + + + + + A central nervous system macrophage that is part of a choroid plexus, a meninx and a perivascular space. A border associated macrophage interacts with various components of the CNS vasculature and meninges, it participates in immune surveillance and in the regulation of the blood brain barrier. + + 2024-03-26T16:39:56Z + BAM + CAM + CNS-associated macrophage + In humans, a border associate macrophage expresses CD45 and CD11B. This cell is also known to have the following molecular signature: CD206, CD38, LYVE1, CD163, CD169. + border associated macrophage + + + + + A central nervous system macrophage that is part of a choroid plexus, a meninx and a perivascular space. A border associated macrophage interacts with various components of the CNS vasculature and meninges, it participates in immune surveillance and in the regulation of the blood brain barrier. + PMID:37232741 + PMID:37626977 + + + + + BAM + PMID:36945367 + + + + + + CAM + PMID:33556248 + + + + + + CNS-associated macrophage + PMID:37232741 + + + + + In humans, a border associate macrophage expresses CD45 and CD11B. This cell is also known to have the following molecular signature: CD206, CD38, LYVE1, CD163, CD169. + PMID:29426702 + PMID:37232741 + + + + + + + + + + + + + + + A choroid plexus macrophage that is part of the apical surface of some choroid plexus epithelium. This macrophage has a star-like shaped body. + + 2024-03-26T19:14:58Z + Kolmer’s cell + cpepiMΦ + epiplexus cpMΦ + choroid epiplexus macrophage + + + + + A choroid plexus macrophage that is part of the apical surface of some choroid plexus epithelium. This macrophage has a star-like shaped body. + PMID:31061494 + PMID:37232741 + + + + + Kolmer’s cell + PMID:31433571 + + + + + cpepiMΦ + PMID:38347231 + + + + + + epiplexus cpMΦ + PMID:38347231 + + + + + + + + + + + + + + + + A choroid plexus macrophage that is part of a choroid plexus stroma. + + 2024-03-26T19:21:51Z + cpstMΦ + stromal cpMΦ + stromal choroid plexus macrophage + + + + + A choroid plexus macrophage that is part of a choroid plexus stroma. + PMID:38347231 + + + + + cpstMΦ + PMID:37626977 + + + + + + stromal cpMΦ + PMID:37232741 + PMID:38347231 + + + + + + + + + + + + + + + + A border associated macrophage which is part of a dura matter. This macrophage phagocytoses intruding pathogens and foreign molecules detected in the bloodstream or in the cerebrospinal fluid. This cell has an amoeboid body with dynamic protrusions in homeostasis. + + 2024-03-26T19:27:03Z + dmMΦ + dural macrophage + + + + + A border associated macrophage which is part of a dura matter. This macrophage phagocytoses intruding pathogens and foreign molecules detected in the bloodstream or in the cerebrospinal fluid. This cell has an amoeboid body with dynamic protrusions in homeostasis. + PMID:31061494 + + + + + dmMΦ + PMID:37232741 + + + + + @@ -99707,17 +114099,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - - - - ID was moved to the CL namespace. Use CL:0017509. - obsolete D96882F1-8709-49AB-BCA9-772A67EA6C33 - true - - - - @@ -100024,6 +114405,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -100450,6 +114837,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -100594,6 +114987,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -100786,12 +115185,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - - - - - @@ -100852,6 +115245,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -100882,12 +115281,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - - - - - @@ -101488,12 +115881,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - - - - - @@ -101518,12 +115905,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - - - - - @@ -102658,12 +117039,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - - - - - @@ -102754,12 +117129,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - - - - - @@ -103012,12 +117381,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - - - - - @@ -103174,6 +117537,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -103264,12 +117633,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - - - - - @@ -103288,12 +117651,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - - - - - @@ -103342,12 +117699,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - - - - - @@ -103540,6 +117891,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -105124,6 +119481,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -105328,12 +119691,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - - - - - @@ -105754,12 +120111,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - - - - - @@ -105886,12 +120237,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - - - - - @@ -105904,6 +120249,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -105964,6 +120315,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -106378,6 +120735,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -106786,12 +121149,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - - - - - @@ -107500,30 +121857,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - - - - - - - - - - - - - - - - - @@ -107544,6 +121883,36 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances /////////////////////////////////////////////////////////////////////////////////////// --> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -107584,17 +121953,27 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - + - + - + + + + + + + + + + + diff --git a/cl.obo b/cl.obo index 02649bf25..28511c673 100644 --- a/cl.obo +++ b/cl.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: releases/2024-02-13 +data-version: releases/2024-04-05 subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -89,20 +89,20 @@ synonymtypedef: SYSTEMATIC "" synonymtypedef: systematic_synonym "" remark: See PMID:15693950, PMID:12799354, PMID:20123131, PMID:21208450; Contact Alexander Diehl, addiehl@buffalo.edu, University at Buffalo. ontology: cl -property_value: dc-contributor https://orcid.org/0000-0001-5208-3432 -property_value: dc-contributor https://orcid.org/0000-0001-9114-8737 -property_value: dc-contributor https://orcid.org/0000-0001-9990-8331 -property_value: dc-contributor https://orcid.org/0000-0002-2244-7917 -property_value: dc-contributor https://orcid.org/0000-0002-6601-2165 -property_value: dc-contributor https://orcid.org/0000-0002-7073-9172 -property_value: dc-contributor https://orcid.org/0000-0002-8688-6599 -property_value: dc-contributor https://orcid.org/0000-0002-9900-7880 -property_value: dc-contributor https://orcid.org/0000-0003-1980-3228 -property_value: dc-description "An ontology of cell types." xsd:string -property_value: dc-title "Cell Ontology" xsd:string -property_value: dcterms-license http://creativecommons.org/licenses/by/4.0/ property_value: has_ontology_root_term CL:0000000 -property_value: owl:versionInfo "2024-02-13" xsd:string +property_value: http://purl.org/dc/elements/1.1/description "An ontology of cell types." xsd:string +property_value: http://purl.org/dc/elements/1.1/title "Cell Ontology" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2244-7917 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9900-7880 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/license http://creativecommons.org/licenses/by/4.0/ +property_value: owl:versionInfo "2024-04-05" xsd:string [Term] id: BFO:0000002 @@ -230,7 +230,7 @@ disjoint_from: GO:0032991 ! protein-containing complex disjoint_from: GO:0043226 ! organelle relationship: has_part GO:0005634 {gci_filler="PATO:0001407", gci_relation="bearer_of"} ! nucleus relationship: has_part GO:0005634 {gci_filler="PATO:0001908", gci_relation="bearer_of"} ! nucleus -relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms +relationship: RO:0002160 NCBITaxon:131567 ! only in taxon cellular organisms [Term] id: CL:0000001 @@ -278,12 +278,13 @@ consider: CL:0001034 [Term] id: CL:0000005 -name: fibroblast neural crest derived -def: "Any fibroblast that is deriived from the neural crest." [https://orcid.org/0000-0001-5208-3432] +name: neural crest derived fibroblast +def: "Any fibroblast that is derived from the neural crest." [https://orcid.org/0000-0001-5208-3432] +synonym: "fibroblast neural crest derived" EXACT [] is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast -intersection_of: develops_from CL:0000333 ! migratory neural crest cell -relationship: develops_from CL:0000008 ! migratory cranial neural crest cell +intersection_of: RO:0002202 CL:0000333 ! develops from migratory neural crest cell +relationship: RO:0002202 CL:0000008 ! develops from migratory cranial neural crest cell [Term] id: CL:0000006 @@ -393,7 +394,7 @@ is_a: CL:0000015 ! male germ cell intersection_of: CL:0000015 ! male germ cell intersection_of: capable_of GO:0048137 ! spermatocyte division relationship: capable_of GO:0048137 ! spermatocyte division -relationship: develops_from CL:0000020 ! spermatogonium +relationship: RO:0002202 CL:0000020 ! develops from spermatogonium [Term] id: CL:0000018 @@ -416,7 +417,7 @@ intersection_of: capable_of GO:0007289 ! spermatid nucleus differentiation relationship: capable_of GO:0001675 ! acrosome assembly relationship: capable_of GO:0007288 ! sperm axoneme assembly relationship: capable_of GO:0007289 ! spermatid nucleus differentiation -relationship: develops_from CL:0000657 ! secondary spermatocyte +relationship: RO:0002202 CL:0000657 ! develops from secondary spermatocyte [Term] id: CL:0000019 @@ -433,7 +434,7 @@ xref: FBbt:00004954 xref: FMA:67338 xref: WBbt:0006798 is_a: CL:0000408 {is_inferred="true"} ! male gamete -relationship: develops_from CL:0000018 ! spermatid +relationship: RO:0002202 CL:0000018 ! develops from spermatid [Term] id: CL:0000020 @@ -490,8 +491,8 @@ xref: MESH:D009865 xref: WBbt:0006797 is_a: CL:0000021 {is_inferred="true"} ! female germ cell is_a: CL:0000255 ! eukaryotic cell -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa relationship: participates_in GO:0007143 ! female meiotic nuclear division +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa [Term] id: CL:0000024 @@ -503,7 +504,7 @@ is_a: CL:0000021 {is_inferred="true"} ! female germ cell intersection_of: CL:0000021 ! female germ cell intersection_of: capable_of GO:0000278 ! mitotic cell cycle relationship: capable_of GO:0000278 ! mitotic cell cycle -relationship: develops_from CL:0000670 ! primordial germ cell +relationship: RO:0002202 CL:0000670 ! develops from primordial germ cell [Term] id: CL:0000025 @@ -518,9 +519,9 @@ xref: FBbt:00057012 xref: FMA:67343 xref: MESH:D010063 is_a: CL:0000675 {is_inferred="true"} ! female gamete -relationship: develops_from CL:0000023 ! oocyte relationship: participates_in GO:0007143 ! female meiotic nuclear division -property_value: depiction "https://www.swissbiopics.org/api/image/Egg_cell.svg" xsd:anyURI +relationship: RO:0002202 CL:0000023 ! develops from oocyte +property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Egg_cell.svg" xsd:anyURI [Term] id: CL:0000026 @@ -531,7 +532,7 @@ xref: BTO:0000953 xref: FBbt:00004878 is_a: CL:0000412 ! polyploid cell is_a: CL:4029002 ! germline-derived nurse cell -relationship: develops_from CL:0000722 ! cystoblast +relationship: RO:0002202 CL:0000722 ! develops from cystoblast [Term] id: CL:0000027 @@ -539,15 +540,15 @@ name: smooth muscle cell neural crest derived def: "A smooth muscle cell derived from the neural crest." [https://orcid.org/0000-0001-5208-3432] is_a: CL:0000192 {is_inferred="true"} ! smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell -intersection_of: develops_from CL:0000333 ! migratory neural crest cell -relationship: develops_from CL:0000008 ! migratory cranial neural crest cell +intersection_of: RO:0002202 CL:0000333 ! develops from migratory neural crest cell +relationship: RO:0002202 CL:0000008 ! develops from migratory cranial neural crest cell [Term] id: CL:0000028 name: CNS neuron (sensu Nematoda and Protostomia) is_a: CL:0000540 ! neuron -relationship: develops_from CL:0000338 ! neuroblast (sensu Nematoda and Protostomia) relationship: part_of UBERON:0001017 ! central nervous system +relationship: RO:0002202 CL:0000338 ! develops from neuroblast (sensu Nematoda and Protostomia) [Term] id: CL:0000029 @@ -555,15 +556,15 @@ name: neural crest derived neuron synonym: "neuron neural crest derived" EXACT [] is_a: CL:0000540 {is_inferred="true"} ! neuron intersection_of: CL:0000540 ! neuron -intersection_of: develops_from CL:0000333 ! migratory neural crest cell -relationship: develops_from CL:0002676 ! neural crest derived neuroblast +intersection_of: RO:0002202 CL:0000333 ! develops from migratory neural crest cell +relationship: RO:0002202 CL:0002676 ! develops from neural crest derived neuroblast [Term] id: CL:0000030 name: glioblast subset: cellxgene_subset is_a: CL:0000055 ! non-terminally differentiated cell -relationship: develops_from CL:0000133 ! neurectodermal cell +relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell [Term] id: CL:0000031 @@ -576,7 +577,7 @@ xref: BTO:0000930 xref: FMA:70563 is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0000255 ! eukaryotic cell -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata [Term] id: CL:0000032 @@ -584,7 +585,7 @@ name: neuroplacodal cell def: "A cell of a platelike structure, especially a thickened plate of ectoderm in the early embryo, from which a sense organ develops." [GOC:tfm, ISBN:0618947256] synonym: "neural placode cell" EXACT [] is_a: CL:0002321 ! embryonic cell (metazoa) -relationship: develops_from CL:0000114 ! surface ectodermal cell +relationship: RO:0002202 CL:0000114 ! develops from surface ectodermal cell [Term] id: CL:0000033 @@ -592,7 +593,7 @@ name: apocrine cell def: "An exocrine cell characterized by loss of part of the cytoplasm during the process of secretion. The secreted substance is accumulated at the apical end and is either budded off through the plasma membrane producing secreted vesicles or dissolved in the cytoplasm that is lost during secretion." [GOC:tfm, ISBN:0721662544, PMID:25960390] subset: human_reference_atlas is_a: CL:0000152 ! exocrine cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000034 @@ -609,8 +610,8 @@ is_a: CL:0011115 ! precursor cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0017145 ! stem cell division relationship: capable_of GO:0017145 ! stem cell division -relationship: in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000035 @@ -632,7 +633,7 @@ subset: cellxgene_subset subset: human_reference_atlas synonym: "epithelial stem cell" EXACT [] is_a: CL:0000035 ! single fate stem cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000037 @@ -682,8 +683,8 @@ relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surfac relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -relationship: develops_from CL:0000566 ! angioblastic mesenchymal cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0000566 ! develops from angioblastic mesenchymal cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000038 @@ -700,7 +701,7 @@ synonym: "erythroid stem cell" RELATED [] xref: BTO:0004911 is_a: CL:0000764 ! erythroid lineage cell is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor cell -relationship: develops_from CL:0000050 ! megakaryocyte-erythroid progenitor cell +relationship: RO:0002202 CL:0000050 ! develops from megakaryocyte-erythroid progenitor cell [Term] id: CL:0000039 @@ -732,11 +733,11 @@ intersection_of: has_part CL:0017503 ! basophilic cytoplasm intersection_of: has_part GO:0000791 ! euchromatin intersection_of: has_part GO:0005730 ! nucleolus intersection_of: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M -relationship: develops_from CL:0002009 ! macrophage dendritic cell progenitor relationship: has_part CL:0017503 ! basophilic cytoplasm relationship: has_part GO:0000791 ! euchromatin relationship: has_part GO:0005730 ! nucleolus relationship: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M +relationship: RO:0002202 CL:0002009 ! develops from macrophage dendritic cell progenitor [Term] id: CL:0000041 @@ -754,16 +755,16 @@ is_a: CL:0000771 {is_inferred="true"} ! eosinophil relationship: capable_of GO:0002495 ! antigen processing and presentation of peptide antigen via MHC class II relationship: capable_of GO:0002540 ! leukotriene production involved in inflammatory response relationship: capable_of GO:0045730 ! respiratory burst -relationship: develops_from CL:0000774 ! band form eosinophil relationship: has_part PR:000007152 ! eosinophil peroxidase relationship: has_part PR:000007857 ! erythroid transcription factor relationship: has_part PR:000007858 ! endothelial transcription factor GATA-2 relationship: has_part PR:000014046 ! non-secretory ribonuclease relationship: has_part PR:000014047 ! eosinophil cationic protein relationship: has_part PR:000022006 ! eosinophil granule major basic protein -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000009129 ! has plasma membrane part integrin alpha-4 -property_value: editor_note "The status of eosinophils as true professional antigen presenting cells is unclear, despite their ability to present exogenous peptides and peptides processed from exogenous proteins (in certain studies) via MHC Class II and activate T cells. Per the equivalence axioms, 'eosinophil' is reasoned to be a subclass of 'professional antigen presenting cell', though the role of eosinophils as such in the body may be limited." xsd:string +relationship: RO:0002202 CL:0000774 ! develops from band form eosinophil +property_value: IAO:0000116 "The status of eosinophils as true professional antigen presenting cells is unclear, despite their ability to present exogenous peptides and peptides processed from exogenous proteins (in certain studies) via MHC Class II and activate T cells. Per the equivalence axioms, 'eosinophil' is reasoned to be a subclass of 'professional antigen presenting cell', though the role of eosinophils as such in the body may be limited." xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000042 @@ -780,12 +781,12 @@ intersection_of: has_part PR:000005307 ! CCAAT/enhancer-binding protein alpha intersection_of: has_part PR:000007857 ! erythroid transcription factor intersection_of: has_part PR:000010799 ! myb proto-oncogene protein intersection_of: has_part PR:000014362 ! runt-related transcription factor 1 -relationship: develops_from CL:0000834 ! neutrophil progenitor cell relationship: has_part PR:000001944 ! transcription factor PU.1 relationship: has_part PR:000005307 ! CCAAT/enhancer-binding protein alpha relationship: has_part PR:000007857 ! erythroid transcription factor relationship: has_part PR:000010799 ! myb proto-oncogene protein relationship: has_part PR:000014362 ! runt-related transcription factor 1 +relationship: RO:0002202 CL:0000834 ! develops from neutrophil progenitor cell [Term] id: CL:0000043 @@ -807,7 +808,7 @@ relationship: capable_of GO:0002830 ! positive regulation of type 2 immune respo relationship: capable_of GO:0032616 ! interleukin-13 production relationship: capable_of GO:0032633 ! interleukin-4 production relationship: capable_of GO:0048295 ! positive regulation of isotype switching to IgE isotypes -relationship: develops_from CL:0000770 ! band form basophil +relationship: RO:0002202 CL:0000770 ! develops from band form basophil [Term] id: CL:0000045 @@ -834,7 +835,7 @@ xref: BTO:0002881 xref: CALOHA:TS-2360 xref: FMA:86684 is_a: CL:0002319 ! neural cell -relationship: develops_from CL:0000133 ! neurectodermal cell +relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell [Term] id: CL:0000048 @@ -871,7 +872,7 @@ is_a: CL:0002032 {is_inferred="true"} ! hematopoietic oligopotent progenitor cel disjoint_from: CL:0000050 ! megakaryocyte-erythroid progenitor cell disjoint_from: CL:0000051 ! common lymphoid progenitor disjoint_from: CL:0000557 ! granulocyte monocyte progenitor cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000050 @@ -897,7 +898,7 @@ disjoint_from: CL:0000557 ! granulocyte monocyte progenitor cell disjoint_from: CL:0002009 ! macrophage dendritic cell progenitor relationship: capable_of GO:0030218 ! erythrocyte differentiation relationship: capable_of GO:0030219 ! megakaryocyte differentiation -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000051 @@ -921,7 +922,7 @@ is_a: CL:0011026 ! progenitor cell intersection_of: CL:0002032 ! hematopoietic oligopotent progenitor cell intersection_of: capable_of GO:0030098 ! lymphocyte differentiation relationship: capable_of GO:0030098 ! lymphocyte differentiation -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000052 @@ -973,8 +974,8 @@ xref: FMA:63877 xref: NCIT:C12482 xref: VHOG:0001482 is_a: CL:0002320 ! connective tissue cell -relationship: develops_from CL:0000134 ! mesenchymal stem cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000058 @@ -985,8 +986,8 @@ xref: BTO:0003607 xref: FMA:66783 is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0002320 ! connective tissue cell -relationship: develops_from CL:0007009 ! prechondroblast relationship: produces UBERON:0002418 ! cartilage tissue +relationship: RO:0002202 CL:0007009 ! develops from prechondroblast [Term] id: CL:0000059 @@ -1004,9 +1005,9 @@ is_a: CL:0000151 ! secretory cell is_a: CL:0002077 ! ecto-epithelial cell relationship: adjacent_to UBERON:0001763 ! odontogenic papilla relationship: capable_of GO:0097186 ! amelogenesis -relationship: develops_from CL:0007000 ! preameloblast relationship: part_of UBERON:0005176 ! tooth enamel organ relationship: produces UBERON:0001752 ! enamel +relationship: RO:0002202 CL:0007000 ! develops from preameloblast [Term] id: CL:0000060 @@ -1021,9 +1022,9 @@ is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0000710 ! neurecto-epithelial cell is_a: CL:0002148 ! dental pulp cell is_a: CL:0011026 ! progenitor cell -relationship: develops_from CL:0007003 ! preodontoblast relationship: part_of UBERON:0005176 ! tooth enamel organ relationship: produces UBERON:0001751 ! dentine +relationship: RO:0002202 CL:0007003 ! develops from preodontoblast [Term] id: CL:0000061 @@ -1036,9 +1037,9 @@ xref: CALOHA:TS-1164 xref: FMA:63002 is_a: CL:0000062 ! osteoblast is_a: CL:0000151 ! secretory cell -relationship: develops_from CL:0007002 ! precementoblast relationship: part_of UBERON:0005176 ! tooth enamel organ relationship: produces UBERON:0001753 ! cementum +relationship: RO:0002202 CL:0007002 ! develops from precementoblast [Term] id: CL:0000062 @@ -1052,8 +1053,8 @@ xref: FMA:66780 is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0002320 ! connective tissue cell is_a: CL:0011026 ! progenitor cell -relationship: develops_from CL:0007010 ! preosteoblast relationship: produces UBERON:0008883 ! osteoid +relationship: RO:0002202 CL:0007010 ! develops from preosteoblast [Term] id: CL:0000063 @@ -1089,7 +1090,7 @@ xref: BTO:0001724 xref: FMA:70550 is_a: CL:0000067 ! ciliated epithelial cell is_a: CL:0000710 ! neurecto-epithelial cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000066 @@ -1108,8 +1109,8 @@ xref: WBbt:0003672 is_a: CL:0000000 ! cell disjoint_from: CL:0000738 ! leukocyte relationship: part_of UBERON:0000483 ! epithelium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000067 @@ -1153,9 +1154,9 @@ is_a: CL:0000076 {is_inferred="true"} ! squamous epithelial cell is_a: CL:0002139 ! endothelial cell of vascular tree intersection_of: CL:0000076 ! squamous epithelial cell intersection_of: part_of UBERON:0004638 ! blood vessel endothelium -relationship: develops_from CL:0002546 ! embryonic blood vessel endothelial progenitor cell relationship: part_of UBERON:0004638 ! blood vessel endothelium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0002546 ! develops from embryonic blood vessel endothelial progenitor cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000072 @@ -1184,7 +1185,7 @@ def: "A columnar/cuboidal epithelial cell is a cell usually found in a two dimen subset: cellxgene_subset subset: human_reference_atlas is_a: CL:0000066 ! epithelial cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000076 @@ -1204,7 +1205,7 @@ xref: FMA:66773 is_a: CL:0000076 ! squamous epithelial cell is_a: CL:0000213 ! lining cell is_a: CL:0002078 ! meso-epithelial cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000078 @@ -1216,7 +1217,7 @@ id: CL:0000079 name: stratified epithelial cell subset: cellxgene_subset is_a: CL:0000066 ! epithelial cell -relationship: develops_from CL:0000357 ! stratified epithelial stem cell +relationship: RO:0002202 CL:0000357 ! develops from stratified epithelial stem cell [Term] id: CL:0000080 @@ -1262,8 +1263,8 @@ xref: BTO:0000028 is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001264 ! pancreas -relationship: develops_from CL:0000223 ! endodermal cell relationship: part_of UBERON:0001264 ! pancreas +relationship: RO:0002202 CL:0000223 ! develops from endodermal cell [Term] id: CL:0000084 @@ -1289,8 +1290,8 @@ intersection_of: CL:0000542 ! lymphocyte intersection_of: capable_of GO:0002456 ! T cell mediated immunity disjoint_from: CL:0000945 ! lymphocyte of B lineage relationship: capable_of GO:0002456 ! T cell mediated immunity -relationship: develops_from CL:0000827 ! pro-T cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0000827 ! develops from pro-T cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000085 @@ -1359,18 +1360,18 @@ is_a: CL:0000864 {is_inferred="true"} ! tissue-resident macrophage is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000864 ! tissue-resident macrophage intersection_of: capable_of GO:0034102 ! erythrocyte clearance -intersection_of: located_in UBERON:0001281 ! hepatic sinusoid +intersection_of: RO:0001025 UBERON:0001281 ! located in hepatic sinusoid intersection_of: RO:0002104 PR:000001813 ! has plasma membrane part adhesion G protein-coupled receptor E1 intersection_of: RO:0002104 PR:000001925 ! has plasma membrane part scavenger receptor cysteine-rich type 1 protein M130 intersection_of: RO:0002104 PR:000002064 ! has plasma membrane part macrosialin intersection_of: RO:0015016 PR:000001012 ! has low plasma membrane amount integrin alpha-M relationship: capable_of GO:0034102 ! erythrocyte clearance -relationship: located_in UBERON:0001281 ! hepatic sinusoid -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0001025 UBERON:0001281 ! located in hepatic sinusoid relationship: RO:0002104 PR:000001813 ! has plasma membrane part adhesion G protein-coupled receptor E1 relationship: RO:0002104 PR:000001925 ! has plasma membrane part scavenger receptor cysteine-rich type 1 protein M130 relationship: RO:0002104 PR:000002064 ! has plasma membrane part macrosialin relationship: RO:0015016 PR:000001012 ! has low plasma membrane amount integrin alpha-M +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000092 @@ -1398,7 +1399,6 @@ intersection_of: part_of UBERON:0001474 ! bone element intersection_of: RO:0002104 PR:000001954 ! has plasma membrane part tumor necrosis factor receptor superfamily member 11A intersection_of: RO:0002104 PR:000002062 ! has plasma membrane part macrophage colony-stimulating factor 1 receptor relationship: capable_of GO:0045453 ! bone resorption -relationship: develops_from CL:0000576 ! monocyte relationship: has_part PR:000001850 ! cathepsin K relationship: has_part PR:000001937 ! tartrate-resistant acid phosphatase type 5 relationship: has_part PR:000001944 ! transcription factor PU.1 @@ -1406,6 +1406,7 @@ relationship: has_part PR:000007597 ! protein c-Fos relationship: has_part PR:000011178 ! nuclear factor NF-kappa-B p100 subunit relationship: RO:0002104 PR:000001954 ! has plasma membrane part tumor necrosis factor receptor superfamily member 11A relationship: RO:0002104 PR:000002062 ! has plasma membrane part macrophage colony-stimulating factor 1 receptor +relationship: RO:0002202 CL:0000576 ! develops from monocyte [Term] id: CL:0000093 @@ -1445,17 +1446,17 @@ relationship: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon relationship: CL:4030046 PR:000001024 ! lacks_plasma_membrane_part neural cell adhesion molecule 1 relationship: CL:4030046 PR:000001084 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD8 alpha chain relationship: has_part GO:0030141 ! secretory granule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M relationship: RO:0002104 PR:000001332 ! has plasma membrane part carcinoembryonic antigen-related cell adhesion molecule 8 relationship: RO:0002104 PR:000001969 ! has plasma membrane part urokinase plasminogen activator surface receptor +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000095 name: neuron associated cell subset: cellxgene_subset is_a: CL:0002319 ! neural cell -relationship: develops_from CL:0000133 ! neurectodermal cell +relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell [Term] id: CL:0000096 @@ -1486,13 +1487,13 @@ relationship: CL:4030045 PR:000010543 ! lacks_part myeloperoxidase relationship: CL:4030045 PR:000010799 ! lacks_part myb proto-oncogene protein relationship: has_part CL:0017500 ! neutrophillic cytoplasm relationship: has_part GO:0070820 ! tertiary granule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001256 ! has plasma membrane part C-X-C chemokine receptor type 1 relationship: RO:0002104 PR:000001257 ! has plasma membrane part C-X-C chemokine receptor type 2 relationship: RO:0002104 PR:000001456 ! has plasma membrane part alpha-(1,3)-fucosyltransferase 4 relationship: RO:0002104 PR:000001483 ! has plasma membrane part low affinity immunoglobulin gamma Fc region receptor III relationship: RO:0002104 PR:000001944 ! has plasma membrane part transcription factor PU.1 relationship: RO:0002104 PR:000007597 ! has plasma membrane part protein c-Fos +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000097 @@ -1532,13 +1533,13 @@ relationship: capable_of GO:0002690 ! positive regulation of leukocyte chemotaxi relationship: capable_of GO:0002830 ! positive regulation of type 2 immune response relationship: capable_of GO:0030210 ! heparin biosynthetic process relationship: CL:4030046 PR:000001865 ! lacks_plasma_membrane_part interleukin-3 receptor class 2 alpha chain -relationship: develops_from CL:0000831 ! mast cell progenitor relationship: has_part GO:0030141 ! secretory granule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001255 ! has plasma membrane part C-C chemokine receptor type 3 relationship: RO:0002104 PR:000006169 ! has plasma membrane part cell surface glycoprotein CD200 receptor 3 +relationship: RO:0002202 CL:0000831 ! develops from mast cell progenitor relationship: RO:0015015 PR:000002065 ! has high plasma membrane amount mast/stem cell growth factor receptor relationship: RO:0015015 PR:000007431 ! has high plasma membrane amount high affinity immunoglobulin epsilon receptor subunit alpha +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000098 @@ -1563,7 +1564,7 @@ xref: FBbt:00005125 xref: FMA:67313 xref: WBbt:0005113 is_a: CL:0000540 ! neuron -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000100 @@ -1577,7 +1578,7 @@ xref: FBbt:00005123 xref: FMA:83617 xref: WBbt:0005409 is_a: CL:0000527 ! efferent neuron -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000101 @@ -1692,7 +1693,7 @@ is_a: CL:0000518 {is_inferred="true"} ! phagocyte (sensu Vertebrata) is_a: CL:0000842 ! mononuclear cell intersection_of: CL:0000518 ! phagocyte (sensu Vertebrata) intersection_of: bearer_of PATO:0001407 ! mononucleate -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000114 @@ -1716,7 +1717,7 @@ xref: CALOHA:TS-0278 xref: FMA:66772 is_a: CL:0000213 ! lining cell is_a: CL:0002078 ! meso-epithelial cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000116 @@ -1729,8 +1730,8 @@ is_a: CL:0000540 ! neuron id: CL:0000117 name: CNS neuron (sensu Vertebrata) is_a: CL:0000540 ! neuron -relationship: develops_from CL:0000031 ! neuroblast (sensu Vertebrata) relationship: part_of UBERON:0001017 ! central nervous system +relationship: RO:0002202 CL:0000031 ! develops from neuroblast (sensu Vertebrata) [Term] id: CL:0000118 @@ -1743,7 +1744,7 @@ intersection_of: CL:0000099 ! interneuron intersection_of: bearer_of PATO:0070002 ! basket cell morphology intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neurotransmission relationship: bearer_of PATO:0070002 ! basket cell morphology -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0000119 @@ -1801,8 +1802,8 @@ name: neuron associated cell (sensu Vertebrata) subset: cellxgene_subset is_a: CL:0000095 ! neuron associated cell is_a: CL:0000255 ! eukaryotic cell -relationship: develops_from CL:0000333 ! migratory neural crest cell -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell [Term] id: CL:0000124 @@ -1837,7 +1838,7 @@ xref: BTO:0000771 xref: CALOHA:TS-2027 xref: FMA:54538 is_a: CL:0000125 ! glial cell -relationship: develops_from CL:0000339 ! glioblast (sensu Vertebrata) +relationship: RO:0002202 CL:0000339 ! develops from glioblast (sensu Vertebrata) [Term] id: CL:0000127 @@ -1851,7 +1852,7 @@ xref: BTO:0000099 xref: CALOHA:TS-0060 xref: FMA:54537 is_a: CL:0000126 ! macroglial cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000128 @@ -1867,9 +1868,9 @@ xref: CALOHA:TS-0709 xref: FMA:54540 is_a: CL:0000126 {is_inferred="true"} ! macroglial cell is_a: CL:4023154 ! myelinating glial cell -relationship: develops_from CL:0002453 ! oligodendrocyte precursor cell relationship: part_of UBERON:0001017 ! central nervous system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0002453 ! develops from oligodendrocyte precursor cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000129 @@ -1897,25 +1898,25 @@ intersection_of: RO:0002104 PR:000001012 ! has plasma membrane part integrin alp intersection_of: RO:0002104 PR:000001813 ! has plasma membrane part adhesion G protein-coupled receptor E1 intersection_of: RO:0002104 PR:000002064 ! has plasma membrane part macrosialin relationship: capable_of GO:0045087 ! innate immune response -relationship: develops_from CL:0000222 ! mesodermal cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M relationship: RO:0002104 PR:000001813 ! has plasma membrane part adhesion G protein-coupled receptor E1 relationship: RO:0002104 PR:000002064 ! has plasma membrane part macrosialin +relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000130 name: neuron associated cell (sensu Nematoda and Protostomia) is_a: CL:0000095 ! neuron associated cell is_a: CL:0000255 ! eukaryotic cell -relationship: only_in_taxon NCBITaxon:33317 ! Protostomia +relationship: RO:0002160 NCBITaxon:33317 ! only in taxon Protostomia [Term] id: CL:0000131 name: gut endothelial cell subset: cellxgene_subset is_a: CL:0000115 ! endothelial cell -relationship: develops_from CL:0000223 ! endodermal cell +relationship: RO:0002202 CL:0000223 ! develops from endodermal cell [Term] id: CL:0000132 @@ -1928,9 +1929,9 @@ xref: CALOHA:TS-0172 xref: FMA:70614 is_a: CL:0000115 ! endothelial cell is_a: CL:0000710 ! neurecto-epithelial cell -relationship: develops_from CL:0000008 ! migratory cranial neural crest cell relationship: part_of UBERON:0001985 ! corneal endothelium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0000008 ! develops from migratory cranial neural crest cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000133 @@ -1978,7 +1979,7 @@ intersection_of: capable_of GO:0002495 ! antigen processing and presentation of intersection_of: capable_of GO:0045766 ! positive regulation of angiogenesis relationship: capable_of GO:0002495 ! antigen processing and presentation of peptide antigen via MHC class II relationship: capable_of GO:0045766 ! positive regulation of angiogenesis -relationship: develops_from CL:0000057 ! fibroblast +relationship: RO:0002202 CL:0000057 ! develops from fibroblast [Term] id: CL:0000136 @@ -1995,8 +1996,8 @@ xref: CALOHA:TS-0012 xref: FMA:63880 is_a: CL:0000325 ! stuff accumulating cell is_a: CL:0002320 ! connective tissue cell -relationship: develops_from CL:0000134 ! mesenchymal stem cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000137 @@ -2010,8 +2011,8 @@ xref: FMA:66779 xref: VSAO:0000124 is_a: CL:0001035 ! bone cell is_a: CL:0002320 ! connective tissue cell -relationship: develops_from CL:0001040 ! non-terminally differentiated osteoblast relationship: part_of UBERON:0002481 ! bone tissue +relationship: RO:0002202 CL:0001040 ! develops from non-terminally differentiated osteoblast [Term] id: CL:0000138 @@ -2024,17 +2025,17 @@ xref: CALOHA:TS-0138 xref: FMA:66782 is_a: CL:0000153 ! glycosaminoglycan secreting cell is_a: CL:0000667 ! collagen secreting cell -relationship: develops_from CL:0000058 ! chondroblast -relationship: located_in UBERON:0002418 ! cartilage tissue +relationship: RO:0001025 UBERON:0002418 ! located in cartilage tissue +relationship: RO:0002202 CL:0000058 ! develops from chondroblast [Term] id: CL:0000140 name: odontocyte def: "Skeletogenic cell that secretes dentine matrix, is derived from odontogenic papilla. Embedded in dentine tissue, and is the transformation of a non-terminally differentiated odontoblast cell." [GO_REF:0000034] is_a: CL:0002320 ! connective tissue cell -relationship: develops_from CL:0000060 ! odontoblast -relationship: develops_from CL:0000134 ! mesenchymal stem cell relationship: produces UBERON:0001751 ! dentine +relationship: RO:0002202 CL:0000060 ! develops from odontoblast +relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell [Term] id: CL:0000141 @@ -2043,8 +2044,8 @@ def: "An osteocytelike cell with numerous processes, trapped in a lacuna in the comment: CHECK: wikipedia says that cementocytes no longer produce cementum, but the phenoscape def is: Skeletogenic cell that produces cementum, is part of the odontogenic papilla, and is a transformation of a cementoblast cell (no change to existing def). xref: FMA:63003 is_a: CL:0000137 ! osteocyte -relationship: develops_from CL:0000061 ! cementoblast relationship: part_of UBERON:0005176 ! tooth enamel organ +relationship: RO:0002202 CL:0000061 ! develops from cementoblast [Term] id: CL:0000142 @@ -2088,7 +2089,7 @@ id: CL:0000146 name: simple columnar epithelial cell subset: human_reference_atlas is_a: CL:0000075 ! columnar/cuboidal epithelial cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000147 @@ -2115,11 +2116,11 @@ xref: MESH:D008544 xref: VHOG:0001679 is_a: CL:0000147 ! pigment cell intersection_of: CL:0000147 ! pigment cell -intersection_of: develops_from CL:0000541 ! melanoblast intersection_of: has_part GO:0042470 ! melanosome -relationship: develops_from CL:0000541 ! melanoblast +intersection_of: RO:0002202 CL:0000541 ! develops from melanoblast relationship: has_part GO:0042470 ! melanosome -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0000541 ! develops from melanoblast +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000149 @@ -2219,8 +2220,8 @@ xref: FMA:14119 is_a: CL:0000157 ! surfactant secreting cell is_a: CL:0002202 ! epithelial cell of tracheobronchial tree is_a: CL:0011026 ! progenitor cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 GO:0005902 ! has plasma membrane part microvillus +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000159 @@ -2271,7 +2272,7 @@ is_a: CL:0000164 {gci_relation="part_of", gci_filler="UBERON:0000945"} ! enteroe is_a: CL:0000164 {gci_filler="UBERON:0000160", gci_relation="part_of"} ! enteroendocrine cell is_a: CL:0000164 {gci_filler="UBERON:0001264", gci_relation="part_of"} ! enteroendocrine cell relationship: part_of UBERON:0000949 ! endocrine system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000164 @@ -2301,7 +2302,7 @@ is_a: CL:0000527 ! efferent neuron is_a: CL:0000710 ! neurecto-epithelial cell intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0046879 ! hormone secretion -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000166 @@ -2359,9 +2360,9 @@ is_a: CL:0008024 ! pancreatic endocrine cell intersection_of: CL:0000164 ! enteroendocrine cell intersection_of: capable_of GO:0030073 ! insulin secretion intersection_of: part_of UBERON:0000006 ! islet of Langerhans -relationship: develops_from CL:0002351 ! progenitor cell of endocrine pancreas relationship: part_of UBERON:0000006 ! islet of Langerhans -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0002351 ! develops from progenitor cell of endocrine pancreas +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000170 @@ -2389,9 +2390,9 @@ is_a: CL:0002067 ! type A enteroendocrine cell is_a: CL:0008024 ! pancreatic endocrine cell intersection_of: CL:0002067 ! type A enteroendocrine cell intersection_of: part_of UBERON:0001264 ! pancreas -relationship: develops_from CL:0002351 ! progenitor cell of endocrine pancreas relationship: part_of UBERON:0000006 ! islet of Langerhans -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0002351 ! develops from progenitor cell of endocrine pancreas +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000172 @@ -2419,9 +2420,9 @@ is_a: CL:0000502 ! type D enteroendocrine cell is_a: CL:0008024 ! pancreatic endocrine cell intersection_of: CL:0000502 ! type D enteroendocrine cell intersection_of: part_of UBERON:0001264 ! pancreas -relationship: develops_from CL:0002351 ! progenitor cell of endocrine pancreas relationship: part_of UBERON:0000006 ! islet of Langerhans -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0002351 ! develops from progenitor cell of endocrine pancreas +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000174 @@ -2443,7 +2444,7 @@ xref: FMA:18688 is_a: CL:0000179 ! progesterone secreting cell is_a: CL:0002132 ! stromal cell of ovary relationship: part_of UBERON:0002512 ! corpus luteum -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000176 @@ -2476,8 +2477,8 @@ xref: FMA:72297 xref: MESH:D007985 is_a: CL:0000177 ! testosterone secreting cell is_a: CL:4030031 ! interstitial cell -relationship: develops_from CL:0009091 ! Leydig stem cell relationship: part_of UBERON:0005212 ! Leydig cell region of testis +relationship: RO:0002202 CL:0009091 ! develops from Leydig stem cell [Term] id: CL:0000179 @@ -2518,9 +2519,9 @@ is_a: CL:0000066 ! epithelial cell is_a: CL:0000417 ! endopolyploid cell relationship: capable_of GO:0006699 ! bile acid biosynthetic process relationship: capable_of GO:0098754 ! detoxification -relationship: develops_from CL:0005026 ! hepatoblast relationship: part_of UBERON:0002107 ! liver -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0005026 ! develops from hepatoblast +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000183 @@ -2553,7 +2554,7 @@ subset: human_reference_atlas synonym: "MFB" EXACT [PMID:8731193] is_a: CL:0000183 ! contractile cell is_a: CL:0002320 ! connective tissue cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000187 @@ -2570,8 +2571,8 @@ xref: FMA:67328 xref: WBbt:0003675 is_a: CL:0000183 ! contractile cell is_a: CL:0000393 ! electrically responsive cell -relationship: develops_from CL:0000056 ! myoblast -property_value: depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI +relationship: RO:0002202 CL:0000056 ! develops from myoblast +property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI [Term] id: CL:0000188 @@ -2588,7 +2589,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001134 ! skeletal muscle tissue relationship: part_of UBERON:0001134 ! skeletal muscle tissue -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000189 @@ -2597,7 +2598,7 @@ def: "A muscle cell that develops tension more slowly than a fast-twitch fiber." subset: cellxgene_subset synonym: "slow muscle fiber" RELATED [ISBN:0815316208] is_a: CL:0008046 ! extrafusal muscle fiber -relationship: develops_from CL:0000857 ! slow muscle myoblast +relationship: RO:0002202 CL:0000857 ! develops from slow muscle myoblast [Term] id: CL:0000190 @@ -2606,7 +2607,7 @@ def: "A muscle cell that can develop high tension rapidly. It is usually innerva subset: cellxgene_subset synonym: "glycolytic muscle fiber" EXACT [] is_a: CL:0008046 ! extrafusal muscle fiber -relationship: develops_from CL:0000858 ! fast muscle myoblast +relationship: RO:0002202 CL:0000858 ! develops from fast muscle myoblast [Term] id: CL:0000192 @@ -2625,8 +2626,8 @@ xref: CALOHA:TS-2159 xref: FMA:14072 is_a: CL:0008000 ! non-striated muscle cell is_a: CL:0008007 ! visceral muscle cell -relationship: develops_from CL:0000514 ! smooth muscle myoblast -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0000514 ! develops from smooth muscle myoblast +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000193 @@ -2635,8 +2636,8 @@ alt_id: CL:0000466 def: "A striated muscle cell of an arthropod heart that participates in heart contraction." [MESH:D032383] is_a: CL:0000746 ! cardiac muscle cell intersection_of: CL:0000746 ! cardiac muscle cell -intersection_of: develops_from CL:0000465 ! cardioblast (sensu Arthropoda) -relationship: develops_from CL:0000465 ! cardioblast (sensu Arthropoda) +intersection_of: RO:0002202 CL:0000465 ! develops from cardioblast (sensu Arthropoda) +relationship: RO:0002202 CL:0000465 ! develops from cardioblast (sensu Arthropoda) [Term] id: CL:0000194 @@ -2691,9 +2692,7 @@ relationship: capable_of GO:0050974 ! detection of mechanical stimulus involved [Term] id: CL:0000200 name: touch receptor cell -is_a: CL:0000006 ! neuronal receptor cell is_a: CL:0000199 ! mechanoreceptor cell -is_a: CL:4023168 ! somatosensory neuron intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0050976 ! detection of mechanical stimulus involved in sensory perception of touch relationship: capable_of GO:0050976 ! detection of mechanical stimulus involved in sensory perception of touch @@ -2789,7 +2788,7 @@ is_a: CL:0000006 {is_inferred="true"} ! neuronal receptor cell intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0050962 ! detection of light stimulus involved in sensory perception relationship: capable_of GO:0050962 ! detection of light stimulus involved in sensory perception -property_value: depiction "https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg" xsd:anyURI [Term] id: CL:0000211 @@ -2803,7 +2802,7 @@ name: absorptive cell def: "A cell that takes up and metabolizes substances." [CL:CVS] subset: human_reference_atlas is_a: CL:0000000 ! cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000213 @@ -2860,7 +2859,7 @@ xref: FMA:62121 is_a: CL:0000217 ! insulating cell is_a: CL:0002573 ! Schwann cell is_a: CL:4023154 ! myelinating glial cell -relationship: develops_from CL:0002377 ! immature Schwann cell +relationship: RO:0002202 CL:0002377 ! develops from immature Schwann cell [Term] id: CL:0000219 @@ -3007,8 +3006,8 @@ intersection_of: CL:4030046 PR:000001945 ! lacks_plasma_membrane_part transferri relationship: bearer_of PATO:0002039 ! biconcave relationship: CL:4030045 GO:0005840 ! lacks_part ribosome relationship: CL:4030046 PR:000001945 ! lacks_plasma_membrane_part transferrin receptor protein 1 -relationship: develops_from CL:0000558 ! reticulocyte -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0000558 ! develops from reticulocyte +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000233 @@ -3030,8 +3029,8 @@ is_a: CL:0000458 ! serotonin secreting cell is_a: CL:0000763 {is_inferred="true"} ! myeloid cell relationship: bearer_of PATO:0001874 ! discoid relationship: capable_of_part_of GO:0007596 ! blood coagulation -relationship: develops_from CL:0000556 ! megakaryocyte -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0000556 ! develops from megakaryocyte +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000234 @@ -3071,8 +3070,8 @@ intersection_of: capable_of GO:0002504 ! antigen processing and presentation of intersection_of: capable_of GO:0006909 ! phagocytosis intersection_of: capable_of GO:0031268 ! pseudopodium organization relationship: capable_of GO:0031268 ! pseudopodium organization -relationship: develops_from CL:0000576 ! monocyte -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0000576 ! develops from monocyte +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000236 @@ -3094,7 +3093,7 @@ is_a: CL:0000945 {is_inferred="true"} ! lymphocyte of B lineage intersection_of: CL:0000945 ! lymphocyte of B lineage intersection_of: capable_of GO:0019724 ! B cell mediated immunity relationship: capable_of GO:0019724 ! B cell mediated immunity -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000237 @@ -3102,7 +3101,7 @@ name: keratinizing barrier epithelial cell is_a: CL:0000240 ! stratified squamous epithelial cell is_a: CL:0000311 ! keratin accumulating cell is_a: CL:0002077 ! ecto-epithelial cell -relationship: develops_from CL:0000114 ! surface ectodermal cell +relationship: RO:0002202 CL:0000114 ! develops from surface ectodermal cell [Term] id: CL:0000238 @@ -3121,7 +3120,7 @@ name: stratified squamous epithelial cell subset: human_reference_atlas is_a: CL:0000076 ! squamous epithelial cell is_a: CL:0000079 ! stratified epithelial cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000241 @@ -3129,7 +3128,7 @@ name: stratified cuboidal epithelial cell subset: human_reference_atlas is_a: CL:0000075 ! columnar/cuboidal epithelial cell is_a: CL:0000079 ! stratified epithelial cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000242 @@ -3143,7 +3142,7 @@ is_a: CL:0000123 ! neuron associated cell (sensu Vertebrata) is_a: CL:0000312 {xref="PMID:19782676"} ! keratinocyte is_a: CL:0000710 ! neurecto-epithelial cell relationship: part_of UBERON:0002025 ! stratum basale of epidermis -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000243 @@ -3160,7 +3159,7 @@ def: "A cell characteristically found lining hollow organs that are subject to g subset: human_reference_atlas xref: FMA:66778 is_a: CL:0000066 ! epithelial cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000245 @@ -3243,9 +3242,9 @@ subset: cellxgene_subset xref: MESH:D005057 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell -intersection_of: only_in_taxon NCBITaxon:2759 ! Eukaryota +intersection_of: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota disjoint_from: CL:0000520 ! prokaryotic cell -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota [Term] id: CL:0000256 @@ -3257,8 +3256,8 @@ id: CL:0000257 name: Eumycetozoan cell is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell -intersection_of: only_in_taxon NCBITaxon:142796 ! Eumycetozoa -relationship: only_in_taxon NCBITaxon:142796 ! Eumycetozoa +intersection_of: RO:0002160 NCBITaxon:142796 ! only in taxon Eumycetozoa +relationship: RO:0002160 NCBITaxon:142796 ! only in taxon Eumycetozoa [Term] id: CL:0000258 @@ -3455,7 +3454,7 @@ is_a: CL:0000210 ! photoreceptor cell intersection_of: CL:0000210 ! photoreceptor cell intersection_of: part_of UBERON:0000970 ! eye relationship: part_of UBERON:0000970 ! eye -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000288 @@ -3612,8 +3611,8 @@ xref: FMA:74793 is_a: CL:0002202 {is_inferred="true"} ! epithelial cell of tracheobronchial tree intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0003126 ! trachea -relationship: develops_from CL:0000377 ! tracheoblast relationship: part_of UBERON:0003126 ! trachea +relationship: RO:0002202 CL:0000377 ! develops from tracheoblast [Term] id: CL:0000308 @@ -3657,7 +3656,7 @@ relationship: capable_of GO:0002775 ! antimicrobial peptide production relationship: capable_of GO:0002776 ! antimicrobial peptide secretion relationship: capable_of GO:0090023 ! positive regulation of neutrophil chemotaxis relationship: part_of UBERON:0001003 ! skin epidermis -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000313 @@ -3699,7 +3698,7 @@ is_a: CL:0000152 ! exocrine cell is_a: CL:2000021 ! sebaceous gland cell intersection_of: CL:0000151 ! secretory cell intersection_of: part_of UBERON:0001821 ! sebaceous gland -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000318 @@ -3757,7 +3756,7 @@ is_a: CL:0000154 ! protein secreting cell id: CL:0000324 name: metanephric mesenchyme stem cell is_a: CL:0000134 ! mesenchymal stem cell -relationship: develops_from CL:0000222 ! mesodermal cell +relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell [Term] id: CL:0000325 @@ -3814,7 +3813,7 @@ xref: FMA:86667 is_a: CL:0000219 ! motile cell is_a: CL:0011012 ! neural crest cell is_a: CL:0011026 ! progenitor cell -relationship: develops_from CL:0007004 ! premigratory neural crest cell +relationship: RO:0002202 CL:0007004 ! develops from premigratory neural crest cell [Term] id: CL:0000334 @@ -3841,8 +3840,8 @@ is_a: CL:0000457 ! biogenic amine secreting cell is_a: CL:1000426 ! chromaffin cell of adrenal gland intersection_of: CL:0000166 ! chromaffin cell intersection_of: part_of UBERON:0001236 ! adrenal medulla -relationship: develops_from CL:0000011 ! migratory trunk neural crest cell relationship: part_of UBERON:0001236 ! adrenal medulla +relationship: RO:0002202 CL:0000011 ! develops from migratory trunk neural crest cell [Term] id: CL:0000338 @@ -3852,7 +3851,7 @@ synonym: "neuroblast" BROAD [] xref: FBbt:00005146 is_a: CL:0000047 ! neural stem cell is_a: CL:0000255 ! eukaryotic cell -relationship: only_in_taxon NCBITaxon:33317 ! Protostomia +relationship: RO:0002160 NCBITaxon:33317 ! only in taxon Protostomia [Term] id: CL:0000339 @@ -3876,7 +3875,7 @@ is_a: CL:0000130 ! neuron associated cell (sensu Nematoda and Protostomia) id: CL:0000341 name: pigment cell (sensu Nematoda and Protostomia) is_a: CL:0000147 ! pigment cell -relationship: never_in_taxon NCBITaxon:33511 ! Deuterostomia +property_value: RO:0002161 NCBITaxon:33511 [Term] id: CL:0000342 @@ -3884,7 +3883,7 @@ name: pigment cell (sensu Vertebrata) def: "Any animal cell containing pigment granules." [GOC:tfm, ISBN:0721662544] is_a: CL:0000147 ! pigment cell is_a: CL:0000255 ! eukaryotic cell -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata [Term] id: CL:0000343 @@ -3908,8 +3907,8 @@ name: dental papilla cell def: "A mesenchymal cell that is part of a small mass of condensed mesenchyme in the enamel organ; it differentiates into the dentin and dental pulp." [GOC:tfm, ISBN:0721662544] comment: Merge with odontoblast? is_a: CL:0008019 ! mesenchymal cell -relationship: develops_from CL:0000008 ! migratory cranial neural crest cell relationship: part_of UBERON:0001763 ! odontogenic papilla +relationship: RO:0002202 CL:0000008 ! develops from migratory cranial neural crest cell [Term] id: CL:0000346 @@ -3920,8 +3919,8 @@ is_a: CL:0000134 {is_inferred="true"} ! mesenchymal stem cell is_a: CL:0011026 ! progenitor cell intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: part_of UBERON:0000412 ! dermal papilla -relationship: develops_from CL:0000333 ! migratory neural crest cell relationship: part_of UBERON:0000412 ! dermal papilla +relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell [Term] id: CL:0000347 @@ -3931,8 +3930,8 @@ subset: eye_upper_slim is_a: CL:0000293 ! structural cell intersection_of: CL:0000293 ! structural cell intersection_of: part_of UBERON:0001773 ! sclera -relationship: develops_from CL:0000008 ! migratory cranial neural crest cell relationship: part_of UBERON:0001773 ! sclera +relationship: RO:0002202 CL:0000008 ! develops from migratory cranial neural crest cell [Term] id: CL:0000348 @@ -3942,8 +3941,8 @@ subset: eye_upper_slim is_a: CL:0000293 ! structural cell intersection_of: CL:0000293 ! structural cell intersection_of: part_of UBERON:0001776 ! optic choroid -relationship: develops_from CL:0000008 ! migratory cranial neural crest cell relationship: part_of UBERON:0001776 ! optic choroid +relationship: RO:0002202 CL:0000008 ! develops from migratory cranial neural crest cell [Term] id: CL:0000349 @@ -4036,7 +4035,7 @@ is_a: CL:4033054 ! perivascular cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0002049 ! vasculature relationship: part_of UBERON:0002049 ! vasculature -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000360 @@ -4094,8 +4093,8 @@ is_a: CL:0000007 ! early embryonic cell (metazoa) is_a: CL:0000255 ! eukaryotic cell is_a: CL:0010017 ! zygote intersection_of: CL:0010017 ! zygote -intersection_of: only_in_taxon NCBITaxon:33208 ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +intersection_of: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa [Term] id: CL:0000366 @@ -4134,7 +4133,7 @@ name: protoplast def: "The cell protoplasm after removal of the cell wall." [ISBN:08199377X] xref: MESH:D011523 is_a: CL:0000578 ! experimentally modified cell in vitro -relationship: never_in_taxon NCBITaxon:33208 ! Metazoa +property_value: RO:0002161 NCBITaxon:33208 [Term] id: CL:0000372 @@ -4151,7 +4150,7 @@ def: "A progenitor cell found in the larval epidermis of insects and that gives xref: FBbt:00001789 is_a: CL:0000255 ! eukaryotic cell is_a: CL:0011026 ! progenitor cell -relationship: only_in_taxon NCBITaxon:50557 ! Insecta +relationship: RO:0002160 NCBITaxon:50557 ! only in taxon Insecta [Term] id: CL:0000374 @@ -4220,7 +4219,7 @@ id: CL:0000383 name: nephrogenic mesenchyme stem cell is_a: CL:0000134 ! mesenchymal stem cell is_a: CL:0011026 ! progenitor cell -relationship: develops_from CL:0000134 ! mesenchymal stem cell +relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell [Term] id: CL:0000384 @@ -4233,7 +4232,7 @@ name: prohemocyte (sensu Nematoda and Protostomia) def: "A precursor of mature hemocytes." [doi:10.1016/B978-012369493-5.50008-0] xref: FBbt:00005062 is_a: CL:0008001 ! hematopoietic precursor cell -relationship: never_in_taxon NCBITaxon:33511 ! Deuterostomia +property_value: RO:0002161 NCBITaxon:33511 [Term] id: CL:0000386 @@ -4247,8 +4246,8 @@ def: "A blood cell of the circulatory system of arthropods." [doi:10.1016/B978-0 xref: FBbt:00005063 is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000390 ! blood cell (sensu Nematoda and Protostomia) -relationship: develops_from CL:0000385 ! prohemocyte (sensu Nematoda and Protostomia) -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda +relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda +relationship: RO:0002202 CL:0000385 ! develops from prohemocyte (sensu Nematoda and Protostomia) [Term] id: CL:0000388 @@ -4273,7 +4272,7 @@ is_a: CL:0000658 ! cuticle secreting cell id: CL:0000390 name: blood cell (sensu Nematoda and Protostomia) is_a: CL:0000081 ! blood cell -relationship: never_in_taxon NCBITaxon:33511 ! Deuterostomia +property_value: RO:0002161 NCBITaxon:33511 [Term] id: CL:0000391 @@ -4288,7 +4287,7 @@ id: CL:0000392 name: crystal cell def: "A hemocyte that synthesizes and secretes melanins as part of the antimicrobial immune response. It is characterized morphologically by crystal inclusions of phenoloxidases in its cytoplasm, hence its name." [doi:10.1016/B978-012369493-5.50008-0] is_a: CL:0000387 ! hemocyte (sensu Arthropoda) -relationship: develops_from CL:0000395 ! procrystal cell +relationship: RO:0002202 CL:0000395 ! develops from procrystal cell [Term] id: CL:0000393 @@ -4369,7 +4368,7 @@ is_a: CL:0000099 ! interneuron is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000099 ! interneuron intersection_of: RO:0002100 UBERON:0001017 ! has soma location central nervous system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000404 @@ -4429,7 +4428,7 @@ synonym: "roundworm hypodermal cell" BROAD [] xref: WBbt:0007846 is_a: CL:0000076 ! squamous epithelial cell is_a: CL:0000228 ! multinucleate cell -relationship: in_taxon NCBITaxon:6237 ! Caenorhabditis +relationship: RO:0002162 NCBITaxon:6237 ! in taxon Caenorhabditis [Term] id: CL:0000412 @@ -4483,7 +4482,7 @@ name: arcade cell def: "An epithelial cell found in C. elegans that firmly hold the outer body wall and the lips to the inner cylinder of the pharynx in a manner that keeps these organs from breaking apart, while still giving each organ freedom of movement during feeding." [GOC:tfm, http://www.wormatlas.org/ver1/handbook/hypodermis/hypsupportother.htm#arcadecells] xref: WBbt:0005793 is_a: CL:0000066 ! epithelial cell -relationship: in_taxon NCBITaxon:6237 ! Caenorhabditis +relationship: RO:0002162 NCBITaxon:6237 ! in taxon Caenorhabditis [Term] id: CL:0000419 @@ -4558,8 +4557,8 @@ comment: This term does not encompass all the cell types that may be found in an xref: FBbt:00007108 is_a: CL:0000146 ! simple columnar epithelial cell is_a: CL:0000255 ! eukaryotic cell -relationship: only_in_taxon NCBITaxon:50557 ! Insecta relationship: part_of UBERON:0000939 ! imaginal disc +relationship: RO:0002160 NCBITaxon:50557 ! only in taxon Insecta [Term] id: CL:0000430 @@ -4567,7 +4566,7 @@ name: xanthophore cell def: "A pigment cell derived from the neural crest. Contains cartenoid pigments in structures called pterinosomes or xanthosomes. This gives an appearance ranging from a golden yellow to orange and red." [SANBI:mhl] synonym: "xanthophore" RELATED [] is_a: CL:0000147 ! pigment cell -relationship: develops_from CL:0005002 ! xanthoblast +relationship: RO:0002202 CL:0005002 ! develops from xanthoblast [Term] id: CL:0000431 @@ -4575,7 +4574,7 @@ name: iridophore def: "A pigment cell derived from the neural crest. The cell contains flat light-reflecting platelets, probably of guanine, in stacks called reflecting platelets or iridisomes. The color-generating components produce a silver, gold, or iridescent color." [SANBI:mhl] synonym: "guanophore" RELATED [] is_a: CL:0000147 ! pigment cell -relationship: develops_from CL:0005001 ! iridoblast +relationship: RO:0002202 CL:0005001 ! develops from iridoblast [Term] id: CL:0000432 @@ -4586,7 +4585,7 @@ subset: human_reference_atlas synonym: "reticulum cell" EXACT [] xref: FMA:62877 is_a: CL:0000057 ! fibroblast -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/1472" xsd:string [Term] @@ -4602,7 +4601,7 @@ name: eccrine cell def: "A secretory cell that discharges its product without loss of cytoplasm." [ISBN:0198547684] subset: human_reference_atlas is_a: CL:0000150 ! glandular epithelial cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000435 @@ -4670,7 +4669,7 @@ synonym: "somatic stem cell" BROAD [doi:10.1016/j.devcel.2005.08.012] xref: FBbt:00004903 is_a: CL:0000036 ! epithelial fate stem cell is_a: CL:0000255 ! eukaryotic cell -relationship: only_in_taxon NCBITaxon:6656 {IAO:0000233="https://github.com/obophenotype/cell-ontology/issues/1943"} ! Arthropoda +relationship: RO:0002160 NCBITaxon:6656 {IAO:0000233="https://github.com/obophenotype/cell-ontology/issues/1943"} ! only in taxon Arthropoda [Term] id: CL:0000442 @@ -4683,7 +4682,7 @@ xref: BTO:0004267 xref: FMA:83037 xref: MESH:D020566 is_a: CL:0000473 ! defensive cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000443 @@ -4737,8 +4736,8 @@ synonym: "white fat cell" RELATED [] xref: CALOHA:TS-1119 xref: FMA:83434 is_a: CL:0000136 ! adipocyte -relationship: develops_from CL:0002334 ! preadipocyte relationship: part_of UBERON:0001347 ! white adipose tissue +relationship: RO:0002202 CL:0002334 ! develops from preadipocyte [Term] id: CL:0000449 @@ -4749,8 +4748,8 @@ synonym: "brown fat cell" EXACT [] xref: CALOHA:TS-0099 xref: FMA:83435 is_a: CL:0000136 ! adipocyte -relationship: develops_from CL:0002335 ! brown preadipocyte relationship: part_of UBERON:0001348 ! brown adipose tissue +relationship: RO:0002202 CL:0002335 ! develops from brown preadipocyte [Term] id: CL:0000451 @@ -4789,7 +4788,7 @@ relationship: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon relationship: CL:4030046 PR:000001024 ! lacks_plasma_membrane_part neural cell adhesion molecule 1 relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-spanning 4-domains subfamily A member 1 relationship: has_part GO:0042613 ! MHC class II protein complex -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000452 @@ -4814,9 +4813,9 @@ intersection_of: CL:0000990 ! conventional dendritic cell intersection_of: capable_of GO:0002828 ! regulation of type 2 immune response intersection_of: RO:0002104 PR:000001293 ! has plasma membrane part C-type lectin domain family 4 member K relationship: capable_of GO:0002828 ! regulation of type 2 immune response -relationship: develops_from CL:0000763 ! myeloid cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001293 ! has plasma membrane part C-type lectin domain family 4 member K +relationship: RO:0002202 CL:0000763 ! develops from myeloid cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000454 @@ -4887,7 +4886,7 @@ def: "A cell of mesodermal origin that is closely associated with the epithelium xref: FBbt:00003219 is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000680 ! muscle precursor cell -relationship: only_in_taxon NCBITaxon:50557 ! Insecta +relationship: RO:0002160 NCBITaxon:50557 ! only in taxon Insecta [Term] id: CL:0000463 @@ -4898,8 +4897,8 @@ xref: FBbt:00007325 is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000362 ! epidermal cell is_a: CL:0000710 ! neurecto-epithelial cell -relationship: develops_from CL:0000464 ! epidermoblast -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda +relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda +relationship: RO:0002202 CL:0000464 ! develops from epidermoblast [Term] id: CL:0000464 @@ -4908,7 +4907,7 @@ def: "An epidermal progenitor cell that arises from neuroectoderm and in turn gi xref: FBbt:00004994 is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0000710 ! neurecto-epithelial cell -relationship: develops_from CL:0000114 ! surface ectodermal cell +relationship: RO:0002202 CL:0000114 ! develops from surface ectodermal cell [Term] id: CL:0000465 @@ -4917,7 +4916,7 @@ def: "A precursor of the cells that form the dorsal vessel of arthropods." [doi: xref: FBbt:00001666 is_a: CL:0000255 ! eukaryotic cell is_a: CL:0010021 ! cardiac myoblast -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda +relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda [Term] id: CL:0000467 @@ -4943,7 +4942,7 @@ synonym: "neuroglioblast" EXACT [] xref: FBbt:00005147 is_a: CL:0000047 ! neural stem cell is_a: CL:0000255 ! eukaryotic cell -relationship: only_in_taxon NCBITaxon:33317 ! Protostomia +relationship: RO:0002160 NCBITaxon:33317 ! only in taxon Protostomia [Term] id: CL:0000469 @@ -4951,7 +4950,7 @@ name: ganglion mother cell def: "A neural progenitor cell that is the daughter of a neuroblast (sensu arthopoda). The progeny of ganglion mother cells develop into neurons, glia and (occasionally) epithelial cells." [] xref: FBbt:00005149 is_a: CL:0011020 ! neural progenitor cell -relationship: develops_from CL:0000338 ! neuroblast (sensu Nematoda and Protostomia) +relationship: RO:0002202 CL:0000338 ! develops from neuroblast (sensu Nematoda and Protostomia) [Term] id: CL:0000470 @@ -5009,8 +5008,8 @@ xref: FBbt:00004904 is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000500 ! follicular epithelial cell is_a: CL:2000064 ! ovarian surface epithelial cell -relationship: develops_from CL:0000441 ! follicle stem cell (sensu Arthropoda) -relationship: only_in_taxon NCBITaxon:50557 {source="https://github.com/obophenotype/cell-ontology/issues/589"} ! Insecta +relationship: RO:0002160 NCBITaxon:50557 {source="https://github.com/obophenotype/cell-ontology/issues/589"} ! only in taxon Insecta +relationship: RO:0002202 CL:0000441 ! develops from follicle stem cell (sensu Arthropoda) [Term] id: CL:0000478 @@ -5065,7 +5064,7 @@ is_a: CL:0000097 {is_inferred="true"} ! mast cell is_a: CL:0002320 ! connective tissue cell intersection_of: CL:0000097 ! mast cell intersection_of: part_of UBERON:0002384 ! connective tissue -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000485 @@ -5082,7 +5081,7 @@ intersection_of: capable_of GO:0002540 ! leukotriene production involved in infl intersection_of: part_of UBERON:0001961 ! mucosa-associated lymphoid tissue relationship: capable_of GO:0002540 ! leukotriene production involved in inflammatory response relationship: part_of UBERON:0001961 ! mucosa-associated lymphoid tissue -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000486 @@ -5103,7 +5102,7 @@ comment: Oenocytes are highly variable in size, shape, cluster formation and ana xref: FBbt:00004995 is_a: CL:0000151 ! secretory cell is_a: CL:0000255 ! eukaryotic cell -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda +relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda [Term] id: CL:0000488 @@ -5147,9 +5146,9 @@ is_a: CL:0000624 {is_inferred="true"} ! CD4-positive, alpha-beta T cell intersection_of: CL:0000624 ! CD4-positive, alpha-beta T cell intersection_of: capable_of GO:0001816 ! cytokine production relationship: capable_of GO:0001816 ! cytokine production -relationship: develops_from CL:0000896 ! activated CD4-positive, alpha-beta T cell relationship: output_of GO:0030217 ! T cell differentiation -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0000896 ! develops from activated CD4-positive, alpha-beta T cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000493 @@ -5203,8 +5202,8 @@ subset: human_reference_atlas xref: BTO:0002064 xref: FMA:83624 is_a: CL:0002320 ! connective tissue cell -relationship: develops_from CL:0000134 ! mesenchymal stem cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000500 @@ -5244,7 +5243,7 @@ xref: BTO:0002850 is_a: CL:0000593 ! androgen secreting cell is_a: CL:0002132 ! stromal cell of ovary relationship: part_of UBERON:0001305 ! ovarian follicle -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000504 @@ -5294,7 +5293,7 @@ name: gastrin secreting cell def: "A peptide hormone secreting cell that secretes gastrin." [GO:tfm] subset: human_reference_atlas is_a: CL:0000167 ! peptide hormone secreting cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000510 @@ -5332,8 +5331,8 @@ xref: FMA:84797 is_a: CL:0002494 ! cardiocyte is_a: CL:0010021 ! cardiac myoblast intersection_of: CL:0000056 ! myoblast -intersection_of: develops_into CL:0000746 ! cardiac muscle cell intersection_of: part_of UBERON:0001133 ! cardiac muscle tissue +intersection_of: RO:0002203 CL:0000746 ! develops into cardiac muscle cell relationship: part_of UBERON:0001133 ! cardiac muscle tissue [Term] @@ -5346,8 +5345,8 @@ synonym: "satellite cell" RELATED [] xref: FMA:84798 is_a: CL:0000056 ! myoblast intersection_of: CL:0000056 ! myoblast -intersection_of: develops_into CL:0000192 ! smooth muscle cell -relationship: develops_into CL:0000192 ! smooth muscle cell +intersection_of: RO:0002203 CL:0000192 ! develops into smooth muscle cell +relationship: RO:0002203 CL:0000192 ! develops into smooth muscle cell [Term] id: CL:0000515 @@ -5358,9 +5357,9 @@ xref: FMA:84799 is_a: CL:0000056 ! myoblast is_a: CL:0011026 ! progenitor cell intersection_of: CL:0000056 ! myoblast -intersection_of: develops_into CL:0008002 ! skeletal muscle fiber -relationship: develops_from CL:0000355 ! multi-potent skeletal muscle stem cell -relationship: develops_into CL:0008002 ! skeletal muscle fiber +intersection_of: RO:0002203 CL:0008002 ! develops into skeletal muscle fiber +relationship: RO:0002202 CL:0000355 ! develops from multi-potent skeletal muscle stem cell +relationship: RO:0002203 CL:0008002 ! develops into skeletal muscle fiber [Term] id: CL:0000516 @@ -5371,7 +5370,7 @@ synonym: "perineuronal satellite oligodendroglial cell" EXACT [] synonym: "satellite oligodendrocyte" EXACT [] xref: FMA:54550 is_a: CL:0000123 ! neuron associated cell (sensu Vertebrata) -relationship: develops_from CL:0000339 ! glioblast (sensu Vertebrata) +relationship: RO:0002202 CL:0000339 ! develops from glioblast (sensu Vertebrata) [Term] id: CL:0000517 @@ -5379,7 +5378,7 @@ name: macrophage derived foam cell def: "A type of foam cell derived from a macrophage containing lipids in small vacuoles and typically seen in atherolosclerotic lesions, as well as other conditions." [GOC:add, PMID:20213546] synonym: "lipophage" EXACT [] is_a: CL:0000891 ! foam cell -relationship: develops_from CL:0000235 ! macrophage +relationship: RO:0002202 CL:0000235 ! develops from macrophage [Term] id: CL:0000518 @@ -5387,29 +5386,29 @@ name: phagocyte (sensu Vertebrata) def: "A phagocyte in vertebrates that is able to phagocytosis." [GOC:tfm] is_a: CL:0000234 ! phagocyte is_a: CL:0000255 ! eukaryotic cell -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata [Term] id: CL:0000519 name: phagocyte (sensu Nematoda and Protostomia) def: "A phagocyte from organisms in the Nematoda or Protostomia clades." [GOC:tfm] is_a: CL:0000234 ! phagocyte -relationship: never_in_taxon NCBITaxon:33511 ! Deuterostomia +property_value: RO:0002161 NCBITaxon:33511 [Term] id: CL:0000520 name: prokaryotic cell xref: MESH:D011387 is_a: CL:0000000 ! cell -relationship: never_in_taxon NCBITaxon:2759 ! Eukaryota +property_value: RO:0002161 NCBITaxon:2759 [Term] id: CL:0000521 name: fungal cell is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell -intersection_of: only_in_taxon NCBITaxon:4751 ! Fungi -relationship: only_in_taxon NCBITaxon:4751 ! Fungi +intersection_of: RO:0002160 NCBITaxon:4751 ! only in taxon Fungi +relationship: RO:0002160 NCBITaxon:4751 ! only in taxon Fungi [Term] id: CL:0000522 @@ -5424,7 +5423,7 @@ def: "A cell from the inner layer of the trophoblast of the early mammalian embr subset: human_reference_atlas xref: FMA:83042 is_a: CL:0000351 ! trophoblast cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000524 @@ -5449,7 +5448,7 @@ is_a: CL:0000351 ! trophoblast cell intersection_of: CL:0000351 ! trophoblast cell intersection_of: bearer_of PATO:0001908 ! multinucleate relationship: part_of UBERON:0000371 ! syncytiotrophoblast -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/2100" xsd:string [Term] @@ -5460,7 +5459,7 @@ subset: human_reference_atlas synonym: "input neuron" EXACT [] xref: FMA:87653 is_a: CL:0000540 ! neuron -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000527 @@ -5488,7 +5487,7 @@ name: primary neuron (sensu Teleostei) def: "A neuron that develops during the early segmentation stages in teleosts, before the neural tube is formed." [doi:10.1242/dev.108.1.121, PMID:1842357] is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000540 ! neuron -relationship: only_in_taxon NCBITaxon:32443 {IAO:0000233="https://github.com/obophenotype/cell-ontology/pull/1950"} ! Teleostei +relationship: RO:0002160 NCBITaxon:32443 {IAO:0000233="https://github.com/obophenotype/cell-ontology/pull/1950"} ! only in taxon Teleostei [Term] id: CL:0000531 @@ -5525,7 +5524,7 @@ name: secondary neuron (sensu Teleostei) def: "A neuron of teleosts that develops later than a primary neuron, typically during the larval stages." [doi:10.1242/dev.108.1.121, PMID:1842357] is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000540 ! neuron -relationship: only_in_taxon NCBITaxon:32443 {IAO:0000233="https://github.com/obophenotype/cell-ontology/pull/1950"} ! Teleostei +relationship: RO:0002160 NCBITaxon:32443 {IAO:0000233="https://github.com/obophenotype/cell-ontology/pull/1950"} ! only in taxon Teleostei [Term] id: CL:0000536 @@ -5575,9 +5574,9 @@ is_a: CL:0000393 ! electrically responsive cell is_a: CL:0000404 ! electrically signaling cell is_a: CL:0002319 ! neural cell relationship: capable_of GO:0019226 ! transmission of nerve impulse -relationship: develops_from CL:0000031 {gci_relation="in_taxon", gci_filler="NCBITaxon:7742", xref="https://github.com/obophenotype/cell-ontology/issues/757"} ! neuroblast (sensu Vertebrata) -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://www.swissbiopics.org/api/image/Neuron_cells.svg" xsd:anyURI +relationship: RO:0002202 CL:0000031 {gci_filler="NCBITaxon:7742", gci_relation="RO:0002162", xref="https://github.com/obophenotype/cell-ontology/issues/757"} ! develops from neuroblast (sensu Vertebrata) +property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Neuron_cells.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000541 @@ -5588,7 +5587,7 @@ xref: BTO:0003217 xref: FMA:83377 is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0011026 ! progenitor cell -relationship: develops_from CL:0000333 ! migratory neural crest cell +relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell [Term] id: CL:0000542 @@ -5611,10 +5610,10 @@ intersection_of: has_part CL:0017500 ! neutrophillic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin disjoint_from: CL:0000766 ! myeloid leukocyte relationship: bearer_of PATO:0040072 ! high nuclear/cytoplasmic ratio -relationship: develops_from CL:0000051 ! common lymphoid progenitor relationship: has_part CL:0017500 ! neutrophillic cytoplasm relationship: has_part GO:0000792 ! heterochromatin -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0000051 ! develops from common lymphoid progenitor +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000543 @@ -5656,8 +5655,8 @@ intersection_of: RO:0002104 PR:000001207 ! has plasma membrane part C-X-C chemok relationship: capable_of GO:0032609 ! type II interferon production relationship: CL:4030046 PR:000001202 ! lacks_plasma_membrane_part C-C chemokine receptor type 6 relationship: has_part PR:000001835 ! T-box transcription factor TBX21 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001207 ! has plasma membrane part C-X-C chemokine receptor type 3 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000546 @@ -5686,7 +5685,7 @@ intersection_of: CL:4030046 PR:000001207 ! lacks_plasma_membrane_part C-X-C chem intersection_of: has_part PR:000001941 ! trans-acting T-cell-specific transcription factor GATA-3 relationship: capable_of GO:0032633 ! interleukin-4 production relationship: has_part PR:000001941 ! trans-acting T-cell-specific transcription factor GATA-3 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000547 @@ -5729,10 +5728,10 @@ relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-span relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD5 relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G -relationship: develops_from CL:0000038 ! erythroid progenitor cell relationship: has_part CL:0017503 ! basophilic cytoplasm relationship: has_part GO:0005730 ! nucleolus relationship: RO:0002104 PR:000001945 ! has plasma membrane part transferrin receptor protein 1 +relationship: RO:0002202 CL:0000038 ! develops from erythroid progenitor cell [Term] id: CL:0000548 @@ -5742,7 +5741,7 @@ subset: cellxgene_subset subset: ubprop:upper_level synonym: "metazoan cell" EXACT [] relationship: term_tracker_item https://github.com/obophenotype/cell-ontology/issues/2124 -property_value: depiction "https://www.swissbiopics.org/api/image/Animal_cells.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Animal_cells.svg" xsd:anyURI is_obsolete: true replaced_by: CL:0000000 @@ -5782,10 +5781,10 @@ intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017504 ! polychromatophilic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin intersection_of: RO:0002104 PR:000001945 ! has plasma membrane part transferrin receptor protein 1 -relationship: develops_from CL:0000549 ! basophilic erythroblast relationship: has_part CL:0017504 ! polychromatophilic cytoplasm relationship: has_part GO:0000792 ! heterochromatin relationship: RO:0002104 PR:000001945 ! has plasma membrane part transferrin receptor protein 1 +relationship: RO:0002202 CL:0000549 ! develops from basophilic erythroblast [Term] id: CL:0000551 @@ -5806,9 +5805,9 @@ is_a: CL:0000765 {is_inferred="true"} ! erythroblast intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017502 ! acidophilic cytoplasm intersection_of: participates_in GO:0030263 ! apoptotic chromosome condensation -relationship: develops_from CL:0000550 ! polychromatophilic erythroblast relationship: has_part CL:0017502 ! acidophilic cytoplasm relationship: participates_in GO:0030263 ! apoptotic chromosome condensation +relationship: RO:0002202 CL:0000550 ! develops from polychromatophilic erythroblast [Term] id: CL:0000553 @@ -5862,8 +5861,8 @@ relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surfac relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -relationship: develops_from CL:0000050 ! megakaryocyte-erythroid progenitor cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0000050 ! develops from megakaryocyte-erythroid progenitor cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000554 @@ -5894,8 +5893,8 @@ xref: FMA:83555 is_a: CL:0000763 {is_inferred="true"} ! myeloid cell disjoint_from: CL:0000764 ! erythroid lineage cell relationship: bearer_of PATO:0001393 ! euploid -relationship: develops_from CL:0000553 ! megakaryocyte progenitor cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0000553 ! develops from megakaryocyte progenitor cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000557 @@ -5931,8 +5930,8 @@ relationship: CL:4030045 PR:000007857 ! lacks_part erythroid transcription facto relationship: CL:4030045 PR:000007858 ! lacks_part endothelial transcription factor GATA-2 relationship: has_part PR:000001944 ! transcription factor PU.1 relationship: has_part PR:000005307 ! CCAAT/enhancer-binding protein alpha -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001865 ! has plasma membrane part interleukin-3 receptor class 2 alpha chain +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000558 @@ -5971,8 +5970,8 @@ relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-span relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD5 relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G -relationship: develops_from CL:0000552 ! orthochromatic erythroblast relationship: RO:0002104 PR:000001945 ! has plasma membrane part transferrin receptor protein 1 +relationship: RO:0002202 CL:0000552 ! develops from orthochromatic erythroblast [Term] id: CL:0000559 @@ -5990,10 +5989,10 @@ intersection_of: CL:0002194 ! monopoietic cell intersection_of: capable_of GO:0030224 ! monocyte differentiation intersection_of: has_part GO:0042582 ! azurophil granule intersection_of: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M -relationship: develops_from CL:0000040 ! monoblast relationship: has_part GO:0042582 ! azurophil granule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M +relationship: RO:0002202 CL:0000040 ! develops from monoblast +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000560 @@ -6020,13 +6019,13 @@ intersection_of: RO:0002104 PR:000001337 ! has plasma membrane part complement r intersection_of: RO:0002104 PR:000001580 ! has plasma membrane part fMet-Leu-Phe receptor relationship: CL:4030046 PR:000009129 ! lacks_plasma_membrane_part integrin alpha-4 relationship: CL:4030046 PR:000010543 ! lacks_plasma_membrane_part myeloperoxidase -relationship: develops_from CL:0000582 ! neutrophilic metamyelocyte relationship: has_part CL:0017506 ! banded nucleus relationship: has_part PR:000001944 ! transcription factor PU.1 relationship: has_part PR:000005307 ! CCAAT/enhancer-binding protein alpha relationship: has_part PR:000007597 ! protein c-Fos relationship: RO:0002104 PR:000001337 ! has plasma membrane part complement receptor type 1 relationship: RO:0002104 PR:000001580 ! has plasma membrane part fMet-Leu-Phe receptor +relationship: RO:0002202 CL:0000582 ! develops from neutrophilic metamyelocyte [Term] id: CL:0000561 @@ -6042,10 +6041,10 @@ xref: BTO:0004044 xref: FMA:67766 is_a: CL:0000099 ! interneuron is_a: CL:0009004 ! retinal cell -relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0000966 ! retina -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002120 CL:0000740 ! synapsed to retinal ganglion cell +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000562 @@ -6057,7 +6056,7 @@ is_a: CL:0000232 {is_inferred="true"} ! erythrocyte is_a: CL:0002242 ! nucleate cell intersection_of: CL:0000232 ! erythrocyte intersection_of: bearer_of PATO:0002505 ! nucleated -relationship: develops_from CL:0002421 ! nucleated reticulocyte +relationship: RO:0002202 CL:0002421 ! develops from nucleated reticulocyte [Term] id: CL:0000563 @@ -6086,12 +6085,12 @@ intersection_of: has_part PR:000007857 ! erythroid transcription factor intersection_of: has_part PR:000010543 ! myeloperoxidase intersection_of: has_part PR:000014362 ! runt-related transcription factor 1 relationship: CL:4030045 PR:000009978 ! lacks_part lactotransferrin -relationship: develops_from CL:0000042 ! neutrophilic myeloblast relationship: has_part PR:000001944 ! transcription factor PU.1 relationship: has_part PR:000005307 ! CCAAT/enhancer-binding protein alpha relationship: has_part PR:000007857 ! erythroid transcription factor relationship: has_part PR:000010543 ! myeloperoxidase relationship: has_part PR:000014362 ! runt-related transcription factor 1 +relationship: RO:0002202 CL:0000042 ! develops from neutrophilic myeloblast [Term] id: CL:0000565 @@ -6113,10 +6112,10 @@ intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: RO:0002104 PR:000001444 ! has plasma membrane part cadherin-5 intersection_of: RO:0002104 PR:000002112 ! has plasma membrane part vascular endothelial growth factor receptor 2 intersection_of: RO:0002104 PR:000016043 ! has plasma membrane part T-cell acute lymphocytic leukemia protein 1 -relationship: develops_from CL:0000134 ! mesenchymal stem cell relationship: RO:0002104 PR:000001444 ! has plasma membrane part cadherin-5 relationship: RO:0002104 PR:000002112 ! has plasma membrane part vascular endothelial growth factor receptor 2 relationship: RO:0002104 PR:000016043 ! has plasma membrane part T-cell acute lymphocytic leukemia protein 1 +relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell [Term] id: CL:0000567 @@ -6141,8 +6140,8 @@ subset: cellxgene_subset is_a: CL:0008019 ! mesenchymal cell is_a: CL:2000073 ! migratory cardiac neural crest cell intersection_of: CL:0008019 ! mesenchymal cell -intersection_of: develops_into CL:0002494 ! cardiocyte -relationship: develops_into CL:0002494 ! cardiocyte +intersection_of: RO:0002203 CL:0002494 ! develops into cardiocyte +relationship: RO:0002203 CL:0002494 ! develops into cardiocyte [Term] id: CL:0000570 @@ -6165,16 +6164,16 @@ intersection_of: capable_of GO:0014046 ! dopamine secretion intersection_of: capable_of GO:0036161 ! calcitonin secretion intersection_of: RO:0002104 PR:000001024 ! has plasma membrane part neural cell adhesion molecule 1 relationship: capable_of GO:0014046 ! dopamine secretion -relationship: develops_from CL:0000333 ! migratory neural crest cell relationship: part_of UBERON:0001747 ! parenchyma of thyroid gland relationship: RO:0002104 PR:000001024 ! has plasma membrane part neural cell adhesion molecule 1 +relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell [Term] id: CL:0000571 name: leucophore def: "A pigment cell derived from the neural crest. Contains uric acid or other purine crystals deposited in stacks called leucosomes. The crystals reflect light and this gives a white appearance under white light." [SANBI:mhl] is_a: CL:0000147 ! pigment cell -relationship: develops_from CL:0005003 ! leucoblast +relationship: RO:0002202 CL:0005003 ! develops from leucoblast [Term] id: CL:0000573 @@ -6187,15 +6186,15 @@ xref: BTO:0001036 xref: CALOHA:TS-0866 xref: FMA:67748 is_a: CL:0010009 ! camera-type eye photoreceptor cell -relationship: develops_from CL:0002672 ! retinal progenitor cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0002672 ! develops from retinal progenitor cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000574 name: erythrophore def: "A pigment cell derived from the neural crest. Contains pteridine and/or carotenoid pigments in structures called pterinosomes or erythrosomes. This gives an orange to red appearance." [SANBI:mhl] is_a: CL:0000147 ! pigment cell -relationship: develops_from CL:0005004 ! pigment erythroblast +relationship: RO:0002202 CL:0005004 ! develops from pigment erythroblast [Term] id: CL:0000575 @@ -6214,7 +6213,7 @@ is_a: CL:0002159 ! general ecto-epithelial cell intersection_of: CL:0000076 ! squamous epithelial cell intersection_of: part_of UBERON:0001772 ! corneal epithelium relationship: part_of UBERON:0001772 ! corneal epithelium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000576 @@ -6239,8 +6238,8 @@ intersection_of: capable_of GO:0043011 ! myeloid dendritic cell differentiation relationship: capable_of GO:0030225 ! macrophage differentiation relationship: capable_of GO:0030316 ! osteoclast differentiation relationship: capable_of GO:0043011 ! myeloid dendritic cell differentiation -relationship: develops_from CL:0000559 ! promonocyte -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0000559 ! develops from promonocyte +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000577 @@ -6261,7 +6260,7 @@ is_a: CL:0000458 ! serotonin secreting cell is_a: CL:0000506 ! enkephalin secreting cell is_a: CL:0002251 ! epithelial cell of alimentary canal relationship: part_of UBERON:0004786 ! gastrointestinal system mucosa -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000578 @@ -6330,7 +6329,7 @@ is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000864 ! tissue-resident macrophage intersection_of: capable_of GO:0042742 ! defense response to bacterium intersection_of: CL:4030046 GO:0042613 ! lacks_plasma_membrane_part MHC class II protein complex -intersection_of: located_in UBERON:0001179 ! peritoneal cavity +intersection_of: RO:0001025 UBERON:0001179 ! located in peritoneal cavity intersection_of: RO:0002104 PR:000001807 ! has plasma membrane part C-type lectin domain family 7 member A intersection_of: RO:0002104 PR:000002064 ! has plasma membrane part macrosialin intersection_of: RO:0002104 PR:000006172 ! has plasma membrane part CD209 molecule-like protein B @@ -6339,7 +6338,7 @@ intersection_of: RO:0015015 PR:000001813 ! has high plasma membrane amount adhes intersection_of: RO:0015015 PR:000002062 ! has high plasma membrane amount macrophage colony-stimulating factor 1 receptor relationship: capable_of GO:0042742 ! defense response to bacterium relationship: CL:4030046 GO:0042613 ! lacks_plasma_membrane_part MHC class II protein complex -relationship: located_in UBERON:0001179 ! peritoneal cavity +relationship: RO:0001025 UBERON:0001179 ! located in peritoneal cavity relationship: RO:0002104 PR:000001807 ! has plasma membrane part C-type lectin domain family 7 member A relationship: RO:0002104 PR:000002064 ! has plasma membrane part macrosialin relationship: RO:0002104 PR:000006172 ! has plasma membrane part CD209 molecule-like protein B @@ -6376,7 +6375,6 @@ intersection_of: RO:0002104 PR:000001892 ! has plasma membrane part CD33 molecul intersection_of: RO:0002104 PR:000001932 ! has plasma membrane part signal transducer CD24 intersection_of: RO:0002104 PR:000002031 ! has plasma membrane part aminopeptidase N relationship: CL:4030046 PR:000001580 ! lacks_plasma_membrane_part fMet-Leu-Phe receptor -relationship: develops_from CL:0000580 ! neutrophilic myelocyte relationship: has_part CL:0017502 ! acidophilic cytoplasm relationship: has_part CL:0017507 ! reniform nucleus relationship: has_part GO:0000792 ! heterochromatin @@ -6393,6 +6391,7 @@ relationship: RO:0002104 PR:000001483 ! has plasma membrane part low affinity im relationship: RO:0002104 PR:000001892 ! has plasma membrane part CD33 molecule relationship: RO:0002104 PR:000001932 ! has plasma membrane part signal transducer CD24 relationship: RO:0002104 PR:000002031 ! has plasma membrane part aminopeptidase N +relationship: RO:0002202 CL:0000580 ! develops from neutrophilic myelocyte [Term] id: CL:0000583 @@ -6412,7 +6411,7 @@ is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000864 ! tissue-resident macrophage intersection_of: capable_of GO:0019882 ! antigen processing and presentation intersection_of: CL:4030046 PR:000001206 ! lacks_plasma_membrane_part CX3C chemokine receptor 1 -intersection_of: located_in UBERON:0002299 ! alveolus of lung +intersection_of: RO:0001025 UBERON:0002299 ! located in alveolus of lung intersection_of: RO:0002104 PR:000001013 ! has plasma membrane part integrin alpha-X intersection_of: RO:0002104 PR:000001807 ! has plasma membrane part C-type lectin domain family 7 member A intersection_of: RO:0002104 PR:000001813 ! has plasma membrane part adhesion G protein-coupled receptor E1 @@ -6421,8 +6420,7 @@ intersection_of: RO:0002104 PR:000002064 ! has plasma membrane part macrosialin intersection_of: RO:0002104 PR:000002972 ! has plasma membrane part macrophage mannose receptor 1 intersection_of: RO:0015016 PR:000001012 ! has low plasma membrane amount integrin alpha-M relationship: CL:4030046 PR:000001206 ! lacks_plasma_membrane_part CX3C chemokine receptor 1 -relationship: located_in UBERON:0002299 ! alveolus of lung -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0001025 UBERON:0002299 ! located in alveolus of lung relationship: RO:0002104 PR:000001013 ! has plasma membrane part integrin alpha-X relationship: RO:0002104 PR:000001807 ! has plasma membrane part C-type lectin domain family 7 member A relationship: RO:0002104 PR:000001813 ! has plasma membrane part adhesion G protein-coupled receptor E1 @@ -6430,6 +6428,7 @@ relationship: RO:0002104 PR:000001931 ! has plasma membrane part sialoadhesin relationship: RO:0002104 PR:000002064 ! has plasma membrane part macrosialin relationship: RO:0002104 PR:000002972 ! has plasma membrane part macrophage mannose receptor 1 relationship: RO:0015016 PR:000001012 ! has low plasma membrane amount integrin alpha-M +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000584 @@ -6445,7 +6444,7 @@ xref: MESH:D020895 is_a: CL:0000239 ! brush border epithelial cell is_a: CL:0000677 ! gut absorptive cell is_a: CL:0002563 ! intestinal epithelial cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000585 @@ -6501,7 +6500,7 @@ synonym: "theca lutein cell" EXACT [] xref: BTO:0002850 xref: FMA:18690 is_a: CL:0000175 ! luteal cell -relationship: develops_from CL:0000503 ! theca cell +relationship: RO:0002202 CL:0000503 ! develops from theca cell [Term] id: CL:0000591 @@ -6518,7 +6517,7 @@ synonym: "granulosoluteocytus" RELATED [] xref: FMA:18689 is_a: CL:0000175 ! luteal cell is_a: CL:0000177 ! testosterone secreting cell -relationship: develops_from CL:0000501 ! granulosa cell +relationship: RO:0002202 CL:0000501 ! develops from granulosa cell [Term] id: CL:0000593 @@ -6549,7 +6548,7 @@ is_a: CL:0000225 ! anucleate cell is_a: CL:0000232 {is_inferred="true"} ! erythrocyte intersection_of: CL:0000232 ! erythrocyte intersection_of: bearer_of PATO:0001405 ! anucleate -relationship: develops_from CL:0002422 ! enucleated reticulocyte +relationship: RO:0002202 CL:0002422 ! develops from enucleated reticulocyte [Term] id: CL:0000596 @@ -6630,8 +6629,8 @@ xref: BTO:0001024 xref: CALOHA:TS-0870 xref: FMA:67747 is_a: CL:0010009 ! camera-type eye photoreceptor cell -relationship: develops_from CL:0002672 ! retinal progenitor cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0002672 ! develops from retinal progenitor cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000605 @@ -6723,7 +6722,6 @@ relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surfac relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -relationship: develops_from CL:0000557 ! granulocyte monocyte progenitor cell relationship: has_part PR:000001944 ! transcription factor PU.1 relationship: has_part PR:000005307 ! CCAAT/enhancer-binding protein alpha relationship: has_part PR:000007857 ! erythroid transcription factor @@ -6732,6 +6730,7 @@ relationship: RO:0002104 PR:000001408 ! has plasma membrane part ADP-ribosyl cyc relationship: RO:0002104 PR:000001865 ! has plasma membrane part interleukin-3 receptor class 2 alpha chain relationship: RO:0002104 PR:000001867 ! has plasma membrane part interleukin-5 receptor subunit alpha relationship: RO:0002104 PR:000002065 ! has plasma membrane part mast/stem cell growth factor receptor +relationship: RO:0002202 CL:0000557 ! develops from granulocyte monocyte progenitor cell [Term] id: CL:0000612 @@ -6805,10 +6804,10 @@ relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002065 ! lacks_plasma_membrane_part mast/stem cell growth factor receptor relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -relationship: develops_from CL:0002028 ! basophil mast progenitor cell relationship: has_part PR:000005307 ! CCAAT/enhancer-binding protein alpha relationship: has_part PR:000007857 ! erythroid transcription factor relationship: has_part PR:000007858 ! endothelial transcription factor GATA-2 +relationship: RO:0002202 CL:0002028 ! develops from basophil mast progenitor cell relationship: RO:0015015 PR:000007431 ! has high plasma membrane amount high affinity immunoglobulin epsilon receptor subunit alpha relationship: RO:0015016 PR:000016401 ! has low plasma membrane amount transmembrane emp24 domain-containing protein 1 @@ -6935,8 +6934,8 @@ relationship: capable_of GO:0002228 ! natural killer cell mediated immunity relationship: capable_of GO:0050776 ! regulation of immune response relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-spanning 4-domains subfamily A member 1 relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule -relationship: develops_from CL:0000825 ! pro-NK cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0000825 ! develops from pro-NK cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000624 @@ -6953,8 +6952,8 @@ intersection_of: CL:4030046 PR:000025402 ! lacks_plasma_membrane_part T cell rec intersection_of: RO:0002104 PR:000001004 ! has plasma membrane part CD4 molecule disjoint_from: CL:0000625 ! CD8-positive, alpha-beta T cell relationship: CL:4030046 PR:000025402 ! lacks_plasma_membrane_part T cell receptor co-receptor CD8 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001004 ! has plasma membrane part CD4 molecule +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000625 @@ -6970,8 +6969,8 @@ intersection_of: CL:0000791 ! mature alpha-beta T cell intersection_of: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecule intersection_of: RO:0002104 PR:000025402 ! has plasma membrane part T cell receptor co-receptor CD8 relationship: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000025402 ! has plasma membrane part T cell receptor co-receptor CD8 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000626 @@ -6985,11 +6984,11 @@ is_a: CL:1001434 ! olfactory bulb interneuron intersection_of: CL:0000120 ! granule cell intersection_of: RO:0002100 UBERON:0005378 ! has soma location olfactory bulb granule cell layer relationship: RO:0002100 UBERON:0005378 ! has soma location olfactory bulb granule cell layer +relationship: RO:0002103 CL:1001502 ! synapsed by mitral cell +relationship: RO:0002103 CL:1001503 ! synapsed by olfactory bulb tufted cell relationship: RO:0002120 CL:1001502 ! synapsed to mitral cell relationship: RO:0002120 CL:1001503 ! synapsed to olfactory bulb tufted cell relationship: RO:0002428 GO:0007608 ! involved in regulation of sensory perception of smell -relationship: synapsed_by CL:1001502 ! mitral cell -relationship: synapsed_by CL:1001503 ! olfactory bulb tufted cell [Term] id: CL:0000627 @@ -7049,8 +7048,8 @@ intersection_of: CL:0002320 ! connective tissue cell intersection_of: part_of UBERON:0002107 ! liver intersection_of: RO:0002104 PR:000007939 ! has plasma membrane part glial fibrillary acidic protein relationship: part_of UBERON:0002107 ! liver -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000007939 ! has plasma membrane part glial fibrillary acidic protein +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000633 @@ -7094,7 +7093,7 @@ xref: BTO:0003064 is_a: CL:0000681 ! radial glial cell is_a: CL:0009004 ! retinal cell relationship: part_of UBERON:0000966 ! retina -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000637 @@ -7164,7 +7163,7 @@ synonym: "Bergmann astrocyte" EXACT [] synonym: "Bergmann glial cell of cerebellum" EXACT [] xref: FMA:54559 is_a: CL:0000127 ! astrocyte -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000645 @@ -7185,7 +7184,7 @@ subset: human_reference_atlas xref: BTO:0000939 xref: FMA:62516 is_a: CL:0000036 ! epithelial fate stem cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000647 @@ -7207,9 +7206,9 @@ intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: bearer_of PATO:0001908 ! multinucleate intersection_of: participates_in GO:0002432 ! granuloma formation intersection_of: participates_in GO:0002544 ! chronic inflammatory response -relationship: develops_from CL:0000235 ! macrophage relationship: participates_in GO:0002432 ! granuloma formation relationship: participates_in GO:0002544 ! chronic inflammatory response +relationship: RO:0002202 CL:0000235 ! develops from macrophage [Term] id: CL:0000648 @@ -7228,7 +7227,7 @@ intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0002001 ! renin secretion into blood stream intersection_of: part_of UBERON:0002113 ! kidney relationship: capable_of GO:0002001 ! renin secretion into blood stream -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000649 @@ -7241,7 +7240,7 @@ synonym: "prickle cell of epidermis" EXACT [] xref: FMA:69059 is_a: CL:0000312 ! keratinocyte relationship: part_of UBERON:0002026 ! stratum spinosum of epidermis -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000650 @@ -7255,7 +7254,7 @@ xref: CALOHA:TS-0617 xref: FMA:70972 xref: MESH:D050527 is_a: CL:0000669 ! pericyte -relationship: develops_from CL:0000134 ! mesenchymal stem cell +relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell [Term] id: CL:0000651 @@ -7296,7 +7295,7 @@ is_a: CL:1000450 ! epithelial cell of glomerular capsule intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0005751 ! glomerular visceral epithelium relationship: part_of UBERON:0005751 ! glomerular visceral epithelium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/1460" xsd:string [Term] @@ -7311,8 +7310,8 @@ is_a: CL:0000023 {is_inferred="true"} ! oocyte intersection_of: CL:0000023 ! oocyte intersection_of: CL:4030044 GO:0051321 ! has_not_completed meiotic cell cycle relationship: CL:4030044 GO:0051321 ! has_not_completed meiotic cell cycle -relationship: develops_from CL:0000024 ! oogonial cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0000024 ! develops from oogonial cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000655 @@ -7325,7 +7324,7 @@ is_a: CL:0000023 {is_inferred="true"} ! oocyte intersection_of: CL:0000023 ! oocyte intersection_of: CL:4030044 GO:0007147 ! has_not_completed female meiosis II relationship: CL:4030044 GO:0007147 ! has_not_completed female meiosis II -relationship: develops_from CL:0000654 ! primary oocyte +relationship: RO:0002202 CL:0000654 ! develops from primary oocyte [Term] id: CL:0000656 @@ -7355,7 +7354,7 @@ intersection_of: CL:0000017 ! spermatocyte intersection_of: bearer_of PATO:0001375 ! haploid intersection_of: capable_of GO:0007142 ! male meiosis II relationship: capable_of GO:0007142 ! male meiosis II -relationship: develops_from CL:0000656 ! primary spermatocyte +relationship: RO:0002202 CL:0000656 ! develops from primary spermatocyte [Term] id: CL:0000658 @@ -7451,7 +7450,7 @@ is_a: CL:0000183 ! contractile cell is_a: CL:0000630 ! supporting cell is_a: CL:0002320 ! connective tissue cell is_a: CL:0008034 ! mural cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000670 @@ -7541,7 +7540,7 @@ is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0061535 ! glutamate secretion, neurotransmission relationship: capable_of GO:0061535 ! glutamate secretion, neurotransmission -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000680 @@ -7550,9 +7549,9 @@ def: "A non-terminally differentiated cell that is capable of developing into a subset: cellxgene_subset is_a: CL:0000055 ! non-terminally differentiated cell intersection_of: CL:0011115 ! precursor cell -intersection_of: develops_into CL:0000187 ! muscle cell -relationship: develops_from CL:0000222 ! mesodermal cell -relationship: develops_into CL:0000187 ! muscle cell +intersection_of: RO:0002203 CL:0000187 ! develops into muscle cell +relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell +relationship: RO:0002203 CL:0000187 ! develops into muscle cell [Term] id: CL:0000681 @@ -7562,7 +7561,7 @@ comment: Unlike that of mammals, the brain of adult teleost fish exhibits an int subset: cellxgene_subset synonym: "forebrain radial glial cell" NARROW [] is_a: CL:0000125 ! glial cell -relationship: develops_from CL:0000710 ! neurecto-epithelial cell +relationship: RO:0002202 CL:0000710 ! develops from neurecto-epithelial cell [Term] id: CL:0000682 @@ -7580,7 +7579,7 @@ is_a: CL:0000473 ! defensive cell is_a: CL:0000627 ! transporting cell is_a: CL:0002251 ! epithelial cell of alimentary canal relationship: part_of UBERON:0003929 ! digestive tract epithelium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000683 @@ -7612,7 +7611,7 @@ is_a: CL:0000710 ! neurecto-epithelial cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0033326 ! cerebrospinal fluid secretion relationship: capable_of GO:0033326 ! cerebrospinal fluid secretion -relationship: develops_from CL:0000333 ! migratory neural crest cell +relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell [Term] id: CL:0000687 @@ -7694,8 +7693,8 @@ synonym: "Horizontal cells of Cajal" EXACT [WikipediaVersioned:Cajal–Retzius_c is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) is_a: CL:2000029 ! central nervous system neuron relationship: bearer_of PATO:0070006 ! cortical bipolar morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: RO:0002100 UBERON:0010403 ! has soma location brain marginal zone +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:0000696 @@ -7795,8 +7794,8 @@ is_a: CL:0002319 ! neural cell intersection_of: CL:0000065 ! ependymal cell intersection_of: part_of UBERON:0001886 ! choroid plexus relationship: part_of UBERON:0001886 ! choroid plexus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2023-08-04T08:48:30Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2023-08-04T08:48:30Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000707 @@ -7836,8 +7835,8 @@ xref: FMA:70557 is_a: CL:0000075 ! columnar/cuboidal epithelial cell is_a: CL:0002077 ! ecto-epithelial cell intersection_of: CL:0002077 ! ecto-epithelial cell -intersection_of: develops_from CL:0000133 ! neurectodermal cell -relationship: develops_from CL:0000133 ! neurectodermal cell +intersection_of: RO:0002202 CL:0000133 ! develops from neurectodermal cell +relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell [Term] id: CL:0000711 @@ -7848,8 +7847,8 @@ xref: BTO:0002236 xref: MESH:D054885 is_a: CL:0000154 ! protein secreting cell is_a: CL:0002174 ! follicular cell of ovary -relationship: develops_from CL:0000501 ! granulosa cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0000501 ! develops from granulosa cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000712 @@ -7920,7 +7919,7 @@ id: CL:0000722 name: cystoblast is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000586 ! germ cell -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda +relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda [Term] id: CL:0000723 @@ -8065,10 +8064,10 @@ intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0002505 ! nucleated intersection_of: capable_of GO:0001667 ! ameboidal-type cell migration relationship: capable_of GO:0001667 ! ameboidal-type cell migration -relationship: develops_from CL:0000037 ! hematopoietic stem cell -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0002405 ! immune system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002202 CL:0000037 ! develops from hematopoietic stem cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000740 @@ -8085,8 +8084,8 @@ xref: BTO:0001800 xref: FMA:67765 xref: MESH:D012165 is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002100 UBERON:0000966 ! has soma location retina +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000741 @@ -8108,7 +8107,7 @@ def: "Chondrocyte that is terminally differentiated, produces type X collagen, i comment: is hypertrophic pathological or normal? and can it be described using a pato term? subset: human_reference_atlas is_a: CL:0000138 ! chondrocyte -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000744 @@ -8128,8 +8127,8 @@ synonym: "HCs" RELATED OMO:0003004 [doi:10.1038/s41598-020-66092-9] synonym: "horizontal cell" EXACT [] xref: BTO:0004120 is_a: CL:0000099 ! interneuron -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002100 UBERON:0003902 ! has soma location retinal neural layer +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000746 @@ -8157,9 +8156,9 @@ intersection_of: has_part GO:0030017 ! sarcomere intersection_of: part_of UBERON:0007100 ! primary circulatory organ intersection_of: participates_in GO:0060047 ! heart contraction relationship: bearer_of PATO:0002478 ! transversely striated -relationship: develops_from CL:0000513 ! cardiac muscle myoblast relationship: participates_in GO:0060047 ! heart contraction -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0000513 ! develops from cardiac muscle myoblast +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000747 @@ -8167,7 +8166,7 @@ name: cyanophore def: "A pigment cell derived from the neural crest. Contains blue pigment of unknown chemical composition in fibrous organelles termed cyanosomes. This gives a blue appearance." [SANBI:mhl] synonym: "blue chromatophore" RELATED [] is_a: CL:0000147 ! pigment cell -relationship: develops_from CL:0005005 ! cyanoblast +relationship: RO:0002202 CL:0005005 ! develops from cyanoblast [Term] id: CL:0000748 @@ -8185,8 +8184,8 @@ is_a: CL:0008028 ! visual system neuron is_a: CL:0009004 ! retinal cell intersection_of: CL:0000103 ! bipolar neuron intersection_of: RO:0002100 UBERON:0001791 ! has soma location inner nuclear layer of retina -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002100 UBERON:0001791 ! has soma location inner nuclear layer of retina +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000749 @@ -8195,7 +8194,7 @@ def: "A bipolar neuron found in the retina and having connections with photorece subset: cellxgene_subset subset: human_reference_atlas is_a: CL:0000748 ! retinal bipolar neuron -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000750 @@ -8204,7 +8203,7 @@ def: "A bipolar neuron found in the retina and having connections with photorece subset: cellxgene_subset subset: human_reference_atlas is_a: CL:0000748 ! retinal bipolar neuron -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000751 @@ -8215,11 +8214,11 @@ subset: human_reference_atlas xref: FMA:67750 is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000749 ! ON-bipolar cell -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002102 UBERON:0008925 ! axon synapses in sublaminar layer S4 relationship: RO:0002102 UBERON:0008926 ! axon synapses in sublaminar layer S5 -relationship: synapsed_by CL:0000604 ! retinal rod cell +relationship: RO:0002103 CL:0000604 ! synapsed by retinal rod cell +relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000752 @@ -8227,8 +8226,8 @@ name: cone retinal bipolar cell def: "A bipolar neuron found in the retina and having connections with cone photoreceptor cells and neurons in the inner plexiform layer." [PMID:14689473] is_a: CL:0000748 ! retinal bipolar neuron intersection_of: CL:0000748 ! retinal bipolar neuron -intersection_of: synapsed_by CL:0000573 ! retinal cone cell -relationship: synapsed_by CL:0000573 ! retinal cone cell +intersection_of: RO:0002103 CL:0000573 ! synapsed by retinal cone cell +relationship: RO:0002103 CL:0000573 ! synapsed by retinal cone cell [Term] id: CL:0000753 @@ -8260,7 +8259,7 @@ def: "An OFF-bipolar neuron found in the retina and having connections with cone synonym: "DB2 cone bipolar cell" EXACT [] is_a: CL:0000752 ! cone retinal bipolar cell relationship: RO:0002102 UBERON:0008923 ! axon synapses in sublaminar layer S2 -relationship: synapsed_by CL:0000604 ! retinal rod cell +relationship: RO:0002103 CL:0000604 ! synapsed by retinal rod cell [Term] id: CL:0000756 @@ -8270,7 +8269,7 @@ synonym: "DB3 cone bipolar cell" EXACT [] is_a: CL:0000752 ! cone retinal bipolar cell relationship: RO:0002102 UBERON:0008923 ! axon synapses in sublaminar layer S2 relationship: RO:0002102 UBERON:0008924 ! axon synapses in sublaminar layer S3 -relationship: synapsed_by CL:0000604 ! retinal rod cell +relationship: RO:0002103 CL:0000604 ! synapsed by retinal rod cell [Term] id: CL:0000757 @@ -8325,7 +8324,7 @@ intersection_of: CL:0000763 ! myeloid cell intersection_of: bearer_of PATO:0001407 ! mononucleate intersection_of: capable_of GO:0007596 ! blood coagulation relationship: capable_of GO:0007596 ! blood coagulation -relationship: develops_from CL:0000828 ! thromboblast +relationship: RO:0002202 CL:0000828 ! develops from thromboblast [Term] id: CL:0000763 @@ -8337,8 +8336,8 @@ xref: CALOHA:TS-0647 xref: MESH:D022423 is_a: CL:0000988 {is_inferred="true"} ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell -intersection_of: develops_from CL:0000049 ! common myeloid progenitor -relationship: develops_from CL:0000049 ! common myeloid progenitor +intersection_of: RO:0002202 CL:0000049 ! develops from common myeloid progenitor +relationship: RO:0002202 CL:0000049 ! develops from common myeloid progenitor [Term] id: CL:0000764 @@ -8353,7 +8352,7 @@ xref: CALOHA:TS-0290 xref: FMA:62845 xref: FMA:83516 is_a: CL:0000763 ! myeloid cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000765 @@ -8396,8 +8395,8 @@ relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-span relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD5 relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G -relationship: develops_from CL:0000547 ! proerythroblast relationship: has_part GO:0005634 ! nucleus +relationship: RO:0002202 CL:0000547 ! develops from proerythroblast [Term] id: CL:0000766 @@ -8407,7 +8406,7 @@ subset: cellxgene_subset is_a: CL:0000738 {is_inferred="true"} ! leukocyte is_a: CL:0000763 ! myeloid cell intersection_of: CL:0000738 ! leukocyte -intersection_of: develops_from CL:0000049 ! common myeloid progenitor +intersection_of: RO:0002202 CL:0000049 ! develops from common myeloid progenitor [Term] id: CL:0000767 @@ -8431,12 +8430,12 @@ intersection_of: RO:0002104 PR:000001950 ! has plasma membrane part tumor necros intersection_of: RO:0015015 PR:000001255 ! has high plasma membrane amount C-C chemokine receptor type 3 intersection_of: RO:0015015 PR:000001865 ! has high plasma membrane amount interleukin-3 receptor class 2 alpha chain intersection_of: RO:0015015 PR:000007431 ! has high plasma membrane amount high affinity immunoglobulin epsilon receptor subunit alpha -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001344 ! has plasma membrane part ectonucleotide pyrophosphatase/phosphodiesterase family member 3 relationship: RO:0002104 PR:000001950 ! has plasma membrane part tumor necrosis factor ligand superfamily member 5 relationship: RO:0015015 PR:000001255 ! has high plasma membrane amount C-C chemokine receptor type 3 relationship: RO:0015015 PR:000001865 ! has high plasma membrane amount interleukin-3 receptor class 2 alpha chain relationship: RO:0015015 PR:000007431 ! has high plasma membrane amount high affinity immunoglobulin epsilon receptor subunit alpha +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000768 @@ -8447,8 +8446,8 @@ synonym: "immature basophilic leukocyte" EXACT [] is_a: CL:0000767 {is_inferred="true"} ! basophil intersection_of: CL:0000767 ! basophil intersection_of: has_part CL:0017509 ! alobate nucleus -relationship: develops_from CL:0000830 ! basophilic promyelocyte relationship: has_part CL:0017509 ! alobate nucleus +relationship: RO:0002202 CL:0000830 ! develops from basophilic promyelocyte [Term] id: CL:0000769 @@ -8468,7 +8467,6 @@ intersection_of: RO:0002104 PR:000001483 ! has plasma membrane part low affinity intersection_of: RO:0002104 PR:000001892 ! has plasma membrane part CD33 molecule intersection_of: RO:0002104 PR:000001932 ! has plasma membrane part signal transducer CD24 intersection_of: RO:0002104 PR:000002031 ! has plasma membrane part aminopeptidase N -relationship: develops_from CL:0000614 ! basophilic myelocyte relationship: has_part CL:0017507 ! reniform nucleus relationship: has_part GO:0000792 ! heterochromatin relationship: has_part GO:0042582 ! azurophil granule @@ -8478,6 +8476,7 @@ relationship: RO:0002104 PR:000001483 ! has plasma membrane part low affinity im relationship: RO:0002104 PR:000001892 ! has plasma membrane part CD33 molecule relationship: RO:0002104 PR:000001932 ! has plasma membrane part signal transducer CD24 relationship: RO:0002104 PR:000002031 ! has plasma membrane part aminopeptidase N +relationship: RO:0002202 CL:0000614 ! develops from basophilic myelocyte [Term] id: CL:0000770 @@ -8486,8 +8485,8 @@ def: "A late basophilic metamyelocyte in which the nucleus is in the form of a c is_a: CL:0000768 {is_inferred="true"} ! immature basophil intersection_of: CL:0000768 ! immature basophil intersection_of: has_part CL:0017506 ! banded nucleus -relationship: develops_from CL:0000769 ! basophilic metamyelocyte relationship: has_part CL:0017506 ! banded nucleus +relationship: RO:0002202 CL:0000769 ! develops from basophilic metamyelocyte [Term] id: CL:0000771 @@ -8514,12 +8513,12 @@ intersection_of: RO:0002104 PR:000001255 ! has plasma membrane part C-C chemokin intersection_of: RO:0002104 PR:000001307 ! has plasma membrane part CD44 molecule intersection_of: RO:0002104 PR:000001343 ! has plasma membrane part CD69 molecule intersection_of: RO:0002104 PR:000005178 ! has plasma membrane part CD9 molecule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001254 ! has plasma membrane part C-C chemokine receptor type 1 relationship: RO:0002104 PR:000001255 ! has plasma membrane part C-C chemokine receptor type 3 relationship: RO:0002104 PR:000001307 ! has plasma membrane part CD44 molecule relationship: RO:0002104 PR:000001343 ! has plasma membrane part CD69 molecule relationship: RO:0002104 PR:000005178 ! has plasma membrane part CD9 molecule +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000772 @@ -8531,8 +8530,8 @@ synonym: "immature eosinophilic leukocyte" EXACT [] is_a: CL:0000771 {is_inferred="true"} ! eosinophil intersection_of: CL:0000771 ! eosinophil intersection_of: has_part CL:0017509 ! alobate nucleus -relationship: develops_from CL:0000833 ! eosinophilic promyelocyte relationship: has_part CL:0017509 ! alobate nucleus +relationship: RO:0002202 CL:0000833 ! develops from eosinophilic promyelocyte [Term] id: CL:0000773 @@ -8552,7 +8551,6 @@ intersection_of: RO:0002104 PR:000001483 ! has plasma membrane part low affinity intersection_of: RO:0002104 PR:000001892 ! has plasma membrane part CD33 molecule intersection_of: RO:0002104 PR:000001932 ! has plasma membrane part signal transducer CD24 intersection_of: RO:0002104 PR:000002031 ! has plasma membrane part aminopeptidase N -relationship: develops_from CL:0000612 ! eosinophilic myelocyte relationship: has_part CL:0017502 ! acidophilic cytoplasm relationship: has_part CL:0017507 ! reniform nucleus relationship: has_part GO:0000792 ! heterochromatin @@ -8563,6 +8561,7 @@ relationship: RO:0002104 PR:000001483 ! has plasma membrane part low affinity im relationship: RO:0002104 PR:000001892 ! has plasma membrane part CD33 molecule relationship: RO:0002104 PR:000001932 ! has plasma membrane part signal transducer CD24 relationship: RO:0002104 PR:000002031 ! has plasma membrane part aminopeptidase N +relationship: RO:0002202 CL:0000612 ! develops from eosinophilic myelocyte [Term] id: CL:0000774 @@ -8571,8 +8570,8 @@ def: "A late eosinophilic metamyelocyte in which the nucleus is in the form of a is_a: CL:0000772 {is_inferred="true"} ! immature eosinophil intersection_of: CL:0000772 ! immature eosinophil intersection_of: has_part CL:0017506 ! banded nucleus -relationship: develops_from CL:0000773 ! eosinophilic metamyelocyte relationship: has_part CL:0017506 ! banded nucleus +relationship: RO:0002202 CL:0000773 ! develops from eosinophilic metamyelocyte [Term] id: CL:0000775 @@ -8601,9 +8600,9 @@ is_a: CL:0000094 {is_inferred="true"} ! granulocyte intersection_of: CL:0000094 ! granulocyte intersection_of: RO:0002104 PR:000001479 ! has plasma membrane part low affinity immunoglobulin gamma Fc region receptor II intersection_of: RO:0002104 PR:000001879 ! has plasma membrane part leukosialin -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001479 ! has plasma membrane part low affinity immunoglobulin gamma Fc region receptor II relationship: RO:0002104 PR:000001879 ! has plasma membrane part leukosialin +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000776 @@ -8618,8 +8617,8 @@ synonym: "immature neutrophilic leucocyte" EXACT [] is_a: CL:0000775 {is_inferred="true"} ! neutrophil intersection_of: CL:0000775 ! neutrophil intersection_of: has_part CL:0017509 ! alobate nucleus -relationship: develops_from CL:0000564 ! neutrophilic promyelocyte relationship: has_part CL:0017509 ! alobate nucleus +relationship: RO:0002202 CL:0000564 ! develops from neutrophilic promyelocyte [Term] id: CL:0000777 @@ -8630,9 +8629,9 @@ is_a: CL:0000864 {is_inferred="true"} ! tissue-resident macrophage intersection_of: CL:0000864 ! tissue-resident macrophage intersection_of: capable_of GO:0019882 ! antigen processing and presentation intersection_of: capable_of GO:0048771 ! tissue remodeling -intersection_of: located_in UBERON:0002320 ! glomerular mesangium +intersection_of: RO:0001025 UBERON:0002320 ! located in glomerular mesangium relationship: capable_of GO:0048771 ! tissue remodeling -relationship: located_in UBERON:0002320 ! glomerular mesangium +relationship: RO:0001025 UBERON:0002320 ! located in glomerular mesangium [Term] id: CL:0000778 @@ -8654,7 +8653,7 @@ is_a: CL:0000092 {is_inferred="true"} ! osteoclast is_a: CL:0000783 ! multinucleated phagocyte intersection_of: CL:0000092 ! osteoclast intersection_of: bearer_of PATO:0001908 ! multinucleate -relationship: develops_from CL:0000778 ! mononuclear osteoclast +relationship: RO:0002202 CL:0000778 ! develops from mononuclear osteoclast [Term] id: CL:0000780 @@ -8666,7 +8665,7 @@ is_a: CL:0000588 {is_inferred="true"} ! odontoclast is_a: CL:0000779 ! multinuclear osteoclast intersection_of: CL:0000588 ! odontoclast intersection_of: bearer_of PATO:0001908 ! multinucleate -relationship: develops_from CL:0000781 ! mononuclear odontoclast +relationship: RO:0002202 CL:0000781 ! develops from mononuclear odontoclast [Term] id: CL:0000781 @@ -8693,9 +8692,9 @@ is_a: CL:0000766 ! myeloid leukocyte is_a: CL:0000990 {is_inferred="true"} ! conventional dendritic cell intersection_of: CL:0000990 ! conventional dendritic cell intersection_of: CL:4030046 PR:000001865 ! lacks_plasma_membrane_part interleukin-3 receptor class 2 alpha chain -intersection_of: develops_from CL:0000763 ! myeloid cell +intersection_of: RO:0002202 CL:0000763 ! develops from myeloid cell relationship: CL:4030046 PR:000001865 ! lacks_plasma_membrane_part interleukin-3 receptor class 2 alpha chain -relationship: develops_from CL:0000763 ! myeloid cell +relationship: RO:0002202 CL:0000763 ! develops from myeloid cell [Term] id: CL:0000783 @@ -8727,7 +8726,7 @@ is_a: CL:0000451 {is_inferred="true"} ! dendritic cell intersection_of: CL:0000451 ! dendritic cell intersection_of: capable_of GO:0032606 ! type I interferon production relationship: capable_of GO:0032606 ! type I interferon production -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000785 @@ -8748,8 +8747,8 @@ disjoint_from: CL:0000816 ! immature B cell disjoint_from: CL:0000817 ! precursor B cell disjoint_from: CL:0000818 ! transitional stage B cell relationship: capable_of GO:0042113 ! B cell activation -relationship: develops_from CL:0000818 ! transitional stage B cell relationship: output_of GO:0002335 ! mature B cell differentiation +relationship: RO:0002202 CL:0000818 ! develops from transitional stage B cell [Term] id: CL:0000786 @@ -8779,11 +8778,11 @@ intersection_of: RO:0002104 PR:000001935 ! has plasma membrane part syndecan-1 relationship: CL:4030046 GO:0019814 ! lacks_plasma_membrane_part immunoglobulin complex relationship: CL:4030046 GO:0042613 ! lacks_plasma_membrane_part MHC class II protein complex relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-spanning 4-domains subfamily A member 1 -relationship: develops_from CL:0000980 ! plasmablast relationship: has_part CL:0017508 ! cartwheel heterochromatin relationship: has_part GO:0005794 ! Golgi apparatus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001935 ! has plasma membrane part syndecan-1 +relationship: RO:0002202 CL:0000980 ! develops from plasmablast +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000787 @@ -8803,9 +8802,9 @@ intersection_of: RO:0002104 GO:0042613 ! has plasma membrane part MHC class II p intersection_of: RO:0002104 PR:000001289 ! has plasma membrane part membrane-spanning 4-domains subfamily A member 1 relationship: CL:4030046 PR:000001935 ! lacks_plasma_membrane_part syndecan-1 relationship: output_of GO:0002344 ! B cell affinity maturation -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 GO:0042613 ! has plasma membrane part MHC class II protein complex relationship: RO:0002104 PR:000001289 ! has plasma membrane part membrane-spanning 4-domains subfamily A member 1 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000788 @@ -8826,10 +8825,10 @@ intersection_of: RO:0002104 GO:0071753 ! has plasma membrane part IgM immunoglob intersection_of: RO:0002104 PR:000001289 ! has plasma membrane part membrane-spanning 4-domains subfamily A member 1 relationship: CL:4030044 GO:0002344 ! has_not_completed B cell affinity maturation relationship: CL:4030046 PR:000001963 ! lacks_plasma_membrane_part CD27 molecule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 GO:0071738 ! has plasma membrane part IgD immunoglobulin complex relationship: RO:0002104 GO:0071753 ! has plasma membrane part IgM immunoglobulin complex relationship: RO:0002104 PR:000001289 ! has plasma membrane part membrane-spanning 4-domains subfamily A member 1 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000789 @@ -8871,7 +8870,7 @@ is_a: CL:0000789 {is_inferred="true"} ! alpha-beta T cell is_a: CL:0002419 ! mature T cell intersection_of: CL:0000789 ! alpha-beta T cell intersection_of: output_of GO:0045058 ! T cell selection -relationship: develops_from CL:0000790 ! immature alpha-beta T cell +relationship: RO:0002202 CL:0000790 ! develops from immature alpha-beta T cell [Term] id: CL:0000792 @@ -8910,9 +8909,9 @@ is_a: CL:0000624 {is_inferred="true"} ! CD4-positive, alpha-beta T cell is_a: CL:0000797 ! alpha-beta intraepithelial T cell intersection_of: CL:0000624 ! CD4-positive, alpha-beta T cell intersection_of: capable_of GO:0002385 ! mucosal immune response -intersection_of: located_in UBERON:0001277 ! intestinal epithelium -relationship: develops_from CL:0000810 ! CD4-positive, alpha-beta thymocyte -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0001025 UBERON:0001277 ! located in intestinal epithelium +relationship: RO:0002202 CL:0000810 ! develops from CD4-positive, alpha-beta thymocyte +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000794 @@ -8942,11 +8941,11 @@ intersection_of: has_part PR:000003499 ! granzyme B intersection_of: output_of GO:0030217 ! T cell differentiation relationship: capable_of GO:0001913 ! T cell mediated cytotoxicity relationship: capable_of GO:0033380 ! granzyme B localization to T cell secretory granule -relationship: develops_from CL:0000906 ! activated CD8-positive, alpha-beta T cell relationship: has_part PR:000003466 ! perforin-1 relationship: has_part PR:000003499 ! granzyme B relationship: output_of GO:0030217 ! T cell differentiation -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0000906 ! develops from activated CD8-positive, alpha-beta T cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000795 @@ -8984,8 +8983,8 @@ synonym: "intraepithelial lymphocyte" BROAD [] is_a: CL:0000797 {is_inferred="true"} ! alpha-beta intraepithelial T cell intersection_of: CL:0000797 ! alpha-beta intraepithelial T cell intersection_of: RO:0002104 PR:000025402 ! has plasma membrane part T cell receptor co-receptor CD8 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000025402 ! has plasma membrane part T cell receptor co-receptor CD8 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000797 @@ -9000,7 +8999,7 @@ is_a: CL:0000791 {is_inferred="true"} ! mature alpha-beta T cell is_a: CL:0002496 ! intraepithelial lymphocyte intersection_of: CL:0000791 ! mature alpha-beta T cell intersection_of: capable_of GO:0002385 ! mucosal immune response -intersection_of: located_in UBERON:0001277 ! intestinal epithelium +intersection_of: RO:0001025 UBERON:0001277 ! located in intestinal epithelium [Term] id: CL:0000798 @@ -9018,8 +9017,8 @@ synonym: "gd T cell" RELATED OMO:0003000 [] is_a: CL:0000084 {is_inferred="true"} ! T cell intersection_of: CL:0000084 ! T cell intersection_of: RO:0002104 GO:0042106 ! has plasma membrane part gamma-delta T cell receptor complex -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 GO:0042106 ! has plasma membrane part gamma-delta T cell receptor complex +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000799 @@ -9035,7 +9034,7 @@ intersection_of: CL:0000798 ! gamma-delta T cell intersection_of: CL:4030044 GO:0042492 ! has_not_completed gamma-delta T cell differentiation intersection_of: CL:4030044 GO:0045058 ! has_not_completed T cell selection relationship: CL:4030044 GO:0042492 ! has_not_completed gamma-delta T cell differentiation -relationship: develops_from CL:0000807 ! DN3 thymocyte +relationship: RO:0002202 CL:0000807 ! develops from DN3 thymocyte [Term] id: CL:0000800 @@ -9049,7 +9048,7 @@ is_a: CL:0000798 {is_inferred="true"} ! gamma-delta T cell is_a: CL:0002419 ! mature T cell intersection_of: CL:0000798 ! gamma-delta T cell intersection_of: output_of GO:0045058 ! T cell selection -relationship: develops_from CL:0000799 ! immature gamma-delta T cell +relationship: RO:0002202 CL:0000799 ! develops from immature gamma-delta T cell [Term] id: CL:0000801 @@ -9064,7 +9063,7 @@ is_a: CL:0000800 {is_inferred="true"} ! mature gamma-delta T cell is_a: CL:0002496 ! intraepithelial lymphocyte intersection_of: CL:0000800 ! mature gamma-delta T cell intersection_of: capable_of GO:0002385 ! mucosal immune response -intersection_of: located_in UBERON:0001277 ! intestinal epithelium +intersection_of: RO:0001025 UBERON:0001277 ! located in intestinal epithelium [Term] id: CL:0000802 @@ -9080,8 +9079,8 @@ synonym: "intraepithelial lymphocyte" BROAD [] is_a: CL:0000801 {is_inferred="true"} ! gamma-delta intraepithelial T cell intersection_of: CL:0000801 ! gamma-delta intraepithelial T cell intersection_of: RO:0002104 PR:000001084 ! has plasma membrane part T-cell surface glycoprotein CD8 alpha chain -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001084 ! has plasma membrane part T-cell surface glycoprotein CD8 alpha chain +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000803 @@ -9120,9 +9119,9 @@ intersection_of: RO:0015015 PR:000001932 ! has high plasma membrane amount signa relationship: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecule relationship: CL:4030046 PR:000001307 ! lacks_plasma_membrane_part CD44 molecule relationship: CL:4030046 PR:000001380 ! lacks_plasma_membrane_part interleukin-2 receptor subunit alpha -relationship: develops_from CL:0000808 ! DN4 thymocyte relationship: RO:0002104 GO:0043384 ! has plasma membrane part pre-T cell receptor complex relationship: RO:0002104 PR:000025402 ! has plasma membrane part T cell receptor co-receptor CD8 +relationship: RO:0002202 CL:0000808 ! develops from DN4 thymocyte relationship: RO:0015015 PR:000001932 ! has high plasma membrane amount signal transducer CD24 [Term] @@ -9145,9 +9144,9 @@ intersection_of: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecu intersection_of: CL:4030046 PR:000025402 ! lacks_plasma_membrane_part T cell receptor co-receptor CD8 intersection_of: RO:0002104 PR:000001307 ! has plasma membrane part CD44 molecule intersection_of: RO:0002104 PR:000001380 ! has plasma membrane part interleukin-2 receptor subunit alpha -relationship: develops_from CL:0000894 ! DN1 thymic pro-T cell relationship: RO:0002104 PR:000001307 ! has plasma membrane part CD44 molecule relationship: RO:0002104 PR:000001380 ! has plasma membrane part interleukin-2 receptor subunit alpha +relationship: RO:0002202 CL:0000894 ! develops from DN1 thymic pro-T cell [Term] id: CL:0000807 @@ -9173,9 +9172,9 @@ intersection_of: CL:4030046 PR:000025402 ! lacks_plasma_membrane_part T cell rec intersection_of: RO:0002104 GO:0043384 ! has plasma membrane part pre-T cell receptor complex intersection_of: RO:0002104 PR:000001380 ! has plasma membrane part interleukin-2 receptor subunit alpha relationship: CL:4030046 PR:000001307 ! lacks_plasma_membrane_part CD44 molecule -relationship: develops_from CL:0000806 ! DN2 thymocyte relationship: RO:0002104 GO:0043384 ! has plasma membrane part pre-T cell receptor complex relationship: RO:0002104 PR:000001380 ! has plasma membrane part interleukin-2 receptor subunit alpha +relationship: RO:0002202 CL:0000806 ! develops from DN2 thymocyte [Term] id: CL:0000808 @@ -9200,8 +9199,8 @@ intersection_of: CL:4030046 PR:000025402 ! lacks_plasma_membrane_part T cell rec intersection_of: RO:0002104 GO:0043384 ! has plasma membrane part pre-T cell receptor complex relationship: CL:4030046 PR:000001307 ! lacks_plasma_membrane_part CD44 molecule relationship: CL:4030046 PR:000001380 ! lacks_plasma_membrane_part interleukin-2 receptor subunit alpha -relationship: develops_from CL:0000807 ! DN3 thymocyte relationship: RO:0002104 GO:0043384 ! has plasma membrane part pre-T cell receptor complex +relationship: RO:0002202 CL:0000807 ! develops from DN3 thymocyte [Term] id: CL:0000809 @@ -9220,10 +9219,10 @@ intersection_of: CL:0000790 ! immature alpha-beta T cell intersection_of: part_of UBERON:0002370 ! thymus intersection_of: RO:0002104 PR:000001004 ! has plasma membrane part CD4 molecule intersection_of: RO:0002104 PR:000025402 ! has plasma membrane part T cell receptor co-receptor CD8 -relationship: develops_from CL:0000805 ! immature single positive thymocyte -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001004 ! has plasma membrane part CD4 molecule relationship: RO:0002104 PR:000025402 ! has plasma membrane part T cell receptor co-receptor CD8 +relationship: RO:0002202 CL:0000805 ! develops from immature single positive thymocyte +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000810 @@ -9241,8 +9240,8 @@ intersection_of: CL:4030046 PR:000001084 ! lacks_plasma_membrane_part T-cell sur intersection_of: part_of UBERON:0002370 ! thymus intersection_of: RO:0002104 PR:000001004 ! has plasma membrane part CD4 molecule relationship: CL:4030046 PR:000001084 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD8 alpha chain -relationship: develops_from CL:0000809 ! double-positive, alpha-beta thymocyte relationship: RO:0002104 PR:000001004 ! has plasma membrane part CD4 molecule +relationship: RO:0002202 CL:0000809 ! develops from double-positive, alpha-beta thymocyte [Term] id: CL:0000811 @@ -9261,8 +9260,8 @@ intersection_of: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecu intersection_of: part_of UBERON:0002370 ! thymus intersection_of: RO:0002104 PR:000025402 ! has plasma membrane part T cell receptor co-receptor CD8 relationship: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecule -relationship: develops_from CL:0000809 ! double-positive, alpha-beta thymocyte relationship: RO:0002104 PR:000025402 ! has plasma membrane part T cell receptor co-receptor CD8 +relationship: RO:0002202 CL:0000809 ! develops from double-positive, alpha-beta thymocyte [Term] id: CL:0000813 @@ -9304,10 +9303,10 @@ intersection_of: output_of GO:0030217 ! T cell differentiation intersection_of: RO:0002104 PR:000001874 ! has plasma membrane part KLRB1-like protein relationship: capable_of GO:0032394 ! MHC class Ib receptor activity relationship: capable_of GO:0045087 ! innate immune response -relationship: develops_from CL:0002042 ! immature NK T cell stage IV relationship: output_of GO:0030217 ! T cell differentiation -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001874 ! has plasma membrane part KLRB1-like protein +relationship: RO:0002202 CL:0002042 ! develops from immature NK T cell stage IV +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000815 @@ -9331,7 +9330,7 @@ is_a: CL:0002419 {is_inferred="true"} ! mature T cell intersection_of: CL:0002419 ! mature T cell intersection_of: capable_of GO:0050777 ! negative regulation of immune response relationship: capable_of GO:0050777 ! negative regulation of immune response -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000816 @@ -9353,10 +9352,10 @@ intersection_of: RO:0002104 GO:0071753 ! has plasma membrane part IgM immunoglob intersection_of: RO:0002104 PR:000001289 ! has plasma membrane part membrane-spanning 4-domains subfamily A member 1 relationship: CL:4030044 GO:0045190 ! has_not_completed isotype switching relationship: CL:4030046 GO:0071738 ! lacks_plasma_membrane_part IgD immunoglobulin complex -relationship: develops_from CL:0000954 ! small pre-B-II cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 GO:0071753 ! has plasma membrane part IgM immunoglobulin complex relationship: RO:0002104 PR:000001289 ! has plasma membrane part membrane-spanning 4-domains subfamily A member 1 +relationship: RO:0002202 CL:0000954 ! develops from small pre-B-II cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000817 @@ -9373,8 +9372,8 @@ intersection_of: CL:4030046 GO:0071753 ! lacks_plasma_membrane_part IgM immunogl intersection_of: RO:0002104 PR:000001898 ! has plasma membrane part neprilysin disjoint_from: CL:0000826 ! pro-B cell relationship: CL:4030046 GO:0071753 ! lacks_plasma_membrane_part IgM immunoglobulin complex -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001898 ! has plasma membrane part neprilysin +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000818 @@ -9398,12 +9397,12 @@ intersection_of: RO:0002104 PR:000001289 ! has plasma membrane part membrane-spa intersection_of: RO:0015015 PR:000001408 ! has high plasma membrane amount ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 intersection_of: RO:0015015 PR:000001932 ! has high plasma membrane amount signal transducer CD24 relationship: CL:4030044 GO:0002335 ! has_not_completed mature B cell differentiation -relationship: develops_from CL:0000816 ! immature B cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 GO:0071753 ! has plasma membrane part IgM immunoglobulin complex relationship: RO:0002104 PR:000001289 ! has plasma membrane part membrane-spanning 4-domains subfamily A member 1 +relationship: RO:0002202 CL:0000816 ! develops from immature B cell relationship: RO:0015015 PR:000001408 ! has high plasma membrane amount ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 relationship: RO:0015015 PR:000001932 ! has high plasma membrane amount signal transducer CD24 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000819 @@ -9508,7 +9507,7 @@ intersection_of: CL:0000623 ! natural killer cell intersection_of: bearer_of PATO:0001501 ! immature disjoint_from: CL:0000824 ! mature natural killer cell disjoint_from: CL:0000937 ! pre-natural killer cell -relationship: develops_from CL:0000937 ! pre-natural killer cell +relationship: RO:0002202 CL:0000937 ! develops from pre-natural killer cell [Term] id: CL:0000824 @@ -9519,8 +9518,8 @@ synonym: "LAK cell" BROAD [PMID:14685782] synonym: "lymphokine activated killer cell" BROAD [PMID:14685782] synonym: "mature NK cell" EXACT [] is_a: CL:0000623 ! natural killer cell -relationship: develops_from CL:0000823 ! immature natural killer cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0000823 ! develops from immature natural killer cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000825 @@ -9543,11 +9542,11 @@ intersection_of: RO:0002104 PR:000001381 ! has plasma membrane part interleukin- intersection_of: RO:0002104 PR:000001898 ! has plasma membrane part neprilysin relationship: CL:4030046 PR:000001874 ! lacks_plasma_membrane_part KLRB1-like protein relationship: CL:4030046 PR:000002065 ! lacks_plasma_membrane_part mast/stem cell growth factor receptor -relationship: develops_from CL:0000051 ! common lymphoid progenitor relationship: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule relationship: RO:0002104 PR:000001015 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RA relationship: RO:0002104 PR:000001381 ! has plasma membrane part interleukin-2 receptor subunit beta relationship: RO:0002104 PR:000001898 ! has plasma membrane part neprilysin +relationship: RO:0002202 CL:0000051 ! develops from common lymphoid progenitor [Term] id: CL:0000826 @@ -9572,11 +9571,11 @@ intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: has_part PR:000001903 ! paired box protein PAX-5 intersection_of: has_part PR:000006611 ! DNA nucleotidylexotransferase intersection_of: participates_in GO:0033152 ! immunoglobulin V(D)J recombination -relationship: develops_from CL:0000051 ! common lymphoid progenitor relationship: has_part PR:000001903 ! paired box protein PAX-5 relationship: has_part PR:000006611 ! DNA nucleotidylexotransferase relationship: participates_in GO:0033152 ! immunoglobulin V(D)J recombination -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0000051 ! develops from common lymphoid progenitor +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000827 @@ -9592,7 +9591,7 @@ is_a: CL:0000838 {is_inferred="true"} ! lymphoid lineage restricted progenitor c intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: capable_of GO:0030217 ! T cell differentiation relationship: capable_of GO:0030217 ! T cell differentiation -relationship: develops_from CL:0000051 ! common lymphoid progenitor +relationship: RO:0002202 CL:0000051 ! develops from common lymphoid progenitor [Term] id: CL:0000828 @@ -9606,7 +9605,7 @@ intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: bearer_of PATO:0001407 ! mononucleate intersection_of: capable_of GO:0002574 ! thrombocyte differentiation relationship: capable_of GO:0002574 ! thrombocyte differentiation -relationship: develops_from CL:0000050 ! megakaryocyte-erythroid progenitor cell +relationship: RO:0002202 CL:0000050 ! develops from megakaryocyte-erythroid progenitor cell [Term] id: CL:0000829 @@ -9616,7 +9615,7 @@ is_a: CL:0000835 {is_inferred="true"} ! myeloblast intersection_of: CL:0000835 ! myeloblast intersection_of: capable_of GO:0030221 ! basophil differentiation relationship: capable_of GO:0030221 ! basophil differentiation -relationship: develops_from CL:0000613 ! basophil progenitor cell +relationship: RO:0002202 CL:0000613 ! develops from basophil progenitor cell [Term] id: CL:0000830 @@ -9627,7 +9626,7 @@ is_a: CL:0000836 {is_inferred="true"} ! promyelocyte intersection_of: CL:0000836 ! promyelocyte intersection_of: capable_of GO:0030221 ! basophil differentiation relationship: capable_of GO:0030221 ! basophil differentiation -relationship: develops_from CL:0000829 ! basophilic myeloblast +relationship: RO:0002202 CL:0000829 ! develops from basophilic myeloblast [Term] id: CL:0000831 @@ -9683,11 +9682,11 @@ relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte an relationship: CL:4030046 PR:000002979 ! lacks_plasma_membrane_part lymphocyte antigen 6A-2/6E-1 relationship: CL:4030046 PR:000002980 ! lacks_plasma_membrane_part lymphocyte antigen 6C2 relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -relationship: develops_from CL:0002028 ! basophil mast progenitor cell relationship: has_part PR:000007857 ! erythroid transcription factor relationship: has_part PR:000007858 ! endothelial transcription factor GATA-2 relationship: RO:0002104 PR:000005178 ! has plasma membrane part CD9 molecule relationship: RO:0002104 PR:000016401 ! has plasma membrane part transmembrane emp24 domain-containing protein 1 +relationship: RO:0002202 CL:0002028 ! develops from basophil mast progenitor cell relationship: RO:0015015 PR:000009143 ! has high plasma membrane amount integrin beta-7 relationship: RO:0015016 PR:000002065 ! has low plasma membrane amount mast/stem cell growth factor receptor relationship: RO:0015016 PR:000007431 ! has low plasma membrane amount high affinity immunoglobulin epsilon receptor subunit alpha @@ -9700,7 +9699,7 @@ is_a: CL:0000835 {is_inferred="true"} ! myeloblast intersection_of: CL:0000835 ! myeloblast intersection_of: capable_of GO:0030222 ! eosinophil differentiation relationship: capable_of GO:0030222 ! eosinophil differentiation -relationship: develops_from CL:0000611 ! eosinophil progenitor cell +relationship: RO:0002202 CL:0000611 ! develops from eosinophil progenitor cell [Term] id: CL:0000833 @@ -9711,7 +9710,7 @@ is_a: CL:0000836 {is_inferred="true"} ! promyelocyte intersection_of: CL:0000836 ! promyelocyte intersection_of: capable_of GO:0030222 ! eosinophil differentiation relationship: capable_of GO:0030222 ! eosinophil differentiation -relationship: develops_from CL:0000832 ! eosinophilic myeloblast +relationship: RO:0002202 CL:0000832 ! develops from eosinophilic myeloblast [Term] id: CL:0000834 @@ -9724,7 +9723,7 @@ is_a: CL:0002191 {is_inferred="true"} ! granulocytopoietic cell intersection_of: CL:0002191 ! granulocytopoietic cell intersection_of: capable_of GO:0030223 ! neutrophil differentiation relationship: capable_of GO:0030223 ! neutrophil differentiation -relationship: develops_from CL:0000557 ! granulocyte monocyte progenitor cell +relationship: RO:0002202 CL:0000557 ! develops from granulocyte monocyte progenitor cell [Term] id: CL:0000835 @@ -9742,9 +9741,9 @@ intersection_of: has_part CL:0017503 ! basophilic cytoplasm intersection_of: has_part GO:0000791 ! euchromatin relationship: bearer_of PATO:0040072 ! high nuclear/cytoplasmic ratio relationship: CL:4030045 GO:0042582 ! lacks_part azurophil granule -relationship: develops_from CL:0000557 ! granulocyte monocyte progenitor cell relationship: has_part CL:0017503 ! basophilic cytoplasm relationship: has_part GO:0000791 ! euchromatin +relationship: RO:0002202 CL:0000557 ! develops from granulocyte monocyte progenitor cell [Term] id: CL:0000836 @@ -9771,13 +9770,13 @@ relationship: bearer_of PATO:0040072 ! high nuclear/cytoplasmic ratio relationship: CL:4030046 PR:000001012 ! lacks_plasma_membrane_part integrin alpha-M relationship: CL:4030046 PR:000001483 ! lacks_plasma_membrane_part low affinity immunoglobulin gamma Fc region receptor III relationship: CL:4030046 PR:000001932 ! lacks_plasma_membrane_part signal transducer CD24 -relationship: develops_from CL:0000835 ! myeloblast relationship: has_part CL:0017503 ! basophilic cytoplasm relationship: has_part GO:0005730 ! nucleolus relationship: has_part GO:0042582 ! azurophil granule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001456 ! has plasma membrane part alpha-(1,3)-fucosyltransferase 4 relationship: RO:0002104 PR:000001892 ! has plasma membrane part CD33 molecule +relationship: RO:0002202 CL:0000835 ! develops from myeloblast +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000837 @@ -9824,9 +9823,9 @@ relationship: CL:4030046 PR:000001869 ! lacks_plasma_membrane_part interleukin-7 relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -relationship: develops_from CL:0000037 ! hematopoietic stem cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule +relationship: RO:0002202 CL:0000037 ! develops from hematopoietic stem cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000838 @@ -9861,7 +9860,7 @@ is_a: CL:0011026 ! progenitor cell intersection_of: CL:0002031 ! hematopoietic lineage restricted progenitor cell intersection_of: capable_of GO:0030099 ! myeloid cell differentiation relationship: capable_of GO:0030099 ! myeloid cell differentiation -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000840 @@ -9875,11 +9874,11 @@ intersection_of: CL:0000990 ! conventional dendritic cell intersection_of: RO:0015016 GO:0042613 ! has low plasma membrane amount MHC class II protein complex intersection_of: RO:0015016 PR:000001412 ! has low plasma membrane amount CD86 molecule intersection_of: RO:0015016 PR:000001438 ! has low plasma membrane amount CD80 molecule -relationship: develops_from CL:0001029 ! common dendritic progenitor -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0001029 ! develops from common dendritic progenitor relationship: RO:0015016 GO:0042613 ! has low plasma membrane amount MHC class II protein complex relationship: RO:0015016 PR:000001412 ! has low plasma membrane amount CD86 molecule relationship: RO:0015016 PR:000001438 ! has low plasma membrane amount CD80 molecule +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000841 @@ -9896,8 +9895,8 @@ intersection_of: RO:0002104 PR:000001310 ! has plasma membrane part CD83 molecul intersection_of: RO:0015015 GO:0042613 ! has high plasma membrane amount MHC class II protein complex intersection_of: RO:0015015 PR:000001412 ! has high plasma membrane amount CD86 molecule intersection_of: RO:0015015 PR:000001438 ! has high plasma membrane amount CD80 molecule -relationship: develops_from CL:0000840 ! immature conventional dendritic cell relationship: RO:0002104 PR:000001310 ! has plasma membrane part CD83 molecule +relationship: RO:0002202 CL:0000840 ! develops from immature conventional dendritic cell relationship: RO:0015015 GO:0042613 ! has high plasma membrane amount MHC class II protein complex relationship: RO:0015015 PR:000001412 ! has high plasma membrane amount CD86 molecule relationship: RO:0015015 PR:000001438 ! has high plasma membrane amount CD80 molecule @@ -9964,10 +9963,10 @@ is_a: CL:0000785 {is_inferred="true"} ! mature B cell intersection_of: CL:0000785 ! mature B cell intersection_of: part_of UBERON:0001745 ! secondary nodular lymphoid tissue intersection_of: RO:0002104 PR:000001289 ! has plasma membrane part membrane-spanning 4-domains subfamily A member 1 -relationship: develops_from CL:0000843 ! follicular B cell relationship: part_of UBERON:0001745 ! secondary nodular lymphoid tissue -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001289 ! has plasma membrane part membrane-spanning 4-domains subfamily A member 1 +relationship: RO:0002202 CL:0000843 ! develops from follicular B cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000845 @@ -9999,10 +9998,10 @@ relationship: capable_of GO:0042742 ! defense response to bacterium relationship: CL:4030046 PR:000001880 ! lacks_plasma_membrane_part low affinity immunoglobulin epsilon Fc receptor relationship: CL:4030046 PR:000002037 ! lacks_plasma_membrane_part complement component C1q receptor relationship: part_of UBERON:0001251 ! marginal zone of spleen -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001289 ! has plasma membrane part membrane-spanning 4-domains subfamily A member 1 relationship: RO:0002104 PR:000001338 ! has plasma membrane part complement receptor type 2 relationship: RO:0015015 GO:0071753 ! has high plasma membrane amount IgM immunoglobulin complex +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000846 @@ -10091,7 +10090,7 @@ id: CL:0000854 name: interneuromast cell def: "Interneuromast cell is a neuroectodermal cell deposited by the migrating lateral line primordium between the neuromasts. Interneuromast cells proliferate and migrate to form additional neuromasts." [SANBI:mhl] is_a: CL:0000133 ! neurectodermal cell -relationship: develops_from CL:0000032 ! neuroplacodal cell +relationship: RO:0002202 CL:0000032 ! develops from neuroplacodal cell [Term] id: CL:0000855 @@ -10117,8 +10116,8 @@ name: slow muscle myoblast def: "A skeletal muscle myoblast that differentiates into slow muscle fibers." [SANBI:mhl] is_a: CL:0000515 ! skeletal muscle myoblast intersection_of: CL:0000056 ! myoblast -intersection_of: develops_into CL:0000189 ! slow muscle cell -relationship: develops_into CL:0000189 ! slow muscle cell +intersection_of: RO:0002203 CL:0000189 ! develops into slow muscle cell +relationship: RO:0002203 CL:0000189 ! develops into slow muscle cell [Term] id: CL:0000858 @@ -10126,8 +10125,8 @@ name: fast muscle myoblast def: "A skeletal muscle myoblast that differentiates into fast muscle fibers." [SANBI:mhl] is_a: CL:0000515 ! skeletal muscle myoblast intersection_of: CL:0000056 ! myoblast -intersection_of: develops_into CL:0000190 ! fast muscle cell -relationship: develops_into CL:0000190 ! fast muscle cell +intersection_of: RO:0002203 CL:0000190 ! develops into fast muscle cell +relationship: RO:0002203 CL:0000190 ! develops into fast muscle cell [Term] id: CL:0000860 @@ -10152,8 +10151,8 @@ relationship: capable_of GO:0006954 ! inflammatory response relationship: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule relationship: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-spanning 4-domains subfamily A member 1 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0015015 PR:000001199 ! has high plasma membrane amount C-C chemokine receptor type 2 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000861 @@ -10172,11 +10171,11 @@ intersection_of: participates_in GO:0006954 ! inflammatory response intersection_of: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M intersection_of: RO:0002104 PR:000001813 ! has plasma membrane part adhesion G protein-coupled receptor E1 intersection_of: RO:0002104 PR:000002064 ! has plasma membrane part macrosialin -relationship: develops_from CL:0000860 ! classical monocyte relationship: participates_in GO:0006954 ! inflammatory response relationship: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M relationship: RO:0002104 PR:000001813 ! has plasma membrane part adhesion G protein-coupled receptor E1 relationship: RO:0002104 PR:000002064 ! has plasma membrane part macrosialin +relationship: RO:0002202 CL:0000860 ! develops from classical monocyte [Term] id: CL:0000862 @@ -10225,7 +10224,7 @@ is_a: CL:0000235 {is_inferred="true"} ! macrophage intersection_of: CL:0000235 ! macrophage intersection_of: part_of UBERON:0000479 ! tissue relationship: part_of UBERON:0000479 ! tissue -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000865 @@ -10251,7 +10250,7 @@ intersection_of: capable_of GO:0043277 ! apoptotic cell clearance intersection_of: part_of UBERON:0002370 ! thymus relationship: capable_of GO:0043277 ! apoptotic cell clearance relationship: part_of UBERON:0002370 ! thymus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000867 @@ -10327,11 +10326,11 @@ intersection_of: RO:0002104 PR:000001885 ! has plasma membrane part macrophage s intersection_of: RO:0002104 PR:000006172 ! has plasma membrane part CD209 molecule-like protein B relationship: CL:4030046 PR:000001012 ! lacks_plasma_membrane_part integrin alpha-M relationship: part_of UBERON:0001251 ! marginal zone of spleen -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001806 ! has plasma membrane part C-type lectin domain family 6 member A relationship: RO:0002104 PR:000001884 ! has plasma membrane part macrophage receptor MARCO relationship: RO:0002104 PR:000001885 ! has plasma membrane part macrophage scavenger receptor types I and II relationship: RO:0002104 PR:000006172 ! has plasma membrane part CD209 molecule-like protein B +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000873 @@ -10374,13 +10373,13 @@ intersection_of: RO:0015016 PR:000001931 ! has low plasma membrane amount sialoa relationship: capable_of GO:0006955 ! immune response relationship: CL:4030046 PR:000001013 ! lacks_plasma_membrane_part integrin alpha-X relationship: part_of UBERON:0001250 ! red pulp of spleen -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001806 ! has plasma membrane part C-type lectin domain family 6 member A relationship: RO:0002104 PR:000001813 ! has plasma membrane part adhesion G protein-coupled receptor E1 relationship: RO:0002104 PR:000002064 ! has plasma membrane part macrosialin relationship: RO:0002104 PR:000002972 ! has plasma membrane part macrophage mannose receptor 1 relationship: RO:0015016 PR:000001012 ! has low plasma membrane amount integrin alpha-M relationship: RO:0015016 PR:000001931 ! has low plasma membrane amount sialoadhesin +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000875 @@ -10406,10 +10405,10 @@ relationship: capable_of GO:0031294 ! lymphocyte costimulation relationship: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule relationship: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-spanning 4-domains subfamily A member 1 -relationship: develops_from CL:0002393 ! intermediate monocyte relationship: output_of GO:0030224 ! monocyte differentiation -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0002393 ! develops from intermediate monocyte relationship: RO:0015015 PR:000001206 ! has high plasma membrane amount CX3C chemokine receptor 1 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000876 @@ -10425,8 +10424,8 @@ intersection_of: part_of UBERON:0001959 ! white pulp of spleen intersection_of: RO:0002104 PR:000002064 ! has plasma membrane part macrosialin relationship: CL:4030046 PR:000001813 ! lacks_plasma_membrane_part adhesion G protein-coupled receptor E1 relationship: part_of UBERON:0001959 ! white pulp of spleen -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000002064 ! has plasma membrane part macrosialin +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000877 @@ -10440,8 +10439,8 @@ intersection_of: part_of UBERON:0001249 ! spleen lymphoid follicle intersection_of: RO:0002104 PR:000010329 ! has plasma membrane part tyrosine-protein kinase Mer relationship: capable_of GO:0043277 ! apoptotic cell clearance relationship: part_of UBERON:0001249 ! spleen lymphoid follicle -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000010329 ! has plasma membrane part tyrosine-protein kinase Mer +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000878 @@ -10458,9 +10457,14 @@ relationship: part_of UBERON:0001017 ! central nervous system [Term] id: CL:0000879 name: meningeal macrophage -def: "A central nervous system macrophage found in the meninges (the three membranes that surround the brain). This macrophage types is highly phagocytic and expresses scavenger receptors." [GO_REF:0000031, GOC:ana, PMID:11591794] -is_a: CL:0000878 {is_inferred="true"} ! central nervous system macrophage -intersection_of: CL:0000878 ! central nervous system macrophage +def: "A border associated macrophage that is part of a meninx. This macrophage type is elongated and amoeboid spindle-shaped with limited mobility. This macrophage is highly phagocytic, expresses scavenger receptors, has dynamic protrusions and extends its processes during inflammation." [GO_REF:0000031, GOC:ana, PMID:11591794, PMID:24078900, PMID:37232741] +synonym: "MM" RELATED OMO:0003000 [PMID:33556248] +synonym: "MnMΦ" RELATED OMO:0003000 [PMID:38347231] +synonym: "sdΜΦ" RELATED OMO:0003000 [PMID:37232741] +synonym: "subdural leptomeningeal macrophage" EXACT [PMID:33556248] +synonym: "subdural meningeal macrophage" EXACT [PMID:28323268] +is_a: CL:4042003 ! border associated macrophage +intersection_of: CL:4042003 ! border associated macrophage intersection_of: capable_of GO:0005044 ! scavenger receptor activity intersection_of: part_of UBERON:0002360 ! meninx relationship: capable_of GO:0005044 ! scavenger receptor activity @@ -10468,24 +10472,25 @@ relationship: part_of UBERON:0002360 ! meninx [Term] id: CL:0000880 -name: choroid-plexus macrophage -def: "A central nervous system macrophage found at the interface between the blood and the cerebrospinal fluid in the brain. This cell expresses scavenger receptors." [GO_REF:0000031, GOC:ana, PMID:9550136] -is_a: CL:0000878 {is_inferred="true"} ! central nervous system macrophage -intersection_of: CL:0000878 ! central nervous system macrophage +name: choroid plexus macrophage +def: "A border associated macrophage found at the interface between the blood and the cerebrospinal fluid in the brain. This central nervous system macrophage has a star-like shaped body and expresses scavenger receptors." [GO_REF:0000031, GOC:ana, PMID:37232741, PMID:9550136] +synonym: "cpMΦ" RELATED OMO:0003000 [PMID:37232741] +is_a: CL:4042003 ! border associated macrophage +intersection_of: CL:4042003 ! border associated macrophage intersection_of: capable_of GO:0005044 ! scavenger receptor activity -intersection_of: located_in UBERON:0001886 ! choroid plexus +intersection_of: part_of UBERON:0001886 ! choroid plexus relationship: capable_of GO:0005044 ! scavenger receptor activity -relationship: located_in UBERON:0001886 ! choroid plexus +relationship: part_of UBERON:0001886 ! choroid plexus [Term] id: CL:0000881 name: perivascular macrophage -def: "A central nervous system macrophage found in small blood vessels in the brain. Markers include CD14+CD16+CD163+." [GO_REF:0000031, GOC:tfm, PMID:16507898] -comment: Markers: Human/monkey, mice: CD163. Human: CD14+CD16+CD163+. -is_a: CL:0000878 {is_inferred="true"} ! central nervous system macrophage +def: "A border associated macrophage that is adjacent to a small blood vessel of a brain. A perivascular macrophage expresses the markers CD14, CD16 and CD163. In homeostatic conditions, this central nervous system macrophage has a non-motile cell body with extending and retracting projections through the blood vessel wall." [GO_REF:0000031, GOC:tfm, PMID:16507898, PMID:37232741] +synonym: "pvMΦ" RELATED OMO:0003000 [PMID:37232741] is_a: CL:4033054 ! perivascular cell +is_a: CL:4042003 {is_inferred="true"} ! border associated macrophage is_a: PR:000050567 ! protein-containing material entity -intersection_of: CL:0000878 ! central nervous system macrophage +intersection_of: CL:4042003 ! border associated macrophage intersection_of: part_of UBERON:0001981 ! blood vessel intersection_of: RO:0002104 PR:000001483 ! has plasma membrane part low affinity immunoglobulin gamma Fc region receptor III intersection_of: RO:0002104 PR:000001889 ! has plasma membrane part CD14 molecule @@ -10504,7 +10509,7 @@ is_a: CL:0000866 {is_inferred="true"} ! thymic macrophage intersection_of: CL:0000866 ! thymic macrophage intersection_of: part_of UBERON:0002124 ! medulla of thymus relationship: part_of UBERON:0002124 ! medulla of thymus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000883 @@ -10515,7 +10520,7 @@ is_a: CL:0000866 {is_inferred="true"} ! thymic macrophage intersection_of: CL:0000866 ! thymic macrophage intersection_of: part_of UBERON:0002123 ! cortex of thymus relationship: part_of UBERON:0002123 ! cortex of thymus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000884 @@ -10560,8 +10565,8 @@ intersection_of: capable_of GO:0032816 ! positive regulation of natural killer c intersection_of: RO:0002104 PR:000001931 ! has plasma membrane part sialoadhesin relationship: adjacent_to UBERON:0002194 ! capsule of lymph node relationship: capable_of GO:0032816 ! positive regulation of natural killer cell activation -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001931 ! has plasma membrane part sialoadhesin +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000888 @@ -10576,7 +10581,7 @@ intersection_of: part_of UBERON:0002006 ! cortex of lymph node relationship: capable_of GO:0002905 ! regulation of mature B cell apoptotic process relationship: capable_of GO:0043277 ! apoptotic cell clearance relationship: part_of UBERON:0002006 ! cortex of lymph node -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000889 @@ -10624,7 +10629,7 @@ id: CL:0000892 name: smooth muscle cell derived foam cell def: "A type of foam cell derived from a smooth muscle cell containing lipids in small vacuoles and typically seen in atherolosclerotic lesions, as well as other conditions." [GOC:add, PMID:30664015] is_a: CL:0000891 ! foam cell -relationship: develops_from CL:0000192 ! smooth muscle cell +relationship: RO:0002202 CL:0000192 ! develops from smooth muscle cell [Term] id: CL:0000893 @@ -10670,9 +10675,9 @@ intersection_of: RO:0002104 PR:000001307 ! has plasma membrane part CD44 molecul relationship: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecule relationship: CL:4030046 PR:000001084 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD8 alpha chain relationship: CL:4030046 PR:000001380 ! lacks_plasma_membrane_part interleukin-2 receptor subunit alpha -relationship: develops_from CL:0002425 ! early T lineage precursor relationship: part_of UBERON:0002370 ! thymus relationship: RO:0002104 PR:000001307 ! has plasma membrane part CD44 molecule +relationship: RO:0002202 CL:0002425 ! develops from early T lineage precursor [Term] id: CL:0000895 @@ -10697,8 +10702,8 @@ intersection_of: RO:0002104 PR:000001869 ! has plasma membrane part interleukin- intersection_of: RO:0015015 PR:000001318 ! has high plasma membrane amount L-selectin intersection_of: RO:0015016 PR:000001307 ! has low plasma membrane amount CD44 molecule relationship: CL:4030046 PR:000001380 ! lacks_plasma_membrane_part interleukin-2 receptor subunit alpha -relationship: develops_from CL:0002436 ! mature CD4 single-positive thymocyte -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0002436 ! develops from mature CD4 single-positive thymocyte +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000896 @@ -10716,9 +10721,9 @@ intersection_of: RO:0002104 PR:000001343 ! has plasma membrane part CD69 molecul intersection_of: RO:0002104 PR:000001380 ! has plasma membrane part interleukin-2 receptor subunit alpha relationship: CL:4030046 PR:000001318 ! lacks_plasma_membrane_part L-selectin relationship: CL:4030046 PR:000001869 ! lacks_plasma_membrane_part interleukin-7 receptor subunit alpha -relationship: develops_from CL:0000895 ! naive thymus-derived CD4-positive, alpha-beta T cell relationship: RO:0002104 PR:000001343 ! has plasma membrane part CD69 molecule relationship: RO:0002104 PR:000001380 ! has plasma membrane part interleukin-2 receptor subunit alpha +relationship: RO:0002202 CL:0000895 ! develops from naive thymus-derived CD4-positive, alpha-beta T cell [Term] id: CL:0000897 @@ -10736,8 +10741,8 @@ intersection_of: CL:0000624 ! CD4-positive, alpha-beta T cell intersection_of: bearer_of PATO:0001603 ! increased life span intersection_of: output_of GO:0002286 ! T cell activation involved in immune response intersection_of: output_of GO:0043379 ! memory T cell differentiation -relationship: dc-contributor https://orcid.org/0000-0001-9990-8331 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000898 @@ -10788,8 +10793,8 @@ intersection_of: RO:0002104 PR:000001202 ! has plasma membrane part C-C chemokin relationship: capable_of GO:0032620 ! interleukin-17 production relationship: CL:4030046 PR:000001207 ! lacks_plasma_membrane_part C-X-C chemokine receptor type 3 relationship: has_part PR:000003455 ! nuclear receptor ROR-gamma isoform 2 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001202 ! has plasma membrane part C-C chemokine receptor type 6 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000900 @@ -10813,8 +10818,8 @@ intersection_of: RO:0002104 PR:000001869 ! has plasma membrane part interleukin- intersection_of: RO:0015015 PR:000001318 ! has high plasma membrane amount L-selectin intersection_of: RO:0015016 PR:000001307 ! has low plasma membrane amount CD44 molecule relationship: CL:4030046 PR:000001380 ! lacks_plasma_membrane_part interleukin-2 receptor subunit alpha -relationship: develops_from CL:0002437 ! mature CD8 single-positive thymocyte -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0002437 ! develops from mature CD8 single-positive thymocyte +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000901 @@ -10847,12 +10852,12 @@ synonym: "induced Treg" EXACT [] synonym: "iTreg" EXACT [] is_a: CL:0000792 {is_inferred="true"} ! CD4-positive, CD25-positive, alpha-beta regulatory T cell intersection_of: CL:0000792 ! CD4-positive, CD25-positive, alpha-beta regulatory T cell -intersection_of: develops_from CL:0000896 ! activated CD4-positive, alpha-beta T cell intersection_of: has_part PR:000001350 ! forkhead box protein P3 intersection_of: RO:0002104 PR:000001852 ! has plasma membrane part cytotoxic T-lymphocyte protein 4 -relationship: develops_from CL:0000896 ! activated CD4-positive, alpha-beta T cell +intersection_of: RO:0002202 CL:0000896 ! develops from activated CD4-positive, alpha-beta T cell relationship: has_part PR:000001350 ! forkhead box protein P3 relationship: RO:0002104 PR:000001852 ! has plasma membrane part cytotoxic T-lymphocyte protein 4 +relationship: RO:0002202 CL:0000896 ! develops from activated CD4-positive, alpha-beta T cell [Term] id: CL:0000903 @@ -10867,14 +10872,14 @@ synonym: "natural Treg" EXACT [] synonym: "nTreg" EXACT [] is_a: CL:0000792 {is_inferred="true"} ! CD4-positive, CD25-positive, alpha-beta regulatory T cell intersection_of: CL:0000792 ! CD4-positive, CD25-positive, alpha-beta regulatory T cell -intersection_of: develops_from CL:0000809 ! double-positive, alpha-beta thymocyte intersection_of: has_part PR:000001350 ! forkhead box protein P3 intersection_of: RO:0002104 PR:000001318 ! has plasma membrane part L-selectin intersection_of: RO:0002104 PR:000001852 ! has plasma membrane part cytotoxic T-lymphocyte protein 4 -relationship: develops_from CL:0000809 ! double-positive, alpha-beta thymocyte +intersection_of: RO:0002202 CL:0000809 ! develops from double-positive, alpha-beta thymocyte relationship: has_part PR:000001350 ! forkhead box protein P3 relationship: RO:0002104 PR:000001318 ! has plasma membrane part L-selectin relationship: RO:0002104 PR:000001852 ! has plasma membrane part cytotoxic T-lymphocyte protein 4 +relationship: RO:0002202 CL:0000809 ! develops from double-positive, alpha-beta thymocyte [Term] id: CL:0000904 @@ -10920,7 +10925,7 @@ intersection_of: CL:4030046 PR:000001203 ! lacks_plasma_membrane_part C-C chemok intersection_of: CL:4030046 PR:000001380 ! lacks_plasma_membrane_part interleukin-2 receptor subunit alpha relationship: CL:4030046 PR:000001015 ! lacks_plasma_membrane_part receptor-type tyrosine-protein phosphatase C isoform CD45RA relationship: CL:4030046 PR:000001203 ! lacks_plasma_membrane_part C-C chemokine receptor type 7 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000906 @@ -10940,9 +10945,9 @@ intersection_of: RO:0002104 PR:000001380 ! has plasma membrane part interleukin- relationship: CL:4030046 PR:000001203 ! lacks_plasma_membrane_part C-C chemokine receptor type 7 relationship: CL:4030046 PR:000001318 ! lacks_plasma_membrane_part L-selectin relationship: CL:4030046 PR:000001869 ! lacks_plasma_membrane_part interleukin-7 receptor subunit alpha -relationship: develops_from CL:0000900 ! naive thymus-derived CD8-positive, alpha-beta T cell relationship: RO:0002104 PR:000001343 ! has plasma membrane part CD69 molecule relationship: RO:0002104 PR:000001380 ! has plasma membrane part interleukin-2 receptor subunit alpha +relationship: RO:0002202 CL:0000900 ! develops from naive thymus-derived CD8-positive, alpha-beta T cell [Term] id: CL:0000907 @@ -10985,10 +10990,10 @@ intersection_of: RO:0002104 PR:000001380 ! has plasma membrane part interleukin- relationship: capable_of GO:0001816 ! cytokine production relationship: CL:4030046 PR:000001318 ! lacks_plasma_membrane_part L-selectin relationship: CL:4030046 PR:000001869 ! lacks_plasma_membrane_part interleukin-7 receptor subunit alpha -relationship: develops_from CL:0000906 ! activated CD8-positive, alpha-beta T cell relationship: output_of GO:0030217 ! T cell differentiation relationship: RO:0002104 PR:000001343 ! has plasma membrane part CD69 molecule relationship: RO:0002104 PR:000001380 ! has plasma membrane part interleukin-2 receptor subunit alpha +relationship: RO:0002202 CL:0000906 ! develops from activated CD8-positive, alpha-beta T cell [Term] id: CL:0000909 @@ -11006,8 +11011,8 @@ intersection_of: CL:0000625 ! CD8-positive, alpha-beta T cell intersection_of: bearer_of PATO:0001603 ! increased life span intersection_of: output_of GO:0002286 ! T cell activation involved in immune response intersection_of: output_of GO:0043379 ! memory T cell differentiation -relationship: dc-contributor https://orcid.org/0000-0001-9990-8331 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000910 @@ -11025,7 +11030,7 @@ is_a: CL:0000911 {is_inferred="true"} ! effector T cell intersection_of: CL:0000911 ! effector T cell intersection_of: capable_of GO:0001913 ! T cell mediated cytotoxicity relationship: capable_of GO:0001913 ! T cell mediated cytotoxicity -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000911 @@ -11080,7 +11085,7 @@ intersection_of: CL:4030046 PR:000001203 ! lacks_plasma_membrane_part C-C chemok intersection_of: CL:4030046 PR:000001380 ! lacks_plasma_membrane_part interleukin-2 receptor subunit alpha relationship: CL:4030046 PR:000001015 ! lacks_plasma_membrane_part receptor-type tyrosine-protein phosphatase C isoform CD45RA relationship: CL:4030046 PR:000001203 ! lacks_plasma_membrane_part C-C chemokine receptor type 7 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000914 @@ -11095,9 +11100,9 @@ synonym: "immature NKT cell" EXACT [] is_a: CL:0000790 {is_inferred="true"} ! immature alpha-beta T cell intersection_of: CL:0000790 ! immature alpha-beta T cell intersection_of: has_part PR:000003469 ! early growth response protein 2 -relationship: develops_from CL:0000809 ! double-positive, alpha-beta thymocyte relationship: has_part PR:000003469 ! early growth response protein 2 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0000809 ! develops from double-positive, alpha-beta thymocyte +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000915 @@ -11115,9 +11120,9 @@ intersection_of: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell sur intersection_of: RO:0002104 PR:000001084 ! has plasma membrane part T-cell surface glycoprotein CD8 alpha chain relationship: CL:4030046 PR:000001083 ! lacks_plasma_membrane_part CD2 molecule relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD5 -relationship: develops_from CL:0000811 ! CD8-positive, alpha-beta thymocyte -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001084 ! has plasma membrane part T-cell surface glycoprotein CD8 alpha chain +relationship: RO:0002202 CL:0000811 ! develops from CD8-positive, alpha-beta thymocyte +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000916 @@ -11131,10 +11136,10 @@ synonym: "DETC" EXACT [] is_a: CL:0000800 {is_inferred="true"} ! mature gamma-delta T cell intersection_of: CL:0000800 ! mature gamma-delta T cell intersection_of: capable_of GO:0060054 ! positive regulation of epithelial cell proliferation involved in wound healing -intersection_of: located_in UBERON:0001003 ! skin epidermis +intersection_of: RO:0001025 UBERON:0001003 ! located in skin epidermis relationship: capable_of GO:0060054 ! positive regulation of epithelial cell proliferation involved in wound healing -relationship: develops_from CL:0002401 ! mature dendritic epithelial T cell precursor -relationship: located_in UBERON:0001003 ! skin epidermis +relationship: RO:0001025 UBERON:0001003 ! located in skin epidermis +relationship: RO:0002202 CL:0002401 ! develops from mature dendritic epithelial T cell precursor [Term] id: CL:0000917 @@ -11209,9 +11214,9 @@ is_a: CL:0000795 {is_inferred="true"} ! CD8-positive, alpha-beta regulatory T ce intersection_of: CL:0000795 ! CD8-positive, alpha-beta regulatory T cell intersection_of: has_part PR:000001350 ! forkhead box protein P3 intersection_of: RO:0002104 PR:000001380 ! has plasma membrane part interleukin-2 receptor subunit alpha -relationship: develops_from CL:0000906 ! activated CD8-positive, alpha-beta T cell relationship: has_part PR:000001350 ! forkhead box protein P3 relationship: RO:0002104 PR:000001380 ! has plasma membrane part interleukin-2 receptor subunit alpha +relationship: RO:0002202 CL:0000906 ! develops from activated CD8-positive, alpha-beta T cell [Term] id: CL:0000920 @@ -11233,8 +11238,8 @@ intersection_of: CL:0000795 ! CD8-positive, alpha-beta regulatory T cell intersection_of: CL:4030046 PR:000001841 ! lacks_plasma_membrane_part T-cell-specific surface glycoprotein CD28 intersection_of: has_part PR:000001350 ! forkhead box protein P3 relationship: CL:4030046 PR:000001841 ! lacks_plasma_membrane_part T-cell-specific surface glycoprotein CD28 -relationship: develops_from CL:0000906 ! activated CD8-positive, alpha-beta T cell relationship: has_part PR:000001350 ! forkhead box protein P3 +relationship: RO:0002202 CL:0000906 ! develops from activated CD8-positive, alpha-beta T cell [Term] id: CL:0000921 @@ -11253,7 +11258,7 @@ is_a: CL:0000814 {is_inferred="true"} ! mature NK T cell intersection_of: CL:0000814 ! mature NK T cell intersection_of: capable_of GO:0043208 ! glycosphingolipid binding relationship: capable_of GO:0043208 ! glycosphingolipid binding -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000922 @@ -11315,8 +11320,8 @@ intersection_of: RO:0002104 PR:000001004 ! has plasma membrane part CD4 molecule intersection_of: RO:0002104 PR:000001343 ! has plasma membrane part CD69 molecule relationship: capable_of GO:0032609 ! type II interferon production relationship: capable_of GO:0032633 ! interleukin-4 production -relationship: develops_from CL:0000923 ! CD4-positive type I NK T cell relationship: RO:0002104 PR:000001343 ! has plasma membrane part CD69 molecule +relationship: RO:0002202 CL:0000923 ! develops from CD4-positive type I NK T cell [Term] id: CL:0000926 @@ -11334,7 +11339,7 @@ intersection_of: capable_of GO:0032609 ! type II interferon production intersection_of: RO:0002104 PR:000001004 ! has plasma membrane part CD4 molecule relationship: capable_of GO:0002827 ! positive regulation of T-helper 1 type immune response relationship: capable_of GO:0032609 ! type II interferon production -relationship: develops_from CL:0000925 ! activated CD4-positive type I NK T cell +relationship: RO:0002202 CL:0000925 ! develops from activated CD4-positive type I NK T cell [Term] id: CL:0000927 @@ -11354,7 +11359,7 @@ intersection_of: RO:0002104 PR:000001004 ! has plasma membrane part CD4 molecule relationship: capable_of GO:0002830 ! positive regulation of type 2 immune response relationship: capable_of GO:0032616 ! interleukin-13 production relationship: capable_of GO:0032633 ! interleukin-4 production -relationship: develops_from CL:0000925 ! activated CD4-positive type I NK T cell +relationship: RO:0002202 CL:0000925 ! develops from activated CD4-positive type I NK T cell [Term] id: CL:0000928 @@ -11371,8 +11376,8 @@ intersection_of: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecu intersection_of: CL:4030046 PR:000001084 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD8 alpha chain intersection_of: RO:0002104 PR:000001343 ! has plasma membrane part CD69 molecule relationship: capable_of GO:0002369 ! T cell cytokine production -relationship: develops_from CL:0000924 ! CD4-negative, CD8-negative type I NK T cell relationship: RO:0002104 PR:000001343 ! has plasma membrane part CD69 molecule +relationship: RO:0002202 CL:0000924 ! develops from CD4-negative, CD8-negative type I NK T cell [Term] id: CL:0000929 @@ -11391,7 +11396,7 @@ intersection_of: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecu intersection_of: CL:4030046 PR:000001084 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD8 alpha chain relationship: capable_of GO:0002827 ! positive regulation of T-helper 1 type immune response relationship: capable_of GO:0032609 ! type II interferon production -relationship: develops_from CL:0000928 ! activated CD4-negative, CD8-negative type I NK T cell +relationship: RO:0002202 CL:0000928 ! develops from activated CD4-negative, CD8-negative type I NK T cell [Term] id: CL:0000930 @@ -11410,7 +11415,7 @@ intersection_of: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecu intersection_of: CL:4030046 PR:000001084 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD8 alpha chain relationship: capable_of GO:0002830 ! positive regulation of type 2 immune response relationship: capable_of GO:0032633 ! interleukin-4 production -relationship: develops_from CL:0000928 ! activated CD4-negative, CD8-negative type I NK T cell +relationship: RO:0002202 CL:0000928 ! develops from activated CD4-negative, CD8-negative type I NK T cell [Term] id: CL:0000931 @@ -11442,8 +11447,8 @@ intersection_of: CL:0000922 ! type II NK T cell intersection_of: capable_of GO:0032609 ! type II interferon production intersection_of: RO:0002104 PR:000001343 ! has plasma membrane part CD69 molecule relationship: capable_of GO:0032609 ! type II interferon production -relationship: develops_from CL:0000931 ! activated type II NK T cell relationship: RO:0002104 PR:000001343 ! has plasma membrane part CD69 molecule +relationship: RO:0002202 CL:0000931 ! develops from activated type II NK T cell [Term] id: CL:0000933 @@ -11459,8 +11464,8 @@ intersection_of: CL:0000922 ! type II NK T cell intersection_of: capable_of GO:0032633 ! interleukin-4 production intersection_of: RO:0002104 PR:000001343 ! has plasma membrane part CD69 molecule relationship: capable_of GO:0032633 ! interleukin-4 production -relationship: develops_from CL:0000931 ! activated type II NK T cell relationship: RO:0002104 PR:000001343 ! has plasma membrane part CD69 molecule +relationship: RO:0002202 CL:0000931 ! develops from activated type II NK T cell [Term] id: CL:0000934 @@ -11476,9 +11481,9 @@ intersection_of: CL:0000624 ! CD4-positive, alpha-beta T cell intersection_of: capable_of GO:0001913 ! T cell mediated cytotoxicity intersection_of: output_of GO:0030217 ! T cell differentiation relationship: capable_of GO:0001913 ! T cell mediated cytotoxicity -relationship: develops_from CL:0000896 ! activated CD4-positive, alpha-beta T cell relationship: output_of GO:0030217 ! T cell differentiation -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0000896 ! develops from activated CD4-positive, alpha-beta T cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000935 @@ -11494,7 +11499,7 @@ intersection_of: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecu intersection_of: CL:4030046 PR:000025403 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD8 alpha chain isoform 1 relationship: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecule relationship: CL:4030046 PR:000025403 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD8 alpha chain isoform 1 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000936 @@ -11518,11 +11523,11 @@ intersection_of: RO:0002104 PR:000002065 ! has plasma membrane part mast/stem ce intersection_of: RO:0002104 PR:000002979 ! has plasma membrane part lymphocyte antigen 6A-2/6E-1 relationship: capable_of GO:0030098 ! lymphocyte differentiation relationship: CL:4030046 PR:000001460 ! lacks_plasma_membrane_part glycophorin-A -relationship: develops_from CL:0002035 ! Slamf1-negative multipotent progenitor cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000002001 ! has plasma membrane part receptor-type tyrosine-protein kinase FLT3 relationship: RO:0002104 PR:000002065 ! has plasma membrane part mast/stem cell growth factor receptor relationship: RO:0002104 PR:000002979 ! has plasma membrane part lymphocyte antigen 6A-2/6E-1 +relationship: RO:0002202 CL:0002035 ! develops from Slamf1-negative multipotent progenitor cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000937 @@ -11556,15 +11561,15 @@ intersection_of: CL:0000824 ! mature natural killer cell intersection_of: capable_of GO:0032609 ! type II interferon production intersection_of: CL:4030046 PR:000001483 ! lacks_plasma_membrane_part low affinity immunoglobulin gamma Fc region receptor III intersection_of: CL:4030046 PR:000002015 ! lacks_plasma_membrane_part MHC class II histocompatibility antigen alpha chain DRA -intersection_of: in_taxon NCBITaxon:9606 ! Homo sapiens intersection_of: RO:0002104 PR:000001319 ! has plasma membrane part SLAM family member 5 +intersection_of: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens intersection_of: RO:0015015 PR:000001024 ! has high plasma membrane amount neural cell adhesion molecule 1 relationship: CL:4030046 PR:000001483 ! lacks_plasma_membrane_part low affinity immunoglobulin gamma Fc region receptor III relationship: CL:4030046 PR:000002015 ! lacks_plasma_membrane_part MHC class II histocompatibility antigen alpha chain DRA -relationship: in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001319 ! has plasma membrane part SLAM family member 5 +relationship: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens relationship: RO:0015015 PR:000001024 ! has high plasma membrane amount neural cell adhesion molecule 1 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000939 @@ -11585,13 +11590,13 @@ intersection_of: CL:0000824 ! mature natural killer cell intersection_of: capable_of GO:0001816 ! cytokine production intersection_of: capable_of GO:0042267 ! natural killer cell mediated cytotoxicity intersection_of: CL:4030046 PR:000002015 ! lacks_plasma_membrane_part MHC class II histocompatibility antigen alpha chain DRA -intersection_of: in_taxon NCBITaxon:9606 ! Homo sapiens intersection_of: RO:0002104 PR:000001483 ! has plasma membrane part low affinity immunoglobulin gamma Fc region receptor III +intersection_of: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens intersection_of: RO:0015016 PR:000001024 ! has low plasma membrane amount neural cell adhesion molecule 1 relationship: capable_of GO:0042267 ! natural killer cell mediated cytotoxicity relationship: CL:4030046 PR:000002015 ! lacks_plasma_membrane_part MHC class II histocompatibility antigen alpha chain DRA -relationship: in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001483 ! has plasma membrane part low affinity immunoglobulin gamma Fc region receptor III +relationship: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens relationship: RO:0015016 PR:000001024 ! has low plasma membrane amount neural cell adhesion molecule 1 [Term] @@ -11611,7 +11616,7 @@ intersection_of: output_of GO:0030217 ! T cell differentiation relationship: capable_of GO:0002227 ! innate immune response in mucosa relationship: capable_of GO:0032394 ! MHC class Ib receptor activity relationship: output_of GO:0030217 ! T cell differentiation -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000941 @@ -11626,9 +11631,9 @@ intersection_of: part_of UBERON:0002370 ! thymus intersection_of: RO:0002104 PR:000001013 ! has plasma membrane part integrin alpha-X relationship: CL:4030046 PR:000001012 ! lacks_plasma_membrane_part integrin alpha-M relationship: CL:4030046 PR:000001015 ! lacks_plasma_membrane_part receptor-type tyrosine-protein phosphatase C isoform CD45RA -relationship: develops_from CL:0000894 ! DN1 thymic pro-T cell relationship: part_of UBERON:0002370 ! thymus relationship: RO:0002104 PR:000001013 ! has plasma membrane part integrin alpha-X +relationship: RO:0002202 CL:0000894 ! develops from DN1 thymic pro-T cell [Term] id: CL:0000942 @@ -11641,10 +11646,10 @@ intersection_of: CL:4030046 PR:000001012 ! lacks_plasma_membrane_part integrin a intersection_of: RO:0002104 PR:000001015 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RA intersection_of: RO:0002104 PR:000001865 ! has plasma membrane part interleukin-3 receptor class 2 alpha chain relationship: CL:4030046 PR:000001012 ! lacks_plasma_membrane_part integrin alpha-M -relationship: develops_from CL:0000894 ! DN1 thymic pro-T cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001015 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RA relationship: RO:0002104 PR:000001865 ! has plasma membrane part interleukin-3 receptor class 2 alpha chain +relationship: RO:0002202 CL:0000894 ! develops from DN1 thymic pro-T cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000943 @@ -11691,8 +11696,8 @@ def: "A lymphocyte of B lineage with the commitment to express an immunoglobulin comment: Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells). Lymphocytes of B cell lineage can be distinguished from those of T cell lineage by their lack of CD3e (as part of the T cell receptor complex). subset: human_reference_atlas is_a: CL:0000542 {is_inferred="true"} ! lymphocyte -relationship: develops_from CL:0000826 ! pro-B cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0000826 ! develops from pro-B cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000946 @@ -11906,11 +11911,11 @@ intersection_of: RO:0002104 PR:000001338 ! has plasma membrane part complement r intersection_of: RO:0002104 PR:000001880 ! has plasma membrane part low affinity immunoglobulin epsilon Fc receptor intersection_of: RO:0002104 PR:000002037 ! has plasma membrane part complement component C1q receptor relationship: CL:4030046 PR:000001318 ! lacks_plasma_membrane_part L-selectin -relationship: develops_from CL:0000958 ! T1 B cell relationship: RO:0002104 GO:0071738 ! has plasma membrane part IgD immunoglobulin complex relationship: RO:0002104 PR:000001338 ! has plasma membrane part complement receptor type 2 relationship: RO:0002104 PR:000001880 ! has plasma membrane part low affinity immunoglobulin epsilon Fc receptor relationship: RO:0002104 PR:000002037 ! has plasma membrane part complement component C1q receptor +relationship: RO:0002202 CL:0000958 ! develops from T1 B cell [Term] id: CL:0000960 @@ -11929,12 +11934,12 @@ intersection_of: RO:0002104 GO:0071753 ! has plasma membrane part IgM immunoglob intersection_of: RO:0002104 PR:000001318 ! has plasma membrane part L-selectin intersection_of: RO:0002104 PR:000001338 ! has plasma membrane part complement receptor type 2 intersection_of: RO:0002104 PR:000001880 ! has plasma membrane part low affinity immunoglobulin epsilon Fc receptor -relationship: develops_from CL:0000959 ! T2 B cell relationship: participates_in GO:0002515 ! B cell anergy relationship: RO:0002104 GO:0071738 ! has plasma membrane part IgD immunoglobulin complex relationship: RO:0002104 PR:000001318 ! has plasma membrane part L-selectin relationship: RO:0002104 PR:000001338 ! has plasma membrane part complement receptor type 2 relationship: RO:0002104 PR:000001880 ! has plasma membrane part low affinity immunoglobulin epsilon Fc receptor +relationship: RO:0002202 CL:0000959 ! develops from T2 B cell [Term] id: CL:0000961 @@ -11965,9 +11970,9 @@ intersection_of: CL:0000843 ! follicular B cell intersection_of: RO:0002104 GO:0071738 ! has plasma membrane part IgD immunoglobulin complex intersection_of: RO:0002104 PR:000001408 ! has plasma membrane part ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 intersection_of: RO:0002104 PR:000001880 ! has plasma membrane part low affinity immunoglobulin epsilon Fc receptor -relationship: develops_from CL:0000961 ! Bm1 B cell relationship: RO:0002104 PR:000001408 ! has plasma membrane part ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 relationship: RO:0002104 PR:000001880 ! has plasma membrane part low affinity immunoglobulin epsilon Fc receptor +relationship: RO:0002202 CL:0000961 ! develops from Bm1 B cell [Term] id: CL:0000963 @@ -11982,9 +11987,9 @@ intersection_of: CL:4030046 GO:0071753 ! lacks_plasma_membrane_part IgM immunogl intersection_of: RO:0002104 GO:0071738 ! has plasma membrane part IgD immunoglobulin complex intersection_of: RO:0002104 PR:000001408 ! has plasma membrane part ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 relationship: CL:4030046 GO:0071753 ! lacks_plasma_membrane_part IgM immunoglobulin complex -relationship: develops_from CL:0000965 ! Bm3 B cell relationship: RO:0002104 GO:0071738 ! has plasma membrane part IgD immunoglobulin complex relationship: RO:0002104 PR:000001408 ! has plasma membrane part ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 +relationship: RO:0002202 CL:0000965 ! develops from Bm3 B cell [Term] id: CL:0000964 @@ -12004,9 +12009,9 @@ intersection_of: RO:0002104 GO:0071738 ! has plasma membrane part IgD immunoglob intersection_of: RO:0002104 PR:000001408 ! has plasma membrane part ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 relationship: capable_of GO:0002634 ! regulation of germinal center formation relationship: CL:4030046 PR:000001880 ! lacks_plasma_membrane_part low affinity immunoglobulin epsilon Fc receptor -relationship: develops_from CL:0000962 ! Bm2 B cell relationship: RO:0002104 GO:0071738 ! has plasma membrane part IgD immunoglobulin complex relationship: RO:0002104 PR:000001408 ! has plasma membrane part ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 +relationship: RO:0002202 CL:0000962 ! develops from Bm2 B cell [Term] id: CL:0000965 @@ -12025,9 +12030,9 @@ intersection_of: RO:0002104 PR:000001408 ! has plasma membrane part ADP-ribosyl intersection_of: RO:0002104 PR:000003516 ! has plasma membrane part lactosylceramide 4-alpha-galactosyltransferase relationship: capable_of GO:0016446 ! somatic hypermutation of immunoglobulin genes relationship: CL:4030046 GO:0071738 ! lacks_plasma_membrane_part IgD immunoglobulin complex -relationship: develops_from CL:0000964 ! Bm2' B cell relationship: RO:0002104 PR:000001408 ! has plasma membrane part ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 relationship: RO:0002104 PR:000003516 ! has plasma membrane part lactosylceramide 4-alpha-galactosyltransferase +relationship: RO:0002202 CL:0000964 ! develops from Bm2' B cell [Term] id: CL:0000966 @@ -12046,9 +12051,9 @@ intersection_of: output_of GO:0016446 ! somatic hypermutation of immunoglobulin intersection_of: RO:0002104 PR:000001408 ! has plasma membrane part ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 relationship: CL:4030046 GO:0071738 ! lacks_plasma_membrane_part IgD immunoglobulin complex relationship: CL:4030046 PR:000003516 ! lacks_plasma_membrane_part lactosylceramide 4-alpha-galactosyltransferase -relationship: develops_from CL:0000963 ! Bm3-delta B cell relationship: output_of GO:0016446 ! somatic hypermutation of immunoglobulin genes relationship: RO:0002104 PR:000001408 ! has plasma membrane part ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 +relationship: RO:0002202 CL:0000963 ! develops from Bm3-delta B cell [Term] id: CL:0000967 @@ -12063,9 +12068,9 @@ intersection_of: CL:0000787 ! memory B cell intersection_of: CL:4030046 GO:0071738 ! lacks_plasma_membrane_part IgD immunoglobulin complex intersection_of: output_of GO:0002314 ! germinal center B cell differentiation intersection_of: output_of GO:0016446 ! somatic hypermutation of immunoglobulin genes -relationship: develops_from CL:0000966 ! Bm4 B cell relationship: output_of GO:0002314 ! germinal center B cell differentiation relationship: output_of GO:0016446 ! somatic hypermutation of immunoglobulin genes +relationship: RO:0002202 CL:0000966 ! develops from Bm4 B cell [Term] id: CL:0000968 @@ -12131,11 +12136,11 @@ intersection_of: RO:0002104 PR:000001963 ! has plasma membrane part CD27 molecul relationship: CL:4030046 GO:0071735 ! lacks_plasma_membrane_part IgG immunoglobulin complex relationship: CL:4030046 GO:0071742 ! lacks_plasma_membrane_part IgE immunoglobulin complex relationship: CL:4030046 GO:0071745 ! lacks_plasma_membrane_part IgA immunoglobulin complex -relationship: develops_from CL:0000980 ! plasmablast -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 GO:0071738 ! has plasma membrane part IgD immunoglobulin complex relationship: RO:0002104 GO:0071753 ! has plasma membrane part IgM immunoglobulin complex relationship: RO:0002104 PR:000001963 ! has plasma membrane part CD27 molecule +relationship: RO:0002202 CL:0000980 ! develops from plasmablast +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000971 @@ -12171,10 +12176,10 @@ intersection_of: CL:4030046 GO:0071753 ! lacks_plasma_membrane_part IgM immunogl intersection_of: output_of GO:0045190 ! isotype switching intersection_of: RO:0002104 PR:000001963 ! has plasma membrane part CD27 molecule relationship: CL:4030046 GO:0071753 ! lacks_plasma_membrane_part IgM immunoglobulin complex -relationship: develops_from CL:0000970 ! unswitched memory B cell relationship: output_of GO:0045190 ! isotype switching -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001963 ! has plasma membrane part CD27 molecule +relationship: RO:0002202 CL:0000970 ! develops from unswitched memory B cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000973 @@ -12207,7 +12212,7 @@ intersection_of: RO:0015015 PR:000001208 ! has high plasma membrane amount C-X-C intersection_of: RO:0015015 PR:000001935 ! has high plasma membrane amount syndecan-1 intersection_of: RO:0015016 PR:000001002 ! has low plasma membrane amount CD19 molecule relationship: CL:4030046 PR:000001408 ! lacks_plasma_membrane_part ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 -relationship: develops_from CL:0000975 ! short lived plasma cell +relationship: RO:0002202 CL:0000975 ! develops from short lived plasma cell relationship: RO:0015015 PR:000001208 ! has high plasma membrane amount C-X-C chemokine receptor type 4 relationship: RO:0015015 PR:000001935 ! has high plasma membrane amount syndecan-1 relationship: RO:0015016 PR:000001002 ! has low plasma membrane amount CD19 molecule @@ -12285,10 +12290,10 @@ intersection_of: RO:0015015 PR:000001408 ! has high plasma membrane amount ADP-r intersection_of: RO:0015015 PR:000001963 ! has high plasma membrane amount CD27 molecule relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-spanning 4-domains subfamily A member 1 relationship: CL:4030046 PR:000001935 ! lacks_plasma_membrane_part syndecan-1 -relationship: develops_from CL:0000785 ! mature B cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0000785 ! develops from mature B cell relationship: RO:0015015 PR:000001408 ! has high plasma membrane amount ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 relationship: RO:0015015 PR:000001963 ! has high plasma membrane amount CD27 molecule +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000981 @@ -12414,8 +12419,8 @@ xref: FMA:84191 is_a: CL:0000451 {is_inferred="true"} ! dendritic cell intersection_of: CL:0000451 ! dendritic cell intersection_of: RO:0015015 PR:000001013 ! has high plasma membrane amount integrin alpha-X -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0015015 PR:000001013 ! has high plasma membrane amount integrin alpha-X +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000991 @@ -12446,7 +12451,7 @@ is_a: CL:0000989 {is_inferred="true"} ! CD11c-low plasmacytoid dendritic cell intersection_of: CL:0000989 ! CD11c-low plasmacytoid dendritic cell intersection_of: RO:0015016 PR:000001412 ! has low plasma membrane amount CD86 molecule intersection_of: RO:0015016 PR:000001438 ! has low plasma membrane amount CD80 molecule -relationship: develops_from CL:0001029 ! common dendritic progenitor +relationship: RO:0002202 CL:0001029 ! develops from common dendritic progenitor relationship: RO:0015016 PR:000001412 ! has low plasma membrane amount CD86 molecule relationship: RO:0015016 PR:000001438 ! has low plasma membrane amount CD80 molecule @@ -12462,8 +12467,8 @@ intersection_of: RO:0002104 PR:000001310 ! has plasma membrane part CD83 molecul intersection_of: RO:0015015 GO:0042613 ! has high plasma membrane amount MHC class II protein complex intersection_of: RO:0015015 PR:000001412 ! has high plasma membrane amount CD86 molecule intersection_of: RO:0015015 PR:000001438 ! has high plasma membrane amount CD80 molecule -relationship: develops_from CL:0000992 ! immature CD11c-low plasmacytoid dendritic cell relationship: RO:0002104 PR:000001310 ! has plasma membrane part CD83 molecule +relationship: RO:0002202 CL:0000992 ! develops from immature CD11c-low plasmacytoid dendritic cell relationship: RO:0015015 GO:0042613 ! has high plasma membrane amount MHC class II protein complex relationship: RO:0015015 PR:000001412 ! has high plasma membrane amount CD86 molecule relationship: RO:0015015 PR:000001438 ! has high plasma membrane amount CD80 molecule @@ -12480,7 +12485,7 @@ intersection_of: CL:4030046 PR:000001438 ! lacks_plasma_membrane_part CD80 molec intersection_of: RO:0015016 GO:0042613 ! has low plasma membrane amount MHC class II protein complex intersection_of: RO:0015016 PR:000001412 ! has low plasma membrane amount CD86 molecule relationship: CL:4030046 PR:000001438 ! lacks_plasma_membrane_part CD80 molecule -relationship: develops_from CL:0000995 ! CD34-positive, CD38-positive common myeloid progenitor OR CD34-positive, CD38-positive common lymphoid progenitor +relationship: RO:0002202 CL:0000995 ! develops from CD34-positive, CD38-positive common myeloid progenitor OR CD34-positive, CD38-positive common lymphoid progenitor relationship: RO:0015016 GO:0042613 ! has low plasma membrane amount MHC class II protein complex relationship: RO:0015016 PR:000001412 ! has low plasma membrane amount CD86 molecule @@ -12504,8 +12509,8 @@ intersection_of: RO:0002104 PR:000001310 ! has plasma membrane part CD83 molecul intersection_of: RO:0015015 GO:0042613 ! has high plasma membrane amount MHC class II protein complex intersection_of: RO:0015015 PR:000001412 ! has high plasma membrane amount CD86 molecule intersection_of: RO:0015015 PR:000001438 ! has high plasma membrane amount CD80 molecule -relationship: develops_from CL:0000994 ! immature CD11c-negative plasmacytoid dendritic cell relationship: RO:0002104 PR:000001310 ! has plasma membrane part CD83 molecule +relationship: RO:0002202 CL:0000994 ! develops from immature CD11c-negative plasmacytoid dendritic cell relationship: RO:0015015 GO:0042613 ! has high plasma membrane amount MHC class II protein complex relationship: RO:0015015 PR:000001412 ! has high plasma membrane amount CD86 molecule relationship: RO:0015015 PR:000001438 ! has high plasma membrane amount CD80 molecule @@ -12541,8 +12546,8 @@ relationship: capable_of GO:0002474 ! antigen processing and presentation of pep relationship: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecule relationship: CL:4030046 PR:000001012 ! lacks_plasma_membrane_part integrin alpha-M relationship: CL:4030046 PR:000001084 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD8 alpha chain -relationship: develops_from CL:0002010 ! pre-conventional dendritic cell relationship: RO:0002104 PR:000001026 ! has plasma membrane part lymphocyte antigen 75 +relationship: RO:0002202 CL:0002010 ! develops from pre-conventional dendritic cell [Term] id: CL:0000999 @@ -12561,8 +12566,8 @@ intersection_of: RO:0002104 PR:000001004 ! has plasma membrane part CD4 molecule relationship: capable_of GO:0050728 ! negative regulation of inflammatory response relationship: CL:4030046 PR:000001026 ! lacks_plasma_membrane_part lymphocyte antigen 75 relationship: CL:4030046 PR:000001084 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD8 alpha chain -relationship: develops_from CL:0002010 ! pre-conventional dendritic cell relationship: RO:0002104 PR:000001004 ! has plasma membrane part CD4 molecule +relationship: RO:0002202 CL:0002010 ! develops from pre-conventional dendritic cell [Term] id: CL:0001000 @@ -12584,9 +12589,9 @@ relationship: capable_of GO:0042590 ! antigen processing and presentation of exo relationship: capable_of GO:0050729 ! positive regulation of inflammatory response relationship: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecule relationship: CL:4030046 PR:000001012 ! lacks_plasma_membrane_part integrin alpha-M -relationship: develops_from CL:0002010 ! pre-conventional dendritic cell relationship: RO:0002104 PR:000001026 ! has plasma membrane part lymphocyte antigen 75 relationship: RO:0002104 PR:000001084 ! has plasma membrane part T-cell surface glycoprotein CD8 alpha chain +relationship: RO:0002202 CL:0002010 ! develops from pre-conventional dendritic cell [Term] id: CL:0001001 @@ -12613,7 +12618,7 @@ intersection_of: RO:0002104 PR:000001310 ! has plasma membrane part CD83 molecul intersection_of: RO:0015015 GO:0042613 ! has high plasma membrane amount MHC class II protein complex intersection_of: RO:0015015 PR:000001412 ! has high plasma membrane amount CD86 molecule intersection_of: RO:0015015 PR:000001438 ! has high plasma membrane amount CD80 molecule -relationship: develops_from CL:0001001 ! immature CD8_alpha-negative CD11b-negative dendritic cell +relationship: RO:0002202 CL:0001001 ! develops from immature CD8_alpha-negative CD11b-negative dendritic cell [Term] id: CL:0001003 @@ -12627,7 +12632,7 @@ intersection_of: RO:0002104 PR:000001310 ! has plasma membrane part CD83 molecul intersection_of: RO:0015015 GO:0042613 ! has high plasma membrane amount MHC class II protein complex intersection_of: RO:0015015 PR:000001412 ! has high plasma membrane amount CD86 molecule intersection_of: RO:0015015 PR:000001438 ! has high plasma membrane amount CD80 molecule -relationship: develops_from CL:0000997 ! immature CD8_alpha-negative CD11b-positive dendritic cell +relationship: RO:0002202 CL:0000997 ! develops from immature CD8_alpha-negative CD11b-positive dendritic cell [Term] id: CL:0001004 @@ -12653,7 +12658,7 @@ intersection_of: RO:0002104 PR:000001310 ! has plasma membrane part CD83 molecul intersection_of: RO:0015015 GO:0042613 ! has high plasma membrane amount MHC class II protein complex intersection_of: RO:0015015 PR:000001412 ! has high plasma membrane amount CD86 molecule intersection_of: RO:0015015 PR:000001438 ! has high plasma membrane amount CD80 molecule -relationship: develops_from CL:0001004 ! immature CD8_alpha-positive CD11b-negative dendritic cell +relationship: RO:0002202 CL:0001004 ! develops from immature CD8_alpha-positive CD11b-negative dendritic cell [Term] id: CL:0001006 @@ -12669,9 +12674,9 @@ intersection_of: RO:0002104 PR:000001012 ! has plasma membrane part integrin alp intersection_of: RO:0002104 PR:000001026 ! has plasma membrane part lymphocyte antigen 75 intersection_of: RO:0002104 PR:000001084 ! has plasma membrane part T-cell surface glycoprotein CD8 alpha chain relationship: part_of UBERON:0002067 ! dermis -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001026 ! has plasma membrane part lymphocyte antigen 75 relationship: RO:0002104 PR:000001084 ! has plasma membrane part T-cell surface glycoprotein CD8 alpha chain +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0001007 @@ -12745,7 +12750,7 @@ intersection_of: RO:0002104 PR:000001310 ! has plasma membrane part CD83 molecul intersection_of: RO:0015015 GO:0042613 ! has high plasma membrane amount MHC class II protein complex intersection_of: RO:0015015 PR:000001412 ! has high plasma membrane amount CD86 molecule intersection_of: RO:0015015 PR:000001438 ! has high plasma membrane amount CD80 molecule -relationship: develops_from CL:0001009 ! immature dermal dendritic cell +relationship: RO:0002202 CL:0001009 ! develops from immature dermal dendritic cell [Term] id: CL:0001011 @@ -12779,7 +12784,7 @@ intersection_of: RO:0002104 PR:000001310 ! has plasma membrane part CD83 molecul intersection_of: RO:0015015 GO:0042613 ! has high plasma membrane amount MHC class II protein complex intersection_of: RO:0015015 PR:000001412 ! has high plasma membrane amount CD86 molecule intersection_of: RO:0015015 PR:000001438 ! has high plasma membrane amount CD80 molecule -relationship: develops_from CL:0001011 ! immature interstitial dendritic cell +relationship: RO:0002202 CL:0001011 ! develops from immature interstitial dendritic cell [Term] id: CL:0001014 @@ -12830,7 +12835,7 @@ intersection_of: RO:0002104 PR:000001310 ! has plasma membrane part CD83 molecul intersection_of: RO:0015015 GO:0042613 ! has high plasma membrane amount MHC class II protein complex intersection_of: RO:0015015 PR:000001412 ! has high plasma membrane amount CD86 molecule intersection_of: RO:0015015 PR:000001438 ! has high plasma membrane amount CD80 molecule -relationship: develops_from CL:0001016 ! immature CD1a-positive Langerhans cell +relationship: RO:0002202 CL:0001016 ! develops from immature CD1a-positive Langerhans cell [Term] id: CL:0001018 @@ -12864,7 +12869,7 @@ intersection_of: RO:0002104 PR:000001310 ! has plasma membrane part CD83 molecul intersection_of: RO:0015015 GO:0042613 ! has high plasma membrane amount MHC class II protein complex intersection_of: RO:0015015 PR:000001412 ! has high plasma membrane amount CD86 molecule intersection_of: RO:0015015 PR:000001438 ! has high plasma membrane amount CD80 molecule -relationship: develops_from CL:0001018 ! immature CD8_alpha-low Langerhans cell +relationship: RO:0002202 CL:0001018 ! develops from immature CD8_alpha-low Langerhans cell [Term] id: CL:0001021 @@ -12883,11 +12888,11 @@ intersection_of: RO:0002104 PR:000001015 ! has plasma membrane part receptor-typ intersection_of: RO:0002104 PR:000001408 ! has plasma membrane part ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 intersection_of: RO:0002104 PR:000001898 ! has plasma membrane part neprilysin disjoint_from: CL:0001025 ! Kit-positive, Sca1-positive common lymphoid progenitor -relationship: develops_from CL:0002043 ! CD34-positive, CD38-negative multipotent progenitor cell relationship: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule relationship: RO:0002104 PR:000001015 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RA relationship: RO:0002104 PR:000001408 ! has plasma membrane part ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 relationship: RO:0002104 PR:000001898 ! has plasma membrane part neprilysin +relationship: RO:0002202 CL:0002043 ! develops from CD34-positive, CD38-negative multipotent progenitor cell [Term] id: CL:0001022 @@ -12901,9 +12906,9 @@ is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000576 ! monocyte intersection_of: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M intersection_of: RO:0002104 PR:000002062 ! has plasma membrane part macrophage colony-stimulating factor 1 receptor -relationship: develops_from CL:0002001 ! CD34-positive, CD38-positive granulocyte monocyte progenitor relationship: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M relationship: RO:0002104 PR:000002062 ! has plasma membrane part macrophage colony-stimulating factor 1 receptor +relationship: RO:0002202 CL:0002001 ! develops from CD34-positive, CD38-positive granulocyte monocyte progenitor [Term] id: CL:0001023 @@ -12922,8 +12927,8 @@ intersection_of: RO:0015016 PR:000001481 ! has low plasma membrane amount low af disjoint_from: CL:0001026 ! CD34-positive, CD38-positive common myeloid progenitor relationship: CL:4030046 PR:000001869 ! lacks_plasma_membrane_part interleukin-7 receptor subunit alpha relationship: CL:4030046 PR:000002979 ! lacks_plasma_membrane_part lymphocyte antigen 6A-2/6E-1 -relationship: develops_from CL:0002035 ! Slamf1-negative multipotent progenitor cell relationship: RO:0002104 PR:000002065 ! has plasma membrane part mast/stem cell growth factor receptor +relationship: RO:0002202 CL:0002035 ! develops from Slamf1-negative multipotent progenitor cell relationship: RO:0015016 GO:0033001 ! has low plasma membrane amount Fc-gamma receptor III complex relationship: RO:0015016 PR:000001481 ! has low plasma membrane amount low affinity immunoglobulin gamma Fc region receptor II-b @@ -12976,11 +12981,11 @@ intersection_of: RO:0002104 PR:000002037 ! has plasma membrane part complement c intersection_of: RO:0015016 PR:000002065 ! has low plasma membrane amount mast/stem cell growth factor receptor intersection_of: RO:0015016 PR:000002979 ! has low plasma membrane amount lymphocyte antigen 6A-2/6E-1 relationship: CL:4030046 PR:000001014 ! lacks_plasma_membrane_part receptor-type tyrosine-protein phosphatase C isoform CD45RABC -relationship: develops_from CL:0000936 ! early lymphoid progenitor relationship: RO:0002104 PR:000001869 ! has plasma membrane part interleukin-7 receptor subunit alpha relationship: RO:0002104 PR:000001963 ! has plasma membrane part CD27 molecule relationship: RO:0002104 PR:000002001 ! has plasma membrane part receptor-type tyrosine-protein kinase FLT3 relationship: RO:0002104 PR:000002037 ! has plasma membrane part complement component C1q receptor +relationship: RO:0002202 CL:0000936 ! develops from early lymphoid progenitor relationship: RO:0015016 PR:000002065 ! has low plasma membrane amount mast/stem cell growth factor receptor relationship: RO:0015016 PR:000002979 ! has low plasma membrane amount lymphocyte antigen 6A-2/6E-1 @@ -13003,8 +13008,8 @@ relationship: CL:4030046 PR:000001015 ! lacks_plasma_membrane_part receptor-type relationship: CL:4030046 PR:000001836 ! lacks_plasma_membrane_part CD7 molecule relationship: CL:4030046 PR:000001867 ! lacks_plasma_membrane_part interleukin-5 receptor subunit alpha relationship: CL:4030046 PR:000001898 ! lacks_plasma_membrane_part neprilysin -relationship: develops_from CL:0002043 ! CD34-positive, CD38-negative multipotent progenitor cell relationship: RO:0002104 PR:000001408 ! has plasma membrane part ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 +relationship: RO:0002202 CL:0002043 ! develops from CD34-positive, CD38-negative multipotent progenitor cell relationship: RO:0015016 PR:000001865 ! has low plasma membrane amount interleukin-3 receptor class 2 alpha chain [Term] @@ -13022,8 +13027,8 @@ intersection_of: CL:4030046 PR:000001836 ! lacks_plasma_membrane_part CD7 molecu intersection_of: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule relationship: CL:4030046 PR:000001015 ! lacks_plasma_membrane_part receptor-type tyrosine-protein phosphatase C isoform CD45RA relationship: CL:4030046 PR:000001836 ! lacks_plasma_membrane_part CD7 molecule -relationship: develops_from CL:0001021 ! CD34-positive, CD38-positive common lymphoid progenitor relationship: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule +relationship: RO:0002202 CL:0001021 ! develops from CD34-positive, CD38-positive common lymphoid progenitor [Term] id: CL:0001028 @@ -13038,9 +13043,9 @@ intersection_of: CL:4030046 PR:000001015 ! lacks_plasma_membrane_part receptor-t intersection_of: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule intersection_of: RO:0002104 PR:000001836 ! has plasma membrane part CD7 molecule relationship: CL:4030046 PR:000001015 ! lacks_plasma_membrane_part receptor-type tyrosine-protein phosphatase C isoform CD45RA -relationship: develops_from CL:0001027 ! CD7-negative lymphoid progenitor cell relationship: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule relationship: RO:0002104 PR:000001836 ! has plasma membrane part CD7 molecule +relationship: RO:0002202 CL:0001027 ! develops from CD7-negative lymphoid progenitor cell [Term] id: CL:0001029 @@ -13082,9 +13087,9 @@ relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surfac relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -relationship: develops_from CL:0002009 ! macrophage dendritic cell progenitor relationship: RO:0002104 PR:000002001 ! has plasma membrane part receptor-type tyrosine-protein kinase FLT3 relationship: RO:0002104 PR:000002062 ! has plasma membrane part macrophage colony-stimulating factor 1 receptor +relationship: RO:0002202 CL:0002009 ! develops from macrophage dendritic cell progenitor relationship: RO:0015016 PR:000002065 ! has low plasma membrane amount mast/stem cell growth factor receptor [Term] @@ -13108,7 +13113,7 @@ is_a: CL:2000028 ! cerebellum glutamatergic neuron is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: CL:0000120 ! granule cell intersection_of: RO:0002100 UBERON:0002037 ! has soma location cerebellum -relationship: directly_develops_from CL:0002362 ! cerebellar granule cell precursor +relationship: RO:0002207 CL:0002362 ! directly develops from cerebellar granule cell precursor [Term] id: CL:0001032 @@ -13135,7 +13140,7 @@ name: cell in vitro def: "A cell that is maintained or propagated in a controlled artificial environment for use in an investigation." [ReO:mhb] comment: 'In vitro', translating literally to 'in glass', typically refers to a controlled, often sterile, laboratory setting where cells or other specimens are placed by some agent for the purpose of studying or manipulating them as part of some research investigation. 'In vitro' is intended to contrast with 'native',which refers to cells or other biological entities that are found in a natural setting. It describes unicellular organisms removed from a natural environement and multicellular organism cells removed from an organism, or cells derived in culture from such displaced cells. is_a: CL:0000000 ! cell -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-01-12T09:58:38Z [Term] @@ -13147,9 +13152,9 @@ subset: human_reference_atlas is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001474 ! bone element -relationship: dc-contributor https://orcid.org/0000-0001-9990-8331 relationship: part_of UBERON:0001474 ! bone element -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2011-11-16T04:28:16Z [Term] @@ -13279,11 +13284,11 @@ synonym: "memory CCR4-positive regulatory T-lymphocyte" EXACT [] is_a: CL:0001047 ! CD4-positive, CD25-positive, CCR4-positive, alpha-beta regulatory T cell is_a: CL:0002678 ! memory regulatory T cell intersection_of: CL:0002678 ! memory regulatory T cell -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens intersection_of: RO:0002104 PR:000001017 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RO intersection_of: RO:0002104 PR:000001200 ! has plasma membrane part C-C chemokine receptor type 4 -relationship: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens relationship: RO:0002104 PR:000001017 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RO +relationship: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: CL:0001047 @@ -13350,8 +13355,8 @@ intersection_of: RO:0002104 GO:0042105 ! has plasma membrane part alpha-beta T c intersection_of: RO:0002104 PR:000001015 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RA intersection_of: RO:0002104 PR:000025402 ! has plasma membrane part T cell receptor co-receptor CD8 relationship: CL:4030046 PR:000001203 ! lacks_plasma_membrane_part C-C chemokine receptor type 7 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001015 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RA +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0001051 @@ -13414,8 +13419,8 @@ intersection_of: RO:0002104 PR:000001889 ! has plasma membrane part CD14 molecul relationship: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule relationship: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-spanning 4-domains subfamily A member 1 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001889 ! has plasma membrane part CD14 molecule +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0001055 @@ -13429,8 +13434,8 @@ is_a: CL:0002397 ! CD14-positive, CD16-positive monocyte intersection_of: CL:0002393 ! intermediate monocyte intersection_of: RO:0002104 PR:000001889 ! has plasma membrane part CD14 molecule intersection_of: RO:0015016 PR:000001483 ! has low plasma membrane amount low affinity immunoglobulin gamma Fc region receptor III -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0015016 PR:000001483 ! has low plasma membrane amount low affinity immunoglobulin gamma Fc region receptor III +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0001056 @@ -13443,8 +13448,8 @@ synonym: "dendritic cell" BROAD [PMID:22343568] is_a: CL:0000451 ! dendritic cell intersection_of: CL:0000451 ! dendritic cell intersection_of: RO:0002104 PR:000002015 ! has plasma membrane part MHC class II histocompatibility antigen alpha chain DRA -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000002015 ! has plasma membrane part MHC class II histocompatibility antigen alpha chain DRA +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0001057 @@ -13473,8 +13478,8 @@ intersection_of: CL:4030046 PR:000001013 ! lacks_plasma_membrane_part integrin a intersection_of: RO:0002104 PR:000001865 ! has plasma membrane part interleukin-3 receptor class 2 alpha chain intersection_of: RO:0002104 PR:000002015 ! has plasma membrane part MHC class II histocompatibility antigen alpha chain DRA relationship: CL:4030046 PR:000001013 ! lacks_plasma_membrane_part integrin alpha-X -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001865 ! has plasma membrane part interleukin-3 receptor class 2 alpha chain +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0001059 @@ -13538,7 +13543,7 @@ relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surfac relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:27Z [Term] @@ -13552,8 +13557,8 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0000460 ! abnormal relationship: bearer_of PATO:0000460 ! abnormal -relationship: dc-contributor https://orcid.org/0000-0001-9990-8331 -property_value: dcterms-date "2017-01-30T18:53:32Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 +property_value: http://purl.org/dc/terms/date "2017-01-30T18:53:32Z" xsd:dateTime [Term] id: CL:0001062 @@ -13570,15 +13575,15 @@ is_a: CL:4030002 ! effector memory CD45RA-positive, alpha-beta T cell, terminall intersection_of: CL:0000909 ! CD8-positive, alpha-beta memory T cell intersection_of: CL:4030046 PR:000001017 ! lacks_plasma_membrane_part receptor-type tyrosine-protein phosphatase C isoform CD45RO intersection_of: CL:4030046 PR:000001203 ! lacks_plasma_membrane_part C-C chemokine receptor type 7 -intersection_of: in_taxon NCBITaxon:9606 ! Homo sapiens intersection_of: output_of GO:0043379 ! memory T cell differentiation intersection_of: RO:0002104 PR:000001015 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RA +intersection_of: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens relationship: CL:4030046 PR:000001017 ! lacks_plasma_membrane_part receptor-type tyrosine-protein phosphatase C isoform CD45RO relationship: CL:4030046 PR:000001203 ! lacks_plasma_membrane_part C-C chemokine receptor type 7 -relationship: develops_from CL:0000913 ! effector memory CD8-positive, alpha-beta T cell -relationship: in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001015 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RA +relationship: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens +relationship: RO:0002202 CL:0000913 ! develops from effector memory CD8-positive, alpha-beta T cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0001063 @@ -13593,8 +13598,8 @@ is_a: CL:0001061 ! abnormal cell intersection_of: CL:0001061 ! abnormal cell intersection_of: bearer_of PATO:0002011 ! neoplastic relationship: bearer_of PATO:0002011 ! neoplastic -relationship: dc-contributor https://orcid.org/0000-0001-9990-8331 -property_value: dcterms-date "2017-01-30T19:16:26Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 +property_value: http://purl.org/dc/terms/date "2017-01-30T19:16:26Z" xsd:dateTime [Term] id: CL:0001064 @@ -13608,8 +13613,8 @@ is_a: CL:0001063 ! neoplastic cell intersection_of: CL:0001063 ! neoplastic cell intersection_of: bearer_of PATO:0002097 ! neoplastic, malignant relationship: bearer_of PATO:0002097 ! neoplastic, malignant -relationship: dc-contributor https://orcid.org/0000-0001-9990-8331 -property_value: dcterms-date "2017-01-30T19:39:12Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 +property_value: http://purl.org/dc/terms/date "2017-01-30T19:39:12Z" xsd:dateTime [Term] id: CL:0001065 @@ -13628,9 +13633,9 @@ relationship: capable_of GO:0001816 ! cytokine production relationship: capable_of GO:0045087 ! innate immune response relationship: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule relationship: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon -relationship: dc-contributor https://orcid.org/0000-0001-9990-8331 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2017-01-30T20:20:48Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 +property_value: http://purl.org/dc/terms/date "2017-01-30T20:20:48Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0001066 @@ -13683,17 +13688,17 @@ is_a: CL:0001065 ! innate lymphoid cell intersection_of: CL:0001065 ! innate lymphoid cell intersection_of: capable_of GO:0032609 ! type II interferon production relationship: capable_of GO:0032609 ! type II interferon production -relationship: dc-contributor https://orcid.org/0000-0001-9990-8331 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2017-01-30T20:42:44Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 +property_value: http://purl.org/dc/terms/date "2017-01-30T20:42:44Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0001068 name: ILC1 def: "A group 1 innate lymphoid cell that is non-cytotoxic." [GOC:add, GOC:dsd, PMID:23292121, PMID:23348417] is_a: CL:0001067 ! group 1 innate lymphoid cell -relationship: dc-contributor https://orcid.org/0000-0001-9990-8331 -property_value: dcterms-date "2017-01-30T20:54:12Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 +property_value: http://purl.org/dc/terms/date "2017-01-30T20:54:12Z" xsd:dateTime [Term] id: CL:0001069 @@ -13708,9 +13713,9 @@ is_a: CL:0001065 ! innate lymphoid cell intersection_of: CL:0001065 ! innate lymphoid cell intersection_of: capable_of GO:0032634 ! interleukin-5 production relationship: capable_of GO:0032634 ! interleukin-5 production -relationship: dc-contributor https://orcid.org/0000-0001-9990-8331 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2017-01-30T21:20:08Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 +property_value: http://purl.org/dc/terms/date "2017-01-30T21:20:08Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0001070 @@ -13726,7 +13731,7 @@ synonym: "brite fat cell" EXACT [] xref: MESH:D000069797 is_a: CL:0000136 ! adipocyte relationship: part_of UBERON:0001347 ! white adipose tissue -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0001071 @@ -13738,10 +13743,10 @@ synonym: "ILC3" EXACT [] is_a: CL:0001065 ! innate lymphoid cell intersection_of: CL:0001065 ! innate lymphoid cell intersection_of: has_part PR:000003455 ! nuclear receptor ROR-gamma isoform 2 -relationship: dc-contributor https://orcid.org/0000-0001-9990-8331 relationship: has_part PR:000003455 ! nuclear receptor ROR-gamma isoform 2 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2017-01-31T20:21:26Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 +property_value: http://purl.org/dc/terms/date "2017-01-31T20:21:26Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0001072 @@ -13754,12 +13759,12 @@ is_a: CL:0001082 ! immature innate lymphoid cell intersection_of: CL:0001065 ! innate lymphoid cell intersection_of: bearer_of PATO:0001501 ! immature intersection_of: CL:4030046 PR:P28906 ! lacks_plasma_membrane_part hematopoietic progenitor cell antigen CD34 (human) -intersection_of: in_taxon NCBITaxon:9606 ! Homo sapiens intersection_of: RO:0002104 PR:P10721 ! has plasma membrane part mast/stem cell growth factor receptor Kit (human) +intersection_of: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens relationship: CL:4030046 PR:P28906 ! lacks_plasma_membrane_part hematopoietic progenitor cell antigen CD34 (human) -relationship: develops_from CL:0001074 ! CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human -relationship: in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:P10721 ! has plasma membrane part mast/stem cell growth factor receptor Kit (human) +relationship: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens +relationship: RO:0002202 CL:0001074 ! develops from CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human [Term] id: CL:0001073 @@ -13770,9 +13775,9 @@ synonym: "CD34-negative, CD56-positive, CD117-positive ILCP" EXACT [] synonym: "CD34-negative, CD56-positive, CD117-positive innate lymphoid cell precursor" EXACT [] is_a: CL:0001072 ! CD34-negative, CD117-positive innate lymphoid cell, human intersection_of: CL:0001072 ! CD34-negative, CD117-positive innate lymphoid cell, human -intersection_of: in_taxon NCBITaxon:9606 ! Homo sapiens intersection_of: RO:0002104 PR:P10721 ! has plasma membrane part mast/stem cell growth factor receptor Kit (human) intersection_of: RO:0002104 PR:P13591 ! has plasma membrane part neural cell adhesion molecule 1 (human) +intersection_of: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens relationship: RO:0002104 PR:P13591 ! has plasma membrane part neural cell adhesion molecule 1 (human) [Term] @@ -13784,14 +13789,14 @@ synonym: "CD34-positive, CD56-positive, CD117-positive CILP" EXACT [] is_a: CL:0001082 ! immature innate lymphoid cell intersection_of: CL:0001065 ! innate lymphoid cell intersection_of: bearer_of PATO:0001501 ! immature -intersection_of: in_taxon NCBITaxon:9606 ! Homo sapiens intersection_of: RO:0002104 PR:P10721 ! has plasma membrane part mast/stem cell growth factor receptor Kit (human) intersection_of: RO:0002104 PR:P13591 ! has plasma membrane part neural cell adhesion molecule 1 (human) intersection_of: RO:0002104 PR:P28906 ! has plasma membrane part hematopoietic progenitor cell antigen CD34 (human) -relationship: in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens relationship: RO:0002104 PR:P10721 ! has plasma membrane part mast/stem cell growth factor receptor Kit (human) relationship: RO:0002104 PR:P13591 ! has plasma membrane part neural cell adhesion molecule 1 (human) relationship: RO:0002104 PR:P28906 ! has plasma membrane part hematopoietic progenitor cell antigen CD34 (human) +relationship: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens [Term] id: CL:0001075 @@ -13800,8 +13805,8 @@ def: "An innate lymphoid cell in the human with the phenotype KLRG1-positive tha synonym: "KLRG1-positive ILC" EXACT [] is_a: CL:0001072 ! CD34-negative, CD117-positive innate lymphoid cell, human intersection_of: CL:0001072 ! CD34-negative, CD117-positive innate lymphoid cell, human -intersection_of: in_taxon NCBITaxon:9606 ! Homo sapiens intersection_of: RO:0002104 PR:Q96E93 ! has plasma membrane part killer cell lectin-like receptor subfamily G member 1 (human) +intersection_of: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens relationship: RO:0002104 PR:Q96E93 ! has plasma membrane part killer cell lectin-like receptor subfamily G member 1 (human) [Term] @@ -13812,8 +13817,8 @@ subset: cellxgene_subset synonym: "NKp46-positive ILC" EXACT [] is_a: CL:0001074 ! CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human intersection_of: CL:0001074 ! CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human -intersection_of: in_taxon NCBITaxon:9606 ! Homo sapiens intersection_of: RO:0002104 PR:O76036 ! has plasma membrane part natural cytotoxicity triggering receptor 1 (human) +intersection_of: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens relationship: RO:0002104 PR:O76036 ! has plasma membrane part natural cytotoxicity triggering receptor 1 (human) [Term] @@ -13825,11 +13830,11 @@ synonym: "innate lymphoid cell 1, human" EXACT [] is_a: CL:0001068 ! ILC1 intersection_of: CL:0001068 ! ILC1 intersection_of: has_part PR:Q9UL17 ! T-box transcription factor TBX21 (human) -intersection_of: in_taxon NCBITaxon:9606 ! Homo sapiens intersection_of: RO:0002104 PR:P16871 ! has plasma membrane part interleukin-7 receptor subunit alpha (human) +intersection_of: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens relationship: has_part PR:Q9UL17 ! T-box transcription factor TBX21 (human) -relationship: in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:P16871 ! has plasma membrane part interleukin-7 receptor subunit alpha (human) +relationship: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens [Term] id: CL:0001078 @@ -13840,11 +13845,11 @@ subset: human_reference_atlas synonym: "ILC3, human" EXACT [] is_a: CL:0001071 ! group 3 innate lymphoid cell intersection_of: CL:0001071 ! group 3 innate lymphoid cell -intersection_of: in_taxon NCBITaxon:9606 ! Homo sapiens intersection_of: RO:0002104 PR:P16871 ! has plasma membrane part interleukin-7 receptor subunit alpha (human) -relationship: in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens relationship: RO:0002104 PR:P16871 ! has plasma membrane part interleukin-7 receptor subunit alpha (human) +relationship: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0001079 @@ -13853,9 +13858,9 @@ def: "A group 3 innate lymphoid cell in the human with the phenotype IL-7Ralpha- subset: cellxgene_subset is_a: CL:0001078 ! group 3 innate lymphoid cell, human intersection_of: CL:0001071 ! group 3 innate lymphoid cell -intersection_of: in_taxon NCBITaxon:9606 ! Homo sapiens intersection_of: RO:0002104 PR:O95944 ! has plasma membrane part natural cytotoxicity triggering receptor 2 (human) intersection_of: RO:0002104 PR:P16871 ! has plasma membrane part interleukin-7 receptor subunit alpha (human) +intersection_of: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens relationship: RO:0002104 PR:O95944 ! has plasma membrane part natural cytotoxicity triggering receptor 2 (human) [Term] @@ -13866,8 +13871,8 @@ subset: cellxgene_subset is_a: CL:0001078 ! group 3 innate lymphoid cell, human intersection_of: CL:0001071 ! group 3 innate lymphoid cell intersection_of: CL:4030046 PR:O95944 ! lacks_plasma_membrane_part natural cytotoxicity triggering receptor 2 (human) -intersection_of: in_taxon NCBITaxon:9606 ! Homo sapiens intersection_of: RO:0002104 PR:P16871 ! has plasma membrane part interleukin-7 receptor subunit alpha (human) +intersection_of: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens relationship: CL:4030046 PR:O95944 ! lacks_plasma_membrane_part natural cytotoxicity triggering receptor 2 (human) [Term] @@ -13879,17 +13884,17 @@ synonym: "ILC2, human" EXACT [] is_a: CL:0001069 ! group 2 innate lymphoid cell intersection_of: CL:0001069 ! group 2 innate lymphoid cell intersection_of: has_part PR:P23771 ! trans-acting T-cell-specific transcription factor GATA-3 (human) -intersection_of: in_taxon NCBITaxon:9606 ! Homo sapiens intersection_of: RO:0002104 PR:P01589 ! has plasma membrane part interleukin-2 receptor subunit alpha (human) intersection_of: RO:0002104 PR:P16871 ! has plasma membrane part interleukin-7 receptor subunit alpha (human) intersection_of: RO:0002104 PR:Q12918 ! has plasma membrane part killer cell lectin-like receptor subfamily B member 1 (human) intersection_of: RO:0002104 PR:Q9Y5Y4 ! has plasma membrane part prostaglandin D2 receptor 2 (human) +intersection_of: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens relationship: has_part PR:P23771 ! trans-acting T-cell-specific transcription factor GATA-3 (human) -relationship: in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:P01589 ! has plasma membrane part interleukin-2 receptor subunit alpha (human) relationship: RO:0002104 PR:P16871 ! has plasma membrane part interleukin-7 receptor subunit alpha (human) relationship: RO:0002104 PR:Q12918 ! has plasma membrane part killer cell lectin-like receptor subfamily B member 1 (human) relationship: RO:0002104 PR:Q9Y5Y4 ! has plasma membrane part prostaglandin D2 receptor 2 (human) +relationship: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens [Term] id: CL:0001082 @@ -13916,17 +13921,17 @@ is_a: CL:4030002 ! effector memory CD45RA-positive, alpha-beta T cell, terminall intersection_of: CL:0000897 ! CD4-positive, alpha-beta memory T cell intersection_of: CL:4030046 PR:000001017 ! lacks_plasma_membrane_part receptor-type tyrosine-protein phosphatase C isoform CD45RO intersection_of: CL:4030046 PR:000001203 ! lacks_plasma_membrane_part C-C chemokine receptor type 7 -intersection_of: in_taxon NCBITaxon:9606 ! Homo sapiens intersection_of: output_of GO:0043379 ! memory T cell differentiation intersection_of: RO:0002104 PR:000001015 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RA +intersection_of: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens relationship: CL:4030046 PR:000001017 ! lacks_plasma_membrane_part receptor-type tyrosine-protein phosphatase C isoform CD45RO relationship: CL:4030046 PR:000001203 ! lacks_plasma_membrane_part C-C chemokine receptor type 7 -relationship: dc-contributor https://orcid.org/0000-0001-9990-8331 -relationship: develops_from CL:0000905 ! effector memory CD4-positive, alpha-beta T cell -relationship: in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001015 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RA -property_value: dcterms-date "2021-01-18T16:32:44Z" xsd:dateTime +relationship: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens +relationship: RO:0002202 CL:0000905 ! develops from effector memory CD4-positive, alpha-beta T cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 +property_value: http://purl.org/dc/terms/date "2021-01-18T16:32:44Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0001200 @@ -13936,12 +13941,12 @@ comment: Types of B lineage lymphocytes include B cells and antibody secreting c is_a: CL:0000945 ! lymphocyte of B lineage intersection_of: CL:0000945 ! lymphocyte of B lineage intersection_of: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon -intersection_of: in_taxon NCBITaxon:40674 ! Mammalia intersection_of: RO:0002104 PR:000001002 ! has plasma membrane part CD19 molecule +intersection_of: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia relationship: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon -relationship: dc-contributor https://orcid.org/0000-0001-9990-8331 -relationship: in_taxon NCBITaxon:40674 ! Mammalia relationship: RO:0002104 PR:000001002 ! has plasma membrane part CD19 molecule +relationship: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 [Term] id: CL:0001201 @@ -13956,9 +13961,9 @@ is_a: CL:0000236 ! B cell is_a: CL:0001200 ! lymphocyte of B lineage, CD19-positive intersection_of: CL:0001200 ! lymphocyte of B lineage, CD19-positive intersection_of: capable_of GO:0019724 ! B cell mediated immunity -intersection_of: in_taxon NCBITaxon:40674 ! Mammalia intersection_of: RO:0002104 PR:000001002 ! has plasma membrane part CD19 molecule -relationship: dc-contributor https://orcid.org/0000-0001-9990-8331 +intersection_of: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 [Term] id: CL:0001202 @@ -13969,8 +13974,8 @@ synonym: "CD86-positive, CD20-negative plasmablast" BROAD [] is_a: CL:0000980 ! plasmablast intersection_of: CL:0000980 ! plasmablast intersection_of: RO:0002104 PR:000001412 ! has plasma membrane part CD86 molecule -relationship: dc-contributor https://orcid.org/0000-0001-9990-8331 relationship: RO:0002104 PR:000001412 ! has plasma membrane part CD86 molecule +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 [Term] id: CL:0001203 @@ -13984,20 +13989,20 @@ synonym: "CD8-positive, alpha-beta memory T-lymphocyte, CD45RO-positive" EXACT [ is_a: CL:0000909 {is_inferred="true"} ! CD8-positive, alpha-beta memory T cell intersection_of: CL:0000909 ! CD8-positive, alpha-beta memory T cell intersection_of: CL:4030046 PR:000001380 ! lacks_plasma_membrane_part interleukin-2 receptor subunit alpha -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens intersection_of: output_of GO:0043379 ! memory T cell differentiation intersection_of: RO:0002104 PR:000001017 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RO intersection_of: RO:0002104 PR:000001869 ! has plasma membrane part interleukin-7 receptor subunit alpha +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens intersection_of: RO:0015015 PR:000001307 ! has high plasma membrane amount CD44 molecule intersection_of: RO:0015015 PR:000001381 ! has high plasma membrane amount interleukin-2 receptor subunit beta relationship: CL:4030046 PR:000001380 ! lacks_plasma_membrane_part interleukin-2 receptor subunit alpha -relationship: develops_from CL:0000906 ! activated CD8-positive, alpha-beta T cell -relationship: only_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001017 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RO relationship: RO:0002104 PR:000001869 ! has plasma membrane part interleukin-7 receptor subunit alpha +relationship: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens +relationship: RO:0002202 CL:0000906 ! develops from activated CD8-positive, alpha-beta T cell relationship: RO:0015015 PR:000001307 ! has high plasma membrane amount CD44 molecule relationship: RO:0015015 PR:000001381 ! has high plasma membrane amount interleukin-2 receptor subunit beta +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0001204 @@ -14009,17 +14014,17 @@ synonym: "CD4-positive, alpha-beta memory T-lymphocyte, CD45RO-positive" EXACT [ is_a: CL:0000897 {is_inferred="true"} ! CD4-positive, alpha-beta memory T cell intersection_of: CL:0000897 ! CD4-positive, alpha-beta memory T cell intersection_of: CL:4030046 PR:000001380 ! lacks_plasma_membrane_part interleukin-2 receptor subunit alpha -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens intersection_of: output_of GO:0043379 ! memory T cell differentiation intersection_of: RO:0002104 PR:000001017 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RO intersection_of: RO:0002104 PR:000001869 ! has plasma membrane part interleukin-7 receptor subunit alpha +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens intersection_of: RO:0015015 PR:000001307 ! has high plasma membrane amount CD44 molecule intersection_of: RO:0015015 PR:000001381 ! has high plasma membrane amount interleukin-2 receptor subunit beta relationship: CL:4030046 PR:000001380 ! lacks_plasma_membrane_part interleukin-2 receptor subunit alpha -relationship: develops_from CL:0000896 ! activated CD4-positive, alpha-beta T cell -relationship: only_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001017 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RO relationship: RO:0002104 PR:000001869 ! has plasma membrane part interleukin-7 receptor subunit alpha +relationship: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens +relationship: RO:0002202 CL:0000896 ! develops from activated CD4-positive, alpha-beta T cell relationship: RO:0015015 PR:000001307 ! has high plasma membrane amount CD44 molecule relationship: RO:0015015 PR:000001381 ! has high plasma membrane amount interleukin-2 receptor subunit beta @@ -14052,10 +14057,10 @@ relationship: CL:4030046 PR:000001865 ! lacks_plasma_membrane_part interleukin-3 relationship: CL:4030046 PR:000001869 ! lacks_plasma_membrane_part interleukin-7 receptor subunit alpha relationship: CL:4030046 PR:000002979 ! lacks_plasma_membrane_part lymphocyte antigen 6A-2/6E-1 relationship: CL:4030046 PR:000009127 ! lacks_plasma_membrane_part integrin alpha-IIb -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002006 ! Kit-positive, CD34-negative megakaryocyte erythroid progenitor cell relationship: RO:0002104 PR:000001345 ! has plasma membrane part endoglin relationship: RO:0002104 PR:000002065 ! has plasma membrane part mast/stem cell growth factor receptor +relationship: RO:0002202 CL:0002006 ! develops from Kit-positive, CD34-negative megakaryocyte erythroid progenitor cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-26T10:14:16Z [Term] @@ -14068,10 +14073,10 @@ intersection_of: CL:0000557 ! granulocyte monocyte progenitor cell intersection_of: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule intersection_of: RO:0002104 PR:000001408 ! has plasma membrane part ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 intersection_of: RO:0002104 PR:000001865 ! has plasma membrane part interleukin-3 receptor class 2 alpha chain -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0001026 ! CD34-positive, CD38-positive common myeloid progenitor relationship: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule relationship: RO:0002104 PR:000001408 ! has plasma membrane part ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 +relationship: RO:0002202 CL:0001026 ! develops from CD34-positive, CD38-positive common myeloid progenitor +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-13T03:19:22Z [Term] @@ -14093,12 +14098,12 @@ relationship: CL:4030046 PR:000001206 ! lacks_plasma_membrane_part CX3C chemokin relationship: CL:4030046 PR:000001843 ! lacks_plasma_membrane_part Thy-1 membrane glycoprotein relationship: CL:4030046 PR:000001869 ! lacks_plasma_membrane_part interleukin-7 receptor subunit alpha relationship: CL:4030046 PR:000002979 ! lacks_plasma_membrane_part lymphocyte antigen 6A-2/6E-1 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0001023 ! Kit-positive, CD34-positive common myeloid progenitor relationship: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule relationship: RO:0002104 PR:000002065 ! has plasma membrane part mast/stem cell growth factor receptor +relationship: RO:0002202 CL:0001023 ! develops from Kit-positive, CD34-positive common myeloid progenitor relationship: RO:0015015 GO:0033001 ! has high plasma membrane amount Fc-gamma receptor III complex relationship: RO:0015015 PR:000001479 ! has high plasma membrane amount low affinity immunoglobulin gamma Fc region receptor II +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-13T03:19:28Z [Term] @@ -14112,9 +14117,9 @@ intersection_of: CL:0001066 ! erythroid progenitor cell, mammalian intersection_of: CL:4030046 PR:000001460 ! lacks_plasma_membrane_part glycophorin-A intersection_of: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule relationship: CL:4030046 PR:000001460 ! lacks_plasma_membrane_part glycophorin-A -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002005 ! CD34-positive, CD38-positive megakaryocyte erythroid progenitor cell relationship: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule +relationship: RO:0002202 CL:0002005 ! develops from CD34-positive, CD38-positive megakaryocyte erythroid progenitor cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-26T10:14:30Z [Term] @@ -14128,8 +14133,8 @@ intersection_of: CL:4030046 PR:000001003 ! lacks_plasma_membrane_part CD34 molec intersection_of: CL:4030046 PR:000001460 ! lacks_plasma_membrane_part glycophorin-A relationship: CL:4030046 PR:000001003 ! lacks_plasma_membrane_part CD34 molecule relationship: CL:4030046 PR:000001460 ! lacks_plasma_membrane_part glycophorin-A -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002003 ! CD34-positive, GlyA-negative erythroid progenitor cell +relationship: RO:0002202 CL:0002003 ! develops from CD34-positive, GlyA-negative erythroid progenitor cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-26T10:31:50Z [Term] @@ -14146,9 +14151,9 @@ intersection_of: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecul intersection_of: RO:0002104 PR:000001408 ! has plasma membrane part ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 relationship: CL:4030046 PR:000001015 ! lacks_plasma_membrane_part receptor-type tyrosine-protein phosphatase C isoform CD45RA relationship: CL:4030046 PR:000001865 ! lacks_plasma_membrane_part interleukin-3 receptor class 2 alpha chain -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule relationship: RO:0002104 PR:000001408 ! has plasma membrane part ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-13T03:43:10Z [Term] @@ -14171,9 +14176,9 @@ relationship: CL:4030046 PR:000001479 ! lacks_plasma_membrane_part low affinity relationship: CL:4030046 PR:000001843 ! lacks_plasma_membrane_part Thy-1 membrane glycoprotein relationship: CL:4030046 PR:000001869 ! lacks_plasma_membrane_part interleukin-7 receptor subunit alpha relationship: CL:4030046 PR:000002979 ! lacks_plasma_membrane_part lymphocyte antigen 6A-2/6E-1 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0002104 PR:000002065 ! has plasma membrane part mast/stem cell growth factor receptor relationship: RO:0015016 GO:0033001 ! has low plasma membrane amount Fc-gamma receptor III complex +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-13T03:43:12Z [Term] @@ -14188,9 +14193,9 @@ intersection_of: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecul intersection_of: RO:0002104 PR:000001867 ! has plasma membrane part interleukin-5 receptor subunit alpha intersection_of: RO:0015016 PR:000002065 ! has low plasma membrane amount mast/stem cell growth factor receptor relationship: CL:4030046 PR:000002979 ! lacks_plasma_membrane_part lymphocyte antigen 6A-2/6E-1 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002002 ! Kit-positive granulocyte monocyte progenitor +relationship: RO:0002202 CL:0002002 ! develops from Kit-positive granulocyte monocyte progenitor relationship: RO:0015016 PR:000002065 ! has low plasma membrane amount mast/stem cell growth factor receptor +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-14T03:25:15Z [Term] @@ -14203,9 +14208,9 @@ intersection_of: CL:0000611 ! eosinophil progenitor cell intersection_of: RO:0002104 PR:000001015 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RA intersection_of: RO:0002104 PR:000001408 ! has plasma membrane part ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 intersection_of: RO:0002104 PR:000001865 ! has plasma membrane part interleukin-3 receptor class 2 alpha chain -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002001 ! CD34-positive, CD38-positive granulocyte monocyte progenitor relationship: RO:0002104 PR:000001015 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RA +relationship: RO:0002202 CL:0002001 ! develops from CD34-positive, CD38-positive granulocyte monocyte progenitor +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-14T03:25:17Z [Term] @@ -14222,8 +14227,8 @@ intersection_of: capable_of GO:0030224 ! monocyte differentiation intersection_of: capable_of GO:0043011 ! myeloid dendritic cell differentiation relationship: capable_of GO:0030224 ! monocyte differentiation relationship: capable_of GO:0043011 ! myeloid dendritic cell differentiation -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000557 ! granulocyte monocyte progenitor cell +relationship: RO:0002202 CL:0000557 ! develops from granulocyte monocyte progenitor cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-19T02:51:58Z [Term] @@ -14264,10 +14269,10 @@ relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surfac relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -relationship: develops_from CL:0001029 ! common dendritic progenitor relationship: RO:0002104 PR:000001013 ! has plasma membrane part integrin alpha-X relationship: RO:0002104 PR:000001968 ! has plasma membrane part tyrosine-protein phosphatase non-receptor type substrate 1 relationship: RO:0002104 PR:000002001 ! has plasma membrane part receptor-type tyrosine-protein kinase FLT3 +relationship: RO:0002202 CL:0001029 ! develops from common dendritic progenitor creation_date: 2010-01-19T03:39:30Z [Term] @@ -14283,12 +14288,12 @@ intersection_of: RO:0002104 PR:000001206 ! has plasma membrane part CX3C chemoki intersection_of: RO:0002104 PR:000002001 ! has plasma membrane part receptor-type tyrosine-protein kinase FLT3 intersection_of: RO:0002104 PR:000002062 ! has plasma membrane part macrophage colony-stimulating factor 1 receptor intersection_of: RO:0015015 PR:000002065 ! has high plasma membrane amount mast/stem cell growth factor receptor -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002002 ! Kit-positive granulocyte monocyte progenitor relationship: RO:0002104 PR:000001206 ! has plasma membrane part CX3C chemokine receptor 1 relationship: RO:0002104 PR:000002001 ! has plasma membrane part receptor-type tyrosine-protein kinase FLT3 relationship: RO:0002104 PR:000002062 ! has plasma membrane part macrophage colony-stimulating factor 1 receptor +relationship: RO:0002202 CL:0002002 ! develops from Kit-positive granulocyte monocyte progenitor relationship: RO:0015015 PR:000002065 ! has high plasma membrane amount mast/stem cell growth factor receptor +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-26T02:43:40Z [Term] @@ -14305,11 +14310,11 @@ intersection_of: RO:0015015 PR:000001945 ! has high plasma membrane amount trans intersection_of: RO:0015016 PR:000002065 ! has low plasma membrane amount mast/stem cell growth factor receptor relationship: CL:4030046 PR:000001869 ! lacks_plasma_membrane_part interleukin-7 receptor subunit alpha relationship: CL:4030046 PR:000002979 ! lacks_plasma_membrane_part lymphocyte antigen 6A-2/6E-1 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002000 ! Kit-positive erythroid progenitor cell relationship: RO:0002104 PR:000002981 ! has plasma membrane part lymphocyte antigen 76 (mouse) +relationship: RO:0002202 CL:0002000 ! develops from Kit-positive erythroid progenitor cell relationship: RO:0015015 PR:000001945 ! has high plasma membrane amount transferrin receptor protein 1 relationship: RO:0015016 PR:000002065 ! has low plasma membrane amount mast/stem cell growth factor receptor +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-26T10:31:56Z [Term] @@ -14322,9 +14327,9 @@ intersection_of: CL:0000549 ! basophilic erythroblast intersection_of: CL:4030046 PR:000001003 ! lacks_plasma_membrane_part CD34 molecule intersection_of: RO:0002104 PR:000001460 ! has plasma membrane part glycophorin-A relationship: CL:4030046 PR:000001003 ! lacks_plasma_membrane_part CD34 molecule -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002004 ! CD34-negative, GlyA-negative proerythroblast relationship: RO:0002104 PR:000001460 ! has plasma membrane part glycophorin-A +relationship: RO:0002202 CL:0002004 ! develops from CD34-negative, GlyA-negative proerythroblast +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-26T10:41:15Z [Term] @@ -14341,9 +14346,9 @@ intersection_of: RO:0015015 PR:000002981 ! has high plasma membrane amount lymph relationship: CL:4030046 PR:000001869 ! lacks_plasma_membrane_part interleukin-7 receptor subunit alpha relationship: CL:4030046 PR:000002065 ! lacks_plasma_membrane_part mast/stem cell growth factor receptor relationship: CL:4030046 PR:000002979 ! lacks_plasma_membrane_part lymphocyte antigen 6A-2/6E-1 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002012 ! Kit-low proerythroblast +relationship: RO:0002202 CL:0002012 ! develops from Kit-low proerythroblast relationship: RO:0015015 PR:000002981 ! has high plasma membrane amount lymphocyte antigen 76 (mouse) +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-26T10:41:22Z [Term] @@ -14360,9 +14365,9 @@ intersection_of: RO:0015015 PR:000002981 ! has high plasma membrane amount lymph relationship: CL:4030046 PR:000001869 ! lacks_plasma_membrane_part interleukin-7 receptor subunit alpha relationship: CL:4030046 PR:000002065 ! lacks_plasma_membrane_part mast/stem cell growth factor receptor relationship: CL:4030046 PR:000002979 ! lacks_plasma_membrane_part lymphocyte antigen 6A-2/6E-1 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002014 ! Kit-negative, Ly-76 high basophilic erythroblast +relationship: RO:0002202 CL:0002014 ! develops from Kit-negative, Ly-76 high basophilic erythroblast relationship: RO:0015015 PR:000002981 ! has high plasma membrane amount lymphocyte antigen 76 (mouse) +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-26T10:53:11Z [Term] @@ -14374,10 +14379,10 @@ is_a: CL:0000550 {is_inferred="true"} ! polychromatophilic erythroblast intersection_of: CL:0000550 ! polychromatophilic erythroblast intersection_of: RO:0002104 PR:000001460 ! has plasma membrane part glycophorin-A intersection_of: RO:0015016 PR:000001945 ! has low plasma membrane amount transferrin receptor protein 1 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002013 ! GlyA-positive basophilic erythroblast relationship: RO:0002104 PR:000001460 ! has plasma membrane part glycophorin-A +relationship: RO:0002202 CL:0002013 ! develops from GlyA-positive basophilic erythroblast relationship: RO:0015016 PR:000001945 ! has low plasma membrane amount transferrin receptor protein 1 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-26T10:53:16Z [Term] @@ -14396,10 +14401,10 @@ intersection_of: RO:0015016 PR:000001945 ! has low plasma membrane amount transf relationship: CL:4030046 PR:000001869 ! lacks_plasma_membrane_part interleukin-7 receptor subunit alpha relationship: CL:4030046 PR:000002065 ! lacks_plasma_membrane_part mast/stem cell growth factor receptor relationship: CL:4030046 PR:000002979 ! lacks_plasma_membrane_part lymphocyte antigen 6A-2/6E-1 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002015 ! Kit-negative, Ly-76 high polychromatophilic erythroblast +relationship: RO:0002202 CL:0002015 ! develops from Kit-negative, Ly-76 high polychromatophilic erythroblast relationship: RO:0015015 PR:000002981 ! has high plasma membrane amount lymphocyte antigen 76 (mouse) relationship: RO:0015016 PR:000001945 ! has low plasma membrane amount transferrin receptor protein 1 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-26T11:04:15Z [Term] @@ -14413,9 +14418,9 @@ intersection_of: CL:0000552 ! orthochromatic erythroblast intersection_of: CL:4030046 PR:000001945 ! lacks_plasma_membrane_part transferrin receptor protein 1 intersection_of: RO:0002104 PR:000001460 ! has plasma membrane part glycophorin-A relationship: CL:4030046 PR:000001945 ! lacks_plasma_membrane_part transferrin receptor protein 1 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002016 ! CD71-low, GlyA-positive polychromatic erythroblast relationship: RO:0002104 PR:000001460 ! has plasma membrane part glycophorin-A +relationship: RO:0002202 CL:0002016 ! develops from CD71-low, GlyA-positive polychromatic erythroblast +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-26T11:04:21Z [Term] @@ -14426,9 +14431,9 @@ comment: Marker associated with mouse cells. is_a: CL:0002422 {is_inferred="true"} ! enucleated reticulocyte intersection_of: CL:0002422 ! enucleated reticulocyte intersection_of: RO:0015015 PR:000002981 ! has high plasma membrane amount lymphocyte antigen 76 (mouse) -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002017 ! Kit-negative, Ly-76 high orthochromatophilic erythroblasts +relationship: RO:0002202 CL:0002017 ! develops from Kit-negative, Ly-76 high orthochromatophilic erythroblasts relationship: RO:0015015 PR:000002981 ! has high plasma membrane amount lymphocyte antigen 76 (mouse) +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-26T11:37:00Z [Term] @@ -14439,9 +14444,9 @@ comment: Markers is associated with human cells. is_a: CL:0002422 {is_inferred="true"} ! enucleated reticulocyte intersection_of: CL:0002422 ! enucleated reticulocyte intersection_of: RO:0002104 PR:000001460 ! has plasma membrane part glycophorin-A -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002018 ! CD71-negative, GlyA-positive orthochromatic erythroblast relationship: RO:0002104 PR:000001460 ! has plasma membrane part glycophorin-A +relationship: RO:0002202 CL:0002018 ! develops from CD71-negative, GlyA-positive orthochromatic erythroblast +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-26T11:48:25Z [Term] @@ -14453,9 +14458,9 @@ is_a: CL:0000595 {is_inferred="true"} ! enucleate erythrocyte is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000595 ! enucleate erythrocyte intersection_of: RO:0002104 PR:000001460 ! has plasma membrane part glycophorin-A -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002020 ! GlyA-positive reticulocytes relationship: RO:0002104 PR:000001460 ! has plasma membrane part glycophorin-A +relationship: RO:0002202 CL:0002020 ! develops from GlyA-positive reticulocytes +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-26T11:51:22Z [Term] @@ -14467,9 +14472,9 @@ is_a: CL:0000595 {is_inferred="true"} ! enucleate erythrocyte is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000595 ! enucleate erythrocyte intersection_of: RO:0015015 PR:000002981 ! has high plasma membrane amount lymphocyte antigen 76 (mouse) -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002019 ! Ly-76 high reticulocyte +relationship: RO:0002202 CL:0002019 ! develops from Ly-76 high reticulocyte relationship: RO:0015015 PR:000002981 ! has high plasma membrane amount lymphocyte antigen 76 (mouse) +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-26T11:51:27Z [Term] @@ -14483,11 +14488,11 @@ intersection_of: CL:0000553 ! megakaryocyte progenitor cell intersection_of: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule intersection_of: RO:0002104 PR:000001907 ! has plasma membrane part platelet glycoprotein Ib alpha chain intersection_of: RO:0002104 PR:000009127 ! has plasma membrane part integrin alpha-IIb -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002025 ! CD34-positive, CD41-positive, CD42-negative megakaryocyte progenitor cell relationship: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule relationship: RO:0002104 PR:000001907 ! has plasma membrane part platelet glycoprotein Ib alpha chain relationship: RO:0002104 PR:000009127 ! has plasma membrane part integrin alpha-IIb +relationship: RO:0002202 CL:0002025 ! develops from CD34-positive, CD41-positive, CD42-negative megakaryocyte progenitor cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-26T02:39:09Z [Term] @@ -14508,12 +14513,12 @@ intersection_of: RO:0015016 PR:000001483 ! has low plasma membrane amount low af relationship: CL:4030046 PR:000001833 ! lacks_plasma_membrane_part SLAM family member 1 relationship: CL:4030046 PR:000001869 ! lacks_plasma_membrane_part interleukin-7 receptor subunit alpha relationship: CL:4030046 PR:000002979 ! lacks_plasma_membrane_part lymphocyte antigen 6A-2/6E-1 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002006 ! Kit-positive, CD34-negative megakaryocyte erythroid progenitor cell relationship: RO:0002104 PR:000002065 ! has plasma membrane part mast/stem cell growth factor receptor relationship: RO:0002104 PR:000005178 ! has plasma membrane part CD9 molecule +relationship: RO:0002202 CL:0002006 ! develops from Kit-positive, CD34-negative megakaryocyte erythroid progenitor cell relationship: RO:0015016 PR:000001479 ! has low plasma membrane amount low affinity immunoglobulin gamma Fc region receptor II relationship: RO:0015016 PR:000001483 ! has low plasma membrane amount low affinity immunoglobulin gamma Fc region receptor III +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-26T02:39:15Z [Term] @@ -14528,10 +14533,10 @@ intersection_of: CL:4030046 PR:000001907 ! lacks_plasma_membrane_part platelet g intersection_of: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule intersection_of: RO:0002104 PR:000009127 ! has plasma membrane part integrin alpha-IIb relationship: CL:4030046 PR:000001907 ! lacks_plasma_membrane_part platelet glycoprotein Ib alpha chain -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002005 ! CD34-positive, CD38-positive megakaryocyte erythroid progenitor cell relationship: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule relationship: RO:0002104 PR:000009127 ! has plasma membrane part integrin alpha-IIb +relationship: RO:0002202 CL:0002005 ! develops from CD34-positive, CD38-positive megakaryocyte erythroid progenitor cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-26T03:52:47Z [Term] @@ -14546,10 +14551,10 @@ intersection_of: CL:4030046 PR:000001003 ! lacks_plasma_membrane_part CD34 molec intersection_of: RO:0002104 PR:000001907 ! has plasma membrane part platelet glycoprotein Ib alpha chain intersection_of: RO:0002104 PR:000009127 ! has plasma membrane part integrin alpha-IIb relationship: CL:4030046 PR:000001003 ! lacks_plasma_membrane_part CD34 molecule -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002023 ! CD34-positive, CD41-positive, CD42-positive megakaryocyte progenitor cell relationship: RO:0002104 PR:000001907 ! has plasma membrane part platelet glycoprotein Ib alpha chain relationship: RO:0002104 PR:000009127 ! has plasma membrane part integrin alpha-IIb +relationship: RO:0002202 CL:0002023 ! develops from CD34-positive, CD41-positive, CD42-positive megakaryocyte progenitor cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-26T03:59:22Z [Term] @@ -14562,10 +14567,10 @@ is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000556 ! megakaryocyte intersection_of: RO:0002104 PR:000005178 ! has plasma membrane part CD9 molecule intersection_of: RO:0002104 PR:000009127 ! has plasma membrane part integrin alpha-IIb -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002024 ! Kit-positive megakaryocyte progenitor cell relationship: RO:0002104 PR:000005178 ! has plasma membrane part CD9 molecule relationship: RO:0002104 PR:000009127 ! has plasma membrane part integrin alpha-IIb +relationship: RO:0002202 CL:0002024 ! develops from Kit-positive megakaryocyte progenitor cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-27T10:39:07Z [Term] @@ -14591,12 +14596,12 @@ relationship: capable_of GO:0030221 ! basophil differentiation relationship: capable_of GO:0060374 ! mast cell differentiation relationship: CL:4030046 PR:000007431 ! lacks_plasma_membrane_part high affinity immunoglobulin epsilon receptor subunit alpha relationship: CL:4030046 PR:000016401 ! lacks_plasma_membrane_part transmembrane emp24 domain-containing protein 1 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000557 ! granulocyte monocyte progenitor cell relationship: has_part PR:000005307 ! CCAAT/enhancer-binding protein alpha relationship: has_part PR:000007857 ! erythroid transcription factor relationship: has_part PR:000007858 ! endothelial transcription factor GATA-2 relationship: RO:0002104 PR:000001867 ! has plasma membrane part interleukin-5 receptor subunit alpha +relationship: RO:0002202 CL:0000557 ! develops from granulocyte monocyte progenitor cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-27T12:46:33Z [Term] @@ -14610,11 +14615,11 @@ intersection_of: RO:0002104 PR:000001006 ! has plasma membrane part receptor-typ intersection_of: RO:0002104 PR:000002065 ! has plasma membrane part mast/stem cell growth factor receptor intersection_of: RO:0002104 PR:000009143 ! has plasma membrane part integrin beta-7 intersection_of: RO:0015016 PR:000007431 ! has low plasma membrane amount high affinity immunoglobulin epsilon receptor subunit alpha -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002044 ! Kit-positive, integrin beta7-high basophil mast progenitor cell relationship: RO:0002104 PR:000001006 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C relationship: RO:0002104 PR:000002065 ! has plasma membrane part mast/stem cell growth factor receptor relationship: RO:0002104 PR:000009143 ! has plasma membrane part integrin beta-7 +relationship: RO:0002202 CL:0002044 ! develops from Kit-positive, integrin beta7-high basophil mast progenitor cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-27T01:22:19Z [Term] @@ -14629,9 +14634,9 @@ intersection_of: CL:4030046 PR:000002979 ! lacks_plasma_membrane_part lymphocyte intersection_of: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule intersection_of: RO:0015015 PR:000007431 ! has high plasma membrane amount high affinity immunoglobulin epsilon receptor subunit alpha relationship: CL:4030046 PR:000002979 ! lacks_plasma_membrane_part lymphocyte antigen 6A-2/6E-1 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002044 ! Kit-positive, integrin beta7-high basophil mast progenitor cell relationship: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule +relationship: RO:0002202 CL:0002044 ! develops from Kit-positive, integrin beta7-high basophil mast progenitor cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-27T01:22:32Z [Term] @@ -14644,8 +14649,8 @@ intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001400 ! unipotent disjoint_from: CL:0002032 ! hematopoietic oligopotent progenitor cell relationship: bearer_of PATO:0001400 ! unipotent -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002032 ! hematopoietic oligopotent progenitor cell +relationship: RO:0002202 CL:0002032 ! develops from hematopoietic oligopotent progenitor cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:20Z [Term] @@ -14658,8 +14663,8 @@ is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001401 ! oligopotent relationship: bearer_of PATO:0001401 ! oligopotent -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000837 ! hematopoietic multipotent progenitor cell +relationship: RO:0002202 CL:0000837 ! develops from hematopoietic multipotent progenitor cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:27Z [Term] @@ -14675,9 +14680,9 @@ intersection_of: CL:4030046 PR:000002001 ! lacks_plasma_membrane_part receptor-t intersection_of: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule intersection_of: RO:0002104 PR:000001833 ! has plasma membrane part SLAM family member 1 relationship: CL:4030046 PR:000002001 ! lacks_plasma_membrane_part receptor-type tyrosine-protein kinase FLT3 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002034 ! long term hematopoietic stem cell relationship: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule +relationship: RO:0002202 CL:0002034 ! develops from long term hematopoietic stem cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-08T09:19:25Z [Term] @@ -14695,8 +14700,8 @@ intersection_of: RO:0002104 PR:000001833 ! has plasma membrane part SLAM family intersection_of: RO:0015016 PR:000001843 ! has low plasma membrane amount Thy-1 membrane glycoprotein relationship: CL:4030046 PR:000001003 ! lacks_plasma_membrane_part CD34 molecule relationship: CL:4030046 PR:000002001 ! lacks_plasma_membrane_part receptor-type tyrosine-protein kinase FLT3 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0015016 PR:000001843 ! has low plasma membrane amount Thy-1 membrane glycoprotein +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-08T09:19:28Z [Term] @@ -14712,10 +14717,10 @@ intersection_of: RO:0002104 PR:000002065 ! has plasma membrane part mast/stem ce intersection_of: RO:0002104 PR:000002979 ! has plasma membrane part lymphocyte antigen 6A-2/6E-1 relationship: CL:4030046 PR:000001833 ! lacks_plasma_membrane_part SLAM family member 1 relationship: CL:4030046 PR:000002001 ! lacks_plasma_membrane_part receptor-type tyrosine-protein kinase FLT3 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002036 ! Slamf1-positive multipotent progenitor cell relationship: RO:0002104 PR:000002065 ! has plasma membrane part mast/stem cell growth factor receptor relationship: RO:0002104 PR:000002979 ! has plasma membrane part lymphocyte antigen 6A-2/6E-1 +relationship: RO:0002202 CL:0002036 ! develops from Slamf1-positive multipotent progenitor cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-08T11:16:33Z [Term] @@ -14730,11 +14735,11 @@ intersection_of: RO:0002104 PR:000001833 ! has plasma membrane part SLAM family intersection_of: RO:0002104 PR:000002065 ! has plasma membrane part mast/stem cell growth factor receptor intersection_of: RO:0002104 PR:000002979 ! has plasma membrane part lymphocyte antigen 6A-2/6E-1 disjoint_from: CL:0002043 ! CD34-positive, CD38-negative multipotent progenitor cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002033 ! short term hematopoietic stem cell relationship: RO:0002104 PR:000001833 ! has plasma membrane part SLAM family member 1 relationship: RO:0002104 PR:000002065 ! has plasma membrane part mast/stem cell growth factor receptor relationship: RO:0002104 PR:000002979 ! has plasma membrane part lymphocyte antigen 6A-2/6E-1 +relationship: RO:0002202 CL:0002033 ! develops from short term hematopoietic stem cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-08T11:16:35Z [Term] @@ -14747,10 +14752,10 @@ intersection_of: CL:0000793 ! CD4-positive, alpha-beta intraepithelial T cell intersection_of: RO:0002104 PR:000001083 ! has plasma membrane part CD2 molecule intersection_of: RO:0002104 PR:000001307 ! has plasma membrane part CD44 molecule intersection_of: RO:0002104 PR:000001839 ! has plasma membrane part T-cell surface glycoprotein CD5 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0002104 PR:000001083 ! has plasma membrane part CD2 molecule relationship: RO:0002104 PR:000001307 ! has plasma membrane part CD44 molecule relationship: RO:0002104 PR:000001839 ! has plasma membrane part T-cell surface glycoprotein CD5 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-10-20T02:20:43Z [Term] @@ -14779,12 +14784,12 @@ intersection_of: RO:0002104 PR:000001919 ! has plasma membrane part programmed c relationship: capable_of GO:0045830 ! positive regulation of isotype switching relationship: capable_of GO:0051024 relationship: CL:4030046 PR:000001203 ! lacks_plasma_membrane_part C-C chemokine receptor type 7 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: has_part PR:000003450 ! B-cell lymphoma 6 protein -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001209 ! has plasma membrane part C-X-C chemokine receptor type 5 relationship: RO:0002104 PR:000001860 ! has plasma membrane part inducible T-cell costimulator relationship: RO:0002104 PR:000001919 ! has plasma membrane part programmed cell death protein 1 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2009-10-29T04:01:27Z [Term] @@ -14800,10 +14805,10 @@ intersection_of: RO:0015016 PR:000001004 ! has low plasma membrane amount CD4 mo intersection_of: RO:0015016 PR:000025402 ! has low plasma membrane amount T cell receptor co-receptor CD8 relationship: CL:4030046 PR:000001307 ! lacks_plasma_membrane_part CD44 molecule relationship: CL:4030046 PR:000001874 ! lacks_plasma_membrane_part KLRB1-like protein -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0015015 PR:000001932 ! has high plasma membrane amount signal transducer CD24 relationship: RO:0015016 PR:000001004 ! has low plasma membrane amount CD4 molecule relationship: RO:0015016 PR:000025402 ! has low plasma membrane amount T cell receptor co-receptor CD8 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-10-29T04:09:16Z [Term] @@ -14819,9 +14824,9 @@ intersection_of: CL:4030046 PR:000001874 ! lacks_plasma_membrane_part KLRB1-like intersection_of: RO:0015016 PR:000001932 ! has low plasma membrane amount signal transducer CD24 relationship: CL:4030046 PR:000001307 ! lacks_plasma_membrane_part CD44 molecule relationship: CL:4030046 PR:000001874 ! lacks_plasma_membrane_part KLRB1-like protein -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002039 ! immature NK T cell stage I +relationship: RO:0002202 CL:0002039 ! develops from immature NK T cell stage I relationship: RO:0015016 PR:000001932 ! has low plasma membrane amount signal transducer CD24 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-10-29T04:13:43Z [Term] @@ -14836,11 +14841,11 @@ intersection_of: RO:0002104 PR:000001307 ! has plasma membrane part CD44 molecul intersection_of: RO:0015016 PR:000001008 ! has low plasma membrane amount integrin alpha-2 intersection_of: RO:0015016 PR:000001932 ! has low plasma membrane amount signal transducer CD24 relationship: CL:4030046 PR:000001874 ! lacks_plasma_membrane_part KLRB1-like protein -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002040 ! immature NK T cell stage II relationship: RO:0002104 PR:000001307 ! has plasma membrane part CD44 molecule +relationship: RO:0002202 CL:0002040 ! develops from immature NK T cell stage II relationship: RO:0015016 PR:000001008 ! has low plasma membrane amount integrin alpha-2 relationship: RO:0015016 PR:000001932 ! has low plasma membrane amount signal transducer CD24 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-10-29T04:14:48Z [Term] @@ -14856,12 +14861,12 @@ intersection_of: RO:0002104 PR:000001307 ! has plasma membrane part CD44 molecul intersection_of: RO:0015015 PR:000001008 ! has high plasma membrane amount integrin alpha-2 intersection_of: RO:0015016 PR:000001932 ! has low plasma membrane amount signal transducer CD24 relationship: CL:4030046 PR:000001874 ! lacks_plasma_membrane_part KLRB1-like protein -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002041 ! immature NK T cell stage III -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001307 ! has plasma membrane part CD44 molecule +relationship: RO:0002202 CL:0002041 ! develops from immature NK T cell stage III relationship: RO:0015015 PR:000001008 ! has high plasma membrane amount integrin alpha-2 relationship: RO:0015016 PR:000001932 ! has low plasma membrane amount signal transducer CD24 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2009-10-29T04:17:38Z [Term] @@ -14878,8 +14883,8 @@ intersection_of: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecul relationship: CL:4030046 PR:000001015 ! lacks_plasma_membrane_part receptor-type tyrosine-protein phosphatase C isoform CD45RA relationship: CL:4030046 PR:000001408 ! lacks_plasma_membrane_part ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 relationship: CL:4030046 PR:000001843 ! lacks_plasma_membrane_part Thy-1 membrane glycoprotein -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0001024 ! CD34-positive, CD38-negative hematopoietic stem cell +relationship: RO:0002202 CL:0001024 ! develops from CD34-positive, CD38-negative hematopoietic stem cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-12T11:14:15Z [Term] @@ -14896,10 +14901,10 @@ intersection_of: RO:0002104 PR:000001483 ! has plasma membrane part low affinity intersection_of: RO:0015015 PR:000009143 ! has high plasma membrane amount integrin beta-7 relationship: CL:4030046 PR:000002065 ! lacks_plasma_membrane_part mast/stem cell growth factor receptor relationship: CL:4030046 PR:000002979 ! lacks_plasma_membrane_part lymphocyte antigen 6A-2/6E-1 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0002104 PR:000001479 ! has plasma membrane part low affinity immunoglobulin gamma Fc region receptor II relationship: RO:0002104 PR:000001483 ! has plasma membrane part low affinity immunoglobulin gamma Fc region receptor III relationship: RO:0015015 PR:000009143 ! has high plasma membrane amount integrin beta-7 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-27T01:22:38Z [Term] @@ -14921,12 +14926,12 @@ intersection_of: RO:0002104 PR:000002065 ! has plasma membrane part mast/stem ce intersection_of: RO:0015016 PR:000001932 ! has low plasma membrane amount signal transducer CD24 relationship: CL:4030046 PR:000002039 ! lacks_plasma_membrane_part glutamyl aminopeptidase relationship: CL:4030046 PR:000002980 ! lacks_plasma_membrane_part lymphocyte antigen 6C2 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0002104 PR:000001015 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RA relationship: RO:0002104 PR:000001879 ! has plasma membrane part leukosialin relationship: RO:0002104 PR:000002037 ! has plasma membrane part complement component C1q receptor relationship: RO:0002104 PR:000002065 ! has plasma membrane part mast/stem cell growth factor receptor relationship: RO:0015016 PR:000001932 ! has low plasma membrane amount signal transducer CD24 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-28T10:50:07Z [Term] @@ -14949,13 +14954,13 @@ intersection_of: RO:0015016 PR:000001898 ! has low plasma membrane amount nepril relationship: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-spanning 4-domains subfamily A member 1 relationship: CL:4030046 PR:000001338 ! lacks_plasma_membrane_part complement receptor type 2 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: participates_in GO:0071707 ! immunoglobulin heavy chain V-D-J recombination relationship: RO:0002104 GO:0035369 ! has plasma membrane part pre-B cell receptor complex relationship: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule relationship: RO:0002104 PR:000001288 ! has plasma membrane part B-cell receptor CD22 relationship: RO:0002104 PR:000001408 ! has plasma membrane part ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 relationship: RO:0015016 PR:000001898 ! has low plasma membrane amount neprilysin +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-28T11:19:11Z [Term] @@ -14971,9 +14976,9 @@ intersection_of: CL:4030046 PR:000002039 ! lacks_plasma_membrane_part glutamyl a intersection_of: RO:0002104 PR:000001014 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RABC intersection_of: RO:0002104 PR:000001932 ! has plasma membrane part signal transducer CD24 relationship: CL:4030046 PR:000002039 ! lacks_plasma_membrane_part glutamyl aminopeptidase -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002045 ! fraction A pre-pro B cell relationship: RO:0002104 PR:000001014 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RABC +relationship: RO:0002202 CL:0002045 ! develops from fraction A pre-pro B cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-28T11:56:21Z [Term] @@ -14988,12 +14993,12 @@ intersection_of: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecul intersection_of: RO:0002104 PR:000001288 ! has plasma membrane part B-cell receptor CD22 intersection_of: RO:0002104 PR:000001408 ! has plasma membrane part ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 intersection_of: RO:0015016 PR:000001002 ! has low plasma membrane amount CD19 molecule -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002046 ! early pro-B cell relationship: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule relationship: RO:0002104 PR:000001288 ! has plasma membrane part B-cell receptor CD22 relationship: RO:0002104 PR:000001408 ! has plasma membrane part ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 +relationship: RO:0002202 CL:0002046 ! develops from early pro-B cell relationship: RO:0015016 PR:000001002 ! has low plasma membrane amount CD19 molecule +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-28T12:06:06Z [Term] @@ -15012,14 +15017,14 @@ intersection_of: RO:0002104 PR:000002039 ! has plasma membrane part glutamyl ami intersection_of: RO:0002104 PR:000003457 ! has plasma membrane part V(D)J recombination-activating protein 1 intersection_of: RO:0002104 PR:000003460 ! has plasma membrane part V(D)J recombination-activating protein 2 relationship: CL:4030044 GO:0071707 ! has_not_completed immunoglobulin heavy chain V-D-J recombination -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002047 ! fraction B precursor B cell relationship: has_part PR:000001858 ! immunoglobulin iota chain relationship: has_part PR:000001859 ! immunoglobulin lambda-like polypeptide 1 relationship: RO:0002104 PR:000001014 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RABC relationship: RO:0002104 PR:000002039 ! has plasma membrane part glutamyl aminopeptidase relationship: RO:0002104 PR:000003457 ! has plasma membrane part V(D)J recombination-activating protein 1 relationship: RO:0002104 PR:000003460 ! has plasma membrane part V(D)J recombination-activating protein 2 +relationship: RO:0002202 CL:0002047 ! develops from fraction B precursor B cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-28T02:04:01Z [Term] @@ -15036,14 +15041,14 @@ intersection_of: RO:0002104 PR:000001380 ! has plasma membrane part interleukin- intersection_of: RO:0002104 PR:000001879 ! has plasma membrane part leukosialin intersection_of: RO:0002104 PR:000002039 ! has plasma membrane part glutamyl aminopeptidase intersection_of: RO:0015015 PR:000001932 ! has high plasma membrane amount signal transducer CD24 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002049 ! fraction C precursor B cell relationship: RO:0002104 GO:0035369 ! has plasma membrane part pre-B cell receptor complex relationship: RO:0002104 PR:000001014 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RABC relationship: RO:0002104 PR:000001380 ! has plasma membrane part interleukin-2 receptor subunit alpha relationship: RO:0002104 PR:000001879 ! has plasma membrane part leukosialin relationship: RO:0002104 PR:000002039 ! has plasma membrane part glutamyl aminopeptidase +relationship: RO:0002202 CL:0002049 ! develops from fraction C precursor B cell relationship: RO:0015015 PR:000001932 ! has high plasma membrane amount signal transducer CD24 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-28T02:13:46Z [Term] @@ -15056,10 +15061,10 @@ is_a: CL:0000952 {is_inferred="true"} ! preBCR-positive large pre-B-II cell intersection_of: CL:0000952 ! preBCR-positive large pre-B-II cell intersection_of: RO:0002104 PR:000001288 ! has plasma membrane part B-cell receptor CD22 intersection_of: RO:0015015 PR:000001408 ! has high plasma membrane amount ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002048 ! late pro-B cell relationship: RO:0002104 PR:000001288 ! has plasma membrane part B-cell receptor CD22 +relationship: RO:0002202 CL:0002048 ! develops from late pro-B cell relationship: RO:0015015 PR:000001408 ! has high plasma membrane amount ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-28T02:27:47Z [Term] @@ -15082,12 +15087,12 @@ intersection_of: RO:0002104 PR:000002039 ! has plasma membrane part glutamyl ami intersection_of: RO:0015016 PR:000001879 ! has low plasma membrane amount leukosialin relationship: CL:4030044 GO:0071708 ! has_not_completed immunoglobulin light chain V-J recombination relationship: CL:4030046 GO:0035369 ! lacks_plasma_membrane_part pre-B cell receptor complex -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002050 ! fraction C' precursor B cell relationship: RO:0002104 PR:000001014 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RABC relationship: RO:0002104 PR:000001380 ! has plasma membrane part interleukin-2 receptor subunit alpha relationship: RO:0002104 PR:000002039 ! has plasma membrane part glutamyl aminopeptidase +relationship: RO:0002202 CL:0002050 ! develops from fraction C' precursor B cell relationship: RO:0015016 PR:000001879 ! has low plasma membrane amount leukosialin +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-28T02:55:16Z [Term] @@ -15100,10 +15105,10 @@ is_a: CL:0000954 {is_inferred="true"} ! small pre-B-II cell intersection_of: CL:0000954 ! small pre-B-II cell intersection_of: RO:0002104 PR:000001288 ! has plasma membrane part B-cell receptor CD22 intersection_of: RO:0015016 PR:000001408 ! has low plasma membrane amount ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002051 ! CD38-high pre-BCR positive cell relationship: RO:0002104 PR:000001288 ! has plasma membrane part B-cell receptor CD22 +relationship: RO:0002202 CL:0002051 ! develops from CD38-high pre-BCR positive cell relationship: RO:0015016 PR:000001408 ! has low plasma membrane amount ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-28T03:04:48Z [Term] @@ -15121,11 +15126,11 @@ intersection_of: RO:0002104 PR:000002037 ! has plasma membrane part complement c intersection_of: RO:0015016 PR:000001879 ! has low plasma membrane amount leukosialin relationship: CL:4030046 PR:000001380 ! lacks_plasma_membrane_part interleukin-2 receptor subunit alpha relationship: CL:4030046 PR:000001869 ! lacks_plasma_membrane_part interleukin-7 receptor subunit alpha -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002052 ! fraction D precursor B cell relationship: RO:0002104 PR:000001932 ! has plasma membrane part signal transducer CD24 relationship: RO:0002104 PR:000002037 ! has plasma membrane part complement component C1q receptor +relationship: RO:0002202 CL:0002052 ! develops from fraction D precursor B cell relationship: RO:0015016 PR:000001879 ! has low plasma membrane amount leukosialin +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-28T03:13:47Z [Term] @@ -15140,11 +15145,11 @@ intersection_of: RO:0015015 PR:000001288 ! has high plasma membrane amount B-cel intersection_of: RO:0015016 PR:000001338 ! has low plasma membrane amount complement receptor type 2 intersection_of: RO:0015016 PR:000001898 ! has low plasma membrane amount neprilysin relationship: CL:4030046 PR:000001408 ! lacks_plasma_membrane_part ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002053 ! CD22-positive, CD38-low small pre-B cell +relationship: RO:0002202 CL:0002053 ! develops from CD22-positive, CD38-low small pre-B cell relationship: RO:0015015 PR:000001288 ! has high plasma membrane amount B-cell receptor CD22 relationship: RO:0015016 PR:000001338 ! has low plasma membrane amount complement receptor type 2 relationship: RO:0015016 PR:000001898 ! has low plasma membrane amount neprilysin +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-28T03:19:14Z [Term] @@ -15163,12 +15168,12 @@ intersection_of: RO:0002104 PR:000001289 ! has plasma membrane part membrane-spa intersection_of: RO:0002104 PR:000001338 ! has plasma membrane part complement receptor type 2 relationship: CL:4030046 PR:000001880 ! lacks_plasma_membrane_part low affinity immunoglobulin epsilon Fc receptor relationship: CL:4030046 PR:000002037 ! lacks_plasma_membrane_part complement component C1q receptor -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002054 ! fraction E immature B cell relationship: RO:0002104 GO:0071738 ! has plasma membrane part IgD immunoglobulin complex relationship: RO:0002104 GO:0071753 ! has plasma membrane part IgM immunoglobulin complex relationship: RO:0002104 PR:000001014 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RABC relationship: RO:0002104 PR:000001338 ! has plasma membrane part complement receptor type 2 +relationship: RO:0002202 CL:0002054 ! develops from fraction E immature B cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-30T03:01:48Z [Term] @@ -15187,9 +15192,9 @@ intersection_of: RO:0002104 PR:000001465 ! has plasma membrane part high affinit intersection_of: RO:0002104 PR:000001889 ! has plasma membrane part CD14 molecule intersection_of: RO:0002104 PR:000001925 ! has plasma membrane part scavenger receptor cysteine-rich type 1 protein M130 relationship: CL:4030046 PR:000001483 ! lacks_plasma_membrane_part low affinity immunoglobulin gamma Fc region receptor III -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0002104 PR:000001465 ! has plasma membrane part high affinity immunoglobulin gamma Fc receptor I relationship: RO:0002104 PR:000001925 ! has plasma membrane part scavenger receptor cysteine-rich type 1 protein M130 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-05T08:25:41Z [Term] @@ -15208,11 +15213,11 @@ intersection_of: RO:0002104 PR:000002062 ! has plasma membrane part macrophage c intersection_of: RO:0015016 PR:000001199 ! has low plasma membrane amount C-C chemokine receptor type 2 intersection_of: RO:0015016 PR:000002980 ! has low plasma membrane amount lymphocyte antigen 6C2 relationship: CL:4030046 PR:000001014 ! lacks_plasma_membrane_part receptor-type tyrosine-protein phosphatase C isoform CD45RABC -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002398 ! Gr1-positive, CD43-positive monocyte relationship: RO:0002104 PR:000001206 ! has plasma membrane part CX3C chemokine receptor 1 +relationship: RO:0002202 CL:0002398 ! develops from Gr1-positive, CD43-positive monocyte relationship: RO:0015016 PR:000001199 ! has low plasma membrane amount C-C chemokine receptor type 2 relationship: RO:0015016 PR:000002980 ! has low plasma membrane amount lymphocyte antigen 6C2 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-05T08:25:44Z [Term] @@ -15225,9 +15230,9 @@ synonym: "DC.8+.Th" EXACT [] is_a: CL:0000941 {is_inferred="true"} ! thymic conventional dendritic cell intersection_of: CL:0000941 ! thymic conventional dendritic cell intersection_of: RO:0002104 PR:000001084 ! has plasma membrane part T-cell surface glycoprotein CD8 alpha chain -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001084 ! has plasma membrane part T-cell surface glycoprotein CD8 alpha chain +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-06-07T02:48:36Z [Term] @@ -15235,8 +15240,8 @@ id: CL:0002060 name: melanophage def: "A melanin-containing macrophage that obtains the pigment by phagocytosis of melanosomes." [GOC:tfm, PMID:20479296, PMID:2943821] is_a: CL:0000864 {is_inferred="true"} ! tissue-resident macrophage -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002097 ! skin of body +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-22T10:46:12Z [Term] @@ -15253,8 +15258,8 @@ intersection_of: capable_of GO:0032638 ! interleukin-9 production intersection_of: RO:0002104 PR:000008982 ! has plasma membrane part interleukin-17 receptor B relationship: capable_of GO:0002215 ! defense response to nematode relationship: capable_of GO:0032638 ! interleukin-9 production -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0002104 PR:000008982 ! has plasma membrane part interleukin-17 receptor B +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-22T11:18:44Z [Term] @@ -15281,8 +15286,8 @@ is_a: CL:0000322 ! pneumocyte intersection_of: CL:0000322 ! pneumocyte intersection_of: capable_of GO:0007585 ! respiratory gaseous exchange by respiratory system relationship: capable_of GO:0007585 ! respiratory gaseous exchange by respiratory system -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-06-23T04:37:54Z [Term] @@ -15313,9 +15318,9 @@ is_a: CL:1000272 ! lung secretory cell intersection_of: CL:0000322 ! pneumocyte intersection_of: capable_of GO:0032940 ! secretion by cell intersection_of: capable_of GO:0043129 ! surfactant homeostasis -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:4040003 ! fetal pre-type II pneumocyte -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:4040003 ! develops from fetal pre-type II pneumocyte +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-06-24T12:04:13Z [Term] @@ -15332,10 +15337,10 @@ is_a: CL:0000622 {is_inferred="true"} ! acinar cell is_a: CL:1001599 ! pancreas exocrine glandular cell intersection_of: CL:0000622 ! acinar cell intersection_of: part_of UBERON:0001263 ! pancreatic acinus -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: has_part GO:0042589 ! zymogen granule membrane relationship: part_of UBERON:0001263 ! pancreatic acinus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-06-24T03:16:29Z [Term] @@ -15348,7 +15353,7 @@ synonym: "P cell" RELATED OMO:0003000 [] synonym: "respiratory enterochromaffin cell" EXACT [] xref: FMA:14118 is_a: CL:0000165 ! neuroendocrine cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-28T08:24:30Z [Term] @@ -15360,7 +15365,7 @@ is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0000170 ! glucagon secreting cell intersection_of: CL:0000164 ! enteroendocrine cell intersection_of: capable_of GO:0070091 ! glucagon secretion -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T10:48:54Z [Term] @@ -15374,8 +15379,8 @@ synonym: "Purkinje muscle cell" EXACT [] xref: BTO:0001032 xref: FMA:14146 is_a: CL:0002086 ! specialized cardiac myocyte -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-06-28T08:36:15Z [Term] @@ -15387,7 +15392,7 @@ synonym: "type 2 vestibular sensory cell" EXACT [] synonym: "type II hair cell" EXACT [] xref: FMA:67909 is_a: CL:0000609 ! vestibular hair cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T09:58:13Z [Term] @@ -15399,7 +15404,7 @@ synonym: "type 1 vestibular sensory cell" EXACT [] synonym: "type I hair cell" EXACT [] xref: FMA:62352 is_a: CL:0000609 ! vestibular hair cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T09:58:19Z [Term] @@ -15418,9 +15423,9 @@ is_a: CL:0000584 ! enterocyte is_a: CL:0002253 {is_inferred="true"} ! epithelial cell of large intestine intersection_of: CL:0000584 ! enterocyte intersection_of: part_of UBERON:0001278 ! epithelium of large intestine -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001278 ! epithelium of large intestine -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-06-29T11:07:25Z [Term] @@ -15434,7 +15439,7 @@ synonym: "pacemaker cell" BROAD [] xref: BTO:0004190 xref: FMA:67101 is_a: CL:0002086 ! specialized cardiac myocyte -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T11:41:37Z [Term] @@ -15443,7 +15448,7 @@ name: transitional myocyte def: "Specialized cardiac myocyte which is in the internodal tract and atrioventricular node. The cell is more slender than ordinary atrial myocytes and has more myofibrils than nodal myocytes." [FMA:67142, GOC:tfm] xref: FMA:67142 is_a: CL:0002086 ! specialized cardiac myocyte -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T02:39:32Z [Term] @@ -15453,7 +15458,7 @@ def: "The myoendocrine cellis a specialized myocyte localized mainly in the righ xref: FMA:67111 is_a: CL:0000163 ! endocrine cell is_a: CL:0002086 ! specialized cardiac myocyte -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T11:50:47Z [Term] @@ -15466,7 +15471,7 @@ is_a: CL:0002202 ! epithelial cell of tracheobronchial tree is_a: CL:0002204 ! brush cell intersection_of: CL:0002204 ! brush cell intersection_of: part_of UBERON:0007196 ! tracheobronchial tree -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T03:22:46Z [Term] @@ -15475,8 +15480,8 @@ name: endo-epithelial cell def: "An epithelial cell derived from endoderm." [FMA:69075, GOC:tfm] xref: FMA:69075 is_a: CL:0000066 ! epithelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000223 ! endodermal cell +relationship: RO:0002202 CL:0000223 ! develops from endodermal cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T03:38:14Z [Term] @@ -15486,9 +15491,9 @@ def: "An epithelial cell derived from ectoderm." [FMA:69074, GOC:tfm] xref: FMA:69074 is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell -intersection_of: develops_from CL:0000221 ! ectodermal cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000221 ! ectodermal cell +intersection_of: RO:0002202 CL:0000221 ! develops from ectodermal cell +relationship: RO:0002202 CL:0000221 ! develops from ectodermal cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T03:38:22Z [Term] @@ -15499,9 +15504,9 @@ synonym: "epithelial mesenchymal cell" EXACT [] xref: FMA:69076 is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell -intersection_of: develops_from CL:0000222 ! mesodermal cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000222 ! mesodermal cell +intersection_of: RO:0002202 CL:0000222 ! develops from mesodermal cell +relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T03:49:14Z [Term] @@ -15517,9 +15522,9 @@ intersection_of: CL:0000083 ! epithelial cell of pancreas intersection_of: capable_of GO:0015106 ! bicarbonate transmembrane transporter activity intersection_of: part_of UBERON:0001064 ! ventral pancreatic duct relationship: capable_of GO:0015106 ! bicarbonate transmembrane transporter activity -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001064 ! ventral pancreatic duct -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-06-30T08:49:43Z [Term] @@ -15535,9 +15540,9 @@ intersection_of: CL:0000083 ! epithelial cell of pancreas intersection_of: capable_of GO:0015106 ! bicarbonate transmembrane transporter activity intersection_of: part_of UBERON:0001263 ! pancreatic acinus relationship: capable_of GO:0015106 ! bicarbonate transmembrane transporter activity -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001263 ! pancreatic acinus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-06-30T08:49:52Z [Term] @@ -15548,7 +15553,7 @@ synonym: "sheath cell of carotid body" EXACT [] xref: FMA:84187 is_a: CL:0000703 ! sustentacular cell is_a: CL:0002256 ! supporting cell of carotid body -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-30T04:23:42Z [Term] @@ -15564,7 +15569,7 @@ is_a: CL:0000454 ! epinephrine secreting cell intersection_of: CL:0000336 ! adrenal medulla chromaffin cell intersection_of: capable_of GO:0048242 ! epinephrine secretion intersection_of: part_of UBERON:0001236 ! adrenal medulla -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-07-14T09:41:42Z [Term] @@ -15578,7 +15583,7 @@ is_a: CL:0000459 ! noradrenergic cell intersection_of: CL:0000336 ! adrenal medulla chromaffin cell intersection_of: capable_of GO:0048243 ! norepinephrine secretion intersection_of: part_of UBERON:0001236 ! adrenal medulla -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-07-14T10:12:24Z [Term] @@ -15589,7 +15594,7 @@ synonym: "Boettcher's cell" EXACT [] synonym: "Bottcher cell" EXACT [] synonym: "Bottcher's cell" EXACT [] is_a: CL:0002315 ! supporting cell of cochlea -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-07-14T03:22:02Z [Term] @@ -15602,7 +15607,7 @@ synonym: "stretch cell" EXACT [] xref: BTO:0001953 xref: FMA:54560 is_a: CL:0000683 ! ependymoglial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-07-15T11:21:11Z [Term] @@ -15611,7 +15616,7 @@ name: specialized cardiac myocyte def: "A cardiac myocyte that is an excitable cells in the myocardium, specifically in the conducting system of heart." [FMA:67968, GOC:tfm] xref: FMA:67968 is_a: CL:0000746 ! cardiac muscle cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-07-21T01:33:38Z [Term] @@ -15625,7 +15630,7 @@ is_a: CL:0000738 {is_inferred="true"} ! leukocyte intersection_of: CL:0000738 ! leukocyte intersection_of: CL:4030045 GO:0030141 ! lacks_part secretory granule relationship: CL:4030045 GO:0030141 ! lacks_part secretory granule -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-07-22T11:30:33Z [Term] @@ -15643,8 +15648,8 @@ is_a: CL:0000710 {is_inferred="true"} ! neurecto-epithelial cell intersection_of: CL:0000710 ! neurecto-epithelial cell intersection_of: capable_of GO:0043134 ! regulation of hindgut contraction relationship: capable_of GO:0043134 ! regulation of hindgut contraction -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-07-22T03:26:00Z [Term] @@ -15667,11 +15672,11 @@ intersection_of: CL:4030046 PR:000001326 ! lacks_plasma_membrane_part bone marro intersection_of: CL:4030046 PR:000001893 ! lacks_plasma_membrane_part natural cytotoxicity triggering receptor 1 intersection_of: CL:4030046 PR:000001927 ! lacks_plasma_membrane_part sialic acid-binding Ig-like lectin 5 intersection_of: CL:4030046 PR:000007431 ! lacks_plasma_membrane_part high affinity immunoglobulin epsilon receptor subunit alpha -intersection_of: in_taxon NCBITaxon:10090 ! Mus musculus intersection_of: RO:0002104 PR:000001860 ! has plasma membrane part inducible T-cell costimulator intersection_of: RO:0002104 PR:000001869 ! has plasma membrane part interleukin-7 receptor subunit alpha intersection_of: RO:0002104 PR:000008982 ! has plasma membrane part interleukin-17 receptor B intersection_of: RO:0002104 PR:000008994 ! has plasma membrane part interleukin-1 receptor-like 1 +intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: capable_of GO:0002830 ! positive regulation of type 2 immune response relationship: capable_of GO:0032616 ! interleukin-13 production relationship: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecule @@ -15683,12 +15688,12 @@ relationship: CL:4030046 PR:000001326 ! lacks_plasma_membrane_part bone marrow s relationship: CL:4030046 PR:000001893 ! lacks_plasma_membrane_part natural cytotoxicity triggering receptor 1 relationship: CL:4030046 PR:000001927 ! lacks_plasma_membrane_part sialic acid-binding Ig-like lectin 5 relationship: CL:4030046 PR:000007431 ! lacks_plasma_membrane_part high affinity immunoglobulin epsilon receptor subunit alpha -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: in_taxon NCBITaxon:10090 ! Mus musculus relationship: RO:0002104 PR:000001860 ! has plasma membrane part inducible T-cell costimulator relationship: RO:0002104 PR:000001869 ! has plasma membrane part interleukin-7 receptor subunit alpha relationship: RO:0002104 PR:000008982 ! has plasma membrane part interleukin-17 receptor B relationship: RO:0002104 PR:000008994 ! has plasma membrane part interleukin-1 receptor-like 1 +relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-12T02:22:19Z [Term] @@ -15701,7 +15706,7 @@ xref: MESH:D059705 xref: WBbt:0008429 xref: XAO:0000262 is_a: CL:0000021 ! female germ cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-23T09:49:53Z [Term] @@ -15715,7 +15720,7 @@ xref: EMAPA:16032 xref: FMA:18650 xref: VHOG:0000464 is_a: CL:0002090 ! polar body -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-23T09:49:58Z [Term] @@ -15730,8 +15735,8 @@ xref: MESH:D001854 is_a: CL:0001035 {is_inferred="true"} ! bone cell intersection_of: CL:0001035 ! bone cell intersection_of: part_of UBERON:0002371 ! bone marrow -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002371 ! bone marrow +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-07-22T04:48:15Z [Term] @@ -15745,7 +15750,7 @@ xref: EMAPA:16034 xref: EMAPA:16045 xref: FMA:18651 is_a: CL:0002090 ! polar body -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-23T09:50:01Z [Term] @@ -15755,7 +15760,7 @@ def: "A cell that makes up the loose connective tissue of the ovary." [GOC:tfm] subset: cellxgene_subset xref: FMA:18709 is_a: CL:0002132 ! stromal cell of ovary -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-23T11:11:34Z [Term] @@ -15767,8 +15772,8 @@ synonym: "hilar cell of ovary" EXACT [] xref: FMA:18710 is_a: CL:0000593 ! androgen secreting cell is_a: CL:0002132 ! stromal cell of ovary -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-08-23T11:18:18Z [Term] @@ -15780,8 +15785,8 @@ is_a: CL:0002086 ! specialized cardiac myocyte is_a: CL:0008009 ! transversely striated visceral muscle cell intersection_of: CL:0000187 ! muscle cell intersection_of: part_of UBERON:0009966 ! internodal tract -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0009966 ! internodal tract +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-23T11:24:11Z [Term] @@ -15797,7 +15802,7 @@ is_a: CL:0002078 {is_inferred="true"} ! meso-epithelial cell is_a: CL:1001601 ! adrenal gland glandular cell intersection_of: CL:0002078 ! meso-epithelial cell intersection_of: part_of UBERON:0001235 ! adrenal cortex -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T01:37:44Z [Term] @@ -15808,7 +15813,7 @@ synonym: "regular cardiac muscle cell" EXACT [] synonym: "regular cardiac muscle fiber" EXACT [] xref: FMA:67967 is_a: CL:0000746 ! cardiac muscle cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-23T11:33:10Z [Term] @@ -15822,8 +15827,8 @@ is_a: CL:0000456 ! mineralocorticoid secreting cell is_a: CL:0002097 {is_inferred="true"} ! cortical cell of adrenal gland intersection_of: CL:0002097 ! cortical cell of adrenal gland intersection_of: part_of UBERON:0002053 ! zona glomerulosa of adrenal gland -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002053 ! zona glomerulosa of adrenal gland +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T01:42:02Z [Term] @@ -15832,7 +15837,7 @@ name: regular interventricular cardiac myocyte def: "A regular cardiac myocyte of the interventricular region of the heart." [GOC:tfm] xref: FMA:228792 is_a: CL:0002098 ! regular cardiac myocyte -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-23T11:40:52Z [Term] @@ -16140,10 +16145,10 @@ intersection_of: capable_of GO:0032609 ! type II interferon production intersection_of: output_of GO:0030217 ! T cell differentiation intersection_of: RO:0002104 PR:000001963 ! has plasma membrane part CD27 molecule relationship: capable_of GO:0032609 ! type II interferon production -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002126 ! CD25-positive, CD27-positive immature gamma-delta T cell relationship: output_of GO:0030217 ! T cell differentiation relationship: RO:0002104 PR:000001963 ! has plasma membrane part CD27 molecule +relationship: RO:0002202 CL:0002126 ! develops from CD25-positive, CD27-positive immature gamma-delta T cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-18T09:57:19Z [Term] @@ -16159,10 +16164,10 @@ intersection_of: has_part PR:000003455 ! nuclear receptor ROR-gamma isoform 2 intersection_of: output_of GO:0030217 ! T cell differentiation relationship: capable_of GO:0032620 ! interleukin-17 production relationship: CL:4030046 PR:000001963 ! lacks_plasma_membrane_part CD27 molecule -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002126 ! CD25-positive, CD27-positive immature gamma-delta T cell relationship: has_part PR:000003455 ! nuclear receptor ROR-gamma isoform 2 relationship: output_of GO:0030217 ! T cell differentiation +relationship: RO:0002202 CL:0002126 ! develops from CD25-positive, CD27-positive immature gamma-delta T cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-18T09:57:29Z [Term] @@ -16180,7 +16185,6 @@ intersection_of: RO:0015015 PR:000001318 ! has high plasma membrane amount L-sel intersection_of: RO:0015015 PR:000001932 ! has high plasma membrane amount signal transducer CD24 intersection_of: RO:0015016 PR:000001083 ! has low plasma membrane amount CD2 molecule intersection_of: RO:0015016 PR:000001839 ! has low plasma membrane amount T-cell surface glycoprotein CD5 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0002104 PR:000001380 ! has plasma membrane part interleukin-2 receptor subunit alpha relationship: RO:0002104 PR:000001919 ! has plasma membrane part programmed cell death protein 1 relationship: RO:0015015 PR:000001307 ! has high plasma membrane amount CD44 molecule @@ -16188,6 +16192,7 @@ relationship: RO:0015015 PR:000001318 ! has high plasma membrane amount L-select relationship: RO:0015015 PR:000001932 ! has high plasma membrane amount signal transducer CD24 relationship: RO:0015016 PR:000001083 ! has low plasma membrane amount CD2 molecule relationship: RO:0015016 PR:000001839 ! has low plasma membrane amount T-cell surface glycoprotein CD5 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-18T10:35:37Z [Term] @@ -16198,7 +16203,7 @@ is_a: CL:0000911 {is_inferred="true"} ! effector T cell intersection_of: CL:0000911 ! effector T cell intersection_of: capable_of GO:0045087 ! innate immune response relationship: capable_of GO:0045087 ! innate immune response -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-20T02:14:25Z [Term] @@ -16236,7 +16241,7 @@ synonym: "regular atrial cardiac muscle fiber" EXACT [] synonym: "regular cardiac muscle cell of atrium" EXACT [] xref: FMA:83108 is_a: CL:0002098 ! regular cardiac myocyte -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-23T11:41:03Z [Term] @@ -16245,7 +16250,7 @@ name: regular interatrial cardiac myocyte def: "A cardiac myocyte of the interatrial region of the heart." [GOC:tfm] xref: FMA:228790 is_a: CL:0002098 ! regular cardiac myocyte -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-23T11:41:09Z [Term] @@ -16259,7 +16264,7 @@ synonym: "ventricular cardiac muscle cell" BROAD [GOC:pr] synonym: "ventricular myocyte" EXACT [] xref: FMA:83109 is_a: CL:0002098 ! regular cardiac myocyte -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-23T11:41:13Z [Term] @@ -16272,8 +16277,8 @@ xref: FMA:72299 is_a: CL:0000499 ! stromal cell intersection_of: CL:0000499 ! stromal cell intersection_of: part_of UBERON:0000992 ! ovary -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0000992 ! ovary +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-23T12:10:31Z [Term] @@ -16282,7 +16287,7 @@ name: stromal cell of ovarian cortex def: "A stromal cell of the ovarian cortex." [GOC:tfm] xref: FMA:256169 is_a: CL:0002132 ! stromal cell of ovary -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-23T12:12:15Z [Term] @@ -16293,8 +16298,8 @@ xref: FMA:256171 is_a: CL:0002132 {is_inferred="true"} ! stromal cell of ovary intersection_of: CL:0000499 ! stromal cell intersection_of: part_of UBERON:0013192 ! ovarian medulla -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0013192 ! ovarian medulla +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-23T12:12:17Z [Term] @@ -16303,8 +16308,8 @@ name: nonkeratinized cell of epidermis def: "Epidermal cells that do not contain keratin. Cell type is usually associated with moist epidermal tissues." [GO:tfm, PMID:1987287] xref: FMA:62880 is_a: CL:0000362 ! epidermal cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001003 ! skin epidermis +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T08:43:27Z [Term] @@ -16315,7 +16320,7 @@ synonym: "type II cortical cell of adrenal gland" EXACT [] xref: FMA:69547 is_a: CL:0000460 ! glucocorticoid secreting cell is_a: CL:0002097 ! cortical cell of adrenal gland -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T01:50:42Z [Term] @@ -16325,7 +16330,7 @@ def: "A cell in the zona reticularis that produce sex hormones." [GOC:tfm, ISBN: xref: FMA:69564 is_a: CL:0000593 ! androgen secreting cell is_a: CL:0002097 ! cortical cell of adrenal gland -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T01:50:44Z [Term] @@ -16341,12 +16346,12 @@ xref: BTO:0004167 xref: FMA:68458 is_a: CL:0002139 {is_inferred="true"} ! endothelial cell of vascular tree intersection_of: CL:0002139 ! endothelial cell of vascular tree -intersection_of: develops_from CL:0005022 ! vascular lymphangioblast intersection_of: part_of UBERON:0001473 ! lymphatic vessel -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0005022 ! vascular lymphangioblast +intersection_of: RO:0002202 CL:0005022 ! develops from vascular lymphangioblast relationship: part_of UBERON:0001473 ! lymphatic vessel -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0005022 ! develops from vascular lymphangioblast +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-08-24T02:05:28Z [Term] @@ -16361,7 +16366,7 @@ xref: BTO:0001854 xref: CALOHA:TS-1106 xref: FMA:67755 is_a: CL:0000115 ! endothelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T02:06:40Z [Term] @@ -16377,8 +16382,8 @@ is_a: CL:0000622 ! acinar cell is_a: CL:1000448 ! epithelial cell of sweat gland intersection_of: CL:0000317 ! sebum secreting cell intersection_of: part_of UBERON:0003487 ! skin sebaceous gland -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0003487 ! skin sebaceous gland +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T09:27:52Z [Term] @@ -16387,7 +16392,7 @@ name: active chief cell of parathyroid gland def: "A parathyroid chief cell that is actively secreting hormone. Have large Golgi complexes with numerous vesicles and small membrane-bound granules; secretory granules are rare, cytoplasmic glycogen sparse, much of the cytoplasm being occupied by flat sacs of granular endoplasmic reticulum in parallel arrays; in normal humans, inactive chief cells outnumber active chief cells in a ratio of 3-5:1" [FMA:0517223651, GOC:tfm] xref: FMA:69082 is_a: CL:0000446 ! chief cell of parathyroid gland -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T09:30:15Z [Term] @@ -16399,8 +16404,8 @@ is_a: CL:0000152 ! exocrine cell is_a: CL:0000318 ! sweat secreting cell is_a: CL:0000434 ! eccrine cell is_a: CL:1000448 ! epithelial cell of sweat gland -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0000423 ! eccrine sweat gland +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T02:15:16Z [Term] @@ -16409,7 +16414,7 @@ name: dark chief cell of parathyroid gland def: "A chief cell that is smaller than light chief cells and has a smaller and darker nucleus and a finely granular cytoplasm with many granules." [GOC:tfm, ISBN:0721662544] xref: FMA:69080 is_a: CL:0000446 ! chief cell of parathyroid gland -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T02:18:36Z [Term] @@ -16424,9 +16429,9 @@ xref: FMA:67756 is_a: CL:2000008 ! microvascular endothelial cell intersection_of: CL:0000071 ! blood vessel endothelial cell intersection_of: part_of UBERON:0001915 ! endothelium of capillary -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001915 ! endothelium of capillary -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-08-24T10:15:00Z [Term] @@ -16439,9 +16444,9 @@ xref: FMA:70542 is_a: CL:0002202 ! epithelial cell of tracheobronchial tree is_a: CL:0005012 ! multi-ciliated epithelial cell is_a: CL:4030034 ! respiratory ciliated cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002209 ! intermediate epitheliocyte -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0002209 ! develops from intermediate epitheliocyte +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-08-24T03:38:29Z [Term] @@ -16453,8 +16458,8 @@ is_a: CL:0000152 ! exocrine cell is_a: CL:0000318 ! sweat secreting cell is_a: CL:0000434 ! eccrine cell is_a: CL:1000448 ! epithelial cell of sweat gland -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0000423 ! eccrine sweat gland +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T10:33:02Z [Term] @@ -16464,7 +16469,7 @@ def: "A chief cell of parathyroid glands that does not stain with hematoxylin or synonym: "clear chief cell of parathyroid cell" EXACT [] xref: FMA:69081 is_a: CL:0000446 ! chief cell of parathyroid gland -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T10:39:42Z [Term] @@ -16477,8 +16482,8 @@ is_a: CL:0002159 ! general ecto-epithelial cell is_a: CL:0002320 ! connective tissue cell intersection_of: CL:0002159 ! general ecto-epithelial cell intersection_of: part_of UBERON:0001754 ! dental pulp -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001754 ! dental pulp +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T02:52:09Z [Term] @@ -16491,8 +16496,8 @@ xref: FMA:256161 is_a: CL:0002076 {is_inferred="true"} ! endo-epithelial cell intersection_of: CL:0002076 ! endo-epithelial cell intersection_of: part_of UBERON:0000995 ! uterus -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0000995 ! uterus +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T10:45:54Z [Term] @@ -16504,8 +16509,8 @@ synonym: "epithelioid histocyte" EXACT [MESH:D015622, PMID:12673090] synonym: "epitheloid macrophage" EXACT [] xref: FMA:83514 is_a: CL:0000235 ! macrophage -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000861 ! elicited macrophage +relationship: RO:0002202 CL:0000861 ! develops from elicited macrophage +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T03:48:30Z [Term] @@ -16515,7 +16520,7 @@ def: "A promyelocyte that is considerably smaller, with more condensed chromatin subset: cellxgene_subset xref: FMA:83534 is_a: CL:0000836 ! promyelocyte -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T03:07:50Z [Term] @@ -16524,8 +16529,8 @@ name: columnar cell of endocervix def: "A columnar cell of the cervix uteri." [GOC:tfm, ISBN:0721662544] xref: FMA:86486 is_a: CL:0002149 ! epithelial cell of uterus -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0000458 ! endocervix +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T10:47:47Z [Term] @@ -16537,10 +16542,10 @@ xref: BTO:0001943 xref: FMA:68650 is_a: CL:0000225 ! anucleate cell is_a: CL:0000311 ! keratin accumulating cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000312 ! keratinocyte relationship: part_of UBERON:0002027 ! stratum corneum of epidermis -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0000312 ! develops from keratinocyte +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-08-24T10:53:03Z [Term] @@ -16550,7 +16555,7 @@ def: "A promyelocyte with a nucleus that is indented and contains more marginate subset: cellxgene_subset xref: FMA:83533 is_a: CL:0000836 ! promyelocyte -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T03:07:53Z [Term] @@ -16560,7 +16565,7 @@ def: "A crenated erythrocyte with 30+ crenations, bumps or spurs that are the re synonym: "burr cell" EXACT [] xref: FMA:81099 is_a: CL:0000595 ! enucleate erythrocyte -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T03:15:21Z [Term] @@ -16571,8 +16576,8 @@ subset: cellxgene_subset xref: FMA:86495 is_a: CL:0001035 ! bone cell is_a: CL:0002078 ! meso-epithelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0009859 ! endosteum +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T03:33:58Z [Term] @@ -16581,7 +16586,7 @@ name: external epithelial cell of tympanic membrane def: "Epithelial cell found on the external side of the tympanic membrane" [GOC:tfm, PMID:5686391] xref: FMA:70558 is_a: CL:0002159 ! general ecto-epithelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T10:25:31Z [Term] @@ -16590,7 +16595,7 @@ name: general ecto-epithelial cell def: "Epithelial cells derived from general body ectoderm and ectoderm placodes." [GOC:tfm] xref: FMA:70556 is_a: CL:0002077 ! ecto-epithelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-26T08:31:08Z [Term] @@ -16598,7 +16603,7 @@ id: CL:0002160 name: basal external epithelial cell of tympanic membrane def: "A cell type found in the basal epithelial layer on the external side of the tympanic membrane. Cell type is flattened with intracellular spaces of variable dimensions." [PMID:5686391] is_a: CL:0002158 ! external epithelial cell of tympanic membrane -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T10:28:44Z [Term] @@ -16606,7 +16611,7 @@ id: CL:0002161 name: superficial external epithelial cell of tympanic membrane def: "A cell type found on the superficial layer of the external side of the tympanic membrane. This cell-type lacks a nucleus." [PMID:5686391] is_a: CL:0002158 ! external epithelial cell of tympanic membrane -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T10:28:48Z [Term] @@ -16615,8 +16620,8 @@ name: internal epithelial cell of tympanic membrane def: "An extremely flattened cell type found on the inner side of the tympanic membrane. The surface of this cell type carries sparse pleomorphic microvilli that are more common near the junctional zones." [FMA:5686391, GOC:tfm] xref: FMA:70626 is_a: CL:0002076 ! endo-epithelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002364 ! tympanic membrane +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T10:49:46Z [Term] @@ -16625,7 +16630,7 @@ name: internal pillar cell of cochlea def: "A rod-shpaed cell that forms a single row adjacent to and supporting the inner hair cells." [GOC:tfm, http://www.theodora.com/anatomy/the_internal_ear_or_labyrinth.html] xref: FMA:75726 is_a: CL:1000191 ! pillar cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T11:05:21Z [Term] @@ -16634,7 +16639,7 @@ name: external pillar cell of cochlea def: "A rod-shaped cell found in 3 or 4 rows that lie adjacent to and support the outer hair cells." [GOC:tfm, http://www.theodora.com/anatomy/the_internal_ear_or_labyrinth.html] xref: FMA:75727 is_a: CL:1000191 ! pillar cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T11:05:23Z [Term] @@ -16643,7 +16648,7 @@ name: phalangeal cell def: "A supporting cell that is attached to the basement membrane and forms rows that support the hair cells." [GOC:tfm, ISBN:0618947256] xref: FMA:79800 is_a: CL:0002490 ! organ of Corti supporting cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T01:29:07Z [Term] @@ -16655,8 +16660,8 @@ synonym: "epithelial debris of Malassez" EXACT [] xref: FMA:62987 is_a: CL:0002159 {is_inferred="true"} ! general ecto-epithelial cell is_a: CL:0002251 ! epithelial cell of alimentary canal -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0011595 ! jaw region +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-26T08:51:27Z [Term] @@ -16670,7 +16675,7 @@ is_a: CL:0000710 ! neurecto-epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: capable_of GO:0050911 ! detection of chemical stimulus involved in sensory perception of smell relationship: capable_of GO:0050911 ! detection of chemical stimulus involved in sensory perception of smell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-26T01:47:13Z [Term] @@ -16679,7 +16684,7 @@ name: border cell of cochlea def: "A border cell is a slender columnar cell on the medial portion of the basilar membrane." [FMA:0412046911, GOC:tfm] xref: FMA:79798 is_a: CL:0002315 ! supporting cell of cochlea -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T01:47:12Z [Term] @@ -16693,8 +16698,8 @@ is_a: CL:0002167 {is_inferred="true"} ! olfactory epithelial cell is_a: CL:0002319 ! neural cell intersection_of: CL:0002167 ! olfactory epithelial cell intersection_of: part_of UBERON:0001997 ! olfactory epithelium -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001997 ! olfactory epithelium +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-26T01:58:54Z [Term] @@ -16706,8 +16711,8 @@ is_a: CL:0002251 ! epithelial cell of alimentary canal is_a: CL:0002336 ! buccal mucosa cell intersection_of: CL:0000237 ! keratinizing barrier epithelial cell intersection_of: part_of UBERON:0003729 ! mouth mucosa -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0003729 ! mouth mucosa +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-26T02:51:30Z [Term] @@ -16717,7 +16722,7 @@ def: "A rounded or elliptical epithelial cell, with pale-staining open face nucl synonym: "blastema cell of olfactory epithelium" EXACT [] xref: FMA:67874 is_a: CL:0002169 ! basal cell of olfactory epithelium -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-26T01:59:18Z [Term] @@ -16727,8 +16732,8 @@ def: "A long, spindle-shaped supporting cells arranged in parallel rows that sec synonym: "interdental cell" EXACT [] xref: FMA:79797 is_a: CL:0002315 ! supporting cell of cochlea -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002276 ! lamina of spiral limbus +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T02:02:48Z [Term] @@ -16745,8 +16750,8 @@ is_a: CL:1000618 {is_inferred="true"} ! juxtaglomerular complex cell is_a: CL:1001318 ! renal interstitial pericyte intersection_of: CL:0002320 ! connective tissue cell intersection_of: part_of UBERON:0002321 ! extraglomerular mesangium -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002321 ! extraglomerular mesangium +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T02:20:55Z [Term] @@ -16757,8 +16762,8 @@ xref: EMAPA:31247 xref: FMA:70589 is_a: CL:0000500 ! follicular epithelial cell is_a: CL:0002078 ! meso-epithelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: never_in_taxon NCBITaxon:50557 {source="https://github.com/obophenotype/cell-ontology/issues/589"} ! Insecta +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002161 NCBITaxon:50557 {source="https://github.com/obophenotype/cell-ontology/issues/589"} creation_date: 2010-08-25T03:01:27Z [Term] @@ -16767,7 +16772,7 @@ name: primary follicular cell of ovary def: "A cell within the primary follicle of the ovary." [GOC:tfm] xref: FMA:70590 is_a: CL:0002174 ! follicular cell of ovary -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T03:03:42Z [Term] @@ -16776,7 +16781,7 @@ name: secondary follicular cell of ovary def: "A cell of a secondary follicile within the ovary." [GOC:tfm] xref: FMA:70591 is_a: CL:0002174 ! follicular cell of ovary -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T03:03:48Z [Term] @@ -16789,8 +16794,8 @@ is_a: CL:0000642 {is_inferred="true"} ! folliculostellate cell is_a: CL:0000710 ! neurecto-epithelial cell intersection_of: CL:0000642 ! folliculostellate cell intersection_of: part_of UBERON:0006964 ! pars distalis of adenohypophysis -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0006964 ! pars distalis of adenohypophysis +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T03:10:10Z [Term] @@ -16802,8 +16807,8 @@ xref: FMA:62948 is_a: CL:0002251 {is_inferred="true"} ! epithelial cell of alimentary canal intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0000945 ! stomach -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0000945 ! stomach +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T03:22:08Z [Term] @@ -16813,7 +16818,7 @@ def: "An epithelial cell within one of the pits in the embryonic gastric mucosa subset: cellxgene_subset xref: FMA:86552 is_a: CL:0002178 ! epithelial cell of stomach -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T03:23:22Z [Term] @@ -16825,8 +16830,8 @@ xref: FMA:63464 is_a: CL:0002659 ! glandular cell of stomach intersection_of: CL:0002178 ! epithelial cell of stomach intersection_of: part_of UBERON:0001199 ! mucosa of stomach -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001199 ! mucosa of stomach +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T03:38:51Z [Term] @@ -16841,8 +16846,8 @@ is_a: CL:0000651 {is_inferred="true"} ! mucous neck cell is_a: CL:0002180 {is_inferred="true"} ! mucous cell of stomach intersection_of: CL:0000651 ! mucous neck cell intersection_of: part_of UBERON:0000325 ! gastric gland -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0000325 ! gastric gland +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T03:41:30Z [Term] @@ -16852,7 +16857,7 @@ def: "A simple columnar cell that populates the entire luminal surface including xref: FMA:62949 is_a: CL:0000319 ! mucus secreting cell is_a: CL:0002180 ! mucous cell of stomach -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T03:45:10Z [Term] @@ -16866,8 +16871,8 @@ is_a: CL:0000152 ! exocrine cell is_a: CL:0002180 ! mucous cell of stomach intersection_of: CL:0000048 ! multi fate stem cell intersection_of: part_of UBERON:0000325 ! gastric gland -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0000325 ! gastric gland +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T03:57:08Z [Term] @@ -16877,7 +16882,7 @@ def: "A flat or angular epithelial cell with condensed nuclei and darkly stainin synonym: "horizontal basal cells" EXACT [] xref: FMA:62304 is_a: CL:0002169 ! basal cell of olfactory epithelium -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-26T01:59:22Z [Term] @@ -16893,7 +16898,7 @@ is_a: CL:0011026 ! progenitor cell is_a: CL:1000428 ! stem cell of epidermis intersection_of: CL:0000646 ! basal cell intersection_of: part_of UBERON:0001003 ! skin epidermis -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-26T03:12:49Z [Term] @@ -16909,7 +16914,7 @@ is_a: CL:0000666 ! fenestrated cell is_a: CL:1000746 ! glomerular cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0000074 ! renal glomerulus -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-26T10:59:44Z [Term] @@ -16919,7 +16924,7 @@ def: "A keratinocyte of the epidermis that is characterized by containing granul subset: cellxgene_subset xref: FMA:70543 is_a: CL:0000312 ! keratinocyte -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-26T03:19:00Z [Term] @@ -16928,7 +16933,7 @@ name: squamous cell of epidermis def: "A flat keratinocyte immediately below the cornified layer." [GOC:tfm, ISBN:0517223651] xref: FMA:86925 is_a: CL:0000312 ! keratinocyte -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-26T03:37:02Z [Term] @@ -16941,7 +16946,7 @@ is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor ce intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: capable_of GO:0030851 ! granulocyte differentiation relationship: capable_of GO:0030851 ! granulocyte differentiation -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-30T12:54:27Z [Term] @@ -16951,8 +16956,8 @@ def: "A eosinophil precursor in the granulocytic series, being a cell intermedia xref: FMA:83541 is_a: CL:0000763 ! myeloid cell is_a: CL:0002191 ! granulocytopoietic cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002193 ! myelocyte +relationship: RO:0002202 CL:0002193 ! develops from myelocyte +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-30T01:08:15Z [Term] @@ -16965,9 +16970,9 @@ xref: BTO:0000734 xref: FMA:83525 is_a: CL:0000763 ! myeloid cell is_a: CL:0002191 ! granulocytopoietic cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000836 ! promyelocyte -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0000836 ! develops from promyelocyte +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-08-30T01:08:19Z [Term] @@ -16979,7 +16984,7 @@ is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor ce intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: capable_of GO:0030224 ! monocyte differentiation relationship: capable_of GO:0030224 ! monocyte differentiation -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-30T01:27:48Z [Term] @@ -16991,8 +16996,8 @@ xref: FMA:86577 is_a: CL:0000048 {is_inferred="true"} ! multi fate stem cell intersection_of: CL:0000048 ! multi fate stem cell intersection_of: part_of UBERON:0002107 ! liver -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002107 ! liver +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/800" xsd:string creation_date: 2010-08-30T02:00:42Z @@ -17008,9 +17013,9 @@ synonym: "liver progenitor cell" EXACT [https://doi.org/10.1038/s12276-020-0483- xref: BTO:0004270 xref: FMA:86576 is_a: CL:0011026 ! progenitor cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002107 ! liver -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 property_value: RO:0004050 "Liver progenitor cells have been variously named in rodent and human studies as oval cells, hepatic progenitor cells, liver stem cells, ductular reactions, or atypical ductular cells. They were first described as oval cells in rats due to their large nuclear-to-cytoplasm ratio and oval-shaped nuclei. On the difference between 'hepatic liver stem cells' (HLSC) and 'oval cells': \"... unlike a well-known hepatic progenitor cell population, known as oval cells in rodents, HLSCs do not express CK-7, CK-19, c-kit, CD133 and alpha-smooth muscle actin (α-SMA) (Gaudio et al., 2009)\"." xsd:string {xref="https://doi.org/10.1038/s12276-020-0483-0", xref="https://doi.org/10.3389/fcell.2021.644088"} creation_date: 2010-08-30T02:01:49Z @@ -17019,7 +17024,7 @@ id: CL:0002197 name: inactive chief cell of parathyoid gland def: "A parathyroid chief cell that is not actively secreting hormone. Contains small Golgi complexes with only a few grouped vesicles and membrane-bound secretory granules; glycogen and many lipofuscin granules abound but sacs of granular endoplasmic reticulum are rare and dispersed. In normal humans, inactive chief cells out number active chief cells in a ratio of 3-5:1." [GOC:tfm, ISBN:0517223651] is_a: CL:0000446 ! chief cell of parathyroid gland -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T11:14:01Z [Term] @@ -17030,7 +17035,7 @@ synonym: "oxyphil" EXACT [] xref: FMA:67606 xref: MESH:D024862 is_a: CL:0002076 ! endo-epithelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T11:26:49Z [Term] @@ -17040,7 +17045,7 @@ def: "An oncocyte located in the parathyroid gland." [PMID:20013317] xref: FMA:69084 is_a: CL:0002198 ! oncocyte is_a: CL:0002260 ! epithelial cell of parathyroid gland -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T11:33:23Z [Term] @@ -17054,7 +17059,7 @@ is_a: CL:0002198 ! oncocyte is_a: CL:0002257 ! epithelial cell of thyroid gland intersection_of: CL:0002198 ! oncocyte intersection_of: part_of UBERON:0002046 ! thyroid gland -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T11:33:26Z [Term] @@ -17066,8 +17071,8 @@ subset: human_reference_atlas synonym: "type B intercalated cell" EXACT [PMID:25632105] synonym: "type B-IC" EXACT [PMID:25632105] is_a: CL:0005010 ! renal intercalated cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-09-02T01:43:55Z [Term] @@ -17079,8 +17084,8 @@ xref: FMA:66816 is_a: CL:0002632 ! epithelial cell of lower respiratory tract intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0007196 ! tracheobronchial tree -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0007196 ! tracheobronchial tree +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T02:09:14Z [Term] @@ -17098,7 +17103,7 @@ is_a: CL:0002253 ! epithelial cell of large intestine is_a: CL:0019032 ! intestinal tuft cell intersection_of: CL:0002204 ! brush cell intersection_of: part_of UBERON:0000059 ! large intestine -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T02:20:50Z [Term] @@ -17112,7 +17117,7 @@ synonym: "multivesicular cell" EXACT [] synonym: "tuft cell" EXACT [] xref: FMA:67978 is_a: CL:0002076 ! endo-epithelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T02:28:53Z [Term] @@ -17125,8 +17130,8 @@ is_a: CL:0000082 ! epithelial cell of lung is_a: CL:0002075 ! brush cell of trachebronchial tree intersection_of: CL:0002204 ! brush cell intersection_of: part_of UBERON:8600001 ! epithelium of lobular bronchiole -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:8600001 ! epithelium of lobular bronchiole +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T02:38:34Z [Term] @@ -17139,8 +17144,8 @@ is_a: CL:0000082 ! epithelial cell of lung is_a: CL:0002075 ! brush cell of trachebronchial tree intersection_of: CL:0002204 ! brush cell intersection_of: part_of UBERON:0001958 ! terminal bronchiole epithelium -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001958 ! terminal bronchiole epithelium +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T02:38:36Z [Term] @@ -17155,9 +17160,9 @@ is_a: CL:0000307 {is_inferred="true"} ! tracheal epithelial cell is_a: CL:0002075 {is_inferred="true"} ! brush cell of trachebronchial tree intersection_of: CL:0002204 ! brush cell intersection_of: part_of UBERON:0001901 ! epithelium of trachea -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001901 ! epithelium of trachea -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-09-02T02:38:37Z [Term] @@ -17171,8 +17176,8 @@ is_a: CL:0002075 ! brush cell of trachebronchial tree is_a: CL:0002328 ! bronchial epithelial cell intersection_of: CL:0002204 ! brush cell intersection_of: part_of UBERON:0002031 ! epithelium of bronchus -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-09-02T02:38:42Z [Term] @@ -17182,7 +17187,7 @@ def: "An epithelial cell present in the trachea and bronchi; columnar in shape; synonym: "undifferentiated columnar cell of tracheobronchial tree" EXACT [] xref: FMA:69060 is_a: CL:0002202 ! epithelial cell of tracheobronchial tree -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T02:53:59Z [Term] @@ -17193,7 +17198,7 @@ synonym: "oxidative muscle fiber" EXACT [] synonym: "red muscle fiber" EXACT [] xref: FMA:84448 is_a: CL:0008046 ! extrafusal muscle fiber -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T03:20:03Z [Term] @@ -17213,7 +17218,7 @@ xref: CALOHA:TS-0940 xref: FMA:84413 is_a: CL:0000189 ! slow muscle cell is_a: CL:0002210 ! red muscle cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T03:24:05Z [Term] @@ -17226,7 +17231,7 @@ synonym: "type II muscle fiber" EXACT [] xref: BTO:0001813 xref: FMA:84414 is_a: CL:0000190 ! fast muscle cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T03:28:45Z [Term] @@ -17235,7 +17240,7 @@ name: white muscle cell def: "A muscle cell with low content of myoglobin and other oxygen storing proteins. This muscle cell has a white appearance." [GOC:tfm, ISBN:0517223651] xref: FMA:84449 is_a: CL:0000190 ! fast muscle cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T03:28:48Z [Term] @@ -17251,7 +17256,7 @@ xref: BTO:0001813 xref: FMA:84415 is_a: CL:0002210 ! red muscle cell is_a: CL:0002212 ! type II muscle cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T03:31:38Z [Term] @@ -17264,7 +17269,7 @@ synonym: "type IIb muscle fiber" EXACT [] xref: FMA:84416 is_a: CL:0002212 ! type II muscle cell is_a: CL:0002213 ! white muscle cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T03:31:42Z [Term] @@ -17273,7 +17278,7 @@ name: intermediate muscle cell def: "An intermediate muscle cell that has characteristics of both fast and slow muscle cells." [GOC:tfm] xref: FMA:84450 is_a: CL:0008046 ! extrafusal muscle fiber -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T03:51:17Z [Term] @@ -17283,7 +17288,7 @@ def: "A trophoblast that leaves the placenta and invades the endometrium and myo xref: BTO:0002366 xref: FMA:86564 is_a: CL:0000351 ! trophoblast cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T04:04:36Z [Term] @@ -17294,7 +17299,7 @@ comment: NOTE: currently variable immune gene segments are not represented in th synonym: "immature DEC precursor" EXACT [] synonym: "immature DETC precursor" EXACT [] is_a: CL:0002404 ! fetal thymocyte -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-07T01:58:00Z [Term] @@ -17302,7 +17307,7 @@ id: CL:0002219 name: anchoring trophoblast def: "A trophoblast found at the junction of the placenta. This cell type makes a unique fibronectin-trophouteronectin junction that helps mediate attachment of the placenta to the uterus. This cell type is also found junction of the chorion layer of the external membranes and the decidua." [GOC:tfm, http://www.med.yale.edu/obgyn/kliman/placenta/articles/EOR_Placenta/Trophtoplacenta.html] is_a: CL:0000351 ! trophoblast cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T04:14:28Z [Term] @@ -17311,7 +17316,7 @@ name: interstitial cell of pineal gland def: "A cell located between the pinealocytes." [GOC:tfm, ISBN:0517223651] xref: FMA:86575 is_a: CL:0000710 ! neurecto-epithelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-02T04:28:41Z [Term] @@ -17321,7 +17326,7 @@ def: "A squamous cell that has keratin in the esophagus." [GOC:tfm, PMID:1169455 xref: FMA:86549 is_a: CL:0000237 ! keratinizing barrier epithelial cell is_a: CL:0002252 ! epithelial cell of esophagus -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T10:11:06Z [Term] @@ -17332,8 +17337,8 @@ subset: eye_upper_slim xref: FMA:70950 is_a: CL:0000066 ! epithelial cell is_a: CL:0000306 ! crystallin accumulating cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0000965 ! lens of camera-type eye +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T10:38:03Z [Term] @@ -17343,7 +17348,7 @@ def: "A cell of the transparent layer of simple cuboidal epithelium over the ant subset: cellxgene_subset xref: FMA:63181 is_a: CL:0002224 ! lens epithelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T10:45:45Z [Term] @@ -17357,9 +17362,9 @@ is_a: CL:0000075 {is_inferred="true"} ! columnar/cuboidal epithelial cell is_a: CL:0002222 ! vertebrate lens cell intersection_of: CL:0000075 ! columnar/cuboidal epithelial cell intersection_of: part_of UBERON:0001803 ! epithelium of lens -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001803 ! epithelium of lens -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-09-07T10:45:47Z [Term] @@ -17370,9 +17375,9 @@ subset: cellxgene_subset subset: human_reference_atlas synonym: "secondary lens fibre" EXACT [] is_a: CL:0011004 ! lens fiber cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002228 ! primary lens fiber -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0002228 ! develops from primary lens fiber +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-09-07T10:53:39Z [Term] @@ -17382,8 +17387,8 @@ def: "A secondary lens fiber cell that lacks a nucleus." [GOC:tfm] synonym: "non-nucleated secondary lens fibre" EXACT [] xref: FMA:67561 is_a: CL:0002225 ! secondary lens fiber -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002227 ! nucleated secondary lens fiber +relationship: RO:0002202 CL:0002227 ! develops from nucleated secondary lens fiber +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T11:15:23Z [Term] @@ -17393,7 +17398,7 @@ def: "A secondary fiber cell that contains a nucleus." [GOC:tfm] synonym: "nucleated secondary lens fibre" EXACT [] xref: FMA:70949 is_a: CL:0002225 ! secondary lens fiber -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T11:15:26Z [Term] @@ -17404,9 +17409,9 @@ subset: human_reference_atlas synonym: "primary lens fibre" EXACT [] xref: FMA:70613 is_a: CL:0011004 ! lens fiber cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002223 ! anterior lens cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0002223 ! develops from anterior lens cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-09-07T11:19:01Z [Term] @@ -17415,7 +17420,7 @@ name: light chief cell of parathyroid gland def: "A chief cell that is bigger than dark chief cells and has a larger and lighter nucleus and a cytoplasm with few granules." [GOC:tfm, ISBN:0721662544] xref: FMA:69079 is_a: CL:0000446 ! chief cell of parathyroid gland -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T11:46:54Z [Term] @@ -17431,8 +17436,8 @@ xref: FMA:66817 is_a: CL:0002076 {is_inferred="true"} ! endo-epithelial cell intersection_of: CL:0002076 ! endo-epithelial cell intersection_of: part_of UBERON:0002367 ! prostate gland -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002367 ! prostate gland +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T01:49:29Z [Term] @@ -17446,8 +17451,8 @@ is_a: CL:0000072 {is_inferred="true"} ! non-branched duct epithelial cell is_a: CL:0002231 ! epithelial cell of prostate intersection_of: CL:0000072 ! non-branched duct epithelial cell intersection_of: part_of UBERON:0002485 ! prostate duct -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002485 ! prostate duct +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T01:55:51Z [Term] @@ -17460,8 +17465,8 @@ xref: FMA:74223 is_a: CL:0002231 {is_inferred="true"} ! epithelial cell of prostate intersection_of: CL:0002231 ! epithelial cell of prostate intersection_of: part_of UBERON:0004179 ! prostate glandular acinus -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0004179 ! prostate glandular acinus +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T01:55:53Z [Term] @@ -17475,7 +17480,7 @@ is_a: CL:0002233 ! epithelial cell of prostatic acinus is_a: CL:0002341 ! basal cell of prostate epithelium intersection_of: CL:0002341 ! basal cell of prostate epithelium intersection_of: part_of UBERON:0004179 ! prostate glandular acinus -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T01:59:08Z [Term] @@ -17487,7 +17492,7 @@ is_a: CL:0002233 ! epithelial cell of prostatic acinus is_a: CL:0002340 ! luminal cell of prostate epithelium intersection_of: CL:0002340 ! luminal cell of prostate epithelium intersection_of: part_of UBERON:0004179 ! prostate glandular acinus -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T01:59:10Z [Term] @@ -17501,8 +17506,8 @@ is_a: CL:0000068 ! duct epithelial cell is_a: CL:0002341 ! basal cell of prostate epithelium intersection_of: CL:0002341 ! basal cell of prostate epithelium intersection_of: part_of UBERON:0002485 ! prostate duct -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002485 ! prostate duct +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T01:59:12Z [Term] @@ -17514,8 +17519,8 @@ is_a: CL:0000068 ! duct epithelial cell is_a: CL:0002340 ! luminal cell of prostate epithelium intersection_of: CL:0002340 ! luminal cell of prostate epithelium intersection_of: part_of UBERON:0002485 ! prostate duct -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002485 ! prostate duct +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T01:59:16Z [Term] @@ -17529,8 +17534,8 @@ xref: EMAPA:18686 xref: FMA:84771 xref: VHOG:0000662 is_a: CL:0000670 ! primordial germ cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0000473 ! testis +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T02:11:13Z [Term] @@ -17545,8 +17550,8 @@ xref: FMA:84772 xref: ISBN:0721662544 xref: VHOG:0000661 is_a: CL:0000670 ! primordial germ cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0000992 ! ovary +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T02:11:16Z [Term] @@ -17558,7 +17563,7 @@ is_a: CL:0000057 ! fibroblast is_a: CL:0002092 ! bone marrow cell intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0002371 ! bone marrow -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T02:25:18Z [Term] @@ -17574,8 +17579,8 @@ is_a: CL:4030031 ! interstitial cell intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001004 ! respiratory system intersection_of: part_of UBERON:0005169 ! interstitial tissue -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001004 ! respiratory system +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T02:29:38Z [Term] @@ -17587,7 +17592,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0002505 ! nucleated relationship: bearer_of PATO:0002505 ! nucleated -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T03:32:33Z [Term] @@ -17601,9 +17606,9 @@ xref: FMA:70611 is_a: CL:0000358 {is_inferred="true"} ! sphincter associated smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0001607 ! sphincter pupillae -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000133 ! neurectodermal cell relationship: part_of UBERON:0001607 ! sphincter pupillae +relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-08T08:53:42Z [Term] @@ -17614,7 +17619,7 @@ synonym: "ectocervical squamous cell" EXACT [] xref: FMA:86483 is_a: CL:0000076 ! squamous epithelial cell is_a: CL:0002149 ! epithelial cell of uterus -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-08T09:12:23Z [Term] @@ -17622,7 +17627,7 @@ id: CL:0002245 name: obsolete null lymphocyte def: "OBSOLETE: A lymphocyte that lacks T or B cell surface markers." [GOC:tfm, ISBN:068340007X] xref: FMA:83601 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 is_obsolete: true creation_date: 2010-09-07T03:43:42Z @@ -17638,8 +17643,8 @@ is_a: CL:0000037 {is_inferred="true"} ! hematopoietic stem cell is_a: CL:0000080 ! circulating cell intersection_of: CL:0000037 ! hematopoietic stem cell intersection_of: part_of UBERON:0000178 ! blood -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0000178 ! blood +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T03:57:09Z [Term] @@ -17648,7 +17653,7 @@ name: pleural macrophage def: "A tissue macrophage that is in the pleural space." [GOC:tfm] xref: FMA:83024 is_a: CL:0000864 ! tissue-resident macrophage -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T04:16:43Z [Term] @@ -17658,7 +17663,7 @@ def: "A pluripotent stem cell has the ability to form cells from all three germ xref: FMA:70570 xref: MESH:D039904 is_a: CL:0000723 ! somatic stem cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T04:26:06Z [Term] @@ -17668,7 +17673,7 @@ def: "A stem cell that can differentiate into a cardiac myocyte." [GOC:tfm, PMID xref: FMA:75620 is_a: CL:0000035 ! single fate stem cell is_a: CL:0002078 ! meso-epithelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T04:40:32Z [Term] @@ -17682,8 +17687,8 @@ is_a: CL:0000048 ! multi fate stem cell is_a: CL:0002563 ! intestinal epithelial cell intersection_of: CL:0000034 ! stem cell intersection_of: part_of UBERON:0001983 ! crypt of Lieberkuhn -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001983 ! crypt of Lieberkuhn +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-08T09:21:22Z [Term] @@ -17693,8 +17698,8 @@ def: "An epithelial cell of the musculomembranous digestive tube extending from is_a: CL:0002076 ! endo-epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001555 ! digestive tract -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001555 ! digestive tract +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-08T09:26:53Z [Term] @@ -17707,8 +17712,8 @@ xref: FMA:63071 is_a: CL:0002251 {is_inferred="true"} ! epithelial cell of alimentary canal intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001043 ! esophagus -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001043 ! esophagus +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-08T09:28:20Z [Term] @@ -17723,8 +17728,8 @@ xref: FMA:256157 is_a: CL:0002563 {is_inferred="true"} ! intestinal epithelial cell intersection_of: CL:0002563 ! intestinal epithelial cell intersection_of: part_of UBERON:0000059 ! large intestine -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0000059 ! large intestine +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-08T09:28:22Z [Term] @@ -17737,8 +17742,8 @@ xref: FMA:256159 is_a: CL:0002563 {is_inferred="true"} ! intestinal epithelial cell intersection_of: CL:0002563 ! intestinal epithelial cell intersection_of: part_of UBERON:0002108 ! small intestine -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002108 ! small intestine +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-08T09:41:46Z [Term] @@ -17753,10 +17758,10 @@ xref: FMA:86490 is_a: CL:0000499 {is_inferred="true"} ! stromal cell intersection_of: CL:0000499 ! stromal cell intersection_of: part_of UBERON:0001295 ! endometrium -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002337 ! endometrial stroma -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002388 CL:2000002 ! has potential to directly develop into decidual cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-09-08T09:50:04Z [Term] @@ -17767,7 +17772,7 @@ synonym: "carotid body sustentacular cell" EXACT [] xref: FMA:84188 is_a: CL:0000630 ! supporting cell is_a: CL:0000710 ! neurecto-epithelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-08T10:34:45Z [Term] @@ -17781,8 +17786,8 @@ is_a: CL:0000150 ! glandular epithelial cell is_a: CL:0002076 {is_inferred="true"} ! endo-epithelial cell intersection_of: CL:0002076 ! endo-epithelial cell intersection_of: part_of UBERON:0002046 ! thyroid gland -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002046 ! thyroid gland +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-08T01:46:51Z [Term] @@ -17797,7 +17802,7 @@ xref: BTO:0003736 xref: CALOHA:TS-1285 xref: FMA:68782 is_a: CL:0002257 ! epithelial cell of thyroid gland -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-08T01:50:08Z [Term] @@ -17808,7 +17813,7 @@ subset: cellxgene_subset synonym: "totipotent neuroepithelial stem cell" NARROW [] xref: FMA:87171 is_a: CL:0000723 ! somatic stem cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-08T02:14:14Z [Term] @@ -17821,7 +17826,7 @@ is_a: CL:0002076 {is_inferred="true"} ! endo-epithelial cell is_a: CL:1001593 ! parathyroid glandular cell intersection_of: CL:0002076 ! endo-epithelial cell intersection_of: part_of UBERON:0001132 ! parathyroid gland -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-08T02:29:38Z [Term] @@ -17831,7 +17836,7 @@ alt_id: CL:1000446 def: "An endothelial cell found in the mucosa associated with the facial skeleton." [GOC:tfm, ISBN:0618947256] xref: FMA:70627 is_a: CL:0002076 ! endo-epithelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-14T10:40:12Z [Term] @@ -17845,9 +17850,9 @@ xref: FMA:63134 is_a: CL:0000115 ! endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0003909 ! sinusoid -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0003909 ! sinusoid -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-09-14T10:57:26Z [Term] @@ -17856,7 +17861,7 @@ name: transitional cell of parathyroid gland def: "One of three types of epithelial cells that populate the parathyroid gland; cytological characteristics intermediate between those of the chief cell and of the oxyphil cell. Because only one hormone is produced, the three cell forms are widely believed to be different phases in the life cycle of a single cell type, with the chief cell being its physiologically active stage." [GOC:tfm, ISBN:0412046911] xref: FMA:69324 is_a: CL:0002260 ! epithelial cell of parathyroid gland -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-08T02:33:50Z [Term] @@ -17868,7 +17873,7 @@ is_a: CL:0002067 ! type A enteroendocrine cell is_a: CL:0002659 ! glandular cell of stomach intersection_of: CL:0002067 ! type A enteroendocrine cell intersection_of: part_of UBERON:0000945 ! stomach -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T10:54:42Z [Term] @@ -17883,7 +17888,7 @@ is_a: CL:0000502 ! type D enteroendocrine cell is_a: CL:0009042 ! enteroendocrine cell of colon intersection_of: CL:0000502 ! type D enteroendocrine cell intersection_of: part_of UBERON:0001155 ! colon -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T11:37:35Z [Term] @@ -17898,7 +17903,7 @@ is_a: CL:0000502 ! type D enteroendocrine cell is_a: CL:0009006 ! enteroendocrine cell of small intestine intersection_of: CL:0000502 ! type D enteroendocrine cell intersection_of: part_of UBERON:0002108 ! small intestine -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T01:34:22Z [Term] @@ -17913,7 +17918,7 @@ is_a: CL:0000502 ! type D enteroendocrine cell is_a: CL:0002659 ! glandular cell of stomach intersection_of: CL:0000502 ! type D enteroendocrine cell intersection_of: part_of UBERON:0000945 ! stomach -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T01:36:03Z [Term] @@ -17924,7 +17929,7 @@ subset: cellxgene_subset xref: FMA:63418 is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0002269 ! vasoactive intestinal peptide secreting cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T01:47:45Z [Term] @@ -17932,7 +17937,7 @@ id: CL:0002269 name: vasoactive intestinal peptide secreting cell def: "An endocrine cell that secretes vasoactive intestinal peptide." [GOC:tfm] is_a: CL:0000167 ! peptide hormone secreting cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T01:52:20Z [Term] @@ -17943,7 +17948,7 @@ synonym: "Mo enteroendocrine cell" BROAD [] xref: FMA:62941 is_a: CL:0000577 ! type EC enteroendocrine cell is_a: CL:0002272 ! motilin secreting cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T02:13:47Z [Term] @@ -17953,7 +17958,7 @@ def: "A type EC enteredocrine cell in the intestines that stores and secretes su xref: FMA:62940 is_a: CL:0000505 ! substance P secreting cell is_a: CL:0000577 ! type EC enteroendocrine cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T02:13:49Z [Term] @@ -17961,7 +17966,7 @@ id: CL:0002272 name: motilin secreting cell def: "A cell that secretes motilin, a gastric hormone that at low pH inhibits gastric motor activity, whereas at high pH has a stimulating effect." [GOC:tfm, MESH:D009037] is_a: CL:0000167 ! peptide hormone secreting cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T02:31:13Z [Term] @@ -17971,7 +17976,7 @@ def: "A type EC enteroendocrine cell type that is numerous in the fundus of the xref: FMA:63208 is_a: CL:0000577 ! type EC enteroendocrine cell is_a: CL:0002274 ! histamine secreting cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T02:35:17Z [Term] @@ -17982,7 +17987,7 @@ is_a: CL:0000457 ! biogenic amine secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0001821 ! histamine secretion relationship: capable_of GO:0001821 ! histamine secretion -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T03:04:42Z [Term] @@ -18003,9 +18008,9 @@ is_a: CL:0008024 ! pancreatic endocrine cell intersection_of: CL:0000696 ! PP cell intersection_of: part_of UBERON:0000006 ! islet of Langerhans intersection_of: part_of UBERON:0001264 ! pancreas -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0000006 ! islet of Langerhans -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-09-10T03:30:31Z [Term] @@ -18014,7 +18019,7 @@ name: obsolete PP cell of pancreatic acinus def: "OBSOLETE: A PP cell located in the pancreatic acinus. Obsoleted due to a lack of published evidence that this cell type is actually found in the pancreatic acinus." [GOC:tfm] synonym: "type F cell of pancreatic acinus" EXACT [] xref: FMA:85400 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 is_obsolete: true creation_date: 2010-09-10T03:30:33Z @@ -18027,7 +18032,7 @@ synonym: "CCK cell" EXACT [] xref: FMA:62937 is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0000167 ! peptide hormone secreting cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T03:44:36Z [Term] @@ -18039,7 +18044,7 @@ synonym: "type K enteroendocrine cell" EXACT [] xref: FMA:62942 is_a: CL:0000167 ! peptide hormone secreting cell is_a: CL:0009006 ! enteroendocrine cell of small intestine -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T03:51:47Z [Term] @@ -18050,7 +18055,7 @@ subset: cellxgene_subset xref: FMA:62944 is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0000167 ! peptide hormone secreting cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T03:59:09Z [Term] @@ -18062,7 +18067,7 @@ synonym: "N cell" EXACT [] xref: FMA:62943 is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0000167 ! peptide hormone secreting cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T04:08:29Z [Term] @@ -18073,7 +18078,7 @@ xref: FMA:62936 is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0000167 ! peptide hormone secreting cell is_a: CL:0000458 ! serotonin secreting cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T04:44:46Z [Term] @@ -18083,7 +18088,7 @@ def: "An enteroendocrine cell which produces a gastrin- and cholecystokinin-like xref: FMA:63421 is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0000509 ! gastrin secreting cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T09:48:34Z [Term] @@ -18093,7 +18098,7 @@ alt_id: CL:1000440 def: "An epithelial cell of the mucosa associated with facial skeleton." [GOC:tfm, ISBN:0323052908] xref: FMA:70581 is_a: CL:0002159 ! general ecto-epithelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-14T11:04:02Z [Term] @@ -18105,7 +18110,7 @@ synonym: "X/A-like" EXACT [] xref: FMA:63209 is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0005018 ! ghrelin secreting cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T10:12:12Z [Term] @@ -18117,7 +18122,7 @@ synonym: "type 3 taste cell" EXACT [] xref: FMA:67940 is_a: CL:0000048 ! multi fate stem cell is_a: CL:0000209 ! taste receptor cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T10:57:21Z [Term] @@ -18127,7 +18132,7 @@ def: "A taste receptor cell that has a short microvilli, a projecting apical reg synonym: "type 2 taste cell" EXACT [] xref: FMA:62381 is_a: CL:0000209 ! taste receptor cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T10:57:26Z [Term] @@ -18140,7 +18145,7 @@ synonym: "type 4 taste cell" EXACT [] xref: FMA:62380 is_a: CL:0000034 ! stem cell is_a: CL:0000209 ! taste receptor cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T10:57:29Z [Term] @@ -18149,7 +18154,7 @@ name: type V taste receptor cell def: "A cell type that forms the boundary with the surrounding epithelium." [GOC:tfm, ISBN:0517223651] xref: FMA:67941 is_a: CL:0000209 ! taste receptor cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T10:57:31Z [Term] @@ -18162,7 +18167,7 @@ synonym: "type taste 1 cell" EXACT [] xref: FMA:62356 is_a: CL:0000209 ! taste receptor cell is_a: CL:0000703 ! sustentacular cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T10:57:35Z [Term] @@ -18173,7 +18178,7 @@ synonym: "Y bearing sperm" EXACT [] synonym: "Y-bearing sperm" EXACT [] xref: FMA:84058 is_a: CL:0000019 ! sperm -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T11:35:24Z [Term] @@ -18184,7 +18189,7 @@ synonym: "X bearing sperm" EXACT [] synonym: "X-bearing sperm" EXACT [] xref: FMA:84057 is_a: CL:0000019 ! sperm -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T11:35:26Z [Term] @@ -18195,8 +18200,8 @@ subset: human_reference_atlas synonym: "glomus cell" EXACT [] xref: FMA:84186 is_a: CL:0000710 ! neurecto-epithelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-09-13T01:40:21Z [Term] @@ -18214,8 +18219,8 @@ xref: FMA:72208 is_a: CL:0002076 {is_inferred="true"} ! endo-epithelial cell intersection_of: CL:0002076 ! endo-epithelial cell intersection_of: part_of UBERON:0002370 ! thymus -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002370 ! thymus +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T02:34:22Z [Term] @@ -18225,7 +18230,7 @@ def: "An epithelial cell with a well defined Golgi apparatus that makes up the c synonym: "subcapsular thymic epithelial cell" RELATED [PMID:18194204, PMID:2694455] xref: FMA:72209 is_a: CL:0002364 ! cortical thymic epithelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T02:37:23Z [Term] @@ -18237,7 +18242,7 @@ synonym: "large medullary thymic epithelial cells" EXACT [] synonym: "large mTEC" EXACT [] xref: FMA:72214 is_a: CL:0002365 ! medullary thymic epithelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T02:37:26Z [Term] @@ -18248,7 +18253,7 @@ synonym: "dark thymic epithelial cell" EXACT [] xref: FMA:72212 is_a: CL:0002364 ! cortical thymic epithelial cell is_a: CL:0002365 ! medullary thymic epithelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T02:37:45Z [Term] @@ -18258,7 +18263,7 @@ def: "A thymic epithelial cell with moderate nuclear and cytoplasmic electron-de synonym: "intermediate thymic epithelial cell" EXACT [] xref: FMA:72211 is_a: CL:0002364 ! cortical thymic epithelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T02:37:51Z [Term] @@ -18270,7 +18275,7 @@ synonym: "undifferentiated mTEC" EXACT [] synonym: "undifferentiated thymic epithelial cell" EXACT [] xref: FMA:72213 is_a: CL:0002365 ! medullary thymic epithelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T02:37:54Z [Term] @@ -18280,7 +18285,7 @@ def: "An epithelial cell scattered in the cortex, predominant in the outer corte synonym: "pale thymic epithelial cell" EXACT [] xref: FMA:72210 is_a: CL:0002364 ! cortical thymic epithelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T02:37:58Z [Term] @@ -18290,7 +18295,7 @@ def: "A small medullary thymic epithelial cell with a spindle shape, often arran synonym: "spindle shaped medullary thymic epithelial cell" EXACT [] synonym: "spindle shaped mTEC" EXACT [] is_a: CL:0002365 ! medullary thymic epithelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T03:23:25Z [Term] @@ -18307,9 +18312,9 @@ is_a: CL:0000499 ! stromal cell intersection_of: CL:0000499 ! stromal cell intersection_of: part_of UBERON:0002018 ! synovial membrane of synovial joint relationship: capable_of GO:0030213 ! hyaluronan biosynthetic process -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002018 ! synovial membrane of synovial joint relationship: produces UBERON:0001090 ! synovial fluid +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T03:39:14Z [Term] @@ -18321,9 +18326,9 @@ synonym: "type A synoviocyte" EXACT [] xref: FMA:66787 is_a: CL:0000214 ! synovial cell is_a: CL:0000234 ! phagocyte -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002018 ! synovial membrane of synovial joint relationship: RO:0001000 CL:0000842 {xref="PMID:10770586"} ! derives from mononuclear cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T03:39:17Z [Term] @@ -18337,9 +18342,9 @@ subset: human_reference_atlas synonym: "PE cell" EXACT [https://doi.org/10.1016/j.exer.2003.09.021] xref: FMA:70606 is_a: CL:0000529 ! pigmented epithelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001778 ! ciliary epithelium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-09-13T04:09:27Z [Term] @@ -18354,9 +18359,9 @@ synonym: "nonpigmented ciliary epithelial cell" EXACT [PMID:10913011] synonym: "NPE cell" EXACT [https://doi.org/10.1016/j.exer.2003.09.021] xref: FMA:70607 is_a: CL:0000710 ! neurecto-epithelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001778 ! ciliary epithelium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-09-13T04:09:31Z [Term] @@ -18391,14 +18396,14 @@ is_a: CL:1000615 ! kidney cortex tubule cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0004134 ! proximal tubule relationship: part_of UBERON:0004134 ! proximal tubule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0002307 name: brush border cell of the proximal tubule def: "A brush border epithelial cell located in the proximal tubule of the kidney that detects fluid flow." [GOC:tfm, ISBN:1-4160-2328-3] is_a: CL:0002306 ! epithelial cell of proximal tubule -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-14T11:29:20Z [Term] @@ -18410,8 +18415,8 @@ xref: FMA:70657 is_a: CL:0002159 ! general ecto-epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0002419 ! skin gland -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002419 ! skin gland +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-14T12:00:07Z [Term] @@ -18423,7 +18428,7 @@ xref: FMA:83098 xref: MESH:D052680 is_a: CL:0000467 ! adrenocorticotropic hormone secreting cell is_a: CL:0000639 ! basophil cell of pars distalis of adenohypophysis -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-14T02:08:23Z [Term] @@ -18434,7 +18439,7 @@ xref: FMA:83097 is_a: CL:0000295 ! somatotropin secreting cell is_a: CL:0000439 ! prolactin secreting cell is_a: CL:0000638 ! acidophil cell of pars distalis of adenohypophysis -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-14T02:25:34Z [Term] @@ -18451,7 +18456,7 @@ synonym: "mammotropic cell" EXACT [] xref: FMA:83096 is_a: CL:0000439 ! prolactin secreting cell is_a: CL:0000638 ! acidophil cell of pars distalis of adenohypophysis -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-14T02:30:57Z [Term] @@ -18465,7 +18470,7 @@ xref: FMA:83095 xref: MESH:D052683 is_a: CL:0000295 ! somatotropin secreting cell is_a: CL:0000638 ! acidophil cell of pars distalis of adenohypophysis -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-14T02:33:09Z [Term] @@ -18483,8 +18488,8 @@ intersection_of: CL:0002159 ! general ecto-epithelial cell intersection_of: capable_of GO:0046879 ! hormone secretion intersection_of: part_of UBERON:0002367 ! prostate gland relationship: capable_of GO:0046879 ! hormone secretion -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002367 ! prostate gland +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-14T03:01:58Z [Term] @@ -18493,7 +18498,7 @@ name: external supporting cell of vestibular epithelium def: "An auditory epithelial support cell located in the vestibular epithelium that has many hallmarks of glial cells. This cell type express glial markers such as vimentin, S100, glutamate-aspartate transporter, low affinity neurotrophin receptor p75, glial fibrillary acidic protein, and proteolipid protein." [GOC:tfm, PMID:20837532] xref: FMA:75809 is_a: CL:0002316 ! supporting cell of vestibular epithelium -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-14T03:20:01Z [Term] @@ -18505,8 +18510,8 @@ is_a: CL:0001035 ! bone cell is_a: CL:0005014 ! auditory epithelial supporting cell intersection_of: CL:0005014 ! auditory epithelial supporting cell intersection_of: part_of UBERON:0001844 ! cochlea -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001844 ! cochlea +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-14T03:31:38Z [Term] @@ -18517,8 +18522,8 @@ xref: FMA:75607 is_a: CL:0005014 ! auditory epithelial supporting cell intersection_of: CL:0005014 ! auditory epithelial supporting cell intersection_of: part_of UBERON:0001862 ! vestibular labyrinth -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001862 ! vestibular labyrinth +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-14T03:31:44Z [Term] @@ -18527,7 +18532,7 @@ name: external limiting cell of vestibular epithelium def: "An external limiting cell found in the vestibular epithelium." [GOC:tfm] xref: FMA:75808 is_a: CL:0002316 ! supporting cell of vestibular epithelium -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-14T03:33:50Z [Term] @@ -18536,8 +18541,8 @@ name: peripheral blood mesothelial cell def: "A mesothelial cell capable of circulating in the blood by first losing its squamous character. This cell can incorporate into the regenerating mesothelium." [GOC:tfm, PMID:14592528] xref: FMA:86712 is_a: CL:0000081 ! blood cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000077 ! mesothelial cell +relationship: RO:0002202 CL:0000077 ! develops from mesothelial cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T10:47:11Z [Term] @@ -18550,8 +18555,8 @@ xref: FMA:70333 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001016 ! nervous system -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001016 ! nervous system +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T01:34:57Z [Term] @@ -18566,8 +18571,8 @@ xref: MESH:D003239 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0002384 ! connective tissue -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002384 ! connective tissue +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T03:01:54Z [Term] @@ -18578,7 +18583,7 @@ xref: CALOHA:TS-0263 xref: FMA:82840 xref: WBbt:0007028 is_a: CL:0000000 ! cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T03:39:21Z [Term] @@ -18594,7 +18599,7 @@ xref: FMA:82841 xref: MESH:D053595 is_a: CL:0000034 ! stem cell is_a: CL:0002321 ! embryonic cell (metazoa) -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T03:44:35Z [Term] @@ -18604,25 +18609,34 @@ def: "A cell of a fetus which is suspended in the amniotic fluid. Amniocytes ar xref: BTO:0000066 is_a: CL:0000349 {is_inferred="true"} ! extraembryonic cell intersection_of: CL:0000349 ! extraembryonic cell -intersection_of: located_in UBERON:0000173 ! amniotic fluid -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: located_in UBERON:0000173 ! amniotic fluid +intersection_of: RO:0001025 UBERON:0000173 ! located in amniotic fluid +relationship: RO:0001025 UBERON:0000173 ! located in amniotic fluid +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-20T10:13:37Z [Term] id: CL:0002324 -name: myoepithelial cell of mammary gland -def: "A myoepithelial cell that surrounds milk-secreting luminal epithelial cells. This cell type contracts under the stimulation of oxytocin and is attached to the basement membrane by hemidesmosomes and to the adjacent luminal cells by desmosomes. This cell type expresses high level of keratin-14 and is estrogen receptor alpha negative." [GOC:tfm, PMID:11250738, PMID:19022771] -subset: cellxgene_subset -synonym: "basal cell of lactiferous duct" EXACT [FMA:67800] -synonym: "myoepithelial cell of lactiferous gland" EXACT [] +name: basal-myoepithelial cell of mammary gland +def: "A myoepithelial cell that is part of a mammary gland and is located in the basal layer. During lactation, a basal-myoepithelial cell of mammary gland contracts under the stimulation of oxytocin. In humans, a basal-myoepithelial cell of mammary gland can be identified by high levels of CD49f and low levels of EpCAM." [GOC:tfm, PMID:11250738, PMID:19022771, PMID:38059556] +comment: Due inconsistencies in naming this and other mammary gland epithelial cell types, several mammary gland experts gathered for a breast atlas annotation jamboree organized by Chan-Zuckerberg initiative. They agreed to label this cell type as basal-myoepithelial cell (and abbreviated: B-Myo cell). {xref="PMID:38059556"} +subset: cellxgene_subset +synonym: "B-Myo cell" RELATED OMO:0003000 [] +synonym: "basal" RELATED OMO:0003000 [PMID:37380767] +synonym: "basal cell of lactiferous duct" NARROW [FMA:67800] +synonym: "basal myoepithelial cell" BROAD [PMID:37694522] +synonym: "basal-myoepithelial cell" BROAD [PMID:37380767] +synonym: "BM" RELATED OMO:0003000 [PMID:38059556] +synonym: "myoepithelial cell of lactiferous gland" NARROW [] +synonym: "myoepithelial cell of mammary gland" EXACT [PMID:11250738] xref: CALOHA:TS-2378 xref: FMA:67800 is_a: CL:0000185 ! myoepithelial cell is_a: CL:0002327 ! mammary gland epithelial cell intersection_of: CL:0000185 ! myoepithelial cell intersection_of: part_of UBERON:0001911 ! mammary gland -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-4969-670X creation_date: 2010-09-20T11:42:14Z [Term] @@ -18647,11 +18661,11 @@ is_a: CL:0002159 {is_inferred="true"} ! general ecto-epithelial cell is_a: CL:1001586 ! mammary gland glandular cell intersection_of: CL:0000150 ! glandular epithelial cell intersection_of: part_of UBERON:0003214 ! mammary gland alveolus -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: dc-contributor https://orcid.org/0000-0003-4361-817X -relationship: develops_from CL:4033057 ! luminal adaptive secretory precursor cell of mammary gland relationship: part_of UBERON:0003214 ! mammary gland alveolus +relationship: RO:0002202 CL:4033057 ! develops from luminal adaptive secretory precursor cell of mammary gland +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-4361-817X creation_date: 2010-09-20T01:30:57Z [Term] @@ -18663,8 +18677,8 @@ synonym: "mature luminal cell" BROAD [PMID:21930782] xref: FMA:73280 is_a: CL:0000069 ! branched duct epithelial cell is_a: CL:0002327 ! mammary gland epithelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0009116 ! progenitor cell of mammary luminal epithelium +relationship: RO:0002202 CL:0009116 ! develops from progenitor cell of mammary luminal epithelium +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-20T01:37:53Z [Term] @@ -18678,8 +18692,8 @@ xref: BTO:0004300 is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001911 ! mammary gland -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001911 ! mammary gland +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-20T01:49:37Z [Term] @@ -18691,8 +18705,8 @@ xref: BTO:0002922 is_a: CL:0002202 ! epithelial cell of tracheobronchial tree intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0002185 ! bronchus -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002031 ! epithelium of bronchus +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-20T02:00:00Z [Term] @@ -18702,8 +18716,8 @@ def: "An epithelial cell type that lacks the columnar shape typical for other re subset: cellxgene_subset subset: human_reference_atlas is_a: CL:0002202 ! epithelial cell of tracheobronchial tree -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-09-20T02:10:36Z [Term] @@ -18711,7 +18725,7 @@ id: CL:0002330 name: undifferentiated cell of bronchus epithelium def: "An undifferentiated columnar cell of the bronchus epithelium" [GOC:tfm, PMID:18757316] is_a: CL:0002328 ! bronchial epithelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-20T02:17:58Z [Term] @@ -18724,8 +18738,8 @@ is_a: CL:0002145 ! ciliated columnar cell of tracheobronchial tree is_a: CL:0002328 ! bronchial epithelial cell intersection_of: CL:0000064 ! ciliated cell intersection_of: part_of UBERON:0002185 ! bronchus -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-09-20T02:21:12Z [Term] @@ -18734,9 +18748,9 @@ name: neural crest derived adipocyte def: "An adipocyte derived from a neural crest cell." [GOC:tfm, PMID:17507398] is_a: CL:0000136 ! adipocyte intersection_of: CL:0000136 ! adipocyte -intersection_of: develops_from CL:0000333 ! migratory neural crest cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000005 ! fibroblast neural crest derived +intersection_of: RO:0002202 CL:0000333 ! develops from migratory neural crest cell +relationship: RO:0002202 CL:0000005 ! develops from neural crest derived fibroblast +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-20T02:25:25Z [Term] @@ -18745,7 +18759,7 @@ name: preadipocyte def: "An undifferentiated fibroblast that can be stimulated to form a fat cell." [GOC:tfm, PMID:18793119] xref: BTO:0001107 is_a: CL:0000057 ! fibroblast -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-20T02:31:53Z [Term] @@ -18753,7 +18767,7 @@ id: CL:0002335 name: brown preadipocyte def: "A preadipocyte that is capable of differentiating into a brown adipocyte. This cell type expresses uncoupling protein-1, PPAR-gamma, PR-domain-containing 16; and PGC-1alpha (peroxisome proliferator-activated receptor-gamma (PPARgamma) coactivator-1alpha)." [GOC:tfm, PMID:18719589] is_a: CL:0002334 ! preadipocyte -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-20T02:38:38Z [Term] @@ -18761,7 +18775,7 @@ id: CL:0002336 name: buccal mucosa cell def: "An endothelial cell that lines the oral cavitiy including the mucosa of the gums, the palate, the lip, and the cheek." [GOC:tfm, MESH:D009061] is_a: CL:0002261 ! endothelial cell of viscerocranial mucosa -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-20T02:52:54Z [Term] @@ -18774,8 +18788,8 @@ synonym: "bulge keratinocyte" EXACT [] is_a: CL:0000048 ! multi fate stem cell is_a: CL:0000312 ! keratinocyte is_a: CL:0011026 ! progenitor cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-09-20T03:07:03Z [Term] @@ -18788,19 +18802,19 @@ synonym: "p-NK" RELATED [PMID:12457618] is_a: CL:0000823 ! immature natural killer cell intersection_of: CL:0000823 ! immature natural killer cell intersection_of: CL:4030046 PR:000001003 ! lacks_plasma_membrane_part CD34 molecule -intersection_of: in_taxon NCBITaxon:9606 ! Homo sapiens intersection_of: RO:0002104 PR:000001024 ! has plasma membrane part neural cell adhesion molecule 1 intersection_of: RO:0002104 PR:000001381 ! has plasma membrane part interleukin-2 receptor subunit beta intersection_of: RO:0002104 PR:000001874 ! has plasma membrane part KLRB1-like protein intersection_of: RO:0002104 PR:000002065 ! has plasma membrane part mast/stem cell growth factor receptor +intersection_of: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens relationship: CL:4030046 PR:000001003 ! lacks_plasma_membrane_part CD34 molecule -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002344 ! CD56-negative, CD161-positive immature natural killer cell, human -relationship: in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001024 ! has plasma membrane part neural cell adhesion molecule 1 relationship: RO:0002104 PR:000001381 ! has plasma membrane part interleukin-2 receptor subunit beta relationship: RO:0002104 PR:000001874 ! has plasma membrane part KLRB1-like protein relationship: RO:0002104 PR:000002065 ! has plasma membrane part mast/stem cell growth factor receptor +relationship: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens +relationship: RO:0002202 CL:0002344 ! develops from CD56-negative, CD161-positive immature natural killer cell, human +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-21T10:06:53Z [Term] @@ -18812,7 +18826,7 @@ is_a: CL:0000048 ! multi fate stem cell is_a: CL:0002341 ! basal cell of prostate epithelium intersection_of: CL:0000034 ! stem cell intersection_of: part_of UBERON:0002367 ! prostate gland -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-20T03:21:06Z [Term] @@ -18822,8 +18836,8 @@ def: "The exocrine cell of the prostate, this epithelial cell secretes prostatic subset: cellxgene_subset subset: human_reference_atlas is_a: CL:0002231 ! epithelial cell of prostate -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-09-20T03:34:05Z [Term] @@ -18833,8 +18847,8 @@ def: "An undifferentiated cell of the prostate epithelium that lacks secretory a subset: cellxgene_subset subset: human_reference_atlas is_a: CL:0002231 ! epithelial cell of prostate -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-09-20T03:34:10Z [Term] @@ -18842,7 +18856,7 @@ id: CL:0002342 name: circulating endothelial cell def: "A circulating endothelial cell of the phenotype CD146-positive, CD105-positive, CD45-negative. This cell type is indicative of recent vascular damage." [GOC:tfm, PMID:19652886] is_a: CL:0000115 ! endothelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-20T03:49:58Z [Term] @@ -18856,15 +18870,15 @@ synonym: "dNK cell" EXACT [] is_a: CL:0000824 ! mature natural killer cell intersection_of: CL:0000824 ! mature natural killer cell intersection_of: CL:4030046 PR:000001483 ! lacks_plasma_membrane_part low affinity immunoglobulin gamma Fc region receptor III -intersection_of: in_taxon NCBITaxon:9606 ! Homo sapiens intersection_of: RO:0002104 PR:000009766 ! has plasma membrane part galectin-1 +intersection_of: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens intersection_of: RO:0015015 PR:000001024 ! has high plasma membrane amount neural cell adhesion molecule 1 relationship: CL:4030046 PR:000001483 ! lacks_plasma_membrane_part low affinity immunoglobulin gamma Fc region receptor III -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000009766 ! has plasma membrane part galectin-1 +relationship: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens relationship: RO:0015015 PR:000001024 ! has high plasma membrane amount neural cell adhesion molecule 1 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-09-20T04:00:02Z [Term] @@ -18877,17 +18891,17 @@ is_a: CL:0000823 ! immature natural killer cell intersection_of: CL:0000823 ! immature natural killer cell intersection_of: CL:4030046 PR:000001003 ! lacks_plasma_membrane_part CD34 molecule intersection_of: CL:4030046 PR:000001024 ! lacks_plasma_membrane_part neural cell adhesion molecule 1 -intersection_of: in_taxon NCBITaxon:9606 ! Homo sapiens intersection_of: RO:0002104 PR:000001381 ! has plasma membrane part interleukin-2 receptor subunit beta intersection_of: RO:0002104 PR:000001874 ! has plasma membrane part KLRB1-like protein intersection_of: RO:0002104 PR:000002065 ! has plasma membrane part mast/stem cell growth factor receptor +intersection_of: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens relationship: CL:4030046 PR:000001003 ! lacks_plasma_membrane_part CD34 molecule relationship: CL:4030046 PR:000001024 ! lacks_plasma_membrane_part neural cell adhesion molecule 1 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001381 ! has plasma membrane part interleukin-2 receptor subunit beta relationship: RO:0002104 PR:000001874 ! has plasma membrane part KLRB1-like protein relationship: RO:0002104 PR:000002065 ! has plasma membrane part mast/stem cell growth factor receptor +relationship: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-20T04:33:11Z [Term] @@ -18898,20 +18912,20 @@ comment: Markers are associated with mouse cells. synonym: "preNK.BM" BROAD [] is_a: CL:0000823 ! immature natural killer cell intersection_of: CL:0000823 ! immature natural killer cell -intersection_of: in_taxon NCBITaxon:10090 ! Mus musculus intersection_of: RO:0002104 PR:000001008 ! has plasma membrane part integrin alpha-2 intersection_of: RO:0002104 PR:000002977 ! has plasma membrane part killer cell lectin-like receptor subfamily B member 1C intersection_of: RO:0002104 PR:000009616 ! has plasma membrane part T-cell surface glycoprotein YE1/48 +intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus intersection_of: RO:0015016 PR:000001012 ! has low plasma membrane amount integrin alpha-M intersection_of: RO:0015016 PR:000001963 ! has low plasma membrane amount CD27 molecule -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002346 ! Dx5-negative, NK1.1-positive immature natural killer cell, mouse -relationship: in_taxon NCBITaxon:10090 ! Mus musculus relationship: RO:0002104 PR:000001008 ! has plasma membrane part integrin alpha-2 relationship: RO:0002104 PR:000002977 ! has plasma membrane part killer cell lectin-like receptor subfamily B member 1C relationship: RO:0002104 PR:000009616 ! has plasma membrane part T-cell surface glycoprotein YE1/48 +relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus +relationship: RO:0002202 CL:0002346 ! develops from Dx5-negative, NK1.1-positive immature natural killer cell, mouse relationship: RO:0015016 PR:000001012 ! has low plasma membrane amount integrin alpha-M relationship: RO:0015016 PR:000001963 ! has low plasma membrane amount CD27 molecule +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-20T04:41:01Z [Term] @@ -18921,12 +18935,12 @@ def: "An immature natural killer cell that is NK1.1-positive and DX-5 negative." is_a: CL:0000823 ! immature natural killer cell intersection_of: CL:0000823 ! immature natural killer cell intersection_of: CL:4030046 PR:000001008 ! lacks_plasma_membrane_part integrin alpha-2 -intersection_of: in_taxon NCBITaxon:10090 ! Mus musculus intersection_of: RO:0002104 PR:000002977 ! has plasma membrane part killer cell lectin-like receptor subfamily B member 1C +intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: CL:4030046 PR:000001008 ! lacks_plasma_membrane_part integrin alpha-2 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: in_taxon NCBITaxon:10090 ! Mus musculus relationship: RO:0002104 PR:000002977 ! has plasma membrane part killer cell lectin-like receptor subfamily B member 1C +relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-21T10:11:44Z [Term] @@ -18936,14 +18950,14 @@ def: "A mature natural killer cell that is CD27-high and CD11b-high. This cell t is_a: CL:0000824 ! mature natural killer cell intersection_of: CL:0000824 ! mature natural killer cell intersection_of: capable_of GO:0032609 ! type II interferon production -intersection_of: in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus intersection_of: RO:0015015 PR:000001012 ! has high plasma membrane amount integrin alpha-M intersection_of: RO:0015015 PR:000001963 ! has high plasma membrane amount CD27 molecule -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002349 ! CD27-high, CD11b-low natural killer cell, mouse -relationship: in_taxon NCBITaxon:10090 ! Mus musculus +relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus +relationship: RO:0002202 CL:0002349 ! develops from CD27-high, CD11b-low natural killer cell, mouse relationship: RO:0015015 PR:000001012 ! has high plasma membrane amount integrin alpha-M relationship: RO:0015015 PR:000001963 ! has high plasma membrane amount CD27 molecule +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-21T10:19:49Z [Term] @@ -18952,14 +18966,14 @@ name: CD27-low, CD11b-high natural killer cell, mouse def: "A CD27-low, CD11b-high natural killer cell that has a higher threshold of activation due to higher expression of inhibitory receptors." [GOC:tfm, PMID:1994922] is_a: CL:0000824 ! mature natural killer cell intersection_of: CL:0000824 ! mature natural killer cell -intersection_of: in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus intersection_of: RO:0015015 PR:000001012 ! has high plasma membrane amount integrin alpha-M intersection_of: RO:0015016 PR:000001963 ! has low plasma membrane amount CD27 molecule -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002347 ! CD27-high, CD11b-high natural killer cell, mouse -relationship: in_taxon NCBITaxon:10090 ! Mus musculus +relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus +relationship: RO:0002202 CL:0002347 ! develops from CD27-high, CD11b-high natural killer cell, mouse relationship: RO:0015015 PR:000001012 ! has high plasma membrane amount integrin alpha-M relationship: RO:0015016 PR:000001963 ! has low plasma membrane amount CD27 molecule +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-21T10:19:54Z [Term] @@ -18968,14 +18982,14 @@ name: CD27-high, CD11b-low natural killer cell, mouse def: "A natural killer cell that is CD27-high and CD11b-low." [GOC:tfm, PMID:1994922] is_a: CL:0000824 ! mature natural killer cell intersection_of: CL:0000824 ! mature natural killer cell -intersection_of: in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus intersection_of: RO:0015015 PR:000001963 ! has high plasma membrane amount CD27 molecule intersection_of: RO:0015016 PR:000001012 ! has low plasma membrane amount integrin alpha-M -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002345 ! CD27-low, CD11b-low immature natural killer cell, mouse -relationship: in_taxon NCBITaxon:10090 ! Mus musculus +relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus +relationship: RO:0002202 CL:0002345 ! develops from CD27-low, CD11b-low immature natural killer cell, mouse relationship: RO:0015015 PR:000001963 ! has high plasma membrane amount CD27 molecule relationship: RO:0015016 PR:000001012 ! has low plasma membrane amount integrin alpha-M +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-21T10:20:00Z [Term] @@ -18991,9 +19005,9 @@ xref: FMA:75621 is_a: CL:0010008 ! cardiac endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0002165 ! endocardium -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002165 ! endocardium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-09-21T04:33:05Z [Term] @@ -19004,7 +19018,7 @@ subset: cellxgene_subset synonym: "pancreatic endocrine progenitor" EXACT [] synonym: "pancreatic islet progenitor cell" EXACT [] is_a: CL:0011026 ! progenitor cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-21T04:41:06Z [Term] @@ -19014,8 +19028,8 @@ def: "A hematopoietic stem cell that exists during embryogenesis." [GOC:tfm, ISB is_a: CL:0000037 ! hematopoietic stem cell intersection_of: CL:0000037 ! hematopoietic stem cell intersection_of: part_of UBERON:0000922 ! embryo -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0000922 ! embryo +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-22T09:05:13Z [Term] @@ -19035,7 +19049,6 @@ intersection_of: RO:0002104 PR:000002037 ! has plasma membrane part complement c intersection_of: RO:0002104 PR:000002979 ! has plasma membrane part lymphocyte antigen 6A-2/6E-1 relationship: CL:4030046 PR:000001308 ! lacks_plasma_membrane_part CD48 molecule relationship: CL:4030046 PR:000001896 ! lacks_plasma_membrane_part natural killer cell receptor 2B4 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002107 ! liver relationship: RO:0002104 GO:0042611 ! has plasma membrane part MHC protein complex relationship: RO:0002104 PR:000001006 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C @@ -19043,6 +19056,7 @@ relationship: RO:0002104 PR:000001833 ! has plasma membrane part SLAM family mem relationship: RO:0002104 PR:000001932 ! has plasma membrane part signal transducer CD24 relationship: RO:0002104 PR:000002037 ! has plasma membrane part complement component C1q receptor relationship: RO:0002104 PR:000002979 ! has plasma membrane part lymphocyte antigen 6A-2/6E-1 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-22T09:08:32Z [Term] @@ -19062,11 +19076,11 @@ intersection_of: RO:0002104 PR:000002037 ! has plasma membrane part complement c relationship: CL:4030046 GO:0042611 ! lacks_plasma_membrane_part MHC protein complex relationship: CL:4030046 PR:000001006 ! lacks_plasma_membrane_part receptor-type tyrosine-protein phosphatase C relationship: CL:4030046 PR:000002979 ! lacks_plasma_membrane_part lymphocyte antigen 6A-2/6E-1 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001040 ! yolk sac relationship: RO:0002104 PR:000001307 ! has plasma membrane part CD44 molecule relationship: RO:0002104 PR:000001932 ! has plasma membrane part signal transducer CD24 relationship: RO:0002104 PR:000002037 ! has plasma membrane part complement component C1q receptor +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-22T09:08:34Z [Term] @@ -19085,11 +19099,11 @@ intersection_of: has_part PR:000008467 ! hemoglobin subunit zeta intersection_of: has_part PR:000008857 ! hemoglobin subunit beta-1 intersection_of: part_of UBERON:0000922 ! embryo relationship: bearer_of PATO:0000586 ! increased size -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002361 ! primitive erythroid progenitor relationship: has_part PR:000008467 ! hemoglobin subunit zeta relationship: has_part PR:000008857 ! hemoglobin subunit beta-1 relationship: part_of UBERON:0000922 ! embryo +relationship: RO:0002202 CL:0002361 ! develops from primitive erythroid progenitor +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-22T09:27:05Z [Term] @@ -19100,10 +19114,10 @@ synonym: "megalocyte" EXACT [] is_a: CL:0002417 {is_inferred="true"} ! primitive erythroid lineage cell intersection_of: CL:0002417 ! primitive erythroid lineage cell intersection_of: bearer_of PATO:0000586 ! increased size -intersection_of: develops_from CL:0002355 ! primitive red blood cell +intersection_of: RO:0002202 CL:0002355 ! develops from primitive red blood cell relationship: bearer_of PATO:0000586 ! increased size -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002355 ! primitive red blood cell +relationship: RO:0002202 CL:0002355 ! develops from primitive red blood cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-22T09:35:16Z [Term] @@ -19116,10 +19130,10 @@ is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000595 ! enucleate erythrocyte intersection_of: has_part PR:000008857 ! hemoglobin subunit beta-1 intersection_of: part_of UBERON:0000922 ! embryo -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002353 ! fetal liver hematopoietic progenitor cell relationship: has_part PR:000008857 ! hemoglobin subunit beta-1 relationship: part_of UBERON:0000922 ! embryo +relationship: RO:0002202 CL:0002353 ! develops from fetal liver hematopoietic progenitor cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-22T09:38:32Z [Term] @@ -19129,10 +19143,10 @@ def: "Derived from the Greek word pyren (the pit of a stone fruit), this is a tr is_a: CL:0002417 {is_inferred="true"} ! primitive erythroid lineage cell intersection_of: CL:0002417 ! primitive erythroid lineage cell intersection_of: bearer_of PATO:0000587 ! decreased size -intersection_of: develops_from CL:0002355 ! primitive red blood cell +intersection_of: RO:0002202 CL:0002355 ! develops from primitive red blood cell relationship: bearer_of PATO:0000587 ! decreased size -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002355 ! primitive red blood cell +relationship: RO:0002202 CL:0002355 ! develops from primitive red blood cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-22T10:02:37Z [Term] @@ -19142,8 +19156,8 @@ def: "A hematopoietic stem cell of the placenta. This cell type is first observe is_a: CL:0002352 ! gestational hematopoietic stem cell intersection_of: CL:0000037 ! hematopoietic stem cell intersection_of: part_of UBERON:0001987 ! placenta -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001987 ! placenta +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-22T10:30:02Z [Term] @@ -19151,7 +19165,7 @@ id: CL:0002360 name: AGM hematopoietic stem cell def: "A hematopoietic stem cell from the aorta-gonad-mesonephros region of the developing embryo. First seen at E10.5 in mouse embryos. May give rise to fetal liver HSC." [GOC:tfm, ISBN:978-1-60327-346-6] is_a: CL:0002352 ! gestational hematopoietic stem cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-22T10:31:49Z [Term] @@ -19164,9 +19178,9 @@ is_a: CL:0002417 {is_inferred="true"} ! primitive erythroid lineage cell is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002417 ! primitive erythroid lineage cell intersection_of: RO:0002104 PR:000009127 ! has plasma membrane part integrin alpha-IIb -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002418 ! hemangioblast relationship: RO:0002104 PR:000009127 ! has plasma membrane part integrin alpha-IIb +relationship: RO:0002202 CL:0002418 ! develops from hemangioblast +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-22T10:47:28Z [Term] @@ -19178,8 +19192,8 @@ synonym: "granule cell precursor" BROAD [doi:10.3389/fncir.2020.611841] synonym: "granule cell progenitor" BROAD [doi:10.3389/fncir.2020.611841] is_a: CL:0000031 ! neuroblast (sensu Vertebrata) is_a: CL:0002319 ! neural cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0009841 ! upper rhombic lip +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-22T01:40:44Z [Term] @@ -19191,12 +19205,12 @@ subset: eye_upper_slim subset: human_reference_atlas synonym: "corneal fibroblast" EXACT [] synonym: "corneal keratocyte" EXACT [] -is_a: CL:0000005 ! fibroblast neural crest derived +is_a: CL:0000005 ! neural crest derived fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001777 ! substantia propria of cornea -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001777 ! substantia propria of cornea -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-09-22T01:57:40Z [Term] @@ -19210,9 +19224,9 @@ xref: BTO:0004562 is_a: CL:0002293 ! epithelial cell of thymus intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0002123 ! cortex of thymus -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002123 ! cortex of thymus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-09-23T03:17:12Z [Term] @@ -19225,8 +19239,8 @@ xref: BTO:0004563 is_a: CL:0002293 ! epithelial cell of thymus intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0002124 ! medulla of thymus -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002124 ! medulla of thymus +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-23T03:17:14Z [Term] @@ -19239,8 +19253,8 @@ xref: BTO:0004519 is_a: CL:0002601 ! uterine smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0001296 ! myometrium -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001296 ! myometrium +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-23T03:46:34Z [Term] @@ -19251,8 +19265,8 @@ synonym: "trabeculocyte" EXACT [] is_a: CL:0000115 {is_inferred="true"} ! endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0005969 ! eye trabecular meshwork -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0005969 ! eye trabecular meshwork +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-23T04:18:50Z [Term] @@ -19265,8 +19279,8 @@ xref: BTO:0004533 is_a: CL:0002076 {is_inferred="true"} ! endo-epithelial cell intersection_of: CL:0002076 ! endo-epithelial cell intersection_of: part_of UBERON:0000065 ! respiratory tract -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0000065 ! respiratory tract +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-23T04:38:49Z [Term] @@ -19275,7 +19289,7 @@ name: fungal spore def: "A differentiated form of a fungus produced during or as a result of an asexual or sexual reproductive process; usually a cell with a thick cell wall that stores and protects one or more nuclei. Spores may be produced in response to, and are characteristically resistant to, adverse environmental conditions." [FAO:0000019, GOC:tfm] xref: MESH:D013172 is_a: CL:0000521 ! fungal cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-01T09:02:42Z [Term] @@ -19287,8 +19301,8 @@ synonym: "respiratory mucosa goblet cells" EXACT [MP:0010863] is_a: CL:0000160 ! goblet cell intersection_of: CL:0000160 ! goblet cell intersection_of: part_of UBERON:0000065 ! respiratory tract -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0004802 ! respiratory tract epithelium +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-23T04:42:27Z [Term] @@ -19300,8 +19314,8 @@ subset: ubprop:upper_level xref: BTO:0001268 xref: FMA:72300 xref: WBbt:0008378 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: term_tracker_item https://github.com/obophenotype/cell-ontology/issues/1150 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 is_obsolete: true replaced_by: CL:0000000 creation_date: 2010-09-24T09:44:42Z @@ -19321,7 +19335,7 @@ intersection_of: bearer_of PATO:0001908 ! multinucleate intersection_of: bearer_of PATO:0002478 ! transversely striated intersection_of: has_part GO:0030017 ! sarcomere relationship: bearer_of PATO:0002478 ! transversely striated -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-24T01:13:01Z [Term] @@ -19331,7 +19345,7 @@ def: "A peptide hormone secreting cell that secretes growth hormone releasing ho synonym: "GHRH secreting cell" EXACT [] synonym: "somatocrinin secreting cell" EXACT [] is_a: CL:0000167 ! peptide hormone secreting cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-24T01:36:44Z [Term] @@ -19343,8 +19357,8 @@ is_a: CL:0000006 ! neuronal receptor cell is_a: CL:0000855 ! sensory hair cell intersection_of: CL:0000855 ! sensory hair cell intersection_of: part_of UBERON:0001690 ! ear -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001690 ! ear +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-24T01:49:31Z [Term] @@ -19355,8 +19369,8 @@ subset: cellxgene_subset synonym: "Schwann cell precursor cell" EXACT [] is_a: CL:0000030 ! glioblast is_a: CL:0011026 ! progenitor cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000333 ! migratory neural crest cell +relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-24T02:06:10Z [Term] @@ -19365,8 +19379,8 @@ name: non-myelinating Schwann cell def: "A glial cell that ensheaths multiple small diameter axons in the peripheral nervous system. The non-myelinating Schwann cell is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has a basal lamina. Cells can survive without an axon present. These cells can de-differentiate into immature Schwann cells." [GOC:cvs, GOC:tfm, ISBN:0721662544] synonym: "Schwann cell" BROAD [] is_a: CL:0002573 ! Schwann cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002377 ! immature Schwann cell +relationship: RO:0002202 CL:0002377 ! develops from immature Schwann cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-24T02:10:26Z [Term] @@ -19377,8 +19391,8 @@ subset: cellxgene_subset synonym: "Schwann cell" BROAD [] xref: ZFA:0001725 is_a: CL:0002573 ! Schwann cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002375 ! Schwann cell precursor +relationship: RO:0002202 CL:0002375 ! develops from Schwann cell precursor +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-24T02:10:31Z [Term] @@ -19388,7 +19402,7 @@ def: "A double negative thymocyte that has a T cell receptor consisting of a gam comment: NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments. synonym: "fetal Vgamma2+ thymocyte" BROAD [] is_a: CL:0002404 ! fetal thymocyte -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-07T02:21:07Z [Term] @@ -19398,7 +19412,7 @@ def: "A neurecto-epithelial cell found in the arachnoid villi of dura mater. Thi synonym: "arachnoid cap cell" EXACT [] xref: FMA:86588 is_a: CL:0000710 ! neurecto-epithelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-28T02:23:46Z [Term] @@ -19407,7 +19421,7 @@ name: oospore def: "An asexual spore formed by Oomycetes; formed upon fertilization of an oosphere." [GOC:tfm, ISBN:0851988857, SGD:clt] xref: FAO:0000039 is_a: CL:0000605 ! fungal asexual spore -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-01T09:22:45Z [Term] @@ -19416,7 +19430,7 @@ name: uninucleate conidium def: "A conidium that has only one nucleus." [GOC:tfm, SGD:clt] xref: FAO:0000025 is_a: CL:0000599 ! conidium -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-01T09:26:39Z [Term] @@ -19425,7 +19439,7 @@ name: multinucleate conidium def: "A conidium that has more than one nucleus." [GOC:tfm, SGD:clt] xref: FAO:0000033 is_a: CL:0000599 ! conidium -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-01T09:31:28Z [Term] @@ -19524,8 +19538,8 @@ relationship: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule relationship: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon relationship: CL:4030046 PR:000001199 ! lacks_plasma_membrane_part C-C chemokine receptor type 2 relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-spanning 4-domains subfamily A member 1 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000860 ! classical monocyte +relationship: RO:0002202 CL:0000860 ! develops from classical monocyte +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-04T10:52:03Z [Term] @@ -19544,9 +19558,9 @@ intersection_of: capable_of GO:0042590 ! antigen processing and presentation of intersection_of: RO:0002104 PR:000002105 ! has plasma membrane part thrombomodulin relationship: capable_of GO:0002827 ! positive regulation of T-helper 1 type immune response relationship: capable_of GO:0042590 ! antigen processing and presentation of exogenous peptide antigen via MHC class I -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000002105 ! has plasma membrane part thrombomodulin +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-10-04T02:38:58Z [Term] @@ -19566,8 +19580,8 @@ intersection_of: RO:0015015 PR:000002980 ! has high plasma membrane amount lymph relationship: CL:4030046 PR:000001014 ! lacks_plasma_membrane_part receptor-type tyrosine-protein phosphatase C isoform CD45RABC relationship: CL:4030046 PR:000001206 ! lacks_plasma_membrane_part CX3C chemokine receptor 1 relationship: CL:4030046 PR:000001879 ! lacks_plasma_membrane_part leukosialin -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0015015 PR:000002980 ! has high plasma membrane amount lymphocyte antigen 6C2 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-04T11:26:18Z [Term] @@ -19583,11 +19597,11 @@ is_a: CL:0001054 ! CD14-positive monocyte intersection_of: CL:0000875 ! non-classical monocyte intersection_of: RO:0002104 PR:000001483 ! has plasma membrane part low affinity immunoglobulin gamma Fc region receptor III intersection_of: RO:0015016 PR:000001889 ! has low plasma membrane amount CD14 molecule -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002397 ! CD14-positive, CD16-positive monocyte -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001483 ! has plasma membrane part low affinity immunoglobulin gamma Fc region receptor III +relationship: RO:0002202 CL:0002397 ! develops from CD14-positive, CD16-positive monocyte relationship: RO:0015016 PR:000001889 ! has low plasma membrane amount CD14 molecule +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-10-04T12:25:42Z [Term] @@ -19602,8 +19616,8 @@ intersection_of: CL:0001054 ! CD14-positive monocyte intersection_of: CL:4030046 PR:000001199 ! lacks_plasma_membrane_part C-C chemokine receptor type 2 intersection_of: RO:0002104 PR:000001483 ! has plasma membrane part low affinity immunoglobulin gamma Fc region receptor III relationship: CL:4030046 PR:000001199 ! lacks_plasma_membrane_part C-C chemokine receptor type 2 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0002104 PR:000001483 ! has plasma membrane part low affinity immunoglobulin gamma Fc region receptor III +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-04T12:49:47Z [Term] @@ -19617,10 +19631,10 @@ intersection_of: RO:0002104 PR:000001012 ! has plasma membrane part integrin alp intersection_of: RO:0002104 PR:000001879 ! has plasma membrane part leukosialin intersection_of: RO:0002104 PR:000002062 ! has plasma membrane part macrophage colony-stimulating factor 1 receptor intersection_of: RO:0002104 PR:000002980 ! has plasma membrane part lymphocyte antigen 6C2 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002395 ! Gr1-high classical monocyte relationship: RO:0002104 PR:000001879 ! has plasma membrane part leukosialin relationship: RO:0002104 PR:000002980 ! has plasma membrane part lymphocyte antigen 6C2 +relationship: RO:0002202 CL:0002395 ! develops from Gr1-high classical monocyte +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-04T12:49:49Z [Term] @@ -19635,9 +19649,9 @@ intersection_of: CL:0000782 ! myeloid dendritic cell intersection_of: capable_of GO:0032637 ! interleukin-8 production intersection_of: RO:0002104 PR:000002027 ! has plasma membrane part T-cell surface glycoprotein CD1c relationship: capable_of GO:0032637 ! interleukin-8 production -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000002027 ! has plasma membrane part T-cell surface glycoprotein CD1c +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-10-04T02:39:01Z [Term] @@ -19651,10 +19665,10 @@ intersection_of: RO:0002104 PR:000001002 ! has plasma membrane part CD19 molecul intersection_of: RO:0002104 PR:000001879 ! has plasma membrane part leukosialin intersection_of: RO:0002104 PR:000001932 ! has plasma membrane part signal transducer CD24 intersection_of: RO:0002104 PR:000002037 ! has plasma membrane part complement component C1q receptor -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0002104 PR:000001879 ! has plasma membrane part leukosialin relationship: RO:0002104 PR:000001932 ! has plasma membrane part signal transducer CD24 relationship: RO:0002104 PR:000002037 ! has plasma membrane part complement component C1q receptor +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-05T10:11:38Z [Term] @@ -19665,8 +19679,8 @@ comment: NOTE: currently variable immune gene segments are not represented in th synonym: "mature DEC precursor" EXACT [] synonym: "mature DETC precursor" EXACT [] is_a: CL:0002404 ! fetal thymocyte -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002218 ! immature dendritic epithelial T cell precursor +relationship: RO:0002202 CL:0002218 ! develops from immature dendritic epithelial T cell precursor +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-07T02:05:46Z [Term] @@ -19687,10 +19701,10 @@ intersection_of: RO:0002104 PR:000001289 ! has plasma membrane part membrane-spa intersection_of: RO:0002104 PR:000001338 ! has plasma membrane part complement receptor type 2 relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD5 relationship: CL:4030046 PR:000002037 ! lacks_plasma_membrane_part complement component C1q receptor -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0002104 GO:0071753 ! has plasma membrane part IgM immunoglobulin complex relationship: RO:0002104 PR:000001014 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RABC relationship: RO:0002104 PR:000001338 ! has plasma membrane part complement receptor type 2 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-05T11:18:03Z [Term] @@ -19700,8 +19714,8 @@ def: "A thymocyte that has a T cell receptor consisting of a gamma chain contain comment: NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments. synonym: "fetal Vgamma2-positive" EXACT [] is_a: CL:0002404 ! fetal thymocyte -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002378 ! immature Vgamma2-positive fetal thymocyte +relationship: RO:0002202 CL:0002378 ! develops from immature Vgamma2-positive fetal thymocyte +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-07T02:24:36Z [Term] @@ -19709,7 +19723,7 @@ id: CL:0002404 name: fetal thymocyte def: "A thymocyte found in the fetal thymus." [GOC:tfm] is_a: CL:0000893 ! thymocyte -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-07T02:28:25Z [Term] @@ -19724,7 +19738,7 @@ intersection_of: CL:0000893 ! thymocyte intersection_of: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecule intersection_of: CL:4030046 PR:000025402 ! lacks_plasma_membrane_part T cell receptor co-receptor CD8 intersection_of: RO:0002104 GO:0042106 ! has plasma membrane part gamma-delta T cell receptor complex -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-07T02:33:39Z [Term] @@ -19734,7 +19748,7 @@ def: "A double negative post-natal thymocyte that has a T cell receptor consisti comment: NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments. synonym: "Vgamma2-positive thymocyte" BROAD [] is_a: CL:0002405 ! gamma-delta thymocyte -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-07T02:53:44Z [Term] @@ -19744,8 +19758,8 @@ def: "A thymocyte that has a T cell receptor consisting of a gamma chain contain comment: NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments. synonym: "Vgamma2-positive" EXACT [] is_a: CL:0002405 ! gamma-delta thymocyte -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002406 ! immature Vgamma2-positive thymocyte +relationship: RO:0002202 CL:0002406 ! develops from immature Vgamma2-positive thymocyte +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-07T02:53:48Z [Term] @@ -19755,7 +19769,7 @@ def: "A double negative post-natal thymocyte that has a T cell receptor consisti comment: NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments. synonym: "Vgamma2-negative thymocyte" BROAD [] is_a: CL:0002405 ! gamma-delta thymocyte -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-07T02:59:05Z [Term] @@ -19765,8 +19779,8 @@ def: "A thymocyte that has a T cell receptor consisting of a gamma chain that do comment: NOTE: currently variable immune gene segments are not represented in the OBO Foundry. Cross-product definitions were not made as a result. Also, there are three different nomenclatures for the variable gamma segments. synonym: "Vgamma2-negative" EXACT [] is_a: CL:0002405 ! gamma-delta thymocyte -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002408 ! immature Vgamma2-negative thymocyte +relationship: RO:0002202 CL:0002408 ! develops from immature Vgamma2-negative thymocyte +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-07T02:59:08Z [Term] @@ -19779,9 +19793,9 @@ synonym: "pancreas stellate cell" EXACT [] synonym: "PaSC" EXACT [] xref: MESH:D058954 is_a: CL:0000057 ! fibroblast -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001264 ! pancreas -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-11-10T09:40:33Z [Term] @@ -19790,7 +19804,7 @@ name: Vgamma1.1-positive, Vdelta6.3-negative thymocyte def: "A gamma-delta receptor that expresses Vgamma1.1 but does not express Vdelta6.3 chains in the T-cell receptor." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "Vg1.1-positive, Vd6.3-negative T cell" EXACT [] is_a: CL:0002405 ! gamma-delta thymocyte -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-07T03:07:44Z [Term] @@ -19799,7 +19813,7 @@ name: Vgamma1.1-positive, Vdelta6.3-positive thymocyte def: "A gamma-delta receptor that expresses Vgamma1.1-Vdelta6.3 chains in the T-cell receptor." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "Vg1.1+Vd6.3+ T cell" EXACT [] is_a: CL:0002405 ! gamma-delta thymocyte -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-07T03:03:00Z [Term] @@ -19808,7 +19822,7 @@ name: mature Vgamma1.1-positive, Vdelta6.3-negative thymocyte def: "A Vgamma1.1-positive, Vdelta6.3-negative thymocyte that is CD24-negative." [GOC:tfm, http://www.immgen.org] synonym: "mature Vg1.1-positive, Vd6.3-negative T cell" RELATED [] is_a: CL:0002411 ! Vgamma1.1-positive, Vdelta6.3-negative thymocyte -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-07T03:10:32Z [Term] @@ -19817,7 +19831,7 @@ name: immature Vgamma1.1-positive, Vdelta6.3-negative thymocyte def: "A Vgamma1.1-positive, Vdelta6.3-negative thymocyte that is CD24-positive." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "immature Vg1.1-positive, Vd6.3-negative T cell" RELATED [] is_a: CL:0002411 ! Vgamma1.1-positive, Vdelta6.3-negative thymocyte -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-07T03:10:35Z [Term] @@ -19826,7 +19840,7 @@ name: immature Vgamma1.1-positive, Vdelta6.3-positive thymocyte def: "A Vgamma1.1-positive, Vdelta6.3-positive thymocyte that is CD24-positive." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "immature Vg1.1+Vd6.3+ T cell" EXACT [] is_a: CL:0002412 ! Vgamma1.1-positive, Vdelta6.3-positive thymocyte -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-07T03:10:39Z [Term] @@ -19835,7 +19849,7 @@ name: mature Vgamma1.1-positive, Vdelta6.3-positive thymocyte def: "A Vgamma1.1-positive, Vdelta6.3-positive thymocyte that is CD24-negative." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "mature Vg1.1+Vd6.3+ T cell" EXACT [] is_a: CL:0002412 ! Vgamma1.1-positive, Vdelta6.3-positive thymocyte -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-07T03:10:41Z [Term] @@ -19843,7 +19857,7 @@ id: CL:0002417 name: primitive erythroid lineage cell def: "An immature or mature cell of the first erythroid lineage to arise during embryonic development." [GOC:tfm] is_a: CL:0000764 ! erythroid lineage cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-12T11:22:41Z [Term] @@ -19852,8 +19866,8 @@ name: hemangioblast def: "A pluripotent cell in the yolk sac that can give rise to mesenchymal cells including erythrocytes and endothelial cells." [GOC:tfm, ISBN:0813817986, PMID:11495698] xref: MESH:D055018 is_a: CL:0000222 ! mesodermal cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002354 ! yolk sac hematopoietic stem cell +relationship: RO:0002202 CL:0002354 ! develops from yolk sac hematopoietic stem cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-12T12:21:16Z [Term] @@ -19868,9 +19882,9 @@ is_a: CL:0000084 {is_inferred="true"} ! T cell intersection_of: CL:0000084 ! T cell intersection_of: output_of GO:0045058 ! T cell selection intersection_of: RO:0002104 GO:0042101 ! has plasma membrane part T cell receptor complex -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: output_of GO:0045058 ! T cell selection relationship: RO:0002104 GO:0042101 ! has plasma membrane part T cell receptor complex +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-12T01:56:15Z [Term] @@ -19886,7 +19900,7 @@ is_a: CL:0000084 {is_inferred="true"} ! T cell intersection_of: CL:0000084 ! T cell intersection_of: CL:4030044 GO:0045058 ! has_not_completed T cell selection relationship: CL:4030044 GO:0045058 ! has_not_completed T cell selection -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-12T01:56:17Z [Term] @@ -19897,7 +19911,7 @@ is_a: CL:0000558 {is_inferred="true"} ! reticulocyte is_a: CL:0002242 ! nucleate cell intersection_of: CL:0000558 ! reticulocyte intersection_of: bearer_of PATO:0002505 ! nucleated -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-15T09:24:05Z [Term] @@ -19912,8 +19926,8 @@ is_a: CL:0000558 {is_inferred="true"} ! reticulocyte intersection_of: CL:0000558 ! reticulocyte intersection_of: bearer_of PATO:0001405 ! anucleate intersection_of: has_part GO:0005840 ! ribosome -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: has_part GO:0005840 ! ribosome +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-15T09:24:08Z [Term] @@ -19924,8 +19938,8 @@ comment: Observed in mice. There is growing evidence that molecular markers char is_a: CL:0000806 {is_inferred="true"} ! DN2 thymocyte intersection_of: CL:0000806 ! DN2 thymocyte intersection_of: RO:0015015 PR:000002065 ! has high plasma membrane amount mast/stem cell growth factor receptor -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0015015 PR:000002065 ! has high plasma membrane amount mast/stem cell growth factor receptor +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-21T10:12:05Z [Term] @@ -19936,9 +19950,9 @@ comment: Observed in mice. There is growing evidence that molecular markers char is_a: CL:0000806 {is_inferred="true"} ! DN2 thymocyte intersection_of: CL:0000806 ! DN2 thymocyte intersection_of: RO:0015016 PR:000002065 ! has low plasma membrane amount mast/stem cell growth factor receptor -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002423 ! DN2a thymocyte +relationship: RO:0002202 CL:0002423 ! develops from DN2a thymocyte relationship: RO:0015016 PR:000002065 ! has low plasma membrane amount mast/stem cell growth factor receptor +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-21T10:12:08Z [Term] @@ -19958,11 +19972,11 @@ intersection_of: RO:0002104 PR:000001307 ! has plasma membrane part CD44 molecul intersection_of: RO:0002104 PR:000001869 ! has plasma membrane part interleukin-7 receptor subunit alpha intersection_of: RO:0002104 PR:000002065 ! has plasma membrane part mast/stem cell growth factor receptor relationship: CL:4030046 PR:000001380 ! lacks_plasma_membrane_part interleukin-2 receptor subunit alpha -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002104 PR:000001307 ! has plasma membrane part CD44 molecule relationship: RO:0002104 PR:000001869 ! has plasma membrane part interleukin-7 receptor subunit alpha relationship: RO:0002104 PR:000002065 ! has plasma membrane part mast/stem cell growth factor receptor +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-10-21T01:16:24Z [Term] @@ -19972,12 +19986,12 @@ def: "A mature natural killer cell that is CD11b-positive and CD27-positive." [G comment: A natural killer cell that is NK1.1-positive, CD11b-positive, and CD27-positive. is_a: CL:0002438 ! NK1.1-positive natural killer cell, mouse intersection_of: CL:0002438 ! NK1.1-positive natural killer cell, mouse -intersection_of: in_taxon NCBITaxon:10090 ! Mus musculus intersection_of: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M intersection_of: RO:0002104 PR:000001963 ! has plasma membrane part CD27 molecule -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M relationship: RO:0002104 PR:000001963 ! has plasma membrane part CD27 molecule +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-25T03:07:59Z [Term] @@ -19989,7 +20003,7 @@ is_a: CL:0000809 {is_inferred="true"} ! double-positive, alpha-beta thymocyte intersection_of: CL:0000809 ! double-positive, alpha-beta thymocyte intersection_of: bearer_of PATO:0000587 ! decreased size relationship: bearer_of PATO:0000587 ! decreased size -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-21T01:59:06Z [Term] @@ -20003,9 +20017,9 @@ intersection_of: CL:0000809 ! double-positive, alpha-beta thymocyte intersection_of: bearer_of PATO:0000586 ! increased size intersection_of: participates_in GO:0008283 ! cell population proliferation relationship: bearer_of PATO:0000586 ! increased size -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002427 ! resting double-positive thymocyte relationship: participates_in GO:0008283 ! cell population proliferation +relationship: RO:0002202 CL:0002427 ! develops from resting double-positive thymocyte +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-21T01:59:11Z [Term] @@ -20018,11 +20032,11 @@ intersection_of: CL:0000809 ! double-positive, alpha-beta thymocyte intersection_of: participates_in GO:0043368 ! positive T cell selection intersection_of: RO:0002104 PR:000001343 ! has plasma membrane part CD69 molecule intersection_of: RO:0015016 GO:0042105 ! has low plasma membrane amount alpha-beta T cell receptor complex -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002428 ! double-positive blast relationship: participates_in GO:0043368 ! positive T cell selection relationship: RO:0002104 PR:000001343 ! has plasma membrane part CD69 molecule +relationship: RO:0002202 CL:0002428 ! develops from double-positive blast relationship: RO:0015016 GO:0042105 ! has low plasma membrane amount alpha-beta T cell receptor complex +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-21T02:11:52Z [Term] @@ -20037,12 +20051,12 @@ intersection_of: participates_in GO:0043368 ! positive T cell selection intersection_of: RO:0002104 PR:000001343 ! has plasma membrane part CD69 molecule intersection_of: RO:0015015 GO:0042105 ! has high plasma membrane amount alpha-beta T cell receptor complex intersection_of: RO:0015016 PR:000001004 ! has low plasma membrane amount CD4 molecule -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002429 ! CD69-positive double-positive thymocyte relationship: participates_in GO:0043368 ! positive T cell selection relationship: RO:0002104 PR:000001343 ! has plasma membrane part CD69 molecule +relationship: RO:0002202 CL:0002429 ! develops from CD69-positive double-positive thymocyte relationship: RO:0015015 GO:0042105 ! has high plasma membrane amount alpha-beta T cell receptor complex relationship: RO:0015016 PR:000001004 ! has low plasma membrane amount CD4 molecule +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-21T02:29:19Z [Term] @@ -20057,12 +20071,12 @@ intersection_of: participates_in GO:0043368 ! positive T cell selection intersection_of: RO:0002104 PR:000001343 ! has plasma membrane part CD69 molecule intersection_of: RO:0015015 GO:0042105 ! has high plasma membrane amount alpha-beta T cell receptor complex intersection_of: RO:0015016 PR:000025402 ! has low plasma membrane amount T cell receptor co-receptor CD8 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002429 ! CD69-positive double-positive thymocyte relationship: participates_in GO:0043368 ! positive T cell selection relationship: RO:0002104 PR:000001343 ! has plasma membrane part CD69 molecule +relationship: RO:0002202 CL:0002429 ! develops from CD69-positive double-positive thymocyte relationship: RO:0015015 GO:0042105 ! has high plasma membrane amount alpha-beta T cell receptor complex relationship: RO:0015016 PR:000025402 ! has low plasma membrane amount T cell receptor co-receptor CD8 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-21T02:29:23Z [Term] @@ -20076,10 +20090,10 @@ is_a: CL:0000810 {is_inferred="true"} ! CD4-positive, alpha-beta thymocyte intersection_of: CL:0000810 ! CD4-positive, alpha-beta thymocyte intersection_of: RO:0002104 PR:000001932 ! has plasma membrane part signal transducer CD24 intersection_of: RO:0015015 GO:0042105 ! has high plasma membrane amount alpha-beta T cell receptor complex -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002433 ! CD69-positive, CD4-positive single-positive thymocyte relationship: RO:0002104 PR:000001932 ! has plasma membrane part signal transducer CD24 +relationship: RO:0002202 CL:0002433 ! develops from CD69-positive, CD4-positive single-positive thymocyte relationship: RO:0015015 GO:0042105 ! has high plasma membrane amount alpha-beta T cell receptor complex +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-21T02:43:52Z [Term] @@ -20092,10 +20106,10 @@ is_a: CL:0000810 {is_inferred="true"} ! CD4-positive, alpha-beta thymocyte intersection_of: CL:0000810 ! CD4-positive, alpha-beta thymocyte intersection_of: RO:0002104 PR:000001343 ! has plasma membrane part CD69 molecule intersection_of: RO:0015015 GO:0042105 ! has high plasma membrane amount alpha-beta T cell receptor complex -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002431 ! CD4-positive, CD8-intermediate double-positive thymocyte relationship: RO:0002104 PR:000001343 ! has plasma membrane part CD69 molecule +relationship: RO:0002202 CL:0002431 ! develops from CD4-positive, CD8-intermediate double-positive thymocyte relationship: RO:0015015 GO:0042105 ! has high plasma membrane amount alpha-beta T cell receptor complex +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-21T02:46:02Z [Term] @@ -20109,10 +20123,10 @@ is_a: CL:0000811 {is_inferred="true"} ! CD8-positive, alpha-beta thymocyte intersection_of: CL:0000811 ! CD8-positive, alpha-beta thymocyte intersection_of: RO:0002104 PR:000001932 ! has plasma membrane part signal transducer CD24 intersection_of: RO:0015015 GO:0042105 ! has high plasma membrane amount alpha-beta T cell receptor complex -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002435 ! CD69-positive, CD8-positive single-positive thymocyte relationship: RO:0002104 PR:000001932 ! has plasma membrane part signal transducer CD24 +relationship: RO:0002202 CL:0002435 ! develops from CD69-positive, CD8-positive single-positive thymocyte relationship: RO:0015015 GO:0042105 ! has high plasma membrane amount alpha-beta T cell receptor complex +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-21T02:59:10Z [Term] @@ -20125,10 +20139,10 @@ is_a: CL:0000811 {is_inferred="true"} ! CD8-positive, alpha-beta thymocyte intersection_of: CL:0000811 ! CD8-positive, alpha-beta thymocyte intersection_of: RO:0002104 PR:000001343 ! has plasma membrane part CD69 molecule intersection_of: RO:0015015 GO:0042105 ! has high plasma membrane amount alpha-beta T cell receptor complex -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002430 ! CD4-intermediate, CD8-positive double-positive thymocyte relationship: RO:0002104 PR:000001343 ! has plasma membrane part CD69 molecule +relationship: RO:0002202 CL:0002430 ! develops from CD4-intermediate, CD8-positive double-positive thymocyte relationship: RO:0015015 GO:0042105 ! has high plasma membrane amount alpha-beta T cell receptor complex +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-21T02:59:14Z [Term] @@ -20141,11 +20155,11 @@ is_a: CL:0000624 {is_inferred="true"} ! CD4-positive, alpha-beta T cell intersection_of: CL:0000624 ! CD4-positive, alpha-beta T cell intersection_of: RO:0015015 GO:0042105 ! has high plasma membrane amount alpha-beta T cell receptor complex intersection_of: RO:0015016 PR:000001932 ! has low plasma membrane amount signal transducer CD24 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002432 ! CD24-positive, CD4 single-positive thymocyte -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0002432 ! develops from CD24-positive, CD4 single-positive thymocyte relationship: RO:0015015 GO:0042105 ! has high plasma membrane amount alpha-beta T cell receptor complex relationship: RO:0015016 PR:000001932 ! has low plasma membrane amount signal transducer CD24 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-10-21T03:31:19Z [Term] @@ -20158,11 +20172,11 @@ is_a: CL:0000625 {is_inferred="true"} ! CD8-positive, alpha-beta T cell intersection_of: CL:0000625 ! CD8-positive, alpha-beta T cell intersection_of: RO:0015015 GO:0042105 ! has high plasma membrane amount alpha-beta T cell receptor complex intersection_of: RO:0015016 PR:000001932 ! has low plasma membrane amount signal transducer CD24 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002434 ! CD24-positive, CD8 single-positive thymocyte -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0002434 ! develops from CD24-positive, CD8 single-positive thymocyte relationship: RO:0015015 GO:0042105 ! has high plasma membrane amount alpha-beta T cell receptor complex relationship: RO:0015016 PR:000001932 ! has low plasma membrane amount signal transducer CD24 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-10-21T03:51:50Z [Term] @@ -20174,11 +20188,11 @@ synonym: "NK.sp" EXACT [] synonym: "NK1.1-positive NK cell" EXACT [] is_a: CL:0000824 ! mature natural killer cell intersection_of: CL:0000824 ! mature natural killer cell -intersection_of: in_taxon NCBITaxon:10090 ! Mus musculus intersection_of: RO:0002104 PR:000002977 ! has plasma membrane part killer cell lectin-like receptor subfamily B member 1C -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002104 PR:000002977 ! has plasma membrane part killer cell lectin-like receptor subfamily B member 1C +relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-25T03:18:04Z [Term] @@ -20188,10 +20202,10 @@ def: "A NK1.1-positive T cell that is NKGA2-positive." [GOC:tfm, http://www.immg synonym: "NK.G2A+.SP" EXACT [] is_a: CL:0002438 ! NK1.1-positive natural killer cell, mouse intersection_of: CL:0002438 ! NK1.1-positive natural killer cell, mouse -intersection_of: in_taxon NCBITaxon:10090 ! Mus musculus intersection_of: RO:0002104 PR:000002023 ! has plasma membrane part NKG2-A/NKG2-B type II integral membrane protein -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002104 PR:000002023 ! has plasma membrane part NKG2-A/NKG2-B type II integral membrane protein +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-25T03:31:09Z [Term] @@ -20201,10 +20215,10 @@ def: "A NK1.1-positive T cell that is Ly49D-positive." [GOC:tfm, http://www.immg synonym: "NK.49D+.Sp" EXACT [] is_a: CL:0002438 ! NK1.1-positive natural killer cell, mouse intersection_of: CL:0002438 ! NK1.1-positive natural killer cell, mouse -intersection_of: in_taxon NCBITaxon:10090 ! Mus musculus intersection_of: RO:0002104 PR:000009619 ! has plasma membrane part killer cell lectin-like receptor 4 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002104 PR:000009619 ! has plasma membrane part killer cell lectin-like receptor 4 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-25T03:36:19Z [Term] @@ -20214,10 +20228,10 @@ def: "A NK1.1-positive T cell that is CD94-positive." [GOC:tfm, http://www.immge synonym: "NK.94+.Sp" EXACT [] is_a: CL:0002438 ! NK1.1-positive natural killer cell, mouse intersection_of: CL:0002438 ! NK1.1-positive natural killer cell, mouse -intersection_of: in_taxon NCBITaxon:10090 ! Mus musculus intersection_of: RO:0002104 PR:000001402 ! has plasma membrane part killer cell lectin-like receptor subfamily D member 1 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002104 PR:000001402 ! has plasma membrane part killer cell lectin-like receptor subfamily D member 1 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-25T03:36:28Z [Term] @@ -20230,11 +20244,11 @@ is_a: CL:0000623 ! natural killer cell intersection_of: CL:0000623 ! natural killer cell intersection_of: CL:4030046 PR:000001402 ! lacks_plasma_membrane_part killer cell lectin-like receptor subfamily D member 1 intersection_of: CL:4030046 PR:000009618 ! lacks_plasma_membrane_part killer cell lectin-like receptor 3 -intersection_of: in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: CL:4030046 PR:000001402 ! lacks_plasma_membrane_part killer cell lectin-like receptor subfamily D member 1 relationship: CL:4030046 PR:000009618 ! lacks_plasma_membrane_part killer cell lectin-like receptor 3 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: in_taxon NCBITaxon:10090 ! Mus musculus +relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-25T03:56:21Z [Term] @@ -20245,10 +20259,10 @@ synonym: "Ly49I-positive NK cell" EXACT [] synonym: "NK.49Cl+.Sp" EXACT [] is_a: CL:0002438 ! NK1.1-positive natural killer cell, mouse intersection_of: CL:0002438 ! NK1.1-positive natural killer cell, mouse -intersection_of: in_taxon NCBITaxon:10090 ! Mus musculus intersection_of: RO:0002104 PR:000009618 ! has plasma membrane part killer cell lectin-like receptor 3 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002104 PR:000009618 ! has plasma membrane part killer cell lectin-like receptor 3 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-25T03:36:38Z [Term] @@ -20258,10 +20272,10 @@ def: "A NK1.1-positive T cell that is Ly49H-positive." [GOC:tfm, http://www.immg synonym: "LyH49H-positive" EXACT [] is_a: CL:0002438 ! NK1.1-positive natural killer cell, mouse intersection_of: CL:0002438 ! NK1.1-positive natural killer cell, mouse -intersection_of: in_taxon NCBITaxon:10090 ! Mus musculus intersection_of: RO:0002104 PR:000009623 ! has plasma membrane part killer cell lectin-like receptor 8 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002104 PR:000009623 ! has plasma membrane part killer cell lectin-like receptor 8 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-25T03:36:43Z [Term] @@ -20272,9 +20286,9 @@ synonym: "NK.49D-.Sp" EXACT [] is_a: CL:0002438 ! NK1.1-positive natural killer cell, mouse intersection_of: CL:0002438 ! NK1.1-positive natural killer cell, mouse intersection_of: CL:4030046 PR:000009619 ! lacks_plasma_membrane_part killer cell lectin-like receptor 4 -intersection_of: in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: CL:4030046 PR:000009619 ! lacks_plasma_membrane_part killer cell lectin-like receptor 4 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-25T03:39:02Z [Term] @@ -20286,9 +20300,9 @@ synonym: "NK.49Cl-.Sp" EXACT [] is_a: CL:0002438 ! NK1.1-positive natural killer cell, mouse intersection_of: CL:0002438 ! NK1.1-positive natural killer cell, mouse intersection_of: CL:4030046 PR:000009618 ! lacks_plasma_membrane_part killer cell lectin-like receptor 3 -intersection_of: in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: CL:4030046 PR:000009618 ! lacks_plasma_membrane_part killer cell lectin-like receptor 3 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-25T03:52:04Z [Term] @@ -20299,9 +20313,9 @@ synonym: "NK.94-.Sp" EXACT [] is_a: CL:0002438 ! NK1.1-positive natural killer cell, mouse intersection_of: CL:0002438 ! NK1.1-positive natural killer cell, mouse intersection_of: CL:4030046 PR:000001402 ! lacks_plasma_membrane_part killer cell lectin-like receptor subfamily D member 1 -intersection_of: in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: CL:4030046 PR:000001402 ! lacks_plasma_membrane_part killer cell lectin-like receptor subfamily D member 1 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-25T03:54:18Z [Term] @@ -20312,9 +20326,9 @@ synonym: "LyH49H-negative" EXACT [] is_a: CL:0002438 ! NK1.1-positive natural killer cell, mouse intersection_of: CL:0002438 ! NK1.1-positive natural killer cell, mouse intersection_of: CL:4030046 PR:000009623 ! lacks_plasma_membrane_part killer cell lectin-like receptor 8 -intersection_of: in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: CL:4030046 PR:000009623 ! lacks_plasma_membrane_part killer cell lectin-like receptor 8 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-25T03:42:42Z [Term] @@ -20325,10 +20339,10 @@ synonym: "NK.49Cl+94+.Sp" EXACT [] is_a: CL:0002441 ! CD94-positive natural killer cell, mouse is_a: CL:0002443 ! Ly49CI-positive natural killer cell, mouse intersection_of: CL:0002438 ! NK1.1-positive natural killer cell, mouse -intersection_of: in_taxon NCBITaxon:10090 ! Mus musculus intersection_of: RO:0002104 PR:000001402 ! has plasma membrane part killer cell lectin-like receptor subfamily D member 1 intersection_of: RO:0002104 PR:000009618 ! has plasma membrane part killer cell lectin-like receptor 3 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-25T03:56:27Z [Term] @@ -20336,7 +20350,7 @@ id: CL:0002450 name: tether cell def: "A specialized hair cell that has an elongated kinocilium upon which an otolith accretes. The tether cell then anchors the otolith in place." [GOC:cvs, GOC:tfm, PMID:9398434] is_a: CL:0002374 ! ear hair cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-10T01:41:00Z [Term] @@ -20344,7 +20358,7 @@ id: CL:0002451 name: mammary stem cell def: "A multi-fate stem cell that is the source of cells for growth of the mammary gland during puberty and gestation. This cell type gives rise to both the luminal and myoepithelial cell types of the gland, and have been shown to have the ability to regenerate the entire organ in mice. This cell type also plays an important role in carcinogenesis of the breast. This cell type is Lin-, CD24-positive, CD29-hi." [GOC:hjd, GOC:tfm, PMID:15987436, PMID:16397499, PMID:17851544] is_a: CL:0000048 ! multi fate stem cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-10T01:46:51Z [Term] @@ -20360,9 +20374,9 @@ synonym: "oligodendrocyte-type 2 astrocyte (O-2A) progenitor cell" BROAD [PMID:2 synonym: "oligodendrocyte/type-2 astrocyte progenitor cell" BROAD [PMID:24133281] {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0002-0819-0473"} xref: MESH:D000073637 is_a: CL:0011026 ! progenitor cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000339 ! glioblast (sensu Vertebrata) -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0000339 ! develops from glioblast (sensu Vertebrata) +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-11-10T02:51:34Z [Term] @@ -20377,7 +20391,7 @@ intersection_of: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecu intersection_of: CL:4030046 PR:000001084 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD8 alpha chain relationship: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecule relationship: CL:4030046 PR:000001084 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD8 alpha chain -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-22T01:10:28Z [Term] @@ -20390,8 +20404,8 @@ intersection_of: CL:0000989 ! CD11c-low plasmacytoid dendritic cell intersection_of: CL:4030046 PR:000001084 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD8 alpha chain intersection_of: RO:0002104 PR:000001004 ! has plasma membrane part CD4 molecule relationship: CL:4030046 PR:000001084 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD8 alpha chain -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0002104 PR:000001004 ! has plasma membrane part CD4 molecule +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-22T01:27:37Z [Term] @@ -20403,9 +20417,9 @@ is_a: CL:0000989 {is_inferred="true"} ! CD11c-low plasmacytoid dendritic cell intersection_of: CL:0000989 ! CD11c-low plasmacytoid dendritic cell intersection_of: RO:0002104 PR:000001004 ! has plasma membrane part CD4 molecule intersection_of: RO:0002104 PR:000001084 ! has plasma membrane part T-cell surface glycoprotein CD8 alpha chain -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0002104 PR:000001004 ! has plasma membrane part CD4 molecule relationship: RO:0002104 PR:000001084 ! has plasma membrane part T-cell surface glycoprotein CD8 alpha chain +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-22T01:23:07Z [Term] @@ -20417,15 +20431,15 @@ subset: human_reference_atlas is_a: CL:0000453 {is_inferred="true"} ! Langerhans cell is_a: CL:0002465 ! CD11b-positive dendritic cell intersection_of: CL:0000453 ! Langerhans cell -intersection_of: located_in UBERON:0001003 ! skin epidermis +intersection_of: RO:0001025 UBERON:0001003 ! located in skin epidermis intersection_of: RO:0002104 GO:0042613 ! has plasma membrane part MHC class II protein complex intersection_of: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M intersection_of: RO:0002104 PR:000001014 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RABC -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: located_in UBERON:0001003 ! skin epidermis -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0001025 UBERON:0001003 ! located in skin epidermis relationship: RO:0002104 GO:0042613 ! has plasma membrane part MHC class II protein complex relationship: RO:0002104 PR:000001014 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RABC +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-11-22T03:57:57Z [Term] @@ -20436,7 +20450,7 @@ is_a: CL:0001006 {is_inferred="true"} ! dermal dendritic cell is_a: CL:0002461 ! CD103-positive dendritic cell intersection_of: CL:0001006 ! dermal dendritic cell intersection_of: RO:0002104 PR:000001010 ! has plasma membrane part integrin alpha-E -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-22T04:06:22Z [Term] @@ -20448,7 +20462,7 @@ intersection_of: CL:0001006 ! dermal dendritic cell intersection_of: CL:4030046 PR:000001010 ! lacks_plasma_membrane_part integrin alpha-E intersection_of: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M relationship: CL:4030046 PR:000001010 ! lacks_plasma_membrane_part integrin alpha-E -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-22T04:09:44Z [Term] @@ -20461,8 +20475,8 @@ is_a: CL:0000941 {is_inferred="true"} ! thymic conventional dendritic cell intersection_of: CL:0000941 ! thymic conventional dendritic cell intersection_of: CL:4030046 PR:000001084 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD8 alpha chain relationship: CL:4030046 PR:000001084 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD8 alpha chain -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-11-23T10:58:53Z [Term] @@ -20473,9 +20487,9 @@ is_a: CL:0000766 ! myeloid leukocyte is_a: CL:0000990 {is_inferred="true"} ! conventional dendritic cell intersection_of: CL:0000990 ! conventional dendritic cell intersection_of: RO:0002104 PR:000001010 ! has plasma membrane part integrin alpha-E -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002010 ! pre-conventional dendritic cell relationship: RO:0002104 PR:000001010 ! has plasma membrane part integrin alpha-E +relationship: RO:0002202 CL:0002010 ! develops from pre-conventional dendritic cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-23T01:32:43Z [Term] @@ -20489,9 +20503,9 @@ intersection_of: CL:0000990 ! conventional dendritic cell intersection_of: CL:4030046 PR:000001813 ! lacks_plasma_membrane_part adhesion G protein-coupled receptor E1 intersection_of: part_of UBERON:0001013 ! adipose tissue relationship: CL:4030046 PR:000001813 ! lacks_plasma_membrane_part adhesion G protein-coupled receptor E1 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002010 ! pre-conventional dendritic cell relationship: part_of UBERON:0001013 ! adipose tissue +relationship: RO:0002202 CL:0002010 ! develops from pre-conventional dendritic cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-23T01:38:21Z [Term] @@ -20502,8 +20516,8 @@ synonym: "DC.SIRPa+.Ad" EXACT [] is_a: CL:0002462 ! adipose dendritic cell intersection_of: CL:0000990 ! conventional dendritic cell intersection_of: RO:0002104 PR:000001968 ! has plasma membrane part tyrosine-protein phosphatase non-receptor type substrate 1 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0002104 PR:000001968 ! has plasma membrane part tyrosine-protein phosphatase non-receptor type substrate 1 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-23T01:40:44Z [Term] @@ -20515,7 +20529,7 @@ is_a: CL:0002462 ! adipose dendritic cell intersection_of: CL:0000990 ! conventional dendritic cell intersection_of: CL:4030046 PR:000001968 ! lacks_plasma_membrane_part tyrosine-protein phosphatase non-receptor type substrate 1 relationship: CL:4030046 PR:000001968 ! lacks_plasma_membrane_part tyrosine-protein phosphatase non-receptor type substrate 1 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-23T01:40:46Z [Term] @@ -20525,8 +20539,8 @@ def: "A conventional dendritic cell that expresses CD11b (ITGAM)." [GOC:tfm, htt is_a: CL:0000990 {is_inferred="true"} ! conventional dendritic cell intersection_of: CL:0000990 ! conventional dendritic cell intersection_of: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-23T01:50:05Z [Term] @@ -20541,10 +20555,10 @@ intersection_of: RO:0002104 GO:0042613 ! has plasma membrane part MHC class II p intersection_of: RO:0002104 PR:000001006 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C intersection_of: RO:0015016 PR:000001013 ! has low plasma membrane amount integrin alpha-X relationship: CL:4030046 PR:000001010 ! lacks_plasma_membrane_part integrin alpha-E -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0002104 GO:0042613 ! has plasma membrane part MHC class II protein complex relationship: RO:0002104 PR:000001006 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C relationship: RO:0015016 PR:000001013 ! has low plasma membrane amount integrin alpha-X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-23T02:00:21Z [Term] @@ -20557,8 +20571,8 @@ intersection_of: CL:0000889 ! myeloid suppressor cell intersection_of: CL:4030046 PR:000001013 ! lacks_plasma_membrane_part integrin alpha-X intersection_of: RO:0015015 PR:000002980 ! has high plasma membrane amount lymphocyte antigen 6C2 relationship: CL:4030046 PR:000001013 ! lacks_plasma_membrane_part integrin alpha-X -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0015015 PR:000002980 ! has high plasma membrane amount lymphocyte antigen 6C2 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-23T02:15:12Z [Term] @@ -20570,9 +20584,9 @@ is_a: CL:0000889 {is_inferred="true"} ! myeloid suppressor cell intersection_of: CL:0000889 ! myeloid suppressor cell intersection_of: RO:0002104 PR:000001013 ! has plasma membrane part integrin alpha-X intersection_of: RO:0015016 PR:000002980 ! has low plasma membrane amount lymphocyte antigen 6C2 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0002104 PR:000001013 ! has plasma membrane part integrin alpha-X relationship: RO:0015016 PR:000002980 ! has low plasma membrane amount lymphocyte antigen 6C2 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-23T02:19:43Z [Term] @@ -20584,7 +20598,7 @@ is_a: CL:0002395 {is_inferred="true"} ! Gr1-high classical monocyte intersection_of: CL:0002395 ! Gr1-high classical monocyte intersection_of: CL:4030046 GO:0042613 ! lacks_plasma_membrane_part MHC class II protein complex relationship: CL:4030046 GO:0042613 ! lacks_plasma_membrane_part MHC class II protein complex -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-23T03:27:12Z [Term] @@ -20596,8 +20610,8 @@ synonym: "Mo.6c+II" EXACT [] is_a: CL:0002395 {is_inferred="true"} ! Gr1-high classical monocyte intersection_of: CL:0002395 ! Gr1-high classical monocyte intersection_of: RO:0002104 GO:0042613 ! has plasma membrane part MHC class II protein complex -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0002104 GO:0042613 ! has plasma membrane part MHC class II protein complex +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-23T03:30:21Z [Term] @@ -20609,7 +20623,7 @@ is_a: CL:0002058 {is_inferred="true"} ! Gr1-low non-classical monocyte intersection_of: CL:0002058 ! Gr1-low non-classical monocyte intersection_of: CL:4030046 GO:0042613 ! lacks_plasma_membrane_part MHC class II protein complex relationship: CL:4030046 GO:0042613 ! lacks_plasma_membrane_part MHC class II protein complex -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-23T03:38:15Z [Term] @@ -20620,8 +20634,8 @@ synonym: "Mo.6C-IIint" EXACT [] is_a: CL:0002058 {is_inferred="true"} ! Gr1-low non-classical monocyte intersection_of: CL:0002058 ! Gr1-low non-classical monocyte intersection_of: RO:0015016 GO:0042613 ! has low plasma membrane amount MHC class II protein complex -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0015016 GO:0042613 ! has low plasma membrane amount MHC class II protein complex +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-23T03:47:53Z [Term] @@ -20632,8 +20646,8 @@ synonym: "Mo.6C-II+" EXACT [] is_a: CL:0002058 {is_inferred="true"} ! Gr1-low non-classical monocyte intersection_of: CL:0002058 ! Gr1-low non-classical monocyte intersection_of: RO:0015015 GO:0042613 ! has high plasma membrane amount MHC class II protein complex -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0015015 GO:0042613 ! has high plasma membrane amount MHC class II protein complex +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-23T03:47:55Z [Term] @@ -20646,9 +20660,9 @@ intersection_of: CL:4030046 PR:000001013 ! lacks_plasma_membrane_part integrin a intersection_of: RO:0002104 PR:000001813 ! has plasma membrane part adhesion G protein-coupled receptor E1 intersection_of: RO:0015015 PR:000001012 ! has high plasma membrane amount integrin alpha-M relationship: CL:4030046 PR:000001013 ! lacks_plasma_membrane_part integrin alpha-X -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0002104 PR:000001813 ! has plasma membrane part adhesion G protein-coupled receptor E1 relationship: RO:0015015 PR:000001012 ! has high plasma membrane amount integrin alpha-M +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-23T04:00:52Z [Term] @@ -20660,10 +20674,10 @@ intersection_of: CL:0002471 ! MHC-II-negative non-classical monocyte intersection_of: RO:0002104 PR:000001013 ! has plasma membrane part integrin alpha-X intersection_of: RO:0002104 PR:000001813 ! has plasma membrane part adhesion G protein-coupled receptor E1 intersection_of: RO:0015015 PR:000001012 ! has high plasma membrane amount integrin alpha-M -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0002104 PR:000001013 ! has plasma membrane part integrin alpha-X relationship: RO:0002104 PR:000001813 ! has plasma membrane part adhesion G protein-coupled receptor E1 relationship: RO:0015015 PR:000001012 ! has high plasma membrane amount integrin alpha-M +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-23T04:09:09Z [Term] @@ -20684,9 +20698,9 @@ intersection_of: RO:0002104 PR:000002062 ! has plasma membrane part macrophage c relationship: CL:4030046 PR:000001014 ! lacks_plasma_membrane_part receptor-type tyrosine-protein phosphatase C isoform CD45RABC relationship: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon relationship: CL:4030046 PR:000002980 ! lacks_plasma_membrane_part lymphocyte antigen 6C2 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0002104 PR:000001813 ! has plasma membrane part adhesion G protein-coupled receptor E1 relationship: RO:0002104 PR:000002062 ! has plasma membrane part macrophage colony-stimulating factor 1 receptor +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-23T04:19:25Z [Term] @@ -20699,10 +20713,10 @@ intersection_of: CL:0000864 ! tissue-resident macrophage intersection_of: RO:0002104 PR:000001006 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C intersection_of: RO:0002104 PR:000001013 ! has plasma membrane part integrin alpha-X intersection_of: RO:0002104 PR:000001968 ! has plasma membrane part tyrosine-protein phosphatase non-receptor type substrate 1 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0002104 PR:000001006 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C relationship: RO:0002104 PR:000001013 ! has plasma membrane part integrin alpha-X relationship: RO:0002104 PR:000001968 ! has plasma membrane part tyrosine-protein phosphatase non-receptor type substrate 1 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-23T04:31:28Z [Term] @@ -20715,8 +20729,8 @@ intersection_of: CL:0002477 ! adipose macrophage intersection_of: CL:4030046 PR:000001813 ! lacks_plasma_membrane_part adhesion G protein-coupled receptor E1 intersection_of: RO:0002104 GO:0042613 ! has plasma membrane part MHC class II protein complex relationship: CL:4030046 PR:000001813 ! lacks_plasma_membrane_part adhesion G protein-coupled receptor E1 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0002104 GO:0042613 ! has plasma membrane part MHC class II protein complex +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-23T04:40:50Z [Term] @@ -20729,8 +20743,8 @@ intersection_of: CL:0002477 ! adipose macrophage intersection_of: CL:4030046 GO:0042613 ! lacks_plasma_membrane_part MHC class II protein complex intersection_of: RO:0002104 PR:000001813 ! has plasma membrane part adhesion G protein-coupled receptor E1 relationship: CL:4030046 GO:0042613 ! lacks_plasma_membrane_part MHC class II protein complex -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0002104 PR:000001813 ! has plasma membrane part adhesion G protein-coupled receptor E1 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-11-23T04:35:53Z [Term] @@ -20742,8 +20756,8 @@ xref: MP:0002262 is_a: CL:0002370 ! respiratory goblet cell intersection_of: CL:0000160 ! goblet cell intersection_of: part_of UBERON:0001826 ! nasal cavity mucosa -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0005384 ! nasal cavity epithelium +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-03T03:03:02Z [Term] @@ -20754,7 +20768,7 @@ is_a: CL:0000185 {is_inferred="true"} ! myoepithelial cell is_a: CL:0002625 ! seminiferous tubule epithelial cell intersection_of: CL:0000185 ! myoepithelial cell intersection_of: part_of UBERON:0001343 ! seminiferous tubule of testis -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-03T03:11:48Z [Term] @@ -20764,8 +20778,8 @@ def: "A melanocyte that produces pigment in the dermis." [GOC:cjm, GOC:tfm, MP:0 is_a: CL:1000458 ! melanocyte of skin intersection_of: CL:0000148 ! melanocyte intersection_of: part_of UBERON:0002067 ! dermis -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002067 ! dermis +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-03T03:17:05Z [Term] @@ -20776,7 +20790,7 @@ is_a: CL:0002559 ! hair follicle cell is_a: CL:2000000 ! epidermal melanocyte intersection_of: CL:0000148 ! melanocyte intersection_of: part_of UBERON:0002073 ! hair follicle -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-03T03:17:09Z [Term] @@ -20787,8 +20801,8 @@ comment: The text defintion reference to the MP term appears to reference an epi is_a: CL:0000148 {is_inferred="true"} ! melanocyte intersection_of: CL:0000148 ! melanocyte intersection_of: part_of UBERON:0000483 ! epithelium -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0000483 ! epithelium +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-03T03:17:14Z [Term] @@ -20800,8 +20814,8 @@ is_a: CL:0000148 ! melanocyte is_a: CL:0009004 ! retinal cell intersection_of: CL:0000148 ! melanocyte intersection_of: part_of UBERON:0000966 ! retina -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0000966 ! retina +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-03T03:25:32Z [Term] @@ -20813,8 +20827,8 @@ is_a: CL:0002484 ! epithelial melanocyte is_a: CL:0002491 ! auditory epithelial cell intersection_of: CL:0000148 ! melanocyte intersection_of: part_of UBERON:0002282 ! stria vascularis of cochlear duct -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002282 ! stria vascularis of cochlear duct +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-03T03:29:15Z [Term] @@ -20822,7 +20836,7 @@ id: CL:0002487 name: cutaneous/subcutaneous mechanoreceptor cell def: "A neuronal receptor that respond to mechanical pressure or distortion in the skin." [GOC:tfm, MP:0000973] is_a: CL:0000199 ! mechanoreceptor cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-06T02:53:30Z [Term] @@ -20837,7 +20851,7 @@ intersection_of: bearer_of PATO:0000586 ! increased size intersection_of: capable_of GO:0001974 ! blood vessel remodeling relationship: bearer_of PATO:0000586 ! increased size relationship: capable_of GO:0001974 ! blood vessel remodeling -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-06T02:55:24Z [Term] @@ -20854,7 +20868,7 @@ intersection_of: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecu intersection_of: CL:4030046 PR:000025402 ! lacks_plasma_membrane_part T cell receptor co-receptor CD8 relationship: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecule relationship: CL:4030046 PR:000025402 ! lacks_plasma_membrane_part T cell receptor co-receptor CD8 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-06T03:03:38Z [Term] @@ -20864,8 +20878,8 @@ def: "A supporting cell of the organ of Corti." [GOC:tfm, MP:0004300] is_a: CL:0002315 ! supporting cell of cochlea intersection_of: CL:0005014 ! auditory epithelial supporting cell intersection_of: part_of UBERON:0002227 ! spiral organ of cochlea -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002227 ! spiral organ of cochlea +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-06T03:09:01Z [Term] @@ -20876,7 +20890,7 @@ is_a: CL:0000098 ! sensory epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: capable_of GO:0050910 ! detection of mechanical stimulus involved in sensory perception of sound relationship: capable_of GO:0050910 ! detection of mechanical stimulus involved in sensory perception of sound -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-06T03:18:43Z [Term] @@ -20884,7 +20898,7 @@ id: CL:0002492 name: strial marginal cell def: "A polarized columnar cell that covesr the lateral surface of the cochlear duct, secretes potassium ions and forms a continuous sheet in contact with the endolymph; marginal cells form extensive interdigitations with the basal and intermediate cells in the normal adult stria." [GOC:tfm, MP:0004366] is_a: CL:0002491 ! auditory epithelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-06T03:20:41Z [Term] @@ -20893,8 +20907,8 @@ name: strial basal cell def: "A polarized cell that is juxtaposed to fibrocytes in the underlying spiral ligament. This cell type secretes potassium ions derived from fibrocytes through gap junctions." [GOC:tfm, MP:0004365] comment: Basal cells form a multi-layered epithelial barrier that separates the extracellular spaces of the stria vascularis and the spiral ligament[PMID:18353863] is_a: CL:0002491 ! auditory epithelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002282 ! stria vascularis of cochlear duct +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-06T03:26:53Z [Term] @@ -20910,8 +20924,8 @@ xref: FMA:84791 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0007100 ! primary circulatory organ -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0007100 ! primary circulatory organ +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T09:37:22Z [Term] @@ -20922,7 +20936,7 @@ subset: cellxgene_subset synonym: "embryonic cardiomyocyte" EXACT [] synonym: "neonatal cardiomyocyte" EXACT [] is_a: CL:0000746 ! cardiac muscle cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T09:50:41Z [Term] @@ -20937,10 +20951,10 @@ xref: MESH:D000075942 is_a: CL:0002419 {is_inferred="true"} ! mature T cell intersection_of: CL:0002419 ! mature T cell intersection_of: capable_of GO:0002385 ! mucosal immune response -intersection_of: located_in UBERON:0001277 ! intestinal epithelium +intersection_of: RO:0001025 UBERON:0001277 ! located in intestinal epithelium relationship: capable_of GO:0002385 ! mucosal immune response -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: located_in UBERON:0001277 ! intestinal epithelium +relationship: RO:0001025 UBERON:0001277 ! located in intestinal epithelium +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T09:54:50Z [Term] @@ -20949,7 +20963,7 @@ name: primary trophoblast giant cell def: "A trophoblast giant cell derived from the mural trophectoderm." [GOC:tfm, PMCID:PMC85124] xref: EMAPA:16066 is_a: CL:0002488 ! trophoblast giant cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T10:07:47Z [Term] @@ -20957,7 +20971,7 @@ id: CL:0002498 name: secondary trophoblast giant cell def: "A trophoblast giant cell that is derived from ectoplacental cone and, later in gestation, the spongiotrophoblast." [GOC:tfm, PMCID:PMC85124] is_a: CL:0002488 ! trophoblast giant cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T10:07:52Z [Term] @@ -20966,8 +20980,8 @@ name: spongiotrophoblast cell def: "A trophoblast cell that arises in the junctional zone (basal plate) of the placenta." [GOC:tfm, MP:0008959] synonym: "spongiotrophoblast" EXACT [] is_a: CL:0000351 ! trophoblast cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0004021 ! spongiotrophoblast layer +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T12:56:56Z [Term] @@ -20975,7 +20989,7 @@ id: CL:0002500 name: P enteroendocrine cell def: "A P/D1 enteroendocrine cell that is Grimelius positive and stores bombesin-like polypeptide." [FMA:63418, GOC:tfm] is_a: CL:0002268 ! P/D1 enteroendocrine cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T03:42:06Z [Term] @@ -20984,7 +20998,7 @@ name: type D1 enteroendocrine cell def: "A P/D1 enteroendocrine cell that is argyrophilic and stores vasoactive intestinal polypeptide." [FMA:63207, GOC:tfm] xref: FMA:63207 is_a: CL:0002268 ! P/D1 enteroendocrine cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T03:42:09Z [Term] @@ -20995,7 +21009,7 @@ synonym: "Mo enteroendocrine cell" BROAD [] xref: FMA:63420 is_a: CL:0002272 ! motilin secreting cell is_a: CL:0009006 ! enteroendocrine cell of small intestine -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T03:55:49Z [Term] @@ -21009,8 +21023,8 @@ is_a: CL:0000630 ! supporting cell is_a: CL:0002320 ! connective tissue cell intersection_of: CL:0002320 ! connective tissue cell intersection_of: part_of UBERON:0005742 ! adventitia -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0005742 ! adventitia +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T04:03:56Z [Term] @@ -21022,8 +21036,8 @@ synonym: "intestinal smooth muscle cell" EXACT [] is_a: CL:0000192 {is_inferred="true"} ! smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0000160 ! intestine -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0000160 ! intestine +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-01-17T03:39:38Z [Term] @@ -21034,16 +21048,16 @@ synonym: "DC.103-11b+.Lv" EXACT [] is_a: CL:0002454 {is_inferred="true"} ! Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic cell intersection_of: CL:0002454 ! Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic cell intersection_of: CL:4030046 PR:000001010 ! lacks_plasma_membrane_part integrin alpha-E -intersection_of: located_in UBERON:0001281 ! hepatic sinusoid +intersection_of: RO:0001025 UBERON:0001281 ! located in hepatic sinusoid intersection_of: RO:0002104 GO:0042613 ! has plasma membrane part MHC class II protein complex intersection_of: RO:0002104 PR:000001006 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C intersection_of: RO:0015015 PR:000001012 ! has high plasma membrane amount integrin alpha-M relationship: CL:4030046 PR:000001010 ! lacks_plasma_membrane_part integrin alpha-E -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: located_in UBERON:0001281 ! hepatic sinusoid +relationship: RO:0001025 UBERON:0001281 ! located in hepatic sinusoid relationship: RO:0002104 GO:0042613 ! has plasma membrane part MHC class II protein complex relationship: RO:0002104 PR:000001006 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C relationship: RO:0015015 PR:000001012 ! has high plasma membrane amount integrin alpha-M +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-01-21T01:27:41Z [Term] @@ -21054,16 +21068,16 @@ synonym: "DC.103+11b-.Lv" EXACT [] is_a: CL:0002454 {is_inferred="true"} ! Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic cell is_a: CL:0002461 ! CD103-positive dendritic cell intersection_of: CL:0002454 ! Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic cell -intersection_of: located_in UBERON:0001281 ! hepatic sinusoid +intersection_of: RO:0001025 UBERON:0001281 ! located in hepatic sinusoid intersection_of: RO:0002104 GO:0042613 ! has plasma membrane part MHC class II protein complex intersection_of: RO:0002104 PR:000001006 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C intersection_of: RO:0002104 PR:000001010 ! has plasma membrane part integrin alpha-E intersection_of: RO:0015016 PR:000001012 ! has low plasma membrane amount integrin alpha-M -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: located_in UBERON:0001281 ! hepatic sinusoid +relationship: RO:0001025 UBERON:0001281 ! located in hepatic sinusoid relationship: RO:0002104 GO:0042613 ! has plasma membrane part MHC class II protein complex relationship: RO:0002104 PR:000001006 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C relationship: RO:0015016 PR:000001012 ! has low plasma membrane amount integrin alpha-M +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-01-21T01:27:45Z [Term] @@ -21078,9 +21092,9 @@ intersection_of: RO:0002104 GO:0042613 ! has plasma membrane part MHC class II p intersection_of: RO:0002104 PR:000001293 ! has plasma membrane part C-type lectin domain family 4 member K relationship: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecule relationship: CL:4030046 PR:000001084 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD8 alpha chain -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0002104 GO:0042613 ! has plasma membrane part MHC class II protein complex relationship: RO:0002104 PR:000001293 ! has plasma membrane part C-type lectin domain family 4 member K +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-01-21T01:57:00Z [Term] @@ -21098,8 +21112,8 @@ relationship: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecule relationship: CL:4030046 PR:000001010 ! lacks_plasma_membrane_part integrin alpha-E relationship: CL:4030046 PR:000001084 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD8 alpha chain relationship: CL:4030046 PR:000001293 ! lacks_plasma_membrane_part C-type lectin domain family 4 member K -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0002104 GO:0042613 ! has plasma membrane part MHC class II protein complex +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-01-21T02:13:58Z [Term] @@ -21112,8 +21126,8 @@ is_a: CL:0002507 {is_inferred="true"} ! langerin-positive lymph node dendritic c intersection_of: CL:0002507 ! langerin-positive lymph node dendritic cell intersection_of: RO:0002104 PR:000001010 ! has plasma membrane part integrin alpha-E intersection_of: RO:0015016 PR:000001012 ! has low plasma membrane amount integrin alpha-M -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0015016 PR:000001012 ! has low plasma membrane amount integrin alpha-M +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-01-21T02:07:54Z [Term] @@ -21126,8 +21140,8 @@ intersection_of: CL:0002507 ! langerin-positive lymph node dendritic cell intersection_of: CL:4030046 PR:000001010 ! lacks_plasma_membrane_part integrin alpha-E intersection_of: RO:0015015 PR:000001012 ! has high plasma membrane amount integrin alpha-M relationship: CL:4030046 PR:000001010 ! lacks_plasma_membrane_part integrin alpha-E -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0015015 PR:000001012 ! has high plasma membrane amount integrin alpha-M +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-01-21T02:11:14Z [Term] @@ -21138,8 +21152,8 @@ is_a: CL:0002454 ! Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic ce is_a: CL:0002508 {is_inferred="true"} ! langerin-negative, CD103-negative lymph node dendritic cell intersection_of: CL:0002508 ! langerin-negative, CD103-negative lymph node dendritic cell intersection_of: RO:0015016 PR:000001012 ! has low plasma membrane amount integrin alpha-M -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0015016 PR:000001012 ! has low plasma membrane amount integrin alpha-M +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-01-21T02:22:15Z [Term] @@ -21150,8 +21164,8 @@ is_a: CL:0002454 ! Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic ce is_a: CL:0002508 {is_inferred="true"} ! langerin-negative, CD103-negative lymph node dendritic cell intersection_of: CL:0002508 ! langerin-negative, CD103-negative lymph node dendritic cell intersection_of: RO:0015015 PR:000001012 ! has high plasma membrane amount integrin alpha-M -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0015015 PR:000001012 ! has high plasma membrane amount integrin alpha-M +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-01-21T02:16:21Z [Term] @@ -21160,7 +21174,7 @@ name: Vgamma5-positive CD8alpha alpha positive gamma-delta intraepithelial T cel def: "A CD8alpha alpha positive gamma-delta intraepithelial T cell that expresses a TCR encoded in part by the Vgamma5 gene segment." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "tgd.vg5+.IEL" EXACT [] is_a: CL:0000802 ! CD8-alpha alpha positive, gamma-delta intraepithelial T cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-01-24T10:22:18Z [Term] @@ -21169,7 +21183,7 @@ name: Vgamma5-negative CD8alpha alpha positive gamma-delta intraepithelial T cel def: "A CD8alpha alpha positive gamma-delta intraepithelial T cell that does not express a TCR partially encoded by the Vgamma5 gene segment." [GOC:tfm, http://www.immgen.org/index_content.html] synonym: "tgd.vg5-.IEL" EXACT [] is_a: CL:0000802 ! CD8-alpha alpha positive, gamma-delta intraepithelial T cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-01-24T10:25:44Z [Term] @@ -21180,7 +21194,7 @@ synonym: "interrenal noradrenaline type cell" EXACT [] synonym: "type n interrenal cell" EXACT [] is_a: CL:0000459 ! noradrenergic cell is_a: CL:0002516 ! interrenal chromaffin cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-08T10:11:55Z [Term] @@ -21188,7 +21202,7 @@ id: CL:0002516 name: interrenal chromaffin cell def: "A chromaffin cell interspersed among the interrenal epithelial layer of the anterior kidney of teloest fish." [GOC:MH, GOC:tfm, PMID:12668625] is_a: CL:0000166 ! chromaffin cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-08T10:21:35Z [Term] @@ -21199,7 +21213,7 @@ synonym: "interrenal adrenaline secreting cell" RELATED [] synonym: "type a interrenal cell" EXACT [] is_a: CL:0000454 ! epinephrine secreting cell is_a: CL:0002516 ! interrenal chromaffin cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-08T10:27:05Z [Term] @@ -21212,7 +21226,7 @@ is_a: CL:0000066 ! epithelial cell is_a: CL:1000497 {is_inferred="true"} ! kidney cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0002113 ! kidney -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-08T10:46:34Z [Term] @@ -21220,7 +21234,7 @@ id: CL:0002519 name: interrenal epithelial cell def: "An interrenal epithelial kidney cell is an epithelial cell found in the anterior kidney of teleosts fish. This cell type is arranged in layers around the posterior cardinal vein and contains many mitochondria with tubulovesicular cristae. Interrenal chromaffin cells are interspersed among the tissue layer created by this cell type." [GOC:mh, GOC:tfm, PMID:12668625] is_a: CL:0002518 ! kidney epithelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-08T11:03:32Z [Term] @@ -21230,8 +21244,8 @@ def: "An insect excretory cell that regulates hemolymph composition by filtratio xref: BTO:0004597 is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002522 ! renal filtration cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: only_in_taxon NCBITaxon:50557 ! Insecta +relationship: RO:0002160 NCBITaxon:50557 ! only in taxon Insecta +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-08T01:34:56Z [Term] @@ -21244,9 +21258,9 @@ synonym: "subcutaneous fat cell" EXACT [] is_a: CL:0000136 {is_inferred="true"} ! adipocyte intersection_of: CL:0000136 ! adipocyte intersection_of: part_of UBERON:0002190 ! subcutaneous adipose tissue -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002190 ! subcutaneous adipose tissue -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2011-02-21T02:51:22Z [Term] @@ -21254,8 +21268,8 @@ id: CL:0002522 name: renal filtration cell def: "A renal filtration cell is a specialized cell of the renal system that filter fluids by charge, size or both." [GOC:tfm] is_a: CL:0000424 ! excretory cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001008 ! renal system +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-08T01:37:59Z [Term] @@ -21266,8 +21280,8 @@ synonym: "mesonephric glomerular visceral epithelial cell" EXACT [ZFA:0001674] is_a: CL:0000653 ! podocyte intersection_of: CL:0000653 ! podocyte intersection_of: part_of UBERON:0000080 ! mesonephros -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0000080 ! mesonephros +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-08T01:58:30Z [Term] @@ -21275,7 +21289,7 @@ id: CL:0002524 name: disseminated nephrocyte def: "A disseminated nephrocyte is a nephrocyte that filters hemolymph and is found at scattered locations in the fat body or other tissues." [GOC:tfm, PMID:19783135] is_a: CL:0002520 ! nephrocyte -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-08T02:07:33Z [Term] @@ -21286,8 +21300,8 @@ synonym: "metanephric glomerular visceral epithelial cell" EXACT [10.1007/s00418 is_a: CL:0000653 ! podocyte intersection_of: CL:0000653 ! podocyte intersection_of: part_of UBERON:0000081 ! metanephros -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0000081 ! metanephros +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-08T02:02:13Z [Term] @@ -21327,7 +21341,7 @@ intersection_of: RO:0002104 PR:000001310 ! has plasma membrane part CD83 molecul intersection_of: RO:0015015 GO:0042613 ! has high plasma membrane amount MHC class II protein complex intersection_of: RO:0015015 PR:000001412 ! has high plasma membrane amount CD86 molecule intersection_of: RO:0015015 PR:000001438 ! has high plasma membrane amount CD80 molecule -relationship: develops_from CL:0002527 ! immature CD14-positive dermal dendritic cell +relationship: RO:0002202 CL:0002527 ! develops from immature CD14-positive dermal dendritic cell [Term] id: CL:0002529 @@ -21362,7 +21376,7 @@ intersection_of: RO:0002104 PR:000001310 ! has plasma membrane part CD83 molecul intersection_of: RO:0015015 GO:0042613 ! has high plasma membrane amount MHC class II protein complex intersection_of: RO:0015015 PR:000001412 ! has high plasma membrane amount CD86 molecule intersection_of: RO:0015015 PR:000001438 ! has high plasma membrane amount CD80 molecule -relationship: develops_from CL:0002530 ! immature CD1a-positive dermal dendritic cell +relationship: RO:0002202 CL:0002530 ! develops from immature CD1a-positive dermal dendritic cell [Term] id: CL:0002532 @@ -21400,7 +21414,7 @@ intersection_of: RO:0002104 PR:000001310 ! has plasma membrane part CD83 molecul intersection_of: RO:0015015 GO:0042613 ! has high plasma membrane amount MHC class II protein complex intersection_of: RO:0015015 PR:000001412 ! has high plasma membrane amount CD86 molecule intersection_of: RO:0015015 PR:000001438 ! has high plasma membrane amount CD80 molecule -relationship: develops_from CL:0002533 ! immature CD16-positive myeloid dendritic cell +relationship: RO:0002202 CL:0002533 ! develops from immature CD16-positive myeloid dendritic cell [Term] id: CL:0002535 @@ -21420,8 +21434,8 @@ synonym: "uterine cervix epithelial cell" EXACT [GOC:tfm] is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0000002 ! uterine cervix -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0004801 ! cervix epithelium +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-24T08:20:08Z [Term] @@ -21433,9 +21447,9 @@ synonym: "amniotic epithelial cell" EXACT [] is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0000305 ! amnion -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0000305 ! amnion -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2011-02-28T12:38:01Z [Term] @@ -21446,8 +21460,8 @@ synonym: "amniotic membrane stem cell" EXACT [] is_a: CL:0000134 ! mesenchymal stem cell intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: part_of UBERON:0000305 ! amnion -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0000305 ! amnion +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T12:44:24Z [Term] @@ -21459,8 +21473,8 @@ synonym: "small bile duct cholangiocyte" EXACT [PMID:23720296] is_a: CL:1000488 {is_inferred="true"} ! cholangiocyte intersection_of: CL:1000488 ! cholangiocyte intersection_of: part_of UBERON:0004823 ! intrahepatic bile duct epithelium -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0004823 ! intrahepatic bile duct epithelium +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T01:20:20Z [Term] @@ -21472,8 +21486,8 @@ xref: BTO:0004577 is_a: CL:0019018 ! blood vessel smooth muscle cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0004178 ! aorta smooth muscle tissue -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0004178 ! aorta smooth muscle tissue +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T01:42:12Z [Term] @@ -21484,7 +21498,7 @@ is_a: CL:0000134 ! mesenchymal stem cell is_a: CL:0002092 ! bone marrow cell intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: part_of UBERON:0002371 ! bone marrow -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T01:47:47Z [Term] @@ -21495,9 +21509,9 @@ subset: human_reference_atlas is_a: CL:0000134 ! mesenchymal stem cell intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: part_of UBERON:0003124 ! chorion membrane -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0003124 ! chorion membrane -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2011-02-28T03:04:35Z [Term] @@ -21514,9 +21528,9 @@ xref: KUPO:0001099 is_a: CL:0000071 {is_inferred="true"} ! blood vessel endothelial cell intersection_of: CL:0000071 ! blood vessel endothelial cell intersection_of: part_of UBERON:0001638 ! vein -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001638 ! vein -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2011-02-28T03:48:11Z [Term] @@ -21527,7 +21541,7 @@ subset: cellxgene_subset xref: BTO:0003245 xref: CALOHA:TS-0047 is_a: CL:1000413 ! endothelial cell of artery -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T03:54:42Z [Term] @@ -21537,8 +21551,8 @@ def: "An endothelial cell that is part of the thoracic endothelium." [GOC:tfm] is_a: CL:0002544 {is_inferred="true"} ! aortic endothelial cell intersection_of: CL:0002544 ! aortic endothelial cell intersection_of: part_of UBERON:0001515 ! thoracic aorta -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001515 ! thoracic aorta +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T03:59:09Z [Term] @@ -21547,7 +21561,7 @@ name: embryonic blood vessel endothelial progenitor cell def: "An endothelial progenitor cell that participates in angiogenesis during development." [GOC:tfm] comment: See CL:0002619. is_a: CL:0000222 ! mesodermal cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T04:20:39Z [Term] @@ -21557,8 +21571,8 @@ def: "A fibroblast of the aortic adventitia." [GOC:tfm] is_a: CL:1000306 {is_inferred="true"} ! fibroblast of tunica adventitia of artery intersection_of: CL:1000306 ! fibroblast of tunica adventitia of artery intersection_of: part_of UBERON:0004664 ! aorta tunica adventitia -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0004664 ! aorta tunica adventitia +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T04:43:41Z [Term] @@ -21571,8 +21585,8 @@ is_a: CL:0000057 {is_inferred="true"} ! fibroblast is_a: CL:0002494 {is_inferred="true"} ! cardiocyte intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0000948 ! heart -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0000948 ! heart +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T04:57:44Z [Term] @@ -21583,8 +21597,8 @@ is_a: CL:0000057 {is_inferred="true"} ! fibroblast is_a: CL:0002319 ! neural cell intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001886 ! choroid plexus -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001886 ! choroid plexus +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T05:01:39Z [Term] @@ -21594,8 +21608,8 @@ def: "A fibroblast that is part of the conjuctiva of the eye." [GOC:tfm] is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001811 ! conjunctiva -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001811 ! conjunctiva +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T05:03:44Z [Term] @@ -21604,8 +21618,8 @@ name: fibroblast of dermis is_a: CL:0002620 {is_inferred="true"} ! skin fibroblast intersection_of: CL:0002620 ! skin fibroblast intersection_of: part_of UBERON:0002067 ! dermis -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002067 ! dermis +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T05:05:33Z [Term] @@ -21614,8 +21628,8 @@ name: fibroblast of gingiva is_a: CL:0000057 {is_inferred="true"} ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001828 ! gingiva -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001828 ! gingiva +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T05:09:12Z [Term] @@ -21628,8 +21642,8 @@ xref: CALOHA:TS-0575 is_a: CL:0000057 {is_inferred="true"} ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0002048 ! lung -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002048 ! lung +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T05:11:03Z [Term] @@ -21639,8 +21653,8 @@ def: "A fibroblast of the lymphatic system." [GOC:tfm] is_a: CL:0000057 {is_inferred="true"} ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001473 ! lymphatic vessel -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001473 ! lymphatic vessel +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T05:16:18Z [Term] @@ -21651,8 +21665,8 @@ subset: cellxgene_subset is_a: CL:0000057 {is_inferred="true"} ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001911 ! mammary gland -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001911 ! mammary gland +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T05:18:38Z [Term] @@ -21662,8 +21676,8 @@ def: "A fibroblast of the periodontium." [GOC:tfm] is_a: CL:0000057 {is_inferred="true"} ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001758 ! periodontium -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001758 ! periodontium +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T05:19:48Z [Term] @@ -21674,9 +21688,9 @@ subset: human_reference_atlas is_a: CL:0000057 {is_inferred="true"} ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0002012 ! pulmonary artery -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002012 ! pulmonary artery -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2011-02-28T05:22:27Z [Term] @@ -21685,9 +21699,9 @@ name: fibroblast of villous mesenchyme def: "A fibroblast that is part of villous mesenchyme." [GOC:tfm] subset: human_reference_atlas is_a: CL:0000057 ! fibroblast -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001987 ! placenta -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2011-02-28T05:24:28Z [Term] @@ -21697,8 +21711,8 @@ def: "An animal cell that is part of a hair follicle." [GOC:tfm] is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0002073 ! hair follicle -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002073 ! hair follicle +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-01T04:11:01Z [Term] @@ -21709,8 +21723,8 @@ is_a: CL:0000362 ! epidermal cell is_a: CL:0002559 {is_inferred="true"} ! hair follicle cell intersection_of: CL:0002559 ! hair follicle cell intersection_of: part_of UBERON:0005941 ! hair inner root sheath -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0005941 ! hair inner root sheath +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-01T04:27:51Z [Term] @@ -21721,8 +21735,8 @@ is_a: CL:0000362 ! epidermal cell is_a: CL:0002559 {is_inferred="true"} ! hair follicle cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0005942 ! hair outer root sheath -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0005942 ! hair outer root sheath +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-01T04:29:47Z [Term] @@ -21734,8 +21748,8 @@ is_a: CL:0000362 {is_inferred="true"} ! epidermal cell is_a: CL:0002559 ! hair follicle cell intersection_of: CL:0000362 ! epidermal cell intersection_of: part_of UBERON:0006004 ! hair follicle matrix region -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0006004 ! hair follicle matrix region +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-01T04:31:06Z [Term] @@ -21746,8 +21760,8 @@ subset: cellxgene_subset is_a: CL:0002251 ! epithelial cell of alimentary canal intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0000160 ! intestine -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001277 ! intestinal epithelium +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-01T05:18:31Z [Term] @@ -21757,8 +21771,8 @@ def: "A connective tissue cell of the nucleus pulposus cell of intervertebral di is_a: CL:0002320 ! connective tissue cell intersection_of: CL:0002320 ! connective tissue cell intersection_of: part_of UBERON:0002242 ! nucleus pulposus -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002242 ! nucleus pulposus +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-02T02:12:23Z [Term] @@ -21771,9 +21785,9 @@ is_a: CL:0000066 ! epithelial cell is_a: CL:0000342 {is_inferred="true"} ! pigment cell (sensu Vertebrata) intersection_of: CL:0000342 ! pigment cell (sensu Vertebrata) intersection_of: part_of UBERON:0002506 ! iris epithelium -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002506 ! iris epithelium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2011-03-01T05:28:52Z [Term] @@ -21783,7 +21797,7 @@ def: "A melanocyte that appears darker due to content or amount of melanin granu synonym: "melanotic melanocyte" EXACT [PMID:10985850] synonym: "melanotic melanophore" EXACT [PMID:10985850] is_a: CL:0000148 ! melanocyte -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-01T05:57:11Z [Term] @@ -21793,7 +21807,7 @@ def: "A melanocyte that appears lighter in color." [GOC:tfm] synonym: "amelanotic melanocyte" EXACT [PMID:10985850] synonym: "amelanotic melanophore" EXACT [PMID:10985850] is_a: CL:0000148 ! melanocyte -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-01T05:58:23Z [Term] @@ -21802,8 +21816,8 @@ name: mesenchymal stem cell of Wharton's jelly def: "A mesenchymal stem cell that is part of Wharton's jelly." [GOC:tfm] subset: human_reference_atlas is_a: CL:0002569 ! mesenchymal stem cell of umbilical cord -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2011-03-01T09:51:18Z [Term] @@ -21814,8 +21828,8 @@ is_a: CL:0000134 ! mesenchymal stem cell is_a: CL:0000349 ! extraembryonic cell intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: part_of UBERON:0003422 ! mesenchyme of umbilical cord -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0003422 ! mesenchyme of umbilical cord +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-01T09:55:12Z [Term] @@ -21827,8 +21841,8 @@ synonym: "mesenchymal stem cell of adipose" EXACT [] is_a: CL:0000134 ! mesenchymal stem cell intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: part_of UBERON:0001013 ! adipose tissue -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001013 ! adipose tissue +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-01T09:57:17Z [Term] @@ -21839,7 +21853,7 @@ is_a: CL:0000134 {is_inferred="true"} ! mesenchymal stem cell is_a: CL:0002195 ! hepatic stem cell intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: part_of UBERON:0002107 ! liver -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-01T09:58:51Z [Term] @@ -21850,8 +21864,8 @@ is_a: CL:0000134 {is_inferred="true"} ! mesenchymal stem cell is_a: CL:0001035 ! bone cell intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: part_of UBERON:0002412 ! vertebra -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002412 ! vertebra +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-01T10:40:27Z [Term] @@ -21865,9 +21879,9 @@ xref: BTO:0001220 xref: CALOHA:TS-0898 xref: MESH:D012583 is_a: CL:0000125 ! glial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0000010 ! peripheral nervous system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2011-03-02T01:19:27Z [Term] @@ -21878,9 +21892,9 @@ subset: human_reference_atlas is_a: CL:0000499 {is_inferred="true"} ! stromal cell intersection_of: CL:0000499 ! stromal cell intersection_of: part_of UBERON:0001264 ! pancreas -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001264 ! pancreas -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2011-03-02T02:40:41Z [Term] @@ -21891,8 +21905,8 @@ is_a: CL:0000669 {is_inferred="true"} ! pericyte is_a: CL:0002319 ! neural cell intersection_of: CL:0000669 ! pericyte intersection_of: part_of UBERON:0001017 ! central nervous system -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001017 ! central nervous system +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-02T02:54:18Z [Term] @@ -21904,9 +21918,9 @@ subset: human_reference_atlas synonym: "perineurial glial cell" EXACT [PMID:25818566] is_a: CL:0000125 ! glial cell is_a: CL:0002320 ! connective tissue cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0000121 ! perineurium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2011-03-02T03:03:58Z [Term] @@ -21917,8 +21931,8 @@ is_a: CL:0000066 ! epithelial cell is_a: CL:0000349 {is_inferred="true"} ! extraembryonic cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001987 ! placenta -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001987 ! placenta +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-02T03:21:30Z [Term] @@ -21928,18 +21942,19 @@ def: "A preadipocyte found in mesenteric tissue." [GOC:tfm] is_a: CL:0002334 {is_inferred="true"} ! preadipocyte intersection_of: CL:0002334 ! preadipocyte intersection_of: part_of UBERON:0002095 ! mesentery -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002095 ! mesentery +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-03T04:19:40Z [Term] id: CL:0002579 name: omentum preadipocyte +def: "A preadipocyte that is part of an omentum." [PMID:21484051] is_a: CL:0002334 {is_inferred="true"} ! preadipocyte intersection_of: CL:0002334 ! preadipocyte intersection_of: part_of UBERON:0003688 ! omentum -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0003688 ! omentum +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-03T04:19:42Z [Term] @@ -21950,17 +21965,18 @@ is_a: CL:0002334 {is_inferred="true"} ! preadipocyte is_a: CL:4006000 ! fibroblast of breast intersection_of: CL:0002334 ! preadipocyte intersection_of: part_of UBERON:0000310 ! breast -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-03T04:19:46Z [Term] id: CL:0002581 name: perirenal preadipocyte +def: "A preadipocyte that is part of a perirenal fat tissue." [PMID:20106964, PMID:31079959] is_a: CL:0002334 {is_inferred="true"} ! preadipocyte intersection_of: CL:0002334 ! preadipocyte intersection_of: part_of UBERON:0005406 ! perirenal fat -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0005406 ! perirenal fat +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-03T04:20:04Z [Term] @@ -21968,7 +21984,7 @@ id: CL:0002582 name: visceral preadipocyte def: "A preadipocyte that is part of visceral tissue." [GOC:tfm] is_a: CL:0002334 ! preadipocyte -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-03T04:32:56Z [Term] @@ -21978,8 +21994,8 @@ def: "A preadipocyte that is part of subcutaneous tissue." [GOC:tfm] is_a: CL:0002334 {is_inferred="true"} ! preadipocyte intersection_of: CL:0002334 ! preadipocyte intersection_of: part_of UBERON:0002072 ! hypodermis -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002072 ! hypodermis +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-03T04:33:01Z [Term] @@ -22003,9 +22019,9 @@ is_a: CL:0000071 {is_inferred="true"} ! blood vessel endothelial cell is_a: CL:0009004 ! retinal cell intersection_of: CL:0000071 ! blood vessel endothelial cell intersection_of: part_of UBERON:0000966 ! retina -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0000966 ! retina -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2011-03-06T03:28:27Z [Term] @@ -22022,10 +22038,10 @@ is_a: CL:0000149 ! visual pigment cell is_a: CL:0009004 ! retinal cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001782 ! pigmented layer of retina -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: has_part GO:0042470 ! melanosome relationship: part_of UBERON:0001782 ! pigmented layer of retina -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2011-03-06T03:37:09Z [Term] @@ -22035,8 +22051,8 @@ def: "A smooth muscle cell of the umbilical vein." [GOC:tfm] is_a: CL:0019018 ! blood vessel smooth muscle cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0002066 ! umbilical vein -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002066 ! umbilical vein +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T05:00:51Z [Term] @@ -22046,8 +22062,8 @@ def: "A smooth muscle cell of the bachiocephalic vasculature." [GOC:tfm] is_a: CL:0019018 ! blood vessel smooth muscle cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0001529 ! brachiocephalic artery -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001529 ! brachiocephalic artery +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T05:00:58Z [Term] @@ -22058,8 +22074,8 @@ is_a: CL:0000359 {is_inferred="true"} ! vascular associated smooth muscle cell is_a: CL:0002319 ! neural cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0000955 ! brain -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0000955 ! brain +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T05:01:20Z [Term] @@ -22072,9 +22088,9 @@ xref: BTO:0003336 is_a: CL:0019018 ! blood vessel smooth muscle cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0002012 ! pulmonary artery -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002012 ! pulmonary artery -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2011-03-06T05:01:28Z [Term] @@ -22086,9 +22102,9 @@ is_a: CL:0002494 ! cardiocyte is_a: CL:0019018 ! blood vessel smooth muscle cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0001621 ! coronary artery -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001621 ! coronary artery -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2011-03-06T05:01:34Z [Term] @@ -22098,8 +22114,8 @@ def: "A smooth muscle of the internal thoracic artery." [GOC:tfm] is_a: CL:0002595 ! smooth muscle cell of the subclavian artery intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0002456 ! internal thoracic artery -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002456 ! internal thoracic artery +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T05:01:41Z [Term] @@ -22109,8 +22125,8 @@ def: "A smooth muscle cell of the umbilical artery." [GOC:tfm] is_a: CL:0019018 ! blood vessel smooth muscle cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0001310 ! umbilical artery -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001310 ! umbilical artery +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T05:01:48Z [Term] @@ -22120,8 +22136,8 @@ def: "A smooth muscle cell of the subclavian artery." [GOC:tfm] is_a: CL:0019018 ! blood vessel smooth muscle cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0001533 ! subclavian artery -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001533 ! subclavian artery +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T05:01:52Z [Term] @@ -22131,8 +22147,8 @@ def: "Smooth muscle cell of the carotid artery." [GOC:tfm] is_a: CL:0019018 ! blood vessel smooth muscle cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0005396 ! carotid artery segment -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0005396 ! carotid artery segment +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T05:01:56Z [Term] @@ -22145,8 +22161,8 @@ is_a: CL:0000192 {is_inferred="true"} ! smooth muscle cell is_a: CL:1001319 ! bladder cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0001255 ! urinary bladder -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2011-03-06T05:43:24Z [Term] @@ -22158,9 +22174,9 @@ xref: BTO:0004402 is_a: CL:0019019 ! tracheobronchial smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0002185 ! bronchus -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002185 ! bronchus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2011-03-06T05:46:39Z [Term] @@ -22170,8 +22186,8 @@ def: "A smooth muscle cell of the esophagus." [GOC:tfm] is_a: CL:0000192 {is_inferred="true"} ! smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0001043 ! esophagus -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001043 ! esophagus +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T05:48:17Z [Term] @@ -22182,8 +22198,8 @@ subset: cellxgene_subset is_a: CL:0019019 ! tracheobronchial smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0003126 ! trachea -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0003126 ! trachea +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T05:50:28Z [Term] @@ -22194,8 +22210,8 @@ subset: cellxgene_subset is_a: CL:0000192 {is_inferred="true"} ! smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0000995 ! uterus -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0000995 ! uterus +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T05:53:28Z [Term] @@ -22205,8 +22221,8 @@ synonym: "anulus pulposus cell" EXACT [] is_a: CL:0002320 {is_inferred="true"} ! connective tissue cell intersection_of: CL:0002320 ! connective tissue cell intersection_of: part_of UBERON:0004715 ! annulus fibrosus disci intervertebralis -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0004715 ! annulus fibrosus disci intervertebralis +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T06:50:53Z [Term] @@ -22218,8 +22234,8 @@ is_a: CL:0000127 {is_inferred="true"} ! astrocyte is_a: CL:2000005 ! brain macroglial cell intersection_of: CL:0000127 ! astrocyte intersection_of: part_of UBERON:0002037 ! cerebellum -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002037 ! cerebellum +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T06:57:27Z [Term] @@ -22233,8 +22249,8 @@ is_a: CL:0002605 ! astrocyte of the cerebral cortex is_a: CL:1001580 ! hippocampal glial cell intersection_of: CL:0000127 ! astrocyte intersection_of: part_of UBERON:0002421 ! hippocampal formation -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2011-03-06T06:57:33Z [Term] @@ -22247,8 +22263,8 @@ is_a: CL:0012000 ! astrocyte of the forebrain is_a: CL:1001579 ! cerebral cortex glial cell intersection_of: CL:0000127 ! astrocyte intersection_of: part_of UBERON:0000956 ! cerebral cortex -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2011-03-06T06:57:36Z [Term] @@ -22258,8 +22274,8 @@ def: "An astrocyte of the spinal cord." [GOC:tfm] is_a: CL:0000127 {is_inferred="true"} ! astrocyte intersection_of: CL:0000127 ! astrocyte intersection_of: part_of UBERON:0002240 ! spinal cord -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002240 ! spinal cord +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T07:11:26Z [Term] @@ -22268,7 +22284,7 @@ name: migratory enteric neural crest cell def: "A neural crest cell that gives rise to cells of the enteric nervous system." [GOC:tfm] subset: cellxgene_subset is_a: CL:0000333 ! migratory neural crest cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T07:24:35Z [Term] @@ -22279,8 +22295,8 @@ subset: cellxgene_subset is_a: CL:0010012 ! cerebral cortex neuron intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0002421 ! has soma location hippocampal formation -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0002100 UBERON:0002421 ! has soma location hippocampal formation +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T07:31:49Z [Term] @@ -22291,8 +22307,8 @@ is_a: CL:0000117 {is_inferred="true"} ! CNS neuron (sensu Vertebrata) is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) intersection_of: RO:0002100 UBERON:0004684 ! has soma location raphe nuclei -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0002100 UBERON:0004684 ! has soma location raphe nuclei +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T07:42:06Z [Term] @@ -22303,8 +22319,8 @@ is_a: CL:0000117 {is_inferred="true"} ! CNS neuron (sensu Vertebrata) is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) intersection_of: RO:0002100 UBERON:0002256 ! has soma location dorsal horn of spinal cord -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0002100 UBERON:0002256 ! has soma location dorsal horn of spinal cord +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T07:43:34Z [Term] @@ -22315,8 +22331,8 @@ is_a: CL:0000117 {is_inferred="true"} ! CNS neuron (sensu Vertebrata) is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) intersection_of: RO:0002100 UBERON:0002257 ! has soma location ventral horn of spinal cord -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0002100 UBERON:0002257 ! has soma location ventral horn of spinal cord +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T07:46:03Z [Term] @@ -22326,8 +22342,8 @@ def: "A neuron of the striatum." [GOC:tfm] is_a: CL:0012001 ! neuron of the forebrain intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) intersection_of: RO:0002100 UBERON:0002435 ! has soma location striatum -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0002100 UBERON:0002435 ! has soma location striatum +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T07:47:12Z [Term] @@ -22338,8 +22354,8 @@ is_a: CL:0000117 {is_inferred="true"} ! CNS neuron (sensu Vertebrata) is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) intersection_of: RO:0002100 UBERON:0002038 ! has soma location substantia nigra -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0002100 UBERON:0002038 ! has soma location substantia nigra +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-06T07:48:42Z [Term] @@ -22351,8 +22367,8 @@ synonym: "omental fat cell" EXACT [] is_a: CL:0000136 {is_inferred="true"} ! adipocyte intersection_of: CL:0000136 ! adipocyte intersection_of: part_of UBERON:0003688 ! omentum -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0003688 ! omentum +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-14T10:17:00Z [Term] @@ -22364,8 +22380,8 @@ synonym: "perirenal fat cell" EXACT [] is_a: CL:0000136 {is_inferred="true"} ! adipocyte intersection_of: CL:0000136 ! adipocyte intersection_of: part_of UBERON:0005406 ! perirenal fat -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0005406 ! perirenal fat +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-14T10:17:05Z [Term] @@ -22380,8 +22396,8 @@ xref: CALOHA:TS-2377 is_a: CL:0000136 {is_inferred="true"} ! adipocyte intersection_of: CL:0000136 ! adipocyte intersection_of: part_of UBERON:0000310 ! breast -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0000310 ! breast +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-14T10:17:07Z [Term] @@ -22392,8 +22408,8 @@ xref: BTO:0004296 is_a: CL:0002543 ! vein endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0002066 ! umbilical vein -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002066 ! umbilical vein +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-14T11:36:51Z [Term] @@ -22404,8 +22420,8 @@ comment: The existence of adult endothelial progenitor cells has been controvers subset: human_reference_atlas synonym: "EPC" EXACT [] is_a: CL:0000566 ! angioblastic mesenchymal cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/1410" xsd:string property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/348" xsd:string creation_date: 2011-03-14T12:11:18Z @@ -22421,9 +22437,9 @@ xref: CALOHA:TS-0935 is_a: CL:0000057 {is_inferred="true"} ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0002097 ! skin of body -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002097 ! skin of body -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2011-03-14T12:31:49Z [Term] @@ -22432,8 +22448,8 @@ name: gingival epithelial cell is_a: CL:0002251 ! epithelial cell of alimentary canal intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001949 ! gingival epithelium -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001949 ! gingival epithelium +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-14T12:46:28Z [Term] @@ -22445,8 +22461,8 @@ xref: BTO:0003972 is_a: CL:0000499 {is_inferred="true"} ! stromal cell intersection_of: CL:0000499 ! stromal cell intersection_of: part_of UBERON:0002367 ! prostate gland -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002367 ! prostate gland +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-14T02:11:10Z [Term] @@ -22458,7 +22474,7 @@ is_a: CL:0000622 {is_inferred="true"} ! acinar cell is_a: CL:1001596 ! salivary gland glandular cell intersection_of: CL:0000622 ! acinar cell intersection_of: part_of UBERON:0001044 ! saliva-secreting gland -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-14T02:22:22Z [Term] @@ -22469,7 +22485,7 @@ is_a: CL:0000510 {is_inferred="true"} ! paneth cell is_a: CL:1001585 ! appendix glandular cell intersection_of: CL:0000510 ! paneth cell intersection_of: part_of UBERON:0001154 ! vermiform appendix -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-15T09:38:18Z [Term] @@ -22480,8 +22496,8 @@ is_a: CL:0000068 ! duct epithelial cell is_a: CL:0000077 {is_inferred="true"} ! mesothelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001343 ! seminiferous tubule of testis -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0004813 ! seminiferous tubule epithelium +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-15T11:59:23Z [Term] @@ -22536,7 +22552,7 @@ id: CL:0002630 name: actinomycete-type spore def: "A spore formed from bacteria in the order Actinomycetales." [GO:0034304, GOC:tfm] is_a: CL:0000520 ! prokaryotic cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-06-16T01:01:41Z [Term] @@ -22545,8 +22561,8 @@ name: epithelial cell of upper respiratory tract is_a: CL:0002368 {is_inferred="true"} ! respiratory epithelial cell intersection_of: CL:0002368 ! respiratory epithelial cell intersection_of: part_of UBERON:0001557 ! upper respiratory tract -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001557 ! upper respiratory tract +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-06-21T12:28:55Z [Term] @@ -22556,8 +22572,8 @@ subset: cellxgene_subset is_a: CL:0002368 {is_inferred="true"} ! respiratory epithelial cell intersection_of: CL:0002368 ! respiratory epithelial cell intersection_of: part_of UBERON:0001558 ! lower respiratory tract -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001558 ! lower respiratory tract +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-06-21T12:29:31Z [Term] @@ -22569,7 +22585,7 @@ synonym: "airway basal cell" EXACT [] synonym: "airway basal stem cell" EXACT [] is_a: CL:0000646 ! basal cell is_a: CL:0002368 ! respiratory epithelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-06-21T03:11:10Z [Term] @@ -22579,8 +22595,8 @@ def: "An epithelial cell of the anal column." [GOC:tfm] is_a: CL:0002253 ! epithelial cell of large intestine intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0009882 ! anal column -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0009882 ! anal column +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-08T12:11:38Z [Term] @@ -22589,7 +22605,7 @@ name: nonkeratinized epithelial cell of anal column def: "A nonkeratinized epithelial cell of the anal canal." [GOC:tfm] xref: FMA:263146 is_a: CL:0002634 ! epithelial cell of anal column -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-08T02:05:33Z [Term] @@ -22599,7 +22615,7 @@ def: "A nonkeratinized cell epithleial cell of the inferior part of the anal can xref: FMA:263144 is_a: CL:0002635 ! nonkeratinized epithelial cell of anal column is_a: CL:1000438 ! epithelial cell of wall of inferior part of anal canal -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-08T02:06:53Z [Term] @@ -22611,7 +22627,7 @@ is_a: CL:0002634 ! epithelial cell of anal column is_a: CL:0009066 ! stratified squamous epithelial cell of anal canal intersection_of: CL:0000237 ! keratinizing barrier epithelial cell intersection_of: part_of UBERON:0000159 ! anal canal -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-08T02:08:40Z [Term] @@ -22625,8 +22641,8 @@ is_a: CL:1000351 ! basal cell of epithelium of respiratory bronchiole intersection_of: CL:0002633 ! respiratory basal cell intersection_of: part_of UBERON:0001955 ! epithelium of respiratory bronchiole intersection_of: part_of UBERON:0001958 ! terminal bronchiole epithelium -relationship: dc-contributor http://orcid.org/0000-0001-7258-9596 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-06-21T03:26:08Z [Term] @@ -22636,7 +22652,7 @@ def: "An amniotic stem cell is a mesenchymalstem cell extracted from amniotic fl comment: Not clear to me if amniotic stem cell is a different cell type from amnion mesenchymal stem cells. They are treated as distinct in the literature as isolations methods are different, so I will keep them as separate terms for now. is_a: CL:0000134 ! mesenchymal stem cell is_a: CL:0002323 ! amniocyte -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-06-21T03:55:39Z [Term] @@ -22644,7 +22660,7 @@ id: CL:0002640 name: amniotic epithelial stem cell def: "An epithelial fate stem cell derived form the amnion membrane." [GOC:tfm, PMID:20446274] is_a: CL:0000036 ! epithelial fate stem cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-06-21T04:06:17Z [Term] @@ -22653,7 +22669,7 @@ name: epithelial cell of esophageal gland proper def: "An epithelial cell of the esophageal gland proper." [GOC:tfm] xref: FMA:256141 is_a: CL:0002657 ! glandular cell of esophagus -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-08T02:16:51Z [Term] @@ -22662,7 +22678,7 @@ name: epithelial cell of esophageal cardiac gland def: "An epithelial cell of the esophageal cardiac gland that occurs both in the proximal and distal esophagus, within the lamina propia." [GOC:tfm, http://web.mac.com/wjkrause/iWeb/Histology/Blog/E3FA5916-1AA9-4885-B579-5051838D98CB.html] xref: FMA:256143 is_a: CL:0002657 ! glandular cell of esophagus -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-08T02:16:54Z [Term] @@ -22671,7 +22687,7 @@ name: nonkeratinized cell of stratum corneum of esophageal epithelium def: "An epithelial cell of stratum corneum of esophageal epithelium that lacks keratin." [GOC:tfm] xref: FMA:263148 is_a: CL:0002654 ! epithelial cell of stratum corneum of esophageal epithelium -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-08T02:22:09Z [Term] @@ -22680,7 +22696,7 @@ name: endo-epithelial cell of tympanic part of viscerocranial mucosa def: "An endothelial cell of viscerocranial mucosa that is part of the tympanic region of the viscerocranial mucosa." [GOC:tfm] xref: FMA:70628 is_a: CL:0002261 ! endothelial cell of viscerocranial mucosa -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-08T02:25:44Z [Term] @@ -22689,7 +22705,7 @@ name: endo-epithelial cell of pharyngotympanic part of viscerocranial mucosa def: "An endocranial viscerocranial mucosa cell that is part of viscerocranial mucosa." [GOC:tfm] xref: FMA:70629 is_a: CL:0002261 ! endothelial cell of viscerocranial mucosa -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-08T02:25:46Z [Term] @@ -22697,7 +22713,7 @@ id: CL:0002646 name: obsolete epithelial cell of buccal part of viscerocranial mucosa def: "An ecto-epithelial cell of the buccal region of the viscerocranial mucosa." [GOC:tfm] xref: FMA:70577 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 is_obsolete: true creation_date: 2011-07-08T02:34:12Z @@ -22706,7 +22722,7 @@ id: CL:0002647 name: obsolete epithelial cell of anterior palatal part of viscerocranial mucosa def: "An ecto-epithelial cell of the palatal region of the viscerocranial mucosa." [GOC:tfm] xref: FMA:70580 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 is_obsolete: true creation_date: 2011-07-08T02:34:14Z @@ -22715,7 +22731,7 @@ id: CL:0002648 name: obsolete epithelial cell of nasal part of viscerocranial mucosa def: "An ecto-epithelial cell of the nasal region of the viscerocranial mucosa." [GOC:tfm] xref: FMA:70554 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 is_obsolete: true creation_date: 2011-07-08T02:36:06Z @@ -22724,7 +22740,7 @@ id: CL:0002649 name: obsolete epithelial cell of gingival part of viscerocranial mucosa def: "An ecto-epithelial cell of the gingival region of the viscerocranial mucosa." [GOC:tfm] xref: FMA:70579 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 is_obsolete: true creation_date: 2011-07-08T02:36:11Z @@ -22733,7 +22749,7 @@ id: CL:0002650 name: obsolete epithelial cell of paranasal sinus part of viscerocranial mucosa def: "An ecto-epithelial cell of the paranasal region of the viscerocranial mucosa." [GOC:tfm] xref: FMA:70578 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 is_obsolete: true creation_date: 2011-07-08T02:38:18Z @@ -22744,7 +22760,7 @@ def: "An endothelial cell that is part of the venous sinus of spleen. This endot synonym: "stave cell" EXACT [FMA:62817] xref: FMA:72140 is_a: CL:0002262 ! endothelial cell of sinusoid -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-08T03:06:49Z [Term] @@ -22760,9 +22776,9 @@ is_a: CL:0000075 ! columnar/cuboidal epithelial cell is_a: CL:1000414 ! endothelial cell of venule intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:8410037 ! high endothelial venule -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:8410037 ! high endothelial venule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2011-07-08T03:14:10Z [Term] @@ -22771,7 +22787,7 @@ name: squamous endothelial cell def: "A endothelial cell of the venule that is squamous shaped. This is in contrast to the cubodial shape of high endothelial venule cells." [GOC:tfm] is_a: CL:0000076 ! squamous epithelial cell is_a: CL:1000414 ! endothelial cell of venule -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-08T03:31:25Z [Term] @@ -22780,7 +22796,7 @@ name: epithelial cell of stratum corneum of esophageal epithelium def: "An epithelial cell of stratum corneum of esophageal epithelium." [GOC:tfm] xref: FMA:70733 is_a: CL:0002252 ! epithelial cell of esophagus -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-08T03:46:35Z [Term] @@ -22789,7 +22805,7 @@ name: epithelial cell of stratum spinosum of esophageal epithelium def: "An epithelial cell of stratum spinosum of esophageal epithelium." [GOC:tfm] xref: FMA:70732 is_a: CL:0002252 ! epithelial cell of esophagus -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-08T03:48:26Z [Term] @@ -22800,8 +22816,8 @@ xref: FMA:86489 is_a: CL:1001591 ! oviduct glandular cell intersection_of: CL:0000150 ! glandular epithelial cell intersection_of: part_of UBERON:0001295 ! endometrium -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001295 ! endometrium +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-08T03:54:08Z [Term] @@ -22814,7 +22830,7 @@ is_a: CL:0000150 {is_inferred="true"} ! glandular epithelial cell is_a: CL:0002252 {is_inferred="true"} ! epithelial cell of esophagus intersection_of: CL:0000150 ! glandular epithelial cell intersection_of: part_of UBERON:0001043 ! esophagus -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-08T03:55:57Z [Term] @@ -22826,7 +22842,7 @@ is_a: CL:0000150 {is_inferred="true"} ! glandular epithelial cell is_a: CL:0002253 ! epithelial cell of large intestine intersection_of: CL:0000150 ! glandular epithelial cell intersection_of: part_of UBERON:0000059 ! large intestine -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-08T04:03:01Z [Term] @@ -22839,7 +22855,7 @@ is_a: CL:0000150 {is_inferred="true"} ! glandular epithelial cell is_a: CL:0002178 ! epithelial cell of stomach intersection_of: CL:0000150 ! glandular epithelial cell intersection_of: part_of UBERON:0000945 ! stomach -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-11T01:20:35Z [Term] @@ -22849,7 +22865,7 @@ def: "A luminal epithelial cell of mammary gland located in acinus of structure. comment: Consider if synonymous with mammary alveolar cell CL:0002325. Some use this term to refer to the non-lactating cell type that gives rise to the lactating cell type. xref: FMA:74505 is_a: CL:0002326 ! luminal epithelial cell of mammary gland -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-11T01:44:31Z [Term] @@ -22858,7 +22874,7 @@ name: luminal cell of lactiferous terminal ductal lobular unit def: "A luminal cell of terminal ducts, i.e.e the terminal branch of a lactiferous duct which alveolar cells drain into." [GOC:tfm] xref: FMA:87168 is_a: CL:0002662 ! luminal cell of lactiferous duct -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-11T01:44:33Z [Term] @@ -22867,7 +22883,7 @@ name: luminal cell of lactiferous duct def: "A luminal epithelial cell of the lactiferous duct. This cuboidal epithelial cell expresses keratin-18 and is estrogen-receptor alpha positive." [GOC:tfm, PMID:19022771] xref: FMA:74504 is_a: CL:0002326 ! luminal epithelial cell of mammary gland -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-11T01:44:48Z [Term] @@ -22878,8 +22894,8 @@ xref: FMA:83389 is_a: CL:0002074 {is_inferred="true"} ! myocardial endocrine cell intersection_of: CL:0002074 ! myocardial endocrine cell intersection_of: part_of UBERON:0002081 ! cardiac atrium -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002081 ! cardiac atrium +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-11T02:45:39Z [Term] @@ -22890,7 +22906,7 @@ comment: Discrepancy in develops from origins prevents me from making the assert synonym: "cardiovascular progenitor cell" EXACT [PMID:17519333, PMID:19745164] synonym: "CPC" RELATED OMO:0003000 [PMID:19745164] is_a: CL:0000048 ! multi fate stem cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-11T03:15:38Z [Term] @@ -22898,8 +22914,8 @@ id: CL:0002665 name: otic fibrocyte def: "A fibrocyte of the cochlea that has specialized structural and molecular adaptions." [GOC:tfm, PMID:18353863] is_a: CL:0000135 ! fibrocyte -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0006725 ! spiral ligament +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-11T03:35:01Z [Term] @@ -22909,7 +22925,7 @@ def: "An otic fibrocyte that underlies the spiral prominence and is part of a me synonym: "type II otic fibrocyte" EXACT [] synonym: "type II spiral ligament fibrocyte" EXACT [MP:0004488] is_a: CL:0002665 ! otic fibrocyte -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-11T03:40:40Z [Term] @@ -22919,7 +22935,7 @@ def: "An otic fibrocyte that resides above the stria vasularis and is part of a synonym: "type V otic fibrocyte" EXACT [] synonym: "type V spiral ligament fibrocyte" EXACT [] is_a: CL:0002665 ! otic fibrocyte -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-11T03:40:42Z [Term] @@ -22929,7 +22945,7 @@ def: "An otic fibrocyte that is lateral to the basilar membrane and anchoris it synonym: "type IV otic fibrocyte" EXACT [] synonym: "type IV spiral ligament fibrocyte" EXACT [MP:0004490] is_a: CL:0002665 ! otic fibrocyte -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-11T03:40:46Z [Term] @@ -22939,7 +22955,7 @@ def: "An otic fibrocyte that lines the otic capsule." [GOC:tfm, PMID:18353863] synonym: "type III otic fibrocyte" EXACT [] synonym: "type III spiral ligament fibrocyte" EXACT [MP:0004489] is_a: CL:0002665 ! otic fibrocyte -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-11T03:40:50Z [Term] @@ -22949,7 +22965,7 @@ def: "An otic fibrocyte that underlies the stria vascularis and is part of a mes synonym: "type I otic fibrocyte" EXACT [] synonym: "type I spiral ligament fibrocyte" EXACT [MP:0004487] is_a: CL:0002665 ! otic fibrocyte -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-07-11T03:39:27Z [Term] @@ -22958,7 +22974,7 @@ name: endothelial stalk cell def: "An endothelial stalk cell is a specialized endothelial cell that follows behind the tip cell of an angiogenic sprout." [GOC:tfm, PMID:21521739] subset: cellxgene_subset is_a: CL:0000071 ! blood vessel endothelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-08-16T01:49:32Z [Term] @@ -22966,8 +22982,8 @@ id: CL:0002672 name: retinal progenitor cell def: "A multi-fate stem cell that can give rise to different retinal cell types including rod and cone cells." [GOC:tfm, PMID:20959166, PMID:21148186] is_a: CL:0000048 ! multi fate stem cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000133 ! neurectodermal cell +relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-08-16T02:38:01Z [Term] @@ -22978,8 +22994,8 @@ subset: cellxgene_subset is_a: CL:0008002 ! skeletal muscle fiber intersection_of: CL:0008002 ! skeletal muscle fiber intersection_of: part_of UBERON:0000378 ! tongue muscle -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0000378 ! tongue muscle +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-08-16T03:10:02Z [Term] @@ -22988,8 +23004,8 @@ name: H minus def: "A S. pombe mating type determined by the mat1-Mc and mat1-Mi on the mat1 locus." [GOC:tfm] synonym: "H- cell" EXACT [] is_a: CL:0000521 ! fungal cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe +relationship: RO:0002162 NCBITaxon:4896 ! in taxon Schizosaccharomyces pombe +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-08-16T03:20:53Z [Term] @@ -22997,8 +23013,8 @@ id: CL:0002675 name: H plus def: "A S. pombe cell type determined by mat1-Pc and mat1-Pi on the mat1 locus." [GOC:tfm] is_a: CL:0000521 ! fungal cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe +relationship: RO:0002162 NCBITaxon:4896 ! in taxon Schizosaccharomyces pombe +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-08-16T03:20:58Z [Term] @@ -23007,8 +23023,8 @@ name: neural crest derived neuroblast def: "A neuroblast derived from a neural crest cell." [GOC:tfm, PMID:17407019] is_a: CL:0000031 ! neuroblast (sensu Vertebrata) is_a: CL:0011026 ! progenitor cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000333 ! migratory neural crest cell +relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-08-22T09:24:15Z [Term] @@ -23023,8 +23039,8 @@ synonym: "naive regulatory T-cell" EXACT [] synonym: "naive regulatory T-lymphocyte" EXACT [] is_a: CL:0000792 ! CD4-positive, CD25-positive, alpha-beta regulatory T cell is_a: CL:0000898 ! naive T cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2011-08-25T03:17:21Z [Term] @@ -23037,7 +23053,7 @@ is_a: CL:0000792 ! CD4-positive, CD25-positive, alpha-beta regulatory T cell is_a: CL:0000897 ! CD4-positive, alpha-beta memory T cell intersection_of: CL:0000792 ! CD4-positive, CD25-positive, alpha-beta regulatory T cell intersection_of: output_of GO:0043379 ! memory T cell differentiation -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-08-25T03:17:34Z [Term] @@ -23065,9 +23081,9 @@ relationship: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon relationship: CL:4030046 PR:000001084 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD8 alpha chain relationship: CL:4030046 PR:000001874 ! lacks_plasma_membrane_part KLRB1-like protein relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0002104 PR:000002065 ! has plasma membrane part mast/stem cell growth factor receptor relationship: RO:0002104 PR:000002979 ! has plasma membrane part lymphocyte antigen 6A-2/6E-1 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-08-29T10:08:02Z [Term] @@ -23078,7 +23094,7 @@ is_a: CL:0000696 {is_inferred="true"} ! PP cell is_a: CL:1001516 ! intestinal enteroendocrine cell intersection_of: CL:0000696 ! PP cell intersection_of: part_of UBERON:0000160 ! intestine -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-09-27T11:59:01Z [Term] @@ -23088,8 +23104,8 @@ def: "A cell that is part of a cortex of kidney." [] is_a: CL:1000497 ! kidney cell intersection_of: CL:1000497 ! kidney cell intersection_of: part_of UBERON:0001225 ! cortex of kidney -relationship: dc-contributor https://orcid.org/0000-0002-0956-8634 relationship: part_of UBERON:0001225 ! cortex of kidney +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0956-8634 creation_date: 2011-10-25T03:49:41Z [Term] @@ -23102,8 +23118,8 @@ is_a: CL:0000740 ! retinal ganglion cell is_a: CL:0004247 ! bistratified cell intersection_of: CL:0000740 ! retinal ganglion cell intersection_of: bearer_of PATO:0070062 ! bistratified dendrite cell morphology -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003002 @@ -23112,8 +23128,8 @@ namespace: cell def: "A retinal ganglion cell that has a small dendritic field and a medium dendritic arbor with post sympatic terminals in sublaminar layer S3." [PMID:11978858] is_a: CL:0000740 ! retinal ganglion cell relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003003 @@ -23123,8 +23139,8 @@ def: "A mono-stratified retinal ganglion cell that has a small dendritic field a is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003004 @@ -23136,8 +23152,8 @@ is_a: CL:0003001 ! bistratified retinal ganglion cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 relationship: RO:0013001 UBERON:0009851 ! has synaptic IO in region border of sublaminar layers S4 and S5 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003005 @@ -23147,8 +23163,8 @@ def: "A mono-stratified retinal ganglion cell that has a small dendritic field a comment: Masland nomenclature PMID:11978858 is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003006 @@ -23159,8 +23175,8 @@ is_a: CL:0003005 ! G4 retinal ganglion cell is_a: CL:4023032 ! ON retinal ganglion cell relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003007 @@ -23172,8 +23188,8 @@ is_a: CL:0003005 ! G4 retinal ganglion cell is_a: CL:4023033 ! OFF retinal ganglion cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003008 @@ -23183,8 +23199,8 @@ def: "A mono-stratified retinal ganglion cell that has a medium dendritic field is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003009 @@ -23195,8 +23211,8 @@ is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 relationship: RO:0013001 UBERON:0008926 ! has synaptic IO in region sublaminar layer S5 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003010 @@ -23207,8 +23223,8 @@ synonym: "ON-OFF DS" EXACT [] is_a: CL:0003001 ! bistratified retinal ganglion cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003011 @@ -23218,8 +23234,8 @@ def: "A mono-stratified retinal ganglion cell that has a large dendritic field a is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003012 @@ -23230,8 +23246,8 @@ is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology relationship: RO:0013001 UBERON:0008922 ! has synaptic IO in region sublaminar layer S1 relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003013 @@ -23285,8 +23301,8 @@ namespace: cell def: "A retinal ganglion B cell that has post synaptic terminals in S2." [PMID:12209831] is_a: CL:0004183 ! retinal ganglion cell B3 relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003018 @@ -23296,8 +23312,8 @@ def: "A retinal ganglion B3 cell with dentrites terminating in S4." [PMID:122098 xref: BAMS:1010 is_a: CL:0004183 ! retinal ganglion cell B3 relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003020 @@ -23306,8 +23322,8 @@ namespace: cell def: "A retinal ganglion cell C that has post-synaptic terminals in S2." [PMID:12209831] is_a: CL:0004116 ! retinal ganglion cell C relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003021 @@ -23315,8 +23331,8 @@ name: retinal ganglion cell C4 namespace: cell def: "A retinal ganglion cell C outer that has a medium dendritic field and a dense dendritic arbor." [PMID:12209831] is_a: CL:0003020 ! retinal ganglion cell C outer -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003022 @@ -23324,8 +23340,8 @@ name: retinal ganglion cell C5 namespace: cell def: "A retinal ganglion cell C outer that has medium dendritic density and field size." [PMID:12209831] is_a: CL:0003020 ! retinal ganglion cell C outer -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003023 @@ -23333,8 +23349,8 @@ name: retinal ganglion cell C6 namespace: cell def: "A retinal ganglion cell C outer that has dense dendritic diversity." [PMID:12209831] is_a: CL:0003020 ! retinal ganglion cell C outer -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003024 @@ -23343,8 +23359,8 @@ namespace: cell def: "A retinal ganglion cell C with medium cell bodies and large dendritic field." [PMID:12209831] is_a: CL:0004116 ! retinal ganglion cell C relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003025 @@ -23353,8 +23369,8 @@ namespace: cell def: "A retinal ganglion cell C inner that has sparse dendritic density, and large dendritic field." [PMID:12209831] synonym: "epsilon" RELATED [] is_a: CL:0003024 ! retinal ganglion cell C inner -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003026 @@ -23364,8 +23380,8 @@ def: "A bistratified retinal ganglion cell that has a small dendrite fields with is_a: CL:0003001 ! bistratified retinal ganglion cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003027 @@ -23377,8 +23393,8 @@ synonym: "ON-OFF direction selective" RELATED [] is_a: CL:0003001 ! bistratified retinal ganglion cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003028 @@ -23388,8 +23404,8 @@ def: "A monostratified retinal ganglion cell that has a small dendrite field wit is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003029 @@ -23400,8 +23416,8 @@ is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003030 @@ -23410,8 +23426,8 @@ namespace: cell def: "A monostratified retinal ganglion cell that has a medium soma and a small dendrite field." [PMID:16626866] is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003031 @@ -23421,8 +23437,8 @@ def: "A monostratified retinal ganglion cell that has post synaptic terminals in is_a: CL:0003030 ! M3 retinal ganglion cell is_a: CL:4023032 ! ON retinal ganglion cell relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003032 @@ -23432,8 +23448,8 @@ def: "A monostratified retinal ganglion cell that has post synaptic terminals in is_a: CL:0003030 ! M3 retinal ganglion cell is_a: CL:4023033 ! OFF retinal ganglion cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003033 @@ -23443,8 +23459,8 @@ def: "A monostratified retinal ganglion cell that has a large soma, a medium den is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003034 @@ -23454,8 +23470,8 @@ def: "A monostratified retinal ganglion cell that has a small soma, an assymetri is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003035 @@ -23465,8 +23481,8 @@ def: "A monostratified retinal ganglion cell that contains opsin." [PMID:1662686 is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology relationship: RO:0002292 PR:000001243 ! expresses melanopsin -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003036 @@ -23475,8 +23491,8 @@ namespace: cell def: "A monostratified retinal ganglion cell with large soma and large dendritic field, with medium dendritic arbor, and has dendrites in layers 2 and 5." [PMID:16626866] is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003037 @@ -23486,8 +23502,8 @@ def: "An M7 retinal ganglion cells with synaptic terminals in S4 and is depolari is_a: CL:0003036 ! M7 retinal ganglion cell is_a: CL:4023032 ! ON retinal ganglion cell relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003038 @@ -23497,8 +23513,8 @@ def: "An M7 retinal ganglion cells with synaptic terminals in S2 and is depolari is_a: CL:0003036 ! M7 retinal ganglion cell is_a: CL:4023033 ! OFF retinal ganglion cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003039 @@ -23507,8 +23523,8 @@ namespace: cell def: "A monostratified retinal ganglion cell with large soma and medium dendritic field, with dense dendritic arbor." [PMID:16626866] is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003040 @@ -23517,8 +23533,8 @@ namespace: cell def: "A monostratified retinal ganglion cell with large soma and large dendritic field, with medium dendritic arbor, and has dendrites in layers 1 and 5." [PMID:16626866] is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003041 @@ -23528,8 +23544,8 @@ def: "An M9 retinal ganglion cells with synaptic terminals in S2 and is depolari is_a: CL:0003040 ! M9 retinal ganglion cell is_a: CL:4023032 ! ON retinal ganglion cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003042 @@ -23539,8 +23555,8 @@ def: "An M9 retinal ganglion cell with synaptic terminals in S4 that is depolari is_a: CL:0003040 ! M9 retinal ganglion cell is_a: CL:4023033 ! OFF retinal ganglion cell relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003043 @@ -23549,8 +23565,8 @@ namespace: cell def: "A monostratified retinal ganglion cell with large soma and large dendritic field, with dense dendritic arbor." [PMID:16626866] is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003044 @@ -23560,8 +23576,8 @@ def: "A bistratified ganglion cell with small, dense dendritic fields that termi is_a: CL:0003001 ! bistratified retinal ganglion cell relationship: RO:0013001 UBERON:0008922 ! has synaptic IO in region sublaminar layer S1 relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003045 @@ -23571,8 +23587,8 @@ def: "A bistratified ganglion cell with larger, asymetric dendritic fields that is_a: CL:0003001 ! bistratified retinal ganglion cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003046 @@ -23582,8 +23598,8 @@ def: "A bistratifed retinal ganglion cell that has small, symmetric dendritic fi is_a: CL:0003001 ! bistratified retinal ganglion cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003047 @@ -23593,8 +23609,8 @@ def: "A bistratifed retinal ganglion cell that has small, symmetric dendritic fi is_a: CL:0003001 ! bistratified retinal ganglion cell relationship: RO:0013001 UBERON:0008922 ! has synaptic IO in region sublaminar layer S1 relationship: RO:0013001 UBERON:0008929 ! has synaptic IO in region sublaminar layers S4 or S5 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003048 @@ -23609,7 +23625,7 @@ synonym: "long-wavelength cone" EXACT [https://doi.org/10.1038/323623a0] is_a: CL:0000573 ! retinal cone cell is_a: PR:000050567 ! protein-containing material entity relationship: has_part PR:000001244 ! long-wave-sensitive opsin 1 -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003049 @@ -23624,7 +23640,7 @@ synonym: "middle-wavelength-sensitive (M) cone" EXACT [https://opg.optica.org/jo is_a: CL:0000573 ! retinal cone cell is_a: PR:000050567 ! protein-containing material entity relationship: has_part PR:000001224 ! medium-wave-sensitive opsin -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003050 @@ -23641,7 +23657,7 @@ synonym: "short- (S) wavelength-sensitive cone" EXACT [https://doi.org/10.7554/e synonym: "short-wavelength sensitive cone" EXACT [PMID:31117170] synonym: "short-wavelength-sensitive (S) cone" EXACT [https://opg.optica.org/josaa/abstract.cfm?URI=josaa-6-1-153] is_a: CL:0000573 ! retinal cone cell -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0003051 @@ -23649,7 +23665,7 @@ name: UV cone cell namespace: cell def: "A cone cell that detects ultraviolet (UV) wavelength light." [] is_a: CL:0000573 ! retinal cone cell -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004001 @@ -23668,8 +23684,8 @@ namespace: cell def: "A monostratified retinal ganglion cell with small to medium soma and small to medium dendritic field." [PMID:12209831] is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004116 @@ -23678,8 +23694,8 @@ namespace: cell def: "A retinal ganglion with cell medium cell bodies and medium to large dendritic fields." [PMID:12209831] comment: Group RGC cells are defined as having small to medium cell bodies and medium to large dendritic fields. Their morphology was more heterogeneous than that of Groups RGA and RGB. We classified cells with a large soma and a large dendritic field as RGA, cells with a small to medium to sized soma and a small to medium to sized dendritic field as RGB, and cells with a small to medium to sized soma but a medium to large dendritic field RGC. is_a: CL:0000740 ! retinal ganglion cell -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004117 @@ -23691,8 +23707,8 @@ synonym: "alpha cell" EXACT [] xref: BAMS:1009 is_a: CL:0000740 ! retinal ganglion cell relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004119 @@ -23704,8 +23720,8 @@ synonym: "retinal ganglion cell B4" EXACT [] xref: BAMS:1047 is_a: CL:0004115 ! retinal ganglion cell B relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004120 @@ -23718,8 +23734,8 @@ synonym: "type I" BROAD [] xref: BAMS:1045 is_a: CL:0004117 ! retinal ganglion cell A relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004121 @@ -23729,8 +23745,8 @@ def: "A retinal ganglion cell B that has a very small but very dense dendritic f xref: BAMS:1048 is_a: CL:0004115 ! retinal ganglion cell B relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004124 @@ -23742,8 +23758,8 @@ synonym: "MTN projecting" RELATED [] synonym: "ON-direction-selective" RELATED [] xref: BAMS:1050 is_a: CL:0003024 ! retinal ganglion cell C inner -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004125 @@ -23752,8 +23768,8 @@ namespace: cell def: "A retinal ganglion cell C inner that has dense dendritic diversity." [PMID:12209831] xref: BAMS:1067 is_a: CL:0003024 ! retinal ganglion cell C inner -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004126 @@ -23762,8 +23778,8 @@ namespace: cell def: "A retinal ganglion cell C outer that has symmetrical and dense dendritic dendritic tree with a large dendritic field." [PMID:12209831] xref: BAMS:1066 is_a: CL:0003020 ! retinal ganglion cell C outer -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004137 @@ -23773,8 +23789,8 @@ def: "A retinal ganglion A2 cell with dendrites terminating in S4." [PMID:122098 xref: BAMS:1061 is_a: CL:0004138 ! retinal ganglion cell A2 relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004138 @@ -23785,8 +23801,8 @@ synonym: "I-1" RELATED [] synonym: "outer alpha retinal ganglion cell" EXACT [] synonym: "type I" RELATED [] is_a: CL:0004117 ! retinal ganglion cell A -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004139 @@ -23796,8 +23812,8 @@ def: "A retinal ganglion A2 cell with dendrites terminating in S2." [PMID:122098 xref: BAMS:1065 is_a: CL:0004138 ! retinal ganglion cell A2 relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004161 @@ -23806,8 +23822,8 @@ namespace: cell def: "A cone whose sensitivity measurements have an average spectral peak of 510 nm. These cones are described in rat." [] xref: BAMS:1028 "MB" is_a: CL:0003049 ! M cone cell -relationship: present_in_taxon NCBITaxon:9989 ! Rodentia -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: RO:0002175 NCBITaxon:9989 [Term] id: CL:0004162 @@ -23817,8 +23833,8 @@ def: "A cone whose sensitivity measurements have an average spectral peak of 358 comment: The photopigment curves that provide best fits to...sensitivity measurements have an average spectral peak of 358.2 nm. xref: BAMS:1029 "MB" is_a: CL:0003051 ! UV cone cell -relationship: present_in_taxon NCBITaxon:9989 ! Rodentia -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: RO:0002175 NCBITaxon:9989 [Term] id: CL:0004183 @@ -23828,8 +23844,8 @@ def: "A monostratified retinal ganglion cell with medium soma, sparse dendritic comment: Sixty to eighty neurons with small somata (12 to 24 micrometers in diameter), small dendritic fields (99 to 289 micrometers in diameter), and small axonal diameters (04. to 07. micrometers in diameter) make up Group RGB. We classified cells with a large soma and a large dendritic field as RGA, cells with a small to medium to sized soma and a small to medium to sized dendritic field as RGB, and cells with a small to medium to sized soma but a medium to large dendritic field RGC. xref: BAMS:1049 is_a: CL:0004115 ! retinal ganglion cell B -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004213 @@ -23837,8 +23853,8 @@ name: type 3a cone bipolar cell namespace: cell def: "A type of type 3 cone bipolar cell with distinctive curly dendrites." [PMID:19129389] is_a: CL:0000755 ! type 3 cone bipolar cell (sensu Mus) -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004214 @@ -23846,8 +23862,8 @@ name: type 3b cone bipolar cell namespace: cell def: "A type of type 3 cone bipolar cell with distinctive crescent-shaped dendrites." [PMID:19129389] is_a: CL:0000755 ! type 3 cone bipolar cell (sensu Mus) -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004215 @@ -23855,8 +23871,8 @@ name: type 5a cone bipolar cell namespace: cell def: "A type 5 cone bipolar cell with narrowly stratified post synaptic terminals." [] is_a: CL:0000757 ! type 5 cone bipolar cell (sensu Mus) -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004216 @@ -23864,8 +23880,8 @@ name: type 5b cone bipolar cell namespace: cell def: "A type 5 cone bipolar cell with diffuse axonal branches." [] is_a: CL:0000757 ! type 5 cone bipolar cell (sensu Mus) -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004217 @@ -23876,8 +23892,8 @@ synonym: "A Horizontal Cell" EXACT [] synonym: "H1" RELATED OMO:0003000 [doi:10.1038/s41598-020-66092-9] is_a: CL:0000745 ! retina horizontal cell relationship: CL:4030045 GO:0030424 ! lacks_part axon -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004218 @@ -23888,8 +23904,8 @@ synonym: "B Horizontal Cell" EXACT [] synonym: "H2" RELATED OMO:0003000 [doi:10.1038/s41598-020-66092-9] is_a: CL:0000745 ! retina horizontal cell relationship: RO:0002120 GO:0044316 ! synapsed to cone cell pedicle -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004219 @@ -23901,11 +23917,11 @@ subset: human_reference_atlas is_a: CL:0004250 ! bistratified retinal amacrine cell is_a: CL:0004251 ! narrow field retinal amacrine cell is_a: CL:4030028 ! glycinergic amacrine cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0013001 UBERON:0008926 ! has synaptic IO in region sublaminar layer S5 relationship: RO:0013001 UBERON:0008927 ! has synaptic IO in region sublaminar layers S1 or S2 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0004220 @@ -23913,8 +23929,8 @@ name: flag amacrine cell namespace: cell def: "An amacrine cell with a small, asymteric dendritic field." [PMID:9620701] is_a: CL:0004251 ! narrow field retinal amacrine cell -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004221 @@ -23925,8 +23941,8 @@ is_a: CL:0004220 ! flag amacrine cell is_a: CL:4030028 ! glycinergic amacrine cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004222 @@ -23938,8 +23954,8 @@ is_a: CL:4030028 ! glycinergic amacrine cell relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 relationship: RO:0013001 UBERON:0008926 ! has synaptic IO in region sublaminar layer S5 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004223 @@ -23951,8 +23967,8 @@ relationship: RO:0013001 UBERON:0008922 ! has synaptic IO in region sublaminar l relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004224 @@ -23963,8 +23979,8 @@ is_a: CL:0004251 ! narrow field retinal amacrine cell is_a: CL:4030028 ! glycinergic amacrine cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004225 @@ -23975,8 +23991,8 @@ is_a: CL:0004251 ! narrow field retinal amacrine cell relationship: RO:0013001 UBERON:0008922 ! has synaptic IO in region sublaminar layer S1 relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004226 @@ -23989,8 +24005,8 @@ intersection_of: bearer_of PATO:0070063 ! monostratified dendrite cell morpholog relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004227 @@ -24002,8 +24018,8 @@ is_a: CL:0004251 ! narrow field retinal amacrine cell is_a: CL:4030028 ! glycinergic amacrine cell relationship: RO:0013001 UBERON:0009738 ! has synaptic IO in region border of sublaminar layers S1 and S2 relationship: RO:0013001 UBERON:0009739 ! has synaptic IO in region border of sublaminar layers S3 and S4 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004228 @@ -24015,8 +24031,8 @@ relationship: RO:0013001 UBERON:0008922 ! has synaptic IO in region sublaminar l relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004229 @@ -24027,8 +24043,8 @@ is_a: CL:0004250 ! bistratified retinal amacrine cell is_a: CL:0004251 ! narrow field retinal amacrine cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0009731 ! has synaptic IO in region sublaminar layers S3 or S4 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004230 @@ -24041,8 +24057,8 @@ relationship: RO:0013001 UBERON:0008922 ! has synaptic IO in region sublaminar l relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 relationship: RO:0013001 UBERON:0009738 ! has synaptic IO in region border of sublaminar layers S1 and S2 relationship: RO:0013001 UBERON:0009852 ! has synaptic IO in region border of sublaminar layers S2 and S3 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004231 @@ -24053,8 +24069,8 @@ is_a: CL:0004251 ! narrow field retinal amacrine cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004232 @@ -24065,10 +24081,10 @@ subset: cellxgene_subset subset: human_reference_atlas is_a: CL:0000108 ! cholinergic neuron is_a: CL:4030027 ! GABAergic amacrine cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0004233 @@ -24080,8 +24096,8 @@ is_a: CL:0004252 ! medium field retinal amacrine cell is_a: CL:4030028 ! glycinergic amacrine cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0009731 ! has synaptic IO in region sublaminar layers S3 or S4 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004234 @@ -24091,8 +24107,8 @@ def: "An amacrine cell with a medium dendritic field and post-synaptic terminals is_a: CL:0004252 ! medium field retinal amacrine cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0009731 ! has synaptic IO in region sublaminar layers S3 or S4 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004235 @@ -24103,8 +24119,8 @@ is_a: CL:0004252 ! medium field retinal amacrine cell is_a: CL:4030027 ! GABAergic amacrine cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004236 @@ -24116,8 +24132,8 @@ is_a: CL:4030027 ! GABAergic amacrine cell relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004237 @@ -24130,8 +24146,8 @@ relationship: RO:0013001 UBERON:0008922 ! has synaptic IO in region sublaminar l relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004238 @@ -24142,8 +24158,8 @@ is_a: CL:0004250 ! bistratified retinal amacrine cell is_a: CL:0004252 ! medium field retinal amacrine cell relationship: RO:0013001 UBERON:0009738 ! has synaptic IO in region border of sublaminar layers S1 and S2 relationship: RO:0013001 UBERON:0009739 ! has synaptic IO in region border of sublaminar layers S3 and S4 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004239 @@ -24155,8 +24171,8 @@ is_a: CL:0004252 ! medium field retinal amacrine cell relationship: RO:0013001 UBERON:0008922 ! has synaptic IO in region sublaminar layer S1 relationship: RO:0013001 UBERON:0008923 ! has synaptic IO in region sublaminar layer S2 relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004240 @@ -24165,8 +24181,8 @@ namespace: cell def: "An amacrine cell with a wide dendritic field, dendrites in S1, and post-synaptic terminals in S1." [PMID:9620701] is_a: CL:0004253 ! wide field retinal amacrine cell relationship: RO:0013001 UBERON:0008922 ! has synaptic IO in region sublaminar layer S1 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004241 @@ -24175,8 +24191,8 @@ namespace: cell def: "An amacrine cell with a wide dendritic field, dendrites in S2, and post-synaptic terminals in S1." [PMID:9620701] is_a: CL:0004253 ! wide field retinal amacrine cell relationship: RO:0013001 UBERON:0008922 ! has synaptic IO in region sublaminar layer S1 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004242 @@ -24185,8 +24201,8 @@ namespace: cell def: "An amacrine cell with a wide dendritic field, dendrites in S3, and post-synaptic terminals in S3. Dendrites of this cell type are straight and minimally branched." [PMID:9620701] is_a: CL:0004253 ! wide field retinal amacrine cell relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004243 @@ -24195,8 +24211,8 @@ namespace: cell def: "An amacrine cell with a wild dendritic field, dendrites in S3, and post-synaptic terminals in S3. Dendrites have spikes, cross over each other, and cover a larger volume than dendrties of W3-1 retinal amacrine cells." [PMID:9620701] is_a: CL:0004253 ! wide field retinal amacrine cell relationship: RO:0013001 UBERON:0008924 ! has synaptic IO in region sublaminar layer S3 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004244 @@ -24205,8 +24221,8 @@ namespace: cell def: "An amacrine cell with a wide dendritic field, dendrites in S4, and post-synaptic terminals in S4." [PMID:9620701] is_a: CL:0004253 ! wide field retinal amacrine cell relationship: RO:0013001 UBERON:0008925 ! has synaptic IO in region sublaminar layer S4 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004245 @@ -24217,8 +24233,8 @@ is_a: CL:0000850 ! serotonergic neuron is_a: CL:0004253 ! wide field retinal amacrine cell is_a: CL:4030027 ! GABAergic amacrine cell relationship: RO:0013001 UBERON:0008926 ! has synaptic IO in region sublaminar layer S5 -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004246 @@ -24230,8 +24246,8 @@ intersection_of: CL:0000540 ! neuron intersection_of: bearer_of PATO:0070063 ! monostratified dendrite cell morphology intersection_of: RO:0002100 UBERON:0001017 ! has soma location central nervous system relationship: bearer_of PATO:0070063 ! monostratified dendrite cell morphology -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004247 @@ -24242,7 +24258,7 @@ is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron intersection_of: bearer_of PATO:0070062 ! bistratified dendrite cell morphology relationship: bearer_of PATO:0070062 ! bistratified dendrite cell morphology -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string [Term] id: CL:0004250 @@ -24253,8 +24269,8 @@ is_a: CL:0000561 ! amacrine cell is_a: CL:0004247 ! bistratified cell intersection_of: CL:0000561 ! amacrine cell intersection_of: bearer_of PATO:0070062 ! bistratified dendrite cell morphology -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004251 @@ -24262,8 +24278,8 @@ name: narrow field retinal amacrine cell namespace: cell def: "An amicrine that has a narrow dendritic field." [PMID:9620701] is_a: CL:0000561 ! amacrine cell -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string [Term] id: CL:0004252 @@ -24272,9 +24288,9 @@ namespace: cell def: "An amicrine that has a medium dendritic field." [PMID:9620701] subset: human_reference_atlas is_a: CL:0000561 ! amacrine cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0004253 @@ -24283,9 +24299,9 @@ namespace: cell def: "An amicrine that has a wide dendritic field." [PMID:9620701] subset: human_reference_atlas is_a: CL:0000561 ! amacrine cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-5260-9315" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0005000 @@ -24304,7 +24320,7 @@ def: "A non-terminally differentiated cell that originates from the neural crest comment: Derived from UBERON:0002342 neural crest. is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0011026 ! progenitor cell -relationship: develops_from CL:0000333 ! migratory neural crest cell +relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell [Term] id: CL:0005002 @@ -24312,7 +24328,7 @@ name: xanthoblast def: "A non-terminally differentiated cell that differentiates into a xanthophore." [CL:CVS] is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0011026 ! progenitor cell -relationship: develops_from CL:0000333 ! migratory neural crest cell +relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell [Term] id: CL:0005003 @@ -24320,7 +24336,7 @@ name: leucoblast def: "A non-terminally differentiated cell that originates from the neural crest and differentiates into a leucophore." [CL:CVS] is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0011026 ! progenitor cell -relationship: develops_from CL:0000333 ! migratory neural crest cell +relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell [Term] id: CL:0005004 @@ -24328,7 +24344,7 @@ name: pigment erythroblast def: "A non-terminally differentiated cell that originates from the neural crest and differentiates into an erythrophore." [CL:CVS] is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0011026 ! progenitor cell -relationship: develops_from CL:0000333 ! migratory neural crest cell +relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell [Term] id: CL:0005005 @@ -24336,7 +24352,7 @@ name: cyanoblast def: "A non-terminally differentiated cell that originates from the neural crest and differentiates into a cyanophore." [CL:CVS] is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0011026 ! progenitor cell -relationship: develops_from CL:0000333 ! migratory neural crest cell +relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell [Term] id: CL:0005006 @@ -24345,7 +24361,7 @@ def: "Specialized epithelial cells involved in the maintenance of osmotic homeos subset: cellxgene_subset subset: human_reference_atlas is_a: CL:0000066 ! epithelial cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0005007 @@ -24467,7 +24483,7 @@ is_a: CL:0005018 ! ghrelin secreting cell is_a: CL:0008024 ! pancreatic endocrine cell intersection_of: CL:0008024 ! pancreatic endocrine cell intersection_of: capable_of GO:0036321 ! ghrelin secretion -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0005020 @@ -24479,7 +24495,7 @@ is_a: CL:4033054 ! perivascular cell intersection_of: CL:0000048 ! multi fate stem cell intersection_of: adjacent_to UBERON:0004536 ! lymph vasculature relationship: adjacent_to UBERON:0004536 ! lymph vasculature -relationship: dc-contributor https://orcid.org/0000-0002-2244-7917 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2244-7917 creation_date: 2012-01-12T04:44:34Z [Term] @@ -24489,7 +24505,7 @@ def: "Mesenchymal derived lymphatic progenitor cells that give rise to the super subset: cellxgene_subset is_a: CL:0000134 ! mesenchymal stem cell is_a: CL:0005020 ! lymphangioblast -relationship: dc-contributor https://orcid.org/0000-0002-2244-7917 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2244-7917 creation_date: 2012-01-12T05:01:22Z [Term] @@ -24502,7 +24518,7 @@ is_a: CL:0005020 {is_inferred="true"} ! lymphangioblast intersection_of: CL:0005020 ! lymphangioblast intersection_of: adjacent_to UBERON:0001638 ! vein relationship: adjacent_to UBERON:0001638 ! vein -relationship: dc-contributor https://orcid.org/0000-0002-2244-7917 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2244-7917 creation_date: 2012-01-12T05:21:09Z [Term] @@ -24553,9 +24569,9 @@ def: "Skeletogenic cell that has the potential to develop into an ameloblast. Lo comment: unsure of neural crest contribution. In VSAO we have develops_from CL:0000008 is_a: CL:0000055 ! non-terminally differentiated cell relationship: adjacent_to UBERON:0001763 ! odontogenic papilla -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 -relationship: develops_from CL:0002077 ! ecto-epithelial cell relationship: part_of UBERON:0005176 ! tooth enamel organ +relationship: RO:0002202 CL:0002077 ! develops from ecto-epithelial cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-15T01:27:01Z [Term] @@ -24565,7 +24581,7 @@ def: "Cell that has the potential to form a skeletal cell type (e.g. cells in pe comment: Needs logical definition. Should be capable_of skeletal system morphogenesis? or skeletal tissue development? needs to be added to GO. NOTES:a cell type of the early embryo (see also: mesenchymal cells) that will give rise to mineralized connective tissue. Scleroblasts can differentiate into osteoblasts (bone-forming cells), chondroblasts (cartilage-forming cells), odontoblasts (dentin-forming cells), ameloblasts (enamel-forming cells). The mesenchymal cells developing into osteoblasts and chondroblasts are derived from the mesoderm. Those developing into odontoblasts are neural crest cells. Those developing into ameloblasts are derived from the ectoderm. (http://www.copewithcytokines.de/cope.cgi?key=scleroblasts) synonym: "scleroblast" EXACT [GO_REF:0000034] is_a: CL:0000000 ! cell -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-15T02:51:27Z [Term] @@ -24573,8 +24589,8 @@ id: CL:0007002 name: precementoblast def: "Skeletogenic cell that has the potential to develop into a cementoblast." [GO_REF:0000034] is_a: CL:0000055 ! non-terminally differentiated cell -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 relationship: part_of UBERON:0005176 ! tooth enamel organ +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-15T04:37:13Z [Term] @@ -24583,9 +24599,9 @@ name: preodontoblast def: "Skeletogenic cell that has the potential to form an odontoblast, deposits predentine, and arises from a cranial neural crest cell." [GO_REF:0000034] is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0011026 ! progenitor cell -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 -relationship: develops_from CL:0000008 ! migratory cranial neural crest cell relationship: part_of UBERON:0005176 ! tooth enamel organ +relationship: RO:0002202 CL:0000008 ! develops from migratory cranial neural crest cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-15T05:15:11Z [Term] @@ -24593,9 +24609,9 @@ id: CL:0007004 name: premigratory neural crest cell def: "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells." [UBERONREF:0000002] is_a: CL:0011012 ! neural crest cell -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 -relationship: develops_from CL:0000133 ! neurectodermal cell relationship: part_of UBERON:0002342 ! neural crest +relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-27T08:27:35Z [Term] @@ -24604,9 +24620,9 @@ name: notochordal cell def: "Cell that is part of the notochord." [GO_REF:0000034] comment: NOTE: TO DO, notochord development still needs work. is_a: CL:0000000 ! cell -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 -relationship: develops_from CL:0007006 ! chordamesodermal cell relationship: part_of UBERON:0002328 ! notochord +relationship: RO:0002202 CL:0007006 ! develops from chordamesodermal cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-27T08:47:31Z [Term] @@ -24615,8 +24631,8 @@ name: chordamesodermal cell def: "Mesodermal cell that is axially located and gives rise to the cells of the notochord." [GO_REF:0000034] synonym: "axial mesodermal cell" EXACT [] is_a: CL:0000222 ! mesodermal cell -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 relationship: part_of UBERON:0004880 ! chordamesoderm +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-27T08:52:41Z [Term] @@ -24624,7 +24640,7 @@ id: CL:0007007 name: notochordal sheath cell def: "Notochordal cell that is part of the outer epithelium of the notochord and surrounds the vacuolated notochord cells." [CL:MAH] is_a: CL:0007005 ! notochordal cell -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-27T09:26:37Z [Term] @@ -24634,7 +24650,7 @@ def: "Notochordal cell that is inner portion of the notochord and becomes vacuol synonym: "chordablast" EXACT [GO_REF:0000034] synonym: "chordoblast" EXACT [PMID:14574572] is_a: CL:0007005 ! notochordal cell -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-27T09:29:30Z [Term] @@ -24642,7 +24658,7 @@ id: CL:0007009 name: prechondroblast def: "Skeletogenic cell that has the potential to develop into a chondroblast; and arises from neural crest, meseosdermal and notochordal and connective tissue cells." [GO_REF:0000034] is_a: CL:0000055 ! non-terminally differentiated cell -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-27T10:44:01Z [Term] @@ -24655,10 +24671,10 @@ is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0001035 ! bone cell is_a: CL:0002320 ! connective tissue cell is_a: CL:0011026 ! progenitor cell -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 -relationship: develops_from CL:0000222 ! mesodermal cell -relationship: develops_from CL:0000333 ! migratory neural crest cell relationship: part_of UBERON:0008883 ! osteoid +relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell +relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-27T10:57:21Z [Term] @@ -24670,10 +24686,10 @@ is_a: CL:0000029 ! neural crest derived neuron is_a: CL:0000107 ! autonomic neuron intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0002005 ! has soma location enteric nervous system -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 -relationship: develops_from CL:0002607 ! migratory enteric neural crest cell relationship: part_of UBERON:0002005 ! enteric nervous system relationship: RO:0002100 UBERON:0002005 ! has soma location enteric nervous system +relationship: RO:0002202 CL:0002607 ! develops from migratory enteric neural crest cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-28T08:20:31Z [Term] @@ -24694,7 +24710,7 @@ name: obsolete cell line cell def: "OBSOLETE: A cultured cell that has been passaged at least one time in culture." [ReO:mhb] comment: Obsoleted in July 2013 and replaced by the CLO 'cell line cell' class, as a result of CLO-OBI-CL alignment efforts.\n\nCovers cells actively being cultured or stored in a quiescent state for future use. synonym: "passaged cultured cell" EXACT [] -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 is_obsolete: true replaced_by: CLO:0000001 creation_date: 2012-11-28T11:54:59Z @@ -24706,7 +24722,7 @@ def: "OBSOLETE: A cell line cell that is expected to be capable of replicating a comment: Obsoleted in July 2013 and replaced by the CLO 'mortal cell line cell' class, as a result of CLO-OBI-CL alignment efforts.\n\nCovers cells actively being cultured or stored in a quiescent state for future use. synonym: "finite cell line cell" EXACT [] synonym: "primary cell line cell" RELATED [] -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 is_obsolete: true replaced_by: CLO:0000018 creation_date: 2012-11-28T11:56:20Z @@ -24717,8 +24733,8 @@ name: adaxial cell def: "Muscle precursor cell that is adjacent to the notochord and part of the presomitic mesoderm." [PMID:8951054] comment: In teleosts, adaxial cells give rise to slow muscle myoblasts. is_a: CL:0000680 ! muscle precursor cell -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 relationship: part_of UBERON:0003059 ! presomitic mesoderm +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-12-30T12:43:15Z [Term] @@ -24727,9 +24743,9 @@ name: Stiftchenzellen def: "An epidermal cell with apical microvilli or a single apical projection have synaptic associations with nerve fibres in the epidermis." [PMID:1087183] comment: Taxon specificity not yet fully known, but are known in anuran larvae but not in adults. is_a: CL:0000206 ! chemoreceptor cell -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 relationship: has_part GO:0005902 ! microvillus relationship: part_of UBERON:0001003 ! skin epidermis +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 [Term] id: CL:0007018 @@ -24738,22 +24754,22 @@ def: "Ciliated cell of the embryonic epidermis and functions in embryonic moveme comment: Taxon specificity not clear -present in embryonic anurans. is_a: CL:0000064 ! ciliated cell is_a: CL:0002321 ! embryonic cell (metazoa) -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 relationship: part_of UBERON:0001003 ! skin epidermis +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 [Term] id: CL:0007019 name: epidermal mucus secreting cell comment: taxon specificity not clear. Appears in early larval stages of anurans and persists after metamorphosis. is_a: CL:0000319 ! mucus secreting cell -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 [Term] id: CL:0007020 name: bottle cell def: "Characteristic early embryonic cell with a bottle or flask shape that is first to migrate inwards at the blastopore during gastrulation in amphibians." [PMID:3197630] is_a: CL:0000007 ! early embryonic cell (metazoa) -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 [Term] id: CL:0007021 @@ -24764,8 +24780,8 @@ synonym: "club cell" RELATED [https://github.com/obophenotype/cell-ontology/issu synonym: "club cell (zebrafish)" EXACT [https://github.com/obophenotype/cell-ontology/issues/583] is_a: CL:0000151 ! secretory cell is_a: CL:0000473 ! defensive cell -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 relationship: part_of UBERON:0001003 ! skin epidermis +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 [Term] id: CL:0007022 @@ -24773,16 +24789,16 @@ name: micropylar cell def: "A specialized pore forming cell of the follicle, located adjacent to the animal pole of the oocyte. The micropylar cell makes the single micropyle (pore) through the chorion through which the sperm fertilizes the egg." [PMID:18582455, ZFA:0005239] synonym: "plug cell" EXACT [] is_a: CL:0000000 ! cell -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 relationship: part_of UBERON:0001305 ! ovarian follicle +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 [Term] id: CL:0007023 name: flask cell def: "Epidermal cell rich in mitochondria. In amphibians, appears during metamorphosis." [DOI:10.1007/BF00717048] is_a: CL:0000000 ! cell -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 relationship: part_of UBERON:0001003 ! skin epidermis +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 [Term] id: CL:0008000 @@ -24810,7 +24826,7 @@ intersection_of: bearer_of PATO:0001908 ! multinucleate intersection_of: bearer_of PATO:0002478 ! transversely striated intersection_of: has_part GO:0030017 ! sarcomere intersection_of: part_of UBERON:0001134 ! skeletal muscle tissue -relationship: develops_from CL:0000515 ! skeletal muscle myoblast +relationship: RO:0002202 CL:0000515 ! develops from skeletal muscle myoblast [Term] id: CL:0008003 @@ -24928,14 +24944,14 @@ def: "A motor neuron that is capable of directly inhibiting muscle contraction." comment: In vertebrates, all motor neurons are excitatory, but various types of inhibitory motor neurons exist in invertebrates. subset: cellxgene_subset is_a: CL:0000100 ! motor neuron -relationship: never_in_taxon NCBITaxon:7742 ! Vertebrata +property_value: RO:0002161 NCBITaxon:7742 [Term] id: CL:0008016 name: activated skeletal muscle satellite cell def: "A skeletal muscle satellite cell that has become mitotically active - typically following muscle damage." [PMID:21849021, PMID:23303905] is_a: CL:0000594 ! skeletal muscle satellite cell -relationship: develops_from CL:0008012 {comment="More accurately - transformation_of ?"} ! quiescent skeletal muscle satellite cell +relationship: RO:0002202 CL:0008012 {comment="More accurately - transformation_of ?"} ! develops from quiescent skeletal muscle satellite cell [Term] id: CL:0008017 @@ -24946,8 +24962,8 @@ synonym: "myogenic precursor cell" BROAD [PMID:23303905] is_a: CL:0000188 ! cell of skeletal muscle is_a: CL:0000515 ! skeletal muscle myoblast intersection_of: CL:0000056 ! myoblast -intersection_of: develops_into CL:0008002 ! skeletal muscle fiber intersection_of: part_of UBERON:0001134 ! skeletal muscle tissue +intersection_of: RO:0002203 CL:0008002 ! develops into skeletal muscle fiber [Term] id: CL:0008018 @@ -24955,8 +24971,8 @@ name: somatic muscle myoblast def: "A myoblast that is commited to developing into a somatic muscle." [] is_a: CL:0000056 ! myoblast intersection_of: CL:0000056 ! myoblast -intersection_of: develops_into CL:0008003 ! somatic muscle myotube -relationship: develops_into CL:0008003 ! somatic muscle myotube +intersection_of: RO:0002203 CL:0008003 ! develops into somatic muscle myotube +relationship: RO:0002203 CL:0008003 ! develops into somatic muscle myotube [Term] id: CL:0008019 @@ -24968,14 +24984,14 @@ synonym: "mesenchyme cell" EXACT [] is_a: CL:0000219 ! motile cell relationship: capable_of GO:0016477 ! cell migration relationship: part_of UBERON:0003104 ! mesenchyme -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0008020 name: skeletal muscle satellite myogenic cell def: "A skeletal muscle satellite cell that undergoes symmetric division to produce two adult skeleltal muscle myoblasts." [GOC:dos, PMID:23303905] is_a: CL:0000594 ! skeletal muscle satellite cell -relationship: develops_into CL:0008017 ! adult skeletal muscle myoblast +relationship: RO:0002203 CL:0008017 ! develops into adult skeletal muscle myoblast [Term] id: CL:0008021 @@ -25012,7 +25028,7 @@ is_a: CL:0000083 ! epithelial cell of pancreas is_a: CL:0000164 ! enteroendocrine cell intersection_of: CL:0000163 ! endocrine cell intersection_of: part_of UBERON:0001264 ! pancreas -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0008025 @@ -25039,7 +25055,7 @@ id: CL:0008027 name: rod bipolar cell (sensu Mus) def: "A bipolar neuron found in the retina that is synapsed by rod photoreceptor cells. These neurons have axons that arborize and synapse to targets in inner plexiform layers 4 and 5 and depolarize in response to light." [] is_a: CL:0000751 ! rod bipolar cell -relationship: dc-contributor https://orcid.org/0000-0002-7073-9172 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2017-06-29T11:05:22Z [Term] @@ -25049,15 +25065,15 @@ is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron intersection_of: capable_of_part_of GO:0007601 ! visual perception relationship: capable_of_part_of GO:0007601 ! visual perception -relationship: dc-contributor https://orcid.org/0000-0002-7073-9172 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-09T19:12:36Z [Term] id: CL:0008029 name: obsolete inhibitory neuron comment: Consider GABAergic neuron or inhibitory interneuron instead. Do note that not all GABAergic neurons are inhibitory (see PMID:12209121) and replacing inhibitory neuron with GABAergic neuron should be done with caution. -relationship: dc-contributor https://orcid.org/0000-0002-7073-9172 relationship: term_tracker_item https://github.com/obophenotype/cell-ontology/issues/1540 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 is_obsolete: true creation_date: 2017-07-12T11:10:52Z @@ -25065,8 +25081,8 @@ creation_date: 2017-07-12T11:10:52Z id: CL:0008030 name: obsolete excitatory neuron comment: Consider using glutamatergic neuron instead. Do note that not all glutamatergic neurons are excitatory and replacing excitatory neuron with glutamatergic neuron should be done with caution. -relationship: dc-contributor https://orcid.org/0000-0002-7073-9172 relationship: term_tracker_item https://github.com/obophenotype/cell-ontology/issues/1540 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 is_obsolete: true creation_date: 2017-07-12T11:11:06Z @@ -25088,8 +25104,8 @@ def: "A GABAergic interneuron in human cortical layer 1 that has large rosehip-s comment: A rosehip cell has been shown to have an immunohistochemical profile GAD1+CCK+, CNR1–SST–CALB2–PVALB– that matches a single transcriptomically defined cell type whose specific molecular marker signature is not seen in mouse cortex. {xref="doi:10.1038/s41593-018-0205-2"} is_a: CL:0000255 ! eukaryotic cell is_a: CL:0010011 ! cerebral cortex GABAergic interneuron -relationship: only_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002100 UBERON:0005390 ! has soma location cortical layer I +relationship: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens relationship: RO:0002292 PR:000005110 ! expresses cholecystokinin relationship: RO:0002292 PR:000007785 ! expresses glutamate decarboxylase 1 relationship: RO:0002292 PR:000011467 ! expresses netrin-G1 @@ -25104,8 +25120,8 @@ is_a: CL:0000349 ! extraembryonic cell is_a: CL:2000078 ! placental pericyte intersection_of: CL:0000669 ! pericyte intersection_of: part_of UBERON:0002450 ! decidua -relationship: dc-contributor https://orcid.org/0000-0002-7073-9172 relationship: part_of UBERON:0002450 ! decidua +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2020-02-29T11:45:57Z [Term] @@ -25116,8 +25132,8 @@ subset: added_for_HCA subset: cellxgene_subset subset: human_reference_atlas is_a: CL:4033054 ! perivascular cell -relationship: dc-contributor https://orcid.org/0000-0002-7073-9172 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2020-02-29T17:33:55Z [Term] @@ -25127,8 +25143,8 @@ is_a: CL:0000359 ! vascular associated smooth muscle cell is_a: CL:0008034 ! mural cell intersection_of: CL:0000359 ! vascular associated smooth muscle cell intersection_of: part_of UBERON:0010523 ! microcirculatory vessel -relationship: dc-contributor https://orcid.org/0000-0002-7073-9172 relationship: part_of UBERON:0010523 ! microcirculatory vessel +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2020-02-29T17:37:00Z [Term] @@ -25141,8 +25157,8 @@ subset: human_reference_atlas synonym: "EVT" EXACT [PMID:31049600] synonym: "extravillous cytotrophloblast" EXACT [] is_a: CL:0000351 ! trophoblast cell -relationship: dc-contributor https://orcid.org/0000-0002-7073-9172 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2020-03-02T08:45:06Z [Term] @@ -25162,8 +25178,8 @@ name: alpha motor neuron def: "A large, multipolar lower motor neuron of the brainstem and spinal cord that innervates the extrafusal muscle fibers of skeletal muscle and are directly responsible for initiating their contraction. While their cell bodies are in the CNS (in the anterior gray horn of the spinal cord), they are part of the somatic nervous system - a branch of the PNS." [DOI:10.1016/B978-0-12-801238-3.05364-2, Wikipedia:Alpha_motor_neuron&oldid=957148643] synonym: "alpha motoneuron" EXACT [] is_a: CL:0008039 ! lower motor neuron -relationship: dc-contributor https://orcid.org/0000-0002-7073-9172 relationship: RO:0002120 CL:0008046 ! synapsed to extrafusal muscle fiber +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2020-09-23T20:16:26Z [Term] @@ -25172,8 +25188,8 @@ name: lower motor neuron def: "The motor neurons of vertebrates that directly innervate skeletal muscles. They receive input from upper motor neurons." [Wikipedia:Lower_motor_neuron&oldid=952547294] xref: FMA:84632 is_a: CL:0005024 ! somatomotor neuron -relationship: dc-contributor https://orcid.org/0000-0002-7073-9172 -relationship: in_taxon NCBITaxon:7742 ! Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2020-09-23T20:22:07Z [Term] @@ -25184,8 +25200,8 @@ synonym: "myofibra extrafusalis" EXACT [] xref: TH:H3.03.00.0.00007 is_a: CL:0008002 ! skeletal muscle fiber disjoint_from: CL:0008047 ! intrafusal muscle fiber -relationship: dc-contributor https://orcid.org/0000-0002-7073-9172 -relationship: synapsed_by CL:0008038 ! alpha motor neuron +relationship: RO:0002103 CL:0008038 ! synapsed by alpha motor neuron +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2020-09-26T21:06:15Z [Term] @@ -25198,8 +25214,8 @@ is_a: CL:0002319 ! neural cell is_a: CL:0008002 ! skeletal muscle fiber intersection_of: CL:0008002 ! skeletal muscle fiber intersection_of: part_of UBERON:0003718 ! muscle spindle -relationship: dc-contributor https://orcid.org/0000-0002-7073-9172 relationship: part_of UBERON:0003718 ! muscle spindle +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2020-09-26T21:07:01Z [Term] @@ -25208,9 +25224,9 @@ name: upper motor neuron def: "A glutamatergic motor neuron with a soma in the brainstem or cerebral cortex. They do not synapse directly to muscles but rather to lower motor neurons, which do. They are the main controllers of voluntary movement." [Wikipedia:Upper_motor_neuron&oldid=943248837] is_a: CL:0000100 ! motor neuron is_a: CL:0000679 ! glutamatergic neuron -relationship: dc-contributor https://orcid.org/0000-0002-7073-9172 -relationship: in_taxon NCBITaxon:33208 ! Metazoa relationship: RO:0002120 CL:0008039 ! synapsed to lower motor neuron +relationship: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2020-09-28T09:41:48Z [Term] @@ -25221,11 +25237,11 @@ synonym: "pyramidal cell of Betz" EXACT [] is_a: CL:2000049 ! primary motor cortex pyramidal cell is_a: CL:4023041 ! L5 extratelencephalic projecting glutamatergic cortical neuron relationship: bearer_of PATO:0070017 ! standard pyramidal morphology -relationship: dc-contributor https://orcid.org/0000-0002-7073-9172 -relationship: present_in_taxon NCBITaxon:9443 ! Primates relationship: RO:0002100 UBERON:0022315 ! has soma location primary motor cortex layer 5 relationship: RO:0002101 UBERON:0002707 ! fasciculates with corticospinal tract -property_value: depiction "https://en.wikipedia.org/w/index.php?title=Betz_cell&oldid=977472330#/media/File:GolgiStainedPyramidalCell.jpg" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: http://xmlns.com/foaf/0.1/depiction "https://en.wikipedia.org/w/index.php?title=Betz_cell&oldid=977472330#/media/File:GolgiStainedPyramidalCell.jpg" xsd:string +property_value: RO:0002175 NCBITaxon:9443 creation_date: 2020-09-28T09:52:58Z [Term] @@ -25263,9 +25279,9 @@ def: "Any cell in the midgut (middle subdivision of a digestive tract) of an ins xref: GOC:pr xref: http://en.wikipedia.org/wiki/Insect#Midgut is_a: CL:0000000 ! cell -relationship: in_taxon NCBITaxon:50557 ! Insecta relationship: part_of UBERON:0001555 ! digestive tract relationship: part_of UBERON:0002548 ! larva +relationship: RO:0002162 NCBITaxon:50557 ! in taxon Insecta property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/710" xsd:string [Term] @@ -25300,7 +25316,7 @@ is_a: CL:1001516 ! intestinal enteroendocrine cell is_a: CL:1001598 ! small intestine glandular cell intersection_of: CL:0000164 ! enteroendocrine cell intersection_of: part_of UBERON:0002108 ! small intestine -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009007 @@ -25312,8 +25328,8 @@ synonym: "small intestine lamina propria resident macrophage" EXACT [] is_a: CL:0000865 ! gastrointestinal tract (lamina propria) macrophage intersection_of: CL:0000885 ! gut-associated lymphoid tissue macrophage intersection_of: part_of UBERON:0001238 ! lamina propria of small intestine -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0001238 ! lamina propria of small intestine +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009008 @@ -25325,8 +25341,8 @@ synonym: "macrophage of large intestine" BROAD [] is_a: CL:0000865 ! gastrointestinal tract (lamina propria) macrophage intersection_of: CL:0000885 ! gut-associated lymphoid tissue macrophage intersection_of: part_of UBERON:0011189 ! lamina propria of large intestine -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0011189 ! lamina propria of large intestine +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009009 @@ -25342,8 +25358,8 @@ is_a: CL:0000510 ! paneth cell is_a: CL:1001588 ! colon glandular cell intersection_of: CL:0000510 ! paneth cell intersection_of: part_of UBERON:0000397 ! colonic epithelium -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0009010 @@ -25356,8 +25372,8 @@ synonym: "transient amplifying cell" EXACT [] synonym: "transit amplifying progenitor cell" EXACT [PMID:30827895] synonym: "transit-amplifying cell" EXACT [] is_a: CL:0000000 ! cell -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 -relationship: develops_from CL:0000034 ! stem cell +relationship: RO:0002202 CL:0000034 ! develops from stem cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009011 @@ -25375,10 +25391,10 @@ synonym: "transit-amplifying cell of colon" EXACT [] is_a: CL:0009010 ! transit amplifying cell intersection_of: CL:0009010 ! transit amplifying cell intersection_of: part_of UBERON:0013485 ! crypt of Lieberkuhn of colon -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 -relationship: develops_from CL:0002250 ! intestinal crypt stem cell relationship: part_of UBERON:0013485 ! crypt of Lieberkuhn of colon -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0002250 ! develops from intestinal crypt stem cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0009012 @@ -25394,9 +25410,9 @@ synonym: "transit-amplifying cell of small intestine" EXACT [] is_a: CL:0009010 ! transit amplifying cell intersection_of: CL:0009010 ! transit amplifying cell intersection_of: part_of UBERON:0001241 ! crypt of Lieberkuhn of small intestine -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 -relationship: develops_from CL:0002250 ! intestinal crypt stem cell relationship: part_of UBERON:0001241 ! crypt of Lieberkuhn of small intestine +relationship: RO:0002202 CL:0002250 ! develops from intestinal crypt stem cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009013 @@ -25406,9 +25422,9 @@ subset: added_for_HCA synonym: "fetal hepatobiliary hybrid progenitor cell" EXACT [] synonym: "HHyP cell" EXACT [] is_a: CL:0011026 ! progenitor cell -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 -relationship: in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:8410003 ! ductal plate +relationship: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009014 @@ -25420,8 +25436,8 @@ synonym: "small intestine Peyer's patch lymphocyte" NARROW [] is_a: CL:0000542 ! lymphocyte intersection_of: CL:0000542 ! lymphocyte intersection_of: part_of UBERON:0001211 ! Peyer's patch -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0001211 ! Peyer's patch +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009015 @@ -25431,8 +25447,8 @@ subset: location_grouping is_a: CL:0000442 ! follicular dendritic cell intersection_of: CL:0000442 ! follicular dendritic cell intersection_of: part_of UBERON:0001211 ! Peyer's patch -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0001211 ! Peyer's patch +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009016 @@ -25447,9 +25463,9 @@ is_a: CL:0002250 ! intestinal crypt stem cell is_a: CL:0002253 ! epithelial cell of large intestine intersection_of: CL:0002250 ! intestinal crypt stem cell intersection_of: part_of UBERON:0001984 ! crypt of Lieberkuhn of large intestine -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0001984 ! crypt of Lieberkuhn of large intestine -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0009017 @@ -25463,8 +25479,8 @@ is_a: CL:0002250 ! intestinal crypt stem cell is_a: CL:0002254 ! epithelial cell of small intestine intersection_of: CL:0002250 ! intestinal crypt stem cell intersection_of: part_of UBERON:0001241 ! crypt of Lieberkuhn of small intestine -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0001241 ! crypt of Lieberkuhn of small intestine +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009018 @@ -25477,9 +25493,9 @@ synonym: "lamina propria lymphocyte of large intestine" EXACT [] is_a: CL:0000542 ! lymphocyte intersection_of: CL:0000542 ! lymphocyte intersection_of: part_of UBERON:0011189 ! lamina propria of large intestine -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0011189 ! lamina propria of large intestine -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0009019 @@ -25491,8 +25507,8 @@ synonym: "cortical nephrogenic zone cell" EXACT [] is_a: CL:0002681 ! kidney cortical cell intersection_of: CL:0002681 ! kidney cortical cell intersection_of: part_of UBERON:0009871 ! nephrogenic zone -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0009871 ! nephrogenic zone +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009020 @@ -25506,7 +25522,7 @@ is_a: CL:0002203 ! brush cell of epithelium proper of large intestine is_a: CL:1000405 ! epithelial cell of appendix intersection_of: CL:0019032 ! intestinal tuft cell intersection_of: part_of UBERON:0001154 ! vermiform appendix -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009021 @@ -25516,8 +25532,8 @@ subset: location_grouping is_a: CL:0000499 ! stromal cell intersection_of: CL:0000499 ! stromal cell intersection_of: part_of UBERON:0011189 ! lamina propria of large intestine -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0011189 ! lamina propria of large intestine +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009022 @@ -25528,8 +25544,8 @@ subset: location_grouping is_a: CL:0000499 ! stromal cell intersection_of: CL:0000499 ! stromal cell intersection_of: part_of UBERON:0001238 ! lamina propria of small intestine -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0001238 ! lamina propria of small intestine +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009023 @@ -25542,8 +25558,8 @@ is_a: CL:0002419 ! mature T cell is_a: CL:0009014 ! Peyer's patch lymphocyte intersection_of: CL:0002419 ! mature T cell intersection_of: part_of UBERON:0003454 ! small intestine Peyer's patch -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0003454 ! small intestine Peyer's patch +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009024 @@ -25554,7 +25570,7 @@ is_a: CL:0000077 ! mesothelial cell is_a: CL:0002254 ! epithelial cell of small intestine intersection_of: CL:0000077 ! mesothelial cell intersection_of: part_of UBERON:0002108 ! small intestine -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009025 @@ -25566,7 +25582,7 @@ is_a: CL:0000077 ! mesothelial cell is_a: CL:0011108 ! colon epithelial cell intersection_of: CL:0000077 ! mesothelial cell intersection_of: part_of UBERON:0001155 ! colon -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009026 @@ -25580,7 +25596,7 @@ is_a: CL:0000584 ! enterocyte is_a: CL:1000405 ! epithelial cell of appendix intersection_of: CL:0000584 ! enterocyte intersection_of: part_of UBERON:0001154 ! vermiform appendix -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009027 @@ -25593,9 +25609,9 @@ synonym: "transit amplifying cell of vermiform appendix" EXACT [] is_a: CL:0009010 ! transit amplifying cell intersection_of: CL:0009010 ! transit amplifying cell intersection_of: part_of UBERON:0013486 ! crypt of Lieberkuhn of appendix -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 -relationship: develops_from CL:0009028 ! intestinal crypt stem cell of appendix relationship: part_of UBERON:0013486 ! crypt of Lieberkuhn of appendix +relationship: RO:0002202 CL:0009028 ! develops from intestinal crypt stem cell of appendix +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009028 @@ -25611,8 +25627,8 @@ is_a: CL:0009016 ! intestinal crypt stem cell of large intestine is_a: CL:1000405 ! epithelial cell of appendix intersection_of: CL:0002250 ! intestinal crypt stem cell intersection_of: part_of UBERON:0013486 ! crypt of Lieberkuhn of appendix -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0013486 ! crypt of Lieberkuhn of appendix +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009029 @@ -25626,7 +25642,7 @@ is_a: CL:0000077 ! mesothelial cell is_a: CL:1000405 ! epithelial cell of appendix intersection_of: CL:0000077 ! mesothelial cell intersection_of: part_of UBERON:0001154 ! vermiform appendix -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009030 @@ -25640,7 +25656,7 @@ is_a: CL:1001516 ! intestinal enteroendocrine cell is_a: CL:1001585 ! appendix glandular cell intersection_of: CL:1001516 ! intestinal enteroendocrine cell intersection_of: part_of UBERON:0001154 ! vermiform appendix -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009031 @@ -25654,8 +25670,8 @@ synonym: "T cell of vermiform appendix" EXACT [] is_a: CL:0000084 ! T cell intersection_of: CL:0000084 ! T cell intersection_of: part_of UBERON:0001154 ! vermiform appendix -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0001154 ! vermiform appendix +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009032 @@ -25669,8 +25685,8 @@ synonym: "B cell of vermiform appendix" EXACT [] is_a: CL:0000236 ! B cell intersection_of: CL:0000236 ! B cell intersection_of: part_of UBERON:0001154 ! vermiform appendix -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0001154 ! vermiform appendix +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009033 @@ -25684,8 +25700,8 @@ synonym: "plasma cell of vermiform appendix" EXACT [] is_a: CL:0000786 ! plasma cell intersection_of: CL:0000786 ! plasma cell intersection_of: part_of UBERON:0001154 ! vermiform appendix -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0001154 ! vermiform appendix +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009034 @@ -25699,8 +25715,8 @@ synonym: "dendritic cell of vermiform appendix" EXACT [] is_a: CL:0000451 ! dendritic cell intersection_of: CL:0000451 ! dendritic cell intersection_of: part_of UBERON:0001154 ! vermiform appendix -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0001154 ! vermiform appendix +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009035 @@ -25713,8 +25729,8 @@ is_a: CL:0009021 ! stromal cell of lamina propria of large intestine intersection_of: CL:0000499 ! stromal cell intersection_of: part_of UBERON:0001154 ! vermiform appendix intersection_of: part_of UBERON:0011189 ! lamina propria of large intestine -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0001154 ! vermiform appendix +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009036 @@ -25728,8 +25744,8 @@ synonym: "macrophage of vermiform appendix" EXACT [] is_a: CL:0000235 ! macrophage intersection_of: CL:0000235 ! macrophage intersection_of: part_of UBERON:0001154 ! vermiform appendix -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0001154 ! vermiform appendix +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009037 @@ -25742,8 +25758,8 @@ synonym: "mantle zone B cell of lymph node" EXACT [] is_a: CL:0000236 ! B cell intersection_of: CL:0000236 ! B cell intersection_of: part_of UBERON:0010420 ! lymph node germinal center mantle zone -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0010420 ! lymph node germinal center mantle zone +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009038 @@ -25756,8 +25772,8 @@ synonym: "macrophage of colon" EXACT [] is_a: CL:0000235 ! macrophage intersection_of: CL:0000235 ! macrophage intersection_of: part_of UBERON:0001155 ! colon -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0001155 ! colon +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009039 @@ -25770,7 +25786,7 @@ is_a: CL:1000320 ! large intestine goblet cell is_a: CL:1001588 ! colon glandular cell intersection_of: CL:0000160 ! goblet cell intersection_of: part_of UBERON:0001155 ! colon -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009040 @@ -25781,8 +25797,8 @@ synonym: "stromal cell of colon lamina propria" EXACT [] is_a: CL:0009021 ! stromal cell of lamina propria of large intestine intersection_of: CL:0000499 ! stromal cell intersection_of: part_of UBERON:0007177 ! lamina propria of mucosa of colon -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0007177 ! lamina propria of mucosa of colon +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009041 @@ -25795,7 +25811,7 @@ is_a: CL:0002203 ! brush cell of epithelium proper of large intestine is_a: CL:0011108 ! colon epithelial cell intersection_of: CL:0019032 ! intestinal tuft cell intersection_of: part_of UBERON:0001155 ! colon -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009042 @@ -25808,7 +25824,7 @@ is_a: CL:1001516 ! intestinal enteroendocrine cell is_a: CL:1001588 ! colon glandular cell intersection_of: CL:0000164 ! enteroendocrine cell intersection_of: part_of UBERON:0001155 ! colon -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009043 @@ -25820,7 +25836,7 @@ is_a: CL:0002250 ! intestinal crypt stem cell is_a: CL:0011108 ! colon epithelial cell intersection_of: CL:0002250 ! intestinal crypt stem cell intersection_of: part_of UBERON:0001155 ! colon -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009044 @@ -25837,8 +25853,8 @@ synonym: "small intestine lamina propria lymphocyte" EXACT [] is_a: CL:0000542 ! lymphocyte intersection_of: CL:0000542 ! lymphocyte intersection_of: part_of UBERON:0001238 ! lamina propria of small intestine -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0001238 ! lamina propria of small intestine +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009045 @@ -25849,8 +25865,8 @@ subset: location_grouping is_a: CL:0000236 ! B cell intersection_of: CL:0000236 ! B cell intersection_of: part_of UBERON:0009744 ! lymph node medullary sinus -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0009744 ! lymph node medullary sinus +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009046 @@ -25861,8 +25877,8 @@ subset: location_grouping is_a: CL:0000084 ! T cell intersection_of: CL:0000084 ! T cell intersection_of: part_of UBERON:0009744 ! lymph node medullary sinus -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0009744 ! lymph node medullary sinus +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009047 @@ -25875,8 +25891,8 @@ synonym: "medullary sinus macrophage" BROAD [] is_a: CL:0000235 ! macrophage intersection_of: CL:0000235 ! macrophage intersection_of: part_of UBERON:0009744 ! lymph node medullary sinus -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0009744 ! lymph node medullary sinus +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009048 @@ -25888,8 +25904,8 @@ synonym: "macrophage of anorectum" EXACT [] is_a: CL:0000235 ! macrophage intersection_of: CL:0000235 ! macrophage intersection_of: part_of UBERON:8410050 ! anorectum -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:8410050 ! anorectum +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009049 @@ -25902,8 +25918,8 @@ is_a: CL:0008035 ! microcirculation associated smooth muscle cell is_a: CL:0019018 ! blood vessel smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:8410038 ! high endothelial venule of lymph node -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:8410038 ! high endothelial venule of lymph node +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009050 @@ -25914,8 +25930,8 @@ subset: location_grouping is_a: CL:0000236 ! B cell intersection_of: CL:0000236 ! B cell intersection_of: part_of UBERON:8410050 ! anorectum -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:8410050 ! anorectum +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009051 @@ -25926,8 +25942,8 @@ subset: location_grouping is_a: CL:0000084 ! T cell intersection_of: CL:0000084 ! T cell intersection_of: part_of UBERON:8410050 ! anorectum -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:8410050 ! anorectum +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009052 @@ -25938,8 +25954,8 @@ synonym: "anorectum smooth muscle cell" EXACT [] is_a: CL:1000279 ! smooth muscle cell of large intestine intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:8410050 ! anorectum -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:8410050 ! anorectum +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009053 @@ -25950,8 +25966,8 @@ is_a: CL:0009021 ! stromal cell of lamina propria of large intestine intersection_of: CL:0000499 ! stromal cell intersection_of: part_of UBERON:0011189 ! lamina propria of large intestine intersection_of: part_of UBERON:8410050 ! anorectum -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:8410050 ! anorectum +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009054 @@ -25962,8 +25978,8 @@ synonym: "M cell of anorectum" EXACT [] is_a: CL:1000360 ! microfold cell of epithelium proper of large intestine intersection_of: CL:0000682 ! M cell of gut intersection_of: part_of UBERON:8410050 ! anorectum -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:8410050 ! anorectum +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009055 @@ -25975,8 +25991,8 @@ is_a: CL:0000510 ! paneth cell is_a: CL:0002658 ! glandular cell of the large intestine intersection_of: CL:0000510 ! paneth cell intersection_of: part_of UBERON:8410050 ! anorectum -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:8410050 ! anorectum +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009056 @@ -25987,8 +26003,8 @@ synonym: "anorectum transit amplifying cell" EXACT [] is_a: CL:0009010 ! transit amplifying cell intersection_of: CL:0009010 ! transit amplifying cell intersection_of: part_of UBERON:8410050 ! anorectum -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:8410050 ! anorectum +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009057 @@ -25999,8 +26015,8 @@ synonym: "goblet cell of anorectum" EXACT [] is_a: CL:1000320 ! large intestine goblet cell intersection_of: CL:0000160 ! goblet cell intersection_of: part_of UBERON:8410050 ! anorectum -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:8410050 ! anorectum +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009058 @@ -26012,8 +26028,8 @@ is_a: CL:0000584 ! enterocyte is_a: CL:0002253 ! epithelial cell of large intestine intersection_of: CL:0000584 ! enterocyte intersection_of: part_of UBERON:8410050 ! anorectum -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:8410050 ! anorectum +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009059 @@ -26027,8 +26043,8 @@ synonym: "plasma cell of medullary sinus" BROAD [] is_a: CL:0000786 ! plasma cell intersection_of: CL:0000786 ! plasma cell intersection_of: part_of UBERON:0009744 ! lymph node medullary sinus -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0009744 ! lymph node medullary sinus +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009060 @@ -26040,8 +26056,8 @@ synonym: "marginal zone B cell" BROAD [] is_a: CL:0000785 ! mature B cell intersection_of: CL:0000785 ! mature B cell intersection_of: part_of UBERON:8410065 ! lymph node follicle marginal zone -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:8410065 ! lymph node follicle marginal zone +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009061 @@ -26053,8 +26069,8 @@ is_a: CL:0002250 ! intestinal crypt stem cell is_a: CL:0002253 ! epithelial cell of large intestine intersection_of: CL:0002250 ! intestinal crypt stem cell intersection_of: part_of UBERON:8410050 ! anorectum -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:8410050 ! anorectum +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009062 @@ -26067,8 +26083,8 @@ synonym: "T follicular helper cell of lymph node germinal center" EXACT [] is_a: CL:0002038 ! T follicular helper cell intersection_of: CL:0002038 ! T follicular helper cell intersection_of: part_of UBERON:0009039 ! lymph node germinal center -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0009039 ! lymph node germinal center +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009063 @@ -26080,8 +26096,8 @@ is_a: CL:0002658 ! glandular cell of the large intestine is_a: CL:1001516 ! intestinal enteroendocrine cell intersection_of: CL:0000164 ! enteroendocrine cell intersection_of: part_of UBERON:8410050 ! anorectum -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:8410050 ! anorectum +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009064 @@ -26094,8 +26110,8 @@ synonym: "T cell of lymph node paracortex" EXACT [] is_a: CL:0000084 ! T cell intersection_of: CL:0000084 ! T cell intersection_of: part_of UBERON:8410066 ! lymph node paracortex -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:8410066 ! lymph node paracortex +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009065 @@ -26106,8 +26122,8 @@ synonym: "anorectum tuft cell" EXACT [] is_a: CL:0002203 ! brush cell of epithelium proper of large intestine intersection_of: CL:0019032 ! intestinal tuft cell intersection_of: part_of UBERON:8410050 ! anorectum -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:8410050 ! anorectum +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009066 @@ -26120,8 +26136,8 @@ is_a: CL:0000240 ! stratified squamous epithelial cell is_a: CL:0002253 ! epithelial cell of large intestine intersection_of: CL:0000240 ! stratified squamous epithelial cell intersection_of: part_of UBERON:0000159 ! anal canal -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0000159 ! anal canal +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009067 @@ -26132,8 +26148,8 @@ synonym: "immature enterocyte" RELATED [https://orcid.org/0000-0001-9610-7627, P synonym: "vacuolated enterocyte" BROAD [] is_a: CL:0000584 ! enterocyte is_a: CL:0002254 ! epithelial cell of small intestine -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 -relationship: in_taxon NCBITaxon:40674 ! Mammalia +relationship: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0009068 @@ -26141,9 +26157,9 @@ name: CD8aa(I) thymocyte def: "An unconventional T lymphocyte population within the thymic medulla that is potentially a thymic resident population." [PMID:32079746] subset: human_reference_atlas is_a: CL:0000893 ! thymocyte -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0002124 ! medulla of thymus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0009069 @@ -26151,9 +26167,9 @@ name: CD8aa(II) thymocyte def: "An unconventional T lymphocyte population within the thymic medulla that expresses both alpha/beta and gamma/delta T cell signatures." [PMID:32079746] subset: human_reference_atlas is_a: CL:0000893 ! thymocyte -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0002124 ! medulla of thymus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0009070 @@ -26161,9 +26177,9 @@ name: corticomedullary thymic epithelial cell def: "A thymic epithelial cell located at the corticomedullary junction." [PMID:32079746, PMID:33597545] subset: human_reference_atlas is_a: CL:0002293 ! epithelial cell of thymus -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0003988 ! thymus corticomedullary boundary -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0009071 @@ -26171,9 +26187,9 @@ name: medullary thymic epithelial cell type 1 def: "A thymic medullary epithelial cell considered to be a pre-AIRE mTEC population." [PMID:24084687, PMID:32079746, PMID:33597545] subset: human_reference_atlas is_a: CL:0002365 ! medullary thymic epithelial cell -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0003846 ! thymus epithelium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0009072 @@ -26181,9 +26197,9 @@ name: medullary thymic epithelial cell type 2 def: "A thymic medullary epithelial cell that expresses AIRE or other canonical markers of mature mTECs like Fezf2." [PMID:17067941, PMID:24084687, PMID:32079746, PMID:33597545] subset: human_reference_atlas is_a: CL:0002365 ! medullary thymic epithelial cell -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0003846 ! thymus epithelium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0009073 @@ -26191,9 +26207,9 @@ name: medullary thymic epithelial cell type 3 def: "A thymic medullary epithelial cell considered to be a post-AIRE cell. This group of AIRE-mTECs is heterogeneous and also includes mTECs within Hassall's Corpuscles." [PMID:16121185, PMID:17067941, PMID:20861360, PMID:24084687, PMID:32079746, PMID:33597545] subset: human_reference_atlas is_a: CL:0002365 ! medullary thymic epithelial cell -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0003846 ! thymus epithelium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0009074 @@ -26202,9 +26218,9 @@ def: "A thymic medullary epithelial cell that expresses typical tuft cell marker subset: human_reference_atlas synonym: "thymic tuft cell" BROAD [] is_a: CL:0002365 ! medullary thymic epithelial cell -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0003846 ! thymus epithelium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0009075 @@ -26212,9 +26228,9 @@ name: myo-medullary thymic epithelial cell def: "A thymic medullary epithelial cell that expresses muscle-specific biomarkers." [PMID:32079746, PMID:33597545] subset: human_reference_atlas is_a: CL:0002365 ! medullary thymic epithelial cell -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0003846 ! thymus epithelium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0009076 @@ -26222,9 +26238,9 @@ name: neuro-medullary thymic epithelial cell def: "A thymic medullary epithelial cell that expresses neuroendocrine biomarkers." [PMID:32079746, PMID:33597545] subset: human_reference_atlas is_a: CL:0002365 ! medullary thymic epithelial cell -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0003846 ! thymus epithelium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0009077 @@ -26232,9 +26248,9 @@ name: subcapsular thymic epithelial cell def: "A thymic epithelial cell located within the subcapsular region of the thymus." [PMID:6209968] subset: human_reference_atlas is_a: CL:0002364 ! cortical thymic epithelial cell -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0006936 ! thymus subcapsular epithelium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0009078 @@ -26243,9 +26259,9 @@ def: "A fibroblast located in the thymic capsule." [PMID:32079746] subset: human_reference_atlas synonym: "thymic capsular fibroblast" EXACT [] is_a: CL:0000057 ! fibroblast -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0002122 ! capsule of thymus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0009079 @@ -26254,9 +26270,9 @@ def: "A fibroblast located between thymic lobules." [PMID:32079746] subset: human_reference_atlas synonym: "thymic interlobular fibroblast" EXACT [] is_a: CL:0000057 ! fibroblast -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0004791 ! thymus trabecula -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0009080 @@ -26271,8 +26287,8 @@ is_a: CL:0002254 ! epithelial cell of small intestine is_a: CL:0019032 ! intestinal tuft cell intersection_of: CL:0019032 ! intestinal tuft cell intersection_of: part_of UBERON:0002108 ! small intestine -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0009081 @@ -26281,9 +26297,9 @@ def: "The human equivalent of a DN2 thymocyte; typically contains two phases, in comment: There is growing evidence that molecular markers characterizing double negative thymocytes are different across species, especially in human versus mouse thymus. This term is restricted for use with human data. subset: human_reference_atlas is_a: CL:0002489 ! double negative thymocyte -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2021-11-25T09:26:32Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/date "2021-11-25T09:26:32Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0009082 @@ -26292,9 +26308,9 @@ def: "The human equivalent of a DN3 thymocyte; these thymocytes finish the proce comment: There is growing evidence that molecular markers characterizing double negative thymocytes are different across species, especially in human versus mouse thymus. This term is restricted for use with human data. subset: human_reference_atlas is_a: CL:0002489 ! double negative thymocyte -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2021-11-25T09:30:45Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/date "2021-11-25T09:30:45Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0009083 @@ -26303,9 +26319,9 @@ def: "The human equivalent of a DN4 thymocyte." [PMID:32304633] comment: There is growing evidence that molecular markers characterizing double negative thymocytes are different across species, especially in human versus mouse thymus. This term is restricted for use with human data. subset: human_reference_atlas is_a: CL:0002489 ! double negative thymocyte -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2021-11-25T09:32:13Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/date "2021-11-25T09:32:13Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0009084 @@ -26318,10 +26334,10 @@ xref: EFO:0010710 is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0002451 ! endometrial gland -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0002451 ! endometrial gland -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2021-11-30T16:13:30Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/date "2021-11-30T16:13:30Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0009085 @@ -26329,8 +26345,8 @@ name: colony forming unit – Hill cell def: "An adult endothelial progenitor cell characterised in vivo by homing to ischemic sites and paracrine support of angiogenesis. They may form discrete colonies." [WikipediaVersioned:Endothelial_progenitor_cell&oldid=1069930016#Colony_forming_unit_–_Hill] synonym: "CFU-Hill" EXACT [] is_a: CL:0002619 ! adult endothelial progenitor cell -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 -property_value: dcterms-date "2022-02-18T09:55:33Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/date "2022-02-18T09:55:33Z" xsd:dateTime [Term] id: CL:0009086 @@ -26342,10 +26358,10 @@ xref: EFO:0010667 is_a: CL:0000115 ! endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0003456 ! respiratory system lymphatic vessel -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0003529 ! respiratory system lymphatic vessel endothelium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2021-12-03T14:00:44Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/date "2021-12-03T14:00:44Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0009087 @@ -26354,16 +26370,16 @@ def: "An extravillous trophoblast that is polynuclear." [https://orcid.org/0000- synonym: "fused EVT" EXACT [] xref: EFO:0010712 is_a: CL:0008036 ! extravillous trophoblast -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 -property_value: dcterms-date "2021-12-03T14:37:32Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/date "2021-12-03T14:37:32Z" xsd:dateTime [Term] id: CL:0009088 name: circulating angiogenic cell def: "An adult endothelial progenitor cell characterised in vivo by homing to ischemic sites and paracrine support of angiogenesis. These cells do not form colonies." [WikipediaVersioned:Endothelial_progenitor_cell&oldid=1069930016#Circulating_angiogenic_cell] is_a: CL:0002619 ! adult endothelial progenitor cell -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 -property_value: dcterms-date "2022-02-18T10:12:57Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/date "2022-02-18T10:12:57Z" xsd:dateTime [Term] id: CL:0009089 @@ -26378,10 +26394,10 @@ xref: EFO:0010669 is_a: CL:0000669 ! pericyte intersection_of: CL:0000669 ! pericyte intersection_of: part_of UBERON:0002048 ! lung -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0002048 ! lung -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2021-12-03T17:13:33Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/date "2021-12-03T17:13:33Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0009090 @@ -26389,9 +26405,9 @@ name: endothelial colony forming cell def: "An adult endothelial progenitor cell that is resident of adult vasculature and capable of differentiating to regenerate endothelial cell populations. Endothelial colony forming cells are characterised in vivo by clonal proliferative status, de novo vessel formation, homing to ischemic sites and paracrine support of angiogenesis. These cells are phenotypically similar to endothelial cells." [http://orcid.org/0000-0002-0819-0473, PMID:33419165, WikipediaVersioned:Endothelial_colony_forming_cell&oldid=1068242094] synonym: "ECFC" EXACT [] is_a: CL:0002619 ! adult endothelial progenitor cell -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0004537 ! blood vasculature -property_value: dcterms-date "2022-02-18T10:15:32Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/date "2022-02-18T10:15:32Z" xsd:dateTime [Term] id: CL:0009091 @@ -26400,9 +26416,9 @@ def: "A stem cell found in the interstitial compartment of the neonatal testis; synonym: "stem Leydig cell" EXACT [] is_a: CL:0000034 ! stem cell is_a: CL:4030031 ! interstitial cell -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0005212 ! Leydig cell region of testis -property_value: dcterms-date "2022-02-18T14:09:25Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/date "2022-02-18T14:09:25Z" xsd:dateTime [Term] id: CL:0009092 @@ -26416,8 +26432,8 @@ is_a: CL:0000115 ! endothelial cell is_a: CL:0002577 ! placental epithelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0001987 ! placenta -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 -property_value: dcterms-date "2021-12-13T13:53:01Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/date "2021-12-13T13:53:01Z" xsd:dateTime [Term] id: CL:0009093 @@ -26429,9 +26445,9 @@ xref: EFO:0010709 is_a: CL:0000192 ! smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0001987 ! placenta -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0001987 ! placenta -property_value: dcterms-date "2021-12-13T13:56:42Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/date "2021-12-13T13:56:42Z" xsd:dateTime [Term] id: CL:0009094 @@ -26443,9 +26459,9 @@ xref: EFO:0010704 is_a: CL:0000115 ! endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0001639 ! hepatic portal vein -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0001639 ! hepatic portal vein -property_value: dcterms-date "2021-12-13T14:01:05Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/date "2021-12-13T14:01:05Z" xsd:dateTime [Term] id: CL:0009095 @@ -26458,9 +26474,9 @@ xref: EFO:0010711 is_a: CL:0000115 ! endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0000995 ! uterus -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0000995 ! uterus -property_value: dcterms-date "2021-12-13T14:39:25Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/date "2021-12-13T14:39:25Z" xsd:dateTime [Term] id: CL:0009096 @@ -26478,10 +26494,10 @@ is_a: CL:0000238 ! non keratinizing barrier epithelial cell is_a: CL:0002252 ! epithelial cell of esophagus intersection_of: CL:0000238 ! non keratinizing barrier epithelial cell intersection_of: part_of UBERON:0006920 ! esophagus squamous epithelium -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0006920 ! esophagus squamous epithelium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2022-02-21T15:00:13Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/date "2022-02-21T15:00:13Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0009097 @@ -26489,10 +26505,10 @@ name: embryonic skeletal muscle fiber def: "A skeletal muscle fiber found in an embryo. In mammalian embryos, skeletal muscle expresses myosin heavy chain-embryonic (MyHC-emb, encoded by the MYH3 gene), which regulates skeletal muscle development." [http://orcid.org/0000-0003-2034-601X, PMID:32094117, PMID:7196501] is_a: CL:0008002 ! skeletal muscle fiber intersection_of: CL:0008002 ! skeletal muscle fiber -intersection_of: existence_starts_and_ends_during UBERON:0000068 ! embryo stage -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 -relationship: existence_starts_and_ends_during UBERON:0000068 ! embryo stage -property_value: dcterms-date "2022-02-21T15:39:10Z" xsd:dateTime +intersection_of: RO:0002491 UBERON:0000068 ! existence starts and ends during embryo stage +relationship: RO:0002491 UBERON:0000068 ! existence starts and ends during embryo stage +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/date "2022-02-21T15:39:10Z" xsd:dateTime [Term] id: CL:0009098 @@ -26500,12 +26516,12 @@ name: fetal and neonatal skeletal muscle fiber def: "A skeletal muscle fiber found at the fetal and neonatal stages. In mammalian fetuses and neonates, skeletal muscle expresses myosin heavy chain-neonatal (MyHC-neo, encoded by the MYH8 gene). This expression disappears shortly after birth and is replaced by expression of adult heavy chain myosins." [http://orcid.org/0000-0003-2034-601X, PMID:26180627, PMID:7196501] is_a: CL:0008002 ! skeletal muscle fiber intersection_of: CL:0008002 ! skeletal muscle fiber -intersection_of: existence_ends_during UBERON:0007221 ! neonate stage -intersection_of: existence_starts_during UBERON:0000092 ! post-embryonic stage -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 -relationship: existence_ends_during UBERON:0007221 ! neonate stage -relationship: existence_starts_during UBERON:0000092 ! post-embryonic stage -property_value: dcterms-date "2022-02-21T15:43:16Z" xsd:dateTime +intersection_of: RO:0002488 UBERON:0000092 ! existence starts during post-embryonic stage +intersection_of: RO:0002492 UBERON:0007221 ! existence ends during neonate stage +relationship: RO:0002488 UBERON:0000092 ! existence starts during post-embryonic stage +relationship: RO:0002492 UBERON:0007221 ! existence ends during neonate stage +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/date "2022-02-21T15:43:16Z" xsd:dateTime [Term] id: CL:0009099 @@ -26515,8 +26531,8 @@ subset: cellxgene_subset synonym: "fibro/adipogenic progenitor" EXACT [] is_a: CL:0008019 ! mesenchymal cell is_a: CL:0011026 ! progenitor cell -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 -property_value: dcterms-date "2022-02-21T16:50:02Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/date "2022-02-21T16:50:02Z" xsd:dateTime [Term] id: CL:0009100 @@ -26527,10 +26543,10 @@ synonym: "portal fibroblast" BROAD [] is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001279 ! portal triad -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0001279 ! portal triad -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2022-03-17T12:00:44Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/date "2022-03-17T12:00:44Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0009101 @@ -26538,8 +26554,8 @@ name: fibroblastic reticular cell def: "A reticular cell involved in directing B cells and T cells to specific regions within a tissue." [] is_a: CL:0000186 ! myofibroblast cell is_a: CL:0000432 ! reticular cell -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 -property_value: dcterms-date "2022-03-21T15:20:33Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/date "2022-03-21T15:20:33Z" xsd:dateTime property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/1472" xsd:string [Term] @@ -26550,10 +26566,10 @@ synonym: "fibroblastic reticular cell" BROAD [] is_a: CL:0009101 ! fibroblastic reticular cell intersection_of: CL:0009101 ! fibroblastic reticular cell intersection_of: part_of UBERON:0000029 ! lymph node -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0000029 ! lymph node -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2022-03-21T15:24:01Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/date "2022-03-21T15:24:01Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/1472" xsd:string [Term] @@ -26563,10 +26579,10 @@ def: "A fibroblastic reticular cell found in the lymph node subcapsular sinus." subset: human_reference_atlas synonym: "marginal reticular cell" BROAD [] is_a: CL:0009102 ! lymph node fibroblastic reticular cell -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 -relationship: located_in UBERON:0005463 ! subcapsular sinus of lymph node -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2022-03-21T15:59:56Z" xsd:dateTime +relationship: RO:0001025 UBERON:0005463 ! located in subcapsular sinus of lymph node +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/date "2022-03-21T15:59:56Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/1472" xsd:string [Term] @@ -26578,10 +26594,10 @@ subset: human_reference_atlas synonym: "lymph node germinal center dark zone fibroblastic reticular cell" EXACT [] synonym: "T-B boundary reticular cell" RELATED [] is_a: CL:0009102 ! lymph node fibroblastic reticular cell -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:8410053 ! lymph node germinal center dark zone -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2022-03-21T16:55:46Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/date "2022-03-21T16:55:46Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/1472" xsd:string [Term] @@ -26592,10 +26608,10 @@ subset: human_reference_atlas synonym: "interfollicular reticular cell" RELATED [PMID:34256989] synonym: "lymph node T cell domain fibroblastic reticular cell" EXACT [] is_a: CL:0009102 ! lymph node fibroblastic reticular cell -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0010417 ! lymph node T cell domain -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2022-03-21T17:19:56Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/date "2022-03-21T17:19:56Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/1472" xsd:string [Term] @@ -26608,10 +26624,10 @@ synonym: "lymph node medullary reticular cell" EXACT [] synonym: "MedRC" RELATED OMO:0003000 [] synonym: "medullary reticular cell of lymph node" EXACT [] is_a: CL:0009102 ! lymph node fibroblastic reticular cell -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0002007 ! medulla of lymph node -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2022-03-22T09:03:15Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/date "2022-03-22T09:03:15Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/1472" xsd:string [Term] @@ -26622,10 +26638,10 @@ subset: human_reference_atlas synonym: "lymphatic endothelial cell of subcapsular sinus ceiling of lymph node" EXACT [] is_a: CL:0002138 ! endothelial cell of lymphatic vessel is_a: CL:0009115 ! lymph node lymphatic vessel endothelial cell -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:8410071 ! subcapsular sinus ceiling -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2022-03-22T10:30:28Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/date "2022-03-22T10:30:28Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0009108 @@ -26635,10 +26651,10 @@ subset: human_reference_atlas synonym: "lymphatic endothelial cell of subcapsular sinus floor of lymph node" EXACT [] is_a: CL:0002138 ! endothelial cell of lymphatic vessel is_a: CL:0009115 ! lymph node lymphatic vessel endothelial cell -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:8410072 ! subcapsular sinus floor -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2022-03-22T10:39:28Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/date "2022-03-22T10:39:28Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0009109 @@ -26649,10 +26665,10 @@ synonym: "lymphatic endothelial cell of lymph node trabecula" EXACT [] synonym: "lymphatic endothelial cell of trabeculae" EXACT [] is_a: CL:0002138 ! endothelial cell of lymphatic vessel is_a: CL:0009115 ! lymph node lymphatic vessel endothelial cell -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0002195 ! trabecula of lymph node -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2022-03-23T15:08:44Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/date "2022-03-23T15:08:44Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0009110 @@ -26662,10 +26678,10 @@ subset: human_reference_atlas synonym: "lymphatic endothelial cell of lymph node medulla ceiling" EXACT [] is_a: CL:0002138 ! endothelial cell of lymphatic vessel is_a: CL:0009115 ! lymph node lymphatic vessel endothelial cell -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0002007 ! medulla of lymph node -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2022-03-23T15:13:30Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/date "2022-03-23T15:13:30Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0009111 @@ -26675,10 +26691,10 @@ subset: cellxgene_subset subset: human_reference_atlas synonym: "lymph node centrocyte" EXACT [] is_a: CL:0000844 ! germinal center B cell -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:8410052 ! lymph node germinal center light zone -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2022-03-24T09:03:44Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/date "2022-03-24T09:03:44Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0009112 @@ -26688,10 +26704,10 @@ subset: cellxgene_subset subset: human_reference_atlas synonym: "lymph node centroblast" EXACT [] is_a: CL:0000844 ! germinal center B cell -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:8410053 ! lymph node germinal center dark zone -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2022-03-24T09:12:41Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/date "2022-03-24T09:12:41Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0009113 @@ -26701,10 +26717,10 @@ subset: cellxgene_subset subset: human_reference_atlas synonym: "follicular regulatory T cell" EXACT [] is_a: CL:0000815 ! regulatory T cell -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0001744 ! lymphoid tissue -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2022-03-24T09:36:29Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/date "2022-03-24T09:36:29Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0009114 @@ -26712,10 +26728,10 @@ name: monocytoid B cell def: "A B cell found in the perisinusoidal area of a lymph node. In humans, monocytoid B cells are a morphologically distinct B cell population\n(oval nuclei, abundant cytoplasm, monocyte-like appearance), share many similarities with marginal zone B cells including marker expression, and are increased in disease settings." [https://orcid.org/0000-0001-7655-4833, PMID:33324003] subset: human_reference_atlas is_a: CL:0000236 ! B cell -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:8410066 ! lymph node paracortex -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2022-03-24T10:18:12Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/date "2022-03-24T10:18:12Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0009115 @@ -26726,10 +26742,10 @@ is_a: CL:0000115 ! endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0000029 ! lymph node intersection_of: part_of UBERON:0001473 ! lymphatic vessel -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0000029 ! lymph node relationship: part_of UBERON:0001473 ! lymphatic vessel -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/1472" xsd:string [Term] @@ -26740,8 +26756,8 @@ subset: cellxgene_subset synonym: "luminal progenitor cell" BROAD [] synonym: "progenitor cell of luminal mammary epithelium" EXACT [] is_a: CL:0011026 ! progenitor cell -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0001911 ! mammary gland +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: CL:0010000 @@ -26759,7 +26775,7 @@ is_a: CL:0000499 ! stromal cell is_a: CL:0002092 ! bone marrow cell intersection_of: CL:0000499 ! stromal cell intersection_of: part_of UBERON:0002371 ! bone marrow -relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 [Term] id: CL:0010002 @@ -26769,8 +26785,8 @@ synonym: "umbilical artery epithelial cell" EXACT [] is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001310 ! umbilical artery -relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 relationship: part_of UBERON:0001310 ! umbilical artery +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 [Term] id: CL:0010003 @@ -26783,8 +26799,8 @@ xref: MESH:D056809 is_a: CL:0000082 ! epithelial cell of lung intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0002299 ! alveolus of lung -relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 relationship: part_of UBERON:0002299 ! alveolus of lung +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 [Term] id: CL:0010004 @@ -26795,7 +26811,7 @@ is_a: CL:0000842 ! mononuclear cell is_a: CL:1001610 ! bone marrow hematopoietic cell intersection_of: CL:0000842 ! mononuclear cell intersection_of: part_of UBERON:0002371 ! bone marrow -relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 [Term] id: CL:0010005 @@ -26833,16 +26849,17 @@ is_a: CL:0002494 ! cardiocyte intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0000948 ! heart relationship: part_of UBERON:0000948 ! heart -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0010009 name: camera-type eye photoreceptor cell synonym: "camera type eye photoreceptor cell" EXACT [] is_a: CL:0000287 ! eye photoreceptor cell +is_a: CL:0009004 ! retinal cell intersection_of: CL:0000210 ! photoreceptor cell intersection_of: part_of UBERON:0000019 ! camera-type eye -relationship: part_of UBERON:0000019 ! camera-type eye +relationship: part_of UBERON:0000966 {seeAlso="https://github.com/obophenotype/cell-ontology/issues/2245"} ! retina [Term] id: CL:0010010 @@ -26876,9 +26893,9 @@ xref: FMA:84104 is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/1359" xsd:string [Term] @@ -26912,7 +26929,7 @@ name: zygote def: "A zygote in a plant or an animal." [] xref: MESH:D015053 is_a: CL:0000000 ! cell -relationship: seeAlso https://github.com/obophenotype/cell-ontology/issues/786 +property_value: seeAlso https://github.com/obophenotype/cell-ontology/issues/786 [Term] id: CL:0010020 @@ -26929,8 +26946,8 @@ name: cardiac myoblast xref: MESH:D032386 is_a: CL:0000056 ! myoblast intersection_of: CL:0000056 ! myoblast -intersection_of: develops_into CL:0000746 ! cardiac muscle cell -relationship: develops_into CL:0000746 ! cardiac muscle cell +intersection_of: RO:0002203 CL:0000746 ! develops into cardiac muscle cell +relationship: RO:0002203 CL:0000746 ! develops into cardiac muscle cell [Term] id: CL:0010022 @@ -26979,8 +26996,8 @@ synonym: "magnocellular neuron" EXACT [] xref: ILX:0107463 is_a: CL:0000165 ! neuroendocrine cell is_a: CL:2000029 ! central nervous system neuron -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: RO:0002100 UBERON:0001898 ! has soma location hypothalamus +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:0011004 @@ -26990,7 +27007,7 @@ subset: cellxgene_subset subset: human_reference_atlas synonym: "lens fibre cell" EXACT [] is_a: CL:0002222 ! vertebrate lens cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0011005 @@ -27003,7 +27020,7 @@ is_a: CL:0000498 ! inhibitory interneuron is_a: CL:0000617 ! GABAergic neuron intersection_of: CL:0000099 ! interneuron intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neurotransmission -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0011006 @@ -27065,21 +27082,21 @@ is_a: CL:0000219 ! motile cell intersection_of: CL:0000019 ! sperm intersection_of: capable_of GO:0097722 ! sperm motility relationship: capable_of GO:0097722 ! sperm motility -relationship: dc-contributor https://orcid.org/0000-0001-5208-3432 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011014 name: non-motile sperm cell def: "A sperm cell that is not cabaple of motion (motility)." [PMID:30612620] is_a: CL:0000019 ! sperm -relationship: dc-contributor https://orcid.org/0000-0001-5208-3432 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011015 name: amoeboid sperm cell def: "A motile sperm cell that contain no F-actin, and their motility is powered by a dynamic filament system." [PMID:17708982] is_a: CL:0011013 ! motile sperm cell -relationship: dc-contributor https://orcid.org/0000-0001-5208-3432 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011016 @@ -27089,14 +27106,14 @@ is_a: CL:0011013 ! motile sperm cell intersection_of: CL:0011013 ! motile sperm cell intersection_of: capable_of GO:0030317 ! flagellated sperm motility relationship: capable_of GO:0030317 ! flagellated sperm motility -relationship: dc-contributor https://orcid.org/0000-0001-5208-3432 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011017 name: vagal neural crest cell def: "Cell that is part of the vagal neural crest population. The vagal neural crest arises from the axial level of somites 1-7 and has been described as a hybrid between the head and the trunk populations." [PMID:22016183] is_a: CL:0011012 ! neural crest cell -relationship: dc-contributor https://orcid.org/0000-0001-5208-3432 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011018 @@ -27105,8 +27122,8 @@ def: "A group 3 innate lymphoid cell that express ROR gamma t and IL-7R alpha in synonym: "LTi" EXACT [] synonym: "lymphoid tissue inducer cell" EXACT [] is_a: CL:0001071 ! group 3 innate lymphoid cell -relationship: dc-contributor https://orcid.org/0000-0001-5208-3432 relationship: RO:0002104 PR:000001869 ! has plasma membrane part interleukin-7 receptor subunit alpha +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011019 @@ -27117,8 +27134,8 @@ is_a: CL:0000077 ! mesothelial cell is_a: CL:0002494 ! cardiocyte intersection_of: CL:0000077 ! mesothelial cell intersection_of: part_of UBERON:0002348 ! epicardium -relationship: dc-contributor https://orcid.org/0000-0001-5208-3432 relationship: part_of UBERON:0002348 ! epicardium +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011020 @@ -27126,7 +27143,7 @@ name: neural progenitor cell def: "An undifferentiated cell that originates from a neural stem cell and has the capacity to generate multiple types of lineage-restricted progenitors but not to self-renew." [PMID:30574073] subset: cellxgene_subset is_a: CL:0000055 ! non-terminally differentiated cell -relationship: dc-contributor https://orcid.org/0000-0001-5208-3432 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011021 @@ -27135,8 +27152,8 @@ def: "A fibroblast that is part of upper back skin." [] is_a: CL:0011022 ! fibroblast of skin of back intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0009015 ! upper back skin -relationship: dc-contributor https://orcid.org/0000-0001-5208-3432 relationship: part_of UBERON:0009015 ! upper back skin +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011022 @@ -27145,8 +27162,8 @@ def: "A fibroblast that is part of skin of back." [] is_a: CL:0002620 ! skin fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001068 ! skin of back -relationship: dc-contributor https://orcid.org/0000-0001-5208-3432 relationship: part_of UBERON:0001068 ! skin of back +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011023 @@ -27159,9 +27176,9 @@ is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0001063 ! neoplastic cell intersection_of: RO:0001000 CL:0000097 ! derives from mast cell intersection_of: RO:0002104 PR:000001380 ! has plasma membrane part interleukin-2 receptor subunit alpha -relationship: dc-contributor https://orcid.org/0000-0001-5208-3432 relationship: RO:0001000 CL:0000097 ! derives from mast cell relationship: RO:0002104 PR:000001380 ! has plasma membrane part interleukin-2 receptor subunit alpha +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011024 @@ -27175,7 +27192,7 @@ is_a: CL:0002489 ! double negative thymocyte intersection_of: CL:0002489 ! double negative thymocyte intersection_of: capable_of GO:0050777 ! negative regulation of immune response relationship: capable_of GO:0050777 ! negative regulation of immune response -relationship: dc-contributor https://orcid.org/0000-0001-5208-3432 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011025 @@ -27184,7 +27201,7 @@ subset: cellxgene_subset synonym: "An effector T cell that displays impaired effector functions (e.g., rapid production of effector cytokines, cytotoxicity) and has limited proliferative potential." EXACT [PMID:26544946] synonym: "Tex cell" EXACT [] is_a: CL:0000911 ! effector T cell -relationship: dc-contributor https://orcid.org/0000-0001-5208-3432 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011026 @@ -27193,9 +27210,9 @@ def: "A precursor cell that has a tendency to differentiate into a specific type subset: cellxgene_subset is_a: CL:0011115 ! precursor cell intersection_of: CL:0011115 ! precursor cell -intersection_of: develops_from CL:0000034 ! stem cell -relationship: dc-contributor https://orcid.org/0000-0001-5208-3432 -relationship: develops_from CL:0000034 ! stem cell +intersection_of: RO:0002202 CL:0000034 ! develops from stem cell +relationship: RO:0002202 CL:0000034 ! develops from stem cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011027 @@ -27207,7 +27224,7 @@ is_a: CL:0000188 ! cell of skeletal muscle is_a: CL:1001609 ! muscle fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001134 ! skeletal muscle tissue -relationship: dc-contributor https://orcid.org/0000-0001-5208-3432 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011028 @@ -27216,7 +27233,7 @@ synonym: "A neural-crest derived glial cell that supports the growth and surviva synonym: "OEC" EXACT [] xref: BTO:0002771 is_a: CL:0000125 ! glial cell -relationship: dc-contributor https://orcid.org/0000-0001-5208-3432 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011029 @@ -27225,9 +27242,9 @@ def: "An explosive cell containing one giant secretory organelle called a cnidoc synonym: "cnidoblast" EXACT [] synonym: "nematocyte" EXACT [] is_a: CL:0000151 ! secretory cell -relationship: dc-contributor https://orcid.org/0000-0001-5208-3432 relationship: has_part GO:0042151 ! nematocyst -relationship: in_taxon NCBITaxon:6073 ! Cnidaria +relationship: RO:0002162 NCBITaxon:6073 ! in taxon Cnidaria +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011030 @@ -27239,7 +27256,7 @@ is_a: CL:2000008 ! microvascular endothelial cell is_a: CL:2000010 ! dermis blood vessel endothelial cell intersection_of: CL:2000008 ! microvascular endothelial cell intersection_of: part_of UBERON:0002067 ! dermis -relationship: dc-contributor https://orcid.org/0000-0001-5208-3432 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011031 @@ -27248,9 +27265,9 @@ def: "A dendritic cell that develops from a monocyte." [BTO:0002900, PMID:307190 subset: human_reference_atlas synonym: "MDDC cell" EXACT [] is_a: CL:0000782 ! myeloid dendritic cell -relationship: dc-contributor https://orcid.org/0000-0001-5208-3432 -relationship: develops_from CL:0000576 ! monocyte -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0000576 ! develops from monocyte +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0011032 @@ -27261,7 +27278,7 @@ synonym: "immature enterocyte" RELATED [https://orcid.org/0000-0001-9610-7627, P synonym: "LRE" EXACT [] synonym: "vacuolated enterocyte" BROAD [] is_a: CL:0000584 ! enterocyte -relationship: dc-contributor https://orcid.org/0000-0001-5208-3432 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011100 @@ -27292,7 +27309,7 @@ def: "Sympathetic neurons are part of the sympathetic nervous system and are pri subset: cellxgene_subset subset: human_reference_atlas is_a: CL:0000107 ! autonomic neuron -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0011104 @@ -27421,9 +27438,9 @@ is_a: CL:0000127 {is_inferred="true"} ! astrocyte is_a: CL:2000005 ! brain macroglial cell intersection_of: CL:0000127 ! astrocyte intersection_of: part_of UBERON:0001890 ! forebrain -relationship: dc-contributor https://orcid.org/0000-0002-3837-8864 relationship: part_of UBERON:0001890 ! forebrain -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3837-8864 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0012001 @@ -27435,9 +27452,9 @@ is_a: CL:0000117 {is_inferred="true"} ! CNS neuron (sensu Vertebrata) is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) intersection_of: RO:0002100 UBERON:0001890 ! has soma location forebrain -relationship: dc-contributor https://orcid.org/0000-0002-3837-8864 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002100 UBERON:0001890 ! has soma location forebrain +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3837-8864 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0013000 @@ -27464,16 +27481,16 @@ subset: cellxgene_subset subset: human_reference_atlas is_a: CL:0000082 ! epithelial cell of lung is_a: CL:0005006 ! ionocyte -relationship: dc-contributor https://orcid.org/0000-0003-2473-2313 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2473-2313 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0017001 name: splanchnic mesodermal cell def: "A mesodermal cell that is part of the splanchnic layer of lateral plate mesoderm." [] is_a: CL:0011010 ! lateral mesodermal cell -relationship: dc-contributor https://orcid.org/0000-0003-2473-2313 relationship: part_of UBERON:0004872 ! splanchnic layer of lateral plate mesoderm +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2473-2313 [Term] id: CL:0017002 @@ -27486,7 +27503,7 @@ is_a: CL:0000165 ! neuroendocrine cell intersection_of: CL:0000165 ! neuroendocrine cell intersection_of: part_of UBERON:0000428 ! prostate epithelium relationship: part_of UBERON:0000428 ! prostate epithelium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 created_by: http://orcid.org/0000-0003-2473-2313 [Term] @@ -27511,7 +27528,7 @@ synonym: "interstitial Cajal-like cell" NARROW [PMID:20367664] synonym: "interstitial neuron" RELATED [PMID:31311805] is_a: CL:0002320 ! connective tissue cell relationship: has_part GO:0120327 ! telopode -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 created_by: http://orcid.org/0000-0003-2473-2313 [Term] @@ -27559,8 +27576,8 @@ is_a: CL:1000296 ! epithelial cell of urethra is_a: CL:4030024 ! hillock cell intersection_of: CL:4030024 ! hillock cell intersection_of: part_of UBERON:0000057 ! urethra -relationship: dc-contributor http://orcid.org/0000-0003-2473-2313 -property_value: dcterms-date "2022-10-13T13:51:35Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-2473-2313 +property_value: http://purl.org/dc/terms/date "2022-10-13T13:51:35Z" xsd:dateTime [Term] id: CL:0017011 @@ -27572,9 +27589,9 @@ is_a: CL:0017003 ! epithelial cell of prostatic urethra is_a: CL:0017010 ! hillock cell of urethral epithelium intersection_of: CL:4030024 ! hillock cell intersection_of: part_of UBERON:0001335 ! prostatic urethra -relationship: dc-contributor http://orcid.org/0000-0003-2473-2313 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2022-10-13T13:58:15Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0003-2473-2313 +property_value: http://purl.org/dc/terms/date "2022-10-13T13:58:15Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0017500 @@ -27584,7 +27601,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0070046 ! neutrophillic relationship: bearer_of PATO:0070046 ! neutrophillic -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-05-25T01:36:34Z [Term] @@ -27592,8 +27609,8 @@ id: CL:0017501 name: obsolete lobed nucleus def: "Nucleus with two or more lobes connected by a thin filament that contains no internal chromatin." [GOC:tfm] comment: Obsoleted because duplicate with GO term. -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: term_tracker_item https://github.com/obophenotype/cell-ontology/issues/734 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 is_obsolete: true replaced_by: GO:0098537 creation_date: 2009-12-22T03:54:43Z @@ -27607,7 +27624,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0002418 ! acidophilic relationship: bearer_of PATO:0002418 ! acidophilic -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-22T04:23:25Z [Term] @@ -27618,7 +27635,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0002094 ! basophilic relationship: bearer_of PATO:0002094 ! basophilic -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-22T04:24:54Z [Term] @@ -27629,7 +27646,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0070047 ! polychromatophilic relationship: bearer_of PATO:0070047 ! polychromatophilic -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-28T04:25:23Z [Term] @@ -27637,8 +27654,8 @@ id: CL:0017505 name: obsolete increased nucleus size def: "OBSOLETE. A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell." [GOC:tfm] comment: This class was a phenotype, not a cell type. -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: term_tracker_item https://github.com/obophenotype/cell-ontology/issues/2251 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 is_obsolete: true replaced_by: PATO:0040072 creation_date: 2009-12-23T10:53:24Z @@ -27648,7 +27665,7 @@ id: CL:0017506 name: banded nucleus def: "A concave nuclear shape where the nucleus is indented to more than half the distance to the farthest nuclear margin, but in no area is the chromatin condensed to a single filament." [GOC:tfm] is_a: GO:0005634 ! nucleus -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-23T02:18:43Z [Term] @@ -27659,7 +27676,7 @@ is_a: GO:0005634 ! nucleus intersection_of: GO:0005634 ! nucleus intersection_of: bearer_of PATO:0001871 ! reniform relationship: bearer_of PATO:0001871 ! reniform -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-23T02:31:25Z [Term] @@ -27667,7 +27684,7 @@ id: CL:0017508 name: cartwheel heterochromatin def: "Heterochromatin that is arranged in a carthwheel pattern." [GOC:tfm] is_a: GO:0000792 ! heterochromatin -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-28T04:28:35Z [Term] @@ -27688,9 +27705,9 @@ synonym: "serous cell of tracheobronchial tree" EXACT [] is_a: CL:0000313 ! serous secreting cell intersection_of: CL:0000313 ! serous secreting cell intersection_of: part_of UBERON:0007196 ! tracheobronchial tree -relationship: dc-contributor https://orcid.org/0000-0003-2034-601X relationship: part_of UBERON:0007196 ! tracheobronchial tree -property_value: dcterms-date "2020-05-07T16:03:27Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X +property_value: http://purl.org/dc/terms/date "2020-05-07T16:03:27Z" xsd:dateTime [Term] id: CL:0019002 @@ -27702,10 +27719,10 @@ synonym: "chondrocyte of tracheobronchial tree" EXACT [] is_a: CL:0000138 ! chondrocyte intersection_of: CL:0000138 ! chondrocyte intersection_of: part_of UBERON:0007196 ! tracheobronchial tree -relationship: dc-contributor https://orcid.org/0000-0003-2034-601X relationship: part_of UBERON:0007196 ! tracheobronchial tree -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2020-05-07T17:29:51Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X +property_value: http://purl.org/dc/terms/date "2020-05-07T17:29:51Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0019003 @@ -27719,9 +27736,9 @@ is_a: CL:0002202 ! epithelial cell of tracheobronchial tree is_a: CL:0002370 ! respiratory goblet cell intersection_of: CL:0000160 ! goblet cell intersection_of: part_of UBERON:0007196 ! tracheobronchial tree -relationship: dc-contributor https://orcid.org/0000-0003-2034-601X -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2020-05-07T18:14:52Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X +property_value: http://purl.org/dc/terms/date "2020-05-07T18:14:52Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0019015 @@ -27733,10 +27750,10 @@ synonym: "rEos" EXACT [PMID:27548519] is_a: CL:0000774 ! band form eosinophil intersection_of: CL:0000774 ! band form eosinophil intersection_of: part_of UBERON:0008946 ! lung parenchyma -relationship: dc-contributor https://orcid.org/0000-0003-2034-601X relationship: part_of UBERON:0008946 ! lung parenchyma -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2020-05-26T09:42:19Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X +property_value: http://purl.org/dc/terms/date "2020-05-26T09:42:19Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0019017 @@ -27747,10 +27764,10 @@ synonym: "smooth muscle cell of lymphatic vessel" EXACT [] is_a: CL:0000359 ! vascular associated smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0001473 ! lymphatic vessel -relationship: dc-contributor https://orcid.org/0000-0003-2034-601X relationship: part_of UBERON:0001473 ! lymphatic vessel -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2020-07-21T12:29:51Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X +property_value: http://purl.org/dc/terms/date "2020-07-21T12:29:51Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0019018 @@ -27761,10 +27778,10 @@ synonym: "smooth muscle cell of blood vessel" EXACT [] is_a: CL:0000359 ! vascular associated smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0001981 ! blood vessel -relationship: dc-contributor https://orcid.org/0000-0003-2034-601X relationship: part_of UBERON:0001981 ! blood vessel -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2020-07-21T12:42:48Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X +property_value: http://purl.org/dc/terms/date "2020-07-21T12:42:48Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0019019 @@ -27776,10 +27793,10 @@ synonym: "smooth muscle cell of tracheobronchial tree" EXACT [] is_a: CL:0000192 ! smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0007196 ! tracheobronchial tree -relationship: dc-contributor https://orcid.org/0000-0003-2034-601X relationship: part_of UBERON:0007196 ! tracheobronchial tree -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2020-07-21T12:50:22Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X +property_value: http://purl.org/dc/terms/date "2020-07-21T12:50:22Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0019020 @@ -27789,9 +27806,9 @@ synonym: "large bile duct cholangiocyte" EXACT [PMID:23720296] is_a: CL:1000488 ! cholangiocyte intersection_of: CL:1000488 ! cholangiocyte intersection_of: part_of UBERON:0004822 ! extrahepatic bile duct epithelium -relationship: dc-contributor https://orcid.org/0000-0003-2034-601X relationship: part_of UBERON:0004822 ! extrahepatic bile duct epithelium -property_value: dcterms-date "2020-09-03T12:24:24Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X +property_value: http://purl.org/dc/terms/date "2020-09-03T12:24:24Z" xsd:dateTime [Term] id: CL:0019021 @@ -27805,8 +27822,8 @@ is_a: CL:1000398 ! endothelial cell of hepatic sinusoid intersection_of: CL:1000398 ! endothelial cell of hepatic sinusoid intersection_of: adjacent_to UBERON:0001279 ! portal triad relationship: adjacent_to UBERON:0001279 ! portal triad -relationship: dc-contributor https://orcid.org/0000-0003-2034-601X -property_value: dcterms-date "2020-09-09T13:56:47Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X +property_value: http://purl.org/dc/terms/date "2020-09-09T13:56:47Z" xsd:dateTime [Term] id: CL:0019022 @@ -27820,8 +27837,8 @@ is_a: CL:1000398 ! endothelial cell of hepatic sinusoid intersection_of: CL:1000398 ! endothelial cell of hepatic sinusoid intersection_of: adjacent_to UBERON:0006841 ! central vein of liver relationship: adjacent_to UBERON:0006841 ! central vein of liver -relationship: dc-contributor https://orcid.org/0000-0003-2034-601X -property_value: dcterms-date "2020-09-10T12:38:29Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X +property_value: http://purl.org/dc/terms/date "2020-09-10T12:38:29Z" xsd:dateTime [Term] id: CL:0019026 @@ -27833,10 +27850,10 @@ synonym: "periportal hepatocyte" EXACT [PMID:29763190] is_a: CL:0000182 ! hepatocyte intersection_of: CL:0000182 ! hepatocyte intersection_of: part_of UBERON:8400006 ! liver lobule periportal region -relationship: dc-contributor https://orcid.org/0000-0003-2034-601X relationship: part_of UBERON:8400006 ! liver lobule periportal region -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2020-10-12T10:29:31Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X +property_value: http://purl.org/dc/terms/date "2020-10-12T10:29:31Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0019028 @@ -27848,10 +27865,10 @@ synonym: "midzonal hepatocyte" EXACT [PMID:29763190] is_a: CL:0000182 ! hepatocyte intersection_of: CL:0000182 ! hepatocyte intersection_of: part_of UBERON:8400007 ! liver lobule centrilobular region -relationship: dc-contributor https://orcid.org/0000-0003-2034-601X relationship: part_of UBERON:8400007 ! liver lobule centrilobular region -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2020-10-12T10:57:40Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X +property_value: http://purl.org/dc/terms/date "2020-10-12T10:57:40Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0019029 @@ -27863,10 +27880,10 @@ synonym: "centrilobular hepatocyte" EXACT [PMID:29763190] is_a: CL:0000182 ! hepatocyte intersection_of: CL:0000182 ! hepatocyte intersection_of: part_of UBERON:8400008 ! liver lobule midzonal region -relationship: dc-contributor https://orcid.org/0000-0003-2034-601X relationship: part_of UBERON:8400008 ! liver lobule midzonal region -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2020-10-12T11:03:51Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X +property_value: http://purl.org/dc/terms/date "2020-10-12T11:03:51Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0019031 @@ -27878,8 +27895,8 @@ is_a: CL:0000160 ! goblet cell is_a: CL:0002563 ! intestinal epithelial cell intersection_of: CL:0000160 ! goblet cell intersection_of: part_of UBERON:0001277 ! intestinal epithelium -relationship: dc-contributor https://orcid.org/0000-0003-2034-601X -property_value: dcterms-date "2020-10-14T14:59:07Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X +property_value: http://purl.org/dc/terms/date "2020-10-14T14:59:07Z" xsd:dateTime [Term] id: CL:0019032 @@ -27892,9 +27909,9 @@ is_a: CL:0002204 ! brush cell is_a: CL:0002563 ! intestinal epithelial cell intersection_of: CL:0002204 ! brush cell intersection_of: part_of UBERON:0001277 ! intestinal epithelium -relationship: dc-contributor https://orcid.org/0000-0003-2034-601X -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2020-10-15T12:47:46Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X +property_value: http://purl.org/dc/terms/date "2020-10-15T12:47:46Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0700009 @@ -27903,7 +27920,7 @@ def: "OBSOLETE. A renal beta-intercalated cell that is part of the cortical coll comment: Created with IRI in incorrect ID range synonym: "B-IC" EXACT [PMID:32016094] synonym: "kidney collecting duct intercalated cell type B" EXACT [PMID:31300091] -property_value: dcterms-date "2022-08-26T10:31:29Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2022-08-26T10:31:29Z" xsd:dateTime is_obsolete: true replaced_by: CL:4030005 @@ -28067,7 +28084,7 @@ intersection_of: CL:0000165 ! neuroendocrine cell intersection_of: part_of UBERON:0002048 ! lung relationship: capable_of GO:0070483 ! detection of hypoxia relationship: has_part GO:0031045 ! dense core granule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000236 @@ -28102,7 +28119,7 @@ is_a: CL:4030034 ! respiratory ciliated cell intersection_of: CL:0000064 ! ciliated cell intersection_of: part_of UBERON:0002048 ! lung relationship: part_of UBERON:0002048 ! lung -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000272 @@ -28177,7 +28194,7 @@ is_a: CL:0002504 {is_inferred="true"} ! enteric smooth muscle cell intersection_of: CL:0002504 ! enteric smooth muscle cell intersection_of: part_of UBERON:0000059 ! large intestine relationship: part_of UBERON:0000059 ! large intestine -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000280 @@ -28325,7 +28342,7 @@ subset: human_reference_atlas xref: FMA:261271 is_a: CL:0000057 ! fibroblast relationship: part_of UBERON:0002367 ! prostate gland -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000300 @@ -28343,7 +28360,7 @@ subset: human_reference_atlas xref: FMA:261275 is_a: CL:0000057 ! fibroblast relationship: part_of UBERON:0002367 ! prostate gland -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000302 @@ -28415,7 +28432,7 @@ is_a: CL:0000135 {is_inferred="true"} ! fibrocyte is_a: CL:1000708 ! ureter adventitial cell intersection_of: CL:0000135 ! fibrocyte intersection_of: part_of UBERON:0001252 ! adventitia of ureter -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000309 @@ -28429,7 +28446,7 @@ xref: FMA:261293 is_a: CL:0000136 ! adipocyte is_a: CL:0002494 ! cardiocyte relationship: part_of UBERON:0002348 ! epicardium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000310 @@ -28556,7 +28573,7 @@ def: "A goblet cell that is part of the epithelium of crypt of Lieberkuhn of lar subset: human_reference_atlas xref: FMA:263056 is_a: CL:1000320 ! large intestine goblet cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000322 @@ -28571,7 +28588,7 @@ is_a: CL:1001599 ! pancreas exocrine glandular cell intersection_of: CL:0000160 ! goblet cell intersection_of: part_of UBERON:0001264 ! pancreas relationship: part_of UBERON:0009970 ! epithelium of pancreatic duct -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000323 @@ -28595,7 +28612,7 @@ is_a: CL:1000317 ! intestinal villus goblet cell is_a: CL:1001589 ! duodenum glandular cell intersection_of: CL:0000160 ! goblet cell intersection_of: part_of UBERON:0002114 ! duodenum -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000325 @@ -28607,7 +28624,7 @@ xref: FMA:263065 is_a: CL:1000317 ! intestinal villus goblet cell intersection_of: CL:0000160 ! goblet cell intersection_of: part_of UBERON:0002115 ! jejunum -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000326 @@ -28651,7 +28668,7 @@ is_a: CL:0019003 ! tracheobronchial goblet cell intersection_of: CL:0000160 ! goblet cell intersection_of: part_of UBERON:0003126 ! trachea relationship: part_of UBERON:0001901 ! epithelium of trachea -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000330 @@ -28664,7 +28681,7 @@ is_a: CL:0019001 ! tracheobronchial serous cell intersection_of: CL:0000313 ! serous secreting cell intersection_of: part_of UBERON:0001901 ! epithelium of trachea relationship: part_of UBERON:0001901 ! epithelium of trachea -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000331 @@ -28677,7 +28694,7 @@ is_a: CL:0019001 ! tracheobronchial serous cell intersection_of: CL:0000313 ! serous secreting cell intersection_of: part_of UBERON:0002031 ! epithelium of bronchus relationship: part_of UBERON:0002031 ! epithelium of bronchus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000332 @@ -28790,7 +28807,7 @@ def: "A Paneth cell that is part of the epithelium proper of small intestine." [ subset: human_reference_atlas xref: FMA:263106 is_a: CL:1000343 ! paneth cell of epithelium of small intestine -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000345 @@ -28833,7 +28850,7 @@ is_a: CL:0002633 {is_inferred="true"} ! respiratory basal cell intersection_of: CL:0002633 ! respiratory basal cell intersection_of: part_of UBERON:0001901 ! epithelium of trachea relationship: part_of UBERON:0001901 ! epithelium of trachea -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000349 @@ -28848,7 +28865,7 @@ is_a: CL:0002329 ! basal epithelial cell of tracheobronchial tree is_a: CL:0002633 ! respiratory basal cell intersection_of: CL:0002633 ! respiratory basal cell intersection_of: part_of UBERON:0002031 ! epithelium of bronchus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000350 @@ -28862,7 +28879,7 @@ is_a: CL:0002633 {is_inferred="true"} ! respiratory basal cell intersection_of: CL:0002633 ! respiratory basal cell intersection_of: part_of UBERON:0001958 ! terminal bronchiole epithelium relationship: part_of UBERON:0001958 ! terminal bronchiole epithelium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000351 @@ -28876,7 +28893,7 @@ is_a: CL:0002633 {is_inferred="true"} ! respiratory basal cell intersection_of: CL:0002633 ! respiratory basal cell intersection_of: part_of UBERON:0001955 ! epithelium of respiratory bronchiole relationship: part_of UBERON:0001955 ! epithelium of respiratory bronchiole -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000352 @@ -28890,7 +28907,7 @@ is_a: CL:0002633 {is_inferred="true"} ! respiratory basal cell intersection_of: CL:0002633 ! respiratory basal cell intersection_of: part_of UBERON:8600001 ! epithelium of lobular bronchiole relationship: part_of UBERON:8600001 ! epithelium of lobular bronchiole -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000353 @@ -29245,7 +29262,7 @@ is_a: CL:0002262 ! endothelial cell of sinusoid intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0001281 ! hepatic sinusoid relationship: part_of UBERON:0001281 ! hepatic sinusoid -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000405 @@ -29314,7 +29331,7 @@ is_a: CL:0000071 {is_inferred="true"} ! blood vessel endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0001980 ! arteriole relationship: part_of UBERON:0001980 ! arteriole -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000413 @@ -29331,7 +29348,7 @@ is_a: CL:0000071 ! blood vessel endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0001637 ! artery relationship: part_of UBERON:0001917 ! endothelium of artery -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000414 @@ -29344,7 +29361,7 @@ is_a: CL:0002139 {is_inferred="true"} ! endothelial cell of vascular tree intersection_of: CL:0002139 ! endothelial cell of vascular tree intersection_of: part_of UBERON:0001979 ! venule relationship: part_of UBERON:0001979 ! venule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000415 @@ -29374,7 +29391,7 @@ is_a: CL:0000185 {is_inferred="true"} ! myoepithelial cell is_a: CL:1000448 ! epithelial cell of sweat gland intersection_of: CL:0000185 ! myoepithelial cell intersection_of: part_of UBERON:0001820 ! sweat gland -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000418 @@ -29383,7 +29400,7 @@ def: "A myoepithelial cell that is part of the mammary gland alveolus." [GOC:tfm synonym: "basal cell of alveolus of lactiferous gland" EXACT [FMA:67802] synonym: "myoepithelial cell of mammary alveolus" EXACT [FMA:67802] xref: FMA:67802 -is_a: CL:0002324 ! myoepithelial cell of mammary gland +is_a: CL:0002324 ! basal-myoepithelial cell of mammary gland intersection_of: CL:0000185 ! myoepithelial cell intersection_of: part_of UBERON:0003214 ! mammary gland alveolus relationship: part_of UBERON:0003214 ! mammary gland alveolus @@ -29394,7 +29411,7 @@ name: myoepithelial cell of lactiferous duct def: "A myoepithelial cell that is part of the lactiferous duct." [GOC:tfm] xref: FMA:67803 is_a: CL:0000068 ! duct epithelial cell -is_a: CL:0002324 ! myoepithelial cell of mammary gland +is_a: CL:0002324 ! basal-myoepithelial cell of mammary gland intersection_of: CL:0000185 ! myoepithelial cell intersection_of: part_of UBERON:0001765 ! mammary duct relationship: part_of UBERON:0001765 ! mammary duct @@ -29653,7 +29670,7 @@ is_a: CL:1000450 ! epithelial cell of glomerular capsule intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0005750 ! glomerular parietal epithelium relationship: part_of UBERON:0005750 ! glomerular parietal epithelium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000453 @@ -29680,7 +29697,7 @@ is_a: CL:1000449 ! epithelial cell of nephron is_a: CL:1001225 {is_inferred="true"} ! kidney collecting duct cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001232 ! collecting duct of renal tubule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000456 @@ -29702,7 +29719,7 @@ is_a: CL:1000490 ! mesothelial cell of peritoneum intersection_of: CL:0000077 ! mesothelial cell intersection_of: part_of UBERON:0001178 ! visceral peritoneum relationship: part_of UBERON:0001178 ! visceral peritoneum -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000458 @@ -29717,7 +29734,7 @@ is_a: CL:0000148 {is_inferred="true"} ! melanocyte intersection_of: CL:0000148 ! melanocyte intersection_of: part_of UBERON:0002097 ! skin of body relationship: part_of UBERON:0002097 ! skin of body -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000465 @@ -29755,7 +29772,7 @@ name: myoepithelial cell of acinus of lactiferous gland def: "A myoepithelial cell that is part of the acinus of lactiferous gland." [GOC:tfm] synonym: "basal cell of acinus of lactiferous gland" EXACT [FMA:74469] xref: FMA:74469 -is_a: CL:0002324 ! myoepithelial cell of mammary gland +is_a: CL:0002324 ! basal-myoepithelial cell of mammary gland relationship: part_of UBERON:0001912 ! lobule of mammary gland [Term] @@ -29803,7 +29820,7 @@ synonym: "pacemaker cell of sinoatrial node" EXACT [] synonym: "pacemaker cell of sinuatrial node" EXACT [] xref: FMA:83383 is_a: CL:1000409 ! myocyte of sinoatrial node -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000478 @@ -29893,7 +29910,7 @@ is_a: CL:0000646 {is_inferred="true"} ! basal cell is_a: CL:0000731 ! urothelial cell intersection_of: CL:0000646 ! basal cell intersection_of: part_of UBERON:0000365 ! urothelium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000487 @@ -29907,7 +29924,7 @@ is_a: CL:0000192 {is_inferred="true"} ! smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0002367 ! prostate gland relationship: part_of UBERON:0002367 ! prostate gland -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000488 @@ -29920,8 +29937,8 @@ is_a: CL:0000069 {is_inferred="true"} ! branched duct epithelial cell intersection_of: CL:0000069 ! branched duct epithelial cell intersection_of: capable_of GO:0015106 ! bicarbonate transmembrane transporter activity intersection_of: part_of UBERON:0002394 ! bile duct -relationship: develops_from CL:0005026 ! hepatoblast relationship: part_of UBERON:0002394 ! bile duct +relationship: RO:0002202 CL:0005026 ! develops from hepatoblast [Term] id: CL:1000489 @@ -29934,7 +29951,7 @@ is_a: CL:2000051 ! splenic fibroblast intersection_of: CL:0000432 ! reticular cell intersection_of: part_of UBERON:0001266 ! splenic cord relationship: part_of UBERON:0001266 ! splenic cord -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000490 @@ -29981,7 +29998,7 @@ is_a: CL:1000491 ! mesothelial cell of pleura intersection_of: CL:0000077 ! mesothelial cell intersection_of: part_of UBERON:0002401 ! visceral pleura relationship: part_of UBERON:0002401 ! visceral pleura -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000494 @@ -30039,7 +30056,7 @@ relationship: part_of UBERON:0005215 ! kidney interstitium [Term] id: CL:1000504 name: kidney medulla cell -def: "A cell that is part of a renal medulla." [] +def: "A cell that is part of a renal medulla." [PMID:22343825] xref: KUPO:0001017 is_a: CL:1000497 ! kidney cell intersection_of: CL:1000497 ! kidney cell @@ -30154,7 +30171,7 @@ is_a: CL:1000617 ! kidney inner medulla cell intersection_of: CL:1000497 ! kidney cell intersection_of: part_of UBERON:0009095 ! tip of renal papilla relationship: part_of UBERON:0009095 ! tip of renal papilla -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000600 @@ -30239,6 +30256,7 @@ relationship: part_of UBERON:0002303 ! juxtaglomerular apparatus [Term] id: CL:1000681 name: kidney cortex interstitial cell +def: "A cell that is part of an interstitial compartment of a renal cortex." [PMID:18575881] xref: KUPO:0001091 is_a: CL:0002584 ! renal cortical epithelial cell is_a: CL:1000500 {is_inferred="true"} ! kidney interstitial cell @@ -30249,6 +30267,7 @@ relationship: part_of UBERON:0005270 ! renal cortex interstitium [Term] id: CL:1000682 name: kidney medulla interstitial cell +def: "A cell that is part of an interstitum of a renal medulla." [PMID:21359760] xref: KUPO:0001092 is_a: CL:1000500 {is_inferred="true"} ! kidney interstitial cell is_a: CL:1000504 {is_inferred="true"} ! kidney medulla cell @@ -30263,11 +30282,12 @@ subset: human_reference_atlas xref: KUPO:0001101 is_a: CL:0000186 ! myofibroblast cell is_a: CL:1000500 ! kidney interstitial cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000692 name: kidney interstitial fibroblast +def: "A fibroblast that is part of an interstitial compartment of a kidney." [PMID:10559635] subset: cellxgene_subset subset: human_reference_atlas xref: KUPO:0001102 @@ -30275,7 +30295,7 @@ is_a: CL:0000057 ! fibroblast is_a: CL:1000500 ! kidney interstitial cell intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0005215 ! kidney interstitium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000693 @@ -30291,7 +30311,7 @@ subset: human_reference_atlas xref: KUPO:0001106 is_a: CL:0000890 ! alternatively activated macrophage is_a: CL:1000500 ! kidney interstitial cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000696 @@ -30319,6 +30339,7 @@ is_a: CL:1000500 ! kidney interstitial cell [Term] id: CL:1000699 name: kidney resident dendritic cell +def: "A resident-dendritic cell that is part of a kidney." [PMID:25266210] xref: KUPO:0001110 is_a: CL:0001007 ! interstitial dendritic cell is_a: CL:1000500 ! kidney interstitial cell @@ -30366,7 +30387,7 @@ is_a: CL:1000601 {is_inferred="true"} ! ureteral cell intersection_of: CL:1000601 ! ureteral cell intersection_of: part_of UBERON:0001252 ! adventitia of ureter relationship: part_of UBERON:0001252 ! adventitia of ureter -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000714 @@ -30377,7 +30398,7 @@ is_a: CL:1000549 {is_inferred="true"} ! kidney cortex collecting duct epithelial is_a: CL:1001431 ! kidney collecting duct principal cell intersection_of: CL:0005009 ! renal principal cell intersection_of: part_of UBERON:0004203 ! cortical collecting duct -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000715 @@ -30388,7 +30409,7 @@ is_a: CL:1000549 {is_inferred="true"} ! kidney cortex collecting duct epithelial is_a: CL:1001432 ! kidney collecting duct intercalated cell intersection_of: CL:0005010 ! renal intercalated cell intersection_of: part_of UBERON:0004203 ! cortical collecting duct -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000716 @@ -30400,7 +30421,7 @@ is_a: CL:1000548 {is_inferred="true"} ! kidney outer medulla collecting duct epi is_a: CL:1001431 ! kidney collecting duct principal cell intersection_of: CL:0005009 ! renal principal cell intersection_of: part_of UBERON:0004204 ! outer medullary collecting duct -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000717 @@ -30412,7 +30433,7 @@ is_a: CL:1000548 {is_inferred="true"} ! kidney outer medulla collecting duct epi is_a: CL:1001432 ! kidney collecting duct intercalated cell intersection_of: CL:0005010 ! renal intercalated cell intersection_of: part_of UBERON:0004204 ! outer medullary collecting duct -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000718 @@ -30423,7 +30444,7 @@ is_a: CL:1000547 {is_inferred="true"} ! kidney inner medulla collecting duct epi is_a: CL:1001431 ! kidney collecting duct principal cell intersection_of: CL:0005009 ! renal principal cell intersection_of: part_of UBERON:0004205 ! inner medullary collecting duct -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000719 @@ -30466,7 +30487,7 @@ is_a: CL:1000746 ! glomerular cell is_a: CL:1001318 ! renal interstitial pericyte relationship: capable_of GO:0070252 ! actin-mediated cell contraction relationship: part_of UBERON:0002320 ! glomerular mesangium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000746 @@ -30489,11 +30510,12 @@ is_a: CL:1000615 ! kidney cortex tubule cell intersection_of: CL:1000494 ! nephron tubule epithelial cell intersection_of: part_of UBERON:0005097 ! renal connecting tubule relationship: part_of UBERON:0005097 ! renal connecting tubule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000803 name: kidney inner medulla interstitial cell +def: "A cell that is part of an interstitial compartment of an inner renal medulla." [PMID:21359760] xref: KUPO:0001093 is_a: CL:1000617 {is_inferred="true"} ! kidney inner medulla cell is_a: CL:1000682 {is_inferred="true"} ! kidney medulla interstitial cell @@ -30504,6 +30526,7 @@ relationship: part_of UBERON:0005214 ! inner renal medulla interstitium [Term] id: CL:1000804 name: kidney outer medulla interstitial cell +def: "A kidney cell that is part of an interstitial compartment of an outer renal medulla." [PMID:8694267] xref: KUPO:0001094 is_a: CL:1000616 {is_inferred="true"} ! kidney outer medulla cell is_a: CL:1000682 {is_inferred="true"} ! kidney medulla interstitial cell @@ -30544,7 +30567,7 @@ is_a: CL:0002305 {is_inferred="true"} ! epithelial cell of distal tubule intersection_of: CL:0002305 ! epithelial cell of distal tubule intersection_of: part_of UBERON:0001292 ! distal convoluted tubule relationship: part_of UBERON:0001292 ! distal convoluted tubule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000850 @@ -30557,15 +30580,16 @@ is_a: CL:1000618 {is_inferred="true"} ! juxtaglomerular complex cell intersection_of: CL:0002305 ! epithelial cell of distal tubule intersection_of: part_of UBERON:0002335 ! macula densa relationship: part_of UBERON:0002335 ! macula densa -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000854 name: kidney blood vessel cell +def: "A blood vessel cell that is part of a kidney." [PMID:34843404] xref: KUPO:0001014 is_a: CL:0002584 ! renal cortical epithelial cell is_a: CL:1000504 {is_inferred="true"} ! kidney medulla cell -intersection_of: CL:1000504 ! kidney medulla cell +intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0003517 ! kidney blood vessel relationship: part_of UBERON:0003517 ! kidney blood vessel relationship: participates_in GO:0008015 ! blood circulation @@ -30635,7 +30659,7 @@ is_a: CL:1000892 {is_inferred="true"} ! kidney capillary endothelial cell intersection_of: CL:1000892 ! kidney capillary endothelial cell intersection_of: part_of UBERON:0004294 ! glomerular capillary endothelium relationship: part_of UBERON:0004294 ! glomerular capillary endothelium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1001006 @@ -30691,11 +30715,12 @@ is_a: CL:1000892 {is_inferred="true"} ! kidney capillary endothelial cell intersection_of: CL:1000892 ! kidney capillary endothelial cell intersection_of: part_of UBERON:0005272 ! peritubular capillary relationship: part_of UBERON:0012441 ! endothelium of peritubular capillary -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1001036 name: vasa recta cell +def: "A cell that is part of a vasa recta." [PMID:12529271, PMID:24381184] xref: KUPO:0001068 is_a: CL:0002543 ! vein endothelial cell is_a: CL:1000892 {is_inferred="true"} ! kidney capillary endothelial cell @@ -30761,7 +30786,7 @@ is_a: CL:1000413 ! endothelial cell of artery is_a: CL:1001006 ! kidney afferent arteriole cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0004639 ! renal afferent arteriole -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1001097 @@ -30783,7 +30808,7 @@ is_a: CL:1000412 {is_inferred="true"} ! endothelial cell of arteriole is_a: CL:1001009 ! kidney efferent arteriole cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0004640 ! renal efferent arteriole -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1001100 @@ -30807,7 +30832,7 @@ is_a: CL:1001016 {is_inferred="true"} ! kidney loop of Henle ascending limb epit intersection_of: CL:1001016 ! kidney loop of Henle ascending limb epithelial cell intersection_of: part_of UBERON:0001291 ! thick ascending limb of loop of Henle relationship: part_of UBERON:0001291 ! thick ascending limb of loop of Henle -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1001107 @@ -30821,7 +30846,7 @@ is_a: CL:1001016 {is_inferred="true"} ! kidney loop of Henle ascending limb epit intersection_of: CL:1001016 ! kidney loop of Henle ascending limb epithelial cell intersection_of: part_of UBERON:0004193 ! loop of Henle ascending limb thin segment relationship: part_of UBERON:0004193 ! loop of Henle ascending limb thin segment -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1001108 @@ -30835,7 +30860,7 @@ is_a: CL:1001106 ! kidney loop of Henle thick ascending limb epithelial cell intersection_of: CL:1001016 ! kidney loop of Henle ascending limb epithelial cell intersection_of: part_of UBERON:0006376 ! premacula segment of distal straight tubule relationship: part_of UBERON:0006376 ! premacula segment of distal straight tubule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1001109 @@ -30848,7 +30873,7 @@ is_a: CL:1001106 ! kidney loop of Henle thick ascending limb epithelial cell intersection_of: CL:1001016 ! kidney loop of Henle ascending limb epithelial cell intersection_of: part_of UBERON:0006854 ! distal straight tubule postmacula segment relationship: part_of UBERON:0006854 ! distal straight tubule postmacula segment -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1001111 @@ -30863,7 +30888,7 @@ is_a: CL:1001021 {is_inferred="true"} ! kidney loop of Henle descending limb epi intersection_of: CL:1001021 ! kidney loop of Henle descending limb epithelial cell intersection_of: part_of UBERON:0005096 ! descending thin limb relationship: part_of UBERON:0005096 ! descending thin limb -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1001123 @@ -30916,7 +30941,7 @@ is_a: CL:1001036 {is_inferred="true"} ! vasa recta cell intersection_of: CL:1001036 ! vasa recta cell intersection_of: part_of UBERON:0009091 ! vasa recta ascending limb relationship: part_of UBERON:0009091 ! vasa recta ascending limb -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1001135 @@ -31070,7 +31095,7 @@ is_a: CL:1001036 {is_inferred="true"} ! vasa recta cell intersection_of: CL:1001036 ! vasa recta cell intersection_of: part_of UBERON:0009202 ! vasa recta descending limb relationship: part_of UBERON:0009202 ! vasa recta descending limb -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1001286 @@ -31103,7 +31128,7 @@ is_a: CL:0000669 {is_inferred="true"} ! pericyte is_a: CL:1000500 ! kidney interstitial cell intersection_of: CL:0000669 ! pericyte intersection_of: part_of UBERON:0005215 ! kidney interstitium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1001319 @@ -31115,7 +31140,7 @@ is_a: CL:1000600 ! lower urinary tract cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001255 ! urinary bladder relationship: part_of UBERON:0001255 ! urinary bladder -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1001320 @@ -31141,7 +31166,7 @@ is_a: CL:1001319 ! bladder cell intersection_of: CL:0000731 ! urothelial cell intersection_of: part_of UBERON:0004645 ! urinary bladder urothelium relationship: part_of UBERON:0004645 ! urinary bladder urothelium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1001430 @@ -31164,7 +31189,7 @@ is_a: CL:0005009 {is_inferred="true"} ! renal principal cell is_a: CL:1000454 ! kidney collecting duct epithelial cell intersection_of: CL:0005009 ! renal principal cell intersection_of: part_of UBERON:0001232 ! collecting duct of renal tubule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1001432 @@ -31177,7 +31202,7 @@ is_a: CL:0005010 {is_inferred="true"} ! renal intercalated cell is_a: CL:1000454 ! kidney collecting duct epithelial cell intersection_of: CL:0005010 ! renal intercalated cell intersection_of: part_of UBERON:0001232 ! collecting duct of renal tubule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1001433 @@ -31191,7 +31216,7 @@ is_a: CL:0000083 ! epithelial cell of pancreas intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0000017 ! exocrine pancreas relationship: part_of UBERON:0000017 ! exocrine pancreas -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1001434 @@ -31255,8 +31280,8 @@ synonym: "striatal medium spiny neuron" EXACT [GO:0021773] xref: BTO:0004778 is_a: CL:0000617 ! GABAergic neuron is_a: CL:2000029 ! central nervous system neuron -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002100 UBERON:0000369 ! has soma location corpus striatum +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1001502 @@ -31357,7 +31382,7 @@ is_a: CL:1000413 ! endothelial cell of artery intersection_of: CL:0002139 ! endothelial cell of vascular tree intersection_of: part_of UBERON:0002012 ! pulmonary artery relationship: part_of UBERON:0005317 ! pulmonary artery endothelium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1001569 @@ -31453,7 +31478,7 @@ is_a: CL:0002251 ! epithelial cell of alimentary canal intersection_of: CL:0000076 ! squamous epithelial cell intersection_of: part_of UBERON:0002372 ! tonsil relationship: part_of UBERON:0013696 ! tonsil epithelium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1001578 @@ -31712,7 +31737,7 @@ is_a: CL:1001433 ! epithelial cell of exocrine pancreas intersection_of: CL:0000150 ! glandular epithelial cell intersection_of: part_of UBERON:0000017 ! exocrine pancreas relationship: part_of UBERON:0013697 ! exocrine pancreas epithelium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1001601 @@ -31774,7 +31799,7 @@ is_a: CL:0000138 ! chondrocyte intersection_of: CL:0000138 ! chondrocyte intersection_of: part_of UBERON:0010996 ! articular cartilage of joint relationship: part_of UBERON:0010996 ! articular cartilage of joint -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1001608 @@ -31831,8 +31856,8 @@ is_a: CL:0002484 ! epithelial melanocyte is_a: CL:1000458 ! melanocyte of skin intersection_of: CL:0000148 ! melanocyte intersection_of: part_of UBERON:0001003 ! skin epidermis -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0001003 ! skin epidermis +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-02-03T23:03:09Z [Term] @@ -31844,8 +31869,8 @@ is_a: CL:0000080 ! circulating cell is_a: CL:0000842 ! mononuclear cell intersection_of: CL:0000842 ! mononuclear cell intersection_of: part_of UBERON:0000178 ! blood -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0000178 ! blood +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-02-11T17:29:04Z [Term] @@ -31860,8 +31885,8 @@ xref: BTO:0005756 xref: NCIT:C32429 is_a: CL:0000349 ! extraembryonic cell is_a: CL:0000499 ! stromal cell -relationship: develops_from CL:0002255 ! stromal cell of endometrium relationship: part_of UBERON:0002450 ! decidua +relationship: RO:0002202 CL:0002255 ! develops from stromal cell of endometrium creation_date: 2014-02-20T23:06:41Z [Term] @@ -31872,8 +31897,8 @@ subset: cellxgene_subset is_a: CL:0002319 ! neural cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0000007 ! pituitary gland -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0000007 ! pituitary gland +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-03-26T22:14:56Z [Term] @@ -31883,8 +31908,8 @@ def: "Any macroglial cell that is part of a brain." [GOC:TermGenie] is_a: CL:0000126 ! macroglial cell intersection_of: CL:0000126 ! macroglial cell intersection_of: part_of UBERON:0000955 ! brain -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0000955 ! brain +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-03-28T21:35:27Z [Term] @@ -31895,8 +31920,8 @@ subset: cellxgene_subset is_a: CL:0000844 ! germinal center B cell intersection_of: CL:0000844 ! germinal center B cell intersection_of: part_of UBERON:0002372 ! tonsil -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0002372 ! tonsil +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-03-28T21:35:33Z [Term] @@ -31906,8 +31931,8 @@ def: "Chondrocyte forming the hyaline cartilage found in the knee joint." [GOC:T is_a: CL:1001607 ! articular chondrocyte intersection_of: CL:1001607 ! articular chondrocyte intersection_of: part_of UBERON:0001485 ! knee joint -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0001485 ! knee joint +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-04T14:40:11Z [Term] @@ -31917,15 +31942,15 @@ def: "Any blood vessel endothelial cell that is part of a microvascular endothel is_a: CL:0000071 ! blood vessel endothelial cell intersection_of: CL:0000071 ! blood vessel endothelial cell intersection_of: part_of UBERON:0008339 ! microvascular endothelium -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0008339 ! microvascular endothelium +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-04T15:07:42Z [Term] id: CL:2000009 name: obsolete microvascular endothelium blood vessel endothelial cell def: "Any blood vessel endothelial cell that is part of a microvascular endothelium." [GOC:TermGenie] -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 is_obsolete: true replaced_by: CL:2000008 creation_date: 2014-06-04T15:09:18Z @@ -31937,8 +31962,8 @@ def: "Any blood vessel endothelial cell that is part of a dermis." [GOC:TermGeni is_a: CL:0000071 ! blood vessel endothelial cell intersection_of: CL:0000071 ! blood vessel endothelial cell intersection_of: part_of UBERON:0002067 ! dermis -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0002067 ! dermis +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-04T15:12:06Z [Term] @@ -31948,8 +31973,8 @@ def: "Any endothelial cell of lymphatic vessel that is part of a dermis." [GOC:T is_a: CL:0002138 ! endothelial cell of lymphatic vessel intersection_of: CL:0002138 ! endothelial cell of lymphatic vessel intersection_of: part_of UBERON:0002067 ! dermis -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0002067 ! dermis +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-04T15:15:08Z [Term] @@ -31959,8 +31984,8 @@ def: "Any skin fibroblast that is part of a pedal digit skin." [GOC:TermGenie] is_a: CL:0002620 ! skin fibroblast intersection_of: CL:0002620 ! skin fibroblast intersection_of: part_of UBERON:0003530 ! pedal digit skin -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0003530 ! pedal digit skin +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-04T15:16:44Z [Term] @@ -31970,8 +31995,8 @@ def: "Any skin fibroblast that is part of a skin of abdomen." [GOC:TermGenie] is_a: CL:0002620 ! skin fibroblast intersection_of: CL:0002620 ! skin fibroblast intersection_of: part_of UBERON:0001416 ! skin of abdomen -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0001416 ! skin of abdomen +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-04T15:18:16Z [Term] @@ -31981,8 +32006,8 @@ def: "Any skin fibroblast that is part of a upper leg skin." [GOC:TermGenie] is_a: CL:0002620 ! skin fibroblast intersection_of: CL:0002620 ! skin fibroblast intersection_of: part_of UBERON:0004262 ! upper leg skin -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0004262 ! upper leg skin +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-04T15:19:44Z [Term] @@ -31992,8 +32017,8 @@ def: "Any skin fibroblast that is part of a arm." [GOC:TermGenie] is_a: CL:0002620 ! skin fibroblast intersection_of: CL:0002620 ! skin fibroblast intersection_of: part_of UBERON:0001460 ! arm -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0001460 ! arm +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-04T15:29:06Z [Term] @@ -32005,7 +32030,7 @@ is_a: CL:1001567 ! lung endothelial cell is_a: CL:2000008 ! microvascular endothelial cell intersection_of: CL:1001567 ! lung endothelial cell intersection_of: part_of UBERON:0008339 ! microvascular endothelium -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-04T16:00:56Z [Term] @@ -32015,8 +32040,8 @@ def: "Any fibroblast that is part of a periodontal ligament." [GOC:TermGenie] is_a: CL:0002556 ! fibroblast of periodontium intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0008266 ! periodontal ligament -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0008266 ! periodontal ligament +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-04T16:50:33Z [Term] @@ -32028,8 +32053,8 @@ is_a: CL:0010006 ! cardiac blood vessel endothelial cell is_a: CL:1000413 ! endothelial cell of artery intersection_of: CL:1000413 ! endothelial cell of artery intersection_of: part_of UBERON:0001621 ! coronary artery -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0001621 ! coronary artery +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-04T17:08:47Z [Term] @@ -32040,8 +32065,8 @@ xref: FBbt:00004211 is_a: CL:0000287 ! eye photoreceptor cell intersection_of: CL:0000210 ! photoreceptor cell intersection_of: part_of UBERON:0000018 ! compound eye -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0000018 ! compound eye +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-24T23:16:45Z [Term] @@ -32051,8 +32076,8 @@ def: "Any native cell that is part of a inner cell mass." [GOC:TermGenie] is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0000087 ! inner cell mass -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0000087 ! inner cell mass +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-24T23:16:53Z [Term] @@ -32063,8 +32088,8 @@ subset: cellxgene_subset is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001821 ! sebaceous gland -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0001821 ! sebaceous gland +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-24T23:17:00Z [Term] @@ -32074,8 +32099,8 @@ def: "Any native cell that is part of a cardiac septum." [GOC:TermGenie] is_a: CL:0002494 ! cardiocyte intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0002099 ! cardiac septum -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0002099 ! cardiac septum +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-24T23:17:07Z [Term] @@ -32085,8 +32110,8 @@ def: "Any interneuron that is part of a spinal cord ventral column." [GOC:TermGe is_a: CL:0005000 ! spinal cord interneuron intersection_of: CL:0000099 ! interneuron intersection_of: RO:0002100 UBERON:0005375 ! has soma location spinal cord ventral column -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: RO:0002100 UBERON:0005375 ! has soma location spinal cord ventral column +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-25T00:23:36Z [Term] @@ -32096,8 +32121,8 @@ def: "Any neuron that is part of a spinal cord medial motor column." [GOC:TermGe is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0004059 ! has soma location spinal cord medial motor column -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: RO:0002100 UBERON:0004059 ! has soma location spinal cord medial motor column +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-25T00:23:43Z [Term] @@ -32107,15 +32132,15 @@ def: "Any oligodendrocyte that is part of a spinal cord." [GOC:TermGenie] is_a: CL:0000128 ! oligodendrocyte intersection_of: CL:0000128 ! oligodendrocyte intersection_of: part_of UBERON:0002240 ! spinal cord -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0002240 ! spinal cord +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-25T00:23:50Z [Term] id: CL:2000026 name: obsolete cerebellum Golgi cell def: "Any Golgi cell that is part of a cerebellum." [GOC:TermGenie] -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 is_obsolete: true creation_date: 2014-06-25T00:23:57Z @@ -32128,7 +32153,7 @@ is_a: CL:0000402 ! CNS interneuron is_a: CL:1001611 ! cerebellar neuron intersection_of: CL:0000118 ! basket cell intersection_of: RO:0002100 UBERON:0002037 ! has soma location cerebellum -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-25T00:24:03Z [Term] @@ -32139,7 +32164,7 @@ is_a: CL:0000679 ! glutamatergic neuron is_a: CL:1001611 ! cerebellar neuron intersection_of: CL:0000679 ! glutamatergic neuron intersection_of: RO:0002100 UBERON:0002037 ! has soma location cerebellum -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-25T00:24:10Z [Term] @@ -32149,8 +32174,8 @@ def: "Any neuron that is part of a central nervous system." [GOC:TermGenie] is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0001017 ! has soma location central nervous system -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: RO:0002100 UBERON:0001017 ! has soma location central nervous system +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-25T01:17:43Z [Term] @@ -32160,8 +32185,8 @@ def: "Any native cell that is part of a hypothalamus." [GOC:TermGenie] is_a: CL:0002319 ! neural cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001898 ! hypothalamus -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0001898 ! hypothalamus +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-25T01:17:50Z [Term] @@ -32171,8 +32196,8 @@ def: "Any neuron that is part of a lateral line ganglion." [GOC:TermGenie] is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:2000120 ! has soma location lateral line ganglion -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: RO:0002100 UBERON:2000120 ! has soma location lateral line ganglion +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-25T01:17:57Z [Term] @@ -32187,8 +32212,8 @@ xref: FMA:84664 is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0000010 ! has soma location peripheral nervous system -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: RO:0002100 UBERON:0000010 ! has soma location peripheral nervous system +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-25T02:28:17Z [Term] @@ -32198,8 +32223,8 @@ def: "Any basal cell of epidermis that is part of a limb." [GOC:TermGenie] is_a: CL:0002187 ! basal cell of epidermis intersection_of: CL:0002187 ! basal cell of epidermis intersection_of: part_of UBERON:0002101 ! limb -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0002101 ! limb +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-25T02:28:25Z [Term] @@ -32209,8 +32234,8 @@ def: "Any neuromast hair cell that is part of a anterior lateral line." [GOC:Ter is_a: CL:0000856 ! neuromast hair cell intersection_of: CL:0000856 ! neuromast hair cell intersection_of: part_of UBERON:2001470 ! anterior lateral line -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:2001470 ! anterior lateral line +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-25T03:44:37Z [Term] @@ -32220,8 +32245,8 @@ def: "Any neuromast mantle cell that is part of an anterior lateral line." [GOC: is_a: CL:0000851 ! neuromast mantle cell intersection_of: CL:0000851 ! neuromast mantle cell intersection_of: part_of UBERON:2001470 ! anterior lateral line -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:2001470 ! anterior lateral line +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-25T03:44:44Z [Term] @@ -32232,8 +32257,8 @@ synonym: "anterior lateral line neuromast support cell" EXACT [] is_a: CL:0000852 ! neuromast supporting cell intersection_of: CL:0000852 ! neuromast supporting cell intersection_of: part_of UBERON:2001470 ! anterior lateral line -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:2001470 ! anterior lateral line +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-25T03:44:51Z [Term] @@ -32243,8 +32268,8 @@ def: "Any neuromast hair cell that is part of a posterior lateral line." [GOC:Te is_a: CL:0000856 ! neuromast hair cell intersection_of: CL:0000856 ! neuromast hair cell intersection_of: part_of UBERON:0006334 ! posterior lateral line -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0006334 ! posterior lateral line +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-25T03:44:57Z [Term] @@ -32254,8 +32279,8 @@ def: "Any neuromast mantle cell that is part of a posterior lateral line." [GOC: is_a: CL:0000851 ! neuromast mantle cell intersection_of: CL:0000851 ! neuromast mantle cell intersection_of: part_of UBERON:0006334 ! posterior lateral line -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0006334 ! posterior lateral line +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-25T03:45:04Z [Term] @@ -32266,8 +32291,8 @@ synonym: "posterior lateral line neuromast support cell" EXACT [] is_a: CL:0000852 ! neuromast supporting cell intersection_of: CL:0000852 ! neuromast supporting cell intersection_of: part_of UBERON:0006334 ! posterior lateral line -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0006334 ! posterior lateral line +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-25T03:45:11Z [Term] @@ -32279,8 +32304,8 @@ is_a: CL:1001319 ! bladder cell is_a: CL:2000008 ! microvascular endothelial cell intersection_of: CL:2000008 ! microvascular endothelial cell intersection_of: part_of UBERON:0001255 ! urinary bladder -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2014-07-09T00:04:47Z [Term] @@ -32291,8 +32316,8 @@ subset: cellxgene_subset is_a: CL:2000011 ! dermis lymphatic vessel endothelial cell intersection_of: CL:2000011 ! dermis lymphatic vessel endothelial cell intersection_of: part_of UBERON:0008339 ! microvascular endothelium -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0008339 ! microvascular endothelium +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-07-09T00:09:54Z [Term] @@ -32303,8 +32328,8 @@ subset: cellxgene_subset is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0000922 ! embryo -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0000922 ! embryo +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-07-09T00:12:00Z [Term] @@ -32315,8 +32340,8 @@ subset: cellxgene_subset is_a: CL:0002575 ! central nervous system pericyte intersection_of: CL:0000669 ! pericyte intersection_of: part_of UBERON:0000955 ! brain -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0000955 ! brain +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-07-09T00:18:22Z [Term] @@ -32327,8 +32352,8 @@ is_a: CL:0002319 ! neural cell is_a: CL:2000008 ! microvascular endothelial cell intersection_of: CL:2000008 ! microvascular endothelial cell intersection_of: part_of UBERON:0000955 ! brain -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0000955 ! brain +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-07-09T00:24:53Z [Term] @@ -32338,8 +32363,8 @@ def: "Any melanocyte that is part of a prepuce of penis." [GOC:TermGenie] is_a: CL:0000148 ! melanocyte intersection_of: CL:0000148 ! melanocyte intersection_of: part_of UBERON:0001332 ! prepuce of penis -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0001332 ! prepuce of penis +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-07-09T00:45:07Z [Term] @@ -32350,8 +32375,8 @@ subset: cellxgene_subset is_a: CL:0000746 ! cardiac muscle cell intersection_of: CL:0000746 ! cardiac muscle cell intersection_of: part_of UBERON:0002082 ! cardiac ventricle -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0002082 ! cardiac ventricle +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-08-12T20:50:28Z [Term] @@ -32362,8 +32387,8 @@ is_a: CL:0000100 ! motor neuron is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000100 ! motor neuron intersection_of: RO:0002100 UBERON:0002298 ! has soma location brainstem -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: RO:0002100 UBERON:0002298 ! has soma location brainstem +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-02T23:52:53Z [Term] @@ -32376,8 +32401,8 @@ synonym: "ventral horn of spinal cord spinal cord motor neuron" EXACT [] xref: NCIT:C12645 is_a: CL:0008039 ! lower motor neuron is_a: CL:0011001 ! spinal cord motor neuron -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: RO:0002100 UBERON:0002257 ! has soma location ventral horn of spinal cord +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-03T00:26:27Z [Term] @@ -32388,8 +32413,8 @@ comment: http://www.ncbi.nlm.nih.gov/pubmed/12524689 is_a: CL:4023111 ! cerebral cortex pyramidal neuron intersection_of: CL:0000598 ! pyramidal neuron intersection_of: RO:0002100 UBERON:0001384 ! has soma location primary motor cortex -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: RO:0002100 UBERON:0001384 ! has soma location primary motor cortex +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-06T17:39:04Z [Term] @@ -32397,7 +32422,7 @@ id: CL:2000050 name: obsolete retina retinal ganglion cell def: "Any retinal ganglion cell that is part of a retina." [GOC:TermGenie] comment: http://www.ncbi.nlm.nih.gov/pubmed/2889210 -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 is_obsolete: true creation_date: 2014-10-06T17:43:59Z @@ -32408,8 +32433,8 @@ def: "Any fibroblast that is part of a spleen." [GOC:TermGenie] is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0002106 ! spleen -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0002106 ! spleen +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-06T18:58:47Z [Term] @@ -32421,8 +32446,8 @@ is_a: CL:0000349 ! extraembryonic cell is_a: CL:1000413 ! endothelial cell of artery intersection_of: CL:1000413 ! endothelial cell of artery intersection_of: part_of UBERON:0002331 ! umbilical cord -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0002331 ! umbilical cord +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-06T19:01:48Z [Term] @@ -32434,9 +32459,9 @@ subset: human_reference_atlas is_a: CL:0000115 ! endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0002106 ! spleen -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0002106 ! spleen -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2014-10-06T19:06:04Z [Term] @@ -32446,8 +32471,8 @@ def: "A large, granular, liver specific natural killer cell that adheres to the comment: Pit cells are named for the presence of large cytoplasmic granules that resemble pits (pips) of fruit. subset: human_reference_atlas is_a: CL:0000623 ! natural killer cell -relationship: located_in UBERON:0001281 ! hepatic sinusoid -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0001025 UBERON:0001281 ! located in hepatic sinusoid +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:2000055 @@ -32459,8 +32484,8 @@ synonym: "hepatic dendritic cell" EXACT [] is_a: CL:0000451 ! dendritic cell intersection_of: CL:0000451 ! dendritic cell intersection_of: part_of UBERON:0002107 ! liver -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0002107 ! liver +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-06T19:16:11Z [Term] @@ -32468,7 +32493,7 @@ id: CL:2000056 name: Meynert cell def: "Any pyramidal cell that is part of a regional part of cerebral cortex." [GOC:TermGenie] is_a: CL:2000049 ! primary motor cortex pyramidal cell -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-06T19:20:41Z [Term] @@ -32480,8 +32505,8 @@ is_a: CL:0000062 ! osteoblast is_a: CL:0001035 ! bone cell intersection_of: CL:0000062 ! osteoblast intersection_of: part_of UBERON:0000981 ! femur -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0000981 ! femur +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-06T19:29:45Z [Term] @@ -32492,8 +32517,8 @@ comment: http://www.sciencellonline.com/site/productInformation.php?keyword=4600 is_a: CL:0000062 ! osteoblast intersection_of: CL:0000062 ! osteoblast intersection_of: part_of UBERON:0003129 ! skull -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0003129 ! skull +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-06T19:48:30Z [Term] @@ -32505,8 +32530,8 @@ subset: cellxgene_subset is_a: CL:2000008 ! microvascular endothelial cell intersection_of: CL:2000008 ! microvascular endothelial cell intersection_of: part_of UBERON:0002367 ! prostate gland -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0002367 ! prostate gland +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-07T17:46:27Z [Term] @@ -32522,8 +32547,8 @@ xref: BTO:0006208 is_a: CL:0000351 ! trophoblast cell intersection_of: CL:0000351 ! trophoblast cell intersection_of: part_of UBERON:0010005 ! placental labyrinth villous -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0010005 ! placental labyrinth villous +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 property_value: seeAlso "http://www.sciencellonline.com/site/productInformation.php?keyword=7120" xsd:string creation_date: 2014-10-07T17:48:27Z @@ -32536,9 +32561,9 @@ subset: human_reference_atlas is_a: CL:0000134 ! mesenchymal stem cell intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: part_of UBERON:0001987 ! placenta -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0001987 ! placenta -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2014-10-07T17:51:11Z [Term] @@ -32550,8 +32575,8 @@ is_a: CL:0002144 ! capillary endothelial cell is_a: CL:0009092 ! endothelial cell of placenta intersection_of: CL:0002144 ! capillary endothelial cell intersection_of: part_of UBERON:0010005 ! placental labyrinth villous -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0010005 ! placental labyrinth villous +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-07T17:55:56Z [Term] @@ -32562,8 +32587,8 @@ comment: http://www.sciencellonline.com/site/productInformation.php?keyword=7330 is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0000992 ! ovary -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0000992 ! ovary +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-07T17:57:42Z [Term] @@ -32575,8 +32600,8 @@ subset: cellxgene_subset is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0000992 ! ovary -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0000992 ! ovary +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-07T17:59:13Z [Term] @@ -32588,8 +32613,8 @@ is_a: CL:1000296 ! epithelial cell of urethra is_a: CL:2000008 ! microvascular endothelial cell intersection_of: CL:2000008 ! microvascular endothelial cell intersection_of: part_of UBERON:0001334 ! female urethra -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0001334 ! female urethra +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-07T18:18:01Z [Term] @@ -32601,9 +32626,9 @@ subset: human_reference_atlas is_a: CL:0002548 ! fibroblast of cardiac tissue intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0002082 ! cardiac ventricle -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0002082 ! cardiac ventricle -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2014-10-07T18:35:38Z [Term] @@ -32615,9 +32640,9 @@ subset: human_reference_atlas is_a: CL:0002548 ! fibroblast of cardiac tissue intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0002081 ! cardiac atrium -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0002081 ! cardiac atrium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2014-10-07T18:36:54Z [Term] @@ -32628,8 +32653,8 @@ comment: http://www.sciencellonline.com/site/productInformation.php?keyword=6430 is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0002407 ! pericardium -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0002407 ! pericardium +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-07T18:38:06Z [Term] @@ -32640,8 +32665,8 @@ comment: http://www.sciencellonline.com/site/productInformation.php?keyword=5430 is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0002110 ! gallbladder -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0002110 ! gallbladder +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-07T18:41:43Z [Term] @@ -32652,8 +32677,8 @@ comment: http://www.sciencellonline.com/site/productInformation.php?keyword=6620 is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001776 ! optic choroid -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0001776 ! optic choroid +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-07T18:50:43Z [Term] @@ -32664,8 +32689,8 @@ comment: http://www.sciencellonline.com/site/productInformation.php?keyword=7600 is_a: CL:2000008 ! microvascular endothelial cell intersection_of: CL:2000008 ! microvascular endothelial cell intersection_of: part_of UBERON:0000310 ! breast -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0000310 ! breast +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-07T19:55:30Z [Term] @@ -32677,8 +32702,8 @@ is_a: CL:0002320 ! connective tissue cell is_a: CL:2000008 ! microvascular endothelial cell intersection_of: CL:2000008 ! microvascular endothelial cell intersection_of: part_of UBERON:0001013 ! adipose tissue -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0001013 ! adipose tissue +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-10-07T22:13:45Z [Term] @@ -32689,8 +32714,8 @@ synonym: "cardiac neural crest cell" EXACT [PMID:33060096] is_a: CL:0000333 ! migratory neural crest cell intersection_of: CL:0000333 ! migratory neural crest cell intersection_of: part_of UBERON:0000095 ! cardiac neural crest -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0000095 ! cardiac neural crest +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-11-05T01:18:43Z [Term] @@ -32701,8 +32726,8 @@ comment: Splenocytes is a vague term that refers to any one of the different whi is_a: CL:0000738 ! leukocyte intersection_of: CL:0000738 ! leukocyte intersection_of: part_of UBERON:0002106 ! spleen -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0002106 ! spleen +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-11-05T01:26:50Z [Term] @@ -32712,8 +32737,8 @@ def: "Any endodermal cell that is part of a anterior visceral endoderm." [GOC:Te is_a: CL:0000223 ! endodermal cell intersection_of: CL:0000223 ! endodermal cell intersection_of: part_of UBERON:0004044 ! anterior visceral endoderm -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0004044 ! anterior visceral endoderm +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-11-05T01:34:13Z [Term] @@ -32723,8 +32748,8 @@ def: "Any vein endothelial cell that is part of a hindlimb stylopod." [GOC:TermG is_a: CL:0002543 ! vein endothelial cell intersection_of: CL:0002543 ! vein endothelial cell intersection_of: part_of UBERON:0000376 ! hindlimb stylopod -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0000376 ! hindlimb stylopod +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-12-02T18:40:47Z [Term] @@ -32735,8 +32760,8 @@ is_a: CL:0000188 ! cell of skeletal muscle is_a: CL:0000737 ! striated muscle cell intersection_of: CL:0000737 ! striated muscle cell intersection_of: part_of UBERON:0004510 ! skeletal muscle tissue of pectoralis major -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0004510 ! skeletal muscle tissue of pectoralis major +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-12-02T18:48:17Z [Term] @@ -32746,8 +32771,8 @@ def: "Any pericyte cell that is part of a placenta." [GOC:TermGenie] is_a: CL:0000669 ! pericyte intersection_of: CL:0000669 ! pericyte intersection_of: part_of UBERON:0001987 ! placenta -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0001987 ! placenta +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-12-02T18:51:03Z [Term] @@ -32757,8 +32782,8 @@ def: "Any mesenchymal stem cell of the bone marrow that is part of a femur." [GO is_a: CL:0002540 ! mesenchymal stem cell of the bone marrow intersection_of: CL:0002540 ! mesenchymal stem cell of the bone marrow intersection_of: part_of UBERON:0000981 ! femur -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0000981 ! femur +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-12-02T19:07:31Z [Term] @@ -32769,8 +32794,8 @@ synonym: "mesenchymal stem cell of abdominal adipose" EXACT [] is_a: CL:0002570 ! mesenchymal stem cell of adipose tissue intersection_of: CL:0002570 ! mesenchymal stem cell of adipose tissue intersection_of: part_of UBERON:0000916 ! abdomen -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0000916 ! abdomen +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-12-02T19:10:34Z [Term] @@ -32780,8 +32805,8 @@ def: "Any melanocyte of skin that is part of a skin of face." [GOC:TermGenie] is_a: CL:1000458 ! melanocyte of skin intersection_of: CL:1000458 ! melanocyte of skin intersection_of: part_of UBERON:1000021 ! skin of face -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:1000021 ! skin of face +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-12-02T19:10:40Z [Term] @@ -32792,8 +32817,8 @@ is_a: CL:1000458 ! melanocyte of skin is_a: CL:2000045 ! foreskin melanocyte intersection_of: CL:1000458 ! melanocyte of skin intersection_of: part_of UBERON:0001471 ! skin of prepuce of penis -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0001471 ! skin of prepuce of penis +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-12-02T19:10:45Z [Term] @@ -32803,8 +32828,8 @@ def: "Any hair follicle dermal papilla cell that is part of a scalp." [GOC:TermG is_a: CL:0000346 ! hair follicle dermal papilla cell intersection_of: CL:0000346 ! hair follicle dermal papilla cell intersection_of: part_of UBERON:0000403 ! scalp -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0000403 ! scalp +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-12-02T19:10:50Z [Term] @@ -32815,7 +32840,7 @@ is_a: CL:0000160 ! goblet cell is_a: CL:1000432 ! conjunctival epithelial cell intersection_of: CL:0000160 ! goblet cell intersection_of: part_of UBERON:0001811 ! conjunctiva -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-12-02T19:28:38Z [Term] @@ -32826,8 +32851,8 @@ is_a: CL:0000349 ! extraembryonic cell is_a: CL:0000842 ! mononuclear cell intersection_of: CL:0000842 ! mononuclear cell intersection_of: part_of UBERON:0002331 ! umbilical cord -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0002331 ! umbilical cord +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-12-02T20:14:16Z [Term] @@ -32838,8 +32863,8 @@ is_a: CL:0000118 ! basket cell is_a: CL:0010011 ! cerebral cortex GABAergic interneuron intersection_of: CL:0000118 ! basket cell intersection_of: RO:0002100 UBERON:0001950 ! has soma location neocortex -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: RO:0002100 UBERON:0001950 ! has soma location neocortex +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-12-24T00:37:19Z [Term] @@ -32852,7 +32877,7 @@ is_a: CL:1001569 ! hippocampal interneuron is_a: CL:4023062 ! dentate gyrus neuron intersection_of: CL:0000118 ! basket cell intersection_of: RO:0002100 UBERON:0001885 ! has soma location dentate gyrus of hippocampal formation -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-12-24T00:37:24Z [Term] @@ -32864,8 +32889,8 @@ is_a: CL:0010011 ! cerebral cortex GABAergic interneuron is_a: CL:1001569 ! hippocampal interneuron intersection_of: CL:0000118 ! basket cell intersection_of: RO:0002100 UBERON:0001954 ! has soma location Ammon's horn -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: RO:0002100 UBERON:0001954 ! has soma location Ammon's horn +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-12-24T00:37:30Z [Term] @@ -32878,8 +32903,8 @@ is_a: CL:0001033 ! hippocampal granule cell is_a: CL:4023062 ! dentate gyrus neuron intersection_of: CL:0001033 ! hippocampal granule cell intersection_of: RO:0002100 UBERON:0005381 ! has soma location dentate gyrus granule cell layer -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: RO:0002100 UBERON:0005381 ! has soma location dentate gyrus granule cell layer +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2015-02-23T05:48:23Z [Term] @@ -32891,7 +32916,7 @@ is_a: CL:0012001 ! neuron of the forebrain is_a: CL:4023062 ! dentate gyrus neuron intersection_of: CL:0000122 ! stellate neuron intersection_of: RO:0002100 UBERON:0001885 ! has soma location dentate gyrus of hippocampal formation -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2015-02-23T05:48:40Z [Term] @@ -32903,9 +32928,9 @@ is_a: CL:0009095 ! endothelial cell of uterus is_a: CL:2000008 ! microvascular endothelial cell intersection_of: CL:2000008 ! microvascular endothelial cell intersection_of: part_of UBERON:0015172 ! endometrial blood vessel -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0015172 ! endometrial blood vessel -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2015-03-31T21:02:36Z [Term] @@ -32917,7 +32942,7 @@ is_a: CL:0000312 ! keratinocyte is_a: CL:0002559 ! hair follicle cell intersection_of: CL:0000312 ! keratinocyte intersection_of: part_of UBERON:0002073 ! hair follicle -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2015-03-31T21:07:02Z [Term] @@ -32928,8 +32953,8 @@ subset: cellxgene_subset is_a: CL:0002553 ! fibroblast of lung intersection_of: CL:0002553 ! fibroblast of lung intersection_of: part_of UBERON:0002185 ! bronchus -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0002185 ! bronchus +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2015-03-31T21:16:22Z [Term] @@ -32939,8 +32964,8 @@ def: "Any epithelial cell of viscerocranial mucosa that is part of a nasal cavit is_a: CL:1000441 ! epithelial cell of viscerocranial mucosa intersection_of: CL:1000441 ! epithelial cell of viscerocranial mucosa intersection_of: part_of UBERON:0005385 ! nasal cavity respiratory epithelium -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0005385 ! nasal cavity respiratory epithelium +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2015-03-31T22:25:17Z [Term] @@ -32952,8 +32977,8 @@ is_a: CL:0002246 ! peripheral blood stem cell is_a: CL:0002352 ! gestational hematopoietic stem cell intersection_of: CL:0000037 ! hematopoietic stem cell intersection_of: part_of UBERON:0012168 ! umbilical cord blood -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0012168 ! umbilical cord blood +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2015-05-26T18:58:34Z [Term] @@ -32963,8 +32988,8 @@ def: "Any fibroblast that is part of a reticular layer of dermis." [GOC:TermGeni is_a: CL:0002551 ! fibroblast of dermis intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001993 ! reticular layer of dermis -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0001993 ! reticular layer of dermis +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2015-08-11T16:28:16Z [Term] @@ -32975,8 +33000,8 @@ is_a: CL:0000700 ! dopaminergic neuron is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000700 ! dopaminergic neuron intersection_of: RO:0002100 UBERON:0001891 ! has soma location midbrain -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: RO:0002100 UBERON:0001891 ! has soma location midbrain +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2015-12-03T16:42:40Z [Term] @@ -32987,8 +33012,8 @@ is_a: CL:0000067 ! ciliated epithelial cell is_a: CL:0002252 ! epithelial cell of esophagus intersection_of: CL:0000067 ! ciliated epithelial cell intersection_of: part_of UBERON:0001976 ! epithelium of esophagus -relationship: dc-contributor https://www.wikidata.org/entity/Q97529981 relationship: part_of UBERON:0001976 ! epithelium of esophagus +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q97529981 creation_date: 2019-02-09T16:40:30Z [Term] @@ -32999,9 +33024,9 @@ comment: Hofbauer cells are a heterogenic group of macrophages that resemble M2- subset: cellxgene_subset synonym: "HBC" RELATED OMO:0003000 [] is_a: CL:0000864 ! tissue-resident macrophage -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: dc-contributor https://www.wikidata.org/entity/Q97529981 relationship: part_of UBERON:0001987 ! placenta +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q97529981 creation_date: 2019-02-18T19:41:20Z [Term] @@ -33013,8 +33038,8 @@ is_a: CL:0008025 ! noradrenergic neuron is_a: CL:0011103 ! sympathetic neuron intersection_of: CL:0011103 ! sympathetic neuron intersection_of: capable_of GO:0061533 ! norepinephrine secretion, neurotransmission -relationship: dc-contributor https://www.wikidata.org/entity/Q97529981 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q97529981 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2019-02-25T19:30:14Z [Term] @@ -33025,7 +33050,7 @@ is_a: CL:0000108 ! cholinergic neuron is_a: CL:0011103 ! sympathetic neuron intersection_of: CL:0011103 ! sympathetic neuron intersection_of: capable_of GO:0014055 ! acetylcholine secretion, neurotransmission -relationship: dc-contributor https://www.wikidata.org/entity/Q97529981 +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q97529981 creation_date: 2019-02-25T19:32:20Z [Term] @@ -33036,7 +33061,7 @@ is_a: CL:0000101 ! sensory neuron is_a: CL:2000032 ! peripheral nervous system neuron intersection_of: CL:2000032 ! peripheral nervous system neuron intersection_of: capable_of GO:0050906 ! detection of stimulus involved in sensory perception -relationship: dc-contributor https://www.wikidata.org/entity/Q97529981 +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q97529981 creation_date: 2019-02-25T19:34:33Z [Term] @@ -33048,8 +33073,8 @@ synonym: "breast fibroblast" EXACT [] is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0000310 ! breast -relationship: dc-contributor https://orcid.org/0000-0001-9897-3238 relationship: part_of UBERON:0000310 ! breast +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9897-3238 [Term] id: CL:4006001 @@ -33059,45 +33084,45 @@ synonym: "skin of scalp fibroblast" EXACT [] is_a: CL:0002620 ! skin fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:8300000 ! skin of scalp -relationship: dc-contributor https://orcid.org/0000-0001-9897-3238 relationship: part_of UBERON:8300000 ! skin of scalp +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9897-3238 [Term] id: CL:4023000 name: beta motor neuron def: "A motor neuron that innervates both intrafusal and extrafusal muscle fibers. Low abundancy. They control both muscle contraction and responsiveness of the sensory feedback from muscle spindles." [PMID:25346659] is_a: CL:0008039 ! lower motor neuron -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: RO:0002120 CL:0008046 ! synapsed to extrafusal muscle fiber relationship: RO:0002120 CL:0008047 ! synapsed to intrafusal muscle fiber +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023001 name: static beta motor neuron def: "A beta motor neuron that innervates nuclear chain fibers." [PMID:25346659] is_a: CL:4023000 ! beta motor neuron -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023002 name: dynamic beta motor neuron def: "A beta motor neuron that innervates the nuclear bag fibers of muscle spindles." [PMID:25346659] is_a: CL:4023000 ! beta motor neuron -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023003 name: nuclear chain fiber def: "A type of intrafusal muscle fiber that has nuclei arranged in a linear row. Unlike nuclear bag fibers, the equatorial region of these fibers (in the centre of the spindle) is not expanded. These fibers are responsible for the detection of changes in muscle length. They are innervated by static gamma motor neurons and are principally associated with type II sensory fibers." [DOI:10.1016/B978-0-323-39632-5.00024-4, PMID:139469] is_a: CL:0008047 ! intrafusal muscle fiber -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023004 name: nuclear bag fiber def: "A type of intrafusal muscle fiber that lies in the center of a muscle spindle. Nuclei are clustered centrally and give the equatorial region a swollen appearance. They are associated with associated with dynamic gamma motor neurons, and the stretching of the equatorial region of the nuclear bag fibers results in an increase in the firing rate of type Ia sensory fibers." [DOI:10.1016/B978-0-323-39632-5.00024-4, PMID:139469] is_a: CL:0008047 ! intrafusal muscle fiber -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023005 @@ -33106,7 +33131,7 @@ def: "A nuclear bag fiber that is sensitive mainly to the rate of change in musc synonym: "bag1 fiber" EXACT [] synonym: "nuclear bag1 intrafusal fiber" EXACT [] is_a: CL:4023004 ! nuclear bag fiber -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023006 @@ -33115,7 +33140,7 @@ def: "A nuclear bag fiber that is sensitive only changes in muscle length but no synonym: "bag2 fiber" EXACT [] synonym: "nuclear bag2 intrafusal fiber" EXACT [] is_a: CL:4023004 ! nuclear bag fiber -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023007 @@ -33125,10 +33150,10 @@ subset: BDS_subset synonym: "L2/3 bipolar Vip (Mus musculus)" EXACT [] is_a: CL:0000103 ! bipolar neuron is_a: CL:4023016 ! vip GABAergic cortical interneuron -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 -relationship: in_taxon NCBITaxon:10090 ! Mus musculus relationship: RO:0002100 UBERON:8440000 ! has soma location cortical layer II/III +relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002292 PR:P32648 ! expresses VIP peptides (mouse) +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "L2/3 bipolar vip interneuron (Mus)" xsd:string [Term] @@ -33145,9 +33170,9 @@ intersection_of: CL:0000679 ! glutamatergic neuron intersection_of: bearer_of PATO:0070034 ! intratelencephalic projecting intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex relationship: bearer_of PATO:0070034 ! intratelencephalic projecting -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "IT glut" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4023009 @@ -33163,9 +33188,9 @@ intersection_of: CL:0000679 ! glutamatergic neuron intersection_of: bearer_of PATO:0070028 ! extratelencephalic projecting intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex relationship: bearer_of PATO:0070028 ! extratelencephalic projecting -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "ET glut" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4023010 @@ -33175,9 +33200,9 @@ comment: Unlike typical Lamp5 electrophysiology, A7 cells have Vip- and Sst-like subset: BDS_subset synonym: "A7 cell (Mus musculus)" EXACT [] is_a: CL:0010011 ! cerebral cortex GABAergic interneuron -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 -relationship: in_taxon NCBITaxon:10090 ! Mus musculus +relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002292 PR:000005460 ! expresses neuronal acetylcholine receptor subunit alpha-7 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "A7 interneuron" xsd:string [Term] @@ -33192,8 +33217,8 @@ intersection_of: CL:0000099 ! interneuron intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neurotransmission intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex intersection_of: RO:0002292 PR:000032148 ! expresses lysosome-associated membrane glycoprotein 5 -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: RO:0002292 PR:000032148 ! expresses lysosome-associated membrane glycoprotein 5 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "Lamp5 cortical interneuron" xsd:string [Term] @@ -33211,9 +33236,9 @@ intersection_of: CL:0000679 ! glutamatergic neuron intersection_of: bearer_of PATO:0070030 ! near projecting intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex relationship: bearer_of PATO:0070030 ! near projecting -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "NP glut neuron" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4023013 @@ -33229,9 +33254,9 @@ intersection_of: CL:0000679 ! glutamatergic neuron intersection_of: bearer_of PATO:0070029 ! corticothalamic projecting intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex relationship: bearer_of PATO:0070029 ! corticothalamic projecting -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "CT glut" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4023014 @@ -33240,10 +33265,10 @@ def: "A vip GABAergic cortical interneuron with a soma found in L5. L5 vip cells subset: BDS_subset synonym: "L5 VIP (Mus musculus)" EXACT [] is_a: CL:4023016 ! vip GABAergic cortical interneuron -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 -relationship: in_taxon NCBITaxon:10090 ! Mus musculus relationship: RO:0002100 UBERON:0005394 ! has soma location cortical layer V +relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002292 PR:P32648 ! expresses VIP peptides (mouse) +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "L5 vip interneuron (Mus)" xsd:string [Term] @@ -33258,8 +33283,8 @@ intersection_of: CL:0000099 ! interneuron intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neurotransmission intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex intersection_of: RO:0002292 PR:000015325 ! expresses gamma-synuclein -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: RO:0002292 PR:000015325 ! expresses gamma-synuclein +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "sncg cortical interneuron" xsd:string [Term] @@ -33274,8 +33299,8 @@ intersection_of: CL:0000099 ! interneuron intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neurotransmission intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex intersection_of: RO:0002292 PR:000017299 ! expresses VIP peptides -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: RO:0002292 PR:000017299 ! expresses VIP peptides +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "vip cortical interneuron" xsd:string [Term] @@ -33290,8 +33315,8 @@ intersection_of: CL:0000099 ! interneuron intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neurotransmission intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex intersection_of: RO:0002292 PR:000015665 ! expresses somatostatin -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: RO:0002292 PR:000015665 ! expresses somatostatin +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "sst cortical interneuron" xsd:string [Term] @@ -33306,8 +33331,8 @@ intersection_of: CL:0000099 ! interneuron intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neurotransmission intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex intersection_of: RO:0002292 PR:000013502 ! expresses parvalbumin alpha -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: RO:0002292 PR:000013502 ! expresses parvalbumin alpha +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "pvalb cortical interneuron" xsd:string [Term] @@ -33320,24 +33345,24 @@ is_a: CL:4023016 ! vip GABAergic cortical interneuron is_a: CL:4023071 ! L5/6 cck GABAergic interneuron (Mmus) intersection_of: CL:4023071 ! L5/6 cck GABAergic interneuron (Mmus) intersection_of: RO:0002292 PR:P32648 ! expresses VIP peptides (mouse) -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: RO:0002292 PR:P32648 ! expresses VIP peptides (mouse) +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023020 name: dynamic gamma motor neuron def: "A gamma motor neuron that innervates dynamic nuclear bag fibers (bag1 fibers) and enhances the sensitivities of Ia sensory neurons. They alter muscle spindle sensitivity and increases its discharge in response to velocity of muscle length (rather than just magnitude)." [PMID:13933877, PMID:139469, WikipediaVersion:Gamma_motor_neuron&oldid=906640465] is_a: CL:0008037 ! gamma motor neuron -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: RO:0002120 CL:4023005 ! synapsed to dynamic nuclear bag fiber +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023021 name: static gamma motor neuron def: "A gamma motor neuron that innervates static nuclear bag fibers (bag2 fibers) and increases their firing, in response to an increase in the magnitude of change in length, and controls the static sensitivity of the stretch reflex." [PMID:13933877, PMID:139469, WikipediaVersion:Gamma_motor_neuron&oldid=906640465] is_a: CL:0008037 ! gamma motor neuron -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: RO:0002120 CL:4023006 ! synapsed to static nuclear bag fiber +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023022 @@ -33345,9 +33370,9 @@ name: canopy lamp5 GABAergic cortical interneuron (Mmus) def: "A Lamp5 GABAergic cortical interneuron that has extended axons in the surface of L1. Canopy Lamp5 cells resemble neurogliaform cells in having elongated horizontal axonal arbors largely confined to L1; but the dendritic arbors are wider and have fewer branches, while the axon is less tortuous and extends further from the soma" [PMID:30413647] subset: BDS_subset is_a: CL:4023011 ! lamp5 GABAergic cortical interneuron -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 -relationship: in_taxon NCBITaxon:10090 ! Mus musculus +relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002292 PR:Q9D387 ! expresses lysosome-associated membrane glycoprotein 5 (mouse) +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "canopy lamp5 interneuron" xsd:string [Term] @@ -33358,9 +33383,9 @@ subset: BDS_subset synonym: "L5,6 NGC Lamp5 (Mus musculus)" EXACT [] is_a: CL:0000693 ! neurogliaform cell is_a: CL:4023011 ! lamp5 GABAergic cortical interneuron -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 -relationship: in_taxon NCBITaxon:10090 ! Mus musculus +relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002292 PR:Q9D387 ! expresses lysosome-associated membrane glycoprotein 5 (mouse) +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "L5,6 NGC Lamp5 interneuron (Mus)" xsd:string [Term] @@ -33371,9 +33396,9 @@ subset: BDS_subset synonym: "NGC Lamp5 (Mus musculus)" EXACT [] is_a: CL:0000693 ! neurogliaform cell is_a: CL:4023011 ! lamp5 GABAergic cortical interneuron -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 -relationship: in_taxon NCBITaxon:10090 ! Mus musculus +relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002292 PR:Q9D387 ! expresses lysosome-associated membrane glycoprotein 5 (mouse) +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "NGC Lamp5 interneuron (Mus)" xsd:string [Term] @@ -33383,9 +33408,9 @@ def: "A sst GABAergic cortical interneuron that is both an interneuron and a pro subset: BDS_subset synonym: "LP SST (Mus musculus)" EXACT [] is_a: CL:4023121 ! sst chodl GABAergic cortical interneuron -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 -relationship: in_taxon NCBITaxon:10090 ! Mus musculus +relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002292 PR:P60041 ! expresses somatostatin (mouse) +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023026 @@ -33395,8 +33420,8 @@ synonym: "D1-MSN" EXACT OMO:0003000 [PMID:34727523] synonym: "dopamine 1 medium spiny neuron" EXACT [https://orcid.org/0000-0001-7258-9596] synonym: "dSPN" EXACT OMO:0003000 [PMID:30096299] is_a: CL:1001474 ! medium spiny neuron -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: RO:0002292 PR:000001175 ! expresses D(1A) dopamine receptor +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023027 @@ -33406,10 +33431,10 @@ subset: BDS_subset synonym: "L5 T Martinotti SST (Mus musculus)" EXACT [] is_a: CL:4023017 ! sst GABAergic cortical interneuron is_a: CL:4023086 ! T Martinotti neuron -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 -relationship: in_taxon NCBITaxon:10090 ! Mus musculus relationship: RO:0002100 UBERON:0005394 ! has soma location cortical layer V +relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002292 PR:P60041 ! expresses somatostatin (mouse) +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "L5 T Martinotti sst interneuron (Mus)" xsd:string [Term] @@ -33419,10 +33444,10 @@ def: "A sst GABAergic cortical interneuron with a soma found in lower L5 with mo subset: BDS_subset synonym: "L5 non-Martinotti SST (Mus musculus)" EXACT [] is_a: CL:4023017 ! sst GABAergic cortical interneuron -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 -relationship: in_taxon NCBITaxon:10090 ! Mus musculus relationship: RO:0002100 UBERON:0005394 ! has soma location cortical layer V +relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002292 PR:P60041 ! expresses somatostatin (mouse) +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "L5 non-Martinotti sst interneuron (Mus)" xsd:string [Term] @@ -33433,8 +33458,8 @@ synonym: "D2-MSN" EXACT OMO:0003000 [PMID:34727523] synonym: "dopamine 2 medium spiny neuron" EXACT [https://orcid.org/0000-0001-7258-9596] synonym: "iSPN" EXACT OMO:0003000 [PMID:30096299] is_a: CL:1001474 ! medium spiny neuron -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: RO:0002292 PR:000001177 ! expresses D(2) dopamine receptor +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023030 @@ -33445,9 +33470,9 @@ subset: BDS_subset synonym: "L2/3/5 fan Martinotti SST (Mus musculus)" EXACT [] is_a: CL:4023017 ! sst GABAergic cortical interneuron is_a: CL:4023087 ! fan Martinotti neuron -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 -relationship: in_taxon NCBITaxon:10090 ! Mus musculus +relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002292 PR:P60041 ! expresses somatostatin (mouse) +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "L2/3/5 fan Martinotti sst interneuron (Mus)" xsd:string [Term] @@ -33458,10 +33483,10 @@ subset: BDS_subset synonym: "L4 SST (Mus musculus)" EXACT [] is_a: CL:4023017 ! sst GABAergic cortical interneuron is_a: CL:4023076 ! Martinotti neuron -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 -relationship: in_taxon NCBITaxon:10090 ! Mus musculus relationship: RO:0002100 UBERON:0005393 ! has soma location cortical layer IV +relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002292 PR:P60041 ! expresses somatostatin (mouse) +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "L4 sst interneuron (Mus)" xsd:string [Term] @@ -33470,7 +33495,7 @@ name: ON retinal ganglion cell comment: A retinal ganglion cell that is depolarized by illumination of its receptive field center. {xref="PMID:19602302"} subset: cellxgene_subset is_a: CL:0000740 ! retinal ganglion cell -relationship: dc-contributor http://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023033 @@ -33478,7 +33503,7 @@ name: OFF retinal ganglion cell def: "A retinal ganglion cell that is depolarized by decreased illumination of their receptive field center." [PMID:19602302] subset: cellxgene_subset is_a: CL:0000740 ! retinal ganglion cell -relationship: dc-contributor http://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023034 @@ -33486,8 +33511,8 @@ name: obsolete L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus) def: "OBSOLETE A sst GABAergic cortical interneuron transcriptomically between the sst and the pvalb families with a soma found in L2/3. Some L2/3 PV-like sst cells have Martinotti morphology while some have basket cell morphology. L2/3 PV-like sst cells have lower AP width and higher firing rate than typical Sst subclass cells. L2/3 PV-like sst cells have high maximum firing rate variability, with many classified as belonging to the pvalb subclass on the basis of electrophysiology." [PMID:33184512] comment: Moved to PCL. Use PCL:1000002 instead. synonym: "L2/3 PV-like SST Mus)" EXACT [] -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: term_tracker_item https://github.com/obophenotype/brain_data_standards_ontologies/issues/231 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 is_obsolete: true replaced_by: PCL:1000002 @@ -33498,10 +33523,10 @@ def: "A neuron that is derived from a precursor cell in the lateral ganglion emi synonym: "LGE-derived neuron" EXACT [PMID:10377350] is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron -intersection_of: develops_from UBERON:0004025 ! lateral ganglionic eminence -relationship: develops_from UBERON:0004025 ! lateral ganglionic eminence -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0002-7073-9172" xsd:string +intersection_of: RO:0002202 UBERON:0004025 ! develops from lateral ganglionic eminence +relationship: RO:0002202 UBERON:0004025 ! develops from lateral ganglionic eminence +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-7073-9172" xsd:string [Term] id: CL:4023036 @@ -33514,7 +33539,7 @@ synonym: "Chandelier PV" EXACT [] xref: ILX:0107356 is_a: CL:4023018 ! pvalb GABAergic cortical interneuron is_a: CL:4023083 ! chandelier cell -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "chandelier PV interneuron" xsd:string [Term] @@ -33528,8 +33553,8 @@ is_a: CL:0000679 ! glutamatergic neuron is_a: CL:0010012 ! cerebral cortex neuron intersection_of: CL:0000679 ! glutamatergic neuron intersection_of: RO:0002100 UBERON:8440003 ! has soma location cortical layer VIb -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: RO:0002100 UBERON:8440003 ! has soma location cortical layer VIb +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "L6b glut" xsd:string [Term] @@ -33542,9 +33567,9 @@ is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0061535 ! glutamate secretion, neurotransmission intersection_of: RO:0002100 UBERON:0001876 ! has soma location amygdala -relationship: dc-contributor http://orcid.org/0000-0001-7258-9596 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002100 UBERON:0001876 ! has soma location amygdala +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4023040 @@ -33554,7 +33579,7 @@ subset: BDS_subset subset: cellxgene_subset synonym: "L2/3-6 IT projecting neuron" EXACT [] is_a: CL:4023008 ! intratelencephalic-projecting glutamatergic cortical neuron -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "L2/3-6 IT glut" xsd:string [Term] @@ -33573,8 +33598,8 @@ is_a: CL:4023009 ! extratelencephalic-projecting glutamatergic cortical neuron is_a: CL:4023111 ! cerebral cortex pyramidal neuron intersection_of: CL:4023009 ! extratelencephalic-projecting glutamatergic cortical neuron intersection_of: RO:0002100 UBERON:0005394 ! has soma location cortical layer V -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: RO:0002100 UBERON:0005394 ! has soma location cortical layer V +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "L5 ET glut" xsd:string [Term] @@ -33587,9 +33612,9 @@ synonym: "L6 CT" EXACT [] is_a: CL:4023013 ! corticothalamic-projecting glutamatergic cortical neuron intersection_of: CL:4023013 ! corticothalamic-projecting glutamatergic cortical neuron intersection_of: RO:0002100 UBERON:0005395 ! has soma location cortical layer VI -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: RO:0002100 UBERON:0005395 ! has soma location cortical layer VI relationship: RO:0013001 UBERON:0010225 ! has synaptic IO in region thalamic complex +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "L6 CT glut" xsd:string [Term] @@ -33604,8 +33629,8 @@ xref: ILX:0770161 is_a: CL:4030067 ! L5/6 near-projecting glutamatergic neuron intersection_of: CL:4030067 ! L5/6 near-projecting glutamatergic neuron intersection_of: RO:0002100 UBERON:0001384 ! has soma location primary motor cortex -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: RO:0002100 UBERON:0001384 ! has soma location primary motor cortex +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "L5/6 NP glut MOp" xsd:string [Term] @@ -33617,7 +33642,7 @@ synonym: "non-MY ET M1" EXACT [] synonym: "non-MY ET MOp (Mus)" EXACT [] is_a: CL:2000049 ! primary motor cortex pyramidal cell is_a: CL:4023041 ! L5 extratelencephalic projecting glutamatergic cortical neuron -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "non-MY ET glut MOp" xsd:string [Term] @@ -33631,8 +33656,8 @@ synonym: "MY ET MOp" EXACT [] is_a: CL:2000049 ! primary motor cortex pyramidal cell is_a: CL:4023041 ! L5 extratelencephalic projecting glutamatergic cortical neuron relationship: bearer_of PATO:0070031 ! corticomedulla projecting -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: RO:0013001 UBERON:0001896 ! has synaptic IO in region medulla oblongata +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "MY ET glut MOp" xsd:string [Term] @@ -33642,8 +33667,8 @@ def: "An excitatory glutamatergic neuron transcriptomically related to the CT su subset: BDS_subset synonym: "L6b subplate glutamatergic neuron of the primary motor cortex" EXACT [] is_a: CL:4023038 ! L6b glutamatergic cortical neuron -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: RO:0002100 UBERON:0001384 ! has soma location primary motor cortex +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "L6b subplate glut" xsd:string [Term] @@ -33657,8 +33682,8 @@ synonym: "L2/3 IT MOp" EXACT [] is_a: CL:4030059 ! L2/3 intratelencephalic projecting glutamatergic neuron intersection_of: CL:4030059 ! L2/3 intratelencephalic projecting glutamatergic neuron intersection_of: RO:0002100 UBERON:0001384 ! has soma location primary motor cortex -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: RO:0002100 UBERON:0001384 ! has soma location primary motor cortex +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "L2/3 IT glut MOp" xsd:string [Term] @@ -33673,8 +33698,8 @@ xref: ILX:0770174 is_a: CL:4030062 ! L4/5 intratelencephalic projecting glutamatergic neuron intersection_of: CL:4030062 ! L4/5 intratelencephalic projecting glutamatergic neuron intersection_of: RO:0002100 UBERON:0001384 ! has soma location primary motor cortex -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: RO:0002100 UBERON:0001384 ! has soma location primary motor cortex +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "L4/5 IT glut MOp" xsd:string [Term] @@ -33688,8 +33713,8 @@ xref: ILX:0770157 is_a: CL:4030064 ! L5 intratelencephalic projecting glutamatergic neuron intersection_of: CL:4030064 ! L5 intratelencephalic projecting glutamatergic neuron intersection_of: RO:0002100 UBERON:0001384 ! has soma location primary motor cortex -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: RO:0002100 UBERON:0001384 ! has soma location primary motor cortex +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "L5 IT glut MOp" xsd:string [Term] @@ -33706,7 +33731,7 @@ is_a: CL:4030065 ! L6 intratelencephalic projecting glutamatergic neuron intersection_of: CL:4030065 ! L6 intratelencephalic projecting glutamatergic neuron intersection_of: RO:0002100 UBERON:0001384 ! has soma location primary motor cortex relationship: bearer_of PATO:0070019 ! untufted pyramidal morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "L6 IT glut MOp" xsd:string [Term] @@ -33718,27 +33743,27 @@ subset: cellxgene_subset synonym: "VLMC" EXACT [] xref: ILX:0770143 is_a: CL:4023058 ! mesothelial fibroblast of the leptomeninx -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 -relationship: develops_from CL:0011012 ! neural crest cell +relationship: RO:0002202 CL:0011012 ! develops from neural crest cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023052 name: Betz upper motor neuron def: "A Betz cell that synapses with lower motor neurons directly." [DOI:10.1101/2020.03.31.016972, PMID:18558853, PMID:28751609] is_a: CL:0008049 ! Betz cell -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002120 CL:0008039 ! synapsed to lower motor neuron +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4023053 name: spinal interneuron synapsing Betz cell def: "A Betz cell that syanpses with spinal interneurons." [DOI:10.1101/2020.03.31.016972, PMID:18558853] is_a: CL:0008049 ! Betz cell -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 -relationship: present_in_taxon NCBITaxon:9685 ! Felis catus -relationship: present_in_taxon NCBITaxon:9989 ! Rodentia relationship: RO:0002120 CL:0005000 ! synapsed to spinal cord interneuron +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: RO:0002175 NCBITaxon:9685 +property_value: RO:0002175 NCBITaxon:9989 [Term] id: CL:4023054 @@ -33746,8 +33771,8 @@ name: mesothelial fibroblast def: "A mesothelial cell that has undergone mesothelial-to-mesenchymal transition (MMT) to become a fibroblast cell." [PMID:26106328] subset: cellxgene_subset is_a: CL:0000057 ! fibroblast -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 -relationship: develops_from CL:0000077 ! mesothelial cell +relationship: RO:0002202 CL:0000077 ! develops from mesothelial cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023055 @@ -33760,7 +33785,7 @@ synonym: "CT VAL/VM MOp" EXACT [] is_a: CL:2000049 ! primary motor cortex pyramidal cell is_a: CL:4023042 ! L6 corticothalamic-projecting glutamatergic cortical neuron relationship: bearer_of PATO:0070019 ! untufted pyramidal morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "CT VAL/VM glut MOp" xsd:string [Term] @@ -33771,11 +33796,11 @@ subset: BDS_subset subset: cellxgene_subset synonym: "VLMC (Mus musculus)" EXACT [] is_a: CL:4023051 ! vascular leptomeningeal cell -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 -relationship: in_taxon NCBITaxon:10090 ! Mus musculus +relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002292 PR:P11087 {xref="PMID:30096314"} ! expresses collagen alpha-1(I) chain (mouse) relationship: RO:0002292 PR:P26618 {xref="PMID:30096314"} ! expresses platelet-derived growth factor receptor alpha (mouse) relationship: RO:0002292 PR:P51885 {xref="PMID:30096314"} ! expresses lumican (mouse) +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023057 @@ -33787,9 +33812,9 @@ is_a: CL:0011005 ! GABAergic interneuron is_a: CL:1001611 ! cerebellar neuron intersection_of: CL:0011005 ! GABAergic interneuron intersection_of: RO:0002100 UBERON:0002129 ! has soma location cerebellar cortex -relationship: dc-contributor http://orcid.org/0000-0001-7258-9596 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002100 UBERON:0002129 ! has soma location cerebellar cortex +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4023058 @@ -33799,8 +33824,8 @@ is_a: CL:0002319 ! neural cell is_a: CL:4023054 ! mesothelial fibroblast intersection_of: CL:4023054 ! mesothelial fibroblast intersection_of: part_of UBERON:0000391 ! leptomeninx -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: part_of UBERON:0000391 ! leptomeninx +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023059 @@ -33812,9 +33837,9 @@ subset: human_reference_atlas synonym: "committed oligodendrocyte precursor" EXACT [] synonym: "COP" EXACT OMO:0003000 [] is_a: CL:0000123 ! neuron associated cell (sensu Vertebrata) -relationship: dc-contributor http://orcid.org/0000-0001-7258-9596 -relationship: develops_from CL:0002453 ! oligodendrocyte precursor cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 CL:0002453 ! develops from oligodendrocyte precursor cell +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4023060 @@ -33822,10 +33847,10 @@ name: hippocampal CA1-3 neuron def: "A neuron that has its soma located in CA1-3 of the hippocampus." [DOI:10.1101/2022.10.12.511898] subset: human_reference_atlas is_a: CL:0002608 ! hippocampal neuron -relationship: dc-contributor http://orcid.org/0000-0001-7258-9596 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002100 UBERON:0001954 ! has soma location Ammon's horn -property_value: editor_note "It is unclear as to if the modelling of Ammon's horn includes CA4 (which could be considered part of the dentate gyrus) in Uberon, hence no equivalent class axiom was made." xsd:string +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 +property_value: IAO:0000116 "It is unclear as to if the modelling of Ammon's horn includes CA4 (which could be considered part of the dentate gyrus) in Uberon, hence no equivalent class axiom was made." xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4023061 @@ -33833,8 +33858,8 @@ name: hippocampal CA4 neuron def: "A neuron that has its soma located in CA4 of the hippocampus." [DOI:10.1101/2022.10.12.511898] subset: human_reference_atlas is_a: CL:0000540 ! neuron -relationship: dc-contributor http://orcid.org/0000-0001-7258-9596 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4023062 @@ -33844,9 +33869,9 @@ subset: human_reference_atlas is_a: CL:0002608 ! hippocampal neuron intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0001885 ! has soma location dentate gyrus of hippocampal formation -relationship: dc-contributor http://orcid.org/0000-0001-7258-9596 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002100 UBERON:0001885 ! has soma location dentate gyrus of hippocampal formation +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4023063 @@ -33856,11 +33881,11 @@ subset: human_reference_atlas synonym: "MGE interneuron" EXACT [] is_a: CL:0000099 ! interneuron intersection_of: CL:0000099 ! interneuron -intersection_of: develops_from UBERON:0004024 ! medial ganglionic eminence -relationship: dc-contributor http://orcid.org/0000-0001-7258-9596 -relationship: develops_from UBERON:0004024 ! medial ganglionic eminence -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002202 UBERON:0004024 ! develops from medial ganglionic eminence +relationship: RO:0002202 UBERON:0004024 ! develops from medial ganglionic eminence +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "MGE interneuron" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4023064 @@ -33870,11 +33895,11 @@ subset: human_reference_atlas synonym: "CGE interneuron" EXACT [] is_a: CL:0000099 ! interneuron intersection_of: CL:0000099 ! interneuron -intersection_of: develops_from UBERON:0004026 ! caudal ganglionic eminence -relationship: dc-contributor http://orcid.org/0000-0001-7258-9596 -relationship: develops_from UBERON:0004026 ! caudal ganglionic eminence -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002202 UBERON:0004026 ! develops from caudal ganglionic eminence +relationship: RO:0002202 UBERON:0004026 ! develops from caudal ganglionic eminence +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "CGE interneuron" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4023065 @@ -33884,8 +33909,8 @@ subset: BDS_subset subset: cellxgene_subset is_a: CL:0000617 ! GABAergic neuron is_a: CL:0010012 ! cerebral cortex neuron -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: RO:0002292 PR:000010317 ! expresses homeobox protein Meis2 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "meis2 GABA" xsd:string [Term] @@ -33898,7 +33923,7 @@ is_a: CL:0000598 ! pyramidal neuron intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) intersection_of: bearer_of PATO:0070016 ! horizontal pyramidal morphology relationship: bearer_of PATO:0070016 ! horizontal pyramidal morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023067 @@ -33906,8 +33931,8 @@ name: obsolete Martinotti morphology L2/3 pvalb-like sst GABAergic cortical inte def: "OBSOLETE A L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus) that has Martinotti morphology." [PMID:33184512] comment: Moved to PCL. Use PCL:1000004 instead. synonym: "Martinotti L2/3 PV-like SST (Mus)" EXACT [] -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: term_tracker_item https://github.com/obophenotype/brain_data_standards_ontologies/issues/231 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 is_obsolete: true replaced_by: PCL:1000004 @@ -33921,9 +33946,9 @@ is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0061535 ! glutamate secretion, neurotransmission intersection_of: RO:0002100 UBERON:0010225 ! has soma location thalamic complex -relationship: dc-contributor http://orcid.org/0000-0001-7258-9596 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002100 UBERON:0010225 ! has soma location thalamic complex +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4023069 @@ -33934,9 +33959,9 @@ is_a: CL:0010011 ! cerebral cortex GABAergic interneuron is_a: CL:4023063 ! medial ganglionic eminence derived interneuron intersection_of: CL:0000099 ! interneuron intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neurotransmission -intersection_of: develops_from UBERON:0004024 ! medial ganglionic eminence intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +intersection_of: RO:0002202 UBERON:0004024 ! develops from medial ganglionic eminence +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "MGE cortical gaba interneuron" xsd:string [Term] @@ -33949,9 +33974,9 @@ is_a: CL:0010011 ! cerebral cortex GABAergic interneuron is_a: CL:4023064 ! caudal ganglionic eminence derived interneuron intersection_of: CL:0000099 ! interneuron intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neurotransmission -intersection_of: develops_from UBERON:0004026 ! caudal ganglionic eminence intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +intersection_of: RO:0002202 UBERON:0004026 ! develops from caudal ganglionic eminence +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "CGE gaba cortical interneuron" xsd:string [Term] @@ -33961,10 +33986,10 @@ def: "A GABAergic cortical interneuron that expresses cck. L5/6 cck cells have s subset: BDS_subset synonym: "L5/6 CCK (Mus musculus)" EXACT [] is_a: CL:0010011 ! cerebral cortex GABAergic interneuron -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 -relationship: in_taxon NCBITaxon:10090 ! Mus musculus relationship: RO:0002100 UBERON:8440002 ! has soma location cortical layer V/VI +relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002292 PR:P09240 ! expresses cholecystokinin (mouse) +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "L5/6 cck interneuron (Mus)" xsd:string [Term] @@ -33975,16 +34000,16 @@ subset: human_reference_atlas is_a: CL:0002319 ! neural cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0008998 ! vasculature of brain -relationship: dc-contributor http://orcid.org/0000-0001-7258-9596 relationship: part_of UBERON:0008998 ! vasculature of brain -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4023073 name: obsolete choroid plexus cell def: "OBSOLETE. A cell that is part of the choroid plexus." [DOI:10.1101/2022.10.12.511898] -relationship: dc-contributor http://orcid.org/0000-0001-7258-9596 relationship: term_tracker_item https://github.com/obophenotype/cell-ontology/issues/2043 +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 is_obsolete: true replaced_by: CL:0000706 @@ -33996,9 +34021,9 @@ subset: human_reference_atlas is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0002206 ! has soma location mammillary body -relationship: dc-contributor http://orcid.org/0000-0001-7258-9596 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002100 UBERON:0002206 ! has soma location mammillary body +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4023075 @@ -34008,11 +34033,11 @@ subset: BDS_subset synonym: "L6 Th+ SST (Mus musculus)" EXACT [] synonym: "L6 tyrosine hydroxylase positive sst expressing GABAergic cortical interneuron (Mus musculus)" EXACT [] is_a: CL:4023017 ! sst GABAergic cortical interneuron -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 -relationship: in_taxon NCBITaxon:10090 ! Mus musculus relationship: RO:0002100 UBERON:0005395 ! has soma location cortical layer VI +relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002292 PR:P24529 ! expresses tyrosine 3-monooxygenase (mouse) relationship: RO:0002292 PR:P60041 ! expresses somatostatin (mouse) +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "L6 th sst interneuron (Mus)" xsd:string [Term] @@ -34028,7 +34053,7 @@ intersection_of: CL:0000099 ! interneuron intersection_of: bearer_of PATO:0070007 ! Martinotti morphology intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neurotransmission relationship: bearer_of PATO:0070007 ! Martinotti morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023077 @@ -34040,7 +34065,7 @@ is_a: CL:0000099 ! interneuron intersection_of: CL:0000099 ! interneuron intersection_of: bearer_of PATO:0070012 ! bitufted cell morphology relationship: bearer_of PATO:0070012 ! bitufted cell morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023078 @@ -34048,8 +34073,8 @@ name: obsolete basket morphology L2/3 pvalb-like sst GABAergic cortical interneu def: "OBSOLETE A L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus) that has basket morphology." [PMID:33184512] comment: Moved to PCL. Use PCL:1000003 instead. synonym: "basket L2/3 PV-like SST (Mus)" EXACT [] -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: term_tracker_item https://github.com/obophenotype/brain_data_standards_ontologies/issues/231 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 is_obsolete: true replaced_by: PCL:1000003 @@ -34061,10 +34086,10 @@ subset: human_reference_atlas is_a: CL:0000540 ! neuron is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: CL:0000540 ! neuron -intersection_of: develops_from UBERON:0001891 ! midbrain -relationship: dc-contributor http://orcid.org/0000-0001-7258-9596 -relationship: develops_from UBERON:0001891 ! midbrain -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002202 UBERON:0001891 ! develops from midbrain +relationship: RO:0002202 UBERON:0001891 ! develops from midbrain +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4023080 @@ -34074,7 +34099,7 @@ subset: BDS_subset synonym: "stellate L6 IT MOp (Mus musculus)" EXACT [] is_a: CL:4023050 ! L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex relationship: bearer_of PATO:0070020 ! stellate pyramidal morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "stellate L6 IT glut MOp" xsd:string [Term] @@ -34085,7 +34110,7 @@ subset: BDS_subset synonym: "inverted L6 IT MOp (Mus musculus)" EXACT [] is_a: CL:4023050 ! L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex relationship: bearer_of PATO:0070021 ! inverted pyramidal morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "inverted L6 IT glut MOp" xsd:string [Term] @@ -34100,7 +34125,7 @@ is_a: CL:0011005 ! GABAergic interneuron intersection_of: CL:0011005 ! GABAergic interneuron intersection_of: bearer_of PATO:0070011 ! chandelier cell morphology relationship: bearer_of PATO:0070011 ! chandelier cell morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023086 @@ -34113,7 +34138,7 @@ intersection_of: CL:0000099 ! interneuron intersection_of: bearer_of PATO:0070008 ! T Martinotti morphology intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neurotransmission relationship: bearer_of PATO:0070008 ! T Martinotti morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023087 @@ -34126,7 +34151,7 @@ intersection_of: CL:0000099 ! interneuron intersection_of: bearer_of PATO:0070009 ! fan Martinotti morphology intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neurotransmission relationship: bearer_of PATO:0070009 ! fan Martinotti morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023088 @@ -34139,7 +34164,7 @@ intersection_of: bearer_of PATO:0070004 ! large basket cell morphology intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neurotransmission intersection_of: RO:0002100 UBERON:0001950 ! has soma location neocortex relationship: bearer_of PATO:0070004 ! large basket cell morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023089 @@ -34152,7 +34177,7 @@ intersection_of: bearer_of PATO:0070005 ! nest basket cell morphology intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neurotransmission intersection_of: RO:0002100 UBERON:0001950 ! has soma location neocortex relationship: bearer_of PATO:0070005 ! nest basket cell morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023090 @@ -34165,7 +34190,7 @@ intersection_of: bearer_of PATO:0070003 ! small basket cell morphology intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neurotransmission intersection_of: RO:0002100 UBERON:0001950 ! has soma location neocortex relationship: bearer_of PATO:0070003 ! small basket cell morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023092 @@ -34177,7 +34202,7 @@ is_a: CL:0000598 ! pyramidal neuron intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) intersection_of: bearer_of PATO:0070021 ! inverted pyramidal morphology relationship: bearer_of PATO:0070021 ! inverted pyramidal morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023093 @@ -34189,7 +34214,7 @@ is_a: CL:0000598 ! pyramidal neuron intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) intersection_of: bearer_of PATO:0070020 ! stellate pyramidal morphology relationship: bearer_of PATO:0070020 ! stellate pyramidal morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023094 @@ -34201,7 +34226,7 @@ is_a: CL:0000598 ! pyramidal neuron intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) intersection_of: bearer_of PATO:0070018 ! tufted pyramidal morphology relationship: bearer_of PATO:0070018 ! tufted pyramidal morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023095 @@ -34213,7 +34238,7 @@ is_a: CL:0000598 ! pyramidal neuron intersection_of: CL:0000117 ! CNS neuron (sensu Vertebrata) intersection_of: bearer_of PATO:0070019 ! untufted pyramidal morphology relationship: bearer_of PATO:0070019 ! untufted pyramidal morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023097 @@ -34222,8 +34247,8 @@ def: "A mesothelial fibroblast of the arachnoid barrier layer. Arachnoid barrier synonym: "AB cell" RELATED OMO:0003000 [PMID:23298861] synonym: "ABC" RELATED OMO:0003000 [PMID:30096314] is_a: CL:4023058 ! mesothelial fibroblast of the leptomeninx -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: part_of UBERON:0000437 ! arachnoid barrier layer +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023098 @@ -34231,7 +34256,7 @@ name: obsolete L2/3 intratelencephalic projecting glutamatergic neuron of the pr def: "OBSOLETE An intratelencephalic-projecting glutamatergic neuron with a soma found in layer 2/3 of the human primary motor cortex." [DOI:10.1101/2020.03.31.016972] comment: Made terms species agnostic, use CL:4023047 instead. synonym: "L2/3 IT MOp (human)" EXACT [] -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 is_obsolete: true replaced_by: CL:4023047 @@ -34242,7 +34267,7 @@ def: "OBSOLETE. An intratelencephalic-projecting glutamatergic neuron with a som comment: Made terms species agnostic, use CL:4023049 instead. synonym: "L5 IT MOp (human)" EXACT [] xref: ILX:0770157 -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 is_obsolete: true replaced_by: CL:4023049 @@ -34253,7 +34278,7 @@ def: "OBSOLETE. An intratelencephalic-projecting glutamatergic neuron with a som comment: Made terms species agnostic, use CL:4023050 instead. synonym: "L6 IT MOp (human)" EXACT [] xref: ILX:0770158 -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 is_obsolete: true replaced_by: CL:4023050 @@ -34264,7 +34289,7 @@ def: "OBSOLETE. A near-projecting glutamatergic neuron with a soma found in laye comment: Made terms species agnostic, use CL:4023043 instead. synonym: "L5/6 NP MOp (human)" EXACT [] xref: ILX:0770161 -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 is_obsolete: true replaced_by: CL:4023043 @@ -34275,7 +34300,7 @@ def: "OBSOLETE. A near-projecting glutamatergic neuron with a soma found in laye comment: Made terms species agnostic, use CL:4023043 instead. synonym: "L5/6 NP MOp (marmoset)" EXACT [] xref: ILX:0770161 -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 is_obsolete: true replaced_by: CL:4023043 @@ -34285,7 +34310,7 @@ name: obsolete L2/3 intratelencephalic projecting glutamatergic neuron of the pr def: "OBSOLETE. An intratelencephalic-projecting glutamatergic neuron with a soma found in layer 2/3 of the marmoset primary motor cortex." [DOI:10.1101/2020.03.31.016972] comment: Made terms species agnostic, use CL:4023047 instead. synonym: "L2/3 IT MOp (marmoset)" EXACT [] -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 is_obsolete: true replaced_by: CL:4023047 @@ -34296,7 +34321,7 @@ def: "OBSOLETE An intratelencephalic-projecting glutamatergic neuron with a soma comment: Made terms species agnostic, use CL:4023049 instead. synonym: "L5 IT MOp (marmoset)" EXACT [] xref: ILX:0770157 -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 is_obsolete: true replaced_by: CL:4023049 @@ -34308,7 +34333,7 @@ comment: Made terms species agnostic, use CL:4023050 instead. subset: BDS_subset synonym: "L6 IT MOp (marmoset)" EXACT [] xref: ILX:0770158 -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 is_obsolete: true replaced_by: CL:4023050 @@ -34318,7 +34343,7 @@ name: obsolete meis2 expressing cortical GABAergic cell (Callithrix jacchus) def: "OBSOLETE. A mouse GABAergic cell located in the marmoset cerebral cortex that expresses meis2." [DOI:10.1101/2020.03.31.016972] comment: false synonym: "Meis2 (Marmoset)" EXACT [] -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 is_obsolete: true replaced_by: CL:4023065 @@ -34331,9 +34356,9 @@ is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0002275 ! has soma location reticular formation intersection_of: RO:0013001 UBERON:0002240 ! has synaptic IO in region spinal cord -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: RO:0002100 UBERON:0002275 ! has soma location reticular formation relationship: RO:0013001 UBERON:0002240 ! has synaptic IO in region spinal cord +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023108 @@ -34343,7 +34368,7 @@ is_a: CL:0011003 ! magnocellular neurosecretory cell intersection_of: CL:0011003 ! magnocellular neurosecretory cell intersection_of: capable_of GO:0036162 ! oxytocin production relationship: capable_of GO:0036162 ! oxytocin production -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023109 @@ -34354,7 +34379,7 @@ is_a: CL:0011003 ! magnocellular neurosecretory cell intersection_of: CL:0011003 ! magnocellular neurosecretory cell intersection_of: capable_of GO:0030103 ! vasopressin secretion relationship: capable_of GO:0030103 ! vasopressin secretion -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023110 @@ -34364,8 +34389,8 @@ is_a: CL:0000598 ! pyramidal neuron is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000598 ! pyramidal neuron intersection_of: RO:0002100 UBERON:0001876 ! has soma location amygdala -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: RO:0002100 UBERON:0001876 ! has soma location amygdala +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023111 @@ -34375,33 +34400,33 @@ is_a: CL:0000598 ! pyramidal neuron is_a: CL:0010012 ! cerebral cortex neuron intersection_of: CL:0000598 ! pyramidal neuron intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023112 name: vestibular afferent neuron def: "An afferent neuron of the vestibular system that innervate the base of the hair cell and increase or decrease their neural firing rate as the receptor cell is excited or inhibited." [PMID:2585041] is_a: CL:0000101 ! sensory neuron -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: RO:0002120 CL:0000609 ! synapsed to vestibular hair cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023113 name: bouton vestibular afferent neuron def: "A vestibular afferent neuron that makes bouton synapses to type II hair cells." [PMID:10706428] is_a: CL:4023112 ! vestibular afferent neuron -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: has_part GO:0043195 ! terminal bouton relationship: RO:0002130 CL:0002069 ! has synaptic terminal in type II vestibular sensory cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023114 name: calyx vestibular afferent neuron def: "A vestibular afferent neuron which posseses a unique postsynaptic terminal, the calyx, which completely covers the basolateral walls of type I hair cells and receives input from multiple ribbon synapses." [PMID:25355208] is_a: CL:4023112 ! vestibular afferent neuron -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: has_part GO:0099096 ! vestibular calyx terminal relationship: RO:0002130 CL:0002070 ! has synaptic terminal in type I vestibular sensory cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023115 @@ -34412,10 +34437,10 @@ synonym: "type I spiral ganglion cell" EXACT [] is_a: CL:0011113 ! spiral ganglion neuron is_a: UBERON:0000122 ! neuron projection bundle intersection_of: CL:0011113 ! spiral ganglion neuron -intersection_of: innervates CL:0000589 ! cochlear inner hair cell +intersection_of: RO:0002134 CL:0000589 ! innervates cochlear inner hair cell relationship: bearer_of PATO:0070006 ! cortical bipolar morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 -relationship: innervates CL:0000589 ! cochlear inner hair cell +relationship: RO:0002134 CL:0000589 ! innervates cochlear inner hair cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023116 @@ -34426,10 +34451,10 @@ synonym: "type II spiral ganglion cell" EXACT [] is_a: CL:0011113 ! spiral ganglion neuron is_a: UBERON:0000122 ! neuron projection bundle intersection_of: CL:0011113 ! spiral ganglion neuron -intersection_of: innervates CL:0000601 ! cochlear outer hair cell +intersection_of: RO:0002134 CL:0000601 ! innervates cochlear outer hair cell relationship: bearer_of PATO:0070025 ! unipolar neuron morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 -relationship: innervates CL:0000601 ! cochlear outer hair cell +relationship: RO:0002134 CL:0000601 ! innervates cochlear outer hair cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023118 @@ -34440,10 +34465,10 @@ subset: BDS_subset synonym: "L5/6 non-Martinotti morphology sst expressing GABAergic cortical interneuron (Mus musculus)" EXACT [] synonym: "L5/6 non-Martinotti SST (Mus musculus)" EXACT [] is_a: CL:4023017 ! sst GABAergic cortical interneuron -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 -relationship: in_taxon NCBITaxon:10090 ! Mus musculus relationship: RO:0002100 UBERON:8440002 ! has soma location cortical layer V/VI +relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002292 PR:P60041 ! expresses somatostatin (mouse) +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "L5/6 non-Martinotti sst interneuron (Mus)" xsd:string [Term] @@ -34454,8 +34479,8 @@ comment: Displaced amacrine cells are a subset of Sox2 expressing amacrine cells synonym: "dACs" EXACT [] synonym: "inverted amacrine cell" EXACT [] is_a: CL:0000561 ! amacrine cell -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: RO:0002292 PR:000015426 ! expresses transcription factor SOX-2 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023120 @@ -34467,8 +34492,8 @@ is_a: CL:0000202 ! auditory hair cell is_a: CL:0002374 ! ear hair cell intersection_of: CL:0000202 ! auditory hair cell intersection_of: part_of UBERON:0002227 ! spiral organ of cochlea -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: part_of UBERON:0002227 ! spiral organ of cochlea +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023121 @@ -34477,8 +34502,8 @@ def: "A sst GABAergic cortical interneuron that also expresses Chodl. These neur subset: cellxgene_subset synonym: "long-range GABAergic interneuron" BROAD [] is_a: CL:4023017 ! sst GABAergic cortical interneuron -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: RO:0002292 PR:000005444 ! expresses chondrolectin +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 property_value: IAO:0000028 "sst chodl cortical interneuron" xsd:string [Term] @@ -34488,9 +34513,9 @@ def: "An interneuron located in the cerebral cortex that expresses the oxytocin comment: These cells were first identified in mouse. {xref="PMID:25303526"} synonym: "OxtrINs" RELATED OMO:0003000 [PMID:25303526] is_a: CL:4023017 ! sst GABAergic cortical interneuron -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 -relationship: present_in_taxon NCBITaxon:10090 {xref="PMID:25303526"} ! Mus musculus relationship: RO:0002292 PR:000001635 ! expresses oxytocin receptor +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: RO:0002175 NCBITaxon:10090 {xref="PMID:25303526"} [Term] id: CL:4023123 @@ -34500,9 +34525,9 @@ is_a: CL:2000029 ! central nervous system neuron is_a: CL:4023130 ! kisspeptin neuron intersection_of: CL:4023130 ! kisspeptin neuron intersection_of: RO:0002100 UBERON:0001898 ! has soma location hypothalamus -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 -relationship: dc-contributor https://orcid.org/0000-0002-0819-0473 relationship: RO:0002100 UBERON:0001898 ! has soma location hypothalamus +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 [Term] id: CL:4023124 @@ -34512,8 +34537,8 @@ is_a: CL:4023062 ! dentate gyrus neuron is_a: CL:4023130 ! kisspeptin neuron intersection_of: CL:4023130 ! kisspeptin neuron intersection_of: RO:0002100 UBERON:0001885 ! has soma location dentate gyrus of hippocampal formation -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 -relationship: dc-contributor https://orcid.org/0000-0002-0819-0473 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 [Term] id: CL:4023125 @@ -34525,10 +34550,10 @@ is_a: CL:4023123 ! hypothalamus kisspeptin neuron intersection_of: CL:4023123 ! hypothalamus kisspeptin neuron intersection_of: RO:0002292 PR:000012526 ! expresses proenkephalin-B intersection_of: RO:0002292 PR:000016004 ! expresses tachykinin-3 -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 -relationship: dc-contributor https://orcid.org/0000-0002-0819-0473 relationship: RO:0002292 PR:000012526 ! expresses proenkephalin-B relationship: RO:0002292 PR:000016004 ! expresses tachykinin-3 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 [Term] id: CL:4023127 @@ -34537,9 +34562,9 @@ def: "a KNDy neuron that is located in the arcuate nucleus of the hypothalamus." is_a: CL:4023125 ! KNDy neuron intersection_of: CL:4023125 ! KNDy neuron intersection_of: RO:0002100 UBERON:0001932 ! has soma location arcuate nucleus of hypothalamus -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 -relationship: dc-contributor https://orcid.org/0000-0002-0819-0473 relationship: RO:0002100 UBERON:0001932 ! has soma location arcuate nucleus of hypothalamus +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 [Term] id: CL:4023128 @@ -34549,10 +34574,10 @@ synonym: "RP3V KNDy neuron" EXACT [] is_a: CL:4023125 ! KNDy neuron intersection_of: CL:4023125 ! KNDy neuron intersection_of: RO:0002100 UBERON:8440005 ! has soma location rostral periventricular region of the third ventricle -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 -relationship: dc-contributor https://orcid.org/0000-0002-0819-0473 relationship: RO:0002100 UBERON:8440005 ! has soma location rostral periventricular region of the third ventricle -property_value: editor_note "In rats and mice, the anteroventral periventricular nucleus plus the periventricular nucleus make up the rostral periventricular region of the third ventricle (RP3V)." xsd:string {xref="WikipediaVersioned:Anteroventral_periventricular_nucleus&oldid=966137187"} +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 +property_value: IAO:0000116 "In rats and mice, the anteroventral periventricular nucleus plus the periventricular nucleus make up the rostral periventricular region of the third ventricle (RP3V)." xsd:string {xref="WikipediaVersioned:Anteroventral_periventricular_nucleus&oldid=966137187"} [Term] id: CL:4023129 @@ -34561,9 +34586,9 @@ def: "A retinal cell that is immature or undifferentiated." [PMID:17565741] subset: eye_upper_slim synonym: "retinal stem cell" EXACT [PMID:17565741] is_a: CL:0009004 ! retinal cell -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 -relationship: dc-contributor https://orcid.org/0000-0002-0819-0473 relationship: part_of UBERON:0000966 ! retina +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 [Term] id: CL:4023130 @@ -34573,9 +34598,9 @@ comment: Gonadal sex steroids stimulate kisspeptin neurons in the RP3V, but inhi is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron intersection_of: RO:0002292 PR:000009344 ! expresses metastasis-suppressor KiSS-1 -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 -relationship: dc-contributor https://orcid.org/0000-0002-0819-0473 relationship: RO:0002292 PR:000009344 ! expresses metastasis-suppressor KiSS-1 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 [Term] id: CL:4023154 @@ -34585,8 +34610,8 @@ def: "A glial cell that myelinates axonal processes." [DOI:10.1007/3-540-29623-9 is_a: CL:0000125 ! glial cell intersection_of: CL:0000125 ! glial cell intersection_of: has_part GO:0043209 ! myelin sheath -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: has_part GO:0043209 ! myelin sheath +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023158 @@ -34594,10 +34619,10 @@ name: octopus cell of the mammalian cochlear nucleus def: "A neuron in the posterior ventral cochlear nucleus that is distinguished by their long, thick and tentacle-shaped dendrites that typically emanate from one side of the cell body." [WikipediaVersioned:title=Cochlear_nucleus&oldid=1090176664] comment: Octopus cells respond only at the onset of a broad-band simple tonal stimulus and form a pathway to the superior paraolivary nucleus and to the ventral nucleus of the lateral lemniscus. {xref="WikipediaVersioned:title=Cochlear_nucleus&oldid=1090176664", xref="PMID:11976365"} is_a: CL:2000029 ! central nervous system neuron -relationship: dc-contributor http://orcid.org/0000-0001-7258-9596 relationship: RO:0002100 UBERON:0002831 ! has soma location posteroventral cochlear nucleus relationship: RO:0013001 UBERON:8440043 ! has synaptic IO in region superior paraolivary nucleus -property_value: editor_note "This term is restricted to the mammalian cochlear nucleus to disambiguate for cells of octopus." xsd:string +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 +property_value: IAO:0000116 "This term is restricted to the mammalian cochlear nucleus to disambiguate for cells of octopus." xsd:string [Term] id: CL:4023159 @@ -34607,7 +34632,7 @@ is_a: CL:0000099 ! interneuron intersection_of: CL:0000099 ! interneuron intersection_of: bearer_of PATO:0070061 ! double bouquet morphology relationship: bearer_of PATO:0070061 ! double bouquet morphology -relationship: dc-contributor http://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023160 @@ -34618,9 +34643,9 @@ xref: ILX:0102311 is_a: CL:0000617 ! GABAergic neuron is_a: CL:1001509 ! glycinergic neuron is_a: CL:2000029 ! central nervous system neuron -relationship: dc-contributor http://orcid.org/0000-0001-7258-9596 relationship: RO:0002100 UBERON:0002829 ! has soma location dorsal cochlear nucleus -relationship: synapsed_by CL:0000120 ! granule cell +relationship: RO:0002103 CL:0000120 ! synapsed by granule cell +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023161 @@ -34629,17 +34654,17 @@ def: "An excitatory glutamatergic interneuron found in the granular layer of the is_a: CL:0000402 ! CNS interneuron is_a: CL:0000679 ! glutamatergic neuron relationship: bearer_of PATO:0070025 ! unipolar neuron morphology -relationship: dc-contributor http://orcid.org/0000-0001-7258-9596 relationship: RO:0002100 UBERON:0002028 ! has soma location hindbrain +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023162 name: bushy cell def: "A neuron found in the anterior part of the ventral cochlear nucleus that has the appearance of bushes, having short dendrites. Bushy cells give outputs to different parts of the superior olivary complex." [WikipediaVersioned:Bushy_cell&oldid=879061753] is_a: CL:2000029 ! central nervous system neuron -relationship: dc-contributor http://orcid.org/0000-0001-7258-9596 relationship: RO:0002100 UBERON:0002830 ! has soma location anteroventral cochlear nucleus relationship: RO:0013001 UBERON:0002128 ! has synaptic IO in region superior olivary complex +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023163 @@ -34647,7 +34672,7 @@ name: spherical bushy cell def: "A bushy cell that receives only few large excitatory endbulb synapses from auditory nerves. Spherical bush cells give excitatory input to the lateral and medial parts of the superior olive." [PMID:31881018, WikipediaVersioned:Bushy_cell&oldid=879061753] synonym: "SBC" RELATED OMO:0003000 [PMID:31881018] is_a: CL:4023162 ! bushy cell -relationship: dc-contributor http://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023164 @@ -34655,7 +34680,7 @@ name: globular bushy cell def: "A bushy cell that receives a large number of medium-sized synapses, called modified endbulbs. Globular bushy cells extend to the superior olive on both sides of the brainstem where they give input to the bipolar neurons." [PMID:31881018, WikipediaVersioned:Bushy_cell&oldid=879061753] synonym: "GBC" EXACT OMO:0003000 [PMID:31881018] is_a: CL:4023162 ! bushy cell -relationship: dc-contributor http://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023168 @@ -34664,15 +34689,15 @@ def: "A neuron that is part of the somatic sensory system. Somatosensory neurons is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron intersection_of: part_of UBERON:0003942 ! somatosensory system -relationship: dc-contributor http://orcid.org/0000-0001-7258-9596 relationship: part_of UBERON:0003942 ! somatosensory system +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023169 name: trigeminal neuron def: "A neuron that is responsible for sensation in the face or motor functions such as biting and chewing. Trigeminal neurons extend a single axon shaft along the lateral white matter of the hindbrain and spinal cord. The highly branched axons innervate the integument of the head." [PMID:22190641, WikipediaVersioned:Trigeminal_nerve&oldid=1099897926] is_a: CL:0000540 ! neuron -relationship: dc-contributor http://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023170 @@ -34683,7 +34708,7 @@ is_a: CL:4023168 ! somatosensory neuron is_a: CL:4023169 ! trigeminal neuron intersection_of: CL:4023169 ! trigeminal neuron intersection_of: capable_of GO:0050906 ! detection of stimulus involved in sensory perception -relationship: dc-contributor http://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023171 @@ -34693,7 +34718,7 @@ is_a: CL:0000100 ! motor neuron is_a: CL:4023169 ! trigeminal neuron intersection_of: CL:0000100 ! motor neuron intersection_of: CL:4023169 ! trigeminal neuron -relationship: dc-contributor http://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023181 @@ -34702,9 +34727,9 @@ def: "A neurecto-epithelial cell that is part of the basal layer of the subcommi subset: cellxgene_subset is_a: CL:0000710 ! neurecto-epithelial cell is_a: CL:0002319 ! neural cell -relationship: dc-contributor http://orcid.org/0000-0002-2105-0715 relationship: part_of UBERON:0002139 ! subcommissural organ relationship: RO:0002292 PR:000015658 ! expresses SCO-spondin +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-2105-0715 [Term] id: CL:4023187 @@ -34716,8 +34741,8 @@ xref: NIFEXT:44 is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0013615 ! has soma location koniocellular layer of dorsal nucleus of lateral geniculate body -relationship: dc-contributor http://orcid.org/0000-0001-7258-9596 relationship: RO:0002100 UBERON:0013615 ! has soma location koniocellular layer of dorsal nucleus of lateral geniculate body +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023188 @@ -34726,10 +34751,10 @@ def: "A retinal ganglion cell that originate in the ganglion cell layer of the r comment: There are midget bipolar cells of retina and midget ganglion cells of retina and they are not the same:\nMidget bipolar cells (imb, fmb) have larger axon terminals at greater distances from the fovea (retinal eccentricity of 4.5mm as compared to 12 mm). Midget ganglion cells (MGC) have larger dendritic fields (here seen at 8 mm) as they increase in eccentricity. subset: human_reference_atlas is_a: CL:0000740 ! retinal ganglion cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0013001 UBERON:0013607 ! has synaptic IO in region parvocellular layer of dorsal nucleus of lateral geniculate body -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0001-7655-4833" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7655-4833" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4023189 @@ -34740,10 +34765,10 @@ subset: human_reference_atlas synonym: "M cell" RELATED [] synonym: "M ganglion cell" RELATED [] is_a: CL:0000740 ! retinal ganglion cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0013001 UBERON:0013606 ! has synaptic IO in region magnocellular layer of dorsal nucleus of lateral geniculate body -property_value: dc-contributor "https://orcid.org/0000-0001-7258-9596" xsd:string -property_value: dc-contributor "https://orcid.org/0000-0001-7655-4833" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7258-9596" xsd:string +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0001-7655-4833" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4028001 @@ -34754,8 +34779,8 @@ is_a: CL:0002144 ! capillary endothelial cell is_a: CL:2000016 ! lung microvascular endothelial cell intersection_of: CL:0002144 ! capillary endothelial cell intersection_of: part_of UBERON:0002048 ! lung -relationship: dc-contributor https://orcid.org/0000-0002-3293-5463 relationship: part_of UBERON:0016405 ! pulmonary capillary +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3293-5463 creation_date: 2021-11-23T02:31:40Z [Term] @@ -34769,8 +34794,8 @@ synonym: "gCAP" RELATED OMO:0003000 [PMID:33057196] synonym: "general capillary cell" BROAD [PMID:33057196] is_a: CL:0010003 ! epithelial cell of alveolus of lung is_a: CL:4028001 ! pulmonary capillary endothelial cell -relationship: dc-contributor https://orcid.org/0000-0002-3293-5463 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3293-5463 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2021-11-23T03:23:53Z [Term] @@ -34786,8 +34811,8 @@ synonym: "Car4+ capillary endothelial cell" BROAD [] synonym: "CD34hi endothelial cells" BROAD [] is_a: CL:0010003 ! epithelial cell of alveolus of lung is_a: CL:4028001 ! pulmonary capillary endothelial cell -relationship: dc-contributor https://orcid.org/0000-0002-3293-5463 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3293-5463 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2021-11-23T03:23:53Z [Term] @@ -34805,12 +34830,12 @@ synonym: "matrix fibroblast 1" BROAD [] synonym: "pulmonary lipofibroblast" BROAD [] is_a: CL:0002241 ! pulmonary interstitial fibroblast is_a: CL:0002553 ! fibroblast of lung -relationship: dc-contributor https://orcid.org/0000-0001-9610-7627 -relationship: dc-contributor https://orcid.org/0000-0002-1425-877X -relationship: dc-contributor https://orcid.org/0000-0002-3293-5463 -relationship: dc-contributor https://orcid.org/0000-0002-8445-4565 relationship: part_of UBERON:0002299 ! alveolus of lung -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9610-7627 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-1425-877X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3293-5463 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8445-4565 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2021-12-09T15:34:13Z [Term] @@ -34828,9 +34853,9 @@ synonym: "mesenchymal alveolar niche cell" BROAD [] synonym: "type-2 associated stromal cell" BROAD [] is_a: CL:0002241 ! pulmonary interstitial fibroblast is_a: CL:0002553 ! fibroblast of lung -relationship: dc-contributor https://orcid.org/0000-0002-3293-5463 relationship: part_of UBERON:0002299 ! alveolus of lung -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-3293-5463 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2021-12-09T15:53:21Z [Term] @@ -34840,8 +34865,8 @@ namespace: cell def: "A cell that supports the development of a gamete by providing it cytoplasmic material (including entire organelles) by direct cross-membrane channels (del Pino, 2021)." [doi:10.1016/bs.ctdb.2020.10.008] xref: BTO:0000953 is_a: CL:0000000 ! cell -relationship: dc-contributor http://orcid.org/0000-0002-6095-8718 -property_value: dcterms-date "2022-06-08T15:29:54Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-6095-8718 +property_value: http://purl.org/dc/terms/date "2022-06-08T15:29:54Z" xsd:dateTime [Term] id: CL:4029002 @@ -34851,8 +34876,8 @@ def: "A gamete-nursing cell that derives from a germline cell (del Pino, 2021)." comment: Nurse cells were first described in insects, but recent works suggest they also exist in some mammals (Lei and Spradling, 2016). {xref="doi:10.1126/science.aad2156"} is_a: CL:0000039 ! germ line cell is_a: CL:4029001 ! gamete-nursing cell -relationship: dc-contributor http://orcid.org/0000-0002-6095-8718 -property_value: dcterms-date "2022-06-08T15:32:29Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-6095-8718 +property_value: http://purl.org/dc/terms/date "2022-06-08T15:32:29Z" xsd:dateTime [Term] id: CL:4029003 @@ -34861,8 +34886,8 @@ namespace: cell def: "A gamete-nursing cell that derives from the somatic tissues of the gonad (del Pino, 2021)." [doi:10.1016/bs.ctdb.2020.10.008] comment: We follow what seems to be a common usage in the literature, which is to reserve the term “nurse cell” proper to cells from the germ line, hence the label “nurse-like”. This term encompasses pyriform cells described in reptiles, bird, and amphibians (del Pino, 2021); it does not encompass mammalian Sertoli cells, which do not appear to transfer cytoplasmic material to spermatogonia (França et al., 2016). {xref="doi:10.1111/andr.12165"} is_a: CL:4029001 ! gamete-nursing cell -relationship: dc-contributor http://orcid.org/0000-0002-6095-8718 -property_value: dcterms-date "2022-06-08T15:38:03Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0002-6095-8718 +property_value: http://purl.org/dc/terms/date "2022-06-08T15:38:03Z" xsd:dateTime [Term] id: CL:4030000 @@ -34885,7 +34910,7 @@ is_a: CL:0000499 ! stromal cell intersection_of: CL:0000499 ! stromal cell intersection_of: part_of UBERON:0002370 ! thymus relationship: part_of UBERON:0002370 ! thymus -property_value: dcterms-date "2022-07-08T11:39:38Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2022-07-08T11:39:38Z" xsd:dateTime [Term] id: CL:4030002 @@ -34905,14 +34930,14 @@ name: interstitial cell of thymus def: "A cell that makes up the loose connective tissue of the thymus." [doi:10.1038/s41467-020-20082-7] synonym: "thymic interstitial cell" EXACT [] is_a: CL:4030001 ! stromal cell of thymus -property_value: dcterms-date "2022-07-08T11:48:36Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2022-07-08T11:48:36Z" xsd:dateTime [Term] id: CL:4030004 name: thymic nurse cell def: "A large epithelial cell found in the thymus. This cell type may internalize thymocytes through extensions of plasma membrane. The cell surface and cytoplasmic vacuoles of a thymic nurse cell express MHC Class I and MHC Class II antigens. The interaction of these antigens with a developing thymocyte determines whether the thymocyte undergoes positive or negative selection." [https://en.wikipedia.org/wiki/Thymic_nurse_cell] {http://purl.org/dc/terms/contributor="https://orcid.org/0000-0002-0819-0473"} is_a: CL:0002293 ! epithelial cell of thymus -property_value: dcterms-date "2022-02-18T12:43:20Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2022-02-18T12:43:20Z" xsd:dateTime [Term] id: CL:4030005 @@ -34924,7 +34949,7 @@ is_a: CL:0002201 ! renal beta-intercalated cell is_a: CL:1000715 ! kidney cortex collecting duct intercalated cell intersection_of: CL:0002201 ! renal beta-intercalated cell intersection_of: part_of UBERON:0004203 ! cortical collecting duct -property_value: dcterms-date "2022-09-14T16:19:11Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2022-09-14T16:19:11Z" xsd:dateTime [Term] id: CL:4030006 @@ -34935,8 +34960,8 @@ subset: human_reference_atlas synonym: "oviduct secretory epithelial cell" BROAD [] synonym: "uterine tube secretory epithelial cell" EXACT [] is_a: CL:1001591 ! oviduct glandular cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2022-03-03T10:39:31Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2022-03-03T10:39:31Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4030007 @@ -34947,8 +34972,8 @@ synonym: "oviduct ciliated cell" BROAD [] synonym: "uterine tube ciliated epithelial cell" EXACT [] is_a: CL:0005012 ! multi-ciliated epithelial cell relationship: part_of UBERON:0007589 ! ciliated columnar oviduct epithelium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2022-03-08T12:40:19Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2022-03-08T12:40:19Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4030008 @@ -34959,7 +34984,7 @@ is_a: CL:0000653 ! podocyte intersection_of: CL:0000653 ! podocyte intersection_of: part_of UBERON:0002120 ! pronephros relationship: part_of UBERON:0002120 ! pronephros -property_value: dcterms-date "2022-03-11T14:38:32Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2022-03-11T14:38:32Z" xsd:dateTime [Term] id: CL:4030009 @@ -34969,8 +34994,8 @@ subset: cellxgene_subset subset: human_reference_atlas synonym: "epithelial cell of segment 1 of proximal tubule" EXACT [] is_a: CL:0002306 ! epithelial cell of proximal tubule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2022-05-10T13:14:00Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2022-05-10T13:14:00Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4030010 @@ -34979,8 +35004,8 @@ def: "Epithelial cell that is part of segment 2 (S2) of the proximal tubule epit subset: human_reference_atlas synonym: "epithelial cell of segment 2 of proximal tubule" EXACT [] is_a: CL:0002306 ! epithelial cell of proximal tubule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2022-05-10T13:26:13Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2022-05-10T13:26:13Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4030011 @@ -34990,8 +35015,8 @@ subset: cellxgene_subset subset: human_reference_atlas synonym: "epithelial cell of segment 3 of proximal tubule" EXACT [] is_a: CL:0002306 ! epithelial cell of proximal tubule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2022-05-10T13:31:06Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2022-05-10T13:31:06Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4030012 @@ -35003,8 +35028,8 @@ is_a: CL:1001111 ! kidney loop of Henle thin descending limb epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0005099 ! short descending thin limb relationship: part_of UBERON:0005099 ! short descending thin limb -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2022-05-13T11:00:29Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2022-05-13T11:00:29Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4030013 @@ -35014,8 +35039,8 @@ subset: human_reference_atlas synonym: "epithelial cell of the outer medulla of the long descending limb of the loop of Henle" EXACT [] is_a: CL:1001111 ! kidney loop of Henle thin descending limb epithelial cell relationship: part_of UBERON:0005100 ! long descending thin limb -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2022-05-13T11:11:07Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2022-05-13T11:11:07Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4030014 @@ -35025,8 +35050,8 @@ subset: human_reference_atlas synonym: "epithelial cell of the inner medulla of the long descending limb of the loop of Henle" EXACT [] is_a: CL:1001111 ! kidney loop of Henle thin descending limb epithelial cell relationship: part_of UBERON:0005100 ! long descending thin limb -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2022-05-13T11:16:54Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2022-05-13T11:16:54Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4030015 @@ -35038,8 +35063,8 @@ is_a: CL:0005011 ! renal alpha-intercalated cell is_a: CL:1001432 ! kidney collecting duct intercalated cell intersection_of: CL:0005011 ! renal alpha-intercalated cell intersection_of: part_of UBERON:0001232 ! collecting duct of renal tubule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2022-05-31T11:15:10Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2022-05-31T11:15:10Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4030016 @@ -35051,8 +35076,8 @@ is_a: CL:1000849 ! kidney distal convoluted tubule epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0005101 ! early distal convoluted tubule relationship: part_of UBERON:0005101 ! early distal convoluted tubule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2022-06-21T12:47:48Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2022-06-21T12:47:48Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4030017 @@ -35065,8 +35090,8 @@ is_a: CL:1000849 ! kidney distal convoluted tubule epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0005102 ! late distal convoluted tubule relationship: part_of UBERON:0005102 ! late distal convoluted tubule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2022-06-21T13:51:46Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2022-06-21T13:51:46Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4030018 @@ -35078,8 +35103,8 @@ is_a: CL:0005009 ! renal principal cell is_a: CL:1000768 ! kidney connecting tubule epithelial cell intersection_of: CL:0005009 ! renal principal cell intersection_of: part_of UBERON:0005097 ! renal connecting tubule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2022-06-27T15:25:10Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2022-06-27T15:25:10Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4030019 @@ -35090,8 +35115,8 @@ is_a: CL:0005010 ! renal intercalated cell is_a: CL:1000768 ! kidney connecting tubule epithelial cell intersection_of: CL:0005010 ! renal intercalated cell intersection_of: part_of UBERON:0005097 ! renal connecting tubule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2022-06-29T11:25:22Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2022-06-29T11:25:22Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4030020 @@ -35104,8 +35129,8 @@ is_a: CL:0005011 ! renal alpha-intercalated cell is_a: CL:4030019 ! kidney connecting tubule intercalated cell intersection_of: CL:0005011 ! renal alpha-intercalated cell intersection_of: part_of UBERON:0005097 ! renal connecting tubule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2022-06-29T12:48:43Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2022-06-29T12:48:43Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4030021 @@ -35118,8 +35143,8 @@ is_a: CL:0002201 ! renal beta-intercalated cell is_a: CL:4030019 ! kidney connecting tubule intercalated cell intersection_of: CL:0002201 ! renal beta-intercalated cell intersection_of: part_of UBERON:0005097 ! renal connecting tubule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2022-06-29T14:31:18Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2022-06-29T14:31:18Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4030022 @@ -35132,8 +35157,8 @@ is_a: CL:1000682 ! kidney medulla interstitial cell is_a: CL:1000692 ! kidney interstitial fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0005211 ! renal medulla interstitium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2022-07-05T12:13:40Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2022-07-05T12:13:40Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4030023 @@ -35145,14 +35170,14 @@ is_a: CL:0002368 ! respiratory epithelial cell is_a: CL:4030024 ! hillock cell intersection_of: CL:4030024 ! hillock cell intersection_of: part_of UBERON:0000065 ! respiratory tract -property_value: dcterms-date "2022-06-06T08:31:09Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2022-06-06T08:31:09Z" xsd:dateTime [Term] id: CL:4030024 name: hillock cell def: "An epithelial, transitional cell type between basal and secretory; located in stratified, non-ciliated structures (called hillocks) with high cell turnover in epithelium. In some mammalian species, this cell type has been noted to express KRT13 and is postulated to play a role in squamous barrier function and immunomodulation." [PMID:30069044] is_a: CL:0000066 ! epithelial cell -property_value: dcterms-date "2022-06-24T14:52:24Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2022-06-24T14:52:24Z" xsd:dateTime [Term] id: CL:4030025 @@ -35164,7 +35189,7 @@ is_a: CL:1000681 ! kidney cortex interstitial cell is_a: CL:1000692 ! kidney interstitial fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0005270 ! renal cortex interstitium -property_value: dcterms-date "2022-07-05T15:50:17Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2022-07-05T15:50:17Z" xsd:dateTime [Term] id: CL:4030026 @@ -35173,9 +35198,9 @@ def: "An absorptive epithelial cell of the human intestine expressing bestrophin subset: cellxgene_subset is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000677 ! gut absorptive cell -relationship: only_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens relationship: RO:0002292 PR:Q8NFU0 ! expresses bestrophin-4 (human) -property_value: dcterms-date "2022-09-07T12:34:20Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2022-09-07T12:34:20Z" xsd:dateTime [Term] id: CL:4030027 @@ -35187,7 +35212,7 @@ is_a: CL:0000561 ! amacrine cell is_a: CL:0011005 ! GABAergic interneuron intersection_of: CL:0000561 ! amacrine cell intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neurotransmission -property_value: dcterms-date "2022-10-17T12:35:11Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2022-10-17T12:35:11Z" xsd:dateTime [Term] id: CL:4030028 @@ -35200,8 +35225,8 @@ is_a: CL:0000561 ! amacrine cell is_a: CL:1001509 ! glycinergic neuron intersection_of: CL:0000561 ! amacrine cell intersection_of: capable_of GO:0061537 ! glycine secretion, neurotransmission -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2022-10-17T12:40:06Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2022-10-17T12:40:06Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4030029 @@ -35212,16 +35237,16 @@ is_a: CL:0000542 ! lymphocyte is_a: CL:2000001 ! peripheral blood mononuclear cell intersection_of: CL:0000542 ! lymphocyte intersection_of: part_of UBERON:0000178 ! blood -property_value: dcterms-date "2022-11-04T14:40:00Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2022-11-04T14:40:00Z" xsd:dateTime [Term] id: CL:4030030 name: peripheral blood lymphocyte def: "A blood lymphocyte located in the flowing, circulating blood of the body." [https://orcid.org/0000-0001-9990-8331, https://orcid.org/0000-0003-2534-198X, https://sciencing.com/what-peripheral-blood-4672930.html, PMID:31092833] is_a: CL:4030029 ! blood lymphocyte -relationship: located_in UBERON:0013755 ! arterial blood -relationship: located_in UBERON:0013756 ! venous blood -property_value: dcterms-date "2022-11-14T10:08:14Z" xsd:dateTime +relationship: RO:0001025 UBERON:0013755 ! located in arterial blood +relationship: RO:0001025 UBERON:0013756 ! located in venous blood +property_value: http://purl.org/dc/terms/date "2022-11-14T10:08:14Z" xsd:dateTime property_value: seeAlso "https://github.com/obophenotype/cell-ontology/pull/1725" xsd:string [Term] @@ -35232,7 +35257,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0005169 ! interstitial tissue relationship: part_of UBERON:0005169 ! interstitial tissue -property_value: dcterms-date "2022-11-30T14:35:08Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2022-11-30T14:35:08Z" xsd:dateTime [Term] id: CL:4030032 @@ -35249,8 +35274,8 @@ is_a: CL:4030031 ! interstitial cell intersection_of: CL:4030031 ! interstitial cell intersection_of: part_of UBERON:0000946 ! cardiac valve relationship: capable_of GO:0070278 ! extracellular matrix constituent secretion -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2022-12-06T14:18:45Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2022-12-06T14:18:45Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4030033 @@ -35263,7 +35288,7 @@ is_a: CL:0010008 ! cardiac endothelial cell is_a: CL:1000147 ! cardiac valve cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0000946 ! cardiac valve -property_value: dcterms-date "2022-12-09T11:58:49Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2022-12-09T11:58:49Z" xsd:dateTime [Term] id: CL:4030034 @@ -35274,7 +35299,7 @@ is_a: CL:0000064 ! ciliated cell intersection_of: CL:0000064 ! ciliated cell intersection_of: part_of UBERON:0004802 ! respiratory tract epithelium relationship: part_of UBERON:0004802 ! respiratory tract epithelium -property_value: dcterms-date "2023-01-25T11:06:01Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2023-01-25T11:06:01Z" xsd:dateTime [Term] id: CL:4030035 @@ -35285,7 +35310,7 @@ is_a: CL:0000034 ! stem cell is_a: CL:0002148 ! dental pulp cell intersection_of: CL:0000034 ! stem cell intersection_of: part_of UBERON:0001754 ! dental pulp -property_value: dcterms-date "2023-01-10T14:02:02Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2023-01-10T14:02:02Z" xsd:dateTime [Term] id: CL:4030036 @@ -35295,7 +35320,7 @@ synonym: "round spermatid" EXACT [https://doi.org/10.1016/B978-0-323-01970-5.500 is_a: CL:0000018 ! spermatid relationship: capable_of GO:0007286 ! spermatid development relationship: part_of UBERON:0000079 ! male reproductive system -property_value: dcterms-date "2023-02-01T13:56:00Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2023-02-01T13:56:00Z" xsd:dateTime [Term] id: CL:4030037 @@ -35304,9 +35329,9 @@ def: "A spermatid in a late stage of maturation that has an elongated morphology synonym: "elongated spermatid" EXACT [https://doi.org/10.1016/B978-0-323-01970-5.50014-2] is_a: CL:0000018 ! spermatid relationship: capable_of GO:0007286 ! spermatid development -relationship: develops_from CL:4030036 ! early spermatid relationship: part_of UBERON:0000079 ! male reproductive system -property_value: dcterms-date "2023-02-01T14:02:15Z" xsd:dateTime +relationship: RO:0002202 CL:4030036 ! develops from early spermatid +property_value: http://purl.org/dc/terms/date "2023-02-01T14:02:15Z" xsd:dateTime [Term] id: CL:4030038 @@ -35321,7 +35346,7 @@ relationship: part_of UBERON:0008404 ! proximal tubular epithelium relationship: RO:0002292 PR:000001786 ! expresses prominin-1 relationship: RO:0002292 PR:000001932 ! expresses signal transducer CD24 relationship: RO:0002292 PR:000017298 ! expresses vimentin -property_value: dcterms-date "2023-03-07T14:17:39Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2023-03-07T14:17:39Z" xsd:dateTime [Term] id: CL:4030039 @@ -35331,7 +35356,7 @@ comment: In humans, a von Economo neuron is restricted to layer 5 of the anterio synonym: "VEN" RELATED OMO:0003000 [PMID:32127543] is_a: CL:4023009 ! extratelencephalic-projecting glutamatergic cortical neuron relationship: bearer_of PATO:0070006 ! cortical bipolar morphology -property_value: dcterms-date "2023-05-25T07:29:21Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2023-05-25T07:29:21Z" xsd:dateTime [Term] id: CL:4030040 @@ -35347,7 +35372,7 @@ intersection_of: CL:0000064 ! ciliated cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0004811 ! endometrium epithelium relationship: part_of UBERON:0004811 ! endometrium epithelium -property_value: dcterms-date "2023-02-09T11:25:14Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2023-02-09T11:25:14Z" xsd:dateTime [Term] id: CL:4030041 @@ -35355,7 +35380,7 @@ name: luminal endometrial ciliated epithelial cell def: "A ciliated cell of the endometrial luminal epithelium." [doi:10.1038/s41591-020-1040-z] is_a: CL:4030040 ! endometrial ciliated epithelial cell relationship: part_of UBERON:0011949 ! endometrium luminal epithelium -property_value: dcterms-date "2023-02-09T11:34:42Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2023-02-09T11:34:42Z" xsd:dateTime [Term] id: CL:4030042 @@ -35363,7 +35388,7 @@ name: glandular endometrial ciliated epithelial cell def: "A ciliated cell of the endometrial glandular epithelium." [doi:10.1038/s41591-020-1040-z] is_a: CL:4030040 ! endometrial ciliated epithelial cell relationship: part_of UBERON:0012276 ! endometrium glandular epithelium -property_value: dcterms-date "2023-02-09T11:37:30Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2023-02-09T11:37:30Z" xsd:dateTime [Term] id: CL:4030043 @@ -35374,7 +35399,7 @@ synonym: "D1-matrix" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] synonym: "D1M" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] synonym: "matrix D1-MSN" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] is_a: CL:4023026 ! direct pathway medium spiny neuron -property_value: dcterms-date "2023-06-02T14:05:03Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2023-06-02T14:05:03Z" xsd:dateTime [Term] id: CL:4030047 @@ -35385,7 +35410,7 @@ synonym: "D2-matrix" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] synonym: "D2M" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] synonym: "matrix D2-MSN" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] is_a: CL:4023029 ! indirect pathway medium spiny neuron -property_value: dcterms-date "2023-06-02T14:40:25Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2023-06-02T14:40:25Z" xsd:dateTime [Term] id: CL:4030048 @@ -35397,7 +35422,7 @@ synonym: "D1S" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] synonym: "striosome D1 medium spiny neuron" EXACT [doi:10.1016/j.cub.2021.10.015] synonym: "striosome D1-MSN" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] is_a: CL:4023026 ! direct pathway medium spiny neuron -property_value: dcterms-date "2023-06-02T14:50:43Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2023-06-02T14:50:43Z" xsd:dateTime [Term] id: CL:4030049 @@ -35409,7 +35434,7 @@ synonym: "D2S" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] synonym: "striosome D2 medium spiny neuron" EXACT [doi:10.1016/j.cub.2021.10.015] synonym: "striosome D2-MSN" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] is_a: CL:4023029 ! indirect pathway medium spiny neuron -property_value: dcterms-date "2023-06-02T15:03:08Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2023-06-02T15:03:08Z" xsd:dateTime [Term] id: CL:4030050 @@ -35424,7 +35449,7 @@ is_a: CL:1001474 ! medium spiny neuron relationship: RO:0002100 UBERON:0005382 ! has soma location dorsal striatum relationship: RO:0002292 PR:000001175 ! expresses D(1A) dopamine receptor relationship: RO:0002292 PR:000001177 ! expresses D(2) dopamine receptor -property_value: dcterms-date "2023-06-02T15:19:45Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2023-06-02T15:19:45Z" xsd:dateTime [Term] id: CL:4030051 @@ -35437,7 +35462,7 @@ synonym: "NAc shell and OT D1-MSN" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.1 is_a: CL:1001474 ! medium spiny neuron relationship: RO:0002100 UBERON:0005403 ! has soma location ventral striatum relationship: RO:0002292 PR:000001175 ! expresses D(1A) dopamine receptor -property_value: dcterms-date "2023-06-14T13:03:50Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2023-06-14T13:03:50Z" xsd:dateTime [Term] id: CL:4030052 @@ -35451,7 +35476,7 @@ synonym: "nucleus accumbens shell and olfactory tubercle D2-MSN" RELATED OMO:000 is_a: CL:1001474 ! medium spiny neuron relationship: RO:0002100 UBERON:0005403 ! has soma location ventral striatum relationship: RO:0002292 PR:000001177 ! expresses D(2) dopamine receptor -property_value: dcterms-date "2023-06-14T13:27:51Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2023-06-14T13:27:51Z" xsd:dateTime [Term] id: CL:4030053 @@ -35462,7 +35487,7 @@ synonym: "D1-ICj" RELATED OMO:0003000 [doi:10.1016/j.cub.2021.10.015] is_a: CL:0000120 ! granule cell is_a: CL:0002613 ! striatum neuron relationship: RO:0002292 PR:000001175 ! expresses D(1A) dopamine receptor -property_value: dcterms-date "2023-06-14T13:37:45Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2023-06-14T13:37:45Z" xsd:dateTime [Term] id: CL:4030054 @@ -35475,7 +35500,7 @@ is_a: CL:1001474 ! medium spiny neuron relationship: RO:0002100 UBERON:0005403 ! has soma location ventral striatum relationship: RO:0002292 PR:000001175 ! expresses D(1A) dopamine receptor relationship: RO:0002292 PR:000001666 ! expresses relaxin receptor 1 -property_value: dcterms-date "2023-06-14T14:46:08Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2023-06-14T14:46:08Z" xsd:dateTime [Term] id: CL:4030055 @@ -35485,8 +35510,8 @@ comment: It has been noted in at least some mammalian species that the urothelia synonym: "urothelial intermediate cell" EXACT [doi:10.1007/978-3-030-14366-4_8] xref: FMA:84155 is_a: CL:0000731 ! urothelial cell -property_value: dc-contributor "https://orcid.org/0000-0003-3065-9183" xsd:string -property_value: dcterms-date "2023-06-16T07:53:43Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0003-3065-9183" xsd:string +property_value: http://purl.org/dc/terms/date "2023-06-16T07:53:43Z" xsd:dateTime [Term] id: CL:4030056 @@ -35497,8 +35522,8 @@ synonym: "facet cell of urothelium" EXACT [doi:10.1038/s41385-022-00565-0] synonym: "superficial cell of urothelium" EXACT [doi:10.1038/s41385-022-00565-0] xref: FMA:84149 is_a: CL:0000731 ! urothelial cell -property_value: dc-contributor "https://orcid.org/0000-0003-3065-9183" xsd:string -property_value: dcterms-date "2023-06-16T07:59:43Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0003-3065-9183" xsd:string +property_value: http://purl.org/dc/terms/date "2023-06-16T07:59:43Z" xsd:dateTime [Term] id: CL:4030057 @@ -35510,7 +35535,7 @@ synonym: "eccentric spiny projection neuron" EXACT [doi:10.1016/j.cell.2018.07.0 synonym: "eccentric SPN" RELATED OMO:0003000 [doi:10.1016/j.cell.2018.07.028] synonym: "eSPN" RELATED OMO:0003000 [doi:10.1016/j.cell.2018.07.028] is_a: CL:1001474 ! medium spiny neuron -property_value: dcterms-date "2023-06-23T14:59:36Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2023-06-23T14:59:36Z" xsd:dateTime [Term] id: CL:4030058 @@ -35523,9 +35548,9 @@ is_a: CL:0000235 ! macrophage is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000235 ! macrophage intersection_of: RO:0002104 GO:0042101 ! has plasma membrane part T cell receptor complex -relationship: dc-contributor https://orcid.org/0000-0003-3308-6245 relationship: RO:0002104 GO:0042101 ! has plasma membrane part T cell receptor complex -property_value: dcterms-date "2023-09-26T12:27:14Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3308-6245 +property_value: http://purl.org/dc/terms/date "2023-09-26T12:27:14Z" xsd:dateTime [Term] id: CL:4030059 @@ -35535,9 +35560,9 @@ synonym: "L2/3 IT" RELATED OMO:0003000 [PMID:34004146] is_a: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron intersection_of: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron intersection_of: RO:0002100 UBERON:8440000 ! has soma location cortical layer II/III -relationship: dc-contributor https://orcid.org/0000-0003-4389-9821 relationship: RO:0002100 UBERON:8440000 ! has soma location cortical layer II/III -property_value: dcterms-date "2023-10-10T14:10:21Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-4389-9821 +property_value: http://purl.org/dc/terms/date "2023-10-10T14:10:21Z" xsd:dateTime [Term] id: CL:4030060 @@ -35547,9 +35572,9 @@ synonym: "L2 IT" RELATED OMO:0003000 [PMID:34004146] is_a: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron intersection_of: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron intersection_of: RO:0002100 UBERON:0005391 ! has soma location cortical layer II -relationship: dc-contributor https://orcid.org/0000-0003-4389-9821 relationship: RO:0002100 UBERON:0005391 ! has soma location cortical layer II -property_value: dcterms-date "2023-10-10T14:10:36Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-4389-9821 +property_value: http://purl.org/dc/terms/date "2023-10-10T14:10:36Z" xsd:dateTime [Term] id: CL:4030061 @@ -35559,9 +35584,9 @@ synonym: "L3 IT" RELATED OMO:0003000 [PMID:34004146] is_a: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron intersection_of: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron intersection_of: RO:0002100 UBERON:0005392 ! has soma location cortical layer III -relationship: dc-contributor https://orcid.org/0000-0003-4389-9821 relationship: RO:0002100 UBERON:0005392 ! has soma location cortical layer III -property_value: dcterms-date "2023-10-10T14:10:47Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-4389-9821 +property_value: http://purl.org/dc/terms/date "2023-10-10T14:10:47Z" xsd:dateTime [Term] id: CL:4030062 @@ -35571,9 +35596,9 @@ synonym: "L4/5 IT" RELATED OMO:0003000 [PMID:34004146] is_a: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron intersection_of: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron intersection_of: RO:0002100 UBERON:8440001 ! has soma location cortical layer IV/V -relationship: dc-contributor https://orcid.org/0000-0003-4389-9821 relationship: RO:0002100 UBERON:8440001 ! has soma location cortical layer IV/V -property_value: dcterms-date "2023-10-10T14:11:04Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-4389-9821 +property_value: http://purl.org/dc/terms/date "2023-10-10T14:11:04Z" xsd:dateTime [Term] id: CL:4030063 @@ -35583,9 +35608,9 @@ synonym: "L4 IT" RELATED OMO:0003000 [PMID:37292694] is_a: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron intersection_of: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron intersection_of: RO:0002100 UBERON:0005393 ! has soma location cortical layer IV -relationship: dc-contributor https://orcid.org/0000-0003-4389-9821 relationship: RO:0002100 UBERON:0005393 ! has soma location cortical layer IV -property_value: dcterms-date "2023-10-10T14:11:25Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-4389-9821 +property_value: http://purl.org/dc/terms/date "2023-10-10T14:11:25Z" xsd:dateTime [Term] id: CL:4030064 @@ -35595,9 +35620,9 @@ synonym: "L5 IT" RELATED [PMID:37292694] {synonymtypedef="OMO:0003000"} is_a: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron intersection_of: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron intersection_of: RO:0002100 UBERON:0005394 ! has soma location cortical layer V -relationship: dc-contributor https://orcid.org/0000-0003-4389-9821 relationship: RO:0002100 UBERON:0005394 ! has soma location cortical layer V -property_value: dcterms-date "2023-10-10T14:11:59Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-4389-9821 +property_value: http://purl.org/dc/terms/date "2023-10-10T14:11:59Z" xsd:dateTime [Term] id: CL:4030065 @@ -35607,9 +35632,9 @@ synonym: "L6 IT" RELATED OMO:0003000 [PMID:37292694] is_a: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron intersection_of: CL:4023040 ! L2/3-6 intratelencephalic projecting glutamatergic neuron intersection_of: RO:0002100 UBERON:0005395 ! has soma location cortical layer VI -relationship: dc-contributor https://orcid.org/0000-0003-4389-9821 relationship: RO:0002100 UBERON:0005395 ! has soma location cortical layer VI -property_value: dcterms-date "2023-10-10T14:12:23Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-4389-9821 +property_value: http://purl.org/dc/terms/date "2023-10-10T14:12:23Z" xsd:dateTime [Term] id: CL:4030066 @@ -35622,8 +35647,8 @@ intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0000084 ! ureteric bud relationship: part_of UBERON:0000084 ! ureteric bud relationship: participates_in GO:2001013 {xref="PMID:9374839"} ! epithelial cell proliferation involved in renal tubule morphogenesis -property_value: dc-contributor "https://orcid.org/0000-0002-1425-877X" xsd:string -property_value: dcterms-date "2023-10-13T11:22:42Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-1425-877X" xsd:string +property_value: http://purl.org/dc/terms/date "2023-10-13T11:22:42Z" xsd:dateTime [Term] id: CL:4030067 @@ -35633,9 +35658,9 @@ synonym: "L5/6 NP" RELATED OMO:0003000 [PMID:34004146] is_a: CL:4023012 ! near-projecting glutamatergic cortical neuron intersection_of: CL:4023012 ! near-projecting glutamatergic cortical neuron intersection_of: RO:0002100 UBERON:8440002 ! has soma location cortical layer V/VI -relationship: dc-contributor https://orcid.org/0000-0003-4389-9821 relationship: RO:0002100 UBERON:8440002 ! has soma location cortical layer V/VI -property_value: dcterms-date "2023-11-17T11:35:06Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-4389-9821 +property_value: http://purl.org/dc/terms/date "2023-11-17T11:35:06Z" xsd:dateTime [Term] id: CL:4030068 @@ -35650,9 +35675,9 @@ is_a: CL:4030065 ! L6 intratelencephalic projecting glutamatergic neuron intersection_of: CL:4030065 ! L6 intratelencephalic projecting glutamatergic neuron intersection_of: RO:0002100 UBERON:0005395 ! has soma location cortical layer VI intersection_of: RO:0002292 PR:000004919 ! expresses -relationship: dc-contributor https://orcid.org/0000-0003-4389-9821 relationship: RO:0002292 PR:000004919 ! expresses -property_value: dcterms-date "2023-11-23T09:16:14Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-4389-9821 +property_value: http://purl.org/dc/terms/date "2023-11-23T09:16:14Z" xsd:dateTime [Term] id: CL:4032000 @@ -35664,10 +35689,10 @@ synonym: "club cell of the urethra epithelium" EXACT [] synonym: "club-like cell of the prostatic urethra epithelium" EXACT [https://orcid.org/0000-0001-7258-9596] synonym: "prostate club cell" EXACT [PMID:30566875] is_a: CL:1000296 ! epithelial cell of urethra -relationship: dc-contributor http://orcid.org/0000-0001-6757-4744 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002292 PR:000014505 ! expresses uteroglobin -property_value: editor_note "The term \"club-like\" is used to disambiguate from club cells which CL defines as a type of bronchial epithelial cell. This seems to reflect common usage of club cell when used without location (club cell seems to mean bronchial club cell, unless it is proceded or preceded by something that says it is not bronchial). In the literature, the name \"club-like\" isn't used." xsd:string +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-6757-4744 +property_value: IAO:0000116 "The term \"club-like\" is used to disambiguate from club cells which CL defines as a type of bronchial epithelial cell. This seems to reflect common usage of club cell when used without location (club cell seems to mean bronchial club cell, unless it is proceded or preceded by something that says it is not bronchial). In the literature, the name \"club-like\" isn't used." xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4032001 @@ -35679,10 +35704,10 @@ intersection_of: CL:0000099 ! interneuron intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neurotransmission intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex intersection_of: RO:0002292 PR:000013879 ! expresses reelin -relationship: dc-contributor http://orcid.org/0000-0001-6757-4744 relationship: RO:0002292 PR:000013879 ! expresses reelin -property_value: dc-contributor "http://orcid.org/0000-0001-5501-853X" xsd:string -property_value: dc-contributor "http://orcid.org/0000-0001-7476-6306" xsd:string +property_value: http://purl.org/dc/terms/contributor "http://orcid.org/0000-0001-5501-853X" xsd:string +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-6757-4744 +property_value: http://purl.org/dc/terms/contributor "http://orcid.org/0000-0001-7476-6306" xsd:string [Term] id: CL:4033000 @@ -35691,8 +35716,8 @@ def: "A(n) endothelial cell that is part of a(n) venule of lymph node." [PMID:28 is_a: CL:0000115 ! endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:8410041 ! venule of lymph node -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: part_of UBERON:8410041 ! venule of lymph node +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 [Term] id: CL:4033001 @@ -35701,8 +35726,8 @@ def: "A(n) endothelial cell that is part of a(n) arteriole of lymph node." [PMID is_a: CL:1000412 ! endothelial cell of arteriole intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:8410042 ! arteriole of lymph node -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: part_of UBERON:8410042 ! arteriole of lymph node +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 [Term] id: CL:4033002 @@ -35712,8 +35737,8 @@ is_a: CL:0000165 ! neuroendocrine cell is_a: CL:1001516 ! intestinal enteroendocrine cell intersection_of: CL:0000165 ! neuroendocrine cell intersection_of: part_of UBERON:0011184 ! epithelium of crypt of Lieberkuhn -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: part_of UBERON:0011184 ! epithelium of crypt of Lieberkuhn +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 [Term] id: CL:4033003 @@ -35724,9 +35749,9 @@ is_a: CL:0000185 ! myoepithelial cell is_a: CL:0002328 ! bronchial epithelial cell intersection_of: CL:0000185 ! myoepithelial cell intersection_of: part_of UBERON:8410043 ! bronchus submucosal gland -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: part_of UBERON:8410043 ! bronchus submucosal gland -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4033004 @@ -35735,8 +35760,8 @@ def: "A(n) smooth muscle cell that is part of a(n) taenia coli." [PMID:10715339, is_a: CL:1000279 ! smooth muscle cell of large intestine intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0012419 ! taenia coli -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: part_of UBERON:0012419 ! taenia coli +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 [Term] id: CL:4033005 @@ -35747,9 +35772,9 @@ is_a: CL:0000152 ! exocrine cell is_a: CL:0019001 ! tracheobronchial serous cell intersection_of: CL:0000313 ! serous secreting cell intersection_of: part_of UBERON:8410043 ! bronchus submucosal gland -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: part_of UBERON:8410043 ! bronchus submucosal gland -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4033006 @@ -35758,8 +35783,8 @@ def: "A(n) endothelial cell that is part of a(n) efferent lymphatic vessel." [PM is_a: CL:0000115 ! endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0010397 ! efferent lymphatic vessel -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: part_of UBERON:0010397 ! efferent lymphatic vessel +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 [Term] id: CL:4033007 @@ -35770,9 +35795,9 @@ is_a: CL:0000082 ! epithelial cell of lung is_a: CL:0002208 ! brush cell of bronchus intersection_of: CL:0002204 ! brush cell intersection_of: part_of UBERON:0002339 ! epithelium of lobar bronchus -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: part_of UBERON:0002339 ! epithelium of lobar bronchus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4033008 @@ -35782,9 +35807,9 @@ subset: human_reference_atlas is_a: CL:0002543 ! vein endothelial cell intersection_of: CL:0002543 ! vein endothelial cell intersection_of: part_of UBERON:0001004 ! respiratory system -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: part_of UBERON:0001004 ! respiratory system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4033009 @@ -35795,9 +35820,9 @@ is_a: CL:1000143 ! lung goblet cell is_a: CL:1000312 ! bronchial goblet cell intersection_of: CL:0000160 ! goblet cell intersection_of: part_of UBERON:0002339 ! epithelium of lobar bronchus -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: part_of UBERON:0002339 ! epithelium of lobar bronchus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4033010 @@ -35808,9 +35833,9 @@ is_a: CL:0002328 ! bronchial epithelial cell is_a: CL:1000223 ! lung neuroendocrine cell intersection_of: CL:0000165 ! neuroendocrine cell intersection_of: part_of UBERON:0002339 ! epithelium of lobar bronchus -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: part_of UBERON:0002339 ! epithelium of lobar bronchus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4033011 @@ -35819,8 +35844,8 @@ def: "A(n) smooth muscle cell that is part of a(n) large intestine smooth muscle is_a: CL:1000279 ! smooth muscle cell of large intestine intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0012398 ! large intestine smooth muscle circular layer -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: part_of UBERON:0012398 ! large intestine smooth muscle circular layer +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 [Term] id: CL:4033012 @@ -35829,8 +35854,8 @@ def: "A(n) smooth muscle cell that is part of a(n) large intestine smooth muscle is_a: CL:1000279 ! smooth muscle cell of large intestine intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0012399 ! large intestine smooth muscle longitudinal layer -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: part_of UBERON:0012399 ! large intestine smooth muscle longitudinal layer +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 [Term] id: CL:4033013 @@ -35839,8 +35864,8 @@ def: "A keratinocyte of the epidermis suprabasal layer. This cell may express th is_a: CL:0000312 ! keratinocyte intersection_of: CL:0000312 ! keratinocyte intersection_of: part_of UBERON:0010402 ! epidermis suprabasal layer -relationship: dc-contributor http://orcid.org/0000-0001-6677-8489 relationship: part_of UBERON:0010402 ! epidermis suprabasal layer +property_value: http://purl.org/dc/terms/contributor http://orcid.org/0000-0001-6677-8489 creation_date: 2023-02-02T11:17:04Z [Term] @@ -35854,10 +35879,10 @@ synonym: "FTE stem-like cell" EXACT [PMID:22911892] synonym: "FTESC" EXACT OMO:0003000 [PMID:22911892] synonym: "intercalary cell" EXACT [PMID:22911892] is_a: CL:0000066 ! epithelial cell -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: part_of UBERON:0004804 ! oviduct epithelium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2023-02-02T15:07:12Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-02-02T15:07:12Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4033015 @@ -35870,9 +35895,9 @@ is_a: CL:0000127 ! astrocyte is_a: CL:0009004 ! retinal cell intersection_of: CL:0000127 ! astrocyte intersection_of: part_of UBERON:0000966 ! retina -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: part_of UBERON:0000966 ! retina -property_value: dcterms-date "2023-03-02T14:38:32Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-03-02T14:38:32Z" xsd:dateTime [Term] id: CL:4033016 @@ -35884,12 +35909,12 @@ synonym: "SCMF" RELATED OMO:0003000 [PMID:33624948] synonym: "SCMFs" RELATED OMO:0003004 [PMID:25448080] synonym: "secondary-crest myofibroblast" EXACT [PMID:31331942] is_a: CL:0000186 ! myofibroblast cell -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: dc-contributor https://orcid.org/0000-0002-9185-3994 relationship: part_of UBERON:0000114 ! lung connective tissue relationship: participates_in GO:0048286 ! lung alveolus development -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2023-03-16T09:17:47Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 +property_value: http://purl.org/dc/terms/date "2023-03-16T09:17:47Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4033017 @@ -35899,11 +35924,11 @@ subset: human_reference_atlas is_a: CL:0019019 ! tracheobronchial smooth muscle cell intersection_of: CL:0000192 ! smooth muscle cell intersection_of: part_of UBERON:0002186 ! bronchiole -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: dc-contributor https://orcid.org/0000-0002-9185-3994 relationship: part_of UBERON:0004515 ! smooth muscle tissue of bronchiole -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2023-03-16T09:38:17Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 +property_value: http://purl.org/dc/terms/date "2023-03-16T09:38:17Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4033018 @@ -35918,11 +35943,11 @@ is_a: CL:0000556 ! megakaryocyte is_a: CL:0002320 ! connective tissue cell intersection_of: CL:0000556 ! megakaryocyte intersection_of: part_of UBERON:0000114 ! lung connective tissue -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: dc-contributor https://orcid.org/0000-0002-9185-3994 relationship: part_of UBERON:0000114 ! lung connective tissue -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2023-03-16T11:31:23Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 +property_value: http://purl.org/dc/terms/date "2023-03-16T11:31:23Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4033019 @@ -35932,9 +35957,9 @@ comment: The axons of a blue cone bipolar cell terminate close to the ganglion c subset: human_reference_atlas synonym: "BB cell" RELATED OMO:0003000 [PMID:32032773] is_a: CL:0000749 ! ON-bipolar cell -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2023-04-04T09:48:15Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-04-04T09:48:15Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4033020 @@ -35946,11 +35971,11 @@ is_a: CL:0000307 ! tracheal epithelial cell is_a: CL:4033037 ! mucus secreting cell of tracheobronchial tree submucosal gland intersection_of: CL:0000319 ! mucus secreting cell intersection_of: part_of UBERON:0005203 ! trachea gland -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: dc-contributor https://orcid.org/0000-0002-9185-3994 relationship: part_of UBERON:0005203 ! trachea gland -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2023-03-16T13:03:13Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 +property_value: http://purl.org/dc/terms/date "2023-03-16T13:03:13Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4033021 @@ -35961,11 +35986,11 @@ is_a: CL:0000185 ! myoepithelial cell is_a: CL:0000307 ! tracheal epithelial cell intersection_of: CL:0000185 ! myoepithelial cell intersection_of: part_of UBERON:0005203 ! trachea gland -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: dc-contributor https://orcid.org/0000-0002-9185-3994 relationship: part_of UBERON:0005203 ! trachea gland -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2023-03-16T13:36:43Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 +property_value: http://purl.org/dc/terms/date "2023-03-16T13:36:43Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4033022 @@ -35977,11 +36002,11 @@ is_a: CL:0002328 ! bronchial epithelial cell is_a: CL:4033037 ! mucus secreting cell of tracheobronchial tree submucosal gland intersection_of: CL:0000319 ! mucus secreting cell intersection_of: part_of UBERON:8410043 ! bronchus submucosal gland -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: dc-contributor https://orcid.org/0000-0002-9185-3994 relationship: part_of UBERON:8410043 ! bronchus submucosal gland -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2023-03-16T15:12:52Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 +property_value: http://purl.org/dc/terms/date "2023-03-16T15:12:52Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4033023 @@ -35989,11 +36014,11 @@ name: airway submucosal gland collecting duct epithelial cell def: "An epithelial cell that is part of a collecting duct of an airway submucosal gland." [PMID:25648514, PMID:29656943] subset: human_reference_atlas is_a: CL:0000066 ! epithelial cell -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: dc-contributor https://orcid.org/0000-0002-9185-3994 relationship: part_of UBERON:8410077 ! airway submucosal gland -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2023-03-16T15:20:28Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 +property_value: http://purl.org/dc/terms/date "2023-03-16T15:20:28Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4033024 @@ -36001,11 +36026,11 @@ name: airway submucosal gland duct basal cell def: "A basal cell that is part of a duct of an airway submucosal gland." [PMID:29656943, PMID:35046051] subset: human_reference_atlas is_a: CL:0000646 ! basal cell -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: part_of UBERON:8410077 ! airway submucosal gland -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dc-contributor "https://orcid.org/0000-0002-9185-3994" xsd:string -property_value: dcterms-date "2023-03-16T15:51:39Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/contributor "https://orcid.org/0000-0002-9185-3994" xsd:string +property_value: http://purl.org/dc/terms/date "2023-03-16T15:51:39Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4033025 @@ -36015,11 +36040,11 @@ subset: human_reference_atlas is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0008305 ! outer fibrous layer of perichondrium -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: dc-contributor https://orcid.org/0000-0002-9185-3994 relationship: part_of UBERON:0008305 ! outer fibrous layer of perichondrium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2023-03-16T16:12:50Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 +property_value: http://purl.org/dc/terms/date "2023-03-16T16:12:50Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4033026 @@ -36031,10 +36056,10 @@ is_a: CL:0002553 ! fibroblast of lung is_a: CL:4033025 ! perichondrial fibroblast intersection_of: CL:4033025 ! perichondrial fibroblast intersection_of: part_of UBERON:0002048 ! lung -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: dc-contributor https://orcid.org/0000-0002-9185-3994 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2023-03-16T16:15:39Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 +property_value: http://purl.org/dc/terms/date "2023-03-16T16:15:39Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4033027 @@ -36047,9 +36072,9 @@ synonym: "DB1 bipolar cell" RELATED OMO:0003000 [PMID:22006647] synonym: "DB1 cell" RELATED OMO:0003000 [PMID:32032773] synonym: "Diffuse Bipolar Cell Type DB1" EXACT [PMID:22006647] is_a: CL:0000750 ! OFF-bipolar cell -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2023-04-04T10:48:29Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-04-04T10:48:29Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4033028 @@ -36059,9 +36084,9 @@ comment: In primates, a diffuse bipolar 2 cell makes an average of 133 ribbon sy subset: human_reference_atlas synonym: "DB2 cell" RELATED OMO:0003000 [PMID:32032773] is_a: CL:0000750 ! OFF-bipolar cell -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2023-04-04T10:49:07Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-04-04T10:49:07Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4033029 @@ -36072,9 +36097,9 @@ subset: human_reference_atlas synonym: "DB3 cell" RELATED OMO:0003000 [DOI:10.3389/fnana.2015.00122] synonym: "DB3a cell" RELATED OMO:0003000 [PMID:32032773] is_a: CL:0000750 ! OFF-bipolar cell -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2023-04-04T10:53:33Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-04-04T10:53:33Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4033030 @@ -36084,9 +36109,9 @@ comment: In humans, a DB3b cell is CD15 positive. A DB3b cell might make sparse subset: human_reference_atlas synonym: "DB3b cell" RELATED OMO:0003000 [PMID:32032773] is_a: CL:0000750 ! OFF-bipolar cell -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2023-04-04T10:53:42Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-04-04T10:53:42Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4033031 @@ -36095,9 +36120,9 @@ def: "An ON diffuse bipolar cell that predominantly connects to ON parasol cells subset: human_reference_atlas synonym: "DB4 cell" RELATED OMO:0003000 [PMID:32032773] is_a: CL:0000749 ! ON-bipolar cell -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2023-04-04T09:51:10Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-04-04T09:51:10Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4033032 @@ -36106,9 +36131,9 @@ def: "An ON diffuse bipolar cell that has a large dendritic field and large axon subset: human_reference_atlas synonym: "DB6 cell" RELATED OMO:0003000 [PMID:32032773] is_a: CL:0000749 ! ON-bipolar cell -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2023-04-04T09:51:22Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-04-04T09:51:22Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4033033 @@ -36117,9 +36142,9 @@ def: "An OFF bipolar cell with a small dendritic tree that provides most of the subset: human_reference_atlas synonym: "FMB cell" RELATED OMO:0003000 [PMID:32032773] is_a: CL:0000750 ! OFF-bipolar cell -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2023-04-04T10:54:00Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-04-04T10:54:00Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4033034 @@ -36128,9 +36153,9 @@ def: "An ON bipolar cell with a small dendritic tree that forms most of the cent subset: human_reference_atlas synonym: "IMB cell" RELATED OMO:0003000 [PMID:32032773] is_a: CL:0000749 ! ON-bipolar cell -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2023-04-04T09:51:44Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-04-04T09:51:44Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4033035 @@ -36139,18 +36164,18 @@ def: "An ON bipolar cell that has large dendritic and axonal fields." [PMID:3203 comment: A giant bipolar cell is usually monostratified, although, very rarely, it can be bistratified. {xref="PMID:32032773"} synonym: "GB cell" RELATED OMO:0003000 [PMID:32032773] is_a: CL:0000749 ! ON-bipolar cell -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -property_value: dcterms-date "2023-04-04T09:54:15Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-04-04T09:54:15Z" xsd:dateTime [Term] id: CL:4033036 name: OFFx cell def: "An OFF bipolar cell that is fovea-specific and expresses FEZF1, NXPH1 and NXPH2." [PMID:30712875, PMID:31995762, PMID:32555229] is_a: CL:0000750 ! OFF-bipolar cell -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: part_of UBERON:0001786 ! fovea centralis -relationship: present_in_taxon NCBITaxon:9443 ! Primates -property_value: dcterms-date "2023-04-04T10:54:15Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-04-04T10:54:15Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9443 [Term] id: CL:4033037 @@ -36162,9 +36187,9 @@ is_a: CL:0002202 ! epithelial cell of tracheobronchial tree intersection_of: CL:0000319 ! mucus secreting cell intersection_of: part_of UBERON:0007196 ! tracheobronchial tree intersection_of: part_of UBERON:8410077 ! airway submucosal gland -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: part_of UBERON:8410077 ! airway submucosal gland -property_value: dcterms-date "2023-04-20T10:55:50Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-04-20T10:55:50Z" xsd:dateTime [Term] id: CL:4033038 @@ -36174,11 +36199,11 @@ subset: human_reference_atlas synonym: "lung CD4-positive TRM" RELATED OMO:0003000 [PMID:31265968] synonym: "lung resident memory CD4 T cell" EXACT [PMID:24064670] is_a: CL:0000897 ! CD4-positive, alpha-beta memory T cell -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: dc-contributor https://orcid.org/0000-0002-9185-3994 relationship: part_of UBERON:0002048 ! lung -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2023-04-27T10:15:45Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 +property_value: http://purl.org/dc/terms/date "2023-04-27T10:15:45Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4033039 @@ -36188,11 +36213,11 @@ comment: In the lung, CXCR6 regulates the localization of lung resident memory C subset: human_reference_atlas synonym: "lung CD8-positive TRM" RELATED OMO:0003000 [PMID:31265968] is_a: CL:0000909 ! CD8-positive, alpha-beta memory T cell -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: dc-contributor https://orcid.org/0000-0002-9185-3994 relationship: part_of UBERON:0002048 ! lung -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2023-04-27T10:16:07Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 +property_value: http://purl.org/dc/terms/date "2023-04-27T10:16:07Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4033040 @@ -36204,10 +36229,10 @@ synonym: "lung TRM CD8-positive, integrin alpha E-positive cell" EXACT [PMID:277 is_a: CL:4033039 ! lung resident memory CD8-positive, alpha-beta T cell intersection_of: CL:4033039 ! lung resident memory CD8-positive, alpha-beta T cell intersection_of: RO:0002104 PR:000001010 ! has plasma membrane part integrin alpha-E -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: dc-contributor https://orcid.org/0000-0002-9185-3994 relationship: RO:0002104 PR:000001010 ! has plasma membrane part integrin alpha-E -property_value: dcterms-date "2023-05-24T12:23:35Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 +property_value: http://purl.org/dc/terms/date "2023-05-24T12:23:35Z" xsd:dateTime [Term] id: CL:4033041 @@ -36216,11 +36241,11 @@ def: "An alveolar macrophage that expresses CCL3." [PMID:37291214] subset: human_reference_atlas synonym: "alveolar macrophage CCL3-positive" EXACT [PMID:37291214] is_a: CL:0000583 ! alveolar macrophage -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: dc-contributor https://orcid.org/0000-0002-9185-3994 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: RO:0002292 PR:000002123 ! expresses C-C motif chemokine 3 -property_value: dcterms-date "2023-06-15T12:53:08Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 +property_value: http://purl.org/dc/terms/date "2023-06-15T12:53:08Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4033042 @@ -36230,10 +36255,10 @@ subset: human_reference_atlas synonym: "alveolar macrophage metallothionein-positive" EXACT [PMID:37291214] synonym: "alveolar macrophage MT-positive" EXACT [PMID:37291214] is_a: CL:0000583 ! alveolar macrophage -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: dc-contributor https://orcid.org/0000-0002-9185-3994 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2023-06-15T12:55:34Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 +property_value: http://purl.org/dc/terms/date "2023-06-15T12:55:34Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4033043 @@ -36244,11 +36269,11 @@ synonym: "lung IM" RELATED OMO:0003000 [PMID:36211428] is_a: CL:0000864 ! tissue-resident macrophage is_a: CL:0002320 ! connective tissue cell is_a: CL:1001603 ! lung macrophage -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: dc-contributor https://orcid.org/0000-0002-9185-3994 relationship: part_of UBERON:0000114 ! lung connective tissue -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2023-06-15T12:58:11Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 +property_value: http://purl.org/dc/terms/date "2023-06-15T12:58:11Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4033044 @@ -36257,11 +36282,11 @@ def: "An epithelial cell part of respiratory tract epithelium that is a precurso comment: In humans, deuterosomal cells have been noted to have enriched expression of the following: PLK4, FOXJ1, DEUP1, FOXN4, YPEL1, HES6 and CDC20B. Deuterosomal cells were termed after deuterosomes, the platforms of active centriole amplification. {xref="PMID:31558434", xref="PMID:36883528", xref="PMID:331922198"} subset: human_reference_atlas is_a: CL:0002368 ! respiratory epithelial cell -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: dc-contributor https://orcid.org/0000-0002-9185-3994 relationship: part_of UBERON:0004802 ! respiratory tract epithelium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2023-06-20T10:27:17Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 +property_value: http://purl.org/dc/terms/date "2023-06-20T10:27:17Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4033045 @@ -36271,10 +36296,10 @@ subset: human_reference_atlas synonym: "lung mDC" RELATED OMO:0003000 [PMID:34516781] synonym: "lung mDCs" RELATED OMO:0003004 [PMID:34516781] is_a: CL:0000451 ! dendritic cell -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: dc-contributor https://orcid.org/0000-0002-9185-3994 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2023-06-21T10:04:46Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 +property_value: http://purl.org/dc/terms/date "2023-06-21T10:04:46Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4033046 @@ -36287,8 +36312,8 @@ is_a: CL:4023032 ! ON retinal ganglion cell is_a: CL:4023188 ! midget ganglion cell of retina intersection_of: CL:4023032 ! ON retinal ganglion cell intersection_of: CL:4023188 ! midget ganglion cell of retina -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -property_value: dcterms-date "2023-08-08T09:40:08Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-08-08T09:40:08Z" xsd:dateTime [Term] id: CL:4033047 @@ -36301,8 +36326,8 @@ is_a: CL:4023033 ! OFF retinal ganglion cell is_a: CL:4023188 ! midget ganglion cell of retina intersection_of: CL:4023033 ! OFF retinal ganglion cell intersection_of: CL:4023188 ! midget ganglion cell of retina -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -property_value: dcterms-date "2023-08-08T11:05:37Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-08-08T11:05:37Z" xsd:dateTime [Term] id: CL:4033048 @@ -36314,12 +36339,12 @@ synonym: "respiratory parabasal cell" EXACT [PMID:25564622] synonym: "respiratory suprabasal progenitor cell" EXACT [PMID:25658372] is_a: CL:0002368 ! respiratory epithelial cell is_a: CL:0011026 ! progenitor cell -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: dc-contributor https://orcid.org/0000-0002-9185-3994 -relationship: develops_from CL:0002633 ! respiratory basal cell relationship: part_of UBERON:0004802 ! respiratory tract epithelium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2023-06-20T10:44:30Z" xsd:dateTime +relationship: RO:0002202 CL:0002633 ! develops from respiratory basal cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 +property_value: http://purl.org/dc/terms/date "2023-06-20T10:44:30Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4033049 @@ -36331,9 +36356,9 @@ is_a: CL:0002251 ! epithelial cell of alimentary canal is_a: CL:0002319 ! neural cell intersection_of: CL:0000209 ! taste receptor cell intersection_of: part_of UBERON:0014451 ! tongue taste bud -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: part_of UBERON:0014451 ! tongue taste bud -property_value: dcterms-date "2023-05-03T07:59:58Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-05-03T07:59:58Z" xsd:dateTime [Term] id: CL:4033050 @@ -36345,8 +36370,8 @@ is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0160043 ! catecholamine secretion, neurotransmission relationship: capable_of GO:0160043 ! catecholamine secretion, neurotransmission -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -property_value: dcterms-date "2023-05-18T12:07:45Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-05-18T12:07:45Z" xsd:dateTime [Term] id: CL:4033051 @@ -36359,8 +36384,8 @@ is_a: CL:4023033 ! OFF retinal ganglion cell is_a: CL:4023189 ! parasol ganglion cell of retina intersection_of: CL:4023033 ! OFF retinal ganglion cell intersection_of: CL:4023189 ! parasol ganglion cell of retina -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -property_value: dcterms-date "2023-08-08T12:34:57Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-08-08T12:34:57Z" xsd:dateTime [Term] id: CL:4033052 @@ -36373,8 +36398,8 @@ is_a: CL:4023032 ! ON retinal ganglion cell is_a: CL:4023189 ! parasol ganglion cell of retina intersection_of: CL:4023032 ! ON retinal ganglion cell intersection_of: CL:4023189 ! parasol ganglion cell of retina -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -property_value: dcterms-date "2023-08-08T12:39:35Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-08-08T12:39:35Z" xsd:dateTime [Term] id: CL:4033053 @@ -36386,9 +36411,9 @@ synonym: "SBS ganglion cell" RELATED OMO:0003000 [PMID:32032773] synonym: "small bistratified cell" EXACT [PMID:32032773] synonym: "small bistratified cell, blue-ON/yellow-OFF ganglion cell" EXACT [doi:10.1002/cne.22183] is_a: CL:0003001 ! bistratified retinal ganglion cell -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: RO:0002100 UBERON:0001792 ! has soma location ganglionic layer of retina -property_value: dcterms-date "2023-08-08T12:43:56Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-08-08T12:43:56Z" xsd:dateTime [Term] id: CL:4033054 @@ -36398,8 +36423,8 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: adjacent_to UBERON:0002049 ! vasculature relationship: adjacent_to UBERON:0002049 ! vasculature -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -property_value: dcterms-date "2023-08-22T13:40:28Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-08-22T13:40:28Z" xsd:dateTime [Term] id: CL:4033055 @@ -36410,12 +36435,12 @@ is_a: CL:0000064 ! ciliated cell intersection_of: CL:0000064 ! ciliated cell intersection_of: part_of UBERON:8410077 ! airway submucosal gland intersection_of: part_of UBERON:8600014 ! submucosal gland ciliated duct -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: dc-contributor https://orcid.org/0000-0002-9185-3994 relationship: part_of UBERON:8410077 ! airway submucosal gland relationship: part_of UBERON:8600014 ! submucosal gland ciliated duct -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2023-09-08T10:32:27Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 +property_value: http://purl.org/dc/terms/date "2023-09-08T10:32:27Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4033056 @@ -36423,10 +36448,10 @@ name: onychocyte def: "A differentiated flat keratinocyte that is part of a nail plate. An onychocyte is firmly adherent and does not desquamate." [PMID:24079581] subset: human_reference_atlas is_a: CL:0000312 ! keratinocyte -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: part_of UBERON:0008198 ! nail plate -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2023-10-03T12:49:46Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-10-03T12:49:46Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4033057 @@ -36445,9 +36470,9 @@ synonym: "luminal secretory cell" BROAD [PMID:37380767] synonym: "LumSec" RELATED OMO:0003000 [PMID:37380767] is_a: CL:0002326 ! luminal epithelial cell of mammary gland is_a: CL:0011026 ! progenitor cell -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: dc-contributor https://orcid.org/0000-0003-4969-670X -property_value: dcterms-date "2023-10-13T13:02:55Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-4969-670X +property_value: http://purl.org/dc/terms/date "2023-10-13T13:02:55Z" xsd:dateTime [Term] id: CL:4033058 @@ -36467,10 +36492,10 @@ is_a: CL:0000152 ! exocrine cell is_a: CL:0000512 ! paracrine cell is_a: CL:0002326 ! luminal epithelial cell of mammary gland is_a: PR:000050567 ! protein-containing material entity -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: dc-contributor https://orcid.org/0000-0003-4969-670X relationship: RO:0002104 PR:000007204 ! has plasma membrane part estrogen receptor -property_value: dcterms-date "2023-10-16T08:30:25Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-4969-670X +property_value: http://purl.org/dc/terms/date "2023-10-16T08:30:25Z" xsd:dateTime [Term] id: CL:4033059 @@ -36481,9 +36506,9 @@ synonym: "LMC major luminal cluster 1" RELATED [PMID:35091553] synonym: "luminal cluster 1 cell" BROAD [PMID:34097179] synonym: "progenitor MEC" RELATED OMO:0003000 [PMID:35091553] is_a: CL:0002325 ! lactocyte -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: dc-contributor https://orcid.org/0000-0003-4361-817X -property_value: dcterms-date "2023-10-16T13:15:36Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-4361-817X +property_value: http://purl.org/dc/terms/date "2023-10-16T13:15:36Z" xsd:dateTime [Term] id: CL:4033060 @@ -36493,9 +36518,9 @@ synonym: "LC2" RELATED OMO:0003000 [PMID:35091553] synonym: "LMC major luminal cluster 2" RELATED [PMID:35091553] synonym: "luminal cluster 2 cell" BROAD [PMID:35377806] is_a: CL:0002325 ! lactocyte -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: dc-contributor https://orcid.org/0000-0003-4361-817X -property_value: dcterms-date "2023-10-16T13:15:55Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-4361-817X +property_value: http://purl.org/dc/terms/date "2023-10-16T13:15:55Z" xsd:dateTime [Term] id: CL:4033061 @@ -36505,8 +36530,8 @@ synonym: "endothelial cell of central vein" BROAD [PMID:28287163] is_a: CL:0000115 ! endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0006841 ! central vein of liver -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: part_of UBERON:0006841 ! central vein of liver +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 [Term] id: CL:4033062 @@ -36517,9 +36542,9 @@ synonym: "interstitial extravillous trophoblast" RELATED [PMID:37630754] synonym: "interstitial trophoblast" RELATED [PMID:11337369] synonym: "invasive interstitial extravillous trophoblast cell" EXACT [doi:10.1007/978-3-030-84725-8] is_a: CL:0000351 ! trophoblast cell -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: develops_from CL:0008036 ! extravillous trophoblast -property_value: dcterms-date "2024-01-08T15:43:15Z" xsd:dateTime +relationship: RO:0002202 CL:0008036 ! develops from extravillous trophoblast +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-01-08T15:43:15Z" xsd:dateTime [Term] id: CL:4033063 @@ -36530,9 +36555,9 @@ synonym: "eEVT" RELATED OMO:0003000 [PMID:37630754] synonym: "endovascular extravillous trophoblast" RELATED [PMID:37630754] synonym: "endovascular trophoblast" RELATED [PMID:11337369] is_a: CL:0000351 ! trophoblast cell -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: develops_from CL:0008036 ! extravillous trophoblast -property_value: dcterms-date "2024-01-08T15:43:32Z" xsd:dateTime +relationship: RO:0002202 CL:0008036 ! develops from extravillous trophoblast +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-01-08T15:43:32Z" xsd:dateTime [Term] id: CL:4033064 @@ -36543,9 +36568,9 @@ synonym: "uterine macrophage" BROAD [PMID:36113384] is_a: CL:0000864 ! tissue-resident macrophage intersection_of: CL:0000864 ! tissue-resident macrophage intersection_of: part_of UBERON:0000995 ! uterus -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: part_of UBERON:0000995 ! uterus -property_value: dcterms-date "2024-01-08T16:05:09Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-01-08T16:05:09Z" xsd:dateTime [Term] id: CL:4040000 @@ -36556,8 +36581,8 @@ synonym: "GRP cell" RELATED OMO:0003000 [PMID:11756508] synonym: "tripotential glial-restricted precursor cell" EXACT [PMID:11921204] is_a: CL:0000123 ! neuron associated cell (sensu Vertebrata) is_a: CL:0011026 ! progenitor cell -relationship: dc-contributor https://orcid.org/0000-0002-0819-0473 -property_value: dcterms-date "2023-04-03T14:54:32Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 +property_value: http://purl.org/dc/terms/date "2023-04-03T14:54:32Z" xsd:dateTime [Term] id: CL:4040001 @@ -36565,10 +36590,10 @@ name: chorionic girdle cell def: "A horse-specific, highly invasive trophoblast cell that invades the endometrium where it forms endometrial cups." [PMID:27280409, PMID:35328607] synonym: "equine chorionic girdle cell" EXACT [PMID:35328607] is_a: CL:0011101 ! chorionic trophoblast cell -relationship: dc-contributor https://orcid.org/0000-0002-0819-0473 -relationship: present_in_taxon NCBITaxon:9789 ! Equus -property_value: dcterms-date "2023-04-03T15:08:05Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 +property_value: http://purl.org/dc/terms/date "2023-04-03T15:08:05Z" xsd:dateTime property_value: note "Humans, mice and rats have a highly invasive (hemochorial) placentation. Horses have a non-invasive epitheliochorial placenta, except for the transient endometrial cup." xsd:string {xref="PMID:27280409"} +property_value: RO:0002175 NCBITaxon:9789 [Term] id: CL:4040002 @@ -36579,10 +36604,10 @@ synonym: "enteric glial cell" EXACT [PMID:11169131, PMID:25170211] is_a: CL:0000125 ! glial cell intersection_of: CL:0000125 ! glial cell intersection_of: part_of UBERON:0002005 ! enteric nervous system -relationship: dc-contributor https://orcid.org/0000-0002-0819-0473 relationship: part_of UBERON:0002005 ! enteric nervous system relationship: RO:0002292 PR:000007939 ! expresses glial fibrillary acidic protein -property_value: dcterms-date "2023-04-03T15:15:40Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 +property_value: http://purl.org/dc/terms/date "2023-04-03T15:15:40Z" xsd:dateTime [Term] id: CL:4040003 @@ -36592,8 +36617,8 @@ synonym: "fetal alveolar pre-type II epithelial cell" EXACT [PMID:9624168] synonym: "fetal pre-type 2 pneumocyte" EXACT [https://orcid.org/0000-0002-0819-0473] synonym: "fetal pre-type II alveolar epithelial cell" EXACT [PMID:12114192] is_a: CL:0000322 ! pneumocyte -relationship: dc-contributor https://orcid.org/0000-0002-0819-0473 -property_value: dcterms-date "2023-06-02T09:19:31Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 +property_value: http://purl.org/dc/terms/date "2023-06-02T09:19:31Z" xsd:dateTime property_value: note "According to PMID:1316350 this cell type does not yet produce surfactant. According to PMID:9109447 and PMID:12114192 this cell type produces low levels of surfactant that can be increased by administration of very low-density lipoproteins. This cell type is of medical relevance, as a central feature of the fetal respiratory distress syndrome seems to be the presence in the lung of abundant pre-type II alveolar epithelial cells (PMID:1316350)." xsd:string [Term] @@ -36606,9 +36631,9 @@ synonym: "Orbital ASCs" EXACT [PMID:30210548] is_a: CL:0002570 ! mesenchymal stem cell of adipose tissue intersection_of: CL:0002570 ! mesenchymal stem cell of adipose tissue intersection_of: part_of UBERON:0004088 ! orbital region -relationship: dc-contributor https://orcid.org/0000-0002-0819-0473 relationship: part_of UBERON:0004088 ! orbital region -property_value: dcterms-date "2023-09-18T10:43:00Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 +property_value: http://purl.org/dc/terms/date "2023-09-18T10:43:00Z" xsd:dateTime [Term] id: CL:4040005 @@ -36619,9 +36644,90 @@ synonym: "SCAP" RELATED OMO:0003000 [PMID:37887345] synonym: "SCAPs" RELATED OMO:0003004 [PMID:30834270] synonym: "stem cells from the apical papilla" BROAD OMO:0003004 [PMID:30834270] is_a: CL:0000134 ! mesenchymal stem cell -relationship: dc-contributor https://orcid.org/0000-0002-0819-0473 relationship: part_of UBERON:0003677 ! tooth root -property_value: dcterms-date "2023-11-02T09:44:47Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 +property_value: http://purl.org/dc/terms/date "2023-11-02T09:44:47Z" xsd:dateTime + +[Term] +id: CL:4040006 +name: dermal chromatophore +def: "A chromatophore that is part of the dermis." [PMID:28553007] +is_a: CL:0000147 ! pigment cell +relationship: part_of UBERON:0002067 ! dermis +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 +property_value: http://purl.org/dc/terms/date "2024-03-07T09:37:14Z" xsd:dateTime + +[Term] +id: CL:4042001 +name: TAC3-positive striatal interneuron +def: "A GABAergic interneuron that has its soma located in the striatum and that has an enriched expression of the gene TAC3." [PMID:32999462, PMID:34727523] +synonym: "TAC3 interneuron" EXACT [PMID:34727523] +is_a: CL:0000402 ! CNS interneuron +is_a: CL:0011005 ! GABAergic interneuron +is_a: PR:000050567 ! protein-containing material entity +relationship: RO:0002100 UBERON:0002435 ! has soma location striatum +relationship: RO:0002104 PR:000016004 ! has plasma membrane part tachykinin-3 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0098-8958 +property_value: http://purl.org/dc/terms/date "2024-03-05T14:29:32Z" xsd:dateTime + +[Term] +id: CL:4042002 +name: TAC3-positive medium spiny neuron +def: "A nucleus accumbens shell and olfactory tubercle D1 medium spiny neuron that co-expresses TAC3 and the DRD1 receptor." [PMID:34727523] +comment: A TAC3-positive medium spiny neuron has its soma in a cluster in the medial shell region of the nucleus accumbens. In Rhesus Macaque, this medium spiny neuron has an enriched expression of the genes MPPED1, HPCAL1, MEIS3. {xref="PMID:34727523"} +synonym: "D1Sh TAC3 archetype" RELATED OMO:0003000 [PMID:34727523] +synonym: "TAC3-positive D1Sh-MSN" RELATED OMO:0003000 [PMID:34727523] +synonym: "TAC3-positive MSN" RELATED OMO:0003000 [PMID:34727523] +is_a: CL:4030051 ! nucleus accumbens shell and olfactory tubercle D1 medium spiny neuron +is_a: PR:000050567 ! protein-containing material entity +relationship: RO:0002104 PR:000016004 ! has plasma membrane part tachykinin-3 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0098-8958 +property_value: http://purl.org/dc/terms/date "2024-03-05T13:36:54Z" xsd:dateTime + +[Term] +id: CL:4042003 +name: border associated macrophage +def: "A central nervous system macrophage that is part of a choroid plexus, a meninx and a perivascular space. A border associated macrophage interacts with various components of the CNS vasculature and meninges, it participates in immune surveillance and in the regulation of the blood brain barrier." [PMID:37232741, PMID:37626977] +comment: In humans, a border associate macrophage expresses CD45 and CD11B. This cell is also known to have the following molecular signature: CD206, CD38, LYVE1, CD163, CD169. {xref="PMID:29426702", xref="PMID:37232741"} +synonym: "BAM" RELATED OMO:0003000 [PMID:36945367] +synonym: "CAM" RELATED OMO:0003000 [PMID:33556248] +synonym: "CNS-associated macrophage" RELATED [PMID:37232741] +is_a: CL:0000878 ! central nervous system macrophage +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0098-8958 +property_value: http://purl.org/dc/terms/date "2024-03-26T16:39:56Z" xsd:dateTime + +[Term] +id: CL:4042004 +name: choroid epiplexus macrophage +def: "A choroid plexus macrophage that is part of the apical surface of some choroid plexus epithelium. This macrophage has a star-like shaped body." [PMID:31061494, PMID:37232741] +synonym: "cpepiMΦ" RELATED OMO:0003000 [PMID:38347231] +synonym: "epiplexus cpMΦ" RELATED OMO:0003000 [PMID:38347231] +synonym: "Kolmer’s cell" EXACT [PMID:31433571] +is_a: CL:0000880 ! choroid plexus macrophage +relationship: part_of UBERON:0003911 ! choroid plexus epithelium +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0098-8958 +property_value: http://purl.org/dc/terms/date "2024-03-26T19:14:58Z" xsd:dateTime + +[Term] +id: CL:4042005 +name: stromal choroid plexus macrophage +def: "A choroid plexus macrophage that is part of a choroid plexus stroma." [PMID:38347231] +synonym: "cpstMΦ" RELATED OMO:0003000 [PMID:37626977] +synonym: "stromal cpMΦ" RELATED OMO:0003000 [PMID:37232741, PMID:38347231] +is_a: CL:0000880 ! choroid plexus macrophage +relationship: part_of UBERON:0005206 ! choroid plexus stroma +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0098-8958 +property_value: http://purl.org/dc/terms/date "2024-03-26T19:21:51Z" xsd:dateTime + +[Term] +id: CL:4042006 +name: dural macrophage +def: "A border associated macrophage which is part of a dura matter. This macrophage phagocytoses intruding pathogens and foreign molecules detected in the bloodstream or in the cerebrospinal fluid. This cell has an amoeboid body with dynamic protrusions in homeostasis." [PMID:31061494] +synonym: "dmMΦ" RELATED OMO:0003000 [PMID:37232741] +is_a: CL:4042003 ! border associated macrophage +relationship: part_of UBERON:0002092 ! brain dura mater +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0098-8958 +property_value: http://purl.org/dc/terms/date "2024-03-26T19:27:03Z" xsd:dateTime [Term] id: CP:0000000 @@ -36711,8 +36817,8 @@ is_a: GO:0007033 ! vacuole organization is_a: GO:0048308 ! organelle inheritance intersection_of: GO:0048308 ! organelle inheritance intersection_of: results_in_distribution_of GO:0005773 ! vacuole -relationship: never_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe relationship: results_in_distribution_of GO:0005773 ! vacuole +property_value: RO:0002161 NCBITaxon:4896 [Term] id: GO:0000018 @@ -36829,8 +36935,8 @@ is_a: GO:0007049 ! cell cycle intersection_of: GO:0007049 ! cell cycle intersection_of: has_part GO:0140014 ! mitotic nuclear division relationship: has_part GO:0140014 ! mitotic nuclear division -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota [Term] id: GO:0000280 @@ -37056,7 +37162,7 @@ namespace: biological_process def: "A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities." [GOC:dph, GOC:go_curators, GOC:tb, ISBN:978-0-07-139011-8] comment: Action potentials typically propagate across excitable membranes. This class covers both action potentials that propagate and those that fail to do so. is_a: GO:0042391 ! regulation of membrane potential -relationship: never_in_taxon NCBITaxon:4895 ! Schizosaccharomyces +property_value: RO:0002161 NCBITaxon:4895 [Term] id: GO:0001525 @@ -37169,10 +37275,10 @@ is_a: GO:0022412 ! cellular process involved in reproduction in multicellular or is_a: GO:0048588 ! developmental cell growth intersection_of: GO:0040007 ! growth intersection_of: results_in_growth_of CL:0000023 ! oocyte -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa relationship: part_of GO:0048599 ! oocyte development relationship: results_in_growth_of CL:0000023 ! oocyte +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0001556 @@ -37185,10 +37291,10 @@ is_a: GO:0022412 ! cellular process involved in reproduction in multicellular or is_a: GO:0048469 ! cell maturation intersection_of: GO:0021700 ! developmental maturation intersection_of: results_in_maturation_of CL:0000023 ! oocyte -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa relationship: part_of GO:0048599 ! oocyte development relationship: results_in_maturation_of CL:0000023 ! oocyte +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0001558 @@ -37410,8 +37516,8 @@ synonym: "male germ-cell nucleus" EXACT [] is_a: GO:0043073 ! germ cell nucleus intersection_of: GO:0005634 ! nucleus intersection_of: part_of CL:0000015 ! male germ cell -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota relationship: part_of CL:0000015 ! male germ cell +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota [Term] id: GO:0001674 @@ -37423,8 +37529,8 @@ synonym: "female germ-cell nucleus" EXACT [] is_a: GO:0043073 ! germ cell nucleus intersection_of: GO:0005634 ! nucleus intersection_of: part_of CL:0000021 ! female germ cell -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota relationship: part_of CL:0000021 ! female germ cell +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota [Term] id: GO:0001675 @@ -37524,8 +37630,8 @@ name: embryonic development via the syncytial blastoderm namespace: biological_process def: "The process whose specific outcome is the progression of the embryo over time, from zygote formation through syncytial blastoderm to the hatching of the first instar larva. An example of this process is found in Drosophila melanogaster." [GOC:go_curators, GOC:mtg_sensu] is_a: GO:0009792 ! embryo development ending in birth or egg hatching -relationship: in_taxon NCBITaxon:50557 {all_only="true"} ! Insecta -relationship: only_in_taxon NCBITaxon:50557 ! Insecta +relationship: RO:0002160 NCBITaxon:50557 ! only in taxon Insecta +relationship: RO:0002162 NCBITaxon:50557 {all_only="true"} ! in taxon Insecta [Term] id: GO:0001701 @@ -37533,8 +37639,8 @@ name: in utero embryonic development namespace: biological_process def: "The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus." [GOC:go_curators, GOC:mtg_sensu] is_a: GO:0043009 ! chordate embryonic development -relationship: in_taxon NCBITaxon:32525 {all_only="true"} ! Theria -relationship: only_in_taxon NCBITaxon:32525 ! Theria +relationship: RO:0002160 NCBITaxon:32525 ! only in taxon Theria +relationship: RO:0002162 NCBITaxon:32525 {all_only="true"} ! in taxon Theria [Term] id: GO:0001702 @@ -37545,8 +37651,8 @@ alt_id: GO:0048276 def: "A gastrulation process in which the initial invagination becomes the anus and the mouth forms second." [GOC:go_curators, GOC:mtg_sensu] synonym: "deuterostomic gastrulation" EXACT [GOC:dph] is_a: GO:0007369 ! gastrulation -relationship: in_taxon NCBITaxon:33511 {all_only="true"} ! Deuterostomia -relationship: only_in_taxon NCBITaxon:33511 ! Deuterostomia +relationship: RO:0002160 NCBITaxon:33511 ! only in taxon Deuterostomia +relationship: RO:0002162 NCBITaxon:33511 {all_only="true"} ! in taxon Deuterostomia [Term] id: GO:0001703 @@ -37555,8 +37661,8 @@ namespace: biological_process def: "A gastrulation process in which the initial invagination becomes the mouth and the anus forms second." [GOC:go_curators, GOC:mtg_sensu] synonym: "protostomic gastrulation" NARROW [GOC:dph] is_a: GO:0007369 ! gastrulation -relationship: in_taxon NCBITaxon:33317 {all_only="true"} ! Protostomia -relationship: only_in_taxon NCBITaxon:33317 ! Protostomia +relationship: RO:0002160 NCBITaxon:33317 ! only in taxon Protostomia +relationship: RO:0002162 NCBITaxon:33317 {all_only="true"} ! in taxon Protostomia [Term] id: GO:0001704 @@ -37635,10 +37741,10 @@ synonym: "insect-type retina morphogenesis" EXACT [PMID:11735386] is_a: GO:0048592 ! eye morphogenesis intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0000018 ! compound eye -relationship: in_taxon NCBITaxon:6656 {all_only="true"} ! Arthropoda -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda relationship: part_of GO:0048749 ! compound eye development relationship: results_in_morphogenesis_of UBERON:0000018 ! compound eye +relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda +relationship: RO:0002162 NCBITaxon:6656 {all_only="true"} ! in taxon Arthropoda [Term] id: GO:0001751 @@ -37805,8 +37911,8 @@ def: "A multicellular organismal process by which exposure to an activating fact subset: goslim_pir is_a: GO:0009987 ! cellular process is_a: GO:0032501 ! multicellular organismal process -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24416" xsd:anyURI [Term] @@ -37822,8 +37928,8 @@ is_a: GO:0048872 ! homeostasis of number of cells intersection_of: GO:0048872 ! homeostasis of number of cells intersection_of: acts_on_population_of CL:0000738 ! leukocyte relationship: acts_on_population_of CL:0000738 ! leukocyte -relationship: in_taxon NCBITaxon:7742 {all_only="true"} ! Vertebrata -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 {all_only="true"} ! in taxon Vertebrata [Term] id: GO:0001777 @@ -38088,10 +38194,10 @@ comment: See also the Anatomical Dictionary for Mouse Development ontology terms is_a: GO:0048856 ! anatomical structure development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0000358 ! blastocyst -relationship: in_taxon NCBITaxon:32525 {all_only="true"} ! Theria -relationship: only_in_taxon NCBITaxon:32525 ! Theria relationship: part_of GO:0001701 ! in utero embryonic development relationship: results_in_development_of UBERON:0000358 ! blastocyst +relationship: RO:0002160 NCBITaxon:32525 ! only in taxon Theria +relationship: RO:0002162 NCBITaxon:32525 {all_only="true"} ! in taxon Theria [Term] id: GO:0001825 @@ -38358,9 +38464,9 @@ synonym: "placentation" EXACT [GOC:dph, GOC:tb] is_a: GO:0048513 ! animal organ development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001987 ! placenta -relationship: in_taxon NCBITaxon:32525 {all_only="true"} ! Theria -relationship: only_in_taxon NCBITaxon:32525 ! Theria relationship: results_in_development_of UBERON:0001987 ! placenta +relationship: RO:0002160 NCBITaxon:32525 ! only in taxon Theria +relationship: RO:0002162 NCBITaxon:32525 {all_only="true"} ! in taxon Theria [Term] id: GO:0001892 @@ -38421,7 +38527,7 @@ is_a: GO:0001906 ! cell killing is_a: GO:0002443 ! leukocyte mediated immunity intersection_of: GO:0001906 ! cell killing intersection_of: process_has_causal_agent CL:0000738 ! leukocyte -relationship: in_taxon NCBITaxon:7742 {all_only="true"} ! Vertebrata +relationship: RO:0002162 NCBITaxon:7742 {all_only="true"} ! in taxon Vertebrata [Term] id: GO:0001910 @@ -39416,8 +39522,8 @@ namespace: biological_process def: "The process whose specific outcome is the progression of the instar larva or pupa over time, from its formation to the mature structure. An example of this process is found in Drosophila melanogaster." [GOC:jid, GOC:mtg_sensu] is_a: GO:0007275 ! multicellular organism development is_a: GO:0009791 ! post-embryonic development -relationship: in_taxon NCBITaxon:6656 {all_only="true"} ! Arthropoda -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda +relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda +relationship: RO:0002162 NCBITaxon:6656 {all_only="true"} ! in taxon Arthropoda [Term] id: GO:0002176 @@ -39564,9 +39670,9 @@ is_a: GO:0002385 ! mucosal immune response is_a: GO:0045087 ! innate immune response intersection_of: GO:0045087 ! innate immune response intersection_of: occurs_in UBERON:0000344 ! mucosa -relationship: in_taxon NCBITaxon:7711 {all_only="true"} ! Chordata relationship: occurs_in UBERON:0000344 ! mucosa -relationship: only_in_taxon NCBITaxon:7711 ! Chordata +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {all_only="true"} ! in taxon Chordata [Term] id: GO:0002228 @@ -39648,8 +39754,8 @@ synonym: "acquired immune response" EXACT [ISBN:068340007X] synonym: "immune memory response" EXACT [GOC:add] xref: Wikipedia:Adaptive_immune_system is_a: GO:0006955 ! immune response -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0002251 @@ -40790,7 +40896,7 @@ subset: goslim_mouse subset: goslim_pir xref: Wikipedia:Immune_system is_a: GO:0008150 ! biological_process -relationship: never_in_taxon NCBITaxon:4895 ! Schizosaccharomyces +property_value: RO:0002161 NCBITaxon:4895 [Term] id: GO:0002377 @@ -40835,9 +40941,9 @@ def: "An immune response taking place in the liver." [GO_REF:0000022, GOC:jal, I is_a: GO:0002251 ! organ or tissue specific immune response intersection_of: GO:0006955 ! immune response intersection_of: occurs_in UBERON:0002107 ! liver -relationship: in_taxon NCBITaxon:7742 {all_only="true"} ! Vertebrata relationship: occurs_in UBERON:0002107 ! liver -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 {all_only="true"} ! in taxon Vertebrata [Term] id: GO:0002385 @@ -40870,9 +40976,9 @@ def: "Immune response taking place in the Peyer's patch, nodular lymphoid struct is_a: GO:0002387 ! immune response in gut-associated lymphoid tissue intersection_of: GO:0006955 ! immune response intersection_of: occurs_in UBERON:0001211 ! Peyer's patch -relationship: in_taxon NCBITaxon:32524 {all_only="true"} ! Amniota relationship: occurs_in UBERON:0001211 ! Peyer's patch -relationship: only_in_taxon NCBITaxon:32524 ! Amniota +relationship: RO:0002160 NCBITaxon:32524 ! only in taxon Amniota +relationship: RO:0002162 NCBITaxon:32524 {all_only="true"} ! in taxon Amniota [Term] id: GO:0002389 @@ -40883,7 +40989,7 @@ is_a: GO:0002388 ! immune response in Peyer's patch is_a: GO:0002394 ! tolerance induction in gut-associated lymphoid tissue intersection_of: GO:0002507 ! tolerance induction intersection_of: occurs_in UBERON:0001211 ! Peyer's patch -relationship: in_taxon NCBITaxon:32524 {all_only="true"} ! Amniota +relationship: RO:0002162 NCBITaxon:32524 {all_only="true"} ! in taxon Amniota [Term] id: GO:0002394 @@ -41082,9 +41188,9 @@ synonym: "leukocyte immune effector process" EXACT [] is_a: GO:0002252 ! immune effector process intersection_of: GO:0002376 ! immune system process intersection_of: process_has_causal_agent CL:0000738 ! leukocyte -relationship: in_taxon NCBITaxon:7742 {all_only="true"} ! Vertebrata -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: process_has_causal_agent CL:0000738 ! leukocyte +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 {all_only="true"} ! in taxon Vertebrata [Term] id: GO:0002444 @@ -44100,9 +44206,9 @@ def: "Any process that modulates the frequency, rate, or extent of an adaptive i is_a: GO:0002819 ! regulation of adaptive immune response intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0002460 ! adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains -relationship: in_taxon NCBITaxon:7776 {all_only="true"} ! Gnathostomata -relationship: only_in_taxon NCBITaxon:7776 ! Gnathostomata relationship: regulates GO:0002460 ! adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains +relationship: RO:0002160 NCBITaxon:7776 ! only in taxon Gnathostomata +relationship: RO:0002162 NCBITaxon:7776 {all_only="true"} ! in taxon Gnathostomata [Term] id: GO:0002823 @@ -46383,15 +46489,15 @@ is_a: GO:0007018 ! microtubule-based movement intersection_of: GO:0007018 ! microtubule-based movement intersection_of: process_has_causal_agent GO:0005874 ! microtubule intersection_of: results_in_movement_of GO:0005929 ! cilium -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: never_in_taxon NCBITaxon:3176 ! Zygnematales -relationship: never_in_taxon NCBITaxon:3312 ! Coniferophyta -relationship: never_in_taxon NCBITaxon:3378 ! Gnetales -relationship: never_in_taxon NCBITaxon:3398 ! Magnoliopsida -relationship: never_in_taxon NCBITaxon:4890 ! Ascomycota -relationship: never_in_taxon NCBITaxon:5782 ! Dictyostelium -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota relationship: results_in_movement_of GO:0005929 ! cilium +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota +property_value: RO:0002161 NCBITaxon:3176 +property_value: RO:0002161 NCBITaxon:3312 +property_value: RO:0002161 NCBITaxon:3378 +property_value: RO:0002161 NCBITaxon:3398 +property_value: RO:0002161 NCBITaxon:4890 +property_value: RO:0002161 NCBITaxon:5782 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19809" xsd:anyURI created_by: dph creation_date: 2009-11-24T09:56:26Z @@ -46559,8 +46665,8 @@ def: "The specification and formation of anisotropic intracellular organization is_a: GO:0030010 ! establishment of cell polarity intersection_of: GO:0030010 ! establishment of cell polarity intersection_of: part_of GO:0001667 ! ameboidal-type cell migration -relationship: never_in_taxon NCBITaxon:4751 ! Fungi relationship: part_of GO:0001667 ! ameboidal-type cell migration +property_value: RO:0002161 NCBITaxon:4751 created_by: dph creation_date: 2009-12-08T04:50:41Z @@ -47540,8 +47646,8 @@ is_a: GO:0004896 ! cytokine receptor activity intersection_of: GO:0038023 ! signaling receptor activity intersection_of: has_primary_input PR:000013246 ! prolactin relationship: has_primary_input PR:000013246 ! prolactin -relationship: never_in_taxon NCBITaxon:4751 ! Fungi relationship: part_of GO:0038161 ! prolactin signaling pathway +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0004930 @@ -47731,9 +47837,9 @@ intersection_of: GO:0038023 ! signaling receptor activity intersection_of: has_primary_input PR:000009054 ! insulin gene translation product relationship: has_part GO:0043559 ! insulin binding relationship: has_primary_input PR:000009054 ! insulin gene translation product -relationship: in_taxon NCBITaxon:6072 {all_only="true"} ! Eumetazoa -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of GO:0008286 ! insulin receptor signaling pathway +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 {all_only="true"} ! in taxon Eumetazoa property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23056" xsd:anyURI [Term] @@ -48014,7 +48120,7 @@ is_a: GO:0005215 ! transporter activity intersection_of: GO:0005215 ! transporter activity intersection_of: has_primary_input CHEBI:18059 relationship: has_primary_input CHEBI:18059 -relationship: part_of GO:0006869 {http://purl.org/dc/terms/source="GO_REF:0000090"} ! lipid transport +relationship: part_of GO:0006869 ! lipid transport [Term] id: GO:0005326 @@ -48024,9 +48130,9 @@ def: "Enables the directed movement of a neurotransmitter into, out of or within synonym: "neurotransmitter transporter activity" RELATED [] xref: Reactome:R-HSA-374896 "Uptake of Noradrenaline" xref: Reactome:R-HSA-374919 "Noradrenaline clearance from the synaptic cleft" -relationship: in_taxon NCBITaxon:6072 {all_only="true"} ! Eumetazoa -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: part_of GO:0006836 {http://purl.org/dc/terms/source="GO_REF:0000090"} ! neurotransmitter transport +relationship: part_of GO:0006836 ! neurotransmitter transport +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 {all_only="true"} ! in taxon Eumetazoa [Term] id: GO:0005342 @@ -48299,8 +48405,8 @@ namespace: cellular_component def: "A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures." [GOC:dos, GOC:mah, ISBN:0721639976, PMID:19693541, PMID:21421911] xref: Wikipedia:Collagen is_a: GO:0032991 ! protein-containing complex -relationship: in_taxon NCBITaxon:33208 {all_only="true", source="PMID:12382326"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 {source="PMID:12382326"} ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 {source="PMID:12382326"} ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true", source="PMID:12382326"} ! in taxon Metazoa [Term] id: GO:0005583 @@ -48409,8 +48515,8 @@ xref: Wikipedia:Cell_nucleus is_a: GO:0043231 ! intracellular membrane-bounded organelle disjoint_from: GO:0005737 ! cytoplasm disjoint_from: GO:0005829 ! cytosol -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota [Term] id: GO:0005635 @@ -48508,7 +48614,7 @@ subset: goslim_plant xref: NIF_Subcellular:sao585356902 xref: Wikipedia:Lysosome is_a: GO:0000323 ! lytic vacuole -relationship: never_in_taxon NCBITaxon:4751 ! Fungi +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0005765 @@ -48520,8 +48626,8 @@ is_a: GO:0098852 ! lytic vacuole membrane intersection_of: GO:0016020 ! membrane intersection_of: bounding_layer_of GO:0005764 ! lysosome relationship: bounding_layer_of GO:0005764 ! lysosome -relationship: never_in_taxon NCBITaxon:4751 ! Fungi relationship: part_of GO:0005764 ! lysosome +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0005766 @@ -48593,10 +48699,10 @@ synonym: "Golgi ribbon" NARROW [] xref: NIF_Subcellular:sao451912436 xref: Wikipedia:Golgi_apparatus is_a: GO:0043231 ! intracellular membrane-bounded organelle -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota relationship: part_of GO:0005737 ! cytoplasm relationship: part_of GO:0012505 ! endomembrane system +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota [Term] id: GO:0005798 @@ -48782,8 +48888,8 @@ is_a: GO:1902911 ! protein kinase complex intersection_of: GO:0032991 ! protein-containing complex intersection_of: capable_of GO:0005009 ! insulin receptor activity relationship: capable_of GO:0005009 ! insulin receptor activity -relationship: in_taxon NCBITaxon:6072 {all_only="true"} ! Eumetazoa -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 {all_only="true"} ! in taxon Eumetazoa [Term] id: GO:0005902 @@ -48797,8 +48903,8 @@ xref: NIF_Subcellular:sao671419673 xref: Wikipedia:Microvillus is_a: GO:0098858 ! actin-based cell projection relationship: has_part GO:0032432 ! actin filament bundle -relationship: never_in_taxon NCBITaxon:4751 ! Fungi relationship: part_of CL:0000066 ! epithelial cell +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0005911 @@ -48845,14 +48951,14 @@ is_a: GO:0043227 ! membrane-bounded organelle is_a: GO:0120025 ! plasma membrane bounded cell projection is_a: PR:000050567 ! protein-containing material entity relationship: has_part GO:0030990 ! intraciliary transport particle -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: never_in_taxon NCBITaxon:3176 ! Zygnematales -relationship: never_in_taxon NCBITaxon:3312 ! Coniferophyta -relationship: never_in_taxon NCBITaxon:3378 ! Gnetales -relationship: never_in_taxon NCBITaxon:3398 ! Magnoliopsida -relationship: never_in_taxon NCBITaxon:4890 ! Ascomycota -relationship: never_in_taxon NCBITaxon:5782 ! Dictyostelium -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota +property_value: RO:0002161 NCBITaxon:3176 +property_value: RO:0002161 NCBITaxon:3312 +property_value: RO:0002161 NCBITaxon:3378 +property_value: RO:0002161 NCBITaxon:3398 +property_value: RO:0002161 NCBITaxon:4890 +property_value: RO:0002161 NCBITaxon:5782 [Term] id: GO:0005930 @@ -50245,8 +50351,8 @@ def: "The directed movement of a neurotransmitter into, out of or within a cell, subset: goslim_pir synonym: "sodium:neurotransmitter transport" NARROW [] is_a: GO:0006810 ! transport -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0006837 @@ -50491,7 +50597,7 @@ namespace: biological_process def: "A vesicle-mediated transport process that results in the engulfment of external particulate material by phagocytes and their delivery to the lysosome. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles." [ISBN:0198506732] xref: Wikipedia:Phagocytosis is_a: GO:0006897 ! endocytosis -relationship: never_in_taxon NCBITaxon:4751 ! Fungi +property_value: RO:0002161 NCBITaxon:4751 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24907" xsd:anyURI [Term] @@ -50541,11 +50647,11 @@ synonym: "type I programmed cell death" NARROW [] xref: Wikipedia:Apoptosis is_a: GO:0012501 ! programmed cell death relationship: ends_with GO:0097194 ! execution phase of apoptosis -relationship: in_taxon NCBITaxon:33154 {all_only="true"} ! Opisthokonta -relationship: never_in_taxon NCBITaxon:2 ! Bacteria -relationship: never_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe -relationship: only_in_taxon NCBITaxon:33154 ! Opisthokonta +relationship: RO:0002160 NCBITaxon:33154 ! only in taxon Opisthokonta +relationship: RO:0002162 NCBITaxon:33154 {all_only="true"} ! in taxon Opisthokonta relationship: starts_with GO:0097190 ! apoptotic signaling pathway +property_value: RO:0002161 NCBITaxon:2 +property_value: RO:0002161 NCBITaxon:4896 [Term] id: GO:0006921 @@ -50693,8 +50799,8 @@ subset: goslim_generic synonym: "inflammation" BROAD [] xref: Wikipedia:Inflammation is_a: GO:0006952 ! defense response -relationship: in_taxon NCBITaxon:7742 {all_only="true"} ! Vertebrata -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 {all_only="true"} ! in taxon Vertebrata [Term] id: GO:0006955 @@ -51152,8 +51258,8 @@ is_a: GO:0140013 ! meiotic nuclear division intersection_of: GO:0000280 ! nuclear division intersection_of: part_of GO:0048232 ! male gamete generation intersection_of: part_of GO:0051321 ! meiotic cell cycle -relationship: never_in_taxon NCBITaxon:4751 ! Fungi relationship: part_of GO:0048232 ! male gamete generation +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0007142 @@ -51180,8 +51286,8 @@ is_a: GO:0140013 ! meiotic nuclear division intersection_of: GO:0000280 ! nuclear division intersection_of: part_of GO:0007292 ! female gamete generation intersection_of: part_of GO:0051321 ! meiotic cell cycle -relationship: never_in_taxon NCBITaxon:4751 ! Fungi relationship: part_of GO:0007292 ! female gamete generation +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0007147 @@ -51237,9 +51343,9 @@ is_a: GO:0098609 ! cell-cell adhesion intersection_of: GO:0098609 ! cell-cell adhesion intersection_of: has_participant CL:0000738 ! leukocyte relationship: has_participant CL:0000738 ! leukocyte -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: in_taxon NCBITaxon:7742 {all_only="true"} ! Vertebrata -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa +relationship: RO:0002162 NCBITaxon:7742 {all_only="true"} ! in taxon Vertebrata [Term] id: GO:0007162 @@ -51430,7 +51536,7 @@ namespace: biological_process def: "A G protein-coupled receptor signaling pathway initiated by a neuropeptide binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process." [GOC:mah, ISBN:0815316194] synonym: "neuropeptide signalling pathway" EXACT [] is_a: GO:0007186 ! G protein-coupled receptor signaling pathway -relationship: never_in_taxon NCBITaxon:4751 ! Fungi +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0007267 @@ -51588,9 +51694,9 @@ is_a: GO:0022412 ! cellular process involved in reproduction in multicellular or intersection_of: GO:0008356 ! asymmetric cell division intersection_of: has_primary_input CL:0000722 ! cystoblast relationship: has_primary_input CL:0000722 ! cystoblast -relationship: in_taxon NCBITaxon:6656 {all_only="true"} ! Arthropoda -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda relationship: part_of GO:0007281 ! germ cell development +relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda +relationship: RO:0002162 NCBITaxon:6656 {all_only="true"} ! in taxon Arthropoda [Term] id: GO:0007283 @@ -51681,9 +51787,9 @@ namespace: biological_process def: "Construction of a stage-1 egg chamber in the anterior part of the germarium, from the progeny of germ-line and somatic stem cells. An example of this is found in Drosophila melanogaster." [GOC:mtg_sensu, ISBN:0879694238] is_a: GO:0003006 ! developmental process involved in reproduction is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis -relationship: in_taxon NCBITaxon:6656 {all_only="true"} ! Arthropoda -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda relationship: part_of GO:0048477 ! oogenesis +relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda +relationship: RO:0002162 NCBITaxon:6656 {all_only="true"} ! in taxon Arthropoda [Term] id: GO:0007297 @@ -51695,10 +51801,10 @@ is_a: GO:0010631 ! epithelial cell migration is_a: GO:0022412 ! cellular process involved in reproduction in multicellular organism intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0000477 ! follicle cell of egg chamber -relationship: in_taxon NCBITaxon:50557 {all_only="true"} ! Insecta -relationship: only_in_taxon NCBITaxon:50557 ! Insecta relationship: part_of GO:0030707 ! follicle cell of egg chamber development relationship: results_in_movement_of CL:0000477 ! follicle cell of egg chamber +relationship: RO:0002160 NCBITaxon:50557 ! only in taxon Insecta +relationship: RO:0002162 NCBITaxon:50557 {all_only="true"} ! in taxon Insecta [Term] id: GO:0007298 @@ -51772,9 +51878,9 @@ def: "The union of male and female gametes to form a zygote." [GOC:ems, GOC:mtg_ synonym: "zygote biosynthesis" RELATED [] synonym: "zygote formation" RELATED [] is_a: GO:0009566 ! fertilization -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: never_in_taxon NCBITaxon:58024 ! Spermatophyta -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota +property_value: RO:0002161 NCBITaxon:58024 [Term] id: GO:0007343 @@ -51907,9 +52013,9 @@ is_a: GO:0061351 ! neural precursor cell proliferation intersection_of: GO:0008283 ! cell population proliferation intersection_of: acts_on_population_of CL:0000031 ! neuroblast (sensu Vertebrata) relationship: acts_on_population_of CL:0000031 ! neuroblast (sensu Vertebrata) -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa relationship: part_of GO:0048699 ! generation of neurons +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0007406 @@ -51939,8 +52045,8 @@ is_a: GO:0001775 ! cell activation intersection_of: GO:0001775 ! cell activation intersection_of: has_primary_input CL:0000031 ! neuroblast (sensu Vertebrata) relationship: has_primary_input CL:0000031 ! neuroblast (sensu Vertebrata) -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa relationship: part_of GO:0048699 ! generation of neurons +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0007409 @@ -52032,9 +52138,9 @@ comment: See also the fly_anatomy.ontology term 'tracheal system ; FBbt:00005024 is_a: GO:0060541 ! respiratory system development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005155 ! open tracheal system -relationship: in_taxon NCBITaxon:6656 {all_only="true"} ! Arthropoda -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda relationship: results_in_development_of UBERON:0005155 ! open tracheal system +relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda +relationship: RO:0002162 NCBITaxon:6656 {all_only="true"} ! in taxon Arthropoda [Term] id: GO:0007431 @@ -52127,9 +52233,9 @@ def: "The process whose specific outcome is the progression of the imaginal disc is_a: GO:0048513 ! animal organ development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0000939 ! imaginal disc -relationship: in_taxon NCBITaxon:6656 {all_only="true"} ! Arthropoda -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda relationship: results_in_development_of UBERON:0000939 ! imaginal disc +relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda +relationship: RO:0002162 NCBITaxon:6656 {all_only="true"} ! in taxon Arthropoda [Term] id: GO:0007446 @@ -52222,10 +52328,10 @@ synonym: "arthropod blood cell development" EXACT [] is_a: GO:0030097 ! hemopoiesis intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of CL:0000387 ! hemocyte (sensu Arthropoda) -relationship: in_taxon NCBITaxon:6656 {all_only="true"} ! Arthropoda -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda relationship: part_of GO:0042386 ! hemocyte differentiation relationship: results_in_development_of CL:0000387 ! hemocyte (sensu Arthropoda) +relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda +relationship: RO:0002162 NCBITaxon:6656 {all_only="true"} ! in taxon Arthropoda [Term] id: GO:0007517 @@ -52385,8 +52491,8 @@ synonym: "gestation" EXACT [] xref: Wikipedia:Gestation is_a: GO:0044703 ! multi-organism reproductive process is_a: GO:0044706 ! multi-multicellular organism process -relationship: in_taxon NCBITaxon:40674 {all_only="true"} ! Mammalia -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia +relationship: RO:0002162 NCBITaxon:40674 {all_only="true"} ! in taxon Mammalia [Term] id: GO:0007566 @@ -52446,9 +52552,9 @@ synonym: "milk secretion" EXACT [GOC:pr] xref: Wikipedia:Lactation is_a: GO:0007589 ! body fluid secretion relationship: has_part GO:0060156 ! milk ejection reflex -relationship: in_taxon NCBITaxon:40674 {all_only="true"} ! Mammalia -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of GO:0030879 ! mammary gland development +relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia +relationship: RO:0002162 NCBITaxon:40674 {all_only="true"} ! in taxon Mammalia [Term] id: GO:0007596 @@ -52541,9 +52647,9 @@ synonym: "single-organism behavior" RELATED [] xref: Wikipedia:Behavior is_a: GO:0032501 ! multicellular organismal process disjoint_from: GO:0032502 ! developmental process -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa relationship: process_has_causal_agent UBERON:0001016 ! nervous system +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa created_by: jl creation_date: 2012-09-20T14:06:08Z @@ -52825,8 +52931,8 @@ namespace: molecular_function def: "Combining with a neuropeptide to initiate a change in cell activity." [GOC:ai] is_a: GO:0008528 ! G protein-coupled peptide receptor activity relationship: has_part GO:0042923 ! neuropeptide binding -relationship: never_in_taxon NCBITaxon:4751 ! Fungi relationship: part_of GO:0007218 ! neuropeptide signaling pathway +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0008201 @@ -52986,7 +53092,7 @@ subset: goslim_mouse subset: goslim_pir synonym: "cell proliferation" RELATED [] is_a: GO:0009987 ! cellular process -relationship: never_in_taxon NCBITaxon:4751 ! Fungi +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0008284 @@ -53003,8 +53109,8 @@ is_a: GO:0042127 ! regulation of cell population proliferation is_a: GO:0048522 ! positive regulation of cellular process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0008283 ! cell population proliferation -relationship: never_in_taxon NCBITaxon:4751 ! Fungi relationship: positively_regulates GO:0008283 ! cell population proliferation +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0008285 @@ -53021,7 +53127,7 @@ is_a: GO:0048523 ! negative regulation of cellular process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0008283 ! cell population proliferation relationship: negatively_regulates GO:0008283 ! cell population proliferation -relationship: never_in_taxon NCBITaxon:4751 ! Fungi +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0008286 @@ -53031,9 +53137,9 @@ def: "The series of molecular signals generated as a consequence of the insulin synonym: "daf-2 receptor signaling pathway" NARROW [] synonym: "insulin receptor signalling pathway" EXACT [] is_a: GO:0007169 ! transmembrane receptor protein tyrosine kinase signaling pathway -relationship: in_taxon NCBITaxon:6072 {all_only="true"} ! Eumetazoa -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of GO:0032869 ! cellular response to insulin stimulus +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 {all_only="true"} ! in taxon Eumetazoa [Term] id: GO:0008289 @@ -53127,7 +53233,7 @@ is_a: GO:0140318 ! protein transporter activity intersection_of: GO:0005215 ! transporter activity intersection_of: has_primary_input PR:000000001 ! protein intersection_of: results_in_transport_across GO:0016020 ! membrane -relationship: part_of GO:0071806 {http://purl.org/dc/terms/source="GO_REF:0000090"} ! protein transmembrane transport +relationship: part_of GO:0071806 ! protein transmembrane transport [Term] id: GO:0008324 @@ -53164,10 +53270,10 @@ synonym: "glia cell migration" EXACT [] is_a: GO:0016477 ! cell migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0000125 ! glial cell -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa relationship: part_of GO:0042063 ! gliogenesis relationship: results_in_movement_of CL:0000125 ! glial cell +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0008348 @@ -53280,14 +53386,13 @@ xref: Reactome:R-HSA-446277 "RhCG mediates ammonium efflux out of kidney collect xref: Reactome:R-HSA-446278 "RhBG mediates ammonium influx into kidney collecting duct cells" xref: Reactome:R-HSA-5623051 "Defective RHAG does not transport NH4+ from cytosol to extracellular region (rbc)" xref: RHEA:28747 -xref: TC:1.A.11 {http://purl.obolibrary.org/obo/IAO_0000233="https://github.com/geneontology/go-ontology/issues/23129"} is_a: GO:0015267 ! channel activity intersection_of: GO:0015267 ! channel activity intersection_of: GO:0022857 ! transmembrane transporter activity intersection_of: has_primary_input CHEBI:28938 relationship: has_participant CHEBI:28938 relationship: has_primary_input CHEBI:28938 -relationship: part_of GO:0072488 {http://purl.org/dc/terms/source="GO_REF:0000090"} ! ammonium transmembrane transport +relationship: part_of GO:0072488 ! ammonium transmembrane transport property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22368" xsd:anyURI [Term] @@ -53309,7 +53414,7 @@ namespace: biological_process def: "The process whose specific outcome is the progression of the epidermis over time, from its formation to the mature structure. The epidermis is the outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species." [GOC:go_curators, UBERON:0001003] synonym: "hypodermis development" RELATED [GOC:kmv, GOC:rk] is_a: GO:0009888 ! tissue development -relationship: never_in_taxon NCBITaxon:33090 ! Viridiplantae +property_value: RO:0002161 NCBITaxon:33090 [Term] id: GO:0008584 @@ -53335,9 +53440,9 @@ synonym: "ovary development" RELATED [GOC:sl] is_a: GO:0008406 ! gonad development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0000992 ! ovary -relationship: never_in_taxon NCBITaxon:3398 ! Magnoliopsida relationship: part_of GO:0046545 ! development of primary female sexual characteristics relationship: results_in_development_of UBERON:0000992 ! ovary +property_value: RO:0002161 NCBITaxon:3398 [Term] id: GO:0008594 @@ -54170,8 +54275,8 @@ namespace: biological_process def: "The process whose specific outcome is the progression of an embryo over time, from zygote formation until the end of the embryonic life stage. The end of the embryonic life stage is organism-specific and may be somewhat arbitrary; for mammals it is usually considered to be birth, for insects the hatching of the first instar larva from the eggshell." [GOC:go_curators, GOC:isa_complete, GOC:mtg_sensu] synonym: "embryogenesis" BROAD [] is_a: GO:0009790 ! embryo development -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0009798 @@ -54224,14 +54329,14 @@ xref: Wikipedia:Histogenesis is_a: GO:0048856 ! anatomical structure development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0000479 ! tissue -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: never_in_taxon NCBITaxon:147554 ! Schizosaccharomycetes -relationship: never_in_taxon NCBITaxon:33630 ! Alveolata -relationship: never_in_taxon NCBITaxon:33682 ! Euglenozoa -relationship: never_in_taxon NCBITaxon:38254 ! Glaucocystophyceae -relationship: never_in_taxon NCBITaxon:4891 ! Saccharomycetes -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota relationship: results_in_development_of UBERON:0000479 ! tissue +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota +property_value: RO:0002161 NCBITaxon:147554 +property_value: RO:0002161 NCBITaxon:33630 +property_value: RO:0002161 NCBITaxon:33682 +property_value: RO:0002161 NCBITaxon:38254 +property_value: RO:0002161 NCBITaxon:4891 [Term] id: GO:0009889 @@ -54530,10 +54635,10 @@ synonym: "neuroglia differentiation" EXACT [] is_a: GO:0030154 ! cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000125 ! glial cell -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa relationship: part_of GO:0042063 ! gliogenesis relationship: results_in_acquisition_of_features_of CL:0000125 ! glial cell +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0010002 @@ -55325,9 +55430,9 @@ synonym: "muscle cell apoptosis" NARROW [] is_a: GO:0006915 ! apoptotic process intersection_of: GO:0006915 ! apoptotic process intersection_of: occurs_in CL:0000187 ! muscle cell -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa relationship: occurs_in CL:0000187 ! muscle cell -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0010658 @@ -56529,10 +56634,10 @@ def: "The formation of a solid rod of neurectoderm derived from the neural keel. is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis intersection_of: GO:0048646 ! anatomical structure formation involved in morphogenesis intersection_of: results_in_formation_of UBERON:0005068 ! neural rod -relationship: in_taxon NCBITaxon:32443 {all_only="true"} ! Teleostei -relationship: only_in_taxon NCBITaxon:32443 ! Teleostei relationship: part_of GO:0014020 ! primary neural tube formation relationship: results_in_formation_of UBERON:0005068 ! neural rod +relationship: RO:0002160 NCBITaxon:32443 ! only in taxon Teleostei +relationship: RO:0002162 NCBITaxon:32443 {all_only="true"} ! in taxon Teleostei [Term] id: GO:0014025 @@ -57084,8 +57189,8 @@ intersection_of: GO:0001775 ! cell activation intersection_of: has_primary_input CL:0008012 ! quiescent skeletal muscle satellite cell intersection_of: results_in_acquisition_of_features_of CL:0008016 ! activated skeletal muscle satellite cell relationship: has_primary_input CL:0008012 ! quiescent skeletal muscle satellite cell -relationship: never_in_taxon NCBITaxon:4751 ! Fungi relationship: results_in_acquisition_of_features_of CL:0008016 ! activated skeletal muscle satellite cell +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0014722 @@ -57257,7 +57362,7 @@ name: urinary bladder smooth muscle contraction namespace: biological_process def: "A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. This process occurs in the urinary bladder. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. The urinary bladder is a musculomembranous sac along the urinary tract." [GOC:mr, GOC:mtg_muscle, PMID:11768524, PMID:18276178, PMID:538956] is_a: GO:0014848 ! urinary tract smooth muscle contraction -relationship: never_in_taxon NCBITaxon:8782 ! Aves +property_value: RO:0002161 NCBITaxon:8782 [Term] id: GO:0014833 @@ -57659,7 +57764,7 @@ is_a: GO:0022857 ! transmembrane transporter activity intersection_of: GO:0022857 ! transmembrane transporter activity intersection_of: has_primary_input CHEBI:24867 relationship: has_primary_input CHEBI:24867 -relationship: part_of GO:0034220 {http://purl.org/dc/terms/source="GO_REF:0000090"} ! monoatomic ion transmembrane transport +relationship: part_of GO:0034220 ! monoatomic ion transmembrane transport property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24479" xsd:anyURI [Term] @@ -57719,7 +57824,7 @@ is_a: GO:0022857 ! transmembrane transporter activity intersection_of: GO:0022857 ! transmembrane transporter activity intersection_of: has_primary_input CHEBI:16646 relationship: has_primary_input CHEBI:16646 -relationship: part_of GO:0034219 {http://purl.org/dc/terms/source="GO_REF:0000090"} ! carbohydrate transmembrane transport +relationship: part_of GO:0034219 ! carbohydrate transmembrane transport [Term] id: GO:0015149 @@ -57732,7 +57837,7 @@ is_a: GO:0022857 ! transmembrane transporter activity intersection_of: GO:0022857 ! transmembrane transporter activity intersection_of: has_primary_input CHEBI:18133 relationship: has_primary_input CHEBI:18133 -relationship: part_of GO:0008645 {http://purl.org/dc/terms/source="GO_REF:0000090"} ! hexose transmembrane transport +relationship: part_of GO:0008645 ! hexose transmembrane transport [Term] id: GO:0015159 @@ -57806,7 +57911,7 @@ is_a: GO:0022857 ! transmembrane transporter activity intersection_of: GO:0022857 ! transmembrane transporter activity intersection_of: has_primary_input CHEBI:33709 relationship: has_primary_input CHEBI:33709 -relationship: part_of GO:0003333 {http://purl.org/dc/terms/source="GO_REF:0000090"} ! amino acid transmembrane transport +relationship: part_of GO:0003333 ! amino acid transmembrane transport [Term] id: GO:0015172 @@ -58261,8 +58366,8 @@ subset: goslim_plant subset: goslim_prokaryote xref: Wikipedia:Photosynthesis is_a: GO:0044237 ! cellular metabolic process -relationship: never_in_taxon NCBITaxon:33208 ! Metazoa -relationship: never_in_taxon NCBITaxon:4895 ! Schizosaccharomyces +property_value: RO:0002161 NCBITaxon:33208 +property_value: RO:0002161 NCBITaxon:4895 [Term] id: GO:0015980 @@ -58672,7 +58777,7 @@ namespace: biological_process def: "The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues." [GOC:cjm, GOC:dph, GOC:ems, GOC:pf, Wikipedia:Cell_migration] xref: Wikipedia:Cell_migration is_a: GO:0048870 ! cell motility -relationship: never_in_taxon NCBITaxon:4890 ! Ascomycota +property_value: RO:0002161 NCBITaxon:4890 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24787" xsd:anyURI [Term] @@ -58742,8 +58847,8 @@ xref: Wikipedia:Sarcoplasm is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: part_of CL:0000187 ! muscle cell -relationship: never_in_taxon NCBITaxon:4751 ! Fungi relationship: part_of CL:0000187 ! muscle cell +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0016594 @@ -59395,9 +59500,9 @@ is_a: GO:0042592 ! homeostatic process intersection_of: GO:0042592 ! homeostatic process intersection_of: occurs_in CL:0000000 ! cell disjoint_from: GO:0048872 ! homeostasis of number of cells -relationship: in_taxon NCBITaxon:131567 {all_only="true"} ! cellular organisms relationship: occurs_in CL:0000000 ! cell -relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms +relationship: RO:0002160 NCBITaxon:131567 ! only in taxon cellular organisms +relationship: RO:0002162 NCBITaxon:131567 {all_only="true"} ! in taxon cellular organisms [Term] id: GO:0019730 @@ -59544,7 +59649,7 @@ def: "Binding to a cytokine, any of a group of proteins that function to control synonym: "IL binding" NARROW [] synonym: "interleukin binding" NARROW [] is_a: GO:0005515 ! protein binding -relationship: never_in_taxon NCBITaxon:4751 ! Fungi +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0021501 @@ -59675,10 +59780,10 @@ def: "The process in which relatively unspecialized cells acquire specialized st is_a: GO:0030154 ! cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: occurs_in UBERON:0002028 ! hindbrain -relationship: in_taxon NCBITaxon:89593 {all_only="true"} ! Craniata relationship: occurs_in UBERON:0002028 ! hindbrain -relationship: only_in_taxon NCBITaxon:89593 ! Craniata relationship: part_of GO:0030902 ! hindbrain development +relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata +relationship: RO:0002162 NCBITaxon:89593 {all_only="true"} ! in taxon Craniata [Term] id: GO:0021534 @@ -59688,10 +59793,10 @@ def: "The multiplication or reproduction of cells, resulting in the expansion of is_a: GO:0061351 ! neural precursor cell proliferation intersection_of: GO:0008283 ! cell population proliferation intersection_of: occurs_in UBERON:0002028 ! hindbrain -relationship: in_taxon NCBITaxon:89593 {all_only="true"} ! Craniata relationship: occurs_in UBERON:0002028 ! hindbrain -relationship: only_in_taxon NCBITaxon:89593 ! Craniata relationship: part_of GO:0030902 ! hindbrain development +relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata +relationship: RO:0002162 NCBITaxon:89593 {all_only="true"} ! in taxon Craniata [Term] id: GO:0021535 @@ -59701,10 +59806,10 @@ def: "The orderly movement of a cell that will reside in the hindbrain." [GO_REF is_a: GO:0016477 ! cell migration intersection_of: GO:0016477 ! cell migration intersection_of: occurs_in UBERON:0002028 ! hindbrain -relationship: in_taxon NCBITaxon:89593 {all_only="true"} ! Craniata relationship: occurs_in UBERON:0002028 ! hindbrain -relationship: only_in_taxon NCBITaxon:89593 ! Craniata relationship: part_of GO:0030902 ! hindbrain development +relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata +relationship: RO:0002162 NCBITaxon:89593 {all_only="true"} ! in taxon Craniata [Term] id: GO:0021536 @@ -61883,8 +61988,8 @@ is_a: GO:0032291 ! axon ensheathment in central nervous system is_a: GO:0042552 ! myelination intersection_of: GO:0042552 ! myelination intersection_of: occurs_in UBERON:0001017 ! central nervous system -relationship: in_taxon NCBITaxon:33213 {all_only="true"} ! Bilateria relationship: part_of GO:0014003 ! oligodendrocyte development +relationship: RO:0002162 NCBITaxon:33213 {all_only="true"} ! in taxon Bilateria [Term] id: GO:0022011 @@ -62127,9 +62232,9 @@ synonym: "estrous cycle process" RELATED [] synonym: "menstrual cycle process" RELATED [] is_a: GO:0022414 ! reproductive process is_a: GO:0048511 ! rhythmic process -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa relationship: part_of GO:0042698 ! ovulation cycle +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0022603 @@ -62240,9 +62345,9 @@ synonym: "80S ribosome" NARROW [] is_a: GO:0005840 ! ribosome intersection_of: GO:0005840 ! ribosome intersection_of: part_of GO:0005829 ! cytosol -relationship: in_taxon NCBITaxon:131567 {all_only="true"} ! cellular organisms -relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms relationship: part_of GO:0005829 ! cytosol +relationship: RO:0002160 NCBITaxon:131567 ! only in taxon cellular organisms +relationship: RO:0002162 NCBITaxon:131567 {all_only="true"} ! in taxon cellular organisms [Term] id: GO:0022803 @@ -62672,7 +62777,7 @@ subset: goslim_drosophila subset: goslim_flybase_ribbon xref: Wikipedia:Cell_junction is_a: GO:0110165 ! cellular anatomical entity -relationship: never_in_taxon NCBITaxon:4751 ! Fungi +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0030070 @@ -62705,8 +62810,8 @@ is_a: GO:0030072 ! peptide hormone secretion intersection_of: GO:0046903 ! secretion intersection_of: has_primary_input PR:000009054 ! insulin gene translation product relationship: has_primary_input PR:000009054 ! insulin gene translation product -relationship: in_taxon NCBITaxon:6072 {all_only="true"} ! Eumetazoa -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 {all_only="true"} ! in taxon Eumetazoa property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/11255#issuecomment-426191045" xsd:anyURI [Term] @@ -62806,8 +62911,8 @@ def: "A small subcellular vesicle, surrounded by a membrane, that is formed from comment: Note that the term 'secretory vesicle' is sometimes used in this sense, but can also mean 'transport vesicle ; GO:0030133'. synonym: "secretory vesicle" BROAD [] is_a: GO:0099503 ! secretory vesicle -relationship: never_in_taxon NCBITaxon:4890 ! Ascomycota relationship: part_of GO:0012505 ! endomembrane system +property_value: RO:0002161 NCBITaxon:4890 [Term] id: GO:0030154 @@ -63054,8 +63159,8 @@ is_a: GO:0030198 ! extracellular matrix organization is_a: GO:0097435 ! supramolecular fiber organization intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0098643 ! banded collagen fibril -relationship: never_in_taxon NCBITaxon:4751 ! Fungi relationship: results_in_organization_of GO:0098643 ! banded collagen fibril +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0030202 @@ -63629,8 +63734,8 @@ def: "Any process that modulates the frequency, rate or extent of cell migration is_a: GO:2000145 ! regulation of cell motility intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0016477 ! cell migration -relationship: never_in_taxon NCBITaxon:4890 ! Ascomycota relationship: regulates GO:0016477 ! cell migration +property_value: RO:0002161 NCBITaxon:4890 [Term] id: GO:0030335 @@ -63745,9 +63850,9 @@ is_a: GO:0048468 ! cell development is_a: GO:1903046 ! meiotic cell cycle process intersection_of: GO:0048646 ! anatomical structure formation involved in morphogenesis intersection_of: results_in_formation_of CL:0000607 ! ascospore -relationship: in_taxon NCBITaxon:4890 {all_only="true"} ! Ascomycota -relationship: only_in_taxon NCBITaxon:4890 ! Ascomycota relationship: results_in_formation_of CL:0000607 ! ascospore +relationship: RO:0002160 NCBITaxon:4890 ! only in taxon Ascomycota +relationship: RO:0002162 NCBITaxon:4890 {all_only="true"} ! in taxon Ascomycota [Term] id: GO:0030473 @@ -63915,8 +64020,8 @@ namespace: molecular_function def: "Combining with a neurotransmitter and transmitting the signal to initiate a change in cell activity." [GOC:jl, GOC:signaling] comment: A strict definition of neurotransmitter receptor activity would limit its use to receptor activity at the postsynaptic membrane as part of synaptic transmission, but we recognize that usage is often much broader than this. For the strict use case, please see 'postsynaptic neurotransmitter receptor activity' is_a: GO:0038023 ! signaling receptor activity -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0030595 @@ -64014,10 +64119,10 @@ is_a: GO:0003006 ! developmental process involved in reproduction is_a: GO:0022412 ! cellular process involved in reproduction in multicellular organism intersection_of: GO:0048468 ! cell development intersection_of: results_in_development_of CL:0000477 ! follicle cell of egg chamber -relationship: in_taxon NCBITaxon:6656 {all_only="true"} ! Arthropoda -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda relationship: part_of GO:0048477 ! oogenesis relationship: results_in_development_of CL:0000477 ! follicle cell of egg chamber +relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda +relationship: RO:0002162 NCBITaxon:6656 {all_only="true"} ! in taxon Arthropoda [Term] id: GO:0030718 @@ -64047,9 +64152,9 @@ is_a: GO:0051674 ! localization of cell intersection_of: GO:0051179 ! localization intersection_of: has_primary_input CL:0000023 ! oocyte relationship: has_primary_input CL:0000023 ! oocyte -relationship: in_taxon NCBITaxon:50557 {all_only="true"} ! Insecta -relationship: only_in_taxon NCBITaxon:50557 ! Insecta relationship: part_of GO:0007293 ! germarium-derived egg chamber formation +relationship: RO:0002160 NCBITaxon:50557 ! only in taxon Insecta +relationship: RO:0002162 NCBITaxon:50557 {all_only="true"} ! in taxon Insecta [Term] id: GO:0030850 @@ -64189,9 +64294,9 @@ synonym: "mammogenesis" NARROW [GOC:dph] is_a: GO:0048732 ! gland development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001911 ! mammary gland -relationship: in_taxon NCBITaxon:40674 {all_only="true"} ! Mammalia -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia relationship: results_in_development_of UBERON:0001911 ! mammary gland +relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia +relationship: RO:0002162 NCBITaxon:40674 {all_only="true"} ! in taxon Mammalia [Term] id: GO:0030885 @@ -64713,7 +64818,7 @@ is_a: GO:0032502 ! developmental process intersection_of: GO:0032502 ! developmental process intersection_of: has_part GO:0045168 ! cell-cell signaling involved in cell fate commitment relationship: has_part GO:0045168 ! cell-cell signaling involved in cell fate commitment -relationship: never_in_taxon NCBITaxon:4895 ! Schizosaccharomyces +property_value: RO:0002161 NCBITaxon:4895 [Term] id: GO:0031143 @@ -66500,10 +66605,10 @@ synonym: "myelin formation in central nervous system" EXACT [] is_a: GO:0032288 ! myelin assembly intersection_of: GO:0032288 ! myelin assembly intersection_of: occurs_in UBERON:0001017 ! central nervous system -relationship: in_taxon NCBITaxon:33213 {all_only="true"} ! Bilateria relationship: occurs_in UBERON:0001017 ! central nervous system -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of GO:0022010 ! central nervous system myelination +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 {all_only="true"} ! in taxon Bilateria [Term] id: GO:0032290 @@ -66528,9 +66633,9 @@ synonym: "ensheathment of axons in central nervous system" EXACT [] is_a: GO:0008366 ! axon ensheathment intersection_of: GO:0008366 ! axon ensheathment intersection_of: occurs_in UBERON:0001017 ! central nervous system -relationship: in_taxon NCBITaxon:33213 {all_only="true"} ! Bilateria relationship: occurs_in UBERON:0001017 ! central nervous system -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 {all_only="true"} ! in taxon Bilateria [Term] id: GO:0032292 @@ -67143,9 +67248,9 @@ is_a: GO:0055074 ! calcium ion homeostasis is_a: GO:0055082 ! intracellular chemical homeostasis intersection_of: GO:0055074 ! calcium ion homeostasis intersection_of: occurs_in GO:0005794 ! Golgi apparatus -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota relationship: occurs_in GO:0005794 ! Golgi apparatus -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota [Term] id: GO:0032472 @@ -67215,10 +67320,10 @@ subset: goslim_pir synonym: "organismal physiological process" EXACT [] synonym: "single-multicellular organism process" RELATED [] is_a: GO:0008150 ! biological_process -relationship: never_in_taxon NCBITaxon:2 ! Bacteria -relationship: never_in_taxon NCBITaxon:2157 ! Archaea -relationship: never_in_taxon NCBITaxon:4896 ! Schizosaccharomyces pombe -relationship: never_in_taxon NCBITaxon:4932 ! Saccharomyces cerevisiae +property_value: RO:0002161 NCBITaxon:2 +property_value: RO:0002161 NCBITaxon:2157 +property_value: RO:0002161 NCBITaxon:4896 +property_value: RO:0002161 NCBITaxon:4932 created_by: jl creation_date: 2012-09-19T16:07:47Z @@ -67264,8 +67369,8 @@ is_a: GO:0045185 ! maintenance of protein location is_a: GO:0051651 ! maintenance of location in cell intersection_of: GO:0045185 ! maintenance of protein location intersection_of: occurs_in CL:0000000 ! cell -relationship: in_taxon NCBITaxon:131567 {all_only="true"} ! cellular organisms -relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms +relationship: RO:0002160 NCBITaxon:131567 ! only in taxon cellular organisms +relationship: RO:0002162 NCBITaxon:131567 {all_only="true"} ! in taxon cellular organisms [Term] id: GO:0032528 @@ -67277,8 +67382,8 @@ synonym: "microvillus organization and biogenesis" RELATED [GOC:mah] is_a: GO:0120036 ! plasma membrane bounded cell projection organization intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0005902 ! microvillus -relationship: never_in_taxon NCBITaxon:4751 ! Fungi relationship: results_in_organization_of GO:0005902 ! microvillus +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0032529 @@ -69409,7 +69514,7 @@ is_a: GO:0001775 ! cell activation intersection_of: GO:0001775 ! cell activation intersection_of: has_primary_input CL:0000312 ! keratinocyte relationship: has_primary_input CL:0000312 ! keratinocyte -relationship: never_in_taxon NCBITaxon:6656 ! Arthropoda +property_value: RO:0002161 NCBITaxon:6656 [Term] id: GO:0032984 @@ -71028,8 +71133,8 @@ is_a: GO:0003006 ! developmental process involved in reproduction is_a: GO:0043934 ! sporulation intersection_of: GO:0043934 ! sporulation intersection_of: part_of GO:0051321 ! meiotic cell cycle -relationship: never_in_taxon NCBITaxon:33083 ! Dictyostelia relationship: part_of GO:0051321 ! meiotic cell cycle +property_value: RO:0002161 NCBITaxon:33083 [Term] id: GO:0034295 @@ -71065,9 +71170,9 @@ is_a: GO:0043937 ! regulation of sporulation is_a: GO:0051445 ! regulation of meiotic cell cycle intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0034293 ! sexual sporulation -relationship: in_taxon NCBITaxon:4751 {all_only="true"} ! Fungi -relationship: only_in_taxon NCBITaxon:4751 ! Fungi relationship: regulates GO:0034293 ! sexual sporulation +relationship: RO:0002160 NCBITaxon:4751 ! only in taxon Fungi +relationship: RO:0002162 NCBITaxon:4751 {all_only="true"} ! in taxon Fungi [Term] id: GO:0034307 @@ -71835,10 +71940,10 @@ synonym: "hemocyte cell migration" EXACT [] is_a: GO:0016477 ! cell migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0000387 ! hemocyte (sensu Arthropoda) -relationship: in_taxon NCBITaxon:6656 {all_only="true"} ! Arthropoda -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda relationship: part_of GO:0035162 ! embryonic hemopoiesis relationship: results_in_movement_of CL:0000387 ! hemocyte (sensu Arthropoda) +relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda +relationship: RO:0002162 NCBITaxon:6656 {all_only="true"} ! in taxon Arthropoda [Term] id: GO:0035107 @@ -72021,8 +72126,8 @@ is_a: GO:0008283 ! cell population proliferation intersection_of: GO:0008283 ! cell population proliferation intersection_of: acts_on_population_of CL:0000387 ! hemocyte (sensu Arthropoda) relationship: acts_on_population_of CL:0000387 ! hemocyte (sensu Arthropoda) -relationship: in_taxon NCBITaxon:6656 {all_only="true"} ! Arthropoda -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda +relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda +relationship: RO:0002162 NCBITaxon:6656 {all_only="true"} ! in taxon Arthropoda [Term] id: GO:0035190 @@ -72106,9 +72211,9 @@ is_a: GO:0008285 ! negative regulation of cell population proliferation is_a: GO:0035206 ! regulation of hemocyte proliferation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0035172 ! hemocyte proliferation -relationship: in_taxon NCBITaxon:6656 {all_only="true"} ! Arthropoda relationship: negatively_regulates GO:0035172 ! hemocyte proliferation -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda +relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda +relationship: RO:0002162 NCBITaxon:6656 {all_only="true"} ! in taxon Arthropoda [Term] id: GO:0035208 @@ -72307,10 +72412,10 @@ synonym: "trichome organization and biogenesis" BROAD [] is_a: GO:0120036 ! plasma membrane bounded cell projection organization intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0070451 ! cell hair -relationship: in_taxon NCBITaxon:6656 {all_only="true"} ! Arthropoda -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda relationship: part_of GO:0035315 ! hair cell differentiation relationship: results_in_organization_of GO:0070451 ! cell hair +relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda +relationship: RO:0002162 NCBITaxon:6656 {all_only="true"} ! in taxon Arthropoda [Term] id: GO:0035322 @@ -73150,9 +73255,9 @@ synonym: "zona pellucida" NARROW [PMID:16944418, PMID:17163408] is_a: GO:0031012 ! extracellular matrix intersection_of: GO:0031012 ! extracellular matrix intersection_of: part_of CL:0000025 ! egg cell -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa relationship: part_of CL:0000025 ! egg cell +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa created_by: bf creation_date: 2011-04-19T02:07:23Z @@ -74003,9 +74108,9 @@ def: "The process in which a post-anal tail is generated and organized. A post-a is_a: GO:0009653 ! anatomical structure morphogenesis intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0007812 ! post-anal tail -relationship: in_taxon NCBITaxon:7711 {all_only="true"} ! Chordata -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: results_in_morphogenesis_of UBERON:0007812 ! post-anal tail +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {all_only="true"} ! in taxon Chordata created_by: bf creation_date: 2012-09-11T13:54:49Z @@ -74168,7 +74273,7 @@ synonym: "PRL signaling pathway" EXACT [PMID:21664429, PR:000013246] synonym: "prolactin-mediated signaling pathway" EXACT [GOC:bf] is_a: GO:0009755 ! hormone-mediated signaling pathway is_a: GO:0019221 ! cytokine-mediated signaling pathway -relationship: never_in_taxon NCBITaxon:4751 ! Fungi +property_value: RO:0002161 NCBITaxon:4751 created_by: bf creation_date: 2012-05-14T01:52:59Z @@ -74441,8 +74546,8 @@ subset: goslim_plant synonym: "growth pattern" RELATED [] synonym: "non-developmental growth" RELATED [GOC:mah] is_a: GO:0008150 ! biological_process -relationship: in_taxon NCBITaxon:131567 {all_only="true"} ! cellular organisms -relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms +relationship: RO:0002160 NCBITaxon:131567 ! only in taxon cellular organisms +relationship: RO:0002162 NCBITaxon:131567 {all_only="true"} ! in taxon cellular organisms [Term] id: GO:0040008 @@ -74462,7 +74567,7 @@ def: "Self-propelled movement of a cell or organism from one location to another subset: goslim_chembl subset: goslim_pir is_a: GO:0008150 ! biological_process -relationship: never_in_taxon NCBITaxon:451864 ! Dikarya +property_value: RO:0002161 NCBITaxon:451864 [Term] id: GO:0040012 @@ -74708,16 +74813,16 @@ intersection_of: GO:0006810 ! transport intersection_of: has_primary_input GO:0032991 ! protein-containing complex intersection_of: occurs_in GO:0005929 ! cilium intersection_of: results_in_transport_along GO:0005874 ! microtubule -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: never_in_taxon NCBITaxon:3176 ! Zygnematales -relationship: never_in_taxon NCBITaxon:3312 ! Coniferophyta -relationship: never_in_taxon NCBITaxon:3378 ! Gnetales -relationship: never_in_taxon NCBITaxon:3398 ! Magnoliopsida -relationship: never_in_taxon NCBITaxon:4890 ! Ascomycota -relationship: never_in_taxon NCBITaxon:5782 ! Dictyostelium relationship: occurs_in GO:0005929 ! cilium -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota relationship: part_of GO:0044782 ! cilium organization +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota +property_value: RO:0002161 NCBITaxon:3176 +property_value: RO:0002161 NCBITaxon:3312 +property_value: RO:0002161 NCBITaxon:3378 +property_value: RO:0002161 NCBITaxon:3398 +property_value: RO:0002161 NCBITaxon:4890 +property_value: RO:0002161 NCBITaxon:5782 [Term] id: GO:0042074 @@ -74953,8 +75058,8 @@ synonym: "regulation of cell proliferation" RELATED [] is_a: GO:0050794 ! regulation of cellular process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0008283 ! cell population proliferation -relationship: never_in_taxon NCBITaxon:4751 ! Fungi relationship: regulates GO:0008283 ! cell population proliferation +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0042129 @@ -74997,9 +75102,9 @@ def: "An organelle found in cnidoblast (nematoblast) cells. When matured, these synonym: "cnidocyst" EXACT [] xref: Wikipedia:Cnidocyte is_a: GO:0043232 ! intracellular non-membrane-bounded organelle -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa relationship: part_of GO:0005938 ! cell cortex +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0042157 @@ -75257,8 +75362,8 @@ is_a: GO:0031099 ! regeneration is_a: GO:0048589 ! developmental growth intersection_of: GO:0031099 ! regeneration intersection_of: results_in_maturation_of UBERON:0000479 ! tissue -relationship: never_in_taxon NCBITaxon:4751 ! Fungi relationship: results_in_maturation_of UBERON:0000479 ! tissue +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0042254 @@ -75518,9 +75623,9 @@ is_a: GO:0002376 ! immune system process is_a: GO:0030154 ! cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000387 ! hemocyte (sensu Arthropoda) -relationship: in_taxon NCBITaxon:6656 {all_only="true"} ! Arthropoda -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda relationship: results_in_acquisition_of_features_of CL:0000387 ! hemocyte (sensu Arthropoda) +relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda +relationship: RO:0002162 NCBITaxon:6656 {all_only="true"} ! in taxon Arthropoda [Term] id: GO:0042387 @@ -75891,7 +75996,7 @@ subset: goslim_pir synonym: "cellular hormone metabolic process" RELATED [] synonym: "hormone metabolism" EXACT [] is_a: GO:0010817 ! regulation of hormone levels -relationship: never_in_taxon NCBITaxon:4895 ! Schizosaccharomyces +property_value: RO:0002161 NCBITaxon:4895 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23965" xsd:anyURI [Term] @@ -75958,11 +76063,11 @@ namespace: cellular_component def: "A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells." [GOC:jl, PMID:11584301] xref: Wikipedia:Melanosome is_a: GO:0048770 ! pigment granule -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: never_in_taxon NCBITaxon:4895 ! Schizosaccharomyces -relationship: never_in_taxon NCBITaxon:6237 {source="GOC:kmv"} ! Caenorhabditis -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa relationship: part_of CL:0000148 ! melanocyte +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa +property_value: RO:0002161 NCBITaxon:4895 +property_value: RO:0002161 NCBITaxon:6237 {source="GOC:kmv"} [Term] id: GO:0042471 @@ -76025,9 +76130,9 @@ synonym: "tooth development" BROAD [] is_a: GO:0042476 ! odontogenesis intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0001091 ! calcareous tooth -relationship: in_taxon NCBITaxon:7711 {all_only="true"} ! Chordata -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: results_in_morphogenesis_of UBERON:0001091 ! calcareous tooth +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {all_only="true"} ! in taxon Chordata [Term] id: GO:0042476 @@ -76044,8 +76149,8 @@ xref: Wikipedia:Odontogenesis is_a: GO:0009887 ! animal organ morphogenesis intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0003913 ! tooth-like structure -relationship: never_in_taxon NCBITaxon:8782 ! Aves relationship: results_in_morphogenesis_of UBERON:0003913 ! tooth-like structure +property_value: RO:0002161 NCBITaxon:8782 [Term] id: GO:0042478 @@ -76417,9 +76522,9 @@ name: hair cycle namespace: biological_process def: "The cyclical phases of growth (anagen), regression (catagen), quiescence (telogen), and shedding (exogen) in the life of a hair; one of the collection or mass of filaments growing from the skin of an animal, and forming a covering for a part of the head or for any part or the whole of the body." [GOC:go_curators, PMID:12230507] is_a: GO:0042303 ! molting cycle -relationship: in_taxon NCBITaxon:40674 {all_only="true"} ! Mammalia -relationship: never_in_taxon NCBITaxon:8782 ! Aves -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia +relationship: RO:0002162 NCBITaxon:40674 {all_only="true"} ! in taxon Mammalia +property_value: RO:0002161 NCBITaxon:8782 [Term] id: GO:0042634 @@ -76564,8 +76669,8 @@ namespace: biological_process def: "The type of sexual cycle seen in females, often with physiologic changes in the endometrium that recur at regular intervals during the reproductive years." [ISBN:0721662544] is_a: GO:0048511 ! rhythmic process is_a: GO:0048609 ! multicellular organismal reproductive process -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota [Term] id: GO:0042701 @@ -76769,8 +76874,8 @@ xref: NIF_Subcellular:sao867568886 is_a: GO:0120025 ! plasma membrane bounded cell projection intersection_of: GO:0120025 ! plasma membrane bounded cell projection intersection_of: part_of CL:0000540 ! neuron -relationship: never_in_taxon NCBITaxon:4751 ! Fungi relationship: part_of CL:0000540 ! neuron +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0043009 @@ -76778,8 +76883,8 @@ name: chordate embryonic development namespace: biological_process def: "The process whose specific outcome is the progression of the embryo over time, from zygote formation through a stage including a notochord and neural tube until birth or egg hatching." [GOC:mtg_sensu] is_a: GO:0009792 ! embryo development ending in birth or egg hatching -relationship: in_taxon NCBITaxon:7711 {all_only="true"} ! Chordata -relationship: only_in_taxon NCBITaxon:7711 ! Chordata +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {all_only="true"} ! in taxon Chordata [Term] id: GO:0043010 @@ -76791,8 +76896,8 @@ def: "The process whose specific outcome is the progression of the camera-type e is_a: GO:0001654 ! eye development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0000019 ! camera-type eye -relationship: never_in_taxon NCBITaxon:6656 ! Arthropoda relationship: results_in_development_of UBERON:0000019 ! camera-type eye +property_value: RO:0002161 NCBITaxon:6656 [Term] id: GO:0043011 @@ -77314,9 +77419,9 @@ xref: FMA:62983 xref: NIF_Subcellular:sao593830697 xref: Wikipedia:Myelin is_a: GO:0110165 ! cellular anatomical entity -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa relationship: part_of CL:0000125 ! glial cell +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0043226 @@ -77631,9 +77736,9 @@ is_a: GO:0045055 ! regulated exocytosis is_a: GO:0051649 ! establishment of localization in cell intersection_of: GO:0045055 ! regulated exocytosis intersection_of: occurs_in CL:0000738 ! leukocyte -relationship: in_taxon NCBITaxon:7742 {all_only="true"} ! Vertebrata relationship: occurs_in CL:0000738 ! leukocyte -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 {all_only="true"} ! in taxon Vertebrata [Term] id: GO:0043300 @@ -78561,8 +78666,8 @@ def: "The accumulation of pigment in an organism, tissue or cell, either by incr subset: goslim_chembl subset: goslim_pir is_a: GO:0008150 ! biological_process -relationship: in_taxon NCBITaxon:131567 {all_only="true"} ! cellular organisms -relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms +relationship: RO:0002160 NCBITaxon:131567 ! only in taxon cellular organisms +relationship: RO:0002162 NCBITaxon:131567 {all_only="true"} ! in taxon cellular organisms [Term] id: GO:0043500 @@ -78746,7 +78851,7 @@ is_a: GO:0017046 ! peptide hormone binding intersection_of: GO:0005488 ! binding intersection_of: has_primary_input PR:000009054 ! insulin gene translation product relationship: has_primary_input PR:000009054 ! insulin gene translation product -relationship: never_in_taxon NCBITaxon:4751 ! Fungi +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0043576 @@ -78827,9 +78932,9 @@ synonym: "animal skin development" EXACT [] is_a: GO:0048513 ! animal organ development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0002097 ! skin of body -relationship: never_in_taxon NCBITaxon:50557 ! Insecta -relationship: never_in_taxon NCBITaxon:6656 ! Arthropoda relationship: results_in_development_of UBERON:0002097 ! skin of body +property_value: RO:0002161 NCBITaxon:50557 +property_value: RO:0002161 NCBITaxon:6656 [Term] id: GO:0043589 @@ -78899,7 +79004,7 @@ is_a: GO:0050673 ! epithelial cell proliferation intersection_of: GO:0008283 ! cell population proliferation intersection_of: acts_on_population_of CL:0000312 ! keratinocyte relationship: acts_on_population_of CL:0000312 ! keratinocyte -relationship: never_in_taxon NCBITaxon:6656 ! Arthropoda +property_value: RO:0002161 NCBITaxon:6656 [Term] id: GO:0043648 @@ -79425,8 +79530,8 @@ xref: FBbt:00005107 xref: FMA:67301 xref: Wikipedia:Cell_body is_a: GO:0110165 ! cellular anatomical entity -relationship: never_in_taxon NCBITaxon:4890 ! Ascomycota relationship: part_of CL:0000000 ! cell +property_value: RO:0002161 NCBITaxon:4890 created_by: jl creation_date: 2010-02-05T10:37:16Z @@ -79506,7 +79611,7 @@ synonym: "interspecies interaction" EXACT [] synonym: "interspecies interaction between organisms" EXACT [] synonym: "interspecies interaction with other organisms" EXACT [] is_a: GO:0008150 ! biological_process -relationship: never_in_taxon NCBITaxon:4895 ! Schizosaccharomyces +property_value: RO:0002161 NCBITaxon:4895 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20191" xsd:anyURI [Term] @@ -79603,9 +79708,9 @@ is_a: GO:0006996 ! organelle organization is_a: GO:0120036 ! plasma membrane bounded cell projection organization intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0005929 ! cilium -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota relationship: results_in_organization_of GO:0005929 ! cilium +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota created_by: jl creation_date: 2013-03-27T15:09:58Z @@ -79882,8 +79987,8 @@ namespace: cellular_component def: "The nucleus of either the ovum or the spermatozoon following fertilization. Thus, in the fertilized ovum, there are two pronuclei, one originating from the ovum, the other from the spermatozoon that brought about fertilization; they approach each other, but do not fuse until just before the first cleavage, when each pronucleus loses its membrane to release its contents." [ISBN:0198506732] xref: Wikipedia:Pronucleus is_a: GO:0005634 ! nucleus -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0045124 @@ -80051,8 +80156,8 @@ synonym: "synaptic junction" EXACT [] xref: NIF_Subcellular:sao914572699 xref: Wikipedia:Chemical_synapse is_a: GO:0030054 ! cell junction -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0045211 @@ -80209,10 +80314,10 @@ synonym: "regulation of eye photoreceptor development" BROAD [] is_a: GO:0042478 ! regulation of eye photoreceptor cell development intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0042051 ! compound eye photoreceptor development -relationship: in_taxon NCBITaxon:6656 {all_only="true"} ! Arthropoda -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda relationship: part_of GO:0046532 ! regulation of photoreceptor cell differentiation relationship: regulates GO:0042051 ! compound eye photoreceptor development +relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda +relationship: RO:0002162 NCBITaxon:6656 {all_only="true"} ! in taxon Arthropoda [Term] id: GO:0045315 @@ -80260,8 +80365,8 @@ is_a: GO:0002376 ! immune system process intersection_of: GO:0001775 ! cell activation intersection_of: has_primary_input CL:0000738 ! leukocyte relationship: has_primary_input CL:0000738 ! leukocyte -relationship: in_taxon NCBITaxon:7742 {all_only="true"} ! Vertebrata -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 {all_only="true"} ! in taxon Vertebrata [Term] id: GO:0045443 @@ -81869,9 +81974,9 @@ def: "Any process that modulates the frequency, rate or extent of neuron differe is_a: GO:0045595 ! regulation of cell differentiation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0030182 ! neuron differentiation -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa relationship: regulates GO:0030182 ! neuron differentiation +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0045665 @@ -84300,9 +84405,9 @@ synonym: "regulation of insulin receptor signalling pathway" EXACT [] is_a: GO:0009966 ! regulation of signal transduction intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0008286 ! insulin receptor signaling pathway -relationship: in_taxon NCBITaxon:6072 {all_only="true"} ! Eumetazoa -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: regulates GO:0008286 ! insulin receptor signaling pathway +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 {all_only="true"} ! in taxon Eumetazoa [Term] id: GO:0046627 @@ -84867,8 +84972,8 @@ synonym: "muscle homeostasis" RELATED [GOC:dph] is_a: GO:0019725 ! cellular homeostasis intersection_of: GO:0019725 ! cellular homeostasis intersection_of: occurs_in CL:0000187 ! muscle cell -relationship: never_in_taxon NCBITaxon:4751 ! Fungi relationship: occurs_in CL:0000187 ! muscle cell +property_value: RO:0002161 NCBITaxon:4751 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24218" xsd:anyURI [Term] @@ -85505,9 +85610,9 @@ is_a: GO:0098728 ! germline stem cell asymmetric division intersection_of: GO:0008356 ! asymmetric cell division intersection_of: has_primary_input CL:0000022 ! female germ line stem cell relationship: has_primary_input CL:0000022 ! female germ line stem cell -relationship: in_taxon NCBITaxon:6656 {all_only="true"} ! Arthropoda -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda relationship: part_of GO:0048477 ! oogenesis +relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda +relationship: RO:0002162 NCBITaxon:6656 {all_only="true"} ! in taxon Arthropoda [Term] id: GO:0048133 @@ -85603,8 +85708,8 @@ namespace: biological_process def: "The stage in oogenesis when many layers of follicle cells surround the oocyte. There is a yolk nucleus (Balbiani's Body) near the germinal vesicle." [GOC:jid, GOC:mtg_sensu, ISBN:0198542771] synonym: "mammalian oogenesis stage 5" EXACT [] is_a: GO:0022605 ! mammalian oogenesis stage -relationship: in_taxon NCBITaxon:40674 {all_only="true"} ! Mammalia -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia +relationship: RO:0002162 NCBITaxon:40674 {all_only="true"} ! in taxon Mammalia [Term] id: GO:0048165 @@ -85613,8 +85718,8 @@ namespace: biological_process def: "The stage in oogenesis when the antral spaces fuse to form a single antral space. The oocyte is suspended in the cumulus oophorous and the first polar body in the perivitelline space." [GOC:jid, GOC:mtg_sensu, ISBN:0198542771] synonym: "mammalian oogenesis stage 8" EXACT [] is_a: GO:0022605 ! mammalian oogenesis stage -relationship: in_taxon NCBITaxon:40674 {all_only="true"} ! Mammalia -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia +relationship: RO:0002162 NCBITaxon:40674 {all_only="true"} ! in taxon Mammalia [Term] id: GO:0048193 @@ -86124,9 +86229,9 @@ is_a: GO:0007281 ! germ cell development is_a: GO:0007292 ! female gamete generation intersection_of: GO:0048468 ! cell development intersection_of: results_in_development_of CL:0000025 ! egg cell -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa relationship: results_in_development_of CL:0000025 ! egg cell +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0048483 @@ -86189,8 +86294,8 @@ def: "Any process pertinent to the generation and maintenance of rhythms in the subset: goslim_pir synonym: "rhythm" RELATED [] is_a: GO:0008150 ! biological_process -relationship: in_taxon NCBITaxon:131567 {all_only="true"} ! cellular organisms -relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms +relationship: RO:0002160 NCBITaxon:131567 ! only in taxon cellular organisms +relationship: RO:0002162 NCBITaxon:131567 {all_only="true"} ! in taxon cellular organisms [Term] id: GO:0048513 @@ -86429,8 +86534,8 @@ synonym: "hematopoietic organ development" BROAD [] synonym: "hemopoietic organ development" BROAD [] is_a: GO:0048534 ! hematopoietic or lymphoid organ development is_a: GO:0048732 ! gland development -relationship: in_taxon NCBITaxon:6656 {all_only="true"} ! Arthropoda -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda +relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda +relationship: RO:0002162 NCBITaxon:6656 {all_only="true"} ! in taxon Arthropoda [Term] id: GO:0048545 @@ -86686,10 +86791,10 @@ is_a: GO:0000902 ! cell morphogenesis is_a: GO:0003006 ! developmental process involved in reproduction intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of CL:0000023 ! oocyte -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa relationship: part_of GO:0048599 ! oocyte development relationship: results_in_morphogenesis_of CL:0000023 ! oocyte +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0048608 @@ -87976,8 +88081,8 @@ xref: Wikipedia:Stem_cell_differentiation is_a: GO:0030154 ! cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000034 ! stem cell -relationship: never_in_taxon NCBITaxon:4751 ! Fungi relationship: results_in_acquisition_of_features_of CL:0000034 ! stem cell +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0048864 @@ -88934,8 +89039,8 @@ def: "Any process that modulates the frequency, rate or extent of phagocytosis, is_a: GO:0030100 ! regulation of endocytosis intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006909 ! phagocytosis -relationship: never_in_taxon NCBITaxon:147537 ! Saccharomycotina relationship: regulates GO:0006909 ! phagocytosis +property_value: RO:0002161 NCBITaxon:147537 [Term] id: GO:0050765 @@ -89240,8 +89345,8 @@ id: GO:0050803 name: regulation of synapse structure or activity namespace: biological_process def: "Any process that modulates the physical form or the activity of a synapse, the junction between a neuron and a target (neuron, muscle, or secretory cell)." [GOC:ai] -relationship: in_taxon NCBITaxon:6072 {all_only="true"} ! Eumetazoa -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 {all_only="true"} ! in taxon Eumetazoa [Term] id: GO:0050804 @@ -89663,8 +89768,8 @@ synonym: "brown adipocyte differentiation" EXACT [] is_a: GO:0045444 ! fat cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000449 ! brown adipocyte -relationship: never_in_taxon NCBITaxon:8782 ! Aves relationship: results_in_acquisition_of_features_of CL:0000449 ! brown adipocyte +property_value: RO:0002161 NCBITaxon:8782 [Term] id: GO:0050877 @@ -89683,8 +89788,8 @@ is_a: GO:0003008 ! system process intersection_of: GO:0003008 ! system process intersection_of: has_participant UBERON:0001016 ! nervous system relationship: has_participant UBERON:0001016 ! nervous system -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13824" xsd:anyURI [Term] @@ -89792,9 +89897,9 @@ is_a: GO:0002376 ! immune system process is_a: GO:0016477 ! cell migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0000738 ! leukocyte -relationship: in_taxon NCBITaxon:7742 {all_only="true"} ! Vertebrata -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: results_in_movement_of CL:0000738 ! leukocyte +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 {all_only="true"} ! in taxon Vertebrata [Term] id: GO:0050905 @@ -91930,9 +92035,9 @@ is_a: GO:0022414 ! reproductive process intersection_of: GO:0007049 ! cell cycle intersection_of: has_part GO:0140013 ! meiotic nuclear division relationship: has_part GO:0140013 ! meiotic nuclear division -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota relationship: part_of GO:0019953 ! sexual reproduction +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24599" xsd:anyURI [Term] @@ -92254,10 +92359,10 @@ synonym: "storage of protein in nucleus" NARROW [] is_a: GO:0072595 ! maintenance of protein localization in organelle intersection_of: GO:0045185 ! maintenance of protein location intersection_of: occurs_in GO:0005634 ! nucleus -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota relationship: occurs_in GO:0005634 ! nucleus -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota relationship: part_of GO:0034504 ! protein localization to nucleus +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota [Term] id: GO:0051458 @@ -92408,8 +92513,8 @@ def: "The directed movement of a keratinocyte, epidermal cells which synthesize is_a: GO:0010631 ! epithelial cell migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0000312 ! keratinocyte -relationship: never_in_taxon NCBITaxon:6656 ! Arthropoda relationship: results_in_movement_of CL:0000312 ! keratinocyte +property_value: RO:0002161 NCBITaxon:6656 [Term] id: GO:0051547 @@ -92869,8 +92974,8 @@ is_a: GO:0051179 ! localization intersection_of: GO:0051179 ! localization intersection_of: has_primary_input GO:0043226 ! organelle relationship: has_primary_input GO:0043226 ! organelle -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19809" xsd:anyURI [Term] @@ -92946,10 +93051,10 @@ synonym: "positioning within cell" NARROW [] is_a: GO:0051234 ! establishment of localization intersection_of: GO:0051234 ! establishment of localization intersection_of: occurs_in CL:0000000 ! cell -relationship: in_taxon NCBITaxon:131567 {all_only="true"} ! cellular organisms relationship: occurs_in CL:0000000 ! cell -relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms relationship: part_of GO:0051641 ! cellular localization +relationship: RO:0002160 NCBITaxon:131567 ! only in taxon cellular organisms +relationship: RO:0002162 NCBITaxon:131567 {all_only="true"} ! in taxon cellular organisms [Term] id: GO:0051650 @@ -93177,7 +93282,7 @@ synonym: "NOS2 synthase biosynthesis" NARROW [] synonym: "NOS2 synthase biosynthetic process" NARROW [] synonym: "NOS3 biosynthesis" NARROW [GOC:bf] is_a: GO:0009059 ! macromolecule biosynthetic process -relationship: never_in_taxon NCBITaxon:4751 ! Fungi +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0051769 @@ -95174,9 +95279,9 @@ synonym: "milk ejection" EXACT [] is_a: GO:0007589 ! body fluid secretion is_a: GO:0032941 ! secretion by tissue is_a: GO:0060004 ! reflex -relationship: in_taxon NCBITaxon:40674 {all_only="true"} ! Mammalia -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of GO:0007595 ! lactation +relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia +relationship: RO:0002162 NCBITaxon:40674 {all_only="true"} ! in taxon Mammalia [Term] id: GO:0060157 @@ -95186,9 +95291,9 @@ def: "The process whose specific outcome is the progression of the urinary bladd is_a: GO:0048513 ! animal organ development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001255 ! urinary bladder -relationship: never_in_taxon NCBITaxon:8782 ! Aves relationship: part_of GO:0072001 ! renal system development relationship: results_in_development_of UBERON:0001255 ! urinary bladder +property_value: RO:0002161 NCBITaxon:8782 [Term] id: GO:0060166 @@ -95493,15 +95598,15 @@ relationship: has_part GO:0035735 ! intraciliary transport involved in cilium as relationship: has_part GO:0061512 ! protein localization to cilium relationship: has_part GO:0097712 ! vesicle targeting, trans-Golgi to periciliary membrane compartment relationship: has_part GO:1905349 ! ciliary transition zone assembly -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: never_in_taxon NCBITaxon:3176 ! Zygnematales -relationship: never_in_taxon NCBITaxon:3312 ! Coniferophyta -relationship: never_in_taxon NCBITaxon:3378 ! Gnetales -relationship: never_in_taxon NCBITaxon:3398 ! Magnoliopsida -relationship: never_in_taxon NCBITaxon:4890 ! Ascomycota -relationship: never_in_taxon NCBITaxon:5782 ! Dictyostelium relationship: results_in_assembly_of GO:0005929 ! cilium +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota relationship: starts_with GO:0097711 ! ciliary basal body-plasma membrane docking +property_value: RO:0002161 NCBITaxon:3176 +property_value: RO:0002161 NCBITaxon:3312 +property_value: RO:0002161 NCBITaxon:3378 +property_value: RO:0002161 NCBITaxon:3398 +property_value: RO:0002161 NCBITaxon:4890 +property_value: RO:0002161 NCBITaxon:5782 [Term] id: GO:0060281 @@ -96894,9 +96999,9 @@ def: "The progression of the diaphragm over time from its initial formation to t is_a: GO:0060538 ! skeletal muscle organ development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001103 ! diaphragm -relationship: never_in_taxon NCBITaxon:8782 ! Aves relationship: part_of GO:0060541 ! respiratory system development relationship: results_in_development_of UBERON:0001103 ! diaphragm +property_value: RO:0002161 NCBITaxon:8782 created_by: dph creation_date: 2009-04-10T08:44:56Z @@ -96908,9 +97013,9 @@ def: "The process in which the anatomical structures of the diaphragm are genera is_a: GO:0048644 ! muscle organ morphogenesis intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0001103 ! diaphragm -relationship: never_in_taxon NCBITaxon:8782 ! Aves relationship: part_of GO:0060539 ! diaphragm development relationship: results_in_morphogenesis_of UBERON:0001103 ! diaphragm +property_value: RO:0002161 NCBITaxon:8782 created_by: dph creation_date: 2009-04-10T08:47:51Z @@ -99518,9 +99623,9 @@ subset: goslim_drosophila is_a: GO:0048856 ! anatomical structure development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0005090 ! muscle structure -relationship: in_taxon NCBITaxon:6072 {all_only="true"} ! Eumetazoa -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: results_in_development_of UBERON:0005090 ! muscle structure +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 {all_only="true"} ! in taxon Eumetazoa created_by: dph creation_date: 2010-03-09T08:55:14Z @@ -101131,9 +101236,9 @@ def: "The process in which a relatively unspecialized cell acquires the speciali is_a: GO:0061318 ! renal filtration cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0002520 ! nephrocyte -relationship: in_taxon NCBITaxon:50557 {all_only="true"} ! Insecta -relationship: only_in_taxon NCBITaxon:50557 ! Insecta relationship: results_in_acquisition_of_features_of CL:0002520 ! nephrocyte +relationship: RO:0002160 NCBITaxon:50557 ! only in taxon Insecta +relationship: RO:0002162 NCBITaxon:50557 {all_only="true"} ! in taxon Insecta created_by: dph creation_date: 2010-09-24T12:23:29Z @@ -101687,14 +101792,14 @@ is_a: GO:0033365 ! protein localization to organelle intersection_of: GO:0008104 ! protein localization intersection_of: has_target_end_location GO:0005929 ! cilium relationship: has_target_end_location GO:0005929 ! cilium -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: never_in_taxon NCBITaxon:3176 ! Zygnematales -relationship: never_in_taxon NCBITaxon:3312 ! Coniferophyta -relationship: never_in_taxon NCBITaxon:3378 ! Gnetales -relationship: never_in_taxon NCBITaxon:3398 ! Magnoliopsida -relationship: never_in_taxon NCBITaxon:4890 ! Ascomycota -relationship: never_in_taxon NCBITaxon:5782 ! Dictyostelium -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota +property_value: RO:0002161 NCBITaxon:3176 +property_value: RO:0002161 NCBITaxon:3312 +property_value: RO:0002161 NCBITaxon:3378 +property_value: RO:0002161 NCBITaxon:3398 +property_value: RO:0002161 NCBITaxon:4890 +property_value: RO:0002161 NCBITaxon:5782 created_by: dph creation_date: 2013-03-22T15:41:44Z @@ -102601,8 +102706,8 @@ name: collagen-containing extracellular matrix namespace: cellular_component def: "An extracellular matrix consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that provides not only essential physical scaffolding for the cellular constituents but can also initiate crucial biochemical and biomechanical cues required for tissue morphogenesis, differentiation and homeostasis. The components are secreted by cells in the vicinity and form a sheet underlying or overlying cells such as endothelial and epithelial cells." [GOC:BHF, GOC:rph, PMID:21123617] is_a: GO:0031012 ! extracellular matrix -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa created_by: dph creation_date: 2018-04-13T12:47:21Z @@ -103481,7 +103586,7 @@ is_a: GO:0070341 ! fat cell proliferation intersection_of: GO:0008283 ! cell population proliferation intersection_of: acts_on_population_of CL:0000449 ! brown adipocyte relationship: acts_on_population_of CL:0000449 ! brown adipocyte -relationship: never_in_taxon NCBITaxon:8782 ! Aves +property_value: RO:0002161 NCBITaxon:8782 [Term] id: GO:0070343 @@ -103913,8 +104018,8 @@ is_a: GO:0008283 ! cell population proliferation intersection_of: GO:0008283 ! cell population proliferation intersection_of: acts_on_population_of CL:0000738 ! leukocyte relationship: acts_on_population_of CL:0000738 ! leukocyte -relationship: in_taxon NCBITaxon:7742 {all_only="true"} ! Vertebrata -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 {all_only="true"} ! in taxon Vertebrata created_by: mah creation_date: 2009-05-28T05:25:28Z @@ -105508,9 +105613,9 @@ synonym: "leukocyte apoptosis" NARROW [] is_a: GO:0006915 ! apoptotic process intersection_of: GO:0006915 ! apoptotic process intersection_of: occurs_in CL:0000738 ! leukocyte -relationship: in_taxon NCBITaxon:7742 {all_only="true"} ! Vertebrata relationship: occurs_in CL:0000738 ! leukocyte -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 {all_only="true"} ! in taxon Vertebrata created_by: mah creation_date: 2010-09-14T12:44:09Z @@ -105650,9 +105755,9 @@ is_a: GO:0048513 ! animal organ development is_a: GO:0061326 ! renal tubule development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0001054 ! Malpighian tubule -relationship: in_taxon NCBITaxon:50557 {all_only="true"} ! Insecta -relationship: only_in_taxon NCBITaxon:50557 ! Insecta relationship: results_in_development_of UBERON:0001054 ! Malpighian tubule +relationship: RO:0002160 NCBITaxon:50557 ! only in taxon Insecta +relationship: RO:0002162 NCBITaxon:50557 {all_only="true"} ! in taxon Insecta created_by: mah creation_date: 2010-01-25T10:54:30Z @@ -109583,8 +109688,8 @@ def: "The process in which a smooth muscle cell acquires the specialized feature is_a: GO:0090077 ! foam cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000892 ! smooth muscle cell derived foam cell -relationship: never_in_taxon NCBITaxon:4751 ! Fungi relationship: results_in_acquisition_of_features_of CL:0000892 ! smooth muscle cell derived foam cell +property_value: RO:0002161 NCBITaxon:4751 created_by: tb creation_date: 2009-09-15T03:48:10Z @@ -110756,11 +110861,11 @@ def: "The process in which any suture between cranial and/or facial bones is gen is_a: GO:0009653 ! anatomical structure morphogenesis intersection_of: GO:0009653 ! anatomical structure morphogenesis intersection_of: results_in_morphogenesis_of UBERON:0009198 ! craniofacial suture -relationship: in_taxon NCBITaxon:7742 {all_only="true"} ! Vertebrata -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of GO:0060349 ! bone morphogenesis relationship: part_of GO:1904888 ! cranial skeletal system development relationship: results_in_morphogenesis_of UBERON:0009198 ! craniofacial suture +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 {all_only="true"} ! in taxon Vertebrata created_by: pr creation_date: 2011-07-05T02:51:54Z @@ -111019,8 +111124,8 @@ synonym: "keratinocyte apoptosis" NARROW [] is_a: GO:1904019 ! epithelial cell apoptotic process intersection_of: GO:0006915 ! apoptotic process intersection_of: occurs_in CL:0000312 ! keratinocyte -relationship: never_in_taxon NCBITaxon:6656 ! Arthropoda relationship: occurs_in CL:0000312 ! keratinocyte +property_value: RO:0002161 NCBITaxon:6656 created_by: pr creation_date: 2012-03-29T10:20:51Z @@ -112809,9 +112914,9 @@ subset: goslim_synapse is_a: GO:0016192 ! vesicle-mediated transport intersection_of: GO:0016192 ! vesicle-mediated transport intersection_of: occurs_in GO:0045202 ! synapse -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa relationship: occurs_in GO:0045202 ! synapse -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0099012 @@ -113444,9 +113549,9 @@ subset: goslim_synapse is_a: GO:0007267 ! cell-cell signaling intersection_of: GO:0007267 ! cell-cell signaling intersection_of: occurs_in GO:0045202 ! synapse -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa relationship: occurs_in GO:0045202 ! synapse -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0099537 @@ -113501,8 +113606,8 @@ intersection_of: GO:0009056 ! catabolic process intersection_of: has_primary_input CHEBI:36080 intersection_of: occurs_in GO:0045202 ! synapse intersection_of: regulates GO:0007268 ! chemical synaptic transmission -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa relationship: regulates GO:0007268 ! chemical synaptic transmission +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0099547 @@ -113517,7 +113622,7 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: occurs_in GO:0045202 ! synapse intersection_of: regulates GO:0006412 ! translation intersection_of: regulates GO:0007268 ! chemical synaptic transmission -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0099550 @@ -113619,7 +113724,7 @@ intersection_of: has_primary_input CHEBI:36080 intersection_of: occurs_in GO:0045202 ! synapse intersection_of: regulates GO:0007268 ! chemical synaptic transmission intersection_of: regulates GO:0009056 ! catabolic process -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0099575 @@ -113845,10 +113950,10 @@ subset: goslim_synapse is_a: GO:0023061 ! signal release intersection_of: GO:0023061 ! signal release intersection_of: occurs_in GO:0045202 ! synapse -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa relationship: occurs_in GO:0045202 ! synapse -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa relationship: part_of GO:0099536 ! synaptic signaling +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0099738 @@ -113908,9 +114013,9 @@ is_a: GO:0071763 ! nuclear membrane organization is_a: GO:1903047 ! mitotic cell cycle process intersection_of: GO:0071763 ! nuclear membrane organization intersection_of: part_of GO:0140014 ! mitotic nuclear division -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota relationship: part_of GO:0140014 ! mitotic nuclear division +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19949" xsd:anyURI [Term] @@ -115336,9 +115441,9 @@ subset: goslim_synapse is_a: GO:0006412 ! translation intersection_of: GO:0006412 ! translation intersection_of: occurs_in GO:0045202 ! synapse -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa relationship: occurs_in GO:0045202 ! synapse -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa property_value: term_tracker_item "https://github.com/geneontology/synapse/issues/210" xsd:anyURI created_by: pg creation_date: 2018-07-15T09:23:12Z @@ -115369,9 +115474,9 @@ is_a: GO:0006417 ! regulation of translation intersection_of: GO:0065007 ! biological regulation intersection_of: occurs_in GO:0045202 ! synapse intersection_of: regulates GO:0006412 ! translation -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa relationship: occurs_in GO:0045202 ! synapse -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa property_value: term_tracker_item "https://github.com/geneontology/synapse/issues/210" xsd:anyURI created_by: pg creation_date: 2018-07-15T09:38:26Z @@ -115419,9 +115524,9 @@ is_a: GO:0030163 ! protein catabolic process intersection_of: GO:0009056 ! catabolic process intersection_of: has_primary_input CHEBI:36080 intersection_of: occurs_in GO:0045202 ! synapse -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa relationship: occurs_in GO:0045202 ! synapse -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa property_value: term_tracker_item "https://github.com/geneontology/synapse/issues/210" xsd:anyURI created_by: pg creation_date: 2018-07-15T10:12:51Z @@ -115471,9 +115576,9 @@ intersection_of: has_primary_input CHEBI:36080 intersection_of: occurs_in GO:0045202 ! synapse intersection_of: regulates GO:0009056 ! catabolic process relationship: has_primary_input CHEBI:36080 -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa relationship: occurs_in GO:0045202 ! synapse -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa property_value: term_tracker_item "https://github.com/geneontology/synapse/issues/204" xsd:anyURI created_by: pg creation_date: 2018-07-15T10:34:56Z @@ -115916,9 +116021,9 @@ def: "Any process that modulates the frequency, rate or extent of neuroinflammat is_a: GO:0050727 ! regulation of inflammatory response intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0150076 ! neuroinflammatory response -relationship: in_taxon NCBITaxon:7742 {all_only="true"} ! Vertebrata -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: regulates GO:0150076 ! neuroinflammatory response +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 {all_only="true"} ! in taxon Vertebrata created_by: bc creation_date: 2018-07-26T12:32:18Z @@ -116013,9 +116118,9 @@ synonym: "transport across blood brain barrier" EXACT [] is_a: GO:0010232 ! vascular transport intersection_of: GO:0010232 ! vascular transport intersection_of: results_in_transport_across UBERON:0000120 ! blood brain barrier -relationship: in_taxon NCBITaxon:6072 {all_only="true"} ! Eumetazoa -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: results_in_transport_across UBERON:0000120 ! blood brain barrier +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 {all_only="true"} ! in taxon Eumetazoa created_by: bc creation_date: 2019-05-27T09:12:03Z @@ -118054,7 +118159,7 @@ is_a: GO:0019538 ! protein metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output PR:000009054 ! insulin gene translation product relationship: has_primary_input_or_output PR:000009054 ! insulin gene translation product -relationship: never_in_taxon NCBITaxon:33090 ! Viridiplantae +property_value: RO:0002161 NCBITaxon:33090 created_by: pm creation_date: 2012-07-13T12:32:40Z @@ -118917,7 +119022,7 @@ is_a: GO:0022857 ! transmembrane transporter activity intersection_of: GO:0022857 ! transmembrane transporter activity intersection_of: has_primary_input CHEBI:63299 relationship: has_primary_input CHEBI:63299 -relationship: part_of GO:1901264 {http://purl.org/dc/terms/source="GO_REF:0000090"} ! carbohydrate derivative transport +relationship: part_of GO:1901264 ! carbohydrate derivative transport created_by: pr creation_date: 2012-10-17T10:31:22Z @@ -120944,8 +121049,8 @@ synonym: "red blood cell apoptotic process" EXACT [GOC:TermGenie] is_a: GO:0033028 ! myeloid cell apoptotic process intersection_of: GO:0006915 ! apoptotic process intersection_of: occurs_in CL:0000232 ! erythrocyte -relationship: never_in_taxon NCBITaxon:4751 ! Fungi relationship: occurs_in CL:0000232 ! erythrocyte +property_value: RO:0002161 NCBITaxon:4751 created_by: rl creation_date: 2013-06-13T10:02:29Z @@ -121005,7 +121110,7 @@ is_a: GO:1902250 ! regulation of erythrocyte apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:1902217 ! erythrocyte apoptotic process relationship: negatively_regulates GO:1902217 ! erythrocyte apoptotic process -relationship: never_in_taxon NCBITaxon:4751 ! Fungi +property_value: RO:0002161 NCBITaxon:4751 created_by: rl creation_date: 2013-06-20T19:30:59Z @@ -121047,8 +121152,8 @@ is_a: GO:0033034 ! positive regulation of myeloid cell apoptotic process is_a: GO:1902250 ! regulation of erythrocyte apoptotic process intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:1902217 ! erythrocyte apoptotic process -relationship: never_in_taxon NCBITaxon:4751 ! Fungi relationship: positively_regulates GO:1902217 ! erythrocyte apoptotic process +property_value: RO:0002161 NCBITaxon:4751 created_by: rl creation_date: 2013-06-20T19:31:04Z @@ -123252,9 +123357,9 @@ is_a: GO:0032368 ! regulation of lipid transport is_a: GO:0150200 ! regulation of transport across blood-brain barrier intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:1990379 ! lipid transport across blood-brain barrier -relationship: in_taxon NCBITaxon:6072 {all_only="true"} ! Eumetazoa -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: regulates GO:1990379 ! lipid transport across blood-brain barrier +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 {all_only="true"} ! in taxon Eumetazoa created_by: sjp creation_date: 2014-05-09T09:30:04Z @@ -126921,8 +127026,8 @@ synonym: "epitheliocyte apoptotic process" EXACT [GOC:TermGenie] is_a: GO:0006915 ! apoptotic process intersection_of: GO:0006915 ! apoptotic process intersection_of: occurs_in CL:0000066 ! epithelial cell -relationship: never_in_taxon NCBITaxon:33090 ! Viridiplantae relationship: occurs_in CL:0000066 ! epithelial cell +property_value: RO:0002161 NCBITaxon:33090 created_by: sl creation_date: 2015-03-06T22:27:17Z @@ -136130,8 +136235,8 @@ is_a: GO:0051650 ! establishment of vesicle localization intersection_of: GO:0006887 ! exocytosis intersection_of: has_primary_input GO:0070062 ! extracellular exosome relationship: has_primary_input GO:0070062 ! extracellular exosome -relationship: never_in_taxon NCBITaxon:4890 ! Ascomycota relationship: part_of GO:0097734 ! extracellular exosome biogenesis +property_value: RO:0002161 NCBITaxon:4890 created_by: hjd creation_date: 2013-09-04T21:08:14Z @@ -136248,7 +136353,7 @@ is_a: GO:0150104 ! transport across blood-brain barrier intersection_of: GO:0150104 ! transport across blood-brain barrier intersection_of: has_primary_input CHEBI:18059 intersection_of: results_in_transport_across UBERON:0000120 ! blood brain barrier -relationship: in_taxon NCBITaxon:6072 {all_only="true"} ! Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 {all_only="true"} ! in taxon Eumetazoa created_by: sjp creation_date: 2014-05-08T09:52:28Z @@ -136362,10 +136467,10 @@ def: "A process in which force is generated within smooth muscle tissue, resulti is_a: GO:0006939 ! smooth muscle contraction intersection_of: GO:0006939 ! smooth muscle contraction intersection_of: occurs_in UBERON:0001155 ! colon -relationship: in_taxon NCBITaxon:7742 {all_only="true"} ! Vertebrata relationship: occurs_in UBERON:0001155 ! colon -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of GO:0014827 ! intestine smooth muscle contraction +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 {all_only="true"} ! in taxon Vertebrata created_by: sl creation_date: 2015-06-10T18:29:21Z @@ -136390,10 +136495,10 @@ def: "A process in which force is generated within smooth muscle tissue, resulti is_a: GO:0006939 ! smooth muscle contraction intersection_of: GO:0006939 ! smooth muscle contraction intersection_of: occurs_in UBERON:0002108 ! small intestine -relationship: in_taxon NCBITaxon:7742 {all_only="true"} ! Vertebrata relationship: occurs_in UBERON:0002108 ! small intestine -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of GO:0014827 ! intestine smooth muscle contraction +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 {all_only="true"} ! in taxon Vertebrata created_by: sl creation_date: 2015-06-11T18:02:33Z @@ -136536,8 +136641,8 @@ def: "The cytoplasm of an ovum." [PMID:19022436] is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: part_of CL:0000025 ! egg cell -relationship: never_in_taxon NCBITaxon:4751 ! Fungi relationship: part_of CL:0000025 ! egg cell +property_value: RO:0002161 NCBITaxon:4751 created_by: sl creation_date: 2015-12-10T21:40:16Z @@ -141287,9 +141392,9 @@ synonym: "regulation of neuronal migration" EXACT [GOC:obol] is_a: GO:0030334 ! regulation of cell migration intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0001764 ! neuron migration -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa relationship: regulates GO:0001764 ! neuron migration +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa created_by: kmv creation_date: 2011-11-17T10:01:38Z @@ -141457,54 +141562,37 @@ creation_date: 2011-12-07T07:14:57Z id: IAO:0000027 name: data item is_a: IAO:0000030 ! information content entity -property_value: IAO:0000111 "data item" xsd:string [Term] id: IAO:0000030 name: information content entity is_a: BFO:0000031 ! generically dependent continuant -property_value: IAO:0000111 "information content entity" xsd:string [Term] id: IAO:0000078 name: curation status specification def: "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." [] is_a: IAO:0000102 ! data about an ontology part -property_value: editor_note "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" xsd:string -property_value: IAO:0000111 "curation status specification" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "PERSON:Bill Bug" xsd:string -property_value: IAO:0000119 "GROUP:OBI:" xsd:string -property_value: IAO:0000119 "OBI_0000266" xsd:string +property_value: IAO:0000116 "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" xsd:string [Term] id: IAO:0000102 name: data about an ontology part def: "Data about an ontology part is a data item about a part of an ontology, for example a term" [] is_a: IAO:0000027 ! data item -property_value: IAO:0000111 "data about an ontology part" xsd:string -property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string [Term] id: IAO:0000225 name: obsolescence reason specification def: "The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." [] is_a: IAO:0000102 ! data about an ontology part -property_value: editor_note "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." xsd:string -property_value: IAO:0000111 "obsolescence reason specification" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string -property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string +property_value: IAO:0000116 "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." xsd:string [Term] id: IAO:0000409 name: denotator type def: "A denotator type indicates how a term should be interpreted from an ontological perspective." [] is_a: IAO:0000102 ! data about an ontology part -property_value: IAO:0000111 "denotator type" xsd:string -property_value: IAO:0000112 "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities." xsd:string -property_value: IAO:0000117 "Alan Ruttenberg" xsd:string -property_value: IAO:0000119 "Barry Smith, Werner Ceusters" xsd:string [Term] id: NCBITaxon:1 @@ -141522,18 +141610,16 @@ namespace: ncbi_taxonomy xref: GC_ID:1 xref: PMID:15371245 is_a: NCBITaxon:337687 ! Muroidea -property_value: has_rank NCBITaxon:family [Term] id: NCBITaxon:10088 name: Mus namespace: ncbi_taxonomy -synonym: "mice" EXACT OMO:0003003 [] +synonym: "mice" EXACT genbank_common_name [] synonym: "mouse" EXACT OMO:0003003 [] synonym: "Mus" EXACT scientific_name [] xref: GC_ID:1 is_a: NCBITaxon:39107 ! Murinae -property_value: has_rank NCBITaxon:genus [Term] id: NCBITaxon:10090 @@ -141544,7 +141630,6 @@ synonym: "house mouse" EXACT genbank_common_name [] synonym: "mouse" EXACT OMO:0003003 [] xref: GC_ID:1 is_a: NCBITaxon:862507 ! Mus -property_value: has_rank NCBITaxon:species [Term] id: NCBITaxon:117570 @@ -141552,7 +141637,6 @@ name: Teleostomi namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:7776 ! Gnathostomata -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:117571 @@ -141562,7 +141646,6 @@ alt_id: NCBITaxon:40673 synonym: "bony vertebrates" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:117570 ! Teleostomi -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:119089 @@ -141572,7 +141655,6 @@ alt_id: NCBITaxon:27837 synonym: "Adenophorea" RELATED synonym [] xref: GC_ID:1 is_a: NCBITaxon:6231 ! Nematoda -property_value: has_rank NCBITaxon:class [Term] id: NCBITaxon:1206794 @@ -141580,7 +141662,6 @@ name: Ecdysozoa namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:33317 ! Protostomia -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:1206795 @@ -141588,7 +141669,6 @@ name: Lophotrochozoa namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:2697495 ! Spiralia -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:131209 @@ -141601,7 +141681,6 @@ synonym: "gamophytes" EXACT OMO:0003003 [] synonym: "Zygnematophyceae" RELATED synonym [] xref: GC_ID:1 is_a: NCBITaxon:131221 ! Streptophytina -property_value: has_rank NCBITaxon:class [Term] id: NCBITaxon:131221 @@ -141611,7 +141690,6 @@ synonym: "Charophyta/Embryophyta group" RELATED synonym [] synonym: "charophyte/embryophyte group" EXACT equivalent_name [] xref: GC_ID:1 is_a: NCBITaxon:35493 ! Streptophyta -property_value: has_rank NCBITaxon:subphylum [Term] id: NCBITaxon:131567 @@ -141631,7 +141709,6 @@ xref: GC_ID:1 xref: PMID:22839753 xref: PMID:25450099 is_a: NCBITaxon:32561 ! Sauria -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:1338369 @@ -141639,7 +141716,6 @@ name: Dipnotetrapodomorpha namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:8287 ! Sarcopterygii -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:142796 @@ -141652,7 +141728,6 @@ xref: GC_ID:1 xref: PMID:11062127 xref: PMID:9342353 is_a: NCBITaxon:2605435 ! Evosea -property_value: has_rank NCBITaxon:class [Term] id: NCBITaxon:1437010 @@ -141663,7 +141738,6 @@ xref: GC_ID:1 xref: PMID:11743200 xref: PMID:11791233 is_a: NCBITaxon:9347 ! Eutheria -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:1437180 @@ -141671,7 +141745,6 @@ name: Acrogymnospermae namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:58024 ! Spermatophyta -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:1445966 @@ -141679,7 +141752,6 @@ name: Gnetidae namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:3372 ! Gnetopsida -property_value: has_rank NCBITaxon:subclass [Term] id: NCBITaxon:147537 @@ -141688,7 +141760,6 @@ namespace: ncbi_taxonomy synonym: "true yeasts" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:716545 ! saccharomyceta -property_value: has_rank NCBITaxon:subphylum [Term] id: NCBITaxon:147554 @@ -141697,7 +141768,6 @@ namespace: ncbi_taxonomy synonym: "Archiascomycota" RELATED in_part [] xref: GC_ID:1 is_a: NCBITaxon:451866 ! Taphrinomycotina -property_value: has_rank NCBITaxon:class [Term] id: NCBITaxon:186623 @@ -141705,7 +141775,6 @@ name: Actinopteri namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:7898 ! Actinopterygii -property_value: has_rank NCBITaxon:class [Term] id: NCBITaxon:1963758 @@ -141715,7 +141784,6 @@ synonym: "mice and others" EXACT genbank_common_name [] synonym: "Sciurognathi" RELATED in_part [] xref: GC_ID:1 is_a: NCBITaxon:9989 ! Rodentia -property_value: has_rank NCBITaxon:suborder [Term] id: NCBITaxon:1965096 @@ -141724,7 +141792,6 @@ namespace: ncbi_taxonomy synonym: "Callithrix" EXACT scientific_name [] xref: GC_ID:1 is_a: NCBITaxon:9481 ! Callithrix -property_value: has_rank NCBITaxon:subgenus [Term] id: NCBITaxon:197562 @@ -141734,7 +141801,6 @@ xref: GC_ID:1 xref: PMID:10874751 xref: PMID:11557979 is_a: NCBITaxon:197563 ! Mandibulata -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:197563 @@ -141745,7 +141811,6 @@ xref: GC_ID:1 xref: PMID:11557979 xref: PMID:9727836 is_a: NCBITaxon:6656 ! Arthropoda -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:2 @@ -141788,7 +141853,6 @@ xref: PMID:8590690 xref: PMID:9103655 xref: PMID:9336922 is_a: NCBITaxon:131567 ! cellular organisms -property_value: has_rank NCBITaxon:superkingdom [Term] id: NCBITaxon:2058185 @@ -141797,7 +141861,6 @@ namespace: ncbi_taxonomy xref: GC_ID:1 xref: PMID:29367151 is_a: NCBITaxon:2058949 ! Dictyosteliales -property_value: has_rank NCBITaxon:family [Term] id: NCBITaxon:2058949 @@ -141806,7 +141869,6 @@ namespace: ncbi_taxonomy xref: GC_ID:1 xref: PMID:29367151 is_a: NCBITaxon:33083 ! Dictyostelia -property_value: has_rank NCBITaxon:order [Term] id: NCBITaxon:207598 @@ -141815,7 +141877,6 @@ namespace: ncbi_taxonomy synonym: "Homo/Pan/Gorilla group" RELATED synonym [] xref: GC_ID:1 is_a: NCBITaxon:9604 ! Hominidae -property_value: has_rank NCBITaxon:subfamily [Term] id: NCBITaxon:2157 @@ -141860,7 +141921,6 @@ xref: PMID:8590690 xref: PMID:9103655 xref: PMID:9336922 is_a: NCBITaxon:131567 ! cellular organisms -property_value: has_rank NCBITaxon:superkingdom [Term] id: NCBITaxon:2301116 @@ -141868,7 +141928,6 @@ name: Rhabditina namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:6236 ! Rhabditida -property_value: has_rank NCBITaxon:suborder [Term] id: NCBITaxon:2301119 @@ -141876,7 +141935,6 @@ name: Rhabditomorpha namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:2301116 ! Rhabditina -property_value: has_rank NCBITaxon:infraorder [Term] id: NCBITaxon:2605435 @@ -141884,7 +141942,6 @@ name: Evosea namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:554915 ! Amoebozoa -property_value: has_rank NCBITaxon:phylum [Term] id: NCBITaxon:2611352 @@ -141892,7 +141949,6 @@ name: Discoba namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:2759 ! Eukaryota -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:2684882 @@ -141900,7 +141956,6 @@ name: Zygnematophycidae namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:131209 ! Zygnemophyceae -property_value: has_rank NCBITaxon:subclass [Term] id: NCBITaxon:2697495 @@ -141908,7 +141963,6 @@ name: Spiralia namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:33317 ! Protostomia -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:2698737 @@ -141917,7 +141971,6 @@ namespace: ncbi_taxonomy synonym: "SAR supergroup" RELATED synonym [] xref: GC_ID:1 is_a: NCBITaxon:2759 ! Eukaryota -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:2759 @@ -141934,7 +141987,6 @@ xref: GC_ID:1 xref: PMID:23020233 xref: PMID:30257078 is_a: NCBITaxon:131567 ! cellular organisms -property_value: has_rank NCBITaxon:superkingdom [Term] id: NCBITaxon:314145 @@ -141945,7 +141997,6 @@ xref: PMID:11214318 xref: PMID:11214319 xref: PMID:12878460 is_a: NCBITaxon:1437010 ! Boreoeutheria -property_value: has_rank NCBITaxon:superorder [Term] id: NCBITaxon:314146 @@ -141957,7 +142008,6 @@ xref: PMID:12082125 xref: PMID:12878460 xref: PMID:15522813 is_a: NCBITaxon:1437010 ! Boreoeutheria -property_value: has_rank NCBITaxon:superorder [Term] id: NCBITaxon:314147 @@ -141969,7 +142019,6 @@ xref: PMID:11214319 xref: PMID:12082125 xref: PMID:15522813 is_a: NCBITaxon:314146 ! Euarchontoglires -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:314293 @@ -141978,7 +142027,6 @@ namespace: ncbi_taxonomy synonym: "Anthropoidea" RELATED synonym [] xref: GC_ID:1 is_a: NCBITaxon:376913 ! Haplorrhini -property_value: has_rank NCBITaxon:infraorder [Term] id: NCBITaxon:314295 @@ -141988,7 +142036,6 @@ synonym: "ape" EXACT OMO:0003003 [] synonym: "apes" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:9526 ! Catarrhini -property_value: has_rank NCBITaxon:superfamily [Term] id: NCBITaxon:3176 @@ -141996,7 +142043,6 @@ name: Zygnematales namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:2684882 ! Zygnematophycidae -property_value: has_rank NCBITaxon:order [Term] id: NCBITaxon:3193 @@ -142008,7 +142054,6 @@ synonym: "land plants" RELATED blast_name [] synonym: "plants" EXACT OMO:0003003 [] xref: GC_ID:1 is_a: NCBITaxon:131221 ! Streptophytina -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:32443 @@ -142017,7 +142062,6 @@ namespace: ncbi_taxonomy synonym: "teleost fishes" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:41665 ! Neopterygii -property_value: has_rank NCBITaxon:infraclass [Term] id: NCBITaxon:32523 @@ -142026,7 +142070,6 @@ namespace: ncbi_taxonomy synonym: "tetrapods" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:1338369 ! Dipnotetrapodomorpha -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:32524 @@ -142035,7 +142078,6 @@ namespace: ncbi_taxonomy synonym: "amniotes" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:32523 ! Tetrapoda -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:32525 @@ -142044,7 +142086,6 @@ namespace: ncbi_taxonomy synonym: "Theria" EXACT scientific_name [] xref: GC_ID:1 is_a: NCBITaxon:40674 ! Mammalia -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:32561 @@ -142054,7 +142095,6 @@ synonym: "Diapsida" RELATED synonym [] synonym: "diapsids" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:8457 ! Sauropsida -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:33083 @@ -142070,7 +142110,6 @@ xref: PMID:11062127 xref: PMID:29367151 xref: PMID:9342353 is_a: NCBITaxon:142796 ! Eumycetozoa -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:33090 @@ -142086,7 +142125,6 @@ xref: GC_ID:1 xref: PMID:16248873 xref: PMID:30257078 is_a: NCBITaxon:2759 ! Eukaryota -property_value: has_rank NCBITaxon:kingdom [Term] id: NCBITaxon:3312 @@ -142095,7 +142133,6 @@ namespace: ncbi_taxonomy synonym: "conifers" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:1437180 ! Acrogymnospermae -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:33154 @@ -142105,7 +142142,6 @@ synonym: "Fungi/Metazoa group" RELATED synonym [] synonym: "opisthokonts" RELATED synonym [] xref: GC_ID:1 is_a: NCBITaxon:2759 ! Eukaryota -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:33208 @@ -142117,7 +142153,6 @@ synonym: "metazoans" EXACT genbank_common_name [] synonym: "multicellular animals" EXACT OMO:0003003 [] xref: GC_ID:1 is_a: NCBITaxon:33154 ! Opisthokonta -property_value: has_rank NCBITaxon:kingdom [Term] id: NCBITaxon:33213 @@ -142125,7 +142160,6 @@ name: Bilateria namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:6072 ! Eumetazoa -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:33317 @@ -142133,7 +142167,6 @@ name: Protostomia namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:33213 ! Bilateria -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:33511 @@ -142142,7 +142175,6 @@ namespace: ncbi_taxonomy synonym: "deuterostomes" EXACT OMO:0003003 [] xref: GC_ID:1 is_a: NCBITaxon:33213 ! Bilateria -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:33554 @@ -142152,7 +142184,6 @@ synonym: "carnivores" EXACT genbank_common_name [] synonym: "carnivores" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:314145 ! Laurasiatheria -property_value: has_rank NCBITaxon:order [Term] id: NCBITaxon:33630 @@ -142161,7 +142192,6 @@ namespace: ncbi_taxonomy synonym: "alveolates" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:2698737 ! Sar -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:33682 @@ -142170,7 +142200,6 @@ namespace: ncbi_taxonomy synonym: "Euglenozoans" RELATED synonym [] xref: GC_ID:1 is_a: NCBITaxon:2611352 ! Discoba -property_value: has_rank NCBITaxon:phylum [Term] id: NCBITaxon:3372 @@ -142180,7 +142209,6 @@ synonym: "Chlamydospermopsida" RELATED synonym [] synonym: "Gneticae" RELATED synonym [] xref: GC_ID:1 is_a: NCBITaxon:1437180 ! Acrogymnospermae -property_value: has_rank NCBITaxon:class [Term] id: NCBITaxon:337687 @@ -142190,7 +142218,6 @@ xref: GC_ID:1 xref: PMID:15019624 xref: PMID:15371245 is_a: NCBITaxon:1963758 ! Myomorpha -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:3378 @@ -142198,7 +142225,6 @@ name: Gnetales namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:1445966 ! Gnetidae -property_value: has_rank NCBITaxon:order [Term] id: NCBITaxon:338152 @@ -142206,7 +142232,6 @@ name: Felinae namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:9681 ! Felidae -property_value: has_rank NCBITaxon:subfamily [Term] id: NCBITaxon:3398 @@ -142220,7 +142245,6 @@ synonym: "Magnoliophyta" RELATED synonym [] xref: GC_ID:1 xref: PMID:25249442 is_a: NCBITaxon:58024 ! Spermatophyta -property_value: has_rank NCBITaxon:class [Term] id: NCBITaxon:34346 @@ -142228,7 +142252,6 @@ name: Schizosaccharomycetales namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:147554 ! Schizosaccharomycetes -property_value: has_rank NCBITaxon:order [Term] id: NCBITaxon:35493 @@ -142236,7 +142259,6 @@ name: Streptophyta namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:33090 ! Viridiplantae -property_value: has_rank NCBITaxon:phylum [Term] id: NCBITaxon:376913 @@ -142244,7 +142266,6 @@ name: Haplorrhini namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:9443 ! Primates -property_value: has_rank NCBITaxon:suborder [Term] id: NCBITaxon:379583 @@ -142252,7 +142273,6 @@ name: Feliformia namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:33554 ! Carnivora -property_value: has_rank NCBITaxon:suborder [Term] id: NCBITaxon:38254 @@ -142264,7 +142284,6 @@ synonym: "Glaucophyceae" RELATED synonym [] synonym: "Glaucophyta" RELATED synonym [] xref: GC_ID:1 is_a: NCBITaxon:2759 ! Eukaryota -property_value: has_rank NCBITaxon:class [Term] id: NCBITaxon:39107 @@ -142273,7 +142292,6 @@ namespace: ncbi_taxonomy alt_id: NCBITaxon:109679 xref: GC_ID:1 is_a: NCBITaxon:10066 ! Muridae -property_value: has_rank NCBITaxon:subfamily [Term] id: NCBITaxon:40674 @@ -142283,7 +142301,6 @@ synonym: "mammals" EXACT genbank_common_name [] synonym: "mammals" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:32524 ! Amniota -property_value: has_rank NCBITaxon:class [Term] id: NCBITaxon:41665 @@ -142292,7 +142309,6 @@ namespace: ncbi_taxonomy synonym: "Neopterygi" RELATED synonym [] xref: GC_ID:1 is_a: NCBITaxon:186623 ! Actinopteri -property_value: has_rank NCBITaxon:subclass [Term] id: NCBITaxon:436486 @@ -142302,7 +142318,6 @@ synonym: "dinosaur" EXACT OMO:0003003 [] synonym: "dinosaurs" EXACT OMO:0003003 [] xref: GC_ID:1 is_a: NCBITaxon:8492 ! Archosauria -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:436489 @@ -142310,7 +142325,6 @@ name: Saurischia namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:436486 ! Dinosauria -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:436491 @@ -142318,7 +142332,6 @@ name: Theropoda namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:436489 ! Saurischia -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:436492 @@ -142326,7 +142339,6 @@ name: Coelurosauria namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:436491 ! Theropoda -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:451864 @@ -142339,7 +142351,6 @@ xref: PMID:17010206 xref: PMID:17051209 xref: PMID:17572334 is_a: NCBITaxon:4751 ! Fungi -property_value: has_rank NCBITaxon:subkingdom [Term] id: NCBITaxon:451866 @@ -142347,7 +142358,6 @@ name: Taphrinomycotina namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:4890 ! Ascomycota -property_value: has_rank NCBITaxon:subphylum [Term] id: NCBITaxon:4751 @@ -142359,7 +142369,6 @@ xref: GC_ID:1 xref: PMID:11062127 xref: PMID:12684019 is_a: NCBITaxon:33154 ! Opisthokonta -property_value: has_rank NCBITaxon:kingdom [Term] id: NCBITaxon:4890 @@ -142371,7 +142380,6 @@ synonym: "sac fungi" EXACT OMO:0003003 [] xref: GC_ID:1 xref: PMID:17572334 is_a: NCBITaxon:451864 ! Dikarya -property_value: has_rank NCBITaxon:phylum [Term] id: NCBITaxon:4891 @@ -142380,7 +142388,6 @@ namespace: ncbi_taxonomy synonym: "Hemiascomycetes" RELATED synonym [] xref: GC_ID:1 is_a: NCBITaxon:147537 ! Saccharomycotina -property_value: has_rank NCBITaxon:class [Term] id: NCBITaxon:4892 @@ -142390,7 +142397,6 @@ synonym: "budding yeasts" RELATED blast_name [] synonym: "Endomycetales" RELATED synonym [] xref: GC_ID:1 is_a: NCBITaxon:4891 ! Saccharomycetes -property_value: has_rank NCBITaxon:order [Term] id: NCBITaxon:4893 @@ -142400,7 +142406,6 @@ alt_id: NCBITaxon:221665 alt_id: NCBITaxon:44280 xref: GC_ID:1 is_a: NCBITaxon:4892 ! Saccharomycetales -property_value: has_rank NCBITaxon:family [Term] id: NCBITaxon:4894 @@ -142410,7 +142415,6 @@ synonym: "fission yeasts" EXACT genbank_common_name [] synonym: "Schizosaccharomycetoideae" RELATED synonym [] xref: GC_ID:1 is_a: NCBITaxon:34346 ! Schizosaccharomycetales -property_value: has_rank NCBITaxon:family [Term] id: NCBITaxon:4895 @@ -142418,7 +142422,6 @@ name: Schizosaccharomyces namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:4894 ! Schizosaccharomycetaceae -property_value: has_rank NCBITaxon:genus [Term] id: NCBITaxon:4896 @@ -142429,7 +142432,6 @@ synonym: "fission yeast" EXACT genbank_common_name [] synonym: "Schizosaccharomyces malidevorans" RELATED synonym [] xref: GC_ID:1 is_a: NCBITaxon:4895 ! Schizosaccharomyces -property_value: has_rank NCBITaxon:species [Term] id: NCBITaxon:4930 @@ -142439,7 +142441,6 @@ alt_id: NCBITaxon:36915 synonym: "Pachytichospora" RELATED synonym [] xref: GC_ID:1 is_a: NCBITaxon:4893 ! Saccharomycetaceae -property_value: has_rank NCBITaxon:genus [Term] id: NCBITaxon:4932 @@ -142458,7 +142459,6 @@ synonym: "Saccharomyces oviformis" RELATED synonym [] synonym: "Saccharomyces uvarum var. melibiosus" RELATED synonym [] xref: GC_ID:1 is_a: NCBITaxon:4930 ! Saccharomyces -property_value: has_rank NCBITaxon:species [Term] id: NCBITaxon:50557 @@ -142468,7 +142468,6 @@ synonym: "insects" RELATED blast_name [] synonym: "true insects" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:6960 ! Hexapoda -property_value: has_rank NCBITaxon:class [Term] id: NCBITaxon:554915 @@ -142478,7 +142477,6 @@ xref: GC_ID:1 xref: PMID:23020233 xref: PMID:30257078 is_a: NCBITaxon:2759 ! Eukaryota -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:55879 @@ -142486,7 +142484,6 @@ name: Rhabditoidea namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:2301119 ! Rhabditomorpha -property_value: has_rank NCBITaxon:superfamily [Term] id: NCBITaxon:55885 @@ -142494,7 +142491,6 @@ name: Peloderinae namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:6243 ! Rhabditidae -property_value: has_rank NCBITaxon:subfamily [Term] id: NCBITaxon:5782 @@ -142504,7 +142500,6 @@ synonym: "Hyalostilbum" RELATED synonym [] xref: GC_ID:1 xref: PMID:29367151 is_a: NCBITaxon:2058185 ! Dictyosteliaceae -property_value: has_rank NCBITaxon:genus [Term] id: NCBITaxon:58023 @@ -142514,7 +142509,6 @@ synonym: "vascular plants" EXACT OMO:0003003 [] synonym: "vascular plants" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:3193 ! Embryophyta -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:58024 @@ -142524,7 +142518,6 @@ synonym: "seed plants" EXACT OMO:0003003 [] synonym: "seed plants" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:78536 ! Euphyllophyta -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:6072 @@ -142532,7 +142525,6 @@ name: Eumetazoa namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:33208 ! Metazoa -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:6073 @@ -142544,7 +142536,6 @@ synonym: "Coelenterata" RELATED in_part [] synonym: "coelenterates" EXACT OMO:0003003 [] xref: GC_ID:1 is_a: NCBITaxon:6072 ! Eumetazoa -property_value: has_rank NCBITaxon:phylum [Term] id: NCBITaxon:6157 @@ -142555,7 +142546,6 @@ synonym: "flatworms" EXACT genbank_common_name [] synonym: "flatworms" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:1206795 ! Lophotrochozoa -property_value: has_rank NCBITaxon:phylum [Term] id: NCBITaxon:6231 @@ -142569,7 +142559,6 @@ synonym: "roundworm" EXACT OMO:0003003 [] synonym: "roundworms" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:1206794 ! Ecdysozoa -property_value: has_rank NCBITaxon:phylum [Term] id: NCBITaxon:6236 @@ -142580,7 +142569,6 @@ alt_id: NCBITaxon:6308 synonym: "Strongylida" RELATED synonym [] xref: GC_ID:1 is_a: NCBITaxon:119089 ! Chromadorea -property_value: has_rank NCBITaxon:order [Term] id: NCBITaxon:6237 @@ -142588,7 +142576,6 @@ name: Caenorhabditis namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:55885 ! Peloderinae -property_value: has_rank NCBITaxon:genus [Term] id: NCBITaxon:6243 @@ -142597,7 +142584,6 @@ namespace: ncbi_taxonomy alt_id: NCBITaxon:54603 xref: GC_ID:1 is_a: NCBITaxon:55879 ! Rhabditoidea -property_value: has_rank NCBITaxon:family [Term] id: NCBITaxon:6656 @@ -142607,7 +142593,6 @@ synonym: "arthropods" EXACT genbank_common_name [] synonym: "arthropods" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:88770 ! Panarthropoda -property_value: has_rank NCBITaxon:phylum [Term] id: NCBITaxon:6960 @@ -142620,7 +142605,6 @@ synonym: "Tracheata" RELATED in_part [] synonym: "Uniramia" RELATED in_part [] xref: GC_ID:1 is_a: NCBITaxon:197562 ! Pancrustacea -property_value: has_rank NCBITaxon:subphylum [Term] id: NCBITaxon:716545 @@ -142628,7 +142612,6 @@ name: saccharomyceta namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:4890 ! Ascomycota -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:7586 @@ -142638,7 +142621,6 @@ synonym: "echinoderms" EXACT genbank_common_name [] synonym: "echinoderms" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:33511 ! Deuterostomia -property_value: has_rank NCBITaxon:phylum [Term] id: NCBITaxon:7711 @@ -142648,7 +142630,6 @@ synonym: "chordates" EXACT genbank_common_name [] synonym: "chordates" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:33511 ! Deuterostomia -property_value: has_rank NCBITaxon:phylum [Term] id: NCBITaxon:7742 @@ -142659,7 +142640,6 @@ synonym: "vertebrates" EXACT genbank_common_name [] synonym: "vertebrates" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:89593 ! Craniata -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:7776 @@ -142669,7 +142649,6 @@ synonym: "Gnathostomata" EXACT scientific_name [] synonym: "jawed vertebrates" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:7742 ! Vertebrata -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:78536 @@ -142678,7 +142657,6 @@ namespace: ncbi_taxonomy synonym: "euphyllophytes" EXACT equivalent_name [] xref: GC_ID:1 is_a: NCBITaxon:58023 ! Tracheophyta -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:7898 @@ -142692,7 +142670,6 @@ synonym: "Osteichthyes" RELATED in_part [] synonym: "ray-finned fishes" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:117571 ! Euteleostomi -property_value: has_rank NCBITaxon:superclass [Term] id: NCBITaxon:8287 @@ -142700,7 +142677,6 @@ name: Sarcopterygii namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:117571 ! Euteleostomi -property_value: has_rank NCBITaxon:superclass [Term] id: NCBITaxon:8457 @@ -142709,7 +142685,6 @@ namespace: ncbi_taxonomy synonym: "sauropsids" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:32524 ! Amniota -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:8492 @@ -142717,7 +142692,6 @@ name: Archosauria namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:1329799 ! Archelosauria -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:862507 @@ -142726,7 +142700,6 @@ namespace: ncbi_taxonomy synonym: "Mus" EXACT scientific_name [] xref: GC_ID:1 is_a: NCBITaxon:10088 ! Mus -property_value: has_rank NCBITaxon:subgenus [Term] id: NCBITaxon:8782 @@ -142737,7 +142710,6 @@ synonym: "birds" EXACT genbank_common_name [] synonym: "birds" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:436492 ! Coelurosauria -property_value: has_rank NCBITaxon:class [Term] id: NCBITaxon:88770 @@ -142745,7 +142717,6 @@ name: Panarthropoda namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:1206794 ! Ecdysozoa -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:89593 @@ -142754,7 +142725,6 @@ namespace: ncbi_taxonomy synonym: "Craniata" EXACT scientific_name [] xref: GC_ID:1 is_a: NCBITaxon:7711 ! Chordata -property_value: has_rank NCBITaxon:subphylum [Term] id: NCBITaxon:9347 @@ -142767,7 +142737,6 @@ synonym: "placentals" EXACT genbank_common_name [] synonym: "placentals" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:32525 ! Theria -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:9443 @@ -142778,7 +142747,6 @@ synonym: "primate" EXACT equivalent_name [] synonym: "primates" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:314146 ! Euarchontoglires -property_value: has_rank NCBITaxon:order [Term] id: NCBITaxon:9479 @@ -142789,7 +142757,6 @@ synonym: "monkeys" EXACT OMO:0003003 [] synonym: "New World monkeys" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:314293 ! Simiiformes -property_value: has_rank NCBITaxon:parvorder [Term] id: NCBITaxon:9480 @@ -142800,7 +142767,6 @@ synonym: "Callitrichidae" RELATED synonym [] synonym: "marmosets and tamarins" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:9498 ! Cebidae -property_value: has_rank NCBITaxon:subfamily [Term] id: NCBITaxon:9481 @@ -142810,7 +142776,6 @@ alt_id: NCBITaxon:9492 synonym: "Callithrix" EXACT scientific_name [] xref: GC_ID:1 is_a: NCBITaxon:9480 ! Callitrichinae -property_value: has_rank NCBITaxon:genus [Term] id: NCBITaxon:9483 @@ -142824,7 +142789,6 @@ synonym: "white ear-tufted marmoset" EXACT OMO:0003003 [] synonym: "white-tufted-ear marmoset" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:1965096 ! Callithrix -property_value: has_rank NCBITaxon:species [Term] id: NCBITaxon:9498 @@ -142832,7 +142796,6 @@ name: Cebidae namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:9479 ! Platyrrhini -property_value: has_rank NCBITaxon:family [Term] id: NCBITaxon:9526 @@ -142840,7 +142803,6 @@ name: Catarrhini namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:314293 ! Simiiformes -property_value: has_rank NCBITaxon:parvorder [Term] id: NCBITaxon:9604 @@ -142850,7 +142812,6 @@ synonym: "great apes" EXACT genbank_common_name [] synonym: "Pongidae" RELATED synonym [] xref: GC_ID:1 is_a: NCBITaxon:314295 ! Hominoidea -property_value: has_rank NCBITaxon:family [Term] id: NCBITaxon:9605 @@ -142859,7 +142820,6 @@ namespace: ncbi_taxonomy synonym: "humans" EXACT OMO:0003003 [] xref: GC_ID:1 is_a: NCBITaxon:207598 ! Homininae -property_value: has_rank NCBITaxon:genus [Term] id: NCBITaxon:9606 @@ -142868,7 +142828,6 @@ namespace: ncbi_taxonomy synonym: "human" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:9605 ! Homo -property_value: has_rank NCBITaxon:species [Term] id: NCBITaxon:9681 @@ -142877,7 +142836,6 @@ namespace: ncbi_taxonomy synonym: "cat family" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:379583 ! Feliformia -property_value: has_rank NCBITaxon:family [Term] id: NCBITaxon:9682 @@ -142885,7 +142843,6 @@ name: Felis namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:338152 ! Felinae -property_value: has_rank NCBITaxon:genus [Term] id: NCBITaxon:9685 @@ -142902,7 +142859,6 @@ xref: PMID:17600185 xref: PMID:8581300 xref: PMID:8603894 is_a: NCBITaxon:9682 ! Felis -property_value: has_rank NCBITaxon:species [Term] id: NCBITaxon:9787 @@ -142912,7 +142868,6 @@ synonym: "odd-toed ungulates" EXACT genbank_common_name [] synonym: "odd-toed ungulates" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:314145 ! Laurasiatheria -property_value: has_rank NCBITaxon:order [Term] id: NCBITaxon:9788 @@ -142921,7 +142876,6 @@ namespace: ncbi_taxonomy synonym: "horses" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:9787 ! Perissodactyla -property_value: has_rank NCBITaxon:family [Term] id: NCBITaxon:9789 @@ -142949,7 +142903,6 @@ synonym: "Hippotigris" RELATED synonym [] synonym: "Sussemionus" RELATED synonym [] xref: GC_ID:1 is_a: NCBITaxon:9788 ! Equidae -property_value: has_rank NCBITaxon:genus [Term] id: NCBITaxon:9989 @@ -142959,7 +142912,6 @@ synonym: "rodent" EXACT genbank_common_name [] synonym: "rodents" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:314147 ! Glires -property_value: has_rank NCBITaxon:order [Term] id: PATO:0000001 @@ -143090,7 +143042,6 @@ subset: value_slim synonym: "ramified" EXACT [] synonym: "ramiform" EXACT [] is_a: PATO:0002009 ! branchiness -property_value: RO:0002604 PATO:0000414 [Term] id: PATO:0000404 @@ -143107,7 +143058,6 @@ synonym: "helicoidal" RELATED [] synonym: "helix-shaped" RELATED [] synonym: "spiral" EXACT [] is_a: PATO:0001794 ! coiling -property_value: RO:0002604 PATO:0000415 [Term] id: PATO:0000405 @@ -143155,7 +143105,6 @@ synonym: "atypia" RELATED [] synonym: "atypical" RELATED [] synonym: "defective" RELATED [] is_a: PATO:0000069 ! deviation (from_normal) -property_value: RO:0002604 PATO:0000461 [Term] id: PATO:0000461 @@ -143167,7 +143116,6 @@ subset: mpath_slim subset: value_slim synonym: "average" RELATED [] is_a: PATO:0000068 ! qualitative -property_value: RO:0002604 PATO:0000460 [Term] id: PATO:0000586 @@ -143185,7 +143133,6 @@ is_a: PATO:0000117 ! size is_a: PATO:0002305 ! increased object quality intersection_of: PATO:0000117 ! size intersection_of: RO:0015007 PATO:0000461 ! increased in magnitude relative to normal -property_value: RO:0002604 PATO:0000587 [Term] id: PATO:0000587 @@ -143202,7 +143149,6 @@ is_a: PATO:0000117 ! size is_a: PATO:0002303 ! decreased object quality intersection_of: PATO:0000117 ! size intersection_of: RO:0015008 PATO:0000461 ! decreased in magnitude relative to normal -property_value: RO:0002604 PATO:0000586 [Term] id: PATO:0000588 @@ -143222,7 +143168,6 @@ subset: value_slim synonym: "blocked" RELATED [] is_a: PATO:0000136 ! closure disjoint_from: PATO:0000610 ! open -property_value: RO:0002604 PATO:0000610 [Term] id: PATO:0000610 @@ -143231,7 +143176,6 @@ namespace: quality def: "A morphological quality inhering in a bearer by virtue of the bearer's affording unobstructed passage or view." [answers.com:answers.com] subset: value_slim is_a: PATO:0000136 ! closure -property_value: RO:0002604 PATO:0000608 [Term] id: PATO:0000947 @@ -143267,7 +143211,6 @@ synonym: "clouding" RELATED [] synonym: "cloudy" RELATED [] synonym: "non-transparent" EXACT [] is_a: PATO:0000957 ! opacity -property_value: RO:0002604 PATO:0000964 [Term] id: PATO:0000964 @@ -143279,7 +143222,6 @@ subset: value_slim synonym: "clear" EXACT [] synonym: "hyaline" EXACT [] is_a: PATO:0000957 ! opacity -property_value: RO:0002604 PATO:0000963 [Term] id: PATO:0000992 @@ -143330,7 +143272,6 @@ subset: disposition_slim subset: mpath_slim subset: value_slim is_a: PATO:0001031 ! elasticity -property_value: RO:0002604 PATO:0001172 [Term] id: PATO:0001185 @@ -143558,7 +143499,6 @@ def: "A quality inhering in a bearer by virtue of the bearer's lacking complete subset: value_slim synonym: "underdeveloped" RELATED [] is_a: PATO:0000261 ! maturity -property_value: RO:0002604 PATO:0001701 [Term] id: PATO:0001543 @@ -143578,7 +143518,6 @@ subset: disposition_slim subset: value_slim synonym: "bendy" EXACT [] is_a: PATO:0001543 ! flexibility -property_value: RO:0002604 PATO:0001545 [Term] id: PATO:0001546 @@ -143629,7 +143568,6 @@ is_a: PATO:0001690 ! contractile is_a: PATO:0002305 ! increased object quality intersection_of: PATO:0001690 ! contractile intersection_of: RO:0015007 PATO:0000461 ! increased in magnitude relative to normal -property_value: RO:0002604 PATO:0001581 [Term] id: PATO:0001581 @@ -143643,7 +143581,6 @@ is_a: PATO:0001690 ! contractile is_a: PATO:0002303 ! decreased object quality intersection_of: PATO:0001690 ! contractile intersection_of: RO:0015008 PATO:0000461 ! decreased in magnitude relative to normal -property_value: RO:0002604 PATO:0001580 [Term] id: PATO:0001591 @@ -143663,7 +143600,6 @@ is_a: PATO:0000050 ! life span is_a: PATO:0002305 ! increased object quality intersection_of: PATO:0000050 ! life span intersection_of: RO:0015007 PATO:0000461 ! increased in magnitude relative to normal -property_value: RO:0002604 PATO:0001604 [Term] id: PATO:0001604 @@ -143675,7 +143611,6 @@ is_a: PATO:0000050 ! life span is_a: PATO:0002303 ! decreased object quality intersection_of: PATO:0000050 ! life span intersection_of: RO:0015008 PATO:0000461 ! decreased in magnitude relative to normal -property_value: RO:0002604 PATO:0001603 [Term] id: PATO:0001690 @@ -143686,7 +143621,6 @@ comment: This refers to the disposition of the bearer. subset: disposition_slim subset: value_slim is_a: PATO:0001579 ! contractility -property_value: RO:0002604 PATO:0001691 [Term] id: PATO:0001693 @@ -143700,7 +143634,6 @@ is_a: PATO:0000998 ! viscous is_a: PATO:0002305 ! increased object quality intersection_of: PATO:0000998 ! viscous intersection_of: RO:0015007 PATO:0000461 ! increased in magnitude relative to normal -property_value: RO:0002604 PATO:0001694 [Term] id: PATO:0001694 @@ -143714,7 +143647,6 @@ is_a: PATO:0000998 ! viscous is_a: PATO:0002303 ! decreased object quality intersection_of: PATO:0000998 ! viscous intersection_of: RO:0015008 PATO:0000461 ! decreased in magnitude relative to normal -property_value: RO:0002604 PATO:0001693 [Term] id: PATO:0001735 @@ -143755,7 +143687,6 @@ is_a: PATO:0001544 ! flexible is_a: PATO:0002305 ! increased object quality intersection_of: PATO:0001544 ! flexible intersection_of: RO:0015007 PATO:0000461 ! increased in magnitude relative to normal -property_value: RO:0002604 PATO:0001777 [Term] id: PATO:0001777 @@ -143769,7 +143700,6 @@ is_a: PATO:0001544 ! flexible is_a: PATO:0002303 ! decreased object quality intersection_of: PATO:0001544 ! flexible intersection_of: RO:0015008 PATO:0000461 ! decreased in magnitude relative to normal -property_value: RO:0002604 PATO:0001776 [Term] id: PATO:0001794 @@ -143791,7 +143721,6 @@ is_a: PATO:0000404 ! coiled is_a: PATO:0002305 ! increased object quality intersection_of: PATO:0000404 ! coiled intersection_of: RO:0015007 PATO:0000461 ! increased in magnitude relative to normal -property_value: RO:0002604 PATO:0001796 [Term] id: PATO:0001796 @@ -143805,7 +143734,6 @@ is_a: PATO:0000404 ! coiled is_a: PATO:0002303 ! decreased object quality intersection_of: PATO:0000404 ! coiled intersection_of: RO:0015008 PATO:0000461 ! decreased in magnitude relative to normal -property_value: RO:0002604 PATO:0001795 [Term] id: PATO:0001857 @@ -143815,7 +143743,6 @@ def: "A shape quality in a bearer by virtue of the bearer's curving inward." [Wo subset: cell_quality subset: value_slim is_a: PATO:0002005 ! concavity -property_value: RO:0002604 PATO:0001355 [Term] id: PATO:0001870 @@ -143961,7 +143888,6 @@ subset: attribute_slim xref: Image:http\://upload.wikimedia.org/wikipedia/commons/0/06/Convex_polygon_illustration1.png is_a: PATO:0002266 ! 3-D shape relationship: RO:0015011 PATO:0002006 ! has cross section 2-D shape -property_value: RO:0002604 PATO:0002008 [Term] id: PATO:0002008 @@ -143972,7 +143898,6 @@ subset: attribute_slim xref: Image:http\://en.wikipedia.org/wiki/Image\:Convex_polygon_illustration2.png is_a: PATO:0002266 ! 3-D shape relationship: has_part PATO:0001857 ! concave -property_value: RO:0002604 PATO:0002007 [Term] id: PATO:0002009 @@ -144009,7 +143934,6 @@ namespace: quality def: "A concave quality inhering in a bearer by virtue of the bearer's curving inward on both sides or surfaces." [PATOC:GVG] subset: value_slim is_a: PATO:0001857 ! concave -property_value: RO:0002604 PATO:0002040 [Term] id: PATO:0002045 @@ -144021,7 +143945,7 @@ synonym: "dendriform" EXACT [] synonym: "dendroid" EXACT [] synonym: "dendroidal" EXACT [] is_a: PATO:0000402 ! branched -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-02-15T08:11:41Z [Term] @@ -144031,7 +143955,7 @@ namespace: quality def: "A quality inhering in a bearer by virtue of the bearer's having an empty space or cavity within." [url:http\://www.merriam-webster.com/dictionary/hollow] subset: value_slim is_a: PATO:0002014 ! structure, cavities -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-09-18T02:19:20Z [Term] @@ -144043,7 +143967,7 @@ subset: disposition_slim subset: mpath_slim subset: value_slim is_a: PATO:0070045 ! anatomical histological quality -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-10-05T12:05:23Z [Term] @@ -144055,7 +143979,7 @@ subset: disposition_slim subset: mpath_slim subset: value_slim is_a: PATO:0002011 ! neoplastic -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-10-05T12:50:22Z [Term] @@ -144066,7 +143990,7 @@ def: "A quality inhering in a bearer by virtue of the bearer's processing the fo subset: mpath_slim subset: value_slim is_a: PATO:0000141 ! structure -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-10-06T04:37:14Z [Term] @@ -144076,7 +144000,7 @@ namespace: quality def: "A quality inhering in a bearer by virtue of its constitution." [PATOC:GVG] subset: attribute_slim is_a: PATO:0001018 ! physical quality -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-03-15T04:35:27Z [Term] @@ -144086,7 +144010,7 @@ namespace: quality def: "A cylindrical shape quality inhering in a bearer by virtue of the bearer's being imperfectly cylindrical or approximately cylindrical." [url:http\://www.thefreedictionary.com/Subcylindrical] subset: value_slim is_a: PATO:0001873 ! cylindrical -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-07-13T04:22:30Z [Term] @@ -144098,7 +144022,7 @@ comment: Becoming flat but not necessarily completely flat. subset: value_slim synonym: "compressed" RELATED [] is_a: PATO:0001591 ! curvature -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-08-16T03:59:34Z [Term] @@ -144110,7 +144034,7 @@ subset: value_slim synonym: "channeled" RELATED [] synonym: "creased" RELATED [] is_a: PATO:0000150 ! texture -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-09-01T10:27:48Z [Term] @@ -144119,7 +144043,7 @@ name: 3-D shape namespace: quality def: "A shape that inheres in a 3 dimensional entity." [PATOC:OREGON] is_a: PATO:0000052 ! shape -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-10-05T12:31:16Z [Term] @@ -144132,8 +144056,7 @@ is_a: PATO:0001171 ! elastic is_a: PATO:0002305 ! increased object quality intersection_of: PATO:0001171 ! elastic intersection_of: RO:0015007 PATO:0000461 ! increased in magnitude relative to normal -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X -property_value: RO:0002604 PATO:0002288 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-03-30T11:50:21Z [Term] @@ -144146,8 +144069,7 @@ is_a: PATO:0001171 ! elastic is_a: PATO:0002303 ! decreased object quality intersection_of: PATO:0001171 ! elastic intersection_of: RO:0015008 PATO:0000461 ! decreased in magnitude relative to normal -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X -property_value: RO:0002604 PATO:0002287 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-03-30T11:50:39Z [Term] @@ -144160,7 +144082,7 @@ synonym: "tube-shaped" EXACT [] synonym: "tubulate" EXACT [] is_a: PATO:0001873 ! cylindrical is_a: PATO:0002078 ! hollow -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-06-08T06:33:50Z [Term] @@ -144171,9 +144093,8 @@ def: "A quality that has a value that is increased compared to normal or average is_a: PATO:0000069 ! deviation (from_normal) intersection_of: PATO:0000001 ! quality intersection_of: RO:0015007 PATO:0000461 ! increased in magnitude relative to normal -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X relationship: RO:0015007 PATO:0000461 ! increased in magnitude relative to normal -property_value: RO:0002604 PATO:0002301 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-06-16T06:39:43Z [Term] @@ -144184,9 +144105,8 @@ def: "A quality that has a value that is decreased compared to normal or average is_a: PATO:0000069 ! deviation (from_normal) intersection_of: PATO:0000001 ! quality intersection_of: RO:0015008 PATO:0000461 ! decreased in magnitude relative to normal -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X relationship: RO:0015008 PATO:0000461 ! decreased in magnitude relative to normal -property_value: RO:0002604 PATO:0002300 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-06-16T06:40:15Z [Term] @@ -144198,8 +144118,7 @@ is_a: PATO:0001241 ! physical object quality is_a: PATO:0002301 ! decreased quality intersection_of: PATO:0001241 ! physical object quality intersection_of: RO:0015008 PATO:0000461 ! decreased in magnitude relative to normal -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X -property_value: RO:0002604 PATO:0002305 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-06-16T06:51:54Z [Term] @@ -144211,8 +144130,7 @@ is_a: PATO:0001241 ! physical object quality is_a: PATO:0002300 ! increased quality intersection_of: PATO:0001241 ! physical object quality intersection_of: RO:0015007 PATO:0000461 ! increased in magnitude relative to normal -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X -property_value: RO:0002604 PATO:0002303 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-06-16T06:54:01Z [Term] @@ -144223,7 +144141,7 @@ def: "A convex 3-D shape quality inhering in a bearer by virtue of the bearer's comment: Note that a fiber shaped object may take any circuitous or straight path through space (think of a length of string or rope). subset: value_slim is_a: PATO:0002226 ! subcylindrical -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-09-09T04:50:10Z [Term] @@ -144233,7 +144151,7 @@ namespace: quality def: "A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt" [wiktionary:superellipse] synonym: "Lamé curve" EXACT [] is_a: PATO:0002006 ! 2-D shape -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-10-12T12:45:16Z [Term] @@ -144246,7 +144164,7 @@ subset: mpath_slim subset: value_slim synonym: "eosinophilic" EXACT [] is_a: PATO:0070045 ! anatomical histological quality -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2012-12-17T03:01:19Z [Term] @@ -144257,7 +144175,7 @@ def: "Having both hydrophilic and hydrophobic (or lipophilic) groups." [wikipedi subset: mpath_slim subset: value_slim is_a: PATO:0070045 ! anatomical histological quality -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2012-12-17T03:04:39Z [Term] @@ -144269,7 +144187,7 @@ comment: Acinus is Latin for berry. subset: mpath_slim subset: value_slim is_a: PATO:0000141 ! structure -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2012-12-17T03:11:10Z [Term] @@ -144279,7 +144197,7 @@ namespace: quality def: "A composition quality inhering in a bearer by virtue of the bearer's being composed of or possessing inorganic material." [PATOC:WC] subset: value_slim is_a: PATO:0000025 ! composition -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2013-01-29T11:03:49Z [Term] @@ -144289,7 +144207,7 @@ namespace: quality def: "A composition quality inhering in an bearer by virtue of the bearer's consisting of collagen." [PATOC:WD] subset: value_slim is_a: PATO:0000025 ! composition -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2013-09-15T11:34:15Z [Term] @@ -144299,7 +144217,7 @@ namespace: quality def: "A structure quality inhering in a bearer by virtue of the bearer's being capable of swelling or stretching." [PATOC:WD] subset: value_slim is_a: PATO:0015008 ! distensibility -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2013-09-15T11:48:26Z [Term] @@ -144311,7 +144229,7 @@ subset: cell_quality subset: mpath_slim subset: value_slim is_a: PATO:0001410 ! striated -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2013-09-15T12:29:15Z [Term] @@ -144323,7 +144241,7 @@ subset: cell_quality subset: mpath_slim subset: value_slim is_a: PATO:0001410 ! striated -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2013-09-15T12:29:42Z [Term] @@ -144334,7 +144252,7 @@ def: "A nucleate quality inhering in a bearer by virtue of the bearer's having o subset: mpath_slim subset: value_slim is_a: PATO:0001404 ! nucleate quality -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2013-10-21T05:44:34Z [Term] @@ -144344,7 +144262,7 @@ namespace: quality def: "A surface feature shape quality inhering in a bearer by virtue of the bearer's not having undulating edges forming lobes." [PATOC:DOS] subset: value_slim is_a: PATO:0001925 ! surface feature shape -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2013-10-25T04:42:40Z [Term] @@ -144354,7 +144272,7 @@ namespace: quality def: "A composition quality inhering in a bearer by virtue of the bearer's consisting of keratin." [PATOC:EJS] subset: value_slim is_a: PATO:0000025 ! composition -relationship: dc-contributor https://orcid.org/0000-0002-9611-1279 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9611-1279 creation_date: 2014-02-04T12:38:14Z [Term] @@ -144363,7 +144281,7 @@ name: disconnected namespace: quality def: "A structural quality inhering in the bearer by virtue of the bearer consisting of multiple structures lacking any physical connection to each other." [GOC:dos] is_a: PATO:0000141 ! structure -relationship: dc-contributor https://orcid.org/0000-0002-7073-9172 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2014-12-12T08:43:17Z [Term] @@ -144373,7 +144291,7 @@ namespace: quality def: "A quality of a single cell inhering in the bearer by virtue of the bearer's size or shape or structure." [ORCID:0000-0002-7073-9172] comment: Use this term for morphologies that can *only* inhere in a cell, e.g. morphological qualities inhering in a cell by virtue of the presence, location or shape of one or more cell parts. is_a: PATO:0000051 ! morphology -relationship: dc-contributor https://orcid.org/0000-0002-7073-9172 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2021-01-23T11:31:53Z [Term] @@ -144411,8 +144329,8 @@ def: "A quality of an object that has a value that is normal or average." [] is_a: PATO:0001241 ! physical object quality intersection_of: PATO:0001241 ! physical object quality intersection_of: RO:0015010 PATO:0000461 ! has relative magnitude normal -relationship: dc-contributor https://orcid.org/0000-0001-9227-0670 relationship: RO:0015010 PATO:0000461 ! has relative magnitude normal +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9227-0670 creation_date: 2017-12-21T14:11:01Z [Term] @@ -144426,7 +144344,7 @@ is_a: PATO:0000404 ! coiled is_a: PATO:0045001 ! normal object quality intersection_of: PATO:0000404 ! coiled intersection_of: RO:0015010 PATO:0000461 ! has relative magnitude normal -relationship: dc-contributor https://orcid.org/0000-0001-9227-0670 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9227-0670 creation_date: 2017-12-22T14:16:43Z [Term] @@ -144440,7 +144358,7 @@ is_a: PATO:0001690 ! contractile is_a: PATO:0045001 ! normal object quality intersection_of: PATO:0001690 ! contractile intersection_of: RO:0015010 PATO:0000461 ! has relative magnitude normal -relationship: dc-contributor https://orcid.org/0000-0001-9227-0670 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9227-0670 creation_date: 2017-12-22T14:16:43Z [Term] @@ -144453,7 +144371,7 @@ is_a: PATO:0001171 ! elastic is_a: PATO:0045001 ! normal object quality intersection_of: PATO:0001171 ! elastic intersection_of: RO:0015010 PATO:0000461 ! has relative magnitude normal -relationship: dc-contributor https://orcid.org/0000-0001-9227-0670 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9227-0670 creation_date: 2017-12-22T14:16:43Z [Term] @@ -144467,7 +144385,7 @@ is_a: PATO:0001544 ! flexible is_a: PATO:0045001 ! normal object quality intersection_of: PATO:0001544 ! flexible intersection_of: RO:0015010 PATO:0000461 ! has relative magnitude normal -relationship: dc-contributor https://orcid.org/0000-0001-9227-0670 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9227-0670 creation_date: 2017-12-22T14:16:43Z [Term] @@ -144479,7 +144397,7 @@ is_a: PATO:0000050 ! life span is_a: PATO:0045001 ! normal object quality intersection_of: PATO:0000050 ! life span intersection_of: RO:0015010 PATO:0000461 ! has relative magnitude normal -relationship: dc-contributor https://orcid.org/0000-0001-9227-0670 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9227-0670 creation_date: 2017-12-22T14:16:43Z [Term] @@ -144492,7 +144410,7 @@ is_a: PATO:0000117 ! size is_a: PATO:0045001 ! normal object quality intersection_of: PATO:0000117 ! size intersection_of: RO:0015010 PATO:0000461 ! has relative magnitude normal -relationship: dc-contributor https://orcid.org/0000-0001-9227-0670 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9227-0670 creation_date: 2017-12-22T14:16:43Z [Term] @@ -144505,7 +144423,7 @@ is_a: PATO:0000998 ! viscous is_a: PATO:0045001 ! normal object quality intersection_of: PATO:0000998 ! viscous intersection_of: RO:0015010 PATO:0000461 ! has relative magnitude normal -relationship: dc-contributor https://orcid.org/0000-0001-9227-0670 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9227-0670 creation_date: 2017-12-22T14:16:43Z [Term] @@ -144515,7 +144433,7 @@ namespace: quality def: "A cell morphology that inheres in neurons which have a small round soma, a large number of short, smooth, or slightly beaded primary dendrites that give rise to only a few secondary branches, and a branched axon that establishes a dense axonal mesh with thin shafts." [PMID:17122314] xref: ilxtr:NeurogliaformPhenotype is_a: PATO:0070026 ! multipolar neuron morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070002 @@ -144526,7 +144444,7 @@ xref: ILX:0101123 xref: ilxtr:BasketPhenotype xref: nifext:3 is_a: PATO:0070026 ! multipolar neuron morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070003 @@ -144535,7 +144453,7 @@ namespace: quality def: "A basket cell morphology that inheres in neurons with axonal arbors composed of frequent, short, curvy axonal branches that tend to be near their somata and within the same layer." [PMID:11884355] xref: ilxtr:SmallBasketPhenotype is_a: PATO:0070002 ! basket cell morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070004 @@ -144544,7 +144462,7 @@ namespace: quality def: "A basket cell morphology that inheres in neurons that are large, and typically ascend to give rise to many long horizontally and vertically projecting axon collaterals that traverse neighboring columns and can extend through all cortical layers." [PMID:11884355] xref: ilxtr:LargeBasketPhenotype is_a: PATO:0070002 ! basket cell morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070005 @@ -144553,7 +144471,7 @@ namespace: quality def: "A basket cell morphology that inheres in neurons which have simpler dendritic arbors (compared to small or large basket cell morphology), and an axonal plexus of intermediate density, composed of a few long, smooth axonal branches." [PMID:11884355] xref: ilxtr:NestBasketPhenotype is_a: PATO:0070002 ! basket cell morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070006 @@ -144565,7 +144483,7 @@ xref: ILX:0101312 xref: ilxtr:BipolarPhenotype xref: nifext:2 is_a: PATO:0070027 ! bitufted dendrite cell morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070007 @@ -144574,7 +144492,7 @@ namespace: quality def: "A cell morphology that inheres in neurons which are large and non-spiny, with dendrites radiating in a multipolar or bitufted pattern, often favouring the descending side, and axons that ascend directly from the superficial side of the soma, and travel upward without branching." [doi:10.1016/b978-0-12-369497-3.10004-4] xref: ilxtr:MartinottiPhenotype is_a: PATO:0070026 ! multipolar neuron morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070008 @@ -144583,7 +144501,7 @@ namespace: quality def: "A Martinotti cell morphology that inheres in neurons which have axons that form a horizontal ramification, making it T-shaped." [doi:10.1016/b978-0-12-369497-3.10004-4] synonym: "'T-shaped' Martinotti morphology" EXACT [] is_a: PATO:0070007 ! Martinotti morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070009 @@ -144592,7 +144510,7 @@ namespace: quality def: "A Martinotti cell morphology that inheres in neurons which have axons that form a fan-like plexus." [doi:10.1016/b978-0-12-369497-3.10004-4] synonym: "'fanning-out' Martinotti morphology" EXACT [] is_a: PATO:0070007 ! Martinotti morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070010 @@ -144602,7 +144520,7 @@ def: "A cell morphology that inheres in neurons that have dendritic processes ra xref: ILX:0111036 xref: SAO:9271919883 is_a: PATO:0070026 ! multipolar neuron morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070011 @@ -144614,7 +144532,7 @@ xref: ILX:0102028 xref: ilxtr:ChandelierPhenotype xref: nifext:4 is_a: PATO:0010006 ! cell morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070012 @@ -144623,7 +144541,7 @@ namespace: quality def: "A cell morphology that inheres in neurons which have two clusters of primary dendrites that originate directly and extend from opposite ends of the soma, and axons that form a plexus which spreads widely. Compared to the narrow vertical axonal projection of bipolar morphology, and the 'horse-tail' axonal cluster of double boquet cells, bitufted morphology has wide horizontal axonal spans, and branching that occur close to the soma. Their vertical projection is also less extensive and crosses mostly to neighboring layers." [doi:10.1016/b978-0-12-369497-3.10004-4, PMID:15378039, PMID:18568015] xref: ilxtr:BituftedPhenotype is_a: PATO:0070027 ! bitufted dendrite cell morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070013 @@ -144632,7 +144550,7 @@ namespace: quality def: "A cell morphology that inheres in neurons which have spiny basal dendrites and resemble pyramidal cells but lose their apical dendrites as they mature. Their axons nearly always emerge from the descending side of the soma, but often recurve and ascend with arc-like collaterals." [doi:10.1016/b978-0-12-369497-3.10004-4] xref: ilxtr:SpinyStellatePhenotype is_a: PATO:0070026 ! multipolar neuron morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070015 @@ -144642,7 +144560,7 @@ def: "A cell morphology that inheres in neurons which have a pyramidal shaped so xref: ILX:0109553 xref: SAO:1465673360 is_a: PATO:0070026 ! multipolar neuron morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070016 @@ -144652,7 +144570,7 @@ def: "A pyramidal family morphology that inheres in neurons which have an apical xref: ilxtr:HorizontalPyramidalPhenotype is_a: PATO:0070015 ! pyramidal family morphology disjoint_from: PATO:0070017 ! standard pyramidal morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070017 @@ -144663,7 +144581,7 @@ synonym: "pyramidal cell morphology" EXACT [] synonym: "vertical pyramidal morphology" EXACT [] xref: ilxtr:PyramidalPhenotype is_a: PATO:0070015 ! pyramidal family morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070018 @@ -144672,7 +144590,7 @@ namespace: quality def: "A pyramidal cell morphology that inheres in neurons which have a distinct tuft formation, distal from the soma." [PMID:30715238] xref: ilxtr:TuftedPyramidalPhenotype is_a: PATO:0070017 ! standard pyramidal morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070019 @@ -144681,7 +144599,7 @@ namespace: quality def: "A pyramidal cell morphology that inheres in neurons which lack a clear tuft formation but extend to large radial distances." [PMID:30715238] xref: ilxtr:UntuftedPyramidalPhenotype is_a: PATO:0070017 ! standard pyramidal morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070020 @@ -144690,7 +144608,7 @@ namespace: quality def: "A pyramidal cell morphology that inheres in neurons which lack a tuft formation but extend to small radial distances forming a star-like shape." [PMID:30715238] xref: ilxtr:StarPyramidalPhenotype is_a: PATO:0070017 ! standard pyramidal morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070021 @@ -144699,7 +144617,7 @@ namespace: quality def: "A pyramidal cell morphology that inheres in neurons which have an apical tree which is oriented towards the white matter." [PMID:30715238] xref: ilxtr:InvertedPyramidalPhenotype is_a: PATO:0070017 ! standard pyramidal morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070025 @@ -144707,7 +144625,7 @@ name: unipolar neuron morphology namespace: quality def: "A cell morphology that inheres in neurons with only one process, a neurite, that extends from the cell body. The neurite then branches to form dendritic and axonal processes." [WikipediaVersioned:Unipolar_neuron&oldid=994458581] is_a: PATO:0010006 ! cell morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070026 @@ -144717,7 +144635,7 @@ def: "A cell morphology that inheres in neurons which possess three or more neur xref: ILX:0107196 xref: NLX:378 is_a: PATO:0010006 ! cell morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070027 @@ -144726,7 +144644,7 @@ namespace: quality def: "A cell morphology that inheres in neurons with dendrites that are bidirectional, emerging from opposite ends of the soma, with the two arbors extending in radial or tangential directions." [PMID:18568015] comment: This morphology type is distinct from bitufted cell morphology in that it refers to bitufted dendrite morphology rather than bitufted cell morphology. is_a: PATO:0010006 ! cell morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070028 @@ -144736,7 +144654,7 @@ def: "A neuron projection quality that is a characteristic of neurons whose soma synonym: "ET projecting" EXACT [] xref: ILX:0770101 is_a: PATO:0070033 ! neuron projection quality -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070029 @@ -144746,7 +144664,7 @@ def: "A neuron projection quality that is a characteristic of neurons with soma synonym: "CT projecting" EXACT [] xref: ILX:0770102 is_a: PATO:0070033 ! neuron projection quality -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070030 @@ -144756,7 +144674,7 @@ def: "A neuron projection quality that is a characteristic of neurons with proje synonym: "NP" EXACT [] xref: ILX:0770103 is_a: PATO:0070033 ! neuron projection quality -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070031 @@ -144765,7 +144683,7 @@ namespace: quality def: "A neuron projection quality that is a characteristic of neurons that project to the medulla oblongata from other brain regions." [DOI:10.1101/2020.10.19.343129] synonym: "MY projecting" EXACT [] is_a: PATO:0070033 ! neuron projection quality -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070033 @@ -144773,7 +144691,7 @@ name: neuron projection quality namespace: quality def: "A physical quality inhering in a neuron by virtue of the relative location of its soma and the regions to which it projects and makes synaptic contacts in." [DOI:10.1101/2020.10.19.343129] is_a: PATO:0001018 ! physical quality -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070034 @@ -144783,7 +144701,7 @@ def: "A neuron projection quality that is a characteristic of neurons with both synonym: "IT projecting" EXACT [] xref: ILX:0770100 is_a: PATO:0070033 ! neuron projection quality -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070044 @@ -144838,7 +144756,7 @@ name: bistratified dendrite cell morphology namespace: quality def: "A cell morphology that inheres in neurons with dendrites that stratify at two and only two locations." [PMID:34093409] is_a: PATO:0010006 ! cell morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070063 @@ -144846,7 +144764,7 @@ name: monostratified dendrite cell morphology namespace: quality def: "A cell morphology that inheres in neurons with dendrites that stratify at one and only one location." [PMID:34093409] is_a: PATO:0010006 ! cell morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PR:000000001 @@ -144926,7 +144844,6 @@ xref: IUPHARobj:1852 xref: PIRSF:PIRSF002004 is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P08575 [Term] id: PR:000001008 @@ -144944,7 +144861,6 @@ synonym: "platelet membrane glycoprotein Ia" EXACT [] synonym: "VLA-2 subunit alpha" EXACT [] xref: IUPHARobj:2440 is_a: PR:000001005 ! integrin alpha with A domain -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P17301 [Term] id: PR:000001010 @@ -144960,7 +144876,6 @@ synonym: "ITGAE" EXACT PRO-short-label [PRO:DNx] synonym: "mucosal lymphocyte 1 antigen" EXACT [] xref: IUPHARobj:2450 is_a: PR:000001005 ! integrin alpha with A domain -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P38570 [Term] id: PR:000001012 @@ -144979,7 +144894,6 @@ synonym: "leukocyte adhesion receptor MO1" EXACT [] synonym: "neutrophil adherence receptor" EXACT [] xref: IUPHARobj:2452 is_a: PR:000001005 ! integrin alpha with A domain -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P11215 [Term] id: PR:000001013 @@ -144996,7 +144910,6 @@ synonym: "leukocyte adhesion glycoprotein p150,95 alpha chain" EXACT [] synonym: "leukocyte adhesion receptor p150,95" EXACT [] xref: IUPHARobj:2454 is_a: PR:000001005 ! integrin alpha with A domain -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P20702 [Term] id: PR:000001014 @@ -145009,7 +144922,6 @@ synonym: "CD45R" RELATED [] synonym: "CD45RABC" EXACT [] synonym: "PTPRC/iso:CD45RABC" EXACT PRO-short-label [PRO:DNx] is_a: PR:000001006 ! receptor-type tyrosine-protein phosphatase C -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P08575-3 [Term] id: PR:000001015 @@ -145020,7 +144932,6 @@ comment: Category=sequence. Requested by=CL. Note: This isoform includes the reg synonym: "CD45RA" EXACT [] synonym: "PTPRC/iso:CD45RA" EXACT PRO-short-label [PRO:DNx] is_a: PR:000050216 ! receptor-type tyrosine-protein phosphatase C isoform CD45R -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P08575-8 [Term] id: PR:000001017 @@ -145033,7 +144944,6 @@ synonym: "CD45RO" EXACT [GOC:add, PRO:ADD] synonym: "PTPRC/iso:CD45RO" EXACT PRO-short-label [PRO:DNx] synonym: "T200" RELATED [] is_a: PR:000001006 ! receptor-type tyrosine-protein phosphatase C -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P08575-4 [Term] id: PR:000001018 @@ -145091,7 +145001,6 @@ synonym: "NCAM-1" EXACT [] synonym: "NCAM1" EXACT PRO-short-label [PRO:DNx] xref: IUPHARobj:2769 is_a: PR:000001023 ! neural cell adhesion molecule NCAM -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P13591 [Term] id: PR:000001025 @@ -145117,7 +145026,6 @@ synonym: "gp200-MR6" EXACT [] synonym: "ly-75" EXACT [] synonym: "LY75" EXACT PRO-short-label [PRO:DNx] is_a: PR:000001025 ! C-type lectin with multiple lectin domains -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:000034294 [Term] id: PR:000001083 @@ -145156,7 +145064,6 @@ synonym: "T-cell surface glycoprotein Lyt-2" EXACT [] synonym: "T-lymphocyte differentiation antigen T8/Leu-2" EXACT [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P01732 [Term] id: PR:000001085 @@ -145175,7 +145082,6 @@ synonym: "T-cell surface glycoprotein Lyt-3" EXACT [] xref: PIRSF:PIRSF002020 is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P10966 [Term] id: PR:000001087 @@ -145234,7 +145140,7 @@ xref: IUPHARfam:975 xref: PIRSF:PIRSF038544 is_a: PR:000001094 ! rhodopsin-like G-protein coupled receptor is_a: PR:000036194 ! eukaryotic protein -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa [Term] id: PR:000001128 @@ -145258,7 +145164,6 @@ synonym: "Drd1a" RELATED Gene-based [] synonym: "Gpcr15" RELATED Gene-based [] xref: IUPHARobj:214 is_a: PR:000001107 ! D(1)-like dopamine receptor -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P21728 [Term] id: PR:000001177 @@ -145270,7 +145175,6 @@ synonym: "dopamine D2 receptor" EXACT [] synonym: "DRD2" EXACT PRO-short-label [PRO:DNx] xref: IUPHARobj:215 is_a: PR:000001108 ! D(2)-like dopamine receptor -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P14416 [Term] id: PR:000001197 @@ -145300,7 +145204,6 @@ synonym: "MCP-1-R" EXACT [] synonym: "monocyte chemoattractant protein 1 receptor" EXACT [] xref: IUPHARobj:59 is_a: PR:000001128 ! chemokine receptor -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P41597 [Term] id: PR:000001200 @@ -145318,7 +145221,6 @@ synonym: "CMKBR4" RELATED Gene-based [] synonym: "K5-5" EXACT [] xref: IUPHARobj:61 is_a: PR:000001128 ! chemokine receptor -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P51679 [Term] id: PR:000001201 @@ -145338,7 +145240,6 @@ synonym: "HIV-1 fusion coreceptor" EXACT [] synonym: "MIP-1 alpha receptor" EXACT [] xref: IUPHARobj:62 is_a: PR:000001128 ! chemokine receptor -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P51681 [Term] id: PR:000001202 @@ -145366,7 +145267,6 @@ synonym: "LARC receptor" EXACT [] synonym: "STRL22" RELATED Gene-based [] xref: IUPHARobj:63 is_a: PR:000001128 ! chemokine receptor -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P51684 [Term] id: PR:000001203 @@ -145391,7 +145291,6 @@ synonym: "EVI1" RELATED Gene-based [] synonym: "MIP-3 beta receptor" EXACT [] xref: IUPHARobj:64 is_a: PR:000001128 ! chemokine receptor -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P32248 [Term] id: PR:000001206 @@ -145413,7 +145312,6 @@ synonym: "V28" EXACT [] xref: IUPHARobj:74 xref: PIRSF:PIRSF501025 is_a: PR:000001128 ! chemokine receptor -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P49238 [Term] id: PR:000001207 @@ -145435,7 +145333,6 @@ synonym: "IP-10 receptor" EXACT [] xref: IUPHARobj:70 xref: PIRSF:PIRSF501023 is_a: PR:000001128 ! chemokine receptor -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P49682 [Term] id: PR:000001208 @@ -145464,7 +145361,6 @@ synonym: "stromal cell-derived factor 1 receptor" EXACT [] xref: IUPHARobj:71 xref: PIRSF:PIRSF501021 is_a: PR:000001128 ! chemokine receptor -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P61073 [Term] id: PR:000001209 @@ -145486,7 +145382,6 @@ synonym: "MDR15" RELATED Gene-based [] synonym: "monocyte-derived receptor 15" EXACT [] xref: IUPHARobj:72 is_a: PR:000001128 ! chemokine receptor -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P32302 [Term] id: PR:000001224 @@ -145505,7 +145400,6 @@ synonym: "Opn1mw" RELATED [] synonym: "OPN1MW2" RELATED [] xref: IUPHARobj:2962 is_a: PR:000001119 ! animal opsin -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:000050522 [Term] id: PR:000001226 @@ -145528,7 +145422,6 @@ synonym: "OPN4" EXACT PRO-short-label [PRO:DNx] synonym: "opsin-4" EXACT [] xref: IUPHARobj:2758 is_a: PR:000001119 ! animal opsin -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q9UHM6 [Term] id: PR:000001244 @@ -145543,7 +145436,6 @@ synonym: "red-sensitive opsin" EXACT [] synonym: "ROP" EXACT [] xref: IUPHARobj:2961 is_a: PR:000001119 ! animal opsin -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P04000 [Term] id: PR:000001254 @@ -145567,7 +145459,6 @@ synonym: "RANTES-R" EXACT [] synonym: "SCYAR1" RELATED Gene-based [] xref: IUPHARobj:58 is_a: PR:000001197 ! chemokine receptor CCR1/3/1L -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P32246 [Term] id: PR:000001255 @@ -145589,7 +145480,6 @@ synonym: "macrophage inflammatory protein 1-alpha receptor-like 2" EXACT [] synonym: "MIP-1 alpha RL2" EXACT [] xref: IUPHARobj:60 is_a: PR:000001197 ! chemokine receptor CCR1/3/1L -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P51677 [Term] id: PR:000001256 @@ -145609,7 +145499,6 @@ synonym: "IL-8R A" EXACT [] synonym: "IL8RA" RELATED Gene-based [] xref: IUPHARobj:68 is_a: PR:000001226 ! high affinity interleukin-8 receptor -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P25024 [Term] id: PR:000001257 @@ -145631,7 +145520,6 @@ synonym: "IL-8R B" EXACT [] synonym: "IL8RB" RELATED Gene-based [] xref: IUPHARobj:69 is_a: PR:000001226 ! high affinity interleukin-8 receptor -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P25025 [Term] id: PR:000001281 @@ -145660,7 +145548,6 @@ synonym: "T-cell surface antigen Leu-14" EXACT [] xref: IUPHARobj:2786 is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P20273 [Term] id: PR:000001289 @@ -145713,7 +145600,6 @@ synonym: "HECL" RELATED Gene-based [] synonym: "UNQ9361/PRO34150" RELATED Gene-based [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q8WTT0 [Term] id: PR:000001293 @@ -145726,7 +145612,6 @@ synonym: "CLEC4K" RELATED Gene-based [] synonym: "langerin" EXACT [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q9UJ71 [Term] id: PR:000001300 @@ -145840,7 +145725,6 @@ synonym: "TQ1" EXACT [] xref: PIRSF:PIRSF002421 is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P14151 [Term] id: PR:000001319 @@ -145856,7 +145740,6 @@ synonym: "signaling lymphocytic activation molecule 5" EXACT [] synonym: "SLAMF5" RELATED Gene-based [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q9UIB8 [Term] id: PR:000001320 @@ -145882,7 +145765,6 @@ synonym: "tetherin" EXACT [] xref: PIRSF:PIRSF023920 is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q10589 [Term] id: PR:000001327 @@ -145908,7 +145790,6 @@ synonym: "CGM6" RELATED Gene-based [] synonym: "non-specific cross-reacting antigen NCA-95" EXACT [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P31997 [Term] id: PR:000001337 @@ -145922,7 +145803,6 @@ synonym: "CD35" EXACT [] synonym: "CR1" EXACT PRO-short-label [PRO:DNx] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P17927 [Term] id: PR:000001338 @@ -145940,7 +145820,6 @@ synonym: "epstein-Barr virus receptor" EXACT [] xref: PIRSF:PIRSF002484 is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P20023 [Term] id: PR:000001343 @@ -145979,7 +145858,6 @@ synonym: "phosphodiesterase I beta" EXACT [] synonym: "phosphodiesterase I/nucleotide pyrophosphatase 3" EXACT [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:O14638 [Term] id: PR:000001345 @@ -145996,7 +145874,6 @@ xref: IUPHARobj:2895 xref: PIRSF:PIRSF038746 is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P17813 [Term] id: PR:000001350 @@ -146010,7 +145887,6 @@ synonym: "JM2" RELATED Gene-based [] synonym: "scurfin" EXACT [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q9BZS1 [Term] id: PR:000001352 @@ -146062,7 +145938,6 @@ xref: IUPHARobj:1695 xref: PIRSF:PIRSF001954 is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P01589 [Term] id: PR:000001381 @@ -146082,7 +145957,6 @@ synonym: "p75" BROAD [PRO:DNx] xref: IUPHARobj:1696 is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P14784 [Term] id: PR:000001398 @@ -146098,7 +145972,6 @@ synonym: "immunoglobulin-like transcript 7" EXACT [] synonym: "LILRA4" EXACT PRO-short-label [PRO:DNx] xref: IUPHARobj:2896 is_a: PR:000044780 ! leukocyte immunoglobulin-like receptor subfamily member -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P59901 [Term] id: PR:000001402 @@ -146143,7 +146016,6 @@ synonym: "NIM-R5 antigen" EXACT [] synonym: "T10" EXACT [] xref: IUPHARobj:2766 is_a: PR:000001281 ! ADP-ribosyl cyclase -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P28907 [Term] id: PR:000001412 @@ -146206,7 +146078,6 @@ synonym: "CDH5" EXACT PRO-short-label [PRO:DNx] synonym: "vascular endothelial cadherin" EXACT [] synonym: "VE-cadherin" EXACT [] is_a: PR:000001327 ! cadherin -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P33151 [Term] id: PR:000001447 @@ -146224,7 +146095,6 @@ synonym: "epithelial cadherin" EXACT [] synonym: "UVO" RELATED Gene-based [] synonym: "uvomorulin" EXACT [] is_a: PR:000001327 ! cadherin -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P12830 [Term] id: PR:000001456 @@ -146245,7 +146115,6 @@ synonym: "FucT-IV" EXACT [] synonym: "FUT4" EXACT PRO-short-label [PRO:DNx] synonym: "galactoside 3-L-fucosyltransferase" BROAD [PRO:DNx] is_a: PR:000001320 ! alpha-(1,3)-fucosyltransferase -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P22083 [Term] id: PR:000001460 @@ -146260,7 +146129,6 @@ synonym: "MN sialoglycoprotein" EXACT [] synonym: "PAS-2" EXACT [] synonym: "sialoglycoprotein alpha" EXACT [] is_a: PR:000001352 ! glycophorin -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P02724 [Term] id: PR:000001465 @@ -146277,7 +146145,6 @@ synonym: "FcRI" EXACT [] synonym: "IGFR1" RELATED Gene-based [] synonym: "IgG Fc receptor I" EXACT [] is_a: PR:000001356 ! immunoglobulin gamma Fc receptor I -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P12314 [Term] id: PR:000001479 @@ -146313,7 +146180,6 @@ synonym: "FcRII-b" EXACT [] synonym: "IGFR2" RELATED Gene-based [] synonym: "IgG Fc receptor II-b" EXACT [] is_a: PR:000001355 ! immunoglobulin gamma Fc receptor II/III/IV -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P31994 [Term] id: PR:000001483 @@ -146391,7 +146257,6 @@ synonym: "N-formyl peptide receptor" BROAD [PRO:DNx] synonym: "N-formylpeptide chemoattractant receptor" EXACT [] xref: IUPHARobj:222 is_a: PR:000001431 ! N-formyl peptide receptor -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P21462 [Term] id: PR:000001635 @@ -146403,7 +146268,6 @@ synonym: "OT-R" EXACT [] synonym: "OXTR" EXACT PRO-short-label [PRO:DNx] xref: IUPHARobj:369 is_a: PR:000001562 ! vasopressin/oxytocin receptor -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P30559 [Term] id: PR:000001666 @@ -146418,7 +146282,6 @@ synonym: "relaxin family peptide receptor 1" EXACT [] synonym: "RXFP1" EXACT PRO-short-label [PRO:DNx] xref: IUPHARobj:351 is_a: PR:000001551 ! relaxin family peptide receptor protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q9HBX9 [Term] id: PR:000001753 @@ -146457,7 +146320,6 @@ synonym: "PROM1" EXACT PRO-short-label [PRO:DNx] synonym: "prominin-like protein 1" EXACT [] synonym: "PROML1" RELATED Gene-based [] is_a: PR:000001785 ! prominin -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:O43490 [Term] id: PR:000001806 @@ -146476,7 +146338,6 @@ synonym: "dendritic cell-associated C-type lectin 2" EXACT [] xref: IUPHARobj:2928 is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q6EIG7 [Term] id: PR:000001807 @@ -146498,7 +146359,6 @@ synonym: "UNQ539/PRO1082" RELATED Gene-based [] xref: IUPHARobj:2927 is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q9BXN2 [Term] id: PR:000001808 @@ -146549,7 +146409,6 @@ synonym: "TM7LN3" RELATED Gene-based [] xref: IUPHARobj:182 xref: PIRSF:PIRSF038685 is_a: PR:000001087 ! adhesion G-protein coupled receptor -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q14246 [Term] id: PR:000001820 @@ -146599,7 +146458,6 @@ synonym: "TBX21" EXACT PRO-short-label [PRO:DNx] synonym: "transcription factor TBLYM" EXACT [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q9UL17 [Term] id: PR:000001836 @@ -146642,7 +146500,6 @@ synonym: "lymphocyte antigen T1/Leu-1" EXACT [] synonym: "Lyt-1" EXACT [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P06127 [Term] id: PR:000001841 @@ -146655,7 +146512,6 @@ synonym: "TP44" EXACT [] xref: IUPHARobj:2863 is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P10747 [Term] id: PR:000001843 @@ -146671,7 +146527,6 @@ synonym: "THY1" EXACT PRO-short-label [PRO:DNx] xref: PIRSF:PIRSF038777 is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P04216 [Term] id: PR:000001844 @@ -146685,7 +146540,6 @@ synonym: "type I arginase" EXACT [] xref: IUPHARobj:1244 is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P05089 [Term] id: PR:000001850 @@ -146701,7 +146555,6 @@ synonym: "CTSO" RELATED Gene-based [] synonym: "CTSO2" RELATED Gene-based [] xref: IUPHARobj:2350 is_a: PR:000040662 ! cathepsin-like protease -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P43235 [Term] id: PR:000001852 @@ -146716,7 +146569,6 @@ synonym: "cytotoxic T-lymphocyte-associated antigen 4" EXACT [] xref: IUPHARobj:2743 is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P16410 [Term] id: PR:000001858 @@ -146734,7 +146586,6 @@ synonym: "VPREB1" EXACT PRO-short-label [PRO:DNx] xref: PIRSF:PIRSF038787 is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P12018 [Term] id: PR:000001859 @@ -146752,7 +146603,6 @@ synonym: "immunoglobulin omega polypeptide" EXACT [] synonym: "immunoglobulin-related protein 14.1" EXACT [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P15814 [Term] id: PR:000001860 @@ -146771,7 +146621,6 @@ synonym: "ICOS" EXACT PRO-short-label [PRO:DNx] xref: IUPHARobj:2939 is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q9Y6W8 [Term] id: PR:000001861 @@ -146820,7 +146669,6 @@ xref: IUPHARobj:1706 xref: PIRSF:PIRSF018419 is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q01344 [Term] id: PR:000001869 @@ -146839,7 +146687,6 @@ xref: IUPHARobj:1698 xref: PIRSF:PIRSF001960 is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P16871 [Term] id: PR:000001874 @@ -146869,7 +146716,6 @@ synonym: "SPN" EXACT PRO-short-label [PRO:DNx] xref: PIRSF:PIRSF001994 is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P16150 [Term] id: PR:000001880 @@ -146893,7 +146739,6 @@ xref: IUPHARobj:2935 xref: PIRSF:PIRSF002426 is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P06734 [Term] id: PR:000001883 @@ -146917,7 +146762,6 @@ synonym: "SCARA2" RELATED Gene-based [] synonym: "scavenger receptor class A member 2" EXACT [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q9UEW3 [Term] id: PR:000001885 @@ -146935,7 +146779,6 @@ synonym: "Scvr" RELATED Gene-based [] synonym: "SR-A" EXACT [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P21757 [Term] id: PR:000001888 @@ -146995,7 +146838,6 @@ synonym: "NK-p46" EXACT [] synonym: "NKp46" EXACT [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:O76036 [Term] id: PR:000001894 @@ -147014,7 +146856,6 @@ synonym: "NKp44" EXACT [] xref: PIRSF:PIRSF037963 is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:O95944 [Term] id: PR:000001896 @@ -147035,7 +146876,6 @@ synonym: "SLAM family member 4" EXACT [] synonym: "SLAMF4" EXACT [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q9BZW8 [Term] id: PR:000001897 @@ -147069,7 +146909,6 @@ xref: IUPHARobj:1611 xref: PIRSF:PIRSF501074 is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P08473 [Term] id: PR:000001902 @@ -147091,7 +146930,6 @@ synonym: "TOR" EXACT [] xref: IUPHARobj:600 is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P51449 [Term] id: PR:000001903 @@ -147105,7 +146943,6 @@ synonym: "Pax-5" RELATED Gene-based [] synonym: "PAX5" EXACT PRO-short-label [PRO:DNx] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q02548 [Term] id: PR:000001905 @@ -147129,7 +146966,6 @@ synonym: "platelet glycoprotein IV" EXACT [] synonym: "thrombospondin receptor" EXACT [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P16671 [Term] id: PR:000001907 @@ -147147,7 +146983,6 @@ synonym: "GPIbA" EXACT [] xref: PIRSF:PIRSF002493 is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P07359 [Term] id: PR:000001919 @@ -147164,7 +146999,6 @@ xref: IUPHARobj:2760 xref: PIRSF:PIRSF018380 is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q15116 [Term] id: PR:000001925 @@ -147177,7 +147011,6 @@ synonym: "hemoglobin scavenger receptor" EXACT [] synonym: "M130" RELATED Gene-based [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q86VB7 [Term] id: PR:000001927 @@ -147199,7 +147032,6 @@ synonym: "SIGLEC5" EXACT PRO-short-label [PRO:DNx] synonym: "Siglecf" RELATED [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:O15389 [Term] id: PR:000001928 @@ -147219,7 +147051,6 @@ synonym: "siglec-6" EXACT [] synonym: "SIGLEC6" EXACT PRO-short-label [PRO:DNx] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:O43699 [Term] id: PR:000001931 @@ -147237,7 +147068,6 @@ synonym: "SIGLEC1" EXACT PRO-short-label [PRO:DNx] synonym: "SN" RELATED Gene-based [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q9BZZ2 [Term] id: PR:000001932 @@ -147257,7 +147087,6 @@ synonym: "small cell lung carcinoma cluster 4 antigen" EXACT [] synonym: "X62 heat stable antigen" EXACT [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P25063 [Term] id: PR:000001935 @@ -147273,7 +147102,6 @@ synonym: "SYND1" EXACT [] xref: PIRSF:PIRSF015854 is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P18827 [Term] id: PR:000001937 @@ -147291,7 +147119,6 @@ synonym: "type 5 acid phosphatase" EXACT [] xref: PIRSF:PIRSF000898 is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P13686 [Term] id: PR:000001938 @@ -147314,7 +147141,6 @@ synonym: "GATA-binding factor 3" EXACT [] synonym: "GATA3" EXACT PRO-short-label [PRO:DNx] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P23771 [Term] id: PR:000001944 @@ -147329,7 +147155,6 @@ synonym: "Sfpi1" RELATED Gene-based [] synonym: "SPI1" EXACT PRO-short-label [PRO:DNx] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P17947 [Term] id: PR:000001945 @@ -147347,7 +147172,6 @@ synonym: "TR" RELATED [] synonym: "Trfr" RELATED Gene-based [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P02786 [Term] id: PR:000001950 @@ -147383,7 +147207,6 @@ xref: IUPHARobj:1881 xref: PIRSF:PIRSF038806 is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q9Y6Q6 [Term] id: PR:000001963 @@ -147433,7 +147256,6 @@ synonym: "Sirp-alpha-3" EXACT [] synonym: "SIRPA" EXACT PRO-short-label [PRO:DNx] xref: IUPHARobj:2942 is_a: PR:000001832 ! SIRP/SHPS-1 family protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P78324 [Term] id: PR:000001969 @@ -147451,7 +147273,6 @@ synonym: "uPAR" EXACT [] xref: PIRSF:PIRSF002022 is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q03405 [Term] id: PR:000001971 @@ -147495,7 +147316,6 @@ synonym: "tyrosine-protein kinase receptor FLT3" EXACT [] xref: IUPHARobj:1807 xref: PIRSF:PIRSF500949 is_a: PR:000001810 ! CSF-1/PDGF receptor-type tyrosine-protein kinase -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P36888 [Term] id: PR:000002015 @@ -147525,7 +147345,6 @@ synonym: "NKG2-A/B-activating NK receptor" EXACT [] synonym: "NKG2A" RELATED Gene-based [] xref: IUPHARobj:2849 is_a: PR:000001897 ! natural killer cell receptor NKG2 -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P26715 [Term] id: PR:000002025 @@ -147538,7 +147357,6 @@ synonym: "CD1a" EXACT [] synonym: "T-cell surface antigen T6/Leu-6" EXACT [] synonym: "Ta1 thymocyte antigen" EXACT [] is_a: PR:000001838 ! T-cell surface glycoprotein CD1 -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P06126 [Term] id: PR:000002027 @@ -147549,7 +147367,6 @@ comment: Category=gene. Requested by=CL. synonym: "CD1C" EXACT PRO-short-label [PRO:DNx] synonym: "CD1c" EXACT [] is_a: PR:000001838 ! T-cell surface glycoprotein CD1 -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P29017 [Term] id: PR:000002028 @@ -147565,7 +147382,6 @@ synonym: "Cd1d1" RELATED Gene-based [] synonym: "R3G1" EXACT [] synonym: "T-cell surface glycoprotein CD1d" EXACT [] is_a: PR:000001838 ! T-cell surface glycoprotein CD1 -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P15813 [Term] id: PR:000002030 @@ -147609,7 +147425,6 @@ synonym: "myeloid plasma membrane glycoprotein CD13" EXACT [] synonym: "PEPN" RELATED Gene-based [] xref: IUPHARobj:1560 is_a: PR:000001888 ! membrane alanyl aminopeptidase-like metallopeptidase -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P15144 [Term] id: PR:000002037 @@ -147633,7 +147448,6 @@ synonym: "lymphocyte antigen 68" EXACT [] synonym: "matrix-remodeling-associated protein 4" EXACT [] synonym: "MXRA4" RELATED Gene-based [] is_a: PR:000001938 ! thrombomodulin-like receptor -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q9NPY3 [Term] id: PR:000002039 @@ -147650,7 +147464,6 @@ synonym: "EAP" RELATED [] synonym: "ENPEP" EXACT PRO-short-label [PRO:DNx] xref: IUPHARobj:1568 is_a: PR:000001888 ! membrane alanyl aminopeptidase-like metallopeptidase -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q07075 [Term] id: PR:000002062 @@ -147670,7 +147483,6 @@ synonym: "proto-oncogene c-Fms" EXACT [] xref: IUPHARobj:1806 xref: PIRSF:PIRSF500947 is_a: PR:000001810 ! CSF-1/PDGF receptor-type tyrosine-protein kinase -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P07333 [Term] id: PR:000002064 @@ -147681,7 +147493,6 @@ comment: Category=gene. Requested by=CL. synonym: "CD68" EXACT PRO-short-label [PRO:DNx] synonym: "gp110" RELATED [] is_a: PR:000001883 ! lysosome-associated membrane protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P34810 [Term] id: PR:000002065 @@ -147713,7 +147524,6 @@ synonym: "THBD" EXACT PRO-short-label [PRO:DNx] synonym: "THRM" RELATED Gene-based [] synonym: "TM" EXACT [] is_a: PR:000001938 ! thrombomodulin-like receptor -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P07204 [Term] id: PR:000002112 @@ -147733,7 +147543,6 @@ synonym: "VEGFR-2" EXACT [] synonym: "VEGFR2" RELATED Gene-based [] xref: IUPHARobj:1813 is_a: PR:000001971 ! vascular endothelial growth factor receptor -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P35968 [Term] id: PR:000002123 @@ -147757,7 +147566,6 @@ synonym: "small-inducible cytokine A3" EXACT [] synonym: "tonsillar lymphocyte LD78 alpha protein" EXACT [] synonym: "TY-5" EXACT [] is_a: PR:000001998 ! C-C motif chemokine 3/4 -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P10147 [Term] id: PR:000002972 @@ -147775,7 +147583,6 @@ synonym: "MMR" EXACT [] synonym: "MRC1" EXACT PRO-short-label [PRO:DNx] synonym: "MRC1L1" RELATED Gene-based [] is_a: PR:000001025 ! C-type lectin with multiple lectin domains -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P22897 [Term] id: PR:000002976 @@ -147882,7 +147689,6 @@ synonym: "alpha-1 type I collagen" EXACT [] synonym: "COL1A1" EXACT PRO-short-label [PRO:DNx] synonym: "Cola1" RELATED Gene-based [] is_a: PR:000003263 ! collagen type I alpha chain -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P02452 [Term] id: PR:000003450 @@ -147904,7 +147710,6 @@ synonym: "ZNF51" RELATED Gene-based [] xref: IUPHARobj:2957 is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P41182 [Term] id: PR:000003455 @@ -147927,7 +147732,6 @@ synonym: "RING finger protein 74" EXACT [] synonym: "RNF74" RELATED Gene-based [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P15918 [Term] id: PR:000003460 @@ -147939,7 +147743,6 @@ synonym: "RAG-2" EXACT [] synonym: "RAG2" EXACT PRO-short-label [PRO:DNx] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P55895 [Term] id: PR:000003463 @@ -147967,7 +147770,6 @@ synonym: "PFP" RELATED Gene-based [] synonym: "PRF1" EXACT PRO-short-label [PRO:DNx] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P14222 [Term] id: PR:000003469 @@ -148010,7 +147812,6 @@ synonym: "SECT" EXACT [] synonym: "T-cell serine protease 1-3E" EXACT [] xref: IUPHARobj:2369 is_a: PR:000003505 ! leukocyte granule-associated proteinase -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P10144 [Term] id: PR:000003505 @@ -148049,7 +147850,6 @@ synonym: "P1/Pk synthase" EXACT [] synonym: "UDP-galactose:beta-D-galactosyl-beta1-R 4-alpha-D-galactosyltransferase" EXACT [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q9NPC4 [Term] id: PR:000004528 @@ -148065,7 +147865,6 @@ synonym: "UFO" RELATED Gene-based [] xref: IUPHARobj:1835 is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P30530 [Term] id: PR:000004724 @@ -148078,7 +147877,6 @@ synonym: "vitelliform macular dystrophy 2-like protein 2" EXACT [] synonym: "VMD2L2" RELATED Gene-based [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q8NFU0 [Term] id: PR:000005110 @@ -148089,7 +147887,6 @@ comment: Category=gene. synonym: "CCK" EXACT PRO-short-label [PRO:DNx] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P06307 [Term] id: PR:000005178 @@ -148123,7 +147920,6 @@ synonym: "CEBP" RELATED Gene-based [] synonym: "CEBPA" EXACT PRO-short-label [PRO:DNx] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P49715 [Term] id: PR:000005310 @@ -148136,7 +147932,6 @@ synonym: "CEBPE" EXACT PRO-short-label [PRO:DNx] synonym: "Gm294" RELATED Gene-based [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q15744 [Term] id: PR:000005444 @@ -148151,7 +147946,6 @@ synonym: "transmembrane protein MT75" EXACT [] synonym: "UNQ872/PRO1890" RELATED Gene-based [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q9H9P2 [Term] id: PR:000005460 @@ -148164,7 +147958,6 @@ synonym: "CHRNA7" EXACT PRO-short-label [PRO:DNx] synonym: "NACHRA7" RELATED Gene-based [] xref: IUPHARobj:468 is_a: PR:000044668 ! nicotinic acetylcholine receptor protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P36544 [Term] id: PR:000006169 @@ -148207,7 +148000,6 @@ synonym: "terminal deoxynucleotidyltransferase" EXACT [] synonym: "terminal transferase" EXACT [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P04053 [Term] id: PR:000007152 @@ -148221,7 +148013,6 @@ synonym: "EPP" RELATED Gene-based [] synonym: "EPX" EXACT PRO-short-label [PRO:DNx] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P11678 [Term] id: PR:000007204 @@ -148241,7 +148032,6 @@ synonym: "nuclear receptor subfamily 3 group A member 1" EXACT [] xref: IUPHARobj:620 is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P03372 [Term] id: PR:000007431 @@ -148256,7 +148046,6 @@ synonym: "FcERI" RELATED [] synonym: "IgE Fc receptor subunit alpha" EXACT [] xref: IUPHARobj:2933 is_a: PR:000001355 ! immunoglobulin gamma Fc receptor II/III/IV -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P12319 [Term] id: PR:000007499 @@ -148272,7 +148061,6 @@ synonym: "HBGF-8" RELATED [] synonym: "heparin-binding growth factor 8" RELATED [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P55075 [Term] id: PR:000007597 @@ -148288,7 +148076,6 @@ synonym: "proto-oncogene protein c-fos" EXACT [] synonym: "transcription factor AP-1 subunit c-Fos" EXACT [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P01100 [Term] id: PR:000007636 @@ -148308,7 +148095,6 @@ synonym: "winged-helix transcription factor nude" EXACT [] xref: IUPHARobj:2958 is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:O15353 [Term] id: PR:000007785 @@ -148325,7 +148111,6 @@ synonym: "glutamate decarboxylase 67 kDa isoform" EXACT [] xref: IUPHARobj:1272 is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q99259 [Term] id: PR:000007857 @@ -148343,7 +148128,6 @@ synonym: "GF1" RELATED Gene-based [] synonym: "NF-E1 DNA-binding protein" EXACT [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P15976 [Term] id: PR:000007858 @@ -148355,7 +148139,6 @@ synonym: "GATA-binding protein 2" EXACT [] synonym: "GATA2" EXACT PRO-short-label [PRO:DNx] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P23769 [Term] id: PR:000007939 @@ -148366,7 +148149,6 @@ comment: Category=gene. Requested by=CL. synonym: "GFAP" EXACT PRO-short-label [PRO:DNx] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P14136 [Term] id: PR:000008457 @@ -148392,7 +148174,6 @@ synonym: "HBZ2" RELATED Gene-based [] synonym: "hemoglobin zeta chain" EXACT [] synonym: "zeta-globin" EXACT [] is_a: PR:000050467 ! hemoglobin subunit -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P02008 [Term] id: PR:000008857 @@ -148429,7 +148210,6 @@ synonym: "UNQ2501/PRO19612" RELATED Gene-based [] xref: IUPHARobj:1739 is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q9NRM6 [Term] id: PR:000008994 @@ -148449,7 +148229,6 @@ synonym: "T1" RELATED Gene-based [] xref: IUPHARobj:1735 is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q01638 [Term] id: PR:000009054 @@ -148460,7 +148239,6 @@ comment: Category=gene. synonym: "INS" EXACT PRO-short-label [PRO:DNx] synonym: "insulin" BROAD [PRO:DAN] is_a: PR:000045358 ! insulin family protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P01308 [Term] id: PR:000009127 @@ -148477,7 +148255,6 @@ synonym: "ITGAB" RELATED Gene-based [] synonym: "platelet membrane glycoprotein IIb" EXACT [] xref: IUPHARobj:2441 is_a: PR:000025797 ! integrin alpha lacking A domain -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P08514 [Term] id: PR:000009129 @@ -148495,7 +148272,6 @@ synonym: "lymphocyte Peyer patch adhesion molecules subunit alpha" EXACT [] synonym: "VLA-4 subunit alpha" EXACT [] xref: IUPHARobj:2443 is_a: PR:000025797 ! integrin alpha lacking A domain -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P13612 [Term] id: PR:000009143 @@ -148509,7 +148285,6 @@ synonym: "ITGB7" EXACT PRO-short-label [PRO:DNx] synonym: "M290 IEL antigen" EXACT [] xref: IUPHARobj:2461 is_a: PR:000001861 ! integrin beta -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P26010 [Term] id: PR:000009344 @@ -148522,7 +148297,6 @@ synonym: "kisspeptin-1" EXACT [] synonym: "PP5098" RELATED Gene-based [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q15726 [Term] id: PR:000009426 @@ -148541,7 +148315,6 @@ synonym: "mast cell function-associated antigen" EXACT [] synonym: "mast cell function-associated antigen 2F1" EXACT [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q96E93 [Term] id: PR:000009616 @@ -148620,7 +148393,6 @@ synonym: "p25" BROAD [PRO:DNx] synonym: "SV-40-induced 24P3 protein" EXACT [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P80188 [Term] id: PR:000009766 @@ -148644,7 +148416,6 @@ synonym: "putative MAPK-activating protein PM12" EXACT [] synonym: "S-Lac lectin 1" EXACT [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P09382 [Term] id: PR:000009793 @@ -148675,7 +148446,6 @@ synonym: "LTF" EXACT PRO-short-label [PRO:DNx] synonym: "talalactoferrin" EXACT [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P02788 [Term] id: PR:000009981 @@ -148691,7 +148461,6 @@ synonym: "LUM" EXACT PRO-short-label [PRO:DNx] synonym: "SLRR2D" RELATED Gene-based [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P51884 [Term] id: PR:000010317 @@ -148705,7 +148474,6 @@ synonym: "MRG1" RELATED Gene-based [] synonym: "Stra10" RELATED Gene-based [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:O14770 [Term] id: PR:000010329 @@ -148721,7 +148489,6 @@ synonym: "receptor tyrosine kinase MerTK" EXACT [] xref: IUPHARobj:1837 is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q12866 [Term] id: PR:000010543 @@ -148733,7 +148500,6 @@ synonym: "MPO" EXACT PRO-short-label [PRO:DNx] xref: IUPHARobj:2789 is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P05164 [Term] id: PR:000010799 @@ -148757,7 +148523,6 @@ synonym: "BTCL1" RELATED Gene-based [] synonym: "NETO1" EXACT PRO-short-label [PRO:DNx] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q8TDF5 [Term] id: PR:000011178 @@ -148774,7 +148539,6 @@ synonym: "NFKB2" EXACT PRO-short-label [PRO:DNx] synonym: "nuclear factor of kappa light polypeptide gene enhancer in B-cells 2" EXACT [] synonym: "oncogene Lyt-10" EXACT [] is_a: PR:000001753 ! transcription factor NF-kappa-B subunit -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q00653 [Term] id: PR:000011467 @@ -148789,7 +148553,6 @@ synonym: "NTNG1" EXACT PRO-short-label [PRO:DNx] synonym: "UNQ571/PRO1133" RELATED Gene-based [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q9Y2I2 [Term] id: PR:000012526 @@ -148802,7 +148565,6 @@ synonym: "PDYN" EXACT PRO-short-label [PRO:DNx] synonym: "preprodynorphin" EXACT [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P01213 [Term] id: PR:000013206 @@ -148817,7 +148579,6 @@ synonym: "PRG2" EXACT PRO-short-label [PRO:DNx] synonym: "proteoglycan 2" EXACT [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P13727 [Term] id: PR:000013246 @@ -148827,7 +148588,6 @@ def: "A somatotropin hormone family member that is a translation product of the comment: Category=gene. synonym: "PRL" EXACT PRO-short-label [PRO:DNx] is_a: PR:000029968 ! somatotropin hormone family member -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P01236 [Term] id: PR:000013502 @@ -148839,7 +148599,6 @@ synonym: "Pva" RELATED Gene-based [] synonym: "PVALB" EXACT PRO-short-label [PRO:DNx] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P20472 [Term] id: PR:000013879 @@ -148852,7 +148611,6 @@ synonym: "RELN" EXACT PRO-short-label [PRO:DNx] synonym: "Rl" RELATED Gene-based [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P78509 [Term] id: PR:000013883 @@ -148864,7 +148622,6 @@ synonym: "angiotensinogenase" RELATED [] synonym: "REN" EXACT PRO-short-label [PRO:DNx] xref: IUPHARobj:2413 is_a: PR:000050025 ! angiotensinogenase -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P00797 [Term] id: PR:000014046 @@ -148885,7 +148642,6 @@ synonym: "RNASE2" EXACT PRO-short-label [PRO:DNx] synonym: "RNS2" RELATED Gene-based [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P10153 [Term] id: PR:000014047 @@ -148900,7 +148656,6 @@ synonym: "RNASE3" EXACT PRO-short-label [PRO:DNx] synonym: "RNS3" RELATED Gene-based [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P12724 [Term] id: PR:000014362 @@ -148923,7 +148678,6 @@ synonym: "SL3-3 enhancer factor 1 alpha B subunit" EXACT [] synonym: "SL3/AKV core-binding factor alpha B subunit" EXACT [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q01196 [Term] id: PR:000014505 @@ -148950,7 +148704,6 @@ synonym: "urine protein 1" EXACT [] synonym: "Utg" RELATED Gene-based [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P11684 [Term] id: PR:000014841 @@ -148965,7 +148718,6 @@ synonym: "Shh unprocessed N-terminal signaling and C-terminal autoprocessing dom synonym: "ShhNC" EXACT [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q15465 [Term] id: PR:000015325 @@ -148983,7 +148735,6 @@ synonym: "SR" EXACT [] synonym: "synoretin" EXACT [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:O76070 [Term] id: PR:000015426 @@ -148995,7 +148746,6 @@ synonym: "Sox-2" RELATED Gene-based [] synonym: "SOX2" EXACT PRO-short-label [PRO:DNx] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P48431 [Term] id: PR:000015658 @@ -149008,7 +148758,6 @@ synonym: "SSPO" EXACT PRO-short-label [PRO:DNx] synonym: "SSPOP" RELATED Gene-based [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:A2VEC9 [Term] id: PR:000015665 @@ -149021,7 +148770,6 @@ synonym: "Smst" RELATED Gene-based [] synonym: "SST" EXACT PRO-short-label [PRO:DNx] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P61278 [Term] id: PR:000016004 @@ -149039,7 +148787,6 @@ synonym: "UNQ585/PRO1155" RELATED Gene-based [] synonym: "ZNEUROK1" EXACT [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q9UHF0 [Term] id: PR:000016043 @@ -149058,7 +148805,6 @@ synonym: "TAL1" EXACT PRO-short-label [PRO:DNx] synonym: "TCL5" RELATED Gene-based [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P17542 [Term] id: PR:000016301 @@ -149088,7 +148834,6 @@ synonym: "putative T1/ST2 receptor-binding protein" EXACT [] synonym: "TMED1" EXACT PRO-short-label [PRO:DNx] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q13445 [Term] id: PR:000017298 @@ -149099,7 +148844,6 @@ comment: Category=gene. synonym: "VIM" EXACT PRO-short-label [PRO:DNx] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P08670 [Term] id: PR:000017299 @@ -149113,7 +148857,6 @@ synonym: "vasoactive intestinal polypeptides precursor" EXACT [] synonym: "VIP" EXACT PRO-short-label [PRO:DNx] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P01282 [Term] id: PR:000018263 @@ -149531,7 +149274,6 @@ comment: Category=sequence. Requested by=CL. synonym: "CD8A/iso:1" EXACT PRO-short-label [PRO:DNx] synonym: "mCD8alpha" EXACT [] is_a: PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P01732-1 [Term] id: PR:000025405 @@ -149621,7 +149363,6 @@ synonym: "Natural killer cell surface protein P1A" EXACT [] synonym: "NKR-P1A" BROAD [PRO:DNx] synonym: "NKRP1A" RELATED Gene-based [] is_a: PR:000001874 ! KLRB1-like protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q12918 [Term] id: PR:000025796 @@ -149669,8 +149410,8 @@ def: "A protein that is encoded in the genome of Mus musculus." [PRO:DAN] synonym: "mouse protein" EXACT PRO-short-label [PRO:DAN] is_a: PR:000036194 ! eukaryotic protein intersection_of: PR:000000001 ! protein -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus -relationship: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus +relationship: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:000029067 @@ -149680,8 +149421,8 @@ def: "A protein that is encoded in the genome of Homo sapiens." [PRO:DAN] synonym: "human protein" EXACT PRO-short-label [PRO:DAN] is_a: PR:000036194 ! eukaryotic protein intersection_of: PR:000000001 ! protein -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens +relationship: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:000029562 @@ -149738,7 +149479,6 @@ synonym: "LAMP5" EXACT PRO-short-label [PRO:DNx] synonym: "lysosome-associated membrane protein 5" EXACT [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q9UJQ1 [Term] id: PR:000034294 @@ -149756,7 +149496,7 @@ synonym: "ly-75 (human)" EXACT [UniProtKB:O60449] is_a: PR:000001026 ! lymphocyte antigen 75 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001026 ! lymphocyte antigen 75 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:000036194 @@ -149767,8 +149507,8 @@ synonym: "Eukaryota protein" EXACT [PRO:DAN] is_a: CHEBI:36080 is_a: PR:000000001 ! protein intersection_of: PR:000000001 ! protein -intersection_of: only_in_taxon NCBITaxon:2759 ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +intersection_of: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota [Term] id: PR:000036947 @@ -149782,7 +149522,7 @@ xref: MRO:0000634 is_a: PR:000001838 ! T-cell surface glycoprotein CD1 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001838 ! T-cell surface glycoprotein CD1 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:000037069 @@ -149805,7 +149545,7 @@ comment: Category=family. synonym: "cathepsin" NARROW [PRO:DAN] synonym: "fam:CTS" EXACT PRO-short-label [PRO:DNx] is_a: PR:000036194 ! eukaryotic protein -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa [Term] id: PR:000044633 @@ -149931,7 +149671,7 @@ synonym: "mH2-Ea" EXACT PRO-short-label [PRO:DAN] is_a: PR:000002015 ! MHC class II histocompatibility antigen alpha chain DRA is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000002015 ! MHC class II histocompatibility antigen alpha chain DRA -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:000050467 @@ -149956,7 +149696,7 @@ synonym: "OPN1MW3" NARROW Gene-based [UniProtKB:P0DN78] is_a: PR:000001224 ! medium-wave-sensitive opsin is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001224 ! medium-wave-sensitive opsin -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens union_of: PR:P04001 ! medium-wave-sensitive opsin 1 (human) union_of: PR:P0DN77 ! medium-wave-sensitive opsin 2 (human) union_of: PR:P0DN78 ! medium-wave-sensitive opsin 3 (human) @@ -149991,7 +149731,7 @@ xref: UniProtKB:A2VEC9 is_a: PR:000015658 ! SCO-spondin is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000015658 ! SCO-spondin -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:O09100 @@ -150006,7 +149746,7 @@ xref: UniProtKB:O09100 is_a: PR:000007858 ! endothelial transcription factor GATA-2 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000007858 ! endothelial transcription factor GATA-2 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:O14638 @@ -150028,7 +149768,7 @@ xref: UniProtKB:O14638 is_a: PR:000001344 ! ectonucleotide pyrophosphatase/phosphodiesterase family member 3 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001344 ! ectonucleotide pyrophosphatase/phosphodiesterase family member 3 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:O14770 @@ -150044,7 +149784,7 @@ xref: UniProtKB:O14770 is_a: PR:000010317 ! homeobox protein Meis2 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000010317 ! homeobox protein Meis2 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:O15353 @@ -150061,7 +149801,7 @@ xref: UniProtKB:O15353 is_a: PR:000007636 ! forkhead box protein N1 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000007636 ! forkhead box protein N1 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:O15389 @@ -150083,7 +149823,7 @@ xref: UniProtKB:O15389 is_a: PR:000001927 ! sialic acid-binding Ig-like lectin 5 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001927 ! sialic acid-binding Ig-like lectin 5 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:O35305 @@ -150102,7 +149842,7 @@ xref: UniProtKB:O35305 is_a: PR:000001954 ! tumor necrosis factor receptor superfamily member 11A is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001954 ! tumor necrosis factor receptor superfamily member 11A -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:O35417 @@ -150118,7 +149858,7 @@ xref: UniProtKB:O35417 is_a: PR:000012526 ! proenkephalin-B is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000012526 ! proenkephalin-B -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:O35930 @@ -150137,7 +149877,7 @@ xref: UniProtKB:O35930 is_a: PR:000001907 ! platelet glycoprotein Ib alpha chain is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001907 ! platelet glycoprotein Ib alpha chain -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:O43490 @@ -150156,7 +149896,7 @@ xref: UniProtKB:O43490 is_a: PR:000001786 ! prominin-1 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001786 ! prominin-1 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:O43699 @@ -150179,7 +149919,7 @@ xref: UniProtKB:O43699 is_a: PR:000001928 ! sialic acid-binding Ig-like lectin 6 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001928 ! sialic acid-binding Ig-like lectin 6 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:O54689 @@ -150199,7 +149939,7 @@ xref: UniProtKB:O54689 is_a: PR:000001202 ! C-C chemokine receptor type 6 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001202 ! C-C chemokine receptor type 6 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:O54707 @@ -150216,7 +149956,7 @@ xref: UniProtKB:O54707 is_a: PR:000001402 ! killer cell lectin-like receptor subfamily D member 1 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001402 ! killer cell lectin-like receptor subfamily D member 1 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:O54839 @@ -150234,7 +149974,7 @@ xref: UniProtKB:O54839 is_a: PR:000003463 ! eomesodermin is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000003463 ! eomesodermin -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:O54990 @@ -150253,7 +149993,7 @@ xref: UniProtKB:O54990 is_a: PR:000001786 ! prominin-1 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001786 ! prominin-1 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:O76036 @@ -150275,7 +150015,7 @@ xref: UniProtKB:O76036 is_a: PR:000001893 ! natural cytotoxicity triggering receptor 1 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001893 ! natural cytotoxicity triggering receptor 1 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:O76070 @@ -150295,7 +150035,7 @@ xref: UniProtKB:O76070 is_a: PR:000015325 ! gamma-synuclein is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000015325 ! gamma-synuclein -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:O88324 @@ -150310,7 +150050,7 @@ xref: UniProtKB:O88324 is_a: PR:000001310 ! CD83 molecule is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001310 ! CD83 molecule -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:O88410 @@ -150330,7 +150070,7 @@ xref: UniProtKB:O88410 is_a: PR:000001207 ! C-X-C chemokine receptor type 3 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001207 ! C-X-C chemokine receptor type 3 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:O88713 @@ -150346,7 +150086,7 @@ xref: UniProtKB:O88713 is_a: PR:000009426 ! killer cell lectin-like receptor subfamily G member 1 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000009426 ! killer cell lectin-like receptor subfamily G member 1 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:O89103 @@ -150372,7 +150112,7 @@ xref: UniProtKB:O89103 is_a: PR:000002037 ! complement component C1q receptor is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000002037 ! complement component C1q receptor -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:O95936 @@ -150390,7 +150130,7 @@ xref: UniProtKB:O95936 is_a: PR:000003463 ! eomesodermin is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000003463 ! eomesodermin -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:O95944 @@ -150411,7 +150151,7 @@ xref: UniProtKB:O95944 is_a: PR:000001894 ! natural cytotoxicity triggering receptor 2 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001894 ! natural cytotoxicity triggering receptor 2 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P00797 @@ -150426,7 +150166,7 @@ xref: UniProtKB:P00797 is_a: PR:000013883 ! renin is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000013883 ! renin -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P01100 @@ -150447,7 +150187,7 @@ xref: UniProtKB:P01100 is_a: PR:000007597 ! protein c-Fos is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000007597 ! protein c-Fos -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P01101 @@ -150464,7 +150204,7 @@ xref: UniProtKB:P01101 is_a: PR:000007597 ! protein c-Fos is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000007597 ! protein c-Fos -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P01213 @@ -150480,7 +150220,7 @@ xref: UniProtKB:P01213 is_a: PR:000012526 ! proenkephalin-B is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000012526 ! proenkephalin-B -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P01236 @@ -150494,7 +150234,7 @@ xref: UniProtKB:P01236 is_a: PR:000013246 ! prolactin is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000013246 ! prolactin -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P01282 @@ -150510,7 +150250,7 @@ xref: UniProtKB:P01282 is_a: PR:000017299 ! VIP peptides is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000017299 ! VIP peptides -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P01308 @@ -150523,7 +150263,7 @@ xref: UniProtKB:P01308 is_a: PR:000009054 ! insulin gene translation product is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000009054 ! insulin gene translation product -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P01589 @@ -150544,7 +150284,7 @@ xref: UniProtKB:P01589 is_a: PR:000001380 ! interleukin-2 receptor subunit alpha is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001380 ! interleukin-2 receptor subunit alpha -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P01590 @@ -150565,7 +150305,7 @@ xref: UniProtKB:P01590 is_a: PR:000001380 ! interleukin-2 receptor subunit alpha is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001380 ! interleukin-2 receptor subunit alpha -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P01730 @@ -150580,7 +150320,7 @@ xref: UniProtKB:P01730 is_a: PR:000001004 ! CD4 molecule is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001004 ! CD4 molecule -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P01731 @@ -150598,7 +150338,7 @@ xref: UniProtKB:P01731 is_a: PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P01732 @@ -150615,7 +150355,7 @@ xref: UniProtKB:P01732 is_a: PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001084 ! T-cell surface glycoprotein CD8 alpha chain -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P01732-1 @@ -150630,7 +150370,7 @@ xref: UniProtKB:P01732-1 is_a: PR:000025403 ! T-cell surface glycoprotein CD8 alpha chain isoform 1 is_a: PR:P01732 ! T-cell surface glycoprotein CD8 alpha chain (human) intersection_of: PR:000025403 ! T-cell surface glycoprotein CD8 alpha chain isoform 1 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P01831 @@ -150647,7 +150387,7 @@ xref: UniProtKB:P01831 is_a: PR:000001843 ! Thy-1 membrane glycoprotein is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001843 ! Thy-1 membrane glycoprotein -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P01903 @@ -150665,7 +150405,7 @@ xref: UniProtKB:P01903 is_a: PR:000002015 ! MHC class II histocompatibility antigen alpha chain DRA is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000002015 ! MHC class II histocompatibility antigen alpha chain DRA -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P02008 @@ -150683,7 +150423,7 @@ xref: UniProtKB:P02008 is_a: PR:000008467 ! hemoglobin subunit zeta is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000008467 ! hemoglobin subunit zeta -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P02088 @@ -150700,7 +150440,7 @@ xref: UniProtKB:P02088 is_a: PR:000008857 ! hemoglobin subunit beta-1 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000008857 ! hemoglobin subunit beta-1 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P02452 @@ -150715,7 +150455,7 @@ xref: UniProtKB:P02452 is_a: PR:000003264 ! collagen alpha-1(I) chain is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000003264 ! collagen alpha-1(I) chain -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P02724 @@ -150734,7 +150474,7 @@ xref: UniProtKB:P02724 is_a: PR:000001460 ! glycophorin-A is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001460 ! glycophorin-A -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P02786 @@ -150760,7 +150500,7 @@ xref: UniProtKB:P02786 is_a: PR:000001945 ! transferrin receptor protein 1 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001945 ! transferrin receptor protein 1 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P02788 @@ -150779,7 +150519,7 @@ xref: UniProtKB:P02788 is_a: PR:000009978 ! lactotransferrin is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000009978 ! lactotransferrin -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P03372 @@ -150802,7 +150542,7 @@ xref: UniProtKB:P03372 is_a: PR:000007204 ! estrogen receptor is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000007204 ! estrogen receptor -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P03995 @@ -150817,7 +150557,7 @@ xref: UniProtKB:P03995 is_a: PR:000007939 ! glial fibrillary acidic protein is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000007939 ! glial fibrillary acidic protein -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P04000 @@ -150837,7 +150577,7 @@ xref: UniProtKB:P04000 is_a: PR:000001244 ! long-wave-sensitive opsin 1 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001244 ! long-wave-sensitive opsin 1 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P04001 @@ -150872,7 +150612,7 @@ xref: UniProtKB:P04053 is_a: PR:000006611 ! DNA nucleotidylexotransferase is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000006611 ! DNA nucleotidylexotransferase -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P04216 @@ -150889,7 +150629,7 @@ xref: UniProtKB:P04216 is_a: PR:000001843 ! Thy-1 membrane glycoprotein is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001843 ! Thy-1 membrane glycoprotein -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P05089 @@ -150909,7 +150649,7 @@ xref: UniProtKB:P05089 is_a: PR:000001844 ! arginase-1 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001844 ! arginase-1 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P05164 @@ -150923,7 +150663,7 @@ xref: UniProtKB:P05164 is_a: PR:000010543 ! myeloperoxidase is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000010543 ! myeloperoxidase -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P05532 @@ -150942,7 +150682,7 @@ xref: UniProtKB:P05532 is_a: PR:000002065 ! mast/stem cell growth factor receptor is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000002065 ! mast/stem cell growth factor receptor -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P05533 @@ -150962,7 +150702,7 @@ xref: UniProtKB:P05533 is_a: PR:000002979 ! lymphocyte antigen 6A-2/6E-1 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000002979 ! lymphocyte antigen 6A-2/6E-1 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P05555 @@ -150981,7 +150721,7 @@ xref: UniProtKB:P05555 is_a: PR:000001012 ! integrin alpha-M is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001012 ! integrin alpha-M -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P06126 @@ -151000,7 +150740,7 @@ xref: UniProtKB:P06126 is_a: PR:000002025 ! T-cell surface glycoprotein CD1a is_a: PR:000036947 ! T-cell surface glycoprotein CD1 (human) intersection_of: PR:000002025 ! T-cell surface glycoprotein CD1a -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P06127 @@ -151016,7 +150756,7 @@ xref: UniProtKB:P06127 is_a: PR:000001839 ! T-cell surface glycoprotein CD5 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001839 ! T-cell surface glycoprotein CD5 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P06307 @@ -151030,7 +150770,7 @@ xref: UniProtKB:P06307 is_a: PR:000005110 ! cholecystokinin is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000005110 ! cholecystokinin -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P06332 @@ -151047,7 +150787,7 @@ xref: UniProtKB:P06332 is_a: PR:000001004 ! CD4 molecule is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001004 ! CD4 molecule -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P06467 @@ -151066,7 +150806,7 @@ xref: UniProtKB:P06467 is_a: PR:000008467 ! hemoglobin subunit zeta is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000008467 ! hemoglobin subunit zeta -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P06729 @@ -151086,7 +150826,7 @@ xref: UniProtKB:P06729 is_a: PR:000001083 ! CD2 molecule is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001083 ! CD2 molecule -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P06734 @@ -151111,7 +150851,7 @@ xref: UniProtKB:P06734 is_a: PR:000001880 ! low affinity immunoglobulin epsilon Fc receptor is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001880 ! low affinity immunoglobulin epsilon Fc receptor -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P06800 @@ -151131,7 +150871,7 @@ xref: UniProtKB:P06800 is_a: PR:000001006 ! receptor-type tyrosine-protein phosphatase C is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001006 ! receptor-type tyrosine-protein phosphatase C -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P06876 @@ -151146,7 +150886,7 @@ xref: UniProtKB:P06876 is_a: PR:000010799 ! myb proto-oncogene protein is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000010799 ! myb proto-oncogene protein -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P06879 @@ -151161,7 +150901,7 @@ xref: UniProtKB:P06879 is_a: PR:000013246 ! prolactin is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000013246 ! prolactin -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P07101 @@ -151177,7 +150917,7 @@ xref: UniProtKB:P07101 is_a: PR:000016301 ! tyrosine 3-monooxygenase is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000016301 ! tyrosine 3-monooxygenase -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P07204 @@ -151195,7 +150935,7 @@ xref: UniProtKB:P07204 is_a: PR:000002105 ! thrombomodulin is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000002105 ! thrombomodulin -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P07333 @@ -151217,7 +150957,7 @@ xref: UniProtKB:P07333 is_a: PR:000002062 ! macrophage colony-stimulating factor 1 receptor is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000002062 ! macrophage colony-stimulating factor 1 receptor -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P07359 @@ -151237,7 +150977,7 @@ xref: UniProtKB:P07359 is_a: PR:000001907 ! platelet glycoprotein Ib alpha chain is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001907 ! platelet glycoprotein Ib alpha chain -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P07766 @@ -151254,7 +150994,7 @@ xref: UniProtKB:P07766 is_a: PR:000001020 ! CD3 epsilon is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001020 ! CD3 epsilon -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P08071 @@ -151269,7 +151009,7 @@ xref: UniProtKB:P08071 is_a: PR:000009978 ! lactotransferrin is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000009978 ! lactotransferrin -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P08101 @@ -151292,7 +151032,7 @@ xref: UniProtKB:P08101 is_a: PR:000001479 ! low affinity immunoglobulin gamma Fc region receptor II is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001479 ! low affinity immunoglobulin gamma Fc region receptor II -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P08152 @@ -151313,7 +151053,7 @@ xref: UniProtKB:P08152 is_a: PR:000003469 ! early growth response protein 2 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000003469 ! early growth response protein 2 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P08473 @@ -151338,7 +151078,7 @@ xref: UniProtKB:P08473 is_a: PR:000001898 ! neprilysin is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001898 ! neprilysin -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P08508 @@ -151356,7 +151096,7 @@ xref: UniProtKB:P08508 is_a: PR:000001483 ! low affinity immunoglobulin gamma Fc region receptor III is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001483 ! low affinity immunoglobulin gamma Fc region receptor III -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P08514 @@ -151376,7 +151116,7 @@ xref: UniProtKB:P08514 is_a: PR:000009127 ! integrin alpha-IIb is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000009127 ! integrin alpha-IIb -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P08571 @@ -151391,7 +151131,7 @@ xref: UniProtKB:P08571 is_a: PR:000001889 ! CD14 molecule is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001889 ! CD14 molecule -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P08575 @@ -151409,7 +151149,7 @@ xref: UniProtKB:P08575 is_a: PR:000001006 ! receptor-type tyrosine-protein phosphatase C is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001006 ! receptor-type tyrosine-protein phosphatase C -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P08575-3 @@ -151422,7 +151162,7 @@ xref: UniProtKB:P08575-3 is_a: PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45RABC is_a: PR:P08575 ! receptor-type tyrosine-protein phosphatase C (human) intersection_of: PR:000001014 ! receptor-type tyrosine-protein phosphatase C isoform CD45RABC -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P08575-4 @@ -151436,7 +151176,7 @@ xref: UniProtKB:P08575-4 is_a: PR:000001017 ! receptor-type tyrosine-protein phosphatase C isoform CD45RO is_a: PR:P08575 ! receptor-type tyrosine-protein phosphatase C (human) intersection_of: PR:000001017 ! receptor-type tyrosine-protein phosphatase C isoform CD45RO -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P08575-8 @@ -151450,7 +151190,7 @@ xref: UniProtKB:P08575-8 is_a: PR:000001015 ! receptor-type tyrosine-protein phosphatase C isoform CD45RA is_a: PR:P08575 ! receptor-type tyrosine-protein phosphatase C (human) intersection_of: PR:000001015 ! receptor-type tyrosine-protein phosphatase C isoform CD45RA -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P08670 @@ -151468,7 +151208,7 @@ xref: UniProtKB:P08670 is_a: PR:000017298 ! vimentin is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000017298 ! vimentin -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P08920 @@ -151488,7 +151228,7 @@ xref: UniProtKB:P08920 is_a: PR:000001083 ! CD2 molecule is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001083 ! CD2 molecule -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P09240 @@ -151503,7 +151243,7 @@ xref: UniProtKB:P09240 is_a: PR:000005110 ! cholecystokinin is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000005110 ! cholecystokinin -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P09326 @@ -151526,7 +151266,7 @@ xref: UniProtKB:P09326 is_a: PR:000001308 ! CD48 molecule is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001308 ! CD48 molecule -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P09382 @@ -151552,7 +151292,7 @@ xref: UniProtKB:P09382 is_a: PR:000009766 ! galectin-1 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000009766 ! galectin-1 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P09564 @@ -151570,7 +151310,7 @@ xref: UniProtKB:P09564 is_a: PR:000001836 ! CD7 molecule is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001836 ! CD7 molecule -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P09581 @@ -151592,7 +151332,7 @@ xref: UniProtKB:P09581 is_a: PR:000002062 ! macrophage colony-stimulating factor 1 receptor is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000002062 ! macrophage colony-stimulating factor 1 receptor -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P09793 @@ -151610,7 +151350,7 @@ xref: UniProtKB:P09793 is_a: PR:000001852 ! cytotoxic T-lymphocyte protein 4 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001852 ! cytotoxic T-lymphocyte protein 4 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P09803 @@ -151629,7 +151369,7 @@ xref: UniProtKB:P09803 is_a: PR:000001447 ! cadherin-1 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001447 ! cadherin-1 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P09838 @@ -151648,7 +151388,7 @@ xref: UniProtKB:P09838 is_a: PR:000006611 ! DNA nucleotidylexotransferase is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000006611 ! DNA nucleotidylexotransferase -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P0CW03 @@ -151664,7 +151404,7 @@ xref: UniProtKB:P0CW03 is_a: PR:000002980 ! lymphocyte antigen 6C2 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000002980 ! lymphocyte antigen 6C2 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P0DN77 @@ -151724,7 +151464,7 @@ xref: UniProtKB:P10144 is_a: PR:000003499 ! granzyme B is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000003499 ! granzyme B -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P10147 @@ -151748,7 +151488,7 @@ xref: UniProtKB:P10147 is_a: PR:000002123 ! C-C motif chemokine 3 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000002123 ! C-C motif chemokine 3 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P10153 @@ -151769,7 +151509,7 @@ xref: UniProtKB:P10153 is_a: PR:000014046 ! non-secretory ribonuclease is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000014046 ! non-secretory ribonuclease -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P10242 @@ -151785,7 +151525,7 @@ xref: UniProtKB:P10242 is_a: PR:000010799 ! myb proto-oncogene protein is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000010799 ! myb proto-oncogene protein -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P10300 @@ -151807,7 +151547,7 @@ xref: UniProtKB:P10300 is_a: PR:000001085 ! T-cell surface glycoprotein CD8 beta chain is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001085 ! T-cell surface glycoprotein CD8 beta chain -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P10721 @@ -151830,7 +151570,7 @@ xref: UniProtKB:P10721 is_a: PR:000002065 ! mast/stem cell growth factor receptor is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000002065 ! mast/stem cell growth factor receptor -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P10747 @@ -151845,7 +151585,7 @@ xref: UniProtKB:P10747 is_a: PR:000001841 ! T-cell-specific surface glycoprotein CD28 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001841 ! T-cell-specific surface glycoprotein CD28 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P10810 @@ -151861,7 +151601,7 @@ xref: UniProtKB:P10810 is_a: PR:000001889 ! CD14 molecule is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001889 ! CD14 molecule -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P10820 @@ -151879,7 +151619,7 @@ xref: UniProtKB:P10820 is_a: PR:000003466 ! perforin-1 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000003466 ! perforin-1 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P10855 @@ -151902,7 +151642,7 @@ xref: UniProtKB:P10855 is_a: PR:000002123 ! C-C motif chemokine 3 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000002123 ! C-C motif chemokine 3 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P10966 @@ -151918,7 +151658,7 @@ xref: UniProtKB:P10966 is_a: PR:000001085 ! T-cell surface glycoprotein CD8 beta chain is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001085 ! T-cell surface glycoprotein CD8 beta chain -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P10966-1 @@ -151933,7 +151673,7 @@ xref: UniProtKB:P10966-1 is_a: PR:000025405 ! T-cell surface glycoprotein CD8 beta chain isoform 1 is_a: PR:P10966 ! T-cell surface glycoprotein CD8 beta chain (human) intersection_of: PR:000025405 ! T-cell surface glycoprotein CD8 beta chain isoform 1 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P11087 @@ -151949,7 +151689,7 @@ xref: UniProtKB:P11087 is_a: PR:000003264 ! collagen alpha-1(I) chain is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000003264 ! collagen alpha-1(I) chain -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P11161 @@ -151970,7 +151710,7 @@ xref: UniProtKB:P11161 is_a: PR:000003469 ! early growth response protein 2 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000003469 ! early growth response protein 2 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P11215 @@ -151991,7 +151731,7 @@ xref: UniProtKB:P11215 is_a: PR:000001012 ! integrin alpha-M is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001012 ! integrin alpha-M -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P11247 @@ -152006,7 +151746,7 @@ xref: UniProtKB:P11247 is_a: PR:000010543 ! myeloperoxidase is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000010543 ! myeloperoxidase -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P11609 @@ -152022,7 +151762,7 @@ xref: UniProtKB:P11609 is_a: PR:000002028 ! antigen-presenting glycoprotein CD1d is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000002028 ! antigen-presenting glycoprotein CD1d -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P11672 @@ -152043,7 +151783,7 @@ xref: UniProtKB:P11672 is_a: PR:000009725 ! neutrophil gelatinase-associated lipocalin is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000009725 ! neutrophil gelatinase-associated lipocalin -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P11678 @@ -152060,7 +151800,7 @@ xref: UniProtKB:P11678 is_a: PR:000007152 ! eosinophil peroxidase is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000007152 ! eosinophil peroxidase -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P11684 @@ -152085,7 +151825,7 @@ xref: UniProtKB:P11684 is_a: PR:000014505 ! uteroglobin is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000014505 ! uteroglobin -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P11836 @@ -152104,7 +151844,7 @@ xref: UniProtKB:P11836 is_a: PR:000001289 ! membrane-spanning 4-domains subfamily A member 1 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001289 ! membrane-spanning 4-domains subfamily A member 1 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P12018 @@ -152124,7 +151864,7 @@ xref: UniProtKB:P12018 is_a: PR:000001858 ! immunoglobulin iota chain is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001858 ! immunoglobulin iota chain -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P12314 @@ -152147,7 +151887,7 @@ xref: UniProtKB:P12314 is_a: PR:000001465 ! high affinity immunoglobulin gamma Fc receptor I is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001465 ! high affinity immunoglobulin gamma Fc receptor I -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P12319 @@ -152165,7 +151905,7 @@ xref: UniProtKB:P12319 is_a: PR:000007431 ! high affinity immunoglobulin epsilon receptor subunit alpha is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000007431 ! high affinity immunoglobulin epsilon receptor subunit alpha -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P12724 @@ -152183,7 +151923,7 @@ xref: UniProtKB:P12724 is_a: PR:000014047 ! eosinophil cationic protein is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000014047 ! eosinophil cationic protein -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P12830 @@ -152204,7 +151944,7 @@ xref: UniProtKB:P12830 is_a: PR:000001447 ! cadherin-1 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001447 ! cadherin-1 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P13379 @@ -152222,7 +151962,7 @@ xref: UniProtKB:P13379 is_a: PR:000001839 ! T-cell surface glycoprotein CD5 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001839 ! T-cell surface glycoprotein CD5 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P13591 @@ -152240,7 +151980,7 @@ xref: UniProtKB:P13591 is_a: PR:000001024 ! neural cell adhesion molecule 1 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001024 ! neural cell adhesion molecule 1 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P13595 @@ -152258,7 +151998,7 @@ xref: UniProtKB:P13595 is_a: PR:000001024 ! neural cell adhesion molecule 1 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001024 ! neural cell adhesion molecule 1 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P13612 @@ -152276,7 +152016,7 @@ xref: UniProtKB:P13612 is_a: PR:000009129 ! integrin alpha-4 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000009129 ! integrin alpha-4 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P13686 @@ -152294,7 +152034,7 @@ xref: UniProtKB:P13686 is_a: PR:000001937 ! tartrate-resistant acid phosphatase type 5 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001937 ! tartrate-resistant acid phosphatase type 5 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P13727 @@ -152311,7 +152051,7 @@ xref: UniProtKB:P13727 is_a: PR:000013206 ! bone marrow proteoglycan is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000013206 ! bone marrow proteoglycan -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P13727-1 @@ -152324,7 +152064,7 @@ xref: UniProtKB:P13727-1 is_a: PR:000022003 ! bone marrow proteoglycan isoform 1 is_a: PR:P13727 ! bone marrow proteoglycan (human) intersection_of: PR:000022003 ! bone marrow proteoglycan isoform 1 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P14136 @@ -152340,7 +152080,7 @@ xref: UniProtKB:P14136 is_a: PR:000007939 ! glial fibrillary acidic protein is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000007939 ! glial fibrillary acidic protein -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P14151 @@ -152366,7 +152106,7 @@ xref: UniProtKB:P14151 is_a: PR:000001318 ! L-selectin is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001318 ! L-selectin -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P14222 @@ -152384,7 +152124,7 @@ xref: UniProtKB:P14222 is_a: PR:000003466 ! perforin-1 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000003466 ! perforin-1 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P14416 @@ -152401,7 +152141,7 @@ xref: UniProtKB:P14416 is_a: PR:000001177 ! D(2) dopamine receptor is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001177 ! D(2) dopamine receptor -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P14719 @@ -152422,7 +152162,7 @@ xref: UniProtKB:P14719 is_a: PR:000008994 ! interleukin-1 receptor-like 1 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000008994 ! interleukin-1 receptor-like 1 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P14784 @@ -152445,7 +152185,7 @@ xref: UniProtKB:P14784 is_a: PR:000001381 ! interleukin-2 receptor subunit beta is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001381 ! interleukin-2 receptor subunit beta -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P15144 @@ -152470,7 +152210,7 @@ xref: UniProtKB:P15144 is_a: PR:000002031 ! aminopeptidase N is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000002031 ! aminopeptidase N -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P15306 @@ -152487,7 +152227,7 @@ xref: UniProtKB:P15306 is_a: PR:000002105 ! thrombomodulin is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000002105 ! thrombomodulin -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P15379 @@ -152514,7 +152254,7 @@ xref: UniProtKB:P15379 is_a: PR:000001307 ! CD44 molecule is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001307 ! CD44 molecule -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P15391 @@ -152531,7 +152271,7 @@ xref: UniProtKB:P15391 is_a: PR:000001002 ! CD19 molecule is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001002 ! CD19 molecule -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P15702 @@ -152551,7 +152291,7 @@ xref: UniProtKB:P15702 is_a: PR:000001879 ! leukosialin is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001879 ! leukosialin -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P15813 @@ -152569,7 +152309,7 @@ xref: UniProtKB:P15813 is_a: PR:000002028 ! antigen-presenting glycoprotein CD1d is_a: PR:000036947 ! T-cell surface glycoprotein CD1 (human) intersection_of: PR:000002028 ! antigen-presenting glycoprotein CD1d -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P15814 @@ -152589,7 +152329,7 @@ xref: UniProtKB:P15814 is_a: PR:000001859 ! immunoglobulin lambda-like polypeptide 1 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001859 ! immunoglobulin lambda-like polypeptide 1 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P15918 @@ -152607,7 +152347,7 @@ xref: UniProtKB:P15918 is_a: PR:000003457 ! V(D)J recombination-activating protein 1 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000003457 ! V(D)J recombination-activating protein 1 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P15919 @@ -152622,7 +152362,7 @@ xref: UniProtKB:P15919 is_a: PR:000003457 ! V(D)J recombination-activating protein 1 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000003457 ! V(D)J recombination-activating protein 1 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P15976 @@ -152643,7 +152383,7 @@ xref: UniProtKB:P15976 is_a: PR:000007857 ! erythroid transcription factor is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000007857 ! erythroid transcription factor -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P16045 @@ -152665,7 +152405,7 @@ xref: UniProtKB:P16045 is_a: PR:000009766 ! galectin-1 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000009766 ! galectin-1 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P16070 @@ -152696,7 +152436,7 @@ xref: UniProtKB:P16070 is_a: PR:000001307 ! CD44 molecule is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001307 ! CD44 molecule -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P16150 @@ -152716,7 +152456,7 @@ xref: UniProtKB:P16150 is_a: PR:000001879 ! leukosialin is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001879 ! leukosialin -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P16234 @@ -152743,7 +152483,7 @@ xref: UniProtKB:P16234 is_a: PR:000002030 ! alpha-type platelet-derived growth factor receptor is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000002030 ! alpha-type platelet-derived growth factor receptor -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P16297 @@ -152763,7 +152503,7 @@ xref: UniProtKB:P16297 is_a: PR:000001381 ! interleukin-2 receptor subunit beta is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001381 ! interleukin-2 receptor subunit beta -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P16406 @@ -152782,7 +152522,7 @@ xref: UniProtKB:P16406 is_a: PR:000002039 ! glutamyl aminopeptidase is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000002039 ! glutamyl aminopeptidase -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P16410 @@ -152799,7 +152539,7 @@ xref: UniProtKB:P16410 is_a: PR:000001852 ! cytotoxic T-lymphocyte protein 4 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001852 ! cytotoxic T-lymphocyte protein 4 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P16671 @@ -152826,7 +152566,7 @@ xref: UniProtKB:P16671 is_a: PR:000001905 ! platelet glycoprotein 4 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001905 ! platelet glycoprotein 4 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P16871 @@ -152846,7 +152586,7 @@ xref: UniProtKB:P16871 is_a: PR:000001869 ! interleukin-7 receptor subunit alpha is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001869 ! interleukin-7 receptor subunit alpha -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P16872 @@ -152865,7 +152605,7 @@ xref: UniProtKB:P16872 is_a: PR:000001869 ! interleukin-7 receptor subunit alpha is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001869 ! interleukin-7 receptor subunit alpha -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P17301 @@ -152885,7 +152625,7 @@ xref: UniProtKB:P17301 is_a: PR:000001008 ! integrin alpha-2 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001008 ! integrin alpha-2 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P17433 @@ -152903,7 +152643,7 @@ xref: UniProtKB:P17433 is_a: PR:000001944 ! transcription factor PU.1 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001944 ! transcription factor PU.1 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P17542 @@ -152925,7 +152665,7 @@ xref: UniProtKB:P17542 is_a: PR:000016043 ! T-cell acute lymphocytic leukemia protein 1 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000016043 ! T-cell acute lymphocytic leukemia protein 1 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P17679 @@ -152945,7 +152685,7 @@ xref: UniProtKB:P17679 is_a: PR:000007857 ! erythroid transcription factor is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000007857 ! erythroid transcription factor -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P17813 @@ -152961,7 +152701,7 @@ xref: UniProtKB:P17813 is_a: PR:000001345 ! endoglin is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001345 ! endoglin -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P17927 @@ -152978,7 +152718,7 @@ xref: UniProtKB:P17927 is_a: PR:000001337 ! complement receptor type 1 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001337 ! complement receptor type 1 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P17947 @@ -152994,7 +152734,7 @@ xref: UniProtKB:P17947 is_a: PR:000001944 ! transcription factor PU.1 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001944 ! transcription factor PU.1 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P18181 @@ -153018,7 +152758,7 @@ xref: UniProtKB:P18181 is_a: PR:000001308 ! CD48 molecule is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001308 ! CD48 molecule -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P18337 @@ -153044,7 +152784,7 @@ xref: UniProtKB:P18337 is_a: PR:000001318 ! L-selectin is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001318 ! L-selectin -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P18827 @@ -153061,7 +152801,7 @@ xref: UniProtKB:P18827 is_a: PR:000001935 ! syndecan-1 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001935 ! syndecan-1 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P18828 @@ -153079,7 +152819,7 @@ xref: UniProtKB:P18828 is_a: PR:000001935 ! syndecan-1 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001935 ! syndecan-1 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P19070 @@ -153095,7 +152835,7 @@ xref: UniProtKB:P19070 is_a: PR:000001338 ! complement receptor type 2 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001338 ! complement receptor type 2 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P19437 @@ -153116,7 +152856,7 @@ xref: UniProtKB:P19437 is_a: PR:000001289 ! membrane-spanning 4-domains subfamily A member 1 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001289 ! membrane-spanning 4-domains subfamily A member 1 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P19785 @@ -153138,7 +152878,7 @@ xref: UniProtKB:P19785 is_a: PR:000007204 ! estrogen receptor is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000007204 ! estrogen receptor -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P20023 @@ -153158,7 +152898,7 @@ xref: UniProtKB:P20023 is_a: PR:000001338 ! complement receptor type 2 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001338 ! complement receptor type 2 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P20138 @@ -153176,7 +152916,7 @@ xref: UniProtKB:P20138 is_a: PR:000001892 ! CD33 molecule is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001892 ! CD33 molecule -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P20152 @@ -153190,7 +152930,7 @@ xref: UniProtKB:P20152 is_a: PR:000017298 ! vimentin is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000017298 ! vimentin -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P20273 @@ -153210,7 +152950,7 @@ xref: UniProtKB:P20273 is_a: PR:000001288 ! B-cell receptor CD22 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001288 ! B-cell receptor CD22 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P20472 @@ -153224,7 +152964,7 @@ xref: UniProtKB:P20472 is_a: PR:000013502 ! parvalbumin alpha is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000013502 ! parvalbumin alpha -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P20489 @@ -153242,7 +152982,7 @@ xref: UniProtKB:P20489 is_a: PR:000007431 ! high affinity immunoglobulin epsilon receptor subunit alpha is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000007431 ! high affinity immunoglobulin epsilon receptor subunit alpha -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P20693 @@ -153260,7 +153000,7 @@ xref: UniProtKB:P20693 is_a: PR:000001880 ! low affinity immunoglobulin epsilon Fc receptor is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001880 ! low affinity immunoglobulin epsilon Fc receptor -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P20702 @@ -153279,7 +153019,7 @@ xref: UniProtKB:P20702 is_a: PR:000001013 ! integrin alpha-X is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001013 ! integrin alpha-X -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P20937 @@ -153299,7 +153039,7 @@ xref: UniProtKB:P20937 is_a: PR:000009616 ! T-cell surface glycoprotein YE1/48 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000009616 ! T-cell surface glycoprotein YE1/48 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P21183 @@ -153319,7 +153059,7 @@ xref: UniProtKB:P21183 is_a: PR:000001867 ! interleukin-5 receptor subunit alpha is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001867 ! interleukin-5 receptor subunit alpha -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P21462 @@ -153342,7 +153082,7 @@ xref: UniProtKB:P21462 is_a: PR:000001580 ! fMet-Leu-Phe receptor is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001580 ! fMet-Leu-Phe receptor -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P21728 @@ -153359,7 +153099,7 @@ xref: UniProtKB:P21728 is_a: PR:000001175 ! D(1A) dopamine receptor is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001175 ! D(1A) dopamine receptor -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P21757 @@ -153377,7 +153117,7 @@ xref: UniProtKB:P21757 is_a: PR:000001885 ! macrophage scavenger receptor types I and II is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001885 ! macrophage scavenger receptor types I and II -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P21784 @@ -153393,7 +153133,7 @@ xref: UniProtKB:P21784 is_a: PR:000003460 ! V(D)J recombination-activating protein 2 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000003460 ! V(D)J recombination-activating protein 2 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P21926 @@ -153418,7 +153158,7 @@ xref: UniProtKB:P21926 is_a: PR:000005178 ! CD9 molecule is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000005178 ! CD9 molecule -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P22083 @@ -153442,7 +153182,7 @@ xref: UniProtKB:P22083 is_a: PR:000001456 ! alpha-(1,3)-fucosyltransferase 4 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001456 ! alpha-(1,3)-fucosyltransferase 4 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P22091 @@ -153460,7 +153200,7 @@ xref: UniProtKB:P22091 is_a: PR:000016043 ! T-cell acute lymphocytic leukemia protein 1 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000016043 ! T-cell acute lymphocytic leukemia protein 1 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P22646 @@ -153476,7 +153216,7 @@ xref: UniProtKB:P22646 is_a: PR:000001020 ! CD3 epsilon is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001020 ! CD3 epsilon -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P22897 @@ -153500,7 +153240,7 @@ xref: UniProtKB:P22897 is_a: PR:000002972 ! macrophage mannose receptor 1 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000002972 ! macrophage mannose receptor 1 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P23769 @@ -153516,7 +153256,7 @@ xref: UniProtKB:P23769 is_a: PR:000007858 ! endothelial transcription factor GATA-2 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000007858 ! endothelial transcription factor GATA-2 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P23771 @@ -153532,7 +153272,7 @@ xref: UniProtKB:P23771 is_a: PR:000001941 ! trans-acting T-cell-specific transcription factor GATA-3 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001941 ! trans-acting T-cell-specific transcription factor GATA-3 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P23772 @@ -153548,7 +153288,7 @@ xref: UniProtKB:P23772 is_a: PR:000001941 ! trans-acting T-cell-specific transcription factor GATA-3 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001941 ! trans-acting T-cell-specific transcription factor GATA-3 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P24529 @@ -153564,7 +153304,7 @@ xref: UniProtKB:P24529 is_a: PR:000016301 ! tyrosine 3-monooxygenase is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000016301 ! tyrosine 3-monooxygenase -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P24807 @@ -153587,7 +153327,7 @@ xref: UniProtKB:P24807 is_a: PR:000001932 ! signal transducer CD24 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001932 ! signal transducer CD24 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P25024 @@ -153613,7 +153353,7 @@ xref: UniProtKB:P25024 is_a: PR:000001256 ! C-X-C chemokine receptor type 1 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001256 ! C-X-C chemokine receptor type 1 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P25025 @@ -153639,7 +153379,7 @@ xref: UniProtKB:P25025 is_a: PR:000001257 ! C-X-C chemokine receptor type 2 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001257 ! C-X-C chemokine receptor type 2 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P25063 @@ -153655,7 +153395,7 @@ xref: UniProtKB:P25063 is_a: PR:000001932 ! signal transducer CD24 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001932 ! signal transducer CD24 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P25918 @@ -153671,7 +153411,7 @@ xref: UniProtKB:P25918 is_a: PR:000001002 ! CD19 molecule is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001002 ! CD19 molecule -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P26010 @@ -153686,7 +153426,7 @@ xref: UniProtKB:P26010 is_a: PR:000009143 ! integrin beta-7 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000009143 ! integrin beta-7 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P26011 @@ -153702,7 +153442,7 @@ xref: UniProtKB:P26011 is_a: PR:000009143 ! integrin beta-7 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000009143 ! integrin beta-7 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P26151 @@ -153721,7 +153461,7 @@ xref: UniProtKB:P26151 is_a: PR:000001465 ! high affinity immunoglobulin gamma Fc receptor I is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001465 ! high affinity immunoglobulin gamma Fc receptor I -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P26618 @@ -153742,7 +153482,7 @@ xref: UniProtKB:P26618 is_a: PR:000002030 ! alpha-type platelet-derived growth factor receptor is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000002030 ! alpha-type platelet-derived growth factor receptor -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P26715 @@ -153762,7 +153502,7 @@ xref: UniProtKB:P26715 is_a: PR:000002023 ! NKG2-A/NKG2-B type II integral membrane protein is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000002023 ! NKG2-A/NKG2-B type II integral membrane protein -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P26842 @@ -153781,7 +153521,7 @@ xref: UniProtKB:P26842 is_a: PR:000001963 ! CD27 molecule is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001963 ! CD27 molecule -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P26951 @@ -153801,7 +153541,7 @@ xref: UniProtKB:P26951 is_a: PR:000001865 ! interleukin-3 receptor class 2 alpha chain is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001865 ! interleukin-3 receptor class 2 alpha chain -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P26952 @@ -153822,7 +153562,7 @@ xref: UniProtKB:P26952 is_a: PR:000001865 ! interleukin-3 receptor class 2 alpha chain is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001865 ! interleukin-3 receptor class 2 alpha chain -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P27548 @@ -153844,7 +153584,7 @@ xref: UniProtKB:P27548 is_a: PR:000001950 ! tumor necrosis factor ligand superfamily member 5 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001950 ! tumor necrosis factor ligand superfamily member 5 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P27814 @@ -153869,7 +153609,7 @@ xref: UniProtKB:P27814 is_a: PR:000002977 ! killer cell lectin-like receptor subfamily B member 1C is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000002977 ! killer cell lectin-like receptor subfamily B member 1C -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P28906 @@ -153883,7 +153623,7 @@ xref: UniProtKB:P28906 is_a: PR:000001003 ! CD34 molecule is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001003 ! CD34 molecule -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P28907 @@ -153906,7 +153646,7 @@ xref: UniProtKB:P28907 is_a: PR:000001408 ! ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001408 ! ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P29017 @@ -153923,7 +153663,7 @@ xref: UniProtKB:P29017 is_a: PR:000002027 ! T-cell surface glycoprotein CD1c is_a: PR:000036947 ! T-cell surface glycoprotein CD1 (human) intersection_of: PR:000002027 ! T-cell surface glycoprotein CD1c -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P29965 @@ -153946,7 +153686,7 @@ xref: UniProtKB:P29965 is_a: PR:000001950 ! tumor necrosis factor ligand superfamily member 5 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001950 ! tumor necrosis factor ligand superfamily member 5 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P30204 @@ -153965,7 +153705,7 @@ xref: UniProtKB:P30204 is_a: PR:000001885 ! macrophage scavenger receptor types I and II is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001885 ! macrophage scavenger receptor types I and II -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P30530 @@ -153982,7 +153722,7 @@ xref: UniProtKB:P30530 is_a: PR:000004528 ! tyrosine-protein kinase receptor UFO is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000004528 ! tyrosine-protein kinase receptor UFO -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P30559 @@ -153999,7 +153739,7 @@ xref: UniProtKB:P30559 is_a: PR:000001635 ! oxytocin receptor is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001635 ! oxytocin receptor -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P31041 @@ -154014,7 +153754,7 @@ xref: UniProtKB:P31041 is_a: PR:000001841 ! T-cell-specific surface glycoprotein CD28 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001841 ! T-cell-specific surface glycoprotein CD28 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P31994 @@ -154037,7 +153777,7 @@ xref: UniProtKB:P31994 is_a: PR:000001481 ! low affinity immunoglobulin gamma Fc region receptor II-b is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001481 ! low affinity immunoglobulin gamma Fc region receptor II-b -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P31996 @@ -154052,7 +153792,7 @@ xref: UniProtKB:P31996 is_a: PR:000002064 ! macrosialin is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000002064 ! macrosialin -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P31997 @@ -154071,7 +153811,7 @@ xref: UniProtKB:P31997 is_a: PR:000001332 ! carcinoembryonic antigen-related cell adhesion molecule 8 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001332 ! carcinoembryonic antigen-related cell adhesion molecule 8 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P32246 @@ -154099,7 +153839,7 @@ xref: UniProtKB:P32246 is_a: PR:000001254 ! C-C chemokine receptor type 1 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001254 ! C-C chemokine receptor type 1 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P32248 @@ -154126,7 +153866,7 @@ xref: UniProtKB:P32248 is_a: PR:000001203 ! C-C chemokine receptor type 7 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001203 ! C-C chemokine receptor type 7 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P32302 @@ -154150,7 +153890,7 @@ xref: UniProtKB:P32302 is_a: PR:000001209 ! C-X-C chemokine receptor type 5 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001209 ! C-X-C chemokine receptor type 5 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P32648 @@ -154164,7 +153904,7 @@ xref: UniProtKB:P32648 is_a: PR:000017299 ! VIP peptides is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000017299 ! VIP peptides -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P32848 @@ -154179,7 +153919,7 @@ xref: UniProtKB:P32848 is_a: PR:000013502 ! parvalbumin alpha is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000013502 ! parvalbumin alpha -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P33151 @@ -154197,7 +153937,7 @@ xref: UniProtKB:P33151 is_a: PR:000001444 ! cadherin-5 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001444 ! cadherin-5 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P33681 @@ -154218,7 +153958,7 @@ xref: UniProtKB:P33681 is_a: PR:000001438 ! CD80 molecule is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001438 ! CD80 molecule -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P33766 @@ -154236,7 +153976,7 @@ xref: UniProtKB:P33766 is_a: PR:000001580 ! fMet-Leu-Phe receptor is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001580 ! fMet-Leu-Phe receptor -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P34810 @@ -154251,7 +153991,7 @@ xref: UniProtKB:P34810 is_a: PR:000002064 ! macrosialin is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000002064 ! macrosialin -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P35329 @@ -154273,7 +154013,7 @@ xref: UniProtKB:P35329 is_a: PR:000001288 ! B-cell receptor CD22 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001288 ! B-cell receptor CD22 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P35343 @@ -154296,7 +154036,7 @@ xref: UniProtKB:P35343 is_a: PR:000001257 ! C-X-C chemokine receptor type 2 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001257 ! C-X-C chemokine receptor type 2 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P35456 @@ -154313,7 +154053,7 @@ xref: UniProtKB:P35456 is_a: PR:000001969 ! urokinase plasminogen activator surface receptor is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001969 ! urokinase plasminogen activator surface receptor -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P35461 @@ -154329,7 +154069,7 @@ xref: UniProtKB:P35461 is_a: PR:000002978 ! lymphocyte antigen 6G is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000002978 ! lymphocyte antigen 6G -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P35918 @@ -154351,7 +154091,7 @@ xref: UniProtKB:P35918 is_a: PR:000002112 ! vascular endothelial growth factor receptor 2 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000002112 ! vascular endothelial growth factor receptor 2 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P35968 @@ -154374,7 +154114,7 @@ xref: UniProtKB:P35968 is_a: PR:000002112 ! vascular endothelial growth factor receptor 2 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000002112 ! vascular endothelial growth factor receptor 2 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P36544 @@ -154390,7 +154130,7 @@ xref: UniProtKB:P36544 is_a: PR:000005460 ! neuronal acetylcholine receptor subunit alpha-7 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000005460 ! neuronal acetylcholine receptor subunit alpha-7 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P36888 @@ -154415,7 +154155,7 @@ xref: UniProtKB:P36888 is_a: PR:000002001 ! receptor-type tyrosine-protein kinase FLT3 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000002001 ! receptor-type tyrosine-protein kinase FLT3 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P37217 @@ -154430,7 +154170,7 @@ xref: UniProtKB:P37217 is_a: PR:000001343 ! CD69 molecule is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001343 ! CD69 molecule -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P37237 @@ -154450,7 +154190,7 @@ xref: UniProtKB:P37237 is_a: PR:000007499 ! fibroblast growth factor 8 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000007499 ! fibroblast growth factor 8 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P38570 @@ -154468,7 +154208,7 @@ xref: UniProtKB:P38570 is_a: PR:000001010 ! integrin alpha-E is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001010 ! integrin alpha-E -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P40240 @@ -154483,7 +154223,7 @@ xref: UniProtKB:P40240 is_a: PR:000005178 ! CD9 molecule is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000005178 ! CD9 molecule -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P41182 @@ -154508,7 +154248,7 @@ xref: UniProtKB:P41182 is_a: PR:000003450 ! B-cell lymphoma 6 protein is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000003450 ! B-cell lymphoma 6 protein -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P41183 @@ -154523,7 +154263,7 @@ xref: UniProtKB:P41183 is_a: PR:000003450 ! B-cell lymphoma 6 protein is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000003450 ! B-cell lymphoma 6 protein -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P41272 @@ -154542,7 +154282,7 @@ xref: UniProtKB:P41272 is_a: PR:000001963 ! CD27 molecule is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001963 ! CD27 molecule -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P41597 @@ -154565,7 +154305,7 @@ xref: UniProtKB:P41597 is_a: PR:000001199 ! C-C chemokine receptor type 2 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001199 ! C-C chemokine receptor type 2 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P42081 @@ -154585,7 +154325,7 @@ xref: UniProtKB:P42081 is_a: PR:000001412 ! CD86 molecule is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001412 ! CD86 molecule -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P42082 @@ -154603,7 +154343,7 @@ xref: UniProtKB:P42082 is_a: PR:000001412 ! CD86 molecule is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001412 ! CD86 molecule -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P43235 @@ -154622,7 +154362,7 @@ xref: UniProtKB:P43235 is_a: PR:000001850 ! cathepsin K is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001850 ! cathepsin K -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P47774 @@ -154647,7 +154387,7 @@ xref: UniProtKB:P47774 is_a: PR:000001203 ! C-C chemokine receptor type 7 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001203 ! C-C chemokine receptor type 7 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P48318 @@ -154665,7 +154405,7 @@ xref: UniProtKB:P48318 is_a: PR:000007785 ! glutamate decarboxylase 1 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000007785 ! glutamate decarboxylase 1 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P48431 @@ -154680,7 +154420,7 @@ xref: UniProtKB:P48431 is_a: PR:000015426 ! transcription factor SOX-2 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000015426 ! transcription factor SOX-2 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P48432 @@ -154695,7 +154435,7 @@ xref: UniProtKB:P48432 is_a: PR:000015426 ! transcription factor SOX-2 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000015426 ! transcription factor SOX-2 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P49238 @@ -154720,7 +154460,7 @@ xref: UniProtKB:P49238 is_a: PR:000001206 ! CX3C chemokine receptor 1 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001206 ! CX3C chemokine receptor 1 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P49290 @@ -154736,7 +154476,7 @@ xref: UniProtKB:P49290 is_a: PR:000007152 ! eosinophil peroxidase is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000007152 ! eosinophil peroxidase -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P49582 @@ -154751,7 +154491,7 @@ xref: UniProtKB:P49582 is_a: PR:000005460 ! neuronal acetylcholine receptor subunit alpha-7 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000005460 ! neuronal acetylcholine receptor subunit alpha-7 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P49682 @@ -154775,7 +154515,7 @@ xref: UniProtKB:P49682 is_a: PR:000001207 ! C-X-C chemokine receptor type 3 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001207 ! C-X-C chemokine receptor type 3 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P49715 @@ -154792,7 +154532,7 @@ xref: UniProtKB:P49715 is_a: PR:000005307 ! CCAAT/enhancer-binding protein alpha is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000005307 ! CCAAT/enhancer-binding protein alpha -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P50283 @@ -154807,7 +154547,7 @@ xref: UniProtKB:P50283 is_a: PR:000001836 ! CD7 molecule is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001836 ! CD7 molecule -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P50481 @@ -154827,7 +154567,7 @@ xref: UniProtKB:P50481 is_a: PR:000009793 ! LIM/homeobox protein Lhx3 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000009793 ! LIM/homeobox protein Lhx3 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P51449 @@ -154850,7 +154590,7 @@ xref: UniProtKB:P51449 is_a: PR:000001902 ! nuclear receptor ROR-gamma is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001902 ! nuclear receptor ROR-gamma -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P51450 @@ -154873,7 +154613,7 @@ xref: UniProtKB:P51450 is_a: PR:000001902 ! nuclear receptor ROR-gamma is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001902 ! nuclear receptor ROR-gamma -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P51450-2 @@ -154887,7 +154627,7 @@ xref: UniProtKB:P51450-2 is_a: PR:000003455 ! nuclear receptor ROR-gamma isoform 2 is_a: PR:P51450 ! nuclear receptor ROR-gamma (mouse) intersection_of: PR:000003455 ! nuclear receptor ROR-gamma isoform 2 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P51675 @@ -154910,7 +154650,7 @@ xref: UniProtKB:P51675 is_a: PR:000001254 ! C-C chemokine receptor type 1 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001254 ! C-C chemokine receptor type 1 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P51677 @@ -154935,7 +154675,7 @@ xref: UniProtKB:P51677 is_a: PR:000001255 ! C-C chemokine receptor type 3 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001255 ! C-C chemokine receptor type 3 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P51678 @@ -154959,7 +154699,7 @@ xref: UniProtKB:P51678 is_a: PR:000001255 ! C-C chemokine receptor type 3 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001255 ! C-C chemokine receptor type 3 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P51679 @@ -154981,7 +154721,7 @@ xref: UniProtKB:P51679 is_a: PR:000001200 ! C-C chemokine receptor type 4 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001200 ! C-C chemokine receptor type 4 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P51680 @@ -155001,7 +154741,7 @@ xref: UniProtKB:P51680 is_a: PR:000001200 ! C-C chemokine receptor type 4 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001200 ! C-C chemokine receptor type 4 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P51681 @@ -155024,7 +154764,7 @@ xref: UniProtKB:P51681 is_a: PR:000001201 ! C-C chemokine receptor type 5 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001201 ! C-C chemokine receptor type 5 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P51682 @@ -155044,7 +154784,7 @@ xref: UniProtKB:P51682 is_a: PR:000001201 ! C-C chemokine receptor type 5 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001201 ! C-C chemokine receptor type 5 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P51683 @@ -155066,7 +154806,7 @@ xref: UniProtKB:P51683 is_a: PR:000001199 ! C-C chemokine receptor type 2 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001199 ! C-C chemokine receptor type 2 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P51684 @@ -155097,7 +154837,7 @@ xref: UniProtKB:P51684 is_a: PR:000001202 ! C-C chemokine receptor type 6 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001202 ! C-C chemokine receptor type 6 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P51884 @@ -155115,7 +154855,7 @@ xref: UniProtKB:P51884 is_a: PR:000009981 ! lumican is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000009981 ! lumican -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P51885 @@ -155133,7 +154873,7 @@ xref: UniProtKB:P51885 is_a: PR:000009981 ! lumican is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000009981 ! lumican -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P53566 @@ -155149,7 +154889,7 @@ xref: UniProtKB:P53566 is_a: PR:000005307 ! CCAAT/enhancer-binding protein alpha is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000005307 ! CCAAT/enhancer-binding protein alpha -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P55075 @@ -155168,7 +154908,7 @@ xref: UniProtKB:P55075 is_a: PR:000007499 ! fibroblast growth factor 8 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000007499 ! fibroblast growth factor 8 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P55097 @@ -155182,7 +154922,7 @@ xref: UniProtKB:P55097 is_a: PR:000001850 ! cathepsin K is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001850 ! cathepsin K -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P55099 @@ -155201,7 +154941,7 @@ xref: UniProtKB:P55099 is_a: PR:000016004 ! tachykinin-3 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000016004 ! tachykinin-3 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P55284 @@ -155218,7 +154958,7 @@ xref: UniProtKB:P55284 is_a: PR:000001444 ! cadherin-5 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001444 ! cadherin-5 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P55895 @@ -155234,7 +154974,7 @@ xref: UniProtKB:P55895 is_a: PR:000003460 ! V(D)J recombination-activating protein 2 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000003460 ! V(D)J recombination-activating protein 2 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P56528 @@ -155258,7 +154998,7 @@ xref: UniProtKB:P56528 is_a: PR:000001408 ! ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001408 ! ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P59901 @@ -155277,7 +155017,7 @@ xref: UniProtKB:P59901 is_a: PR:000001398 ! leukocyte immunoglobulin-like receptor subfamily A member 4 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001398 ! leukocyte immunoglobulin-like receptor subfamily A member 4 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P60041 @@ -155292,7 +155032,7 @@ xref: UniProtKB:P60041 is_a: PR:000015665 ! somatostatin is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000015665 ! somatostatin -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P61073 @@ -155323,7 +155063,7 @@ xref: UniProtKB:P61073 is_a: PR:000001208 ! C-X-C chemokine receptor type 4 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001208 ! C-X-C chemokine receptor type 4 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P61168 @@ -155338,7 +155078,7 @@ xref: UniProtKB:P61168 is_a: PR:000001177 ! D(2) dopamine receptor is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001177 ! D(2) dopamine receptor -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P61278 @@ -155353,7 +155093,7 @@ xref: UniProtKB:P61278 is_a: PR:000015665 ! somatostatin is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000015665 ! somatostatin -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P70658 @@ -155380,7 +155120,7 @@ xref: UniProtKB:P70658 is_a: PR:000001208 ! C-X-C chemokine receptor type 4 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001208 ! C-X-C chemokine receptor type 4 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P78324 @@ -155415,7 +155155,7 @@ xref: UniProtKB:P78324 is_a: PR:000001968 ! tyrosine-protein phosphatase non-receptor type substrate 1 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001968 ! tyrosine-protein phosphatase non-receptor type substrate 1 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P78412 @@ -155433,7 +155173,7 @@ xref: UniProtKB:P78412 is_a: PR:000029067 ! Homo sapiens protein is_a: PR:000029562 ! iroquois-class homeodomain protein IRX-6 intersection_of: PR:000029562 ! iroquois-class homeodomain protein IRX-6 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P78509 @@ -155447,7 +155187,7 @@ xref: UniProtKB:P78509 is_a: PR:000013879 ! reelin is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000013879 ! reelin -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P80188 @@ -155468,7 +155208,7 @@ xref: UniProtKB:P80188 is_a: PR:000009725 ! neutrophil gelatinase-associated lipocalin is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000009725 ! neutrophil gelatinase-associated lipocalin -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:P97367 @@ -155485,7 +155225,7 @@ xref: UniProtKB:P97367 is_a: PR:000010317 ! homeobox protein Meis2 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000010317 ! homeobox protein Meis2 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P97449 @@ -155509,7 +155249,7 @@ xref: UniProtKB:P97449 is_a: PR:000002031 ! aminopeptidase N is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000002031 ! aminopeptidase N -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P97797 @@ -155539,7 +155279,7 @@ xref: UniProtKB:P97797 is_a: PR:000001968 ! tyrosine-protein phosphatase non-receptor type substrate 1 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001968 ! tyrosine-protein phosphatase non-receptor type substrate 1 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:P97926 @@ -155554,7 +155294,7 @@ xref: UniProtKB:P97926 is_a: PR:000001635 ! oxytocin receptor is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001635 ! oxytocin receptor -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q00342 @@ -155577,7 +155317,7 @@ xref: UniProtKB:Q00342 is_a: PR:000002001 ! receptor-type tyrosine-protein kinase FLT3 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000002001 ! receptor-type tyrosine-protein kinase FLT3 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q00609 @@ -155594,7 +155334,7 @@ xref: UniProtKB:Q00609 is_a: PR:000001438 ! CD80 molecule is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001438 ! CD80 molecule -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q00651 @@ -155614,7 +155354,7 @@ xref: UniProtKB:Q00651 is_a: PR:000009129 ! integrin alpha-4 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000009129 ! integrin alpha-4 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q00653 @@ -155635,7 +155375,7 @@ xref: UniProtKB:Q00653 is_a: PR:000011178 ! nuclear factor NF-kappa-B p100 subunit is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000011178 ! nuclear factor NF-kappa-B p100 subunit -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q00993 @@ -155652,7 +155392,7 @@ xref: UniProtKB:Q00993 is_a: PR:000004528 ! tyrosine-protein kinase receptor UFO is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000004528 ! tyrosine-protein kinase receptor UFO -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q01151 @@ -155668,7 +155408,7 @@ xref: UniProtKB:Q01151 is_a: PR:000001310 ! CD83 molecule is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001310 ! CD83 molecule -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q01196 @@ -155695,7 +155435,7 @@ xref: UniProtKB:Q01196 is_a: PR:000014362 ! runt-related transcription factor 1 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000014362 ! runt-related transcription factor 1 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q01344 @@ -155716,7 +155456,7 @@ xref: UniProtKB:Q01344 is_a: PR:000001867 ! interleukin-5 receptor subunit alpha is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001867 ! interleukin-5 receptor subunit alpha -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q01638 @@ -155734,7 +155474,7 @@ xref: UniProtKB:Q01638 is_a: PR:000008994 ! interleukin-1 receptor-like 1 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000008994 ! interleukin-1 receptor-like 1 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q02242 @@ -155752,7 +155492,7 @@ xref: UniProtKB:Q02242 is_a: PR:000001919 ! programmed cell death protein 1 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001919 ! programmed cell death protein 1 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q02548 @@ -155769,7 +155509,7 @@ xref: UniProtKB:Q02548 is_a: PR:000001903 ! paired box protein PAX-5 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001903 ! paired box protein PAX-5 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q02650 @@ -155786,7 +155526,7 @@ xref: UniProtKB:Q02650 is_a: PR:000001903 ! paired box protein PAX-5 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001903 ! paired box protein PAX-5 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q03347 @@ -155812,7 +155552,7 @@ xref: UniProtKB:Q03347 is_a: PR:000014362 ! runt-related transcription factor 1 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000014362 ! runt-related transcription factor 1 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q03405 @@ -155831,7 +155571,7 @@ xref: UniProtKB:Q03405 is_a: PR:000001969 ! urokinase plasminogen activator surface receptor is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001969 ! urokinase plasminogen activator surface receptor -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q04683 @@ -155851,7 +155591,7 @@ xref: UniProtKB:Q04683 is_a: PR:000001209 ! C-X-C chemokine receptor type 5 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001209 ! C-X-C chemokine receptor type 5 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q05117 @@ -155871,7 +155611,7 @@ xref: UniProtKB:Q05117 is_a: PR:000001937 ! tartrate-resistant acid phosphatase type 5 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001937 ! tartrate-resistant acid phosphatase type 5 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q06318 @@ -155895,7 +155635,7 @@ xref: UniProtKB:Q06318 is_a: PR:000014505 ! uteroglobin is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000014505 ! uteroglobin -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q07075 @@ -155915,7 +155655,7 @@ xref: UniProtKB:Q07075 is_a: PR:000002039 ! glutamyl aminopeptidase is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000002039 ! glutamyl aminopeptidase -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q07108 @@ -155939,7 +155679,7 @@ xref: UniProtKB:Q07108 is_a: PR:000001343 ! CD69 molecule is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001343 ! CD69 molecule -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q07763 @@ -155962,7 +155702,7 @@ xref: UniProtKB:Q07763 is_a: PR:000001896 ! natural killer cell receptor 2B4 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001896 ! natural killer cell receptor 2B4 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q08857 @@ -155983,7 +155723,7 @@ xref: UniProtKB:Q08857 is_a: PR:000001905 ! platelet glycoprotein 4 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001905 ! platelet glycoprotein 4 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q10589 @@ -156001,7 +155741,7 @@ xref: UniProtKB:Q10589 is_a: PR:000001326 ! bone marrow stromal antigen 2 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001326 ! bone marrow stromal antigen 2 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q11127 @@ -156022,7 +155762,7 @@ xref: UniProtKB:Q11127 is_a: PR:000001456 ! alpha-(1,3)-fucosyltransferase 4 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001456 ! alpha-(1,3)-fucosyltransferase 4 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q12866 @@ -156040,7 +155780,7 @@ xref: UniProtKB:Q12866 is_a: PR:000010329 ! tyrosine-protein kinase Mer is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000010329 ! tyrosine-protein kinase Mer -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q12918 @@ -156062,7 +155802,7 @@ xref: UniProtKB:Q12918 is_a: PR:000025670 ! killer cell lectin-like receptor subfamily B member 1 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000025670 ! killer cell lectin-like receptor subfamily B member 1 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q13241 @@ -156081,7 +155821,7 @@ xref: UniProtKB:Q13241 is_a: PR:000001402 ! killer cell lectin-like receptor subfamily D member 1 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001402 ! killer cell lectin-like receptor subfamily D member 1 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q13291 @@ -156100,7 +155840,7 @@ xref: UniProtKB:Q13291 is_a: PR:000001833 ! SLAM family member 1 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001833 ! SLAM family member 1 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q13445 @@ -156121,7 +155861,7 @@ xref: UniProtKB:Q13445 is_a: PR:000016401 ! transmembrane emp24 domain-containing protein 1 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000016401 ! transmembrane emp24 domain-containing protein 1 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q14246 @@ -156141,7 +155881,7 @@ xref: UniProtKB:Q14246 is_a: PR:000001813 ! adhesion G protein-coupled receptor E1 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001813 ! adhesion G protein-coupled receptor E1 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q15116 @@ -156159,7 +155899,7 @@ xref: UniProtKB:Q15116 is_a: PR:000001919 ! programmed cell death protein 1 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001919 ! programmed cell death protein 1 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q15465 @@ -156176,7 +155916,7 @@ xref: UniProtKB:Q15465 is_a: PR:000014841 ! sonic hedgehog protein is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000014841 ! sonic hedgehog protein -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q15726 @@ -156192,7 +155932,7 @@ xref: UniProtKB:Q15726 is_a: PR:000009344 ! metastasis-suppressor KiSS-1 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000009344 ! metastasis-suppressor KiSS-1 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q15744 @@ -156208,7 +155948,7 @@ xref: UniProtKB:Q15744 is_a: PR:000005310 ! CCAAT/enhancer-binding protein epsilon is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000005310 ! CCAAT/enhancer-binding protein epsilon -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q18PI6 @@ -156226,7 +155966,7 @@ xref: UniProtKB:Q18PI6 is_a: PR:000001319 ! SLAM family member 5 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001319 ! SLAM family member 5 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q2VLH6 @@ -156242,7 +155982,7 @@ xref: UniProtKB:Q2VLH6 is_a: PR:000001925 ! scavenger receptor cysteine-rich type 1 protein M130 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001925 ! scavenger receptor cysteine-rich type 1 protein M130 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q3V009 @@ -156261,7 +156001,7 @@ xref: UniProtKB:Q3V009 is_a: PR:000016401 ! transmembrane emp24 domain-containing protein 1 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000016401 ! transmembrane emp24 domain-containing protein 1 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q5UKY4 @@ -156280,7 +156020,7 @@ xref: UniProtKB:Q5UKY4 is_a: PR:000006169 ! cell surface glycoprotein CD200 receptor 3 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000006169 ! cell surface glycoprotein CD200 receptor 3 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q60651 @@ -156299,7 +156039,7 @@ xref: UniProtKB:Q60651 is_a: PR:000009619 ! killer cell lectin-like receptor 4 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000009619 ! killer cell lectin-like receptor 4 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q60677 @@ -156315,7 +156055,7 @@ xref: UniProtKB:Q60677 is_a: PR:000001010 ! integrin alpha-E is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001010 ! integrin alpha-E -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q60682 @@ -156334,7 +156074,7 @@ xref: UniProtKB:Q60682 is_a: PR:000009623 ! killer cell lectin-like receptor 8 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000009623 ! killer cell lectin-like receptor 8 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q60754 @@ -156349,7 +156089,7 @@ xref: UniProtKB:Q60754 is_a: PR:000001884 ! macrophage receptor MARCO is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001884 ! macrophage receptor MARCO -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q60767 @@ -156367,7 +156107,7 @@ xref: UniProtKB:Q60767 is_a: PR:000001026 ! lymphocyte antigen 75 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001026 ! lymphocyte antigen 75 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q60805 @@ -156384,7 +156124,7 @@ xref: UniProtKB:Q60805 is_a: PR:000010329 ! tyrosine-protein kinase Mer is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000010329 ! tyrosine-protein kinase Mer -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q60841 @@ -156400,7 +156140,7 @@ xref: UniProtKB:Q60841 is_a: PR:000013879 ! reelin is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000013879 ! reelin -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q61176 @@ -156416,7 +156156,7 @@ xref: UniProtKB:Q61176 is_a: PR:000001844 ! arginase-1 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001844 ! arginase-1 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q61391 @@ -156438,7 +156178,7 @@ xref: UniProtKB:Q61391 is_a: PR:000001898 ! neprilysin is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001898 ! neprilysin -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q61549 @@ -156458,7 +156198,7 @@ xref: UniProtKB:Q61549 is_a: PR:000001813 ! adhesion G protein-coupled receptor E1 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001813 ! adhesion G protein-coupled receptor E1 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q61575 @@ -156479,7 +156219,7 @@ xref: UniProtKB:Q61575 is_a: PR:000007636 ! forkhead box protein N1 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000007636 ! forkhead box protein N1 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q61616 @@ -156496,7 +156236,7 @@ xref: UniProtKB:Q61616 is_a: PR:000001175 ! D(1A) dopamine receptor is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001175 ! D(1A) dopamine receptor -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q61830 @@ -156512,7 +156252,7 @@ xref: UniProtKB:Q61830 is_a: PR:000002972 ! macrophage mannose receptor 1 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000002972 ! macrophage mannose receptor 1 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q61878 @@ -156529,7 +156269,7 @@ xref: UniProtKB:Q61878 is_a: PR:000013206 ! bone marrow proteoglycan is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000013206 ! bone marrow proteoglycan -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q61878-1 @@ -156542,7 +156282,7 @@ xref: UniProtKB:Q61878-1 is_a: PR:000022003 ! bone marrow proteoglycan isoform 1 is_a: PR:Q61878 ! bone marrow proteoglycan (mouse) intersection_of: PR:000022003 ! bone marrow proteoglycan isoform 1 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q62226 @@ -156561,7 +156301,7 @@ xref: UniProtKB:Q62226 is_a: PR:000014841 ! sonic hedgehog protein is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000014841 ! sonic hedgehog protein -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q62230 @@ -156582,7 +156322,7 @@ xref: UniProtKB:Q62230 is_a: PR:000001931 ! sialoadhesin is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001931 ! sialoadhesin -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q62351 @@ -156601,7 +156341,7 @@ xref: UniProtKB:Q62351 is_a: PR:000001945 ! transferrin receptor protein 1 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001945 ! transferrin receptor protein 1 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q62469 @@ -156621,7 +156361,7 @@ xref: UniProtKB:Q62469 is_a: PR:000001008 ! integrin alpha-2 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001008 ! integrin alpha-2 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q63961 @@ -156638,7 +156378,7 @@ xref: UniProtKB:Q63961 is_a: PR:000001345 ! endoglin is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001345 ! endoglin -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q63994 @@ -156656,7 +156396,7 @@ xref: UniProtKB:Q63994 is_a: PR:000001892 ! CD33 molecule is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001892 ! CD33 molecule -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q64314 @@ -156671,7 +156411,7 @@ xref: UniProtKB:Q64314 is_a: PR:000001003 ! CD34 molecule is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001003 ! CD34 molecule -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q64329 @@ -156691,7 +156431,7 @@ xref: UniProtKB:Q64329 is_a: PR:000009618 ! killer cell lectin-like receptor 3 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000009618 ! killer cell lectin-like receptor 3 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q67BJ4 @@ -156711,7 +156451,7 @@ xref: UniProtKB:Q67BJ4 is_a: PR:000003516 ! lactosylceramide 4-alpha-galactosyltransferase is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000003516 ! lactosylceramide 4-alpha-galactosyltransferase -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q6DYE8 @@ -156730,7 +156470,7 @@ xref: UniProtKB:Q6DYE8 is_a: PR:000001344 ! ectonucleotide pyrophosphatase/phosphodiesterase family member 3 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001344 ! ectonucleotide pyrophosphatase/phosphodiesterase family member 3 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q6EIG7 @@ -156751,7 +156491,7 @@ xref: UniProtKB:Q6EIG7 is_a: PR:000001806 ! C-type lectin domain family 6 member A is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001806 ! C-type lectin domain family 6 member A -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q6PZD9 @@ -156767,7 +156507,7 @@ xref: UniProtKB:Q6PZD9 is_a: PR:000005310 ! CCAAT/enhancer-binding protein epsilon is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000005310 ! CCAAT/enhancer-binding protein epsilon -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q6QLQ4 @@ -156790,7 +156530,7 @@ xref: UniProtKB:Q6QLQ4 is_a: PR:000001807 ! C-type lectin domain family 7 member A is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001807 ! C-type lectin domain family 7 member A -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q6R6I7 @@ -156808,7 +156548,7 @@ xref: UniProtKB:Q6R6I7 is_a: PR:000001666 ! relaxin receptor 1 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001666 ! relaxin receptor 1 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q6Y4S4 @@ -156823,7 +156563,7 @@ xref: UniProtKB:Q6Y4S4 is_a: PR:000009344 ! metastasis-suppressor KiSS-1 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000009344 ! metastasis-suppressor KiSS-1 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q86VB7 @@ -156839,7 +156579,7 @@ xref: UniProtKB:Q86VB7 is_a: PR:000001925 ! scavenger receptor cysteine-rich type 1 protein M130 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001925 ! scavenger receptor cysteine-rich type 1 protein M130 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q8C567 @@ -156862,7 +156602,7 @@ xref: UniProtKB:Q8C567 is_a: PR:000001893 ! natural cytotoxicity triggering receptor 1 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001893 ! natural cytotoxicity triggering receptor 1 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q8CG65 @@ -156876,7 +156616,7 @@ xref: UniProtKB:Q8CG65 is_a: PR:000015658 ! SCO-spondin is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000015658 ! SCO-spondin -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q8CJ91 @@ -156894,7 +156634,7 @@ xref: UniProtKB:Q8CJ91 is_a: PR:000006172 ! CD209 molecule-like protein B is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000006172 ! CD209 molecule-like protein B -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q8NFU0 @@ -156912,7 +156652,7 @@ xref: UniProtKB:Q8NFU0 is_a: PR:000004724 ! bestrophin-4 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000004724 ! bestrophin-4 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q8R2Q8 @@ -156929,7 +156669,7 @@ xref: UniProtKB:Q8R2Q8 is_a: PR:000001326 ! bone marrow stromal antigen 2 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001326 ! bone marrow stromal antigen 2 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q8R4G0 @@ -156946,7 +156686,7 @@ xref: UniProtKB:Q8R4G0 is_a: PR:000011467 ! netrin-G1 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000011467 ! netrin-G1 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q8R4I7 @@ -156962,7 +156702,7 @@ xref: UniProtKB:Q8R4I7 is_a: PR:000011143 ! neuropilin and tolloid-like protein 1 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000011143 ! neuropilin and tolloid-like protein 1 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q8TDF5 @@ -156978,7 +156718,7 @@ xref: UniProtKB:Q8TDF5 is_a: PR:000011143 ! neuropilin and tolloid-like protein 1 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000011143 ! neuropilin and tolloid-like protein 1 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q8VBX4 @@ -156995,7 +156735,7 @@ xref: UniProtKB:Q8VBX4 is_a: PR:000001293 ! C-type lectin domain family 4 member K is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001293 ! C-type lectin domain family 4 member K -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q8WTT0 @@ -157024,7 +156764,7 @@ xref: UniProtKB:Q8WTT0 is_a: PR:000001292 ! C-type lectin domain family 4 member C is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001292 ! C-type lectin domain family 4 member C -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q920G3 @@ -157044,7 +156784,7 @@ xref: UniProtKB:Q920G3 is_a: PR:000001928 ! sialic acid-binding Ig-like lectin 6 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001928 ! sialic acid-binding Ig-like lectin 6 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q96E93 @@ -157066,7 +156806,7 @@ xref: UniProtKB:Q96E93 is_a: PR:000009426 ! killer cell lectin-like receptor subfamily G member 1 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000009426 ! killer cell lectin-like receptor subfamily G member 1 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q99259 @@ -157085,7 +156825,7 @@ xref: UniProtKB:Q99259 is_a: PR:000007785 ! glutamate decarboxylase 1 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000007785 ! glutamate decarboxylase 1 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q99JB6 @@ -157100,7 +156840,7 @@ xref: UniProtKB:Q99JB6 is_a: PR:000001350 ! forkhead box protein P3 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001350 ! forkhead box protein P3 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q9BXN2 @@ -157125,7 +156865,7 @@ xref: UniProtKB:Q9BXN2 is_a: PR:000001807 ! C-type lectin domain family 7 member A is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001807 ! C-type lectin domain family 7 member A -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q9BZS1 @@ -157143,7 +156883,7 @@ xref: UniProtKB:Q9BZS1 is_a: PR:000001350 ! forkhead box protein P3 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001350 ! forkhead box protein P3 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q9BZW8 @@ -157166,7 +156906,7 @@ xref: UniProtKB:Q9BZW8 is_a: PR:000001896 ! natural killer cell receptor 2B4 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001896 ! natural killer cell receptor 2B4 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q9BZZ2 @@ -157184,7 +156924,7 @@ xref: UniProtKB:Q9BZZ2 is_a: PR:000001931 ! sialoadhesin is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001931 ! sialoadhesin -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q9CXM0 @@ -157199,7 +156939,7 @@ xref: UniProtKB:Q9CXM0 is_a: PR:000005444 ! chondrolectin is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000005444 ! chondrolectin -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q9D387 @@ -157218,7 +156958,7 @@ xref: UniProtKB:Q9D387 is_a: PR:000029032 ! Mus musculus protein is_a: PR:000032148 ! lysosome-associated membrane glycoprotein 5 intersection_of: PR:000032148 ! lysosome-associated membrane glycoprotein 5 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q9ER75 @@ -157235,7 +156975,7 @@ xref: UniProtKB:Q9ER75 is_a: PR:000029032 ! Mus musculus protein is_a: PR:000029562 ! iroquois-class homeodomain protein IRX-6 intersection_of: PR:000029562 ! iroquois-class homeodomain protein IRX-6 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q9H9P2 @@ -157253,7 +156993,7 @@ xref: UniProtKB:Q9H9P2 is_a: PR:000005444 ! chondrolectin is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000005444 ! chondrolectin -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q9HBX9 @@ -157272,7 +157012,7 @@ xref: UniProtKB:Q9HBX9 is_a: PR:000001666 ! relaxin receptor 1 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001666 ! relaxin receptor 1 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q9JIP3 @@ -157296,7 +157036,7 @@ xref: UniProtKB:Q9JIP3 is_a: PR:000008982 ! interleukin-17 receptor B is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000008982 ! interleukin-17 receptor B -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q9JKD8 @@ -157315,7 +157055,7 @@ xref: UniProtKB:Q9JKD8 is_a: PR:000001835 ! T-box transcription factor TBX21 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001835 ! T-box transcription factor TBX21 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q9JKF4 @@ -157336,7 +157076,7 @@ xref: UniProtKB:Q9JKF4 is_a: PR:000001806 ! C-type lectin domain family 6 member A is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001806 ! C-type lectin domain family 6 member A -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q9NNX6 @@ -157356,7 +157096,7 @@ xref: UniProtKB:Q9NNX6 is_a: PR:000001300 ! CD209 molecule is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001300 ! CD209 molecule -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q9NPC4 @@ -157380,7 +157120,7 @@ xref: UniProtKB:Q9NPC4 is_a: PR:000003516 ! lactosylceramide 4-alpha-galactosyltransferase is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000003516 ! lactosylceramide 4-alpha-galactosyltransferase -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q9NPY3 @@ -157403,7 +157143,7 @@ xref: UniProtKB:Q9NPY3 is_a: PR:000002037 ! complement component C1q receptor is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000002037 ! complement component C1q receptor -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q9NRM6 @@ -157429,7 +157169,7 @@ xref: UniProtKB:Q9NRM6 is_a: PR:000008982 ! interleukin-17 receptor B is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000008982 ! interleukin-17 receptor B -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q9QUM0 @@ -157447,7 +157187,7 @@ xref: UniProtKB:Q9QUM0 is_a: PR:000009127 ! integrin alpha-IIb is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000009127 ! integrin alpha-IIb -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q9QUM4 @@ -157464,7 +157204,7 @@ xref: UniProtKB:Q9QUM4 is_a: PR:000001833 ! SLAM family member 1 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001833 ! SLAM family member 1 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q9QXH4 @@ -157482,7 +157222,7 @@ xref: UniProtKB:Q9QXH4 is_a: PR:000001013 ! integrin alpha-X is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001013 ! integrin alpha-X -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q9QXZ9 @@ -157499,7 +157239,7 @@ xref: UniProtKB:Q9QXZ9 is_a: PR:000001243 ! melanopsin is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001243 ! melanopsin -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q9UBR4 @@ -157515,7 +157255,7 @@ xref: UniProtKB:Q9UBR4 is_a: PR:000009793 ! LIM/homeobox protein Lhx3 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000009793 ! LIM/homeobox protein Lhx3 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q9UEW3 @@ -157532,7 +157272,7 @@ xref: UniProtKB:Q9UEW3 is_a: PR:000001884 ! macrophage receptor MARCO is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001884 ! macrophage receptor MARCO -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q9UHF0 @@ -157549,7 +157289,7 @@ xref: UniProtKB:Q9UHF0 is_a: PR:000016004 ! tachykinin-3 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000016004 ! tachykinin-3 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q9UHM6 @@ -157567,7 +157307,7 @@ xref: UniProtKB:Q9UHM6 is_a: PR:000001243 ! melanopsin is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001243 ! melanopsin -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q9UIB8 @@ -157586,7 +157326,7 @@ xref: UniProtKB:Q9UIB8 is_a: PR:000001319 ! SLAM family member 5 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001319 ! SLAM family member 5 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q9UJ71 @@ -157605,7 +157345,7 @@ xref: UniProtKB:Q9UJ71 is_a: PR:000001293 ! C-type lectin domain family 4 member K is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001293 ! C-type lectin domain family 4 member K -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q9UJQ1 @@ -157625,7 +157365,7 @@ xref: UniProtKB:Q9UJQ1 is_a: PR:000029067 ! Homo sapiens protein is_a: PR:000032148 ! lysosome-associated membrane glycoprotein 5 intersection_of: PR:000032148 ! lysosome-associated membrane glycoprotein 5 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q9UL17 @@ -157644,7 +157384,7 @@ xref: UniProtKB:Q9UL17 is_a: PR:000001835 ! T-box transcription factor TBX21 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001835 ! T-box transcription factor TBX21 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q9WTK5 @@ -157660,7 +157400,7 @@ xref: UniProtKB:Q9WTK5 is_a: PR:000011178 ! nuclear factor NF-kappa-B p100 subunit is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000011178 ! nuclear factor NF-kappa-B p100 subunit -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q9WVS0 @@ -157681,7 +157421,7 @@ xref: UniProtKB:Q9WVS0 is_a: PR:000001860 ! inducible T-cell costimulator is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001860 ! inducible T-cell costimulator -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q9Y2I2 @@ -157699,7 +157439,7 @@ xref: UniProtKB:Q9Y2I2 is_a: PR:000011467 ! netrin-G1 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000011467 ! netrin-G1 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q9Y5Y4 @@ -157721,7 +157461,7 @@ xref: UniProtKB:Q9Y5Y4 is_a: PR:000001547 ! prostaglandin D2 receptor DP2 is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001547 ! prostaglandin D2 receptor DP2 -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q9Y6Q6 @@ -157740,7 +157480,7 @@ xref: UniProtKB:Q9Y6Q6 is_a: PR:000001954 ! tumor necrosis factor receptor superfamily member 11A is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001954 ! tumor necrosis factor receptor superfamily member 11A -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q9Y6W8 @@ -157757,7 +157497,7 @@ xref: UniProtKB:Q9Y6W8 is_a: PR:000001860 ! inducible T-cell costimulator is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001860 ! inducible T-cell costimulator -intersection_of: only_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens [Term] id: PR:Q9Z0D9 @@ -157774,7 +157514,7 @@ xref: UniProtKB:Q9Z0D9 is_a: PR:000001206 ! CX3C chemokine receptor 1 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001206 ! CX3C chemokine receptor 1 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q9Z0F7 @@ -157790,7 +157530,7 @@ xref: UniProtKB:Q9Z0F7 is_a: PR:000015325 ! gamma-synuclein is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000015325 ! gamma-synuclein -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:Q9Z2J6 @@ -157809,16 +157549,14 @@ xref: UniProtKB:Q9Z2J6 is_a: PR:000001547 ! prostaglandin D2 receptor DP2 is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001547 ! prostaglandin D2 receptor DP2 -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: RO:0002577 name: system def: "A material entity consisting of multiple components that are causally integrated." [] is_a: BFO:0000040 ! material entity -property_value: editor_note "May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "http://www.jbiomedsem.com/content/4/1/43" xsd:string +property_value: IAO:0000116 "May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43" xsd:string [Term] id: UBERON:0000000 @@ -157829,9 +157567,9 @@ subset: common_anatomy subset: upper_level xref: BFO:0000003 disjoint_from: UBERON:0001062 ! anatomical entity -relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 ! Fungi +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000002 @@ -157871,16 +157609,13 @@ xref: Wikipedia:Cervix is_a: UBERON:0001560 ! neck of organ is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0001560 ! neck of organ -intersection_of: continuous_with UBERON:0000996 ! vagina intersection_of: part_of UBERON:0000995 ! uterus -relationship: continuous_with UBERON:0000996 ! vagina -relationship: contributes_to_morphology_of UBERON:0000995 ! uterus +intersection_of: RO:0002150 UBERON:0000996 ! continuous with vagina relationship: part_of UBERON:0000995 ! uterus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Uterus.glb" xsd:anyURI -property_value: UBPROP:0000001 "The narrow caudal end of the uterus that opens into the vagina. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001359", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/uterine+cervix"} -property_value: UBPROP:0000003 "The evolution of mammals is associated with radical changes in their reproductive biology, particularly the structure and function of the female reproductive organs. These changes include the evolution of the uterus, cervix, vagina, placenta and specialized cell types associated with each of those structures.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001359", ontology="VHOG", source="DOI:10.1098/rspb.2004.2848 Lynch VJ, Roth JJ, Takahashi K, Dunn CW, Nonaka DF, Stopper GF, Wagner GP, Adaptive evolution of HoxA-11 and HoxA-13 at the origin of the uterus in mammals. Proceedings of the Royal Society of London, Series B (2004)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "cervical" xsd:string +relationship: RO:0002150 UBERON:0000996 ! continuous with vagina +relationship: RO:0002433 UBERON:0000995 ! contributes to morphology of uterus +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Uterus.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000003 @@ -157899,17 +157634,12 @@ xref: SCTID:272650008 xref: VHOG:0000663 is_a: UBERON:0000161 ! orifice intersection_of: UBERON:0000161 ! orifice -intersection_of: connects UBERON:0001707 ! nasal cavity intersection_of: part_of UBERON:0005725 ! olfactory system -relationship: connects UBERON:0001707 ! nasal cavity -relationship: in_lateral_side_of UBERON:0000033 {gci_relation="part_of", gci_filler="NCBITaxon:7776", notes="hagfish have median nostril"} ! head -relationship: only_in_taxon NCBITaxon:7711 ! Chordata +intersection_of: RO:0002176 UBERON:0001707 ! connects nasal cavity relationship: part_of UBERON:0000033 {source="ZFA"} ! head relationship: part_of UBERON:0005725 ! olfactory system -property_value: UBPROP:0000001 "One of paired external openings of the nasal chamber.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000311", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "Naris refer to the external and interior naris (choana) of tetrapods, and to anterior and posterior naris of zebrafish. It seems now accepted that the structure is homologous: The choana, a unique 'internal nostril' opening from the nasal sac into the roof of the mouth, is a key part of the tetrapod (land vertebrate) respiratory system. It was the first component of the tetrapod body plan to evolve, well before the origin of limbs, and is therefore crucial to our understanding of the beginning of the fish-tetrapod transition. (...) Here we present new material of Kenichthys, a 395-million-year-old fossil fish from China, that provides direct evidence for the origin of the choana and establishes its homology: it is indeed a displaced posterior external nostril that, during a brief transitional stage illustrated by Kenichthys, separated the maxilla from the premaxilla.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000663", ontology="VHOG", source="DOI:10.1038/nature02843 Zhu M, Ahlberg PE, The origin of the internal nostril in tetrapodes. Nature (2004)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "in actinopterygians, both pairs of nares are external. In tetrapods, the exhalant empties into the buccal cavity" xsd:string -property_value: UBPROP:0000012 "we have classified this as an orifice, according to FMA. Note that in FMA, orifices are immaterial entities, but in ZFA this is a surface structure" xsd:string {external_ontology="FMA"} +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002176 UBERON:0001707 ! connects nasal cavity [Term] id: UBERON:0000004 @@ -157951,19 +157681,14 @@ is_a: UBERON:0000475 ! organism subdivision is_a: UBERON:0002268 ! olfactory organ is_a: UBERON:0004121 ! ectoderm-derived structure relationship: capable_of_part_of GO:0007608 ! sensory perception of smell -relationship: contributes_to_morphology_of UBERON:0001004 ! respiratory system -relationship: contributes_to_morphology_of UBERON:0001456 ! face -relationship: develops_from UBERON:0003050 {source="ZFA"} ! olfactory placode -relationship: has_skeleton UBERON:0006813 ! nasal skeleton -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0001004 {gci_relation="part_of", gci_filler="NCBITaxon:32523", source="PMID:25312359"} ! respiratory system relationship: part_of UBERON:0001456 {source="FMA", source="ZFA-def"} ! face -relationship: part_of UBERON:0004089 {gci_relation="part_of", gci_filler="NCBITaxon:7776", notes="midface division only makes sense for gnathostomes"} ! midface -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/d0/Canine-nose.jpg" xsd:anyURI -property_value: UBPROP:0000001 "a protuberance in vertebrates that houses the nostrils, or nares, which admit and expel air for respiration in conjunction with the mouth. Behind the nose are the olfactory mucosa and the sinuses. Behind the nasal cavity, air next passes through the pharynx, shared with the digestive system, and then into the rest of the respiratory system. In humans, the nose is located centrally on the face; on most other mammals, it is on the upper tip of the snout[WP]. GO: The nose is the specialized structure of the face that serves as the organ of the sense of smell and as part of the respiratory system. Includes the nasi externus (external nose) and cavitas nasi (nasal cavity)[Wikipedia:Nose]." xsd:string {source="Wikipedia:Nose"} -property_value: UBPROP:0000001 "Organ that is the specialized structure of the face that contains olfactory neurons. The peripheral olfactory organ is paired[ZFA:0000047]." xsd:string {source="ZFA:0000047"} -property_value: UBPROP:0000001 "the organ that is specialized for smell and is part of the respiratory system" xsd:string {source="MP:0002233"} -property_value: UBPROP:0000008 "the structure of the nose varies across vertebrates. In tetrapods the nose is part of the respiratory system.[PMID:25312359]" xsd:string +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002202 UBERON:0003050 {source="ZFA"} ! develops from olfactory placode +relationship: RO:0002433 UBERON:0001004 ! contributes to morphology of respiratory system +relationship: RO:0002433 UBERON:0001456 ! contributes to morphology of face +relationship: RO:0002551 UBERON:0006813 ! has skeleton nasal skeleton +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d0/Canine-nose.jpg" xsd:anyURI [Term] id: UBERON:0000005 @@ -157972,7 +157697,6 @@ namespace: uberon subset: functional_classification subset: uberon_slim synonym: "chemosensory sensory organ" EXACT [FBbt:00005157] -xref: FBbt:00005157 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000020 ! sense organ intersection_of: UBERON:0000020 ! sense organ intersection_of: capable_of GO:0007606 ! sensory perception of chemical stimulus @@ -158011,19 +157735,16 @@ xref: UMLS:C0022131 {source="ncithesaurus:Islet_of_Langerhans"} xref: VHOG:0000646 xref: Wikipedia:Islets_of_Langerhans xref: XAO:0000159 +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0034922 ! cell cluster -relationship: contributes_to_morphology_of UBERON:0000016 ! endocrine pancreas relationship: has_part CL:0000168 {source="PMID:16417468"} ! insulin secreting cell relationship: has_part CL:0000172 {source="PMID:16417468"} ! somatostatin secreting cell relationship: has_part CL:0000696 {gci_filler="NCBITaxon:117570", gci_relation="part_of", source="PMID:16417468"} ! PP cell relationship: has_part CL:0002067 {source="PMID:16417468"} ! type A enteroendocrine cell relationship: part_of UBERON:0000016 ! endocrine pancreas -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/99/Gray1105.png" xsd:anyURI -property_value: UBPROP:0000001 "Anatomical structure which consists of glands developed from pancreatic ducts in the larvae and secrete insulin.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010406", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "Mammals, birds, reptiles and amphibians have a pancreas with similar histology and mode of development, while in some fish, the islet cells are segregated as Brockmann bodies.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000646", ontology="VHOG", source="PMID:7600975 Slack JMW, Developmental biology of the pancreas. Development (1995)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "A primitive exocrine pancreas can be found in holocephalan cartilaginous fish; a pancreatic duct directly ending in the gut lumen is connected to a glandular structure made of exocrine cells and associated with cell islets, which comprises three different hormone-producing cell types: insulin, somatostatin and glucagon (Yui and Fujita, 1986)" xsd:string {source="PMID:16417468"} -property_value: UBPROP:0000202 FMA:76489 +relationship: RO:0002433 UBERON:0000016 ! contributes to morphology of endocrine pancreas +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/99/Gray1105.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000007 @@ -158074,20 +157795,16 @@ xref: XAO:0000017 xref: ZFA:0000118 is_a: UBERON:0002368 {source="BTO", source="EFO", source="VHOG"} ! endocrine gland is_a: UBERON:0003296 ! gland of diencephalon -is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: capable_of_part_of GO:0007276 ! gamete generation -relationship: contributes_to_morphology_of UBERON:0001894 ! diencephalon relationship: has_part CL:0000440 {source="ZFA"} ! melanocyte stimulating hormone secreting cell relationship: has_part CL:0000642 {source="ZFA"} ! folliculostellate cell relationship: has_part UBERON:0002196 ! adenohypophysis relationship: has_part UBERON:0002198 ! neurohypophysis -relationship: immediate_transformation_of UBERON:0034875 {source="https://orcid.org/0000-0003-3308-6245"} ! future pituitary gland -relationship: only_in_taxon NCBITaxon:7742 {source="PMID:19084529"} ! Vertebrata -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/97/Gray1180.png" xsd:anyURI -property_value: UBPROP:0000001 "An endocrine gland derived from infundibulum of the floor of the diencephalon and an ectodermal dorsal protrusion from the buccal cavity which controls the secretion of many hormones influencing the function of various organs of the body.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010536", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000118", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000143", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "The lamprey possesses a distinct pituitary organ and hormones, the ascidian does not show distinct evidence of them [Sower S, Freamat M, Kavanaugh S. The origins of the vertebrate hypothalamic-pituitary-gonadal (HPG) and hypothalamic-pituitary-thyroid (HPT) endocrine systems: new insights from lampreys. Gen Comp Endocrinol 2009;161:20-9]" xsd:string +relationship: RO:0002160 NCBITaxon:7742 {source="PMID:19084529"} ! only in taxon Vertebrata +relationship: RO:0002433 UBERON:0001894 ! contributes to morphology of diencephalon +relationship: RO:0002495 UBERON:0034875 {source="https://orcid.org/0000-0003-3308-6245"} ! immediate transformation of future pituitary gland +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/97/Gray1180.png" xsd:anyURI [Term] id: UBERON:0000009 @@ -158111,12 +157828,11 @@ xref: SCTID:68439008 xref: UMLS:C0225344 {source="ncithesaurus:Submucosa"} xref: Wikipedia:Submucosa is_a: UBERON:0004923 ! organ component layer -relationship: composed_primarily_of UBERON:0002384 ! connective tissue -relationship: immediately_deep_to UBERON:0000344 ! mucosa -relationship: only_in_taxon NCBITaxon:7711 ! Chordata -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png" xsd:anyURI -property_value: UBPROP:0000007 "submucosal" xsd:string +relationship: BSPO:0001107 UBERON:0000344 ! mucosa +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002473 UBERON:0002384 ! composed primarily of connective tissue +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png" xsd:anyURI [Term] id: UBERON:0000010 @@ -158143,7 +157859,6 @@ xref: EHDAA2:0001445 xref: EHDAA:2893 xref: EMAPA:16665 xref: EV:0100335 -xref: FBbt:00005098 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9903 xref: GAID:715 xref: MA:0000218 @@ -158162,12 +157877,8 @@ xref: XAO:0000178 xref: ZFA:0000142 is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision relationship: part_of UBERON:0001016 ! nervous system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI -property_value: UBPROP:0000001 "Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000142", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Part of nervous system in which nerves extend throughout the body outside of the brain and spinal cord.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000429", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "The peripheral nervous system (PNS) is the part of the nervous system connected to the CNS which contains cranial nerves III - XII, spinal, peripheral and autonomic nerves. (CUMBO)" xsd:string {source="http://neurolex.org/wiki/Cumbo_terms"} -property_value: UBPROP:0000003 "(...) specific vertebrate traits within the chordate phylum such as skeletal tissues, PNS, and spectacular head and brain development, are linked to the NC (neural crest) and its derivatives.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000399", ontology="VHOG", source="DOI:10.1007/978-0-387-46954-6_6 Dupin E, Creuzet S, Le Douarin NM, The contribution of the neural crest to the vertebrate body. Advances in experimental medicine and biology (2006)", source="http://bgee.unil.ch/"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000011 @@ -158207,11 +157918,9 @@ xref: Wikipedia:Parasympathetic_nervous_system xref: ZFA:0001575 is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision -relationship: contributes_to_morphology_of UBERON:0002410 ! autonomic nervous system relationship: part_of UBERON:0002410 {source="FMA", source="MA", source="WP", source="ZFA-modified-from-isa"} ! autonomic nervous system -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png" xsd:anyURI -property_value: UBPROP:0000001 "Part of the autonomic nervous system which has opposing physiological effects of the sympathetic nervous system. Examples include decreasing the heart rate or dilating the blood vessels.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010488", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "In mammals, the autonomic nervous system is divided into two contrasting, antagonistic systems of control over visceral activity: the sympathetic system and the parasympathetic system (reference 1); In general, the teleosts may be considered phylogenetically the first class of vertebrates in which the heart is regulated by both sympathetic and parasympathetic neural pathways (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000755", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.634, DOI:10.1016/S0306-4530(98)00057-2 Porges SW, Love: an emergent property of the mammalian autonomic nervous system. Psychoneuroendocrinology (1998)", source="http://bgee.unil.ch/"} +relationship: RO:0002433 UBERON:0002410 ! contributes to morphology of autonomic nervous system +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png" xsd:anyURI [Term] id: UBERON:0000012 @@ -158232,8 +157941,8 @@ xref: MIAA:0000099 xref: NLXANAT:100301 xref: Wikipedia:Somatic_nervous_system is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision -relationship: contributes_to_morphology_of UBERON:0001016 ! nervous system relationship: part_of UBERON:0000010 ! peripheral nervous system +relationship: RO:0002433 UBERON:0001016 ! contributes to morphology of nervous system [Term] id: UBERON:0000013 @@ -158270,13 +157979,9 @@ xref: VHOG:0000384 xref: Wikipedia:Sympathetic_nervous_system xref: ZFA:0001576 is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision -relationship: contributes_to_morphology_of UBERON:0002410 ! autonomic nervous system relationship: part_of UBERON:0002410 {source="FMA", source="MA", source="ZFA-modified-from-isa"} ! autonomic nervous system -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/77/Gray838.png" xsd:anyURI -property_value: UBPROP:0000001 "Part of the autonomic nervous system which has opposing physiological effects of the parasympathetic nervous system. Examples include increasing the heart rate or constricting the blood vessels.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010487", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "The part of the autonomic nervous system which chiefly contains adrenergic fibres and tends to control and reduce secretions, decrease the contractility and hence the tone of smooth muscles and provoke the contraction of blood vessels. Essentially, it consists of preganglionic fibres from the thoracic and upper lumbar parts of the spinal cord. These fibres, by means of delicate rami communicantes, cross over to ganglia sited in a pair of ganglionated cords on each side of the vertebral column or to more peripheral ganglia. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000384", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "The autonomic nervous system is composed of three divisions: the sympathetic division, the parasympathetic division, and the enteric division. (...) In ray-finned teleost fishes, a sympathetic chain is present, and dual innervation of additional organs can be observed. A similar pattern can be found in amphibians (...). The evolution of the autonomic nervous system has been quite conservative, especially in the tetrapod lineage.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000384", ontology="VHOG", source="ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.461-463", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000011 "has developmental contribution from NC in verteberates (https://github.com/obophenotype/uberon/wiki/The-neural-crest)" xsd:string +relationship: RO:0002433 UBERON:0002410 ! contributes to morphology of autonomic nervous system +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/77/Gray838.png" xsd:anyURI [Term] id: UBERON:0000014 @@ -158289,9 +157994,7 @@ synonym: "region of skin" EXACT [] synonym: "skin" EXACT [MA:0000151] synonym: "skin region" EXACT [] synonym: "skin zone" EXACT [] -xref: EHDAA2:0001844 xref: EHDAA:6530 -xref: EMAPA:17525 xref: EV:0100152 xref: FMA:86166 xref: GAID:933 @@ -158303,15 +158006,13 @@ xref: SCTID:20795001 xref: VHOG:0000860 xref: Wikipedia:Skin is_a: PR:000050567 ! protein-containing material entity +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0034944 {source="FMA"} ! zone of organ relationship: has_part UBERON:0001003 ! skin epidermis relationship: has_part UBERON:0002067 ! dermis relationship: part_of UBERON:0002097 ! skin of body -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/HumanSkinDiagram.jpg" xsd:anyURI -property_value: IAO:0000232 "Note the distinction between the entire skin of the body, of which there is only 1 in an organism, and zones of skin, of which there can be many. Examples: skin of knee" xsd:string -property_value: UBPROP:0000003 "(...) it is well-established that neural crest cells contribute to both the dermal skeleton (craniofacial bone, teeth, and the caudal fin rays of teleosts) and the integument, including craniofacial dermis and all pigment cells outside the retina (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000860", ontology="VHOG", source="DOI:10.1111/j.1469-7580.2008.01043.x Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "we assume that mouse, HOG and GAID all mean zone of skin when they say skin. We also choose skin as an exact synonym, as it is more intuitive" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/HumanSkinDiagram.jpg" xsd:anyURI [Term] id: UBERON:0000015 @@ -158326,9 +158027,9 @@ xref: AEO:0000192 xref: CARO:0000010 xref: FMA:50705 is_a: UBERON:0000466 {source="CARO"} ! immaterial anatomical entity -relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 ! Fungi +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000016 @@ -158352,7 +158053,6 @@ xref: EMAPA:35305 xref: EV:0100129 xref: FMA:16018 xref: MA:0001582 -xref: MESH:D007515 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: NCIT:C32509 xref: SCTID:361339003 xref: TAO:0001260 @@ -158364,17 +158064,13 @@ is_a: UBERON:0004119 ! endoderm-derived structure relationship: capable_of GO:0030073 {source="GO"} ! insulin secretion relationship: capable_of GO:0070091 {source="GO"} ! glucagon secretion relationship: capable_of GO:0070253 {source="GO"} ! somatostatin secretion -relationship: composed_primarily_of UBERON:0000006 ! islet of Langerhans -relationship: contributes_to_morphology_of UBERON:0001264 ! pancreas -relationship: develops_from UBERON:0003923 ! dorsal pancreatic bud relationship: part_of UBERON:0000949 {source="AAO", source="FMA", source="XAO"} ! endocrine system relationship: part_of UBERON:0001264 ! pancreas -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: editor_note "create a separate class for distributed pancreas, eg cyclostomes?" xsd:string -property_value: UBPROP:0000001 "The part of the pancreas that acts as an endocrine gland, consisting of the islets of Langerhans, which secrete insulin and other hormones. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000049", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/Pancreas"} -property_value: UBPROP:0000001 "The zebrafish endocrine pancreas is composed of small groups of islet cells that are distributed throughout the exocrine pancreas. The islet cells produce insulin, glucagon and somatostatin.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001260", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000049", ontology="VHOG", source="DOI:10.1016/j.crvi.2007.03.006 Madsen OD, Pancreas phylogeny and ontogeny in relation to a 'pancreatic stem cell'. C.R. Biologies (2007)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "endocrine and exocrine pancreas are not co-associated in hagfishes or lampreys" xsd:string {source="PMID:20959416"} +relationship: RO:0002202 UBERON:0003923 ! develops from dorsal pancreatic bud +relationship: RO:0002433 UBERON:0001264 ! contributes to morphology of pancreas +relationship: RO:0002473 UBERON:0000006 ! composed primarily of islet of Langerhans +property_value: IAO:0000116 "create a separate class for distributed pancreas, eg cyclostomes?" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000017 @@ -158397,7 +158093,6 @@ xref: EMAPA:35328 xref: EV:0100093 xref: FMA:16017 xref: MA:0002415 -xref: MESH:D046790 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C32546 xref: SCTID:248202004 xref: TAO:0001249 @@ -158409,16 +158104,14 @@ xref: ZFA:0001249 is_a: UBERON:0000409 ! serous gland is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0005177 ! trunk region element +is_a: UBERON:0013765 ! digestive system element relationship: capable_of_part_of GO:0007586 ! digestion -relationship: contributes_to_morphology_of UBERON:0001264 ! pancreas -relationship: develops_from UBERON:0003924 ! ventral pancreatic bud relationship: has_part UBERON:0001263 ! pancreatic acinus relationship: has_part UBERON:0007329 ! pancreatic duct relationship: part_of UBERON:0001264 ! pancreas -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000001 "The exocrine pancreas is composed of acinar epithelial cells and ductal epithelium that manufacture the proteolytic enzymes and bicarbonate required for digestion.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001249", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "The part of the pancreas that acts as an exocrine gland, consisting of the pancreatic acini, which produce pancreatic juice and secrete it into the intestine to aid in protein digestion. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000048", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/Pancreas"} -property_value: UBPROP:0000003 "In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000048", ontology="VHOG", source="DOI:10.1016/j.crvi.2007.03.006 Madsen OD, Pancreas phylogeny and ontogeny in relation to a 'pancreatic stem cell'. C.R. Biologies (2007)", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003924 ! develops from ventral pancreatic bud +relationship: RO:0002433 UBERON:0001264 ! contributes to morphology of pancreas +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000018 @@ -158434,18 +158127,15 @@ synonym: "insect eye" RELATED [] synonym: "Komplexauge" RELATED [BTO:0001921] synonym: "zusammengesetztes Auge" RELATED [BTO:0001921] xref: BTO:0001921 -xref: FBbt:00004508 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: HAO:0000217 -xref: IDOMAL:0002421 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: TGMA:0000024 xref: Wikipedia:Compound_eye is_a: UBERON:0015165 ! multi-unit eye intersection_of: UBERON:0000970 ! eye -intersection_of: composed_primarily_of UBERON:0000971 ! ommatidium -relationship: composed_primarily_of UBERON:0000971 ! ommatidium -relationship: only_in_taxon NCBITaxon:6656 {source="PMID:21062451"} ! Arthropoda +intersection_of: RO:0002473 UBERON:0000971 ! composed primarily of ommatidium +relationship: RO:0002160 NCBITaxon:6656 {source="PMID:21062451"} ! only in taxon Arthropoda +relationship: RO:0002473 UBERON:0000971 ! composed primarily of ommatidium property_value: seeAlso "https://github.com/obophenotype/uberon/issues/457" xsd:anyURI -property_value: UBPROP:0000008 "The term compound eye is sometimes used for the multi-unit eyes of annelids, bivalves, echinoderms. We follow Richter et al and restrict this class to the arthropod structure for these structures" xsd:string {source="PMID:21062451"} [Term] id: UBERON:0000019 @@ -158482,15 +158172,12 @@ is_a: UBERON:0000047 ! simple eye is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0015212 ! lateral structure -relationship: develops_from UBERON:0003072 {evidence="definitional"} ! optic cup -relationship: existence_ends_during UBERON:0000066 ! fully formed stage +relationship: BSPO:0000126 UBERON:0000033 ! head relationship: has_part UBERON:0000965 ! lens of camera-type eye relationship: has_part UBERON:0000966 ! retina -relationship: in_lateral_side_of UBERON:0000033 ! head relationship: part_of UBERON:0004088 ! orbital region -property_value: UBPROP:0000001 "A cavitated compound organ that transduces light waves into neural signals.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000107", ontology="TAO", source="TAO:wd"} -property_value: UBPROP:0000003 "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000275", ontology="VHOG", source="DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "FMA distinguishes Eye (subdivision of face) which has its parts an Eyeball (organ), as well as other structures, and the orbit of skull. MA includes eyelid, conjunctiva and lacrimal apparatus as part of MA:eye - consistent with FMA - so we can infer that MA:eye is more like FMA:eye than FMA:eyeball. For other AOs this distinction is less meaningful - e.g. ZFA has no eyelid; XAO has no eyelid, but it has conjuctiva, which is considered part of the xao:eye. GO considers eyelid development part of eye development. See also notes on optic nerve - XAO, AAO and BTO consider this part of the eye. MA considers the eye muscles part of the eye, whereas FMA has a class 'orbital content' for this" xsd:string {external_ontology="FMA"} +relationship: RO:0002202 UBERON:0003072 ! develops from optic cup +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage [Term] id: UBERON:0000020 @@ -158515,7 +158202,6 @@ xref: CALOHA:TS-2043 xref: EHDAA2:0001824 xref: EHDAA:500 xref: EMAPA:35955 -xref: FBbt:00005155 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: GAID:63 xref: HAO:0000930 xref: MA:0000017 @@ -158530,7 +158216,7 @@ intersection_of: UBERON:0000062 ! organ intersection_of: capable_of GO:0050906 ! detection of stimulus involved in sensory perception relationship: capable_of GO:0050906 ! detection of stimulus involved in sensory perception relationship: part_of UBERON:0001032 ! sensory system -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" xsd:anyURI [Term] id: UBERON:0000021 @@ -158545,8 +158231,8 @@ xref: CALOHA:TS-0051 xref: FMA:71012 xref: SCTID:276160000 is_a: UBERON:0013703 ! integumentary projection -relationship: attaches_to UBERON:0002097 ! skin of body -property_value: editor_note "Mammary glands develop by similar mechanisms, and there is an argument for including them here (e.g. http://www.ncbi.nlm.nih.gov/pubmed/20484386), but these structures do not fit the current definition (lactiferous glands are part of the integumentary system in FMA). Note the FMA class is a subdivision of epidermis, which may be too restrictive for our purposes here." xsd:string +relationship: RO:0002371 UBERON:0002097 ! attached to skin of body +property_value: IAO:0000116 "Mammary glands develop by similar mechanisms, and there is an argument for including them here (e.g. http://www.ncbi.nlm.nih.gov/pubmed/20484386), but these structures do not fit the current definition (lactiferous glands are part of the integumentary system in FMA). Note the FMA class is a subdivision of epidermis, which may be too restrictive for our purposes here." xsd:string [Term] id: UBERON:0000025 @@ -158558,11 +158244,9 @@ synonym: "duct" NARROW [] xref: galen:Tube is_a: UBERON:0004111 ! anatomical conduit intersection_of: UBERON:0004111 ! anatomical conduit -intersection_of: has_quality PATO:0002299 ! tubular +intersection_of: RO:0000086 PATO:0002299 ! has quality tubular relationship: has_part UBERON:0013522 ! subdivision of tube -relationship: has_quality PATO:0002299 ! tubular -property_value: IAO:0000232 "not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts)" xsd:string -property_value: UBPROP:0000007 "tubular" xsd:string +relationship: RO:0000086 PATO:0002299 ! has quality tubular [Term] id: UBERON:0000026 @@ -158584,7 +158268,6 @@ xref: EFO:0000799 xref: EHDAA2:0003193 xref: EMAPA:37283 {source="MA:th"} xref: EV:0100155 -xref: FBbt:00007000 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: HAO:0000144 xref: MAT:0000023 xref: MESH:D005121 @@ -158595,11 +158278,7 @@ xref: VSAO:0000075 xref: Wikipedia:Appendage xref: XAO:0000218 is_a: UBERON:0000475 ! organism subdivision -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: UBPROP:0000001 "An appendage is an external body part, or natural prolongation, that protrudes from an organism's body, such as a vertebrate's limbs[BILA][BILA:0000018]." xsd:string {source="BILA:0000018"} -property_value: UBPROP:0000001 "Organ or organ part that is attached to the body of an organism. For example a limb[GO, modified][GO:0048736]." xsd:string {source="GO:0048736"} -property_value: UBPROP:0000007 "appendicular" xsd:string -property_value: UBPROP:0000008 "this is currently a subtype of organism subdivision - which would exclude feathers" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0000029 @@ -158635,21 +158314,20 @@ xref: ZFA_RETIRED:0005318 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005057 ! immune organ intersection_of: UBERON:0000062 ! organ -intersection_of: composed_primarily_of UBERON:0001744 ! lymphoid tissue -intersection_of: continuous_with UBERON:0001473 ! lymphatic vessel -relationship: composed_primarily_of UBERON:0001744 ! lymphoid tissue -relationship: continuous_with UBERON:0001473 ! lymphatic vessel -relationship: develops_from UBERON:0034953 ! embryonic lymph sac +intersection_of: RO:0002150 UBERON:0001473 ! continuous with lymphatic vessel +intersection_of: RO:0002473 UBERON:0001744 ! composed primarily of lymphoid tissue relationship: has_part UBERON:0002006 ! cortex of lymph node relationship: has_part UBERON:0002007 ! medulla of lymph node relationship: has_part UBERON:0002194 ! capsule of lymph node relationship: has_part UBERON:0002391 ! lymph -relationship: in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0002465 ! lymphoid system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b8/Illu_lymph_node_structure.png" xsd:anyURI +relationship: RO:0002150 UBERON:0001473 ! continuous with lymphatic vessel +relationship: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia +relationship: RO:0002202 UBERON:0034953 ! develops from embryonic lymph sac +relationship: RO:0002473 UBERON:0001744 ! composed primarily of lymphoid tissue +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b8/Illu_lymph_node_structure.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/uberon/issues/650" xsd:anyURI -property_value: UBPROP:0000003 "Lymph nodes that are associated with the lymphatic system have evolved in mammals.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001273", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.630", source="http://bgee.unil.ch/"} [Term] id: UBERON:0000030 @@ -158667,10 +158345,10 @@ xref: SCTID:298225002 xref: UMLS:C1179187 {source="ncithesaurus:Lamina_Propria"} xref: Wikipedia:Lamina_propria is_a: UBERON:0004923 ! organ component layer -relationship: composed_primarily_of UBERON:0011825 ! loose connective tissue -relationship: immediately_deep_to UBERON:0000483 ! epithelium +relationship: BSPO:0001107 UBERON:0000483 ! epithelium relationship: part_of UBERON:0000344 ! mucosa -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/f/fb/GI_Organization.svg" xsd:anyURI +relationship: RO:0002473 UBERON:0011825 ! composed primarily of loose connective tissue +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/f/fb/GI_Organization.svg" xsd:anyURI [Term] id: UBERON:0000031 @@ -158740,13 +158418,9 @@ xref: Wikipedia:Head xref: XAO:0003024 xref: ZFA:0001114 is_a: UBERON:0011676 ! subdivision of organism along main body axis -relationship: has_skeleton UBERON:0003129 {gci_relation="part_of", gci_filler="NCBITaxon:7776"} ! skull -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0007811 ! craniocervical region -property_value: RO:0002171 UBERON:0000948 -property_value: UBPROP:0000001 "Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010335", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001114", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001644", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.82", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002551 UBERON:0003129 {gci_relation="part_of", gci_filler="NCBITaxon:7776"} ! has skeleton skull [Term] id: UBERON:0000035 @@ -158767,12 +158441,13 @@ xref: EMAPA:35631 xref: FMA:18634 xref: MA:0002907 xref: SCTID:258665002 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0001305 ! ovarian follicle intersection_of: UBERON:0001305 ! ovarian follicle intersection_of: has_component UBERON:0005170 {cardinality="1"} ! granulosa cell layer -relationship: develops_from UBERON:0003981 ! primordial ovarian follicle relationship: has_component UBERON:0005170 ! granulosa cell layer -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 UBERON:0003981 ! develops from primordial ovarian follicle +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000036 @@ -158793,15 +158468,16 @@ synonym: "secondary follicle of ovary" EXACT [] xref: EMAPA:35632 xref: FMA:18637 xref: MA:0002908 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0001305 ! ovarian follicle intersection_of: UBERON:0001305 ! ovarian follicle intersection_of: has_component UBERON:0005170 {minCardinality="2"} ! granulosa cell layer -intersection_of: has_potential_to_develop_into UBERON:0000037 ! tertiary ovarian follicle -relationship: develops_from UBERON:0000035 ! primary ovarian follicle +intersection_of: RO:0002387 UBERON:0000037 ! has potential to develop into tertiary ovarian follicle relationship: has_component UBERON:0005170 ! granulosa cell layer -relationship: has_potential_to_develop_into UBERON:0000037 ! tertiary ovarian follicle -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: editor_note "consider adopting distinction in MA" xsd:string +relationship: RO:0002202 UBERON:0000035 ! develops from primary ovarian follicle +relationship: RO:0002387 UBERON:0000037 ! has potential to develop into tertiary ovarian follicle +property_value: IAO:0000116 "consider adopting distinction in MA" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000037 @@ -158828,14 +158504,15 @@ xref: MA:0002909 xref: NCIT:C32692 xref: SCTID:362261008 xref: UMLS:C0600225 {source="ncithesaurus:Graafian_Follicle"} +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0001305 ! ovarian follicle intersection_of: UBERON:0001305 ! ovarian follicle intersection_of: has_component UBERON:0005170 {minCardinality="2"} ! granulosa cell layer intersection_of: has_part UBERON:0000039 ! follicular antrum -relationship: develops_from UBERON:0000036 ! secondary ovarian follicle relationship: has_component UBERON:0005170 ! granulosa cell layer relationship: has_part UBERON:0000039 ! follicular antrum -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/e/e6/Primary_follicle-4.JPG" xsd:anyURI +relationship: RO:0002202 UBERON:0000036 ! develops from secondary ovarian follicle +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/e/e6/Primary_follicle-4.JPG" xsd:anyURI [Term] id: UBERON:0000038 @@ -158864,13 +158541,11 @@ is_a: UBERON:0000463 ! organism substance relationship: has_part CHEBI:17089 relationship: has_part UBERON:0000456 ! secretion of exocrine gland relationship: has_part UBERON:0007779 ! transudate -relationship: located_in UBERON:0000039 ! follicular antrum relationship: part_of UBERON:0001305 ! ovarian follicle -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: surrounds CL:0000025 ! egg cell -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/81/Gray3.png" xsd:anyURI -property_value: UBPROP:0000008 "Generally, larger species such as ovine, equine, porcine, human, and bovine have larger follicles, with the fluid comprising a substantial proportion of the volume of the follicles at ovulation (estimated at >95% in bovine [3]). Smaller species such as rats and mice have smaller follicles with fractionally less follicular fluid[20164441]" xsd:string -property_value: UBPROP:0000010 "The follicular fluid contains sex steroids, glycoprotein hormones, plasma proteins, mucopolysaccharides, and enzymes and is rich in hyaluronic acid." xsd:string +relationship: RO:0001025 UBERON:0000039 ! located in follicular antrum +relationship: RO:0002221 CL:0000025 ! surrounds egg cell +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/81/Gray3.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000039 @@ -158888,11 +158563,11 @@ xref: FMA:18675 xref: Wikipedia:Follicular_antrum is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: location_of UBERON:0000038 ! follicular fluid intersection_of: part_of UBERON:0001305 ! ovarian follicle -relationship: location_of UBERON:0000038 ! follicular fluid +intersection_of: RO:0001015 UBERON:0000038 ! location of follicular fluid relationship: part_of UBERON:0001305 ! ovarian follicle -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0001015 UBERON:0000038 ! location of follicular fluid +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000042 @@ -158919,11 +158594,8 @@ is_a: UBERON:0004120 ! mesoderm-derived structure relationship: has_part UBERON:0001136 ! mesothelium relationship: has_part UBERON:0002384 ! connective tissue relationship: part_of UBERON:0000060 ! anatomical wall -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png" xsd:anyURI -property_value: UBPROP:0000001 "A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005425", ontology="TAO", source="Wikipedia:Serous_membrane"} -property_value: UBPROP:0000001 "a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP]" xsd:string {source="Wikipedia:Serous_membrane"} -property_value: UBPROP:0000012 "in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA." xsd:string {external_ontology="FMA"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png" xsd:anyURI [Term] id: UBERON:0000043 @@ -158954,15 +158626,12 @@ xref: Wikipedia:Tendon xref: XAO:0000173 xref: ZFA:0005647 is_a: UBERON:0007846 {source="VSAO"} ! dense regular connective tissue -relationship: connects UBERON:0001474 ! bone element -relationship: connects UBERON:0001630 ! muscle organ relationship: has_part CL:0000327 {source="AEO"} ! extracellular matrix secreting cell -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0002204 {source="OG"} ! musculoskeletal system -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Dense regular connective tissue that connects muscle to bone.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000073", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000003 "Phylogenetically, tendinous tissue first appears in the invertebrate chordate Branchiostoma as myosepta. This two-dimensional array of collagen fibers is highly organized, with fibers running along two primary axes. In hagfish the first linear tendons appear and the myosepta have developed specialized regions with unidirectional fiber orientation - a linear tendon within the flat sheet of myoseptum.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001286", ontology="VHOG", source="DOI:10.1016/S1095-6433(02)00241-6 Summers AP, Koob TJ, The evolution of tendon - morphology and material properties. Comparative Biochemistry and Physiology-Part A: Molecular and Integrative Physiology (2002)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "in FMA, tendon is an organ component that with parts dense-irregular-connective-tissue of tendon and dense-irregular-connective-tissue of tendon sheath; we follow VSAO in making it a subtype of the former. In VSAO tendons connect muscle to bone; in WP the def states integument (e.g. auricular muscles) - but JB confirms this is not actually tendon but aponeurosis" xsd:string {external_ontology="FMA"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002176 UBERON:0001474 ! connects bone element +relationship: RO:0002176 UBERON:0001630 ! connects muscle organ +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg" xsd:anyURI [Term] id: UBERON:0000044 @@ -159002,7 +158671,6 @@ xref: FMA:5888 xref: MA:0000231 xref: MA:0000232 xref: MAT:0000162 -xref: MESH:D005727 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: MIAA:0000162 xref: NCIT:C12462 xref: SCTID:244455004 @@ -159013,19 +158681,16 @@ xref: Wikipedia:Dorsal_root_ganglion xref: XAO:0000210 xref: ZFA:0000200 is_a: UBERON:0001800 {source="MA"} ! sensory ganglion +is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0000045 ! ganglion intersection_of: extends_fibers_into UBERON:0001780 ! spinal nerve intersection_of: extends_fibers_into UBERON:0002261 ! dorsal root of spinal cord -relationship: develops_from UBERON:0003083 {source="DOI:10.1101/gr.157586.113", source="ZFA", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! trunk neural crest relationship: extends_fibers_into UBERON:0001780 ! spinal nerve relationship: extends_fibers_into UBERON:0002261 ! dorsal root of spinal cord -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/71/DRG_Chicken_e7.jpg" xsd:anyURI +relationship: RO:0002202 UBERON:0003083 {source="DOI:10.1101/gr.157586.113", source="ZFA", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! develops from trunk neural crest +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/71/DRG_Chicken_e7.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/uberon/issues/2644" xsd:string -property_value: UBPROP:0000001 "Trunk ganglion which is located adjacent to the spine on a dorsal root and contains the cell bodies of afferent sensory nerves.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000200", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "From comparative analyses of craniate brains, a morphotype of the brain in the earliest craniate stock can be constructed. In marked contrast to cephalochordates, the ancestral craniate morphotype had a plethora of unique features, which included a telencephalon with pallial and subpallial parts, paired olfactory bulbs with substantial projections to most or all of the telencephalic pallium, paired lateral eyes and ears, a lateral line system for both electroreception and mechanoreception, spinal cord dorsal root ganglia, and an autonomic nervous system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000222", ontology="VHOG", source="DOI:10.1002/1097-0185(20000615)261:3<111::AID-AR6>3.0.CO;2-F Butler AB, Chordate evolution and the origin of craniates: An old brain in a new head. AnaT Rec (New Anat) (2000)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000011 "The sensory ganglia of spinal nerves arise only from the neural crest, whereas many sensory ganglia of the 'dorsal' cranial nerves arise from epibranchial placodes as well as the neural crest[DOI:10.1093/icb/icn065]" xsd:string -property_value: UBPROP:0000012 "MA and EMAPA introduce distinct classes for what appears to be the same thing" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0000045 @@ -159070,18 +158735,11 @@ xref: Wikipedia:Ganglion xref: XAO:0000209 xref: ZFA:0000190 is_a: UBERON:0000061 {source="https://github.com/obophenotype/uberon/issues/2495#issuecomment-1187364719"} ! anatomical structure -disjoint_from: UBERON:0002420 {inconsistent_with="BTO"} ! basal ganglion -relationship: composed_primarily_of UBERON:0003714 {source="EHDAA2"} ! neural tissue -relationship: immediate_transformation_of UBERON:0003869 {source="Bgee:AN"} ! presumptive ganglion relationship: part_of UBERON:0001016 ! nervous system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: editor_note "TODO - check vert vs invert. Other species: Any of a number of aggregations of neurons, glial cells and their processes, surrounded by a glial cell and connective tissue sheath (plural: ganglia). // Subdivision of neural tree (organ) which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord); together with a nucleus and its associated nerve, it constitutes a neural tree (organ). Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion. // a cluster of nerve cells and associated glial cells (nuclear location) // Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system." xsd:string -property_value: UBPROP:0000001 "A ganglion is a cluster of neurons. It is part of a nervous system. It may include glial cells. The neurons are arranged in a specific constellation: neuronal somata are concentrated at the surface, thus forming a cell cortex, and neurites are concentrated in the centre of the ganglion to form the neuropil. A ganglion is a distinct unit but several ganglia may be anterio-posteriorly joined by connectives or transversally by commissures" xsd:string {source="PMID:21062451"} -property_value: UBPROP:0000001 "Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010426", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000001 "Structures containing a collection of nerve cell bodies. (Source: BioGlossary, www.Biology-Text.com)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000190", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Subdivision of nervous system which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord. Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion (adapted from Foundational Model of Anatomy)[NLXANAT:100302]." xsd:string {source="NLXANAT:100302"} -property_value: UBPROP:0000003 "Cranial sensory placodes are focused areas of the head ectoderm of vertebrates that contribute to the development of the cranial sense organs and their associated ganglia. Placodes have long been considered a key character of vertebrates, and their evolution is proposed to have been essential for the evolution of an active predatory lifestyle by early vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000156", ontology="VHOG", source="DOI:10.1016/j.ydbio.2005.02.021 Mazet F, Hutt JA, Milloz J, Millard J, Graham A, Shimeld SM, Molecular evidence from Ciona intestinalis for the evolutionary origin of vertebrate sensory placodes. Developmental Biology (2005)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "ganglionic" xsd:string +relationship: RO:0002473 UBERON:0003714 {source="EHDAA2"} ! composed primarily of neural tissue +relationship: RO:0002495 UBERON:0003869 {source="Bgee:AN"} ! immediate transformation of presumptive ganglion +property_value: IAO:0000116 "TODO - check vert vs invert. Other species: Any of a number of aggregations of neurons, glial cells and their processes, surrounded by a glial cell and connective tissue sheath (plural: ganglia). // Subdivision of neural tree (organ) which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord); together with a nucleus and its associated nerve, it constitutes a neural tree (organ). Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion. // a cluster of nerve cells and associated glial cells (nuclear location) // Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system." xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000047 @@ -159117,7 +158775,6 @@ xref: BIRNLEX:705 xref: DHBA:10576 xref: DMBA:17767 xref: EMAPA:35352 -xref: FMA:61965 {notes="inferred"} xref: FMA:83865 xref: HBA:9249 xref: MA:0002747 @@ -159131,10 +158788,10 @@ is_a: UBERON:0007702 ! tract of brain relationship: extends_fibers_into UBERON:0002206 ! mammillary body relationship: extends_fibers_into UBERON:0002663 ! septal nuclear complex relationship: part_of UBERON:0002421 {source="NIFSTD"} ! hippocampal formation -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/21/Gray747.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/21/Gray747.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000053 @@ -159162,9 +158819,10 @@ xref: UMLS:C0450295 {source="ncithesaurus:Macula_Lutea", source="BIRNLEX:2540"} xref: UMLS:C1284755 {source="BIRNLEX:2540"} xref: Wikipedia:Macula_of_retina is_a: UBERON:0000064 ! organ part +is_a: UBERON:0004121 ! ectoderm-derived structure disjoint_from: UBERON:0000054 ! macula relationship: part_of UBERON:0000966 ! retina -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png" xsd:anyURI [Term] id: UBERON:0000054 @@ -159184,11 +158842,9 @@ xref: MESH:D008267 xref: TAO:0000386 xref: ZFA:0000386 is_a: UBERON:0000479 ! tissue +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: has_part GO:0070451 ! cell hair relationship: part_of UBERON:0001846 ! internal ear -property_value: IAO:0000232 "this refers to the inner ear structure, not the macula of the retina. We follow ZFA in including a grouping class for the macula of utricle and sacule" xsd:string -property_value: UBPROP:0000001 "Patches of thickened, pseudostratified epithelium of the inner ear, consisting of regular arrays of sensory hair cells interspersed with supporting cells. Each patch has its own charcteristic shape and polarity pattern. (See Anatomical Atlas entry for sensory patches of the ear by T. Whitfield.)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000386", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000007 "macular" xsd:string [Term] id: UBERON:0000055 @@ -159200,7 +158856,7 @@ subset: human_reference_atlas subset: pheno_slim is_a: UBERON:0004111 ! anatomical conduit relationship: channel_for UBERON:0006314 ! bodily fluid -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000056 @@ -159239,20 +158895,14 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005179 ! pelvic region element is_a: UBERON:0006555 ! excretory tube is_a: UBERON:0015212 ! lateral structure +relationship: BSPO:0000126 UBERON:0000468 ! multicellular organism relationship: channel_for UBERON:0001088 ! urine relationship: channels_from UBERON:0001224 ! renal pelvis relationship: channels_into UBERON:0001255 ! urinary bladder -relationship: develops_from UBERON:0005081 {source="GO"} ! ureter ureteric bud -relationship: in_lateral_side_of UBERON:0000468 ! multicellular organism relationship: part_of UBERON:0036295 ! renal pelvis/ureter -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg" xsd:anyURI -property_value: UBPROP:0000001 "Anatomical structure consisting of long narrow duct which carries urine from the kidney to the urinary bladder.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010254", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "The duct of amniotes that carries urine from a metanephric kidney to the urinary bladder. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000605", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000605", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "ureteral" xsd:string -property_value: UBPROP:0000007 "ureteric" xsd:string -property_value: UBPROP:0000010 "in humans, consists of adventitial, muscular and mucoa layers" xsd:string +relationship: RO:0002202 UBERON:0005081 {source="GO"} ! develops from ureter ureteric bud +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000057 @@ -159288,13 +158938,11 @@ is_a: UBERON:0004120 ! mesoderm-derived structure relationship: capable_of_part_of GO:0060073 ! micturition relationship: channel_for UBERON:0001088 ! urine relationship: channels_from UBERON:0001255 ! urinary bladder -relationship: continuous_with UBERON:0001255 ! urinary bladder -relationship: develops_from UBERON:0000164 {notes="pelvic part of UG sinus gives rise to prostatic and membranous parts of urethra", source="Wikipedia"} ! primitive urogenital sinus -relationship: develops_from UBERON:0013241 {source="Wikipedia"} ! embryonic urethral groove relationship: part_of UBERON:0001556 ! lower urinary tract -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png" xsd:anyURI -property_value: UBPROP:0000007 "urethral" xsd:string -property_value: UBPROP:0000008 "In human males, the urethra travels through the penis, and carries semen as well as urine. In females, the urethra is shorter and emerges above the vaginal opening." xsd:string +relationship: RO:0002150 UBERON:0001255 ! continuous with urinary bladder +relationship: RO:0002202 UBERON:0000164 ! develops from primitive urogenital sinus +relationship: RO:0002202 UBERON:0013241 {source="Wikipedia"} ! develops from embryonic urethral groove +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png" xsd:anyURI [Term] id: UBERON:0000058 @@ -159307,7 +158955,6 @@ synonym: "ducts" RELATED OMO:0003004 [XAO:0004000] synonym: "exocrine duct" NARROW [] synonym: "exocrine gland duct" NARROW [] xref: AAO:0011123 -xref: FBbt:00100314 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:30320 xref: galen:Duct xref: NCIT:C12948 @@ -159319,11 +158966,9 @@ xref: XAO:0004000 xref: ZFA:0005171 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000063 ! organ subunit -relationship: conduit_for UBERON:0000463 ! organism substance relationship: has_part UBERON:0034969 ! epithelial layer of duct -relationship: has_quality PATO:0002299 ! tubular -property_value: UBPROP:0000001 "A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171]." xsd:string {source="ZFA:0005171"} -property_value: UBPROP:0000012 "Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here." xsd:string +relationship: RO:0000086 PATO:0002299 ! has quality tubular +relationship: RO:0002570 UBERON:0000463 ! conduit for organism substance [Term] id: UBERON:0000059 @@ -159356,15 +159001,14 @@ xref: Wikipedia:Large_intestine_(anatomy) xref: XAO:0000131 is_a: UBERON:0004921 {source="cjm"} ! subdivision of digestive tract is_a: UBERON:0013765 ! digestive system element -relationship: contributes_to_morphology_of UBERON:0000160 ! intestine -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0000160 ! intestine relationship: part_of UBERON:0004907 ! lower digestive tract -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/SBU_F_Intestine_Large.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb" xsd:anyURI -property_value: UBPROP:0000003 "Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000054", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.566", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002433 UBERON:0000160 ! contributes to morphology of intestine +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/SBU_F_Intestine_Large.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000060 @@ -159376,13 +159020,11 @@ subset: upper_level synonym: "organ wall" RELATED [FMA:82482] synonym: "wall" BROAD [] synonym: "wall of organ" EXACT [FMA:82482] -xref: EMAPA:25036 xref: FMA:82482 xref: galen:Wall is_a: UBERON:0000064 ! organ part relationship: adjacent_to UBERON:0002553 ! anatomical cavity relationship: has_part UBERON:0004923 ! organ component layer -property_value: UBPROP:0000012 "in FMA, serosa is a wall" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0000061 @@ -159399,7 +159041,6 @@ xref: BILA:0000003 xref: CARO:0000003 xref: EHDAA2:0003003 xref: EMAPA:0 -xref: FBbt:00007001 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:305751 xref: FMA:67135 xref: GAID:781 @@ -159414,11 +159055,11 @@ xref: VHOG:0001759 xref: XAO:0003000 xref: ZFA:0000037 is_a: UBERON:0000465 ! material anatomical entity -relationship: existence_ends_during_or_before UBERON:0000071 ! death stage -relationship: existence_starts_during_or_after UBERON:0000106 {gci_relation="in_taxon", gci_filler="NCBITaxon:33208"} ! zygote stage -relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 ! Fungi +relationship: RO:0002496 UBERON:0000106 {gci_filler="NCBITaxon:33208", gci_relation="RO:0002162"} ! existence starts during or after zygote stage +relationship: RO:0002497 UBERON:0000071 ! existence ends during or before death stage +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000062 @@ -159446,15 +159087,13 @@ is_a: UBERON:0010000 ! multicellular anatomical structure disjoint_from: UBERON:0002095 {source="PMID:28192867"} ! mesentery disjoint_from: UBERON:0034921 ! multi organ part structure relationship: capable_of GO:0008150 ! biological_process -relationship: existence_starts_during_or_after UBERON:0000111 {gci_filler="NCBITaxon:6072", gci_relation="in_taxon"} ! organogenesis stage -relationship: has_boundary UBERON:0006984 ! anatomical surface -relationship: never_in_taxon NCBITaxon:110815 {source="Wikipedia"} relationship: part_of UBERON:0000467 ! anatomical system -relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 ! Fungi -property_value: UBPROP:0000001 "Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." xsd:string {source="GO:0048513"} -property_value: UBPROP:0000012 "CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4" xsd:string +relationship: RO:0002002 UBERON:0006984 ! has 2D boundary anatomical surface +relationship: RO:0002496 UBERON:0000111 {gci_filler="NCBITaxon:6072", gci_relation="RO:0002162"} ! existence starts during or after organogenesis stage +property_value: RO:0002161 NCBITaxon:110815 {source="Wikipedia"} +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000063 @@ -159467,9 +159106,7 @@ synonym: "organ segment" RELATED [FMA:86140] synonym: "segment of organ" RELATED [FMA:86140] xref: FMA:86140 is_a: UBERON:0000064 ! organ part -property_value: editor_note "FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction" xsd:string -property_value: UBPROP:0000001 "Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball." xsd:string {source="FMA:86140", version="3"} -property_value: UBPROP:0000001 "Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal." xsd:string {source="FMA:86140", version="1"} +property_value: IAO:0000116 "FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction" xsd:string [Term] id: UBERON:0000064 @@ -159490,10 +159127,9 @@ xref: SCTID:113343008 xref: SCTID:91717005 is_a: UBERON:0010000 ! multicellular anatomical structure relationship: part_of UBERON:0000062 ! organ -relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 ! Fungi -property_value: IAO:0000232 "currently defined in a very broad sense, may be replaced by more specific classes in the future" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000065 @@ -159509,9 +159145,10 @@ xref: FMA:265130 xref: SCTID:361110005 xref: VHOG:0000393 is_a: UBERON:0001005 ! respiratory airway -relationship: develops_from UBERON:0007026 {source="NCBIBook:NBK10107"} ! presumptive gut -relationship: develops_from UBERON:0008947 ! respiratory primordium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +is_a: UBERON:0004119 ! endoderm-derived structure +relationship: RO:0002202 UBERON:0007026 {source="NCBIBook:NBK10107"} ! develops from presumptive gut +relationship: RO:0002202 UBERON:0008947 ! develops from respiratory primordium +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000066 @@ -159560,7 +159197,7 @@ is_a: UBERON:0000105 ! life cycle stage disjoint_from: UBERON:0000092 ! post-embryonic stage relationship: precedes UBERON:0000066 ! fully formed stage relationship: precedes UBERON:0000092 ! post-embryonic stage -relationship: simultaneous_with GO:0009790 ! embryo development +relationship: RO:0002082 GO:0009790 ! simultaneous with embryo development [Term] id: UBERON:0000069 @@ -159605,7 +159242,6 @@ synonym: "zoea stage" NARROW SENSU [Wikipedia:Larva] xref: BTO:0000915 xref: BTO:0000954 xref: EFO:0001303 -xref: FBdv:00005336 xref: MIAA:0000400 xref: OGES:000008 xref: Wikipedia:Larva @@ -159613,11 +159249,9 @@ xref: ZFS:0000048 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage relationship: immediately_preceded_by UBERON:0000068 ! embryo stage -relationship: never_in_taxon NCBITaxon:32524 ! Amniota relationship: part_of UBERON:0000092 ! post-embryonic stage -relationship: simultaneous_with GO:0002164 ! larval development -property_value: IAO:0000232 "Uberon includes clade-specific subclasses, e.g. nematod larva" xsd:string -property_value: UBPROP:0000008 "It is a misunderstanding that the larval form always reflects the group's evolutionary history. It could be the case, but often the larval stage has evolved secondarily, as in insects. In these cases the larval form might differ more from the group's common origin than the adult form" xsd:string {source="WP"} +relationship: RO:0002082 GO:0002164 ! simultaneous with larval development +property_value: RO:0002161 NCBITaxon:32524 [Term] id: UBERON:0000071 @@ -159630,11 +159264,10 @@ xref: XAO:0000437 xref: XtroDO:0000085 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage -relationship: ends UBERON:0000104 ! life cycle -relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 ! Fungi -property_value: UBPROP:0000012 "ncit:Death is an outcome" xsd:string {external_ontology="ncit"} +relationship: RO:0002229 UBERON:0000104 ! ends life cycle +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000072 @@ -159644,14 +159277,13 @@ def: "An section of a respiratory tract." [http://orcid.org/0000-0002-6601-2165] subset: non_informative synonym: "respiratory tract" RELATED [MA:0000434] synonym: "subdivision of respiratory tract" RELATED [] -xref: EMAPA:16737 xref: FMA:45660 xref: MA:0000434 +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0013522 ! subdivision of tube intersection_of: UBERON:0013522 ! subdivision of tube intersection_of: part_of UBERON:0000065 ! respiratory tract relationship: part_of UBERON:0000065 ! respiratory tract -property_value: UBPROP:0000012 "MA:0000434 has subclasses upper and lower, so it corresponds to a segment of the tract, rather than the tract as a whole" xsd:string {external_ontology="MA"} [Term] id: UBERON:0000073 @@ -159668,8 +159300,8 @@ xref: UMLS:C1518256 {source="ncithesaurus:Nervous_System_Part"} is_a: UBERON:0000481 ! multi-tissue structure intersection_of: UBERON:0000481 ! multi-tissue structure intersection_of: part_of UBERON:0001016 ! nervous system -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 relationship: part_of UBERON:0001016 ! nervous system +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2009-06-18T09:00:04Z [Term] @@ -159706,14 +159338,13 @@ xref: Wikipedia:Glomerulus xref: ZFA:0001288 is_a: UBERON:0000064 ! organ part is_a: UBERON:0004120 ! mesoderm-derived structure -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 -relationship: develops_from UBERON:0005749 ! glomerular tuft relationship: part_of UBERON:0001229 {source="FMA", source="MA"} ! renal corpuscle -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: surrounded_by UBERON:0001230 ! glomerular capsule -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg" xsd:anyURI -property_value: UBPROP:0000012 "ZFA - The multi-tissue structure where the glomerular basement membrane supported by mesonephric podocytes filters blood from the glomerular capillaries. GUDMAP: 'Together, the Bowman's capsule and the glomerulus comprise the definitive renal corpuscle.' - here the glomerulus is part of the capsule?" xsd:string {external_ontology="ZFA"} +relationship: RO:0002202 UBERON:0005749 ! develops from glomerular tuft +relationship: RO:0002219 UBERON:0001230 ! surrounded by glomerular capsule +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2009-06-18T09:26:37Z [Term] @@ -159731,9 +159362,9 @@ xref: NCIT:C34076 xref: SCTID:118966000 xref: UMLS:C1519343 {source="ncithesaurus:Skeletal_System_Part"} is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision -relationship: composed_primarily_of UBERON:0004765 ! skeletal element -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0001434 ! skeletal system +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002473 UBERON:0004765 ! composed primarily of skeletal element [Term] id: UBERON:0000076 @@ -159743,7 +159374,6 @@ def: "The surface (external) layer of ectoderm which begins to proliferate short subset: pheno_slim synonym: "surface (external) ectoderm" EXACT [] synonym: "surface ectoderm" EXACT [MP:0012532] -xref: BTO:0006242 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: EHDAA2:0001968 xref: EHDAA:1494 xref: EHDAA:350 @@ -159759,10 +159389,8 @@ xref: Wikipedia:External_ectoderm is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0005291 ! embryonic tissue relationship: part_of UBERON:0000924 {source="EHDAA2"} ! ectoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1d/Ectoderm.png" xsd:anyURI -property_value: editor_note "merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube)" xsd:string -property_value: RO:0002171 UBERON:0002346 -property_value: UBPROP:0000011 "(or external ectoderm) forms the following structures: Skin Epithelium of the mouth and nasal cavity saliavary glands, and glands of mouth and nasal cavity Enamel - as a side note dentin and dental pulp are formed from ectomesenchyme which is derived from ectoderm Epithelium of pineal and pituitary glands Lens and cornea of the eye Apical ectodermal ridge inducing development of the limb buds of the embryo. Sensory receptors in epidermis" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1d/Ectoderm.png" xsd:anyURI +property_value: IAO:0000116 "merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube)" xsd:string [Term] id: UBERON:0000077 @@ -159773,9 +159401,8 @@ subset: grouping_class is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: develops_from UBERON:0000925 ! endoderm -intersection_of: develops_from UBERON:0000926 ! mesoderm -property_value: IAO:0000232 "Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple" xsd:string +intersection_of: RO:0002202 UBERON:0000925 ! develops from endoderm +intersection_of: RO:0002202 UBERON:0000926 ! develops from mesoderm [Term] id: UBERON:0000078 @@ -159786,10 +159413,9 @@ subset: grouping_class is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: develops_from UBERON:0000924 ! ectoderm -intersection_of: develops_from UBERON:0000925 ! endoderm -intersection_of: develops_from UBERON:0000926 ! mesoderm -property_value: IAO:0000232 "Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple" xsd:string +intersection_of: RO:0002202 UBERON:0000924 ! develops from ectoderm +intersection_of: RO:0002202 UBERON:0000925 ! develops from endoderm +intersection_of: RO:0002202 UBERON:0000926 ! develops from mesoderm [Term] id: UBERON:0000079 @@ -159817,7 +159443,6 @@ xref: EHDAA2:0001054 xref: EHDAA:8136 xref: EMAPA:17968 xref: EV:0100101 -xref: FBbt:00004927 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45664 xref: GAID:386 xref: HAO:0000505 @@ -159836,9 +159461,8 @@ intersection_of: UBERON:0000990 ! reproductive system intersection_of: part_of UBERON:0003101 ! male organism disjoint_from: UBERON:0000474 ! female reproductive system relationship: part_of UBERON:0003101 ! male organism -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Prostate.glb" xsd:anyURI -property_value: UBPROP:0000003 "By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000725", ontology="VHOG", source="ISBN:978-0792383369 Lombardi J, Comparative vertebrate reproduction (1998) p.43", source="http://bgee.unil.ch/"} +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Prostate.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000080 @@ -159879,14 +159503,8 @@ xref: XAO:0000141 xref: ZFA:0000529 is_a: UBERON:0002113 ! kidney is_a: UBERON:0004120 ! mesoderm-derived structure -relationship: develops_from UBERON:0002120 ! pronephros -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray986.png" xsd:anyURI -property_value: UBPROP:0000001 "A kidney formed of nephric tubules arising in the middle region of the nephric ridge; a transient embryonic stage that replaces the pronephros, but is itself replaced by the adult metanephros [in mammals; in fishes and amphibians it is the adult kidney]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000038", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000001 "Organ that is the definitive adult kidney. It replaces the earlier pronephros, which degenerates as the mesonephros becomes functional in feeding stage tadpoles.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010384", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates. (...) In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000038", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "mesonephric" xsd:string -property_value: UBPROP:0000008 "In mammals, the mesonephros is the second of the three embryonic kidneys to be established and exists only transiently. In fish and amphibians, the mesonephros will form the mature kidney" xsd:string -property_value: UBPROP:0000009 "By contrast to the pronephros, the histological features of the mammalian mesonephros, with its primitive glomeruli, suggest that it probably functions as a primitive kidney, and is involved in the production of much of the amniotic fluid. Within the two mesonephroi, one located on either side of the dorsal mesentery of the hindgut, a substantial number (in the region of about 40 or more) of cranio-caudally segmented mesonephric tubules are formed. It has, however, been suggested that only the most rostrally located 4-6 pairs of mesonephric tubules drain into the mesonephric portion of the nephric duct. This is now seen to extend along the length of the mesonephroi, being located towards their lateral sides. The mesonephros is also retained over a considerably longer period than the pronephros, but gradually undergoes regression in a cranio-caudal direction. While the rostral part displays clear evidence of regression its more caudal part appears to display evidence of functional activity. Within the medial part of the mesonephros, vesicles are formed, although no glomeruli are formed there in this species. It is, however, difficult to believe that the relatively enormous mesonephroi do not have an excretory role in the mouse, only serving as a base for gonadal differentiation. In the human embryo, the medial part of the mesonephric tubules enlarges, become invaginated by capillaries, and form glomeruli. These then take on an excretory role. In the mouse, the mesonephric ducts appear to be patent throughout their length[GUDMAP, modified]" xsd:string +relationship: RO:0002202 UBERON:0002120 ! develops from pronephros +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray986.png" xsd:anyURI [Term] id: UBERON:0000081 @@ -159914,16 +159532,12 @@ xref: VHOG:0000039 xref: Wikipedia:Metanephros#Metanephros is_a: UBERON:0002113 ! kidney is_a: UBERON:0004120 ! mesoderm-derived structure -relationship: developmentally_replaces UBERON:0000080 {source="ISBN:9780878932504"} ! mesonephros -relationship: develops_from UBERON:0003220 {evidence="definitional"} ! metanephric mesenchyme -relationship: develops_from UBERON:0005080 {source="GO"} ! metanephric ureteric bud -relationship: develops_from UBERON:0005753 ! caudal part of nephrogenic cord -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -property_value: editor_note "TODO check developmental relationships" xsd:string -property_value: UBPROP:0000001 "A kidney formed of nephric tubules arising in the posterior region of the nephric ridge and drained by a ureter; replaces the embryonic pronephros and mesonephros [in mammals]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000039", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000039", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "metanephric" xsd:string -property_value: UBPROP:0000011 "During the fifth week of gestation, the mesonephric duct develops an outpouching, the ureteric bud, near its attachment to the cloaca. This bud, also called the metanephrogenic diverticulum, grows posteriorly and towards the head of the embryo. The elongated stalk of the ureteric bud, the metanephric duct, later forms the ureter. As the cranial end of the bud extends into the intermediate mesoderm, it undergoes a series of branchings to form the collecting duct system of the kidney. It also forms the major and minor calyces and the renal pelvis" xsd:string +relationship: RO:0002202 UBERON:0003220 ! develops from metanephric mesenchyme +relationship: RO:0002202 UBERON:0005080 {source="GO"} ! develops from metanephric ureteric bud +relationship: RO:0002202 UBERON:0005753 ! develops from caudal part of nephrogenic cord +relationship: RO:0002285 UBERON:0000080 {source="ISBN:9780878932504"} ! developmentally replaces mesonephros +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +property_value: IAO:0000116 "TODO check developmental relationships" xsd:string [Term] id: UBERON:0000083 @@ -159943,9 +159557,7 @@ is_a: UBERON:0005103 ! mesonephric epithelium is_a: UBERON:0006555 ! excretory tube intersection_of: UBERON:0003914 ! epithelial tube intersection_of: part_of UBERON:0000080 ! mesonephros -property_value: editor_note "TODO check" xsd:string -property_value: UBPROP:0000001 "Any of the renal tubules composing the mesonephros. In mammals they function as excretory structures during the early embryonic development but are later incorporated into the reproductive system. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000500", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/mesonephric+tubule"} -property_value: UBPROP:0000003 "As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000500", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639", source="http://bgee.unil.ch/"} +property_value: IAO:0000116 "TODO check" xsd:string [Term] id: UBERON:0000084 @@ -159972,14 +159584,10 @@ xref: VHOG:0000541 xref: Wikipedia:Ureteric_bud is_a: UBERON:0000083 ! mesonephric tubule is_a: UBERON:0007499 {source="EHDAA2"} ! epithelial sac -is_a: UBERON:0012275 ! meso-epithelium is_a: UBERON:0034969 ! epithelial layer of duct -relationship: developmentally_induced_by UBERON:0003220 {source="ISBN:9780878932504"} ! metanephric mesenchyme -relationship: develops_from UBERON:0003074 {source="EHDAA2"} ! mesonephric duct relationship: part_of UBERON:0003074 ! mesonephric duct -property_value: UBPROP:0000001 "Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts. [Embryology, See_Dudek_RW_and_Fix_JD, Third_Edition_(2004)_Philadelphia:_Lippincott_William_and_Wilkins, p.137][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000541", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000001 "Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts[VHOG:0000541]." xsd:string {source="VHOG:0000541"} -property_value: UBPROP:0000003 "The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000541", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003074 {source="EHDAA2"} ! develops from mesonephric duct +relationship: RO:0002256 UBERON:0003220 {source="ISBN:9780878932504"} ! developmentally induced by metanephric mesenchyme [Term] id: UBERON:0000085 @@ -159998,13 +159606,12 @@ xref: SCTID:361474003 xref: UMLS:C0026573 {source="ncithesaurus:Morula"} xref: Wikipedia:Morula is_a: UBERON:0000922 ! embryo -relationship: existence_ends_during UBERON:0000107 ! cleavage stage -relationship: existence_starts_during UBERON:0000107 ! cleavage stage relationship: has_part CL:0000353 ! blastoderm cell relationship: part_of UBERON:0004716 {source="EHDAA2"} ! conceptus -relationship: surrounded_by UBERON:0000086 ! zona pellucida -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI -property_value: UBPROP:0000012 "EHDAA2 has embryo starting later" xsd:string {external_ontology="EHDAA2"} +relationship: RO:0002219 UBERON:0000086 ! surrounded by zona pellucida +relationship: RO:0002488 UBERON:0000107 ! existence starts during cleavage stage +relationship: RO:0002492 UBERON:0000107 ! existence ends during cleavage stage +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI [Term] id: UBERON:0000086 @@ -160034,16 +159641,14 @@ xref: MESH:D015044 xref: NCIT:C33896 xref: TAO:0001111 xref: UMLS:C0043519 {source="ncithesaurus:Zona_Pellucida"} -xref: VHOG:0000720 xref: Wikipedia:Zona_pellucida xref: ZFA:0001111 is_a: UBERON:0005764 ! acellular membrane relationship: bounding_layer_of CL:0000023 ! oocyte relationship: has_part CHEBI:17089 relationship: part_of UBERON:0000992 ! ovary -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/81/Gray3.png" xsd:anyURI -property_value: UBPROP:0000003 "Outside the plasma membrane, three envelopes surround the ovum. The first, the primary egg envelope, lies between the plasma membrane and the surrounding cells of the ovary. The most consistent component of this primary layer is the vitelline membrane, a transparent jacket of fibrous protein. In mammals, the homologous structure is called the zona pellucida.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000720", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.159", source="http://bgee.unil.ch/"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/81/Gray3.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000087 @@ -160069,12 +159674,9 @@ xref: UMLS:C1283994 {source="ncithesaurus:Inner_Cell_Mass"} xref: VHOG:0000742 xref: Wikipedia:Inner_cell_mass is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0000358 {source="Wikipedia"} ! blastocyst -relationship: surrounded_by UBERON:0000088 {source="Wikipedia"} ! trophoblast -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/7/72/Blastocyst_English.svg" xsd:anyURI -property_value: UBPROP:0000001 "A group of cells found in the mammalian blastocyst that give rise to the embryo. [Biology_Online][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000742", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "A small sphere of cells known as the inner cell mass lies within the trophoblast (of all eutherian mammals).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000742", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.144", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000011 "This structure forms in the earliest steps of development, before implantation into the endometrium of the uterus has occurred.The ICM lies within the blastocyst cavity and is entirely surrounded by the single layer of cells called trophoblast. [Wikipedia:Inner_cell_mass]" xsd:string +relationship: RO:0002202 UBERON:0000358 {source="Wikipedia"} ! develops from blastocyst +relationship: RO:0002219 UBERON:0000088 {source="Wikipedia"} ! surrounded by trophoblast +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/72/Blastocyst_English.svg" xsd:anyURI [Term] id: UBERON:0000088 @@ -160099,13 +159701,10 @@ xref: SCTID:362839005 xref: UMLS:C0041178 {source="ncithesaurus:Trophoblast"} xref: Wikipedia:Trophoblast is_a: UBERON:0002050 ! embryonic structure -relationship: composed_primarily_of CL:0000351 ! trophoblast cell -relationship: develops_from UBERON:0004345 {source="MP-def", source="PMID:19829370"} ! trophectoderm relationship: part_of UBERON:0000358 ! blastocyst -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/7/72/Blastocyst_English.svg" xsd:anyURI -property_value: UBPROP:0000001 "the mesectodermal cell layer arising from the trophectoderm that erodes the uterine mucosa and contributes to the formation of the placenta[MP]" xsd:string {date_retrieved="2012-08-23", external_class="MP:0005031", external_class_label="trophoblast layer", ontology="MP", source="ISBN:0-683-40008-8"} -property_value: UBPROP:0000007 "trophoblastic" xsd:string -property_value: UBPROP:0000011 "The postimplantation derivatives of the trophectoderm, which make up most of the fetal part of the placenta" xsd:string {source="PMID:19829370"} +relationship: RO:0002202 UBERON:0004345 {source="MP-def", source="PMID:19829370"} ! develops from trophectoderm +relationship: RO:0002473 CL:0000351 ! composed primarily of trophoblast cell +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/72/Blastocyst_English.svg" xsd:anyURI [Term] id: UBERON:0000091 @@ -160126,8 +159725,8 @@ xref: NCIT:C34112 xref: UMLS:C1283997 {source="ncithesaurus:Bilaminar_Embryonic_Disc"} xref: Wikipedia:Bilaminar_disc is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0000087 {source="Wikipedia"} ! inner cell mass -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" xsd:anyURI +relationship: RO:0002202 UBERON:0000087 {source="Wikipedia"} ! develops from inner cell mass +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" xsd:anyURI [Term] id: UBERON:0000092 @@ -160147,9 +159746,8 @@ xref: WBls:0000103 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage relationship: preceded_by UBERON:0000068 ! embryo stage -relationship: simultaneous_with GO:0009791 ! post-embryonic development +relationship: RO:0002082 GO:0009791 ! simultaneous with post-embryonic development property_value: seeAlso "https://github.com/obophenotype/uberon/issues/344" xsd:anyURI -property_value: UBPROP:0000008 "In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)" xsd:string [Term] id: UBERON:0000093 @@ -160160,7 +159758,7 @@ subset: grouping_class subset: non_informative xref: Wikipedia:Sulcus_(anatomy) is_a: UBERON:0000464 ! anatomical space -relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 creation_date: 2009-04-09T06:23:22Z [Term] @@ -160173,8 +159771,8 @@ synonym: "membrane of organ" EXACT [] xref: FMA:7145 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000062 ! organ -relationship: composed_primarily_of UBERON:0011823 {source="FMA-def"} ! dense connective tissue -relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 +relationship: RO:0002473 UBERON:0011823 {source="FMA-def"} ! composed primarily of dense connective tissue +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 creation_date: 2009-07-30T05:19:13Z [Term] @@ -160189,12 +159787,11 @@ xref: TAO:0002173 xref: Wikipedia:Cardiac_neural_crest xref: XAO:0004190 xref: ZFA:0001648 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue -relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 relationship: overlaps UBERON:0005428 {source="Wikipedia"} ! vagal neural crest relationship: part_of UBERON:0002342 ! neural crest -property_value: UBPROP:0000001 "A subpopulation of the cephalic neural crest that emerges from the otic level to the anterior limit of somite 4. It migrates to the heart and is essential for the septation of the outflow track[DOI:10.1242/dev.091751]." xsd:string {source="DOI:10.1242/dev.091751"} -property_value: UBPROP:0000012 "ZFA treats this as a subtype of NC." xsd:string {external_ontology="ZFA"} +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 creation_date: 2009-07-30T07:57:38Z [Term] @@ -160213,9 +159810,10 @@ xref: MA:0003098 xref: NCIT:C34021 xref: SCTID:245524004 xref: UMLS:C0225752 {source="ncithesaurus:Lung_Lobe"} +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0009912 {source="FMA"} ! anatomical lobe -relationship: contributes_to_morphology_of UBERON:0002048 ! lung relationship: part_of UBERON:0002048 ! lung +relationship: RO:0002433 UBERON:0002048 ! contributes to morphology of lung [Term] id: UBERON:0000102 @@ -160254,10 +159852,10 @@ is_a: BFO:0000003 ! occurrent is_a: UBERON:0000000 ! processual entity relationship: ends_with UBERON:0000071 ! death stage relationship: has_part UBERON:0000105 ! life cycle stage -relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 ! Fungi -relationship: starts_with UBERON:0000106 {gci_relation="in_taxon", gci_filler="NCBITaxon:33208"} ! zygote stage +relationship: starts_with UBERON:0000106 {gci_filler="NCBITaxon:33208", gci_relation="RO:0002162"} ! zygote stage +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 property_value: seeAlso "https://github.com/obophenotype/uberon/issues/532" xsd:anyURI [Term] @@ -160286,12 +159884,10 @@ xref: ZFS:0000000 xref: ZFS:0100000 is_a: UBERON:0000000 ! processual entity relationship: part_of UBERON:0000104 ! life cycle -relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 ! Fungi -property_value: editor_note "this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here" xsd:string -property_value: UBPROP:0000012 "the WBls class 'all stages' belongs here as it is the superclass of other WBls stages" xsd:string -property_value: UBPROP:0000012 "we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage" xsd:string +property_value: IAO:0000116 "this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000106 @@ -160311,7 +159907,6 @@ xref: BILS:0000106 xref: EFO:0001322 xref: EHDAA:27 xref: FBdv:00005288 -xref: IDOMAL:0000302 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C12601 xref: PdumDv:0000100 xref: VHOG:0000745 @@ -160321,9 +159916,8 @@ xref: ZFS:0000001 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage -relationship: seeAlso EMAPA:16033 -relationship: starts UBERON:0000104 ! life cycle -property_value: UBPROP:0000003 "As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000745", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107", source="http://bgee.unil.ch/"} +relationship: RO:0002223 UBERON:0000104 ! starts life cycle +property_value: seeAlso EMAPA:16033 [Term] id: UBERON:0000107 @@ -160346,10 +159940,10 @@ xref: ZFS:0000046 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage intersection_of: UBERON:0000105 ! life cycle stage -intersection_of: simultaneous_with GO:0040016 ! embryonic cleavage +intersection_of: RO:0002082 GO:0040016 ! simultaneous with embryonic cleavage relationship: immediately_preceded_by UBERON:0000106 ! zygote stage relationship: part_of UBERON:0000068 ! embryo stage -relationship: simultaneous_with GO:0040016 ! embryonic cleavage +relationship: RO:0002082 GO:0040016 ! simultaneous with embryonic cleavage [Term] id: UBERON:0000108 @@ -160373,8 +159967,8 @@ is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000107 ! cleavage stage -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI -property_value: editor_note "consider adding a preceding stage 'morula stage' as part of cleavage" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI +property_value: IAO:0000116 "consider adding a preceding stage 'morula stage' as part of cleavage" xsd:string [Term] id: UBERON:0000109 @@ -160401,10 +159995,10 @@ xref: XAO:1000005 xref: ZFS:0000047 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000108 {source="BILS"} ! blastula stage -relationship: simultaneous_with GO:0007369 ! gastrulation +relationship: RO:0002082 GO:0007369 ! simultaneous with gastrulation +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0000110 @@ -160418,14 +160012,12 @@ xref: MmusDv:0000017 xref: XAO:1000006 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000109 ! gastrula stage -relationship: simultaneous_with GO:0001841 ! neural tube formation -property_value: RO:0002174 NCBITaxon:7955 +relationship: RO:0002082 GO:0001841 ! simultaneous with neural tube formation +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa property_value: seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/343" xsd:anyURI -property_value: UBPROP:0000008 "In zebrafish, the times of neurulation and segmentation overlap so extensively there is no distinct neurula period of development, such as occurs largely before segmentation in amphibian embryos." xsd:string [Term] id: UBERON:0000111 @@ -160442,10 +160034,10 @@ xref: OGES:000032 xref: Wikipedia:Organogenesis is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000110 {gci_relation="part_of", gci_filler="NCBITaxon:32523"} ! neurula stage -relationship: simultaneous_with GO:0048513 ! animal organ development +relationship: RO:0002082 GO:0048513 ! simultaneous with animal organ development +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa property_value: seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/533" xsd:anyURI @@ -160470,8 +160062,6 @@ is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000066 ! fully formed stage property_value: seeAlso "https://github.com/obophenotype/uberon/issues/427" xsd:anyURI -property_value: UBPROP:0000001 "The stage of being a sexually immature adult animal[XAO:1000010]." xsd:string {source="XAO:1000010"} -property_value: UBPROP:0000008 "In mammals this would include infant (nourishment from lactation) and juvenile (prepubertal no longer dependent on mother)" xsd:string [Term] id: UBERON:0000113 @@ -160512,16 +160102,15 @@ xref: EMAPA:35521 xref: FMA:27533 xref: MA:0001782 xref: SCTID:201609008 +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0003580 ! lower respiratory tract connective tissue is_a: UBERON:0003837 ! thoracic segment connective tissue -is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0002048 ! lung -relationship: contributes_to_morphology_of UBERON:0002048 ! lung relationship: part_of UBERON:0002048 ! lung -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: transformation_of UBERON:0004883 ! lung mesenchyme -property_value: UBPROP:0000009 "it functions in the mechanical behavior of the lung, and forms a barrier to regulate the flow of plasma constituents from the capillaries to the airway and alveolar spaces" xsd:string +relationship: RO:0002433 UBERON:0002048 ! contributes to morphology of lung +relationship: RO:0002494 UBERON:0004883 ! transformation of lung mesenchyme +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000115 @@ -160539,10 +160128,9 @@ xref: MA:0001783 is_a: UBERON:0004815 ! lower respiratory tract epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002048 ! lung -relationship: contributes_to_morphology_of UBERON:0002048 ! lung -relationship: develops_from UBERON:0001041 ! foregut relationship: part_of UBERON:0002048 ! lung -property_value: UBPROP:0000008 "A pseudostratified epithelium, containing basal cells, stem cells of the airway, submucosal glands and cartilage rings, is limited to the trachea and large lobar airways in the mouse (Morrisey and Hogan, 2010). This more complex epithelium extends to terminal bronchioles in the human[DOI:10.1242/dev.115469]" xsd:string +relationship: RO:0002202 UBERON:0001041 ! develops from foregut +relationship: RO:0002433 UBERON:0002048 ! contributes to morphology of lung [Term] id: UBERON:0000117 @@ -160558,11 +160146,11 @@ xref: EMAPA:37946 {source="MA:th"} xref: FMA:12224 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000025 ! tube +is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0000025 ! tube intersection_of: part_of UBERON:0000065 ! respiratory tract relationship: has_part UBERON:0000483 ! epithelium relationship: part_of UBERON:0000065 ! respiratory tract -property_value: UBPROP:0000012 "in GO lung development is part of respiratory tube development. This can lead to inconsistencies with other ontologies, e.g. VT. The GO structure may be better represented by a tree of tubes (see the FMA class)" xsd:string {external_ontology="GO"} [Term] id: UBERON:0000118 @@ -160584,11 +160172,12 @@ xref: UMLS:C1514420 {source="ncithesaurus:Primary_Bronchial_Bud"} xref: UMLS:C1514897 {source="ncithesaurus:Respiratory_Diverticulum"} xref: Wikipedia:Respiratory_bud is_a: UBERON:0005153 {source="GO:0060441"} ! epithelial bud +is_a: UBERON:0005911 ! endo-epithelium relationship: adjacent_to UBERON:0004872 ! splanchnic layer of lateral plate mesoderm -relationship: develops_from UBERON:0005597 ! lung primordium -relationship: develops_from UBERON:0008947 {source="EHDAA2"} ! respiratory primordium -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/71/Gray948.png" xsd:anyURI -property_value: editor_note "clarify successors - include bronchi?" xsd:string +relationship: RO:0002202 UBERON:0005597 ! develops from lung primordium +relationship: RO:0002202 UBERON:0008947 {source="EHDAA2"} ! develops from respiratory primordium +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/71/Gray948.png" xsd:anyURI +property_value: IAO:0000116 "clarify successors - include bronchi?" xsd:string [Term] id: UBERON:0000119 @@ -160602,7 +160191,7 @@ synonym: "layer of cells" EXACT [] synonym: "sheath of cells" RELATED [] xref: NCIT:C66831 is_a: UBERON:0000957 ! lamina -property_value: editor_note "consider adding to caro" xsd:string +property_value: IAO:0000116 "consider adding to caro" xsd:string [Term] id: UBERON:0000120 @@ -160612,7 +160201,6 @@ def: "Cell layer consisting of lining cells that separates the central nervous s synonym: "BBB" RELATED [] synonym: "blood-brain barrier" EXACT [] xref: http://uri.neuinfo.org/nif/nifstd/nlx_subcell_100205 -xref: MESH:D001812 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C13194 xref: UMLS:C0005854 {source="ncithesaurus:Blood-Brain_Barrier"} xref: Wikipedia:Blood-brain_barrier @@ -160638,12 +160226,9 @@ xref: Wikipedia:Perineurium is_a: UBERON:0011822 {source="FMA"} ! dense irregular connective tissue relationship: bounding_layer_of UBERON:0001019 ! nerve fasciculus relationship: has_part GO:0005581 ! collagen trimer -relationship: located_in UBERON:0000124 ! epineurium relationship: part_of UBERON:0003209 ! blood nerve barrier -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/9c/Gray636.png" xsd:anyURI -property_value: UBPROP:0000001 "Connective tissue surrounding a fascicle[Wikipedia:Perineurium]." xsd:string {source="Wikipedia:Perineurium"} -property_value: UBPROP:0000007 "perineurial" xsd:string -property_value: UBPROP:0000012 "consider FBbt:00007090 (perineurium): The outer two layers of glial cells that cover the central nervous system and the nerves. The outer layer is the perineurial sheath (sometimes referred to as the perineurial sheath outer layer); the inner layer is the sub-perineural glial sheath (sometimes referred to as the perineurial sheath inner layer)" xsd:string {external_ontology="FBbt"} +relationship: RO:0001025 UBERON:0000124 ! located in epineurium +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/9c/Gray636.png" xsd:anyURI [Term] id: UBERON:0000122 @@ -160655,7 +160240,6 @@ synonym: "funiculus" EXACT [] synonym: "nerve fiber bundle" EXACT [FBbt:00005099] synonym: "neural fiber bundle" EXACT [] xref: CARO:0001001 -xref: FBbt:00005099 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: NLX:147821 is_a: UBERON:0005162 ! multi cell part structure relationship: has_part GO:0043005 ! neuron projection @@ -160676,9 +160260,8 @@ xref: UMLS:C0205889 {source="ncithesaurus:Epineurium"} xref: Wikipedia:Epineurium is_a: UBERON:0011822 {source="FMA"} ! dense irregular connective tissue relationship: part_of UBERON:0000010 ! peripheral nervous system -relationship: surrounds UBERON:0001021 ! nerve -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/9c/Gray636.png" xsd:anyURI -property_value: UBPROP:0000001 "outermost layer of connective tissue surrounding a peripheral nerve. It includes the blood vessels supplying the nerve. It consists of adipose tissue and fibrocollagenous tissues[Wikipedia:Epineurium]." xsd:string {source="Wikipedia:Epineurium"} +relationship: RO:0002221 UBERON:0001021 ! surrounds nerve +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/9c/Gray636.png" xsd:anyURI [Term] id: UBERON:0000125 @@ -160698,10 +160281,8 @@ xref: NCIT:C13197 xref: NLX:28443 xref: Wikipedia:Nucleus_(neuroanatomy) is_a: UBERON:0011215 ! central nervous system cell part cluster -relationship: composed_primarily_of UBERON:0002020 ! gray matter -relationship: only_in_taxon NCBITaxon:7711 {notes="we limit this structure by definition to chordate and vertebrate nervous systems"} ! Chordata -property_value: UBPROP:0000001 "Anatomical structure consisting of a discrete aggregate of neuronal soma[GO][GO_REF:0000021]." xsd:string {source="GO_REF:0000021"} -property_value: UBPROP:0000012 "Proposed CUMBO def from MM: A subcortical part of the nervous system consisting of a relatively compact group of cells that is distinguishable histologically that share a commonality of cytoarchitecture, chemoarchitecturel and connectivity. (comments: I put in 'subcortical' because I don't think we consider either the cerebellar cortex or cerebral cortex to be nuclei. Some people distinguish between a nucleus and a laminar structure (see Wikipedia definition). However, there are structures identified as nuclei that are laminar, e.g., lateral geniculate nucleus, although they are not laminated in all species. Also, I put in 'relatively compact' and 'distiguishable by histology' because we have groups of cells, e.g., cholinergic cell groups, doparminergic cell groups that are related on the 3 criteria but which we don't tend to consider nuclei because they don't occupy an easily defined territory. But all is open to debate." xsd:string +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002473 UBERON:0002020 ! composed primarily of gray matter [Term] id: UBERON:0000126 @@ -160720,7 +160301,7 @@ is_a: UBERON:0002308 ! nucleus of brain intersection_of: UBERON:0002308 ! nucleus of brain intersection_of: extends_fibers_into UBERON:0001785 ! cranial nerve relationship: extends_fibers_into UBERON:0001785 ! cranial nerve -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray696.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray696.png" xsd:anyURI [Term] id: UBERON:0000127 @@ -160748,16 +160329,14 @@ xref: SCTID:280166009 xref: UMLS:C0228740 {source="ncithesaurus:Facial_Nerve_Nucleus"} xref: VHOG:0001412 is_a: UBERON:0000126 ! cranial nerve nucleus -is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0006331 ! brainstem nucleus is_a: UBERON:0009662 ! hindbrain nucleus intersection_of: UBERON:0000126 ! cranial nerve nucleus intersection_of: extends_fibers_into UBERON:0001647 ! facial nerve -relationship: contributes_to_morphology_of UBERON:0000988 ! pons relationship: extends_fibers_into UBERON:0001647 ! facial nerve -relationship: immediate_transformation_of UBERON:0010123 {evidence="definitional"} ! future facial nucleus relationship: part_of UBERON:0000988 ! pons -property_value: UBPROP:0000012 "FMA has 3 subclasses - left, right and motor nucleus of facial nerve, but no defs. It's not clear how facial nucleus is distinct from facial motor nucleus." xsd:string {external_ontology="FMA"} +relationship: RO:0002433 UBERON:0000988 ! contributes to morphology of pons +relationship: RO:0002495 UBERON:0010123 ! immediate transformation of future facial nucleus [Term] id: UBERON:0000153 @@ -160765,15 +160344,15 @@ name: anterior region of body namespace: uberon is_a: UBERON:0000475 ! organism subdivision disjoint_from: UBERON:0000154 {source="lexical"} ! posterior region of body -relationship: anterior_to UBERON:0000154 ! posterior region of body -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +relationship: BSPO:0000096 UBERON:0000154 ! posterior region of body +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria [Term] id: UBERON:0000154 name: posterior region of body namespace: uberon is_a: UBERON:0000475 ! organism subdivision -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria [Term] id: UBERON:0000155 @@ -160802,14 +160381,14 @@ xref: TAO:0001113 xref: Wikipedia:Theca_of_follicle xref: ZFA:0001113 is_a: UBERON:0000119 ! cell layer +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0000119 ! cell layer -intersection_of: composed_primarily_of CL:0000503 ! theca cell intersection_of: part_of UBERON:0001305 ! ovarian follicle -relationship: composed_primarily_of CL:0000503 ! theca cell +intersection_of: RO:0002473 CL:0000503 ! composed primarily of theca cell relationship: part_of UBERON:0001305 ! ovarian follicle -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000009 "The theca folliculi are responsible for the production of testosterone from androstenedione in females, and indirectly the production of estrogens by supplying the neighboring granulosa cells with androstenedione that can then be used as a substrate for aromatase. [Wikipedia:Theca_of_follicle]" xsd:string +relationship: RO:0002473 CL:0000503 ! composed primarily of theca cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000158 @@ -160823,7 +160402,6 @@ xref: MESH:D008566 xref: NCIT:C12749 is_a: UBERON:0004923 ! organ component layer relationship: bounding_layer_of UBERON:0000064 ! organ part -property_value: UBPROP:0000001 "A thin sheet or layer of pliable tissue, serving as a covering or envelope of a part, as the lining of a cavity, as a partition or septum, or to connect two structures." xsd:string {source="ncithesaurus:Membrane"} [Term] id: UBERON:0000159 @@ -160849,21 +160427,21 @@ xref: EMAPA:18256 xref: FMA:15703 xref: galen:AnalCanal xref: MA:0000330 -xref: MESH:D001003 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C12375 xref: SCTID:245438008 xref: UMLS:C0227411 {source="ncithesaurus:Anal_Canal"} xref: Wikipedia:Anal_canal is_a: UBERON:0004111 ! anatomical conduit +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: channel_for UBERON:0001988 ! feces -relationship: continuous_with UBERON:0001052 ! rectum -relationship: continuous_with UBERON:0001245 ! anus -relationship: develops_from UBERON:0011272 {source="Wikipathways:WP2062"} ! embryonic skin basal layer relationship: part_of UBERON:0000059 ! large intestine relationship: part_of UBERON:0001353 ! anal region -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/0/01/Gray1078.png" xsd:anyURI -property_value: editor_note "requires alignment with EHDAA2 and complete developmental relationships" xsd:string +relationship: RO:0002150 UBERON:0001052 ! continuous with rectum +relationship: RO:0002150 UBERON:0001245 ! continuous with anus +relationship: RO:0002202 UBERON:0011272 {source="Wikipathways:WP2062"} ! develops from embryonic skin basal layer +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/0/01/Gray1078.png" xsd:anyURI +property_value: IAO:0000116 "requires alignment with EHDAA2 and complete developmental relationships" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000160 @@ -160901,13 +160479,9 @@ xref: Wikipedia:Intestine xref: XAO:0000129 xref: ZFA:0001338 is_a: UBERON:0004921 {source="cjm"} ! subdivision of digestive tract -relationship: contributes_to_morphology_of UBERON:0001007 ! digestive system relationship: part_of UBERON:0005409 ! alimentary part of gastrointestinal system -property_value: editor_note "This class is probably too inclusive" xsd:string -property_value: UBPROP:0000001 "Portion of the alimentary canal bounded anteriorly by the pyloric sphincter and posteriorly by the cloacal sphincter.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000246", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000001 "The tract of the alimentary canal. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000056", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "intestinal" xsd:string -property_value: UBPROP:0000008 "In zebrafish, No stomach, small intestine, or large intestine can be distinguished. However, differences can be found in the morphology of the mucosa columnar epithelial cells and the number of goblet cells, suggesting functional differentiation. The intestine has numerous folds that become progressively shorter in a rostral-to-caudal direction. Proportionally, these folds are significantly larger than the finger-like intestinal villi of mammals and other amniotes (Wallace et al. 2005). Columnar-shaped absorptive enterocytes are the most numerous in the zebrafish intestinal epithelium. Goblet cells are the second most populous epithelial cell type." xsd:string +relationship: RO:0002433 UBERON:0001007 ! contributes to morphology of digestive system +property_value: IAO:0000116 "This class is probably too inclusive" xsd:string [Term] id: UBERON:0000161 @@ -160921,7 +160495,6 @@ synonym: "ostium" BROAD [] xref: FMA:3724 xref: SCTID:91837002 is_a: UBERON:0004111 ! anatomical conduit -property_value: UBPROP:0000012 "in FMA, this is an anatomical conduit *space*, rather than anatomical conduit" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0000162 @@ -160942,17 +160515,10 @@ xref: Wikipedia:Cloaca xref: XAO:0000244 xref: ZFA:0005781 is_a: UBERON:0013522 ! subdivision of tube -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0001555 {source="ZFA"} ! digestive tract relationship: part_of UBERON:0004122 {source="AAO"} ! genitourinary system -relationship: present_in_taxon NCBITaxon:9369 {notes="most adult placentals have no trace of a cloaca. However, the tenrecs and golden moles, small placental mammals native to Africa, retain a cloaca as adults."} -property_value: editor_note "adding df link to embryonic cloaca leads to a cycle in uberon-simple, as cloaca is a suberclass of embryonic cloaca" xsd:string -property_value: UBPROP:0000001 "A common passage for fecal, urinary, and reproductive discharge in most lower vertebrates as well as the terminal end of the hindgut before division into rectum, bladder, and genital primordia in mammalian embryos. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001186", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/cloaca"} -property_value: UBPROP:0000001 "Anatomical structure which is the common receptacle for the alimentary canal, Wolffian ducts, oviducts, and the bladder.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000095", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "A cloaca is apparently a primitive vertebrate feature because it occurs in most primitive gnathostomes and persists in the embryos of almost all vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001186", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.572", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "cloacal" xsd:string -property_value: UBPROP:0000008 "Human beings only have an embryonic cloaca, which is split up into separate tracts during the development of the urinary and reproductive organs" xsd:string -property_value: UBPROP:0000011 "hindgut endoderm and proctodeal ectoderm." xsd:string {source="WP"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +property_value: IAO:0000116 "adding df link to embryonic cloaca leads to a cycle in uberon-simple, as cloaca is a suberclass of embryonic cloaca" xsd:string [Term] id: UBERON:0000163 @@ -160966,11 +160532,10 @@ xref: EHDAA:4895 xref: EMAPA:27573 xref: Wikipedia:Cloaca_(embryology) is_a: UBERON:0000162 ! cloaca -relationship: has_developmental_contribution_from UBERON:0003064 ! intermediate mesoderm relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0001008 {source="EHDAA2"} ! renal system relationship: part_of UBERON:0012361 {source="EHDAA2"} ! internal anal region -property_value: IAO:0000232 "this class represents the embryonic form of the cloaca, as found in both mammals and non-mammals." xsd:string +relationship: RO:0002254 UBERON:0003064 ! has developmental contribution from intermediate mesoderm [Term] id: UBERON:0000164 @@ -160992,14 +160557,11 @@ xref: UMLS:C0231057 {source="ncithesaurus:Urogenital_Sinus"} xref: VHOG:0000414 xref: Wikipedia:Definitive_urogenital_sinus is_a: UBERON:0002050 ! embryonic structure -relationship: contributes_to_morphology_of UBERON:0000163 ! embryonic cloaca -relationship: develops_from UBERON:0003064 ! intermediate mesoderm -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0000163 {source="MP-def"} ! embryonic cloaca -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png" xsd:anyURI -property_value: UBPROP:0000001 "The ventral part of the cloaca after its separation from the rectum, giving rise to the lower part of the bladder in both sexes, to the prostatic portion of the male urethra, and to the urethra and vestibule in the female. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000414", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/urogenital+sinus"} -property_value: UBPROP:0000003 "In mammals the lowly monotremes still have a cloaca. Higher types have done away with this structure and have a separate anal outlet for the rectum. The monotreme cloaca shows the initiation of this subdivision. The cloaca has such includes only the distal part, roughly comparable to the proctodeum. The more proximal part is divided into (1) a large dorsal passage into which the intestine opens, the coprodeum, and (2) a ventral portion, the urodeum with which the bladder connects. (...) the development of the placental mammals recapitulates in many respects the phylogenetic story. In the sexually indifferent stage of placental mammal there is a cloaca. While the indifferent stage still persists, a septum develops, and extends out to the closing membrane. This divides the cloaca into two chambers: a coprodeum continuous with the gut above, and a urodeum or urogenital sinus below.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000414", ontology="VHOG", source="ISBN:978-0721676678 Romer AS, Vertebrate body (1970)p.388-89 and Figure 300", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000013 "the term 'urogenital sinus' may refer to the primitive urogenital sinus present as a transient developmental structure in most mammals or it may refer to a condition in which an unseptated cloaca persists in animals longer than normal" xsd:string {source="MP"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002202 UBERON:0003064 ! develops from intermediate mesoderm +relationship: RO:0002433 UBERON:0000163 ! contributes to morphology of embryonic cloaca +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png" xsd:anyURI [Term] id: UBERON:0000165 @@ -161033,7 +160595,6 @@ xref: EFO:0000825 xref: EHDAA2:0001326 xref: EHDAA:542 xref: EMAPA:16262 -xref: FBbt:00003126 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:49184 xref: GAID:75 xref: galen:Mouth @@ -161054,19 +160615,14 @@ xref: Wikipedia:Mouth xref: XAO:0003029 xref: ZFA:0000547 xref: ZFA:0000590 -is_a: UBERON:0004921 {notes="the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts"} ! subdivision of digestive tract +is_a: UBERON:0004921 ! subdivision of digestive tract intersection_of: UBERON:0004921 ! subdivision of digestive tract -intersection_of: proximalmost_part_of UBERON:0001555 ! digestive tract -relationship: develops_from UBERON:0035804 ! future mouth -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: proximalmost_part_of UBERON:0001555 ! digestive tract -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI +intersection_of: BSPO:0001106 UBERON:0001555 ! digestive tract +relationship: BSPO:0001106 UBERON:0001555 ! digestive tract +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002202 UBERON:0035804 ! develops from future mouth +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/661" xsd:anyURI -property_value: UBPROP:0000001 "Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010355", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000812", ontology="VHOG", source="DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "oral" xsd:string -property_value: UBPROP:0000011 "some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives" xsd:string -property_value: UBPROP:0000012 "in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0000166 @@ -161083,7 +160639,6 @@ xref: FMA:59806 is_a: UBERON:0000161 {source="FMA"} ! orifice relationship: overlaps UBERON:0001004 {gci_relation="part_of", gci_filler="NCBITaxon:32523"} ! respiratory system relationship: part_of UBERON:0000165 ! mouth -property_value: UBPROP:0000003 "(...) mouth development is very similar in protostomes and 'basal' deuterostomes, whereas the chordate mouth seems to develop at a new position. Recent data for echinoderms and hemichordates further suggest that this change in mouth position may result from change in the influence of a conserved ectodermal patterning system on mouth development. It has been suggested that the mouths of vertebrates and urochordates may constitute a 'new' mouth.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000280", ontology="VHOG", source="DOI:10.1016/j.semcdb.2007.06.002 Christiaen L, Jaszczyszyn Y, Kerfant M, Kanob S, Thermes V, Joly JS, Evolutionary modification of mouth position in deuterostomes. Seminars in Cell and Developmental Biology (2007)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0000167 @@ -161108,7 +160663,6 @@ xref: EMAPA:18399 xref: EV:0100057 xref: FMA:20292 xref: HAO:0000669 -xref: MESH:D009055 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: NCIT:C12421 xref: SCTID:181220002 xref: TAO:0001027 @@ -161120,13 +160674,10 @@ xref: XAO:0000126 xref: ZFA:0001027 is_a: UBERON:0002553 ! anatomical cavity intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0000165 ! mouth -relationship: contributes_to_morphology_of UBERON:0000165 ! mouth -relationship: luminal_space_of UBERON:0000165 ! mouth +intersection_of: RO:0002572 UBERON:0000165 ! luminal space of mouth relationship: part_of UBERON:0000165 ! mouth -property_value: UBPROP:0000001 "Anatomical cavity bounded anteriorly by the mouth and posteriorly by the derivatives of the branchial arches.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000960", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000001 "The cavity of the mouth, bounded by the jaw bones and associated structures (muscles and mucosa). [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000188", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/oral+cavity"} -property_value: UBPROP:0000003 "Echinoderms, hemichordates, and chordates are called deuterostomes because the mouth arises not from the blastopore but from a second invagination at the anterior end of the larva that pushes in to connect with the archenteron.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000188", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.32", source="http://bgee.unil.ch/"} +relationship: RO:0002433 UBERON:0000165 ! contributes to morphology of mouth +relationship: RO:0002572 UBERON:0000165 ! luminal space of mouth [Term] id: UBERON:0000168 @@ -161136,7 +160687,7 @@ def: "A section dividing a colon along a proximal-distal axis." [http://orcid.or subset: non_informative synonym: "segment of colon" RELATED [FMA:222905] xref: FMA:222905 -is_a: UBERON:0004921 {order="4", source="cjm"} ! subdivision of digestive tract +is_a: UBERON:0004921 ! subdivision of digestive tract intersection_of: UBERON:0013522 ! subdivision of tube intersection_of: subdivision_of UBERON:0001155 ! colon relationship: part_of UBERON:0001155 ! colon @@ -161156,15 +160707,15 @@ synonym: "set of lungs" EXACT [] xref: FMA:68877 is_a: UBERON:0034925 ! anatomical collection intersection_of: UBERON:0034925 ! anatomical collection -intersection_of: has_member UBERON:0002167 ! right lung -intersection_of: has_member UBERON:0002168 ! left lung -relationship: has_member UBERON:0002167 ! right lung -relationship: has_member UBERON:0002167 {cardinality="1"} ! right lung -relationship: has_member UBERON:0002168 ! left lung -relationship: has_member UBERON:0002168 {cardinality="1"} ! left lung -relationship: located_in UBERON:0002224 ! thoracic cavity +intersection_of: RO:0002351 UBERON:0002167 ! has member right lung +intersection_of: RO:0002351 UBERON:0002168 ! has member left lung relationship: part_of UBERON:0001558 {source="FMA-abduced"} ! lower respiratory tract -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0001025 UBERON:0002224 ! located in thoracic cavity +relationship: RO:0002351 UBERON:0002167 ! has member right lung +relationship: RO:0002351 UBERON:0002167 {cardinality="1"} ! has member right lung +relationship: RO:0002351 UBERON:0002168 ! has member left lung +relationship: RO:0002351 UBERON:0002168 {cardinality="1"} ! has member left lung +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000171 @@ -161180,7 +160731,6 @@ synonym: "organ of apparatus respiratorius" EXACT [OBOL:automatic] synonym: "organ of respiratory system" EXACT [OBOL:automatic] synonym: "respiratory organ" EXACT [] synonym: "respiratory system organ" EXACT [OBOL:automatic] -xref: EMAPA:17607 xref: SCTID:272626006 xref: SPD:0000428 xref: TGMA:0001247 @@ -161211,10 +160761,10 @@ xref: NCIT:C13188 xref: UMLS:C0002638 {source="ncithesaurus:Amniotic_Fluid"} xref: VHOG:0001267 is_a: UBERON:0000463 ! organism substance -relationship: functionally_related_to GO:0001701 ! in utero embryonic development -relationship: located_in UBERON:0000305 ! amnion -relationship: only_in_taxon NCBITaxon:32524 ! Amniota -relationship: surrounds UBERON:0000922 ! embryo +relationship: RO:0001025 UBERON:0000305 ! located in amnion +relationship: RO:0002160 NCBITaxon:32524 ! only in taxon Amniota +relationship: RO:0002221 UBERON:0000922 ! surrounds embryo +relationship: RO:0002328 GO:0001701 ! functionally related to in utero embryonic development [Term] id: UBERON:0000174 @@ -161277,15 +160827,10 @@ is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000179 ! haemolymphatic fluid relationship: has_part CL:0000232 {source="CL:tm"} ! erythrocyte relationship: has_part UBERON:0001969 ! blood plasma -relationship: immediate_transformation_of UBERON:0006596 {source="Bgee:AN"} ! presumptive blood -relationship: located_in UBERON:0002049 {source="https://github.com/obophenotype/uberon/issues/1330"} ! vasculature relationship: part_of UBERON:0002390 ! hematopoietic system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: IAO:0000232 "This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid." xsd:string -property_value: UBPROP:0000001 "A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000007", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000046", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000002 "relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000046", ontology="AAO"} -property_value: UBPROP:0000003 "Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000224", ontology="VHOG", source="DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006) ", source="http://bgee.unil.ch/"} +relationship: RO:0001025 UBERON:0002049 {source="https://github.com/obophenotype/uberon/issues/1330"} ! located in vasculature +relationship: RO:0002495 UBERON:0006596 {source="Bgee:AN"} ! immediate transformation of presumptive blood +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000179 @@ -161298,9 +160843,9 @@ xref: CARO:0000081 is_a: UBERON:0006314 ! bodily fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: part_of UBERON:0002193 ! hemolymphoid system -relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0002193 ! hemolymphoid system +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 creation_date: 2009-04-08T04:38:19Z [Term] @@ -161326,13 +160871,12 @@ xref: neuronames:1211 xref: SCTID:279165009 xref: UMLS:C0458308 {source="ncithesaurus:Cerebral_Gyrus"} xref: Wikipedia:Gyrus +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0034768 ! morphological feature -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0000956 ! cerebral cortex -relationship: surrounded_by UBERON:0013118 ! sulcus of brain -property_value: RO:0002174 NCBITaxon:10088 +relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia +relationship: RO:0002219 UBERON:0013118 ! surrounded by sulcus of brain property_value: seeAlso "https://github.com/obophenotype/uberon/issues/573" xsd:anyURI -property_value: UBPROP:0000202 FMA:72015 [Term] id: UBERON:0000201 @@ -161343,8 +160887,8 @@ xref: NIF_Subcellular:nlx_subcell_100205 is_a: UBERON:0000120 ! blood brain barrier is_a: UBERON:0001986 ! endothelium intersection_of: UBERON:0000120 ! blood brain barrier -intersection_of: composed_primarily_of CL:0000115 ! endothelial cell -relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 +intersection_of: RO:0002473 CL:0000115 ! composed primarily of endothelial cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 creation_date: 2009-04-10T08:15:44Z [Term] @@ -161352,12 +160896,11 @@ id: UBERON:0000202 name: glial blood brain barrier namespace: uberon def: "A blood brain barrier composed of glial cells." [https://orcid.org/0000-0002-6601-2165] -xref: FBbt:00007091 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000120 ! blood brain barrier intersection_of: UBERON:0000120 ! blood brain barrier -intersection_of: composed_primarily_of CL:0000125 ! glial cell -relationship: composed_primarily_of CL:0000125 ! glial cell -relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 +intersection_of: RO:0002473 CL:0000125 ! composed primarily of glial cell +relationship: RO:0002473 CL:0000125 ! composed primarily of glial cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 creation_date: 2009-04-10T08:42:24Z [Term] @@ -161383,12 +160926,10 @@ xref: Wikipedia:Avian_pallium xref: Wikipedia:Pallium_(neuroanatomy) xref: ZFA:0000505 is_a: UBERON:0002616 ! regional part of brain -relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 relationship: part_of UBERON:0001893 ! telencephalon -relationship: present_in_taxon NCBITaxon:7762 {source="PMID:8932866"} +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 +property_value: RO:0002175 NCBITaxon:7762 {source="PMID:8932866"} property_value: seeAlso "https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/87" xsd:anyURI -property_value: UBPROP:0000003 "In the anatomy of animals, an avian pallium is the dorsal telencephalon of a bird's brain. Pallium of avian species tend to be relatively large, comprising ~75% of the telencephalic volume." xsd:string {source="Wikipedia:Avian_pallium", taxon="NCBITaxon:8782"} -property_value: UBPROP:0000008 "In humans the cerebrum has three parts: the archipallium, the paleopallium and the neopallium. The developing telencephalon or forebrain is divided into pallium and subpallium. In amphibians, the cerebrum includes archipallium, paleopallium and some of the basal nuclei. Reptiles first developed a neopallium, which continued to develop in the brains of more recent species to become the neocortex of humans and Old World monkeys. In fish, the archipallium is the largest part of the cerebrum. Some researchers suggest the early archipallium gave rise to the human hippocampus" xsd:string {source="WP"} creation_date: 2009-04-18T12:03:09Z [Term] @@ -161408,10 +160949,9 @@ xref: EFO:0003522 xref: TAO:0000304 xref: ZFA:0000304 is_a: UBERON:0002616 ! regional part of brain -relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 -relationship: dorsal_to UBERON:0000203 {notes="separated by cell-free region"} ! pallium +relationship: BSPO:0000098 UBERON:0000203 ! pallium relationship: part_of UBERON:0001893 ! telencephalon -property_value: UBPROP:0000012 "BTO term refers specifically to the avian structure" xsd:string {external_ontology="BTO"} +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 creation_date: 2009-04-18T12:12:27Z [Term] @@ -161434,22 +160974,19 @@ xref: MESH:D005624 xref: NCIT:C32635 xref: SCTID:181793006 xref: UMLS:C0016732 {source="ncithesaurus:Frontal_Bone"} -xref: VHOG:0001324 xref: VSAO:0000208 xref: Wikipedia:Frontal_bone is_a: UBERON:0002514 ! intramembranous bone is_a: UBERON:0008907 ! dermal bone is_a: UBERON:0010428 {source="FMA"} ! flat bone is_a: UBERON:0011164 ! neurocranium bone -relationship: connected_to UBERON:0001677 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! sphenoid bone -relationship: connected_to UBERON:0001679 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! ethmoid bone relationship: overlaps UBERON:0001697 ! orbit of skull relationship: part_of UBERON:0003113 {source="cjm"} ! dermatocranium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/97/Gray136.png" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/5/5b/Frontal_bone.png" xsd:anyURI -property_value: UBPROP:0000008 "fused in humans, paired in other animals" xsd:string -property_value: UBPROP:0000011 "In the mouse the parietal originates from cephalic paraxial mesoderm (Jiang 2000; Morriss-Kay 2001), whereas in the chicken it is traced back to either mesodermal (Noden 1978) or neural crest (Couly 1992, 1993)." xsd:string +relationship: RO:0002170 UBERON:0001677 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to sphenoid bone +relationship: RO:0002170 UBERON:0001679 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to ethmoid bone +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/97/Gray136.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/5/5b/Frontal_bone.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000211 @@ -161479,12 +161016,8 @@ xref: XAO:0004031 xref: ZFA:0001675 is_a: UBERON:0000062 ! organ relationship: has_part UBERON:0002384 ! connective tissue -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/9/9a/Knee_diagram.svg" xsd:anyURI -property_value: UBPROP:0000001 "Nonparenchymatous organ that primarily consists of dense connective tissue aggregated into fasciculi by connective tissue. Examples: sutural ligament, radiate sternocostal ligament, ligament of liver, ovarian ligament[FMA][FMA:21496]." xsd:string {source="FMA:21496"} -property_value: UBPROP:0000001 "Portion of connective tissue that connects bone or cartilage.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001682", ontology="TAO", source="TAO:wd"} -property_value: UBPROP:0000003 "Compared with their Ediacarian predecessor, Cambrian animals in general were characterized by their much stouter bodies. The stoutness of the body is likely due to the formation of ligaments and tendons, which in turn requires the crosslinking of collagen triple helices.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001272", ontology="VHOG", source="PMID:8710894 Ohno S, The notion of the Cambrian pananimalia genome. PNAS (1996)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "this groups both skeletal and non-skeletal ligaments. What is called a 'ligament' in many AOs is actually a skeletal ligament" xsd:string +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/9/9a/Knee_diagram.svg" xsd:anyURI [Term] id: UBERON:0000218 @@ -161525,7 +161058,6 @@ synonym: "craniovertebral joint" EXACT [FMA:24939] synonym: "occipito atlantal joint" EXACT [] synonym: "occipito-atlantal joint" EXACT [] xref: FMA:24939 -xref: MESH:D001269 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C32158 xref: ncithesaurus:Atlanto-occipital_Joint-Atlanto xref: SCTID:361831006 @@ -161534,13 +161066,13 @@ xref: Wikipedia:Atlanto-occipital_joint is_a: UBERON:0002217 ! synovial joint is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0002217 ! synovial joint -intersection_of: connects UBERON:0001092 ! vertebral bone 1 -intersection_of: connects UBERON:0001676 ! occipital bone -relationship: connects UBERON:0001092 ! vertebral bone 1 -relationship: connects UBERON:0001676 ! occipital bone -relationship: in_lateral_side_of UBERON:0006072 {source="FMA-abduced-lr"} ! cervical region of vertebral column +intersection_of: RO:0002176 UBERON:0001092 ! connects vertebral bone 1 +intersection_of: RO:0002176 UBERON:0001676 ! connects occipital bone +relationship: BSPO:0000126 UBERON:0006072 {source="FMA-abduced-lr"} ! cervical region of vertebral column relationship: part_of UBERON:0011138 ! postcranial axial skeletal system -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray304.png" xsd:anyURI +relationship: RO:0002176 UBERON:0001092 ! connects vertebral bone 1 +relationship: RO:0002176 UBERON:0001676 ! connects occipital bone +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray304.png" xsd:anyURI [Term] id: UBERON:0000304 @@ -161563,7 +161095,7 @@ intersection_of: bounding_layer_of UBERON:0000043 ! tendon relationship: bounding_layer_of UBERON:0000043 ! tendon relationship: has_part UBERON:0011233 ! synovial membrane of synovial tendon sheath relationship: has_part UBERON:0011234 ! fibrous membrane of synovial tendon sheath -property_value: editor_note "TODO - add layer relations. 'tendon sheath' GAT in FMA." xsd:string +property_value: IAO:0000116 "TODO - add layer relations. 'tendon sheath' GAT in FMA." xsd:string [Term] id: UBERON:0000305 @@ -161588,20 +161120,18 @@ xref: UMLS:C0002630 {source="ncithesaurus:Amnion"} xref: VHOG:0000721 xref: Wikipedia:Amnion is_a: PR:000050567 ! protein-containing material entity +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005631 ! extraembryonic membrane -relationship: develops_from UBERON:0005971 {source="ISBN:0073040584"} ! amniotic fold -relationship: has_developmental_contribution_from UBERON:0000924 {source="ISBN:0073040584-table5.4"} ! ectoderm -relationship: has_developmental_contribution_from UBERON:0004871 {source="ISBN:0073040584-table5.4"} ! somatic layer of lateral plate mesoderm relationship: has_part UBERON:0003254 ! amniotic ectoderm relationship: has_part UBERON:0003262 ! amniotic mesoderm -relationship: only_in_taxon NCBITaxon:32524 {source="Hymans"} ! Amniota -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: surrounds UBERON:0000922 ! embryo -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e7/Gray14.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Placenta.glb" xsd:anyURI -property_value: UBPROP:0000001 "A thin but tough extraembryonic membrane of reptiles, birds and mammals that lines the chorion and contains the fEtus and the amniotic fluid around it. [Biology_Online][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000721", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000721", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.187", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "amniotic" xsd:string +relationship: RO:0002160 NCBITaxon:32524 {source="Hymans"} ! only in taxon Amniota +relationship: RO:0002202 UBERON:0005971 {source="ISBN:0073040584"} ! develops from amniotic fold +relationship: RO:0002221 UBERON:0000922 ! surrounds embryo +relationship: RO:0002254 UBERON:0000924 {source="ISBN:0073040584-table5.4"} ! has developmental contribution from ectoderm +relationship: RO:0002254 UBERON:0004871 {source="ISBN:0073040584-table5.4"} ! has developmental contribution from somatic layer of lateral plate mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e7/Gray14.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Placenta.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000307 @@ -161620,11 +161150,11 @@ xref: OGEM:000006 xref: Wikipedia:Blastula is_a: UBERON:0000922 ! embryo intersection_of: UBERON:0000468 ! multicellular organism -intersection_of: existence_starts_and_ends_during UBERON:0000108 ! blastula stage -relationship: develops_from UBERON:0007010 ! cleaving embryo -relationship: existence_starts_and_ends_during UBERON:0000108 ! blastula stage -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI -property_value: editor_note "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" xsd:string +intersection_of: RO:0002491 UBERON:0000108 ! existence starts and ends during blastula stage +relationship: RO:0002202 UBERON:0007010 ! develops from cleaving embryo +relationship: RO:0002491 UBERON:0000108 ! existence starts and ends during blastula stage +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI +property_value: IAO:0000116 "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" xsd:string [Term] id: UBERON:0000309 @@ -161641,8 +161171,6 @@ xref: FMA:10427 xref: galen:BodyWall xref: SCTID:281483004 is_a: UBERON:0000475 ! organism subdivision -property_value: UBPROP:0000008 "defined generically to encompass both vertebrates and invertebrates" xsd:string -property_value: UBPROP:0000012 "the BTO class refers to earthworms." xsd:string {external_ontology="BTO"} [Term] id: UBERON:0000310 @@ -161666,8 +161194,7 @@ xref: UMLS:C0006141 {source="ncithesaurus:Breast"} xref: Wikipedia:Breast is_a: UBERON:0034929 ! external soft tissue zone relationship: part_of UBERON:0001443 ! chest -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/6e/Closeup_of_female_breast.jpg" xsd:anyURI -property_value: UBPROP:0000008 "The breasts of a female primate's body contain the mammary glands, which secrete milk used to feed infants. Both men and women develop breasts from the same embryological tissues. However, at puberty female sex hormones, mainly estrogens, promote breast development, which does not happen with men. As a result women's breasts become more prominent than men's." xsd:string {source="WP,unvetted"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6e/Closeup_of_female_breast.jpg" xsd:anyURI [Term] id: UBERON:0000313 @@ -161683,7 +161210,6 @@ is_a: UBERON:0007391 ! pelvic appendage cartilage tissue intersection_of: UBERON:0002418 ! cartilage tissue intersection_of: part_of UBERON:0000979 ! tibia relationship: part_of UBERON:0000979 ! tibia -property_value: IAO:0000232 "This class represents a portion of cartilage tissue located in the tibia, *not* the cartilaginous condensation of an emrbyonic tibia" xsd:string [Term] id: UBERON:0000314 @@ -161721,7 +161247,7 @@ is_a: UBERON:0000317 ! colonic mucosa intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0001153 ! caecum relationship: part_of UBERON:0001153 ! caecum -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000315 @@ -161750,11 +161276,11 @@ intersection_of: adjacent_to UBERON:0002361 ! pia mater intersection_of: adjacent_to UBERON:0002362 ! arachnoid mater relationship: adjacent_to UBERON:0002361 ! pia mater relationship: adjacent_to UBERON:0002362 ! arachnoid mater -relationship: location_of UBERON:0001359 ! cerebrospinal fluid -relationship: location_of UBERON:0001981 {source="ISBN:0471888893"} ! blood vessel relationship: part_of UBERON:0010743 ! meningeal cluster -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray769-en.svg" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/f8/Gray769.png" xsd:anyURI +relationship: RO:0001015 UBERON:0001359 ! location of cerebrospinal fluid +relationship: RO:0001015 UBERON:0001981 {source="ISBN:0471888893"} ! location of blood vessel +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray769-en.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f8/Gray769.png" xsd:anyURI [Term] id: UBERON:0000316 @@ -161799,7 +161325,7 @@ is_a: UBERON:0001207 ! mucosa of large intestine intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0001155 ! colon relationship: part_of UBERON:0001155 ! colon -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000320 @@ -161823,7 +161349,7 @@ is_a: UBERON:0001204 ! mucosa of small intestine intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0002114 ! duodenum relationship: part_of UBERON:0002114 ! duodenum -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000323 @@ -161838,7 +161364,6 @@ synonym: "fetus" NARROW [BTO:0000449] xref: BTO:0000449 xref: CALOHA:TS-0360 xref: EFO:0001323 -xref: FBbt:00005333 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:63919 xref: GAID:552 xref: MESH:D005333 @@ -161847,10 +161372,9 @@ xref: SCTID:83418008 xref: UMLS:C0015965 {source="ncithesaurus:Fetus"} is_a: UBERON:0000922 ! embryo intersection_of: UBERON:0000922 ! embryo -intersection_of: existence_starts_and_ends_during UBERON:0007220 ! late embryonic stage -relationship: existence_starts_and_ends_during UBERON:0007220 ! late embryonic stage -property_value: editor_note "TODO - check fetus/embryo. WP: An embryo is a multicellular diploid eukaryote in its earliest stage of development, from the time of first cell division until birth, hatching, or germination. In humans, it is called an embryo until about eight weeks after fertilization (i.e. ten weeks LMP), and from then it is instead called a fetus." xsd:string -property_value: UBPROP:0000001 "Fetal structure, which is a developmental form of a vertebrate animal at any given time point from 8 weeks of gestation to birth (or hatching). Examples: There is only one fetus[FMA:63919]." xsd:string {source="FMA:63919"} +intersection_of: RO:0002491 UBERON:0007220 ! existence starts and ends during late embryonic stage +relationship: RO:0002491 UBERON:0007220 ! existence starts and ends during late embryonic stage +property_value: IAO:0000116 "TODO - check fetus/embryo. WP: An embryo is a multicellular diploid eukaryote in its earliest stage of development, from the time of first cell division until birth, hatching, or germination. In humans, it is called an embryo until about eight weeks after fertilization (i.e. ten weeks LMP), and from then it is instead called a fetus." xsd:string [Term] id: UBERON:0000325 @@ -161899,7 +161423,6 @@ is_a: UBERON:0000060 ! anatomical wall intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0001555 ! digestive tract relationship: part_of UBERON:0001555 ! digestive tract -property_value: IAO:0000232 "We model the digestive tract as consisting of two parts: the wall and the lumen." xsd:string [Term] id: UBERON:0000331 @@ -161926,7 +161449,7 @@ is_a: UBERON:0001204 ! mucosa of small intestine intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0002116 ! ileum relationship: part_of UBERON:0002116 ! ileum -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000332 @@ -161942,9 +161465,9 @@ xref: SCTID:328639002 xref: SCTID:5023006 is_a: UBERON:0002371 ! bone marrow intersection_of: UBERON:0002371 ! bone marrow -intersection_of: composed_primarily_of CL:0000136 ! adipocyte -relationship: composed_primarily_of CL:0000136 ! adipocyte +intersection_of: RO:0002473 CL:0000136 ! composed primarily of adipocyte relationship: part_of UBERON:0007195 ! stroma of bone marrow +relationship: RO:0002473 CL:0000136 ! composed primarily of adipocyte [Term] id: UBERON:0000333 @@ -161995,7 +161518,6 @@ is_a: UBERON:0003408 ! gland of digestive tract intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0001242 ! intestinal mucosa relationship: part_of UBERON:0001242 ! intestinal mucosa -property_value: UBPROP:0000012 "Note that some sources treat 'intestinal gland' as synonymous with crypts" xsd:string [Term] id: UBERON:0000344 @@ -162028,12 +161550,9 @@ is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004923 ! organ component layer relationship: has_part UBERON:0000483 ! epithelium relationship: has_part UBERON:0002384 ! connective tissue -relationship: only_in_taxon NCBITaxon:7711 ! Chordata -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png" xsd:anyURI -property_value: RO:0002171 UBERON:0000009 -property_value: UBPROP:0000007 "mucosal" xsd:string -property_value: UBPROP:0000012 "FMA has mucosa vs region of mucosa; these are subtypes of Mucosa: Mucosa of gallbladder, tongue, .... The following are subtypes of Region of mucosa: Mucosa of zone of stomach, trachea, bronchus, dorsum of tongue.... Depends on whether the covered area is an organ or organ component. Uberon does not regard organ vs organ component as crucial distinction and thus collapses these into a single class deliberately" xsd:string {external_ontology="FMA"} +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png" xsd:anyURI [Term] id: UBERON:0000348 @@ -162083,14 +161602,12 @@ xref: SCTID:280210000 xref: UMLS:C0029082 {source="ncithesaurus:Ophthalmic_Nerve"} xref: VHOG:0001349 xref: Wikipedia:Ophthalmic_nerve -is_a: UBERON:0001021 ! nerve is_a: UBERON:0004121 ! ectoderm-derived structure -relationship: branching_part_of UBERON:0001645 {notes="may be a distinct nerve in teleosts", source="multiple"} ! trigeminal nerve -relationship: develops_from UBERON:0035597 ! profundal placode -relationship: innervates UBERON:1000021 ! skin of face -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000001 "Sensory medial ramus of the trigeminal nerve.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010648", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "The profundus nerve is a distinct nerve only in fishes. (...) In mammals, the profundus nerve is the same as the most rostral (ophthalmic) branch of the trigeminal nerve.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001349", ontology="VHOG", source="ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.177", source="http://bgee.unil.ch/"} +is_a: UBERON:0011779 ! nerve of head region +relationship: RO:0002134 UBERON:1000021 ! innervates skin of face +relationship: RO:0002202 UBERON:0035597 ! develops from profundal placode +relationship: RO:0002380 UBERON:0001645 ! branching part of trigeminal nerve +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000349 @@ -162111,10 +161628,11 @@ xref: neuronames:2055 xref: SCTID:361342009 xref: UMLS:C0023715 {source="ncithesaurus:Limbic_System"} xref: Wikipedia:Limbic_system +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0011216 ! organ system subdivision relationship: part_of UBERON:0001890 ! forebrain -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/5/5c/Brain_limbicsystem.jpg" xsd:anyURI -property_value: editor_note "obsoletion proposes. The current part_of children were chosen as the intersection of what is stated in wikipedia and in the FMA. NIF: We are including Limbic System because it is still used by neuroscientists and others, but as a data annotation term, it is very poor because it is not a clearly defined entity." xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/5/5c/Brain_limbicsystem.jpg" xsd:anyURI +property_value: IAO:0000116 "obsoletion proposes. The current part_of children were chosen as the intersection of what is stated in wikipedia and in the FMA. NIF: We are including Limbic System because it is still used by neuroscientists and others, but as a data annotation term, it is very poor because it is not a clearly defined entity." xsd:string [Term] id: UBERON:0000351 @@ -162132,24 +161650,20 @@ xref: SCTID:166962007 xref: Wikipedia:Nuchal_ligament is_a: UBERON:0005174 ! dorsal region element is_a: UBERON:0008846 ! skeletal ligament -relationship: attaches_to UBERON:0001676 ! occipital bone -relationship: attaches_to UBERON:0002413 {notes="C7 in humans"} ! cervical vertebra -relationship: never_in_taxon NCBITaxon:9596 relationship: part_of UBERON:0012477 {source="BTO"} ! dorsal part of neck -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: present_in_taxon NCBITaxon:9608 -relationship: present_in_taxon NCBITaxon:9788 ! Equidae -relationship: present_in_taxon NCBITaxon:9895 -property_value: UBPROP:0000008 "In humans it is a tendon-like structure that has developed independently in humans and other animals well adapted for running. In some four legged animals, particularly ungulates, the nuchal ligament serves to sustain the weight of the head" xsd:string -property_value: UBPROP:0000009 "As it is required for running, not all animals have a nuchal ligament" xsd:string +relationship: RO:0002371 UBERON:0001676 ! attached to occipital bone +relationship: RO:0002371 UBERON:0002413 ! attached to cervical vertebra +property_value: RO:0002161 NCBITaxon:9596 +property_value: RO:0002175 NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9608 +property_value: RO:0002175 NCBITaxon:9788 +property_value: RO:0002175 NCBITaxon:9895 [Term] id: UBERON:0000353 name: parenchyma namespace: uberon def: "Functional part of an organ in the body. This is in contrast to the stroma, which refers to the structural tissue of organs, being exactly, connective tissues." [Wikipedia:Parenchyma] -xref: BTO:0000999 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} -xref: BTO:0001539 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: EHDAA:3015 xref: EHDAA:3905 xref: EHDAA:3999 @@ -162169,10 +161683,7 @@ xref: Wikipedia:Parenchyma is_a: UBERON:0000064 ! organ part disjoint_from: UBERON:0003891 ! stroma relationship: capable_of GO:0032501 ! multicellular organismal process -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: UBPROP:0000007 "parenchymal" xsd:string -property_value: UBPROP:0000011 "Early in development the mammalian embryo has three distinct layers: ectoderm (external layer), endoderm (internal layer) and in between those two layers the middle layer or mesoderm. The parenchyma of most organs is of ectodermal (brain, skin) or endodermal origin (lungs, gastrointestinal tract, liver, pancreas). The parenchyma of a few organs (spleen, kidneys, heart) is of mesodermal origin. The stroma of all organs is of mesodermal origin" xsd:string {source="WP"} -property_value: UBPROP:0000012 "the FMA definition is more restrictive, and limits this to solid organs. This would seem to cause problems for the lung parenchyma, except FMA classifies Lung as solid rather than cavitated" xsd:string {external_ontology="FMA"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0000355 @@ -162222,14 +161733,14 @@ xref: SCTID:308837009 xref: UMLS:C1281743 {source="ncithesaurus:Blastocyst"} xref: Wikipedia:Blastocyst is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0000085 ! morula -relationship: existence_starts_and_ends_during UBERON:0000108 ! blastula stage relationship: has_part UBERON:0000087 ! inner cell mass relationship: has_part UBERON:0000088 ! trophoblast -relationship: only_in_taxon NCBITaxon:32525 ! Theria relationship: part_of UBERON:0000307 ! blastula -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/7/72/Blastocyst_English.svg" xsd:anyURI -property_value: editor_note "Gilbert fig11.32 has blastocyst has giving rise to ICM and trophoblast (which in this source is a synonym for trophectoderm)" xsd:string +relationship: RO:0002160 NCBITaxon:32525 ! only in taxon Theria +relationship: RO:0002202 UBERON:0000085 ! develops from morula +relationship: RO:0002491 UBERON:0000108 ! existence starts and ends during blastula stage +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/72/Blastocyst_English.svg" xsd:anyURI +property_value: IAO:0000116 "Gilbert fig11.32 has blastocyst has giving rise to ICM and trophoblast (which in this source is a synonym for trophectoderm)" xsd:string [Term] id: UBERON:0000361 @@ -162246,9 +161757,9 @@ xref: SCTID:328538003 xref: SCTID:75330005 is_a: UBERON:0002371 ! bone marrow intersection_of: UBERON:0002371 ! bone marrow -intersection_of: composed_primarily_of CL:0000988 ! hematopoietic cell -relationship: composed_primarily_of CL:0000988 ! hematopoietic cell +intersection_of: RO:0002473 CL:0000988 ! composed primarily of hematopoietic cell relationship: part_of UBERON:0012429 ! hematopoietic tissue +relationship: RO:0002473 CL:0000988 ! composed primarily of hematopoietic cell [Term] id: UBERON:0000362 @@ -162283,16 +161794,15 @@ is_a: UBERON:0000958 ! medulla of organ intersection_of: UBERON:0000958 ! medulla of organ intersection_of: part_of UBERON:0002113 ! kidney relationship: capable_of_part_of GO:0070295 ! renal water absorption -relationship: contributes_to_morphology_of UBERON:0002113 ! kidney relationship: has_part UBERON:0004200 ! kidney pyramid relationship: part_of UBERON:0002113 ! kidney -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" xsd:anyURI -property_value: UBPROP:0000010 "The renal medulla is split up into a number of sections, known as the renal pyramids. Blood enters into the kidney via the renal artery, which then splits up to form the arcuate arterioles. The arcuate arterioles each in turn branch into interlobular arterioles, which finally reach the glomeruli. At the glomerulus the blood reaches a highly disfavourable pressure gradient and a large exchange surface area, which forces the serum portion of the blood out of the vessel into the renal tubules. Flow continues through the renal tubules, including the proximal tubule, the Loop of Henle, and finally leaves the kidney by means of the collecting duct, leading to the renal ureter. The renal medulla contains the structures of the nephrons responsible for maintaining the salt and water balance of the blood. The renal medulla is hypertonic to the filtrate in the nephron and aids in the reabsorption of water" xsd:string +relationship: RO:0002433 UBERON:0002113 ! contributes to morphology of kidney +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000365 @@ -162312,7 +161822,6 @@ xref: FMA:67695 xref: GAID:935 xref: MESH:D019459 xref: NCIT:C12884 -xref: NCIT:C13318 xref: SCTID:30117005 xref: SCTID:57789003 xref: UMLS:C0225339 {source="ncithesaurus:Transitional_Epithelium"} @@ -162322,8 +161831,7 @@ xref: Wikipedia:Urothelium is_a: UBERON:0000486 ! multilaminar epithelium is_a: UBERON:0005911 ! endo-epithelium relationship: part_of UBERON:0001008 ! renal system -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/9/91/Harnblase_Urothel.png" xsd:anyURI -property_value: UBPROP:0000007 "urothelial" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/9/91/Harnblase_Urothel.png" xsd:anyURI [Term] id: UBERON:0000369 @@ -162353,9 +161861,7 @@ xref: VHOG:0001175 xref: Wikipedia:Corpus_striatum is_a: UBERON:0002616 ! regional part of brain relationship: part_of UBERON:0002420 {source="MA"} ! basal ganglion -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b3/Gray656.png" xsd:anyURI -property_value: UBPROP:0000003 "Thus, certain telencephalic characters - such as the presence of a pallium divided into lateral, dorsal, and medial formations and a subpallium divided into striatum and septum - appear to characterize all vertebrates. They are primitive characters and are homologous among all vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001175", ontology="VHOG", source="DOI:10.1146/annurev.ne.04.030181.001505, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.487 Figure 14-10", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000013 "The term has been used in a few different ways: * It is a pair of nuclear masses which form the basal ganglia, along with the subthalamic nucleus and the substantia nigra. * It may also refer to both the basal ganglia and internal capsule collectively.[2]" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b3/Gray656.png" xsd:anyURI [Term] id: UBERON:0000371 @@ -162377,9 +161883,9 @@ xref: SCTID:256965005 xref: UMLS:C1135936 {source="ncithesaurus:Syncytiotrophoblast"} xref: Wikipedia:Syncytiotrophoblast is_a: UBERON:0002050 {source="FMA"} ! embryonic structure -relationship: composed_primarily_of CL:0000525 ! syncytiotrophoblast cell relationship: part_of UBERON:0004364 {source="EMAPA"} ! ectoplacental cone -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray36.png" xsd:anyURI +relationship: RO:0002473 CL:0000525 ! composed primarily of syncytiotrophoblast cell +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray36.png" xsd:anyURI [Term] id: UBERON:0000375 @@ -162419,10 +161925,10 @@ xref: SCTID:280212008 xref: UMLS:C0024695 {source="ncithesaurus:Inferior_Maxillary_Nerve"} xref: VHOG:0001345 xref: Wikipedia:Mandibular_nerve -is_a: UBERON:0001021 ! nerve -relationship: branching_part_of UBERON:0001645 ! trigeminal nerve -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray781.png" xsd:anyURI +is_a: UBERON:0011779 ! nerve of head region +relationship: RO:0002380 UBERON:0001645 ! branching part of trigeminal nerve +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray781.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000376 @@ -162465,12 +161971,10 @@ is_a: UBERON:0002472 ! stylopod is_a: UBERON:0008784 ! lower limb segment intersection_of: UBERON:0002472 ! stylopod intersection_of: part_of UBERON:0002103 ! hindlimb -relationship: contributes_to_morphology_of UBERON:0002103 ! hindlimb -relationship: has_skeleton UBERON:0015052 ! femur endochondral element relationship: part_of UBERON:0000978 {source="MA"} ! leg -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/4b/Gray1238.png" xsd:anyURI -property_value: UBPROP:0000003 "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000349", ontology="VHOG", source="ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000013 "Naming conventions for pod terms under discussion within phenoscape group." xsd:string {seeAlso="https://github.com/obophenotype/uberon/issues/61"} +relationship: RO:0002433 UBERON:0002103 ! contributes to morphology of hindlimb +relationship: RO:0002551 UBERON:0015052 ! has skeleton femur endochondral element +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4b/Gray1238.png" xsd:anyURI [Term] id: UBERON:0000377 @@ -162506,12 +162010,10 @@ xref: MESH:D008442 xref: SCTID:280211001 xref: VHOG:0001346 xref: Wikipedia:Maxillary_nerve -is_a: UBERON:0001021 ! nerve -relationship: branching_part_of UBERON:0001645 ! trigeminal nerve -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/a9/Gray779.png" xsd:anyURI -property_value: UBPROP:0000001 "Medial ramus (sensory) of the trigeminal nerve.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010670", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000002 "relationship loss: part_of trunk maxillary-mandibularis (AAO:0010669)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010670", ontology="AAO"} +is_a: UBERON:0011779 ! nerve of head region +relationship: RO:0002380 UBERON:0001645 ! branching part of trigeminal nerve +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/a9/Gray779.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000378 @@ -162541,15 +162043,14 @@ xref: Wikipedia:Muscles_of_tongue is_a: UBERON:0013765 ! digestive system element is_a: UBERON:0014892 {source="FEED:rd"} ! skeletal muscle organ, vertebrate intersection_of: UBERON:0014892 ! skeletal muscle organ, vertebrate -intersection_of: attaches_to_part_of UBERON:0001723 ! tongue +intersection_of: RO:0002177 UBERON:0001723 ! attached to part of tongue union_of: UBERON:0001575 ! extrinsic muscle of tongue union_of: UBERON:0001576 ! intrinsic muscle of tongue -relationship: attaches_to_part_of UBERON:0001723 ! tongue -relationship: contributes_to_morphology_of UBERON:0001723 ! tongue -relationship: develops_from UBERON:0005594 {source="FEED:rd", source="ISBN:1607950324"} ! head somite relationship: part_of UBERON:0000165 ! mouth -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Gray1019.png" xsd:anyURI -property_value: UBPROP:0000003 "The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001390", ontology="VHOG", source="DOI:10.1002/dvdy.20587 Kusakabe R, Kuratani S, Evolution and developmental patterning of the vertebrate skeletal muscles: perspectives from the lamprey. Developmental Dynamics (2005)", source="http://bgee.unil.ch/"} +relationship: RO:0002177 UBERON:0001723 ! attached to part of tongue +relationship: RO:0002202 UBERON:0005594 {source="FEED:rd", source="ISBN:1607950324"} ! develops from head somite +relationship: RO:0002433 UBERON:0001723 ! contributes to morphology of tongue +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Gray1019.png" xsd:anyURI [Term] id: UBERON:0000379 @@ -162602,9 +162103,8 @@ xref: Wikipedia:Apocrine_sweat_gland is_a: UBERON:0001820 {source="FMA"} ! sweat gland is_a: UBERON:0012177 ! skin apocrine gland disjoint_from: UBERON:0000423 ! eccrine sweat gland -relationship: never_in_taxon NCBITaxon:9822 {source="http://www.nal.usda.gov/awic/pubs/swine/swine.htm"} +property_value: RO:0002161 NCBITaxon:9822 {source="http://www.nal.usda.gov/awic/pubs/swine/swine.htm"} property_value: seeAlso "https://github.com/obophenotype/uberon/issues/2111" xsd:string -property_value: UBPROP:0000008 "In humans, apocrine sweat glands are found only in certain locations of the body: the axillae (armpits), the areola of the nipples, and the genitoanal region." xsd:string [Term] id: UBERON:0000383 @@ -162627,7 +162127,6 @@ xref: BILA:0000088 xref: BTO:0001369 xref: BTO:0001485 xref: EFO:0000801 -xref: EMAPA:35578 xref: FMA:72954 xref: MA:0002888 xref: MAT:0000025 @@ -162636,15 +162135,13 @@ xref: VSAO:0000033 xref: XAO:0004042 is_a: UBERON:0011216 ! organ system subdivision intersection_of: UBERON:0011216 ! organ system subdivision -intersection_of: composed_primarily_of UBERON:0001015 ! musculature +intersection_of: RO:0002473 UBERON:0001015 ! composed primarily of musculature relationship: capable_of GO:0003012 ! muscle system process -relationship: composed_primarily_of UBERON:0001015 ! musculature -relationship: never_in_taxon NCBITaxon:6040 -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: editor_note "consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77" xsd:string -property_value: UBPROP:0000001 "Anatomical system that consists of the muscles of the body.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000033", ontology="VSAO", source="VSAO:curator"} -property_value: UBPROP:0000012 "we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA" xsd:string {external_ontology="MA"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002473 UBERON:0001015 ! composed primarily of musculature +property_value: IAO:0000116 "consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77" xsd:string +property_value: RO:0002161 NCBITaxon:6040 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000389 @@ -162661,11 +162158,11 @@ xref: SCTID:280626006 is_a: UBERON:0000479 ! tissue is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000479 ! tissue -intersection_of: surrounds UBERON:0000390 ! lens nucleus -relationship: develops_from UBERON:0005614 ! lens anterior epithelium +intersection_of: RO:0002221 UBERON:0000390 ! surrounds lens nucleus relationship: part_of UBERON:0000965 ! lens of camera-type eye -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: surrounds UBERON:0000390 ! lens nucleus +relationship: RO:0002202 UBERON:0005614 ! develops from lens anterior epithelium +relationship: RO:0002221 UBERON:0000390 ! surrounds lens nucleus +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000390 @@ -162681,11 +162178,11 @@ xref: SCTID:280628007 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0034944 ! zone of organ intersection_of: UBERON:0034944 ! zone of organ -intersection_of: surrounded_by UBERON:0000389 ! lens cortex -relationship: develops_from UBERON:0005614 ! lens anterior epithelium +intersection_of: RO:0002219 UBERON:0000389 ! surrounded by lens cortex relationship: part_of UBERON:0000965 ! lens of camera-type eye -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: surrounded_by UBERON:0000389 ! lens cortex +relationship: RO:0002202 UBERON:0005614 ! develops from lens anterior epithelium +relationship: RO:0002219 UBERON:0000389 ! surrounded by lens cortex +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000391 @@ -162708,9 +162205,9 @@ xref: SCTID:362303006 xref: UMLS:C0228126 {source="ncithesaurus:Leptomeninges"} xref: Wikipedia:Leptomeninges is_a: UBERON:0002360 ! meninx -relationship: immediate_transformation_of UBERON:0007646 ! endomeninx -property_value: editor_note "check relationship to secondary meninx" xsd:string -property_value: UBPROP:0000012 "in FMA/NIF this is a superclass of PM/AM - in BTO it is the mereological sum. We go with superclass here, as we are naming the class in the singular" xsd:string {external_ontology="FMA"} +is_a: UBERON:0010313 ! neural crest-derived structure +relationship: RO:0002495 UBERON:0007646 ! immediate transformation of endomeninx +property_value: IAO:0000116 "check relationship to secondary meninx" xsd:string [Term] id: UBERON:0000395 @@ -162741,14 +162238,15 @@ xref: SCTID:368955007 xref: VHOG:0001183 xref: Wikipedia:Spiral_ganglion is_a: UBERON:0001714 ! cranial ganglion +is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0001714 ! cranial ganglion intersection_of: extends_fibers_into UBERON:0004727 ! cochlear nerve relationship: extends_fibers_into UBERON:0004727 ! cochlear nerve -relationship: located_in UBERON:0006723 {notes="cell bodies", source="BTO-modified", source="Wikipedia"} ! cochlear modiolus relationship: part_of UBERON:0002827 ! vestibulocochlear ganglion relationship: part_of UBERON:0016490 ! auditory system -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b1/Gray903.png" xsd:anyURI -property_value: editor_note "in BTO this is part of the cochlear modiolus, but this leads to the CG being in both the nervous and skeletal systems" xsd:string +relationship: RO:0001025 UBERON:0006723 ! located in cochlear modiolus +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b1/Gray903.png" xsd:anyURI +property_value: IAO:0000116 "in BTO this is part of the cochlear modiolus, but this leads to the CG being in both the nervous and skeletal systems" xsd:string [Term] id: UBERON:0000397 @@ -162778,8 +162276,7 @@ is_a: UBERON:0001278 ! epithelium of large intestine intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001155 ! colon relationship: part_of UBERON:0001155 ! colon -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000001 "Intestinal epithelium which lines the lumen of the posterior intestine.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005128", ontology="TAO", source="ZFIN:curator"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000398 @@ -162820,7 +162317,7 @@ is_a: UBERON:0001204 ! mucosa of small intestine intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0002115 ! jejunum relationship: part_of UBERON:0002115 ! jejunum -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000400 @@ -162839,7 +162336,7 @@ is_a: UBERON:0013636 ! epithelium of intestinal villus intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002115 ! jejunum relationship: part_of UBERON:0008343 {source="FMA"} ! intestinal villus of jejunum -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000402 @@ -162856,7 +162353,7 @@ xref: SCTID:278940000 xref: Wikipedia:Nasal_vestibule is_a: UBERON:0002553 ! anatomical cavity relationship: part_of UBERON:0001707 ! nasal cavity -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/7c/Gray994.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7c/Gray994.png" xsd:anyURI [Term] id: UBERON:0000403 @@ -162884,8 +162381,8 @@ relationship: has_part UBERON:0002515 ! periosteum relationship: overlaps UBERON:0001084 ! skin of head relationship: overlaps UBERON:0006661 ! epicranial aponeurosis relationship: part_of UBERON:0000033 {source="BTO"} ! head -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Layers_of_the_scalp_and_meninges.png" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/e/eb/Double_cowlick.jpg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Layers_of_the_scalp_and_meninges.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/e/eb/Double_cowlick.jpg" xsd:anyURI [Term] id: UBERON:0000407 @@ -162907,9 +162404,9 @@ xref: Wikipedia:Sympathetic_trunk xref: XAO:0000211 is_a: UBERON:0000062 ! organ is_a: UBERON:0015212 ! lateral structure -relationship: in_lateral_side_of UBERON:0000013 {source="FMA-abduced-lr"} ! sympathetic nervous system +relationship: BSPO:0000126 UBERON:0000013 {source="FMA-abduced-lr"} ! sympathetic nervous system relationship: part_of UBERON:0000013 ! sympathetic nervous system -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray847.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray847.png" xsd:anyURI [Term] id: UBERON:0000409 @@ -162928,8 +162425,7 @@ intersection_of: has_part CL:0000313 ! serous secreting cell relationship: has_part CL:0000313 ! serous secreting cell relationship: has_part UBERON:0013232 ! serous acinus relationship: produces UBERON:0007794 ! secretion of serous gland -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray1021.png" xsd:anyURI -property_value: UBPROP:0000001 "glands that secrete watery albuminous material that often contains enzymes[MP:0008052]." xsd:string {source="MP:0008052"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray1021.png" xsd:anyURI [Term] id: UBERON:0000410 @@ -162965,6 +162461,7 @@ xref: BTO:0001846 xref: FMA:62652 xref: SCTID:30802009 is_a: UBERON:0000379 ! tracheal mucosa +is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0002185 ! bronchus relationship: part_of UBERON:0002185 ! bronchus @@ -162996,13 +162493,11 @@ xref: SCTID:320101005 xref: UMLS:C0221931 {source="ncithesaurus:Dermal_Papilla"} xref: Wikipedia:Dermal_papillae is_a: UBERON:0000479 ! tissue -relationship: composed_primarily_of CL:0000057 ! fibroblast +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001992 ! papillary layer of dermis -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/34/Skin.jpg" xsd:anyURI -property_value: editor_note "consider adding grouping class for TAO:0001995 ! papilla" xsd:string -property_value: UBPROP:0000008 "In humans, at the surface of the skin in hands and feet, they appear as epidermal or papillary ridges (colloquially known as fingerprints)" xsd:string -property_value: UBPROP:0000009 "Blood vessels in the dermal papillae nourish all hair follicles and bring nutrients and oxygen to the lower layers of epidermal cells." xsd:string -property_value: UBPROP:0000012 "ncit has 'hair papilla' as part of hypodermis" xsd:string {external_ontology="ncit"} +relationship: RO:0002473 CL:0000057 ! composed primarily of fibroblast +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/34/Skin.jpg" xsd:anyURI +property_value: IAO:0000116 "consider adding grouping class for TAO:0001995 ! papilla" xsd:string [Term] id: UBERON:0000414 @@ -163026,8 +162521,7 @@ intersection_of: has_part CL:0000319 ! mucus secreting cell relationship: capable_of GO:0070254 ! mucus secretion relationship: has_part CL:0000319 ! mucus secreting cell relationship: produces UBERON:0000912 ! mucus -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray1021.png" xsd:anyURI -property_value: UBPROP:0000008 "In frogs and salamanders, this is the smaller of the two types of gland, the other being the granular (poison) gland. In these species the mucous gland is a cluster of cells that release secretion into a common duct[Kardong]" xsd:string {scope="NCBITaxon:8292", source="ISBN:0073040584"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray1021.png" xsd:anyURI [Term] id: UBERON:0000415 @@ -163056,9 +162550,9 @@ xref: FMA:67805 xref: Wikipedia:Myoepithelial_cell is_a: UBERON:0000488 ! atypical epithelium intersection_of: UBERON:0000488 ! atypical epithelium -intersection_of: composed_primarily_of CL:0000185 ! myoepithelial cell -relationship: composed_primarily_of CL:0000185 ! myoepithelial cell +intersection_of: RO:0002473 CL:0000185 ! composed primarily of myoepithelial cell relationship: has_part GO:0036379 ! myofilament +relationship: RO:0002473 CL:0000185 ! composed primarily of myoepithelial cell [Term] id: UBERON:0000423 @@ -163084,8 +162578,7 @@ xref: Wikipedia:Eccrine_sweat_gland is_a: UBERON:0001820 ! sweat gland is_a: UBERON:0010243 {source="MGI:anna"} ! merocrine gland relationship: part_of UBERON:0008837 {gci_relation="part_of", gci_filler="NCBITaxon:10088", source="PMID:15843440"} ! palmar/plantar part of autopod -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000008 "in mice, found only on footpads; in humans, entire body including soles and palms" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000428 @@ -163113,14 +162606,16 @@ xref: FMA:79643 xref: MA:0001737 xref: NCIT:C13103 xref: UMLS:C1179826 {source="ncithesaurus:Prostatic_Epithelium"} +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0000485 ! simple columnar epithelium is_a: UBERON:0005156 ! reproductive structure is_a: UBERON:0005911 ! endo-epithelium +is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002367 ! prostate gland relationship: part_of UBERON:0002367 ! prostate gland -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: editor_note "TODO - check 2 FMA IDs" xsd:string +property_value: IAO:0000116 "TODO - check 2 FMA IDs" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000429 @@ -163139,10 +162634,11 @@ xref: EMAPA:35446 xref: FMA:77597 xref: MA:0001147 is_a: UBERON:0001816 ! autonomic nerve plexus +is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0001810 ! nerve plexus intersection_of: part_of UBERON:0002005 ! enteric nervous system relationship: part_of UBERON:0002005 ! enteric nervous system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000437 @@ -163151,10 +162647,12 @@ namespace: uberon def: "The arachnoid barrier layer is a part of the arachnoid meningeal layer. It is formed by tight junctions between the endothelial cells of cerebral capillaries in the arachnoid mater." [BTO:0002498] xref: BTO:0002498 xref: FMA:231559 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004923 {source="FMA"} ! organ component layer -relationship: composed_primarily_of GO:0005923 ! bicellular tight junction +is_a: UBERON:0010313 ! neural crest-derived structure relationship: part_of UBERON:0000201 {source="cjm"} ! endothelial blood brain barrier relationship: part_of UBERON:0002362 {source="FMA"} ! arachnoid mater +relationship: RO:0002473 GO:0005923 ! composed primarily of bicellular tight junction [Term] id: UBERON:0000439 @@ -163168,6 +162666,7 @@ xref: FMA:83979 xref: Wikipedia:Arachnoid_trabeculae is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000440 ! trabecula +is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0000440 ! trabecula intersection_of: part_of UBERON:0002362 ! arachnoid mater relationship: has_part GO:0005581 ! collagen trimer @@ -163186,8 +162685,7 @@ xref: FMA:85273 xref: Wikipedia:Trabecula is_a: UBERON:0000064 ! organ part relationship: has_part UBERON:0002384 ! connective tissue -relationship: has_quality PATO:0001873 ! cylindrical -property_value: UBPROP:0000007 "trabecular" xsd:string +relationship: RO:0000086 PATO:0001873 ! has quality cylindrical [Term] id: UBERON:0000442 @@ -163207,11 +162705,11 @@ xref: NCIT:C52697 xref: SCTID:53500001 is_a: UBERON:0001144 ! testicular vein intersection_of: UBERON:0001144 ! testicular vein -intersection_of: drains UBERON:0004534 ! right testis -relationship: connected_to UBERON:0001142 ! left renal vein -relationship: drains UBERON:0004534 ! right testis -relationship: in_left_side_of UBERON:0000468 ! multicellular organism -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002179 UBERON:0004534 ! drains right testis +relationship: BSPO:0000120 UBERON:0000468 ! multicellular organism +relationship: RO:0002170 UBERON:0001142 ! connected to left renal vein +relationship: RO:0002179 UBERON:0004534 ! drains right testis +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000443 @@ -163230,11 +162728,11 @@ xref: NCIT:C52696 xref: SCTID:90988008 is_a: UBERON:0001144 ! testicular vein intersection_of: UBERON:0001144 ! testicular vein -intersection_of: drains UBERON:0004533 ! left testis -relationship: connected_to UBERON:0001142 ! left renal vein -relationship: drains UBERON:0004533 ! left testis -relationship: in_left_side_of UBERON:0000468 ! multicellular organism -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002179 UBERON:0004533 ! drains left testis +relationship: BSPO:0000120 UBERON:0000468 ! multicellular organism +relationship: RO:0002170 UBERON:0001142 ! connected to left renal vein +relationship: RO:0002179 UBERON:0004533 ! drains left testis +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000444 @@ -163253,7 +162751,7 @@ xref: NCIT:C33040 xref: SCTID:64626006 xref: UMLS:C0229654 {source="ncithesaurus:Lymphoid_Follicle"} is_a: UBERON:0001744 {source="FMA"} ! lymphoid tissue -property_value: editor_note "introducing part_of to 'cortex of lymph node' as in issue 7 introduces equivalencies; the part_of has instead been added to 'lymph node follicle'" xsd:string +property_value: IAO:0000116 "introducing part_of to 'cortex of lymph node' as in issue 7 introduces equivalencies; the part_of has instead been added to 'lymph node follicle'" xsd:string property_value: seeAlso "https://github.com/obophenotype/uberon/issues/6" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/7" xsd:anyURI @@ -163286,7 +162784,6 @@ xref: MA:0000924 xref: neuronames:255 {source="BIRNLEX:963"} xref: UMLS:C0752060 {source="BIRNLEX:963"} is_a: UBERON:0005401 ! cerebral hemisphere gray matter -property_value: UBPROP:0000001 "Subdivision of the telencephalon on the midline between the lateral ventricles which contains the septum pellucidum and the septal nuclei[FMA][FMA:61842]." xsd:string {source="FMA:61842"} [Term] id: UBERON:0000454 @@ -163301,6 +162798,7 @@ xref: FMA:242188 xref: NCIT:C98712 xref: UMLS:C0815008 {source="ncithesaurus:Cerebral_Subcortex"} is_a: UBERON:0000064 ! organ part +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0000955 ! brain [Term] @@ -163331,7 +162829,6 @@ is_a: UBERON:0000463 ! organism substance intersection_of: UBERON:0000463 ! organism substance intersection_of: produced_by UBERON:0002365 ! exocrine gland relationship: produced_by UBERON:0002365 ! exocrine gland -property_value: UBPROP:0000012 "BTO has two distunct classes, with exocrine glandular secretion a subtype of secretion - however, all examples in BTO directly under secretion appear to be exocrine gland secretions" xsd:string {external_ontology="BTO"} [Term] id: UBERON:0000457 @@ -163344,10 +162841,10 @@ xref: BTO:0002996 xref: FMA:70527 is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery -intersection_of: connecting_branch_of UBERON:0001532 ! internal carotid artery -intersection_of: supplies UBERON:0001675 ! trigeminal ganglion -relationship: connecting_branch_of UBERON:0001532 ! internal carotid artery -relationship: supplies UBERON:0001675 ! trigeminal ganglion +intersection_of: RO:0002178 UBERON:0001675 ! supplies trigeminal ganglion +intersection_of: RO:0002252 UBERON:0001532 ! connecting branch of internal carotid artery +relationship: RO:0002178 UBERON:0001675 ! supplies trigeminal ganglion +relationship: RO:0002252 UBERON:0001532 ! connecting branch of internal carotid artery [Term] id: UBERON:0000458 @@ -163362,11 +162859,12 @@ xref: SCTID:264460007 xref: UMLS:C0227837 {source="ncithesaurus:Endocervix"} is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000064 ! organ part +is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0000064 ! organ part -intersection_of: proximalmost_part_of UBERON:0000002 ! uterine cervix +intersection_of: BSPO:0001106 UBERON:0000002 ! uterine cervix +relationship: BSPO:0001106 UBERON:0000002 ! uterine cervix relationship: has_part UBERON:0000485 ! simple columnar epithelium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: proximalmost_part_of UBERON:0000002 ! uterine cervix +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000459 @@ -163406,7 +162904,6 @@ xref: CALOHA:TS-2101 xref: CARO:0000004 xref: EHDAA2:0003004 xref: EMAPA:35178 -xref: FBbt:00007019 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9669 xref: galen:BodySubstance xref: HAO:0000004 @@ -163419,11 +162916,11 @@ xref: VHOG:0001726 xref: XAO:0004001 xref: ZFA:0001487 is_a: UBERON:0000465 ! material anatomical entity -relationship: has_quality PATO:0002198 ! quality of a substance -relationship: part_of UBERON:0000468 {notes="this relationship may be too strong and may be weakened in future"} ! multicellular organism -relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 ! Fungi +relationship: part_of UBERON:0000468 ! multicellular organism +relationship: RO:0000086 PATO:0002198 ! has quality quality of a substance +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000464 @@ -163441,7 +162938,6 @@ xref: AEO:0000005 xref: BILA:0000005 xref: CARO:0000005 xref: EHDAA2:0003005 -xref: FBbt:00007017 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:5897 xref: HAO:0000005 xref: NCIT:C94478 @@ -163452,10 +162948,10 @@ xref: VHOG:0001728 xref: XAO:0003190 xref: ZFA:0001643 is_a: UBERON:0000466 ! immaterial anatomical entity -relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 ! Fungi -relationship: surrounded_by UBERON:0000061 ! anatomical structure +relationship: RO:0002219 UBERON:0000061 ! surrounded by anatomical structure +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000465 @@ -163469,7 +162965,6 @@ xref: AEO:0000006 xref: BILA:0000006 xref: CARO:0000006 xref: EHDAA2:0003006 -xref: FBbt:00007016 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67165 xref: HAO:0000006 xref: TAO:0001836 @@ -163478,9 +162973,9 @@ xref: VHOG:0001721 is_a: BFO:0000040 ! material entity is_a: UBERON:0001062 ! anatomical entity disjoint_from: UBERON:0000466 ! immaterial anatomical entity -relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 ! Fungi +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000466 @@ -163495,7 +162990,6 @@ xref: AEO:0000007 xref: BILA:0000007 xref: CARO:0000007 xref: EHDAA2:0003007 -xref: FBbt:00007015 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67112 xref: HAO:0000007 xref: TAO:0001835 @@ -163503,9 +162997,9 @@ xref: TGMA:0001827 xref: VHOG:0001727 is_a: BFO:0000141 ! immaterial entity is_a: UBERON:0001062 ! anatomical entity -relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 ! Fungi +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000467 @@ -163533,11 +163027,9 @@ xref: EHDAA2:0003011 xref: EHDAA:392 xref: EMAPA:16103 xref: EV:0100000 -xref: FBbt:00004856 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7149 xref: galen:AnatomicalSystem xref: HAO:0000011 -xref: IDOMAL:0002460 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: MA:0000003 xref: NCIT:C12919 xref: SCTID:278195005 @@ -163551,14 +163043,14 @@ xref: Wikipedia:Organ_system xref: XAO:0003002 xref: ZFA:0001439 is_a: UBERON:0000061 ! anatomical structure -relationship: existence_starts_during_or_after UBERON:0000111 {gci_filler="NCBITaxon:6072", gci_relation="in_taxon"} ! organogenesis stage relationship: has_part UBERON:0000062 ! organ relationship: part_of UBERON:0000468 ! multicellular organism -relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 ! Fungi -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: seeAlso EHDAA2:0001330 +relationship: RO:0002496 UBERON:0000111 {gci_filler="NCBITaxon:6072", gci_relation="RO:0002162"} ! existence starts during or after organogenesis stage +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:9606 +property_value: seeAlso EHDAA2:0001330 [Term] id: UBERON:0000468 @@ -163589,7 +163081,6 @@ xref: EHDAA2:0003191 xref: EHDAA:1 xref: EMAPA:25765 xref: EV:0100016 -xref: FBbt:00000001 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:256135 xref: galen:Organism xref: HAO:0000012 @@ -163605,11 +163096,10 @@ xref: Wikipedia:Multi-cellular_organism xref: XAO:0003004 xref: ZFA:0001094 is_a: UBERON:0010000 ! multicellular anatomical structure -relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 ! Fungi -property_value: editor_note "TODO - split body and mc organism? body continues after death stage" xsd:string -property_value: UBPROP:0000007 "organismal" xsd:string +property_value: IAO:0000116 "TODO - split body and mc organism? body continues after death stage" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000471 @@ -163630,7 +163120,6 @@ xref: XAO:0003039 xref: ZFA:0001489 is_a: UBERON:0000481 ! multi-tissue structure relationship: part_of UBERON:0003103 ! compound organ -property_value: IAO:0000232 "this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future" xsd:string [Term] id: UBERON:0000473 @@ -163660,7 +163149,6 @@ xref: EHDAA2:0002007 xref: EHDAA:8146 xref: EMAPA:17972 xref: EV:0100102 -xref: FBbt:00004928 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7210 xref: GAID:396 xref: galen:Testis @@ -163684,13 +163172,8 @@ intersection_of: UBERON:0000991 ! gonad intersection_of: part_of UBERON:0000079 ! male reproductive system disjoint_from: UBERON:0000992 ! ovary disjoint_from: UBERON:0009117 ! indifferent gonad -relationship: develops_from UBERON:0009117 ! indifferent gonad -relationship: in_lateral_side_of UBERON:0000468 {gci_relation="part_of", gci_filler="NCBITaxon:7742", notes="vertebrates"} ! multicellular organism -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c3/Gray1144.png" xsd:anyURI -property_value: UBPROP:0000001 "Male reproductive organ.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000598", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "(...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000252", ontology="VHOG", source="DOI:10.1093/icb/icm052 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across the Bilateria. Integrative and Comparative Biology (2007), DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T and Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "testicular" xsd:string -property_value: UBPROP:0000008 "The testes are descended in metatherian and eutherian mammals, first transabdominally, then inguinoscrotally" xsd:string {source="ISBN:0123971756", taxon="NCBITaxon:40674"} +relationship: RO:0002202 UBERON:0009117 ! develops from indifferent gonad +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c3/Gray1144.png" xsd:anyURI [Term] id: UBERON:0000474 @@ -163719,7 +163202,6 @@ xref: EHDAA2:0000506 xref: EHDAA:8116 xref: EMAPA:17959 xref: EV:0100110 -xref: FBbt:00004864 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45663 xref: GAID:364 xref: HAO:0000324 @@ -163738,9 +163220,8 @@ is_a: UBERON:0000990 ! reproductive system intersection_of: UBERON:0000990 ! reproductive system intersection_of: part_of UBERON:0003100 ! female organism relationship: part_of UBERON:0003100 ! female organism -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/68/Scheme_female_reproductive_system-en.svg" xsd:anyURI -property_value: UBPROP:0000003 "By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000726", ontology="VHOG", source="ISBN:978-0792383369 Lombardi J, Comparative vertebrate reproduction (1998) p.43", source="http://bgee.unil.ch/"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/68/Scheme_female_reproductive_system-en.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000475 @@ -163765,7 +163246,6 @@ xref: CARO:0000032 xref: EFO:0000808 xref: EHDAA2:0003032 xref: EMAPA:36031 -xref: FBbt:00007009 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7153 xref: galen:BodyPart xref: HAO:0000032 @@ -163784,16 +163264,16 @@ xref: ZFA:0001308 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure relationship: has_part UBERON:0000075 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! subdivision of skeletal system relationship: has_part UBERON:0034929 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! external soft tissue zone -relationship: overlaps UBERON:0001009 {gci_filler="NCBITaxon:33213", gci_relation="in_taxon"} ! circulatory system -relationship: overlaps UBERON:0001015 {gci_filler="NCBITaxon:6072", gci_relation="in_taxon"} ! musculature -relationship: overlaps UBERON:0001016 {gci_filler="NCBITaxon:6072", gci_relation="in_taxon"} ! nervous system -relationship: overlaps UBERON:0001434 {gci_filler="NCBITaxon:33213", gci_relation="in_taxon"} ! skeletal system -relationship: overlaps UBERON:0002416 {gci_filler="NCBITaxon:6072", gci_relation="in_taxon"} ! integumental system +relationship: overlaps UBERON:0001009 {gci_filler="NCBITaxon:33213", gci_relation="RO:0002162"} ! circulatory system +relationship: overlaps UBERON:0001015 {gci_filler="NCBITaxon:6072", gci_relation="RO:0002162"} ! musculature +relationship: overlaps UBERON:0001016 {gci_filler="NCBITaxon:6072", gci_relation="RO:0002162"} ! nervous system +relationship: overlaps UBERON:0001434 {gci_filler="NCBITaxon:33213", gci_relation="RO:0002162"} ! skeletal system +relationship: overlaps UBERON:0002416 {gci_filler="NCBITaxon:6072", gci_relation="RO:0002162"} ! integumental system relationship: part_of UBERON:0000468 ! multicellular organism -relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 ! Fungi -property_value: editor_note "Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency" xsd:string +property_value: IAO:0000116 "Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000476 @@ -163808,7 +163288,6 @@ xref: AEO:0000040 xref: BILA:0000040 xref: CARO:0000040 xref: EHDAA2:0003040 -xref: FBbt:00007013 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:63863 xref: HAO:0000040 xref: TAO:0000382 @@ -163817,9 +163296,9 @@ xref: XAO:0003162 xref: ZFA:0000382 is_a: UBERON:0000061 ! anatomical structure disjoint_from: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure -relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 ! Fungi +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000477 @@ -163828,12 +163307,11 @@ namespace: uberon def: "Anatomical group whose component anatomical structures lie in close proximity to each other." [FBbt:00007277] subset: common_anatomy subset: upper_level -xref: FBbt:00007277 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: VHOG:0001737 is_a: UBERON:0034923 ! disconnected anatomical group -relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 ! Fungi +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000478 @@ -163854,7 +163332,6 @@ xref: CALOHA:TS-2119 xref: CARO:0000042 xref: EHDAA2:0003042 xref: EHDAA:46 -xref: FBbt:00005835 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:85537 xref: HAO:0000042 xref: NCIT:C34055 @@ -163868,8 +163345,8 @@ xref: ZFA:0000020 is_a: UBERON:0005423 ! developing anatomical structure intersection_of: UBERON:0005423 ! developing anatomical structure intersection_of: part_of UBERON:0016887 ! entire extraembryonic component -relationship: existence_starts_and_ends_during UBERON:0000068 {gci_filler="NCBITaxon:6072", gci_relation="in_taxon"} ! embryo stage relationship: part_of UBERON:0016887 ! entire extraembryonic component +relationship: RO:0002491 UBERON:0000068 {gci_filler="NCBITaxon:6072", gci_relation="RO:0002162"} ! existence starts and ends during embryo stage [Term] id: UBERON:0000479 @@ -163891,7 +163368,6 @@ xref: CALOHA:TS-2090 xref: CARO:0000043 xref: EHDAA2:0003043 xref: EMAPA:35868 -xref: FBbt:00007003 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9637 xref: galen:Tissue xref: HAO:0000043 @@ -163908,10 +163384,10 @@ xref: ZFA:0001477 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure relationship: has_part GO:0031012 ! extracellular matrix relationship: part_of UBERON:0000468 ! multicellular organism -relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 ! Fungi -property_value: editor_note "changed label and definition to reflect CARO2" xsd:string +property_value: IAO:0000116 "changed label and definition to reflect CARO2" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000481 @@ -163926,7 +163402,6 @@ xref: AEO:0000055 xref: BILA:0000055 xref: CARO:0000055 xref: EHDAA2:0003055 -xref: FBbt:00007010 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: HAO:0000055 xref: TAO:0001488 xref: TGMA:0001847 @@ -163935,10 +163410,10 @@ xref: XAO:0003037 xref: ZFA:0001488 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure relationship: has_part UBERON:0000479 ! tissue -relationship: part_of NCBITaxon:6072 {gci_filler="NCBITaxon:6072", gci_relation="in_taxon"} ! Eumetazoa -relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 ! Fungi +relationship: part_of NCBITaxon:6072 {gci_filler="NCBITaxon:6072", gci_relation="RO:0002162"} ! Eumetazoa +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000483 @@ -163960,7 +163435,6 @@ xref: CALOHA:TS-0288 xref: CARO:0000066 xref: EHDAA2:0003066 xref: EMAPA:32738 -xref: FBbt:00007005 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9639 xref: GAID:402 xref: HAO:0000066 @@ -163977,16 +163451,14 @@ xref: ZFA:0001486 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue -intersection_of: composed_primarily_of CL:0000066 ! epithelial cell +intersection_of: RO:0002473 CL:0000066 ! composed primarily of epithelial cell union_of: UBERON:0000486 ! multilaminar epithelium union_of: UBERON:0000490 ! unilaminar epithelium -relationship: composed_primarily_of CL:0000066 ! epithelial cell relationship: has_part GO:0005911 ! cell-cell junction relationship: has_part UBERON:0005769 ! basement membrane of epithelium -relationship: only_in_taxon NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! Metazoa -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI -property_value: UBPROP:0000003 "The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000387", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.59", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "epithelial" xsd:string +relationship: RO:0002160 NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! only in taxon Metazoa +relationship: RO:0002473 CL:0000066 ! composed primarily of epithelial cell +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI [Term] id: UBERON:0000484 @@ -164012,8 +163484,8 @@ xref: XAO:0004009 xref: ZFA:0001497 is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0010077 ! cuboidal epithelium -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/d0/Gray1133.png" xsd:anyURI -property_value: editor_note "needs to be synchronized with CL - there is no distinct cuboidal cell in CL" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d0/Gray1133.png" xsd:anyURI +property_value: IAO:0000116 "needs to be synchronized with CL - there is no distinct cuboidal cell in CL" xsd:string [Term] id: UBERON:0000485 @@ -164032,7 +163504,6 @@ xref: AEO:0000068 xref: BILA:0000068 xref: CARO:0000068 xref: EHDAA2_RETIRED:0003068 -xref: FBbt:00007027 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45567 xref: HAO:0000068 xref: NCIT:C33552 @@ -164044,7 +163515,7 @@ xref: XAO:0004008 xref: ZFA:0001496 is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0012274 ! columnar epithelium -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray1059.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray1059.png" xsd:anyURI [Term] id: UBERON:0000486 @@ -164071,7 +163542,6 @@ xref: Wikipedia:Stratified_epithelium xref: XAO:0004006 xref: ZFA:0001494 is_a: UBERON:0000483 ! epithelium -property_value: UBPROP:0000001 "Epithelium that consists of more than one layer of epithelial cells.[CARO]" xsd:string {date_retrieved="2012-06-20", external_class="CARO:0000069", ontology="CARO", source="FMA:45562", source="http://orcid.org/0000-0001-9114-8737"} [Term] id: UBERON:0000487 @@ -164100,8 +163570,7 @@ is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0006914 ! squamous epithelium intersection_of: UBERON:0000490 ! unilaminar epithelium intersection_of: has_part CL:0000076 ! squamous epithelial cell -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Unilaminar epithelium that consists of a single layer of squamous cells.[CARO]" xsd:string {date_retrieved="2012-06-20", external_class="CARO:0000070", ontology="CARO", source="FMA:45565", source="http://orcid.org/0000-0001-9114-8737"} +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI [Term] id: UBERON:0000488 @@ -164148,7 +163617,6 @@ is_a: UBERON:0003103 ! compound organ intersection_of: UBERON:0003103 ! compound organ intersection_of: has_part UBERON:0002553 ! anatomical cavity relationship: has_part UBERON:0002553 ! anatomical cavity -property_value: IAO:0000232 "this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future" xsd:string [Term] id: UBERON:0000490 @@ -164173,8 +163641,7 @@ xref: UMLS:C0682574 {source="ncithesaurus:Simple_Epithelium"} xref: XAO:0004007 xref: ZFA:0001495 is_a: UBERON:0000483 ! epithelium -property_value: editor_note "consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable" xsd:string -property_value: UBPROP:0000001 "Epithelium that consists of a single layer of epithelial cells.[CARO]" xsd:string {date_retrieved="2012-06-20", external_class="CARO:0000073", ontology="CARO", source="FMA:45561", source="http://orcid.org/0000-0001-9114-8737"} +property_value: IAO:0000116 "consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable" xsd:string [Term] id: UBERON:0000912 @@ -164193,10 +163660,8 @@ xref: Wikipedia:Mucus is_a: UBERON:0000456 ! secretion of exocrine gland is_a: UBERON:0006314 ! bodily fluid relationship: has_part CHEBI:37395 -relationship: has_quality PATO:0000998 ! viscous relationship: produced_by UBERON:0000344 ! mucosa -property_value: UBPROP:0000007 "mucoid" xsd:string -property_value: UBPROP:0000007 "mucous" xsd:string +relationship: RO:0000086 PATO:0000998 ! has quality viscous [Term] id: UBERON:0000913 @@ -164211,10 +163676,9 @@ xref: FMA:9673 xref: NCIT:C120839 xref: Wikipedia:Interstitial_fluid is_a: UBERON:0000463 ! organism substance -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000479 ! tissue -relationship: surrounds CL:0000000 ! cell -property_value: RO:0002171 UBERON:0001969 +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002221 CL:0000000 ! surrounds cell [Term] id: UBERON:0000915 @@ -164234,12 +163698,8 @@ xref: Wikipedia:Thorax is_a: UBERON:0009569 {source="FMA"} ! subdivision of trunk is_a: UBERON:0011676 ! subdivision of organism along main body axis intersection_of: UBERON:0011676 ! subdivision of organism along main body axis -intersection_of: has_skeleton UBERON:0014477 ! thoracic skeleton -relationship: has_skeleton UBERON:0014477 ! thoracic skeleton -property_value: IAO:0000232 "note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest" xsd:string -property_value: RO:0002171 UBERON:0000026 -property_value: RO:0002171 UBERON:0000033 -property_value: RO:0002171 UBERON:0002417 +intersection_of: RO:0002551 UBERON:0014477 ! has skeleton thoracic skeleton +relationship: RO:0002551 UBERON:0014477 ! has skeleton thoracic skeleton [Term] id: UBERON:0000916 @@ -164269,11 +163729,9 @@ xref: MIAA:0000298 xref: SCTID:302553009 xref: Wikipedia:Abdomen is_a: UBERON:0009569 ! subdivision of trunk -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0002417 {source="MA"} ! abdominal segment of trunk -property_value: editor_note "Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class" xsd:string -property_value: UBPROP:0000007 "abdominal" xsd:string -property_value: UBPROP:0000007 "celiac" xsd:string +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +property_value: IAO:0000116 "Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class" xsd:string [Term] id: UBERON:0000922 @@ -164298,11 +163756,9 @@ xref: EHDAA2:0000002 xref: EHDAA2_RETIRED:0003236 xref: EHDAA:38 xref: EMAPA:16039 -xref: FBbt:00000052 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69068 xref: GAID:963 xref: http://neurolex.org/wiki/Category\:Embryonic_organism -xref: IDOMAL:0000646 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: MAT:0000226 xref: MESH:D004622 xref: MIAA:0000019 @@ -164316,14 +163772,12 @@ xref: XAO:0000113 xref: ZFA:0000103 is_a: UBERON:0000468 ! multicellular organism intersection_of: UBERON:0000468 ! multicellular organism -intersection_of: existence_ends_with UBERON:0000068 ! embryo stage -intersection_of: existence_starts_with UBERON:0000068 ! embryo stage -relationship: existence_ends_with UBERON:0000068 ! embryo stage -relationship: existence_starts_with UBERON:0000068 ! embryo stage -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" xsd:anyURI +intersection_of: RO:0002489 UBERON:0000068 ! existence starts with embryo stage +intersection_of: RO:0002493 UBERON:0000068 ! existence ends with embryo stage +relationship: RO:0002489 UBERON:0000068 ! existence starts with embryo stage +relationship: RO:0002493 UBERON:0000068 ! existence ends with embryo stage +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/503" xsd:anyURI -property_value: UBPROP:0000007 "embryonic" xsd:string -property_value: UBPROP:0000012 "Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo" xsd:string {external_ontology="ZFA"} [Term] id: UBERON:0000923 @@ -164342,7 +163796,6 @@ xref: AAO:0000480 xref: BILA:0000035 xref: BTO:0000556 xref: EMAPA:36033 -xref: FBbt:00000110 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69069 xref: GAID:1303 xref: MESH:D005855 @@ -164356,8 +163809,7 @@ xref: Wikipedia:Germ_layer xref: XAO:0003011 xref: ZFA:0001122 is_a: UBERON:0010316 ! germ layer / neural crest -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001223", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0000924 @@ -164377,7 +163829,6 @@ xref: EFO:0000414 xref: EHDAA2:0000428 xref: EMAPA:16069 xref: EV:0100003 -xref: FBbt:00000111 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69070 xref: GAID:1304 xref: MAT:0000155 @@ -164394,11 +163845,8 @@ xref: XAO:0000001 xref: ZFA:0000016 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000221 ! ectodermal cell -relationship: immediate_transformation_of UBERON:0006601 {source="Bgee:AN"} ! presumptive ectoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png" xsd:anyURI -property_value: UBPROP:0000001 "Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000137", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000153", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "ectodermal" xsd:string +relationship: RO:0002495 UBERON:0006601 {source="Bgee:AN"} ! immediate transformation of presumptive ectoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png" xsd:anyURI [Term] id: UBERON:0000925 @@ -164418,7 +163866,6 @@ xref: EFO:0002545 xref: EHDAA2:0000436 xref: EMAPA:16062 xref: EV:0100005 -xref: FBbt:00000125 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69071 xref: GAID:1305 xref: MAT:0000175 @@ -164434,11 +163881,9 @@ xref: XAO:0000090 xref: ZFA:0000017 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000223 ! endodermal cell -relationship: immediate_transformation_of UBERON:0006595 {source="Bgee:AN"} ! presumptive endoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png" xsd:anyURI -property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000154", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "endodermal" xsd:string +relationship: RO:0002495 UBERON:0006595 {source="Bgee:AN"} ! immediate transformation of presumptive endoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png" xsd:anyURI [Term] id: UBERON:0000926 @@ -164464,7 +163909,6 @@ xref: EHDAA:160 xref: EHDAA:183 xref: EMAPA:16083 xref: EV:0100006 -xref: FBbt:00000126 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69072 xref: GAID:522 xref: MAT:0000174 @@ -164478,15 +163922,11 @@ xref: VHOG:0000152 xref: Wikipedia:Mesoderm xref: XAO:0000050 xref: ZFA:0000041 -is_a: UBERON:0000923 {notes="sometimes not considered primary"} ! germ layer +is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000222 ! mesodermal cell -relationship: immediate_transformation_of UBERON:0006603 {source="Bgee:AN"} ! presumptive mesoderm -relationship: never_in_taxon NCBITaxon:6040 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" xsd:anyURI -property_value: UBPROP:0000001 "Primary germ layer that is the middle of the embryonic germ layers.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000304", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000152", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "mesodermal" xsd:string -property_value: UBPROP:0000008 "sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates" xsd:string {source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} +relationship: RO:0002495 UBERON:0006603 {source="Bgee:AN"} ! immediate transformation of presumptive mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" xsd:anyURI +property_value: RO:0002161 NCBITaxon:6040 [Term] id: UBERON:0000930 @@ -164508,7 +163948,6 @@ synonym: "stomodeal-hypophyseal primordium" BROAD [XAO:0000269] xref: BTO:0004224 xref: EHDAA2:0001929 xref: EMAPA:16263 -xref: FBbt:00000439 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:295846 xref: NCIT:C34306 xref: TAO:0001290 @@ -164518,15 +163957,11 @@ xref: Wikipedia:Stomodeum xref: XAO:0000269 xref: ZFA:0001290 is_a: UBERON:0013522 ! subdivision of tube -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000924 ! ectoderm relationship: part_of UBERON:0035804 ! future mouth -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI -property_value: editor_note "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" xsd:string -property_value: UBPROP:0000001 "Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001290", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx" xsd:string {source="MP:0012522", taxon="NCBITaxon:40674"} -property_value: UBPROP:0000007 "stomodeal" xsd:string -property_value: UBPROP:0000008 "This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity." xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI +property_value: IAO:0000116 "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" xsd:string [Term] id: UBERON:0000931 @@ -164542,7 +163977,6 @@ synonym: "proctodaeum" EXACT [] xref: AAO:0011087 xref: EHDAA2:0000121 xref: EMAPA:25038 -xref: FBbt:00000123 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: NCIT:C34278 xref: TAO:0000066 xref: UMLS:C0231054 {source="ncithesaurus:Proctodeum"} @@ -164551,16 +163985,13 @@ xref: Wikipedia:Proctodeum xref: XAO:0001019 xref: ZFA:0000066 is_a: UBERON:0016566 {source="EHDAA2"} ! pit -relationship: develops_from UBERON:0000924 ! ectoderm -relationship: has_potential_to_develop_into UBERON:0001353 ! anal region -relationship: located_in UBERON:0012469 {source="EHDAA2"} ! external anal region -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0007026 ! presumptive gut -property_value: editor_note "removed WBbt:0006795 'proctodeum' - junction between the alimentary and genital tracts in the male." xsd:string +relationship: RO:0001025 UBERON:0012469 {source="EHDAA2"} ! located in external anal region +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002202 UBERON:0000924 ! develops from ectoderm +relationship: RO:0002387 UBERON:0001353 ! has potential to develop into anal region +property_value: IAO:0000116 "removed WBbt:0006795 'proctodeum' - junction between the alimentary and genital tracts in the male." xsd:string property_value: seeAlso "https://github.com/obophenotype/uberon/issues/685" xsd:anyURI -property_value: UBPROP:0000001 "An inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000066", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011087", ontology="AAO", source="ZFA:0000066"} -property_value: UBPROP:0000007 "proctodeal" xsd:string [Term] id: UBERON:0000933 @@ -164582,7 +164013,6 @@ synonym: "pharynx muscle organ" EXACT [OBOL:automatic] synonym: "tunica muscularis pharyngis" RELATED OMO:0003011 [Wikipedia:Pharyngeal_muscles] xref: BTO:0001048 xref: EFO:0003504 -xref: EMAPA:18963 xref: FMA:46619 xref: GAID:154 xref: MA:0001797 @@ -164596,11 +164026,9 @@ xref: ZFA:0000172 is_a: UBERON:0001630 ! muscle organ intersection_of: UBERON:0001630 ! muscle organ intersection_of: part_of UBERON:0004467 ! musculature of pharynx -relationship: contributes_to_morphology_of UBERON:0001015 ! musculature relationship: part_of UBERON:0004467 ! musculature of pharynx -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/35/Gray1030.png" xsd:anyURI -property_value: UBPROP:0000001 "A pharyngeal muscle is any muscle that forms part of the pharynx[GO]." xsd:string {date_retrieved="2012-06-30", external_class="GO:0043282", notes="does not quite work for some muscles such as stylopharyngeus", ontology="GO", source="GOC:go_curators"} -property_value: UBPROP:0000202 FMA:67169 +relationship: RO:0002433 UBERON:0001015 ! contributes to morphology of musculature +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/35/Gray1030.png" xsd:anyURI [Term] id: UBERON:0000939 @@ -164611,14 +164039,12 @@ comment: Though inaginal discs are sometimes described as “epithelial sacs”, subset: uberon_slim synonym: "imaginal disk" RELATED [] xref: BTO:0004658 -xref: FBbt:00001761 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: MAT:0000064 -xref: MESH:D060227 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: MIAA:0000064 xref: Wikipedia:Imaginal_disc is_a: UBERON:0000481 {source="FBbt text definition"} ! multi-tissue structure -relationship: only_in_taxon NCBITaxon:50557 {source="Wikipedia"} ! Insecta relationship: part_of UBERON:0002548 ! larva +relationship: RO:0002160 NCBITaxon:50557 {source="Wikipedia"} ! only in taxon Insecta [Term] id: UBERON:0000941 @@ -164668,22 +164094,17 @@ xref: VHOG:0000543 xref: Wikipedia:Optic_nerve xref: XAO:0000188 xref: ZFA:0000435 -is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0011215 ! central nervous system cell part cluster is_a: UBERON:0034713 ! cranial neuron projection bundle intersection_of: UBERON:0034713 ! cranial neuron projection bundle intersection_of: extends_fibers_into UBERON:0000959 ! optic chiasma -intersection_of: innervates UBERON:0000966 ! retina -relationship: develops_from UBERON:0003902 {source="EHDAA2"} ! retinal neural layer +intersection_of: RO:0002134 UBERON:0000966 ! innervates retina relationship: extends_fibers_into UBERON:0000959 ! optic chiasma relationship: extends_fibers_into UBERON:0003098 ! optic stalk -relationship: innervates UBERON:0000966 ! retina relationship: part_of UBERON:0002104 ! visual system -property_value: editor_note "Do not classify under 'cranial nerve', as this is not a true nerve - should be classified as evaginated sensory afferent[ISBN:0471888893]" xsd:string -property_value: UBPROP:0000001 "A collection of nerve cells that project visual information from the eyes to the brain. (Source: BioGlossary, www.Biology-Text.com)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000435", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Fibrous, somatic sensory element covered by a fibrous connective-tissue sheath and is continuous with the layer of nerve cells on the inner surface of the eye.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010345", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup (reference 1); The (optic) stalk persists as the optic nerve (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000543", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429, http://medical-dictionary.thefreedictionary.com/optic+stalk", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "(relaion to eye): MA, XAO, AAO and BTO consider this part of the eye. This is in contrast to GO, FMA, EHDAA2 (FMA has a class 'intra-ocular part of optic nerve' which represents the region of overlap). Relation to brain: part of diencephalon in EHDAA2, ZFA. In NIF, has the optic nerve root as part, which is a feature part of the diencphalon" xsd:string {external_ontology="MA"} +relationship: RO:0002134 UBERON:0000966 ! innervates retina +relationship: RO:0002202 UBERON:0003902 {source="EHDAA2"} ! develops from retinal neural layer +property_value: IAO:0000116 "Do not classify under 'cranial nerve', as this is not a true nerve - should be classified as evaginated sensory afferent[ISBN:0471888893]" xsd:string [Term] id: UBERON:0000945 @@ -164727,19 +164148,16 @@ xref: Wikipedia:Stomach xref: XAO:0000128 is_a: UBERON:0004921 {source="cjm"} ! subdivision of digestive tract is_a: UBERON:0010039 {source="cjm"} ! food storage organ -relationship: capable_of GO:0001696 {evidence="ISBN:0486692132"} ! gastric acid secretion -relationship: contributes_to_morphology_of UBERON:0001007 ! digestive system -relationship: never_in_taxon NCBITaxon:7864 {source="Wikipedia"} -relationship: never_in_taxon NCBITaxon:7878 {source="Wikipedia"} -relationship: never_in_taxon NCBITaxon:7955 {source="ZFA"} -relationship: never_in_taxon NCBITaxon:9259 {source="Wikipedia"} -relationship: only_in_taxon NCBITaxon:7776 {notes="absent in lampreys and hagfishes", source="ISBN:0073040584"} ! Gnathostomata +relationship: capable_of GO:0001696 ! gastric acid secretion relationship: part_of UBERON:0001041 ! foregut -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/e/e0/Stomach_diagram.svg" xsd:anyURI -property_value: UBPROP:0000001 "Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000579", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "It appears that the stomach has an ancient origin. The stomach first appears in the fish lineage. The prevertebrate chordates do not have a true stomach, whereas the cartilaginous and bony fish do. Although most fish do have a true stomach, some fish species appear to have lost the stomach secondarily. The remaining vertebrate lineages do have a true stomach (at least in the adult animal), although there is great variation in the size and shape of the stomach.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000408", ontology="VHOG", source="DOI:10.1046/j.1525-142x.2000.00076.x Smith DM, Grasty RC, Theodosiou NA, Tabin CJ, Nascone-Yoder NM, Evolutionary relationships between the amphibian, avian, and mammalian stomachs. Evolution and development (2000)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "We restrict this to the vertebrate specific structure - see the grouping class 'food storage organ' for analogous structures in other species. Teleosts: Zebrafish is functionally stomach-less, but may retain ontogenic footprint. Although the precise shape and size of the stomach varies widely among different vertebrates, the relative positions of the oesophageal and duodenal openings remain relatively constant. As a result, the organ always curves somewhat to the left before curving back to meet the pyloric sphincter. However, lampreys, hagfishes, chimaeras, lungfishes, and some teleost fish have no stomach at all, with the oesophagus opening directly into the intestine. The gastric lining is usually divided into two regions, an anterior portion lined by fundic glands, and a posterior with pyloric glands. Cardiac glands are unique to mammals, and even then are absent in a number of species. The distributions of these glands vary between species, and do not always correspond with the same regions as in man. Furthermore, in many non-human mammals, a portion of the stomach anterior to the cardiac glands is lined with epithelium essentially identical to that of the oesophagus. Ruminants, in particular, have a complex stomach, the first three chambers of which are all lined with oesophageal mucosa" xsd:string {source="WP:Stomach#In_other_animals"} +relationship: RO:0002160 NCBITaxon:7776 ! only in taxon Gnathostomata +relationship: RO:0002433 UBERON:0001007 ! contributes to morphology of digestive system +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/e/e0/Stomach_diagram.svg" xsd:anyURI +property_value: RO:0002161 NCBITaxon:7864 {source="Wikipedia"} +property_value: RO:0002161 NCBITaxon:7878 {source="Wikipedia"} +property_value: RO:0002161 NCBITaxon:7955 {source="ZFA"} +property_value: RO:0002161 NCBITaxon:9259 {source="Wikipedia"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000946 @@ -164773,13 +164191,11 @@ xref: Wikipedia:Cardiac_valve xref: XAO:0004126 xref: ZFA:0005065 is_a: UBERON:0003978 ! valve +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010313 ! neural crest-derived structure -relationship: develops_from UBERON:0002062 {source="PMID:15797462"} ! endocardial cushion relationship: part_of UBERON:0000948 ! heart -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000001 "One of the four structures within the heart that prevent backflow of blood by opening and closing with each heartbeat. The valves include two semilunar valves, the aortic and pulmonary; the mitral or bicuspid valve; and the tricuspid valve. The valves permit blood flow in only one direction. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000818", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/heart+valve"} -property_value: UBPROP:0000003 "Extensive conservation of valve developmental mechanisms also has been observed among vertebrate species including chicken, mouse, and human.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000818", ontology="VHOG", source="DOI:10.1161/CIRCRESAHA.109.201566 Combs MD, Yutzey KE, Heart valve development. Circulatory Research (2009)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000013 "Rector et al: One might be tempted to define 'heart valve' equivalently to 'valve in the heart', and 'valve' as a 'structure which functions as a valve'. But this combination results in the 'foramen ovale' being classified as a kind of 'heart valve', since it is undoubtedly located in the heart and functions as a valve" xsd:string +relationship: RO:0002202 UBERON:0002062 {source="PMID:15797462"} ! develops from endocardial cushion +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000947 @@ -164817,17 +164233,13 @@ xref: XAO:0003010 is_a: UBERON:0003509 {source="MA"} ! arterial blood vessel is_a: UBERON:0003519 ! thoracic cavity blood vessel is_a: UBERON:0013768 ! great vessel of heart -relationship: connected_to UBERON:0002084 ! heart left ventricle relationship: part_of UBERON:0010191 {source="EHDAA2"} ! aortic system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/9/91/Aorta_scheme.jpg" xsd:anyURI -property_value: editor_note "This class is currently a mixed bag, encompassing (1) the entirety of the mammalian aorta together with (2) the developmental and phylogenetic homologs of its segments: the ventral aorta and dorsal aortae." xsd:string {source="WP"} -property_value: UBPROP:0000001 "The main artery of the circulatory system which carries oxygenated blood from the heart to all the arteries of the body except those of the lungs.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010213", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001523", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "aortic" xsd:string -property_value: UBPROP:0000008 "All amniotes have a broadly similar arrangement to that of humans, albeit with a number of individual variations. In fish, however, there are two separate vessels referred to as aortas. The ventral aorta carries de-oxygenated blood from the heart to the gills; part of this vessel forms the ascending aorta in tetrapods (the remainder forms the pulmonary artery). A second, dorsal aorta carries oxygenated blood from the gills to the rest of the body, and is homologous with the descending aorta of tetrapods. The two aortas are connected by a number of vessels, one passing through each of the gills. Amphibians also retain the fifth connecting vessel, so that the aorta has two parallel arches" xsd:string +relationship: RO:0002170 UBERON:0002084 ! connected to heart left ventricle +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/9/91/Aorta_scheme.jpg" xsd:anyURI +property_value: IAO:0000116 "This class is currently a mixed bag, encompassing (1) the entirety of the mammalian aorta together with (2) the developmental and phylogenetic homologs of its segments: the ventral aorta and dorsal aortae." xsd:string {source="WP"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000948 @@ -164876,22 +164288,17 @@ is_a: UBERON:0007100 ! primary circulatory organ is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0007100 ! primary circulatory organ intersection_of: has_part UBERON:0004151 ! cardiac chamber -relationship: contributes_to_morphology_of UBERON:0004535 ! cardiovascular system -relationship: develops_from UBERON:0004141 ! heart tube relationship: has_part UBERON:0004151 ! cardiac chamber -relationship: never_in_taxon NCBITaxon:6239 -relationship: never_in_taxon NCBITaxon:7227 -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0015410 {source="MA"} ! heart plus pericardium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI -property_value: UBPROP:0000001 "Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000114", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010210", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000002 "relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010210", ontology="AAO"} -property_value: UBPROP:0000003 "As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000276", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "cardiac" xsd:string +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002202 UBERON:0004141 ! develops from heart tube +relationship: RO:0002433 UBERON:0004535 ! contributes to morphology of cardiovascular system +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI +property_value: RO:0002161 NCBITaxon:6239 +property_value: RO:0002161 NCBITaxon:7227 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000949 @@ -164911,7 +164318,6 @@ xref: EFO:0002969 xref: EHDAA2:0002224 xref: EMAPA:35306 xref: EV:0100128 -xref: FBbt:00005068 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9668 xref: GAID:439 xref: MA:0000012 @@ -164941,12 +164347,9 @@ disjoint_from: UBERON:0002416 ! integumental system disjoint_from: UBERON:0002423 ! hepatobiliary system disjoint_from: UBERON:0004456 ! entire sense organ system disjoint_from: UBERON:8450002 ! excretory system -relationship: composed_primarily_of UBERON:0002368 ! endocrine gland -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: UBPROP:0000001 "Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010279", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000098", ontology="VHOG", source="DOI:10.1073/pnas.0812138106 Markov GV, Tavares R, Dauphin-Villemant C, Demeneix BA, Baker ME, Laudet V, Independent elaboration of steroid hormone signaling pathways in metazoans. PNAS (2009)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "endocrine" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002473 UBERON:0002368 ! composed primarily of endocrine gland +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage [Term] id: UBERON:0000951 @@ -164959,11 +164362,11 @@ xref: SCTID:244872002 is_a: UBERON:0001630 ! muscle organ is_a: UBERON:0005174 ! dorsal region element intersection_of: UBERON:0001630 ! muscle organ -intersection_of: has_muscle_insertion UBERON:0001076 ! neural spine -intersection_of: has_muscle_origin UBERON:0001077 ! transverse process of vertebra intersection_of: part_of UBERON:0001137 ! dorsum -relationship: has_muscle_insertion UBERON:0001076 ! neural spine -relationship: has_muscle_origin UBERON:0001077 ! transverse process of vertebra +intersection_of: RO:0002372 UBERON:0001077 ! has muscle origin transverse process of vertebra +intersection_of: RO:0002373 UBERON:0001076 ! has muscle insertion neural spine +relationship: RO:0002372 UBERON:0001077 ! has muscle origin transverse process of vertebra +relationship: RO:0002373 UBERON:0001076 ! has muscle insertion neural spine [Term] id: UBERON:0000955 @@ -164997,7 +164400,6 @@ xref: EHDAA:2641 xref: EHDAA:6485 xref: EMAPA:16894 xref: EV:0100164 -xref: FBbt:00005095 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:50801 xref: GAID:571 xref: galen:Brain @@ -165021,22 +164423,18 @@ xref: XAO:0000010 xref: ZFA:0000008 is_a: UBERON:0000062 {source="GO"} ! organ is_a: UBERON:0004121 ! ectoderm-derived structure +relationship: BSPO:0000123 UBERON:0000468 ! multicellular organism relationship: capable_of GO:0050890 {gci_relation="part_of", gci_filler="NCBITaxon:9606"} ! cognition -relationship: composed_primarily_of CL:0002319 ! neural cell -relationship: contributes_to_morphology_of UBERON:0001016 ! nervous system -relationship: develops_from UBERON:0001049 {gci_relation="part_of", gci_filler="NCBITaxon:7711"} ! neural tube -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: immediate_transformation_of UBERON:0006238 {source="Bgee:AN"} ! future brain -relationship: in_anterior_side_of UBERON:0000468 ! multicellular organism relationship: part_of UBERON:0001017 {source="FMA"} ! central nervous system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI -property_value: editor_note "requires review for applicability to invertebrate structures, e.g. synganglion" xsd:string -property_value: UBPROP:0000001 "Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000008", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010478", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO)" xsd:string {source="http://neurolex.org/wiki/Cumbo_terms"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000157", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0001049 {gci_relation="part_of", gci_filler="NCBITaxon:7711"} ! develops from neural tube +relationship: RO:0002433 UBERON:0001016 ! contributes to morphology of nervous system +relationship: RO:0002473 CL:0002319 ! composed primarily of neural cell +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +relationship: RO:0002495 UBERON:0006238 {source="Bgee:AN"} ! immediate transformation of future brain +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI +property_value: IAO:0000116 "requires review for applicability to invertebrate structures, e.g. synganglion" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000956 @@ -165086,19 +164484,15 @@ xref: Wikipedia:Cerebral_cortex is_a: UBERON:0011215 ! central nervous system cell part cluster is_a: UBERON:0016548 {source="FMA"} ! central nervous system gray matter layer relationship: capable_of_part_of GO:0007613 {source="Wikipedia"} ! memory -relationship: contributes_to_morphology_of UBERON:0001893 ! telencephalon -relationship: has_developmental_contribution_from UBERON:0004035 ! cortical subplate -relationship: has_developmental_contribution_from UBERON:0005343 ! cortical plate relationship: part_of UBERON:0000203 {source="GO", source="ISBN:0471888893"} ! pallium relationship: part_of UBERON:0005401 {source="FMA", source="MA"} ! cerebral hemisphere gray matter -relationship: present_in_taxon NCBITaxon:117569 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/7b/Cerebral_Cortex_location.jpg" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/9a/Brainmaps-macaque-hippocampus.jpg" xsd:anyURI -property_value: IAO:0000232 "We follow NIFSTD in defining cerebral cortex and including both neocortex and hippocampal formation (DG+hippocampus)." xsd:string -property_value: UBPROP:0000001 "The cerebral cortex is a structure within the brain that plays a key role in memory, attention, perceptual awareness, thought, language, and consciousness. It constitutes the outermost layer of the cerebrum. In preserved brains, it has a grey color, hence the name 'grey matter'. Grey matter is formed by neurons and their unmyelinated fibers, whereas the white matter below the grey matter of the cortex is formed predominantly by myelinated axons interconnecting different regions of the central nervous system. The human cerebral cortex is 2-4 mm (0.08-0.16 inches) thick. The surface of the cerebral cortex is folded in large mammals, such that more than two-thirds of the cortical surface is buried in the grooves, called 'sulci. ' The phylogenetically most recent part of the cerebral cortex, the neocortex, also called isocortex, is differentiated into six horizontal layers; the more ancient part of the cerebral cortex, the hippocampus (also called archicortex), has at most three cellular layers, and is divided into subfields. Relative variations in thickness or cell type (among other parameters) allow us to distinguish between different neocortical architectonic fields. The geometry of at least some of these fields seems to be related to the anatomy of the cortical folds, and, for example, layers in the upper part of the cortical ridges seem to be more clearly differentiated than in its deeper parts. [WP,unvetted][Wikipedia:Cerebral_cortex]." xsd:string {source="Wikipedia:Cerebral_cortex"} -property_value: UBPROP:0000003 "Migration of neurons from the basal or striatal portions of the anterior part of the neural tube occurs to varying degrees in different vertebrate classes, but a true cerebral cortex is generally acknowledged to have made its first appearance in reptiles. The definition can be unambiguous, since 'cortex' simply implies the existence of a surface neuronal layer with an overlying 'zonal lamina' or 'molecular' layer containing dendrites and axons, which is separated from the underlying basal 'matrix' by white matter. Although reptilian cerebral cortex does indeed fulfill these conditions in certain locations, the separation from striatal structures is often indistinct, so that it may even be argued that some primitive dipnoans possess a pallium or cortex. Nevertheless, an extensive laminated layer separated by underlying white matter is well represented only in reptiles and mammals.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000722", ontology="VHOG", source="DOI:10.1111/j.1749-6632.1969.tb20437.x Kruger L, Experimental analyses of the reptilian nervous system. Annals of the New York Academy of Sciences (1969)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "hagfishes have independently evolved a highly laminated cerebral cortex, comparable in many ways to the cerebral cortex of mammals [http://icb.oxfordjournals.org/content/42/4/743]" xsd:string +relationship: RO:0002254 UBERON:0004035 ! has developmental contribution from cortical subplate +relationship: RO:0002254 UBERON:0005343 ! has developmental contribution from cortical plate +relationship: RO:0002433 UBERON:0001893 ! contributes to morphology of telencephalon +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7b/Cerebral_Cortex_location.jpg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/9a/Brainmaps-macaque-hippocampus.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:117569 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000957 @@ -165112,11 +164506,10 @@ synonym: "laminar tissue" EXACT [] xref: Wikipedia:Lamina_of_the_vertebral_arch is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue -intersection_of: has_quality PATO:0002124 ! laminar -relationship: has_quality PATO:0002124 ! laminar -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/80/Laminaarcusvertebrae.png" xsd:anyURI -property_value: editor_note "TODO - merge with cell layer?" xsd:string -property_value: UBPROP:0000007 "laminar" xsd:string +intersection_of: RO:0000086 PATO:0002124 ! has quality laminar +relationship: RO:0000086 PATO:0002124 ! has quality laminar +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/80/Laminaarcusvertebrae.png" xsd:anyURI +property_value: IAO:0000116 "TODO - merge with cell layer?" xsd:string [Term] id: UBERON:0000958 @@ -165128,10 +164521,8 @@ synonym: "medulla" EXACT [FMA:61108] xref: FMA:61108 xref: galen:Medulla is_a: UBERON:0000471 ! compound organ component -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: surrounded_by UBERON:0001851 ! cortex -property_value: IAO:0000232 "this class is used in a very general sense" xsd:string -property_value: UBPROP:0000007 "medullary" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002219 UBERON:0001851 ! surrounded by cortex [Term] id: UBERON:0000959 @@ -165181,9 +164572,7 @@ intersection_of: extends_fibers_into UBERON:0001908 ! optic tract intersection_of: part_of UBERON:0001894 ! diencephalon relationship: extends_fibers_into UBERON:0000941 ! cranial nerve II relationship: extends_fibers_into UBERON:0001908 ! optic tract -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b3/1543%2CVisalius%27OpticChiasma.jpg" xsd:anyURI -property_value: UBPROP:0000001 "The point at which fibers of the optic nerves cross.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010622", ontology="AAO", source="AAO:DSM"} -property_value: UBPROP:0000003 "The chiasm has been studied in great detail in some animals, while in others relatively little or nothing is known. Although there are some gross architectural features that are conserved within some animals, such as birds and fish, the general picture is one of diversity. This review will attempt to consider the key features of such diversity of chiasmatic organisation in vertebrates and the mechanisms that sculpt them from the limited literature that is available. However, as so much research has been undertaken on the structure and development of the chiasm in laboratory animals, any review must consider the information that has been gleaned from them and hope that future studies will determine whether the features revealed in these animals, and the underlying mechanisms that generate them, have a common vertebrate plan.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000190", ontology="VHOG", source="DOI:10.1016/j.preteyeres.2005.04.005 Jeffery G, Erskine L, Variations in the architecture and development of the vertebrate optic chiasm. Progress in retinal and eye research (2005)", source="http://bgee.unil.ch/"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b3/1543%2CVisalius%27OpticChiasma.jpg" xsd:anyURI [Term] id: UBERON:0000961 @@ -165214,8 +164603,8 @@ intersection_of: UBERON:0001807 ! paravertebral ganglion intersection_of: part_of UBERON:0004863 ! thoracic sympathetic nerve trunk relationship: extends_fibers_into UBERON:0018679 ! thoracic splanchnic nerve relationship: part_of UBERON:0004863 ! thoracic sympathetic nerve trunk -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/3e/Gray849.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3e/Gray849.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000962 @@ -165240,20 +164629,19 @@ is_a: UBERON:0001780 ! spinal nerve intersection_of: UBERON:0001780 ! spinal nerve intersection_of: extends_fibers_into UBERON:0002726 ! cervical spinal cord relationship: extends_fibers_into UBERON:0002726 ! cervical spinal cord -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray795.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray795.png" xsd:anyURI [Term] id: UBERON:0000963 name: head sensillum namespace: uberon -xref: FBbt:00004114 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: MAT:0000204 xref: MIAA:0000204 is_a: UBERON:0002536 ! arthropod sensillum intersection_of: UBERON:0002536 ! arthropod sensillum intersection_of: part_of UBERON:0000033 ! head relationship: part_of UBERON:0000033 ! head -property_value: editor_note "this term should be ceded to the arthropod anatomy ontology" xsd:string +property_value: IAO:0000116 "this term should be ceded to the arthropod anatomy ontology" xsd:string [Term] id: UBERON:0000964 @@ -165291,21 +164679,19 @@ xref: ZFA:0000640 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0010000 ! multicellular anatomical structure is_a: UBERON:0010313 ! neural crest-derived structure -relationship: continuous_with UBERON:0001773 ! sclera -relationship: contributes_to_morphology_of UBERON:0001801 ! anterior segment of eyeball -relationship: developmentally_induced_by UBERON:0005426 ! lens vesicle -relationship: develops_from UBERON:0004348 {evidence="definitional"} ! optic eminence -relationship: develops_from UBERON:0005427 ! corneal primordium relationship: has_part UBERON:0001772 ! corneal epithelium relationship: has_part UBERON:0004370 ! anterior limiting lamina of cornea -relationship: has_quality PATO:0000964 ! transparent relationship: part_of UBERON:0001801 {source="MA"} ! anterior segment of eyeball relationship: part_of UBERON:0010409 {source="MA"} ! ocular surface region relationship: part_of UBERON:0012430 {source="FMA-isa"} ! tunica fibrosa of eyeball -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI -property_value: UBPROP:0000007 "corneal" xsd:string -property_value: UBPROP:0000008 "Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals. In fish, and aquatic vertebrates in general, the cornea plays no role in focusing light, since it has virtually the same refractive index as water" xsd:string +relationship: RO:0000086 PATO:0000964 ! has quality transparent +relationship: RO:0002150 UBERON:0001773 ! continuous with sclera +relationship: RO:0002202 UBERON:0004348 ! develops from optic eminence +relationship: RO:0002202 UBERON:0005427 ! develops from corneal primordium +relationship: RO:0002256 UBERON:0005426 ! developmentally induced by lens vesicle +relationship: RO:0002433 UBERON:0001801 ! contributes to morphology of anterior segment of eyeball +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000965 @@ -165344,15 +164730,13 @@ xref: VHOG:0000169 xref: Wikipedia:Lens_(anatomy) xref: XAO:0000008 xref: ZFA:0000035 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005389 ! transparent eye structure -relationship: contributes_to_morphology_of UBERON:0001801 ! anterior segment of eyeball -relationship: developmentally_induced_by UBERON:0003902 ! retinal neural layer -relationship: develops_from UBERON:0005426 ! lens vesicle relationship: part_of UBERON:0001801 ! anterior segment of eyeball -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: RO:0002171 UBERON:0002049 -property_value: UBPROP:0000003 "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000169", ontology="VHOG", source="DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "This class excludes compound eye corneal lenses." xsd:string +relationship: RO:0002202 UBERON:0005426 ! develops from lens vesicle +relationship: RO:0002256 UBERON:0003902 ! developmentally induced by retinal neural layer +relationship: RO:0002433 UBERON:0001801 ! contributes to morphology of anterior segment of eyeball +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000966 @@ -165400,18 +164784,15 @@ xref: XAO:0000009 xref: ZFA:0000152 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005388 ! photoreceptor array -relationship: develops_from UBERON:0003072 {source="EHDAA2"} ! optic cup relationship: has_part CL:0000573 {source="FMA"} ! retinal cone cell relationship: has_part CL:0000604 {source="FMA"} ! retinal rod cell relationship: has_part CL:0000740 {source="FMA"} ! retinal ganglion cell -relationship: never_in_taxon NCBITaxon:6656 ! Arthropoda relationship: part_of UBERON:0001802 ! posterior segment of eyeball relationship: part_of UBERON:0019207 ! chorioretinal region -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png" xsd:anyURI -property_value: UBPROP:0000001 "The portion of the eye developing from the optic primordium and including the neural retina and the retinal pigment layer. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000152", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000229", ontology="VHOG", source="DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "retinal" xsd:string +relationship: RO:0002202 UBERON:0003072 {source="EHDAA2"} ! develops from optic cup +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png" xsd:anyURI +property_value: RO:0002161 NCBITaxon:6656 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000970 @@ -165431,7 +164812,6 @@ xref: BTO:0000439 xref: CALOHA:TS-0309 xref: EFO:0000827 xref: EV:0100336 -xref: FBbt:00005162 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: GAID:69 xref: MAT:0000140 xref: MESH:D005123 @@ -165442,11 +164822,7 @@ relationship: capable_of GO:0009584 ! detection of visible light relationship: has_part CL:0000149 {source="PMID:21062451"} ! visual pigment cell relationship: has_part CL:0000210 {source="PMID:21062451"} ! photoreceptor cell relationship: part_of UBERON:0002104 ! visual system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: IAO:0000232 "This class encompasses a variety of light-detecting structures from different phyla with no implication of homology, from the compound insect eye to the vertebrate camera-type eye (distinct classes are provided for each)" xsd:string -property_value: UBPROP:0000007 "ocular" xsd:string -property_value: UBPROP:0000007 "optic" xsd:string -property_value: UBPROP:0000010 "Note that whilst this is classified as an organ, it is in fact more of a unit composed of different structures: in Drosophila, it includes the interommatidial bristle as a part; we consider here the vertebrate eye to include the eyeball/eye proper as a part, with the eye having as parts (when present): eyelids, conjuctiva," xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000971 @@ -165457,7 +164833,6 @@ subset: uberon_slim synonym: "omatidia" RELATED OMO:0003004 [] synonym: "omatidium" EXACT [] xref: BTO:0001922 -xref: FBbt:00004510 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: HAO:0000666 xref: MAT:0000143 xref: MIAA:0000143 @@ -165465,7 +164840,6 @@ xref: Wikipedia:Ommatidium is_a: UBERON:0000970 {source="PMID:21062451"} ! eye is_a: UBERON:0002536 ! arthropod sensillum relationship: part_of UBERON:0000018 ! compound eye -property_value: UBPROP:0000007 "ommatidial" xsd:string [Term] id: UBERON:0000974 @@ -165498,10 +164872,7 @@ is_a: UBERON:0000475 ! organism subdivision relationship: anteriorly_connected_to UBERON:0000033 ! head relationship: part_of UBERON:0000153 ! anterior region of body relationship: posteriorly_connected_to UBERON:0002100 ! trunk -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/9/99/Female_neck.jpg" xsd:anyURI -property_value: IAO:0000232 "true necks are considered to be present when the pectoral girdle is separate from the skull - Tiktaalik is the earliest known fish to have a true neck." xsd:string -property_value: RO:0002174 NCBITaxon:32443 {source="ISBN:9780674021839"} -property_value: UBPROP:0000007 "cervical" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/9/99/Female_neck.jpg" xsd:anyURI [Term] id: UBERON:0000975 @@ -165531,24 +164902,17 @@ xref: VHOG:0000856 xref: Wikipedia:Sternum is_a: UBERON:0005181 ! thoracic segment organ is_a: UBERON:0010363 {source="ISBN:0073040584"} ! endochondral element -relationship: connected_to UBERON:0002228 ! rib -relationship: connected_to UBERON:0007831 ! pectoral girdle skeleton -relationship: connected_to UBERON:0008255 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! right clavicle -relationship: connected_to UBERON:0008256 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! left clavicle -relationship: contributes_to_morphology_of UBERON:0003252 ! thoracic rib cage -relationship: never_in_taxon NCBITaxon:8570 {source="Wikipedia"} -relationship: only_in_taxon NCBITaxon:32523 {source="ISBN:0073040584"} ! Tetrapoda relationship: part_of UBERON:0003252 {source="FMA"} ! thoracic rib cage -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/12/Illu_thoracic_cage.jpg" xsd:anyURI -property_value: editor_note "in EMAPA and EHDAA2 this is part of the skeleton of pectoral girdle; the classic def of pectoral girdle (see WP) excludes the rib cage and sternum" xsd:string -property_value: UBPROP:0000001 "Single element that constitutes the postzonal area of the pectoral girdle.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000765", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000002 "relationship loss: part_of postzonal element (AAO:0000938)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000765", ontology="AAO"} -property_value: UBPROP:0000003 "Fishes lack a sternum. (...) A sternum is absent in the first fossil tetrapods, but it is present in modern amphibians. (...) Thus, a sternum occurs in some modern amphibians, birds, mammals and archosaurs. However, its absence in the common ancestors to these groups means that it has arisen independently several times within the field of the midventral connective tissue.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000856", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.294", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "sternal" xsd:string -property_value: UBPROP:0000008 "in birds, either ratite (no keel or carina) or carinate (keel and carina present)" xsd:string -property_value: UBPROP:0000008 "It probably first evolved in early tetrapods as an extension of the pectoral girdle; it is not found in fish. In amphibians and reptiles it is typically a shield-shaped structure, often composed entirely of cartilage. It is absent in both turtles and snakes. In birds it is a relatively large bone and typically bears an enormous projecting keel to which the flight muscles are attached. Only in mammals does the sternum take on the elongated, segmented form seen in humans. In some mammals, such as opossums, the individual segments never fuse and remain separated by cartilagenous plates throughout life" xsd:string -property_value: UBPROP:0000011 "While its developmental origins are similar to the ribs (from the myospetum and septum of the trunk region), it is often associated with the pectoral skeleton, due to both function and physical connections (i.e. the coracoid of archosaurs). It may be a single element or a series of smaller structure (sternebrae). Based on Kardong 2012. [PHENOSCAPE:ad]." xsd:string {source="WP"} +relationship: RO:0002160 NCBITaxon:32523 {source="ISBN:0073040584"} ! only in taxon Tetrapoda +relationship: RO:0002170 UBERON:0002228 ! connected to rib +relationship: RO:0002170 UBERON:0007831 ! connected to pectoral girdle skeleton +relationship: RO:0002170 UBERON:0008255 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to right clavicle +relationship: RO:0002170 UBERON:0008256 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to left clavicle +relationship: RO:0002433 UBERON:0003252 ! contributes to morphology of thoracic rib cage +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/12/Illu_thoracic_cage.jpg" xsd:anyURI +property_value: IAO:0000116 "in EMAPA and EHDAA2 this is part of the skeleton of pectoral girdle; the classic def of pectoral girdle (see WP) excludes the rib cage and sternum" xsd:string +property_value: RO:0002161 NCBITaxon:8570 {source="Wikipedia"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000976 @@ -165584,15 +164948,12 @@ is_a: UBERON:0003607 ! forelimb long bone is_a: UBERON:0004250 ! upper arm bone is_a: UBERON:0015053 ! humerus endochondral element intersection_of: UBERON:0015053 ! humerus endochondral element -intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue -relationship: develops_from UBERON:0006245 {evidence="definitional"} ! humerus cartilage element +intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue relationship: overlaps UBERON:0001470 ! glenohumeral joint -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: proximally_connected_to UBERON:0007831 ! pectoral girdle skeleton -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/67/Illu_upper_extremity.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Paired, elongate, cylindrical bones of endochondral origin that extend from the pectoral girdle to the elbows.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000679", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000003 "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001158", ontology="VHOG", source="ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "humeral" xsd:string +relationship: RO:0002202 UBERON:0006245 ! develops from humerus cartilage element +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/67/Illu_upper_extremity.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000977 @@ -165608,7 +164969,6 @@ synonym: "wall of pleural sac" EXACT [] xref: BTO:0001791 xref: CALOHA:TS-2081 xref: EFO:0001980 -xref: EMAPA:16775 xref: EV:0100044 xref: FMA:9583 xref: GAID:360 @@ -165620,22 +164980,20 @@ xref: UMLS:C0032225 {source="ncithesaurus:Pleural_Tissue"} xref: VHOG:0000394 xref: Wikipedia:Pleura is_a: UBERON:0000042 ! serous membrane +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure intersection_of: UBERON:0000042 ! serous membrane intersection_of: has_part UBERON:0002400 ! parietal pleura intersection_of: has_part UBERON:0002401 ! visceral pleura intersection_of: part_of UBERON:0009778 ! pleural sac -relationship: contributes_to_morphology_of UBERON:0001004 ! respiratory system -relationship: develops_from UBERON:0003081 ! lateral plate mesoderm relationship: has_part UBERON:0002400 ! parietal pleura relationship: has_part UBERON:0002401 ! visceral pleura -relationship: has_quality PATO:0001748 ! invaginated -relationship: only_in_taxon NCBITaxon:32524 ! Amniota relationship: part_of UBERON:0009778 {source="https://github.com/obophenotype/uberon/issues/86"} ! pleural sac -relationship: present_in_taxon NCBITaxon:8782 {source="ISBN:978-0030223693", source="https://orcid.org/0000-0003-3308-6245"} ! Aves -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/ab/Gray965.png" xsd:anyURI -property_value: UBPROP:0000001 "The serous membrane that covers the lungs and lines the pleural cavity. [Kaufman_MH_and_Bard_JBL, The_anatomical_basis_of_mouse_development_(1999)_San_Diego:_Academic_Press, p.264][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000394", ontology="VHOG", source="ISBN:0124020607", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "pleural" xsd:string -property_value: UBPROP:0000012 "In MA, is_a cavity lining (which we equate to parietal). In FMA, is_a (viscous) serous membrane (which includes mesothelium plus connective tissue). Note the MA structure should probably be associated with the mesothelium of pleura in FMA. JB/EHDAA2 argues the term 'pleura' is best used for the mesothelial lining (thus excluding connective tissue). See https://github.com/obophenotype/uberon/issues/86" xsd:string +relationship: RO:0000086 PATO:0001748 ! has quality invaginated +relationship: RO:0002160 NCBITaxon:32524 ! only in taxon Amniota +relationship: RO:0002202 UBERON:0003081 ! develops from lateral plate mesoderm +relationship: RO:0002433 UBERON:0001004 ! contributes to morphology of respiratory system +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/ab/Gray965.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:8782 {source="ISBN:978-0030223693", source="https://orcid.org/0000-0003-3308-6245"} [Term] id: UBERON:0000978 @@ -165665,8 +165023,6 @@ is_a: UBERON:0006058 ! multi-limb segment region is_a: UBERON:0008784 ! lower limb segment relationship: distally_connected_to UBERON:0002387 ! pes relationship: proximally_connected_to UBERON:0001464 ! hip -property_value: UBPROP:0000003 "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000345", ontology="VHOG", source="ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000013 "The term leg can mean: [1] an appendage on which an animal walks [2] the entire hindlimb of a tetrapod [3] the segment of a human leg between knee and ankle (cf FMA) [4] the region of a hindlimb include the stylopod and zeugopod, but excluding the autopod. We define this class as [4], and thus 'leg' is compltely analagous to 'arm'. For [1], see the class 'locomotive weight-bearing appendage'. For [2] we use 'hindlimb'. For" xsd:string {source="3"} [Term] id: UBERON:0000979 @@ -165697,12 +165053,11 @@ is_a: UBERON:0003608 ! hindlimb long bone is_a: UBERON:0004251 ! hindlimb zeugopod bone is_a: UBERON:0015004 ! tibia endochondral element intersection_of: UBERON:0015004 ! tibia endochondral element -intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue -relationship: develops_from UBERON:0010849 ! tibia cartilage element -relationship: preaxialmost_part_of UBERON:0010720 ! hindlimb zeugopod skeleton -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/2a/Gray260.png" xsd:anyURI -property_value: UBPROP:0000001 "One of the two long bones of endochondral origin of the hind-epipodium; it is a straight, simple bone whose section is more or less rectangular at the ends and circular at its central portion.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000890", ontology="AAO", source="AAO:LAP"} +intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue +relationship: BSPO:0001113 UBERON:0010720 ! hindlimb zeugopod skeleton +relationship: RO:0002202 UBERON:0010849 ! develops from tibia cartilage element +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2a/Gray260.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000981 @@ -165744,18 +165099,14 @@ is_a: UBERON:0003826 ! upper leg bone is_a: UBERON:0008202 {source="MA"} ! bone of hip region is_a: UBERON:0015052 ! femur endochondral element intersection_of: UBERON:0015052 ! femur endochondral element -intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue -relationship: connected_to UBERON:0000979 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! tibia -relationship: connected_to UBERON:0001272 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! innominate bone -relationship: connected_to UBERON:0002446 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! patella -relationship: develops_from UBERON:0010129 {evidence="definitional"} ! femur cartilage element -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue relationship: proximally_connected_to UBERON:0007832 ! pelvic girdle skeleton -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/73/Gray252.png" xsd:anyURI -property_value: UBPROP:0000001 "Endochondral longbone connecting the pelvic girdle with posterior zeugopodium.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000186", ontology="VSAO", source="VSAO:NI"} -property_value: UBPROP:0000001 "Paired, elongate, cylindrical bones of endochondral origin that form the thighs, extending from the pelvic girdles to the knees.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000889", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000003 "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001159", ontology="VHOG", source="ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "femoral" xsd:string +relationship: RO:0002170 UBERON:0000979 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to tibia +relationship: RO:0002170 UBERON:0001272 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to innominate bone +relationship: RO:0002170 UBERON:0002446 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to patella +relationship: RO:0002202 UBERON:0010129 ! develops from femur cartilage element +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/73/Gray252.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000982 @@ -165797,10 +165148,8 @@ is_a: UBERON:0004905 ! articulation union_of: UBERON:0002217 ! synovial joint union_of: UBERON:0011134 ! nonsynovial joint disjoint_from: UBERON:0001474 ! bone element -relationship: connects UBERON:0004765 ! skeletal element -relationship: contributes_to_morphology_of UBERON:0001434 ! skeletal system -property_value: UBPROP:0000001 "Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000101", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000367", ontology="TAO", source="TAO:pem"} +relationship: RO:0002176 UBERON:0004765 ! connects skeletal element +relationship: RO:0002433 UBERON:0001434 ! contributes to morphology of skeletal system [Term] id: UBERON:0000983 @@ -165824,9 +165173,8 @@ is_a: UBERON:0008784 ! lower limb segment is_a: UBERON:0009877 ! metapodium region intersection_of: UBERON:0009877 ! metapodium region intersection_of: part_of UBERON:0002387 ! pes -relationship: has_skeleton UBERON:0010545 ! metatarsus skeleton relationship: part_of UBERON:0012142 {source="PHENOSCAPE:ni"} ! pedal digitopodium region -property_value: UBPROP:0000012 "mammalian and non-mammalian AOs differ in whether they consider this a part of the skeleton" xsd:string +relationship: RO:0002551 UBERON:0010545 ! has skeleton metatarsus skeleton [Term] id: UBERON:0000985 @@ -165849,13 +165197,12 @@ xref: UMLS:C0004456 {source="ncithesaurus:Axillary_Vein"} xref: Wikipedia:Axillary_vein is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein -intersection_of: drains UBERON:0009472 ! axilla -relationship: connected_to UBERON:0001587 ! subclavian vein -relationship: drains UBERON:0009472 ! axilla +intersection_of: RO:0002179 UBERON:0009472 ! drains axilla relationship: part_of UBERON:0001467 ! shoulder -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e9/Gray576.png" xsd:anyURI -property_value: UBPROP:0000008 "In human anatomy, the axillary vein is a large blood vessel that conveys blood from the lateral aspect of the thorax, axilla (armpit) and upper limb toward the heart. There is one axillary vein on each side of the body. Its origin is at the lower margin of the teres major muscle and a continuation of the brachial vein. Its tributaries include the basilic vein and cephalic vein, which are both superficial veins. It terminates at the lateral margin of the first rib, at which it becomes the subclavian vein. It is accompanied along its course by a similarly named artery, the axillary artery" xsd:string {source="WP"} +relationship: RO:0002170 UBERON:0001587 ! connected to subclavian vein +relationship: RO:0002179 UBERON:0009472 ! drains axilla +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e9/Gray576.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000988 @@ -165896,17 +165243,14 @@ xref: UMLS:C1280999 {source="BIRNLEX:733"} xref: VHOG:0001176 xref: Wikipedia:Pons is_a: UBERON:0002616 ! regional part of brain -relationship: contributes_to_morphology_of UBERON:0001895 ! metencephalon -relationship: contributes_to_morphology_of UBERON:0002298 ! brainstem -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0001895 {source="neuronames"} ! metencephalon relationship: part_of UBERON:0002298 ! brainstem -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/36/Gray768.png" xsd:anyURI -property_value: editor_note "The pons is not present in zebrafish. In this ontology we currently have some structures which are applicable to zebrafish appearing as parts of the pons. Currently we only include the weaker dubious_for_taxon relationship ubtil this is resolved" xsd:string -property_value: RO:0002174 NCBITaxon:7955 -property_value: UBPROP:0000001 "The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001176", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/pons"} -property_value: UBPROP:0000003 "During the embryonic development of birds and mammals, neuroblasts migrate from the cerebellum into the ventral part of the rhombencephalon and differentiate into pontine and other nuclei, which relay information from between the cerebrum and cerebellum, and a conspicuous band of transverse fibers. This region is known as the pons. A pons does not differentiate in reptiles and anamniotes (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001176", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.474", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002433 UBERON:0001895 ! contributes to morphology of metencephalon +relationship: RO:0002433 UBERON:0002298 ! contributes to morphology of brainstem +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/36/Gray768.png" xsd:anyURI +property_value: IAO:0000116 "The pons is not present in zebrafish. In this ontology we currently have some structures which are applicable to zebrafish appearing as parts of the pons. Currently we only include the weaker dubious_for_taxon relationship ubtil this is resolved" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000989 @@ -165941,12 +165285,9 @@ xref: VHOG:0000727 xref: Wikipedia:Penis is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0008811 {source="Wikipedia"} ! intromittent organ -relationship: develops_from UBERON:0004876 {source="Wikipedia"} ! urogenital fold -relationship: develops_from UBERON:0005876 {source="EHDAA2"} ! undifferentiated genital tubercle -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/87/Labelled_flaccid_penis.jpg" xsd:anyURI -property_value: UBPROP:0000007 "penile" xsd:string -property_value: UBPROP:0000007 "phallic" xsd:string -property_value: UBPROP:0000008 "Most male birds (e.g., roosters and turkeys) have a cloaca (also present on the female), but not a penis. Among bird species with a penis are paleognathes (tinamous and ratites), Anatidae (ducks, geese and swans), and a very few other species (such as flamingoes). A bird penis is different in structure from mammal penises, being an erectile expansion of the cloacal wall and being erected by lymph, not blood. It is usually partially feathered and in some species features spines and brush-like filaments, and in flaccid state curls up inside the cloaca" xsd:string {source="WP"} +relationship: RO:0002202 UBERON:0004876 {source="Wikipedia"} ! develops from urogenital fold +relationship: RO:0002202 UBERON:0005876 {source="EHDAA2"} ! develops from undifferentiated genital tubercle +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/87/Labelled_flaccid_penis.jpg" xsd:anyURI [Term] id: UBERON:0000990 @@ -165977,13 +165318,11 @@ xref: EHDAA2:0001603 xref: EHDAA:5923 xref: EMAPA:17381 xref: EV:0100100 -xref: FBbt:00004857 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7160 xref: GAID:363 xref: HAO:0000374 xref: HAO:0000895 xref: MA:0000326 -xref: MESH:D005835 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: MIAA:0000305 xref: NCIT:C12841 xref: SCTID:278875001 @@ -166013,15 +165352,12 @@ disjoint_from: UBERON:0002423 ! hepatobiliary system disjoint_from: UBERON:0004456 ! entire sense organ system disjoint_from: UBERON:8450002 ! excretory system relationship: capable_of_part_of GO:0000003 ! reproduction -relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: has_part UBERON:0000991 ! gonad -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2022-06-10T18:22:34Z" xsd:dateTime -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/52/Penis.svg" xsd:anyURI -property_value: editor_note "consider splitting genitalia from reproductive system" xsd:string -property_value: UBPROP:0000001 "Anatomical system which consists of organs and tissues associated with sexual reproduction of the organism.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010258", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "Arguably, one of the most important aspects of urbilaterian organogenesis would have been gonadogenesis, since Urbilateria must have successfully generated gametes and developed a strategy for extrusion and fertilization, in order to be the ancestor of all living Bilateria.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000182", ontology="VHOG", source="PMID:21672850 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across Bilateria. Integrative and Comparative Biology (2007)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000202 FMA:75572 +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +property_value: http://purl.org/dc/terms/date "2022-06-10T18:22:34Z" xsd:dateTime +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/52/Penis.svg" xsd:anyURI +property_value: IAO:0000116 "consider splitting genitalia from reproductive system" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000991 @@ -166040,7 +165376,6 @@ xref: BILA:0000123 xref: BSA:0000079 xref: BTO:0000534 xref: EMAPA:17383 -xref: FBbt:00004858 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:18250 xref: GAID:368 xref: HAO:0000379 @@ -166058,14 +165393,9 @@ xref: ZFA:0000413 is_a: UBERON:0003133 ! reproductive organ intersection_of: UBERON:0003133 ! reproductive organ intersection_of: has_part CL:0000586 ! germ cell -relationship: contains_process GO:0007276 ! gamete generation -relationship: develops_from UBERON:0005564 ! gonad primordium +relationship: BFO:0000067 GO:0007276 ! contains process gamete generation relationship: has_part CL:0000586 ! germ cell -property_value: UBPROP:0000001 "Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000213", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000413", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000397", ontology="VHOG", source="DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T, Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "gonadal" xsd:string -property_value: UBPROP:0000012 "FMA xref is a 'general anatomical term'" xsd:string {external_ontology="FMA"} +relationship: RO:0002202 UBERON:0005564 ! develops from gonad primordium [Term] id: UBERON:0000992 @@ -166113,7 +165443,6 @@ xref: EHDAA2:0001360 xref: EHDAA:8124 xref: EMAPA:17962 xref: EV:0100111 -xref: FBbt:00004865 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7209 xref: GAID:367 xref: MA:0000384 @@ -166132,17 +165461,12 @@ is_a: UBERON:0003134 ! female reproductive organ intersection_of: UBERON:0000991 ! gonad intersection_of: part_of UBERON:0000474 ! female reproductive system disjoint_from: UBERON:0009117 ! indifferent gonad -relationship: develops_from UBERON:0009117 ! indifferent gonad -relationship: in_lateral_side_of UBERON:0003975 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="FMA-abduced-lr"} ! internal female genitalia -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray589.png" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png" xsd:anyURI -property_value: UBPROP:0000001 "Either of paired female reproductive organs involved in production of ova and female sex hormones.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000371", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "Female reproductive organ.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000403", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "(...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000251", ontology="VHOG", source="DOI:10.1093/icb/icm052 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across the Bilateria. Integrative and Comparative Biology (2007), DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T and Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "ovarian" xsd:string -property_value: UBPROP:0000008 "Ovaries of some kind are found in the female reproductive system of many animals that employ sexual reproduction, including invertebrates. However, they develop in a very different way in most invertebrates than they do in vertebrates, and are not truly homologous. Many of the features found in human ovaries are common to all vertebrates, including the presence of follicular cells, tunica albuginea, and so on. However, many species produce a far greater number of eggs during their lifetime than do humans, so that, in fish and amphibians, there may be hundreds, or even millions of fertile eggs present in the ovary at any given time. In these species, fresh eggs may be developing from the germinal epithelium throughout life. Corpora lutea are found only in mammals, and in some elasmobranch fish; in other species, the remnants of the follicle are quickly resorbed by the ovary. In birds, reptiles, and monotremes, the egg is relatively large, filling the follicle, and distorting the shape of the ovary at maturity. Amphibians and reptiles have no ovarian medulla; the central part of the ovary is a hollow, lymph-filled space. The ovary of teleosts is also often hollow, but in this case, the eggs are shed into the cavity, which opens into the oviduct. Although most normal female vertebrates have two ovaries, this is not the case in all species. In birds and platypuses, the right ovary never matures, so that only the left is functional. In some elasmobranchs, the reverse is true, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo" xsd:string {source="WP"} +relationship: BSPO:0000126 UBERON:0003975 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="FMA-abduced-lr"} ! internal female genitalia +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002202 UBERON:0009117 ! develops from indifferent gonad +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray589.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000993 @@ -166178,15 +165502,10 @@ xref: XAO:0003052 xref: ZFA:0000560 is_a: UBERON:0000025 ! tube is_a: UBERON:0005156 ! reproductive structure -relationship: connects UBERON:0000992 ! ovary -relationship: connects UBERON:0013514 ! space surrounding organism -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000474 ! female reproductive system -property_value: IAO:0000232 "sometimes oviduct is used interchangeably with follaopian tube. Here they are different - the oviduct connects the gonad to the outside in a variety of animals. The mammal-class fallopian tube is derived from the mullerian duct and connects the gonads/infubdibulum to the uterus" xsd:string -property_value: UBPROP:0000001 "A passage through which ova leave the maternal body or pass to an organ communicating with the exterior of the body. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001136", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/oviduct"} -property_value: UBPROP:0000003 "In all remaining vertebrates (i.e., coelacanths, lungfishes, amphibians, reptiles, birds, and mammals), the oviduct arises in ontogeny as a longitudinal, groovelike invagination of the coelomic epithelium on the lateral surface of the mesonephros.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001136", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.687-688", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "in birds divided into infundibulum, magnum, isthmus, uterus, and vagina" xsd:string -property_value: UBPROP:0000008 "The only female vertebrates to lack oviducts are the jawless fishes. In these species, the single fused ovary releases eggs directly into the body cavity. The fish eventually extrudes the eggs through small genital pores towards the rear of the body[WP]" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002176 UBERON:0000992 ! connects ovary +relationship: RO:0002176 UBERON:0013514 ! connects space surrounding organism [Term] id: UBERON:0000995 @@ -166216,18 +165535,13 @@ xref: UMLS:C0042149 {source="ncithesaurus:Uterus"} xref: VHOG:0001137 xref: Wikipedia:Uterus is_a: UBERON:0013515 {source="cjm"} ! subdivision of oviduct -relationship: immediate_transformation_of UBERON:0005795 ! embryonic uterus -relationship: only_in_taxon NCBITaxon:32525 ! Theria relationship: part_of UBERON:0004175 ! internal genitalia -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/6a/Female_reproductive_system_lateral_nolabel.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Uterus.glb" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png" xsd:anyURI -property_value: UBPROP:0000001 "The hollow muscular organ in female mammals in which the blastocyst normally becomes embedded and in which the developing embryo and fetus is nourished. Its cavity opens into the vagina below and into a uterine tube on either side. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001137", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/uterus"} -property_value: UBPROP:0000003 "An infundibulum, uterine tube, uterus, and vagina also differentiate along the oviducts of eutherian mammals.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001137", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.678", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "uterine" xsd:string -property_value: UBPROP:0000008 "Most animals that lay eggs, such as birds and reptiles, have an oviduct instead of a uterus. In monotremes, mammals which lay eggs and include the platypus, either the term uterus or oviduct is used to describe the same organ, but the egg does not develop a placenta within the mother and thus does not receive further nourishment after formation and fertilization. Marsupials have two uteruses, each of which connect to a lateral vagina and which both use a third, middle 'vagina' which functions as the birth canal. Marsupial embryos form a choriovitelline 'placenta' (which can be thought of as something between a monotreme egg and a 'true' placenta), in which the egg's yolk sac supplies a large part of the embryo's nutrition but also attaches to the uterine wall and takes nutrients from the mother's bloodstream." xsd:string -property_value: UBPROP:0000011 "Two uteruses usually form initially in a female fetus, and in placental mammals they may partially or completely fuse into a single uterus depending on the species. In many species with two uteruses, only one is functional. Humans and other higher primates such as chimpanzees, along with horses, usually have a single completely fused uterus, although in some individuals the uteruses may not have completely fused [Wikipedia:Uterus]" xsd:string +relationship: RO:0002160 NCBITaxon:32525 ! only in taxon Theria +relationship: RO:0002495 UBERON:0005795 ! immediate transformation of embryonic uterus +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6a/Female_reproductive_system_lateral_nolabel.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Uterus.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000996 @@ -166259,16 +165573,11 @@ xref: VHOG:0001138 xref: Wikipedia:Vagina is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0013515 {source="cjm"} ! subdivision of oviduct -relationship: contributes_to_morphology_of UBERON:0003975 ! internal female genitalia -relationship: develops_from UBERON:0000164 {source="Wikipedia"} ! primitive urogenital sinus relationship: part_of UBERON:0003975 {source="FMA"} ! internal female genitalia -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1b/Illu_repdt_female.jpg" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/a4/Vaginal_opening_-_english_description.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Organ with organ cavity which connects the cervical canal of uterus to the vestibule of vagina.[FMA]" xsd:string {date_retrieved="2012-11-29", external_class="FMA:19949", ontology="FMA"} -property_value: UBPROP:0000001 "The genital canal in the female, leading from the opening of the vulva to the cervix of the uterus. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001138", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/vagina"} -property_value: UBPROP:0000003 "The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001138", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.688", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "vaginal" xsd:string -property_value: UBPROP:0000011 "'The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.' Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective, Third Edition (2001) Orlando Fla.: Harcourt College Publishers, p.688" xsd:string +relationship: RO:0002202 UBERON:0000164 {source="Wikipedia"} ! develops from primitive urogenital sinus +relationship: RO:0002433 UBERON:0003975 ! contributes to morphology of internal female genitalia +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1b/Illu_repdt_female.jpg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/a4/Vaginal_opening_-_english_description.jpg" xsd:anyURI [Term] id: UBERON:0000997 @@ -166305,11 +165614,9 @@ xref: VHOG:0001458 xref: Wikipedia:Vulva is_a: UBERON:0000062 ! organ is_a: UBERON:0005156 ! reproductive structure -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0005056 ! external female genitalia -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/da/Female_unshaved_genitalia.jpg" xsd:anyURI -property_value: UBPROP:0000001 "The external genital organs of the female, including the labia majora, labia minora, clitoris, and vestibule of the vagina. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001458", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/vulva"} -property_value: UBPROP:0000007 "vulval" xsd:string +relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/da/Female_unshaved_genitalia.jpg" xsd:anyURI [Term] id: UBERON:0000998 @@ -166350,15 +165657,12 @@ xref: VHOG:0001379 xref: Wikipedia:Seminal_vesicle is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0006868 ! seminal fluid secreting gland -relationship: contributes_to_morphology_of UBERON:0004054 ! internal male genitalia -relationship: develops_from UBERON:0000080 ! mesonephros relationship: part_of UBERON:0000473 ! testis relationship: produces UBERON:0010143 ! seminal vesicle fluid -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/d1/Male_anatomy_en.svg" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Prostate.glb" xsd:anyURI -property_value: UBPROP:0000001 "Either of a pair of pouchlike glands situated on each side of the male urinary bladder that secrete seminal fluid and nourish and promote the movement of spermatozoa through the urethra. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001379", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/prominence"} -property_value: UBPROP:0000003 "(In mammalian testis) Along the way (the sperm travel), three accessory sex glands, the seminal vesicle, prostate, and bulbourethral (Cowper's) gland, respectively, add their secretions as sperm move from the testes to the urethra.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001379", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.556", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000009 "The seminal vesicles secrete a significant proportion of the fluid that ultimately becomes semen. Lipofuscin granules from dead epithelial cells give the secretion its yellowish color. About 50-70% of the seminal fluid in humans originates from the seminal vesicles, but is not expelled in the first ejaculate fractions which are dominated by spermatozoa and zinc-rich prostatic fluid." xsd:string +relationship: RO:0002202 UBERON:0000080 ! develops from mesonephros +relationship: RO:0002433 UBERON:0004054 ! contributes to morphology of internal male genitalia +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d1/Male_anatomy_en.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Prostate.glb" xsd:anyURI [Term] id: UBERON:0000999 @@ -166387,16 +165691,16 @@ xref: Wikipedia:Ejaculatory_duct is_a: UBERON:0000025 ! tube is_a: UBERON:0005904 ! duct of male reproductive system is_a: UBERON:0015212 ! lateral structure +relationship: BSPO:0000126 UBERON:0000079 ! male reproductive system relationship: capable_of_part_of GO:0042713 ! sperm ejaculation relationship: channel_for UBERON:0001968 ! semen relationship: channel_for UBERON:0010143 ! seminal vesicle fluid relationship: channels_from UBERON:0000998 ! seminal vesicle relationship: channels_from UBERON:0001000 ! vas deferens relationship: channels_into UBERON:0000057 ! urethra -relationship: in_lateral_side_of UBERON:0000079 ! male reproductive system -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Prostate.glb" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/3/35/Male_anatomy.png" xsd:anyURI +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Prostate.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/3/35/Male_anatomy.png" xsd:anyURI [Term] id: UBERON:0001000 @@ -166433,13 +165737,11 @@ is_a: UBERON:0005904 ! duct of male reproductive system relationship: channel_for UBERON:0001968 ! semen relationship: channels_from UBERON:0001301 ! epididymis relationship: channels_into UBERON:0000999 ! ejaculatory duct -relationship: contributes_to_morphology_of UBERON:0004054 ! internal male genitalia -relationship: only_in_taxon NCBITaxon:32524 ! Amniota relationship: part_of UBERON:0005352 {source="FMA"} ! spermatic cord relationship: part_of UBERON:0006947 ! male genital duct -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/d1/Male_anatomy_en.svg" xsd:anyURI -property_value: UBPROP:0000003 "The continuation of the archinephric duct, now called the deferent duct, extends caudally to the cloaca or to the part of the mammalian urethra that is derived from the cloaca.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001135", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.670", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "Most vertebrates have some form of duct to transfer the sperm from the testes to the urethra. In cartilaginous fish and amphibians, sperm is carried through the archinephric duct, which also partially helps to transport urine from the kidneys. In teleosts, there is a distinct sperm duct, separate from the ureters, and often called the vas deferens, although probably not truly homologous with that in humans. In cartilaginous fishes, the part of the archinephric duct closest to the testis is coiled up to form an epididymis. Below this are a number of small glands secreting components of the seminal fluid. The final portion of the duct also receives ducts from the kidneys in most species. In amniotes, however, the archinephric duct has become a true vas deferens, and is used only for conducting sperm, never urine. As in cartilaginous fish, the upper part of the duct forms the epididymis. In many species, the vas deferens ends in a small sac for storing sperm. The only vertebrates to lack any structure resembling a vas deferens are the primitive jawless fishes, which release sperm directly into the body cavity, and then into the surrounding water through a simple opening in the body wall." xsd:string {source="WP"} +relationship: RO:0002160 NCBITaxon:32524 ! only in taxon Amniota +relationship: RO:0002433 UBERON:0004054 ! contributes to morphology of internal male genitalia +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d1/Male_anatomy_en.svg" xsd:anyURI [Term] id: UBERON:0001003 @@ -166479,15 +165781,9 @@ is_a: UBERON:3000961 ! external integument structure intersection_of: UBERON:0007376 ! outer epithelium intersection_of: part_of UBERON:0002097 ! skin of body relationship: adjacent_to UBERON:0002067 ! dermis -relationship: developmentally_replaces UBERON:0003055 ! periderm relationship: part_of UBERON:0002097 ! skin of body -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000001 "A cellular, multilayered epithelium derived from the ectoderm. Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. Le Guellec et al, 2004.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000105", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "The outer epithelial layer of the external integument of the body that is derived from the embryonic epiblast.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000143", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000002 "relationship loss: subclass external integument structures (AAO:0000961)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000143", ontology="AAO"} -property_value: UBPROP:0000003 "(...) outer epithelia in all metazoan animals are homologous. (...) The ancestor of all metazoans likely had an epidermis with a basal extracellular matrix (ECM), an apical extracellular glycocalyx, and one cilium with a striated rootlet per cell.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000077", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.71-72", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "epidermal" xsd:string -property_value: UBPROP:0000008 "Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. In terrestrial vertebrates the epidermis often forms an outer keratinized or cornified layer, the stratum corneum. Interaction between the epideris and dermis gives rise to feathers (birds), hair and mammary glands (mammals), teeth and scales (placoid: chondrichthyans; cosmoids, ganoid, cycloid in bony fishes)." xsd:string +relationship: RO:0002285 UBERON:0003055 ! developmentally replaces periderm +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001004 @@ -166546,18 +165842,16 @@ disjoint_from: UBERON:0004456 ! entire sense organ system disjoint_from: UBERON:8450002 ! excretory system relationship: capable_of GO:0003016 ! respiratory system process relationship: capable_of GO:0007585 ! respiratory gaseous exchange by respiratory system -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/5e/Respiratory_system_complete_en.svg" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Lung.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Lung.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Lung.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb" xsd:anyURI -property_value: UBPROP:0000001 "The anatomical system in which the exchange of oxygen and carbon dioxide between the organism and its environment.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000541", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "There is no doubt that the primitive pattern of vertebrate air-breathing is the buccal pulse pump found in actinopterygian fishes.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000202", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.599 and Figure 18-23", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5e/Respiratory_system_complete_en.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Lung.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Lung.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Lung.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb" xsd:anyURI +property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001005 @@ -166568,14 +165862,12 @@ subset: grouping_class subset: uberon_slim synonym: "airway" BROAD [http://orcid.org/0000-0002-6601-2165] synonym: "airways" BROAD OMO:0003004 [http://orcid.org/0000-0002-6601-2165] -xref: FMA:265130 xref: SCTID:361380005 xref: Wikipedia:Trachea is_a: UBERON:0003103 ! compound organ is_a: UBERON:0004111 ! anatomical conduit relationship: channel_for UBERON:0034874 ! air in respiratory system relationship: part_of UBERON:0001004 ! respiratory system -property_value: IAO:0000232 "This class generically groups trachea and analagous structures throughout metazoa. Consider renaming, as the term could be taken to mean lumen of tracheal system (e.g. in SNOMED). As a grouping class this is quite vague, as it is not clear where the airway begins and ends" xsd:string [Term] id: UBERON:0001007 @@ -166596,8 +165888,6 @@ xref: BILA:0000082 xref: BTO:0000058 xref: CALOHA:TS-1293 xref: EFO:0000793 -xref: EV:0100056 -xref: FBbt:00005055 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7152 xref: GAID:278 xref: galen:DigestiveSystem @@ -166630,11 +165920,8 @@ disjoint_from: UBERON:0002423 ! hepatobiliary system disjoint_from: UBERON:0004456 ! entire sense organ system disjoint_from: UBERON:8450002 ! excretory system relationship: capable_of GO:0022600 ! digestive system process -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000001 "An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000129", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000007 "digestive" xsd:string -property_value: UBPROP:0000012 "many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class" xsd:string {external_ontology="MA"} +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001008 @@ -166664,7 +165951,6 @@ xref: EHDAA2:0001601 xref: EHDAA:5901 xref: EMAPA:17366 xref: EV:0100095 -xref: FBbt:00005056 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7159 xref: GAID:391 xref: galen:UrinaryTract @@ -166686,15 +165972,11 @@ is_a: UBERON:8450002 ! excretory system intersection_of: UBERON:8450002 ! excretory system intersection_of: capable_of GO:0097254 ! renal tubular secretion relationship: capable_of GO:0097254 ! renal tubular secretion -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: never_in_taxon NCBITaxon:110815 {source="Wikipedia"} -relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000001 "An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010257", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "Evolution of vertebrate renal anatomy appears quite conservative when compared, for example, to evolution of respiratory and cardiovascular systems in vertebrates. Major anatomical changes in vertebrates kidneys separate those of birds and mammals from kidneys of lower vertebrates. General increase in animal size from fish to mammals is reflected by an increase in total number of nephrons per kidney, rather than by constant change in tubular dimensions.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000723", ontology="VHOG", source="ISBN:978-3540428541 Kapoor BG, Bhavna Khanna, Ichthyology Handbook (2004) p.406", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels" xsd:string {source="GO"} -property_value: UBPROP:0000008 "This definition is inclusive of the organs of the vertebrate renal system, as well as the Malpighian tubules of insects, and allows for future incorporation of structures such as the antennal glands of crustaceans" xsd:string {source="DOI:10.1371/journal.pone.0099864"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +property_value: RO:0002161 NCBITaxon:110815 {source="Wikipedia"} +property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001009 @@ -166706,7 +165988,6 @@ subset: uberon_slim synonym: "systema cardiovasculare" RELATED OMO:0003011 [Wikipedia:Circulatory_system] xref: AAO:0000959 xref: CALOHA:TS-2103 -xref: MESH:D002319 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: VHOG:0001248 xref: Wikipedia:Circulatory_system is_a: UBERON:0000467 ! anatomical system @@ -166723,17 +166004,13 @@ disjoint_from: UBERON:0002423 ! hepatobiliary system disjoint_from: UBERON:0004456 ! entire sense organ system disjoint_from: UBERON:8450002 ! excretory system relationship: capable_of GO:0003013 ! circulatory system process -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} -relationship: never_in_taxon NCBITaxon:6073 ! Cnidaria -relationship: never_in_taxon NCBITaxon:6157 ! Platyhelminthes -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI -property_value: IAO:0000232 "the cardiovascular system and the lymphatic system are parts of the circulatory system" xsd:string -property_value: RO:0002174 NCBITaxon:6231 {notes="WBbt coelomocyte currently classified as circulating cell"} -property_value: UBPROP:0000001 "Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000959", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001248", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.493", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} +property_value: RO:0002161 NCBITaxon:6073 +property_value: RO:0002161 NCBITaxon:6157 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001013 @@ -166776,17 +166053,10 @@ xref: XAO:0003049 xref: ZFA:0005345 is_a: UBERON:0011822 {source="FMA"} ! dense irregular connective tissue intersection_of: UBERON:0002384 ! connective tissue -intersection_of: composed_primarily_of CL:0000136 ! adipocyte +intersection_of: RO:0002473 CL:0000136 ! composed primarily of adipocyte disjoint_from: UBERON:0003714 ! neural tissue -relationship: composed_primarily_of CL:0000136 ! adipocyte -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000001 "Connective tissue in which fat is stored.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002134", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Tissue that contains adipocytes, used for cushioning, thermal insulation, lubrication (primarily in the pericardium) and energy storage.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000001", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000002 "relationship loss: subclass connective tissue proper (AAO:0000099)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000001", ontology="AAO"} -property_value: UBPROP:0000003 "Adipose tissue is unique to vertebrates. It is found in mostmammals, birds, reptiles and amphibians, and a variety is found in some species of fish. Furthermore, in insects the fat body found in larvae as well as in adults shares some homology with adipose tissue.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001284", ontology="VHOG", source="DOI:10.1017/S0029665107005423 Haugen F, Drevon CA, The interplay between nutrients and the adipose tissue. The Proceedings of the Nutrition Society (2007)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "adipose" xsd:string -property_value: UBPROP:0000008 "In humans, adipose tissue is located beneath the skin (subcutaneous fat), around internal organs (visceral fat), in bone marrow (yellow bone marrow) and in breast tissue. Adipose tissue is found in specific locations, which are referred to as adipose depots. Adipose tissue contains several cell types, with the highest percentage of cells being adipocytes, which contain fat droplets. Other cell types include fibroblasts, macrophages, and endothelial cells. Adipose tissue contains many small blood vessels.; Mice have eight major adipose depots, four of which are within the abdominal cavity. The paired gonadal depots are attached to the uterus and ovaries in females and the epididymis and testes in males; the paired retroperitoneal depots are found along the dorsal wall of the abdomen, surrounding the kidney, and, when massive, extend into the pelvis. The mesenteric depot forms a glue-like web that supports the intestines, and the omental depot, which originates near the stomach and spleen, and, when massive, extends into the ventral abdomen." xsd:string -property_value: UBPROP:0000012 "in FMA this is dense irregular connective tissue" xsd:string {external_ontology="FMA"} +relationship: RO:0002473 CL:0000136 ! composed primarily of adipocyte +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001015 @@ -166806,10 +166076,8 @@ synonym: "musculature system" RELATED [] synonym: "musculi" EXACT OMO:0003011 [FMA:32558, FMA:TA] synonym: "set of muscles" EXACT [FMA:32558] synonym: "set of skeletal muscles" EXACT [MA:0000165] -xref: AAO:0011066 xref: BTO:0000887 xref: EFO:0001949 -xref: EMAPA:32715 xref: EMAPA:35577 xref: FMA:32558 xref: MA:0000165 @@ -166821,11 +166089,9 @@ xref: WBbt:0005737 xref: Wikipedia:Muscular_system xref: ZFA:0000548 is_a: UBERON:0011216 ! organ system subdivision -relationship: composed_primarily_of UBERON:0001630 ! muscle organ relationship: part_of UBERON:0000383 ! musculature of body -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png" xsd:anyURI -property_value: RO:0002171 UBERON:0001474 -property_value: UBPROP:0000012 "In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here." xsd:string {external_ontology="FMA"} +relationship: RO:0002473 UBERON:0001630 ! composed primarily of muscle organ +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png" xsd:anyURI [Term] id: UBERON:0001016 @@ -166851,7 +166117,6 @@ xref: EHDAA2:0001246 xref: EHDAA:826 xref: EMAPA:16469 xref: EV:0100162 -xref: FBbt:00005093 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7157 xref: GAID:466 xref: MA:0000016 @@ -166881,20 +166146,15 @@ disjoint_from: UBERON:0002423 ! hepatobiliary system disjoint_from: UBERON:0004456 ! entire sense organ system disjoint_from: UBERON:8450002 ! excretory system relationship: capable_of GO:0050877 ! nervous system process -relationship: composed_primarily_of CL:0002319 ! neural cell -relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: has_part CL:0000540 ! neuron -relationship: immediate_transformation_of UBERON:0016880 {source="Bgee:AN"} ! future nervous system -relationship: never_in_taxon NCBITaxon:6040 -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI -property_value: UBPROP:0000001 "A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000396", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000324", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000402", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.117", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "nervous" xsd:string -property_value: UBPROP:0000007 "neural" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002473 CL:0002319 ! composed primarily of neural cell +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +relationship: RO:0002495 UBERON:0016880 {source="Bgee:AN"} ! immediate transformation of future nervous system +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI +property_value: RO:0002161 NCBITaxon:6040 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001017 @@ -166923,7 +166183,6 @@ xref: EHDAA:828 xref: EMAPA:16470 xref: EMAPA:16754 xref: EV:0100163 -xref: FBbt:00005094 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:55675 xref: GAID:570 xref: MA:0000167 @@ -166940,16 +166199,11 @@ xref: XAO:0000215 xref: ZFA:0000012 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0011216 {source="FBbt", source="cjm"} ! organ system subdivision -relationship: develops_from UBERON:0001049 {gci_relation="part_of", gci_filler="NCBITaxon:7742", evidence="definitional"} ! neural tube -relationship: immediate_transformation_of UBERON:0016879 {source="Bgee:AN"} ! future central nervous system -relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0001016 ! nervous system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000001 "Part of the nervous system which includes the brain and spinal cord.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000090", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "The brain and spinal cord. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000012", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO)." xsd:string {source="BIRNLEX:1099"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000293", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 (reference 1), ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 (reference 2), DOI:10.1016/j.cell.2007.02.040 Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud'homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007) (reference 3)", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002495 UBERON:0016879 {source="Bgee:AN"} ! immediate transformation of future central nervous system +property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001018 @@ -166967,12 +166221,10 @@ synonym: "tract" RELATED [] synonym: "tract of neuraxis" EXACT [FMA:83847] xref: BIRNLEX:1649 xref: EV:0100304 -xref: FBbt:00005100 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:83847 xref: NLX:147822 is_a: UBERON:0000122 ! neuron projection bundle is_a: UBERON:0011215 ! central nervous system cell part cluster -property_value: UBPROP:0000001 "White matter structure of CNS that contains axons that arise predominantly in one central nervous system part and terminate in another. Tracts are generally named by their region or origin followed by their region of primary termination, e.g., mammillothalamic tract contains axons that arise from neurons in the mammillary bodies and terminate in the thalamus. (CUMBO)" xsd:string {source="http://neurolex.org/wiki/Cumbo_terms"} [Term] id: UBERON:0001019 @@ -167024,7 +166276,6 @@ xref: EHDAA:4657 xref: EMAPA:32808 xref: EMAPA:32815 xref: EV:0100371 -xref: FBbt:00005105 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:65132 xref: FMA:65239 xref: GAID:747 @@ -167047,12 +166298,10 @@ xref: XAO:0000204 xref: XAO:0003047 xref: ZFA:0007009 is_a: UBERON:0000122 {source="FBbt"} ! neuron projection bundle -relationship: has_developmental_contribution_from UBERON:0002342 {gci_relation="part_of", gci_filler="NCBITaxon:7742", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! neural crest -relationship: has_quality PATO:0002045 ! dendritic relationship: part_of UBERON:0000010 ! peripheral nervous system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000001 "A portion of tissue which is a fasiculated group of axons.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0007009", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000007 "nervous" xsd:string +relationship: RO:0000086 PATO:0002045 ! has quality dendritic +relationship: RO:0002254 UBERON:0002342 {gci_relation="part_of", gci_filler="NCBITaxon:7742", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! has developmental contribution from neural crest +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001027 @@ -167065,7 +166314,6 @@ synonym: "afferent nerve" RELATED [] synonym: "nervus sensorius" EXACT OMO:0003011 [Wikipedia:Sensory_nerve] xref: AEO:0000201 xref: EHDAA2:0003200 -xref: FBbt:00005136 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:5868 xref: Wikipedia:Sensory_nerve is_a: UBERON:0001021 ! nerve @@ -167094,7 +166342,6 @@ xref: BILA:0000099 xref: EFO:0000805 xref: EHDAA2:0003094 xref: EMAPA:16192 -xref: FBbt:00007692 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:75259 xref: MA:0002442 xref: MAT:0000031 @@ -167109,9 +166356,7 @@ is_a: UBERON:0015203 ! non-connected functional system relationship: capable_of_part_of GO:0007600 ! sensory perception relationship: overlaps UBERON:0001016 ! nervous system relationship: part_of UBERON:0004456 ! entire sense organ system -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" xsd:anyURI -property_value: UBPROP:0000003 "An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001674", ontology="VHOG", source="DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" xsd:anyURI [Term] id: UBERON:0001033 @@ -167152,12 +166397,8 @@ disjoint_from: UBERON:0002423 ! hepatobiliary system disjoint_from: UBERON:0004456 ! entire sense organ system disjoint_from: UBERON:8450002 ! excretory system relationship: capable_of_part_of GO:0050912 ! detection of chemical stimulus involved in sensory perception of taste -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: UBPROP:0000001 "The sensory system for the sense of taste[NLXANAT:090803]." xsd:string {source="NLXANAT:090803"} -property_value: UBPROP:0000001 "The sensory system used for the sense of taste.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010577", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000007 "gustatory" xsd:string -property_value: UBPROP:0000012 "in ZFA and MA this is a subtype of sensory system. we should change sensory system to disambiguate parts and wholes" xsd:string {external_ontology="ZFA"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage [Term] id: UBERON:0001037 @@ -167193,14 +166434,14 @@ xref: UMLS:C0018494 {source="ncithesaurus:Hair"} xref: VHOG:0001191 xref: Wikipedia:Hair is_a: UBERON:0000021 {source="FMA"} ! cutaneous appendage -relationship: develops_from UBERON:0002073 ! hair follicle +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: has_part GO:0045095 ! keratin filament -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0001003 {source="FMA"} ! skin epidermis relationship: part_of UBERON:0011932 {source="FMA"} ! pilosebaceous unit -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/25/Gray945.png" xsd:anyURI -property_value: editor_note "TODO for now we treat vibrissa/whisker as a syonym, but these have different follicles. We could introduce subclasses (see also: Pangolin scales)" xsd:string -property_value: IAO:0000232 "this class defines an individual hair" xsd:string +relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia +relationship: RO:0002202 UBERON:0002073 ! develops from hair follicle +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/25/Gray945.png" xsd:anyURI +property_value: IAO:0000116 "TODO for now we treat vibrissa/whisker as a syonym, but these have different follicles. We could introduce subclasses (see also: Pangolin scales)" xsd:string [Term] id: UBERON:0001038 @@ -167214,12 +166455,11 @@ subset: uberon_slim synonym: "ch" RELATED [] synonym: "scolopophorous organ" RELATED [] xref: EFO:0000940 -xref: FBbt:00005215 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: MAT:0000209 xref: MIAA:0000209 xref: Wikipedia:Chordotonal_organ is_a: UBERON:0000020 ! sense organ -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda +relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda [Term] id: UBERON:0001040 @@ -167248,14 +166488,10 @@ xref: Wikipedia:Yolk_sac is_a: UBERON:0005292 ! extraembryonic tissue is_a: UBERON:0005631 {seeAlso="https://github.com/obophenotype/uberon/issues/635"} ! extraembryonic membrane is_a: UBERON:0007499 {source="EHDAA2"} ! epithelial sac -relationship: has_developmental_contribution_from UBERON:0000925 {source="ISBN:0073040584"} ! endoderm -relationship: has_developmental_contribution_from UBERON:0004872 {source="ISBN:0073040584"} ! splanchnic layer of lateral plate mesoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/17/Gray22.png" xsd:anyURI -property_value: editor_note "consider splitting class" xsd:string -property_value: UBPROP:0000001 "One of the extraembryonic fetal membranes that balloons out from the fetal midgut. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000830", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/yolk+sac"} -property_value: UBPROP:0000001 "the extraembryonic tissue membrane, formed from the visceral endoderm and the extraembryonic mesoderm, which is located ventral to the embryonic disc and is connected to the presumptive midgut of the embryo; the yolk that it contains is the site of embryonic hematopoiesis and vitelline circulation is involved in early embryonic circulation; it is the origin of the primordial germ cells" xsd:string {source="MP:0001718"} -property_value: UBPROP:0000003 "Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000830", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.187", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "In therians, a structure homologous to the yolk sac is is present, but contains no yolk platelets. Instead it is filled with fluid [ISBN:0073040584 (Vertebrates, Kardong)]" xsd:string +relationship: RO:0002254 UBERON:0000925 {source="ISBN:0073040584"} ! has developmental contribution from endoderm +relationship: RO:0002254 UBERON:0004872 {source="ISBN:0073040584"} ! has developmental contribution from splanchnic layer of lateral plate mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/17/Gray22.png" xsd:anyURI +property_value: IAO:0000116 "consider splitting class" xsd:string [Term] id: UBERON:0001041 @@ -167273,7 +166509,6 @@ xref: BTO:0000507 xref: EHDAA2:0000557 xref: EHDAA:520 xref: EMAPA:16548 -xref: FBbt:00005379 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45616 xref: MA:0001526 xref: NCIT:C34180 @@ -167284,10 +166519,8 @@ xref: VHOG:0000285 xref: Wikipedia:Foregut xref: XAO:0000232 is_a: UBERON:0004921 ! subdivision of digestive tract -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/9a/Gray27.png" xsd:anyURI -property_value: editor_note "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. In vertebrates the term may refer to a developmental structure" xsd:string -property_value: UBPROP:0000001 "The anterior portion of the primitive digestive tube of the embryo that lies cephalic to the junction of the yolk stalk, consists of endodermal tissue, and gives rise to the the pharynx, lower respiratory system, esophagus, stomach, duodenum proximal to the biliary tract, liver, pancreas, biliary tract, and gall bladder." xsd:string {source="MP:0000474"} -property_value: UBPROP:0000003 "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000285", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11", source="http://bgee.unil.ch/"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/9a/Gray27.png" xsd:anyURI +property_value: IAO:0000116 "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. In vertebrates the term may refer to a developmental structure" xsd:string [Term] id: UBERON:0001042 @@ -167322,21 +166555,12 @@ xref: Wikipedia:Pharynx xref: XAO:0003227 xref: ZFA:0000056 is_a: UBERON:0006562 ! pharynx -relationship: continuous_with UBERON:0001043 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! esophagus -relationship: develops_from UBERON:0009145 {source="EHDAA2"} ! pharyngeal region of foregut relationship: distally_connected_to UBERON:0001043 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! esophagus -relationship: has_skeleton UBERON:0008895 {gci_relation="part_of", gci_filler="NCBITaxon:89593"} ! splanchnocranium -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0001004 ! respiratory system -property_value: UBPROP:0000001 "A funnel-shaped fibromuscular tube that conducts food to the ESOPHAGUS, and air to the LARYNYX and LUNGS. It is located posterior to the NASAL CAVITY; ORAL CAVITY; and LARYNX, and extends from the SKULL BASE to the inferior border of the CRICOID CARTILAGE anteriorly and to the inferior border of the C6 vertebra posteriorly. It is divided into the NASOPHARYNX; OROPHARYNX; and HYPOPHARYNX (laryngopharynx)[MESH:A03.867]." xsd:string {source="MESH:A03.867"} -property_value: UBPROP:0000001 "Anatomical cavity bounded by the derivatives of the branchial arches.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000967", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000001 "Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000056", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills[ZFA:0000056, ZFIN:ZDB-PUB-961014-576]." xsd:string {source="ZFIN:ZDB-PUB-961014-576"} -property_value: UBPROP:0000001 "The portion of the alimentary canal between the mouth and the oesophagus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000462", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000002 "relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: develops_from respiratory system (UBERON:0001004)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000967", ontology="AAO"} -property_value: UBPROP:0000002 "relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: part_of respiratory system (UBERON:0001004)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000967", ontology="AAO"} -property_value: UBPROP:0000003 "(...) the earliest vertebrates possessed unjointed internal and external branchial arches, and musculature encircling the pharynx.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000462", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) Box essay 13.1 and Box figure I, p.502-503", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "MA/FMA pharynx not part of digestive/alimentary system, we are consistent with this scheme" xsd:string {external_ontology="MA"} +relationship: RO:0002150 UBERON:0001043 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! continuous with esophagus +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002202 UBERON:0009145 {source="EHDAA2"} ! develops from pharyngeal region of foregut +relationship: RO:0002551 UBERON:0008895 {gci_relation="part_of", gci_filler="NCBITaxon:89593"} ! has skeleton splanchnocranium [Term] id: UBERON:0001043 @@ -167379,16 +166603,11 @@ xref: ZFA:0000204 is_a: UBERON:0004921 ! subdivision of digestive tract is_a: UBERON:0005178 ! thoracic cavity element is_a: UBERON:0013765 ! digestive system element -relationship: develops_from UBERON:0001041 ! foregut -relationship: distally_connected_to UBERON:0000945 {gci_relation="part_of", gci_filler="NCBITaxon:40674", notes="only in species that have a stomach"} ! stomach relationship: part_of UBERON:0004908 ! upper digestive tract -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: proximally_connected_to UBERON:0001042 ! chordate pharynx -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/d4/Illu01_head_neck.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Anterior end of the alimentary canal lined with smooth muscle. Bounded anteriorly by a constriction in the pharynx. Bounded posteriorly by and increase in circular and/or longitudinal smooth muscle associated with the stomach.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000145", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "The few structural specializations in (adult lampreys) pharynx include complex valves on the external gill openings that direct the tidal flow, and the division of the ancestral pharynx into an oesophagus and a respiratory pharynx.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000450", ontology="VHOG", source="DOI:10.1111/j.1096-3642.1996.tb01658.x Mallatt J, Ventilation and the origin of jawed vertebrates: a new mouth. Zoological Journal of the Linnean Society (1996)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "esophageal" xsd:string -property_value: UBPROP:0000012 "esophagus NOT part of gut in MA. part of gut in ZFA. part_of gut (via UGIT) in FMA. Consider splitting. Interspecies: The human oesophagus is 25 cm long and has a diameter of ca. 2 cm. Only little information was found on the oesophagus in rat, rabbit and pig. The oesophagus of rat (75 x 2 mm) and rabbit has no mucous glands and the cardia of the stomach has a well-developed sphincter, which prevents them from vomiting (Hebel and Stromberg, 1988; Manning et al., 1994). Morphologically the oesophagus is similar in man and pig; both are omnivores and have a non-keratinised epithelium, submucous glands and similar membrane enzymes. Like in humans, pigs can suffer from reflux oesophagitis and stress ulceration of the oesophagus. The pig oesophagus may therefore be a good model for investigation compared to the human oesophagus (Christie et al., 1995)" xsd:string {external_ontology="MA"} +relationship: RO:0002202 UBERON:0001041 ! develops from foregut +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d4/Illu01_head_neck.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001044 @@ -167409,7 +166628,6 @@ xref: EHDAA2:0001775 xref: EHDAA:7987 xref: EMAPA:17751 xref: EV:0100059 -xref: FBbt:00005382 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9597 xref: GAID:937 xref: galen:SalivaryGland @@ -167426,15 +166644,11 @@ is_a: UBERON:0010047 ! oral gland intersection_of: UBERON:0002530 ! gland intersection_of: produces UBERON:0001836 ! saliva relationship: capable_of GO:0046541 ! saliva secretion -relationship: contributes_to_morphology_of UBERON:0001007 ! digestive system -relationship: located_in UBERON:0000167 ! oral cavity -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria relationship: produces UBERON:0001836 ! saliva -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/51/Illu_quiz_hn_02.jpg" xsd:anyURI -property_value: IAO:0000232 "currently we define saliva and salivary glands very generally in functional terms but it may be more appropriate to split this class. From WP: In most vertebrates, saliva does not contain any enzymes, consisting of mucus and water only, and its primary function is to moisten food while eating. As a result, true salivary glands are rarely found in fish or aquatic tetrapods, although there are often individual mucus-secreting cells. Amphibians have a single salivary gland, the intermaxillary gland, located in the forward part of the palate. Reptiles and birds normally have only very small glands on the lips, palate, and base of the mouth, although there are some birds with large glands, which produce a sticky saliva that helps in nest-building. The distinct parotid, submandibular, and sublingual glands are only developed in mammals." xsd:string {source="3"} -property_value: UBPROP:0000001 "A gland that produces the saliva. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-25, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000376", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "In air-feeding animals, the lack of water column to lubricate the food has been compensated for by the evolution of the salivary glands. These glands are present only in amniotes and are controlled by the parasympathetic system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000376", ontology="VHOG", source="ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptationm(2005) p.211", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "The salivary glands in mammals are exocrine glands, glands with ducts, that produce saliva. They also secrete amylase, an enzyme that breaks down starch into maltose. In other organisms such as insects, salivary glands are often used to produce biologically important proteins like silk or glues, and fly salivary glands contain polytene chromosomes that have been useful in genetic research. The salivary glands of some species are modified to produce enzymes; salivary amylase is found in many, but by no means all, bird and mammal species (including humans, as noted above). Furthermore, the venom glands of poisonous snakes, Gila monsters, and some shrews, are modified salivary glands" xsd:string +relationship: RO:0001025 UBERON:0000167 ! located in oral cavity +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002433 UBERON:0001007 ! contributes to morphology of digestive system +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/51/Illu_quiz_hn_02.jpg" xsd:anyURI [Term] id: UBERON:0001045 @@ -167452,7 +166666,6 @@ xref: EFO:0001950 xref: EHDAA2:0001185 xref: EHDAA:983 xref: EMAPA:16255 -xref: FBbt:00005383 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45617 xref: MA:0001564 xref: NCIT:C34210 @@ -167464,11 +166677,8 @@ xref: Wikipedia:Midgut xref: XAO:0000103 is_a: UBERON:0004921 ! subdivision of digestive tract relationship: proximally_connected_to UBERON:0001041 ! foregut -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/3d/Illu_small_intestine.jpg" xsd:anyURI -property_value: editor_note "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. We may explicitly make this a developmental class" xsd:string -property_value: UBPROP:0000003 "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000290", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "In humans: originates from the foregut at the opening of the bile duct into the duodenum and continues through the small intestine and much of the large intestine until the transition to the hindgut about two-thirds of the way through the transverse colon" xsd:string {source="WP"} -property_value: UBPROP:0000012 "in FMA this represents an embryonic region." xsd:string {external_ontology="FMA"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3d/Illu_small_intestine.jpg" xsd:anyURI +property_value: IAO:0000116 "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. We may explicitly make this a developmental class" xsd:string [Term] id: UBERON:0001046 @@ -167485,7 +166695,6 @@ xref: BTO:0000510 xref: EHDAA2:0000779 xref: EHDAA:975 xref: EMAPA:16715 -xref: FBbt:00005384 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45618 xref: MA:0001527 xref: NCIT:C34188 @@ -167496,13 +166705,10 @@ xref: VHOG:0000459 xref: Wikipedia:Hindgut xref: XAO:0000104 is_a: UBERON:0004921 ! subdivision of digestive tract -relationship: develops_from UBERON:0003104 {source="Wikipedia"} ! mesenchyme relationship: proximally_connected_to UBERON:0001045 ! midgut -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray472.png" xsd:anyURI -property_value: editor_note "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future (vertebrates have some contribution from NC - https://github.com/obophenotype/uberon/wiki/The-neural-crest). We may explicitly make this a developmental class" xsd:string -property_value: UBPROP:0000001 "the caudal portion of the primitive digestive tube of the embryo" xsd:string {source="MP:0008786"} -property_value: UBPROP:0000003 "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000459", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "in FMA this class has no children. In MA it has a single child hindgut epithelium" xsd:string {external_ontology="FMA"} +relationship: RO:0002202 UBERON:0003104 {source="Wikipedia"} ! develops from mesenchyme +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray472.png" xsd:anyURI +property_value: IAO:0000116 "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future (vertebrates have some contribution from NC - https://github.com/obophenotype/uberon/wiki/The-neural-crest). We may explicitly make this a developmental class" xsd:string [Term] id: UBERON:0001048 @@ -167521,7 +166727,6 @@ xref: AEO:0000171 xref: BTO:0001886 xref: EFO:0001652 xref: EHDAA2:0003171 -xref: FBbt:00005495 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:86589 xref: MAT:0000482 xref: NCIT:C34275 @@ -167553,7 +166758,6 @@ xref: EMAPA:16164 xref: EMAPA:16757 xref: FMA:293882 xref: MAT:0000069 -xref: MESH:D054259 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: MIAA:0000069 xref: NCIT:C34226 xref: neuronames:1365 @@ -167568,12 +166772,8 @@ is_a: UBERON:0003914 {source="EHDAA2"} ! epithelial tube is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0016879 ! future central nervous system -relationship: develops_from UBERON:0005068 ! neural rod -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010617", ontology="AAO", source="AAO:JOR"} -property_value: UBPROP:0000001 "The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000307", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/neural+tube"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000307", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000011 "The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium" xsd:string {source="GO:0021915"} +relationship: RO:0002202 UBERON:0005068 ! develops from neural rod +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0001052 @@ -167609,20 +166809,17 @@ xref: UMLS:C0034896 {source="ncithesaurus:Rectum"} xref: VHOG:0001751 xref: Wikipedia:Rectum xref: XAO:0000238 -is_a: UBERON:0004921 {order="4", source="cjm"} ! subdivision of digestive tract -relationship: continuous_with UBERON:0001159 ! sigmoid colon -relationship: contributes_to_morphology_of UBERON:0000059 ! large intestine -relationship: distalmost_part_of UBERON:0000059 {source="ISBN:0073040584"} ! large intestine +is_a: UBERON:0004921 ! subdivision of digestive tract +relationship: BSPO:0001108 UBERON:0000059 {source="ISBN:0073040584"} ! large intestine relationship: part_of UBERON:0000059 {source="MA"} ! large intestine relationship: part_of UBERON:0006866 ! terminal part of digestive tract relationship: part_of UBERON:0012361 {source="EHDAA2"} ! internal anal region -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/75/Anorectum.gif" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb" xsd:anyURI -property_value: UBPROP:0000001 "The terminal portion of the large intestine between the ileo-pelvic colon and the anus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001751", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "rectal" xsd:string -property_value: UBPROP:0000008 "In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html" xsd:string +relationship: RO:0002150 UBERON:0001159 ! continuous with sigmoid colon +relationship: RO:0002433 UBERON:0000059 ! contributes to morphology of large intestine +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/75/Anorectum.gif" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001054 @@ -167637,7 +166834,6 @@ synonym: "Malpighian tube" RELATED [UBERON:cjm] synonym: "tuba Malpighii" RELATED [BTO:0000810] xref: BTO:0000810 xref: EFO:0000243 -xref: FBbt:00005786 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: GAID:1228 xref: MAT:0000123 xref: MESH:D008317 @@ -167647,8 +166843,7 @@ xref: TADS:0000163 xref: TGMA:0001038 xref: Wikipedia:Malpighian_tubule is_a: UBERON:0009773 {source="GO"} ! renal tubule -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda -property_value: UBPROP:0000008 "It is unclear as to whether the Malpighian tubules of arachnids and those of the Uniramia are homologous or the result of convergent evolution.[Wikipedia:Malpighian_tubule_system]" xsd:string +relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda [Term] id: UBERON:0001058 @@ -167661,7 +166856,6 @@ synonym: "corpora pedunculata" RELATED [FBbt:00005801, PMID:21062451] synonym: "mushroom bodies" EXACT OMO:0003004 [] xref: BTO:0002675 xref: EFO:0000925 -xref: FBbt:00005801 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: GAID:1231 xref: MAT:0000336 xref: MESH:D024521 @@ -167670,12 +166864,11 @@ xref: Wikipedia:Mushroom_body is_a: UBERON:0000477 ! anatomical cluster relationship: capable_of_part_of GO:0007613 {source="Wikipedia"} ! memory relationship: capable_of_part_of GO:0008355 {source="Wikipedia"} ! olfactory learning -relationship: never_in_taxon NCBITaxon:6217 -relationship: only_in_taxon NCBITaxon:33317 {notes="annelids and arthropods"} ! Protostomia relationship: part_of UBERON:0000955 ! brain -relationship: present_in_taxon NCBITaxon:6340 -relationship: present_in_taxon NCBITaxon:6656 ! Arthropoda -property_value: UBPROP:0000008 "Also in annelids. 'Comparison to the vertebrate pallium reveals that the annelid mushroom bodies develop from similar molecular coordinates within a conserved overall molecular brain topology and that their development involves conserved patterning mechanisms and produces conserved neuron types that existed already in the proto- stome-deuterostome ancestors. These data indicate deep homology of pallium and mushroom bodies and date back the origin of higher brain centers to prebilaterian times'" xsd:string {source="PMID:20813265"} +relationship: RO:0002160 NCBITaxon:33317 ! only in taxon Protostomia +property_value: RO:0002161 NCBITaxon:6217 +property_value: RO:0002175 NCBITaxon:6340 +property_value: RO:0002175 NCBITaxon:6656 [Term] id: UBERON:0001062 @@ -167691,7 +166884,6 @@ xref: BILA:0000000 xref: BIRNLEX:6 xref: CARO:0000000 xref: EHDAA2:0002229 -xref: FBbt:10000000 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:62955 xref: HAO:0000000 xref: MA:0000001 @@ -167704,9 +166896,9 @@ xref: XAO:0000000 xref: ZFA:0100000 relationship: part_of UBERON:0003942 {gci_filler="GO:0050975", gci_relation="capable_of_part_of"} ! somatosensory system relationship: part_of UBERON:0003942 {gci_relation="capable_of_part_of", gci_filler="GO:0019233"} ! somatosensory system -relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 ! Fungi +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0001064 @@ -167742,12 +166934,10 @@ is_a: UBERON:0000025 ! tube is_a: UBERON:0007329 {source="FMA"} ! pancreatic duct relationship: channel_for UBERON:0001970 ! bile relationship: channels_into UBERON:0004913 ! hepatopancreatic ampulla -relationship: continuous_with UBERON:0001174 ! common bile duct -relationship: develops_from UBERON:0003924 {source="EHDAA2"} ! ventral pancreatic bud -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1100.png" xsd:anyURI -property_value: UBPROP:0000003 "These data show that ducts within the zebrafish pancreas originally arise in situ from isolated progenitor cells rather than arising from reiterative branching of the pancreatic epithelium. This process of pancreatic duct formation in zebrafish may be analogous to the mechanism of duct formation in the mammalian mammary and salivary glands. (...) A related mechanism of duct formation has also been proposed to occur within the mammalian pancreatic epithelium.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000256", ontology="VHOG", source="DOI:10.1016/j.ydbio.2005.04.035 Yee NS, Lorent K, Pack M, Exocrine pancreas development in zebrafish. Developmental Biology (2005)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000011 "Upon reaching its final destination, the ventral pancreatic bud fuses with the much larger dorsal pancreatic bud. At this point of fusion, the main ducts of the ventral and dorsal pancreatic buds fuse, forming the duct of Wirsung, the main pancreatic duct." xsd:string {source="WP"} +relationship: RO:0002150 UBERON:0001174 ! continuous with common bile duct +relationship: RO:0002202 UBERON:0003924 {source="EHDAA2"} ! develops from ventral pancreatic bud +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1100.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001066 @@ -167779,8 +166969,7 @@ is_a: UBERON:0011135 ! intervertebral cartilage intersection_of: UBERON:0011135 ! intervertebral cartilage intersection_of: has_part UBERON:0002242 ! nucleus pulposus relationship: has_part UBERON:0002242 ! nucleus pulposus -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/92/Gray301.png" xsd:anyURI -property_value: UBPROP:0000008 "strictly speaking the term intervertebral disk [applies to intervertebral cartilage]" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/92/Gray301.png" xsd:anyURI [Term] id: UBERON:0001068 @@ -167832,13 +167021,12 @@ xref: VHOG:0000265 xref: Wikipedia:External_carotid_artery xref: XAO:0000345 is_a: UBERON:0005396 {source="MA"} ! carotid artery segment -relationship: branching_part_of UBERON:0001530 {source="FMA"} ! common carotid artery plus branches -relationship: develops_from UBERON:0001530 {source="EHDAA2"} ! common carotid artery plus branches relationship: part_of UBERON:0001530 {source="FMA"} ! common carotid artery plus branches -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/13/External_carotid_a.gif" xsd:anyURI +relationship: RO:0002202 UBERON:0001530 {source="EHDAA2"} ! develops from common carotid artery plus branches +relationship: RO:0002380 UBERON:0001530 {source="FMA"} ! branching part of common carotid artery plus branches +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/13/External_carotid_a.gif" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://sourceforge.net/tracker/?func=detail&aid=3486863&group_id=76834&atid=1127722" xsd:anyURI -property_value: UBPROP:0000008 "not homologous to the external carotid of zebrafish (Goodrich, 1958) - http://zfish.nichd.nih.gov/zfatlas/Intro%20Page/comparative.html; check XAO" xsd:string [Term] id: UBERON:0001071 @@ -167859,9 +167047,9 @@ xref: Wikipedia:Superficial_part_of_transverse_cervical_artery is_a: UBERON:0012320 ! cervical artery intersection_of: UBERON:0012320 ! cervical artery intersection_of: part_of UBERON:0035549 ! vasculature of integument -relationship: connected_to UBERON:0012324 ! transverse cervical artery relationship: part_of UBERON:0035549 ! vasculature of integument -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002170 UBERON:0012324 ! connected to transverse cervical artery +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001072 @@ -167894,16 +167082,14 @@ xref: Wikipedia:Inferior_vena_cava xref: XAO:0000388 is_a: UBERON:0004087 ! vena cava intersection_of: UBERON:0004087 ! vena cava -intersection_of: drains UBERON:0000154 ! posterior region of body +intersection_of: RO:0002179 UBERON:0000154 ! drains posterior region of body disjoint_from: UBERON:0001585 {source="lexical"} ! anterior vena cava relationship: channels_into UBERON:0002078 {gci_relation="part_of", gci_filler="NCBITaxon:40674"} ! right cardiac atrium -relationship: connected_to UBERON:0002078 ! right cardiac atrium -relationship: develops_from UBERON:0005487 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="Wikipedia:Vitelline_vein"} ! vitelline vein -relationship: drains UBERON:0000154 ! posterior region of body -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray577.png" xsd:anyURI -property_value: UBPROP:0000001 "Trunk of systemic vein which is formed by the union of the right common iliac vein and the left common iliac vein and terminates in the right atrium[FMA]." xsd:string {source="FMA:10951"} -property_value: UBPROP:0000003 "Phylogenetic modifications within this basic pattern of arteries and veins are largely correlated with functional changes. In the transition from water to land, gills gave way to lungs, accompanied by the establishment of a pulmonary circulation. In some fishes and certainly in tetrapods, the cardinal veins become less involved in blood return. Instead, the composite, prominent postcava (posterior vena cava) arose to drain the posterior part of the body and the precava (anterior vena cava) developed to drain the anterior part of the body.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001194", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.454-455", source="http://bgee.unil.ch/"} +relationship: RO:0002170 UBERON:0002078 ! connected to right cardiac atrium +relationship: RO:0002179 UBERON:0000154 ! drains posterior region of body +relationship: RO:0002202 UBERON:0005487 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="Wikipedia:Vitelline_vein"} ! develops from vitelline vein +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray577.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001073 @@ -167917,11 +167103,11 @@ xref: MA:0000332 xref: SCTID:264021000 is_a: UBERON:8410024 ! intestinal junction intersection_of: UBERON:0007651 ! anatomical junction -intersection_of: connects UBERON:0000059 ! large intestine -intersection_of: connects UBERON:0002108 ! small intestine -relationship: connects UBERON:0000059 ! large intestine -relationship: connects UBERON:0002108 ! small intestine -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +intersection_of: RO:0002176 UBERON:0000059 ! connects large intestine +intersection_of: RO:0002176 UBERON:0002108 ! connects small intestine +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002176 UBERON:0000059 ! connects large intestine +relationship: RO:0002176 UBERON:0002108 ! connects small intestine [Term] id: UBERON:0001074 @@ -167951,15 +167137,12 @@ xref: ZFA:0001655 is_a: UBERON:0002323 {source="MA"} ! coelemic cavity lumen is_a: UBERON:0035809 ! serous cavity intersection_of: UBERON:0002553 ! anatomical cavity -intersection_of: luminal_space_of UBERON:0002406 ! pericardial sac -relationship: develops_from UBERON:0003887 {source="Wikipedia"} ! intraembryonic coelom -relationship: location_of UBERON:0002409 ! pericardial fluid -relationship: luminal_space_of UBERON:0002406 ! pericardial sac +intersection_of: RO:0002572 UBERON:0002406 ! luminal space of pericardial sac relationship: part_of UBERON:0002406 {source="FMA"} ! pericardial sac -relationship: surrounded_by UBERON:0002357 ! serous pericardium -property_value: UBPROP:0000001 "Anatomical space in which the heart is located and is surrounded by the pericardium.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002220", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart (of other tetrapods) is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000556", ontology="VHOG", source="ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "check ZFA, should actually be thoracic cavity. Note that Hyman defines the cavity as the space between the heart and the sac (but defines the sac as parietal)" xsd:string {external_ontology="ZFA"} +relationship: RO:0001015 UBERON:0002409 ! location of pericardial fluid +relationship: RO:0002202 UBERON:0003887 {source="Wikipedia"} ! develops from intraembryonic coelom +relationship: RO:0002219 UBERON:0002357 ! surrounded by serous pericardium +relationship: RO:0002572 UBERON:0002406 ! luminal space of pericardial sac [Term] id: UBERON:0001075 @@ -167991,17 +167174,12 @@ xref: TAO:0000126 xref: UMLS:C0223084 {source="ncithesaurus:Vertebral_Body"} xref: Wikipedia:Body_of_vertebra xref: ZFA:0000126 -is_a: UBERON:0001474 ! bone element +is_a: UBERON:0002513 ! endochondral bone is_a: UBERON:0016491 ! vertebral centrum element intersection_of: UBERON:0016491 ! vertebral centrum element -intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue +intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue relationship: part_of UBERON:0002412 ! vertebra -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/63/Corpusvertebrae.png" xsd:anyURI -property_value: UBPROP:0000001 "Centra are represented by mineralized, calcified, or ossified portions that surround the notochord. The autocentrum, present in Danio and all other living teleosts, is formed by direct ossification outside the elastica externa of the notochord (Arratia, 1999).[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000126", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Cylindrical body of bone, round or oval in cross section, which functionally replaces the notochord.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000697", ontology="AAO", source="AAO:Duellman_and_Trueb_2008"} -property_value: UBPROP:0000001 "The body is the largest part of a vertebra, and is more or less cylindrical in shape. Its upper and lower surfaces are flattened and rough, and give attachment to the intervertebral fibrocartilages, and each presents a rim around its circumference. In front, the body is convex from side to side and concave from above downward. Behind, it is flat from above downward and slightly concave from side to side. Its anterior surface presents a few small apertures, for the passage of nutrient vessels. On the posterior surface is a single large, irregular aperture, or occasionally more than one, for the exit of the basi-vertebral veins from the body of the vertebra. [WP,unvetted][Wikipedia:Body_of_vertebra]." xsd:string {source="Wikipedia:Body_of_vertebra"} -property_value: UBPROP:0000005 "The vertebral centrum may be cartilaginous, develop as cartilage but be replaced by bone or mineralized, or form directly through intramembranous ossification.[VSAO]" xsd:string {date_retrieved="2012-09-06", external_class="VSAO:0000183", ontology="VSAO", source="Curator"} -property_value: UBPROP:0000012 "VSAO definition states it surrounds notochord but not applicable to post-natal." xsd:string {external_ontology="VSAO"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/63/Corpusvertebrae.png" xsd:anyURI [Term] id: UBERON:0001076 @@ -168030,12 +167208,7 @@ xref: Wikipedia:Spinous_process xref: ZFA:0001336 is_a: UBERON:0006061 ! process of vertebra relationship: part_of UBERON:0003861 ! neural arch -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/48/Processusspinosusvertebrae.png" xsd:anyURI -property_value: UBPROP:0000001 "Elaboration of the mid-dorsal keel into a posterior or posterolateral process.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000705", ontology="AAO", source="AAO:Pugener_and_Maglia_2008"} -property_value: UBPROP:0000001 "Neural spines are extensions of neural arches dorsal to the neural canal in the median skeletogenous septum. Neural spines are typically unpaired median structures but can be paired in some instances, e.g., in the abdominal region of basal teleosts such as Leptolepis, Elops, Megalops, and Hiodon).[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001336", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Small, posteriorly directed process at the posterior margin of each neural arch lamina; it is not a neural spine.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000739", ontology="AAO", source="AAO:Pugener_2002"} -property_value: UBPROP:0000002 "relationship loss: part_of mid-dorsal keel (AAO:0000735)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000705", ontology="AAO"} -property_value: UBPROP:0000008 "The spinous process of a vertebra is directed backward and downward from the junction of the laminae (in humans), and serves for the attachment of muscles and ligaments. In animals without an erect stance, the process points upward and may slant forward or backward. Spinous processes are exaggerated in some animals, such as the extinct Dimetrodon and Spinosaurus, where they form a sail- or finback. [Wikipedia:Spinous_process]" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/48/Processusspinosusvertebrae.png" xsd:anyURI [Term] id: UBERON:0001077 @@ -168057,8 +167230,7 @@ xref: SCTID:264238006 xref: Wikipedia:Transverse_process xref: XAO:0003102 is_a: UBERON:0006061 ! process of vertebra -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/a1/Processustransversusvertebrae.PNG" xsd:anyURI -property_value: UBPROP:0000001 "Projections on each side of the vertebra from the point where the neural arch lamina joins the pedicel for the articulation with the head of a single-headed rib or the upper head of a double-headed rib. Also called diapophyses. They provide surfaces for the attachment of muscles. In anurans, the term transverse process is used in reference to the processes associated with the presacral and postsacral vertebrae." xsd:string {source="AAO:0000698"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/a1/Processustransversusvertebrae.PNG" xsd:anyURI [Term] id: UBERON:0001081 @@ -168090,8 +167262,8 @@ is_a: UBERON:0002165 ! endocardium is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0002165 ! endocardium intersection_of: part_of UBERON:0002082 ! cardiac ventricle -relationship: contributes_to_morphology_of UBERON:0002082 ! cardiac ventricle relationship: part_of UBERON:0004784 {source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! heart ventricle wall +relationship: RO:0002433 UBERON:0002082 ! contributes to morphology of cardiac ventricle [Term] id: UBERON:0001082 @@ -168108,7 +167280,6 @@ is_a: UBERON:0002348 ! epicardium intersection_of: UBERON:0002348 ! epicardium intersection_of: part_of UBERON:0002082 ! cardiac ventricle relationship: part_of UBERON:0002082 ! cardiac ventricle -property_value: UBPROP:0000001 "The external layer of the ventricle bounding the ventricular myocardium. It is formed by a single layer of mesothelial cells supported by a basal lamina, and imbricated with collagen, fibroblasts, and vascular structures in the subepicardial space. Hu et al. 2001.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005058", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0001083 @@ -168132,10 +167303,8 @@ xref: ZFA:0005061 is_a: UBERON:0002349 ! myocardium intersection_of: UBERON:0002349 ! myocardium intersection_of: part_of UBERON:0002082 ! cardiac ventricle -relationship: contributes_to_morphology_of UBERON:0002082 ! cardiac ventricle relationship: part_of UBERON:0004784 {source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! heart ventricle wall -property_value: UBPROP:0000001 "Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer Hu et al. 2001.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005061", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000604", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481", source="http://bgee.unil.ch/"} +relationship: RO:0002433 UBERON:0002082 ! contributes to morphology of cardiac ventricle [Term] id: UBERON:0001084 @@ -168196,8 +167365,8 @@ xref: ncithesaurus:Pleural_Fluid xref: Wikipedia:Pleural_fluid is_a: UBERON:0036244 ! secretion of serous membrane intersection_of: UBERON:0007779 ! transudate -intersection_of: located_in UBERON:0002402 ! pleural cavity -relationship: located_in UBERON:0002402 ! pleural cavity +intersection_of: RO:0001025 UBERON:0002402 ! located in pleural cavity +relationship: RO:0001025 UBERON:0002402 ! located in pleural cavity [Term] id: UBERON:0001088 @@ -168225,9 +167394,8 @@ xref: Wikipedia:Urine is_a: UBERON:0000174 ! excreta intersection_of: UBERON:0000174 ! excreta intersection_of: produced_by UBERON:0002113 ! kidney -relationship: has_quality PATO:0001548 {gci_relation="part_of", gci_filler="NCBITaxon:40674"} ! quality of a liquid relationship: produced_by UBERON:0002113 ! kidney -property_value: UBPROP:0000008 "kidney excreta from some taxa (e.g. in aves) may not be liquid" xsd:string +relationship: RO:0000086 PATO:0001548 {gci_relation="part_of", gci_filler="NCBITaxon:40674"} ! has quality quality of a liquid [Term] id: UBERON:0001089 @@ -168278,11 +167446,8 @@ is_a: UBERON:0007794 {source="FMA"} ! secretion of serous gland intersection_of: UBERON:0007779 ! transudate intersection_of: produced_by CL:0000214 ! synovial cell relationship: has_part CHEBI:16336 -relationship: located_in UBERON:0007617 ! synovial cavity of joint relationship: produced_by CL:0000214 ! synovial cell -property_value: UBPROP:0000001 "Portion of organism substance that is a clear fluid that occupies the space in synovial joints.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005154", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000009 "It provides nutrients and lubrication for articular cartilage" xsd:string -property_value: UBPROP:0000010 "The fluid contains hyaluronan secreted by fibroblast-like cells in the synovial membrane, lubricin (proteoglycan 4; PRG4) secreted by the surface chondrocytes of the articular cartilage and interstitial fluid filtered from the blood plasma" xsd:string +relationship: RO:0001025 UBERON:0007617 ! located in synovial cavity of joint [Term] id: UBERON:0001091 @@ -168318,24 +167483,21 @@ xref: UMLS:C0040426 {source="ncithesaurus:Tooth"} xref: VHOG:0001733 xref: Wikipedia:Tooth xref: XAO:0000431 -xref: ZFA:0000694 is_a: UBERON:0003913 ! tooth-like structure +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest -relationship: has_developmental_contribution_from UBERON:0000930 {source="XAO-modified"} ! stomodeum -relationship: has_developmental_contribution_from UBERON:0005176 {source="ZFA-modified"} ! tooth enamel organ +relationship: BSPO:0000126 UBERON:0011595 {gci_relation="part_of", gci_filler="NCBITaxon:9606"} ! jaw region relationship: has_part UBERON:0001751 ! dentine relationship: has_part UBERON:0001752 {gci_relation="part_of", gci_filler="NCBITaxon:9606"} ! enamel -relationship: immediate_transformation_of UBERON:0008281 {source="cjm"} ! tooth bud -relationship: in_lateral_side_of UBERON:0011595 {gci_relation="part_of", gci_filler="NCBITaxon:9606"} ! jaw region -relationship: never_in_taxon NCBITaxon:189497 {source="Wikipedia"} -relationship: never_in_taxon NCBITaxon:8782 ! Aves -relationship: never_in_taxon NCBITaxon:9257 {source="PMID:10210685"} -relationship: never_in_taxon NCBITaxon:9761 relationship: part_of UBERON:0011595 {gci_relation="part_of", gci_filler="NCBITaxon:32523"} ! jaw region -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/14/Teeth_by_David_Shankbone.jpg" xsd:anyURI -property_value: UBPROP:0000003 "The ancestor of recent vertebrate teeth was a tooth-like structure on the outer body surface of jawless fishes.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001733", ontology="VHOG", source="PMID:19266065 Koussoulakou DS, Margaritis LH, Koussoulakos SL, A curriculum vitae of teeth: evolution, generation, regeneration. International Journal of Biological Sciences (2009)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "dental" xsd:string -property_value: UBPROP:0000008 "absent in living platypus, present in toothed Miocene platypus Obduron dicksoni" xsd:string {source="PMID:10210685"} +relationship: RO:0002254 UBERON:0000930 {source="XAO-modified"} ! has developmental contribution from stomodeum +relationship: RO:0002254 UBERON:0005176 {source="ZFA-modified"} ! has developmental contribution from tooth enamel organ +relationship: RO:0002495 UBERON:0008281 {source="cjm"} ! immediate transformation of tooth bud +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/14/Teeth_by_David_Shankbone.jpg" xsd:anyURI +property_value: RO:0002161 NCBITaxon:189497 {source="Wikipedia"} +property_value: RO:0002161 NCBITaxon:8782 +property_value: RO:0002161 NCBITaxon:9257 {source="PMID:10210685"} +property_value: RO:0002161 NCBITaxon:9761 [Term] id: UBERON:0001092 @@ -168370,13 +167532,10 @@ xref: UMLS:C0004170 {source="ncithesaurus:C1_Vertebra"} xref: Wikipedia:Atlas_(anatomy) xref: ZFA:0001167 is_a: UBERON:0002412 ! vertebra -relationship: anterior_to UBERON:0001093 ! vertebral bone 2 relationship: anteriorly_connected_to UBERON:0001676 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="FMA"} ! occipital bone +relationship: BSPO:0000096 UBERON:0001093 ! vertebral bone 2 relationship: part_of UBERON:0006072 {gci_relation="part_of", gci_filler="NCBITaxon:32523"} ! cervical region of vertebral column -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000001 "First postcranial vertebra, which is modified anteriorly to articulate with the skull.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000709", ontology="AAO", source="AAO:Duellman_and_Trueb_1994"} -property_value: UBPROP:0000001 "Vertebra that is posteriorly adjacent to the neurocranium.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001167", ontology="TAO", source="TAO:wd"} -property_value: UBPROP:0000107 "1" xsd:nonNegativeInteger +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001093 @@ -168412,10 +167571,7 @@ xref: ZFA:0001168 is_a: UBERON:0002412 ! vertebra relationship: anteriorly_connected_to UBERON:0001092 {source="FMA"} ! vertebral bone 1 relationship: part_of UBERON:0006072 {gci_relation="part_of", gci_filler="NCBITaxon:32523"} ! cervical region of vertebral column -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000001 "Vertebra that is posteriorly adjacent to vertebra 1.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001168", ontology="TAO", source="TAO:wd"} -property_value: UBPROP:0000013 "not the same as ZFA term 'axis'" xsd:string -property_value: UBPROP:0000107 "2" xsd:nonNegativeInteger +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001095 @@ -168453,10 +167609,8 @@ is_a: UBERON:0002412 ! vertebra is_a: UBERON:0004247 ! bone of dorsum is_a: UBERON:0018142 ! caudal vertebra endochondral element intersection_of: UBERON:0018142 ! caudal vertebra endochondral element -intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000001 "Vertebrae bearing a hemal arch and spine. The most posterior caudal vertebrae support the caudal fin and are referred to as preural vertebrae.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000326", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000012 "we deliberately merge the MA classes as we believe them equivalent" xsd:string {external_ontology="MA"} +intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001096 @@ -168507,10 +167661,10 @@ xref: UMLS:C0224347 {source="ncithesaurus:Pectoralis_Minor"} xref: VHOG:0000902 xref: Wikipedia:Pectoralis_minor_muscle is_a: UBERON:0001495 {source="FMA"} ! pectoral muscle -relationship: has_muscle_insertion UBERON:0007174 {notes="medial border and superior surface of the coracoid process of the scapula", source="dbpedia"} ! medial border of scapula -relationship: has_muscle_origin UBERON:0002228 {notes="third to fifth ribs near their costal cartilages", source="dbpedia"} ! rib -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/5/5d/Pectoralis_minor.png" xsd:anyURI +relationship: RO:0002372 UBERON:0002228 ! has muscle origin rib +relationship: RO:0002373 UBERON:0007174 ! has muscle insertion medial border of scapula +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/5/5d/Pectoralis_minor.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001103 @@ -168544,18 +167698,10 @@ xref: VHOG:0000713 xref: Wikipedia:Thoracid_diaphragm is_a: UBERON:0003830 ! thoracic segment muscle is_a: UBERON:0003831 ! respiratory system muscle -relationship: immediate_transformation_of UBERON:0010084 {evidence="definitional"} ! future diaphragm -relationship: innervated_by UBERON:0001884 ! phrenic nerve -relationship: never_in_taxon NCBITaxon:8782 {source="Wikipedia:Thoracic_diaphragm#Comparative_anatomy_and_evolution"} ! Aves -relationship: only_in_taxon NCBITaxon:40674 {source="PMID:23586979"} ! Mammalia -property_value: UBPROP:0000001 "The diaphragm is a skeletal muscle that is responsible for contraction and expansion of the lungs[GO]." xsd:string {source="GO:0060539"} -property_value: UBPROP:0000003 "The mammals are characterized by a diaphragm, which separates the thoracic portion of the body cavity from the abdominal region and assists in drawing air into the lungs and forcing it out. Modern reptiles lack a muscular diaphragm and it is reasonable to suppose that the diaphragm developed as a new device that made possible a large degree of oxygen intake for active animals. The change may have taken place during the transition from reptile to mammal (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000713", ontology="VHOG", source="ISBN:978-0471384618 Colbert EH, Evolution of the vertebrates: a history of the backboned animals through time (2001) p.278", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "phrenic" xsd:string -property_value: UBPROP:0000008 "The existence of some membrane separating the pharynx from the stomach can be traced widely among the chordates. Thus amphioxus possesses an atrium by which water exits the pharynx, which has been argued (and disputed) to be homologous to structures in ascidians and hagfishes.[3]" xsd:string -property_value: UBPROP:0000008 "The urochordate epicardium separates digestive organs from the pharynx and heart, but the anus returns to the upper compartment to discharge wastes through an outgoing siphon (Thoracic_diaphragm#Comparative_anatomy_and_evolution)" xsd:string -property_value: UBPROP:0000009 "barrier between thoracic and abdominal cavities; stop gastric contents from refluxing into the oesophagus" xsd:string -property_value: UBPROP:0000009 "breathing control" xsd:string -property_value: UBPROP:0000011 "originate from the cervical somites, likely C3-C5[PMID:23586979]" xsd:string +relationship: RO:0002005 UBERON:0001884 ! innervated_by phrenic nerve +relationship: RO:0002160 NCBITaxon:40674 {source="PMID:23586979"} ! only in taxon Mammalia +relationship: RO:0002495 UBERON:0010084 ! immediate transformation of future diaphragm +property_value: RO:0002161 NCBITaxon:8782 {source="Wikipedia:Thoracic_diaphragm#Comparative_anatomy_and_evolution"} [Term] id: UBERON:0001105 @@ -168587,20 +167733,13 @@ is_a: UBERON:0002495 {source="FMA"} ! long bone is_a: UBERON:0003461 {gci_relation="part_of", gci_filler="NCBITaxon:32523"} ! shoulder bone is_a: UBERON:0007829 ! pectoral girdle bone is_a: UBERON:0015212 ! lateral structure -relationship: connected_to UBERON:0000975 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! sternum -relationship: develops_from UBERON:0010905 {editor="mah", source="ISBN:978-0-12-319060-4"} ! clavicle bone primordium -relationship: has_developmental_contribution_from UBERON:0010843 {notes="from secondary cartilage of fusion", source="ISBN:978-0-12-319060-4"} ! clavicle cartilage element -relationship: in_lateral_side_of UBERON:0002091 ! appendicular skeleton +relationship: BSPO:0000126 UBERON:0002091 ! appendicular skeleton relationship: overlaps UBERON:0001469 {gci_relation="part_of", gci_filler="NCBITaxon:32523"} ! sternoclavicular joint -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/5/59/Pectoral_girdles-en.svg" xsd:anyURI -property_value: UBPROP:0000001 "Slender, paired bones of intramembranous origin that invest the anterior margins of the procoracoids.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000761", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000002 "relationship loss: part_of zonal element (AAO:0000936)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000761", ontology="AAO"} -property_value: UBPROP:0000003 "In early tetrapods, the connecting skull bone, the posttemporal, and adjoining shoulder bones, supracleithrum and postcleithrum (=anocleithrum), are absent, leaving a dermal shoulder girdle composed of the remaining ventral elements: the paired cleithrum and clavicle, and an unpaired midventral interclavicle that joins both halves of the girdle across the midline. (...) Several dermal elements of the shoulder persist in early synapsids. The clavicle and interclavicle are present in therapsids and monotremes, but in marsupials and placentals, the interclavicle is absent, the clavicle often is reduced in size, and the scapula becomes the predominant shoulder element.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000849", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.330-333 and Figure 9.18", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "clavicular" xsd:string -property_value: UBPROP:0000008 "The clavicle first appears as part of the skeleton in primitive bony fish, where it is associated with the pectoral fin; they also have a bone called the cleithrum. In such fish, the paired clavicles run behind and below the gills on each side, and are joined by a solid symphysis on the fish's underside. They are, however, absent in cartilagenous fish and in the vast majority of living bony fish, including all of the teleosts[ISBN 0-03-910284-X]." xsd:string -property_value: UBPROP:0000011 "In most birds and mammals the clavicles are the only dermal elements in the trunk, and is the only membrane bone associated with the pectoral girdle in these taxa. However, there can be secondary cartilage, or subsequent endochondral ossification, or fusion with endochondral elements. In rodents, the lateral ends of the clavicle are endochondral but the main portion is dermal." xsd:string {source="ISBN:978-0-12-319060-4"} -property_value: UBPROP:0000012 "FMA and MA differ in whether they consider this part of the shoulder" xsd:string {external_ontology="FMA"} +relationship: RO:0002170 UBERON:0000975 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to sternum +relationship: RO:0002202 UBERON:0010905 ! develops from clavicle bone primordium +relationship: RO:0002254 UBERON:0010843 ! has developmental contribution from clavicle cartilage element +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/5/59/Pectoral_girdles-en.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001112 @@ -168629,17 +167768,17 @@ xref: UMLS:C0224362 {source="ncithesaurus:Musculus_Latissimus_Dorsi"} xref: VHOG:0000930 xref: Wikipedia:Latissimus_dorsi_muscle is_a: UBERON:0001482 ! muscle of shoulder +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0034908 ! scapular muscle -relationship: develops_from UBERON:0010982 {source="EHDAA2"} ! latissimus dorsi pre-muscle mass -relationship: has_muscle_antagonist UBERON:0001476 {source="dbpedia"} ! deltoid -relationship: has_muscle_antagonist UBERON:0002380 {source="dbpedia"} ! trapezius muscle -relationship: has_muscle_insertion UBERON:0000976 {notes="floor of intertubercular groove of the humerus", source="dbpedia"} ! humerus -relationship: has_muscle_origin UBERON:0006849 ! scapula -relationship: has_muscle_origin UBERON:0007175 {notes="spinous processes of thoracic T7-T12 thoracolumbar fascia iliac crest and inferior 3 or 4 ribs inferior angle of scapula", source="dbpedia"} ! inferior angle of scapula relationship: part_of UBERON:0008713 {source="EHDAA2"} ! pectoral girdle and thoracic body wall skeletal muscle -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/7/7d/Latissimus_dorsi.png" xsd:anyURI -property_value: UBPROP:0000008 "In humans it inserts along a roughened line deep in the groove. In other mammals (most, I believe) it is an actual projection, the latissimus dorsi process [FEED:rd] [https://github.com/obophenotype/uberon/issues/1192]" xsd:string +relationship: RO:0002202 UBERON:0010982 {source="EHDAA2"} ! develops from latissimus dorsi pre-muscle mass +relationship: RO:0002372 UBERON:0006849 ! has muscle origin scapula +relationship: RO:0002372 UBERON:0007175 ! has muscle origin inferior angle of scapula +relationship: RO:0002373 UBERON:0000976 ! has muscle insertion humerus +relationship: RO:0002568 UBERON:0001476 {source="dbpedia"} ! has muscle antagonist deltoid +relationship: RO:0002568 UBERON:0002380 {source="dbpedia"} ! has muscle antagonist trapezius muscle +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/7d/Latissimus_dorsi.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001113 @@ -168656,9 +167795,10 @@ xref: NCIT:C49579 xref: SCTID:245378000 xref: UMLS:C0447541 {source="ncithesaurus:Liver_Lobe"} xref: Wikipedia:Liver#Lobes +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0009912 {source="FMA"} ! anatomical lobe relationship: part_of UBERON:0002107 ! liver -property_value: editor_note "some work needs to be done to ensure the child terms of this class have correct isa/partof placement. in MA they are subclasses, in FMA they are parts" xsd:string +property_value: IAO:0000116 "some work needs to be done to ensure the child terms of this class have correct isa/partof placement. in MA they are subclasses, in FMA they are parts" xsd:string [Term] id: UBERON:0001114 @@ -168688,10 +167828,9 @@ xref: VHOG:0001424 xref: Wikipedia:Right_lobe_of_liver xref: ZFA:0005173 is_a: UBERON:0001113 ! lobe of liver -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/a3/Gray1087-liver.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Liver.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Liver.glb" xsd:anyURI -property_value: UBPROP:0000001 "Portion of the liver which develops on the fish's right side adjacent to the gall bladder.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005173", ontology="TAO", source="ZFIN:curator"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/a3/Gray1087-liver.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Liver.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Liver.glb" xsd:anyURI [Term] id: UBERON:0001115 @@ -168718,10 +167857,9 @@ xref: VHOG:0001423 xref: Wikipedia:Left_lobe_of_liver xref: ZFA:0005172 is_a: UBERON:0001113 ! lobe of liver -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/a3/Gray1087-liver.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Liver.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Liver.glb" xsd:anyURI -property_value: UBPROP:0000001 "Portion of the liver which develops on the fish's left side.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005172", ontology="TAO", source="ZFIN:curator"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/a3/Gray1087-liver.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Liver.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Liver.glb" xsd:anyURI [Term] id: UBERON:0001118 @@ -168743,14 +167881,14 @@ xref: SCTID:245537001 xref: UMLS:C0447647 {source="ncithesaurus:Thyroid_Gland_Lobe"} xref: VHOG:0000732 xref: Wikipedia:Lobes_of_thyroid_gland +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0009912 ! anatomical lobe is_a: UBERON:0015212 ! lateral structure -is_a: UBERON:0035075 ! thymus subunit intersection_of: UBERON:0009912 ! anatomical lobe intersection_of: part_of UBERON:0002046 ! thyroid gland -relationship: in_lateral_side_of UBERON:0002046 {source="FMA-abduced-lr"} ! thyroid gland -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/9e/Gray1174.png" xsd:anyURI -property_value: UBPROP:0000003 "Thus, a thyroid capable of forming iodotyrosines and iodothyronines is present in all vertebrates. (...) Certain morphologic changes occur after the biochemical evolution of the thyroid has ceased. In the adult lamprey and in most bony fishes, the gland is not encapsulated. (...) In cartilaginous fish, the thyroid is encapsulated. In the higher vertebrate forms, the thyroid is a one- or two-lobed encapsulated structure.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000732", ontology="VHOG", source="http://bgee.unil.ch/", source="http://www.thyroidmanager.org/Chapter1/chapter01.htm"} +relationship: BSPO:0000126 UBERON:0002046 {source="FMA-abduced-lr"} ! thyroid gland +relationship: part_of UBERON:0002046 ! thyroid gland +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/9e/Gray1174.png" xsd:anyURI [Term] id: UBERON:0001119 @@ -168770,10 +167908,8 @@ xref: UMLS:C0229581 {source="ncithesaurus:Right_Thyroid_Gland_Lobe"} xref: VHOG:0000733 is_a: UBERON:0001118 ! lobe of thyroid gland intersection_of: UBERON:0001118 ! lobe of thyroid gland -intersection_of: in_right_side_of UBERON:0002046 ! thyroid gland -relationship: in_right_side_of UBERON:0002046 ! thyroid gland -property_value: UBPROP:0000003 "Thus, a thyroid capable of forming iodotyrosines and iodothyronines is present in all vertebrates. (...) Certain morphologic changes occur after the biochemical evolution of the thyroid has ceased. In the adult lamprey and in most bony fishes, the gland is not encapsulated. (...) In cartilaginous fish, the thyroid is encapsulated. In the higher vertebrate forms, the thyroid is a one- or two-lobed encapsulated structure.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000733", ontology="VHOG", source="http://bgee.unil.ch/", source="http://www.thyroidmanager.org/Chapter1/chapter01.htm"} -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +intersection_of: BSPO:0000121 UBERON:0002046 ! thyroid gland +relationship: BSPO:0000121 UBERON:0002046 ! thyroid gland [Term] id: UBERON:0001120 @@ -168793,10 +167929,8 @@ xref: UMLS:C0229582 {source="ncithesaurus:Left_Thyroid_Gland_Lobe"} xref: VHOG:0000734 is_a: UBERON:0001118 ! lobe of thyroid gland intersection_of: UBERON:0001118 ! lobe of thyroid gland -intersection_of: in_left_side_of UBERON:0002046 ! thyroid gland -relationship: in_left_side_of UBERON:0002046 ! thyroid gland -property_value: UBPROP:0000003 "Thus, a thyroid capable of forming iodotyrosines and iodothyronines is present in all vertebrates. (...) Certain morphologic changes occur after the biochemical evolution of the thyroid has ceased. In the adult lamprey and in most bony fishes, the gland is not encapsulated. (...) In cartilaginous fish, the thyroid is encapsulated. In the higher vertebrate forms, the thyroid is a one- or two-lobed encapsulated structure.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000734", ontology="VHOG", source="http://bgee.unil.ch/", source="http://www.thyroidmanager.org/Chapter1/chapter01.htm"} -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +intersection_of: BSPO:0000120 UBERON:0002046 ! thyroid gland +relationship: BSPO:0000120 UBERON:0002046 ! thyroid gland [Term] id: UBERON:0001125 @@ -168824,13 +167958,13 @@ xref: VHOG:0000679 xref: Wikipedia:Serratus_anterior_muscle is_a: UBERON:0001482 ! muscle of shoulder is_a: UBERON:0034908 ! scapular muscle -relationship: develops_from UBERON:0010986 {source="EHDAA2"} ! serratus ventralis pre-muscle mass -relationship: has_muscle_antagonist UBERON:0002380 {source="dbpedia"} ! trapezius muscle -relationship: has_muscle_insertion UBERON:0006849 {notes="costal aspect of medial margin of the scapula", source="dbpedia"} ! scapula -relationship: has_muscle_origin UBERON:0002228 {notes="fleshy slips from the outer surface of upper 8 or 9 ribs", source="dbpedia"} ! rib -relationship: innervated_by UBERON:0003726 {notes="long thoracic nerve", source="dbpedia"} ! thoracic nerve -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/c/c6/Serratus_anterior.png" xsd:anyURI +relationship: RO:0002005 UBERON:0003726 ! innervated_by thoracic nerve +relationship: RO:0002202 UBERON:0010986 {source="EHDAA2"} ! develops from serratus ventralis pre-muscle mass +relationship: RO:0002372 UBERON:0002228 ! has muscle origin rib +relationship: RO:0002373 UBERON:0006849 ! has muscle insertion scapula +relationship: RO:0002568 UBERON:0002380 {source="dbpedia"} ! has muscle antagonist trapezius muscle +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/c/c6/Serratus_anterior.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001130 @@ -168874,17 +168008,14 @@ xref: XAO:0003074 xref: ZFA:0001559 is_a: UBERON:0000075 ! subdivision of skeletal system intersection_of: UBERON:0000075 ! subdivision of skeletal system -intersection_of: composed_primarily_of UBERON:0010913 ! vertebral element -relationship: composed_primarily_of UBERON:0010913 ! vertebral element -relationship: never_in_taxon NCBITaxon:7762 -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +intersection_of: RO:0002473 UBERON:0010913 ! composed primarily of vertebral element relationship: part_of UBERON:0011138 {source="cjm"} ! postcranial axial skeletal system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: protects UBERON:0002240 ! spinal cord -property_value: editor_note "Note that in contrast to VSAO, this is a subset of the skeletal system, and thus includes intervertebral joints, cartilage and ligaments etc. Some ontologies such as AAO seem to purely refer to the skeleton" xsd:string -property_value: UBPROP:0000001 "Anatomical cluster that consists of all the vertebra in the body.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000185", ontology="VSAO", source="VSAO:curator"} -property_value: UBPROP:0000001 "The vertebral column consists of a series of vertebrae connected by ligaments. It provides a supporting axis for the body and protects the spinal cord. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001142", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/vertebral+column"} -property_value: UBPROP:0000003 "Vertebrata is characterized by three synapomorphies. First, vertebrates have a backbone composed of vertebrae (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001142", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.53", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002473 UBERON:0010913 ! composed primarily of vertebral element +property_value: IAO:0000116 "Note that in contrast to VSAO, this is a subset of the skeletal system, and thus includes intervertebral joints, cartilage and ligaments etc. Some ontologies such as AAO seem to purely refer to the skeleton" xsd:string +property_value: RO:0002161 NCBITaxon:7762 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001131 @@ -168902,14 +168033,13 @@ xref: SCTID:280734009 xref: Wikipedia:Vertebral_foramen is_a: UBERON:0004111 ! anatomical conduit intersection_of: UBERON:0004111 ! anatomical conduit -intersection_of: conduit_for UBERON:0002240 ! spinal cord -intersection_of: lumen_of UBERON:0010913 ! vertebral element -relationship: conduit_for UBERON:0002240 ! spinal cord -relationship: lumen_of UBERON:0010913 ! vertebral element +intersection_of: RO:0002570 UBERON:0002240 ! conduit for spinal cord +intersection_of: RO:0002571 UBERON:0010913 ! lumen of vertebral element relationship: part_of UBERON:0006692 ! vertebral canal relationship: part_of UBERON:0010913 ! vertebral element -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/10/Foramenvertebrale.png" xsd:anyURI -property_value: UBPROP:0000001 "Opening on the vertebra for a spinal nerve as it emerges from the spinal canal.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000729", ontology="AAO", source="AAO:LAP"} +relationship: RO:0002570 UBERON:0002240 ! conduit for spinal cord +relationship: RO:0002571 UBERON:0010913 ! lumen of vertebral element +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/10/Foramenvertebrale.png" xsd:anyURI [Term] id: UBERON:0001132 @@ -168943,19 +168073,8 @@ xref: XAO:0000167 is_a: UBERON:0002368 ! endocrine gland relationship: capable_of GO:0035898 ! parathyroid hormone secretion relationship: capable_of_part_of GO:0055074 {source="Wikipedia"} ! calcium ion homeostasis -relationship: develops_from UBERON:0007124 {gci_relation="part_of", gci_filler="NCBITaxon:10090", source="PMID:16313389"} ! pharyngeal pouch 3 -relationship: develops_from UBERON:0007125 {gci_relation="part_of", gci_filler="NCBITaxon:9606", notes="pouches 3 and 4 in human", source="PMID:16313389"} ! pharyngeal pouch 4 -relationship: has_developmental_contribution_from UBERON:0010025 {gci_relation="part_of", gci_filler="NCBITaxon:40674", notes="Mammals", source="ISBN:0073040584-table13.1"} ! dorsal part of pharyngeal pouch 3 -relationship: has_developmental_contribution_from UBERON:0010026 {gci_relation="part_of", gci_filler="NCBITaxon:8782", notes="Aves", source="ISBN:0073040584-table13.1"} ! ventral part of pharyngeal pouch 3 -relationship: has_developmental_contribution_from UBERON:0010027 {gci_relation="part_of", gci_filler="NCBITaxon:40674", notes="Mammals", source="ISBN:0073040584-table13.1"} ! dorsal part of pharyngeal pouch 4 -relationship: has_developmental_contribution_from UBERON:0010028 {gci_relation="part_of", gci_filler="NCBITaxon:8782", notes="Aves", source="ISBN:0073040584-table13.1"} ! ventral part of pharyngeal pouch 4 -relationship: only_in_taxon NCBITaxon:32523 {source="PMID:16313389"} ! Tetrapoda -property_value: UBPROP:0000001 "Any one of several small structures, usually four, attached to the dorsal surfaces of the lateral lobes of the thyroid gland. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001188", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/parathyroid+gland"} -property_value: UBPROP:0000001 "Either of the two pairs of small, spherical, encapsulated glands which develop from ventral growths of the third and fourth pharyngeal pouches and are closely associated with the external jugular veins. Calcitonin and parathyroid hormone are secreted by these glands.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010545", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "The evolution of the tetrapods, and the shift from an aquatic to a terrestrial environment, was believed to have required new controls for regulating calcium homeostasis, and thus the evolution of parathyroid glands (...) both the tetrapod parathyroid and the gills of fish contribute to the regulation of extracellular calcium levels. It is therefore reasonable to suggest that the parathyroid gland evolved as a result of the transformation of the gills into the parathyroid glands of tetrapods and the transition from an aquatic to a terrestrial environment. This interpretation would also explain the positioning of the parathyroid gland within the pharynx in the tetrapod body. Were the parathyroid gland to have emerged de novo with the evolution of the tetrapods it could, as an endocrine organ, have been placed anywhere in the body and still exert its effect.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001188", ontology="VHOG", source="DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M, Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "Parathyroid glands are found in all adult tetrapods, although they vary in their number, and in their exact position. Mammals typically have four parathyroids, while other groups typically have six. Fish do not possess parathyroid glands, although the ultimobranchial glands, which are found close to the oesophagus, may have a similar function and could even be homologous with the tetrapod parathyroids. Even these glands are absent in the most primitive vertebrates, the jawless fish, but as these species have no bone in their skeletons, only cartilage, it may be that they have less need to regulate calcium metabolism. The conserved homology of genes and calcium-sensing receptors in fish gills with those in the parathryroid glands of birds and mammals is recognized by evolutionary developmental biology as evolution-using genes and gene networks in novel ways to generate new structures with some similar functions and novel functions[WP]" xsd:string -property_value: UBPROP:0000011 "In humans and chick it emerges from pouches 3 and 4, but in mice it is exclusively generated by the third pouch" xsd:string -property_value: UBPROP:0000011 "table 13.1 of Kardong is used to create the taxon-specific developmental relationships here, although some omissions are made for simplicity." xsd:string {source="PMID:16313389"} +relationship: RO:0002160 NCBITaxon:32523 {source="PMID:16313389"} ! only in taxon Tetrapoda +relationship: RO:0002202 UBERON:0007124 {gci_relation="part_of", gci_filler="NCBITaxon:10090", source="PMID:16313389"} ! develops from pharyngeal pouch 3 [Term] id: UBERON:0001133 @@ -169006,10 +168125,10 @@ is_a: UBERON:8600006 ! visceral striated muscle tissue intersection_of: UBERON:0002036 ! striated muscle tissue intersection_of: has_part CL:0000746 ! cardiac muscle cell disjoint_from: UBERON:0001134 ! skeletal muscle tissue -relationship: composed_primarily_of CL:0000746 ! cardiac muscle cell relationship: has_part CL:0000746 ! cardiac muscle cell relationship: part_of UBERON:0007100 ! primary circulatory organ -property_value: editor_note "check relationship with myocardium. part_of in MA - but we also have a more specific class 'cardiac muscle tissue of myocardium'. Check ncit" xsd:string +relationship: RO:0002473 CL:0000746 ! composed primarily of cardiac muscle cell +property_value: IAO:0000116 "check relationship with myocardium. part_of in MA - but we also have a more specific class 'cardiac muscle tissue of myocardium'. Check ncit" xsd:string [Term] id: UBERON:0001134 @@ -169031,15 +168150,12 @@ xref: UMLS:C0242692 {source="ncithesaurus:Skeletal_Muscle_Tissue"} xref: Wikipedia:Skeletal_striated_muscle is_a: UBERON:0002036 ! striated muscle tissue intersection_of: UBERON:0002385 ! muscle tissue -intersection_of: composed_primarily_of CL:0008002 ! skeletal muscle fiber -relationship: composed_primarily_of CL:0008002 ! skeletal muscle fiber -relationship: develops_from UBERON:0003082 ! myotome +intersection_of: RO:0002473 CL:0008002 ! composed primarily of skeletal muscle fiber relationship: part_of UBERON:0014892 ! skeletal muscle organ, vertebrate -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/c/c0/Skeletal_muscle.jpg" xsd:anyURI -property_value: editor_note "TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle." xsd:string -property_value: UBPROP:0000001 "Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005277", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA]" xsd:string {external_class="FMA:14069", ontology="FMA"} -property_value: UBPROP:0000003 "This result implies the following views in terms of evolutionary differentiation: (1) Arthropod striated muscle and vertebrate skeletal and cardiac muscles share a common ancestor. In other words, they did not evolve independently (...) (5) The divergence of vertebrate skeletal and cardiac muscles/vertebrate smooth muscle and nonmuscle is at least before that of vertebrates/arthropods. In other words, emergence of skeletal and cardiac musle type tissues preceded the vertebrate/arthropod divergence (ca. 700 MYA).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000319", ontology="VHOG", source="PMID:10368962 Oota S, Saitou N, Phylogenetic relationship of muscle tissues deduced from superimposition of gene trees. Mol Biol Evol (1999)", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003082 ! develops from myotome +relationship: RO:0002473 CL:0008002 ! composed primarily of skeletal muscle fiber +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/c/c0/Skeletal_muscle.jpg" xsd:anyURI +property_value: IAO:0000116 "TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle." xsd:string [Term] id: UBERON:0001135 @@ -169085,14 +168201,10 @@ is_a: UBERON:0002385 ! muscle tissue intersection_of: UBERON:0002385 ! muscle tissue intersection_of: has_part CL:0000192 ! smooth muscle cell disjoint_from: UBERON:0002036 ! striated muscle tissue -relationship: composed_primarily_of CL:0000192 ! smooth muscle cell relationship: has_part CL:0000192 ! smooth muscle cell relationship: has_part GO:0071953 ! elastic fiber -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/3/3b/Glatte_Muskelzellen.jpg" xsd:anyURI -property_value: UBPROP:0000001 "A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005274", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010244", ontology="AAO", source="AAO:CAM"} -property_value: UBPROP:0000003 "(...) the first bilateral animals possessed only smooth muscles with the molecular repertoire necessary to build a striated muscle. (...) it is more parsimonious to regard striated muscle cells as a sister cell type to the smooth muscle cells. In this scenario, striated and smooth muscles would have arisen in the stem lineage that led to the Nephrozoa (i.e. all Bilateria exclusive the acoelomorphs) (Hejnol et al., 2009), from an 'acoel-like' smooth muscle, by segregation and divergence of functions and through differential recruitment of additional genes[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001246", ontology="VHOG", source="DOI:10.1002/jez.b.21416 Chiodin M, Achatz JG, Wanninger A, Martinez P, Molecular architecture of muscles in an acoel and its evolutionary implications. Journal of Experimental Zoology (2011)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000013 "GO uses visceral and smooth interchangeably. However visceral can also be used in the sense of the viscera. Many fly annotations to smooth muscle terms. If we want to be inclusive of insects have to have a general definition of tissue that includes cells." xsd:string +relationship: RO:0002473 CL:0000192 ! composed primarily of smooth muscle cell +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/3/3b/Glatte_Muskelzellen.jpg" xsd:anyURI [Term] id: UBERON:0001136 @@ -169120,11 +168232,11 @@ xref: Wikipedia:Mesothelium is_a: UBERON:0000487 ! simple squamous epithelium is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0000487 ! simple squamous epithelium -intersection_of: develops_from UBERON:0000926 ! mesoderm intersection_of: part_of UBERON:0000042 ! serous membrane -relationship: composed_primarily_of CL:0000077 {source="FMA"} ! mesothelial cell +intersection_of: RO:0002202 UBERON:0000926 ! develops from mesoderm relationship: part_of UBERON:0000042 ! serous membrane -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/25/Mesothelium_peritoneal_wash_high_mag.jpg" xsd:anyURI +relationship: RO:0002473 CL:0000077 {source="FMA"} ! composed primarily of mesothelial cell +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/25/Mesothelium_peritoneal_wash_high_mag.jpg" xsd:anyURI [Term] id: UBERON:0001137 @@ -169148,10 +168260,8 @@ xref: SCTID:123961009 xref: UMLS:C0004600 {source="ncithesaurus:Back"} xref: Wikipedia:Dorsum_(anatomy) is_a: UBERON:0000475 ! organism subdivision -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/432px-Gray-back.PNG" xsd:anyURI -property_value: UBPROP:0000007 "dorsal" xsd:string -property_value: UBPROP:0000008 "In humans, called the back, a large posterior area of the human body, rising from the top of the buttocks to the back of the neck and the shoulders. It is the surface opposite to the chest, its height being defined by the vertebral column (commonly referred to as the spine or backbone) and its breadth being supported by the ribcage and shoulders. The spinal canal runs through the spine and provides nerves to the rest of the body" xsd:string +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/432px-Gray-back.PNG" xsd:anyURI [Term] id: UBERON:0001138 @@ -169175,13 +168285,13 @@ xref: VHOG:0000552 xref: Wikipedia:Superior_mesenteric_vein is_a: UBERON:0005617 ! mesenteric vein intersection_of: UBERON:0005617 ! mesenteric vein -intersection_of: drains UBERON:0002108 ! small intestine -relationship: connected_to UBERON:0001639 ! hepatic portal vein -relationship: develops_from UBERON:0005487 {source="Wikipedia:Vitelline_vein"} ! vitelline vein -relationship: drains UBERON:0002108 ! small intestine +intersection_of: RO:0002179 UBERON:0002108 ! drains small intestine relationship: part_of UBERON:0005806 ! portal system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png" xsd:anyURI +relationship: RO:0002170 UBERON:0001639 ! connected to hepatic portal vein +relationship: RO:0002179 UBERON:0002108 ! drains small intestine +relationship: RO:0002202 UBERON:0005487 {source="Wikipedia:Vitelline_vein"} ! develops from vitelline vein +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001139 @@ -169202,12 +168312,11 @@ xref: UMLS:C0226758 {source="ncithesaurus:Common_Iliac_Vein"} xref: Wikipedia:Common_iliac_vein is_a: UBERON:0005610 {source="MA"} ! iliac vein is_a: UBERON:0015212 ! lateral structure -relationship: in_lateral_side_of UBERON:0001072 {source="FMA-abduced-lr"} ! posterior vena cava -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/6/65/Iliac_veins.gif" xsd:anyURI -property_value: UBPROP:0000008 "In human anatomy, the common iliac veins are formed by the external iliac veins and internal iliac veins and together, in the abdomen at the level of the fifth lumbar vertebrae, form the inferior vena cava. They drain blood from the pelvis and lower limbs. Both common iliac veins are accompanied along their course by common iliac arteries." xsd:string {source="Wikipedia:Common_iliac_vein"} +relationship: BSPO:0000126 UBERON:0001072 {source="FMA-abduced-lr"} ! posterior vena cava +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/65/Iliac_veins.gif" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001140 @@ -169236,15 +168345,13 @@ xref: UMLS:C0035092 {source="ncithesaurus:Renal_Vein"} xref: Wikipedia:Renal_vein is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein -intersection_of: drains UBERON:0002113 ! kidney -relationship: drains UBERON:0002113 ! kidney -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: tributary_of UBERON:0001072 ! posterior vena cava -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI -property_value: UBPROP:0000001 "The renal veins are veins that drain the kidney. They connect the kidney to the inferior vena cava. It is usually singular to each kidney, except in the condition 'multiple renal veins'. It also divides into 2 divisions upon entering the kidney: the anterior branch which receives blood from the anterior portion of the kidney and, the posterior branch which receives blood from the posterior portion. Often, each renal vein will have a branch that receives blood from the ureter. [WP,unvetted][Wikipedia:Renal_vein]." xsd:string {source="Wikipedia:Renal_vein"} -property_value: UBPROP:0000012 "in EHDAA2, the renal vein is part of the kidney" xsd:string {external_ontology="EHDAA2"} +intersection_of: RO:0002179 UBERON:0002113 ! drains kidney +relationship: RO:0002179 UBERON:0002113 ! drains kidney +relationship: RO:0002376 UBERON:0001072 ! tributary of posterior vena cava +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001141 @@ -169261,12 +168368,11 @@ xref: SCTID:116357001 xref: UMLS:C0508000 {source="ncithesaurus:Right_Renal_Vein"} is_a: UBERON:0001140 ! renal vein intersection_of: UBERON:0001140 ! renal vein -intersection_of: drains UBERON:0004539 ! right kidney -relationship: drains UBERON:0004539 ! right kidney -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI -property_value: UBPROP:0000001 "A vein that drains blood from the right kidney into the inferior vena cava[ncithesaurus]." xsd:string {source="ncithesaurus:Right_Renal_Vein"} +intersection_of: RO:0002179 UBERON:0004539 ! drains right kidney +relationship: RO:0002179 UBERON:0004539 ! drains right kidney +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001142 @@ -169283,13 +168389,12 @@ xref: SCTID:116356005 xref: UMLS:C0508001 {source="ncithesaurus:Left_Renal_Vein"} is_a: UBERON:0001140 ! renal vein intersection_of: UBERON:0001140 ! renal vein -intersection_of: drains UBERON:0004538 ! left kidney -relationship: drains UBERON:0004538 ! left kidney -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI -property_value: UBPROP:0000001 "A vein that drains blood from the left kidney into the inferior vena cava[ncithesaurus]." xsd:string {source="ncithesaurus:Left_Renal_Vein"} +intersection_of: RO:0002179 UBERON:0004538 ! drains left kidney +relationship: RO:0002179 UBERON:0004538 ! drains left kidney +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001143 @@ -169321,14 +168426,14 @@ xref: ZFA:0000670 is_a: UBERON:0013126 ! vein of abdomen is_a: UBERON:0015796 ! liver blood vessel intersection_of: UBERON:0001638 ! vein -intersection_of: drains UBERON:0002107 ! liver +intersection_of: RO:0002179 UBERON:0002107 ! drains liver disjoint_from: UBERON:0001639 ! hepatic portal vein -relationship: develops_from UBERON:0005487 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="Wikipedia:Vitelline_vein"} ! vitelline vein -relationship: drains UBERON:0002107 ! liver relationship: part_of UBERON:0006877 ! vasculature of liver -relationship: tributary_of UBERON:0001072 {source="FMA-abduced-lr"} ! posterior vena cava -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/61/Gray1121.png" xsd:anyURI -property_value: editor_note "todo - add developmental relationships for other taxa" xsd:string +relationship: RO:0002179 UBERON:0002107 ! drains liver +relationship: RO:0002202 UBERON:0005487 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="Wikipedia:Vitelline_vein"} ! develops from vitelline vein +relationship: RO:0002376 UBERON:0001072 {source="FMA-abduced-lr"} ! tributary of posterior vena cava +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/61/Gray1121.png" xsd:anyURI +property_value: IAO:0000116 "todo - add developmental relationships for other taxa" xsd:string [Term] id: UBERON:0001144 @@ -169357,15 +168462,14 @@ xref: Wikipedia:Testicular_vein is_a: UBERON:0001638 ! vein is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0001638 ! vein -intersection_of: drains UBERON:0000473 ! testis -relationship: connected_to UBERON:0001072 ! posterior vena cava -relationship: connected_to UBERON:0001330 ! pampiniform plexus -relationship: drains UBERON:0000473 ! testis -relationship: in_lateral_side_of UBERON:0000468 ! multicellular organism +intersection_of: RO:0002179 UBERON:0000473 ! drains testis +relationship: BSPO:0000126 UBERON:0000468 ! multicellular organism +relationship: RO:0002170 UBERON:0001072 ! connected to posterior vena cava +relationship: RO:0002170 UBERON:0001330 ! connected to pampiniform plexus +relationship: RO:0002179 UBERON:0000473 ! drains testis relationship: sexually_homologous_to UBERON:0001145 ! ovarian vein -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1b/Gray590.png" xsd:anyURI -property_value: editor_note "TODO - check testicular vs spermatic vein (MA:0002218)" xsd:string -property_value: UBPROP:0000008 "In humans, the right testicular vein generally joins the inferior vena cava; the left testicular vein, unlike the right, often joins the left renal vein instead of the inferior vena cava. The veins emerge from the back of the testis, and receive tributaries from the epididymis; they unite and form a convoluted plexus, called the pampiniform plexus, which constitutes the greater mass of the spermatic cord; the vessels composing this plexus are very numerous, and ascend along the cord, in front of the ductus deferens. Below the subcutaneous inguinal ring, they unite to form three or four veins, which pass along the inguinal canal, and, entering the abdomen through the abdominal inguinal ring, coalesce to form two veins, which ascend on the Psoas major, behind the peritoneum, lying one on either side of the internal spermatic artery. These unite to form a single vein, which opens, on the right side, into the inferior vena cava (at an acute angle), on the left side into the left renal vein (at a right angle). The spermatic veins are provided with valves. The left spermatic vein passes behind the iliac colon and is thus exposed to pressure from the contents of that part of the bowel" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1b/Gray590.png" xsd:anyURI +property_value: IAO:0000116 "TODO - check testicular vs spermatic vein (MA:0002218)" xsd:string [Term] id: UBERON:0001145 @@ -169395,10 +168499,10 @@ xref: Wikipedia:Ovarian_vein is_a: UBERON:0001638 ! vein is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0001638 ! vein -intersection_of: drains UBERON:0000992 ! ovary -relationship: drains UBERON:0000992 ! ovary -relationship: in_lateral_side_of UBERON:0000468 ! multicellular organism -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/cf/Ovarschaf.jpg" xsd:anyURI +intersection_of: RO:0002179 UBERON:0000992 ! drains ovary +relationship: BSPO:0000126 UBERON:0000468 ! multicellular organism +relationship: RO:0002179 UBERON:0000992 ! drains ovary +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/cf/Ovarschaf.jpg" xsd:anyURI [Term] id: UBERON:0001146 @@ -169418,9 +168522,9 @@ xref: UMLS:C0226717 {source="ncithesaurus:Suprarenal_Vein"} xref: Wikipedia:Suprarenal_vein is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein -intersection_of: drains UBERON:0002369 ! adrenal gland -relationship: drains UBERON:0002369 ! adrenal gland -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png" xsd:anyURI +intersection_of: RO:0002179 UBERON:0002369 ! drains adrenal gland +relationship: RO:0002179 UBERON:0002369 ! drains adrenal gland +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png" xsd:anyURI [Term] id: UBERON:0001152 @@ -169448,17 +168552,15 @@ xref: Wikipedia:Cystic_duct xref: ZFA:0005166 is_a: UBERON:0003703 {source="FMA"} ! extrahepatic bile duct intersection_of: UBERON:0000058 ! duct -intersection_of: continuous_with UBERON:0001174 ! common bile duct -intersection_of: continuous_with UBERON:0002110 ! gallbladder +intersection_of: RO:0002150 UBERON:0001174 ! continuous with common bile duct +intersection_of: RO:0002150 UBERON:0002110 ! continuous with gallbladder disjoint_from: UBERON:0005171 ! hepatic duct relationship: channels_into UBERON:0001174 ! common bile duct -relationship: continuous_with UBERON:0001174 ! common bile duct -relationship: continuous_with UBERON:0002110 ! gallbladder -relationship: develops_from UBERON:0005604 {source="EHDAA2"} ! extrahepatic part of hepatic duct -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/48/Illu_liver_gallbladder.jpg" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png" xsd:anyURI -property_value: UBPROP:0000001 "Duct that connects the gall bladder and the common bile duct.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005166", ontology="TAO", source="ZFIN:Curator"} -property_value: UBPROP:0000001 "The duct of the gallbladder which joins the common hepatic duct, thus forming the common biliary duct. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000213", ontology="VHOG", source="http://bgee.unil.ch/"} +relationship: RO:0002150 UBERON:0001174 ! continuous with common bile duct +relationship: RO:0002150 UBERON:0002110 ! continuous with gallbladder +relationship: RO:0002202 UBERON:0005604 {source="EHDAA2"} ! develops from extrahepatic part of hepatic duct +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/48/Illu_liver_gallbladder.jpg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png" xsd:anyURI [Term] id: UBERON:0001153 @@ -169498,18 +168600,16 @@ xref: UMLS:C0007531 {source="ncithesaurus:Cecum"} xref: VHOG:0001559 xref: Wikipedia:Cecum is_a: UBERON:0009854 ! digestive tract diverticulum -relationship: continuous_with UBERON:0001156 {source="Wikipedia"} ! ascending colon -relationship: contributes_to_morphology_of UBERON:0000059 ! large intestine -relationship: develops_from UBERON:0001045 {source="Wikipedia"} ! midgut -relationship: never_in_taxon NCBITaxon:32443 {source="Wikipedia"} ! Teleostei -relationship: only_in_taxon NCBITaxon:7776 ! Gnathostomata relationship: part_of UBERON:0001155 {source="EHDAA2"} ! colon -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/82/Stomach_colon_rectum_diagram.svg" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb" xsd:anyURI -property_value: UBPROP:0000007 "caecal" xsd:string -property_value: UBPROP:0000008 "A cecum is present in most amniote species, and also in lungfish, but not in any living species of amphibian. In reptiles, it is usually a single median structure, arising from the dorsal side of the large intestine. Birds typically have two paired ceca, as, unlike other mammals, do hyraxes. Most mammalian herbivores have a relatively large cecum, hosting a large number of bacteria, which aid in the enzymatic breakdown of plant materials such as cellulose; in many species, it is considerably wider than the colon. In contrast, obligatory carnivores, whose diets contain little or no plant material, have a reduced cecum, which is often partially or wholly replaced by the vermiform appendix. Many fish have a number of small outpocketings, called pyloric ceca, along their intestine; despite the name they are not homologous with the cecum of amniotes, and their purpose is to increase the overall area of the digestive epithelium.[2] Some invertebrates, such as squid,[3] may also have structures with the same name, but these have no relationship with those of vertebrates." xsd:string {source="WP"} +relationship: RO:0002150 UBERON:0001156 {source="Wikipedia"} ! continuous with ascending colon +relationship: RO:0002160 NCBITaxon:7776 ! only in taxon Gnathostomata +relationship: RO:0002202 UBERON:0001045 {source="Wikipedia"} ! develops from midgut +relationship: RO:0002433 UBERON:0000059 ! contributes to morphology of large intestine +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/82/Stomach_colon_rectum_diagram.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb" xsd:anyURI +property_value: RO:0002161 NCBITaxon:32443 {source="Wikipedia"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001154 @@ -169548,17 +168648,14 @@ xref: UMLS:C0003617 {source="ncithesaurus:Vermiform_Appendix"} xref: VHOG:0001306 xref: Wikipedia:Vermiform_appendix is_a: UBERON:0013765 ! digestive system element -relationship: continuous_with UBERON:0001153 {xref="http://orcid.org/0000-0002-1572-1316"} ! caecum -relationship: develops_from UBERON:0001045 {source="Wikipedia"} ! midgut relationship: part_of UBERON:0000059 ! large intestine -relationship: present_in_taxon NCBITaxon:40674 ! Mammalia -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray536.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb" xsd:anyURI -property_value: UBPROP:0000001 "Organ with organ cavity which is continuous proximally with the cecum and distally terminates in the tip of the appendix. Examples: There is only one appendix[FMA:14542]." xsd:string {source="FMA:14542"} -property_value: UBPROP:0000003 "A comparative anatomical approach reveals three apparent morphotypes of the cecal appendix, as well as appendix-like structures in some species that lack a true cecal appendix. Cladistic analyses indicate that the appendix has evolved independently at least twice (at least once in diprotodont marsupials and at least once in Euarchontoglires), shows a highly significant (P < 0.0001) phylogenetic signal in its distribution, and has been maintained in mammalian evolution for 80 million years or longer.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001306", ontology="VHOG", source="DOI:10.1111/j.1420-9101.2009.01809.x Smith HF, Fisher RE, Everett ML, Thomas AD, Randal Bollinger R, Parker W, Comparative anatomy and phylogenetic distribution of the mammalian cecal appendix. Journal of Evolutionary Biology (2009)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "appendiceal" xsd:string +relationship: RO:0002150 UBERON:0001153 {xref="http://orcid.org/0000-0002-1572-1316"} ! continuous with caecum +relationship: RO:0002202 UBERON:0001045 {source="Wikipedia"} ! develops from midgut +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray536.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:40674 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001155 @@ -169593,19 +168690,12 @@ xref: VHOG:0000648 xref: Wikipedia:Colon_(anatomy) xref: XAO:0000243 xref: ZFA:0000706 -is_a: UBERON:0004921 {order="3", source="cjm"} ! subdivision of digestive tract -relationship: contributes_to_morphology_of UBERON:0000059 ! large intestine -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +is_a: UBERON:0004921 ! subdivision of digestive tract relationship: part_of UBERON:0000059 {source="FMA"} ! large intestine -property_value: editor_note "Some references do not consider the caecum to be part of the colon." xsd:string {xref="http://orcid.org/0000-0002-1572-1316"} -property_value: editor_note "TODO - abstract this such that it legitimately covers all vertebrates" xsd:string -property_value: UBPROP:0000001 "The last portion of the digestive system, it extracts water and salt from solid wastes before they are eliminated from the body.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010400", ontology="AAO", source="UBERON:0001155"} -property_value: UBPROP:0000001 "The posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates. Wallace et al, 2005.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000706", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000648", ontology="VHOG", source="ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "colonic" xsd:string -property_value: UBPROP:0000008 "In mammals, the colon consists of four sections: the ascending colon, the transverse colon, the descending colon, and the sigmoid colon[WP]" xsd:string -property_value: UBPROP:0000008 "In zebrafish, the posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates[ZFIN]" xsd:string -property_value: UBPROP:0000009 "it extracts water and salt from solid wastes before they are eliminated from the body[WP]" xsd:string +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002433 UBERON:0000059 ! contributes to morphology of large intestine +property_value: IAO:0000116 "Some references do not consider the caecum to be part of the colon." xsd:string {xref="http://orcid.org/0000-0002-1572-1316"} +property_value: IAO:0000116 "TODO - abstract this such that it legitimately covers all vertebrates" xsd:string [Term] id: UBERON:0001156 @@ -169625,20 +168715,18 @@ xref: FMA:14545 xref: galen:AscendingColon xref: MA:0001541 xref: MAT:0000311 -xref: MESH:D044682 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: MIAA:0000311 xref: NCIT:C12265 xref: SCTID:362162009 xref: UMLS:C0227375 {source="ncithesaurus:Ascending_Colon"} xref: Wikipedia:Ascending_colon is_a: UBERON:0000168 {source="FMA"} ! proximal-distal subdivision of colon -relationship: continuous_with UBERON:0001157 ! transverse colon -relationship: develops_from UBERON:0001045 {source="Wikipedia"} ! midgut -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/3b/Dickdarm-Schema.svg" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb" xsd:anyURI -property_value: UBPROP:0000012 "in MA, this is a subclass of colon" xsd:string {external_ontology="MA"} +relationship: RO:0002150 UBERON:0001157 ! continuous with transverse colon +relationship: RO:0002202 UBERON:0001045 {source="Wikipedia"} ! develops from midgut +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3b/Dickdarm-Schema.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001157 @@ -169657,19 +168745,18 @@ xref: FMA:14546 xref: galen:TransverseColon xref: MA:0001543 xref: MAT:0000312 -xref: MESH:D044684 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: MIAA:0000312 xref: NCIT:C12385 xref: SCTID:362163004 xref: UMLS:C0227386 {source="ncithesaurus:Transverse_Colon"} xref: Wikipedia:Transverse_colon is_a: UBERON:0000168 {source="FMA"} ! proximal-distal subdivision of colon -relationship: continuous_with UBERON:0001158 ! descending colon -relationship: develops_from UBERON:0001045 {source="Wikipedia"} ! midgut -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/3b/Dickdarm-Schema.svg" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb" xsd:anyURI +relationship: RO:0002150 UBERON:0001158 ! continuous with descending colon +relationship: RO:0002202 UBERON:0001045 {source="Wikipedia"} ! develops from midgut +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3b/Dickdarm-Schema.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001158 @@ -169688,19 +168775,18 @@ xref: FMA:14547 xref: galen:DescendingColon xref: MA:0001542 xref: MAT:0000313 -xref: MESH:D044683 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: MIAA:0000313 xref: NCIT:C12268 xref: SCTID:362165006 xref: UMLS:C0227389 {source="ncithesaurus:Descending_Colon"} xref: Wikipedia:Descending_colon is_a: UBERON:0000168 {source="FMA"} ! proximal-distal subdivision of colon -relationship: continuous_with UBERON:0001159 ! sigmoid colon -relationship: develops_from UBERON:0001046 {source="Wikipedia"} ! hindgut -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/ca/Gray1223.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb" xsd:anyURI +relationship: RO:0002150 UBERON:0001159 ! continuous with sigmoid colon +relationship: RO:0002202 UBERON:0001046 {source="Wikipedia"} ! develops from hindgut +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/ca/Gray1223.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001159 @@ -169730,12 +168816,12 @@ xref: UMLS:C0227391 {source="ncithesaurus:Sigmoid_Colon"} xref: UMLS:C0682612 {source="ncithesaurus:Sigmoid_Flexure"} xref: Wikipedia:Sigmoid_colon is_a: UBERON:0000168 {source="FMA"} ! proximal-distal subdivision of colon -relationship: continuous_with UBERON:0001052 ! rectum -relationship: develops_from UBERON:0001046 {source="Wikipedia"} ! hindgut -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/3b/Dickdarm-Schema.svg" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb" xsd:anyURI +relationship: RO:0002150 UBERON:0001052 ! continuous with rectum +relationship: RO:0002202 UBERON:0001046 {source="Wikipedia"} ! develops from hindgut +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3b/Dickdarm-Schema.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_F_Intestine_Large.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/SBU_M_Intestine_Large.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001160 @@ -169769,11 +168855,9 @@ xref: VHOG:0000421 xref: Wikipedia:Fundus_(stomach) is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0009870 ! zone of stomach -relationship: contributes_to_morphology_of UBERON:0000945 ! stomach relationship: has_part UBERON:0010038 ! fundic gastric gland -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg" xsd:anyURI -property_value: UBPROP:0000001 "The greater curvature of the stomach. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000421", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000421", ontology="VHOG", source="ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11", source="http://bgee.unil.ch/"} +relationship: RO:0002433 UBERON:0000945 ! contributes to morphology of stomach +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg" xsd:anyURI [Term] id: UBERON:0001161 @@ -169798,8 +168882,8 @@ xref: SCTID:362140009 xref: UMLS:C0227230 {source="ncithesaurus:Body_of_Stomach"} xref: Wikipedia:Body_of_stomach is_a: UBERON:0009870 {source="FMA"} ! zone of stomach -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg" xsd:anyURI -property_value: editor_note "we include this as zone of stomach even though it is not distinguished by gland type" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg" xsd:anyURI +property_value: IAO:0000116 "we include this as zone of stomach even though it is not distinguished by gland type" xsd:string [Term] id: UBERON:0001162 @@ -169832,14 +168916,14 @@ is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0009870 ! zone of stomach intersection_of: UBERON:0009870 ! zone of stomach intersection_of: has_part UBERON:0008859 ! cardiac gastric gland -relationship: continuous_with UBERON:0001043 ! esophagus -relationship: continuous_with UBERON:0001161 ! body of stomach -relationship: contributes_to_morphology_of UBERON:0000945 ! stomach relationship: has_part UBERON:0008859 ! cardiac gastric gland -relationship: only_in_taxon NCBITaxon:40674 {source="ISBN:0073040584"} ! Mammalia -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/3/33/Illu_stomach.jpg" xsd:anyURI -property_value: editor_note "There were previously conflicting statements in the academic anatomy community[10][11][12] over whether the cardia is part of the stomach, part of the esophagus or a distinct entity. Modern surgical and medical textbooks have agreed that 'The gastric cardia is now clearly considered to be part of the stomach'[13][14]. Classical anatomy textbooks, and some other resources[15], describe the cardia as the first of 4 regions of the stomach. This makes sense histologically because the mucosa of the cardia is the same as that of the stomach[WP]" xsd:string -property_value: editor_note "We follow Kardong in defining stomach regions by glands." xsd:string +relationship: RO:0002150 UBERON:0001043 ! continuous with esophagus +relationship: RO:0002150 UBERON:0001161 ! continuous with body of stomach +relationship: RO:0002160 NCBITaxon:40674 {source="ISBN:0073040584"} ! only in taxon Mammalia +relationship: RO:0002433 UBERON:0000945 ! contributes to morphology of stomach +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/3/33/Illu_stomach.jpg" xsd:anyURI +property_value: IAO:0000116 "There were previously conflicting statements in the academic anatomy community[10][11][12] over whether the cardia is part of the stomach, part of the esophagus or a distinct entity. Modern surgical and medical textbooks have agreed that 'The gastric cardia is now clearly considered to be part of the stomach'[13][14]. Classical anatomy textbooks, and some other resources[15], describe the cardia as the first of 4 regions of the stomach. This makes sense histologically because the mucosa of the cardia is the same as that of the stomach[WP]" xsd:string +property_value: IAO:0000116 "We follow Kardong in defining stomach regions by glands." xsd:string [Term] id: UBERON:0001165 @@ -169870,12 +168954,12 @@ xref: SCTID:362142001 xref: UMLS:C0034193 {source="ncithesaurus:Antrum_Pylori"} xref: Wikipedia:Pyloric_antrum is_a: UBERON:0009870 {source="FMA"} ! zone of stomach -relationship: continuous_with UBERON:0001161 ! body of stomach -relationship: contributes_to_morphology_of UBERON:0001166 ! pylorus relationship: has_part CL:0000502 ! type D enteroendocrine cell relationship: has_part CL:0000508 ! type G enteroendocrine cell relationship: part_of UBERON:0001166 {source="Wikipedia"} ! pylorus -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg" xsd:anyURI +relationship: RO:0002150 UBERON:0001161 ! continuous with body of stomach +relationship: RO:0002433 UBERON:0001166 ! contributes to morphology of pylorus +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg" xsd:anyURI [Term] id: UBERON:0001166 @@ -169910,15 +168994,12 @@ intersection_of: UBERON:0009870 ! zone of stomach intersection_of: has_part UBERON:0001165 ! pyloric antrum intersection_of: has_part UBERON:0008858 ! pyloric canal intersection_of: has_part UBERON:0008861 ! pyloric gastric gland -relationship: contributes_to_morphology_of UBERON:0000945 ! stomach relationship: has_part UBERON:0001165 ! pyloric antrum relationship: has_part UBERON:0008858 ! pyloric canal relationship: has_part UBERON:0008861 ! pyloric gastric gland -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg" xsd:anyURI -property_value: editor_note "We follow Kardong in defining stomach regions by glands" xsd:string -property_value: UBPROP:0000001 "The orifice which allows the passage from the stomach into the intestine. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000420", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000420", ontology="VHOG", source="ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "pyloric" xsd:string +relationship: RO:0002433 UBERON:0000945 ! contributes to morphology of stomach +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/31/Gray1046.svg" xsd:anyURI +property_value: IAO:0000116 "We follow Kardong in defining stomach regions by glands" xsd:string [Term] id: UBERON:0001167 @@ -169942,8 +169023,8 @@ xref: SCTID:279995000 is_a: UBERON:0000328 ! gut wall intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0000945 ! stomach -relationship: contributes_to_morphology_of UBERON:0000945 ! stomach relationship: part_of UBERON:0000945 ! stomach +relationship: RO:0002433 UBERON:0000945 ! contributes to morphology of stomach [Term] id: UBERON:0001168 @@ -170015,9 +169096,10 @@ xref: FMA:14653 xref: MA:0002498 xref: NCIT:C33341 xref: UMLS:C0682620 {source="ncithesaurus:Portal_Lobule"} +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0009911 {source="FMA"} ! lobule -relationship: contributes_to_morphology_of UBERON:0001280 ! liver parenchyma relationship: part_of UBERON:0001280 {source="MA", source="MP"} ! liver parenchyma +relationship: RO:0002433 UBERON:0001280 ! contributes to morphology of liver parenchyma [Term] id: UBERON:0001172 @@ -170032,6 +169114,7 @@ xref: MA:0002496 xref: NCIT:C32992 xref: SCTID:272214009 xref: UMLS:C0227519 {source="ncithesaurus:Liver_Acinus"} +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0011858 ! acinus of exocrine gland relationship: overlaps UBERON:0001171 ! portal lobule relationship: overlaps UBERON:0004647 ! liver lobule @@ -170050,7 +169133,6 @@ synonym: "biliary tract" RELATED [MA:0001273] xref: AAO:0011020 xref: EMAPA:35172 xref: FMA:14665 -xref: MESH:D001659 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: SCTID:181267003 xref: UMLS:C0005423 {source="ncithesaurus:Biliary_Tract"} xref: Wikipedia:Biliary_tract @@ -170059,17 +169141,15 @@ is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0013765 ! digestive system element intersection_of: UBERON:0000062 ! organ -intersection_of: composed_primarily_of UBERON:0002394 ! bile duct intersection_of: part_of UBERON:0002294 ! biliary system -relationship: composed_primarily_of UBERON:0002394 ! bile duct -relationship: contributes_to_morphology_of UBERON:0002423 ! hepatobiliary system -relationship: develops_from UBERON:0004912 ! biliary bud +intersection_of: RO:0002473 UBERON:0002394 ! composed primarily of bile duct relationship: has_part UBERON:0001246 ! interlobular bile duct relationship: has_part UBERON:0001282 ! intralobular bile duct relationship: has_part UBERON:0003703 ! extrahepatic bile duct relationship: part_of UBERON:0002294 ! biliary system -property_value: RO:0002171 UBERON:0002110 -property_value: UBPROP:0000001 "Hollow tree organ, the organ parts of which consist of the bile ducts.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011020", ontology="AAO", source="UBERON:0001173"} +relationship: RO:0002202 UBERON:0004912 ! develops from biliary bud +relationship: RO:0002433 UBERON:0002423 ! contributes to morphology of hepatobiliary system +relationship: RO:0002473 UBERON:0002394 ! composed primarily of bile duct [Term] id: UBERON:0001174 @@ -170099,12 +169179,10 @@ xref: Wikipedia:Common_bile_duct xref: ZFA:0005165 is_a: UBERON:0003703 ! extrahepatic bile duct relationship: channels_into UBERON:0001064 ! ventral pancreatic duct -relationship: continuous_with UBERON:0001152 ! cystic duct -relationship: continuous_with UBERON:0001175 ! common hepatic duct -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png" xsd:anyURI -property_value: UBPROP:0000001 "Digestive system duct that collects bile from the hepatic bile duct and the cystic duct.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005165", ontology="TAO", source="ZFIN:Curator"} -property_value: UBPROP:0000001 "The duct formed by the union of the common hepatic and cystic ducts. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000214", ontology="VHOG", source="http://bgee.unil.ch/"} +relationship: RO:0002150 UBERON:0001152 ! continuous with cystic duct +relationship: RO:0002150 UBERON:0001175 ! continuous with common hepatic duct +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001175 @@ -170127,13 +169205,12 @@ xref: VHOG:0000220 xref: Wikipedia:Common_hepatic_duct is_a: UBERON:0003703 {source="FMA"} ! extrahepatic bile duct relationship: channels_into UBERON:0001174 ! common bile duct -relationship: continuous_with UBERON:0001176 {source="Wikipedia"} ! right hepatic duct -relationship: continuous_with UBERON:0001177 {source="Wikipedia"} ! left hepatic duct -relationship: immediate_transformation_of UBERON:0010081 {evidence="definitional"} ! future common hepatic duct relationship: part_of UBERON:0005604 {source="MA"} ! extrahepatic part of hepatic duct -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/48/Illu_liver_gallbladder.jpg" xsd:anyURI -property_value: editor_note "TODO - MA distinguishes between bile duct, hepatic duct, common bile duct and common hepatic duct. in FMA hepatic duct and common hepatic duct are the same. Common is part of extra-hepatic part" xsd:string -property_value: UBPROP:0000001 "The duct which conveys the bile from the liver and unites with the cystic duct to form the common bile duct. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000220", ontology="VHOG", source="http://bgee.unil.ch/"} +relationship: RO:0002150 UBERON:0001176 {source="Wikipedia"} ! continuous with right hepatic duct +relationship: RO:0002150 UBERON:0001177 {source="Wikipedia"} ! continuous with left hepatic duct +relationship: RO:0002495 UBERON:0010081 ! immediate transformation of future common hepatic duct +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/48/Illu_liver_gallbladder.jpg" xsd:anyURI +property_value: IAO:0000116 "TODO - MA distinguishes between bile duct, hepatic duct, common bile duct and common hepatic duct. in FMA hepatic duct and common hepatic duct are the same. Common is part of extra-hepatic part" xsd:string [Term] id: UBERON:0001176 @@ -170152,10 +169229,9 @@ xref: UMLS:C0227557 {source="ncithesaurus:Right_Hepatic_Duct"} xref: VHOG:0000217 is_a: UBERON:0003703 ! extrahepatic bile duct intersection_of: UBERON:0003703 ! extrahepatic bile duct -intersection_of: continuous_with UBERON:0001114 ! right lobe of liver -relationship: continuous_with UBERON:0001114 ! right lobe of liver +intersection_of: RO:0002150 UBERON:0001114 ! continuous with right lobe of liver relationship: part_of UBERON:0005171 ! hepatic duct -property_value: UBPROP:0000001 "The duct which drains bile from the right half of the liver and unites with the left hepatic duct to form the common hepatic duct. [adapted_from_http://www.medterms.com/script/main/art.asp?articlekey=26032][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000217", ontology="VHOG", source="http://bgee.unil.ch/"} +relationship: RO:0002150 UBERON:0001114 ! continuous with right lobe of liver [Term] id: UBERON:0001177 @@ -170174,10 +169250,9 @@ xref: UMLS:C0227560 {source="ncithesaurus:Left_Hepatic_Duct"} xref: VHOG:0000218 is_a: UBERON:0003703 ! extrahepatic bile duct intersection_of: UBERON:0003703 ! extrahepatic bile duct -intersection_of: continuous_with UBERON:0001115 ! left lobe of liver -relationship: continuous_with UBERON:0001115 ! left lobe of liver +intersection_of: RO:0002150 UBERON:0001115 ! continuous with left lobe of liver relationship: part_of UBERON:0005171 ! hepatic duct -property_value: UBPROP:0000001 "The duct which drains bile from the left half of the liver and unites with the right hepatic duct to form the common hepatic duct. [adapted_from_http://www.medterms.com/script/main/art.asp?articlekey=26032][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000218", ontology="VHOG", source="http://bgee.unil.ch/"} +relationship: RO:0002150 UBERON:0001115 ! continuous with left lobe of liver [Term] id: UBERON:0001178 @@ -170198,7 +169273,7 @@ is_a: UBERON:0022350 ! visceral serous membrane intersection_of: UBERON:0022350 ! visceral serous membrane intersection_of: part_of UBERON:0002358 ! peritoneum relationship: part_of UBERON:0002358 ! peritoneum -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray1040.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray1040.png" xsd:anyURI [Term] id: UBERON:0001179 @@ -170225,14 +169300,12 @@ is_a: UBERON:0035809 ! serous cavity intersection_of: UBERON:0002553 ! anatomical cavity intersection_of: adjacent_to UBERON:0001178 ! visceral peritoneum intersection_of: adjacent_to UBERON:0001366 ! parietal peritoneum -intersection_of: luminal_space_of UBERON:0035820 ! peritoneal sac +intersection_of: RO:0002572 UBERON:0035820 ! luminal space of peritoneal sac relationship: adjacent_to UBERON:0001178 ! visceral peritoneum relationship: adjacent_to UBERON:0001366 ! parietal peritoneum -relationship: develops_from UBERON:0003887 {source="Wikipedia"} ! intraembryonic coelom -relationship: luminal_space_of UBERON:0035820 ! peritoneal sac relationship: part_of UBERON:0035820 ! peritoneal sac -property_value: UBPROP:0000001 "The potential space between the parietal and visceral layers of the peritoneum, which are normally in contact. The peritoneal cavity is divided into the greater and lesser sac. The greater sac is the peritoneal cavity, and the lesser sac is the omental bursa. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000852", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/peritoneal+cavity"} -property_value: UBPROP:0000003 "In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes) Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000852", ontology="VHOG", source="ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003887 {source="Wikipedia"} ! develops from intraembryonic coelom +relationship: RO:0002572 UBERON:0035820 ! luminal space of peritoneal sac [Term] id: UBERON:0001182 @@ -170261,16 +169334,15 @@ xref: VHOG:0000754 xref: Wikipedia:Superior_mesenteric_artery is_a: UBERON:0005616 ! mesenteric artery intersection_of: UBERON:0005616 ! mesenteric artery -intersection_of: supplies UBERON:0002115 ! jejunum -intersection_of: supplies UBERON:0002116 ! ileum -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: supplies UBERON:0002115 ! jejunum -relationship: supplies UBERON:0002116 ! ileum -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/68/Gray1099.png" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Superior_mesenteric_a.gif" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI -property_value: UBPROP:0000010 "Origin: abdominal aorta; branches, inferior pancreaticoduodenal, jejunal, ileal, ileocolic, right colic, and middle colic arteries; distribution: small intestine, proximal half of colon" xsd:string {source="BTO"} +intersection_of: RO:0002178 UBERON:0002115 ! supplies jejunum +intersection_of: RO:0002178 UBERON:0002116 ! supplies ileum +relationship: RO:0002178 UBERON:0002115 ! supplies jejunum +relationship: RO:0002178 UBERON:0002116 ! supplies ileum +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/68/Gray1099.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Superior_mesenteric_a.gif" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001183 @@ -170300,15 +169372,15 @@ xref: Wikipedia:Inferior_mesenteric_artery is_a: UBERON:0005616 ! mesenteric artery is_a: UBERON:0035039 ! rectal artery intersection_of: UBERON:0005616 ! mesenteric artery -intersection_of: supplies UBERON:0001052 ! rectum -intersection_of: supplies UBERON:0001158 ! descending colon -intersection_of: supplies UBERON:0001159 ! sigmoid colon -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: supplies UBERON:0001158 ! descending colon -relationship: supplies UBERON:0001159 ! sigmoid colon -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e4/Gray538.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +intersection_of: RO:0002178 UBERON:0001052 ! supplies rectum +intersection_of: RO:0002178 UBERON:0001158 ! supplies descending colon +intersection_of: RO:0002178 UBERON:0001159 ! supplies sigmoid colon +relationship: RO:0002178 UBERON:0001158 ! supplies descending colon +relationship: RO:0002178 UBERON:0001159 ! supplies sigmoid colon +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e4/Gray538.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001184 @@ -170344,15 +169416,13 @@ xref: Wikipedia:Renal_artery xref: ZFA:0000420 is_a: UBERON:0012254 ! abdominal aorta artery intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0002113 ! kidney -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: supplies UBERON:0002113 ! kidney -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/da/Gray1120.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI -property_value: editor_note "renal arteries vary widely even in humans. Sub-structures should be checked for taxon variability." xsd:string -property_value: UBPROP:0000001 "Artery which supplies blood via branches to the gonads, oviducts, and kidneys.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010223", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "The renal arteries normally arise off the side of the abdominal aorta, immediately below the superior mesenteric artery, and supply the kidneys with blood. Each is directed across the crus of the diaphragm, so as to form nearly a right angle with the aorta. The renal arteries carry a large portion of total blood flow to the kidneys. Up to a third of total cardiac output can pass through the renal arteries to be filtered by the kidneys. The arterial supply of the kidneys is variable and there may be one or more renal arteries supplying each kidney. It is located above the renal vein. It has a radius of approximately 0.25cm, 0.26 cm at the root. The measured mean diameter can differ depending on the imaging method used. For example, the diameter was found to be 5.04 ± 0.74 mm using ultrasound, but 5.68 ± 1.19 mm using angiography. [WP,unvetted].[Wikipedia]" xsd:string {ontology="Wikipedia", source="Wikipedia:Renal_artery"} +intersection_of: RO:0002178 UBERON:0002113 ! supplies kidney +relationship: RO:0002178 UBERON:0002113 ! supplies kidney +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/da/Gray1120.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: IAO:0000116 "renal arteries vary widely even in humans. Sub-structures should be checked for taxon variability." xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001185 @@ -170372,12 +169442,12 @@ xref: SCTID:36800007 xref: UMLS:C0226332 {source="ncithesaurus:Right_Renal_Artery"} is_a: UBERON:0001184 ! renal artery intersection_of: UBERON:0001184 ! renal artery -intersection_of: supplies UBERON:0004539 ! right kidney -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: supplies UBERON:0004539 ! right kidney -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/da/Gray1120.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +intersection_of: RO:0002178 UBERON:0004539 ! supplies right kidney +relationship: RO:0002178 UBERON:0004539 ! supplies right kidney +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/da/Gray1120.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001186 @@ -170396,11 +169466,11 @@ xref: SCTID:19215005 xref: UMLS:C0226333 {source="ncithesaurus:Left_Renal_Artery"} is_a: UBERON:0001184 ! renal artery intersection_of: UBERON:0001184 ! renal artery -intersection_of: supplies UBERON:0004538 ! left kidney -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: supplies UBERON:0004538 ! left kidney -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +intersection_of: RO:0002178 UBERON:0004538 ! supplies left kidney +relationship: RO:0002178 UBERON:0004538 ! supplies left kidney +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001187 @@ -170426,10 +169496,10 @@ xref: SCTID:244281003 xref: Wikipedia:Testicular_artery is_a: UBERON:0010192 ! genital artery intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0000473 ! testis -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: supplies UBERON:0000473 ! testis -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/af/Gray531.png" xsd:anyURI +intersection_of: RO:0002178 UBERON:0000473 ! supplies testis +relationship: RO:0002178 UBERON:0000473 ! supplies testis +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/af/Gray531.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001188 @@ -170447,10 +169517,10 @@ xref: UMLS:C0734076 {source="ncithesaurus:Right_Spermatic_Artery"} is_a: UBERON:0001187 ! testicular artery is_a: UBERON:0003468 ! ureteric segment of renal artery intersection_of: UBERON:0001187 ! testicular artery -intersection_of: supplies UBERON:0004534 ! right testis -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: supplies UBERON:0001222 ! right ureter -relationship: supplies UBERON:0004534 ! right testis +intersection_of: RO:0002178 UBERON:0004534 ! supplies right testis +relationship: RO:0002178 UBERON:0001222 ! supplies right ureter +relationship: RO:0002178 UBERON:0004534 ! supplies right testis +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001189 @@ -170468,10 +169538,10 @@ xref: UMLS:C0734077 {source="ncithesaurus:Left_Spermatic_Artery"} is_a: UBERON:0001187 ! testicular artery is_a: UBERON:0003468 ! ureteric segment of renal artery intersection_of: UBERON:0001187 ! testicular artery -intersection_of: supplies UBERON:0004533 ! left testis -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: supplies UBERON:0001223 ! left ureter -relationship: supplies UBERON:0004533 ! left testis +intersection_of: RO:0002178 UBERON:0004533 ! supplies left testis +relationship: RO:0002178 UBERON:0001223 ! supplies left ureter +relationship: RO:0002178 UBERON:0004533 ! supplies left testis +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001190 @@ -170491,12 +169561,11 @@ xref: UMLS:C0226411 {source="ncithesaurus:Ovarian_Artery"} xref: Wikipedia:Ovarian_artery is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0000992 ! ovary -relationship: connected_to UBERON:0001516 ! abdominal aorta -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: supplies UBERON:0000992 ! ovary -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/ae/Gray1170.png" xsd:anyURI -property_value: UBPROP:0000001 "In human anatomy, the ovarian artery is a blood vessel that supplies oxygenated blood to the ovary. It arises from the abdominal aorta below the renal artery, and does not pass out of the abdomiproperty_value external_definitioncavity. It can be found in the suspensory ligament of the ovary. [WP]." xsd:string {source="Wikipedia:Ovarian_artery"} +intersection_of: RO:0002178 UBERON:0000992 ! supplies ovary +relationship: RO:0002170 UBERON:0001516 ! connected to abdominal aorta +relationship: RO:0002178 UBERON:0000992 ! supplies ovary +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/ae/Gray1170.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001191 @@ -170519,10 +169588,8 @@ xref: UMLS:C1261084 {source="ncithesaurus:Common_Iliac_Artery"} xref: Wikipedia:Common_iliac_artery is_a: UBERON:0005609 {source="MA"} ! iliac artery is_a: UBERON:0012254 ! abdominal aorta artery -relationship: develops_from UBERON:0005458 {gci_relation="part_of", gci_filler="NCBITaxon:9606", notes="requires review", source="EHDAA2"} ! left umbilical artery -relationship: develops_from UBERON:0005470 {gci_relation="part_of", gci_filler="NCBITaxon:9606", notes="requires review", source="EHDAA2"} ! right umbilical artery -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/6e/Iliac_artery_bifurcation_and_aorta.PNG" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6e/Iliac_artery_bifurcation_and_aorta.PNG" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001193 @@ -170548,12 +169615,10 @@ xref: UMLS:C0019145 {source="ncithesaurus:Hepatic_Artery"} xref: ZFA:0005161 is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0002107 ! liver -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: supplies UBERON:0002107 ! liver -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/4c/Common_and_proper_hepatic_artery.png" xsd:anyURI -property_value: IAO:0000232 "currently defined in a generic fashion." xsd:string -property_value: UBPROP:0000001 "Artery that supplies blood to the liver.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005161", ontology="TAO", source="ZFIN:curator"} +intersection_of: RO:0002178 UBERON:0002107 ! supplies liver +relationship: RO:0002178 UBERON:0002107 ! supplies liver +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4c/Common_and_proper_hepatic_artery.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001194 @@ -170578,14 +169643,14 @@ xref: UMLS:C0037996 {source="ncithesaurus:Splenic_Artery"} xref: Wikipedia:Splenic_artery is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0002106 ! spleen +intersection_of: RO:0002178 UBERON:0002106 ! supplies spleen disjoint_from: UBERON:0001640 ! celiac artery -relationship: connecting_branch_of UBERON:0001640 ! celiac artery -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: supplies UBERON:0002106 ! spleen -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/a2/Gray1188.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +relationship: RO:0002178 UBERON:0002106 ! supplies spleen +relationship: RO:0002252 UBERON:0001640 ! connecting branch of celiac artery +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/a2/Gray1188.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/uberon/issues/268" xsd:anyURI [Term] @@ -170606,14 +169671,14 @@ xref: UMLS:C0226328 {source="ncithesaurus:Middle_Colic_Artery"} xref: Wikipedia:Middle_colic_artery is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery -intersection_of: connecting_branch_of UBERON:0001182 ! superior mesenteric artery -intersection_of: supplies UBERON:0001157 ! transverse colon -relationship: connecting_branch_of UBERON:0001182 ! superior mesenteric artery -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: supplies UBERON:0001157 ! transverse colon -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/cb/Gray537.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +intersection_of: RO:0002178 UBERON:0001157 ! supplies transverse colon +intersection_of: RO:0002252 UBERON:0001182 ! connecting branch of superior mesenteric artery +relationship: RO:0002178 UBERON:0001157 ! supplies transverse colon +relationship: RO:0002252 UBERON:0001182 ! connecting branch of superior mesenteric artery +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/cb/Gray537.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001197 @@ -170633,18 +169698,18 @@ xref: UMLS:C0226323 {source="ncithesaurus:Ileo-colic_Artery"} xref: Wikipedia:Ileocolic_artery is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery -intersection_of: connecting_branch_of UBERON:0001182 ! superior mesenteric artery -intersection_of: supplies UBERON:0001153 ! caecum -intersection_of: supplies UBERON:0001154 ! vermiform appendix -intersection_of: supplies UBERON:0002116 ! ileum -relationship: connecting_branch_of UBERON:0001182 ! superior mesenteric artery -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: supplies UBERON:0001153 ! caecum -relationship: supplies UBERON:0001154 ! vermiform appendix -relationship: supplies UBERON:0002116 ! ileum -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray536.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +intersection_of: RO:0002178 UBERON:0001153 ! supplies caecum +intersection_of: RO:0002178 UBERON:0001154 ! supplies vermiform appendix +intersection_of: RO:0002178 UBERON:0002116 ! supplies ileum +intersection_of: RO:0002252 UBERON:0001182 ! connecting branch of superior mesenteric artery +relationship: RO:0002178 UBERON:0001153 ! supplies caecum +relationship: RO:0002178 UBERON:0001154 ! supplies vermiform appendix +relationship: RO:0002178 UBERON:0002116 ! supplies ileum +relationship: RO:0002252 UBERON:0001182 ! connecting branch of superior mesenteric artery +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray536.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001199 @@ -170690,10 +169755,9 @@ is_a: UBERON:0004786 ! gastrointestinal system mucosa intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0000945 ! stomach relationship: capable_of GO:0001696 ! gastric acid secretion -relationship: contributes_to_morphology_of UBERON:0001167 ! wall of stomach relationship: part_of UBERON:0001167 ! wall of stomach -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/1/1c/Normal_gastric_mucosa_intermed_mag.jpg" xsd:anyURI -property_value: UBPROP:0000001 "The gastric mucosa is the mucous membrane layer of the stomach which contains the glands and the gastric pits. In men it is about 1 mm thick and its surface is smooth, soft, and velvety. It consists of epithelium, lamina propria, and the muscularis mucosae. In its fresh state, it is of a pinkish tinge at the pyloric end and of a red or reddish-brown color over the rest of its surface. In infancy it is of a brighter hue, the vascular redness being more marked. It is thin at the cardiac extremity, but thicker toward the pylorus. During the contracted state of the organ it is thrown into numerous plaits or rugae, which, for the most part, have a longitudinal direction, and are most marked toward the pyloric end of the stomach, and along the greater curvature. These folds are entirely obliterated when the organ becomes distended. When examined with a lens, the inner surface of the mucous membrane presents a peculiar honeycomb appearance from being covered with funnel-like depressions or foveolae of a polygonal or hexagonal form, which vary from 0.12 to 0.25 mm. in diameter. These are the ducts of the gastric glands, and at the bottom of each may be seen one or more minute orifices, the openings of the gland tubes. Gastric glands are simple or branched tubular glands that emerge on the deeper part of the gastric foveola, inside the gastric areas and outlined by the folds of the mucosa. There are three types of glands: cardiac glands (in the proximal part of the stomach), oxyntic glands (the dominating type of gland), and pyloric glands. The cardiac glands mainly contain mucus producing cells. The bottom part of the oxyntic glands is dominated by zymogen (chief) cells that produce pepsinogen (an inactive precursor of the pepsin enzyme). Parietal cells, which secrete hydrochloric acid are scattered in the glands, with most of them in the middle part. The upper part of the glands consist of mucous neck cells; in this part the dividing cells are seen. The pyloric glands contain mucus-secreting cells. Several types of endocrine cells are found in all regions of the gastric mucosa. In the pyloric glands contain gastrin producing cells (G cells); this hormone stimulates acid production from the parietal cells. ECL (enterochromaffine-like) cells, found in the oxyntic glands release histamine, which also is a powerful stimulant of the acid secretion. The A cells produce glucagon, which mobilizes the hepatic glycogen, and the enterochromaffin cells that produce serotonin, which stimulates the contraction of the smooth muscles. The surface of the mucous membrane is covered by a single layer of columnar epithelium . This epithelium commences very abruptly at the cardiac orifice, where there is a sudden transition from the stratified epithelium of the esophagus. The epithelial lining of the gland ducts is of the same character and is continuous with the general lining of the stomach. [WP,unvetted][Wikipedia:Gastric_mucosa]." xsd:string {source="Wikipedia:Gastric_mucosa"} +relationship: RO:0002433 UBERON:0001167 ! contributes to morphology of wall of stomach +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/1/1c/Normal_gastric_mucosa_intermed_mag.jpg" xsd:anyURI [Term] id: UBERON:0001200 @@ -170719,8 +169783,8 @@ xref: UMLS:C0227211 {source="ncithesaurus:Gastric_Submucosa"} is_a: UBERON:0018257 ! submucosa of digestive tract intersection_of: UBERON:0000009 ! submucosa intersection_of: part_of UBERON:0000945 ! stomach -relationship: contributes_to_morphology_of UBERON:0001167 ! wall of stomach relationship: part_of UBERON:0001167 ! wall of stomach +relationship: RO:0002433 UBERON:0001167 ! contributes to morphology of wall of stomach [Term] id: UBERON:0001201 @@ -170779,9 +169843,9 @@ xref: UMLS:C1517453 {source="ncithesaurus:Gastric_Serosal_Surface"} is_a: UBERON:0004782 ! gastrointestinal system serosa intersection_of: UBERON:0000042 ! serous membrane intersection_of: part_of UBERON:0001167 ! wall of stomach -relationship: contributes_to_morphology_of UBERON:0001167 ! wall of stomach relationship: part_of UBERON:0001167 ! wall of stomach -property_value: editor_note "TODO - check serosa/peritoneum" xsd:string +relationship: RO:0002433 UBERON:0001167 ! contributes to morphology of wall of stomach +property_value: IAO:0000116 "TODO - check serosa/peritoneum" xsd:string [Term] id: UBERON:0001202 @@ -170804,11 +169868,10 @@ is_a: UBERON:0011185 ! gastrointestinal sphincter intersection_of: UBERON:0004590 ! sphincter muscle intersection_of: part_of UBERON:0001166 ! pylorus relationship: adjacent_to UBERON:0002114 ! duodenum -relationship: continuous_with UBERON:0008858 ! pyloric canal -relationship: contributes_to_morphology_of UBERON:0001166 ! pylorus -relationship: never_in_taxon NCBITaxon:8355 relationship: part_of UBERON:0001166 ! pylorus -property_value: UBPROP:0000003 "(...) the adult Xenopus stomach exhibits both glandular and aglandular regions and a distinct pyloric sphincter similar to that of the amniotic vertebrates (...).[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001466", ontology="VHOG", source="DOI:10.1046/j.1525-142x.2000.00076.x", source="http://bgee.unil.ch/"} +relationship: RO:0002150 UBERON:0008858 ! continuous with pyloric canal +relationship: RO:0002433 UBERON:0001166 ! contributes to morphology of pylorus +property_value: RO:0002161 NCBITaxon:8355 [Term] id: UBERON:0001204 @@ -170898,7 +169961,6 @@ intersection_of: UBERON:0000042 ! serous membrane intersection_of: part_of UBERON:0002108 ! small intestine relationship: part_of UBERON:0001168 ! wall of small intestine relationship: part_of UBERON:0001243 ! serosa of intestine -property_value: UBPROP:0000010 "duodenum, 1st part serosa, 2nd - 4th adventitia" xsd:string [Term] id: UBERON:0001207 @@ -170968,7 +170030,7 @@ intersection_of: UBERON:0000042 ! serous membrane intersection_of: part_of UBERON:0000059 ! large intestine relationship: part_of UBERON:0001169 ! wall of large intestine relationship: part_of UBERON:0001243 ! serosa of intestine -property_value: editor_note "TODO - check serosa/peritoneum" xsd:string +property_value: IAO:0000116 "TODO - check serosa/peritoneum" xsd:string [Term] id: UBERON:0001211 @@ -170994,13 +170056,10 @@ xref: NCIT:C12771 xref: UMLS:C0031272 {source="ncithesaurus:Peyer_s_Patch"} xref: Wikipedia:Peyer's_patch is_a: UBERON:0001962 {source="FMA", source="MA"} ! gut-associated lymphoid tissue -relationship: never_in_taxon NCBITaxon:8459 {source="PMID:PMID:20181529"} -relationship: only_in_taxon NCBITaxon:32524 {source="PMID:PMID:20181529"} ! Amniota relationship: part_of UBERON:0000030 {comment="EDITOR_NOTE check this"} ! lamina propria relationship: part_of UBERON:0001242 ! intestinal mucosa -property_value: UBPROP:0000008 "Reptiles have accumulations of lymphocytes in their guts that may be primitive Peyer's patches (Zapata and Solas)." xsd:string -property_value: UBPROP:0000012 "FMA has [set of?] [aggregated,small] lymphoid [follice,nodule] of [colon, SI, I, etc]" xsd:string {external_ontology="FMA"} -property_value: UBPROP:0000012 "Pp is a syn for Aggregated lymphoid follicle of small intestine; but MA uses Pp as covering both SI and LI. MA also includes follicle as a part. WP says duodenum and jejunum lack PPs" xsd:string {external_ontology="MA"} +relationship: RO:0002160 NCBITaxon:32524 {source="PMID:PMID:20181529"} ! only in taxon Amniota +property_value: RO:0002161 NCBITaxon:8459 {source="PMID:PMID:20181529"} [Term] id: UBERON:0001212 @@ -171026,14 +170085,13 @@ xref: SCTID:41298001 xref: UMLS:C0006323 {source="ncithesaurus:Brunner_s_Gland"} xref: Wikipedia:Brunner's_glands is_a: UBERON:0003408 ! gland of digestive tract -is_a: UBERON:0011148 {notes="compound tubular"} ! submucosal gland +is_a: UBERON:0011148 ! submucosal gland intersection_of: UBERON:0011148 ! submucosal gland intersection_of: part_of UBERON:0002114 ! duodenum -relationship: located_in UBERON:0003332 {source="FMA, modified"} ! submucosa of duodenum -relationship: only_in_taxon NCBITaxon:40674 {notes="unclear for Aves", source="ISBN:9780521617147"} ! Mammalia relationship: part_of UBERON:0002114 ! duodenum -property_value: editor_note "currently defined as equivalent to any submucosal gland in the duodenum." xsd:string -property_value: UBPROP:0000008 "Said to be absent outside mammlian (Andrew 1959) but Ziswiler and Farner (1972) noted similar glands at the gastroduodenal junction of some birds" xsd:string {source="ISBN:9780521617147"} +relationship: RO:0001025 UBERON:0003332 {source="FMA, modified"} ! located in submucosa of duodenum +relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia +property_value: IAO:0000116 "currently defined as equivalent to any submucosal gland in the duodenum." xsd:string [Term] id: UBERON:0001213 @@ -171068,12 +170126,9 @@ is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004923 {source="FMA"} ! organ component layer relationship: has_part UBERON:0001981 ! blood vessel relationship: has_part UBERON:0012425 ! striated border microvillus layer -relationship: part_of UBERON:0001204 {gci_relation="part_of", gci_filler="NCBITaxon:9606", notes="may be present in other parts in other species", source="FMA"} ! mucosa of small intestine relationship: part_of UBERON:0001277 {source="ZFA"} ! intestinal epithelium -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/38/Small_intestine_low_mag.jpg" xsd:anyURI -property_value: editor_note "in mammals, villi are (largely?) absent from the large intestine, so we treat this as equivalent to small intestinal villus. small/large subdivision may not make sense for all species for which this is present (see ZFA). Note that VHOG quotes ISBN:978-0030223693 as suggesting there are some villi in the large intestine" xsd:string -property_value: UBPROP:0000001 "The entire digestive tract is lined by well developed villi, which are longest in the intestinal bulb and decrease progressively in size towards the caudal end of the intestine. No crypts are present, but, the regions between the villi, the intervillus pockets, have a crypt-like function. Cells are produced in the intervillus pockets and shed from the villus tips. Crosnier et al. 2005[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005125", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000012 "the BTO class refers to a generic villous" xsd:string {external_ontology="BTO"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/38/Small_intestine_low_mag.jpg" xsd:anyURI +property_value: IAO:0000116 "in mammals, villi are (largely?) absent from the large intestine, so we treat this as equivalent to small intestinal villus. small/large subdivision may not make sense for all species for which this is present (see ZFA). Note that VHOG quotes ISBN:978-0030223693 as suggesting there are some villi in the large intestine" xsd:string [Term] id: UBERON:0001215 @@ -171097,12 +170152,12 @@ xref: VHOG:0001118 xref: Wikipedia:Inferior_mesenteric_vein is_a: UBERON:0005617 ! mesenteric vein intersection_of: UBERON:0005617 ! mesenteric vein -intersection_of: drains UBERON:0000059 ! large intestine -relationship: drains UBERON:0000059 ! large intestine -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: tributary_of UBERON:0003713 {source="FMA/obol"} ! splenic vein -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +intersection_of: RO:0002179 UBERON:0000059 ! drains large intestine +relationship: RO:0002179 UBERON:0000059 ! drains large intestine +relationship: RO:0002376 UBERON:0003713 {source="FMA/obol"} ! tributary of splenic vein +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001216 @@ -171117,11 +170172,11 @@ xref: MA:0002153 xref: Wikipedia:Jejunal_veins is_a: UBERON:0002017 {source="FMA"} ! portal vein intersection_of: UBERON:0001638 ! vein -intersection_of: drains UBERON:0002115 ! jejunum -relationship: drains UBERON:0002115 ! jejunum -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: tributary_of UBERON:0001138 {source="FMA/obol"} ! superior mesenteric vein -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png" xsd:anyURI +intersection_of: RO:0002179 UBERON:0002115 ! drains jejunum +relationship: RO:0002179 UBERON:0002115 ! drains jejunum +relationship: RO:0002376 UBERON:0001138 {source="FMA/obol"} ! tributary of superior mesenteric vein +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001217 @@ -171137,11 +170192,11 @@ xref: UMLS:C1301431 {source="ncithesaurus:Ileal_Vein"} xref: Wikipedia:Ileal_veins is_a: UBERON:0002017 ! portal vein intersection_of: UBERON:0001638 ! vein -intersection_of: drains UBERON:0002116 ! ileum -relationship: drains UBERON:0002116 ! ileum +intersection_of: RO:0002179 UBERON:0002116 ! drains ileum relationship: part_of UBERON:0001138 ! superior mesenteric vein -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: tributary_of UBERON:0001138 {source="FMA", source="Wikipedia"} ! superior mesenteric vein +relationship: RO:0002179 UBERON:0002116 ! drains ileum +relationship: RO:0002376 UBERON:0001138 {source="FMA", source="Wikipedia"} ! tributary of superior mesenteric vein +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001218 @@ -171159,14 +170214,14 @@ xref: SCTID:9018004 xref: Wikipedia:Middle_colic_vein is_a: UBERON:0002017 ! portal vein intersection_of: UBERON:0002017 ! portal vein -intersection_of: drains UBERON:0001157 ! transverse colon -intersection_of: tributary_of UBERON:0001138 ! superior mesenteric vein -relationship: drains UBERON:0001157 ! transverse colon -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: tributary_of UBERON:0001138 ! superior mesenteric vein -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +intersection_of: RO:0002179 UBERON:0001157 ! drains transverse colon +intersection_of: RO:0002376 UBERON:0001138 ! tributary of superior mesenteric vein +relationship: RO:0002179 UBERON:0001157 ! drains transverse colon +relationship: RO:0002376 UBERON:0001138 ! tributary of superior mesenteric vein +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001219 @@ -171185,16 +170240,16 @@ xref: UMLS:C0226744 {source="ncithesaurus:Ileocolic_Vein"} xref: Wikipedia:Ileocolic_vein is_a: UBERON:0001217 ! ileal vein intersection_of: UBERON:0002017 ! portal vein -intersection_of: drains UBERON:0001153 ! caecum -intersection_of: drains UBERON:0001155 ! colon -intersection_of: drains UBERON:0002116 ! ileum -intersection_of: tributary_of UBERON:0001138 ! superior mesenteric vein -relationship: drains UBERON:0001153 ! caecum -relationship: drains UBERON:0001155 ! colon -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +intersection_of: RO:0002179 UBERON:0001153 ! drains caecum +intersection_of: RO:0002179 UBERON:0001155 ! drains colon +intersection_of: RO:0002179 UBERON:0002116 ! drains ileum +intersection_of: RO:0002376 UBERON:0001138 ! tributary of superior mesenteric vein +relationship: RO:0002179 UBERON:0001153 ! drains caecum +relationship: RO:0002179 UBERON:0001155 ! drains colon +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001222 @@ -171209,11 +170264,10 @@ xref: SCTID:276251000 xref: UMLS:C0227682 {source="ncithesaurus:Right_Ureter"} is_a: UBERON:0000056 ! ureter intersection_of: UBERON:0000056 ! ureter -intersection_of: in_right_side_of UBERON:0000468 ! multicellular organism -relationship: in_right_side_of UBERON:0000468 ! multicellular organism -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Ureter_R.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Ureter_R.glb" xsd:anyURI -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +intersection_of: BSPO:0000121 UBERON:0000468 ! multicellular organism +relationship: BSPO:0000121 UBERON:0000468 ! multicellular organism +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Ureter_R.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Ureter_R.glb" xsd:anyURI [Term] id: UBERON:0001223 @@ -171228,11 +170282,10 @@ xref: SCTID:276340002 xref: UMLS:C0227683 {source="ncithesaurus:Left_Ureter"} is_a: UBERON:0000056 ! ureter intersection_of: UBERON:0000056 ! ureter -intersection_of: in_left_side_of UBERON:0000468 ! multicellular organism -relationship: in_left_side_of UBERON:0000468 ! multicellular organism -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Ureter_L.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Ureter_L.glb" xsd:anyURI -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +intersection_of: BSPO:0000120 UBERON:0000468 ! multicellular organism +relationship: BSPO:0000120 UBERON:0000468 ! multicellular organism +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Ureter_L.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Ureter_L.glb" xsd:anyURI [Term] id: UBERON:0001224 @@ -171264,12 +170317,12 @@ disjoint_from: UBERON:0002355 ! pelvic region of trunk relationship: channel_for UBERON:0001088 ! urine relationship: channels_from UBERON:0002113 ! kidney relationship: channels_into UBERON:0000056 ! ureter -relationship: continuous_with UBERON:0000056 {source="FMA"} ! ureter -relationship: contributes_to_morphology_of UBERON:0000056 ! ureter relationship: part_of UBERON:0002113 {source="MA"} ! kidney relationship: part_of UBERON:0036295 ! renal pelvis/ureter -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/c/c0/Illu_kidney2.jpg" xsd:anyURI +relationship: RO:0002150 UBERON:0000056 {source="FMA"} ! continuous with ureter +relationship: RO:0002433 UBERON:0000056 ! contributes to morphology of ureter +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/c/c0/Illu_kidney2.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001225 @@ -171297,15 +170350,14 @@ xref: Wikipedia:Renal_cortex is_a: UBERON:0001851 ! cortex intersection_of: UBERON:0001851 ! cortex intersection_of: part_of UBERON:0002113 ! kidney -relationship: contributes_to_morphology_of UBERON:0002113 ! kidney relationship: part_of UBERON:0008987 {source="FMA"} ! renal parenchyma -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" xsd:anyURI -property_value: UBPROP:0000010 "In the adult metanephros, it forms a continuous smooth outer zone with a number of projections that extend down between the pyramids. It contains the renal corpuscles and the renal tubules except for parts of the loop of Henle which descend into the renal medulla. It also contains blood vessels and cortical collecting ducts. The renal cortex is the part of the kidney where ultrafiltration occurs.[WP]" xsd:string +relationship: RO:0002433 UBERON:0002113 ! contributes to morphology of kidney +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001228 @@ -171327,15 +170379,15 @@ xref: SCTID:362214007 xref: UMLS:C0022666 {source="ncithesaurus:Renal_Papilla"} xref: Wikipedia:Renal_papilla is_a: UBERON:0000064 ! organ part -relationship: contributes_to_morphology_of UBERON:0001224 ! renal pelvis relationship: part_of UBERON:0001224 ! renal pelvis relationship: part_of UBERON:0001294 ! inner medulla of kidney -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Ureter_L.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Ureter_R.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI +relationship: RO:0002433 UBERON:0001224 ! contributes to morphology of renal pelvis +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Ureter_L.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Ureter_R.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001229 @@ -171368,15 +170420,12 @@ xref: VHOG:0001262 xref: Wikipedia:Renal_corpuscle xref: ZFA:0005281 is_a: UBERON:0000063 ! organ subunit -relationship: contributes_to_morphology_of UBERON:0001225 ! cortex of kidney -relationship: contributes_to_morphology_of UBERON:0001285 ! nephron relationship: part_of UBERON:0001225 ! cortex of kidney relationship: part_of UBERON:0001285 {source="MA", source="ZFA"} ! nephron -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg" xsd:anyURI -property_value: UBPROP:0000001 "A mass of arterial capillaries enveloped in a capsule and attached to a tubule in the kidney[BTO]" xsd:string {date_retrieved="2012-11-28", external_class="BTO:0000333", ontology="BTO", source="BTO:curator"} -property_value: UBPROP:0000001 "A tuft of capillaries found in a Bowman's capsule in which waste products are filtered from the blood and urine formation is initiated. Paired highly vascularized structures of the pronephros, responsible for blood filtration.[XAO]" xsd:string {date_retrieved="2012-11-28", external_class="XAO:0000146", ontology="XAO", source="XAO:curator"} -property_value: UBPROP:0000001 "The part of the nephron that filters blood.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005281", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002433 UBERON:0001225 ! contributes to morphology of cortex of kidney +relationship: RO:0002433 UBERON:0001285 ! contributes to morphology of nephron +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001230 @@ -171415,13 +170464,10 @@ xref: ZFA:0005310 is_a: UBERON:0000064 ! organ part disjoint_from: UBERON:0002015 ! kidney capsule relationship: capable_of_part_of GO:0003094 {source="Wikipedia"} ! glomerular filtration -relationship: contributes_to_morphology_of UBERON:0001229 ! renal corpuscle -relationship: develops_from UBERON:0004199 ! S-shaped body relationship: part_of UBERON:0001229 ! renal corpuscle -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg" xsd:anyURI -property_value: UBPROP:0000001 "Anatomical structure found in the kidney consisting of an expanded end of a kidney tubule surrounding a glomerulus and is the major site of filtration.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010526", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000009 "Fluids from blood in the glomerulus are collected in the Bowman's capsule and further processed along the nephron to form urine. This process is known as ultrafiltration[WP]." xsd:string -property_value: UBPROP:0000011 "One fold of the S-shaped body gives rise to Bowman's capsule[GUDMAP]" xsd:string +relationship: RO:0002202 UBERON:0004199 ! develops from S-shaped body +relationship: RO:0002433 UBERON:0001229 ! contributes to morphology of renal corpuscle +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg" xsd:anyURI [Term] id: UBERON:0001231 @@ -171457,11 +170503,10 @@ is_a: UBERON:0004211 ! nephron epithelium is_a: UBERON:0009773 {source="GO"} ! renal tubule intersection_of: UBERON:0003914 {source="GO", source="MA", source="ZFA"} ! epithelial tube intersection_of: part_of UBERON:0001285 {source="GO", source="MA", source="ZFA"} ! nephron -relationship: contributes_to_morphology_of UBERON:0001285 ! nephron -relationship: develops_from UBERON:0003918 {notes="checkme"} ! kidney mesenchyme relationship: has_part CL:0005009 {source="ZFA"} ! renal principal cell -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000012 "note that in ISBN:0073040584 (Vertebrates, Kardong), the uriniferous tubule contains the nephron, so we have a separate class, rather than using a synonym, as in MA" xsd:string {external_ontology="MA"} +relationship: RO:0002202 UBERON:0003918 ! develops from kidney mesenchyme +relationship: RO:0002433 UBERON:0001285 ! contributes to morphology of nephron +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001232 @@ -171496,12 +170541,10 @@ xref: TAO:0005294 xref: Wikipedia:Collecting_tubule xref: ZFA:0005294 is_a: UBERON:0006555 ! excretory tube -relationship: contributes_to_morphology_of UBERON:0002113 ! kidney -relationship: part_of UBERON:0001285 {notes="checkme", source="GO"} ! nephron +relationship: part_of UBERON:0001285 ! nephron relationship: part_of UBERON:0004100 ! renal collecting system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000001 "Renal duct that collects the output from renal tubules.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005294", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000012 "in ISBN:0073040584 (Vertebrates, Kardong), the nephron is adjacent to the collecting tubule, consistent with FMA, but not GO. Wikipedia says: Many sources include the connecting tubule as part of the collecting duct system. However, the embryological origin is more similar to the nephron than it is to the rest of the collecting duct (which derives from the ureteric bud), and other sources therefore classify the connecting tubule with the nephron" xsd:string {external_ontology="FMA"} +relationship: RO:0002433 UBERON:0002113 ! contributes to morphology of kidney +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001233 @@ -171518,10 +170561,8 @@ xref: SCTID:281625001 xref: UMLS:C0229559 {source="ncithesaurus:Right_Adrenal_Gland"} is_a: UBERON:0002369 ! adrenal gland intersection_of: UBERON:0002369 ! adrenal gland -intersection_of: in_right_side_of UBERON:0000916 ! abdomen -relationship: in_right_side_of UBERON:0000916 ! abdomen -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI -property_value: UBPROP:0000008 "In humans, the right adrenal gland is triangular shaped" xsd:string {source="WP"} +intersection_of: BSPO:0000121 UBERON:0000916 ! abdomen +relationship: BSPO:0000121 UBERON:0000916 ! abdomen [Term] id: UBERON:0001234 @@ -171538,10 +170579,8 @@ xref: SCTID:281626000 xref: UMLS:C0229560 {source="ncithesaurus:Left_Adrenal_Gland"} is_a: UBERON:0002369 ! adrenal gland intersection_of: UBERON:0002369 ! adrenal gland -intersection_of: in_left_side_of UBERON:0000916 ! abdomen -relationship: in_left_side_of UBERON:0000916 ! abdomen -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI -property_value: UBPROP:0000008 "In humans, the left adrenal gland is semilunar shaped" xsd:string {source="WP"} +intersection_of: BSPO:0000120 UBERON:0000916 ! abdomen +relationship: BSPO:0000120 UBERON:0000916 ! abdomen [Term] id: UBERON:0001235 @@ -171577,16 +170616,15 @@ xref: Wikipedia:Adrenal_cortex xref: XAO:0000165 is_a: UBERON:0001851 ! cortex is_a: UBERON:0004120 ! mesoderm-derived structure +is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0001851 ! cortex intersection_of: part_of UBERON:0002369 ! adrenal gland relationship: capable_of GO:0006704 ! glucocorticoid biosynthetic process relationship: capable_of GO:0006705 ! mineralocorticoid biosynthetic process relationship: capable_of GO:0035932 ! aldosterone secretion -relationship: contributes_to_morphology_of UBERON:0002369 ! adrenal gland relationship: part_of UBERON:0002369 ! adrenal gland -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray1185.png" xsd:anyURI -property_value: UBPROP:0000003 "All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues (medulla), but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001481", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "Kardong states that mammals are the first to have distinct cortext and medulla, but this contradicts XAO" xsd:string +relationship: RO:0002433 UBERON:0002369 ! contributes to morphology of adrenal gland +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray1185.png" xsd:anyURI [Term] id: UBERON:0001236 @@ -171623,16 +170661,16 @@ xref: VHOG:0001378 xref: Wikipedia:Adrenal_medulla xref: XAO:0000166 is_a: UBERON:0000958 ! medulla of organ +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0000958 ! medulla of organ intersection_of: part_of UBERON:0002369 ! adrenal gland -relationship: contributes_to_morphology_of UBERON:0002369 ! adrenal gland relationship: has_part CL:0002082 {source="FMA"} ! type II cell of adrenal medulla relationship: has_part CL:0002083 {source="FMA"} ! type I cell of adrenal medulla relationship: part_of UBERON:0002369 ! adrenal gland -relationship: surrounded_by UBERON:0001235 {source="Wikipedia"} ! adrenal cortex -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray1185.png" xsd:anyURI -property_value: UBPROP:0000003 "All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues (medulla), but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001378", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9", source="http://bgee.unil.ch/"} +relationship: RO:0002219 UBERON:0001235 {source="Wikipedia"} ! surrounded by adrenal cortex +relationship: RO:0002433 UBERON:0002369 ! contributes to morphology of adrenal gland +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray1185.png" xsd:anyURI [Term] id: UBERON:0001237 @@ -171656,7 +170694,7 @@ xref: SCTID:276159005 xref: UMLS:C0442134 {source="ncithesaurus:Paraaortic"} xref: Wikipedia:Organ_of_Zuckerkandl is_a: UBERON:0012279 ! chromaffin paraganglion -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/af/Gray531.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/af/Gray531.png" xsd:anyURI [Term] id: UBERON:0001238 @@ -171714,8 +170752,8 @@ xref: UMLS:C0227267 {source="ncithesaurus:Small_Intestinal_Crypt_of_Lieberkuhn"} is_a: UBERON:0001983 ! crypt of Lieberkuhn intersection_of: UBERON:0001983 ! crypt of Lieberkuhn intersection_of: part_of UBERON:0002108 ! small intestine -relationship: contributes_to_morphology_of UBERON:0002108 ! small intestine relationship: part_of UBERON:0002108 ! small intestine +relationship: RO:0002433 UBERON:0002108 ! contributes to morphology of small intestine [Term] id: UBERON:0001242 @@ -171806,7 +170844,7 @@ is_a: UBERON:0004782 ! gastrointestinal system serosa intersection_of: UBERON:0000042 ! serous membrane intersection_of: part_of UBERON:0000160 ! intestine relationship: part_of UBERON:0001262 ! wall of intestine -property_value: editor_note "TODO - check serosa/peritoneum" xsd:string +property_value: IAO:0000116 "TODO - check serosa/peritoneum" xsd:string [Term] id: UBERON:0001245 @@ -171823,7 +170861,6 @@ synonym: "proctodeum" RELATED [] xref: BTO:0001680 xref: CALOHA:TS-2005 xref: EV:0100082 -xref: FBbt:00047153 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:15711 xref: GAID:312 xref: galen:Anus @@ -171838,15 +170875,13 @@ xref: Wikipedia:Anus is_a: UBERON:0000161 ! orifice is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000161 ! orifice -intersection_of: distalmost_part_of UBERON:0001555 ! digestive tract -relationship: develops_from UBERON:0000931 ! proctodeum -relationship: distalmost_part_of UBERON:0001555 ! digestive tract +intersection_of: BSPO:0001108 UBERON:0001555 ! digestive tract +relationship: BSPO:0001108 UBERON:0001555 ! digestive tract relationship: part_of UBERON:0001555 ! digestive tract -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/65/Protovsdeuterostomes.svg" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/75/Anorectum.gif" xsd:anyURI -property_value: UBPROP:0000007 "anal" xsd:string -property_value: UBPROP:0000008 "In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html" xsd:string +relationship: RO:0002202 UBERON:0000931 ! develops from proctodeum +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/65/Protovsdeuterostomes.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/75/Anorectum.gif" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001246 @@ -171862,10 +170897,10 @@ xref: SCTID:83488001 xref: UMLS:C0227515 {source="ncithesaurus:Interlobular_Bile_Duct"} xref: Wikipedia:Interlobular_bile_ducts is_a: UBERON:0003704 {source="FMA", source="MA-part-of"} ! intrahepatic bile duct -relationship: connects UBERON:0004058 ! biliary ductule -relationship: connects UBERON:0014719 ! intralobular duct -relationship: contributes_to_morphology_of UBERON:0001279 ! portal triad relationship: part_of UBERON:0001279 {source="FMA", source="MA", source="MP"} ! portal triad +relationship: RO:0002176 UBERON:0004058 ! connects biliary ductule +relationship: RO:0002176 UBERON:0014719 ! connects intralobular duct +relationship: RO:0002433 UBERON:0001279 ! contributes to morphology of portal triad [Term] id: UBERON:0001247 @@ -171886,16 +170921,16 @@ xref: SCTID:362705001 xref: UMLS:C0230240 {source="ncithesaurus:Falciform_Ligament"} xref: VHOG:0000355 xref: Wikipedia:Falciform_ligament +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0013139 ! ligament of liver intersection_of: UBERON:0008845 ! nonskeletal ligament -intersection_of: attaches_to UBERON:0000309 ! body wall -intersection_of: attaches_to UBERON:0002107 ! liver -relationship: attaches_to UBERON:0000309 ! body wall -relationship: attaches_to UBERON:0002107 ! liver +intersection_of: RO:0002371 UBERON:0000309 ! attached to body wall +intersection_of: RO:0002371 UBERON:0002107 ! attached to liver relationship: part_of UBERON:0005626 {source="MA"} ! ventral mesogastrium -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Liver.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Liver.glb" xsd:anyURI -property_value: UBPROP:0000012 "in FMA this is a subclass of mesentery. In MA it is a subclass of ligament, we infer and assert this is a nonskeletal ligament" xsd:string {external_ontology="FMA"} +relationship: RO:0002371 UBERON:0000309 ! attached to body wall +relationship: RO:0002371 UBERON:0002107 ! attached to liver +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Liver.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Liver.glb" xsd:anyURI [Term] id: UBERON:0001249 @@ -171920,12 +170955,13 @@ xref: NCIT:C33602 xref: SCTID:35845000 xref: UMLS:C1519475 {source="ncithesaurus:Splenic_Lymphoid_Follicle"} is_a: UBERON:0000444 ! lymphoid follicle +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000444 ! lymphoid follicle intersection_of: part_of UBERON:0002106 ! spleen -relationship: contains_process GO:0002319 ! memory B cell differentiation -relationship: contributes_to_morphology_of UBERON:0001959 ! white pulp of spleen +relationship: BFO:0000067 GO:0002319 ! contains process memory B cell differentiation relationship: part_of UBERON:0001959 {source="CL:tm", source="MA"} ! white pulp of spleen relationship: part_of UBERON:0006561 {source="FMA"} ! non-lymphatic part of lymphoid system +relationship: RO:0002433 UBERON:0001959 ! contributes to morphology of white pulp of spleen [Term] id: UBERON:0001250 @@ -171950,11 +170986,11 @@ xref: UMLS:C0229687 {source="ncithesaurus:Splenic_Red_Pulp"} xref: Wikipedia:Red_pulp is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:1000023 ! spleen pulp -relationship: composed_primarily_of CL:0000542 ! lymphocyte -relationship: contributes_to_morphology_of UBERON:0002106 ! spleen -relationship: present_in_taxon NCBITaxon:7955 {source="DOI:10.1177/0192623311409597"} -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1191.png" xsd:anyURI +relationship: RO:0002433 UBERON:0002106 ! contributes to morphology of spleen +relationship: RO:0002473 CL:0000542 ! composed primarily of lymphocyte +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1191.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:7955 {source="DOI:10.1177/0192623311409597"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001251 @@ -171974,12 +171010,12 @@ xref: NCIT:C49767 xref: UMLS:C1711368 {source="ncithesaurus:Marginal_Zone"} xref: Wikipedia:Marginal_zone is_a: UBERON:0000064 ! organ part +is_a: UBERON:0004120 ! mesoderm-derived structure relationship: adjacent_to UBERON:0001250 ! red pulp of spleen relationship: adjacent_to UBERON:0001959 ! white pulp of spleen relationship: part_of UBERON:0002106 ! spleen -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1191.png" xsd:anyURI -property_value: UBPROP:0000012 "WP says - (Some sources consider it to be the part of red pulp which borders on the white pulp, while other sources consider it to be neither red pulp nor white pulp.) - we use the adjacency relation here so it overlaps neither. FMA considers this an anatomical line." xsd:string {external_ontology="FMA"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1191.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001252 @@ -171996,6 +171032,7 @@ xref: FMA:15892 xref: MA:0002652 xref: SCTID:392273001 xref: SCTID:47879001 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005742 ! adventitia intersection_of: UBERON:0005742 ! adventitia intersection_of: part_of UBERON:0000056 ! ureter @@ -172017,10 +171054,11 @@ xref: FMA:15896 xref: MA:0002653 xref: SCTID:2771005 is_a: UBERON:0000030 ! lamina propria +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000030 ! lamina propria intersection_of: part_of UBERON:0000056 ! ureter relationship: part_of UBERON:0004980 {is_inferred="true", source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! mucosa of ureter -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001254 @@ -172036,13 +171074,14 @@ synonym: "ureter urothelium" EXACT [] xref: EMAPA:28089 xref: FMA:15897 xref: MA:0002655 +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0000365 ! urothelium +is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0000365 ! urothelium intersection_of: part_of UBERON:0000056 ! ureter -relationship: contributes_to_morphology_of UBERON:0000056 ! ureter relationship: part_of UBERON:0000056 ! ureter -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000012 "MP treats ureter urothelium and ureter luminal urothelium as exact synonyms, yes MA treats these as distinct; see also: transitional epithelium vs urothelium" xsd:string {external_ontology="MP"} +relationship: RO:0002433 UBERON:0000056 ! contributes to morphology of ureter +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001255 @@ -172083,18 +171122,12 @@ xref: XAO:0000154 is_a: UBERON:0002075 ! viscus is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0018707 {source="BTO"} ! bladder organ -relationship: develops_from UBERON:0000164 {notes="upper part of UG sinus"} ! primitive urogenital sinus -relationship: never_in_taxon NCBITaxon:8782 {editor="https://orcid.org/0000-0003-3308-6245", id="GOTAX:0010073", source="https://github.com/obophenotype/uberon/issues/454"} ! Aves relationship: part_of UBERON:0001556 {source="FMA"} ! lower urinary tract -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Urinary_Bladder.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urinary_Bladder.glb" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg" xsd:anyURI -property_value: UBPROP:0000001 "A saccular organ in which urine accumulates before discharge from the body. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000740", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000001 "Anatomical structure which consists of a membranous sac used to temporarily store urine until it is excreted from the body.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000623", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "In tetrapods, the urinary bladder arises as an outpocketing of the cloaca. (...) The tetrapod urinary bladder appears first among amphibians and is present in Sphenodon, turtles, most lizards, ostriches among birds, and all mammals.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000740", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.577-78", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "vesical" xsd:string -property_value: UBPROP:0000008 "The urinary bladder evolved in tetrapods. Birds to not possess a true urinary bladder, although Palaeognathae have an undifferentiated cloacal outpocketing that serves a similar function[https://github.com/obophenotype/uberon/issues/454]" xsd:string +relationship: RO:0002202 UBERON:0000164 ! develops from primitive urogenital sinus +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Urinary_Bladder.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urinary_Bladder.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001256 @@ -172118,10 +171151,11 @@ xref: NCIT:C48941 xref: SCTID:362225003 xref: UMLS:C0458421 {source="ncithesaurus:Bladder_Wall"} is_a: UBERON:0000060 ! anatomical wall +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0001255 ! urinary bladder relationship: part_of UBERON:0001255 ! urinary bladder -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001257 @@ -172150,14 +171184,13 @@ xref: SCTID:272663002 xref: UMLS:C0447586 {source="ncithesaurus:Bladder_Trigone"} xref: Wikipedia:Trigone_of_urinary_bladder is_a: UBERON:0000064 ! organ part -relationship: contributes_to_morphology_of UBERON:0001255 ! urinary bladder +is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0006082 ! fundus of urinary bladder -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Urinary_Bladder.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urinary_Bladder.glb" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/5/57/Illu_bladder.jpg" xsd:anyURI -property_value: UBPROP:0000009 "The area is very sensitive to expansion and once stretched to a certain degree, the urinary bladder signals the brain of its need to empty. The signals become stronger as the bladder continues to fill." xsd:string -property_value: UBPROP:0000011 "Embryologically, the trigone of the bladder is derived from the caudal end of mesonephric ducts, which is of mesodermal origin (the rest of the bladder is endodermal). In the female the mesonephric ducts regresses, causing the trigone to be less prominent, but still present" xsd:string {source="WP"} +relationship: RO:0002433 UBERON:0001255 ! contributes to morphology of urinary bladder +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Urinary_Bladder.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urinary_Bladder.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/5/57/Illu_bladder.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001258 @@ -172182,11 +171215,12 @@ xref: SCTID:362227006 xref: UMLS:C0227716 {source="ncithesaurus:Bladder_Neck"} xref: Wikipedia:Neck_of_urinary_bladder is_a: UBERON:0001560 ! neck of organ +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0001560 ! neck of organ intersection_of: part_of UBERON:0001255 ! urinary bladder -relationship: contributes_to_morphology_of UBERON:0001255 ! urinary bladder relationship: part_of UBERON:0001255 ! urinary bladder -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/63/Gray1156.png" xsd:anyURI +relationship: RO:0002433 UBERON:0001255 ! contributes to morphology of urinary bladder +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/63/Gray1156.png" xsd:anyURI [Term] id: UBERON:0001259 @@ -172216,11 +171250,12 @@ xref: NCIT:C32205 xref: SCTID:362224004 xref: UMLS:C0227691 {source="ncithesaurus:Bladder_Mucosa"} is_a: UBERON:0000344 ! mucosa +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0001255 ! urinary bladder -relationship: contributes_to_morphology_of UBERON:0001255 ! urinary bladder relationship: part_of UBERON:0001256 ! wall of urinary bladder -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002433 UBERON:0001255 ! contributes to morphology of urinary bladder +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001260 @@ -172247,7 +171282,7 @@ is_a: UBERON:0000042 ! serous membrane intersection_of: UBERON:0000042 ! serous membrane intersection_of: part_of UBERON:0001255 ! urinary bladder relationship: part_of UBERON:0001256 {source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! wall of urinary bladder -property_value: editor_note "TODO - check serosa/peritoneum" xsd:string +property_value: IAO:0000116 "TODO - check serosa/peritoneum" xsd:string [Term] id: UBERON:0001261 @@ -172272,11 +171307,11 @@ xref: MA:0001695 xref: NCIT:C48940 xref: UMLS:C1706967 {source="ncithesaurus:Bladder_Lamina_Propria"} is_a: UBERON:0000030 ! lamina propria +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000030 ! lamina propria intersection_of: part_of UBERON:0001255 ! urinary bladder relationship: part_of UBERON:0001259 ! mucosa of urinary bladder -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000010 "Contains loose to dense connective tissue, variably sized blood vessels that may be close to epithelium, lymphatics, variable adipose tissue" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001262 @@ -172303,7 +171338,7 @@ is_a: UBERON:0000328 ! gut wall intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0000160 ! intestine relationship: part_of UBERON:0000160 ! intestine -property_value: editor_note "we place two MA classes here due to the official ncit2ma mapping to intestinal wall tissue; not clear how bowel and intestine are different" xsd:string +property_value: IAO:0000116 "we place two MA classes here due to the official ncit2ma mapping to intestinal wall tissue; not clear how bowel and intestine are different" xsd:string [Term] id: UBERON:0001263 @@ -172316,20 +171351,20 @@ synonym: "acinus pancreaticus" EXACT OMO:0003011 [FMA:16011] synonym: "pancreas acinus" EXACT [] synonym: "pancreatic acinar" RELATED [] synonym: "pancreatic acini" RELATED OMO:0003004 [] -xref: BTO:0000028 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: EMAPA:35651 xref: FMA:16011 xref: MA:0002417 xref: NCIT:C49268 xref: SCTID:247604006 xref: UMLS:C0227578 {source="ncithesaurus:Pancreatic_Acinus"} +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0013232 ! serous acinus intersection_of: UBERON:0009842 ! glandular acinus intersection_of: part_of UBERON:0000017 ! exocrine pancreas -relationship: composed_primarily_of CL:0002064 ! pancreatic acinar cell -relationship: contributes_to_morphology_of UBERON:0000017 ! exocrine pancreas relationship: part_of UBERON:0007324 {source="FMA"} ! pancreatic lobule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002433 UBERON:0000017 ! contributes to morphology of exocrine pancreas +relationship: RO:0002473 CL:0002064 ! composed primarily of pancreatic acinar cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001264 @@ -172367,21 +171402,15 @@ xref: Wikipedia:Pancreas xref: XAO:0000136 xref: ZFA:0000140 is_a: UBERON:0002075 ! viscus -relationship: has_developmental_contribution_from UBERON:0003923 {source="Wikipedia"} ! dorsal pancreatic bud -relationship: has_developmental_contribution_from UBERON:0003924 {source="Wikipedia"} ! ventral pancreatic bud relationship: has_part UBERON:0000016 ! endocrine pancreas relationship: has_part UBERON:0000017 {gci_relation="part_of", gci_filler="NCBITaxon:89593"} ! exocrine pancreas -relationship: only_in_taxon NCBITaxon:7742 {source="PMID:16417468"} ! Vertebrata -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Pancreas.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Pancreas.glb" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Blausen_0699_PancreasAnatomy2.png" xsd:anyURI -property_value: UBPROP:0000001 "Organ which secretes a fluid containing enzymes that aid in the digestion of food.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010112", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000050", ontology="VHOG", source="DOI:10.1016/j.crvi.2007.03.006 Madsen OD, Pancreas phylogeny and ontogeny in relation to a 'pancreatic stem cell'. C.R. Biologies (2007)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "pancreatic" xsd:string -property_value: UBPROP:0000008 "As a secretory organ serving exocrine and endocrine functions, the pancreas is specific to the vertebrates[PMID:16417468] Hagfishes and lampreys are unique in the complete separation of their endocrine pancreas (islet or- gan) and their exocrine pancreas (50). The endocrine and exocrine pancreas are coassociated in crown gnathostomes (50). In Branchiostoma and Ciona, there is no diverticulum as there is in hagfishes, lampreys, and gnathostomes, only dispersed insulin-secreting cells in the walls of the gastrointestinal tract (51, 52)" xsd:string {source="PMID:20959416"} -property_value: UBPROP:0000008 "The zebrafish does not have a discrete pancreas. Exocrine pancreatic tissue can be found scattered along the intestinal tract. The acinar structure of the exocrine pancreas is very similar to that of mammals and comprises cells with a very dark, basophilic cytoplasm" xsd:string -property_value: UBPROP:0000009 "The mature pancreas of higher vertebrates and mammals comprises two major functional units: the exocrine pancreas, which is responsible for the production of digestive enzymes to be secreted into the gut lumen, and the endocrine pancreas, which has its role in the synthesis of several hormones with key regulatory functions in food uptake and metabolism. The exocrine portion constitutes the majority of the mass of the pancreas, and contains only two different cell types, the secretory acinar cells and the ductular cells. The endocrine portion, which comprises only 1-2% of the total mass, contains five different cell types, which are organized into mixed functional assemblies referred to as the islets of Langerhans" xsd:string {source="PMID:16417468"} +relationship: RO:0002160 NCBITaxon:7742 {source="PMID:16417468"} ! only in taxon Vertebrata +relationship: RO:0002254 UBERON:0003923 {source="Wikipedia"} ! has developmental contribution from dorsal pancreatic bud +relationship: RO:0002254 UBERON:0003924 {source="Wikipedia"} ! has developmental contribution from ventral pancreatic bud +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Pancreas.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Pancreas.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Blausen_0699_PancreasAnatomy2.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001265 @@ -172400,10 +171429,11 @@ xref: SCTID:61987002 xref: UMLS:C0229688 {source="ncithesaurus:Splenic_Trabecula"} xref: Wikipedia:Trabeculae_of_spleen is_a: UBERON:0000440 ! trabecula +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000440 ! trabecula intersection_of: part_of UBERON:0002106 ! spleen relationship: part_of UBERON:1000024 {source="FMA"} ! parenchyma of spleen -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001266 @@ -172420,8 +171450,9 @@ xref: NCIT:C33599 xref: UMLS:C0735011 {source="ncithesaurus:Splenic_Cord"} xref: Wikipedia:Cords_of_Billroth is_a: UBERON:0000064 ! organ part +is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0001250 {source="MA"} ! red pulp of spleen -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001268 @@ -172434,15 +171465,14 @@ xref: BTO:0001031 xref: EMAPA:35683 xref: FMA:16515 xref: MA:0002531 -xref: MESH:D001202 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: ncithesaurus:Peritoneal_Fluid xref: Wikipedia:Peritoneal_fluid is_a: UBERON:0007779 ! transudate is_a: UBERON:0007794 {source="FMA"} ! secretion of serous gland is_a: UBERON:0036217 ! coelomic fluid intersection_of: UBERON:0007779 ! transudate -intersection_of: located_in UBERON:0001179 ! peritoneal cavity -relationship: located_in UBERON:0001179 ! peritoneal cavity +intersection_of: RO:0001025 UBERON:0001179 ! located in peritoneal cavity +relationship: RO:0001025 UBERON:0001179 ! located in peritoneal cavity [Term] id: UBERON:0001271 @@ -172464,12 +171494,10 @@ is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0007823 ! appendage girdle region intersection_of: part_of UBERON:0010709 ! pelvic complex disjoint_from: UBERON:0007832 ! pelvic girdle skeleton -relationship: has_skeleton UBERON:0007832 ! pelvic girdle skeleton -relationship: in_lateral_side_of UBERON:0002355 ! pelvic region of trunk +relationship: BSPO:0000126 UBERON:0002355 ! pelvic region of trunk relationship: part_of UBERON:0002355 ! pelvic region of trunk relationship: part_of UBERON:0010709 ! pelvic complex -property_value: IAO:0000232 "this class describes the subdivision of the limb/fin, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831). See also comments on obo-anatomy mail list. Note that even though the class includes soft tissue it is more restrictive than 'pelvis' which also includes structures in cavities etc. TODO this needs to be better documented" xsd:string -property_value: UBPROP:0000001 "Subdivision of lower limb or fin which links the limb/fin to the body[FMA,modified]. There is only one instance of the pelvic girdle region per organism.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000304", ontology="VSAO", source="https://orcid.org/0000-0002-6601-2165"} +relationship: RO:0002551 UBERON:0007832 ! has skeleton pelvic girdle skeleton [Term] id: UBERON:0001272 @@ -172495,13 +171523,11 @@ xref: Wikipedia:Hip_bone is_a: UBERON:0007830 ! pelvic girdle bone/zone is_a: UBERON:0010428 {source="FMA"} ! flat bone is_a: UBERON:0015212 ! lateral structure -relationship: in_lateral_side_of UBERON:0007832 ! pelvic girdle skeleton +relationship: BSPO:0000126 UBERON:0007832 ! pelvic girdle skeleton relationship: part_of UBERON:0001464 {source="FMA"} ! hip -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray341.png" xsd:anyURI -property_value: editor_note "currently this class is restricted to exclude the teleost bone as the definition mentions ilium, ischium and pubis. In future we may add a grouping class for girdle bones that supports the appendage" xsd:string -property_value: UBPROP:0000008 "The hip/pelvic bone/basipterygium first appears in fishes, where it consists of a simple, usually triangular bone, to which the pelvic fin articulates. The hip bones on each side usually connect with each other at the forward end, and are even solidly fused in lungfishes and sharks, but they never attach to the vertebral column" xsd:string {source="WP"} -property_value: UBPROP:0000012 "in FMA this is a paired structure. NCITA has 'pelvic bone' but this is the *superclass* of ilium/ischium/pubis. The MA class 'pelvis bone' is actually a superclass of 'pelvic girdle bone' and caudal/sacral vertebra." xsd:string {external_ontology="FMA"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray341.png" xsd:anyURI +property_value: IAO:0000116 "currently this class is restricted to exclude the teleost bone as the definition mentions ilium, ischium and pubis. In future we may add a grouping class for girdle bones that supports the appendage" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001273 @@ -172535,19 +171561,14 @@ is_a: UBERON:0007830 ! pelvic girdle bone/zone is_a: UBERON:0015054 ! iliac endochondral element is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0015054 ! iliac endochondral element -intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue -relationship: contributes_to_morphology_of UBERON:0007830 ! pelvic girdle bone/zone -relationship: develops_from UBERON:0010714 {source="cjm"} ! iliac cartilage element -relationship: in_lateral_side_of UBERON:0007832 ! pelvic girdle skeleton -relationship: never_in_taxon NCBITaxon:32443 {source="Wikipedia"} ! Teleostei +intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue +relationship: BSPO:0000126 UBERON:0007832 ! pelvic girdle skeleton relationship: part_of UBERON:0001272 {source="FMA"} ! innominate bone -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Pelvis.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Pelvis.glb" xsd:anyURI -property_value: RO:0002174 NCBITaxon:8570 {source="Wikipedia"} -property_value: UBPROP:0000001 "Paired, rodlike endochondral bones that constitute the anterior pelvic girdle.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000772", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000007 "iliac" xsd:string -property_value: UBPROP:0000008 "All reptiles have an ilium except snakes, although some snake species have a tiny bone which is considered to be an ilium" xsd:string {source="WP"} -property_value: UBPROP:0000012 "this is_a hip bone in MA." xsd:string {external_ontology="MA"} +relationship: RO:0002202 UBERON:0010714 {source="cjm"} ! develops from iliac cartilage element +relationship: RO:0002433 UBERON:0007830 ! contributes to morphology of pelvic girdle bone/zone +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Pelvis.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Pelvis.glb" xsd:anyURI +property_value: RO:0002161 NCBITaxon:32443 {source="Wikipedia"} [Term] id: UBERON:0001274 @@ -172577,17 +171598,14 @@ is_a: UBERON:0008202 {source="MA"} ! bone of hip region is_a: UBERON:0015056 ! ischial endochondral element is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0015056 ! ischial endochondral element -intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue -relationship: contributes_to_morphology_of UBERON:0007830 ! pelvic girdle bone/zone -relationship: develops_from UBERON:0006254 {source="cjm"} ! ischial cartilage element -relationship: in_lateral_side_of UBERON:0007832 ! pelvic girdle skeleton +intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue +relationship: BSPO:0000126 UBERON:0007832 ! pelvic girdle skeleton relationship: part_of UBERON:0001272 ! innominate bone -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Illu_pelvic_girdle.jpg" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Pelvis.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Pelvis.glb" xsd:anyURI -property_value: UBPROP:0000001 "Paired bones of endochondral origin that constitute the posterior elements of the pelvic girdle. They are synostotically fused to each other and form the posterior part of the acetabulum.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000860", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000007 "ischial" xsd:string -property_value: UBPROP:0000012 "this is_a hip bone in MA; in FMA it is a zone of bone organ." xsd:string {external_ontology="MA"} +relationship: RO:0002202 UBERON:0006254 {source="cjm"} ! develops from ischial cartilage element +relationship: RO:0002433 UBERON:0007830 ! contributes to morphology of pelvic girdle bone/zone +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Illu_pelvic_girdle.jpg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Pelvis.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Pelvis.glb" xsd:anyURI [Term] id: UBERON:0001276 @@ -172617,9 +171635,8 @@ is_a: UBERON:0004808 ! gastrointestinal system epithelium is_a: UBERON:0015833 ! foregut epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000945 ! stomach -relationship: contributes_to_morphology_of UBERON:0001199 ! mucosa of stomach relationship: part_of UBERON:0001199 ! mucosa of stomach -property_value: UBPROP:0000012 "in FMA this is classified as simple columnar, MA divides this into squamous and glandular" xsd:string {external_ontology="FMA"} +relationship: RO:0002433 UBERON:0001199 ! contributes to morphology of mucosa of stomach [Term] id: UBERON:0001277 @@ -172654,9 +171671,8 @@ is_a: UBERON:0003929 ! digestive tract epithelium is_a: UBERON:0004808 ! gastrointestinal system epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000160 ! intestine -relationship: contributes_to_morphology_of UBERON:0000160 ! intestine relationship: part_of UBERON:0001242 ! intestinal mucosa -property_value: UBPROP:0000001 "Simple columnar epithelium that lines the intestine, sometimes pseudostratified, with absorptive brush-border cells and mucous goblet cells clearly visible. Crosnier et al. 2005[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005124", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002433 UBERON:0000160 ! contributes to morphology of intestine [Term] id: UBERON:0001278 @@ -172693,15 +171709,15 @@ xref: SCTID:362192000 xref: UMLS:C0227514 {source="ncithesaurus:Portal_Triad"} xref: Wikipedia:Portal_triad is_a: PR:000050567 ! protein-containing material entity +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0034921 ! multi organ part structure -relationship: contributes_to_morphology_of UBERON:0001171 ! portal lobule relationship: has_part UBERON:0001193 ! hepatic artery relationship: has_part UBERON:0002017 ! portal vein relationship: has_part UBERON:0003704 ! intrahepatic bile duct relationship: part_of UBERON:0001172 ! hepatic acinus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/6/62/Portal_triad.JPG" xsd:anyURI -property_value: UBPROP:0000013 "The misnomer 'portal triad' traditionally has included only the first three structures, and was named before lymphatic vessels were discovered in the structure. It can refer both to the largest branch of each of these vessels running inside the hepatoduodenal ligament, and to the smaller branches of these vessels inside the liver." xsd:string +relationship: RO:0002433 UBERON:0001171 ! contributes to morphology of portal lobule +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/62/Portal_triad.JPG" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001280 @@ -172729,10 +171745,9 @@ is_a: UBERON:0000353 ! parenchyma is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0000353 ! parenchyma intersection_of: part_of UBERON:0002107 ! liver -relationship: contributes_to_morphology_of UBERON:0002107 ! liver -relationship: develops_from UBERON:0008835 {source="XAO"} ! hepatic diverticulum relationship: part_of UBERON:0002107 ! liver -property_value: UBPROP:0000003 "the (liver) tubular structure (dual layered parenchyma) appears to be conserved among all embryonic vertebrates (...) it is not unlikely that all vertebrate livers share the same fundamental functional unit.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000539", ontology="VHOG", source="DOI:10.1002/ar.20524 Hardman RC, Volz DC, Kullman SW, Hinton DE, An in vivo look at vertebrate liver architecture: three-dimensional reconstruction from Medaka (Oryzias latipes). The Anatomical Record (2007)", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0008835 {source="XAO"} ! develops from hepatic diverticulum +relationship: RO:0002433 UBERON:0002107 ! contributes to morphology of liver [Term] id: UBERON:0001281 @@ -172764,16 +171779,16 @@ xref: VHOG:0000708 xref: Wikipedia:Hepatic_sinusoid xref: ZFA:0005091 is_a: UBERON:0003909 ! sinusoid +is_a: UBERON:0005911 ! endo-epithelium is_a: UBERON:0015796 ! liver blood vessel intersection_of: UBERON:0003909 ! sinusoid intersection_of: part_of UBERON:0002107 ! liver -relationship: connected_to UBERON:0006841 ! central vein of liver -relationship: contributes_to_morphology_of UBERON:0004647 ! liver lobule -relationship: develops_in UBERON:0001113 ! lobe of liver relationship: part_of UBERON:0004647 ! liver lobule relationship: part_of UBERON:0006877 {source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! vasculature of liver -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000003 "(...) the amphibian liver has characteristics in common with both fish and terrestrial vertebrates. (...) The histological structure of the liver is similar to that in other vertebrates, with hepatocytes arranged in clusters and cords separated by a meshwork of sinusoids and the presence of the traditional triad of portal venule, hepatic arteriole, and bile duct.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000708", ontology="VHOG", source="DOI:10.1053/ax.2000.7133 Crawshaw GJ, Weinkle TK, Clinical and pathological aspects of the amphibian liver. Seminars in Avian and Exotic Pet Medicine (2000)", source="http://bgee.unil.ch/"} +relationship: RO:0002170 UBERON:0006841 ! connected to central vein of liver +relationship: RO:0002226 UBERON:0001113 ! develops in lobe of liver +relationship: RO:0002433 UBERON:0004647 ! contributes to morphology of liver lobule +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001282 @@ -172799,13 +171814,13 @@ xref: UMLS:C0227517 {source="ncithesaurus:Canal_of_Hering"} xref: Wikipedia:Canals_of_Hering is_a: UBERON:0003704 {source="FMA"} ! intrahepatic bile duct is_a: UBERON:0014716 ! interlobular duct -relationship: contributes_to_morphology_of UBERON:0004647 ! liver lobule relationship: has_part CL:0000182 ! hepatocyte relationship: has_part CL:1000488 ! cholangiocyte relationship: part_of UBERON:0001172 {source="FMA"} ! hepatic acinus relationship: part_of UBERON:0004647 {source="FMA"} ! liver lobule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: editor_note "Note that this is part of the intrahepatic bile duct in MA, as this class is more alike the tree in FMA. Note also that SCT has canal of Hering and Entire IBduct as the only sibling terms under 'Structure of intralobular bile duct' (i.e. the CoH is the only part of the entire IBduct)" xsd:string +relationship: RO:0002433 UBERON:0004647 ! contributes to morphology of liver lobule +property_value: IAO:0000116 "Note that this is part of the intrahepatic bile duct in MA, as this class is more alike the tree in FMA. Note also that SCT has canal of Hering and Entire IBduct as the only sibling terms under 'Structure of intralobular bile duct' (i.e. the CoH is the only part of the entire IBduct)" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001285 @@ -172835,15 +171850,13 @@ xref: UMLS:C0027713 {source="ncithesaurus:Nephron"} xref: Wikipedia:Nephron xref: ZFA:0005282 is_a: UBERON:0000064 ! organ part -relationship: contributes_to_morphology_of UBERON:0002113 ! kidney -relationship: develops_from UBERON:0004208 {evidence="definitional"} ! nephrogenic mesenchyme -relationship: immediate_transformation_of UBERON:0010532 {source="Bgee:AN"} ! primitive nephron relationship: part_of UBERON:0007684 {source="FMA"} ! uriniferous tubule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI -property_value: editor_note "kidney terms require review for cross-vertebrate compatibility and developmental relationships." xsd:string -property_value: UBPROP:0000001 "Functional unit of the kidney that filters waste.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002153", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000008 "In the avian kidney, three types of nephron are identified: mammalian-type nephrons with long and short loops of Henle, and reptilian type nephrons (Gambaryan, 1992)" xsd:string {source="GO"} +relationship: RO:0002202 UBERON:0004208 ! develops from nephrogenic mesenchyme +relationship: RO:0002433 UBERON:0002113 ! contributes to morphology of kidney +relationship: RO:0002495 UBERON:0010532 {source="Bgee:AN"} ! immediate transformation of primitive nephron +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: IAO:0000116 "kidney terms require review for cross-vertebrate compatibility and developmental relationships." xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001286 @@ -172876,10 +171889,9 @@ xref: Wikipedia:Bowman's_space xref: ZFA:0005283 xref: ZFA:0005312 is_a: UBERON:0000464 ! anatomical space -relationship: contributes_to_morphology_of UBERON:0001230 ! glomerular capsule relationship: part_of UBERON:0001230 ! glomerular capsule -property_value: editor_note "TODO - fix ZFA" xsd:string -property_value: UBPROP:0000001 "Space between the renal glomerulus and the glomerular capsule. Renal filtrate collects here then passes into the renal tubule.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005283", external_class="TAO:0005312", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002433 UBERON:0001230 ! contributes to morphology of glomerular capsule +property_value: IAO:0000116 "TODO - fix ZFA" xsd:string [Term] id: UBERON:0001287 @@ -172912,13 +171924,12 @@ xref: ZFA:0005290 is_a: UBERON:0006534 {source="MA"} ! renal convoluted tubule is_a: UBERON:0006853 ! renal cortex tubule is_a: UBERON:0012275 ! meso-epithelium -relationship: continuous_with UBERON:0001230 {source="GO"} ! glomerular capsule -relationship: continuous_with UBERON:0001290 ! proximal straight tubule -relationship: contributes_to_morphology_of UBERON:0001231 ! nephron tubule -relationship: develops_from UBERON:0003220 {source="Wikipedia"} ! metanephric mesenchyme -relationship: part_of UBERON:0004134 {notes="MA uses subclass", source="GOC:mtg_kidney_jan10"} ! proximal tubule -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI -property_value: UBPROP:0000001 "Renal tubule that connects to the renal corpuscle.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005290", ontology="TAO", source="ZFIN:curator"} +relationship: part_of UBERON:0004134 ! proximal tubule +relationship: RO:0002150 UBERON:0001230 {source="GO"} ! continuous with glomerular capsule +relationship: RO:0002150 UBERON:0001290 ! continuous with proximal straight tubule +relationship: RO:0002202 UBERON:0003220 {source="Wikipedia"} ! develops from metanephric mesenchyme +relationship: RO:0002433 UBERON:0001231 ! contributes to morphology of nephron tubule +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI [Term] id: UBERON:0001288 @@ -172944,18 +171955,14 @@ xref: VHOG:0001270 xref: Wikipedia:Loop_of_Henle is_a: UBERON:0007685 ! region of nephron tubule intersection_of: UBERON:0007685 ! region of nephron tubule -intersection_of: continuous_with UBERON:0001287 ! proximal convoluted tubule -intersection_of: continuous_with UBERON:0001292 ! distal convoluted tubule -relationship: continuous_with UBERON:0001287 ! proximal convoluted tubule -relationship: continuous_with UBERON:0001292 ! distal convoluted tubule -relationship: contributes_to_morphology_of UBERON:0001231 ! nephron tubule -relationship: present_in_taxon NCBITaxon:8782 ! Aves -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI -property_value: editor_note "the definitions of some kidney parts (e.g. proximal straight tubule) refer to Henle's loop, even in species where this may not be present. Requires review." xsd:string -property_value: RO:0002174 NCBITaxon:8353 -property_value: UBPROP:0000001 "A highly specialized segment of the mammalian kidney tubules, that dips into the medulla. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, p.648, see_Liem_KF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001270", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "The structure differs considerably between species; there is a definite physical loop of Henle in the mammalian and avian renal systems but this seems to be absent in Xenopus. However, homologs of some, but not all, molecular markers (e.g. cldn8 and clcnk) of the mammalian loop of Henle were found to be present in the pronephros of the frog larva ." xsd:string {source="DOI:10.1371/journal.pone.0099864"} -property_value: UBPROP:0000009 "The loop of Henle plays an important role in creating a concentration gradient in the medulla of the kidney. It is involved in reabsorption of filtered water and ions including sodium, potassium and calcium, and independently regulates both the volume and osmolarity of body fluids." xsd:string {source="DOI:10.1371/journal.pone.0099864"} +intersection_of: RO:0002150 UBERON:0001287 ! continuous with proximal convoluted tubule +intersection_of: RO:0002150 UBERON:0001292 ! continuous with distal convoluted tubule +relationship: RO:0002150 UBERON:0001287 ! continuous with proximal convoluted tubule +relationship: RO:0002150 UBERON:0001292 ! continuous with distal convoluted tubule +relationship: RO:0002433 UBERON:0001231 ! contributes to morphology of nephron tubule +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: IAO:0000116 "the definitions of some kidney parts (e.g. proximal straight tubule) refer to Henle's loop, even in species where this may not be present. Requires review." xsd:string +property_value: RO:0002175 NCBITaxon:8782 [Term] id: UBERON:0001289 @@ -172976,10 +171983,10 @@ xref: SCTID:245350001 xref: UMLS:C0227657 {source="ncithesaurus:Descending_Limb_of_the_Henle_s_Loop"} xref: Wikipedia:Descending_limb_of_loop_of_henle is_a: UBERON:0007685 {source="FMA"} ! region of nephron tubule -relationship: contributes_to_morphology_of UBERON:0001288 ! loop of Henle relationship: part_of UBERON:0001288 {source="FMA"} ! loop of Henle -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +relationship: RO:0002433 UBERON:0001288 ! contributes to morphology of loop of Henle +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001290 @@ -173007,14 +172014,13 @@ xref: Wikipedia:Proximal_straight_tubule xref: ZFA:0005291 is_a: UBERON:0006853 ! renal cortex tubule is_a: UBERON:0009035 {source="MA"} ! renal straight tubule -relationship: continuous_with UBERON:0001287 ! proximal convoluted tubule -relationship: continuous_with UBERON:0005096 ! descending thin limb relationship: part_of UBERON:0001289 {source="MA"} ! descending limb of loop of Henle -relationship: part_of UBERON:0004134 {notes="MA uses subclass", source="GOC:mtg_kidney_jan10"} ! proximal tubule +relationship: part_of UBERON:0004134 ! proximal tubule relationship: part_of UBERON:0006542 {source="MA"} ! outer medulla outer stripe loop of Henle -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: editor_note "TODO - is S3 exactly coincident with PST? todo - ensure relationships work across species (loop of Henle)" xsd:string -property_value: UBPROP:0000001 "Portion of the renal tubule which is just posterior to the proximal convoluted tubule.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005291", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002150 UBERON:0001287 ! continuous with proximal convoluted tubule +relationship: RO:0002150 UBERON:0005096 ! continuous with descending thin limb +property_value: IAO:0000116 "TODO - is S3 exactly coincident with PST? todo - ensure relationships work across species (loop of Henle)" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001291 @@ -173042,11 +172048,11 @@ xref: MA:0001677 xref: SCTID:244953001 xref: Wikipedia:Thick_ascending_limb_of_loop_of_Henle is_a: UBERON:0009035 {source="MA"} ! renal straight tubule -relationship: contributes_to_morphology_of UBERON:0005164 ! ascending limb of loop of Henle relationship: part_of UBERON:0005164 ! ascending limb of loop of Henle -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI -property_value: editor_note "TODO - thick/thin check. Also - does the loop of Henle overlap the distal convoluted tubule? FMA divides DCT into straight and convoluted portions" xsd:string +relationship: RO:0002433 UBERON:0005164 ! contributes to morphology of ascending limb of loop of Henle +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: IAO:0000116 "TODO - thick/thin check. Also - does the loop of Henle overlap the distal convoluted tubule? FMA divides DCT into straight and convoluted portions" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001292 @@ -173072,13 +172078,11 @@ xref: Wikipedia:Distal_convoluted_tubule is_a: UBERON:0006534 {source="MA"} ! renal convoluted tubule is_a: UBERON:0006853 ! renal cortex tubule is_a: UBERON:0012275 ! meso-epithelium -relationship: contributes_to_morphology_of UBERON:0001231 ! nephron tubule -relationship: develops_from UBERON:0003220 ! metanephric mesenchyme relationship: part_of UBERON:0004135 {source="EMAPA", source="GO", source="MA-modified-from-isa"} ! distal tubule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/2/21/Kidney_nephron.png" xsd:anyURI -property_value: UBPROP:0000001 "a portion of kidney nephron between the loop of Henle and the collecting duct system[Wikipedia:Distal_convoluted_tubule]." xsd:string {source="Wikipedia:Distal_convoluted_tubule"} -property_value: UBPROP:0000009 "in humans it is responsible for the reabsorption of about 5% of filtered sodium via the thiazide-sensitive Na-Cl symporter." xsd:string +relationship: RO:0002202 UBERON:0003220 ! develops from metanephric mesenchyme +relationship: RO:0002433 UBERON:0001231 ! contributes to morphology of nephron tubule +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/21/Kidney_nephron.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001293 @@ -173100,8 +172104,8 @@ xref: EMAPA:28310 xref: FMA:17733 xref: MA:0001653 is_a: UBERON:0000064 ! organ part -relationship: contributes_to_morphology_of UBERON:0000362 ! renal medulla relationship: part_of UBERON:0000362 ! renal medulla +relationship: RO:0002433 UBERON:0000362 ! contributes to morphology of renal medulla [Term] id: UBERON:0001294 @@ -173124,11 +172128,10 @@ xref: EMAPA:28349 xref: FMA:17734 xref: MA:0001652 is_a: UBERON:0000064 ! organ part -relationship: contributes_to_morphology_of UBERON:0000362 ! renal medulla -relationship: only_in_taxon NCBITaxon:40674 {source="GO:0072053"} ! Mammalia relationship: part_of UBERON:0000362 ! renal medulla -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000008 "unique to mammals" xsd:string {source="GO:0072053"} +relationship: RO:0002160 NCBITaxon:40674 {source="GO:0072053"} ! only in taxon Mammalia +relationship: RO:0002433 UBERON:0000362 ! contributes to morphology of renal medulla +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001295 @@ -173163,16 +172166,11 @@ xref: Wikipedia:Endometrium is_a: UBERON:0019042 ! reproductive system mucosa intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0000995 ! uterus -relationship: contributes_to_morphology_of UBERON:0000995 ! uterus -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0000459 {source="FMA"} ! uterine wall -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cervix.jpg" xsd:anyURI -property_value: UBPROP:0000001 "The mucous membrane lining the uterus. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001285", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/Endometrium"} -property_value: UBPROP:0000003 "The maternal part of the placenta (of eutherian mammals) is the vascularized and glandular uterine lining, or endometrium.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001285", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.144", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "endometrial" xsd:string -property_value: UBPROP:0000008 "Animals that have estrous cycles reabsorb the endometrium if conception does not occur during that cycle. Animals that have menstrual cycles shed the endometrium through menstruation instead" xsd:string -property_value: UBPROP:0000012 "in FMA this is subdivided into basal and outer" xsd:string {external_ontology="FMA"} +relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia +relationship: RO:0002433 UBERON:0000995 ! contributes to morphology of uterus +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cervix.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001296 @@ -173202,15 +172200,11 @@ xref: VHOG:0001281 xref: Wikipedia:Myometrium is_a: UBERON:0005156 ! reproductive structure is_a: UBERON:0034933 ! layer of smooth muscle tissue -relationship: contributes_to_morphology_of UBERON:0000995 ! uterus relationship: part_of UBERON:0000459 {source="FMA"} ! uterine wall -relationship: surrounded_by UBERON:0001297 ! serosa of uterus -relationship: surrounds UBERON:0001295 ! endometrium -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cervix.jpg" xsd:anyURI -property_value: UBPROP:0000001 "The muscular wall of the uterus. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001281", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/myometrium"} -property_value: UBPROP:0000003 "In all mammals, the uterus develops as a specialization of the paramesonephric or Müllerian ducts, which gives rise to the infundibula, oviducts, uterus, cervix, and anterior vagina. Morphogenetic events common to development of all uteri include: 1) differentiation and growth of the myometrium, 2) differentiation and morphogenesis of the endometrial glands, and 3) organization and stratification of endometrial stroma. Uterine development is initiated in the fetus, but is only completed postnatally with differentiation and development of the endometrial glands.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001281", ontology="VHOG", source="PMID:15471813 Spencer TE, Bazer FW, Uterine and placental factors regulating conceptus growth in domestic animals. Journal of Animal Science (2004)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "myometrial" xsd:string -property_value: UBPROP:0000009 "The myometrium stretches (the smooth muscle cells expand in both size and number) during pregnancy to allow for the harboring of the pregnancy, and contracts in a coordinated fashion during the process of labor. After delivery the myometrium contracts to expel the placenta and reduce blood loss." xsd:string +relationship: RO:0002219 UBERON:0001297 ! surrounded by serosa of uterus +relationship: RO:0002221 UBERON:0001295 ! surrounds endometrium +relationship: RO:0002433 UBERON:0000995 ! contributes to morphology of uterus +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cervix.jpg" xsd:anyURI [Term] id: UBERON:0001297 @@ -173238,8 +172232,8 @@ is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0000042 ! serous membrane intersection_of: part_of UBERON:0000995 ! uterus relationship: part_of UBERON:0000459 {source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! uterine wall -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cervix.jpg" xsd:anyURI -property_value: editor_note "TODO - check for parallel structure with peritoneum" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cervix.jpg" xsd:anyURI +property_value: IAO:0000116 "TODO - check for parallel structure with peritoneum" xsd:string [Term] id: UBERON:0001299 @@ -173265,12 +172259,12 @@ xref: Wikipedia:Glans_penis is_a: UBERON:0035651 ! glans intersection_of: UBERON:0035651 ! glans intersection_of: part_of UBERON:0000989 ! penis -relationship: contributes_to_morphology_of UBERON:0000989 ! penis -relationship: immediate_transformation_of UBERON:0013239 {source="Bgee:AN"} ! future glans penis relationship: part_of UBERON:0000989 ! penis +relationship: RO:0002433 UBERON:0000989 ! contributes to morphology of penis +relationship: RO:0002495 UBERON:0013239 {source="Bgee:AN"} ! immediate transformation of future glans penis relationship: sexually_homologous_to UBERON:0006653 ! glans clitoris -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/13/Anteriorglanspenis.jpg" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/3/35/Male_anatomy.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/13/Anteriorglanspenis.jpg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/3/35/Male_anatomy.png" xsd:anyURI [Term] id: UBERON:0001301 @@ -173303,15 +172297,12 @@ is_a: UBERON:0005904 ! duct of male reproductive system relationship: channel_for CL:0000019 ! sperm relationship: channels_from UBERON:0006946 ! efferent duct relationship: channels_into UBERON:0001000 ! vas deferens -relationship: contributes_to_morphology_of UBERON:0004054 ! internal male genitalia -relationship: develops_from UBERON:0003074 {source="Wikipedia"} ! mesonephric duct -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0006947 {source="FMA"} ! male genital duct -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c3/Illu_testis_surface.jpg" xsd:anyURI -property_value: editor_note "Kardong has epididymis in elasmobranch" xsd:string -property_value: UBPROP:0000007 "epididymal" xsd:string -property_value: UBPROP:0000008 "A similar, but probably non-homologous, structure is found in cartilaginous fishes" xsd:string {source="WP"} -property_value: UBPROP:0000010 "Typically divided into three main regions. In reptiles, there is an additional canal between the testis and the head of the epididymis, which receives the various efferent ducts. This is, however, absent in all birds and mammals. The epididymis is covered by a two layered pseudostratified epithelium. The epithelium is separated by a basement membrane from the connective tissue wall which has smooth muscle cells." xsd:string +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002202 UBERON:0003074 {source="Wikipedia"} ! develops from mesonephric duct +relationship: RO:0002433 UBERON:0004054 ! contributes to morphology of internal male genitalia +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c3/Illu_testis_surface.jpg" xsd:anyURI +property_value: IAO:0000116 "Kardong has epididymis in elasmobranch" xsd:string [Term] id: UBERON:0001302 @@ -173328,11 +172319,9 @@ xref: SCTID:280106006 xref: UMLS:C0227900 {source="ncithesaurus:Right_Fallopian_Tube"} is_a: UBERON:0003889 ! fallopian tube intersection_of: UBERON:0003889 ! fallopian tube -intersection_of: in_right_side_of UBERON:0000468 ! multicellular organism -relationship: in_right_side_of UBERON:0000468 ! multicellular organism -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Fallopian_Tube_R.glb" xsd:anyURI -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI -property_value: UBPROP:0000008 "non-functional in monotremes[ISBN:978-0226870137]" xsd:string +intersection_of: BSPO:0000121 UBERON:0000468 ! multicellular organism +relationship: BSPO:0000121 UBERON:0000468 ! multicellular organism +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Fallopian_Tube_R.glb" xsd:anyURI [Term] id: UBERON:0001303 @@ -173349,10 +172338,9 @@ xref: SCTID:280107002 xref: UMLS:C0227902 {source="ncithesaurus:Left_Fallopian_Tube"} is_a: UBERON:0003889 ! fallopian tube intersection_of: UBERON:0003889 ! fallopian tube -intersection_of: in_left_side_of UBERON:0000468 ! multicellular organism -relationship: in_left_side_of UBERON:0000468 ! multicellular organism -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Fallopian_Tube_L.glb" xsd:anyURI -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +intersection_of: BSPO:0000120 UBERON:0000468 ! multicellular organism +relationship: BSPO:0000120 UBERON:0000468 ! multicellular organism +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Fallopian_Tube_L.glb" xsd:anyURI [Term] id: UBERON:0001304 @@ -173416,18 +172404,14 @@ xref: Wikipedia:Ovarian_follicle xref: ZFA:0001110 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:8450001 ! egg follicle -relationship: develops_from UBERON:0005296 {source="Wikipedia"} ! ovary sex cord relationship: has_part CL:0000023 ! oocyte relationship: has_part CL:0002174 ! follicular cell of ovary relationship: has_part UBERON:0000038 ! follicular fluid -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/ca/Human_ovarian_follicle.jpg" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/e/e6/Primary_follicle-4.JPG" xsd:anyURI -property_value: editor_note "TODO - align subtypes based on staging, which is taxon-specific" xsd:string -property_value: UBPROP:0000001 "Oocyte development of zebrafish has been divided into five stages based on morphological criteria and on physiological and biochemical events. Stage I follicles (less than 140 microns) are primary growth stage, stage II follicles (140-340 microns) are cortical alveolus stage, stage III (340-690 microns) are vitellogenesis, stage IV (690-730 microns) are oocyte maturation, and stage V follicles are matured egg. Selman et al, 1993.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001110", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001536", ontology="VHOG", source="DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T, Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "These structures are periodically initiated to grow and develop, culminating in ovulation of usually a single competent oocyte in humans. These eggs/ova are only developed once every menstrual cycle (e.g. once a month in humans)" xsd:string -property_value: UBPROP:0000009 "The somatic cell component of the follicle produces hormones important for oocyte development and proper endocrine function" xsd:string +relationship: RO:0002202 UBERON:0005296 {source="Wikipedia"} ! develops from ovary sex cord +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/ca/Human_ovarian_follicle.jpg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/e/e6/Primary_follicle-4.JPG" xsd:anyURI +property_value: IAO:0000116 "TODO - align subtypes based on staging, which is taxon-specific" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001307 @@ -173470,8 +172454,8 @@ xref: UMLS:C0226398 {source="ncithesaurus:External_Iliac_Artery"} xref: Wikipedia:External_iliac_artery is_a: UBERON:0005609 {source="MA"} ! iliac artery relationship: part_of UBERON:0001191 ! common iliac artery -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/3e/Gray539.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3e/Gray539.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001309 @@ -173493,8 +172477,8 @@ xref: UMLS:C0226364 {source="ncithesaurus:Internal_Iliac_Artery"} xref: Wikipedia:Internal_iliac_artery is_a: UBERON:0005609 {source="MA"} ! iliac artery relationship: part_of UBERON:0001191 ! common iliac artery -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/d3/Iliac_artery_bifurcation.PNG" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d3/Iliac_artery_bifurcation.PNG" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001310 @@ -173522,10 +172506,10 @@ xref: UMLS:C0041632 {source="ncithesaurus:Umbilical_Artery"} xref: Wikipedia:Umbilical_artery is_a: UBERON:0001637 ! artery is_a: UBERON:0010260 ! umbilical blood vessel -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Gray502.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Placenta.glb" xsd:anyURI -property_value: editor_note "todo - compare with EHDAA2. Check embryonic vs extraembryonic, developmental relationships" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Gray502.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Placenta.glb" xsd:anyURI +property_value: IAO:0000116 "todo - compare with EHDAA2. Check embryonic vs extraembryonic, developmental relationships" xsd:string +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/uberon/issues/328" xsd:anyURI [Term] @@ -173547,14 +172531,14 @@ xref: UMLS:C0226377 {source="ncithesaurus:Inferior_Vesical_Artery"} xref: Wikipedia:Inferior_vesical_artery is_a: UBERON:0009027 ! vesical artery intersection_of: UBERON:0009027 ! vesical artery -intersection_of: supplies UBERON:0006082 ! fundus of urinary bladder -relationship: connecting_branch_of UBERON:0001309 ! internal iliac artery -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: supplies UBERON:0000998 {gci_filler="UBERON:0003101", gci_relation="part_of"} ! seminal vesicle -relationship: supplies UBERON:0001000 {gci_filler="UBERON:0003101", gci_relation="part_of"} ! vas deferens -relationship: supplies UBERON:0002367 {gci_filler="UBERON:0003101", gci_relation="part_of"} ! prostate gland -relationship: supplies UBERON:0006082 ! fundus of urinary bladder -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/1/13/Inferiorvesical.png" xsd:anyURI +intersection_of: RO:0002178 UBERON:0006082 ! supplies fundus of urinary bladder +relationship: RO:0002178 UBERON:0000998 {gci_filler="UBERON:0003101", gci_relation="part_of"} ! supplies seminal vesicle +relationship: RO:0002178 UBERON:0001000 {gci_filler="UBERON:0003101", gci_relation="part_of"} ! supplies vas deferens +relationship: RO:0002178 UBERON:0002367 {gci_filler="UBERON:0003101", gci_relation="part_of"} ! supplies prostate gland +relationship: RO:0002178 UBERON:0006082 ! supplies fundus of urinary bladder +relationship: RO:0002252 UBERON:0001309 ! connecting branch of internal iliac artery +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/1/13/Inferiorvesical.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001312 @@ -173576,11 +172560,10 @@ xref: Wikipedia:Superior_vesical_artery is_a: UBERON:0003468 ! ureteric segment of renal artery is_a: UBERON:0009027 ! vesical artery intersection_of: UBERON:0009027 ! vesical artery -intersection_of: supplies UBERON:0000056 ! ureter -relationship: connecting_branch_of UBERON:0001310 ! umbilical artery -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/0/02/Internal_iliac_branches.PNG" xsd:anyURI -property_value: UBPROP:0000011 "The first part of the superior vesical artery represents the terminal section of the previous portion of the umbilical artery (fetal hypogastric artery)[WP]" xsd:string +intersection_of: RO:0002178 UBERON:0000056 ! supplies ureter +relationship: RO:0002252 UBERON:0001310 ! connecting branch of umbilical artery +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/0/02/Internal_iliac_branches.PNG" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001316 @@ -173600,11 +172583,11 @@ xref: SCTID:181400000 xref: UMLS:C0226761 {source="ncithesaurus:External_Iliac_Vein"} xref: Wikipedia:External_iliac_vein is_a: UBERON:0005610 {source="MA"} ! iliac vein -relationship: connected_to UBERON:0001139 ! common iliac vein -relationship: drains UBERON:0002103 ! hindlimb -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/6/65/Iliac_veins.gif" xsd:anyURI +relationship: RO:0002170 UBERON:0001139 ! connected to common iliac vein +relationship: RO:0002179 UBERON:0002103 ! drains hindlimb +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/65/Iliac_veins.gif" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001317 @@ -173628,12 +172611,12 @@ xref: UMLS:C0226764 {source="ncithesaurus:Internal_Iliac_Vein"} xref: VHOG:0000749 xref: Wikipedia:Internal_iliac_vein is_a: UBERON:0005610 {source="MA"} ! iliac vein -relationship: connected_to UBERON:0001139 ! common iliac vein -relationship: drains UBERON:0005179 ! pelvic region element -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/cb/Internaliliacv.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +relationship: RO:0002170 UBERON:0001139 ! connected to common iliac vein +relationship: RO:0002179 UBERON:0005179 ! drains pelvic region element +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/cb/Internaliliacv.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001318 @@ -173645,10 +172628,10 @@ xref: FMA:18890 xref: MA:0002264 is_a: UBERON:0002460 {is_inferred="true", source="MA"} ! vesical vein intersection_of: UBERON:0001638 ! vein -intersection_of: drains UBERON:0006082 ! fundus of urinary bladder -relationship: drains UBERON:0006082 ! fundus of urinary bladder -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: editor_note "inferred from artery" xsd:string +intersection_of: RO:0002179 UBERON:0006082 ! drains fundus of urinary bladder +relationship: RO:0002179 UBERON:0006082 ! drains fundus of urinary bladder +property_value: IAO:0000116 "inferred from artery" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001319 @@ -173668,9 +172651,9 @@ is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0001638 ! vein intersection_of: part_of UBERON:0000996 ! vagina relationship: part_of UBERON:0000996 ! vagina -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: tributary_of UBERON:0001317 {source="FMA/obol"} ! internal iliac vein -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray589.png" xsd:anyURI +relationship: RO:0002376 UBERON:0001317 {source="FMA/obol"} ! tributary of internal iliac vein +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray589.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001322 @@ -173702,12 +172685,11 @@ xref: UMLS:C0036394 {source="BIRNLEX:1133", source="ncithesaurus:Sciatic_Nerve"} xref: VHOG:0000894 xref: Wikipedia:Sciatic_nerve is_a: UBERON:0001021 ! nerve -relationship: innervates UBERON:0001511 ! skin of leg relationship: overlaps UBERON:0000978 ! leg relationship: part_of UBERON:0001815 ! lumbosacral nerve plexus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/3a/Gray1244.png" xsd:anyURI -property_value: UBPROP:0000008 "mouse sciatic nerve origins predominantly from the third lumbar (L3) and L4 spinal nerves, unlike the L4 and L5 in rats - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700063/" xsd:string +relationship: RO:0002134 UBERON:0001511 ! innervates skin of leg +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3a/Gray1244.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001323 @@ -173727,8 +172709,8 @@ xref: SCTID:181078002 xref: UMLS:C0040186 {source="ncithesaurus:Tibial_Nerve"} xref: Wikipedia:Tibial_nerve is_a: UBERON:0003431 ! leg nerve -relationship: branching_part_of UBERON:0001322 {source="FMA", source="WP"} ! sciatic nerve -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1a/Gray828.png" xsd:anyURI +relationship: RO:0002380 UBERON:0001322 {source="FMA", source="WP"} ! branching part of sciatic nerve +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1a/Gray828.png" xsd:anyURI [Term] id: UBERON:0001325 @@ -173741,7 +172723,6 @@ synonym: "muscle organ of pelvis" EXACT [OBOL:automatic] synonym: "pelvic muscle" EXACT [FMA:19086] synonym: "pelvis muscle" EXACT [] synonym: "pelvis muscle organ" EXACT [OBOL:automatic] -xref: EMAPA:18184 xref: EMAPA:37481 {source="MA:th"} xref: FMA:19086 xref: MA:0000534 @@ -173765,12 +172746,12 @@ xref: MA:0001738 xref: NCIT:C52726 xref: SCTID:279692004 xref: UMLS:C0227970 {source="ncithesaurus:Prostate_Gland_Lobe"} +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0005156 ! reproductive structure is_a: UBERON:0009912 ! anatomical lobe intersection_of: UBERON:0009912 ! anatomical lobe intersection_of: part_of UBERON:0002367 ! prostate gland relationship: part_of UBERON:0002367 ! prostate gland -property_value: UBPROP:0000008 "Anatomically, the human prostate gland is located between the base of the bladder and the rectum, and it completely surrounds the proximal urethra (Fig. 1A). It is a single alobular structure with central (CZ), peripheral (PZ) and transitional (TZ) zones. In contrast, the mouse prostate is not merged into one compact anatomical structure. It comprises four paired lobes situated circumferentially around the urethra, immediately caudal to the urinary bladder-namely, anterior (AP), dorsal (DP), lateral (LP), and ventral (VP) prostate (Fig. 1B). Often, the dorsal and the lateral lobes are thought of in combination and referred to as the dorsolateral (DLP) lobe as they share a ductal system. The mouse AP is considered analogous to the human CZ, which is rarely a site of neoplastic transformation in humans. The mouse DLP is considered most similar to the human PZ, which is the zone in which most carcinomas arise (Xue et al. 1997). These analogies, however, are limited as they are based solely on descriptive data and need to be re-evaluated using molecular techniques before the relationship between specific mouse prostate lobes and the human prostate zones is definitively asserted (Abate-Shen & Shen 2000). The mouse VP does not have a human homologue, and the human TZ does not have a murine homologue" xsd:string {source="PMID:15163300", source="https://github.com/obophenotype/uberon/issues/665"} [Term] id: UBERON:0001330 @@ -173790,10 +172771,10 @@ xref: MA:0001866 xref: SCTID:279661001 xref: Wikipedia:Pampiniform_venous_plexus is_a: UBERON:0001593 ! venous plexus -relationship: connected_to UBERON:0000442 ! right testicular vein -relationship: located_in UBERON:0005352 ! spermatic cord -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/af/Gray1147.png" xsd:anyURI +relationship: RO:0001025 UBERON:0005352 ! located in spermatic cord +relationship: RO:0002170 UBERON:0000442 ! connected to right testicular vein +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/af/Gray1147.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001331 @@ -173809,11 +172790,12 @@ xref: FMA:19638 xref: MA:0002727 xref: SCTID:35900000 is_a: UBERON:0000014 ! zone of skin +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0000989 ! penis -relationship: continuous_with UBERON:0001085 ! skin of trunk relationship: part_of UBERON:0000989 ! penis +relationship: RO:0002150 UBERON:0001085 ! continuous with skin of trunk [Term] id: UBERON:0001332 @@ -173835,7 +172817,6 @@ xref: BTO:0001113 xref: CALOHA:TS-0383 xref: EFO:0001664 xref: EMAPA:18989 -xref: EV:0100109 xref: FMA:19639 xref: MA:0000407 xref: NCIT:C33049 @@ -173847,9 +172828,9 @@ intersection_of: UBERON:0011374 ! prepuce intersection_of: part_of UBERON:0000989 ! penis relationship: adjacent_to UBERON:0001299 ! glans penis relationship: part_of UBERON:0000989 ! penis -relationship: transformation_of UBERON:0035005 ! preputial swelling of male -property_value: depiction "http://upload.wikimedia.org/wikipedia/en/thumb/c/cc/Foreskin2.jpg/200px-Foreskin2.jpg" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/e/e6/Foreskin_CloseupV2.jpg" xsd:anyURI +relationship: RO:0002494 UBERON:0035005 ! transformation of preputial swelling of male +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/en/thumb/c/cc/Foreskin2.jpg/200px-Foreskin2.jpg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/e/e6/Foreskin_CloseupV2.jpg" xsd:anyURI [Term] id: UBERON:0001333 @@ -173870,8 +172851,8 @@ is_a: UBERON:0000057 ! urethra intersection_of: UBERON:0000057 ! urethra intersection_of: part_of UBERON:0003101 ! male organism relationship: part_of UBERON:0003101 ! male organism -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urethra.glb" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urethra.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png" xsd:anyURI [Term] id: UBERON:0001334 @@ -173894,7 +172875,7 @@ is_a: UBERON:0000057 ! urethra intersection_of: UBERON:0000057 ! urethra intersection_of: part_of UBERON:0003100 ! female organism relationship: part_of UBERON:0003100 ! female organism -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png" xsd:anyURI [Term] id: UBERON:0001335 @@ -173917,13 +172898,14 @@ xref: NCIT:C13101 xref: SCTID:279434009 xref: UMLS:C0458450 {source="ncithesaurus:Prostatic_Portion_of_the_Male_Urethra"} xref: Wikipedia:Prostatic_urethra +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0013522 ! subdivision of tube -relationship: contributes_to_morphology_of UBERON:0001333 ! male urethra -relationship: located_in UBERON:0002367 {source="FMA"} ! prostate gland relationship: part_of UBERON:0001333 {source="FMA", source="MA"} ! male urethra -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/d7/Gray1142.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urethra.glb" xsd:anyURI +relationship: RO:0001025 UBERON:0002367 {source="FMA"} ! located in prostate gland +relationship: RO:0002433 UBERON:0001333 ! contributes to morphology of male urethra +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d7/Gray1142.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urethra.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001338 @@ -173942,12 +172924,12 @@ xref: FMA:19683 xref: MA:0001688 xref: SCTID:279477005 is_a: UBERON:0000414 {source="MP"} ! mucous gland +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0000057 ! urethra -relationship: contributes_to_morphology_of UBERON:0000057 ! urethra -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0000057 ! urethra -property_value: UBPROP:0000012 "NCIT:C12339 paraurethral gland belongs here" xsd:string {external_ontology="NCIT"} +relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia +relationship: RO:0002433 UBERON:0000057 ! contributes to morphology of urethra [Term] id: UBERON:0001343 @@ -173985,16 +172967,13 @@ xref: XAO:0003088 is_a: UBERON:0000025 ! tube is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005904 ! duct of male reproductive system +relationship: BFO:0000067 GO:0007283 ! contains process spermatogenesis relationship: channel_for CL:0000019 ! sperm relationship: channels_into UBERON:0003959 {gci_relation="part_of", gci_filler="NCBITaxon:40674"} ! rete testis -relationship: contains_process GO:0007283 ! spermatogenesis -relationship: develops_from UBERON:0005297 {source="Wikipedia"} ! testis sex cord relationship: part_of UBERON:0000473 ! testis -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/49/Seminiferous_tubule_and_sperm_low_mag.jpg" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/6a/Gray1145.png" xsd:anyURI -property_value: UBPROP:0000001 "Any of the coiled tubules located in the testes in which spermatozoa are produced.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010399", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "One of two or three twisted curved tubules in each lobule of the testis in which spermatogenesis occurs. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001363", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/SEMINIFEROUS+TUBULE"} -property_value: UBPROP:0000003 "Frogs among amphibians and the amniotes have males with testes that are composed of seminiferous tubules, which differ from ampullae in being long, highly convoluted ductules.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001363", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.688 and Figure 21-28", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0005297 {source="Wikipedia"} ! develops from testis sex cord +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/49/Seminiferous_tubule_and_sperm_low_mag.jpg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6a/Gray1145.png" xsd:anyURI [Term] id: UBERON:0001344 @@ -174018,9 +172997,8 @@ is_a: UBERON:0000486 ! multilaminar epithelium is_a: UBERON:0004804 ! oviduct epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000996 ! vagina -relationship: contributes_to_morphology_of UBERON:0000996 ! vagina relationship: part_of UBERON:0000996 ! vagina -property_value: UBPROP:0000012 "FMA: nonkeratinizing stratified squamous epithelium; BTO: Vaginal epithelium is stratified squamous epithelium having a thickness of 15-200 microns; MA has single subclass (squamous)" xsd:string {external_ontology="FMA"} +relationship: RO:0002433 UBERON:0000996 ! contributes to morphology of vagina [Term] id: UBERON:0001347 @@ -174042,16 +173020,14 @@ xref: EMAPA:35926 xref: FMA:20117 xref: MA:0000058 xref: MAT:0000199 -xref: MESH:D052436 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: MIAA:0000199 xref: NCIT:C33889 xref: UMLS:C1704223 {source="ncithesaurus:White_Adipose_Tissue"} xref: Wikipedia:White_adipose_tissue is_a: UBERON:0001013 ! adipose tissue intersection_of: UBERON:0001013 ! adipose tissue -intersection_of: composed_primarily_of CL:0000448 ! white adipocyte -relationship: composed_primarily_of CL:0000448 ! white adipocyte -property_value: UBPROP:0000001 "Adipose tissue, cells of which contain a single large lipid droplet." xsd:string {source="FMA"} +intersection_of: RO:0002473 CL:0000448 ! composed primarily of white adipocyte +relationship: RO:0002473 CL:0000448 ! composed primarily of white adipocyte [Term] id: UBERON:0001348 @@ -174083,13 +173059,10 @@ xref: UMLS:C0006298 {source="ncithesaurus:Brown_Adipose_Tissue"} xref: Wikipedia:Brown_adipose_tissue is_a: UBERON:0001013 ! adipose tissue intersection_of: UBERON:0001013 ! adipose tissue -intersection_of: composed_primarily_of CL:0000449 ! brown adipocyte +intersection_of: RO:0002473 CL:0000449 ! composed primarily of brown adipocyte relationship: capable_of GO:1990845 ! adaptive thermogenesis -relationship: composed_primarily_of CL:0000449 ! brown adipocyte -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Brownfat_PETCT.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Adipose tissue, cells of which contain multiple small lipid droplets.[FMA]" xsd:string {source="FMA"} -property_value: UBPROP:0000008 "especially abundant in newborns and in hibernating mammals" xsd:string -property_value: UBPROP:0000009 "thermogenesis" xsd:string +relationship: RO:0002473 CL:0000449 ! composed primarily of brown adipocyte +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Brownfat_PETCT.jpg" xsd:anyURI [Term] id: UBERON:0001351 @@ -174107,9 +173080,10 @@ xref: NCIT:C32909 xref: SCTID:362534009 xref: UMLS:C0229289 {source="ncithesaurus:Lacrimal_Sac"} xref: Wikipedia:Lacrimal_sac +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0034944 ! zone of organ relationship: part_of UBERON:0002392 ! nasolacrimal duct -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray896.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray896.png" xsd:anyURI [Term] id: UBERON:0001352 @@ -174140,13 +173114,13 @@ xref: UMLS:C0013444 {source="ncithesaurus:External_Acoustic_Meatus"} xref: VHOG:0000977 xref: Wikipedia:External_acoustic_meatus is_a: UBERON:0004111 ! anatomical conduit +is_a: UBERON:0004119 ! endoderm-derived structure +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: capable_of_part_of GO:0055127 ! vibrational conductance of sound to the inner ear -relationship: develops_from UBERON:0005872 {source="PMID:11237469"} ! 1st arch pharyngeal cleft relationship: part_of UBERON:0001691 {source="FMA"} ! external ear -relationship: surrounded_by UBERON:0010065 {source="EHDAA2"} ! auditory meatus epithelium -property_value: editor_note "consider revisiting superclass after refinement of CARO/EAO, conduit may not be quite correct." xsd:string -property_value: UBPROP:0000011 "tympanic ring, which serves as support for the tympanic membrane, directs invagination of the first pharingeal cleft ectoderm to form the external acoustic meatus (EAM), which provides the outer layer of the membrane[PMID 11237469]" xsd:string -property_value: UBPROP:0000012 "subdivision of head in FMA." xsd:string {external_ontology="FMA"} +relationship: RO:0002202 UBERON:0005872 {source="PMID:11237469"} ! develops from 1st arch pharyngeal cleft +relationship: RO:0002219 UBERON:0010065 {source="EHDAA2"} ! surrounded by auditory meatus epithelium +property_value: IAO:0000116 "consider revisiting superclass after refinement of CARO/EAO, conduit may not be quite correct." xsd:string [Term] id: UBERON:0001353 @@ -174171,11 +173145,10 @@ xref: UMLS:C0230120 {source="ncithesaurus:Anal_Region"} xref: VHOG:0000395 xref: WBbt:0006919 is_a: UBERON:0000475 ! organism subdivision -relationship: has_developmental_contribution_from UBERON:0000931 {evidence="cjm"} ! proctodeum relationship: overlaps UBERON:0006866 ! terminal part of digestive tract -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray408.png" xsd:anyURI +relationship: RO:0002254 UBERON:0000931 ! has developmental contribution from proctodeum +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray408.png" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/507" xsd:anyURI -property_value: UBPROP:0000003 "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000395", ontology="VHOG", source="ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11", source="http://bgee.unil.ch/"} [Term] id: UBERON:0001355 @@ -174195,12 +173168,12 @@ xref: UMLS:C0226455 {source="ncithesaurus:Deep_Femoral_Artery"} xref: Wikipedia:Deep_femoral_artery is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery -intersection_of: connecting_branch_of UBERON:0002060 ! femoral artery intersection_of: part_of UBERON:0035551 ! deep vasculature -relationship: connecting_branch_of UBERON:0002060 ! femoral artery +intersection_of: RO:0002252 UBERON:0002060 ! connecting branch of femoral artery relationship: part_of UBERON:0035551 ! deep vasculature -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray548.png" xsd:anyURI +relationship: RO:0002252 UBERON:0002060 ! connecting branch of femoral artery +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray548.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001356 @@ -174218,11 +173191,11 @@ xref: SCTID:244326008 xref: Wikipedia:Medial_circumflex_femoral_artery is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0007119 ! neck of femur -relationship: connecting_branch_of UBERON:0001355 {source="FMA"} ! deep femoral artery -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: supplies UBERON:0007119 ! neck of femur -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c5/Circumflex_femoral_arteries.png" xsd:anyURI +intersection_of: RO:0002178 UBERON:0007119 ! supplies neck of femur +relationship: RO:0002178 UBERON:0007119 ! supplies neck of femur +relationship: RO:0002252 UBERON:0001355 {source="FMA"} ! connecting branch of deep femoral artery +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c5/Circumflex_femoral_arteries.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001359 @@ -174256,14 +173229,10 @@ xref: VHOG:0001278 xref: Wikipedia:Cerebrospinal_fluid xref: ZFA:0001626 is_a: UBERON:0007779 {source="Wikipedia"} ! transudate -relationship: develops_from UBERON:0002307 {notes="see notes", source="EHDAA2"} ! choroid plexus of lateral ventricle relationship: filtered_through UBERON:0001886 ! choroid plexus -relationship: located_in UBERON:0005281 {source="EHDAA2"} ! ventricular system of central nervous system -property_value: editor_note "many sources state the CP as sole producer of CSF, but this is disputed [DOI:10.1007/s11064-015-1581-6]" xsd:string -property_value: UBPROP:0000001 "Portion of organism substance that is a clear fluid that occupies the subarachnoid space and the ventricular system around and inside the brain.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002184", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "In vertebrates, at early stages of Central Nervous System (CNS) development, the architecture of the brain primordium reveals the presence of the cavity of brain vesicles, which is filled by Embryonic Cerebro-Spinal Fluid (E-CSF). (...) Rat and chick E-CSF proteomes are similar, although rat is more complex in certain groups of proteins, e.g., apolipoproteins, which may be involved in the control of neural diversity, and has soluble enzymes present, just like adult human CSF, but unlike chick E-CSF, revealing phylogenetic brain differences between these groups of vertebrates.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001278", ontology="VHOG", source="DOI:10.1021/pr050213t Parada C, Gato A, Bueno D, Mammalian embryonic cerebrospinal fluid proteome has greater apolipoprotein and enzyme pattern complexity than the avian proteome. Journal of Proteome Research (2005)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "EHDAA2 models this as developing from CP, which is wrong" xsd:string {external_ontology="EHDAA2"} -property_value: UBPROP:0000012 "the FMA def states that this is subarachnoid spaces only. ZFA def states subarachnoid spaces and brain ventricles, but not SC (and has part_of to brain). Circulation: It circulates from the lateral ventricles to the foramen of Monro (Interventricular foramen), third ventricle, aqueduct of Sylvius (Cerebral aqueduct), fourth ventricle, foramen of Magendie (Median aperture) and foramina of Luschka (Lateral apertures), subarachnoid space over brain and spinal cord. It should be noted that the CSF moves in a pulsatile manner throughout the CSF system with nearly zero net flow. CSF is reabsorbed into venous sinus blood via arachnoid granulations." xsd:string {external_ontology="FMA"} +relationship: RO:0001025 UBERON:0005281 {source="EHDAA2"} ! located in ventricular system of central nervous system +relationship: RO:0002202 UBERON:0002307 ! develops from choroid plexus of lateral ventricle +property_value: IAO:0000116 "many sources state the CP as sole producer of CSF, but this is disputed [DOI:10.1007/s11064-015-1581-6]" xsd:string [Term] id: UBERON:0001361 @@ -174286,9 +173255,8 @@ xref: UMLS:C0015809 {source="ncithesaurus:Femoral_Vein"} xref: Wikipedia:Femoral_vein is_a: UBERON:0001638 ! vein is_a: UBERON:0003516 ! hindlimb blood vessel -relationship: connected_to UBERON:0001316 ! external iliac vein -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000001 "Either of the primary veins in the hindlimbs which collect blood from the hindlimb region.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010237", ontology="AAO", source="AAO:BJB"} +relationship: RO:0002170 UBERON:0001316 ! connected to external iliac vein +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001363 @@ -174312,9 +173280,9 @@ xref: SCTID:181402008 xref: UMLS:C0392907 {source="ncithesaurus:Long_Saphenous_Vein"} xref: Wikipedia:Great_saphenous_vein is_a: UBERON:0007318 ! saphenous vein -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: tributary_of UBERON:0001361 {source="FMA/obol"} ! femoral vein -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/51/Great_saphenous_vein.png" xsd:anyURI +relationship: RO:0002376 UBERON:0001361 {source="FMA/obol"} ! tributary of femoral vein +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/51/Great_saphenous_vein.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001366 @@ -174337,10 +173305,9 @@ xref: ZFA:0005131 is_a: UBERON:0022351 ! parietal serous membrane intersection_of: UBERON:0022351 ! parietal serous membrane intersection_of: part_of UBERON:0002358 ! peritoneum -relationship: attaches_to UBERON:0003697 ! abdominal wall relationship: part_of UBERON:0002358 ! peritoneum -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray1040.png" xsd:anyURI -property_value: UBPROP:0000001 "Peritoneum attached to the abdominal wall.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010816", ontology="AAO", source="AAO:JMG"} +relationship: RO:0002371 UBERON:0003697 ! attached to abdominal wall +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray1040.png" xsd:anyURI [Term] id: UBERON:0001383 @@ -174363,8 +173330,6 @@ synonym: "muscle organ of leg" EXACT [OBOL:automatic] synonym: "skeletal muscle of leg" EXACT [OBOL:automatic] xref: BTO:0000722 xref: EHDAA:8291 -xref: EMAPA:19144 -xref: EMAPA:19318 xref: MA:0000672 xref: RETIRED_EHDAA2:0000974 xref: Wikipedia:Leg_muscle @@ -174372,8 +173337,7 @@ is_a: UBERON:0003663 ! hindlimb muscle intersection_of: UBERON:0014892 ! skeletal muscle organ, vertebrate intersection_of: part_of UBERON:0000978 ! leg relationship: part_of UBERON:0004466 {source="prolog"} ! musculature of leg -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000013 "see notes on UBERON:0000978 for possible confusion over the term 'leg'." xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001384 @@ -174412,14 +173376,12 @@ xref: SCTID:11931008 xref: UMLS:C0026607 {source="ncithesaurus:Primary_Motor_Cortex"} xref: Wikipedia:Primary_motor_cortex is_a: UBERON:0002616 ! regional part of brain -relationship: contributes_to_morphology_of UBERON:0000956 ! cerebral cortex -relationship: contributes_to_morphology_of UBERON:0001870 ! frontal cortex relationship: part_of UBERON:0001870 {source="MA", source="Wikipedia"} ! frontal cortex -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/eb/Ba4.png" xsd:anyURI -property_value: editor_note "TODO - in MA this is asserted to be part_of BOTH frontal and parietal cortex. in ABA these are disjoint. FMA makes no commitment beyond cerebral cortex. Wikipedia says frontal lobe. Check if species difference or difference in definition. Removed relationship: part_of UBERON:0001872 parietal lobe" xsd:string -property_value: UBPROP:0000001 "the area of the frontal lobe that is involved with integration of voluntary movements and with speech.[MP]" xsd:string {date_retrieved="2012-08-31", external_class="MP:0000800", ontology="MP", source="MGI:csmith"} -property_value: UBPROP:0000001 "The part of the cerebral cortex that receives projections from the motor thalamus and which projects to motor neurons in the brainstem and spinal cord. The motor cortex corresponds to Brodmann's area 4 (MM). The primary motor cortex, or M1, is located on the precentral gyrus and on the anterior paracentral lobule on the medial surface of the brain. Of the three motor cortex areas, stimulation of the primary motor cortex requires the least amount of electrical current to elicit a movement. http://neuroscience.uth.tmc.edu/s3/chapter03.html" xsd:string {source="NLX:143555"} +relationship: RO:0002433 UBERON:0000956 ! contributes to morphology of cerebral cortex +relationship: RO:0002433 UBERON:0001870 ! contributes to morphology of frontal cortex +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/eb/Ba4.png" xsd:anyURI +property_value: IAO:0000116 "TODO - in MA this is asserted to be part_of BOTH frontal and parietal cortex. in ABA these are disjoint. FMA makes no commitment beyond cerebral cortex. Wikipedia says frontal lobe. Check if species difference or difference in definition. Removed relationship: part_of UBERON:0001872 parietal lobe" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001394 @@ -174443,14 +173405,13 @@ xref: UMLS:C0004455 {source="ncithesaurus:Axillary_Artery"} xref: Wikipedia:Axillary_artery is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0009472 ! axilla -relationship: connected_to UBERON:0001533 ! subclavian artery -relationship: connecting_branch_of UBERON:0001394 ! axillary artery +intersection_of: RO:0002178 UBERON:0009472 ! supplies axilla relationship: part_of UBERON:0001467 ! shoulder -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: supplies UBERON:0009472 ! axilla -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/88/Axillary_limits.PNG" xsd:anyURI -property_value: UBPROP:0000008 "In human anatomy, the axillary artery is a large blood vessel that conveys oxygenated blood to the lateral aspect of the thorax, the axilla (armpit) and the upper limb. Its origin is at the lateral margin of the first rib, before which it is called the subclavian artery. After passing the lower margin of teres major it becomes the brachial artery." xsd:string +relationship: RO:0002170 UBERON:0001533 ! connected to subclavian artery +relationship: RO:0002178 UBERON:0009472 ! supplies axilla +relationship: RO:0002252 UBERON:0001394 ! connecting branch of axillary artery +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/88/Axillary_limits.PNG" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001397 @@ -174468,9 +173429,9 @@ xref: SCTID:244311006 xref: UMLS:C0226422 {source="ncithesaurus:Subscapular_Artery"} xref: Wikipedia:Subscapular_artery is_a: UBERON:0001637 ! artery -relationship: connected_to UBERON:0001394 ! axillary artery -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/4/4c/Axillary_branches.PNG" xsd:anyURI +relationship: RO:0002170 UBERON:0001394 ! connected to axillary artery +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/4/4c/Axillary_branches.PNG" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001415 @@ -174601,13 +173562,9 @@ is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0007823 ! appendage girdle region intersection_of: part_of UBERON:0010708 ! pectoral complex disjoint_from: UBERON:0007831 ! pectoral girdle skeleton -relationship: has_skeleton UBERON:0007831 ! pectoral girdle skeleton -relationship: in_lateral_side_of UBERON:0000468 ! multicellular organism +relationship: BSPO:0000126 UBERON:0000468 ! multicellular organism relationship: part_of UBERON:0010708 ! pectoral complex -property_value: IAO:0000232 "this class describes the organism subdivision, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831)." xsd:string -property_value: RO:0002171 UBERON:0001271 -property_value: UBPROP:0000001 "An organism subdivision that includes the pectoral girdle skeleton. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There is only one instance of the pectoral girdle region per organism.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000305", ontology="VSAO", source="https://orcid.org/0000-0002-6601-2165"} -property_value: UBPROP:0000005 "Note that this class describes the central subdivision of the pectoral girdle complex, NOT the skeleton within.[VSAO]" xsd:string {date_retrieved="2012-09-06", external_class="VSAO:0000305", ontology="VSAO", source="Curator"} +relationship: RO:0002551 UBERON:0007831 ! has skeleton pectoral girdle skeleton [Term] id: UBERON:0001422 @@ -174685,18 +173642,11 @@ disjoint_from: UBERON:0002416 ! integumental system disjoint_from: UBERON:0002423 ! hepatobiliary system disjoint_from: UBERON:0004456 ! entire sense organ system disjoint_from: UBERON:8450002 ! excretory system -relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: has_part UBERON:0004288 ! skeleton relationship: has_part UBERON:0004770 ! articular system relationship: part_of UBERON:0002204 ! musculoskeletal system -property_value: RO:0002171 UBERON:0001016 +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/The-skeletal-system" xsd:anyURI -property_value: UBPROP:0000001 "Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000434", ontology="TAO", source="TAO:wd"} -property_value: UBPROP:0000001 "Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000027", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "System that provides physical support to the organism.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000566", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000003 "By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001254", ontology="VHOG", source="DOI:10.1159/000324245 Donoghue PCJ, Sansom IJ, Origin and early evolution of vertebrate skeletonization. Microscopy research and technique (2002)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "skeletal" xsd:string -property_value: UBPROP:0000012 "GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates" xsd:string {external_ontology="GO"} [Term] id: UBERON:0001435 @@ -174725,9 +173675,8 @@ is_a: UBERON:0015049 ! carpus endochondral element intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0004452 ! carpal region disjoint_from: UBERON:0012358 ! manual digitopodium bone -relationship: develops_from UBERON:0006213 ! carpus cartilage element -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/58/Carpus.svg" xsd:anyURI -property_value: UBPROP:0000008 "In tetrapods, the carpals is the sole cluster of the bones in the wrist between the radius and ulna and the metacarpus. The bones of the carpus do not belong to individual fingers (or toes in quadrupeds), whereas those of the metacarpus do. The corresponding part of the foot is the tarsus. The carpal bones allow the wrist to move and rotate vertically, horizontally and laterally. In human anatomy, the main role of the carpus is to facilitate effective positioning of the hand and powerful use of the extensors and flexors of the forearm, but the mobility of individual carpal bones increase the freedom of movements at the wrist." xsd:string {source="Wikipedia:Carpus"} +relationship: RO:0002202 UBERON:0006213 ! develops from carpus cartilage element +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/58/Carpus.svg" xsd:anyURI [Term] id: UBERON:0001436 @@ -174766,8 +173715,7 @@ is_a: UBERON:0004249 ! manual digit bone is_a: UBERON:0015024 ! manual digit phalanx endochondral element intersection_of: UBERON:0003221 ! phalanx intersection_of: part_of UBERON:0002389 ! manual digit -relationship: develops_from UBERON:0010686 ! manual digit phalanx cartilage element -property_value: UBPROP:0000001 "Dumb-bell shaped bones of endochondral origin with cartilaginous epiphyses that make the four digits of the manus. The terminal phalanges are much smaller than the proximal and penultimate phalanges. The typical phalangeal formula of the manus, in a medial to lateral sequence, is 2-2-3-3.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000947", ontology="AAO", source="AAO:LAP"} +relationship: RO:0002202 UBERON:0010686 ! develops from manual digit phalanx cartilage element [Term] id: UBERON:0001437 @@ -174792,13 +173740,9 @@ xref: SCTID:244701002 xref: UMLS:C1708734 {source="ncithesaurus:Long_Bone_Epiphysis"} xref: Wikipedia:Epiphysis is_a: UBERON:0005055 ! zone of long bone -relationship: contributes_to_morphology_of UBERON:0002495 ! long bone -relationship: seeAlso UBERON:0006776 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/94/Illu_long_bone.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Cartilaginous expansion at the distal end of an anterior rib or transverse process that serves for the attachment of muscles suspending the pectoral girdle to the vertebral column.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000742", ontology="AAO", source="AAO:Pugener_2002"} -property_value: UBPROP:0000001 "Subdivision of long bone which forms its expanded proximal or distal articular end; together with other the subdivisions of long bone, it constitutes the long bone. Examples: proximal epiphysis of humerus, distal epiphysis of femur." xsd:string {source="FMA:24012"} -property_value: UBPROP:0000007 "epiphyseal" xsd:string -property_value: UBPROP:0000007 "epiphysial" xsd:string +relationship: RO:0002433 UBERON:0002495 ! contributes to morphology of long bone +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/94/Illu_long_bone.jpg" xsd:anyURI +property_value: seeAlso UBERON:0006776 [Term] id: UBERON:0001438 @@ -174819,10 +173763,9 @@ xref: UMLS:C0222671 {source="ncithesaurus:Metaphysis"} xref: Wikipedia:Metaphysis is_a: UBERON:0005055 ! zone of long bone relationship: adjacent_to UBERON:0006861 ! diaphysis proper -relationship: contributes_to_morphology_of UBERON:0002495 ! long bone relationship: part_of UBERON:0004769 ! diaphysis -property_value: editor_note "todo - decide - adjacent to or containing epiphyseal plate? AO Notes: FMA the metaphysis is part of the diaphysis, but not in MA." xsd:string -property_value: UBPROP:0000001 "Subdivision of diaphysis which forms the proximal or distal end of diaphysis next to the epiphysis; together with diaphysis proper, it constitutes the diaphysis. Examples: proximal metaphysis of humerus, distal metaphysis of femur.[FMA]" xsd:string {source="FMA:24014"} +relationship: RO:0002433 UBERON:0002495 ! contributes to morphology of long bone +property_value: IAO:0000116 "todo - decide - adjacent to or containing epiphyseal plate? AO Notes: FMA the metaphysis is part of the diaphysis, but not in MA." xsd:string [Term] id: UBERON:0001439 @@ -174845,15 +173788,14 @@ xref: EMAPA:35250 xref: FMA:24018 xref: galen:CorticalBone xref: MA:0001461 -xref: MESH:D000071538 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: NCIT:C52714 xref: SCTID:361728003 xref: UMLS:C0222661 {source="ncithesaurus:Cortical_Bone"} xref: Wikipedia:Compact_bone is_a: UBERON:0002481 ! bone tissue relationship: part_of UBERON:0002482 ! lamellar bone -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Pelvis.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Pelvis.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Pelvis.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Pelvis.glb" xsd:anyURI [Term] id: UBERON:0001440 @@ -174883,16 +173825,12 @@ xref: XAO:0003061 is_a: UBERON:0004381 ! skeleton of limb is_a: UBERON:0007272 ! pectoral appendage skeleton intersection_of: UBERON:0010912 ! subdivision of skeleton -intersection_of: skeleton_of UBERON:0002102 ! forelimb +intersection_of: RO:0002576 UBERON:0002102 ! skeleton of forelimb relationship: part_of UBERON:0002102 {source="FMA"} ! forelimb relationship: part_of UBERON:0012475 ! skeleton of pectoral complex relationship: proximally_connected_to UBERON:0007831 ! pectoral girdle skeleton -relationship: skeleton_of UBERON:0002102 ! forelimb -property_value: editor_note "TODO - find a home for: FMA:24139 ! skeleton of upper limb" xsd:string -property_value: RO:0002475 UBERON:0001441 -property_value: UBPROP:0000001 "Skeletal structure of the paired, anterior appendages.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000202", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000002 "relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000202", ontology="AAO"} -property_value: UBPROP:0000003 "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001256", ontology="VHOG", source="ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268", source="http://bgee.unil.ch/"} +relationship: RO:0002576 UBERON:0002102 ! skeleton of forelimb +property_value: IAO:0000116 "TODO - find a home for: FMA:24139 ! skeleton of upper limb" xsd:string [Term] id: UBERON:0001441 @@ -174921,14 +173859,11 @@ xref: XAO:0003062 is_a: UBERON:0004381 ! skeleton of limb is_a: UBERON:0007273 ! pelvic appendage skeleton intersection_of: UBERON:0010912 ! subdivision of skeleton -intersection_of: skeleton_of UBERON:0002103 ! hindlimb +intersection_of: RO:0002576 UBERON:0002103 ! skeleton of hindlimb relationship: part_of UBERON:0002103 {source="FMA"} ! hindlimb relationship: part_of UBERON:0012476 ! skeleton of pelvic complex relationship: proximally_connected_to UBERON:0007832 ! pelvic girdle skeleton -relationship: skeleton_of UBERON:0002103 ! hindlimb -property_value: UBPROP:0000001 "Skeletal structure of the paired, posterior appendages.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000217", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000002 "relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000217", ontology="AAO"} -property_value: UBPROP:0000003 "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001255", ontology="VHOG", source="ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268", source="http://bgee.unil.ch/"} +relationship: RO:0002576 UBERON:0002103 ! skeleton of hindlimb [Term] id: UBERON:0001442 @@ -174956,12 +173891,11 @@ xref: FMA:24159 xref: VSAO:0005020 is_a: UBERON:0006717 ! autopodial skeleton intersection_of: UBERON:0010912 ! subdivision of skeleton -intersection_of: skeleton_of UBERON:0002398 ! manus +intersection_of: RO:0002576 UBERON:0002398 ! skeleton of manus disjoint_from: UBERON:0001445 {source="lexical"} ! skeleton of pes relationship: part_of UBERON:0001440 {source="EHDAA2"} ! forelimb skeleton relationship: part_of UBERON:0002398 ! manus -relationship: skeleton_of UBERON:0002398 ! manus -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern" xsd:anyURI +relationship: RO:0002576 UBERON:0002398 ! skeleton of manus [Term] id: UBERON:0001443 @@ -174997,11 +173931,8 @@ xref: UMLS:C1527391 {source="ncithesaurus:Chest"} xref: Wikipedia:Chest is_a: UBERON:0009569 {source="FMA-modified"} ! subdivision of trunk relationship: part_of UBERON:0000915 {source="FMA", source="MA"} ! thoracic segment of trunk -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/db/Chest.jpg" xsd:anyURI -property_value: editor_note "FMA:24216 present in FMA1, but gone in subsequent versions" xsd:string -property_value: RO:0002171 UBERON:0000916 -property_value: UBPROP:0000007 "pectoral" xsd:string -property_value: UBPROP:0000007 "thoracic" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/db/Chest.jpg" xsd:anyURI +property_value: IAO:0000116 "FMA:24216 present in FMA1, but gone in subsequent versions" xsd:string [Term] id: UBERON:0001444 @@ -175038,11 +173969,10 @@ xref: FMA:24222 xref: VSAO:0005021 is_a: UBERON:0006717 ! autopodial skeleton intersection_of: UBERON:0010912 ! subdivision of skeleton -intersection_of: skeleton_of UBERON:0002387 ! pes +intersection_of: RO:0002576 UBERON:0002387 ! skeleton of pes relationship: part_of UBERON:0001441 {source="EHDAA2"} ! hindlimb skeleton relationship: part_of UBERON:0002387 ! pes -relationship: skeleton_of UBERON:0002387 ! pes -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern" xsd:anyURI +relationship: RO:0002576 UBERON:0002387 ! skeleton of pes [Term] id: UBERON:0001446 @@ -175071,13 +174001,11 @@ is_a: UBERON:0003608 ! hindlimb long bone is_a: UBERON:0004251 ! hindlimb zeugopod bone is_a: UBERON:0015013 ! fibula endochondral element intersection_of: UBERON:0015013 ! fibula endochondral element -intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue -relationship: develops_from UBERON:0010851 ! fibula cartilage element -relationship: postaxialmost_part_of UBERON:0010720 ! hindlimb zeugopod skeleton -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/16/Illu_lower_extremity.jpg" xsd:anyURI -property_value: UBPROP:0000001 "One of the two long bones of endochondral origin of the hind-epipodium; it is a rather more slender bone than the tibia but of about the same length.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000891", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000007 "fibular" xsd:string +intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue +relationship: BSPO:0001115 UBERON:0010720 ! hindlimb zeugopod skeleton +relationship: RO:0002202 UBERON:0010851 ! develops from fibula cartilage element +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/16/Illu_lower_extremity.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001447 @@ -175112,9 +174040,8 @@ is_a: UBERON:0015050 ! tarsus endochondral element intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0004454 ! tarsal region disjoint_from: UBERON:0012359 ! pedal digitopodium bone -relationship: develops_from UBERON:0010541 ! tarsus cartilage element -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/b/bf/Ankle_en.svg" xsd:anyURI -property_value: UBPROP:0000008 "In primitive tetrapods, such as Trematops, the tarsus consists of three rows of bones. There are three proximal tarsals, the tibiale, intermedium, and fibulare, named for their points of articulation with the bones of the lower limb. These are followed by a second row of four bones, referred to as the centralia (singular: centrale), and then a row of five distal tarsals, each articulating with a single metatarsal. In the great majority of tetrapods, including all of those alive today, this simple pattern is modified by the loss and fusion of various of the bones.[3] In reptiles and mammals, there are normally just two proximal tarsals, the calcaneus (equivalent to the amphibian fibulare) and the talus (probably derived from a fusion of multiple bones). In mammals, including humans, the talus forms a hinge joint with the tibia, a feature especially well developed in the artiodactyls. The calcaneus is also modified, forming a heel for the attachment of the Achilles tendon. Neither of these adaptations is found in reptiles, which have a relatively simple structure to both bones.[3] The fifth distal tarsal disappears relatively early in evolution, with the remainder becoming the cuneiform and cuboid bones. Reptiles usually retain two centralia, while mammals typically have only one (the navicular).[3] In birds, the tarsus has disappeared, with the proximal tarsals having fused with the tibia, the centralia having disappeared, and the distal bones having fused with the metatarsals to form a single tarsometatarsus bone, effectively giving the leg a third segment" xsd:string {source="Wikipedia:Tarsus_(skeleton)"} +relationship: RO:0002202 UBERON:0010541 ! develops from tarsus cartilage element +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/b/bf/Ankle_en.svg" xsd:anyURI [Term] id: UBERON:0001448 @@ -175144,10 +174071,10 @@ is_a: UBERON:0012359 ! pedal digitopodium bone is_a: UBERON:0015036 ! pedal digit metatarsal endochondral element intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0000983 ! metatarsus region -relationship: connected_to UBERON:0001447 ! tarsal bone -relationship: connected_to UBERON:0001449 ! phalanx of pes relationship: part_of UBERON:0010545 ! metatarsus skeleton -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/52/Gray291.png" xsd:anyURI +relationship: RO:0002170 UBERON:0001447 ! connected to tarsal bone +relationship: RO:0002170 UBERON:0001449 ! connected to phalanx of pes +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/52/Gray291.png" xsd:anyURI [Term] id: UBERON:0001449 @@ -175185,8 +174112,7 @@ is_a: UBERON:0004248 ! pedal digit bone is_a: UBERON:0015030 ! pedal digit phalanx endochondral element intersection_of: UBERON:0003221 ! phalanx intersection_of: part_of UBERON:0002387 ! pes -relationship: develops_from UBERON:0010685 ! pedal digit phalanx cartilage element -property_value: UBPROP:0000001 "Dumb-bell shaped bones of endochondral origin with cartilaginous epiphyses that make the five digits of the pes. The terminal phalanges are much smaller than the proximal and penultimate phalanges. The typical phalangeal formula of the pes, in a medial to lateral sequence, is 2(1)-2-3-4(3)-3(2).[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000930", ontology="AAO", source="AAO:LAP"} +relationship: RO:0002202 UBERON:0010685 ! develops from pedal digit phalanx cartilage element [Term] id: UBERON:0001456 @@ -175211,16 +174137,12 @@ xref: SCTID:302549007 xref: UMLS:C0015450 {source="ncithesaurus:Face"} xref: Wikipedia:Face is_a: UBERON:0001444 ! subdivision of head -relationship: contributes_to_morphology_of UBERON:0000033 ! head relationship: has_part UBERON:0000018 {gci_filler="NCBITaxon:50557", gci_relation="part_of"} ! compound eye relationship: has_part UBERON:0000165 ! mouth relationship: has_part UBERON:0011156 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! facial skeleton -relationship: has_skeleton UBERON:0011156 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! facial skeleton -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Mona_Lisa_headcrop.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face." xsd:string {source="FMA:24728"} -property_value: UBPROP:0000001 "The area that extends from the median ocellus to the oral foramen[HAO]." xsd:string {source="HAO:0000316", source="http://api.hymao.org/api/ref/67791", taxon="NCBITaxon:7399"} -property_value: UBPROP:0000007 "facial" xsd:string -property_value: UBPROP:0000011 "The face develops from outward growth of tissue located rostral to the cranium & pharynx. The lower jaw and most of the upper jaw are formed by growth of the first pharyngeal (branchial) arch. The upper incisor region and the nose and forehead (frontal region) are formed from tissue located rostral to the neural tube (frontonasal prominence)" xsd:string {source="vanat.cvm.umn.edu/TFFlectPDFs/LectFaceDevelop.pdf"} +relationship: RO:0002433 UBERON:0000033 ! contributes to morphology of head +relationship: RO:0002551 UBERON:0011156 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! has skeleton facial skeleton +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Mona_Lisa_headcrop.jpg" xsd:anyURI [Term] id: UBERON:0001457 @@ -175318,10 +174240,8 @@ is_a: UBERON:0006058 ! multi-limb segment region is_a: UBERON:0008785 ! upper limb segment relationship: distally_connected_to UBERON:0002398 ! manus relationship: proximally_connected_to UBERON:0001467 ! shoulder -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Upperarm.jpg" xsd:anyURI -property_value: editor_note "currently declared as overlapping hand, as AOs disagree over whether some wrist parts are in the arm or hand" xsd:string -property_value: IAO:0000232 "this class refers to the combination of the stylopod and zeugopod of a forelimb. Sometimes (cf FMA), 'arm' denotes the stylopod only; sometimes (cf MA), 'arm' denotes the part of the forelimb covering both (i.e. shoulder to hand). Also note distinction between arm and forelimb: hand is part of forelimb, but not part of arm" xsd:string -property_value: UBPROP:0000003 "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000339", ontology="VHOG", source="ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268", source="http://bgee.unil.ch/"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Upperarm.jpg" xsd:anyURI +property_value: IAO:0000116 "currently declared as overlapping hand, as AOs disagree over whether some wrist parts are in the arm or hand" xsd:string [Term] id: UBERON:0001461 @@ -175351,9 +174271,7 @@ xref: VHOG:0000340 xref: Wikipedia:Elbow is_a: UBERON:0008785 ! upper limb segment relationship: part_of UBERON:0001460 {source="EHDAA2"} ! arm -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/5/5c/Elbow_coude.JPG" xsd:anyURI -property_value: UBPROP:0000007 "cubital" xsd:string -property_value: UBPROP:0000013 "Naming conventions for pod terms under discussion within phenoscape group" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/5/5c/Elbow_coude.JPG" xsd:anyURI [Term] id: UBERON:0001464 @@ -175386,10 +174304,7 @@ xref: Wikipedia:Hip is_a: UBERON:0000475 ! organism subdivision relationship: overlaps UBERON:0001271 {source="FMA-modified"} ! pelvic girdle region relationship: part_of UBERON:0010709 ! pelvic complex -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/9f/Hip.jpg" xsd:anyURI -property_value: UBPROP:0000003 "The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000346", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.333", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "coxal" xsd:string -property_value: UBPROP:0000012 "See notes for shoulder. in BTO this is part of the abdomen - this creates an inconsistency if limb and abdomen are spatially disjoint" xsd:string {external_ontology="BTO"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/9f/Hip.jpg" xsd:anyURI [Term] id: UBERON:0001465 @@ -175416,8 +174331,8 @@ xref: SCTID:361291001 xref: VHOG:0000347 is_a: UBERON:0008784 ! lower limb segment relationship: part_of UBERON:0000978 ! leg -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/8d/Male_Knee_by_David_Shankbone.jpg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8d/Male_Knee_by_David_Shankbone.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001466 @@ -175457,7 +174372,7 @@ intersection_of: UBERON:0002544 ! digit intersection_of: part_of UBERON:0002387 ! pes relationship: part_of UBERON:0012142 {source="PHENOSCAPE:ni"} ! pedal digitopodium region relationship: part_of UBERON:5001466 ! pedal digit plus metapodial segment -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/5e/Toes.jpg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5e/Toes.jpg" xsd:anyURI [Term] id: UBERON:0001467 @@ -175487,12 +174402,10 @@ xref: VHOG:0000342 xref: Wikipedia:Shoulder is_a: UBERON:0000475 ! organism subdivision relationship: has_part UBERON:0016884 ! shoulder joint -relationship: only_in_taxon NCBITaxon:32523 ! Tetrapoda relationship: overlaps UBERON:0001421 {source="FMA-modified"} ! pectoral girdle region relationship: part_of UBERON:0010708 ! pectoral complex -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/90/Shoulderjoint.PNG" xsd:anyURI -property_value: UBPROP:0000003 "(...) endochondral elements of the early tetrapod shoulder develop from two centers of ossification, giving rise to a scapula and a 'coracoid'.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000342", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.332", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "In FMA, the shoulder is part of the pectoral girdle region. in MA, shoulder structures like shoulder joints, bones, nerves etc are part of the shoulder and the forelimb. E.g. humerus is a shoulder bone" xsd:string {external_ontology="FMA"} +relationship: RO:0002160 NCBITaxon:32523 ! only in taxon Tetrapoda +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/90/Shoulderjoint.PNG" xsd:anyURI [Term] id: UBERON:0001468 @@ -175512,10 +174425,9 @@ xref: SCTID:244512000 xref: UMLS:C1182940 {source="ncithesaurus:Vertebral_Joint"} is_a: UBERON:0002216 {source="FMA"} ! symphysis intersection_of: UBERON:0000982 ! skeletal joint -intersection_of: connects UBERON:0001075 {cardinality="2"} ! bony vertebral centrum -relationship: connects UBERON:0001075 {notes="connects successive pairs of centra"} ! bony vertebral centrum +intersection_of: RO:0002176 UBERON:0001075 {cardinality="2"} ! connects bony vertebral centrum relationship: part_of UBERON:0001130 {source="FMA"} ! vertebral column -property_value: UBPROP:0000012 "FMA has 'intervertebral joint' as a GAT, and has two distinct classes 'intervertebral symphysis' and 'intervertebral syndesmosis', but note that the latter do not connect the centra" xsd:string {external_ontology="FMA"} +relationship: RO:0002176 UBERON:0001075 ! connects bony vertebral centrum [Term] id: UBERON:0001469 @@ -175539,11 +174451,11 @@ xref: Wikipedia:Sternoclavicular_articulation is_a: UBERON:0011108 {source="FMA"} ! synovial joint of pectoral girdle is_a: UBERON:0011965 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="Wikipedia"} ! saddle joint intersection_of: UBERON:0000982 ! skeletal joint -intersection_of: connects UBERON:0000975 ! sternum -intersection_of: connects UBERON:0001105 ! clavicle bone -relationship: connects UBERON:0000975 {notes="clavicular notch of the manubrium sterni"} ! sternum -relationship: connects UBERON:0001105 {notes="sternal end of the clavicle and first rib"} ! clavicle bone -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/3f/Gray325.png" xsd:anyURI +intersection_of: RO:0002176 UBERON:0000975 ! connects sternum +intersection_of: RO:0002176 UBERON:0001105 ! connects clavicle bone +relationship: RO:0002176 UBERON:0000975 ! connects sternum +relationship: RO:0002176 UBERON:0001105 ! connects clavicle bone +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3f/Gray325.png" xsd:anyURI [Term] id: UBERON:0001470 @@ -175571,15 +174483,14 @@ is_a: UBERON:0011108 ! synovial joint of pectoral girdle is_a: UBERON:0011139 {source="FMA"} ! synovial limb joint is_a: UBERON:0016884 ! shoulder joint intersection_of: UBERON:0000982 ! skeletal joint -intersection_of: connects UBERON:0000976 ! humerus -intersection_of: connects UBERON:0006849 ! scapula +intersection_of: RO:0002176 UBERON:0000976 ! connects humerus +intersection_of: RO:0002176 UBERON:0006849 ! connects scapula relationship: adjacent_to UBERON:0006657 ! glenoid fossa -relationship: connects UBERON:0000976 ! humerus -relationship: connects UBERON:0006849 ! scapula relationship: part_of UBERON:0004753 ! scapulocoracoid -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/a3/Gray327.png" xsd:anyURI -property_value: editor_note "note that in this ontology 'glenoid fossa' is a cavity (consistent with FMA) - consider adding a class for the surface of the scapula that is adjacent to this cavity, and making a more explicit connects relationship" xsd:string -property_value: UBPROP:0000012 "in FMA, this is part of the bony pectoral girdle, alongside the skeleton of pectoral girdle" xsd:string {external_ontology="FMA"} +relationship: RO:0002176 UBERON:0000976 ! connects humerus +relationship: RO:0002176 UBERON:0006849 ! connects scapula +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/a3/Gray327.png" xsd:anyURI +property_value: IAO:0000116 "note that in this ontology 'glenoid fossa' is a cavity (consistent with FMA) - consider adding a class for the surface of the scapula that is adjacent to this cavity, and making a more explicit connects relationship" xsd:string [Term] id: UBERON:0001471 @@ -175590,7 +174501,6 @@ subset: pheno_slim synonym: "foreskin of penis" EXACT [] synonym: "penis foreskin" EXACT [] synonym: "preputial skin" EXACT [] -xref: EV:0100109 xref: FMA:27648 xref: MA:0001744 xref: SCTID:39059001 @@ -175598,8 +174508,8 @@ xref: VHOG:0001342 is_a: UBERON:0001331 ! skin of penis intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0001332 ! prepuce of penis -relationship: contributes_to_morphology_of UBERON:0000989 ! penis relationship: part_of UBERON:0001332 ! prepuce of penis +relationship: RO:0002433 UBERON:0000989 ! contributes to morphology of penis [Term] id: UBERON:0001472 @@ -175619,7 +174529,7 @@ is_a: UBERON:0006876 ! vasculature of organ intersection_of: UBERON:0001593 ! venous plexus intersection_of: part_of UBERON:0000996 ! vagina relationship: part_of UBERON:0000996 ! vagina -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray589.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray589.png" xsd:anyURI [Term] id: UBERON:0001473 @@ -175641,10 +174551,8 @@ xref: EMAPA:35532 xref: FMA:30315 xref: MA:0000138 xref: MAT:0000443 -xref: MESH:D042601 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C33038 xref: SCTID:279089004 -xref: TAO:0005105 xref: UMLS:C0229889 {source="ncithesaurus:Lymphatic_Vessel"} xref: VHOG:0001249 xref: Wikipedia:Lymphatic_vessel @@ -175653,15 +174561,11 @@ is_a: UBERON:0000055 ! vessel intersection_of: UBERON:0000055 ! vessel intersection_of: part_of UBERON:0004536 ! lymph vasculature disjoint_from: UBERON:0001981 ! blood vessel -relationship: contributes_to_morphology_of UBERON:0002405 ! immune system relationship: has_part UBERON:0002391 ! lymph relationship: part_of UBERON:0004536 ! lymph vasculature -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/44/Illu_lymph_capillary.jpg" xsd:anyURI -property_value: RO:0002174 NCBITaxon:8342 {source="DOI:10.1152/japplphysiol.00201.2013"} -property_value: UBPROP:0000001 "A network of blunt ended vessels lacking direct connection to the blood vascular system. These vessels collect and drain fluids and macromolecules from interstitial spaces throughout the animal. They derive from a subpopulation of endothelial cells and have walls that are much thinner than the blood carrying vessels. Lymphatic vessels are usually classified as either superficial or deep.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005105", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "A vessel that contains or conveys lymph.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011005", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "Tetrapods have evolved distinct lymphatic systems, in which lymphatic capillaries help drain most of the tissues of the body.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001249", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.627", source="http://bgee.unil.ch/"} +relationship: RO:0002433 UBERON:0002405 ! contributes to morphology of immune system +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/44/Illu_lymph_capillary.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001474 @@ -175704,20 +174608,12 @@ xref: XAO:0000169 xref: ZFA:0001514 is_a: UBERON:0004765 ! skeletal element intersection_of: UBERON:0004765 ! skeletal element -intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue +intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue disjoint_from: UBERON:0001630 ! muscle organ disjoint_from: UBERON:0005090 ! muscle structure disjoint_from: UBERON:0010538 ! paired limb/fin segment -relationship: composed_primarily_of UBERON:0002481 {source="VSAO-modified"} ! bone tissue -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata -property_value: RO:0002171 UBERON:0001015 -property_value: RO:0002171 UBERON:0001630 -property_value: RO:0002171 UBERON:0002385 -property_value: UBPROP:0000001 "Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000047", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000001 "Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001514", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Skeletal element that is composed of bone tissue.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000057", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000002 "relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000047", ontology="AAO"} -property_value: UBPROP:0000003 "The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001190", ontology="VHOG", source="DOI:10.1159/000324245 Murdock DJ, Donoghue PC, Evolutionary Origins of Animal Skeletal Biomineralization. Cells Tissues Organs (2011)", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002473 UBERON:0002481 {source="VSAO-modified"} ! composed primarily of bone tissue [Term] id: UBERON:0001476 @@ -175748,25 +174644,25 @@ xref: UMLS:C0224234 {source="ncithesaurus:Deltoid"} xref: VHOG:0000846 xref: Wikipedia:Deltoid_muscle is_a: UBERON:0001482 {source="FMA"} ! muscle of shoulder +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0034908 ! scapular muscle intersection_of: UBERON:0014892 ! skeletal muscle organ, vertebrate -intersection_of: attaches_to UBERON:0000976 ! humerus -intersection_of: attaches_to UBERON:0001105 ! clavicle bone -intersection_of: attaches_to UBERON:0006849 ! scapula -relationship: attaches_to UBERON:0000976 ! humerus -relationship: attaches_to UBERON:0001105 ! clavicle bone -relationship: attaches_to UBERON:0002498 {source="FMA"} ! deltopectoral crest -relationship: develops_from UBERON:0006219 {source="EHDAA2"} ! deltoid pre-muscle mass -relationship: has_muscle_antagonist UBERON:0001112 {source="dbpedia"} ! latissimus dorsi muscle -relationship: has_muscle_insertion UBERON:0002498 {notes="deltoid tuberosity of humerus", source="dbpedia"} ! deltopectoral crest -relationship: has_muscle_origin UBERON:0001105 {notes="the anterior border and upper surface of the lateral third of the clavicle acromion spine of the scapula", source="dbpedia"} ! clavicle bone -relationship: has_muscle_origin UBERON:0002497 {notes="the anterior border and upper surface of the lateral third of the clavicle acromion spine of the scapula", source="dbpedia"} ! acromion -relationship: has_muscle_origin UBERON:0006849 {notes="the anterior border and upper surface of the lateral third of the clavicle acromion spine of the scapula", source="dbpedia"} ! scapula -relationship: innervated_by UBERON:0001493 {source="dbpedia"} ! axillary nerve +intersection_of: RO:0002371 UBERON:0000976 ! attached to humerus +intersection_of: RO:0002371 UBERON:0001105 ! attached to clavicle bone +intersection_of: RO:0002371 UBERON:0006849 ! attached to scapula relationship: part_of UBERON:0008713 {source="EHDAA2"} ! pectoral girdle and thoracic body wall skeletal muscle -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Deltoideus.png" xsd:anyURI -property_value: UBPROP:0000001 "Muscle which originates as three heads, the pars externalis, pars clavicularis, and pars scapularis. The pars externalis originates from the lateral border of the omosternum and inserts on the distal portion of the humerus. The pars clavicularis originates from the ventro-lateral surface of the clavicle and inserts on the deltoid crest of the humerus. The pars scapularis originates from the lateral surface of the clavicle and inserts on the deltoid crest of the humerus.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010716", ontology="AAO", source="AAO:MEJ"} +relationship: RO:0002005 UBERON:0001493 {source="dbpedia"} ! innervated_by axillary nerve +relationship: RO:0002202 UBERON:0006219 {source="EHDAA2"} ! develops from deltoid pre-muscle mass +relationship: RO:0002371 UBERON:0000976 ! attached to humerus +relationship: RO:0002371 UBERON:0001105 ! attached to clavicle bone +relationship: RO:0002371 UBERON:0002498 {source="FMA"} ! attached to deltopectoral crest +relationship: RO:0002372 UBERON:0001105 ! has muscle origin clavicle bone +relationship: RO:0002372 UBERON:0002497 ! has muscle origin acromion +relationship: RO:0002372 UBERON:0006849 ! has muscle origin scapula +relationship: RO:0002373 UBERON:0002498 ! has muscle insertion deltopectoral crest +relationship: RO:0002568 UBERON:0001112 {source="dbpedia"} ! has muscle antagonist latissimus dorsi muscle +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Deltoideus.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001479 @@ -175792,8 +174688,8 @@ xref: Wikipedia:Sesamoid_bone is_a: UBERON:0013630 {source="UBERON:cjm"} ! short bone is_a: UBERON:0013631 ! sesamoid element intersection_of: UBERON:0013631 ! sesamoid element -intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b3/Gray350.png" xsd:anyURI +intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b3/Gray350.png" xsd:anyURI [Term] id: UBERON:0001480 @@ -175808,8 +174704,8 @@ is_a: UBERON:0001435 ! carpal bone is_a: UBERON:0014395 ! proximal mesopodial bone is_a: UBERON:0015078 ! proximal carpal endochondral element intersection_of: UBERON:0015078 ! proximal carpal endochondral element -intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue -relationship: develops_from UBERON:0015079 ! proximal carpal cartilage +intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue +relationship: RO:0002202 UBERON:0015079 ! develops from proximal carpal cartilage [Term] id: UBERON:0001482 @@ -175825,11 +174721,11 @@ xref: FMA:33531 xref: MA:0000633 is_a: UBERON:0014892 ! skeletal muscle organ, vertebrate intersection_of: UBERON:0014892 ! skeletal muscle organ, vertebrate -intersection_of: attaches_to UBERON:0003461 ! shoulder bone -relationship: attaches_to UBERON:0003461 ! shoulder bone +intersection_of: RO:0002371 UBERON:0003461 ! attached to shoulder bone relationship: overlaps UBERON:0001467 ! shoulder relationship: part_of UBERON:0004476 {source="prolog"} ! musculature of shoulder -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002371 UBERON:0003461 ! attached to shoulder bone +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001483 @@ -175847,7 +174743,6 @@ is_a: UBERON:0000014 ! zone of skin intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0001467 ! shoulder relationship: part_of UBERON:0001467 ! shoulder -property_value: UBPROP:0000012 "in MA this is a subclass of forelimb skin, but this violates part-disjointness in Uberon" xsd:string {external_ontology="MA"} [Term] id: UBERON:0001484 @@ -175875,12 +174770,11 @@ xref: Wikipedia:Articular_capsule is_a: UBERON:0000094 ! membrane organ intersection_of: UBERON:0000094 ! membrane organ intersection_of: has_part UBERON:0007616 ! layer of synovial tissue -intersection_of: surrounds UBERON:0002217 ! synovial joint +intersection_of: RO:0002221 UBERON:0002217 ! surrounds synovial joint relationship: has_part UBERON:0007616 ! layer of synovial tissue -relationship: surrounds UBERON:0002217 ! synovial joint -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Joint.png" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/4a/Gray299.png" xsd:anyURI -property_value: UBPROP:0000012 "check ncita" xsd:string {external_ontology="ncit"} +relationship: RO:0002221 UBERON:0002217 ! surrounds synovial joint +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Joint.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4a/Gray299.png" xsd:anyURI [Term] id: UBERON:0001485 @@ -175908,16 +174802,16 @@ xref: Wikipedia:Knee is_a: UBERON:0003840 ! hindlimb joint is_a: UBERON:0011139 ! synovial limb joint intersection_of: UBERON:0000982 ! skeletal joint -intersection_of: connects UBERON:0000979 ! tibia -intersection_of: connects UBERON:0000981 ! femur -intersection_of: connects UBERON:0002446 ! patella -relationship: connects UBERON:0000979 ! tibia -relationship: connects UBERON:0000981 ! femur -relationship: connects UBERON:0002446 ! patella -relationship: develops_from UBERON:0006256 {evidence="definitional"} ! knee joint primordium +intersection_of: RO:0002176 UBERON:0000979 ! connects tibia +intersection_of: RO:0002176 UBERON:0000981 ! connects femur +intersection_of: RO:0002176 UBERON:0002446 ! connects patella relationship: part_of UBERON:0001465 ! knee -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/ca/Knee.agr.jpg" xsd:anyURI +relationship: RO:0002176 UBERON:0000979 ! connects tibia +relationship: RO:0002176 UBERON:0000981 ! connects femur +relationship: RO:0002176 UBERON:0002446 ! connects patella +relationship: RO:0002202 UBERON:0006256 ! develops from knee joint primordium +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/ca/Knee.agr.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001487 @@ -175945,8 +174839,7 @@ is_a: UBERON:0011139 ! synovial limb joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: part_of UBERON:0002387 ! pes relationship: part_of UBERON:0002387 ! pes -property_value: editor_note "TODO check FMA - use the set class for now" xsd:string -property_value: UBPROP:0000202 FMA:71349 +property_value: IAO:0000116 "TODO check FMA - use the set class for now" xsd:string [Term] id: UBERON:0001488 @@ -175976,15 +174869,14 @@ xref: Wikipedia:Ankle is_a: UBERON:0003840 ! hindlimb joint is_a: UBERON:0011139 ! synovial limb joint intersection_of: UBERON:0000982 ! skeletal joint -intersection_of: connects UBERON:0001445 ! skeleton of pes -intersection_of: connects UBERON:0010720 ! hindlimb zeugopod skeleton -relationship: connects UBERON:0000979 {gci_relation="part_of", gci_filler="NCBITaxon:9606"} ! tibia -relationship: connects UBERON:0001445 ! skeleton of pes -relationship: connects UBERON:0001446 {gci_relation="part_of", gci_filler="NCBITaxon:9606"} ! fibula -relationship: connects UBERON:0010720 ! hindlimb zeugopod skeleton +intersection_of: RO:0002176 UBERON:0001445 ! connects skeleton of pes +intersection_of: RO:0002176 UBERON:0010720 ! connects hindlimb zeugopod skeleton relationship: overlaps UBERON:0002387 ! pes -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/b/bf/Ankle_en.svg" xsd:anyURI -property_value: UBPROP:0000008 "todo - accurately represent different types of ankle joint" xsd:string +relationship: RO:0002176 UBERON:0000979 {gci_relation="part_of", gci_filler="NCBITaxon:9606"} ! connects tibia +relationship: RO:0002176 UBERON:0001445 ! connects skeleton of pes +relationship: RO:0002176 UBERON:0001446 {gci_relation="part_of", gci_filler="NCBITaxon:9606"} ! connects fibula +relationship: RO:0002176 UBERON:0010720 ! connects hindlimb zeugopod skeleton +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/b/bf/Ankle_en.svg" xsd:anyURI [Term] id: UBERON:0001489 @@ -176008,8 +174900,7 @@ is_a: UBERON:0011139 ! synovial limb joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: part_of UBERON:0002398 ! manus relationship: part_of UBERON:0002398 ! manus -property_value: editor_note "TODO check FMA - use the set class for now" xsd:string -property_value: UBPROP:0000202 FMA:71345 +property_value: IAO:0000116 "TODO check FMA - use the set class for now" xsd:string [Term] id: UBERON:0001490 @@ -176036,13 +174927,12 @@ xref: Wikipedia:Elbow is_a: UBERON:0003839 ! forelimb joint is_a: UBERON:0011139 ! synovial limb joint intersection_of: UBERON:0000982 ! skeletal joint -intersection_of: connects UBERON:0000976 ! humerus -intersection_of: connects UBERON:0010703 ! forelimb zeugopod skeleton -relationship: connects UBERON:0000976 ! humerus -relationship: connects UBERON:0010703 ! forelimb zeugopod skeleton -relationship: develops_from UBERON:0006224 {evidence="definitional"} ! elbow joint primordium +intersection_of: RO:0002176 UBERON:0000976 ! connects humerus +intersection_of: RO:0002176 UBERON:0010703 ! connects forelimb zeugopod skeleton relationship: part_of UBERON:0001461 ! elbow -property_value: UBPROP:0000008 "In human anatomy, the elbow joint is a compound joint that actually comprises three separate joints: the joints connecting the upper and lower arm: 1) Articulatio humero-ulnaris and 2) Articulatio humero-radialis as well as the proximal joint connecting the forarm bones: 3) Articulatio radio-ulnaris proximalis" xsd:string {source="HP"} +relationship: RO:0002176 UBERON:0000976 ! connects humerus +relationship: RO:0002176 UBERON:0010703 ! connects forelimb zeugopod skeleton +relationship: RO:0002202 UBERON:0006224 ! develops from elbow joint primordium [Term] id: UBERON:0001491 @@ -176054,7 +174944,6 @@ synonym: "carpal region joint" EXACT [OBOL:automatic] synonym: "joint of carpal region" EXACT [OBOL:automatic] synonym: "joint of wrist" EXACT [] synonym: "radiocarpal joint" NARROW INCONSISTENT [FMA:35291] -xref: EMAPA:19205 xref: FMA:321842 xref: GAID:274 xref: galen:WristJoint @@ -176066,13 +174955,12 @@ xref: UMLS:C1322271 {source="ncithesaurus:Wrist_Joint"} xref: Wikipedia:Wrist is_a: UBERON:0001489 ! manus joint intersection_of: UBERON:0000982 ! skeletal joint -intersection_of: connects UBERON:0009880 ! carpal skeleton -intersection_of: connects UBERON:0010703 ! forelimb zeugopod skeleton -relationship: connects UBERON:0009880 ! carpal skeleton -relationship: connects UBERON:0010703 ! forelimb zeugopod skeleton +intersection_of: RO:0002176 UBERON:0009880 ! connects carpal skeleton +intersection_of: RO:0002176 UBERON:0010703 ! connects forelimb zeugopod skeleton relationship: part_of UBERON:0004452 ! carpal region -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/4/4a/Human_wrist.png" xsd:anyURI -property_value: UBPROP:0000012 "in FMA this includes radio-carpal and radio-ulnar *ligaments*" xsd:string {external_ontology="FMA"} +relationship: RO:0002176 UBERON:0009880 ! connects carpal skeleton +relationship: RO:0002176 UBERON:0010703 ! connects forelimb zeugopod skeleton +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/4/4a/Human_wrist.png" xsd:anyURI [Term] id: UBERON:0001493 @@ -176093,11 +174981,11 @@ xref: SCTID:181009006 xref: UMLS:C0228885 {source="ncithesaurus:Axillary_Nerve"} xref: Wikipedia:Axillary_nerve is_a: UBERON:0003433 ! arm nerve -relationship: innervates UBERON:0009472 ! axilla relationship: part_of UBERON:0001814 {source="MA"} ! brachial nerve plexus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/ea/Brachial_plexus_2.svg" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/d/d4/Brachial_plexus.jpg" xsd:anyURI +relationship: RO:0002134 UBERON:0009472 ! innervates axilla +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ea/Brachial_plexus_2.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/d4/Brachial_plexus.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001495 @@ -176128,11 +175016,11 @@ xref: NCIT:C33286 xref: SCTID:181621006 xref: UMLS:C0030747 {source="ncithesaurus:Pectoralis_Muscle"} is_a: UBERON:0003830 ! thoracic segment muscle +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0008196 {source="FMA"} ! muscle of pectoral girdle -relationship: develops_from UBERON:0010984 ! pectoral pre-muscle mass -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/6/6c/Pectoralis_major.png" xsd:anyURI -property_value: UBPROP:0000001 "Muscle which is comprised of three heads. The anterior head is the portio epicoracoidea that originates on the epicoracoid cartilage and inserts on the deltoid crest of the humerus. The next more posterior head, portio sternalis, originates on the sternum and inserts in the groove next to the deltoid crest of the humerus. The most posterior head, portio abdominalis, arises from the M. rectus abdominis and inserts on the deltoid crest of the humerus.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010727", ontology="AAO", source="AAO:MEJ"} +relationship: RO:0002202 UBERON:0010984 ! develops from pectoral pre-muscle mass +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/6c/Pectoralis_major.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001496 @@ -176156,15 +175044,15 @@ xref: SCTID:181299009 xref: UMLS:C0003956 {source="ncithesaurus:Ascending_Aorta"} xref: Wikipedia:Ascending_aorta is_a: UBERON:0001515 ! thoracic aorta -relationship: contributes_to_morphology_of UBERON:0001515 ! thoracic aorta -relationship: develops_from UBERON:0005338 {source="EHDAA2"} ! outflow tract aortic component -relationship: has_developmental_contribution_from UBERON:0002061 ! truncus arteriosus -relationship: has_developmental_contribution_from UBERON:0005432 ! aortic sac relationship: part_of UBERON:0001515 ! thoracic aorta -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +relationship: RO:0002202 UBERON:0005338 {source="EHDAA2"} ! develops from outflow tract aortic component +relationship: RO:0002254 UBERON:0002061 ! has developmental contribution from truncus arteriosus +relationship: RO:0002254 UBERON:0005432 ! has developmental contribution from aortic sac +relationship: RO:0002433 UBERON:0001515 ! contributes to morphology of thoracic aorta +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001497 @@ -176181,7 +175069,6 @@ synonym: "pelvic girdle muscle" EXACT [] synonym: "pelvic girdle muscle organ" EXACT [OBOL:automatic] synonym: "pelvic girdle skeletal muscle" EXACT [EMAPA:18185] xref: EHDAA:8326 -xref: EMAPA:18184 xref: EMAPA:18185 xref: FMA:37367 xref: MA:0000537 @@ -176191,7 +175078,6 @@ is_a: UBERON:0010890 ! pelvic complex muscle intersection_of: UBERON:0014892 ! skeletal muscle organ, vertebrate intersection_of: part_of UBERON:0001271 ! pelvic girdle region relationship: part_of UBERON:0004470 {source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! musculature of pelvic girdle -property_value: UBPROP:0000012 "Note that in MA, this is a subclass of pelvis muscle; in FMA this is a hindlimb muscle, but recall in FMA hindlimb includes the girdle." xsd:string {external_ontology="MA"} [Term] id: UBERON:0001498 @@ -176234,8 +175120,7 @@ is_a: UBERON:0003662 ! forelimb muscle intersection_of: UBERON:0014892 ! skeletal muscle organ, vertebrate intersection_of: part_of UBERON:0001460 ! arm relationship: part_of UBERON:0004474 {source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! musculature of arm -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000013 "See notes on UBERON:0001460 for possible terminological confusion over term 'arm'. MA uses this consistent with uberon (forelimb muscle is subdivided into shoulder, arm and hand)" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001500 @@ -176256,7 +175141,7 @@ is_a: UBERON:0003662 ! forelimb muscle intersection_of: UBERON:0014892 ! skeletal muscle organ, vertebrate intersection_of: part_of UBERON:0002398 ! manus relationship: part_of UBERON:0004489 {source="prolog"} ! musculature of manus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001508 @@ -176280,20 +175165,16 @@ xref: SCTID:181300001 xref: VHOG:0001196 xref: Wikipedia:Arch_of_aorta is_a: UBERON:0001515 ! thoracic aorta -relationship: connected_to UBERON:0001496 ! ascending aorta -relationship: contributes_to_morphology_of UBERON:0001515 ! thoracic aorta -relationship: develops_from UBERON:0003121 {notes="left arch 4 in human", source="embryology.ch"} ! pharyngeal arch artery 4 -relationship: has_developmental_contribution_from UBERON:0005432 ! aortic sac -relationship: has_developmental_contribution_from UBERON:0005613 ! left dorsal aorta relationship: part_of UBERON:0001515 ! thoracic aorta -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI -property_value: IAO:0000232 "Do not confuse with aortic arch" xsd:string -property_value: UBPROP:0000001 "The curving portion between the ascending aorta and the descending aorta, giving rise to the brachiocephalic trunk, the left common carotid artery, and the left subclavian artery. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001196", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/arch+of+aorta"} -property_value: UBPROP:0000003 "The double systemic arch arches (left and right) present in amphibians and reptiles become reduced to a single systemic arch - the right in birds, the left in mammals.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001196", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.460 and p.461 Figure 12.20", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "birds have right aortic arch, mammals left." xsd:string +relationship: RO:0002170 UBERON:0001496 ! connected to ascending aorta +relationship: RO:0002202 UBERON:0003121 ! develops from pharyngeal arch artery 4 +relationship: RO:0002254 UBERON:0005432 ! has developmental contribution from aortic sac +relationship: RO:0002254 UBERON:0005613 ! has developmental contribution from left dorsal aorta +relationship: RO:0002433 UBERON:0001515 ! contributes to morphology of thoracic aorta +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001510 @@ -176322,8 +175203,6 @@ def: "A zone of skin that is part of a leg [Automatically generated definition]. synonym: "leg skin" EXACT [] synonym: "leg zone of skin" EXACT [OBOL:automatic] synonym: "zone of skin of leg" EXACT [OBOL:automatic] -xref: EMAPA:18156 -xref: EMAPA:18159 xref: EMAPA:37352 {source="MA:th"} xref: FMA:37828 xref: MA:0000674 @@ -176393,17 +175272,15 @@ xref: NCIT:C32455 xref: SCTID:261399002 xref: UMLS:C0011666 {source="ncithesaurus:Descending_Aorta"} xref: Wikipedia:Descending_aorta -is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005800 {source="FMA"} ! section of aorta -relationship: connected_to UBERON:0001508 ! arch of aorta -relationship: develops_from UBERON:0005805 {source="Wikipedia"} ! dorsal aorta -relationship: has_developmental_contribution_from UBERON:0005613 ! left dorsal aorta -relationship: has_developmental_contribution_from UBERON:0005622 ! right dorsal aorta -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI -property_value: UBPROP:0000011 "results from fusion of left and right dorsal aortae" xsd:string +relationship: RO:0002170 UBERON:0001508 ! connected to arch of aorta +relationship: RO:0002202 UBERON:0005805 {source="Wikipedia"} ! develops from dorsal aorta +relationship: RO:0002254 UBERON:0005613 ! has developmental contribution from left dorsal aorta +relationship: RO:0002254 UBERON:0005622 ! has developmental contribution from right dorsal aorta +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001515 @@ -176432,9 +175309,9 @@ xref: Wikipedia:Thoracic_aorta is_a: UBERON:0005800 {source="FMA"} ! section of aorta intersection_of: UBERON:0005800 ! section of aorta intersection_of: part_of UBERON:0000915 ! thoracic segment of trunk -relationship: contributes_to_morphology_of UBERON:0000947 ! aorta relationship: part_of UBERON:0000915 ! thoracic segment of trunk -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/75/Gray530.png" xsd:anyURI +relationship: RO:0002433 UBERON:0000947 ! contributes to morphology of aorta +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/75/Gray530.png" xsd:anyURI [Term] id: UBERON:0001516 @@ -176464,13 +175341,13 @@ xref: SCTID:244231007 xref: UMLS:C0003484 {source="ncithesaurus:Abdominal_Aorta"} xref: Wikipedia:Abdominal_aorta is_a: UBERON:0005800 ! section of aorta -relationship: connected_to UBERON:0002345 ! descending thoracic aorta -relationship: contributes_to_morphology_of UBERON:0001514 ! descending aorta relationship: overlaps UBERON:0000916 ! abdomen relationship: part_of UBERON:0001514 {source="FMA"} ! descending aorta -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/af/Gray531.png" xsd:anyURI -property_value: editor_note "Many of the branches of the abdominal aorta in mammals may be branches of the dorsal aorta in other vertebrates" xsd:string +relationship: RO:0002170 UBERON:0002345 ! connected to descending thoracic aorta +relationship: RO:0002433 UBERON:0001514 ! contributes to morphology of descending aorta +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/af/Gray531.png" xsd:anyURI +property_value: IAO:0000116 "Many of the branches of the abdominal aorta in mammals may be branches of the dorsal aorta in other vertebrates" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001517 @@ -176565,12 +175442,12 @@ xref: UMLS:C0006094 {source="ncithesaurus:Innominate_Artery"} xref: Wikipedia:Brachiocephalic_artery is_a: UBERON:0004573 ! systemic artery relationship: channels_from UBERON:0001508 ! arch of aorta -relationship: connected_to UBERON:0001508 ! arch of aorta relationship: part_of UBERON:0007204 ! brachiocephalic vasculature -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +relationship: RO:0002170 UBERON:0001508 ! connected to arch of aorta +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001530 @@ -176599,14 +175476,12 @@ xref: UMLS:C0162859 {source="ncithesaurus:Common_Carotid_Artery"} xref: VHOG:0000272 xref: Wikipedia:Common_carotid_artery is_a: UBERON:0004573 {source="FMA"} ! systemic artery -relationship: connected_to UBERON:0001508 ! arch of aorta -relationship: develops_from UBERON:0004363 {source="Wikipedia"} ! pharyngeal arch artery -relationship: existence_starts_during UBERON:0000068 ! embryo stage -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI -property_value: editor_note "we follow the FMA and treat the artery as a tree-structure - here we include the internal and external as parts. For the part that excludes the branches, see 'trunk of common carotid artery'" xsd:string -property_value: IAO:0000232 "This class represents the adult and developing structures'" xsd:string -property_value: UBPROP:0000011 "in birds and reptiles, develops from arch III and parts of ventral and dorsal aortae" xsd:string +relationship: RO:0002170 UBERON:0001508 ! connected to arch of aorta +relationship: RO:0002202 UBERON:0004363 {source="Wikipedia"} ! develops from pharyngeal arch artery +relationship: RO:0002488 UBERON:0000068 ! existence starts during embryo stage +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI +property_value: IAO:0000116 "we follow the FMA and treat the artery as a tree-structure - here we include the internal and external as parts. For the part that excludes the branches, see 'trunk of common carotid artery'" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001531 @@ -176626,11 +175501,10 @@ xref: SCTID:362042003 xref: UMLS:C0226086 {source="ncithesaurus:Right_Common_Carotid_Artery"} xref: Wikipedia:Right_common_carotid_artery is_a: UBERON:0001530 {source="FMA"} ! common carotid artery plus branches -relationship: branching_part_of UBERON:0001529 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="FMA"} ! brachiocephalic artery -relationship: connected_to UBERON:0001529 ! brachiocephalic artery -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI -property_value: UBPROP:0000012 "placement of the MA class here is not strictly correct, as the MA class does not include the branches" xsd:string +relationship: RO:0002170 UBERON:0001529 ! connected to brachiocephalic artery +relationship: RO:0002380 UBERON:0001529 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="FMA"} ! branching part of brachiocephalic artery +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001532 @@ -176668,14 +175542,12 @@ xref: XAO:0000366 xref: ZFA:0005081 is_a: UBERON:0003496 ! head blood vessel is_a: UBERON:0005396 {source="MA"} ! carotid artery segment -relationship: branching_part_of UBERON:0001530 {source="FMA"} ! common carotid artery plus branches -relationship: develops_from UBERON:2001053 {source="cjm"} ! future internal carotid artery -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: supplies UBERON:0000955 ! brain -relationship: supplies UBERON:0000970 ! eye -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/9c/Gray513.png" xsd:anyURI -property_value: UBPROP:0000001 "Each of two arteries starting at the bifurcation of the common carotid arteries through which blood circulates to many structures and organs in the head. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000267", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/Internal+carotid+artery"} -property_value: UBPROP:0000001 "One of the major arteries of the head, it is the as the cranial continuation of the aortic arches and the dorsal aorta. It curves ventrally before resuming a dorsal course as it enters the head proper, and it lies ventral to the internal jugular vein. The internal carotid artery gives off palatine, ophthalmic, and cerebral branches by stage NF stage 41.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011054", ontology="AAO", source="PMID:12606281"} +relationship: RO:0002178 UBERON:0000955 ! supplies brain +relationship: RO:0002178 UBERON:0000970 ! supplies eye +relationship: RO:0002202 UBERON:2001053 {source="cjm"} ! develops from future internal carotid artery +relationship: RO:0002380 UBERON:0001530 {source="FMA"} ! branching part of common carotid artery plus branches +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/9c/Gray513.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001533 @@ -176708,19 +175580,15 @@ xref: UMLS:C0038530 {source="ncithesaurus:Subclavian_Artery"} xref: Wikipedia:Subclavian_artery xref: XAO:0000365 xref: ZFA:0005086 -is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004573 ! systemic artery -relationship: connected_to UBERON:0001508 ! arch of aorta -relationship: develops_from UBERON:0002457 {source="EHDAA2"} ! intersomitic artery -relationship: develops_from UBERON:0005622 {source="EHDAA2"} ! right dorsal aorta relationship: overlaps UBERON:0000915 ! thoracic segment of trunk -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: supplies UBERON:0004710 ! pectoral appendage -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI -property_value: editor_note "Developmental relationships should be added (intersegmental artery and right dorsal aorta in EHDAA2, occipitovertebral artery in XAO)" xsd:string -property_value: UBPROP:0000001 "Artery which supplies blood via branches to the various muscles of the shoulder region and to the forelimb.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010232", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "In human anatomy, the subclavian artery is a major artery of the upper thorax that mainly supplies blood to the head and arms. It is located below the clavicle, hence the name. There is a left subclavian and a right subclavian. On the left side of the body, the subclavian comes directly off the arch of aorta. On the right side of the body, the subclavian arises from the relatively short brachiocephalic artery (trunk) when it bifurcates into the subclavian and the right common carotid artery. The usual branches of the subclavian on both sides of the body are the vertebral artery, the internal thoracic artery, the thyrocervical trunk, the costocervical trunk and the dorsal scapular artery. The subclavian becomes the axillary artery at the lateral border of the first rib[WP]" xsd:string {source="Wikipedia:Subclavian_artery"} -property_value: UBPROP:0000001 "The pectoral (subclavian) arteries originate from the dorsal aorta and takes the blood outward into the fin from the paired portion of the dorsal aorta posterior to the last aortic arch. Kimmel et al. 1993[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005086", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002170 UBERON:0001508 ! connected to arch of aorta +relationship: RO:0002178 UBERON:0004710 ! supplies pectoral appendage +relationship: RO:0002202 UBERON:0002457 {source="EHDAA2"} ! develops from intersomitic artery +relationship: RO:0002202 UBERON:0005622 {source="EHDAA2"} ! develops from right dorsal aorta +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI +property_value: IAO:0000116 "Developmental relationships should be added (intersegmental artery and right dorsal aorta in EHDAA2, occipitovertebral artery in XAO)" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001534 @@ -176740,16 +175608,14 @@ xref: SCTID:244246000 xref: UMLS:C0226261 {source="ncithesaurus:Right_Subclavian_Artery"} xref: Wikipedia:Subclavian_artery is_a: UBERON:0001533 ! subclavian artery +is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0001533 ! subclavian artery -intersection_of: in_right_side_of UBERON:0000468 ! multicellular organism -relationship: branching_part_of UBERON:0001529 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="FMA"} ! brachiocephalic artery -relationship: connected_to UBERON:0001529 ! brachiocephalic artery -relationship: develops_from UBERON:0003121 {gci_relation="part_of", gci_filler="NCBITaxon:40674", notes="right arch 4 in human", source="embryology.ch"} ! pharyngeal arch artery 4 -relationship: in_right_side_of UBERON:0000468 ! multicellular organism -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI -property_value: UBPROP:0000008 "in humans, arises from the relatively short brachiocephalic artery (trunk) when it bifurcates into the subclavian and the right common carotid artery" xsd:string -property_value: UBPROP:0000011 "proximal part arises from right 4th aortic arch in humans" xsd:string +intersection_of: BSPO:0000121 UBERON:0000468 ! multicellular organism +relationship: BSPO:0000121 UBERON:0000468 ! multicellular organism +relationship: RO:0002170 UBERON:0001529 ! connected to brachiocephalic artery +relationship: RO:0002380 UBERON:0001529 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="FMA"} ! branching part of brachiocephalic artery +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001536 @@ -176769,11 +175635,10 @@ xref: SCTID:362043008 xref: UMLS:C0226087 {source="ncithesaurus:Left_Common_Carotid_Artery"} xref: Wikipedia:Left_common_carotid_artery is_a: UBERON:0001530 {source="FMA"} ! common carotid artery plus branches -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI -property_value: UBPROP:0000012 "placement of the MA class here is not strictly correct, as the MA class does not include the branches" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001544 @@ -176795,9 +175660,9 @@ xref: UMLS:C0032652 {source="ncithesaurus:Popliteal_Vein"} xref: Wikipedia:Popliteal_vein is_a: UBERON:0001638 ! vein relationship: overlaps UBERON:0001465 ! knee -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: tributary_of UBERON:0001361 {source="FMA/obol"} ! femoral vein -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray609.png" xsd:anyURI +relationship: RO:0002376 UBERON:0001361 {source="FMA/obol"} ! tributary of femoral vein +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray609.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001545 @@ -176816,10 +175681,10 @@ xref: SCTID:281066000 xref: UMLS:C0226833 {source="ncithesaurus:Anterior_Tibial_Vein"} xref: Wikipedia:Anterior_tibial_vein is_a: UBERON:0010370 {source="MA"} ! tibial vein -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: tributary_of UBERON:0001361 {source="FMA/obol"} ! femoral vein -relationship: tributary_of UBERON:0001544 {source="FMA/obol"} ! popliteal vein -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/4/4e/Gray440_color.png" xsd:anyURI +relationship: RO:0002376 UBERON:0001361 {source="FMA/obol"} ! tributary of femoral vein +relationship: RO:0002376 UBERON:0001544 {source="FMA/obol"} ! tributary of popliteal vein +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/4/4e/Gray440_color.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001547 @@ -176841,9 +175706,9 @@ xref: SCTID:181404009 xref: UMLS:C0226827 {source="ncithesaurus:Short_Saphenous_Vein"} xref: Wikipedia:Small_saphenous_vein is_a: UBERON:0007318 ! saphenous vein -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: tributary_of UBERON:0001544 {source="FMA"} ! popliteal vein -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/62/Gray582.png" xsd:anyURI +relationship: RO:0002376 UBERON:0001544 {source="FMA"} ! tributary of popliteal vein +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/62/Gray582.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001549 @@ -176861,10 +175726,10 @@ xref: UMLS:C0835053 {source="ncithesaurus:Dorsal_Metatarsal_Vein"} xref: Wikipedia:Dorsal_metatarsal_veins is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein -intersection_of: drains UBERON:0000983 ! metatarsus region -relationship: drains UBERON:0000983 ! metatarsus region -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: tributary_of UBERON:0008783 ! dorsal venous arch +intersection_of: RO:0002179 UBERON:0000983 ! drains metatarsus region +relationship: RO:0002179 UBERON:0000983 ! drains metatarsus region +relationship: RO:0002376 UBERON:0008783 ! tributary of dorsal venous arch +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001550 @@ -176880,8 +175745,8 @@ xref: FMA:44420 xref: MA:0002171 xref: Wikipedia:Medial_marginal_vein is_a: UBERON:0001638 ! vein -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: tributary_of UBERON:0001363 {source="FMA/obol"} ! great saphenous vein +relationship: RO:0002376 UBERON:0001363 {source="FMA/obol"} ! tributary of great saphenous vein +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001552 @@ -176899,10 +175764,10 @@ xref: MA:0002583 xref: Wikipedia:Arcuate_arteries_of_the_kidney is_a: UBERON:0001637 ! artery is_a: UBERON:0003644 ! kidney arterial blood vessel -relationship: connecting_branch_of UBERON:0009885 ! interlobar artery relationship: part_of UBERON:0001225 {source="MA"} ! cortex of kidney -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/87/2610_The_Kidney.jpg" xsd:anyURI +relationship: RO:0002252 UBERON:0009885 ! connecting branch of interlobar artery +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/87/2610_The_Kidney.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001554 @@ -176924,7 +175789,6 @@ is_a: UBERON:0000014 ! zone of skin intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0001464 ! hip relationship: part_of UBERON:0001464 ! hip -property_value: UBPROP:0000012 "in MA this isa hindlimb skin" xsd:string {external_ontology="MA"} [Term] id: UBERON:0001555 @@ -176948,11 +175812,9 @@ xref: BTO:0000545 xref: EHDAA2:0000726 xref: EHDAA:518 xref: EMAPA:16247 -xref: FBbt:00003125 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45615 xref: galen:AlimentaryTract xref: MA:0000917 -xref: MESH:D041981 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: NCIT:C34082 xref: TAO:0000112 xref: TGMA:0001819 @@ -176961,18 +175823,13 @@ xref: VHOG:0000309 xref: WBbt:0005743 xref: ZFA:0000112 is_a: UBERON:0000025 ! tube -relationship: connects UBERON:0000165 ! mouth -relationship: immediate_transformation_of UBERON:0007026 {source="NCBIBook:NBK10107"} ! presumptive gut -relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} -relationship: never_in_taxon NCBITaxon:41324 {source="DOI:10.1371/journal.pone.0016309"} -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0001007 ! digestive system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000001 "The alimentary or digestive tract, and associated organs.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000112", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000309", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "FMA also has a term 'gastrointestinal tract', but this includes the liver." xsd:string {external_ontology="FMA"} -property_value: UBPROP:0000012 "we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509" xsd:string {external_ontology="MA"} -property_value: UBPROP:0000013 "we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002176 UBERON:0000165 ! connects mouth +relationship: RO:0002495 UBERON:0007026 {source="NCBIBook:NBK10107"} ! immediate transformation of presumptive gut +property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} +property_value: RO:0002161 NCBITaxon:41324 {source="DOI:10.1371/journal.pone.0016309"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001556 @@ -176990,7 +175847,7 @@ is_a: UBERON:0011216 ! organ system subdivision relationship: has_part UBERON:0000057 ! urethra relationship: has_part UBERON:0001255 ! urinary bladder relationship: part_of UBERON:0001008 ! renal system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001557 @@ -177009,11 +175866,9 @@ xref: VHOG:0000406 xref: Wikipedia:Upper_respiratory_tract is_a: UBERON:0000072 ! proximo-distal subdivision of respiratory tract relationship: has_part UBERON:0000004 ! nose -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/9f/Illu_conducting_passages.svg" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c3/Illu_conducting_passages.jpg" xsd:anyURI -property_value: RO:0002171 UBERON:0001558 -property_value: UBPROP:0000012 "Some specify that the glottis (vocal cords) is the defining line between the upper and lower respiratory tracts;[2] yet even others make the line at the cricoid cartilage. The FMA includes nose, nasopharynx, oropharynx and larynx[WP]" xsd:string {external_ontology="FMA"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/9f/Illu_conducting_passages.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c3/Illu_conducting_passages.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001558 @@ -177033,9 +175888,9 @@ xref: VHOG:0000382 xref: Wikipedia:Lower_respiratory_tract is_a: UBERON:0000072 ! proximo-distal subdivision of respiratory tract relationship: has_part UBERON:0000170 ! pair of lungs -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/9f/Illu_conducting_passages.svg" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c3/Illu_conducting_passages.jpg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/9f/Illu_conducting_passages.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c3/Illu_conducting_passages.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001560 @@ -177045,7 +175900,7 @@ subset: non_informative synonym: "organ neck" EXACT [] xref: FMA:45733 is_a: UBERON:0034944 {source="FMA"} ! zone of organ -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0001568 @@ -177071,12 +175926,13 @@ xref: UMLS:C0023054 {source="ncithesaurus:Laryngeal_Muscle"} xref: Wikipedia:Muscles_of_larynx is_a: UBERON:0002377 ! muscle of neck is_a: UBERON:0003831 ! respiratory system muscle +is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0014892 ! skeletal muscle organ, vertebrate intersection_of: part_of UBERON:0001737 ! larynx -relationship: contributes_to_morphology_of UBERON:0001015 ! musculature -relationship: contributes_to_morphology_of UBERON:0001737 ! larynx relationship: part_of UBERON:0004478 {source="prolog"} ! musculature of larynx -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002433 UBERON:0001015 ! contributes to morphology of musculature +relationship: RO:0002433 UBERON:0001737 ! contributes to morphology of larynx +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001571 @@ -177101,17 +175957,11 @@ xref: VHOG:0000847 xref: Wikipedia:Genioglossus_muscle is_a: UBERON:0001575 {source="FMA"} ! extrinsic muscle of tongue is_a: UBERON:0004120 ! mesoderm-derived structure -relationship: develops_from UBERON:0010059 {source="EHDAA2"} ! hypoglossal cord -relationship: has_muscle_insertion UBERON:0009471 {source="Wikipedia"} ! dorsum of tongue -relationship: has_muscle_origin UBERON:0006606 ! mandibular symphysis -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/7e/Genioglossus.png" xsd:anyURI -property_value: UBPROP:0000001 "Either of a pair of lingual muscles with origin in the mandible, with insertion to the lingual fascia below the mucous membrane and epiglottis, with nerve supply from the hypoglossal nerve, and whose action depresses and protrudes the tongue. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000847", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/genioglossus"} -property_value: UBPROP:0000001 "Makes up bulk of tongue in frogs and salamanders; makes up entire tongue in caecilians.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010660", ontology="AAO", source="AAO:BMZ"} -property_value: UBPROP:0000001 "see Intrinsic Tongue.[FEED]" xsd:string {date_retrieved="2012-07-02", ontology="FEED", url="http://www.feedexp.org"} -property_value: UBPROP:0000002 "relationship loss: subclass hyobranchial muscles (AAO:0000224)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010660", ontology="AAO"} -property_value: UBPROP:0000003 "The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000847", ontology="VHOG", source="DOI:10.1002/dvdy.20587, DOI:10.1186/1471-213X-8-24 Table 7", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "Makes up bulk of tongue in frogs and salamanders; makes up entire tongue in caecilians." xsd:string {source="AAO:0010660"} +relationship: RO:0002202 UBERON:0010059 {source="EHDAA2"} ! develops from hypoglossal cord +relationship: RO:0002372 UBERON:0006606 ! has muscle origin mandibular symphysis +relationship: RO:0002373 UBERON:0009471 {source="Wikipedia"} ! has muscle insertion dorsum of tongue +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7e/Genioglossus.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001572 @@ -177133,18 +175983,15 @@ xref: UMLS:C0224196 {source="ncithesaurus:Hyoglossus_Muscle"} xref: Wikipedia:Hyoglossus_muscle is_a: UBERON:0001575 {source="FMA"} ! extrinsic muscle of tongue intersection_of: UBERON:0014892 ! skeletal muscle organ, vertebrate -intersection_of: attaches_to UBERON:0001685 ! hyoid bone -intersection_of: attaches_to UBERON:0001723 ! tongue -intersection_of: innervated_by UBERON:0001650 ! hypoglossal nerve -relationship: attaches_to UBERON:0001685 ! hyoid bone -relationship: attaches_to UBERON:0001723 ! tongue -relationship: has_muscle_insertion UBERON:0001723 ! tongue -relationship: has_muscle_origin UBERON:0001685 {notes="lingual process in horse", source="dbpedia"} ! hyoid bone -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/7e/Hyoglossus.png" xsd:anyURI -property_value: UBPROP:0000001 "Makes up part of the tongue in frogs and salamanders.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010663", ontology="AAO", source="AAO:BMZ"} -property_value: UBPROP:0000001 "The hyoglossus is a muscle that attaches to the hyoid and tongue and is innervated by Cranial Nerve XII.[FEED]" xsd:string {date_retrieved="2012-07-02", ontology="FEED", url="http://www.feedexp.org"} -property_value: UBPROP:0000002 "relationship loss: subclass hyobranchial muscles (AAO:0000224)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010663", ontology="AAO"} +intersection_of: RO:0002005 UBERON:0001650 ! innervated_by hypoglossal nerve +intersection_of: RO:0002371 UBERON:0001685 ! attached to hyoid bone +intersection_of: RO:0002371 UBERON:0001723 ! attached to tongue +relationship: RO:0002371 UBERON:0001685 ! attached to hyoid bone +relationship: RO:0002371 UBERON:0001723 ! attached to tongue +relationship: RO:0002372 UBERON:0001685 ! has muscle origin hyoid bone +relationship: RO:0002373 UBERON:0001723 ! has muscle insertion tongue +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7e/Hyoglossus.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001575 @@ -177163,16 +176010,13 @@ xref: SCTID:244782006 xref: VHOG:0000825 is_a: UBERON:0000378 {is_inferred="true"} ! tongue muscle intersection_of: UBERON:0014892 ! skeletal muscle organ, vertebrate -intersection_of: attaches_to UBERON:0004765 ! skeletal element -intersection_of: attaches_to_part_of UBERON:0001723 ! tongue -intersection_of: innervated_by UBERON:0001650 ! hypoglossal nerve -relationship: attaches_to UBERON:0004765 ! skeletal element -relationship: immediate_transformation_of UBERON:0011332 ! extrinsic tongue pre-muscle mass -relationship: innervated_by UBERON:0001650 {notes="check palatoglossus", source="Wikipedia"} ! hypoglossal nerve -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000003 "The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000825", ontology="VHOG", source="DOI:10.1002/dvdy.20587 Kusakabe R, Kuratani S, Evolution and developmental patterning of the vertebrate skeletal muscles: perspectives from the lamprey. Developmental Dynamics (2005)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000009 "main functions are altering the tongue's position allowing for protrusion, retraction, and side-to-side movement" xsd:string {source="WP"} -property_value: UBPROP:0000010 "All intrinsic and extrinsic muscles of the tongue are supplied by the hypoglossal nerve (CN XII), except for one of the extrinsic muscles, palatoglossus, which is innervated by the Vagus nerve CN X of the pharyngeal plexus." xsd:string {source="WP"} +intersection_of: RO:0002005 UBERON:0001650 ! innervated_by hypoglossal nerve +intersection_of: RO:0002177 UBERON:0001723 ! attached to part of tongue +intersection_of: RO:0002371 UBERON:0004765 ! attached to skeletal element +relationship: RO:0002005 UBERON:0001650 ! innervated_by hypoglossal nerve +relationship: RO:0002371 UBERON:0004765 ! attached to skeletal element +relationship: RO:0002495 UBERON:0011332 ! immediate transformation of extrinsic tongue pre-muscle mass +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001576 @@ -177192,16 +176036,13 @@ xref: VHOG:0000748 is_a: UBERON:0000378 {is_inferred="true"} ! tongue muscle is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0014892 ! skeletal muscle organ, vertebrate -intersection_of: attaches_to_part_of UBERON:0001723 ! tongue -intersection_of: innervated_by UBERON:0001650 ! hypoglossal nerve intersection_of: part_of UBERON:0001723 ! tongue -relationship: develops_from UBERON:0010059 {source="EHDAA2"} ! hypoglossal cord -relationship: innervated_by UBERON:0001650 {source="FEED", source="Wikipedia"} ! hypoglossal nerve +intersection_of: RO:0002005 UBERON:0001650 ! innervated_by hypoglossal nerve +intersection_of: RO:0002177 UBERON:0001723 ! attached to part of tongue relationship: part_of UBERON:0001723 ! tongue -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000001 "The intrinsic tongue muscles are an integral part of the tongue that are innervated by Cranial Nerve XII.[FEED]" xsd:string {date_retrieved="2012-07-02", ontology="FEED", url="http://www.feedexp.org"} -property_value: UBPROP:0000003 "The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000748", ontology="VHOG", source="DOI:10.1002/dvdy.20587 Kusakabe R, Kuratani S, Evolution and developmental patterning of the vertebrate skeletal muscles: perspectives from the lamprey. Developmental Dynamics (2005)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000009 "The main function of the intrinsic muscles is to provide shape. They are not involved with changing the position of the tongue and are not attached to bone" xsd:string {source="WP"} +relationship: RO:0002005 UBERON:0001650 {source="FEED", source="Wikipedia"} ! innervated_by hypoglossal nerve +relationship: RO:0002202 UBERON:0010059 {source="EHDAA2"} ! develops from hypoglossal cord +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001577 @@ -177237,10 +176078,10 @@ xref: Wikipedia:Facial_muscles xref: XAO:0001013 is_a: UBERON:0015789 ! cranial or facial muscle intersection_of: UBERON:0014892 ! skeletal muscle organ, vertebrate -intersection_of: innervated_by UBERON:0001647 ! facial nerve -relationship: develops_from UBERON:0003066 {source="FEED", source="Wikipedia"} ! pharyngeal arch 2 -relationship: innervated_by UBERON:0001647 ! facial nerve -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/fa/Gray378.png" xsd:anyURI +intersection_of: RO:0002005 UBERON:0001647 ! innervated_by facial nerve +relationship: RO:0002005 UBERON:0001647 ! innervated_by facial nerve +relationship: RO:0002202 UBERON:0003066 {source="FEED", source="Wikipedia"} ! develops from pharyngeal arch 2 +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/fa/Gray378.png" xsd:anyURI [Term] id: UBERON:0001579 @@ -177293,17 +176134,12 @@ is_a: UBERON:0001785 ! cranial nerve is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0001785 ! cranial nerve intersection_of: extends_fibers_into UBERON:0002264 ! olfactory bulb -intersection_of: innervates UBERON:0001997 ! olfactory epithelium -relationship: develops_from UBERON:0003050 {source="ISBN:0471888893"} ! olfactory placode +intersection_of: RO:0002134 UBERON:0001997 ! innervates olfactory epithelium relationship: extends_fibers_into UBERON:0002264 ! olfactory bulb -relationship: innervates UBERON:0001997 {source="ISBN:0471888893"} ! olfactory epithelium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/be/Gray771.png" xsd:anyURI -property_value: UBPROP:0000001 "Nerve that carries information from the olfactory epithelium through the olfactory bulb to the olfactory cortex of the telencephalon.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010088", ontology="AAO", source="AAO:DSM"} -property_value: UBPROP:0000001 "Segment of neural tree organ which is continuous with the olfactory epithelium and an olfactory bulb[FMA:46787]." xsd:string {source="FMA:46787"} -property_value: UBPROP:0000001 "The 1st cranial nerve. The olfactory nerve conveys the sense of smell. It is formed by the axons of OLFACTORY RECEPTOR NEURONS which project from the olfactory epithelium (in the nasal epithelium) to the OLFACTORY BULB[MESH:A08.800.800.120.640]." xsd:string {source="MESH:A08.800.800.120.640"} -property_value: UBPROP:0000003 "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000703", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "connects to main OB (in taxa where main/accessory distinction is important)" xsd:string +relationship: RO:0002134 UBERON:0001997 {source="ISBN:0471888893"} ! innervates olfactory epithelium +relationship: RO:0002202 UBERON:0003050 {source="ISBN:0471888893"} ! develops from olfactory placode +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/be/Gray771.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001584 @@ -177322,16 +176158,15 @@ xref: SCTID:244245001 xref: UMLS:C0226262 {source="ncithesaurus:Left_Subclavian_Artery"} xref: Wikipedia:Subclavian_artery is_a: UBERON:0001533 ! subclavian artery +is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0001533 ! subclavian artery -intersection_of: in_left_side_of UBERON:0000468 ! multicellular organism +intersection_of: BSPO:0000120 UBERON:0000468 ! multicellular organism +relationship: BSPO:0000120 UBERON:0000468 ! multicellular organism relationship: channels_from UBERON:0001508 ! arch of aorta -relationship: in_left_side_of UBERON:0000468 ! multicellular organism -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI -property_value: UBPROP:0000008 "in humans, branches off the arch of aorta" xsd:string -property_value: UBPROP:0000011 "arises from left intersegmental 6th artery in the region of the 6th -7th cervical segment in humans" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Gray506.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001585 @@ -177363,13 +176198,11 @@ xref: VHOG:0001195 xref: Wikipedia:Superior_vena_cava is_a: UBERON:0004087 ! vena cava intersection_of: UBERON:0004087 ! vena cava -intersection_of: drains UBERON:0000153 ! anterior region of body -relationship: connected_to UBERON:0002078 ! right cardiac atrium -relationship: drains UBERON:0000153 ! anterior region of body -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b4/Venenwinkel.png" xsd:anyURI -property_value: UBPROP:0000003 "Phylogenetic modifications within this basic pattern of arteries and veins are largely correlated with functional changes. In the transition from water to land, gills gave way to lungs, accompanied by the establishment of a pulmonary circulation. In some fishes and certainly in tetrapods, the cardinal veins become less involved in blood return. Instead, the composite, prominent postcava (posterior vena cava) arose to drain the posterior part of the body and the precava (anterior vena cava) developed to drain the anterior part of the body.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001195", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.454-455", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "The mouse has both left and right anterior vena cava. adult humans only have a right. Postnatally the left regresses and becomes non-functional (Wessels and Sedmera 2003). In the mouse, The right pulmonary vein passes dorsal to the right superior vena cava, the left pulmonary dorsal to the left superior vena cava (Biology of the Laboratory Mouse, Green)." xsd:string +intersection_of: RO:0002179 UBERON:0000153 ! drains anterior region of body +relationship: RO:0002170 UBERON:0002078 ! connected to right cardiac atrium +relationship: RO:0002179 UBERON:0000153 ! drains anterior region of body +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b4/Venenwinkel.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001586 @@ -177395,12 +176228,11 @@ xref: UMLS:C0226550 {source="ncithesaurus:Internal_Jugular_Vein"} xref: Wikipedia:Internal_jugular_vein xref: XAO:0000382 is_a: UBERON:0004711 ! jugular vein -relationship: connected_to UBERON:0003711 ! brachiocephalic vein -relationship: drains UBERON:0000955 ! brain -relationship: drains UBERON:0001456 ! face -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e9/Gray562.png" xsd:anyURI -property_value: UBPROP:0000001 "Vein which receives many veins draining the palate, brain, and the orbital, nasal, and auditory regions.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010236", ontology="AAO", source="AAO:BJB"} +relationship: RO:0002170 UBERON:0003711 ! connected to brachiocephalic vein +relationship: RO:0002179 UBERON:0000955 ! drains brain +relationship: RO:0002179 UBERON:0001456 ! drains face +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e9/Gray562.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001587 @@ -177425,11 +176257,10 @@ xref: SCTID:181388005 xref: UMLS:C0038532 {source="ncithesaurus:Subclavian_Vein"} xref: Wikipedia:Subclavian_vein is_a: UBERON:0001638 ! vein -relationship: connected_to UBERON:0003711 ! brachiocephalic vein -relationship: drains UBERON:0004710 ! pectoral appendage -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/9e/Gray1174.png" xsd:anyURI -property_value: UBPROP:0000001 "Vein which collects blood from the forelimb via the brachial veins and from the muscles and skin of the trunk via the anterior epigastric and lateral veins.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010510", ontology="AAO", source="AAO:BJB"} +relationship: RO:0002170 UBERON:0003711 ! connected to brachiocephalic vein +relationship: RO:0002179 UBERON:0004710 ! drains pectoral appendage +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/9e/Gray1174.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001591 @@ -177449,10 +176280,10 @@ xref: UMLS:C0226698 {source="ncithesaurus:Thymic_Vein"} xref: Wikipedia:Thymic_veins is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein -intersection_of: drains UBERON:0002370 ! thymus -relationship: drains UBERON:0002370 ! thymus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: tributary_of UBERON:0003711 ! brachiocephalic vein +intersection_of: RO:0002179 UBERON:0002370 ! drains thymus +relationship: RO:0002179 UBERON:0002370 ! drains thymus +relationship: RO:0002376 UBERON:0003711 ! tributary of brachiocephalic vein +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001592 @@ -177471,9 +176302,9 @@ xref: UMLS:C0226650 {source="ncithesaurus:Bronchial_Vein"} xref: Wikipedia:Bronchial_veins is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein -intersection_of: drains UBERON:0002185 ! bronchus -relationship: drains UBERON:0002185 ! bronchus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002179 UBERON:0002185 ! drains bronchus +relationship: RO:0002179 UBERON:0002185 ! drains bronchus +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001593 @@ -177492,9 +176323,9 @@ xref: Wikipedia:Venous_plexus is_a: UBERON:0004537 ! blood vasculature is_a: UBERON:0005629 ! vascular plexus intersection_of: UBERON:0005629 ! vascular plexus -intersection_of: composed_primarily_of UBERON:0001638 ! vein -relationship: composed_primarily_of UBERON:0001638 ! vein -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/bd/Gray585.png" xsd:anyURI +intersection_of: RO:0002473 UBERON:0001638 ! composed primarily of vein +relationship: RO:0002473 UBERON:0001638 ! composed primarily of vein +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/bd/Gray585.png" xsd:anyURI [Term] id: UBERON:0001605 @@ -177520,8 +176351,8 @@ is_a: UBERON:0003386 {source="MA"} ! smooth muscle of eye is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0011222 {source="FMA"} ! intra-ocular muscle relationship: part_of UBERON:0001775 {source="FMA"} ! ciliary body -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/28/Gray872.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/28/Gray872.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001606 @@ -177531,7 +176362,6 @@ subset: uberon_slim synonym: "iris muscle" EXACT [] synonym: "iris muscle organ" EXACT [OBOL:automatic] synonym: "muscle organ of iris" EXACT [OBOL:automatic] -xref: EMAPA:35448 xref: FMA:49154 xref: MA:0001287 xref: SCTID:280888007 @@ -177540,9 +176370,7 @@ is_a: UBERON:0011222 {source="FMA"} ! intra-ocular muscle intersection_of: UBERON:0001630 ! muscle organ intersection_of: part_of UBERON:0001769 ! iris relationship: part_of UBERON:0001769 ! iris -property_value: editor_note "revisit this, see issue #331" xsd:string -property_value: UBPROP:0000008 "in aves, stromal mesenchymal cells may migrate to the iris and become skeletal" xsd:string -property_value: UBPROP:0000008 "The muscle cells of the iris are smooth muscle in mammals and amphibians, but are striated muscle in birds and reptiles. Many fish have neither, and, as a result, their irides are unable to dilate and contract, so that the pupil always remains of a fixed size[Romer, via WP]" xsd:string +property_value: IAO:0000116 "revisit this, see issue #331" xsd:string [Term] id: UBERON:0001607 @@ -177575,19 +176403,15 @@ xref: SCTID:280889004 xref: UMLS:C0229189 {source="ncithesaurus:Sphincter_Pupillae_Muscle"} xref: Wikipedia:Iris_sphincter_muscle is_a: UBERON:0001606 ! muscle of iris -is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004234 {source="BTO"} ! iris smooth muscle is_a: UBERON:0007521 ! smooth muscle sphincter intersection_of: UBERON:0004590 ! sphincter muscle intersection_of: part_of UBERON:0001769 ! iris -relationship: develops_from UBERON:0002346 {source="ISBN:0781772214"} ! neurectoderm -relationship: has_muscle_antagonist UBERON:0001608 {source="dbpedia"} ! dilatator pupillae -relationship: has_muscle_insertion UBERON:0001769 {notes="encircles iris", source="dbpedia"} ! iris -relationship: has_muscle_origin UBERON:0001769 {notes="encircles iris", source="dbpedia"} ! iris -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray878.png" xsd:anyURI -property_value: UBPROP:0000008 "In humans, it functions to constrict the pupil in bright light or during accommodation. Its dimensions are about 0.75 mm wide by 0.15 mm thick. It is controlled by parasympathetic fibers that originate from the Edinger-Westphal nucleus, travel along the oculomotor nerve (CN III), synapse in the ciliary ganglion, and then enter the eye via the short ciliary nerves. Initially, all the myocytes are of the smooth muscle type, but much later in life, so that ultimately most cells are of the striated muscle type. [WP,unvetted]" xsd:string -property_value: UBPROP:0000008 "WP says: It is found in vertebrates and some cephalopods; this class refers to the vertebrate structure" xsd:string -property_value: UBPROP:0000009 "constricts iris" xsd:string +relationship: RO:0002202 UBERON:0002346 {source="ISBN:0781772214"} ! develops from neurectoderm +relationship: RO:0002372 UBERON:0001769 ! has muscle origin iris +relationship: RO:0002373 UBERON:0001769 ! has muscle insertion iris +relationship: RO:0002568 UBERON:0001608 {source="dbpedia"} ! has muscle antagonist dilatator pupillae +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray878.png" xsd:anyURI [Term] id: UBERON:0001608 @@ -177622,15 +176446,13 @@ xref: NCIT:C32463 xref: SCTID:280890008 xref: UMLS:C0229190 {source="ncithesaurus:Dilator_Pupillae_Muscle"} xref: Wikipedia:Iris_dilator_muscle -is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004234 {source="BTO"} ! iris smooth muscle -relationship: develops_from UBERON:0002346 {source="ISBN:0781772214"} ! neurectoderm -relationship: has_muscle_antagonist UBERON:0001607 {source="dbpedia"} ! sphincter pupillae -relationship: has_muscle_insertion UBERON:0001769 {notes="inner margins of iris", source="dbpedia"} ! iris -relationship: has_muscle_origin UBERON:0001769 {notes="outer margins of iris", source="dbpedia"} ! iris -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray878.png" xsd:anyURI -property_value: UBPROP:0000009 "It is innervated by the sympathetic system, which acts by releasing noradrenaline, which acts on alpha1-receptors. Thus, when presented with a threatening stimuli that activates the fight-or-flight response, this innervation dilates the iris, thus temporarily letting more light reach the retina" xsd:string +relationship: RO:0002202 UBERON:0002346 {source="ISBN:0781772214"} ! develops from neurectoderm +relationship: RO:0002372 UBERON:0001769 ! has muscle origin iris +relationship: RO:0002373 UBERON:0001769 ! has muscle insertion iris +relationship: RO:0002568 UBERON:0001607 {source="dbpedia"} ! has muscle antagonist sphincter pupillae +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray878.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001610 @@ -177652,13 +176474,11 @@ xref: Wikipedia:Lingual_artery is_a: UBERON:0015212 ! lateral structure is_a: UBERON:0035398 ! branch of external carotid artery intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0001723 ! tongue -relationship: in_lateral_side_of UBERON:0001723 {source="FMA-abduced-lr"} ! tongue -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: supplies UBERON:0001723 ! tongue -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/3/3c/Lingual_artery.PNG" xsd:anyURI -property_value: UBPROP:0000001 "Part of the external carotid which supplies blood to the tongue.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010492", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000002 "relationship loss: part_of external carotid (AAO:0010218)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010492", ontology="AAO"} +intersection_of: RO:0002178 UBERON:0001723 ! supplies tongue +relationship: BSPO:0000126 UBERON:0001723 {source="FMA-abduced-lr"} ! tongue +relationship: RO:0002178 UBERON:0001723 ! supplies tongue +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/3/3c/Lingual_artery.PNG" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001612 @@ -177678,11 +176498,11 @@ xref: UMLS:C0226109 {source="ncithesaurus:Facial_Artery"} xref: Wikipedia:Facial_artery is_a: UBERON:0035398 ! branch of external carotid artery intersection_of: UBERON:0001637 ! artery -intersection_of: connecting_branch_of UBERON:0001070 ! external carotid artery -intersection_of: supplies UBERON:0001456 ! face -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: supplies UBERON:0001456 ! face -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/7b/Gray508.png" xsd:anyURI +intersection_of: RO:0002178 UBERON:0001456 ! supplies face +intersection_of: RO:0002252 UBERON:0001070 ! connecting branch of external carotid artery +relationship: RO:0002178 UBERON:0001456 ! supplies face +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7b/Gray508.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001613 @@ -177701,13 +176521,13 @@ xref: UMLS:C0226117 {source="ncithesaurus:Occipital_Artery"} xref: Wikipedia:Occipital_artery is_a: UBERON:0035398 ! branch of external carotid artery intersection_of: UBERON:0001637 ! artery -intersection_of: connecting_branch_of UBERON:0001070 ! external carotid artery -intersection_of: supplies UBERON:0000403 ! scalp -intersection_of: supplies UBERON:0002377 ! muscle of neck -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: supplies UBERON:0000403 ! scalp -relationship: supplies UBERON:0002377 ! muscle of neck -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/7b/Gray508.png" xsd:anyURI +intersection_of: RO:0002178 UBERON:0000403 ! supplies scalp +intersection_of: RO:0002178 UBERON:0002377 ! supplies muscle of neck +intersection_of: RO:0002252 UBERON:0001070 ! connecting branch of external carotid artery +relationship: RO:0002178 UBERON:0000403 ! supplies scalp +relationship: RO:0002178 UBERON:0002377 ! supplies muscle of neck +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7b/Gray508.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001616 @@ -177731,12 +176551,11 @@ xref: UMLS:C0024949 {source="ncithesaurus:Maxillary_Artery"} xref: Wikipedia:Maxillary_artery is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery -intersection_of: directly_develops_from UBERON:0003118 ! pharyngeal arch artery 1 -relationship: connected_to UBERON:0001070 ! external carotid artery -relationship: directly_develops_from UBERON:0003118 ! pharyngeal arch artery 1 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/39/Gray510.png" xsd:anyURI -property_value: UBPROP:0000011 "...1st pair undergoes partial regression, the remnants of which becomes part of the maxillary arteries" xsd:string {source="http://download.videohelp.com/vitualis/med/Vascular_Devt.html"} +intersection_of: RO:0002207 UBERON:0003118 ! directly develops from pharyngeal arch artery 1 +relationship: RO:0002170 UBERON:0001070 ! connected to external carotid artery +relationship: RO:0002207 UBERON:0003118 ! directly develops from pharyngeal arch artery 1 +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/39/Gray510.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001619 @@ -177761,13 +176580,11 @@ xref: UMLS:C0029078 {source="ncithesaurus:Opthalmic_Artery"} xref: Wikipedia:Ophthalmic_artery xref: XAO:0000368 is_a: UBERON:0001637 ! artery -relationship: connecting_branch_of UBERON:0001532 ! internal carotid artery -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray514.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI -property_value: UBPROP:0000001 "Part of internal carotid which carries blood via branches to the eye, the eye muscles, and eyelids.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010497", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000002 "relationship loss: part_of internal carotid (AAO:0010219)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010497", ontology="AAO"} +relationship: RO:0002252 UBERON:0001532 ! connecting branch of internal carotid artery +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray514.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001621 @@ -177795,8 +176612,8 @@ xref: Wikipedia:Coronary_circulation#Coronary_anatomy xref: ZFA:0005812 is_a: UBERON:0003498 ! heart blood vessel is_a: UBERON:0004573 ! systemic artery -relationship: supplies UBERON:0002349 ! myocardium -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/46/Gray492.png" xsd:anyURI +relationship: RO:0002178 UBERON:0002349 ! supplies myocardium +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/46/Gray492.png" xsd:anyURI [Term] id: UBERON:0001622 @@ -177815,11 +176632,11 @@ xref: UMLS:C0226171 {source="ncithesaurus:Lacrimal_Artery"} xref: Wikipedia:Lacrimal_artery is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0001817 ! lacrimal gland -relationship: connecting_branch_of UBERON:0001619 {source="FMA"} ! ophthalmic artery -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: supplies UBERON:0001817 ! lacrimal gland -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray514.png" xsd:anyURI +intersection_of: RO:0002178 UBERON:0001817 ! supplies lacrimal gland +relationship: RO:0002178 UBERON:0001817 ! supplies lacrimal gland +relationship: RO:0002252 UBERON:0001619 {source="FMA"} ! connecting branch of ophthalmic artery +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray514.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001628 @@ -177850,15 +176667,13 @@ is_a: UBERON:0004573 ! systemic artery is_a: UBERON:0006347 ! communicating artery is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0006347 ! communicating artery -intersection_of: connecting_branch_of UBERON:0001532 ! internal carotid artery intersection_of: part_of UBERON:0003709 ! circle of Willis -relationship: connecting_branch_of UBERON:0001532 {source="FMA", source="ZFA"} ! internal carotid artery -relationship: in_lateral_side_of UBERON:0003709 {source="FMA-abduced-lr"} ! circle of Willis +intersection_of: RO:0002252 UBERON:0001532 ! connecting branch of internal carotid artery +relationship: BSPO:0000126 UBERON:0003709 {source="FMA-abduced-lr"} ! circle of Willis relationship: part_of UBERON:0003709 ! circle of Willis -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/2e/Circle_of_Willis_en.svg" xsd:anyURI -property_value: UBPROP:0000001 "An artery that connects caudal division of the internal carotid artery and the basal communicating artery to the basilar artery. Isogai et al. 2001.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005001", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000008 "todo - verify ZFA link: An artery that connects caudal division of the internal carotid artery and the basal communicating artery to the basilar artery" xsd:string +relationship: RO:0002252 UBERON:0001532 {source="FMA", source="ZFA"} ! connecting branch of internal carotid artery +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2e/Circle_of_Willis_en.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001630 @@ -177870,8 +176685,6 @@ subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "muscle" BROAD [ZFA:0005145] -xref: AAO:0011066 -xref: EMAPA:32715 xref: EMAPA:37474 {source="MA:th"} xref: EV:0100146 xref: FMA:5022 @@ -177886,12 +176699,9 @@ xref: ZFA:0005145 is_a: UBERON:0000062 ! organ is_a: UBERON:0005090 ! muscle structure intersection_of: UBERON:0000062 ! organ -intersection_of: composed_primarily_of UBERON:0002385 ! muscle tissue -relationship: composed_primarily_of UBERON:0002385 ! muscle tissue +intersection_of: RO:0002473 UBERON:0002385 ! composed primarily of muscle tissue relationship: part_of UBERON:0001015 ! musculature -property_value: UBPROP:0000001 "Portion of tissue composed of contractile fibers.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005145", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001245", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.75", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "muscular" xsd:string +relationship: RO:0002473 UBERON:0002385 ! composed primarily of muscle tissue [Term] id: UBERON:0001637 @@ -177912,7 +176722,6 @@ xref: AEO:0000208 xref: BTO:0000573 xref: CALOHA:TS-0054 xref: EFO:0000814 -xref: EHDAA2:0000143 xref: EHDAA2:0003253 xref: EMAPA:35147 xref: EV:0100026 @@ -177933,12 +176742,7 @@ xref: XAO:0000114 xref: ZFA:0000005 is_a: UBERON:0003509 ! arterial blood vessel relationship: channels_from UBERON:0000948 ! heart -property_value: editor_note "Note that in FMA an artery is a tree, whereas AEO/JB defines it as a tube; FMA includes a separate class for what it calls the trunk. Classification in this ontology may currently (Jan 2012) represent a mix of both schemes, although we are gradually revising in the direction of the AEO scheme." xsd:string -property_value: UBPROP:0000001 "Part of the circulatory system composed of blood vessels which carry oxygenated blood away from the heart to the rest of the body.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010211", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001251", ontology="VHOG", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "arterial" xsd:string -property_value: UBPROP:0000012 "Some arthropods have primitive arterial systems but this term refers to arteries in a true closed circulatory system." xsd:string -property_value: UBPROP:0000202 FMA:63812 +property_value: IAO:0000116 "Note that in FMA an artery is a tree, whereas AEO/JB defines it as a tube; FMA includes a separate class for what it calls the trunk. Classification in this ontology may currently (Jan 2012) represent a mix of both schemes, although we are gradually revising in the direction of the AEO scheme." xsd:string [Term] id: UBERON:0001638 @@ -177983,12 +176787,8 @@ intersection_of: UBERON:0003920 ! venous blood vessel intersection_of: channel_for UBERON:0013756 ! venous blood relationship: channel_for UBERON:0013756 ! venous blood relationship: channels_from UBERON:0001982 ! capillary -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c2/Venous_system_en.svg" xsd:anyURI -property_value: editor_note "TODO - check with MA - vein vs venous blood vessel" xsd:string -property_value: UBPROP:0000001 "Part of the circulatory system composed of blood vessels which carry blood from other organs, tissues, and cells to the heart.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010212", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001743", ontology="VHOG", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "venous" xsd:string -property_value: UBPROP:0000202 FMA:63814 +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c2/Venous_system_en.svg" xsd:anyURI +property_value: IAO:0000116 "TODO - check with MA - vein vs venous blood vessel" xsd:string [Term] id: UBERON:0001639 @@ -178016,15 +176816,13 @@ xref: Wikipedia:Hepatic_portal_vein xref: ZFA:0005090 is_a: UBERON:0002017 {source="MA"} ! portal vein relationship: channels_into UBERON:0002107 ! liver -relationship: develops_from UBERON:0005487 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="Wikipedia:Vitelline_vein"} ! vitelline vein relationship: overlaps UBERON:0002107 ! liver relationship: part_of UBERON:0010194 ! hepatic portal system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI -property_value: UBPROP:0000003 "Adults of all vertebrates lose the vitelline veins and establish a single large hepatic portal vein (...) by the selective retention of parts of the left and right subintestinals and of several anastomoses that occur between them within and just posterior to the liver.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000642", ontology="VHOG", source="ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.265", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "In humans A vein in the abdominal cavity that drains blood from the gastrointestinal tract and spleen. It is usually formed by the confluence of the superior mesenteric and splenic veins, and also receives blood from the inferior mesenteric, gastric, and cystic veins. The hepatic portal vein is a major component of the hepatic portal system, one of the main portal venous systems in the body. Conditions involving the hepatic portal vein cause considerable illness and death. An important example of such a condition is elevated blood pressure in the hepatic portal vein. This condition, called portal hypertension, is a major complication of cirrhosis worldwide. [WP,unvetted]" xsd:string +relationship: RO:0002202 UBERON:0005487 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="Wikipedia:Vitelline_vein"} ! develops from vitelline vein +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001640 @@ -178056,13 +176854,13 @@ xref: SCTID:181340007 xref: UMLS:C0007569 {source="ncithesaurus:Coeliac_Artery"} xref: Wikipedia:Celiac_artery is_a: UBERON:0012254 ! abdominal aorta artery -relationship: develops_from UBERON:0006002 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="Wikipedia"} ! vitelline artery relationship: indirectly_supplies UBERON:0000160 {source="ISBN:0073040584"} ! intestine relationship: indirectly_supplies UBERON:0000945 {source="ISBN:0073040584"} ! stomach relationship: indirectly_supplies UBERON:0002106 {source="ISBN:0073040584"} ! spleen relationship: indirectly_supplies UBERON:0002107 {source="ISBN:0073040584"} ! liver -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/65/Gray532.png" xsd:anyURI +relationship: RO:0002202 UBERON:0006002 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="Wikipedia"} ! develops from vitelline artery +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/65/Gray532.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001645 @@ -178117,19 +176915,16 @@ xref: ZFA:0000697 is_a: UBERON:0001785 ! cranial nerve intersection_of: UBERON:0001785 ! cranial nerve intersection_of: extends_fibers_into UBERON:0002925 ! trigeminal nucleus -intersection_of: innervates UBERON:0000165 ! mouth -intersection_of: innervates UBERON:0011648 ! jaw muscle -intersection_of: innervates UBERON:1000021 ! skin of face +intersection_of: RO:0002134 UBERON:0000165 ! innervates mouth +intersection_of: RO:0002134 UBERON:0011648 ! innervates jaw muscle +intersection_of: RO:0002134 UBERON:1000021 ! innervates skin of face relationship: extends_fibers_into UBERON:0002925 ! trigeminal nucleus -relationship: has_developmental_contribution_from UBERON:0005239 {source="Wikipedia"} ! basal plate metencephalon -relationship: innervates UBERON:0000165 ! mouth -relationship: innervates UBERON:0011648 ! jaw muscle -relationship: innervates UBERON:1000021 ! skin of face -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/9/99/Gray778_Trigeminal.png" xsd:anyURI -property_value: UBPROP:0000001 "Nerve consists of motor and sensory components. Ganglion cells of the sensory component form the proximal part of the trigeminal (Gasserian) ganglion. From the ganglion 3 major rami innervate jaws, snout, and buccal roof.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010470", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000704", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "the ophthalmic usually usually merges with the other two. In some vertebrates, the ophthalmic emerges from the brain separately[Kardong] The trigeminal nerve has 3 branches in mammals - similar branches are present in nonmammalian vertebrates, but in some a separate profundus nerve that corresponds to opthalmic branch in mammls" xsd:string {source="ISBN:0471888893"} +relationship: RO:0002134 UBERON:0000165 ! innervates mouth +relationship: RO:0002134 UBERON:0011648 ! innervates jaw muscle +relationship: RO:0002134 UBERON:1000021 ! innervates skin of face +relationship: RO:0002254 UBERON:0005239 {source="Wikipedia"} ! has developmental contribution from basal plate metencephalon +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/9/99/Gray778_Trigeminal.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001647 @@ -178186,16 +176981,14 @@ is_a: UBERON:0001785 ! cranial nerve is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0001021 ! nerve intersection_of: extends_fibers_into UBERON:0000127 ! facial nucleus -intersection_of: innervates UBERON:0001577 ! facial muscle +intersection_of: RO:0002134 UBERON:0001577 ! innervates facial muscle relationship: extends_fibers_into UBERON:0000127 ! facial nucleus -relationship: has_developmental_contribution_from UBERON:0003066 {source="Wikipedia"} ! pharyngeal arch 2 -relationship: has_developmental_contribution_from UBERON:0005239 {source="Wikipedia"} ! basal plate metencephalon -relationship: innervates UBERON:0001577 ! facial muscle relationship: part_of UBERON:0001033 {source="ZFA"} ! gustatory system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1f/Cranial_nerve_VII.svg" xsd:anyURI -property_value: UBPROP:0000001 "Slender nerve composed of branchiomotor and visceral efferent fibers innervating the mouth and various muscles within the jaw. Sensory components innervate the bucccal roof and somatomotor components innervate the depressor musculature and muscle interhyoideus.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010472", ontology="AAO", source="AAO:DSM"} -property_value: UBPROP:0000003 "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000706", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625", source="http://bgee.unil.ch/"} +relationship: RO:0002134 UBERON:0001577 ! innervates facial muscle +relationship: RO:0002254 UBERON:0003066 {source="Wikipedia"} ! has developmental contribution from pharyngeal arch 2 +relationship: RO:0002254 UBERON:0005239 {source="Wikipedia"} ! has developmental contribution from basal plate metencephalon +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1f/Cranial_nerve_VII.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001648 @@ -178255,15 +177048,13 @@ is_a: UBERON:0001785 ! cranial nerve is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0001785 ! cranial nerve intersection_of: extends_fibers_into UBERON:0001720 ! cochlear nucleus -intersection_of: innervates UBERON:0001844 ! cochlea -relationship: develops_from UBERON:0003069 {source="ISBN:0471888893"} ! otic placode +intersection_of: RO:0002134 UBERON:0001844 ! innervates cochlea relationship: extends_fibers_into UBERON:0001720 ! cochlear nucleus -relationship: innervates UBERON:0001844 ! cochlea relationship: part_of UBERON:0002105 ! vestibulo-auditory system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray789.png" xsd:anyURI -property_value: UBPROP:0000001 "Nerve primarily composed of special somatic afferent fibers innervating the inner ear, and is involved in balance, position, and hearing.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010473", ontology="AAO", source="AAO:DSM"} -property_value: UBPROP:0000003 "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000695", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625", source="http://bgee.unil.ch/"} +relationship: RO:0002134 UBERON:0001844 ! innervates cochlea +relationship: RO:0002202 UBERON:0003069 {source="ISBN:0471888893"} ! develops from otic placode +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray789.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001649 @@ -178312,14 +177103,12 @@ xref: XAO:0003096 xref: ZFA:0000668 is_a: UBERON:0001785 ! cranial nerve relationship: extends_fibers_into UBERON:0001896 ! medulla oblongata -relationship: has_developmental_contribution_from UBERON:0005239 {notes="motor", source="Wikipedia"} ! basal plate metencephalon -relationship: innervates UBERON:0001727 ! taste bud -relationship: innervates UBERON:0006562 ! pharynx relationship: part_of UBERON:0001033 ! gustatory system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/5e/Gray791.png" xsd:anyURI -property_value: UBPROP:0000001 "Small nerve consisting of branchiomotor and visceral efferent and afferent fibers which innervate the m. subarculais rectus I, dorsal buccal mucosa, and the tongue.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010474", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000701", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625", source="http://bgee.unil.ch/"} +relationship: RO:0002134 UBERON:0001727 ! innervates taste bud +relationship: RO:0002134 UBERON:0006562 ! innervates pharynx +relationship: RO:0002254 UBERON:0005239 ! has developmental contribution from basal plate metencephalon +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5e/Gray791.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001650 @@ -178367,19 +177156,13 @@ xref: XAO:0004215 is_a: UBERON:0001785 ! cranial nerve intersection_of: UBERON:0001785 ! cranial nerve intersection_of: extends_fibers_into UBERON:0002871 ! hypoglossal nucleus -intersection_of: innervates UBERON:0000378 ! tongue muscle +intersection_of: RO:0002134 UBERON:0000378 ! innervates tongue muscle relationship: extends_fibers_into UBERON:0002871 ! hypoglossal nucleus -relationship: innervates UBERON:0001571 ! genioglossus muscle -relationship: innervates UBERON:0001572 ! hyoglossus muscle -relationship: only_in_taxon NCBITaxon:32523 ! Tetrapoda -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/ef/Gray794.png" xsd:anyURI -property_value: RO:0002174 NCBITaxon:8292 -property_value: UBPROP:0000001 "Cranial nerve that innervates muscles in the tongue. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-14, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000693", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000001 "In amphibians, represents the hypoglossal nerve in amniotes. Innverates mm. geniohyoideus, genioglossus, hyoglossus, rectus cervicis" xsd:string {source="ISBN:080184780X"} -property_value: UBPROP:0000001 "Nerve which innervates the muscles associated with the tongue including mm geniohyoideus, genioglossus, hyoglossus and rectus cervicis.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010477", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "Cranial nerves XI and XII evolved in the common ancestor to amniotes (non-amphibian tetrapods) thus totalling twelve pairs.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000693", ontology="VHOG", source="Wikipedia:Cranial_nerves", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "we use a broad definition of this cranial nerve that encompasses the amphibian predecessor of true amniote hypoglossal nerves" xsd:string +relationship: RO:0002134 UBERON:0001571 ! innervates genioglossus muscle +relationship: RO:0002134 UBERON:0001572 ! innervates hyoglossus muscle +relationship: RO:0002160 NCBITaxon:32523 ! only in taxon Tetrapoda +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ef/Gray794.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001651 @@ -178401,15 +177184,15 @@ xref: UMLS:C0923924 {source="ncithesaurus:Right_Pulmonary_Artery"} xref: Wikipedia:Right_pulmonary_artery is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0002167 ! right lung -relationship: connected_to UBERON:0002333 ! pulmonary trunk -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: supplies UBERON:0002167 ! right lung -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray504.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png" xsd:anyURI -property_value: editor_note "TODO - add class 'pulmonary artery tree organ'" xsd:string +intersection_of: RO:0002178 UBERON:0002167 ! supplies right lung +relationship: RO:0002170 UBERON:0002333 ! connected to pulmonary trunk +relationship: RO:0002178 UBERON:0002167 ! supplies right lung +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray504.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png" xsd:anyURI +property_value: IAO:0000116 "TODO - add class 'pulmonary artery tree organ'" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001652 @@ -178431,15 +177214,15 @@ xref: UMLS:C0923925 {source="ncithesaurus:Left_Pulmonary_Artery"} xref: Wikipedia:Left_pulmonary_artery is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0002168 ! left lung -relationship: connected_to UBERON:0002333 ! pulmonary trunk -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: supplies UBERON:0002168 ! left lung -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray504.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png" xsd:anyURI -property_value: editor_note "TODO - add class 'pulmonary artery tree organ'" xsd:string +intersection_of: RO:0002178 UBERON:0002168 ! supplies left lung +relationship: RO:0002170 UBERON:0002333 ! connected to pulmonary trunk +relationship: RO:0002178 UBERON:0002168 ! supplies left lung +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray504.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png" xsd:anyURI +property_value: IAO:0000116 "TODO - add class 'pulmonary artery tree organ'" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001653 @@ -178463,11 +177246,9 @@ xref: Wikipedia:Facial_vein is_a: UBERON:0003496 ! head blood vessel is_a: UBERON:0009141 ! craniocervical region vein relationship: part_of UBERON:0001456 ! face -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: tributary_of UBERON:0001586 {source="FMA"} ! internal jugular vein -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray557.png" xsd:anyURI -property_value: UBPROP:0000001 "Vein which collects blood from muscles of the head and drains into the external jugular vein.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010513", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000012 "MA and NCITA also has 'anterior facial vein'" xsd:string {external_ontology="MA"} +relationship: RO:0002376 UBERON:0001586 {source="FMA"} ! tributary of internal jugular vein +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray557.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001663 @@ -178490,11 +177271,10 @@ xref: XAO:0004160 is_a: UBERON:0001638 ! vein is_a: UBERON:0003499 ! brain blood vessel intersection_of: UBERON:0001638 ! vein -intersection_of: drains UBERON:0001893 ! telencephalon -relationship: drains UBERON:0001893 ! telencephalon +intersection_of: RO:0002179 UBERON:0001893 ! drains telencephalon relationship: part_of UBERON:0001893 ! telencephalon -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/9f/Gray568.png" xsd:anyURI -property_value: UBPROP:0000202 FMA:70861 +relationship: RO:0002179 UBERON:0001893 ! drains telencephalon +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/9f/Gray568.png" xsd:anyURI [Term] id: UBERON:0001668 @@ -178514,8 +177294,8 @@ xref: UMLS:C0226601 {source="ncithesaurus:Cerebellar_Vein"} xref: Wikipedia:Cerebellar_veins is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein -intersection_of: drains UBERON:0002037 ! cerebellum -relationship: drains UBERON:0002037 ! cerebellum +intersection_of: RO:0002179 UBERON:0002037 ! drains cerebellum +relationship: RO:0002179 UBERON:0002037 ! drains cerebellum [Term] id: UBERON:0001675 @@ -178566,15 +177346,13 @@ xref: XAO:0000428 xref: ZFA:0000295 is_a: UBERON:0001714 ! cranial ganglion is_a: UBERON:0001800 {source="ncithesaurus"} ! sensory ganglion -is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0001714 ! cranial ganglion intersection_of: extends_fibers_into UBERON:0001645 ! trigeminal nerve relationship: extends_fibers_into UBERON:0001645 ! trigeminal nerve -relationship: immediate_transformation_of UBERON:0006304 {source="Bgee:AN"} ! future trigeminal ganglion -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/69/Gray776.png" xsd:anyURI -property_value: editor_note "consider renaming this 'trigeminal ganglion complex'. The complex may be fused (amniotes) partially fused (xenopus) or separate (sharks)" xsd:string -property_value: UBPROP:0000001 "A prominent collection of touch-sensory neurons of the trigeminal or fifth cranial nerve, positioned beside the brain between the eye and the ear. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000295", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000008 "In Xenopus, the profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24." xsd:string {source="PMID:21452441", source="XAO:0004093"} +relationship: RO:0002495 UBERON:0006304 {source="Bgee:AN"} ! immediate transformation of future trigeminal ganglion +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/69/Gray776.png" xsd:anyURI +property_value: IAO:0000116 "consider renaming this 'trigeminal ganglion complex'. The complex may be fused (amniotes) partially fused (xenopus) or separate (sharks)" xsd:string [Term] id: UBERON:0001676 @@ -178598,18 +177376,16 @@ xref: UMLS:C0028784 {source="ncithesaurus:Occipital_Bone"} xref: Wikipedia:Occipital_bone is_a: UBERON:0010428 {source="FMA"} ! flat bone is_a: UBERON:0011164 ! neurocranium bone -relationship: connected_to UBERON:0001092 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! vertebral bone 1 -relationship: connected_to UBERON:0001677 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! sphenoid bone -relationship: develops_from UBERON:0003089 {source="PMID:11523816"} ! sclerotome -relationship: only_in_taxon NCBITaxon:117570 {source="WP"} ! Teleostomi -relationship: overlaps UBERON:0002241 {notes="basi paired exo and supra occipital bones", source="MA-modified"} ! chondrocranium -relationship: overlaps UBERON:0003113 {notes="interparietal (postparietal)"} ! dermatocranium +relationship: overlaps UBERON:0002241 ! chondrocranium +relationship: overlaps UBERON:0003113 ! dermatocranium relationship: part_of UBERON:0005902 {source="FMA"} ! occipital region -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: surrounds UBERON:0003687 ! foramen magnum -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/27/Gray194.png" xsd:anyURI -property_value: UBPROP:0000008 "formed from the sclerotome of the occipital somites. It is not present in living or fossil agnathans or cartilaginous fishes, but appears to have arisen in parallel in many bony fishes. Incorporation of the occipital ver- tebrae into the skull was associated with the annexation of the upper part of the spinal cord into the brain, together with the first 2 spinal nerves as cranial nerves XI and XII" xsd:string {source="PMID:11523816"} -property_value: UBPROP:0000008 "fusion of basi-, exo- and supra-occipitals (and maybe tabular)" xsd:string {source="Kardong"} +relationship: RO:0002160 NCBITaxon:117570 {source="WP"} ! only in taxon Teleostomi +relationship: RO:0002170 UBERON:0001092 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to vertebral bone 1 +relationship: RO:0002170 UBERON:0001677 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to sphenoid bone +relationship: RO:0002202 UBERON:0003089 {source="PMID:11523816"} ! develops from sclerotome +relationship: RO:0002221 UBERON:0003687 ! surrounds foramen magnum +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/27/Gray194.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001677 @@ -178641,18 +177417,17 @@ is_a: UBERON:0003462 ! facial bone is_a: UBERON:0008193 {source="FMA"} ! pneumatized bone is_a: UBERON:0015060 ! sphenoid endochondral element intersection_of: UBERON:0015060 ! sphenoid endochondral element -intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue -relationship: connected_to UBERON:0000209 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! tetrapod frontal bone -relationship: connected_to UBERON:0001676 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! occipital bone -relationship: connected_to UBERON:0001679 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! ethmoid bone -relationship: connected_to UBERON:0002396 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! vomer -relationship: develops_from UBERON:0009193 {source="cjm"} ! sphenoid cartilage element -relationship: overlaps UBERON:0002241 {notes="orbito pre and basi sphenoid"} ! chondrocranium -relationship: overlaps UBERON:0003113 {notes="pterygoid process"} ! dermatocranium -relationship: overlaps UBERON:0008895 {notes="alisphenoid"} ! splanchnocranium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cranial_bones2.jpg" xsd:anyURI -property_value: UBPROP:0000012 "part of viscerocranium (facial skeleton) in FMA" xsd:string {external_ontology="FMA"} +intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue +relationship: overlaps UBERON:0002241 ! chondrocranium +relationship: overlaps UBERON:0003113 ! dermatocranium +relationship: overlaps UBERON:0008895 ! splanchnocranium +relationship: RO:0002170 UBERON:0000209 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to tetrapod frontal bone +relationship: RO:0002170 UBERON:0001676 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to occipital bone +relationship: RO:0002170 UBERON:0001679 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to ethmoid bone +relationship: RO:0002170 UBERON:0002396 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to vomer +relationship: RO:0002202 UBERON:0009193 {source="cjm"} ! develops from sphenoid cartilage element +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cranial_bones2.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001678 @@ -178675,15 +177450,11 @@ xref: UMLS:C0039484 {source="ncithesaurus:Temporal_Bone"} xref: VHOG:0000800 xref: Wikipedia:Temporal_bone is_a: UBERON:0008193 {source="FMA"} ! pneumatized bone -relationship: overlaps UBERON:0002241 {notes="petrosal"} ! chondrocranium -relationship: overlaps UBERON:0003113 {notes="squamosal plus angular", notes="temporal series"} ! dermatocranium -relationship: overlaps UBERON:0008895 {notes="styloid process"} ! splanchnocranium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cranial_bones2.jpg" xsd:anyURI -property_value: UBPROP:0000008 "fusion of squamosal + angular (tympanic annulus) [derm.] + petrosal (prootic + opisthotic)" xsd:string {source="chond."} -property_value: UBPROP:0000008 "In many mammals, as in humans, the petrosal, ectotympanic and squamosal bones synostose to form the temporal bone + styloid process" xsd:string -property_value: UBPROP:0000010 "The temporal bone consists of four parts: * Squama temporalis * Mastoid portion * Petrous portion (Petrosal ridge) * Tympanic part[WP]." xsd:string {source="[WP]"} -property_value: UBPROP:0000012 "Note the Temporal bone is not explicitly categorized to a part of the cranium in FMA" xsd:string {external_ontology="FMA"} +relationship: overlaps UBERON:0002241 ! chondrocranium +relationship: overlaps UBERON:0003113 ! dermatocranium +relationship: overlaps UBERON:0008895 ! splanchnocranium +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cranial_bones2.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001679 @@ -178710,20 +177481,15 @@ xref: Wikipedia:Ethmoid_bone is_a: UBERON:0002513 {source="ISBN:0073040584"} ! endochondral bone is_a: UBERON:0003462 ! facial bone is_a: UBERON:0011164 ! neurocranium bone -relationship: connected_to UBERON:0000209 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! tetrapod frontal bone -relationship: connected_to UBERON:0001677 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! sphenoid bone -relationship: connected_to UBERON:0002396 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! vomer -relationship: contributes_to_morphology_of UBERON:0011156 ! facial skeleton -relationship: develops_from UBERON:0006227 {evidence="definitional"} ! ethmoid bone primordium relationship: part_of UBERON:0002517 ! basicranium relationship: part_of UBERON:0011241 ! ethmoid region -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cranial_bones2.jpg" xsd:anyURI -property_value: UBPROP:0000001 "A light spongy bone located between the eye sockets, forming part of the walls and septum of the superior nasal cavity, and containing perforations for the passage of olfactory nerve fibers. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001317", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/ethmoid+bone"} -property_value: UBPROP:0000003 "The ethmoid region of the chondrocranium and the nasal capsules, which were largely unossified in early tetrapods and ancestral amniotes, are represented in mammals by the ethmoid and turbinates bones, respectively.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001317", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.259", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "ethmoidal" xsd:string -property_value: UBPROP:0000008 "todo - homology e.g. mesethmoid of teleost" xsd:string -property_value: UBPROP:0000012 "Note the WP states the Neurocranium contains the ethmoid bone, both MA and FMA place the ethmoid as part of the viscerocranium. FMA also has it in neurocranium (via basicranium). Ideally we would have non-overlapping divisions of the skull, but for now we follow FMA" xsd:string {external_ontology="MA"} +relationship: RO:0002170 UBERON:0000209 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to tetrapod frontal bone +relationship: RO:0002170 UBERON:0001677 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to sphenoid bone +relationship: RO:0002170 UBERON:0002396 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to vomer +relationship: RO:0002202 UBERON:0006227 ! develops from ethmoid bone primordium +relationship: RO:0002433 UBERON:0011156 ! contributes to morphology of facial skeleton +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cranial_bones2.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001685 @@ -178750,14 +177516,11 @@ xref: UMLS:C0020417 {source="ncithesaurus:Hyoid_Bone"} xref: VHOG:0001325 xref: Wikipedia:Hyoid_bone is_a: UBERON:0008001 {source="FMA"} ! irregular bone -relationship: has_developmental_contribution_from UBERON:0003066 {source="Wikipedia"} ! pharyngeal arch 2 -relationship: has_developmental_contribution_from UBERON:0003114 {source="Wikipedia"} ! pharyngeal arch 3 relationship: part_of UBERON:0010272 ! hyoid apparatus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1f/Gray186.png" xsd:anyURI -property_value: UBPROP:0000001 "Paired processes that extend posterolaterally from the posterior margin of the hyoid plate. These processes are the ossified posteromedial processes and invest the laryngeal apparatus.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000684", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000002 "relationship loss: part_of hyoid plate (AAO:0000664)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000684", ontology="AAO"} -property_value: UBPROP:0000008 "The hyoid bone is derived from the lower half of the second gill arch in fish, which separates the first gill slit from the spiracle. In many animals, it also incorporates elements of other gill arches, and has a correspondingly greater number of cornua. Amphibians and reptiles may have many cornua, while mammals (including humans) have two pairs, and birds only one. In birds, and some reptiles, the body of the hyoid is greatly extended forward, creating a solid bony support for the tongue. The howler monkey Alouatta has a pneumatized hyoid bone, one of the few cases of postcranial pneumatization of bones outside Saurischia." xsd:string {source="WP", seeAlso="https://github.com/obophenotype/uberon/issues/548"} +relationship: RO:0002254 UBERON:0003066 {source="Wikipedia"} ! has developmental contribution from pharyngeal arch 2 +relationship: RO:0002254 UBERON:0003114 {source="Wikipedia"} ! has developmental contribution from pharyngeal arch 3 +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1f/Gray186.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001686 @@ -178793,12 +177556,9 @@ xref: XAO:0000214 is_a: UBERON:0003457 ! head bone is_a: UBERON:0035130 ! auditory ossicle endochondral element intersection_of: UBERON:0035130 ! auditory ossicle endochondral element -intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b0/Illu_auditory_ossicles.jpg" xsd:anyURI -property_value: editor_note "This should probably be restricted to mammals - the AAO/XAO structures may group non-homologous structures [Wikipedia:Evolution_of_mammalian_auditory_ossicles] see https://github.com/seger/aao/issues/5." xsd:string -property_value: UBPROP:0000001 "The small bones of the middle ear: incus, malleus, and stapes. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000461", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/auditory+ossicles"} -property_value: UBPROP:0000003 "Additional structural analysis within a phylogenetic context has led to the remarkable discovery that in synapsids, thought to be ancestral to mammals, both the quadrate and articular have become reduced and less firmly articulated with their surrounding bones, reducing their jaw-joint-bearing role. This trend culminated with the incorporation of the quadrate, the columella (which remains articulated with the quadrate), and the articular into the expanded middle ear in mammals.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000461", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.695", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000011 "Studies have shown that ear bones in mammal embryos are attached to the dentary, which is part of the jaw. These are ossified portions of cartilage -- called Meckel's cartilage -- that are attached to the jaw. As the embryo develops, the cartilage hardens to form bone. Later in development, the bone structure breaks loose from the jaw and migrates to the inner ear area. The structure is known as the middle ear, and is made up of the incus, stapes, malleus, and tympanic membrane. These correspond to the quadrate, prearticular, articular, and angular structures in the reptile jaw. For this reason, researchers believe the similarity of the results shows that mammals and reptiles have a common ancestry." xsd:string {source="WP"} +intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b0/Illu_auditory_ossicles.jpg" xsd:anyURI +property_value: IAO:0000116 "This should probably be restricted to mammals - the AAO/XAO structures may group non-homologous structures [Wikipedia:Evolution_of_mammalian_auditory_ossicles] see https://github.com/seger/aao/issues/5." xsd:string [Term] id: UBERON:0001690 @@ -178839,10 +177599,7 @@ is_a: UBERON:0010314 ! structure with developmental contribution from neural cre relationship: capable_of GO:0050910 ! detection of mechanical stimulus involved in sensory perception of sound relationship: part_of UBERON:0000033 ! head relationship: part_of UBERON:0002105 ! vestibulo-auditory system -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b8/Ear.jpg" xsd:anyURI -property_value: UBPROP:0000001 "The organ of hearing and of equilibrium. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000330", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/ear"} -property_value: UBPROP:0000003 "Both vertebrate and invertebrate auditory organs are thought to have evolved from primitive mechanosensors, but the nature of the ancestral structure and the evolutionary trajectories followed in distinct animal lineages remain unknown. In particular, we do not know how many types of mechanosensor existed in the protostome-deuterostome ancestor from which insects and vertebrates evolved or whether the PDA had an auditory organ.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000330", ontology="VHOG", source="DOI:10.1002/dvdy.20207 Boekhoff-Falk G, Hearing in Drosophila: Development of Johnston's organ and emerging parallels to vertebrate ear development. Developmental Dynamics (2005)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "auricular" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b8/Ear.jpg" xsd:anyURI [Term] id: UBERON:0001691 @@ -178879,16 +177636,13 @@ xref: Wikipedia:External_ear xref: XAO:0000190 is_a: UBERON:0001444 ! subdivision of head is_a: UBERON:0015212 ! lateral structure -relationship: contributes_to_morphology_of UBERON:0000033 ! head -relationship: contributes_to_morphology_of UBERON:0001690 ! ear -relationship: in_lateral_side_of UBERON:0000033 ! head -relationship: never_in_taxon NCBITaxon:9709 {source="Wikipedia"} -relationship: only_in_taxon NCBITaxon:32523 ! Tetrapoda +relationship: BSPO:0000126 UBERON:0000033 ! head relationship: part_of UBERON:0001690 ! ear -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Gray907.png" xsd:anyURI -property_value: UBPROP:0000001 "The external part of the organ, which consists of an outer portion (external auditory meatus) which leads to the tympanum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000311", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "Some species, like Amolops tormotus (Feng et al. 2006), have a cavity in front of the tympanic membrane which is considered to be an ear canal and thus an outer ear. (...) The ancestral lineage of amphibians separated from the mammalian lineage, approximately 350 million years ago, in the paleozoic era. Many of the important developments in the auditory systems emerged after the ancestral paths separated (Manley and Clack 2003). This implies that shared features, like the tympanic middle ear, developed independently in different vertebrate lineages.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000311", ontology="VHOG", source="DOI:10.1007/s00359-008-0327-1 Schoffelen RLM, Segenhout JM, Van Dijk P, Mechanics of the exceptional anuran ear. Journal of Comparative Physiology A (2008)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "in XAO this includes and is only the tympanum" xsd:string {external_ontology="XAO"} +relationship: RO:0002160 NCBITaxon:32523 ! only in taxon Tetrapoda +relationship: RO:0002433 UBERON:0000033 ! contributes to morphology of head +relationship: RO:0002433 UBERON:0001690 ! contributes to morphology of ear +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Gray907.png" xsd:anyURI +property_value: RO:0002161 NCBITaxon:9709 {source="Wikipedia"} [Term] id: UBERON:0001694 @@ -178917,9 +177671,7 @@ xref: Wikipedia:Petrous_part_of_the_temporal_bone is_a: UBERON:0005913 ! zone of bone organ relationship: part_of UBERON:0001678 ! temporal bone relationship: part_of UBERON:0002517 {source="FMA"} ! basicranium -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray137.png" xsd:anyURI -property_value: UBPROP:0000001 "The petrosal bone arises from the two otic bones on the lateral wall of the chondrocranium and encases the inner ear of mammals. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, p.258, see_Liem_KF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001553", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "derivative of prootic and opisthotic" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray137.png" xsd:anyURI [Term] id: UBERON:0001697 @@ -178945,14 +177697,13 @@ xref: UMLS:C0029180 {source="ncithesaurus:Orbit"} xref: Wikipedia:Orbit_(anatomy) xref: XAO:0003171 xref: ZFA:0001410 +is_a: UBERON:0010313 ! neural crest-derived structure is_a: UBERON:0010912 ! subdivision of skeleton is_a: UBERON:0015212 ! lateral structure -relationship: in_lateral_side_of UBERON:0011156 {source="FMA-abduced-lr"} ! facial skeleton -relationship: location_of UBERON:0000019 ! camera-type eye +relationship: BSPO:0000126 UBERON:0011156 {source="FMA-abduced-lr"} ! facial skeleton relationship: part_of UBERON:0004088 ! orbital region relationship: part_of UBERON:0011156 ! facial skeleton -property_value: UBPROP:0000001 "Anatomical cluster that is a anterolateral part of the cranium and structurally supports the eye.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001410", ontology="TAO", source="TAO:MAH"} -property_value: UBPROP:0000012 "in FMA, this overlaps with bones such as the maxilla and sphenoid; in ZFA, individual bones are part of the orbit" xsd:string {external_ontology="FMA"} +relationship: RO:0001015 UBERON:0000019 ! location of camera-type eye [Term] id: UBERON:0001700 @@ -178997,13 +177748,12 @@ is_a: UBERON:0009127 ! epibranchial ganglion is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0001714 ! cranial ganglion intersection_of: extends_fibers_into UBERON:0001647 ! facial nerve -relationship: develops_from UBERON:0009124 {source="EHDAA2:0004623", source="ZFA"} ! geniculate placode -relationship: develops_from UBERON:0010258 {source="EHDAA2:0004623"} ! mesenchyme from rhombencephalic neural crest -relationship: develops_from UBERON:0012175 {source="EHDAA2:0000491"} ! acoustico-facial VII-VIII ganglion complex relationship: extends_fibers_into UBERON:0001647 ! facial nerve -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray789.png" xsd:anyURI -property_value: editor_note "resolve facial VII vs geniculate (see EHDAA2)" xsd:string -property_value: UBPROP:0000003 "These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia. (...) The one substantial difference between the vertebrate pharyngeal arches and those of the protochordates is the presence of the epibranchial placodes but the evolution of these structures was undoubtedly driven by the endoderm.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000707", ontology="VHOG", source="DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0009124 {source="EHDAA2:0004623", source="ZFA"} ! develops from geniculate placode +relationship: RO:0002202 UBERON:0010258 {source="EHDAA2:0004623"} ! develops from mesenchyme from rhombencephalic neural crest +relationship: RO:0002202 UBERON:0012175 {source="EHDAA2:0000491"} ! develops from acoustico-facial VII-VIII ganglion complex +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray789.png" xsd:anyURI +property_value: IAO:0000116 "resolve facial VII vs geniculate (see EHDAA2)" xsd:string [Term] id: UBERON:0001701 @@ -179031,10 +177781,9 @@ is_a: UBERON:0009127 {source="ZFA"} ! epibranchial ganglion intersection_of: UBERON:0001714 ! cranial ganglion intersection_of: extends_fibers_into UBERON:0001649 ! glossopharyngeal nerve relationship: extends_fibers_into UBERON:0001649 ! glossopharyngeal nerve -relationship: has_developmental_contribution_from UBERON:0005491 {notes="dorsal", source="EHDAA2", source="ISBN:0471888893", source="ZFA"} ! glossopharyngeal neural crest -relationship: has_developmental_contribution_from UBERON:0009125 {notes="ventrolateral", source="EHDAA2", source="ISBN:0471888893", source="ZFA"} ! petrosal placode -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000003 "These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia. (...) The one substantial difference between the vertebrate pharyngeal arches and those of the protochordates is the presence of the epibranchial placodes but the evolution of these structures was undoubtedly driven by the endoderm.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000702", ontology="VHOG", source="DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)", source="http://bgee.unil.ch/"} +relationship: RO:0002254 UBERON:0005491 ! has developmental contribution from glossopharyngeal neural crest +relationship: RO:0002254 UBERON:0009125 ! has developmental contribution from petrosal placode +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001703 @@ -179049,9 +177798,6 @@ synonym: "brain box" EXACT [] synonym: "brain case" RELATED [ZFA:0001580] synonym: "brain pan" RELATED [http://www.thefreedictionary.com/braincase] synonym: "braincase" RELATED [ZFA:0001580] -xref: AAO:0010153 -xref: EHDAA2:0000243 -xref: EMAPA:17681 xref: FMA:53672 xref: MA:0000317 xref: SCTID:361731002 @@ -179060,16 +177806,11 @@ xref: Wikipedia:Neuroranium xref: XAO:0003170 xref: ZFA:0001580 is_a: UBERON:0011158 {source="FMA"} ! primary subdivision of skull -relationship: develops_from UBERON:0004761 ! cartilaginous neurocranium -relationship: location_of UBERON:0000955 ! brain relationship: part_of UBERON:0003128 ! cranium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: protects UBERON:0000955 ! brain -property_value: UBPROP:0000001 "Anatomical cluster that consists of the cartilages and bones that surround the brain.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001580", ontology="TAO", source="TAO:MAH"} -property_value: UBPROP:0000007 "neurocranial" xsd:string -property_value: UBPROP:0000010 "It includes the following bones: Ethmoid bone, Frontal bone, Occipital bone, Parietal bone, Sphenoid bone, Temporal bone. The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton" xsd:string -property_value: UBPROP:0000011 "The cartilaginous parts of the neurocranium undergo endochondral ossification in most species; ossification has been lost in cartilaginous fishes, but the cartilaginous condition of the skull of lampreys is considered to be primitive (Kardong, 1995)[PMID:11523816]. The neurocranium arises from paraxial mesoderm in the head (first five somites and the unsegmented somitomeres rostral to the first somite) and from ectoderm via the neural crest. In Chondrichthyes and other cartilaginous vertebrates this portion of the cranium does not ossify; it is not replaced via endochondral ossification[WP]." xsd:string {source="WP"} -property_value: UBPROP:0000012 "It seems MA uses 'neurocranium' as a synonym for chondrocranium. Note there are currently some structures part of both viscero and neurocranium - ethmoid, zyogomatic, ..." xsd:string {external_ontology="MA"} +relationship: RO:0001015 UBERON:0000955 ! location of brain +relationship: RO:0002202 UBERON:0004761 ! develops from cartilaginous neurocranium +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001705 @@ -179101,9 +177842,7 @@ xref: UMLS:C0027342 {source="ncithesaurus:Nail"} xref: VHOG:0001361 xref: Wikipedia:Nail_(anatomy) is_a: UBERON:0009564 ! distal limb integumentary appendage -relationship: composed_primarily_of GO:0045095 ! keratin filament -property_value: IAO:0000232 "Use this class for both the nails of primates and the homologous claws of mammals such as mouse." xsd:string -property_value: UBPROP:0000008 "A primate's nail consists of the unguis alone; the subunguis has disappeared" xsd:string +relationship: RO:0002473 GO:0045095 ! composed primarily of keratin filament [Term] id: UBERON:0001707 @@ -179143,14 +177882,10 @@ xref: VHOG:0000271 xref: Wikipedia:Nasal_cavity xref: ZFA:0000130 is_a: UBERON:0002553 ! anatomical cavity -relationship: develops_from UBERON:0005870 ! olfactory pit relationship: part_of UBERON:0015788 {source="cjm"} ! olfactory apparatus chamber -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/d4/Illu01_head_neck.jpg" xsd:anyURI -property_value: editor_note "define the boundaries of this cavity for a variety of species and check that parthood relations are not too strong." xsd:string -property_value: UBPROP:0000001 "a large air filled space above and behind the nose in the middle of the face[WP][Wikipedia:Nasal_cavity]." xsd:string {source="Wikipedia:Nasal_cavity"} -property_value: UBPROP:0000001 "Saclike space internal to the nasal capsule lined by respiratory and sensory epithelium and glandular tissue.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000314", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000003 "Despite significant modification to the nasal cavity within Archosauria and its extreme hypertrophy and supraorbital development in Lambeosaurinae, the neural olfactory system and the olfactory region of the nasal cavity proper retain their plesiomorphic positions and associations, suggesting that this system is highly conserved in vertebrate evolution.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000271", ontology="VHOG", source="DOI:10.1666/0094-8373(2006)032[0109:NCHACC]2.0.CO;2 Evans DC, Nasal cavity homologies and cranial crest function in lambeosaurine dinosaurs. Paleobiology (2006)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "in humans, the cavity includes and starts at the nares and reaches all the way through to the and includes the choanae, the posterior nasal apertures" xsd:string {source="HP"} +relationship: RO:0002202 UBERON:0005870 ! develops from olfactory pit +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d4/Illu01_head_neck.jpg" xsd:anyURI +property_value: IAO:0000116 "define the boundaries of this cavity for a variety of species and check that parthood relations are not too strong." xsd:string [Term] id: UBERON:0001708 @@ -179183,19 +177918,16 @@ xref: TAO:0001227 xref: UMLS:C0022359 {source="ncithesaurus:Jaw"} xref: Wikipedia:Jaw xref: ZFA:0001227 -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +is_a: UBERON:0010313 ! neural crest-derived structure is_a: UBERON:0010912 ! subdivision of skeleton intersection_of: UBERON:0010912 ! subdivision of skeleton -intersection_of: skeleton_of UBERON:0011595 ! jaw region -relationship: only_in_taxon NCBITaxon:7776 ! Gnathostomata +intersection_of: RO:0002576 UBERON:0011595 ! skeleton of jaw region relationship: overlaps UBERON:0008895 ! splanchnocranium relationship: part_of UBERON:0011156 {source="cjm"} ! facial skeleton relationship: part_of UBERON:0011595 ! jaw region -relationship: skeleton_of UBERON:0011595 ! jaw region -property_value: editor_note "TODO - move ZFA:0001227 (it is the entire jaw skeleton)." xsd:string -property_value: UBPROP:0000001 "Skeletal and cartilage elements of the first pharyngeal arch.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001227", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000011 "There are cellular contributions from all three embryonic germ layers: pharyngeal mesoderm, endoderm and neural crest that migrates out of the ectoderm (Noden, 1983)." xsd:string -property_value: UBPROP:0000012 "in FMA, the jaw is an organism subdivision cluster, and includes mucosal tissue such as the gingiva as parts. It appears to be skeletal in MA (and has teeth as parts). It is reasonable to assume that ZFA and XAO consider the upper and lower jaws to be skeletal elements or clusters. EHDAA2 also considers these clusters. TODO - follow EHDAA2 model. These arbitrary differences in terminology and classification have to be reconciled with the genuine well-known biological differences in the skeletal elements across vertebrates" xsd:string {external_ontology="FMA"} +relationship: RO:0002160 NCBITaxon:7776 ! only in taxon Gnathostomata +relationship: RO:0002576 UBERON:0011595 ! skeleton of jaw region +property_value: IAO:0000116 "TODO - move ZFA:0001227 (it is the entire jaw skeleton)." xsd:string [Term] id: UBERON:0001709 @@ -179223,17 +177955,14 @@ xref: SCTID:362636001 xref: VHOG:0000454 xref: Wikipedia:Upper_jaw is_a: UBERON:0000475 ! organism subdivision +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0000475 ! organism subdivision -intersection_of: has_skeleton UBERON:0003277 ! skeleton of upper jaw +intersection_of: RO:0002551 UBERON:0003277 ! has skeleton skeleton of upper jaw disjoint_from: UBERON:0001710 ! lower jaw region -relationship: has_skeleton UBERON:0003277 ! skeleton of upper jaw relationship: part_of UBERON:0004089 ! midface relationship: part_of UBERON:0011595 ! jaw region -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/a7/Gray189.png" xsd:anyURI -property_value: RO:0002171 UBERON:0001710 -property_value: UBPROP:0000001 "Superior maxillary arch located on the anterior and lateral sides of the skull.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000620", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000003 "Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000454", ontology="VHOG", source="DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "Note isa/partof difference MA/FMA" xsd:string {external_ontology="MA"} +relationship: RO:0002551 UBERON:0003277 ! has skeleton skeleton of upper jaw +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/a7/Gray189.png" xsd:anyURI [Term] id: UBERON:0001710 @@ -179259,16 +177988,13 @@ xref: SCTID:362637005 xref: VHOG:0000453 xref: Wikipedia:Lower_jaw is_a: UBERON:0000475 ! organism subdivision +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0000475 ! organism subdivision -intersection_of: has_skeleton UBERON:0003278 ! skeleton of lower jaw -relationship: develops_from UBERON:0005867 {source="Wikipedia:Mandibular_prominence"} ! mandibular prominence -relationship: has_skeleton UBERON:0003278 ! skeleton of lower jaw +intersection_of: RO:0002551 UBERON:0003278 ! has skeleton skeleton of lower jaw relationship: part_of UBERON:0011595 ! jaw region -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray176.png" xsd:anyURI -property_value: RO:0002171 UBERON:0001709 -property_value: UBPROP:0000001 "Inferior mandibular arch located on the anterior and lateral sides of the skull.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000272", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000003 "Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000453", ontology="VHOG", source="DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "Note isa/partof difference MA/FMA" xsd:string {external_ontology="MA"} +relationship: RO:0002202 UBERON:0005867 {source="Wikipedia:Mandibular_prominence"} ! develops from mandibular prominence +relationship: RO:0002551 UBERON:0003278 ! has skeleton skeleton of lower jaw +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray176.png" xsd:anyURI [Term] id: UBERON:0001711 @@ -179297,17 +178023,12 @@ xref: UMLS:C0015426 {source="ncithesaurus:Eyelid"} xref: VHOG:0000016 xref: Wikipedia:Eyelid is_a: UBERON:0000064 ! organ part +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: capable_of GO:0060082 ! eye blink reflex -relationship: contributes_to_morphology_of UBERON:0000019 ! camera-type eye relationship: part_of UBERON:0000019 {source="multiple"} ! camera-type eye relationship: protects UBERON:0010409 ! ocular surface region -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/84/Eye_makeup.jpg" xsd:anyURI -property_value: UBPROP:0000007 "blepharic" xsd:string -property_value: UBPROP:0000007 "palpebral" xsd:string -property_value: UBPROP:0000008 "In humans the upper and lower eyelid consists of the following layers, starting anteriorly: (1) skin, (2) a layer of subcutaneous connective tissue, (3) a layer of striated muscle fibres of the orbicularis muscle, (4) a layer of submuscular connective tissue, (5) a fibrous layer, including the tarsal plates, (6) a layer of smooth muscle, (7) the palpebral conjunctiva." xsd:string -property_value: UBPROP:0000012 "Consider adding 'eye surface', like MA" xsd:string {external_ontology="MA"} -property_value: UBPROP:0000012 "FMA divides this into skin, fascia, conjunctiva" xsd:string {external_ontology="FMA"} -property_value: UBPROP:0000202 FMA:75178 +relationship: RO:0002433 UBERON:0000019 ! contributes to morphology of camera-type eye +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/84/Eye_makeup.jpg" xsd:anyURI [Term] id: UBERON:0001714 @@ -179352,8 +178073,7 @@ intersection_of: UBERON:0000045 ! ganglion intersection_of: extends_fibers_into UBERON:0034713 ! cranial neuron projection bundle relationship: extends_fibers_into UBERON:0034713 ! cranial neuron projection bundle relationship: part_of UBERON:0000033 ! head -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000001 "Ganglion which is located in the head.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000013", ontology="TAO", source="ZFIN:curator"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001720 @@ -179382,10 +178102,10 @@ xref: ZFA:0001638 is_a: UBERON:0007635 ! nucleus of medulla oblongata intersection_of: UBERON:0000125 ! neural nucleus intersection_of: part_of UBERON:0002610 ! cochlear nuclear complex -relationship: contributes_to_morphology_of UBERON:0002298 ! brainstem relationship: extends_fibers_into UBERON:0004727 ! cochlear nerve relationship: part_of UBERON:0002610 ! cochlear nuclear complex -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/52/Gray691.png" xsd:anyURI +relationship: RO:0002433 UBERON:0002298 ! contributes to morphology of brainstem +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/52/Gray691.png" xsd:anyURI [Term] id: UBERON:0001723 @@ -179423,24 +178143,16 @@ xref: ZFA:0005333 is_a: UBERON:0000020 {source="GO"} ! sense organ is_a: UBERON:0013765 ! digestive system element relationship: adjacent_to UBERON:0000166 ! oral opening -relationship: contributes_to_morphology_of UBERON:0001007 ! digestive system -relationship: develops_from UBERON:0008814 ! pharyngeal arch system -relationship: has_developmental_contribution_from UBERON:0006260 {notes="anterior 2/3"} ! lingual swellings -relationship: has_developmental_contribution_from UBERON:0006756 {source="Wikipedia"} ! median lingual swelling -relationship: has_developmental_contribution_from UBERON:0006757 {source="Wikipedia"} ! lateral lingual swelling -relationship: immediate_transformation_of UBERON:0010056 {evidence="definitional"} ! future tongue relationship: part_of UBERON:0000165 {source="BTO", source="EHDAA2", source="FMA", source="ZFA"} ! mouth relationship: part_of UBERON:0001033 {source="MA"} ! gustatory system -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/a6/Tongue.agr.jpg" xsd:anyURI -property_value: editor_note "in MA the tongue is part of the oral region, which in uberon is treated as the oral opening. consider revising oral opening - oral region equivalence." xsd:string -property_value: UBPROP:0000001 "A mobile mass of muscular tissue that is covered with mucous membrane, occupies much of the cavity of the mouth, forms part of its floor, bears the organ of taste, and assists in chewing and swallowing. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000419", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/tongue"} -property_value: UBPROP:0000001 "Muscular organ in the floor of the mouth.[FEED]" xsd:string {date_retrieved="2012-07-02", ontology="FEED", url="http://www.feedexp.org"} -property_value: UBPROP:0000001 "The tongue is the movable, muscular organ on the floor of the mouth of most vertebrates, in many other mammals is the principal organ of taste, aids in the prehension of food, in swallowing, and in modifying the voice as in speech[GO][GO:0043586]." xsd:string {source="GO:0043586"} -property_value: UBPROP:0000003 "Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000419", ontology="VHOG", source="DOI:10.1046/j.1469-7580.2002.00073.x Iwasaki S, Evolution of the structure and function of the vertebrate tongue. J Anat (2002)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "glossal" xsd:string -property_value: UBPROP:0000007 "lingual" xsd:string -property_value: UBPROP:0000008 "Many species of fish have small folds at the base of their mouths that might informally be called tongues, but they lack a muscular structure like the true tongues found in most tetrapods" xsd:string -property_value: UBPROP:0000011 "The tongue has contributions from all pharyngeal arches which changes with time. The tongue initially begins as swelling rostral to foramen cecum, the median tongue bud.. tongue muscles derive from the somites - http://php.med.unsw.edu.au/embryology/index.php?title=Tongue_Development#Pharyngeal_Arch_Contributions" xsd:string +relationship: RO:0002202 UBERON:0008814 ! develops from pharyngeal arch system +relationship: RO:0002254 UBERON:0006260 ! has developmental contribution from lingual swellings +relationship: RO:0002254 UBERON:0006756 {source="Wikipedia"} ! has developmental contribution from median lingual swelling +relationship: RO:0002254 UBERON:0006757 {source="Wikipedia"} ! has developmental contribution from lateral lingual swelling +relationship: RO:0002433 UBERON:0001007 ! contributes to morphology of digestive system +relationship: RO:0002495 UBERON:0010056 ! immediate transformation of future tongue +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/a6/Tongue.agr.jpg" xsd:anyURI +property_value: IAO:0000116 "in MA the tongue is part of the oral region, which in uberon is treated as the oral opening. consider revising oral opening - oral region equivalence." xsd:string [Term] id: UBERON:0001725 @@ -179509,17 +178221,11 @@ xref: ZFA:0001074 is_a: UBERON:0003212 ! gustatory organ is_a: UBERON:0004119 ! endoderm-derived structure relationship: capable_of GO:0050912 ! detection of chemical stimulus involved in sensory perception of taste -relationship: contributes_to_morphology_of UBERON:0001033 ! gustatory system -relationship: develops_from UBERON:0007690 {source="http://dev.biologists.org/content/128/22/4573.full"} ! early pharyngeal endoderm relationship: has_part CL:0000209 {source="FMA"} ! taste receptor cell relationship: part_of UBERON:0002926 {source="NIF"} ! gustatory epithelium -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/5a/Gray1018.png" xsd:anyURI -property_value: RO:0002171 UBERON:0002467 {source="http://periowiki.wikispot.org/Taste_bud_histology"} -property_value: UBPROP:0000001 "A chemoreceptive organ.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010573", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000001 "One of a number of receptor cell nests located in the epithelium of the papillae of the tongue and in the soft palate, epiglottis, and pharynx that mediate the sense of taste. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000130", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/taste+bud"} -property_value: UBPROP:0000003 "Experients in amphibia have shown that an intrinsic feature of the pharyngeal endoderm is its ability to generate taste buds and this capacity must have been acquired by the endoderm at the origin of the vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000130", ontology="VHOG", source="DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "In humans, saste buds may be found on the tongue, soft palatte, epiglottis and upper pharynx. In other species they may be found in more unusual places, such as the trunk, or on the barbels or fins of fish." xsd:string -property_value: UBPROP:0000011 "arise by inductive interactions between epithelial cells and invading gustatory cells from chorda tympani (facial), glossophrayngeal and vagues nerves ISBN:1607950324 (todo - request cell terms from CL)" xsd:string +relationship: RO:0002202 UBERON:0007690 {source="http://dev.biologists.org/content/128/22/4573.full"} ! develops from early pharyngeal endoderm +relationship: RO:0002433 UBERON:0001033 ! contributes to morphology of gustatory system +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5a/Gray1018.png" xsd:anyURI [Term] id: UBERON:0001728 @@ -179550,13 +178256,10 @@ xref: UMLS:C0027442 {source="ncithesaurus:Nasopharynx"} xref: VHOG:0000375 xref: Wikipedia:Nasopharynx is_a: UBERON:0000072 ! proximo-distal subdivision of respiratory tract -relationship: contributes_to_morphology_of UBERON:0001042 ! chordate pharynx relationship: part_of UBERON:0001042 ! chordate pharynx relationship: part_of UBERON:0001557 ! upper respiratory tract -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/4/4a/Illu_pharynx.jpg" xsd:anyURI -property_value: UBPROP:0000001 "The uppermost of the three regions of the throat (pharynx), situated behind the nasal cavity and extending from the posterior nares to the level above the soft palate. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000375", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/nasopharynx"} -property_value: UBPROP:0000007 "nasopharyngeal" xsd:string -property_value: UBPROP:0000008 "In humans - in front it communicates through the choanae with the nasal cavities. On its lateral wall is the pharyngeal ostium of the auditory tube, somewhat triangular in shape, and bounded behind by a firm prominence, the torus tubarius or cushion, caused by the medial end of the cartilage of the tube which elevates the mucous membrane" xsd:string +relationship: RO:0002433 UBERON:0001042 ! contributes to morphology of chordate pharynx +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/4/4a/Illu_pharynx.jpg" xsd:anyURI [Term] id: UBERON:0001731 @@ -179576,18 +178279,16 @@ xref: SCTID:180543003 xref: XAO:0000105 is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0006562 ! pharynx -relationship: develops_from UBERON:0001041 {source="XAO"} ! foregut -relationship: luminal_space_of UBERON:0006562 ! pharynx +intersection_of: RO:0002572 UBERON:0006562 ! luminal space of pharynx relationship: part_of UBERON:0006562 ! pharynx -property_value: UBPROP:0000008 "See notes for pharynx - as a grouping class this is probably too bad. We exclude WBbt:0005790 (pharyngeal lumen) because of the developmental relationship" xsd:string -property_value: UBPROP:0000011 "TOODO check" xsd:string +relationship: RO:0002202 UBERON:0001041 {source="XAO"} ! develops from foregut +relationship: RO:0002572 UBERON:0006562 ! luminal space of pharynx [Term] id: UBERON:0001735 name: tonsillar ring namespace: uberon -def: "The circular lymphoid tissue formed by the lingual, pharyngeal, and facial tonsils." [MGI:cwg, MP:0002379] +def: "The circular lymphoid tissue formed by the lingual, pharyngeal, and faucial tonsils." [MGI:cwg, MP:0002379] subset: pheno_slim subset: uberon_slim synonym: "anulus lymphoideus pharyngis" EXACT OMO:0003011 [FMA:55070, FMA:TA] @@ -179604,7 +178305,7 @@ xref: UMLS:C0459892 {source="ncithesaurus:Waldeyers_Tonsillar_Ring"} xref: Wikipedia:Waldeyer's_ring is_a: UBERON:0001962 ! gut-associated lymphoid tissue relationship: part_of UBERON:0001042 ! chordate pharynx -relationship: seeAlso FMA:79771 +property_value: seeAlso FMA:79771 [Term] id: UBERON:0001737 @@ -179635,16 +178336,12 @@ xref: VHOG:0001279 xref: Wikipedia:Larynx xref: XAO:0003081 is_a: UBERON:0000072 ! proximo-distal subdivision of respiratory tract -relationship: contributes_to_morphology_of UBERON:0001004 ! respiratory system -relationship: develops_from UBERON:0008947 {source="EHDAA2"} ! respiratory primordium -relationship: innervated_by UBERON:0003716 ! recurrent laryngeal nerve -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/8a/Larynx_external_en.svg" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-larynx.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-larynx.glb" xsd:anyURI -property_value: UBPROP:0000001 "An anatomical cluster consisting of the epiglottus, the arytenoid cartilages, the thyroid cartilage, the cricoid cartilage and the muscles, membranes, and ligaments connecting them, and also of the mucosal covering these structures.[FEED]" xsd:string {date_retrieved="2012-07-02", ontology="FEED", url="http://www.feedexp.org"} -property_value: UBPROP:0000001 "Anatomical structure consisting of a narrowly triangular chamber supported by a series of semicircular cartilages in which part of the sound-production system is located.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000268", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "(In anura) a dorsal pair of arytenoid cartilages (...), which support vocal cords, and a ventral pair (often fused) of cricoid cartilage (...). These cartilages are regarded as derivatives of posterior visceral arches of ancestors. Together they constitute the larynx, a structure characteristic of tetrapods. (...) (In mammals) Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (...) and a cartilage in the epiglottis.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001279", ontology="VHOG", source="ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.239-241", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "laryngeal" xsd:string +relationship: RO:0002005 UBERON:0003716 ! innervated_by recurrent laryngeal nerve +relationship: RO:0002202 UBERON:0008947 {source="EHDAA2"} ! develops from respiratory primordium +relationship: RO:0002433 UBERON:0001004 ! contributes to morphology of respiratory system +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8a/Larynx_external_en.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-larynx.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-larynx.glb" xsd:anyURI [Term] id: UBERON:0001739 @@ -179667,15 +178364,14 @@ xref: SCTID:263482005 xref: UMLS:C0023050 {source="ncithesaurus:Laryngeal_Cartilage"} xref: VHOG:0001550 is_a: UBERON:0003406 ! cartilage of respiratory system +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0011004 ! pharyngeal arch cartilage intersection_of: UBERON:0007844 ! cartilage element intersection_of: part_of UBERON:0001737 ! larynx -relationship: develops_from UBERON:0010213 ! laryngeal pre-cartilage condensation relationship: part_of UBERON:0010212 ! laryngeal apparatus -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-larynx.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-larynx.glb" xsd:anyURI -property_value: UBPROP:0000003 "(In anura) a dorsal pair of arytenoid cartilages (...), which support vocal cords, and a ventral pair (often fused) of cricoid cartilage (...). These cartilages are regarded as derivatives of posterior visceral arches of ancestors. Together they constitute the larynx, a structure characteristic of tetrapods. (...) (In mammals) Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (...) and a cartilage in the epiglottis.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001550", ontology="VHOG", source="ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.239-241", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000202 FMA:64159 +relationship: RO:0002202 UBERON:0010213 ! develops from laryngeal pre-cartilage condensation +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-larynx.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-larynx.glb" xsd:anyURI [Term] id: UBERON:0001743 @@ -179690,6 +178386,7 @@ xref: MA:0001755 xref: NCIT:C32933 xref: SCTID:279508004 xref: UMLS:C0458519 {source="ncithesaurus:Laryngeal_Ligament"} +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0008845 {source="FMA"} ! nonskeletal ligament intersection_of: UBERON:0000211 ! ligament intersection_of: part_of UBERON:0001737 ! larynx @@ -179718,9 +178415,8 @@ xref: Wikipedia:Lymphoid_tissue is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0034769 {source="FMA"} ! lymphomyeloid tissue relationship: has_part CL:0000542 ! lymphocyte -relationship: only_in_taxon NCBITaxon:7742 {source="NCBIBook:NBK27108"} ! Vertebrata relationship: part_of UBERON:0002465 ! lymphoid system -property_value: RO:0002174 NCBITaxon:7776 {notes="lampreys lack organized lymphoid tissue", source="NCBIBook:NBK27108"} +relationship: RO:0002160 NCBITaxon:7742 {source="NCBIBook:NBK27108"} ! only in taxon Vertebrata [Term] id: UBERON:0001745 @@ -179736,10 +178432,10 @@ xref: GAID:946 is_a: UBERON:0000444 ! lymphoid follicle intersection_of: UBERON:0000444 ! lymphoid follicle intersection_of: has_part UBERON:0010754 ! germinal center -relationship: contains_process GO:0042100 ! B cell proliferation -relationship: develops_from UBERON:0010422 ! primary nodular lymphoid tissue +relationship: BFO:0000067 GO:0042100 ! contains process B cell proliferation relationship: has_part UBERON:0010754 ! germinal center -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/Keimzentrum.jpg" xsd:anyURI +relationship: RO:0002202 UBERON:0010422 ! develops from primary nodular lymphoid tissue +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/Keimzentrum.jpg" xsd:anyURI [Term] id: UBERON:0001746 @@ -179756,6 +178452,7 @@ xref: NCIT:C33781 xref: SCTID:176859009 xref: UMLS:C0229575 {source="ncithesaurus:Thyroid_Gland_Capsule"} is_a: UBERON:0003893 ! capsule +is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0003893 ! capsule intersection_of: part_of UBERON:0002046 ! thyroid gland relationship: part_of UBERON:0002046 ! thyroid gland @@ -179780,6 +178477,8 @@ xref: MA:0000730 xref: SCTID:371402001 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000353 ! parenchyma +is_a: UBERON:0004119 ! endoderm-derived structure +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0000353 ! parenchyma intersection_of: part_of UBERON:0002046 ! thyroid gland relationship: has_part CL:0000570 {source="FMA"} ! parafollicular cell @@ -179803,8 +178502,8 @@ is_a: UBERON:0003893 ! capsule intersection_of: UBERON:0003893 ! capsule intersection_of: bounding_layer_of UBERON:0001132 ! parathyroid gland relationship: bounding_layer_of UBERON:0001132 ! parathyroid gland -relationship: composed_primarily_of UBERON:0011822 ! dense irregular connective tissue relationship: part_of UBERON:0001132 {source="MA"} ! parathyroid gland +relationship: RO:0002473 UBERON:0011822 ! composed primarily of dense irregular connective tissue [Term] id: UBERON:0001749 @@ -179845,14 +178544,14 @@ xref: NCIT:C32905 xref: UMLS:C0022903 {source="ncithesaurus:Lacrimal_Apparatus"} xref: Wikipedia:Lacrimal_apparatus is_a: UBERON:0000467 ! anatomical system -relationship: contributes_to_morphology_of UBERON:0000019 ! camera-type eye -relationship: develops_from UBERON:0000076 {source="ISBN:0781772214"} ! external ectoderm -relationship: only_in_taxon NCBITaxon:32523 ! Tetrapoda +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0010409 {source="MA"} ! ocular surface region relationship: part_of UBERON:0035639 {source="HPO:pr"} ! ocular adnexa -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray896.png" xsd:anyURI -property_value: editor_note "TODO - resolve canaliculus vs tear duct vs lacrimal vs nasolacrimal" xsd:string -property_value: UBPROP:0000012 "this is an eye appendage in ncit, along with eyelid and eyebrow. in MA, part of eye surface part_of eye" xsd:string {external_ontology="ncit"} +relationship: RO:0002160 NCBITaxon:32523 ! only in taxon Tetrapoda +relationship: RO:0002202 UBERON:0000076 {source="ISBN:0781772214"} ! develops from external ectoderm +relationship: RO:0002433 UBERON:0000019 ! contributes to morphology of camera-type eye +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray896.png" xsd:anyURI +property_value: IAO:0000116 "TODO - resolve canaliculus vs tear duct vs lacrimal vs nasolacrimal" xsd:string [Term] id: UBERON:0001751 @@ -179881,15 +178580,10 @@ xref: VSAO:0000069 xref: Wikipedia:Dentin xref: XAO:0004051 xref: ZFA:0005143 -is_a: UBERON:0010313 ! neural crest-derived structure is_a: UBERON:0010365 {source="VSAO"} ! odontoid tissue is_a: UBERON:4000013 ! mineralized skeletal tissue -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata -relationship: transformation_of UBERON:0011587 {source="VSAO"} ! pre-dentine -property_value: UBPROP:0000001 "Mineralized collagen containing substance that forms the tooth structure.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005143", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "Dentine is a bona fide vertebrate novelty, and dentine-secreting odontoblasts represent a cell type that is exclusively derived from the neural crest.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001589", ontology="VHOG", source="DOI:10.1111/j.1469-7580.2012.01495.x Hall BK, Gillis JA, Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues. J Anat (2012)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "dentinal" xsd:string -property_value: UBPROP:0000008 "Dentine is found in the fossil record as early as the late Cambrian, in fish, where it may have had a role in electrochemical sensing of the environment as well as assisting in defense[WP]" xsd:string +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002494 UBERON:0011587 {source="VSAO"} ! transformation of pre-dentine [Term] id: UBERON:0001752 @@ -179917,15 +178611,13 @@ xref: Wikipedia:Enamel_organ xref: XAO:0004198 is_a: UBERON:0010365 {source="VSAO"} ! odontoid tissue is_a: UBERON:4000013 ! mineralized skeletal tissue -relationship: composed_primarily_of CHEBI:52255 {proportion="85", source="Wikipedia:ENAM"} -relationship: develops_from UBERON:0011588 {source="VSAO"} ! pre-enamel -relationship: never_in_taxon NCBITaxon:9359 {source="PMID:19730686"} -relationship: never_in_taxon NCBITaxon:9816 {source="PMID:19730686"} -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Enamelorgan11-17-05.jpg" xsd:anyURI -property_value: editor_note "current classification under substance of tooth may be turned into taxon GCI (e.g. sharks have enamel in dermal denticles)" xsd:string -property_value: UBPROP:0000001 "Skeletal tissue that consists of an avascular, noncollagenous, hypermineralized matrix that is deposited by ameloblasts that are excluded from the matrix. Enamel develops from organic pre-enamel tissue that is replaced by a largely inorganic matrix.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000065", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000012 "part_of tooth enamel organ in MA" xsd:string {external_ontology="MA"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002202 UBERON:0011588 {source="VSAO"} ! develops from pre-enamel +relationship: RO:0002473 CHEBI:52255 ! composed primarily of +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Enamelorgan11-17-05.jpg" xsd:anyURI +property_value: IAO:0000116 "current classification under substance of tooth may be turned into taxon GCI (e.g. sharks have enamel in dermal denticles)" xsd:string +property_value: RO:0002161 NCBITaxon:9359 {source="PMID:19730686"} +property_value: RO:0002161 NCBITaxon:9816 {source="PMID:19730686"} [Term] id: UBERON:0001753 @@ -179951,11 +178643,8 @@ xref: VSAO:0000062 xref: Wikipedia:Cementum xref: XAO:0004196 is_a: UBERON:0010365 {source="VSAO"} ! odontoid tissue -relationship: has_developmental_contribution_from UBERON:0008969 {source="PMID:19767574", source="Wikipedia"} ! dental follicle -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/d/dc/The_Periodontium.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Odontoid tissue that is deposited by cementoblasts onto dentine tissue and functions to attach teeth, odontodes and other odontogenic derivatives to bone tissue and the integument.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000062", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "Substance of tooth produced by cementoblasts; surrounds the dentine of the root of the tooth[FMA:55630]." xsd:string {source="FMA:55630"} -property_value: UBPROP:0000008 "Cementum, the supporting tissue that anchors mammalian and crocodylian teeth into their sockets, differs among species and can have features of dentine, of bone, and of calcified cartilage, as well as unique features. Cementum is deposited by cementoblasts onto existing dentine. As in bone and dentine, cementoblasts produce an organic matrix, the main constituent of which is collagen type I (Bosshardt, 2005), but cementum, dentine, and bone also share a number of important noncollagenous matrix components such as osteopontin, osteocalcin, bone sialoprotein, a2-HS- glycoprotein, dentine matrix protein, dentine sialoprotein, and den- tine phosphoprotein (McKee et al., 1996; Bosshardt, 2005). it has been argued that in all rodents and ruminants, cementum is a form of calcified cartilage[H&W]" xsd:string +relationship: RO:0002254 UBERON:0008969 {source="PMID:19767574", source="Wikipedia"} ! has developmental contribution from dental follicle +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/dc/The_Periodontium.jpg" xsd:anyURI [Term] id: UBERON:0001754 @@ -179982,13 +178671,12 @@ xref: UMLS:C0011399 {source="ncithesaurus:Dental_Pulp"} xref: VHOG:0001469 xref: Wikipedia:Dental_pulp xref: ZFA:0005141 +is_a: UBERON:0010313 ! neural crest-derived structure is_a: UBERON:0011825 {source="FMA"} ! loose connective tissue -relationship: develops_from UBERON:0001763 {source="ZFA"} ! odontogenic papilla relationship: has_part CL:0000060 ! odontoblast relationship: part_of UBERON:0001091 ! calcareous tooth -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/2/2e/Tooth_Section.svg" xsd:anyURI -property_value: UBPROP:0000001 "Material in the center of the dentine of the mature tooth. In secondary teeth the pulp contains blood vessels and odontoblast.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005141", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "The oral cavity of vertebrates is generally thought to arise as an ectodermal invagination. Consistent with this, oral teeth are proposed to arise exclusively from ectoderm, contributing to tooth enamel epithelium, and from neural crest derived mesenchyme, contributing to dentin and pulp (reference 1); Teeth and tooth-like structures, together named odontodes, are repeated organs thought to share a common evolutionary origin. These structures can be found in gnathostomes at different locations along the body: oral teeth in the jaws, teeth and denticles in the oral-pharyngeal cavity, and dermal denticles on elasmobranch skin (reference 2).[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001469", ontology="VHOG", source="DOI:10.1038/nature07304 Soukup V, Epperlein HH, Horacek I, Cerny R, Dual epithelial origin of vertebrate oral teeth. Nature (2008), DOI:10.1186/1471-2148-11-307 The homology of odontodes in gnathostomes: insights from Dlx gene expression in the dogfish, Scyliorhinus canicula. BMC Evolutionary Biology (2011)", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0001763 {source="ZFA"} ! develops from odontogenic papilla +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/2e/Tooth_Section.svg" xsd:anyURI [Term] id: UBERON:0001756 @@ -180020,10 +178708,8 @@ xref: VHOG:0000312 xref: Wikipedia:Middle_ear xref: XAO:0000191 is_a: UBERON:0034921 ! multi organ part structure -relationship: contributes_to_morphology_of UBERON:0001690 ! ear relationship: part_of UBERON:0001690 ! ear -property_value: UBPROP:0000001 "The intermediate portion of the ear which consists of a small air-filled and membrane-lined chamber. It is lodged in the temporal bone and continues with the nasopharynx through the Eustachian tube. It is separated from the external ear by the tympanic membrane and from the inner ear by the fenestrae. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000312", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "The tympanic cavity and auditory tube of an amniote develop from the first embryonic pharyngeal pouch, so they are homologous to the first gill pouch, or spiracle, of a fish. We are uncertain whether this homology strictly applies to the middle ear cavity and auditory tube of lissamphibians, which show certain peculiarities in their development.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000312", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.417", source="http://bgee.unil.ch/"} +relationship: RO:0002433 UBERON:0001690 ! contributes to morphology of ear [Term] id: UBERON:0001757 @@ -180051,15 +178737,11 @@ xref: UMLS:C0928075 {source="ncithesaurus:Auricle"} xref: VHOG:0000460 xref: Wikipedia:Pinna_(anatomy) is_a: UBERON:0001444 ! subdivision of head -relationship: continuous_with UBERON:0001352 ! external acoustic meatus -relationship: develops_from UBERON:0006208 ! auditory hillocks -relationship: has_quality PATO:0001297 ! reflectivity -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0001691 ! external ear -property_value: UBPROP:0000001 "The external expanded part of the ear characterized by a funnel-shaped structure through which the sound vibrations are received. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000460", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "Mammals have a third type of tympanic ear. An external flap, the auricle or pinna, helps funnel sound waves down the external acoustic meatus to the tympanic membrane.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000460", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.420", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "In various species, the pinna can also signal mood and radiate heat" xsd:string -property_value: UBPROP:0000009 "The purpose of the pinna is to collect sound. It does so by acting as a funnel, amplifying the sound and directing it to the ear canal. While reflecting from the pinna, sound also goes through a filtering process which adds directional information to the sound (see sound localization, head-related transfer function, pinna notch)." xsd:string +relationship: RO:0000086 PATO:0001297 ! has quality reflectivity +relationship: RO:0002150 UBERON:0001352 ! continuous with external acoustic meatus +relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia +relationship: RO:0002202 UBERON:0006208 ! develops from auditory hillocks [Term] id: UBERON:0001758 @@ -180082,8 +178764,7 @@ is_a: UBERON:0000479 {source="cjm"} ! tissue relationship: adjacent_to UBERON:0001091 ! calcareous tooth relationship: has_part CL:0002166 {source="FMA"} ! epithelial cell of Malassez relationship: part_of UBERON:0003672 {source="cjm"} ! dentition -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/d/dc/The_Periodontium.jpg" xsd:anyURI -property_value: UBPROP:0000012 "FMA treats periodontium and periodontal ligament as the same" xsd:string {external_ontology="FMA"} +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/dc/The_Periodontium.jpg" xsd:anyURI [Term] id: UBERON:0001759 @@ -180139,12 +178820,10 @@ intersection_of: UBERON:0001785 ! cranial nerve intersection_of: extends_fibers_into UBERON:0011775 ! vagus nerve nucleus relationship: extends_fibers_into UBERON:0002075 ! viscus relationship: extends_fibers_into UBERON:0011775 ! vagus nerve nucleus -relationship: has_developmental_contribution_from UBERON:0005239 {notes="motor", source="Wikipedia"} ! basal plate metencephalon relationship: part_of UBERON:0001033 ! gustatory system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/5e/Gray791.png" xsd:anyURI -property_value: UBPROP:0000001 "Nerve consisting of branchiomotor and visceral efferent fibers which branch and innervate the smooth muscles and glands of the heart, lungs, esophagus, and stomach as well as some throat muscles. Sensory fibers supply mucosa of the mouth and pharynx.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010475", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000737", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625", source="http://bgee.unil.ch/"} +relationship: RO:0002254 UBERON:0005239 ! has developmental contribution from basal plate metencephalon +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5e/Gray791.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001763 @@ -180175,18 +178854,14 @@ xref: ZFA:0005140 is_a: UBERON:0005856 ! developing mesenchymal condensation is_a: UBERON:0007213 ! mesenchyme derived from head neural crest intersection_of: UBERON:0005856 ! developing mesenchymal condensation -intersection_of: composed_primarily_of CL:0007003 ! preodontoblast intersection_of: part_of UBERON:0008281 ! tooth bud -relationship: composed_primarily_of CL:0007003 ! preodontoblast -relationship: develops_from UBERON:0003856 {source="ZFA"} ! uncondensed odontogenic mesenchyme -relationship: immediately_deep_to UBERON:0005176 ! tooth enamel organ -relationship: located_in UBERON:0001828 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA-implied"} ! gingiva +intersection_of: RO:0002473 CL:0007003 ! composed primarily of preodontoblast +relationship: BSPO:0001107 UBERON:0005176 ! tooth enamel organ relationship: part_of UBERON:0008281 ! tooth bud -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/22/Gray1011.png" xsd:anyURI -property_value: UBPROP:0000001 "Cell condensation that is a well-defined population of densely organized mesenchymal cells that aggregates adjacent to an epithelium.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000025", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "Tissue of the developing tooth. It is composed of pre-odontoblast and undiffentiated mesnchyme cells and connects to the basal lamina.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005140", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "Teeth and tooth-like structures, together named odontodes, are repeated organs thought to share a common evolutionary origin. These structures can be found in gnathostomes at different locations along the body: oral teeth in the jaws, teeth and denticles in the oral-pharyngeal cavity, and dermal denticles on elasmobranch skin.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001465", ontology="VHOG", source="DOI:10.1186/1471-2148-11-307 The homology of odontodes in gnathostomes: insights from Dlx gene expression in the dogfish, Scyliorhinus canicula. BMC Evolutionary Biology (2011)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000011 "In humans, the dental papilla appears after 8-10 weeks intra uteral life" xsd:string +relationship: RO:0001025 UBERON:0001828 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA-implied"} ! located in gingiva +relationship: RO:0002202 UBERON:0003856 {source="ZFA"} ! develops from uncondensed odontogenic mesenchyme +relationship: RO:0002473 CL:0007003 ! composed primarily of preodontoblast +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/22/Gray1011.png" xsd:anyURI [Term] id: UBERON:0001765 @@ -180220,7 +178895,7 @@ intersection_of: UBERON:0000058 ! duct intersection_of: part_of UBERON:0001911 ! mammary gland relationship: channel_for UBERON:0001913 ! milk relationship: channels_into UBERON:0002030 ! nipple -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Illu_breast_anatomy.jpg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Illu_breast_anatomy.jpg" xsd:anyURI [Term] id: UBERON:0001766 @@ -180249,11 +178924,9 @@ xref: UMLS:C0003151 {source="ncithesaurus:Anterior_Chamber_of_the_Eye"} xref: VHOG:0001431 xref: Wikipedia:Anterior_chamber_of_eyeball is_a: UBERON:0006311 {source="FMA"} ! chamber of eyeball -relationship: contributes_to_morphology_of UBERON:0001801 ! anterior segment of eyeball relationship: part_of UBERON:0001801 ! anterior segment of eyeball -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI -property_value: UBPROP:0000001 "The part of the eyeball between the cornea and the iris, filled with aqueous humor. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001431", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/anterior+chamber"} -property_value: UBPROP:0000012 "space in EHDAA2 - consider adding Cavity of anterior chamber of eyeball" xsd:string {external_ontology="EHDAA2"} +relationship: RO:0002433 UBERON:0001801 ! contributes to morphology of anterior segment of eyeball +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI [Term] id: UBERON:0001768 @@ -180279,16 +178952,17 @@ xref: NCIT:C12811 xref: SCTID:280648000 xref: UMLS:C0042160 {source="ncithesaurus:Uvea"} xref: Wikipedia:Uvea +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004923 {source="FMA"} ! organ component layer -relationship: contributes_to_morphology_of UBERON:0000019 ! camera-type eye +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: has_part UBERON:0001769 ! iris relationship: has_part UBERON:0001775 ! ciliary body relationship: has_part UBERON:0001776 ! optic choroid relationship: part_of UBERON:0001801 ! anterior segment of eyeball -relationship: present_in_taxon NCBITaxon:7955 {source="DOI:10.1177/0192623311409597"} -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/eb/Gray869.png" xsd:anyURI -property_value: editor_note "TODO - check child terms, isa vs partof. See also MA:0001284 ! tunica vasculosa plexus" xsd:string -property_value: UBPROP:0000007 "uveal" xsd:string +relationship: RO:0002433 UBERON:0000019 ! contributes to morphology of camera-type eye +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/eb/Gray869.png" xsd:anyURI +property_value: IAO:0000116 "TODO - check child terms, isa vs partof. See also MA:0001284 ! tunica vasculosa plexus" xsd:string +property_value: RO:0002175 NCBITaxon:7955 {source="DOI:10.1177/0192623311409597"} [Term] id: UBERON:0001769 @@ -180323,14 +178997,10 @@ xref: XAO:0000185 xref: ZFA:0001238 is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004121 ! ectoderm-derived structure -relationship: contributes_to_morphology_of UBERON:0011892 ! anterior uvea -relationship: develops_from UBERON:0004128 {source="XAO"} ! optic vesicle relationship: part_of UBERON:0011892 ! anterior uvea -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000001 "The opaque muscular contractile diaphragm suspended in the aqueous humour in front of the lens of the eye. The organ is perforated by the pupil and continues peripherally with the ciliary body. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000101", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000101", ontology="VHOG", source="DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "iridial" xsd:string -property_value: UBPROP:0000008 "The avian iris and ciliary body undergoes a transition from smooth-to-striated muscle during embryonic development [DOI:dx.doi.org/10.1006/dbio.1998.9019]" xsd:string +relationship: RO:0002202 UBERON:0004128 {source="XAO"} ! develops from optic vesicle +relationship: RO:0002433 UBERON:0011892 ! contributes to morphology of anterior uvea +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001770 @@ -180348,9 +179018,10 @@ xref: SCTID:263348000 xref: UMLS:C0459631 {source="ncithesaurus:Lacrimal_Canaliculus"} xref: Wikipedia:Lacrimal_canaliculi is_a: UBERON:0004111 ! anatomical conduit -relationship: connects UBERON:0001351 ! lacrimal sac -relationship: connects UBERON:0010284 ! lacrimal punctum +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001850 {source="FMA"} ! lacrimal drainage system +relationship: RO:0002176 UBERON:0001351 ! connects lacrimal sac +relationship: RO:0002176 UBERON:0010284 ! connects lacrimal punctum [Term] id: UBERON:0001772 @@ -180393,17 +179064,15 @@ xref: UMLS:C0459875 {source="ncithesaurus:Corneal_Epithelium"} xref: Wikipedia:Corneal_epithelium xref: ZFA:0001683 is_a: UBERON:0000488 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! atypical epithelium +is_a: UBERON:0010313 ! neural crest-derived structure is_a: UBERON:0015808 ! eye epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: bounding_layer_of UBERON:0000964 ! cornea relationship: bounding_layer_of UBERON:0000964 ! cornea -relationship: contributes_to_morphology_of UBERON:0000964 ! cornea -relationship: develops_from UBERON:0000076 {source="ISBN:0781772214"} ! external ectoderm -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png" xsd:anyURI -property_value: UBPROP:0000001 "Portion of tissue comprised of four to six layers of nonkeratinized, stratified squamous cells and represents approximately 60% of the thickness of the cornea.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002187", ontology="TAO", source="ZFIN:ZDB-PUB-061010-3"} -property_value: UBPROP:0000008 "In Humans: It consists of several layers of cells. The cells of the deepest layer are columnar; then follow two or three layers of polyhedral cells, the majority of which are prickle cells similar to those found in the stratum mucosum of the cuticle. Lastly, there are three or four layers of squamous cells, with flattened nuclei" xsd:string -property_value: UBPROP:0000008 "In zebrafish: nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals" xsd:string +relationship: RO:0002202 UBERON:0000076 {source="ISBN:0781772214"} ! develops from external ectoderm +relationship: RO:0002433 UBERON:0000964 ! contributes to morphology of cornea +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001773 @@ -180432,21 +179101,14 @@ xref: Wikipedia:Sclera xref: XAO:0000183 xref: ZFA:0005563 is_a: UBERON:0000064 ! organ part -relationship: contributes_to_morphology_of UBERON:0000019 ! camera-type eye -relationship: develops_from UBERON:0003314 {source="ISBN:0781772214"} ! eye mesenchyme -relationship: develops_from UBERON:0007213 {inferred_by="cjm", source="ISBN:0781772214", source="Wikipedia"} ! mesenchyme derived from head neural crest +is_a: UBERON:0010313 ! neural crest-derived structure relationship: has_part CL:0000347 {source="ZFA"} ! scleral cell -relationship: has_quality PATO:0000963 ! opaque relationship: part_of UBERON:0012430 {source="FMA"} ! tunica fibrosa of eyeball -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI -property_value: UBPROP:0000001 "The sclera, also known as the white part of the eye, is the opaque (usually white, though certain animals, such as horses and lizards, can have black sclera), fibrous, protective, outer layer of the eye containing collagen and elastic fiber. It is derived from the neural crest. In children, it is thinner and shows some of the underlying pigment, appearing slightly blue. In the elderly, however, fatty deposits on the sclera can make it appear slightly yellow. The sclera forms the posterior five sixths of the connective tissue coat of the globe. It is continuous with the dura mater and the cornea, and maintains the shape of the globe, offering resistance to internal and external forces, and provides an attachment for the extraocular muscle insertions. The sclera is perforated by plenty of nerves and vessels passing through the posterior scleral foramen, the hole that is formed by the optic nerve. At the optic disk the outer two-thirds of the sclera continues with the dura mater (outer coat of the brain) via the dural sheath of the optic nerve. The inner third joins with some choroidal tissue to form a plate (lamina cribrosa) across the optic nerve with perforations through which the optic fibers (fasciculi). The thickness of the sclera varies from 1mm at the posterior pole to 0.3 mm just behind the rectus muscle insertions. The sclera's blood vessels are mainly on the surface, and together with the conjunctiva (which lies on top) This is a thin layer covering the sclera. Along with the vessels of the conjunctiva, those of the sclera renders the inflamed eye bright red. [WP,unvetted][Wikipedia:Sclera]." xsd:string {source="Wikipedia:Sclera"} -property_value: UBPROP:0000001 "The tough, usually white, outer coat of the eyeball, covering all the posterior surface and continuous anteriorly with the cornea. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001274", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/sclera"} -property_value: UBPROP:0000007 "scleral" xsd:string -property_value: UBPROP:0000008 "in fish, reptiles and monotremes the connective tissue of the sclera is skeletal" xsd:string -property_value: UBPROP:0000010 "continuous with the dura mater and the cornea; The sclera forms the posterior five-sixths of the connective tissue coat of the globe." xsd:string -property_value: UBPROP:0000011 "Majority derives from NC that surrounds optic cup of neurectoderm; a small temporal portion develops from the mesoderm that contributes to striated extra-ocular muscles and vascular endothelia[Rada&Johnson]." xsd:string -property_value: UBPROP:0000011 "Seko et al demonstrate chondrogenic potential and identify this as connective tissue[DOI:10.1371/journal.pone.0003709]." xsd:string +relationship: RO:0000086 PATO:0000963 ! has quality opaque +relationship: RO:0002202 UBERON:0003314 {source="ISBN:0781772214"} ! develops from eye mesenchyme +relationship: RO:0002433 UBERON:0000019 ! contributes to morphology of camera-type eye +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001774 @@ -180475,8 +179137,7 @@ is_a: UBERON:0014892 ! skeletal muscle organ, vertebrate intersection_of: UBERON:0014892 ! skeletal muscle organ, vertebrate intersection_of: part_of UBERON:0002100 ! trunk relationship: part_of UBERON:0004479 {source="prolog"} ! musculature of trunk -property_value: editor_note "Note that this class excludes smooth muscle elements in the trunk region, such as the internal anal sphincter. This appears to be consistent with other ontologies such as FMA and ZFA which appear to only include skeletal muscles here. In fact the MA class 'trunk muscle' is classified as a 'set of skeletal muscles'." xsd:string -property_value: UBPROP:0000012 "Many ontologies do not appear to have a coherent distinction between an individual muscle and the musculature (i.e. the set of muscles in a region), so we group all together here." xsd:string +property_value: IAO:0000116 "Note that this class excludes smooth muscle elements in the trunk region, such as the internal anal sphincter. This appears to be consistent with other ontologies such as FMA and ZFA which appear to only include skeletal muscles here. In fact the MA class 'trunk muscle' is classified as a 'set of skeletal muscles'." xsd:string [Term] id: UBERON:0001775 @@ -180509,14 +179170,13 @@ xref: Wikipedia:Ciliary_body xref: XAO:0000186 is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004121 ! ectoderm-derived structure -relationship: contributes_to_morphology_of UBERON:0011892 ! anterior uvea -relationship: develops_from UBERON:0002346 {source="ISBN:0781772214"} ! neurectoderm relationship: has_part UBERON:0001605 ! ciliary muscle relationship: has_part UBERON:0010427 ! ciliary processes relationship: part_of UBERON:0011892 ! anterior uvea -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI -property_value: UBPROP:0000003 "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000102", ontology="VHOG", source="DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0002346 {source="ISBN:0781772214"} ! develops from neurectoderm +relationship: RO:0002433 UBERON:0011892 ! contributes to morphology of anterior uvea +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001776 @@ -180555,15 +179215,13 @@ disjoint_from: UBERON:0011892 {source="lexical"} ! anterior uvea relationship: adjacent_to UBERON:0000966 ! retina relationship: adjacent_to UBERON:0001773 ! sclera relationship: adjacent_to UBERON:0011892 ! anterior uvea -relationship: contributes_to_morphology_of UBERON:0001768 ! uvea relationship: overlaps UBERON:0001802 {source="Wikipedia"} ! posterior segment of eyeball relationship: part_of UBERON:0001768 {source="MA"} ! uvea relationship: part_of UBERON:0019207 ! chorioretinal region -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI -property_value: editor_note "check choroid vs choroid layer; check ZFA/TAO placement - no homology assertion in VHOG. Note this is entirely in the posterior region of eyeball in ZFA" xsd:string -property_value: UBPROP:0000007 "choroidal" xsd:string -property_value: UBPROP:0000012 "MP treats posterior uvea and optic choroid as distinct" xsd:string {external_ontology="MP"} +relationship: RO:0002433 UBERON:0001768 ! contributes to morphology of uvea +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: IAO:0000116 "check choroid vs choroid layer; check ZFA/TAO placement - no homology assertion in VHOG. Note this is entirely in the posterior region of eyeball in ZFA" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001777 @@ -180592,17 +179250,15 @@ xref: UMLS:C0010040 {source="ncithesaurus:Corneal_Stroma"} xref: Wikipedia:Corneal_stroma xref: ZFA:0001685 is_a: UBERON:0003891 ! stroma +is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0003891 ! stroma intersection_of: part_of UBERON:0000964 ! cornea relationship: adjacent_to UBERON:0004367 ! Descemet's membrane relationship: adjacent_to UBERON:0004370 ! anterior limiting lamina of cornea -relationship: contributes_to_morphology_of UBERON:0000964 ! cornea -relationship: develops_from UBERON:0007213 {inferred_by="cjm", source="ISBN:0781772214", source="Wikipedia"} ! mesenchyme derived from head neural crest relationship: part_of UBERON:0000964 ! cornea -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png" xsd:anyURI -property_value: UBPROP:0000001 "Portion of tissue that is located basal to Bowman's layer and distal to Descemet's membrane and is comprised largely of connective tissue.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002189", ontology="TAO", source="ZFIN:ZDB-PUB-061010-3"} -property_value: UBPROP:0000002 "relationship type change: subclass tissue (CARO:0000043) CHANGED TO: develops_from tissue (UBERON:0000479)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002189", ontology="TAO"} -property_value: UBPROP:0000002 "relationship type change: subclass tissue (CARO:0000043) CHANGED TO: has_developmental_contribution_from tissue (UBERON:0000479)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002189", ontology="TAO"} +relationship: RO:0002202 UBERON:0007213 ! develops from mesenchyme derived from head neural crest +relationship: RO:0002433 UBERON:0000964 ! contributes to morphology of cornea +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png" xsd:anyURI [Term] id: UBERON:0001778 @@ -180628,8 +179284,8 @@ intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001775 ! ciliary body relationship: has_part GO:0048770 {source="MP"} ! pigment granule relationship: part_of UBERON:0001775 {source="MA"} ! ciliary body -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: produces UBERON:0001796 {source="Wikipedia"} ! aqueous humor of eyeball +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001779 @@ -180648,11 +179304,12 @@ xref: SCTID:280882008 xref: Wikipedia:Iris_stroma xref: ZFA:0005569 is_a: UBERON:0003891 ! stroma +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0003891 ! stroma intersection_of: part_of UBERON:0001769 ! iris -relationship: contributes_to_morphology_of UBERON:0001769 ! iris relationship: part_of UBERON:0001769 ! iris -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png" xsd:anyURI +relationship: RO:0002433 UBERON:0001769 ! contributes to morphology of iris +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png" xsd:anyURI [Term] id: UBERON:0001780 @@ -180693,9 +179350,8 @@ is_a: UBERON:0001021 ! nerve intersection_of: UBERON:0001021 ! nerve intersection_of: extends_fibers_into UBERON:0002240 ! spinal cord relationship: extends_fibers_into UBERON:0002240 ! spinal cord -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg" xsd:anyURI -property_value: UBPROP:0000001 "Any of the paired nerves emerging from the spinal cord, each attached to the cord by two roots: ventral and dorsal, and passing out between the vertebrae. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000824", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/spinal+nerve"} +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001781 @@ -180716,10 +179372,10 @@ xref: NCIT:C49328 xref: SCTID:280657006 xref: UMLS:C0459649 {source="ncithesaurus:Retina_Layer"} xref: XAO:0000266 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0022303 ! nervous system cell part layer -relationship: contributes_to_morphology_of UBERON:0000966 ! retina relationship: part_of UBERON:0000966 ! retina -property_value: UBPROP:0000012 "MA does not treat internal/external limiting memranes as layers - these are classified as laminae. Here we follow other ontologies in grouping with other layers. MA also treats retinal pigment epithelium and neural retina epithelium as distinct from the layers. We follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers - these are also classified as layers, giving us over the usual 10 layers" xsd:string {external_ontology="MA"} +relationship: RO:0002433 UBERON:0000966 ! contributes to morphology of retina [Term] id: UBERON:0001782 @@ -180766,19 +179422,15 @@ xref: XAO:0003217 xref: ZFA:0000144 is_a: UBERON:0000957 ! lamina is_a: UBERON:0001781 ! layer of retina -is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0015808 ! eye epithelium intersection_of: UBERON:0001781 ! layer of retina -intersection_of: immediate_transformation_of UBERON:0005424 ! presumptive retinal pigmented epithelium +intersection_of: RO:0002495 UBERON:0005424 ! immediate transformation of presumptive retinal pigmented epithelium relationship: adjacent_to UBERON:0001787 {source="Wikipedia"} ! photoreceptor layer of retina relationship: adjacent_to UBERON:0003902 ! retinal neural layer relationship: has_part GO:0048770 ! pigment granule -relationship: immediate_transformation_of UBERON:0005424 ! presumptive retinal pigmented epithelium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI -property_value: UBPROP:0000001 "A monolayer of pigmented epithelium covering the neural retina; develops from the outer of the two layers of the optic cup. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000144", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "The monolayer of pigmented epithelium covering the neural retina.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011096", ontology="AAO", source="ZFA:0000144"} -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000536", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} +relationship: RO:0002495 UBERON:0005424 ! immediate transformation of presumptive retinal pigmented epithelium +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001785 @@ -180815,20 +179467,17 @@ xref: Wikipedia:Cranial_nerve xref: XAO:0000429 xref: XAO:0003089 xref: ZFA:0000641 -is_a: UBERON:0001021 ! nerve +is_a: UBERON:0011779 ! nerve of head region is_a: UBERON:0034713 ! cranial neuron projection bundle intersection_of: UBERON:0001021 ! nerve -intersection_of: anterior_to UBERON:0001780 ! spinal nerve +intersection_of: BSPO:0000096 UBERON:0001780 ! spinal nerve intersection_of: extends_fibers_into UBERON:0000955 ! brain -relationship: anterior_to UBERON:0001780 ! spinal nerve -relationship: has_developmental_contribution_from UBERON:0003099 ! cranial neural crest -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/18/Brain_human_normal_inferior_view_with_labels_en-2.svg" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/84/Brain_human_normal_inferior_view_with_labels_en.svg" xsd:anyURI -property_value: editor_note "classified as neural tree organ, not nerve in FMA. CN II poses a challenge here as it is not strictly a nerve, yet is expected to be classified under CN." xsd:string -property_value: UBPROP:0000001 "Twelve pairs of cranial nerves exit/enter the cranium through openings in the skull. The nerves contain efferent axons with motor and glandular functions, as well as afferent axons from cranial ganglia with sensory functions. The nerves are numbered in a rostral to caudal sequence, with the exception of the lateral line nerves.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000641", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000279", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "See https://github.com/obophenotype/mouse-anatomy-ontology/issues/6" xsd:string +relationship: BSPO:0000096 UBERON:0001780 ! spinal nerve +relationship: RO:0002254 UBERON:0003099 ! has developmental contribution from cranial neural crest +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/18/Brain_human_normal_inferior_view_with_labels_en-2.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/84/Brain_human_normal_inferior_view_with_labels_en.svg" xsd:anyURI +property_value: IAO:0000116 "classified as neural tree organ, not nerve in FMA. CN II poses a challenge here as it is not strictly a nerve, yet is expected to be classified under CN." xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001786 @@ -180856,17 +179505,13 @@ xref: UMLS:C0450290 {source="BIRNLEX:2543"} xref: VHOG:0001572 xref: Wikipedia:Fovea_centralis_in_macula is_a: UBERON:0000064 ! organ part +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: has_part CHEBI:27547 relationship: has_part CHEBI:28838 relationship: has_part CL:0000573 ! retinal cone cell -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0000053 ! macula lutea -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI -property_value: UBPROP:0000001 "A small pit in the center of the macula lutea, the area of clearest vision, where the retinal layers are spread aside, and light falls directly on the cones. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001572", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/fovea"} -property_value: UBPROP:0000003 "Definition of fovea centralis should be considered here as 'an area centralis at the visual axis' (reference 1). There is an uncertaincy of the relation, because: 1.-The fovea first appeared in evolution in the temporal retina of fishes. Then, in birds, the nasal fovea and bifoveal system with nasal and temporal foveas developed. The fovea disappeared in primitive mammals, and reappeared in primates. A residue of the fovea is conserved in the visual streak, and the disappearance and reappearance of the fovea, in primitive mammals and primates respectively, correlates with degeneration and restoration of cone pigment genes in photoreceptors (reference 2). 2.-Many retinal features (foveas, trichromacy, midget pathways and associated cell types) appear specific to primates. This has led to investigations in parallel with other mammalian models such as cat or rabbit. Correlation of the results often proves to be difficult, since an evolutionary scenario with transitions between the mammalian models is largely lacking (reference 3).[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001572", ontology="VHOG", source="DOI:10.1017/S095252380623342X Ahnelt PK, Schubert C, Kübber-Heiss A, Schiviz A, Anger E, Independent variation of retinal S and M cone photoreceptor topographies: A survey of four families of mammals. Visual neuroscience (2006), http://www.ncbi.nlm.nih.gov/pubmed/11193946 Azuma N, Molecular cell biology on morphogenesis of the fovea and evolution of the central vision. Nihon Ganka Gakkai Zasshi (2000), DOI:10.1016/S1350-9462(00)00012-4 Ahnelt PK, Kolb H, The mammalian photoreceptor mosaic-adaptive design. Progress in Retinal and Eye Research (2000)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "foveal" xsd:string -property_value: UBPROP:0000008 "The fovea is also a pit in the surface of the retinas of many types of fish, reptiles, and birds. Among mammals, it is found only in simian primates. The retinal fovea takes slightly different forms in different types of animals. For example, in primates, cone photoreceptors line the base of the foveal pit, the cells that elsewhere in the retina form more superficial layers having been displaced away from the foveal region during late fetal and early postnatal life. Other foveae may show only a reduced thickness in the inner cell layers, rather than an almost complete absence" xsd:string -property_value: UBPROP:0000009 "high acuity vision" xsd:string +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI [Term] id: UBERON:0001787 @@ -180896,9 +179541,7 @@ is_a: UBERON:0001781 ! layer of retina relationship: adjacent_to UBERON:0001788 ! outer limiting layer of retina relationship: has_part CL:0000287 {source="ZFA"} ! eye photoreceptor cell relationship: part_of UBERON:0003902 ! retinal neural layer -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001165", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "we follow MA and ZFA in subdividing this into inner and outer segments" xsd:string {external_ontology="MA"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI [Term] id: UBERON:0001788 @@ -180966,11 +179609,10 @@ xref: XAO:0003219 xref: ZFA:0001464 is_a: UBERON:0001781 ! layer of retina relationship: adjacent_to UBERON:0001790 ! outer plexiform layer of retina -relationship: contributes_to_morphology_of UBERON:0003902 ! retinal neural layer -relationship: overlaps CL:0000287 {notes="soma", source="ZFA"} ! eye photoreceptor cell +relationship: overlaps CL:0000287 ! eye photoreceptor cell relationship: part_of UBERON:0003902 ! retinal neural layer -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001170", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} +relationship: RO:0002433 UBERON:0003902 ! contributes to morphology of retinal neural layer +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001790 @@ -181004,10 +179646,8 @@ xref: ZFA:0001330 is_a: UBERON:0001781 ! layer of retina disjoint_from: UBERON:0005376 ! olfactory bulb external plexiform layer relationship: adjacent_to UBERON:0001791 ! inner nuclear layer of retina -relationship: contributes_to_morphology_of UBERON:0003902 ! retinal neural layer relationship: part_of UBERON:0003902 ! retinal neural layer -property_value: UBPROP:0000001 "The layer within the retina where the bipolar cells synapse with the photoreceptor cells.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001330", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001171", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} +relationship: RO:0002433 UBERON:0003902 ! contributes to morphology of retinal neural layer [Term] id: UBERON:0001791 @@ -181045,14 +179685,12 @@ xref: XAO:0003221 xref: ZFA:0000119 is_a: UBERON:0001781 ! layer of retina relationship: adjacent_to UBERON:0001795 ! inner plexiform layer of retina -relationship: contributes_to_morphology_of UBERON:0003902 ! retinal neural layer relationship: has_part CL:0000561 ! amacrine cell relationship: has_part CL:0000745 ! retina horizontal cell relationship: has_part CL:0000748 ! retinal bipolar neuron relationship: part_of UBERON:0003902 ! retinal neural layer -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000001 "The layer of the retina composed of the cell bodies of bipolar cells, horizontal cells, and some of the cell bodies of amacrine cells[BTO:0003176]." xsd:string {source="BTO:0003176"} -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001167", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} +relationship: RO:0002433 UBERON:0003902 ! contributes to morphology of retinal neural layer +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001792 @@ -181091,14 +179729,11 @@ xref: XAO:0003223 xref: ZFA:0000024 is_a: UBERON:0001781 {source="FMA"} ! layer of retina relationship: adjacent_to UBERON:0001793 ! nerve fiber layer of retina -relationship: composed_primarily_of CL:0000740 ! retinal ganglion cell -relationship: contributes_to_morphology_of UBERON:0003902 ! retinal neural layer relationship: part_of UBERON:0003902 {source="FMA"} ! retinal neural layer -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI -property_value: UBPROP:0000001 "a layer of the retina that consists of retinal ganglion cells[WP]. innermost nuclear layer of the retina, which contains neurons that project axons through the optic nerve to the brain[Wikipedia:Ganglion_cell_layer]." xsd:string {source="Wikipedia:Ganglion_cell_layer"} -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001166", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "NIFSTD class appears to be retired in nlx[http://neurolex.org/wiki/Nlx_anat_1005030]" xsd:string {external_ontology="NIF"} +relationship: RO:0002433 UBERON:0003902 ! contributes to morphology of retinal neural layer +relationship: RO:0002473 CL:0000740 ! composed primarily of retinal ganglion cell +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001793 @@ -181132,11 +179767,10 @@ xref: XAO:0003220 xref: ZFA:0001619 is_a: UBERON:0001781 ! layer of retina relationship: adjacent_to UBERON:0001794 ! inner limiting layer of retina -relationship: composed_primarily_of GO:0030424 ! axon -relationship: contributes_to_morphology_of UBERON:0003902 ! retinal neural layer relationship: overlaps UBERON:0000941 ! cranial nerve II relationship: part_of UBERON:0003902 {source="FMA"} ! retinal neural layer -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001169", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} +relationship: RO:0002433 UBERON:0003902 ! contributes to morphology of retinal neural layer +relationship: RO:0002473 GO:0030424 ! composed primarily of axon [Term] id: UBERON:0001794 @@ -181165,12 +179799,12 @@ xref: Wikipedia:Inner_limiting_membrane xref: XAO:0003222 xref: ZFA:0001029 is_a: UBERON:0007619 {source="MA"} ! limiting membrane of retina +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: adjacent_to UBERON:0001797 ! vitreous humor relationship: has_part CL:0000127 ! astrocyte relationship: has_part GO:0043005 ! neuron projection relationship: overlaps CL:0000636 ! Mueller cell -property_value: editor_note "TODO - check frog/fish" xsd:string -property_value: UBPROP:0000001 "Membrane on the apical surface of the retina. The retinal vasculature becomes adhered to the apical surface of the ILM by 30dpf[ZFIN:ZDB-PUB-071023-7, ZFIN:ZDB-PUB-120529-3]." xsd:string {source="ZFIN:ZDB-PUB-071023-7, ZFIN:ZDB-PUB-120529-3"} +property_value: IAO:0000116 "TODO - check frog/fish" xsd:string [Term] id: UBERON:0001795 @@ -181210,16 +179844,12 @@ intersection_of: adjacent_to UBERON:0001791 ! inner nuclear layer of retina intersection_of: adjacent_to UBERON:0001792 ! ganglionic layer of retina relationship: adjacent_to UBERON:0001791 ! inner nuclear layer of retina relationship: adjacent_to UBERON:0001792 ! ganglionic layer of retina -relationship: contributes_to_morphology_of UBERON:0003902 ! retinal neural layer relationship: has_part GO:0030425 ! dendrite relationship: overlaps CL:0000740 ! retinal ganglion cell relationship: overlaps CL:0000748 ! retinal bipolar neuron relationship: part_of UBERON:0003902 ! retinal neural layer -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI -property_value: UBPROP:0000001 "The inner plexiform layer (IPL) is positioned between the INL and the ganglion cell layer and contains the dendrites of RGCs and processes of bipolar and amacrine cells[GO][GO:0010842]." xsd:string {source="GO:0010842"} -property_value: UBPROP:0000001 "The layer within the retina where the bipolar cells synapse with the dendrites of the ganglion cells.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001329", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001168", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "http://neurolex.org/wiki/Nlx_anat_1005032 appears to be retired" xsd:string +relationship: RO:0002433 UBERON:0003902 ! contributes to morphology of retinal neural layer +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI [Term] id: UBERON:0001796 @@ -181248,12 +179878,9 @@ xref: Wikipedia:Aqueous_humor xref: ZFA:0005564 is_a: UBERON:0006312 ! ocular refractive media is_a: UBERON:0006314 ! bodily fluid -relationship: contributes_to_morphology_of UBERON:0001766 ! anterior chamber of eyeball -relationship: part_of UBERON:0001766 {notes="FMA def states A and P", notes="located_in in EHDAA2", source="VHOG"} ! anterior chamber of eyeball -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI -property_value: UBPROP:0000001 "The fluid produced by the ciliary process in the eye and occupying the anterior and posterior chambers. It provides nourishment for the lens and cornea and maintains the ocular pressure, and hence the optical integrity of the eyeball. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000548", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/aqueous+humour"} -property_value: UBPROP:0000003 "(...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000548", ontology="VHOG", source="DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424 and p.426 and p.429 and Figure 12-24", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "FMA says A+P chambers, and MA states A chamber. ZFA states A chamber and tha it is produced primarily by dorsal ciliary epithelial cells.To be investigated across taxa." xsd:string {external_ontology="FMA"} +relationship: part_of UBERON:0001766 ! anterior chamber of eyeball +relationship: RO:0002433 UBERON:0001766 ! contributes to morphology of anterior chamber of eyeball +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI [Term] id: UBERON:0001797 @@ -181279,17 +179906,16 @@ xref: ENVO:02000032 xref: EV:0100344 xref: FMA:58822 xref: MA:0001286 -xref: MESH:D014822 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: NCIT:C13323 xref: UMLS:C0229096 {source="ncithesaurus:Vitreous_Humor"} xref: VHOG:0000795 xref: Wikipedia:Vitreous_humour xref: ZFA:0005561 is_a: UBERON:0006312 ! ocular refractive media -relationship: has_quality PATO:0000964 ! transparent -relationship: located_in UBERON:0005606 ! hyaloid cavity relationship: part_of UBERON:0001798 ! vitreous body -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +relationship: RO:0000086 PATO:0000964 ! has quality transparent +relationship: RO:0001025 UBERON:0005606 ! located in hyaloid cavity +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI [Term] id: UBERON:0001798 @@ -181307,12 +179933,13 @@ xref: NCIT:C33884 xref: SCTID:181170006 xref: UMLS:C0042905 {source="ncithesaurus:Vitreous_Body"} is_a: UBERON:0003566 ! head connective tissue +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0011825 {source="FMA"} ! loose connective tissue -relationship: composed_primarily_of UBERON:0001797 ! vitreous humor -relationship: has_developmental_contribution_from UBERON:0002346 {notes="neural ectoderm of optic cup", source="ISBN:0781772214"} ! neurectoderm relationship: part_of UBERON:0001799 ! vitreous chamber of eyeball -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI -property_value: editor_note "distinciton between body and humor requires more work. These may be merged in future. Note that FMA includes the hyaloid canal as part of the vitreous body" xsd:string +relationship: RO:0002254 UBERON:0002346 ! has developmental contribution from neurectoderm +relationship: RO:0002473 UBERON:0001797 ! composed primarily of vitreous humor +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: IAO:0000116 "distinciton between body and humor requires more work. These may be merged in future. Note that FMA includes the hyaloid canal as part of the vitreous body" xsd:string [Term] id: UBERON:0001799 @@ -181336,9 +179963,9 @@ xref: UMLS:C0229095 {source="ncithesaurus:Vitreous_Chamber"} xref: Wikipedia:Vitreous_chamber is_a: UBERON:0006311 ! chamber of eyeball intersection_of: UBERON:0006311 ! chamber of eyeball -intersection_of: location_of UBERON:0001798 ! vitreous body -relationship: location_of UBERON:0001798 ! vitreous body +intersection_of: RO:0001015 UBERON:0001798 ! location of vitreous body relationship: part_of UBERON:0001802 ! posterior segment of eyeball +relationship: RO:0001015 UBERON:0001798 ! location of vitreous body [Term] id: UBERON:0001800 @@ -181360,7 +179987,7 @@ is_a: UBERON:0000045 ! ganglion intersection_of: UBERON:0000045 ! ganglion intersection_of: extends_fibers_into UBERON:0001027 ! sensory nerve relationship: extends_fibers_into UBERON:0001027 ! sensory nerve -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001801 @@ -181386,12 +180013,12 @@ xref: UMLS:C0003153 {source="ncithesaurus:Anterior_Eye_Segment"} xref: Wikipedia:Anterior_segment_of_eyeball xref: ZFA:0005566 is_a: UBERON:0000063 ! organ subunit +is_a: UBERON:0004121 ! ectoderm-derived structure disjoint_from: UBERON:0001802 {source="lexical"} ! posterior segment of eyeball -relationship: contributes_to_morphology_of UBERON:0000019 ! camera-type eye -relationship: in_anterior_side_of UBERON:0010230 {source="cjm"} ! eyeball of camera-type eye +relationship: BSPO:0000123 UBERON:0010230 {source="cjm"} ! eyeball of camera-type eye relationship: part_of UBERON:0010230 {source="FMA"} ! eyeball of camera-type eye -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Cataract_in_human_eye.png" xsd:anyURI -property_value: RO:0002171 UBERON:0001802 {exceptions="ZFA", source="https://github.com/obophenotype/uberon/issues/378", status="pending"} +relationship: RO:0002433 UBERON:0000019 ! contributes to morphology of camera-type eye +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Cataract_in_human_eye.png" xsd:anyURI [Term] id: UBERON:0001802 @@ -181416,10 +180043,11 @@ xref: UMLS:C0278450 {source="ncithesaurus:Posterior_Eye_Segment"} xref: Wikipedia:Posterior_segment_of_eyeball xref: ZFA:0005567 is_a: UBERON:0000063 ! organ subunit -relationship: contributes_to_morphology_of UBERON:0000019 ! camera-type eye -relationship: in_posterior_side_of UBERON:0010230 {source="cjm"} ! eyeball of camera-type eye +is_a: UBERON:0004121 ! ectoderm-derived structure +relationship: BSPO:0000122 UBERON:0010230 {source="cjm"} ! eyeball of camera-type eye relationship: part_of UBERON:0010230 {source="FMA"} ! eyeball of camera-type eye -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +relationship: RO:0002433 UBERON:0000019 ! contributes to morphology of camera-type eye +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI [Term] id: UBERON:0001803 @@ -181451,10 +180079,9 @@ is_a: UBERON:0000484 ! simple cuboidal epithelium is_a: UBERON:0015808 ! eye epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000965 ! lens of camera-type eye -relationship: contributes_to_morphology_of UBERON:0000965 ! lens of camera-type eye relationship: part_of UBERON:0000965 ! lens of camera-type eye -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: IAO:0000232 "this class is the superclass of the anterior epithelium and equatorial epithlium, although the term 'lens epithelium' may refer specifically to the former" xsd:string +relationship: RO:0002433 UBERON:0000965 ! contributes to morphology of lens of camera-type eye +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001804 @@ -181482,15 +180109,11 @@ is_a: UBERON:0005764 ! acellular membrane intersection_of: UBERON:0000476 ! acellular anatomical structure intersection_of: bounding_layer_of UBERON:0000965 ! lens of camera-type eye relationship: bounding_layer_of UBERON:0000965 ! lens of camera-type eye -relationship: develops_from UBERON:0005614 {source="EHDAA2"} ! lens anterior epithelium relationship: has_part CHEBI:35722 relationship: has_part GO:0005587 ! collagen type IV trimer -relationship: has_quality PATO:0000964 ! transparent -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png" xsd:anyURI -property_value: UBPROP:0000001 "The transparent membrane which surrounds the lens of the eye. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000550", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "(...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000550", ontology="VHOG", source="DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424 and p.426 and p.429 and Figure 12-24", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000010 "synthesized by the lens epithelium and its main components are Type IV collagen and sulfated glycosaminoglycans (GAGs). [Wikipedia:Capsule_of_lens" xsd:string -property_value: UBPROP:0000012 "FMA classifies this is a capsule and hence an organ part. In contrast we classify this as acellular" xsd:string {external_ontology="FMA"} +relationship: RO:0000086 PATO:0000964 ! has quality transparent +relationship: RO:0002202 UBERON:0005614 {source="EHDAA2"} ! develops from lens anterior epithelium +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png" xsd:anyURI [Term] id: UBERON:0001805 @@ -181506,7 +180129,6 @@ synonym: "ganglion of visceral nervous system" EXACT [OBOL:automatic] synonym: "visceral nervous system ganglion" EXACT [OBOL:automatic] xref: AEO:0001001 xref: CALOHA:TS-2340 -xref: EMAPA:17157 xref: EMAPA:18221 xref: FMA:5889 xref: MA:0000220 @@ -181519,8 +180141,8 @@ intersection_of: UBERON:0000045 ! ganglion intersection_of: part_of UBERON:0002410 ! autonomic nervous system relationship: extends_fibers_into UBERON:0034728 ! autonomic nerve relationship: part_of UBERON:0002410 ! autonomic nervous system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001806 @@ -181542,19 +180164,19 @@ xref: EHDAA2:0001969 xref: EMAPA:17157 xref: FMA:5890 xref: MA:0000226 -xref: MESH:D005728 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C12467 xref: SCTID:362485003 xref: UMLS:C0017071 {source="ncithesaurus:Sympathetic_Ganglion"} xref: Wikipedia:Sympathetic_ganglion is_a: UBERON:0001805 ! autonomic ganglion +is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0000045 ! ganglion intersection_of: part_of UBERON:0000013 ! sympathetic nervous system -relationship: contributes_to_morphology_of UBERON:0000013 ! sympathetic nervous system -relationship: develops_from UBERON:0003083 {source="DOI:10.1101/gr.157586.113", source="ISBN:0073040584"} ! trunk neural crest relationship: extends_fibers_into UBERON:0034729 ! sympathetic nerve relationship: part_of UBERON:0000013 ! sympathetic nervous system -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png" xsd:anyURI +relationship: RO:0002202 UBERON:0003083 {source="DOI:10.1101/gr.157586.113", source="ISBN:0073040584"} ! develops from trunk neural crest +relationship: RO:0002433 UBERON:0000013 ! contributes to morphology of sympathetic nervous system +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png" xsd:anyURI [Term] id: UBERON:0001807 @@ -181587,9 +180209,8 @@ is_a: UBERON:0007134 {source="ZFA"} ! trunk ganglion intersection_of: UBERON:0000045 ! ganglion intersection_of: part_of UBERON:0000407 ! sympathetic trunk relationship: part_of UBERON:0000407 ! sympathetic trunk -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray847.png" xsd:anyURI -property_value: UBPROP:0000202 FMA:80128 +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray847.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001808 @@ -181605,7 +180226,6 @@ xref: EHDAA2:0001400 xref: EMAPA:32813 xref: FMA:5894 xref: MA:0002469 -xref: MESH:D005726 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C52557 xref: NLXANAT:100303 xref: SCTID:279284004 @@ -181615,11 +180235,11 @@ is_a: UBERON:0001805 ! autonomic ganglion is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0001805 ! autonomic ganglion intersection_of: part_of UBERON:0000011 ! parasympathetic nervous system -relationship: contributes_to_morphology_of UBERON:0000011 ! parasympathetic nervous system relationship: extends_fibers_into UBERON:0004293 ! parasympathetic nerve relationship: part_of UBERON:0000011 ! parasympathetic nervous system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png" xsd:anyURI +relationship: RO:0002433 UBERON:0000011 ! contributes to morphology of parasympathetic nervous system +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001809 @@ -181636,8 +180256,8 @@ xref: Wikipedia:Enteric_ganglia is_a: UBERON:0001808 {source="FMA"} ! parasympathetic ganglion intersection_of: UBERON:0001808 ! parasympathetic ganglion intersection_of: part_of UBERON:0002005 ! enteric nervous system -relationship: contributes_to_morphology_of UBERON:0002005 ! enteric nervous system relationship: part_of UBERON:0002005 ! enteric nervous system +relationship: RO:0002433 UBERON:0002005 ! contributes to morphology of enteric nervous system [Term] id: UBERON:0001810 @@ -181662,8 +180282,7 @@ is_a: UBERON:0007651 ! anatomical junction relationship: has_part CL:0000526 {source="AEO"} ! afferent neuron relationship: has_part CL:0000527 {source="AEO"} ! efferent neuron relationship: part_of UBERON:0001016 ! nervous system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000012 "Made to be a subtype of junction rather than tissue to be consistent with FMA" xsd:string {external_ontology="FMA"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001811 @@ -181682,7 +180301,6 @@ xref: AAO:0010343 xref: BTO:0003415 xref: CALOHA:TS-2232 xref: EFO:0000374 -xref: EMAPA:18233 xref: EV:0100340 xref: FMA:59011 xref: GAID:898 @@ -181694,15 +180312,15 @@ xref: UMLS:C0009758 {source="ncithesaurus:Conjunctiva"} xref: Wikipedia:Conjunctiva xref: XAO:0000182 is_a: UBERON:0000060 {source="FMA"} ! anatomical wall +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: adjacent_to UBERON:0001711 ! eyelid relationship: adjacent_to UBERON:0001773 ! sclera -relationship: contributes_to_morphology_of UBERON:0001801 ! anterior segment of eyeball -relationship: develops_from UBERON:0000076 {source="ISBN:0781772214"} ! external ectoderm relationship: part_of UBERON:0005908 {source="cjm"} ! conjunctival sac relationship: part_of UBERON:0010409 {source="MA"} ! ocular surface region -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png" xsd:anyURI -property_value: UBPROP:0000007 "conjunctival" xsd:string +relationship: RO:0002202 UBERON:0000076 {source="ISBN:0781772214"} ! develops from external ectoderm +relationship: RO:0002433 UBERON:0001801 ! contributes to morphology of anterior segment of eyeball +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001813 @@ -181725,7 +180343,6 @@ is_a: UBERON:0001810 ! nerve plexus intersection_of: UBERON:0001810 ! nerve plexus intersection_of: extends_fibers_into UBERON:0001780 ! spinal nerve relationship: extends_fibers_into UBERON:0001780 ! spinal nerve -property_value: UBPROP:0000003 "To reach the muscles, dermatomes, and other structures of the limbs, some of the neurons in the spinal nerves come together in the plexus at the base of the limb. Such plexuses occur in all gnathostomes, and they reach their highest complexity among mammals and birds in which the cervical plexus supplies many ventral neck muscles, the brachial plexus supplies the pectoral appendage, a lumbosacral plexus supplies the pelvic appendage, and a coccygeal plexus supplies some of the pelvic muscles.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000926", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.436", source="http://bgee.unil.ch/"} [Term] id: UBERON:0001814 @@ -181750,13 +180367,11 @@ xref: VHOG:0000372 xref: Wikipedia:Brachial_plexus is_a: UBERON:0000122 ! neuron projection bundle is_a: UBERON:0001813 ! spinal nerve plexus -relationship: innervates UBERON:0002102 ! forelimb -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/3a/Gray808.png" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c9/Brachial_plexus_color.svg" xsd:anyURI -property_value: editor_note "check superclass - nerve vs collection of fibers vs junction; note that FMA also has 'brachial autonomic nerve plexus'" xsd:string -property_value: UBPROP:0000001 "A nerve plexus originating from the anterior branches of the last four cervical and the first thoracic spinal nerves, giving off many of the principal nerves of the shoulder, chest, and arms. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000372", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/brachial+plexus"} -property_value: UBPROP:0000003 "To reach the muscles, dermatomes, and other structures of the limbs, some of the neurons in the spinal nerves come together in the plexus at the base of the limb. Such plexuses occur in all gnathostomes, and they reach their highest complexity among mammals and birds in which the cervical plexus supplies many ventral neck muscles, the brachial plexus supplies the pectoral appendage, a lumbosacral plexus supplies the pelvic appendage, and a coccygeal plexus supplies some of the pelvic muscles.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000372", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.436", source="http://bgee.unil.ch/"} +relationship: RO:0002134 UBERON:0002102 ! innervates forelimb +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3a/Gray808.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c9/Brachial_plexus_color.svg" xsd:anyURI +property_value: IAO:0000116 "check superclass - nerve vs collection of fibers vs junction; note that FMA also has 'brachial autonomic nerve plexus'" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001815 @@ -181782,8 +180397,8 @@ xref: VHOG:0000926 xref: Wikipedia:Lumbosacral_plexus is_a: UBERON:0000122 ! neuron projection bundle is_a: UBERON:0001813 ! spinal nerve plexus -relationship: innervates UBERON:0002103 ! hindlimb -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/8d/Gray822.png" xsd:anyURI +relationship: RO:0002134 UBERON:0002103 ! innervates hindlimb +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8d/Gray822.png" xsd:anyURI [Term] id: UBERON:0001816 @@ -181833,20 +180448,16 @@ xref: VHOG:0001476 xref: Wikipedia:Lacrimal_gland xref: Wikipedia:Preorbital_gland is_a: UBERON:0002365 ! exocrine gland +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004859 ! eye gland is_a: UBERON:0015154 ! lateral gland of orbital region intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0001750 ! lacrimal apparatus -relationship: contributes_to_morphology_of UBERON:0001750 ! lacrimal apparatus -relationship: develops_from UBERON:0022284 ! lacrimal gland bud -relationship: never_in_taxon NCBITaxon:8570 {source="PMID:7559104"} relationship: part_of UBERON:0001750 ! lacrimal apparatus -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray896.png" xsd:anyURI -property_value: UBPROP:0000001 "Lobular organ the parenchyma of which consists of glandular acini which communicate the lacrimal sac. Examples: There only two instances, right lacrimal and left lacrimal glands." xsd:string {source="FMA:59101"} -property_value: UBPROP:0000001 "The preorbital gland is a paired exocrine gland found in many species of hoofed animals, which is homologous to the lacrimal gland found in humans. These glands are trenchlike slits of dark blue to black, nearly bare skin extending from the medial canthus of each eye. They are lined by a combination of sebaceous and sudoriferous glands, and they produce secretions which contain pheromones and other semiochemical compounds. Ungulates frequently deposit these secretions on twigs and grass as a means of communication with other animals. The preorbital gland serves different roles in different species. Pheromone-containing secretions from the preorbital gland may serve to establish an animal's dominance (especially in preparation for breeding), mark its territory, or simply to produce a pleasurable sensation to the animal. Because of its critical role in scent marking, the preorbital gland is usually considered as a type of scent gland. A further function of these glands may be to produce antimicrobial compounds against skin pathogens. Antimicrobial compounds found in these glands may be biosynthesized by the animal itself, or by microorganisms that live in these glands[Wikipedia:Preorbital_gland]." xsd:string {source="Wikipedia:Preorbital_gland"} -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI -property_value: UBPROP:0000008 "In humans, they are situated in the upper, outer portion of each orbit" xsd:string -property_value: UBPROP:0000008 "Innervation is highly complex and species-specific" xsd:string +relationship: RO:0002202 UBERON:0022284 ! develops from lacrimal gland bud +relationship: RO:0002433 UBERON:0001750 ! contributes to morphology of lacrimal apparatus +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray896.png" xsd:anyURI +property_value: RO:0002161 NCBITaxon:8570 {source="PMID:7559104"} [Term] id: UBERON:0001820 @@ -181876,15 +180487,12 @@ is_a: UBERON:0007771 ! epidermis gland is_a: UBERON:0019319 ! exocrine gland of integumental system intersection_of: UBERON:0002530 ! gland intersection_of: produces UBERON:0001089 ! sweat -relationship: develops_from UBERON:0005089 {evidence="definitional"} ! sweat gland placode -relationship: has_quality PATO:0002299 {notes="coiled tubular", source="Wikipedia:Tubular_gland"} ! tubular -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia relationship: produces UBERON:0001089 ! sweat -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg" xsd:anyURI -property_value: editor_note "TODO - check if all sweat glands are epidermal - see EMAPA:29743" xsd:string -property_value: UBPROP:0000001 "A gland that secretes sweat, found in the dermis or subcutaneous tissue, opening by a duct on the body surface. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001467", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/sweat+gland"} -property_value: UBPROP:0000003 "Sweat glands (also called sudoriferous glands) are unique to mammals.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001467", ontology="VHOG", source="ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.101", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "In humans a system of apocrine - and merocrine sweat glands is the main method of cooling. Many other mammals rely on panting or other means as a primary source of cooling, but still use sweat glands to aid in body temperature regulation" xsd:string +relationship: RO:0000086 PATO:0002299 ! has quality tubular +relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia +relationship: RO:0002202 UBERON:0005089 ! develops from sweat gland placode +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg" xsd:anyURI +property_value: IAO:0000116 "TODO - check if all sweat glands are epidermal - see EMAPA:29743" xsd:string [Term] id: UBERON:0001821 @@ -181914,15 +180522,12 @@ xref: Wikipedia:Sebaceous_gland is_a: UBERON:0007771 ! epidermis gland is_a: UBERON:0012344 {source="Wikipedia"} ! holocrine gland is_a: UBERON:0019319 ! exocrine gland of integumental system -relationship: develops_from UBERON:0005088 {evidence="definitional"} ! sebaceous gland placode -relationship: only_in_taxon NCBITaxon:40674 {source="VHOG"} ! Mammalia relationship: part_of UBERON:0011932 ! pilosebaceous unit -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: produces UBERON:0001866 ! sebum -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/49/HairFollicle.png" xsd:anyURI -property_value: IAO:0000232 "sebaceous glands are also found in glabrous areas of eyelids, nose, penis, labia minora and nipples, and do not always secrete into hair follices. This causes some confusion in classification. In addition some structures, such as preputial glands are sometimes called 'modified' sebaceous glands, implying a non-subclass relationship. we follow MP and MA in keeping this class generic and creating a distinct subclass for sebaceuous glands of the skin. The FMA class may be better placed under this subclass." xsd:string -property_value: UBPROP:0000001 "Any of the numerous holocrine glands in the dermis that empty into a hair follicle and produce and secrete sebum. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001468", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/sebaceous+gland"} -property_value: UBPROP:0000003 "Sebaceous glands are also limited to mammals.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001468", ontology="VHOG", source="ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.102", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:40674 {source="VHOG"} ! only in taxon Mammalia +relationship: RO:0002202 UBERON:0005088 ! develops from sebaceous gland placode +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/49/HairFollicle.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001823 @@ -181936,19 +180541,19 @@ xref: CALOHA:TS-0655 xref: EMAPA:37681 {source="MA:th"} xref: FMA:59502 xref: MA:0001883 -xref: MESH:D055171 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C49593 xref: SCTID:278941001 xref: UMLS:C0225415 {source="ncithesaurus:Nasal_Cartilage"} xref: Wikipedia:Nasal_cartilage is_a: UBERON:0002418 {source="MA"} ! cartilage tissue is_a: UBERON:0003566 ! head connective tissue +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0007844 ! cartilage element intersection_of: UBERON:0007844 ! cartilage element intersection_of: part_of UBERON:0000004 ! nose -relationship: location_of UBERON:0000402 ! nasal vestibule relationship: part_of UBERON:0000004 ! nose -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e1/Gray852.png" xsd:anyURI +relationship: RO:0001015 UBERON:0000402 ! location of nasal vestibule +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e1/Gray852.png" xsd:anyURI [Term] id: UBERON:0001824 @@ -181974,6 +180579,7 @@ xref: NCIT:C49246 xref: SCTID:361940006 xref: UMLS:C0023053 {source="ncithesaurus:Laryngeal_Mucosa"} is_a: UBERON:0000379 ! tracheal mucosa +is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0001737 ! larynx relationship: part_of UBERON:0001737 ! larynx @@ -181997,11 +180603,13 @@ xref: GAID:302 xref: SCTID:310211009 xref: Wikipedia:Mucous_membrane_of_nose is_a: UBERON:0000379 ! tracheal mucosa +is_a: UBERON:0004119 ! endoderm-derived structure +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0015788 ! olfactory apparatus chamber relationship: bounding_layer_of UBERON:0015788 ! olfactory apparatus chamber relationship: part_of UBERON:0015788 ! olfactory apparatus chamber -property_value: editor_note "TODO - check lining vs part of. split olfactory and nasal mucosa?" xsd:string +property_value: IAO:0000116 "TODO - check lining vs part of. split olfactory and nasal mucosa?" xsd:string [Term] id: UBERON:0001827 @@ -182065,12 +180673,11 @@ xref: Wikipedia:Gingiva is_a: UBERON:0003729 ! mouth mucosa relationship: adjacent_to UBERON:0004103 ! alveolar ridge relationship: adjacent_to UBERON:0008266 ! periodontal ligament -relationship: continuous_with UBERON:0003729 {source="ISBN:0013002015"} ! mouth mucosa relationship: part_of UBERON:0003729 {source="Carranza"} ! mouth mucosa relationship: part_of UBERON:0011595 ! jaw region -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/2/2e/Tooth_Section.svg" xsd:anyURI -property_value: editor_note "FMA has a 3-level breakdown of jaws into: region, jaw (skeleton+gums), skeleton." xsd:string -property_value: UBPROP:0000007 "gingival" xsd:string +relationship: RO:0002150 UBERON:0003729 {source="ISBN:0013002015"} ! continuous with mouth mucosa +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/2e/Tooth_Section.svg" xsd:anyURI +property_value: IAO:0000116 "FMA has a 3-level breakdown of jaws into: region, jaw (skeleton+gums), skeleton." xsd:string [Term] id: UBERON:0001833 @@ -182098,14 +180705,12 @@ xref: VHOG:0000677 xref: Wikipedia:Lip xref: ZFA:0007006 is_a: UBERON:0003102 {source="ZFA"} ! surface structure -relationship: contributes_to_morphology_of UBERON:0000165 ! mouth -relationship: never_in_taxon NCBITaxon:8782 ! Aves relationship: part_of UBERON:0000165 {source="BTO", source="FMA-implicit", source="VHOG", source="ZFA"} ! mouth -relationship: surrounds UBERON:0000166 {source="cjm"} ! oral opening -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/90/Lips.JPG" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/99/Mouth.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Surface structure that is one of the two fleshy folds surrounding the opening of the mouth.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0007006", ontology="TAO", source="ZFIN:curator", source="http//:www.medterms.com/script/main/art.asp?articlekey=9458"} -property_value: UBPROP:0000007 "labial" xsd:string +relationship: RO:0002221 UBERON:0000166 {source="cjm"} ! surrounds oral opening +relationship: RO:0002433 UBERON:0000165 ! contributes to morphology of mouth +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/90/Lips.JPG" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/99/Mouth.jpg" xsd:anyURI +property_value: RO:0002161 NCBITaxon:8782 [Term] id: UBERON:0001834 @@ -182129,11 +180734,9 @@ xref: ZFA:0005226 is_a: UBERON:0001833 ! lip intersection_of: UBERON:0001833 ! lip intersection_of: part_of UBERON:0001709 ! upper jaw region -relationship: immediate_transformation_of UBERON:0011592 ! future upper lip relationship: part_of UBERON:0001709 ! upper jaw region -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/d4/Illu01_head_neck.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Lip that covers the lower portion of the mouth. [ZFIN:Curator][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001750", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000001 "Lip that covers the upper portion of the mouth.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001970", ontology="TAO", source="TAO:wd"} +relationship: RO:0002495 UBERON:0011592 ! immediate transformation of future upper lip +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d4/Illu01_head_neck.jpg" xsd:anyURI [Term] id: UBERON:0001835 @@ -182146,7 +180749,6 @@ subset: uberon_slim subset: vertebrate_core synonym: "labium inferius oris" RELATED OMO:0003011 [Wikipedia:Lower_lip] synonym: "lower jaw lip" EXACT [https://orcid.org/0000-0002-6601-2165] -xref: EHDAA2:0001020 xref: EMAPA:17909 xref: FMA:59818 xref: MA:0000921 @@ -182159,10 +180761,9 @@ xref: ZFA:0005225 is_a: UBERON:0001833 ! lip intersection_of: UBERON:0001833 ! lip intersection_of: part_of UBERON:0001710 ! lower jaw region -relationship: develops_from UBERON:0011596 ! future lower lip relationship: part_of UBERON:0001710 ! lower jaw region -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/99/Mouth.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Lip that covers the lower portion of the mouth.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002060", ontology="TAO", source="TAO:wd"} +relationship: RO:0002202 UBERON:0011596 ! develops from future lower lip +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/99/Mouth.jpg" xsd:anyURI [Term] id: UBERON:0001836 @@ -182189,8 +180790,6 @@ xref: UMLS:C0036087 {source="ncithesaurus:Saliva"} xref: Wikipedia:Saliva is_a: UBERON:0000456 ! secretion of exocrine gland relationship: capable_of_part_of GO:0007586 ! digestion -property_value: UBPROP:0000007 "salivary" xsd:string -property_value: UBPROP:0000008 "We classify a wide variety of not necessarily homologous fluids here. In humans, the saliva is a turbid and slightly viscous fluid, generally of an alkaline reaction, and is secreted by the parotid, submaxillary, and sublingual glands. In the mouth the saliva is mixed with the secretion from the buccal glands. In man and many animals, saliva is an important digestive fluid on account of the presence of the peculiar enzyme, ptyalin" xsd:string {source="GO"} [Term] id: UBERON:0001837 @@ -182218,8 +180817,8 @@ intersection_of: part_of UBERON:0001044 ! saliva-secreting gland relationship: channel_for UBERON:0001836 ! saliva relationship: channels_from UBERON:0001044 ! saliva-secreting gland relationship: channels_into UBERON:0000165 ! mouth -relationship: contributes_to_morphology_of UBERON:0001044 ! saliva-secreting gland relationship: part_of UBERON:0001044 ! saliva-secreting gland +relationship: RO:0002433 UBERON:0001044 ! contributes to morphology of saliva-secreting gland [Term] id: UBERON:0001839 @@ -182245,11 +180844,12 @@ xref: UMLS:C0458699 {source="ncithesaurus:Osseous_Labyrinth"} xref: VHOG:0001219 xref: Wikipedia:Bony_labyrinth xref: XAO:0000193 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0034921 ! multi organ part structure relationship: part_of UBERON:0001694 {source="FMA", source="MA"} ! petrous part of temporal bone relationship: part_of UBERON:0001846 {source="FMA"} ! internal ear relationship: part_of UBERON:0004681 ! vestibular system -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/22/Gray920.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/22/Gray920.png" xsd:anyURI [Term] id: UBERON:0001840 @@ -182282,13 +180882,10 @@ xref: Wikipedia:Semicircular_canal xref: XAO:0000198 xref: ZFA:0000431 is_a: UBERON:0000025 {source="GO"} ! tube -relationship: develops_from UBERON:0003051 ! ear vesicle +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001849 {source="OG"} ! membranous labyrinth -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/33/Balance_Disorder_Illustration_A.png" xsd:anyURI -property_value: UBPROP:0000001 "Fluid-filled toroidal spaces, arranged orthogonally to each other in the ear, that detect angular accelerations. (See Anatomical Atlas entry for semicircular canals by T. Whitfield.)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000431", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "In gnathostomes, each membranous labyrinth has three semicircular ducts that connect with a chamber known as the utriculus. These ducts are sometimes called canals, but technically the term semicircular canal applies to the spaces in the osseus labyrinth in which the semicircular ducts lie.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001144", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.414", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000009 "detects angular acceleration" xsd:string -property_value: UBPROP:0000012 "MA divides this into osseous and duct. In FMA, this is systemically part of the bony labyrinth. Note this is an anatomical space in ZFA. The MA treatment has advantages for representing the neuroepithelium, which should not be part of bone. Also check duct vs canal" xsd:string {external_ontology="MA"} +relationship: RO:0002202 UBERON:0003051 ! develops from ear vesicle +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/33/Balance_Disorder_Illustration_A.png" xsd:anyURI [Term] id: UBERON:0001844 @@ -182328,18 +180925,13 @@ xref: VHOG:0000691 xref: Wikipedia:Cochlea xref: XAO:0000197 xref: ZFA:0000374 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0034921 ! multi organ part structure -relationship: contributes_to_morphology_of UBERON:0001846 ! internal ear -relationship: has_quality PATO:0000404 {gci_relation="part_of", gci_filler="NCBITaxon:32525", source="Wikipedia"} ! coiled relationship: part_of UBERON:0001839 {source="FMA", source="VHOG", source="XAO", source="ncit"} ! bony labyrinth -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c7/Cochlea-crosssection.png" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/cb/Cochlea-crosssection.svg" xsd:anyURI -property_value: UBPROP:0000001 "A spiral-shaped cavity in the petrous portion of the temporal bone of the inner ear, containing the nerve endings essential for hearing and forming one of the divisions of the labyrinth. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000691", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/cochlea"} -property_value: UBPROP:0000003 "Because achieving high sensitivity is generally advantageous for auditory organs, it is not surprising that evidence for cochlear amplification is also seen in nonmammals. Spontaneous otoacoustic emissions (SOAEs) are narrow-band sound signals emitted from the inner ear, and it is generally assumed that their energy derives from the hair-cell molecular motors underlying cochlear amplification. However, all terrestrial vertebrates studied so far (including amphibians) show very similar SOAEs. The most parsimonious explanation for the universality of this phenomena is that some kind of amplifying mechanism is at least as old as land vertebrates themselves.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000691", ontology="VHOG", source="DOI:10.1016/S0959-4388(98)80033-0 Manley GA, Koeppl C, Phylogenetic development of the cochlea and its innervation. Current Opinion in Neurobiology (1998)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "cochlear" xsd:string -property_value: UBPROP:0000008 "The association with 'lagena' in frog and fish comes from HOG, although HOG is inconsistent here, associating lagena with XAO cochlea and ZFA cochlear duct. NBK53175 says: 'In contrast, the ventrally located auditory chambers have undergone more extensive evolutionary modifications. The saccule and lagena are prominent auditory organs in fish but the saccule has a vestibular role in mammals and birds, and the lagena is absent in mammals. The primary au- ditory organ in mammals and birds is the cochlea, which has no known counterpart in amphibians and fish (Riley and Phillips, 2003)'" xsd:string -property_value: UBPROP:0000008 "the cochlea is coiled in most mammals, monotremes being the exceptions." xsd:string -property_value: UBPROP:0000012 "sources vary in connection to bony labyrinth" xsd:string {external_ontology="XAO"} +relationship: RO:0000086 PATO:0000404 {gci_relation="part_of", gci_filler="NCBITaxon:32525", source="Wikipedia"} ! has quality coiled +relationship: RO:0002433 UBERON:0001846 ! contributes to morphology of internal ear +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c7/Cochlea-crosssection.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/cb/Cochlea-crosssection.svg" xsd:anyURI [Term] id: UBERON:0001845 @@ -182362,8 +180954,8 @@ xref: UMLS:C0031059 {source="ncithesaurus:Perilymph"} xref: Wikipedia:Perilymph xref: ZFA:0005413 is_a: UBERON:0006586 ! otolymph -relationship: located_in UBERON:0002278 ! perilymphatic space -relationship: surrounds UBERON:0001849 {source="Wikipedia"} ! membranous labyrinth +relationship: RO:0001025 UBERON:0002278 ! located in perilymphatic space +relationship: RO:0002221 UBERON:0001849 {source="Wikipedia"} ! surrounds membranous labyrinth [Term] id: UBERON:0001846 @@ -182404,12 +180996,11 @@ xref: VHOG:0000284 xref: Wikipedia:Internal_ear xref: XAO:0000192 xref: ZFA:0000217 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0034921 ! multi organ part structure -relationship: develops_from UBERON:0003051 {evidence="definitional"} ! ear vesicle relationship: part_of UBERON:0001690 ! ear -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray923.png" xsd:anyURI -property_value: UBPROP:0000001 "The auditory (hearing) and vestibular (balance) organ of the fish, equivalent to the inner ear of amniotes. (See Anatomical Atlas entry for ear by T. Whitfield.)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000217", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "The labyrinth, or inner ear, evolved very early in vertebrate history and, with many variations in configuration but none of basic design and function, has been retained by all vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000284", ontology="VHOG", source="ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.366", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003051 ! develops from ear vesicle +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray923.png" xsd:anyURI [Term] id: UBERON:0001848 @@ -182443,7 +181034,6 @@ synonym: "labyrinthus membranaceus" EXACT OMO:0003011 [Wikipedia:Membranous_laby xref: AAO:0011060 xref: EHDAA2:0000899 xref: EHDAA:4698 -xref: EMAPA:17815 xref: EV:0100367 xref: FMA:61022 xref: MA:0000242 @@ -182454,13 +181044,11 @@ xref: VHOG:0000729 xref: Wikipedia:Membranous_labyrinth xref: XAO:0000194 is_a: UBERON:0000062 ! organ -relationship: develops_from UBERON:0003051 ! ear vesicle -relationship: located_in UBERON:0004637 ! otic capsule +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001846 {source="FMA", source="MA"} ! internal ear -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray924.png" xsd:anyURI -property_value: UBPROP:0000001 "A system of communicating epithelial sacs and ducts within the bony labyrinth, containing the endolymph. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000729", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/membranous+labyrinth"} -property_value: UBPROP:0000003 "The labyrinth, or inner ear, evolved very early in vertebrate history and, with many variations in configuration but none of basic design and function, has been retained by all vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000729", ontology="VHOG", source="ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.366", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "inner ear has parts membranous and osseuous/bony labyrinth. it's not clear where the EMAPA term 'labyrinth' belong, we place them here for now" xsd:string {external_ontology="EMAPA"} +relationship: RO:0001025 UBERON:0004637 ! located in otic capsule +relationship: RO:0002202 UBERON:0003051 ! develops from ear vesicle +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray924.png" xsd:anyURI [Term] id: UBERON:0001850 @@ -182477,13 +181065,13 @@ xref: MA:0001295 xref: SCTID:280426002 is_a: UBERON:0000062 {source="FMA"} ! organ is_a: UBERON:0004111 ! anatomical conduit +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: channel_for UBERON:0001827 ! secretion of lacrimal gland -relationship: connects UBERON:0001707 ! nasal cavity -relationship: connects UBERON:0010284 ! lacrimal punctum -relationship: never_in_taxon NCBITaxon:8459 {source="PMID:7559104"} -relationship: only_in_taxon NCBITaxon:32523 {source="ISBN:9780674021839"} ! Tetrapoda relationship: part_of UBERON:0001750 {source="FMA"} ! lacrimal apparatus -property_value: UBPROP:0000008 "chelonians lack a lacrimal duct, and lacrimal/harderian secretions remain in or spill from the conjunctival sac[PMID:7559104]" xsd:string +relationship: RO:0002160 NCBITaxon:32523 {source="ISBN:9780674021839"} ! only in taxon Tetrapoda +relationship: RO:0002176 UBERON:0001707 ! connects nasal cavity +relationship: RO:0002176 UBERON:0010284 ! connects lacrimal punctum +property_value: RO:0002161 NCBITaxon:8459 {source="PMID:7559104"} [Term] id: UBERON:0001851 @@ -182502,8 +181090,6 @@ xref: galen:Cortex xref: Wikipedia:Cortex_(anatomy) is_a: UBERON:0000064 ! organ part relationship: bounding_layer_of UBERON:0000062 ! organ -property_value: UBPROP:0000007 "cortical" xsd:string -property_value: UBPROP:0000012 "this class is used more generically than in FMA, and includes e.g. cortex of hair" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0001853 @@ -182537,8 +181123,6 @@ xref: Wikipedia:Utricle_(ear) xref: XAO:0000195 xref: ZFA:0000700 is_a: UBERON:0002518 {source="Wikipedia", source="ZFA"} ! otolith organ -property_value: UBPROP:0000001 "The portion of the membranous labyrinth of the ear into which the semicircular ducts find their outlet. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000289", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "In gnathostomes, each membranous labyrinth has three semicircular ducts that connect with a chamber known as the utriculus.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000289", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.413-414", source="http://bgee.unil.ch/"} [Term] id: UBERON:0001854 @@ -182572,9 +181156,7 @@ xref: Wikipedia:Saccule xref: XAO:0000196 xref: ZFA:0000428 is_a: UBERON:0002518 {source="Wikipedia", source="ZFA"} ! otolith organ -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/cb/Bigotolith.jpg" xsd:anyURI -property_value: UBPROP:0000001 "The most ventral chamber of the membranous labyrinth. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-25, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000374", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "In gnathostomes, each membranous labyrinth has three semicircular ducts that connect with a chamber known as the utriculus. (...) In all gnathostomes, the utriculus connects ventrally with a larger sac, called the sacculus (...) .[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000374", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.413-414", source="http://bgee.unil.ch/"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/cb/Bigotolith.jpg" xsd:anyURI [Term] id: UBERON:0001855 @@ -182610,11 +181192,10 @@ xref: UMLS:C1323110 {source="ncithesaurus:Cochlear_Duct", source="BIRNLEX:2562"} xref: VHOG:0000507 xref: Wikipedia:Cochlear_duct is_a: UBERON:0000025 ! tube +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0002499 {source="FMA", source="MA"} ! cochlear labyrinth -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/bc/Gray928.png" xsd:anyURI -property_value: editor_note "TODO - check cochlear duct vs cochlear aqueduct vs scala media" xsd:string -property_value: UBPROP:0000001 "The coiled portion of the membranous labyrinth located inside the cochlea. It contains endolymph. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000507", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/cochlear+duct"} -property_value: UBPROP:0000003 "In gnathostomes, each membranous labyrinth has three semicircular ducts that connect with a chamber known as the utriculus. (...) In all gnathostomes, the utriculus connects ventrally with a larger sac, called the sacculus (...) In most groups of gnathostomes, the caudoventral evagination of the sacculus forms a small lagena, and in some diapsids and mammals the lagena develops into a longer duct. The lagena becomes greatly elongated in therians and coils to form the cochlear duct.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000507", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.413-414", source="http://bgee.unil.ch/"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/bc/Gray928.png" xsd:anyURI +property_value: IAO:0000116 "TODO - check cochlear duct vs cochlear aqueduct vs scala media" xsd:string [Term] id: UBERON:0001856 @@ -182626,16 +181207,15 @@ synonym: "membranous semicircular canal" RELATED [MA:0000251] xref: EMAPA:32830 xref: FMA:61122 xref: MA:0000251 -xref: MESH:D054776 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C33528 xref: SCTID:279833009 xref: UMLS:C1323109 {source="ncithesaurus:Semicircular_Duct"} xref: VHOG:0000238 is_a: UBERON:0000025 ! tube +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001840 {source="MA"} ! semicircular canal relationship: part_of UBERON:0001862 {source="FMA", source="MA"} ! vestibular labyrinth -property_value: editor_note "TODO - check canal vs duct. see Wikipedia:File:Gray927.png" xsd:string -property_value: UBPROP:0000003 "In gnathostomes, each membranous labyrinth has three semicircular ducts that connect with a chamber known as the utriculus (...); Gnathostome ears have a horizontal semicircular duct. This brings their complement to three semicircular ducts, a pattern retained throughout gnathostome evolution.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000238", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.413-414 and p.58", source="http://bgee.unil.ch/"} +property_value: IAO:0000116 "TODO - check canal vs duct. see Wikipedia:File:Gray927.png" xsd:string [Term] id: UBERON:0001862 @@ -182652,16 +181232,14 @@ xref: CALOHA:TS-0479 xref: EHDAA2:0000832 xref: EHDAA:4706 xref: EMAPA:17286 -xref: EMAPA:17815 xref: FMA:61255 xref: MA:0000245 -xref: MESH:D014722 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C33871 -xref: SCTID:181188003 xref: UMLS:C0042606 {source="ncithesaurus:Vestibular_Labyrinth"} xref: Wikipedia:Inner_ear xref: XAO:0004145 is_a: UBERON:0000064 ! organ part +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001849 ! membranous labyrinth [Term] @@ -182684,8 +181262,6 @@ intersection_of: UBERON:0000456 ! secretion of exocrine gland intersection_of: produced_by UBERON:0001821 ! sebaceous gland relationship: has_part CHEBI:15440 relationship: produced_by UBERON:0001821 ! sebaceous gland -property_value: UBPROP:0000008 "The composition of sebum varies across species. In humans, the lipid content is as follows: 25% wax monoesters, 41% triglycerides, 16% free fatty acids, 12% squalene; Sapienic acid is a sebum fatty acid that is unique to humans." xsd:string -property_value: UBPROP:0000009 "waterproofs skin" xsd:string [Term] id: UBERON:0001867 @@ -182704,8 +181280,8 @@ xref: UMLS:C0013445 {source="ncithesaurus:External_Ear_Cartilage"} is_a: UBERON:0007844 ! cartilage element intersection_of: UBERON:0007844 ! cartilage element intersection_of: part_of UBERON:0001691 ! external ear -relationship: composed_primarily_of UBERON:0001996 ! elastic cartilage tissue relationship: part_of UBERON:0001691 ! external ear +relationship: RO:0002473 UBERON:0001996 ! composed primarily of elastic cartilage tissue [Term] id: UBERON:0001868 @@ -182733,7 +181309,7 @@ is_a: UBERON:0001418 ! skin of thorax intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0001443 ! chest relationship: part_of UBERON:0001443 ! chest -property_value: editor_note "check FMA:61415" xsd:string +property_value: IAO:0000116 "check FMA:61415" xsd:string [Term] id: UBERON:0001869 @@ -182770,13 +181346,12 @@ xref: UMLS:C0242202 {source="BIRNLEX:1042"} xref: VHOG:0001639 xref: Wikipedia:Cerebral_hemisphere is_a: UBERON:0000064 ! organ part +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0015212 ! lateral structure -relationship: in_lateral_side_of UBERON:0000955 ! brain -relationship: in_lateral_side_of UBERON:0001893 {source="FMA-abduced-lr"} ! telencephalon +relationship: BSPO:0000126 UBERON:0000955 ! brain +relationship: BSPO:0000126 UBERON:0001893 {source="FMA-abduced-lr"} ! telencephalon relationship: part_of UBERON:0001893 ! telencephalon -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/92/Hemispheres.png" xsd:anyURI -property_value: UBPROP:0000001 "Part of the telencephalon consisting of either of the two smooth, elongated halves of the cerebrum.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010480", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "The presence of paired evaginated hemispheres and olfactory bulbs in both agnathan and gnathostome radiations suggests that such hemispheres were also present in the common ancestor.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001639", ontology="VHOG", source="DOI:10.1146/annurev.ne.04.030181.001505 Northcutt RG, Evolution of the telencephalon in nonmammals. Ann. Rev. Neurosci. (1981)", source="http://bgee.unil.ch/"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/92/Hemispheres.png" xsd:anyURI [Term] id: UBERON:0001870 @@ -182799,16 +181374,14 @@ xref: EMAPA:35357 xref: FMA:242199 xref: GAID:674 xref: MA:0000905 -xref: MESH:D005625 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: NLXANAT:20090601 xref: Wikipedia:Frontal_lobe is_a: UBERON:0016529 ! cortex of cerebral lobe intersection_of: UBERON:0016529 ! cortex of cerebral lobe intersection_of: part_of UBERON:0016525 ! frontal lobe relationship: part_of UBERON:0016525 ! frontal lobe -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b4/Gray729.png" xsd:anyURI -property_value: UBPROP:0000001 "Anterior portion of the frontal cortex, lying anterior to the central sulcus. It is bounded by the parietal cortex posteriorly and the temporal cortex laterally." xsd:string {source="NLXANAT:20090601"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b4/Gray729.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001871 @@ -182843,9 +181416,9 @@ xref: UMLS:C0039485 {source="BIRNLEX:1160", source="ncithesaurus:Temporal_Lobe"} xref: UMLS:C1268978 {source="BIRNLEX:1160"} xref: Wikipedia:Temporal_lobe is_a: UBERON:0016526 {source="FMA"} ! lobe of cerebral hemisphere -relationship: contributes_to_morphology_of UBERON:0001893 ! telencephalon -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/91/Gray730.png" xsd:anyURI +relationship: RO:0002433 UBERON:0001893 ! contributes to morphology of telencephalon +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/91/Gray730.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001872 @@ -182878,9 +181451,9 @@ xref: UMLS:C0030560 {source="BIRNLEX:1148", source="ncithesaurus:Parietal_Lobe_o xref: Wikipedia:Parietal_lobe is_a: UBERON:0016526 {source="FMA"} ! lobe of cerebral hemisphere relationship: adjacent_to UBERON:0001871 ! temporal lobe -relationship: contributes_to_morphology_of UBERON:0001893 ! telencephalon -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/Gray726_parietal_lobe.png" xsd:anyURI +relationship: RO:0002433 UBERON:0001893 ! contributes to morphology of telencephalon +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/Gray726_parietal_lobe.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001873 @@ -182921,11 +181494,10 @@ xref: SCTID:279297002 xref: UMLS:C0007461 {source="ncithesaurus:Caudate_Nucleus", source="BIRNLEX:1373"} xref: Wikipedia:Caudate_nucleus is_a: UBERON:0009663 ! telencephalic nucleus -relationship: contributes_to_morphology_of UBERON:0005383 ! caudate-putamen relationship: part_of UBERON:0005383 {source="MA"} ! caudate-putamen -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/91/Telencephalon-Horiconatal.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Nucleus of brain which is an elongated crescent-shaped mass lying parallel and adjacent to the lateral ventricle throughout its extent[FMA:61833]." xsd:string {source="FMA:61833"} +relationship: RO:0002433 UBERON:0005383 ! contributes to morphology of caudate-putamen +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/91/Telencephalon-Horiconatal.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001874 @@ -182958,14 +181530,12 @@ xref: UMLS:C0034169 {source="ncithesaurus:Putamen"} xref: VHOG:0001456 xref: Wikipedia:Putamen is_a: UBERON:0009663 ! telencephalic nucleus -relationship: contributes_to_morphology_of UBERON:0005383 ! caudate-putamen relationship: part_of UBERON:0001869 {source="FMA"} ! cerebral hemisphere relationship: part_of UBERON:0005383 ! caudate-putamen -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/33/BrainCaudatePutamen.svg" xsd:anyURI -property_value: editor_note "check - rodents. The caudate nucleus and putamen are separated by a clear white matter bundle in most species but not in rodents (MM)" xsd:string -property_value: UBPROP:0000001 "Nucleus of brain which lies ventral to the caudate nucleus and internal capsule and medial to the external capsule. The putamen and caudate nucleus together form the dorsal striatum. It is also one of the structures that comprises the basal ganglia. Through various pathways, the putamen is connected to the substantia nigra and globus pallidus. The main function of the putamen is to regulate movements and influence various types of learning. It employs dopamine to perform its functions. The putamen also plays a role in degenerative neurological disorders, such as Parkinson's disease[Wikipedia:Putamen]." xsd:string {source="Wikipedia:Putamen"} -property_value: UBPROP:0000003 "All nuclei of the mammalian basal ganglia are also present in the oldest vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001456", ontology="VHOG", source="DOI:10.1016/j.cub.2011.05.001 Stephenson-Jones M, Samuelsson E, Ericsson J, Robertson B, Grillner S, Evolutionary conservation of the basal ganglia as a common vertebrate mechanism for action selection. Current Biology (2011)", source="http://bgee.unil.ch/"} +relationship: RO:0002433 UBERON:0005383 ! contributes to morphology of caudate-putamen +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/33/BrainCaudatePutamen.svg" xsd:anyURI +property_value: IAO:0000116 "check - rodents. The caudate nucleus and putamen are separated by a clear white matter bundle in most species but not in rodents (MM)" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001876 @@ -183020,12 +181590,8 @@ is_a: UBERON:0002420 {source="FMA"} ! basal ganglion is_a: UBERON:0005401 ! cerebral hemisphere gray matter relationship: part_of UBERON:0000349 {source="FMA"} ! limbic system relationship: part_of UBERON:0001871 {source="BTO"} ! temporal lobe -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Amyg.png" xsd:anyURI -property_value: UBPROP:0000001 "Subdivision of basal ganglion of telencephalon which is an almond-shaped gray mass in the dorsomedial part of the temporal lobe[FMA:61841]" xsd:string {source="FMA:61841"} -property_value: UBPROP:0000003 "One part of the striatum is called the archistriatum. (...) The archistriatum of fishes consists of several indistinctly segregated nuclei called the amygdaloid (...) complex. Tetrapods retain the structure, and in mammals the corresponding amygdala is a globular mass that tends to be ventral to the other basal nuclei.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001277", ontology="VHOG", source="ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.342", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "amygdalar" xsd:string -property_value: UBPROP:0000012 "MA and FMA differ on relationship to basal ganglion. The FMA text def suggests a subdivision, but it is classified as a subtype" xsd:string {external_ontology="MA"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Amyg.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001881 @@ -183058,13 +181624,12 @@ xref: PBA:10095 xref: UMLS:C0262264 {source="BIRNLEX:1113"} xref: Wikipedia:Islands_of_Calleja is_a: UBERON:0009663 ! telencephalic nucleus -relationship: contributes_to_morphology_of UBERON:0001882 ! nucleus accumbens -relationship: contributes_to_morphology_of UBERON:0001883 ! olfactory tubercle relationship: part_of UBERON:0001869 ! cerebral hemisphere relationship: part_of UBERON:0001882 {gci_relation="part_of", gci_filler="NCBITaxon:9443", source="MP"} ! nucleus accumbens relationship: part_of UBERON:0001883 {gci_relation="part_of", gci_filler="NCBITaxon:9989", source="MP"} ! olfactory tubercle -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Islands_of_Calleja_Rat.jpg" xsd:anyURI -property_value: UBPROP:0000008 "The islands of Calleja are located within the olfactory tubercle in most species; however, in primates these islands are located within the nucleus accumbens, since the olfactory tubercle is absent or extremely rudimentary in the brains of primates" xsd:string {source="MP:0010010"} +relationship: RO:0002433 UBERON:0001882 ! contributes to morphology of nucleus accumbens +relationship: RO:0002433 UBERON:0001883 ! contributes to morphology of olfactory tubercle +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Islands_of_Calleja_Rat.jpg" xsd:anyURI [Term] id: UBERON:0001882 @@ -183103,16 +181668,13 @@ xref: SCTID:427667007 xref: UMLS:C0028633 {source="ncithesaurus:Accumbens_Nucleus"} xref: Wikipedia:Nucleus_accumbens is_a: UBERON:0009663 ! telencephalic nucleus -relationship: contributes_to_morphology_of UBERON:0005403 ! ventral striatum relationship: part_of UBERON:0000349 {source="FMA", source="GO"} ! limbic system relationship: part_of UBERON:0001869 ! cerebral hemisphere relationship: part_of UBERON:0005403 {source="MA"} ! ventral striatum -relationship: present_in_taxon NCBITaxon:8782 {source="ISBN:0471888893"} ! Aves -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Circuit_du_syst%C3%A8me_de_recompense.jpg" xsd:anyURI -property_value: RO:0002171 UBERON:0001883 {source="ABA"} -property_value: UBPROP:0000001 "a collection of pleomorphic cells in the caudal part of the anterior horn of the lateral ventricle, in the region of the olfactory tubercle, lying between the head of the caudate nucleus and the anterior perforated substance. It is part of the ventral striatum, a composite structure considered part of the basal ganglia[GO][GO:0021768]." xsd:string {source="GO:0021768"} -property_value: UBPROP:0000008 "The ventral striatopallidal complex in birds corresponds closely to its counterpart in mammals, with a nucleus accumbes present in the rostral telenceaphalon. Note that in birds, a region previously called the nucleus accumbens is now recognized as the lateral part of the bed nucleus of stria terminalis.[ISBN:0471888893]" xsd:string +relationship: RO:0002433 UBERON:0005403 ! contributes to morphology of ventral striatum +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Circuit_du_syst%C3%A8me_de_recompense.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:8782 {source="ISBN:0471888893"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001883 @@ -183141,13 +181703,9 @@ xref: PBA:10096 xref: VHOG:0001625 xref: Wikipedia:Olfactory_tubercle is_a: UBERON:0009663 ! telencephalic nucleus -relationship: contributes_to_morphology_of UBERON:0002894 ! olfactory cortex relationship: part_of UBERON:0002894 {source="EHDAA2-inferred", source="MA", source="VHOG", source="Wikipedia"} ! olfactory cortex -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray732.png" xsd:anyURI -property_value: RO:0002171 UBERON:0001882 {source="ABA"} -property_value: RO:0002174 NCBITaxon:9443 {source="MP", comment="EDITOR_NOTE check EHDAA2"} -property_value: UBPROP:0000001 "The olfactory tubercle is a structure involved in Olfaction. It is present in humans, but much smaller than it is in some other animals. It is a frequent subject of research." xsd:string {source="Wikipedia:Olfactory_tubercle"} -property_value: UBPROP:0000008 "Absent in primates" xsd:string {source="MP"} +relationship: RO:0002433 UBERON:0002894 ! contributes to morphology of olfactory cortex +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray732.png" xsd:anyURI [Term] id: UBERON:0001884 @@ -183175,12 +181733,11 @@ xref: VHOG:0000728 xref: Wikipedia:Phrenic_nerve is_a: UBERON:0003443 ! thoracic cavity nerve intersection_of: UBERON:0001021 ! nerve -intersection_of: innervates UBERON:0001103 ! diaphragm -relationship: branching_part_of UBERON:0000962 ! nerve of cervical vertebra -relationship: innervates UBERON:0001103 ! diaphragm -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/3c/Gray806.png" xsd:anyURI -property_value: UBPROP:0000001 "A nerve that arises from the caudal cervical nerves and is primarily the motor nerve of the diaphragm but also sends sensory fibers to the pericardium. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000728", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/phrenic+nerve"} +intersection_of: RO:0002134 UBERON:0001103 ! innervates diaphragm +relationship: RO:0002134 UBERON:0001103 ! innervates diaphragm +relationship: RO:0002380 UBERON:0000962 ! branching part of nerve of cervical vertebra +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3c/Gray806.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001885 @@ -183222,10 +181779,7 @@ xref: Wikipedia:Dentate_gyrus is_a: UBERON:0000200 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! gyrus is_a: UBERON:0002616 ! regional part of brain relationship: part_of UBERON:0002421 {source="MA"} ! hippocampal formation -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/ab/HippocampalRegions.jpg" xsd:anyURI -property_value: RO:0002171 UBERON:0001954 {source="ABA"} -property_value: RO:0002171 UBERON:0002601 {source="ABA"} -property_value: UBPROP:0000001 "The dentate gyrus is one of two interlocking gyri of the hippocampus. It contains granule cells, which project to the pyramidal cells and interneurons of the CA3 region of the ammon gyrus[GO][GO:0021542]." xsd:string {source="GO:0021542"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/ab/HippocampalRegions.jpg" xsd:anyURI [Term] id: UBERON:0001886 @@ -183267,14 +181821,11 @@ is_a: UBERON:0003947 ! brain ventricle/choroid plexus is_a: UBERON:0005629 ! vascular plexus is_a: UBERON:0006876 ! vasculature of organ is_a: UBERON:0036303 ! vasculature of central nervous system -relationship: contributes_to_morphology_of UBERON:0003947 ! brain ventricle/choroid plexus relationship: part_of UBERON:0004086 ! brain ventricle relationship: part_of UBERON:0005283 ! tela choroidea -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b9/Gray708.svg" xsd:anyURI -property_value: editor_note "TODO - check relationship to ventricle. Check subclass - ZFA says vasculature. Note that FMA:61934 (choroid plexus of cerebral hemisphere) has exact synonym 'choroid plexus' but it is not clear that this belongs here, as the fourth ventricle is not in the cerebral hemisphere" xsd:string -property_value: UBPROP:0000001 "A tuft of capillaries that project into the ventricles of the brain and secretes cerebral spinal fluid. The choroid plexus is covered by a cuboidal epithelium which maintains the integrity of the blood-brain barrier.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001443", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Fringe of the tela choroidea of the brain ventricles[MP]" xsd:string {source="MP:0000820"} -property_value: UBPROP:0000007 "choroidal" xsd:string +relationship: RO:0002433 UBERON:0003947 ! contributes to morphology of brain ventricle/choroid plexus +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b9/Gray708.svg" xsd:anyURI +property_value: IAO:0000116 "TODO - check relationship to ventricle. Check subclass - ZFA says vasculature. Note that FMA:61934 (choroid plexus of cerebral hemisphere) has exact synonym 'choroid plexus' but it is not clear that this belongs here, as the fourth ventricle is not in the cerebral hemisphere" xsd:string [Term] id: UBERON:0001888 @@ -183312,8 +181863,7 @@ is_a: UBERON:0034730 ! olfactory tract linking bulb to ipsilateral dorsal telenc intersection_of: UBERON:0002265 ! olfactory tract intersection_of: overlaps UBERON:0002894 ! olfactory cortex relationship: overlaps UBERON:0002894 ! olfactory cortex -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray732.png" xsd:anyURI -property_value: UBPROP:0000008 "In mammals the fibers of the dorsal lateral olfactory tract either pass under the accessory olfactory formation, or they penetrate through it separating the internal granule cells from the output cells." xsd:string {source="PMID:7437895"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray732.png" xsd:anyURI [Term] id: UBERON:0001889 @@ -183369,18 +181919,12 @@ xref: Wikipedia:Forebrain xref: XAO:0000011 xref: ZFA:0000109 is_a: UBERON:0002616 ! regional part of brain -is_a: UBERON:0004121 ! ectoderm-derived structure disjoint_from: UBERON:0002298 ! brainstem -relationship: contributes_to_morphology_of UBERON:0000955 ! brain -relationship: develops_from UBERON:0003080 ! anterior neural tube -relationship: immediate_transformation_of UBERON:0006240 {evidence="definitional"} ! future forebrain -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI -property_value: UBPROP:0000001 "Most anterior of the three regions of the brain consisting of the telencephalon and diencephalon.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010147", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "The most anterior region the brain including both the telencephalon and diencephalon. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000109", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000002 "relationship loss: develops_from forebrain neural tube (TAO:0007041)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000109", ontology="TAO"} -property_value: UBPROP:0000003 "In craniate embryos, neural expression of Distal-less-related genes is exclusively in the forebrain (...). Because the major neural expression domain of amphioxus AmphiDll is in the anterior three-fourths of the cerebral vesicle, we suggest that this region of the neural tube is homologous to parts of the craniate forebrain. This conclusion is strongly supported by three-dimensional, computer-assisted reconstruction of the neural tube of amphioxus based on serial transmission electron microscopy. At the neuroanatomical level, a number of detailed homologies are indicated between the anterior three-fourths of the amphioxus cerebral vesicle and the diencephalic region of the craniate forebrain. If one assumes that the amphioxus condition fairly represents the nervous system of the proximate ancestor of the craniates, one can suggest that they evolved from a creature that had the beginnings of a forebrain.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000383", ontology="VHOG", source="PMID:8787764 Holland ND, Panganiban G, Henyey EL, Holland LZ, Sequence and developmental expression of AmphiDll, an amphioxus Distal-less gene transcribed in the ectoderm, epidermis and nervous system: insights into evolution of craniate forebrain and neural crest. Development (1996)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "prosencephalic" xsd:string +relationship: RO:0002202 UBERON:0003080 ! develops from anterior neural tube +relationship: RO:0002433 UBERON:0000955 ! contributes to morphology of brain +relationship: RO:0002495 UBERON:0006240 ! immediate transformation of future forebrain +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001891 @@ -183425,21 +181969,13 @@ xref: Wikipedia:Midbrain xref: XAO:0000014 xref: ZFA:0000128 is_a: UBERON:0002616 ! regional part of brain -is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest -relationship: contributes_to_morphology_of UBERON:0000955 ! brain -relationship: has_developmental_contribution_from UBERON:0003849 {evidence="definitional"} ! mesencephalic neural crest -relationship: immediate_transformation_of UBERON:0009616 {source="Bgee:AN"} ! presumptive midbrain -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/f9/Human_brain_inferior_view_description.JPG" xsd:anyURI -property_value: editor_note "developmental relationships need revised" xsd:string -property_value: RO:0002171 UBERON:0001894 {exceptions="ZFA", exceptions_url="https://github.com/obophenotype/uberon/issues/378", source="ABA", status="pending"} -property_value: RO:0002171 UBERON:0002028 {exceptions="ZFA", source="ABA", status="pending"} -property_value: UBPROP:0000001 "Middle part of the brain composed of the optic tectum and penducular region.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010149", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000128", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000069", ontology="VHOG", source="DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "mesencephalic" xsd:string -property_value: UBPROP:0000012 "part of brainstem in ABA - we reject this in favor of ISBN:0471888893 which has an implicit overlaps relationships" xsd:string {external_ontology="ABA"} +relationship: RO:0002254 UBERON:0003849 ! has developmental contribution from mesencephalic neural crest +relationship: RO:0002433 UBERON:0000955 ! contributes to morphology of brain +relationship: RO:0002495 UBERON:0009616 {source="Bgee:AN"} ! immediate transformation of presumptive midbrain +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f9/Human_brain_inferior_view_description.JPG" xsd:anyURI +property_value: IAO:0000116 "developmental relationships need revised" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001892 @@ -183473,10 +182009,6 @@ is_a: UBERON:0004731 ! neuromere intersection_of: UBERON:0004731 ! neuromere intersection_of: part_of UBERON:0007277 ! presumptive hindbrain relationship: part_of UBERON:0007277 ! presumptive hindbrain -property_value: UBPROP:0000001 "A segment of the developing hindbrain. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001064", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "Rhombomeric segmentation is found in all living vertebrates and is of fundamental importance to the development of the vertebrate head.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000672", ontology="VHOG", source="DOI:10.1006/dbio.2002.0831 Mazet F, Shimeld SM, The Evolution of Chordate Neural Segmentation. Developmental Biology (2002)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "In human embryonic development, the rhombomeres are present by day 29" xsd:string -property_value: UBPROP:0000012 "DHBA divides this into A(1-3),B(4),C(5-7) and D(8)" xsd:string [Term] id: UBERON:0001893 @@ -183522,25 +182054,8 @@ xref: Wikipedia:Telencephalon xref: XAO:0000012 xref: ZFA:0000079 is_a: UBERON:0002616 ! regional part of brain -is_a: UBERON:0004121 ! ectoderm-derived structure -relationship: immediate_transformation_of UBERON:0014371 {source="Bgee:AN"} ! future telencephalon relationship: part_of UBERON:0001890 ! forebrain -property_value: RO:0002171 UBERON:0002037 {source="ABA"} -property_value: UBPROP:0000001 "Organ component of neuraxis that has as its parts the cerebral cortex, cerebral white matter, basal ganglia, septum and fornix, as well as subcortical gray and white matter structures[FMA:62000]." xsd:string {source="FMA:62000"} -property_value: UBPROP:0000001 "Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010479", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "The anterior and dorsal forebrain neuromere, includes the olfactory bulb. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000079", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000002 "relationship loss: develops_from presumptive telencephalon (TAO:0000571)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000079", ontology="TAO"} -property_value: UBPROP:0000003 "From an evolutionary standpoint, the telencephalon is the most recent brain structure: the amphioxus does not have this structure as a morphological entity. Overt telencephalon is present in the hagfish and lamprey to receive numerous input fibers from various parts of the CNS, similar to gnathostomes.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000283", ontology="VHOG", source="DOI:10.1016/j.ydbio.2005.02.008 Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "cerebral" xsd:string -property_value: UBPROP:0000007 "telencephalic" xsd:string -property_value: UBPROP:0000007 "telenencephalic" xsd:string -property_value: UBPROP:0000008 "dolphins are the only species (other than humans) to have cerebra accounting for as much as 2 percent of their body weight." xsd:string {source="Wikipedia:Telencephalon#Variation_among_species"} -property_value: UBPROP:0000008 "In mammals the cortex covers almost the whole of the cerebral hemispheres." xsd:string {source="Wikipedia:Telencephalon#Variation_among_species"} -property_value: UBPROP:0000008 "In ray-finned fishes and most pronounced in teleosts the roof plate of the embryonic telencephalon extends laterally with the effect that the paired alar plates forming the hemispheric walls roll out lateroventrally in a process called eversion. This is unlike the development in other vertebrate groups. [ZFA:0000079, ISBN:3764351209]" xsd:string -property_value: UBPROP:0000008 "In ray-finned fishes the inner surfaces of the lateral and ventral regions of the cerebrum bulge up into the ventricles." xsd:string {source="Wikipedia:Telencephalon#Variation_among_species"} -property_value: UBPROP:0000008 "In the amniotes, the cerebrum becomes increasingly large and complex. In reptiles, the paleopallium is much larger than in amphibians, and its growth has pushed the basal nuclei into the central regions of the cerebrum." xsd:string {source="Wikipedia:Telencephalon#Variation_among_species"} -property_value: UBPROP:0000008 "In the most primitive living vertebrates, the hagfishes and lampreys, the cerebrum is a relatively simple structure receiving nerve impulses from the olfactory bulb." xsd:string {source="Wikipedia:Telencephalon#Variation_among_species"} -property_value: UBPROP:0000008 "The cerebrum of birds has evolved along different lines to that of mammals, although they are similarly enlarged, by comparison with reptiles. However, this enlargement is largely due to the basal ganglia, with the other areas remaining relatively primitive in structure." xsd:string {source="Wikipedia:Telencephalon#Variation_among_species"} +relationship: RO:0002495 UBERON:0014371 {source="Bgee:AN"} ! immediate transformation of future telencephalon [Term] id: UBERON:0001894 @@ -183596,21 +182111,12 @@ xref: Wikipedia:Diencephalon xref: XAO:0000013 xref: ZFA:0000101 is_a: UBERON:0002616 ! regional part of brain -is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest -relationship: contributes_to_morphology_of UBERON:0001890 ! forebrain -relationship: has_developmental_contribution_from UBERON:0003851 {evidence="definitional"} ! diencephalon neural crest -relationship: immediate_transformation_of UBERON:0006222 {evidence="definitional"} ! future diencephalon relationship: part_of UBERON:0001890 ! forebrain -relationship: present_in_taxon NCBITaxon:7762 {notes="not well differentiated from the cerebrum. (Ariens, p. 868)", source="PMID:8932866"} -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI -property_value: RO:0002171 UBERON:0001891 {exceptions="ZFA", source="ABA", source="https://github.com/obophenotype/uberon/issues/378", status="pending"} -property_value: RO:0002171 UBERON:0002028 {source="ABA"} -property_value: UBPROP:0000001 "The more posterior and ventral of two forebrain neuromeres, the other being the telencephalon; major derivatives are the eye cups, the brain pretectal region, the thalamus, hypothalamus, and epithalamus (including the habenula and epiphysis). Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000101", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Unpaired part of the forebrain comprised of three major parts; the epithalamus, thalamus, and hypothalamus.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010481", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000318", ontology="VHOG", source="DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "diencephalic" xsd:string -property_value: UBPROP:0000012 "in ABA, this is part of the brain stem" xsd:string {external_ontology="ABA"} +relationship: RO:0002254 UBERON:0003851 ! has developmental contribution from diencephalon neural crest +relationship: RO:0002433 UBERON:0001890 ! contributes to morphology of forebrain +relationship: RO:0002495 UBERON:0006222 ! immediate transformation of future diencephalon +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI [Term] id: UBERON:0001895 @@ -183641,15 +182147,10 @@ xref: UMLS:C0376353 {source="BIRNLEX:965"} xref: UMLS:C1516904 {source="ncithesaurus:Epencephalon"} xref: VHOG:0000741 xref: Wikipedia:Metencephalon -is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004733 ! segmental subdivision of hindbrain -relationship: contributes_to_morphology_of UBERON:0002028 ! hindbrain -relationship: immediate_transformation_of UBERON:0010092 {evidence="definitional"} ! future metencephalon -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI -property_value: RO:0002174 NCBITaxon:7955 -property_value: UBPROP:0000001 "Anterior part of the hindbrain ventral to the cerebellum[BIRNLEX:965]." xsd:string {source="BIRNLEX:965"} -property_value: UBPROP:0000001 "The anterior of two brain vesicles formed by specialization of the rhombencephalon in the developing embryo. It gives rise to cerebellum and pons. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000741", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/metencephalon"} -property_value: UBPROP:0000003 "The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000741", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500", source="http://bgee.unil.ch/"} +relationship: RO:0002433 UBERON:0002028 ! contributes to morphology of hindbrain +relationship: RO:0002495 UBERON:0010092 ! immediate transformation of future metencephalon +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI [Term] id: UBERON:0001896 @@ -183698,16 +182199,14 @@ xref: Wikipedia:Bone_marrow_of_ovary_oblongata xref: XAO:0003100 xref: ZFA:0000545 is_a: UBERON:0000064 ! organ part +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: capable_of GO:0002027 ! regulation of heart rate relationship: capable_of GO:0043576 ! regulation of respiratory gaseous exchange relationship: capable_of GO:0044058 ! regulation of digestive system process relationship: part_of UBERON:0002298 ! brainstem relationship: part_of UBERON:0005290 ! myelencephalon -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/6b/Illu_pituitary_pineal_glands.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Posterior portion of the hindbrain which controls respiration, heartbeat, digestion, and swallowing as well as some locomotor responses.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010486", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "The posterior region of the brain that is continuous with the spinal cord. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-17, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000181", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "Classical anatomical studies subdivided the vertebrate rhombencephalon into pons and medulla oblongata. (...) The medulla oblongata appears therefore as a tagma, that is, a group of segmental units (pseudorhombomeres, in this case) sharing some morphological and molecular characteristics, and in some aspects different from the segmental units present in adjoining brain regions, pons and spinal cord.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000181", ontology="VHOG", source="DOI:10.1016/j.ydbio.2008.08.017 Marin F, Aroca P, Puelles L, Hox gene colinear expression in the avian medulla oblongata is correlated with pseudorhombomeric domains. Developmental Biology (2008)", source="http://bgee.unil.ch/"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6b/Illu_pituitary_pineal_glands.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001897 @@ -183754,16 +182253,11 @@ xref: Wikipedia:Thalamus xref: ZFA:0001215 is_a: UBERON:0002616 ! regional part of brain is_a: UBERON:0015212 ! lateral structure -relationship: contributes_to_morphology_of UBERON:0001894 ! diencephalon -relationship: in_lateral_side_of UBERON:0010225 {source="FMA-abduced-lr"} ! thalamic complex +relationship: BSPO:0000126 UBERON:0010225 {source="FMA-abduced-lr"} ! thalamic complex relationship: part_of UBERON:0010225 ! thalamic complex -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/ce/Brain_chrischan_thalamus.jpg" xsd:anyURI -property_value: RO:0002171 UBERON:0001898 {source="ABA"} -property_value: UBPROP:0000001 "One of a pair of large oval nervous structures made of gray matter and forming most of the lateral walls of the third ventricle of the brain and part of the diencephalon. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000657", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/thalamus"} -property_value: UBPROP:0000001 "Part of the diencephalon consisting of a mass of connecting fibers which relay sensory information to the cerebral cortex.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010483", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "(...) the brain regions of tetrapods, the structures they contain, and their basic organizational features are the same as in fishes.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000657", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.484", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "thalamic" xsd:string +relationship: RO:0002433 UBERON:0001894 ! contributes to morphology of diencephalon +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/ce/Brain_chrischan_thalamus.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001898 @@ -183812,22 +182306,15 @@ xref: XAO:0004070 xref: ZFA:0000032 is_a: UBERON:0002616 ! regional part of brain relationship: capable_of GO:0046883 {source="WP"} ! regulation of hormone secretion -relationship: contributes_to_morphology_of UBERON:0001894 ! diencephalon relationship: part_of UBERON:0000349 ! limbic system -relationship: part_of UBERON:0010225 {missing_from="FMA", source="EHDAA2", source="Wikipedia"} ! thalamic complex -relationship: present_in_taxon NCBITaxon:117569 {source="Ariens, p. 1192"} -relationship: present_in_taxon NCBITaxon:7742 ! Vertebrata -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/9f/LocationOfHypothalamus.jpg" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI -property_value: RO:0002171 UBERON:0001897 {source="ABA"} -property_value: RO:0002174 NCBITaxon:7737 {notes="Lancelets possess a region similar to the hypothalamus (Murakami, 2005)"} -property_value: UBPROP:0000001 "A specialized brain region of the ventral diencephalon arising near the end of the segmentation period; the embryonic hypothalamic region will give rise to the posterior pituitary gland as well as a number of brain nuclei. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000032", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Part of the diencephalon ventral to the thalamus consisting of connecting fibers and is a center for control of the autonomous nervous system.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010484", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "For instance, the vertebrate ventral diencephalon generates the hypothalamus which functions as a major endocrine center in cooperation with the hypophysis, the anterior part of the pituitary gland, located just ventral to the hypothalamus. In the amphioxus brain, the presence of a hypothalamus-like structure has been reported associated with the ventrally located Hatschek's pit, the hypothetical hypophysial homologue. It is thus conceivable that a hypothalamus-like structure originally involved in endocrine functions may have already been present before the establishment of vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000179", ontology="VHOG", source="DOI:10.1016/j.ydbio.2005.02.008 Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "hypothalamic" xsd:string -property_value: UBPROP:0000008 "all vertebrates contain a hypothalamus" xsd:string {source="WP"} +relationship: part_of UBERON:0010225 ! thalamic complex +relationship: RO:0002433 UBERON:0001894 ! contributes to morphology of diencephalon +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/9f/LocationOfHypothalamus.jpg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:117569 {source="Ariens, p. 1192"} +property_value: RO:0002175 NCBITaxon:7742 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001899 @@ -183874,18 +182361,11 @@ xref: VHOG:0000178 xref: Wikipedia:Epithalamus xref: ZFA:0000509 is_a: UBERON:0002616 ! regional part of brain -relationship: contributes_to_morphology_of UBERON:0001894 ! diencephalon relationship: part_of UBERON:0001897 ! dorsal plus ventral thalamus -relationship: present_in_taxon NCBITaxon:7742 ! Vertebrata -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/cb/Epithalamus.png" xsd:anyURI -property_value: RO:0002171 UBERON:0001903 {source="ABA"} -property_value: RO:0002171 UBERON:0002733 {source="ABA"} -property_value: RO:0002171 UBERON:0002736 {source="ABA"} -property_value: UBPROP:0000001 "Dorsal segment of the diencephalon containing the habenular ganglia, a choroid plexus, and the pineal organ.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010482", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "The roof of the diencephalon lying above the thalamus. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-11, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000178", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "The epithalamus has been historically conceived as a distinct neuroanatomical moiety within the diencephalon of all vertebrates. (...) The evolutionary origins of epithalamic structures are uncertain but asymmetry in this region is likely to have existed at the origin of the vertebrate, perhaps even the chordate, lineage.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000178", ontology="VHOG", source="DOI:10.1046/j.1469-7580.2001.19910063.x Concha ML and Wilson SW, Asymmetry in the epithalamus of vertebrates. J Anat (2001)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "epithalamic" xsd:string +relationship: RO:0002433 UBERON:0001894 ! contributes to morphology of diencephalon +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/cb/Epithalamus.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:7742 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001901 @@ -183914,14 +182394,13 @@ xref: MA:0001862 xref: NCIT:C33797 xref: UMLS:C1179002 {source="ncithesaurus:Tracheal_Epithelium"} xref: VHOG:0001045 -is_a: UBERON:0005911 ! endo-epithelium is_a: UBERON:0008397 ! tracheobronchial epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0003126 ! trachea -relationship: contributes_to_morphology_of UBERON:0003126 ! trachea -relationship: develops_from UBERON:0003258 ! endoderm of foregut relationship: part_of UBERON:0003126 ! trachea -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 UBERON:0003258 ! develops from endoderm of foregut +relationship: RO:0002433 UBERON:0003126 ! contributes to morphology of trachea +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001902 @@ -183951,7 +182430,6 @@ intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002108 ! small intestine relationship: has_part CL:0000164 {source="FMA"} ! enteroendocrine cell relationship: part_of UBERON:0001204 ! mucosa of small intestine -property_value: UBPROP:0000001 "Intestinal epithelium which lines the lumen of the mid intestine.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005127", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0001905 @@ -184011,24 +182489,15 @@ xref: ZFA:0000019 is_a: UBERON:0003296 ! gland of diencephalon is_a: UBERON:0010134 {source="MA"} ! secretory circumventricular organ relationship: capable_of GO:0030187 {comment="EDITOR_NOTE add secretion"} ! melatonin biosynthetic process -relationship: contributes_to_morphology_of UBERON:0001899 ! epithalamus relationship: has_part CL:0000652 ! pinealocyte relationship: has_part CL:0002220 ! interstitial cell of pineal gland relationship: part_of UBERON:0015238 {source="ZFA", source="various"} ! pineal complex -relationship: present_in_taxon NCBITaxon:117569 {source="Hardisty, p. 310"} -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/6b/Illu_pituitary_pineal_glands.jpg" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI -property_value: RO:0002171 UBERON:0001941 {source="ABA"} -property_value: RO:0002171 UBERON:0001942 {source="ABA"} -property_value: UBPROP:0000001 "A circumscribed swelling, includes the pineal primordium that appears late in the segmentation period in the dorsal midline of the diencephalon. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000019", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Anatomical structure which is a medial outgrowth of the thalamus on the dorsal surface of the brain. This structure is light sensitive and secretes melatonin when exposed to prolonged darkness.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010549", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000002 "relationship loss: part_of pineal complex (TAO:0001359)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000019", ontology="TAO"} -property_value: UBPROP:0000003 "The pineal gland has evolved from a part of the epiphyseal complex of anamniotes, which includes a median light-receptive pineal eye, parietal eye, or both.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000051", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.516", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "epiphyseal" xsd:string -property_value: UBPROP:0000007 "epiphysial" xsd:string -property_value: UBPROP:0000008 "lobulated in humans, homogeneous in mouse. Calcifies with age in humans." xsd:string +relationship: RO:0002433 UBERON:0001899 ! contributes to morphology of epithalamus +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6b/Illu_pituitary_pineal_glands.jpg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:117569 {source="Hardisty, p. 310"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001908 @@ -184049,7 +182518,6 @@ xref: BIRNLEX:1684 xref: BM:Tel-OT xref: DHBA:10589 xref: DMBA:17785 -xref: EMAPA:16678 xref: EMAPA:35617 xref: FMA:62046 xref: GAID:735 @@ -184067,17 +182535,17 @@ xref: Wikipedia:Optic_tract xref: XAO:0004101 xref: ZFA:0000252 is_a: UBERON:0011591 ! tract of diencephalon -relationship: contributes_to_morphology_of UBERON:0003544 ! brain white matter relationship: extends_fibers_into UBERON:0000941 ! cranial nerve II relationship: extends_fibers_into UBERON:0000959 ! optic chiasma -relationship: innervates UBERON:0000966 ! retina relationship: part_of UBERON:0002104 ! visual system relationship: part_of UBERON:0003931 ! diencephalic white matter -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray773.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI -property_value: editor_note "relationships need checking by expert. NIF and ZFA both state part of diencepahalon; MA says part of optic nerve II. in uberon, CNS and PNS are spatially disjoint, and axon tracts are part of the CNS so we make the relationship to CNII 'continuous_with'" xsd:string +relationship: RO:0002134 UBERON:0000966 ! innervates retina +relationship: RO:0002433 UBERON:0003544 ! contributes to morphology of brain white matter +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray773.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI +property_value: IAO:0000116 "relationships need checking by expert. NIF and ZFA both state part of diencepahalon; MA says part of optic nerve II. in uberon, CNS and PNS are spatially disjoint, and axon tracts are part of the CNS so we make the relationship to CNII 'continuous_with'" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001911 @@ -184119,21 +182587,12 @@ is_a: UBERON:0019319 ! exocrine gland of integumental system intersection_of: UBERON:0002530 ! gland intersection_of: capable_of GO:0007595 ! lactation relationship: capable_of GO:0007595 ! lactation -relationship: develops_from UBERON:0005333 ! mammary bud -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: produces UBERON:0001913 ! milk -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Illu_breast_anatomy.jpg" xsd:anyURI -property_value: editor_note "Originally this was classified as a female reproductive structure, as it was in the MP in 2011" xsd:string -property_value: UBPROP:0000001 "Any of the milk-producing apocrine glands typically occurring in pairs in female mammals and consisting of lobes containing clusters of alveoli with a system of ducts to convey the milk to an external nipple or teat. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000398", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/mammary+gland"} -property_value: UBPROP:0000003 "The detailed similarities of mammary glands in living monotremes, marsupials, and eutherians argue for a monophyletic origin of these glands, perhaps by the combination of parts of preexisting sebaceous and sweat glands.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000398", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.224", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "mammary" xsd:string -property_value: UBPROP:0000008 "A mouse mammary gland contains a single duct or sinus, forming 5-10 secondary ducts" xsd:string -property_value: UBPROP:0000008 "The male Dayak fruit bat has lactating mammary glands" xsd:string -property_value: UBPROP:0000008 "The mammary glands of humans are in the thoracid/breast region. In other mammals they may be located elsewhere on the mammary ridges." xsd:string -property_value: UBPROP:0000012 "The BTO class represents the combination of nipple plus lobe" xsd:string -property_value: UBPROP:0000012 "The FMA class represents an individule lobe. The nipple is not a part" xsd:string -property_value: UBPROP:0000012 "The MA class represents a composite structure, including the nipple, fat, connective tissue, smooth muscle as parts" xsd:string +relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia +relationship: RO:0002202 UBERON:0005333 ! develops from mammary bud +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Illu_breast_anatomy.jpg" xsd:anyURI +property_value: IAO:0000116 "Originally this was classified as a female reproductive structure, as it was in the MP in 2011" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001912 @@ -184153,10 +182612,11 @@ synonym: "mammary gland lobule" EXACT [MA:0000793] xref: EMAPA:36634 xref: FMA:62090 xref: MA:0000793 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0009911 {source="FMA"} ! lobule -relationship: contributes_to_morphology_of UBERON:0001911 ! mammary gland relationship: part_of UBERON:0001911 ! mammary gland -property_value: editor_note "TODO - ensure correct terminology for lobes/lobules. In mouse there are no distinct lobes (ISBN:0123813611), here lobule appears to be synonymous with acinus" xsd:string +relationship: RO:0002433 UBERON:0001911 ! contributes to morphology of mammary gland +property_value: IAO:0000116 "TODO - ensure correct terminology for lobes/lobules. In mouse there are no distinct lobes (ISBN:0123813611), here lobule appears to be synonymous with acinus" xsd:string [Term] id: UBERON:0001913 @@ -184188,9 +182648,7 @@ is_a: UBERON:0006539 ! mammary gland fluid/secretion relationship: has_part CHEBI:18059 relationship: has_part PR:000028527 ! casein derived peptide relationship: output_of GO:0007595 ! lactation -property_value: editor_note "to axiomatize the different forms of mammary gland secretion an ontology of the phases of pregnancy/lactation is required. Using the existing GO def of lactation is circular." xsd:string -property_value: UBPROP:0000003 "The detailed similarities of mammary glands in living monotremes, marsupials, and eutherians argue for a monophyletic origin of these glands, perhaps by the combination of parts of preexisting sebaceous and sweat glands.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001263", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.224", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "ncit:Milk refers specifically to cow milk" xsd:string {external_ontology="ncit"} +property_value: IAO:0000116 "to axiomatize the different forms of mammary gland secretion an ontology of the phases of pregnancy/lactation is required. Using the existing GO def of lactation is circular." xsd:string [Term] id: UBERON:0001915 @@ -184253,8 +182711,6 @@ is_a: UBERON:0004700 ! arterial system endothelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0001637 ! artery relationship: part_of UBERON:0001637 ! artery -property_value: UBPROP:0000001 "The endothelium is the thin layer of cells that lines the interior surface of blood vessels, forming an interface between circulating blood in the lumen and the rest of the vessel wall.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011013", ontology="AAO", source="XAO:curator"} -property_value: UBPROP:0000003 "Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001215", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207", source="http://bgee.unil.ch/"} [Term] id: UBERON:0001918 @@ -184295,7 +182751,6 @@ is_a: UBERON:0004701 ! venous system endothelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0001638 ! vein relationship: part_of UBERON:0001638 ! vein -property_value: UBPROP:0000003 "Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001216", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207", source="http://bgee.unil.ch/"} [Term] id: UBERON:0001926 @@ -184335,12 +182790,11 @@ xref: SCTID:362377006 xref: UMLS:C0086526 {source="ncithesaurus:External_Geniculate_Body", source="BIRNLEX:1662"} xref: Wikipedia:Lateral_geniculate_body is_a: UBERON:0015233 ! nucleus of dorsal thalamus -relationship: contributes_to_morphology_of UBERON:0001897 ! dorsal plus ventral thalamus relationship: part_of UBERON:0002704 {source="FMA"} ! metathalamus -relationship: present_in_taxon NCBITaxon:117569 {source="Ariens, p. 1192"} -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b7/Gray719.png" xsd:anyURI -property_value: UBPROP:0000012 "BTO has distinct classes for body and nucleus, but other sources treat as identical" xsd:string {external_ontology="BTO"} +relationship: RO:0002433 UBERON:0001897 ! contributes to morphology of dorsal plus ventral thalamus +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b7/Gray719.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:117569 {source="Ariens, p. 1192"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001928 @@ -184383,10 +182837,8 @@ xref: ZFA:0000470 is_a: UBERON:0002616 ! regional part of brain relationship: part_of UBERON:0001894 ! diencephalon relationship: part_of UBERON:0001898 {gci_relation="part_of", gci_filler="NCBITaxon:32524", source="PMC4038951"} ! hypothalamus -relationship: present_in_taxon NCBITaxon:7742 ! Vertebrata -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/8c/HypothalamicNuclei.PNG" xsd:anyURI -property_value: UBPROP:0000001 "Area of the forebrain anterior to the posterior tuberculum and the hypothalamus and ventral to the ventral thalamus. See Figure 7, Atlas of Early Zebrafish Brain Development.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000470", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000008 "Located in the hypothalamus in amniotes[PMC4038951]" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8c/HypothalamicNuclei.PNG" xsd:anyURI +property_value: RO:0002175 NCBITaxon:7742 [Term] id: UBERON:0001930 @@ -184431,12 +182883,10 @@ xref: SCTID:369131006 xref: UMLS:C0030532 {source="BIRNLEX:1407"} xref: Wikipedia:Paraventricular_nucleus_of_hypothalamus is_a: UBERON:0006568 ! hypothalamic nucleus -relationship: contributes_to_morphology_of UBERON:0001898 ! hypothalamus relationship: part_of UBERON:0002271 ! periventricular zone of hypothalamus -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/ef/PVNss.jpg" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/en/thumb/e/ef/PVNss.jpg/200px-PVNss.jpg" xsd:anyURI -property_value: RO:0002171 UBERON:0001929 {source="ABA"} -property_value: RO:0002171 UBERON:0001932 {source="ABA"} +relationship: RO:0002433 UBERON:0001898 ! contributes to morphology of hypothalamus +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ef/PVNss.jpg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/en/thumb/e/ef/PVNss.jpg/200px-PVNss.jpg" xsd:anyURI [Term] id: UBERON:0001932 @@ -184482,10 +182932,7 @@ xref: Wikipedia:Arcuate_nucleus is_a: UBERON:0006568 ! hypothalamic nucleus relationship: part_of UBERON:0002271 ! periventricular zone of hypothalamus relationship: part_of UBERON:0002555 {source="NIFSTD"} ! intermediate hypothalamic region -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/8c/HypothalamicNuclei.PNG" xsd:anyURI -property_value: RO:0002171 UBERON:0001929 {source="ABA"} -property_value: RO:0002171 UBERON:0001930 {source="ABA"} -property_value: UBPROP:0000012 "the semantics of the BTO class arcuate nucleus are not clear" xsd:string {external_ontology="BTO"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8c/HypothalamicNuclei.PNG" xsd:anyURI [Term] id: UBERON:0001943 @@ -184515,7 +182962,6 @@ xref: FMA:62393 xref: HBA:9002 xref: MA:0000212 xref: MAT:0000452 -xref: MESH:D013681 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: neuronames:491 {source="BIRNLEX:1200"} xref: SCTID:362392007 xref: TAO:0000160 @@ -184525,12 +182971,11 @@ xref: Wikipedia:Midbrain_tegmentum xref: XAO:0004271 xref: ZFA:0000160 is_a: UBERON:0002616 ! regional part of brain -relationship: develops_from UBERON:0010285 {source="ZFA"} ! midbrain basal plate relationship: part_of UBERON:0001891 ! midbrain relationship: part_of UBERON:0002298 ! brainstem -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray712.png" xsd:anyURI -property_value: UBPROP:0000003 "Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001367", ontology="VHOG", source="DOI:10.1016/j.brainresbull.2005.05.001 Villar-Cheda B, Abalo XM, Anadon R, Rodicio MC, The tegmental proliferation region in the sea lamprey. Brain Research Bulletin (2005)", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0010285 {source="ZFA"} ! develops from midbrain basal plate +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray712.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001948 @@ -184544,6 +182989,7 @@ xref: NCIT:C33969 xref: SCTID:244437008 xref: UMLS:C1268166 {source="ncithesaurus:Spinal_Cord_Part"} is_a: UBERON:0000073 ! regional part of nervous system +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000481 ! multi-tissue structure intersection_of: part_of UBERON:0002240 ! spinal cord relationship: part_of UBERON:0002240 ! spinal cord @@ -184568,7 +183014,6 @@ is_a: UBERON:0035037 ! jaw epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001828 ! gingiva relationship: part_of UBERON:0001828 ! gingiva -property_value: UBPROP:0000008 "In humans: 15% orthokeratinized, 75% parakeratinized, 10% non-keratinized; diurnal; decreased keratinization with age. Note that in FMA this is classified as keratinized squamous - this perhaps refers to the epithelium of the attached or free gingiva" xsd:string [Term] id: UBERON:0001950 @@ -184607,12 +183052,10 @@ xref: PBA:294021746 xref: UMLS:C0175173 {source="BIRNLEX:2547"} xref: Wikipedia:Neocortex is_a: UBERON:0002616 ! regional part of brain -relationship: contributes_to_morphology_of UBERON:0000956 ! cerebral cortex -relationship: only_in_taxon NCBITaxon:7742 {source="Wikipedia"} ! Vertebrata relationship: part_of UBERON:0000956 ! cerebral cortex -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/77/Neocortex.jpg" xsd:anyURI -property_value: RO:0002171 UBERON:0002264 {source="ABA"} -property_value: UBPROP:0000003 "The 6-layer neocortex is well conserved in all extant mammals, but not present in birds or reptils" xsd:string {source="PMID:23027930"} +relationship: RO:0002160 NCBITaxon:7742 {source="Wikipedia"} ! only in taxon Vertebrata +relationship: RO:0002433 UBERON:0000956 ! contributes to morphology of cerebral cortex +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/77/Neocortex.jpg" xsd:anyURI [Term] id: UBERON:0001951 @@ -184678,7 +183121,6 @@ xref: DHBA:10296 xref: DMBA:16124 xref: EFO:0000530 xref: EHDAA2:0004443 -xref: EMAPA:32772 xref: EMAPA:32845 xref: EV:0100180 xref: FMA:62493 @@ -184699,15 +183141,11 @@ xref: VHOG:0001177 xref: Wikipedia:Hippocampus is_a: UBERON:0002616 ! regional part of brain relationship: capable_of_part_of GO:0007613 {source="Wikipedia"} ! memory -relationship: only_in_taxon NCBITaxon:40674 {source="Wikipedia:Hippocampus"} ! Mammalia relationship: part_of UBERON:0000349 {source="FMA"} ! limbic system relationship: part_of UBERON:0002421 {source="ABA"} ! hippocampal formation relationship: part_of UBERON:0002600 {source="FMA"} ! limbic lobe -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/2e/Gray739-emphasizing-hippocampus.png" xsd:anyURI -property_value: RO:0002171 UBERON:0001885 {source="ABA"} -property_value: RO:0002171 UBERON:0002601 {source="ABA"} -property_value: UBPROP:0000007 "hippocampal" xsd:string -property_value: UBPROP:0000012 "Non-mammalian species do not have a brain structure that looks like the mammalian hippocampus, but they have one that is considered homologous to it. The hippocampus, as pointed out above, is essentially the medial edge of the cortex. Only mammals have a fully developed cortex, but the structure it evolved from, called the pallium, is present in all vertebrates, even the most primitive ones such as the lamprey or hagfish. The pallium is usually divided into three zones: medial, lateral, and dorsal. The medial pallium forms the precursor of the hippocampus. It does not resemble the hippocampus visually, because the layers are not warped into an S shape or enwrapped by the dentate gyrus, but the homology is indicated by strong chemical and functional affinities. There is now evidence that these hippocampal-like structures are involved in spatial cognition in birds, reptiles, and fish. In birds, the correspondence is sufficiently well established that most anatomists refer to the medial pallial zone as the 'avian hippocampus'. The story for fish is more complex. In teleost fish (which make up the great majority of existing species), the forebrain is distorted in comparison to other types of vertebrates: most neuroanatomists believe that the teleost forebrain is essentially everted, like a sock turned inside-out, so that structures that lie in the interior, next to the ventricles, for most vertebrates, are found on the outside in teleost fish, and vice versa. One of the consequences of this is that the medial pallium ('hippocampal' zone) of a typical vertebrate is thought to correspond to the lateral pallium of a typical fish. Several types of fish (particularly goldfish) have been shown experimentally to have strong spatial memory abilities, even forming 'cognitive maps' of the areas they inhabit.[WP]" xsd:string +relationship: RO:0002160 NCBITaxon:40674 {source="Wikipedia:Hippocampus"} ! only in taxon Mammalia +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2e/Gray739-emphasizing-hippocampus.png" xsd:anyURI [Term] id: UBERON:0001955 @@ -184731,7 +183169,7 @@ is_a: UBERON:0002051 ! epithelium of bronchiole intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002188 ! respiratory bronchiole relationship: part_of UBERON:0002188 ! respiratory bronchiole -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001956 @@ -184758,12 +183196,12 @@ is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0003603 ! lower respiratory tract cartilage intersection_of: UBERON:0007844 ! cartilage element intersection_of: part_of UBERON:0002185 ! bronchus -relationship: composed_primarily_of UBERON:0001994 {source="MP"} ! hyaline cartilage tissue -relationship: contributes_to_morphology_of UBERON:0002185 ! bronchus -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: has_part CL:0019002 ! tracheobronchial chondrocyte relationship: part_of UBERON:0002185 ! bronchus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002433 UBERON:0002185 ! contributes to morphology of bronchus +relationship: RO:0002473 UBERON:0001994 {source="MP"} ! composed primarily of hyaline cartilage tissue +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001957 @@ -184785,6 +183223,7 @@ xref: MA:0001837 xref: NCIT:C49214 xref: SCTID:85546005 xref: UMLS:C0225601 {source="ncithesaurus:Bronchus_Submucosa"} +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0004777 ! respiratory system submucosa intersection_of: UBERON:0000009 ! submucosa intersection_of: part_of UBERON:0002185 ! bronchus @@ -184812,10 +183251,9 @@ xref: UMLS:C1179400 {source="ncithesaurus:Terminal_Bronchiole_Epithelium"} is_a: UBERON:0002051 ! epithelium of bronchiole intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002187 ! terminal bronchiole -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: part_of UBERON:0002187 ! terminal bronchiole -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000008 "A pseudostratified epithelium, containing basal cells, stem cells of the airway, submucosal glands and cartilage rings, is limited to the trachea and large lobar airways in the mouse (Morrisey and Hogan, 2010). This more complex epithelium extends to terminal bronchioles in the human[DOI:10.1242/dev.115469]" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001959 @@ -184839,11 +183277,10 @@ xref: UMLS:C0229686 {source="ncithesaurus:Splenic_White_Pulp"} xref: Wikipedia:White_pulp is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:1000023 ! spleen pulp -relationship: composed_primarily_of CL:0000542 ! lymphocyte -relationship: contributes_to_morphology_of UBERON:0002106 ! spleen -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1191.png" xsd:anyURI -property_value: UBPROP:0000009 "The white pulp contains T cells, B cells and accessory cells. The function of the white pulp is to mount an immunological response to antigens within the blood. The white pulp is present in the form of a periarteriolar lymphoid sheath. This sheath contains B cell follicles and T cells. At the edge of the T zone is a region known as the marginal zone where larger lymphocytes and antigen presenting dendritic cells are located. [Wikipedia:White_pulp]" xsd:string +relationship: RO:0002433 UBERON:0002106 ! contributes to morphology of spleen +relationship: RO:0002473 CL:0000542 ! composed primarily of lymphocyte +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1191.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001960 @@ -184864,13 +183301,11 @@ xref: MA:0000765 is_a: UBERON:0004177 ! hemopoietic organ is_a: UBERON:0005172 ! abdomen element is_a: UBERON:0010393 ! T cell domain -is_a: UBERON:0013765 ! digestive system element intersection_of: UBERON:0010393 ! T cell domain intersection_of: part_of UBERON:0001959 ! white pulp of spleen -relationship: contributes_to_morphology_of UBERON:0001959 ! white pulp of spleen relationship: part_of UBERON:0001959 ! white pulp of spleen -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000012 "FMA distinguishes periarterial (PALS) from periarteriolar (FMA:62806)" xsd:string {external_ontology="FMA"} +relationship: RO:0002433 UBERON:0001959 ! contributes to morphology of white pulp of spleen +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001961 @@ -184893,10 +183328,10 @@ xref: NCIT:C12910 xref: UMLS:C0599921 {source="ncithesaurus:Mucosa-Associated_Lymphoid_Tissue"} xref: Wikipedia:Mucosa-associated_lymphoid_tissue is_a: UBERON:0012069 {source="FMA"} ! epithelium-associated lymphoid tissue -relationship: contains_process GO:0046649 ! lymphocyte activation +relationship: BFO:0000067 GO:0046649 ! contains process lymphocyte activation relationship: overlaps UBERON:0000344 ! mucosa -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: editor_note "todo - add part relationships to specific layers" xsd:string +property_value: IAO:0000116 "todo - add part relationships to specific layers" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001962 @@ -184917,9 +183352,8 @@ is_a: UBERON:0001961 ! mucosa-associated lymphoid tissue intersection_of: UBERON:0001961 ! mucosa-associated lymphoid tissue intersection_of: part_of UBERON:0001555 ! digestive tract relationship: part_of UBERON:0001555 ! digestive tract -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: editor_note "phylogenetic relationships to be added" xsd:string -property_value: UBPROP:0000008 "guts of jawless fish contains cells with lymphocyte-like morphology (Mayer 2002)." xsd:string +property_value: IAO:0000116 "phylogenetic relationships to be added" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001963 @@ -184935,6 +183369,7 @@ xref: MA:0000135 xref: NCIT:C32234 xref: UMLS:C1179418 {source="ncithesaurus:Bronchus-Associated_Lymphoid_Tissue"} is_a: UBERON:0001961 ! mucosa-associated lymphoid tissue +is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0001961 ! mucosa-associated lymphoid tissue intersection_of: part_of UBERON:0002185 ! bronchus relationship: overlaps UBERON:0001957 {source="ISBN:0123813611"} ! submucosa of bronchus @@ -184965,9 +183400,7 @@ is_a: UBERON:0000463 ! organism substance relationship: has_part CL:0000019 ! sperm relationship: has_part UBERON:0006530 ! seminal fluid relationship: output_of GO:0042713 ! sperm ejaculation -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/40/Human_semen_in_petri_dish2.jpg" xsd:anyURI -property_value: UBPROP:0000007 "seminal" xsd:string -property_value: UBPROP:0000008 "Note that in this ontology, semen is defined as the sum of sperm and seminal fluid, where seminal fluid is defined in taxonomically generic way (see comments for UBERON:0006530)." xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/40/Human_semen_in_petri_dish2.jpg" xsd:anyURI [Term] id: UBERON:0001969 @@ -184998,12 +183431,12 @@ is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000179 ! haemolymphatic fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: has_part GO:0005577 ! fibrinogen complex -intersection_of: has_quality PATO:0001548 ! quality of a liquid intersection_of: part_of UBERON:0000178 ! blood -intersection_of: surrounds CL:0000232 ! erythrocyte +intersection_of: RO:0000086 PATO:0001548 ! has quality quality of a liquid +intersection_of: RO:0002221 CL:0000232 ! surrounds erythrocyte relationship: has_part GO:0005577 ! fibrinogen complex relationship: part_of UBERON:0000178 ! blood -relationship: surrounds CL:0000232 ! erythrocyte +relationship: RO:0002221 CL:0000232 ! surrounds erythrocyte [Term] id: UBERON:0001970 @@ -185031,18 +183464,11 @@ is_a: UBERON:0006314 ! bodily fluid intersection_of: UBERON:0000456 ! secretion of exocrine gland intersection_of: produced_by UBERON:0002107 ! liver relationship: capable_of_part_of GO:0007586 ! digestion -relationship: has_part CHEBI:16990 {composition="0.3% in humans"} +relationship: has_part CHEBI:16990 relationship: has_part CHEBI:22868 relationship: has_part CHEBI:36277 -relationship: has_quality PATO:0001735 ! liquid configuration relationship: produced_by UBERON:0002107 ! liver -property_value: UBPROP:0000008 "In many species, bile is stored in the gallbladder and upon eating is discharged into the duodenum." xsd:string -property_value: UBPROP:0000009 "aids the process of digestion of lipids in the small intestine" xsd:string -property_value: UBPROP:0000009 "bile salts function to emulsify dietary fats and facilitate their intestinal absorption" xsd:string -property_value: UBPROP:0000009 "elimination of cholesterol" xsd:string -property_value: UBPROP:0000009 "major excretory route for potentially harmful exogenous lipophilic substances" xsd:string -property_value: UBPROP:0000009 "many hormones and pheromones are excreted in bile, and contribute to growth and development of the intestine in some species and provide attractants for the weaning of non-human vertebrates" xsd:string -property_value: UBPROP:0000009 "protects the organism from enteric infections by excreting immune globulin A (IgA), inflammatory cytokines, and stimulating the innate immune system in the intestine" xsd:string +relationship: RO:0000086 PATO:0001735 ! has quality liquid configuration [Term] id: UBERON:0001971 @@ -185190,10 +183616,9 @@ is_a: UBERON:0003350 ! epithelium of mucosa is_a: UBERON:0003929 ! digestive tract epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001043 ! esophagus -relationship: contributes_to_morphology_of UBERON:0001043 ! esophagus relationship: part_of UBERON:0002469 {source="FMA"} ! esophagus mucosa -property_value: editor_note "TODO check epithelium types: in FMA: Nonkeratinizing stratified squamous epithelium; mouse has basal and squamous subtypes; in ZFA it is columnar" xsd:string -property_value: UBPROP:0000001 "Simple columnar epithelium that lines the esophagus. Chen et al, 2007.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001499", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002433 UBERON:0001043 ! contributes to morphology of esophagus +property_value: IAO:0000116 "TODO check epithelium types: in FMA: Nonkeratinizing stratified squamous epithelium; mouse has basal and squamous subtypes; in ZFA it is columnar" xsd:string [Term] id: UBERON:0001978 @@ -185211,7 +183636,7 @@ is_a: UBERON:0000353 ! parenchyma intersection_of: UBERON:0000353 ! parenchyma intersection_of: part_of UBERON:0001264 ! pancreas relationship: part_of UBERON:0001264 ! pancreas -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001979 @@ -185237,11 +183662,10 @@ xref: Wikipedia:Venule xref: ZFA:0005315 is_a: UBERON:0003920 ! venous blood vessel is_a: UBERON:8410081 ! blood microvessel -relationship: connects UBERON:0001638 ! vein -relationship: connects UBERON:0001982 ! capillary -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/d/da/Illu_capillary.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Multi-tissue structure part of the blood vasculature formed by the anastomosis of capillaries. Venules carry blood toward the heart.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005315", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002176 UBERON:0001638 ! connects vein +relationship: RO:0002176 UBERON:0001982 ! connects capillary +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/da/Illu_capillary.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001980 @@ -185268,14 +183692,12 @@ xref: ZFA:0005255 is_a: UBERON:0003509 {source="MA"} ! arterial blood vessel is_a: UBERON:8410081 ! blood microvessel intersection_of: UBERON:0001981 ! blood vessel -intersection_of: connects UBERON:0001637 ! artery -intersection_of: connects UBERON:0001982 ! capillary -relationship: connects UBERON:0001637 ! artery -relationship: connects UBERON:0001982 ! capillary -relationship: contributes_to_morphology_of UBERON:0001637 ! artery -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/d/da/Illu_capillary.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Multi-tissue structure part of the blood vasculature, feeds into capillaries. Arterioles carry blood away from the heart.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002138", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Small, terminal branch of an artery which generally connects to capillaries.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010253", ontology="AAO", source="AAO:BJB"} +intersection_of: RO:0002176 UBERON:0001637 ! connects artery +intersection_of: RO:0002176 UBERON:0001982 ! connects capillary +relationship: RO:0002176 UBERON:0001637 ! connects artery +relationship: RO:0002176 UBERON:0001982 ! connects capillary +relationship: RO:0002433 UBERON:0001637 ! contributes to morphology of artery +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/da/Illu_capillary.jpg" xsd:anyURI [Term] id: UBERON:0001981 @@ -185317,22 +183739,18 @@ xref: XAO:0001011 xref: ZFA:0005314 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000055 ! vessel +is_a: UBERON:0004120 ! mesoderm-derived structure relationship: capable_of_part_of GO:0008015 ! blood circulation relationship: channel_for UBERON:0000178 ! blood -relationship: develops_from UBERON:0004872 ! splanchnic layer of lateral plate mesoderm -relationship: develops_from UBERON:0006965 {source="GO:0072360"} ! vascular cord relationship: has_part CL:0000071 {source="AEO"} ! blood vessel endothelial cell relationship: has_part UBERON:0007500 {source="EHDAA2"} ! epithelial tube open at both ends -relationship: has_quality PATO:0002045 ! dendritic relationship: part_of UBERON:0004537 ! blood vasculature -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI -property_value: editor_note "consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus" xsd:string -property_value: UBPROP:0000001 "Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001250", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000001 "Any of the vessels through which blood circulates in the body.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011004", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001250", ontology="VHOG", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "annelids have blood vessels, but this class is not applicable to annelids." xsd:string -property_value: UBPROP:0000012 "FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX" xsd:string {external_ontology="FMA"} +relationship: RO:0000086 PATO:0002045 ! has quality dendritic +relationship: RO:0002202 UBERON:0004872 ! develops from splanchnic layer of lateral plate mesoderm +relationship: RO:0002202 UBERON:0006965 {source="GO:0072360"} ! develops from vascular cord +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: IAO:0000116 "consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001982 @@ -185365,17 +183783,14 @@ xref: XAO:0000116 xref: ZFA:0005250 is_a: UBERON:8410081 ! blood microvessel intersection_of: UBERON:8410081 ! blood microvessel -intersection_of: connects UBERON:0001979 ! venule -intersection_of: connects UBERON:0001980 ! arteriole -relationship: connects UBERON:0001979 ! venule -relationship: connects UBERON:0001980 ! arteriole -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/A_red_blood_cell_in_a_capillary,_pancreatic_tissue_-_TEM.jpg" xsd:anyURI -property_value: editor_note "not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element" xsd:string +intersection_of: RO:0002176 UBERON:0001979 ! connects venule +intersection_of: RO:0002176 UBERON:0001980 ! connects arteriole +relationship: RO:0002176 UBERON:0001979 ! connects venule +relationship: RO:0002176 UBERON:0001980 ! connects arteriole +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/A_red_blood_cell_in_a_capillary,_pancreatic_tissue_-_TEM.jpg" xsd:anyURI +property_value: IAO:0000116 "not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element" xsd:string +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/uberon/issues/2186" xsd:string -property_value: UBPROP:0000001 "Any of the tiny blood vessels connecting the arterioles to the venules.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010252", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001253", ontology="VHOG", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000010 "capillaries lack tunica media and tunica adventitia; only the endothelial wall of the tunica intima belongs" xsd:string [Term] id: UBERON:0001983 @@ -185405,13 +183820,11 @@ xref: SCTID:118652008 xref: UMLS:C1621887 {source="ncithesaurus:Crypts_of_the_Lieberkuhn"} xref: Wikipedia:Intestinal_crypt is_a: UBERON:0000333 ! intestinal gland -relationship: contributes_to_morphology_of UBERON:0001242 ! intestinal mucosa -relationship: has_quality PATO:0002299 {source="Wikipedia:Tubular_gland"} ! tubular -relationship: only_in_taxon NCBITaxon:32523 {notes="further investigation required", source="ISBN:9780521617147"} ! Tetrapoda -relationship: seeAlso UBERON:2005256 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/38/Small_intestine_low_mag.jpg" xsd:anyURI -property_value: UBPROP:0000001 "In histology, an intestinal crypt, also crypt of LieberkC -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000007 "endothelial" xsd:string +intersection_of: RO:0002473 CL:0000115 ! composed primarily of endothelial cell +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002473 CL:0000115 ! composed primarily of endothelial cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001987 @@ -185530,20 +183941,18 @@ xref: UMLS:C0032043 {source="ncithesaurus:Placenta"} xref: VHOG:0001266 xref: Wikipedia:Placenta is_a: UBERON:0000062 ! organ +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005156 ! reproductive structure -relationship: develops_from UBERON:0000995 {source="ISBN:0073040584"} ! uterus -relationship: develops_from UBERON:0003124 {source="Wikipedia"} ! chorion membrane -relationship: develops_from UBERON:0004340 {source="ISBN:0073040584"} ! allantois -relationship: only_in_taxon NCBITaxon:32525 {source="https://github.com/obophenotype/uberon/issues/1376"} ! Theria relationship: part_of UBERON:0000474 ! female reproductive system relationship: part_of UBERON:0016887 ! entire extraembryonic component -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Placenta.jpg" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/f1/Placenta.svg" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Placenta.glb" xsd:anyURI -property_value: UBPROP:0000003 "Phylogenetic analyses of the concatenated data set using maximum parsimony, maximum likelihood and distance based (neighbour joining) methods all converged on a nearly identical, well supported topology defining four principal eutherian lineages. The results affirm monophyly of traditional placental orders (except Artiodactyla and Insectivora), and also support some previously proposed, as well as new, superordinal clades.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001266", ontology="VHOG", source="DOI:10.1038/35054550 Murphy WJ, Eizirik E, Johnson WE, Zhang YP, Ryder OA, O'Brien SJ, Molecular phylogenetics and the origins of placental mammals. Nature (2001)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "placental" xsd:string -property_value: UBPROP:0000008 "Eutherians: In eutherians, the chorioallantoic membrane of the fetus establishes intimate contact with the adjacent vascular wall of the mother's uterus to produce the placenta, a composite structure formed in part from tissues of the fetus and in part from tissues of the mother [ISBN:0073040584 (Vertebrates, Kardong)]. TODO - is taxon restriction too strict, even if we restrict def to allantoic placenta? - WP says: also found in some snakes and lizards with varying levels of development up to mammalian levels. Pough et al. 1992. Herpetology: Third Edition. Pearson Prentice Hall:Pearson Education, Inc., 2002. // See also: DOI:10.1002/jmor.11011" xsd:string +relationship: RO:0002160 NCBITaxon:32525 {source="https://github.com/obophenotype/uberon/issues/1376"} ! only in taxon Theria +relationship: RO:0002202 UBERON:0000995 {source="ISBN:0073040584"} ! develops from uterus +relationship: RO:0002202 UBERON:0003124 {source="Wikipedia"} ! develops from chorion membrane +relationship: RO:0002202 UBERON:0004340 {source="ISBN:0073040584"} ! develops from allantois +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Placenta.jpg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f1/Placenta.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Placenta.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001988 @@ -185596,8 +184005,6 @@ is_a: UBERON:0000174 ! excreta intersection_of: UBERON:0000174 ! excreta intersection_of: output_of GO:0030421 ! defecation relationship: output_of GO:0030421 ! defecation -property_value: UBPROP:0000001 "Excretion in semisolid state processed by the intestine.[FMA]" xsd:string {source="FMA:64183"} -property_value: UBPROP:0000007 "fecal" xsd:string [Term] id: UBERON:0001992 @@ -185628,13 +184035,13 @@ xref: UMLS:C0221930 {source="ncithesaurus:Stratum_Papillare"} xref: UMLS:C0682598 {source="ncithesaurus:Papillary_Dermis"} xref: Wikipedia:Papillary_dermis is_a: PR:000050567 ! protein-containing material entity +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0013754 ! integumentary system layer -relationship: composed_primarily_of UBERON:0006815 {source="WP"} ! areolar connective tissue -relationship: composed_primarily_of UBERON:0011822 {source="FMA-text"} ! dense irregular connective tissue relationship: part_of UBERON:0002067 ! dermis -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b4/Normal_Epidermis_and_Dermis_with_Intradermal_Nevus_10x.JPG" xsd:anyURI -property_value: editor_note "todo - check tissue composition" xsd:string -property_value: UBPROP:0000001 "Dense irregular connective tissue of the skin that consists of fibroblasts, various connective tissue cell types, and collagen, predominantly type III." xsd:string {source="FMA:64776"} +relationship: RO:0002473 UBERON:0006815 {source="WP"} ! composed primarily of areolar connective tissue +relationship: RO:0002473 UBERON:0011822 {source="FMA-text"} ! composed primarily of dense irregular connective tissue +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b4/Normal_Epidermis_and_Dermis_with_Intradermal_Nevus_10x.JPG" xsd:anyURI +property_value: IAO:0000116 "todo - check tissue composition" xsd:string [Term] id: UBERON:0001993 @@ -185658,11 +184065,12 @@ xref: NCIT:C94818 xref: UMLS:C0682599 {source="ncithesaurus:Reticular_Dermis"} xref: UMLS:C1514988 {source="ncithesaurus:Stratum_Reticulare"} xref: Wikipedia:Reticular_dermis +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0013754 ! integumentary system layer -relationship: contributes_to_morphology_of UBERON:0000014 ! zone of skin -relationship: deep_to UBERON:0001992 ! papillary layer of dermis +relationship: BSPO:0000107 UBERON:0001992 ! papillary layer of dermis relationship: part_of UBERON:0002067 ! dermis relationship: part_of UBERON:0008877 {source="FMA"} ! epidermal-dermal junction +relationship: RO:0002433 UBERON:0000014 ! contributes to morphology of zone of skin [Term] id: UBERON:0001994 @@ -185684,11 +184092,9 @@ xref: Wikipedia:Hyaline_cartilage xref: XAO:0004029 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002418 {source="FMA"} ! cartilage tissue -relationship: composed_primarily_of GO:0005585 {source="VSAO-text-def"} ! collagen type II trimer -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/2a/Gray292.png" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Hypertrophic_Zone_of_Epiphyseal_Plate.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Cartilage (tissue) which consists of chondrocytes and collagen, the intercellular matrix of which is an amorphous gel with a perichondrium[FMA:64783]." xsd:string {source="FMA:64783"} -property_value: UBPROP:0000001 "Cartilage tissue primarily composed of type II collagen (thin fibrils) and a glassy appearance.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000094", ontology="VSAO", source="PSPUB:0000170"} +relationship: RO:0002473 GO:0005585 {source="VSAO-text-def"} ! composed primarily of collagen type II trimer +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2a/Gray292.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Hypertrophic_Zone_of_Epiphyseal_Plate.jpg" xsd:anyURI [Term] id: UBERON:0001995 @@ -185703,7 +184109,6 @@ synonym: "stratified cartilage tissue" EXACT [http://orcid.org/0000-0002-6601-21 xref: FMA:64784 xref: galen:Fibrocartilage xref: MA:0000108 -xref: MESH:D051445 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C32599 xref: SCTID:91685003 xref: UMLS:C0684077 {source="ncithesaurus:Fibrocartilage"} @@ -185713,11 +184118,7 @@ xref: XAO:0004028 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002418 ! cartilage tissue relationship: has_part GO:0005584 ! collagen type I trimer -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/2e/Gray295.png" xsd:anyURI -property_value: UBPROP:0000001 "A mixture of white fibrous tissue and cartilaginous tissue in various proportions. It owes its flexibility and toughness to the former of these constituents, and its elasticity to the latter. It is the only type of cartilage that contains type I collagen in addition to the normal type I[Wikipedia:Fibrocartilage]I" xsd:string {source="Wikipedia:Fibrocartilage"} -property_value: UBPROP:0000001 "Cartilage (tissue) which consists of chondrocytes and collagen, the intercellular matrix of which is an amorphous gel without a well-defined perichondrium[FMA:64784]." xsd:string {source="FMA:64784"} -property_value: UBPROP:0000001 "Cartilage tissue intermediate between hyaline cartilage and dense connective tissue; contains of abundant collagen fibers; chondrocytes often arranged in columns.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000103", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000007 "fibrocartilaginous" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2e/Gray295.png" xsd:anyURI [Term] id: UBERON:0001996 @@ -185741,13 +184142,10 @@ xref: VSAO:0000091 xref: Wikipedia:Elastic_cartilage xref: XAO:0004197 is_a: UBERON:0011589 {source="VSAO"} ! non-mineralized cartilage tissue -relationship: develops_from UBERON:0005863 {source="VSAO"} ! cartilaginous condensation relationship: has_part GO:0071953 {source="Wikipedia"} ! elastic fiber -relationship: has_quality PATO:0001544 ! flexible -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/ca/Gray904.png" xsd:anyURI -property_value: UBPROP:0000001 "Cartilage (tissue) which consists of chondrocytes and collagen, the intercellular matrix of which consists of elastic fibers[FMA:64785]." xsd:string {source="FMA:64785"} -property_value: UBPROP:0000001 "Cartilage tissue that is flexible and contains abundant elastic fibers.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000091", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000012 "MA has a distinct class for yellow" xsd:string {external_ontology="MA"} +relationship: RO:0000086 PATO:0001544 ! has quality flexible +relationship: RO:0002202 UBERON:0005863 {source="VSAO"} ! develops from cartilaginous condensation +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/ca/Gray904.png" xsd:anyURI [Term] id: UBERON:0001997 @@ -185790,20 +184188,17 @@ xref: Wikipedia:Olfactory_epithelium xref: ZFA:0000554 is_a: UBERON:0005384 ! nasal cavity epithelium is_a: UBERON:0006934 ! sensory epithelium -is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0006934 ! sensory epithelium intersection_of: part_of UBERON:0005386 ! olfactory segment of nasal mucosa relationship: capable_of_part_of GO:0050911 ! detection of chemical stimulus involved in sensory perception of smell -relationship: contributes_to_morphology_of UBERON:0005725 ! olfactory system relationship: has_part CL:0000207 {source="NBK26868"} ! olfactory receptor cell relationship: has_part CL:0000853 {source="NBK26868"} ! olfactory epithelial supporting cell -relationship: immediate_transformation_of UBERON:2001431 ! primitive olfactory epithelium relationship: part_of UBERON:0000012 {source="NIFSTD"} ! somatic nervous system relationship: part_of UBERON:0005386 ! olfactory segment of nasal mucosa +relationship: RO:0002433 UBERON:0005725 ! contributes to morphology of olfactory system +relationship: RO:0002495 UBERON:2001431 ! immediate transformation of primitive olfactory epithelium relationship: site_of GO:0022008 {source="NCBIBook:NBK55982"} ! neurogenesis -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray857.png" xsd:anyURI -property_value: UBPROP:0000001 "Sensory lining of the medial wall, roof and anterior aspects of the main olfactory cavity (cavum principale).[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010158", ontology="AAO", source="AAO:DSM"} -property_value: UBPROP:0000002 "relationship loss: part_of principal cavity (AAO:0000992)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010158", ontology="AAO"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray857.png" xsd:anyURI [Term] id: UBERON:0002001 @@ -185818,9 +184213,9 @@ xref: SCTID:263314001 xref: UMLS:C1261194 {source="ncithesaurus:Joint_of_the_Rib"} is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint -intersection_of: connects UBERON:0002228 ! rib -relationship: connects UBERON:0002228 ! rib +intersection_of: RO:0002176 UBERON:0002228 ! connects rib relationship: part_of UBERON:0014478 {source="cjm"} ! rib skeletal system +relationship: RO:0002176 UBERON:0002228 ! connects rib [Term] id: UBERON:0002004 @@ -185828,7 +184223,6 @@ name: trunk of sciatic nerve namespace: uberon synonym: "sciatic nerve trunk" EXACT [] synonym: "sciatic neural trunk" EXACT [] -xref: EMAPA:18577 xref: FMA:65507 xref: MA:0001178 is_a: UBERON:0002464 ! nerve trunk @@ -185864,11 +184258,11 @@ xref: TAO:0001155 xref: UMLS:C0206111 {source="BIRNLEX:1166"} xref: Wikipedia:Enteric_nervous_system xref: ZFA:0001155 +is_a: UBERON:0010313 ! neural crest-derived structure is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision -relationship: contributes_to_morphology_of UBERON:0002410 ! autonomic nervous system -relationship: develops_from UBERON:0005428 {source="Wikipedia", source="ZFA", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! vagal neural crest relationship: part_of UBERON:0002410 {source="FMA", source="MA", source="NIF", source="ZFA-isa-changed"} ! autonomic nervous system -property_value: UBPROP:0000012 "most sources classify this as autonomic, but in FMA it is placed directly under nervous system." xsd:string {external_ontology="FMA"} +relationship: RO:0002202 UBERON:0005428 {source="Wikipedia", source="ZFA", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! develops from vagal neural crest +relationship: RO:0002433 UBERON:0002410 ! contributes to morphology of autonomic nervous system [Term] id: UBERON:0002006 @@ -185891,8 +184285,8 @@ intersection_of: UBERON:0001851 ! cortex intersection_of: part_of UBERON:0000029 ! lymph node relationship: adjacent_to UBERON:0002194 ! capsule of lymph node relationship: part_of UBERON:0000029 ! lymph node -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b8/Illu_lymph_node_structure.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b8/Illu_lymph_node_structure.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002007 @@ -185913,9 +184307,9 @@ intersection_of: part_of UBERON:0000029 ! lymph node relationship: has_part UBERON:0009744 ! lymph node medullary sinus relationship: has_part UBERON:0009745 ! lymph node medullary cord relationship: part_of UBERON:0000029 ! lymph node -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_F_Lymph_Node.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_M_Lymph_Node.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_F_Lymph_Node.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_M_Lymph_Node.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002008 @@ -185939,9 +184333,9 @@ xref: Wikipedia:Cardiac_plexus is_a: UBERON:0000122 ! neuron projection bundle is_a: UBERON:0001816 ! autonomic nerve plexus intersection_of: UBERON:0001816 ! autonomic nerve plexus -intersection_of: innervates UBERON:0000948 ! heart -relationship: innervates UBERON:0000948 ! heart -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/77/Gray838.png" xsd:anyURI +intersection_of: RO:0002134 UBERON:0000948 ! innervates heart +relationship: RO:0002134 UBERON:0000948 ! innervates heart +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/77/Gray838.png" xsd:anyURI [Term] id: UBERON:0002011 @@ -185959,11 +184353,11 @@ xref: UMLS:C0933449 {source="ncithesaurus:Thoracodorsal_Artery"} xref: Wikipedia:Thoracodorsal_artery is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0001112 ! latissimus dorsi muscle -relationship: connected_to UBERON:0001397 ! subscapular artery -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: supplies UBERON:0001112 ! latissimus dorsi muscle -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/7/7d/Latissimus_dorsi.png" xsd:anyURI +intersection_of: RO:0002178 UBERON:0001112 ! supplies latissimus dorsi muscle +relationship: RO:0002170 UBERON:0001397 ! connected to subscapular artery +relationship: RO:0002178 UBERON:0001112 ! supplies latissimus dorsi muscle +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/7d/Latissimus_dorsi.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002012 @@ -186001,22 +184395,18 @@ is_a: UBERON:0001637 ! artery is_a: UBERON:0013768 ! great vessel of heart intersection_of: UBERON:0001637 ! artery intersection_of: part_of UBERON:0008886 ! pulmonary vascular system -intersection_of: supplies UBERON:0002048 ! lung +intersection_of: RO:0002178 UBERON:0002048 ! supplies lung disjoint_from: UBERON:0004573 ! systemic artery -relationship: continuous_with UBERON:0002333 ! pulmonary trunk -relationship: develops_from UBERON:0002061 {source="Wikipedia"} ! truncus arteriosus -relationship: develops_from UBERON:0003123 {source="EHDAA2", source="XAO"} ! pharyngeal arch artery 6 -relationship: develops_from UBERON:0005339 {source="EHDAA2"} ! outflow tract pulmonary component relationship: part_of UBERON:0008886 ! pulmonary vascular system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: supplies UBERON:0002048 ! lung -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png" xsd:anyURI -property_value: UBPROP:0000001 "Major artery which supplies blood to the lungs.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010221", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "One of two arteries, leaving from the heart, the left one supplying the left lung and the right one supplying the right lung. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000982", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/pulmonary+artery"} -property_value: UBPROP:0000003 "On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000982", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "In the human heart, the pulmonary trunk (pulmonary artery or main pulmonary artery) begins at the base of the right ventricle. It is short and wide - approximately 5 cm (2 inches) in length and 3 cm (1.2 inches) in diameter. It then branches into two pulmonary arteries (left and right), which deliver deoxygenated blood to the corresponding lung[WP]" xsd:string +relationship: RO:0002150 UBERON:0002333 ! continuous with pulmonary trunk +relationship: RO:0002178 UBERON:0002048 ! supplies lung +relationship: RO:0002202 UBERON:0002061 {source="Wikipedia"} ! develops from truncus arteriosus +relationship: RO:0002202 UBERON:0003123 {source="EHDAA2", source="XAO"} ! develops from pharyngeal arch artery 6 +relationship: RO:0002202 UBERON:0005339 {source="EHDAA2"} ! develops from outflow tract pulmonary component +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002015 @@ -186043,15 +184433,13 @@ is_a: UBERON:0011824 ! fibrous connective tissue intersection_of: UBERON:0011824 ! fibrous connective tissue intersection_of: bounding_layer_of UBERON:0002113 ! kidney relationship: bounding_layer_of UBERON:0002113 ! kidney -relationship: contributes_to_morphology_of UBERON:0002113 ! kidney -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" xsd:anyURI -property_value: UBPROP:0000009 "provides some protection from trauma and damage." xsd:string -property_value: UBPROP:0000010 "The renal capsule relates to the other layers in the following order (moving from innermost to outermost): renal medulla renal cortex renal capsule perinephric fat (or 'perirenal fat') renal fascia paranephric fat (or 'pararenal fat') peritoneum (anteriorly), and transversalis fascia (posteriorly).[Wikipedia:Kidney_capsule]" xsd:string +relationship: RO:0002433 UBERON:0002113 ! contributes to morphology of kidney +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002016 @@ -186083,20 +184471,15 @@ xref: XAO:0000394 is_a: UBERON:0001638 ! vein is_a: UBERON:0013768 ! great vessel of heart intersection_of: UBERON:0001638 ! vein -intersection_of: drains UBERON:0002048 ! lung -relationship: connected_to UBERON:0002079 ! left cardiac atrium -relationship: develops_from UBERON:0002061 ! truncus arteriosus -relationship: drains UBERON:0002048 ! lung +intersection_of: RO:0002179 UBERON:0002048 ! drains lung relationship: part_of UBERON:0008886 ! pulmonary vascular system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png" xsd:anyURI -property_value: UBPROP:0000001 "Any of the veins which collect blood from the lungs and some small vesicles received from the esophagus.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010521", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "One of two pairs of large vessels that return oxygenated blood from each lung to the left atrium of the heart. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001133", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/pulmonary+vein"} -property_value: UBPROP:0000001 "the veins that return oxygenated blood from the lungs to the left atrium of the heart" xsd:string {source="MP:0002726,MGI:cwg"} -property_value: UBPROP:0000003 "On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001133", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000202 FMA:70827 +relationship: RO:0002170 UBERON:0002079 ! connected to left cardiac atrium +relationship: RO:0002179 UBERON:0002048 ! drains lung +relationship: RO:0002202 UBERON:0002061 ! develops from truncus arteriosus +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002017 @@ -186124,8 +184507,8 @@ xref: VHOG:0000656 xref: XAO:0000392 is_a: UBERON:0001638 {source="FMA"} ! vein relationship: part_of UBERON:0005806 ! portal system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/33/Gray591.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002018 @@ -186163,12 +184546,11 @@ xref: Wikipedia:Synovial_membrane is_a: UBERON:0006915 ! stratified squamous epithelium is_a: UBERON:0007616 {source="FMA"} ! layer of synovial tissue is_a: UBERON:0012275 ! meso-epithelium -relationship: attaches_to UBERON:0001484 {source="GAID"} ! articular capsule relationship: has_part CL:0000214 ! synovial cell relationship: part_of UBERON:0002217 {source="EHDAA2"} ! synovial joint -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Joint.png" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/5d/Synovium.png" xsd:anyURI -property_value: UBPROP:0000003 "Phylogenetically, synovium is one of the newer attributes of the vertebrate locomotor apparatus. The first synovial joints developed in the piscine jaw of ancestors of modern lungfish by an evolutionary process that modified preexisting fibrous and cartilaginous joints, which were the predominant articulation of the early sea- and land-dwelling vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001282", ontology="VHOG", source="PMID:11068553 O'Connel JX, Pathology of the synovium. American Journal of Clinical Pathology (2000)", source="http://bgee.unil.ch/"} +relationship: RO:0002371 UBERON:0001484 {source="GAID"} ! attached to articular capsule +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Joint.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5d/Synovium.png" xsd:anyURI [Term] id: UBERON:0002019 @@ -186219,15 +184601,8 @@ is_a: UBERON:0035642 ! laryngeal nerve intersection_of: UBERON:0001021 ! nerve intersection_of: extends_fibers_into UBERON:0020358 ! accessory XI nerve nucleus relationship: extends_fibers_into UBERON:0020358 ! accessory XI nerve nucleus -relationship: only_in_taxon NCBITaxon:32523 ! Tetrapoda -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/5e/Gray791.png" xsd:anyURI -property_value: RO:0002174 NCBITaxon:8292 {source="VHOG", source="Wikipedia", seeAlso="http://code.google.com/p/xenopus-anatomy-ontology/issues/detail?id=7"} -property_value: UBPROP:0000001 "A small motor nerve which emerges from the lateral wall of the medulla with the roots of the vagus nerve, and innervates a single pectoral suspensory muscle, the m.cucullaris." xsd:string {source="ISBN:080184780X", source="XAO:0004214"} -property_value: UBPROP:0000001 "Cranial nerve that innervates the sternocleidomastoid and trapezius complex of muscles. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-1, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000699", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000001 "Small motor nerve which innervates a single pectoral suspensory muscle, the m. cucullaris.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010476", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "Cranial nerves XI and XII evolved in the common ancestor to amniotes (non-amphibian tetrapods) thus totalling twelve pairs.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000699", ontology="VHOG", source="Wikipedia:Cranial_nerves", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "In mice, the spinal branch of this motor nerve innervates the trapezius and the sternocleidomastoid muscles. The cranial branch joins the vagus nerve and innervates the same targets as the vagus nerve" xsd:string {source="GO"} -property_value: UBPROP:0000012 "FMA has distinct cranial and spinal parts - WP says 'Traditional descriptions of the accessory nerve divide it into two parts: a spinal part and a cranial part.[1] However, because the cranial component rapidly joins the vagus nerve, becoming an integral part of said nerve, modern descriptions often consider the cranial component to be part of the vagus nerve and not part of the accessory nerve proper.[2]" xsd:string {external_ontology="FMA"} +relationship: RO:0002160 NCBITaxon:32523 ! only in taxon Tetrapoda +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5e/Gray791.png" xsd:anyURI [Term] id: UBERON:0002020 @@ -186253,7 +184628,6 @@ xref: EMAPA:37596 {source="MA:th"} xref: FMA:67242 xref: HBA:4006 xref: MA:0001112 -xref: MESH:D066128 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C32695 xref: neuronames:2869 xref: TAO:0002197 @@ -186262,9 +184636,8 @@ xref: VHOG:0001768 xref: Wikipedia:Gray_matter xref: ZFA:0001681 is_a: UBERON:0011215 ! central nervous system cell part cluster -relationship: composed_primarily_of GO:0043025 ! neuronal cell body -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg" xsd:anyURI -property_value: UBPROP:0000001 "Multi-tissue comprised of neurons, dendrites, axon terminals, glial cells, and capillaries.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002197", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002473 GO:0043025 ! composed primarily of neuronal cell body +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg" xsd:anyURI [Term] id: UBERON:0002025 @@ -186305,16 +184678,16 @@ xref: UMLS:C0221925 {source="ncithesaurus:Stratum_Basale"} xref: Wikipedia:Stratum_germinativum xref: XAO:0000041 xref: ZFA:0001180 +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0013754 ! integumentary system layer intersection_of: UBERON:0013754 ! integumentary system layer -intersection_of: composed_primarily_of CL:0002187 ! basal cell of epidermis -relationship: composed_primarily_of CL:0002187 ! basal cell of epidermis +intersection_of: RO:0002473 CL:0002187 ! composed primarily of basal cell of epidermis relationship: has_part CL:0000148 ! melanocyte relationship: has_part CL:0000242 ! Merkel cell relationship: part_of UBERON:0001003 ! skin epidermis -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000009 "replaces damaged cells on outside of body" xsd:string -property_value: UBPROP:0000010 "consisting of non-keratinized, viable cells, in contrast to the outer (upper) layer of epidermis made up of keratinized, anucleated, non-viable cells" xsd:string +relationship: RO:0002473 CL:0002187 ! composed primarily of basal cell of epidermis +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002026 @@ -186340,16 +184713,16 @@ xref: SCTID:420086000 xref: UMLS:C0221924 {source="ncithesaurus:Stratum_Spinosum"} xref: Wikipedia:Stratum_spinosum is_a: PR:000050567 ! protein-containing material entity +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0013754 ! integumentary system layer intersection_of: UBERON:0013754 ! integumentary system layer -intersection_of: composed_primarily_of CL:0000649 ! prickle cell +intersection_of: RO:0002473 CL:0000649 ! composed primarily of prickle cell relationship: adjacent_to UBERON:0002025 ! stratum basale of epidermis relationship: adjacent_to UBERON:0002069 ! stratum granulosum of epidermis -relationship: composed_primarily_of CL:0000649 ! prickle cell relationship: has_part CL:0000453 ! Langerhans cell relationship: part_of UBERON:0001003 ! skin epidermis -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000009 "Has cells that produce and secrete bipolar lipids which prevent evaporation, helping to 'water-proof' the skin. Keratinization begins in the stratum spinosum. [Wikipedia:Stratum_spinosum]" xsd:string +relationship: RO:0002473 CL:0000649 ! composed primarily of prickle cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002027 @@ -186376,16 +184749,15 @@ xref: NCIT:C33625 xref: SCTID:361695002 xref: UMLS:C0221921 {source="ncithesaurus:Stratum_Corneum"} xref: Wikipedia:Stratum_corneum -is_a: UBERON:0003055 ! periderm +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0013754 ! integumentary system layer -relationship: contains_process GO:0031424 ! keratinization +relationship: BFO:0000067 GO:0031424 ! contains process keratinization +relationship: BSPO:0000108 UBERON:0002069 ! stratum granulosum of epidermis relationship: has_part CL:0002153 {source="FMA"} ! corneocyte -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: superficial_to UBERON:0002069 ! stratum granulosum of epidermis -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/20/Skinlayers.png" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/e/e4/Epidermal_layers.png" xsd:anyURI -property_value: UBPROP:0000001 "The keratinized outermost layer of the epidermis, which is periodically shed.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010597", ontology="AAO", source="AAO:CAM"} -property_value: UBPROP:0000010 "some oral epitehlium also has cornified layer / stratum corneum" xsd:string +relationship: part_of UBERON:0001003 ! skin epidermis +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/20/Skinlayers.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/e/e4/Epidermal_layers.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002028 @@ -186427,22 +184799,13 @@ xref: Wikipedia:Rhombencephalon xref: XAO:0000015 xref: ZFA:0000029 is_a: UBERON:0002616 ! regional part of brain -is_a: UBERON:0004121 ! ectoderm-derived structure -relationship: contributes_to_morphology_of UBERON:0000955 ! brain -relationship: immediate_transformation_of UBERON:0007277 {source="Bgee:AN"} ! presumptive hindbrain -relationship: only_in_taxon NCBITaxon:89593 ! Craniata -relationship: overlaps UBERON:0002298 {notes="modified-source-relation", source="ABA"} ! brainstem -relationship: present_in_taxon NCBITaxon:7762 {source="PMID:8932866"} -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI -property_value: RO:0002171 UBERON:0001891 {exceptions="ZFA", source="ABA", source="https://github.com/obophenotype/uberon/issues/378", status="pending"} -property_value: RO:0002171 UBERON:0001894 {source="ABA"} -property_value: UBPROP:0000001 "Posterior part of the brain consisting of the cerebellum and medulla oblongata.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010150", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "The most posterior of the three principal regions of the brain, forming the rhombencephalon and all or most of the metencephalon. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000029", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000002 "relationship loss: develops_from hindbrain neural tube (TAO:0007043)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000029", ontology="TAO"} -property_value: UBPROP:0000003 "Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000070", ontology="VHOG", source="DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "rhombencephalic" xsd:string -property_value: UBPROP:0000012 "in MA, brainstem and hindbrain and part-of siblings under brain, consistent with FMA and NIF. See also notes for cerebellum. We weaken the relation in ABA to overlaps" xsd:string {external_ontology="MA"} +relationship: overlaps UBERON:0002298 ! brainstem +relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata +relationship: RO:0002433 UBERON:0000955 ! contributes to morphology of brain +relationship: RO:0002495 UBERON:0007277 {source="Bgee:AN"} ! immediate transformation of presumptive hindbrain +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:7762 {source="PMID:8932866"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002029 @@ -186466,11 +184829,12 @@ xref: MA:0001632 xref: NCIT:C49227 xref: UMLS:C1180206 {source="ncithesaurus:Gallbladder_Epithelium"} is_a: UBERON:0000485 ! simple columnar epithelium +is_a: UBERON:0005911 ! endo-epithelium is_a: UBERON:0034932 ! epithelium of biliary system intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002110 ! gallbladder -relationship: contributes_to_morphology_of UBERON:0002110 ! gallbladder relationship: part_of UBERON:0002110 ! gallbladder +relationship: RO:0002433 UBERON:0002110 ! contributes to morphology of gallbladder [Term] id: UBERON:0002030 @@ -186501,14 +184865,12 @@ xref: UMLS:C0028109 {source="ncithesaurus:Nipple"} xref: Wikipedia:Nipple is_a: UBERON:0000475 ! organism subdivision is_a: UBERON:0004121 ! ectoderm-derived structure -relationship: develops_from UBERON:0008425 {source="Stedmans"} ! mammary ridge -relationship: only_in_taxon NCBITaxon:32525 ! Theria relationship: part_of UBERON:0000310 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! breast relationship: part_of UBERON:0001911 ! mammary gland -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/59/Female_nipple_profile.jpg" xsd:anyURI +relationship: RO:0002160 NCBITaxon:32525 ! only in taxon Theria +relationship: RO:0002202 UBERON:0008425 {source="Stedmans"} ! develops from mammary ridge +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/59/Female_nipple_profile.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/1873" xsd:string -property_value: UBPROP:0000008 "a male mouse has no nipples - mammary tissue regresses during embryonic development" xsd:string -property_value: UBPROP:0000012 "FMA makes this part of the breast, whereas in MA it is part of the mammary gland -" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0002031 @@ -186540,9 +184902,9 @@ xref: UMLS:C0599333 {source="ncithesaurus:Bronchial_Epithelium"} is_a: UBERON:0008397 ! tracheobronchial epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002185 ! bronchus -relationship: contributes_to_morphology_of UBERON:0002185 ! bronchus relationship: has_part CL:0002209 {source="FMA"} ! intermediate epitheliocyte relationship: part_of UBERON:0002185 ! bronchus +relationship: RO:0002433 UBERON:0002185 ! contributes to morphology of bronchus [Term] id: UBERON:0002033 @@ -186569,9 +184931,8 @@ xref: MA:0000778 xref: SCTID:319910005 xref: Wikipedia:Arrector_pili_muscle is_a: UBERON:0001135 {source="FMA"} ! smooth muscle tissue -relationship: attaches_to UBERON:0002073 ! hair follicle relationship: part_of UBERON:0011932 {source="FMA"} ! pilosebaceous unit -property_value: UBPROP:0000009 "When contracted the arrector pili causes the raising of the hair" xsd:string +relationship: RO:0002371 UBERON:0002073 ! attached to hair follicle [Term] id: UBERON:0002036 @@ -186595,9 +184956,8 @@ xref: WBbt:0005779 xref: Wikipedia:Striated_muscle is_a: UBERON:0002385 ! muscle tissue intersection_of: UBERON:0002385 ! muscle tissue -intersection_of: composed_primarily_of CL:0000737 ! striated muscle cell -relationship: composed_primarily_of CL:0000737 ! striated muscle cell -property_value: UBPROP:0000001 "Voluntary muscle tissue arranged in bundles of fibers.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010762", ontology="AAO", source="AAO:CAM"} +intersection_of: RO:0002473 CL:0000737 ! composed primarily of striated muscle cell +relationship: RO:0002473 CL:0000737 ! composed primarily of striated muscle cell [Term] id: UBERON:0002037 @@ -186644,23 +185004,14 @@ xref: Wikipedia:Cerebellum xref: XAO:0003098 xref: ZFA:0000100 is_a: UBERON:0002616 ! regional part of brain -relationship: contributes_to_morphology_of UBERON:0001895 ! metencephalon -relationship: develops_from UBERON:0006215 {evidence="definitional"} ! rhombic lip -relationship: never_in_taxon NCBITaxon:117565 {source="ISBN:0471888893"} -relationship: only_in_taxon NCBITaxon:7742 {source="ISBN:0471888893"} ! Vertebrata relationship: part_of UBERON:0001895 {source="FMA", source="MA"} ! metencephalon -relationship: present_in_taxon NCBITaxon:117569 {source="ISBN:0471888893"} -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/a/a7/Cerebellum_NIH.png" xsd:anyURI -property_value: RO:0002171 UBERON:0001893 {source="ABA"} -property_value: RO:0002171 UBERON:0002298 {exceptions="ZFA", source="ABA", source="https://github.com/obophenotype/uberon/issues/378", status="pending"} -property_value: RO:0002174 NCBITaxon:117569 {source="http://icb.oxfordjournals.org/content/42/4/743.full"} -property_value: UBPROP:0000001 "Dorsal part of the hindbrain that coordinates muscle movement, posture, and balance.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010485", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "Specialized brain region derived from the dorsal metencephalon (anterior hindbrain, and perhaps including posterior midbrain) and becoming distinctive late in the segmentation period. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000100", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "However, although the lamprey possesses a region comparable to the cerebellum and display expression of LjFgf8/17 at the MHB (midbrain hindbrain boundary), it does not have Purkinje cells and cerebellar nuclei, as well as components of the rhombic lip-derived cerebellar and pre-cerebellar systems. It is noteworthy that the latter structures require specific expression of Pax6 in the rhombic lip of the gnathostome hindbrain. Interestingly, the lamprey rhombic lip does not express Pax6. Thus, it is tempting to speculate that in vertebrate evolution the rostral hindbrain is incapable of differentiating into the cerebellum before the co-option of Pax6 in that region. In other words, cerebellum has been brought about as an evolutionary innovation in gnathostomes, based on exaptation of MHB, rhombic lip, and some regulatory gene expression already present in the vertebrate common ancestor.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000024", ontology="VHOG", source="DOI:10.1016/j.ydbio.2005.02.008 Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "cerebellar" xsd:string -property_value: UBPROP:0000008 "The absence of a cerebellum in hagfishes and lampreys appears to be the only exception [to the rule that vertebrates possess the same number of brain divisions]. Both hagfishes and lampreys do possess a thin band of cells located medial to the lateral line centers of the medulla (Ronan and Northcutt, 1998), which has been interpreted as a primitive cerebellum (Larsell, 1967), but more recent experimental studies (Kishida et al., 1987; Weigle and Northcutt, 1998) fail to support Larsell's claim[http://icb.oxfordjournals.org/content/42/4/743.full]" xsd:string -property_value: UBPROP:0000012 "almost all AOs agree that the cerebellum is part of the hindbrain (sometimes specifically part of the metencephalon, which, when present, is part of the hindbrain). However, ABA has cerebellum and brain stem as partof siblings, with the hindbrain part of the brainstem" xsd:string {external_ontology="ABA"} +relationship: RO:0002160 NCBITaxon:7742 {source="ISBN:0471888893"} ! only in taxon Vertebrata +relationship: RO:0002202 UBERON:0006215 ! develops from rhombic lip +relationship: RO:0002433 UBERON:0001895 ! contributes to morphology of metencephalon +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/a/a7/Cerebellum_NIH.png" xsd:anyURI +property_value: RO:0002161 NCBITaxon:117565 {source="ISBN:0471888893"} +property_value: RO:0002175 NCBITaxon:117569 {source="ISBN:0471888893"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002038 @@ -186701,17 +185052,15 @@ xref: VHOG:0001573 xref: Wikipedia:Substantia_nigra is_a: UBERON:0009661 ! midbrain nucleus is_a: UBERON:0015212 ! lateral structure -relationship: contributes_to_morphology_of UBERON:0001891 ! midbrain -relationship: contributes_to_morphology_of UBERON:0010011 ! collection of basal ganglia -relationship: in_lateral_side_of UBERON:0001891 {source="FMA-abduced-lr"} ! midbrain +relationship: BSPO:0000126 UBERON:0001891 {source="FMA-abduced-lr"} ! midbrain relationship: part_of UBERON:0002420 {source="NIF"} ! basal ganglion -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Midbraincrosssection.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI -property_value: editor_note "TODO - In BTO and NIF, part of basal ganglion which is part of telencephalon - but this is inconsistent with being part of midbrain, if these are spatially disjoint, as in ABA" xsd:string -property_value: UBPROP:0000001 "Subdivision of the midbrain anterior to the midbrain tegmentum which contains darkly pigmented neurons[FMA][FMA:67947]." xsd:string {source="FMA:67947"} -property_value: UBPROP:0000003 "(...) the substantia nigra first appears in reptiles and is best developed in primates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001573", ontology="VHOG", source="ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.336", source="http://bgee.unil.ch/"} +relationship: RO:0002433 UBERON:0001891 ! contributes to morphology of midbrain +relationship: RO:0002433 UBERON:0010011 ! contributes to morphology of collection of basal ganglia +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Midbraincrosssection.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI +property_value: IAO:0000116 "TODO - In BTO and NIF, part of basal ganglion which is part of telencephalon - but this is inconsistent with being part of midbrain, if these are spatially disjoint, as in ABA" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002040 @@ -186736,12 +185085,12 @@ xref: Wikipedia:Bronchial_artery is_a: UBERON:0004573 ! systemic artery intersection_of: UBERON:0004573 ! systemic artery intersection_of: part_of UBERON:0004571 ! systemic arterial system -intersection_of: supplies UBERON:0002048 ! lung +intersection_of: RO:0002178 UBERON:0002048 ! supplies lung relationship: has_part UBERON:0004848 ! respiratory system arterial endothelium relationship: has_part UBERON:0012416 ! respiratory system arterial smooth muscle -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: supplies UBERON:0002048 ! lung -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/a7/Gray1032.png" xsd:anyURI +relationship: RO:0002178 UBERON:0002048 ! supplies lung +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/a7/Gray1032.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002042 @@ -186769,11 +185118,10 @@ xref: ZFA:0005258 is_a: UBERON:0004852 ! cardiovascular system endothelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0001473 ! lymphatic vessel -relationship: contributes_to_morphology_of UBERON:0001473 ! lymphatic vessel relationship: has_part CL:0002138 {source="FMA"} ! endothelial cell of lymphatic vessel relationship: part_of UBERON:0001473 ! lymphatic vessel -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000001 "The vascular endothelium that lines the lymph vessels.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005258", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002433 UBERON:0001473 ! contributes to morphology of lymphatic vessel +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002046 @@ -186811,18 +185159,13 @@ xref: XAO:0000162 is_a: UBERON:0002368 ! endocrine gland is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest +relationship: BFO:0000067 GO:0006590 ! contains process thyroid hormone generation relationship: capable_of GO:0036161 {source="Wikipedia"} ! calcitonin secretion relationship: capable_of_part_of GO:0055074 {source="Wikipedia"} ! calcium ion homeostasis -relationship: contains_process GO:0006590 ! thyroid hormone generation -relationship: only_in_taxon NCBITaxon:7711 {source="Wikipedia:Endostyle"} ! Chordata -relationship: transformation_of UBERON:0007689 ! thyroid diverticulum -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/a3/Illu_thyroid_parathyroid.jpg" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Illu_endocrine_system.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Either of paired structures located in the throat which develop from the ventral wall of the pharynx and excretes hormones involved in the morphological and functional changes during metamorphosis as well as influencing other tissues.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010544", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (2) a groove in the pharyngeal floor known as the endostyle, or a thyroid gland derived from part of the endostyle (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000418", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "In fish, it is usually located below the gills and is not always divided into distinct lobes. However, in some teleosts, patches of thyroid tissue are found elsewhere in the body, associated with the kidneys, spleen, heart, or eyes" xsd:string {scope="NCBITaxon:32443", source="Romer", source="Wikipedia:Thyroid_gland#Other_animals"} -property_value: UBPROP:0000008 "In larval lampreys, the thyroid originates as an exocrine gland, secreting its hormones into the gut, and associated with the larva's filter-feeding apparatus. In the adult lamprey, the gland separates from the gut, and becomes endocrine, but this path of development may reflect the evolutionary origin of the thyroid. For instance, the closest living relatives of vertebrates, the tunicates and Amphioxus, have a structure very similar to that of larval lampreys, and this also secretes iodine-containing compounds (albeit not thyroxine)" xsd:string {scope="NCBITaxon:7746", source="Romer", source="Wikipedia:Thyroid_gland#Other_animals"} -property_value: UBPROP:0000008 "In tetrapods, the thyroid is always found somewhere in the neck region. In most tetrapod species, there are two paired thyroid glands - that is, the right and left lobes are not joined together. However, there is only ever a single thyroid gland in most mammals, and the shape found in humans is common to many other species" xsd:string {scope="NCBITaxon:32523", source="Romer", source="Wikipedia:Thyroid_gland#Other_animals"} +relationship: RO:0002160 NCBITaxon:7711 {source="Wikipedia:Endostyle"} ! only in taxon Chordata +relationship: RO:0002494 UBERON:0007689 ! transformation of thyroid diverticulum +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/a3/Illu_thyroid_parathyroid.jpg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Illu_endocrine_system.jpg" xsd:anyURI [Term] id: UBERON:0002047 @@ -186854,10 +185197,6 @@ is_a: UBERON:0006331 ! brainstem nucleus is_a: UBERON:0009662 ! hindbrain nucleus relationship: part_of UBERON:0003023 ! pontine tegmentum relationship: part_of UBERON:0004684 {source="Wikipedia"} ! raphe nuclei -property_value: RO:0002171 UBERON:0002148 {source="ABA"} -property_value: RO:0002171 UBERON:0002267 {source="ABA"} -property_value: RO:0002171 UBERON:0002587 {source="ABA"} -property_value: RO:0002171 UBERON:0003004 {source="ABA"} [Term] id: UBERON:0002048 @@ -186892,28 +185231,22 @@ xref: MIAA:0000135 xref: NCIT:C12468 xref: SCTID:181216001 xref: UMLS:C0024109 {source="ncithesaurus:Lung"} -xref: VHOG:0000310 xref: Wikipedia:Lung xref: XAO:0000119 is_a: UBERON:0000171 ! respiration organ +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0005178 ! thoracic cavity element is_a: UBERON:0015212 ! lateral structure -relationship: contributes_to_morphology_of UBERON:0001004 ! respiratory system -relationship: develops_from UBERON:0000118 ! lung bud -relationship: in_lateral_side_of UBERON:0000170 ! pair of lungs -relationship: never_in_taxon NCBITaxon:32443 {editor="https://orcid.org/0000-0002-9415-5104", source="https://github.com/obophenotype/uberon/issues/701"} ! Teleostei -relationship: never_in_taxon NCBITaxon:7777 {editor="https://orcid.org/0000-0002-9415-5104", source="https://github.com/obophenotype/uberon/issues/701"} -relationship: only_in_taxon NCBITaxon:7776 ! Gnathostomata +relationship: BSPO:0000126 UBERON:0000170 ! pair of lungs relationship: part_of UBERON:0000170 {note="some species only have a single lung"} ! pair of lungs -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: surrounded_by UBERON:0009778 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! pleural sac -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb" xsd:anyURI +relationship: RO:0002160 NCBITaxon:7776 ! only in taxon Gnathostomata +relationship: RO:0002202 UBERON:0000118 ! develops from lung bud +relationship: RO:0002219 UBERON:0009778 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! surrounded by pleural sac +relationship: RO:0002433 UBERON:0001004 ! contributes to morphology of respiratory system +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/uberon/issues/701" xsd:anyURI -property_value: UBPROP:0000001 "Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010567", ontology="AAO", source="AAO:SBH"} -property_value: UBPROP:0000003 "Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata. (...) In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ (reference 1); Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000310", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210, DOI:10.1371/journal.pone.0024019 Zheng W, Wang Z, Collins JE, Andrews RM, Stemple D, Gong Z, Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung. PLoS One (2011)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "pulmonary" xsd:string -property_value: UBPROP:0000008 "respiration organ in all air-breathing animals, including most tetrapods, a few fish and a few snails. In mammals and the more complex life forms, the two lungs are located in the chest on either side of the heart. Their principal function is to transport oxygen from the atmosphere into the bloodstream, and to release carbon dioxide from the bloodstream into the atmosphere. This exchange of gases is accomplished in the mosaic of specialized cells that form millions of tiny, exceptionally thin-walled air sacs called alveoli. // Avian lungs do not have alveoli as mammalian lungs do, they have Faveolar lungs. They contain millions of tiny passages known as para-bronchi, connected at both ends by the dorsobronchi" xsd:string [Term] id: UBERON:0002049 @@ -186930,13 +185263,12 @@ xref: FMA:69050 xref: TAO:0005249 xref: ZFA:0005249 is_a: UBERON:0000477 {source="FMA"} ! anatomical cluster -relationship: composed_primarily_of UBERON:0000055 ! vessel relationship: has_part UBERON:0000179 ! haemolymphatic fluid relationship: part_of UBERON:0007798 ! vascular system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI -property_value: editor_note "see also: vascular system. Consider merging?" xsd:string -property_value: UBPROP:0000007 "vascular" xsd:string +relationship: RO:0002473 UBERON:0000055 ! composed primarily of vessel +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: IAO:0000116 "see also: vascular system. Consider merging?" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002050 @@ -186956,7 +185288,6 @@ xref: BILA:0000034 xref: BTO:0000174 xref: CALOHA:TS-2110 xref: EFO:0000461 -xref: FBbt:00004208 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69067 xref: GAID:407 xref: MESH:D004628 @@ -186972,10 +185303,6 @@ is_a: UBERON:0005423 ! developing anatomical structure intersection_of: UBERON:0005423 ! developing anatomical structure intersection_of: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0000922 ! embryo -property_value: UBPROP:0000001 "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000138", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001105", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000178", ontology="VSAO", source="ZFIN:curator"} -property_value: UBPROP:0000012 "in FMA embryo is_a embryonic structure" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0002051 @@ -187000,13 +185327,13 @@ is_a: UBERON:0003350 ! epithelium of mucosa is_a: UBERON:0008397 ! tracheobronchial epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002186 ! bronchiole -relationship: contributes_to_morphology_of UBERON:0002186 ! bronchiole -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: has_part CL:0000158 ! club cell relationship: has_part CL:0002145 {source="FMA"} ! ciliated columnar cell of tracheobronchial tree relationship: has_part CL:1000271 ! lung ciliated cell relationship: part_of UBERON:0005039 ! mucosa of bronchiole -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002433 UBERON:0002186 ! contributes to morphology of bronchiole +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002052 @@ -187022,11 +185349,13 @@ xref: NCIT:C32050 xref: UMLS:C1181304 {source="ncithesaurus:Adrenal_Gland_Capsule"} is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0003893 ! capsule +is_a: UBERON:0004120 ! mesoderm-derived structure +is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0003893 ! capsule intersection_of: bounding_layer_of UBERON:0002369 ! adrenal gland relationship: bounding_layer_of UBERON:0002369 ! adrenal gland -relationship: composed_primarily_of UBERON:0011822 ! dense irregular connective tissue -relationship: contributes_to_morphology_of UBERON:0001235 ! adrenal cortex +relationship: RO:0002433 UBERON:0001235 ! contributes to morphology of adrenal cortex +relationship: RO:0002473 UBERON:0011822 ! composed primarily of dense irregular connective tissue [Term] id: UBERON:0002053 @@ -187050,9 +185379,9 @@ xref: SCTID:21476003 xref: Wikipedia:Zona_glomerulosa is_a: UBERON:0009753 {source="MA"} ! adrenal gland cortex zone relationship: capable_of GO:0032342 ! aldosterone biosynthetic process -relationship: contributes_to_morphology_of UBERON:0001235 ! adrenal cortex relationship: has_part CL:1000427 {source="FMA"} ! adrenal cortex chromaffin cell -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray1185.png" xsd:anyURI +relationship: RO:0002433 UBERON:0001235 ! contributes to morphology of adrenal cortex +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray1185.png" xsd:anyURI [Term] id: UBERON:0002056 @@ -187071,10 +185400,10 @@ xref: UMLS:C0226334 {source="ncithesaurus:Inferior_Suprarenal_Artery"} xref: Wikipedia:Inferior_suprarenal_artery is_a: UBERON:0005624 ! suprarenal artery intersection_of: UBERON:0005624 ! suprarenal artery -intersection_of: connecting_branch_of UBERON:0001184 ! renal artery -relationship: connecting_branch_of UBERON:0001184 ! renal artery -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/61/Gray1121.png" xsd:anyURI +intersection_of: RO:0002252 UBERON:0001184 ! connecting branch of renal artery +relationship: RO:0002252 UBERON:0001184 ! connecting branch of renal artery +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/61/Gray1121.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002057 @@ -187089,9 +185418,8 @@ xref: NCIT:C33320 xref: UMLS:C1181536 {source="ncithesaurus:Phrenic_Artery"} is_a: UBERON:0004573 ! systemic artery intersection_of: UBERON:0004573 ! systemic artery -intersection_of: supplies UBERON:0001103 ! diaphragm -relationship: supplies UBERON:0001103 ! diaphragm -property_value: UBPROP:0000008 "In humans this includes the superior and inferior phrenic arteries" xsd:string +intersection_of: RO:0002178 UBERON:0001103 ! supplies diaphragm +relationship: RO:0002178 UBERON:0001103 ! supplies diaphragm [Term] id: UBERON:0002060 @@ -187114,9 +185442,8 @@ xref: SCTID:244332003 xref: UMLS:C0015801 {source="ncithesaurus:Femoral_Artery"} xref: Wikipedia:Femoral_artery is_a: UBERON:0001637 ! artery -relationship: connecting_branch_of UBERON:0001308 {source="FMA", source="WP"} ! external iliac artery -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray546.png" xsd:anyURI -property_value: UBPROP:0000001 "Artery which supplies blood via branches to the hindlimbs.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010222", ontology="AAO", source="AAO:BJB"} +relationship: RO:0002252 UBERON:0001308 {source="FMA", source="WP"} ! connecting branch of external iliac artery +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray546.png" xsd:anyURI [Term] id: UBERON:0002061 @@ -187137,10 +185464,9 @@ xref: Wikipedia:Truncus_arteriosus_(embryology) is_a: UBERON:0001637 {source="EHDAA2"} ! artery is_a: UBERON:0002050 {source="FMA"} ! embryonic structure is_a: UBERON:0003498 ! heart blood vessel -relationship: develops_from UBERON:0005432 {source="EHDAA2"} ! aortic sac relationship: part_of UBERON:0004145 {source="MA"} ! outflow tract relationship: part_of UBERON:0005498 {source="EHDAA2"} ! primitive heart tube -property_value: UBPROP:0000012 "assume spelling error for ncit" xsd:string {external_ontology="ncit"} +relationship: RO:0002202 UBERON:0005432 {source="EHDAA2"} ! develops from aortic sac [Term] id: UBERON:0002062 @@ -187163,7 +185489,6 @@ xref: EHDAA:2586 xref: EMAPA:16696 xref: FMA:70302 xref: MA:0000078 -xref: MESH:D054089 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: TAO:0001317 xref: VHOG:0000932 xref: Wikipedia:Atrioventricular_cushions @@ -187174,10 +185499,7 @@ is_a: UBERON:0005256 ! trunk mesenchyme is_a: UBERON:0009751 ! cardiac mesenchyme is_a: UBERON:0014387 ! mesenchyme derived from neural crest relationship: part_of UBERON:0002165 {source="ZFA"} ! endocardium -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c7/Gray465.png" xsd:anyURI -property_value: UBPROP:0000001 "Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001317", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000002 "relationship loss: develops_from endocardial ring (TAO:0005072)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001317", ontology="TAO"} -property_value: UBPROP:0000003 "(Cardiac valve formation in vertebrates) In response to a myocardial signal, endocardial cells at chamber boundaries take on a mesenchymal character, delaminate and migrate into the cardiac jelly. There, they form an endocardial cushion that is later remodelled into a valve.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000932", ontology="VHOG", source="DOI:10.1038/35047564 Stainier DYR, Zebrafish genetics and vertebrate heart formation. Nature Reviews Genetics (2001) Figure 3", source="http://bgee.unil.ch/"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c7/Gray465.png" xsd:anyURI [Term] id: UBERON:0002063 @@ -187206,18 +185528,11 @@ xref: UMLS:C0231084 {source="ncithesaurus:Sinus_Venosus"} xref: VHOG:0000177 xref: Wikipedia:Sinus_venosus xref: ZFA:0000154 -is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004151 ! cardiac chamber disjoint_from: UBERON:0006615 ! venous sinus -relationship: immediate_transformation_of UBERON:0007278 {source="Bgee:AN"} ! presumptive sinus venosus relationship: part_of UBERON:0002350 {source="VHOG"} ! conducting system of heart -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c7/Gray465.png" xsd:anyURI -property_value: UBPROP:0000001 "Heart region collecting blood from the paired common cardinal veins and delivering to the atrium. One of four components of the heart. The sinus venosus also acts as a pacemaker and is the first to contract. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000154", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Part of the circulatory system which receives blood from the systemic veins and contracts to pump the blood into the atrium of the heart.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010505", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000177", ontology="VHOG", source="ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.428", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "In fish, receives venous blood from the systemic circulation through paired hepatic veins, anterior jugular veins and Cuvierian ducts[PMID:20735616]" xsd:string -property_value: UBPROP:0000008 "In humans, it exists distinctly only in the embryonic heart, where it is found between the two venae cavae. In the adult, it is incorporated into the wall of the right atrium to form a smooth part called the sinus venarum, also known as the venarum sinus, which is separated from the rest of the atrium by a ridge of fibres called the crista terminalis. The sinus venosus also forms the SA node and the coronary sinus. In the embryo, the thin walls of the sinus venosus are connected below with the right ventricle, and medially with the left atrium, but are free in the rest of their extent. It receives blood from the vitelline vein, umbilical vein and common cardinal vein. It originally starts as a paired structure but shifts towards associating only with the right atrium as the embryonic heart develops. The left portion shrinks in size and eventually forms the coronary sinus and oblique vein of the left atrium, whereas the right part becomes incorporated into the right atrium to form the sinus venarmu" xsd:string -property_value: UBPROP:0000008 "In zebrafish, the sinus venosus also acts as a pacemaker and is the first to contract" xsd:string {source="ZFA:0000154"} +relationship: RO:0002495 UBERON:0007278 {source="Bgee:AN"} ! immediate transformation of presumptive sinus venosus +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c7/Gray465.png" xsd:anyURI [Term] id: UBERON:0002066 @@ -187248,9 +185563,9 @@ xref: UMLS:C0041637 {source="ncithesaurus:Umbilical_Vein"} xref: Wikipedia:Umbilical_vein is_a: UBERON:0001638 ! vein is_a: UBERON:0010260 ! umbilical blood vessel -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Gray502.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Placenta.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Gray502.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Placenta.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002067 @@ -187286,21 +185601,19 @@ xref: Wikipedia:Dermis xref: XAO:0000217 xref: ZFA:0001119 is_a: PR:000050567 ! protein-containing material entity +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0013754 ! integumentary system layer -relationship: composed_primarily_of UBERON:0002384 ! connective tissue -relationship: deep_to UBERON:0001003 ! skin epidermis +relationship: BSPO:0000107 UBERON:0001003 ! skin epidermis +relationship: BSPO:0000108 UBERON:0002072 ! hypodermis relationship: has_part GO:0071953 ! elastic fiber relationship: has_part UBERON:0011860 ! collection of collagen fibrils -relationship: immediate_transformation_of UBERON:0010083 {evidence="definitional"} ! future dermis relationship: part_of UBERON:0002097 {source="FMA"} ! skin of body -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: superficial_to UBERON:0002072 ! hypodermis -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/23/EpidermisPainted.svg" xsd:anyURI -property_value: editor_note "Consider adding a layer-of-skin grouping class for all skin layers" xsd:string -property_value: UBPROP:0000001 "A collagenous layer of the skin subjacent to the epidermis and covering the hypodermis. It contains various types of cells (e.g. fibroblasts, pigment cells, nerve, blood vessels and scales. Le Guellec et al, 2004.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001119", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "When approaching controversies surrounding skin evolution, we need to remember that the skin consists of two layers, an epidermis and a dermis, not a single evolving structure. (...) It is little wonder that controversies about homology exist. If we think of the epidermis, the dermis, and their interactions as an evolving unit, then their specialized products (hair, feathers, and reptilian scales) are broadly homologous.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000108", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.231-232 see also p.209 and p.228 and Figure 6-1", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "dermal" xsd:string +relationship: RO:0002473 UBERON:0002384 ! composed primarily of connective tissue +relationship: RO:0002495 UBERON:0010083 ! immediate transformation of future dermis +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/23/EpidermisPainted.svg" xsd:anyURI +property_value: IAO:0000116 "Consider adding a layer-of-skin grouping class for all skin layers" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002069 @@ -187321,13 +185634,14 @@ xref: NCIT:C33627 xref: SCTID:418563001 xref: UMLS:C0221923 {source="ncithesaurus:Stratum_Granulosum"} xref: Wikipedia:Stratum_granulosum +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0013754 ! integumentary system layer intersection_of: UBERON:0013754 ! integumentary system layer -intersection_of: composed_primarily_of CL:0000712 ! stratum granulosum cell -relationship: composed_primarily_of CL:0000712 ! stratum granulosum cell -relationship: immediately_superficial_to UBERON:0002026 ! stratum spinosum of epidermis +intersection_of: RO:0002473 CL:0000712 ! composed primarily of stratum granulosum cell +relationship: BSPO:0015014 UBERON:0002026 ! stratum spinosum of epidermis relationship: part_of UBERON:0001003 ! skin epidermis -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002473 CL:0000712 ! composed primarily of stratum granulosum cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002072 @@ -187350,7 +185664,6 @@ xref: BTO:0001314 xref: CALOHA:TS-2366 xref: EMAPA:37505 {source="MA:th"} xref: FMA:70544 -xref: MESH:D040521 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: NCIT:C33645 xref: TAO:0001136 xref: UMLS:C0278403 {source="ncithesaurus:Subcutis"} @@ -187359,19 +185672,13 @@ xref: ZFA:0001136 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0013754 ! integumentary system layer -relationship: composed_primarily_of UBERON:0001013 ! adipose tissue -relationship: composed_primarily_of UBERON:0011825 {source="FMA-modified"} ! loose connective tissue -relationship: deep_to UBERON:0002067 ! dermis +relationship: BSPO:0000107 UBERON:0002067 ! dermis +relationship: BSPO:0000108 UBERON:0001015 ! musculature relationship: part_of UBERON:0002199 {source="ZFA"} ! integument -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: superficial_to UBERON:0001015 ! musculature -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg" xsd:anyURI -property_value: UBPROP:0000001 "A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells. Le Guellec et al, 2004.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001136", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells[FMA:70544]." xsd:string {source="FMA:70544"} -property_value: UBPROP:0000007 "hypodermal" xsd:string -property_value: UBPROP:0000007 "subcutaneous" xsd:string -property_value: UBPROP:0000007 "subcutaneus" xsd:string -property_value: UBPROP:0000012 "BTO has 'subcutis', as part of dermis. We follow FMA in having distinct classes for hypodermis and superficial fascia, and including these as part of the non-skin intgeument." xsd:string {external_ontology="BTO"} +relationship: RO:0002473 UBERON:0001013 ! composed primarily of adipose tissue +relationship: RO:0002473 UBERON:0011825 {source="FMA-modified"} ! composed primarily of loose connective tissue +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002073 @@ -187401,13 +185708,12 @@ xref: UMLS:C0221971 {source="ncithesaurus:Hair_Follicle"} xref: VHOG:0001268 xref: Wikipedia:Hair_follicle is_a: UBERON:0036150 ! skin appendage follicle -relationship: develops_from UBERON:0005086 ! hair follicle placode relationship: overlaps UBERON:0001037 ! strand of hair relationship: part_of UBERON:0001003 {source="FMA"} ! skin epidermis relationship: part_of UBERON:0011932 {source="DOI:10.1016/j.cub.2008.12.005"} ! pilosebaceous unit -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/4/4d/Hair_follicle-en.svg" xsd:anyURI -property_value: UBPROP:0000003 "The earliest reliable record of hair is found in a fossil of the Paleocene period, in which the structure of hair cuticles is preserved. Its appearance suggests that the complicated structure of the hair follicle, closely similar to that of present-day mammals, had already appeared at this time.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001268", ontology="VHOG", source="ISBN:978-4431998051 Morioka K, Hair follicle: differentiation under the electron microscope, An atlas (2005) p.3", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0005086 ! develops from hair follicle placode +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/4/4d/Hair_follicle-en.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002074 @@ -187425,9 +185731,10 @@ xref: NCIT:C33543 xref: SCTID:361359004 xref: UMLS:C0221961 {source="ncithesaurus:Shaft_of_the_Hair"} is_a: UBERON:0000021 ! cutaneous appendage +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001037 {source="DOI:10.1016/j.cub.2008.12.005"} ! strand of hair -property_value: editor_note "TODO - add distinct subclasses for coat hair vs vibrissa hair" xsd:string -property_value: editor_note "TODO - check definition of trichocyte in CL" xsd:string +property_value: IAO:0000116 "TODO - add distinct subclasses for coat hair vs vibrissa hair" xsd:string +property_value: IAO:0000116 "TODO - check definition of trichocyte in CL" xsd:string [Term] id: UBERON:0002075 @@ -187458,10 +185765,8 @@ xref: Wikipedia:Viscus xref: XAO:0003034 is_a: UBERON:0005177 ! trunk region element intersection_of: UBERON:0000062 ! organ -intersection_of: located_in UBERON:0002323 ! coelemic cavity lumen -relationship: located_in UBERON:0002323 ! coelemic cavity lumen -property_value: UBPROP:0000001 "An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010386", ontology="AAO", source="BTO:0001491"} -property_value: UBPROP:0000012 "general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs." xsd:string {external_ontology="FMA"} +intersection_of: RO:0001025 UBERON:0002323 ! located in coelemic cavity lumen +relationship: RO:0001025 UBERON:0002323 ! located in coelemic cavity lumen [Term] id: UBERON:0002076 @@ -187474,6 +185779,7 @@ xref: EMAPA:35388 xref: FMA:70933 xref: MA:0000157 is_a: UBERON:0000119 ! cell layer +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000119 ! cell layer intersection_of: bounding_layer_of UBERON:0002074 ! hair shaft relationship: bounding_layer_of UBERON:0002074 ! hair shaft @@ -187495,6 +185801,7 @@ xref: FMA:70934 xref: MA:0000156 xref: SCTID:318832008 is_a: UBERON:0001851 ! cortex +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0001851 ! cortex intersection_of: part_of UBERON:0001037 ! strand of hair relationship: part_of UBERON:0002074 ! hair shaft @@ -187529,15 +185836,12 @@ xref: XAO:0003192 is_a: UBERON:0002081 ! cardiac atrium is_a: UBERON:0035554 ! right cardiac chamber intersection_of: UBERON:0002081 ! cardiac atrium -intersection_of: in_right_side_of UBERON:0000948 ! heart -relationship: connected_to UBERON:0004537 ! blood vasculature -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI -property_value: UBPROP:0000001 "Right cardiac chamber which is continuous with the superior vena cava and inferior vena cava.[FMA]" xsd:string {source="FMA:7096"} -property_value: UBPROP:0000003 "The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000328", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +intersection_of: BSPO:0000121 UBERON:0000948 ! heart +relationship: RO:0002170 UBERON:0004537 ! connected to blood vasculature +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002079 @@ -187569,16 +185873,12 @@ xref: XAO:0003191 is_a: UBERON:0002081 ! cardiac atrium is_a: UBERON:0035553 ! left cardiac chamber intersection_of: UBERON:0002081 ! cardiac atrium -intersection_of: in_left_side_of UBERON:0000948 ! heart -relationship: connected_to UBERON:0004537 ! blood vasculature -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI -property_value: UBPROP:0000001 "Left cardiac chamber which is continuous with the pulmonary venous trunk.[FMA]" xsd:string {source="FMA:7097"} -property_value: UBPROP:0000001 "The chamber of the heart that receives blood from the lungs[XAO:EJS]." xsd:string {source="XAO:EJS"} -property_value: UBPROP:0000003 "The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000369", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +intersection_of: BSPO:0000120 UBERON:0000948 ! heart +relationship: RO:0002170 UBERON:0004537 ! connected to blood vasculature +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002080 @@ -187608,17 +185908,14 @@ xref: Wikipedia:Right_ventricle is_a: UBERON:0002082 ! cardiac ventricle is_a: UBERON:0035554 ! right cardiac chamber intersection_of: UBERON:0002082 ! cardiac ventricle -intersection_of: in_right_side_of UBERON:0000948 ! heart -relationship: connected_to UBERON:0004537 ! blood vasculature -relationship: develops_from UBERON:0009889 {source="PMID:17276708"} ! secondary heart field -relationship: has_developmental_contribution_from UBERON:0004706 {source="cjm"} ! bulbus cordis -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI -property_value: UBPROP:0000001 "The muscular chamber on the right and in front of the left ventricle. It generally receives venous blood from the right atrium and conveys it into the pulmonary artery. [(1988)_Dorian_AF, Amsterdam, Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B._Anatomy, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier's_Encyclopaedic_Dictionary_of_Medicine][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000717", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI -property_value: UBPROP:0000008 "In mammals continuous with the pulmonary arteries" xsd:string +intersection_of: BSPO:0000121 UBERON:0000948 ! heart +relationship: RO:0002170 UBERON:0004537 ! connected to blood vasculature +relationship: RO:0002202 UBERON:0009889 {source="PMID:17276708"} ! develops from secondary heart field +relationship: RO:0002254 UBERON:0004706 {source="cjm"} ! has developmental contribution from bulbus cordis +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002081 @@ -187656,13 +185953,9 @@ xref: UMLS:C0018792 {source="ncithesaurus:Cardiac_Atrium"} xref: VHOG:0000175 xref: Wikipedia:Heart_atrium xref: ZFA:0000471 -is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004151 ! cardiac chamber -relationship: contributes_to_morphology_of UBERON:0000948 ! heart -relationship: immediate_transformation_of UBERON:0010227 ! future cardiac atrium -property_value: UBPROP:0000001 "One of four heart chambers.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000471", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "One of two chambers of the heart which receive blood from the veins and forces it by muscular contration to the ventricle.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010246", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000175", ontology="VHOG", source="ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.428", source="http://bgee.unil.ch/"} +relationship: RO:0002433 UBERON:0000948 ! contributes to morphology of heart +relationship: RO:0002495 UBERON:0010227 ! immediate transformation of future cardiac atrium [Term] id: UBERON:0002082 @@ -187699,13 +185992,9 @@ xref: VHOG:0000435 xref: Wikipedia:Ventricle_(heart) xref: XAO:0003193 xref: ZFA:0000009 -is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004151 ! cardiac chamber -relationship: contributes_to_morphology_of UBERON:0000948 ! heart -relationship: immediate_transformation_of UBERON:0006283 {source="Bgee:AN"} ! future cardiac ventricle -property_value: UBPROP:0000001 "A chamber of the heart that receives blood from one or more atria and pumps it by muscular contraction into the arteries.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010249", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "One of four heart chambers.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000009", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...)[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000435", ontology="VHOG", source="ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.428", source="http://bgee.unil.ch/"} +relationship: RO:0002433 UBERON:0000948 ! contributes to morphology of heart +relationship: RO:0002495 UBERON:0006283 {source="Bgee:AN"} ! immediate transformation of future cardiac ventricle [Term] id: UBERON:0002084 @@ -187735,18 +186024,14 @@ xref: Wikipedia:Left_ventricle is_a: UBERON:0002082 ! cardiac ventricle is_a: UBERON:0035553 ! left cardiac chamber intersection_of: UBERON:0002082 ! cardiac ventricle -intersection_of: in_left_side_of UBERON:0000948 ! heart -relationship: connected_to UBERON:0004537 ! blood vasculature -relationship: continuous_with UBERON:0000947 ! aorta -relationship: develops_from UBERON:0004140 {source="GO"} ! primary heart field -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI -property_value: UBPROP:0000001 "Thick-walled muscular chamber constituting the left border and apex of the heart. It receives oxygenated blood from the left atrium through the mitral orifice and send it off into the aorta. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000718", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "The vertebrate heart initially forms as a tube from a population of precursor cells termed the first heart field (FHF). Cells from the adjacent second heart field (SHF) are then progressively added to the developing heart. In avian and mammalian hearts, the FHF contributes mainly to the left ventricle, whereas the SHF gives rise to the outflow tract and large portions of the right ventricle and atria. Both fields arise from common mesodermal progenitors, although the detailed lineage relationships between FHF and SHF remain uncertain.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000718", ontology="VHOG", source="DOI:10.1126/science.1190181 Stolfi A, Gainous TB, Young JJ, Mori A, Levine M, Christiaen L, Early chordate origins of the vertebrate second heart field. Science (2010)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI -property_value: UBPROP:0000008 "In mammals continuous with aorta" xsd:string +intersection_of: BSPO:0000120 UBERON:0000948 ! heart +relationship: RO:0002150 UBERON:0000947 ! continuous with aorta +relationship: RO:0002170 UBERON:0004537 ! connected to blood vasculature +relationship: RO:0002202 UBERON:0004140 {source="GO"} ! develops from primary heart field +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002085 @@ -187775,9 +186060,7 @@ intersection_of: adjacent_to UBERON:0002078 ! right cardiac atrium intersection_of: adjacent_to UBERON:0002079 ! left cardiac atrium relationship: adjacent_to UBERON:0002078 ! right cardiac atrium relationship: adjacent_to UBERON:0002079 ! left cardiac atrium -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/6c/Gray493.png" xsd:anyURI -property_value: UBPROP:0000001 "The partition separating the right and left atria of the heart. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000385", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/interatrial+septum"} -property_value: UBPROP:0000003 "The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000385", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620", source="http://bgee.unil.ch/"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6c/Gray493.png" xsd:anyURI [Term] id: UBERON:0002089 @@ -187790,10 +186073,10 @@ xref: FMA:71213 xref: MA:0002238 is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein -intersection_of: drains UBERON:0001112 ! latissimus dorsi muscle -relationship: drains UBERON:0001112 ! latissimus dorsi muscle -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: tributary_of UBERON:0000985 {source="FMA/obol"} ! axillary vein +intersection_of: RO:0002179 UBERON:0001112 ! drains latissimus dorsi muscle +relationship: RO:0002179 UBERON:0001112 ! drains latissimus dorsi muscle +relationship: RO:0002376 UBERON:0000985 {source="FMA/obol"} ! tributary of axillary vein +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002090 @@ -187811,12 +186094,10 @@ xref: AAO:0000034 xref: EFO:0000942 xref: EHDAA2:0000161 xref: EHDAA:5049 -xref: EMAPA:17214 xref: EMAPA:37721 {source="MA:th"} xref: FMA:71221 xref: MA:0002986 xref: MAT:0000148 -xref: MESH:D013131 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: MIAA:0000148 xref: TAO:0000317 xref: VHOG:0000317 @@ -187824,14 +186105,10 @@ xref: VSAO:0000093 xref: XAO:0003073 xref: ZFA:0000317 is_a: UBERON:0010912 ! subdivision of skeleton -relationship: develops_from UBERON:0003089 ! sclerotome relationship: part_of UBERON:0005944 ! axial skeleton plus cranial skeleton relationship: part_of UBERON:0011138 ! postcranial axial skeletal system +relationship: RO:0002202 UBERON:0003089 ! develops from sclerotome property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" xsd:anyURI -property_value: UBPROP:0000001 "Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000093", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000034", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000001 "The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000317", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000317", ontology="VHOG", source="DOI:10.1186/1742-9994-8-4 Schilling N, Evolution of the axial system in craniates: morphology and function of the perivertebral musculature. Frontiers in Zoology (2011)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0002091 @@ -187857,22 +186134,17 @@ xref: MIAA:0000278 xref: NCIT:C49477 xref: SCTID:322050006 xref: UMLS:C0222646 {source="ncithesaurus:Appendicular_Skeleton"} -xref: VHOG:0001666 xref: VSAO:0000076 xref: Wikipedia:Appendicular_skeleton xref: XAO:0003166 is_a: UBERON:0010912 ! subdivision of skeleton -relationship: contributes_to_morphology_of UBERON:0001434 ! skeletal system -relationship: only_in_taxon NCBITaxon:7776 ! Gnathostomata relationship: overlaps UBERON:0000026 ! appendage relationship: part_of UBERON:0011249 ! appendicular skeletal system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/7c/Appendicular_skeleton_diagram.svg" xsd:anyURI +relationship: RO:0002160 NCBITaxon:7776 ! only in taxon Gnathostomata +relationship: RO:0002433 UBERON:0001434 ! contributes to morphology of skeletal system +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7c/Appendicular_skeleton_diagram.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton" xsd:anyURI -property_value: UBPROP:0000001 "Skeletal subdivision consisting of all the skeletal elements in the pectoral and pelvic appendage complexes.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000076", ontology="VSAO", source="PSPUB:0000170", source="https://orcid.org/0000-0002-6601-2165"} -property_value: UBPROP:0000001 "Skeletal system that consists of the paired fins (pectoral or pelvic fins).[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000027", ontology="TAO", source="TAO:wd"} -property_value: UBPROP:0000001 "The pectoral and pelvic girdles, which articulate with the axial skeleton, together with their associated limbs, the forelimbs and hind limbs, form the appendicular skeleton.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000747", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000012 "ontologies differ in whether they treat the term appendicular skeleton as being the entire set of bones in the limbs, or whether the fore and hind limbs/fins are treated as seperate appendicular skeletons. Here we follow FMA, and treat the appendicular skeleton as the sum total of skeletal elements in the organism (this is evidenced by the fact that in FMA, skeleton of left/right upper/lower limb is part_of a appendicular skeleton, and subtypes of 'subdivision of appendicular skeleton'). We have separate classes such as 'skeleton of limb', and 'skeleton of hindlimb' for the 4 parts of the appendicular skeleton. In future the ZFA/TAO classes may be moved." xsd:string {external_ontology="FMA"} [Term] id: UBERON:0002092 @@ -187885,7 +186157,6 @@ synonym: "dura mater cranialis" EXACT OMO:0003011 [FMA:71236, FMA:TA] synonym: "dura mater encephali" EXACT [] synonym: "dura mater of brain" EXACT [] xref: EMAPA:32668 -xref: EV:0100313 xref: FMA:71236 xref: MA:0000815 xref: NCIT:C49332 @@ -187896,8 +186167,6 @@ is_a: UBERON:0002363 ! dura mater is_a: UBERON:0003547 ! brain meninx intersection_of: UBERON:0002363 ! dura mater intersection_of: part_of UBERON:0000955 ! brain -property_value: UBPROP:0000001 "The outermost and densest membrane of the three mammalian meninges covering the brain and spinal cord. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000270", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000270", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639", source="http://bgee.unil.ch/"} [Term] id: UBERON:0002093 @@ -187921,8 +186190,6 @@ is_a: UBERON:0002363 ! dura mater is_a: UBERON:0003292 ! meninx of spinal cord intersection_of: UBERON:0002363 ! dura mater intersection_of: part_of UBERON:0002240 ! spinal cord -property_value: UBPROP:0000001 "The outermost and densest membrane of the three mammalian meninges covering the brain and spinal cord. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000411", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000411", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639", source="http://bgee.unil.ch/"} [Term] id: UBERON:0002094 @@ -187961,13 +186228,10 @@ intersection_of: adjacent_to UBERON:0002080 ! heart right ventricle intersection_of: adjacent_to UBERON:0002084 ! heart left ventricle relationship: adjacent_to UBERON:0002080 ! heart right ventricle relationship: adjacent_to UBERON:0002084 ! heart left ventricle -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray498.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI -property_value: UBPROP:0000001 "The partition separating the right and left ventricles of the heart. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000386", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/interventricular+septum"} -property_value: UBPROP:0000003 "The two most progressive vertebrate classes, the birds and mammals, have completed the ventricular septum and at long last have completely separated the two blood streams along the length of the major heart chambers. This development has obviously been brought about independently in the two cases, since mammals and birds have evolved independently from primitive reptiles.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000386", ontology="VHOG", source="ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.430", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000011 "involves the recruitment of myocardial cells as well as of non- muscular mesenchymal cells (Kaufman and Bard, 1999)" xsd:string {source="ISBN:0124020607"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray498.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002095 @@ -187991,10 +186255,8 @@ xref: SCTID:362707009 xref: UMLS:C0025474 {source="ncithesaurus:Mesentery"} xref: Wikipedia:Mesentery#Mesentery_.28general.29 is_a: UBERON:0000042 ! serous membrane -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray1038.png" xsd:anyURI -property_value: UBPROP:0000007 "mesenteric" xsd:string -property_value: UBPROP:0000012 "in Uberon, this term is used in the generic sense, not necessarily restricted to the peritoneum, consistent with FMA. WP: 'In anatomy, the mesentery is the double layer of peritoneum that suspends the jejunum and ileum from the posterior wall of the abdomen. Its meaning, however, is frequently extended to include double layers of peritoneum connecting various components of the abdominal cavity.'. TODO - check. Consider FMA:259286 - Region of mesentery." xsd:string {external_ontology="FMA"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray1038.png" xsd:anyURI [Term] id: UBERON:0002097 @@ -188029,17 +186291,16 @@ xref: Wikipedia:Skin xref: XAO:0000023 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000062 ! organ -relationship: composed_primarily_of UBERON:0000014 ! zone of skin -relationship: develops_from UBERON:0011272 {source="Wikipathways:WP2062"} ! embryonic skin basal layer +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0002199 ! integument -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Skin.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_M_Skin.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Skin.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.3/3d-vh-f-skin.glb" xsd:anyURI -property_value: IAO:0000232 "consider 'integumentary system' for invertebrates" xsd:string -property_value: UBPROP:0000012 "MA uses the term skin to refer to what is called here: zone of skin" xsd:string {external_ontology="FMA"} +relationship: RO:0002202 UBERON:0011272 {source="Wikipathways:WP2062"} ! develops from embryonic skin basal layer +relationship: RO:0002473 UBERON:0000014 ! composed primarily of zone of skin +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Skin.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_M_Skin.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Skin.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.3/3d-vh-f-skin.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002099 @@ -188062,13 +186323,12 @@ xref: NCIT:C49485 xref: SCTID:362014000 xref: UMLS:C0018819 {source="ncithesaurus:Heart_Septum"} is_a: UBERON:0003037 ! septum +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0003037 ! septum intersection_of: part_of UBERON:0000948 ! heart relationship: adjacent_to UBERON:0004151 ! cardiac chamber -relationship: contributes_to_morphology_of UBERON:0000948 ! heart relationship: part_of UBERON:0000948 ! heart -property_value: UBPROP:0000008 "'Terrestrial vertebrates have divided hearts in which septae separate the oxygenated and deoxygenated blood within the pulmonary and systemic circulations'" xsd:string -property_value: UBPROP:0000012 "in GO, septum morphogenesis is part of cardiac chamber morphogenesis; need to add axioms to infer this" xsd:string {external_ontology="GO"} +relationship: RO:0002433 UBERON:0000948 ! contributes to morphology of heart [Term] id: UBERON:0002100 @@ -188107,10 +186367,6 @@ disjoint_from: UBERON:0002464 ! nerve trunk relationship: has_part UBERON:0000915 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! thoracic segment of trunk relationship: has_part UBERON:0000916 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! abdomen relationship: part_of UBERON:0013702 ! body proper -property_value: RO:0002171 UBERON:0000026 {exceptions="ZFA", source="https://github.com/obophenotype/uberon/issues/378", status="pending"} -property_value: RO:0002171 UBERON:0000033 -property_value: UBPROP:0000001 "Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010339", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001115", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0002101 @@ -188140,7 +186396,6 @@ xref: GAID:36 xref: galen:Extremity xref: MA:0000007 xref: MAT:0000090 -xref: MESH:D005121 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: MIAA:0000090 xref: NCIT:C12429 xref: SCTID:243996003 @@ -188149,15 +186404,13 @@ xref: VHOG:0000336 xref: VSAO:0000121 xref: Wikipedia:Limb xref: XAO:0003027 -is_a: UBERON:0004708 {specialization_within="Sarcopterygians"} ! paired limb/fin +is_a: UBERON:0004708 ! paired limb/fin intersection_of: UBERON:0000475 ! organism subdivision -intersection_of: has_skeleton UBERON:0004381 ! skeleton of limb -relationship: develops_from UBERON:0004347 ! limb bud -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: has_skeleton UBERON:0004381 ! skeleton of limb -relationship: only_in_taxon NCBITaxon:32523 {note="extends to stem tetrapods such as Eusthenopteron"} ! Tetrapoda -property_value: UBPROP:0000001 "Organism subdivision that has as its parts the jointed appendages used for locomotion and manipulation.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010336", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000336", ontology="VHOG", source="ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268", source="http://bgee.unil.ch/"} +intersection_of: RO:0002551 UBERON:0004381 ! has skeleton skeleton of limb +relationship: RO:0002160 NCBITaxon:32523 {note="extends to stem tetrapods such as Eusthenopteron"} ! only in taxon Tetrapoda +relationship: RO:0002202 UBERON:0004347 ! develops from limb bud +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +relationship: RO:0002551 UBERON:0004381 ! has skeleton skeleton of limb [Term] id: UBERON:0002102 @@ -188206,14 +186459,10 @@ is_a: UBERON:0002101 ! limb is_a: UBERON:0004710 ! pectoral appendage intersection_of: UBERON:0002101 ! limb intersection_of: part_of UBERON:0010708 ! pectoral complex -relationship: anterior_to UBERON:0002103 ! hindlimb -relationship: develops_from UBERON:0005417 ! forelimb bud -relationship: has_skeleton UBERON:0001440 ! forelimb skeleton +relationship: BSPO:0000096 UBERON:0002103 ! hindlimb relationship: part_of UBERON:0000153 ! anterior region of body -property_value: IAO:0000232 "Note distinction between arm and forelimb. hand is part of forelimb, but not part of arm" xsd:string -property_value: RO:0002171 UBERON:0002103 -property_value: UBPROP:0000001 "Upper limb, which connects the manus with the pectoral girdle.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000205", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000012 "note that this corresponds to FMA:'free upper limb' (a limb segment), NOT FMA:'upper limb'. Both MA and FMA consider shoulder (and shoulder bones) part of upper limb" xsd:string {external_ontology="FMA"} +relationship: RO:0002202 UBERON:0005417 ! develops from forelimb bud +relationship: RO:0002551 UBERON:0001440 ! has skeleton forelimb skeleton [Term] id: UBERON:0002103 @@ -188263,14 +186512,10 @@ is_a: UBERON:0002101 ! limb is_a: UBERON:0004709 ! pelvic appendage intersection_of: UBERON:0002101 ! limb intersection_of: part_of UBERON:0010709 ! pelvic complex -relationship: develops_from UBERON:0005418 ! hindlimb bud -relationship: has_skeleton UBERON:0001441 ! hindlimb skeleton relationship: part_of UBERON:0000154 ! posterior region of body -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/dc/Gray1239.png" xsd:anyURI -property_value: UBPROP:0000001 "Lower limb, which connects the pes with the pelvic girdle.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000219", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000003 "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000337", ontology="VHOG", source="ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "crural" xsd:string -property_value: UBPROP:0000012 "note that this corresponds to FMA:'free lower limb' (a limb segment), NOT 'lower limb'. Both MA and FMA consider shoulder (and shoulder bones) part of upper limb. Note that AAO class probably refers to skeleton" xsd:string {external_ontology="FMA"} +relationship: RO:0002202 UBERON:0005418 ! develops from hindlimb bud +relationship: RO:0002551 UBERON:0001441 ! has skeleton hindlimb skeleton +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/dc/Gray1239.png" xsd:anyURI [Term] id: UBERON:0002104 @@ -188298,7 +186543,6 @@ xref: XAO:0003198 xref: ZFA:0001127 is_a: UBERON:0001032 ! sensory system relationship: capable_of_part_of GO:0007601 ! visual perception -property_value: UBPROP:0000001 "The sensory system used for sight.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000632", ontology="AAO", source="AAO:EJS"} [Term] id: UBERON:0002105 @@ -188315,7 +186559,6 @@ synonym: "auditory/vestibular system" RELATED [] synonym: "vestibuloauditory system" EXACT [] synonym: "vestibuloauditory system" RELATED [] xref: AAO:0000631 -xref: EMAPA:36002 xref: EMAPA:37985 {source="MA:th"} xref: FMA:78500 xref: TAO:0001138 @@ -188323,8 +186566,7 @@ xref: XAO:0003195 xref: ZFA:0001138 is_a: UBERON:0001032 ! sensory system relationship: capable_of_part_of GO:0007605 ! sensory perception of sound -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/d2/Anatomy_of_the_Human_Ear.svg" xsd:anyURI -property_value: UBPROP:0000001 "The sensory system used for balance and hearing.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000631", ontology="AAO", source="AAO:EJS"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d2/Anatomy_of_the_Human_Ear.svg" xsd:anyURI [Term] id: UBERON:0002106 @@ -188361,22 +186603,14 @@ xref: XAO:0000328 xref: ZFA:0000436 is_a: UBERON:0004177 ! hemopoietic organ is_a: UBERON:0005057 ! immune organ -is_a: UBERON:0013765 ! digestive system element is_a: UBERON:0017672 ! abdominal viscera -relationship: develops_from UBERON:0006293 ! spleen primordium -relationship: only_in_taxon NCBITaxon:7776 {source="multiple sources - true spleen appear in jawed vertebrates"} ! Gnathostomata -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Spleen.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Spleen.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Spleen.glb" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/d/d6/Illu_spleen.jpg" xsd:anyURI -property_value: UBPROP:0000001 "An organ involved in red blood cell filtration and immune response.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010395", ontology="AAO", source="AAO:BMZ"} -property_value: UBPROP:0000003 "With the advent of clonal selection, the accumulation and segregation of T and B cells in specialized organs for antigen presentation became necessary, and indeed the spleen is found in all jawed vertebrates, but not in agnathans or invertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000120", ontology="VHOG", source="ISBN:978-0781765190 Paul WE, Fundamental Immunology (2008) p.94", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "lienal" xsd:string -property_value: UBPROP:0000007 "splenic" xsd:string -property_value: UBPROP:0000008 "In humans, it is located in the left upper quadrant of the abdomen. It removes old red blood cells and holds a reserve in case of hemorrhagic shock, especially in animals like horses (not in humans), while recycling iron" xsd:string -property_value: UBPROP:0000008 "Neither hagfish nor lampreys possess what might be considered a discrete and condensed spleen. Hagfish possess dispersed lymphoid tissue within the submucosa of the intestine (96) associated with the portal vein (97), whereas lymphoid tissue is associated with the typhlosole portion of the intestine in lampreys (96)" xsd:string {source="PMID:20959416"} -property_value: UBPROP:0000009 "It synthesizes antibodies in its white pulp and removes, from blood and lymph node circulation, antibody-coated bacteria along with antibody-coated blood cells" xsd:string +relationship: RO:0002160 NCBITaxon:7776 {source="multiple sources - true spleen appear in jawed vertebrates"} ! only in taxon Gnathostomata +relationship: RO:0002202 UBERON:0006293 ! develops from spleen primordium +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Spleen.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Spleen.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Spleen.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/d6/Illu_spleen.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002107 @@ -188419,29 +186653,21 @@ is_a: UBERON:0002365 {source="BTO", source="EHDAA2", source="GO-def"} ! exocrine is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0005172 ! abdomen element is_a: UBERON:0006925 ! digestive system gland -relationship: contributes_to_morphology_of UBERON:0002423 ! hepatobiliary system -relationship: develops_from UBERON:0004161 {source="EHDAA2"} ! septum transversum -relationship: develops_from UBERON:0008836 {source="http://www.stembook.org/node/512"} ! liver bud relationship: has_part UBERON:0004647 ! liver lobule -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: overlaps UBERON:0002405 {source="ZFA-weakened"} ! immune system relationship: part_of UBERON:0002423 {source="ZFA"} ! hepatobiliary system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: produces UBERON:0001970 ! bile +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002202 UBERON:0004161 {source="EHDAA2"} ! develops from septum transversum +relationship: RO:0002202 UBERON:0008836 {source="http://www.stembook.org/node/512"} ! develops from liver bud +relationship: RO:0002433 UBERON:0002423 ! contributes to morphology of hepatobiliary system relationship: site_of GO:0002384 ! hepatic immune response relationship: site_of GO:0005978 ! glycogen biosynthetic process relationship: site_of GO:0005980 ! glycogen catabolic process -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Liver.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Liver.glb" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/6/64/Leber_Schaf.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Organ which secretes bile and participates in formation of certain blood proteins.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010111", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000002 "relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010111", ontology="AAO"} -property_value: UBPROP:0000003 "All vertebrates possess a liver (reference 1); Later in craniate evolution, an anterior gill arch was transformed into jaws, and many new types of feeding subsequently evolved.(...) A liver evolved that, among its many functions, stores considerable energy as glycogen or lipid (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000257", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.526, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "hepatic" xsd:string -property_value: UBPROP:0000008 "An organ sometimes referred to as a liver is found associated with the digestive tract of the primitive chordate Amphioxus. However, this is an enzyme secreting gland, not a metabolic organ, and it is unclear how truly homologous it is to the vertebrate liver. The zebrafish liver differs from the mammalian liver in that the hepatocytes are not clearly organized in cords or lobules and the typical portal triads are not apparent. In addition, the zebrafish liver does not have Kuppfer cells. Furthermore, a clear distinction can be made between the male and female liver in the adult zebrafish. The female hepatocytes are very basophilic (Figure 15c) as a result of the production of vitellogenin (Van der Ven et al. 2003)." xsd:string -property_value: UBPROP:0000008 "The liver is found in all vertebrates, and is typically the largest visceral organ. Its form varies considerably in different species, and is largely determined by the shape and arrangement of the surrounding organs. Nonetheless, in most species it is divided into right and left lobes; exceptions to this general rule include snakes, where the shape of the body necessitates a simple cigar-like form. The internal structure of the liver is broadly similar in all vertebrates." xsd:string -property_value: UBPROP:0000009 "secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]." xsd:string -property_value: UBPROP:0000012 "Only ZFA considers this part_of immune system - we weaken this to an overlaps relation, as in general it's only a subset of cells that have clear immune function." xsd:string {external_ontology="ZFA"} +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Liver.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Liver.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/64/Leber_Schaf.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002108 @@ -188481,17 +186707,15 @@ xref: VHOG:0000055 xref: Wikipedia:Small_intestine xref: XAO:0000130 xref: ZFA:0001323 -is_a: UBERON:0004921 {order="2", source="cjm"} ! subdivision of digestive tract +is_a: UBERON:0004921 ! subdivision of digestive tract is_a: UBERON:0013765 ! digestive system element -relationship: contributes_to_morphology_of UBERON:0000160 ! intestine -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0000160 ! intestine -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/82/Stomach_colon_rectum_diagram.svg" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Small_Intestine.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Small_Intestine.glb" xsd:anyURI -property_value: UBPROP:0000001 "The terminal region of the mid intestine is comprised of specialized enterocytes that appear to play a role in mucosal immunity. Wallace et al, 2005.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001323", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000055", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.566", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002433 UBERON:0000160 ! contributes to morphology of intestine +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/82/Stomach_colon_rectum_diagram.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Small_Intestine.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Small_Intestine.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002109 @@ -188508,12 +186732,11 @@ xref: FMA:72005 xref: Wikipedia:Nares is_a: UBERON:0034925 ! anatomical collection intersection_of: UBERON:0034925 ! anatomical collection -intersection_of: has_member UBERON:0000003 {cardinality="2"} ! naris -relationship: has_member UBERON:0000003 ! naris +intersection_of: RO:0002351 UBERON:0000003 {cardinality="2"} ! has member naris relationship: has_part UBERON:0000003 ! naris -relationship: never_in_taxon NCBITaxon:7745 {source="http://webs.lander.edu/rsfox/invertebrates/ammocoetes.html"} relationship: part_of UBERON:0000004 ! nose -property_value: UBPROP:0000012 "this is a 'set of anatomical planes' in FMA" xsd:string {external_ontology="FMA"} +relationship: RO:0002351 UBERON:0000003 ! has member naris +property_value: RO:0002161 NCBITaxon:7745 {source="http://webs.lander.edu/rsfox/invertebrates/ammocoetes.html"} [Term] id: UBERON:0002110 @@ -188556,19 +186779,15 @@ is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0013765 ! digestive system element is_a: UBERON:0017672 ! abdominal viscera is_a: UBERON:0018707 {source="BTO"} ! bladder organ -relationship: contributes_to_morphology_of UBERON:0001173 ! biliary tree -relationship: develops_from UBERON:0004912 ! biliary bud -relationship: develops_from UBERON:0006242 {evidence="definitional"} ! gallbladder primordium -relationship: never_in_taxon NCBITaxon:10114 {source="ISBN:9780120749034"} -relationship: never_in_taxon NCBITaxon:8801 {source="GOC:mr", source="ISBN:9781840761122"} -relationship: never_in_taxon NCBITaxon:8930 {source="GOC:mr", source="ISBN:9781840761122"} relationship: part_of UBERON:0002294 ! biliary system -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/b/b1/GallbladderAnatomy-en.svg" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/f/f4/Abdomal_organs.svg" xsd:anyURI -property_value: UBPROP:0000001 "Membranous muscular sac in which the bile from the liver remains stored until it is required. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000221", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000001 "Organ attached to the liver which stores bile and empties into the duodenum via the bile duct as needed for digestion.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010114", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000002 "relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010114", ontology="AAO"} -property_value: UBPROP:0000003 "The presence of a gallbladder appears to be a primitive trait. It is found in most fish and all adult reptiles and amphibians and has been well conserved in mammals, for the most part.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000221", ontology="VHOG", source="DOI:10.1002/(SICI)1097-0029(19970915)38:6<571::AID-JEMT3>3.0.CO;2-I Oldham-Ott CK, Gilloteaux J, Comparative morphology of the gallbladder and biliary tract in vertebrates: Variation in structure, homology in function and gallstones. Microscopy research and technique (1997)", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0004912 ! develops from biliary bud +relationship: RO:0002202 UBERON:0006242 ! develops from gallbladder primordium +relationship: RO:0002433 UBERON:0001173 ! contributes to morphology of biliary tree +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/b/b1/GallbladderAnatomy-en.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/f/f4/Abdomal_organs.svg" xsd:anyURI +property_value: RO:0002161 NCBITaxon:10114 {source="ISBN:9780120749034"} +property_value: RO:0002161 NCBITaxon:8801 {source="GOC:mr", source="ISBN:9781840761122"} +property_value: RO:0002161 NCBITaxon:8930 {source="GOC:mr", source="ISBN:9781840761122"} [Term] id: UBERON:0002111 @@ -188629,14 +186848,14 @@ xref: MA:0001573 is_a: UBERON:0001135 ! smooth muscle tissue intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0001043 ! esophagus -relationship: contributes_to_morphology_of UBERON:0001043 ! esophagus relationship: part_of UBERON:0003832 ! esophagus muscle +relationship: RO:0002433 UBERON:0001043 ! contributes to morphology of esophagus [Term] id: UBERON:0002113 name: kidney namespace: uberon -def: "A paired organ of the urinary tract which has the production of urine as its primary function." [http://anatomy.uams.edu/anatomyhtml/kidney.html, Wikipedia:Kidney] +def: "A paired organ of the urinary tract that produces urine and maintains bodily fluid homeostasis, blood pressure, pH levels, red blood cell production and skeleton mineralization." [http://anatomy.uams.edu/anatomyhtml/kidney.html, https://www.kidney.org/kidneydisease/top-5-jobs-kidneys-do, PMID:25140012, PMID:35003210, Wikipedia:Kidney] subset: efo_slim subset: human_reference_atlas subset: major_organ @@ -188648,35 +186867,26 @@ synonym: "reniculate kidney" NARROW SENSU [Wikipedia:Reniculate_kidney] xref: AAO:0000250 xref: BTO:0000671 xref: CALOHA:TS-0510 -xref: EFO:0000929 -xref: EMAPA:17373 -xref: EV:0100096 -xref: FMA:7203 xref: GAID:423 xref: galen:Kidney -xref: MA:0000368 xref: MAT:0000119 xref: MESH:D007668 xref: MIAA:0000119 -xref: NCIT:C12415 -xref: SCTID:181414000 xref: UMLS:C0022646 {source="ncithesaurus:Kidney"} xref: Wikipedia:Kidney xref: XAO:0003267 is_a: UBERON:0000489 ! cavitated compound organ is_a: UBERON:0005172 ! abdomen element is_a: UBERON:0015212 ! lateral structure -relationship: contributes_to_morphology_of UBERON:0001008 ! renal system -relationship: develops_from UBERON:0003918 {evidence="definitional"} ! kidney mesenchyme -relationship: develops_from UBERON:0005095 ! kidney rudiment -relationship: in_lateral_side_of UBERON:0000468 ! multicellular organism -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: BSPO:0000126 UBERON:0000468 ! multicellular organism relationship: part_of UBERON:0011143 {source="FMA"} ! upper urinary tract -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: RO:0002171 UBERON:0000160 -property_value: UBPROP:0000001 "One of either of a pair of structures lying on either side of the dorsal aorta in which fluid balance is regulated and waste is excreted out in the form of urine.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000250", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000007 "renal" xsd:string -property_value: UBPROP:0000202 FMA:264815 +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002202 UBERON:0003918 ! develops from kidney mesenchyme +relationship: RO:0002202 UBERON:0005095 ! develops from kidney rudiment +relationship: RO:0002433 UBERON:0001008 ! contributes to morphology of renal system +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7655-4833 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2804-127X +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002114 @@ -188709,20 +186919,16 @@ xref: UMLS:C0013303 {source="ncithesaurus:Duodenum"} xref: VHOG:0000052 xref: Wikipedia:Duodenum xref: XAO:0000236 -is_a: UBERON:0004921 {order="3", source="cjm"} ! subdivision of digestive tract -relationship: continuous_with UBERON:0001166 ! pylorus -relationship: contributes_to_morphology_of UBERON:0002108 ! small intestine -relationship: never_in_taxon NCBITaxon:7955 {source="ZFA:0000348"} +is_a: UBERON:0004921 ! subdivision of digestive tract +relationship: BSPO:0001106 UBERON:0002108 ! small intestine relationship: part_of UBERON:0002108 ! small intestine -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: proximalmost_part_of UBERON:0002108 ! small intestine -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b3/Tractus_intestinalis_duodenum.svg" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Small_Intestine.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Small_Intestine.glb" xsd:anyURI -property_value: UBPROP:0000001 "The fixed portion of the small intestine deeply lodged in the posterior wall of the abdomen and extending from the pylorus to the beginning of the jejunum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000052", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "duodenal" xsd:string -property_value: UBPROP:0000008 "In fish, the divisions of the small intestine are not as clear, and the terms anterior intestine or proximal intestine may be used instead of duodenum." xsd:string {scope="NCBITaxon:32443", source="Wikipedia:Duodenum"} -property_value: UBPROP:0000008 "In humans, the duodenum is a hollow jointed tube about 10-15 inches (25-38 centimetres) long connecting the stomach to the jejunum. It begins with the duodenal bulb and ends at the ligament of Treitz." xsd:string {scope="NCBITaxon:9606", source="Wikipedia:Duodenum"} +relationship: RO:0002150 UBERON:0001166 ! continuous with pylorus +relationship: RO:0002433 UBERON:0002108 ! contributes to morphology of small intestine +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b3/Tractus_intestinalis_duodenum.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Small_Intestine.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Small_Intestine.glb" xsd:anyURI +property_value: RO:0002161 NCBITaxon:7955 {source="ZFA:0000348"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002115 @@ -188753,18 +186959,15 @@ xref: SCTID:181248002 xref: UMLS:C0022378 {source="ncithesaurus:Jejunum"} xref: VHOG:0000053 xref: Wikipedia:Jejunum -is_a: UBERON:0004921 {order="3", source="cjm"} ! subdivision of digestive tract -relationship: contributes_to_morphology_of UBERON:0002108 ! small intestine -relationship: develops_from UBERON:0001045 {source="Wikipedia"} ! midgut +is_a: UBERON:0004921 ! subdivision of digestive tract relationship: part_of UBERON:0002108 ! small intestine -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/3d/Illu_small_intestine.jpg" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Small_Intestine.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Small_Intestine.glb" xsd:anyURI -property_value: editor_note "TODO consider ZFA:0001323 mid intestine, see also small intestine" xsd:string -property_value: UBPROP:0000001 "The first two fifth of the small intestine beyond the duodenum. It extends from the end of the duodenum to the ileum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000053", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "jejunal" xsd:string -property_value: UBPROP:0000008 "The jejunum is the middle section of the small intestine in most higher vertebrates, including mammals, reptiles, and birds. In fish, the divisions of the small intestine are not as clear and the terms middle intestine or mid-gut may be used instead of jejunum.[Wikipedia:Jejunum]" xsd:string +relationship: RO:0002202 UBERON:0001045 {source="Wikipedia"} ! develops from midgut +relationship: RO:0002433 UBERON:0002108 ! contributes to morphology of small intestine +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3d/Illu_small_intestine.jpg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Small_Intestine.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Small_Intestine.glb" xsd:anyURI +property_value: IAO:0000116 "TODO consider ZFA:0001323 mid intestine, see also small intestine" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002116 @@ -188798,17 +187001,14 @@ xref: UMLS:C0020885 {source="ncithesaurus:Ileum"} xref: VHOG:0000647 xref: Wikipedia:Ileum xref: XAO:0000237 -is_a: UBERON:0004921 {order="3", source="cjm"} ! subdivision of digestive tract -relationship: contributes_to_morphology_of UBERON:0002108 ! small intestine +is_a: UBERON:0004921 ! subdivision of digestive tract relationship: part_of UBERON:0002108 ! small intestine -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/3d/Illu_small_intestine.jpg" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Small_Intestine.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Small_Intestine.glb" xsd:anyURI -property_value: editor_note "TODO consider ZFA:0000706 posterior intestine, see also colon" xsd:string -property_value: UBPROP:0000003 "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000647", ontology="VHOG", source="ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "ileal" xsd:string -property_value: UBPROP:0000008 "The ileum is the final section of the small intestine in most higher vertebrates, including mammals, reptiles, and birds. In fish, the divisions of the small intestine are not as clear and the terms posterior intestine or distal intestine may be used instead of ileum.[Wikipedia:Ileum]" xsd:string +relationship: RO:0002433 UBERON:0002108 ! contributes to morphology of small intestine +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3d/Illu_small_intestine.jpg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Small_Intestine.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Small_Intestine.glb" xsd:anyURI +property_value: IAO:0000116 "TODO consider ZFA:0000706 posterior intestine, see also colon" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002118 @@ -188822,10 +187022,10 @@ xref: NCIT:C33487 xref: SCTID:280123002 xref: UMLS:C0227873 {source="ncithesaurus:Right_Ovary"} is_a: UBERON:0000992 ! ovary +is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0000992 ! ovary -intersection_of: in_right_side_of UBERON:0000468 ! multicellular organism -relationship: in_right_side_of UBERON:0000468 ! multicellular organism -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +intersection_of: BSPO:0000121 UBERON:0000468 ! multicellular organism +relationship: BSPO:0000121 UBERON:0000468 ! multicellular organism [Term] id: UBERON:0002119 @@ -188839,11 +187039,10 @@ xref: NCIT:C32969 xref: SCTID:280124008 xref: UMLS:C0227874 {source="ncithesaurus:Left_Ovary"} is_a: UBERON:0000992 ! ovary +is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0000992 ! ovary -intersection_of: in_left_side_of UBERON:0000468 ! multicellular organism -relationship: in_left_side_of UBERON:0000468 ! multicellular organism -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI -property_value: UBPROP:0000008 "In some elasmobranchs, the left ovary does not mature, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo" xsd:string {source="Wikipedia:Ovary#In_other_animals"} +intersection_of: BSPO:0000120 UBERON:0000468 ! multicellular organism +relationship: BSPO:0000120 UBERON:0000468 ! multicellular organism [Term] id: UBERON:0002120 @@ -188867,7 +187066,6 @@ xref: EHDAA:1017 xref: EMAPA:16579 xref: FMA:72170 xref: MAT:0000117 -xref: MESH:D060910 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: MIAA:0000117 xref: NCIT:C34280 xref: SCTID:308804007 @@ -188880,14 +187078,9 @@ xref: ZFA:0000151 is_a: UBERON:0002113 {source="GO"} ! kidney is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005423 ! developing anatomical structure -relationship: develops_from UBERON:0005721 {source="ZFA"} ! pronephric mesoderm -relationship: develops_from UBERON:0005754 ! rostral part of nephrogenic cord -relationship: located_in UBERON:0003887 {source="OG"} ! intraembryonic coelom -property_value: UBPROP:0000001 "A kidney formed of nephric tubules arising in the anterior region of the nephric ridge; forms only as a transient embryonic structure. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.748][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000037", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000001 "Organ that serves as a transient kidney, providing osmoregulation during early developmental stages and then degenerating during metamorphosis.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011089", ontology="AAO", source="XAO:curator"} -property_value: UBPROP:0000001 "The embryonic kidney, present at the level of the third somite, is composed of two glomeruli fused at the midline, two pronephric tubules, and paired bilateral pronephric ducts that modify the composition of the blood filtrate before delivering it to the cloaca for excretion.Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000151", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000037", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.637", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "pronephric" xsd:string +relationship: RO:0001025 UBERON:0003887 {source="OG"} ! located in intraembryonic coelom +relationship: RO:0002202 UBERON:0005721 {source="ZFA"} ! develops from pronephric mesoderm +relationship: RO:0002202 UBERON:0005754 ! develops from rostral part of nephrogenic cord [Term] id: UBERON:0002122 @@ -188904,11 +187097,12 @@ xref: MA:0000766 xref: NCIT:C33770 xref: SCTID:188181003 xref: UMLS:C0229945 {source="ncithesaurus:Thymic_Capsule"} +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0003893 ! capsule intersection_of: UBERON:0003893 ! capsule intersection_of: bounding_layer_of UBERON:0002370 ! thymus relationship: bounding_layer_of UBERON:0002370 ! thymus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002123 @@ -188928,6 +187122,7 @@ xref: SCTID:188262003 xref: UMLS:C0229948 {source="ncithesaurus:Thymus_Cortex"} xref: Wikipedia:Thymus#Cortex is_a: PR:000050567 ! protein-containing material entity +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0001851 ! cortex intersection_of: UBERON:0001851 ! cortex intersection_of: part_of UBERON:0002370 ! thymus @@ -188935,9 +187130,8 @@ relationship: capable_of_part_of GO:0045058 ! T cell selection relationship: has_part CL:0000542 ! lymphocyte relationship: has_part CL:0002293 ! epithelial cell of thymus relationship: part_of UBERON:0002370 ! thymus -relationship: present_in_taxon NCBITaxon:7955 {source="DOI:10.1177/0192623311409597"} -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000010 "Histologically, the thymus can be divided into a central medulla and a peripheral cortex which is surrounded by an outer capsule. The cortex and medulla play different roles in the development of T cells. Cells in the thymus can be divided into thymic stromal cells and cells of hematopoietic origin[WP]" xsd:string +property_value: RO:0002175 NCBITaxon:7955 {source="DOI:10.1177/0192623311409597"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002124 @@ -188959,12 +187153,13 @@ xref: NCIT:C33775 xref: SCTID:188344009 xref: UMLS:C0229949 {source="ncithesaurus:Thymus_Medulla"} xref: Wikipedia:Thymus#Medulla +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0000958 ! medulla of organ intersection_of: UBERON:0000958 ! medulla of organ intersection_of: part_of UBERON:0002370 ! thymus relationship: part_of UBERON:0002370 ! thymus -relationship: present_in_taxon NCBITaxon:7955 {source="DOI:10.1177/0192623311409597"} -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:7955 {source="DOI:10.1177/0192623311409597"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002125 @@ -188982,17 +187177,16 @@ xref: NCIT:C33772 xref: SCTID:187882006 xref: UMLS:C1522462 {source="ncithesaurus:Thymic_Lobule"} is_a: PR:000050567 ! protein-containing material entity +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0009911 ! lobule intersection_of: UBERON:0009911 ! lobule intersection_of: part_of UBERON:0002370 ! thymus -relationship: contributes_to_morphology_of UBERON:0002370 ! thymus relationship: has_part CL:0000235 ! macrophage relationship: has_part CL:0000432 ! reticular cell relationship: has_part CL:0000542 ! lymphocyte relationship: part_of UBERON:0005483 ! thymus lobe -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000008 "in the mouse, the lobes of the thymus are not subdivided into lobules but only in the central medulla and a peripheral cortex (i.e. there is no distinct sublobulation). In humans, the two thymus lobes are composed of many lobules of various sizes which contain follicles, each comprising a medulla and a cortex. in the rat, the thymus is partially subdivided into lobules separated by thin bands of connective tissue which are continuous with the thin connective tissue capsule.[MP]" xsd:string -property_value: UBPROP:0000010 "Lymphocytes, reticular cells and macrophages are found in the lobules" xsd:string +relationship: RO:0002433 UBERON:0002370 ! contributes to morphology of thymus +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002128 @@ -189015,7 +187209,6 @@ xref: FMA:72247 xref: HBA:9177 xref: MA:0001026 xref: MBA:398 -xref: MESH:D065832 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: neuronames:569 {source="BIRNLEX:1307"} xref: UMLS:C0175427 {source="BIRNLEX:1307"} xref: VHOG:0001381 @@ -189024,12 +187217,7 @@ is_a: UBERON:0007245 ! nuclear complex of neuraxis is_a: UBERON:0019263 ! gray matter of hindbrain relationship: part_of UBERON:0003023 {source="NIFSTD"} ! pontine tegmentum relationship: part_of UBERON:0016490 ! auditory system -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/46/Gray713.png" xsd:anyURI -property_value: RO:0002171 UBERON:0002597 {source="ABA"} -property_value: RO:0002171 UBERON:0006840 {source="ABA"} -property_value: RO:0002171 UBERON:0007634 {source="ABA"} -property_value: UBPROP:0000008 "In mice, the superior olivary nucleus is a small cylindrical mass on the dorsal surface of the lateral part of the trapezoid body of the pons, and it is situated immediately above the inferior olivary nucleus. It receives projections from the cochlear nucleus and thus is involved in the perception of sound[GO:0021718]" xsd:string -property_value: UBPROP:0000008 "The SOC displays a significant interspecies variation, being largest in bats and rodents and smaller in primates." xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/46/Gray713.png" xsd:anyURI [Term] id: UBERON:0002129 @@ -189069,12 +187257,10 @@ xref: VHOG:0001597 xref: Wikipedia:Cerebellar_cortex is_a: UBERON:0019263 ! gray matter of hindbrain relationship: capable_of_part_of GO:0007613 {source="Wikipedia"} ! memory -relationship: contributes_to_morphology_of UBERON:0002037 ! cerebellum relationship: part_of UBERON:0002037 ! cerebellum -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/a/a7/Cerebellum_NIH.png" xsd:anyURI -property_value: RO:0002171 UBERON:0002130 {source="ABA"} -property_value: UBPROP:0000001 "The cerebellar cortex is a thin mantle of gray matter that covers the surface of each cerebral hemisphere. It has a characteristic morphology with convolutions (gyri) and crevices (sulci) that have specific functions. Six layers of nerve cells and the nerve pathways that connect them comprise the cerebellar cortex. Together, these regions are responsible for the processes of conscious thought, perception, emotion and memory as well as advanced motor function[GO][GO:0021695]." xsd:string {source="GO:0021695"} +relationship: RO:0002433 UBERON:0002037 ! contributes to morphology of cerebellum +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/a/a7/Cerebellum_NIH.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002139 @@ -189113,10 +187299,9 @@ is_a: UBERON:0010134 {source="MA"} ! secretory circumventricular organ relationship: has_part CL:0000065 ! ependymal cell relationship: part_of UBERON:0002314 {source="MA"} ! midbrain tectum relationship: part_of UBERON:0011357 ! Reissner's fiber -relationship: present_in_taxon NCBITaxon:7742 {source="multiple"} ! Vertebrata relationship: produces PR:000015658 ! SCO-spondin -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/d7/Gray715.png" xsd:anyURI -property_value: IAO:0000232 "Hypendymal cells being part of the subcommissural organ is not axiomatized as it is rare in non-mammals. Consider using GCIs if this axiom needs to be added." xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d7/Gray715.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:7742 {source="multiple"} [Term] id: UBERON:0002148 @@ -189167,13 +187352,9 @@ is_a: UBERON:0006331 ! brainstem nucleus is_a: UBERON:0009662 ! hindbrain nucleus is_a: UBERON:8440015 ! noradrenergic cell groups relationship: capable_of GO:0048243 ! norepinephrine secretion -relationship: part_of UBERON:0003023 {notes="check ZFA", source="NIFSTD"} ! pontine tegmentum -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/77/Gray709.png" xsd:anyURI -property_value: editor_note "TODO - check ZFA/pons. also GO says part of dorsorostral pons" xsd:string -property_value: RO:0002171 UBERON:0002047 {source="ABA"} -property_value: RO:0002171 UBERON:0002267 {source="ABA"} -property_value: RO:0002171 UBERON:0002587 {source="ABA"} -property_value: RO:0002171 UBERON:0003004 {source="ABA"} +relationship: part_of UBERON:0003023 ! pontine tegmentum +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/77/Gray709.png" xsd:anyURI +property_value: IAO:0000116 "TODO - check ZFA/pons. also GO says part of dorsorostral pons" xsd:string [Term] id: UBERON:0002149 @@ -189201,21 +187382,11 @@ xref: SCTID:369028007 xref: UMLS:C0175447 {source="BIRNLEX:1131"} xref: Wikipedia:Superior_salivatory_nucleus is_a: UBERON:0000126 ! cranial nerve nucleus -is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004133 ! salivatory nucleus is_a: UBERON:0007635 ! nucleus of medulla oblongata -relationship: immediate_transformation_of UBERON:0010125 {evidence="definitional"} ! future superior salivatory nucleus relationship: part_of UBERON:0003023 ! pontine tegmentum -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/6b/Gray788.png" xsd:anyURI -property_value: RO:0002171 UBERON:0002143 {source="ABA"} -property_value: RO:0002171 UBERON:0002147 {source="ABA"} -property_value: RO:0002171 UBERON:0002151 {source="ABA"} -property_value: RO:0002171 UBERON:0002633 {source="ABA"} -property_value: RO:0002171 UBERON:0002682 {source="ABA"} -property_value: RO:0002171 UBERON:0002963 {source="ABA"} -property_value: RO:0002171 UBERON:0002968 {source="ABA"} -property_value: RO:0002171 UBERON:0003011 {source="ABA"} -property_value: RO:0002171 UBERON:0007632 {source="ABA"} +relationship: RO:0002495 UBERON:0010125 ! immediate transformation of future superior salivatory nucleus +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6b/Gray788.png" xsd:anyURI [Term] id: UBERON:0002165 @@ -189255,14 +187426,10 @@ xref: Wikipedia:Endocardium xref: XAO:0000066 xref: ZFA:0001320 is_a: UBERON:0002523 ! tunica intima -is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005983 ! heart layer relationship: has_part UBERON:0005316 ! endocardial endothelium -relationship: immediate_transformation_of UBERON:0007280 {source="Bgee:AN"} ! presumptive endocardium -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/6c/Gray493.png" xsd:anyURI -property_value: UBPROP:0000001 "Layer that lines the lumen of the heart.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001320", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Part of the heart comprised of thin serous membrane, composed of endothelial tissue, that lines the interior of the heart.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010408", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "Tunica intima which has as its parts the endothelium of endocardium and the fibroelastic connective tissue that surrounds the cavity of a cardiac chamber." xsd:string {source="FMA:7280"} +relationship: RO:0002495 UBERON:0007280 {source="Bgee:AN"} ! immediate transformation of presumptive endocardium +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6c/Gray493.png" xsd:anyURI [Term] id: UBERON:0002166 @@ -189292,8 +187459,8 @@ xref: ZFA:0001614 is_a: UBERON:0002165 ! endocardium intersection_of: UBERON:0002165 ! endocardium intersection_of: part_of UBERON:0002081 ! cardiac atrium -relationship: contributes_to_morphology_of UBERON:0002081 ! cardiac atrium relationship: part_of UBERON:0002081 ! cardiac atrium +relationship: RO:0002433 UBERON:0002081 ! contributes to morphology of cardiac atrium [Term] id: UBERON:0002167 @@ -189314,13 +187481,11 @@ xref: VHOG:0000301 xref: Wikipedia:Right_lung is_a: UBERON:0002048 ! lung intersection_of: UBERON:0002048 ! lung -intersection_of: in_right_side_of UBERON:0000170 ! pair of lungs -relationship: in_right_side_of UBERON:0000170 ! pair of lungs -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/32/Gray972.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb" xsd:anyURI -property_value: UBPROP:0000003 "Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000301", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +intersection_of: BSPO:0000121 UBERON:0000170 ! pair of lungs +relationship: BSPO:0000121 UBERON:0000170 ! pair of lungs +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/32/Gray972.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb" xsd:anyURI [Term] id: UBERON:0002168 @@ -189341,13 +187506,11 @@ xref: VHOG:0000618 xref: Wikipedia:Left_lung is_a: UBERON:0002048 ! lung intersection_of: UBERON:0002048 ! lung -intersection_of: in_left_side_of UBERON:0000170 ! pair of lungs -relationship: in_left_side_of UBERON:0000170 ! pair of lungs -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/dd/Gray973.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb" xsd:anyURI -property_value: UBPROP:0000003 "Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000618", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +intersection_of: BSPO:0000120 UBERON:0000170 ! pair of lungs +relationship: BSPO:0000120 UBERON:0000170 ! pair of lungs +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/dd/Gray973.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb" xsd:anyURI [Term] id: UBERON:0002169 @@ -189373,10 +187536,10 @@ is_a: UBERON:0000117 ! respiratory tube is_a: UBERON:0007499 ! epithelial sac intersection_of: UBERON:0007499 ! epithelial sac intersection_of: part_of UBERON:0008874 ! pulmonary acinus -relationship: contributes_to_morphology_of UBERON:0008874 ! pulmonary acinus relationship: has_part UBERON:0002299 ! alveolus of lung relationship: part_of UBERON:0006524 {source="MA"} ! alveolar system relationship: part_of UBERON:0008874 {source="FMA"} ! pulmonary acinus +relationship: RO:0002433 UBERON:0008874 ! contributes to morphology of pulmonary acinus [Term] id: UBERON:0002173 @@ -189397,9 +187560,8 @@ xref: UMLS:C0391892 {source="ncithesaurus:Alveolar_Duct"} xref: Wikipedia:Alveolar_duct is_a: UBERON:0000117 ! respiratory tube relationship: part_of UBERON:0006524 ! alveolar system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/8f/Gray975.png" xsd:anyURI -property_value: UBPROP:0000008 "In human anatomy, respiratory bronchioles exists proximal to the alveolar ducts. The epithelial lining consists of smooth muscle knobs covered by nonciliated, simple cuboidal cells. The smooth muscle constricts under parasympathetic innervation and relax under sympathetic innervation" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8f/Gray975.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002180 @@ -189425,8 +187587,8 @@ xref: Wikipedia:Ventral_funiculus xref: ZFA:0000605 is_a: UBERON:0006127 ! funiculus of spinal cord is_a: UBERON:0015212 ! lateral structure -relationship: in_lateral_side_of UBERON:0002318 {source="FMA-abduced-lr"} ! white matter of spinal cord -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/dc/Medulla_spinalis_-_Section_-_English.svg" xsd:anyURI +relationship: BSPO:0000126 UBERON:0002318 {source="FMA-abduced-lr"} ! white matter of spinal cord +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/dc/Medulla_spinalis_-_Section_-_English.svg" xsd:anyURI [Term] id: UBERON:0002183 @@ -189463,9 +187625,8 @@ relationship: has_part UBERON:0001956 ! cartilage of bronchus relationship: has_part UBERON:0004242 ! bronchus smooth muscle relationship: has_part UBERON:8410043 ! bronchus submucosal gland relationship: part_of UBERON:0000101 {source="FMA"} ! lobe of lung -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Illu_quiz_lung05.jpg" xsd:anyURI -property_value: UBPROP:0000010 "They have relatively large lumens that are lined by respiratory epithelium. There is a smooth muscle layer below the epithelium arranged as two ribbons of muscle that spiral in opposite directions. This smooth muscle layer contains seromucous glands. Irregularly arranged plates of hyaline cartilage surround the smooth muscle. These plates give structural support to the bronchus and maintain the patency of the lumen." xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Illu_quiz_lung05.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002184 @@ -189496,11 +187657,11 @@ relationship: has_part UBERON:0004883 ! lung mesenchyme relationship: has_part UBERON:8410043 ! bronchus submucosal gland relationship: overlaps UBERON:8600017 ! bronchopulmonary segment relationship: part_of UBERON:0000101 {source="FMA"} ! lobe of lung -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: proximally_connected_to UBERON:0002183 ! lobar bronchus -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Illu_quiz_lung05.jpg" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Illu_quiz_lung05.jpg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002185 @@ -189533,16 +187694,13 @@ xref: VHOG:0000262 xref: Wikipedia:Bronchus xref: XAO:0000121 is_a: UBERON:0000117 ! respiratory tube -relationship: located_in UBERON:0002224 ! thoracic cavity -relationship: never_in_taxon NCBITaxon:8507 {source="Wikipedia"} relationship: part_of UBERON:0007196 ! tracheobronchial tree -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/18/Respiratory_system_complete_numbered.svg" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb" xsd:anyURI -property_value: UBPROP:0000001 "Each of the two primary divisions of the trachea leading respectively into the right and the left lung. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000262", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "bronchial" xsd:string -property_value: UBPROP:0000008 "In humans, the main bronchus is histologically identical to trachea; 2ary and 3ary bronchi are not; epithelium becomes simple columnar, goblet cell number decreases, elastic fibers in lamina propria increases, distribution more uniform. Muscular layer between mucosa and submucosa appears. cartilage rings become discontinuous plates connected by fibrous connective tissue" xsd:string +relationship: RO:0001025 UBERON:0002224 ! located in thoracic cavity +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/18/Respiratory_system_complete_numbered.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb" xsd:anyURI +property_value: RO:0002161 NCBITaxon:8507 {source="Wikipedia"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002186 @@ -189563,19 +187721,15 @@ xref: EHDAA:8221 xref: EMAPA:32697 xref: FMA:7410 xref: MA:0000422 -xref: MESH:D055745 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C12684 xref: SCTID:278982001 xref: UMLS:C0006270 {source="ncithesaurus:Bronchiole"} xref: VHOG:0000675 xref: Wikipedia:Bronchiole is_a: UBERON:0000117 ! respiratory tube -relationship: branching_part_of UBERON:0007196 {source="FMA"} ! tracheobronchial tree relationship: part_of UBERON:0002048 {source="MA"} ! lung -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png" xsd:anyURI -property_value: UBPROP:0000007 "bronchiolar" xsd:string -property_value: UBPROP:0000010 "lacks submucosa and cartilage plates; they have 3 layers: mucosa, muscular layer and outer layer" xsd:string {source="ISBN:0123813611"} -property_value: UBPROP:0000012 "In FMA2 and FMA3, lobular bronchiole is an exact synonym of bronchiole; however, there are two distinct terms for the corresponding epithelium." xsd:string {external_ontology="FMA"} +relationship: RO:0002380 UBERON:0007196 {source="FMA"} ! branching part of tracheobronchial tree +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png" xsd:anyURI [Term] id: UBERON:0002187 @@ -189600,8 +187754,8 @@ is_a: UBERON:0002186 ! bronchiole relationship: distally_connected_to UBERON:0002188 ! respiratory bronchiole relationship: distally_connected_to UBERON:0008874 ! pulmonary acinus relationship: part_of UBERON:0010369 ! secondary pulmonary lobule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002188 @@ -189622,13 +187776,12 @@ xref: SCTID:128517006 xref: UMLS:C1261270 {source="ncithesaurus:Respiratory_Bronchiole"} xref: Wikipedia:Respiratory_bronchiole is_a: UBERON:0002186 ! bronchiole -relationship: contributes_to_morphology_of UBERON:0008874 ! pulmonary acinus relationship: distally_connected_to UBERON:0002173 ! pulmonary alveolar duct relationship: part_of UBERON:0008874 {source="ISBN:0123813611"} ! pulmonary acinus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: proximally_connected_to UBERON:0002187 ! terminal bronchiole -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png" xsd:anyURI -property_value: UBPROP:0000008 "mice have few or none of these structures, with the terminal bronchioles transitioning directly to the alveolary ducts" xsd:string {source="ISBN:0123813611"} +relationship: RO:0002433 UBERON:0008874 ! contributes to morphology of pulmonary acinus +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002190 @@ -189650,14 +187803,13 @@ xref: BTO:0004042 xref: EMAPA:35829 xref: FMA:74315 xref: MA:0000473 -xref: MESH:D015434 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} is_a: UBERON:0001013 ! adipose tissue +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0001013 ! adipose tissue intersection_of: part_of UBERON:0002072 ! hypodermis -relationship: contributes_to_morphology_of UBERON:0002072 ! hypodermis relationship: part_of UBERON:0002072 ! hypodermis -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000001 "the superficial portion of the subcutaneous tissue which is specialized for fat storage[MP:0011156]" xsd:string {source="MP:0011156"} +relationship: RO:0002433 UBERON:0002072 ! contributes to morphology of hypodermis +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002191 @@ -189693,14 +187845,7 @@ xref: Wikipedia:Subiculum is_a: UBERON:0002616 ! regional part of brain relationship: capable_of_part_of GO:0007613 {source="Wikipedia"} ! memory relationship: part_of UBERON:0002421 {source="NIFSTD"} ! hippocampal formation -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/9/99/Hippocampus.gif" xsd:anyURI -property_value: RO:0002171 UBERON:0001953 {source="ABA"} -property_value: RO:0002171 UBERON:0002728 {source="ABA"} -property_value: RO:0002171 UBERON:0004683 {source="ABA"} -property_value: UBPROP:0000007 "subicular" xsd:string -property_value: UBPROP:0000009 "The pyramidal neurons in the subiculum exhibit transitions between two modes of action potential output: bursting and single spiking. The transitions between these two modes is thought to be important for routing information out of the hippocampus. It is the site responsible for ictal activity in some cases of human epilepsy. It has also been implicated in working memory and drug addiction.[Wikipedia:Subiculum]" xsd:string -property_value: UBPROP:0000012 "In ABA SUB is part of the retrohippocampal region, along with the entorhinal area. this is in the hippocampal formation but not the hippocampal region" xsd:string {external_ontology="ABA"} -property_value: UBPROP:0000012 "in DHBA subicular cortex is divided into subiculum, prosubiculum and supracallosal subiculum" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/9/99/Hippocampus.gif" xsd:anyURI [Term] id: UBERON:0002193 @@ -189716,7 +187861,7 @@ xref: EMAPA:18765 xref: FMA:74562 xref: MA:0000013 is_a: UBERON:0000467 {source="MA"} ! anatomical system -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria [Term] id: UBERON:0002194 @@ -189738,12 +187883,11 @@ is_a: UBERON:0003893 ! capsule intersection_of: UBERON:0003893 ! capsule intersection_of: bounding_layer_of UBERON:0000029 ! lymph node relationship: bounding_layer_of UBERON:0000029 ! lymph node -relationship: composed_primarily_of UBERON:0002384 ! connective tissue -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_F_Lymph_Node.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_M_Lymph_Node.glb" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/9/92/Lymphknoten_(Schwein).jpg" xsd:anyURI -property_value: UBPROP:0000008 "from its internal surface are given off a number of membranous processes or trabeculae, consisting, in man, of connective tissue, with a small admixture of plain muscle fibers; but in many of the lower animals composed almost entirely of involuntary muscle[WP]" xsd:string +relationship: RO:0002473 UBERON:0002384 ! composed primarily of connective tissue +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_F_Lymph_Node.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_M_Lymph_Node.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/9/92/Lymphknoten_(Schwein).jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002195 @@ -189765,8 +187909,8 @@ is_a: UBERON:0000440 ! trabecula intersection_of: UBERON:0000440 ! trabecula intersection_of: part_of UBERON:0000029 ! lymph node relationship: part_of UBERON:0000029 ! lymph node -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b3/Gray598.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b3/Gray598.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002196 @@ -189819,22 +187963,17 @@ xref: Wikipedia:Adenohypophysis xref: ZFA:0001282 is_a: UBERON:0000064 ! organ part is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest disjoint_from: UBERON:0002198 {source="lexical"} ! neurohypophysis -relationship: contributes_to_morphology_of UBERON:0000007 ! pituitary gland -relationship: develops_from UBERON:0005356 {gci_relation="part_of", gci_filler="NCBITaxon:32523", exception="teleost", source="NCBIBook:NBK53175"} ! Rathke's pouch -relationship: develops_from UBERON:0009122 {source="NCBIBook:NBK53175", source="ZFA"} ! adenohypophyseal placode relationship: has_part CL:0000438 ! luteinizing hormone secreting cell relationship: has_part CL:0000439 {source="ZFA"} ! prolactin secreting cell relationship: has_part CL:0000467 {source="ZFA"} ! adrenocorticotropic hormone secreting cell relationship: has_part CL:0002312 ! somatotroph -relationship: only_in_taxon NCBITaxon:7742 {source="PMID:19084529"} ! Vertebrata relationship: part_of UBERON:0000007 ! pituitary gland -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray1181.png" xsd:anyURI -property_value: UBPROP:0000001 "Region of the pituitary gland derived from the buccal protrusion consisting of three regions.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010540", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "The anterior lobe of the hypophysis (pituitary gland). This lobe contains cells that produce prolactin, growth hormone, thyroid-stimulating hormone, follicle-stimulating hormone and proopiomelanocortin. In contrast to mamalian vertebrates, the adenohypophysis remains in a subepithelial position and there exists no equivalent of Rathke's pouch in zebrafish. Herzog et al, 2004.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001282", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. An infundibulum grows ventrally from the diencephalon of the brain, and Rathke's pouch extends dorsally from the roof of the developing mouth, or stomodaeum. The infundibulum remains connected to the floor of the diencephalon, which becomes the hypothalamus, and gives rise to the part of the gland known as the neurohypophysis. (...) Rathke's pouch loses its connection with the stomodaeum in most adult vertebrates and gives rise to the rest of the gland, the adenohypophysis. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000141", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510 and Figure 15-5", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "In contrast to mammalian vertebrates, the adenohypophysis remains in a subepithelial position and there exists no equivalent of Rathke's pouch in zebrafish" xsd:string {source="ZFA"} -property_value: UBPROP:0000008 "While in most basal fish and tetrapods the adenohypophyseal anlagen invaginates to form Rathke's pouch, in teleost fish the adenohypophyseal placode does not invaginate but rather maintains its initial organization forming a solid structure in the head[NCBIBook:NBK53175]." xsd:string +relationship: RO:0002160 NCBITaxon:7742 {source="PMID:19084529"} ! only in taxon Vertebrata +relationship: RO:0002202 UBERON:0009122 {source="NCBIBook:NBK53175", source="ZFA"} ! develops from adenohypophyseal placode +relationship: RO:0002433 UBERON:0000007 ! contributes to morphology of pituitary gland +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray1181.png" xsd:anyURI [Term] id: UBERON:0002198 @@ -189890,19 +188029,15 @@ xref: VHOG:0000142 xref: Wikipedia:Neurohypophysis xref: ZFA:0001271 is_a: UBERON:0003296 ! gland of diencephalon -is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010134 {source="MA"} ! secretory circumventricular organ relationship: capable_of GO:0001992 {source="Wikipedia"} ! regulation of systemic arterial blood pressure by vasopressin relationship: capable_of GO:0030103 {source="Wikipedia"} ! vasopressin secretion -relationship: develops_from UBERON:0002346 ! neurectoderm -relationship: only_in_taxon NCBITaxon:7742 {source="PMID:19084529"} ! Vertebrata relationship: part_of UBERON:0000007 {source="ZFA"} ! pituitary gland -relationship: present_in_taxon NCBITaxon:117569 {source="Ariens, p. 1192"} -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b9/Pituitary_gland_representation.PNG" xsd:anyURI -property_value: editor_note "request magnocellular cell from CL. Request oxytocin secretion from GO. Notes: 'The hypophysis or pituitary gland is derived, in part from an ectodermal outpocketing of the stomodeum (Rathke's Pouch) and in part from the floor of the diencephalon'" xsd:string {source="http://syllabus.med.unc.edu/courseware/embryo_images/"} -property_value: UBPROP:0000001 "The infundibular part of the pituitary gland consisting of two regions.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010537", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. An infundibulum grows ventrally from the diencephalon of the brain, and Rathke's pouch extends dorsally from the roof of the developing mouth, or stomodaeum. The infundibulum remains connected to the floor of the diencephalon, which becomes the hypothalamus, and gives rise to the part of the gland known as the neurohypophysis. (...) Rathke's pouch loses its connection with the stomodaeum in most adult vertebrates and gives rise to the rest of the gland, the adenohypophysis. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000142", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510 and Figure 15-5", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "todo - resolve EMAPA and EHDAA2 models, include future neurohypophysis (TS15-19)? relationship to infundibular recess of 3rd ventricle (TS15-19)" xsd:string {external_ontology="EMAPA"} +relationship: RO:0002160 NCBITaxon:7742 {source="PMID:19084529"} ! only in taxon Vertebrata +relationship: RO:0002202 UBERON:0002346 ! develops from neurectoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b9/Pituitary_gland_representation.PNG" xsd:anyURI +property_value: IAO:0000116 "request magnocellular cell from CL. Request oxytocin secretion from GO. Notes: 'The hypophysis or pituitary gland is derived, in part from an ectodermal outpocketing of the stomodeum (Rathke's Pouch) and in part from the floor of the diencephalon'" xsd:string {source="http://syllabus.med.unc.edu/courseware/embryo_images/"} +property_value: RO:0002175 NCBITaxon:117569 {source="Ariens, p. 1192"} [Term] id: UBERON:0002199 @@ -189937,15 +188072,9 @@ is_a: UBERON:0011216 {source="FMA"} ! organ system subdivision relationship: bounding_layer_of UBERON:0000468 ! multicellular organism relationship: has_part UBERON:0002072 ! hypodermis relationship: has_part UBERON:0002097 ! skin of body -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0002416 {source="FMA"} ! integumental system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: IAO:0000232 "in FMA intergument = skin+superficial fascia(hypodermis), skin=dermis+epidermis+hair_nail. Note that the definition provided here excludes the more general sense of the term 'integument' used in invertebrates; consider 'integumental system'. Note that the VSAO class appears to include adnexa by its definition." xsd:string -property_value: UBPROP:0000001 "Anatomical system that protects the body from damage, comprising the skin and its appendages.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000239", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000001 "Surface structure that is the outer protective covering of the body.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000029", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "The outer protective barrier that separates the animal from its aquatic environment. Le Guellec et al, 2004.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000368", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000007 "integumental" xsd:string -property_value: UBPROP:0000007 "integumentary" xsd:string +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002200 @@ -190012,11 +188141,12 @@ xref: MA:0001860 xref: NCIT:C49307 xref: SCTID:4419000 xref: UMLS:C0225586 {source="ncithesaurus:Trachea_Submucosa"} +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0004777 ! respiratory system submucosa intersection_of: UBERON:0000009 ! submucosa intersection_of: part_of UBERON:0003126 ! trachea relationship: part_of UBERON:0003126 ! trachea -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002203 @@ -190040,12 +188170,11 @@ is_a: UBERON:0002200 ! vasculature of head is_a: UBERON:0006876 ! vasculature of organ intersection_of: UBERON:0002049 ! vasculature intersection_of: part_of UBERON:0000019 ! camera-type eye -relationship: develops_from UBERON:0003314 {source="ISBN:0781772214"} ! eye mesenchyme relationship: part_of UBERON:0000019 ! camera-type eye -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI -property_value: UBPROP:0000012 "not part of the eye in ZFA. Note this changed to a blood vessel in ZFA" xsd:string {external_ontology="ZFA"} +relationship: RO:0002202 UBERON:0003314 {source="ISBN:0781772214"} ! develops from eye mesenchyme +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002204 @@ -190079,13 +188208,10 @@ disjoint_from: UBERON:0002423 ! hepatobiliary system disjoint_from: UBERON:0004456 ! entire sense organ system disjoint_from: UBERON:8450002 ! excretory system relationship: capable_of_part_of GO:0040011 ! locomotion -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: has_developmental_contribution_from UBERON:0000926 {notes="check ctenophore"} ! mesoderm relationship: has_part UBERON:0000383 ! musculature of body relationship: has_part UBERON:0001434 ! skeletal system -property_value: UBPROP:0000001 "Anatomical system that provides locomotion and physical support to the organism.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010546", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001275", ontology="VHOG", source="DOI:10.1002/jez.b.21246 Shearman RM, Burke AC, The lateral somitic frontier in ontogeny and phylogeny. Journal of Experimental Zoology (2009)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "musculoskeletal" xsd:string +relationship: RO:0002254 UBERON:0000926 ! has developmental contribution from mesoderm +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage [Term] id: UBERON:0002206 @@ -190126,16 +188252,13 @@ xref: UMLS:C1305759 {source="BIRNLEX:865"} xref: Wikipedia:Mammillary_body xref: ZFA:0000334 is_a: UBERON:0000064 ! organ part -relationship: contributes_to_morphology_of UBERON:0001894 ! diencephalon +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0002272 {source="ABA"} ! medial zone of hypothalamus relationship: part_of UBERON:0002770 {source="GO definition"} ! posterior hypothalamic region -relationship: present_in_taxon NCBITaxon:117569 {source="Hardisty, p. 320-1"} -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/97/Gray1180.png" xsd:anyURI -property_value: RO:0002171 UBERON:0001935 {source="ABA"} -property_value: RO:0002171 UBERON:0002035 {source="ABA"} -property_value: RO:0002171 UBERON:0002634 {source="ABA"} -property_value: RO:0002171 UBERON:0002706 {source="ABA"} +relationship: RO:0002433 UBERON:0001894 ! contributes to morphology of diencephalon +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/97/Gray1180.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:117569 {source="Hardisty, p. 320-1"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002209 @@ -190157,7 +188280,6 @@ xref: Wikipedia:Fibrous_joint xref: ZFA:0005156 is_a: UBERON:0011134 {source="FMA"} ! nonsynovial joint relationship: has_part CL:0002320 {source="AEO"} ! connective tissue cell -property_value: UBPROP:0000001 "A joint where fibrous tissue such as ligament connects two calcified tissues.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005156", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0002210 @@ -190191,9 +188313,7 @@ xref: Wikipedia:Nerve_root is_a: UBERON:0000122 ! neuron projection bundle relationship: extends_fibers_into UBERON:0001017 ! central nervous system relationship: extends_fibers_into UBERON:0001021 ! nerve -property_value: editor_note "We consider cranial nerve roots to be primarily CNS structures, but model spinal nerve roots as PNS structures, due to the existence of ganglia on the roots." xsd:string -property_value: UBPROP:0000001 "The continuation of the neurite bundle and associated glia of a nerve, inside the central nervous system[FBbt:00007602, FBC:DOS]." xsd:string {source="FBbt:00007602, FBC:DOS"} -property_value: UBPROP:0000012 "FMA has 'central zone of nerve' which is the superclass of cranial nerve tracts, which the FMA sometimes calls roots" xsd:string {external_ontology="FMA"} +property_value: IAO:0000116 "We consider cranial nerve roots to be primarily CNS structures, but model spinal nerve roots as PNS structures, due to the existence of ganglia on the roots." xsd:string [Term] id: UBERON:0002212 @@ -190229,8 +188349,8 @@ xref: ZFA:0007000 is_a: UBERON:0000054 ! macula intersection_of: UBERON:0000054 ! macula intersection_of: part_of UBERON:0001854 ! saccule of membranous labyrinth -relationship: contributes_to_morphology_of UBERON:0001854 ! saccule of membranous labyrinth relationship: part_of UBERON:0001854 ! saccule of membranous labyrinth +relationship: RO:0002433 UBERON:0001854 ! contributes to morphology of saccule of membranous labyrinth [Term] id: UBERON:0002213 @@ -190250,8 +188370,8 @@ xref: Wikipedia:Cartilaginous_joint xref: ZFA:0005155 is_a: UBERON:0011134 {source="FMA"} ! nonsynovial joint intersection_of: UBERON:0011134 ! nonsynovial joint -intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue -relationship: composed_primarily_of UBERON:0002418 ! cartilage tissue +intersection_of: RO:0002473 UBERON:0002418 ! composed primarily of cartilage tissue +relationship: RO:0002473 UBERON:0002418 ! composed primarily of cartilage tissue [Term] id: UBERON:0002214 @@ -190287,9 +188407,9 @@ xref: ZFA:0000030 is_a: UBERON:0000054 ! macula intersection_of: UBERON:0000054 ! macula intersection_of: part_of UBERON:0001853 ! utricle of membranous labyrinth -relationship: contributes_to_morphology_of UBERON:0001853 ! utricle of membranous labyrinth relationship: part_of UBERON:0001853 ! utricle of membranous labyrinth -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/cb/Bigotolith.jpg" xsd:anyURI +relationship: RO:0002433 UBERON:0001853 ! contributes to morphology of utricle of membranous labyrinth +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/cb/Bigotolith.jpg" xsd:anyURI [Term] id: UBERON:0002215 @@ -190310,11 +188430,11 @@ is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002209 ! fibrous joint is_a: UBERON:0002213 ! cartilaginous joint intersection_of: UBERON:0002209 ! fibrous joint -intersection_of: composed_primarily_of UBERON:0001994 ! hyaline cartilage tissue -relationship: composed_primarily_of UBERON:0001994 ! hyaline cartilage tissue -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/76/Gray297.png" xsd:anyURI -property_value: editor_note "consider adding link to hyaline cartilage" xsd:string -property_value: editor_note "WP considers epiphyseal plates as subtypes of this" xsd:string +intersection_of: RO:0002473 UBERON:0001994 ! composed primarily of hyaline cartilage tissue +relationship: RO:0002473 UBERON:0001994 ! composed primarily of hyaline cartilage tissue +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/76/Gray297.png" xsd:anyURI +property_value: IAO:0000116 "consider adding link to hyaline cartilage" xsd:string +property_value: IAO:0000116 "WP considers epiphyseal plates as subtypes of this" xsd:string [Term] id: UBERON:0002216 @@ -190330,8 +188450,8 @@ xref: SCTID:1584001 xref: Wikipedia:Symphysis is_a: UBERON:0002209 {source="MA"} ! fibrous joint is_a: UBERON:0002213 {source="FMA"} ! cartilaginous joint -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b1/Gray298.png" xsd:anyURI -property_value: editor_note "consider adding fibrocartilage class" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b1/Gray298.png" xsd:anyURI +property_value: IAO:0000116 "consider adding fibrocartilage class" xsd:string [Term] id: UBERON:0002217 @@ -190359,11 +188479,10 @@ xref: Wikipedia:Synovial_joint xref: ZFA:0005153 is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint -intersection_of: surrounded_by UBERON:0001484 ! articular capsule +intersection_of: RO:0002219 UBERON:0001484 ! surrounded by articular capsule disjoint_from: UBERON:0011134 ! nonsynovial joint -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata -relationship: surrounded_by UBERON:0001484 ! articular capsule -property_value: UBPROP:0000001 "Is a joint that is located at the point of contact of articulating bones allowing movement. The joint has a capsule containing synovial fluid surrounding the articulating bone surfaces.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005153", ontology="TAO", source="ZFIN:Curator"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002219 UBERON:0001484 ! surrounded by articular capsule [Term] id: UBERON:0002222 @@ -190389,7 +188508,6 @@ xref: XAO:0004049 xref: ZFA:0001634 is_a: UBERON:0002384 {source="VSAO"} ! connective tissue relationship: bounding_layer_of UBERON:0007844 ! cartilage element -property_value: UBPROP:0000001 "Portion of connective tissue which surrounds cartilage.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001643", ontology="TAO", source="TAO:wd"} [Term] id: UBERON:0002224 @@ -190416,13 +188534,12 @@ xref: UMLS:C0230139 {source="ncithesaurus:Thoracic_Cavity"} xref: Wikipedia:Thoracic_cavity is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0000915 ! thoracic segment of trunk intersection_of: part_of UBERON:0002323 ! coelemic cavity lumen -relationship: luminal_space_of UBERON:0000915 ! thoracic segment of trunk +intersection_of: RO:0002572 UBERON:0000915 ! luminal space of thoracic segment of trunk relationship: part_of UBERON:0002323 ! coelemic cavity lumen -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI -property_value: UBPROP:0000008 "In many species, the diaphragm separates thoracic and abdominal cavities" xsd:string +relationship: RO:0002572 UBERON:0000915 ! luminal space of thoracic segment of trunk +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI [Term] id: UBERON:0002227 @@ -190455,21 +188572,17 @@ xref: NCIT:C33223 xref: ncithesaurus:Spiral_Organ_of_Corti xref: SCTID:279841009 xref: UMLS:C0029207 {source="BIRNLEX:2526", source="ncithesaurus:Organ_of_Corti"} -xref: VHOG:0001567 xref: Wikipedia:Organ_of_Corti is_a: UBERON:0000020 ! sense organ +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: capable_of GO:0050910 ! detection of mechanical stimulus involved in sensory perception of sound relationship: has_part CL:0000202 ! auditory hair cell -relationship: located_in UBERON:0002295 {source="Wikipedia:Scala_media"} ! scala media -relationship: only_in_taxon NCBITaxon:32523 {notes="https://github.com/obophenotype/uberon/issues/387"} ! Tetrapoda relationship: part_of UBERON:0001855 {source="MA"} ! cochlear duct of membranous labyrinth -relationship: present_in_taxon NCBITaxon:40674 ! Mammalia -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c7/Cochlea-crosssection.png" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/cb/Cochlea-crosssection.svg" xsd:anyURI -property_value: RO:0002174 NCBITaxon:8292 -property_value: RO:0002174 NCBITaxon:8457 -property_value: UBPROP:0000003 "The auditory hair cells in tetrapods are located in the inner ear in a structure known as the basilar papilla. In mammals this structure (along with some related structure) is called the organ of Corti.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001567", ontology="VHOG", source="ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.33", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "in basal early lizards, organized into 3 tonotopically organized areas, the outer areas lack a tectorial membrane[ISBN:9780387714691]" xsd:string +relationship: RO:0001025 UBERON:0002295 {source="Wikipedia:Scala_media"} ! located in scala media +relationship: RO:0002160 NCBITaxon:32523 ! only in taxon Tetrapoda +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c7/Cochlea-crosssection.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/cb/Cochlea-crosssection.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:40674 [Term] id: UBERON:0002228 @@ -190497,20 +188610,13 @@ xref: SCTID:302523002 xref: TAO:0000538 xref: UMLS:C0035561 {source="ncithesaurus:Rib"} xref: VHOG:0001154 -xref: VO:0012403 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: Wikipedia:Rib xref: ZFA:0000538 is_a: UBERON:0002513 ! endochondral bone is_a: UBERON:0015019 ! rib endochondral element intersection_of: UBERON:0015019 ! rib endochondral element -intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue -relationship: develops_from UBERON:0006288 {evidence="definitional"} ! rib cartilage element -relationship: part_of UBERON:0003252 {gci_filler="NCBITaxon:314146", gci_relation="part_of", notes="Euarchontoglires"} ! thoracic rib cage -property_value: UBPROP:0000001 "Endochondral bone that is intersegmental and rod-shaped, forming in the peritoneal membrane and attached to the vertebral parapophyses. Ribs protect and support internal organs.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000538", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Endochondral, rodlike element that articulates with the transverse process and parapophysis (double-headed rib), or with the transverse process only (single-headed rib); it extends into the body wall and provides a site for muscle attachment.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000545", ontology="AAO", source="AAO:Pugener_2002"} -property_value: UBPROP:0000007 "costal" xsd:string -property_value: UBPROP:0000008 "In most vertebrates, ribs surround the chest. In some species, especially snakes, ribs may provide support and protection for the entire body" xsd:string -property_value: UBPROP:0000009 "They protect and support internal organs and enable lungs to expand by expanding the chest." xsd:string +intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue +relationship: RO:0002202 UBERON:0006288 ! develops from rib cartilage element [Term] id: UBERON:0002234 @@ -190552,9 +188658,9 @@ xref: SCTID:368044009 xref: Wikipedia:True_ribs is_a: UBERON:0002228 ! rib intersection_of: UBERON:0002228 ! rib -intersection_of: connected_to UBERON:0000975 ! sternum -relationship: connected_to UBERON:0000975 ! sternum -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/3d/Gray115.png" xsd:anyURI +intersection_of: RO:0002170 UBERON:0000975 ! connected to sternum +relationship: RO:0002170 UBERON:0000975 ! connected to sternum +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3d/Gray115.png" xsd:anyURI [Term] id: UBERON:0002240 @@ -190610,19 +188716,16 @@ is_a: UBERON:0000489 ! cavitated compound organ is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005174 ! dorsal region element is_a: UBERON:0010314 ! structure with developmental contribution from neural crest -relationship: develops_from UBERON:0003076 ! posterior neural tube -relationship: has_developmental_contribution_from UBERON:0003853 {evidence="definitional"} ! spinal cord neural crest relationship: has_part CL:0005000 {source="ZFA"} ! spinal cord interneuron -relationship: immediate_transformation_of UBERON:0006241 {evidence="definitional"} ! future spinal cord relationship: part_of UBERON:0001017 ! central nervous system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/58/Spinal_cord_direv.svg" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Spinal_Cord.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Spinal_Cord.glb" xsd:anyURI -property_value: editor_note "TODO - add superclass to unify with VNC?" xsd:string -property_value: RO:0002171 UBERON:0000955 {exceptions="ZFA", source="https://github.com/obophenotype/uberon/issues/378", status="pending"} -property_value: UBPROP:0000001 "Part of the central nervous system which descends from the hindbrain within the vertebral column.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010151", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000601", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003076 ! develops from posterior neural tube +relationship: RO:0002254 UBERON:0003853 ! has developmental contribution from spinal cord neural crest +relationship: RO:0002495 UBERON:0006241 ! immediate transformation of future spinal cord +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/58/Spinal_cord_direv.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Spinal_Cord.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Spinal_Cord.glb" xsd:anyURI +property_value: IAO:0000116 "TODO - add superclass to unify with VNC?" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002241 @@ -190641,11 +188744,7 @@ xref: Wikipedia:Chondrocranium xref: ZFA:0001424 is_a: UBERON:0011159 ! primary subdivision of cranial skeletal system relationship: overlaps UBERON:0001703 ! neurocranium -property_value: editor_note "we follow the standard evolutionary classification and treat this as endoskeletal. This means what MA calls 'chondrocranium' must in fact be neurocranium, as it includes parts of the dermatocranium (e.g. frontal, parietal)" xsd:string -property_value: UBPROP:0000001 "Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010169", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001424", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000007 "chondrocranial" xsd:string -property_value: UBPROP:0000008 "covers the brain dorsally in chondrichthyans" xsd:string +property_value: IAO:0000116 "we follow the standard evolutionary classification and treat this as endoskeletal. This means what MA calls 'chondrocranium' must in fact be neurocranium, as it includes parts of the dermatocranium (e.g. frontal, parietal)" xsd:string [Term] id: UBERON:0002242 @@ -190665,23 +188764,21 @@ xref: EMAPA:18008 xref: FMA:13550 xref: FMA:76703 xref: MA:0000112 -xref: MESH:D000070614 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: SCTID:316586000 xref: Wikipedia:Nucleus_pulposus is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000062 ! organ is_a: UBERON:0002384 ! connective tissue +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004121 ! ectoderm-derived structure -relationship: contributes_to_morphology_of UBERON:0001066 ! intervertebral disk -relationship: develops_from UBERON:0002328 {editor="mah", source="ISBN:0073040584", source="Wikipedia"} ! notochord relationship: has_part CHEBI:37397 relationship: has_part CHEBI:60924 relationship: has_part CL:0000138 ! chondrocyte relationship: has_part UBERON:0011860 ! collection of collagen fibrils relationship: part_of UBERON:0001066 ! intervertebral disk -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/d9/Cervical_vertebra_english.png" xsd:anyURI -property_value: UBPROP:0000010 "The nucleus pulposus consists of chondrocytes, collagen fibrils, and proteoglycan aggrecans that have hyaluronic long chains which attract water. Attached to each hyaluronic chain are side chains of chondroitin sulfate and keratan sulfate[Wikipedia:Nucleus_pulposus]" xsd:string -property_value: UBPROP:0000012 "we group two FMA classes together" xsd:string {external_ontology="FMA"} +relationship: RO:0002202 UBERON:0002328 ! develops from notochord +relationship: RO:0002433 UBERON:0001066 ! contributes to morphology of intervertebral disk +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d9/Cervical_vertebra_english.png" xsd:anyURI [Term] id: UBERON:0002255 @@ -190715,16 +188812,13 @@ xref: XAO:0000272 is_a: UBERON:0000020 ! sense organ is_a: UBERON:0004121 ! ectoderm-derived structure relationship: capable_of GO:0043695 {source="Wikipedia"} ! detection of pheromone -relationship: develops_from UBERON:0003050 {source="Wikipedia"} ! olfactory placode -relationship: has_developmental_contribution_from UBERON:0009714 {source="EHDAA2-abduced"} ! intermaxillary process -relationship: has_quality PATO:0000588 {gci_relation="part_of", gci_filler="NCBITaxon:314295"} ! vestigial -relationship: only_in_taxon NCBITaxon:8287 ! Sarcopterygii relationship: part_of UBERON:0000004 ! nose relationship: part_of UBERON:0009954 ! vomeronasal system -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/84/Gray51.png" xsd:anyURI -property_value: UBPROP:0000001 "An organ thought to supplement the olfactory system in receiving pheromonic communication. The sensory part of the organ is in two long, thin sacs, situated on either side of the nasal septum at its base. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000665", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/vomeronasal+organ"} -property_value: UBPROP:0000003 "(...) the vomeronasal organ is known only in some tetrapods. It is absent in most turtles, crocodiles, birds, some bats, and aquatic mammals. In amphibians, it is in a recessed area off the main nasal cavity. (...) In mammals possesing this organ, it is an isolated area of olfactory membrane within the nasal cavity that is usually connected to the mouth via the nasopalatine duct (reference 1); The opinions concerning the presence and functioning of the vomeronasal organ in humans are controversial. The vomeronasal cavities appear early in human foetuses. (...) Historical examination of the nasal septum revealed the presence of vomeronasal cavities in approximately 70% of adults. In contrast to the situation in other mammals, the organ is not supported by a rigid tube of bone or cartilage (reference 2); (...) the best evidence for the homology of the human VNO to that of other primates (and of mammals in general) is ontogenetic in nature, based on a common embryonic origin from a thickening (vomeronasal primordium) on the medial aspect of each olfactory pit (reference 3); (...) suggesting that lungfish possess a region homologous to the accessory olfactory bulb of tetrapods. Based on these results, it seems appropriate to refer to the recess epithelium as a primordium of the vomeronasal organ (reference 4). [debated][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000665", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.669 (ref.1), http://www.ncbi.nlm.nih.gov/pubmed/9866877 Doving KB, Trotier D, Review: Structure and function of the vomeronasal organ. The Journal of Experimental Biology (1998) (ref.2), DOI:10.1046/j.1469-7580.2001.19810077.x Smith TD, Siegel MI, Bonar CJ, Bhatnagar KP, Mooney MP, Burrows AM, Smith MA, Maico LM, The existence of the vomeronasal organ in postnatal chimpanzees and evidence for its homology with that of humans. J Anat (2001) (ref.3) , DOI:10.1002/ar.22415 Nakamuta S, Nakamuta N, Taniguchi K, Taniguchi K, Histological and ultrastructural characteristics of the primordial vomeronasal organ in lungfish. Anat Rec (Hoboken) (2012) (ref.4)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "Generally formed only in tetrapods; lungfish have rudimentary VN organs; true VN organs are not normally found in recent fishes, birds, aquatic reptiles, aquatic mammals (Bertmar 1980). Humans: Its presence in many animals has been widely studied and the importance of the vomeronasal system to the role of reproduction and social behavior (through influence on anterior hypothalamus) has been shown in many studies. Its presence and functionality in humans was controversial, though most studies agree the organ regresses during fetal development. Many genes essential for VNO function in animals (such as TRPC2) are non-functional in humans (Liman ER. Use it or lose it: molecular evolution of sensory signaling in primates. Pflugers Arch. 2006;453(2):125-31.)" xsd:string +relationship: RO:0000086 PATO:0000588 {gci_relation="part_of", gci_filler="NCBITaxon:314295"} ! has quality vestigial +relationship: RO:0002160 NCBITaxon:8287 ! only in taxon Sarcopterygii +relationship: RO:0002202 UBERON:0003050 {source="Wikipedia"} ! develops from olfactory placode +relationship: RO:0002254 UBERON:0009714 {source="EHDAA2-abduced"} ! has developmental contribution from intermaxillary process +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/84/Gray51.png" xsd:anyURI [Term] id: UBERON:0002256 @@ -190773,12 +188867,12 @@ xref: ZFA:0000649 is_a: UBERON:0015212 ! lateral structure is_a: UBERON:0016550 ! spinal cord column disjoint_from: UBERON:0002257 {source="lexical"} ! ventral horn of spinal cord +relationship: BSPO:0000126 UBERON:0002315 {source="FMA-abduced-lr"} ! gray matter of spinal cord relationship: capable_of_part_of GO:0019230 {source="GO"} ! proprioception -relationship: contributes_to_morphology_of UBERON:0002315 ! gray matter of spinal cord relationship: has_part CL:0000101 ! sensory neuron -relationship: in_lateral_side_of UBERON:0002315 {source="FMA-abduced-lr"} ! gray matter of spinal cord relationship: part_of UBERON:0002315 ! gray matter of spinal cord -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/dc/Medulla_spinalis_-_Section_-_English.svg" xsd:anyURI +relationship: RO:0002433 UBERON:0002315 ! contributes to morphology of gray matter of spinal cord +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/dc/Medulla_spinalis_-_Section_-_English.svg" xsd:anyURI [Term] id: UBERON:0002257 @@ -190825,11 +188919,10 @@ xref: Wikipedia:Anterior_horn_of_spinal_cord xref: ZFA:0000702 is_a: UBERON:0015212 ! lateral structure is_a: UBERON:0016550 ! spinal cord column -relationship: contributes_to_morphology_of UBERON:0002315 ! gray matter of spinal cord +relationship: BSPO:0000126 UBERON:0002315 {source="FMA-abduced-lr"} ! gray matter of spinal cord relationship: has_part CL:0000100 ! motor neuron -relationship: in_lateral_side_of UBERON:0002315 {source="FMA-abduced-lr"} ! gray matter of spinal cord relationship: part_of UBERON:0002315 ! gray matter of spinal cord -property_value: UBPROP:0000001 "The anterior horn of the spinal cord (or anterior cornu, or anterior column, or ventral horn) is the ventral (front) grey matter section of the spinal cord. The anterior horn contains motor neurons that affect the axial muscles while the posterior horn receives information regarding touch and sensation. The anterior horn is where the cell bodies of alpha motorneurons are located[Wikipedia:Anterior_horn_of_spinal_cord]." xsd:string {source="Wikipedia:Anterior_horn_of_spinal_cord"} +relationship: RO:0002433 UBERON:0002315 ! contributes to morphology of gray matter of spinal cord [Term] id: UBERON:0002261 @@ -190868,8 +188961,7 @@ xref: ZFA:0000652 is_a: UBERON:0009623 {source="FMA"} ! spinal nerve root relationship: capable_of_part_of GO:0019230 {source="Wikipedia"} ! proprioception relationship: extends_fibers_into UBERON:0000044 ! dorsal root ganglion -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg" xsd:anyURI -property_value: UBPROP:0000001 "In anatomy and neurology, the dorsal root (or posterior root) is the afferent sensory root of a spinal nerve. At the distal end of the dorsal root is the dorsal root ganglion, which contains the neuron cell bodies of the nerve fibres conveyed by the root. If the dorsal root of a spinal nerve were severed it would lead to numbness in certain areas of the body. The lateral division of the dorsal root contains lightly myelinated and unmyelinated axons of small diameter. These transmit pain and temperature sensation from the body. These fibers cross through the anterior white commissure to form the Anterior lateral system in the lateral funiculus. The medial division of the dorsal root contains myelinated axons of larger diameter. These transmit information of discriminative touch, pressure, vibration, and conscious proprioception originating from spinal levels C2 through S5. These fibers are pushed in towards the posterior medial sulcus to form the fasciculus gracilis and the fasciculus cuneatus. [WP,unvetted][Wikipedia:Posterior_root_of_spinal_nerve]." xsd:string {source="Wikipedia:Posterior_root_of_spinal_nerve"} +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg" xsd:anyURI [Term] id: UBERON:0002264 @@ -190913,26 +189005,16 @@ xref: XAO:0004180 xref: ZFA:0000402 is_a: UBERON:0002616 ! regional part of brain is_a: UBERON:0015212 ! lateral structure +relationship: BSPO:0000126 UBERON:0001893 {source="ISBN:0471888893"} ! telencephalon relationship: capable_of GO:0007608 ! sensory perception of smell -relationship: contributes_to_morphology_of UBERON:0005366 ! olfactory lobe relationship: has_part CL:0000626 {source="ZFA"} ! olfactory granule cell -relationship: in_lateral_side_of UBERON:0001893 {source="ISBN:0471888893"} ! telencephalon relationship: part_of UBERON:0005366 ! olfactory lobe -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/d2/1543%2CVesalius%27OlfactoryBulbs.jpg" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/f9/1543,Vesalius%27OlfactoryBulbs.jpg" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI -property_value: RO:0002171 UBERON:0001950 {source="ABA"} -property_value: RO:0002171 UBERON:0002421 {source="ABA"} -property_value: UBPROP:0000001 "Part of the rostral part of the cerebrum where axons of olfactory cells from the nasal mucosa terminate. Projects onto olfactory parts of pallium via olfactory tracts" xsd:string {source="ISBN:0471888893"} -property_value: UBPROP:0000001 "Part of the telencephalon comprised of anterior outgrowths of either of the cerebral hemispheres in which the olfactory nerve exits.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010165", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "Segment of neural tree organ which is continuous with a set of olfactory nerves and an olfactory tract[FMA:77624]." xsd:string {source="FMA:77624"} -property_value: UBPROP:0000001 "The part of the forebrain in which the olfactory nerves end and the olfactory tracts originate. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000033", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "The presence of paired evaginated hemispheres and olfactory bulbs in both agnathan and gnathostome radiations suggests that such hemispheres were also present in the common ancestor.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000033", ontology="VHOG", source="DOI:10.1146/annurev.ne.04.030181.001505 Northcutt RG, Evolution of the telencephalon in nonmammals. Ann. Rev. Neurosci. (1981)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "In most vertebrates, the olfactory bulb is the most rostral (forward) part of the brain. In humans, however, the olfactory bulb is on the inferior (bottom) side of the brain. The olfactory bulb is supported and protected by the cribriform plate which in mammals, separates it from the olfactory epithelium, and which is perforated by olfactory nerve axons. The bulb is divided into two distinct structures, the main olfactory bulb, and the accessory olfactory bulb" xsd:string {source="WP"} -property_value: UBPROP:0000008 "Note that in uberon 'main olfactory bulb' is a separate class, but some ontologies may treat this as partially synonymous. The distinction may only make sense in tetrapods with a vomeronasal organ (olfactory nerves terminate in OB in fishes and in main OB in tetrapods - Butler and Hodos)" xsd:string -property_value: UBPROP:0000011 "the olfactory bulbs develop as bilateral evaginations from a region of the prosencephalic neural plate intercalated between the septal and the cortical anlagen (Cobos et al. 2001b, Rubenstein et al. 1998). Comparing the structure of the olfactory bulb among vertebrate species, such as the leopard frog and the lab mouse, reveals that they all share the same fundamental layout(WP)." xsd:string +relationship: RO:0002433 UBERON:0005366 ! contributes to morphology of olfactory lobe +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d2/1543%2CVesalius%27OlfactoryBulbs.jpg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f9/1543,Vesalius%27OlfactoryBulbs.jpg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002265 @@ -190966,14 +189048,8 @@ intersection_of: UBERON:0007702 ! tract of brain intersection_of: overlaps UBERON:0002264 ! olfactory bulb relationship: overlaps UBERON:0002264 ! olfactory bulb relationship: part_of UBERON:0011299 ! white matter of telencephalon -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray732.png" xsd:anyURI -property_value: UBPROP:0000001 "A nervelike, white band composed primarily of nerve fibres originating from the mitral cells and tufted cells of the olfactory bulb but also containing the scattered cells of the anterior olfactory nucleus[BTO:0003647]." xsd:string {source="BTO:0003647"} -property_value: UBPROP:0000001 "The olfactory tract is a bundle of axons connecting the mitral and tufted cells of the olfactory bulb to several target regions in the brain, including piriform cortex, amygdala, and entorhinal cortex. It is a narrow white band, triangular on coronal section, the apex being directed upward. It lies in the olfactory sulcus on the inferior surface of the frontal lobe, and divides posteriorly into two striæ, a medial olfactory stria and a lateral olfactory stria.[Wikipedia]." xsd:string {source="Wikipedia:Olfactory_tract"} -property_value: UBPROP:0000001 "Tract of brain which is continuous with olfactory bulb and the cerebral cortex.[FMA]" xsd:string {source="FMA"} -property_value: UBPROP:0000001 "White matter tract that contains projections from the olfactory bulb to the olfactory cortex (Maryann Martone)" xsd:string {notes="deprecated class", source="BIRNLEX:1663"} -property_value: UBPROP:0000008 "in animals with a long snout, the olfactory tract is long, whereas it is short in short-snouted animals such as primates. In some birds the tract per se does not exist as the bulb is connected directly to the cerebral hemisphere.[ISBN:0471888893]" xsd:string -property_value: UBPROP:0000012 "The definition was adapted from the NIFSTD class which has been retired. It has been generalized so it is applicable to various different kinds of olfactory tracts found in different taxa." xsd:string {editor="cjm", source="ISBN:0471888893"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray732.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002268 @@ -190991,7 +189067,6 @@ synonym: "organum olfactorium" RELATED [BTO:0001772] synonym: "primary olfactory organ" NARROW [] xref: AAO:0010180 xref: BTO:0001772 -xref: FBbt:00005158 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:77659 xref: VHOG:0000287 xref: XAO:0000273 @@ -191001,8 +189076,7 @@ intersection_of: capable_of GO:0050911 ! detection of chemical stimulus involved relationship: capable_of GO:0050911 ! detection of chemical stimulus involved in sensory perception of smell relationship: has_part CL:0000207 ! olfactory receptor cell relationship: overlaps UBERON:0005725 ! olfactory system -property_value: editor_note "An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint" xsd:string -property_value: UBPROP:0000012 "fma general anatomical term. xao has no subtypes (but Johnstons organ develops from this). An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint" xsd:string +property_value: IAO:0000116 "An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint" xsd:string [Term] id: UBERON:0002271 @@ -191019,6 +189093,7 @@ xref: MBA:157 xref: neuronames:2292 xref: VHOG:0000623 is_a: UBERON:0000064 ! organ part +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001898 ! hypothalamus [Term] @@ -191037,6 +189112,7 @@ xref: MA:0000837 xref: MBA:467 xref: neuronames:2291 is_a: UBERON:0000064 ! organ part +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001898 ! hypothalamus [Term] @@ -191060,10 +189136,7 @@ xref: SCTID:361552007 xref: Wikipedia:Reticular_formation is_a: UBERON:0002616 ! regional part of brain relationship: part_of UBERON:0002298 ! brainstem -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/9b/Gray701.png" xsd:anyURI -property_value: IAO:0000232 "this class denotes the generic structure, and not a specific one such as medullary or pontine reticular formation." xsd:string -property_value: UBPROP:0000008 "It is essential for governing some of the basic functions of higher organisms, and is one of the phylogenetically oldest portions of the brain." xsd:string -property_value: UBPROP:0000012 "FMA has a spinal cord reticular formation but we follow NNs (classical) to restrict this to brainstem structures. This means we also include the MA class for brainstem reticular formation here. FMA has subtypes of reticular formation but we treat this as a composite structure" xsd:string {external_ontology="FMA"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/9b/Gray701.png" xsd:anyURI [Term] id: UBERON:0002276 @@ -191083,9 +189156,10 @@ xref: FMA:77721 xref: MA:0001191 xref: Wikipedia:Limbus_laminae_spiralis is_a: UBERON:0000064 ! organ part +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001855 {source="MA"} ! cochlear duct of membranous labyrinth -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/a5/Gray930.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/a5/Gray930.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002278 @@ -191133,10 +189207,10 @@ xref: SCTID:279842002 xref: UMLS:C0229477 {source="BIRNLEX:2525"} xref: Wikipedia:Stria_vascularis is_a: UBERON:0000064 ! organ part +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0001855 {source="FMA", source="MA"} ! cochlear duct of membranous labyrinth -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c7/Cochlea-crosssection.png" xsd:anyURI -property_value: UBPROP:0000012 "represented as a wall in FMA. MESH def implies part of spiral ligament but better represented as adjacency / overlaps" xsd:string {external_ontology="FMA"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c7/Cochlea-crosssection.png" xsd:anyURI [Term] id: UBERON:0002285 @@ -191188,15 +189262,10 @@ xref: ZFA:0000696 is_a: UBERON:0004086 ! brain ventricle intersection_of: UBERON:0004086 ! brain ventricle intersection_of: part_of UBERON:0001893 ! telencephalon -relationship: in_lateral_side_of UBERON:0001893 {gci_relation="part_of", gci_filler="NCBITaxon:32523", notes="evaginated"} ! telencephalon -relationship: part_of UBERON:0001869 {gci_relation="part_of", gci_filler="NCBITaxon:32523", notes="evaginated"} ! cerebral hemisphere relationship: part_of UBERON:0001893 ! telencephalon -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: transformation_of UBERON:0009676 {notes="material to immaterial", source="EHDAA2"} ! early telencephalic vesicle -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray734.png" xsd:anyURI -property_value: UBPROP:0000001 "The lateral ventricles are part of the ventricular system of the brain. Classified as part of the telencephalon, they are the largest of the ventricles. The lateral ventricles connect to the central third ventricle through the interventricular foramina of Monro[WP]." xsd:string {source="Wikipedia:Lateral_ventricle"} -property_value: UBPROP:0000001 "The two lateral ventricles are a cavity in each of the cerebral hemispheres derived from the cavity of the embryonic neural tube. They are separated from each other by the septum pellucidum, and each communicates with the third ventricle by the foramen of Monro, through which also the choroid plexuses of the lateral ventricles become continuous with that of the third ventricle[GO]." xsd:string {source="GO:0021670"} -property_value: UBPROP:0000003 "The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000643", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500", source="http://bgee.unil.ch/"} +relationship: RO:0002494 UBERON:0009676 ! transformation of early telencephalic vesicle +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray734.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002290 @@ -191269,13 +189338,13 @@ xref: ZFA:0000938 is_a: UBERON:0004111 {source="cjm"} ! anatomical conduit is_a: UBERON:0004121 ! ectoderm-derived structure relationship: channel_for UBERON:0001359 ! cerebrospinal fluid -relationship: contributes_to_morphology_of UBERON:0002240 ! spinal cord -relationship: develops_from UBERON:0001049 ! neural tube relationship: has_part UBERON:0001359 ! cerebrospinal fluid relationship: part_of UBERON:0002240 {source="MA"} ! spinal cord relationship: part_of UBERON:0005281 {source="FMA"} ! ventricular system of central nervous system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/dc/Medulla_spinalis_-_Section_-_English.svg" xsd:anyURI +relationship: RO:0002202 UBERON:0001049 ! develops from neural tube +relationship: RO:0002433 UBERON:0002240 ! contributes to morphology of spinal cord +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/dc/Medulla_spinalis_-_Section_-_English.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002294 @@ -191310,8 +189379,7 @@ relationship: capable_of GO:0006699 ! bile acid biosynthetic process relationship: capable_of GO:0015721 ! bile acid and bile salt transport relationship: has_part UBERON:0001173 ! biliary tree relationship: part_of UBERON:0002423 ! hepatobiliary system -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png" xsd:anyURI -property_value: RO:0002171 UBERON:0016478 +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png" xsd:anyURI [Term] id: UBERON:0002295 @@ -191322,18 +189390,16 @@ comment: located in between the scala tympani and the scala vestibuli, separated subset: pheno_slim subset: uberon_slim synonym: "cochlear duct" RELATED [] -xref: EHDAA2:0000262 xref: EMAPA:35751 xref: FMA:79789 xref: MA:0002458 -xref: MESH:D003053 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: Wikipedia:Scala_media is_a: UBERON:0011060 {source="MA"} ! perilymphatic channel is_a: UBERON:0013685 ! foramen of skull -relationship: contributes_to_morphology_of UBERON:0001844 ! cochlea relationship: part_of UBERON:0001844 {source="FMA"} ! cochlea -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/bc/Gray928.png" xsd:anyURI -property_value: editor_note "TODO - check cochlear duct vs cochlear aqueduct vs scala media" xsd:string +relationship: RO:0002433 UBERON:0001844 ! contributes to morphology of cochlea +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/bc/Gray928.png" xsd:anyURI +property_value: IAO:0000116 "TODO - check cochlear duct vs cochlear aqueduct vs scala media" xsd:string [Term] id: UBERON:0002296 @@ -191357,10 +189423,9 @@ xref: TAO:0005130 xref: Wikipedia:Mesentery#Development xref: ZFA:0005130 is_a: UBERON:0006598 ! presumptive structure -relationship: has_potential_to_develop_into UBERON:0002095 ! mesentery relationship: part_of UBERON:0009664 {source="EHDAA2"} ! gut mesentery -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/85/Gray985.png" xsd:anyURI -property_value: UBPROP:0000001 "The mesentery that originates from the dorsal side of the peritoneal cavity.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005130", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002387 UBERON:0002095 ! has potential to develop into mesentery +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/85/Gray985.png" xsd:anyURI [Term] id: UBERON:0002298 @@ -191400,17 +189465,11 @@ xref: VHOG:0001457 xref: Wikipedia:Brainstem xref: ZFA:0001707 is_a: UBERON:0002616 ! regional part of brain -relationship: continuous_with UBERON:0002240 ! spinal cord -relationship: contributes_to_morphology_of UBERON:0000955 ! brain relationship: has_part UBERON:0001896 ! medulla oblongata relationship: has_part UBERON:0001943 ! midbrain tegmentum -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b7/Gray719.png" xsd:anyURI -property_value: RO:0002171 UBERON:0001890 {notes="we apply a strict definition"} -property_value: RO:0002171 UBERON:0002037 {exceptions="ZFA", source="ABA", source="https://github.com/obophenotype/uberon/issues/378", status="pending"} -property_value: RO:0002171 UBERON:0002314 {notes="we apply a strict definition"} -property_value: UBPROP:0000001 "Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002156", ontology="TAO", source="ISBN:3764351209"} -property_value: UBPROP:0000001 "Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,adopted][ZFA:0001707]." xsd:string {source="ZFA:0001707"} -property_value: UBPROP:0000001 "the stalk-like part of the brain that comprises the midbrain (aka mesencephalon), the pons (aka pons Varolii), and the medulla oblongata, and connects the cerebral hemispheres with the cervical spinal cord[MP]" xsd:string {source="MP:0005277"} +relationship: RO:0002150 UBERON:0002240 ! continuous with spinal cord +relationship: RO:0002433 UBERON:0000955 ! contributes to morphology of brain +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b7/Gray719.png" xsd:anyURI [Term] id: UBERON:0002299 @@ -191433,7 +189492,6 @@ xref: BTO:0000060 xref: CALOHA:TS-0031 xref: EFO:0001985 xref: EMAPA:32682 -xref: EV:0100043 xref: FMA:7318 xref: GAID:349 xref: MA:0000420 @@ -191442,15 +189500,16 @@ xref: SCTID:361364000 xref: VHOG:0001445 xref: Wikipedia:Pulmonary_alveolus is_a: UBERON:0003215 ! alveolus +is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0003215 ! alveolus intersection_of: part_of UBERON:0002048 ! lung -relationship: contains_process GO:0007585 ! respiratory gaseous exchange by respiratory system -relationship: contributes_to_morphology_of UBERON:0008874 ! pulmonary acinus -relationship: only_in_taxon NCBITaxon:40674 {source="PMID:12625309", source="PMID:12869615"} ! Mammalia +relationship: BFO:0000067 GO:0007585 ! contains process respiratory gaseous exchange by respiratory system relationship: part_of UBERON:0006524 {source="MA"} ! alveolar system relationship: part_of UBERON:0008874 ! pulmonary acinus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/4/46/Alveolus_diagram.svg" xsd:anyURI +relationship: RO:0002160 NCBITaxon:40674 {source="PMID:12625309", source="PMID:12869615"} ! only in taxon Mammalia +relationship: RO:0002433 UBERON:0008874 ! contributes to morphology of pulmonary acinus +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/4/46/Alveolus_diagram.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002301 @@ -191493,9 +189552,8 @@ xref: ZFA:0001374 is_a: UBERON:0002349 ! myocardium intersection_of: UBERON:0002349 ! myocardium intersection_of: part_of UBERON:0002081 ! cardiac atrium -relationship: contributes_to_morphology_of UBERON:0002081 ! cardiac atrium relationship: part_of UBERON:0002081 ! cardiac atrium -property_value: UBPROP:0000003 "As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000602", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481", source="http://bgee.unil.ch/"} +relationship: RO:0002433 UBERON:0002081 ! contributes to morphology of cardiac atrium [Term] id: UBERON:0002303 @@ -191524,7 +189582,7 @@ relationship: has_part CL:0000648 ! kidney granular cell relationship: has_part CL:0002173 ! extraglomerular mesangial cell relationship: has_part UBERON:0002335 ! macula densa relationship: part_of UBERON:0001225 {source="MA"} ! cortex of kidney -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002304 @@ -191541,7 +189599,6 @@ is_a: UBERON:0022303 ! nervous system cell part layer intersection_of: UBERON:0022303 ! nervous system cell part layer intersection_of: part_of UBERON:0001885 ! dentate gyrus of hippocampal formation relationship: part_of UBERON:0001885 ! dentate gyrus of hippocampal formation -property_value: UBPROP:0000008 "the basic trilaminar structure of the dentate gyrus is common across all species studied, with relatively minimal phylogenetic variation[PMC2492885]" xsd:string [Term] id: UBERON:0002305 @@ -191564,8 +189621,8 @@ is_a: UBERON:0011215 ! central nervous system cell part cluster is_a: UBERON:0016548 ! central nervous system gray matter layer intersection_of: UBERON:0016548 ! central nervous system gray matter layer intersection_of: part_of UBERON:0002421 ! hippocampal formation -relationship: contributes_to_morphology_of UBERON:0002421 ! hippocampal formation relationship: part_of UBERON:0002421 ! hippocampal formation +relationship: RO:0002433 UBERON:0002421 ! contributes to morphology of hippocampal formation [Term] id: UBERON:0002306 @@ -191587,7 +189644,6 @@ is_a: UBERON:0016553 ! respiratory system mucus intersection_of: UBERON:0000912 ! mucus intersection_of: produced_by UBERON:0015786 ! respiratory segment of nasal mucosa relationship: produced_by UBERON:0015786 ! respiratory segment of nasal mucosa -property_value: UBPROP:0000009 "protects the olfactory epithelium and allows odors to dissolve so that they can be detected by olfactory receptor neurons" xsd:string [Term] id: UBERON:0002307 @@ -191674,10 +189730,10 @@ xref: SCTID:369096000 xref: UMLS:C0152315 {source="BIRNLEX:1502", source="ncithesaurus:Fimbria"} xref: Wikipedia:Fimbria_of_hippocampus is_a: UBERON:0011215 ! central nervous system cell part cluster -relationship: part_of UBERON:0000052 {notes="Need to determine whether the fimbria is part of the fornix. Sometimes the language suggests it isn't always thought of that way, but I see no useful reason why it should be separate; it all forms one continuous white matter tract. Neuronames and others include this as part of the hippocampal formation (MM)", source="NIFSTD"} ! fornix of brain +relationship: part_of UBERON:0000052 ! fornix of brain relationship: part_of UBERON:0001954 {source="MA", source="NIFSTD"} ! Ammon's horn relationship: part_of UBERON:0011299 ! white matter of telencephalon -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/6b/Gray749.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6b/Gray749.png" xsd:anyURI [Term] id: UBERON:0002313 @@ -191706,11 +189762,11 @@ xref: MA:0000956 xref: neuronames:156 {source="BIRNLEX:1444"} is_a: UBERON:0002305 ! layer of hippocampus intersection_of: UBERON:0002305 ! layer of hippocampus -intersection_of: deep_to UBERON:0007637 ! hippocampus stratum lucidum -intersection_of: immediately_superficial_to UBERON:0005371 ! hippocampus stratum oriens -relationship: composed_primarily_of CL:0000598 ! pyramidal neuron -relationship: deep_to UBERON:0007637 ! hippocampus stratum lucidum -relationship: immediately_superficial_to UBERON:0005371 ! hippocampus stratum oriens +intersection_of: BSPO:0000107 UBERON:0007637 ! hippocampus stratum lucidum +intersection_of: BSPO:0015014 UBERON:0005371 ! hippocampus stratum oriens +relationship: BSPO:0000107 UBERON:0007637 ! hippocampus stratum lucidum +relationship: BSPO:0015014 UBERON:0005371 ! hippocampus stratum oriens +relationship: RO:0002473 CL:0000598 ! composed primarily of pyramidal neuron [Term] id: UBERON:0002314 @@ -191748,11 +189804,9 @@ xref: UMLS:C0039433 {source="ncithesaurus:Tectum_Mesencephali", source="BIRNLEX: xref: VHOG:0001388 xref: Wikipedia:Midbrain_tectum is_a: UBERON:0002616 ! regional part of brain -relationship: develops_from UBERON:0005882 {source="Wikipedia"} ! neural tube alar plate relationship: part_of UBERON:0001891 ! midbrain -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray685.png" xsd:anyURI -property_value: UBPROP:0000003 "The tectum - a multisensory, topologically mapped structure in the roof of the midbrain presents a remarkable degree of conservation in all vertebrate radiations; although it varies in the extent of its development in different vertebrate classes, there is considerable evidence now to deem its layered structure, its cell types, and its hodological pattern as homologous in all vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001388", ontology="VHOG", source="DOI:10.1371/journal.pone.0003582 Maximino C, Evolutionary Changes in the Complexity of the Tectum of Nontetrapods: A Cladistic Approach. PLoS ONE (2008)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "In adult humans it is present only in the mesencephalon as the inferior and the superior colliculi" xsd:string {source="WP"} +relationship: RO:0002202 UBERON:0005882 {source="Wikipedia"} ! develops from neural tube alar plate +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray685.png" xsd:anyURI [Term] id: UBERON:0002315 @@ -191781,8 +189835,8 @@ xref: UMLS:C0475853 {source="ncithesaurus:Gray_Matter_of_the_Spinal_Cord"} is_a: UBERON:0002020 ! gray matter intersection_of: UBERON:0002020 ! gray matter intersection_of: part_of UBERON:0002240 ! spinal cord -relationship: contributes_to_morphology_of UBERON:0002240 ! spinal cord relationship: part_of UBERON:0002240 ! spinal cord +relationship: RO:0002433 UBERON:0002240 ! contributes to morphology of spinal cord [Term] id: UBERON:0002316 @@ -191805,7 +189859,6 @@ xref: EMAPA:35927 xref: FMA:83929 xref: HBA:9218 xref: MA:0001135 -xref: MESH:D066127 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C33892 xref: neuronames:2870 xref: NLX:412 @@ -191819,13 +189872,9 @@ xref: VHOG:0001764 xref: Wikipedia:White_matter xref: ZFA:0001682 is_a: UBERON:0011215 ! central nervous system cell part cluster -relationship: composed_primarily_of UBERON:0006135 ! myelinated nerve fiber -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/d7/Grey_matter_and_white_matter_-_very_high_mag.jpg" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg" xsd:anyURI -property_value: UBPROP:0000001 "Cell part cluster consisting predominantly of neurites in the brain and the spinal cord[FMA:83929]." xsd:string {source="FMA:83929"} -property_value: UBPROP:0000001 "Multi-tissue structure comprised largely of myelinated axons.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002142", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "The myelination of axons by glial cells was the last major step in the evolution of cells in the vertebrate nervous system, and white-matter tracts are key to the architecture of the mammalian brain.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001764", ontology="VHOG", source="DOI:10.1038/nature09614 Nave KA, Myelination and support of axonal integrity by glia. Nature (2010)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "nlx_anat_101177 seems to have been lost in the transition from NIFGA to Neurolex" xsd:string {external_ontology="NIF", seeAlso="https://github.com/SciCrunch/NIF-Ontology/issues/83"} +relationship: RO:0002473 UBERON:0006135 ! composed primarily of myelinated nerve fiber +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d7/Grey_matter_and_white_matter_-_very_high_mag.jpg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg" xsd:anyURI [Term] id: UBERON:0002318 @@ -191850,8 +189899,8 @@ xref: UMLS:C0458457 {source="ncithesaurus:White_Matter_of_the_Spinal_Cord"} is_a: UBERON:0002316 ! white matter intersection_of: UBERON:0002316 ! white matter intersection_of: part_of UBERON:0002240 ! spinal cord -relationship: contributes_to_morphology_of UBERON:0002240 ! spinal cord relationship: part_of UBERON:0002240 ! spinal cord +relationship: RO:0002433 UBERON:0002240 ! contributes to morphology of spinal cord [Term] id: UBERON:0002319 @@ -191862,7 +189911,6 @@ subset: human_reference_atlas subset: pheno_slim subset: uberon_slim xref: BTO:0002494 -xref: EMAPA:28248 xref: EMAPA:36561 {source="MA:th"} xref: FMA:84139 xref: MA:0002617 @@ -191870,17 +189918,16 @@ xref: NCIT:C33101 xref: UMLS:C0017655 {source="ncithesaurus:Mesangium"} xref: Wikipedia:Mesangium is_a: UBERON:0000119 ! cell layer +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000119 ! cell layer -intersection_of: composed_primarily_of CL:0000650 ! mesangial cell -intersection_of: located_in UBERON:0005777 ! glomerular basement membrane -relationship: composed_primarily_of CL:0000650 ! mesangial cell -relationship: located_in UBERON:0005777 ! glomerular basement membrane +intersection_of: RO:0001025 UBERON:0005777 ! located in glomerular basement membrane +intersection_of: RO:0002473 CL:0000650 ! composed primarily of mesangial cell relationship: part_of UBERON:0000074 ! renal glomerulus relationship: part_of UBERON:0005215 ! kidney interstitium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: surrounds UBERON:0004212 ! glomerular capillary -property_value: UBPROP:0000007 "mesangial" xsd:string -property_value: UBPROP:0000012 "WP considers this the same as glomerular mesangium. In MA, glomerular and extraglomerular are distingsuished. FMA class has no definition and is a type of stroma, which is inconsistent with our classification of this here." xsd:string {external_ontology="MA"} +relationship: RO:0001025 UBERON:0005777 ! located in glomerular basement membrane +relationship: RO:0002221 UBERON:0004212 ! surrounds glomerular capillary +relationship: RO:0002473 CL:0000650 ! composed primarily of mesangial cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002320 @@ -191891,7 +189938,6 @@ subset: human_reference_atlas subset: pheno_slim subset: uberon_slim xref: EMAPA:27961 -xref: EMAPA:28248 xref: FMA:84140 xref: GAID:430 xref: MA:0002606 @@ -191899,10 +189945,11 @@ xref: MESH:D005920 xref: SCTID:244574009 xref: Wikipedia:Glomerular_mesangium is_a: UBERON:0003891 ! stroma -relationship: contributes_to_morphology_of UBERON:0000074 ! renal glomerulus +is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0002319 ! mesangium relationship: part_of UBERON:0004190 {source="GO"} ! renal glomerulus vasculature -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002433 UBERON:0000074 ! contributes to morphology of renal glomerulus +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002321 @@ -191915,6 +189962,7 @@ xref: EMAPA:28278 xref: FMA:84141 xref: MA:0002602 is_a: UBERON:0003891 ! stroma +is_a: UBERON:0004120 ! mesoderm-derived structure relationship: overlaps UBERON:0000074 ! renal glomerulus relationship: part_of UBERON:0002303 {source="MA"} ! juxtaglomerular apparatus relationship: part_of UBERON:0002319 {source="MA"} ! mesangium @@ -191933,7 +189981,6 @@ xref: TAO:0000260 xref: Wikipedia:Periventricular_nucleus xref: ZFA:0000260 is_a: UBERON:0002308 ! nucleus of brain -property_value: UBPROP:0000001 "Diencephalic nucleus which is the periventricular part of the ventral hypothalamic zone. From Neuroanatomy of the Zebrafish Brain." xsd:string {source="ZFA:0000260, GOC:MAH, ISBN:3764351209"} [Term] id: UBERON:0002323 @@ -191957,7 +190004,6 @@ synonym: "ventral body cavity" NARROW [NCBITaxon:7742] xref: AEO:0000186 xref: BTO:0001707 xref: EHDAA2:0000267 -xref: FBbt:00005060 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:85006 xref: galen:BodyCavity xref: NCIT:C25444 @@ -191967,11 +190013,8 @@ xref: TAO:0001438 xref: UMLS:C0333343 {source="ncithesaurus:Cavity"} xref: ZFA:0001438 is_a: UBERON:0002553 ! anatomical cavity -relationship: luminal_space_of UBERON:0011997 ! coelom -relationship: transformation_of UBERON:0003886 {evidence="definitional"} ! future coelemic cavity lumen -property_value: UBPROP:0000001 "Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]." xsd:string {date_retrieved="2012-09-12", external_class="ZFA:0001438", ontology="ZFA", source="ZFIN:curator"} -property_value: UBPROP:0000001 "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]." xsd:string {date_retrieved="2012-09-12", external_class="BTO:0001707", ontology="BTO", source="BTO"} -property_value: UBPROP:0000008 "In mammals it forms the peritoneal, pleural, and pericardial cavities" xsd:string +relationship: RO:0002494 UBERON:0003886 ! transformation of future coelemic cavity lumen +relationship: RO:0002572 UBERON:0011997 ! luminal space of coelom [Term] id: UBERON:0002324 @@ -191990,7 +190033,7 @@ is_a: UBERON:0005174 ! dorsal region element intersection_of: UBERON:0014892 ! skeletal muscle organ, vertebrate intersection_of: part_of UBERON:0001137 ! dorsum relationship: part_of UBERON:0004469 {source="prolog"} ! musculature of back -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002325 @@ -192008,9 +190051,11 @@ xref: FMA:85275 xref: MA:0001686 xref: NCIT:C49309 xref: UMLS:C1710584 {source="ncithesaurus:Urethra_Epithelium"} +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0003914 {source="GO"} ! epithelial tube is_a: UBERON:0005911 ! endo-epithelium is_a: UBERON:0006555 ! excretory tube +is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000057 ! urethra relationship: part_of UBERON:0000057 ! urethra @@ -192030,6 +190075,7 @@ xref: EMAPA:37785 {source="MA:th"} xref: FMA:85276 xref: MA:0001689 is_a: UBERON:0000030 ! lamina propria +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000030 ! lamina propria intersection_of: part_of UBERON:0000057 ! urethra relationship: part_of UBERON:0000057 ! urethra @@ -192040,7 +190086,6 @@ name: trunk of intercostal nerve namespace: uberon synonym: "intercostal nerve trunk" EXACT [] synonym: "intercostal neural trunk" EXACT [] -xref: EMAPA:18227 xref: EMAPA:37720 {source="MA:th"} xref: FMA:85315 xref: MA:0001176 @@ -192085,24 +190130,18 @@ xref: XAO:0000055 xref: ZFA:0000135 is_a: UBERON:0000062 {source="PMID:15890825"} ! organ is_a: UBERON:0000481 {source="VSAO"} ! multi-tissue structure +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004121 ! ectoderm-derived structure -relationship: develops_from UBERON:0004880 {source="ZFA"} ! chordamesoderm -relationship: develops_from UBERON:0006267 {source="EHDAA2"} ! notochordal plate -relationship: dorsal_to UBERON:0001555 ! digestive tract -relationship: existence_starts_during UBERON:0000068 ! embryo stage -relationship: only_in_taxon NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! Chordata +relationship: BSPO:0000098 UBERON:0001555 ! digestive tract +relationship: BSPO:0000102 UBERON:0001049 ! neural tube relationship: part_of UBERON:0000922 {gci_relation="part_of", gci_filler="NCBITaxon:40674"} ! embryo relationship: part_of UBERON:0011137 ! axial skeletal system relationship: produces PR:000014841 ! sonic hedgehog protein -relationship: ventral_to UBERON:0001049 ! neural tube -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000032", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000135", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000327", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000002 "relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000327", ontology="AAO"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000199", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "notochordal" xsd:string -property_value: UBPROP:0000011 "In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord." xsd:string +relationship: RO:0002160 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! only in taxon Chordata +relationship: RO:0002202 UBERON:0004880 {source="ZFA"} ! develops from chordamesoderm +relationship: RO:0002202 UBERON:0006267 {source="EHDAA2"} ! develops from notochordal plate +relationship: RO:0002488 UBERON:0000068 ! existence starts during embryo stage +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0002329 @@ -192141,18 +190180,10 @@ xref: XAO:0000058 xref: ZFA:0000155 is_a: UBERON:0005423 ! developing anatomical structure is_a: UBERON:0007503 {source="EHDAA2"} ! epithelial vesicle -relationship: develops_from UBERON:0003059 {source="ZFA"} ! presomitic mesoderm -relationship: never_in_taxon NCBITaxon:7712 {source="PMID:17237766"} -relationship: only_in_taxon NCBITaxon:7711 {source="GOTAX:0000352"} ! Chordata -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: IAO:0000232 "EDITOR_NOTE currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk" xsd:string -property_value: UBPROP:0000001 "Post-cranial axial segments which form sclerotome and dermomyotome.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010569", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000001 "Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000155", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000002 "relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000155", ontology="TAO"} -property_value: UBPROP:0000002 "relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000155", ontology="TAO"} -property_value: UBPROP:0000002 "relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010569", ontology="AAO"} -property_value: UBPROP:0000003 "(...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000191", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.40, DOI:10.1093/icb/43.1.137 Balavoine G, Adoutte A, The segmented urbilateria: a testable scenario. Integrative and Comparative Biology (2003)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "somitic" xsd:string +relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata +relationship: RO:0002202 UBERON:0003059 {source="ZFA"} ! develops from presomitic mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: RO:0002161 NCBITaxon:7712 {source="PMID:17237766"} [Term] id: UBERON:0002330 @@ -192179,9 +190210,9 @@ disjoint_from: UBERON:0002416 ! integumental system disjoint_from: UBERON:0002423 ! hepatobiliary system disjoint_from: UBERON:0004456 ! entire sense organ system disjoint_from: UBERON:8450002 ! excretory system -relationship: composed_primarily_of UBERON:0002365 ! exocrine gland -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002473 UBERON:0002365 ! composed primarily of exocrine gland +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage [Term] id: UBERON:0002331 @@ -192216,14 +190247,12 @@ xref: SCTID:280644003 xref: UMLS:C0041633 {source="ncithesaurus:Umbilical_Cord"} xref: Wikipedia:Umbilical_cord is_a: UBERON:0000478 ! extraembryonic structure -relationship: connects UBERON:0000922 ! embryo -relationship: connects UBERON:0001987 ! placenta -relationship: develops_from UBERON:0007806 ! connecting stalk -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/f3/Umbilicalcord.jpg" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Placenta.glb" xsd:anyURI -property_value: UBPROP:0000001 "The connecting cord from the developing embryo or fetus to the placenta. During prenatal development, the umbilical cord comes from the same zygote as the fetus and (in humans) normally contains two arteries (the umbilical arteries) and one vein (the umbilical vein), buried within Wharton's jelly. The umbilical vein supplies the fetus with oxygenated, nutrient-rich blood from the placenta.property_value, external_definition the umbilical arteries return the deoxygenated, nutrient-depleted blood[WP]." xsd:string {source="Wikipedia:Umbilical_cord"} -property_value: UBPROP:0000007 "umbilical" xsd:string +relationship: RO:0002176 UBERON:0000922 ! connects embryo +relationship: RO:0002176 UBERON:0001987 ! connects placenta +relationship: RO:0002202 UBERON:0007806 ! develops from connecting stalk +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f3/Umbilicalcord.jpg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Placenta.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002333 @@ -192246,16 +190275,14 @@ xref: MA:0002033 xref: NCIT:C116918 xref: VHOG:0001134 is_a: UBERON:0001637 {source="MA"} ! artery -relationship: connected_to UBERON:0002080 ! heart right ventricle -relationship: continuous_with UBERON:0000948 ! heart -relationship: continuous_with UBERON:0002080 {gci_relation="part_of", gci_filler="NCBITaxon:40674"} ! heart right ventricle relationship: part_of UBERON:0008886 ! pulmonary vascular system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png" xsd:anyURI -property_value: UBPROP:0000001 "An arterial trunk with origin from the right ventricle of the heart, and dividing into the right and left pulmonary arteries, which enter the corresponding lungs and branch with the bronchi. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001134", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/pulmonary+trunk"} -property_value: UBPROP:0000003 "As in birds, the conus arteriosus split during embryonic development in mammals to produce the pulmonary trunk and single aortic trunk of the adult.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001134", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481", source="http://bgee.unil.ch/"} +relationship: RO:0002150 UBERON:0000948 ! continuous with heart +relationship: RO:0002150 UBERON:0002080 {gci_relation="part_of", gci_filler="NCBITaxon:40674"} ! continuous with heart right ventricle +relationship: RO:0002170 UBERON:0002080 ! connected to heart right ventricle +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/db/Alveoli_diagram.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002335 @@ -192276,8 +190303,7 @@ xref: Wikipedia:Macula_densa is_a: UBERON:0004211 ! nephron epithelium relationship: part_of UBERON:0002303 {source="MA"} ! juxtaglomerular apparatus relationship: part_of UBERON:0004135 {source="GO"} ! distal tubule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000012 "not part of a nephron or distal tubule in MA and FMA" xsd:string {external_ontology="MA"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002337 @@ -192299,7 +190325,7 @@ is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0003891 ! stroma intersection_of: part_of UBERON:0001295 ! endometrium relationship: part_of UBERON:0001295 ! endometrium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002338 @@ -192330,6 +190356,7 @@ xref: MA:0001836 xref: NCIT:C49212 xref: UMLS:C1707054 {source="ncithesaurus:Bronchus_Lamina_Propria"} is_a: UBERON:0000031 ! lamina propria of trachea +is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0000030 ! lamina propria intersection_of: part_of UBERON:0002185 ! bronchus relationship: part_of UBERON:0000410 {is_inferred="true", source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! bronchial mucosa @@ -192355,12 +190382,12 @@ is_a: UBERON:0000115 ! lung epithelium is_a: UBERON:0002031 ! epithelium of bronchus intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002183 ! lobar bronchus -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: has_part CL:0002329 ! basal epithelial cell of tracheobronchial tree relationship: has_part CL:0002332 ! ciliated cell of the bronchus relationship: has_part CL:0017000 ! pulmonary ionocyte relationship: part_of UBERON:0002183 ! lobar bronchus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002341 @@ -192384,7 +190411,6 @@ is_a: UBERON:0002031 ! epithelium of bronchus is_a: UBERON:0006934 ! sensory epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002184 ! segmental bronchus -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: has_part CL:0000158 ! club cell relationship: has_part CL:0002208 ! brush cell of bronchus relationship: has_part CL:0002329 ! basal epithelial cell of tracheobronchial tree @@ -192393,7 +190419,8 @@ relationship: has_part CL:0017000 ! pulmonary ionocyte relationship: has_part CL:1000143 ! lung goblet cell relationship: has_part CL:1000223 ! lung neuroendocrine cell relationship: part_of UBERON:0002184 ! segmental bronchus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002342 @@ -192420,28 +190447,22 @@ xref: MIAA:0000066 xref: NCIT:C34222 xref: neuronames:1366 xref: SCTID:361462002 -xref: TAO:0000045 xref: UMLS:C0027789 {source="ncithesaurus:Neural_Crest"} xref: VHOG:0000057 xref: Wikipedia:Neural_crest xref: XAO:0000048 xref: ZFA:0000045 is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0010316 ! germ layer / neural crest -relationship: composed_primarily_of CL:0000333 {notes="pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! migratory neural crest cell -relationship: develops_from UBERON:0003075 {source="BTO"} ! neural plate -relationship: develops_from UBERON:0005062 {source="PMID:11523831"} ! neural fold -relationship: existence_starts_during UBERON:0000110 {source="PMID:11523831"} ! neurula stage -relationship: only_in_taxon NCBITaxon:89593 {notes="Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells", source="ISBN:0073040584"} ! Craniata relationship: part_of UBERON:0002346 {source="XAO", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! neurectoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI -property_value: IAO:0000232 "EDITOR_NOTE consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams)." xsd:string -property_value: RO:0002174 NCBITaxon:117565 {source="ISBN:0073040584", source="PMID:17377535"} -property_value: UBPROP:0000001 "A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000045", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010578", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831]" xsd:string {source="PMID:11523831"} -property_value: UBPROP:0000003 "We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000057", ontology="VHOG", source="DOI:10.1111/j.1469-7580.2012.01495.x Hall BK, Gillis JA, Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues. J Anat (2012)", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata +relationship: RO:0002202 UBERON:0003075 {source="BTO"} ! develops from neural plate +relationship: RO:0002202 UBERON:0005062 {source="PMID:11523831"} ! develops from neural fold +relationship: RO:0002473 CL:0000333 ! composed primarily of migratory neural crest cell +relationship: RO:0002488 UBERON:0000110 {source="PMID:11523831"} ! existence starts during neurula stage +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI [Term] id: UBERON:0002343 @@ -192464,7 +190485,6 @@ is_a: UBERON:0004479 ! musculature of trunk intersection_of: UBERON:0001015 ! musculature intersection_of: part_of UBERON:0000916 ! abdomen relationship: part_of UBERON:0000916 ! abdomen -property_value: IAO:0000232 "distinction between abdomen muscle and abdomen musculature" xsd:string [Term] id: UBERON:0002345 @@ -192479,12 +190499,13 @@ xref: EMAPA:18605 xref: FMA:87217 xref: MA:0002572 xref: SCTID:181301002 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0013522 ! subdivision of tube -relationship: contributes_to_morphology_of UBERON:0001514 ! descending aorta -relationship: contributes_to_morphology_of UBERON:0001515 ! thoracic aorta relationship: part_of UBERON:0001514 ! descending aorta relationship: part_of UBERON:0001515 ! thoracic aorta -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002433 UBERON:0001514 ! contributes to morphology of descending aorta +relationship: RO:0002433 UBERON:0001515 ! contributes to morphology of thoracic aorta +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002346 @@ -192507,7 +190528,6 @@ xref: EHDAA:1498 xref: EHDAA:255 xref: EMAPA:16073 xref: EV:0100004 -xref: FBbt:00001057 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:87657 xref: MAT:0000176 xref: MIAA:0000176 @@ -192521,9 +190541,6 @@ xref: ZFA:0001120 is_a: UBERON:0000923 ! germ layer is_a: UBERON:0004121 ! ectoderm-derived structure relationship: has_part CL:0000133 ! neurectodermal cell -property_value: UBPROP:0000003 "(...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000150", ontology="VHOG", source="DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "neurectodermal" xsd:string -property_value: UBPROP:0000013 "we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here" xsd:string [Term] id: UBERON:0002347 @@ -192551,11 +190568,10 @@ is_a: UBERON:0003827 ! thoracic segment bone is_a: UBERON:0004247 ! bone of dorsum is_a: UBERON:0015008 ! thoracic vertebra endochondral element intersection_of: UBERON:0015008 ! thoracic vertebra endochondral element -intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue -relationship: develops_from UBERON:0013507 ! thoracic vertebra cartilage element -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray90.png" xsd:anyURI -property_value: UBPROP:0000008 "Thoracic vertebrae in all species are defined as those vertebrae which also carry a pair of ribs, and lie caudal to the cervical vertebrae. In humans, they are distinguished by the presence of facets on the sides of the bodies for articulation with the heads of the ribs, and facets on the transverse processes of all, except the eleventh and twelfth, for articulation with the tubercles of the ribs" xsd:string +intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue +relationship: RO:0002202 UBERON:0013507 ! develops from thoracic vertebra cartilage element +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray90.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002348 @@ -192583,14 +190599,12 @@ xref: Wikipedia:Epicardium xref: XAO:0000316 xref: ZFA:0005057 is_a: UBERON:0000481 ! multi-tissue structure -relationship: attaches_to UBERON:0002349 {source="FMA"} ! myocardium -relationship: develops_from UBERON:0004160 ! proepicardium +is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0000948 {source="multiple"} ! heart relationship: part_of UBERON:0002425 {source="FMA-inferred"} ! visceral serous pericardium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000001 "External layer of the heart.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005057", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "The inner layer of the pericardium that is in contact with the surface of the heart.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010409", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000009 "The visceral pericardium apparently produces the pericardial fluid, which lubricates motion between the inner and outer layers of the pericardium. During ventricular contraction, the wave of depolarization moves from endocardial to epicardial surface. [Wikipedia:Epicardium]" xsd:string +relationship: RO:0002202 UBERON:0004160 ! develops from proepicardium +relationship: RO:0002371 UBERON:0002349 {source="FMA"} ! attached to myocardium +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002349 @@ -192612,7 +190626,6 @@ xref: BTO:0000901 xref: CALOHA:TS-0440 xref: EFO:0000819 xref: EHDAA2:0004150 -xref: EMAPA:32688 xref: EV:0100022 xref: FMA:9462 xref: GAID:173 @@ -192632,14 +190645,11 @@ xref: ZFA:0001319 is_a: UBERON:0005983 ! heart layer is_a: UBERON:0018260 ! layer of muscle tissue intersection_of: UBERON:0005983 ! heart layer -intersection_of: composed_primarily_of UBERON:0001133 ! cardiac muscle tissue -relationship: composed_primarily_of UBERON:0001133 ! cardiac muscle tissue +intersection_of: RO:0002473 UBERON:0001133 ! composed primarily of cardiac muscle tissue relationship: has_part UBERON:0002350 ! conducting system of heart relationship: part_of UBERON:0000383 ! musculature of body -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/6e/Glanzstreifen.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Robust muscular tunic of the heart which forms the basic part of its walls. Its external surface is covered by the pericardium and its internal one by the endocardium. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000083", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000001 "The middle layer of the heart, consisting of cardiac muscle.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010410", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000007 "myocardial" xsd:string +relationship: RO:0002473 UBERON:0001133 ! composed primarily of cardiac muscle tissue +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6e/Glanzstreifen.jpg" xsd:anyURI [Term] id: UBERON:0002350 @@ -192671,14 +190681,13 @@ xref: VHOG:0001271 xref: ZFA:0005063 is_a: UBERON:0004493 ! cardiac muscle tissue of myocardium is_a: UBERON:0010131 {source="FMA"} ! conducting tissue of heart -relationship: contributes_to_morphology_of UBERON:0000948 ! heart relationship: has_part CL:0002068 {source="FMA"} ! Purkinje myocyte relationship: has_part CL:0002073 {source="FMA"} ! transitional myocyte relationship: has_part CL:0002074 {source="FMA"} ! myocardial endocrine cell relationship: has_part CL:1000409 {source="FMA"} ! myocyte of sinoatrial node relationship: has_part CL:1000410 {source="FMA"} ! myocyte of atrioventricular node -property_value: editor_note "EHDAA2 divides the system from the tissue" xsd:string -property_value: UBPROP:0000003 "The fish heart displays clear polarity of contraction in a posterior-to-anterior direction. The contraction waves originate in the sinus venosus and terminate in the conus arteriosus. The nodal phenotype persists in the inflow region of the heart, varying from the venosinus to the sinoatrial junctional areas in different species . Similar to the mammalian situation, pacemaker tissue with a lower intrinsic rhythmicity is also found at the atrioventricular junction.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001271", ontology="VHOG", source="DOI:10.1152/physrev.00006.2003 Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003)", source="http://bgee.unil.ch/"} +relationship: RO:0002433 UBERON:0000948 ! contributes to morphology of heart +property_value: IAO:0000116 "EHDAA2 divides the system from the tissue" xsd:string [Term] id: UBERON:0002351 @@ -192720,12 +190729,12 @@ is_a: UBERON:0003379 ! cardiac muscle of right atrium is_a: UBERON:0010131 {source="cjm"} ! conducting tissue of heart relationship: capable_of GO:0002027 ! regulation of heart rate relationship: capable_of_part_of GO:0060048 ! cardiac muscle contraction -relationship: contributes_to_morphology_of UBERON:0002350 ! conducting system of heart -relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0002350 {source="ZFA"} ! conducting system of heart -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/d2/Sinoatrial_node_low_mag.jpg" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/de/Sinoatrial_node_2_low_mag.jpg" xsd:anyURI +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata +relationship: RO:0002433 UBERON:0002350 ! contributes to morphology of conducting system of heart +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d2/Sinoatrial_node_low_mag.jpg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/de/Sinoatrial_node_2_low_mag.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002352 @@ -192767,14 +190776,13 @@ xref: ZFA:0005070 is_a: UBERON:0004491 ! cardiac muscle tissue of interatrial septum is_a: UBERON:0004493 ! cardiac muscle tissue of myocardium is_a: UBERON:0010131 {source="cjm"} ! conducting tissue of heart -relationship: connected_to UBERON:0002085 ! interatrial septum -relationship: connected_to UBERON:0005979 ! crista terminalis -relationship: contributes_to_morphology_of UBERON:0002350 ! conducting system of heart relationship: part_of UBERON:0002350 ! conducting system of heart -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/50/ConductionsystemoftheheartwithouttheHeart.png" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/92/Gray501.png" xsd:anyURI -property_value: UBPROP:0000003 "Three major adaptations, or 'novel cardiac components', that were not present in the ancestor chordate heart tube can be distinguished in the lower vertebrate heart: the atrium, ventricle, and possibly the muscular sinus venosus. Furthermore, within the ventricular component a compact outer myocardial component and an interiorly localized extensive trabecular component can be distinguished. The specific activation of the ventricle adds to its complexity as follows. The depolarizing impulse travels rapidly from the atrioventricular node toward the apex and then toward the conal region, achieving activation from apex to base.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001474", ontology="VHOG", source="DOI:10.1152/physrev.00006.2003 Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003)", source="http://bgee.unil.ch/"} +relationship: RO:0002170 UBERON:0002085 ! connected to interatrial septum +relationship: RO:0002170 UBERON:0005979 ! connected to crista terminalis +relationship: RO:0002433 UBERON:0002350 ! contributes to morphology of conducting system of heart +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/50/ConductionsystemoftheheartwithouttheHeart.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/92/Gray501.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002353 @@ -192806,12 +190814,12 @@ xref: UMLS:C0006382 {source="ncithesaurus:Atrioventricular_Bundle"} xref: Wikipedia:Bundle_of_His is_a: UBERON:0010131 {source="cjm"} ! conducting tissue of heart is_a: UBERON:0018649 ! cardiac muscle tissue of ventricle -relationship: contributes_to_morphology_of UBERON:0002350 ! conducting system of heart relationship: has_part CL:1000410 {source="FMA"} ! myocyte of atrioventricular node relationship: part_of UBERON:0004146 {source="GO"} ! His-Purkinje system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/50/ConductionsystemoftheheartwithouttheHeart.png" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b6/ECG_Principle_fast.gif" xsd:anyURI +relationship: RO:0002433 UBERON:0002350 ! contributes to morphology of conducting system of heart +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/50/ConductionsystemoftheheartwithouttheHeart.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b6/ECG_Principle_fast.gif" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002354 @@ -192837,10 +190845,10 @@ xref: UMLS:C0034144 {source="ncithesaurus:Purkinje_Fiber"} xref: Wikipedia:Purkinje_fiber is_a: UBERON:0010131 {source="FMA"} ! conducting tissue of heart is_a: UBERON:0018649 ! cardiac muscle tissue of ventricle -relationship: contributes_to_morphology_of UBERON:0002350 ! conducting system of heart relationship: has_part CL:0002068 {source="FMA"} ! Purkinje myocyte relationship: part_of UBERON:8000009 {source="https://github.com/obophenotype/uberon/issues/1785", source="https://orcid.org/0000-0001-5208-3432", source="https://orcid.org/0000-0002-9791-0064"} ! Purkinje fiber network -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray498.png" xsd:anyURI +relationship: RO:0002433 UBERON:0002350 ! contributes to morphology of conducting system of heart +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray498.png" xsd:anyURI [Term] id: UBERON:0002355 @@ -192872,8 +190880,6 @@ xref: Wikipedia:Pelvis is_a: UBERON:0000475 ! organism subdivision relationship: has_part UBERON:0007832 ! pelvic girdle skeleton relationship: part_of UBERON:0002417 ! abdominal segment of trunk -property_value: UBPROP:0000007 "pelvic" xsd:string -property_value: UBPROP:0000012 "MA and FMA differ in what they consider to be parts of the pelvis. MA includes ureter, urethra, urinary bladder, reproductive organs" xsd:string {external_ontology="MA"} [Term] id: UBERON:0002357 @@ -192889,10 +190895,10 @@ xref: MA:0002739 xref: SCTID:243954002 xref: Wikipedia:Serous_pericardium is_a: UBERON:0000042 ! serous membrane -relationship: attaches_to UBERON:0002359 {source="FMA"} ! fibrous pericardium relationship: has_part UBERON:0002408 ! parietal serous pericardium relationship: has_part UBERON:0002425 ! visceral serous pericardium relationship: part_of UBERON:0002406 {source="FMA"} ! pericardial sac +relationship: RO:0002371 UBERON:0002359 {source="FMA"} ! attached to fibrous pericardium [Term] id: UBERON:0002358 @@ -192924,12 +190930,8 @@ intersection_of: UBERON:0000042 ! serous membrane intersection_of: part_of UBERON:0035820 ! peritoneal sac relationship: part_of UBERON:0003697 {source="MP"} ! abdominal wall relationship: part_of UBERON:0035820 ! peritoneal sac -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray1040.png" xsd:anyURI -property_value: editor_note "TODO - in ZFA is_a epithelium" xsd:string -property_value: UBPROP:0000001 "An epithelium that lines the peritoneal cavity.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005120", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Serous membrane that forms the lining of the abdominal cavity or the coelom. It covers most of the intra-abdominal organs, supports the abdominal organs, and serves as a conduit for their blood and lymph vessels and nerves. It is composed of a layer of mesothelium.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010814", ontology="AAO", source="AAO:JMG"} -property_value: UBPROP:0000007 "peritoneal" xsd:string -property_value: UBPROP:0000012 "todo: check MA/EMAPA." xsd:string {external_ontology="MA"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray1040.png" xsd:anyURI +property_value: IAO:0000116 "TODO - in ZFA is_a epithelium" xsd:string [Term] id: UBERON:0002359 @@ -192947,10 +190949,9 @@ xref: SCTID:243953008 xref: Wikipedia:Fibrous_pericardium is_a: UBERON:0000094 {source="FMA"} ! membrane organ is_a: UBERON:0005181 ! thoracic segment organ -relationship: composed_primarily_of UBERON:0006815 {source="WP"} ! areolar connective tissue -relationship: continuous_with UBERON:0002408 ! parietal serous pericardium relationship: part_of UBERON:0002407 {source="FMA"} ! pericardium -property_value: UBPROP:0000010 "most superficial part of pericardium; continuous with the outer adventitial layer of the neighboring great blood vessels. [Wikipedia:Pericardium]" xsd:string +relationship: RO:0002150 UBERON:0002408 ! continuous with parietal serous pericardium +relationship: RO:0002473 UBERON:0006815 {source="WP"} ! composed primarily of areolar connective tissue [Term] id: UBERON:0002360 @@ -192969,7 +190970,6 @@ xref: BTO:0000144 xref: CALOHA:TS-1177 xref: EFO:0000867 xref: EMAPA:32660 -xref: EV:0100312 xref: FMA:9589 xref: GAID:687 xref: MA:0001113 @@ -192984,15 +190984,9 @@ xref: Wikipedia:Meninx xref: ZFA:0001355 is_a: UBERON:0000094 {source="FMA"} ! membrane organ is_a: UBERON:0004121 ! ectoderm-derived structure -relationship: immediate_transformation_of UBERON:0007645 {source="Bgee:AN"} ! future meninx relationship: part_of UBERON:0010743 ! meningeal cluster -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/4/48/Illu_meninges.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Membrane covering the brain and spinal cord. It is represented by a single layer in fishes, two in amphibians, reptiles and birds and three in mammals (named dura mater, arachnoid and pia mater). [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001295", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/meninges"} -property_value: UBPROP:0000003 "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001295", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "meningeal" xsd:string -property_value: UBPROP:0000008 "Whereas cyclostomes and fishes only have a single envelope called the primitive meninx, amphibians have two layers, consisting of an outer dura mater which is extremely dense and protective, and a pia-arachnoid or secondary meninx which is more delicate and vascular. Mammals have three meninges: pia mater (which follows all the convolutions of the brain and is the most interior), the arachnoid layer (which is delicate and sends strands to the pia mater), and the dura mater (the outer, more protective meninx)." xsd:string -property_value: UBPROP:0000012 "Not consider part of the CNS/neuraxis in FMA" xsd:string {external_ontology="FMA", seeAlso="https://github.com/obophenotype/uberon/issues/1261"} -property_value: UBPROP:0000202 FMA:76821 +relationship: RO:0002495 UBERON:0007645 {source="Bgee:AN"} ! immediate transformation of future meninx +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/4/48/Illu_meninges.jpg" xsd:anyURI [Term] id: UBERON:0002361 @@ -193018,7 +191012,6 @@ xref: EHDAA:3710 xref: EHDAA:6566 xref: EHDAA:6583 xref: EMAPA:32663 -xref: EV:0100315 xref: FMA:9590 xref: GAID:693 xref: MA:0001116 @@ -193031,12 +191024,11 @@ xref: SCTID:362305004 xref: UMLS:C0031869 {source="ncithesaurus:Pia_Mater"} xref: Wikipedia:Pia_mater is_a: UBERON:0000391 ! leptomeninx -relationship: composed_primarily_of UBERON:0011825 ! loose connective tissue -relationship: only_in_taxon NCBITaxon:40674 {notes="check-aves", source="ISBN:0073040584"} ! Mammalia -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/31/Gray770-en.svg" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/65/Gray770.png" xsd:anyURI -property_value: editor_note "consider adding adjacency relationship to neuraxis (brain+spinal cord); however note that at this time the meninges may be considered part of the nervous system" xsd:string -property_value: UBPROP:0000001 "delicate innermost layer of the meninges-the membranes surrounding the brain and spinal cord. The thin, mesh-like pia mater closely envelops the entire surface of the brain, running down into the fissures of the cortex. It joins with the ependyma which lines the ventricles to form choroid plexuses that produce cerebrospinal fluid. In the spinal cord, the pia mater attaches to the dura mater by the denticular ligaments through the arachnoid membrane. The pia mater is a neural crest derivative[Wikipedia:Pia_mater]." xsd:string {source="Wikipedia:Pia_mater"} +relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia +relationship: RO:0002473 UBERON:0011825 ! composed primarily of loose connective tissue +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/31/Gray770-en.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/65/Gray770.png" xsd:anyURI +property_value: IAO:0000116 "consider adding adjacency relationship to neuraxis (brain+spinal cord); however note that at this time the meninges may be considered part of the nervous system" xsd:string [Term] id: UBERON:0002362 @@ -193064,10 +191056,9 @@ xref: SCTID:362304000 xref: UMLS:C1510935 {source="ncithesaurus:Arachnoid_Membrane"} xref: Wikipedia:Arachnoid_mater is_a: UBERON:0000391 ! leptomeninx -relationship: composed_primarily_of GO:0071953 ! elastic fiber -relationship: only_in_taxon NCBITaxon:40674 {source="ISBN:0073040584"} ! Mammalia -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/a0/Gray767.png" xsd:anyURI -property_value: RO:0002171 UBERON:0002049 {source="ISBN:0471888893"} +relationship: RO:0002160 NCBITaxon:40674 {source="ISBN:0073040584"} ! only in taxon Mammalia +relationship: RO:0002473 GO:0071953 ! composed primarily of elastic fiber +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/a0/Gray767.png" xsd:anyURI [Term] id: UBERON:0002363 @@ -193083,7 +191074,6 @@ synonym: "pachymeninges" EXACT [NLXANAT:090206] xref: BTO:0001637 xref: CALOHA:TS-2008 xref: EMAPA:32664 -xref: EV:0100313 xref: FMA:9592 xref: GAID:691 xref: MA:0001115 @@ -193095,13 +191085,10 @@ xref: SCTID:362301008 xref: UMLS:C0013313 {source="ncithesaurus:Dura_Mater"} xref: Wikipedia:Dura_mater is_a: UBERON:0002360 ! meninx -relationship: continuous_with UBERON:0001773 {source="PMID:16496288"} ! sclera -relationship: immediate_transformation_of UBERON:0007647 {evidence="definitional"} ! ectomeninx -relationship: never_in_taxon NCBITaxon:32443 {source="ISBN:0073040584"} ! Teleostei -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/8e/Meninges-en.svg" xsd:anyURI -property_value: UBPROP:0000001 "the outermost of the three layers of the meninges surrounding the brain and spinal cord. The other two meningeal layers are the pia mater and the arachnoid mater. The dura surrounds the brain and the spinal cord and is responsible for keeping in the cerebrospinal fluid[Wikipedia:Dura_mater]." xsd:string {source="Wikipedia:Dura_mater"} -property_value: UBPROP:0000009 "capable of inducing chondrogenesis - requires contact with an epithelium - http://www.ncbi.nlm.nih.gov/pubmed/16496288" xsd:string -property_value: UBPROP:0000012 "some ontologies consider dura mater part of the CNS, others dispute this and claim it surrounds it (e.g. DOI:10.1111/joa.12381)[https://github.com/obophenotype/uberon/issues/1261]" xsd:string +relationship: RO:0002150 UBERON:0001773 {source="PMID:16496288"} ! continuous with sclera +relationship: RO:0002495 UBERON:0007647 ! immediate transformation of ectomeninx +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8e/Meninges-en.svg" xsd:anyURI +property_value: RO:0002161 NCBITaxon:32443 {source="ISBN:0073040584"} [Term] id: UBERON:0002364 @@ -193132,19 +191119,15 @@ xref: Wikipedia:Tympanic_membrane xref: XAO:0000212 is_a: UBERON:0000094 {source="FMA"} ! membrane organ relationship: adjacent_to UBERON:0004114 {source="cjm"} ! tympanic cavity -relationship: contributes_to_morphology_of UBERON:0001756 ! middle ear -relationship: develops_from UBERON:0009213 {source="Wikipedia"} ! pharyngeal membrane of 1st arch relationship: has_part UBERON:0005042 ! inner epithelial layer of tympanic membrane relationship: has_part UBERON:0010069 ! outer epithelial layer of tympanic membrane relationship: has_part UBERON:0010070 ! intermediate layer of tympanic membrane -relationship: never_in_taxon NCBITaxon:8459 {source="Wikipedia"} relationship: overlaps UBERON:0001352 ! external acoustic meatus relationship: overlaps UBERON:0001691 {source="cjm"} ! external ear relationship: part_of UBERON:0001756 {source="MA"} ! middle ear -property_value: UBPROP:0000001 "The thin membrane which closes externally the cavity of the middle ear and is deeply sited at the bottom of the external auditory meatus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001146", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "In particular, a tympanic membrane was not present in the earliest tetrapods (...). An ear utilizing a tympanic membrane evolved independently at least three times in tetrapods: (1) in the lineage that leads to anurans (frogs), (2) in the line of evolution to turtles and diapsids, and (3) in the late synapsid lineage that gave rise to mammals.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001146", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.418", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000011 "The tympanic membrane (TM) has three layers, two epithelia provided by the external acoustic meatus (EAM) and the MEC, derived respectively from the first pharyngeal cleft and pouch, and a mesenchymally derived fibrous stratum" xsd:string -property_value: UBPROP:0000012 "most AOs consider this part of the middle ear, so we go with this and place it in the middle ear as a border to the external, although it could be considered to overlap the external ear in that it has an EAM layer as part - for this reason we do not consider middle and external ear to be spatially disjoint." xsd:string {source="PMID:11237469"} +relationship: RO:0002202 UBERON:0009213 {source="Wikipedia"} ! develops from pharyngeal membrane of 1st arch +relationship: RO:0002433 UBERON:0001756 ! contributes to morphology of middle ear +property_value: RO:0002161 NCBITaxon:8459 {source="Wikipedia"} [Term] id: UBERON:0002365 @@ -193175,7 +191158,7 @@ intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0002330 ! exocrine system relationship: has_part UBERON:0000058 ! duct relationship: part_of UBERON:0002330 ! exocrine system -property_value: editor_note "Currently this is logically defined by the system it belongs to, but a better system may be base this on presence/absence of ducts. However, the dual nature of the liver should be taken into consideration here. Consider adding subclasses" xsd:string +property_value: IAO:0000116 "Currently this is logically defined by the system it belongs to, but a better system may be base this on presence/absence of ducts. However, the dual nature of the liver should be taken into consideration here. Consider adding subclasses" xsd:string [Term] id: UBERON:0002367 @@ -193208,15 +191191,14 @@ xref: SCTID:181422007 xref: UMLS:C0033572 {source="ncithesaurus:Prostate_Gland"} xref: VHOG:0001261 xref: Wikipedia:Prostate -is_a: UBERON:0004119 ! endoderm-derived structure +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0010147 ! male accessory sex gland -relationship: develops_from UBERON:0003820 ! prostate bud -relationship: only_in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/a1/Prostatelead.jpg" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Prostate.glb" xsd:anyURI -property_value: editor_note "TODO - FMA treats the gland as part of the prostate - see also FMA:74119." xsd:string -property_value: UBPROP:0000007 "prostatic" xsd:string +relationship: RO:0002160 NCBITaxon:40674 {source="Wikipedia"} ! only in taxon Mammalia +relationship: RO:0002202 UBERON:0003820 ! develops from prostate bud +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/a1/Prostatelead.jpg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Prostate.glb" xsd:anyURI +property_value: IAO:0000116 "TODO - FMA treats the gland as part of the prostate - see also FMA:74119." xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002368 @@ -193248,7 +191230,7 @@ intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0000949 ! endocrine system relationship: capable_of GO:0046879 ! hormone secretion relationship: part_of UBERON:0000949 ! endocrine system -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/da/Illu_endocrine_system.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/da/Illu_endocrine_system.png" xsd:anyURI [Term] id: UBERON:0002369 @@ -193286,21 +191268,15 @@ xref: MIAA:0000071 xref: NCIT:C12666 xref: SCTID:181127006 xref: UMLS:C0001625 {source="ncithesaurus:Adrenal_Gland"} -xref: VHOG:0001141 xref: Wikipedia:Adrenal_gland xref: XAO:0000164 is_a: UBERON:0005172 ! abdomen element is_a: UBERON:0006858 ! adrenal/interrenal gland -is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0015212 ! lateral structure -relationship: has_developmental_contribution_from UBERON:0000926 {source="Wikipedia"} ! mesoderm -relationship: in_lateral_side_of UBERON:0000949 {source="FMA-abduced-lr"} ! endocrine system -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/9d/Illu_endocrine_system_New.png" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Illu_endocrine_system.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Anatomical structure which is found on the surface of the kidney and secretes various hormones including epinephrine, norephinephrine, aldosterone, corticosterone, and cortisol.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010551", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001141", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "The origin of the adrenal gland is still controversial. It is thought to share the same origin as the kidney and gonads, derived from coelomic epithelium of the urogenital ridge and/or the underlying mesenchyme (Keegan and Hammer, 2002; Morohashi, 1997). We follow Kardong and state homology at the level of the cortex and medulla rather than gland as a whole" xsd:string -property_value: UBPROP:0000009 "suprarenal cortex manufactures corticosteroids; suprarenal medulla manufactures epinephrine and norepinephrine; suprarenal medulla receives preganglionic sympathetic innervation from the greater thoracic splanchnic n." xsd:string +relationship: BSPO:0000126 UBERON:0000949 {source="FMA-abduced-lr"} ! endocrine system +relationship: RO:0002254 UBERON:0000926 {source="Wikipedia"} ! has developmental contribution from mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/9d/Illu_endocrine_system_New.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Illu_endocrine_system.jpg" xsd:anyURI [Term] id: UBERON:0002370 @@ -193339,26 +191315,23 @@ xref: Wikipedia:Thymus xref: XAO:0000163 xref: ZFA:0001078 is_a: PR:000050567 ! protein-containing material entity +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0002368 {source="EHDAA2"} ! endocrine gland -is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0004177 ! hemopoietic organ is_a: UBERON:0005057 ! immune organ is_a: UBERON:0005058 ! hemolymphoid system gland -relationship: contains_process GO:0030217 ! T cell differentiation -relationship: develops_from UBERON:0005562 {source="ZFA"} ! thymus primordium +relationship: BFO:0000067 GO:0030217 ! contains process T cell differentiation relationship: has_part UBERON:0003483 ! thymus lymphoid tissue relationship: has_part UBERON:0003846 ! thymus epithelium -relationship: only_in_taxon NCBITaxon:7776 {source="multiple sources - true thymus appears in jawed vertebrates"} ! Gnathostomata relationship: part_of UBERON:0000153 ! anterior region of body -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Thymus.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Thymus.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Thymus.glb" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/c/cf/Illu_thymus.jpg" xsd:anyURI -property_value: editor_note "check - a subtype of gland? not in GO. NCIT has thymus and thymus gland. EHDAA2 has ductless gland." xsd:string -property_value: UBPROP:0000001 "Anatomical structure which originates as several paired thickenings on the dorsal side of the pharyngeal pouches and secretes thymosin.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010548", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "A thymus develops in all vertebrates from the endodermal epithelium of certain pharyngeal pouches and from the adjacent ectodermal epithelium. In fishes, all the pouches, or the first four, contribute to thymus formation, but in tetrapods, the number is more restricted. In mammals, only the third and fourth are involved, and the contribution of the third is by far the greater.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000253", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.558", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "thymic" xsd:string +relationship: RO:0002160 NCBITaxon:7776 {source="multiple sources - true thymus appears in jawed vertebrates"} ! only in taxon Gnathostomata +relationship: RO:0002202 UBERON:0005562 {source="ZFA"} ! develops from thymus primordium +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Thymus.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Thymus.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Thymus.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/c/cf/Illu_thymus.jpg" xsd:anyURI +property_value: IAO:0000116 "check - a subtype of gland? not in GO. NCIT has thymus and thymus gland. EHDAA2 has ductless gland." xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002371 @@ -193394,6 +191367,7 @@ xref: VHOG:0001218 xref: Wikipedia:Bone_marrow xref: XAO:0000123 is_a: UBERON:0000479 ! tissue +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000479 ! tissue intersection_of: has_part UBERON:0012429 ! hematopoietic tissue intersection_of: part_of UBERON:0001474 ! bone element @@ -193402,12 +191376,10 @@ relationship: has_part UBERON:0012429 ! hematopoietic tissue relationship: part_of UBERON:0001474 ! bone element relationship: part_of UBERON:0002390 {source="FMA", source="MA"} ! hematopoietic system relationship: part_of UBERON:0002405 ! immune system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg" xsd:anyURI -property_value: editor_note "consider placement of NCIT:C53466 medullary bone" xsd:string -property_value: editor_note "TODO - create superclass for bone marrow / head kidney. both are portions of tissue in the hematopoetic system. also consider adding as subclass of zone of bone organ for consistency with FMA. See also: Leydig and epigonal organs" xsd:string -property_value: UBPROP:0000003 "The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001218", ontology="VHOG", source="DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood Cells and Blood Cell Development in the Animal Kingdom. Annual Review of Cell and Developmental Biology (2006)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000009 "In adults, marrow in large bones produces new blood cells[Wikipedia:Bone_marrow]" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg" xsd:anyURI +property_value: IAO:0000116 "consider placement of NCIT:C53466 medullary bone" xsd:string +property_value: IAO:0000116 "TODO - create superclass for bone marrow / head kidney. both are portions of tissue in the hematopoetic system. also consider adding as subclass of zone of bone organ for consistency with FMA. See also: Leydig and epigonal organs" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002372 @@ -193436,11 +191408,10 @@ xref: UMLS:C1519548 {source="ncithesaurus:Tonsillar_Lymphoid_Tissue"} xref: VHOG:0001139 xref: Wikipedia:Tonsil is_a: UBERON:0001962 ! gut-associated lymphoid tissue -relationship: contributes_to_morphology_of UBERON:0001735 ! tonsillar ring -relationship: located_in UBERON:0000167 ! oral cavity relationship: part_of UBERON:0001735 {source="cjm"} ! tonsillar ring -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: IAO:0000232 "the term 'tonsil' can be ambiguous, sometimes refering specifically to the palatine tonsil, sometimes generically to include the cecal tonsils of avians. This class represents lymphoid tissue that is part of the tonsillar ring, in the mouth/throat region" xsd:string +relationship: RO:0001025 UBERON:0000167 ! located in oral cavity +relationship: RO:0002433 UBERON:0001735 ! contributes to morphology of tonsillar ring +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002374 @@ -193467,10 +191438,10 @@ is_a: UBERON:0012358 ! manual digitopodium bone is_a: UBERON:0015042 ! manual digit metacarpus endochondral element intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0004453 ! metacarpus region -relationship: connected_to UBERON:0001435 ! carpal bone -relationship: connected_to UBERON:0001436 ! phalanx of manus relationship: part_of UBERON:0010544 ! metacarpus skeleton -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/2/2f/Metacarpals_numbered-en.svg" xsd:anyURI +relationship: RO:0002170 UBERON:0001435 ! connected to carpal bone +relationship: RO:0002170 UBERON:0001436 ! connected to phalanx of manus +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/2f/Metacarpals_numbered-en.svg" xsd:anyURI [Term] id: UBERON:0002376 @@ -193506,13 +191477,13 @@ xref: ZFA:0001652 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010959 ! craniocervical muscle intersection_of: UBERON:0014892 ! skeletal muscle organ, vertebrate -intersection_of: attaches_to UBERON:0003129 ! skull intersection_of: part_of UBERON:0000033 ! head -relationship: attaches_to UBERON:0003129 ! skull -relationship: develops_from UBERON:0006904 {source="EHDAA2-abduced"} ! head mesenchyme from mesoderm -relationship: has_developmental_contribution_from UBERON:0002342 {gci_relation="part_of", gci_filler="NCBITaxon:7742", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! neural crest +intersection_of: RO:0002371 UBERON:0003129 ! attached to skull relationship: part_of UBERON:0004461 {source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! skeletal musculature of head -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 UBERON:0006904 {source="EHDAA2-abduced"} ! develops from head mesenchyme from mesoderm +relationship: RO:0002254 UBERON:0002342 {gci_relation="part_of", gci_filler="NCBITaxon:7742", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! has developmental contribution from neural crest +relationship: RO:0002371 UBERON:0003129 ! attached to skull +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002377 @@ -193527,7 +191498,6 @@ synonym: "muscle organ of neck (volume)" EXACT [OBOL:automatic] synonym: "neck (volume) muscle organ" EXACT [OBOL:automatic] synonym: "neck muscle" EXACT [] synonym: "neck muscle organ" EXACT [OBOL:automatic] -xref: EMAPA:36050 xref: FMA:9617 xref: GAID:149 xref: MA:0000587 @@ -193538,7 +191508,7 @@ is_a: UBERON:0010959 ! craniocervical muscle intersection_of: UBERON:0014892 ! skeletal muscle organ, vertebrate intersection_of: part_of UBERON:0000974 ! neck relationship: part_of UBERON:0004465 {source="prolog"} ! musculature of neck -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002378 @@ -193570,7 +191540,7 @@ intersection_of: UBERON:0014892 ! skeletal muscle organ, vertebrate intersection_of: part_of UBERON:0000916 ! abdomen relationship: part_of UBERON:0002343 {source="prolog"} ! abdomen musculature relationship: part_of UBERON:0003697 ! abdominal wall -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002380 @@ -193591,17 +191561,17 @@ xref: UMLS:C0224361 {source="ncithesaurus:Trapezius_Muscle"} xref: VHOG:0000834 xref: Wikipedia:Trapezius_muscle is_a: UBERON:0001482 ! muscle of shoulder +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010313 ! neural crest-derived structure -relationship: develops_from UBERON:0010955 ! trapezius pre-muscle mass -relationship: has_muscle_antagonist UBERON:0001112 {source="dbpedia"} ! latissimus dorsi muscle -relationship: has_muscle_antagonist UBERON:0001125 {source="dbpedia"} ! serratus ventralis -relationship: has_muscle_insertion UBERON:0002497 {notes="posterior border of the lateral third of the clavicle acromion process and spine of scapula", source="dbpedia"} ! acromion -relationship: has_muscle_insertion UBERON:0007173 {notes="posterior border of the lateral third of the clavicle acromion process and spine of scapula", source="dbpedia"} ! lateral border of scapula -relationship: has_muscle_origin UBERON:0000351 {notes="external occipital protuberance nuchal ligament medial superior nuchal line spinous processes of vertebrae C7-T12", source="dbpedia"} ! nuchal ligament -relationship: has_muscle_origin UBERON:0001076 {notes="external occipital protuberance nuchal ligament medial superior nuchal line spinous processes of vertebrae C7-T12", source="dbpedia"} ! neural spine -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/60/Trapezius.png" xsd:anyURI -property_value: UBPROP:0000003 "The sternomastoid and the three parts of the trapezius are branchiomeric muscles that have secondarily acquired an attachment to the pectoral girdle. They evolved from the fish cucullaris.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000834", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.345", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0010955 ! develops from trapezius pre-muscle mass +relationship: RO:0002372 UBERON:0000351 ! has muscle origin nuchal ligament +relationship: RO:0002372 UBERON:0001076 ! has muscle origin neural spine +relationship: RO:0002373 UBERON:0002497 ! has muscle insertion acromion +relationship: RO:0002373 UBERON:0007173 ! has muscle insertion lateral border of scapula +relationship: RO:0002568 UBERON:0001112 {source="dbpedia"} ! has muscle antagonist latissimus dorsi muscle +relationship: RO:0002568 UBERON:0001125 {source="dbpedia"} ! has muscle antagonist serratus ventralis +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/60/Trapezius.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002381 @@ -193627,14 +191597,13 @@ xref: VHOG:0000895 xref: Wikipedia:Pectoralis_major_muscle is_a: UBERON:0001482 ! muscle of shoulder is_a: UBERON:0001495 {source="FMA"} ! pectoral muscle -is_a: UBERON:0003897 ! axial muscle -relationship: has_muscle_insertion UBERON:0000976 {notes="Lateral lip of intertubercular groove of the humerus", source="dbpedia"} ! humerus -relationship: has_muscle_origin UBERON:0000975 {notes="anterior surface of the sternum and the superior six costal cartilages and the aponeurosis of the external oblique muscle", source="dbpedia"} ! sternum -relationship: has_muscle_origin UBERON:0001105 {notes="anterior surface of the medial half of the clavicle", source="dbpedia"} ! clavicle bone -relationship: innervated_by UBERON:0003726 {notes="lateral pectoral nerve and medial pectoral nerveClavicular head: C5 and C6Sternocostal head: C7 C8 and T1", source="dbpedia"} ! thoracic nerve -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: superficial_to UBERON:0001100 ! pectoralis minor -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/6/6c/Pectoralis_major.png" xsd:anyURI +relationship: BSPO:0000108 UBERON:0001100 ! pectoralis minor +relationship: RO:0002005 UBERON:0003726 ! innervated_by thoracic nerve +relationship: RO:0002372 UBERON:0000975 ! has muscle origin sternum +relationship: RO:0002372 UBERON:0001105 ! has muscle origin clavicle bone +relationship: RO:0002373 UBERON:0000976 ! has muscle insertion humerus +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/6c/Pectoralis_major.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002384 @@ -193668,12 +191637,8 @@ xref: VSAO:0000017 xref: XAO:0001017 xref: ZFA:0001632 is_a: UBERON:0000479 ! tissue -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000001 "One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000098", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000001 "Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001641", ontology="TAO", source="TAO:wd"} -property_value: UBPROP:0000001 "Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000017", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} -property_value: UBPROP:0000012 "MA also has set of connective tissues" xsd:string {external_ontology="MA"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002385 @@ -193701,14 +191666,12 @@ xref: Wikipedia:Muscle_tissue is_a: UBERON:0000479 ! tissue is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000479 ! tissue -intersection_of: composed_primarily_of CL:0000187 ! muscle cell +intersection_of: RO:0002473 CL:0000187 ! composed primarily of muscle cell disjoint_from: UBERON:0003714 ! neural tissue relationship: capable_of GO:0006936 ! muscle contraction -relationship: composed_primarily_of CL:0000187 ! muscle cell -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0001015 ! musculature -property_value: RO:0002171 UBERON:0003714 -property_value: UBPROP:0000001 "One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000306", ontology="AAO", source="AAO:LAP"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002473 CL:0000187 ! composed primarily of muscle cell [Term] id: UBERON:0002386 @@ -193766,13 +191729,10 @@ is_a: UBERON:0002471 ! zeugopod is_a: UBERON:0008785 ! upper limb segment intersection_of: UBERON:0002471 ! zeugopod intersection_of: part_of UBERON:0002102 ! forelimb -relationship: has_skeleton UBERON:0010703 ! forelimb zeugopod skeleton relationship: part_of UBERON:0001460 {source="MA"} ! arm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/3b/Veins.jpg" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/5/50/Forearm_labeled.png" xsd:anyURI -property_value: UBPROP:0000001 "The middle forelimb region. [Evolution, Fourth_Edition_(2006)_Boston_etc.:_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.321, see_Kardong_KV][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000341", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000341", ontology="VHOG", source="ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000013 "Naming conventions for pod terms under discussion within phenoscape group. TODO - add distinct term for skeleton and place AAO class here" xsd:string +relationship: RO:0002551 UBERON:0010703 ! has skeleton forelimb zeugopod skeleton +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3b/Veins.jpg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/5/50/Forearm_labeled.png" xsd:anyURI [Term] id: UBERON:0002387 @@ -193815,10 +191775,9 @@ is_a: UBERON:0002470 ! autopod region is_a: UBERON:0008784 ! lower limb segment intersection_of: UBERON:0002470 ! autopod region intersection_of: part_of UBERON:0002103 ! hindlimb -relationship: develops_from UBERON:0006871 ! embryonic footplate -relationship: has_skeleton UBERON:0001445 ! skeleton of pes -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/ae/Male_Right_Foot_1.jpg" xsd:anyURI -property_value: UBPROP:0000007 "pedal" xsd:string +relationship: RO:0002202 UBERON:0006871 ! develops from embryonic footplate +relationship: RO:0002551 UBERON:0001445 ! has skeleton skeleton of pes +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/ae/Male_Right_Foot_1.jpg" xsd:anyURI [Term] id: UBERON:0002389 @@ -193856,7 +191815,6 @@ intersection_of: UBERON:0002544 ! digit intersection_of: part_of UBERON:0002102 ! forelimb relationship: part_of UBERON:0012141 {source="PHENOSCAPE:ni"} ! manual digitopodium region relationship: part_of UBERON:5002389 ! manual digit plus metapodial segment -property_value: UBPROP:0000001 "One of the fingers of the manus.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000857", ontology="AAO", source="AAO:LAP"} [Term] id: UBERON:0002390 @@ -193903,14 +191861,10 @@ disjoint_from: UBERON:0002416 ! integumental system disjoint_from: UBERON:0002423 ! hepatobiliary system disjoint_from: UBERON:0004456 ! entire sense organ system disjoint_from: UBERON:8450002 ! excretory system -relationship: develops_from UBERON:0003061 {evidence="definitional"} ! blood island -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0002193 {source="FMA"} ! hemolymphoid system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000001 "Anatomical system that consists of the blood and blood forming tissues.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011002", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001624", ontology="VHOG", source="DOI:10.1016/j.coph.2010.05.004 Ellett F, Lieschke GJ, Zebrafish as a model for vertebrate hematopoiesis. Current Opinion in Pharmacology (2010)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "hematopoietic" xsd:string -property_value: UBPROP:0000008 "In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes" xsd:string {source="WP"} +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002202 UBERON:0003061 ! develops from blood island +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002391 @@ -193940,8 +191894,8 @@ xref: Wikipedia:Lymph xref: ZFA:0005658 is_a: UBERON:0000179 ! haemolymphatic fluid relationship: part_of UBERON:0006558 ! lymphatic part of lymphoid system -relationship: transformation_of UBERON:0000913 ! interstitial fluid -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Illu_lymph_capillary.png" xsd:anyURI +relationship: RO:0002494 UBERON:0000913 ! transformation of interstitial fluid +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Illu_lymph_capillary.png" xsd:anyURI [Term] id: UBERON:0002392 @@ -193970,17 +191924,16 @@ xref: VHOG:0000664 xref: Wikipedia:Nasolacrimal_duct is_a: UBERON:0000025 ! tube is_a: UBERON:0000058 ! duct +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: channel_for UBERON:0001827 ! secretion of lacrimal gland -relationship: connects UBERON:0001351 ! lacrimal sac -relationship: connects UBERON:0001707 ! nasal cavity -relationship: contributes_to_morphology_of UBERON:0001750 ! lacrimal apparatus -relationship: develops_from UBERON:0006266 ! nasolacrimal groove relationship: has_part CL:0000160 ! goblet cell relationship: has_part UBERON:0007602 ! stratified columnar epithelium relationship: part_of UBERON:0001850 ! lacrimal drainage system -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray896.png" xsd:anyURI -property_value: UBPROP:0000003 "The nasolacrimal duct is probably homologous to the posterior (excurrent) naris of actinopterygian fishes.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000664", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.256", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000010 "the nasolacrimal duct, the sac is lined by stratified columnar epithelium with mucus-secreting goblet cells, and is surrounded by connective tissue" xsd:string +relationship: RO:0002176 UBERON:0001351 ! connects lacrimal sac +relationship: RO:0002176 UBERON:0001707 ! connects nasal cavity +relationship: RO:0002202 UBERON:0006266 ! develops from nasolacrimal groove +relationship: RO:0002433 UBERON:0001750 ! contributes to morphology of lacrimal apparatus +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray896.png" xsd:anyURI [Term] id: UBERON:0002394 @@ -193996,7 +191949,6 @@ synonym: "hepatic duct" RELATED INCONSISTENT [ZFA:0001100] xref: AAO:0011019 xref: BTO:0000122 xref: CALOHA:TS-0075 -xref: EHDAA2:0000741 xref: EMAPA:35171 xref: EV:0100091 xref: FMA:9706 @@ -194017,14 +191969,10 @@ is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0000058 ! duct intersection_of: part_of UBERON:0001173 ! biliary tree relationship: channel_for UBERON:0001970 ! bile -relationship: contributes_to_morphology_of UBERON:0001173 ! biliary tree -relationship: develops_from UBERON:0008835 {source="XAO"} ! hepatic diverticulum relationship: part_of UBERON:0001173 {source="EMAPA", source="MA"} ! biliary tree -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png" xsd:anyURI -property_value: UBPROP:0000001 "A duct that carries bile from the liver to the intestine." xsd:string {source="ZFA:0001100, ZFA:curator"} -property_value: UBPROP:0000001 "Any of the excretory ducts in the liver that convey bile between the liver and the intestine. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000212", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/bile+duct"} -property_value: UBPROP:0000003 "(...) the amphibian liver has characteristics in common with both fish and terrestrial vertebrates. (...) The histological structure of the liver is similar to that in other vertebrates, with hepatocytes arranged in clusters and cords separated by a meshwork of sinusoids and the presence of the traditional triad of portal venule, hepatic arteriole, and bile duct.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000212", ontology="VHOG", source="DOI:10.1053/ax.2000.7133 Crawshaw GJ, Weinkle TK, Clinical and pathological aspects of the amphibian liver. Seminars in Avian and Exotic Pet Medicine (2000)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "we place the ZFA class here as this fits its textual definition and child nodes. We may recommend a label change for ZFA" xsd:string {external_ontology="ZFA"} +relationship: RO:0002202 UBERON:0008835 {source="XAO"} ! develops from hepatic diverticulum +relationship: RO:0002433 UBERON:0001173 ! contributes to morphology of biliary tree +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5d/Digestive_system_showing_bile_duct.png" xsd:anyURI [Term] id: UBERON:0002396 @@ -194040,7 +191988,6 @@ synonym: "vomer bone" EXACT [] xref: AAO:0000633 xref: FMA:9710 xref: MA:0001496 -xref: MESH:D055172 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C33888 xref: SCTID:272678009 xref: TAO:0000308 @@ -194050,18 +191997,12 @@ xref: ZFA:0000308 is_a: UBERON:0008001 {source="FMA"} ! irregular bone is_a: UBERON:0011597 ! bone of upper jaw is_a: UBERON:0012071 ! palate bone -relationship: connected_to UBERON:0001677 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! sphenoid bone -relationship: connected_to UBERON:0001679 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! ethmoid bone -relationship: contributes_to_morphology_of UBERON:0011156 ! facial skeleton relationship: part_of UBERON:0011085 ! palatoquadrate arch -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Dermal bone that underlies the mesethmoid and inserts in a fossa on the anteroventral surface of the parasphenoid.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000308", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Paired, palatal bones of intramembranous origin that lie ventral to the olfactory region and help to floor the nasal capsules.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000633", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000002 "relationship loss: overlaps autopalatine-vomer joint (TAO:0001784)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000308", ontology="TAO"} -property_value: UBPROP:0000002 "relationship loss: overlaps mesethmoid-vomer joint (TAO:0001680)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000308", ontology="TAO"} -property_value: UBPROP:0000003 "In bony fish, the vomers are flattened, paired, bones forming the anterior part of the roof of the mouth, just behind the premaxillary bones. In many species, they have teeth, supplementing those in the jaw proper; in some extinct species the teeth on the vomers were actually larger than the primary set. In amphibians and reptiles, the vomers become narrower, due to the presence of the enlarged choanae (the inner part of the nostrils) on either side, and they may extend further back in the jaw. They are typically small in birds, where they form the upper hind part of the beak, again being located between the choanae. In mammals, the vomers have become narrower still, and are fused into a single, vertically oriented bone. The development of the hard palate beneath the vomer means that the bone is now located in a nasal chamber, separate from the mouth[WP]" xsd:string {source="Wikipedia:Vomer#In_other_animals"} -property_value: UBPROP:0000005 "The vomer is paired in some taxa (e.g., Amia) while unpaired in others (e.g., teleosts).[TAO]" xsd:string {date_retrieved="2012-09-06", external_class="TAO:0000308", ontology="TAO", source="Curator"} +relationship: RO:0002170 UBERON:0001677 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to sphenoid bone +relationship: RO:0002170 UBERON:0001679 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to ethmoid bone +relationship: RO:0002433 UBERON:0011156 ! contributes to morphology of facial skeleton +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002398 @@ -194102,11 +192043,9 @@ is_a: UBERON:0002470 ! autopod region is_a: UBERON:0008785 ! upper limb segment intersection_of: UBERON:0002470 ! autopod region intersection_of: part_of UBERON:0002102 ! forelimb -relationship: develops_from UBERON:0006875 ! embryonic handplate -relationship: has_skeleton UBERON:0001442 ! skeleton of manus -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/76/LeftHand0.jpg" xsd:anyURI -property_value: IAO:0000232 "like all limb segments, this class encompasses both the unformed hand region of the embryo to the fully formed structure complete with skeleton" xsd:string -property_value: UBPROP:0000007 "manual" xsd:string +relationship: RO:0002202 UBERON:0006875 ! develops from embryonic handplate +relationship: RO:0002551 UBERON:0001442 ! has skeleton skeleton of manus +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/76/LeftHand0.jpg" xsd:anyURI [Term] id: UBERON:0002400 @@ -194125,14 +192064,15 @@ xref: SCTID:361998003 xref: UMLS:C0225777 {source="ncithesaurus:Parietal_Pleura"} xref: VHOG:0001495 xref: Wikipedia:Parietal_pleura +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0004923 ! organ component layer intersection_of: UBERON:0004923 ! organ component layer intersection_of: adjacent_to UBERON:0002224 ! thoracic cavity intersection_of: part_of UBERON:0000977 ! pleura relationship: adjacent_to UBERON:0002224 ! thoracic cavity -relationship: contributes_to_morphology_of UBERON:0000977 ! pleura -relationship: innervated_by UBERON:0003727 ! intercostal nerve relationship: part_of UBERON:0000977 ! pleura +relationship: RO:0002005 UBERON:0003727 ! innervated_by intercostal nerve +relationship: RO:0002433 UBERON:0000977 ! contributes to morphology of pleura [Term] id: UBERON:0002401 @@ -194157,18 +192097,17 @@ xref: NCIT:C33881 xref: SCTID:361997008 xref: UMLS:C0225776 {source="ncithesaurus:Visceral_Pleura"} xref: VHOG:0001496 +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0022350 ! visceral serous membrane intersection_of: UBERON:0004923 ! organ component layer intersection_of: adjacent_to UBERON:0002048 ! lung intersection_of: part_of UBERON:0000977 ! pleura relationship: adjacent_to UBERON:0002048 ! lung -relationship: attaches_to UBERON:0008946 ! lung parenchyma -relationship: contributes_to_morphology_of UBERON:0000977 ! pleura relationship: part_of UBERON:0000977 ! pleura relationship: part_of UBERON:0002048 {source="FMA"} ! lung -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000001 "Each lung is invested by an exceedingly delicate serous membrane, the pleura, which is arranged in the form of a closed invaginated sac. A portion of the serous membrane covers the surface of the lung and dips into the fissures between its lobes; it is called the pulmonary pleura (or visceral pleura). The visceral pleura is attached directly to the lungs[Wikipedia:Visceral_pleura]." xsd:string {source="Wikipedia:Visceral_pleura"} -property_value: UBPROP:0000012 "FMA treats this as part of the lungs" xsd:string {external_ontology="FMA"} +relationship: RO:0002371 UBERON:0008946 ! attached to lung parenchyma +relationship: RO:0002433 UBERON:0000977 ! contributes to morphology of pleura +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002402 @@ -194195,15 +192134,12 @@ xref: VHOG:0000581 xref: Wikipedia:Pleural_cavity is_a: UBERON:0035809 ! serous cavity intersection_of: UBERON:0002553 ! anatomical cavity -intersection_of: luminal_space_of UBERON:0009778 ! pleural sac +intersection_of: RO:0002572 UBERON:0009778 ! luminal space of pleural sac relationship: adjacent_to UBERON:0002400 ! parietal pleura relationship: adjacent_to UBERON:0002401 ! visceral pleura -relationship: develops_from UBERON:0003887 {source="Wikipedia"} ! intraembryonic coelom -relationship: luminal_space_of UBERON:0009778 ! pleural sac -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/ab/Gray965.png" xsd:anyURI -property_value: UBPROP:0000003 "In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000581", ontology="VHOG", source="ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000009 "The contraction of the diaphragm creates a negative pressure within the pleural cavity which forces the lungs to expand resulting in passive exhalation and active inhalation. This breathing process can be made forceful through the contraction of the external intercostal muscles which forces the rib cage to expand and add to the negative pressure in the pleural cavity causing the lungs to fill with air. The fluid in the cavity provides lubrication and cushioning" xsd:string -property_value: UBPROP:0000012 "the EHDAA2 class of the same is not equivalent. See https://github.com/obophenotype/uberon/issues/86" xsd:string {external_ontology="EHDAA2"} +relationship: RO:0002202 UBERON:0003887 {source="Wikipedia"} ! develops from intraembryonic coelom +relationship: RO:0002572 UBERON:0009778 ! luminal space of pleural sac +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/ab/Gray965.png" xsd:anyURI [Term] id: UBERON:0002405 @@ -194235,10 +192171,9 @@ disjoint_from: UBERON:0002423 ! hepatobiliary system disjoint_from: UBERON:0004456 ! entire sense organ system disjoint_from: UBERON:8450002 ! excretory system relationship: capable_of GO:0002376 ! immune system process -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: protects UBERON:0000468 ! multicellular organism -property_value: UBPROP:0000003 "The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001247", ontology="VHOG", source="PMID:21046016 Dzik JM, The ancestry and cumulative evolution of immune reactions. Acta biochimica Polonica (2010)", source="http://bgee.unil.ch/"} +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002406 @@ -194251,7 +192186,6 @@ synonym: "pericardium" RELATED [] xref: FMA:9868 xref: RETIRED_EHDAA2:0001443 xref: SCTID:361326002 -xref: TAO:0000054 is_a: UBERON:0005181 ! thoracic segment organ is_a: UBERON:0005906 ! serous sac intersection_of: UBERON:0005906 ! serous sac @@ -194260,8 +192194,8 @@ intersection_of: has_part UBERON:0002357 ! serous pericardium relationship: has_part UBERON:0001074 ! pericardial cavity relationship: has_part UBERON:0002357 ! serous pericardium relationship: part_of UBERON:0002407 ! pericardium -relationship: surrounded_by UBERON:0002359 {source="FMA"} ! fibrous pericardium -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png" xsd:anyURI +relationship: RO:0002219 UBERON:0002359 {source="FMA"} ! surrounded by fibrous pericardium +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png" xsd:anyURI [Term] id: UBERON:0002407 @@ -194279,7 +192213,6 @@ xref: BTO:0000717 xref: CALOHA:TS-0761 xref: EFO:0000820 xref: EHDAA:5376 -xref: EMAPA:16133 xref: EV:0100023 xref: FMA:9869 xref: GAID:569 @@ -194290,7 +192223,6 @@ xref: MESH:D010496 xref: NCIT:C13005 xref: RETIRED_EHDAA2:0001443 xref: SCTID:181295003 -xref: TAO:0000054 xref: UMLS:C0031050 {source="ncithesaurus:Pericardium"} xref: VHOG:0001280 xref: Wikipedia:Pericardium @@ -194301,14 +192233,9 @@ is_a: UBERON:0000481 ! multi-tissue structure relationship: has_part UBERON:0002359 ! fibrous pericardium relationship: has_part UBERON:0002406 ! pericardial sac relationship: part_of UBERON:0015410 {source="MA"} ! heart plus pericardium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: surrounds UBERON:0002349 ! myocardium -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png" xsd:anyURI -property_value: UBPROP:0000001 "Peritoneum that surrounds the heart.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010817", ontology="AAO", source="AAO:JMG"} -property_value: UBPROP:0000007 "pericardial" xsd:string -property_value: UBPROP:0000012 "In GO the concept of pericardium is developmental implicitly epithelial, but here it represents a multi-tissue structure encompassing the sac (epithelium plus connective) and cavity" xsd:string {external_ontology="FMA"} -property_value: UBPROP:0000012 "this class denotes a combination of fibrous PC + PC sac (itself a combination of cavity, epithelium and connective tissue). Many sources use the term 'pericardium' to denote either just the serous membrane (ZFA) or the epithelium (GO)" xsd:string {external_ontology="ZFA"} -property_value: UBPROP:0000012 "we follow FMA in dividing pericardium into pericardial sac and fibrous pericardium" xsd:string {external_ontology="FMA"} +relationship: RO:0002221 UBERON:0002349 ! surrounds myocardium +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002408 @@ -194335,9 +192262,9 @@ xref: Wikipedia:Parietal_pericardium is_a: UBERON:0022351 ! parietal serous membrane intersection_of: UBERON:0022351 ! parietal serous membrane intersection_of: part_of UBERON:0002357 ! serous pericardium -relationship: attaches_to UBERON:0006670 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="FMA"} ! central tendon of diaphragm relationship: part_of UBERON:0002357 ! serous pericardium -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png" xsd:anyURI +relationship: RO:0002371 UBERON:0006670 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="FMA"} ! attached to central tendon of diaphragm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray489.png" xsd:anyURI [Term] id: UBERON:0002409 @@ -194348,14 +192275,13 @@ subset: uberon_slim xref: BTO:0001016 xref: FMA:9887 xref: MA:0002530 -xref: MESH:D000069236 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: Wikipedia:Pericardial_fluid is_a: UBERON:0007794 {source="FMA"} ! secretion of serous gland is_a: UBERON:0036217 ! coelomic fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: produced_by UBERON:0002425 ! visceral serous pericardium -relationship: located_in UBERON:0001074 ! pericardial cavity relationship: produced_by UBERON:0002425 ! visceral serous pericardium +relationship: RO:0001025 UBERON:0001074 ! located in pericardial cavity [Term] id: UBERON:0002410 @@ -194383,7 +192309,6 @@ xref: EHDAA:3767 xref: EMAPA:16984 xref: FMA:65553 xref: GAID:706 -xref: IDOMAL:0002126 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: MA:0000219 xref: MESH:D001341 xref: NCIT:C12673 @@ -194396,14 +192321,10 @@ xref: VHOG:0000396 xref: Wikipedia:Autonomic_nervous_system xref: ZFA:0001574 is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision -relationship: contributes_to_morphology_of UBERON:0001016 ! nervous system -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0000010 {source="EMAPA", source="MA", source="NIFSTD", source="ZFA-modified-from-isa"} ! peripheral nervous system -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png" xsd:anyURI -property_value: UBPROP:0000001 "Nervous system including a portion of the central and peripheral systems and presiding over the control and coordination of the vegetative functions of the organism. It innervates smooth and cardiac muscles and glandular tissues and is responsible for many actions which are more or less automatic (e.g. secretion, vasoconstriction etc.). It consists of the sympathetic and parasympathetic nervous systems. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000396", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000001 "Part of the peripheral nervous system which regulates involuntary functions of the body and consists of the sympathetic and parasympathetic system.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000033", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "From comparative analyses of craniate brains, a morphotype of the brain in the earliest craniate stock can be constructed. In marked contrast to cephalochordates, the ancestral craniate morphotype had a plethora of unique features, which included a telencephalon with pallial and subpallial parts, paired olfactory bulbs with substantial projections to most or all of the telencephalic pallium, paired lateral eyes and ears, a lateral line system for both electroreception and mechanoreception, spinal cord dorsal root ganglia, and an autonomic nervous system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000396", ontology="VHOG", source="DOI:10.1002/1097-0185(20000615)261:3<111::AID-AR6>3.0.CO;2-F Butler AB, Chordate evolution and the origin of craniates: An old brain in a new head. AnaT Rec (New Anat) (2000)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "FMA splits this into peripheral and nervous parts; GO has ANS directly under NS; PNS is a sib" xsd:string {external_ontology="FMA"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002433 UBERON:0001016 ! contributes to morphology of nervous system +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png" xsd:anyURI [Term] id: UBERON:0002411 @@ -194428,13 +192349,13 @@ xref: UMLS:C0008984 {source="ncithesaurus:Clitoris"} xref: VHOG:0000700 xref: Wikipedia:Clitoris is_a: UBERON:0000062 {source="Wikipedia"} ! organ +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005156 ! reproductive structure -relationship: contributes_to_morphology_of UBERON:0005056 ! external female genitalia -relationship: develops_from UBERON:0005876 {source="EHDAA2", source="Wikipedia"} ! undifferentiated genital tubercle -relationship: only_in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia relationship: part_of UBERON:0000997 {source="MA"} ! mammalian vulva -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/cf/Clitoris_anatomy_labeled-en.svg" xsd:anyURI -property_value: UBPROP:0000007 "clitoral" xsd:string +relationship: RO:0002160 NCBITaxon:40674 {source="Wikipedia"} ! only in taxon Mammalia +relationship: RO:0002202 UBERON:0005876 {source="EHDAA2", source="Wikipedia"} ! develops from undifferentiated genital tubercle +relationship: RO:0002433 UBERON:0005056 ! contributes to morphology of external female genitalia +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/cf/Clitoris_anatomy_labeled-en.svg" xsd:anyURI [Term] id: UBERON:0002412 @@ -194448,7 +192369,6 @@ subset: vertebrate_core synonym: "vertebra bone" EXACT [] synonym: "vertebrae" EXACT OMO:0003004 [PHENOSCAPE:ad] xref: AAO:0000691 -xref: BTO:0006196 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: CALOHA:TS-2352 xref: EFO:0001371 xref: EMAPA:32740 @@ -194466,14 +192386,12 @@ is_a: UBERON:0002513 ! endochondral bone is_a: UBERON:0008001 {source="FMA"} ! irregular bone is_a: UBERON:0010913 ! vertebral element intersection_of: UBERON:0010913 ! vertebral element -intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue -relationship: develops_from UBERON:0011094 ! vertebra cartilage element -relationship: never_in_taxon NCBITaxon:7901 {source="Wikipedia"} +intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue relationship: part_of UBERON:0001130 ! vertebral column -property_value: editor_note "Consider changing name to make distinction from inferred superclass 'vertebral element' clear" xsd:string -property_value: editor_note "we follow FMA in making this an irregular bone - however vertebra have 'epiphyses' which are currently classified as belonging to long bones" xsd:string -property_value: UBPROP:0000001 "Endochondral bone that forms around the notochord and is part of the vertebral column.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001189", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Main component of the vertebral column. It consists of two essential parts, a dorsal neural arch and a ventral centrum.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000691", ontology="AAO", source="AAO:Pugener_and_Maglia_2008"} +relationship: RO:0002202 UBERON:0011094 ! develops from vertebra cartilage element +property_value: IAO:0000116 "Consider changing name to make distinction from inferred superclass 'vertebral element' clear" xsd:string +property_value: IAO:0000116 "we follow FMA in making this an irregular bone - however vertebra have 'epiphyses' which are currently classified as belonging to long bones" xsd:string +property_value: RO:0002161 NCBITaxon:7901 {source="Wikipedia"} [Term] id: UBERON:0002413 @@ -194500,11 +192418,10 @@ is_a: UBERON:0004247 ! bone of dorsum is_a: UBERON:0004451 {is_inferred="true"} ! trunk or cervical vertebra is_a: UBERON:0015007 ! cervical vertebra endochondral element intersection_of: UBERON:0015007 ! cervical vertebra endochondral element -intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue -relationship: develops_from UBERON:0013505 ! cervical vertebra cartilage element -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/f8/Illu_vertebral_column.jpg" xsd:anyURI -property_value: UBPROP:0000008 "In some species, some parts of the skull may be composed of vertebra-like elements, e.g. the occipital bone in humans is composed of four vertebra-like segments. In many vertebrate species, cervical vertebrae are variable in number; however, almost all mammals have seven (including those with very short necks relative to body size, such as elephants or whales, and those with very long necks, such as giraffes). The few exceptions include the manatee and the sloths, of which the two-toed sloth has six cervical vertebrae and the three-toed sloth has up to nine cervical vertebrae. In many species, though not in mammals, the cervical vertebrae bear ribs. In many other groups, such as lizards and saurischian dinosaurs, the cervical ribs are large; in birds they are small and completely fused to the vertebrae. The transverse processes of mammals are homologous to the cervical ribs of other amniotes. Thoracic vertebrae in all species are defined as those vertebrae which also carry a pair of ribs, and lie caudal to the cervical vertebrae. In humans, cervical vertebrae are the smallest of the true vertebrae, and can be readily distinguished from those of the thoracic or lumbar regions by the presence of a foramen (hole) in each transverse process, through which passes the vertebral artery." xsd:string +intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue +relationship: RO:0002202 UBERON:0013505 ! develops from cervical vertebra cartilage element +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f8/Illu_vertebral_column.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002415 @@ -194528,10 +192445,10 @@ xref: MIAA:0000094 xref: WBbt:0005741 xref: Wikipedia:Tail is_a: UBERON:0011676 ! subdivision of organism along main body axis -relationship: never_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0000154 ! posterior region of body -property_value: editor_note "Note we also have a subclass post-anal tail, for the chordate specific structure. currently defined very generally, inclusive of caudal fin" xsd:string +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +property_value: IAO:0000116 "Note we also have a subclass post-anal tail, for the chordate specific structure. currently defined very generally, inclusive of caudal fin" xsd:string +property_value: RO:0002161 NCBITaxon:9606 [Term] id: UBERON:0002416 @@ -194560,7 +192477,6 @@ xref: EHDAA2_RETIRED:0003154 xref: EHDAA:6520 xref: EMAPA:17524 xref: EV:0100151 -xref: FBbt:00004969 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:72979 xref: galen:Surface xref: HAO:0000421 @@ -194581,11 +192497,10 @@ disjoint_from: UBERON:0002423 ! hepatobiliary system disjoint_from: UBERON:0004456 ! entire sense organ system disjoint_from: UBERON:8450002 ! excretory system relationship: bounding_layer_of UBERON:0000468 ! multicellular organism -relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: has_part UBERON:0007376 ! outer epithelium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: surrounded_by UBERON:0013514 ! space surrounding organism -property_value: UBPROP:0000003 "(...) the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000403", ontology="VHOG", source="DOI:10.1111/j.1469-7580.2008.01043.x Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009)", source="http://bgee.unil.ch/"} +relationship: RO:0002219 UBERON:0013514 ! surrounded by space surrounding organism +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002417 @@ -194646,16 +192561,11 @@ xref: XAO:0000170 xref: ZFA:0005622 is_a: UBERON:0004755 ! skeletal tissue disjoint_from: UBERON:0002481 {source="https://github.com/obophenotype/uberon/issues/117"} ! bone tissue -relationship: contributes_to_morphology_of UBERON:0001434 ! skeletal system relationship: has_part CHEBI:18085 relationship: has_part CL:0000138 ! chondrocyte -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Hypertrophic_Zone_of_Epiphyseal_Plate.jpg" xsd:anyURI -property_value: UBPROP:0000001 "A type of dense connective tissue. It is composed of cells called chondrocytes which are dispersed in a firm gel-like ground substance, called the matrix. Cartilage is avascular (contains no blood vessels) and nutrients are diffused through the matrix. Cartilage is found in the joints, the rib cage, the ear, the nose, in the throat and between intervertebral disks. It makes up virtually the entire skeleton in chondrichthyes.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000060", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000001 "Portion of tissue which is connective tissue composed of collagen and/or elastin fibers and chondrocytes. Cartilage is avascular and provides both skeletal functions and a framework upon which bone is deposited.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001501", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000040", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} -property_value: UBPROP:0000002 "relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000060", ontology="AAO"} -property_value: UBPROP:0000003 "Phylogenetic analysis suggests that cartilage arose independently in cnidarians, hemichordates, vertebrates, arthropods, annelids, brachiopods, and molluscs - or a common ancestor of brachiopods and molluscs (...). Analyses of cartilage as a tissue and of the development of invertebrate cartilages are consistent with homology between invertebrate and vertebrate cartilage. From the discussion above, it will be clear that understanding genetic changes underlying cartilage evolution is key to determining whether the multiple origins of cartilage represent parallel evolution.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001207", ontology="VHOG", source="DOI:10.1111/j.1525-142X.2011.00520.x Hall BK, Parallelism, deep homology, and evo-devo. Evolution and Development (2012)", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002433 UBERON:0001434 ! contributes to morphology of skeletal system +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Hypertrophic_Zone_of_Epiphyseal_Plate.jpg" xsd:anyURI [Term] id: UBERON:0002419 @@ -194672,11 +192582,12 @@ xref: FMA:71878 xref: MA:0000146 xref: SCTID:110485007 is_a: UBERON:0003297 ! gland of integumental system +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0006003 ! integumentary adnexa intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0002097 ! skin of body relationship: part_of UBERON:0002097 ! skin of body -property_value: editor_note "check FMA, use plural for now as general class not there" xsd:string +property_value: IAO:0000116 "check FMA, use plural for now as general class not there" xsd:string [Term] id: UBERON:0002420 @@ -194699,8 +192610,8 @@ xref: SCTID:244434001 is_a: UBERON:0003528 ! brain gray matter is_a: UBERON:0007245 {source="FMA"} ! nuclear complex of neuraxis relationship: part_of UBERON:0010011 ! collection of basal ganglia -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1b/Basal_Ganglia_and_Related_Structures.svg" xsd:anyURI -property_value: editor_note "it is necessary to introduce two classes, one representing an individual basal ganglion, another representing the aggregate structure, in order to have consistent classification amongst AOs (e.g. in MA the aygdala is part of the BG, in FMA and BTO it is a subclass). Apart from achieving this consistency, the value of having two distinct classes is questionable, since the BG-plural is trivially the set of all BGs-singular. it would be better for all AOs to decide on one single way of doing this. Do not merge until this is done." xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1b/Basal_Ganglia_and_Related_Structures.svg" xsd:anyURI +property_value: IAO:0000116 "it is necessary to introduce two classes, one representing an individual basal ganglion, another representing the aggregate structure, in order to have consistent classification amongst AOs (e.g. in MA the aygdala is part of the BG, in FMA and BTO it is a subclass). Apart from achieving this consistency, the value of having two distinct classes is questionable, since the BG-plural is trivially the set of all BGs-singular. it would be better for all AOs to decide on one single way of doing this. Do not merge until this is done." xsd:string [Term] id: UBERON:0002421 @@ -194735,12 +192646,9 @@ xref: SCTID:422867004 xref: UMLS:C0175202 {source="BIRNLEX:715"} xref: Wikipedia:Hippocampal_formation is_a: UBERON:0002616 ! regional part of brain -relationship: only_in_taxon NCBITaxon:40674 {source="Wikipedia:Hippocampus"} ! Mammalia relationship: part_of UBERON:0000956 {source="MBA-indirect", source="NIFSTD"} ! cerebral cortex -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: IAO:0000232 "The term hippocampus is often used synonymously with hippocampal formation which consists of the hippocampus proper or Cornu Ammonis, the dentate gyrus and the subiculum" xsd:string {source="NIF"} -property_value: RO:0002171 UBERON:0002264 {source="ABA"} -property_value: UBPROP:0000012 "BTO:0000601 is placed here since it includes the DG. GO also includes dentate gyrus development as part of hippocampus development, so we assume when GO says 'hippocampus' it means 'hippocampal formation'. In ABA HPF = (.. subiculum) + HIP, HIP = DG + AH." xsd:string {external_ontology="BTO"} +relationship: RO:0002160 NCBITaxon:40674 {source="Wikipedia:Hippocampus"} ! only in taxon Mammalia +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002422 @@ -194793,17 +192701,13 @@ xref: ZFA:0000110 is_a: UBERON:0004086 ! brain ventricle intersection_of: UBERON:0004086 ! brain ventricle intersection_of: part_of UBERON:0002028 ! hindbrain -relationship: contributes_to_morphology_of UBERON:0002028 ! hindbrain -relationship: develops_from UBERON:0013149 {source="EHDAA2"} ! hindbrain vesicle relationship: part_of UBERON:0002028 ! hindbrain -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray734.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI -property_value: UBPROP:0000001 "Fluid-filled brain cavity. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000110", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Irregularly shaped cavity in the rhombencephalon, between the medulla oblongata, the pons, and the isthmus in front, and the cerebellum behind. It is continuous with the central canal of the cord below and with the cerebral aqueduct above, and through its lateral and median apertures it communicates with the subarachnoid space.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011043", ontology="AAO", source="UBERON:0002422"} -property_value: UBPROP:0000001 "The fourth ventricle is an irregularly shaped cavity in the rhombencephalon, between the medulla oblongata, the pons, and the isthmus in front, and the cerebellum behind. It is continuous with the central canal of the cord below and with the cerebral aqueduct above, and through its lateral and median apertures it communicates with the subarachnoid space[GO][GO:0021592]." xsd:string {source="GO:0021592"} -property_value: UBPROP:0000003 "The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000006", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0013149 {source="EHDAA2"} ! develops from hindbrain vesicle +relationship: RO:0002433 UBERON:0002028 ! contributes to morphology of hindbrain +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray734.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002423 @@ -194839,13 +192743,11 @@ is_a: UBERON:0011216 ! organ system subdivision disjoint_from: UBERON:0004456 ! entire sense organ system disjoint_from: UBERON:8450002 ! excretory system relationship: capable_of GO:0061007 ! hepaticobiliary system process -relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: has_part UBERON:0002107 ! liver relationship: has_part UBERON:0002294 ! biliary system -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0001007 ! digestive system -property_value: UBPROP:0000001 "System responsible for the production and movement of bile[ZFIN:curator]." xsd:string {source="ZFIN:curator"} -property_value: UBPROP:0000009 "The hepaticobiliary system is responsible for metabolic and catabolic processing of small molecules absorbed from the blood or gut, hormones and serum proteins, detoxification, storage of glycogen, triglycerides, metals and lipid soluble vitamins and excretion of bile. Included are the synthesis of albumin, blood coagulation factors, complement, and specific binding proteins. The parts are: liver, bile duct, gall bladder and hepatic duct [GO:0061008]" xsd:string +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage [Term] id: UBERON:0002424 @@ -194877,9 +192779,7 @@ intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0003729 ! mouth mucosa relationship: adjacent_to UBERON:0000167 {source="AAO-modified"} ! oral cavity relationship: part_of UBERON:0003729 ! mouth mucosa -property_value: editor_note "consider including separate class for developmental structure (adult human is stratified; in EHDAA2 is unilaminar)" xsd:string -property_value: UBPROP:0000001 "The epithelium that lines the oral cavity. The oral epithelium epithelial cells with many short microvilli as well as mucous cells, rodlet cells and taste buds[ZFIN:ZDB-PUB-060921-12, ZFIN:ZDB-PUB-091204-24]." xsd:string {source="ZFA:0000816"} -property_value: UBPROP:0000011 "the avian oral epithelium has the developmental capacity to initiate tooth developmental programs with underlying grafts of non-avian oral ectomesenchyme" xsd:string {source="PMID:16488870"} +property_value: IAO:0000116 "consider including separate class for developmental structure (adult human is stratified; in EHDAA2 is unilaminar)" xsd:string [Term] id: UBERON:0002425 @@ -194895,7 +192795,6 @@ synonym: "serous visceral pericardium" EXACT [] synonym: "visceral lamina of serous pericardium" EXACT [] synonym: "visceral layer of serous pericardium" EXACT [] synonym: "visceral pericardium" EXACT [VHOG:0000538] -xref: EMAPA:16589 xref: EMAPA:19032 xref: FMA:84882 xref: MA:0000484 @@ -194905,10 +192804,10 @@ xref: Wikipedia:Visceral_pericardium is_a: UBERON:0022350 ! visceral serous membrane intersection_of: UBERON:0022350 ! visceral serous membrane intersection_of: part_of UBERON:0002357 ! serous pericardium -relationship: attaches_to UBERON:0002349 {source="FMA"} ! myocardium -relationship: contributes_to_morphology_of UBERON:0002407 ! pericardium relationship: has_part UBERON:0002348 {source="cjm"} ! epicardium relationship: part_of UBERON:0002357 ! serous pericardium +relationship: RO:0002371 UBERON:0002349 {source="FMA"} ! attached to myocardium +relationship: RO:0002433 UBERON:0002407 ! contributes to morphology of pericardium [Term] id: UBERON:0002426 @@ -194930,14 +192829,13 @@ synonym: "thoracic muscle" EXACT [] xref: BTO:0000508 xref: CALOHA:TS-1037 xref: EMAPA:17747 -xref: EMAPA:17748 xref: FMA:9619 xref: MA:0000548 is_a: UBERON:0003830 ! thoracic segment muscle is_a: UBERON:0005175 ! chest organ intersection_of: UBERON:0014892 ! skeletal muscle organ, vertebrate intersection_of: part_of UBERON:0001443 ! chest -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002427 @@ -194976,9 +192874,7 @@ is_a: UBERON:0004375 ! bone of free limb or fin is_a: UBERON:0015061 ! limb endochondral element intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0002101 ! limb -relationship: develops_from UBERON:0010881 ! limb cartilage element -property_value: IAO:0000232 "the formal definition is very inclusive, and includes sesamoids" xsd:string -property_value: UBPROP:0000012 "NCITA includes clavicle. MA:'limb bone' is actually a bone of limb or girdle" xsd:string {external_ontology="NCIT"} +relationship: RO:0002202 UBERON:0010881 ! develops from limb cartilage element [Term] id: UBERON:0002429 @@ -194998,7 +192894,7 @@ is_a: UBERON:0000029 ! lymph node intersection_of: UBERON:0000029 ! lymph node intersection_of: part_of UBERON:0000974 ! neck relationship: part_of UBERON:0000974 ! neck -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/4c/Lymph_node_regions.jpg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4c/Lymph_node_regions.jpg" xsd:anyURI [Term] id: UBERON:0002435 @@ -195040,14 +192936,11 @@ xref: PBA:10080 xref: UMLS:C0162512 {source="BIRNLEX:1672"} xref: Wikipedia:Striatum is_a: UBERON:0011300 ! gray matter of telencephalon -relationship: contributes_to_morphology_of UBERON:0010011 ! collection of basal ganglia relationship: part_of UBERON:0000204 {source="GO"} ! ventral part of telencephalon relationship: part_of UBERON:0000369 {source="BTO"} ! corpus striatum relationship: part_of UBERON:0006098 {source="NIFSTD"} ! basal nuclear complex -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/33/BrainCaudatePutamen.svg" xsd:anyURI -property_value: RO:0002171 UBERON:0006514 {source="ABA"} -property_value: UBPROP:0000007 "striatal" xsd:string -property_value: UBPROP:0000012 "FMA divides 'striatum of neuraxis' into 4, neostriatum is seperate class. In NIF these are synonyms. TODO - check striatum vs corpus striatum see Wikipedia:Striatum#History. Check caudoputamen" xsd:string {external_ontology="FMA"} +relationship: RO:0002433 UBERON:0010011 ! contributes to morphology of collection of basal ganglia +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/33/BrainCaudatePutamen.svg" xsd:anyURI [Term] id: UBERON:0002437 @@ -195079,8 +192972,6 @@ is_a: UBERON:0011299 ! white matter of telencephalon intersection_of: UBERON:0002316 ! white matter intersection_of: part_of UBERON:0001869 ! cerebral hemisphere relationship: part_of UBERON:0001869 ! cerebral hemisphere -property_value: IAO:0000232 "sometimes the term 'cerebral white matter' may be used generically but here is refers specifically to the white matter in a hemisphere" xsd:string -property_value: UBPROP:0000012 "The BTO class is inconsistent as it is part of the brain and spinal cord." xsd:string {external_ontology="BTO"} [Term] id: UBERON:0002442 @@ -195120,6 +193011,7 @@ xref: EMAPA:17828 xref: FMA:76550 xref: MA:0001237 is_a: UBERON:0003496 ! head blood vessel +is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0001776 ! optic choroid relationship: part_of UBERON:0001776 ! optic choroid @@ -195150,15 +193042,14 @@ xref: UMLS:C0229224 {source="ncithesaurus:Lens_Fiber"} xref: VHOG:0000444 xref: Wikipedia:Lens_(anatomy)#Lens_fibers xref: XAO:0004096 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0034944 ! zone of organ intersection_of: UBERON:0034944 ! zone of organ -intersection_of: composed_primarily_of CL:0011004 ! lens fiber cell -relationship: composed_primarily_of CL:0011004 ! lens fiber cell -relationship: contributes_to_morphology_of UBERON:0000965 ! lens of camera-type eye +intersection_of: RO:0002473 CL:0011004 ! composed primarily of lens fiber cell relationship: part_of UBERON:0000965 ! lens of camera-type eye -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000001 "Fibres resembling a ribbon and arranged in very thin plates in the lens. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000444", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "(...) the line, or Y, or star sutures common to mammalian lenses, including those of primates. In the case of line or Y sutures, the overlapping of lens fibers in each successive shell is coincident and results in the formation of four or six three-dimensional suture planes that extend from the lens nucleus to the periphery.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000444", ontology="VHOG", source="DOI:10.1167/iovs.03-0466 Sivak JG, Through the lens clearly: phylogeny and development, The Proctor lecture. Investigative ophthalmology and visual science (2004)", source="http://bgee.unil.ch/"} +relationship: RO:0002433 UBERON:0000965 ! contributes to morphology of lens of camera-type eye +relationship: RO:0002473 CL:0011004 ! composed primarily of lens fiber cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002446 @@ -195186,14 +193077,13 @@ is_a: UBERON:0001479 {source="FMA"} ! sesamoid bone is_a: UBERON:0005893 ! leg bone is_a: UBERON:0011141 ! appendicular ossicle intersection_of: UBERON:0001474 ! bone element -intersection_of: connected_to UBERON:0000981 ! femur intersection_of: part_of UBERON:0001465 ! knee +intersection_of: RO:0002170 UBERON:0000981 ! connected to femur relationship: adjacent_to UBERON:0001485 ! knee joint -relationship: connected_to UBERON:0000981 ! femur relationship: part_of UBERON:0001465 ! knee -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/9/9a/Knee_diagram.svg" xsd:anyURI -property_value: UBPROP:0000007 "patellar" xsd:string +relationship: RO:0002170 UBERON:0000981 ! connected to femur +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/9/9a/Knee_diagram.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002450 @@ -195226,12 +193116,11 @@ xref: SCTID:362842004 xref: UMLS:C0011106 {source="ncithesaurus:Decidua"} xref: Wikipedia:Decidua is_a: UBERON:0000478 {source="FMA"} ! extraembryonic structure -relationship: contributes_to_morphology_of UBERON:0001987 ! placenta -relationship: develops_from UBERON:0000459 ! uterine wall -relationship: part_of UBERON:0001987 {component="maternal", source="MA"} ! placenta -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/fa/Gray33.png" xsd:anyURI -property_value: editor_note "TODO - check mp syn" xsd:string -property_value: UBPROP:0000011 "formed under the influence of progesterone and forms highly-characteristic cells. [Wikipedia:Decidua]" xsd:string +relationship: part_of UBERON:0001987 ! placenta +relationship: RO:0002202 UBERON:0000459 ! develops from uterine wall +relationship: RO:0002433 UBERON:0001987 ! contributes to morphology of placenta +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/fa/Gray33.png" xsd:anyURI +property_value: IAO:0000116 "TODO - check mp syn" xsd:string [Term] id: UBERON:0002451 @@ -195257,16 +193146,15 @@ xref: SCTID:361377009 xref: UMLS:C1183035 {source="ncithesaurus:Uterine_Gland"} xref: Wikipedia:Uterine_glands is_a: UBERON:0000414 {source="MP"} ! mucous gland +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005179 ! pelvic region element is_a: UBERON:0005398 ! female reproductive gland intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0001295 ! endometrium -relationship: has_quality PATO:0002299 {source="Wikipedia:Tubular_gland"} ! tubular relationship: part_of UBERON:0012276 ! endometrium glandular epithelium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/28/Gray1169.png" xsd:anyURI -property_value: UBPROP:0000010 "simple or branched tubular" xsd:string -property_value: UBPROP:0000202 FMA:71647 +relationship: RO:0000086 PATO:0002299 {source="Wikipedia:Tubular_gland"} ! has quality tubular +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/28/Gray1169.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002456 @@ -195291,12 +193179,11 @@ xref: SCTID:244239009 xref: UMLS:C0226276 {source="ncithesaurus:Internal_Mammary_Artery"} xref: Wikipedia:Internal_thoracic_artery is_a: UBERON:0004573 ! systemic artery -relationship: connecting_branch_of UBERON:0001533 ! subclavian artery relationship: part_of UBERON:0001533 ! subclavian artery -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: supplies UBERON:0000310 ! breast -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray522.png" xsd:anyURI -property_value: UBPROP:0000012 "MA has both mammary and thoracic" xsd:string {external_ontology="MA"} +relationship: RO:0002178 UBERON:0000310 ! supplies breast +relationship: RO:0002252 UBERON:0001533 ! connecting branch of subclavian artery +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray522.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002457 @@ -195319,8 +193206,6 @@ xref: XAO:0004165 xref: ZFA:0001061 is_a: UBERON:0001637 ! artery is_a: UBERON:0014907 ! intersomitic vessel -property_value: UBPROP:0000001 "Arteries that connect the dorsal aorta and the dorsal longitudinal anastomotic vessel. They run along the vertical myotomal boundaries. At early stages these vessels don't have venous or arteriproperty_value external_definitionmarkers. They form from the primary sprouts from the dorsal aorta[ZFA:0001061]." xsd:string {source="ZFA:0001061"} -property_value: UBPROP:0000003 "Few changes of evolutionary significance occur in the branching pattern of the dorsal aorta. All vertebrates have (...) paired intersegmental arteries to the trunk, tail, and paired appendages.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000225", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.612", source="http://bgee.unil.ch/"} [Term] id: UBERON:0002458 @@ -195342,8 +193227,8 @@ xref: Wikipedia:Spinal_artery xref: ZFA:0000682 is_a: UBERON:0004573 ! systemic artery intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0002240 ! spinal cord -relationship: supplies UBERON:0002240 ! spinal cord +intersection_of: RO:0002178 UBERON:0002240 ! supplies spinal cord +relationship: RO:0002178 UBERON:0002240 ! supplies spinal cord [Term] id: UBERON:0002460 @@ -195361,12 +193246,11 @@ xref: SCTID:12683000 xref: Wikipedia:Vesical_veins is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein -intersection_of: drains UBERON:0001255 ! urinary bladder -relationship: drains UBERON:0001255 ! urinary bladder -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: tributary_of UBERON:0001317 ! internal iliac vein -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/bd/Gray585.png" xsd:anyURI -property_value: UBPROP:0000202 FMA:70911 +intersection_of: RO:0002179 UBERON:0001255 ! drains urinary bladder +relationship: RO:0002179 UBERON:0001255 ! drains urinary bladder +relationship: RO:0002376 UBERON:0001317 ! tributary of internal iliac vein +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/bd/Gray585.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002464 @@ -195390,7 +193274,6 @@ intersection_of: trunk_part_of UBERON:0001021 ! nerve disjoint_from: UBERON:0003439 ! nerve of trunk region relationship: part_of UBERON:0001021 ! nerve relationship: trunk_part_of UBERON:0001021 ! nerve -property_value: UBPROP:0000001 "Segment of neural tree organ which consists of nerve fiber bundles aggregated to form a cable-like structure that branches off to different nerves; together with all nerves of the same tree. Example: trunk of cranial nerve, trunk of spinal nerve, trunk of peripheral nerve[FMA:5913]." xsd:string {source="FMA:5913"} [Term] id: UBERON:0002465 @@ -195421,16 +193304,10 @@ xref: Wikipedia:Lymphoid_system xref: XAO:0003199 xref: ZFA:0000385 is_a: UBERON:0000467 ! anatomical system -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0002193 {source="FMA"} ! hemolymphoid system relationship: part_of UBERON:0002405 ! immune system -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b3/TE-Lymphatic_system_diagram.svg" xsd:anyURI -property_value: UBPROP:0000001 "Part of the circulatory system which consists of a series of vessels which collect blood (exclusive of erythrocytes) which seep through capillary walls and return it to the veins.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010522", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "Tetrapods have evolved distinct lymphatic systems, in which lymphatic capillaries help drain most of the tissues of the body.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000842", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.627", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "lymphoid" xsd:string -property_value: UBPROP:0000008 "The lymphatic system of anuran amphibians is characterized by large lymphatic sacs and two pairs of lymph hearts that return lymph into the venous circulation but no lymph vessels per se [10.1152/japplphysiol.00201.2013]" xsd:string -property_value: UBPROP:0000008 "The lymphatic systems of reptiles and some birds have lymph hearts, and both groups have extensive lymph vessels, but their functional role in both lymph movement and plasma volume homeostasis is almost completely unknown [10.1152/japplphysiol.00201.2013]" xsd:string -property_value: UBPROP:0000012 "We follow FMA and MA in distinguishing between lymphatic system and lymphoid system, with lymhoid tissue part of the non-lymphatic component, although these terms are often used interchangeably. We assume the ZFA term lymphatic tissue actually corresponds to the broader class (e.g. ZFA lymph node in the ZFA lymphatic system). See tracker for more comments." xsd:string {source="https://github.com/obophenotype/mouse-anatomy-ontology/issues/51"} +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b3/TE-Lymphatic_system_diagram.svg" xsd:anyURI [Term] id: UBERON:0002466 @@ -195482,7 +193359,6 @@ xref: BTO:0002859 xref: EMAPA:26981 xref: FMA:62996 xref: MA:0002680 -xref: MESH:D000071041 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C32538 xref: SCTID:362127004 xref: UMLS:C0227176 {source="ncithesaurus:Esophageal_Mucosa"} @@ -195524,12 +193400,11 @@ xref: SCTID:95936004 xref: UMLS:C0687080 {source="ncithesaurus:Paw"} is_a: UBERON:0002529 ! limb segment intersection_of: UBERON:0002529 ! limb segment -intersection_of: has_skeleton UBERON:0006717 ! autopodial skeleton -relationship: contributes_to_morphology_of UBERON:0002101 ! limb -relationship: develops_from UBERON:0010130 {evidence="definitional"} ! embryonic autopod plate +intersection_of: RO:0002551 UBERON:0006717 ! has skeleton autopodial skeleton relationship: distally_connected_to UBERON:0002471 ! zeugopod -relationship: has_skeleton UBERON:0006717 ! autopodial skeleton -property_value: UBPROP:0000013 "Naming conventions for pod terms under discussion within phenoscape group; note that this refers to the limb segment, not just the skeleton." xsd:string +relationship: RO:0002202 UBERON:0010130 ! develops from embryonic autopod plate +relationship: RO:0002433 UBERON:0002101 ! contributes to morphology of limb +relationship: RO:0002551 UBERON:0006717 ! has skeleton autopodial skeleton [Term] id: UBERON:0002471 @@ -195557,11 +193432,10 @@ xref: MAT:0000092 xref: MIAA:0000092 is_a: UBERON:0002529 ! limb segment intersection_of: UBERON:0002529 ! limb segment -intersection_of: has_skeleton UBERON:0011584 ! zeugopodial skeleton -relationship: distal_to UBERON:0002472 ! stylopod -relationship: has_skeleton UBERON:0011584 ! zeugopodial skeleton -relationship: proximal_to UBERON:0002470 ! autopod region -property_value: UBPROP:0000007 "zeugopodial" xsd:string +intersection_of: RO:0002551 UBERON:0011584 ! has skeleton zeugopodial skeleton +relationship: BSPO:0000097 UBERON:0002472 ! stylopod +relationship: BSPO:0000100 UBERON:0002470 ! autopod region +relationship: RO:0002551 UBERON:0011584 ! has skeleton zeugopodial skeleton [Term] id: UBERON:0002472 @@ -195583,13 +193457,9 @@ xref: MAT:0000093 xref: MIAA:0000093 is_a: UBERON:0002529 ! limb segment intersection_of: UBERON:0002529 ! limb segment -intersection_of: has_skeleton UBERON:0011583 ! stylopodial skeleton -relationship: has_skeleton UBERON:0011583 ! stylopodial skeleton -relationship: proximal_to UBERON:0002471 ! zeugopod -property_value: RO:0002171 UBERON:0002470 -property_value: RO:0002171 UBERON:0002471 -property_value: UBPROP:0000007 "stylopodial" xsd:string -property_value: UBPROP:0000013 "Naming conventions for pod terms under discussion within phenoscape group" xsd:string +intersection_of: RO:0002551 UBERON:0011583 ! has skeleton stylopodial skeleton +relationship: BSPO:0000100 UBERON:0002471 ! zeugopod +relationship: RO:0002551 UBERON:0011583 ! has skeleton stylopodial skeleton [Term] id: UBERON:0002478 @@ -195623,22 +193493,13 @@ is_a: UBERON:0011164 ! neurocranium bone is_a: UBERON:0015059 ! orbitosphenoid endochondral element is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0015059 ! orbitosphenoid endochondral element -intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue -relationship: contributes_to_morphology_of UBERON:0001677 ! sphenoid bone -relationship: develops_from UBERON:0005687 ! orbitosphenoid cartilage element -relationship: develops_from UBERON:0009638 ! orbitosphenoid ossification center -relationship: in_lateral_side_of UBERON:0002517 {source="FMA-abduced-lr"} ! basicranium +intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue +relationship: BSPO:0000126 UBERON:0002517 {source="FMA-abduced-lr"} ! basicranium relationship: part_of UBERON:0001677 ! sphenoid bone -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/35/Gray145.png" xsd:anyURI -property_value: UBPROP:0000001 "Endochondral ossification of the lateral sides of the braincase.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000345", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000001 "Large median unpaired cartilage bone consisting of two diverging plates. Positioned medial to the eye. The orbitosphenoid develops from the Trabeculae communis and forms the anterior and anterolateral boundary of the orbital foramen and constitutes a significant part of the sidewalls and floor of the cranial cavity. Bordered by the lateral ethmoid anteriorly, and the pterosphenoid posteriorly, The orbitosphenoid may extend ventrally to meet the parasphenoid. In the adult, the orbitosphenoid is fused ventrally to the parasphenoid via a thin sheet of bone.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000253", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000002 "relationship loss: develops_from taenia marginalis anterior (TAO:0001505)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000253", ontology="TAO"} -property_value: UBPROP:0000002 "relationship loss: overlaps orbitosphenoid-lateral ethmoid joint (TAO:0001941)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000253", ontology="TAO"} -property_value: UBPROP:0000002 "relationship loss: overlaps orbitosphenoid-prootic joint (TAO:0001794)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000253", ontology="TAO"} -property_value: UBPROP:0000002 "relationship loss: overlaps pterosphenoid-orbitosphenoid joint (TAO:0001831)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000253", ontology="TAO"} -property_value: UBPROP:0000002 "relationship loss: part_of braincase and otic capsule skeleton (AAO:0000052)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000345", ontology="AAO"} -property_value: UBPROP:0000002 "relationship type change: overlaps neurocranium (TAO:0001580) CHANGED TO: develops_from neurocranium (UBERON:0001703)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000253", ontology="TAO"} -property_value: UBPROP:0000002 "relationship type change: overlaps neurocranium (TAO:0001580) CHANGED TO: part_of neurocranium (UBERON:0001703)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000253", ontology="TAO"} +relationship: RO:0002202 UBERON:0005687 ! develops from orbitosphenoid cartilage element +relationship: RO:0002202 UBERON:0009638 ! develops from orbitosphenoid ossification center +relationship: RO:0002433 UBERON:0001677 ! contributes to morphology of sphenoid bone +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/35/Gray145.png" xsd:anyURI [Term] id: UBERON:0002479 @@ -195673,7 +193534,6 @@ xref: UMLS:C0175292 {source="BIRNLEX:1595"} is_a: UBERON:0015233 ! nucleus of dorsal thalamus relationship: part_of UBERON:0001926 ! lateral geniculate body relationship: part_of UBERON:0002104 {source="NIFSTD"} ! visual system -property_value: RO:0002171 UBERON:0001927 {source="ABA"} [Term] id: UBERON:0002481 @@ -195702,10 +193562,9 @@ xref: XAO:0004040 xref: ZFA:0005621 is_a: UBERON:0004755 {source="VSAO"} ! skeletal tissue disjoint_from: UBERON:0005090 ! muscle structure -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0001474 ! bone element -property_value: editor_note "see https://github.com/obophenotype/uberon/issues/27" xsd:string -property_value: UBPROP:0000001 "Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000047", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +property_value: IAO:0000116 "see https://github.com/obophenotype/uberon/issues/27" xsd:string [Term] id: UBERON:0002482 @@ -195735,10 +193594,7 @@ xref: MA:0002783 xref: Wikipedia:Bone_marrow_of_ovaryry_cavity is_a: UBERON:0002553 ! anatomical cavity relationship: part_of UBERON:0001439 ! compact bone tissue -relationship: surrounds UBERON:0002371 ! bone marrow -property_value: RO:0002174 NCBITaxon:7955 {source="DOI:10.1177/0192623311409597"} -property_value: UBPROP:0000010 "Located in the main shaft (cortical bone) of a long bone (diaphysis) (consisting mostly of compact bone), the medullary cavity has walls composed of spongy bone (cancellous bone) and is lined with a thin, vascular membrane (endosteum)[Wikipedia:Bone_marrow_of_ovaryry_cavity]" xsd:string -property_value: UBPROP:0000012 "not clear if the FMA intends to have two classes. MP:0000065: 'the medullary cavities of the bones.'. NCITA also has 'medullary bone'" xsd:string {external_ontology="FMA"} +relationship: RO:0002221 UBERON:0002371 ! surrounds bone marrow [Term] id: UBERON:0002485 @@ -195758,14 +193614,14 @@ xref: NCIT:C13102 xref: SCTID:362276000 xref: UMLS:C0227965 {source="ncithesaurus:Prostatic_Duct"} xref: Wikipedia:Prostatic_ducts -is_a: UBERON:0004119 ! endoderm-derived structure +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0005904 ! duct of male reproductive system intersection_of: UBERON:0000058 ! duct intersection_of: part_of UBERON:0002367 ! prostate gland -relationship: contributes_to_morphology_of UBERON:0002367 ! prostate gland -relationship: develops_from UBERON:0003820 {source="PMID:18977204"} ! prostate bud relationship: part_of UBERON:0002367 ! prostate gland -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Prostate.glb" xsd:anyURI +relationship: RO:0002202 UBERON:0003820 {source="PMID:18977204"} ! develops from prostate bud +relationship: RO:0002433 UBERON:0002367 ! contributes to morphology of prostate gland +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Prostate.glb" xsd:anyURI [Term] id: UBERON:0002490 @@ -195788,11 +193644,10 @@ xref: SCTID:136854008 xref: Wikipedia:Frontal_suture is_a: UBERON:0003685 ! cranial suture intersection_of: UBERON:0003685 ! cranial suture -intersection_of: connects UBERON:0000209 {cardinality="2"} ! tetrapod frontal bone -relationship: connects UBERON:0000209 {notes="two halves of the frontal bone"} ! tetrapod frontal bone -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/17/Gray134.png" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/d/d1/Frontal_suture.png" xsd:anyURI -property_value: UBPROP:0000008 "in humans, the frontal suture is a dense connective tissue structure that divides the two halves of the frontal bone of the skull in infants and children. It usually disappears by the age of six, with the two halves of the frontal bone being fused together. If it does not disappear it may be called a 'metopic suture' or 'sutura frontalis persistens. ' If the suture is not present at birth (craniosynostosis) it will cause a keel-shaped deformity of the skull called 'trigonocephaly. ' It is present in a fetal skull so that the skull can bend and is very elastic at the time of birth. The baby's head literally bends when coming out of the mother's womb. The space is filled as the child grows older. [WP,unvetted]" xsd:string +intersection_of: RO:0002176 UBERON:0000209 {cardinality="2"} ! connects tetrapod frontal bone +relationship: RO:0002176 UBERON:0000209 ! connects tetrapod frontal bone +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/17/Gray134.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/d1/Frontal_suture.png" xsd:anyURI [Term] id: UBERON:0002495 @@ -195813,8 +193668,8 @@ xref: SCTID:332709000 xref: UMLS:C0222647 {source="ncithesaurus:Long_Bone"} xref: Wikipedia:Long_bone is_a: UBERON:0001474 ! bone element -relationship: contributes_to_morphology_of UBERON:0002091 ! appendicular skeleton relationship: part_of UBERON:0002091 ! appendicular skeleton +relationship: RO:0002433 UBERON:0002091 ! contributes to morphology of appendicular skeleton [Term] id: UBERON:0002497 @@ -195840,9 +193695,7 @@ xref: VSAO:0005067 xref: Wikipedia:Acromion is_a: UBERON:0004530 ! bony projection relationship: part_of UBERON:0006849 ! scapula -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/79/Gray206.png" xsd:anyURI -property_value: UBPROP:0000001 "Anterior rounded projection of the pars acromialis of the scapula.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000826", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000002 "relationship loss: part_of pars acromialis (AAO:0000752)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000826", ontology="AAO"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/79/Gray206.png" xsd:anyURI [Term] id: UBERON:0002498 @@ -195868,12 +193721,12 @@ xref: EMAPA:25052 xref: FMA:23418 xref: MA:0002808 xref: Wikipedia:Deltoid_tuberosity +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005813 ! tubercle is_a: UBERON:4100000 ! skeletal element projection -relationship: contributes_to_morphology_of UBERON:0000976 ! humerus relationship: part_of UBERON:0004652 ! humerus diaphysis -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/a7/HumerusFront.png" xsd:anyURI -property_value: UBPROP:0000008 "In basal Tetrapodomorph lineages often the deltoid process and the pectoral processes are separate and thus should not be made exact synonyms to the deltopectoral crest.[PHENOSCAPE:ad]" xsd:string +relationship: RO:0002433 UBERON:0000976 ! contributes to morphology of humerus +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/a7/HumerusFront.png" xsd:anyURI [Term] id: UBERON:0002499 @@ -195890,10 +193743,11 @@ xref: NCIT:C32336 xref: UMLS:C0931689 {source="ncithesaurus:Cochlear_Labyrinth"} xref: Wikipedia:Cochlear_labyrinth is_a: UBERON:0000064 ! organ part -relationship: located_in UBERON:0001844 ! cochlea +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001849 {source="FMA"} ! membranous labyrinth -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray923.png" xsd:anyURI -property_value: editor_note "we follow the FMA in placing this in the membranous labyrinth. Notes: The labyrinth can be divided by layer or by region. Bony vs. membranous / Vestibular vs. cochlear" xsd:string +relationship: RO:0001025 UBERON:0001844 ! located in cochlea +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray923.png" xsd:anyURI +property_value: IAO:0000116 "we follow the FMA in placing this in the membranous labyrinth. Notes: The labyrinth can be divided by layer or by region. Bony vs. membranous / Vestibular vs. cochlear" xsd:string [Term] id: UBERON:0002506 @@ -195917,10 +193771,10 @@ is_a: UBERON:0000488 {source="FMA"} ! atypical epithelium is_a: UBERON:0015808 ! eye epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001769 ! iris -relationship: contributes_to_morphology_of UBERON:0001769 ! iris relationship: has_part GO:0048770 {source="MP"} ! pigment granule relationship: part_of UBERON:0001769 {source="MA"} ! iris -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002433 UBERON:0001769 ! contributes to morphology of iris +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002507 @@ -195956,13 +193810,14 @@ xref: MA:0002829 xref: NCIT:C77641 xref: UMLS:C0229792 {source="ncithesaurus:Mesenteric_Lymph_Node"} xref: Wikipedia:Mesenteric_lymph_nodes +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0015860 {source="FMA"} ! visceral abdominal lymph node intersection_of: UBERON:0002507 ! abdominal lymph node intersection_of: part_of UBERON:0002095 ! mesentery relationship: part_of UBERON:0002095 ! mesentery -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_F_Lymph_Node.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_M_Lymph_Node.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_F_Lymph_Node.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_M_Lymph_Node.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002511 @@ -195984,10 +193839,9 @@ xref: MA:0002831 xref: SCTID:118755002 xref: Wikipedia:Trabeculae_carneae is_a: UBERON:0000440 ! trabecula -relationship: composed_primarily_of UBERON:0001133 ! cardiac muscle tissue +is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0002082 {source="WP"} ! cardiac ventricle -property_value: UBPROP:0000009 "The purpose of the trabeculae carneae is most likely to prevent suction that would occur with a flat surfaced membrane and thus impair the heart's ability to pump efficiently. The trabeculae carneae also serve a similar function to papillary muscles in that their contraction pulls on the chordae tendineae, preventing inversion of the mitral (bicuspid) and tricuspid valves, that is, their bulging towards the atrial chambers, which would lead to subsequent leakage of the blood into the atria. So by the action of papillary muscles on the atrioventricular valves, backflow of the blood from the ventricles into the atria is prevented" xsd:string {source="WP"} -property_value: UBPROP:0000012 "Note that WP states they are ventricular, but MP has classes for atrial ventricular carnea." xsd:string {external_ontology="MP"} +relationship: RO:0002473 UBERON:0001133 ! composed primarily of cardiac muscle tissue [Term] id: UBERON:0002512 @@ -196013,18 +193867,16 @@ xref: SCTID:257943001 xref: UMLS:C0010092 {source="ncithesaurus:Corpus_Luteum"} xref: Wikipedia:Corpus_luteum is_a: UBERON:0002368 {source="PMID:20959416"} ! endocrine gland -is_a: UBERON:0003134 ! female reproductive organ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005398 ! female reproductive gland relationship: capable_of GO:0042701 ! progesterone secretion -relationship: develops_from UBERON:0001305 ! ovarian follicle relationship: has_part CL:0000175 ! luteal cell -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0000992 {source="MA"} ! ovary -relationship: present_in_taxon NCBITaxon:7762 {source="PMID:20959416"} -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/57/Folliclesinovary.jpg" xsd:anyURI -property_value: UBPROP:0000008 "maintains the endometrium in mammals[WP]. A corpus luteum is known in hagfish (100), Squalus (101), and salamander (100) but not lamprey (102). There are no data for Branchiostoma and Ciona, and given that they are multiple spawners, there is no a priori reason to conclude that they lack a corpus luteum" xsd:string {source="PMID:20959416"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002202 UBERON:0001305 ! develops from ovarian follicle +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/57/Folliclesinovary.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:7762 {source="PMID:20959416"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002513 @@ -196048,14 +193900,12 @@ xref: ZFA:0001591 is_a: UBERON:0001474 ! bone element is_a: UBERON:0010363 {source="VSAO"} ! endochondral element intersection_of: UBERON:0001474 ! bone element -intersection_of: develops_from UBERON:0005863 ! cartilaginous condensation -relationship: developmentally_replaces UBERON:0002418 ! cartilage tissue -relationship: develops_from UBERON:0007844 {source="VSAO"} ! cartilage element -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Hypertrophic_Zone_of_Epiphyseal_Plate.jpg" xsd:anyURI -property_value: editor_note "placement in this class to be inferred" xsd:string +intersection_of: RO:0002202 UBERON:0005863 ! develops from cartilaginous condensation +relationship: RO:0002202 UBERON:0007844 {source="VSAO"} ! develops from cartilage element +relationship: RO:0002285 UBERON:0002418 ! developmentally replaces cartilage tissue +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Hypertrophic_Zone_of_Epiphyseal_Plate.jpg" xsd:anyURI +property_value: IAO:0000116 "placement in this class to be inferred" xsd:string property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern" xsd:anyURI -property_value: UBPROP:0000001 "Replacement bone that forms within cartilage.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000145", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} -property_value: UBPROP:0000012 "some structures, e.g. in ZFA are both intramembrane and endochondral" xsd:string {external_ontology="ZFA"} [Term] id: UBERON:0002514 @@ -196069,10 +193919,8 @@ xref: TAO:0001644 xref: Wikipedia:Intramembranous_ossification xref: ZFA:0001635 is_a: UBERON:0001474 {source="VSAO"} ! bone element -relationship: develops_from UBERON:0003104 ! mesenchyme relationship: output_of GO:0001957 ! intramembranous ossification -property_value: UBPROP:0000001 "Bone that forms directly within mesenchyme, and does not replace other tissues.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001644", ontology="TAO", source="TAO:wd"} -property_value: UBPROP:0000005 "[In TAO], This term was made obsolete because it is considered a synonym of membrane bone (VSAO:0000023).[TAO]" xsd:string {date_retrieved="2012-09-06", external_class="TAO:0001644", ontology="TAO", source="Curator"} +relationship: RO:0002202 UBERON:0003104 ! develops from mesenchyme [Term] id: UBERON:0002515 @@ -196094,10 +193942,9 @@ xref: UMLS:C0031110 {source="ncithesaurus:Periosteum"} xref: Wikipedia:Periosteum is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000158 ! membranous layer -relationship: composed_primarily_of UBERON:0011822 ! dense irregular connective tissue relationship: part_of UBERON:0001474 ! bone element -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/c/cf/Bone_growth.png" xsd:anyURI -property_value: UBPROP:0000007 "periosteal" xsd:string +relationship: RO:0002473 UBERON:0011822 ! composed primarily of dense irregular connective tissue +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/c/cf/Bone_growth.png" xsd:anyURI [Term] id: UBERON:0002517 @@ -196120,11 +193967,10 @@ xref: SCTID:181890004 xref: UMLS:C0149543 {source="ncithesaurus:Base_of_the_Skull"} xref: Wikipedia:Base_of_skull is_a: UBERON:0000075 ! subdivision of skeletal system -relationship: contributes_to_morphology_of UBERON:0003128 ! cranium relationship: part_of UBERON:0001703 ! neurocranium relationship: part_of UBERON:0002241 ! chondrocranium -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/81/Gray193.png" xsd:anyURI -property_value: UBPROP:0000007 "basicranial" xsd:string +relationship: RO:0002433 UBERON:0003128 ! contributes to morphology of cranium +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/81/Gray193.png" xsd:anyURI [Term] id: UBERON:0002518 @@ -196147,13 +193993,13 @@ xref: TAO:0000559 xref: VHOG:0001676 xref: Wikipedia:Otolith_organ xref: ZFA:0000559 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0006585 ! vestibular organ relationship: capable_of_part_of GO:0060007 ! linear vestibuloocular reflex -relationship: develops_from UBERON:0003051 ! ear vesicle relationship: part_of UBERON:0001862 ! vestibular labyrinth -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/cb/Bigotolith.jpg" xsd:anyURI -property_value: editor_note "Representation of utricle, sacule and otoliths in correspondence to other ontologies may require review. In EHDAA2, saccule and utricle are epithelia" xsd:string -property_value: UBPROP:0000003 "In fishes, as in other vertebrates, the vestibular end-organs are divided into a gravity receptor system, with three subdivisions and an angular acceleration receptor system. The gravity receptor system on each side consists of utricular, saccular, and lagenar maculae, each covered by an otolith (reference 1); (...)considerations have led to our rethinking issues related to the origin of several aspects of vertebrate hearing, and to the view that many basic auditory functions evolved very early in vertebrate history, and that the functions observed in more `advanced' vertebrates, such as birds and mammals, are frequently modifications of themes first encountered in fishes, and perhaps even more ancestral animals (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001676", ontology="VHOG", source="PMID:11581521 Moorman SJ, Development of sensory systems in zebrafish (Danio rerio). ILAR Journal (2001), DOI:10.1016/S0378-5955(00)00168-4 Fay RR, Popper AN, Evolution of hearing in vertebrates: the inner ears and processing. Hearing research (2000)", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003051 ! develops from ear vesicle +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/cb/Bigotolith.jpg" xsd:anyURI +property_value: IAO:0000116 "Representation of utricle, sacule and otoliths in correspondence to other ontologies may require review. In EHDAA2, saccule and utricle are epithelia" xsd:string [Term] id: UBERON:0002521 @@ -196173,10 +194019,10 @@ xref: SCTID:27197004 xref: Wikipedia:Elastic_fiber is_a: UBERON:0002384 ! connective tissue intersection_of: UBERON:0002384 ! connective tissue -intersection_of: composed_primarily_of GO:0071953 ! elastic fiber -relationship: composed_primarily_of GO:0071953 ! elastic fiber -relationship: has_quality PATO:0001171 ! elastic -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/cb/Gray377.png" xsd:anyURI +intersection_of: RO:0002473 GO:0071953 ! composed primarily of elastic fiber +relationship: RO:0000086 PATO:0001171 ! has quality elastic +relationship: RO:0002473 GO:0071953 ! composed primarily of elastic fiber +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/cb/Gray377.png" xsd:anyURI [Term] id: UBERON:0002522 @@ -196199,8 +194045,8 @@ xref: Wikipedia:Tunica_media is_a: UBERON:0004797 {source="MA"} ! blood vessel layer relationship: has_part UBERON:0002521 {source="cjm"} ! elastic tissue relationship: has_part UBERON:0004237 {source="cjm"} ! blood vessel smooth muscle -relationship: surrounded_by UBERON:0005734 ! tunica adventitia of blood vessel -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/3/32/Illu_artery.jpg" xsd:anyURI +relationship: RO:0002219 UBERON:0005734 ! surrounded by tunica adventitia of blood vessel +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/3/32/Illu_artery.jpg" xsd:anyURI [Term] id: UBERON:0002523 @@ -196226,11 +194072,10 @@ is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004923 {source="FMA"} ! organ component layer relationship: adjacent_to UBERON:0010161 {source="ISBN:0073040584"} ! lumen of blood vessel relationship: has_part UBERON:0001986 ! endothelium -relationship: surrounded_by UBERON:0002522 {notes="check for exceptions, e.g. capillaries"} ! tunica media -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/3/32/Illu_artery.jpg" xsd:anyURI -property_value: editor_note "the FMA class represents a more generic layer which is the superclass of the layer found in both blood vessels and lymph vessels (and also endocardium) - we should probably follow this structure" xsd:string -property_value: editor_note "the FMA class represents a structure which may have both epithelium and fibroelastic connective tissue as parts" xsd:string -property_value: UBPROP:0000001 "The tunica intima (or just intima) is the innermost layer of an artery or vein. It is made up of one layer of endothelial cells and is supported by an internal elastic lamina. The endothelial cells are in direct contact with the blood flow. The inner coat (tunica intima) can be separated from the middle by a little maceration, or it may be stripped off in small pieces; but, on account of its friability, it cannot be separated as a complete membrane. It is a fine, transparent, colorless structure which is highly elastic, and, after death, is commonly corrugated into longitudinal wrinkles. The inner coat consists of: A layer of pavement endothelium, the cells of which are polygonal, oval, or fusiform, and have very distinct round or oval nuclei. This endothelium is brought into view most distinctly by staining with silver nitrate. A subendothelial layer, consisting of delicate connective tissue with branched cells lying in the interspaces of the tissue; in arteries of less than 2 mm. in diameter the subendothelial layer consists of a single stratum of stellate cells, and the connective tissue is only largely developed in vessels of a considerable size. An elastic or fenestrated layer, which consists of a membrane containing a net-work of elastic fibers, having principally a longitudinal direction, and in which, under the microscope, small elongated apertures or perforations may be seen, giving it a fenestrated appearance. It was therefore called by Henle the fenestrated membrane. This membrane forms the chief thickness of the inner coat, and can be separated into several layers, some of which present the appearance of a network of longitudinal elastic fibers, and others a more membranous character, marked by pale lines having a longitudinal direction. In minute arteries the fenestrated membrane is a very thin layer; but in the larger arteries, and especially in the aorta, it has a very considerable thickness. [WP,unvetted].[Wikipedia]" xsd:string {ontology="Wikipedia", source="Wikipedia:Tunica_intima"} +relationship: RO:0002219 UBERON:0002522 ! surrounded by tunica media +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/3/32/Illu_artery.jpg" xsd:anyURI +property_value: IAO:0000116 "the FMA class represents a more generic layer which is the superclass of the layer found in both blood vessels and lymph vessels (and also endocardium) - we should probably follow this structure" xsd:string +property_value: IAO:0000116 "the FMA class represents a structure which may have both epithelium and fibroelastic connective tissue as parts" xsd:string [Term] id: UBERON:0002527 @@ -196271,12 +194116,11 @@ is_a: UBERON:0010538 ! paired limb/fin segment intersection_of: UBERON:0010758 ! subdivision of organism along appendicular axis intersection_of: part_of UBERON:0002101 ! limb disjoint_from: UBERON:0010912 ! subdivision of skeleton -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: existence_starts_during UBERON:0000068 ! embryo stage relationship: has_part UBERON:0014892 ! skeletal muscle organ, vertebrate relationship: part_of UBERON:0002101 ! limb -property_value: editor_note "TODO - align this with the CARO2 class 'appendage segment'; note the FMA class does not appear to require repetition" xsd:string -property_value: UBPROP:0000012 "FMA has both limb segment and free limb segment, the former includes the girdles. Note that MA uses the term more generally and includes A,S,Z,S+Z(arm/leg), whereas FMA is just A,S,Z" xsd:string {external_ontology="FMA"} +relationship: RO:0002488 UBERON:0000068 ! existence starts during embryo stage +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +property_value: IAO:0000116 "TODO - align this with the CARO2 class 'appendage segment'; note the FMA class does not appear to require repetition" xsd:string [Term] id: UBERON:0002530 @@ -196295,10 +194139,7 @@ xref: BTO:0000522 xref: EFO:0000797 xref: EHDAA2:0003096 xref: EHDAA:2161 -xref: EHDAA:4475 -xref: EHDAA:6522 xref: EMAPA:18425 -xref: FBbt:00100317 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7146 xref: FMA:86294 xref: galen:Gland @@ -196313,11 +194154,9 @@ xref: Wikipedia:Gland xref: WikipediaCategory:Glands is_a: UBERON:0000062 ! organ relationship: capable_of GO:0046903 ! secretion -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: produces UBERON:0000463 ! organism substance -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/a1/Gray1026.png" xsd:anyURI -property_value: RO:0002171 UBERON:0001434 -property_value: UBPROP:0000007 "glandular" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/a1/Gray1026.png" xsd:anyURI [Term] id: UBERON:0002532 @@ -196341,9 +194180,8 @@ xref: VHOG:0000243 xref: Wikipedia:Epiblast is_a: UBERON:0002050 ! embryonic structure relationship: has_part CL:0000352 ! epiblast cell -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" xsd:anyURI -property_value: editor_note "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" xsd:string -property_value: UBPROP:0000003 "In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000243", ontology="VHOG", source="DOI:10.1146/annurev.cellbio.042308.113344 Zorn AM, Wells JM, Vertebrate endoderm development and organ formation. Annual Review of Cell Developmental Biology (2009)", source="http://bgee.unil.ch/"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" xsd:anyURI +property_value: IAO:0000116 "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" xsd:string [Term] id: UBERON:0002533 @@ -196371,10 +194209,8 @@ xref: VHOG:0000201 xref: XAO:0000107 xref: ZFA:0000077 is_a: UBERON:0002050 ! embryonic structure -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata -property_value: editor_note "See notes from https://github.com/obophenotype/uberon/wiki/The-neural-crest" xsd:string -property_value: UBPROP:0000001 "Rapidly proliferating mass of cells at the caudal extremity of the embryo. Its formation is reflected in a caudal carving of the posterior portion of the archenteric canal at NF stage 22. With its further outgrowth, the postanal gut primordium becomes stretched. Its lumen is in broad communication with the hindgut at NF stage 25.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011104", ontology="AAO", source="ISBN:0815318960", source="OMD:tail+bud"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (5) a larva or embryo with a postanal tail.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000201", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +property_value: IAO:0000116 "See notes from https://github.com/obophenotype/uberon/wiki/The-neural-crest" xsd:string [Term] id: UBERON:0002536 @@ -196386,16 +194222,15 @@ subset: uberon_slim synonym: "sensillum" EXACT [FBbt:00007152, HAO:0000933] xref: BTO:0001237 xref: EFO:0000939 -xref: FBbt:00007152 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: HAO:0000933 xref: MAT:0000163 xref: MIAA:0000163 xref: TGMA:0000540 xref: Wikipedia:Sensillum is_a: UBERON:0000020 ! sense organ -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda relationship: part_of UBERON:0001016 ! nervous system -property_value: editor_note "this term should be ceded to the arthropod anatomy ontology" xsd:string +relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda +property_value: IAO:0000116 "this term should be ceded to the arthropod anatomy ontology" xsd:string [Term] id: UBERON:0002537 @@ -196455,14 +194290,11 @@ xref: ZFA:0001306 is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0010188 {source="EHDAA2"} ! protuberance is_a: UBERON:0010314 ! structure with developmental contribution from neural crest -relationship: developmentally_induced_by UBERON:0007690 {source="PMID:16313389"} ! early pharyngeal endoderm -relationship: only_in_taxon NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! Chordata relationship: part_of UBERON:0008814 ! pharyngeal arch system relationship: part_of UBERON:0008816 {source="PMID:16313389"} ! embryonic head -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray41.png" xsd:anyURI -property_value: UBPROP:0000001 "One of a series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010359", ontology="AAO", source="NLM:branchial+arch"} -property_value: UBPROP:0000003 "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000155", ontology="VHOG", source="DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000013 "Numbered cranial to caudal. different in mammals. branchial arch = ZFA:0001613 pharyngeal arch 3-7. generally gill arch 1 = pharyngeal arch 3. terminology varies as to whether branchial arch follows gill or pharyngeal numbering" xsd:string +relationship: RO:0002160 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! only in taxon Chordata +relationship: RO:0002256 UBERON:0007690 {source="PMID:16313389"} ! developmentally induced by early pharyngeal endoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray41.png" xsd:anyURI [Term] id: UBERON:0002540 @@ -196479,7 +194311,6 @@ xref: AAO:0000269 xref: AAO:0000975 xref: EFO:0000941 xref: MAT:0000249 -xref: MESH:D053403 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: MIAA:0000249 xref: TAO:0000034 xref: VHOG:0001243 @@ -196488,14 +194319,10 @@ xref: XAO:0000095 xref: ZFA:0000034 is_a: UBERON:0001032 ! sensory system relationship: has_part UBERON:0010202 ! lateral line -relationship: never_in_taxon NCBITaxon:32524 {source="http://tolweb.org/Amniota"} ! Amniota -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: overlaps UBERON:0000010 ! peripheral nervous system -property_value: editor_note "we model this as being potentially inclusive of lateral line scales, and thus overlapping with the skeletal system. This is to accomodate TAO" xsd:string -property_value: UBPROP:0000001 "A sensory system on the surface of the fish, consisting of small sensory patches (neuromasts) distributed in discrete lines over the body surface. The lateral line system is stimulated by local water displacements and vibrations, and detects propulsion of the fish through the water, as well as facilitating shoaling, prey capture, and predator and obstacle avoidance. (See Anatomical Atlas entry for lateral line by T. Whitfield.)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000034", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Sensory system which develops from a specialized series of dorsolateral ectodermal placodes named lateral line placodes.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000975", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000002 "relationship loss: is_formed_by lateral line receptor organ (AAO:0001001)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000975", ontology="AAO"} -property_value: UBPROP:0000003 "The mechanosensory lateral line system is widely distributed in aquatic anamniotes. It was apparently present in the earliest vertebrates, as it has been identified in agnathans, cartilaginous fishes, bony fishes, lungfishes, the crossopterygian Latimeria, and aquatic amphibians.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001243", ontology="VHOG", source="ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.195", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +property_value: IAO:0000116 "we model this as being potentially inclusive of lateral line scales, and thus overlapping with the skeletal system. This is to accomodate TAO" xsd:string +property_value: RO:0002161 NCBITaxon:32524 {source="http://tolweb.org/Amniota"} [Term] id: UBERON:0002544 @@ -196511,7 +194338,6 @@ synonym: "limb digit" EXACT [MA:0000690] xref: AAO:0011126 xref: EFO:0000881 xref: EMAPA:32725 -xref: FMA:85518 {notes="GAT"} xref: galen:Digit xref: MA:0000690 xref: MAT:0000285 @@ -196525,15 +194351,11 @@ xref: XAO:0003032 is_a: UBERON:0005881 ! autopodial extension intersection_of: UBERON:0005881 ! autopodial extension intersection_of: part_of UBERON:0012354 ! acropodium region -relationship: contributes_to_morphology_of UBERON:0002470 ! autopod region relationship: has_part UBERON:0015023 ! phalanx endochondral element -relationship: only_in_taxon NCBITaxon:32523 ! Tetrapoda relationship: part_of UBERON:0012354 ! acropodium region relationship: part_of UBERON:5002544 ! digit plus metapodial segment -property_value: IAO:0000232 "this class represents the entire organism subdivision encompassing soft tissue as well as the underlying skeletal framework. The class represents the phalangeal part only - historically the term 'digit' has also been used to represent the unit consisting of a series of phalanges together with a metapodial bone. We may in future relabel this class to avoid confusion with this concept, but the class will continue to represent the phalangeal portion" xsd:string -property_value: RO:0002171 UBERON:0009877 -property_value: UBPROP:0000003 "Our reinterpretation of the distal fin endoskeleton of Panderichthys removes the final piece of evidence supporting the formerly popular hypothesis that tetrapod digits are wholly new structures without homologues in sarcopterygian fish fins. This hypothesis, which was based partly on the complete absence of plausible digit homologues in Panderichthys (then the closest known relative of tetrapods), has already been called into question by the discovery of digit-like radials in Tiktaalik and the fact that Hox gene expression patterns closely resembling those associated with digit formation in tetrapods occur in the distal fin skeletons of paddlefish and Australian lungfish. Our new data show that Panderichthys is not an anomaly: like Tiktaalik and other fish members of the Tetrapodomorpha, it has distal radials that can be interpreted as digit homologues.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000944", ontology="VHOG", source="DOI:10.1038/nature07339 Boisvert CA, Mark-Kurik E and Ahlberg PE, The pectoral fin of Panderichthys and the origin of digits. Nature (2008)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "digital" xsd:string +relationship: RO:0002160 NCBITaxon:32523 ! only in taxon Tetrapoda +relationship: RO:0002433 UBERON:0002470 ! contributes to morphology of autopod region [Term] id: UBERON:0002546 @@ -196547,16 +194369,13 @@ synonym: "ectodermal placode" BROAD INCONSISTENT [FMA:293966, PMID:22512454] synonym: "placode" BROAD [Wikipedia:Placode] xref: AAO:0010466 xref: EFO:0001650 -xref: FMA:293966 xref: MAT:0000369 xref: MIAA:0000369 xref: XAO:0000305 is_a: UBERON:0005085 {source="cjm"} ! ectodermal placode -relationship: only_in_taxon NCBITaxon:7711 {source="PMID:11523831", source="PMID:22512454"} ! Chordata relationship: part_of UBERON:0000033 ! head -property_value: editor_note "Do not merge with neurogenic placode" xsd:string -property_value: UBPROP:0000008 "Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons" xsd:string {source="PMID:11523831"} -property_value: UBPROP:0000013 "The term placode or placodes also applies to developing organs such as teeth, mammary glands, hair follicles, feathers and scales. We include a separate parent class for this. to avoid confusion, we include neurogenic placode as a subclass" xsd:string +relationship: RO:0002160 NCBITaxon:7711 {source="PMID:11523831", source="PMID:22512454"} ! only in taxon Chordata +property_value: IAO:0000116 "Do not merge with neurogenic placode" xsd:string [Term] id: UBERON:0002548 @@ -196582,19 +194401,15 @@ synonym: "wriggler" NARROW [Wikipedia:Larva] synonym: "zoea" NARROW [Wikipedia:Larva] xref: AEO:0000126 xref: BTO:0000707 -xref: FBbt:00001727 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: HAO:0000459 -xref: MESH:D007814 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: TAO:0002048 xref: Wikipedia:Larva is_a: UBERON:0000468 ! multicellular organism intersection_of: UBERON:0000468 ! multicellular organism -intersection_of: existence_starts_and_ends_during UBERON:0000069 ! larval stage -relationship: existence_starts_and_ends_during UBERON:0000069 ! larval stage -relationship: has_quality PATO:0001185 ! larval -property_value: editor_note "TODO discriminate between stages and organisms" xsd:string -property_value: UBPROP:0000001 "Whole organism that is premetamorphic or a very immature individual.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002048", ontology="TAO", source="TAO:wd"} -property_value: UBPROP:0000007 "larval" xsd:string +intersection_of: RO:0002491 UBERON:0000069 ! existence starts and ends during larval stage +relationship: RO:0000086 PATO:0001185 ! has quality larval +relationship: RO:0002491 UBERON:0000069 ! existence starts and ends during larval stage +property_value: IAO:0000116 "TODO discriminate between stages and organisms" xsd:string [Term] id: UBERON:0002550 @@ -196632,7 +194447,7 @@ xref: galen:Cavity xref: MA:0002447 xref: NCIT:C34007 is_a: UBERON:0000464 ! anatomical space -relationship: location_of UBERON:0000463 ! organism substance +relationship: RO:0001015 UBERON:0000463 ! location of organism substance [Term] id: UBERON:0002555 @@ -196656,9 +194471,6 @@ xref: TAO:0006000 xref: UMLS:C0020669 {source="BIRNLEX:1015"} is_a: UBERON:0002616 ! regional part of brain relationship: part_of UBERON:0001898 ! hypothalamus -property_value: IAO:0000232 "See notes for pars intermedia of adenohypophysis." xsd:string -property_value: UBPROP:0000001 "Brain structure that lies perpendicular to the longitudinal axis of the embryonic neural tube, is continuous with the rostral hypothalamic proliferation and whose most lateral extent is deflected dorsally within the inferior lobe.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0006000", ontology="TAO", source="ZFIN:ZDB-PUB-001018-1", source="ZFIN:ZDB-PUB-020730-6", source="ZFIN:ZDB-PUB-081114-19"} -property_value: UBPROP:0000008 "In humans it contains the following nuclei: dorsal nucleus [TA] (nucleus dorsalis hypothalami [TA]), parts of the dorsomedial nucleus [TA] (nucleus dorsomedialis [TA]), arcuate nucleus [TA] (nucleus arcuatus [TA]), posterior periventricular nucleus [TA] (nucleus periventricularis posterior [TA]), retrochiasmatic area [TA] (area retrochiasmatica [TA]), lateral tuberal nuclei [TA] (nuclei tuberales laterales [TA]), and ventromedial nucleus [TA] (nucleus ventromedialis hypothalami" xsd:string {source="TA"} [Term] id: UBERON:0002558 @@ -196684,11 +194496,11 @@ xref: BIRNLEX:1029 xref: FMA:75007 is_a: UBERON:0002558 ! organ cavity intersection_of: UBERON:0002558 ! organ cavity -intersection_of: luminal_space_of UBERON:0001017 ! central nervous system -relationship: develops_from UBERON:0003842 {gci_relation="part_of", gci_filler="NCBITaxon:7742", source="cjm"} ! neural tube lumen -relationship: luminal_space_of UBERON:0001017 ! central nervous system +intersection_of: RO:0002572 UBERON:0001017 ! luminal space of central nervous system relationship: part_of UBERON:0001017 ! central nervous system -relationship: present_in_taxon NCBITaxon:569425 {source="DOI:10.1186/s12983-014-0089-2"} +relationship: RO:0002202 UBERON:0003842 {gci_relation="part_of", gci_filler="NCBITaxon:7742", source="cjm"} ! develops from neural tube lumen +relationship: RO:0002572 UBERON:0001017 ! luminal space of central nervous system +property_value: RO:0002175 NCBITaxon:569425 {source="DOI:10.1186/s12983-014-0089-2"} [Term] id: UBERON:0002600 @@ -196712,14 +194524,13 @@ xref: CALOHA:TS-2061 xref: DHBA:12155 xref: FMA:72719 xref: HBA:4219 -xref: MESH:D065726 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: neuronames:834 {source="BIRNLEX:1128"} xref: SCTID:279215006 xref: UMLS:C0458337 {source="BIRNLEX:1128"} xref: Wikipedia:Limbic_lobe is_a: UBERON:0016526 {source="FMA"} ! lobe of cerebral hemisphere -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/7e/Human_brain_inferior-medial_view_description.JPG" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7e/Human_brain_inferior-medial_view_description.JPG" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002610 @@ -196741,16 +194552,8 @@ xref: neuronames:720 {source="BIRNLEX:1151"} xref: UMLS:C0152411 {source="ncithesaurus:Cochlear_Nuclei", source="BIRNLEX:1151"} xref: Wikipedia:Cochlear_nuclei is_a: UBERON:0019263 ! gray matter of hindbrain -relationship: part_of UBERON:0001896 {inconsistent_with="MA", source="FMA"} ! medulla oblongata -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/52/Gray691.png" xsd:anyURI -property_value: RO:0002171 UBERON:0002126 {source="ABA"} -property_value: RO:0002171 UBERON:0002162 {source="ABA"} -property_value: RO:0002171 UBERON:0002591 {source="ABA"} -property_value: RO:0002171 UBERON:0002864 {source="ABA"} -property_value: RO:0002171 UBERON:0002866 {source="ABA"} -property_value: RO:0002171 UBERON:0002873 {source="ABA"} -property_value: RO:0002171 UBERON:0007633 {source="ABA"} -property_value: UBPROP:0000015 "WP says 'The CN is located at the dorso-lateral side of the brainstem, spanning the junction of the pons and medulla.'. MA places this in pons, other sources the medulla" xsd:string +relationship: part_of UBERON:0001896 ! medulla oblongata +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/52/Gray691.png" xsd:anyURI [Term] id: UBERON:0002616 @@ -196772,10 +194575,11 @@ xref: NCIT:C13031 xref: SCTID:384763002 xref: UMLS:C0445620 {source="ncithesaurus:Brain_Part"} is_a: UBERON:0000073 ! regional part of nervous system +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000481 ! multi-tissue structure intersection_of: part_of UBERON:0000955 ! brain -relationship: composed_primarily_of UBERON:0003714 ! neural tissue relationship: part_of UBERON:0000955 ! brain +relationship: RO:0002473 UBERON:0003714 ! composed primarily of neural tissue [Term] id: UBERON:0002622 @@ -196821,7 +194625,6 @@ xref: BAMS:MEPO xref: BAMS:MnPO xref: BIRNLEX:1208 xref: BM:MPO -xref: BTO:0006168 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: DHBA:13063 xref: FMA:62323 xref: HBA:4548 @@ -196833,12 +194636,6 @@ is_a: UBERON:0007251 ! preoptic nucleus relationship: capable_of GO:0048243 {source="Wikipedia"} ! norepinephrine secretion relationship: capable_of GO:2000070 {source="Wikipedia"} ! regulation of response to water deprivation relationship: overlaps UBERON:8440005 ! rostral periventricular region of the third ventricle -property_value: RO:0002171 UBERON:0001934 {source="ABA"} -property_value: RO:0002171 UBERON:0002034 {source="ABA"} -property_value: RO:0002171 UBERON:0002219 {source="ABA"} -property_value: RO:0002171 UBERON:0002689 {source="ABA"} -property_value: RO:0002171 UBERON:0002690 {source="ABA"} -property_value: RO:0002171 UBERON:0007626 {source="ABA"} [Term] id: UBERON:0002663 @@ -196869,9 +194666,6 @@ intersection_of: UBERON:0007245 ! nuclear complex of neuraxis intersection_of: part_of UBERON:0000446 ! septum of telencephalon relationship: part_of UBERON:0000446 ! septum of telencephalon relationship: part_of UBERON:0002743 {source="NIFSTD"} ! basal forebrain -property_value: UBPROP:0000001 "Any of the groups of neural nuclei situated in the septal region which have afferent and cholinergic efferent connections with a variety of forebrain and brainstem areas including the hippocampus, the lateral hypothalamus, the tegmentum, and the amygdala." xsd:string {source="MP:0012682"} -property_value: UBPROP:0000001 "The septal nuclei are structures in the middle anteroventral cerebrum that are composed of medium-size neurons grouped into medial, lateral, and posterior groups. The septal nuclei receive reciprocal connections from the olfactory bulb, hippocampus, amygdala, hypothalamus, midbrain, habenula, cingulate gyrus, and thalamus. The septal nuclei play a role in reward and reinforcement along with the nucleus accumbens. In the 1950s, Olds & Milner showed that rats with electrodes implanted in this area will self-stimulate repeatedly in order to experience a euphoric feeling (i.e. press a bar to receive electrical current that will stimulate the neurons). [WP,unvetted][Wikipedia:Septal_nuclei]." xsd:string {source="Wikipedia:Septal_nuclei"} -property_value: UBPROP:0000012 "in NIFSTD this is the mereological sum of the individual complexes - in MA it is the superclass" xsd:string {external_ontology="NIF"} [Term] id: UBERON:0002690 @@ -196894,12 +194688,6 @@ xref: UMLS:C0262200 {source="BIRNLEX:1401"} is_a: UBERON:0006568 ! hypothalamic nucleus relationship: overlaps UBERON:8440005 ! rostral periventricular region of the third ventricle relationship: part_of UBERON:0002550 {source="FMA"} ! anterior hypothalamic region -property_value: RO:0002171 UBERON:0001934 {source="ABA"} -property_value: RO:0002171 UBERON:0002034 {source="ABA"} -property_value: RO:0002171 UBERON:0002219 {source="ABA"} -property_value: RO:0002171 UBERON:0002625 {source="ABA"} -property_value: RO:0002171 UBERON:0002689 {source="ABA"} -property_value: RO:0002171 UBERON:0007626 {source="ABA"} [Term] id: UBERON:0002704 @@ -196924,15 +194712,11 @@ xref: EV:0100217 xref: FMA:62023 xref: MA:0000868 xref: MBA:1008 -xref: MESH:D005829 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: neuronames:351 {source="BIRNLEX:1461"} xref: SCTID:361550004 xref: Wikipedia:Metathalamus is_a: UBERON:0015233 ! nucleus of dorsal thalamus -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1b/ThalamicNuclei.png" xsd:anyURI -property_value: RO:0002171 UBERON:0002144 {source="ABA"} -property_value: RO:0002171 UBERON:0002776 {source="ABA"} -property_value: UBPROP:0000012 "we follow FMA in making this a subtype of nucleus, but in fact it is a group containing two nuclei" xsd:string {external_ontology="FMA"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1b/ThalamicNuclei.png" xsd:anyURI [Term] id: UBERON:0002707 @@ -196956,7 +194740,6 @@ xref: BAMS:P xref: BIRNLEX:1464 xref: BM:CST xref: BM:Me-PyT -xref: BTO:0006132 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: DHBA:12776 xref: DMBA:17756 xref: EMAPA:36600 @@ -196971,11 +194754,11 @@ xref: neuronames:800 {source="BIRNLEX:1464"} xref: SCTID:362325000 xref: UMLS:C0034229 {source="BIRNLEX:1464"} xref: Wikipedia:Corticospinal_tract -is_a: UBERON:0001018 {notes="In NIFSTD this is a tract of brain but this leads to issues due to its overlap with the spinal cord"} ! axon tract +is_a: UBERON:0001018 ! axon tract relationship: part_of UBERON:0025525 ! motor system relationship: part_of UBERON:0036224 ! corticobulbar and corticospinal tracts -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/ac/Gray684.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/ac/Gray684.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002726 @@ -196991,7 +194774,6 @@ synonym: "segmenta cervicalia medullae spinalis [1-8" EXACT OMO:0003011 [FMA:711 xref: BIRNLEX:1499 xref: FMA:71166 xref: MA:0003081 -xref: MESH:D066193 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: NCIT:C12892 xref: neuronames:1654 xref: SCTID:180960003 @@ -197001,8 +194783,8 @@ is_a: UBERON:0005844 ! spinal cord segment intersection_of: UBERON:0005844 ! spinal cord segment intersection_of: adjacent_to UBERON:0005434 ! cervical region relationship: adjacent_to UBERON:0005434 ! cervical region -relationship: only_in_taxon NCBITaxon:8287 ! Sarcopterygii -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002160 NCBITaxon:8287 ! only in taxon Sarcopterygii +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002731 @@ -197046,14 +194828,13 @@ xref: DHBA:10349 xref: EMAPA:35164 xref: FMA:77700 xref: HBA:4300 -xref: MESH:D066187 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: neuronames:1997 {source="BIRNLEX:1560"} xref: PBA:128012976 xref: Wikipedia:Basal_forebrain is_a: UBERON:0002616 ! regional part of brain relationship: part_of UBERON:0001890 {source="BTO"} ! forebrain -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/a4/Basal_Forebrain_Monakhos_2007.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/a4/Basal_Forebrain_Monakhos_2007.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002749 @@ -197108,7 +194889,6 @@ intersection_of: UBERON:0001872 ! parietal lobe intersection_of: part_of UBERON:0002812 ! left cerebral hemisphere relationship: adjacent_to UBERON:0002921 ! longitudinal fissure relationship: part_of UBERON:0002812 ! left cerebral hemisphere -property_value: RO:0002171 UBERON:0002803 [Term] id: UBERON:0002803 @@ -197206,7 +194986,6 @@ intersection_of: UBERON:0001870 ! frontal cortex intersection_of: part_of UBERON:0002812 ! left cerebral hemisphere relationship: adjacent_to UBERON:0002921 ! longitudinal fissure relationship: part_of UBERON:0002812 ! left cerebral hemisphere -property_value: RO:0002171 UBERON:0002810 [Term] id: UBERON:0002812 @@ -197221,11 +195000,10 @@ xref: SCTID:362323007 xref: UMLS:C0228176 {source="ncithesaurus:Left_Cerebral_Hemisphere"} is_a: UBERON:0001869 ! cerebral hemisphere intersection_of: UBERON:0001869 ! cerebral hemisphere -intersection_of: in_left_side_of UBERON:0000955 ! brain -relationship: in_left_side_of UBERON:0000955 ! brain -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +intersection_of: BSPO:0000120 UBERON:0000955 ! brain +relationship: BSPO:0000120 UBERON:0000955 ! brain +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI [Term] id: UBERON:0002813 @@ -197240,11 +195018,10 @@ xref: SCTID:362322002 xref: UMLS:C0228175 {source="ncithesaurus:Right_Cerebral_Hemisphere"} is_a: UBERON:0001869 ! cerebral hemisphere intersection_of: UBERON:0001869 ! cerebral hemisphere -intersection_of: in_right_side_of UBERON:0000955 ! brain -relationship: in_right_side_of UBERON:0000955 ! brain -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +intersection_of: BSPO:0000121 UBERON:0000955 ! brain +relationship: BSPO:0000121 UBERON:0000955 ! brain +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI [Term] id: UBERON:0002827 @@ -197286,13 +195063,10 @@ xref: XAO:0004142 xref: ZFA:0000588 is_a: UBERON:0001714 {source="ZFA"} ! cranial ganglion is_a: UBERON:0010313 ! neural crest-derived structure -relationship: develops_from UBERON:0003249 {source="NCBIBook:NBK53175"} ! epithelium of otic placode -relationship: develops_from UBERON:0012175 {source="EHDAA2"} ! acoustico-facial VII-VIII ganglion complex relationship: part_of UBERON:0002105 {source="ZFA"} ! vestibulo-auditory system -property_value: editor_note "Consider follow MA naming scheme." xsd:string -property_value: UBPROP:0000001 "The sensory ganglion of the ear. (See Anatomical Atlas entry for statoacoustic ganglion by T. Whitfield.)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000588", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "(During the development of the inner ear in a vertebrate embryo) As the otic placode invaginates into a cup neuroblasts delaminate from the anterior ventral aspect of the otic epithelium to give rise to neurons of the vestibulocochlear (statoacoustic) ganglion of cranial nerve VIII.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000696", ontology="VHOG", source="PMID:21452441 Park BY, Saint-Jeannet JP, Induction and Segregation of the Vertebrate Cranial Placodes. Developmental Biology (2010)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000013 "The cell bodies of the cochlear nerve lie within the central aspect of the cochlea and are collectively known as the spiral ganglion. This name reflects the fact that the cell bodies, considered as a unit, have a spiral (or perhaps more accurately, a helical) shape, reflecting the shape of the cochlea. The terms 'cochlear nerve fiber' and 'spiral ganglion cell' are used, to some degree, interchangeably, although the former may be used to more specifically refer to the central axons of the cochlear nerve. These central axons exit the cochlea at its base, where it forms a nerve trunk. In humans, this aspect of the nerve is roughly one inch in length. It projects centrally to the brainstem, where its fibers synapse with the cell bodies of the cochlear nucleus" xsd:string {source="Wikipedia:Cochlear_nerve"} +relationship: RO:0002202 UBERON:0003249 {source="NCBIBook:NBK53175"} ! develops from epithelium of otic placode +relationship: RO:0002202 UBERON:0012175 {source="EHDAA2"} ! develops from acoustico-facial VII-VIII ganglion complex +property_value: IAO:0000116 "Consider follow MA naming scheme." xsd:string [Term] id: UBERON:0002828 @@ -197325,7 +195099,7 @@ xref: UMLS:C0175500 {source="BIRNLEX:2567"} xref: Wikipedia:Ventral_cochlear_nucleus is_a: UBERON:0001720 ! cochlear nucleus disjoint_from: UBERON:0002829 {source="lexical"} ! dorsal cochlear nucleus -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/bb/Gray760.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/bb/Gray760.png" xsd:anyURI [Term] id: UBERON:0002829 @@ -197358,7 +195132,7 @@ xref: UMLS:C0175499 {source="BIRNLEX:2569", source="ncithesaurus:Dorsal_Cochlear xref: UMLS:C1281210 {source="BIRNLEX:2569"} xref: Wikipedia:Dorsal_cochlear_nucleus is_a: UBERON:0001720 ! cochlear nucleus -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/bb/Gray760.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/bb/Gray760.png" xsd:anyURI [Term] id: UBERON:0002830 @@ -197420,7 +195194,7 @@ is_a: UBERON:0000044 ! dorsal root ganglion intersection_of: UBERON:0000044 ! dorsal root ganglion intersection_of: extends_fibers_into UBERON:0009632 ! root of cervical nerve relationship: extends_fibers_into UBERON:0009632 ! root of cervical nerve -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002835 @@ -197445,7 +195219,7 @@ is_a: UBERON:0000961 ! thoracic ganglion intersection_of: UBERON:0000044 ! dorsal root ganglion intersection_of: extends_fibers_into UBERON:0009630 ! root of thoracic nerve relationship: extends_fibers_into UBERON:0009630 ! root of thoracic nerve -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002871 @@ -197487,16 +195261,7 @@ is_a: UBERON:0007635 ! nucleus of medulla oblongata intersection_of: UBERON:0000126 ! cranial nerve nucleus intersection_of: extends_fibers_into UBERON:0001650 ! hypoglossal nerve relationship: extends_fibers_into UBERON:0001650 ! hypoglossal nerve -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/94/Gray694.png" xsd:anyURI -property_value: RO:0002171 UBERON:0001719 {source="ABA"} -property_value: RO:0002171 UBERON:0002127 {source="ABA"} -property_value: RO:0002171 UBERON:0002154 {source="ABA"} -property_value: RO:0002171 UBERON:0002155 {source="ABA"} -property_value: RO:0002171 UBERON:0002559 {source="ABA"} -property_value: RO:0002171 UBERON:0002673 {source="ABA"} -property_value: RO:0002171 UBERON:0002870 {source="ABA"} -property_value: RO:0002171 UBERON:0002872 {source="ABA"} -property_value: RO:0002171 UBERON:0002877 {source="ABA"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/94/Gray694.png" xsd:anyURI [Term] id: UBERON:0002893 @@ -197528,9 +195293,6 @@ intersection_of: extends_fibers_into UBERON:0001888 ! lateral olfactory stria intersection_of: part_of UBERON:0002894 ! olfactory cortex relationship: extends_fibers_into UBERON:0001888 ! lateral olfactory stria relationship: part_of UBERON:0002894 ! olfactory cortex -property_value: RO:0002171 UBERON:0002266 {source="ABA"} -property_value: RO:0002171 UBERON:0002590 {source="ABA"} -property_value: RO:0002171 UBERON:0004069 {source="ABA"} [Term] id: UBERON:0002894 @@ -197558,13 +195320,10 @@ xref: UMLS:C0162434 {source="BIRNLEX:2707"} xref: VHOG:0000325 xref: Wikipedia:Olfactory_cortex is_a: UBERON:0002616 ! regional part of brain -relationship: contributes_to_morphology_of UBERON:0005366 ! olfactory lobe relationship: part_of UBERON:0000956 {source="VHOG"} ! cerebral cortex relationship: part_of UBERON:0005366 {source="MA"} ! olfactory lobe -property_value: editor_note "consider relationship: receives_input_from UBERON:0002264 olfactory bulb" xsd:string -property_value: UBPROP:0000001 "That portion of the cerebral cortex that, with the palaeocortex, develops in association with the olfactory system, and which is phylogenetically older than the neocortex and lacks its layered structure. The embryonic archaeocortex corresponds to the cortex of the dentate gyrus and hippocampus in mature mammals[BTO:0001446]." xsd:string {source="BTO:0001446"} -property_value: UBPROP:0000001 "The olfactory cortex is involved in the perception of smell. It receives input from the olfactory bulb and is responsible for the identification of odors[GO][GO:0021989]." xsd:string {source="GO:0021989"} -property_value: UBPROP:0000003 "(In mammals) Odorant detection is mediated by millions of olfactory sensory neurons located in the olfactory epithelium lining the nasal cavity. These neurons transmit sensory signals to the olfactory bulb of the brain, which in turn sends signals to the olfactory cortex.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000325", ontology="VHOG", source="DOI:10.1111/j.1753-4887.2004.tb00097.x Buck LB, Olfactory receptors and odor coding in mammals. Nutrition Reviews (2008)", source="http://bgee.unil.ch/"} +relationship: RO:0002433 UBERON:0005366 ! contributes to morphology of olfactory lobe +property_value: IAO:0000116 "consider relationship: receives_input_from UBERON:0002264 olfactory bulb" xsd:string [Term] id: UBERON:0002916 @@ -197596,13 +195355,13 @@ xref: UMLS:C1281071 {source="BIRNLEX:4035"} xref: Wikipedia:Central_sulcus is_a: UBERON:0013118 ! sulcus of brain intersection_of: UBERON:0013118 ! sulcus of brain -intersection_of: connects UBERON:0001870 ! frontal cortex -intersection_of: connects UBERON:0001872 ! parietal lobe -relationship: connects UBERON:0001870 ! frontal cortex -relationship: connects UBERON:0001872 ! parietal lobe +intersection_of: RO:0002176 UBERON:0001870 ! connects frontal cortex +intersection_of: RO:0002176 UBERON:0001872 ! connects parietal lobe relationship: part_of UBERON:0000956 {source="NIFSTD"} ! cerebral cortex -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/8e/Gray726_central_sulcus.svg" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/b/b6/Central_sulcus.png" xsd:anyURI +relationship: RO:0002176 UBERON:0001870 ! connects frontal cortex +relationship: RO:0002176 UBERON:0001872 ! connects parietal lobe +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8e/Gray726_central_sulcus.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/b/b6/Central_sulcus.png" xsd:anyURI [Term] id: UBERON:0002921 @@ -197636,7 +195395,7 @@ xref: SCTID:369225004 xref: UMLS:C0228186 {source="BIRNLEX:4041", source="ncithesaurus:Longitudinal_Fissure"} xref: Wikipedia:Medial_longitudinal_fissure is_a: UBERON:0014466 {source="FMA"} ! subarachnoid fissure -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/92/Hemispheres.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/92/Hemispheres.png" xsd:anyURI [Term] id: UBERON:0002925 @@ -197670,7 +195429,6 @@ intersection_of: UBERON:0002308 ! nucleus of brain intersection_of: part_of UBERON:0007641 ! trigeminal nuclear complex relationship: extends_fibers_into UBERON:0001645 ! trigeminal nerve relationship: part_of UBERON:0007641 ! trigeminal nuclear complex -property_value: UBPROP:0000012 "massive inconsistencies between GO, MA, wikipedia. Part of pons in MA, but this leads to inconsistencies with ABA." xsd:string {external_ontology="GO", url="https://github.com/obophenotype/mouse-anatomy-ontology/issues/58"} [Term] id: UBERON:0002926 @@ -197703,10 +195461,10 @@ xref: neuronames:2123 xref: NLX:42439 is_a: UBERON:0002304 ! layer of dentate gyrus intersection_of: UBERON:0002304 ! layer of dentate gyrus -intersection_of: immediately_deep_to UBERON:0005381 ! dentate gyrus granule cell layer -relationship: composed_primarily_of CL:0000540 ! neuron -relationship: immediately_deep_to UBERON:0005381 ! dentate gyrus granule cell layer -property_value: editor_note "TODO: add mossy cell" xsd:string +intersection_of: BSPO:0001107 UBERON:0005381 ! dentate gyrus granule cell layer +relationship: BSPO:0001107 UBERON:0005381 ! dentate gyrus granule cell layer +relationship: RO:0002473 CL:0000540 ! composed primarily of neuron +property_value: IAO:0000116 "TODO: add mossy cell" xsd:string [Term] id: UBERON:0002956 @@ -197735,12 +195493,11 @@ xref: neuronames:363 {source="BIRNLEX:779"} xref: UMLS:C1708253 {source="ncithesaurus:Granular_Layer_of_the_Cerebellum"} is_a: UBERON:0004130 ! cerebellar layer intersection_of: UBERON:0004130 ! cerebellar layer -intersection_of: in_deep_part_of UBERON:0002129 ! cerebellar cortex +intersection_of: BSPO:0001101 UBERON:0002129 ! cerebellar cortex +relationship: BSPO:0001101 UBERON:0002129 ! cerebellar cortex relationship: has_part CL:0000119 ! cerebellar Golgi cell relationship: has_part CL:0000555 ! neuronal brush cell relationship: has_part CL:0001031 ! cerebellar granule cell -relationship: in_deep_part_of UBERON:0002129 ! cerebellar cortex -property_value: RO:0002171 UBERON:0002979 {source="ABA"} [Term] id: UBERON:0002974 @@ -197769,12 +195526,11 @@ xref: UMLS:C1289474 {source="BIRNLEX:810"} xref: UMLS:C1709064 {source="ncithesaurus:Molecular_Layer_of_the_Cerebellum"} is_a: UBERON:0004130 ! cerebellar layer intersection_of: UBERON:0004130 ! cerebellar layer -intersection_of: in_superficial_part_of UBERON:0002129 ! cerebellar cortex +intersection_of: BSPO:0001100 UBERON:0002129 ! cerebellar cortex +relationship: BSPO:0001100 UBERON:0002129 ! cerebellar cortex relationship: has_part CL:0000118 ! basket cell relationship: has_part CL:0000122 ! stellate neuron -relationship: in_superficial_part_of UBERON:0002129 ! cerebellar cortex -property_value: editor_note "revisit logical definition after using brain layer patterns" xsd:string -property_value: UBPROP:0000008 "Compare with ZFA:0000636 - cerebellar crest, which is also composed of parallel fibers but located in a more restricted nucleus within the cerebellum" xsd:string +property_value: IAO:0000116 "revisit logical definition after using brain layer patterns" xsd:string [Term] id: UBERON:0002979 @@ -197806,12 +195562,11 @@ xref: UMLS:C1289475 {source="BIRNLEX:818"} xref: UMLS:C1709776 {source="ncithesaurus:Purkinje_Cell_Layer_of_the_Cerebellum"} is_a: UBERON:0004130 ! cerebellar layer intersection_of: UBERON:0004130 ! cerebellar layer -intersection_of: immediately_deep_to UBERON:0002974 ! molecular layer of cerebellar cortex -intersection_of: immediately_superficial_to UBERON:0002956 ! granular layer of cerebellar cortex -relationship: composed_primarily_of CL:0000121 ! Purkinje cell -relationship: immediately_deep_to UBERON:0002974 ! molecular layer of cerebellar cortex -relationship: immediately_superficial_to UBERON:0002956 ! granular layer of cerebellar cortex -property_value: RO:0002171 UBERON:0002956 {source="ABA"} +intersection_of: BSPO:0001107 UBERON:0002974 ! molecular layer of cerebellar cortex +intersection_of: BSPO:0015014 UBERON:0002956 ! granular layer of cerebellar cortex +relationship: BSPO:0001107 UBERON:0002974 ! molecular layer of cerebellar cortex +relationship: BSPO:0015014 UBERON:0002956 ! granular layer of cerebellar cortex +relationship: RO:0002473 CL:0000121 ! composed primarily of Purkinje cell [Term] id: UBERON:0003023 @@ -197833,22 +195588,21 @@ xref: BIRNLEX:923 xref: DHBA:12416 xref: FMA:71108 xref: HBA:9135 -xref: MESH:D065821 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: neuronames:557 {source="BIRNLEX:923"} xref: SCTID:362401009 xref: UMLS:C0228426 {source="BIRNLEX:923"} xref: Wikipedia:Pontine_tegmentum is_a: UBERON:0000064 ! organ part +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: has_part UBERON:0002047 ! pontine raphe nucleus relationship: has_part UBERON:0002128 ! superior olivary complex relationship: has_part UBERON:0002148 ! locus ceruleus relationship: has_part UBERON:0002149 ! superior salivatory nucleus relationship: part_of UBERON:0000988 ! pons -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/9/9c/Brainstem_Abducens.png" xsd:anyURI -property_value: UBPROP:0000009 "involved in the initiation of REM sleep [Wikipedia:Pontine_tegmentum]" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/9/9c/Brainstem_Abducens.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003037 @@ -197862,8 +195616,7 @@ xref: AAO:0011127 xref: FMA:86461 xref: Wikipedia:Septum is_a: UBERON:0000061 ! anatomical structure -relationship: located_in UBERON:0002553 ! anatomical cavity -property_value: UBPROP:0000007 "septal" xsd:string +relationship: RO:0001025 UBERON:0002553 ! located in anatomical cavity [Term] id: UBERON:0003038 @@ -197890,8 +195643,8 @@ is_a: UBERON:0005844 ! spinal cord segment intersection_of: UBERON:0005844 ! spinal cord segment intersection_of: part_of UBERON:0000915 ! thoracic segment of trunk relationship: part_of UBERON:0008231 ! dorsal thoracic segment of trunk -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/68/Gray820.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/68/Gray820.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003041 @@ -197928,7 +195681,6 @@ synonym: "olfactory placodes" EXACT OMO:0003004 [] synonym: "placoda nasalis" EXACT OMO:0003011 [] synonym: "placoda olfactoria" EXACT OMO:0003011 [] xref: AAO:0011076 -xref: BTO:0006222 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: EFO:0003420 xref: EHDAA2:0001232 xref: EHDAA:1504 @@ -197939,10 +195691,9 @@ xref: VHOG:0000186 xref: Wikipedia:Nasal_placode xref: XAO:0000005 xref: ZFA:0000048 -is_a: UBERON:0009955 {contradicted_by="NCBIBook:NBK53171", source="ZFA"} ! neurogenic placode -relationship: develops_from UBERON:0002346 ! neurectoderm +is_a: UBERON:0009955 ! neurogenic placode relationship: part_of UBERON:0000076 {source="EHDAA2"} ! external ectoderm -property_value: UBPROP:0000003 "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (2) neurogenic placodes (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000186", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0002346 ! develops from neurectoderm [Term] id: UBERON:0003051 @@ -197973,17 +195724,14 @@ xref: ZFA:0000051 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0006598 ! presumptive structure is_a: UBERON:0007499 ! epithelial sac +is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0007499 ! epithelial sac -intersection_of: has_potential_to_develop_into UBERON:0001846 ! internal ear intersection_of: part_of UBERON:0000924 ! ectoderm -relationship: develops_from UBERON:0006273 ! otic pit -relationship: has_potential_to_develop_into UBERON:0001846 ! internal ear +intersection_of: RO:0002387 UBERON:0001846 ! has potential to develop into internal ear relationship: part_of UBERON:0000924 ! ectoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray40.png" xsd:anyURI -property_value: UBPROP:0000001 "Epithelial sac present beside the fifth rhombomere; forms the semicircular canals dorsally and the otolith organs ventrally, and houses the acoustico-vestibular sensory epithelia (maculae) of hair cells. Kimmel et al, 1995. (Also see Anatomical Atlas entry for ear by T. Whitfield.)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000051", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "One of the paired sacs of invaginated ectoderm that develop into the membranous labyrinth of the internal ear. [Biology_online][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001148", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "The inner ear develops embryonically in all vertebrates as an invagination of the ectodermal otic placode to form an otic vesicle.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001148", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.413", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "MP defines as epithelial sac, but EHDAA defines as multi-tissue; See https://github.com/obophenotype/uberon/issues/1305" xsd:string {external_ontology="MP"} +relationship: RO:0002202 UBERON:0006273 ! develops from otic pit +relationship: RO:0002387 UBERON:0001846 ! has potential to develop into internal ear +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray40.png" xsd:anyURI [Term] id: UBERON:0003052 @@ -198013,31 +195761,26 @@ xref: VHOG:0000649 xref: XAO:0000016 xref: ZFA:0000042 is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0007651 {inconsistent_with="ZFA", source="https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/106/"} ! anatomical junction +is_a: UBERON:0007651 ! anatomical junction intersection_of: UBERON:0007651 ! anatomical junction intersection_of: overlaps UBERON:0001891 ! midbrain intersection_of: overlaps UBERON:0002028 ! hindbrain -relationship: immediate_transformation_of UBERON:0009615 {source="ZFA"} ! midbrain hindbrain boundary neural plate relationship: overlaps UBERON:0001891 ! midbrain relationship: overlaps UBERON:0002028 ! hindbrain relationship: part_of UBERON:0000955 {source="ZFA"} ! brain -property_value: editor_note "consider adding class for organizer. Consider adding separate class for isthmus as a structure" xsd:string -property_value: UBPROP:0000003 "Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000649", ontology="VHOG", source="DOI:10.1016/j.ydbio.2005.02.008 Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005)", source="http://bgee.unil.ch/"} +relationship: RO:0002495 UBERON:0009615 {source="ZFA"} ! immediate transformation of midbrain hindbrain boundary neural plate +property_value: IAO:0000116 "consider adding class for organizer. Consider adding separate class for isthmus as a structure" xsd:string [Term] id: UBERON:0003055 name: periderm namespace: uberon -def: "A temporary epithelium that derives from the outer layer of the ectdoerm and is shed once the inner layer differentiates to form a true epidermis." [ISBN:9780878932504] +def: "The outermost layer (or layers, depending on the species) of embryonic skin, essential for the development of the epidermis and establishment of the barrier functions. The periderm derives from the outer layer of the ectoderm." [ISBN:9780878932504, PMID:25133425, PMID:35582825] subset: pheno_slim subset: uberon_slim -synonym: "epidermis epithelial layer" RELATED [] -synonym: "epidermis outer layer" RELATED [] -synonym: "epitrichium" RELATED [MP:0013530] -synonym: "EVL" RELATED [ZFA:0001185] -synonym: "periderm" RELATED [] -synonym: "skin periderm" EXACT [EHDAA2:0001846] -xref: BTO:0003377 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} +synonym: "enveloping layer" RELATED [ZFA:0001185] +synonym: "epitrichium" RELATED [MP:0013530, PMID:28722897] +synonym: "EVL" RELATED OMO:0003000 [ZFA:0001185] xref: EHDAA2:0001846 xref: EHDAA:6538 xref: FMA:295662 @@ -198048,13 +195791,8 @@ xref: VHOG:0001680 xref: XAO:0000029 xref: ZFA:0001185 is_a: UBERON:0000487 {source="EHDAA2"} ! simple squamous epithelium -relationship: develops_from UBERON:0007383 {source="ZFA"} ! enveloping layer of ectoderm -relationship: part_of UBERON:0002199 {source="EHDAA2"} ! integument -property_value: UBPROP:0000001 "The outermost epidermal layer covering the fish at embryonic stages; derived from the EVL and thought to eventually be replaced by the superficial stratum of the epidermis. Sometimes used synonymously with EVL. Le Guellec et al, 2004.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001185", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000002 "relationship type change: OBO_REL:part_of ectoderm (TAO:0000016) CHANGED TO: develops_from ectoderm (UBERON:0000924)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001185", ontology="TAO"} -property_value: UBPROP:0000008 "In mice, the first non-basal layer formed at ~E9.5; it is a temporary structure composed of simple squamous epithelium that serves as the first barrier to the embryo's physical environment, exists throughout the entire keratinocyte stratification process, and sheds off at ~E17, when it is replaced by corneocytes[MP]" xsd:string -property_value: UBPROP:0000011 "In some mammals, Eyelid Fusion is thought to be driven by a population of cells which are derived from the periderm, the outermost layer of the developing epidermis" xsd:string -property_value: UBPROP:0000011 "Originally the epidermis is one layer thick, in most vertebrates it soon becomes a two-layered structure. The outer layer gives rise to the periderm. The periderm goes through distinct developmental phases and is ultimately sloughed into the amniotic fluid when differentiation of the underlying epidermal layers is complete. The function of the periderm is not known, but is thought to be related to transport/exchange between the fetus and the amniotic fluid (http://courses.washington.edu/hubio567/devbio/periderm.html)" xsd:string +is_a: UBERON:0007376 ! outer epithelium +is_a: UBERON:3000961 ! external integument structure [Term] id: UBERON:0003056 @@ -198067,10 +195805,10 @@ xref: TAO:0007016 xref: VHOG:0001200 xref: XAO:0000045 xref: ZFA:0007016 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue -relationship: anterior_to UBERON:0009615 ! midbrain hindbrain boundary neural plate +relationship: BSPO:0000096 UBERON:0009615 ! midbrain hindbrain boundary neural plate relationship: part_of UBERON:0003075 ! neural plate -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001200", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003057 @@ -198083,9 +195821,8 @@ xref: VHOG:0001201 xref: XAO:0000046 xref: ZFA:0007017 is_a: UBERON:0002050 ! embryonic structure +relationship: BSPO:0000099 UBERON:0009615 ! midbrain hindbrain boundary neural plate relationship: part_of UBERON:0003075 ! neural plate -relationship: posterior_to UBERON:0009615 ! midbrain hindbrain boundary neural plate -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001201", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003059 @@ -198111,13 +195848,11 @@ xref: XAO:0000057 xref: ZFA:0000279 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0005423 ! developing anatomical structure -intersection_of: has_potential_to_develop_into UBERON:0002329 ! somite -intersection_of: immediate_transformation_of UBERON:0007282 ! presumptive segmental plate -relationship: has_potential_to_develop_into UBERON:0002329 ! somite -relationship: immediate_transformation_of UBERON:0007282 {source="Bgee:AN"} ! presumptive segmental plate +intersection_of: RO:0002387 UBERON:0002329 ! has potential to develop into somite +intersection_of: RO:0002495 UBERON:0007282 ! immediate transformation of presumptive segmental plate relationship: part_of UBERON:0003077 ! paraxial mesoderm -property_value: UBPROP:0000001 "Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000279", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000559", ontology="VHOG", source="DOI:10.1006/dbio.2001.0460 Schubert M, Holland LZ, Dale Stokes M and Holland ND, Three Amphoxius Wnt Genes (AmphiWnt3, AmphiWnt5, and AmphiWnt6) Associated with the Tail Bud: the Evolution of Somitogenesis in Chordates. Developmental Biology (2001)", source="http://bgee.unil.ch/"} +relationship: RO:0002387 UBERON:0002329 ! has potential to develop into somite +relationship: RO:0002495 UBERON:0007282 {source="Bgee:AN"} ! immediate transformation of presumptive segmental plate [Term] id: UBERON:0003060 @@ -198130,23 +195865,18 @@ synonym: "archinephric duct" RELATED [VHOG:0000082] synonym: "ductus pronephricus" RELATED OMO:0003011 [Wikipedia:Pronephric_duct] synonym: "pronephric ducts" RELATED OMO:0003004 [ZFA:0000150] xref: AAO:0011088 -xref: BTO:0005991 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C34279 xref: SCTID:361406002 xref: TAO:0000150 xref: UMLS:C1283945 {source="ncithesaurus:Pronephric_Duct"} -xref: VHOG:0000082 xref: Wikipedia:Pronephric_duct xref: XAO:0000063 xref: ZFA:0000150 is_a: UBERON:0009201 {source="GO"} ! nephric duct is_a: UBERON:0012275 ! meso-epithelium -relationship: develops_from UBERON:0003064 {source="Wikipedia"} ! intermediate mesoderm -relationship: develops_from UBERON:0005721 {source="XAO"} ! pronephric mesoderm relationship: part_of UBERON:0002120 ! pronephros -property_value: UBPROP:0000001 "Duct of the embryonic kidney, present bilaterally ventral to the somites and leading to the anal region where it empties separately from, and just posterior to the anus. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000150", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000082", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "(...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000082", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.686", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003064 {source="Wikipedia"} ! develops from intermediate mesoderm +relationship: RO:0002202 UBERON:0005721 {source="XAO"} ! develops from pronephric mesoderm [Term] id: UBERON:0003061 @@ -198176,13 +195906,8 @@ xref: Wikipedia:Blood_island_of_umbilical_vesicle xref: XAO:0000067 xref: ZFA:0000094 is_a: UBERON:0006598 ! presumptive structure -relationship: develops_from UBERON:0003081 ! lateral plate mesoderm -relationship: has_potential_to_develop_into UBERON:0002390 ! hematopoietic system -property_value: UBPROP:0000001 "Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000094", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011006", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000002 "relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000094", ontology="TAO"} -property_value: UBPROP:0000003 "Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000085", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450, DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual Review of Cell and Developmental Biology (2006)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac" xsd:string {external_ontology="EHDAA2"} +relationship: RO:0002202 UBERON:0003081 ! develops from lateral plate mesoderm +relationship: RO:0002387 UBERON:0002390 ! has potential to develop into hematopoietic system [Term] id: UBERON:0003063 @@ -198206,11 +195931,8 @@ xref: XAO:0000079 xref: ZFA:0000060 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0003068 {source="ZFA"} ! axial mesoderm -relationship: transformation_of UBERON:0034878 {todo="PMID:16313393"} ! prechordal mesoderm -property_value: editor_note "TODO - check; developmental relationship to anterior hypoblast in ZFA?" xsd:string -property_value: UBPROP:0000001 "Axial hypoblast located anterior to the chorda mesoderm; the polster is its most anterior region. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000060", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Axial mesoderm that lies anterior to the notochord and that underlies the forebrain. [Amphioxus_goosecoid_and_the_evolution_of_the_head_organizer_and_prechordal_plate._Evolution_and_Development_(2008)_2(6):303-310, Neidert_AH, Panopoulou_G_and_Langeland_JA][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000086", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "There are two opposing models that can potentially explain the differences in gsc (goosecoid) expression between amphioxus and vertebrates. In one model, the vertebrate gsc expression pattern more closely resembles the common ancestral state and the amphioxus gsc expression pattern is a derivation associated with its unique morphology. (...) In an alternate model, the amphioxus gsc expression pattern most closely represents the common ancestral state and the vertebrate pattern is derived. This model suggests that the evolution of vertebrates was accompanied by the segregation of gsc expression, from a more general domain underlying the entire brain anlage to a distinct forebrain organizer domain and subsequent prechordal plate. We feel this second model is more parsimonious than the first model in that what would be novel anterior gsc expression in vertebrates directly correlates with a novel vertebrate anterior structure, the prechordal plate.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000086", ontology="VHOG", source="DOI:10.1046/j.1525-142x.2000.00073.x Neidert AH, Panopoulou G and Langeland JA, Amphioxus goosecoid and the evolution of the head organizer and prechordal plate. Evolution and Development (2008)", source="http://bgee.unil.ch/"} +relationship: RO:0002494 UBERON:0034878 ! transformation of prechordal mesoderm +property_value: IAO:0000116 "TODO - check; developmental relationship to anterior hypoblast in ZFA?" xsd:string [Term] id: UBERON:0003064 @@ -198240,13 +195962,10 @@ xref: ZFA:0001206 is_a: UBERON:0002050 ! embryonic structure relationship: adjacent_to UBERON:0003077 ! paraxial mesoderm relationship: adjacent_to UBERON:0003081 ! lateral plate mesoderm -relationship: develops_from UBERON:0000926 {source="XAO"} ! mesoderm relationship: part_of UBERON:0000926 {source="AAO"} ! mesoderm relationship: part_of UBERON:0005256 {source="EMAPA"} ! trunk mesenchyme -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "Mesoderm between somite and lateral plate. Traditionally thought to give rise to the urogenital system.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010575", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "(...)the mesoderm of a developing vertebrate transitionally differentiates into the following sub-types: Chordamesoderm (also known as axial mesoderm) which later on gives rise to notochord in all chordates, Paraxial mesoderm, Intermediate mesoderm, Lateral plate mesoderm (reference 1); The mesoderm is present in Bilateria, therefore they are sometimes called triploblasts. Ectoderm and endoderm are usually organized as epithelial layers, while mesoderm can be epithelial or a compact, three-dimensional tissue.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000087", ontology="VHOG", source="Wikipedia:Mesoderm, ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.43", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm')." xsd:string {external_ontology="ZFA"} +relationship: RO:0002202 UBERON:0000926 {source="XAO"} ! develops from mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003066 @@ -198282,11 +196001,7 @@ xref: Wikipedia:Second_pharyngeal_arch xref: XAO:0000098 xref: ZFA:0001611 is_a: UBERON:0002539 ! pharyngeal arch -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray41.png" xsd:anyURI -property_value: UBPROP:0000001 "The second of the series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010363", ontology="AAO", source="XAO:EJS"} -property_value: UBPROP:0000003 "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000297", ontology="VHOG", source="DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "in XAO, develops from visceral pouch 2" xsd:string {external_ontology="XAO"} -property_value: UBPROP:0000103 "2" xsd:nonNegativeInteger +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray41.png" xsd:anyURI [Term] id: UBERON:0003067 @@ -198300,8 +196015,7 @@ xref: VHOG:0000103 xref: XAO:0000187 xref: ZFA:0001310 is_a: UBERON:0009955 {source="NCBIBook:NBK53175"} ! neurogenic placode -relationship: dorsal_to UBERON:0003078 ! epibranchial placode -property_value: UBPROP:0000003 "In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000103", ontology="VHOG", source="DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)", source="http://bgee.unil.ch/"} +relationship: BSPO:0000098 UBERON:0003078 ! epibranchial placode [Term] id: UBERON:0003068 @@ -198319,11 +196033,10 @@ xref: Wikipedia:Chordamesoderm xref: XAO:0000205 xref: ZFA:0001204 is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0000926 ! mesoderm -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0000926 ! mesoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000107", ontology="VHOG", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002202 UBERON:0000926 ! develops from mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003069 @@ -198353,11 +196066,8 @@ xref: VHOG:0000235 xref: Wikipedia:Otic_placode xref: XAO:0000223 xref: ZFA:0000138 -is_a: UBERON:0003067 {notes="invaginates", source="NCBIBook:NBK53175"} ! dorsolateral placode +is_a: UBERON:0003067 ! dorsolateral placode relationship: part_of UBERON:0001690 ! ear -property_value: UBPROP:0000001 "Primordium of the ear epithelium before it hollows into the otic vesicle, present beside the hindbrain rudiment in the midsegmentation period. Kimmel et al, 1995. (Also see Anatomical Atlas entry for ear by T. Whitfield.)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000138", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (2) neurogenic placodes (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000235", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000011 "With the exception of the pigment cells of the stria vascularis and the secretory epithelium of the cochlea, which are of neural crest origin, all compo- nents of the inner ear derive from the otic placode. In most species the thickening of the ectoderm into a placode occurs in a region adjacent to rhombomere 5 (reviewed in Ohyama et al., 2007), while in amphibians the otic placode is centered onto rhombomere 4 (Ruiz i Altaba and Jessell, 1991)." xsd:string {source="NCBIBook:NBK53175"} [Term] id: UBERON:0003070 @@ -198377,11 +196087,7 @@ xref: VHOG:0000109 xref: XAO:0000225 xref: ZFA:0000162 is_a: UBERON:0003067 {source="ISBN:0471888893"} ! dorsolateral placode -relationship: has_potential_to_developmentally_contribute_to UBERON:0003942 ! somatosensory system -property_value: UBPROP:0000001 "The ectodermal precursor of the trigeminal ganglion. The profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24.[XAO]" xsd:string {ontology="XAO"} -property_value: UBPROP:0000001 "The ectodermal rudiment of the trigeminal ganglion, distinguishable during much of the segmentation period. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000162", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "The dorsolateral placodes (trigeminal and vestibular) develop from ectoderm lateral to the brain (...). In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000109", ontology="VHOG", source="DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000013 "Consider naming this 'trigeminal placode complex'. Also, Fig9-5 of ISBN:0471888893 calls this the profundus placode; XAO says 'profundal and the trigeminal ganglia are separate distally but fused at their proximal end...'" xsd:string +relationship: RO:0002385 UBERON:0003942 ! has potential to developmentally contribute to somatosensory system [Term] id: UBERON:0003071 @@ -198411,12 +196117,12 @@ is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0001048 ! primordium is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0006598 ! presumptive structure +is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0001048 ! primordium -intersection_of: has_potential_to_develop_into UBERON:0000019 ! camera-type eye -relationship: develops_from UBERON:0003056 ! pre-chordal neural plate -relationship: has_potential_to_develop_into UBERON:0000019 ! camera-type eye +intersection_of: RO:0002387 UBERON:0000019 ! has potential to develop into camera-type eye relationship: part_of UBERON:0003056 {source="PMID:16496288", source="XAO"} ! pre-chordal neural plate -property_value: UBPROP:0000012 "TODO - check that GO's optic placode is the same as ZFA's eye primordium; we may want to have separate term for ocular primordium precursor. XAO has both optic field and eye primordium." xsd:string {external_ontology="GO"} +relationship: RO:0002202 UBERON:0003056 ! develops from pre-chordal neural plate +relationship: RO:0002387 UBERON:0000019 ! has potential to develop into camera-type eye [Term] id: UBERON:0003072 @@ -198441,10 +196147,9 @@ xref: VHOG:0000167 xref: ZFA:0001202 is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004121 ! ectoderm-derived structure -relationship: developmentally_induced_by UBERON:0003073 ! lens placode -relationship: develops_from UBERON:0004128 {source="ZFA"} ! optic vesicle relationship: part_of UBERON:0010312 {source="ZFA"} ! immature eye -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000167", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0004128 {source="ZFA"} ! develops from optic vesicle +relationship: RO:0002256 UBERON:0003073 ! developmentally induced by lens placode [Term] id: UBERON:0003073 @@ -198472,16 +196177,14 @@ xref: XAO:0000240 xref: ZFA:0000122 is_a: UBERON:0002546 ! cranial placode is_a: UBERON:0006598 ! presumptive structure +is_a: UBERON:0010312 ! immature eye is_a: UBERON:0011814 {source="NCBIBook:NBK53175"} ! non-neurogenic ectodermal placode intersection_of: UBERON:0005085 ! ectodermal placode -intersection_of: has_potential_to_develop_into UBERON:0000965 ! lens of camera-type eye -relationship: developmentally_induced_by UBERON:0004128 ! optic vesicle -relationship: has_potential_to_develop_into UBERON:0000965 ! lens of camera-type eye +intersection_of: RO:0002387 UBERON:0000965 ! has potential to develop into lens of camera-type eye relationship: part_of UBERON:0010312 {source="ZFA"} ! immature eye -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png" xsd:anyURI -property_value: UBPROP:0000001 "Ectodermal primordium of the lens of the eye. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000122", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000166", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000011 "Classical transplantation experiments using amphibian embryos suggested that the optic vesicle is the source of lens-inducing signals sufficient to generate lens tissues in competent ectoderm (reviewed in Grainger et al., 1996). More recent findings suggest a multistep model for lens induction. There is now good evidence that lens specification occurs at the neurula stage, before the optic vesicle contact the surface ectoderm, and that neural crest cell migration in the frontonasal region is required to restrict the position of the lens placode (Bailey et al., 2006)" xsd:string {source="NCBIBook:NBK53175"} +relationship: RO:0002256 UBERON:0004128 ! developmentally induced by optic vesicle +relationship: RO:0002387 UBERON:0000965 ! has potential to develop into lens of camera-type eye +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png" xsd:anyURI [Term] id: UBERON:0003074 @@ -198497,32 +196200,24 @@ synonym: "Leydig's duct" RELATED [Wikipedia:Wolffian_duct] synonym: "renal duct" RELATED [] synonym: "Wolffian duct" EXACT [GOC:yaf, Wikipedia:Wolffian_duct, ZFA:0000546] xref: AAO:0000637 -xref: BTO:0005990 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: EHDAA2:0001243 xref: EHDAA:1590 -xref: EMAPA:16577 xref: GAID:1315 xref: MESH:D014928 xref: NCIT:C26469 xref: SCTID:308800003 xref: TAO:0000546 xref: UMLS:C0043204 {source="ncithesaurus:Mesonephric_Duct"} -xref: VHOG:0000082 xref: Wikipedia:Mesonephric_duct xref: XAO:0000242 xref: ZFA:0000546 is_a: UBERON:0000083 ! mesonephric tubule is_a: UBERON:0009201 {source="GO"} ! nephric duct -is_a: UBERON:0012275 ! meso-epithelium -relationship: develops_from UBERON:0003060 ! pronephric duct -relationship: develops_from UBERON:0005792 {source="EHDAA2"} ! nephric ridge -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png" xsd:anyURI -property_value: editor_note "Consider adding subclasses for male and female specific variants" xsd:string -property_value: editor_note "TODO - mesonephric portion of the nephric duct" xsd:string -property_value: UBPROP:0000001 "Anatomical structure consisting of either of a pair of longitudinal ducts which carry urine and in males, sperm, to the cloaca.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000637", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000082", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "(...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000082", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.686", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000011 "In the male the Wolffian duct persists, and forms for example the epididymis, the ductus deferens, the ejaculatory duct, seminal vesicle and efferent ducts." xsd:string +relationship: RO:0002202 UBERON:0003060 ! develops from pronephric duct +relationship: RO:0002202 UBERON:0005792 {source="EHDAA2"} ! develops from nephric ridge +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png" xsd:anyURI +property_value: IAO:0000116 "Consider adding subclasses for male and female specific variants" xsd:string +property_value: IAO:0000116 "TODO - mesonephric portion of the nephric duct" xsd:string [Term] id: UBERON:0003075 @@ -198542,7 +196237,6 @@ xref: EHDAA:346 xref: EHDAA:902 xref: EMAPA:35593 xref: FMA:293879 -xref: MESH:D054258 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C34225 xref: neuronames:1362 xref: RETIRED_EHDAA2:0001252 @@ -198555,12 +196249,10 @@ xref: ZFA:0000132 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0016879 ! future central nervous system -relationship: developmentally_induced_by UBERON:0002328 {source="Wikipedia"} ! notochord -relationship: immediate_transformation_of UBERON:0007284 {source="Bgee:AN"} ! presumptive neural plate -relationship: only_in_taxon NCBITaxon:7711 {source="GOTAX:0000352"} ! Chordata -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI -property_value: UBPROP:0000001 "The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000132", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000068", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata +relationship: RO:0002256 UBERON:0002328 {source="Wikipedia"} ! developmentally induced by notochord +relationship: RO:0002495 UBERON:0007284 {source="Bgee:AN"} ! immediate transformation of presumptive neural plate +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI [Term] id: UBERON:0003076 @@ -198573,9 +196265,8 @@ xref: XAO:0000250 xref: ZFA:0007037 is_a: UBERON:0002050 ! embryonic structure disjoint_from: UBERON:0003080 {source="lexical"} ! anterior neural tube -relationship: develops_from UBERON:0003057 ! chordal neural plate relationship: part_of UBERON:0001049 ! neural tube -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001383", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003057 ! develops from chordal neural plate [Term] id: UBERON:0003077 @@ -198604,13 +196295,10 @@ xref: ZFA:0000255 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue is_a: UBERON:0015212 ! lateral structure -relationship: existence_starts_during UBERON:0000109 ! gastrula stage -relationship: immediate_transformation_of UBERON:0007285 {source="Bgee:AN"} ! presumptive paraxial mesoderm -relationship: in_lateral_side_of UBERON:0000922 ! embryo -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010568", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000114", ontology="VHOG", source="DOI:10.1002/dvdy.21177 Kusakabe R and Kuratani S. Evolutionary perspectives from development of mesodermal components in the lamprey. Developmental dynamics (2007)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here)" xsd:string {external_ontology="ZFA"} +relationship: BSPO:0000126 UBERON:0000922 ! embryo +relationship: RO:0002488 UBERON:0000109 ! existence starts during gastrula stage +relationship: RO:0002495 UBERON:0007285 {source="Bgee:AN"} ! immediate transformation of presumptive paraxial mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003078 @@ -198628,13 +196316,9 @@ xref: VHOG:0000117 xref: XAO:0000284 xref: ZFA:0001294 is_a: UBERON:0009955 {source="NCBIBook:NBK53175", source="ZFA"} ! neurogenic placode -relationship: develops_from UBERON:0000076 {source="EHDAA2-abduced"} ! external ectoderm -relationship: has_potential_to_developmentally_contribute_to UBERON:0002410 ! autonomic nervous system relationship: part_of UBERON:0000010 {source="ZFA"} ! peripheral nervous system -property_value: UBPROP:0000001 "Focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches and that produce the neuroblasts that migrate and condense to form the distal cranial ganglia. [Graham_A, The_development_and_evolution_of_the_pharyngeal_arches._J_Anat_(2001)_199:_133-141][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000117", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia. (...) The one substantial difference between the vertebrate pharyngeal arches and those of the protochordates is the presence of the epibranchial placodes but the evolution of these structures was undoubtedly driven by the endoderm.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000117", ontology="VHOG", source="DOI:10.1046/j.1469-7580.2001.19910133.x Graham A, The development and evolution of the pharyngeal arches. J Anat (2001)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000011 "Epibranchial placodes-derived neurons innervate internal organs to transmit information such as heart rate, blood pressure, and visceral distension from the periphery to the central nervous system (Baker and Bronner-Fraser, 2001). From rostral to caudal the epibranchial placodes comprise the geniculate, petrosal, and nodose placodes, each associated in sequence with the first, second and third branchial clefts. Each placode contributes sensory neurons to cranial nerves VII (facial nerve), IX (glossopharyngeal nerve), and X (vagal nerve), respectively" xsd:string {source="NCBIBook:NBK53175"} -property_value: UBPROP:0000012 "in XAO this develops_from dorsolateral placode, but in NBK53175, this is a separate group" xsd:string {external_ontology="XAO"} +relationship: RO:0002202 UBERON:0000076 {source="EHDAA2-abduced"} ! develops from external ectoderm +relationship: RO:0002385 UBERON:0002410 ! has potential to developmentally contribute to autonomic nervous system [Term] id: UBERON:0003080 @@ -198646,10 +196330,9 @@ xref: VHOG:0001384 xref: XAO:0000307 xref: ZFA:0007038 is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0003056 ! pre-chordal neural plate relationship: part_of UBERON:0001049 ! neural tube -property_value: editor_note "TODO - add grouping class for the anterior end of the neural tube at all stages" xsd:string -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001384", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003056 ! develops from pre-chordal neural plate +property_value: IAO:0000116 "TODO - add grouping class for the anterior end of the neural tube at all stages" xsd:string [Term] id: UBERON:0003081 @@ -198681,14 +196364,10 @@ is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0000926 {source="EHDAA2", source="VHOG"} ! mesoderm -relationship: surrounds UBERON:0003887 ! intraembryonic coelom -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010574", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000001 "The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000118", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000118", ontology="VHOG", source="DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "subclass of mesoderm in ZFA." xsd:string {external_ontology="ZFA"} +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002221 UBERON:0003887 ! surrounds intraembryonic coelom +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003082 @@ -198723,12 +196402,10 @@ xref: Wikipedia:Myotome xref: XAO:0000315 xref: ZFA:0001056 is_a: UBERON:0017650 {source="AEO"} ! developing mesenchymal structure -relationship: contributes_to_morphology_of UBERON:0001630 ! muscle organ -relationship: develops_from UBERON:0004290 {source="EHDAA2-abduced"} ! dermomyotome -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI -property_value: editor_note "The term 'myotome' is also used to describe the muscles served by a single nerve root / spinal segment - consider adding new class, myomere." xsd:string -property_value: UBPROP:0000001 "Portion of the somites giving rise to body wall muscle masses. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001056", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "In all vertebrates, the skeletal muscle of the body axis is chiefly derived from an early embryonic compartment, known as the myotome.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001244", ontology="VHOG", source="DOI:10.1038/sj.embor.embor920 Hollway GE, Currie PD, Myotome meanderings. Cellular morphogenesis and the making of muscle. EMBO Rep.(2003)", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0004290 {source="EHDAA2-abduced"} ! develops from dermomyotome +relationship: RO:0002433 UBERON:0001630 ! contributes to morphology of muscle organ +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI +property_value: IAO:0000116 "The term 'myotome' is also used to describe the muscles served by a single nerve root / spinal segment - consider adding new class, myomere." xsd:string [Term] id: UBERON:0003083 @@ -198747,11 +196424,11 @@ xref: VHOG:0000062 xref: Wikipedia:Trunk_neural_crest xref: XAO:0000319 xref: ZFA:0001024 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: has_part CL:0000011 {source="ZFA"} ! migratory trunk neural crest cell relationship: part_of UBERON:0002342 ! neural crest -property_value: UBPROP:0000001 "Post-cranial portion of the neural crest. Exact anatomical derivations not experimentally resolved in amphibians.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010582", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000062", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003084 @@ -198769,14 +196446,11 @@ xref: UMLS:C1514450 {source="ncithesaurus:Primordium_of_the_Heart"} xref: XAO:0000336 xref: ZFA:0000028 is_a: UBERON:0001048 {source="Obol"} ! primordium -relationship: develops_from UBERON:0003081 {source="ZFA"} ! lateral plate mesoderm -relationship: develops_from UBERON:0004140 ! primary heart field -relationship: develops_from UBERON:0007005 {source="XAO"} ! cardiogenic splanchnic mesoderm relationship: part_of UBERON:0004535 {source="ZFA"} ! cardiovascular system -property_value: editor_note "should probably be merged with heart rudiment." xsd:string -property_value: UBPROP:0000001 "Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000028", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011044", ontology="AAO", source="XAO:curator"} -property_value: UBPROP:0000002 "relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000028", ontology="TAO"} +relationship: RO:0002202 UBERON:0003081 {source="ZFA"} ! develops from lateral plate mesoderm +relationship: RO:0002202 UBERON:0004140 ! develops from primary heart field +relationship: RO:0002202 UBERON:0007005 {source="XAO"} ! develops from cardiogenic splanchnic mesoderm +property_value: IAO:0000116 "should probably be merged with heart rudiment." xsd:string [Term] id: UBERON:0003086 @@ -198796,12 +196470,10 @@ xref: ZFA:0000011 is_a: UBERON:0001637 ! artery is_a: UBERON:0003524 ! tail blood vessel intersection_of: UBERON:0001637 ! artery -intersection_of: connecting_branch_of UBERON:0005805 ! dorsal aorta intersection_of: part_of UBERON:0007812 ! post-anal tail -relationship: connecting_branch_of UBERON:0005805 ! dorsal aorta +intersection_of: RO:0002252 UBERON:0005805 ! connecting branch of dorsal aorta relationship: part_of UBERON:2001073 ! axial vasculature -property_value: UBPROP:0000001 "Extension of the dorsal aorta in the tail. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000011", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "The posterior extension of the dorsal aorta to the tail region, which degenerates at metamorphosis.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011023", ontology="AAO", source="ISBN:0-226-55763-4"} +relationship: RO:0002252 UBERON:0005805 ! connecting branch of dorsal aorta [Term] id: UBERON:0003089 @@ -198815,7 +196487,6 @@ synonym: "sclerotomes" EXACT OMO:0003004 [TAO:0001080] synonym: "sclerotomus" RELATED OMO:0003011 [Wikipedia:Sclerotome] xref: AAO:0010571 xref: AEO:0000212 -xref: BTO:0006255 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: EHDAA2:0003439 xref: EMAPA:31159 xref: FMA:295652 @@ -198828,12 +196499,9 @@ xref: XAO:0000397 xref: ZFA:0001080 is_a: UBERON:0005856 {source="EHDAA2"} ! developing mesenchymal condensation is_a: UBERON:0007530 {source="EHDAA2"} ! migrating mesenchyme population -relationship: develops_from UBERON:0002329 {source="ZFA"} ! somite -relationship: only_in_taxon NCBITaxon:7742 {source="VHOG:0000680"} ! Vertebrata -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI -property_value: UBPROP:0000001 "Skeletogenic portion of somites.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010571", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000680", ontology="VHOG", source="DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "part_of somite in XAO" xsd:string {external_ontology="XAO"} +relationship: RO:0002160 NCBITaxon:7742 {source="VHOG:0000680"} ! only in taxon Vertebrata +relationship: RO:0002202 UBERON:0002329 {source="ZFA"} ! develops from somite +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI [Term] id: UBERON:0003091 @@ -198855,12 +196523,9 @@ xref: ZFA:0001081 is_a: UBERON:0000479 {source="ZFA"} ! tissue is_a: UBERON:0001048 ! primordium is_a: UBERON:0004119 ! endoderm-derived structure -relationship: develops_from UBERON:0007123 {source="ISBN:0073040584", source="PMID:16313389"} ! pharyngeal pouch 2 relationship: part_of UBERON:0000949 {source="ZFA"} ! endocrine system relationship: part_of UBERON:0001042 {source="VHOG"} ! chordate pharynx -property_value: UBPROP:0000001 "Portion of tissue part of the pharyngeal endoderm that is fated to become thyroid follicle[ZFIN:curator]." xsd:string {source="ZFIN:curator"} -property_value: UBPROP:0000008 "In all vertebrates the thyroid arises from the ventral aspect of the second pouch" xsd:string {source="PMID:16313389"} -property_value: UBPROP:0000012 "Note that we follow EHDAA2 in dividing this into endoderm and mesenchyme. In this ontology we place the broad developmental relationship at this level, and include specific relationships to the pharyngeal endoderm at the level of the endoderm" xsd:string {external_ontology="EHDAA2"} +relationship: RO:0002202 UBERON:0007123 {source="ISBN:0073040584", source="PMID:16313389"} ! develops from pharyngeal pouch 2 [Term] id: UBERON:0003098 @@ -198886,11 +196551,9 @@ xref: XAO:0000475 xref: ZFA:0000137 is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0034705 {source="EHDAA2"} ! developing neuroepithelium -relationship: develops_from UBERON:0003072 ! optic cup relationship: part_of UBERON:0001894 ! diencephalon -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png" xsd:anyURI -property_value: UBPROP:0000001 "The evagination from the neural tube of the developing embryo which develops the optic cup at its extremity; the stalk persists as the optic nerve. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000223", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/optic+stalk"} -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000223", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003072 ! develops from optic cup +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png" xsd:anyURI [Term] id: UBERON:0003099 @@ -198916,12 +196579,11 @@ xref: VHOG:0000063 xref: Wikipedia:Cranial_neural_crest xref: XAO:0001001 xref: ZFA:0001194 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: has_part CL:0000008 ! migratory cranial neural crest cell relationship: part_of UBERON:0002342 ! neural crest -property_value: UBPROP:0000001 "Anterior most portion of the neural crest. Migrates in three highly conserved streams: mandibular, hyoid and branchial.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010580", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000001 "Neural crest that is part of the head.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001194", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000063", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003100 @@ -198935,7 +196597,6 @@ synonym: "female human body" NARROW SENSU [FMA:67812] xref: AAO:0010030 xref: BILA:0000028 xref: CARO:0000028 -xref: FBbt:00007011 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67812 xref: HAO:0000028 xref: SCTID:362608006 @@ -198945,7 +196606,6 @@ xref: XAO:0003005 xref: ZFA:0000303 is_a: UBERON:0000468 ! multicellular organism disjoint_from: UBERON:0003101 ! male organism -property_value: RO:0002171 UBERON:0003101 [Term] id: UBERON:0003101 @@ -198959,7 +196619,6 @@ synonym: "male human body" NARROW SENSU [FMA:67811] xref: AAO:0010033 xref: BILA:0000027 xref: CARO:0000027 -xref: FBbt:00007004 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67811 xref: HAO:0000027 xref: SCTID:362609003 @@ -198991,8 +196650,7 @@ xref: XAO:0003028 xref: ZFA:0000292 is_a: UBERON:0000061 ! anatomical structure relationship: adjacent_to UBERON:0013514 ! space surrounding organism -property_value: editor_note "consider obsoleting. See issue/1305" xsd:string -property_value: UBPROP:0000001 "Organism subdivision which is the collection of anatomical structures on the body surface.[ZFA]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000292", ontology="TAO", source="ZFIN:curator"} +property_value: IAO:0000116 "consider obsoleting. See issue/1305" xsd:string [Term] id: UBERON:0003103 @@ -199015,7 +196673,6 @@ xref: VHOG:0001723 xref: XAO:0003041 xref: ZFA:0000496 is_a: UBERON:0000062 ! organ -property_value: IAO:0000232 "this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs" xsd:string [Term] id: UBERON:0003104 @@ -199045,16 +196702,13 @@ xref: XAO:0003046 xref: ZFA:0000393 is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue -intersection_of: composed_primarily_of CL:0008019 ! mesenchymal cell -relationship: composed_primarily_of CL:0008019 ! mesenchymal cell -relationship: functionally_related_to GO:0032502 ! developmental process -relationship: has_developmental_contribution_from UBERON:0000926 {gci_relation="part_of", gci_filler="NCBITaxon:7711"} ! mesoderm -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI -property_value: editor_note "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" xsd:string -property_value: UBPROP:0000001 "A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000393", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010427", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000007 "mesenchymal" xsd:string +intersection_of: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002254 UBERON:0000926 {gci_relation="part_of", gci_filler="NCBITaxon:7711"} ! has developmental contribution from mesoderm +relationship: RO:0002328 GO:0032502 ! functionally related to developmental process +relationship: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI +property_value: IAO:0000116 "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" xsd:string [Term] id: UBERON:0003110 @@ -199068,10 +196722,6 @@ xref: ZFA:0000189 is_a: UBERON:0034921 ! multi organ part structure relationship: part_of UBERON:0001703 ! neurocranium relationship: part_of UBERON:0002241 ! chondrocranium -property_value: UBPROP:0000001 "Anatomical cluster that is a posterolateral part of the cranium and structurally supports the vestibuloauditory system.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000189", ontology="TAO", source="TAO:MAH"} -property_value: UBPROP:0000001 "Anatomical cluster that is a posterolateral part of the neurocranium and structurally supports the vestibuloauditory system.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010208", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000002 "relationship loss: overlaps hyomandibular-otic region joint (TAO:0001947)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000189", ontology="TAO"} -property_value: UBPROP:0000012 "UBERONREF:0000007 has this as a syn for otic capsule" xsd:string [Term] id: UBERON:0003111 @@ -199085,7 +196735,6 @@ xref: ZFA:0000290 is_a: UBERON:0034921 ! multi organ part structure relationship: part_of UBERON:0001703 ! neurocranium relationship: part_of UBERON:0002241 ! chondrocranium -property_value: UBPROP:0000001 "Anatomical cluster that forms the floor and sidewalls of the middle part of the neurocranium.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010207", ontology="AAO", source="AAO:EJS"} [Term] id: UBERON:0003112 @@ -199103,8 +196752,6 @@ xref: ZFA:0000351 is_a: UBERON:0034921 ! multi organ part structure relationship: part_of UBERON:0001703 ! neurocranium relationship: part_of UBERON:0002241 ! chondrocranium -property_value: UBPROP:0000001 "Anatomical cluster that is located in the anterior region of the cranium and provides structural support for the peripheral olfactory organ.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000351", ontology="TAO", source="TAO:MAH"} -property_value: UBPROP:0000001 "Anatomical cluster that is located in the anterior region of the neurocranium and provides structural support for the olfactory organs.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010206", ontology="AAO", source="AAO:EJS"} [Term] id: UBERON:0003113 @@ -199129,12 +196776,10 @@ xref: Wikipedia:Skull_roof xref: XAO:0003169 xref: ZFA:0000863 is_a: UBERON:0011159 ! primary subdivision of cranial skeletal system -relationship: never_in_taxon NCBITaxon:7777 {source="ISBN:0073040584"} -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0010364 ! dermal skeleton -property_value: editor_note "wikipedia treats skull roof and dermatocranium as synonymous, but some sources treat the roof as being part of the dermatocranium - see UBERONREF:0000007" xsd:string -property_value: UBPROP:0000001 "Anatomical cluster that is part of the cranium and composed of dermally derived bones.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000863", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Anatomical cluster that is part of the cranium which consists of dermally derived bones.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010154", ontology="AAO", source="AAO:BJB"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +property_value: IAO:0000116 "wikipedia treats skull roof and dermatocranium as synonymous, but some sources treat the roof as being part of the dermatocranium - see UBERONREF:0000007" xsd:string +property_value: RO:0002161 NCBITaxon:7777 {source="ISBN:0073040584"} [Term] id: UBERON:0003114 @@ -199164,10 +196809,6 @@ xref: VHOG:0000298 xref: XAO:0000447 xref: ZFA:0001606 is_a: UBERON:0002539 ! pharyngeal arch -property_value: UBPROP:0000001 "The most anterior, or first, pharygeal/branchial arch, composed of the mandibular process, forming the posterior border of the stomodeum, and the maxillary process anterior to the stomodeum, contains the first aortic arch.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010365", ontology="AAO", source="ISBN:0-02-377110-0"} -property_value: UBPROP:0000003 "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000298", ontology="VHOG", source="DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "in XAO, called branchial arch 1 and df VP3" xsd:string {external_ontology="XAO"} -property_value: UBPROP:0000103 "3" xsd:nonNegativeInteger [Term] id: UBERON:0003115 @@ -199199,10 +196840,6 @@ xref: VHOG:0000299 xref: XAO:0000449 xref: ZFA:0001607 is_a: UBERON:0002539 ! pharyngeal arch -property_value: UBPROP:0000001 "The second pharyngeal/branchial arch; arises as a thickening of the pharygeal wall between the first and second branchial clefts; contains the second aortic arch; forms part of the hyoid bone, tongue and facial musculature.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010366", ontology="AAO", source="ISBN:0-02-377110-0"} -property_value: UBPROP:0000003 "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000299", ontology="VHOG", source="DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "in XAO, called branchial arch 2 and df VP4" xsd:string {external_ontology="XAO"} -property_value: UBPROP:0000103 "4" xsd:nonNegativeInteger [Term] id: UBERON:0003116 @@ -199224,11 +196861,6 @@ xref: VHOG:0001204 xref: XAO:0000451 xref: ZFA:0001608 is_a: UBERON:0002539 ! pharyngeal arch -property_value: UBPROP:0000001 "The third in a series of paired bars in the wall of the pharynx, within which are formed the third aortic arch and the cartilage bar of the visceral skeleton, forms and supports the gills.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010367", ontology="AAO", source="ISBN:0-02-377110-0"} -property_value: UBPROP:0000003 "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001204", ontology="VHOG", source="DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M, Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "A fifth arch never establishes itself in amniotes" xsd:string -property_value: UBPROP:0000012 "in XAO, called branchial arch 3 and df VP5" xsd:string {external_ontology="XAO"} -property_value: UBPROP:0000103 "5" xsd:nonNegativeInteger [Term] id: UBERON:0003117 @@ -199257,9 +196889,6 @@ xref: VHOG:0001205 xref: XAO:0000453 xref: ZFA:0001609 is_a: UBERON:0002539 ! pharyngeal arch -property_value: UBPROP:0000001 "The forth in a series of paired bars in the wall of the pharynx, within which are formed the forth aortic arch and the cartilage bar of the visceral skeleton, forms and supports the gills.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010368", ontology="AAO", source="ISBN:0-02-377110-0"} -property_value: UBPROP:0000003 "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001205", ontology="VHOG", source="DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M, Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000103 "6" xsd:nonNegativeInteger [Term] id: UBERON:0003118 @@ -199291,10 +196920,8 @@ xref: ZFA:0005005 is_a: UBERON:0004363 ! pharyngeal arch artery intersection_of: UBERON:0004363 ! pharyngeal arch artery intersection_of: part_of UBERON:0004362 ! pharyngeal arch 1 -relationship: contributes_to_morphology_of UBERON:0004362 ! pharyngeal arch 1 relationship: part_of UBERON:0004362 ! pharyngeal arch 1 -property_value: UBPROP:0000008 "Disappears early in development in tetrapods" xsd:string -property_value: UBPROP:0000012 "ZFA states that The paired aortic arch 1 arteries branch off of the ventral aorta, and empty into the right and left lateral dorsal aortas" xsd:string {external_ontology="ZFA"} +relationship: RO:0002433 UBERON:0004362 ! contributes to morphology of pharyngeal arch 1 [Term] id: UBERON:0003119 @@ -199326,10 +196953,8 @@ xref: ZFA:0005006 is_a: UBERON:0004363 ! pharyngeal arch artery intersection_of: UBERON:0004363 ! pharyngeal arch artery intersection_of: part_of UBERON:0003066 ! pharyngeal arch 2 -relationship: contributes_to_morphology_of UBERON:0003066 ! pharyngeal arch 2 relationship: part_of UBERON:0003066 ! pharyngeal arch 2 -property_value: UBPROP:0000001 "The first and second arches disappear early, but the dorsal end of the second gives origin to the stapedial artery, a vessel which atrophies in humans but persists in some mammals. It passes through the ring of the stapes and divides into supraorbital, infraorbital, and mandibular branches which follow the three divisions of the trigeminal nerve. The infraorbital and mandibular arise from a common stem, the terminal part of which anastomoses with the external carotid. On the obliteration of the stapedial artery this anastomosis enlarges and forms the internal maxillary artery, and the branches of the stapedial artery are now branches of this vessel. The common stem of the infraorbital and mandibular branches passes between the two roots of the auriculotemporal nerve and becomes the middle meningeal artery; the original supraorbital branch of the stapedial is represented by the orbital twigs of the middle meningeal[WP][Wikipedia:Aortic_arches#Arches_1_and_2]." xsd:string {source="Wikipedia:Aortic_arches#Arches_1_and_2"} -property_value: UBPROP:0000001 "The second in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 2 that is part of hyoid arch.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010418", ontology="AAO", source="ISBN:0-02-377110-0"} +relationship: RO:0002433 UBERON:0003066 ! contributes to morphology of pharyngeal arch 2 [Term] id: UBERON:0003120 @@ -199360,11 +196985,8 @@ xref: ZFA:0005007 is_a: UBERON:0004363 ! pharyngeal arch artery intersection_of: UBERON:0004363 ! pharyngeal arch artery intersection_of: part_of UBERON:0003114 ! pharyngeal arch 3 -relationship: contributes_to_morphology_of UBERON:0003114 ! pharyngeal arch 3 relationship: part_of UBERON:0003114 ! pharyngeal arch 3 -property_value: UBPROP:0000001 "Aortic arches 3 and 4 are not remodeled but are retained largely intact as the branchial arteries providing circulation through the gills. These areches are direct branches from the ventral aorta to the lateral dorsal aorta. Isogai et al. 2001.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005007", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "The third aortic arch constitutes the commencement of the internal carotid artery, and is therefore named the carotid arch[WP][Wikipedia:Aortic_arches#Arch_3]." xsd:string {source="Wikipedia:Aortic_arches#Arch_3"} -property_value: UBPROP:0000001 "The third in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 3 lies within the 3rd branchial arch and branches directly from the ventral aorta to the lateral dorsal aorta, and are retained as the branchial arteries providing circulation through the gills in the adult.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010419", ontology="AAO", source="ISBN:0-02-377110-0"} +relationship: RO:0002433 UBERON:0003114 ! contributes to morphology of pharyngeal arch 3 [Term] id: UBERON:0003121 @@ -199396,10 +197018,6 @@ is_a: UBERON:0004363 ! pharyngeal arch artery intersection_of: UBERON:0004363 ! pharyngeal arch artery intersection_of: part_of UBERON:0003115 ! pharyngeal arch 4 relationship: part_of UBERON:0003115 ! pharyngeal arch 4 -property_value: UBPROP:0000001 "Aortic arches 3 and 4 are not remodeled but are retained largely intact as the branchial arteries providing circulation through the gills. These areches are direct branches from the ventral aorta to the lateral dorsal aorta. Isogai et al. 2001.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005008", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "The forth in a series paired arterial connections between the dorsal and ventral aortae, lies within the 4th branchial arch. The paired aortic arch 4 arteries branch directly from the ventral aorta to the lateral dorsal aorta, and are retained as the branchial arteries providing circulation through the gills in the adult.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010420", ontology="AAO", source="ISBN:0-02-377110-0"} -property_value: UBPROP:0000001 "The fourth right arch forms the right subclavian as far as the origin of its internal mammary branch; while the fourth left arch constitutes the arch of the aorta between the origin of the left carotid artery and the termination of the ductus arteriosus[WP][Wikipedia:Aortic_arches#Arch_4]." xsd:string {source="Wikipedia:Aortic_arches#Arch_4"} -property_value: UBPROP:0000011 "Normally, the left fourth arch becomes the aortic arch, the right fourth arch contributes to the innominate artery[http://emedicine.medscape.com/article/899609-overview] in birds it is the right fourth arch which forms the permanent aorta" xsd:string [Term] id: UBERON:0003122 @@ -199421,10 +197039,6 @@ is_a: UBERON:0004363 ! pharyngeal arch artery intersection_of: UBERON:0004363 ! pharyngeal arch artery intersection_of: part_of UBERON:0003116 ! pharyngeal arch 5 relationship: part_of UBERON:0003116 ! pharyngeal arch 5 -property_value: UBPROP:0000001 "The fifth and sixth arches, which come on-line at approximately 2.5 dpf, have a common trunk from the ventral aorta and drain to the midline dorsal aorta via an independent route. The fifth and sixth aortic arches supply the trunk and tail with oxigenated blood. Isogai et al. 2001.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005009", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "The fifth arch disappears on both sides[WP][Wikipedia:Aortic_arches#Arch_5]." xsd:string {source="Wikipedia:Aortic_arches#Arch_5"} -property_value: UBPROP:0000001 "The fifth in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 5 artery is paired and has a common trunk with aortic arch 6 from the ventral aorta, and drains via a separate branch of the lateral dorsal aorta. Aortic arches 5 and 6 supply the trunk and tail with oxygenated blood.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010421", ontology="AAO", source="ISBN:0-02-377110-0"} -property_value: UBPROP:0000008 "In humans the 5th arch disappears on both sides" xsd:string [Term] id: UBERON:0003123 @@ -199456,10 +197070,6 @@ is_a: UBERON:0004363 ! pharyngeal arch artery intersection_of: UBERON:0004363 ! pharyngeal arch artery intersection_of: part_of UBERON:0003117 ! pharyngeal arch 6 relationship: part_of UBERON:0003117 ! pharyngeal arch 6 -property_value: UBPROP:0000001 "The fifth and sixth arches, which come on-line at approximately 2.5 dpf, have a common trunk from the ventral aorta and drain to the midline dorsal aorta via an independent route. The fifth and sixth aortic arches supply the trunk and tail with oxigenated blood. Isogai et al. 2001.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005016", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "The sixth in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 6 artery is paired and has a common trunk with aortic arch 5 from the ventral aorta, and drains via a separate branch of the lateral dorsal aorta. It forms part of the pulmonary arteries, and in the later embryo, the ductus arteriosis. Aortic arches 5 and 6 together supply the trunk and tail with oxygenated blood.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010422", ontology="AAO", source="ISBN:0-02-377110-0"} -property_value: UBPROP:0000001 "The sixth right arch disappears; the sixth left arch gives off the pulmonary arteries and forms the ductus arteriosus; this duct remains pervious during the whole of fetal life, but then closes within the first few days after birth due to increased O2 concentration. Oxygen concentration causes the production of bradykinin which causes the ductus to constrict occluding all flow. Within 1-3 months, the ductus is obliterated and becomes the ligamentum arteriosus. His showed that in the early embryo the right and left arches each gives a branch to the lungs, but that later both pulmonary arteries take origin from the left arch[WP][Wikipedia:Aortic_arches#Arch_6]." xsd:string {source="Wikipedia:Aortic_arches#Arch_6"} -property_value: UBPROP:0000011 "the distal left sixth arch becomes the ductus arteriosus, the proximal sixth arches bilaterally contribute to the proximal branch pulmonary arteries" xsd:string {source="http://emedicine.medscape.com/article/899609-overview"} [Term] id: UBERON:0003124 @@ -199494,20 +197104,15 @@ xref: UMLS:C0008503 {source="ncithesaurus:Chorion"} xref: UMLS:C1516505 {source="ncithesaurus:Chorionic_Sac"} xref: VHOG:0000200 xref: Wikipedia:Chorion +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005631 ! extraembryonic membrane relationship: adjacent_to UBERON:0000922 ! embryo -relationship: develops_from UBERON:0005971 {source="ISBN:0073040584"} ! amniotic fold relationship: has_part UBERON:0003265 ! chorionic mesenchyme relationship: has_part UBERON:0003374 ! chorionic ectoderm -relationship: only_in_taxon NCBITaxon:32524 {source="Hymans"} ! Amniota -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/51/Gray24.png" xsd:anyURI -property_value: UBPROP:0000001 "The outer membrane enclosing the embryo in reptiles, birds, and mammals. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000200", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/chorion"} -property_value: UBPROP:0000001 "The outer membrane of the two membranes enclosing the embryo in reptiles, birds, and mammals. In placental mammals it contributes to the development of the placenta[BTO:0000252]." xsd:string {source="BTO:0000252"} -property_value: UBPROP:0000003 "Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000200", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.187", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "chorionic" xsd:string -property_value: UBPROP:0000008 "The chorion of placentals is bilaminar as in reptiles and birds, but forms from the trophoblast and includes the ajdacent mesodermal layer [ISBN:0073040584]" xsd:string -property_value: UBPROP:0000011 "Extra-embryonic ectoderm" xsd:string {source="PMID:19829370"} +relationship: RO:0002160 NCBITaxon:32524 {source="Hymans"} ! only in taxon Amniota +relationship: RO:0002202 UBERON:0005971 {source="ISBN:0073040584"} ! develops from amniotic fold +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/51/Gray24.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003126 @@ -199544,22 +197149,16 @@ xref: VHOG:0000371 xref: Wikipedia:Vertebrate_trachea xref: XAO:0000118 is_a: UBERON:0000117 ! respiratory tube -relationship: contributes_to_morphology_of UBERON:0001004 ! respiratory system -relationship: develops_from UBERON:0008947 {source="EHDAA2"} ! respiratory primordium -relationship: located_in UBERON:0002224 ! thoracic cavity -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0007196 ! tracheobronchial tree -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/9f/Illu_conducting_passages.svg" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c3/Illu_conducting_passages.jpg" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-trachea.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-trachea.glb" xsd:anyURI -property_value: UBPROP:0000001 "An elongated tube which carries air to and from the lungs.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010140", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "The respiratory tube between the larynx and the bronchi. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000371", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "In primitive fishes and most tetrapods, the lungs of adults are usually paired. They lie ventral to the digestive tract and are connected to the outside environment through the trachea.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000371", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.409", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "tracheal" xsd:string -property_value: UBPROP:0000008 "In birds, the trachea runs from the pharynx to the syrinx, from which the primary bronchi diverge. Swans have an unusually elongated trachea, part of which is coiled beneath the sternum; this may act as a resonator to amplify sound. In some birds, the cartilagenous rings are complete, and may even be ossified. In amphibians, the trachea is normally extremely short, and leads directly into the lungs, without clear primary bronchi. A longer trachea is, however found in some long-necked salamanders, and in caecilians. While there are irregular cartilagenous nodules on the amphibian trachea, these do not form the rings found in amniotes. The only vertebrate to have lungs, but no trachea, is Polypterus, in which the lungs arise directly from the pharynx." xsd:string -property_value: UBPROP:0000008 "in mouse 15-18 C-rings, 15-20 in human." xsd:string {source="ISBN:0123813611"} +relationship: RO:0001025 UBERON:0002224 ! located in thoracic cavity +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002202 UBERON:0008947 {source="EHDAA2"} ! develops from respiratory primordium +relationship: RO:0002433 UBERON:0001004 ! contributes to morphology of respiratory system +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/9f/Illu_conducting_passages.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c3/Illu_conducting_passages.jpg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-trachea.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-trachea.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003127 @@ -199575,8 +197174,8 @@ xref: Wikipedia:Invertebrate_trachea is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0001005 ! respiratory airway relationship: has_part UBERON:0003914 ! epithelial tube -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda relationship: part_of UBERON:0005155 ! open tracheal system +relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda [Term] id: UBERON:0003128 @@ -199598,21 +197197,15 @@ synonym: "upper part of skull" EXACT [] xref: BTO:0001328 xref: EFO:0000831 xref: EHDAA:6029 -xref: EMAPA:17680 xref: FMA:71325 xref: MA:0000316 xref: MAT:0000340 -xref: MESH:D012886 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: MIAA:0000340 xref: SCTID:181889008 xref: VHOG:0000334 xref: Wikipedia:Cranium_(anatomy) is_a: UBERON:0000075 {source="FMA-inferred"} ! subdivision of skeletal system -relationship: present_in_taxon NCBITaxon:7762 -property_value: RO:0002171 UBERON:0003278 -property_value: UBPROP:0000007 "cranial" xsd:string -property_value: UBPROP:0000012 "the inclusion of the FMA class here is probably not quite correct, as this class includes as parts sutures, whereas this is not part of the bones of the cranium" xsd:string {external_ontology="FMA"} -property_value: UBPROP:0000013 "The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton" xsd:string {source="WP"} +property_value: RO:0002175 NCBITaxon:7762 [Term] id: UBERON:0003129 @@ -199637,14 +197230,12 @@ xref: UMLS:C0037303 {source="ncithesaurus:Skull"} xref: Wikipedia:Skull xref: WikipediaCategory:Skull is_a: UBERON:0000075 {source="FMA"} ! subdivision of skeletal system +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: has_part UBERON:0003128 ! cranium relationship: has_part UBERON:0003278 ! skeleton of lower jaw -relationship: only_in_taxon NCBITaxon:89593 ! Craniata relationship: part_of UBERON:0000033 ! head relationship: part_of UBERON:0010323 ! cranial skeletal system -property_value: UBPROP:0000012 "in FMA the skull is divided into orbit, neurocranium (8 parts), viscerocranium (26 parts). Here we have a separate overlapping division into cranium and mandible." xsd:string {external_ontology="FMA"} -property_value: UBPROP:0000012 "in many ontologies, the structure called the cranium is inclusive of the mandible/lower jaw skeleton" xsd:string -property_value: UBPROP:0000013 "A skull that is missing a mandible is only a cranium; this is the source of a very commonly made error in terminology. Those animals having skulls are called craniates" xsd:string {source="WP"} +relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata [Term] id: UBERON:0003133 @@ -199658,7 +197249,6 @@ synonym: "genital organ" EXACT [] synonym: "genitalia" RELATED OMO:0003004 [] synonym: "reproductive system organ" EXACT [] synonym: "sex organ" EXACT [] -xref: EMAPA:17381 xref: EMAPA:37731 {source="MA:th"} xref: MA:0001752 xref: MESH:D005835 @@ -199672,7 +197262,6 @@ is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0000062 ! organ intersection_of: capable_of_part_of GO:0000003 ! reproduction relationship: capable_of_part_of GO:0000003 ! reproduction -property_value: UBPROP:0000012 "GO uses genitalia for the singular organ" xsd:string {external_ontology="GO"} [Term] id: UBERON:0003134 @@ -199731,13 +197320,12 @@ name: blood nerve barrier namespace: uberon def: "Barrier between the perineurium of peripheral nerves and the vascular endothelium of endoneurial capillaries. The perineurium acts as a diffusion barrier, but ion permeability at the blood-nerve barrier is still higher than at the blood-brain barrier[GO]." [GO:0008065, Wikipedia:Blood-nerve_barrier] synonym: "blood-nerve barrier" EXACT [] -xref: MESH:D049428 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: Wikipedia:Blood-nerve_barrier is_a: UBERON:0000119 ! cell layer relationship: adjacent_to UBERON:0000179 ! haemolymphatic fluid relationship: adjacent_to UBERON:0001021 ! nerve -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0001016 ! nervous system +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata [Term] id: UBERON:0003210 @@ -199747,10 +197335,11 @@ def: "Barrier in the choroid plexus located in the lateral, third, and fourth br subset: pheno_slim synonym: "blood-CSF barrier" EXACT [MP:0006088] is_a: UBERON:0000119 ! cell layer +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: adjacent_to UBERON:0000178 ! blood relationship: adjacent_to UBERON:0001359 ! cerebrospinal fluid -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0001886 ! choroid plexus +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata [Term] id: UBERON:0003212 @@ -199764,7 +197353,6 @@ synonym: "organ of gustatory system" EXACT [OBOL:automatic] synonym: "organ of taste system" EXACT [OBOL:automatic] synonym: "taste organ" EXACT [] synonym: "taste system organ" EXACT [OBOL:automatic] -xref: FBbt:00005159 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:77853 is_a: UBERON:0000005 ! chemosensory organ intersection_of: UBERON:0000062 ! organ @@ -199792,10 +197380,11 @@ xref: EMAPA:36566 xref: FMA:73285 xref: MA:0002760 is_a: UBERON:0003215 ! alveolus +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0003215 ! alveolus intersection_of: part_of UBERON:0001911 ! mammary gland -relationship: contributes_to_morphology_of UBERON:0001912 ! lobule of mammary gland relationship: part_of UBERON:0001912 ! lobule of mammary gland +relationship: RO:0002433 UBERON:0001912 ! contributes to morphology of lobule of mammary gland [Term] id: UBERON:0003215 @@ -199804,13 +197393,11 @@ namespace: uberon def: "Organ part that has the form of a hollow cavity[WP]." [Wikipedia:Alveolus] subset: efo_slim xref: EFO:0002513 -xref: EV:0100043 xref: FMA:82493 xref: NCIT:C12986 xref: UMLS:C0034051 {source="ncithesaurus:Alveolus"} xref: Wikipedia:Alveolus is_a: UBERON:0000064 ! organ part -property_value: UBPROP:0000007 "alveolar" xsd:string [Term] id: UBERON:0003218 @@ -199846,12 +197433,10 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: has_potential_to_develop_into UBERON:0000081 ! metanephros -relationship: developmentally_induced_by UBERON:0000084 {source="ISBN:9780878932504"} ! ureteric bud -relationship: develops_from UBERON:0003074 ! mesonephric duct -relationship: has_potential_to_develop_into UBERON:0000081 ! metanephros -property_value: UBPROP:0000001 "A mass of intermediate mesodermal cells around the distal end of the ureteric bud that gives rise to nephrons in the metanephric kidney. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000540", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/metanephric+mesenchyme"} -property_value: UBPROP:0000003 "When the ureteric buds emerge from the nephric duct, they enter the metanephrogenic mesenchyme. The ureteric buds induce this mesenchymal tissue to condense around them and differentiate into the nephrons of the mammalian kidney. As this mesenchyme differentiates, it tells the ureteric bud to branch and grow.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000540", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.462", source="http://bgee.unil.ch/"} +intersection_of: RO:0002387 UBERON:0000081 ! has potential to develop into metanephros +relationship: RO:0002202 UBERON:0003074 ! develops from mesonephric duct +relationship: RO:0002256 UBERON:0000084 {source="ISBN:9780878932504"} ! developmentally induced by ureteric bud +relationship: RO:0002387 UBERON:0000081 ! has potential to develop into metanephros [Term] id: UBERON:0003221 @@ -199878,11 +197463,9 @@ is_a: UBERON:0003606 ! limb long bone is_a: UBERON:0012357 ! digitopodium bone is_a: UBERON:0015023 ! phalanx endochondral element intersection_of: UBERON:0015023 ! phalanx endochondral element -intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue -relationship: develops_from UBERON:0010701 ! phalanx cartilage element +intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue relationship: part_of UBERON:5102544 ! individual digit of digitopodial skeleton -property_value: UBPROP:0000007 "phalangeal" xsd:string -property_value: UBPROP:0000008 "In primates such as humans and monkeys, the thumb and big toe have two phalanges, while the other fingers and toes consist of three" xsd:string {source="WP"} +relationship: RO:0002202 UBERON:0010701 ! develops from phalanx cartilage element [Term] id: UBERON:0003224 @@ -199893,11 +197476,11 @@ xref: EHDAA2:0001973 xref: EHDAA:156 is_a: UBERON:0000478 ! extraembryonic structure intersection_of: UBERON:0000478 ! extraembryonic structure -intersection_of: develops_from UBERON:0000371 ! syncytiotrophoblast intersection_of: part_of UBERON:0003124 ! chorion membrane -relationship: develops_from UBERON:0000371 {notes="polar trophectoderm syncytiotrophoblast", source="EHDAA2"} ! syncytiotrophoblast +intersection_of: RO:0002202 UBERON:0000371 ! develops from syncytiotrophoblast relationship: part_of UBERON:0003124 {source="EHDAA2"} ! chorion membrane -property_value: editor_note "TODO - check" xsd:string +relationship: RO:0002202 UBERON:0000371 ! develops from syncytiotrophoblast +property_value: IAO:0000116 "TODO - check" xsd:string [Term] id: UBERON:0003229 @@ -199916,11 +197499,11 @@ xref: EHDAA:4168 xref: EHDAA:6214 xref: EMAPA:17415 xref: VHOG:0001044 -is_a: UBERON:0000483 ! epithelium +is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001461 ! elbow -relationship: develops_from UBERON:0003372 {source="EHDAA2"} ! pectoral appendage bud ectoderm relationship: part_of UBERON:0001461 ! elbow +relationship: RO:0002202 UBERON:0003372 {source="EHDAA2"} ! develops from pectoral appendage bud ectoderm [Term] id: UBERON:0003230 @@ -199937,10 +197520,11 @@ synonym: "wrist epithelium" EXACT [OBOL:automatic] xref: EHDAA2:0000219 xref: EHDAA:5198 is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium +is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0004452 ! carpal region -relationship: develops_from UBERON:0003372 {source="EHDAA2"} ! pectoral appendage bud ectoderm relationship: part_of UBERON:0004452 ! carpal region +relationship: RO:0002202 UBERON:0003372 {source="EHDAA2"} ! develops from pectoral appendage bud ectoderm [Term] id: UBERON:0003231 @@ -199963,11 +197547,11 @@ xref: EHDAA:5155 xref: EHDAA:6180 xref: EMAPA:17491 xref: VHOG:0000779 -is_a: UBERON:0000483 ! epithelium +is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001464 ! hip -relationship: develops_from UBERON:0003371 {source="EHDAA2"} ! pelvic appendage bud ectoderm relationship: part_of UBERON:0001464 ! hip +relationship: RO:0002202 UBERON:0003371 {source="EHDAA2"} ! develops from pelvic appendage bud ectoderm [Term] id: UBERON:0003232 @@ -199982,11 +197566,11 @@ xref: EHDAA:5161 xref: EHDAA:6186 xref: EMAPA:17494 xref: VHOG:0000810 -is_a: UBERON:0000483 ! epithelium +is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001465 ! knee -relationship: develops_from UBERON:0003371 {source="EHDAA2"} ! pelvic appendage bud ectoderm relationship: part_of UBERON:0001465 ! knee +relationship: RO:0002202 UBERON:0003371 {source="EHDAA2"} ! develops from pelvic appendage bud ectoderm [Term] id: UBERON:0003233 @@ -200001,11 +197585,11 @@ xref: EHDAA:4182 xref: EHDAA:6230 xref: EMAPA:17422 xref: VHOG:0000761 -is_a: UBERON:0000483 ! epithelium +is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001467 ! shoulder -relationship: develops_from UBERON:0003372 {source="EHDAA2"} ! pectoral appendage bud ectoderm relationship: part_of UBERON:0001467 ! shoulder +relationship: RO:0002202 UBERON:0003372 {source="EHDAA2"} ! develops from pectoral appendage bud ectoderm [Term] id: UBERON:0003235 @@ -200021,7 +197605,6 @@ synonym: "upper jaw epithelial tissue" EXACT [OBOL:automatic] synonym: "upper jaw epithelium" EXACT [OBOL:automatic] xref: EHDAA2:0002119 xref: EHDAA:8027 -xref: EMAPA:17943 xref: EMAPA:18971 is_a: UBERON:0035037 ! jaw epithelium intersection_of: UBERON:0000483 ! epithelium @@ -200072,10 +197655,6 @@ synonym: "utriculus (labyrinthus vestibularis) epithelial tissue" EXACT [OBOL:au synonym: "utriculus (labyrinthus vestibularis) epithelium" EXACT [OBOL:automatic] xref: EHDAA:4730 xref: EMAPA:17295 -xref: EMAPA:17298 -xref: EMAPA:17301 -xref: EMAPA:17820 -xref: EMAPA:17823 xref: FMA:75604 xref: MA:0001204 xref: RETIRED_EHDAA2:0002155 @@ -200087,7 +197666,7 @@ relationship: has_part CL:0002316 {source="FMA"} ! supporting cell of vestibular relationship: has_part CL:1000379 {source="FMA"} ! type 1 vestibular sensory cell of epithelium of macula of utricle of membranous labyrinth relationship: has_part CL:1000383 {source="FMA"} ! type 2 vestibular sensory cell of epithelium of macula of utricle of membranous labyrinth relationship: part_of UBERON:0002214 {source="FMA"} ! macula of utricle of membranous labyrinth -property_value: editor_note "TODO - check relationships w.r.t macula" xsd:string +property_value: IAO:0000116 "TODO - check relationships w.r.t macula" xsd:string [Term] id: UBERON:0003242 @@ -200123,7 +197702,7 @@ relationship: has_part CL:0002316 {source="FMA"} ! supporting cell of vestibular relationship: has_part CL:1000380 {source="FMA"} ! type 1 vestibular sensory cell of epithelium of macula of saccule of membranous labyrinth relationship: has_part CL:1000384 {source="FMA"} ! type 2 vestibular sensory cell of epithelium of macula of saccule of membranous labyrinth relationship: part_of UBERON:0001854 ! saccule of membranous labyrinth -property_value: editor_note "TODO - check relationships w.r.t macula" xsd:string +property_value: IAO:0000116 "TODO - check relationships w.r.t macula" xsd:string [Term] id: UBERON:0003243 @@ -200171,13 +197750,13 @@ xref: MA:0000792 xref: NCIT:C12937 xref: UMLS:C0596882 {source="ncithesaurus:Mammary_Epithelium"} xref: VHOG:0001088 -is_a: UBERON:0000483 ! epithelium +is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001911 ! mammary gland -relationship: contributes_to_morphology_of UBERON:0001911 ! mammary gland -relationship: develops_from UBERON:0011272 {source="EHDAA2", source="Wikipathways:WP2062"} ! embryonic skin basal layer relationship: part_of UBERON:0001911 ! mammary gland relationship: part_of UBERON:0005200 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="EHDAA2"} ! thoracic mammary gland +relationship: RO:0002202 UBERON:0011272 {source="EHDAA2", source="Wikipathways:WP2062"} ! develops from embryonic skin basal layer +relationship: RO:0002433 UBERON:0001911 ! contributes to morphology of mammary gland [Term] id: UBERON:0003247 @@ -200190,11 +197769,11 @@ xref: EHDAA:4174 xref: EHDAA:6220 xref: EMAPA:17418 xref: VHOG:0001096 -is_a: UBERON:0000483 ! epithelium +is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002386 ! forelimb zeugopod -relationship: develops_from UBERON:0003372 {source="EHDAA2"} ! pectoral appendage bud ectoderm relationship: part_of UBERON:0002386 ! forelimb zeugopod +relationship: RO:0002202 UBERON:0003372 {source="EHDAA2"} ! develops from pectoral appendage bud ectoderm [Term] id: UBERON:0003248 @@ -200209,10 +197788,11 @@ xref: EHDAA:6144 xref: EMAPA:32655 is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0006871 ! embryonic footplate -relationship: develops_from UBERON:0003372 {source="EHDAA2"} ! pectoral appendage bud ectoderm relationship: part_of UBERON:0006871 ! embryonic footplate +relationship: RO:0002202 UBERON:0003372 {source="EHDAA2"} ! develops from pectoral appendage bud ectoderm [Term] id: UBERON:0003249 @@ -200229,11 +197809,12 @@ xref: EMAPA:16197 xref: VHOG:0000636 xref: ZFA:0007068 is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0015807 ! ear epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0003069 ! otic placode relationship: part_of UBERON:0003069 ! otic placode -property_value: editor_note "check ZFA, placemeant, appears to refer to both adult structures and primordium" xsd:string +property_value: IAO:0000116 "check ZFA, placemeant, appears to refer to both adult structures and primordium" xsd:string [Term] id: UBERON:0003252 @@ -200251,11 +197832,10 @@ xref: SCTID:361741004 xref: Wikipedia:Human_rib_cage xref: Wikipedia:Rib_cage is_a: UBERON:0010912 ! subdivision of skeleton -relationship: contributes_to_morphology_of UBERON:0005944 ! axial skeleton plus cranial skeleton relationship: part_of UBERON:0014477 ! thoracic skeleton relationship: part_of UBERON:0014478 ! rib skeletal system -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/88/Gray112.png" xsd:anyURI -property_value: UBPROP:0000001 "Anatomical cluster that consists of more than one rib in an individual.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002100", ontology="TAO", source="TAO:wd"} +relationship: RO:0002433 UBERON:0005944 ! contributes to morphology of axial skeleton plus cranial skeleton +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/88/Gray112.png" xsd:anyURI [Term] id: UBERON:0003253 @@ -200273,7 +197853,7 @@ is_a: UBERON:0018664 ! neck of bone element intersection_of: UBERON:0001560 ! neck of organ intersection_of: part_of UBERON:0002228 ! rib relationship: part_of UBERON:0010388 {source="PMID:15906248"} ! proximal segment of rib -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray122.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray122.png" xsd:anyURI [Term] id: UBERON:0003254 @@ -200292,10 +197872,10 @@ xref: VHOG:0000621 is_a: UBERON:0000478 {source="EHDAA2"} ! extraembryonic structure is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0005292 ! extraembryonic tissue -relationship: develops_from UBERON:0002532 {source="EHDAA2-via-amnioblasts", source="ISBN:9780878932504"} ! epiblast (generic) +is_a: UBERON:0012275 ! meso-epithelium relationship: part_of UBERON:0000305 {source="EHDAA2"} ! amnion -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: editor_note "we make the germ layer relationship develops_from, as currently the germ layers are declared to be purely embryonic. TODO - check. WP:Amnion - In the human embryo the earliest stages of the formation of the amnion have not been observed; in the youngest embryo which has been studied the amnion was already present as a closed sac, and appears in the inner cell-mass as a cavity. This cavity is roofed in by a single stratum of flattened, ectodermal cells, the amniotic ectoderm, and its floor consists of the prismatic ectoderm of the embryonic disk-the continuity between the roof and floor being established at the margin of the embryonic disk. Outside the amniotic ectoderm is a thin layer of mesoderm, which is continuous with that of the somatopleure and is connected by the body-stalk with the mesodermal lining of the chorion." xsd:string +property_value: IAO:0000116 "we make the germ layer relationship develops_from, as currently the germ layers are declared to be purely embryonic. TODO - check. WP:Amnion - In the human embryo the earliest stages of the formation of the amnion have not been observed; in the youngest embryo which has been studied the amnion was already present as a closed sac, and appears in the inner cell-mass as a cavity. This cavity is roofed in by a single stratum of flattened, ectodermal cells, the amniotic ectoderm, and its floor consists of the prismatic ectoderm of the embryonic disk-the continuity between the roof and floor being established at the margin of the embryonic disk. Outside the amniotic ectoderm is a thin layer of mesoderm, which is continuous with that of the somatopleure and is connected by the body-stalk with the mesodermal lining of the chorion." xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003257 @@ -200311,7 +197891,7 @@ is_a: UBERON:0005292 ! extraembryonic tissue is_a: UBERON:0005911 ! endo-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: bounding_layer_of UBERON:0001040 ! yolk sac -intersection_of: develops_from UBERON:0000925 ! endoderm +intersection_of: RO:0002202 UBERON:0000925 ! develops from endoderm relationship: bounding_layer_of UBERON:0001040 ! yolk sac [Term] @@ -200326,9 +197906,9 @@ is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0005911 ! endo-epithelium is_a: UBERON:0015833 ! foregut epithelium intersection_of: UBERON:0000490 ! unilaminar epithelium -intersection_of: develops_from UBERON:0000925 ! endoderm intersection_of: part_of UBERON:0001041 ! foregut -property_value: editor_note "TODO - check" xsd:string +intersection_of: RO:0002202 UBERON:0000925 ! develops from endoderm +property_value: IAO:0000116 "TODO - check" xsd:string [Term] id: UBERON:0003259 @@ -200344,9 +197924,9 @@ is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0003352 ! epithelium of midgut is_a: UBERON:0005911 ! endo-epithelium intersection_of: UBERON:0000490 ! unilaminar epithelium -intersection_of: develops_from UBERON:0000925 ! endoderm intersection_of: part_of UBERON:0001045 ! midgut -property_value: editor_note "TODO - check" xsd:string +intersection_of: RO:0002202 UBERON:0000925 ! develops from endoderm +property_value: IAO:0000116 "TODO - check" xsd:string [Term] id: UBERON:0003260 @@ -200360,9 +197940,9 @@ is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0003353 ! epithelium of hindgut is_a: UBERON:0005911 ! endo-epithelium intersection_of: UBERON:0000490 ! unilaminar epithelium -intersection_of: develops_from UBERON:0000925 ! endoderm intersection_of: part_of UBERON:0001046 ! hindgut -property_value: editor_note "TODO - check" xsd:string +intersection_of: RO:0002202 UBERON:0000925 ! develops from endoderm +property_value: IAO:0000116 "TODO - check" xsd:string [Term] id: UBERON:0003261 @@ -200379,8 +197959,8 @@ is_a: UBERON:0000925 ! endoderm is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0000925 ! endoderm intersection_of: part_of UBERON:0003091 ! thyroid primordium -relationship: develops_from UBERON:0007690 {source="ZFA-propagated"} ! early pharyngeal endoderm relationship: part_of UBERON:0003091 ! thyroid primordium +relationship: RO:0002202 UBERON:0007690 {source="ZFA-propagated"} ! develops from early pharyngeal endoderm [Term] id: UBERON:0003262 @@ -200406,8 +197986,8 @@ is_a: UBERON:0010333 ! extraembryonic membrane mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0000305 ! amnion relationship: part_of UBERON:0000305 ! amnion -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: editor_note "we make the germ layer relationship develops_from, as currently the germ layers are declared to be purely embryonic. TODO - check. WP:Amnion - In the human embryo the earliest stages of the formation of the amnion have not been observed; in the youngest embryo which has been studied the amnion was already present as a closed sac, and appears in the inner cell-mass as a cavity. This cavity is roofed in by a single stratum of flattened, ectodermal cells, the amniotic ectoderm, and its floor consists of the prismatic ectoderm of the embryonic disk-the continuity between the roof and floor being established at the margin of the embryonic disk. Outside the amniotic ectoderm is a thin layer of mesoderm, which is continuous with that of the somatopleure and is connected by the body-stalk with the mesodermal lining of the chorion." xsd:string +property_value: IAO:0000116 "we make the germ layer relationship develops_from, as currently the germ layers are declared to be purely embryonic. TODO - check. WP:Amnion - In the human embryo the earliest stages of the formation of the amnion have not been observed; in the youngest embryo which has been studied the amnion was already present as a closed sac, and appears in the inner cell-mass as a cavity. This cavity is roofed in by a single stratum of flattened, ectodermal cells, the amniotic ectoderm, and its floor consists of the prismatic ectoderm of the embryonic disk-the continuity between the roof and floor being established at the margin of the embryonic disk. Outside the amniotic ectoderm is a thin layer of mesoderm, which is continuous with that of the somatopleure and is connected by the body-stalk with the mesodermal lining of the chorion." xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003265 @@ -200431,9 +198011,9 @@ is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue is_a: UBERON:0010333 ! extraembryonic membrane mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0003124 ! chorion membrane -relationship: develops_from UBERON:0004871 {source="ISBN:0073040584"} ! somatic layer of lateral plate mesoderm relationship: part_of UBERON:0003124 ! chorion membrane -property_value: editor_note "TODO - check" xsd:string +relationship: RO:0002202 UBERON:0004871 {source="ISBN:0073040584"} ! develops from somatic layer of lateral plate mesoderm +property_value: IAO:0000116 "TODO - check" xsd:string [Term] id: UBERON:0003267 @@ -200449,12 +198029,13 @@ xref: NCIT:C49792 xref: SCTID:422279005 xref: UMLS:C1710581 {source="ncithesaurus:Upper_Jaw_Tooth"} is_a: UBERON:0001091 ! calcareous tooth +is_a: UBERON:0010313 ! neural crest-derived structure is_a: UBERON:0013765 ! digestive system element intersection_of: UBERON:0001091 ! calcareous tooth intersection_of: part_of UBERON:0001709 ! upper jaw region -relationship: attaches_to UBERON:0011597 ! bone of upper jaw relationship: part_of UBERON:0009680 ! set of upper jaw teeth -property_value: editor_note "Note that we follow EHDAA2 and consider teeth part of the jaw skeleton" xsd:string +relationship: RO:0002371 UBERON:0011597 ! attached to bone of upper jaw +property_value: IAO:0000116 "Note that we follow EHDAA2 and consider teeth part of the jaw skeleton" xsd:string [Term] id: UBERON:0003268 @@ -200467,7 +198048,6 @@ synonym: "lower jaw dentine containing tooth" EXACT [OBOL:automatic] synonym: "lower jaw tooth" EXACT [OBOL:automatic] synonym: "lower jaw vertebrate tooth" EXACT [OBOL:automatic] synonym: "mandibular tooth" NARROW [NCBITaxon:40674] -xref: EHDAA2:0001029 xref: EHDAA:8009 xref: EMAPA:17917 xref: FMA:321647 @@ -200476,11 +198056,12 @@ xref: NCIT:C49582 xref: SCTID:422032003 xref: UMLS:C1708757 {source="ncithesaurus:Lower_Jaw_Tooth"} is_a: UBERON:0001091 ! calcareous tooth +is_a: UBERON:0010313 ! neural crest-derived structure is_a: UBERON:0013765 ! digestive system element intersection_of: UBERON:0001091 ! calcareous tooth intersection_of: part_of UBERON:0001710 ! lower jaw region -relationship: attaches_to UBERON:0004768 ! bone of lower jaw relationship: part_of UBERON:0009679 ! set of lower jaw teeth +relationship: RO:0002371 UBERON:0004768 ! attached to bone of lower jaw [Term] id: UBERON:0003269 @@ -200495,6 +198076,7 @@ xref: EHDAA2:0000486 xref: EHDAA:2923 xref: EMAPA:17844 is_a: UBERON:0001134 ! skeletal muscle tissue +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0001134 ! skeletal muscle tissue intersection_of: part_of UBERON:0000019 ! camera-type eye relationship: part_of UBERON:0000019 ! camera-type eye @@ -200515,14 +198097,13 @@ xref: FMA:54397 xref: MA:0001908 xref: VHOG:0000429 xref: XAO:0003087 +is_a: UBERON:0010313 ! neural crest-derived structure is_a: UBERON:0010912 ! subdivision of skeleton intersection_of: UBERON:0010912 ! subdivision of skeleton -intersection_of: skeleton_of UBERON:0001709 ! upper jaw region +intersection_of: RO:0002576 UBERON:0001709 ! skeleton of upper jaw region relationship: part_of UBERON:0001708 ! jaw skeleton relationship: part_of UBERON:0001709 ! upper jaw region -relationship: skeleton_of UBERON:0001709 ! upper jaw region -property_value: UBPROP:0000003 "The jaw joint of all jawed vertebrates, except for mammals, involves the quadrate and articular bones, or the posterior ends of the palatoquadrate and mandibular cartilages; A correlate of the conversion of the articular and quadrate bones to the malleus and incus is that all adult mammals have a jaw joint that lies between the dentary of the lower jaw and the squamosal bone of the skull roof.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000429", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.241 and p.101", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "EMAPA/MA placement unclear. See https://github.com/obophenotype/mouse-anatomy-ontology/issues/102" xsd:string {external_ontology="EMAPA"} +relationship: RO:0002576 UBERON:0001709 ! skeleton of upper jaw region [Term] id: UBERON:0003278 @@ -200538,7 +198119,6 @@ synonym: "mandibular series" RELATED [ZFA:0001273] xref: AAO:0000274 xref: EHDAA2:0004606 xref: EHDAA:8005 -xref: EMAPA:17906 xref: EMAPA:17910 xref: FMA:54398 xref: MA:0001906 @@ -200546,16 +198126,14 @@ xref: TAO:0001273 xref: VHOG:0000428 xref: XAO:0003084 xref: ZFA:0001273 +is_a: UBERON:0010313 ! neural crest-derived structure is_a: UBERON:0010912 ! subdivision of skeleton intersection_of: UBERON:0010912 ! subdivision of skeleton -intersection_of: skeleton_of UBERON:0001710 ! lower jaw region +intersection_of: RO:0002576 UBERON:0001710 ! skeleton of lower jaw region relationship: overlaps UBERON:0008895 {source="VHOG-modified"} ! splanchnocranium relationship: part_of UBERON:0001708 ! jaw skeleton relationship: part_of UBERON:0001710 {source="EHDAA2"} ! lower jaw region -relationship: skeleton_of UBERON:0001710 ! lower jaw region -property_value: UBPROP:0000001 "The ventral portion of the first pharyngeal arch, comprising the lower jaw.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001273", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "The jaw joint of all jawed vertebrates, except for mammals, involves the quadrate and articular bones, or the posterior ends of the palatoquadrate and mandibular cartilages; A correlate of the conversion of the articular and quadrate bones to the malleus and incus is that all adult mammals have a jaw joint that lies between the dentary of the lower jaw and the squamosal bone of the skull roof.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000428", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.241 and p.101", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "Inclusion of the FMA class 'lower jaw' is debatable - this mostly corresponds to the lower jaw skeleton (with 'maxillary part of mouth' corresponding to the upper jaw region); however, the FMA class also includes gingiva. See also: https://github.com/obophenotype/mouse-anatomy-ontology/issues/102" xsd:string {external_ontology="FMA"} +relationship: RO:0002576 UBERON:0001710 ! skeleton of lower jaw region [Term] id: UBERON:0003279 @@ -200594,10 +198172,9 @@ xref: VHOG:0000358 is_a: UBERON:0004854 {source="MA"} ! gastrointestinal system mesentery intersection_of: UBERON:0002095 ! mesentery intersection_of: part_of UBERON:0000945 ! stomach -relationship: contributes_to_morphology_of UBERON:0000945 ! stomach relationship: part_of UBERON:0000945 {source="MA"} ! stomach -property_value: editor_note "TODO - check primitive vs developed" xsd:string -property_value: UBPROP:0000001 "The portion of the primitive mesentery that encloses the stomach; from its dorsal sheet, the greater omentum develops, and from its ventral sheet, the lesser omentum. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000358", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/mesogastrium"} +relationship: RO:0002433 UBERON:0000945 ! contributes to morphology of stomach +property_value: IAO:0000116 "TODO - check primitive vs developed" xsd:string [Term] id: UBERON:0003282 @@ -200636,7 +198213,6 @@ is_a: UBERON:0001975 ! serosa of esophagus is_a: UBERON:0002095 ! mesentery intersection_of: UBERON:0002095 ! mesentery intersection_of: part_of UBERON:0001043 ! esophagus -property_value: UBPROP:0000003 "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000415", ontology="VHOG", source="ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003284 @@ -200654,7 +198230,6 @@ is_a: UBERON:0002095 ! mesentery intersection_of: UBERON:0002095 ! mesentery intersection_of: part_of UBERON:0001045 ! midgut relationship: part_of UBERON:0001045 ! midgut -property_value: UBPROP:0000003 "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000413", ontology="VHOG", source="ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003288 @@ -200675,9 +198250,7 @@ is_a: UBERON:0003547 ! brain meninx intersection_of: UBERON:0002360 ! meninx intersection_of: part_of UBERON:0001891 ! midbrain relationship: part_of UBERON:0001891 ! midbrain -property_value: editor_note "consider changing genus to subdivision of meninx" xsd:string -property_value: UBPROP:0000001 "Meninges that are part of the midbrain. [Bgee_curator][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000012", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000012", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639", source="http://bgee.unil.ch/"} +property_value: IAO:0000116 "consider changing genus to subdivision of meninx" xsd:string [Term] id: UBERON:0003289 @@ -200696,9 +198269,7 @@ is_a: UBERON:0003548 ! forebrain meninges intersection_of: UBERON:0002360 ! meninx intersection_of: part_of UBERON:0001893 ! telencephalon relationship: part_of UBERON:0001893 ! telencephalon -property_value: editor_note "consider changing genus to subdivision of meninx" xsd:string -property_value: UBPROP:0000001 "Meninges that are part of the telencephalon. [Bgee_curator][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000010", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000010", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639", source="http://bgee.unil.ch/"} +property_value: IAO:0000116 "consider changing genus to subdivision of meninx" xsd:string [Term] id: UBERON:0003290 @@ -200729,9 +198300,7 @@ is_a: UBERON:0003548 ! forebrain meninges intersection_of: UBERON:0002360 ! meninx intersection_of: part_of UBERON:0001894 ! diencephalon relationship: part_of UBERON:0001894 ! diencephalon -property_value: editor_note "consider changing genus to subdivision of meninx" xsd:string -property_value: UBPROP:0000001 "Meninges that are part of the diencephalon. [Bgee_curator][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000009", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000009", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639", source="http://bgee.unil.ch/"} +property_value: IAO:0000116 "consider changing genus to subdivision of meninx" xsd:string [Term] id: UBERON:0003291 @@ -200750,11 +198319,9 @@ xref: VHOG:0000011 is_a: UBERON:0003547 ! brain meninx intersection_of: UBERON:0002360 ! meninx intersection_of: part_of UBERON:0002028 ! hindbrain -relationship: immediate_transformation_of UBERON:0010091 {evidence="definitional"} ! future hindbrain meninx relationship: part_of UBERON:0002028 ! hindbrain -property_value: editor_note "consider changing genus to subdivision of meninx" xsd:string -property_value: UBPROP:0000001 "Meninges that are part of the hindbrain. [Bgee_curator][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000011", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000011", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639", source="http://bgee.unil.ch/"} +relationship: RO:0002495 UBERON:0010091 ! immediate transformation of future hindbrain meninx +property_value: IAO:0000116 "consider changing genus to subdivision of meninx" xsd:string [Term] id: UBERON:0003292 @@ -200782,8 +198349,6 @@ is_a: UBERON:0005174 ! dorsal region element intersection_of: UBERON:0002360 ! meninx intersection_of: part_of UBERON:0002240 ! spinal cord relationship: part_of UBERON:0002240 ! spinal cord -property_value: UBPROP:0000001 "Meninges that are part of the spinal cord. [Bgee_curator][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000443", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000443", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003294 @@ -200826,10 +198391,10 @@ def: "Any gland that is part of the diencephalon. Examples: pineal gland, neuroh synonym: "diencephalon gland" EXACT [OBOL:automatic] synonym: "interbrain gland" EXACT [OBOL:automatic] xref: EHDAA2:0000395 -xref: EHDAA:4475 xref: EMAPA:16897 xref: VHOG:0000653 is_a: UBERON:0002530 ! gland +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0001894 ! diencephalon relationship: part_of UBERON:0001894 ! diencephalon @@ -200843,7 +198408,6 @@ synonym: "integumental gland" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "integumental system gland" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "integumentary gland" EXACT [http://orcid.org/0000-0002-6601-2165] xref: EHDAA2:0000837 -xref: EHDAA:6522 xref: EMAPA:17758 xref: MA:0000144 xref: VHOG:0000654 @@ -200862,7 +198426,6 @@ synonym: "mesenchyme blood island" RELATED [OBOL:automatic] synonym: "mesoderm blood islands" EXACT OMO:0003004 [EHDAA2:0003241] xref: EHDAA2:0003241 xref: EHDAA:170 -xref: EMAPA:16115 is_a: UBERON:0003061 ! blood island is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007503 {source="EHDAA2"} ! epithelial vesicle @@ -200871,7 +198434,6 @@ intersection_of: UBERON:0003061 ! blood island intersection_of: part_of UBERON:0000926 ! mesoderm relationship: part_of UBERON:0000926 ! mesoderm relationship: part_of UBERON:0007798 {source="EHDAA2"} ! vascular system -property_value: UBPROP:0000012 "in EHDAA2, gives rise to blood and dorsal aorta" xsd:string {external_ontology="EHDAA2"} [Term] id: UBERON:0003312 @@ -200898,12 +198460,13 @@ xref: EHDAA2:0000485 xref: EHDAA:2910 xref: EMAPA:16673 xref: VHOG:0001084 +is_a: UBERON:0007213 ! mesenchyme derived from head neural crest is_a: UBERON:0009891 ! facial mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0000019 ! camera-type eye -relationship: develops_from UBERON:0009920 {source="EHDAA2"} ! optic neural crest relationship: part_of UBERON:0000019 ! camera-type eye -property_value: editor_note "TODO - change mesenchyme relationships to precursor_of" xsd:string +relationship: RO:0002202 UBERON:0009920 {source="EHDAA2"} ! develops from optic neural crest +property_value: IAO:0000116 "TODO - change mesenchyme relationships to precursor_of" xsd:string [Term] id: UBERON:0003315 @@ -200927,7 +198490,7 @@ is_a: UBERON:0003855 ! gonad mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0000992 ! ovary relationship: part_of UBERON:0000992 ! ovary -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003316 @@ -200977,7 +198540,6 @@ synonym: "mesenchyme of wrist" EXACT [OBOL:automatic] synonym: "wrist mesenchyme" EXACT [OBOL:automatic] xref: EHDAA2:0000220 xref: EHDAA:5200 -xref: EMAPA:19122 is_a: UBERON:0003859 ! forelimb mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0004452 ! carpal region @@ -201051,8 +198613,8 @@ is_a: UBERON:0009891 ! facial mesenchyme is_a: UBERON:0034995 ! jaw mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0001709 ! upper jaw region -relationship: develops_from UBERON:0009526 {source="EHDAA2"} ! maxillary process mesenchyme relationship: part_of UBERON:0001709 ! upper jaw region +relationship: RO:0002202 UBERON:0009526 {source="EHDAA2"} ! develops from maxillary process mesenchyme [Term] id: UBERON:0003324 @@ -201069,8 +198631,8 @@ xref: VHOG:0001069 is_a: UBERON:0034995 ! jaw mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0001710 ! lower jaw region -relationship: develops_from UBERON:0006905 {source="EHDAA2"} ! mandibular process mesenchyme relationship: part_of UBERON:0001710 ! lower jaw region +relationship: RO:0002202 UBERON:0006905 {source="EHDAA2"} ! develops from mandibular process mesenchyme [Term] id: UBERON:0003325 @@ -201098,7 +198660,6 @@ is_a: UBERON:0005253 ! head mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0001757 ! pinna relationship: part_of UBERON:0001757 ! pinna -property_value: UBPROP:0000012 "EMAPA divides this spatially into condensation + rest, and temporally into mesenchyme and cartilage condensation" xsd:string {external_ontology="EMAPA"} [Term] id: UBERON:0003326 @@ -201118,6 +198679,7 @@ xref: EHDAA:6528 xref: EMAPA:17761 xref: VHOG:0001087 is_a: UBERON:0003104 ! mesenchyme +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0001911 ! mammary gland relationship: part_of UBERON:0001911 ! mammary gland @@ -201153,9 +198715,8 @@ xref: VHOG_RETIRED:0001055 is_a: UBERON:0010377 ! mesenchyme from somatopleure intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0006871 ! embryonic footplate -relationship: develops_from UBERON:0003412 {source="EHDAA2"} ! pelvic appendage bud mesenchyme relationship: part_of UBERON:0006871 ! embryonic footplate -property_value: UBPROP:0000012 "We group two EMAPA classes here but these may need to be separated" xsd:string {external_ontology="EMAPA"} +relationship: RO:0002202 UBERON:0003412 {source="EHDAA2"} ! develops from pelvic appendage bud mesenchyme [Term] id: UBERON:0003329 @@ -201176,10 +198737,11 @@ xref: EMAPA:27535 xref: FMA:85399 xref: SCTID:7892006 is_a: UBERON:0001208 ! submucosa of large intestine +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000009 ! submucosa intersection_of: part_of UBERON:0000159 ! anal canal relationship: part_of UBERON:0000159 ! anal canal -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003330 @@ -201216,7 +198778,7 @@ is_a: UBERON:0001208 ! submucosa of large intestine intersection_of: UBERON:0000009 ! submucosa intersection_of: part_of UBERON:0001155 ! colon relationship: part_of UBERON:0001155 ! colon -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003332 @@ -201237,7 +198799,7 @@ is_a: UBERON:0001205 ! submucosa of small intestine intersection_of: UBERON:0000009 ! submucosa intersection_of: part_of UBERON:0002114 ! duodenum relationship: part_of UBERON:0002114 ! duodenum -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003333 @@ -201254,7 +198816,7 @@ is_a: UBERON:0001205 ! submucosa of small intestine intersection_of: UBERON:0000009 ! submucosa intersection_of: part_of UBERON:0002115 ! jejunum relationship: part_of UBERON:0002115 ! jejunum -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003334 @@ -201296,7 +198858,7 @@ is_a: UBERON:0001209 ! serosa of large intestine intersection_of: UBERON:0000042 ! serous membrane intersection_of: part_of UBERON:0001155 ! colon relationship: part_of UBERON:0001155 ! colon -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003336 @@ -201318,8 +198880,7 @@ is_a: UBERON:0001206 ! serosa of small intestine intersection_of: UBERON:0000042 ! serous membrane intersection_of: part_of UBERON:0002114 ! duodenum relationship: part_of UBERON:0002114 ! duodenum -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000010 "1st part serosa, 2nd - 4th adventitia" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003337 @@ -201338,7 +198899,7 @@ is_a: UBERON:0001206 ! serosa of small intestine intersection_of: UBERON:0000042 ! serous membrane intersection_of: part_of UBERON:0002115 ! jejunum relationship: part_of UBERON:0002115 ! jejunum -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003338 @@ -201355,7 +198916,6 @@ is_a: UBERON:0000045 ! ganglion intersection_of: UBERON:0000045 ! ganglion intersection_of: part_of UBERON:0000010 ! peripheral nervous system relationship: part_of UBERON:0000010 ! peripheral nervous system -property_value: UBPROP:0000012 "we follow MA in including separate classes for ganglion and peripheral nervous system, even though for vertebrates gangia are always in the PNS" xsd:string {external_ontology="MA"} [Term] id: UBERON:0003339 @@ -201369,10 +198929,10 @@ xref: EHDAA2:0000227 xref: EMAPA:16658 xref: FMA:83843 is_a: UBERON:0000045 ! ganglion +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000045 ! ganglion intersection_of: part_of UBERON:0001017 ! central nervous system relationship: part_of UBERON:0001017 ! central nervous system -property_value: UBPROP:0000012 "this has no subclasses in FMA. In EHDAA2 and EMAPA it has only the cranial ganglia" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0003342 @@ -201419,10 +198979,11 @@ xref: NCIT:C60784 xref: SCTID:362170004 xref: UMLS:C0227414 {source="ncithesaurus:Anal_Mucosa"} is_a: UBERON:0001207 ! mucosa of large intestine +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0000159 ! anal canal relationship: part_of UBERON:0000159 ! anal canal -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003343 @@ -201460,7 +199021,6 @@ synonym: "subdivision of mouth mucosa" EXACT [OBOL:automatic] synonym: "subdivision of mouth mucosa of organ" EXACT [OBOL:automatic] synonym: "subdivision of mouth mucous membrane" EXACT [OBOL:automatic] synonym: "subdivision of mouth organ mucosa" EXACT [OBOL:automatic] -xref: EMAPA:26937 xref: SCTID:362083000 is_a: UBERON:0003729 ! mouth mucosa intersection_of: UBERON:0000344 ! mucosa @@ -201528,9 +199088,8 @@ is_a: UBERON:0004807 ! respiratory system epithelium is_a: UBERON:0005911 ! endo-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001042 ! chordate pharynx -relationship: develops_from UBERON:0007690 {source="ZFA"} ! early pharyngeal endoderm relationship: part_of UBERON:0001042 {source="ZFA"} ! chordate pharynx -property_value: UBPROP:0000001 "Epithelium lining the pharynx consisting largely of simple columnar epithelium with a short segment (1mm) of stratified squamous epithelium on the ventral side. Chen et al, 2007.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001174", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002202 UBERON:0007690 {source="ZFA"} ! develops from early pharyngeal endoderm [Term] id: UBERON:0003352 @@ -201609,8 +199168,8 @@ is_a: UBERON:0003929 ! digestive tract epithelium is_a: UBERON:0019304 ! sensory organ epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001723 ! tongue -relationship: contributes_to_morphology_of UBERON:0001723 ! tongue relationship: part_of UBERON:0001723 ! tongue +relationship: RO:0002433 UBERON:0001723 ! contributes to morphology of tongue [Term] id: UBERON:0003364 @@ -201661,13 +199220,13 @@ xref: EMAPA:18444 xref: FMA:301283 xref: MA:0001328 is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium -is_a: UBERON:0010371 ! ecto-epithelium +is_a: UBERON:0005911 ! endo-epithelium is_a: UBERON:0019306 ! nose epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002255 ! vomeronasal organ -relationship: develops_from UBERON:0001997 {source="EHDAA2"} ! olfactory epithelium relationship: part_of UBERON:0002255 ! vomeronasal organ -property_value: editor_note "TODO - add cell types" xsd:string +relationship: RO:0002202 UBERON:0001997 {source="EHDAA2"} ! develops from olfactory epithelium +property_value: IAO:0000116 "TODO - add cell types" xsd:string [Term] id: UBERON:0003371 @@ -201686,12 +199245,13 @@ xref: EMAPA:16780 xref: VHOG:0001048 is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0000490 ! unilaminar epithelium intersection_of: bounding_layer_of UBERON:0005420 ! pelvic appendage bud relationship: bounding_layer_of UBERON:0005420 ! pelvic appendage bud -relationship: develops_from UBERON:0000076 {source="EHDAA2"} ! external ectoderm relationship: part_of UBERON:0000076 {source="EHDAA2"} ! external ectoderm relationship: part_of UBERON:0005420 ! pelvic appendage bud +relationship: RO:0002202 UBERON:0000076 {source="EHDAA2"} ! develops from external ectoderm [Term] id: UBERON:0003372 @@ -201711,12 +199271,13 @@ xref: EMAPA:16407 xref: VHOG:0001047 is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0000490 ! unilaminar epithelium intersection_of: bounding_layer_of UBERON:0005419 ! pectoral appendage bud relationship: bounding_layer_of UBERON:0005419 ! pectoral appendage bud -relationship: develops_from UBERON:0000076 {source="EHDAA2"} ! external ectoderm relationship: part_of UBERON:0000076 {source="EHDAA2"} ! external ectoderm relationship: part_of UBERON:0005419 ! pectoral appendage bud +relationship: RO:0002202 UBERON:0000076 {source="EHDAA2"} ! develops from external ectoderm [Term] id: UBERON:0003373 @@ -201741,10 +199302,10 @@ xref: BTO:0005145 xref: EMAPA:16113 is_a: UBERON:0000478 ! extraembryonic structure intersection_of: UBERON:0000478 ! extraembryonic structure -intersection_of: develops_from UBERON:0000924 ! ectoderm intersection_of: part_of UBERON:0003124 ! chorion membrane -relationship: develops_from UBERON:0000924 {source="ISBN:0073040584"} ! ectoderm +intersection_of: RO:0002202 UBERON:0000924 ! develops from ectoderm relationship: part_of UBERON:0003124 ! chorion membrane +relationship: RO:0002202 UBERON:0000924 {source="ISBN:0073040584"} ! develops from ectoderm [Term] id: UBERON:0003379 @@ -201772,7 +199333,7 @@ is_a: UBERON:0004490 ! cardiac muscle tissue of atrium intersection_of: UBERON:0001133 ! cardiac muscle tissue intersection_of: part_of UBERON:0002078 ! right cardiac atrium relationship: part_of UBERON:0002078 ! right cardiac atrium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003380 @@ -201854,7 +199415,7 @@ is_a: UBERON:0004492 ! cardiac muscle tissue of cardiac septum is_a: UBERON:0004667 ! interventricular septum muscular part intersection_of: UBERON:0001133 ! cardiac muscle tissue intersection_of: part_of UBERON:0002094 ! interventricular septum -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003384 @@ -201880,11 +199441,12 @@ synonym: "ocular smooth muscle" EXACT [MA:0001268] xref: EMAPA:18807 xref: MA:0001268 is_a: UBERON:0001135 ! smooth muscle tissue +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0000019 ! camera-type eye -relationship: contributes_to_morphology_of UBERON:0001015 ! musculature relationship: part_of UBERON:0000019 ! camera-type eye -property_value: editor_note "Not clear if we need this and intra-ocular muscle. See issue #331. MA includes ciliary and iris smooth muscle" xsd:string +relationship: RO:0002433 UBERON:0001015 ! contributes to morphology of musculature +property_value: IAO:0000116 "Not clear if we need this and intra-ocular muscle. See issue #331. MA includes ciliary and iris smooth muscle" xsd:string [Term] id: UBERON:0003387 @@ -201905,9 +199467,9 @@ xref: UMLS:C1710458 {source="ncithesaurus:Trachea_Smooth_Muscle_Tissue"} is_a: UBERON:0004233 ! lower respiratory tract smooth muscle intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0003126 ! trachea -relationship: contributes_to_morphology_of UBERON:0003126 ! trachea relationship: part_of UBERON:0003126 ! trachea -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002433 UBERON:0003126 ! contributes to morphology of trachea +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003388 @@ -201963,8 +199525,8 @@ xref: EMAPA:16775 xref: FMA:18148 is_a: UBERON:0001136 ! mesothelium intersection_of: UBERON:0001136 ! mesothelium -intersection_of: located_in UBERON:0002402 ! pleural cavity -relationship: located_in UBERON:0002402 ! pleural cavity +intersection_of: RO:0001025 UBERON:0002402 ! located in pleural cavity +relationship: RO:0001025 UBERON:0002402 ! located in pleural cavity [Term] id: UBERON:0003393 @@ -202094,8 +199656,8 @@ is_a: UBERON:0002183 ! lobar bronchus intersection_of: UBERON:0002183 ! lobar bronchus intersection_of: part_of UBERON:0002167 ! right lung relationship: part_of UBERON:0006518 {is_inferred="true", source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! right lung lobe -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb" xsd:anyURI [Term] id: UBERON:0003405 @@ -202114,8 +199676,8 @@ is_a: UBERON:0002183 ! lobar bronchus intersection_of: UBERON:0002183 ! lobar bronchus intersection_of: part_of UBERON:0002168 ! left lung relationship: part_of UBERON:0008951 {is_inferred="true", source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! left lung lobe -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-lung.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-lung.glb" xsd:anyURI [Term] id: UBERON:0003406 @@ -202180,9 +199742,8 @@ xref: ZFA:0001386 is_a: UBERON:0010329 ! paired limb/fin bud mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0005420 ! pelvic appendage bud -relationship: develops_from UBERON:0005730 ! pelvic appendage field relationship: part_of UBERON:0005420 ! pelvic appendage bud -property_value: UBPROP:0000001 "Mesoderm part of pelvic fin bud.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001386", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002202 UBERON:0005730 ! develops from pelvic appendage field [Term] id: UBERON:0003413 @@ -202204,9 +199765,8 @@ xref: ZFA:0000789 is_a: UBERON:0010329 ! paired limb/fin bud mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0005419 ! pectoral appendage bud -relationship: develops_from UBERON:0005729 ! pectoral appendage field relationship: part_of UBERON:0005419 ! pectoral appendage bud -property_value: UBPROP:0000001 "Mesoderm that is part of the pectoral fin bud.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000789", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002202 UBERON:0005729 ! develops from pectoral appendage field [Term] id: UBERON:0003416 @@ -202220,7 +199780,7 @@ is_a: UBERON:0003104 ! mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0001723 ! tongue relationship: part_of UBERON:0001723 ! tongue -property_value: editor_note "TODO - develops_from" xsd:string +property_value: IAO:0000116 "TODO - develops_from" xsd:string [Term] id: UBERON:0003421 @@ -202237,8 +199797,8 @@ is_a: UBERON:0007213 ! mesenchyme derived from head neural crest is_a: UBERON:0009891 ! facial mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0002255 ! vomeronasal organ -relationship: develops_from UBERON:0009204 {source="EHDAA2"} ! medial nasal process mesenchyme relationship: part_of UBERON:0002255 {source="EHDAA2"} ! vomeronasal organ +relationship: RO:0002202 UBERON:0009204 {source="EHDAA2"} ! develops from medial nasal process mesenchyme [Term] id: UBERON:0003422 @@ -202253,13 +199813,14 @@ xref: EMAPA:35925 xref: SCTID:368069009 xref: Wikipedia:Wharton's_jelly is_a: UBERON:0003104 ! mesenchyme +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005292 ! extraembryonic tissue intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0002331 ! umbilical cord relationship: has_part CHEBI:37395 {source="Wikipedia"} relationship: part_of UBERON:0002331 ! umbilical cord -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: editor_note "TODO - check" xsd:string +property_value: IAO:0000116 "TODO - check" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003425 @@ -202277,9 +199838,8 @@ xref: NCIT:C77646 xref: UMLS:C2699031 {source="ncithesaurus:Renal_Lymph_Node"} is_a: UBERON:0000029 ! lymph node intersection_of: UBERON:0000029 ! lymph node -intersection_of: located_in UBERON:0002113 ! kidney -relationship: located_in UBERON:0002113 ! kidney -property_value: UBPROP:0000001 "Dorsal to the ipsilateral kidney nearby the renal blood vessels, caudal to the adrenal gland" xsd:string {source="PMID:16624319", taxon="NCBITaxon:10090"} +intersection_of: RO:0001025 UBERON:0002113 ! located in kidney +relationship: RO:0001025 UBERON:0002113 ! located in kidney [Term] id: UBERON:0003426 @@ -202440,8 +200000,8 @@ xref: EMAPA:37535 {source="MA:th"} xref: MA:0001255 is_a: UBERON:0001021 ! nerve intersection_of: UBERON:0001021 ! nerve -intersection_of: innervates UBERON:0001711 ! eyelid -relationship: innervates UBERON:0001711 ! eyelid +intersection_of: RO:0002134 UBERON:0001711 ! innervates eyelid +relationship: RO:0002134 UBERON:0001711 ! innervates eyelid [Term] id: UBERON:0003438 @@ -202454,9 +200014,9 @@ xref: EMAPA:35449 xref: MA:0001291 is_a: UBERON:0001021 ! nerve intersection_of: UBERON:0001021 ! nerve -intersection_of: innervates UBERON:0001769 ! iris -relationship: innervates UBERON:0001769 ! iris -property_value: editor_note "added for consistency with mouse ontologies. The term 'ciliary nerve' is usually used to denote either of the two nerves (with different origins) that innervate the iris, as well as ciliary muscles and cornea" xsd:string +intersection_of: RO:0002134 UBERON:0001769 ! innervates iris +relationship: RO:0002134 UBERON:0001769 ! innervates iris +property_value: IAO:0000116 "added for consistency with mouse ontologies. The term 'ciliary nerve' is usually used to denote either of the two nerves (with different origins) that innervate the iris, as well as ciliary muscles and cornea" xsd:string [Term] id: UBERON:0003439 @@ -202543,9 +200103,9 @@ xref: EMAPA:37267 {source="MA:th"} xref: MA:0000556 is_a: UBERON:0001021 ! nerve intersection_of: UBERON:0001021 ! nerve -intersection_of: located_in UBERON:0002224 ! thoracic cavity -relationship: located_in UBERON:0002224 ! thoracic cavity -property_value: editor_note "consider merging with thoracic nerve. In MA the only subclass is the phrenic nerve, which arises from a cervical nerve" xsd:string +intersection_of: RO:0001025 UBERON:0002224 ! located in thoracic cavity +relationship: RO:0001025 UBERON:0002224 ! located in thoracic cavity +property_value: IAO:0000116 "consider merging with thoracic nerve. In MA the only subclass is the phrenic nerve, which arises from a cervical nerve" xsd:string [Term] id: UBERON:0003444 @@ -202588,8 +200148,7 @@ is_a: UBERON:0003445 ! pes nerve intersection_of: UBERON:0001021 ! nerve intersection_of: part_of UBERON:0004454 ! tarsal region relationship: part_of UBERON:0004454 ! tarsal region -relationship: seeAlso FMA:86901 -property_value: UBPROP:0000012 "FMA placement dubious" xsd:string {external_ontology="FMA"} +property_value: seeAlso FMA:86901 [Term] id: UBERON:0003447 @@ -202722,7 +200281,7 @@ is_a: UBERON:0001211 ! Peyer's patch intersection_of: UBERON:0001211 ! Peyer's patch intersection_of: part_of UBERON:0000059 ! large intestine relationship: part_of UBERON:0000059 ! large intestine -property_value: editor_note "requires expert attention" xsd:string +property_value: IAO:0000116 "requires expert attention" xsd:string [Term] id: UBERON:0003454 @@ -202744,8 +200303,7 @@ is_a: UBERON:0001211 ! Peyer's patch intersection_of: UBERON:0001211 ! Peyer's patch intersection_of: part_of UBERON:0002108 ! small intestine relationship: part_of UBERON:0001204 {source="ncithesaurus"} ! mucosa of small intestine -property_value: editor_note "add subtypes for jejunum, ileum" xsd:string -property_value: UBPROP:0000202 FMA:76466 +property_value: IAO:0000116 "add subtypes for jejunum, ileum" xsd:string [Term] id: UBERON:0003455 @@ -202861,12 +200419,11 @@ synonym: "bone of upper extremity" RELATED [GAID:178] synonym: "bone organ of arm" EXACT [OBOL:automatic] xref: EMAPA:37303 {source="MA:th"} xref: MA:0000592 -xref: MESH:D050280 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} is_a: UBERON:0008962 ! forelimb bone intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0001460 ! arm relationship: part_of UBERON:0001460 ! arm -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003461 @@ -202877,12 +200434,11 @@ subset: pheno_slim synonym: "bone of shoulder" EXACT [OBOL:automatic] synonym: "shoulder-articulating bone" EXACT [] xref: MA:0000631 -is_a: UBERON:0010741 {notes="UBERONREF:0000003", source="MA"} ! bone of pectoral complex +is_a: UBERON:0010741 ! bone of pectoral complex intersection_of: UBERON:0001474 ! bone element intersection_of: overlaps UBERON:0016884 ! shoulder joint relationship: overlaps UBERON:0016884 ! shoulder joint relationship: part_of UBERON:0012475 ! skeleton of pectoral complex -property_value: UBPROP:0000012 "this is a forelimb bone in MA, but this would lead to part-disjointness violations." xsd:string {external_ontology="MA"} [Term] id: UBERON:0003462 @@ -202899,15 +200455,15 @@ xref: EMAPA:19019 xref: EMAPA:35924 xref: MA:0001482 xref: MA:0003159 -xref: MESH:D005147 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C63706 xref: SCTID:181799005 xref: UMLS:C0015455 {source="ncithesaurus:Facial_Bone"} is_a: UBERON:0003457 ! head bone +is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0011156 ! facial skeleton relationship: part_of UBERON:0011156 {source="MA"} ! facial skeleton -property_value: editor_note "test whether 'facial bone' is an exact synonym" xsd:string +property_value: IAO:0000116 "test whether 'facial bone' is an exact synonym" xsd:string [Term] id: UBERON:0003463 @@ -202955,8 +200511,7 @@ is_a: UBERON:0010742 ! bone of pelvic complex is_a: UBERON:0015022 ! hindlimb endochondral element intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0002103 ! hindlimb -relationship: develops_from UBERON:0010885 ! hindlimb cartilage element -property_value: UBPROP:0000012 "the MA class is actually bone of pelvic complex; in contrast the NCIT class excludes ilium etc" xsd:string {external_ontology="MA"} +relationship: RO:0002202 UBERON:0010885 ! develops from hindlimb cartilage element [Term] id: UBERON:0003466 @@ -202993,11 +200548,11 @@ xref: SCTID:65376008 xref: Wikipedia:Ureteral_branches_of_renal_artery is_a: UBERON:0004573 ! systemic artery intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0000056 ! ureter -relationship: connecting_branch_of UBERON:0001184 {source="FMA"} ! renal artery +intersection_of: RO:0002178 UBERON:0000056 ! supplies ureter relationship: part_of UBERON:0001184 {source="FMA"} ! renal artery -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: supplies UBERON:0000056 ! ureter +relationship: RO:0002178 UBERON:0000056 ! supplies ureter +relationship: RO:0002252 UBERON:0001184 {source="FMA"} ! connecting branch of renal artery +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003469 @@ -203029,10 +200584,10 @@ xref: Wikipedia:Superior_labial_artery is_a: UBERON:0003496 ! head blood vessel is_a: UBERON:0009657 ! artery of lip intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0001834 ! upper lip -relationship: connecting_branch_of UBERON:0001612 {source="FMA"} ! facial artery -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: supplies UBERON:0001834 ! upper lip +intersection_of: RO:0002178 UBERON:0001834 ! supplies upper lip +relationship: RO:0002178 UBERON:0001834 ! supplies upper lip +relationship: RO:0002252 UBERON:0001612 {source="FMA"} ! connecting branch of facial artery +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003471 @@ -203053,10 +200608,10 @@ xref: Wikipedia:Inferior_labial_artery is_a: UBERON:0003496 ! head blood vessel is_a: UBERON:0009657 ! artery of lip intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0001835 ! lower lip -relationship: connecting_branch_of UBERON:0001612 {source="FMA"} ! facial artery -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: supplies UBERON:0001835 ! lower lip +intersection_of: RO:0002178 UBERON:0001835 ! supplies lower lip +relationship: RO:0002178 UBERON:0001835 ! supplies lower lip +relationship: RO:0002252 UBERON:0001612 {source="FMA"} ! connecting branch of facial artery +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003472 @@ -203074,9 +200629,9 @@ xref: Wikipedia:Cerebellar_artery is_a: UBERON:0001637 ! artery is_a: UBERON:0003496 ! head blood vessel intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0002037 ! cerebellum -relationship: supplies UBERON:0002037 ! cerebellum -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e1/CerebellumArteries.jpg" xsd:anyURI +intersection_of: RO:0002178 UBERON:0002037 ! supplies cerebellum +relationship: RO:0002178 UBERON:0002037 ! supplies cerebellum +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e1/CerebellumArteries.jpg" xsd:anyURI [Term] id: UBERON:0003473 @@ -203090,8 +200645,7 @@ xref: MESH:D013895 is_a: UBERON:0001637 ! artery is_a: UBERON:0003519 ! thoracic cavity blood vessel intersection_of: UBERON:0001637 ! artery -intersection_of: located_in UBERON:0002224 ! thoracic cavity -property_value: UBPROP:0000012 "in MA, aorta is classified here - but this is problematic because the abdominal aorta is not in the thoracic cavity" xsd:string {external_ontology="MA"} +intersection_of: RO:0001025 UBERON:0002224 ! located in thoracic cavity [Term] id: UBERON:0003474 @@ -203105,8 +200659,8 @@ xref: MESH:D008576 xref: Wikipedia:Meningeal_arteries is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0002360 ! meninx -relationship: supplies UBERON:0002360 ! meninx +intersection_of: RO:0002178 UBERON:0002360 ! supplies meninx +relationship: RO:0002178 UBERON:0002360 ! supplies meninx [Term] id: UBERON:0003475 @@ -203137,8 +200691,8 @@ xref: MA:0001809 xref: MA:0001810 is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein -intersection_of: drains UBERON:0001004 ! respiratory system -relationship: drains UBERON:0001004 ! respiratory system +intersection_of: RO:0002179 UBERON:0001004 ! drains respiratory system +relationship: RO:0002179 UBERON:0001004 ! drains respiratory system [Term] id: UBERON:0003477 @@ -203156,9 +200710,9 @@ xref: SCTID:422755007 xref: Wikipedia:Superior_labial_vein is_a: UBERON:0013136 ! vein of lip intersection_of: UBERON:0001638 ! vein -intersection_of: drains UBERON:0001834 ! upper lip -relationship: drains UBERON:0001834 ! upper lip -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002179 UBERON:0001834 ! drains upper lip +relationship: RO:0002179 UBERON:0001834 ! drains upper lip +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003478 @@ -203177,10 +200731,10 @@ xref: SCTID:422955002 xref: Wikipedia:Inferior_labial_vein is_a: UBERON:0013136 ! vein of lip intersection_of: UBERON:0001638 ! vein -intersection_of: drains UBERON:0001835 ! lower lip -relationship: drains UBERON:0001835 ! lower lip -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray557.png" xsd:anyURI +intersection_of: RO:0002179 UBERON:0001835 ! drains lower lip +relationship: RO:0002179 UBERON:0001835 ! drains lower lip +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8c/Gray557.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003479 @@ -203201,7 +200755,7 @@ xref: MA:0001903 is_a: UBERON:0001638 ! vein is_a: UBERON:0003519 ! thoracic cavity blood vessel intersection_of: UBERON:0001638 ! vein -intersection_of: located_in UBERON:0002224 ! thoracic cavity +intersection_of: RO:0001025 UBERON:0002224 ! located in thoracic cavity [Term] id: UBERON:0003480 @@ -203236,7 +200790,7 @@ is_a: UBERON:0001638 ! vein is_a: UBERON:0003524 ! tail blood vessel intersection_of: UBERON:0001638 ! vein intersection_of: part_of UBERON:0007812 ! post-anal tail -property_value: editor_note "see also caudal vein" xsd:string +property_value: IAO:0000116 "see also caudal vein" xsd:string [Term] id: UBERON:0003483 @@ -203251,6 +200805,7 @@ xref: MA:0002673 xref: MESH:D013950 xref: NCIT:C38515 xref: UMLS:C1515429 {source="ncithesaurus:Thymic_Lymphoid_Tissue"} +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0001744 ! lymphoid tissue intersection_of: UBERON:0001744 ! lymphoid tissue intersection_of: part_of UBERON:0002370 ! thymus @@ -203284,6 +200839,7 @@ synonym: "sebaceous gland of vagina" EXACT [OBOL:automatic] xref: EMAPA:37793 {source="MA:th"} xref: MA:0001732 is_a: UBERON:0001821 ! sebaceous gland +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005398 ! female reproductive gland intersection_of: UBERON:0001821 ! sebaceous gland intersection_of: part_of UBERON:0000996 ! vagina @@ -203322,7 +200878,6 @@ is_a: UBERON:0001911 ! mammary gland is_a: UBERON:0005172 ! abdomen element intersection_of: UBERON:0001911 ! mammary gland intersection_of: part_of UBERON:0000916 ! abdomen -property_value: UBPROP:0000008 "Female mice normally have five pairs of nipples and mammary glands, three in the thoracic and two in the abdominal region. (There is an additional abdominal pair in female rats.) http://www.informatics.jax.org/greenbook/chapters/chapter13.shtml" xsd:string [Term] id: UBERON:0003489 @@ -203415,7 +200970,6 @@ is_a: UBERON:0003835 ! abdominal segment blood vessel intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0000916 ! abdomen relationship: part_of UBERON:0000916 ! abdomen -property_value: seeAlso "UBERON:0012254" xsd:string {notes="abdominal aorta artery"} [Term] id: UBERON:0003498 @@ -203443,6 +200997,7 @@ synonym: "blood vessel of brain" EXACT [OBOL:automatic] xref: EMAPA:35182 xref: MA:0002769 is_a: UBERON:0001981 ! blood vessel +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0000955 ! brain relationship: part_of UBERON:0008998 ! vasculature of brain @@ -203457,11 +201012,12 @@ synonym: "cornea blood vessel" EXACT [OBOL:automatic] xref: EMAPA:36611 xref: MA:0001241 is_a: UBERON:0003496 ! head blood vessel +is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0000964 ! cornea relationship: part_of UBERON:0000964 ! cornea -relationship: present_in_taxon NCBITaxon:9775 {source="PMID:17051153"} -property_value: editor_note "follow up on tracker item" xsd:string +property_value: IAO:0000116 "follow up on tracker item" xsd:string +property_value: RO:0002175 NCBITaxon:9775 {source="PMID:17051153"} [Term] id: UBERON:0003501 @@ -203482,10 +201038,11 @@ xref: MESH:D012171 xref: SCTID:280692003 xref: XAO:0004153 is_a: UBERON:0003496 ! head blood vessel +is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0000966 ! retina -relationship: contributes_to_morphology_of UBERON:0000966 ! retina relationship: part_of UBERON:0004864 ! vasculature of retina +relationship: RO:0002433 UBERON:0000966 ! contributes to morphology of retina [Term] id: UBERON:0003502 @@ -203540,6 +201097,7 @@ def: "A blood vessel that is part of a trachea." [OBOL:automatic] synonym: "blood vessel of trachea" EXACT [OBOL:automatic] xref: EMAPA:35874 xref: MA:0001852 +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0003504 ! respiratory system blood vessel intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0003126 ! trachea @@ -203628,6 +201186,7 @@ synonym: "blood vessel of eyelid" EXACT [OBOL:automatic] xref: EMAPA:37388 {source="MA:th"} xref: MA:0001250 is_a: UBERON:0003496 ! head blood vessel +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0001711 ! eyelid relationship: part_of UBERON:0001711 ! eyelid @@ -203641,8 +201200,8 @@ subset: vertebrate_core synonym: "blood vessel of iris" EXACT [OBOL:automatic] xref: EMAPA:37387 {source="MA:th"} xref: MA:0001290 -xref: ZFA:0005568 is_a: UBERON:0003496 ! head blood vessel +is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0001769 ! iris relationship: part_of UBERON:0004118 ! vasculature of iris @@ -203657,12 +201216,13 @@ synonym: "blood vessel of lung" EXACT [OBOL:automatic] synonym: "pulmonary vascular element" RELATED [EMAPA:32867] xref: EMAPA:32867 xref: MA:0002457 +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0003504 ! respiratory system blood vessel is_a: UBERON:0003834 ! thoracic segment blood vessel intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0002048 ! lung -relationship: contributes_to_morphology_of UBERON:0002048 ! lung relationship: part_of UBERON:0002048 ! lung +relationship: RO:0002433 UBERON:0002048 ! contributes to morphology of lung [Term] id: UBERON:0003513 @@ -203738,7 +201298,6 @@ subset: pheno_slim subset: vertebrate_core synonym: "blood vessel of kidney" EXACT [OBOL:automatic] synonym: "renal blood vessel" EXACT [OBOL:automatic] -xref: EMAPA:28457 xref: MA:0001682 xref: TAO:0005306 xref: ZFA:0005306 @@ -203746,7 +201305,7 @@ is_a: UBERON:0003497 ! abdomen blood vessel intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0002113 ! kidney relationship: part_of UBERON:0006544 ! kidney vasculature -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003519 @@ -203766,8 +201325,8 @@ xref: EMAPA:37240 {source="MA:th"} xref: MA:0000554 is_a: UBERON:0001981 ! blood vessel intersection_of: UBERON:0001981 ! blood vessel -intersection_of: located_in UBERON:0002224 ! thoracic cavity -relationship: located_in UBERON:0002224 ! thoracic cavity +intersection_of: RO:0001025 UBERON:0002224 ! located in thoracic cavity +relationship: RO:0001025 UBERON:0002224 ! located in thoracic cavity [Term] id: UBERON:0003520 @@ -203888,7 +201447,7 @@ is_a: UBERON:0001982 ! capillary is_a: UBERON:0003517 ! kidney blood vessel intersection_of: UBERON:0001982 ! capillary intersection_of: part_of UBERON:0002113 ! kidney -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003528 @@ -203934,7 +201493,7 @@ is_a: UBERON:0004807 ! respiratory system epithelium intersection_of: UBERON:0002042 ! lymphatic vessel endothelium intersection_of: part_of UBERON:0001004 ! respiratory system relationship: part_of UBERON:0003456 ! respiratory system lymphatic vessel -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003530 @@ -203989,7 +201548,7 @@ is_a: UBERON:0001419 ! skin of limb intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0002102 ! forelimb relationship: part_of UBERON:0002102 ! forelimb -property_value: editor_note "TODO - check free limb vs pectoral complex" xsd:string +property_value: IAO:0000116 "TODO - check free limb vs pectoral complex" xsd:string [Term] id: UBERON:0003532 @@ -203997,8 +201556,8 @@ name: hindlimb skin namespace: uberon def: "A zone of skin that is part of a hindlimb [Automatically generated definition]." [OBOL:automatic] synonym: "hind limb skin" EXACT [OBOL:automatic] -synonym: "lower limb skin" EXACT [https://orcid.org/0000-0002-0819-0473] synonym: "lower limb skin" EXACT [FMA:23102] +synonym: "lower limb skin" EXACT [https://orcid.org/0000-0002-0819-0473] synonym: "skin of hind limb" EXACT [OBOL:automatic] synonym: "skin of hindlimb" EXACT [OBOL:automatic] synonym: "skin of lower extremity" EXACT [OBOL:automatic] @@ -204013,7 +201572,7 @@ is_a: UBERON:0001419 ! skin of limb intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0002103 ! hindlimb relationship: part_of UBERON:0002103 ! hindlimb -property_value: editor_note "TODO - check free limb vs pelvic complex" xsd:string +property_value: IAO:0000116 "TODO - check free limb vs pelvic complex" xsd:string [Term] id: UBERON:0003533 @@ -204230,15 +201789,14 @@ synonym: "white matter of brain" EXACT [OBOL:automatic] synonym: "white matter of neuraxis of brain" EXACT [OBOL:automatic] synonym: "white substance of brain" EXACT [OBOL:automatic] xref: EMAPA:35187 -xref: HBA:9218 xref: MA:0000820 xref: NCIT:C49334 xref: UMLS:C1706995 {source="ncithesaurus:Brain_White_Matter"} is_a: UBERON:0002316 ! white matter intersection_of: UBERON:0002316 ! white matter intersection_of: part_of UBERON:0000955 ! brain -relationship: contributes_to_morphology_of UBERON:0000955 ! brain relationship: part_of UBERON:0000955 ! brain +relationship: RO:0002433 UBERON:0000955 ! contributes to morphology of brain [Term] id: UBERON:0003546 @@ -204247,6 +201805,7 @@ namespace: uberon def: "A macula densa that is part of a distal convoluted tubule [Automatically generated definition]." [OBOL:automatic] xref: MA:0001668 is_a: UBERON:0002335 ! macula densa +is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0002335 ! macula densa intersection_of: part_of UBERON:0001292 ! distal convoluted tubule relationship: part_of UBERON:0001292 {source="MA"} ! distal convoluted tubule @@ -204264,7 +201823,6 @@ synonym: "meninges of brain" EXACT [OBOL:automatic] synonym: "meninx of brain" EXACT [OBOL:automatic] xref: CALOHA:TS-2147 xref: EMAPA:32662 -xref: EV:0100312 xref: MA:0000813 xref: SCTID:180949007 xref: VHOG:0000013 @@ -204272,8 +201830,6 @@ is_a: UBERON:0002360 ! meninx intersection_of: UBERON:0002360 ! meninx intersection_of: part_of UBERON:0000955 ! brain relationship: part_of UBERON:0000955 ! brain -property_value: UBPROP:0000001 "Meninges that are part of the brain. [Bgee_curator][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000013", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000013", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003548 @@ -204283,8 +201839,6 @@ def: "A meninx that is part of a forebrain [Automatically generated definition]. synonym: "forebrain meninx" EXACT [OBOL:automatic] synonym: "meninges of forebrain" EXACT [OBOL:automatic] synonym: "meninx of forebrain" EXACT [OBOL:automatic] -xref: EMAPA:17764 -xref: EMAPA:17774 xref: EMAPA:37543 {source="MA:th"} xref: MA:0000883 is_a: UBERON:0003547 ! brain meninx @@ -204302,7 +201856,6 @@ synonym: "brain pia mater of neuraxis" EXACT [OBOL:automatic] synonym: "pia mater of brain" EXACT [OBOL:automatic] synonym: "pia mater of neuraxis of brain" EXACT [OBOL:automatic] xref: EMAPA:32667 -xref: EV:0100315 xref: MA:0000816 xref: NCIT:C49335 xref: UMLS:C1706994 {source="ncithesaurus:Brain_Pia_Mater"} @@ -204311,8 +201864,6 @@ is_a: UBERON:0002361 ! pia mater is_a: UBERON:0003547 ! brain meninx intersection_of: UBERON:0002361 ! pia mater intersection_of: part_of UBERON:0000955 ! brain -property_value: UBPROP:0000001 "The innermost of the three mammalian meninges covering the brain and spinal cord. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000470", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/pia+mater"} -property_value: UBPROP:0000003 "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000470", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003550 @@ -204322,8 +201873,6 @@ def: "A pia mater that is part of a forebrain [Automatically generated definitio synonym: "forebrain pia mater of neuraxis" EXACT [OBOL:automatic] synonym: "pia mater of forebrain" EXACT [OBOL:automatic] synonym: "pia mater of neuraxis of forebrain" EXACT [OBOL:automatic] -xref: EMAPA:17767 -xref: EMAPA:17777 xref: EMAPA:37546 {source="MA:th"} xref: MA:0000886 is_a: UBERON:0003548 ! forebrain meninges @@ -204349,8 +201898,6 @@ is_a: UBERON:0003288 ! meninx of midbrain is_a: UBERON:0003549 ! brain pia mater intersection_of: UBERON:0002361 ! pia mater intersection_of: part_of UBERON:0001891 ! midbrain -property_value: UBPROP:0000001 "Pia mater that is part of the midbrain. [Bgee_curator][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000467", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000467", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003552 @@ -204368,8 +201915,6 @@ is_a: UBERON:0003289 ! meninx of telencephalon is_a: UBERON:0003550 ! forebrain pia mater intersection_of: UBERON:0002361 ! pia mater intersection_of: part_of UBERON:0001893 ! telencephalon -property_value: UBPROP:0000001 "Pia mater that is part of the telencephalon. [Bgee_curator][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000476", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000476", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003553 @@ -204399,8 +201944,6 @@ is_a: UBERON:0003290 ! meninx of diencephalon is_a: UBERON:0003550 ! forebrain pia mater intersection_of: UBERON:0002361 ! pia mater intersection_of: part_of UBERON:0001894 ! diencephalon -property_value: UBPROP:0000001 "Pia mater that is part of the diencephalon. [Bgee_curator][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000475", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000475", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003554 @@ -204419,8 +201962,6 @@ is_a: UBERON:0003291 ! meninx of hindbrain is_a: UBERON:0003549 ! brain pia mater intersection_of: UBERON:0002361 ! pia mater intersection_of: part_of UBERON:0002028 ! hindbrain -property_value: UBPROP:0000001 "Pia mater that is part of the hindbrain. [Bgee_curator][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000466", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000466", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003555 @@ -204441,8 +201982,6 @@ is_a: UBERON:0002361 ! pia mater is_a: UBERON:0003292 ! meninx of spinal cord intersection_of: UBERON:0002361 ! pia mater intersection_of: part_of UBERON:0002240 ! spinal cord -property_value: UBPROP:0000001 "The innermost of the three mammalian meninges covering the brain and spinal cord. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000468", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/pia+mater"} -property_value: UBPROP:0000003 "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000468", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003556 @@ -204454,8 +201993,6 @@ synonym: "arachnoid mater of neuraxis of forebrain" EXACT [OBOL:automatic] synonym: "arachnoid of forebrain" EXACT [OBOL:automatic] synonym: "forebrain arachnoid" EXACT [OBOL:automatic] synonym: "forebrain arachnoid mater of neuraxis" EXACT [OBOL:automatic] -xref: EMAPA:17765 -xref: EMAPA:17775 xref: EMAPA:37544 {source="MA:th"} xref: MA:0000884 is_a: UBERON:0002362 ! arachnoid mater @@ -204481,8 +202018,6 @@ is_a: UBERON:0002362 ! arachnoid mater is_a: UBERON:0003288 ! meninx of midbrain intersection_of: UBERON:0002362 ! arachnoid mater intersection_of: part_of UBERON:0001891 ! midbrain -property_value: UBPROP:0000001 "Arachnoid mater that is part of the midbrain. [Bgee_curator][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000233", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000233", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003558 @@ -204519,8 +202054,6 @@ is_a: UBERON:0003290 ! meninx of diencephalon is_a: UBERON:0003556 ! forebrain arachnoid mater intersection_of: UBERON:0002362 ! arachnoid mater intersection_of: part_of UBERON:0001894 ! diencephalon -property_value: UBPROP:0000001 "Arachnoid mater that is part of the diencephalon. [Bgee_curator][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000231", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000231", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003559 @@ -204540,8 +202073,6 @@ is_a: UBERON:0002362 ! arachnoid mater is_a: UBERON:0003291 ! meninx of hindbrain intersection_of: UBERON:0002362 ! arachnoid mater intersection_of: part_of UBERON:0002028 ! hindbrain -property_value: UBPROP:0000001 "Arachnoid mater that is part of the hindbrain. [Bgee_curator][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000236", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000236", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003560 @@ -204561,8 +202092,6 @@ is_a: UBERON:0002362 ! arachnoid mater is_a: UBERON:0003292 ! meninx of spinal cord intersection_of: UBERON:0002362 ! arachnoid mater intersection_of: part_of UBERON:0002240 ! spinal cord -property_value: UBPROP:0000001 "The middle membrane of the three mammalian meninges covering the brain and spinal cord. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000234", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/arachnoid+mater"} -property_value: UBPROP:0000003 "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000234", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003561 @@ -204572,7 +202101,6 @@ def: "A dura mater that is part of a forebrain." [OBOL:automatic] synonym: "dura mater of forebrain" EXACT [OBOL:automatic] synonym: "dura mater of neuraxis of forebrain" EXACT [OBOL:automatic] synonym: "forebrain dura mater of neuraxis" EXACT [OBOL:automatic] -xref: EMAPA:17766 xref: EMAPA:37545 {source="MA:th"} xref: MA:0000885 is_a: UBERON:0002092 ! brain dura mater @@ -204596,8 +202124,6 @@ is_a: UBERON:0002092 ! brain dura mater is_a: UBERON:0003288 ! meninx of midbrain intersection_of: UBERON:0002363 ! dura mater intersection_of: part_of UBERON:0001891 ! midbrain -property_value: UBPROP:0000001 "Dura mater that is part of the midbrain. [Bgee_curator][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000410", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000410", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003563 @@ -204641,8 +202167,6 @@ is_a: UBERON:0003290 ! meninx of diencephalon is_a: UBERON:0003561 ! forebrain dura mater intersection_of: UBERON:0002363 ! dura mater intersection_of: part_of UBERON:0001894 ! diencephalon -property_value: UBPROP:0000001 "Dura mater that is part of the diencephalon. [Bgee_curator][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000258", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000258", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003565 @@ -204660,8 +202184,6 @@ is_a: UBERON:0002092 ! brain dura mater is_a: UBERON:0003291 ! meninx of hindbrain intersection_of: UBERON:0002363 ! dura mater intersection_of: part_of UBERON:0002028 ! hindbrain -property_value: UBPROP:0000001 "Dura mater that is part of the hindbrain. [Bgee_curator][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000409", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000409", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003566 @@ -204679,13 +202201,12 @@ synonym: "portion of connective tissue of adult head" EXACT [OBOL:automatic] synonym: "portion of connective tissue of head" EXACT [OBOL:automatic] synonym: "textus connectivus of adult head" EXACT [OBOL:automatic] synonym: "textus connectivus of head" EXACT [OBOL:automatic] -xref: EMAPA:16098 xref: MA:0000577 is_a: UBERON:0002384 ! connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0000033 ! head relationship: part_of UBERON:0000033 ! head -relationship: transformation_of UBERON:0005253 ! head mesenchyme +relationship: RO:0002494 UBERON:0005253 ! transformation of head mesenchyme [Term] id: UBERON:0003567 @@ -204781,8 +202302,8 @@ is_a: UBERON:0003580 ! lower respiratory tract connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0003126 ! trachea relationship: part_of UBERON:0003126 ! trachea -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: transformation_of UBERON:0009505 ! mesenchyme of trachea +relationship: RO:0002494 UBERON:0009505 ! transformation of mesenchyme of trachea +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003572 @@ -204845,7 +202366,7 @@ is_a: UBERON:0003573 ! arm connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0001461 ! elbow relationship: part_of UBERON:0001461 ! elbow -relationship: transformation_of UBERON:0003318 ! mesenchyme of elbow +relationship: RO:0002494 UBERON:0003318 ! transformation of mesenchyme of elbow [Term] id: UBERON:0003575 @@ -204861,7 +202382,7 @@ is_a: UBERON:0003598 ! manus connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0004452 ! carpal region relationship: part_of UBERON:0004452 ! carpal region -relationship: transformation_of UBERON:0003319 ! mesenchyme of carpal region +relationship: RO:0002494 UBERON:0003319 ! transformation of mesenchyme of carpal region [Term] id: UBERON:0003576 @@ -204877,7 +202398,7 @@ is_a: UBERON:0002384 ! connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0001464 ! hip relationship: part_of UBERON:0001464 ! hip -relationship: transformation_of UBERON:0003320 ! mesenchyme of hip +relationship: RO:0002494 UBERON:0003320 ! transformation of mesenchyme of hip [Term] id: UBERON:0003577 @@ -204892,7 +202413,7 @@ is_a: UBERON:0003569 ! leg connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0001465 ! knee relationship: part_of UBERON:0001465 ! knee -relationship: transformation_of UBERON:0003321 ! mesenchyme of knee +relationship: RO:0002494 UBERON:0003321 ! transformation of mesenchyme of knee [Term] id: UBERON:0003578 @@ -204914,7 +202435,7 @@ is_a: UBERON:0015791 ! digit connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0001466 ! pedal digit relationship: part_of UBERON:0001466 ! pedal digit -relationship: transformation_of UBERON:0005255 ! pedal digit mesenchyme +relationship: RO:0002494 UBERON:0005255 ! transformation of pedal digit mesenchyme [Term] id: UBERON:0003579 @@ -204932,7 +202453,7 @@ is_a: UBERON:0002384 ! connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0001467 ! shoulder relationship: part_of UBERON:0001467 ! shoulder -relationship: transformation_of UBERON:0003322 ! mesenchyme of shoulder +relationship: RO:0002494 UBERON:0003322 ! transformation of mesenchyme of shoulder [Term] id: UBERON:0003580 @@ -204947,6 +202468,7 @@ synonym: "textus connectivus of lower respiratory tract" EXACT [OBOL:automatic] xref: EMAPA:37548 {source="MA:th"} xref: MA:0002409 is_a: UBERON:0003570 ! respiratory system connective tissue +is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0001558 ! lower respiratory tract relationship: part_of UBERON:0001558 ! lower respiratory tract @@ -204964,10 +202486,11 @@ xref: MA:0001251 xref: NCIT:C49482 xref: UMLS:C1707989 {source="ncithesaurus:Eyelid_Connective_Tissue"} is_a: UBERON:0003566 ! head connective tissue +is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0001711 ! eyelid relationship: part_of UBERON:0001711 ! eyelid -relationship: transformation_of UBERON:0010330 ! eyelid mesenchyme +relationship: RO:0002494 UBERON:0010330 ! transformation of eyelid mesenchyme [Term] id: UBERON:0003582 @@ -204994,6 +202517,7 @@ synonym: "textus connectivus of rhinopharynx" EXACT [OBOL:automatic] xref: EMAPA:37682 {source="MA:th"} xref: MA:0001864 is_a: UBERON:0003570 ! respiratory system connective tissue +is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0001728 ! nasopharynx relationship: part_of UBERON:0001728 ! nasopharynx @@ -205014,6 +202538,7 @@ xref: MA:0001754 xref: NCIT:C49245 xref: UMLS:C1708651 {source="ncithesaurus:Laryngeal_Connective_Tissue"} is_a: UBERON:0003570 ! respiratory system connective tissue +is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0001737 ! larynx relationship: part_of UBERON:0001737 ! larynx @@ -205039,11 +202564,12 @@ xref: FMA:74479 xref: FMA:74483 xref: MA:0002897 is_a: UBERON:0002384 ! connective tissue +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0001911 ! mammary gland -relationship: contributes_to_morphology_of UBERON:0001911 ! mammary gland relationship: part_of UBERON:0001911 ! mammary gland -relationship: transformation_of UBERON:0003326 ! mesenchyme of mammary gland +relationship: RO:0002433 UBERON:0001911 ! contributes to morphology of mammary gland +relationship: RO:0002494 UBERON:0003326 ! transformation of mesenchyme of mammary gland [Term] id: UBERON:0003585 @@ -205062,8 +202588,8 @@ is_a: UBERON:0002384 ! connective tissue is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0002067 ! dermis -relationship: develops_from UBERON:0004016 ! dermatome relationship: part_of UBERON:0002067 ! dermis +relationship: RO:0002202 UBERON:0004016 ! develops from dermatome [Term] id: UBERON:0003586 @@ -205104,7 +202630,7 @@ is_a: UBERON:0002384 ! connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0002101 ! limb relationship: part_of UBERON:0002101 ! limb -relationship: transformation_of UBERON:0009749 ! limb mesenchyme +relationship: RO:0002494 UBERON:0009749 ! transformation of limb mesenchyme [Term] id: UBERON:0003588 @@ -205123,7 +202649,7 @@ is_a: UBERON:0003587 ! limb connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0002102 ! forelimb relationship: part_of UBERON:0002102 ! forelimb -relationship: transformation_of UBERON:0003859 ! forelimb mesenchyme +relationship: RO:0002494 UBERON:0003859 ! transformation of forelimb mesenchyme [Term] id: UBERON:0003589 @@ -205141,7 +202667,7 @@ is_a: UBERON:0003587 ! limb connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0002103 ! hindlimb relationship: part_of UBERON:0002103 ! hindlimb -relationship: transformation_of UBERON:0003860 ! hindlimb mesenchyme +relationship: RO:0002494 UBERON:0003860 ! transformation of hindlimb mesenchyme [Term] id: UBERON:0003591 @@ -205158,8 +202684,8 @@ is_a: UBERON:0003592 ! bronchus connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0002183 ! lobar bronchus relationship: part_of UBERON:0002183 ! lobar bronchus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: transformation_of UBERON:0004884 ! lobar bronchus mesenchyme +relationship: RO:0002494 UBERON:0004884 ! transformation of lobar bronchus mesenchyme +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003592 @@ -205233,8 +202759,8 @@ xref: EMAPA:37255 {source="MA:th"} xref: MA:0000555 is_a: UBERON:0002384 ! connective tissue intersection_of: UBERON:0002384 ! connective tissue -intersection_of: located_in UBERON:0002224 ! thoracic cavity -relationship: located_in UBERON:0002224 ! thoracic cavity +intersection_of: RO:0001025 UBERON:0002224 ! located in thoracic cavity +relationship: RO:0001025 UBERON:0002224 ! located in thoracic cavity [Term] id: UBERON:0003594 @@ -205265,10 +202791,11 @@ synonym: "textus connectivus of pes" EXACT OMO:0003011 [OBOL:automatic] xref: EMAPA:37329 {source="MA:th"} xref: MA:0000644 is_a: UBERON:0003589 ! hindlimb connective tissue +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0002387 ! pes relationship: part_of UBERON:0002387 ! pes -relationship: transformation_of UBERON:0003328 ! mesenchyme of footplate +relationship: RO:0002494 UBERON:0003328 ! transformation of mesenchyme of footplate [Term] id: UBERON:0003596 @@ -205283,7 +202810,7 @@ is_a: UBERON:0003595 ! pes connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0004454 ! tarsal region relationship: part_of UBERON:0004454 ! tarsal region -relationship: transformation_of UBERON:0010695 ! mesenchyme of tarsal region +relationship: RO:0002494 UBERON:0010695 ! transformation of mesenchyme of tarsal region [Term] id: UBERON:0003597 @@ -205304,7 +202831,7 @@ is_a: UBERON:0015791 ! digit connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0002389 ! manual digit relationship: part_of UBERON:0002389 ! manual digit -relationship: transformation_of UBERON:0005257 ! manual digit mesenchyme +relationship: RO:0002494 UBERON:0005257 ! transformation of manual digit mesenchyme [Term] id: UBERON:0003598 @@ -205317,10 +202844,11 @@ synonym: "hand connective tissue" EXACT [MA:0000620] xref: EMAPA:35392 xref: MA:0000620 is_a: UBERON:0003588 ! forelimb connective tissue +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0002398 ! manus relationship: part_of UBERON:0002398 ! manus -relationship: transformation_of UBERON:0009523 ! mesenchyme of handplate +relationship: RO:0002494 UBERON:0009523 ! transformation of mesenchyme of handplate [Term] id: UBERON:0003599 @@ -205371,6 +202899,7 @@ xref: MA:0001819 xref: NCIT:C49256 xref: UMLS:C1708759 {source="ncithesaurus:Lower_Respiratory_Tract_Cartilage"} is_a: UBERON:0003406 ! cartilage of respiratory system +is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0007844 ! cartilage element intersection_of: part_of UBERON:0001558 ! lower respiratory tract relationship: part_of UBERON:0001558 ! lower respiratory tract @@ -205405,14 +202934,13 @@ xref: Wikipedia:Tracheal_rings is_a: UBERON:0003603 ! lower respiratory tract cartilage intersection_of: UBERON:0007844 ! cartilage element intersection_of: part_of UBERON:0003126 ! trachea -relationship: develops_from UBERON:0007267 ! trachea pre-cartilage rings relationship: part_of UBERON:0003126 ! trachea -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/56/Gray952.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-trachea.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-trachea.glb" xsd:anyURI -property_value: editor_note "check whether to classify as part of splanchoncranium" xsd:string -property_value: UBPROP:0000008 "in mammals the rings are incomplete, in avians the rings are complete." xsd:string +relationship: RO:0002202 UBERON:0007267 ! develops from trachea pre-cartilage rings +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/56/Gray952.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-trachea.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-trachea.glb" xsd:anyURI +property_value: IAO:0000116 "check whether to classify as part of splanchoncranium" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003605 @@ -205548,6 +203076,7 @@ synonym: "textus connectivus elasticus of heart" EXACT [OBOL:automatic] xref: MA:0002858 is_a: UBERON:0003613 ! cardiovascular system elastic tissue is_a: UBERON:0003837 ! thoracic segment connective tissue +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0002521 ! elastic tissue intersection_of: part_of UBERON:0000948 ! heart relationship: part_of UBERON:0000948 ! heart @@ -205617,6 +203146,7 @@ synonym: "vascular elastic tissue" EXACT [MP:0006083] xref: EMAPA:36300 xref: MA:0002856 is_a: UBERON:0003613 ! cardiovascular system elastic tissue +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0002521 ! elastic tissue intersection_of: part_of UBERON:0001981 ! blood vessel relationship: part_of UBERON:0001981 ! blood vessel @@ -205699,7 +203229,7 @@ is_a: UBERON:0003611 ! respiratory system elastic tissue intersection_of: UBERON:0002521 ! elastic tissue intersection_of: part_of UBERON:0003126 ! trachea relationship: part_of UBERON:0002202 ! submucosa of trachea -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003618 @@ -205721,8 +203251,8 @@ xref: SCTID:48467007 is_a: UBERON:0002522 ! tunica media intersection_of: UBERON:0002522 ! tunica media intersection_of: part_of UBERON:0000947 ! aorta -relationship: contributes_to_morphology_of UBERON:0004663 ! aorta wall relationship: part_of UBERON:0004663 ! aorta wall +relationship: RO:0002433 UBERON:0004663 ! contributes to morphology of aorta wall [Term] id: UBERON:0003619 @@ -205746,8 +203276,8 @@ is_a: UBERON:0002523 ! tunica intima is_a: UBERON:0004797 ! blood vessel layer intersection_of: UBERON:0002523 ! tunica intima intersection_of: part_of UBERON:0000947 ! aorta -relationship: contributes_to_morphology_of UBERON:0004663 ! aorta wall relationship: part_of UBERON:0004663 ! aorta wall +relationship: RO:0002433 UBERON:0004663 ! contributes to morphology of aorta wall [Term] id: UBERON:0003643 @@ -205791,8 +203321,7 @@ is_a: UBERON:0011250 ! autopod bone is_a: UBERON:0013630 {source="UBERON:cjm"} ! short bone intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0006716 ! mesopodium region -relationship: part_of UBERON:0009878 {notes="https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern"} ! mesopodial skeleton -property_value: UBPROP:0000008 "The carpus (wrist) and tarsus (ankle) of land vertebrates primitively had three rows of carpal or tarsal bones. Often some of these have become lost or fused in evolution. Three proximals. In the hand humans has all three. In the foot the middle proximal appears in 5-15% of people as an os trigonum. Centrale or os centrale, on the medial side. In humans and our closest relatives the African apes (chimpanzees and gorillas) it fuses to the scaphoid where it forms the articulation with the trapezoid bone; occasionally it stays separate. In Man's foot it is the navicular. Some early land vertebrates had more than one (up to three) os centrale per hand or foot. Distals, one per finger / toe at the base of each metacarpal or metatarsal. In mammals the 4th and 5th fuse. In the horse the 1st is lost" xsd:string {source="Wikipedia:Carpus_and_tarsus_of_land_vertebrates"} +relationship: part_of UBERON:0009878 ! mesopodial skeleton [Term] id: UBERON:0003657 @@ -205873,9 +203402,8 @@ xref: NCIT:C52803 xref: UMLS:C1707990 {source="ncithesaurus:Eyelid_Muscle"} is_a: UBERON:0001630 ! muscle organ intersection_of: UBERON:0001630 ! muscle organ -intersection_of: attaches_to UBERON:0001711 ! eyelid -relationship: attaches_to UBERON:0001711 ! eyelid -property_value: UBPROP:0000001 "The muscle in the orbit of the eye that lifts the upper eyelid[ncithesaurus:Eyelid_Muscle]." xsd:string {source="ncithesaurus:Eyelid_Muscle"} +intersection_of: RO:0002371 UBERON:0001711 ! attached to eyelid +relationship: RO:0002371 UBERON:0001711 ! attached to eyelid [Term] id: UBERON:0003661 @@ -205887,14 +203415,13 @@ subset: pheno_slim synonym: "limb muscle organ" EXACT [OBOL:accepted] synonym: "limb skeletal muscle" EXACT [OBOL:exploratory] synonym: "muscle organ of limb" EXACT [OBOL:accepted] -xref: EMAPA:32700 xref: MA:0000692 is_a: UBERON:0014892 ! skeletal muscle organ, vertebrate intersection_of: UBERON:0014892 ! skeletal muscle organ, vertebrate intersection_of: part_of UBERON:0002101 ! limb -relationship: contributes_to_morphology_of UBERON:0001015 ! musculature relationship: part_of UBERON:0004480 {source="prolog"} ! musculature of limb -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002433 UBERON:0001015 ! contributes to morphology of musculature +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003662 @@ -205921,7 +203448,6 @@ is_a: UBERON:0014794 ! pectoral appendage muscle intersection_of: UBERON:0014892 ! skeletal muscle organ, vertebrate intersection_of: part_of UBERON:0002102 ! forelimb relationship: part_of UBERON:0004481 {source="prolog"} ! musculature of upper limb -property_value: UBPROP:0000012 "FMA and MA class actually refer to muscles of entire pectoral complex" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0003663 @@ -205950,7 +203476,7 @@ is_a: UBERON:0014795 ! pelvic appendage muscle intersection_of: UBERON:0014892 ! skeletal muscle organ, vertebrate intersection_of: part_of UBERON:0002103 ! hindlimb relationship: part_of UBERON:0004482 {source="prolog"} ! musculature of lower limb -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003664 @@ -205997,10 +203523,9 @@ xref: MA:0000699 xref: SCTID:113230005 is_a: UBERON:0004518 ! muscle of vertebral column intersection_of: UBERON:0014892 ! skeletal muscle organ, vertebrate -intersection_of: attaches_to UBERON:0001095 ! caudal vertebra -relationship: attaches_to UBERON:0001095 ! caudal vertebra +intersection_of: RO:0002371 UBERON:0001095 ! attached to caudal vertebra relationship: overlaps UBERON:0007812 ! post-anal tail -property_value: UBPROP:0000012 "the BTO class may possibly refer to an invertebrate structure" xsd:string {external_ontology="BTO"} +relationship: RO:0002371 UBERON:0001095 ! attached to caudal vertebra [Term] id: UBERON:0003672 @@ -206023,13 +203548,10 @@ xref: SCTID:245543004 xref: UMLS:C0011443 {source="ncithesaurus:Dentition"} is_a: UBERON:0034925 ! anatomical collection intersection_of: UBERON:0034925 ! anatomical collection -intersection_of: has_member UBERON:0001091 ! calcareous tooth -relationship: has_member UBERON:0001091 ! calcareous tooth +intersection_of: RO:0002351 UBERON:0001091 ! has member calcareous tooth relationship: part_of UBERON:0010323 ! cranial skeletal system relationship: part_of UBERON:0011595 {gci_relation="part_of", gci_filler="NCBITaxon:32523"} ! jaw region -property_value: UBPROP:0000001 "Dentition refers to set of teeth, especially with regard to their number, kind, and arrangement, in the mouth.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000126", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000001 "The teeth collectively in the dental arch. Dentition ordinarily refers to the natural teeth in position in their alveoli. (MeSH[ncithesaurus:Dentition])" xsd:string {source="ncithesaurus:Dentition"} -property_value: UBPROP:0000012 "In FMA this is an anatomical set" xsd:string {external_ontology="FMA"} +relationship: RO:0002351 UBERON:0001091 ! has member calcareous tooth [Term] id: UBERON:0003677 @@ -206046,8 +203568,9 @@ xref: GAID:1280 xref: MESH:D014092 xref: SCTID:245728004 is_a: UBERON:0000063 ! organ subunit -relationship: attaches_to UBERON:0001091 ! calcareous tooth +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001091 ! calcareous tooth +relationship: RO:0002371 UBERON:0001091 ! attached to calcareous tooth [Term] id: UBERON:0003684 @@ -206072,12 +203595,11 @@ xref: UMLS:C0230168 {source="ncithesaurus:Abdominal_Cavity"} xref: Wikipedia:Abdominal_cavity is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0000916 ! abdomen intersection_of: part_of UBERON:0002323 ! coelemic cavity lumen -relationship: luminal_space_of UBERON:0000916 ! abdomen +intersection_of: RO:0002572 UBERON:0000916 ! luminal space of abdomen relationship: part_of UBERON:0035819 ! abdominopelvic cavity -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI -property_value: UBPROP:0000012 "in FMA this contains the pelvic cavity, but this is inconsistent with the concept of abdominopelvic cavity" xsd:string {external_ontology="FMA"} +relationship: RO:0002572 UBERON:0000916 ! luminal space of abdomen +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI [Term] id: UBERON:0003685 @@ -206101,10 +203623,9 @@ xref: Wikipedia:Suture_(joint) is_a: UBERON:0009198 {source="GO"} ! craniofacial suture intersection_of: UBERON:0002209 ! fibrous joint intersection_of: part_of UBERON:0003128 ! cranium -relationship: contributes_to_morphology_of UBERON:0003128 ! cranium -relationship: developmentally_induced_by UBERON:0002363 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="PMID:16496288"} ! dura mater relationship: part_of UBERON:0003128 ! cranium -property_value: UBPROP:0000202 FMA:71385 +relationship: RO:0002256 UBERON:0002363 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="PMID:16496288"} ! developmentally induced by dura mater +relationship: RO:0002433 UBERON:0003128 ! contributes to morphology of cranium [Term] id: UBERON:0003687 @@ -206115,7 +203636,6 @@ comment: Design pattern notes: check whether this fits the foramen design patter subset: pheno_slim subset: vertebrate_core xref: AAO:0010826 -xref: BTO:0006035 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: EMAPA:37868 {source="MA:th"} xref: FMA:75306 xref: GAID:228 @@ -206128,11 +203648,10 @@ xref: Wikipedia:Foramen_magnum xref: ZFA:0005387 is_a: UBERON:0013685 ! foramen of skull intersection_of: UBERON:0013685 ! foramen of skull -intersection_of: conduit_for UBERON:0001896 ! medulla oblongata -relationship: conduit_for UBERON:0001896 ! medulla oblongata -relationship: located_in UBERON:0001676 ! occipital bone -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/39/Gray130.png" xsd:anyURI -property_value: UBPROP:0000001 "Foramen in the occipital region of neurocranium to allow passage of spinal cord.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002045", ontology="TAO", source="TAO:wd"} +intersection_of: RO:0002570 UBERON:0001896 ! conduit for medulla oblongata +relationship: RO:0001025 UBERON:0001676 ! located in occipital bone +relationship: RO:0002570 UBERON:0001896 ! conduit for medulla oblongata +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/39/Gray130.png" xsd:anyURI [Term] id: UBERON:0003688 @@ -206148,9 +203667,9 @@ xref: MESH:D009852 xref: NCIT:C33209 xref: SCTID:362710002 xref: UMLS:C0028977 {source="ncithesaurus:Omentum"} +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0034944 ! zone of organ relationship: part_of UBERON:0001178 ! visceral peritoneum -property_value: UBPROP:0000007 "omental" xsd:string [Term] id: UBERON:0003691 @@ -206171,13 +203690,9 @@ xref: Wikipedia:Epidural_space is_a: UBERON:0010276 ! space in vertebral column intersection_of: UBERON:0000464 ! anatomical space intersection_of: part_of UBERON:0006692 ! vertebral canal -intersection_of: surrounds UBERON:0002363 ! dura mater +intersection_of: RO:0002221 UBERON:0002363 ! surrounds dura mater relationship: part_of UBERON:0006692 ! vertebral canal -relationship: surrounds UBERON:0002363 ! dura mater -property_value: UBPROP:0000007 "epidural" xsd:string -property_value: UBPROP:0000007 "extradural" xsd:string -property_value: UBPROP:0000008 "In humans the epidural space contains lymphatics, spinal nerve roots, loose fatty tissue, small arteries, and a network of large, thin-walled blood vessels called the epidural venous plexus" xsd:string -property_value: UBPROP:0000012 "in the FMA this is treated as a space of the head, but this ontology covers non-humans, where the space may continue into the tail" xsd:string {external_ontology="FMA"} +relationship: RO:0002221 UBERON:0002363 ! surrounds dura mater [Term] id: UBERON:0003692 @@ -206197,12 +203712,11 @@ xref: Wikipedia:Acromioclavicular_joint is_a: UBERON:0011108 {source="FMA"} ! synovial joint of pectoral girdle is_a: UBERON:0016884 ! shoulder joint intersection_of: UBERON:0000982 ! skeletal joint -intersection_of: connects UBERON:0001105 ! clavicle bone -intersection_of: connects UBERON:0002497 ! acromion -relationship: connects UBERON:0001105 ! clavicle bone -relationship: connects UBERON:0002497 ! acromion -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/3b/Gray326.png" xsd:anyURI -property_value: UBPROP:0000001 "The gliding joint formed by the outer extremity of the clavicle and the inner margin of the acromion process of the scapula." xsd:string {source="MESH:A02.835.583.032"} +intersection_of: RO:0002176 UBERON:0001105 ! connects clavicle bone +intersection_of: RO:0002176 UBERON:0002497 ! connects acromion +relationship: RO:0002176 UBERON:0001105 ! connects clavicle bone +relationship: RO:0002176 UBERON:0002497 ! connects acromion +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3b/Gray326.png" xsd:anyURI [Term] id: UBERON:0003694 @@ -206226,12 +203740,12 @@ xref: UMLS:C0004168 {source="ncithesaurus:Atlanto-axial_Joint"} xref: Wikipedia:Atlanto-axial_joint is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint -intersection_of: connects UBERON:0001092 ! vertebral bone 1 -intersection_of: connects UBERON:0001093 ! vertebral bone 2 -relationship: connects UBERON:0001092 ! vertebral bone 1 -relationship: connects UBERON:0001093 ! vertebral bone 2 +intersection_of: RO:0002176 UBERON:0001092 ! connects vertebral bone 1 +intersection_of: RO:0002176 UBERON:0001093 ! connects vertebral bone 2 relationship: part_of UBERON:0011138 ! postcranial axial skeletal system -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray304.png" xsd:anyURI +relationship: RO:0002176 UBERON:0001092 ! connects vertebral bone 1 +relationship: RO:0002176 UBERON:0001093 ! connects vertebral bone 2 +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray304.png" xsd:anyURI [Term] id: UBERON:0003695 @@ -206260,14 +203774,13 @@ xref: UMLS:C0025525 {source="ncithesaurus:Metacarpophalangeal_Joint"} xref: Wikipedia:Metacarpophalangeal_joint is_a: UBERON:0001489 ! manus joint intersection_of: UBERON:0000982 ! skeletal joint -intersection_of: connects UBERON:0002234 ! proximal phalanx of manus -intersection_of: connects UBERON:0002374 ! metacarpal bone -relationship: connects UBERON:0002234 ! proximal phalanx of manus -relationship: connects UBERON:0002374 ! metacarpal bone +intersection_of: RO:0002176 UBERON:0002234 ! connects proximal phalanx of manus +intersection_of: RO:0002176 UBERON:0002374 ! connects metacarpal bone relationship: part_of UBERON:0002389 ! manual digit -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/53/Gray337.png" xsd:anyURI -property_value: editor_note "we follow FMA in making these joints part of digits. We include carpometacarpophalangeal joint as a synonym - these joints connect to the carpometacarpus - this is not necessarily inconsistent with the relationship for this class to metacarpal bone, as the carpometacarpus could be considered to have a metacarpal as part" xsd:string -property_value: UBPROP:0000202 FMA:71364 +relationship: RO:0002176 UBERON:0002234 ! connects proximal phalanx of manus +relationship: RO:0002176 UBERON:0002374 ! connects metacarpal bone +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/53/Gray337.png" xsd:anyURI +property_value: IAO:0000116 "we follow FMA in making these joints part of digits. We include carpometacarpophalangeal joint as a synonym - these joints connect to the carpometacarpus - this is not necessarily inconsistent with the relationship for this class to metacarpal bone, as the carpometacarpus could be considered to have a metacarpal as part" xsd:string [Term] id: UBERON:0003696 @@ -206292,13 +203805,13 @@ xref: UMLS:C0025589 {source="ncithesaurus:Metatarsophalangeal_Joint"} xref: Wikipedia:Metatarsophalangeal_articulations is_a: UBERON:0001487 ! pes joint intersection_of: UBERON:0000982 ! skeletal joint -intersection_of: connects UBERON:0001448 ! metatarsal bone -intersection_of: connects UBERON:0003867 ! distal phalanx of pes -relationship: connects UBERON:0001448 ! metatarsal bone -relationship: connects UBERON:0003867 ! distal phalanx of pes +intersection_of: RO:0002176 UBERON:0001448 ! connects metatarsal bone +intersection_of: RO:0002176 UBERON:0003867 ! connects distal phalanx of pes relationship: part_of UBERON:0001466 ! pedal digit -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/9e/Gray268.png" xsd:anyURI -property_value: editor_note "we follow FMA in making these joints part of digits" xsd:string +relationship: RO:0002176 UBERON:0001448 ! connects metatarsal bone +relationship: RO:0002176 UBERON:0003867 ! connects distal phalanx of pes +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/9e/Gray268.png" xsd:anyURI +property_value: IAO:0000116 "we follow FMA in making these joints part of digits" xsd:string [Term] id: UBERON:0003697 @@ -206325,7 +203838,7 @@ is_a: UBERON:0000060 ! anatomical wall intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0000916 ! abdomen relationship: part_of UBERON:0000916 ! abdomen -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI [Term] id: UBERON:0003703 @@ -206344,8 +203857,7 @@ xref: NCIT:C32573 xref: SCTID:276158002 xref: UMLS:C0206187 {source="ncithesaurus:Extrahepatic_Bile_Duct"} is_a: UBERON:0002394 ! bile duct -property_value: editor_note "includes all the cystic duct, all the common bile duct and the extrahapetic part of the hepatic duct" xsd:string -property_value: RO:0002171 UBERON:0002107 +property_value: IAO:0000116 "includes all the cystic duct, all the common bile duct and the extrahapetic part of the hepatic duct" xsd:string [Term] id: UBERON:0003704 @@ -206368,10 +203880,9 @@ xref: ZFA:0005169 is_a: UBERON:0002394 {source="FMA"} ! bile duct intersection_of: UBERON:0002394 ! bile duct intersection_of: part_of UBERON:0002107 ! liver -relationship: contributes_to_morphology_of UBERON:0002107 ! liver relationship: part_of UBERON:0002107 {source="MA"} ! liver -property_value: editor_note "includes the hepatic duct of the caudate lobe, and the intra- and inter- lobar bile ducts" xsd:string -property_value: UBPROP:0000001 "Duct that collects bile from the bile ductules and connects to the extrahepatic bile duct.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005169", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002433 UBERON:0002107 ! contributes to morphology of liver +property_value: IAO:0000116 "includes the hepatic duct of the caudate lobe, and the intra- and inter- lobar bile ducts" xsd:string [Term] id: UBERON:0003709 @@ -206396,8 +203907,7 @@ xref: Wikipedia:Circle_of_Willis is_a: UBERON:0004573 ! systemic artery relationship: overlaps UBERON:0007142 {source="FMA-modified"} ! left internal carotid artery relationship: overlaps UBERON:0007143 {source="FMA-modified"} ! right internal carotid artery -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/2e/Circle_of_Willis_en.svg" xsd:anyURI -property_value: UBPROP:0000008 "In zebrafish, the circle of vessels comprised of the basal communicating artery (BCA) and posterior communicating segments (PCS) superficially resemble but are not homologous to the human circle of Willis" xsd:string {source="http://zfish.nichd.nih.gov/zfatlas/Intro%20Page/comparative.html"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2e/Circle_of_Willis_en.svg" xsd:anyURI [Term] id: UBERON:0003711 @@ -206424,10 +203934,10 @@ xref: SCTID:181371003 xref: UMLS:C0006095 {source="ncithesaurus:Innominate_Vein"} xref: Wikipedia:Brachiocephalic_vein is_a: UBERON:0001638 ! vein -relationship: connected_to UBERON:0001585 ! anterior vena cava relationship: part_of UBERON:0007204 ! brachiocephalic vasculature -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/9e/Gray1174.png" xsd:anyURI +relationship: RO:0002170 UBERON:0001585 ! connected to anterior vena cava +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/9e/Gray1174.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003712 @@ -206450,9 +203960,8 @@ xref: SCTID:244402005 xref: UMLS:C0007473 {source="ncithesaurus:Cavernous_Sinus"} xref: Wikipedia:Cavernous_sinus is_a: UBERON:0005486 ! venous dural sinus -relationship: connected_to UBERON:0007160 ! inferior petrosal sinus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000001 "An irregularly shaped venous space in the dura mater at either side of the sphenoid bone[MESH:A07.231.908.224.334]." xsd:string {source="MESH:A07.231.908.224.334"} +relationship: RO:0002170 UBERON:0007160 ! connected to inferior petrosal sinus +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003713 @@ -206474,12 +203983,12 @@ xref: SCTID:278029005 xref: UMLS:C0038001 {source="ncithesaurus:Splenic_Vein"} xref: Wikipedia:Splenic_vein is_a: UBERON:0001638 ! vein -relationship: connected_to UBERON:0001639 ! hepatic portal vein -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/5b/Gray1189.png" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e4/Bilebladder.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +relationship: RO:0002170 UBERON:0001639 ! connected to hepatic portal vein +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5b/Gray1189.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e4/Bilebladder.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003714 @@ -206506,8 +204015,6 @@ disjoint_from: UBERON:0004755 ! skeletal tissue relationship: has_part CL:0000125 ! glial cell relationship: has_part CL:0000540 ! neuron relationship: part_of UBERON:0001016 ! nervous system -property_value: UBPROP:0000001 "One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000325", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000012 "FMA definition includes vasculature" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0003715 @@ -206526,10 +204033,9 @@ xref: SCTID:264198001 xref: Wikipedia:Splanchnic_nerves is_a: UBERON:0034729 ! sympathetic nerve intersection_of: UBERON:0001021 ! nerve -intersection_of: innervates UBERON:0000916 ! abdomen -relationship: contributes_to_morphology_of UBERON:0000013 ! sympathetic nervous system -relationship: innervates UBERON:0000916 ! abdomen -property_value: UBPROP:0000010 "All carry sympathetic fibers except for the pelvic splanchnic nerves, which carry parasympathetic fibers" xsd:string +intersection_of: RO:0002134 UBERON:0000916 ! innervates abdomen +relationship: RO:0002134 UBERON:0000916 ! innervates abdomen +relationship: RO:0002433 UBERON:0000013 ! contributes to morphology of sympathetic nervous system [Term] id: UBERON:0003716 @@ -206549,11 +204055,11 @@ xref: MESH:D012009 xref: SCTID:24227007 xref: VHOG:0001347 xref: Wikipedia:Recurrent_laryngeal_nerve +is_a: UBERON:0011779 ! nerve of head region is_a: UBERON:0035642 ! laryngeal nerve -relationship: branching_part_of UBERON:0001759 ! vagus nerve -relationship: develops_from UBERON:0003117 {source="Wikipedia"} ! pharyngeal arch 6 -relationship: only_in_taxon NCBITaxon:32523 ! Tetrapoda -property_value: UBPROP:0000001 "Branch of the vagus nerve that separates from the vagus well postcranially, then continues anteriorly to innervate the larynx[AAO:0010754]." xsd:string {source="AAO:0010754"} +relationship: RO:0002160 NCBITaxon:32523 ! only in taxon Tetrapoda +relationship: RO:0002202 UBERON:0003117 {source="Wikipedia"} ! develops from pharyngeal arch 6 +relationship: RO:0002380 UBERON:0001759 ! branching part of vagus nerve [Term] id: UBERON:0003718 @@ -206589,11 +204095,11 @@ xref: MA:0001102 xref: MESH:D008036 xref: SCTID:280260006 xref: Wikipedia:Lingual_nerve -is_a: UBERON:0001021 ! nerve +is_a: UBERON:0011779 ! nerve of head region intersection_of: UBERON:0001021 ! nerve -intersection_of: innervates UBERON:0001723 ! tongue -relationship: branching_part_of UBERON:0000375 ! mandibular nerve -relationship: innervates UBERON:0001723 ! tongue +intersection_of: RO:0002134 UBERON:0001723 ! innervates tongue +relationship: RO:0002134 UBERON:0001723 ! innervates tongue +relationship: RO:0002380 UBERON:0000375 ! branching part of mandibular nerve [Term] id: UBERON:0003726 @@ -206635,7 +204141,7 @@ xref: SCTID:279568001 xref: UMLS:C1285089 {source="ncithesaurus:Intercostal_Nerve"} xref: Wikipedia:Intercostal_nerves is_a: UBERON:0001780 ! spinal nerve -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b1/Gray819.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b1/Gray819.png" xsd:anyURI [Term] id: UBERON:0003728 @@ -206658,9 +204164,8 @@ xref: UMLS:C0025066 {source="ncithesaurus:Mediastinum"} xref: Wikipedia:Mediastinum is_a: UBERON:0002553 ! anatomical cavity relationship: part_of UBERON:0002224 ! thoracic cavity -relationship: surrounded_by UBERON:0035431 {source="FMA"} ! mediastinal pleura -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/ab/Mediastinum.png" xsd:anyURI -property_value: UBPROP:0000007 "mediastinal" xsd:string +relationship: RO:0002219 UBERON:0035431 {source="FMA"} ! surrounded by mediastinal pleura +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/ab/Mediastinum.png" xsd:anyURI [Term] id: UBERON:0003729 @@ -206694,12 +204199,10 @@ is_a: UBERON:0000344 ! mucosa intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0000165 ! mouth relationship: bounding_layer_of UBERON:0000165 ! mouth -relationship: continuous_with UBERON:0000355 ! pharyngeal mucosa -relationship: continuous_with UBERON:0001458 ! skin of lip -relationship: contributes_to_morphology_of UBERON:0001007 ! digestive system relationship: part_of UBERON:0000165 ! mouth -property_value: IAO:0000232 "this is defined as any mucous membrane of the mouth - including palate, lips, uvula, etc. ncit split mouth/oral mucosa into lip and buccal. In future we may split into masticatory/keratinized (gingiva + hard palate) vs lining/non-keratinized (lips, cheeks, floor of mouth, soft palate). FMA distinguishes between mucosa of mouth and region of mouth (the latter including the buccal mucosa)" xsd:string -property_value: UBPROP:0000001 "the mucous membrane epithelium of the mouth. It can be divided into three categories: masticatory, lining, and specialized[Wikipedia:Oral_mucosa]." xsd:string {source="Wikipedia:Oral_mucosa"} +relationship: RO:0002150 UBERON:0000355 ! continuous with pharyngeal mucosa +relationship: RO:0002150 UBERON:0001458 ! continuous with skin of lip +relationship: RO:0002433 UBERON:0001007 ! contributes to morphology of digestive system [Term] id: UBERON:0003820 @@ -206714,11 +204217,10 @@ xref: EMAPA:36141 is_a: UBERON:0004902 ! urogenital sinus epithelium is_a: UBERON:0005153 ! epithelial bud intersection_of: UBERON:0005153 ! epithelial bud -intersection_of: has_potential_to_develop_into UBERON:0002367 ! prostate gland -relationship: develops_from UBERON:0009847 {source="PMID:18977204"} ! prostate field -relationship: has_potential_to_develop_into UBERON:0002367 ! prostate gland +intersection_of: RO:0002387 UBERON:0002367 ! has potential to develop into prostate gland relationship: part_of UBERON:0004902 ! urogenital sinus epithelium -property_value: UBPROP:0000009 "AR activation releases instructive signals from UGM that acts on UGS epithelium (UGE) to stimulate cell proliferation, form prostate ductal progenitors (prostatic buds), and regulate cell adhesion dynamics to permit prostatic bud outgrowth. There are three phases of prostatic budding: (1) the specification phase, when instructive developmental cues define where buds will form in the UGS, (2) the initiation phase, when prostatic buds begin to form, and (3) the elongation phase, when proliferation, cell adhesion, and cell migration coordinate outgrowth of prostatic buds into UGM. Timing of prostatic bud formation and the quantity and pattern of buds that are formed in the UGS are strictly regulated [3, 4]. The position of prostatic buds as they emerge from the UGS in utero determines the arrangement of prostate ducts in adulthood.[PMID:18977204]" xsd:string +relationship: RO:0002202 UBERON:0009847 {source="PMID:18977204"} ! develops from prostate field +relationship: RO:0002387 UBERON:0002367 ! has potential to develop into prostate gland [Term] id: UBERON:0003821 @@ -206737,7 +204239,7 @@ is_a: UBERON:0003606 ! limb long bone is_a: UBERON:0012357 ! digitopodium bone intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0009877 ! metapodium region -relationship: part_of UBERON:0010546 {notes="https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern"} ! metapodial skeleton +relationship: part_of UBERON:0010546 ! metapodial skeleton [Term] id: UBERON:0003822 @@ -206776,12 +204278,9 @@ is_a: UBERON:0002472 ! stylopod is_a: UBERON:0008785 ! upper limb segment intersection_of: UBERON:0002472 ! stylopod intersection_of: part_of UBERON:0002102 ! forelimb -relationship: contributes_to_morphology_of UBERON:0002102 ! forelimb -relationship: has_skeleton UBERON:0015053 ! humerus endochondral element relationship: part_of UBERON:0001460 {source="MA"} ! arm -property_value: UBPROP:0000001 "Segment of the hindleg corresponding to the humerus.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000887", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000003 "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000343", ontology="VHOG", source="ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000013 "anatomical usage, the term arm refers specifically to the segment between the shoulder and the elbow, while the segment between the elbow and wrist is the forearm. However, in common, literary, and historical usage, arm refers to the entire upper limb from shoulder to wrist. FMA uses the term Arm for this class, so we place it here. Naming conventions for pod terms under discussion within phenoscape group." xsd:string +relationship: RO:0002433 UBERON:0002102 ! contributes to morphology of forelimb +relationship: RO:0002551 UBERON:0015053 ! has skeleton humerus endochondral element [Term] id: UBERON:0003823 @@ -206824,20 +204323,15 @@ xref: NCIT:C32974 xref: SCTID:244015008 xref: UMLS:C1140621 {source="ncithesaurus:Leg"} xref: VHOG:0000348 -xref: VO:0010971 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: VSAO:0005060 xref: Wikipedia:Forearm is_a: UBERON:0002471 ! zeugopod is_a: UBERON:0008784 ! lower limb segment intersection_of: UBERON:0002471 ! zeugopod intersection_of: part_of UBERON:0002103 ! hindlimb -relationship: contributes_to_morphology_of UBERON:0002103 ! hindlimb -relationship: has_skeleton UBERON:0010720 ! hindlimb zeugopod skeleton relationship: part_of UBERON:0000978 {source="MA"} ! leg -property_value: UBPROP:0000003 "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000348", ontology="VHOG", source="ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "sural" xsd:string -property_value: UBPROP:0000012 "FMA:24979 denotes the middle segment (zeugopod), its placement here is correct. See obo-anatomy archives for discussion" xsd:string {external_ontology="FMA"} -property_value: UBPROP:0000013 "Naming conventions for pod terms under discussion within phenoscape group. TODO - add distinct term for skeleton and place AAO class here" xsd:string +relationship: RO:0002433 UBERON:0002103 ! contributes to morphology of hindlimb +relationship: RO:0002551 UBERON:0010720 ! has skeleton hindlimb zeugopod skeleton [Term] id: UBERON:0003824 @@ -206926,6 +204420,7 @@ def: "Any muscle tissue that is part of the urethra." [UBERON:cjm] synonym: "urethral muscle layer" RELATED [MA:0002649] xref: EMAPA:37787 {source="MA:th"} xref: MA:0002649 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005090 ! muscle structure intersection_of: UBERON:0005090 ! muscle structure intersection_of: part_of UBERON:0000057 ! urethra @@ -206983,7 +204478,7 @@ is_a: UBERON:0013765 ! digestive system element intersection_of: UBERON:0001630 ! muscle organ intersection_of: part_of UBERON:0001043 ! esophagus relationship: part_of UBERON:0001096 {source="MA"} ! wall of esophagus -property_value: editor_note "merge muscle and muscle layer?" xsd:string +property_value: IAO:0000116 "merge muscle and muscle layer?" xsd:string [Term] id: UBERON:0003833 @@ -207114,7 +204609,6 @@ is_a: UBERON:0003657 ! limb joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: part_of UBERON:0002102 ! forelimb relationship: part_of UBERON:0002102 ! forelimb -property_value: UBPROP:0000202 FMA:71344 [Term] id: UBERON:0003840 @@ -207147,7 +204641,6 @@ is_a: UBERON:0003657 ! limb joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: part_of UBERON:0002103 ! hindlimb relationship: part_of UBERON:0002103 ! hindlimb -property_value: UBPROP:0000202 FMA:71348 [Term] id: UBERON:0003841 @@ -207192,10 +204685,9 @@ xref: VHOG:0001119 xref: XAO:0000252 is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0001049 ! neural tube -relationship: luminal_space_of UBERON:0001049 ! neural tube +intersection_of: RO:0002572 UBERON:0001049 ! luminal space of neural tube relationship: part_of UBERON:0001049 ! neural tube -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001119", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} +relationship: RO:0002572 UBERON:0001049 ! luminal space of neural tube [Term] id: UBERON:0003843 @@ -207218,14 +204710,13 @@ xref: UMLS:C1709309 {source="ncithesaurus:Odontogenic_Epithelial_Remnants"} xref: VHOG:0001443 xref: XAO:0003203 xref: ZFA:0005134 -is_a: UBERON:0000483 ! epithelium +is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0005176 ! tooth enamel organ -relationship: develops_from UBERON:0004362 {notes="epithelium", source="JB"} ! pharyngeal arch 1 relationship: part_of UBERON:0005176 ! tooth enamel organ -property_value: editor_note "see comments for dental organ." xsd:string -property_value: editor_note "todo - full developmental relationships" xsd:string -property_value: UBPROP:0000011 "In the developing molar dentition of the mouse, tooth inductive po- tential resides in the dental epithelium until embryonic day (E)12.5 (3). Thereafter, tooth inductive potential shifts to neural crest-derived dental mesenchyme, which acquires the ability to direct tooth formation in nonodontogenic tissues (3, 4)" xsd:string {source="PMID:10954731"} +relationship: RO:0002202 UBERON:0004362 ! develops from pharyngeal arch 1 +property_value: IAO:0000116 "see comments for dental organ." xsd:string +property_value: IAO:0000116 "todo - full developmental relationships" xsd:string [Term] id: UBERON:0003846 @@ -207252,15 +204743,17 @@ xref: NCIT:C45713 xref: UMLS:C1711423 {source="ncithesaurus:Thymic_Epithelial_Tissue"} xref: VHOG:0001426 xref: ZFA:0005779 -is_a: UBERON:0000483 ! epithelium +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure +is_a: UBERON:0005911 ! endo-epithelium +is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002370 ! thymus -relationship: contributes_to_morphology_of UBERON:0002370 ! thymus -relationship: develops_from UBERON:0010026 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="MP"} ! ventral part of pharyngeal pouch 3 relationship: has_part CL:0002293 ! epithelial cell of thymus relationship: has_part PR:000007636 {source="PMID:21293377"} ! forkhead box protein N1 relationship: part_of UBERON:0002370 ! thymus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 UBERON:0010026 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="MP"} ! develops from ventral part of pharyngeal pouch 3 +relationship: RO:0002433 UBERON:0002370 ! contributes to morphology of thymus +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003847 @@ -207277,10 +204770,8 @@ xref: UMLS:C1711424 {source="ncithesaurus:Thyroid_Artery"} xref: VHOG:0001366 is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0002046 ! thyroid gland -relationship: supplies UBERON:0002046 ! thyroid gland -property_value: UBPROP:0000001 "Part of the external carotid which supplies blood to the thyroid gland.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010490", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000002 "relationship loss: part_of external carotid (AAO:0010218)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010490", ontology="AAO"} +intersection_of: RO:0002178 UBERON:0002046 ! supplies thyroid gland +relationship: RO:0002178 UBERON:0002046 ! supplies thyroid gland [Term] id: UBERON:0003848 @@ -207298,9 +204789,9 @@ xref: VHOG:0001340 xref: Wikipedia:Gonadal_vein is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein -intersection_of: attaches_to UBERON:0000991 ! gonad -relationship: attaches_to UBERON:0000991 ! gonad -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/da/Gray1120.png" xsd:anyURI +intersection_of: RO:0002371 UBERON:0000991 ! attached to gonad +relationship: RO:0002371 UBERON:0000991 ! attached to gonad +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/da/Gray1120.png" xsd:anyURI [Term] id: UBERON:0003849 @@ -207320,9 +204811,8 @@ xref: ZFA:0000935 is_a: UBERON:0002342 ! neural crest is_a: UBERON:0003099 {source="ZFA"} ! cranial neural crest intersection_of: UBERON:0002342 ! neural crest -intersection_of: has_potential_to_developmentally_contribute_to UBERON:0001891 ! midbrain -relationship: has_potential_to_developmentally_contribute_to UBERON:0001891 ! midbrain -property_value: UBPROP:0000003 "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000796", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43", source="http://bgee.unil.ch/"} +intersection_of: RO:0002385 UBERON:0001891 ! has potential to developmentally contribute to midbrain +relationship: RO:0002385 UBERON:0001891 ! has potential to developmentally contribute to midbrain [Term] id: UBERON:0003850 @@ -207339,10 +204829,8 @@ xref: VHOG:0000799 xref: ZFA:0000812 is_a: UBERON:0002342 ! neural crest intersection_of: UBERON:0002342 ! neural crest -intersection_of: has_potential_to_developmentally_contribute_to UBERON:0001893 ! telencephalon -relationship: has_potential_to_developmentally_contribute_to UBERON:0001893 ! telencephalon -property_value: UBPROP:0000001 "Cranial neural crest that is part of the telencephalon.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000812", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000799", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43", source="http://bgee.unil.ch/"} +intersection_of: RO:0002385 UBERON:0001893 ! has potential to developmentally contribute to telencephalon +relationship: RO:0002385 UBERON:0001893 ! has potential to developmentally contribute to telencephalon [Term] id: UBERON:0003851 @@ -207362,9 +204850,8 @@ xref: VHOG:0000798 xref: ZFA:0000811 is_a: UBERON:0002342 ! neural crest intersection_of: UBERON:0002342 ! neural crest -intersection_of: has_potential_to_developmentally_contribute_to UBERON:0001894 ! diencephalon -relationship: has_potential_to_developmentally_contribute_to UBERON:0001894 ! diencephalon -property_value: UBPROP:0000003 "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000798", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43", source="http://bgee.unil.ch/"} +intersection_of: RO:0002385 UBERON:0001894 ! has potential to developmentally contribute to diencephalon +relationship: RO:0002385 UBERON:0001894 ! has potential to developmentally contribute to diencephalon [Term] id: UBERON:0003852 @@ -207384,10 +204871,8 @@ xref: ZFA:0007063 is_a: UBERON:0002342 ! neural crest is_a: UBERON:0003099 {source="ZFA"} ! cranial neural crest intersection_of: UBERON:0002342 ! neural crest -intersection_of: has_potential_to_developmentally_contribute_to UBERON:0002028 ! hindbrain -relationship: has_potential_to_developmentally_contribute_to UBERON:0002028 ! hindbrain -property_value: UBPROP:0000001 "Cranial neural crest that is part of the hindbrain.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0007063", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001210", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43", source="http://bgee.unil.ch/"} +intersection_of: RO:0002385 UBERON:0002028 ! has potential to developmentally contribute to hindbrain +relationship: RO:0002385 UBERON:0002028 ! has potential to developmentally contribute to hindbrain [Term] id: UBERON:0003853 @@ -207402,9 +204887,8 @@ xref: EMAPA:16881 xref: VHOG:0001006 is_a: UBERON:0002342 ! neural crest intersection_of: UBERON:0002342 ! neural crest -intersection_of: has_potential_to_developmentally_contribute_to UBERON:0002240 ! spinal cord -relationship: has_potential_to_developmentally_contribute_to UBERON:0002240 ! spinal cord -property_value: UBPROP:0000003 "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001006", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43", source="http://bgee.unil.ch/"} +intersection_of: RO:0002385 UBERON:0002240 ! has potential to developmentally contribute to spinal cord +relationship: RO:0002385 UBERON:0002240 ! has potential to developmentally contribute to spinal cord [Term] id: UBERON:0003854 @@ -207418,10 +204902,8 @@ xref: VHOG:0000439 xref: ZFA:0007021 is_a: UBERON:0003075 ! neural plate intersection_of: UBERON:0003075 ! neural plate -intersection_of: develops_from UBERON:0006241 ! future spinal cord -relationship: develops_from UBERON:0006241 {source="ZFA"} ! future spinal cord -property_value: UBPROP:0000001 "Neural plate that is part of the spinal cord. [Bgee_curator][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000439", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000439", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} +intersection_of: RO:0002202 UBERON:0006241 ! develops from future spinal cord +relationship: RO:0002202 UBERON:0006241 {source="ZFA"} ! develops from future spinal cord [Term] id: UBERON:0003855 @@ -207463,12 +204945,10 @@ is_a: UBERON:0007529 ! loose mesenchyme tissue intersection_of: UBERON:0007529 ! loose mesenchyme tissue intersection_of: part_of UBERON:0008281 ! tooth bud relationship: adjacent_to UBERON:0005176 ! tooth enamel organ -relationship: develops_from UBERON:0007213 {notes="see comments"} ! mesenchyme derived from head neural crest -relationship: develops_from UBERON:0010259 {gci_relation="part_of", gci_filler="NCBITaxon:32523", source="JB"} ! 1st arch mesenchyme from neural crest relationship: part_of UBERON:0008281 ! tooth bud -property_value: editor_note "we follow ZFA in introducing an additional distinction between the dental papilla and the (uncondensed) mesenchyme. Note that in some species such as zebrafish teeth are not part of the mouth, and sharks have dermal denticles which share similar developmental origins with teeth. For now we assume a NC origin for all and add a taxon restriction to 1st arch mesenchyme" xsd:string -property_value: UBPROP:0000001 "Mesenchyme enclosed by dental organ.[MP]" xsd:string {ontology="MP", source="J:153554"} -property_value: UBPROP:0000001 "Mesenchyme enclosed by dental organ.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005139", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002202 UBERON:0007213 ! develops from mesenchyme derived from head neural crest +relationship: RO:0002202 UBERON:0010259 {gci_relation="part_of", gci_filler="NCBITaxon:32523", source="JB"} ! develops from 1st arch mesenchyme from neural crest +property_value: IAO:0000116 "we follow ZFA in introducing an additional distinction between the dental papilla and the (uncondensed) mesenchyme. Note that in some species such as zebrafish teeth are not part of the mouth, and sharks have dermal denticles which share similar developmental origins with teeth. For now we assume a NC origin for all and add a taxon restriction to 1st arch mesenchyme" xsd:string [Term] id: UBERON:0003859 @@ -207539,15 +205019,8 @@ xref: Wikipedia:Vertebral_arch xref: ZFA:0001066 is_a: UBERON:0002513 ! endochondral bone is_a: UBERON:0010358 ! arch of centrum of vertebra -relationship: develops_from UBERON:0006063 ! cartilaginous neural arch -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray82.png" xsd:anyURI -property_value: UBPROP:0000001 "A neural arch encloses the neural canal and typically meets its partner to form a neural spine. The neural arch can be a replacement ossification of the basidorsal cartilage or can form directly in membrane bone.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001066", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Bony arch perched on the vertebral centrum; successive arches enclose the neural canal that surrounds and protects the spinal cord dorsally.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000725", ontology="AAO", source="AAO:Pugener_2002"} -property_value: UBPROP:0000001 "the dorsal bony and/or cartilaginous part of a vertebra, consisting of a pair of pedicles, a pair of laminae, and seven processes (four articular processes, two transverse processes, and one spinous process)" xsd:string {source="MP:0004599:csmith"} -property_value: UBPROP:0000002 "relationship loss: develops_from basidorsal (TAO:0001060)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001066", ontology="TAO"} -property_value: UBPROP:0000003 "(...) certain common components [of vertebral structure] are found in nearly all vertebrate. A representative vertebra has a vertebral arch or neural arch, which extends dorsally around the spinal cord.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001670", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.270", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "tiny neural arches present in Hagfish (which lack a true vertebraal column)." xsd:string -property_value: UBPROP:0000011 "The neural arch can be a replacement ossification of the basidorsal cartilage or can form directly in membrane bone" xsd:string +relationship: RO:0002202 UBERON:0006063 ! develops from cartilaginous neural arch +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray82.png" xsd:anyURI [Term] id: UBERON:0003864 @@ -207688,8 +205161,8 @@ namespace: uberon def: "A presumptive structure that has the potential to develop into a ganglion." [OBOL:automatic] is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0000045 ! ganglion -relationship: has_potential_to_develop_into UBERON:0000045 ! ganglion +intersection_of: RO:0002387 UBERON:0000045 ! has potential to develop into ganglion +relationship: RO:0002387 UBERON:0000045 ! has potential to develop into ganglion [Term] id: UBERON:0003885 @@ -207708,7 +205181,7 @@ is_a: UBERON:0002095 ! mesentery intersection_of: UBERON:0002095 ! mesentery intersection_of: part_of UBERON:0000995 ! uterus relationship: part_of UBERON:0012332 ! broad ligament of uterus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003886 @@ -207721,11 +205194,11 @@ synonym: "body cavity precursor" RELATED [] synonym: "future coelomic cavity lumen" EXACT [] is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: has_potential_to_develop_into UBERON:0002323 ! coelemic cavity lumen -relationship: existence_ends_during UBERON:0000111 ! organogenesis stage -relationship: existence_starts_during UBERON:0000109 ! gastrula stage -relationship: has_potential_to_develop_into UBERON:0002323 ! coelemic cavity lumen +intersection_of: RO:0002387 UBERON:0002323 ! has potential to develop into coelemic cavity lumen relationship: part_of UBERON:0000926 ! mesoderm +relationship: RO:0002387 UBERON:0002323 ! has potential to develop into coelemic cavity lumen +relationship: RO:0002488 UBERON:0000109 ! existence starts during gastrula stage +relationship: RO:0002492 UBERON:0000111 ! existence ends during organogenesis stage [Term] id: UBERON:0003887 @@ -207741,10 +205214,9 @@ xref: UMLS:C1512940 {source="ncithesaurus:Intraembryonic_Coelom"} xref: VHOG:0000316 xref: Wikipedia:Intraembryonic_coelom is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0003081 {source="Wikipedia"} ! lateral plate mesoderm relationship: part_of UBERON:0011997 ! coelom -property_value: editor_note "consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults" xsd:string -property_value: UBPROP:0000003 "(...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000316", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.166", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003081 {source="Wikipedia"} ! develops from lateral plate mesoderm +property_value: IAO:0000116 "consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults" xsd:string [Term] id: UBERON:0003889 @@ -207765,7 +205237,6 @@ synonym: "tuba uterina" RELATED OMO:0003011 [Wikipedia:Fallopian_tube] synonym: "uterine tube (sensu Mammalia)" EXACT [] xref: CALOHA:TS-0732 xref: EHDAA2:0000504 -xref: EMAPA:18984 xref: EMAPA:35660 xref: EV:0100112 xref: FMA:18245 @@ -207781,17 +205252,16 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0013515 ! subdivision of oviduct is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0013515 ! subdivision of oviduct -intersection_of: develops_from UBERON:0003890 ! Mullerian duct intersection_of: part_of UBERON:0000993 ! oviduct -relationship: connects UBERON:0000995 ! uterus -relationship: connects UBERON:0003984 ! uterine tube infundibulum -relationship: develops_from UBERON:0003890 ! Mullerian duct -relationship: in_lateral_side_of UBERON:0003975 {source="FMA-abduced-lr"} ! internal female genitalia -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia +intersection_of: RO:0002202 UBERON:0003890 ! develops from Mullerian duct +relationship: BSPO:0000126 UBERON:0003975 {source="FMA-abduced-lr"} ! internal female genitalia relationship: part_of UBERON:0002355 ! pelvic region of trunk -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/68/Scheme_female_reproductive_system-en.svg" xsd:anyURI -property_value: UBPROP:0000008 "Homologous to appendix testis" xsd:string {source="Wikipedia:Talk:Fallopian_tube#Homology"} +relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia +relationship: RO:0002176 UBERON:0000995 ! connects uterus +relationship: RO:0002176 UBERON:0003984 ! connects uterine tube infundibulum +relationship: RO:0002202 UBERON:0003890 ! develops from Mullerian duct +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/68/Scheme_female_reproductive_system-en.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003890 @@ -207820,14 +205290,10 @@ xref: XAO:0000330 is_a: UBERON:0000025 ! tube is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0015212 ! lateral structure -relationship: develops_from UBERON:0003064 {source="Wikipedia"} ! intermediate mesoderm -relationship: in_lateral_side_of UBERON:0000922 ! embryo +relationship: BSPO:0000126 UBERON:0000922 ! embryo relationship: part_of UBERON:0000922 ! embryo -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png" xsd:anyURI -property_value: UBPROP:0000001 "Either of the paired embryonic ducts developing into the uterine tubes, uterus, and vagina in the female and becoming largely obliterated in the male. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001199", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/paramesonephric+duct"} -property_value: UBPROP:0000001 "Transient developmental organ which gives rise to oviducts in female (documented to persist in some male frogs).[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010141", ontology="AAO", source="AAO:RED"} -property_value: UBPROP:0000003 "In females, the archinephric (mesonephric) ducts tend to function only within the urinary systems. The muellerian duct arises embryologically next to the archinephric (wolffian) duct. In males, the muellerian duct regresses if it appears at all, but in females, the muellerian ducts become the oviducts of the reproductive system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001199", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.559", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000011 "Sertoli cells secrete anti-Mullerian hormone (AMH) inducing the demise of this duct" xsd:string +relationship: RO:0002202 UBERON:0003064 {source="Wikipedia"} ! develops from intermediate mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png" xsd:anyURI [Term] id: UBERON:0003891 @@ -207840,9 +205306,8 @@ xref: FMA:81494 xref: NCIT:C67387 xref: UMLS:C0927195 {source="ncithesaurus:Stroma_Connective_Tissue"} is_a: UBERON:0000064 ! organ part -relationship: composed_primarily_of UBERON:0002384 ! connective tissue -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: UBPROP:0000007 "stromal" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002473 UBERON:0002384 ! composed primarily of connective tissue [Term] id: UBERON:0003893 @@ -207858,7 +205323,6 @@ xref: FMA:85272 xref: galen:Capsule xref: Wikipedia:Capsule_(anatomy) is_a: UBERON:0000158 ! membranous layer -property_value: UBPROP:0000007 "capsular" xsd:string [Term] id: UBERON:0003894 @@ -207892,11 +205356,11 @@ is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0006598 ! presumptive structure is_a: UBERON:0009497 ! epithelium of foregut-midgut junction intersection_of: UBERON:0001048 ! primordium -intersection_of: has_potential_to_develop_into UBERON:0002107 ! liver -relationship: develops_from UBERON:0001041 {notes="ventral foregut endoderm", source="Zaret 1996"} ! foregut -relationship: has_potential_to_develop_into UBERON:0002107 ! liver +intersection_of: RO:0002387 UBERON:0002107 ! has potential to develop into liver relationship: part_of UBERON:0009550 {source="EHDAA2"} ! endoderm of foregut-midgut junction -property_value: editor_note "consider adding further subdivisions of the endoderm, e.g. ventral foregut. Note we place two EFO classes here, it's not clear how they differ" xsd:string +relationship: RO:0002202 UBERON:0001041 ! develops from foregut +relationship: RO:0002387 UBERON:0002107 ! has potential to develop into liver +property_value: IAO:0000116 "consider adding further subdivisions of the endoderm, e.g. ventral foregut. Note we place two EFO classes here, it's not clear how they differ" xsd:string [Term] id: UBERON:0003897 @@ -207911,10 +205375,10 @@ xref: RETIRED_EHDAA2:0000160 xref: TAO:0001954 is_a: UBERON:0014892 ! skeletal muscle organ, vertebrate intersection_of: UBERON:0014892 ! skeletal muscle organ, vertebrate -intersection_of: attaches_to_part_of UBERON:0005944 ! axial skeleton plus cranial skeleton intersection_of: part_of UBERON:0013701 ! main body axis -relationship: attaches_to_part_of UBERON:0005944 ! axial skeleton plus cranial skeleton +intersection_of: RO:0002177 UBERON:0005944 ! attached to part of axial skeleton plus cranial skeleton relationship: part_of UBERON:0013700 ! axial musculature +relationship: RO:0002177 UBERON:0005944 ! attached to part of axial skeleton plus cranial skeleton [Term] id: UBERON:0003898 @@ -207965,14 +205429,12 @@ xref: VHOG:0000535 xref: XAO:0003216 xref: ZFA:0000046 is_a: UBERON:0001781 ! layer of retina -is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0001781 ! layer of retina -intersection_of: immediate_transformation_of UBERON:0005425 ! presumptive neural retina -relationship: developmentally_induced_by UBERON:0005426 ! lens vesicle +intersection_of: RO:0002495 UBERON:0005425 ! immediate transformation of presumptive neural retina relationship: has_part CL:0000210 ! photoreceptor cell -relationship: immediate_transformation_of UBERON:0005425 {source="Bgee:AN"} ! presumptive neural retina -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000535", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} +relationship: RO:0002256 UBERON:0005426 ! developmentally induced by lens vesicle +relationship: RO:0002495 UBERON:0005425 {source="Bgee:AN"} ! immediate transformation of presumptive neural retina +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003909 @@ -207991,9 +205453,6 @@ xref: TAO:0005261 xref: Wikipedia:Sinusoid_(blood_vessel) xref: ZFA:0005261 is_a: UBERON:2005260 {source="Wikipedia", source="ZFA"} ! fenestrated capillary -property_value: UBPROP:0000001 "Fenestrated blood vessel endothelium with pores that are large enough for blood cells to pass. The basal lamina and gap junctions may be discontinuous.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005261", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000007 "sinusoidal" xsd:string -property_value: UBPROP:0000012 "some sources give discontinuous capillary as synonym but this may be a subtype - see FMA:63198 discontinuous sinusoid (undefined)." xsd:string {external_ontology="FMA"} [Term] id: UBERON:0003910 @@ -208010,15 +205469,14 @@ is_a: UBERON:0003497 ! abdomen blood vessel is_a: UBERON:0003909 ! sinusoid intersection_of: UBERON:0003909 ! sinusoid intersection_of: part_of UBERON:0001250 ! red pulp of spleen -relationship: connected_to UBERON:0010400 ! spleen trabecular vein -relationship: never_in_taxon NCBITaxon:10088 {source="http://www.informatics.jax.org/greenbook/chapters/chapter13.shtml"} ! Mus -relationship: never_in_taxon NCBITaxon:9681 {source="http://www.informatics.jax.org/greenbook/chapters/chapter13.shtml"} ! Felidae -relationship: never_in_taxon NCBITaxon:9822 {source="http://www.informatics.jax.org/greenbook/chapters/chapter13.shtml"} -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0001250 ! red pulp of spleen -relationship: present_in_taxon NCBITaxon:10114 {source="http://www.informatics.jax.org/greenbook/chapters/chapter13.shtml"} -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000008 "Whereas man and the rat are in the 'sinusal' group, the mouse belongs in the 'nonsinusal' group. The red pulp of spleens of rat, dog, man, and many other mammals contains an elaborate plexus of sinuses; that of mouse, cat, pig and others has no true sinuses and relatively few veins leading from the meshes into collecting veins - http://www.informatics.jax.org/greenbook/chapters/chapter13.shtml" xsd:string +relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia +relationship: RO:0002170 UBERON:0010400 ! connected to spleen trabecular vein +property_value: RO:0002161 NCBITaxon:10088 {source="http://www.informatics.jax.org/greenbook/chapters/chapter13.shtml"} +property_value: RO:0002161 NCBITaxon:9681 {source="http://www.informatics.jax.org/greenbook/chapters/chapter13.shtml"} +property_value: RO:0002161 NCBITaxon:9822 {source="http://www.informatics.jax.org/greenbook/chapters/chapter13.shtml"} +property_value: RO:0002175 NCBITaxon:10114 {source="http://www.informatics.jax.org/greenbook/chapters/chapter13.shtml"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003911 @@ -208029,17 +205487,15 @@ synonym: "choroid plexus epithelial tissue" EXACT [OBOL:automatic] synonym: "epithelial tissue of chorioid plexus of cerebral hemisphere" EXACT [OBOL:automatic] synonym: "epithelial tissue of choroid plexus" EXACT [OBOL:automatic] synonym: "epithelium of choroid plexus" EXACT [FMA:242811] -xref: BTO:0006008 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: EMAPA:36608 xref: FMA:242811 xref: MA:0000824 xref: NCIT:C42079 xref: UMLS:C1516506 {source="ncithesaurus:Choroid_Plexus_Epithelium"} -is_a: UBERON:0000483 ! epithelium +is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001886 ! choroid plexus relationship: part_of UBERON:0001886 ! choroid plexus -property_value: UBPROP:0000010 "The CP epithelial layer is continuous with the ependymal cell layer that lines the ventricles, but unlike the ependyma, the epithelial layer has tight gap junctions between the cells on the side facing the ventricle (apical surface). These gap junctions prevent the majority of substances from crossing the cell layer into the CSF; thus the CP acts as a blood-CSF barrier" xsd:string [Term] id: UBERON:0003913 @@ -208052,7 +205508,7 @@ synonym: "tooth-like organ" EXACT [http://orcid.org/0000-0002-6601-2165] xref: HAO:0001019 is_a: UBERON:0004765 ! skeletal element relationship: capable_of_part_of GO:0071626 ! mastication -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria [Term] id: UBERON:0003914 @@ -208062,12 +205518,10 @@ def: "Epithelial tubes transport gases, liquids and cells from one site to anoth synonym: "epithelial or endothelial tube" EXACT [] xref: AEO:0000114 xref: EHDAA2:0003114 -xref: FBbt:00007474 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000025 ! tube is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium -intersection_of: has_quality PATO:0002299 ! tubular -property_value: IAO:0000232 "contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers" xsd:string +intersection_of: RO:0000086 PATO:0002299 ! has quality tubular [Term] id: UBERON:0003915 @@ -208077,7 +205531,7 @@ def: "Any endothelium that has the quality of being cylindrical [Automatically g is_a: UBERON:0001986 ! endothelium is_a: UBERON:0003914 ! epithelial tube intersection_of: UBERON:0001986 ! endothelium -intersection_of: has_quality PATO:0002299 ! tubular +intersection_of: RO:0000086 PATO:0002299 ! has quality tubular [Term] id: UBERON:0003918 @@ -208088,9 +205542,9 @@ subset: pheno_slim synonym: "mesenchyme of kidney" EXACT [] is_a: UBERON:0003104 ! mesenchyme intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: has_potential_to_develop_into UBERON:0002113 ! kidney -relationship: has_potential_to_develop_into UBERON:0002113 ! kidney -property_value: editor_note "check this" xsd:string +intersection_of: RO:0002387 UBERON:0002113 ! has potential to develop into kidney +relationship: RO:0002387 UBERON:0002113 ! has potential to develop into kidney +property_value: IAO:0000116 "check this" xsd:string [Term] id: UBERON:0003920 @@ -208108,7 +205562,7 @@ is_a: UBERON:0001981 ! blood vessel intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0004582 ! venous system relationship: part_of UBERON:0004582 ! venous system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003921 @@ -208133,13 +205587,11 @@ xref: ZFA:0000254 is_a: UBERON:0001048 ! primordium is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0001048 ! primordium -intersection_of: has_potential_to_develop_into UBERON:0001264 ! pancreas -relationship: develops_from UBERON:0000925 {source="Wikipedia"} ! endoderm -relationship: has_potential_to_develop_into UBERON:0001264 ! pancreas +intersection_of: RO:0002387 UBERON:0001264 ! has potential to develop into pancreas relationship: part_of UBERON:0007026 ! presumptive gut -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png" xsd:anyURI -property_value: UBPROP:0000012 "in EHDAA2 this has dorsal and ventral primordia as parts. the buds are part of the primordium, with the ducts developing from the buds; only parenchyma and ducts have contribution from buds" xsd:string {external_ontology="EHDAA2"} -property_value: UBPROP:0000013 "revisit after standardizing terms 'primordium', 'anlagen', 'bud'" xsd:string +relationship: RO:0002202 UBERON:0000925 {source="Wikipedia"} ! develops from endoderm +relationship: RO:0002387 UBERON:0001264 ! has potential to develop into pancreas +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png" xsd:anyURI [Term] id: UBERON:0003922 @@ -208162,13 +205614,13 @@ xref: ZFA:0001390 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0005911 ! endo-epithelium is_a: UBERON:0007499 {source="EHDAA2"} ! epithelial sac -relationship: develops_from UBERON:0001041 {source="Wikipedia:Pancreas#Embryological_development"} ! foregut -relationship: develops_from UBERON:0001555 ! digestive tract -relationship: develops_from UBERON:0002114 {exception="zebrafish", source="Wikipedia:Pancreatic_bud"} ! duodenum -relationship: develops_from UBERON:0009497 {source="EHDAA2-inferred"} ! epithelium of foregut-midgut junction relationship: part_of UBERON:0003921 {source="EHDAA2"} ! pancreas primordium -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/49/Suckale08FBS_fig1_pancreas_development.jpeg" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png" xsd:anyURI +relationship: RO:0002202 UBERON:0001041 {source="Wikipedia:Pancreas#Embryological_development"} ! develops from foregut +relationship: RO:0002202 UBERON:0001555 ! develops from digestive tract +relationship: RO:0002202 UBERON:0002114 ! develops from duodenum +relationship: RO:0002202 UBERON:0009497 {source="EHDAA2-inferred"} ! develops from epithelium of foregut-midgut junction +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/49/Suckale08FBS_fig1_pancreas_development.jpeg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png" xsd:anyURI [Term] id: UBERON:0003923 @@ -208195,13 +205647,11 @@ xref: Wikipedia:Pancreatic_bud xref: XAO:0000467 xref: ZFA:0001370 is_a: UBERON:0003922 ! pancreatic epithelial bud -relationship: developmentally_induced_by UBERON:0002328 {gci_relation="part_of", gci_filler="NCBITaxon:10088", source="PMID:16417468"} ! notochord -relationship: developmentally_induced_by UBERON:0005805 {gci_relation="part_of", gci_filler="NCBITaxon:10088", source="PMID:16417468"} ! dorsal aorta -relationship: develops_from UBERON:0001045 {source="XAO"} ! midgut relationship: part_of UBERON:0010375 {source="EHDAA2"} ! pancreas dorsal primordium -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png" xsd:anyURI -property_value: UBPROP:0000001 "The pancreatic bud that gives rise to the accessory pancreatic duct.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011031", ontology="AAO", source="XAO:curator"} -property_value: UBPROP:0000003 "In chick, Xenopus laevis, and the teleost fish Medaka, the pancreas develops from three buds that emerge from the gut tube, two from its ventral aspect, and one from its dorsal aspect. In mouse, although there are initially three buds that arise from the gut tube at the point of contact between the endoderm and the vasculature, the pancreas develops from only two of these buds, one dorsal and one ventral. (...) In this study, we use a transgenic zebrafish line (...). We provide evidence for the existence of two distinct pancreatic anlagen - a ventral anterior bud and a dorsal posterior bud - that join to form the definitive pancreas (reference 1); The pancreas develops from the fusion of distinct endoderm-derived dorsal and ventral diverticula. In humans, by day 35 of development, the ventral pancreatic bud begins to migrate backwards and comes into contact and eventually fuses with the dorsal pancreatic bud during the sixth week of development (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001428", ontology="VHOG", source="DOI:10.1016/S0012-1606(03)00308-7 Field HA, Dong PD, Beis D, Stainier DY, Formation of the digestive system in zebrafish. II. Pancreas morphogenesis. Developmental Biology (2003), DOI:10.2337/diabetes.49.2.225 Polak M, Bouchareb-Banaei L, Scharfmann R, Czernichow P, Early pattern of differentiation in the human pancreas. Diabetes (2000)", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0001045 {source="XAO"} ! develops from midgut +relationship: RO:0002256 UBERON:0002328 {gci_relation="part_of", gci_filler="NCBITaxon:10088", source="PMID:16417468"} ! developmentally induced by notochord +relationship: RO:0002256 UBERON:0005805 {gci_relation="part_of", gci_filler="NCBITaxon:10088", source="PMID:16417468"} ! developmentally induced by dorsal aorta +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png" xsd:anyURI [Term] id: UBERON:0003924 @@ -208227,12 +205677,9 @@ xref: Wikipedia:Pancreatic_bud xref: XAO:0001103 xref: ZFA:0001369 is_a: UBERON:0003922 ! pancreatic epithelial bud -relationship: develops_from UBERON:0008835 {source="PMID:16417468", source="WP"} ! hepatic diverticulum relationship: part_of UBERON:0010376 {source="EHDAA2"} ! pancreas ventral primordium -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png" xsd:anyURI -property_value: UBPROP:0000003 "In chick, Xenopus laevis, and the teleost fish Medaka, the pancreas develops from three buds that emerge from the gut tube, two from its ventral aspect, and one from its dorsal aspect. In mouse, although there are initially three buds that arise from the gut tube at the point of contact between the endoderm and the vasculature, the pancreas develops from only two of these buds, one dorsal and one ventral. (...) In this study, we use a transgenic zebrafish line (...). We provide evidence for the existence of two distinct pancreatic anlagen - a ventral anterior bud and a dorsal posterior bud - that join to form the definitive pancreas (reference 1); The pancreas develops from the fusion of distinct endoderm-derived dorsal and ventral diverticula. In humans, by day 35 of development, the ventral pancreatic bud begins to migrate backwards and comes into contact and eventually fuses with the dorsal pancreatic bud during the sixth week of development (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001429", ontology="VHOG", source="DOI:10.1016/S0012-1606(03)00308-7 Field HA, Dong PD, Beis D, Stainier DY, Formation of the digestive system in zebrafish. II. Pancreas morphogenesis. Developmental Biology (2003), DOI:10.2337/diabetes.49.2.225 Polak M, Bouchareb-Banaei L, Scharfmann R, Czernichow P, Early pattern of differentiation in the human pancreas. Diabetes (2000)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000011 "the ventral pancreas and liver are derived from a common precursor cell population[PMID:16417468]. TODO - add this relationship." xsd:string -property_value: UBPROP:0000011 "The ventral pancreatic bud becomes the head and uncinate process, and comes from the hepatic diverticulum[WP]" xsd:string +relationship: RO:0002202 UBERON:0008835 {source="PMID:16417468", source="WP"} ! develops from hepatic diverticulum +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/db/Gray982.png" xsd:anyURI [Term] id: UBERON:0003928 @@ -208266,7 +205713,6 @@ synonym: "gut epithelium" EXACT [EHDAA2:0004567, MA:0003201, ZFA:0005123] xref: BTO:0000956 xref: EHDAA2:0004567 xref: EMAPA:32928 -xref: FBbt:00047166 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: MA:0003201 xref: NCIT:C12963 xref: TAO:0005123 @@ -208277,8 +205723,6 @@ is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001555 ! digestive tract relationship: part_of UBERON:0001555 ! digestive tract -property_value: UBPROP:0000001 "Epithelium lining the lumen of the gut.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005123", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000008 "" xsd:string [Term] id: UBERON:0003931 @@ -208332,7 +205776,6 @@ is_a: UBERON:0007844 ! cartilage element intersection_of: UBERON:0007844 ! cartilage element intersection_of: part_of UBERON:0010323 ! cranial skeletal system relationship: part_of UBERON:0010323 ! cranial skeletal system -property_value: UBPROP:0000001 "Cartilage which is part of the cranium.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001458", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0003937 @@ -208347,7 +205790,6 @@ synonym: "gland of reproductive system" EXACT [OBOL:automatic] synonym: "reproductive gland" EXACT [MA:0001751] synonym: "reproductive system gland" EXACT [OBOL:automatic] synonym: "sex gland" EXACT [MP:0000653] -xref: BTO:0006162 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: MA:0001751 is_a: UBERON:0002530 ! gland is_a: UBERON:0005156 ! reproductive structure @@ -208370,8 +205812,6 @@ xref: Wikipedia:Somatosensory_system is_a: UBERON:0001032 ! sensory system relationship: capable_of_part_of GO:0019233 ! sensory perception of pain relationship: capable_of_part_of GO:0050975 ! sensory perception of touch -property_value: UBPROP:0000001 "The neural tissue involved in the transmission of sensory signals" xsd:string {source="MP:0000959"} -property_value: UBPROP:0000012 "MP defines this in a may more appropriate to somatosensory cortex" xsd:string {external_ontology="MP"} [Term] id: UBERON:0003946 @@ -208382,12 +205822,12 @@ subset: pheno_slim synonym: "labyrinthine layer" EXACT [GO:0060713] synonym: "labyrinthine layer of placenta" EXACT [GO:0060713] synonym: "placental labyrinth" EXACT [] +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005156 ! reproductive structure -relationship: contributes_to_morphology_of UBERON:0001987 ! placenta -relationship: never_in_taxon NCBITaxon:9606 {source="http://placentation.ucsd.edu"} ! Homo sapiens relationship: part_of UBERON:0001987 ! placenta +relationship: RO:0002433 UBERON:0001987 ! contributes to morphology of placenta +property_value: RO:0002161 NCBITaxon:9606 {source="http://placentation.ucsd.edu"} property_value: seeAlso "http://placentation.ucsd.edu/placenta.html" xsd:anyURI -property_value: UBPROP:0000008 "Mouse-human differences: The mouse and human placentas have labyrinthine and villous types of interdigitation between maternal and fetal tissues, respectively ... The mouse placental labyrinth is composed of an intricate network of maternal blood spaces and embryonal blood vessels. Maternal and embryonal blood is separated by a placental barrier that consists of four cellular layers: layer I trophoblasts line the maternal lacunae, trophoblasts in layers II and III form syncytial-like layers, and endothelial cells line the embryonic vessels[DOI: 10.1073/pnas.96.14.8138 ]" xsd:string [Term] id: UBERON:0003947 @@ -208395,13 +205835,14 @@ name: brain ventricle/choroid plexus namespace: uberon def: "The brain ventricles or their associated choroid plexuses." [MP:0002200] subset: pheno_slim +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010000 ! multicellular anatomical structure union_of: UBERON:0001886 ! choroid plexus union_of: UBERON:0004086 ! brain ventricle -relationship: contributes_to_morphology_of UBERON:0000955 ! brain relationship: part_of UBERON:0000955 ! brain -property_value: editor_note "TODO - check relationship between CP and BV. If this is part of then this class should be obsoleted" xsd:string -property_value: editor_note "TODO merge into BV" xsd:string +relationship: RO:0002433 UBERON:0000955 ! contributes to morphology of brain +property_value: IAO:0000116 "TODO - check relationship between CP and BV. If this is part of then this class should be obsoleted" xsd:string +property_value: IAO:0000116 "TODO merge into BV" xsd:string [Term] id: UBERON:0003952 @@ -208414,13 +205855,14 @@ synonym: "anterior stroma" BROAD [MP:0003093] synonym: "cornea anterior stroma" EXACT [MP:0003093] xref: EMAPA:37414 {source="MA:th"} is_a: UBERON:0003566 ! head connective tissue +is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0002384 ! connective tissue -intersection_of: in_anterior_side_of UBERON:0001777 ! substantia propria of cornea +intersection_of: BSPO:0000123 UBERON:0001777 ! substantia propria of cornea disjoint_from: UBERON:0003953 {source="lexical"} ! posterior stroma of cornea -relationship: contributes_to_morphology_of UBERON:0001777 ! substantia propria of cornea -relationship: in_anterior_side_of UBERON:0001777 ! substantia propria of cornea +relationship: BSPO:0000123 UBERON:0001777 ! substantia propria of cornea relationship: part_of UBERON:0001777 ! substantia propria of cornea -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002433 UBERON:0001777 ! contributes to morphology of substantia propria of cornea +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003953 @@ -208432,11 +205874,12 @@ synonym: "cornea posterior stroma" EXACT [MP:0003094] synonym: "posterior stroma" BROAD [MP:0003094] xref: EMAPA:37415 {source="MA:th"} is_a: UBERON:0003566 ! head connective tissue +is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0002384 ! connective tissue -intersection_of: in_posterior_side_of UBERON:0001777 ! substantia propria of cornea -relationship: contributes_to_morphology_of UBERON:0001777 ! substantia propria of cornea -relationship: in_posterior_side_of UBERON:0001777 ! substantia propria of cornea +intersection_of: BSPO:0000122 UBERON:0001777 ! substantia propria of cornea +relationship: BSPO:0000122 UBERON:0001777 ! substantia propria of cornea relationship: part_of UBERON:0001777 ! substantia propria of cornea +relationship: RO:0002433 UBERON:0001777 ! contributes to morphology of substantia propria of cornea [Term] id: UBERON:0003956 @@ -208446,6 +205889,7 @@ def: "The structures associated with drainage of the aqueous humor from the eye, subset: pheno_slim xref: EMAPA:37427 {source="MA:th"} is_a: UBERON:0000467 ! anatomical system +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001768 ! uvea [Term] @@ -208470,10 +205914,10 @@ is_a: UBERON:0005156 ! reproductive structure relationship: channel_for CL:0000019 ! sperm relationship: channels_from UBERON:0001343 ! seminiferous tubule of testis relationship: channels_into UBERON:0006946 ! efferent duct -relationship: develops_from UBERON:0005297 {source="Wikipedia"} ! testis sex cord relationship: part_of UBERON:0005051 ! mediastinum testis -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b5/Hodenschema.svg" xsd:anyURI -property_value: editor_note "add more specific classification e.g. anastomosing network - consider FMA:3726" xsd:string +relationship: RO:0002202 UBERON:0005297 {source="Wikipedia"} ! develops from testis sex cord +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b5/Hodenschema.svg" xsd:anyURI +property_value: IAO:0000116 "add more specific classification e.g. anastomosing network - consider FMA:3726" xsd:string [Term] id: UBERON:0003967 @@ -208485,10 +205929,11 @@ synonym: "cutaneous elastic fiber" NARROW [MP:0008418] synonym: "dermal elastic fiber" NARROW [MP:0008418] xref: EMAPA:37841 {source="MA:th"} is_a: UBERON:0002521 ! elastic tissue +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0002521 ! elastic tissue intersection_of: part_of UBERON:0000014 ! zone of skin -relationship: contributes_to_morphology_of UBERON:0000014 ! zone of skin relationship: part_of UBERON:0000014 ! zone of skin +relationship: RO:0002433 UBERON:0000014 ! contributes to morphology of zone of skin [Term] id: UBERON:0003970 @@ -208524,7 +205969,7 @@ is_a: UBERON:0003134 ! female reproductive organ is_a: UBERON:0004175 ! internal genitalia intersection_of: UBERON:0004175 ! internal genitalia intersection_of: part_of UBERON:0000474 ! female reproductive system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003978 @@ -208539,9 +205984,8 @@ xref: FMA:67611 xref: galen:Valve is_a: UBERON:0000064 ! organ part relationship: capable_of GO:0065008 ! regulation of biological quality -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI -property_value: UBPROP:0000007 "valvular" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI [Term] id: UBERON:0003980 @@ -208568,7 +206012,6 @@ is_a: UBERON:0014466 ! subarachnoid fissure intersection_of: UBERON:0014466 ! subarachnoid fissure intersection_of: part_of UBERON:0002037 ! cerebellum relationship: part_of UBERON:0002037 ! cerebellum -property_value: UBPROP:0000202 FMA:77789 [Term] id: UBERON:0003981 @@ -208584,7 +206027,7 @@ xref: MA:0001710 xref: NCIT:C33400 xref: UMLS:C1514441 {source="ncithesaurus:Primordial_Follicle"} is_a: UBERON:0001305 ! ovarian follicle -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003983 @@ -208595,10 +206038,7 @@ xref: AAO:0010250 xref: Wikipedia:Conus_arteriosus is_a: UBERON:0004151 ! cardiac chamber relationship: part_of UBERON:0002080 ! heart right ventricle -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/46/Gray492.png" xsd:anyURI -property_value: UBPROP:0000001 "Receives blood from the left atrium and becomes the median truncus arteriosus.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010250", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000008 "Kardong says absent in adult tetrapods, check AAO" xsd:string -property_value: UBPROP:0000013 "we use the term CA for the anterior chamber if it is composed of cardiac muscle, contractile, and contains conal valves internally" xsd:string {source="ISBN:0073040584"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/46/Gray492.png" xsd:anyURI [Term] id: UBERON:0003984 @@ -208617,13 +206057,11 @@ xref: FMA:18307 xref: SCTID:362262001 xref: Wikipedia:Infundibulum_of_uterine_tube is_a: UBERON:0013515 {source="FMA"} ! subdivision of oviduct -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0003889 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="FMA"} ! fallopian tube -relationship: present_in_taxon NCBITaxon:8782 ! Aves -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cervix.jpg" xsd:anyURI -property_value: UBPROP:0000001 "The third part of the uterine tube is the infundibulum. It terminates with the ostium of Fallopian tube, surrounded by fimbriae, one of which is attached to the ovary[Wikipedia:Infundibulum_of_uterine_tube]." xsd:string {source="Wikipedia:Infundibulum_of_uterine_tube"} -property_value: UBPROP:0000008 "In mammals, the uterine tube infundibulum is part of the fallopian tube. In birds, where there is no fallopian tube, the uterine tube infundibulum is part of the oviduct." xsd:string {xref="https://orcid.org/0000-0002-2825-0621"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cervix.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:8782 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003988 @@ -208642,11 +206080,11 @@ synonym: "thymus corticomedullary junction" EXACT [MP:0009543] synonym: "thymus corticomedullary zone" EXACT [MP:0009543] xref: EMAPA:37974 {source="MA:th"} is_a: PR:000050567 ! protein-containing material entity +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0007651 ! anatomical junction intersection_of: UBERON:0007651 ! anatomical junction intersection_of: overlaps UBERON:0002123 ! cortex of thymus intersection_of: overlaps UBERON:0002124 ! medulla of thymus -relationship: contributes_to_morphology_of UBERON:0002125 ! thymus lobule relationship: has_part CL:0000451 ! dendritic cell relationship: has_part CL:0000542 ! lymphocyte relationship: has_part CL:0000881 ! perivascular macrophage @@ -208654,7 +206092,8 @@ relationship: has_part UBERON:0001980 ! arteriole relationship: overlaps UBERON:0002123 ! cortex of thymus relationship: overlaps UBERON:0002124 ! medulla of thymus relationship: part_of UBERON:0002125 ! thymus lobule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002433 UBERON:0002125 ! contributes to morphology of thymus lobule +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003990 @@ -208663,8 +206102,8 @@ namespace: uberon def: "The subclasses of motor neurons which are organized into longitudinally oriented columns that occupy distinct and, in some cases, discontinuous domains along the rostrocaudal axis of the spinal cord; motor neurons within a single column send their axons to a common peripheral target." [MP:0009685] subset: pheno_slim is_a: UBERON:0016550 ! spinal cord column -relationship: composed_primarily_of CL:0000100 ! motor neuron -relationship: contributes_to_morphology_of UBERON:0002240 ! spinal cord +relationship: RO:0002433 UBERON:0002240 ! contributes to morphology of spinal cord +relationship: RO:0002473 CL:0000100 ! composed primarily of motor neuron [Term] id: UBERON:0004001 @@ -208679,9 +206118,9 @@ is_a: UBERON:0011215 ! central nervous system cell part cluster is_a: UBERON:0022303 ! nervous system cell part layer intersection_of: UBERON:0022303 ! nervous system cell part layer intersection_of: part_of UBERON:0002264 ! olfactory bulb -relationship: contributes_to_morphology_of UBERON:0002264 ! olfactory bulb relationship: part_of UBERON:0002264 ! olfactory bulb -property_value: editor_note "TODO - check isa parentage" xsd:string +relationship: RO:0002433 UBERON:0002264 ! contributes to morphology of olfactory bulb +property_value: IAO:0000116 "TODO - check isa parentage" xsd:string [Term] id: UBERON:0004015 @@ -208708,7 +206147,6 @@ synonym: "epimere mesoderm" RELATED [] synonym: "mesenchyma dermatomiale" RELATED OMO:0003011 [Wikipedia:Dermatomal_mesenchyme] xref: AAO:0011028 xref: AEO:0001017 -xref: BTO:0006248 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: EHDAA2_RETIRED:0003428 xref: EHDAA:1719 xref: EHDAA:1725 @@ -208721,9 +206159,8 @@ xref: UMLS:C0180383 {source="ncithesaurus:Dermatome"} xref: Wikipedia:Dermatome_(embryology) xref: XAO:0000220 is_a: UBERON:0017650 {source="AEO"} ! developing mesenchymal structure -relationship: develops_from UBERON:0004290 {source="EHDAA2-abduced"} ! dermomyotome -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/f3/Gray64.png" xsd:anyURI -property_value: UBPROP:0000013 "Not to be confused with 'dermatome segment of skin'." xsd:string +relationship: RO:0002202 UBERON:0004290 {source="EHDAA2-abduced"} ! develops from dermomyotome +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f3/Gray64.png" xsd:anyURI [Term] id: UBERON:0004021 @@ -208736,15 +206173,13 @@ synonym: "spongiotrophoblast layer of placenta" EXACT [] xref: BTO:0005402 xref: EMAPA:31876 is_a: UBERON:0000119 ! cell layer +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005156 ! reproductive structure is_a: UBERON:0005292 ! extraembryonic tissue -relationship: composed_primarily_of CL:0002499 ! spongiotrophoblast cell -relationship: develops_from UBERON:0004364 {source="PMID:19829370"} ! ectoplacental cone -relationship: only_in_taxon NCBITaxon:9989 {source="MP:0004255", source="PMID:11433360"} ! Rodentia relationship: part_of UBERON:0001987 ! placenta -property_value: UBPROP:0000008 "restriction to Rodentia may be too strong - we apply it for now as we are inheriting the MP definition" xsd:string -property_value: UBPROP:0000010 "Forms a compact layer of non-syncytial cells between the labyrinth and the outer giant cells" xsd:string -property_value: UBPROP:0000011 "In the absence of direct lineage analysis, it has been assumed, from histological studies and from the continuity of marker gene expression, that the spongiotrophoblast largely derives from the cells of the ectoplacental cone" xsd:string {source="PMID:19829370"} +relationship: RO:0002160 NCBITaxon:9989 {source="MP:0004255", source="PMID:11433360"} ! only in taxon Rodentia +relationship: RO:0002202 UBERON:0004364 {source="PMID:19829370"} ! develops from ectoplacental cone +relationship: RO:0002473 CL:0002499 ! composed primarily of spongiotrophoblast cell [Term] id: UBERON:0004022 @@ -208756,12 +206191,12 @@ synonym: "germinal neuroepithelial layer" EXACT [http://orcid.org/0000-0002-6601 synonym: "germinal neuroepithelium" EXACT [NCBIBook:NBK10047] synonym: "original neural tube" EXACT [NCBIBook:NBK10047] is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0034706 {source="NCBIBook:NBK10047"} ! proliferating neuroepithelium disjoint_from: UBERON:0006934 ! sensory epithelium relationship: adjacent_to UBERON:0003842 ! neural tube lumen relationship: bounding_layer_of UBERON:0001049 ! neural tube relationship: part_of UBERON:0001049 ! neural tube -property_value: UBPROP:0000011 "As the cells adjacent to the lumen continue to divide, the migrating cells form a second layer around the original neural tube. This layer becomes progressively thicker as more cells are added to it from the germinal neuroepithelium. This new layer is called the mantle (or intermediate) zone, and the germinal epithelium is now called the ventricular zone (and, later, the ependyma)[NCBIBook:NBK10047]" xsd:string [Term] id: UBERON:0004023 @@ -208784,7 +206219,6 @@ xref: PBA:128012818 xref: Wikipedia:Ganglionic_eminence is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0001016 ! nervous system -property_value: UBPROP:0000011 "contributes significantly in building up the GABAergic cortical cell population[WP]" xsd:string [Term] id: UBERON:0004024 @@ -208798,8 +206232,8 @@ xref: EMAPA:37471 {source="MA:th"} xref: PBA:128012834 is_a: UBERON:0002050 ! embryonic structure disjoint_from: UBERON:0004025 {source="lexical"} ! lateral ganglionic eminence -relationship: contributes_to_morphology_of UBERON:0004023 ! ganglionic eminence relationship: part_of UBERON:0004023 ! ganglionic eminence +relationship: RO:0002433 UBERON:0004023 ! contributes to morphology of ganglionic eminence [Term] id: UBERON:0004025 @@ -208812,8 +206246,8 @@ xref: DHBA:10551 xref: EMAPA:37470 {source="MA:th"} xref: PBA:128012822 is_a: UBERON:0002050 ! embryonic structure -relationship: contributes_to_morphology_of UBERON:0004023 ! ganglionic eminence relationship: part_of UBERON:0004023 ! ganglionic eminence +relationship: RO:0002433 UBERON:0004023 ! contributes to morphology of ganglionic eminence [Term] id: UBERON:0004026 @@ -208828,8 +206262,8 @@ xref: EFO:0001911 xref: EMAPA:37469 {source="MA:th"} xref: PBA:128012846 is_a: UBERON:0002050 ! embryonic structure -relationship: contributes_to_morphology_of UBERON:0004023 ! ganglionic eminence relationship: part_of UBERON:0004023 ! ganglionic eminence +relationship: RO:0002433 UBERON:0004023 ! contributes to morphology of ganglionic eminence [Term] id: UBERON:0004027 @@ -208843,13 +206277,14 @@ xref: EMAPA:31872 xref: NCIT:C34123 xref: SCTID:256391000 xref: UMLS:C0230972 {source="ncithesaurus:Chorionic_Plate"} +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005156 ! reproductive structure is_a: UBERON:0005292 ! extraembryonic tissue -relationship: contributes_to_morphology_of UBERON:0003124 ! chorion membrane relationship: part_of UBERON:0003124 ! chorion membrane relationship: part_of UBERON:8600038 ! placental disc -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Placenta.glb" xsd:anyURI +relationship: RO:0002433 UBERON:0003124 ! contributes to morphology of chorion membrane +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Placenta.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004035 @@ -208866,7 +206301,6 @@ xref: EMAPA:32703 xref: https://upload.wikimedia.org/wikipedia/commons/thumb/a/ac/Corticogenesis_in_a_wild-type_mouse_with_captions_in_english_copy.png/360px-Corticogenesis_in_a_wild-type_mouse_with_captions_in_english_copy.png xref: neuronames:3233 xref: PBA:294021932 -xref: VO:0011276 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: Wikipedia:Subplate is_a: UBERON:0014950 ! layer of developing cerebral cortex intersection_of: UBERON:0014950 ! layer of developing cerebral cortex @@ -208874,8 +206308,7 @@ intersection_of: adjacent_to UBERON:0004040 ! cortical intermediate zone intersection_of: adjacent_to UBERON:0005343 ! cortical plate relationship: adjacent_to UBERON:0004040 ! cortical intermediate zone relationship: adjacent_to UBERON:0005343 ! cortical plate -relationship: develops_from UBERON:0034711 ! cortical preplate -property_value: UBPROP:0000011 "The transient fetal subplate zone, together with the marginal zone and the cortical plate, represents the developmental anlage of the mammalian cerebral cortex. It serves as a waiting compartment for growing cortical afferents; its cells are involved in the establishment of pioneering cortical efferent projections and transient fetal circuitry, and apparently have a number of other developmental roles. The subplate zone is a phylogenetically recent structure and it is most developed in the human brain. Subplate neurons are among the first generated neurons in the mammalian cerebral cortex [1]. These neurons disappear during postnatal development and are important in establishing the correct wiring [2][3] and functional maturation [4] of the cerebral cortex. Subplate neurons appear to be selectively sensitive to injury (such as hypoxia) which in humans are associated with motor and cognitive defects" xsd:string {source="WP"} +relationship: RO:0002202 UBERON:0034711 ! develops from cortical preplate [Term] id: UBERON:0004040 @@ -208890,8 +206323,8 @@ synonym: "IZ" BROAD OMO:0003000 [BRAINSPAN:BRAINSPAN] xref: EMAPA:17545 xref: EMAPA:32712 is_a: UBERON:0014950 ! layer of developing cerebral cortex -relationship: develops_from UBERON:0004061 ! neural tube mantle layer -relationship: only_in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia +relationship: RO:0002160 NCBITaxon:40674 {source="Wikipedia"} ! only in taxon Mammalia +relationship: RO:0002202 UBERON:0004061 ! develops from neural tube mantle layer [Term] id: UBERON:0004041 @@ -208907,8 +206340,7 @@ is_a: UBERON:0001249 ! spleen lymphoid follicle is_a: UBERON:0010422 ! primary nodular lymphoid tissue intersection_of: UBERON:0010422 ! primary nodular lymphoid tissue intersection_of: part_of UBERON:0002106 ! spleen -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000012 "FMA:15843 is classified as primary follicle so it belongs here" xsd:string {external_ontology="FMA"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004042 @@ -208924,8 +206356,8 @@ is_a: UBERON:0001249 ! spleen lymphoid follicle is_a: UBERON:0001745 ! secondary nodular lymphoid tissue intersection_of: UBERON:0001745 ! secondary nodular lymphoid tissue intersection_of: part_of UBERON:0002106 ! spleen -relationship: develops_from UBERON:0004041 {source="CL:tm"} ! spleen primary B follicle -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 UBERON:0004041 {source="CL:tm"} ! develops from spleen primary B follicle +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004043 @@ -208940,10 +206372,11 @@ xref: EMAPA:32831 xref: MA:0002770 xref: SCTID:279759001 xref: Wikipedia:Osseous_ampullae +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010000 ! multicellular anatomical structure relationship: part_of UBERON:0001856 {source="MA"} ! semicircular duct -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/65/Vestibular_system%27s_semicircular_canal-_a_cross-section.jpg" xsd:anyURI -property_value: editor_note "TODO check duct vs canal. Also check FMA - has many subtypes of semicircular canal such as 'ampulla of anterior semicircular canal'" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/65/Vestibular_system%27s_semicircular_canal-_a_cross-section.jpg" xsd:anyURI +property_value: IAO:0000116 "TODO check duct vs canal. Also check FMA - has many subtypes of semicircular canal such as 'ampulla of anterior semicircular canal'" xsd:string [Term] id: UBERON:0004044 @@ -208955,7 +206388,7 @@ synonym: "AVE" RELATED [BTO:0003361] xref: BTO:0003361 xref: EMAPA:36068 is_a: UBERON:0004877 ! visceral endoderm -relationship: seeAlso UBERON:0004341 ! primitive streak +property_value: seeAlso UBERON:0004341 [Term] id: UBERON:0004053 @@ -208979,7 +206412,7 @@ intersection_of: UBERON:0004176 ! external genitalia intersection_of: part_of UBERON:0000079 ! male reproductive system disjoint_from: UBERON:0005056 ! external female genitalia disjoint_from: UBERON:0009196 ! indifferent external genitalia -relationship: contributes_to_morphology_of UBERON:0000079 ! male reproductive system +relationship: RO:0002433 UBERON:0000079 ! contributes to morphology of male reproductive system [Term] id: UBERON:0004054 @@ -208999,8 +206432,8 @@ is_a: UBERON:0003135 ! male reproductive organ is_a: UBERON:0004175 ! internal genitalia intersection_of: UBERON:0004175 ! internal genitalia intersection_of: part_of UBERON:0000079 ! male reproductive system -relationship: contributes_to_morphology_of UBERON:0000079 ! male reproductive system -property_value: editor_note "consider splitting genitalia from genital organ" xsd:string +relationship: RO:0002433 UBERON:0000079 ! contributes to morphology of male reproductive system +property_value: IAO:0000116 "consider splitting genitalia from genital organ" xsd:string [Term] id: UBERON:0004058 @@ -209021,11 +206454,11 @@ xref: EMAPA:37440 {source="MA:th"} xref: TAO:0005164 xref: ZFA:0005164 is_a: UBERON:0000025 ! tube +is_a: UBERON:0004119 ! endoderm-derived structure relationship: adjacent_to UBERON:0001175 ! common hepatic duct relationship: part_of UBERON:0002107 ! liver relationship: part_of UBERON:0002394 {source="BTO"} ! bile duct -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000012 "In ZFA, Digestive system duct that collects bile from the canaliculus and transports bile through the liver -- (check if the same) // The smallest and the most peripheral branches of the biliary tree consist of a portal part (portal ductule) and an intralobular part (intralobular ductule)" xsd:string {external_ontology="ZFA"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004059 @@ -209054,10 +206487,9 @@ is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0034706 {source="NCBIBook:NBK10047"} ! proliferating neuroepithelium relationship: adjacent_to UBERON:0003842 ! neural tube lumen -relationship: immediate_transformation_of UBERON:0004022 {source="NCBIBook:NBK10047"} ! germinal neuroepithelium relationship: part_of UBERON:0001049 ! neural tube -property_value: editor_note "consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure" xsd:string -property_value: UBPROP:0000001 "The layer of undifferentiated, proliferating cells that line the neural tube lumen" xsd:string {source="MP:0009689"} +relationship: RO:0002495 UBERON:0004022 {source="NCBIBook:NBK10047"} ! immediate transformation of germinal neuroepithelium +property_value: IAO:0000116 "consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure" xsd:string [Term] id: UBERON:0004061 @@ -209071,11 +206503,12 @@ xref: EMAPA:17148 xref: EMAPA:35360 xref: neuronames:1367 is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0034707 {source="NCBIBook:NBK10047"} ! differentiating neuroepithelium relationship: adjacent_to UBERON:0004060 ! neural tube ventricular layer relationship: adjacent_to UBERON:0004062 ! neural tube marginal layer -relationship: develops_from UBERON:0004022 {notes="by division", source="NCBIBook:NBK10047"} ! germinal neuroepithelium relationship: part_of UBERON:0001049 ! neural tube +relationship: RO:0002202 UBERON:0004022 ! develops from germinal neuroepithelium [Term] id: UBERON:0004062 @@ -209087,10 +206520,11 @@ synonym: "brain marginal zone" RELATED [] synonym: "neural tube marginal zone" EXACT [MP:0009691] xref: EMAPA:17151 xref: neuronames:1368 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005162 ! multi cell part structure relationship: adjacent_to UBERON:0004061 ! neural tube mantle layer -relationship: develops_from UBERON:0004061 {notes="forms from axons"} ! neural tube mantle layer relationship: part_of UBERON:0001049 ! neural tube +relationship: RO:0002202 UBERON:0004061 ! develops from neural tube mantle layer [Term] id: UBERON:0004063 @@ -209107,9 +206541,9 @@ xref: VHOG:0000899 is_a: UBERON:0005882 ! neural tube alar plate intersection_of: UBERON:0005882 ! neural tube alar plate intersection_of: part_of UBERON:0006241 ! future spinal cord -relationship: contributes_to_morphology_of UBERON:0004061 ! neural tube mantle layer relationship: part_of UBERON:0006241 ! future spinal cord -property_value: editor_note "TODO - merge with UBERON:0003054 roof plate?" xsd:string +relationship: RO:0002433 UBERON:0004061 ! contributes to morphology of neural tube mantle layer +property_value: IAO:0000116 "TODO - merge with UBERON:0003054 roof plate?" xsd:string [Term] id: UBERON:0004064 @@ -209129,12 +206563,13 @@ xref: NCIT:C34111 xref: neuronames:1372 xref: UMLS:C1511061 {source="ncithesaurus:Basal_Plate"} xref: Wikipedia:Basal_plate_(neural_tube) +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue -relationship: contributes_to_morphology_of UBERON:0004061 ! neural tube mantle layer -relationship: developmentally_induced_by UBERON:0002328 {gene="Shh", source="Swenson"} ! notochord +relationship: BSPO:0000102 UBERON:0005478 ! sulcus limitans of neural tube relationship: has_part CL:0000100 ! motor neuron relationship: part_of UBERON:0004061 ! neural tube mantle layer -relationship: ventral_to UBERON:0005478 ! sulcus limitans of neural tube +relationship: RO:0002256 UBERON:0002328 ! developmentally induced by notochord +relationship: RO:0002433 UBERON:0004061 ! contributes to morphology of neural tube mantle layer [Term] id: UBERON:0004066 @@ -209158,8 +206593,8 @@ xref: UMLS:C1517321 {source="ncithesaurus:Frontonasal_Prominence"} xref: VHOG:0001319 xref: Wikipedia:Frontonasal_prominence is_a: UBERON:0009292 ! embryonic nasal process -relationship: intersects_midsagittal_plane_of UBERON:0000033 ! head -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/98/Gray44.png" xsd:anyURI +relationship: BSPO:0005001 UBERON:0000033 ! head +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/98/Gray44.png" xsd:anyURI [Term] id: UBERON:0004067 @@ -209179,9 +206614,9 @@ xref: SCTID:308880000 xref: Wikipedia:Lateral_nasal_prominence is_a: UBERON:0009292 ! embryonic nasal process disjoint_from: UBERON:0004068 {source="lexical"} ! medial nasal prominence -relationship: develops_from UBERON:0004066 {source="Wikipedia"} ! frontonasal prominence relationship: part_of UBERON:0004066 {source="EHDAA2"} ! frontonasal prominence -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray48.png" xsd:anyURI +relationship: RO:0002202 UBERON:0004066 {source="Wikipedia"} ! develops from frontonasal prominence +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray48.png" xsd:anyURI [Term] id: UBERON:0004068 @@ -209202,11 +206637,10 @@ xref: SCTID:308877001 xref: VHOG:0000804 xref: Wikipedia:Medial_nasal_prominence is_a: UBERON:0009292 ! embryonic nasal process -relationship: develops_from UBERON:0004066 {source="Wikipedia"} ! frontonasal prominence -relationship: in_lateral_side_of UBERON:0008816 ! embryonic head +relationship: BSPO:0000126 UBERON:0008816 ! embryonic head relationship: part_of UBERON:0004066 {source="EHDAA2"} ! frontonasal prominence -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/85/Gray45.png" xsd:anyURI -property_value: UBPROP:0000011 "Fusion of right and left medial nasal processes forms a primary palate rostrally and the nasal septum caudally. The incisive bone, including upper incisor teeth and the rostral up- per lip, are derived from the primary palate. The nasal septum consists of bone, cartilage, and a patch of soft tissue membrane that separates right & left halves of the nasal cavity." xsd:string +relationship: RO:0002202 UBERON:0004066 {source="Wikipedia"} ! develops from frontonasal prominence +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/85/Gray45.png" xsd:anyURI [Term] id: UBERON:0004086 @@ -209234,9 +206668,7 @@ xref: UMLS:C0007799 {source="ncithesaurus:Ventricle_Brain"} is_a: UBERON:0003947 ! brain ventricle/choroid plexus is_a: UBERON:0005358 ! ventricle of nervous system relationship: part_of UBERON:0005282 ! ventricular system of brain -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000001 "Organ cavity of the brain which consists of the lateral ventricles, the third and fourth ventricles and the cerebral aqueduct[BIRNLEX:1356]." xsd:string {source="BIRNLEX:1356"} -property_value: UBPROP:0000012 "FMA draws the distinction between e.g. 'fourth ventricle' and 'cavity of fourth ventricle'. The latter is a cavity, and part of the former, which is a region. The superclass of 'fourth ventricle' is_a 'region of ventricular system of the brain'. We place this class here, although it is not equivalent to ventricles, as it includes ventricle bodies." xsd:string {external_ontology="FMA"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004087 @@ -209259,10 +206691,10 @@ xref: UMLS:C0042460 {source="ncithesaurus:Vena_Cava"} xref: Wikipedia:Venae_cavae is_a: UBERON:0003479 ! thoracic cavity vein is_a: UBERON:0013768 ! great vessel of heart -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/35/Relations_of_the_aorta,_trachea,_esophagus_and_other_heart_structures.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/7/7c/Heart_numlabels.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/35/Relations_of_the_aorta,_trachea,_esophagus_and_other_heart_structures.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/7c/Heart_numlabels.png" xsd:anyURI [Term] id: UBERON:0004088 @@ -209280,8 +206712,7 @@ synonym: "orbital part of face" EXACT [http://orcid.org/0000-0002-6601-2165] xref: FMA:260119 is_a: UBERON:0001444 ! subdivision of head relationship: part_of UBERON:0001456 ! face -property_value: editor_note "note the FMA class is more narrow though, and is more like eye + muscles + vasculature. The FMA also has FMA:72951 orbital part of eye" xsd:string -property_value: UBPROP:0000012 "in HP covers eyelid, eyebrow." xsd:string {external_ontology="HP:0000284"} +property_value: IAO:0000116 "note the FMA class is more narrow though, and is more like eye + muscles + vasculature. The FMA also has FMA:72951 orbital part of eye" xsd:string [Term] id: UBERON:0004089 @@ -209292,15 +206723,13 @@ subset: pheno_slim synonym: "lower face" RELATED [] synonym: "midface/lower face" RELATED [] synonym: "snout" RELATED SENSU [MA:0001910] -xref: EMAPA:32806 xref: FMA:285406 xref: MA:0001910 is_a: UBERON:0001444 ! subdivision of head -relationship: contributes_to_morphology_of UBERON:0001456 ! face -relationship: only_in_taxon NCBITaxon:89593 ! Craniata relationship: part_of UBERON:0001456 ! face -property_value: editor_note "this class is currently a union of the snout (e.g. in mouse), the midface and the lower face. Note that in MA, snout includes the whole jaw and should thus be more alike the lower face than the midface, so its placement here is not strictly accurate. In future we might introduce specific classes for each of these, and include the full parthood relationships. if this is done, then care should be taken to preserve inferences such as an abnormality of the lower face being an abnormality of the midface." xsd:string -property_value: UBPROP:0000007 "midfacial" xsd:string +relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata +relationship: RO:0002433 UBERON:0001456 ! contributes to morphology of face +property_value: IAO:0000116 "this class is currently a union of the snout (e.g. in mouse), the midface and the lower face. Note that in MA, snout includes the whole jaw and should thus be more alike the lower face than the midface, so its placement here is not strictly accurate. In future we might introduce specific classes for each of these, and include the full parthood relationships. if this is done, then care should be taken to preserve inferences such as an abnormality of the lower face being an abnormality of the midface." xsd:string [Term] id: UBERON:0004099 @@ -209312,9 +206741,9 @@ synonym: "synovial cavity of elbow joint" EXACT [FMA:38911] xref: FMA:38911 is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0001490 ! elbow joint -relationship: luminal_space_of UBERON:0001490 ! elbow joint +intersection_of: RO:0002572 UBERON:0001490 ! luminal space of elbow joint relationship: part_of UBERON:0001490 ! elbow joint +relationship: RO:0002572 UBERON:0001490 ! luminal space of elbow joint [Term] id: UBERON:0004100 @@ -209331,8 +206760,8 @@ xref: SCTID:279371005 xref: Wikipedia:Collecting_duct_system is_a: UBERON:0000467 ! anatomical system relationship: part_of UBERON:0002113 ! kidney -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004103 @@ -209356,9 +206785,9 @@ xref: SCTID:245790000 xref: UMLS:C0447411 {source="ncithesaurus:Alveolar_Ridge"} xref: Wikipedia:Alveolar_ridge is_a: UBERON:0005913 ! zone of bone organ -relationship: has_developmental_contribution_from UBERON:0008969 {source="PMID:19767574", source="Wikipedia"} ! dental follicle +is_a: UBERON:0010313 ! neural crest-derived structure relationship: part_of UBERON:0001708 ! jaw skeleton -property_value: UBPROP:0000012 "in BTO, this is part of an embryo" xsd:string {external_ontology="BTO"} +relationship: RO:0002254 UBERON:0008969 {source="PMID:19767574", source="Wikipedia"} ! has developmental contribution from dental follicle [Term] id: UBERON:0004109 @@ -209372,6 +206801,7 @@ synonym: "humerus compact bone" EXACT [] synonym: "humerus cortical bone" EXACT [] xref: FMA:31542 is_a: UBERON:0001439 ! compact bone tissue +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004269 ! upper arm connective tissue is_a: UBERON:0005808 ! bone tissue of long bone intersection_of: UBERON:0001439 ! compact bone tissue @@ -209396,15 +206826,14 @@ xref: SCTID:346902003 xref: Wikipedia:Foramen is_a: UBERON:0010000 ! multicellular anatomical structure intersection_of: UBERON:0010000 ! multicellular anatomical structure -intersection_of: conduit_for UBERON:0000061 ! anatomical structure intersection_of: has_part UBERON:0013686 ! anatomical conduit space -relationship: conduit_for UBERON:0000061 ! anatomical structure -relationship: connects UBERON:0000464 {cardinality="2"} ! anatomical space +intersection_of: RO:0002570 UBERON:0000061 ! conduit for anatomical structure relationship: has_part UBERON:0013686 ! anatomical conduit space -relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 ! Fungi -property_value: UBPROP:0000012 "FMA has both conduit and conduit space. In EHDAA2 this is a surface feature" xsd:string {external_ontology="FMA"} +relationship: RO:0002176 UBERON:0000464 {cardinality="2"} ! connects anatomical space +relationship: RO:0002570 UBERON:0000061 ! conduit for anatomical structure +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0004113 @@ -209427,11 +206856,10 @@ xref: UMLS:C1513769 {source="ncithesaurus:Muscle_of_the_Tympanum"} xref: Wikipedia:Muscles_of_auditory_ossicles is_a: UBERON:0002376 {source="FMA"} ! cranial muscle intersection_of: UBERON:0001630 ! muscle organ -intersection_of: attaches_to UBERON:0001686 ! auditory ossicle bone -relationship: attaches_to UBERON:0001686 ! auditory ossicle bone -relationship: located_in UBERON:0004114 ! tympanic cavity +intersection_of: RO:0002371 UBERON:0001686 ! attached to auditory ossicle bone relationship: part_of UBERON:0001756 ! middle ear -property_value: UBPROP:0000009 "attenuate low-frequency sounds, reduce masking of high-frequency sounds by low-frequency sounds, frequency-selection filter" xsd:string +relationship: RO:0001025 UBERON:0004114 ! located in tympanic cavity +relationship: RO:0002371 UBERON:0001686 ! attached to auditory ossicle bone [Term] id: UBERON:0004114 @@ -209455,13 +206883,13 @@ is_a: UBERON:0002553 ! anatomical cavity is_a: UBERON:0005082 ! tube lumen is_a: UBERON:0010064 {source="EHDAA2"} ! open anatomical space intersection_of: UBERON:0002553 ! anatomical cavity -intersection_of: luminal_space_of UBERON:0001756 ! middle ear -relationship: developmentally_replaces UBERON:0005625 {source="EHDAA2"} ! tubotympanic recess lumen -relationship: luminal_space_of UBERON:0001756 ! middle ear +intersection_of: RO:0002572 UBERON:0001756 ! luminal space of middle ear relationship: part_of UBERON:0001756 ! middle ear -relationship: surrounded_by UBERON:0010063 ! tympanic cavity epithelium -relationship: surrounds UBERON:0001686 ! auditory ossicle bone -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray923.png" xsd:anyURI +relationship: RO:0002219 UBERON:0010063 ! surrounded by tympanic cavity epithelium +relationship: RO:0002221 UBERON:0001686 ! surrounds auditory ossicle bone +relationship: RO:0002285 UBERON:0005625 {source="EHDAA2"} ! developmentally replaces tubotympanic recess lumen +relationship: RO:0002572 UBERON:0001756 ! luminal space of middle ear +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray923.png" xsd:anyURI [Term] id: UBERON:0004115 @@ -209482,9 +206910,9 @@ xref: EMAPA:37775 {source="MA:th"} xref: MA:0001219 is_a: UBERON:0003496 ! head blood vessel intersection_of: UBERON:0001981 ! blood vessel -intersection_of: located_in UBERON:0004114 ! tympanic cavity -relationship: located_in UBERON:0004114 ! tympanic cavity +intersection_of: RO:0001025 UBERON:0004114 ! located in tympanic cavity relationship: part_of UBERON:0001756 ! middle ear +relationship: RO:0001025 UBERON:0004114 ! located in tympanic cavity [Term] id: UBERON:0004116 @@ -209505,9 +206933,9 @@ xref: EMAPA:37777 {source="MA:th"} xref: MA:0001222 is_a: UBERON:0011779 ! nerve of head region intersection_of: UBERON:0001021 ! nerve -intersection_of: located_in UBERON:0004114 ! tympanic cavity -relationship: located_in UBERON:0004114 ! tympanic cavity +intersection_of: RO:0001025 UBERON:0004114 ! located in tympanic cavity relationship: part_of UBERON:0001756 ! middle ear +relationship: RO:0001025 UBERON:0004114 ! located in tympanic cavity [Term] id: UBERON:0004117 @@ -209541,13 +206969,10 @@ xref: ZFA:0001106 is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0003258 ! endoderm of foregut is_a: UBERON:0005291 ! embryonic tissue -relationship: develops_from UBERON:0007690 {source="EHDAA2", source="ZFA"} ! early pharyngeal endoderm -relationship: only_in_taxon NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! Chordata relationship: overlaps UBERON:0002539 ! pharyngeal arch relationship: part_of UBERON:0008814 ! pharyngeal arch system -property_value: UBPROP:0000001 "Outpocketings of pharyngeal endoderm that interdigitate with the neural crest derived pharyngeal arches. The pouches later fuse with the surface ectoderm to form the gill slits. Crump et al, 2004.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001106", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001203", ontology="VHOG", source="DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M, Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "EMAPA also includes a distinct pouch endoderm" xsd:string {external_ontology="EMAPA"} +relationship: RO:0002160 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! only in taxon Chordata +relationship: RO:0002202 UBERON:0007690 {source="EHDAA2", source="ZFA"} ! develops from early pharyngeal endoderm [Term] id: UBERON:0004118 @@ -209573,9 +206998,8 @@ def: "An anatomical structure that develops (entirely or partially) from the end subset: grouping_class is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: develops_from UBERON:0000925 ! endoderm -relationship: develops_from UBERON:0000925 ! endoderm -property_value: IAO:0000232 "Grouping term for query purposes" xsd:string +intersection_of: RO:0002202 UBERON:0000925 ! develops from endoderm +relationship: RO:0002202 UBERON:0000925 ! develops from endoderm [Term] id: UBERON:0004120 @@ -209586,9 +207010,8 @@ subset: grouping_class synonym: "mesodermal derivative" EXACT [FBbt:00025998] is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: develops_from UBERON:0000926 ! mesoderm -relationship: develops_from UBERON:0000926 ! mesoderm -property_value: IAO:0000232 "Grouping term for query purposes" xsd:string +intersection_of: RO:0002202 UBERON:0000926 ! develops from mesoderm +relationship: RO:0002202 UBERON:0000926 ! develops from mesoderm [Term] id: UBERON:0004121 @@ -209599,9 +207022,8 @@ subset: grouping_class synonym: "ectodermal deriviative" EXACT [FBbt:00025990] is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: develops_from UBERON:0000924 ! ectoderm -relationship: develops_from UBERON:0000924 ! ectoderm -property_value: IAO:0000232 "Grouping term for query purposes" xsd:string +intersection_of: RO:0002202 UBERON:0000924 ! develops from ectoderm +relationship: RO:0002202 UBERON:0000924 ! develops from ectoderm [Term] id: UBERON:0004122 @@ -209637,15 +207059,10 @@ is_a: UBERON:0000467 ! anatomical system intersection_of: UBERON:0000467 ! anatomical system intersection_of: has_part UBERON:0000990 ! reproductive system intersection_of: has_part UBERON:0001008 ! renal system -relationship: develops_from UBERON:0003064 {gci_relation="part_of", gci_filler="NCBITaxon:7742", source="AAO", source="https://github.com/geneontology/go-ontology/issues/16143"} ! intermediate mesoderm -relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: has_part UBERON:0000990 ! reproductive system relationship: has_part UBERON:0001008 ! renal system -property_value: UBPROP:0000001 "Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000624", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000002 "relationship type change: differentiates_from intermediate mesoderm (AAO:0010575) CHANGED TO: develops_from intermediate mesoderm (UBERON:0003064)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000624", ontology="AAO"} -property_value: UBPROP:0000003 "Kidneys and gonads (of vertebrates) develop from adjacent tissues, and after the excretory or urinary ducts have developed, the reproductive system usually taps into them or their derivatives.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000286", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.633", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "genitourinary" xsd:string -property_value: UBPROP:0000007 "urogenital" xsd:string +relationship: RO:0002202 UBERON:0003064 {gci_relation="part_of", gci_filler="NCBITaxon:7742", source="AAO", source="https://github.com/geneontology/go-ontology/issues/16143"} ! develops from intermediate mesoderm +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage [Term] id: UBERON:0004123 @@ -209685,10 +207102,9 @@ xref: ZFA:0005059 is_a: UBERON:0004123 ! myocardial layer intersection_of: UBERON:0004123 ! myocardial layer intersection_of: adjacent_to UBERON:0002165 ! endocardium -intersection_of: composed_primarily_of GO:0036194 ! muscle cell projection +intersection_of: RO:0002473 GO:0036194 ! composed primarily of muscle cell projection relationship: adjacent_to UBERON:0002165 ! endocardium -relationship: composed_primarily_of GO:0036194 ! muscle cell projection -property_value: UBPROP:0000001 "The layer of the myocardium composed of projections of contractile myocytes. The trabecular layer is bounded internally by the the endocardium. Unlike the trabeculations of higher vertebrates, both atrial and ventricular trabeculae of the zebrafish have more strut-like character, and are more uniform without apparent regional differences Hu et al. 2001.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005059", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002473 GO:0036194 ! composed primarily of muscle cell projection [Term] id: UBERON:0004126 @@ -209706,7 +207122,7 @@ is_a: UBERON:0004124 ! myocardium trabecular layer intersection_of: UBERON:0004124 ! myocardium trabecular layer intersection_of: part_of UBERON:0002082 ! cardiac ventricle relationship: part_of UBERON:0001083 {source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! myocardium of ventricle -property_value: editor_note "TODO - check FMA" xsd:string +property_value: IAO:0000116 "TODO - check FMA" xsd:string [Term] id: UBERON:0004128 @@ -209734,12 +207150,11 @@ xref: XAO:0000228 xref: ZFA:0000050 is_a: UBERON:0000479 ! tissue is_a: UBERON:0004121 ! ectoderm-derived structure -relationship: developmentally_induced_by UBERON:0004880 ! chordamesoderm -relationship: develops_from UBERON:0002346 {source="GO-def"} ! neurectoderm -relationship: develops_from UBERON:0003071 {source="ZFA"} ! eye primordium relationship: part_of UBERON:0010312 {source="ZFA"} ! immature eye -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e0/Gray863.png" xsd:anyURI -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000165", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0002346 {source="GO-def"} ! develops from neurectoderm +relationship: RO:0002202 UBERON:0003071 {source="ZFA"} ! develops from eye primordium +relationship: RO:0002256 UBERON:0004880 ! developmentally induced by chordamesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e0/Gray863.png" xsd:anyURI [Term] id: UBERON:0004129 @@ -209748,10 +207163,10 @@ namespace: uberon def: "Cartilage that will provide a scaffold for mineralization of endochondral bones as they elongate or grow." [GO:0003417] synonym: "growth plate" RELATED [] is_a: UBERON:0002418 ! cartilage tissue -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0010363 ! endochondral element +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002221 UBERON:0004763 ! surrounds endochondral bone tissue relationship: site_of GO:0030282 ! bone mineralization -relationship: surrounds UBERON:0004763 ! endochondral bone tissue [Term] id: UBERON:0004130 @@ -209775,8 +207190,8 @@ is_a: UBERON:0011215 ! central nervous system cell part cluster is_a: UBERON:0016548 ! central nervous system gray matter layer intersection_of: UBERON:0016548 ! central nervous system gray matter layer intersection_of: part_of UBERON:0002037 ! cerebellum -relationship: contributes_to_morphology_of UBERON:0002129 ! cerebellar cortex relationship: part_of UBERON:0002129 ! cerebellar cortex +relationship: RO:0002433 UBERON:0002129 ! contributes to morphology of cerebellar cortex [Term] id: UBERON:0004133 @@ -209803,10 +207218,10 @@ xref: EMAPA:28281 xref: MA:0002611 xref: MESH:D007687 is_a: UBERON:0006853 ! renal cortex tubule -relationship: continuous_with UBERON:0001230 {source="GO"} ! glomerular capsule -relationship: continuous_with UBERON:0001289 {source="GO"} ! descending limb of loop of Henle -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: editor_note "TODO - ensure definition works across species." xsd:string +relationship: RO:0002150 UBERON:0001230 {source="GO"} ! continuous with glomerular capsule +relationship: RO:0002150 UBERON:0001289 {source="GO"} ! continuous with descending limb of loop of Henle +property_value: IAO:0000116 "TODO - ensure definition works across species." xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004135 @@ -209821,7 +207236,6 @@ xref: EMAPA:28387 xref: MA:0002633 xref: MESH:D007686 is_a: UBERON:0007685 ! region of nephron tubule -property_value: RO:0002171 UBERON:0012424 [Term] id: UBERON:0004136 @@ -209833,7 +207247,7 @@ synonym: "tubulus attenuatus" EXACT [FMA:17718] xref: FMA:17718 is_a: UBERON:0007685 ! region of nephron tubule relationship: part_of UBERON:0001288 {source="FMA"} ! loop of Henle -property_value: editor_note "TODO - check for applicability across species" xsd:string +property_value: IAO:0000116 "TODO - check for applicability across species" xsd:string [Term] id: UBERON:0004139 @@ -209849,9 +207263,8 @@ xref: EHDAA2:0000215 xref: EMAPA:16106 xref: VHOG:0000975 is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0003084 ! heart primordium -property_value: editor_note "TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO" xsd:string -property_value: UBPROP:0000003 "(In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000975", ontology="VHOG", source="PMID:15611355 Gittenberger-de Groot AC, Bartelings MM, Deruiter MC, Poelmann RE, Basics of cardiac development for the understanding of congenital heart malformations. Pediatric Research (2005)", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003084 ! develops from heart primordium +property_value: IAO:0000116 "TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO" xsd:string [Term] id: UBERON:0004140 @@ -209865,11 +207278,11 @@ synonym: "PHF" RELATED OMO:0003000 [XAO:0004185] synonym: "primary heart field" EXACT [PMID:17276708, XAO:0004185] xref: XAO:0004185 is_a: UBERON:0002050 ! embryonic structure +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007688 ! anlage relationship: part_of UBERON:0003081 {source="GO:0003128"} ! lateral plate mesoderm relationship: part_of UBERON:0036146 {source="https://orcid.org/0000-0003-3308-6245"} ! cardiopharyngeal field -property_value: UBPROP:0000012 "this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138]" xsd:string {external_ontology="GO"} [Term] id: UBERON:0004141 @@ -209892,8 +207305,7 @@ xref: ZFA:0000360 is_a: UBERON:0003914 ! epithelial tube is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0012275 ! meso-epithelium -relationship: immediate_transformation_of UBERON:0005498 {source="ZFA-modified"} ! primitive heart tube -property_value: UBPROP:0000001 "the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube." xsd:string {source="MP:0012700"} +relationship: RO:0002495 UBERON:0005498 {source="ZFA-modified"} ! immediate transformation of primitive heart tube [Term] id: UBERON:0004142 @@ -209923,11 +207335,11 @@ xref: MA:0000100 xref: VHOG:0000670 xref: XAO:0004139 is_a: UBERON:0004111 ! anatomical conduit +is_a: UBERON:0004120 ! mesoderm-derived structure relationship: channel_for UBERON:0000178 ! blood relationship: channels_from UBERON:0000948 ! heart relationship: channels_into UBERON:0001637 ! artery relationship: part_of UBERON:0000948 ! heart -property_value: UBPROP:0000008 "Depending on the species, attached at the cardiac outflow are described the conus arteriosus, the truncus arteriosus and, or the bulbus arteriosus. At the distal limit of these outflow structures, but lying outside the pericardial cavity, is the ventral aorta[PMID:20735616]" xsd:string [Term] id: UBERON:0004146 @@ -209940,9 +207352,8 @@ synonym: "VCS" EXACT [] synonym: "ventricular conduction system" EXACT [] is_a: UBERON:0010131 {source="cjm"} ! conducting tissue of heart is_a: UBERON:0018649 ! cardiac muscle tissue of ventricle -relationship: only_in_taxon NCBITaxon:32523 {source="PMID:12626327", source="PMID:21234997", source="github:michaelerice"} ! Tetrapoda relationship: part_of UBERON:0002350 {source="GO"} ! conducting system of heart -property_value: UBPROP:0000001 "the intraventricular conduction system from the bundle of His to the distal Purkinje fibers, which carries the impulse to the ventricles." xsd:string {source="http://medical-dictionary.thefreedictionary.com/His-Purkinje+system"} +relationship: RO:0002160 NCBITaxon:32523 {source="PMID:12626327", source="PMID:21234997", source="github:michaelerice"} ! only in taxon Tetrapoda [Term] id: UBERON:0004148 @@ -209970,11 +207381,11 @@ is_a: UBERON:0003498 ! heart blood vessel is_a: UBERON:0005194 ! thoracic vein is_a: UBERON:0013140 {source="FMA"} ! systemic vein intersection_of: UBERON:0001638 ! vein -intersection_of: drains UBERON:0002349 ! myocardium intersection_of: part_of UBERON:0000948 ! heart -relationship: drains UBERON:0002349 ! myocardium -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +intersection_of: RO:0002179 UBERON:0002349 ! drains myocardium +relationship: RO:0002179 UBERON:0002349 ! drains myocardium +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI [Term] id: UBERON:0004151 @@ -209987,6 +207398,7 @@ synonym: "heart chamber" EXACT [] xref: FMA:7095 xref: SCTID:276456008 is_a: UBERON:0000064 ! organ part +is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0000948 ! heart [Term] @@ -209999,10 +207411,8 @@ synonym: "proepicardial organ" EXACT [ZFIN:ZDB-PUB-080218-16] xref: EMAPA:36025 xref: ZFA:0005808 is_a: UBERON:0003104 ! mesenchyme -relationship: part_of UBERON:0004161 {notes="todo check other taxa"} ! septum transversum +relationship: part_of UBERON:0004161 ! septum transversum relationship: part_of UBERON:0004535 {source="ZFA"} ! cardiovascular system -property_value: UBPROP:0000007 "propepicardial" xsd:string -property_value: UBPROP:0000008 "Proepicardial clusters in Zebrafish form on the pericardial wall, adjacent to the atrioventricular (AV) junction and near the venous pole[ZFA]" xsd:string [Term] id: UBERON:0004161 @@ -210021,12 +207431,8 @@ xref: UMLS:C0231004 {source="ncithesaurus:Septum_Transversum"} xref: VHOG:0000019 xref: Wikipedia:Septum_transversum is_a: UBERON:0003104 ! mesenchyme -relationship: located_in UBERON:0002323 ! coelemic cavity lumen relationship: part_of UBERON:0002100 ! trunk -property_value: UBPROP:0000001 "A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000019", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/transverse+septum"} -property_value: UBPROP:0000003 "In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart (of other tetrapods) is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes) Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000019", ontology="VHOG", source="ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000011 "The cranial part of the septum transversum gives rise to the central tendon of the diaphragm and is the origin of the myoblasts that invade the pleuroperitoneal folds resulting in the formation of the muscular diaphragm. The caudal part of the septum transversum is invaded by the hepatic diverticulum which divides within it to form the liver and thus gives rise to the ventral mesentery of the foregut." xsd:string -property_value: UBPROP:0000012 "in EHDAA2 this is divided into mesenchymal portion and hepatic diverticulum" xsd:string {external_ontology="EHDAA2"} +relationship: RO:0001025 UBERON:0002323 ! located in coelemic cavity lumen [Term] id: UBERON:0004164 @@ -210039,12 +207445,10 @@ xref: Wikipedia:Branchiomeric_musculature xref: XAO:0004325 is_a: UBERON:0001630 ! muscle organ is_a: UBERON:0004120 ! mesoderm-derived structure -relationship: composed_primarily_of UBERON:0001134 ! skeletal muscle tissue -relationship: develops_from UBERON:0010360 {source="PMID:21610022"} ! pharyngeal arch mesenchyme from head mesenchyme -relationship: innervated_by UBERON:0001785 {source="ISBN:0073040584"} ! cranial nerve -relationship: only_in_taxon NCBITaxon:7711 ! Chordata -property_value: UBPROP:0000001 "The branchiomeric muscle is derived from cranial mesoderm and controls facial expression, pharyngeal and laryngeal function, operating the jaw. Branchiomeric muscles of mammals correspond to the musculature of fish[GO][GO:0014707]." xsd:string {source="GO:0014707"} -property_value: UBPROP:0000008 "It has been hypothesized that Haikouella must have been powered by branchiomeric muscles, as in living craniates, rather than by water moving through the pharynx via ciliary currents, as in lancelets[http://icb.oxfordjournals.org/content/42/4/743.full]" xsd:string +relationship: RO:0002005 UBERON:0001785 {source="ISBN:0073040584"} ! innervated_by cranial nerve +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002202 UBERON:0010360 {source="PMID:21610022"} ! develops from pharyngeal arch mesenchyme from head mesenchyme +relationship: RO:0002473 UBERON:0001134 ! composed primarily of skeletal muscle tissue [Term] id: UBERON:0004175 @@ -210061,7 +207465,7 @@ synonym: "internal reproductive organ" RELATED [] synonym: "internal sex organ" RELATED [] xref: FMA:45652 is_a: UBERON:0003133 ! reproductive organ -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004176 @@ -210103,12 +207507,11 @@ xref: FMA:7143 xref: MA:0000747 xref: SCTID:361338006 is_a: UBERON:0000062 ! organ +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000062 ! organ intersection_of: part_of UBERON:0002390 ! hematopoietic system relationship: part_of UBERON:0002390 ! hematopoietic system -property_value: editor_note "consider splitting out lymph organ, compare with lymph node" xsd:string -property_value: UBPROP:0000001 "the organs in which the formed elements of the blood and lymph are produced[http://encyclopedia2.thefreedictionary.com/Hematopoietic+Organs]." xsd:string {source="http://encyclopedia2.thefreedictionary.com/Hematopoietic+Organs"} -property_value: UBPROP:0000012 "the FMA class 'lymphoid organ' is a general anatomical term" xsd:string {external_ontology="FMA"} +property_value: IAO:0000116 "consider splitting out lymph organ, compare with lymph node" xsd:string [Term] id: UBERON:0004178 @@ -210142,13 +207545,13 @@ subset: human_reference_atlas synonym: "prostatic acinus" EXACT [FMA:66808] synonym: "prostatic follicle" EXACT [FMA:66808] xref: FMA:66808 +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0005156 ! reproductive structure is_a: UBERON:0009842 {source="FMA"} ! glandular acinus -relationship: develops_from UBERON:0009843 {source="PMID:18977204"} ! prostate epithelial cord relationship: part_of UBERON:0000428 {source="GO"} ! prostate epithelium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: editor_note "the muscle layer is implicitly treated as outside the acinus" xsd:string -property_value: UBPROP:0000011 "Concurrent with branching morphogenesis, the solid cords of epithelium formed by budding arborize and differentiate postnatally into glandular acin. The basic prostate architecture is established by puberty and acquires secretory function thereafter[PMID:18977204]" xsd:string +relationship: RO:0002202 UBERON:0009843 {source="PMID:18977204"} ! develops from prostate epithelial cord +property_value: IAO:0000116 "the muscle layer is implicitly treated as outside the acinus" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004180 @@ -210194,13 +207597,11 @@ synonym: "mammary cord" EXACT [] synonym: "mammary sprout" RELATED [] is_a: UBERON:0003244 ! epithelium of mammary gland is_a: UBERON:0005154 ! epithelial cord -is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0034969 ! epithelial layer of duct intersection_of: UBERON:0005154 ! epithelial cord intersection_of: part_of UBERON:0001765 ! mammary duct -relationship: develops_from UBERON:0005333 ! mammary bud relationship: part_of UBERON:0001765 ! mammary duct -property_value: UBPROP:0000008 "in female mouse embryos, the primary mammary cord (aka 'mammary sprout') is formed between E15.5 and E16.5; once the primary cord reaches the adipocytes of the fat pad (around E16), it begins to branch in a characteristic dichotomous fashion to form the initial ductal tree" xsd:string +relationship: RO:0002202 UBERON:0005333 ! develops from mammary bud [Term] id: UBERON:0004183 @@ -210235,13 +207636,14 @@ xref: FMA:45719 xref: MA:0002912 xref: NCIT:C13104 xref: UMLS:C1521760 {source="ncithesaurus:Prostatic_Stroma"} +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0003891 ! stroma is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0003891 ! stroma intersection_of: part_of UBERON:0002367 ! prostate gland relationship: part_of UBERON:0002367 ! prostate gland -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: editor_note "TODO - check also FMA Stroma of glandular part of prostate" xsd:string +property_value: IAO:0000116 "TODO - check also FMA Stroma of glandular part of prostate" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004185 @@ -210254,8 +207656,8 @@ xref: EMAPA:32930 is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0004921 ! subdivision of digestive tract intersection_of: UBERON:0004921 ! subdivision of digestive tract -intersection_of: develops_from UBERON:0000925 ! endoderm intersection_of: part_of UBERON:0001555 ! digestive tract +intersection_of: RO:0002202 UBERON:0000925 ! develops from endoderm [Term] id: UBERON:0004186 @@ -210276,7 +207678,6 @@ xref: EMAPA:35611 xref: MA:0000973 xref: NLXANAT:100201 is_a: UBERON:0004001 ! olfactory bulb layer -property_value: UBPROP:0000012 "NIF divides this into main and accessory" xsd:string {external_ontology="NIF"} [Term] id: UBERON:0004188 @@ -210293,11 +207694,12 @@ xref: BTO:0001515 xref: EMAPA:35458 xref: MA:0002847 is_a: UBERON:0004211 ! nephron epithelium +is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000074 ! renal glomerulus relationship: part_of UBERON:0000074 ! renal glomerulus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: editor_note "TODO - check - GO says outer, BTO says inner. Make this a superclass" xsd:string +property_value: IAO:0000116 "TODO - check - GO says outer, BTO says inner. Make this a superclass" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004189 @@ -210328,7 +207730,7 @@ is_a: UBERON:0006544 ! kidney vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: part_of UBERON:0000074 ! renal glomerulus relationship: part_of UBERON:0000074 ! renal glomerulus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004193 @@ -210348,12 +207750,12 @@ xref: FMA:17720 xref: MA:0001678 xref: Wikipedia:Thin_ascending_limb_of_loop_of_Henle is_a: UBERON:0007685 ! region of nephron tubule -relationship: contributes_to_morphology_of UBERON:0005164 ! ascending limb of loop of Henle relationship: part_of UBERON:0003455 ! inner renal medulla loop of Henle relationship: part_of UBERON:0005164 ! ascending limb of loop of Henle -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI -property_value: editor_note "check relationship to distal tubule" xsd:string +relationship: RO:0002433 UBERON:0005164 ! contributes to morphology of ascending limb of loop of Henle +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: IAO:0000116 "check relationship to distal tubule" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004194 @@ -210384,8 +207786,8 @@ synonym: "CSB" EXACT OMO:0003000 [] xref: EMAPA:27681 xref: ZFA:0005588 is_a: UBERON:0005423 ! developing anatomical structure -relationship: develops_from UBERON:0004209 {source="ZFA"} ! renal vesicle relationship: part_of UBERON:0010532 {source="cjm"} ! primitive nephron +relationship: RO:0002202 UBERON:0004209 {source="ZFA"} ! develops from renal vesicle [Term] id: UBERON:0004199 @@ -210396,12 +207798,11 @@ subset: pheno_slim synonym: "SSB" EXACT OMO:0003000 [] synonym: "stage II nephron" EXACT [http://www.gudmap.org/Organ_Summaries/Metanephros/Renal_vesicle.html] xref: EMAPA:27756 -xref: VO:0010896 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: ZFA:0005589 is_a: UBERON:0005423 ! developing anatomical structure -relationship: develops_from UBERON:0004198 {source="GO"} ! comma-shaped body relationship: part_of UBERON:0010532 {source="cjm"} ! primitive nephron -property_value: editor_note "TODO" xsd:string +relationship: RO:0002202 UBERON:0004198 {source="GO"} ! develops from comma-shaped body +property_value: IAO:0000116 "TODO" xsd:string [Term] id: UBERON:0004200 @@ -210433,16 +207834,14 @@ xref: UMLS:C0227629 {source="ncithesaurus:Renal_Pyramid"} xref: UMLS:C1514613 {source="ncithesaurus:Pyramid_of_Malpighi"} xref: Wikipedia:Renal_pyramids is_a: UBERON:0000064 ! organ part -relationship: contributes_to_morphology_of UBERON:0000362 ! renal medulla relationship: part_of UBERON:0000362 ! renal medulla -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI -property_value: UBPROP:0000012 "not the same as FMA:50609 Pyramid (which is a volume / dimensional entity)" xsd:string {external_ontology="FMA"} -property_value: UBPROP:0000202 FMA:74268 +relationship: RO:0002433 UBERON:0000362 ! contributes to morphology of renal medulla +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004201 @@ -210461,9 +207860,9 @@ xref: EMAPA:29675 xref: FMA:76663 xref: MA:0002626 is_a: UBERON:0010000 ! multicellular anatomical structure -relationship: contributes_to_morphology_of UBERON:0001293 ! outer medulla of kidney relationship: part_of UBERON:0001293 ! outer medulla of kidney -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002433 UBERON:0001293 ! contributes to morphology of outer medulla of kidney +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004202 @@ -210482,9 +207881,9 @@ xref: EMAPA:29663 xref: FMA:76662 xref: MA:0002629 is_a: UBERON:0010000 ! multicellular anatomical structure -relationship: contributes_to_morphology_of UBERON:0001293 ! outer medulla of kidney relationship: part_of UBERON:0001293 ! outer medulla of kidney -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002433 UBERON:0001293 ! contributes to morphology of outer medulla of kidney +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004203 @@ -210504,7 +207903,7 @@ intersection_of: part_of UBERON:0001225 ! cortex of kidney intersection_of: part_of UBERON:0001232 ! collecting duct of renal tubule relationship: part_of UBERON:0001225 ! cortex of kidney relationship: part_of UBERON:0001232 ! collecting duct of renal tubule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004204 @@ -210521,7 +207920,7 @@ is_a: UBERON:0001232 ! collecting duct of renal tubule intersection_of: UBERON:0001232 ! collecting duct of renal tubule intersection_of: part_of UBERON:0001293 ! outer medulla of kidney relationship: part_of UBERON:0001293 ! outer medulla of kidney -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004205 @@ -210540,7 +207939,7 @@ is_a: UBERON:0001232 ! collecting duct of renal tubule intersection_of: UBERON:0001232 ! collecting duct of renal tubule intersection_of: part_of UBERON:0001294 ! inner medulla of kidney relationship: part_of UBERON:0001294 ! inner medulla of kidney -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004208 @@ -210552,8 +207951,8 @@ synonym: "mesenchyme of nephron" EXACT [OBOL:automatic] synonym: "nephron mesenchyme" EXACT [OBOL:automatic] is_a: UBERON:0003104 ! mesenchyme intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: has_potential_to_develop_into UBERON:0001285 ! nephron -relationship: has_potential_to_develop_into UBERON:0001285 ! nephron +intersection_of: RO:0002387 UBERON:0001285 ! has potential to develop into nephron +relationship: RO:0002387 UBERON:0001285 ! has potential to develop into nephron [Term] id: UBERON:0004209 @@ -210562,11 +207961,11 @@ namespace: uberon def: "The renal vesicle is the primordial structure of the nephron epithelium, and is formed by the condensation of mesenchymal cells." [GO:0072077] synonym: "stage I nephron" EXACT [http://www.gudmap.org/Organ_Summaries/Metanephros/Renal_vesicle.html, ZFA:0005586] is_a: UBERON:0007503 {source="EHDAA2"} ! epithelial vesicle -relationship: developmentally_induced_by UBERON:0000084 ! ureteric bud -relationship: develops_from UBERON:0004208 ! nephrogenic mesenchyme -relationship: has_potential_to_develop_into UBERON:0004211 ! nephron epithelium relationship: part_of UBERON:0010536 ! nephron progenitor -property_value: editor_note "note that this class includes both metanephric and mesonephric vesicles - ZFA and EHDAA2 associations are placed with these classes. TODO - make a more specific develops_from relationship - see UBERON:0005107 ! metanephric cap" xsd:string +relationship: RO:0002202 UBERON:0004208 ! develops from nephrogenic mesenchyme +relationship: RO:0002256 UBERON:0000084 ! developmentally induced by ureteric bud +relationship: RO:0002387 UBERON:0004211 ! has potential to develop into nephron epithelium +property_value: IAO:0000116 "note that this class includes both metanephric and mesonephric vesicles - ZFA and EHDAA2 associations are placed with these classes. TODO - make a more specific develops_from relationship - see UBERON:0005107 ! metanephric cap" xsd:string [Term] id: UBERON:0004211 @@ -210608,11 +208007,10 @@ xref: ZFA:0005284 is_a: UBERON:0003527 ! kidney capillary intersection_of: UBERON:0001982 ! capillary intersection_of: part_of UBERON:0000074 ! renal glomerulus -relationship: connected_to UBERON:0004639 ! renal afferent arteriole -relationship: contributes_to_morphology_of UBERON:0000074 ! renal glomerulus relationship: part_of UBERON:0004190 {source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! renal glomerulus vasculature -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000001 "Capillary that is part of the renal glomerulus. Glomerular capillary endothelial membranes in zebrafish normally have a fenestrated morphology that is visible at the ultrastructural level.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005284", ontology="TAO", source="ZFIN:ZDB-PUB-000824-1", source="ZFIN:curator"} +relationship: RO:0002170 UBERON:0004639 ! connected to renal afferent arteriole +relationship: RO:0002433 UBERON:0000074 ! contributes to morphology of renal glomerulus +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004214 @@ -210717,9 +208115,8 @@ xref: MA:0001547 is_a: UBERON:0004221 ! intestine smooth muscle intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0000059 ! large intestine -relationship: overlaps UBERON:0011198 {notes="consider merging"} ! muscle layer of large intestine +relationship: overlaps UBERON:0011198 ! muscle layer of large intestine relationship: part_of UBERON:0001169 {source="MA"} ! wall of large intestine -property_value: UBPROP:0000012 "MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa" xsd:string {external_ontology="MA"} [Term] id: UBERON:0004221 @@ -210753,10 +208150,9 @@ xref: UMLS:C1708547 {source="ncithesaurus:Intestinal_Smooth_Muscle_Tissue"} is_a: UBERON:0004226 ! gastrointestinal system smooth muscle intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0000160 ! intestine -relationship: contributes_to_morphology_of UBERON:0000160 ! intestine -relationship: overlaps UBERON:0012367 {notes="consider merging"} ! muscle layer of intestine +relationship: overlaps UBERON:0012367 ! muscle layer of intestine relationship: part_of UBERON:0001262 ! wall of intestine -property_value: UBPROP:0000012 "MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa" xsd:string {external_ontology="MA"} +relationship: RO:0002433 UBERON:0000160 ! contributes to morphology of intestine [Term] id: UBERON:0004222 @@ -210804,7 +208200,6 @@ synonym: "vagina smooth muscle" RELATED [BTO:0004999] synonym: "vagina smooth muscle tissue" EXACT [OBOL:automatic] synonym: "vaginal smooth muscle" EXACT [BTO:0004999] xref: BTO:0004999 -xref: EMAPA:30997 xref: MA:0001733 is_a: UBERON:0001135 ! smooth muscle tissue is_a: UBERON:0005156 ! reproductive structure @@ -210835,7 +208230,7 @@ is_a: UBERON:0034933 ! layer of smooth muscle tissue intersection_of: UBERON:0006660 ! muscular coat intersection_of: part_of UBERON:0001000 ! vas deferens relationship: part_of UBERON:0001000 ! vas deferens -property_value: editor_note "TODO - check MA and FMA classes mean the same thing" xsd:string +property_value: IAO:0000116 "TODO - check MA and FMA classes mean the same thing" xsd:string [Term] id: UBERON:0004225 @@ -210883,8 +208278,8 @@ xref: MA:0002631 is_a: UBERON:0001135 ! smooth muscle tissue intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0001224 ! renal pelvis -relationship: contributes_to_morphology_of UBERON:0001224 ! renal pelvis relationship: part_of UBERON:0001224 ! renal pelvis +relationship: RO:0002433 UBERON:0001224 ! contributes to morphology of renal pelvis [Term] id: UBERON:0004228 @@ -210977,7 +208372,7 @@ is_a: UBERON:0004228 ! urinary bladder smooth muscle intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0001257 ! trigone of urinary bladder relationship: part_of UBERON:0001257 ! trigone of urinary bladder -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004230 @@ -211033,8 +208428,8 @@ is_a: UBERON:0004228 ! urinary bladder smooth muscle intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0001258 ! neck of urinary bladder relationship: part_of UBERON:0001258 ! neck of urinary bladder -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Urinary_Bladder.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urinary_Bladder.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Urinary_Bladder.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urinary_Bladder.glb" xsd:anyURI [Term] id: UBERON:0004231 @@ -211100,8 +208495,8 @@ xref: UMLS:C1708791 {source="ncithesaurus:Lymphatic_Vessel_Smooth_Muscle_Tissue" is_a: UBERON:0001135 ! smooth muscle tissue intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0001473 ! lymphatic vessel -relationship: contributes_to_morphology_of UBERON:0001473 ! lymphatic vessel relationship: part_of UBERON:0001473 ! lymphatic vessel +relationship: RO:0002433 UBERON:0001473 ! contributes to morphology of lymphatic vessel [Term] id: UBERON:0004233 @@ -211117,6 +208512,7 @@ synonym: "smooth muscle of lower respiratory tract" EXACT [OBOL:automatic] synonym: "smooth muscle tissue of lower respiratory tract" EXACT [OBOL:automatic] xref: EMAPA:35520 xref: MA:0002410 +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0004225 ! respiratory system smooth muscle intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0001558 ! lower respiratory tract @@ -211143,7 +208539,7 @@ is_a: UBERON:0003386 {source="MA"} ! smooth muscle of eye intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0001769 ! iris relationship: part_of UBERON:0001606 ! muscle of iris -property_value: editor_note "see notes for muscle of iris." xsd:string +property_value: IAO:0000116 "see notes for muscle of iris." xsd:string [Term] id: UBERON:0004235 @@ -211154,6 +208550,7 @@ synonym: "smooth muscle tissue of mammary gland" EXACT [OBOL:automatic] xref: EMAPA:37669 {source="MA:th"} xref: MA:0000795 is_a: UBERON:0001135 ! smooth muscle tissue +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0001911 ! mammary gland relationship: part_of UBERON:0001911 ! mammary gland @@ -211203,8 +208600,7 @@ is_a: UBERON:0001135 ! smooth muscle tissue intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0001981 ! blood vessel relationship: part_of UBERON:0001981 ! blood vessel -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000009 "Vascular smooth muscle contracts or relaxes to both change the volume of blood vessels and the local blood pressure, a mechanism that is responsible for the redistribution of the blood within the body to areas where it is needed (i.e. areas with temporarily enhanced oxygen consumption). Thus the main function of vascular smooth muscle tonus is to regulate the caliber of the blood vessels in the body. Excessive vasoconstriction leads to hypertension, while excessive vasodilation as in shock leads to hypotension." xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004238 @@ -211251,9 +208647,8 @@ xref: MA:0001559 is_a: UBERON:0004221 ! intestine smooth muscle intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0002108 ! small intestine -relationship: overlaps UBERON:0011201 {notes="consider merging"} ! muscle layer of small intestine +relationship: overlaps UBERON:0011201 ! muscle layer of small intestine relationship: part_of UBERON:0001168 ! wall of small intestine -property_value: UBPROP:0000012 "MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa" xsd:string {external_ontology="MA"} [Term] id: UBERON:0004240 @@ -211280,6 +208675,7 @@ xref: EMAPA:35373 xref: MA:0001635 xref: NCIT:C49483 xref: UMLS:C1708179 {source="ncithesaurus:Gallbladder_Smooth_Muscle_Tissue"} +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0001135 ! smooth muscle tissue intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0002110 ! gallbladder @@ -211323,10 +208719,10 @@ xref: UMLS:C1707055 {source="ncithesaurus:Bronchus_Smooth_Muscle_Tissue"} is_a: UBERON:0004233 ! lower respiratory tract smooth muscle intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0002185 ! bronchus -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: has_part CL:0002598 ! bronchial smooth muscle cell relationship: part_of UBERON:0002185 ! bronchus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004243 @@ -211360,7 +208756,7 @@ is_a: UBERON:0008715 ! muscle tissue of prostate intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0002367 ! prostate gland relationship: has_part CL:1000487 {source="FMA"} ! smooth muscle cell of prostate -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004245 @@ -211375,7 +208771,6 @@ synonym: "involuntary muscle of fallopian tube" EXACT [OBOL:automatic] synonym: "non-striated muscle of fallopian tube" EXACT [OBOL:automatic] synonym: "smooth muscle of fallopian tube" EXACT [OBOL:automatic] synonym: "smooth muscle tissue of fallopian tube" EXACT [OBOL:automatic] -xref: EMAPA:29046 xref: MA:0001721 is_a: UBERON:0001135 ! smooth muscle tissue is_a: UBERON:0005156 ! reproductive structure @@ -211417,8 +208812,6 @@ is_a: UBERON:0001474 ! bone element is_a: UBERON:0005174 ! dorsal region element intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0001137 ! dorsum -property_value: IAO:0000232 "this class may be obsoleted. See: https://github.com/obophenotype/mouse-anatomy-ontology/issues/93" xsd:string -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern" xsd:anyURI [Term] id: UBERON:0004248 @@ -211444,7 +208837,6 @@ intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0001466 ! pedal digit relationship: part_of UBERON:0001466 ! pedal digit relationship: part_of UBERON:5101466 ! pedal digit digitopodial skeleton -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern" xsd:anyURI [Term] id: UBERON:0004249 @@ -211464,7 +208856,6 @@ intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0002389 ! manual digit relationship: part_of UBERON:0002389 ! manual digit relationship: part_of UBERON:5102389 ! manual digit digitopodial skeleton -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern" xsd:anyURI [Term] id: UBERON:0004250 @@ -211479,7 +208870,6 @@ is_a: UBERON:0003460 ! arm bone intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0003822 ! forelimb stylopod relationship: part_of UBERON:0003822 ! forelimb stylopod -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern" xsd:anyURI [Term] id: UBERON:0004251 @@ -211567,7 +208957,6 @@ is_a: UBERON:0005893 ! leg bone intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0003823 ! hindlimb zeugopod relationship: part_of UBERON:0003823 ! hindlimb zeugopod -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern" xsd:anyURI [Term] id: UBERON:0004252 @@ -211606,10 +208995,9 @@ xref: MA:0003139 is_a: UBERON:0001630 ! muscle organ intersection_of: UBERON:0001630 ! muscle organ intersection_of: part_of UBERON:0002416 ! integumental system -relationship: located_in UBERON:0002097 ! skin of body relationship: part_of UBERON:0002416 ! integumental system -property_value: editor_note "review as part of general integumentary system review - part of skin, or more generally, integumental system" xsd:string -property_value: UBPROP:0000012 "in MA, the only skin muscle is arrector pili. The only integumental muscle is panniculus carnosus. In EMAPA, the arrector pili only" xsd:string {external_ontology="MA"} +relationship: RO:0001025 UBERON:0002097 ! located in skin of body +property_value: IAO:0000116 "review as part of general integumentary system review - part of skin, or more generally, integumental system" xsd:string [Term] id: UBERON:0004254 @@ -211648,8 +209036,7 @@ is_a: UBERON:0001499 ! muscle of arm intersection_of: UBERON:0014892 ! skeletal muscle organ, vertebrate intersection_of: part_of UBERON:0003822 ! forelimb stylopod relationship: part_of UBERON:0014791 {source="prolog"} ! musculature of forelimb stylopod -property_value: editor_note "the FMA class 'muscle of arm' belongs here, do not move" xsd:string -property_value: UBPROP:0000013 "See notes on UBERON:0001460 for possible terminological confusion over term 'arm'" xsd:string +property_value: IAO:0000116 "the FMA class 'muscle of arm' belongs here, do not move" xsd:string [Term] id: UBERON:0004256 @@ -211669,9 +209056,8 @@ is_a: UBERON:0001383 ! muscle of leg intersection_of: UBERON:0014892 ! skeletal muscle organ, vertebrate intersection_of: part_of UBERON:0003823 ! hindlimb zeugopod relationship: part_of UBERON:0006067 {source="prolog"} ! musculature of hindlimb zeugopod -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: editor_note "the FMA class 'muscle of leg' belongs here, do not move[cjm]" xsd:string -property_value: UBPROP:0000013 "See notes on UBERON:0000978 for possible terminological confusion over term 'leg'" xsd:string +property_value: IAO:0000116 "the FMA class 'muscle of leg' belongs here, do not move[cjm]" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004257 @@ -211817,7 +209203,6 @@ is_a: UBERON:0002349 ! myocardium intersection_of: UBERON:0002349 ! myocardium intersection_of: part_of UBERON:0004145 ! outflow tract relationship: part_of UBERON:0004145 ! outflow tract -property_value: UBPROP:0000003 "(...) (theme) is how the vertebrate cardiovascular system differs from that of the presumptive evolutionary chordate ancestor. (...) At best we can tell there are two essential new ingredients: (1) vertebrates all have a continuous endothelial lining to the heart and vessels and (2) vertebrates have developed a second chamber in the heart, one designed for generating high systemic blood pressure.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000603", ontology="VHOG", source="PMID:9187138 Fishman MC, Chien KR, Fashioning the vertebrate heart: earliest embryonic decisions. Development (1997)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0004266 @@ -211830,7 +209215,7 @@ is_a: UBERON:0003569 ! leg connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0000376 ! hindlimb stylopod relationship: part_of UBERON:0000376 ! hindlimb stylopod -relationship: transformation_of UBERON:0005254 ! upper leg mesenchyme +relationship: RO:0002494 UBERON:0005254 ! transformation of upper leg mesenchyme [Term] id: UBERON:0004267 @@ -211856,7 +209241,7 @@ is_a: UBERON:0003573 ! arm connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0002386 ! forelimb zeugopod relationship: part_of UBERON:0002386 ! forelimb zeugopod -relationship: transformation_of UBERON:0003327 ! mesenchyme of forearm +relationship: RO:0002494 UBERON:0003327 ! transformation of mesenchyme of forearm [Term] id: UBERON:0004269 @@ -211869,7 +209254,7 @@ is_a: UBERON:0003573 ! arm connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0003822 ! forelimb stylopod relationship: part_of UBERON:0003822 ! forelimb stylopod -relationship: transformation_of UBERON:0005258 ! upper arm mesenchyme +relationship: RO:0002494 UBERON:0005258 ! transformation of upper arm mesenchyme [Term] id: UBERON:0004270 @@ -211882,7 +209267,7 @@ is_a: UBERON:0003569 ! leg connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0003823 ! hindlimb zeugopod relationship: part_of UBERON:0003823 ! hindlimb zeugopod -relationship: transformation_of UBERON:0005259 ! lower leg mesenchyme +relationship: RO:0002494 UBERON:0005259 ! transformation of lower leg mesenchyme [Term] id: UBERON:0004271 @@ -211893,6 +209278,7 @@ synonym: "pericardium of outflow tract" EXACT [OBOL:automatic] xref: EMAPA:37707 {source="MA:th"} xref: MA:0000491 is_a: UBERON:0002407 ! pericardium +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0002407 ! pericardium intersection_of: part_of UBERON:0004145 ! outflow tract relationship: part_of UBERON:0004145 ! outflow tract @@ -211998,10 +209384,11 @@ xref: AAO:0000156 xref: EMAPA:35335 xref: MA:0000271 is_a: UBERON:0001630 ! muscle organ +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0001630 ! muscle organ intersection_of: part_of UBERON:0000019 ! camera-type eye -relationship: contributes_to_morphology_of UBERON:0000019 ! camera-type eye relationship: part_of UBERON:0000019 {source="MA"} ! camera-type eye +relationship: RO:0002433 UBERON:0000019 ! contributes to morphology of camera-type eye [Term] id: UBERON:0004288 @@ -212031,13 +209418,10 @@ xref: Wikipedia:Skeleton xref: XAO:0004053 is_a: UBERON:0034925 ! anatomical collection disjoint_from: UBERON:0004770 ! articular system -relationship: has_member UBERON:0004765 ! skeletal element relationship: part_of UBERON:0001434 ! skeletal system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: RO:0002171 UBERON:0000383 +relationship: RO:0002351 UBERON:0004765 ! has member skeletal element +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/The-skeletal-system" xsd:anyURI -property_value: UBPROP:0000001 "Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000026", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070"} -property_value: UBPROP:0000007 "skeletal" xsd:string [Term] id: UBERON:0004290 @@ -212058,13 +209442,8 @@ xref: VHOG:0000676 xref: ZFA:0001513 is_a: UBERON:0000486 {source="AEO"} ! multilaminar epithelium is_a: UBERON:0016888 {source="AEO"} ! transitional anatomical structure -relationship: develops_from UBERON:0002329 {source="EHDAA2", source="ZFA"} ! somite relationship: has_part CL:0000075 ! columnar/cuboidal epithelial cell -property_value: UBPROP:0000001 "all but the sclerotome of a mesodermal somite; the primordium of skeletal muscle and, perhaps, of the dermis." xsd:string {source="http://medical-dictionary.thefreedictionary.com/dermomyotome"} -property_value: UBPROP:0000001 "Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768]." xsd:string {source="http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768"} -property_value: UBPROP:0000001 "Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001513", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Portion of somites that gives rise to dermis and muscles.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010572", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000676", ontology="VHOG", source="DOI:10.1111/j.1525-142X.2006.05079.x Devoto SH, Stoiber W, Hammond CL, Steinbacher P, Haslett JR, Barresi MJF, Patterson SE, Adiarte EG and Hughes SM, Generality of vertebrate developmental patterns: evidence for a dermomyotome in fish. Evolution and Development (2006)", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0002329 {source="EHDAA2", source="ZFA"} ! develops from somite [Term] id: UBERON:0004291 @@ -212076,8 +209455,7 @@ synonym: "rudimentary heart" EXACT [ZFA:0000115] xref: TAO:0000115 xref: ZFA:0000115 is_a: UBERON:0012275 ! meso-epithelium -relationship: develops_from UBERON:0004139 ! cardiogenic plate -property_value: UBPROP:0000001 "The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000115", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002202 UBERON:0004139 ! develops from cardiogenic plate [Term] id: UBERON:0004292 @@ -212097,11 +209475,11 @@ xref: EMAPA:36645 xref: FMA:9496 xref: Wikipedia:Cardiac_skeleton is_a: UBERON:0003837 ! thoracic segment connective tissue +is_a: UBERON:0004120 ! mesoderm-derived structure relationship: adjacent_to UBERON:0002081 ! cardiac atrium relationship: adjacent_to UBERON:0002082 ! cardiac ventricle relationship: part_of UBERON:0000948 ! heart -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/50/Gray495.png" xsd:anyURI -property_value: UBPROP:0000009 "It is not a true skeleton, but it does provide structure and support for the heart, as well as isolating the atria from the ventricles. This allows the AV node and AV bundle to delay the wave of depolarisation such that the atria can contract and assist in ventricular filling before the ventricles themselves depolarise and contract (the AV bundle is the only part of the conduction system that passes from the atria to the ventricles in a normal heart). It also allows the valves (bicuspid, tricuspid, semilunar) to keep open by giving them structural support[WP]" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/50/Gray495.png" xsd:anyURI [Term] id: UBERON:0004293 @@ -212118,9 +209496,9 @@ is_a: UBERON:0001021 ! nerve intersection_of: UBERON:0001021 ! nerve intersection_of: part_of UBERON:0000011 ! parasympathetic nervous system relationship: extends_fibers_into UBERON:0001808 ! parasympathetic ganglion -relationship: has_developmental_contribution_from UBERON:0005428 {source="NCBIBook:NBK10065"} ! vagal neural crest -relationship: has_developmental_contribution_from UBERON:0010075 {source="NCBIBook:NBK10065"} ! sacral neural crest relationship: part_of UBERON:0000011 ! parasympathetic nervous system +relationship: RO:0002254 UBERON:0005428 {source="NCBIBook:NBK10065"} ! has developmental contribution from vagal neural crest +relationship: RO:0002254 UBERON:0010075 {source="NCBIBook:NBK10065"} ! has developmental contribution from sacral neural crest [Term] id: UBERON:0004294 @@ -212138,9 +209516,9 @@ is_a: UBERON:0001915 ! endothelium of capillary is_a: UBERON:0004189 ! glomerular endothelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0004212 ! glomerular capillary -relationship: contributes_to_morphology_of UBERON:0004212 ! glomerular capillary relationship: part_of UBERON:0004212 ! glomerular capillary -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002433 UBERON:0004212 ! contributes to morphology of glomerular capillary +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004295 @@ -212207,8 +209585,7 @@ intersection_of: UBERON:0003221 ! phalanx intersection_of: proximally_connected_to UBERON:0004301 ! middle phalanx relationship: part_of UBERON:0009551 ! distal segment of digit relationship: proximally_connected_to UBERON:0004301 ! middle phalanx -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/ab/Scheme_human_hand_bones-en.svg" xsd:anyURI -property_value: UBPROP:0000008 "In human anatomy, the distal phalanges of the four fingers and toes articulate proximally with the intermediate phalanges at the distal interphalangeal joints (DIP); in the thumb and big toe, with only two phalanges, the distal phalanges articulate proximally with the proximal phalanges. The distal phalanges carry and shape nails and claws and are therefore occasionally referred to as the ungual phalanges. The distal phalanges are cone-shaped in most mammals, including most primates, but relatively wide and flat in humans." xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/ab/Scheme_human_hand_bones-en.svg" xsd:anyURI [Term] id: UBERON:0004301 @@ -212231,9 +209608,7 @@ intersection_of: distally_connected_to UBERON:0003221 ! phalanx intersection_of: proximally_connected_to UBERON:0003221 ! phalanx relationship: distally_connected_to UBERON:0004300 ! distal phalanx relationship: proximally_connected_to UBERON:0004302 ! proximal phalanx -property_value: editor_note "consider using numbering system, and axioms to the effect that there is a single middle phalanx per finger in humans. This should perhaps be renamed 'intermediate phalanx', leaving the term middle phalanx open for the specific intermediate phalanx of a 3-phalanx digit" xsd:string -property_value: UBPROP:0000008 "in some groups such as whales, there are multiple intermediate phalanges" xsd:string -property_value: UBPROP:0000008 "Intermediate phalanges are bones found in the limbs of most vertebrates. In humans, they are the bones of the finger and toe which lie in the middle, between the two wrinkly joints. The thumb and big toe do not have intermediate phalanges. In most other vertebrates, they have a corresponding place in their limbs, whether they be paw, wing, hoof or fin" xsd:string {source="WP"} +property_value: IAO:0000116 "consider using numbering system, and axioms to the effect that there is a single middle phalanx per finger in humans. This should perhaps be renamed 'intermediate phalanx', leaving the term middle phalanx open for the specific intermediate phalanx of a 3-phalanx digit" xsd:string [Term] id: UBERON:0004302 @@ -212250,10 +209625,8 @@ xref: SCTID:299708005 xref: Wikipedia:Proximal_phalanges is_a: UBERON:0003221 ! phalanx intersection_of: UBERON:0003221 ! phalanx -intersection_of: connected_to UBERON:0003821 ! metapodium bone -relationship: connected_to UBERON:0003821 ! metapodium bone -property_value: UBPROP:0000008 "Proximal phalanges are bones found in the limbs of most vertebrates. In humans, they are the bones at the base of a toe or finger, the prominent, knobby ends of which are often called the knuckles. In other vertebrates, proximal phalanges have a similar placement in the corresponding limbs, be they paw, wing or fin. In many species, they are the longest and thickest phalanx ('finger' bone)" xsd:string {source="WP"} -property_value: UBPROP:0000105 "1" xsd:nonNegativeInteger +intersection_of: RO:0002170 UBERON:0003821 ! connected to metapodium bone +relationship: RO:0002170 UBERON:0003821 ! connected to metapodium bone [Term] id: UBERON:0004340 @@ -212274,17 +209647,12 @@ xref: UMLS:C0002084 {source="ncithesaurus:Allantois"} xref: VHOG:0000738 xref: Wikipedia:Allantois is_a: UBERON:0005631 ! extraembryonic membrane -relationship: develops_from UBERON:0000162 {source="Hymans"} ! cloaca -relationship: has_developmental_contribution_from UBERON:0000925 {notes="hindgut diverticulum endoderm", source="ISBN:0073040584"} ! endoderm -relationship: has_developmental_contribution_from UBERON:0004872 {source="ISBN:0073040584"} ! splanchnic layer of lateral plate mesoderm -relationship: only_in_taxon NCBITaxon:32524 {source="Hymans"} ! Amniota relationship: overlaps UBERON:0001008 {source="EHDAA2-modified"} ! renal system -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/a5/Gray25.png" xsd:anyURI -property_value: UBPROP:0000001 "A membranous sac that develops from the posterior part of the alimentary canal in the embryos of mammals, birds, and reptiles, and it is important in the formation of the umbilical cord and placenta in mammals. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000738", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/allantois"} -property_value: UBPROP:0000003 "Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000738", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.187", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "allantoic" xsd:string -property_value: UBPROP:0000011 "a diverticulum of the hindgut endoderm [ISBN:0073040584 (Vertebrates, Kardong)]" xsd:string -property_value: UBPROP:0000012 "part_of embryo in EHDAA2 - note differences in humans" xsd:string {external_ontology="EHDAA2"} +relationship: RO:0002160 NCBITaxon:32524 {source="Hymans"} ! only in taxon Amniota +relationship: RO:0002202 UBERON:0000162 {source="Hymans"} ! develops from cloaca +relationship: RO:0002254 UBERON:0000925 ! has developmental contribution from endoderm +relationship: RO:0002254 UBERON:0004872 {source="ISBN:0073040584"} ! has developmental contribution from splanchnic layer of lateral plate mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/a5/Gray25.png" xsd:anyURI [Term] id: UBERON:0004341 @@ -212298,7 +209666,6 @@ xref: EHDAA2:0001525 xref: EHDAA:185 xref: EMAPA:16072 xref: FMA:293110 -xref: MESH:D054240 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C28402 xref: SCTID:361438007 xref: UMLS:C0033153 {source="ncithesaurus:Primitive_Streak"} @@ -212306,13 +209673,10 @@ xref: VHOG:0001202 xref: Wikipedia:Primitive_streak is_a: UBERON:0000485 {source="EHDAA2"} ! simple columnar epithelium is_a: UBERON:0005291 ! embryonic tissue -relationship: develops_from UBERON:0008780 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="ISBN:9780878932504"} ! inner cell mass derived epiblast -relationship: has_potential_to_develop_into UBERON:0000925 ! endoderm -relationship: has_potential_to_develop_into UBERON:0000926 ! mesoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Gray13.png" xsd:anyURI -property_value: RO:0002174 NCBITaxon:32443 -property_value: UBPROP:0000003 "(...) the blastopore equivalent of chordates (germ ring in fish, marginal zone/blastopore lip in frog and node/primitive streak in chick and mouse) (...) (reference 1); Indeed, the primitive streak has been considered the homologue of the blastopore since the 1870s (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001202", ontology="VHOG", source="PMID:9609826 Wu LH, Lengyel JA, Role of caudal in hindgut specification and gastrulation suggests homology between Drosophila amnioproctodeal invagination and vertebrate blastopore. Development (1998), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.139", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "VHOG includes a very broad grouping here based on http://www.ncbi.nlm.nih.gov/pubmed/9609826" xsd:string {external_ontology="VHOG"} +relationship: RO:0002202 UBERON:0008780 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="ISBN:9780878932504"} ! develops from inner cell mass derived epiblast +relationship: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm +relationship: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Gray13.png" xsd:anyURI [Term] id: UBERON:0004345 @@ -212328,14 +209692,10 @@ xref: EMAPA:16046 xref: VHOG:0000979 is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0005292 ! extraembryonic tissue -relationship: develops_from UBERON:0000085 {source="EHDAA2"} ! morula relationship: has_part CL:1000274 ! trophectodermal cell relationship: part_of UBERON:0005631 {source="EHDAA2"} ! extraembryonic membrane -property_value: editor_note "distinction between trophectoderm and trophoblast unclear/inconsistent in many sources" xsd:string -property_value: UBPROP:0000001 "The outer cellular layer of the mammalian blastocyst. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.750, see_Kardong_KV][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000979", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "(...) the trophoblast develops rapidly so that contact may be made with the maternal uterine tissues when conditions are appropriate. We have here an excellent example of an embryonic adaptation, the development of a structure never present in either adult or embryo of 'lower' vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000979", ontology="VHOG", source="ISBN:978-0721676685 Romer AS, Parsons TS, Vertebrate body (1977) p.105-106", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "trophectodermal" xsd:string -property_value: UBPROP:0000012 "BTO has this has part of the trophoblast" xsd:string {external_ontology="BTO"} +relationship: RO:0002202 UBERON:0000085 {source="EHDAA2"} ! develops from morula +property_value: IAO:0000116 "distinction between trophectoderm and trophoblast unclear/inconsistent in many sources" xsd:string [Term] id: UBERON:0004347 @@ -212358,11 +209718,10 @@ xref: UMLS:C0282505 {source="ncithesaurus:Limb_Bud"} xref: Wikipedia:Limb_bud xref: XAO:0003161 is_a: UBERON:0004357 ! paired limb/fin bud -relationship: developmentally_induced_by UBERON:0003081 {source="ISBN:9780878932504"} ! lateral plate mesoderm -relationship: has_developmental_contribution_from UBERON:0005733 ! limb field -relationship: has_potential_to_develop_into UBERON:0002101 ! limb -relationship: only_in_taxon NCBITaxon:32523 ! Tetrapoda -property_value: UBPROP:0000001 "Early outgrowth of presumptive limb.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010375", ontology="AAO", source="AAO:EJS"} +relationship: RO:0002160 NCBITaxon:32523 ! only in taxon Tetrapoda +relationship: RO:0002254 UBERON:0005733 ! has developmental contribution from limb field +relationship: RO:0002256 UBERON:0003081 {source="ISBN:9780878932504"} ! developmentally induced by lateral plate mesoderm +relationship: RO:0002387 UBERON:0002101 ! has potential to develop into limb [Term] id: UBERON:0004348 @@ -212375,7 +209734,7 @@ xref: EMAPA:16322 xref: RETIRED_EHDAA2:0001308 xref: VHOG:0001296 is_a: UBERON:0006598 ! presumptive structure -relationship: has_potential_to_develop_into UBERON:0000964 ! cornea +relationship: RO:0002387 UBERON:0000964 ! has potential to develop into cornea [Term] id: UBERON:0004356 @@ -212397,17 +209756,11 @@ xref: ZFA:0001702 is_a: UBERON:0002050 ! embryonic structure relationship: capable_of GO:0010464 ! regulation of mesenchymal cell proliferation relationship: capable_of GO:0061037 ! negative regulation of cartilage development -relationship: developmentally_induced_by UBERON:0003104 ! mesenchyme relationship: part_of UBERON:0000924 ! ectoderm relationship: part_of UBERON:0004357 ! paired limb/fin bud relationship: produces PR:000007499 ! fibroblast growth factor 8 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/56/Limbbuddiagram.jpg" xsd:anyURI -property_value: IAO:0000232 "note that media, dorsal fins etc have AERs." xsd:string -property_value: UBPROP:0000001 "Distal ectodermal thickening which forms along the anterior-posterior limb axis. Signaling from this region influences proximal-distal patterning of the limb. Structure is missing in some lineages (salamanders, Eleutherodactylus coqui) however morphologically their indistinct distal ectoderm may still be involved in signaling.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010760", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000001 "Proliferative region that is part of the developing fin fold or fin.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002146", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000002 "relationship loss: subclass proliferative region (TAO:0000098)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002146", ontology="TAO"} -property_value: UBPROP:0000008 "The AER of tetrapods regresses after specification of skeletal progenitors, the AER of teleosts form an elongating fin fold" xsd:string {source="PMID:20574421"} -property_value: UBPROP:0000009 "maintaining mesenchyme in plastic proliferating state; maintaining expression of A-P axis genes; interacting with D-V proteins. Genes: AER induced by Fgf10 in mesenchyme. AER secretes Fgf8, which stimulates mitosis in the mesenchyme causing Fgf10 production - positive feedback loop" xsd:string +relationship: RO:0002256 UBERON:0003104 ! developmentally induced by mesenchyme +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/56/Limbbuddiagram.jpg" xsd:anyURI [Term] id: UBERON:0004357 @@ -212422,10 +209775,9 @@ synonym: "paired limb/fin bud" EXACT [VHOG:0001258] xref: VHOG:0001258 is_a: UBERON:0003102 ! surface structure is_a: UBERON:0006598 ! presumptive structure -relationship: has_developmental_contribution_from UBERON:0005732 ! paired limb/fin field relationship: has_part UBERON:0004356 ! apical ectodermal ridge -relationship: has_potential_to_develop_into UBERON:0004708 ! paired limb/fin -property_value: UBPROP:0000003 "The tetrapod limb is derived from a posterior part of the fin endoskeleton of elasmobranchs and basal bony fish, the so-called metapterygium, a series of endoskeletal elements that is the first to form in the developing paired fins. (...) In addition, there is an independent endoskeletal element called the protopterygium that develops anterior to the metapterygium in many basal fishes (e.g., the bichir and sturgeon). Teleosts have lost the metapterygium whereas the sarcopterygians, on the other hand, have lost the protopterygium. Sarcopterygians thus develop all their endoskeletal structures from the metapterygium and consequently the tetrapod limb skeleton is derived from the metapterygium.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001258", ontology="VHOG", source="DOI:10.1002/jez.1100 Wagner GP, Chiu C, The tetrapod limb: A hypothesis on its origin. J Exp Zool (Mol Dev Evol) (2001)", source="http://bgee.unil.ch/"} +relationship: RO:0002254 UBERON:0005732 ! has developmental contribution from paired limb/fin field +relationship: RO:0002387 UBERON:0004708 ! has potential to develop into paired limb/fin [Term] id: UBERON:0004362 @@ -212461,11 +209813,7 @@ xref: Wikipedia:First_pharyngeal_arch xref: XAO:0000097 xref: ZFA:0001612 is_a: UBERON:0002539 ! pharyngeal arch -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray48.png" xsd:anyURI -property_value: UBPROP:0000001 "the first arch which contributes to development of mastication muscles, maxilla, mandible, incus, malleus, Meckel's cartilage, trigeminal nerve, and maxillary artery" xsd:string {source="MP:0006337,MGI:smb"} -property_value: UBPROP:0000001 "The first of the series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010364", ontology="AAO", source="XAO:EJS"} -property_value: UBPROP:0000003 "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000296", ontology="VHOG", source="DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000103 "1" xsd:nonNegativeInteger +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray48.png" xsd:anyURI [Term] id: UBERON:0004363 @@ -212507,17 +209855,12 @@ is_a: UBERON:0003469 ! respiratory system artery is_a: UBERON:0003496 ! head blood vessel is_a: UBERON:0006598 ! presumptive structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest -relationship: contributes_to_morphology_of UBERON:0002539 ! pharyngeal arch -relationship: has_potential_to_develop_into UBERON:0001637 ! artery relationship: part_of UBERON:0002539 ! pharyngeal arch relationship: part_of UBERON:0007303 {source="ZFA"} ! pharyngeal vasculature -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/84/Gray473.png" xsd:anyURI -property_value: editor_note "add specific artery derivatives" xsd:string -property_value: IAO:0000232 "Do not confuse with arch of aorta." xsd:string -property_value: UBPROP:0000001 "Paired vessels arching from the ventral to the dorsal aorta through the pharyngeal arches. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000122", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/aortic+arches"} -property_value: UBPROP:0000003 "When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000122", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "Number varies - Lampreys have 8, hagfishes 15; only up to 6 appear in embryonic development in most gnathostome fishes and all tetrapods" xsd:string -property_value: UBPROP:0000011 "The third, fourth, and sixth arches, along with the seventh intersegmental arteries and the left dorsal aorta, are the primary contributors to the normal aortic arch and its major thoracic branches" xsd:string +relationship: RO:0002387 UBERON:0001637 ! has potential to develop into artery +relationship: RO:0002433 UBERON:0002539 ! contributes to morphology of pharyngeal arch +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/84/Gray473.png" xsd:anyURI +property_value: IAO:0000116 "add specific artery derivatives" xsd:string [Term] id: UBERON:0004364 @@ -212531,7 +209874,6 @@ xref: BTO:0001715 xref: EMAPA:16059 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0000088 ! trophoblast -property_value: UBPROP:0000011 "derivative of the early postimplantation trophoblast, which probably gives rise to the spongiotrophoblast." xsd:string {source="PMID:19829370"} [Term] id: UBERON:0004365 @@ -212542,9 +209884,9 @@ subset: pheno_slim xref: EMAPA:36494 is_a: UBERON:0001981 ! blood vessel intersection_of: UBERON:0001981 ! blood vessel -intersection_of: connected_to UBERON:0001040 ! yolk sac -relationship: connected_to UBERON:0001040 ! yolk sac +intersection_of: RO:0002170 UBERON:0001040 ! connected to yolk sac relationship: part_of UBERON:0004374 ! vitelline vasculature +relationship: RO:0002170 UBERON:0001040 ! connected to yolk sac [Term] id: UBERON:0004367 @@ -212573,6 +209915,7 @@ xref: UMLS:C0011665 {source="ncithesaurus:Descemet_s_Membrane"} xref: Wikipedia:Descemet%27s_membrane xref: ZFA:0001686 is_a: UBERON:0005769 ! basement membrane of epithelium +is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0005769 ! basement membrane of epithelium intersection_of: adjacent_to UBERON:0001777 ! substantia propria of cornea intersection_of: adjacent_to UBERON:0001985 ! corneal endothelium @@ -212580,11 +209923,10 @@ intersection_of: part_of UBERON:0000964 ! cornea disjoint_from: UBERON:0004370 {source="lexical"} ! anterior limiting lamina of cornea relationship: adjacent_to UBERON:0001777 ! substantia propria of cornea relationship: adjacent_to UBERON:0001985 ! corneal endothelium -relationship: has_quality PATO:0000964 ! transparent relationship: part_of UBERON:0000964 ! cornea relationship: produced_by UBERON:0001985 {source="Cline et al"} ! corneal endothelium +relationship: RO:0000086 PATO:0000964 ! has quality transparent property_value: seeAlso "https://github.com/obophenotype/uberon/issues/15" xsd:anyURI -property_value: UBPROP:0000001 "Acellular anatomical structure composed of collagen, Descemet's membrane is secreted as a basement membrane of the corneal endothelium. Located between the stroma and the corneal endothelium, it is approximately 0.15 micrometer thick at 6 months post-fertilization.[ZFIN]" xsd:string {date_retrieved="2016-05-01", external_class="TAO:0002157", ontology="ZFIN", source="ZFIN:ZDB-PUB-061010-3", source="https://orcid.org/0000-0001-9114-8737"} [Term] id: UBERON:0004370 @@ -212612,13 +209954,12 @@ xref: UMLS:C0229127 {source="ncithesaurus:Bowman_s_Membrane"} xref: Wikipedia:Bowman%27s_membrane xref: ZFA:0001684 is_a: UBERON:0005769 ! basement membrane of epithelium +is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0005769 ! basement membrane of epithelium -intersection_of: attaches_to UBERON:0001772 ! corneal epithelium intersection_of: part_of UBERON:0000964 ! cornea -relationship: attaches_to UBERON:0001772 ! corneal epithelium +intersection_of: RO:0002371 UBERON:0001772 ! attached to corneal epithelium relationship: part_of UBERON:0000964 ! cornea -property_value: UBPROP:0000001 "Acellular anatomical structure that is the zone of collagen fibers adjacent the basement membrane of the corneal epithelium.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002155", ontology="TAO", source="ZFIN:ZDB-PUB-061010-3"} -property_value: UBPROP:0000008 "Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals" xsd:string +relationship: RO:0002371 UBERON:0001772 ! attached to corneal epithelium [Term] id: UBERON:0004374 @@ -212632,8 +209973,8 @@ synonym: "vitelline system" RELATED [https://orcid.org/0000-0002-6601-2165] xref: Wikipedia:Vitelline_circulation is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature -intersection_of: connected_to UBERON:0001040 ! yolk sac -relationship: connected_to UBERON:0001040 ! yolk sac +intersection_of: RO:0002170 UBERON:0001040 ! connected to yolk sac +relationship: RO:0002170 UBERON:0001040 ! connected to yolk sac [Term] id: UBERON:0004375 @@ -212644,6 +209985,7 @@ subset: homology_grouping synonym: "appendage bone" EXACT [] synonym: "bone of appendage" EXACT [] synonym: "bone of free segment of appendicular skeleton" EXACT [] +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010740 ! bone of appendage girdle complex intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0004708 ! paired limb/fin @@ -212658,8 +210000,8 @@ synonym: "proximal diaphyseal end of long bone" EXACT [FMA:32823] xref: FMA:32823 is_a: UBERON:0001438 ! metaphysis intersection_of: UBERON:0001438 ! metaphysis -intersection_of: in_proximal_side_of UBERON:0004769 ! diaphysis -relationship: in_proximal_side_of UBERON:0004769 ! diaphysis +intersection_of: BSPO:0000124 UBERON:0004769 ! diaphysis +relationship: BSPO:0000124 UBERON:0004769 ! diaphysis [Term] id: UBERON:0004380 @@ -212671,9 +210013,9 @@ xref: FMA:32821 xref: SCTID:279998003 is_a: UBERON:0001437 ! epiphysis intersection_of: UBERON:0001437 ! epiphysis -intersection_of: in_proximal_side_of UBERON:0001474 ! bone element +intersection_of: BSPO:0000124 UBERON:0001474 ! bone element relationship: adjacent_to UBERON:0004378 ! proximal metaphysis -relationship: in_proximal_side_of UBERON:0001474 ! bone element +relationship: BSPO:0000124 UBERON:0001474 ! bone element [Term] id: UBERON:0004381 @@ -212689,10 +210031,8 @@ xref: VSAO:0000300 is_a: UBERON:0010712 ! limb skeleton subdivision is_a: UBERON:0011582 ! paired limb/fin skeleton intersection_of: UBERON:0010912 ! subdivision of skeleton -intersection_of: skeleton_of UBERON:0002101 ! limb -relationship: skeleton_of UBERON:0002101 ! limb -property_value: UBPROP:0000001 "Skeletal subdivision that is part of the limb.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000300", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070"} -property_value: UBPROP:0000012 "EHDAA2 considers hip and shoulder joints part of limb skeleton." xsd:string {external_ontology="EHDAA2"} +intersection_of: RO:0002576 UBERON:0002101 ! skeleton of limb +relationship: RO:0002576 UBERON:0002101 ! skeleton of limb [Term] id: UBERON:0004382 @@ -212704,6 +210044,7 @@ synonym: "humeral epiphysis" EXACT [OBOL:automatic] xref: FMA:32825 xref: SCTID:313054009 is_a: UBERON:0001437 ! epiphysis +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0001437 ! epiphysis intersection_of: part_of UBERON:0000976 ! humerus relationship: part_of UBERON:0000976 ! humerus @@ -212720,6 +210061,7 @@ xref: FMA:33112 xref: MA:0003113 xref: SCTID:314626006 is_a: UBERON:0001437 ! epiphysis +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0001437 ! epiphysis intersection_of: part_of UBERON:0000979 ! tibia relationship: part_of UBERON:0000979 ! tibia @@ -212736,6 +210078,7 @@ xref: FMA:32838 xref: MA:0003056 xref: SCTID:314625005 is_a: UBERON:0001437 ! epiphysis +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0001437 ! epiphysis intersection_of: part_of UBERON:0000981 ! femur relationship: part_of UBERON:0000981 ! femur @@ -212764,6 +210107,7 @@ subset: pheno_slim synonym: "fibula epiphysis" EXACT [FMA:33726] xref: FMA:33726 is_a: UBERON:0001437 ! epiphysis +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0001437 ! epiphysis intersection_of: part_of UBERON:0001446 ! fibula relationship: part_of UBERON:0001446 ! fibula @@ -212779,6 +210123,7 @@ synonym: "metatarsal bone epiphysis" EXACT [FMA:33814] synonym: "metatarsal epiphysis" EXACT [] xref: FMA:33814 xref: SCTID:313057002 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0011973 ! epiphysis of phalanx of pes intersection_of: UBERON:0001437 ! epiphysis intersection_of: part_of UBERON:0001448 ! metatarsal bone @@ -212796,6 +210141,7 @@ synonym: "metacarpal epiphysis" EXACT [] xref: FMA:33792 xref: SCTID:314907001 is_a: UBERON:0001437 ! epiphysis +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0001437 ! epiphysis intersection_of: part_of UBERON:0002374 ! metacarpal bone relationship: part_of UBERON:0002374 ! metacarpal bone @@ -212854,7 +210200,7 @@ is_a: UBERON:0004380 ! proximal epiphysis is_a: UBERON:0004382 ! epiphysis of humerus intersection_of: UBERON:0004380 ! proximal epiphysis intersection_of: part_of UBERON:0000976 ! humerus -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray207.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray207.png" xsd:anyURI [Term] id: UBERON:0004412 @@ -212929,6 +210275,7 @@ def: "An epiphysis that is part of a phalanx [Automatically generated definition subset: pheno_slim xref: SCTID:280033007 is_a: UBERON:0001437 ! epiphysis +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0001437 ! epiphysis intersection_of: part_of UBERON:0003221 ! phalanx relationship: part_of UBERON:0003221 ! phalanx @@ -212965,12 +210312,9 @@ xref: Wikipedia:Cerebral_artery xref: XAO:0000367 is_a: UBERON:0004573 ! systemic artery intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0001893 ! telencephalon +intersection_of: RO:0002178 UBERON:0001893 ! supplies telencephalon relationship: part_of UBERON:0003709 ! circle of Willis -relationship: supplies UBERON:0001893 ! telencephalon -property_value: UBPROP:0000001 "Part of the internal carotid containing many branches supplying blood to the chorioid plexuses of the brain.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010493", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000002 "relationship loss: part_of internal carotid (AAO:0010219)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010493", ontology="AAO"} -property_value: UBPROP:0000012 "in AAO this is part_of the internal carotid, but in humans the PCA intervenes for some cerebral arteries. Proper comparative review required" xsd:string {external_ontology="AAO"} +relationship: RO:0002178 UBERON:0001893 ! supplies telencephalon [Term] id: UBERON:0004451 @@ -212984,12 +210328,10 @@ xref: MA:0002869 xref: XAO:0003077 is_a: UBERON:0002412 ! vertebra intersection_of: UBERON:0002412 ! vertebra -intersection_of: anterior_to UBERON:0001095 ! caudal vertebra +intersection_of: BSPO:0000096 UBERON:0001095 ! caudal vertebra union_of: UBERON:0002413 ! cervical vertebra union_of: UBERON:0011677 ! trunk vertebra -relationship: anterior_to UBERON:0001095 ! caudal vertebra -property_value: UBPROP:0000008 "In humans, there are 24 presacral vertebrae (7 cervical, 12 thoracic, and 5 lumbar)" xsd:string -property_value: UBPROP:0000012 "it's not clear if the XAO class belongs here or below" xsd:string {external_ontology="XAO"} +relationship: BSPO:0000096 UBERON:0001095 ! caudal vertebra [Term] id: UBERON:0004452 @@ -213028,11 +210370,11 @@ is_a: UBERON:0008785 {source="FMA"} ! upper limb segment intersection_of: UBERON:0006716 ! mesopodium region intersection_of: part_of UBERON:0002398 ! manus relationship: distally_connected_to UBERON:0004453 ! metacarpus region -relationship: has_skeleton UBERON:0009880 ! carpal skeleton relationship: part_of UBERON:0002398 ! manus relationship: proximally_connected_to UBERON:0002386 ! forelimb zeugopod -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/4/4a/Human_wrist.png" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/c/cc/Hand_parts.jpg" xsd:anyURI +relationship: RO:0002551 UBERON:0009880 ! has skeleton carpal skeleton +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/4/4a/Human_wrist.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/c/cc/Hand_parts.jpg" xsd:anyURI [Term] id: UBERON:0004453 @@ -213056,12 +210398,10 @@ is_a: UBERON:0005451 {source="FMA"} ! segment of manus is_a: UBERON:0009877 ! metapodium region intersection_of: UBERON:0009877 ! metapodium region intersection_of: part_of UBERON:0002398 ! manus -relationship: has_skeleton UBERON:0010544 ! metacarpus skeleton relationship: part_of UBERON:0012141 {source="PHENOSCAPE:ni"} ! manual digitopodium region -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/2/2f/Metacarpals_numbered-en.svg" xsd:anyURI -property_value: editor_note "Note that along with FMA we treat this as a limb segment rather than a purely skeletal element" xsd:string -property_value: UBPROP:0000007 "metacarpal" xsd:string -property_value: UBPROP:0000012 "Note that mammalian and non-mammalian AOs differ in whether they consider this a part of the skeleton" xsd:string +relationship: RO:0002551 UBERON:0010544 ! has skeleton metacarpus skeleton +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/2f/Metacarpals_numbered-en.svg" xsd:anyURI +property_value: IAO:0000116 "Note that along with FMA we treat this as a limb segment rather than a purely skeletal element" xsd:string [Term] id: UBERON:0004454 @@ -213094,12 +210434,10 @@ is_a: UBERON:0008784 ! lower limb segment intersection_of: UBERON:0006716 ! mesopodium region intersection_of: part_of UBERON:0002387 ! pes relationship: distally_connected_to UBERON:0000983 ! metatarsus region -relationship: has_skeleton UBERON:0009879 ! tarsal skeleton relationship: part_of UBERON:0002387 ! pes relationship: proximally_connected_to UBERON:0003823 ! hindlimb zeugopod -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/b/bf/Ankle_en.svg" xsd:anyURI -property_value: IAO:0000232 "this term refers to the limb segment. See also: tarsal bones and tarsal skeleton" xsd:string -property_value: UBPROP:0000012 "MA has both tarsus (part of foot, has tarsal bone) and ankle (part of hindlimb, has joint, nerve, skin)." xsd:string {external_ontology="MA"} +relationship: RO:0002551 UBERON:0009879 ! has skeleton tarsal skeleton +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/b/bf/Ankle_en.svg" xsd:anyURI [Term] id: UBERON:0004455 @@ -213114,9 +210452,9 @@ xref: NCIT:C34229 xref: UMLS:C1518306 {source="ncithesaurus:Neurula"} is_a: UBERON:0000922 ! embryo intersection_of: UBERON:0000468 ! multicellular organism -intersection_of: existence_starts_and_ends_during UBERON:0000110 ! neurula stage -relationship: develops_from UBERON:0004734 ! gastrula -relationship: existence_starts_and_ends_during UBERON:0000110 ! neurula stage +intersection_of: RO:0002491 UBERON:0000110 ! existence starts and ends during neurula stage +relationship: RO:0002202 UBERON:0004734 ! develops from gastrula +relationship: RO:0002491 UBERON:0000110 ! existence starts and ends during neurula stage [Term] id: UBERON:0004456 @@ -213128,9 +210466,8 @@ synonym: "sense organ system" EXACT [FMA:78499] xref: FMA:78499 is_a: UBERON:0000467 ! anatomical system disjoint_from: UBERON:8450002 ! excretory system -relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: overlaps UBERON:0001016 ! nervous system -property_value: UBPROP:0000012 "note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs" xsd:string +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage [Term] id: UBERON:0004461 @@ -213148,12 +210485,12 @@ xref: EMAPA:18171 xref: FMA:71287 is_a: UBERON:0008229 ! craniocervical region musculature intersection_of: UBERON:0001015 ! musculature -intersection_of: attaches_to UBERON:0003129 ! skull intersection_of: part_of UBERON:0000033 ! head -relationship: attaches_to UBERON:0003129 ! skull -relationship: develops_from UBERON:0005253 ! head mesenchyme +intersection_of: RO:0002371 UBERON:0003129 ! attached to skull relationship: part_of UBERON:0000033 ! head relationship: part_of UBERON:0013700 ! axial musculature +relationship: RO:0002202 UBERON:0005253 ! develops from head mesenchyme +relationship: RO:0002371 UBERON:0003129 ! attached to skull property_value: seeAlso "https://github.com/obophenotype/mouse-anatomy-ontology/issues/4" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/1405" xsd:anyURI @@ -213173,7 +210510,6 @@ is_a: UBERON:0001015 ! musculature intersection_of: UBERON:0001015 ! musculature intersection_of: part_of UBERON:0000309 ! body wall relationship: part_of UBERON:0000309 ! body wall -property_value: UBPROP:0000008 "define generically to encompass both vertebrates and invertebrates" xsd:string [Term] id: UBERON:0004463 @@ -213209,7 +210545,6 @@ is_a: UBERON:0004479 ! musculature of trunk intersection_of: UBERON:0001015 ! musculature intersection_of: part_of UBERON:0000915 ! thoracic segment of trunk relationship: part_of UBERON:0000915 ! thoracic segment of trunk -property_value: UBPROP:0000012 "BTO and FMA do not mean precisely the same thing here. BTO thorax muscle is a pectoral muscle or diaphragm" xsd:string {external_ontology="BTO"} [Term] id: UBERON:0004465 @@ -213245,7 +210580,6 @@ is_a: UBERON:0004482 ! musculature of lower limb intersection_of: UBERON:0001015 ! musculature intersection_of: part_of UBERON:0000978 ! leg relationship: part_of UBERON:0000978 ! leg -property_value: UBPROP:0000013 "see notes on UBERON:0000978 for possible confusion over the term 'leg'. This class represents the class-union of upper leg musculature and lower leg musculature (and thus may not mean precisely the same thing as the EHDAA2 class)" xsd:string [Term] id: UBERON:0004467 @@ -213270,8 +210604,8 @@ synonym: "muscle group of vertebral column" EXACT [FMA:33061] xref: FMA:33061 is_a: UBERON:0001015 ! musculature intersection_of: UBERON:0001015 ! musculature -intersection_of: attaches_to UBERON:0001130 ! vertebral column -relationship: attaches_to UBERON:0001130 ! vertebral column +intersection_of: RO:0002371 UBERON:0001130 ! attached to vertebral column +relationship: RO:0002371 UBERON:0001130 ! attached to vertebral column [Term] id: UBERON:0004469 @@ -213314,7 +210648,6 @@ is_a: UBERON:0014792 ! musculature of pelvic complex intersection_of: UBERON:0001015 ! musculature intersection_of: part_of UBERON:0001271 ! pelvic girdle region relationship: part_of UBERON:0001271 ! pelvic girdle region -property_value: UBPROP:0000012 "we merge two FMA classes here" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0004471 @@ -213351,7 +210684,7 @@ is_a: UBERON:0008229 ! craniocervical region musculature intersection_of: UBERON:0001015 ! musculature intersection_of: part_of UBERON:0001456 ! face relationship: part_of UBERON:0001456 ! face -property_value: editor_note "originally created to reflect the distinction drawn in FMA between a facial muscle and the entire musculature of the face. However, naming both does not serve any particular purpose" xsd:string +property_value: IAO:0000116 "originally created to reflect the distinction drawn in FMA between a facial muscle and the entire musculature of the face. However, naming both does not serve any particular purpose" xsd:string [Term] id: UBERON:0004474 @@ -213381,9 +210714,9 @@ synonym: "set of muscles of hip" EXACT [FMA:50227] xref: FMA:50227 is_a: UBERON:0001015 ! musculature intersection_of: UBERON:0001015 ! musculature -intersection_of: attaches_to UBERON:0008202 ! bone of hip region -relationship: attaches_to UBERON:0008202 ! bone of hip region +intersection_of: RO:0002371 UBERON:0008202 ! attached to bone of hip region relationship: overlaps UBERON:0001464 ! hip +relationship: RO:0002371 UBERON:0008202 ! attached to bone of hip region [Term] id: UBERON:0004476 @@ -213396,9 +210729,9 @@ synonym: "set of muscles of shoulder" EXACT [FMA:50220] xref: FMA:50220 is_a: UBERON:0001015 ! musculature intersection_of: UBERON:0001015 ! musculature -intersection_of: attaches_to UBERON:0003461 ! shoulder bone -relationship: attaches_to UBERON:0003461 ! shoulder bone +intersection_of: RO:0002371 UBERON:0003461 ! attached to shoulder bone relationship: overlaps UBERON:0001467 ! shoulder +relationship: RO:0002371 UBERON:0003461 ! attached to shoulder bone [Term] id: UBERON:0004478 @@ -213415,10 +210748,11 @@ xref: FMA:46616 xref: MESH:D007821 xref: Wikipedia:Muscles_of_larynx is_a: UBERON:0001015 ! musculature +is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0001015 ! musculature intersection_of: part_of UBERON:0001737 ! larynx relationship: part_of UBERON:0001737 ! larynx -property_value: editor_note "currently defined by location rather than attachment" xsd:string +property_value: IAO:0000116 "currently defined by location rather than attachment" xsd:string [Term] id: UBERON:0004479 @@ -213437,7 +210771,7 @@ is_a: UBERON:0001015 ! musculature intersection_of: UBERON:0001015 ! musculature intersection_of: part_of UBERON:0002100 ! trunk relationship: part_of UBERON:0002100 ! trunk -property_value: editor_note "currently defined by location rather than attachment" xsd:string +property_value: IAO:0000116 "currently defined by location rather than attachment" xsd:string [Term] id: UBERON:0004480 @@ -213457,7 +210791,7 @@ is_a: UBERON:0007271 ! appendage musculature intersection_of: UBERON:0001015 ! musculature intersection_of: part_of UBERON:0002101 ! limb relationship: part_of UBERON:0002101 ! limb -property_value: editor_note "currently defined by location rather than attachment" xsd:string +property_value: IAO:0000116 "currently defined by location rather than attachment" xsd:string [Term] id: UBERON:0004481 @@ -213475,7 +210809,7 @@ is_a: UBERON:0007269 ! pectoral appendage musculature intersection_of: UBERON:0001015 ! musculature intersection_of: part_of UBERON:0002102 ! forelimb relationship: part_of UBERON:0002102 ! forelimb -property_value: editor_note "currently defined by location rather than attachment" xsd:string +property_value: IAO:0000116 "currently defined by location rather than attachment" xsd:string [Term] id: UBERON:0004482 @@ -213493,7 +210827,7 @@ is_a: UBERON:0007270 ! pelvic appendage musculature intersection_of: UBERON:0001015 ! musculature intersection_of: part_of UBERON:0002103 ! hindlimb relationship: part_of UBERON:0002103 ! hindlimb -property_value: editor_note "currently defined by location rather than attachment" xsd:string +property_value: IAO:0000116 "currently defined by location rather than attachment" xsd:string [Term] id: UBERON:0004487 @@ -213524,7 +210858,7 @@ is_a: UBERON:0004482 ! musculature of lower limb intersection_of: UBERON:0001015 ! musculature intersection_of: part_of UBERON:0002387 ! pes relationship: part_of UBERON:0002387 ! pes -property_value: editor_note "currently defined by location rather than attachment" xsd:string +property_value: IAO:0000116 "currently defined by location rather than attachment" xsd:string [Term] id: UBERON:0004489 @@ -213541,7 +210875,7 @@ is_a: UBERON:0004481 ! musculature of upper limb intersection_of: UBERON:0001015 ! musculature intersection_of: part_of UBERON:0002398 ! manus relationship: part_of UBERON:0002398 ! manus -property_value: editor_note "currently defined by location rather than attachment" xsd:string +property_value: IAO:0000116 "currently defined by location rather than attachment" xsd:string [Term] id: UBERON:0004490 @@ -213557,7 +210891,6 @@ is_a: UBERON:0004493 ! cardiac muscle tissue of myocardium intersection_of: UBERON:0001133 ! cardiac muscle tissue intersection_of: part_of UBERON:0002081 ! cardiac atrium relationship: part_of UBERON:0002302 ! myocardium of atrium -property_value: UBPROP:0000012 "in GO, this is equivalent to the atrial myocardium, but FMA distinguishes these two. Consider merging." xsd:string {external_ontology="GO"} [Term] id: UBERON:0004491 @@ -213595,14 +210928,13 @@ name: cardiac muscle tissue of myocardium namespace: uberon def: "A portion of cardiac muscle tissue that is part of a myocardium [Automatically generated definition]." [OBOL:automatic] subset: pheno_slim -xref: EMAPA:32688 xref: FMA:261726 xref: MA:0002441 is_a: UBERON:0001133 ! cardiac muscle tissue intersection_of: UBERON:0001133 ! cardiac muscle tissue intersection_of: part_of UBERON:0002349 ! myocardium relationship: part_of UBERON:0002349 {source="MA"} ! myocardium -property_value: editor_note "Note placement of MA class based on parthood relationship" xsd:string +property_value: IAO:0000116 "Note placement of MA class based on parthood relationship" xsd:string [Term] id: UBERON:0004495 @@ -213636,6 +210968,7 @@ def: "A portion of skeletal muscle tissue that is part of a trapezius [Automatic synonym: "skeletal muscle tissue of trapezius muscle" RELATED [FMA:261938] xref: FMA:261938 is_a: UBERON:0001134 ! skeletal muscle tissue +is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0001134 ! skeletal muscle tissue intersection_of: part_of UBERON:0002380 ! trapezius muscle relationship: part_of UBERON:0002380 ! trapezius muscle @@ -213663,7 +210996,7 @@ is_a: UBERON:0004233 ! lower respiratory tract smooth muscle intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0002186 ! bronchiole relationship: part_of UBERON:0002186 ! bronchiole -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004516 @@ -213675,10 +211008,10 @@ xref: FMA:261051 is_a: UBERON:0004515 ! smooth muscle tissue of bronchiole intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0002187 ! terminal bronchiole -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: has_part CL:4033017 ! bronchiolar smooth muscle cell relationship: part_of UBERON:0002187 ! terminal bronchiole -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004517 @@ -213690,10 +211023,10 @@ xref: FMA:261055 is_a: UBERON:0004515 ! smooth muscle tissue of bronchiole intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0002188 ! respiratory bronchiole -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: has_part CL:4033017 ! bronchiolar smooth muscle cell relationship: part_of UBERON:0002188 ! respiratory bronchiole -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004518 @@ -213704,8 +211037,8 @@ synonym: "vertebral column muscle" EXACT [FMA:22594] xref: FMA:22594 is_a: UBERON:0014892 ! skeletal muscle organ, vertebrate intersection_of: UBERON:0014892 ! skeletal muscle organ, vertebrate -intersection_of: attaches_to UBERON:0002412 ! vertebra -relationship: attaches_to UBERON:0002412 ! vertebra +intersection_of: RO:0002371 UBERON:0002412 ! attached to vertebra +relationship: RO:0002371 UBERON:0002412 ! attached to vertebra [Term] id: UBERON:0004520 @@ -213806,13 +211139,10 @@ xref: Wikipedia:Process_(anatomy) xref: XAO:0004020 is_a: UBERON:0034768 ! morphological feature relationship: part_of UBERON:0000062 ! organ -relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 ! Fungi -property_value: editor_note "should be declared disjoint from organ, but in some ontologies (e.g. ZFA), structures such as neural spines are classified as bones (and hence organs)" xsd:string -property_value: UBPROP:0000001 "Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, or tissue.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010278", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, tissue, fin, scale, etc.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001834", ontology="TAO", source="TAO:wd"} -property_value: UBPROP:0000001 "Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, tissue, fin, scale, etc.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000180", ontology="VSAO", source="TAO:curator"} +property_value: IAO:0000116 "should be declared disjoint from organ, but in some ontologies (e.g. ZFA), structures such as neural spines are classified as bones (and hence organs)" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0004530 @@ -213827,9 +211157,9 @@ xref: FMA:75433 xref: ZFA:0001637 is_a: UBERON:4100000 ! skeletal element projection intersection_of: UBERON:4100000 ! skeletal element projection -intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue -relationship: composed_primarily_of UBERON:0002481 ! bone tissue -relationship: continuous_with UBERON:0004765 ! skeletal element +intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue +relationship: RO:0002150 UBERON:0004765 ! continuous with skeletal element +relationship: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue [Term] id: UBERON:0004533 @@ -213844,10 +211174,10 @@ xref: NCIT:C49323 xref: SCTID:367720001 xref: UMLS:C0227998 {source="ncithesaurus:Left_Testis"} is_a: UBERON:0000473 ! testis +is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0000473 ! testis -intersection_of: in_left_side_of UBERON:0000990 ! reproductive system -relationship: in_left_side_of UBERON:0000990 ! reproductive system -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +intersection_of: BSPO:0000120 UBERON:0000990 ! reproductive system +relationship: BSPO:0000120 UBERON:0000990 ! reproductive system [Term] id: UBERON:0004534 @@ -213862,10 +211192,10 @@ xref: NCIT:C49326 xref: SCTID:367719007 xref: UMLS:C0227997 {source="ncithesaurus:Right_Testis"} is_a: UBERON:0000473 ! testis +is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0000473 ! testis -intersection_of: in_right_side_of UBERON:0000990 ! reproductive system -relationship: in_right_side_of UBERON:0000990 ! reproductive system -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +intersection_of: BSPO:0000121 UBERON:0000990 ! reproductive system +relationship: BSPO:0000121 UBERON:0000990 ! reproductive system [Term] id: UBERON:0004535 @@ -213884,10 +211214,8 @@ xref: BILA:0000016 xref: BTO:0000088 xref: CALOHA:TS-1297 xref: EFO:0000791 -xref: EHDAA2:0000216 xref: EHDAA:394 xref: EMAPA:16104 -xref: EMAPA:16370 xref: EV:0100017 xref: FMA:7161 xref: GAID:467 @@ -213913,9 +211241,7 @@ intersection_of: part_of UBERON:0001009 ! circulatory system relationship: has_part UBERON:0000948 ! heart relationship: has_part UBERON:0001981 ! blood vessel relationship: part_of UBERON:0001009 ! circulatory system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: IAO:0000232 "we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph." xsd:string -property_value: UBPROP:0000003 "The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000302", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.451", source="http://bgee.unil.ch/"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004536 @@ -213932,18 +211258,16 @@ synonym: "lymphatic vessels set" EXACT [FMA:63815] synonym: "set of lymphatic vessels" EXACT [] synonym: "trunci et ductus lymphatici" EXACT OMO:0003011 [FMA:63815, FMA:TA] xref: FMA:63815 -xref: TAO:0005105 xref: ZFA:0005105 is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: has_part UBERON:0002391 ! lymph relationship: has_part UBERON:0002391 ! lymph relationship: part_of UBERON:0006558 ! lymphatic part of lymphoid system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_F_Lymph_Node.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_M_Lymph_Node.glb" xsd:anyURI -property_value: editor_note "consider merging with parent" xsd:string -property_value: UBPROP:0000001 "A network of blunt ended vessels lacking direct connection to the blood vascular system. These vessels collect and drain fluids and macromolecules from interstitial spaces throughout the animal. They derive from a subpopulation of endothelial cells and have walls that are much thinner than the blood carrying vessels. Lymphatic vessels are usually classified as either superficial or deep.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005105", ontology="TAO", source="ZFIN:curator"} +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_F_Lymph_Node.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_M_Lymph_Node.glb" xsd:anyURI +property_value: IAO:0000116 "consider merging with parent" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004537 @@ -213961,11 +211285,11 @@ xref: ZFA:0001079 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature -intersection_of: composed_primarily_of UBERON:0001981 ! blood vessel -relationship: composed_primarily_of UBERON:0001981 ! blood vessel -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +intersection_of: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel +relationship: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004538 @@ -213981,12 +211305,11 @@ xref: SCTID:362209008 xref: UMLS:C0227614 {source="ncithesaurus:Left_Kidney"} is_a: UBERON:0002113 ! kidney intersection_of: UBERON:0002113 ! kidney -intersection_of: in_left_side_of UBERON:0000468 ! multicellular organism -relationship: in_left_side_of UBERON:0000468 ! multicellular organism -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Kidney_Left.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +intersection_of: BSPO:0000120 UBERON:0000468 ! multicellular organism +relationship: BSPO:0000120 UBERON:0000468 ! multicellular organism +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Kidney_Left.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI [Term] id: UBERON:0004539 @@ -214002,12 +211325,11 @@ xref: SCTID:362208000 xref: UMLS:C0227613 {source="ncithesaurus:Right_Kidney"} is_a: UBERON:0002113 ! kidney intersection_of: UBERON:0002113 ! kidney -intersection_of: in_right_side_of UBERON:0000468 ! multicellular organism -relationship: in_right_side_of UBERON:0000468 ! multicellular organism -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Kidney_Right.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +intersection_of: BSPO:0000121 UBERON:0000468 ! multicellular organism +relationship: BSPO:0000121 UBERON:0000468 ! multicellular organism +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Kidney_Right.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI [Term] id: UBERON:0004544 @@ -214024,11 +211346,12 @@ xref: FMA:19153 xref: MA:0002825 is_a: UBERON:0000485 ! simple columnar epithelium is_a: UBERON:0005156 ! reproductive structure +is_a: UBERON:0012275 ! meso-epithelium is_a: UBERON:0034969 ! epithelial layer of duct intersection_of: UBERON:0000485 ! simple columnar epithelium intersection_of: part_of UBERON:0001301 ! epididymis -relationship: contributes_to_morphology_of UBERON:0001301 ! epididymis relationship: part_of UBERON:0001301 ! epididymis +relationship: RO:0002433 UBERON:0001301 ! contributes to morphology of epididymis [Term] id: UBERON:0004548 @@ -214045,12 +211368,12 @@ xref: MA:0002949 xref: NCIT:C119334 xref: SCTID:362503005 is_a: UBERON:0000970 ! eye +is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0000970 ! eye -intersection_of: in_left_side_of UBERON:0000468 ! multicellular organism -relationship: in_left_side_of UBERON:0000468 ! multicellular organism -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-l.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-l.glb" xsd:anyURI -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +intersection_of: BSPO:0000120 UBERON:0000468 ! multicellular organism +relationship: BSPO:0000120 UBERON:0000468 ! multicellular organism +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-l.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-l.glb" xsd:anyURI [Term] id: UBERON:0004549 @@ -214067,12 +211390,12 @@ xref: MA:0002950 xref: NCIT:C119333 xref: SCTID:362502000 is_a: UBERON:0000970 ! eye +is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0000970 ! eye -intersection_of: in_right_side_of UBERON:0000468 ! multicellular organism -relationship: in_right_side_of UBERON:0000468 ! multicellular organism -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-r.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-r.glb" xsd:anyURI -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +intersection_of: BSPO:0000121 UBERON:0000468 ! multicellular organism +relationship: BSPO:0000121 UBERON:0000468 ! multicellular organism +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-r.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-r.glb" xsd:anyURI [Term] id: UBERON:0004550 @@ -214101,16 +211424,15 @@ xref: EMAPA:18267 xref: FMA:14915 xref: galen:LowerEsophagealSphincter xref: MA:0002951 -xref: MESH:D049630 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: NCIT:C33009 xref: SCTID:267809009 xref: UMLS:C0227192 {source="ncithesaurus:Lower_Esophageal_Sphincter"} is_a: UBERON:0011185 ! gastrointestinal sphincter intersection_of: UBERON:0004590 {source="MA"} ! sphincter muscle intersection_of: part_of UBERON:0001162 {source="MA"} ! cardia of stomach -relationship: contributes_to_morphology_of UBERON:0001162 ! cardia of stomach relationship: part_of UBERON:0001162 ! cardia of stomach -property_value: editor_note "TODO - split? check FMA:63048 ! circular muscle layer of abdominal part of esophagus" xsd:string +relationship: RO:0002433 UBERON:0001162 ! contributes to morphology of cardia of stomach +property_value: IAO:0000116 "TODO - split? check FMA:63048 ! circular muscle layer of abdominal part of esophagus" xsd:string [Term] id: UBERON:0004552 @@ -214125,7 +211447,7 @@ is_a: UBERON:0003514 ! limb blood vessel intersection_of: UBERON:0001637 ! artery intersection_of: part_of UBERON:0002544 ! digit relationship: part_of UBERON:0002544 ! digit -property_value: editor_note "check part_of - do we need term for digit + metacarpal/tarsal bones?" xsd:string +property_value: IAO:0000116 "check part_of - do we need term for digit + metacarpal/tarsal bones?" xsd:string [Term] id: UBERON:0004553 @@ -214187,9 +211509,8 @@ xref: SCTID:362030008 xref: VHOG:0000273 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0007798 {source="MA"} ! vascular system -relationship: has_member UBERON:0001637 ! artery -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000003 "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000273", ontology="VHOG", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005)", source="http://bgee.unil.ch/"} +relationship: RO:0002351 UBERON:0001637 ! has member artery +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004573 @@ -214206,7 +211527,7 @@ is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery intersection_of: part_of UBERON:0004571 ! systemic arterial system relationship: part_of UBERON:0004571 ! systemic arterial system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004581 @@ -214218,9 +211539,6 @@ xref: FMA:45626 xref: Wikipedia:Systemic_venous_system is_a: UBERON:0002049 ! vasculature relationship: part_of UBERON:0004582 ! venous system -property_value: UBPROP:0000001 "In human anatomy, the systemic venous system refers to veins that drain into the right atrium without passing through two vascular beds (i.e. they originate from a set of capillaries and do not pass through a second set of capillaries before reaching the right side of the heart). The term systemic venous system is often used to differentiate veins from veins that drain the pulmonary system (the pulmonary venous system) and veins that drain the digestive tract (the portal venous system). Large veins that are considered part of the systemic venous system are the: Superior vena cava; Inferior vena cava[WP]" xsd:string {source="Wikipedia:Systemic_venous_system"} -property_value: UBPROP:0000001 "Subdivision of cardiovascular system which has as its parts the right side of heart, the superior vena cava and the inferior vena cava[FMA]" xsd:string {ontology="FMA", source="FMA:45626"} -property_value: UBPROP:0000003 "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000277", ontology="VHOG", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0004582 @@ -214240,9 +211558,8 @@ xref: UMLS:C1267406 {source="ncithesaurus:Venous_System"} xref: VHOG:0000277 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0007798 {source="MA"} ! vascular system -relationship: composed_primarily_of UBERON:0001638 ! vein -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000003 "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000277", ontology="VHOG", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005)", source="http://bgee.unil.ch/"} +relationship: RO:0002473 UBERON:0001638 ! composed primarily of vein +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004590 @@ -214256,7 +211573,6 @@ xref: NCIT:C28381 xref: UMLS:C1409894 {source="ncithesaurus:Sphincter"} xref: Wikipedia:Sphincter is_a: UBERON:0001630 ! muscle organ -property_value: UBPROP:0000012 "FMA class is not a subtype of muscle" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0004637 @@ -214272,19 +211588,14 @@ synonym: "otic region" RELATED [] synonym: "periotic" RELATED [] synonym: "periotic capsule" RELATED [VHOG:0000854] xref: AAO:0010143 -xref: BTO:0005981 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} +xref: EMAPA:17596 xref: SCTID:361515007 xref: VHOG:0000854 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010363 ! endochondral element relationship: part_of UBERON:0001846 ! internal ear relationship: part_of UBERON:0003110 ! otic region -property_value: editor_note "developmental relationships need to be checked" xsd:string -property_value: UBPROP:0000001 "Skeletal elements surrounding the membranous labyrinth of the inner ear. Sensory capsules anterolateral to and confluent with occipital arch.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010143", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000001 "The cartilage capsule surrounding the inner ear mechanism; in the embryos of higher vertebrates, it is cartilaginous at first but later becomes bony. [Biology_online][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000854", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000002 "relationship loss: part_of occipito-petrosal (AAO:0010831)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010143", ontology="AAO"} -property_value: UBPROP:0000002 "relationship loss: part_of otic and occipital (AAO:0000993)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010143", ontology="AAO"} -property_value: UBPROP:0000003 "Otic capsules develop around the parts of the ear that lie within the chondrocranium. This part of the ear, known as the inner ear, is composed of the semicircular ducts and associated sacs that contain the receptive cells for equilibrium and hearing (reference 1); (...) considerations have led to our rethinking issues related to the origin of several aspects of vertebrate hearing, and to the view that many basic auditory functions evolved very early in vertebrate history, and that the functions observed in more `advanced' vertebrates, such as birds and mammals, are frequently modifications of themes first encountered in fishes, and perhaps even more ancestral animals.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000854", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.235, DOI:10.1016/S0378-5955(00)00168-4 Fay RR, Popper AN, Evolution of hearing in vertebrates: the inner ears and processing. Hearing research (2000)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "in elasmobranchs, it remains cartilaginous in the adult; in the embryos of higher vertebrates, it is cartilaginous at first but later becomes bony (at approximately 23 weeks in humans)" xsd:string {source="Biology-Online"} +property_value: IAO:0000116 "developmental relationships need to be checked" xsd:string [Term] id: UBERON:0004638 @@ -214306,7 +211617,7 @@ is_a: UBERON:0004852 ! cardiovascular system endothelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0001981 ! blood vessel relationship: part_of UBERON:0001981 ! blood vessel -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004639 @@ -214334,12 +211645,12 @@ is_a: UBERON:0001637 ! artery is_a: UBERON:0001980 ! arteriole is_a: UBERON:0003644 ! kidney arterial blood vessel relationship: capable_of GO:0003093 {source="Wikipedia"} ! regulation of glomerular filtration -relationship: connecting_branch_of UBERON:0004723 ! interlobular artery -relationship: contributes_to_morphology_of UBERON:0001229 ! renal corpuscle relationship: part_of UBERON:0001229 ! renal corpuscle -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: supplies UBERON:0001285 ! nephron -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +relationship: RO:0002178 UBERON:0001285 ! supplies nephron +relationship: RO:0002252 UBERON:0004723 ! connecting branch of interlobular artery +relationship: RO:0002433 UBERON:0001229 ! contributes to morphology of renal corpuscle +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004640 @@ -214366,11 +211677,11 @@ xref: ZFA:0005308 is_a: UBERON:0001980 ! arteriole is_a: UBERON:0003644 ! kidney arterial blood vessel relationship: capable_of GO:0003093 {source="Wikipedia"} ! regulation of glomerular filtration -relationship: connected_to UBERON:0004212 ! glomerular capillary -relationship: contributes_to_morphology_of UBERON:0001229 ! renal corpuscle relationship: part_of UBERON:0001229 ! renal corpuscle -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +relationship: RO:0002170 UBERON:0004212 ! connected to glomerular capillary +relationship: RO:0002433 UBERON:0001229 ! contributes to morphology of renal corpuscle +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004641 @@ -214394,11 +211705,12 @@ xref: NCIT:C33598 xref: SCTID:329635002 xref: UMLS:C0229681 {source="ncithesaurus:Splenic_Capsule"} is_a: UBERON:0003893 ! capsule +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0003893 ! capsule intersection_of: part_of UBERON:0002106 ! spleen -relationship: contributes_to_morphology_of UBERON:0002106 ! spleen relationship: part_of UBERON:0002106 ! spleen -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002433 UBERON:0002106 ! contributes to morphology of spleen +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004643 @@ -214454,17 +211766,17 @@ xref: CALOHA:TS-1088 xref: EMAPA:28601 xref: FMA:15936 xref: MA:0001693 -xref: NCIT:C13318 xref: SCTID:25631003 xref: UMLS:C0225339 {source="ncithesaurus:Transitional_Epithelium"} +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0000365 ! urothelium is_a: UBERON:0003350 ! epithelium of mucosa +is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0000365 ! urothelium intersection_of: part_of UBERON:0001255 ! urinary bladder -relationship: contributes_to_morphology_of UBERON:0001255 ! urinary bladder relationship: part_of UBERON:0001259 ! mucosa of urinary bladder -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000010 "5-7 cell layers thick in contracted bladder, 2-3 cells thick in distended bladder; lines renal pelvis, ureters, bladder, most of urethra but not distal urethra" xsd:string +relationship: RO:0002433 UBERON:0001255 ! contributes to morphology of urinary bladder +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004647 @@ -214486,11 +211798,11 @@ xref: SCTID:362194004 xref: UMLS:C0227518 {source="ncithesaurus:Hepatic_Lobule"} xref: Wikipedia:Lobules_of_liver is_a: UBERON:0000064 {source="FMA"} ! organ part -relationship: contributes_to_morphology_of UBERON:0001280 ! liver parenchyma +is_a: UBERON:0004119 ! endoderm-derived structure relationship: has_part CL:0000182 ! hepatocyte relationship: part_of UBERON:0001280 {source="FMA", source="MA"} ! liver parenchyma -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: IAO:0000232 "should not be confused with the anatomic lobes of the liver (caudate lobe, quadrate lobe, left lobe, and right lobe), or any of the functional lobe classification systems.[WP]" xsd:string +relationship: RO:0002433 UBERON:0001280 ! contributes to morphology of liver parenchyma +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004650 @@ -214525,6 +211837,7 @@ xref: MA:0002807 xref: NCIT:C120671 xref: SCTID:181927007 xref: Wikipedia:Body_of_humerus +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004769 ! diaphysis intersection_of: UBERON:0004769 ! diaphysis intersection_of: part_of UBERON:0000976 ! humerus @@ -214544,8 +211857,8 @@ xref: MA:0002901 is_a: UBERON:0035965 ! wall of blood vessel intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0000947 ! aorta -relationship: contributes_to_morphology_of UBERON:0000947 ! aorta relationship: part_of UBERON:0000947 ! aorta +relationship: RO:0002433 UBERON:0000947 ! contributes to morphology of aorta [Term] id: UBERON:0004664 @@ -214561,8 +211874,8 @@ xref: SCTID:24996002 is_a: UBERON:0005734 ! tunica adventitia of blood vessel intersection_of: UBERON:0005734 ! tunica adventitia of blood vessel intersection_of: part_of UBERON:0000947 ! aorta -relationship: contributes_to_morphology_of UBERON:0004663 ! aorta wall relationship: part_of UBERON:0004663 ! aorta wall +relationship: RO:0002433 UBERON:0004663 ! contributes to morphology of aorta wall [Term] id: UBERON:0004665 @@ -214577,6 +211890,7 @@ synonym: "tunica muscularis glandulae vesiculosae" EXACT OMO:0003011 [FMA:19404, xref: EMAPA:29773 xref: FMA:19404 xref: MA:0002913 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005156 ! reproductive structure is_a: UBERON:0006660 ! muscular coat intersection_of: UBERON:0006660 ! muscular coat @@ -214609,12 +211923,12 @@ xref: SCTID:278228007 xref: VHOG:0000927 is_a: UBERON:0000158 ! membranous layer is_a: UBERON:0005983 ! heart layer +is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0000158 ! membranous layer intersection_of: part_of UBERON:0002094 ! interventricular septum -relationship: contributes_to_morphology_of UBERON:0002094 ! interventricular septum -relationship: develops_from UBERON:0000095 {source="Wikipedia"} ! cardiac neural crest relationship: part_of UBERON:0002094 ! interventricular septum -property_value: UBPROP:0000001 "The membranous septum is the upper part of ventricular septum[GO:0003149]." xsd:string {source="GO:0003149"} +relationship: RO:0002202 UBERON:0000095 {source="Wikipedia"} ! develops from cardiac neural crest +relationship: RO:0002433 UBERON:0002094 ! contributes to morphology of interventricular septum [Term] id: UBERON:0004667 @@ -214642,9 +211956,8 @@ xref: RETIRED_EHDAA2:0000888 is_a: UBERON:0002385 ! muscle tissue intersection_of: UBERON:0002385 ! muscle tissue intersection_of: part_of UBERON:0002094 ! interventricular septum -relationship: contributes_to_morphology_of UBERON:0002094 ! interventricular septum relationship: part_of UBERON:0002094 ! interventricular septum -property_value: UBPROP:0000001 "The muscular septum is the lower part of the ventricular septum[GO]" xsd:string {source="GO:0003150"} +relationship: RO:0002433 UBERON:0002094 ! contributes to morphology of interventricular septum [Term] id: UBERON:0004668 @@ -214656,6 +211969,7 @@ synonym: "aperture of fourth ventricle" EXACT [FMA:242766] xref: FMA:242766 xref: MA:0002945 is_a: UBERON:0000161 ! orifice +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000161 ! orifice intersection_of: part_of UBERON:0002422 ! fourth ventricle relationship: part_of UBERON:0002422 ! fourth ventricle @@ -214682,16 +211996,12 @@ xref: Wikipedia:Ependyma is_a: UBERON:0007601 ! ciliated epithelium is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0000483 ! epithelium -intersection_of: composed_primarily_of CL:0000065 ! ependymal cell -relationship: composed_primarily_of CL:0000065 ! ependymal cell -relationship: contributes_to_morphology_of UBERON:0001016 ! nervous system -relationship: develops_from UBERON:0004060 ! neural tube ventricular layer +intersection_of: RO:0002473 CL:0000065 ! composed primarily of ependymal cell relationship: part_of UBERON:0005358 ! ventricle of nervous system -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray667.png" xsd:anyURI -property_value: RO:0002171 GO:0005604 -property_value: UBPROP:0000007 "ependymal" xsd:string -property_value: UBPROP:0000010 "unlike other epithelia, there is no basement membrane under the ependymal epithelium[ISBN:0387949542]" xsd:string -property_value: UBPROP:0000012 "FMA breaks ependyma into ependyma proper (a subdivsion of epithelium) and epithelium of choroid plexus" xsd:string {external_ontology="FMA"} +relationship: RO:0002202 UBERON:0004060 ! develops from neural tube ventricular layer +relationship: RO:0002433 UBERON:0001016 ! contributes to morphology of nervous system +relationship: RO:0002473 CL:0000065 ! composed primarily of ependymal cell +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray667.png" xsd:anyURI [Term] id: UBERON:0004673 @@ -214716,7 +212026,7 @@ intersection_of: UBERON:0002211 ! nerve root intersection_of: extends_fibers_into UBERON:0001645 ! trigeminal nerve relationship: extends_fibers_into UBERON:0001645 ! trigeminal nerve relationship: part_of UBERON:0001895 ! metencephalon -property_value: editor_note "TODO - check ZFA" xsd:string +property_value: IAO:0000116 "TODO - check ZFA" xsd:string [Term] id: UBERON:0004674 @@ -214798,9 +212108,9 @@ is_a: UBERON:0002304 ! layer of dentate gyrus intersection_of: UBERON:0002304 ! layer of dentate gyrus intersection_of: bounding_layer_of UBERON:0001885 ! dentate gyrus of hippocampal formation relationship: bounding_layer_of UBERON:0001885 ! dentate gyrus of hippocampal formation +relationship: BSPO:0001107 UBERON:0002361 ! pia mater relationship: has_part GO:0030425 ! dendrite relationship: has_part UBERON:0006134 ! nerve fiber -relationship: immediately_deep_to UBERON:0002361 ! pia mater [Term] id: UBERON:0004681 @@ -214824,8 +212134,6 @@ intersection_of: capable_of GO:0050957 ! equilibrioception relationship: capable_of GO:0050957 ! equilibrioception relationship: capable_of_part_of GO:0060005 ! vestibular reflex relationship: part_of UBERON:0002105 ! vestibulo-auditory system -property_value: UBPROP:0000001 "The vestibular system, which contributes to our balance and our sense of spatial orientation, is the sensory system that provides the dominant input about movement and equilibrioception. Together with the cochlea, a part of the auditory system, it constitutes the labyrinth of the inner ear, situated in the vestibulum in the inner ear. As our movements consist of rotations and translations, the vestibular system comprises two components: the semicircular canal system, which indicate rotational movements; and the otoliths, which indicate linear accelerations. The vestibular system sends signals primarily to the neural structures that control our eye movements, and to the muscles that keep us upright. The projections to the former provide the anatomical basis of the vestibulo-ocular reflex, which is required for clear vision; and the projections to the muscles that control our posture are necessary to keep us upright[Wikipedia:Vestibular_system]." xsd:string {source="Wikipedia:Vestibular_system"} -property_value: UBPROP:0000012 "FMA and NIF have no part information for this class. This is a GAT in FMA" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0004684 @@ -214857,7 +212165,7 @@ xref: ZFA:0001429 is_a: UBERON:0002616 ! regional part of brain relationship: capable_of GO:0001820 {source="Wikipedia"} ! serotonin secretion relationship: part_of UBERON:0002275 {source="GO", source="Wikipedia"} ! reticular formation -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/94/Gray694.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/94/Gray694.png" xsd:anyURI [Term] id: UBERON:0004688 @@ -214874,9 +212182,9 @@ xref: MA:0001939 xref: SCTID:244225009 xref: Wikipedia:Costocervical_trunk is_a: UBERON:0001637 ! artery -relationship: connected_to UBERON:0001533 ! subclavian artery -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b3/Costocervical_trunk_with_branches.png" xsd:anyURI +relationship: RO:0002170 UBERON:0001533 ! connected to subclavian artery +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b3/Costocervical_trunk_with_branches.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004692 @@ -214903,8 +212211,8 @@ xref: MA:0000731 is_a: UBERON:0001277 ! intestinal epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001211 ! Peyer's patch -relationship: contributes_to_morphology_of UBERON:0001211 ! Peyer's patch relationship: part_of UBERON:0001211 ! Peyer's patch +relationship: RO:0002433 UBERON:0001211 ! contributes to morphology of Peyer's patch [Term] id: UBERON:0004695 @@ -214944,8 +212252,8 @@ xref: UMLS:C1711398 {source="ncithesaurus:Peyer_s_Patch_Germinal_Center"} is_a: UBERON:0010754 ! germinal center intersection_of: UBERON:0010754 ! germinal center intersection_of: part_of UBERON:0001211 ! Peyer's patch -relationship: contains_process GO:0002317 ! plasma cell differentiation -relationship: contains_process GO:0042100 ! B cell proliferation +relationship: BFO:0000067 GO:0002317 ! contains process plasma cell differentiation +relationship: BFO:0000067 GO:0042100 ! contains process B cell proliferation relationship: part_of UBERON:0001211 ! Peyer's patch [Term] @@ -214973,7 +212281,6 @@ is_a: UBERON:0008307 ! heart endothelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0004145 ! outflow tract relationship: part_of UBERON:0004145 ! outflow tract -property_value: UBPROP:0000003 "It is assumed that during evolution, a circulatory system composed of the heart and endothelial tubular system first formed in vertebrates, medial smooth muscle then appeared for regulation of the system, and innervation of the muscle tissue took place. This sequence of development assumed for phylogenesis is actually realized in the ontogenetic processes.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001524", ontology="VHOG", source="DOI:10.1254/jjp.87.253 Shigei T, Tsuru H, Ishikawa N, Yoshioka K, Absence of endothelium in invertebrate blood vessels: significance of endothelium and sympathetic nerve/medial smooth muscle in the vertebrate vascular system. Japanese Journal of Pharmacology (2001)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0004700 @@ -215046,11 +212353,10 @@ xref: TAO:0000653 xref: ZFA:0000653 is_a: UBERON:0002616 ! regional part of brain relationship: part_of UBERON:0001897 ! dorsal plus ventral thalamus -relationship: present_in_taxon NCBITaxon:117569 {source="Ariens, p. 1192"} -relationship: present_in_taxon NCBITaxon:7742 ! Vertebrata -relationship: present_in_taxon NCBITaxon:7776 {notes="http://neurolex.org/wiki/Category_talk:Thalamus", source="PMID:8167659"} ! Gnathostomata -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: editor_note "TODO. http://www.ncbi.nlm.nih.gov/pubmed/8167659" xsd:string +property_value: IAO:0000116 "TODO. http://www.ncbi.nlm.nih.gov/pubmed/8167659" xsd:string +property_value: RO:0002175 NCBITaxon:117569 {source="Ariens, p. 1192"} +property_value: RO:0002175 NCBITaxon:7742 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004704 @@ -215074,8 +212380,6 @@ xref: Wikipedia:Fossa#Anatomy xref: ZFA:0005388 is_a: UBERON:0002553 {source="FMA-implied"} ! anatomical cavity relationship: part_of UBERON:0001474 ! bone element -property_value: UBPROP:0000001 "Anatomical space that is a concavity, shallow depression, or groove on a bone.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001743", ontology="TAO", source="TAO:wd"} -property_value: UBPROP:0000012 "General Anatomical term in FMA; not restricted to bone in ncit; surface feature in VSAO; note that entities named 'fossa' are cavities in FMA, hence placement here" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0004706 @@ -215096,9 +212400,8 @@ xref: UMLS:C1284055 {source="ncithesaurus:Bulbus_Cordis"} xref: Wikipedia:Bulbus_cordis is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0000948 ! heart -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c9/Gray466.png" xsd:anyURI -property_value: editor_note "TODO - check relationship to bulbus arteriosus" xsd:string -property_value: UBPROP:0000001 "A pear shaped chamber that functions as a capacitor, maintaining continuous blood flow into the gill arches. The bulbus arteriosus has three distinct layers. Hu et al. 2000.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000173", ontology="TAO", source="ZFIN:curator"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c9/Gray466.png" xsd:anyURI +property_value: IAO:0000116 "TODO - check relationship to bulbus arteriosus" xsd:string [Term] id: UBERON:0004707 @@ -215115,10 +212418,9 @@ xref: Wikipedia:Pharyngula xref: ZFS:0000050 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000111 ! organogenesis stage relationship: preceded_by UBERON:0000110 ! neurula stage -property_value: UBPROP:0000008 "Corresponds to E7-E11 in Mouse (Galis et al, TREE, 2001)" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0004708 @@ -215139,15 +212441,14 @@ is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000026 {source="VSAO"} ! appendage intersection_of: UBERON:0000026 ! appendage intersection_of: part_of UBERON:0010707 ! appendage girdle complex -relationship: connected_to UBERON:0007823 ! appendage girdle region -relationship: develops_from UBERON:0004357 {evidence="definitional"} ! paired limb/fin bud relationship: has_part UBERON:0000014 ! zone of skin relationship: has_part UBERON:0001015 ! musculature relationship: has_part UBERON:0002049 ! vasculature -relationship: has_skeleton UBERON:0011582 ! paired limb/fin skeleton -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0010707 {source="VSAO"} ! appendage girdle complex -property_value: IAO:0000232 "this class is the union of the classes limb, pectoral fin and pelvic fin." xsd:string +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002170 UBERON:0007823 ! connected to appendage girdle region +relationship: RO:0002202 UBERON:0004357 ! develops from paired limb/fin bud +relationship: RO:0002551 UBERON:0011582 ! has skeleton paired limb/fin skeleton [Term] id: UBERON:0004709 @@ -215167,10 +212468,10 @@ is_a: UBERON:0004708 ! paired limb/fin intersection_of: UBERON:0004708 ! paired limb/fin intersection_of: part_of UBERON:0010709 ! pelvic complex disjoint_from: UBERON:0004710 {source="lexical"} ! pectoral appendage -relationship: connected_to UBERON:0001271 ! pelvic girdle region -relationship: develops_from UBERON:0005420 {evidence="definitional"} ! pelvic appendage bud -relationship: has_skeleton UBERON:0007273 ! pelvic appendage skeleton relationship: part_of UBERON:0010709 ! pelvic complex +relationship: RO:0002170 UBERON:0001271 ! connected to pelvic girdle region +relationship: RO:0002202 UBERON:0005420 ! develops from pelvic appendage bud +relationship: RO:0002551 UBERON:0007273 ! has skeleton pelvic appendage skeleton [Term] id: UBERON:0004710 @@ -215191,11 +212492,10 @@ xref: VSAO:0000125 is_a: UBERON:0004708 ! paired limb/fin intersection_of: UBERON:0004708 ! paired limb/fin intersection_of: part_of UBERON:0010708 ! pectoral complex -relationship: connected_to UBERON:0001421 ! pectoral girdle region -relationship: develops_from UBERON:0005419 {evidence="definitional"} ! pectoral appendage bud -relationship: has_skeleton UBERON:0007272 ! pectoral appendage skeleton relationship: part_of UBERON:0010708 ! pectoral complex -property_value: UBPROP:0000003 "While the skeletons of teleost pectoral fins and tetrapod forelimbs are homologous at the level of endoskeletal radials, teleosts and tetrapods do not share homologous skeletal elements at the level of 'individuated' pro-, meso-, and metapterygia. Among osteichthyans, only basal actinopterygians retain the full complement of elements present in non-osteichthyan gnathostomes.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001753", ontology="VHOG", source="DOI:10.1002/jmor.10264 Davis MC, Shubin NH, Force A, Pectoral fin and girdle development in the basal actinopterygians Polyodon spathula and Acipenser transmontanus. Journal of Morphology (2004)", source="http://bgee.unil.ch/"} +relationship: RO:0002170 UBERON:0001421 ! connected to pectoral girdle region +relationship: RO:0002202 UBERON:0005419 ! develops from pectoral appendage bud +relationship: RO:0002551 UBERON:0007272 ! has skeleton pectoral appendage skeleton [Term] id: UBERON:0004711 @@ -215215,9 +212515,9 @@ xref: SCTID:244403000 xref: UMLS:C0022427 {source="ncithesaurus:Jugular_Vein"} xref: Wikipedia:Jugular_vein is_a: UBERON:0001638 ! vein -relationship: drains UBERON:0000033 ! head -relationship: part_of UBERON:0000974 {gci_filler="NCBITaxon:8287", gci_relation="in_taxon"} ! neck -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/f8/Gray558.png" xsd:anyURI +relationship: part_of UBERON:0000974 {gci_filler="NCBITaxon:8287", gci_relation="RO:0002162"} ! neck +relationship: RO:0002179 UBERON:0000033 ! drains head +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f8/Gray558.png" xsd:anyURI [Term] id: UBERON:0004715 @@ -215239,7 +212539,7 @@ intersection_of: UBERON:0006444 ! annulus fibrosus intersection_of: part_of UBERON:0001066 ! intervertebral disk disjoint_from: UBERON:0006008 ! fibrous ring of heart relationship: part_of UBERON:0001066 ! intervertebral disk -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/d9/Cervical_vertebra_english.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d9/Cervical_vertebra_english.png" xsd:anyURI [Term] id: UBERON:0004716 @@ -215256,12 +212556,12 @@ xref: NCIT:C34131 xref: UMLS:C1516779 {source="ncithesaurus:Conceptus"} xref: Wikipedia:Conceptus is_a: UBERON:0000061 ! anatomical structure -relationship: develops_from CL:0000365 ! animal zygote -relationship: existence_ends_with UBERON:0000068 ! embryo stage -relationship: existence_starts_with UBERON:0000068 ! embryo stage relationship: has_part UBERON:0002050 ! embryonic structure relationship: has_part UBERON:0016887 ! entire extraembryonic component -property_value: editor_note "EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus" xsd:string +relationship: RO:0002202 CL:0000365 ! develops from animal zygote +relationship: RO:0002489 UBERON:0000068 ! existence starts with embryo stage +relationship: RO:0002493 UBERON:0000068 ! existence ends with embryo stage +property_value: IAO:0000116 "EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus" xsd:string [Term] id: UBERON:0004719 @@ -215283,10 +212583,9 @@ xref: MA:0002593 xref: Wikipedia:Arcuate_vein is_a: UBERON:0013126 ! vein of abdomen is_a: UBERON:0014401 ! renal venous blood vessel -relationship: connected_to UBERON:0009887 ! interlobar vein -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI -property_value: UBPROP:0000202 FMA:71632 +relationship: RO:0002170 UBERON:0009887 ! connected to interlobar vein +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004721 @@ -215306,9 +212605,10 @@ xref: SCTID:368953000 xref: UMLS:C0229465 {source="ncithesaurus:Ampullary_Crest"} xref: Wikipedia:Crista_ampullaris is_a: UBERON:0000020 ! sense organ -relationship: contributes_to_morphology_of UBERON:0004043 ! semicircular canal ampulla +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0004043 {source="MA"} ! semicircular canal ampulla -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/ec/Semicircular_canal_-_ampulla.png" xsd:anyURI +relationship: RO:0002433 UBERON:0004043 ! contributes to morphology of semicircular canal ampulla +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ec/Semicircular_canal_-_ampulla.png" xsd:anyURI [Term] id: UBERON:0004723 @@ -215333,9 +212633,9 @@ xref: UMLS:C1512856 {source="ncithesaurus:Interlobular_Artery"} xref: Wikipedia:Interlobular_arteries is_a: UBERON:0003644 ! kidney arterial blood vessel disjoint_from: UBERON:0009885 {source="Wikipedia:Renal_circulation"} ! interlobar artery -relationship: connected_to UBERON:0001552 ! kidney arcuate artery -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +relationship: RO:0002170 UBERON:0001552 ! connected to kidney arcuate artery +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004725 @@ -215372,14 +212672,13 @@ xref: SCTID:369098004 xref: UMLS:C0228280 {source="BIRNLEX:1097"} xref: Wikipedia:Piriform_cortex is_a: UBERON:0002616 ! regional part of brain -relationship: contributes_to_morphology_of UBERON:0002894 ! olfactory cortex -relationship: only_in_taxon NCBITaxon:32523 {source="Wikipedia"} ! Tetrapoda relationship: part_of UBERON:0002894 ! olfactory cortex -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b1/Human_brainstem_anterior_view_2_description.JPG" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI -property_value: UBPROP:0000008 "Piriform cortical regions are present in the brains of amphibians, reptiles and mammals. The piriform cortex is among three areas that emerge in the telencephalon of amphibians, situated caudally to a dorsal area, which is caudal to a hippocampal area. Farther along the phylogenic timeline, the telencephalic bulb of reptiles as viewed in a cross section of the transverse plane extends with the archipallial hippocampus folding toward the midline and down as the dorsal area begins to form a recognizable cortex. As mammalian cerebrums developed, volume of the dorsal cortex increased in slightly greater proportion, as compared proportionally with increased overall brain volume, until it enveloped the hippocampal regions. Recognized as neopallium or neocortex, enlarged dorsal areas envelop the paleopallial piriform cortex in humans and Old World monkeys. Among taxonomic groupings of mammals, the piriform cortex and the olfactory bulb become proportionally smaller in the brains of phylogenically younger species. The piriform cortex occupies a greater proportion of the overall brain and of the telencephalic brains of insectivores than in primates. The piriform cortex continues to occupy a consistent albeit small and declining proportion of the increasingly large telencephalon in the most recent primate species while the volume of the olfactory bulb becomes less in proportion" xsd:string {source="WP"} +relationship: RO:0002160 NCBITaxon:32523 {source="Wikipedia"} ! only in taxon Tetrapoda +relationship: RO:0002433 UBERON:0002894 ! contributes to morphology of olfactory cortex +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b1/Human_brainstem_anterior_view_2_description.JPG" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004726 @@ -215406,10 +212705,10 @@ xref: galen:ArteriaeRectae xref: MA:0002595 xref: Wikipedia:Vasa_recta is_a: UBERON:0001140 ! renal vein -relationship: connected_to UBERON:0004640 ! renal efferent arteriole -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/2/21/Kidney_nephron.png" xsd:anyURI -property_value: editor_note "TODO - is this a vein or set of veins? in MA it is a venous blood vessel" xsd:string +relationship: RO:0002170 UBERON:0004640 ! connected to renal efferent arteriole +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/21/Kidney_nephron.png" xsd:anyURI +property_value: IAO:0000116 "TODO - is this a vein or set of veins? in MA it is a venous blood vessel" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004727 @@ -215441,14 +212740,15 @@ xref: SCTID:280286001 xref: UMLS:C0009201 {source="ncithesaurus:Cochlear_Nerve"} xref: VHOG:0001182 xref: Wikipedia:Cochlear_nerve -is_a: UBERON:0001021 ! nerve +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0011779 ! nerve of head region intersection_of: UBERON:0001021 ! nerve -intersection_of: branching_part_of UBERON:0001648 ! vestibulocochlear nerve intersection_of: extends_fibers_into UBERON:0001720 ! cochlear nucleus -intersection_of: innervates UBERON:0001844 ! cochlea -relationship: branching_part_of UBERON:0001648 ! vestibulocochlear nerve +intersection_of: RO:0002134 UBERON:0001844 ! innervates cochlea +intersection_of: RO:0002380 UBERON:0001648 ! branching part of vestibulocochlear nerve relationship: extends_fibers_into UBERON:0001720 ! cochlear nucleus -relationship: innervates UBERON:0001844 ! cochlea +relationship: RO:0002134 UBERON:0001844 ! innervates cochlea +relationship: RO:0002380 UBERON:0001648 ! branching part of vestibulocochlear nerve [Term] id: UBERON:0004731 @@ -215466,13 +212766,13 @@ xref: NLX:147842 xref: TAO:0001328 xref: Wikipedia:Neuromere xref: ZFA:0001328 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004732 ! segmental subdivision of nervous system intersection_of: UBERON:0004732 ! segmental subdivision of nervous system intersection_of: part_of UBERON:0001049 ! neural tube -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 relationship: part_of UBERON:0001049 ! neural tube -property_value: editor_note "We take the definition of neuromere from Puelles et al, although the existence of mesomeres and prosomeres may not be widely accepted" xsd:string -property_value: UBPROP:0000001 "A metameric segment of the central nervous system.[ZFA]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001328", ontology="TAO", source="ZFIN:curator"} +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: IAO:0000116 "We take the definition of neuromere from Puelles et al, although the existence of mesomeres and prosomeres may not be widely accepted" xsd:string creation_date: 2009-06-18T09:00:04Z [Term] @@ -215486,7 +212786,7 @@ is_a: UBERON:0000063 ! organ subunit intersection_of: UBERON:0000063 ! organ subunit intersection_of: part_of UBERON:0001016 ! nervous system relationship: part_of UBERON:0001016 ! nervous system -property_value: editor_note "revisit this after CARO is revised and/or we have defined metameric segment; note that with the additional of an A/P axis constraint this corresponds to what Richter at al call a neuromere (PMID:21062451)" xsd:string +property_value: IAO:0000116 "revisit this after CARO is revised and/or we have defined metameric segment; note that with the additional of an A/P axis constraint this corresponds to what Richter at al call a neuromere (PMID:21062451)" xsd:string [Term] id: UBERON:0004733 @@ -215497,6 +212797,7 @@ subset: non_informative synonym: "hindbrain segment" EXACT [FMA:61998] synonym: "segment of hindbrain" EXACT [FMA:61998] xref: FMA:61998 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004732 ! segmental subdivision of nervous system intersection_of: UBERON:0000063 ! organ subunit intersection_of: part_of UBERON:0002028 ! hindbrain @@ -215520,7 +212821,6 @@ synonym: "trilaminar disk" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "trilaminar germ" RELATED [https://orcid.org/0000-0002-6601-2165] xref: BILA:0000060 xref: BTO:0001403 -xref: FBbt:00005317 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:293108 xref: GAID:1302 xref: MESH:D005775 @@ -215533,10 +212833,9 @@ xref: Wikipedia:Gastrula xref: Wikipedia:Trilaminar_blastocyst is_a: UBERON:0000922 ! embryo intersection_of: UBERON:0000468 ! multicellular organism -intersection_of: existence_starts_and_ends_during UBERON:0000109 ! gastrula stage -relationship: develops_from UBERON:0000307 ! blastula -relationship: existence_starts_and_ends_during UBERON:0000109 ! gastrula stage -property_value: UBPROP:0000012 "We explicitly merge the NCITA terms here" xsd:string {external_ontology="NCIT"} +intersection_of: RO:0002491 UBERON:0000109 ! existence starts and ends during gastrula stage +relationship: RO:0002202 UBERON:0000307 ! develops from blastula +relationship: RO:0002491 UBERON:0000109 ! existence starts and ends during gastrula stage [Term] id: UBERON:0004736 @@ -215562,9 +212861,9 @@ is_a: UBERON:0001232 ! collecting duct of renal tubule is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0001232 ! collecting duct of renal tubule intersection_of: part_of UBERON:0000081 ! metanephros -relationship: develops_from UBERON:0003220 {source="Wikipedia-abduced"} ! metanephric mesenchyme -relationship: develops_from UBERON:0014706 ! primitive renal collecting duct system relationship: part_of UBERON:0005110 {is_inferred="true", source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! metanephric nephron +relationship: RO:0002202 UBERON:0003220 {source="Wikipedia-abduced"} ! develops from metanephric mesenchyme +relationship: RO:0002202 UBERON:0014706 ! develops from primitive renal collecting duct system [Term] id: UBERON:0004738 @@ -215573,6 +212872,7 @@ namespace: uberon def: "Juxtaglomerular apparatus of the mature vertebrate kidney, or metanephros." [GO:0072206] synonym: "juxtaglomerular apparatus of metanephros" EXACT [] is_a: UBERON:0002303 ! juxtaglomerular apparatus +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0002303 ! juxtaglomerular apparatus intersection_of: part_of UBERON:0000081 ! metanephros relationship: part_of UBERON:0010533 {is_inferred="true", source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! metanephros cortex @@ -215599,12 +212899,8 @@ xref: ZFA:0001557 is_a: UBERON:0000074 ! renal glomerulus intersection_of: UBERON:0000074 ! renal glomerulus intersection_of: part_of UBERON:0002120 ! pronephros -relationship: develops_from UBERON:0007128 {source="XAO"} ! glomeral mesenchyme relationship: part_of UBERON:0002120 ! pronephros -property_value: IAO:0000232 "a glomus differs from a glomerulus in that each vascular glomus services several tubules" xsd:string {source="ISBN:0073040584"} -property_value: UBPROP:0000001 "Paired highly vascularized portion of the pronephros. Left and right glomeruli are fused at the midline. Begins to function between 40 and 48hpf. Drummond, 2000.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001557", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "The teleost pronephros shares many essential features with the amphibian pronephros including its derivation from mesoderm associated with the coelom and the derivation of the glomerular blood supply from the medial dorsal aorta. However, unlike the pronephros of amphibians, which have an external glomus and tubules with nephrostomes open to the coelom, the mature teleost pronephros has no connection to the body cavity and instead functions as a closed system (reference 1); This variation in nephron types [with external glomeruli that open into the coelom and with internal glomeruli that do not connect with the coelom] and their pattern of distribution suggest an evolutionary sequence. Ancestral craniates probably had an external glomerulus and nephrostomes, as do the first few to develop in very primitive craniates. (...) The mechanism would become more efficient as the coelomic recess into which each glomerulus discharged became a part of the tubule, that is, grew around the glomerulus as a renal capsule. The glomerulus becomes internal. The nephrostomes were lost during subsequent evolution, leaving the type of renal tubule found in most vertebrates (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001237", ontology="VHOG", source="PMID:9806915 Drummond IA, Majumdar A, Hentschel H, Elger M, Solnica-Krezel L, Schier AF, Neuhauss SCF, Stemple DL, Zwartkruis F, Rangini Z, Driever W, Fishman MC, Early development of the zebrafish pronephros and analysis of mutations affecting pronephric function. Development (1998), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.636", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "GO treats glomus and pronephric glomerulus differently" xsd:string {external_ontology="GO"} +relationship: RO:0002202 UBERON:0007128 {source="XAO"} ! develops from glomeral mesenchyme [Term] id: UBERON:0004742 @@ -215626,16 +212922,10 @@ xref: ZFA:0000191 is_a: UBERON:0004768 ! bone of lower jaw is_a: UBERON:0008907 {source="ZFA"} ! dermal bone is_a: UBERON:0015212 ! lateral structure -relationship: develops_from UBERON:0010336 {source="EHDAA2"} ! mandibular process mesenchyme from neural crest -relationship: has_developmental_contribution_from UBERON:0003324 {source="EHDAA2-modified"} ! mesenchyme of lower jaw -relationship: in_lateral_side_of UBERON:0003278 ! skeleton of lower jaw -relationship: part_of UBERON:0003113 {notes="mandibular series", source="ISBN:0073040584", source="ZFA"} ! dermatocranium -property_value: UBPROP:0000001 "Dermal bone that is usually the anteriormost bone of the lower jaw, and that articulates with the angular, or anguloarticular bone, posteriorly, and carries part of the mandibular sensory canal and pore openings of the mandibular sensory canal on its lateral surface. The dentary is a paired bone.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000191", ontology="TAO", source="TAO:GA_TG"} -property_value: UBPROP:0000001 "Ossified element of intramembranous origin that invests the lateral margin of Meckel's cartilage thereby forming the lateral side of the mandible in anurans and salamanders (Duellman & Trueb, 1994:293). In caecilians, the dentary is part of a compound bone termed the pseudodentary.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000124", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000001 "The dentary is a dermal bone that forms the antero-lateral part of the lower jaw in fishes and amphibians. In mammals the lower jaw consists entirely of the dentary bone. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, ZFA:0000191_and_Liem_KF, p.248][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001022", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000002 "relationship loss: overlaps dentary-anguloarticular joint (TAO:0001749)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000191", ontology="TAO"} -property_value: UBPROP:0000003 "Of all these bones [dentary, splenials, coronoids, angular, surangular and prearticular], only the dentary remains in the lower jaw of a mammal.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001022", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.248", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "In lobe-finned fishes and the early fossil tetrapods, the bone homologous to the mandible of mammals is merely the largest of several bones in the lower jaw. In such animals, it is referred to as the dentary bone, and forms the body of the outer surface of the jaw. It is bordered below by a number of splenial bones, while the angle of the jaw is formed by a lower angular bone and a suprangular bone just above it. The inner surface of the jaw is lined by a prearticular bone, while the articular bone forms the articulation with the skull proper. Finally a set of three narrow coronoid bones lie above the prearticular bone. As the name implies, the majority of the teeth are attached to the dentary, but there are commonly also teeth on the coronoid bones, and sometimes on the prearticular as well. This complex primitive pattern has, however, been simplified to various degrees in the great majority of vertebrates, as bones have either fused or vanished entirely. In teleosts, only the dentary, articular, and angular bones remain, while in living amphibians, the dentary is accompanied only by the prearticular, and, in salamanders, one of the coronoids. The lower jaw of reptiles has only a single coronoid and splenial, but retains all the other primitive bones except the prearticular." xsd:string +relationship: BSPO:0000126 UBERON:0003278 ! skeleton of lower jaw +relationship: part_of UBERON:0003113 ! dermatocranium +relationship: RO:0002202 UBERON:0010336 {source="EHDAA2"} ! develops from mandibular process mesenchyme from neural crest +relationship: RO:0002254 UBERON:0003324 {source="EHDAA2-modified"} ! has developmental contribution from mesenchyme of lower jaw [Term] id: UBERON:0004753 @@ -215653,12 +212943,7 @@ xref: Wikipedia:Scapulocoracoid xref: ZFA:0001455 is_a: UBERON:0004765 ! skeletal element relationship: part_of UBERON:0007831 {source="VSAO"} ! pectoral girdle skeleton -property_value: editor_note "todo - decide whether to create separate classes for cartilage & ossified. Wikipedia considers this absent in Therians, but if considered as a grouping of scapula and coracoid then it would be present" xsd:string -property_value: UBPROP:0000001 "either a fusion of the scapula and coracoid (the two main bones of the shoulder girdle), or the scapula & coracoid considered as a single structural unit.[Palaeos]" xsd:string {date_retrieved="2012-09-10", source="http://palaeos.com/vertebrates/glossary/glossaryS.html"} -property_value: UBPROP:0000001 "Fused, ossified portions of the scapula, procoracoid, and coracoid.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000781", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000001 "Pectoral fin cartilage that consists of a paired cartilaginous plate of the embryonic primary pectoral girdle and from which the scapular and coracaoid bones ossify.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001455", ontology="TAO", source="TAO:GA_TG", source="ZFIN:curator"} -property_value: UBPROP:0000002 "relationship loss: part_of scapular area (AAO:0000935)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000781", ontology="AAO"} -property_value: UBPROP:0000012 "ZFA defines as precursor to scapula and coracoid. Cartilage in TAO" xsd:string {external_ontology="ZFA"} +property_value: IAO:0000116 "todo - decide whether to create separate classes for cartilage & ossified. Wikipedia considers this absent in Therians, but if considered as a grouping of scapula and coracoid then it would be present" xsd:string [Term] id: UBERON:0004755 @@ -215673,9 +212958,8 @@ xref: VSAO:0000015 xref: XAO:0004038 xref: ZFA:0005619 is_a: UBERON:0002384 {source="VSAO"} ! connective tissue -relationship: develops_from CL:0007001 {date_retrieved="2012-08-14", external_class="VSAO:0000015", source="VSAO"} ! skeletogenic cell relationship: part_of UBERON:0004765 ! skeletal element -property_value: UBPROP:0000001 "A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000015", notes="taken from version of VSAO used in TAO and used directly in Uberon", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} +relationship: RO:0002202 CL:0007001 ! develops from skeletogenic cell [Term] id: UBERON:0004756 @@ -215683,12 +212967,13 @@ name: dermal skeletal element namespace: uberon def: "Dermis-derived entity that is made of skeletal tissue." [http://orcid.org/0000-0002-6601-2165, https://github.com/obophenotype/uberon/issues/206] synonym: "dermal element" EXACT [VSAO:curator] +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004765 ! skeletal element intersection_of: UBERON:0004765 ! skeletal element -intersection_of: develops_from UBERON:0002067 ! dermis intersection_of: has_part UBERON:0004755 ! skeletal tissue -relationship: develops_from UBERON:0002067 ! dermis +intersection_of: RO:0002202 UBERON:0002067 ! develops from dermis relationship: has_part UBERON:0004755 ! skeletal tissue +relationship: RO:0002202 UBERON:0002067 ! develops from dermis [Term] id: UBERON:0004760 @@ -215699,7 +212984,7 @@ subset: human_reference_atlas subset: organ_slim synonym: "anal gland" RELATED [] synonym: "anal sac" RELATED SENSU [Wikipedia:Anal_gland] -synonym: "gland of anal canal" EXACT [OBOL:automatic] +synonym: "gland of anal sac" RELATED [] synonym: "gland of anus" RELATED [] synonym: "rectal gland" RELATED [] xref: EMAPA:27221 @@ -215712,10 +212997,11 @@ xref: SCTID:245448005 xref: UMLS:C0162322 {source="ncithesaurus:Anal_Gland"} xref: Wikipedia:Anal_gland is_a: UBERON:0003408 ! gland of digestive tract +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0000159 ! anal canal relationship: part_of UBERON:0000159 ! anal canal -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004761 @@ -215729,7 +213015,6 @@ synonym: "chondocranium" RELATED [Wikipedia:Chondrocranium] synonym: "embryonic chondocranium" RELATED [] synonym: "neurocranium" RELATED SENSU [] xref: AAO:0000094 -xref: AAO:0010153 xref: EHDAA:6031 xref: FMA:76621 xref: NCIT:C34121 @@ -215738,10 +213023,9 @@ xref: UMLS:C1516496 {source="ncithesaurus:Chondrocranium"} xref: Wikipedia:Chondrocranium xref: XAO:0003059 is_a: UBERON:0000075 {source="FMA"} ! subdivision of skeletal system -relationship: develops_from UBERON:0009617 {source="PMC1571569"} ! head paraxial mesoderm relationship: has_part UBERON:0002418 ! cartilage tissue -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata -property_value: UBPROP:0000012 "in contrast to chondrocranium, this structure is entirely cartiliginous. In Chondricthyes this is the same as the neurocranium. FMA:76621 is an undefined fetal structure, so we assume the correct placement is here. Note that this is distinct from MA:0000317 which is the uberon:neurocranium (the part of the cranium that encloses the brain)" xsd:string {external_ontology="FMA"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002202 UBERON:0009617 {source="PMC1571569"} ! develops from head paraxial mesoderm [Term] id: UBERON:0004763 @@ -215757,10 +213041,9 @@ is_a: UBERON:0002481 ! bone tissue intersection_of: UBERON:0002481 ! bone tissue intersection_of: output_of GO:0001958 ! endochondral ossification disjoint_from: UBERON:0004764 ! intramembranous bone tissue -relationship: developmentally_replaces UBERON:0002418 ! cartilage tissue relationship: output_of GO:0001958 ! endochondral ossification relationship: part_of UBERON:0002513 ! endochondral bone -property_value: UBPROP:0000012 "the distinction between endochondral bone and endochondral bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type" xsd:string {external_ontology="MA"} +relationship: RO:0002285 UBERON:0002418 ! developmentally replaces cartilage tissue [Term] id: UBERON:0004764 @@ -215772,10 +213055,9 @@ xref: Wikipedia:Intramembranous_ossification is_a: UBERON:0002481 ! bone tissue intersection_of: UBERON:0002481 ! bone tissue intersection_of: output_of GO:0001957 ! intramembranous ossification -relationship: develops_from UBERON:0003104 ! mesenchyme relationship: output_of GO:0001957 ! intramembranous ossification relationship: part_of UBERON:0002514 ! intramembranous bone -property_value: UBPROP:0000012 "note the distinction between intramembranous bone and intramembranous bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type (it is under bone tissue and connective tissue; there are no child classes)" xsd:string {external_ontology="MA"} +relationship: RO:0002202 UBERON:0003104 ! develops from mesenchyme [Term] id: UBERON:0004765 @@ -215792,8 +213074,6 @@ xref: XAO:0004012 xref: ZFA:0005494 is_a: UBERON:0000062 ! organ relationship: part_of UBERON:0001434 {source="VSAO"} ! skeletal system -property_value: UBPROP:0000001 "Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000128", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001890", ontology="TAO", source="TAO:VSAO_workshop"} [Term] id: UBERON:0004766 @@ -215807,23 +213087,19 @@ is_a: UBERON:0001474 ! bone element intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0003128 ! cranium relationship: part_of UBERON:0003128 ! cranium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: IAO:0000232 "here cranium = skull - mandible" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004767 name: vomerine tooth namespace: uberon def: "A tooth that is on the vomer." [http://www.encyclo.co.uk/define/Vomerine%20teeth] -xref: AAO:0000635 xref: TAO:0001631 is_a: UBERON:0012070 ! palatal tooth intersection_of: UBERON:0001091 ! calcareous tooth -intersection_of: attaches_to UBERON:0002396 ! vomer -relationship: attaches_to UBERON:0002396 ! vomer +intersection_of: RO:0002371 UBERON:0002396 ! attached to vomer relationship: part_of UBERON:0017615 ! vomerine dentition -property_value: UBPROP:0000001 "Tooth that is attached to the vomer.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001631", ontology="TAO", source="TAO:wd"} -property_value: UBPROP:0000002 "relationship type change: OBO_REL:part_of vomer (TAO:0000308) CHANGED TO: attaches_to vomer (UBERON:0002396)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001631", ontology="TAO"} +relationship: RO:0002371 UBERON:0002396 ! attached to vomer [Term] id: UBERON:0004768 @@ -215832,12 +213108,11 @@ namespace: uberon def: "Any bone that is part of the lower jaw skeleton. This includes (when present): the dentary/mandible, the articular, the splenial, the suprangular." [https://orcid.org/0000-0002-6601-2165] subset: grouping_class synonym: "lower jaw bone" EXACT [] -is_a: UBERON:0010313 ! neural crest-derived structure is_a: UBERON:0012360 ! bone of jaw intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0001710 ! lower jaw region relationship: part_of UBERON:0003278 ! skeleton of lower jaw -property_value: editor_note "Do not manually classify under here - bones are automatically classified" xsd:string +property_value: IAO:0000116 "Do not manually classify under here - bones are automatically classified" xsd:string [Term] id: UBERON:0004769 @@ -215856,9 +213131,7 @@ xref: MESH:D018483 xref: SCTID:361729006 xref: Wikipedia:Diaphysis is_a: UBERON:0005055 ! zone of long bone -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/94/Illu_long_bone.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Subdivision of long bone which forms the part of the bone between the two epiphyses; together with other the subdivisions of long bone, it constitutes the long bone. Examples: diaphysis of humerus, diaphysis of femur[FMA]." xsd:string {source="FMA:24013"} -property_value: UBPROP:0000001 "The main or mid section (shaft) of a long bone. It is made up of cortical bone and usually contains bone marrow and adipose tissue (fat)[WP][FMA:24013, Wikipedia:Diaphysis]." xsd:string {source="FMA:24013, Wikipedia:Diaphysis"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/94/Illu_long_bone.jpg" xsd:anyURI [Term] id: UBERON:0004770 @@ -215876,12 +213149,12 @@ xref: SCTID:361827000 xref: VSAO:0000181 is_a: UBERON:0034925 ! anatomical collection intersection_of: UBERON:0034925 ! anatomical collection -intersection_of: has_member UBERON:0000982 ! skeletal joint -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: functionally_related_to GO:0040011 ! locomotion -relationship: has_member UBERON:0000982 ! skeletal joint -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +intersection_of: RO:0002351 UBERON:0000982 ! has member skeletal joint relationship: part_of UBERON:0001434 {source="FMA"} ! skeletal system +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002328 GO:0040011 ! functionally related to locomotion +relationship: RO:0002351 UBERON:0000982 ! has member skeletal joint +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage [Term] id: UBERON:0004771 @@ -215908,16 +213181,11 @@ xref: Wikipedia:Posterior_nasal_apertures xref: XAO:0000277 is_a: UBERON:0010425 ! internal naris intersection_of: UBERON:0010425 ! internal naris -intersection_of: connects UBERON:0001707 ! nasal cavity -intersection_of: connects UBERON:0001728 ! nasopharynx -relationship: connects UBERON:0001728 ! nasopharynx +intersection_of: RO:0002176 UBERON:0001707 ! connects nasal cavity +intersection_of: RO:0002176 UBERON:0001728 ! connects nasopharynx relationship: part_of UBERON:0003128 ! cranium -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/87/Gray855.png" xsd:anyURI -property_value: UBPROP:0000001 "One of the paired openings from the nasal cavities into the pharynx. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-6, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000545", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000001 "Opening between the nasal cavity and the nasopharynx.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000093", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000003 "The choana, a unique 'internal nostril' opening from the nasal sac into the roof of the mouth, is a key part of the tetrapod (land vertebrate) respiratory system. It was the first component of the tetrapod body plan to evolve, well before the origin of limbs, and is therefore crucial to our understanding of the beginning of the fish-tetrapod transition. (...) Here we present new material of Kenichthys, a 395-million-year-old fossil fish from China, that provides direct evidence for the origin of the choana and establishes its homology: it is indeed a displaced posterior external nostril that, during a brief transitional stage illustrated by Kenichthys, separated the maxilla from the premaxilla.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000545", ontology="VHOG", source="DOI:10.1038/nature02843 Zhu M, Ahlberg PE, The origin of the internal nostril in tetrapodes. Nature (2004)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "Fish don't have choanae, instead they have two pairs of external nostrils" xsd:string {source="WP"} -property_value: UBPROP:0000008 "In addition to tetrapods, the lungfish has internal nostrils too. In tetrapods the exhalant nostril (choana) empties into the buccal cavity." xsd:string +relationship: RO:0002176 UBERON:0001728 ! connects nasopharynx +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/87/Gray855.png" xsd:anyURI [Term] id: UBERON:0004775 @@ -215941,8 +213209,8 @@ is_a: UBERON:0013126 ! vein of abdomen is_a: UBERON:0014401 ! renal venous blood vessel intersection_of: UBERON:0004726 ! vasa recta intersection_of: part_of UBERON:0001293 ! outer medulla of kidney -relationship: contributes_to_morphology_of UBERON:0001293 ! outer medulla of kidney relationship: part_of UBERON:0001293 ! outer medulla of kidney +relationship: RO:0002433 UBERON:0001293 ! contributes to morphology of outer medulla of kidney [Term] id: UBERON:0004776 @@ -215966,8 +213234,8 @@ is_a: UBERON:0013126 ! vein of abdomen is_a: UBERON:0014401 ! renal venous blood vessel intersection_of: UBERON:0004726 ! vasa recta intersection_of: part_of UBERON:0001294 ! inner medulla of kidney -relationship: contributes_to_morphology_of UBERON:0001294 ! inner medulla of kidney relationship: part_of UBERON:0001294 ! inner medulla of kidney +relationship: RO:0002433 UBERON:0001294 ! contributes to morphology of inner medulla of kidney [Term] id: UBERON:0004777 @@ -215995,6 +213263,7 @@ xref: EMAPA:35474 xref: FMA:321584 xref: MA:0002728 xref: SCTID:361941005 +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0004777 ! respiratory system submucosa intersection_of: UBERON:0000009 ! submucosa intersection_of: part_of UBERON:0001737 ! larynx @@ -216052,6 +213321,7 @@ xref: MA:0001633 xref: NCIT:C49228 xref: UMLS:C1708175 {source="ncithesaurus:Gallbladder_Lamina_Propria"} is_a: UBERON:0000030 ! lamina propria +is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0000030 ! lamina propria intersection_of: part_of UBERON:0002110 ! gallbladder relationship: part_of UBERON:0005033 {is_inferred="true", source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! mucosa of gallbladder @@ -216096,6 +213366,7 @@ xref: FMA:14659 xref: MA:0001634 xref: SCTID:362197006 is_a: UBERON:0000042 ! serous membrane +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure intersection_of: UBERON:0000042 ! serous membrane intersection_of: part_of UBERON:0002110 ! gallbladder relationship: part_of UBERON:0002110 ! gallbladder @@ -216152,7 +213423,6 @@ synonym: "respiratory system mucosa of organ" EXACT [OBOL:automatic] synonym: "respiratory system mucous membrane" EXACT [OBOL:automatic] synonym: "respiratory tract mucosa" RELATED [] xref: BTO:0000973 -xref: EMAPA:18334 xref: EMAPA:37577 {source="MA:th"} xref: FMA:302092 xref: GAID:304 @@ -216162,7 +213432,7 @@ is_a: UBERON:0000344 ! mucosa intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0001004 ! respiratory system relationship: part_of UBERON:0001004 ! respiratory system -property_value: editor_note "TODO - split respiratory tract mucosa from respiratory system mucosa" xsd:string +property_value: IAO:0000116 "TODO - split respiratory tract mucosa from respiratory system mucosa" xsd:string [Term] id: UBERON:0004786 @@ -216206,7 +213476,7 @@ is_a: UBERON:0000365 ! urothelium is_a: UBERON:0002325 ! epithelium of urethra intersection_of: UBERON:0000365 ! urothelium intersection_of: part_of UBERON:0000057 ! urethra -relationship: contributes_to_morphology_of UBERON:0000057 ! urethra +relationship: RO:0002433 UBERON:0000057 ! contributes to morphology of urethra [Term] id: UBERON:0004788 @@ -216239,8 +213509,8 @@ is_a: UBERON:0000365 ! urothelium is_a: UBERON:0004819 ! kidney epithelium intersection_of: UBERON:0000365 ! urothelium intersection_of: part_of UBERON:0001224 ! renal pelvis -relationship: contributes_to_morphology_of UBERON:0001224 ! renal pelvis relationship: part_of UBERON:0001224 ! renal pelvis +relationship: RO:0002433 UBERON:0001224 ! contributes to morphology of renal pelvis [Term] id: UBERON:0004789 @@ -216251,6 +213521,7 @@ synonym: "mucous gland of larynx" EXACT [OBOL:automatic] xref: EMAPA:37631 {source="MA:th"} xref: MA:0001767 is_a: UBERON:0000414 ! mucous gland +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0036225 ! respiratory system gland intersection_of: UBERON:0000414 ! mucous gland intersection_of: part_of UBERON:0001737 ! larynx @@ -216273,7 +213544,7 @@ is_a: UBERON:0007771 ! epidermis gland is_a: UBERON:0019319 ! exocrine gland of integumental system intersection_of: UBERON:0000414 ! mucous gland intersection_of: part_of UBERON:0002097 ! skin of body -property_value: editor_note "See comments for 'skin mucus'" xsd:string +property_value: IAO:0000116 "See comments for 'skin mucus'" xsd:string [Term] id: UBERON:0004791 @@ -216290,12 +213561,13 @@ synonym: "trabecula of thymus gland" EXACT [OBOL:automatic] xref: MA:0002674 xref: NCIT:C33773 xref: UMLS:C1515431 {source="ncithesaurus:Thymic_Trabecula"} +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0000440 ! trabecula intersection_of: UBERON:0000440 ! trabecula intersection_of: part_of UBERON:0002370 ! thymus -relationship: contributes_to_morphology_of UBERON:0002370 ! thymus relationship: part_of UBERON:0002370 {source="MA"} ! thymus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002433 UBERON:0002370 ! contributes to morphology of thymus +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004792 @@ -216387,8 +213659,6 @@ is_a: UBERON:0006530 {source="FMA"} ! seminal fluid intersection_of: UBERON:0000456 ! secretion of exocrine gland intersection_of: produced_by UBERON:0002367 ! prostate gland relationship: produced_by UBERON:0002367 ! prostate gland -property_value: UBPROP:0000008 "Prostatic secretions vary among species. They are generally composed of simple sugars and are often slightly alkaline." xsd:string -property_value: UBPROP:0000010 "A secretion of the prostate this is slightly alkaline fluid, milky or white in appearance. Usually constitutes 20-30% of the volume of the semen along with spermatozoa and seminal vesicle fluid [Wikipedia:Prostate#Secretions]" xsd:string [Term] id: UBERON:0004797 @@ -216397,11 +213667,12 @@ namespace: uberon def: "Any of the tissue layers that comprise a blood vessel. Examples: tunica media, tunica adventitia." [http://orcid.org/0000-0002-6601-2165] xref: EMAPA:36296 xref: MA:0002854 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004923 ! organ component layer intersection_of: UBERON:0004923 ! organ component layer intersection_of: part_of UBERON:0001981 ! blood vessel relationship: part_of UBERON:0035965 ! wall of blood vessel -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/6/61/Blood_vessels.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/61/Blood_vessels.svg" xsd:anyURI [Term] id: UBERON:0004801 @@ -216426,10 +213697,9 @@ xref: UMLS:C1711358 {source="ncithesaurus:Cervix_Epithelium"} is_a: UBERON:0006955 ! uterine epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000002 ! uterine cervix -relationship: contributes_to_morphology_of UBERON:0000002 ! uterine cervix relationship: part_of UBERON:0000002 ! uterine cervix -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000010 "The epithelium of the cervix is varied. The ectocervix (more distal, by the vagina) is composed of nonkeratinized stratified squamous epithelium. The endocervix (more proximal, within the uterus) is composed of simple columnar epithelium" xsd:string {source="Wikipedia:Cervix#Histology"} +relationship: RO:0002433 UBERON:0000002 ! contributes to morphology of uterine cervix +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004802 @@ -216447,13 +213717,13 @@ xref: CALOHA:TS-0023 xref: EMAPA:32827 xref: MA:0001480 xref: SCTID:321764001 -xref: VHOG:0000981 is_a: UBERON:0004807 ! respiratory system epithelium +is_a: UBERON:0005911 ! endo-epithelium is_a: UBERON:0010499 ! pseudostratified ciliated columnar epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000065 ! respiratory tract -relationship: contributes_to_morphology_of UBERON:0001004 ! respiratory system relationship: part_of UBERON:0000072 ! proximo-distal subdivision of respiratory tract +relationship: RO:0002433 UBERON:0001004 ! contributes to morphology of respiratory system [Term] id: UBERON:0004803 @@ -216466,8 +213736,8 @@ synonym: "penis epithelial tissue" EXACT [OBOL:automatic] xref: EHDAA2:0004039 xref: EMAPA:35674 xref: MA:0001742 -is_a: UBERON:0000483 ! epithelium is_a: UBERON:0005156 ! reproductive structure +is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000989 ! penis relationship: part_of UBERON:0000989 ! penis @@ -216490,13 +213760,12 @@ xref: BTO:0002402 xref: CALOHA:TS-1316 xref: EMAPA:29043 xref: MA:0001718 -is_a: UBERON:0000483 ! epithelium is_a: UBERON:0005156 ! reproductive structure +is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000993 ! oviduct relationship: part_of UBERON:0003889 ! fallopian tube -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000012 "in FMA, epithelium of uterine tube is a subclass of ciliated columnar epithelium. MA introduces subtypes: ciliated columnar and cuboidal. We map the FMA type according to its relationships, not its label" xsd:string {external_ontology="FMA"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004805 @@ -216516,6 +213785,7 @@ xref: MA:0001745 xref: NCIT:C49295 xref: UMLS:C1710049 {source="ncithesaurus:Seminal_Vesicle_Epithelium"} is_a: UBERON:0004910 ! epithelium of male gonad +is_a: UBERON:0012275 ! meso-epithelium is_a: UBERON:0034969 ! epithelial layer of duct intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000998 ! seminal vesicle @@ -216572,7 +213842,6 @@ synonym: "respiratory system epithelial tissue" EXACT [OBOL:automatic] xref: CALOHA:TS-0023 xref: EMAPA:32826 xref: MA:0001823 -xref: VHOG:0000981 is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001004 ! respiratory system @@ -216613,8 +213882,8 @@ xref: MA:0001587 is_a: UBERON:0003929 ! digestive tract epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001044 ! saliva-secreting gland -relationship: develops_from UBERON:0011272 {gci_relation="part_of", gci_filler="NCBITaxon:7742", source="Wikipathways:WP2062"} ! embryonic skin basal layer relationship: part_of UBERON:0001044 ! saliva-secreting gland +relationship: RO:0002202 UBERON:0011272 {gci_relation="part_of", gci_filler="NCBITaxon:7742", source="Wikipathways:WP2062"} ! develops from embryonic skin basal layer [Term] id: UBERON:0004810 @@ -216633,9 +213902,9 @@ intersection_of: UBERON:0000483 ! epithelium intersection_of: adjacent_to UBERON:0000464 ! anatomical space intersection_of: part_of UBERON:0001231 ! nephron tubule relationship: adjacent_to UBERON:0000464 ! anatomical space -relationship: contributes_to_morphology_of UBERON:0001231 ! nephron tubule relationship: part_of UBERON:0001231 ! nephron tubule -property_value: editor_note "See https://github.com/obophenotype/uberon/issues/1305" xsd:string +relationship: RO:0002433 UBERON:0001231 ! contributes to morphology of nephron tubule +property_value: IAO:0000116 "See https://github.com/obophenotype/uberon/issues/1305" xsd:string [Term] id: UBERON:0004811 @@ -216656,7 +213925,6 @@ is_a: UBERON:0006955 ! uterine epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001295 ! endometrium relationship: part_of UBERON:0001295 ! endometrium -property_value: UBPROP:0000008 "In rodents and primates, the uterine epithelium (the endometrium) is eroded away so that maternal blood comes into direct contact with the trophoblast surface (called haemochorial)" xsd:string {source="PMID:19829370"} [Term] id: UBERON:0004812 @@ -216687,7 +213955,7 @@ is_a: UBERON:0004803 ! penis epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001332 ! prepuce of penis relationship: part_of UBERON:0001332 ! prepuce of penis -property_value: editor_note "NCITA term may be sex-neutral" xsd:string +property_value: IAO:0000116 "NCITA term may be sex-neutral" xsd:string [Term] id: UBERON:0004813 @@ -216723,10 +213991,10 @@ is_a: UBERON:0004910 ! epithelium of male gonad is_a: UBERON:0034969 ! epithelial layer of duct intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001343 ! seminiferous tubule of testis -relationship: contributes_to_morphology_of UBERON:0001343 ! seminiferous tubule of testis relationship: has_part CL:0000020 ! spermatogonium relationship: has_part CL:0000216 ! Sertoli cell relationship: part_of UBERON:0001343 ! seminiferous tubule of testis +relationship: RO:0002433 UBERON:0001343 ! contributes to morphology of seminiferous tubule of testis [Term] id: UBERON:0004814 @@ -216776,9 +214044,8 @@ xref: UMLS:C0751258 {source="ncithesaurus:Laryngeal_Epithelium"} is_a: UBERON:0004802 ! respiratory tract epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001737 ! larynx -relationship: contributes_to_morphology_of UBERON:0001737 ! larynx relationship: part_of UBERON:0001737 ! larynx -property_value: UBPROP:0000010 "composed of squamous epithelium in the upper larynx and ciliated columnar epithelium in the lower larynx [ISBN:0-397-51047-0]" xsd:string +relationship: RO:0002433 UBERON:0001737 ! contributes to morphology of larynx [Term] id: UBERON:0004817 @@ -216812,8 +214079,8 @@ xref: MA:0002846 is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002113 ! kidney -relationship: contributes_to_morphology_of UBERON:0002113 ! kidney relationship: part_of UBERON:0002113 ! kidney +relationship: RO:0002433 UBERON:0002113 ! contributes to morphology of kidney [Term] id: UBERON:0004820 @@ -216828,13 +214095,13 @@ xref: BTO:0000417 xref: MA:0001629 xref: NCIT:C43616 xref: UMLS:C1711208 {source="ncithesaurus:Bile_Duct_Epithelium"} +is_a: UBERON:0005911 ! endo-epithelium is_a: UBERON:0034932 ! epithelium of biliary system is_a: UBERON:0034969 ! epithelial layer of duct intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002394 ! bile duct relationship: has_part CL:1000488 ! cholangiocyte relationship: part_of UBERON:0002394 ! bile duct -property_value: UBPROP:0000001 "The irregularly shaped proliferating bile ducts are lined by normal cuboidal epithelium." xsd:string {source="BTO:0000417"} [Term] id: UBERON:0004821 @@ -216859,10 +214126,10 @@ is_a: UBERON:0000115 ! lung epithelium is_a: UBERON:0000487 {source="FMA"} ! simple squamous epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002299 ! alveolus of lung -relationship: contributes_to_morphology_of UBERON:0000115 ! lung epithelium -relationship: contributes_to_morphology_of UBERON:0002299 ! alveolus of lung relationship: has_part CL:0002062 {source="FMA"} ! type I pneumocyte relationship: part_of UBERON:0004894 {source="FMA"} ! alveolar wall +relationship: RO:0002433 UBERON:0000115 ! contributes to morphology of lung epithelium +relationship: RO:0002433 UBERON:0002299 ! contributes to morphology of alveolus of lung [Term] id: UBERON:0004822 @@ -216915,6 +214182,7 @@ synonym: "thyroid medulla" EXACT [OBOL:automatic] xref: EMAPA:37768 {source="MA:th"} xref: MA:0000132 is_a: UBERON:0000958 ! medulla of organ +is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0000958 ! medulla of organ intersection_of: part_of UBERON:0002046 ! thyroid gland relationship: part_of UBERON:0002046 ! thyroid gland @@ -217005,7 +214273,7 @@ is_a: UBERON:0001134 ! skeletal muscle tissue intersection_of: UBERON:0001134 ! skeletal muscle tissue intersection_of: part_of UBERON:0001833 ! lip relationship: part_of UBERON:0001833 ! lip -property_value: editor_note "this class is derived from MA. Consider re-modeling this as being a muscle that acts on the lips. See: Wikipedia:Lip#Muscles_acting_on_the_lips" xsd:string +property_value: IAO:0000116 "this class is derived from MA. Consider re-modeling this as being a muscle that acts on the lips. See: Wikipedia:Lip#Muscles_acting_on_the_lips" xsd:string [Term] id: UBERON:0004834 @@ -217014,6 +214282,7 @@ namespace: uberon def: "Smooth muscle tissue in all or part of a hepatic duct." [http://orcid.org/0000-0002-6601-2165] xref: EMAPA:37598 {source="MA:th"} xref: MA:0001640 +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0001135 ! smooth muscle tissue intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0005171 ! hepatic duct @@ -217031,7 +214300,6 @@ synonym: "involuntary muscle of epididymis" EXACT [OBOL:automatic] synonym: "non-striated muscle of epididymis" EXACT [OBOL:automatic] synonym: "smooth muscle of epididymis" EXACT [OBOL:automatic] synonym: "smooth muscle tissue of epididymis" EXACT [OBOL:automatic] -xref: EMAPA:30747 xref: MA:0001736 is_a: UBERON:0001135 ! smooth muscle tissue is_a: UBERON:0005156 ! reproductive structure @@ -217063,7 +214331,7 @@ is_a: UBERON:0004702 ! respiratory system blood vessel endothelium intersection_of: UBERON:0001917 ! endothelium of artery intersection_of: part_of UBERON:0001004 ! respiratory system relationship: part_of UBERON:0003469 {is_inferred="true", source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! respiratory system artery -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004849 @@ -217089,7 +214357,7 @@ is_a: UBERON:0004702 ! respiratory system blood vessel endothelium intersection_of: UBERON:0001919 ! endothelium of vein intersection_of: part_of UBERON:0001004 ! respiratory system relationship: part_of UBERON:0003476 ! respiratory system venous blood vessel -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004850 @@ -217155,8 +214423,7 @@ is_a: UBERON:0001986 ! endothelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0004535 ! cardiovascular system relationship: part_of UBERON:0004535 ! cardiovascular system -property_value: editor_note "consider merging with 'endothelium'" xsd:string -property_value: UBPROP:0000003 "Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001217", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207", source="http://bgee.unil.ch/"} +property_value: IAO:0000116 "consider merging with 'endothelium'" xsd:string [Term] id: UBERON:0004854 @@ -217196,8 +214463,8 @@ xref: EMAPA:37743 {source="MA:th"} xref: MA:0002868 is_a: UBERON:0002384 ! connective tissue intersection_of: UBERON:0002384 ! connective tissue -intersection_of: surrounds UBERON:0001134 ! skeletal muscle tissue -relationship: surrounds UBERON:0001134 ! skeletal muscle tissue +intersection_of: RO:0002221 UBERON:0001134 ! surrounds skeletal muscle tissue +relationship: RO:0002221 UBERON:0001134 ! surrounds skeletal muscle tissue [Term] id: UBERON:0004859 @@ -217289,14 +214556,12 @@ synonym: "set of retinal blood vessels" EXACT [FMA:76552] synonym: "vasa sanguinea retinae" EXACT OMO:0003011 [FMA:76552, FMA:TA] xref: FMA:76552 xref: MESH:D012171 -xref: XAO:0004153 is_a: UBERON:0002203 ! vasculature of eye is_a: UBERON:0036302 ! vasculature of central nervous system plus retina intersection_of: UBERON:0002049 ! vasculature intersection_of: part_of UBERON:0000966 ! retina -relationship: never_in_taxon NCBITaxon:8782 {source="PMID:21622558", source="PMID:2772405", submitter="michaelerice"} ! Aves relationship: part_of UBERON:0000966 ! retina -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004867 @@ -217311,9 +214576,8 @@ xref: Wikipedia:Orbit_(anatomy) xref: ZFA:0005558 is_a: UBERON:0002553 ! anatomical cavity intersection_of: UBERON:0002553 ! anatomical cavity -intersection_of: luminal_space_of UBERON:0001697 ! orbit of skull -relationship: luminal_space_of UBERON:0001697 ! orbit of skull -property_value: UBPROP:0000012 "note that the AAO and ZFA class is a cavity" xsd:string {external_ontology="AAO", seeAlso="https://github.com/obophenotype/uberon/issues/462"} +intersection_of: RO:0002572 UBERON:0001697 ! luminal space of orbit of skull +relationship: RO:0002572 UBERON:0001697 ! luminal space of orbit of skull [Term] id: UBERON:0004869 @@ -217324,9 +214588,10 @@ synonym: "parietal eye" EXACT [Wikipedia:Parietal_eye] synonym: "third eye" RELATED [Wikipedia:Parietal_eye] xref: Wikipedia:Parietal_eye is_a: UBERON:0003103 {source="cjm"} ! compound organ -relationship: never_in_taxon NCBITaxon:40674 ! Mammalia -relationship: never_in_taxon NCBITaxon:8782 ! Aves +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0015238 {source="cjm"} ! pineal complex +property_value: RO:0002161 NCBITaxon:40674 +property_value: RO:0002161 NCBITaxon:8782 [Term] id: UBERON:0004871 @@ -217344,7 +214609,7 @@ xref: Wikipedia:Lateral_plate_mesoderm#Division_into_layers xref: XAO:0000271 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0003081 ! lateral plate mesoderm -property_value: editor_note "check BILA" xsd:string +property_value: IAO:0000116 "check BILA" xsd:string [Term] id: UBERON:0004872 @@ -217362,7 +214627,6 @@ xref: Wikipedia:Lateral_plate_mesoderm#Division_into_layers xref: XAO:0000276 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0003081 ! lateral plate mesoderm -property_value: UBPROP:0000012 "We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors" xsd:string {external_ontology="BILA"} [Term] id: UBERON:0004873 @@ -217381,8 +214645,8 @@ xref: Wikipedia:Splanchnopleure is_a: UBERON:0002050 ! embryonic structure relationship: overlaps UBERON:0000925 ! endoderm relationship: part_of UBERON:0003081 {source="EHDAA2"} ! lateral plate mesoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png" xsd:anyURI -property_value: editor_note "TODO - check relationship to LPM" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png" xsd:anyURI +property_value: IAO:0000116 "TODO - check relationship to LPM" xsd:string [Term] id: UBERON:0004874 @@ -217400,9 +214664,7 @@ xref: Wikipedia:Somatopleure is_a: UBERON:0002050 ! embryonic structure relationship: overlaps UBERON:0000924 ! ectoderm relationship: part_of UBERON:0003081 {source="EHDAA2"} ! lateral plate mesoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png" xsd:anyURI -property_value: UBPROP:0000011 "Gives rise to the paired appendages in jawed vertebrates. a persistent somatopleure through the redistribution and expansion of the lateral plate mesoderm is a synapomorphy for gnathostomes and a critical step in generating a novel developmental module with dramatic evolutionary potentia (Tulenko et al. 2012) http://burkelab.research.wesleyan.edu/current-projects/lamprey/" xsd:string -property_value: UBPROP:0000012 "sources differ as to whether this is part-of or develops-from the LPM" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png" xsd:anyURI [Term] id: UBERON:0004875 @@ -217417,7 +214679,7 @@ xref: SCTID:361405003 xref: UMLS:C1283944 {source="ncithesaurus:Nephrogenic_Cord"} xref: Wikipedia:Nephrogenic_cord is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0004876 ! urogenital fold +relationship: RO:0002202 UBERON:0004876 ! develops from urogenital fold [Term] id: UBERON:0004876 @@ -217433,11 +214695,10 @@ xref: EMAPA:30888 xref: FMA:321919 xref: Wikipedia:Urogenital_folds is_a: UBERON:0006598 ! presumptive structure -relationship: develops_from UBERON:0003064 {source="Wikipedia"} ! intermediate mesoderm -relationship: develops_from UBERON:0012292 {source="EHDAA2"} ! embryonic cloacal fold -relationship: has_potential_to_develop_into UBERON:0004176 ! external genitalia relationship: part_of UBERON:0009196 {source="EHDAA2"} ! indifferent external genitalia -property_value: UBPROP:0000013 "Less commonly, urogenital fold refers to the fold in the mesonephros which is the precursor of e.g. the suspensory ligament of the ovary. This is the case in older versions of Gray's anatomy[WP]" xsd:string +relationship: RO:0002202 UBERON:0003064 {source="Wikipedia"} ! develops from intermediate mesoderm +relationship: RO:0002202 UBERON:0012292 {source="EHDAA2"} ! develops from embryonic cloacal fold +relationship: RO:0002387 UBERON:0004176 ! has potential to develop into external genitalia [Term] id: UBERON:0004877 @@ -217449,7 +214710,6 @@ xref: BTO:0003487 xref: EMAPA:16058 is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0005292 {source="BTO"} ! extraembryonic tissue -property_value: UBPROP:0000013 "Gilbert uses visceral endoderm as a synonym for primitive endoderm/hypoblast" xsd:string [Term] id: UBERON:0004880 @@ -217467,10 +214727,8 @@ xref: EFO:0003426 xref: TAO:0000091 xref: ZFA:0000091 is_a: UBERON:0002050 ! embryonic structure -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0003068 ! axial mesoderm -property_value: UBPROP:0000001 "Notochord rudiment[ZFIN:ZDB-PUB-961014-576]." xsd:string {source="ZFIN:ZDB-PUB-961014-576"} -property_value: UBPROP:0000012 "WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord." xsd:string +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata [Term] id: UBERON:0004883 @@ -217483,13 +214741,13 @@ synonym: "lung-associated mesenchyme" EXACT [GO:0060484] synonym: "mesenchyme of lung" EXACT [OBOL:automatic] synonym: "pulmonary mesenchyme" EXACT [GO:0060484] xref: EMAPA:32866 +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0003104 ! mesenchyme -is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0002048 ! lung -relationship: develops_from UBERON:0003081 ! lateral plate mesoderm relationship: part_of UBERON:0002048 ! lung -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 UBERON:0003081 ! develops from lateral plate mesoderm +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004884 @@ -217502,10 +214760,10 @@ xref: EMAPA:32698 is_a: UBERON:0004883 ! lung mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0002183 ! lobar bronchus -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: has_part CL:0019019 ! tracheobronchial smooth muscle cell relationship: part_of UBERON:0002183 ! lobar bronchus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004889 @@ -217532,6 +214790,7 @@ xref: NCIT:C49473 xref: UMLS:C1706784 {source="ncithesaurus:Alveolar_Septum"} xref: Wikipedia:Alveolar_septum is_a: UBERON:0003037 ! septum +is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0003037 ! septum intersection_of: adjacent_to UBERON:0002299 ! alveolus of lung relationship: adjacent_to UBERON:0002299 ! alveolus of lung @@ -217556,11 +214815,11 @@ xref: NCIT:C13085 xref: SCTID:361965008 xref: UMLS:C0225695 {source="ncithesaurus:Alveolar_Wall"} is_a: UBERON:0000060 ! anatomical wall +is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0002299 ! alveolus of lung -relationship: contributes_to_morphology_of UBERON:0002299 ! alveolus of lung relationship: part_of UBERON:0002299 ! alveolus of lung -property_value: UBPROP:0000012 "part of wall in FMA" xsd:string {external_ontology="FMA"} +relationship: RO:0002433 UBERON:0002299 ! contributes to morphology of alveolus of lung [Term] id: UBERON:0004895 @@ -217595,12 +214854,13 @@ synonym: "epithelium of urogenital sinus" EXACT [OBOL:automatic] synonym: "UGE" EXACT [PMID:18977204] xref: EHDAA2:0004061 xref: EMAPA:31509 +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0009846 ! embryonic cloacal epithelium +is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000164 ! primitive urogenital sinus -relationship: develops_from UBERON:0009846 {source="EHDAA2"} ! embryonic cloacal epithelium relationship: part_of UBERON:0000164 ! primitive urogenital sinus -property_value: UBPROP:0000012 "we follow EHDAA2 in dividing the UGS into epithelium and lumen" xsd:string {external_ontology="EHDAA2"} +relationship: RO:0002202 UBERON:0009846 {source="EHDAA2"} ! develops from embryonic cloacal epithelium [Term] id: UBERON:0004904 @@ -217615,7 +214875,6 @@ synonym: "optic nerve" BROAD [BTO:0000966] synonym: "optic nerve (generic)" EXACT [] xref: BTO:0000966 xref: EV:0100351 -xref: FBbt:00001956 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: TADS:0000232 is_a: UBERON:0000122 ! neuron projection bundle intersection_of: UBERON:0000122 ! neuron projection bundle @@ -217624,7 +214883,7 @@ intersection_of: extends_fibers_into UBERON:0005388 ! photoreceptor array relationship: extends_fibers_into UBERON:0000955 ! brain relationship: extends_fibers_into UBERON:0005388 ! photoreceptor array relationship: part_of UBERON:0002104 ! visual system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004905 @@ -217633,7 +214892,6 @@ namespace: uberon def: "Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts." [http://orcid.org/0000-0002-6601-2165] subset: grouping_class synonym: "joint" NARROW [] -xref: FBbt:00005811 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0034921 ! multi organ part structure relationship: part_of UBERON:0004770 ! articular system @@ -217647,8 +214905,8 @@ synonym: "gut ectoderm" EXACT [EMAPA:32930] is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004921 ! subdivision of digestive tract intersection_of: UBERON:0004921 ! subdivision of digestive tract -intersection_of: develops_from UBERON:0000924 ! ectoderm intersection_of: part_of UBERON:0001555 ! digestive tract +intersection_of: RO:0002202 UBERON:0000924 ! develops from ectoderm [Term] id: UBERON:0004907 @@ -217666,10 +214924,8 @@ xref: SCTID:279973004 xref: UMLS:C0226875 {source="ncithesaurus:Lower_Gastrointestinal_Tract"} xref: Wikipedia:Alimentary_canal#Upper_gastrointestinal_tract is_a: UBERON:0004921 ! subdivision of digestive tract -relationship: develops_from UBERON:0001046 ! hindgut relationship: part_of UBERON:0005409 ! alimentary part of gastrointestinal system -property_value: UBPROP:0000012 "MA class was moved from here. See https://github.com/obophenotype/uberon/issues/509" xsd:string {external_ontology="MA"} -property_value: UBPROP:0000012 "WP: small intestine, large intestine, anus. Anal canal not part of LGIT according to FMA, but anus is considered part of LGIT according to WP. Duodenum overlaps both U/L" xsd:string {external_ontology="FMA"} +relationship: RO:0002202 UBERON:0001046 ! develops from hindgut [Term] id: UBERON:0004908 @@ -217686,8 +214942,7 @@ xref: SCTID:181244000 xref: UMLS:C0226874 {source="ncithesaurus:Upper_Gastrointestinal_Tract"} xref: Wikipedia:Alimentary_canal#Upper_gastrointestinal_tract is_a: UBERON:0004921 ! subdivision of digestive tract -relationship: develops_from UBERON:0001041 ! foregut -property_value: UBPROP:0000012 "WP: small intestine, large intestine, anus. Anal canal not part of LGIT according to FMA, but anus is considered part of LGIT according to WP. Duodenum overlaps both U/L. In Galen, entire GI tract excludes esophagus" xsd:string {external_ontology="FMA"} +relationship: RO:0002202 UBERON:0001041 ! develops from foregut [Term] id: UBERON:0004909 @@ -217706,7 +214961,7 @@ is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000991 ! gonad relationship: part_of UBERON:0000991 ! gonad -property_value: editor_note "after reasoning this should subsume the more specific germinal epithelium classes. We include the fly structure here although it is not clear if the sheath is an epithelium or a multi-tissue structure that includes epithelium as parts" xsd:string +property_value: IAO:0000116 "after reasoning this should subsume the more specific germinal epithelium classes. We include the fly structure here although it is not clear if the sheath is an epithelium or a multi-tissue structure that includes epithelium as parts" xsd:string [Term] id: UBERON:0004910 @@ -217720,7 +214975,7 @@ is_a: UBERON:0004909 ! epithelium of gonad intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000473 ! testis relationship: part_of UBERON:0000473 ! testis -property_value: editor_note "after reasoning this should subsume the more specific germinal epithelium classes. We include the fly structure here although it is not clear if the sheath is an epithelium or a multi-tissue structure that includes epithelium as parts" xsd:string +property_value: IAO:0000116 "after reasoning this should subsume the more specific germinal epithelium classes. We include the fly structure here although it is not clear if the sheath is an epithelium or a multi-tissue structure that includes epithelium as parts" xsd:string [Term] id: UBERON:0004911 @@ -217735,7 +214990,7 @@ is_a: UBERON:0004909 ! epithelium of gonad intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000992 ! ovary relationship: part_of UBERON:0000992 ! ovary -property_value: editor_note "after reasoning this should subsume the more specific germinal epithelium classes. We include the fly structure here although it is not clear if the sheath is an epithelium or a multi-tissue structure that includes epithelium as parts" xsd:string +property_value: IAO:0000116 "after reasoning this should subsume the more specific germinal epithelium classes. We include the fly structure here although it is not clear if the sheath is an epithelium or a multi-tissue structure that includes epithelium as parts" xsd:string [Term] id: UBERON:0004912 @@ -217750,9 +215005,9 @@ is_a: UBERON:0004185 ! endodermal part of digestive tract is_a: UBERON:0007499 {source="EHDAA2"} ! epithelial sac is_a: UBERON:0009497 ! epithelium of foregut-midgut junction is_a: UBERON:0009854 ! digestive tract diverticulum -relationship: develops_from UBERON:0004161 {source="EHDAA2-modified"} ! septum transversum relationship: part_of UBERON:0002423 {source="EHDAA2"} ! hepatobiliary system -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/4f/Gray1088.png" xsd:anyURI +relationship: RO:0002202 UBERON:0004161 {source="EHDAA2-modified"} ! develops from septum transversum +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4f/Gray1088.png" xsd:anyURI [Term] id: UBERON:0004913 @@ -217787,9 +215042,8 @@ intersection_of: part_of UBERON:0001174 ! common bile duct intersection_of: part_of UBERON:0004914 ! duodenal papilla relationship: part_of UBERON:0001174 ! common bile duct relationship: part_of UBERON:0004914 ! duodenal papilla -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Biliary_system_new.svg" xsd:anyURI -property_value: UBPROP:0000001 "Ampulla formed by the union of the pancreatic duct and the common bile duct where they enter the intestine.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005167", ontology="TAO", source="ZFIN:ZDB-PUB-070212-11", source="ZFIN:ZDB-PUB-080414-12"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Biliary_system_new.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004914 @@ -217806,8 +215060,8 @@ xref: NCIT:C119578 xref: SCTID:245389007 is_a: UBERON:0034944 ! zone of organ relationship: part_of UBERON:0000320 ! duodenal mucosa -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/43/Gray1057.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Small_Intestine.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/43/Gray1057.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Small_Intestine.glb" xsd:anyURI [Term] id: UBERON:0004915 @@ -217829,12 +215083,13 @@ xref: NCIT:C13065 xref: SCTID:181271000 xref: UMLS:C0028872 {source="ncithesaurus:Sphincter_of_Oddi"} xref: Wikipedia:Sphincter_of_ampulla +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0011185 ! gastrointestinal sphincter intersection_of: UBERON:0004590 ! sphincter muscle intersection_of: part_of UBERON:0004913 ! hepatopancreatic ampulla relationship: part_of UBERON:0004913 ! hepatopancreatic ampulla -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/43/Gray1057.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/43/Gray1057.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004916 @@ -217881,15 +215136,13 @@ synonym: "gut section" RELATED [FBbt:00100315] synonym: "intestinal tract" RELATED [] synonym: "segment of intestinal tract" RELATED [] synonym: "subdivision of alimentary system" RELATED [FMA:71131] -xref: FBbt:00100315 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:71131 is_a: UBERON:0013522 ! subdivision of tube intersection_of: UBERON:0013522 ! subdivision of tube intersection_of: subdivision_of UBERON:0001555 ! digestive tract relationship: part_of UBERON:0001555 ! digestive tract -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: subdivision_of UBERON:0001555 ! digestive tract -property_value: IAO:0000232 "intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct." xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004923 @@ -217899,8 +215152,8 @@ def: "A part of a wall of an organ that forms a layer." [http://orcid.org/0000-0 subset: upper_level xref: FMA:82485 is_a: UBERON:0000064 ! organ part -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000060 ! anatomical wall +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0004924 @@ -217952,7 +215205,7 @@ is_a: UBERON:0003331 ! submucosa of colon intersection_of: UBERON:0000009 ! submucosa intersection_of: part_of UBERON:0001153 ! caecum relationship: part_of UBERON:0001153 ! caecum -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004928 @@ -217974,7 +215227,7 @@ is_a: UBERON:0001208 ! submucosa of large intestine intersection_of: UBERON:0000009 ! submucosa intersection_of: part_of UBERON:0001154 ! vermiform appendix relationship: part_of UBERON:0001154 ! vermiform appendix -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004929 @@ -218123,6 +215376,7 @@ synonym: "biliary tree submucosa" EXACT [OBOL:automatic] synonym: "submucosa of biliary tract" EXACT [OBOL:automatic] xref: FMA:18009 is_a: UBERON:0000009 ! submucosa +is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0000009 ! submucosa intersection_of: part_of UBERON:0001173 ! biliary tree relationship: part_of UBERON:0001173 ! biliary tree @@ -218201,10 +215455,11 @@ xref: EMAPA:32275 xref: FMA:15929 xref: SCTID:88384001 is_a: UBERON:0000009 ! submucosa +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000009 ! submucosa intersection_of: part_of UBERON:0001255 ! urinary bladder relationship: part_of UBERON:0001256 {source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! wall of urinary bladder -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004944 @@ -218229,7 +215484,7 @@ is_a: UBERON:0004943 ! submucosa of urinary bladder intersection_of: UBERON:0000009 ! submucosa intersection_of: part_of UBERON:0001257 ! trigone of urinary bladder relationship: part_of UBERON:0001257 ! trigone of urinary bladder -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004945 @@ -218266,7 +215521,7 @@ is_a: UBERON:0001205 ! submucosa of small intestine intersection_of: UBERON:0000009 ! submucosa intersection_of: part_of UBERON:0002116 ! ileum relationship: part_of UBERON:0002116 ! ileum -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004950 @@ -218305,6 +215560,7 @@ namespace: uberon def: "A submucosa that is part of a bronchiole [Automatically generated definition]." [OBOL:automatic] synonym: "bronchiole submucosa" EXACT [OBOL:automatic] xref: FMA:62775 +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0004777 ! respiratory system submucosa intersection_of: UBERON:0000009 ! submucosa intersection_of: part_of UBERON:0002186 ! bronchiole @@ -218331,6 +215587,7 @@ xref: FMA:15894 xref: galen:MucousMembraneOfUreter xref: SCTID:40476001 is_a: UBERON:0000344 ! mucosa +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0000056 ! ureter relationship: part_of UBERON:0009916 {source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! wall of ureter @@ -218352,6 +215609,7 @@ synonym: "vaginal mucosa" EXACT [FMA:19975] xref: BTO:0005676 xref: FMA:19975 xref: SCTID:362245006 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0019042 ! reproductive system mucosa intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0000996 ! vagina @@ -218380,6 +215638,7 @@ synonym: "seminal vesicle organ mucosa" EXACT [OBOL:automatic] synonym: "tunica mucosa glandulae vesiculosae" EXACT OMO:0003011 [FMA:19405, FMA:TA] xref: FMA:19405 xref: SCTID:252260007 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0019042 ! reproductive system mucosa intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0000998 ! seminal vesicle @@ -218522,7 +215781,7 @@ is_a: UBERON:0001207 ! mucosa of large intestine intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0001154 ! vermiform appendix relationship: part_of UBERON:0001154 ! vermiform appendix -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004990 @@ -218820,6 +216079,7 @@ synonym: "organ mucosa of biliary tract" EXACT [OBOL:automatic] synonym: "organ mucosa of biliary tree" EXACT [OBOL:automatic] xref: FMA:14695 is_a: UBERON:0000344 ! mucosa +is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0001173 ! biliary tree relationship: part_of UBERON:0001173 ! biliary tree @@ -218954,7 +216214,7 @@ is_a: UBERON:0004980 ! mucosa of ureter intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0001223 ! left ureter relationship: part_of UBERON:0001223 ! left ureter -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0005006 @@ -219051,7 +216311,7 @@ is_a: UBERON:0001259 ! mucosa of urinary bladder intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0001257 ! trigone of urinary bladder relationship: part_of UBERON:0001257 ! trigone of urinary bladder -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0005010 @@ -219307,6 +216567,7 @@ xref: FMA:54971 xref: SCTID:361938001 is_a: UBERON:0000355 ! pharyngeal mucosa is_a: UBERON:0000379 ! tracheal mucosa +is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0001728 ! nasopharynx relationship: part_of UBERON:0001728 ! nasopharynx @@ -219347,6 +216608,7 @@ synonym: "mucous membrane of lacrimal canaliculus" EXACT [OBOL:automatic] synonym: "organ mucosa of lacrimal canaliculus" EXACT [OBOL:automatic] xref: FMA:85366 is_a: UBERON:0000344 ! mucosa +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0001770 ! lacrimal canaliculus relationship: part_of UBERON:0001770 ! lacrimal canaliculus @@ -219420,6 +216682,7 @@ synonym: "tunica mucosa vesicae biliaris" EXACT OMO:0003011 [FMA:14662, FMA:TA] xref: FMA:14662 xref: SCTID:362196002 is_a: UBERON:0000344 ! mucosa +is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0002110 ! gallbladder relationship: part_of UBERON:0002110 ! gallbladder @@ -219493,6 +216756,7 @@ synonym: "organ mucosa of bronchiole" EXACT [OBOL:automatic] xref: FMA:62774 xref: SCTID:10887006 is_a: UBERON:0000379 ! tracheal mucosa +is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0002186 ! bronchiole relationship: part_of UBERON:0002186 ! bronchiole @@ -219561,11 +216825,11 @@ synonym: "tympanic membrane external middle ear cavity epithelial component" EXA synonym: "tympanic membrane mucosa" EXACT [FMA:56844] xref: FMA:56844 xref: SCTID:36411006 +is_a: UBERON:0005911 ! endo-epithelium is_a: UBERON:0009647 ! tympanic membrane epithelium intersection_of: UBERON:0009647 ! tympanic membrane epithelium intersection_of: part_of UBERON:0010063 ! tympanic cavity epithelium relationship: part_of UBERON:0010063 ! tympanic cavity epithelium -property_value: UBPROP:0000012 "in FMA this is classified as a mucosa" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0005043 @@ -219582,6 +216846,7 @@ synonym: "nasolacrimal ductal mucosa" EXACT [FMA:59664] synonym: "organ mucosa of nasolacrimal duct" EXACT [OBOL:automatic] xref: FMA:59664 is_a: UBERON:0000344 ! mucosa +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0002392 ! nasolacrimal duct relationship: part_of UBERON:0002392 ! nasolacrimal duct @@ -219610,6 +216875,7 @@ synonym: "uterine tube mucosa of organ" EXACT [OBOL:automatic] synonym: "uterine tube mucous membrane" EXACT [OBOL:automatic] synonym: "uterine tube organ mucosa" EXACT [OBOL:automatic] xref: FMA:18319 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0019042 ! reproductive system mucosa intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0003889 ! fallopian tube @@ -219654,7 +216920,7 @@ is_a: UBERON:0002050 ! embryonic structure relationship: has_part UBERON:0002384 ! connective tissue relationship: overlaps UBERON:0003728 ! mediastinum relationship: part_of UBERON:0000473 ! testis -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b5/Hodenschema.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b5/Hodenschema.svg" xsd:anyURI [Term] id: UBERON:0005055 @@ -219691,7 +216957,6 @@ is_a: UBERON:0004176 ! external genitalia intersection_of: UBERON:0004176 ! external genitalia intersection_of: part_of UBERON:0000474 ! female reproductive system disjoint_from: UBERON:0009196 ! indifferent external genitalia -property_value: UBPROP:0000008 "in eutherians, this is known as the vulva in and composed of the mons pubis, the labia majora and minora, the clitoris, the vestibule of the vagina and its glands, and the opening of the urethra and of the vagina [MP:0003126]" xsd:string [Term] id: UBERON:0005057 @@ -219738,7 +217003,6 @@ xref: Wikipedia:Neural_groove xref: XAO:0000248 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0003075 ! neural plate -property_value: UBPROP:0000001 "The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]." xsd:string {source="Wikipedia:Neural_groove"} [Term] id: UBERON:0005062 @@ -219758,10 +217022,10 @@ xref: XAO:0004087 is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0005157 ! epithelial fold is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0015212 ! lateral structure -relationship: in_lateral_side_of UBERON:0005061 ! neural groove +relationship: BSPO:0000126 UBERON:0005061 ! neural groove relationship: part_of UBERON:0005061 ! neural groove -property_value: UBPROP:0000001 "In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]." xsd:string {source="Wikipedia:Neural_fold"} [Term] id: UBERON:0005064 @@ -219794,8 +217058,7 @@ xref: EFO:0003498 xref: TAO:0000133 xref: ZFA:0000133 is_a: UBERON:0016879 ! future central nervous system -relationship: develops_from UBERON:0007135 ! neural keel -property_value: UBPROP:0000001 "An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000133", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002202 UBERON:0007135 ! develops from neural keel [Term] id: UBERON:0005075 @@ -219808,16 +217071,15 @@ synonym: "forebrain-midbrain boundary region" EXACT [EMAPA:36449] xref: EMAPA:36449 xref: TAO:0001367 xref: ZFA:0001367 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0007651 ! anatomical junction intersection_of: UBERON:0007651 ! anatomical junction intersection_of: adjacent_to UBERON:0001890 ! forebrain intersection_of: adjacent_to UBERON:0001891 ! midbrain relationship: adjacent_to UBERON:0001890 ! forebrain relationship: adjacent_to UBERON:0001891 ! midbrain -relationship: develops_from UBERON:0007288 {evidence="definitional"} ! presumptive forebrain midbrain boundary relationship: part_of UBERON:0000955 ! brain -property_value: UBPROP:0000001 "The boundary between the diencephalon and the mesencephalon.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001367", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000002 "relationship loss: develops_from forebrain midbrain boundary neural tube (TAO:0007040)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001367", ontology="TAO"} +relationship: RO:0002202 UBERON:0007288 ! develops from presumptive forebrain midbrain boundary [Term] id: UBERON:0005076 @@ -219825,6 +217087,7 @@ name: hindbrain-spinal cord boundary namespace: uberon def: "An anatomical boundary that adjacent_to a hindbrain and adjacent_to a spinal cord." [OBOL:automatic] synonym: "hindbrain-spinal cord boundary region" EXACT [] +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0007651 ! anatomical junction intersection_of: UBERON:0007651 ! anatomical junction intersection_of: adjacent_to UBERON:0002028 ! hindbrain @@ -219840,8 +217103,8 @@ namespace: uberon def: "The portion of the ureteric bud tube that contributes to the morphogenesis of the metanephros[GO]." [GO:0035502] is_a: UBERON:0000084 ! ureteric bud intersection_of: UBERON:0000084 ! ureteric bud -intersection_of: has_potential_to_develop_into UBERON:0000081 ! metanephros -relationship: has_potential_to_develop_into UBERON:0000081 ! metanephros +intersection_of: RO:0002387 UBERON:0000081 ! has potential to develop into metanephros +relationship: RO:0002387 UBERON:0000081 ! has potential to develop into metanephros [Term] id: UBERON:0005081 @@ -219850,8 +217113,8 @@ namespace: uberon def: "The portion of the ureteric bud that contributes to the morphogenesis of the ureter. The ureter ureteric bud is the initial structure that forms the ureter[GO]." [GO:0035503] is_a: UBERON:0000084 ! ureteric bud intersection_of: UBERON:0000084 ! ureteric bud -intersection_of: has_potential_to_develop_into UBERON:0000056 ! ureter -relationship: has_potential_to_develop_into UBERON:0000056 ! ureter +intersection_of: RO:0002387 UBERON:0000056 ! has potential to develop into ureter +relationship: RO:0002387 UBERON:0000056 ! has potential to develop into ureter [Term] id: UBERON:0005082 @@ -219863,8 +217126,8 @@ xref: EHDAA2:0004618 xref: RETIRED_EHDAA2:0003078 is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: surrounded_by UBERON:0000025 ! tube -relationship: surrounded_by UBERON:0000025 ! tube +intersection_of: RO:0002219 UBERON:0000025 ! surrounded by tube +relationship: RO:0002219 UBERON:0000025 ! surrounded by tube [Term] id: UBERON:0005085 @@ -219876,9 +217139,7 @@ xref: AEO:0000218 is_a: UBERON:0001048 ! primordium is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0000924 ! ectoderm -property_value: editor_note "consder adding placodal ectoderm as a distinct class? Also place placodal ectoderm as develops_from ectoderm; need to check taxon-appropriateness" xsd:string -property_value: UBPROP:0000008 "With the exception of the adenohypophysis, homologues of the nonneurogenic placodes (e.g. placodes giving rise to the teeth, hair follicles and lens), appear to be lacking in invertebrate chordates." xsd:string -property_value: UBPROP:0000012 "in GO, covers optic, otic, olfactory, mammary, hair, tooth, sebaceous - and also insect structures" xsd:string {external_ontology="GO", source="https://github.com/geneontology/go-ontology/issues/12223#issuecomment-215692347"} +property_value: IAO:0000116 "consder adding placodal ectoderm as a distinct class? Also place placodal ectoderm as develops_from ectoderm; need to check taxon-appropriateness" xsd:string [Term] id: UBERON:0005086 @@ -219893,11 +217154,10 @@ synonym: "vibrissa placode" NARROW [] xref: EMAPA:36479 is_a: UBERON:0011817 ! skin appendage placode intersection_of: UBERON:0005085 ! ectodermal placode -intersection_of: has_potential_to_develop_into UBERON:0002073 ! hair follicle -relationship: develops_from UBERON:0001003 ! skin epidermis -relationship: develops_from UBERON:0011272 {source="Wikipathways:WP2062"} ! embryonic skin basal layer -relationship: has_potential_to_develop_into UBERON:0002073 ! hair follicle -property_value: UBPROP:0000001 "An hair follicle placode is a thickening of the ectoderm that will give rise to the hair follicle bud[GO]." xsd:string {source="GO:0060789"} +intersection_of: RO:0002387 UBERON:0002073 ! has potential to develop into hair follicle +relationship: RO:0002202 UBERON:0001003 ! develops from skin epidermis +relationship: RO:0002202 UBERON:0011272 {source="Wikipathways:WP2062"} ! develops from embryonic skin basal layer +relationship: RO:0002387 UBERON:0002073 ! has potential to develop into hair follicle [Term] id: UBERON:0005087 @@ -219917,12 +217177,10 @@ xref: ZFA:0001153 is_a: UBERON:0006598 ! presumptive structure is_a: UBERON:0011814 {source="NCBIBook:NBK53175"} ! non-neurogenic ectodermal placode intersection_of: UBERON:0005085 ! ectodermal placode -intersection_of: has_potential_to_develop_into UBERON:0001091 ! calcareous tooth -relationship: has_developmental_contribution_from UBERON:0004362 {notes="check for other species", source="Wikipedia:Tooth_development"} ! pharyngeal arch 1 -relationship: has_potential_to_develop_into UBERON:0001091 ! calcareous tooth +intersection_of: RO:0002387 UBERON:0001091 ! has potential to develop into calcareous tooth relationship: part_of UBERON:0011595 {gci_relation="part_of", gci_filler="NCBITaxon:40674"} ! jaw region -property_value: UBPROP:0000001 "Placode that develops into a tooth. The placode is a thickening of the pharyngeal epithelium.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001153", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000015 "In mammals this may be located in the alveolar ridges, but note that some species such as zebrafish have ceratobranchial teeth. Sharks have dermal denticles that share developmental origins. Currently we don't include location information due to this diversity, but in future we may include specific subclasses and/or taxon GCIs." xsd:string +relationship: RO:0002254 UBERON:0004362 ! has developmental contribution from pharyngeal arch 1 +relationship: RO:0002387 UBERON:0001091 ! has potential to develop into calcareous tooth [Term] id: UBERON:0005088 @@ -219932,10 +217190,10 @@ def: "A sebaceous gland placode is a thickening of the ectoderm that will give r is_a: UBERON:0006598 ! presumptive structure is_a: UBERON:0011814 {source="NCBIBook:NBK53175"} ! non-neurogenic ectodermal placode intersection_of: UBERON:0005085 ! ectodermal placode -intersection_of: has_potential_to_develop_into UBERON:0001821 ! sebaceous gland -relationship: develops_from UBERON:0011272 {source="Wikipathways:WP2062"} ! embryonic skin basal layer -relationship: has_potential_to_develop_into UBERON:0001821 ! sebaceous gland -property_value: editor_note "TODO - add bud" xsd:string +intersection_of: RO:0002387 UBERON:0001821 ! has potential to develop into sebaceous gland +relationship: RO:0002202 UBERON:0011272 {source="Wikipathways:WP2062"} ! develops from embryonic skin basal layer +relationship: RO:0002387 UBERON:0001821 ! has potential to develop into sebaceous gland +property_value: IAO:0000116 "TODO - add bud" xsd:string [Term] id: UBERON:0005089 @@ -219945,10 +217203,10 @@ def: "An sweat gland placode is a thickening of the ectoderm that will give rise is_a: UBERON:0006598 ! presumptive structure is_a: UBERON:0011814 {source="NCBIBook:NBK53175"} ! non-neurogenic ectodermal placode intersection_of: UBERON:0005085 ! ectodermal placode -intersection_of: has_potential_to_develop_into UBERON:0001820 ! sweat gland -relationship: develops_from UBERON:0011272 {source="Wikipathways:WP2062"} ! embryonic skin basal layer -relationship: has_potential_to_develop_into UBERON:0001820 ! sweat gland -property_value: editor_note "TODO - add bud" xsd:string +intersection_of: RO:0002387 UBERON:0001820 ! has potential to develop into sweat gland +relationship: RO:0002202 UBERON:0011272 {source="Wikipathways:WP2062"} ! develops from embryonic skin basal layer +relationship: RO:0002387 UBERON:0001820 ! has potential to develop into sweat gland +property_value: IAO:0000116 "TODO - add bud" xsd:string [Term] id: UBERON:0005090 @@ -219958,12 +217216,10 @@ def: "Muscle structures are contractile cells, tissues or organs that are found synonym: "muscle" RELATED [] synonym: "muscle element" RELATED [] synonym: "musculus" EXACT [FMA:30316] -xref: EMAPA:32715 xref: FMA:30316 is_a: UBERON:0000061 ! anatomical structure relationship: has_part CL:0000187 ! muscle cell -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: IAO:0000232 "in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0005092 @@ -219976,8 +217232,7 @@ xref: EMAPA:16239 xref: FMA:70318 xref: VHOG:0000489 is_a: UBERON:0002050 {source="FMA"} ! embryonic structure -relationship: in_right_side_of UBERON:0002063 ! sinus venosus -property_value: UBPROP:0000003 "Three major adaptations, or 'novel cardiac components', that were not present in the ancestor chordate heart tube can be distinguished in the lower vertebrate heart: the atrium, ventricle, and possibly the muscular sinus venosus.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000489", ontology="VHOG", source="DOI:10.1152/physrev.00006.2003 Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003", source="http://bgee.unil.ch/"} +relationship: BSPO:0000121 UBERON:0002063 ! sinus venosus [Term] id: UBERON:0005095 @@ -219986,8 +217241,8 @@ namespace: uberon def: "Missing definition for term UBERON:0005095. Please replace it using linked reference." [GO:0072003] synonym: "kidney anlage" RELATED [GOC:mtg_kidney_jan10] is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0007687 {source="GO"} ! kidney field -property_value: editor_note "class added for consistency with GO - consider merging with kidney mesenchyme." xsd:string +relationship: RO:0002202 UBERON:0007687 {source="GO"} ! develops from kidney field +property_value: IAO:0000116 "class added for consistency with GO - consider merging with kidney mesenchyme." xsd:string [Term] id: UBERON:0005096 @@ -220014,8 +217269,8 @@ xref: Wikipedia:Descending_limb_of_loop_of_Henle is_a: UBERON:0000064 ! organ part relationship: part_of UBERON:0001289 ! descending limb of loop of Henle relationship: part_of UBERON:0004136 ! intermediate tubule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/uberon/issues/2276" xsd:string [Term] @@ -220035,9 +217290,9 @@ xref: MA:0002610 xref: Wikipedia:Connecting_tubule is_a: UBERON:0007685 ! region of nephron tubule is_a: UBERON:0012275 ! meso-epithelium -relationship: develops_from UBERON:0003220 {source="Wikipedia"} ! metanephric mesenchyme -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +relationship: RO:0002202 UBERON:0003220 {source="Wikipedia"} ! develops from metanephric mesenchyme +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0005099 @@ -220046,7 +217301,7 @@ namespace: uberon def: "The short descending thin limb is the descending thin limb of a short nephron that has a squamous epithelial morphology[GO]." [GO:0072063] is_a: UBERON:0004211 ! nephron epithelium is_a: UBERON:0006914 ! squamous epithelium -property_value: editor_note "TODO - epithelium types" xsd:string +property_value: IAO:0000116 "TODO - epithelium types" xsd:string [Term] id: UBERON:0005100 @@ -220060,8 +217315,8 @@ id: UBERON:0005101 name: early distal convoluted tubule namespace: uberon def: "The early distal convoluted tubule contains DCT cells and is vasopressin-insensitive[GO]." [GO:0072067] -xref: EMAPA:28393 is_a: UBERON:0004211 ! nephron epithelium +is_a: UBERON:0012275 ! meso-epithelium relationship: part_of UBERON:0001292 ! distal convoluted tubule [Term] @@ -220069,10 +217324,10 @@ id: UBERON:0005102 name: late distal convoluted tubule namespace: uberon def: "The late distal convoluted tubule contains DCT cells and intercalated (IC) alpha and beta cells and is vasopressin-sensitive[GO]." [GO:0072068] -xref: EMAPA:28393 is_a: UBERON:0004211 ! nephron epithelium +is_a: UBERON:0012275 ! meso-epithelium relationship: part_of UBERON:0001292 ! distal convoluted tubule -property_value: editor_note "TODO - CL" xsd:string +property_value: IAO:0000116 "TODO - CL" xsd:string [Term] id: UBERON:0005103 @@ -220080,6 +217335,7 @@ name: mesonephric epithelium namespace: uberon def: "An epithelium that is part of a mesonephros [Automatically generated definition]." [OBOL:automatic] is_a: UBERON:0004819 ! kidney epithelium +is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000080 ! mesonephros relationship: part_of UBERON:0000080 ! mesonephros @@ -220095,7 +217351,6 @@ is_a: UBERON:0005108 ! metanephric epithelium is_a: UBERON:0006555 ! excretory tube intersection_of: UBERON:0003914 ! epithelial tube intersection_of: part_of UBERON:0000081 ! metanephros -property_value: UBPROP:0000003 "The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001526", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543", source="http://bgee.unil.ch/"} [Term] id: UBERON:0005108 @@ -220103,6 +217358,7 @@ name: metanephric epithelium namespace: uberon def: "An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure[GO]." [GO:0072207] is_a: UBERON:0004819 ! kidney epithelium +is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000081 ! metanephros relationship: part_of UBERON:0000081 ! metanephros @@ -220128,16 +217384,16 @@ is_a: UBERON:0001285 ! nephron is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0001285 ! nephron intersection_of: part_of UBERON:0000081 ! metanephros -relationship: develops_from UBERON:0003220 {source="Wikipedia", source="Wikipedia:Nephron"} ! metanephric mesenchyme -relationship: immediate_transformation_of UBERON:0010535 {source="Bgee:AN"} ! primitive metanephric nephron relationship: part_of UBERON:0000081 ! metanephros -property_value: UBPROP:0000003 "The primitive form of the vertebrate nephron consists of a vascular filtration surface overlain with podocytes, a specialized coelomic cavity to receive the ultrafiltrate, and a tubule for modification to final urine. Although previously thought to be unique to the vertebrates, this design is now known to be widespread among invertebrates, including most of the protochordates, and especially their larvae.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000719", ontology="VHOG", source="DOI:10.1093/icb/34.4.542 Ruppert EE, Evolutionary Origin of the Vertebrate Nephron. Integrative and Comparative Biology (1994)", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003220 {source="Wikipedia", source="Wikipedia:Nephron"} ! develops from metanephric mesenchyme +relationship: RO:0002495 UBERON:0010535 {source="Bgee:AN"} ! immediate transformation of primitive metanephric nephron [Term] id: UBERON:0005111 name: metanephric pyramid namespace: uberon def: "Metanephric pyramids are the conical masses that constitute the renal medulla in a metanephros; they contain the loops of Henle and the medullary collecting ducts[GO]." [GO:0072211] +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004200 ! kidney pyramid intersection_of: UBERON:0004200 ! kidney pyramid intersection_of: part_of UBERON:0000081 ! metanephros @@ -220150,7 +217406,7 @@ namespace: uberon xref: EHDAA2:0001140 is_a: UBERON:0003104 ! mesenchyme is_a: UBERON:0004120 ! mesoderm-derived structure -relationship: develops_from UBERON:0010531 {source="EHDAA2"} ! metanephros induced blastemal cells +relationship: RO:0002202 UBERON:0010531 {source="EHDAA2"} ! develops from metanephros induced blastemal cells [Term] id: UBERON:0005114 @@ -220168,6 +217424,7 @@ id: UBERON:0005115 name: metanephric cortical collecting duct namespace: uberon def: "The metanephric cortical collecting duct is the portion of the metanephric collecting duct that resides in the renal cortex[GO]." [GO:0072219] +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004203 ! cortical collecting duct intersection_of: UBERON:0004203 ! cortical collecting duct intersection_of: part_of UBERON:0000081 ! metanephros @@ -220179,6 +217436,7 @@ id: UBERON:0005116 name: metanephric descending thin limb namespace: uberon def: "It extends to the tip of the metanephric loop of Henle[GO]." [GO:0072220] +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005096 ! descending thin limb intersection_of: UBERON:0005096 ! descending thin limb intersection_of: part_of UBERON:0000081 ! metanephros @@ -220263,7 +217521,7 @@ is_a: UBERON:0005146 ! metanephric nephron tubule intersection_of: UBERON:0001290 ! proximal straight tubule intersection_of: part_of UBERON:0000081 ! metanephros relationship: part_of UBERON:0005151 {is_inferred="true", source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! metanephric proximal tubule -property_value: editor_note "TODO - place mammalian xrefs here rather than at parent" xsd:string +property_value: IAO:0000116 "TODO - place mammalian xrefs here rather than at parent" xsd:string [Term] id: UBERON:0005127 @@ -220358,6 +217616,7 @@ namespace: uberon alt_id: UBERON:0005112 def: "The metanephric capsule is the tough fibrous layer surrounding the metanephros, covered in a thick layer of perinephric adipose tissue. It provides some protection from trauma and damage[GO]." [GO:0072213] is_a: UBERON:0002015 ! kidney capsule +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0002015 ! kidney capsule intersection_of: part_of UBERON:0000081 ! metanephros relationship: part_of UBERON:0000081 ! metanephros @@ -220422,10 +217681,9 @@ def: "A metanephric nephron tubule is an epithelial tube that is part of the met is_a: UBERON:0001231 ! nephron tubule is_a: UBERON:0005106 ! metanephric tubule is_a: UBERON:0005134 ! metanephric nephron epithelium -is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0001231 ! nephron tubule intersection_of: part_of UBERON:0000081 ! metanephros -relationship: develops_from UBERON:0003220 {source="ISBN:9780878932504"} ! metanephric mesenchyme +relationship: RO:0002202 UBERON:0003220 {source="ISBN:9780878932504"} ! develops from metanephric mesenchyme [Term] id: UBERON:0005147 @@ -220438,11 +217696,10 @@ xref: EHDAA:9346 xref: EMAPA:27678 is_a: UBERON:0004209 ! renal vesicle is_a: UBERON:0005108 ! metanephric epithelium -is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0004209 ! renal vesicle intersection_of: part_of UBERON:0000081 ! metanephros -relationship: develops_from UBERON:0005113 {source="EHDAA2"} ! metanephric cortex mesenchyme -relationship: has_potential_to_develop_into UBERON:0005134 ! metanephric nephron epithelium +relationship: RO:0002202 UBERON:0005113 {source="EHDAA2"} ! develops from metanephric cortex mesenchyme +relationship: RO:0002387 UBERON:0005134 ! has potential to develop into metanephric nephron epithelium [Term] id: UBERON:0005148 @@ -220503,11 +217760,10 @@ synonym: "invertebrate tracheal system" EXACT [] synonym: "open tracheal system" EXACT [] synonym: "tracheal system" BROAD SENSU [FBbt:00005024] xref: BTO:0003870 -xref: FBbt:00005024 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: SPD:0000427 xref: TADS:0000043 is_a: UBERON:0001004 ! respiratory system -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda +relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda [Term] id: UBERON:0005156 @@ -220539,6 +217795,7 @@ synonym: "CNS parenchyma" EXACT [OBOL:automatic] synonym: "parenchyma of central nervous system" EXACT [] synonym: "parenchyma of CNS" EXACT [OBOL:automatic] is_a: UBERON:0000353 ! parenchyma +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000353 ! parenchyma intersection_of: part_of UBERON:0001017 ! central nervous system relationship: part_of UBERON:0001017 ! central nervous system @@ -220551,8 +217808,8 @@ def: "A remnant structure from earlier development or evolution." [PATOC:MAH] xref: Wikipedia:Vestigiality is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: has_quality PATO:0000588 ! vestigial -relationship: has_quality PATO:0000588 ! vestigial +intersection_of: RO:0000086 PATO:0000588 ! has quality vestigial +relationship: RO:0000086 PATO:0000588 ! has quality vestigial [Term] id: UBERON:0005162 @@ -220565,11 +217822,9 @@ synonym: "multi-cell-component structure" EXACT [CARO:0001000] synonym: "multi-cell-part structure" EXACT [CARO:0001000] xref: AAO:0011000 xref: CARO:0001000 -xref: FBbt:00007060 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:83115 is_a: UBERON:0000061 ! anatomical structure -relationship: composed_primarily_of GO:0005575 ! cellular_component -property_value: UBPROP:0000012 "we go with the FMA classification rather than the CARO one. FMA def: 'Anatomical cluster which has as direct parts cell parts from two or more cells.'" xsd:string {external_ontology="CARO", external_ontology="FMA"} +relationship: RO:0002473 GO:0005575 ! composed primarily of cellular_component [Term] id: UBERON:0005164 @@ -220590,9 +217845,9 @@ xref: SCTID:245434005 xref: UMLS:C0227658 {source="ncithesaurus:Ascending_Limb_of_the_Henle_s_Loop"} xref: Wikipedia:Ascending_limb_of_loop_of_Henle is_a: UBERON:0004135 ! distal tubule -relationship: contributes_to_morphology_of UBERON:0001288 ! loop of Henle relationship: part_of UBERON:0001288 ! loop of Henle -property_value: editor_note "TODO - thick/thin check. Also relationship to distal tubule. We need a home for MA:0002634-renal straight tubule" xsd:string +relationship: RO:0002433 UBERON:0001288 ! contributes to morphology of loop of Henle +property_value: IAO:0000116 "TODO - thick/thin check. Also relationship to distal tubule. We need a home for MA:0002634-renal straight tubule" xsd:string [Term] id: UBERON:0005167 @@ -220631,10 +217886,10 @@ xref: Wikipedia:Interlobular_veins is_a: UBERON:0013126 ! vein of abdomen is_a: UBERON:0014401 ! renal venous blood vessel disjoint_from: UBERON:0009887 ! interlobar vein -relationship: connected_to UBERON:0004719 ! kidney arcuate vein relationship: part_of UBERON:0001225 ! cortex of kidney -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +relationship: RO:0002170 UBERON:0004719 ! connected to kidney arcuate vein +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0005169 @@ -220647,9 +217902,8 @@ synonym: "interstitium" EXACT [] xref: FMA:86301 xref: SCTID:85293002 is_a: UBERON:0003891 {source="FMA"} ! stroma -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: editor_note "specify differentia from stroma" xsd:string -property_value: UBPROP:0000007 "interstital" xsd:string +property_value: IAO:0000116 "specify differentia from stroma" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0005170 @@ -220676,13 +217930,13 @@ xref: Wikipedia:Membrana_granulosa xref: ZFA:0001112 is_a: UBERON:0000119 ! cell layer is_a: UBERON:0004911 ! epithelium of female gonad +is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0000119 ! cell layer -intersection_of: composed_primarily_of CL:0000501 ! granulosa cell intersection_of: part_of UBERON:0001305 ! ovarian follicle -relationship: composed_primarily_of CL:0000501 ! granulosa cell +intersection_of: RO:0002473 CL:0000501 ! composed primarily of granulosa cell relationship: part_of UBERON:0001305 ! ovarian follicle -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000010 "At one part of the mature follicle the cells of the membrana granulosa are collected into a mass which projects into the cavity of the follicle. This is termed the discus proligerus. [Wikipedia:Membrana_granulosa, Wikipedia:Membrana_granulosa]" xsd:string +relationship: RO:0002473 CL:0000501 ! composed primarily of granulosa cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0005171 @@ -220702,12 +217956,9 @@ xref: SCTID:245399002 xref: UMLS:C0917710 {source="ncithesaurus:Hepatic_Duct"} xref: VHOG:0000219 is_a: UBERON:0002394 ! bile duct -relationship: connects UBERON:0001174 ! common bile duct -relationship: connects UBERON:0002107 ! liver -property_value: editor_note "TODO - MA distinguishes between bile duct, hepatic duct, common bile duct and common hepatic duct. in FMA hepatic duct and common hepatic duct are the same" xsd:string -property_value: UBPROP:0000001 "A duct that carries bile from the liver to the small intestine.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001100", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "The excretory duct of the liver or one of its branches in the lobes of the liver. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000219", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/hepatic+duct"} -property_value: UBPROP:0000001 "The hepatic duct is the duct that leads from the liver to the bile duct[GO]." xsd:string {source="GO:0061011"} +relationship: RO:0002176 UBERON:0001174 ! connects common bile duct +relationship: RO:0002176 UBERON:0002107 ! connects liver +property_value: IAO:0000116 "TODO - MA distinguishes between bile duct, hepatic duct, common bile duct and common hepatic duct. in FMA hepatic duct and common hepatic duct are the same" xsd:string [Term] id: UBERON:0005172 @@ -220790,11 +218041,8 @@ xref: Wikipedia:Enamel_organ xref: ZFA:0005138 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0034922 ! cell cluster -relationship: never_in_taxon NCBITaxon:8782 ! Aves relationship: part_of UBERON:0008281 ! tooth bud -property_value: UBPROP:0000001 "A structure that is involved in tooth formation. A bell shape two layer epithelial structure that descends toward the ceratobranchial 5 bone, enclosing the dental mesenchyme. At later times in tooth development the cells at the apex of the bell may be involved in enameloid formation. This structure remains at the base of the erupted tooth and is the source of replacement teeth.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005138", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000011 "NOT develops_from NC[https://github.com/obophenotype/uberon/wiki/The-neural-crest]" xsd:string -property_value: UBPROP:0000013 "Historically, enamel organ has been the term to describe this structure, but it was attempted unsuccessfully in recent years to change the name to dental organ in order to better represent its multiple functions apart from enamel formation" xsd:string +property_value: RO:0002161 NCBITaxon:8782 [Term] id: UBERON:0005177 @@ -220824,8 +218072,8 @@ xref: MA:0000557 is_a: UBERON:0002075 ! viscus is_a: UBERON:0005181 ! thoracic segment organ intersection_of: UBERON:0000062 ! organ -intersection_of: located_in UBERON:0002224 ! thoracic cavity -relationship: located_in UBERON:0002224 ! thoracic cavity +intersection_of: RO:0001025 UBERON:0002224 ! located in thoracic cavity +relationship: RO:0001025 UBERON:0002224 ! located in thoracic cavity [Term] id: UBERON:0005179 @@ -220872,6 +218120,7 @@ xref: MA:0000158 xref: SCTID:318929009 xref: Wikipedia:Bone_marrow_of_ovary_(hair) is_a: UBERON:0000958 ! medulla of organ +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000958 ! medulla of organ intersection_of: part_of UBERON:0001037 ! strand of hair relationship: part_of UBERON:0001037 ! strand of hair @@ -220912,11 +218161,11 @@ xref: Wikipedia:Artery_to_the_ductus_deferens is_a: UBERON:0001637 ! artery is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0001000 ! vas deferens -relationship: connecting_branch_of UBERON:0001312 {source="Wikipedia"} ! superior vesical artery +intersection_of: RO:0002178 UBERON:0001000 ! supplies vas deferens relationship: part_of UBERON:0005352 ! spermatic cord -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: supplies UBERON:0001000 ! vas deferens +relationship: RO:0002178 UBERON:0001000 ! supplies vas deferens +relationship: RO:0002252 UBERON:0001312 {source="Wikipedia"} ! connecting branch of superior vesical artery +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0005194 @@ -220961,12 +218210,13 @@ xref: EMAPA:35803 xref: MA:0000764 xref: NCIT:C49760 xref: UMLS:C1710156 {source="ncithesaurus:Spleen_Germinal_Center"} +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010754 ! germinal center intersection_of: UBERON:0010754 ! germinal center intersection_of: part_of UBERON:0002106 ! spleen -relationship: contributes_to_morphology_of UBERON:0004042 ! spleen secondary B follicle relationship: part_of UBERON:0004042 {source="CL:tm"} ! spleen secondary B follicle -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002433 UBERON:0004042 ! contributes to morphology of spleen secondary B follicle +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0005199 @@ -220978,7 +218228,6 @@ is_a: UBERON:0001911 ! mammary gland intersection_of: UBERON:0001911 ! mammary gland intersection_of: part_of UBERON:0005434 ! cervical region relationship: part_of UBERON:0005434 ! cervical region -property_value: UBPROP:0000008 "mice have a single pair of cervical mammary glands" xsd:string [Term] id: UBERON:0005200 @@ -221002,22 +218251,19 @@ is_a: UBERON:0005175 ! chest organ intersection_of: UBERON:0001911 ! mammary gland intersection_of: part_of UBERON:0000915 ! thoracic segment of trunk relationship: part_of UBERON:0000310 {source="BTO"} ! breast -property_value: UBPROP:0000008 "Most primates have one pair of mammary glands, which are thoracic." xsd:string -property_value: UBPROP:0000202 FMA:57983 [Term] id: UBERON:0005202 name: distal straight tubule macula densa namespace: uberon def: "A macula densa that is part of an ascending limb of loop of Henle [Automatically generated definition]." [OBOL:automatic] -xref: EMAPA:28399 xref: MA:0002604 is_a: UBERON:0002335 ! macula densa intersection_of: UBERON:0002335 ! macula densa intersection_of: part_of UBERON:0001291 ! thick ascending limb of loop of Henle relationship: part_of UBERON:0001291 {source="MA"} ! thick ascending limb of loop of Henle relationship: part_of UBERON:0006853 {source="MA"} ! renal cortex tubule -property_value: editor_note "TODO - unify terminology - check DST = TAL? Note EMAPA class appears to refer to this segment" xsd:string +property_value: IAO:0000116 "TODO - unify terminology - check DST = TAL? Note EMAPA class appears to refer to this segment" xsd:string [Term] id: UBERON:0005203 @@ -221039,8 +218285,7 @@ intersection_of: UBERON:0011148 ! submucosal gland intersection_of: has_part CL:0000159 ! seromucus secreting cell intersection_of: part_of UBERON:0003126 ! trachea relationship: part_of UBERON:0003126 ! trachea -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000009 "These glands secrete mucus, lysozyme, defensins, and other agents that help protect the lungs from particles and infectious agents." xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0005204 @@ -221051,6 +218296,7 @@ subset: organ_slim synonym: "laryngeal submucosa gland" RELATED [EMAPA:35475] xref: EMAPA:35475 xref: MA:0002729 +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0036225 ! respiratory system gland intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0004778 ! larynx submucosa @@ -221065,6 +218311,7 @@ xref: EMAPA:35902 xref: FMA:19979 xref: MA:0002737 is_a: UBERON:0000030 ! lamina propria +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0000030 ! lamina propria intersection_of: part_of UBERON:0000996 ! vagina @@ -221080,6 +218327,7 @@ xref: EMAPA:36609 xref: MA:0000825 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0003891 ! stroma +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0003891 ! stroma intersection_of: part_of UBERON:0001886 ! choroid plexus relationship: has_part CL:0000235 ! macrophage @@ -221098,7 +218346,7 @@ is_a: UBERON:0003893 ! capsule intersection_of: UBERON:0003893 ! capsule intersection_of: part_of UBERON:0002372 ! tonsil relationship: part_of UBERON:0002372 ! tonsil -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0005208 @@ -221112,6 +218360,7 @@ xref: EHDAA2:0000302 xref: EMAPA:17327 xref: MA:0001871 is_a: UBERON:0003978 ! valve +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0003978 ! valve intersection_of: part_of UBERON:0002078 ! right cardiac atrium relationship: part_of UBERON:0002078 ! right cardiac atrium @@ -221136,7 +218385,6 @@ intersection_of: part_of UBERON:0000362 ! renal medulla relationship: capable_of_part_of GO:0070295 ! renal water absorption relationship: part_of UBERON:0000362 ! renal medulla relationship: part_of UBERON:0005215 {source="MA"} ! kidney interstitium -property_value: UBPROP:0000009 "It functions in renal water reabsorption by building up a high hypertonicity, which draws water out of the thin descending limb of the loop of Henle and the collecting duct system. This hypertonicity, in turn, is created by an efflux of urea from the inner medullary collecting duct." xsd:string [Term] id: UBERON:0005212 @@ -221155,12 +218403,12 @@ xref: SCTID:362280005 is_a: UBERON:0005156 ! reproductive structure is_a: UBERON:0005169 ! interstitial tissue intersection_of: UBERON:0005169 ! interstitial tissue -intersection_of: composed_primarily_of CL:0000178 ! Leydig cell intersection_of: part_of UBERON:0000473 ! testis -relationship: composed_primarily_of CL:0000178 ! Leydig cell -relationship: contributes_to_morphology_of UBERON:0000473 ! testis +intersection_of: RO:0002473 CL:0000178 ! composed primarily of Leydig cell relationship: part_of NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0000473 ! testis +relationship: RO:0002433 UBERON:0000473 ! contributes to morphology of testis +relationship: RO:0002473 CL:0000178 ! composed primarily of Leydig cell [Term] id: UBERON:0005213 @@ -221214,26 +218462,11 @@ xref: SCTID:362210003 is_a: UBERON:0005169 ! interstitial tissue intersection_of: UBERON:0005169 ! interstitial tissue intersection_of: part_of UBERON:0002113 ! kidney -relationship: composed_primarily_of CL:1000692 ! kidney interstitial fibroblast -relationship: contributes_to_morphology_of UBERON:0002113 ! kidney relationship: part_of UBERON:0002113 ! kidney -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: editor_note "See https://sourceforge.net/p/geneontology/ontology-requests/10941/" xsd:string -property_value: UBPROP:0000009 "The interstitium is necessarily involved in all intrarenal exchange processes since the reabsorption and secretion of fluid and solutes implicates a transit across the interstitial compartment." xsd:string -property_value: UBPROP:0000010 "The fibroblasts in the interstitium provide the 'skeleton' of the tissue and maintain the three-dimensional architecture of the tissue." xsd:string - -[Term] -id: UBERON:0005216 -name: optic eminence surface ectoderm -namespace: uberon -def: "An external ectoderm that is part of a optic eminence [Automatically generated definition]." [OBOL:automatic] -xref: EMAPA:16539 -xref: RETIRED_EHDAA2:0001311 -xref: VHOG:0000520 -is_a: UBERON:0000076 ! external ectoderm -intersection_of: UBERON:0000076 ! external ectoderm -intersection_of: part_of UBERON:0004348 ! optic eminence -relationship: part_of UBERON:0005234 {is_inferred="true", source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! optic eminence ectoderm +relationship: RO:0002433 UBERON:0002113 ! contributes to morphology of kidney +relationship: RO:0002473 CL:1000692 ! composed primarily of kidney interstitial fibroblast +property_value: IAO:0000116 "See https://sourceforge.net/p/geneontology/ontology-requests/10941/" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0005217 @@ -221248,7 +218481,6 @@ is_a: UBERON:0039175 ! subarachnoid space of brain intersection_of: UBERON:0000315 ! subarachnoid space intersection_of: part_of UBERON:0001891 ! midbrain relationship: part_of UBERON:0001891 ! midbrain -property_value: UBPROP:0000001 "Subarachnoid space that is part of the midbrain. [Bgee_curator][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001304", ontology="VHOG", source="http://bgee.unil.ch/"} [Term] id: UBERON:0005218 @@ -221262,7 +218494,6 @@ is_a: UBERON:0039175 ! subarachnoid space of brain intersection_of: UBERON:0000315 ! subarachnoid space intersection_of: part_of UBERON:0001894 ! diencephalon relationship: part_of UBERON:0001894 ! diencephalon -property_value: UBPROP:0000001 "Subarachnoid space that is part of the diencephalon. [Bgee_curator][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001302", ontology="VHOG", source="http://bgee.unil.ch/"} [Term] id: UBERON:0005219 @@ -221277,7 +218508,6 @@ is_a: UBERON:0039175 ! subarachnoid space of brain intersection_of: UBERON:0000315 ! subarachnoid space intersection_of: part_of UBERON:0002028 ! hindbrain relationship: part_of UBERON:0002028 ! hindbrain -property_value: UBPROP:0000001 "Subarachnoid space that is part of the hindbrain. [Bgee_curator][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001303", ontology="VHOG", source="http://bgee.unil.ch/"} [Term] id: UBERON:0005221 @@ -221317,11 +218547,11 @@ def: "An epithelium that is part of a hindlimb stylopod [Automatically generated xref: EHDAA2:0002131 xref: EMAPA:17500 xref: VHOG:0001041 -is_a: UBERON:0000483 ! epithelium +is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000376 ! hindlimb stylopod -relationship: develops_from UBERON:0003371 {source="EHDAA2"} ! pelvic appendage bud ectoderm relationship: part_of UBERON:0000376 ! hindlimb stylopod +relationship: RO:0002202 UBERON:0003371 {source="EHDAA2"} ! develops from pelvic appendage bud ectoderm [Term] id: UBERON:0005226 @@ -221334,10 +218564,11 @@ synonym: "toe epithelium" EXACT [] xref: EMAPA:32946 xref: VHOG:0001031 is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium +is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001466 ! pedal digit -relationship: develops_from UBERON:0003248 {source="EHDAA2"} ! epithelium of footplate relationship: part_of UBERON:0001466 ! pedal digit +relationship: RO:0002202 UBERON:0003248 {source="EHDAA2"} ! develops from epithelium of footplate [Term] id: UBERON:0005227 @@ -221351,10 +218582,11 @@ xref: EHDAA2:0000406 xref: EMAPA:32647 xref: VHOG:0001032 is_a: UBERON:0000490 ! unilaminar epithelium +is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002389 ! manual digit -relationship: develops_from UBERON:0010332 {source="EHDAA2"} ! epithelium of handplate relationship: part_of UBERON:0002389 ! manual digit +relationship: RO:0002202 UBERON:0010332 {source="EHDAA2"} ! develops from epithelium of handplate [Term] id: UBERON:0005228 @@ -221364,11 +218596,11 @@ def: "An epithelium that is part of a forelimb stylopod [Automatically generated xref: EHDAA2:0002113 xref: EMAPA:17425 xref: VHOG:0000990 -is_a: UBERON:0000483 ! epithelium +is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0003822 ! forelimb stylopod -relationship: develops_from UBERON:0003372 {source="EHDAA2"} ! pectoral appendage bud ectoderm relationship: part_of UBERON:0003822 ! forelimb stylopod +relationship: RO:0002202 UBERON:0003372 {source="EHDAA2"} ! develops from pectoral appendage bud ectoderm [Term] id: UBERON:0005229 @@ -221378,11 +218610,11 @@ def: "An epithelium that is part of a lower leg [Automatically generated definit xref: EHDAA2:0001031 xref: EMAPA:17497 xref: VHOG:0001050 -is_a: UBERON:0000483 ! epithelium +is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0003823 ! hindlimb zeugopod -relationship: develops_from UBERON:0003371 {source="EHDAA2"} ! pelvic appendage bud ectoderm relationship: part_of UBERON:0003823 ! hindlimb zeugopod +relationship: RO:0002202 UBERON:0003371 {source="EHDAA2"} ! develops from pelvic appendage bud ectoderm [Term] id: UBERON:0005233 @@ -221422,7 +218654,6 @@ xref: EHDAA2:0001154 xref: EMAPA:17078 xref: VHOG:0000320 is_a: UBERON:0004064 ! neural tube basal plate -property_value: UBPROP:0000001 "The ventral half of the developing neural tube that is the metencephalon. [Chordate_evolution_and_the_origin_of_craniates:_An_old_brain_in_a_new_head._AnaT_Rec_(New_Anat)_(2000)_261(3):_111-125, See_Butler_AB][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000320", ontology="VHOG", source="http://bgee.unil.ch/"} [Term] id: UBERON:0005243 @@ -221439,7 +218670,7 @@ is_a: UBERON:0002165 ! endocardium intersection_of: UBERON:0002165 ! endocardium intersection_of: part_of UBERON:0002094 ! interventricular septum relationship: part_of UBERON:0002094 ! interventricular septum -property_value: editor_note "TODO - split?" xsd:string +property_value: IAO:0000116 "TODO - split?" xsd:string [Term] id: UBERON:0005248 @@ -221462,10 +218693,10 @@ def: "A renal pelvis that is part of a metanephros." [OBOL:automatic] synonym: "metanephros pelvis" EXACT [VHOG:0000945] xref: VHOG:0000945 is_a: UBERON:0001224 ! renal pelvis +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0001224 ! renal pelvis intersection_of: part_of UBERON:0000081 ! metanephros relationship: part_of UBERON:0000081 ! metanephros -property_value: UBPROP:0000003 "The ureteric bud itself forms the collecting tubules and the ureter that drain the adult kidney. This type of kidney, called the metanephros, occurs in all adult amniotes.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000945", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639", source="http://bgee.unil.ch/"} [Term] id: UBERON:0005250 @@ -221479,7 +218710,7 @@ is_a: UBERON:0002530 ! gland intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0000930 ! stomodeum relationship: part_of UBERON:0000930 ! stomodeum -property_value: editor_note "check this" xsd:string +property_value: IAO:0000116 "check this" xsd:string [Term] id: UBERON:0005251 @@ -221496,10 +218727,8 @@ is_a: UBERON:0002553 ! anatomical cavity is_a: UBERON:0007473 ! lumen of epithelial sac is_a: UBERON:0012466 ! extraembryonic cavity intersection_of: UBERON:0002553 ! anatomical cavity -intersection_of: luminal_space_of UBERON:0001040 ! yolk sac -relationship: luminal_space_of UBERON:0001040 ! yolk sac -property_value: UBPROP:0000008 "In mammals, the yolk sac cavity contains fluid rather than platelets" xsd:string {source="ISBN:0073040584"} -property_value: UBPROP:0000012 "in EHDAA2, there are separate primary and secondary yolk sac cavities" xsd:string {external_ontology="EHDAA2"} +intersection_of: RO:0002572 UBERON:0001040 ! luminal space of yolk sac +relationship: RO:0002572 UBERON:0001040 ! luminal space of yolk sac [Term] id: UBERON:0005253 @@ -221527,7 +218756,6 @@ intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0000033 ! head relationship: part_of UBERON:0000033 ! head relationship: part_of UBERON:0009142 {source="EHDAA2"} ! entire embryonic mesenchyme -property_value: UBPROP:0000001 "Mesoderm that will give rise, along with cranial neural crest cells, to connective tissue, bone and musculature in the head. (Source: BioGlossary, www.Biology-Text.com)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000113", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0005254 @@ -221555,11 +218783,12 @@ synonym: "toe mesenchyme" EXACT [] xref: EMAPA:32947 xref: VHOG:0000463 is_a: UBERON:0003860 ! hindlimb mesenchyme +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010702 ! digit mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0001466 ! pedal digit -relationship: develops_from UBERON:0003328 {source="EHDAA2"} ! mesenchyme of footplate relationship: part_of UBERON:0001466 ! pedal digit +relationship: RO:0002202 UBERON:0003328 {source="EHDAA2"} ! develops from mesenchyme of footplate [Term] id: UBERON:0005256 @@ -221599,12 +218828,13 @@ xref: EHDAA2:0000407 xref: EMAPA:32645 xref: VHOG:0001416 is_a: UBERON:0003859 ! forelimb mesenchyme +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010702 ! digit mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0002389 ! manual digit -relationship: develops_from UBERON:0009523 ! mesenchyme of handplate relationship: part_of UBERON:0002389 ! manual digit -property_value: editor_note "In EHDAA2, the metacarpal cartilage condensation is considered part of the digits - it might be better to call the whole structure digital ray mesenchyme/condensation" xsd:string +relationship: RO:0002202 UBERON:0009523 ! develops from mesenchyme of handplate +property_value: IAO:0000116 "In EHDAA2, the metacarpal cartilage condensation is considered part of the digits - it might be better to call the whole structure digital ray mesenchyme/condensation" xsd:string [Term] id: UBERON:0005258 @@ -221646,10 +218876,10 @@ xref: MA:0002582 is_a: UBERON:0001637 ! artery is_a: UBERON:0003644 ! kidney arterial blood vessel intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0001225 ! cortex of kidney -relationship: contributes_to_morphology_of UBERON:0001225 ! cortex of kidney +intersection_of: RO:0002178 UBERON:0001225 ! supplies cortex of kidney relationship: part_of UBERON:0001225 {source="MA"} ! cortex of kidney -relationship: supplies UBERON:0001225 ! cortex of kidney +relationship: RO:0002178 UBERON:0001225 ! supplies cortex of kidney +relationship: RO:0002433 UBERON:0001225 ! contributes to morphology of cortex of kidney [Term] id: UBERON:0005269 @@ -221664,10 +218894,10 @@ xref: MA:0002592 is_a: UBERON:0013126 ! vein of abdomen is_a: UBERON:0014401 ! renal venous blood vessel intersection_of: UBERON:0001638 ! vein -intersection_of: drains UBERON:0001225 ! cortex of kidney -relationship: contributes_to_morphology_of UBERON:0001225 ! cortex of kidney -relationship: drains UBERON:0001225 ! cortex of kidney +intersection_of: RO:0002179 UBERON:0001225 ! drains cortex of kidney relationship: part_of UBERON:0001225 {source="MA"} ! cortex of kidney +relationship: RO:0002179 UBERON:0001225 ! drains cortex of kidney +relationship: RO:0002433 UBERON:0001225 ! contributes to morphology of cortex of kidney [Term] id: UBERON:0005270 @@ -221689,7 +218919,6 @@ relationship: has_part CL:0000057 ! fibroblast relationship: has_part CL:0000451 ! dendritic cell relationship: part_of UBERON:0001225 {source="MA"} ! cortex of kidney relationship: part_of UBERON:0005215 {source="MA"} ! kidney interstitium -property_value: UBPROP:0000010 "In the renal cortex, interstitial fibroblasts produce erythropoietin and are distinguished from other interstitial cells by their prominent F-actin cytoskeleton, abundance of rough endoplasmic reticulum, and by ecto-5'-nucleotidase expression in their plasma membrane. The resident dendritic cells belong to the mononuclear phagocyte system and fulfil a sentinel function. They are characterized by their expression of MHC class II and CD11c." xsd:string {source="PMID:18575881"} [Term] id: UBERON:0005271 @@ -221706,7 +218935,7 @@ xref: KUPO:0001008 xref: MA:0001648 is_a: UBERON:0000064 ! organ part relationship: part_of UBERON:0001225 {source="FMA", source="KUPO"} ! cortex of kidney -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0005272 @@ -221720,8 +218949,8 @@ xref: MA:0002588 xref: Wikipedia:Peritubular_capillaries is_a: UBERON:0003527 ! kidney capillary relationship: capable_of_part_of GO:0070293 {source="Wikipedia"} ! renal absorption -relationship: connected_to UBERON:0004640 ! renal efferent arteriole -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002170 UBERON:0004640 ! connected to renal efferent arteriole +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0005275 @@ -221745,7 +218974,6 @@ is_a: UBERON:0003533 ! manual digit skin is_a: UBERON:0005275 ! dorsal skin of digit intersection_of: UBERON:0005275 ! dorsal skin of digit intersection_of: part_of UBERON:0002389 ! manual digit -property_value: UBPROP:0000012 "this class is explicitly the union of the two FMA classes" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0005277 @@ -221761,7 +218989,6 @@ is_a: UBERON:0003530 ! pedal digit skin is_a: UBERON:0005275 ! dorsal skin of digit intersection_of: UBERON:0005275 ! dorsal skin of digit intersection_of: part_of UBERON:0001466 ! pedal digit -property_value: UBPROP:0000012 "this class is explicitly the union of the two FMA classes" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0005281 @@ -221785,9 +219012,10 @@ xref: TAO:0001261 xref: Wikipedia:Ventricular_system xref: ZFA:0001261 is_a: UBERON:0000467 {source="ZFA"} ! anatomical system +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001017 ! central nervous system -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray734.png" xsd:anyURI -property_value: editor_note "TODO - resolve space vs structure conflation. We follow FMA in making this and the various ventricles a structure - it follows from this that strutures such as the tela choroidea and choroid plexuses can be part of the ventricles and ventricular system. Note: see also the class 'neuraxis cavity'" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray734.png" xsd:anyURI +property_value: IAO:0000116 "TODO - resolve space vs structure conflation. We follow FMA in making this and the various ventricles a structure - it follows from this that strutures such as the tela choroidea and choroid plexuses can be part of the ventricles and ventricular system. Note: see also the class 'neuraxis cavity'" xsd:string [Term] id: UBERON:0005282 @@ -221799,9 +219027,9 @@ xref: EMAPA:37447 {source="MA:th"} xref: FMA:242787 xref: VHOG:0000005 is_a: UBERON:0000467 ! anatomical system +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0000955 ! brain relationship: part_of UBERON:0005281 ! ventricular system of central nervous system -property_value: UBPROP:0000003 "The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000005", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500", source="http://bgee.unil.ch/"} [Term] id: UBERON:0005283 @@ -221820,9 +219048,6 @@ is_a: UBERON:0004923 ! organ component layer relationship: overlaps UBERON:0001886 ! choroid plexus relationship: overlaps UBERON:0010743 ! meningeal cluster relationship: part_of UBERON:0005358 {source="FMA"} ! ventricle of nervous system -property_value: UBPROP:0000001 "Portion of tissue that is part of the primitive meninx which forms a fold, roofing a ventricle of the brain and supporting the choroid plexus[ZFA:0000447]." xsd:string {source="ZFA:0000447"} -property_value: UBPROP:0000010 "Vascularized tela choroidea is choroid plexus." xsd:string -property_value: UBPROP:0000012 "Note that the structure in ZFA may be different" xsd:string {external_ontology="ZFA"} [Term] id: UBERON:0005287 @@ -221845,11 +219070,11 @@ xref: SCTID:362321009 xref: TAO:0005158 xref: Wikipedia:Tela_chorioidea_of_fourth_ventricle xref: ZFA:0005158 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005283 ! tela choroidea intersection_of: UBERON:0005283 ! tela choroidea intersection_of: part_of UBERON:0002422 ! fourth ventricle relationship: part_of UBERON:0002422 ! fourth ventricle -property_value: UBPROP:0000001 "Tela chorioidea that lines the fourth ventricle.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005158", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0005289 @@ -221869,6 +219094,7 @@ xref: neuronames:219 xref: SCTID:362319004 xref: TAO:0005160 xref: ZFA:0005160 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005283 ! tela choroidea intersection_of: UBERON:0005283 ! tela choroidea intersection_of: part_of UBERON:0002285 ! telencephalic ventricle @@ -221890,17 +219116,11 @@ xref: EHDAA:5526 xref: EMAPA:17082 xref: HBA:9512 xref: MA:0000205 -xref: MESH:D054024 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: VHOG:0000456 xref: Wikipedia:Myelencephalon -is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004733 ! segmental subdivision of hindbrain -relationship: immediate_transformation_of UBERON:0010096 {evidence="definitional"} ! future myelencephalon -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI -property_value: RO:0002174 NCBITaxon:7955 -property_value: UBPROP:0000001 "The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000456", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/myelencephalon"} -property_value: UBPROP:0000003 "The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000456", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000013 "the terms metencephalon and myelencephalon are only meaningful in mammals and birds - Neuroanatomy of the Zebrafish Brain. Note that its not clear if this refers to the developing medulla oblongata - MA (adult) has two distinct classes" xsd:string +relationship: RO:0002495 UBERON:0010096 ! immediate transformation of future myelencephalon +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI [Term] id: UBERON:0005291 @@ -221961,11 +219181,10 @@ xref: UMLS:C1512243 {source="ncithesaurus:Gonadal_Ridge"} xref: Wikipedia:Gonadal_ridge xref: XAO:0000018 is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0004876 ! urogenital fold relationship: part_of UBERON:0004122 ! genitourinary system -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1106.png" xsd:anyURI -property_value: editor_note "TODO - check developmental relationships. merge with urogenital ridge?" xsd:string -property_value: UBPROP:0000011 "in eutherians, SRY transforms the indifferent gonad into testes" xsd:string +relationship: RO:0002202 UBERON:0004876 ! develops from urogenital fold +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1106.png" xsd:anyURI +property_value: IAO:0000116 "TODO - check developmental relationships. merge with urogenital ridge?" xsd:string [Term] id: UBERON:0005295 @@ -221976,7 +219195,6 @@ synonym: "genital cord" RELATED [] synonym: "gonad cord" RELATED [] synonym: "gonadal cord" RELATED [] synonym: "primitive sex cord" RELATED [] -xref: EHDAA2:0004051 xref: NCIT:C34183 xref: RETIRED_EHDAA2:0001523 xref: SCTID:343823004 @@ -221985,7 +219203,7 @@ xref: Wikipedia:Sex_cords is_a: UBERON:0005154 {source="EHDAA2"} ! epithelial cord is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0012275 ! meso-epithelium -relationship: develops_from UBERON:0005294 ! gonadal ridge +relationship: RO:0002202 UBERON:0005294 ! develops from gonadal ridge [Term] id: UBERON:0005296 @@ -222009,8 +219227,8 @@ is_a: UBERON:0004911 ! epithelium of female gonad is_a: UBERON:0005295 ! sex cord intersection_of: UBERON:0005295 ! sex cord intersection_of: part_of UBERON:0000992 ! ovary -relationship: develops_from UBERON:0010141 ! primitive sex cord of indifferent gonad -property_value: editor_note "TODO check secondary vs cortical vs ovary" xsd:string +relationship: RO:0002202 UBERON:0010141 ! develops from primitive sex cord of indifferent gonad +property_value: IAO:0000116 "TODO check secondary vs cortical vs ovary" xsd:string [Term] id: UBERON:0005297 @@ -222031,8 +219249,8 @@ is_a: UBERON:0004910 ! epithelium of male gonad is_a: UBERON:0005295 ! sex cord intersection_of: UBERON:0005295 ! sex cord intersection_of: part_of UBERON:0000473 ! testis -relationship: immediate_transformation_of UBERON:0010141 {source="Bgee:AN"} ! primitive sex cord of indifferent gonad -property_value: editor_note "TODO - check primary vs testis" xsd:string +relationship: RO:0002495 UBERON:0010141 {source="Bgee:AN"} ! immediate transformation of primitive sex cord of indifferent gonad +property_value: IAO:0000116 "TODO - check primary vs testis" xsd:string [Term] id: UBERON:0005298 @@ -222042,6 +219260,7 @@ def: "A zone of skin that is part of a clitoris [Automatically generated definit synonym: "clitoris skin" EXACT [] xref: FMA:20168 xref: SCTID:361374002 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:8480029 ! skin of external genitalia intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0002411 ! clitoris @@ -222069,9 +219288,8 @@ intersection_of: UBERON:0011374 ! prepuce intersection_of: part_of UBERON:0002411 ! clitoris relationship: adjacent_to UBERON:0006653 ! glans clitoris relationship: part_of UBERON:0002411 ! clitoris -relationship: transformation_of UBERON:0035006 ! preputial swelling of female -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/bd/Clitoris_outer_anatomy.gif" xsd:anyURI -property_value: UBPROP:0000008 "FMA has FMA:27886 skin of prepuce of clitoris" xsd:string +relationship: RO:0002494 UBERON:0035006 ! transformation of preputial swelling of female +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/bd/Clitoris_outer_anatomy.gif" xsd:anyURI [Term] id: UBERON:0005309 @@ -222081,10 +219299,10 @@ def: "A pronephric nephron is the functional unit of the pronephros[GO]." [GO:00 xref: AAO:0011091 xref: XAO:0000285 is_a: UBERON:0001285 ! nephron +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0001285 ! nephron intersection_of: part_of UBERON:0002120 ! pronephros relationship: part_of UBERON:0002120 ! pronephros -property_value: UBPROP:0000001 "The structure that is the basic functional unit of the pronephros.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011091", ontology="AAO", source="UBERON:0005309"} [Term] id: UBERON:0005310 @@ -222097,11 +219315,10 @@ xref: TAO:0001558 xref: XAO:0004105 xref: ZFA:0001558 is_a: UBERON:0001231 ! nephron tubule +is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0001231 ! nephron tubule intersection_of: part_of UBERON:0005309 ! pronephric nephron relationship: part_of UBERON:0005309 {source="GO"} ! pronephric nephron -property_value: RO:0002174 NCBITaxon:32524 {source="ISBN:0073040584"} -property_value: UBPROP:0000001 "Bilaterally paired tubes connecting the pronephric glomeruli to the pronephric ducts. In zebrafish and other teleosts, the pronephric nephron and tubules form after the pronephric duct, connecting to the anterior-most tip of the pronephric ducts. Drummond, 2000.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001558", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0005311 @@ -222111,10 +219328,9 @@ def: "The mammary placode is a transient lens shaped structure that will give ri synonym: "mammary anlage" RELATED [] xref: EMAPA:35541 is_a: UBERON:0011814 {source="NCBIBook:NBK53175"} ! non-neurogenic ectodermal placode -relationship: develops_from UBERON:0008425 {source="Stedmans"} ! mammary ridge relationship: part_of UBERON:0000076 {source="PMID:20484386"} ! external ectoderm -property_value: editor_note "TODO develops_from" xsd:string -property_value: UBPROP:0000008 "in mouse, five pairs of symmetrically positioned mammary placodes (three thoracic and two inguinal) form at reproducible locations along the mammary line at E11.5; the individual pairs develop asynchronously and in a distinct order; pair 3 is first, followed by pair 4, then by pairs 1 and 5 (which develop together), and finally by pair 2; the orientation of placodal cells is not uniform, suggesting that placodes are formed by migration of cells from the mammary line; between E11.5 and E12.5, each mammary placode expands and invaginates into the underlying mesenchyme to form an early bulb-shaped mammary bud[MP]" xsd:string +relationship: RO:0002202 UBERON:0008425 {source="Stedmans"} ! develops from mammary ridge +property_value: IAO:0000116 "TODO develops_from" xsd:string [Term] id: UBERON:0005316 @@ -222149,6 +219365,7 @@ def: "The collecting duct is the final common path through which urine flows bef xref: AAO:0010390 xref: XAO:0000151 is_a: UBERON:0001232 ! collecting duct of renal tubule +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0001232 ! collecting duct of renal tubule intersection_of: part_of UBERON:0000080 ! mesonephros relationship: part_of UBERON:0005322 {is_inferred="true", source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! mesonephric nephron @@ -222159,6 +219376,7 @@ name: mesonephric juxtaglomerular apparatus namespace: uberon def: "The juxtaglomerular apparatus lies adjacent to the glomerulus and regulates kidney function by maintaining the blood flow to the kidney and the filtration rate[GO]." [GO:0061212] is_a: UBERON:0002303 ! juxtaglomerular apparatus +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0002303 ! juxtaglomerular apparatus intersection_of: part_of UBERON:0000080 ! mesonephros relationship: part_of UBERON:0000080 ! mesonephros @@ -222184,11 +219402,11 @@ xref: AAO:0010387 xref: XAO:0000292 xref: ZFA:0005592 is_a: UBERON:0001285 ! nephron +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0001285 ! nephron intersection_of: part_of UBERON:0000080 ! mesonephros -relationship: develops_from UBERON:0005323 {source="XAO"} ! mesonephric mesenchyme relationship: part_of UBERON:0000080 ! mesonephros -property_value: UBPROP:0000001 "The structure that is the basic functional unit of the kidney.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010387", ontology="AAO", source="PMID:9268568"} +relationship: RO:0002202 UBERON:0005323 {source="XAO"} ! develops from mesonephric mesenchyme [Term] id: UBERON:0005323 @@ -222201,6 +219419,7 @@ xref: EHDAA2:0001132 xref: EMAPA:16745 xref: XAO:0000291 is_a: UBERON:0003104 ! mesenchyme +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0000080 ! mesonephros relationship: part_of UBERON:0000080 ! mesonephros @@ -222224,16 +219443,12 @@ def: "The mesonephric glomerulus is a capillary tuft which forms a close network synonym: "glomerulus" BROAD SENSU [AAO:0010388] xref: AAO:0010388 xref: EMAPA:30568 -xref: SCTID:362217000 xref: VHOG:0001238 xref: XAO:0000146 is_a: UBERON:0000074 ! renal glomerulus intersection_of: UBERON:0000074 ! renal glomerulus intersection_of: part_of UBERON:0000080 ! mesonephros relationship: part_of UBERON:0000080 ! mesonephros -property_value: UBPROP:0000001 "A tuft of capillaries found in a Bowman's capsule in which waste products are filtered from the blood and urine formation is initiated.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010388", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "In animals in which the mesonephros is the terminal kidney, such as amphibians and fish, the final organ is very complex, containing a large number of nephrons, most of which have an internal glomerulus.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001238", ontology="VHOG", source="ISBN:978-0127224411 Vize PD, Woolf AS, Bard JBL, The kidney: From normal development to congenital disease (2003) p.3", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "XAO/AAO class belongs here, as it refers to mesonephric structure" xsd:string {external_ontology="XAO"} [Term] id: UBERON:0005326 @@ -222299,8 +219514,8 @@ is_a: UBERON:0004209 ! renal vesicle is_a: UBERON:0005103 ! mesonephric epithelium intersection_of: UBERON:0004209 ! renal vesicle intersection_of: part_of UBERON:0000080 ! mesonephros -relationship: develops_from UBERON:0010534 {source="ZFA"} ! primitive mesonephric nephron -relationship: has_potential_to_develop_into UBERON:0005330 ! mesonephric nephron epithelium +relationship: RO:0002202 UBERON:0010534 {source="ZFA"} ! develops from primitive mesonephric nephron +relationship: RO:0002387 UBERON:0005330 ! has potential to develop into mesonephric nephron epithelium [Term] id: UBERON:0005332 @@ -222326,9 +219541,8 @@ xref: EMAPA:35536 is_a: UBERON:0005153 ! epithelial bud is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0005153 ! epithelial bud -intersection_of: transformation_of UBERON:0005311 ! mammary placode -relationship: transformation_of UBERON:0005311 ! mammary placode -property_value: UBPROP:0000011 "produced along the length of the embryonic mammary ridge these buds represent the future locations of the mammary glands. Invagination of ectoderm at each bud leads to the development of epithelial diverticula, later maturing as lactiferous ducts" xsd:string {source="http://medical-dictionary.thefreedictionary.com/mammary+bud"} +intersection_of: RO:0002494 UBERON:0005311 ! transformation of mammary placode +relationship: RO:0002494 UBERON:0005311 ! transformation of mammary placode [Term] id: UBERON:0005334 @@ -222371,7 +219585,7 @@ is_a: UBERON:0004145 ! outflow tract intersection_of: UBERON:0004145 ! outflow tract intersection_of: part_of UBERON:0000947 ! aorta relationship: part_of UBERON:0000947 ! aorta -property_value: editor_note "merge with LVOT?" xsd:string +property_value: IAO:0000116 "merge with LVOT?" xsd:string [Term] id: UBERON:0005339 @@ -222383,7 +219597,7 @@ xref: EMAPA:17330 xref: MA:0000102 xref: VHOG:0001395 is_a: UBERON:0004145 ! outflow tract -property_value: editor_note "merge with RVOT?" xsd:string +property_value: IAO:0000116 "merge with RVOT?" xsd:string [Term] id: UBERON:0005343 @@ -222401,13 +219615,10 @@ xref: BAMS:CTXpl xref: DHBA:10515 xref: EMAPA:32711 xref: MBA:695 -xref: MESH:D002540 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: neuronames:2702 xref: PBA:294021914 is_a: UBERON:0014950 ! layer of developing cerebral cortex -relationship: has_potential_to_develop_into UBERON:0001950 {source="NCBIBook:NBK10047"} ! neocortex -property_value: UBPROP:0000011 "A single stem cell in the ventricular layer can give rise to neurons (and glial cells) in any of the cortical layers (Walsh and Cepko 1988)[NCBIBook:NBK10047]" xsd:string -property_value: UBPROP:0000011 "in humans develops into cortical layers II-VI" xsd:string +relationship: RO:0002387 UBERON:0001950 {source="NCBIBook:NBK10047"} ! has potential to develop into neocortex [Term] id: UBERON:0005352 @@ -222427,10 +219638,10 @@ xref: Wikipedia:Spermatic_cord is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005156 ! reproductive structure is_a: UBERON:0034921 ! multi organ part structure -relationship: contributes_to_morphology_of UBERON:0004054 ! internal male genitalia relationship: has_part UBERON:0001000 ! vas deferens relationship: part_of UBERON:0004054 ! internal male genitalia -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/3/35/Male_anatomy.png" xsd:anyURI +relationship: RO:0002433 UBERON:0004054 ! contributes to morphology of internal male genitalia +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/3/35/Male_anatomy.png" xsd:anyURI [Term] id: UBERON:0005356 @@ -222468,14 +219679,9 @@ xref: XAO:0000430 is_a: UBERON:0005423 ! developing anatomical structure is_a: UBERON:0007499 {source="EHDAA2"} ! epithelial sac is_a: UBERON:0010371 ! ecto-epithelium -relationship: develops_from UBERON:0000930 {source="MP"} ! stomodeum -relationship: develops_from UBERON:0009122 {source="NCBIBook:NBK53175"} ! adenohypophyseal placode relationship: part_of UBERON:0000033 ! head -property_value: RO:0002174 NCBITaxon:7955 -property_value: UBPROP:0000001 "A depression that forms in the roof of the mouth of an embryo, anterior to the buccopharyngeal membrane. The walls of the diverticulum develop into the anterior lobe of the pituitary gland. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000674", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/rathke's+pouch"} -property_value: UBPROP:0000003 "It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. An infundibulum grows ventrally from the diencephalon of the brain, and Rathke's pouch extends dorsally from the roof of the developing mouth, or stomodaeum. The infundibulum remains connected to the floor of the diencephalon, which becomes the hypothalamus, and gives rise to the part of the gland known as the neurohypophysis. (...) Rathke's pouch loses its connection with the stomodaeum in most adult vertebrates and gives rise to the rest of the gland, the adenohypophysis. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000674", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510 and Figure 15-5", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "median funnel­-shaped invagination of ectoderm, the nasohypophyseal pouch. It will contribute to the formation of the pituitary gland of the adult lamprey and is homologous to Rathke's pouch and perhaps to Hatschek 's pit (amphioxus)." xsd:string {source="http://webs.lander.edu/rsfox/invertebrates/ammocoetes.html"} -property_value: UBPROP:0000012 "EHDAA2 distinguishes between the adenohypophyseal pouch and it's precursor Rathke's pouch epithelium." xsd:string {external_ontology="EHDAA2"} +relationship: RO:0002202 UBERON:0000930 {source="MP"} ! develops from stomodeum +relationship: RO:0002202 UBERON:0009122 {source="NCBIBook:NBK53175"} ! develops from adenohypophyseal placode [Term] id: UBERON:0005357 @@ -222491,9 +219697,8 @@ xref: MESH:D004805 is_a: UBERON:0004670 ! ependyma intersection_of: UBERON:0004670 ! ependyma intersection_of: part_of UBERON:0004086 ! brain ventricle -relationship: contributes_to_morphology_of UBERON:0003947 ! brain ventricle/choroid plexus relationship: part_of UBERON:0004086 ! brain ventricle -property_value: UBPROP:0000012 "in FMA this is treated as part of the ependyma, but here we treat ependyma as a portion" xsd:string {external_ontology="FMA"} +relationship: RO:0002433 UBERON:0003947 ! contributes to morphology of brain ventricle/choroid plexus [Term] id: UBERON:0005358 @@ -222523,10 +219728,9 @@ xref: SCTID:369278000 is_a: UBERON:0004670 ! ependyma intersection_of: UBERON:0004670 ! ependyma intersection_of: part_of UBERON:0002240 ! spinal cord -relationship: contributes_to_morphology_of UBERON:0002240 ! spinal cord -relationship: develops_from UBERON:0034710 ! spinal cord ventricular layer relationship: part_of UBERON:0002291 ! central canal of spinal cord -property_value: UBPROP:0000012 "in FMA this is treated as part of the ependyma, but here we treat ependyma as a portion" xsd:string {external_ontology="FMA"} +relationship: RO:0002202 UBERON:0034710 ! develops from spinal cord ventricular layer +relationship: RO:0002433 UBERON:0002240 ! contributes to morphology of spinal cord [Term] id: UBERON:0005362 @@ -222554,7 +219758,7 @@ is_a: UBERON:0009127 {source="ZFA"} ! epibranchial ganglion intersection_of: UBERON:0000045 ! ganglion intersection_of: extends_fibers_into UBERON:0001759 ! vagus nerve relationship: extends_fibers_into UBERON:0001759 ! vagus nerve -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0005366 @@ -222575,8 +219779,6 @@ xref: neuronames:2078 xref: UMLS:C0178780 {source="ncithesaurus:Olfactory_Lobe"} xref: VHOG:0000833 is_a: UBERON:0016526 ! lobe of cerebral hemisphere -property_value: UBPROP:0000001 "Part of the telencephalon, comprised of paired anterior outgrowths of either of the cerebral hemispheres in which the olfactory nerve exits. In Xenopus,the olfactory bulbs begin to fuse at NF stage 50, fusion is complete around NF stage 58. The cerebral vein loops around the olfactory bulb by NF stage 43[XAO:0004180]." xsd:string {source="XAO:0004180"} -property_value: UBPROP:0000003 "(In mammals) Odorant detection is mediated by millions of olfactory sensory neurons located in the olfactory epithelium lining the nasal cavity. These neurons transmit sensory signals to the olfactory bulb of the brain, which in turn sends signals to the olfactory cortex.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000833", ontology="VHOG", source="DOI:10.1111/j.1753-4887.2004.tb00097.x Buck LB, Olfactory receptors and odor coding in mammals. Nutrition Reviews (2008)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0005367 @@ -222588,9 +219790,9 @@ xref: EMAPA:35406 xref: MA:0000954 is_a: UBERON:0002305 ! layer of hippocampus intersection_of: UBERON:0002305 ! layer of hippocampus -intersection_of: composed_primarily_of CL:0001033 ! hippocampal granule cell -relationship: composed_primarily_of CL:0001033 ! hippocampal granule cell -property_value: editor_note "TODO - check this. The granule layer is typically in the dentate gyrus, under some definitions of hippocampus, the DG is included, thus making this layer a hippocampal layer" xsd:string +intersection_of: RO:0002473 CL:0001033 ! composed primarily of hippocampal granule cell +relationship: RO:0002473 CL:0001033 ! composed primarily of hippocampal granule cell +property_value: IAO:0000116 "TODO - check this. The granule layer is typically in the dentate gyrus, under some definitions of hippocampus, the DG is included, thus making this layer a hippocampal layer" xsd:string [Term] id: UBERON:0005371 @@ -222613,10 +219815,10 @@ xref: MA:0000958 xref: neuronames:157 {source="BIRNLEX:4113"} is_a: UBERON:0002305 ! layer of hippocampus intersection_of: UBERON:0002305 ! layer of hippocampus -intersection_of: immediately_deep_to UBERON:0002313 ! hippocampus pyramidal layer -intersection_of: immediately_superficial_to UBERON:0007639 ! hippocampus alveus -relationship: immediately_deep_to UBERON:0002313 ! hippocampus pyramidal layer -relationship: immediately_superficial_to UBERON:0007639 ! hippocampus alveus +intersection_of: BSPO:0001107 UBERON:0002313 ! hippocampus pyramidal layer +intersection_of: BSPO:0015014 UBERON:0007639 ! hippocampus alveus +relationship: BSPO:0001107 UBERON:0002313 ! hippocampus pyramidal layer +relationship: BSPO:0015014 UBERON:0007639 ! hippocampus alveus [Term] id: UBERON:0005372 @@ -222636,11 +219838,10 @@ xref: MA:0000959 xref: neuronames:158 {source="BIRNLEX:1298"} is_a: UBERON:0002305 ! layer of hippocampus intersection_of: UBERON:0002305 ! layer of hippocampus -intersection_of: immediately_deep_to UBERON:0002313 ! hippocampus pyramidal layer -intersection_of: immediately_superficial_to UBERON:0007637 ! hippocampus stratum lucidum -relationship: immediately_deep_to UBERON:0002313 ! hippocampus pyramidal layer -relationship: immediately_superficial_to UBERON:0007637 ! hippocampus stratum lucidum -property_value: UBPROP:0000010 "contains septal and commissural fibers. It also contains Schaffer collateral fibers, which are the projection forward from CA3 to CA1. Some interneurons that can be found in more superficial layers can also be found here, including basket cells, bistratified cells, and radial trilaminar cells" xsd:string +intersection_of: BSPO:0001107 UBERON:0002313 ! hippocampus pyramidal layer +intersection_of: BSPO:0015014 UBERON:0007637 ! hippocampus stratum lucidum +relationship: BSPO:0001107 UBERON:0002313 ! hippocampus pyramidal layer +relationship: BSPO:0015014 UBERON:0007637 ! hippocampus stratum lucidum [Term] id: UBERON:0005375 @@ -222656,10 +219857,8 @@ xref: MA:0002751 xref: neuronames:269 xref: VHOG:0001622 is_a: UBERON:0016550 ! spinal cord column -relationship: contributes_to_morphology_of UBERON:0002318 ! white matter of spinal cord relationship: part_of UBERON:0002180 ! ventral funiculus of spinal cord -property_value: UBPROP:0000001 "The ventral ridge of gray matter in each half of the spinal cord. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001622", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/anterior+column+of+spinal+cord"} -property_value: UBPROP:0000012 "in MA, this is a subclass of white matter, but in WP/Gray's, the anterior column is a synonym of the grey matter section. is this the same as funiculus? See lateral column." xsd:string {external_ontology="MA"} +relationship: RO:0002433 UBERON:0002318 ! contributes to morphology of white matter of spinal cord [Term] id: UBERON:0005376 @@ -222748,10 +219947,10 @@ xref: MBA:632 xref: neuronames:2122 is_a: UBERON:0002304 ! layer of dentate gyrus intersection_of: UBERON:0002304 ! layer of dentate gyrus -intersection_of: immediately_deep_to UBERON:0004679 ! dentate gyrus molecular layer -relationship: composed_primarily_of CL:2000089 ! dentate gyrus granule cell -relationship: immediately_deep_to UBERON:0004679 ! dentate gyrus molecular layer +intersection_of: BSPO:0001107 UBERON:0004679 ! dentate gyrus molecular layer +relationship: BSPO:0001107 UBERON:0004679 ! dentate gyrus molecular layer relationship: overlaps CL:0000118 ! basket cell +relationship: RO:0002473 CL:2000089 ! composed primarily of dentate gyrus granule cell [Term] id: UBERON:0005382 @@ -222781,11 +219980,6 @@ is_a: UBERON:0011300 ! gray matter of telencephalon relationship: has_part UBERON:0001873 ! caudate nucleus relationship: has_part UBERON:0001874 ! putamen relationship: part_of UBERON:0002435 {source="NIFSTD"} ! striatum -property_value: UBPROP:0000001 "According to BrainInfo it is a part of the basal ganglia comprising the globus pallidus and striatum" xsd:string {source="Wikipedia:Dorsal_striatum"} -property_value: UBPROP:0000001 "According to the 1917 version of Gray's Anatomy, it is the combination of the lentiform nucleus (putamen and the globus pallidus) and the caudate nucleus" xsd:string {source="Wikipedia:Dorsal_striatum"} -property_value: UBPROP:0000001 "It may also refer to both the basal ganglia and the internal capsule collectively." xsd:string {source="Wikipedia:Dorsal_striatum"} -property_value: UBPROP:0000001 "It may also refer to the putamen and caudate collectively." xsd:string {source="Wikipedia:Dorsal_striatum"} -property_value: UBPROP:0000001 "The term dorsal striatum refers to a composite structure of the endbrain that is defined in the striatopallidal system by connectivity and neurochemical staining. It includes most of the striatum ( Heimer-1995 ). The boundary between this structure and the ventral striatum is indistinct in sections stained for Nissl substance." xsd:string {source="neuronames:2340"} [Term] id: UBERON:0005383 @@ -222814,14 +220008,13 @@ xref: MA:0000893 xref: MBA:672 xref: NLXANAT:100312 is_a: UBERON:0011215 ! central nervous system cell part cluster -relationship: composed_primarily_of UBERON:0002020 ! gray matter -relationship: contributes_to_morphology_of UBERON:0002435 ! striatum relationship: has_part UBERON:0001873 ! caudate nucleus relationship: has_part UBERON:0001874 ! putamen relationship: part_of UBERON:0005382 {source="MA"} ! dorsal striatum -property_value: editor_note "check - rodents. The caudate nucleus and putamen are separated by a clear white matter bundle in most species but not in rodents (MM)" xsd:string -property_value: editor_note "we do not currently place rodent-specific taxon constraints here as this would cause taxon violations. There is an argument for merging this into dorsal striatum and treating the distinction as phenotypic" xsd:string -property_value: UBPROP:0000011 "In the human, histologically the caudate nucleus and putamen are identically and share a common embryological origin[ISBN:0123813611]" xsd:string +relationship: RO:0002433 UBERON:0002435 ! contributes to morphology of striatum +relationship: RO:0002473 UBERON:0002020 ! composed primarily of gray matter +property_value: IAO:0000116 "check - rodents. The caudate nucleus and putamen are separated by a clear white matter bundle in most species but not in rodents (MM)" xsd:string +property_value: IAO:0000116 "we do not currently place rodent-specific taxon constraints here as this would cause taxon violations. There is an argument for merging this into dorsal striatum and treating the distinction as phenotypic" xsd:string [Term] id: UBERON:0005384 @@ -222846,10 +220039,10 @@ is_a: UBERON:0019306 ! nose epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001826 ! nasal cavity mucosa relationship: bounding_layer_of UBERON:0015788 ! olfactory apparatus chamber -relationship: contributes_to_morphology_of UBERON:0000004 ! nose -relationship: contributes_to_morphology_of UBERON:0004785 ! respiratory system mucosa relationship: part_of UBERON:0001826 ! nasal cavity mucosa -property_value: editor_note "this class may in future be split into the embryonic precursor of the oronasal membrane and the structure that is part of the mucosa in the developed organism" xsd:string +relationship: RO:0002433 UBERON:0000004 ! contributes to morphology of nose +relationship: RO:0002433 UBERON:0004785 ! contributes to morphology of respiratory system mucosa +property_value: IAO:0000116 "this class may in future be split into the embryonic precursor of the oronasal membrane and the structure that is part of the mucosa in the developed organism" xsd:string [Term] id: UBERON:0005385 @@ -222894,7 +220087,6 @@ intersection_of: part_of UBERON:0005725 ! olfactory system disjoint_from: UBERON:0015786 ! respiratory segment of nasal mucosa relationship: has_part UBERON:0001997 ! olfactory epithelium relationship: part_of UBERON:0005725 ! olfactory system -property_value: UBPROP:0000001 "The olfactory mucosa is located in the upper region of the nasal cavity and is made up of the olfactory epithelium and the underlying lamina propria, connective tissue containing fibroblasts, blood vessels, Bowman's glands and bundles of fine axons from the olfactory neurons. The mucus protects the olfactory epithelium and allows odors to dissolve so that they can be detected by olfactory receptor neurons. Electron microscopy studies show that Bowman's glands contain cells with large secretory vesicles. The exact composition of the secretions from Bowman's glands is unclear, but there is evidence that Bowman's glands do not produce odorant binding protein[WP][Wikipedia:Olfactory_mucosa]." xsd:string {source="Wikipedia:Olfactory_mucosa"} [Term] id: UBERON:0005388 @@ -222902,14 +220094,13 @@ name: photoreceptor array namespace: uberon def: "An array of photoreceptors and any supporting cells found in an eye." [https://orcid.org/0000-0002-6601-2165] synonym: "light-sensitive tissue" EXACT [] -xref: FBbt:00004200 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0004923 ! organ component layer intersection_of: UBERON:0004923 ! organ component layer -intersection_of: composed_primarily_of CL:0000210 ! photoreceptor cell intersection_of: part_of UBERON:0000970 ! eye -relationship: composed_primarily_of CL:0000210 ! photoreceptor cell +intersection_of: RO:0002473 CL:0000210 ! composed primarily of photoreceptor cell relationship: part_of UBERON:0000970 ! eye relationship: part_of UBERON:0001016 ! nervous system +relationship: RO:0002473 CL:0000210 ! composed primarily of photoreceptor cell [Term] id: UBERON:0005389 @@ -222919,9 +220110,8 @@ def: "A transparent structure that is part of a visual sense organ, the function subset: grouping_class synonym: "lens" NARROW [] is_a: UBERON:0000061 ! anatomical structure -relationship: has_quality PATO:0000964 ! transparent relationship: part_of UBERON:0000970 ! eye -property_value: UBPROP:0000009 "directing or focusing light onto light receptors" xsd:string +relationship: RO:0000086 PATO:0000964 ! has quality transparent [Term] id: UBERON:0005390 @@ -222953,7 +220143,7 @@ xref: NLXANAT:090807 xref: PBA:294021786 xref: UMLS:C1709063 {source="ncithesaurus:Molecular_Layer"} is_a: UBERON:0002301 ! layer of neocortex -relationship: develops_from UBERON:0014935 {source="NBK10047"} ! cerebral cortex marginal layer +relationship: RO:0002202 UBERON:0014935 {source="NBK10047"} ! develops from cerebral cortex marginal layer [Term] id: UBERON:0005391 @@ -222984,8 +220174,8 @@ xref: NLXANAT:090808 xref: PBA:294021800 xref: UMLS:C1517039 {source="ncithesaurus:External_Granular_Layer"} is_a: UBERON:0002301 ! layer of neocortex -relationship: develops_from UBERON:0005343 {source="BRAINSPAN"} ! cortical plate -relationship: immediately_deep_to UBERON:0005390 ! cortical layer I +relationship: BSPO:0001107 UBERON:0005390 ! cortical layer I +relationship: RO:0002202 UBERON:0005343 {source="BRAINSPAN"} ! develops from cortical plate [Term] id: UBERON:0005392 @@ -223018,9 +220208,9 @@ xref: NLXANAT:090809 xref: PBA:294021824 xref: UMLS:C1517046 {source="ncithesaurus:External_Pyramidal_Cell_Layer"} is_a: UBERON:0002301 ! layer of neocortex -relationship: develops_from UBERON:0005343 {source="BRAINSPAN"} ! cortical plate +relationship: BSPO:0001107 UBERON:0005391 ! cortical layer II relationship: has_part CL:0000598 ! pyramidal neuron -relationship: immediately_deep_to UBERON:0005391 ! cortical layer II +relationship: RO:0002202 UBERON:0005343 {source="BRAINSPAN"} ! develops from cortical plate [Term] id: UBERON:0005393 @@ -223050,10 +220240,8 @@ xref: NLXANAT:090810 xref: PBA:294021852 xref: UMLS:C1512872 {source="ncithesaurus:Internal_Granular_Layer"} is_a: UBERON:0002301 ! layer of neocortex -relationship: develops_from UBERON:0005343 {source="BRAINSPAN"} ! cortical plate -relationship: immediately_deep_to UBERON:0005392 ! cortical layer III -property_value: UBPROP:0000003 "..." xsd:string {source="PMID:23027930"} -property_value: UBPROP:0000003 "Relatively undeveloped in some mammals such as the tenrec." xsd:string {source="ISBN:0471888893"} +relationship: BSPO:0001107 UBERON:0005392 ! cortical layer III +relationship: RO:0002202 UBERON:0005343 {source="BRAINSPAN"} ! develops from cortical plate [Term] id: UBERON:0005394 @@ -223091,9 +220279,9 @@ xref: NLXANAT:090811 xref: PBA:294021878 xref: UMLS:C1517447 {source="ncithesaurus:Ganglionic_Layer"} is_a: UBERON:0002301 ! layer of neocortex -relationship: develops_from UBERON:0005343 {source="BRAINSPAN"} ! cortical plate +relationship: BSPO:0001107 UBERON:0005393 ! cortical layer IV relationship: has_part CL:0000598 ! pyramidal neuron -relationship: immediately_deep_to UBERON:0005393 ! cortical layer IV +relationship: RO:0002202 UBERON:0005343 {source="BRAINSPAN"} ! develops from cortical plate [Term] id: UBERON:0005395 @@ -223124,7 +220312,7 @@ xref: neuronames:2451 xref: NLXANAT:090812 xref: PBA:294021896 is_a: UBERON:0002301 ! layer of neocortex -relationship: immediately_deep_to UBERON:0005394 ! cortical layer V +relationship: BSPO:0001107 UBERON:0005394 ! cortical layer V [Term] id: UBERON:0005396 @@ -223161,8 +220349,7 @@ xref: VHOG:0000266 xref: Wikipedia:Carotid_artery xref: ZFA:0000097 is_a: UBERON:0004573 {source="FMA"} ! systemic artery -property_value: editor_note "This is a generic grouping class that is the superclass of the trunks/branches of the common carotid artery. Note that AOs vary widely in how they divide up and generalize arteries" xsd:string -property_value: UBPROP:0000001 "Artery originating at the junction of the first two aortic arches and supplying the anterior brain. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000097", ontology="TAO", source="ZFIN:curator"} +property_value: IAO:0000116 "This is a generic grouping class that is the superclass of the trunks/branches of the common carotid artery. Note that AOs vary widely in how they divide up and generalize arteries" xsd:string [Term] id: UBERON:0005397 @@ -223182,11 +220369,9 @@ xref: VHOG:0000230 is_a: UBERON:0002362 ! arachnoid mater is_a: UBERON:0003547 ! brain meninx intersection_of: UBERON:0002362 ! arachnoid mater -intersection_of: surrounds UBERON:0000955 ! brain +intersection_of: RO:0002221 UBERON:0000955 ! surrounds brain relationship: part_of UBERON:0003547 ! brain meninx -relationship: surrounds UBERON:0000955 ! brain -property_value: UBPROP:0000001 "The middle membrane of the three mammalian meninges covering the brain and spinal cord. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000230", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/arachnoid+mater"} -property_value: UBPROP:0000003 "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000230", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639", source="http://bgee.unil.ch/"} +relationship: RO:0002221 UBERON:0000955 ! surrounds brain [Term] id: UBERON:0005398 @@ -223248,7 +220433,6 @@ is_a: UBERON:0011300 ! gray matter of telencephalon intersection_of: UBERON:0002020 ! gray matter intersection_of: part_of UBERON:0001869 ! cerebral hemisphere relationship: part_of UBERON:0001869 ! cerebral hemisphere -property_value: UBPROP:0000012 "BTO may actually be a more generic structure; FMA may represent a more specific structure. Consider merging with gray matter of telencephalon" xsd:string {external_ontology="BTO"} [Term] id: UBERON:0005403 @@ -223269,15 +220453,13 @@ xref: EMAPA:36576 xref: FMA:77614 xref: MA:0002972 xref: MBA:493 -xref: MESH:D066328 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: neuronames:2341 xref: NLX:57107 xref: PBA:10091 xref: Wikipedia:Ventral_striatum is_a: UBERON:0011300 ! gray matter of telencephalon -relationship: contributes_to_morphology_of UBERON:0002435 ! striatum relationship: part_of UBERON:0002435 {source="MA"} ! striatum -property_value: UBPROP:0000001 "The term ventral striatum refers to a composite structure of the endbrain that is defined in the striatopallidal system by connectivity and neurochemical staining. It includes the nucleus accumbens, the most ventral portions of the caudate nucleus and the putamen, the rostrolateral portion of the olfactory tubercle, the islands of Calleja and a rostral subcommissural portion of substantia innominata. The boundary between the ventral striatum and dorsal striatum is indistinct in sections stained for Nissl substance ( Heimer-1995 )." xsd:string {source="neuronames:2341"} +relationship: RO:0002433 UBERON:0002435 ! contributes to morphology of striatum [Term] id: UBERON:0005406 @@ -223300,9 +220482,9 @@ xref: MA:0002975 xref: SCTID:246901006 xref: Wikipedia:Adipose_capsule_of_kidney is_a: UBERON:0001013 ! adipose tissue -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" xsd:anyURI -property_value: editor_note "TODO - split perinephric / perirenal" xsd:string +relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" xsd:anyURI +property_value: IAO:0000116 "TODO - split perinephric / perirenal" xsd:string [Term] id: UBERON:0005408 @@ -223313,18 +220495,14 @@ subset: pheno_slim synonym: "circumventricular organ" EXACT [NLXANAT:20090312] synonym: "circumventricular organ of neuraxis" EXACT [FMA:84081] synonym: "CVO" EXACT OMO:0003000 [NLXANAT:20090312] -xref: BTO:0006267 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: EMAPA:35243 xref: FMA:84081 xref: MA:0002942 -xref: MESH:D066280 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: neuronames:1242 xref: NLXANAT:20090312 xref: Wikipedia:Circumventricular_organs is_a: UBERON:0002616 ! regional part of brain -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray734.png" xsd:anyURI -property_value: UBPROP:0000008 "All vertebrates possess at least 4 circumventricular organs (including the hypothalamus) which can monitor the contents of the cerebrospinal fluid and secrete additional substances into it. (Butler, 1996, p. 330)" xsd:string -property_value: UBPROP:0000010 "CVOs contain neural tissue and are an integral part of neuroendocrine function; all of the CVOs, besides the subcommissural organ, contain extensive vasculature and fenestrated capillaries which leads to a leaky BBB at the site of the organs; the lack of a BBB allows CVOs to act as an alternative route for peptides and hormones in the neural tissue to the peripheral blood stream, while still protecting it from toxic substances" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray734.png" xsd:anyURI [Term] id: UBERON:0005409 @@ -223345,7 +220523,6 @@ xref: CALOHA:TS-0407 xref: EHDAA2:0000110 xref: EHDAA:514 xref: EMAPA:16246 -xref: EV:0100056 xref: FMA:71132 xref: GAID:294 xref: galen:GastrointestinalTract @@ -223356,12 +220533,9 @@ xref: SCTID:373871007 xref: UMLS:C0012240 {source="ncithesaurus:Gastrointestinal_System"} xref: VHOG:0000412 is_a: UBERON:0000467 ! anatomical system -relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: part_of UBERON:0001007 ! digestive system -property_value: editor_note "the decision to split digestive and gastrointestinal in this way may be revisited. As it currently stands, this class more closely aligns what MA calls the alimentary system" xsd:string -property_value: UBPROP:0000001 "The system that includes the esophagus, stomach, small and large intestine, anus, liver, biliary tract, and pancreas[ncithesaurus:Gastrointestinal_System]." xsd:string {source="ncithesaurus:Gastrointestinal_System"} -property_value: UBPROP:0000003 "All metazoans (with degenerate exceptions) have some sort of digestive cavity with a means of entrance to and exit from it.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000412", ontology="VHOG", source="ISBN:978-0721676685 Sherwood Romer A and Parsons T, Vertebrate body (1977) p.3", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "that many anatomy ontologies consider this synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class. We have one entity that is part of both gastrointestinal and hepatobiliary systems: hepatopancreatic ampulla." xsd:string {external_ontology="MA"} +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +property_value: IAO:0000116 "the decision to split digestive and gastrointestinal in this way may be revisited. As it currently stands, this class more closely aligns what MA calls the alimentary system" xsd:string [Term] id: UBERON:0005410 @@ -223374,7 +220548,6 @@ synonym: "auditory capsule" EXACT [ZFA:0001500] synonym: "otic capsule cartilage element" EXACT [] xref: EHDAA2:0001333 xref: EHDAA:4704 -xref: EMAPA:17596 xref: EMAPA:18803 xref: EMAPA:37467 {source="MA:th"} xref: TAO:0001500 @@ -223382,12 +220555,8 @@ xref: ZFA:0001500 is_a: UBERON:0003932 ! cartilage element of chondrocranium is_a: UBERON:0004637 ! otic capsule intersection_of: UBERON:0004637 ! otic capsule -intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue -relationship: develops_from UBERON:0010349 {source="EHDAA2"} ! otic capsule pre-cartilage condensation -property_value: UBPROP:0000001 "Bilaterally paired cartilage encasing the semicircular canals of the inner ear.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001500", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000002 "relationship type change: overlaps neurocranium (TAO:0001580) CHANGED TO: develops_from neurocranium (UBERON:0001703)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001500", ontology="TAO"} -property_value: UBPROP:0000002 "relationship type change: overlaps neurocranium (TAO:0001580) CHANGED TO: part_of neurocranium (UBERON:0001703)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001500", ontology="TAO"} -property_value: UBPROP:0000008 "In elasmobranchs, the otic capsule remains cartilaginous in the adult; in the embryos of higher vertebrates, it is cartilaginous at first but later becomes bony (at approximately 23 weeks in humans). todo - check EMAPA" xsd:string +intersection_of: RO:0002473 UBERON:0002418 ! composed primarily of cartilage tissue +relationship: RO:0002202 UBERON:0010349 {source="EHDAA2"} ! develops from otic capsule pre-cartilage condensation [Term] id: UBERON:0005411 @@ -223396,17 +220565,15 @@ namespace: uberon def: "The cartilage or bony capsule surrounding the inner ear mechanism." [ISBN:0-683-40008-8, MP:0000039] subset: pheno_slim synonym: "otic capsule bone" EXACT [] -xref: EMAPA:17596 xref: EMAPA:37466 {source="MA:th"} xref: MA:0000252 is_a: UBERON:0002513 ! endochondral bone is_a: UBERON:0004637 ! otic capsule is_a: UBERON:0011164 ! neurocranium bone intersection_of: UBERON:0004637 ! otic capsule -intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue -relationship: develops_from UBERON:0005410 ! cartilaginous otic capsule +intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue relationship: part_of UBERON:0001694 {source="EHDAA2"} ! petrous part of temporal bone -property_value: UBPROP:0000008 "In elasmobranchs, the otic capsule remains cartilaginous in the adult; in the embryos of higher vertebrates, it is cartilaginous at first but later becomes bony (at approximately 23 weeks in humans)" xsd:string +relationship: RO:0002202 UBERON:0005410 ! develops from cartilaginous otic capsule [Term] id: UBERON:0005417 @@ -223432,9 +220599,9 @@ xref: XAO:0003065 is_a: UBERON:0004347 ! limb bud is_a: UBERON:0005419 ! pectoral appendage bud intersection_of: UBERON:0004347 ! limb bud -intersection_of: has_potential_to_develop_into UBERON:0002102 ! forelimb +intersection_of: RO:0002387 UBERON:0002102 ! has potential to develop into forelimb disjoint_from: UBERON:0005418 {source="lexical"} ! hindlimb bud -relationship: has_potential_to_develop_into UBERON:0002102 ! forelimb +relationship: RO:0002387 UBERON:0002102 ! has potential to develop into forelimb [Term] id: UBERON:0005418 @@ -223457,10 +220624,9 @@ xref: XAO:0003066 is_a: UBERON:0004347 ! limb bud is_a: UBERON:0005420 ! pelvic appendage bud intersection_of: UBERON:0004347 ! limb bud -intersection_of: has_potential_to_develop_into UBERON:0002103 ! hindlimb intersection_of: part_of UBERON:0000154 ! posterior region of body -relationship: has_potential_to_develop_into UBERON:0002103 ! hindlimb -property_value: UBPROP:0000001 "The bilateral thickening of the ectoderm in the region of the first noticeable at NF stage 47, and innervated by NF stage 51. The hind limb buds develop before the forelimb buds.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010382", ontology="AAO", source="XAO:curator"} +intersection_of: RO:0002387 UBERON:0002103 ! has potential to develop into hindlimb +relationship: RO:0002387 UBERON:0002103 ! has potential to develop into hindlimb [Term] id: UBERON:0005419 @@ -223479,12 +220645,10 @@ xref: VHOG_RETIRED:0001259 xref: ZFA:0000141 is_a: UBERON:0004357 ! paired limb/fin bud intersection_of: UBERON:0004357 ! paired limb/fin bud -intersection_of: has_potential_to_develop_into UBERON:0004710 ! pectoral appendage -relationship: has_developmental_contribution_from UBERON:0005729 ! pectoral appendage field -relationship: has_potential_to_develop_into UBERON:0004710 ! pectoral appendage +intersection_of: RO:0002387 UBERON:0004710 ! has potential to develop into pectoral appendage relationship: part_of UBERON:0000153 ! anterior region of body -property_value: UBPROP:0000001 "Fin bud that develops into the pectoral fin.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000141", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "While the skeletons of teleost pectoral fins and tetrapod forelimbs are homologous at the level of endoskeletal radials, teleosts and tetrapods do not share homologous skeletal elements at the level of 'individuated' pro-, meso-, and metapterygia. Among osteichthyans, only basal actinopterygians retain the full complement of elements present in non-osteichthyan gnathostomes.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001754", ontology="VHOG", source="DOI:10.1002/jmor.10264 Davis MC, Shubin NH, Force A, Pectoral fin and girdle development in the basal actinopterygians Polyodon spathula and Acipenser transmontanus. Journal of Morphology (2004)", source="http://bgee.unil.ch/"} +relationship: RO:0002254 UBERON:0005729 ! has developmental contribution from pectoral appendage field +relationship: RO:0002387 UBERON:0004710 ! has potential to develop into pectoral appendage [Term] id: UBERON:0005420 @@ -223502,14 +220666,12 @@ xref: VHOG:0001260 xref: ZFA:0001384 is_a: UBERON:0004357 ! paired limb/fin bud intersection_of: UBERON:0004357 ! paired limb/fin bud -intersection_of: has_potential_to_develop_into UBERON:0004709 ! pelvic appendage intersection_of: part_of UBERON:0000154 ! posterior region of body -relationship: has_developmental_contribution_from UBERON:0005730 ! pelvic appendage field -relationship: has_potential_to_develop_into UBERON:0004709 ! pelvic appendage -relationship: never_in_taxon NCBITaxon:31033 {source="PMID:15893975"} +intersection_of: RO:0002387 UBERON:0004709 ! has potential to develop into pelvic appendage relationship: part_of UBERON:0000154 ! posterior region of body -property_value: UBPROP:0000001 "Fin bud that develops into the pelvic fin.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001384", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001260", ontology="VHOG", source="ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268", source="http://bgee.unil.ch/"} +relationship: RO:0002254 UBERON:0005730 ! has developmental contribution from pelvic appendage field +relationship: RO:0002387 UBERON:0004709 ! has potential to develop into pelvic appendage +property_value: RO:0002161 NCBITaxon:31033 {source="PMID:15893975"} [Term] id: UBERON:0005421 @@ -223537,11 +220699,8 @@ xref: ZFA:0000085 is_a: UBERON:0004356 ! apical ectodermal ridge intersection_of: UBERON:0004356 ! apical ectodermal ridge intersection_of: part_of UBERON:0005419 ! pectoral appendage bud -relationship: develops_from UBERON:0003372 {source="EHDAA2"} ! pectoral appendage bud ectoderm relationship: part_of UBERON:0005419 ! pectoral appendage bud -property_value: UBPROP:0000001 "An ectodermal thickening at the end of the forelimb bud in the developing embryo. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001064", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/apical+ectodermal+ridge"} -property_value: UBPROP:0000001 "Apical ectodermal ridge that is part of the pectoral fin bud.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000085", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "Pectoral and pelvic fins are homologous to the tetrapod fore and hindlimb, respectively. (...) The zebrafish AER [apical ectodermal ridge] is an apical ectodermal thickening at the distal tip of the fin bud and consists of wedge-shaped cells of the basal stratum. The AER is observed only transiently, and from 36 hpf onwards the cells of this region form the apical fold (AF), which consists of a dorsal and a ventral layer of cylindrically-shaped ectodermal cells extending from the anterior to the posterior fin margin. Despite the change in shape, the AF still carries out the same functions as the AER. Indeed, although the AER receives its name from its characteristic shape, being composed of a pseudostratified ectoderm in the chicken and a polystratified ectoderm in the mouse, this independence of AER morphology from its function is also observed in tetrapods. The AF also expresses similar molecular markers to the tetrapod AER, suggesting that it fulfills similar functions in the fin as the AER does in tetrapod limbs.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001064", ontology="VHOG", source="DOI:10.1111/j.1440-169X.2007.00942.x", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003372 {source="EHDAA2"} ! develops from pectoral appendage bud ectoderm [Term] id: UBERON:0005422 @@ -223565,11 +220724,8 @@ xref: ZFA:0001385 is_a: UBERON:0004356 ! apical ectodermal ridge intersection_of: UBERON:0004356 ! apical ectodermal ridge intersection_of: part_of UBERON:0005420 ! pelvic appendage bud -relationship: develops_from UBERON:0003371 {source="EHDAA2"} ! pelvic appendage bud ectoderm relationship: part_of UBERON:0005420 ! pelvic appendage bud -property_value: UBPROP:0000001 "An ectodermal thickening at the end of the hindlimb bud in the developing embryo. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001066", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/apical+ectodermal+ridge"} -property_value: UBPROP:0000001 "Apical ectodermal ridge that is part of the pelvic fin bud.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001385", ontology="TAO", source="ZIFIN:curator"} -property_value: UBPROP:0000003 "Pectoral and pelvic fins are homologous to the tetrapod fore and hindlimb, respectively. (...) The zebrafish AER [apical ectodermal ridge] is an apical ectodermal thickening at the distal tip of the fin bud and consists of wedge-shaped cells of the basal stratum. The AER is observed only transiently, and from 36 hpf onwards the cells of this region form the apical fold (AF), which consists of a dorsal and a ventral layer of cylindrically-shaped ectodermal cells extending from the anterior to the posterior fin margin. Despite the change in shape, the AF still carries out the same functions as the AER. Indeed, although the AER receives its name from its characteristic shape, being composed of a pseudostratified ectoderm in the chicken and a polystratified ectoderm in the mouse, this independence of AER morphology from its function is also observed in tetrapods. The AF also expresses similar molecular markers to the tetrapod AER, suggesting that it fulfills similar functions in the fin as the AER does in tetrapod limbs.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001066", ontology="VHOG", source="DOI:10.1111/j.1440-169X.2007.00942.x", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003371 {source="EHDAA2"} ! develops from pelvic appendage bud ectoderm [Term] id: UBERON:0005423 @@ -223582,14 +220738,13 @@ synonym: "developmental tissue" RELATED [MIAA:0000019] xref: AEO:0000125 xref: CALOHA:TS-2122 xref: EHDAA2:0003125 -xref: FBbt:00007006 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:292313 xref: MIAA:0000019 is_a: UBERON:0000465 ! material anatomical entity relationship: capable_of GO:0032502 ! developmental process -relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 ! Fungi +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0005424 @@ -223612,11 +220767,11 @@ xref: TAO:0000064 xref: VHOG:0000492 xref: ZFA:0000064 is_a: UBERON:0006598 ! presumptive structure +is_a: UBERON:0010312 ! immature eye intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001782 ! pigmented layer of retina -relationship: has_potential_to_develop_into UBERON:0001782 ! pigmented layer of retina +intersection_of: RO:0002387 UBERON:0001782 ! has potential to develop into pigmented layer of retina relationship: part_of UBERON:0003072 ! optic cup -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000492", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} +relationship: RO:0002387 UBERON:0001782 ! has potential to develop into pigmented layer of retina [Term] id: UBERON:0005425 @@ -223639,11 +220794,11 @@ xref: TAO:0001071 xref: VHOG:0000490 xref: ZFA:0001071 is_a: UBERON:0006598 ! presumptive structure +is_a: UBERON:0010312 ! immature eye intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0003902 ! retinal neural layer -relationship: has_potential_to_develop_into UBERON:0003902 ! retinal neural layer +intersection_of: RO:0002387 UBERON:0003902 ! has potential to develop into retinal neural layer relationship: part_of UBERON:0003072 ! optic cup -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000490", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} +relationship: RO:0002387 UBERON:0003902 ! has potential to develop into retinal neural layer [Term] id: UBERON:0005426 @@ -223665,12 +220820,8 @@ xref: TAO:0002205 xref: VHOG:0001163 xref: ZFA:0001679 is_a: UBERON:0000479 ! tissue -relationship: develops_from UBERON:0003073 ! lens placode -relationship: has_quality PATO:0001736 {gci_relation="part_of", gci_filler="NCBITaxon:32443", notes="teleosts"} ! solid configuration -relationship: has_quality PATO:0002078 {gci_relation="part_of", gci_filler="NCBITaxon:40674", notes="Mammals"} ! hollow -property_value: UBPROP:0000001 "A vesicle formed from the lens pit of the embryo, developing into the crystalline lens. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001163", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/lens+vesicle"} -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001163", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000011 "the lens of zebrafish (and other teleosts) forms from delamination of cells from the lens placode; thus, there is no formation of a hollow lens vesicle, in contrast to the situation in mammals and birds (Glass and Dahm, 2004) [PMID:16496288] The lens of the zebrafish forms by delamination of lens placodal cells and not through invagination. This results in a solid spherical mass as opposed to a hollow lens vesicle. Detachment of the solid lens vesicle of zebrafish at 24b26 hpf is accomplished in part by apoptosis, similar to mammals" xsd:string {source="ZFA"} +is_a: UBERON:0004121 ! ectoderm-derived structure +relationship: RO:0002202 UBERON:0003073 ! develops from lens placode [Term] id: UBERON:0005427 @@ -223681,6 +220832,7 @@ xref: TAO:0002188 xref: ZFA:0001688 is_a: UBERON:0000479 {source="ZFA"} ! tissue is_a: UBERON:0001048 {source="Obol"} ! primordium +is_a: UBERON:0010312 ! immature eye is_a: UBERON:0010313 ! neural crest-derived structure relationship: part_of UBERON:0000019 {source="ZFA"} ! camera-type eye @@ -223699,11 +220851,9 @@ xref: TAO:0000818 xref: VHOG:0001208 xref: XAO:0004191 xref: ZFA:0000818 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue relationship: part_of UBERON:0002342 ! neural crest -property_value: UBPROP:0000001 "Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000818", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001208", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "In chicken fate mapping studies it was found to originate from neural crest residing between Somite 1-7 (S1-7); In mouse it is considered to be derived from rhombencephalic (post otic) neural crest cells and trunk neural crest cells (anterior to S5)" xsd:string {source="filemaps.com"} [Term] id: UBERON:0005432 @@ -223721,9 +220871,8 @@ xref: SCTID:361527005 is_a: UBERON:0001637 {source="EHDAA2"} ! artery is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0003498 ! heart blood vessel -relationship: develops_from UBERON:0004363 {source="EHDAA2"} ! pharyngeal arch artery relationship: part_of UBERON:0004145 ! outflow tract -property_value: UBPROP:0000001 "the merged ventral aortae of the embryo which supplies blood to the aortic arches[TMD][http://medical-dictionary.thefreedictionary.com/aortic+sac]." xsd:string {source="http://medical-dictionary.thefreedictionary.com/aortic+sac"} +relationship: RO:0002202 UBERON:0004363 {source="EHDAA2"} ! develops from pharyngeal arch artery [Term] id: UBERON:0005434 @@ -223736,8 +220885,8 @@ synonym: "subdivision of neck" EXACT [FMA:24219] xref: FMA:24219 xref: SCTID:123958008 is_a: UBERON:0011676 ! subdivision of organism along main body axis -relationship: only_in_taxon NCBITaxon:8287 ! Sarcopterygii relationship: part_of UBERON:0000974 ! neck +relationship: RO:0002160 NCBITaxon:8287 ! only in taxon Sarcopterygii [Term] id: UBERON:0005436 @@ -223756,11 +220905,11 @@ xref: MA:0003094 xref: SCTID:244263001 xref: Wikipedia:Common_hepatic_artery is_a: UBERON:0004573 ! systemic artery -relationship: connecting_branch_of UBERON:0001640 ! celiac artery -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/65/Gray532.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +relationship: RO:0002252 UBERON:0001640 ! connecting branch of celiac artery +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/65/Gray532.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0005445 @@ -223797,16 +220946,14 @@ xref: FMA:53154 xref: SCTID:369439002 xref: VHOG:0001543 xref: Wikipedia:Foramen_rotundum +is_a: UBERON:0010313 ! neural crest-derived structure is_a: UBERON:0013685 ! foramen of skull intersection_of: UBERON:0013685 ! foramen of skull -intersection_of: conduit_for UBERON:0000377 ! maxillary nerve intersection_of: part_of UBERON:0001677 ! sphenoid bone -relationship: conduit_for UBERON:0000377 ! maxillary nerve +intersection_of: RO:0002570 UBERON:0000377 ! conduit for maxillary nerve relationship: part_of UBERON:0001677 ! sphenoid bone -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/35/Gray145.png" xsd:anyURI -property_value: UBPROP:0000001 "A circular hole in the sphenoid bone that connects the middle cranial fossa and the pterygopalatine fossa.vity. [Wikipedia:Foramen_rotundum][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001543", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "It is suggested that the mammalian lamina ascendens arose from an upgrowth of the root of the quadrate ramus of the epipterygoid in cynodonts, separating foramen rotundum from foramen ovale.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001543", ontology="VHOG", source="PMID:1018003 Presley R, Steel FLD, On the homology of the alisphenoid. Journal of Anatomy (1976)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "todo - check placement of AAO class" xsd:string {external_ontology="AAO"} +relationship: RO:0002570 UBERON:0000377 ! conduit for maxillary nerve +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/35/Gray145.png" xsd:anyURI [Term] id: UBERON:0005451 @@ -223839,7 +220986,6 @@ xref: EHDAA2:0000893 xref: EHDAA:10631 xref: EMAPA:18713 xref: FMA:56432 -xref: MESH:D000080869 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C12496 xref: SCTID:361735006 xref: UMLS:C0222712 {source="ncithesaurus:Jugular_Foramen"} @@ -223847,16 +220993,13 @@ xref: VHOG:0001113 xref: Wikipedia:Jugular_foramen is_a: UBERON:0018321 ! foramen for glossopharyngeal nerve intersection_of: UBERON:0013685 ! foramen of skull -intersection_of: conduit_for UBERON:0001586 ! internal jugular vein intersection_of: part_of UBERON:0001678 ! temporal bone -relationship: conduit_for UBERON:0001586 ! internal jugular vein -relationship: conduit_for UBERON:0001759 ! vagus nerve -relationship: conduit_for UBERON:0002019 ! accessory XI nerve +intersection_of: RO:0002570 UBERON:0001586 ! conduit for internal jugular vein relationship: part_of UBERON:0001678 ! temporal bone -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/fa/Foramenjugulare.PNG" xsd:anyURI -property_value: UBPROP:0000001 "Large foramen that houses the glossopharyngeal and vagus nerves and is located inside the condyloid fossa.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000249", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000001 "One of a pair of openings between the lateral part of the occipital bone and the petrous part of the temporal bones in the skull. The foramen contains the inferior petrosal sinus; the transverse sinus; some meningeal branches of the occipital and ascending pharyngeal arteries; and the glossopharyngeal, vagus, and accessory nerves. [Free_Online_Medical_Dictionary]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001113", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/jugular+foramen"} -property_value: UBPROP:0000002 "relationship loss: subclass braincase and otic capsule opening (AAO:0000051)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000249", ontology="AAO"} +relationship: RO:0002570 UBERON:0001586 ! conduit for internal jugular vein +relationship: RO:0002570 UBERON:0001759 ! conduit for vagus nerve +relationship: RO:0002570 UBERON:0002019 ! conduit for accessory XI nerve +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/fa/Foramenjugulare.PNG" xsd:anyURI [Term] id: UBERON:0005457 @@ -223870,11 +221013,10 @@ xref: RETIRED_EHDAA2:0000964 xref: SCTID:188079002 is_a: UBERON:0005483 ! thymus lobe intersection_of: UBERON:0005483 ! thymus lobe -intersection_of: in_left_side_of UBERON:0002370 ! thymus -relationship: in_left_side_of UBERON:0002370 ! thymus -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Thymus.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Thymus.glb" xsd:anyURI -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +intersection_of: BSPO:0000120 UBERON:0002370 ! thymus +relationship: BSPO:0000120 UBERON:0002370 ! thymus +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Thymus.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Thymus.glb" xsd:anyURI [Term] id: UBERON:0005458 @@ -223886,8 +221028,8 @@ xref: EMAPA:16544 xref: FMA:18822 xref: VHOG:0000522 is_a: UBERON:0001310 ! umbilical artery -relationship: develops_from UBERON:0005613 {notes="check this", source="EHDAA2"} ! left dorsal aorta -relationship: develops_from UBERON:0011696 {notes="check this", source="EHDAA2"} ! left extraembryonic umbilical artery +relationship: RO:0002202 UBERON:0005613 ! develops from left dorsal aorta +relationship: RO:0002202 UBERON:0011696 ! develops from left extraembryonic umbilical artery [Term] id: UBERON:0005459 @@ -223900,10 +221042,10 @@ xref: EMAPA:16377 xref: FMA:70320 xref: SCTID:308833008 is_a: UBERON:0002066 ! umbilical vein +is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0002066 ! umbilical vein -intersection_of: in_left_side_of UBERON:0000468 ! multicellular organism -relationship: in_left_side_of UBERON:0000468 ! multicellular organism -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +intersection_of: BSPO:0000120 UBERON:0000468 ! multicellular organism +relationship: BSPO:0000120 UBERON:0000468 ! multicellular organism [Term] id: UBERON:0005460 @@ -223916,10 +221058,10 @@ xref: EMAPA:16698 xref: FMA:70307 xref: SCTID:361446008 is_a: UBERON:0005487 ! vitelline vein +is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0005487 ! vitelline vein -intersection_of: in_left_side_of UBERON:0000468 ! multicellular organism -relationship: in_left_side_of UBERON:0000468 ! multicellular organism -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +intersection_of: BSPO:0000120 UBERON:0000468 ! multicellular organism +relationship: BSPO:0000120 UBERON:0000468 ! multicellular organism [Term] id: UBERON:0005461 @@ -223941,20 +221083,21 @@ xref: FMA:32519 xref: SCTID:279236008 xref: Wikipedia:Levator_scapulae_muscle is_a: UBERON:0001482 ! muscle of shoulder -is_a: UBERON:0003897 ! axial muscle +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004518 ! muscle of vertebral column is_a: UBERON:0034908 ! scapular muscle intersection_of: UBERON:0014892 ! skeletal muscle organ, vertebrate -intersection_of: attaches_to UBERON:0002413 ! cervical vertebra -intersection_of: attaches_to UBERON:0006849 ! scapula -relationship: attaches_to UBERON:0002413 ! cervical vertebra -relationship: develops_from UBERON:0010983 {source="EHDAA2"} ! levator scapulae pre-muscle mass -relationship: has_muscle_insertion UBERON:0007174 {notes="Superior part of medial border of scapula", source="dbpedia"} ! medial border of scapula -relationship: has_muscle_origin UBERON:0001077 {notes="Posterior tubercles of transverse processes of C1 - C4 vertebrae", source="dbpedia"} ! transverse process of vertebra -relationship: innervated_by UBERON:0000962 {notes="cervical nerve and dorsal scapular nerve", source="dbpedia"} ! nerve of cervical vertebra +intersection_of: RO:0002371 UBERON:0002413 ! attached to cervical vertebra +intersection_of: RO:0002371 UBERON:0006849 ! attached to scapula relationship: part_of UBERON:0008713 {source="EHDAA2"} ! pectoral girdle and thoracic body wall skeletal muscle -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/b/bc/Levator_scapulae.png" xsd:anyURI +relationship: part_of UBERON:0013700 {source="Kardong"} ! axial musculature +relationship: RO:0002005 UBERON:0000962 ! innervated_by nerve of cervical vertebra +relationship: RO:0002202 UBERON:0010983 {source="EHDAA2"} ! develops from levator scapulae pre-muscle mass +relationship: RO:0002371 UBERON:0002413 ! attached to cervical vertebra +relationship: RO:0002372 UBERON:0001077 ! has muscle origin transverse process of vertebra +relationship: RO:0002373 UBERON:0007174 ! has muscle insertion medial border of scapula +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/b/bc/Levator_scapulae.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0005463 @@ -223984,8 +221127,8 @@ intersection_of: part_of UBERON:0000029 ! lymph node relationship: adjacent_to UBERON:0002006 ! cortex of lymph node relationship: adjacent_to UBERON:0002194 ! capsule of lymph node relationship: part_of UBERON:0000029 ! lymph node -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/68/Gray597.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/68/Gray597.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0005469 @@ -223999,11 +221142,10 @@ xref: RETIRED_EHDAA2:0001758 xref: SCTID:187981000 is_a: UBERON:0005483 ! thymus lobe intersection_of: UBERON:0005483 ! thymus lobe -intersection_of: in_right_side_of UBERON:0002370 ! thymus -relationship: in_right_side_of UBERON:0002370 ! thymus -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Thymus.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Thymus.glb" xsd:anyURI -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +intersection_of: BSPO:0000121 UBERON:0002370 ! thymus +relationship: BSPO:0000121 UBERON:0002370 ! thymus +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Thymus.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Thymus.glb" xsd:anyURI [Term] id: UBERON:0005470 @@ -224015,8 +221157,8 @@ xref: EMAPA:16545 xref: FMA:18821 xref: VHOG:0000523 is_a: UBERON:0001310 ! umbilical artery -relationship: develops_from UBERON:0005622 {notes="check this", source="EHDAA2"} ! right dorsal aorta -relationship: develops_from UBERON:0011697 {notes="check this", source="EHDAA2"} ! right extraembryonic umbilical artery +relationship: RO:0002202 UBERON:0005622 ! develops from right dorsal aorta +relationship: RO:0002202 UBERON:0011697 ! develops from right extraembryonic umbilical artery [Term] id: UBERON:0005471 @@ -224029,10 +221171,10 @@ xref: EMAPA:16378 xref: FMA:70319 xref: SCTID:361447004 is_a: UBERON:0002066 ! umbilical vein +is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0002066 ! umbilical vein -intersection_of: in_right_side_of UBERON:0000468 ! multicellular organism -relationship: in_right_side_of UBERON:0000468 ! multicellular organism -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +intersection_of: BSPO:0000121 UBERON:0000468 ! multicellular organism +relationship: BSPO:0000121 UBERON:0000468 ! multicellular organism [Term] id: UBERON:0005472 @@ -224045,10 +221187,10 @@ xref: EMAPA:16699 xref: FMA:70306 xref: SCTID:361445007 is_a: UBERON:0005487 ! vitelline vein +is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0005487 ! vitelline vein -intersection_of: in_right_side_of UBERON:0000468 ! multicellular organism -relationship: in_right_side_of UBERON:0000468 ! multicellular organism -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +intersection_of: BSPO:0000121 UBERON:0000468 ! multicellular organism +relationship: BSPO:0000121 UBERON:0000468 ! multicellular organism [Term] id: UBERON:0005476 @@ -224103,16 +221245,17 @@ def: "Either of the two lateral lobes that constitute the thymus." [http://orcid subset: human_reference_atlas synonym: "lateral lobe of thymus" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "lobe of thymus" EXACT [FMA:71193] +synonym: "thymus subunit" EXACT [] xref: FMA:71193 xref: RETIRED_EHDAA2:0002021 +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0009912 ! anatomical lobe is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0009912 ! anatomical lobe intersection_of: part_of UBERON:0002370 ! thymus -relationship: in_lateral_side_of UBERON:0002370 {source="FMA-abduced-lr"} ! thymus +relationship: BSPO:0000126 UBERON:0002370 {source="FMA-abduced-lr"} ! thymus relationship: part_of UBERON:0002370 ! thymus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000010 "each lobe of the thymus can be divided into a central medulla and a peripheral cortex which is surrounded by an outer capsule. Each lobe is composed of numerous lobules held together by delicate areolar tissue; the entire organ being enclosed in an investing capsule of a similar but denser structure. The primary lobules vary in size from that of a pin's head to that of a small pea, and are made up of a number of small nodules or follicles.[WP]" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0005486 @@ -224135,14 +221278,15 @@ xref: NCIT:C102627 xref: SCTID:54944003 xref: VHOG:0001004 xref: Wikipedia:Dural_venous_sinuses +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0006615 ! venous sinus intersection_of: UBERON:0006615 ! venous sinus -intersection_of: located_in UBERON:0002363 ! dura mater -relationship: located_in UBERON:0002363 ! dura mater +intersection_of: RO:0001025 UBERON:0002363 ! located in dura mater relationship: part_of UBERON:0003711 {source="FMA"} ! brachiocephalic vein relationship: part_of UBERON:0010743 ! meningeal cluster -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/b/bd/Gray488_blue.gif" xsd:anyURI -property_value: editor_note "the MA placement should be checked" xsd:string +relationship: RO:0001025 UBERON:0002363 ! located in dura mater +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/b/bd/Gray488_blue.gif" xsd:anyURI +property_value: IAO:0000116 "the MA placement should be checked" xsd:string [Term] id: UBERON:0005487 @@ -224171,12 +221315,9 @@ xref: XAO:0004147 is_a: UBERON:0004365 ! vitelline blood vessel is_a: UBERON:0013140 ! systemic vein intersection_of: UBERON:0001638 ! vein -intersection_of: drains UBERON:0001040 ! yolk sac -relationship: drains UBERON:0001040 ! yolk sac -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray475.png" xsd:anyURI -property_value: UBPROP:0000001 "One of two veins that run upward at first in front, and subsequently on either side of the intestinal canal. They unite on the ventral aspect of the canal, and beyond this are connected to one another by two anastomotic branches, one on the dorsal, and the other on the ventral aspect of the duodenal portion of the intestine, which is thus encircled by two venous rings; into the middle or dorsal anastomosis the superior mesenteric vein opens. The portions of the veins above the upper ring become interrupted by the developing liver and broken up by it into a plexus of small capillary-like vessels termed sinusoids.[XAO]" xsd:string {ontology="XAO", source="XAO:0004147"} -property_value: UBPROP:0000003 "Within each vertebrate group, the veins compose a few main functional systems that arise embryologically from what seems to be a common developmental pattern. (...) Early in development, three major sets of paired veins are present: the vitelline veins from the yolk sac, the cardinal veins from the body of the embryo itself, and the lateral abdominal veins from the pelvic region. The paired vitelline veins are among the first vessels to appear in the embryo. They arise over the yolk and follow the yolk stalk into the body. They then turn anteriorly, continue along the gut, and enter the sinus venosus.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000401", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.460", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "check zfa (no text def). Check vitelline/omphalomesenteric distinction in XAO" xsd:string {external_ontology="XAO"} +intersection_of: RO:0002179 UBERON:0001040 ! drains yolk sac +relationship: RO:0002179 UBERON:0001040 ! drains yolk sac +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7e/Gray475.png" xsd:anyURI [Term] id: UBERON:0005491 @@ -224204,7 +221345,7 @@ xref: EMAPA:16166 xref: TAO:0001435 xref: VHOG:0000513 xref: ZFA:0001435 -is_a: UBERON:0000061 ! anatomical structure +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001049 ! neural tube [Term] @@ -224229,10 +221370,7 @@ xref: XAO:0004091 xref: ZFA:0001178 is_a: UBERON:0000479 {source="ZFA"} ! tissue is_a: UBERON:0004121 ! ectoderm-derived structure -property_value: editor_note "todo - epidermis? todo - track down EHDAA2 class in new release" xsd:string -property_value: RO:0002171 UBERON:0002346 -property_value: UBPROP:0000003 "In the early gastrula of vertebrates, factors from the organizer (e.g. noggin, chordin, and follistatin in Xenopus) antagonize the epidermalizing factor bone morphogenetic protein 4 (BMP4), thus dividing the epiblast into neuroectoderm. In Drosophila, decapentaplegic, the homologue of BMP4, interacts similarly with the protein short gastrulation, the homologue of chordin. Thus, a comparable molecular mechanism for distinguishing non-neural ectoderm from neural ectoderm was probably present in the common ancestor of all bilaterally symmetrical animals.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001372", ontology="VHOG", source="DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000011 "After gastrulation, neural crest cells are specified at the border of the neural plate and the non-neural ectoderm." xsd:string +property_value: IAO:0000116 "todo - epidermis? todo - track down EHDAA2 class in new release" xsd:string [Term] id: UBERON:0005498 @@ -224242,7 +221380,6 @@ def: "Multi-tissue structure that arises from the heart rudiment and will become subset: vertebrate_core synonym: "early primitive heart tube" NARROW [EMAPA:16208] synonym: "primitive heart tube" EXACT [EMAPA:16215] -xref: BTO:0006179 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: EHDAA2:0001512 xref: EHDAA:424 xref: EHDAA:436 @@ -224254,8 +221391,8 @@ xref: Wikipedia:Primitive_heart_tube xref: ZFA:0000149 is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004120 ! mesoderm-derived structure -relationship: develops_from UBERON:0004291 {source="ZFA"} ! heart rudiment relationship: part_of UBERON:0000922 ! embryo +relationship: RO:0002202 UBERON:0004291 {source="ZFA"} ! develops from heart rudiment [Term] id: UBERON:0005499 @@ -224275,9 +221412,7 @@ xref: FMA:295790 xref: TAO:0001031 xref: ZFA:0001031 is_a: UBERON:0001892 ! rhombomere -relationship: develops_from UBERON:0007289 {evidence="definitional"} ! presumptive rhombomere 1 -property_value: UBPROP:0000001 "Hindbrain segment or neuromere. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001031", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000111 "1" xsd:nonNegativeInteger +relationship: RO:0002202 UBERON:0007289 ! develops from presumptive rhombomere 1 [Term] id: UBERON:0005501 @@ -224309,17 +221444,11 @@ xref: TAO:0001077 xref: ZFA:0001077 is_a: UBERON:0001048 ! primordium is_a: UBERON:0003351 ! pharyngeal epithelium -relationship: has_developmental_contribution_from UBERON:0005428 {notes="mesenchymal", source="ZFA", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! vagal neural crest -relationship: has_developmental_contribution_from UBERON:0010025 {gci_relation="part_of", gci_filler="NCBITaxon:8782", notes="Aves", source="ISBN:0073040584-table13.1"} ! dorsal part of pharyngeal pouch 3 -relationship: has_developmental_contribution_from UBERON:0010026 {gci_relation="part_of", gci_filler="NCBITaxon:40674", notes="Mammals", source="EHDAA2", source="ISBN:0073040584-table13.1"} ! ventral part of pharyngeal pouch 3 -relationship: has_developmental_contribution_from UBERON:0010027 {gci_relation="part_of", gci_filler="NCBITaxon:8782", notes="Aves", source="ISBN:0073040584-table13.1"} ! dorsal part of pharyngeal pouch 4 -relationship: has_developmental_contribution_from UBERON:0010028 {gci_relation="part_of", gci_filler="NCBITaxon:40674", notes="Mammals", source="ISBN:0073040584-table13.1"} ! ventral part of pharyngeal pouch 4 relationship: part_of UBERON:0000974 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="EHDAA2"} ! neck relationship: part_of UBERON:0002405 {source="ZFA"} ! immune system relationship: part_of UBERON:0003295 {source="EHDAA2"} ! pharyngeal gland -property_value: editor_note "we follow Kardong table 13.1 in having some developmental contribution of pouch 4 in mammals, but this isn't reflected in EHDAA2. Consider adding distinct term for mesenchyme (see EHDAA2), to indicate NC constribution." xsd:string {source="ISBN:0781714125"} -property_value: UBPROP:0000001 "A small outgrowth of the pharyngeal epithelium that is the site of lymphocyte cell production. Willett et al, 1999.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001077", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000008 "variability of developmental origin: In fish, thymic primordia are generated by all the pouches except the first. However, in avians the thymus arises from pouches 3 and 4, whereas in humans it is only generated by the third pouch[PMID:16313389] The thymus arises from the second pouch in frogs, 2-6 in cartilaginous fish, 2-3 in reptiles, 3 or 4 in bony fish, birds and mammals. The final number is variable - 5 paired organs in sharks, 4 in caecilians, 3 in urodeles, 1 in many teleost, anurans and many mammals" xsd:string {source="ISBN:0781714125"} +relationship: RO:0002254 UBERON:0005428 ! has developmental contribution from vagal neural crest +property_value: IAO:0000116 "we follow Kardong table 13.1 in having some developmental contribution of pouch 4 in mammals, but this isn't reflected in EHDAA2. Consider adding distinct term for mesenchyme (see EHDAA2), to indicate NC constribution." xsd:string {source="ISBN:0781714125"} [Term] id: UBERON:0005563 @@ -224336,11 +221465,10 @@ xref: TAO:0000080 xref: VHOG:0000269 xref: ZFA:0000080 is_a: UBERON:0003099 {source="ZFA"} ! cranial neural crest -is_a: UBERON:0005253 ! head mesenchyme +is_a: UBERON:0007213 ! mesenchyme derived from head neural crest is_a: UBERON:0007530 {source="EHDAA2"} ! migrating mesenchyme population relationship: part_of UBERON:0007213 {source="EHDAA2"} ! mesenchyme derived from head neural crest -property_value: editor_note "todo - compare ZFA and EHDAA2 representation" xsd:string -property_value: UBPROP:0000003 "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000269", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43", source="http://bgee.unil.ch/"} +property_value: IAO:0000116 "todo - compare ZFA and EHDAA2 representation" xsd:string [Term] id: UBERON:0005564 @@ -224363,11 +221491,8 @@ xref: TAO:0001262 xref: WBbt:0008366 xref: ZFA:0001262 is_a: UBERON:0001048 {source="Obol"} ! primordium -relationship: has_potential_to_develop_into UBERON:0000991 ! gonad -relationship: located_in UBERON:0002323 {gci_relation="part_of", gci_filler="NCBITaxon:33511", notes="conservatively place at deuterostome, excluding acoelomates"} ! coelemic cavity lumen relationship: part_of UBERON:0000990 {source="ZFA"} ! reproductive system -property_value: UBPROP:0000001 "Immature reproductive tissue that has not undergone final maturation into either testis or ovary.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001262", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000008 "this is a very broad grouping class" xsd:string +relationship: RO:0002387 UBERON:0000991 ! has potential to develop into gonad [Term] id: UBERON:0005565 @@ -224385,9 +221510,7 @@ xref: ZFA:0000762 is_a: UBERON:0003099 ! cranial neural crest is_a: UBERON:0007213 ! mesenchyme derived from head neural crest is_a: UBERON:0007530 {source="EHDAA2"} ! migrating mesenchyme population -is_a: UBERON:0014387 ! mesenchyme derived from neural crest -relationship: develops_from UBERON:0003849 {source="EHDAA2"} ! mesencephalic neural crest -property_value: UBPROP:0000003 "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000268", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003849 {source="EHDAA2"} ! develops from mesencephalic neural crest [Term] id: UBERON:0005567 @@ -224419,12 +221542,9 @@ is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0002329 ! somite is_a: UBERON:0005291 ! embryonic tissue intersection_of: UBERON:0002329 ! somite -intersection_of: develops_from UBERON:0009617 ! head paraxial mesoderm -relationship: develops_from UBERON:0009617 {source="EHDAA2"} ! head paraxial mesoderm +intersection_of: RO:0002202 UBERON:0009617 ! develops from head paraxial mesoderm relationship: part_of UBERON:0009617 {source="EHDAA2"} ! head paraxial mesoderm -property_value: UBPROP:0000008 "in humans this includes somites 1-4" xsd:string -property_value: UBPROP:0000011 "They provide the epaxial and hypaxial muscles of the neck, the pharyngeal and laryngeal muscles that develop in the caudal branchial arches and the musculature of the tongue. Despite their localisation in the head, myogenic precursors from occipital somites essentially follow the trunk programmes (E. H. Walters and S. D., unpublished). during evolution, have been secondarily incorporated into the head (Gans and Northcutt, 1983)" xsd:string {source="PMID:11830559"} -property_value: UBPROP:0000012 "EHDAA2 has both 'head somite' and 'head somite group', with part_of and develops_from for latter" xsd:string {external_ontology="EHDAA2"} +relationship: RO:0002202 UBERON:0009617 {source="EHDAA2"} ! develops from head paraxial mesoderm [Term] id: UBERON:0005597 @@ -224440,9 +221560,9 @@ xref: EFO:0002578 xref: EMAPA:36007 xref: XAO:0001002 is_a: UBERON:0001048 {source="XAO"} ! primordium -relationship: develops_from UBERON:0001041 {source="XAO"} ! foregut -relationship: has_potential_to_develop_into UBERON:0000170 ! pair of lungs relationship: part_of UBERON:0008947 ! respiratory primordium +relationship: RO:0002202 UBERON:0001041 {source="XAO"} ! develops from foregut +relationship: RO:0002387 UBERON:0000170 ! has potential to develop into pair of lungs [Term] id: UBERON:0005598 @@ -224475,7 +221595,6 @@ xref: Wikipedia:Dorsal_mesentery is_a: UBERON:0003281 {source="MA"} ! mesentery of stomach relationship: part_of UBERON:0002296 {source="EHDAA2"} ! dorsal mesentery relationship: part_of UBERON:0003281 {source="EHDAA2"} ! mesentery of stomach -property_value: UBPROP:0000001 "The dorsal sheet of the primitive mesentery that encloses the stomach. The greater omentum develops from the dorsal mesogastrium. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000352", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/mesogastrium"} [Term] id: UBERON:0005604 @@ -224503,7 +221622,6 @@ xref: VHOG:0001477 is_a: UBERON:0002553 ! anatomical cavity is_a: UBERON:0012467 ! enclosed anatomical space relationship: part_of UBERON:0002203 ! vasculature of eye -property_value: UBPROP:0000001 "A depression in the front of the vitreous body, lodging the lens. [adapted_from_the_definition_of_the_hyaloid_fossa]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001477", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/hyaloid+fossa"} [Term] id: UBERON:0005609 @@ -224525,9 +221643,7 @@ xref: Wikipedia:Iliac_artery xref: XAO:0000361 is_a: UBERON:0004573 ! systemic artery relationship: part_of UBERON:0010709 ! pelvic complex -relationship: supplies UBERON:0002355 ! pelvic region of trunk -property_value: IAO:0000232 "this is an extremely loose and flexible grouping class that is the superclass of the mammalian common iliac and its main brahces, together with analagous structures in other tetrapods" xsd:string -property_value: UBPROP:0000012 "we place the XAO structure here for now. In terms of analagy, it is more closely related to common iliac, but the relationships currently attached to this class are mammal specific" xsd:string {external_ontology="XAO"} +relationship: RO:0002178 UBERON:0002355 ! supplies pelvic region of trunk [Term] id: UBERON:0005610 @@ -224543,7 +221659,7 @@ xref: NCIT:C12734 xref: SCTID:281481002 xref: UMLS:C0020888 {source="ncithesaurus:Iliac_Vein"} is_a: UBERON:0001638 ! vein -relationship: drains UBERON:0010708 ! pectoral complex +relationship: RO:0002179 UBERON:0010708 ! drains pectoral complex [Term] id: UBERON:0005613 @@ -224558,8 +221674,6 @@ xref: VHOG:0000484 is_a: UBERON:0000947 ! aorta is_a: UBERON:0003513 ! trunk blood vessel relationship: part_of UBERON:0005805 ! dorsal aorta -property_value: UBPROP:0000003 "A study of embryos shows that in all vertebrates six arterial arches link the ventral aorta with a pair of lateral dorsal aortae on each side of the body. The latter unite posteriorly to form a single median dorsal aorta wich takes blood to the body.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000484", ontology="VHOG", source="ISBN:978-0174480198 Roberts MBV, Biology: a functional approach (1986) p.572", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "Contributes to the arch of aorta in humans" xsd:string {source="http://emedicine.medscape.com/article/899609-overview"} [Term] id: UBERON:0005614 @@ -224583,13 +221697,11 @@ xref: SCTID:362521008 xref: UMLS:C1182652 {source="ncithesaurus:Subcapsular_Epithelium_of_the_Lens"} xref: VHOG:0001425 is_a: UBERON:0001803 ! epithelium of lens -is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: adjacent_to UBERON:0001804 ! capsule of lens intersection_of: part_of UBERON:0000965 ! lens of camera-type eye relationship: adjacent_to UBERON:0000389 ! lens cortex relationship: adjacent_to UBERON:0001804 ! capsule of lens -property_value: UBPROP:0000010 "Cells of the subcapsular epithelium (or anterior lens cells) are mitotically active. In adult individuals they only cover the anterior 'hemisphere' of the lens. As they divide, cells gradually move towards the equator of the lens where they tranform into lens fibres. The apical part of the gradually elongating cell extends between the subcapsular epithelium and adjacent lens fibres towards the anterior pole of the lens. The basal part extends towards the posterior pole. The nucleus remains close to the equatorial plane of the lens - http://www.lab.anhb.uwa.edu.au/mb140/corepages/eye/eye.htm" xsd:string [Term] id: UBERON:0005616 @@ -224610,9 +221722,9 @@ xref: Wikipedia:Mesenteric_artery xref: XAO:0000370 is_a: UBERON:0012254 ! abdominal aorta artery intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0000160 ! intestine -relationship: supplies UBERON:0000160 ! intestine -property_value: editor_note "includes posterior and anterior mesenteric arteries, which branch from the dorsal aorta (see Kardong), and superior and inferior mesenteric arteries" xsd:string +intersection_of: RO:0002178 UBERON:0000160 ! supplies intestine +relationship: RO:0002178 UBERON:0000160 ! supplies intestine +property_value: IAO:0000116 "includes posterior and anterior mesenteric arteries, which branch from the dorsal aorta (see Kardong), and superior and inferior mesenteric arteries" xsd:string [Term] id: UBERON:0005617 @@ -224632,9 +221744,8 @@ xref: UMLS:C0025473 {source="ncithesaurus:Mesenteric_Vein"} xref: Wikipedia:Mesenteric_vein is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein -intersection_of: drains UBERON:0000160 ! intestine -relationship: drains UBERON:0000160 ! intestine -property_value: UBPROP:0000008 "In humans the inferior mesenteric vein empties into the splenic vein, the superior mesenteric vein joins the splenic vein to form the portal vein" xsd:string +intersection_of: RO:0002179 UBERON:0000160 ! drains intestine +relationship: RO:0002179 UBERON:0000160 ! drains intestine [Term] id: UBERON:0005622 @@ -224649,8 +221760,6 @@ xref: VHOG:0000485 is_a: UBERON:0000947 ! aorta is_a: UBERON:0003513 ! trunk blood vessel relationship: part_of UBERON:0005805 ! dorsal aorta -property_value: UBPROP:0000003 "A study of embryos shows that in all vertebrates six arterial arches link the ventral aorta with a pair of lateral dorsal aortae on each side of the body. The latter unite posteriorly to form a single median dorsal aorta wich takes blood to the body.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000485", ontology="VHOG", source="ISBN:978-0174480198 Roberts MBV, Biology: a functional approach (1986) p.572", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "Normally regresses in humans" xsd:string {source="http://emedicine.medscape.com/article/899609-overview"} [Term] id: UBERON:0005624 @@ -224669,8 +221778,8 @@ xref: SCTID:181342004 xref: Wikipedia:Adrenal_artery is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0002369 ! adrenal gland -relationship: supplies UBERON:0002369 ! adrenal gland +intersection_of: RO:0002178 UBERON:0002369 ! supplies adrenal gland +relationship: RO:0002178 UBERON:0002369 ! supplies adrenal gland [Term] id: UBERON:0005625 @@ -224685,10 +221794,10 @@ xref: EHDAA2:0002095 is_a: UBERON:0002553 ! anatomical cavity is_a: UBERON:0007473 ! lumen of epithelial sac intersection_of: UBERON:0002553 ! anatomical cavity -intersection_of: luminal_space_of UBERON:0010020 ! tubotympanic recess epithelium -relationship: develops_from UBERON:0007122 {source="ISBN:0073040584"} ! pharyngeal pouch 1 -relationship: luminal_space_of UBERON:0010020 ! tubotympanic recess epithelium +intersection_of: RO:0002572 UBERON:0010020 ! luminal space of tubotympanic recess epithelium relationship: part_of UBERON:0001756 {source="MA"} ! middle ear +relationship: RO:0002202 UBERON:0007122 {source="ISBN:0073040584"} ! develops from pharyngeal pouch 1 +relationship: RO:0002572 UBERON:0010020 ! luminal space of tubotympanic recess epithelium [Term] id: UBERON:0005626 @@ -224709,9 +221818,7 @@ xref: VHOG:0000351 xref: ZFA:0005133 is_a: UBERON:0003281 ! mesentery of stomach relationship: part_of UBERON:0009668 {source="EHDAA2"} ! ventral mesentery -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray984.png" xsd:anyURI -property_value: UBPROP:0000001 "The mesentery that originates from the ventral side of the peritoneal cavity.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005133", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "The ventral sheet of the primitive mesentery that encloses the stomach. The lesser omentum develops from the ventral mesogastrium. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000351", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/mesogastrium"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray984.png" xsd:anyURI [Term] id: UBERON:0005629 @@ -224727,7 +221834,6 @@ xref: XAO:0004143 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002049 ! vasculature relationship: has_part UBERON:0001981 ! blood vessel -property_value: UBPROP:0000001 "In a vascular plexus, the contents of the vessels mix. A plexus allows blood to flow via multiple routes. If one branch of the plexus is obstructed, the blood may flow via the open branches[Wikipedia:Plexus#Circulatory_system]." xsd:string {source="Wikipedia:Plexus#Circulatory_system"} [Term] id: UBERON:0005631 @@ -224736,13 +221842,10 @@ namespace: uberon def: "Intrinsic membrane that arises from embryonic germ layers and grow to surround the developing embryo." [ISBN:0073040584] xref: EHDAA2:0004714 xref: FMA:305915 -xref: MESH:D005321 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: SCTID:362840007 is_a: UBERON:0000158 ! membranous layer relationship: part_of UBERON:0016887 ! entire extraembryonic component property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-extraembryonic-membranes" xsd:anyURI -property_value: UBPROP:0000008 "stuctures homologous to the four extraembryonic membranes appear in mammals [ISBN:0073040584 (Vertebrates, Kardong)]" xsd:string -property_value: UBPROP:0000012 "EHDAA2 is a mereological sum." xsd:string {external_ontology="EHDAA2"} [Term] id: UBERON:0005636 @@ -224755,7 +221858,7 @@ is_a: UBERON:0000397 ! colonic epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001153 ! caecum relationship: part_of UBERON:0001153 ! caecum -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0005637 @@ -224789,7 +221892,7 @@ def: "An epithelium that is part of a lens vesicle." [OBOL:automatic] xref: EHDAA2:0000987 xref: EMAPA:17165 xref: VHOG:0000532 -is_a: UBERON:0000483 ! epithelium +is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0005426 ! lens vesicle relationship: part_of UBERON:0005426 ! lens vesicle @@ -224810,7 +221913,6 @@ is_a: UBERON:0000924 ! ectoderm intersection_of: UBERON:0000924 ! ectoderm intersection_of: part_of UBERON:0003066 ! pharyngeal arch 2 relationship: part_of UBERON:0003066 ! pharyngeal arch 2 -property_value: UBPROP:0000003 "In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001062", ontology="VHOG", source="DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0005661 @@ -224828,7 +221930,6 @@ is_a: UBERON:0000924 ! ectoderm intersection_of: UBERON:0000924 ! ectoderm intersection_of: part_of UBERON:0003114 ! pharyngeal arch 3 relationship: part_of UBERON:0003114 ! pharyngeal arch 3 -property_value: UBPROP:0000003 "In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000946", ontology="VHOG", source="DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0005662 @@ -224846,7 +221947,6 @@ is_a: UBERON:0000924 ! ectoderm intersection_of: UBERON:0000924 ! ectoderm intersection_of: part_of UBERON:0003115 ! pharyngeal arch 4 relationship: part_of UBERON:0003115 ! pharyngeal arch 4 -property_value: UBPROP:0000003 "In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001095", ontology="VHOG", source="DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0005664 @@ -224864,7 +221964,6 @@ is_a: UBERON:0000925 ! endoderm intersection_of: UBERON:0000925 ! endoderm intersection_of: part_of UBERON:0003066 ! pharyngeal arch 2 relationship: part_of UBERON:0003066 ! pharyngeal arch 2 -property_value: UBPROP:0000003 "In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001108", ontology="VHOG", source="DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0005665 @@ -224882,7 +221981,6 @@ is_a: UBERON:0000925 ! endoderm intersection_of: UBERON:0000925 ! endoderm intersection_of: part_of UBERON:0003114 ! pharyngeal arch 3 relationship: part_of UBERON:0003114 ! pharyngeal arch 3 -property_value: UBPROP:0000003 "In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001081", ontology="VHOG", source="DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0005666 @@ -224900,7 +221998,6 @@ is_a: UBERON:0000925 ! endoderm intersection_of: UBERON:0000925 ! endoderm intersection_of: part_of UBERON:0003115 ! pharyngeal arch 4 relationship: part_of UBERON:0003115 ! pharyngeal arch 4 -property_value: UBPROP:0000003 "In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001092", ontology="VHOG", source="DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0005667 @@ -224908,9 +222005,8 @@ name: connecting stalk mesoderm namespace: uberon xref: EHDAA2:0000314 is_a: UBERON:0003422 ! mesenchyme of umbilical cord -is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue -relationship: develops_from UBERON:0005728 {source="EHDAA2"} ! extraembryonic mesoderm +relationship: RO:0002202 UBERON:0005728 {source="EHDAA2"} ! develops from extraembryonic mesoderm [Term] id: UBERON:0005669 @@ -224929,9 +222025,8 @@ xref: FMA:18147 xref: SCTID:34073007 is_a: UBERON:0001136 ! mesothelium intersection_of: UBERON:0001136 ! mesothelium -intersection_of: located_in UBERON:0001179 ! peritoneal cavity -relationship: located_in UBERON:0001179 ! peritoneal cavity -property_value: UBPROP:0000012 "we believe that this corresponds to EMAPA:16139 based on synonyms and parenthood" xsd:string {external_ontology="EMAPA"} +intersection_of: RO:0001025 UBERON:0001179 ! located in peritoneal cavity +relationship: RO:0001025 UBERON:0001179 ! located in peritoneal cavity [Term] id: UBERON:0005672 @@ -224939,6 +222034,7 @@ name: right lung endothelium namespace: uberon def: "An endothelium that is part of a right lung." [OBOL:automatic] xref: EHDAA2:0001755 +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0001986 ! endothelium is_a: UBERON:0003364 ! epithelium of right lung intersection_of: UBERON:0001986 ! endothelium @@ -224950,6 +222046,7 @@ name: left lung endothelium namespace: uberon def: "An endothelium that is part of a left lung." [OBOL:automatic] xref: EHDAA2:0000961 +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0001986 ! endothelium is_a: UBERON:0003365 ! epithelium of left lung intersection_of: UBERON:0001986 ! endothelium @@ -225004,11 +222101,12 @@ is_a: UBERON:0003932 ! cartilage element of chondrocranium is_a: UBERON:0005863 {source="EHDAA2"} ! cartilaginous condensation is_a: UBERON:0006904 ! head mesenchyme from mesoderm is_a: UBERON:0009891 ! facial mesenchyme +is_a: UBERON:0014387 ! mesenchyme derived from neural crest is_a: UBERON:0015059 ! orbitosphenoid endochondral element intersection_of: UBERON:0015059 ! orbitosphenoid endochondral element -intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue -relationship: develops_from UBERON:0010728 {source="EHDAA2"} ! sphenoid lesser wing pre-cartilage condensation +intersection_of: RO:0002473 UBERON:0002418 ! composed primarily of cartilage tissue relationship: part_of UBERON:0009193 {source="EHDAA2"} ! sphenoid cartilage element +relationship: RO:0002202 UBERON:0010728 {source="EHDAA2"} ! develops from sphenoid lesser wing pre-cartilage condensation [Term] id: UBERON:0005688 @@ -225023,10 +222121,9 @@ xref: EMAPA:17164 xref: VHOG:0000531 is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0005426 ! lens vesicle -relationship: luminal_space_of UBERON:0005426 ! lens vesicle +intersection_of: RO:0002572 UBERON:0005426 ! luminal space of lens vesicle relationship: part_of UBERON:0005426 ! lens vesicle -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000531", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} +relationship: RO:0002572 UBERON:0005426 ! luminal space of lens vesicle [Term] id: UBERON:0005689 @@ -225045,7 +222142,6 @@ is_a: UBERON:0009494 ! pharyngeal arch mesenchymal region intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0003066 ! pharyngeal arch 2 relationship: part_of UBERON:0003066 ! pharyngeal arch 2 -property_value: UBPROP:0000003 "In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001102", ontology="VHOG", source="DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0005690 @@ -225064,7 +222160,6 @@ is_a: UBERON:0009494 ! pharyngeal arch mesenchymal region intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0003114 ! pharyngeal arch 3 relationship: part_of UBERON:0003114 ! pharyngeal arch 3 -property_value: UBPROP:0000003 "In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001083", ontology="VHOG", source="DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0005691 @@ -225083,7 +222178,6 @@ is_a: UBERON:0009494 ! pharyngeal arch mesenchymal region intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0003115 ! pharyngeal arch 4 relationship: part_of UBERON:0003115 ! pharyngeal arch 4 -property_value: UBPROP:0000003 "In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001052", ontology="VHOG", source="DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0005702 @@ -225110,8 +222204,8 @@ is_a: UBERON:0003397 ! mesentery of duodenum is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0003397 ! mesentery of duodenum intersection_of: part_of UBERON:0001041 ! foregut -relationship: develops_from UBERON:0011642 ! oral epithelium from ectoderm relationship: part_of UBERON:0001041 ! foregut +relationship: RO:0002202 UBERON:0011642 ! develops from oral epithelium from ectoderm [Term] id: UBERON:0005712 @@ -225124,7 +222218,7 @@ is_a: UBERON:0003397 ! mesentery of duodenum is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0003397 ! mesentery of duodenum intersection_of: part_of UBERON:0001045 ! midgut -relationship: develops_from UBERON:0011642 ! oral epithelium from ectoderm +relationship: RO:0002202 UBERON:0011642 ! develops from oral epithelium from ectoderm [Term] id: UBERON:0005719 @@ -225147,6 +222241,7 @@ synonym: "rhombencephalon venous system" RELATED [VHOG:0001322] xref: EHDAA2:0000776 xref: EMAPA:18632 xref: VHOG:0001322 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004582 ! venous system intersection_of: UBERON:0004582 ! venous system intersection_of: part_of UBERON:0002028 ! hindbrain @@ -225170,13 +222265,13 @@ xref: VHOG:0001239 xref: XAO:0000264 xref: ZFA:0000067 is_a: UBERON:0000926 ! mesoderm +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0000926 ! mesoderm -intersection_of: has_potential_to_develop_into UBERON:0002120 ! pronephros -relationship: has_potential_to_develop_into UBERON:0002120 ! pronephros -relationship: immediate_transformation_of UBERON:0007297 {source="Bgee:AN"} ! presumptive pronephric mesoderm +intersection_of: RO:0002387 UBERON:0002120 ! has potential to develop into pronephros relationship: part_of UBERON:0003064 {source="ZFA"} ! intermediate mesoderm -property_value: UBPROP:0000001 "Portion of tissue that consists of the mesenchymal precursor to the pronephric kidney and that begins to separate from the intermediate mesoderm at NF stage 21 and epithelializes by NF stage 30.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011090", ontology="AAO", source="XAO:curator"} +relationship: RO:0002387 UBERON:0002120 ! has potential to develop into pronephros +relationship: RO:0002495 UBERON:0007297 {source="Bgee:AN"} ! immediate transformation of presumptive pronephric mesoderm [Term] id: UBERON:0005725 @@ -225205,12 +222300,9 @@ is_a: UBERON:0005726 ! chemosensory system intersection_of: UBERON:0001032 ! sensory system intersection_of: capable_of GO:0007608 ! sensory perception of smell relationship: capable_of GO:0007608 ! sensory perception of smell -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -property_value: editor_note "consider splitting into main and accessory. See also: vomeronasal organ" xsd:string -property_value: editor_note "we make the relationship to nervous system 'overlaps', as the olfactory system includes e.g. apertures in the cranium that are not part of the nervous system" xsd:string -property_value: UBPROP:0000001 "The olfactory system is the sensory system used for olfaction, or the sense of smell. Most mammals and reptiles have two distinct parts to their olfactory system: a main olfactory system and an accessory olfactory system. The main olfactory system detects volatile, airborne substances, while the accessory olfactory system senses fluid-phase stimuli. Behavioral evidence indicates that most often, the stimuli detected by the accessory olfactory system are pheromones. The olfactory system is often spoken of along with the gustatory system as the chemosensory senses because both transduce chemical signals into perception[WP][Wikipedia:Olfactory_system]." xsd:string {source="Wikipedia:Olfactory_system"} -property_value: UBPROP:0000001 "The sensory system used for olfaction (the sense of smell).[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000978", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000008 "In mammals, the main olfactory system detects odorants that are inhaled through the nose, where they contact the main olfactory epithelium, which contains various olfactory receptors. These olfactory receptors are membrane proteins of bipolar olfactory receptor neurons in the olfactory epithelium. Rather than binding specific ligands like most receptors, olfactory receptors display affinity for a range of odor molecules. Olfactory neurons transduce receptor activation into electrical signals in neurons. The signals travel along the olfactory nerve, which belongs to the peripheral nervous system. This nerve terminates in the olfactory bulb, which belongs to the central nervous system. The complex set of olfactory receptors on different olfactory neurons can distinguish a new odor from the background environmental odors and determine the concentration of the odor[WP]." xsd:string +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +property_value: IAO:0000116 "consider splitting into main and accessory. See also: vomeronasal organ" xsd:string +property_value: IAO:0000116 "we make the relationship to nervous system 'overlaps', as the olfactory system includes e.g. apertures in the cranium that are not part of the nervous system" xsd:string [Term] id: UBERON:0005726 @@ -225237,8 +222329,8 @@ xref: VHOG:0000616 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005292 ! extraembryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue -relationship: develops_from UBERON:0003081 ! lateral plate mesoderm -relationship: develops_from UBERON:0008780 {source="EHDAA2"} ! inner cell mass derived epiblast +relationship: RO:0002202 UBERON:0003081 ! develops from lateral plate mesoderm +relationship: RO:0002202 UBERON:0008780 {source="EHDAA2"} ! develops from inner cell mass derived epiblast [Term] id: UBERON:0005729 @@ -225252,9 +222344,8 @@ xref: ZFA:0001453 is_a: UBERON:0005732 ! paired limb/fin field is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0005732 ! paired limb/fin field -intersection_of: has_potential_to_develop_into UBERON:0003413 ! pectoral appendage bud mesenchyme -relationship: has_potential_to_develop_into UBERON:0003413 ! pectoral appendage bud mesenchyme -property_value: UBPROP:0000001 "Embryonic region that develops into the pectoral fin bud.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001453", ontology="TAO", source="ZFIN:curator"} +intersection_of: RO:0002387 UBERON:0003413 ! has potential to develop into pectoral appendage bud mesenchyme +relationship: RO:0002387 UBERON:0003413 ! has potential to develop into pectoral appendage bud mesenchyme [Term] id: UBERON:0005730 @@ -225268,9 +222359,8 @@ xref: ZFA:0001454 is_a: UBERON:0005732 ! paired limb/fin field is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0005732 ! paired limb/fin field -intersection_of: has_potential_to_develop_into UBERON:0003412 ! pelvic appendage bud mesenchyme -relationship: has_potential_to_develop_into UBERON:0003412 ! pelvic appendage bud mesenchyme -property_value: UBPROP:0000001 "Embryonic region that develops into the pelvic fin bud.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001454", ontology="TAO", source="ZFIN:curator"} +intersection_of: RO:0002387 UBERON:0003412 ! has potential to develop into pelvic appendage bud mesenchyme +relationship: RO:0002387 UBERON:0003412 ! has potential to develop into pelvic appendage bud mesenchyme [Term] id: UBERON:0005732 @@ -225281,13 +222371,14 @@ subset: homology_grouping synonym: "limb/fin field of lateral plate mesoderm" EXACT [] synonym: "paired limb/fin field" EXACT [] is_a: UBERON:0002050 ! embryonic structure +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007688 ! anlage intersection_of: UBERON:0007688 ! anlage -intersection_of: has_potential_to_developmentally_contribute_to UBERON:0004357 ! paired limb/fin bud -relationship: has_potential_to_developmentally_contribute_to UBERON:0004357 ! paired limb/fin bud +intersection_of: RO:0002385 UBERON:0004357 ! has potential to developmentally contribute to paired limb/fin bud relationship: part_of UBERON:0003081 {source="ISBN:9780878932504", source="ZFA-inferred"} ! lateral plate mesoderm -property_value: editor_note "we represent the field as being a part of the LPM (consistent with ZFA, Gilbert). As a consequence, the relationship between limb bud (with is ectoderm+mesenchyme) stands in a weaker has_developmental_contribution_from relation to the field - TODO implement this." xsd:string +relationship: RO:0002385 UBERON:0004357 ! has potential to developmentally contribute to paired limb/fin bud +property_value: IAO:0000116 "we represent the field as being a part of the LPM (consistent with ZFA, Gilbert). As a consequence, the relationship between limb bud (with is ectoderm+mesenchyme) stands in a weaker has_developmental_contribution_from relation to the field - TODO implement this." xsd:string [Term] id: UBERON:0005733 @@ -225298,8 +222389,8 @@ comment: the central portion of the limb field gives rise to the limb proper. me synonym: "limb field of lateral plate mesoderm" EXACT [] is_a: UBERON:0005732 ! paired limb/fin field intersection_of: UBERON:0005732 ! paired limb/fin field -intersection_of: has_potential_to_developmentally_contribute_to UBERON:0004347 ! limb bud -relationship: has_potential_to_developmentally_contribute_to UBERON:0004347 ! limb bud +intersection_of: RO:0002385 UBERON:0004347 ! has potential to developmentally contribute to limb bud +relationship: RO:0002385 UBERON:0004347 ! has potential to developmentally contribute to limb bud [Term] id: UBERON:0005734 @@ -225321,11 +222412,10 @@ xref: Wikipedia:Tunica_externa_(vessels) is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004797 {source="cjm"} ! blood vessel layer is_a: UBERON:0005742 ! adventitia -relationship: composed_primarily_of UBERON:0011824 ! fibrous connective tissue -relationship: has_quality PATO:0002462 ! collagenous -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/3/32/Illu_artery.jpg" xsd:anyURI -property_value: editor_note "TODO - note terminological problems. WP says tunica external layer of blood vessel. FMA says tunica externa = adventitia, and is FMA adventitia covers other kinds of vessels. Here we opt for a lengthier name that attempts to disambiguate. There is no precise FMA equivalent, as FMA has tunica externa of arteries, veins, genital ducts etc as siblings" xsd:string -property_value: UBPROP:0000001 "The outermost layer of a blood vessel, surrounding the tunica media. It is mainly composed of collagen. The collagen serves to anchor the blood vessel to nearby organs, giving it stability[Wikipedia:Tunica_externa_(vessels)]." xsd:string {source="Wikipedia:Tunica_externa_(vessels)"} +relationship: RO:0000086 PATO:0002462 ! has quality collagenous +relationship: RO:0002473 UBERON:0011824 ! composed primarily of fibrous connective tissue +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/3/32/Illu_artery.jpg" xsd:anyURI +property_value: IAO:0000116 "TODO - note terminological problems. WP says tunica external layer of blood vessel. FMA says tunica externa = adventitia, and is FMA adventitia covers other kinds of vessels. Here we opt for a lengthier name that attempts to disambiguate. There is no precise FMA equivalent, as FMA has tunica externa of arteries, veins, genital ducts etc as siblings" xsd:string [Term] id: UBERON:0005740 @@ -225356,13 +222446,12 @@ synonym: "tunica advetitia" NARROW [Wikipedia:Adventitia] synonym: "tunica externa" NARROW [FMA:45635] xref: BTO:0002010 xref: FMA:45635 -xref: MESH:D063194 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: SCTID:30180000 xref: Wikipedia:Adventitia is_a: UBERON:0004923 ! organ component layer -relationship: composed_primarily_of UBERON:0002384 ! connective tissue -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Illu_esophageal_layers.jpg" xsd:anyURI +relationship: RO:0002473 UBERON:0002384 ! composed primarily of connective tissue +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Illu_esophageal_layers.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0005744 @@ -225379,8 +222468,7 @@ is_a: UBERON:0004111 ! anatomical conduit intersection_of: UBERON:0004111 ! anatomical conduit intersection_of: part_of UBERON:0001474 ! bone element relationship: part_of UBERON:0001474 ! bone element -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/81/Gray193.png" xsd:anyURI -property_value: UBPROP:0000012 "in FMA and ZFA this is a conduit space, not a conduit. Note there may be some additional disambiguation required: foramen is used loosely in the sense of any opening (e.g. foramen primum). FMA appears to use cranial conduit (undefined) in the sense of any foramen of the skull (includes mental foramen, which is not in the cranium proper)." xsd:string {external_ontology="FMA"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/81/Gray193.png" xsd:anyURI [Term] id: UBERON:0005745 @@ -225407,18 +222495,17 @@ xref: TAO:0002025 xref: VHOG:0001408 xref: Wikipedia:Optic_canal xref: ZFA:0005428 +is_a: UBERON:0004120 ! mesoderm-derived structure +is_a: UBERON:0010313 ! neural crest-derived structure is_a: UBERON:0013685 ! foramen of skull is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0013685 ! foramen of skull -intersection_of: conduit_for UBERON:0000941 ! cranial nerve II -relationship: conduit_for UBERON:0000941 ! cranial nerve II -relationship: conduit_for UBERON:0001619 ! ophthalmic artery -relationship: in_lateral_side_of UBERON:0001677 {source="FMA-abduced-lr"} ! sphenoid bone +intersection_of: RO:0002570 UBERON:0000941 ! conduit for cranial nerve II +relationship: BSPO:0000126 UBERON:0001677 {source="FMA-abduced-lr"} ! sphenoid bone relationship: part_of UBERON:0002478 ! orbitosphenoid -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/8e/Orbita_mensch.jpg" xsd:anyURI -property_value: UBPROP:0000001 "An aperture in the root of the lesser wing of the sphenoid bone transmitting the optic nerve. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001408", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/optic+foramen"} -property_value: UBPROP:0000001 "Foramen in the orbital region of the neurocranium for the passage of the optic nerve (cranial nerve II).[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002025", ontology="TAO", source="TAO:wd"} -property_value: UBPROP:0000001 "The short canal through the orbitosphenoid bone at the apex of the orbit that gives passage to the optic nerve and the opthalmic artery" xsd:string {external_class="MP:0010704", ontology="MP"} +relationship: RO:0002570 UBERON:0000941 ! conduit for cranial nerve II +relationship: RO:0002570 UBERON:0001619 ! conduit for ophthalmic artery +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8e/Orbita_mensch.jpg" xsd:anyURI [Term] id: UBERON:0005749 @@ -225429,14 +222516,12 @@ subset: pheno_slim synonym: "glomerular capillary tuft" RELATED [] synonym: "glomerulus" RELATED INCONSISTENT [EMAPA:28239] xref: EMAPA:28239 -xref: SCTID:362217000 xref: Wikipedia:Glomerulus is_a: UBERON:0000064 ! organ part is_a: UBERON:0004120 ! mesoderm-derived structure relationship: capable_of_part_of GO:0003094 ! glomerular filtration -relationship: develops_from UBERON:0003220 {source="Wikipedia"} ! metanephric mesenchyme relationship: part_of UBERON:0001230 ! glomerular capsule -property_value: UBPROP:0000011 "...Soon afterwards, endothelial cells invade to make a capillary knot-like outgrowth, the glomerular tuft, which goes on to form the glomerulus" xsd:string {source="GudMap"} +relationship: RO:0002202 UBERON:0003220 {source="Wikipedia"} ! develops from metanephric mesenchyme [Term] id: UBERON:0005750 @@ -225473,9 +222558,8 @@ is_a: UBERON:0000487 ! simple squamous epithelium is_a: UBERON:0004188 ! glomerular epithelium relationship: adjacent_to UBERON:0001286 ! Bowman's space relationship: part_of UBERON:0001230 ! glomerular capsule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: editor_note "TODO - check this. BTO has podocytes under here" xsd:string -property_value: UBPROP:0000001 "Simple squamous epithelium that lines the capsule of the renal glomerulus.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005253", ontology="TAO", source="ZFIN:curator"} +property_value: IAO:0000116 "TODO - check this. BTO has podocytes under here" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0005751 @@ -225501,11 +222585,11 @@ xref: SCTID:244093000 xref: UMLS:C0227644 {source="ncithesaurus:Visceral_Layer_of_Bowman_s_Capsule"} is_a: UBERON:0004188 ! glomerular epithelium relationship: adjacent_to UBERON:0001286 ! Bowman's space -relationship: contributes_to_morphology_of UBERON:0001230 ! glomerular capsule relationship: has_part CL:0000653 ! podocyte relationship: part_of UBERON:0001230 ! glomerular capsule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: editor_note "TODO - check - the BTO class 'glomerular epithelium' is the visceral layer. But GO uses 'glomerular epithelium' as the mereological sum of P+V layers" xsd:string +relationship: RO:0002433 UBERON:0001230 ! contributes to morphology of glomerular capsule +property_value: IAO:0000116 "TODO - check - the BTO class 'glomerular epithelium' is the visceral layer. But GO uses 'glomerular epithelium' as the mereological sum of P+V layers" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0005753 @@ -225546,13 +222630,11 @@ xref: UMLS:C1519838 {source="ncithesaurus:Urorectal_Septum"} xref: VHOG:0000018 xref: Wikipedia:Urorectal_septum is_a: UBERON:0003037 ! septum -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0001008 {source="MA"} ! renal system relationship: part_of UBERON:0012361 {source="EHDAA2"} ! internal anal region -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray992.png" xsd:anyURI -property_value: editor_note "todo - use to define cloacal septation in GO" xsd:string -property_value: UBPROP:0000001 "A ridge of mesoderm covered with endoderm that in the early developing embryo divides the endodermal cloaca into the urogenital sinus and the rectum. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000018", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/urorectal+septum"} -property_value: UBPROP:0000003 "In mammals the lowly monotremes still have a cloaca. Higher types have done away with this structure and have a separate anal outlet for the rectum. The monotreme cloaca shows the initiation of this subdivision. The cloaca has such includes only the distal part, roughly comparable to the proctodeum. The more proximal part is divided into (1) a large dorsal passage into which the intestine opens, the coprodeum, and (2) a ventral portion, the urodeum with which the bladder connects. (...) the development of the placental mammals recapitulates in many respects the phylogenetic story. In the sexually indifferent stage of placental mammal there is a cloaca. While the indifferent stage still persists, a septum develops, and extends out to the closing membrane. This divides the cloaca into two chambers: a coprodeum continuous with the gut above, and a urodeum or urogenital sinus below.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000018", ontology="VHOG", source="ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.388-89 and Figure 300", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray992.png" xsd:anyURI +property_value: IAO:0000116 "todo - use to define cloacal septation in GO" xsd:string [Term] id: UBERON:0005764 @@ -225565,9 +222647,9 @@ is_a: UBERON:0000476 ! acellular anatomical structure intersection_of: UBERON:0000476 ! acellular anatomical structure intersection_of: bounding_layer_of UBERON:0000061 ! anatomical structure relationship: bounding_layer_of UBERON:0000061 ! anatomical structure -relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 ! Fungi +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0005769 @@ -225587,12 +222669,11 @@ xref: Wikipedia:Basement_membrane is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005764 {source="FMA"} ! acellular membrane relationship: adjacent_to CL:0000066 ! epithelial cell -relationship: composed_primarily_of GO:0005604 ! basement membrane relationship: has_part GO:0005587 ! collagen type IV trimer -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa relationship: part_of UBERON:0000483 ! epithelium -relationship: present_in_taxon NCBITaxon:80999 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} -property_value: IAO:0000232 "this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell." xsd:string +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002473 GO:0005604 ! composed primarily of basement membrane +property_value: RO:0002175 NCBITaxon:80999 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} [Term] id: UBERON:0005777 @@ -225608,20 +222689,19 @@ xref: EMAPA:28251 xref: EMAPA:30965 xref: FMA:74274 xref: MA:0001659 -xref: MESH:D050533 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C32683 xref: SCTID:243897006 xref: TAO:0005285 xref: UMLS:C0599297 {source="ncithesaurus:Glomerular_Basement_Membrane"} xref: Wikipedia:Glomerular_basement_membrane xref: ZFA:0005285 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005769 ! basement membrane of epithelium intersection_of: UBERON:0005769 ! basement membrane of epithelium intersection_of: part_of UBERON:0000074 ! renal glomerulus relationship: capable_of GO:0003094 ! glomerular filtration relationship: part_of UBERON:0004188 {is_inferred="true", source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! glomerular epithelium -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/de/PhysiologieGlom%C3%A9rulaire.png" xsd:anyURI -property_value: UBPROP:0000001 "Membrane between the mesonephric podocytes and the renal glomerular capillaries. It is a trilaminar structure composed of the fused basement membranes of the glomerular capillaries and basement membrane of the podocytes. The capillary membranes touch the GBM at contact points that are separated by pores. The membrane is semi-permeable allowing water and small molecules to pass into the renal capsular space.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005285", ontology="TAO", source="ZFIN:ZDB-PUB-000824-1"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/de/PhysiologieGlom%C3%A9rulaire.png" xsd:anyURI [Term] id: UBERON:0005787 @@ -225637,6 +222717,7 @@ xref: NCIT:C32916 xref: TAO:0005286 xref: UMLS:C1235665 {source="ncithesaurus:Lamina_Densa"} xref: ZFA:0005286 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005764 ! acellular membrane intersection_of: UBERON:0005764 ! acellular membrane intersection_of: adjacent_to UBERON:0005788 ! lamina rara interna @@ -225644,8 +222725,8 @@ intersection_of: adjacent_to UBERON:0005789 ! lamina rara externa intersection_of: part_of UBERON:0005777 ! glomerular basement membrane relationship: adjacent_to UBERON:0005788 ! lamina rara interna relationship: adjacent_to UBERON:0005789 ! lamina rara externa -relationship: composed_primarily_of GO:0005604 ! basement membrane relationship: part_of UBERON:0005777 ! glomerular basement membrane +relationship: RO:0002473 GO:0005604 ! composed primarily of basement membrane [Term] id: UBERON:0005788 @@ -225661,6 +222742,7 @@ xref: TAO:0005287 xref: UMLS:C1517719 {source="ncithesaurus:Lamina_Rara_Interna"} xref: ZFA:0005287 is_a: UBERON:0000476 ! acellular anatomical structure +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000476 ! acellular anatomical structure intersection_of: adjacent_to UBERON:0001230 ! glomerular capsule intersection_of: part_of UBERON:0005777 ! glomerular basement membrane @@ -225681,6 +222763,7 @@ xref: TAO:0005288 xref: UMLS:C1517718 {source="ncithesaurus:Lamina_Rara_Externa"} xref: ZFA:0005288 is_a: UBERON:0000476 ! acellular anatomical structure +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000476 ! acellular anatomical structure intersection_of: adjacent_to UBERON:0001286 ! Bowman's space intersection_of: part_of UBERON:0005777 ! glomerular basement membrane @@ -225700,7 +222783,7 @@ xref: VHOG:0001240 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0001008 ! renal system relationship: part_of UBERON:0004122 ! genitourinary system -property_value: editor_note "TODO - check ridge vs cord vs nephrogenic cord vs blastema" xsd:string +property_value: IAO:0000116 "TODO - check ridge vs cord vs nephrogenic cord vs blastema" xsd:string [Term] id: UBERON:0005795 @@ -225710,7 +222793,7 @@ synonym: "fetal uterus" EXACT [FMA:72173] xref: FMA:72173 xref: SCTID:255782009 is_a: UBERON:0006598 ! presumptive structure -relationship: has_potential_to_develop_into UBERON:0000995 ! uterus +relationship: RO:0002387 UBERON:0000995 ! has potential to develop into uterus [Term] id: UBERON:0005800 @@ -225725,6 +222808,7 @@ xref: FMA:13087 xref: NCIT:C34027 xref: SCTID:119203005 xref: UMLS:C0506947 {source="ncithesaurus:Aortic_Segment"} +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0013522 ! subdivision of tube relationship: part_of UBERON:0000947 ! aorta @@ -225753,16 +222837,10 @@ xref: XAO:0000051 xref: ZFA:0000014 is_a: UBERON:0000947 ! aorta is_a: UBERON:0003513 ! trunk blood vessel -is_a: UBERON:0004120 ! mesoderm-derived structure -relationship: develops_from UBERON:0001917 ! endothelium of artery -relationship: develops_from UBERON:0003064 ! intermediate mesoderm relationship: part_of UBERON:0002201 ! vasculature of trunk -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray459.png" xsd:anyURI -property_value: UBPROP:0000001 "Each primitive aorta receives anteriorly a vein 'the vitelline vein' from the yolk-sac, and is prolonged backward on the lateral aspect of the notochord under the name of the dorsal aorta. The dorsal aortae give branches to the yolk-sac, and are continued backward through the body-stalk as the umbilical arteries to the villi of the chorion. The two dorsal aortae combine to become the descending aorta in later development[WP]." xsd:string {source="Wikipedia:Dorsal_aorta"} -property_value: UBPROP:0000001 "Principal unpaired, median artery of the trunk, leading from the paired roots (radices) of the dorsal aorta to the caudal artery. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000014", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "The artery in vertebrate embryos that transports blood from the aortic arches to the trunk and limbs. In adult fish it is a major artery that carries oxygenated blood from the efferent branchial arteries to branches that supply the body organ. In adult tetrapods it arises from the systemic arch" xsd:string {source="BTO:0004673"} -property_value: UBPROP:0000002 "relationship loss: part_of axial vasculature (TAO:0001073)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000014", ontology="TAO"} -property_value: UBPROP:0000003 "When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000264", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0001917 ! develops from endothelium of artery +relationship: RO:0002202 UBERON:0003064 ! develops from intermediate mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray459.png" xsd:anyURI [Term] id: UBERON:0005806 @@ -225870,7 +222948,7 @@ xref: FMA:62420 xref: MA:0003080 xref: SCTID:278748001 is_a: UBERON:0001948 ! regional part of spinal cord -property_value: editor_note "This is currently used loosely to refer to cervical, lumbar, etc as well as the metamerically repeated segments, which may correspond more closely with the ZFA neuromere term" xsd:string +property_value: IAO:0000116 "This is currently used loosely to refer to cervical, lumbar, etc as well as the metamerically repeated segments, which may correspond more closely with the ZFA neuromere term" xsd:string [Term] id: UBERON:0005845 @@ -225903,7 +222981,7 @@ xref: EHDAA2_RETIRED:0003148 xref: EHDAA:8979 is_a: UBERON:0007524 {source="AEO"} ! dense mesenchyme tissue is_a: UBERON:0011585 {source="cjm"} ! cell condensation -relationship: composed_primarily_of CL:0000335 {source="AEO-modified-relation"} ! mesenchyme condensation cell +relationship: RO:0002473 CL:0000335 {source="AEO-modified-relation"} ! composed primarily of mesenchyme condensation cell [Term] id: UBERON:0005863 @@ -225919,9 +222997,8 @@ xref: EMAPA:32731 xref: VSAO:0000092 xref: XAO:0004022 is_a: UBERON:0005856 {source="AEO"} ! developing mesenchymal condensation -relationship: develops_from UBERON:0005866 ! pre-cartilage condensation relationship: part_of UBERON:0004288 {source="AEO"} ! skeleton -property_value: UBPROP:0000012 "isa cell condensation in VSAO; has_part chondroblast in AEO" xsd:string {external_ontology="VSAO"} +relationship: RO:0002202 UBERON:0005866 ! develops from pre-cartilage condensation [Term] id: UBERON:0005865 @@ -225934,10 +223011,10 @@ xref: AEO:0000149 xref: EHDAA2_RETIRED:0003149 is_a: UBERON:0005856 ! developing mesenchymal condensation intersection_of: UBERON:0005856 ! developing mesenchymal condensation -intersection_of: composed_primarily_of CL:0000680 ! muscle precursor cell -relationship: composed_primarily_of CL:0000680 ! muscle precursor cell +intersection_of: RO:0002473 CL:0000680 ! composed primarily of muscle precursor cell relationship: has_part CL:0000680 {source="AEO"} ! muscle precursor cell -relationship: has_potential_to_develop_into UBERON:0005090 ! muscle structure +relationship: RO:0002387 UBERON:0005090 ! has potential to develop into muscle structure +relationship: RO:0002473 CL:0000680 ! composed primarily of muscle precursor cell [Term] id: UBERON:0005866 @@ -225953,9 +223030,8 @@ xref: EHDAA2:0003150 xref: EMAPA:32736 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0005856 {source="AEO"} ! developing mesenchymal condensation -relationship: has_potential_to_develop_into UBERON:0007844 ! cartilage element relationship: part_of UBERON:0004288 {source="AEO"} ! skeleton -property_value: UBPROP:0000001 "A closely packed aggregation of mesenchymal cells just prior to their differentiation into embryonic cartilage." xsd:string {source="http://dictionary.reference.com/browse/precartilage"} +relationship: RO:0002387 UBERON:0007844 ! has potential to develop into cartilage element [Term] id: UBERON:0005867 @@ -225974,9 +223050,9 @@ xref: NCIT:C34204 xref: UMLS:C1512982 {source="ncithesaurus:Mandibular_Prominence"} xref: Wikipedia:Mandibular_prominence is_a: UBERON:0012314 ! embryonic facial prominence -relationship: develops_from UBERON:0007237 ! 1st arch mandibular component relationship: part_of UBERON:0000166 ! oral opening -property_value: editor_note "check develops_from" xsd:string +relationship: RO:0002202 UBERON:0007237 ! develops from 1st arch mandibular component +property_value: IAO:0000116 "check develops_from" xsd:string [Term] id: UBERON:0005868 @@ -225997,8 +223073,8 @@ xref: SCTID:346355001 xref: UMLS:C1513037 {source="ncithesaurus:Maxillary_Prominence"} xref: Wikipedia:Maxillary_prominence is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0007238 ! 1st arch maxillary component -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray48.png" xsd:anyURI +relationship: RO:0002202 UBERON:0007238 ! develops from 1st arch maxillary component +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray48.png" xsd:anyURI [Term] id: UBERON:0005870 @@ -226019,12 +223095,11 @@ xref: Wikipedia:Nasal_pit xref: XAO:0000275 xref: XAO:0004073 is_a: UBERON:0016566 {source="EHDAA2"} ! pit -relationship: develops_from UBERON:0003050 {source="XAO:0000275 nasal pit"} ! olfactory placode -relationship: located_in UBERON:0005384 {source="EHDAA2"} ! nasal cavity epithelium relationship: part_of UBERON:0000004 {source="EMAPA"} ! nose relationship: part_of UBERON:0000922 ! embryo -property_value: editor_note "we represent the relationship as develops from, though in fact the pit is formed as an indentation in the placode" xsd:string -property_value: UBPROP:0000001 "By the upgrowth of the surrounding parts the olfactory areas are converted into pits, the nasal pits or olfactory pits, which indent the fronto-nasal process and divide it into a medial and two lateral nasal processes[Wikipedia:Nasal_pit]." xsd:string {source="Wikipedia:Nasal_pit"} +relationship: RO:0001025 UBERON:0005384 {source="EHDAA2"} ! located in nasal cavity epithelium +relationship: RO:0002202 UBERON:0003050 {source="XAO:0000275 nasal pit"} ! develops from olfactory placode +property_value: IAO:0000116 "we represent the relationship as develops from, though in fact the pit is formed as an indentation in the placode" xsd:string [Term] id: UBERON:0005872 @@ -226050,7 +223125,6 @@ intersection_of: overlaps UBERON:0003066 ! pharyngeal arch 2 intersection_of: overlaps UBERON:0004362 ! pharyngeal arch 1 relationship: overlaps UBERON:0003066 ! pharyngeal arch 2 relationship: overlaps UBERON:0004362 ! pharyngeal arch 1 -property_value: UBPROP:0000003 "In all jawed vertebrates the first arch forms the jaw, while the second arch forms the hyoid apparatus. These two arches are separated by the first pharyngeal pouch and cleft.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000969", ontology="VHOG", source="DOI:10.1016/j.semcdb.2010.01.022 Grevellec A, Tucker AS, The pharyngeal pouches and clefts: development, evolution, structure and derivatives. Seminars in Cell and Developmental Biology (2010)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0005873 @@ -226147,18 +223221,11 @@ xref: SCTID:308798005 xref: VHOG:0000583 xref: Wikipedia:Genital_tubercle is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0004874 ! somatopleure -relationship: has_potential_to_develop_into UBERON:0011757 ! differentiated genital tubercle -relationship: only_in_taxon NCBITaxon:32524 {source="https://github.com/obophenotype/uberon/issues/1230"} ! Amniota relationship: part_of UBERON:0009196 {source="EHDAA2"} ! indifferent external genitalia -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/d6/Gray1119.png" xsd:anyURI -property_value: UBPROP:0000001 "embryonic anlage of the external genitalia, which emerges as paired swellings ventral to the cloacal membrane, is proposed to be derived from all three germ layers, and gives rise to the penis, clitoris, scrotum, labia, and foreskin; GT development is indistinguishable in male and female mouse embryos until ~E16, when the urethral plate begins to be masculinized to form the penile urethra, marking the beginning of an androgen-dependent phase of sexual differentiation[MP]" xsd:string {ontology="MP"} -property_value: UBPROP:0000001 "The eminence in the embryo which develops into the clitoris or penis. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000583", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/genital+tubercle"} -property_value: UBPROP:0000003 "In mammalian embryos, male and female external genitalia develop from the genital tubercle.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000583", ontology="VHOG", source="DOI:10.1242/dev.036830 Seifert AW, Yamaguchi T, Cohn MJ, Functional and phylogenetic analysis shows that Fgf8 is a marker of genital induction in mammals but is not required for external genital development. Development (2009)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "All amniotes studied to date initiate external genital development with the formation of paired genital swellings. In mammals, archosaurs, and turtles, these swellings merge to form a single genital tubercle, the precursor of the penis and clitoris[PMID:24960313]" xsd:string -property_value: UBPROP:0000008 "GT development is indistinguishable in male and female mouse embryos until approximately E16, when the urethral plate begins to be masculinized to form the penile urethra, marking the beginning of an androgen-dependent phase of sexual differentiation[MP:0011771]" xsd:string -property_value: UBPROP:0000008 "todo - add taxon constraints" xsd:string -property_value: UBPROP:0000012 "we assume the EMAPA class is the undifferentiated form based on TS timings" xsd:string {external_ontology="EMAPA"} +relationship: RO:0002160 NCBITaxon:32524 {source="https://github.com/obophenotype/uberon/issues/1230"} ! only in taxon Amniota +relationship: RO:0002202 UBERON:0004874 ! develops from somatopleure +relationship: RO:0002387 UBERON:0011757 ! has potential to develop into differentiated genital tubercle +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d6/Gray1119.png" xsd:anyURI [Term] id: UBERON:0005879 @@ -226185,9 +223252,8 @@ is_a: UBERON:0006846 {source="EHDAA2"} ! surface groove relationship: adjacent_to UBERON:0004117 ! pharyngeal pouch relationship: overlaps UBERON:0002539 ! pharyngeal arch relationship: part_of UBERON:0016545 ! pharyngeal ectoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/20/Kiemenbogen.jpg" xsd:anyURI -property_value: editor_note "Note we use overlaps as the relationship to the arches" xsd:string -property_value: UBPROP:0000012 "EMAPA distinguishes between the groove ectoderm and epithelium, with the latter arising after the former" xsd:string {external_ontology="EMAPA"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/20/Kiemenbogen.jpg" xsd:anyURI +property_value: IAO:0000116 "Note we use overlaps as the relationship to the arches" xsd:string [Term] id: UBERON:0005881 @@ -226215,10 +223281,10 @@ synonym: "sensory part of neural tube" RELATED [] xref: neuronames:1370 xref: Wikipedia:Alar_plate is_a: UBERON:0002050 ! embryonic structure -relationship: dorsal_to UBERON:0005478 ! sulcus limitans of neural tube +relationship: BSPO:0000098 UBERON:0005478 ! sulcus limitans of neural tube relationship: has_part CL:0000101 ! sensory neuron relationship: part_of UBERON:0004061 ! neural tube mantle layer -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Gray646.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Gray646.png" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/336" xsd:anyURI [Term] @@ -226237,9 +223303,8 @@ xref: TAO:0001276 xref: XAO:0003177 xref: ZFA:0001276 is_a: UBERON:0010912 ! subdivision of skeleton -relationship: develops_from UBERON:0003066 {source="cjm"} ! pharyngeal arch 2 relationship: part_of UBERON:0008895 {source="ZFA"} ! splanchnocranium -property_value: UBPROP:0000012 "it's not clear where AAO:'hyobranchial skeleton' belongs" xsd:string {external_ontology="AAO"} +relationship: RO:0002202 UBERON:0003066 {source="cjm"} ! develops from pharyngeal arch 2 [Term] id: UBERON:0005891 @@ -226251,11 +223316,10 @@ synonym: "germinal epithelium of Waldeyer" EXACT [Wikipedia:Coelomic_epithelium] xref: Wikipedia:Coelomic_epithelium xref: XAO:0000329 is_a: UBERON:0000483 ! epithelium -relationship: has_developmental_contribution_from UBERON:0004871 {source="XAO"} ! somatic layer of lateral plate mesoderm -relationship: has_developmental_contribution_from UBERON:0004872 {source="XAO"} ! splanchnic layer of lateral plate mesoderm -relationship: located_in UBERON:0002323 ! coelemic cavity lumen relationship: part_of UBERON:0011997 ! coelom -property_value: UBPROP:0000012 "EHDAA2:0004049 used to be called 'coelomic epithelium' but is now 'gonadal ridge mesothelium'" xsd:string {external_ontology="EHDAA2"} +relationship: RO:0001025 UBERON:0002323 ! located in coelemic cavity lumen +relationship: RO:0002254 UBERON:0004871 {source="XAO"} ! has developmental contribution from somatic layer of lateral plate mesoderm +relationship: RO:0002254 UBERON:0004872 {source="XAO"} ! has developmental contribution from splanchnic layer of lateral plate mesoderm [Term] id: UBERON:0005893 @@ -226271,7 +223335,7 @@ is_a: UBERON:0003464 ! hindlimb bone intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0000978 ! leg relationship: part_of UBERON:0000978 ! leg -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0005897 @@ -226295,8 +223359,7 @@ is_a: UBERON:0011250 ! autopod bone intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0002398 ! manus relationship: part_of UBERON:0001442 ! skeleton of manus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0005899 @@ -226321,8 +223384,7 @@ is_a: UBERON:0011250 ! autopod bone intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0002387 ! pes relationship: part_of UBERON:0001445 ! skeleton of pes -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0005902 @@ -226336,7 +223398,6 @@ synonym: "occipital region of head" EXACT [FMA:49187] xref: AAO:0010199 xref: BTO:0004675 xref: FMA:49187 -xref: MESH:D009778 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: neuronames:2431 xref: SCTID:362618001 xref: TAO:0001414 @@ -226344,9 +223405,7 @@ xref: XAO:0003173 xref: ZFA:0001414 is_a: UBERON:0034921 ! multi organ part structure relationship: part_of UBERON:0003128 ! cranium -property_value: editor_note "TODO - check" xsd:string -property_value: UBPROP:0000001 "An anatomical cluster that is located in the posterior region of the neurocranium and forms the margin of the foramen margin and occipital condyles.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010199", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000001 "Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occiptal condyle.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001414", ontology="TAO", source="TAO:MAH"} +property_value: IAO:0000116 "TODO - check" xsd:string [Term] id: UBERON:0005903 @@ -226363,13 +223422,14 @@ xref: FMA:19473 xref: SCTID:279675008 xref: Wikipedia:Excretory_duct_of_seminal_gland is_a: UBERON:0000025 ! tube +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005904 ! duct of male reproductive system intersection_of: UBERON:0000058 ! duct intersection_of: part_of UBERON:0000998 ! seminal vesicle relationship: channel_for UBERON:0010143 ! seminal vesicle fluid relationship: channels_into UBERON:0000999 ! ejaculatory duct relationship: part_of UBERON:0000998 ! seminal vesicle -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/97/Gray1160.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/97/Gray1160.png" xsd:anyURI [Term] id: UBERON:0005904 @@ -226382,7 +223442,6 @@ is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0000058 ! duct intersection_of: part_of UBERON:0000079 ! male reproductive system relationship: part_of UBERON:0000079 ! male reproductive system -property_value: IAO:0000232 "this class groups the individual ducts in a variety of species" xsd:string [Term] id: UBERON:0005906 @@ -226407,8 +223466,9 @@ synonym: "subbrillar sac" NARROW [NCBITaxon:8570] xref: EMAPA:18233 xref: FMA:20291 xref: SCTID:362531001 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005906 {source="FMA"} ! serous sac -relationship: adjacent_to UBERON:0001801 {modified_from="MA"} ! anterior segment of eyeball +relationship: adjacent_to UBERON:0001801 ! anterior segment of eyeball relationship: part_of UBERON:0000019 {source="FMA"} ! camera-type eye relationship: part_of UBERON:0035639 {source="HPO:pr"} ! ocular adnexa @@ -226423,7 +223483,7 @@ xref: FMA:69065 is_a: UBERON:0000483 ! epithelium is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0000483 ! epithelium -intersection_of: develops_from UBERON:0000925 ! endoderm +intersection_of: RO:0002202 UBERON:0000925 ! develops from endoderm [Term] id: UBERON:0005913 @@ -226432,8 +223492,8 @@ namespace: uberon synonym: "bone organ zone" EXACT [FMA:10483] xref: FMA:10483 is_a: UBERON:0034944 {source="FMA"} ! zone of organ -relationship: composed_primarily_of UBERON:0002481 ! bone tissue relationship: part_of UBERON:0001474 ! bone element +relationship: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue [Term] id: UBERON:0005928 @@ -226466,17 +223526,14 @@ xref: XAO:0003033 xref: ZFA:0000550 is_a: UBERON:0000003 ! naris is_a: UBERON:0003102 {source="ZFA"} ! surface structure +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000003 ! naris -intersection_of: connects UBERON:0001707 ! nasal cavity -intersection_of: connects UBERON:0013514 ! space surrounding organism +intersection_of: RO:0002176 UBERON:0001707 ! connects nasal cavity +intersection_of: RO:0002176 UBERON:0013514 ! connects space surrounding organism relationship: capable_of_part_of GO:0007585 ! respiratory gaseous exchange by respiratory system -relationship: connects UBERON:0013514 ! space surrounding organism -relationship: contributes_to_morphology_of UBERON:0000004 ! nose relationship: part_of UBERON:0000004 ! nose -property_value: UBPROP:0000001 "Hole on the nasal capsule that connects the nasal cavity with the exterior.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000024", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000002 "relationship loss: subclass nasal opening (AAO:0000316)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000024", ontology="AAO"} -property_value: UBPROP:0000003 "In a tetrapod, the nasal sac has an external naris (homologous with the anterior naris of the fish) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000544", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.257 and Figure 7.27", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "Fish have two pairs of external nostrils." xsd:string +relationship: RO:0002176 UBERON:0013514 ! connects space surrounding organism +relationship: RO:0002433 UBERON:0000004 ! contributes to morphology of nose [Term] id: UBERON:0005932 @@ -226494,6 +223551,7 @@ xref: NCIT:C32706 xref: SCTID:361360009 xref: UMLS:C0221962 {source="ncithesaurus:Hair_Bulb"} is_a: UBERON:0000479 ! tissue +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0002073 ! hair follicle property_value: seeAlso "https://github.com/obophenotype/mouse-anatomy-ontology/issues/56" xsd:anyURI @@ -226505,6 +223563,7 @@ xref: EMAPA:18772 xref: FMA:294628 xref: MA:0000162 is_a: UBERON:0000479 ! tissue +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0005932 ! bulb of hair follicle property_value: seeAlso "https://github.com/obophenotype/mouse-anatomy-ontology/issues/56" xsd:anyURI @@ -226546,7 +223605,7 @@ xref: NCIT:C62490 xref: SCTID:319224003 xref: Wikipedia:Outer_root_sheath is_a: UBERON:0005933 ! hair root sheath -relationship: continuous_with UBERON:0005932 ! bulb of hair follicle +relationship: RO:0002150 UBERON:0005932 ! continuous with bulb of hair follicle [Term] id: UBERON:0005944 @@ -226559,7 +223618,6 @@ subset: uberon_slim synonym: "skeleton axiale" RELATED OMO:0003011 [Wikipedia:Axial_skeleton] xref: AAO:0000963 xref: EMAPA:17214 -xref: EMAPA:18043 xref: MA:0000308 xref: NCIT:C32172 xref: SCTID:361725000 @@ -226568,14 +223626,13 @@ xref: VSAO:0000056 xref: Wikipedia:Axial_skeleton xref: XAO:0004011 is_a: UBERON:0010912 ! subdivision of skeleton -relationship: connected_to UBERON:0002091 {gci_relation="part_of", gci_filler="NCBITaxon:7776"} ! appendicular skeleton -relationship: contributes_to_morphology_of UBERON:0001434 ! skeletal system -relationship: develops_from UBERON:0003089 ! sclerotome relationship: part_of UBERON:0011137 ! axial skeletal system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg" xsd:anyURI +relationship: RO:0002170 UBERON:0002091 {gci_relation="part_of", gci_filler="NCBITaxon:7776"} ! connected to appendicular skeleton +relationship: RO:0002202 UBERON:0003089 ! develops from sclerotome +relationship: RO:0002433 UBERON:0001434 ! contributes to morphology of skeletal system +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" xsd:anyURI -property_value: UBPROP:0000001 "Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000056", ontology="VSAO", source="PSPUB:0000170"} [Term] id: UBERON:0005945 @@ -226602,8 +223659,8 @@ xref: FMA:14141 is_a: UBERON:0004145 ! outflow tract intersection_of: UBERON:0004145 ! outflow tract intersection_of: part_of UBERON:0002081 ! cardiac atrium -relationship: continuous_with UBERON:0002082 ! cardiac ventricle relationship: part_of UBERON:0002081 ! cardiac atrium +relationship: RO:0002150 UBERON:0002082 ! continuous with cardiac ventricle [Term] id: UBERON:0005953 @@ -226630,9 +223687,9 @@ xref: UMLS:C1881209 {source="ncithesaurus:Infundibulum"} is_a: UBERON:0005337 ! outflow tract of ventricle intersection_of: UBERON:0005337 ! outflow tract of ventricle intersection_of: part_of UBERON:0002080 ! heart right ventricle -relationship: continuous_with UBERON:0002333 ! pulmonary trunk -relationship: develops_from UBERON:0009889 {source="PMID:17276708"} ! secondary heart field relationship: part_of UBERON:0002080 ! heart right ventricle +relationship: RO:0002150 UBERON:0002333 ! continuous with pulmonary trunk +relationship: RO:0002202 UBERON:0009889 {source="PMID:17276708"} ! develops from secondary heart field [Term] id: UBERON:0005956 @@ -226723,16 +223780,17 @@ xref: SCTID:280694002 xref: UMLS:C0040573 {source="ncithesaurus:Trabecular_Meshwork"} xref: Wikipedia:Trabecular_meshwork is_a: UBERON:0000479 ! tissue +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: has_part CL:0002367 ! trabecular meshwork cell relationship: overlaps UBERON:0006206 ! iridocorneal angle relationship: part_of UBERON:0003956 ! aqueous drainage system -relationship: surrounds UBERON:0001766 ! anterior chamber of eyeball -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/22/Gray870.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-l.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-r.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-l.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-r.glb" xsd:anyURI -property_value: editor_note "TODO check syns - ligaments" xsd:string +relationship: RO:0002221 UBERON:0001766 ! surrounds anterior chamber of eyeball +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/22/Gray870.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-l.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-r.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-l.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-r.glb" xsd:anyURI +property_value: IAO:0000116 "TODO check syns - ligaments" xsd:string [Term] id: UBERON:0005971 @@ -226743,8 +223801,8 @@ subset: pheno_slim synonym: "amnionic fold" EXACT [http://placentation.ucsd.edu/glossfs.html] xref: EMAPA:16076 is_a: UBERON:0000478 ! extraembryonic structure -relationship: develops_from UBERON:0004874 {source="ISBN:0073040584"} ! somatopleure -relationship: only_in_taxon NCBITaxon:32524 ! Amniota +relationship: RO:0002160 NCBITaxon:32524 ! only in taxon Amniota +relationship: RO:0002202 UBERON:0004874 {source="ISBN:0073040584"} ! develops from somatopleure [Term] id: UBERON:0005979 @@ -226760,8 +223818,9 @@ xref: FMA:9236 xref: SCTID:277693004 xref: Wikipedia:Crista_terminalis is_a: UBERON:0000064 ! organ part -relationship: contributes_to_morphology_of UBERON:0002078 ! right cardiac atrium +is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0002078 ! right cardiac atrium +relationship: RO:0002433 UBERON:0002078 ! contributes to morphology of right cardiac atrium [Term] id: UBERON:0005983 @@ -226770,11 +223829,12 @@ namespace: uberon def: "The laminar structure of the heart." [MP:0010545] subset: non_informative subset: pheno_slim +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004923 ! organ component layer intersection_of: UBERON:0004923 ! organ component layer intersection_of: part_of UBERON:0000948 ! heart -relationship: contributes_to_morphology_of UBERON:0000948 ! heart relationship: part_of UBERON:0000948 ! heart +relationship: RO:0002433 UBERON:0000948 ! contributes to morphology of heart [Term] id: UBERON:0005985 @@ -226785,11 +223845,12 @@ subset: pheno_slim xref: MESH:D003331 xref: Wikipedia:Coronary_circulation is_a: UBERON:0000055 ! vessel +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000055 ! vessel intersection_of: part_of UBERON:0000948 ! heart -relationship: contributes_to_morphology_of UBERON:0000948 ! heart relationship: part_of UBERON:0000948 ! heart -property_value: editor_note "TODO - change relation from part_of" xsd:string +relationship: RO:0002433 UBERON:0000948 ! contributes to morphology of heart +property_value: IAO:0000116 "TODO - change relation from part_of" xsd:string [Term] id: UBERON:0005986 @@ -226812,8 +223873,9 @@ xref: FMA:9487 xref: galen:LeftBundleBranch xref: SCTID:277690001 is_a: UBERON:0010131 ! conducting tissue of heart +is_a: UBERON:0015212 ! lateral structure is_a: UBERON:0018649 ! cardiac muscle tissue of ventricle -relationship: in_left_side_of UBERON:0002353 ! bundle of His +relationship: BSPO:0000120 UBERON:0002353 ! bundle of His relationship: part_of UBERON:0004146 {source="https://github.com/obophenotype/uberon/issues/1785", source="https://orcid.org/0000-0001-5208-3432", source="https://orcid.org/0000-0002-9791-0064"} ! His-Purkinje system [Term] @@ -226836,8 +223898,9 @@ xref: FMA:9486 xref: galen:RightBundleBranch xref: SCTID:277689005 is_a: UBERON:0010131 ! conducting tissue of heart +is_a: UBERON:0015212 ! lateral structure is_a: UBERON:0018649 ! cardiac muscle tissue of ventricle -relationship: in_right_side_of UBERON:0002353 ! bundle of His +relationship: BSPO:0000121 UBERON:0002353 ! bundle of His relationship: part_of UBERON:0004146 {source="https://github.com/obophenotype/uberon/issues/1785", source="https://orcid.org/0000-0001-5208-3432", source="https://orcid.org/0000-0002-9791-0064"} ! His-Purkinje system [Term] @@ -226854,11 +223917,12 @@ synonym: "trabecular layer of the atrium" EXACT [ZFA:0005810] xref: EMAPA:37432 {source="MA:th"} xref: ZFA:0005810 is_a: UBERON:0000440 ! trabecula +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000440 ! trabecula intersection_of: part_of UBERON:0002302 ! myocardium of atrium -relationship: contributes_to_morphology_of UBERON:0002302 ! myocardium of atrium relationship: part_of UBERON:0002302 ! myocardium of atrium relationship: part_of UBERON:0004124 {source="ZFA"} ! myocardium trabecular layer +relationship: RO:0002433 UBERON:0002302 ! contributes to morphology of myocardium of atrium [Term] id: UBERON:0005989 @@ -226878,7 +223942,7 @@ intersection_of: adjacent_to UBERON:0002078 ! right cardiac atrium intersection_of: adjacent_to UBERON:0002084 ! heart left ventricle relationship: adjacent_to UBERON:0002078 ! right cardiac atrium relationship: adjacent_to UBERON:0002084 ! heart left ventricle -relationship: develops_from UBERON:0002062 {source="PMID:15797462", source="Wikipedia"} ! endocardial cushion +relationship: RO:0002202 UBERON:0002062 {source="PMID:15797462", source="Wikipedia"} ! develops from endocardial cushion [Term] id: UBERON:0006002 @@ -226893,10 +223957,10 @@ xref: Wikipedia:Vitelline_arteries is_a: UBERON:0001637 ! artery is_a: UBERON:0004365 ! vitelline blood vessel intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0001040 ! yolk sac -relationship: connecting_branch_of UBERON:0005805 {notes="ventral branch"} ! dorsal aorta -relationship: supplies UBERON:0001040 ! yolk sac -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray31.png" xsd:anyURI +intersection_of: RO:0002178 UBERON:0001040 ! supplies yolk sac +relationship: RO:0002178 UBERON:0001040 ! supplies yolk sac +relationship: RO:0002252 UBERON:0005805 ! connecting branch of dorsal aorta +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray31.png" xsd:anyURI [Term] id: UBERON:0006003 @@ -226913,8 +223977,7 @@ xref: EMAPA:37883 {source="MA:th"} xref: Wikipedia:Skin_appendage is_a: UBERON:0000064 ! organ part relationship: part_of UBERON:0002416 ! integumental system -property_value: editor_note "add subclasses based on resolution of CARO tracker item. Also check: adnexal gland. Note that MP implicitly includes hypodermis." xsd:string -property_value: UBPROP:0000001 "the tissue or structures associated with or embedded in the skin such as hair and hair follicles, sweat glands, sebaceous glands and claws or nails[MP:0010678]" xsd:string {source="MP:0010678"} +property_value: IAO:0000116 "add subclasses based on resolution of CARO tracker item. Also check: adnexal gland. Note that MP implicitly includes hypodermis." xsd:string [Term] id: UBERON:0006004 @@ -226927,12 +223990,13 @@ synonym: "lower part of bulb of hair follicle" EXACT [FMA:70772] synonym: "lower zone of bulb of hair follicle" EXACT [FMA:70772] xref: EMAPA:37878 {source="MA:th"} xref: FMA:70772 +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0019204 ! skin epithelium relationship: adjacent_to UBERON:0000412 ! dermal papilla -relationship: contributes_to_morphology_of UBERON:0005932 ! bulb of hair follicle relationship: has_part CL:0000148 {source="FMA"} ! melanocyte relationship: has_part CL:0000453 {source="FMA"} ! Langerhans cell relationship: part_of UBERON:0005932 ! bulb of hair follicle +relationship: RO:0002433 UBERON:0005932 ! contributes to morphology of bulb of hair follicle [Term] id: UBERON:0006008 @@ -226952,11 +224016,12 @@ xref: EMAPA:37422 {source="MA:th"} xref: FMA:9497 xref: Wikipedia:Fibrous_rings_of_heart is_a: UBERON:0003837 ! thoracic segment connective tissue +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0006444 ! annulus fibrosus intersection_of: UBERON:0006444 ! annulus fibrosus intersection_of: part_of UBERON:0000948 ! heart relationship: part_of UBERON:0000948 ! heart -property_value: editor_note "TODO - compare with ZFA atrioventricular ring, part of the conduction system" xsd:string +property_value: IAO:0000116 "TODO - compare with ZFA atrioventricular ring, part of the conduction system" xsd:string [Term] id: UBERON:0006056 @@ -226964,8 +224029,8 @@ name: posterior surface of head namespace: uberon is_a: UBERON:0036215 ! anatomical surface region intersection_of: UBERON:0036215 ! anatomical surface region -intersection_of: in_posterior_side_of UBERON:0000033 ! head -relationship: in_posterior_side_of UBERON:0000033 ! head +intersection_of: BSPO:0000122 UBERON:0000033 ! head +relationship: BSPO:0000122 UBERON:0000033 ! head relationship: part_of UBERON:0000033 ! head [Term] @@ -226988,7 +224053,6 @@ synonym: "vertebra process" EXACT [] synonym: "vertebral process" EXACT [FMA:24530] xref: AAO:0000739 xref: FMA:24530 -xref: NCIT:C116112 xref: Wikipedia:Vertebral_column#Structure_of_individual_vertebrae is_a: UBERON:4100000 ! skeletal element projection relationship: part_of UBERON:0002412 ! vertebra @@ -227033,7 +224097,6 @@ is_a: UBERON:0001474 ! bone element intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0007812 ! post-anal tail relationship: part_of UBERON:0007812 ! post-anal tail -property_value: UBPROP:0000012 "MA has distinct classes for 'tail bone', 'caudal vertebra' and 'coccygeal vertebra' but these may all be equivalent. This class may be obsoleted in future." xsd:string {external_ontology="MA"} [Term] id: UBERON:0006071 @@ -227046,11 +224109,9 @@ synonym: "postsacral region" RELATED [AAO:0000082] synonym: "tail region" RELATED [AAO:0000082] xref: XAO:0000087 is_a: UBERON:0011676 ! subdivision of organism along main body axis -relationship: has_skeleton UBERON:0006076 ! caudal region of vertebral column +relationship: BSPO:0000099 UBERON:0001245 ! anus relationship: part_of UBERON:0000154 ! posterior region of body -relationship: posterior_to UBERON:0001245 ! anus -property_value: UBPROP:0000008 "This region is reduced in humans and corresponds to the coccyx" xsd:string -property_value: UBPROP:0000012 "We follow XAO is distinguishing the tail region from the tail; the tail bud is part of the tail region; the tail starts after the tail bud" xsd:string {external_ontology="XAO"} +relationship: RO:0002551 UBERON:0006076 ! has skeleton caudal region of vertebral column [Term] id: UBERON:0006072 @@ -227081,7 +224142,6 @@ intersection_of: subdivision_of UBERON:0005434 ! cervical region relationship: part_of UBERON:0002090 ! postcranial axial skeleton relationship: part_of UBERON:0012477 {source="FMA"} ! dorsal part of neck relationship: subdivision_of UBERON:0005434 ! cervical region -property_value: UBPROP:0000001 "Anterior region of the vertebral column consisting of one to 19 or 20 vertebrae.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000092", ontology="AAO", source="AAO:Duellman_and_Trueb_1994"} [Term] id: UBERON:0006073 @@ -227094,7 +224154,6 @@ synonym: "columna vertebralis thoracicus" EXACT [FMA:9140] synonym: "thoracic spine" EXACT [FMA:9140] synonym: "thoracic vertebrae series" EXACT [] synonym: "thoracic vertebral column" EXACT [FMA:9140] -xref: AAO:0000612 xref: BTO:0004150 xref: EHDAA:5063 xref: EMAPA:17396 @@ -227109,7 +224168,6 @@ intersection_of: subdivision_of UBERON:0000915 ! thoracic segment of trunk relationship: part_of UBERON:0008231 {source="FMA"} ! dorsal thoracic segment of trunk relationship: part_of UBERON:0014477 ! thoracic skeleton relationship: subdivision_of UBERON:0000915 ! thoracic segment of trunk -property_value: UBPROP:0000001 "Region of the vertebral column between the atlas and the sacrum consisting of seven to 285 vertebrae.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000612", ontology="AAO", source="AAO:Duellman_and_Trueb_1994"} [Term] id: UBERON:0006076 @@ -227131,8 +224189,6 @@ intersection_of: subdivision_of UBERON:0006071 ! caudal region relationship: part_of UBERON:0002090 ! postcranial axial skeleton relationship: part_of UBERON:0006071 ! caudal region relationship: subdivision_of UBERON:0006071 ! caudal region -property_value: UBPROP:0000001 "Region of the vertebral column posterior to the caudal-sacral region, that may consists of two or three to more than 100 vertebrae. These vertebrae exhibit a gradual reduction in the sizes of their transverse processes and zygapophyses, but these structures are never entirely absent. All caudal vertebrae bear haemal arches.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000082", ontology="AAO", source="AAO:Duellman_and_Trueb_1994"} -property_value: UBPROP:0000012 "in AAO, this is posterior to the caudal-sacral region" xsd:string {external_ontology="AAO"} [Term] id: UBERON:0006077 @@ -227180,13 +224236,14 @@ xref: UMLS:C0447584 {source="ncithesaurus:Bladder_Fundus"} xref: VHOG:0001184 xref: Wikipedia:Fundus_of_the_urinary_bladder#Fundus is_a: UBERON:0000064 ! organ part -relationship: contributes_to_morphology_of UBERON:0001255 ! urinary bladder -relationship: develops_from UBERON:0005760 {source="EHDAA2-modified"} ! urorectal septum -relationship: develops_from UBERON:0009845 {source="EHDAA2"} ! urogenital sinus mesenchyme +is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0001255 ! urinary bladder -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Urinary_Bladder.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urinary_Bladder.glb" xsd:anyURI +relationship: RO:0002202 UBERON:0005760 {source="EHDAA2-modified"} ! develops from urorectal septum +relationship: RO:0002202 UBERON:0009845 {source="EHDAA2"} ! develops from urogenital sinus mesenchyme +relationship: RO:0002433 UBERON:0001255 ! contributes to morphology of urinary bladder +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Urinary_Bladder.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urinary_Bladder.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0006098 @@ -227203,7 +224260,6 @@ xref: BAMS:BG xref: BAMS:BNC xref: BIRNLEX:1629 xref: EV:0100182 -xref: MESH:D001479 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: neuronames:224 {source="BIRNLEX:1629"} xref: UMLS:C0004781 {source="BIRNLEX:1629"} is_a: UBERON:0007245 ! nuclear complex of neuraxis @@ -227225,6 +224281,7 @@ xref: MA:0003176 xref: SCTID:279779009 xref: UMLS:C0009198 {source="BIRNLEX:2553"} xref: UMLS:C0458767 {source="BIRNLEX:2553"} +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005913 ! zone of bone organ relationship: part_of UBERON:0001844 ! cochlea @@ -227275,8 +224332,7 @@ union_of: UBERON:0006136 ! unmyelinated nerve fiber relationship: extends_fibers_into CL:0000540 ! neuron relationship: has_part GO:0030424 ! axon relationship: part_of UBERON:0001019 ! nerve fasciculus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000007 "neurofibrous" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0006135 @@ -227295,12 +224351,11 @@ intersection_of: UBERON:0006134 ! nerve fiber intersection_of: has_part GO:0043209 ! myelin sheath disjoint_from: UBERON:0006136 ! unmyelinated nerve fiber relationship: has_part GO:0043209 ! myelin sheath -relationship: never_in_taxon NCBITaxon:117569 -relationship: never_in_taxon NCBITaxon:7762 -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -relationship: present_in_taxon NCBITaxon:7776 ! Gnathostomata -property_value: editor_note "consider adding link to UBERON:0002316 ! white matter of neuraxis" xsd:string -property_value: UBPROP:0000008 "http://www1.pbrc.hawaii.edu/~danh/MyelinEvolution/evolution.html, http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=6134604, Wikipedia:Myelin#Invertebrate_myelin" xsd:string +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +property_value: IAO:0000116 "consider adding link to UBERON:0002316 ! white matter of neuraxis" xsd:string +property_value: RO:0002161 NCBITaxon:117569 +property_value: RO:0002161 NCBITaxon:7762 +property_value: RO:0002175 NCBITaxon:7776 [Term] id: UBERON:0006136 @@ -227315,7 +224370,7 @@ xref: NCIT:C33835 xref: SCTID:46920005 xref: UMLS:C0501409 {source="ncithesaurus:Unmyelinated_Nerve_Fiber"} is_a: UBERON:0006134 ! nerve fiber -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0006170 @@ -227323,6 +224378,7 @@ name: mesonephric capsule namespace: uberon def: "The mesonephric capsule is the tough fibrous layer surrounding the mesonephros, covered in a thick layer of perinephric adipose tissue." [DOI:10.1371/journal.pone.0099864, GO:0061285, GOC:mtg_kidney_jan10] is_a: UBERON:0002015 ! kidney capsule +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0002015 ! kidney capsule intersection_of: part_of UBERON:0000080 ! mesonephros relationship: part_of UBERON:0000080 ! mesonephros @@ -227388,7 +224444,6 @@ is_a: UBERON:0004135 ! distal tubule is_a: UBERON:0005330 ! mesonephric nephron epithelium intersection_of: UBERON:0004135 ! distal tubule intersection_of: part_of UBERON:0000080 ! mesonephros -property_value: UBPROP:0000012 "ZFA has terms for developing tubule" xsd:string {external_ontology="ZFA"} [Term] id: UBERON:0006192 @@ -227400,7 +224455,6 @@ is_a: UBERON:0004134 ! proximal tubule is_a: UBERON:0005330 ! mesonephric nephron epithelium intersection_of: UBERON:0004134 ! proximal tubule intersection_of: part_of UBERON:0000080 ! mesonephros -property_value: UBPROP:0000012 "ZFA has terms for developing tubule" xsd:string {external_ontology="ZFA"} [Term] id: UBERON:0006206 @@ -227434,13 +224488,14 @@ xref: EMAPA:16827 xref: VHOG:0000502 xref: Wikipedia:Aorticopulmonary_septum is_a: UBERON:0004142 ! outflow tract septum +is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0002099 ! cardiac septum intersection_of: adjacent_to UBERON:0002333 ! pulmonary trunk intersection_of: adjacent_to UBERON:0005805 ! dorsal aorta relationship: adjacent_to UBERON:0002333 ! pulmonary trunk relationship: adjacent_to UBERON:0005805 ! dorsal aorta -relationship: develops_from UBERON:0000095 {source="PMID:6844926", source="Wikipedia"} ! cardiac neural crest -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b9/Gray470.png" xsd:anyURI +relationship: RO:0002202 UBERON:0000095 {source="PMID:6844926", source="Wikipedia"} ! develops from cardiac neural crest +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b9/Gray470.png" xsd:anyURI [Term] id: UBERON:0006208 @@ -227491,13 +224546,13 @@ xref: SCTID:361412007 xref: VHOG:0000380 xref: Wikipedia:Buccopharyngeal_membrane is_a: UBERON:0003037 ! septum -relationship: has_developmental_contribution_from UBERON:0000924 ! ectoderm -relationship: has_developmental_contribution_from UBERON:0000925 ! endoderm relationship: overlaps UBERON:0000930 ! stomodeum relationship: overlaps UBERON:0001042 ! chordate pharynx relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0006264 {source="EHDAA2"} ! mouth-foregut junction -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI +relationship: RO:0002254 UBERON:0000924 ! has developmental contribution from ectoderm +relationship: RO:0002254 UBERON:0000925 ! has developmental contribution from endoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI [Term] id: UBERON:0006213 @@ -227515,9 +224570,9 @@ is_a: UBERON:0006598 ! presumptive structure is_a: UBERON:0010377 ! mesenchyme from somatopleure is_a: UBERON:0015049 ! carpus endochondral element intersection_of: UBERON:0005863 ! cartilaginous condensation -intersection_of: has_potential_to_develop_into UBERON:0001435 ! carpal bone -relationship: develops_from UBERON:0006214 ! carpus pre-cartilage condensation -relationship: has_potential_to_develop_into UBERON:0001435 ! carpal bone +intersection_of: RO:0002387 UBERON:0001435 ! has potential to develop into carpal bone +relationship: RO:0002202 UBERON:0006214 ! develops from carpus pre-cartilage condensation +relationship: RO:0002387 UBERON:0001435 ! has potential to develop into carpal bone [Term] id: UBERON:0006214 @@ -227535,10 +224590,10 @@ is_a: UBERON:0006598 ! presumptive structure is_a: UBERON:0009523 ! mesenchyme of handplate is_a: UBERON:0015049 ! carpus endochondral element intersection_of: UBERON:0005866 ! pre-cartilage condensation -intersection_of: has_potential_to_develop_into UBERON:0001435 ! carpal bone -relationship: develops_from UBERON:0003319 ! mesenchyme of carpal region -relationship: has_potential_to_develop_into UBERON:0001435 ! carpal bone +intersection_of: RO:0002387 UBERON:0001435 ! has potential to develop into carpal bone relationship: part_of UBERON:0009523 ! mesenchyme of handplate +relationship: RO:0002202 UBERON:0003319 ! develops from mesenchyme of carpal region +relationship: RO:0002387 UBERON:0001435 ! has potential to develop into carpal bone [Term] id: UBERON:0006215 @@ -227565,10 +224620,9 @@ xref: ZFA:0001440 is_a: UBERON:0001048 ! primordium is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0001048 ! primordium -intersection_of: has_potential_to_develop_into UBERON:0002037 ! cerebellum -relationship: has_potential_to_develop_into UBERON:0002037 ! cerebellum +intersection_of: RO:0002387 UBERON:0002037 ! has potential to develop into cerebellum relationship: part_of UBERON:0010092 {source="EHDAA2", source="Wikipedia"} ! future metencephalon -property_value: UBPROP:0000001 "The interface between the dorsal neuroepithelium and the roofplate of the fourth ventricle. The source of a number of migratory neuron populations of the hindbrain.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001440", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002387 UBERON:0002037 ! has potential to develop into cerebellum [Term] id: UBERON:0006217 @@ -227590,14 +224644,12 @@ xref: UMLS:C0231056 {source="ncithesaurus:Cloacal_Membrane"} xref: VHOG:0001198 xref: Wikipedia:Cloacal_membrane is_a: UBERON:0000158 ! membranous layer -relationship: contributes_to_morphology_of UBERON:0000163 ! embryonic cloaca -relationship: develops_from UBERON:0004341 {source="Wikipedia"} ! primitive streak -relationship: has_developmental_contribution_from UBERON:0000924 ! ectoderm -relationship: has_developmental_contribution_from UBERON:0000925 ! endoderm relationship: part_of UBERON:0000163 ! embryonic cloaca -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray991.png" xsd:anyURI -property_value: UBPROP:0000001 "A membrane that separates the proctodeum and the hindgut in the early embryo. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.497, see_Kardong_KV][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001198", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "In mammals, the cloaca exists as an embryonic structure that undergoes septation to become distinct urethral, anal, and genital orifices.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001198", ontology="VHOG", source="PMID:11830557 De Santa Barbara P, Roberts DJ, Tail gut endoderm and gut/genitourinary/tail development: a new tissue-specific role for Hoxa13. Development (2002)", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0004341 {source="Wikipedia"} ! develops from primitive streak +relationship: RO:0002254 UBERON:0000924 ! has developmental contribution from ectoderm +relationship: RO:0002254 UBERON:0000925 ! has developmental contribution from endoderm +relationship: RO:0002433 UBERON:0000163 ! contributes to morphology of embryonic cloaca +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray991.png" xsd:anyURI [Term] id: UBERON:0006218 @@ -227618,9 +224670,10 @@ subset: emapa_ehdaa2 xref: EHDAA2:0000340 xref: EHDAA:6002 xref: EMAPA:17749 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005865 {source="EHDAA2"} ! pre-muscle condensation -relationship: develops_from UBERON:0010963 {source="EHDAA2"} ! trunk and cervical myotome group relationship: part_of UBERON:0008713 {source="EHDAA2"} ! pectoral girdle and thoracic body wall skeletal muscle +relationship: RO:0002202 UBERON:0010963 {source="EHDAA2"} ! develops from trunk and cervical myotome group [Term] id: UBERON:0006222 @@ -227640,9 +224693,9 @@ xref: TAO:0000574 xref: ZFA:0000574 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001894 ! diencephalon -relationship: has_potential_to_develop_into UBERON:0001894 ! diencephalon +intersection_of: RO:0002387 UBERON:0001894 ! has potential to develop into diencephalon relationship: part_of UBERON:0006240 {source="EHDAA2"} ! future forebrain +relationship: RO:0002387 UBERON:0001894 ! has potential to develop into diencephalon [Term] id: UBERON:0006224 @@ -227653,8 +224706,8 @@ xref: EHDAA2:0000431 xref: EHDAA:8483 xref: EMAPA:17710 is_a: UBERON:0001048 ! primordium -relationship: has_potential_to_develop_into UBERON:0001490 ! elbow joint relationship: part_of UBERON:0003318 ! mesenchyme of elbow +relationship: RO:0002387 UBERON:0001490 ! has potential to develop into elbow joint [Term] id: UBERON:0006227 @@ -227667,12 +224720,12 @@ xref: EMAPA:18023 xref: FMA:312597 is_a: UBERON:0001048 ! primordium intersection_of: UBERON:0001048 ! primordium -intersection_of: has_potential_to_develop_into UBERON:0001679 ! ethmoid bone -relationship: develops_from UBERON:0007213 {source="EHDAA2"} ! mesenchyme derived from head neural crest -relationship: has_potential_to_develop_into UBERON:0001679 ! ethmoid bone +intersection_of: RO:0002387 UBERON:0001679 ! has potential to develop into ethmoid bone relationship: part_of UBERON:0002517 {source="FMA"} ! basicranium relationship: part_of UBERON:0011241 {source="AAO"} ! ethmoid region -property_value: editor_note "consider obsoleting, the ethmoid is endochondral?" xsd:string +relationship: RO:0002202 UBERON:0007213 {source="EHDAA2"} ! develops from mesenchyme derived from head neural crest +relationship: RO:0002387 UBERON:0001679 ! has potential to develop into ethmoid bone +property_value: IAO:0000116 "consider obsoleting, the ethmoid is endochondral?" xsd:string [Term] id: UBERON:0006232 @@ -227683,10 +224736,9 @@ synonym: "facio-acoustic preganglion complex" RELATED [EMAPA:16660] xref: EHDAA:1477 xref: EMAPA:16660 xref: RETIRED_EHDAA2:0000496 -xref: VHOG:0000715 is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0005565 ! facio-acoustic neural crest relationship: part_of UBERON:0001714 {source="EHDAA2"} ! cranial ganglion +relationship: RO:0002202 UBERON:0005565 ! develops from facio-acoustic neural crest [Term] id: UBERON:0006233 @@ -227719,8 +224771,8 @@ is_a: UBERON:0005866 ! pre-cartilage condensation is_a: UBERON:0010886 ! hindlimb pre-cartilage condensation is_a: UBERON:0015052 ! femur endochondral element intersection_of: UBERON:0015052 ! femur endochondral element -intersection_of: composed_primarily_of UBERON:0005866 ! pre-cartilage condensation -relationship: has_potential_to_develop_into UBERON:0000981 ! femur +intersection_of: RO:0002473 UBERON:0005866 ! composed primarily of pre-cartilage condensation +relationship: RO:0002387 UBERON:0000981 ! has potential to develop into femur [Term] id: UBERON:0006235 @@ -227734,12 +224786,11 @@ xref: EMAPA:16363 xref: VHOG:0000291 is_a: UBERON:1100000 ! digestive tract junction intersection_of: UBERON:0007651 ! anatomical junction -intersection_of: connects UBERON:0001041 ! foregut -intersection_of: connects UBERON:0001045 ! midgut -relationship: connects UBERON:0001041 ! foregut -relationship: connects UBERON:0001045 ! midgut +intersection_of: RO:0002176 UBERON:0001041 ! connects foregut +intersection_of: RO:0002176 UBERON:0001045 ! connects midgut relationship: part_of UBERON:0001555 ! digestive tract -property_value: UBPROP:0000003 "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000291", ontology="VHOG", source="ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11", source="http://bgee.unil.ch/"} +relationship: RO:0002176 UBERON:0001041 ! connects foregut +relationship: RO:0002176 UBERON:0001045 ! connects midgut [Term] id: UBERON:0006236 @@ -227753,8 +224804,8 @@ xref: EMAPA:18017 xref: FMA:312589 is_a: UBERON:0001048 ! primordium intersection_of: UBERON:0001048 ! primordium -intersection_of: has_potential_to_develop_into UBERON:0000209 ! tetrapod frontal bone -relationship: has_potential_to_develop_into UBERON:0000209 ! tetrapod frontal bone +intersection_of: RO:0002387 UBERON:0000209 ! has potential to develop into tetrapod frontal bone +relationship: RO:0002387 UBERON:0000209 ! has potential to develop into tetrapod frontal bone [Term] id: UBERON:0006238 @@ -227780,9 +224831,8 @@ xref: RETIRED_EHDAA2:0000591 xref: TAO:0000146 xref: ZFA:0000146 is_a: UBERON:0006598 ! presumptive structure -relationship: has_potential_to_develop_into UBERON:0000955 ! brain relationship: part_of UBERON:0002346 ! neurectoderm -property_value: UBPROP:0000001 "The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO)" xsd:string {source="http://neurolex.org/wiki/Cumbo_terms"} +relationship: RO:0002387 UBERON:0000955 ! has potential to develop into brain [Term] id: UBERON:0006239 @@ -227799,11 +224849,10 @@ is_a: UBERON:0000043 ! tendon is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0000043 ! tendon -intersection_of: has_potential_to_develop_into UBERON:0006670 ! central tendon of diaphragm -relationship: develops_from UBERON:0004161 {notes="mesenchyme", region="cranial part", source="Wikipedia"} ! septum transversum -relationship: has_potential_to_develop_into UBERON:0006670 ! central tendon of diaphragm +intersection_of: RO:0002387 UBERON:0006670 ! has potential to develop into central tendon of diaphragm relationship: part_of UBERON:0010084 {source="EHDAA2"} ! future diaphragm -property_value: UBPROP:0000011 "The cranial part of the septum transversum gives rise to the central tendon of the diaphragm and is the origin of the myoblasts that invade the pleuroperitoneal folds resulting in the formation of the muscular diaphragm." xsd:string +relationship: RO:0002202 UBERON:0004161 ! develops from septum transversum +relationship: RO:0002387 UBERON:0006670 ! has potential to develop into central tendon of diaphragm [Term] id: UBERON:0006240 @@ -227827,10 +224876,10 @@ xref: Wikipedia:Prosencephalon xref: ZFA:0000062 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001890 ! forebrain -relationship: has_potential_to_develop_into UBERON:0001890 ! forebrain +intersection_of: RO:0002387 UBERON:0001890 ! has potential to develop into forebrain relationship: part_of UBERON:0006238 ! future brain -property_value: editor_note "TODO. Add relationships to neural plate (both ZFA and EMAPA time this with the neural plate)" xsd:string +relationship: RO:0002387 UBERON:0001890 ! has potential to develop into forebrain +property_value: IAO:0000116 "TODO. Add relationships to neural plate (both ZFA and EMAPA time this with the neural plate)" xsd:string [Term] id: UBERON:0006241 @@ -227850,9 +224899,9 @@ xref: EMAPA:16755 xref: TAO:0000417 xref: ZFA:0000417 is_a: UBERON:0006598 ! presumptive structure -relationship: has_potential_to_develop_into UBERON:0001049 {source="EHDAA2"} ! neural tube -relationship: has_potential_to_develop_into UBERON:0002240 ! spinal cord relationship: part_of UBERON:0001017 ! central nervous system +relationship: RO:0002387 UBERON:0001049 {source="EHDAA2"} ! has potential to develop into neural tube +relationship: RO:0002387 UBERON:0002240 ! has potential to develop into spinal cord [Term] id: UBERON:0006242 @@ -227868,10 +224917,10 @@ xref: XAO:0004205 is_a: UBERON:0001048 ! primordium is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0001048 ! primordium -intersection_of: has_potential_to_develop_into UBERON:0002110 ! gallbladder -relationship: develops_from UBERON:0001152 {source="EHDAA2"} ! cystic duct -relationship: has_potential_to_develop_into UBERON:0002110 ! gallbladder +intersection_of: RO:0002387 UBERON:0002110 ! has potential to develop into gallbladder relationship: part_of UBERON:0004912 {source="EMAPA"} ! biliary bud +relationship: RO:0002202 UBERON:0001152 {source="EHDAA2"} ! develops from cystic duct +relationship: RO:0002387 UBERON:0002110 ! has potential to develop into gallbladder [Term] id: UBERON:0006245 @@ -227889,10 +224938,10 @@ is_a: UBERON:0005863 ! cartilaginous condensation is_a: UBERON:0010883 ! forelimb cartilage element is_a: UBERON:0015053 ! humerus endochondral element intersection_of: UBERON:0015053 ! humerus endochondral element -intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue -relationship: develops_from UBERON:0006246 {source="EHDAA2"} ! humerus pre-cartilage condensation -relationship: has_potential_to_develop_into UBERON:0000976 ! humerus +intersection_of: RO:0002473 UBERON:0002418 ! composed primarily of cartilage tissue relationship: part_of UBERON:0005258 {source="EHDAA2"} ! upper arm mesenchyme +relationship: RO:0002202 UBERON:0006246 {source="EHDAA2"} ! develops from humerus pre-cartilage condensation +relationship: RO:0002387 UBERON:0000976 ! has potential to develop into humerus [Term] id: UBERON:0006246 @@ -227910,9 +224959,9 @@ is_a: UBERON:0005866 ! pre-cartilage condensation is_a: UBERON:0010884 ! forelimb bone pre-cartilage condensation is_a: UBERON:0015053 ! humerus endochondral element intersection_of: UBERON:0015053 ! humerus endochondral element -intersection_of: composed_primarily_of UBERON:0005866 ! pre-cartilage condensation -relationship: has_potential_to_develop_into UBERON:0000976 ! humerus +intersection_of: RO:0002473 UBERON:0005866 ! composed primarily of pre-cartilage condensation relationship: part_of UBERON:0005258 {source="EHDAA2"} ! upper arm mesenchyme +relationship: RO:0002387 UBERON:0000976 ! has potential to develop into humerus [Term] id: UBERON:0006247 @@ -227926,11 +224975,12 @@ xref: EMAPA:18029 xref: VHOG:0000964 is_a: UBERON:0005256 ! trunk mesenchyme is_a: UBERON:0005866 ! pre-cartilage condensation +is_a: UBERON:0010377 ! mesenchyme from somatopleure is_a: UBERON:0015054 ! iliac endochondral element intersection_of: UBERON:0015054 ! iliac endochondral element -intersection_of: composed_primarily_of UBERON:0005866 ! pre-cartilage condensation -relationship: composed_primarily_of UBERON:0005866 ! pre-cartilage condensation -relationship: develops_from UBERON:0006210 {source="EHDAA2"} ! body-wall mesenchyme +intersection_of: RO:0002473 UBERON:0005866 ! composed primarily of pre-cartilage condensation +relationship: RO:0002202 UBERON:0006210 {source="EHDAA2"} ! develops from body-wall mesenchyme +relationship: RO:0002473 UBERON:0005866 ! composed primarily of pre-cartilage condensation [Term] id: UBERON:0006254 @@ -227946,8 +224996,8 @@ is_a: UBERON:0005863 {source="EHDAA2"} ! cartilaginous condensation is_a: UBERON:0007844 ! cartilage element is_a: UBERON:0015056 ! ischial endochondral element intersection_of: UBERON:0015056 ! ischial endochondral element -intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue -relationship: develops_from UBERON:0006255 {source="EHDAA2"} ! ischial pre-cartilage condensation +intersection_of: RO:0002473 UBERON:0002418 ! composed primarily of cartilage tissue +relationship: RO:0002202 UBERON:0006255 {source="EHDAA2"} ! develops from ischial pre-cartilage condensation [Term] id: UBERON:0006255 @@ -227961,10 +225011,11 @@ xref: EMAPA:18348 xref: VHOG:0000962 is_a: UBERON:0005256 ! trunk mesenchyme is_a: UBERON:0005866 {source="EHDAA2"} ! pre-cartilage condensation +is_a: UBERON:0010377 ! mesenchyme from somatopleure is_a: UBERON:0015056 ! ischial endochondral element intersection_of: UBERON:0015056 ! ischial endochondral element -intersection_of: composed_primarily_of UBERON:0005866 ! pre-cartilage condensation -relationship: composed_primarily_of UBERON:0005866 ! pre-cartilage condensation +intersection_of: RO:0002473 UBERON:0005866 ! composed primarily of pre-cartilage condensation +relationship: RO:0002473 UBERON:0005866 ! composed primarily of pre-cartilage condensation [Term] id: UBERON:0006256 @@ -227976,8 +225027,8 @@ xref: EHDAA:8467 xref: EMAPA:17740 is_a: UBERON:0001048 ! primordium is_a: UBERON:0006598 ! presumptive structure -relationship: has_potential_to_develop_into UBERON:0001485 ! knee joint relationship: part_of UBERON:0003321 ! mesenchyme of knee +relationship: RO:0002387 UBERON:0001485 ! has potential to develop into knee joint [Term] id: UBERON:0006260 @@ -227991,10 +225042,8 @@ xref: EMAPA:17186 xref: VHOG:0000449 is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0010188 {source="EHDAA2"} ! protuberance -relationship: develops_from UBERON:0004362 ! pharyngeal arch 1 relationship: part_of UBERON:0010056 {source="EHDAA2"} ! future tongue -property_value: UBPROP:0000001 "Primordium of the tongue; the median swelling and the distal and proximal swellings arise from the ventral aspect of the stomodeum. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000449", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/lingual+swellings"} -property_value: UBPROP:0000003 "Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000449", ontology="VHOG", source="DOI:10.1046/j.1469-7580.2002.00073.x Iwasaki S, Evolution of the structure and function of the vertebrate tongue. J Anat (2002)", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0004362 ! develops from pharyngeal arch 1 [Term] id: UBERON:0006261 @@ -228053,9 +225102,9 @@ is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0019306 ! nose epithelium relationship: adjacent_to UBERON:0004067 ! lateral nasal prominence relationship: adjacent_to UBERON:0005868 ! maxillary prominence -relationship: develops_from UBERON:0012313 {source="EHDAA2"} ! 1st arch maxillary ectoderm relationship: part_of UBERON:0000076 {source="EHDAA2"} ! external ectoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/3f/Gray163.png" xsd:anyURI +relationship: RO:0002202 UBERON:0012313 {source="EHDAA2"} ! develops from 1st arch maxillary ectoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3f/Gray163.png" xsd:anyURI [Term] id: UBERON:0006267 @@ -228073,9 +225122,8 @@ is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium -relationship: develops_from UBERON:0006268 {source="EHDAA2"} ! notochordal process -property_value: editor_note "TODO - check ordering; awaiting confirmation from JB" xsd:string -property_value: UBPROP:0000001 "The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001212", ontology="VHOG", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0006268 {source="EHDAA2"} ! develops from notochordal process +property_value: IAO:0000116 "TODO - check ordering; awaiting confirmation from JB" xsd:string [Term] id: UBERON:0006268 @@ -228094,8 +225142,8 @@ xref: NCIT:C34232 xref: UMLS:C1518430 {source="ncithesaurus:Notochordal_Process"} xref: VHOG:0001213 is_a: UBERON:0005423 ! developing anatomical structure -relationship: develops_from UBERON:0000924 {source="EHDAA2"} ! ectoderm -relationship: only_in_taxon NCBITaxon:7711 ! Chordata +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002202 UBERON:0000924 {source="EHDAA2"} ! develops from ectoderm [Term] id: UBERON:0006271 @@ -228107,6 +225155,7 @@ xref: EHDAA2:0001328 xref: EHDAA:10648 xref: EMAPA:18717 xref: SCTID:280546005 +is_a: UBERON:0010313 ! neural crest-derived structure is_a: UBERON:0013685 ! foramen of skull intersection_of: UBERON:0013685 ! foramen of skull intersection_of: part_of UBERON:0001697 ! orbit of skull @@ -228129,9 +225178,8 @@ xref: NCIT:C34238 xref: VHOG:0001147 xref: Wikipedia:Otic_pit is_a: UBERON:0016566 {source="EHDAA2"} ! pit -relationship: has_potential_to_develop_into UBERON:0003051 ! ear vesicle relationship: part_of UBERON:0003069 ! otic placode -property_value: UBPROP:0000001 "A depression appearing in each otic placode, marking the beginnning of embryonic development of the internal ear. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001147", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/Otic+pit"} +relationship: RO:0002387 UBERON:0003051 ! has potential to develop into ear vesicle [Term] id: UBERON:0006279 @@ -228142,20 +225190,18 @@ subset: emapa_ehdaa2 synonym: "pleuroperitoneal channel" RELATED [VHOG:0001505] xref: EHDAA2:0001481 xref: EHDAA:4128 -xref: EMAPA:17704 xref: EMAPA:17707 xref: SCTID:361413002 xref: VHOG:0001505 is_a: UBERON:0003914 {source="EHDAA2"} ! epithelial tube is_a: UBERON:0005291 ! embryonic tissue intersection_of: UBERON:0003914 ! epithelial tube -intersection_of: connects UBERON:0001179 ! peritoneal cavity -intersection_of: connects UBERON:0002402 ! pleural cavity -relationship: connects UBERON:0001179 ! peritoneal cavity -relationship: connects UBERON:0002402 ! pleural cavity -relationship: only_in_taxon NCBITaxon:7711 ! Chordata +intersection_of: RO:0002176 UBERON:0001179 ! connects peritoneal cavity +intersection_of: RO:0002176 UBERON:0002402 ! connects pleural cavity relationship: part_of UBERON:0011997 {source="EHDAA2"} ! coelom -property_value: UBPROP:0000001 "Each of the canal that links the peritoneal cavity and the caudal part of a pleural cavity. [ISBN:0124020607][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001505", ontology="VHOG", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002176 UBERON:0001179 ! connects peritoneal cavity +relationship: RO:0002176 UBERON:0002402 ! connects pleural cavity [Term] id: UBERON:0006283 @@ -228182,9 +225228,9 @@ xref: TAO:0002231 xref: Wikipedia:Embryonic_ventricle xref: ZFA:0001719 is_a: UBERON:0006598 ! presumptive structure -relationship: has_potential_to_develop_into UBERON:0002082 ! cardiac ventricle relationship: part_of UBERON:0004141 {source="ZFA"} ! heart tube relationship: part_of UBERON:0005498 {source="EMAPA"} ! primitive heart tube +relationship: RO:0002387 UBERON:0002082 ! has potential to develop into cardiac ventricle [Term] id: UBERON:0006284 @@ -228206,7 +225252,6 @@ xref: VHOG:0000644 xref: ZFA:0001259 is_a: UBERON:0013150 ! future brain vesicle relationship: part_of UBERON:0006240 {source="EHDAA2"} ! future forebrain -property_value: UBPROP:0000003 "The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000644", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500", source="http://bgee.unil.ch/"} [Term] id: UBERON:0006288 @@ -228222,9 +225267,9 @@ is_a: UBERON:0005863 {source="EHDAA2"} ! cartilaginous condensation is_a: UBERON:0007844 ! cartilage element is_a: UBERON:0015019 ! rib endochondral element intersection_of: UBERON:0015019 ! rib endochondral element -intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue -relationship: develops_from UBERON:0006289 {source="EHDAA2"} ! rib pre-cartilage condensation -relationship: has_potential_to_develop_into UBERON:0002228 ! rib +intersection_of: RO:0002473 UBERON:0002418 ! composed primarily of cartilage tissue +relationship: RO:0002202 UBERON:0006289 {source="EHDAA2"} ! develops from rib pre-cartilage condensation +relationship: RO:0002387 UBERON:0002228 ! has potential to develop into rib [Term] id: UBERON:0006289 @@ -228239,10 +225284,10 @@ xref: VHOG:0000681 is_a: UBERON:0005866 {source="EHDAA2"} ! pre-cartilage condensation is_a: UBERON:0015019 ! rib endochondral element intersection_of: UBERON:0015019 ! rib endochondral element -intersection_of: composed_primarily_of UBERON:0005866 ! pre-cartilage condensation -relationship: composed_primarily_of UBERON:0005866 ! pre-cartilage condensation -relationship: develops_from UBERON:0003089 {source="EHDAA2-abduced", source="ZFA"} ! sclerotome -relationship: has_potential_to_develop_into UBERON:0002228 ! rib +intersection_of: RO:0002473 UBERON:0005866 ! composed primarily of pre-cartilage condensation +relationship: RO:0002202 UBERON:0003089 {source="EHDAA2-abduced", source="ZFA"} ! develops from sclerotome +relationship: RO:0002387 UBERON:0002228 ! has potential to develop into rib +relationship: RO:0002473 UBERON:0005866 ! composed primarily of pre-cartilage condensation [Term] id: UBERON:0006290 @@ -228257,10 +225302,10 @@ xref: VHOG:0001125 is_a: UBERON:0007844 ! cartilage element is_a: UBERON:0015057 ! scapula endochondral element intersection_of: UBERON:0015057 ! scapula endochondral element -intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue -relationship: develops_from UBERON:0006291 {source="EHDAA2"} ! scapula pre-cartilage condensation -relationship: has_potential_to_develop_into UBERON:0006849 ! scapula +intersection_of: RO:0002473 UBERON:0002418 ! composed primarily of cartilage tissue relationship: part_of UBERON:0000922 ! embryo +relationship: RO:0002202 UBERON:0006291 {source="EHDAA2"} ! develops from scapula pre-cartilage condensation +relationship: RO:0002387 UBERON:0006849 ! has potential to develop into scapula [Term] id: UBERON:0006291 @@ -228274,11 +225319,10 @@ xref: EMAPA:18027 xref: VHOG:0000960 is_a: UBERON:0015057 ! scapula endochondral element intersection_of: UBERON:0015057 ! scapula endochondral element -intersection_of: composed_primarily_of UBERON:0005866 ! pre-cartilage condensation -relationship: composed_primarily_of UBERON:0005866 ! pre-cartilage condensation -relationship: develops_from UBERON:0006210 {source="EHDAA2"} ! body-wall mesenchyme -relationship: has_potential_to_develop_into UBERON:0006849 ! scapula -property_value: UBPROP:0000011 "the scapula has been shown to develop from multiple tissues, such as the dermomyotome of the somites, the mesodermal portion of the soma- topleure (a domain of the lateral plate mesoderm or LPM) and neural crest cell-derived mesenchyme (Huang et al., 2000; Matsuoka et al., 2005; Wang et al., 2005)." xsd:string {source="PMID:21455939"} +intersection_of: RO:0002473 UBERON:0005866 ! composed primarily of pre-cartilage condensation +relationship: RO:0002202 UBERON:0006210 {source="EHDAA2"} ! develops from body-wall mesenchyme +relationship: RO:0002387 UBERON:0006849 ! has potential to develop into scapula +relationship: RO:0002473 UBERON:0005866 ! composed primarily of pre-cartilage condensation [Term] id: UBERON:0006292 @@ -228290,10 +225334,9 @@ xref: EHDAA:8493 xref: EMAPA:17712 is_a: UBERON:0003322 ! mesenchyme of shoulder is_a: UBERON:0005856 {source="EHDAA2"} ! developing mesenchymal condensation -relationship: develops_from UBERON:0003322 {source="EHDAA2"} ! mesenchyme of shoulder -relationship: has_potential_to_develop_into UBERON:0001470 ! glenohumeral joint relationship: part_of UBERON:0003322 ! mesenchyme of shoulder -property_value: UBPROP:0000012 "this is part of the forelimb skeleton in EHDAA2, but this violates part-disjointness" xsd:string {external_ontology="EHDAA2"} +relationship: RO:0002202 UBERON:0003322 {source="EHDAA2"} ! develops from mesenchyme of shoulder +relationship: RO:0002387 UBERON:0001470 ! has potential to develop into glenohumeral joint [Term] id: UBERON:0006293 @@ -228313,10 +225356,10 @@ xref: XAO:0000326 is_a: UBERON:0001048 {source="XAO"} ! primordium is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0003104 ! mesenchyme +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue -relationship: develops_from UBERON:0004872 {source="XAO"} ! splanchnic layer of lateral plate mesoderm relationship: part_of UBERON:0005602 {source="EHDAA2-modified"} ! dorsal mesogastrium -property_value: UBPROP:0000012 "check difference between splenic and spleen in EMAPA; note that in EHDAA2 the class 'spleen' refers to the mesenchyme" xsd:string {external_ontology="EMAPA"} +relationship: RO:0002202 UBERON:0004872 {source="XAO"} ! develops from splanchnic layer of lateral plate mesoderm [Term] id: UBERON:0006304 @@ -228330,9 +225373,9 @@ xref: EHDAA:924 xref: EMAPA:16663 xref: RETIRED_EHDAA2:0002089 is_a: UBERON:0003869 ! presumptive ganglion -relationship: develops_from UBERON:0005563 ! trigeminal neural crest -relationship: has_potential_to_develop_into UBERON:0001675 ! trigeminal ganglion -relationship: transformation_of UBERON:0003070 {source="EHDAA2"} ! trigeminal placode complex +relationship: RO:0002202 UBERON:0005563 ! develops from trigeminal neural crest +relationship: RO:0002387 UBERON:0001675 ! has potential to develop into trigeminal ganglion +relationship: RO:0002494 UBERON:0003070 {source="EHDAA2"} ! transformation of trigeminal placode complex [Term] id: UBERON:0006311 @@ -228350,11 +225393,12 @@ xref: NCIT:C32301 xref: SCTID:280540004 xref: UMLS:C0459556 {source="ncithesaurus:Chamber_of_the_Eye"} is_a: UBERON:0000063 ! organ subunit +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000063 ! organ subunit -intersection_of: location_of UBERON:0006312 ! ocular refractive media intersection_of: part_of UBERON:0000019 ! camera-type eye -relationship: location_of UBERON:0006312 ! ocular refractive media +intersection_of: RO:0001015 UBERON:0006312 ! location of ocular refractive media relationship: part_of UBERON:0000019 ! camera-type eye +relationship: RO:0001015 UBERON:0006312 ! location of ocular refractive media [Term] id: UBERON:0006312 @@ -228364,7 +225408,6 @@ def: "Body substance in a liquid or semi-solid state in the eyeball which serves xref: MA:0001911 is_a: UBERON:0000463 ! organism substance relationship: part_of UBERON:0000019 ! camera-type eye -property_value: UBPROP:0000009 "ocular refraction" xsd:string [Term] id: UBERON:0006314 @@ -228383,8 +225426,8 @@ xref: MESH:D001826 xref: Wikipedia:Body_fluid is_a: UBERON:0000463 ! organism substance intersection_of: UBERON:0000463 ! organism substance -intersection_of: has_quality PATO:0001548 ! quality of a liquid -relationship: has_quality PATO:0001548 ! quality of a liquid +intersection_of: RO:0000086 PATO:0001548 ! has quality quality of a liquid +relationship: RO:0000086 PATO:0001548 ! has quality quality of a liquid [Term] id: UBERON:0006331 @@ -228414,10 +225457,7 @@ xref: XAO:0000465 xref: ZFA:0000944 is_a: UBERON:0010202 ! lateral line disjoint_from: UBERON:2001470 {source="lexical"} ! anterior lateral line -property_value: editor_note "check XAO/AAO" xsd:string -property_value: UBPROP:0000001 "One of eight distinct lateral lines in the 4-day larva. A sensory system on the surface of the fish, consisting of small sensory patches (neuromasts) distributed in discrete lines over the body surface. The lateral line system is stimulated by local water displacements and vibrations, and detects propulsion of the fish through the water, as well as facilitating shoaling, prey capture, and predator and obstacle avoidance. (See Anatomical Atlas entry for lateral line by T. Whitfield.)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000944", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000002 "relationship loss: develops_from posterior lateral line primordium (TAO:0001157)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000944", ontology="TAO"} -property_value: UBPROP:0000002 "relationship loss: part_of posterior lateral line system (TAO:0001471)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000944", ontology="TAO"} +property_value: IAO:0000116 "check XAO/AAO" xsd:string [Term] id: UBERON:0006338 @@ -228429,7 +225469,7 @@ is_a: UBERON:0005206 ! choroid plexus stroma intersection_of: UBERON:0005206 ! choroid plexus stroma intersection_of: part_of UBERON:0002285 ! telencephalic ventricle relationship: part_of UBERON:0002307 ! choroid plexus of lateral ventricle -property_value: editor_note "definitions should be fixed to use generic stroma class" xsd:string +property_value: IAO:0000116 "definitions should be fixed to use generic stroma class" xsd:string [Term] id: UBERON:0006340 @@ -228467,8 +225507,8 @@ xref: NCIT:C52851 xref: UMLS:C1707451 {source="ncithesaurus:Communicating_Artery"} is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery -intersection_of: connects UBERON:0001637 {cardinality="2"} ! artery -relationship: connects UBERON:0001637 ! artery +intersection_of: RO:0002176 UBERON:0001637 {cardinality="2"} ! connects artery +relationship: RO:0002176 UBERON:0001637 ! connects artery [Term] id: UBERON:0006355 @@ -228479,10 +225519,10 @@ xref: EMAPA:18646 xref: MA:0002227 is_a: UBERON:0002460 {is_inferred="true", source="MA"} ! vesical vein intersection_of: UBERON:0001638 ! vein -intersection_of: drains UBERON:0000056 ! ureter -relationship: drains UBERON:0000056 ! ureter -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: editor_note "inferred from artery" xsd:string +intersection_of: RO:0002179 UBERON:0000056 ! drains ureter +relationship: RO:0002179 UBERON:0000056 ! drains ureter +property_value: IAO:0000116 "inferred from artery" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0006376 @@ -228516,13 +225556,13 @@ xref: EMAPA:29769 xref: MA:0000406 xref: SCTID:27962002 xref: Wikipedia:Baculum +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0007719 ! bone of reproductive organ intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0000989 ! penis -relationship: never_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: only_in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia relationship: part_of UBERON:0000989 ! penis -property_value: UBPROP:0000008 "found in most mammals, with the exception of humans" xsd:string +relationship: RO:0002160 NCBITaxon:40674 {source="Wikipedia"} ! only in taxon Mammalia +property_value: RO:0002161 NCBITaxon:9606 [Term] id: UBERON:0006440 @@ -228536,15 +225576,16 @@ synonym: "clitoris bone" EXACT [] synonym: "os clitoridis" EXACT [Wikipedia:Baculum] xref: EMAPA:30823 xref: MA:0000387 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0007719 ! bone of reproductive organ intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0002411 ! clitoris -relationship: contributes_to_morphology_of UBERON:0001434 ! skeletal system -relationship: contributes_to_morphology_of UBERON:0002411 ! clitoris -relationship: never_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: only_in_taxon NCBITaxon:40674 {source="Wikipedia"} ! Mammalia relationship: part_of UBERON:0002411 ! clitoris +relationship: RO:0002160 NCBITaxon:40674 {source="Wikipedia"} ! only in taxon Mammalia +relationship: RO:0002433 UBERON:0001434 ! contributes to morphology of skeletal system +relationship: RO:0002433 UBERON:0002411 ! contributes to morphology of clitoris relationship: sexually_homologous_to UBERON:0006435 ! os penis +property_value: RO:0002161 NCBITaxon:9606 [Term] id: UBERON:0006444 @@ -228557,9 +225598,7 @@ synonym: "anulus fibrosus" EXACT [FMA:76704] synonym: "fibrocartilaginous ring" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "fibrous ring" RELATED [BTO:0003627] xref: BTO:0003627 -xref: EMAPA:32670 xref: FMA:76704 -xref: MESH:D000070616 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} is_a: UBERON:0001995 ! fibrocartilage [Term] @@ -228578,7 +225617,6 @@ is_a: UBERON:0000101 ! lobe of lung intersection_of: UBERON:0000101 ! lobe of lung intersection_of: part_of UBERON:0002167 ! right lung relationship: part_of UBERON:0002167 ! right lung -property_value: UBPROP:0000008 "4 in mice, divided into 3 in human by two interlobal fissures" xsd:string {source="ISBN:0123813611"} [Term] id: UBERON:0006524 @@ -228592,9 +225630,10 @@ xref: BTO:0000136 xref: CALOHA:TS-1296 xref: EMAPA:32692 xref: MA:0000416 +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0011216 ! organ system subdivision -relationship: contributes_to_morphology_of UBERON:0002048 ! lung relationship: part_of UBERON:0002048 ! lung +relationship: RO:0002433 UBERON:0002048 ! contributes to morphology of lung [Term] id: UBERON:0006525 @@ -228602,6 +225641,7 @@ name: left lung alveolar system namespace: uberon xref: EMAPA:19001 xref: MA:0001775 +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0011216 ! organ system subdivision relationship: part_of UBERON:0002168 ! left lung relationship: part_of UBERON:0006524 ! alveolar system @@ -228612,6 +225652,7 @@ name: right lung alveolar system namespace: uberon xref: EMAPA:35717 xref: MA:0001784 +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0011216 ! organ system subdivision relationship: part_of UBERON:0002167 ! right lung relationship: part_of UBERON:0006524 ! alveolar system @@ -228641,10 +225682,6 @@ intersection_of: produced_by UBERON:0005399 ! male reproductive gland relationship: capable_of_part_of GO:0048240 ! sperm capacitation relationship: capable_of_part_of GO:1902093 ! positive regulation of flagellated sperm motility relationship: part_of UBERON:0001968 ! semen -property_value: IAO:0000232 "this ontology contains a number of subtypes of seminal fluid, defined according to glands (which are more taxonomically restricted)" xsd:string -property_value: IAO:0000232 "we follow FMA and make this class a generic superclass of the secretions of different glands (prostate, bulbo-urethreal, seminal vesicle). MA (and ncit) follows a mixture model, where these secretions are part of the seminal fluid" xsd:string -property_value: UBPROP:0000008 "This term covers a variety of species. Example: In D. melanogaster, seminal fluid proteins affect female receptivity, ovulation, oogenesis, sperm storage, sperm competition and mating plug formation" xsd:string {source="DOI:10.1046/j.1365-2540.2001.00961.x"} -property_value: UBPROP:0000009 "seminal fluid may have a role in sperm capacitation, sperm motility" xsd:string [Term] id: UBERON:0006534 @@ -228778,7 +225815,7 @@ is_a: UBERON:0006876 ! vasculature of organ intersection_of: UBERON:0002049 ! vasculature intersection_of: part_of UBERON:0002113 ! kidney relationship: part_of UBERON:0002113 ! kidney -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0006553 @@ -228791,7 +225828,6 @@ is_a: UBERON:0000058 ! duct intersection_of: UBERON:0000058 ! duct intersection_of: part_of UBERON:0002113 ! kidney relationship: part_of UBERON:0002113 ! kidney -property_value: UBPROP:0000012 "in ZFA this is defined as part of mesonephros" xsd:string {external_ontology="ZFA"} [Term] id: UBERON:0006555 @@ -228826,10 +225862,7 @@ xref: Wikipedia:Lymphatic_system is_a: UBERON:0011216 ! organ system subdivision relationship: part_of UBERON:0001009 {source="AAO"} ! circulatory system relationship: part_of UBERON:0002465 {source="FMA", source="MA"} ! lymphoid system -property_value: editor_note "consider merging with lymph vasculature" xsd:string -property_value: UBPROP:0000001 "Part of the circulatory system which consists of a series of vessels which collect blood (exclusive of erythrocytes) which seep through capillary walls and return it to the veins.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010522", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000007 "lymporeticular" xsd:string -property_value: UBPROP:0000012 "in FMA this is part of the cardiovascular system, but here we treat the CV system as a separate component of the circulatory system from the lymphatic system" xsd:string {external_ontology="FMA"} +property_value: IAO:0000116 "consider merging with lymph vasculature" xsd:string [Term] id: UBERON:0006561 @@ -228854,11 +225887,7 @@ xref: MAT:0000049 xref: MESH:D010614 xref: MIAA:0000049 is_a: UBERON:0004921 ! subdivision of digestive tract -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -property_value: IAO:0000232 "currently this is an extremely generic class, encompassing both protostomes and deuterostomes." xsd:string -property_value: IAO:0006012 "2023-04-20" xsd:string -property_value: UBPROP:0000007 "branchial" xsd:string -property_value: UBPROP:0000007 "pharyngeal" xsd:string +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria [Term] id: UBERON:0006563 @@ -228892,7 +225921,6 @@ is_a: UBERON:0012240 ! urethral meatus intersection_of: UBERON:0012240 ! urethral meatus intersection_of: part_of UBERON:0003100 ! female organism relationship: part_of UBERON:0001334 ! female urethra -property_value: UBPROP:0000001 "The external urethral orifice (urinary meatus) is the external opening of the urethra, from which urine is ejected during urination. It is placed about 2.5 cm behind the glans clitoridis and immediately in front of that of the vagina; it usually assumes the form of a short, sagittal cleft with slightly raised margins. To its left and right are the openings of the Skene's ducts." xsd:string {source="Wikipedia:External_urethral_orifice_(female)"} [Term] id: UBERON:0006566 @@ -228902,17 +225930,15 @@ def: "A myocardium that is part of a left ventricle of a heart." [http://orcid.o subset: human_reference_atlas synonym: "left ventricular myocardium" EXACT [FMA:9558] synonym: "myocardium of left ventricle" EXACT [FMA:9558] -xref: EMAPA:17339 xref: FMA:9558 xref: MA:0002983 xref: SCTID:362021000 is_a: UBERON:0001083 ! myocardium of ventricle intersection_of: UBERON:0001083 ! myocardium of ventricle intersection_of: part_of UBERON:0002084 ! heart left ventricle -relationship: continuous_with UBERON:0003618 ! aorta tunica media relationship: part_of UBERON:0002084 ! heart left ventricle -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000001 "Myocardium of ventricle which is continuous with the tunica media of aorta." xsd:string {source="FMA:9558"} +relationship: RO:0002150 UBERON:0003618 ! continuous with aorta tunica media +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0006567 @@ -228923,17 +225949,15 @@ subset: human_reference_atlas subset: pheno_slim synonym: "myocardium of right ventricle" EXACT [FMA:9535] synonym: "right ventricular myocardium" EXACT [FMA:9535] -xref: EMAPA:17342 xref: FMA:9535 xref: MA:0002984 xref: SCTID:362020004 is_a: UBERON:0001083 ! myocardium of ventricle intersection_of: UBERON:0001083 ! myocardium of ventricle intersection_of: part_of UBERON:0002080 ! heart right ventricle -relationship: continuous_with UBERON:0006563 ! tunica media of pulmonary trunk relationship: part_of UBERON:0002080 ! heart right ventricle -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000001 "Myocardium of ventricle which is continuous with the tunica media of the pulmonary trunk." xsd:string {source="FMA:9535"} +relationship: RO:0002150 UBERON:0006563 ! continuous with tunica media of pulmonary trunk +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0006568 @@ -229007,15 +226031,15 @@ xref: NCIT:C34245 xref: SCTID:245445008 xref: UMLS:C0821671 {source="ncithesaurus:Pectinate_Line"} xref: Wikipedia:Pectinate_line +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:8410024 ! intestinal junction intersection_of: UBERON:0007651 ! anatomical junction -intersection_of: connects UBERON:0000931 ! proctodeum -intersection_of: connects UBERON:0001046 ! hindgut -relationship: connects UBERON:0000931 ! proctodeum -relationship: connects UBERON:0001046 ! hindgut +intersection_of: RO:0002176 UBERON:0000931 ! connects proctodeum +intersection_of: RO:0002176 UBERON:0001046 ! connects hindgut relationship: part_of UBERON:0000159 ! anal canal -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/7b/Hemorrhoid.png" xsd:anyURI -property_value: UBPROP:0000012 "FMA also has FMA:29321 but it's not clear how this differs" xsd:string {external_ontology="FMA"} +relationship: RO:0002176 UBERON:0000931 ! connects proctodeum +relationship: RO:0002176 UBERON:0001046 ! connects hindgut +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7b/Hemorrhoid.png" xsd:anyURI [Term] id: UBERON:0006585 @@ -229045,9 +226069,8 @@ xref: MESH:D007761 xref: NCIT:C33231 xref: UMLS:C1518679 {source="ncithesaurus:Otolymph"} is_a: UBERON:0007779 {source="FMA-abduced"} ! transudate -relationship: located_in UBERON:0001839 ! bony labyrinth relationship: part_of UBERON:0001844 {source="Wikipedia:Perilymph"} ! cochlea -property_value: UBPROP:0000001 "Fluids found within the osseous labyrinth (PERILYMPH) and the membranous labyrinth (ENDOLYMPH) of the inner ear. (From Gray's Anatomy, 30th American ed, p1328, 1332[MESH:A12.207.571])" xsd:string {source="MESH:A12.207.571"} +relationship: RO:0001025 UBERON:0001839 ! located in bony labyrinth [Term] id: UBERON:0006595 @@ -229061,11 +226084,11 @@ xref: TAO:0000416 xref: ZFA:0000416 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0000925 ! endoderm intersection_of: part_of UBERON:0000307 ! blastula -relationship: has_potential_to_develop_into UBERON:0000925 ! endoderm -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +intersection_of: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm relationship: part_of UBERON:0000307 ! blastula +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm [Term] id: UBERON:0006596 @@ -229079,8 +226102,8 @@ xref: TAO:0000568 xref: ZFA:0000568 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0000178 ! blood -relationship: has_potential_to_develop_into UBERON:0000178 ! blood +intersection_of: RO:0002387 UBERON:0000178 ! has potential to develop into blood +relationship: RO:0002387 UBERON:0000178 ! has potential to develop into blood [Term] id: UBERON:0006598 @@ -229094,10 +226117,10 @@ xref: TAO:0001116 xref: ZFA:0001116 is_a: UBERON:0002050 ! embryonic structure intersection_of: UBERON:0005423 ! developing anatomical structure -intersection_of: has_potential_to_develop_into UBERON:0000061 ! anatomical structure intersection_of: part_of UBERON:0000922 ! embryo -relationship: has_potential_to_develop_into UBERON:0000061 ! anatomical structure -property_value: editor_note "Consider merging with anlage" xsd:string +intersection_of: RO:0002387 UBERON:0000061 ! has potential to develop into anatomical structure +relationship: RO:0002387 UBERON:0000061 ! has potential to develop into anatomical structure +property_value: IAO:0000116 "Consider merging with anlage" xsd:string [Term] id: UBERON:0006600 @@ -229111,9 +226134,9 @@ xref: TAO:0001334 xref: ZFA:0001334 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0002005 ! enteric nervous system -relationship: develops_from UBERON:0005428 {source="NCBIBook:NBK10065"} ! vagal neural crest -relationship: has_potential_to_develop_into UBERON:0002005 ! enteric nervous system +intersection_of: RO:0002387 UBERON:0002005 ! has potential to develop into enteric nervous system +relationship: RO:0002202 UBERON:0005428 {source="NCBIBook:NBK10065"} ! develops from vagal neural crest +relationship: RO:0002387 UBERON:0002005 ! has potential to develop into enteric nervous system [Term] id: UBERON:0006601 @@ -229129,11 +226152,11 @@ xref: XAO:0004132 xref: ZFA:0001376 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0000924 ! ectoderm intersection_of: part_of UBERON:0000307 ! blastula -relationship: has_potential_to_develop_into UBERON:0000924 ! ectoderm -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +intersection_of: RO:0002387 UBERON:0000924 ! has potential to develop into ectoderm relationship: part_of UBERON:0000307 ! blastula +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002387 UBERON:0000924 ! has potential to develop into ectoderm [Term] id: UBERON:0006603 @@ -229147,11 +226170,11 @@ xref: TAO:0001377 xref: ZFA:0001377 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0000926 ! mesoderm intersection_of: part_of UBERON:0000307 ! blastula -relationship: has_potential_to_develop_into UBERON:0000926 ! mesoderm -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +intersection_of: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm relationship: part_of UBERON:0000307 ! blastula +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm [Term] id: UBERON:0006606 @@ -229174,13 +226197,11 @@ xref: Wikipedia:Symphysis_menti xref: ZFA:0005488 is_a: UBERON:0002216 {source="FMA"} ! symphysis intersection_of: UBERON:0002213 ! cartilaginous joint -intersection_of: connects UBERON:0004742 {cardinality="2"} ! dentary -relationship: connects UBERON:0004742 {notes="connects adjacent mandibles"} ! dentary +intersection_of: RO:0002176 UBERON:0004742 {cardinality="2"} ! connects dentary relationship: part_of UBERON:0001710 ! lower jaw region -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray176.png" xsd:anyURI -property_value: editor_note "this is placed as part of lower jaw region, as in this ontology the skeleton does not include joints" xsd:string -property_value: UBPROP:0000001 "Joint that articulates the left and right dentary bones. Mandibular symphysis is unpaired.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001851", ontology="TAO", source="TAO:wd"} -property_value: UBPROP:0000008 "in snakes, the mandibular symphysis is composed of soft tissues, allowing independent movement of each mandible" xsd:string {source="ISBN:0073040584"} +relationship: RO:0002176 UBERON:0004742 ! connects dentary +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray176.png" xsd:anyURI +property_value: IAO:0000116 "this is placed as part of lower jaw region, as in this ontology the skeleton does not include joints" xsd:string [Term] id: UBERON:0006614 @@ -229192,7 +226213,6 @@ synonym: "aponeurotic" RELATED [Wikipedia:Aponeurosis] xref: AEO:0000092 xref: EHDAA2:0003092 xref: FMA:9722 -xref: MESH:D000070606 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C32133 xref: SCTID:331712004 xref: UMLS:C0225205 {source="ncithesaurus:Aponeurosis"} @@ -229201,9 +226221,7 @@ xref: ZFA:0005652 is_a: UBERON:0000158 {source="FMA"} ! membranous layer relationship: has_part CL:0000327 {source="AEO"} ! extracellular matrix secreting cell relationship: part_of UBERON:0001630 {source="FMA"} ! muscle organ -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Aponeurosis.png" xsd:anyURI -property_value: UBPROP:0000001 "Aponeuroses are layers of flat broad tendons. They have a shiny, whitish-silvery color, and are histologically similar to tendons, but are very sparingly supplied with blood vessels and nerves. When dissected, aponeuroses are papery, and peel off by sections. The primary regions with thick aponeurosis is in the ventral abdominal region, the dorsal lumbar region, and in the palmar region. Their primary function is to join muscles and the body parts the muscles act upon[Wikipedia:Aponeurosis]." xsd:string {source="Wikipedia:Aponeurosis"} -property_value: UBPROP:0000012 "in ZFA, aponeuroses are subtypes of tendons, but this is inconsistent with tendons being muscle-bone connections" xsd:string {external_ontology="ZFA"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e6/Aponeurosis.png" xsd:anyURI [Term] id: UBERON:0006615 @@ -229218,7 +226236,7 @@ xref: SCTID:341586007 xref: UMLS:C0226504 {source="ncithesaurus:Venous_Sinus"} xref: ZFA:0007072 is_a: UBERON:0003920 ! venous blood vessel -property_value: editor_note "check if it is valid to group ZFA class here." xsd:string +property_value: IAO:0000116 "check if it is valid to group ZFA class here." xsd:string [Term] id: UBERON:0006616 @@ -229232,9 +226250,8 @@ xref: FMA:53643 xref: SCTID:368567003 is_a: UBERON:0001691 ! external ear intersection_of: UBERON:0001691 ! external ear -intersection_of: in_right_side_of UBERON:0000468 ! multicellular organism -relationship: in_right_side_of UBERON:0000468 ! multicellular organism -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +intersection_of: BSPO:0000121 UBERON:0000468 ! multicellular organism +relationship: BSPO:0000121 UBERON:0000468 ! multicellular organism [Term] id: UBERON:0006617 @@ -229248,9 +226265,8 @@ xref: FMA:53644 xref: SCTID:368589004 is_a: UBERON:0001691 ! external ear intersection_of: UBERON:0001691 ! external ear -intersection_of: in_left_side_of UBERON:0000468 ! multicellular organism -relationship: in_left_side_of UBERON:0000468 ! multicellular organism -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +intersection_of: BSPO:0000120 UBERON:0000468 ! multicellular organism +relationship: BSPO:0000120 UBERON:0000468 ! multicellular organism [Term] id: UBERON:0006632 @@ -229265,10 +226281,10 @@ xref: SCTID:244242003 xref: Wikipedia:Musculophrenic_artery is_a: UBERON:0002057 ! phrenic artery intersection_of: UBERON:0001637 ! artery -intersection_of: connecting_branch_of UBERON:0002456 ! internal thoracic artery -intersection_of: supplies UBERON:0001103 ! diaphragm -relationship: connecting_branch_of UBERON:0002456 ! internal thoracic artery -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002178 UBERON:0001103 ! supplies diaphragm +intersection_of: RO:0002252 UBERON:0002456 ! connecting branch of internal thoracic artery +relationship: RO:0002252 UBERON:0002456 ! connecting branch of internal thoracic artery +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0006642 @@ -229287,6 +226303,7 @@ synonym: "uterine tubal muscularis" EXACT [FMA:18318] xref: EMAPA:29046 xref: FMA:18318 xref: SCTID:259488000 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005156 ! reproductive structure is_a: UBERON:0006660 ! muscular coat intersection_of: UBERON:0006660 ! muscular coat @@ -229301,6 +226318,7 @@ def: "An adventitia that is part of a epididymis." [OBOL:automatic] synonym: "epididymis adventitia" EXACT [FMA:19136] xref: EMAPA:30443 xref: FMA:19136 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005156 ! reproductive structure is_a: UBERON:0005742 ! adventitia intersection_of: UBERON:0005742 ! adventitia @@ -229314,6 +226332,7 @@ namespace: uberon def: "A muscle layer that is part of a epididymis." [OBOL:automatic] xref: EMAPA:30747 xref: FMA:19149 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005156 ! reproductive structure is_a: UBERON:0006660 ! muscular coat intersection_of: UBERON:0006660 ! muscular coat @@ -229352,6 +226371,7 @@ synonym: "tunica adventitia glandulae vesiculosae" EXACT OMO:0003011 [FMA:19403, xref: EMAPA:29775 xref: FMA:19403 xref: SCTID:252406002 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005156 ! reproductive structure is_a: UBERON:0005742 ! adventitia intersection_of: UBERON:0005742 ! adventitia @@ -229368,6 +226388,7 @@ synonym: "vaginal muscularis" EXACT [] xref: EMAPA:30997 xref: FMA:19976 xref: SCTID:253069005 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005156 ! reproductive structure is_a: UBERON:0006660 ! muscular coat intersection_of: UBERON:0006660 ! muscular coat @@ -229384,7 +226405,6 @@ synonym: "glans clitoridis" RELATED [Wikipedia:Clitoral_glans] synonym: "glans clitoris" RELATED [Wikipedia:Clitoral_glans] synonym: "glans of clitoris" EXACT [FMA:19999] xref: BTO:0003117 -xref: EMAPA:19170 xref: EMAPA:30829 xref: FMA:19999 xref: NCIT:C32681 @@ -229395,9 +226415,9 @@ is_a: UBERON:0008324 ! erectile tissue is_a: UBERON:0035651 ! glans intersection_of: UBERON:0035651 ! glans intersection_of: part_of UBERON:0002411 ! clitoris -relationship: develops_from UBERON:0013240 {source="cjm"} ! future glans clitoris relationship: part_of UBERON:0002411 ! clitoris -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/8c/Clitoris_inner_anatomy.gif" xsd:anyURI +relationship: RO:0002202 UBERON:0013240 {source="cjm"} ! develops from future glans clitoris +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8c/Clitoris_inner_anatomy.gif" xsd:anyURI [Term] id: UBERON:0006657 @@ -229415,19 +226435,14 @@ synonym: "glenoid facet" EXACT [] xref: AAO:0000749 xref: EMAPA:25122 xref: FMA:23275 -xref: MESH:D061165 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: NCIT:C32682 xref: SCTID:181914008 xref: UMLS:C1261046 {source="ncithesaurus:Glenoid_Fossa"} xref: Wikipedia:Glenoid_cavity is_a: UBERON:0004704 ! bone fossa -relationship: adjacent_to UBERON:0006849 {notes="to be revised after scapulocoracoid fixes"} ! scapula +relationship: adjacent_to UBERON:0006849 ! scapula relationship: part_of UBERON:0004753 ! scapulocoracoid -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/ec/Gray328.png" xsd:anyURI -property_value: UBPROP:0000001 "Cavity for the articulation of the forelimb formed by the scapula, coracoid, and clavicle.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000749", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000002 "relationship loss: part_of scapular area (AAO:0000935)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000749", ontology="AAO"} -property_value: UBPROP:0000008 "The glenoid fossa can be associated with the metapterygium in sarcopterygians, or either the meso- or propterygium in basal gnathostomes such as Chondrichthyans" xsd:string {source="ad"} -property_value: UBPROP:0000012 "FMA also has classes for the bony parts around the cavity - these may be more useful than the cavity term itself" xsd:string {external_ontology="FMA"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ec/Gray328.png" xsd:anyURI [Term] id: UBERON:0006658 @@ -229444,10 +226459,9 @@ xref: NCIT:C101527 is_a: UBERON:0003841 ! autopod joint is_a: UBERON:0011139 ! synovial limb joint intersection_of: UBERON:0000982 ! skeletal joint -intersection_of: connects UBERON:0003221 {cardinality="2"} ! phalanx -relationship: connects UBERON:0003221 {notes="two phalanges in series"} ! phalanx +intersection_of: RO:0002176 UBERON:0003221 {cardinality="2"} ! connects phalanx relationship: part_of UBERON:0002544 {source="cjm"} ! digit -property_value: UBPROP:0000001 "Hinge joints between the phalanges of the hand or foot[ncithesaurus:Interphalangeal_Joint]." xsd:string {source="ncithesaurus:Interphalangeal_Joint"} +relationship: RO:0002176 UBERON:0003221 ! connects phalanx [Term] id: UBERON:0006660 @@ -229470,12 +226484,8 @@ xref: UMLS:C0225358 {source="ncithesaurus:Muscle_Layer"} xref: Wikipedia:Muscular_layer is_a: UBERON:0018260 ! layer of muscle tissue relationship: adjacent_to UBERON:0000009 ! submucosa -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata -property_value: editor_note "currently this class conflates a generic layer of muscle and a specific layer found lining the digestive tract (the muscularis externa), typically composed of circular and longitudinal layers (although this varies)" xsd:string -property_value: RO:0002171 UBERON:0000009 -property_value: RO:0002171 UBERON:0006676 -property_value: UBPROP:0000001 "An outer layer of smooth muscle surrounding a hollow or tubular organ as the bladder, esophagus, large intestine, small intestine, stomach, ureter, uterus, and vagina that often consists of an inner layer of circular fibers serving to narrow the lumen of the organ and an outer layer of longitudinal fibers serving to shorten its length[BTO]." xsd:string {source="BTO:0004838"} -property_value: UBPROP:0000008 "typically smooth muscle, but there may be exceptions - in the upper esophagus, part of the externa is skeletal muscle, rather than smooth muscle." xsd:string +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +property_value: IAO:0000116 "currently this class conflates a generic layer of muscle and a specific layer found lining the digestive tract (the muscularis externa), typically composed of circular and longitudinal layers (although this varies)" xsd:string [Term] id: UBERON:0006661 @@ -229498,7 +226508,7 @@ xref: SCTID:368677009 xref: Wikipedia:Galea_aponeurotica is_a: UBERON:0006614 ! aponeurosis relationship: part_of UBERON:0000403 {source="FMA"} ! scalp -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/fa/Gray378.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/fa/Gray378.png" xsd:anyURI [Term] id: UBERON:0006668 @@ -229511,10 +226521,10 @@ xref: FMA:55805 xref: Wikipedia:Carotid_canal is_a: UBERON:0013685 ! foramen of skull intersection_of: UBERON:0013685 ! foramen of skull -intersection_of: conduit_for UBERON:0001532 ! internal carotid artery -relationship: conduit_for UBERON:0001532 ! internal carotid artery +intersection_of: RO:0002570 UBERON:0001532 ! conduit for internal carotid artery relationship: part_of UBERON:0001678 ! temporal bone -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/4c/Gray141.png" xsd:anyURI +relationship: RO:0002570 UBERON:0001532 ! conduit for internal carotid artery +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4c/Gray141.png" xsd:anyURI [Term] id: UBERON:0006670 @@ -229535,10 +226545,9 @@ xref: Wikipedia:Central_tendon_of_diaphragm is_a: UBERON:0000043 ! tendon is_a: UBERON:0003570 ! respiratory system connective tissue is_a: UBERON:0003837 ! thoracic segment connective tissue -relationship: attaches_to UBERON:0002359 ! fibrous pericardium -relationship: immediate_transformation_of UBERON:0006239 {evidence="definitional"} ! future central tendon relationship: part_of UBERON:0001103 {source="VHOG"} ! diaphragm -property_value: UBPROP:0000003 "In mammals, the diaphragm muscle divides the thoracoabdominal cavity into thorax and abdomen. In most mammals, the diaphragm is a flat sheet with muscle fibers radiating outward from a central tendon, and the diaphragm's apposition to the cranial surface of the liver gives it a dome-shape. Muscle fiber contraction reduces the curvature of the dome, thereby expanding the thoracic cavity and aspirating air into the lungs.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001399", ontology="VHOG", source="DOI:10.1016/j.resp.2006.06.003", source="http://bgee.unil.ch/"} +relationship: RO:0002371 UBERON:0002359 ! attached to fibrous pericardium +relationship: RO:0002495 UBERON:0006239 ! immediate transformation of future central tendon [Term] id: UBERON:0006675 @@ -229547,8 +226556,8 @@ namespace: uberon def: "A valve that is part of a vein." [OBOL:automatic] synonym: "valve of vein" EXACT [FMA:68095] xref: FMA:68095 -xref: MESH:D055422 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} is_a: UBERON:0003978 ! valve +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0003978 ! valve intersection_of: part_of UBERON:0001638 ! vein relationship: part_of UBERON:0001638 ! vein @@ -229579,10 +226588,10 @@ xref: SCTID:139380001 xref: Wikipedia:Hypoglossal_canal is_a: UBERON:0013685 ! foramen of skull intersection_of: UBERON:0004111 ! anatomical conduit -intersection_of: conduit_for UBERON:0001650 ! hypoglossal nerve -relationship: conduit_for UBERON:0001650 ! hypoglossal nerve -relationship: only_in_taxon NCBITaxon:7776 ! Gnathostomata +intersection_of: RO:0002570 UBERON:0001650 ! conduit for hypoglossal nerve relationship: part_of UBERON:0001676 ! occipital bone +relationship: RO:0002160 NCBITaxon:7776 ! only in taxon Gnathostomata +relationship: RO:0002570 UBERON:0001650 ! conduit for hypoglossal nerve [Term] id: UBERON:0006686 @@ -229616,7 +226625,6 @@ synonym: "vertebral canal" RELATED [Wikipedia:Spinal_canal] xref: AAO:0000693 xref: FMA:9680 xref: GAID:242 -xref: MESH:D013115 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: NCIT:C33869 xref: NCIT:C34221 xref: SCTID:361746009 @@ -229625,15 +226633,14 @@ xref: UMLS:C1522467 {source="ncithesaurus:Neural_Canal"} xref: Wikipedia:Spinal_canal is_a: UBERON:0004111 ! anatomical conduit intersection_of: UBERON:0004111 ! anatomical conduit -intersection_of: conduit_for UBERON:0002240 ! spinal cord -intersection_of: lumen_of UBERON:0001130 ! vertebral column -relationship: conduit_for UBERON:0002240 ! spinal cord -relationship: lumen_of UBERON:0001130 ! vertebral column +intersection_of: RO:0002570 UBERON:0002240 ! conduit for spinal cord +intersection_of: RO:0002571 UBERON:0001130 ! lumen of vertebral column relationship: part_of UBERON:0001130 ! vertebral column -relationship: surrounds UBERON:0002240 ! spinal cord -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray82.png" xsd:anyURI -property_value: editor_note "TODO - check neural vs vertebral canal; embryonic vs adult?" xsd:string -property_value: UBPROP:0000001 "Canal formed by the vertebral centra ventrally, the pedicels laterally, and the neural arches dorsally that encloses and protects the spinal cord.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000693", ontology="AAO", source="AAO:LAP"} +relationship: RO:0002221 UBERON:0002240 ! surrounds spinal cord +relationship: RO:0002570 UBERON:0002240 ! conduit for spinal cord +relationship: RO:0002571 UBERON:0001130 ! lumen of vertebral column +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray82.png" xsd:anyURI +property_value: IAO:0000116 "TODO - check neural vs vertebral canal; embryonic vs adult?" xsd:string [Term] id: UBERON:0006694 @@ -229662,10 +226669,9 @@ intersection_of: UBERON:0002529 ! limb segment intersection_of: distally_connected_to UBERON:0009877 ! metapodium region intersection_of: proximally_connected_to UBERON:0002471 ! zeugopod relationship: distally_connected_to UBERON:0009877 ! metapodium region -relationship: has_skeleton UBERON:0009878 ! mesopodial skeleton relationship: part_of UBERON:0002470 {source="MA:th"} ! autopod region relationship: proximally_connected_to UBERON:0002471 ! zeugopod -property_value: UBPROP:0000013 "Naming conventions for pod terms under discussion within phenoscape group" xsd:string +relationship: RO:0002551 UBERON:0009878 ! has skeleton mesopodial skeleton [Term] id: UBERON:0006717 @@ -229678,15 +226684,14 @@ synonym: "autopodium" RELATED [VSAO:0005019, VSAO:NI] synonym: "skeletal parts of autopod" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "skeleton of autopod" EXACT [https://orcid.org/0000-0002-6601-2165] xref: VSAO:0005019 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010712 ! limb skeleton subdivision intersection_of: UBERON:0010912 ! subdivision of skeleton -intersection_of: skeleton_of UBERON:0002470 ! autopod region +intersection_of: RO:0002576 UBERON:0002470 ! skeleton of autopod region relationship: part_of UBERON:0002470 ! autopod region relationship: part_of UBERON:0004381 ! skeleton of limb relationship: proximally_connected_to UBERON:0011584 ! zeugopodial skeleton -relationship: skeleton_of UBERON:0002470 ! autopod region -property_value: UBPROP:0000001 "Distal section of the limb skeleton, consisting of the anterior autopodium or posterior autopodium.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0005019", ontology="VSAO", source="VSAO:NI"} -property_value: UBPROP:0000013 "Naming conventions for pod terms under discussion within phenoscape group" xsd:string +relationship: RO:0002576 UBERON:0002470 ! skeleton of autopod region [Term] id: UBERON:0006723 @@ -229708,10 +226713,11 @@ xref: NCIT:C33135 xref: SCTID:361314007 xref: UMLS:C0229503 {source="ncithesaurus:Modiolus"} xref: Wikipedia:Modiolus_(cochlea) +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005913 ! zone of bone organ -relationship: contributes_to_morphology_of UBERON:0001844 ! cochlea relationship: part_of UBERON:0007223 {source="MA"} ! osseus cochlea -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/16/Gray921.png" xsd:anyURI +relationship: RO:0002433 UBERON:0001844 ! contributes to morphology of cochlea +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/16/Gray921.png" xsd:anyURI [Term] id: UBERON:0006725 @@ -229732,11 +226738,11 @@ xref: MESH:D055493 xref: SCTID:279840005 xref: UMLS:C0229477 xref: Wikipedia:Spiral_ligament +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0008845 ! nonskeletal ligament -relationship: attaches_to UBERON:0006106 {source="MESH-def"} ! cochlear canal relationship: has_part CL:0002665 ! otic fibrocyte relationship: part_of UBERON:0001855 ! cochlear duct of membranous labyrinth -property_value: UBPROP:0000012 "this is not classified as a ligament in FMA" xsd:string {external_ontology="FMA"} +relationship: RO:0002371 UBERON:0006106 {source="MESH-def"} ! attached to cochlear canal [Term] id: UBERON:0006756 @@ -229755,10 +226761,9 @@ xref: SCTID:308821003 xref: VHOG:0000730 xref: Wikipedia:Tuberculum_impar is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0004362 ! pharyngeal arch 1 relationship: part_of UBERON:0006260 {source="EHDAA2"} ! lingual swellings -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray979.png" xsd:anyURI -property_value: UBPROP:0000003 "Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000730", ontology="VHOG", source="DOI:10.1046/j.1469-7580.2002.00073.x", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0004362 ! develops from pharyngeal arch 1 +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray979.png" xsd:anyURI [Term] id: UBERON:0006757 @@ -229775,11 +226780,9 @@ xref: FMA:313628 xref: VHOG:0000731 xref: Wikipedia:Lateral_lingual_swelling is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0004362 ! pharyngeal arch 1 relationship: part_of UBERON:0006260 ! lingual swellings -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray979.png" xsd:anyURI -property_value: UBPROP:0000003 "Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000731", ontology="VHOG", source="DOI:10.1046/j.1469-7580.2002.00073.x Iwasaki S, Evolution of the structure and function of the vertebrate tongue. J Anat (2002)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000010 "paired" xsd:string +relationship: RO:0002202 UBERON:0004362 ! develops from pharyngeal arch 1 +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5c/Gray979.png" xsd:anyURI [Term] id: UBERON:0006761 @@ -229807,15 +226810,16 @@ xref: MESH:D016850 xref: SCTID:63716004 xref: Wikipedia:Corneal_limbus xref: ZFA:0005570 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0007651 ! anatomical junction intersection_of: UBERON:0007651 ! anatomical junction -intersection_of: connects UBERON:0000964 ! cornea -intersection_of: connects UBERON:0001773 ! sclera -relationship: connects UBERON:0000964 ! cornea -relationship: connects UBERON:0001773 ! sclera +intersection_of: RO:0002176 UBERON:0000964 ! connects cornea +intersection_of: RO:0002176 UBERON:0001773 ! connects sclera relationship: part_of UBERON:0000019 ! camera-type eye -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/3d/Limbus.png" xsd:anyURI +relationship: RO:0002176 UBERON:0000964 ! connects cornea +relationship: RO:0002176 UBERON:0001773 ! connects sclera +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3d/Limbus.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0006763 @@ -229849,9 +226853,9 @@ xref: UMLS:C0682578 {source="ncithesaurus:Glandular_Epithelium"} xref: UMLS:C1708242 {source="ncithesaurus:Glandular_Epithelial_Tissue"} is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium -intersection_of: composed_primarily_of CL:0000150 ! glandular epithelial cell -relationship: composed_primarily_of CL:0000150 ! glandular epithelial cell -property_value: editor_note "consider splitting epithelium from epithelial tissue" xsd:string +intersection_of: RO:0002473 CL:0000150 ! composed primarily of glandular epithelial cell +relationship: RO:0002473 CL:0000150 ! composed primarily of glandular epithelial cell +property_value: IAO:0000116 "consider splitting epithelium from epithelial tissue" xsd:string [Term] id: UBERON:0006813 @@ -229864,12 +226868,13 @@ xref: AAO:0000320 xref: FMA:60116 xref: SCTID:281486007 is_a: UBERON:0000075 {source="FMA"} ! subdivision of skeletal system +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010912 ! subdivision of skeleton intersection_of: UBERON:0010912 ! subdivision of skeleton -intersection_of: skeleton_of UBERON:0000004 ! nose +intersection_of: RO:0002576 UBERON:0000004 ! skeleton of nose relationship: part_of UBERON:0000004 {source="FMA"} ! nose -relationship: part_of UBERON:0003113 {notes="facial series", source="Kardong-abduced"} ! dermatocranium -relationship: skeleton_of UBERON:0000004 ! nose +relationship: part_of UBERON:0003113 ! dermatocranium +relationship: RO:0002576 UBERON:0000004 ! skeleton of nose [Term] id: UBERON:0006815 @@ -229886,9 +226891,6 @@ is_a: UBERON:0011825 {source="FMA"} ! loose connective tissue relationship: has_part CL:1000303 {source="FMA"} ! fibroblast of areolar connective tissue relationship: part_of UBERON:0000030 ! lamina propria relationship: protects UBERON:0000062 ! organ -property_value: UBPROP:0000001 "Also known as loose connective tissue. A pliable, mesh-like tissue with a fluid matrix that functions to cushion and protect body organs.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000027", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000002 "relationship loss: subclass connective tissue proper (AAO:0000099)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000027", ontology="AAO"} -property_value: UBPROP:0000009 "cushions body organs" xsd:string {source="AAO"} [Term] id: UBERON:0006828 @@ -229899,7 +226901,7 @@ is_a: UBERON:0002511 ! trabecula carnea intersection_of: UBERON:0002511 ! trabecula carnea intersection_of: part_of UBERON:0002081 ! cardiac atrium relationship: part_of UBERON:0002081 ! cardiac atrium -property_value: editor_note "Not present in any AO. Note that WP states that trabecular carnea are ventricular and 'They should not be confused with the pectinate muscles, which are present in the right and left atria only'" xsd:string +property_value: IAO:0000116 "Not present in any AO. Note that WP states that trabecular carnea are ventricular and 'They should not be confused with the pectinate muscles, which are present in the right and left atria only'" xsd:string [Term] id: UBERON:0006832 @@ -229907,12 +226909,11 @@ name: lumen of open tracheal system trachea namespace: uberon def: "An anatomical space that surrounded_by a open tracheal system trachea." [OBOL:automatic] synonym: "tracheal lumen" BROAD SENSU [FBbt:00007410] -xref: FBbt:00007410 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0003127 ! open tracheal system trachea -relationship: luminal_space_of UBERON:0003127 ! open tracheal system trachea +intersection_of: RO:0002572 UBERON:0003127 ! luminal space of open tracheal system trachea relationship: part_of UBERON:0003127 ! open tracheal system trachea +relationship: RO:0002572 UBERON:0003127 ! luminal space of open tracheal system trachea [Term] id: UBERON:0006833 @@ -229925,9 +226926,9 @@ xref: FMA:7469 xref: SCTID:197486000 is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0003126 ! trachea -relationship: luminal_space_of UBERON:0003126 ! trachea +intersection_of: RO:0002572 UBERON:0003126 ! luminal space of trachea relationship: part_of UBERON:0003126 ! trachea +relationship: RO:0002572 UBERON:0003126 ! luminal space of trachea [Term] id: UBERON:0006834 @@ -229936,15 +226937,14 @@ namespace: uberon def: "A subdivision of a the reproductive tract in a female organism that is the site of embryo development." [http://orcid.org/0000-0002-6601-2165] subset: grouping_class synonym: "uterus" BROAD SENSU [FBbt:00004924] -xref: FBbt:00004924 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: TADS:0000421 xref: WBbt:0006760 is_a: UBERON:0005156 ! reproductive structure is_a: UBERON:0013522 ! subdivision of tube intersection_of: UBERON:0013522 ! subdivision of tube intersection_of: site_of GO:0009790 ! embryo development -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa relationship: part_of UBERON:0000474 ! female reproductive system +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa relationship: site_of GO:0009790 ! embryo development [Term] @@ -229967,7 +226967,7 @@ xref: ZFA:0005168 is_a: UBERON:0013126 ! vein of abdomen is_a: UBERON:0015796 ! liver blood vessel relationship: part_of UBERON:0004647 ! liver lobule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0006843 @@ -229987,7 +226987,7 @@ intersection_of: UBERON:0002211 ! nerve root intersection_of: extends_fibers_into UBERON:0001785 ! cranial nerve intersection_of: part_of UBERON:0001017 ! central nervous system relationship: extends_fibers_into UBERON:0001785 ! cranial nerve -property_value: editor_note "recommend asserting under this class rather than relying on inference, as relations may change" xsd:string +property_value: IAO:0000116 "recommend asserting under this class rather than relying on inference, as relations may change" xsd:string [Term] id: UBERON:0006846 @@ -230000,7 +227000,7 @@ synonym: "groove" RELATED [AEO:0000161] xref: AEO:0000161 xref: EHDAA2_RETIRED:0003161 is_a: UBERON:0000466 ! immaterial anatomical entity -relationship: has_quality PATO:0002255 ! grooved +relationship: RO:0000086 PATO:0002255 ! has quality grooved property_value: seeAlso "https://github.com/obophenotype/uberon/issues/2667" xsd:string [Term] @@ -230040,23 +227040,16 @@ is_a: UBERON:0002513 ! endochondral bone is_a: UBERON:0007829 ! pectoral girdle bone is_a: UBERON:0015057 ! scapula endochondral element intersection_of: UBERON:0015057 ! scapula endochondral element -intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue -relationship: develops_from UBERON:0004753 {source="ZFA"} ! scapulocoracoid -relationship: develops_from UBERON:0006290 {evidence="definitional"} ! scapula cartilage element +intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue relationship: distally_connected_to UBERON:0000976 {gci_relation="part_of", gci_filler="NCBITaxon:32523"} ! humerus relationship: distally_connected_to UBERON:0007272 ! pectoral appendage skeleton relationship: overlaps UBERON:0001470 {gci_relation="part_of", gci_filler="NCBITaxon:32523"} ! glenohumeral joint relationship: overlaps UBERON:0003692 {gci_relation="part_of", gci_filler="NCBITaxon:32523"} ! acromioclavicular joint relationship: part_of UBERON:0001467 {gci_relation="part_of", gci_filler="NCBITaxon:32523", source="FMA"} ! shoulder -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/5/59/Pectoral_girdles-en.svg" xsd:anyURI -property_value: UBPROP:0000001 "Endochondral bone that is located medial to the cleithrum, and articulates ventrally with the coracoid, medially with the mesocoracoid when the later is present and posteriorly with the upper one to three proximal radials. The scapula develops from the scapulocoracoid cartilage and belongs to the primary pectoral girdle. It may be perforated by the scapular foramen or it may be notched ventr and forms together with a similar notch of the coracoid the scapulocoracoid foramen[TAO:0000583]." xsd:string {source="TAO:0000583"} -property_value: UBPROP:0000001 "Paired bony elements of endochondral origin. They are situated at the level of the jaw articulation, in a vertical position, with the suprascapular margin being dorsal and the glenoid end being ventral.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000751", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000002 "relationship loss: has pars glenoidalis of scapula (AAO:0000753)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000751", ontology="AAO"} -property_value: UBPROP:0000002 "relationship loss: part_of scapular area (AAO:0000935)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000751", ontology="AAO"} -property_value: UBPROP:0000007 "scapular" xsd:string -property_value: UBPROP:0000008 "present in all tetrapods with even vestiges of anterior limbs, e.g., turtles & birds & mammals." xsd:string {source="ISBN:978-0-12-319060-4"} -property_value: UBPROP:0000011 "chick scapula is of dual origin and segmentally organized" xsd:string +relationship: RO:0002202 UBERON:0004753 {source="ZFA"} ! develops from scapulocoracoid +relationship: RO:0002202 UBERON:0006290 ! develops from scapula cartilage element +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/5/59/Pectoral_girdles-en.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0006851 @@ -230111,10 +227104,10 @@ synonym: "muscularis of ureter" EXACT [FMA:15893] synonym: "tunica muscularis (ureter)" EXACT OMO:0003011 [FMA:TA] synonym: "tunica muscularis ureteris" EXACT OMO:0003011 [FMA:TA] synonym: "ureteral smooth muscle layer" RELATED [EMAPA:28567] -xref: EMAPA:28811 xref: FMA:15893 xref: MA:0002654 xref: SCTID:3563003 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0006660 ! muscular coat intersection_of: UBERON:0006660 ! muscular coat intersection_of: part_of UBERON:0000056 ! ureter @@ -230131,15 +227124,14 @@ synonym: "adrenal - interrenal gland" RELATED [VHOG:0001141] synonym: "adrenal gland - interrenal gland" EXACT [VHOG:0001141] synonym: "adrenal gland/interrenal tissue" EXACT [] synonym: "suprarenal gland - interrenal gland" RELATED [VHOG:0001141] -xref: VHOG:0001141 is_a: UBERON:0002368 ! endocrine gland is_a: UBERON:0004120 ! mesoderm-derived structure -relationship: develops_from UBERON:0003064 ! intermediate mesoderm +is_a: UBERON:0010313 ! neural crest-derived structure relationship: has_part CL:0000166 ! chromaffin cell relationship: has_part CL:0000457 ! biogenic amine secreting cell relationship: part_of UBERON:0010074 ! chromaffin system -property_value: editor_note "keep this grouping class so long as it is required for GO" xsd:string -property_value: UBPROP:0000003 "All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001141", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003064 ! develops from intermediate mesoderm +property_value: IAO:0000116 "keep this grouping class so long as it is required for GO" xsd:string [Term] id: UBERON:0006861 @@ -230153,10 +227145,8 @@ synonym: "shaft proper of long bone" EXACT [FMA:32688] xref: FMA:32688 xref: MA:0002803 is_a: UBERON:0005055 ! zone of long bone -relationship: contributes_to_morphology_of UBERON:0002495 ! long bone relationship: part_of UBERON:0004769 ! diaphysis -property_value: RO:0002171 UBERON:0001438 -property_value: UBPROP:0000012 "The MA class is associated with EMAPA:35505 but we associate this with the more precise concept of diaphyseal plate" xsd:string {external_ontology="MA"} +relationship: RO:0002433 UBERON:0002495 ! contributes to morphology of long bone [Term] id: UBERON:0006862 @@ -230175,12 +227165,12 @@ xref: MA:0003055 xref: NCIT:C96209 xref: SCTID:182048009 xref: Wikipedia:Body_of_femur +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004769 ! diaphysis intersection_of: UBERON:0004769 ! diaphysis intersection_of: part_of UBERON:0000981 ! femur relationship: part_of UBERON:0000981 ! femur -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/2b/Gray244.png" xsd:anyURI -property_value: UBPROP:0000001 "The body of the femur (or shaft), almost cylindrical in form, is a little broader above than in the center, broadest and somewhat flattened from before backward below. It is slightly arched, so as to be convex in front, and concave behind, where it is strengthened by a prominent longitudinal ridge, the linea aspera. It presents for examination three borders, separating three surfaces. Of the borders, one, the linea aspera, is posterior, one is medial, and the other, lateral[Wikipedia:Body_of_femur]." xsd:string {source="Wikipedia:Body_of_femur"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2b/Gray244.png" xsd:anyURI [Term] id: UBERON:0006863 @@ -230205,6 +227195,7 @@ xref: EMAPA:37540 {source="MA:th"} xref: FMA:32875 xref: MA:0003052 is_a: UBERON:0001438 ! metaphysis +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0001438 ! metaphysis intersection_of: part_of UBERON:0000981 ! femur relationship: part_of UBERON:0006862 {is_inferred="true", source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! diaphysis of femur @@ -230217,12 +227208,10 @@ def: "The distalmost portion of the digestive tract, derived from the hindgut, a synonym: "rectal part of digestive tract" RELATED [] synonym: "rectum" NARROW [FBbt:00005756] synonym: "terminal section of digestive tract" RELATED [] -xref: FBbt:00005756 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: WBbt:0005773 is_a: UBERON:0004921 ! subdivision of digestive tract -relationship: continuous_with UBERON:0001245 ! anus -relationship: develops_from UBERON:0001046 ! hindgut -property_value: IAO:0000232 "this class is the superclass of 'rectum', which is currently reserved for the vertebrate structure. May be merged in future." xsd:string +relationship: RO:0002150 UBERON:0001245 ! continuous with anus +relationship: RO:0002202 UBERON:0001046 ! develops from hindgut [Term] id: UBERON:0006868 @@ -230231,7 +227220,6 @@ namespace: uberon def: "A gland that secretes a seminal fluid." [OBOL:automatic] subset: grouping_class subset: organ_slim -xref: FBbt:00004958 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: WBbt:0006870 is_a: UBERON:0005399 ! male reproductive gland intersection_of: UBERON:0002530 ! gland @@ -230258,10 +227246,9 @@ xref: NCIT:C34177 xref: UMLS:C1517291 {source="ncithesaurus:Foot_Plate"} is_a: UBERON:0010130 ! embryonic autopod plate intersection_of: UBERON:0010130 ! embryonic autopod plate -intersection_of: has_potential_to_develop_into UBERON:0002387 ! pes -relationship: develops_from UBERON:0005418 ! hindlimb bud -relationship: has_potential_to_develop_into UBERON:0002387 ! pes -property_value: UBPROP:0000012 "EHDAA2 does not have a single class for footplate, but includes epithelium, mesenchyme and AER" xsd:string {external_ontology="EHDAA2"} +intersection_of: RO:0002387 UBERON:0002387 ! has potential to develop into pes +relationship: RO:0002202 UBERON:0005418 ! develops from hindlimb bud +relationship: RO:0002387 UBERON:0002387 ! has potential to develop into pes [Term] id: UBERON:0006872 @@ -230291,9 +227278,9 @@ xref: NCIT:C34185 xref: UMLS:C1512334 {source="ncithesaurus:Hand_Plate"} is_a: UBERON:0010130 ! embryonic autopod plate intersection_of: UBERON:0010130 ! embryonic autopod plate -intersection_of: has_potential_to_develop_into UBERON:0002398 ! manus -relationship: develops_from UBERON:0005417 ! forelimb bud -relationship: has_potential_to_develop_into UBERON:0002398 ! manus +intersection_of: RO:0002387 UBERON:0002398 ! has potential to develop into manus +relationship: RO:0002202 UBERON:0005417 ! develops from forelimb bud +relationship: RO:0002387 UBERON:0002398 ! has potential to develop into manus [Term] id: UBERON:0006876 @@ -230327,7 +227314,6 @@ is_a: UBERON:0006876 ! vasculature of organ intersection_of: UBERON:0002049 ! vasculature intersection_of: part_of UBERON:0002107 ! liver relationship: part_of UBERON:0002107 ! liver -property_value: UBPROP:0000012 "the EHDAA2 term and the FMA term may not be exact equivalents - check" xsd:string {external_ontology="EHDAA2"} [Term] id: UBERON:0006904 @@ -230358,9 +227344,9 @@ xref: ZFA:0000998 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005253 {source="ZFA"} ! head mesenchyme intersection_of: UBERON:0005253 ! head mesenchyme -intersection_of: develops_from UBERON:0000926 ! mesoderm -relationship: develops_from UBERON:0003063 {source="EHDAA2", source="XAO"} ! prechordal plate -property_value: editor_note "merged in 'head mesoderm' from XAO/AAO and EFO here. Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme" xsd:string +intersection_of: RO:0002202 UBERON:0000926 ! develops from mesoderm +relationship: RO:0002202 UBERON:0003063 {source="EHDAA2", source="XAO"} ! develops from prechordal plate +property_value: IAO:0000116 "merged in 'head mesoderm' from XAO/AAO and EFO here. Partially implements https://github.com/obophenotype/uberon/wiki/The-neural-crest NC meeting scheme" xsd:string [Term] id: UBERON:0006905 @@ -230394,11 +227380,9 @@ xref: UMLS:C0242874 {source="ncithesaurus:Muscle_Fibers_Slow-Twitch"} is_a: UBERON:0001134 ! skeletal muscle tissue intersection_of: UBERON:0001134 ! skeletal muscle tissue intersection_of: has_part CL:0000189 ! slow muscle cell -relationship: composed_primarily_of CL:0000189 ! slow muscle cell relationship: has_part CL:0000189 ! slow muscle cell -property_value: editor_note "check if relationship to cell types should be more specific type I cells" xsd:string -property_value: UBPROP:0000011 "The fast and slow skeletal muscles are different in terms of twitching speed (Fitts 1994), and they are believed to be derived from distinct myogenic precursors (Stockdale 1992)" xsd:string -property_value: UBPROP:0000012 "check if CALOHA term is for fiber or tissue." xsd:string {external_ontology="CALOHA"} +relationship: RO:0002473 CL:0000189 ! composed primarily of slow muscle cell +property_value: IAO:0000116 "check if relationship to cell types should be more specific type I cells" xsd:string [Term] id: UBERON:0006908 @@ -230415,8 +227399,8 @@ xref: UMLS:C0242873 {source="ncithesaurus:Muscle_Fibers_Fast-Twitch"} is_a: UBERON:0001134 ! skeletal muscle tissue intersection_of: UBERON:0001134 ! skeletal muscle tissue intersection_of: has_part CL:0000190 ! fast muscle cell -relationship: composed_primarily_of CL:0000190 ! fast muscle cell relationship: has_part CL:0000190 ! fast muscle cell +relationship: RO:0002473 CL:0000190 ! composed primarily of fast muscle cell [Term] id: UBERON:0006909 @@ -230434,9 +227418,9 @@ xref: EMAPA:32908 xref: FMA:45677 is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0001555 ! digestive tract -relationship: luminal_space_of UBERON:0001555 ! digestive tract +intersection_of: RO:0002572 UBERON:0001555 ! luminal space of digestive tract relationship: part_of UBERON:0001555 ! digestive tract +relationship: RO:0002572 UBERON:0001555 ! luminal space of digestive tract [Term] id: UBERON:0006913 @@ -230450,7 +227434,6 @@ is_a: UBERON:0003929 ! digestive tract epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001833 ! lip relationship: part_of UBERON:0001833 ! lip -property_value: UBPROP:0000001 "The thick, high squamous-stratified epithelium that covers the lips. It contains abundant melanocytes, many mucous cells and has well differentiated taste buds.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005334", ontology="TAO", source="ZFIN:ZDB-PUB-060921-12"} [Term] id: UBERON:0006914 @@ -230466,7 +227449,6 @@ is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: has_part CL:0000076 ! squamous epithelial cell relationship: has_part CL:0000076 ! squamous epithelial cell -property_value: UBPROP:0000012 "FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium" xsd:string {external_ontology="FBbt"} [Term] id: UBERON:0006915 @@ -230509,7 +227491,6 @@ is_a: UBERON:0006914 ! squamous epithelium intersection_of: UBERON:0006914 ! squamous epithelium intersection_of: part_of UBERON:0001723 ! tongue relationship: part_of UBERON:0005020 ! mucosa of tongue -property_value: UBPROP:0000012 "this is a singleton subclass of tongue epithelium in MA" xsd:string {external_ontology="MA"} [Term] id: UBERON:0006920 @@ -230530,7 +227511,6 @@ is_a: UBERON:0001976 ! epithelium of esophagus is_a: UBERON:0006914 ! squamous epithelium intersection_of: UBERON:0006914 ! squamous epithelium intersection_of: part_of UBERON:0001043 ! esophagus -property_value: UBPROP:0000012 "MA introduces basal and squamous subtypes of esophagus epithelium; consider adding the FMA class 'epithelium of esophagus' here, because it is classified as squamous. BTO also has a singleton subclass" xsd:string {external_ontology="MA"} [Term] id: UBERON:0006921 @@ -230560,7 +227540,7 @@ is_a: UBERON:0004801 ! cervix epithelium is_a: UBERON:0010304 ! non-keratinized stratified squamous epithelium intersection_of: UBERON:0006914 ! squamous epithelium intersection_of: part_of UBERON:0000002 ! uterine cervix -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0006923 @@ -230585,7 +227565,6 @@ def: "A glandular epithelium that lines the stomach. The stomach's glandular epi subset: pheno_slim synonym: "epithelium of gastric gland" NARROW [FMA:63458] synonym: "gastric gland epithelium" RELATED [FMA:63458] -xref: EMAPA:17623 xref: EMAPA:35814 xref: FMA:63458 xref: MA:0002784 @@ -230595,7 +227574,7 @@ intersection_of: UBERON:0006799 ! glandular epithelium intersection_of: part_of UBERON:0000945 ! stomach relationship: has_part UBERON:0000325 ! gastric gland relationship: part_of UBERON:0006931 ! stomach glandular region mucosa -property_value: editor_note "we follow Kardong in treating the glandular epithelium as a distinct entity, and thus as an epithelium which has glands; FMA has 'epithelium of gastric gland', which is part of the gastric gland." xsd:string +property_value: IAO:0000116 "we follow Kardong in treating the glandular epithelium as a distinct entity, and thus as an epithelium which has glands; FMA has 'epithelium of gastric gland', which is part of the gastric gland." xsd:string [Term] id: UBERON:0006925 @@ -230622,7 +227601,7 @@ xref: UMLS:C0225337 {source="ncithesaurus:Columnar_Epithelium"} is_a: UBERON:0000485 ! simple columnar epithelium is_a: UBERON:0006799 ! glandular epithelium intersection_of: UBERON:0000485 ! simple columnar epithelium -intersection_of: composed_primarily_of CL:0000150 ! glandular epithelial cell +intersection_of: RO:0002473 CL:0000150 ! composed primarily of glandular epithelial cell [Term] id: UBERON:0006930 @@ -230632,7 +227611,7 @@ xref: FMA:66809 is_a: UBERON:0000484 ! simple cuboidal epithelium is_a: UBERON:0006799 ! glandular epithelium intersection_of: UBERON:0000484 ! simple cuboidal epithelium -intersection_of: composed_primarily_of CL:0000150 ! glandular epithelial cell +intersection_of: RO:0002473 CL:0000150 ! composed primarily of glandular epithelial cell [Term] id: UBERON:0006931 @@ -230681,7 +227660,6 @@ intersection_of: UBERON:0000483 ! epithelium intersection_of: has_part CL:0000098 ! sensory epithelial cell relationship: has_part CL:0000098 ! sensory epithelial cell relationship: part_of UBERON:0000010 ! peripheral nervous system -property_value: UBPROP:0000012 "note that the definition sourced from Dorlands say 'simple columnar', but FMA says atypical" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0006935 @@ -230696,9 +227674,9 @@ xref: MA:0002870 is_a: UBERON:0006932 {source="FMA"} ! vestibular epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0004721 ! crista ampullaris -relationship: contributes_to_morphology_of UBERON:0004721 ! crista ampullaris relationship: has_part CL:0002316 {source="FMA"} ! supporting cell of vestibular epithelium relationship: part_of UBERON:0004721 {source="MA"} ! crista ampullaris +relationship: RO:0002433 UBERON:0004721 ! contributes to morphology of crista ampullaris [Term] id: UBERON:0006936 @@ -230713,8 +227691,8 @@ intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002122 ! capsule of thymus relationship: has_part CL:0002294 ! type-1 epithelial cell of thymus relationship: part_of UBERON:0002122 ! capsule of thymus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: editor_note "TODO - check whether this is part of the thymus or borders it" xsd:string +property_value: IAO:0000116 "TODO - check whether this is part of the thymus or borders it" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0006937 @@ -230724,6 +227702,7 @@ def: "The epithelial cell layer containing the sensory hair cells and their asso subset: pheno_slim xref: EMAPA:32883 xref: MA:0001189 +is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0015807 ! ear epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001846 ! internal ear @@ -230765,12 +227744,9 @@ is_a: UBERON:0005904 ! duct of male reproductive system relationship: channel_for CL:0000019 ! sperm relationship: channels_from UBERON:0003959 ! rete testis relationship: channels_into UBERON:0001301 ! epididymis -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0006947 {source="FMA"} ! male genital duct -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b5/Hodenschema.svg" xsd:anyURI -property_value: UBPROP:0000001 "Any of a group ranging from one to twelve (varies in species) small seminal ducts per testis which transport sperm from the testes to the kidney.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010532", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000008 "There are two basic designs for efferent ductule structure: a) multiple entries into the epididymis, as seen in most large mammals. In humans and other large mammals, there are approximately 15-20 efferent ducts, which also occupy nearly one third of the head of the epididymis. b) single entry, as seen in most small animals such as rodents, whereby the 3-6 ductules merge into a single small ductule prior to entering the epididymis" xsd:string -property_value: UBPROP:0000012 "Check EMAPA" xsd:string {external_ontology="EMAPA"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b5/Hodenschema.svg" xsd:anyURI [Term] id: UBERON:0006947 @@ -230787,13 +227763,11 @@ xref: ZFA:0001268 is_a: UBERON:0000025 ! tube is_a: UBERON:0005904 ! duct of male reproductive system is_a: UBERON:0015212 ! lateral structure +relationship: BSPO:0000126 UBERON:0004054 {source="FMA-abduced-lr"} ! internal male genitalia relationship: channel_for UBERON:0001968 ! semen relationship: channels_from UBERON:0000473 ! testis -relationship: in_lateral_side_of UBERON:0004054 {source="FMA-abduced-lr"} ! internal male genitalia relationship: part_of UBERON:0004054 ! internal male genitalia -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Prostate.glb" xsd:anyURI -property_value: UBPROP:0000008 "we use this as a generic grouping class for a number of taxa" xsd:string -property_value: UBPROP:0000012 "in FMA includes as parts: seminal vesicle, efferent ductule (vas efferentia), epididymis, deferent duct (vas deferens), ejaculatory duct" xsd:string {external_ontology="FMA"} +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Prostate.glb" xsd:anyURI [Term] id: UBERON:0006948 @@ -230822,7 +227796,7 @@ is_a: UBERON:0034969 ! epithelial layer of duct intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000999 ! ejaculatory duct relationship: part_of UBERON:0000999 ! ejaculatory duct -property_value: editor_note "TODO - split off insect classes" xsd:string +property_value: IAO:0000116 "TODO - split off insect classes" xsd:string [Term] id: UBERON:0006954 @@ -230840,8 +227814,7 @@ is_a: UBERON:0000420 ! myoepithelium is_a: UBERON:0003244 ! epithelium of mammary gland intersection_of: UBERON:0000420 ! myoepithelium intersection_of: part_of UBERON:0001911 ! mammary gland -relationship: has_part CL:0002324 ! myoepithelial cell of mammary gland -property_value: UBPROP:0000010 "The cells of this structure are specialized epithelial cells that express smooth muscle-specific contractile and cytoskeletal properties; during lactation, MECs contract in response to oxytocin to generate the contractile force required for milk ejection; MECs are involved in all developmental stages of mammary gland morphogenesis, modulating proliferation and differentiation of luminal cells; they take part in the formation of extracellular matrix, synthesizing its components and secreting proteinases and their inhibitors; in addition, MECs are regarded as natural cancer suppressors: they secrete suppressor proteins limiting cancer growth, invasiveness, and neoangiogenesis; MECs are markedly resistant to malignant transformation and they are able to suppress the transformation of neighboring luminal cells[MP]" xsd:string +relationship: has_part CL:0002324 ! basal-myoepithelial cell of mammary gland [Term] id: UBERON:0006955 @@ -230881,7 +227854,7 @@ intersection_of: UBERON:0003891 ! stroma intersection_of: part_of UBERON:0000992 ! ovary relationship: has_part CL:0002095 {source="FMA"} ! hilus cell of ovary relationship: part_of UBERON:0000992 ! ovary -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0006964 @@ -230919,11 +227892,8 @@ xref: UMLS:C0175322 {source="BIRNLEX:1022"} xref: VHOG:0000244 xref: Wikipedia:Pars_distalis xref: ZFA:0001195 -is_a: UBERON:0000483 {source="EHDAA2"} ! epithelium +is_a: UBERON:0010371 ! ecto-epithelium relationship: part_of UBERON:0002196 {source="MA"} ! adenohypophysis -property_value: UBPROP:0000001 "Region of the adenohypophysis which produces the follicle-stimulating hormone, luteinizing hormone, prolactin, thyrotropin, and adrenocorticotropin.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010542", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "The anterior part of the adenohypophysis. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000244", ontology="VHOG", source="http://bgee.unil.ch/", source="http://www.thefreedictionary.com/pars+anterior"} -property_value: UBPROP:0000003 "It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. An infundibulum grows ventrally from the diencephalon of the brain, and Rathke's pouch extends dorsally from the roof of the developing mouth, or stomodaeum. The infundibulum remains connected to the floor of the diencephalon, which becomes the hypothalamus, and gives rise to the part of the gland known as the neurohypophysis. (...) Rathke's pouch loses its connection with the stomodaeum in most adult vertebrates and gives rise to the rest of the gland, the adenohypophysis. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000244", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510 and Figure 15-5", source="http://bgee.unil.ch/"} [Term] id: UBERON:0006965 @@ -230966,7 +227936,7 @@ xref: EHDAA2_RETIRED:0003192 xref: FMA:24137 xref: NCIT:C34022 xref: UMLS:C1515977 {source="ncithesaurus:Anatomic_Surface"} -is_a: UBERON:0010199 {notes="via morphological boundary in CARO"} ! bona-fide anatomical boundary +is_a: UBERON:0010199 ! bona-fide anatomical boundary [Term] id: UBERON:0007005 @@ -230989,13 +227959,14 @@ xref: FMA:293143 xref: SCTID:360387000 xref: VHOG:0001641 xref: XAO:0000235 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue -relationship: developmentally_induced_by UBERON:0009881 ! anterior lateral plate mesoderm -relationship: develops_from UBERON:0004872 ! splanchnic layer of lateral plate mesoderm relationship: part_of UBERON:0004140 ! primary heart field relationship: part_of UBERON:0009881 ! anterior lateral plate mesoderm -property_value: editor_note "consider FBbt:00005541 ! cardiogenic mesoderm" xsd:string -property_value: editor_note "review EHDAA2 placement" xsd:string +relationship: RO:0002202 UBERON:0004872 ! develops from splanchnic layer of lateral plate mesoderm +relationship: RO:0002256 UBERON:0009881 ! developmentally induced by anterior lateral plate mesoderm +property_value: IAO:0000116 "consider FBbt:00005541 ! cardiogenic mesoderm" xsd:string +property_value: IAO:0000116 "review EHDAA2 placement" xsd:string [Term] id: UBERON:0007010 @@ -231005,10 +227976,10 @@ def: "Organism at the cleavage stage." [OBOL:automatic] xref: BILA:0000058 is_a: UBERON:0000922 ! embryo intersection_of: UBERON:0000468 ! multicellular organism -intersection_of: existence_ends_with UBERON:0000107 ! cleavage stage -intersection_of: existence_starts_with UBERON:0000107 ! cleavage stage -relationship: existence_ends_with UBERON:0000107 ! cleavage stage -relationship: existence_starts_with UBERON:0000107 ! cleavage stage +intersection_of: RO:0002489 UBERON:0000107 ! existence starts with cleavage stage +intersection_of: RO:0002493 UBERON:0000107 ! existence ends with cleavage stage +relationship: RO:0002489 UBERON:0000107 ! existence starts with cleavage stage +relationship: RO:0002493 UBERON:0000107 ! existence ends with cleavage stage [Term] id: UBERON:0007021 @@ -231023,12 +227994,11 @@ xref: http://neurolex.org/wiki/Category\:Juvenile_organism xref: TAO:0002047 is_a: UBERON:0000468 ! multicellular organism intersection_of: UBERON:0000468 ! multicellular organism -intersection_of: existence_ends_with UBERON:0000112 ! sexually immature stage -intersection_of: existence_starts_with UBERON:0000112 ! sexually immature stage -relationship: existence_ends_with UBERON:0000112 ! sexually immature stage -relationship: existence_starts_with UBERON:0000112 ! sexually immature stage -relationship: has_quality PATO:0001190 ! juvenile -property_value: UBPROP:0000001 "Whole organism that is not fully grown or sexually mature.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002047", ontology="TAO", source="TAO:wd"} +intersection_of: RO:0002489 UBERON:0000112 ! existence starts with sexually immature stage +intersection_of: RO:0002493 UBERON:0000112 ! existence ends with sexually immature stage +relationship: RO:0000086 PATO:0001190 ! has quality juvenile +relationship: RO:0002489 UBERON:0000112 ! existence starts with sexually immature stage +relationship: RO:0002493 UBERON:0000112 ! existence ends with sexually immature stage [Term] id: UBERON:0007023 @@ -231038,7 +228008,6 @@ def: "A multicellular organism that existence_ends_with a post-juvenile adult st synonym: "adult" BROAD [] synonym: "adults" EXACT OMO:0003004 [TAO:0002046] xref: BILA:0000078 -xref: FBbt:00003004 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: galen:Adult xref: HAO:0000087 xref: http://neurolex.org/wiki/Category\:Adult_organism @@ -231047,11 +228016,10 @@ xref: TAO:0002046 xref: UMLS:C0001675 {source="ncithesaurus:Adult"} is_a: UBERON:0000468 ! multicellular organism intersection_of: UBERON:0000468 ! multicellular organism -intersection_of: existence_ends_with UBERON:0000113 ! post-juvenile adult stage -intersection_of: existence_starts_with UBERON:0000113 ! post-juvenile adult stage -relationship: existence_ends_with UBERON:0000113 ! post-juvenile adult stage -relationship: existence_starts_with UBERON:0000113 ! post-juvenile adult stage -property_value: UBPROP:0000001 "Whole organism that is fully grown or sexually mature.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002046", ontology="TAO", source="TAO:wd"} +intersection_of: RO:0002489 UBERON:0000113 ! existence starts with post-juvenile adult stage +intersection_of: RO:0002493 UBERON:0000113 ! existence ends with post-juvenile adult stage +relationship: RO:0002489 UBERON:0000113 ! existence starts with post-juvenile adult stage +relationship: RO:0002493 UBERON:0000113 ! existence ends with post-juvenile adult stage [Term] id: UBERON:0007026 @@ -231070,12 +228038,11 @@ xref: SCTID:360394002 xref: UMLS:C1514442 {source="ncithesaurus:Primordial_Gut"} is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001555 ! digestive tract -relationship: existence_starts_during UBERON:0000109 ! gastrula stage -relationship: has_developmental_contribution_from UBERON:0000925 ! endoderm -relationship: has_developmental_contribution_from UBERON:0000926 ! mesoderm -relationship: has_potential_to_develop_into UBERON:0001555 ! digestive tract -property_value: UBPROP:0000011 "The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis" xsd:string {source="NCBIBook:NBK10107"} +intersection_of: RO:0002387 UBERON:0001555 ! has potential to develop into digestive tract +relationship: RO:0002254 UBERON:0000925 ! has developmental contribution from endoderm +relationship: RO:0002254 UBERON:0000926 ! has developmental contribution from mesoderm +relationship: RO:0002387 UBERON:0001555 ! has potential to develop into digestive tract +relationship: RO:0002488 UBERON:0000109 ! existence starts during gastrula stage [Term] id: UBERON:0007037 @@ -231121,14 +228088,12 @@ synonym: "adult heart" RELATED [FBbt:00003154] synonym: "dorsal tube" NARROW [Wikipedia:Heart] synonym: "heart" NARROW [GO:0007507] xref: http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg -xref: SPD:0000130 xref: TADS:0000147 is_a: UBERON:0015228 ! circulatory organ intersection_of: UBERON:0015228 ! circulatory organ intersection_of: capable_of GO:0008015 ! blood circulation -relationship: capable_of GO:0008015 {notes="GO uses blood circulation generically to include the haemolymphatic fluid of arthropods"} ! blood circulation +relationship: capable_of GO:0008015 ! blood circulation relationship: has_part CL:0002494 ! cardiocyte -property_value: UBPROP:0000008 "note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis" xsd:string [Term] id: UBERON:0007106 @@ -231156,11 +228121,9 @@ xref: UMLS:C0008508 {source="ncithesaurus:Chorionic_Villus"} xref: Wikipedia:Chorionic_villi is_a: UBERON:0000478 ! extraembryonic structure is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0004027 {source="MP-def"} ! chorionic plate relationship: part_of UBERON:0003124 {source="BTO"} ! chorion membrane -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Gray29.png" xsd:anyURI -property_value: UBPROP:0000008 "The mouse and human placentas have labyrinthine and villous types of interdigitation between maternal and fetal tissues, respectively" xsd:string -property_value: UBPROP:0000010 "The bulk of the villi consist of connective tissues in which blood vessels are found. Most of the cells in the connective tissue core of the villi are fibroblasts. Macrophages known as Hofbauer cells are also present." xsd:string +relationship: RO:0002202 UBERON:0004027 {source="MP-def"} ! develops from chorionic plate +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Gray29.png" xsd:anyURI [Term] id: UBERON:0007119 @@ -231181,13 +228144,14 @@ xref: NCIT:C61563 xref: SCTID:361792007 xref: UMLS:C0015815 {source="ncithesaurus:Femoral_Neck"} xref: Wikipedia:Femur_neck +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005055 ! zone of long bone is_a: UBERON:0018664 ! neck of bone element intersection_of: UBERON:0001560 ! neck of organ intersection_of: part_of UBERON:0000981 ! femur relationship: part_of UBERON:0006863 ! proximal metaphysis of femur -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/97/Gray243.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/97/Gray243.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0007122 @@ -231230,10 +228194,6 @@ intersection_of: overlaps UBERON:0003066 ! pharyngeal arch 2 intersection_of: overlaps UBERON:0004362 ! pharyngeal arch 1 relationship: overlaps UBERON:0003066 ! pharyngeal arch 2 relationship: overlaps UBERON:0004362 ! pharyngeal arch 1 -property_value: UBPROP:0000001 ". [][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000970", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "In all jawed vertebrates the first arch forms the jaw, while the second arch forms the hyoid apparatus. These two arches are separated by the first pharyngeal pouch and cleft.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000970", ontology="VHOG", source="DOI:10.1016/j.semcdb.2010.01.022 Grevellec A, Tucker AS, The pharyngeal pouches and clefts: development, evolution, structure and derivatives. Seminars in Cell and Developmental Biology (2010)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000011 "The endoderm lines the future auditory tube (Pharyngotympanic Eustachian tube) , middle ear, mastoid antrum, and inner layer of the tympanic membrane. & origin of Mandibular nerve & Maxillary artery" xsd:string {source="WP"} -property_value: UBPROP:0000012 "we use adjacency relations rather than part_of, as in EHDAA2." xsd:string {external_ontology="EHDAA2"} [Term] id: UBERON:0007123 @@ -231258,7 +228218,6 @@ xref: AAO:0011115 xref: EFO:0003633 xref: EHDAA2:0000058 xref: EMAPA:16275 -xref: EMAPA:16276 xref: FMA:295676 xref: NCIT:C34289 xref: RETIRED_EHDAA2:0000060 @@ -231276,11 +228235,6 @@ intersection_of: overlaps UBERON:0003066 ! pharyngeal arch 2 intersection_of: overlaps UBERON:0003114 ! pharyngeal arch 3 relationship: overlaps UBERON:0003066 ! pharyngeal arch 2 relationship: overlaps UBERON:0003114 ! pharyngeal arch 3 -property_value: UBPROP:0000001 "A pouch that is situated between the 2nd and 3rd pharyngeal arch. [ISBN:0124020607][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000967", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000001 "Second of the pharyngeal (endodermal) evaginations between the visceral arches from which the Eustachian tube is derived; pouches 2-4 open as gill slits.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011115", ontology="AAO", source="ISBN:0-226-55763-4"} -property_value: UBPROP:0000003 "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000967", ontology="VHOG", source="DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "the dorsal elongation of the second pouch endoderm of all mammals, with the exception of rodents, gives rise to the epithelial lining of palatine tonsils; in rodents, the ventral portion of the second pouch appears to degenerate whereas the remaining part is incorporated into the lateral border of the pharynx; it appears that rodents no longer require tonsils as their function is carried out by the NALT (Nose/Nasal-Associated Lymphoid Tissue) system in the upper respiratory tract." xsd:string -property_value: UBPROP:0000011 "Contributes to the middle ear, epithelial lining of Crypts (spaces) of the palatine tonsils, supplied by the facial nerve" xsd:string {source="WP"} [Term] id: UBERON:0007124 @@ -231321,10 +228275,6 @@ intersection_of: overlaps UBERON:0003114 ! pharyngeal arch 3 intersection_of: overlaps UBERON:0003115 ! pharyngeal arch 4 relationship: overlaps UBERON:0003114 ! pharyngeal arch 3 relationship: overlaps UBERON:0003115 ! pharyngeal arch 4 -property_value: UBPROP:0000001 "A pouch that is situated between the 3rd and 4th pharyngeal arch. [ISBN:0124020607][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000966", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000001 "Third of the pharyngeal (endodermal) evaginations between the visceral arches from which the Eustachian tube is derived; pouches 2-4 open as gill slits.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011116", ontology="AAO", source="ISBN:0-226-55763-4"} -property_value: UBPROP:0000003 "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000966", ontology="VHOG", source="DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000011 "The third pouch possesses Dorsal and Ventral wings. Derivatives of the dorsal wings include the inferior parathyroid glands, while the ventral wings fuse to form the cytoreticular cells of the thymus. The main nerve supply to the derivatives of this pouch is Cranial Nerve IX, glossopharyngeal nerve" xsd:string {source="WP"} [Term] id: UBERON:0007125 @@ -231365,10 +228315,6 @@ intersection_of: overlaps UBERON:0003115 ! pharyngeal arch 4 intersection_of: overlaps UBERON:0003116 ! pharyngeal arch 5 relationship: overlaps UBERON:0003115 ! pharyngeal arch 4 relationship: overlaps UBERON:0003116 ! pharyngeal arch 5 -property_value: UBPROP:0000001 "A pouch that is situated between the 4th and 5th pharyngeal arch. [ISBN:0124020607][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000971", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000001 "Fourth of the pharyngeal (endodermal) evaginations between the visceral arches from which the Eustachian tube is derived; pouches 2-4 open as gill slits.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011117", ontology="AAO", source="ISBN:0-226-55763-4"} -property_value: UBPROP:0000003 "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000971", ontology="VHOG", source="DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000011 "Derivatives include: superior parathyroid glands and ultimobranchial body which forms the parafollicular C-Cells of the thyroid gland. Musculature and cartilage of larynx (along with the sixth pharyngeal pouch)[WP] in most mammals, excluding rodents, the dorsal part of each fourth pouch develops into a superior parathyroid gland (parathyroid IV), which lies on the dorsal surface of the thyroid gland (the parathyroid glands derived from the third pouches descend with the thymus and are carried to a more inferior position than the parathyroid glands that are derived from the fourth pouches); the elongated ventral part of each fourth pouch develops into the ultimopharyngeal body, which fuses with the thyroid gland, giving rise to the calcitonin-producing parafollicular or C-cells of the thyroid gland. In the mouse, but also in the rat and hamster, the dorsal fourth pouch does not generate a parathyroid. Thus, rodents develop only one pair of parathyroid glands." xsd:string {source="MP"} [Term] id: UBERON:0007128 @@ -231379,7 +228325,7 @@ synonym: "corpuscle" RELATED [XAO:0000110] synonym: "glomerulus" RELATED [XAO:0000110] xref: XAO:0000110 is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0003064 ! intermediate mesoderm +relationship: RO:0002202 UBERON:0003064 ! develops from intermediate mesoderm [Term] id: UBERON:0007134 @@ -231410,8 +228356,7 @@ xref: EFO:0003497 xref: TAO:0000131 xref: ZFA:0000131 is_a: UBERON:0016879 ! future central nervous system -relationship: develops_from UBERON:0003075 ! neural plate -property_value: UBPROP:0000001 "An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000131", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002202 UBERON:0003075 ! develops from neural plate [Term] id: UBERON:0007142 @@ -231424,9 +228369,9 @@ xref: FMA:4062 xref: SCTID:161452006 is_a: UBERON:0001532 ! internal carotid artery intersection_of: UBERON:0001532 ! internal carotid artery -intersection_of: branching_part_of UBERON:0001536 ! left common carotid artery plus branches -relationship: branching_part_of UBERON:0001536 ! left common carotid artery plus branches +intersection_of: RO:0002380 UBERON:0001536 ! branching part of left common carotid artery plus branches relationship: part_of UBERON:0001536 ! left common carotid artery plus branches +relationship: RO:0002380 UBERON:0001536 ! branching part of left common carotid artery plus branches [Term] id: UBERON:0007143 @@ -231439,9 +228384,9 @@ xref: FMA:3949 xref: SCTID:161251001 is_a: UBERON:0001532 ! internal carotid artery intersection_of: UBERON:0001532 ! internal carotid artery -intersection_of: branching_part_of UBERON:0001531 ! right common carotid artery plus branches -relationship: branching_part_of UBERON:0001531 ! right common carotid artery plus branches +intersection_of: RO:0002380 UBERON:0001531 ! branching part of right common carotid artery plus branches relationship: part_of UBERON:0001531 ! right common carotid artery plus branches +relationship: RO:0002380 UBERON:0001531 ! branching part of right common carotid artery plus branches [Term] id: UBERON:0007144 @@ -231454,8 +228399,7 @@ synonym: "tail of embryo" EXACT [FMA:85540] xref: EMAPA:16748 xref: FMA:85540 is_a: UBERON:0002050 ! embryonic structure -relationship: transformation_of UBERON:0002533 ! post-anal tail bud -property_value: UBPROP:0000011 "By the fourth week a clear tail is seen in the human embryo. It recedes after a few weeks and these tissues form what is commonly known as the tailbone (coccyx)." xsd:string +relationship: RO:0002494 UBERON:0002533 ! transformation of post-anal tail bud [Term] id: UBERON:0007147 @@ -231467,9 +228411,9 @@ xref: EMAPA:18377 xref: FMA:54366 is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0001045 ! midgut -relationship: luminal_space_of UBERON:0001045 ! midgut +intersection_of: RO:0002572 UBERON:0001045 ! luminal space of midgut relationship: part_of UBERON:0001045 ! midgut +relationship: RO:0002572 UBERON:0001045 ! luminal space of midgut [Term] id: UBERON:0007148 @@ -231481,9 +228425,9 @@ xref: EMAPA:18396 xref: FMA:54367 is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0001046 ! hindgut -relationship: luminal_space_of UBERON:0001046 ! hindgut +intersection_of: RO:0002572 UBERON:0001046 ! luminal space of hindgut relationship: part_of UBERON:0001046 ! hindgut +relationship: RO:0002572 UBERON:0001046 ! luminal space of hindgut [Term] id: UBERON:0007158 @@ -231495,9 +228439,9 @@ xref: EMAPA:18836 xref: FMA:17357 is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0000159 ! anal canal -relationship: luminal_space_of UBERON:0000159 ! anal canal +intersection_of: RO:0002572 UBERON:0000159 ! luminal space of anal canal relationship: part_of UBERON:0000159 ! anal canal +relationship: RO:0002572 UBERON:0000159 ! luminal space of anal canal [Term] id: UBERON:0007159 @@ -231511,9 +228455,9 @@ xref: FMA:18374 xref: SCTID:362156004 is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0001155 ! colon -relationship: luminal_space_of UBERON:0001155 ! colon +intersection_of: RO:0002572 UBERON:0001155 ! luminal space of colon relationship: part_of UBERON:0001155 ! colon +relationship: RO:0002572 UBERON:0001155 ! luminal space of colon [Term] id: UBERON:0007160 @@ -231527,8 +228471,8 @@ xref: FMA:50770 xref: SCTID:279263009 xref: Wikipedia:Inferior_petrosal_sinus is_a: UBERON:0017635 {source="FMA"} ! paired venous dural sinus -relationship: connected_to UBERON:0001586 ! internal jugular vein -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002170 UBERON:0001586 ! connected to internal jugular vein +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0007171 @@ -231569,7 +228513,7 @@ xref: FMA:23239 xref: Wikipedia:Lateral_border_of_the_scapula is_a: UBERON:0007171 {source="EMAPA-modified"} ! border of scapula disjoint_from: UBERON:0007174 {source="lexical"} ! medial border of scapula -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0007174 @@ -231590,9 +228534,9 @@ xref: FMA:23242 xref: SCTID:368187009 xref: Wikipedia:Medial_border_of_scapula is_a: UBERON:0007171 {source="EMAPA-modified"} ! border of scapula -relationship: has_developmental_contribution_from UBERON:0002329 {source="PMID:20136669"} ! somite -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: editor_note "consider merging with UBERON:1500000 scapular blade, depending on https://github.com/obophenotype/uberon/issues/339. See also http://www.ncbi.nlm.nih.gov/pubmed/20136669" xsd:string +relationship: RO:0002254 UBERON:0002329 {source="PMID:20136669"} ! has developmental contribution from somite +property_value: IAO:0000116 "consider merging with UBERON:1500000 scapular blade, depending on https://github.com/obophenotype/uberon/issues/339. See also http://www.ncbi.nlm.nih.gov/pubmed/20136669" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0007175 @@ -231606,7 +228550,7 @@ xref: EMAPA:25128 xref: FMA:13315 xref: Wikipedia:Inferior_angle_of_scapula is_a: UBERON:0007172 {source="EMAPA-modified"} ! angle of scapula -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0007177 @@ -231626,7 +228570,7 @@ is_a: UBERON:0011189 ! lamina propria of large intestine intersection_of: UBERON:0000030 ! lamina propria intersection_of: part_of UBERON:0000317 ! colonic mucosa relationship: part_of UBERON:0000317 ! colonic mucosa -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0007181 @@ -231690,6 +228634,7 @@ xref: FMA:21426 xref: Wikipedia:Bone_marrow#Stroma is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0003891 ! stroma +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0003891 ! stroma intersection_of: part_of UBERON:0002371 ! bone marrow relationship: has_part CL:0002240 ! marrow fibroblast @@ -231714,11 +228659,12 @@ xref: SCTID:361384001 xref: Wikipedia:Tracheobronchial_tree is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000062 ! organ +is_a: UBERON:0004119 ! endoderm-derived structure relationship: has_part UBERON:0002185 ! bronchus relationship: has_part UBERON:0003126 ! trachea relationship: has_part UBERON:0007592 {source="Wikipedia"} ! ciliated columnar epithelium relationship: part_of UBERON:0001558 ! lower respiratory tract -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0007197 @@ -231774,9 +228720,10 @@ xref: EMAPA_RETIRED:16271 xref: TAO:0000787 xref: ZFA:0000787 is_a: UBERON:0005253 {source="ZFA"} ! head mesenchyme +is_a: UBERON:0014387 ! mesenchyme derived from neural crest intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: develops_from UBERON:0003099 ! cranial neural crest -relationship: develops_from UBERON:0003099 ! cranial neural crest +intersection_of: RO:0002202 UBERON:0003099 ! develops from cranial neural crest +relationship: RO:0002202 UBERON:0003099 ! develops from cranial neural crest [Term] id: UBERON:0007214 @@ -231791,9 +228738,10 @@ xref: EMAPA:16182 xref: TAO:0000999 xref: ZFA:0000999 is_a: UBERON:0005256 ! trunk mesenchyme +is_a: UBERON:0014387 ! mesenchyme derived from neural crest intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: develops_from UBERON:0003083 ! trunk neural crest -relationship: develops_from UBERON:0003083 ! trunk neural crest +intersection_of: RO:0002202 UBERON:0003083 ! develops from trunk neural crest +relationship: RO:0002202 UBERON:0003083 ! develops from trunk neural crest [Term] id: UBERON:0007220 @@ -231850,7 +228798,7 @@ is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000112 ! sexually immature stage relationship: part_of UBERON:0018685 {gci_relation="part_of", gci_filler="NCBITaxon:40674"} ! nursing stage -property_value: editor_note "consider splitting infant/newborn" xsd:string +property_value: IAO:0000116 "consider splitting infant/newborn" xsd:string property_value: seeAlso "https://github.com/obophenotype/uberon/issues/350" xsd:anyURI [Term] @@ -231861,9 +228809,9 @@ def: "The osseous cochlea is the bony foundation that forms the small shell arra subset: pheno_slim xref: EMAPA:35620 xref: MA:0000239 -is_a: UBERON:0000061 ! anatomical structure +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001844 ! cochlea -property_value: editor_note "TODO - check this. in MA, cochlea is not part of the bony labyrinth" xsd:string +property_value: IAO:0000116 "TODO - check this. in MA, cochlea is not part of the bony labyrinth" xsd:string [Term] id: UBERON:0007237 @@ -231878,8 +228826,7 @@ xref: EMAPA:16382 xref: VHOG:0000510 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0004362 {source="EHDAA2"} ! pharyngeal arch 1 -property_value: editor_note "relationship to Meckel's cartilage to be added" xsd:string -property_value: UBPROP:0000003 "Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000510", ontology="VHOG", source="DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)", source="http://bgee.unil.ch/"} +property_value: IAO:0000116 "relationship to Meckel's cartilage to be added" xsd:string [Term] id: UBERON:0007238 @@ -231888,11 +228835,9 @@ namespace: uberon xref: EHDAA2:0000038 xref: EHDAA:595 xref: EMAPA:16388 -xref: VHOG:0000511 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0004362 {source="EHDAA2"} ! pharyngeal arch 1 -property_value: editor_note "relationship to palatoquadrate to be added" xsd:string -property_value: UBPROP:0000003 "Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000511", ontology="VHOG", source="DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)", source="http://bgee.unil.ch/"} +property_value: IAO:0000116 "relationship to palatoquadrate to be added" xsd:string [Term] id: UBERON:0007239 @@ -231990,8 +228935,8 @@ xref: FMA:256381 xref: FMA:84059 is_a: UBERON:0002020 ! gray matter intersection_of: UBERON:0002020 ! gray matter -intersection_of: composed_primarily_of UBERON:0000125 ! neural nucleus -relationship: composed_primarily_of UBERON:0000125 ! neural nucleus +intersection_of: RO:0002473 UBERON:0000125 ! composed primarily of neural nucleus +relationship: RO:0002473 UBERON:0000125 ! composed primarily of neural nucleus [Term] id: UBERON:0007247 @@ -232008,7 +228953,6 @@ is_a: UBERON:0009662 ! hindbrain nucleus intersection_of: UBERON:0002308 ! nucleus of brain intersection_of: part_of UBERON:0002128 ! superior olivary complex relationship: part_of UBERON:0002128 ! superior olivary complex -property_value: IAO:0000232 "this class exists largely for consistency with the FMA. It is defined trivially with respect to the SOC. The class may be removed in future." xsd:string [Term] id: UBERON:0007251 @@ -232017,12 +228961,11 @@ namespace: uberon def: "A nucleus of brain that is part of a preoptic area." [OBOL:automatic] xref: CALOHA:TS-0822 xref: EV:0100226 -xref: MESH:D011301 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} is_a: UBERON:0006569 ! diencephalic nucleus intersection_of: UBERON:0002308 ! nucleus of brain intersection_of: part_of UBERON:0001928 ! preoptic area relationship: part_of UBERON:0001928 ! preoptic area -relationship: present_in_taxon NCBITaxon:117569 {source="Hardisty, p. 320-1"} +property_value: RO:0002175 NCBITaxon:117569 {source="Hardisty, p. 320-1"} [Term] id: UBERON:0007252 @@ -232074,10 +229017,10 @@ synonym: "intervertebral disk, C1-C2" EXACT [] xref: EMAPA:19416 is_a: UBERON:0007252 ! intervertebral disk of cervical vertebra intersection_of: UBERON:0001066 ! intervertebral disk -intersection_of: connects UBERON:0001092 ! vertebral bone 1 -intersection_of: connects UBERON:0001093 ! vertebral bone 2 -relationship: connects UBERON:0001092 ! vertebral bone 1 -relationship: connects UBERON:0001093 ! vertebral bone 2 +intersection_of: RO:0002176 UBERON:0001092 ! connects vertebral bone 1 +intersection_of: RO:0002176 UBERON:0001093 ! connects vertebral bone 2 +relationship: RO:0002176 UBERON:0001092 ! connects vertebral bone 1 +relationship: RO:0002176 UBERON:0001093 ! connects vertebral bone 2 [Term] id: UBERON:0007267 @@ -232090,7 +229033,7 @@ is_a: UBERON:0005866 ! pre-cartilage condensation is_a: UBERON:0009505 ! mesenchyme of trachea intersection_of: UBERON:0005866 ! pre-cartilage condensation intersection_of: part_of UBERON:0003126 ! trachea -relationship: develops_from UBERON:0009505 {source="EHDAA2"} ! mesenchyme of trachea +relationship: RO:0002202 UBERON:0009505 {source="EHDAA2"} ! develops from mesenchyme of trachea [Term] id: UBERON:0007269 @@ -232108,7 +229051,7 @@ is_a: UBERON:0014793 ! musculature of pectoral complex intersection_of: UBERON:0001015 ! musculature intersection_of: part_of UBERON:0004710 ! pectoral appendage relationship: part_of UBERON:0004710 ! pectoral appendage -property_value: editor_note "currently defined by location rather than attachment" xsd:string +property_value: IAO:0000116 "currently defined by location rather than attachment" xsd:string [Term] id: UBERON:0007270 @@ -232123,8 +229066,7 @@ is_a: UBERON:0014792 ! musculature of pelvic complex intersection_of: UBERON:0001015 ! musculature intersection_of: part_of UBERON:0004709 ! pelvic appendage relationship: part_of UBERON:0004709 ! pelvic appendage -property_value: editor_note "currently defined by location rather than attachment" xsd:string -property_value: UBPROP:0000001 "Musculature that is part of the pelvic fin.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000258", ontology="TAO", source="TAO:curator"} +property_value: IAO:0000116 "currently defined by location rather than attachment" xsd:string [Term] id: UBERON:0007271 @@ -232138,7 +229080,7 @@ is_a: UBERON:0001015 ! musculature intersection_of: UBERON:0001015 ! musculature intersection_of: part_of UBERON:0000026 ! appendage relationship: part_of UBERON:0000026 ! appendage -property_value: editor_note "currently defined by location rather than attachment" xsd:string +property_value: IAO:0000116 "currently defined by location rather than attachment" xsd:string [Term] id: UBERON:0007272 @@ -232149,11 +229091,10 @@ synonym: "cheiropterygium" RELATED [VSAO:0005000, VSAO:NI] xref: VSAO:0005000 is_a: UBERON:0011582 ! paired limb/fin skeleton intersection_of: UBERON:0010912 ! subdivision of skeleton -intersection_of: skeleton_of UBERON:0004710 ! pectoral appendage -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +intersection_of: RO:0002576 UBERON:0004710 ! skeleton of pectoral appendage relationship: part_of UBERON:0004710 {source="VSAO"} ! pectoral appendage -relationship: skeleton_of UBERON:0004710 ! pectoral appendage -property_value: RO:0002475 UBERON:0007273 +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002576 UBERON:0004710 ! skeleton of pectoral appendage [Term] id: UBERON:0007273 @@ -232162,10 +229103,10 @@ namespace: uberon def: "The collection of all skeletal elements in a pelvic appendage region." [https://orcid.org/0000-0002-6601-2165] is_a: UBERON:0011582 ! paired limb/fin skeleton intersection_of: UBERON:0010912 ! subdivision of skeleton -intersection_of: skeleton_of UBERON:0004709 ! pelvic appendage -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +intersection_of: RO:0002576 UBERON:0004709 ! skeleton of pelvic appendage relationship: part_of UBERON:0004709 {source="VSAO"} ! pelvic appendage -relationship: skeleton_of UBERON:0004709 ! pelvic appendage +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002576 UBERON:0004709 ! skeleton of pelvic appendage [Term] id: UBERON:0007277 @@ -232187,13 +229128,12 @@ xref: Wikipedia:Rhombencephalon xref: ZFA:0000569 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0002028 ! hindbrain -relationship: develops_from UBERON:0003076 {source="XAO-abduced"} ! posterior neural tube -relationship: has_developmental_contribution_from UBERON:0003852 {source="cjm"} ! rhombencephalon neural crest -relationship: has_potential_to_develop_into UBERON:0002028 ! hindbrain +intersection_of: RO:0002387 UBERON:0002028 ! has potential to develop into hindbrain relationship: part_of UBERON:0006238 ! future brain -property_value: editor_note "TODO - unify naming conventions" xsd:string -property_value: UBPROP:0000001 "The embryonic rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. Rhombomeres Rh7-Rh4 form the myelencephalon that will give the medulla oblongata. Rhombomeres Rh3-Rh1 form the metencephalon that will form the pons and the cerebellum[NPX:PDR]." xsd:string {source="NPX:PDR"} +relationship: RO:0002202 UBERON:0003076 {source="XAO-abduced"} ! develops from posterior neural tube +relationship: RO:0002254 UBERON:0003852 {source="cjm"} ! has developmental contribution from rhombencephalon neural crest +relationship: RO:0002387 UBERON:0002028 ! has potential to develop into hindbrain +property_value: IAO:0000116 "TODO - unify naming conventions" xsd:string [Term] id: UBERON:0007278 @@ -232204,9 +229144,9 @@ xref: TAO:0002234 xref: ZFA:0001722 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0002063 ! sinus venosus -relationship: has_potential_to_develop_into UBERON:0002063 ! sinus venosus +intersection_of: RO:0002387 UBERON:0002063 ! has potential to develop into sinus venosus relationship: part_of UBERON:0004141 {source="ZFA"} ! heart tube +relationship: RO:0002387 UBERON:0002063 ! has potential to develop into sinus venosus [Term] id: UBERON:0007280 @@ -232217,11 +229157,10 @@ xref: TAO:0002233 xref: ZFA:0001724 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0002165 ! endocardium -relationship: develops_from UBERON:0003084 ! heart primordium -relationship: has_potential_to_develop_into UBERON:0002165 ! endocardium +intersection_of: RO:0002387 UBERON:0002165 ! has potential to develop into endocardium relationship: part_of UBERON:0005498 ! primitive heart tube -property_value: UBPROP:0000001 "Portion of tissue that is part of the heart tube and will become the endocardium.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002233", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002202 UBERON:0003084 ! develops from heart primordium +relationship: RO:0002387 UBERON:0002165 ! has potential to develop into endocardium [Term] id: UBERON:0007281 @@ -232237,9 +229176,9 @@ xref: XAO:0004086 xref: ZFA:0001187 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0003052 ! midbrain-hindbrain boundary -relationship: has_potential_to_develop_into UBERON:0003052 ! midbrain-hindbrain boundary +intersection_of: RO:0002387 UBERON:0003052 ! has potential to develop into midbrain-hindbrain boundary relationship: part_of UBERON:0006238 {source="ZFA"} ! future brain +relationship: RO:0002387 UBERON:0003052 ! has potential to develop into midbrain-hindbrain boundary [Term] id: UBERON:0007282 @@ -232253,9 +229192,9 @@ xref: TAO:0000053 xref: ZFA:0000053 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0003059 ! presomitic mesoderm -relationship: develops_from UBERON:0009618 {consistent_with="https://github.com/obophenotype/uberon/wiki/The-neural-crest", source="EDHAA2"} ! trunk paraxial mesoderm -relationship: has_potential_to_develop_into UBERON:0003059 ! presomitic mesoderm +intersection_of: RO:0002387 UBERON:0003059 ! has potential to develop into presomitic mesoderm +relationship: RO:0002202 UBERON:0009618 ! develops from trunk paraxial mesoderm +relationship: RO:0002387 UBERON:0003059 ! has potential to develop into presomitic mesoderm [Term] id: UBERON:0007284 @@ -232270,12 +229209,11 @@ xref: TAO:0000063 xref: ZFA:0000063 is_a: UBERON:0016879 ! future central nervous system intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0003075 ! neural plate -relationship: develops_from UBERON:0002346 ! neurectoderm -relationship: has_potential_to_develop_into UBERON:0003075 ! neural plate +intersection_of: RO:0002387 UBERON:0003075 ! has potential to develop into neural plate relationship: part_of UBERON:0004734 ! gastrula -property_value: editor_note "consider merging" xsd:string -property_value: UBPROP:0000001 "Region of the gastrula which gives rise to the neural plate.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000063", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002202 UBERON:0002346 ! develops from neurectoderm +relationship: RO:0002387 UBERON:0003075 ! has potential to develop into neural plate +property_value: IAO:0000116 "consider merging" xsd:string [Term] id: UBERON:0007285 @@ -232291,10 +229229,10 @@ xref: XAO:0004134 xref: ZFA:0000591 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 {source="https://github.com/obophenotype/uberon/issues/1277"} ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0003077 {source="https://github.com/obophenotype/uberon/issues/1277"} ! paraxial mesoderm intersection_of: part_of UBERON:0000307 {source="https://github.com/obophenotype/uberon/issues/1277"} ! blastula -relationship: has_potential_to_develop_into UBERON:0003077 ! paraxial mesoderm +intersection_of: RO:0002387 UBERON:0003077 {source="https://github.com/obophenotype/uberon/issues/1277"} ! has potential to develop into paraxial mesoderm relationship: part_of UBERON:0000307 ! blastula +relationship: RO:0002387 UBERON:0003077 ! has potential to develop into paraxial mesoderm [Term] id: UBERON:0007288 @@ -232307,9 +229245,9 @@ xref: TAO:0001368 xref: ZFA:0001368 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0005075 ! forebrain-midbrain boundary -relationship: has_potential_to_develop_into UBERON:0005075 ! forebrain-midbrain boundary +intersection_of: RO:0002387 UBERON:0005075 ! has potential to develop into forebrain-midbrain boundary relationship: part_of UBERON:0006238 ! future brain +relationship: RO:0002387 UBERON:0005075 ! has potential to develop into forebrain-midbrain boundary [Term] id: UBERON:0007289 @@ -232320,8 +229258,8 @@ xref: TAO:0001207 xref: ZFA:0001207 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0005499 ! rhombomere 1 -relationship: has_potential_to_develop_into UBERON:0005499 ! rhombomere 1 +intersection_of: RO:0002387 UBERON:0005499 ! has potential to develop into rhombomere 1 +relationship: RO:0002387 UBERON:0005499 ! has potential to develop into rhombomere 1 [Term] id: UBERON:0007297 @@ -232335,8 +229273,8 @@ xref: TAO:0001070 xref: ZFA:0001070 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0005721 ! pronephric mesoderm -relationship: has_potential_to_develop_into UBERON:0005721 ! pronephric mesoderm +intersection_of: RO:0002387 UBERON:0005721 ! has potential to develop into pronephric mesoderm +relationship: RO:0002387 UBERON:0005721 ! has potential to develop into pronephric mesoderm [Term] id: UBERON:0007298 @@ -232471,12 +229409,12 @@ xref: FMA:16012 xref: MA:0000721 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000064 ! organ part +is_a: UBERON:0004119 ! endoderm-derived structure relationship: has_part UBERON:0001263 ! pancreatic acinus relationship: has_part UBERON:0014719 ! intralobular duct relationship: part_of UBERON:0000017 ! exocrine pancreas -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: editor_note "TODO - check" xsd:string -property_value: UBPROP:0000008 "In mice many lobules lack islets, in contrast to other mammals including humans" xsd:string +property_value: IAO:0000116 "TODO - check" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0007329 @@ -232493,7 +229431,6 @@ xref: EHDAA:9194 xref: EMAPA:32952 xref: FMA:10419 xref: MA:0000124 -xref: MESH:D010183 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: SCTID:181278006 xref: TAO:0001372 xref: VHOG:0000254 @@ -232502,18 +229439,14 @@ xref: ZFA:0001372 is_a: UBERON:0003928 {source="ZFA"} ! digestive system duct is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0000058 ! duct -intersection_of: connected_to UBERON:0000160 ! intestine intersection_of: part_of UBERON:0001264 ! pancreas -relationship: connected_to UBERON:0000160 ! intestine -relationship: contributes_to_morphology_of UBERON:0000017 ! exocrine pancreas -relationship: develops_from UBERON:0003922 ! pancreatic epithelial bud +intersection_of: RO:0002170 UBERON:0000160 ! connected to intestine relationship: part_of UBERON:0000017 {source="MA"} ! exocrine pancreas -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1100.png" xsd:anyURI -property_value: IAO:0000232 "this class groups together accessory (dorsal) and main (ventral) pancreatic ducts" xsd:string -property_value: UBPROP:0000001 "Duct connecting the pancreas with the intestine. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000254", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "These data show that ducts within the zebrafish pancreas originally arise in situ from isolated progenitor cells rather than arising from reiterative branching of the pancreatic epithelium. This process of pancreatic duct formation in zebrafish may be analogous to the mechanism of duct formation in the mammalian mammary and salivary glands. (...) A related mechanism of duct formation has also been proposed to occur within the mammalian pancreatic epithelium.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000254", ontology="VHOG", source="DOI:10.1016/j.ydbio.2005.04.035 Yee NS, Lorent K, Pack M, Exocrine pancreas development in zebrafish. Developmental Biology (2005)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "in EHDAA2, the dorsal and ventral ducts are classified as epithelial sacs - review after overhaul of duct/epithelia terms" xsd:string {external_ontology="EHDAA2"} +relationship: RO:0002170 UBERON:0000160 ! connected to intestine +relationship: RO:0002202 UBERON:0003922 ! develops from pancreatic epithelial bud +relationship: RO:0002433 UBERON:0000017 ! contributes to morphology of exocrine pancreas +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/15/Gray1100.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0007352 @@ -232550,9 +229483,9 @@ synonym: "dorsal surface of tongue" EXACT [FMA:54646] xref: FMA:54646 is_a: UBERON:0007367 ! surface of tongue intersection_of: UBERON:0007367 ! surface of tongue -intersection_of: in_dorsal_side_of UBERON:0001723 ! tongue -relationship: in_dorsal_side_of UBERON:0001723 ! tongue -property_value: editor_note "check superior/dorsal" xsd:string +intersection_of: BSPO:0015101 UBERON:0001723 ! tongue +relationship: BSPO:0015101 UBERON:0001723 ! tongue +property_value: IAO:0000116 "check superior/dorsal" xsd:string [Term] id: UBERON:0007375 @@ -232569,7 +229502,7 @@ xref: CALOHA:TS-2212 xref: Wikipedia:Palate is_a: UBERON:0000481 ! multi-tissue structure relationship: part_of UBERON:0000033 ! head -property_value: editor_note "check subclasses to verify if they refer to a multi-tissue structure or a subdivision of the skeleton" xsd:string +property_value: IAO:0000116 "check subclasses to verify if they refer to a multi-tissue structure or a subdivision of the skeleton" xsd:string [Term] id: UBERON:0007376 @@ -232585,20 +229518,19 @@ synonym: "outer epidermal layer" EXACT [] synonym: "outer epithelial layer" EXACT [] xref: BSA:0000073 xref: BTO:0000313 -xref: FBbt:00004993 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: HAO:0000298 xref: TADS:0000109 xref: WBbt:0005733 xref: Wikipedia:Epidermis_(zoology) -is_a: UBERON:0000483 ! epithelium is_a: UBERON:0003102 ! surface structure +is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: bounding_layer_of UBERON:0000468 ! multicellular organism -intersection_of: develops_from UBERON:0007383 ! enveloping layer of ectoderm +intersection_of: RO:0002202 UBERON:0007383 ! develops from enveloping layer of ectoderm relationship: bounding_layer_of UBERON:0000468 ! multicellular organism -relationship: develops_from UBERON:0007383 ! enveloping layer of ectoderm -relationship: only_in_taxon NCBITaxon:6072 {source="Wikipedia:Epidermis_(zoology)"} ! Eumetazoa -property_value: editor_note "this grouping class exists primarily to align with GO - see GO:0008544." xsd:string +relationship: RO:0002160 NCBITaxon:6072 {source="Wikipedia:Epidermis_(zoology)"} ! only in taxon Eumetazoa +relationship: RO:0002202 UBERON:0007383 ! develops from enveloping layer of ectoderm +property_value: IAO:0000116 "this grouping class exists primarily to align with GO - see GO:0008544." xsd:string [Term] id: UBERON:0007383 @@ -232613,11 +229545,9 @@ xref: TAO:0000086 xref: ZFA:0000086 is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010371 ! ecto-epithelium relationship: bounding_layer_of UBERON:0000922 ! embryo -relationship: develops_from UBERON:0000076 ! external ectoderm -property_value: UBPROP:0000001 "Outermost monolayer of cells surrounding the embryo that become very flattened in the blastula and give rise to the periderm. Sometimes used synonymously with periderm. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000086", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000002 "relationship loss: develops_from superficial blastomere (TAO:0001484)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000086", ontology="TAO"} -property_value: UBPROP:0000008 "Originally this tissue is one cell layer thick but in most vertebrates it soon becomes a two layered structure. The outer layer gives rise to the periderm." xsd:string +relationship: RO:0002202 UBERON:0000076 ! develops from external ectoderm [Term] id: UBERON:0007384 @@ -232667,7 +229597,6 @@ intersection_of: UBERON:0002418 ! cartilage tissue intersection_of: part_of UBERON:0004708 ! paired limb/fin relationship: part_of UBERON:0002091 ! appendicular skeleton relationship: part_of UBERON:0004708 ! paired limb/fin -property_value: UBPROP:0000001 "Cartilage which is part of one of the paired fins.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001543", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0007390 @@ -232677,12 +229606,12 @@ def: "A cartilage tissue that is part of a pectoral appendage." [OBOL:automatic] synonym: "pectoral fin cartilage" RELATED [TAO:0000257] xref: TAO:0000257 xref: ZFA:0000257 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0007389 ! paired limb/fin cartilage intersection_of: UBERON:0002418 ! cartilage tissue intersection_of: part_of UBERON:0004710 ! pectoral appendage -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0007272 ! pectoral appendage skeleton -property_value: UBPROP:0000001 "Cartilage which is part of the pectoral fin.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000257", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata [Term] id: UBERON:0007391 @@ -232692,12 +229621,12 @@ def: "A cartilage tissue that is part of a pelvic appendage." [OBOL:automatic] synonym: "pelvic fin cartilage" RELATED [TAO:0001459] xref: TAO:0001459 xref: ZFA:0001459 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0007389 ! paired limb/fin cartilage intersection_of: UBERON:0002418 ! cartilage tissue intersection_of: part_of UBERON:0004709 ! pelvic appendage -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0007273 ! pelvic appendage skeleton -property_value: UBPROP:0000001 "Cartilage which is part of the pelvic fin.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001459", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata [Term] id: UBERON:0007414 @@ -232713,7 +229642,6 @@ is_a: UBERON:0000125 ! neural nucleus intersection_of: UBERON:0000125 ! neural nucleus intersection_of: overlaps UBERON:0001943 ! midbrain tegmentum relationship: overlaps UBERON:0001943 ! midbrain tegmentum -property_value: IAO:0000232 "this class groups together any nuclei in the tegmentum region, possibly including disparate structures across species" xsd:string [Term] id: UBERON:0007418 @@ -232756,8 +229684,8 @@ synonym: "cavity of vesicle" EXACT [AEO:0000079] xref: AEO:0000079 is_a: UBERON:0012467 ! enclosed anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0007499 ! epithelial sac -relationship: luminal_space_of UBERON:0007499 ! epithelial sac +intersection_of: RO:0002572 UBERON:0007499 ! luminal space of epithelial sac +relationship: RO:0002572 UBERON:0007499 ! luminal space of epithelial sac [Term] id: UBERON:0007475 @@ -232768,8 +229696,8 @@ xref: AEO:0000081 xref: EHDAA2:0003081 is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue -intersection_of: composed_primarily_of GO:0031012 ! extracellular matrix -relationship: composed_primarily_of GO:0031012 ! extracellular matrix +intersection_of: RO:0002473 GO:0031012 ! composed primarily of extracellular matrix +relationship: RO:0002473 GO:0031012 ! composed primarily of extracellular matrix [Term] id: UBERON:0007490 @@ -232781,10 +229709,10 @@ xref: AEO:0000099 xref: EHDAA2:0003099 is_a: UBERON:0000476 ! acellular anatomical structure intersection_of: UBERON:0000476 ! acellular anatomical structure -intersection_of: composed_primarily_of GO:0045095 ! keratin filament -relationship: composed_primarily_of GO:0045095 ! keratin filament -relationship: has_quality PATO:0002507 ! keratinous -property_value: editor_note "should all structures composed primarily of keratin be classified here? At what stage of cornification are keratin-filled cells no longer considered cells" xsd:string +intersection_of: RO:0002473 GO:0045095 ! composed primarily of keratin filament +relationship: RO:0000086 PATO:0002507 ! has quality keratinous +relationship: RO:0002473 GO:0045095 ! composed primarily of keratin filament +property_value: IAO:0000116 "should all structures composed primarily of keratin be classified here? At what stage of cornification are keratin-filled cells no longer considered cells" xsd:string [Term] id: UBERON:0007499 @@ -232796,7 +229724,7 @@ xref: EHDAA2:0003115 is_a: UBERON:0003914 {source="AEO"} ! epithelial tube is_a: UBERON:0009856 ! sac intersection_of: UBERON:0000483 ! epithelium -intersection_of: has_quality PATO:0001987 ! saccular +intersection_of: RO:0000086 PATO:0001987 ! has quality saccular [Term] id: UBERON:0007500 @@ -232838,8 +229766,8 @@ xref: SCTID:362915001 is_a: UBERON:0004590 ! sphincter muscle intersection_of: UBERON:0004590 ! sphincter muscle intersection_of: has_part CL:0000192 ! smooth muscle cell -relationship: composed_primarily_of UBERON:0001135 ! smooth muscle tissue relationship: has_part CL:0000192 ! smooth muscle cell +relationship: RO:0002473 UBERON:0001135 ! composed primarily of smooth muscle tissue [Term] id: UBERON:0007522 @@ -232851,8 +229779,8 @@ xref: EHDAA2:0003144 is_a: UBERON:0004590 ! sphincter muscle intersection_of: UBERON:0004590 ! sphincter muscle intersection_of: has_part CL:0000737 ! striated muscle cell -relationship: composed_primarily_of UBERON:0002036 ! striated muscle tissue relationship: has_part CL:0000737 ! striated muscle cell +relationship: RO:0002473 UBERON:0002036 ! composed primarily of striated muscle tissue [Term] id: UBERON:0007524 @@ -232886,7 +229814,7 @@ is_a: UBERON:0003104 ! mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: participates_in GO:0016477 ! cell migration relationship: participates_in GO:0016477 ! cell migration -property_value: editor_note "this class will be an important part of the NC reorganization" xsd:string +property_value: IAO:0000116 "this class will be an important part of the NC reorganization" xsd:string [Term] id: UBERON:0007567 @@ -232906,8 +229834,7 @@ intersection_of: UBERON:0000061 ! anatomical structure intersection_of: participates_in GO:0031099 ! regeneration relationship: part_of UBERON:0000468 ! multicellular organism relationship: participates_in GO:0031099 ! regeneration -property_value: editor_note "we define this in terms of active participation in regeneration, rather that capabilities. In this sense it is different from the AEO structure." xsd:string -property_value: UBPROP:0000001 "A portion of tissue that is regrowing after damage or amputation.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005147", ontology="TAO", source="ZFIN:curator"} +property_value: IAO:0000116 "we define this in terms of active participation in regeneration, rather that capabilities. In this sense it is different from the AEO structure." xsd:string [Term] id: UBERON:0007589 @@ -232923,8 +229850,7 @@ is_a: UBERON:0004804 {source="MA"} ! oviduct epithelium is_a: UBERON:0007592 {source="FMA"} ! ciliated columnar epithelium intersection_of: UBERON:0007592 ! ciliated columnar epithelium intersection_of: part_of UBERON:0000993 ! oviduct -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000012 "in FMA, epithelium of uterine tube is a subclass of ciliated columnar epithelium. MA introduces subtypes: ciliated columnar and cuboidal. We map the FMA type according to its relationships, not its label" xsd:string {external_ontology="FMA"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0007590 @@ -232937,7 +229863,7 @@ is_a: UBERON:0004804 {source="MA"} ! oviduct epithelium is_a: UBERON:0010077 ! cuboidal epithelium intersection_of: UBERON:0010077 ! cuboidal epithelium intersection_of: part_of UBERON:0000993 ! oviduct -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0007592 @@ -232949,8 +229875,6 @@ is_a: UBERON:0000485 {source="FMA"} ! simple columnar epithelium is_a: UBERON:0007601 ! ciliated epithelium intersection_of: UBERON:0000485 ! simple columnar epithelium intersection_of: has_part CL:0000067 ! ciliated epithelial cell -property_value: UBPROP:0000008 "In humans, Ciliated columnar epithelial cells are found mainly in the tracheal and bronchial regions of the pulmonary system and also in the fallopian tubes of the female reproductive system" xsd:string -property_value: UBPROP:0000009 "Ciliated columnar epithelium in the pulmonary system is interspersed with goblet cells that secrete mucous to form a mucosal layer apical to the epithelial layer. The rowing-like action of epithelial cilia work in tandem with goblet cells to propel mucus away from the lungs, preventing particulate matter from causing infection[http://www.bio.davidson.edu/people/kabernd/berndcv/lab/epithelialinfoweb/ciliated%20columnar%20epithelium.html]" xsd:string [Term] id: UBERON:0007601 @@ -233001,8 +229925,8 @@ xref: FMA:66762 is_a: UBERON:0000042 ! serous membrane intersection_of: UBERON:0000042 ! serous membrane intersection_of: produces UBERON:0001090 ! synovial fluid -relationship: composed_primarily_of UBERON:0002384 {source="BTO"} ! connective tissue relationship: produces UBERON:0001090 ! synovial fluid +relationship: RO:0002473 UBERON:0002384 {source="BTO"} ! composed primarily of connective tissue [Term] id: UBERON:0007617 @@ -233017,8 +229941,8 @@ synonym: "synovial cavity" RELATED [FMA:11356] xref: FMA:11356 is_a: UBERON:0002553 ! anatomical cavity intersection_of: UBERON:0002553 ! anatomical cavity -intersection_of: luminal_space_of UBERON:0002217 ! synovial joint -relationship: luminal_space_of UBERON:0002217 ! synovial joint +intersection_of: RO:0002572 UBERON:0002217 ! luminal space of synovial joint +relationship: RO:0002572 UBERON:0002217 ! luminal space of synovial joint [Term] id: UBERON:0007619 @@ -233030,7 +229954,6 @@ xref: MA:0001318 xref: SCTID:280667001 is_a: UBERON:0001781 {source="UBERON"} ! layer of retina relationship: part_of UBERON:0003902 ! retinal neural layer -property_value: UBPROP:0000012 "MA does treat internal/external limiting membranes as layers - these are classified as laminae. We do not follow this convention. However, we do following MA is grouping these terms together" xsd:string {external_ontology="MA"} [Term] id: UBERON:0007625 @@ -233070,19 +229993,17 @@ synonym: "stratum lucidum hippocampus" RELATED [BAMS:SLu] xref: BAMS:SLu xref: BIRNLEX:4108 xref: EMAPA:35411 -xref: NCIT:C33629 xref: neuronames:1777 xref: OldNeuroNames:-975815906 {source="BIRNLEX:4108"} -xref: SCTID:419156002 xref: UMLS:C0221922 {source="ncithesaurus:Stratum_Lucidum"} xref: Wikipedia:Stratum_lucidum_of_hippocampus is_a: UBERON:0002305 ! layer of hippocampus intersection_of: UBERON:0002305 ! layer of hippocampus -intersection_of: immediately_deep_to UBERON:0005372 ! hippocampus stratum radiatum -intersection_of: immediately_superficial_to UBERON:0002313 ! hippocampus pyramidal layer +intersection_of: BSPO:0001107 UBERON:0005372 ! hippocampus stratum radiatum +intersection_of: BSPO:0015014 UBERON:0002313 ! hippocampus pyramidal layer +relationship: BSPO:0001107 UBERON:0005372 ! hippocampus stratum radiatum +relationship: BSPO:0015014 UBERON:0002313 ! hippocampus pyramidal layer relationship: has_part GO:0097457 ! hippocampal mossy fiber -relationship: immediately_deep_to UBERON:0005372 ! hippocampus stratum radiatum -relationship: immediately_superficial_to UBERON:0002313 ! hippocampus pyramidal layer [Term] id: UBERON:0007639 @@ -233109,9 +230030,9 @@ xref: SCTID:369094002 xref: UMLS:C0228247 {source="BIRNLEX:1510", source="ncithesaurus:Alveus"} is_a: UBERON:0011215 ! central nervous system cell part cluster is_a: UBERON:0016549 ! central nervous system white matter layer -relationship: continuous_with UBERON:0002310 ! hippocampus fimbria relationship: part_of UBERON:0002421 {source="NIFSTD"} ! hippocampal formation -property_value: editor_note "TODO - check xref: NCIT:C32058 ! Alveus" xsd:string +relationship: RO:0002150 UBERON:0002310 ! continuous with hippocampus fimbria +property_value: IAO:0000116 "TODO - check xref: NCIT:C32058 ! Alveus" xsd:string [Term] id: UBERON:0007641 @@ -233126,15 +230047,13 @@ xref: CALOHA:TS-2077 xref: DHBA:266441713 xref: FMA:71248 xref: HBA:9203 -xref: MESH:D014278 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: neuronames:2021 xref: UMLS:C0040999 {source="BIRNLEX:4096"} xref: Wikipedia:Trigeminal_nerve_nuclei is_a: UBERON:0007245 {source="FMA"} ! nuclear complex of neuraxis relationship: extends_fibers_into UBERON:0001645 ! trigeminal nerve relationship: overlaps UBERON:0003023 {source="FMA"} ! pontine tegmentum -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray696.png" xsd:anyURI -property_value: UBPROP:0000012 "in MA and FMA this is part of the pons / pontime tegmentum. We weaken this to overlaps to avoid inconsistency. In NIF this is a composite structure spanning multiple regions, which is more appropriate." xsd:string {external_ontology="MA"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray696.png" xsd:anyURI [Term] id: UBERON:0007644 @@ -233167,12 +230086,11 @@ synonym: "primordial meninx" RELATED [] xref: EHDAA2:0004453 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0002360 ! meninx -relationship: has_developmental_contribution_from UBERON:0007213 {source="ISBN:0073040584"} ! mesenchyme derived from head neural crest -relationship: has_potential_to_develop_into UBERON:0002360 ! meninx +intersection_of: RO:0002387 UBERON:0002360 ! has potential to develop into meninx relationship: part_of UBERON:0010743 {source="EHDAA2"} ! meningeal cluster -property_value: editor_note "decide whether to treat the endo and ecto meninx as subtypes or parts of the future meninx" xsd:string -property_value: UBPROP:0000001 "the outermost mesenchymal covering of the developing brain and spinal cord that is composed of tough fibrous connective tissue from which the arachnoid mater, pia mater and dura mater are formed[MP:0009726]d" xsd:string {source="MP:0009726"} +relationship: RO:0002254 UBERON:0007213 {source="ISBN:0073040584"} ! has developmental contribution from mesenchyme derived from head neural crest +relationship: RO:0002387 UBERON:0002360 ! has potential to develop into meninx +property_value: IAO:0000116 "decide whether to treat the endo and ecto meninx as subtypes or parts of the future meninx" xsd:string [Term] id: UBERON:0007646 @@ -233183,9 +230101,9 @@ synonym: "future leptomeninges" EXACT [] synonym: "future leptomeninx" EXACT [] is_a: UBERON:0007645 ! future meninx intersection_of: UBERON:0007645 ! future meninx -intersection_of: has_potential_to_develop_into UBERON:0000391 ! leptomeninx -relationship: develops_from UBERON:0007213 {source="ISBN:9781607950325"} ! mesenchyme derived from head neural crest -relationship: has_potential_to_develop_into UBERON:0000391 ! leptomeninx +intersection_of: RO:0002387 UBERON:0000391 ! has potential to develop into leptomeninx +relationship: RO:0002202 UBERON:0007213 {source="ISBN:9781607950325"} ! develops from mesenchyme derived from head neural crest +relationship: RO:0002387 UBERON:0000391 ! has potential to develop into leptomeninx [Term] id: UBERON:0007647 @@ -233197,9 +230115,9 @@ synonym: "future dura mater" EXACT [EHDAA2:0004317] xref: EHDAA2:0004317 is_a: UBERON:0007645 ! future meninx intersection_of: UBERON:0007645 ! future meninx -intersection_of: has_potential_to_develop_into UBERON:0002363 ! dura mater -relationship: develops_from UBERON:0009617 {source="ISBN:9781607950325"} ! head paraxial mesoderm -relationship: has_potential_to_develop_into UBERON:0002363 ! dura mater +intersection_of: RO:0002387 UBERON:0002363 ! has potential to develop into dura mater +relationship: RO:0002202 UBERON:0009617 {source="ISBN:9781607950325"} ! develops from head paraxial mesoderm +relationship: RO:0002387 UBERON:0002363 ! has potential to develop into dura mater [Term] id: UBERON:0007651 @@ -233213,10 +230131,10 @@ synonym: "junction" BROAD [] xref: FMA:5898 xref: SCTID:91833003 is_a: UBERON:0000061 {source="FMA"} ! anatomical structure -relationship: connects UBERON:0000061 {minCardinality="2"} ! anatomical structure -relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 ! Fungi +relationship: RO:0002176 UBERON:0000061 {minCardinality="2"} ! connects anatomical structure +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0007652 @@ -233228,7 +230146,7 @@ is_a: UBERON:0003832 ! esophagus muscle is_a: UBERON:0004590 ! sphincter muscle intersection_of: UBERON:0004590 ! sphincter muscle intersection_of: part_of UBERON:0001043 ! esophagus -property_value: editor_note "check for specific subtypes across species. Note mammals have upper and lower, but lower is really part of cardia and thus is not classified under here" xsd:string +property_value: IAO:0000116 "check for specific subtypes across species. Note mammals have upper and lower, but lower is really part of cardia and thus is not classified under here" xsd:string [Term] id: UBERON:0007684 @@ -233251,7 +230169,6 @@ synonym: "renal tubule region" EXACT [FMA:17692] xref: FMA:17692 is_a: UBERON:0001231 ! nephron tubule relationship: part_of UBERON:0001231 ! nephron tubule -property_value: UBPROP:0000012 "consider moving MA:0000377 renal tubule here, as it includes the various segments (proximal etc) as subclasses, not parts" xsd:string {external_ontology="MA"} [Term] id: UBERON:0007687 @@ -233263,8 +230180,8 @@ is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0006598 ! presumptive structure is_a: UBERON:0007688 ! anlage intersection_of: UBERON:0007688 ! anlage -intersection_of: has_potential_to_develop_into UBERON:0002113 ! kidney -relationship: has_potential_to_develop_into UBERON:0002113 ! kidney +intersection_of: RO:0002387 UBERON:0002113 ! has potential to develop into kidney +relationship: RO:0002387 UBERON:0002113 ! has potential to develop into kidney [Term] id: UBERON:0007688 @@ -233279,7 +230196,6 @@ synonym: "organ field" RELATED [] xref: AEO:0000170 xref: EFO:0001649 xref: EHDAA2:0003170 -xref: FBbt:00005426 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: Wikipedia:Anlage_(biology) is_a: UBERON:0000479 {source="FBbt"} ! tissue is_a: UBERON:0005423 {source="AEO", source="FBbt"} ! developing anatomical structure @@ -233294,7 +230210,7 @@ synonym: "saccus thyroideus" RELATED OMO:0003011 [Wikipedia:Thyroid_diverticulum xref: Wikipedia:Thyroid_diverticulum is_a: UBERON:0001048 ! primordium relationship: part_of UBERON:0001042 {source="VHOG"} ! chordate pharynx -relationship: transformation_of UBERON:0003091 ! thyroid primordium +relationship: RO:0002494 UBERON:0003091 ! transformation of thyroid primordium [Term] id: UBERON:0007690 @@ -233309,8 +230225,6 @@ synonym: "pharyngeal region endoderm" RELATED [EHDAA2:0001456] xref: EFO:0003626 xref: EHDAA2:0001457 xref: EHDAA:962 -xref: EMAPA:32754 -xref: FMA:293087 xref: TAO:0001104 xref: ZFA:0001104 is_a: UBERON:0003258 ! endoderm of foregut @@ -233330,11 +230244,12 @@ xref: NCIT:C33738 xref: SCTID:368724008 xref: UMLS:C0226971 {source="ncithesaurus:Taste_Pore"} is_a: UBERON:0000161 {source="FMA"} ! orifice +is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0000161 ! orifice intersection_of: part_of UBERON:0001727 ! taste bud -relationship: continuous_with UBERON:0000167 ! oral cavity relationship: part_of UBERON:0001727 {source="FMA"} ! taste bud -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/0/0e/Taste_bud.svg" xsd:anyURI +relationship: RO:0002150 UBERON:0000167 ! continuous with oral cavity +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/0/0e/Taste_bud.svg" xsd:anyURI [Term] id: UBERON:0007692 @@ -233353,7 +230268,7 @@ is_a: UBERON:0006569 ! diencephalic nucleus intersection_of: UBERON:0002308 ! nucleus of brain intersection_of: part_of UBERON:0001897 ! dorsal plus ventral thalamus relationship: part_of UBERON:0001897 ! dorsal plus ventral thalamus -property_value: editor_note "TODO - consider splitting nucleus and complex" xsd:string +property_value: IAO:0000116 "TODO - consider splitting nucleus and complex" xsd:string [Term] id: UBERON:0007699 @@ -233383,7 +230298,7 @@ intersection_of: UBERON:0001018 ! axon tract intersection_of: part_of UBERON:0000955 ! brain relationship: part_of UBERON:0000955 ! brain relationship: part_of UBERON:0002316 {source="cjm"} ! white matter -property_value: editor_note "the NIFSTD class 'nerve tract' is classified under 'regional part of brain', so it may seem like it belongs here, but actually includes spinal cord tracts" xsd:string +property_value: IAO:0000116 "the NIFSTD class 'nerve tract' is classified under 'regional part of brain', so it may seem like it belongs here, but actually includes spinal cord tracts" xsd:string [Term] id: UBERON:0007719 @@ -233396,8 +230311,8 @@ is_a: UBERON:0001474 ! bone element is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0003133 ! reproductive organ -relationship: never_in_taxon NCBITaxon:9606 {source="Wikipedia"} ! Homo sapiens relationship: part_of UBERON:0003133 ! reproductive organ +property_value: RO:0002161 NCBITaxon:9606 {source="Wikipedia"} [Term] id: UBERON:0007721 @@ -233422,9 +230337,9 @@ is_a: UBERON:0001487 ! pes joint is_a: UBERON:0006658 ! interphalangeal joint intersection_of: UBERON:0006658 ! interphalangeal joint intersection_of: part_of UBERON:0001466 ! pedal digit -relationship: connects UBERON:0001449 {notes="two in series"} ! phalanx of pes -relationship: connects UBERON:0001449 {cardinality="2"} ! phalanx of pes relationship: part_of UBERON:0001466 ! pedal digit +relationship: RO:0002176 UBERON:0001449 ! connects phalanx of pes +relationship: RO:0002176 UBERON:0001449 {cardinality="2"} ! connects phalanx of pes [Term] id: UBERON:0007722 @@ -233450,10 +230365,10 @@ is_a: UBERON:0001489 ! manus joint is_a: UBERON:0006658 ! interphalangeal joint intersection_of: UBERON:0006658 ! interphalangeal joint intersection_of: part_of UBERON:0002389 ! manual digit -relationship: connects UBERON:0001436 {notes="two in series"} ! phalanx of manus -relationship: connects UBERON:0001436 {cardinality="2"} ! phalanx of manus relationship: part_of UBERON:0002389 ! manual digit -property_value: editor_note "consider renaming: 'finger' is ambiguous as the term in some usages excludes the thumb (we include it)" xsd:string +relationship: RO:0002176 UBERON:0001436 ! connects phalanx of manus +relationship: RO:0002176 UBERON:0001436 {cardinality="2"} ! connects phalanx of manus +property_value: IAO:0000116 "consider renaming: 'finger' is ambiguous as the term in some usages excludes the thumb (we include it)" xsd:string [Term] id: UBERON:0007771 @@ -233505,13 +230420,11 @@ xref: ncithesaurus:Transudate is_a: UBERON:0006314 ! bodily fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: filtered_through UBERON:0001982 ! capillary -intersection_of: has_quality PATO:0001548 ! quality of a liquid -intersection_of: transformation_of UBERON:0001969 ! blood plasma +intersection_of: RO:0000086 PATO:0001548 ! has quality quality of a liquid +intersection_of: RO:0002494 UBERON:0001969 ! transformation of blood plasma relationship: filtered_through UBERON:0001982 ! capillary -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata -relationship: transformation_of UBERON:0001969 ! blood plasma -property_value: UBPROP:0000007 "transudative" xsd:string -property_value: UBPROP:0000010 "characteristically low in protein and cellular content (unless there has been secondary concentration)" xsd:string +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002494 UBERON:0001969 ! transformation of blood plasma [Term] id: UBERON:0007794 @@ -233544,10 +230457,8 @@ xref: NCIT:C33854 xref: UMLS:C0489903 {source="ncithesaurus:Vascular_System"} is_a: UBERON:0000467 ! anatomical system relationship: part_of UBERON:0004535 {source="MA"} ! cardiovascular system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: editor_note "consider merging with vasculature" xsd:string -property_value: UBPROP:0000001 "The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]." xsd:string {source="ncithesaurus:Vascular_System"} -property_value: UBPROP:0000012 "in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system" xsd:string {external_ontology="MA"} +property_value: IAO:0000116 "consider merging with vasculature" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0007806 @@ -233558,8 +230469,8 @@ xref: BTO:0004705 xref: NCIT:C34132 xref: UMLS:C1516792 {source="ncithesaurus:Connecting_Stalk"} is_a: UBERON:0000478 {source="EHDAA2"} ! extraembryonic structure -relationship: develops_from UBERON:0005728 {source="EHDAA2"} ! extraembryonic mesoderm -property_value: editor_note "TODO - this is currently defined as a bridge of mesoderm, but in EHDAA2 is extraembryonic structure split into mesoderm and blood vessels" xsd:string +relationship: RO:0002202 UBERON:0005728 {source="EHDAA2"} ! develops from extraembryonic mesoderm +property_value: IAO:0000116 "TODO - this is currently defined as a bridge of mesoderm, but in EHDAA2 is extraembryonic structure split into mesoderm and blood vessels" xsd:string [Term] id: UBERON:0007807 @@ -233573,8 +230484,8 @@ xref: EHDAA2:0000313 is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: part_of UBERON:0007806 ! connecting stalk -relationship: develops_from UBERON:0011921 {source="EHDAA2"} ! connecting stalk blood islands relationship: part_of UBERON:0007806 ! connecting stalk +relationship: RO:0002202 UBERON:0011921 {source="EHDAA2"} ! develops from connecting stalk blood islands [Term] id: UBERON:0007808 @@ -233631,7 +230542,6 @@ synonym: "post-anal fin tail" NARROW SENSU [http://purl.oboibrary.org/obo/uberon synonym: "post-vent region" RELATED [TAO:0001117] synonym: "postanal tail" EXACT [] xref: AAO:0010338 -xref: EMAPA:16748 xref: MA:0000008 xref: NCIT:C77663 xref: TAO:0001117 @@ -233642,13 +230552,10 @@ is_a: UBERON:0002415 ! tail intersection_of: UBERON:0002415 ! tail intersection_of: part_of UBERON:0006071 ! caudal region relationship: capable_of_part_of GO:0007626 ! locomotory behavior -relationship: never_in_taxon NCBITaxon:314295 ! Hominoidea -relationship: only_in_taxon NCBITaxon:7711 {notes="possible exception in hemichordates", source="cjm"} ! Chordata relationship: part_of UBERON:0006071 ! caudal region -relationship: transformation_of UBERON:0007144 ! embryonic post-anal tail -property_value: UBPROP:0000001 "Anatomical structure that is the terminal, flexible posterior appendage of the organism.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010338", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000001 "Organism subdivision which is the part of the body posterior to the vent which includes the anal and caudal fins.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001117", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000008 "present at some time in chordate life history (eg in Urochordates, present only in free-swimming larvae). Function: propellor locomotion (in some species)" xsd:string +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002494 UBERON:0007144 ! transformation of embryonic post-anal tail +property_value: RO:0002161 NCBITaxon:314295 [Term] id: UBERON:0007823 @@ -233667,12 +230574,10 @@ xref: FMA:24874 xref: VSAO:0000303 is_a: UBERON:0000475 ! organism subdivision intersection_of: UBERON:0000475 ! organism subdivision -intersection_of: has_skeleton UBERON:0010719 ! girdle skeleton -relationship: has_skeleton UBERON:0010719 ! girdle skeleton -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +intersection_of: RO:0002551 UBERON:0010719 ! has skeleton girdle skeleton relationship: part_of UBERON:0010707 ! appendage girdle complex -property_value: IAO:0000232 "this encompasses non-skeletal tissue" xsd:string -property_value: UBPROP:0000001 "An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There are only two instances of appendage girdle regions per organism.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000303", ontology="VSAO", source="https://orcid.org/0000-0002-6601-2165"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002551 UBERON:0010719 ! has skeleton girdle skeleton [Term] id: UBERON:0007826 @@ -233701,13 +230606,13 @@ xref: FMA:59515 xref: NCIT:C32566 xref: SCTID:265785009 xref: UMLS:C0458561 {source="ncithesaurus:External_Nose"} +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0034929 ! external soft tissue zone intersection_of: UBERON:0034929 ! external soft tissue zone intersection_of: has_part UBERON:0005928 ! external naris intersection_of: part_of UBERON:0000004 ! nose relationship: has_part UBERON:0005928 ! external naris relationship: part_of UBERON:0000004 ! nose -property_value: UBPROP:0000001 "Subdivision of face, the exterior of the nose, which consists of a root, dorsum, tip, columella, and right and left alae[FMA:59515]." xsd:string {source="FMA:59515"} [Term] id: UBERON:0007828 @@ -233737,7 +230642,7 @@ is_a: UBERON:0010741 ! bone of pectoral complex intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0001421 ! pectoral girdle region relationship: part_of UBERON:0007831 ! pectoral girdle skeleton -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0007830 @@ -233749,12 +230654,12 @@ subset: pheno_slim subset: vertebrate_core synonym: "bone of pelvic girdle" EXACT [] synonym: "pelvic girdle bone" EXACT [MA:0000293] -xref: EMAPA:18028 xref: MA:0000293 xref: NCIT:C33287 xref: SCTID:426214007 xref: UMLS:C0030786 {source="ncithesaurus:Pelvic_Bone"} is_a: UBERON:0003828 ! abdominal segment bone +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005179 ! pelvic region element is_a: UBERON:0005913 ! zone of bone organ is_a: UBERON:0007828 {source="MA"} ! girdle bone/zone @@ -233762,9 +230667,8 @@ is_a: UBERON:0010742 ! bone of pelvic complex intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0007832 ! pelvic girdle skeleton relationship: part_of UBERON:0007832 ! pelvic girdle skeleton -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: editor_note "check sacrum, coccyx (MA does NOT include these)" xsd:string -property_value: UBPROP:0000008 "typically the ilium, ischium and pubis. These can alternately be considered individual bones, or zones of a single fused bone" xsd:string +property_value: IAO:0000116 "check sacrum, coccyx (MA does NOT include these)" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0007831 @@ -233796,16 +230700,11 @@ xref: ZFA:0000407 is_a: UBERON:0010719 ! girdle skeleton intersection_of: UBERON:0010912 ! subdivision of skeleton intersection_of: part_of UBERON:0001421 ! pectoral girdle region -intersection_of: skeleton_of UBERON:0001421 ! pectoral girdle region +intersection_of: RO:0002576 UBERON:0001421 ! skeleton of pectoral girdle region relationship: part_of UBERON:0001421 ! pectoral girdle region relationship: part_of UBERON:0012475 ! skeleton of pectoral complex -relationship: skeleton_of UBERON:0001421 ! pectoral girdle region -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/22/Pectoral_girdle_front_diagram.svg" xsd:anyURI -property_value: UBPROP:0000001 "Anatomical cluster of paired dermal and endochondral bones that attaches to the dorso-posterior part of the cranium, and support the radials and pectoral fin. It consists of two components: the primary pectoral girdle consisting of the endochondral coracoid, scapula and mesocoracoid bones, and the secondary pectoral girdle consisting of the dermal posttemporal, supracleithrum, cleithrum and poscleithrum(thra) bones.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000407", ontology="TAO", source="TAO:wd"} -property_value: UBPROP:0000001 "Girdle skeleton consisting of a set of bones linking the axial series to the forelimb/fin skeleton and offering anchoring areas for forelimb/fin and caudal musculature.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000156", ontology="VSAO", source="https://orcid.org/0000-0002-6601-2165"} -property_value: UBPROP:0000001 "Skeletal structure immediately behind the head attached to the vertebral column by muscles and supporting the forelimbs.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000422", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000003 "The pectoral girdle is clearly of dual origin, composed of dermal as well as endochondral bones. The endochondral component, the scapulocoracoid, evolved by fusion or enlargment of several basal fin elements. (...) The dermal component of the shoulder girdle evolved from dermal bones of the body's surface. (...) Like endochondral bones, these dermal bones were passed along to tetrapods (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001156", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.336 and Figure 9.18", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "Note that the VSAO and many ontologies use the label 'pectoral girdle' to denote the skeletal region specifically." xsd:string {external_ontology="VSAO"} +relationship: RO:0002576 UBERON:0001421 ! skeleton of pectoral girdle region +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/22/Pectoral_girdle_front_diagram.svg" xsd:anyURI [Term] id: UBERON:0007832 @@ -233836,21 +230735,17 @@ xref: VSAO:0000155 xref: Wikipedia:Pelvis xref: XAO:0003064 xref: ZFA:0000565 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010719 ! girdle skeleton intersection_of: UBERON:0010912 ! subdivision of skeleton intersection_of: part_of UBERON:0001271 ! pelvic girdle region -intersection_of: skeleton_of UBERON:0001271 ! pelvic girdle region -relationship: develops_from UBERON:0010377 {source="PMID:21455939"} ! mesenchyme from somatopleure +intersection_of: RO:0002576 UBERON:0001271 ! skeleton of pelvic girdle region relationship: part_of UBERON:0001271 ! pelvic girdle region relationship: part_of UBERON:0012476 ! skeleton of pelvic complex -relationship: skeleton_of UBERON:0001271 ! pelvic girdle region -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png" xsd:anyURI -property_value: editor_note "need to resolve whether this is a paired structure or a single belt (Paired in FMA - implicitly paired in VSAO)" xsd:string -property_value: UBPROP:0000001 "Anatomical cluster by which the hind limbs are supported and attached to the vertebral column.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000426", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000001 "Anatomical cluster that consists of the paired basipterygia which support the pelvic fin.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000565", ontology="TAO", source="TAO:wd"} -property_value: UBPROP:0000001 "Girdle skeleton consisting of a set of bones linking the axial series to the hindlimb/fin skeleton and offering anchoring areas for hindlimb/fin and caudal musculature.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000155", ontology="VSAO", source="https://orcid.org/0000-0002-6601-2165"} -property_value: UBPROP:0000003 "The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000305", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.333", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "Note that the VSAO and many ontologies use the label 'pelvic girdle' to denote the skeletal region specifically. We place the EHDAA2 class here, note that this includes the pre-cartilage condensation as parts" xsd:string {external_ontology="VSAO"} +relationship: RO:0002202 UBERON:0010377 {source="PMID:21455939"} ! develops from mesenchyme from somatopleure +relationship: RO:0002576 UBERON:0001271 ! skeleton of pelvic girdle region +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png" xsd:anyURI +property_value: IAO:0000116 "need to resolve whether this is a paired structure or a single belt (Paired in FMA - implicitly paired in VSAO)" xsd:string [Term] id: UBERON:0007842 @@ -233866,8 +230761,6 @@ xref: XAO:0004014 xref: ZFA:0001636 is_a: UBERON:0001474 {source="VSAO"} ! bone element relationship: output_of GO:0001957 ! intramembranous ossification -property_value: UBPROP:0000001 "Bone element that arises as a result of intramembranous ossification.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000023", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "Intramembranous bone that forms deep in the organism.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001645", ontology="TAO", source="TAO:wd"} [Term] id: UBERON:0007844 @@ -233882,18 +230775,16 @@ synonym: "cartilaginous element" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "chondrogenic element" EXACT [VSAO:0000000] xref: AAO:0011130 xref: CALOHA:TS-0118 -xref: EMAPA:32730 xref: FMA:55107 xref: VSAO:0000000 xref: XAO:0004013 xref: ZFA:0001501 is_a: UBERON:0004765 {source="VSAO"} ! skeletal element intersection_of: UBERON:0004765 ! skeletal element -intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue -relationship: composed_primarily_of UBERON:0002418 ! cartilage tissue -relationship: develops_from UBERON:0005863 {source="VSAO"} ! cartilaginous condensation +intersection_of: RO:0002473 UBERON:0002418 ! composed primarily of cartilage tissue relationship: has_part UBERON:0002418 {source="VSAO"} ! cartilage tissue -property_value: UBPROP:0000012 "TAO still mixes tissue and element" xsd:string {external_ontology="TAO"} +relationship: RO:0002202 UBERON:0005863 {source="VSAO"} ! develops from cartilaginous condensation +relationship: RO:0002473 UBERON:0002418 ! composed primarily of cartilage tissue [Term] id: UBERON:0007845 @@ -233907,7 +230798,7 @@ disjoint_from: UBERON:0011821 ! irregular connective tissue relationship: has_part CL:0000057 ! fibroblast relationship: has_part GO:0071953 ! elastic fiber relationship: has_part UBERON:0011860 ! collection of collagen fibrils -property_value: editor_note "the connective tissue hierarchy largely follows FMA with definitions from VSAO. Note that in FMA, loose-CT is irregular-CT. This means regular-CT is necessarily equivalent to dense-regular-CT (assuming a JEPD classification)." xsd:string +property_value: IAO:0000116 "the connective tissue hierarchy largely follows FMA with definitions from VSAO. Note that in FMA, loose-CT is irregular-CT. This means regular-CT is necessarily equivalent to dense-regular-CT (assuming a JEPD classification)." xsd:string [Term] id: UBERON:0007846 @@ -233929,10 +230820,8 @@ xref: XAO:0004030 is_a: UBERON:0007845 {source="FMA"} ! regular connective tissue is_a: UBERON:0011823 {source="ncithesaurus"} ! dense connective tissue intersection_of: UBERON:0007845 ! regular connective tissue -intersection_of: composed_primarily_of UBERON:0011860 ! collection of collagen fibrils intersection_of: has_part GO:0071953 ! elastic fiber -property_value: UBPROP:0000001 "Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000050", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "Regular connective tissue, the intercellular matrix of which consists predominantly of collagen fiber bundles arranged in parallel arrays.[FMA]" xsd:string {date_retrieved="2012-08-29", external_class="FMA:64781", ontology="FMA"} +intersection_of: RO:0002473 UBERON:0011860 ! composed primarily of collection of collagen fibrils [Term] id: UBERON:0007914 @@ -234001,9 +230890,9 @@ xref: MA:0001505 is_a: UBERON:0000982 {source="MA"} ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: part_of UBERON:0007823 ! appendage girdle region -relationship: connects UBERON:0007828 ! girdle bone/zone -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0007823 ! appendage girdle region +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002176 UBERON:0007828 ! connects girdle bone/zone [Term] id: UBERON:0008115 @@ -234033,8 +230922,7 @@ is_a: UBERON:0001474 ! bone element intersection_of: UBERON:0001474 ! bone element intersection_of: has_part UBERON:0010528 ! pneumatic cavity of bone relationship: has_part UBERON:0010528 ! pneumatic cavity of bone -property_value: editor_note "subclasses of this should be checked for taxonomic consistency" xsd:string -property_value: UBPROP:0000008 "Skeletal pneumaticity is the presence of air spaces within bones. Skeletal pneumaticity exists only in synapsids and archosaurs. It is generally produced during development by excavation of bone by pneumatic diverticula (air sacs) from an air-filled space such as the lungs or nasal cavity. Pneumatization is highly variable between individuals, and bones not normally pneumatized can become pneumatized in pathological development. Pneumatization occurs in the skulls of mammals, crocodilians and birds among extant groups, as well as extinct archosaurs including the dinosaurs and pterosaurs. Pneumatic spaces include the paranasal sinuses and some of the mastoid cells[WP]. [Wikipedia:Skeletal_pneumaticity]" xsd:string +property_value: IAO:0000116 "subclasses of this should be checked for taxonomic consistency" xsd:string [Term] id: UBERON:0008196 @@ -234044,13 +230932,11 @@ def: "Any muscle organ that is part of a pectoral girdle region." [OBOL:automati subset: pheno_slim synonym: "muscle of shoulder girdle" EXACT [FMA:37347] synonym: "pectoral girdle muscle" EXACT [FMA:37347] -xref: EMAPA:17748 xref: FMA:37347 is_a: UBERON:0010891 ! pectoral complex muscle intersection_of: UBERON:0014892 ! skeletal muscle organ, vertebrate intersection_of: part_of UBERON:0001421 ! pectoral girdle region relationship: part_of UBERON:0004471 ! musculature of pectoral girdle -property_value: UBPROP:0000012 "EMAPA has both non-skeletal and skeletal types, with the non-skeletal also including a chest muscle, so we place the skeletal class here as the most accurate" xsd:string {external_ontology="EMAPA"} [Term] id: UBERON:0008198 @@ -234064,12 +230950,12 @@ xref: MA:0002708 xref: NCIT:C34216 xref: SCTID:372177002 xref: Wikipedia:Nail_plate +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0013754 ! integumentary system layer relationship: has_part CL:0000312 ! keratinocyte relationship: part_of UBERON:0001705 {source="MA"} ! nail -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/9/9f/Fingernail_label.jpg" xsd:anyURI -property_value: UBPROP:0000012 "in FMA, the nail is the nail plate" xsd:string {external_ontology="FMA"} +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/9/9f/Fingernail_label.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0008202 @@ -234084,8 +230970,7 @@ xref: MA:0000655 xref: SCTID:304907005 is_a: UBERON:0001474 ! bone element relationship: overlaps UBERON:0001464 {source="MA"} ! hip -property_value: editor_note "todo - consider obsoletion" xsd:string -property_value: UBPROP:0000012 "in MA, this includes the femur. i.e. pelvic girdle bone or femur; note that this makes the ilium etc in MA hindlimb bones. in MA this is a hindlimb bone" xsd:string {external_ontology="MA"} +property_value: IAO:0000116 "todo - consider obsoletion" xsd:string [Term] id: UBERON:0008203 @@ -234101,11 +230986,11 @@ xref: SCTID:281903009 xref: Wikipedia:Pelvic_cavity is_a: UBERON:0002553 ! anatomical cavity intersection_of: UBERON:0002553 ! anatomical cavity -intersection_of: luminal_space_of UBERON:0002355 ! pelvic region of trunk intersection_of: part_of UBERON:0002323 ! coelemic cavity lumen -relationship: luminal_space_of UBERON:0002355 ! pelvic region of trunk +intersection_of: RO:0002572 UBERON:0002355 ! luminal space of pelvic region of trunk relationship: part_of UBERON:0035819 ! abdominopelvic cavity -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI +relationship: RO:0002572 UBERON:0002355 ! luminal space of pelvic region of trunk +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI [Term] id: UBERON:0008229 @@ -234123,7 +231008,6 @@ is_a: UBERON:0001015 {source="MA"} ! musculature intersection_of: UBERON:0001015 ! musculature intersection_of: part_of UBERON:0007811 ! craniocervical region relationship: part_of UBERON:0007811 {source="MA"} ! craniocervical region -property_value: UBPROP:0000012 "in MA this is restricted to skeletal muscles" xsd:string {external_ontology="MA"} [Term] id: UBERON:0008231 @@ -234166,9 +231050,8 @@ def: "A clavicle that is in the right side of a entire appendicular skeleton." [ xref: FMA:13322 is_a: UBERON:0001105 {source="FMA"} ! clavicle bone intersection_of: UBERON:0001105 ! clavicle bone -intersection_of: in_right_side_of UBERON:0002091 ! appendicular skeleton -relationship: in_right_side_of UBERON:0002091 ! appendicular skeleton -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +intersection_of: BSPO:0000121 UBERON:0002091 ! appendicular skeleton +relationship: BSPO:0000121 UBERON:0002091 ! appendicular skeleton [Term] id: UBERON:0008256 @@ -234178,9 +231061,8 @@ def: "A clavicle that is in the left side of a entire appendicular skeleton." [O xref: FMA:13323 is_a: UBERON:0001105 {source="FMA"} ! clavicle bone intersection_of: UBERON:0001105 ! clavicle bone -intersection_of: in_left_side_of UBERON:0002091 ! appendicular skeleton -relationship: in_left_side_of UBERON:0002091 ! appendicular skeleton -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +intersection_of: BSPO:0000120 UBERON:0002091 ! appendicular skeleton +relationship: BSPO:0000120 UBERON:0002091 ! appendicular skeleton [Term] id: UBERON:0008266 @@ -234213,20 +231095,16 @@ xref: EMAPA:35679 xref: FMA:56665 xref: GAID:1259 xref: MA:0002467 -xref: MESH:D010513 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: SCTID:245775004 xref: Wikipedia:Periodontal_fiber is_a: UBERON:0008846 {source="FMA-moved"} ! skeletal ligament is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0000211 ! ligament intersection_of: part_of UBERON:0001758 ! periodontium -relationship: develops_from UBERON:0008969 {source="PMID:19767574", source="Wikipedia:Dental_follicle"} ! dental follicle relationship: part_of UBERON:0001758 {source="BTO"} ! periodontium -relationship: seeAlso FMA:76870 -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/d/dc/The_Periodontium.jpg" xsd:anyURI -property_value: UBPROP:0000001 "The collagen fibers, running from the cementum to the alveolar bone, that suspend a tooth in its socket; they include apical, oblique, horizontal, and alveolar crest fibers, indicating that the orientation of the fibers varies at different levels[http://www.drugs.com/dict/desmodentium.html]." xsd:string {source="http://www.drugs.com/dict/desmodentium.html"} -property_value: UBPROP:0000001 "The fibrous connective tissue that surrounds the root of a tooth, separating it from and attaching it to the alveolar bone. It extends from the base of the gingival mucosa to the fundus of the bony socket, and its main function is to hold the tooth in its socket[BTO]. It consist of cells, extracellular compartment of fibers. The cells are fibroblast, epithelial, undifferentiated mesenchymal cells, bone and cementum cells. The extracellular compartment consists of collagen fibers bundles embedded in ground substance. The PDL substance has been estimated to be 70% water and is thought to have a significant effect on the tooth's ability to withstand stress loads[WP][BTO:0001020, Wikipedia:Periodontal_fiber, https://github.com/obophenotype/uberon/issues/21]." xsd:string {source="Wikipedia:Periodontal_fiber"} -property_value: UBPROP:0000012 "FMA treats periodontium and periodontal ligament as the same; it has a separate class desmodentium, which we place here even though it is classified as fetal in FMA" xsd:string {external_ontology="FMA"} +relationship: RO:0002202 UBERON:0008969 {source="PMID:19767574", source="Wikipedia:Dental_follicle"} ! develops from dental follicle +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/dc/The_Periodontium.jpg" xsd:anyURI +property_value: seeAlso FMA:76870 [Term] id: UBERON:0008281 @@ -234243,8 +231121,8 @@ xref: NCIT:C34313 xref: SCTID:53301001 xref: UMLS:C0040442 {source="ncithesaurus:Tooth_Bud"} is_a: UBERON:0005423 ! developing anatomical structure -relationship: develops_from UBERON:0005087 ! tooth placode relationship: part_of UBERON:0011595 {gci_relation="part_of", gci_filler="NCBITaxon:40674"} ! jaw region +relationship: RO:0002202 UBERON:0005087 ! develops from tooth placode [Term] id: UBERON:0008304 @@ -234254,8 +231132,8 @@ def: "The perichondrium consists of two separate layers: an outer fibrous layer xref: BTO:0005090 xref: Wikipedia:The_Free_Encyclopedia is_a: UBERON:0002384 ! connective tissue -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0002222 {source="BTO"} ! perichondrium +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata [Term] id: UBERON:0008305 @@ -234278,7 +231156,6 @@ is_a: UBERON:0004852 ! cardiovascular system endothelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0000948 ! heart relationship: part_of UBERON:0000948 ! heart -property_value: IAO:0000232 "this class includes any endothelia that are part of the heart. This might include the endocardial epithelia, as well as endothelia of vessels that are considered strictly part of the heart (e.g. outflow tract). As a grouping class, this may lack utility, and pending review this class may be obsoleted. For annotation consider a more specific class." xsd:string [Term] id: UBERON:0008310 @@ -234289,6 +231166,7 @@ subset: organ_slim xref: FMA:55076 xref: SCTID:178973008 is_a: UBERON:0003295 ! pharyngeal gland +is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0001728 ! nasopharynx relationship: part_of UBERON:0001728 ! nasopharynx @@ -234301,7 +231179,7 @@ def: "With numerous vascular spaces that may become engorged with blood." [Wikip comment: Examples: corpus cavernosum or penis or clitoris xref: Wikipedia:Erectile_tissue is_a: UBERON:0000479 ! tissue -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria [Term] id: UBERON:0008331 @@ -234345,8 +231223,7 @@ is_a: UBERON:0005445 {source="FMA"} ! segment of pes is_a: UBERON:0008837 ! palmar/plantar part of autopod intersection_of: UBERON:0008837 ! palmar/plantar part of autopod intersection_of: part_of UBERON:0002387 ! pes -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/41/Soles2.jpg" xsd:anyURI -property_value: UBPROP:0000008 "In humans is the sole of the foot anatomically referred to as the plantar aspect. The equivalent surface in ungulates is the hoof" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/41/Soles2.jpg" xsd:anyURI [Term] id: UBERON:0008339 @@ -234407,7 +231284,7 @@ is_a: UBERON:0013636 ! epithelium of intestinal villus intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002116 ! ileum relationship: part_of UBERON:0008344 {source="FMA"} ! intestinal villus of ileum -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0008346 @@ -234425,7 +231302,7 @@ is_a: UBERON:0013636 ! epithelium of intestinal villus intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002114 ! duodenum relationship: part_of UBERON:0008342 {source="FMA"} ! intestinal villus of duodenum -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0008367 @@ -234468,7 +231345,7 @@ intersection_of: UBERON:0000483 ! epithelium intersection_of: adjacent_to UBERON:0000464 ! anatomical space intersection_of: part_of UBERON:0004134 ! proximal tubule relationship: part_of UBERON:0004134 ! proximal tubule -property_value: editor_note "See https://github.com/obophenotype/uberon/issues/1305" xsd:string +property_value: IAO:0000116 "See https://github.com/obophenotype/uberon/issues/1305" xsd:string [Term] id: UBERON:0008408 @@ -234482,7 +231359,7 @@ intersection_of: UBERON:0000483 ! epithelium intersection_of: adjacent_to UBERON:0000464 ! anatomical space intersection_of: part_of UBERON:0004135 ! distal tubule relationship: part_of UBERON:0004135 {source="BTO"} ! distal tubule -property_value: editor_note "See https://github.com/obophenotype/uberon/issues/1305" xsd:string +property_value: IAO:0000116 "See https://github.com/obophenotype/uberon/issues/1305" xsd:string [Term] id: UBERON:0008425 @@ -234496,14 +231373,11 @@ synonym: "milk line" RELATED [Wikipedia:Milk_line] xref: EMAPA:18541 xref: Wikipedia:Milk_line is_a: UBERON:0006598 ! presumptive structure -relationship: develops_from UBERON:0000924 ! ectoderm -relationship: has_potential_to_develop_into UBERON:0001911 ! mammary gland relationship: part_of UBERON:0000915 {gci_relation="part_of", gci_filler="NCBITaxon:9443"} ! thoracic segment of trunk relationship: part_of UBERON:0002100 ! trunk -property_value: editor_note "consider splitting ridge (precursor) and milk line" xsd:string -property_value: UBPROP:0000008 "These buds are either located in the thoracic region in primates, in the inguinal area in ungulates or along the entire length of the trunk in rodents and pigs. In humans, milk lines appear in the seventh week of embryonic development" xsd:string -property_value: UBPROP:0000011 "in mouse, mammary gland development begins shortly after mid-gestation (about E10.5); epidermal cells within the milk line become columnar and multilayered, defining a ridge that protrudes above and below the plane of the single-layered primitive epidermis or periderm; by E11.5, five pairs of lens-shaped placodes form along the mammary line at the site of each future nipple.[MP]" xsd:string -property_value: UBPROP:0000011 "The first manifestation of the mammary gland in many mammals is an elevated ridge or milk line, which then fragments into individual buds in specific regions lateral of the dorsal midline. After initial development of the milk lines they go into remission." xsd:string +relationship: RO:0002202 UBERON:0000924 ! develops from ectoderm +relationship: RO:0002387 UBERON:0001911 ! has potential to develop into mammary gland +property_value: IAO:0000116 "consider splitting ridge (precursor) and milk line" xsd:string [Term] id: UBERON:0008429 @@ -234587,10 +231461,10 @@ xref: UMLS:C1527245 {source="ncithesaurus:Tarsal_Joint"} xref: Wikipedia:Intertarsal_articulations is_a: UBERON:0001487 ! pes joint intersection_of: UBERON:0000982 ! skeletal joint -intersection_of: connects UBERON:0001447 {cardinality="2"} ! tarsal bone -relationship: connects UBERON:0001447 {notes="two adjacent tarsals"} ! tarsal bone +intersection_of: RO:0002176 UBERON:0001447 {cardinality="2"} ! connects tarsal bone relationship: part_of UBERON:0004454 ! tarsal region -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray360.png" xsd:anyURI +relationship: RO:0002176 UBERON:0001447 ! connects tarsal bone +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray360.png" xsd:anyURI [Term] id: UBERON:0008522 @@ -234603,6 +231477,7 @@ xref: NCIT:C33158 xref: SCTID:244730009 xref: UMLS:C0224219 {source="ncithesaurus:Nasal_Muscle"} is_a: UBERON:0001577 {source="FMA"} ! facial muscle +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0001630 ! muscle organ intersection_of: part_of UBERON:0000004 ! nose relationship: part_of UBERON:0000004 ! nose @@ -234628,6 +231503,7 @@ synonym: "prostatic musclular tissue" EXACT [] xref: NCIT:C13100 xref: SCTID:251498008 xref: UMLS:C1183911 {source="ncithesaurus:Prostatic_Muscular_Tissue"} +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0002385 ! muscle tissue is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0002385 ! muscle tissue @@ -234676,7 +231552,6 @@ is_a: UBERON:0004380 ! proximal epiphysis is_a: UBERON:0004388 ! epiphysis of fibula intersection_of: UBERON:0004380 ! proximal epiphysis intersection_of: part_of UBERON:0001446 ! fibula -property_value: UBPROP:0000001 "The upper extremity or head of the fibula is of an irregular quadrate form, presenting above a flattened articular surface, directed upward, forward, and medialward, for articulation with a corresponding surface on the lateral condyle of the tibia. On the lateral side is a thick and rough prominence continued behind into a pointed eminence, the apex, which projects upward from the posterior part of the head. The prominence, at its upper and lateral part, gives attachment to the tendon of the Biceps femoris and to the fibular collateral ligament of the knee-joint, the ligament dividing the tendon into two parts. The remaining part of the circumference of the head is rough, for the attachment of muscles and ligaments. It presents in front a tubercle for the origin of the upper and anterior fibers of the Peronæus longus, and a surface for the attachment of the anterior ligament of the head; and behind, another tubercle, for the attachment of the posterior ligament of the head and the origin of the upper fibers of the Soleus[Wikipedia:Head_of_fibula]." xsd:string {source="Wikipedia:Head_of_fibula"} [Term] id: UBERON:0008780 @@ -234695,9 +231570,9 @@ xref: NCIT:C34164 xref: UMLS:C1516906 {source="ncithesaurus:Epiblast"} is_a: UBERON:0002532 ! epiblast (generic) intersection_of: UBERON:0002532 ! epiblast (generic) -intersection_of: develops_from UBERON:0000087 ! inner cell mass -relationship: develops_from UBERON:0000087 {source="Wikipedia"} ! inner cell mass +intersection_of: RO:0002202 UBERON:0000087 ! develops from inner cell mass relationship: part_of UBERON:0000091 ! bilaminar disc +relationship: RO:0002202 UBERON:0000087 {source="Wikipedia"} ! develops from inner cell mass [Term] id: UBERON:0008783 @@ -234714,11 +231589,11 @@ xref: MA:0002110 xref: SCTID:231189006 xref: Wikipedia:Dorsal_venous_arch_of_the_foot is_a: UBERON:0001638 {source="MA"} ! vein -relationship: connected_to UBERON:0001545 ! anterior tibial vein -relationship: connected_to UBERON:0001547 ! small saphenous vein -relationship: connected_to UBERON:0001550 ! medial marginal vein -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/4e/Gray581.png" xsd:anyURI +relationship: RO:0002170 UBERON:0001545 ! connected to anterior tibial vein +relationship: RO:0002170 UBERON:0001547 ! connected to small saphenous vein +relationship: RO:0002170 UBERON:0001550 ! connected to medial marginal vein +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4e/Gray581.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0008784 @@ -234760,7 +231635,7 @@ is_a: UBERON:0004704 ! bone fossa intersection_of: UBERON:0004704 ! bone fossa intersection_of: part_of UBERON:0003128 ! cranium relationship: part_of UBERON:0004766 {is_inferred="true", source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! cranial bone -property_value: editor_note "todo - review the relationships for this and its subclasses; the relation should be bounded rather than part of, and contains should be used for the brain parts contained by the fossae" xsd:string +property_value: IAO:0000116 "todo - review the relationships for this and its subclasses; the relation should be bounded rather than part of, and contains should be used for the brain parts contained by the fossae" xsd:string [Term] id: UBERON:0008805 @@ -234781,9 +231656,9 @@ intersection_of: adjacent_to UBERON:0001091 ! calcareous tooth intersection_of: adjacent_to UBERON:0001828 ! gingiva relationship: adjacent_to UBERON:0001091 ! calcareous tooth relationship: adjacent_to UBERON:0001828 ! gingiva -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0000165 ! mouth -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/5/5e/Gingival_sulcus.PNG" xsd:anyURI +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/5/5e/Gingival_sulcus.PNG" xsd:anyURI [Term] id: UBERON:0008811 @@ -234796,16 +231671,13 @@ synonym: "aedeagus" NARROW SENSU [FBbt:00004850] synonym: "copulatory organ" RELATED [] synonym: "penis" NARROW [] xref: AAO:0010255 -xref: FBbt:00004850 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: HAO:0000091 xref: TAO:0002036 xref: TGMA:0000585 xref: Wikipedia:Intromittent_organ is_a: UBERON:0003135 ! male reproductive organ relationship: capable_of_part_of GO:0007620 ! copulation -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: IAO:0000232 "this is a broad grouping class connecting a number of different analagous organs by their function. We place the insect aedeagus here rather than penis, although this is somewhat arbitrary given the broadness of the current definition" xsd:string -property_value: UBPROP:0000001 "Surface structure that is an external structure of a male organism through which sperm is transferred to a female organism during mating.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002036", ontology="TAO", source="TAO:wd"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0008814 @@ -234824,10 +231696,10 @@ xref: FMA:293041 xref: NCIT:C34248 xref: UMLS:C1519038 {source="ncithesaurus:Pharyngeal_Apparatus"} is_a: UBERON:0034921 ! multi organ part structure -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0009145 ! pharyngeal region of foregut -property_value: editor_note "Currently defined in a vertebrate specific manner. The arch system has origins in basal deuterostomes, consider generalizing" xsd:string +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +property_value: IAO:0000116 "Currently defined in a vertebrate specific manner. The arch system has origins in basal deuterostomes, consider generalizing" xsd:string [Term] id: UBERON:0008816 @@ -234836,7 +231708,6 @@ namespace: uberon def: "A head that is part of a embryo." [OBOL:automatic] subset: non_informative xref: CALOHA:TS-0246 -xref: FBbt:00000155 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:293011 is_a: UBERON:0000033 ! head intersection_of: UBERON:0000033 ! head @@ -234849,10 +231720,11 @@ name: thymus primordium endoderm namespace: uberon def: "An endoderm that is part of a thymus primordium." [OBOL:automatic] is_a: UBERON:0000925 ! endoderm +is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0000925 ! endoderm intersection_of: part_of UBERON:0005562 ! thymus primordium -relationship: has_developmental_contribution_from UBERON:0007124 {source="PMID:16313389"} ! pharyngeal pouch 3 relationship: part_of UBERON:0005562 ! thymus primordium +relationship: RO:0002254 UBERON:0007124 {source="PMID:16313389"} ! has developmental contribution from pharyngeal pouch 3 [Term] id: UBERON:0008823 @@ -234863,10 +231735,10 @@ synonym: "vertebrate brain" NARROW [] is_a: UBERON:0000489 {source="ZFA"} ! cavitated compound organ is_a: UBERON:0000955 ! brain intersection_of: UBERON:0000955 ! brain -intersection_of: develops_from UBERON:0001049 ! neural tube -relationship: develops_from UBERON:0001049 ! neural tube +intersection_of: RO:0002202 UBERON:0001049 ! develops from neural tube relationship: part_of UBERON:0000033 {source="FMA"} ! head -property_value: editor_note "a reasoner should automatically classify all the vertebrate ontology brain classes here" xsd:string +relationship: RO:0002202 UBERON:0001049 ! develops from neural tube +property_value: IAO:0000116 "a reasoner should automatically classify all the vertebrate ontology brain classes here" xsd:string property_value: seeAlso "https://github.com/obophenotype/uberon/issues/338" xsd:anyURI [Term] @@ -234882,11 +231754,12 @@ xref: MA:0001735 xref: NCIT:C32484 xref: SCTID:279623004 xref: UMLS:C0458632 {source="ncithesaurus:Duct_of_the_Epididymis"} +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005904 ! duct of male reproductive system intersection_of: UBERON:0000058 ! duct -intersection_of: branching_part_of UBERON:0001301 ! epididymis -relationship: branching_part_of UBERON:0001301 ! epididymis +intersection_of: RO:0002380 UBERON:0001301 ! branching part of epididymis relationship: part_of UBERON:0001301 {source="FMA"} ! epididymis +relationship: RO:0002380 UBERON:0001301 ! branching part of epididymis [Term] id: UBERON:0008826 @@ -234900,7 +231773,6 @@ synonym: "type II pneumocyte secretion" EXACT [] xref: EMAPA:36551 xref: FMA:62780 xref: MA:0002534 -xref: MESH:D011663 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C13273 xref: UMLS:C0034085 {source="ncithesaurus:Lung_Surfactant"} xref: Wikipedia:Pulmonary_surfactant @@ -234909,7 +231781,6 @@ intersection_of: UBERON:0006538 ! respiratory system fluid/secretion intersection_of: produced_by CL:0002063 ! type II pneumocyte relationship: has_part CHEBI:6495 relationship: produced_by CL:0002063 ! type II pneumocyte -property_value: UBPROP:0000009 "surfactant" xsd:string [Term] id: UBERON:0008835 @@ -234931,11 +231802,9 @@ is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007499 {source="EHDAA2"} ! epithelial sac is_a: UBERON:0009497 ! epithelium of foregut-midgut junction is_a: UBERON:0009854 ! digestive tract diverticulum -relationship: develops_from UBERON:0003894 {source="EHDAA2"} ! liver primordium -relationship: part_of UBERON:0004161 {notes="caudal part", source="EHDAA2"} ! septum transversum -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/4f/Gray1088.png" xsd:anyURI -property_value: UBPROP:0000008 "in mice, the hepatic diverticulum forms by E9 and expands into an obvious liver bud by E10" xsd:string -property_value: UBPROP:0000011 "The caudal part of the septum transversum is invaded by the hepatic diverticulum which divides within it to form the liver and thus gives rise to the ventral mesentery of the foregut." xsd:string +relationship: part_of UBERON:0004161 ! septum transversum +relationship: RO:0002202 UBERON:0003894 {source="EHDAA2"} ! develops from liver primordium +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4f/Gray1088.png" xsd:anyURI [Term] id: UBERON:0008836 @@ -234946,7 +231815,7 @@ is_a: UBERON:0004185 ! endodermal part of digestive tract is_a: UBERON:0007499 {source="cjm"} ! epithelial sac is_a: UBERON:0009497 ! epithelium of foregut-midgut junction is_a: UBERON:0009854 ! digestive tract diverticulum -relationship: develops_from UBERON:0008835 {source="http://www.stembook.org/node/512"} ! hepatic diverticulum +relationship: RO:0002202 UBERON:0008835 {source="http://www.stembook.org/node/512"} ! develops from hepatic diverticulum [Term] id: UBERON:0008837 @@ -234967,8 +231836,6 @@ xref: MA:0003004 xref: SCTID:410746001 is_a: UBERON:0000211 {source="cjm"} ! ligament disjoint_from: UBERON:0008846 ! skeletal ligament -property_value: UBPROP:0000001 "Ligament organ that primarily consists of dense connective tissue aggregated into fasciculi which may be admixed with smooth muscle. Examples: ligament of liver, ovarian ligament[FMA:25625]." xsd:string {source="FMA:25625"} -property_value: UBPROP:0000012 "this class is used more generally than the FMA class, to include for example folds of mesentery such as the broad ligament of the uterus." xsd:string {external_ontology="FMA"} [Term] id: UBERON:0008846 @@ -234993,17 +231860,15 @@ xref: Wikipedia:Ligament#Articular_ligaments is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000211 ! ligament intersection_of: UBERON:0000211 ! ligament -intersection_of: connects UBERON:0004765 ! skeletal element intersection_of: part_of UBERON:0001434 ! skeletal system -relationship: composed_primarily_of UBERON:0007846 {source="VSAO"} ! dense regular connective tissue -relationship: connects UBERON:0004765 {notes="bones or cartilage organs"} ! skeletal element +intersection_of: RO:0002176 UBERON:0004765 ! connects skeletal element relationship: has_part CL:0000057 {source="AEO"} ! fibroblast relationship: has_part CL:0000327 {source="AEO"} ! extracellular matrix secreting cell relationship: part_of UBERON:0001434 ! skeletal system -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/9/9a/Knee_diagram.svg" xsd:anyURI -property_value: editor_note "logical definition deliberately made strict to avoid classifying MA:spiral ligament as both nonskeletal and skeletal. see https://github.com/obophenotype/mouse-anatomy-ontology/issues/71" xsd:string -property_value: UBPROP:0000001 "Dense regular connective tissue connecting two or more adjacent skeletal elements or supporting an organ.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000072", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "Ligament organ that primarily consists of regular dense connective tissue aggregated into fasciculi; connects bone and cartilage organs. Examples: sutural ligament, ligament of pinna, tarsal ligament[FMA:25624]." xsd:string {source="FMA:25624"} +relationship: RO:0002176 UBERON:0004765 ! connects skeletal element +relationship: RO:0002473 UBERON:0007846 {source="VSAO"} ! composed primarily of dense regular connective tissue +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/9/9a/Knee_diagram.svg" xsd:anyURI +property_value: IAO:0000116 "logical definition deliberately made strict to avoid classifying MA:spiral ligament as both nonskeletal and skeletal. see https://github.com/obophenotype/mouse-anatomy-ontology/issues/71" xsd:string [Term] id: UBERON:0008851 @@ -235016,9 +231881,9 @@ synonym: "epamniotic cavity" RELATED [MP:0011207] xref: EMAPA:16080 is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0004364 ! ectoplacental cone -relationship: luminal_space_of UBERON:0004364 ! ectoplacental cone +intersection_of: RO:0002572 UBERON:0004364 ! luminal space of ectoplacental cone relationship: part_of UBERON:0004364 ! ectoplacental cone +relationship: RO:0002572 UBERON:0004364 ! luminal space of ectoplacental cone [Term] id: UBERON:0008856 @@ -235033,14 +231898,14 @@ synonym: "tunica muscularis (gaster)" EXACT [FMA:14909] synonym: "tunica muscularis gastris" EXACT [] xref: FMA:14909 xref: SCTID:362132003 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0018261 ! muscular coat of digestive tract is_a: UBERON:0034933 ! layer of smooth muscle tissue intersection_of: UBERON:0006660 ! muscular coat intersection_of: part_of UBERON:0001167 ! wall of stomach -relationship: contributes_to_morphology_of UBERON:0001135 ! smooth muscle tissue -relationship: contributes_to_morphology_of UBERON:0001167 ! wall of stomach relationship: part_of UBERON:0004222 {source="MA-abduced"} ! stomach smooth muscle -property_value: UBPROP:0000010 "the muscularis externa in the stomach differs from that of other GI organs in that it has three layers of smooth muscle instead of two" xsd:string {source="WP"} +relationship: RO:0002433 UBERON:0001135 ! contributes to morphology of smooth muscle tissue +relationship: RO:0002433 UBERON:0001167 ! contributes to morphology of wall of stomach [Term] id: UBERON:0008858 @@ -235055,11 +231920,11 @@ xref: FMA:14580 xref: SCTID:245417002 xref: Wikipedia:Pyloric_canal is_a: UBERON:0009870 {source="FMA"} ! zone of stomach -relationship: continuous_with UBERON:0001165 ! pyloric antrum -relationship: continuous_with UBERON:0001202 ! pyloric sphincter -relationship: contributes_to_morphology_of UBERON:0001166 ! pylorus relationship: part_of UBERON:0001166 {source="Wikipedia"} ! pylorus -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/3/33/Illu_stomach.jpg" xsd:anyURI +relationship: RO:0002150 UBERON:0001165 ! continuous with pyloric antrum +relationship: RO:0002150 UBERON:0001202 ! continuous with pyloric sphincter +relationship: RO:0002433 UBERON:0001166 ! contributes to morphology of pylorus +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/3/33/Illu_stomach.jpg" xsd:anyURI [Term] id: UBERON:0008859 @@ -235082,10 +231947,8 @@ is_a: UBERON:0000325 ! gastric gland is_a: UBERON:0000414 {source="MP"} ! mucous gland intersection_of: UBERON:0000325 ! gastric gland intersection_of: part_of UBERON:0001162 ! cardia of stomach -relationship: contributes_to_morphology_of UBERON:0001162 ! cardia of stomach relationship: part_of UBERON:0004996 {source="FMA"} ! mucosa of cardia of stomach -property_value: UBPROP:0000001 "The cardiac glands of the stomach secrete primarily mucus. They are few in number and occur close to the cardiac orifice where the esophagus joins the stomach. In general, they are more shallow than those in the other parts of the stomach. They are of two kinds: (1) simple tubular glands resembling those of the pyloric end of the stomach, but with short ducts. (2) compound racemose glands resembling the duodenal glands. The cardiac gland is both innervated by the parasympathetic and symapthetic nerve fibres of the autonomic nervous system[Wikipedia:Cardiac_glands]." xsd:string {source="Wikipedia:Cardiac_glands"} -property_value: UBPROP:0000012 "Kardong places this in the glandular epithelium, FMA more generally in the mucosa" xsd:string {external_ontology="FMA"} +relationship: RO:0002433 UBERON:0001162 ! contributes to morphology of cardia of stomach [Term] id: UBERON:0008861 @@ -235107,11 +231970,11 @@ is_a: UBERON:0000325 ! gastric gland is_a: UBERON:0000414 {source="MP"} ! mucous gland intersection_of: UBERON:0000325 ! gastric gland intersection_of: part_of UBERON:0001166 ! pylorus -relationship: contributes_to_morphology_of UBERON:0001166 ! pylorus -relationship: has_quality PATO:0002299 {source="Wikipedia:Tubular_gland"} ! tubular relationship: part_of UBERON:0004998 ! mucosa of pylorus -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/bf/Gray1054.png" xsd:anyURI -property_value: editor_note "check relationship to pylorus vs antrum" xsd:string +relationship: RO:0000086 PATO:0002299 {source="Wikipedia:Tubular_gland"} ! has quality tubular +relationship: RO:0002433 UBERON:0001166 ! contributes to morphology of pylorus +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/bf/Gray1054.png" xsd:anyURI +property_value: IAO:0000116 "check relationship to pylorus vs antrum" xsd:string [Term] id: UBERON:0008870 @@ -235124,13 +231987,13 @@ xref: EMAPA:37942 {source="MA:th"} is_a: UBERON:0008946 ! lung parenchyma intersection_of: UBERON:0000353 ! parenchyma intersection_of: part_of UBERON:0002299 ! alveolus of lung -relationship: contributes_to_morphology_of UBERON:0006524 ! alveolar system -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: has_part CL:0002062 ! type I pneumocyte relationship: has_part CL:0002063 ! type II pneumocyte relationship: has_part CL:0009089 ! lung pericyte relationship: part_of UBERON:0002299 ! alveolus of lung -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002433 UBERON:0006524 ! contributes to morphology of alveolar system +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0008874 @@ -235150,10 +232013,10 @@ xref: UMLS:C0225696 {source="ncithesaurus:Pulmonary_Acinus"} xref: Wikipedia:Acinus#The_Lungs is_a: BFO:0000004 ! independent continuant is_a: UBERON:0001062 ! anatomical entity -relationship: connected_to UBERON:0002187 ! terminal bronchiole -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: part_of UBERON:0010369 ! secondary pulmonary lobule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002170 UBERON:0002187 ! connected to terminal bronchiole +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0008876 @@ -235168,16 +232031,17 @@ synonym: "panniculus carnosus" NARROW [MP:0011157] synonym: "superficial fascia muscular layer" EXACT [] xref: EMAPA:18188 xref: MA:0003140 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004253 ! skin muscle is_a: UBERON:0014892 ! skeletal muscle organ, vertebrate intersection_of: UBERON:0014892 ! skeletal muscle organ, vertebrate intersection_of: part_of UBERON:0002072 ! hypodermis -relationship: contributes_to_morphology_of UBERON:0001015 ! musculature -relationship: contributes_to_morphology_of UBERON:0002072 ! hypodermis -relationship: has_muscle_insertion UBERON:0002097 ! skin of body -relationship: located_in UBERON:0002190 {source="MP-def"} ! subcutaneous adipose tissue relationship: part_of UBERON:0002072 ! hypodermis -property_value: editor_note "We follow MP and treat this as part of the hypodermis, although some sources may consider the hypodermis to be superficial to this" xsd:string +relationship: RO:0001025 UBERON:0002190 {source="MP-def"} ! located in subcutaneous adipose tissue +relationship: RO:0002373 UBERON:0002097 ! has muscle insertion skin of body +relationship: RO:0002433 UBERON:0001015 ! contributes to morphology of musculature +relationship: RO:0002433 UBERON:0002072 ! contributes to morphology of hypodermis +property_value: IAO:0000116 "We follow MP and treat this as part of the hypodermis, although some sources may consider the hypodermis to be superficial to this" xsd:string [Term] id: UBERON:0008877 @@ -235193,11 +232057,12 @@ xref: EMAPA:37866 {source="MA:th"} xref: FMA:70963 xref: NCIT:C62356 xref: SCTID:51025007 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005769 ! basement membrane of epithelium relationship: adjacent_to UBERON:0001003 ! skin epidermis relationship: adjacent_to UBERON:0002067 ! dermis -relationship: contributes_to_morphology_of UBERON:0000014 ! zone of skin relationship: part_of UBERON:0000014 {source="MP"} ! zone of skin +relationship: RO:0002433 UBERON:0000014 ! contributes to morphology of zone of skin [Term] id: UBERON:0008883 @@ -235219,10 +232084,7 @@ xref: VSAO:0000046 xref: Wikipedia:Osteoid xref: XAO:0004035 is_a: UBERON:0002481 {source="VSAO"} ! bone tissue -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/9/9c/Active_osteoblasts.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Bone tissue that is an unmineralized bone matrix deposited by osteoblasts prior to the mineralization of bone tissue.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000046", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "Newly formed organic bone matrix secreted by osteoblasts, that exists prior to calcification; it is comprised mainly of type I collagen fibers, chondroitin sulfate and osteocalci[ISBN:0-683-40008-8]n" xsd:string {reference="ISBN:0-683-40008-8", source="MP:0010924"} -property_value: UBPROP:0000012 "Note that in VSAO this was classified both as tissue and acellular extracellular matrix. Consider also the AEO class 'bone condensation'. is_a intercellular matrix in FMA." xsd:string {external_ontology="VSAO"} +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/9/9c/Active_osteoblasts.jpg" xsd:anyURI [Term] id: UBERON:0008884 @@ -235235,8 +232097,8 @@ is_a: UBERON:0001874 ! putamen intersection_of: UBERON:0001874 ! putamen intersection_of: part_of UBERON:0002812 ! left cerebral hemisphere relationship: part_of UBERON:0002812 ! left cerebral hemisphere -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI [Term] id: UBERON:0008885 @@ -235249,8 +232111,8 @@ is_a: UBERON:0001874 ! putamen intersection_of: UBERON:0001874 ! putamen intersection_of: part_of UBERON:0002813 ! right cerebral hemisphere relationship: part_of UBERON:0002813 ! right cerebral hemisphere -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI [Term] id: UBERON:0008886 @@ -235266,8 +232128,7 @@ is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0007798 {source="Obol"} ! vascular system relationship: has_part UBERON:0002012 ! pulmonary artery relationship: has_part UBERON:0002016 ! pulmonary vein -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000001 "Subdivision of cardiovascular system which has as its parts the pulmonary arterial and venous tree organs.[FMA]" xsd:string {ontology="FMA", source="FMA:45621"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0008887 @@ -235285,9 +232146,9 @@ xref: UMLS:C0226766 {source="ncithesaurus:Hemorrhoidal_Plexus"} xref: Wikipedia:Rectal_venous_plexus is_a: UBERON:0001593 {source="FMA"} ! venous plexus intersection_of: UBERON:0001593 ! venous plexus -intersection_of: surrounds UBERON:0001052 ! rectum -relationship: surrounds UBERON:0001052 ! rectum -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/69/Gray587.png" xsd:anyURI +intersection_of: RO:0002221 UBERON:0001052 ! surrounds rectum +relationship: RO:0002221 UBERON:0001052 ! surrounds rectum +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/69/Gray587.png" xsd:anyURI [Term] id: UBERON:0008895 @@ -235314,17 +232175,11 @@ xref: XAO:0003176 xref: ZFA:0001216 is_a: UBERON:0011159 ! primary subdivision of cranial skeletal system disjoint_from: UBERON:0011156 ! facial skeleton -relationship: develops_from UBERON:0002539 {source="https://github.com/obophenotype/uberon/issues/83"} ! pharyngeal arch -relationship: has_developmental_contribution_from UBERON:0003099 {notes="redundant", source="Grays", source="PMID:11237469"} ! cranial neural crest relationship: overlaps UBERON:0011156 {gci_relation="part_of", gci_filler="NCBITaxon:89593"} ! facial skeleton -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Anatomical cluster that is part of the cranium and consists of the jaws, hyoid and branchial arches.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001216", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Anatomical cluster that is part of the cranium and consists of the jaws, hyoid, and branchial arches.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010157", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000001 "The part of the skull derived from the embryonic pharyngeal arches. [Biology_Online][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000315", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "The skull of ancestral tetrapods has the three basic components that we have been considering: (1) chondrocranium, (2) splanchnocranium, and (3) dermatocranium (reference 1); Each part of the skull arises from a separate phylogenetic source. The most ancient part is the splanchnocranium (visceral cranium), which first arose to support pharyngeal slits in protochordates (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000315", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.242, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.235", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "many sources define this as the part of the endoskeletal that is from pharyngeal arches - this would make it part-disjoint from dermatocranium. However, there are many bones in AOs that have part-paths to both" xsd:string -property_value: UBPROP:0000012 "VSAO labels this term 'pharyngeal arch' (2012-06-01) - however, it clearly means pharyngeal arch skeleton." xsd:string {external_ontology="VSAO"} +relationship: RO:0002202 UBERON:0002539 {source="https://github.com/obophenotype/uberon/issues/83"} ! develops from pharyngeal arch +relationship: RO:0002254 UBERON:0003099 ! has developmental contribution from cranial neural crest +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0008896 @@ -235344,15 +232199,13 @@ synonym: "visceral arches 3-7" EXACT [ZFA:0001613] xref: AAO:0010362 xref: BTO:0002152 xref: EFO:0003694 -xref: SCTID:308766004 xref: TAO:0001597 xref: XAO:0000099 xref: ZFA:0001613 is_a: UBERON:0002539 ! pharyngeal arch intersection_of: UBERON:0002539 ! pharyngeal arch -intersection_of: posterior_to UBERON:0003066 ! pharyngeal arch 2 -relationship: posterior_to UBERON:0003066 ! pharyngeal arch 2 -property_value: UBPROP:0000001 "Posterior-most stream of cranial neural crest, which sub-divides during migration.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010362", ontology="AAO", source="AAO:EJS"} +intersection_of: BSPO:0000099 UBERON:0003066 ! pharyngeal arch 2 +relationship: BSPO:0000099 UBERON:0003066 ! pharyngeal arch 2 [Term] id: UBERON:0008904 @@ -235365,21 +232218,16 @@ synonym: "lateral line organ" BROAD [ZFA:0000243] synonym: "neuromast organ" EXACT [PHENOSCAPE:wd] synonym: "neuromasts" EXACT OMO:0003004 [ZFA:0000243] xref: AAO:0001004 -xref: BTO:0006219 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: EFO:0003513 xref: TAO:0000243 xref: ZFA:0000243 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0035555 ! lateral line sense organ -relationship: develops_from UBERON:0009128 {source="DOI:10.1038/ncomms1502"} ! lateral line placode relationship: has_part CL:0000856 ! neuromast hair cell -relationship: located_in UBERON:0001003 ! skin epidermis relationship: part_of UBERON:0010202 ! lateral line -relationship: transformation_of UBERON:2005227 {source="ZFA"} ! protoneuromast -property_value: UBPROP:0000001 "Type of mechanoreceptive organ of the lateral line which are arranged in lines on the body surface. These organs are constituted by hair cells and supporting cells and it is located in the epidermis with its hair cells exposed to the surface. Absent in some caecilians. These receptors receive afferent and efferent innervations.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0001004", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000001 "Volcano-shaped lateral line sensory organ located in characteristic positions within the skin epithelium and containing hair cells and their support elements. Kimmel et al, 1995. (Also see Anatomical Atlas entry for lateral line by T. Whitfield.)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000243", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000002 "relationship loss: part_of lateral line receptor organ (AAO:0001001)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0001004", ontology="AAO"} -property_value: UBPROP:0000002 "relationship loss: subclass lateral line receptor (AAO:0010705)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0001004", ontology="AAO"} +relationship: RO:0001025 UBERON:0001003 ! located in skin epidermis +relationship: RO:0002202 UBERON:0009128 {source="DOI:10.1038/ncomms1502"} ! develops from lateral line placode +relationship: RO:0002494 UBERON:2005227 {source="ZFA"} ! transformation of protoneuromast [Term] id: UBERON:0008906 @@ -235395,13 +232243,10 @@ is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0001785 ! cranial nerve intersection_of: extends_fibers_into UBERON:0008904 ! neuromast intersection_of: extends_fibers_into UBERON:3010706 ! lateral line nucleus -relationship: develops_from UBERON:0009128 {source="NCBIBook:NBK53175"} ! lateral line placode relationship: extends_fibers_into UBERON:0008904 ! neuromast relationship: extends_fibers_into UBERON:3010706 ! lateral line nucleus relationship: part_of UBERON:0002540 ! lateral line system -property_value: UBPROP:0000001 "Any of the sensory nerves that innervate mechano- and electroreceptors of the lateral line system. The lateral line nerves may be separated in two components, anterior and posterior, in relation to the position of its roots with respect to the otic capsule. These nerves develop from lateral line placodes.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010077", ontology="AAO", source="AAO:SIQ"} -property_value: UBPROP:0000002 "relationship loss: innervates lateral line receptor organ (AAO:0001001)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010077", ontology="AAO"} -property_value: UBPROP:0000002 "relationship type change: part_of_proxy lateral line system (AAO:0000975) CHANGED TO: part_of lateral line system (UBERON:0002540)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010077", ontology="AAO"} +relationship: RO:0002202 UBERON:0009128 {source="NCBIBook:NBK53175"} ! develops from lateral line placode [Term] id: UBERON:0008907 @@ -235420,8 +232265,6 @@ is_a: UBERON:0007842 {source="VSAO"} ! membrane bone intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0010364 ! dermal skeleton relationship: part_of UBERON:0010364 {source="VSAO"} ! dermal skeleton -property_value: UBPROP:0000001 "Intramembranous bone that forms superficially in the organism.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001590", ontology="TAO", source="TAO:wd"} -property_value: UBPROP:0000012 "other AOs are not yet in sync with this classification" xsd:string [Term] id: UBERON:0008909 @@ -235434,18 +232277,18 @@ xref: AAO:0010777 xref: TAO:0001639 xref: VSAO:0000307 xref: ZFA:0001629 -is_a: UBERON:0012075 {notes="not in VSAO", source="ZFA"} ! replacement bone +is_a: UBERON:0012075 ! replacement bone intersection_of: UBERON:0001474 ! bone element intersection_of: adjacent_to UBERON:0002328 ! notochord relationship: adjacent_to UBERON:0002328 ! notochord -property_value: editor_note "We go with the latest VSAO in making this a subtype of bone, and add a logical definition based on the textual definition in VSAO. We also include the subtyping under 'replacement bone', for consistency with ZFA" xsd:string -property_value: UBPROP:0000001 "Replacement bone that forms within the connective tissue surrounding the notochord.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001639", ontology="TAO", source="TAO:wd"} +property_value: IAO:0000116 "We go with the latest VSAO in making this a subtype of bone, and add a logical definition based on the textual definition in VSAO. We also include the subtyping under 'replacement bone', for consistency with ZFA" xsd:string [Term] id: UBERON:0008921 name: substratum of layer of retina namespace: uberon def: "Missing definition for term UBERON:0008921. Please replace it using linked reference." [UBERON:CL_meeting_20110725] +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0022303 ! nervous system cell part layer relationship: part_of UBERON:0000966 ! retina @@ -235588,6 +232431,7 @@ xref: FMA:27360 xref: MA:0003168 xref: SCTID:201712001 is_a: UBERON:0000353 {source="FMA"} ! parenchyma +is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0000353 ! parenchyma intersection_of: part_of UBERON:0002048 ! lung relationship: part_of UBERON:0002048 {source="FMA"} ! lung @@ -235600,8 +232444,8 @@ xref: EHDAA2:0004069 xref: NCIT:C34283 xref: UMLS:C1514898 {source="ncithesaurus:Respiratory_Primordium"} is_a: UBERON:0001048 {source="Obol"} ! primordium -relationship: has_potential_to_develop_into UBERON:0001004 ! respiratory system relationship: part_of UBERON:0003258 ! endoderm of foregut +relationship: RO:0002387 UBERON:0001004 ! has potential to develop into respiratory system [Term] id: UBERON:0008951 @@ -235618,7 +232462,6 @@ is_a: UBERON:0000101 ! lobe of lung intersection_of: UBERON:0000101 ! lobe of lung intersection_of: part_of UBERON:0002168 ! left lung relationship: part_of UBERON:0002168 ! left lung -property_value: UBPROP:0000008 "1 in mice, divided into 2 in human by a single interlobar fissure, the oblqiue fissure" xsd:string {source="ISBN:0123813611"} [Term] id: UBERON:0008962 @@ -235636,8 +232479,8 @@ is_a: UBERON:0002428 ! limb bone is_a: UBERON:0010741 ! bone of pectoral complex is_a: UBERON:0015021 ! forelimb endochondral element intersection_of: UBERON:0015021 ! forelimb endochondral element -intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue -relationship: develops_from UBERON:0010883 ! forelimb cartilage element +intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue +relationship: RO:0002202 UBERON:0010883 ! develops from forelimb cartilage element [Term] id: UBERON:0008969 @@ -235649,7 +232492,6 @@ synonym: "tooth follicle" RELATED [BTO:0000337] xref: BTO:0000337 xref: EMAPA:35275 xref: MA:0003121 -xref: MESH:D003795 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: NCIT:C34138 xref: SCTID:110975002 xref: Wikipedia:Dental_follicle @@ -235671,14 +232513,11 @@ synonym: "true apocrine gland" EXACT [] xref: BTO:0001162 xref: EMAPA:35141 xref: MA:0003040 -xref: MESH:D001050 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: SCTID:361698000 xref: Wikipedia:Apocrine is_a: UBERON:0002365 ! exocrine gland disjoint_from: UBERON:0010243 {source="cjm"} ! merocrine gland -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000007 "apocrine" xsd:string -property_value: UBPROP:0000008 "Mammary glands are modified apocrine glands present in both humans and mice; unlike humans, mice do not have axillary apocrine sweat glands[MGI:anna]" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0008987 @@ -235715,9 +232554,9 @@ is_a: UBERON:0005178 ! thoracic cavity element is_a: UBERON:0011148 ! submucosal gland intersection_of: UBERON:0011148 ! submucosal gland intersection_of: part_of UBERON:0001043 ! esophagus -relationship: located_in UBERON:0001972 ! submucosa of esophagus relationship: part_of UBERON:0001043 ! esophagus -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Illu_esophageal_layers.jpg" xsd:anyURI +relationship: RO:0001025 UBERON:0001972 ! located in submucosa of esophagus +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Illu_esophageal_layers.jpg" xsd:anyURI [Term] id: UBERON:0008998 @@ -235750,9 +232589,9 @@ xref: BTO:0005081 xref: SCTID:256880003 is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue -intersection_of: surrounds UBERON:0000057 ! urethra +intersection_of: RO:0002221 UBERON:0000057 ! surrounds urethra relationship: part_of UBERON:0001556 ! lower urinary tract -relationship: surrounds UBERON:0000057 ! urethra +relationship: RO:0002221 UBERON:0000057 ! surrounds urethra [Term] id: UBERON:0009015 @@ -235780,8 +232619,8 @@ xref: MA:0002078 xref: SCTID:244307000 is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0001255 ! urinary bladder -relationship: supplies UBERON:0001255 ! urinary bladder +intersection_of: RO:0002178 UBERON:0001255 ! supplies urinary bladder +relationship: RO:0002178 UBERON:0001255 ! supplies urinary bladder [Term] id: UBERON:0009029 @@ -235809,9 +232648,8 @@ xref: SCTID:304057004 xref: UMLS:C0226670 {source="ncithesaurus:Left_Pulmonary_Vein"} is_a: UBERON:0002016 ! pulmonary vein intersection_of: UBERON:0002016 ! pulmonary vein -intersection_of: drains UBERON:0002168 ! left lung -relationship: drains UBERON:0002168 ! left lung -property_value: UBPROP:0000001 "A vein that returns oxygenated blood from the left lung to the left atrium of the heart[ncithesaurus:Left_Pulmonary_Vein]." xsd:string {source="ncithesaurus:Left_Pulmonary_Vein"} +intersection_of: RO:0002179 UBERON:0002168 ! drains left lung +relationship: RO:0002179 UBERON:0002168 ! drains left lung [Term] id: UBERON:0009032 @@ -235825,9 +232663,8 @@ xref: SCTID:304056008 xref: UMLS:C0226669 {source="ncithesaurus:Right_Pulmonary_Vein"} is_a: UBERON:0002016 ! pulmonary vein intersection_of: UBERON:0002016 ! pulmonary vein -intersection_of: drains UBERON:0002167 ! right lung -relationship: drains UBERON:0002167 ! right lung -property_value: UBPROP:0000001 "A vein that returns oxygenated blood from the right lung to the left atrium of the heart[ncithesaurus:Right_Pulmonary_Vein]." xsd:string {source="ncithesaurus:Right_Pulmonary_Vein"} +intersection_of: RO:0002179 UBERON:0002167 ! drains right lung +relationship: RO:0002179 UBERON:0002167 ! drains right lung [Term] id: UBERON:0009035 @@ -235864,7 +232701,7 @@ is_a: UBERON:0010754 ! germinal center intersection_of: UBERON:0010754 ! germinal center intersection_of: part_of UBERON:0000029 ! lymph node relationship: part_of UBERON:0010753 {source="MA"} ! lymph node secondary follicle -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0009042 @@ -235882,8 +232719,8 @@ is_a: UBERON:0006876 ! vasculature of organ intersection_of: UBERON:0001593 ! venous plexus intersection_of: part_of UBERON:0002367 ! prostate gland relationship: part_of UBERON:0002367 ! prostate gland -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/bd/Gray585.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/bd/Gray585.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0009089 @@ -235891,8 +232728,8 @@ name: inner medulla vasa recta descending limb namespace: uberon xref: KUPO:0001003 is_a: UBERON:0000064 ! organ part +is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0004776 {source="KUPO"} ! inner renal medulla vasa recta -property_value: UBPROP:0000012 "This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta in the inner medullar parallel to the descending limb" xsd:string {external_ontology="CL"} [Term] id: UBERON:0009090 @@ -235900,8 +232737,8 @@ name: outer medulla vasa recta descending limb namespace: uberon xref: KUPO:0001004 is_a: UBERON:0000064 ! organ part +is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0004775 {source="KUPO"} ! outer renal medulla vasa recta -property_value: UBPROP:0000012 "This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta in the outer medullar parallel to the descending limb" xsd:string {external_ontology="CL"} [Term] id: UBERON:0009091 @@ -235910,9 +232747,9 @@ namespace: uberon subset: human_reference_atlas xref: KUPO:0001005 is_a: UBERON:0000064 ! organ part +is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0004726 {source="KUPO"} ! vasa recta -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000012 "This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta parallel to the ascending limb" xsd:string {external_ontology="CL"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0009092 @@ -235920,8 +232757,8 @@ name: inner medulla vasa recta ascending limb namespace: uberon xref: KUPO:0001006 is_a: UBERON:0000064 ! organ part +is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0004776 {source="KUPO"} ! inner renal medulla vasa recta -property_value: UBPROP:0000012 "This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta in the inner medulla parallel to the ascending limb" xsd:string {external_ontology="CL"} [Term] id: UBERON:0009093 @@ -235929,8 +232766,8 @@ name: outer medulla vasa recta ascending limb namespace: uberon xref: KUPO:0001007 is_a: UBERON:0000064 ! organ part +is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0004775 {source="KUPO"} ! outer renal medulla vasa recta -property_value: UBPROP:0000012 "This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta in the outer medulla parallel to the ascending limb" xsd:string {external_ontology="CL"} [Term] id: UBERON:0009095 @@ -235942,7 +232779,7 @@ synonym: "papillary tips" EXACT OMO:0003004 [KUPO:0001009] xref: KUPO:0001009 is_a: UBERON:0000064 ! organ part relationship: part_of UBERON:0001228 {source="KUPO"} ! renal papilla -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0009097 @@ -235955,13 +232792,12 @@ synonym: "pregnant adult stage" RELATED [BTO:0004733] synonym: "pregnant organism" RELATED [] synonym: "pregnant stage" RELATED [BTO:0004733] xref: BTO:0004733 -xref: IDOMAL:0000443 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} is_a: UBERON:0007023 ! adult organism intersection_of: UBERON:0007023 ! adult organism intersection_of: has_part UBERON:0000922 ! embryo relationship: has_part UBERON:0000922 ! embryo -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: participates_in GO:0007565 ! female pregnancy +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0009098 @@ -235975,10 +232811,10 @@ xref: SCTID:362253003 xref: UMLS:C1514389 {source="ncithesaurus:Pregnant_Uterus"} is_a: UBERON:0000995 ! uterus intersection_of: UBERON:0000995 ! uterus -intersection_of: location_of UBERON:0000922 ! embryo -relationship: contains_process GO:0007565 ! female pregnancy -relationship: location_of UBERON:0000922 ! embryo +intersection_of: RO:0001015 UBERON:0000922 ! location of embryo +relationship: BFO:0000067 GO:0007565 ! contains process female pregnancy relationship: part_of UBERON:0009097 ! gravid organism +relationship: RO:0001015 UBERON:0000922 ! location of embryo [Term] id: UBERON:0009114 @@ -235990,9 +232826,8 @@ is_a: UBERON:0002370 ! thymus intersection_of: UBERON:0002370 ! thymus intersection_of: part_of UBERON:0000974 ! neck relationship: part_of UBERON:0000974 ! neck -relationship: present_in_taxon NCBITaxon:39107 ! Murinae -relationship: present_in_taxon NCBITaxon:9263 -property_value: UBPROP:0000008 "A cervical thymus is a pathological structure in a human - it can form during the migration of the thymus to its location in the mediastinum. Some mice have a cervical thymus. There are examples of cervical thymi in marsupials and prosimians[ISBN:0781714125]" xsd:string +property_value: RO:0002175 NCBITaxon:39107 +property_value: RO:0002175 NCBITaxon:9263 [Term] id: UBERON:0009115 @@ -236032,9 +232867,8 @@ xref: XAO:0004208 xref: ZFA:0001198 is_a: UBERON:0002546 ! cranial placode is_a: UBERON:0011814 {source="NCBIBook:NBK53175"} ! non-neurogenic ectodermal placode -relationship: develops_from UBERON:0005497 {source="ZFA"} ! non-neural ectoderm -property_value: editor_note "consider adding more detailed spatial placement - e.g. oral ectoderm and/or rostal ectoderm" xsd:string -property_value: UBPROP:0000011 "Fate-mapping studies in amphibian, chick and mouse embryos (Eagleson et al., 1986; 1995; Couly and Le Douarin, 1985; Cobos et al., 2001; Osumi-Yamachita et al., 1994; Kawamura et al., 2002) have shown that the cells contributing to the adenohypophysis develop at the midline of the anterior neural ridge, which delineates the rostral boundary of the neural plate, a region devoid of neural crest. The anterior neural ridge also gives rise to the olfactory placodes and some forebrain tissues including the olfactory bulbs (reviewed in Papalopulu, 1995). Ablation of this region in chick embryos at the 2-4 somite stage confirmed these lineage analyses as it prevented formation of Rathke's pouch and any further pituitary development (elAmraoui and Dubois, 1993). Upon head folding, the oral ectoderm cells of the adenohypophyseal placode invaginate towards the prospective ventral diencephalon to form Rathke's pouch, the anlage of the adenohypophysis. Rathke's pouch starts as an invagination of the oral ectoderm in response to inductive signals from the prospective diencephalon. The region of the diencephalon above the pouch is known as the infundibulum and forms the posterior lobe of the pituitary or neurohypohysis (Figure 3). While in most basal fish and tetrapods the adenohypophyseal anlagen invaginates to form Rathke's pouch, in teleost fish the adenohypophyseal placode does not invaginate but rather maintains its initial organization forming a solid structure in the head (reviewed in Pogoda and Hammerschmidt; 2009)" xsd:string +relationship: RO:0002202 UBERON:0005497 {source="ZFA"} ! develops from non-neural ectoderm +property_value: IAO:0000116 "consider adding more detailed spatial placement - e.g. oral ectoderm and/or rostal ectoderm" xsd:string [Term] id: UBERON:0009124 @@ -236077,14 +232911,13 @@ namespace: uberon def: "Cranial ganglion which develops from an epibranchial placode." [PMID:20133851, ZFIN:curator] comment: Epibranchial ganglia orchestrate the development of the cranial neurogenic crest synonym: "epibranchial ganglia" EXACT OMO:0003004 [ZFA:0001555] -xref: BTO:0006250 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: TAO:0001555 xref: ZFA:0001555 is_a: UBERON:0001714 {source="ZFA"} ! cranial ganglion is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0001714 ! cranial ganglion -intersection_of: develops_from UBERON:0003078 ! epibranchial placode -relationship: develops_from UBERON:0003078 {source="NCBIBook:NBK53175"} ! epibranchial placode +intersection_of: RO:0002202 UBERON:0003078 ! develops from epibranchial placode +relationship: RO:0002202 UBERON:0003078 {source="NCBIBook:NBK53175"} ! develops from epibranchial placode [Term] id: UBERON:0009128 @@ -236096,12 +232929,11 @@ xref: AAO:0010718 xref: XAO:0000440 is_a: UBERON:0003067 {source="ISBN:0471888893"} ! dorsolateral placode intersection_of: UBERON:0005085 ! ectodermal placode -intersection_of: has_potential_to_develop_into UBERON:0002540 ! lateral line system -relationship: has_potential_to_develop_into UBERON:0002540 ! lateral line system -relationship: never_in_taxon NCBITaxon:32524 {source="http://tolweb.org/Amniota"} ! Amniota -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata -property_value: editor_note "TODO - compare with protoneuromast" xsd:string -property_value: UBPROP:0000001 "Specialized series of dorsolateral ectodermal placodes.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010718", ontology="AAO", source="AAO:SIQ"} +intersection_of: RO:0002387 UBERON:0002540 ! has potential to develop into lateral line system +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002387 UBERON:0002540 ! has potential to develop into lateral line system +property_value: IAO:0000116 "TODO - compare with protoneuromast" xsd:string +property_value: RO:0002161 NCBITaxon:32524 {source="http://tolweb.org/Amniota"} [Term] id: UBERON:0009129 @@ -236122,9 +232954,9 @@ is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0002165 ! endocardium intersection_of: part_of UBERON:0002078 ! right cardiac atrium -relationship: develops_from UBERON:0005092 {source="EHDAA2"} ! right horn of sinus venosus relationship: part_of UBERON:0002078 ! right cardiac atrium relationship: part_of UBERON:0006218 {source="EHDAA2"} ! common atrial chamber +relationship: RO:0002202 UBERON:0005092 {source="EHDAA2"} ! develops from right horn of sinus venosus [Term] id: UBERON:0009133 @@ -236145,7 +232977,6 @@ is_a: UBERON:0002050 {source="EHDAA2"} ! embryonic structure is_a: UBERON:0005291 ! embryonic tissue relationship: adjacent_to UBERON:0001179 ! peritoneal cavity relationship: adjacent_to UBERON:0002402 ! pleural cavity -property_value: UBPROP:0000003 "In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000757", ontology="VHOG", source="ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206", source="http://bgee.unil.ch/"} [Term] id: UBERON:0009141 @@ -236172,10 +233003,10 @@ xref: EHDAA2:0001113 xref: EHDAA:177 xref: EMAPA:16097 is_a: UBERON:0000477 ! anatomical cluster -relationship: composed_primarily_of UBERON:0003104 ! mesenchyme -relationship: has_developmental_contribution_from UBERON:0000926 {source="EHDAA2"} ! mesoderm relationship: part_of UBERON:0000922 ! embryo -property_value: editor_note "consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)" xsd:string +relationship: RO:0002254 UBERON:0000926 {source="EHDAA2"} ! has developmental contribution from mesoderm +relationship: RO:0002473 UBERON:0003104 ! composed primarily of mesenchyme +property_value: IAO:0000116 "consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)" xsd:string [Term] id: UBERON:0009145 @@ -236197,12 +233028,13 @@ xref: EMAPA:18015 is_a: UBERON:0000481 {source="EHDAA2"} ! multi-tissue structure is_a: UBERON:0005866 {source="EHDAA2"} ! pre-cartilage condensation is_a: UBERON:0009891 ! facial mesenchyme +is_a: UBERON:0014387 ! mesenchyme derived from neural crest is_a: UBERON:0015060 ! sphenoid endochondral element intersection_of: UBERON:0015060 ! sphenoid endochondral element -intersection_of: composed_primarily_of UBERON:0005866 ! pre-cartilage condensation -relationship: composed_primarily_of UBERON:0005866 ! pre-cartilage condensation +intersection_of: RO:0002473 UBERON:0005866 ! composed primarily of pre-cartilage condensation relationship: part_of UBERON:0001703 {source="EHDAA2"} ! neurocranium relationship: part_of UBERON:0002241 {source="EHDAA2"} ! chondrocranium +relationship: RO:0002473 UBERON:0005866 ! composed primarily of pre-cartilage condensation [Term] id: UBERON:0009193 @@ -236214,10 +233046,11 @@ xref: EHDAA2:0001888 is_a: UBERON:0003932 ! cartilage element of chondrocranium is_a: UBERON:0005863 {source="EHDAA2"} ! cartilaginous condensation is_a: UBERON:0009891 ! facial mesenchyme +is_a: UBERON:0014387 ! mesenchyme derived from neural crest is_a: UBERON:0015060 ! sphenoid endochondral element intersection_of: UBERON:0015060 ! sphenoid endochondral element -intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue -relationship: develops_from UBERON:0009191 ! sphenoid bone pre-cartilage condensation +intersection_of: RO:0002473 UBERON:0002418 ! composed primarily of cartilage tissue +relationship: RO:0002202 UBERON:0009191 ! develops from sphenoid bone pre-cartilage condensation [Term] id: UBERON:0009196 @@ -236237,10 +233070,10 @@ synonym: "articulation of skull bones" RELATED [OBOL:automatic] synonym: "joint of the skull bones" EXACT [OBOL:automatic] is_a: UBERON:0002209 ! fibrous joint intersection_of: UBERON:0002209 ! fibrous joint -intersection_of: connects UBERON:0003457 {minCardinality="2"} ! head bone -relationship: connects UBERON:0003457 ! head bone +intersection_of: RO:0002176 UBERON:0003457 {minCardinality="2"} ! connects head bone relationship: part_of UBERON:0010323 ! cranial skeletal system -property_value: editor_note "we follow GO in dividing sutures into cranial and facial and making a grouping class, but this is not consistent with FMA" xsd:string +relationship: RO:0002176 UBERON:0003457 ! connects head bone +property_value: IAO:0000116 "we follow GO in dividing sutures into cranial and facial and making a grouping class, but this is not consistent with FMA" xsd:string [Term] id: UBERON:0009199 @@ -236249,9 +233082,9 @@ namespace: uberon def: "Any suture between facial bones." [GO:0097096] is_a: UBERON:0009198 ! craniofacial suture intersection_of: UBERON:0009198 ! craniofacial suture -intersection_of: connects UBERON:0003462 {minCardinality="2"} ! facial bone -relationship: connects UBERON:0003462 {notes="between two adjacent facial bones"} ! facial bone +intersection_of: RO:0002176 UBERON:0003462 {minCardinality="2"} ! connects facial bone relationship: part_of UBERON:0011156 ! facial skeleton +relationship: RO:0002176 UBERON:0003462 ! connects facial bone [Term] id: UBERON:0009200 @@ -236286,9 +233119,9 @@ namespace: uberon subset: human_reference_atlas xref: KUPO:0001002 is_a: UBERON:0000064 ! organ part +is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0004726 {source="KUPO"} ! vasa recta -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000012 "This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta parallel to the descending limb" xsd:string {external_ontology="CL"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0009204 @@ -236353,7 +233186,6 @@ relationship: has_part UBERON:0000925 ! endoderm relationship: overlaps UBERON:0004117 ! pharyngeal pouch relationship: overlaps UBERON:0005879 ! pharyngeal cleft relationship: part_of UBERON:0002539 {source="EMAPA"} ! pharyngeal arch -property_value: UBPROP:0000003 "In all vertebrates, the endodermal epithelium lining each pouch contacts the surface ectoderm of the clefts to form a series of bilayered branchial membranes, that break down in fish to form the gill openings.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001427", ontology="VHOG", source="ISBN:978-0124020603 Kaufman MH, Bard JBL, The anatomical basis of mouse development (1999) p.72", source="http://bgee.unil.ch/"} [Term] id: UBERON:0009213 @@ -236373,7 +233205,7 @@ is_a: UBERON:0009210 ! pharyngeal membrane relationship: overlaps UBERON:0005872 ! 1st arch pharyngeal cleft relationship: overlaps UBERON:0007122 ! pharyngeal pouch 1 relationship: part_of UBERON:0004362 {source="EMAPA"} ! pharyngeal arch 1 -property_value: editor_note "check EMAPA - 3 terms appear to match. We follow EMAPA in making each membrane part of the arch with the same number, though in fact it is between these arches" xsd:string +property_value: IAO:0000116 "check EMAPA - 3 terms appear to match. We follow EMAPA in making each membrane part of the arch with the same number, though in fact it is between these arches" xsd:string [Term] id: UBERON:0009291 @@ -236387,7 +233219,7 @@ xref: SCTID:317278007 is_a: UBERON:0007844 ! cartilage element is_a: UBERON:0016491 ! vertebral centrum element intersection_of: UBERON:0016491 ! vertebral centrum element -intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue +intersection_of: RO:0002473 UBERON:0002418 ! composed primarily of cartilage tissue relationship: part_of UBERON:0011094 ! vertebra cartilage element [Term] @@ -236398,10 +233230,8 @@ synonym: "nasal placode" RELATED [] xref: EHDAA2:0000581 xref: EHDAA:4776 xref: EMAPA:16680 -xref: FMA:293971 xref: SCTID:308881001 is_a: UBERON:0012314 ! embryonic facial prominence -property_value: UBPROP:0000012 "medial or lateral; in EHDAA2 also frontonasal or intermaxillary" xsd:string {external_ontology="EHDAA2"} [Term] id: UBERON:0009471 @@ -236446,8 +233276,7 @@ xref: UMLS:C0004454 {source="ncithesaurus:Axilla"} xref: Wikipedia:Axilla is_a: UBERON:0034929 ! external soft tissue zone relationship: part_of UBERON:0001421 {source="FMA"} ! pectoral girdle region -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/f2/Gray411.png" xsd:anyURI -property_value: UBPROP:0000007 "axillary" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f2/Gray411.png" xsd:anyURI [Term] id: UBERON:0009477 @@ -236460,8 +233289,8 @@ xref: EMAPA:16196 is_a: UBERON:0007213 ! mesenchyme derived from head neural crest intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0003069 ! otic placode -relationship: develops_from UBERON:0007213 ! mesenchyme derived from head neural crest relationship: part_of UBERON:0003069 ! otic placode +relationship: RO:0002202 UBERON:0007213 ! develops from mesenchyme derived from head neural crest [Term] id: UBERON:0009479 @@ -236516,7 +233345,6 @@ is_a: UBERON:0002095 ! mesentery intersection_of: UBERON:0002095 ! mesentery intersection_of: part_of UBERON:0006235 ! foregut-midgut junction relationship: part_of UBERON:0006235 ! foregut-midgut junction -property_value: UBPROP:0000003 "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000430", ontology="VHOG", source="ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11", source="http://bgee.unil.ch/"} [Term] id: UBERON:0009494 @@ -236532,10 +233360,10 @@ is_a: UBERON:0005253 ! head mesenchyme is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0002539 ! pharyngeal arch -relationship: has_developmental_contribution_from UBERON:0003099 {source="cjm"} ! cranial neural crest relationship: part_of UBERON:0002539 ! pharyngeal arch relationship: part_of UBERON:0010046 ! entire pharyngeal arch associated mesenchyme -property_value: editor_note "this represents a part of the entire arch mesenchyme (UBERON:0010046), and is therefore a superclass of the individual arch mesenchyme classes. Alternate definition: primordial embryonic connective tissue associated with the branchial arches, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to facial and cranial nerve-associated structures." xsd:string {source="MP:0011262"} +relationship: RO:0002254 UBERON:0003099 {source="cjm"} ! has developmental contribution from cranial neural crest +property_value: IAO:0000116 "this represents a part of the entire arch mesenchyme (UBERON:0010046), and is therefore a superclass of the individual arch mesenchyme classes. Alternate definition: primordial embryonic connective tissue associated with the branchial arches, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to facial and cranial nerve-associated structures." xsd:string {source="MP:0011262"} [Term] id: UBERON:0009497 @@ -236550,9 +233378,9 @@ is_a: UBERON:0003929 ! digestive tract epithelium is_a: UBERON:0005911 ! endo-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0006235 ! foregut-midgut junction -relationship: develops_from UBERON:0009550 {source="EHDAA2"} ! endoderm of foregut-midgut junction relationship: part_of UBERON:0003929 {source="EHDAA2"} ! digestive tract epithelium relationship: part_of UBERON:0006235 ! foregut-midgut junction +relationship: RO:0002202 UBERON:0009550 {source="EHDAA2"} ! develops from endoderm of foregut-midgut junction [Term] id: UBERON:0009500 @@ -236568,10 +233396,10 @@ xref: EMAPA:16670 xref: XAO:0004474 is_a: UBERON:0007213 ! mesenchyme derived from head neural crest intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: surrounds UBERON:0003051 ! ear vesicle -relationship: develops_from UBERON:0009477 {source="EHDAA2"} ! associated mesenchyme of otic placode +intersection_of: RO:0002221 UBERON:0003051 ! surrounds ear vesicle relationship: part_of UBERON:0001444 {source="XAO"} ! subdivision of head -relationship: surrounds UBERON:0003051 ! ear vesicle +relationship: RO:0002202 UBERON:0009477 {source="EHDAA2"} ! develops from associated mesenchyme of otic placode +relationship: RO:0002221 UBERON:0003051 ! surrounds ear vesicle [Term] id: UBERON:0009501 @@ -236588,8 +233416,8 @@ xref: FMA:295821 is_a: UBERON:0007213 ! mesenchyme derived from head neural crest intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0004066 ! frontonasal prominence -relationship: develops_from UBERON:0007213 ! mesenchyme derived from head neural crest relationship: part_of UBERON:0004066 ! frontonasal prominence +relationship: RO:0002202 UBERON:0007213 ! develops from mesenchyme derived from head neural crest [Term] id: UBERON:0009503 @@ -236614,11 +233442,12 @@ subset: emapa_ehdaa2 synonym: "trachea associated mesenchyme" EXACT [EHDAA2:0002067] xref: EHDAA2:0002067 xref: EMAPA:16854 +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0003126 ! trachea -relationship: develops_from UBERON:0002539 ! pharyngeal arch relationship: part_of UBERON:0003126 ! trachea +relationship: RO:0002202 UBERON:0002539 ! develops from pharyngeal arch [Term] id: UBERON:0009506 @@ -236634,10 +233463,9 @@ is_a: UBERON:0005253 ! head mesenchyme is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0001756 ! middle ear -relationship: has_developmental_contribution_from UBERON:0005689 {source="EHDAA2"} ! 2nd arch mesenchyme -relationship: has_developmental_contribution_from UBERON:0010045 {source="EHDAA2"} ! 1st arch maxillary mesenchyme relationship: part_of UBERON:0001756 ! middle ear -property_value: UBPROP:0000012 "Also 1st arch maxillary mesenchyme in EHDAA2" xsd:string {external_ontology="EHDAA2"} +relationship: RO:0002254 UBERON:0005689 {source="EHDAA2"} ! has developmental contribution from 2nd arch mesenchyme +relationship: RO:0002254 UBERON:0010045 {source="EHDAA2"} ! has developmental contribution from 1st arch maxillary mesenchyme [Term] id: UBERON:0009521 @@ -236650,8 +233478,8 @@ xref: EMAPA:17177 is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0005911 ! endo-epithelium intersection_of: UBERON:0000490 ! unilaminar epithelium -intersection_of: develops_from UBERON:0000925 ! endoderm intersection_of: part_of UBERON:0001353 ! anal region +intersection_of: RO:0002202 UBERON:0000925 ! develops from endoderm relationship: part_of UBERON:0001353 ! anal region [Term] @@ -236684,9 +233512,8 @@ xref: EMAPA:17457 is_a: UBERON:0010377 ! mesenchyme from somatopleure intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0006875 ! embryonic handplate -relationship: develops_from UBERON:0003413 {source="EHDAA2"} ! pectoral appendage bud mesenchyme relationship: part_of UBERON:0006875 ! embryonic handplate -property_value: UBPROP:0000012 "We group two EMAPA classes here but these may need to be separated" xsd:string {external_ontology="EMAPA"} +relationship: RO:0002202 UBERON:0003413 {source="EHDAA2"} ! develops from pectoral appendage bud mesenchyme [Term] id: UBERON:0009526 @@ -236746,8 +233573,8 @@ xref: VHOG:0000709 is_a: UBERON:0001281 ! hepatic sinusoid intersection_of: UBERON:0001281 ! hepatic sinusoid intersection_of: part_of UBERON:0001115 ! left lobe of liver -relationship: develops_in UBERON:0001115 ! left lobe of liver relationship: part_of UBERON:0001115 ! left lobe of liver +relationship: RO:0002226 UBERON:0001115 ! develops in left lobe of liver [Term] id: UBERON:0009549 @@ -236762,8 +233589,8 @@ xref: VHOG:0000710 is_a: UBERON:0001281 ! hepatic sinusoid intersection_of: UBERON:0001281 ! hepatic sinusoid intersection_of: part_of UBERON:0001114 ! right lobe of liver -relationship: develops_in UBERON:0001114 ! right lobe of liver relationship: part_of UBERON:0001114 ! right lobe of liver +relationship: RO:0002226 UBERON:0001114 ! develops in right lobe of liver [Term] id: UBERON:0009550 @@ -236794,7 +233621,6 @@ intersection_of: part_of UBERON:0002544 {source="cjm"} ! digit relationship: has_part UBERON:0004300 ! distal phalanx relationship: overlaps UBERON:0009768 ! distal interphalangeal joint relationship: part_of UBERON:0002544 ! digit -property_value: UBPROP:0000011 "Newborn and adult mice are able to regrow forelimb (finger) and hindlimb (toe) digit tips after their amputation through the distal interphalangeal joint. Regeneration of the digit tip involves the integrated regrowth of multiple tissues within 2-3 months, reaching an external morphology that is cosmetically and functionally similar to normal digits. Most importantly, regeneration of the mouse distal digit shares morphological similarities with clinical cases documenting regrowth of missing distal portions of fingers in both children and adults" xsd:string [Term] id: UBERON:0009552 @@ -236845,12 +233671,12 @@ synonym: "metapodium-phalanx joint" EXACT [https://orcid.org/0000-0002-6601-2165 is_a: UBERON:0003841 ! autopod joint is_a: UBERON:0011139 ! synovial limb joint intersection_of: UBERON:0000982 ! skeletal joint -intersection_of: connects UBERON:0003656 ! mesopodium bone -intersection_of: connects UBERON:0004302 ! proximal phalanx -relationship: connects UBERON:0003656 ! mesopodium bone -relationship: connects UBERON:0004302 ! proximal phalanx +intersection_of: RO:0002176 UBERON:0003656 ! connects mesopodium bone +intersection_of: RO:0002176 UBERON:0004302 ! connects proximal phalanx relationship: part_of UBERON:0002544 ! digit -property_value: editor_note "We include these joints as being part of the digits; this is consistent with the FMA, and makes classification easier. Note that digit and metapodial regions are part-disjoint" xsd:string +relationship: RO:0002176 UBERON:0003656 ! connects mesopodium bone +relationship: RO:0002176 UBERON:0004302 ! connects proximal phalanx +property_value: IAO:0000116 "We include these joints as being part of the digits; this is consistent with the FMA, and makes classification easier. Note that digit and metapodial regions are part-disjoint" xsd:string [Term] id: UBERON:0009564 @@ -236863,10 +233689,11 @@ synonym: "keratin plate" RELATED [] synonym: "keratin sheath" RELATED [] synonym: "unguis" RELATED [] xref: MESH:D006724 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0013703 ! integumentary projection -relationship: develops_from UBERON:0011272 {source="Wikipathways:WP2062"} ! embryonic skin basal layer relationship: part_of UBERON:0001003 ! skin epidermis relationship: part_of UBERON:0009551 {source="cjm"} ! distal segment of digit +relationship: RO:0002202 UBERON:0011272 {source="Wikipathways:WP2062"} ! develops from embryonic skin basal layer [Term] id: UBERON:0009565 @@ -236951,7 +233778,6 @@ synonym: "trunk skeleton" RELATED [] synonym: "trunk spine" RELATED [] synonym: "trunk vertebrae series" EXACT [] synonym: "trunk vertebral column" EXACT [] -xref: AAO:0000612 xref: FMA:72066 xref: NCIT:C92597 xref: SCTID:281699004 @@ -236961,7 +233787,6 @@ intersection_of: part_of UBERON:0002100 ! trunk intersection_of: subdivision_of UBERON:0002100 ! trunk relationship: part_of UBERON:0002100 ! trunk relationship: subdivision_of UBERON:0002100 ! trunk -property_value: UBPROP:0000001 "Region of the vertebral column between the atlas and the sacrum consisting of seven to 285 vertebrae.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000612", ontology="AAO", source="AAO:Duellman_and_Trueb_1994"} [Term] id: UBERON:0009569 @@ -237003,11 +233828,11 @@ xref: FMA:242845 xref: Wikipedia:Central_canal is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0002291 ! central canal of spinal cord -relationship: luminal_space_of UBERON:0002291 ! central canal of spinal cord +intersection_of: RO:0002572 UBERON:0002291 ! luminal space of central canal of spinal cord relationship: part_of UBERON:0002291 ! central canal of spinal cord -relationship: surrounds UBERON:0001359 ! cerebrospinal fluid -relationship: transformation_of UBERON:0003842 ! neural tube lumen +relationship: RO:0002221 UBERON:0001359 ! surrounds cerebrospinal fluid +relationship: RO:0002494 UBERON:0003842 ! transformation of neural tube lumen +relationship: RO:0002572 UBERON:0002291 ! luminal space of central canal of spinal cord [Term] id: UBERON:0009576 @@ -237019,8 +233844,8 @@ xref: EMAPA:17561 is_a: UBERON:0005478 ! sulcus limitans of neural tube intersection_of: UBERON:0005478 ! sulcus limitans of neural tube intersection_of: part_of UBERON:0001896 ! medulla oblongata -relationship: develops_from UBERON:0009578 {source="EHDAA2"} ! myelencephalon sulcus limitans relationship: part_of UBERON:0001896 ! medulla oblongata +relationship: RO:0002202 UBERON:0009578 {source="EHDAA2"} ! develops from myelencephalon sulcus limitans [Term] id: UBERON:0009577 @@ -237140,9 +233965,9 @@ xref: TAO:0007018 xref: ZFA:0007018 is_a: UBERON:0003075 ! neural plate intersection_of: UBERON:0003075 {source="ZFA"} ! neural plate -intersection_of: develops_from UBERON:0006240 {source="ZFA"} ! future forebrain -relationship: develops_from UBERON:0006240 ! future forebrain +intersection_of: RO:0002202 UBERON:0006240 {source="ZFA"} ! develops from future forebrain relationship: part_of UBERON:0003056 {source="ZFA"} ! pre-chordal neural plate +relationship: RO:0002202 UBERON:0006240 ! develops from future forebrain [Term] id: UBERON:0009611 @@ -237153,9 +233978,9 @@ xref: TAO:0007019 xref: ZFA:0007019 is_a: UBERON:0003075 ! neural plate intersection_of: UBERON:0003075 {source="ZFA"} ! neural plate -intersection_of: develops_from UBERON:0009616 {source="ZFA"} ! presumptive midbrain -relationship: develops_from UBERON:0009616 ! presumptive midbrain +intersection_of: RO:0002202 UBERON:0009616 {source="ZFA"} ! develops from presumptive midbrain relationship: part_of UBERON:0003056 {source="ZFA"} ! pre-chordal neural plate +relationship: RO:0002202 UBERON:0009616 ! develops from presumptive midbrain [Term] id: UBERON:0009614 @@ -237166,9 +233991,9 @@ xref: TAO:0007022 xref: ZFA:0007022 is_a: UBERON:0003075 ! neural plate intersection_of: UBERON:0003075 {source="ZFA"} ! neural plate -intersection_of: develops_from UBERON:0007277 {source="ZFA"} ! presumptive hindbrain -relationship: develops_from UBERON:0007277 ! presumptive hindbrain +intersection_of: RO:0002202 UBERON:0007277 {source="ZFA"} ! develops from presumptive hindbrain relationship: part_of UBERON:0003057 {source="ZFA"} ! chordal neural plate +relationship: RO:0002202 UBERON:0007277 ! develops from presumptive hindbrain [Term] id: UBERON:0009615 @@ -237179,9 +234004,9 @@ synonym: "midbrain-hindbrain boundary neural plate" EXACT [ZFA:0007044] xref: TAO:0007044 xref: ZFA:0007044 is_a: UBERON:0006598 ! presumptive structure -relationship: immediate_transformation_of UBERON:0007281 {notes="https://github.com/obophenotype/uberon/issues/438", source="Bgee:AN"} ! presumptive midbrain hindbrain boundary relationship: part_of UBERON:0003075 {source="ZFA"} ! neural plate -property_value: editor_note "TODO - developmental relationships for lines" xsd:string +relationship: RO:0002495 UBERON:0007281 ! immediate transformation of presumptive midbrain hindbrain boundary +property_value: IAO:0000116 "TODO - developmental relationships for lines" xsd:string [Term] id: UBERON:0009616 @@ -237202,12 +234027,12 @@ xref: Wikipedia:Mesencephalon xref: ZFA:0000148 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001891 ! midbrain -relationship: develops_from UBERON:0003080 ! anterior neural tube -relationship: develops_from UBERON:0010286 {source="ZFA"} ! midbrain neural tube -relationship: has_potential_to_develop_into UBERON:0001891 ! midbrain +intersection_of: RO:0002387 UBERON:0001891 ! has potential to develop into midbrain relationship: part_of UBERON:0006238 {source="ZFA"} ! future brain -property_value: editor_note "TODO - unify naming conventions" xsd:string +relationship: RO:0002202 UBERON:0003080 ! develops from anterior neural tube +relationship: RO:0002202 UBERON:0010286 {source="ZFA"} ! develops from midbrain neural tube +relationship: RO:0002387 UBERON:0001891 ! has potential to develop into midbrain +property_value: IAO:0000116 "TODO - unify naming conventions" xsd:string [Term] id: UBERON:0009617 @@ -237227,7 +234052,6 @@ xref: EMAPA:16171 is_a: UBERON:0005253 ! head mesenchyme relationship: part_of UBERON:0003077 ! paraxial mesoderm relationship: part_of UBERON:0005253 {source="EHDAA2"} ! head mesenchyme -property_value: UBPROP:0000011 "A major contributor to neurocranium [PMID:16313393]" xsd:string [Term] id: UBERON:0009618 @@ -237281,19 +234105,17 @@ xref: FMA:14060 xref: GAID:717 xref: MESH:D013126 xref: NCIT:C12791 -xref: SCTID:362436008 xref: UMLS:C0037940 {source="ncithesaurus:Spinal_Nerve_Root"} xref: ZFA:0005578 is_a: UBERON:0002211 {source="FMA"} ! nerve root intersection_of: UBERON:0002211 ! nerve root intersection_of: extends_fibers_into UBERON:0001780 ! spinal nerve intersection_of: extends_fibers_into UBERON:0002240 ! spinal cord -relationship: contributes_to_morphology_of UBERON:0001780 ! spinal nerve -relationship: contributes_to_morphology_of UBERON:0002240 ! spinal cord relationship: extends_fibers_into UBERON:0001780 ! spinal nerve relationship: extends_fibers_into UBERON:0002240 ! spinal cord +relationship: RO:0002433 UBERON:0001780 ! contributes to morphology of spinal nerve +relationship: RO:0002433 UBERON:0002240 ! contributes to morphology of spinal cord property_value: seeAlso "https://github.com/obophenotype/uberon/issues/2644" xsd:string -property_value: UBPROP:0000012 "ZFA has part_of to spinal cord but this causes spatial disjointness violations (CNS/PNS)" xsd:string {external_ontology="ZFA"} [Term] id: UBERON:0009630 @@ -237344,7 +234166,7 @@ subset: human_reference_atlas xref: EMAPA:35878 xref: MA:0001859 is_a: UBERON:0003571 {source="MA"} ! trachea connective tissue -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0009647 @@ -237376,6 +234198,7 @@ xref: MA:0001252 xref: NCIT:C49226 xref: UMLS:C1707991 {source="ncithesaurus:Eyelid_Subcutaneous_Connective_Tissue"} is_a: UBERON:0003581 ! eyelid connective tissue +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0003581 ! eyelid connective tissue intersection_of: part_of UBERON:0002072 ! hypodermis relationship: adjacent_to UBERON:0001457 ! skin of eyelid @@ -237409,11 +234232,11 @@ xref: EMAPA:37809 {source="MA:th"} xref: MA:0001832 xref: NCIT:C49208 xref: UMLS:C1707051 {source="ncithesaurus:Bronchus_Basement_Membrane"} +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0015329 ! respiratory system basement membrane intersection_of: UBERON:0005769 ! basement membrane of epithelium intersection_of: part_of UBERON:0002185 ! bronchus relationship: part_of UBERON:0002031 {is_inferred="true", source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! epithelium of bronchus -property_value: UBPROP:0000012 "MA classifies as type of connective tissue: https://github.com/obophenotype/mouse-anatomy-ontology/issues/108" xsd:string {external_ontology="MA"} [Term] id: UBERON:0009653 @@ -237424,6 +234247,7 @@ xref: EMAPA:37552 {source="MA:th"} xref: MA:0001854 xref: NCIT:C49302 xref: UMLS:C1710455 {source="ncithesaurus:Trachea_Basement_Membrane"} +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0015329 ! respiratory system basement membrane intersection_of: UBERON:0005769 ! basement membrane of epithelium intersection_of: part_of UBERON:0003126 ! trachea @@ -237441,9 +234265,9 @@ xref: NCIT:C52849 xref: UMLS:C1706858 {source="ncithesaurus:Auricular_Artery"} is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0001691 ! external ear -relationship: supplies UBERON:0001691 ! external ear -property_value: editor_note "add child terms" xsd:string +intersection_of: RO:0002178 UBERON:0001691 ! supplies external ear +relationship: RO:0002178 UBERON:0001691 ! supplies external ear +property_value: IAO:0000116 "add child terms" xsd:string [Term] id: UBERON:0009657 @@ -237456,8 +234280,8 @@ xref: NCIT:C52947 xref: UMLS:C1708633 {source="ncithesaurus:Labial_Artery"} is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0001833 ! lip -relationship: supplies UBERON:0001833 ! lip +intersection_of: RO:0002178 UBERON:0001833 ! supplies lip +relationship: RO:0002178 UBERON:0001833 ! supplies lip [Term] id: UBERON:0009661 @@ -237506,7 +234330,7 @@ xref: EHDAA2:0004566 xref: EMAPA:32911 xref: MA:0003203 is_a: UBERON:0002095 ! mesentery -relationship: located_in UBERON:0001179 {source="EHDAA2"} ! peritoneal cavity +relationship: RO:0001025 UBERON:0001179 {source="EHDAA2"} ! located in peritoneal cavity property_value: seeAlso "https://github.com/obophenotype/uberon/issues/509" xsd:anyURI [Term] @@ -237519,7 +234343,6 @@ xref: SCTID:361430000 xref: Wikipedia:Ventral_mesentery is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0009664 {source="EHDAA2"} ! gut mesentery -property_value: UBPROP:0000011 "degenerates during development except foregut portion" xsd:string [Term] id: UBERON:0009669 @@ -237529,10 +234352,10 @@ def: "An anatomical space that surrounded_by a embryonic cloaca." [OBOL:automati xref: EHDAA2:0004586 is_a: UBERON:0012463 ! cloacal lumen intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0000163 ! embryonic cloaca -relationship: luminal_space_of UBERON:0000163 ! embryonic cloaca +intersection_of: RO:0002572 UBERON:0000163 ! luminal space of embryonic cloaca relationship: part_of UBERON:0000163 ! embryonic cloaca -relationship: surrounded_by UBERON:0009846 ! embryonic cloacal epithelium +relationship: RO:0002219 UBERON:0009846 ! surrounded by embryonic cloacal epithelium +relationship: RO:0002572 UBERON:0000163 ! luminal space of embryonic cloaca [Term] id: UBERON:0009670 @@ -237546,11 +234369,11 @@ xref: FMA:14598 xref: SCTID:259740004 is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0001052 ! rectum -relationship: develops_from UBERON:0009669 {source="EHDAA2"} ! embryonic cloacal lumen -relationship: luminal_space_of UBERON:0001052 ! rectum +intersection_of: RO:0002572 UBERON:0001052 ! luminal space of rectum relationship: part_of UBERON:0001052 ! rectum relationship: part_of UBERON:0012465 {source="cjm"} ! lumen of terminal part of digestive tract +relationship: RO:0002202 UBERON:0009669 {source="EHDAA2"} ! develops from embryonic cloacal lumen +relationship: RO:0002572 UBERON:0001052 ! luminal space of rectum [Term] id: UBERON:0009676 @@ -237565,8 +234388,8 @@ xref: EHDAA:1993 xref: EHDAA:2671 xref: EMAPA:16914 is_a: UBERON:0013150 ! future brain vesicle -relationship: develops_from UBERON:0006284 {source="EHDAA2"} ! early prosencephalic vesicle relationship: part_of UBERON:0001893 {source="EHDAA2"} ! telencephalon +relationship: RO:0002202 UBERON:0006284 {source="EHDAA2"} ! develops from early prosencephalic vesicle [Term] id: UBERON:0009678 @@ -237582,7 +234405,7 @@ xref: ZFA:0001642 is_a: UBERON:0003672 ! dentition is_a: UBERON:0034926 ! anatomical row intersection_of: UBERON:0034926 ! anatomical row -intersection_of: has_member UBERON:0001091 ! calcareous tooth +intersection_of: RO:0002351 UBERON:0001091 ! has member calcareous tooth [Term] id: UBERON:0009679 @@ -237633,9 +234456,9 @@ xref: FMA:63581 is_a: UBERON:0001278 ! epithelium of large intestine intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001154 ! vermiform appendix -relationship: develops_from UBERON:0005636 {source="EHDAA2"} ! caecum epithelium relationship: part_of UBERON:0003929 {source="EHDAA2"} ! digestive tract epithelium relationship: part_of UBERON:0004989 ! mucosa of appendix +relationship: RO:0002202 UBERON:0005636 {source="EHDAA2"} ! develops from caecum epithelium [Term] id: UBERON:0009708 @@ -237646,11 +234469,12 @@ subset: organ_slim synonym: "pancreatis dorsalis" RELATED [] xref: EHDAA2:0001371 is_a: UBERON:0002365 {source="EHDAA2"} ! exocrine gland +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0005177 ! trunk region element -relationship: develops_from UBERON:0010375 {source="EHDAA2"} ! pancreas dorsal primordium -relationship: has_developmental_contribution_from UBERON:0003923 {source="cjm"} ! dorsal pancreatic bud relationship: part_of UBERON:0001264 {source="EHDAA2"} ! pancreas -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 UBERON:0010375 {source="EHDAA2"} ! develops from pancreas dorsal primordium +relationship: RO:0002254 UBERON:0003923 {source="cjm"} ! has developmental contribution from dorsal pancreatic bud +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0009709 @@ -237661,11 +234485,12 @@ subset: organ_slim synonym: "pancreatis ventralis" RELATED [] xref: EHDAA2:0001393 is_a: UBERON:0002365 {source="EHDAA2"} ! exocrine gland +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0005177 ! trunk region element -relationship: develops_from UBERON:0010376 {source="EHDAA2"} ! pancreas ventral primordium -relationship: has_developmental_contribution_from UBERON:0003924 {source="cjm"} ! ventral pancreatic bud relationship: part_of UBERON:0001264 {source="EHDAA2"} ! pancreas -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 UBERON:0010376 {source="EHDAA2"} ! develops from pancreas ventral primordium +relationship: RO:0002254 UBERON:0003924 {source="cjm"} ! has developmental contribution from ventral pancreatic bud +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0009712 @@ -237685,10 +234510,9 @@ xref: VHOG:0001235 is_a: UBERON:0001081 ! endocardium of ventricle intersection_of: UBERON:0001081 ! endocardium of ventricle intersection_of: part_of UBERON:0002080 ! heart right ventricle -relationship: attaches_to UBERON:0006567 {source="FMA"} ! right ventricle myocardium -relationship: develops_from UBERON:0004706 {source="EHDAA2"} ! bulbus cordis relationship: part_of UBERON:0002080 ! heart right ventricle -property_value: UBPROP:0000001 "Endocardium of ventricle which is continuous tricuspid valve, pulmonary valve and with the tunica intima of the pulmonary trunk." xsd:string {source="FMA:9536"} +relationship: RO:0002202 UBERON:0004706 {source="EHDAA2"} ! develops from bulbus cordis +relationship: RO:0002371 UBERON:0006567 {source="FMA"} ! attached to right ventricle myocardium [Term] id: UBERON:0009713 @@ -237707,9 +234531,8 @@ xref: VHOG:0001233 is_a: UBERON:0001081 ! endocardium of ventricle intersection_of: UBERON:0001081 ! endocardium of ventricle intersection_of: part_of UBERON:0002084 ! heart left ventricle -relationship: attaches_to UBERON:0006566 {source="FMA"} ! left ventricle myocardium relationship: part_of UBERON:0002084 ! heart left ventricle -property_value: UBPROP:0000001 "Endocardium of ventricle which is continuous with mitral valve, aortic valve, atrioventricular septum and the tunica intima of the aorta." xsd:string {source="FMA:9559"} +relationship: RO:0002371 UBERON:0006566 {source="FMA"} ! attached to left ventricle myocardium [Term] id: UBERON:0009714 @@ -237724,9 +234547,9 @@ xref: EHDAA:7856 xref: FMA:295872 xref: Wikipedia:Intermaxillary_segment is_a: UBERON:0009292 {source="EHDAA2-modified"} ! embryonic nasal process -relationship: develops_from UBERON:0004067 {notes="inconsistent", source="EHDAA2"} ! lateral nasal prominence -relationship: develops_from UBERON:0004068 {source="EHDAA2"} ! medial nasal prominence -property_value: editor_note "requires verification. Note EHDAA2 has this as coming from both lateral and medial prominences. See also: median cleft lip" xsd:string +relationship: RO:0002202 UBERON:0004067 ! develops from lateral nasal prominence +relationship: RO:0002202 UBERON:0004068 {source="EHDAA2"} ! develops from medial nasal prominence +property_value: IAO:0000116 "requires verification. Note EHDAA2 has this as coming from both lateral and medial prominences. See also: median cleft lip" xsd:string [Term] id: UBERON:0009715 @@ -237738,8 +234561,8 @@ synonym: "lumen of stomodeum" EXACT [] synonym: "stomatodeal cavity" EXACT [] is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0000930 ! stomodeum -relationship: luminal_space_of UBERON:0000930 ! stomodeum +intersection_of: RO:0002572 UBERON:0000930 ! luminal space of stomodeum +relationship: RO:0002572 UBERON:0000930 ! luminal space of stomodeum [Term] id: UBERON:0009722 @@ -237865,6 +234688,7 @@ id: UBERON:0009740 name: border between sublaminar layers namespace: uberon def: "A region of the retina corresponding to a portion of two adjacent substratum layers." [https://orcid.org/0000-0002-6601-2165] +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0022303 ! nervous system cell part layer relationship: overlaps UBERON:0008921 ! substratum of layer of retina relationship: part_of UBERON:0000966 ! retina @@ -237884,7 +234708,7 @@ xref: FMA:312359 is_a: UBERON:0004111 ! anatomical conduit relationship: channel_for UBERON:0002391 ! lymph relationship: part_of UBERON:0002007 ! medulla of lymph node -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0009745 @@ -237898,7 +234722,7 @@ xref: EMAPA:37897 {source="MA:th"} is_a: UBERON:0000064 ! organ part relationship: adjacent_to UBERON:0009744 ! lymph node medullary sinus relationship: part_of UBERON:0002007 ! medulla of lymph node -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0009749 @@ -237912,7 +234736,6 @@ is_a: UBERON:0003104 ! mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0002101 ! limb relationship: part_of UBERON:0002101 ! limb -property_value: UBPROP:0000012 "EMAPA mapping from TH" xsd:string {external_ontology="EMAPA"} [Term] id: UBERON:0009751 @@ -237924,10 +234747,11 @@ synonym: "heart mesenchyme" EXACT [EMAPA:36438] xref: EHDAA2:0004162 xref: EMAPA:36438 is_a: UBERON:0003104 ! mesenchyme +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0000948 ! heart relationship: part_of UBERON:0000948 ! heart -property_value: editor_note "decide whether to merge with cardiac mesoderm. In EHDAA2 this lasts CS12->unbounded, includes mesenchyme of individual components as parts" xsd:string +property_value: IAO:0000116 "decide whether to merge with cardiac mesoderm. In EHDAA2 this lasts CS12->unbounded, includes mesenchyme of individual components as parts" xsd:string [Term] id: UBERON:0009752 @@ -237943,7 +234767,7 @@ is_a: UBERON:0003104 ! mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0001264 ! pancreas relationship: part_of UBERON:0001264 ! pancreas -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0009753 @@ -237956,6 +234780,8 @@ xref: FMA:69086 xref: MA:0001887 xref: SCTID:68594002 is_a: UBERON:0000064 ! organ part +is_a: UBERON:0004120 ! mesoderm-derived structure +is_a: UBERON:0010313 ! neural crest-derived structure relationship: part_of UBERON:0001235 {source="MA"} ! adrenal cortex [Term] @@ -237981,9 +234807,9 @@ xref: FMA:65022 xref: NCIT:C101528 is_a: UBERON:0006658 ! interphalangeal joint intersection_of: UBERON:0006658 ! interphalangeal joint -intersection_of: connects UBERON:0004302 ! proximal phalanx -relationship: connects UBERON:0004301 ! middle phalanx -relationship: connects UBERON:0004302 ! proximal phalanx +intersection_of: RO:0002176 UBERON:0004302 ! connects proximal phalanx +relationship: RO:0002176 UBERON:0004301 ! connects middle phalanx +relationship: RO:0002176 UBERON:0004302 ! connects proximal phalanx [Term] id: UBERON:0009768 @@ -237997,8 +234823,8 @@ xref: FMA:65024 xref: NCIT:C101529 is_a: UBERON:0006658 ! interphalangeal joint intersection_of: UBERON:0006658 ! interphalangeal joint -intersection_of: connects UBERON:0004300 ! distal phalanx -relationship: connects UBERON:0004300 ! distal phalanx +intersection_of: RO:0002176 UBERON:0004300 ! connects distal phalanx +relationship: RO:0002176 UBERON:0004300 ! connects distal phalanx [Term] id: UBERON:0009773 @@ -238011,8 +234837,7 @@ synonym: "renal tubule (generic)" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "tubule of excretory system" EXACT [https://orcid.org/0000-0002-6601-2165, OBOL:automatic] is_a: UBERON:0003914 ! epithelial tube is_a: UBERON:0006555 ! excretory tube -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -property_value: IAO:0000232 "this class groups vertebrate nephron tubules with analagous structures such as insect Malpighian tubules" xsd:string +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria [Term] id: UBERON:0009778 @@ -238023,16 +234848,16 @@ subset: non_informative xref: EHDAA2:0004737 xref: FMA:9690 xref: SCTID:361996004 +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0005906 ! serous sac is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0005906 ! serous sac intersection_of: has_part UBERON:0000977 ! pleura intersection_of: has_part UBERON:0002402 ! pleural cavity +relationship: BSPO:0000126 UBERON:0001004 {source="FMA-abduced-lr"} ! respiratory system relationship: has_part UBERON:0000977 ! pleura relationship: has_part UBERON:0002402 ! pleural cavity -relationship: in_lateral_side_of UBERON:0001004 {source="FMA-abduced-lr"} ! respiratory system relationship: part_of UBERON:0001558 {source="FMA"} ! lower respiratory tract -property_value: UBPROP:0000012 "despite its name the class EHDAA2:0004737 is not a true cavity, it corresponds to what we call the sac" xsd:string {external_ontology="EHDAA2"} [Term] id: UBERON:0009841 @@ -238066,13 +234891,12 @@ xref: Wikipedia:Acinus is_a: UBERON:0034922 ! cell cluster intersection_of: UBERON:0034922 ! cell cluster intersection_of: has_part CL:0000151 ! secretory cell -intersection_of: has_quality PATO:0002422 ! acinar intersection_of: part_of UBERON:0002530 ! gland +intersection_of: RO:0000086 PATO:0002422 ! has quality acinar relationship: has_part CL:0000151 ! secretory cell -relationship: has_quality PATO:0002422 ! acinar relationship: part_of UBERON:0002530 ! gland -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/99/Gray1105.png" xsd:anyURI -property_value: UBPROP:0000007 "acinar" xsd:string +relationship: RO:0000086 PATO:0002422 ! has quality acinar +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/99/Gray1105.png" xsd:anyURI [Term] id: UBERON:0009843 @@ -238084,8 +234908,8 @@ synonym: "cord of prostate epithelium" EXACT [PMID:18977204] synonym: "epithelial cord of prostate" EXACT [] is_a: UBERON:0005154 ! epithelial cord intersection_of: UBERON:0005154 ! epithelial cord -intersection_of: has_potential_to_develop_into UBERON:0002367 ! prostate gland -relationship: has_potential_to_develop_into UBERON:0002367 ! prostate gland +intersection_of: RO:0002387 UBERON:0002367 ! has potential to develop into prostate gland +relationship: RO:0002387 UBERON:0002367 ! has potential to develop into prostate gland [Term] id: UBERON:0009844 @@ -238095,11 +234919,11 @@ def: "An anatomical space that surrounded_by a primitive urogenital sinus." [OBO xref: EHDAA2:0002142 is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0000164 ! primitive urogenital sinus -relationship: develops_from UBERON:0009669 {source="EHDAA2"} ! embryonic cloacal lumen -relationship: luminal_space_of UBERON:0000164 ! primitive urogenital sinus +intersection_of: RO:0002572 UBERON:0000164 ! luminal space of primitive urogenital sinus relationship: part_of UBERON:0000164 ! primitive urogenital sinus -relationship: surrounded_by UBERON:0004902 ! urogenital sinus epithelium +relationship: RO:0002202 UBERON:0009669 {source="EHDAA2"} ! develops from embryonic cloacal lumen +relationship: RO:0002219 UBERON:0004902 ! surrounded by urogenital sinus epithelium +relationship: RO:0002572 UBERON:0000164 ! luminal space of primitive urogenital sinus [Term] id: UBERON:0009845 @@ -238110,9 +234934,8 @@ synonym: "UGM" EXACT OMO:0003000 [PMID:18977204] xref: EMAPA:31500 is_a: UBERON:0003104 ! mesenchyme intersection_of: UBERON:0003104 {source="PMID:18977204"} ! mesenchyme -intersection_of: surrounds UBERON:0000164 {source="PMID:18977204"} ! primitive urogenital sinus -relationship: surrounds UBERON:0000164 ! primitive urogenital sinus -property_value: UBPROP:0000011 "Androgen receptor (AR) activation releases instructive signals from UGM that acts on UGS epithelium (UGE) to stimulate cell proliferation, form prostate ductal progenitors (prostatic buds), and regulate cell adhesion dynamics to permit prostatic bud outgrowth" xsd:string +intersection_of: RO:0002221 UBERON:0000164 {source="PMID:18977204"} ! surrounds primitive urogenital sinus +relationship: RO:0002221 UBERON:0000164 ! surrounds primitive urogenital sinus [Term] id: UBERON:0009846 @@ -238126,9 +234949,9 @@ is_a: UBERON:0009521 ! anal membrane endodermal component is_a: UBERON:0012481 ! cloacal epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000163 ! embryonic cloaca -relationship: develops_from UBERON:0003353 {source="EHDAA2"} ! epithelium of hindgut relationship: part_of UBERON:0000163 ! embryonic cloaca relationship: part_of UBERON:0003929 {source="EHDAA2"} ! digestive tract epithelium +relationship: RO:0002202 UBERON:0003353 {source="EHDAA2"} ! develops from epithelium of hindgut [Term] id: UBERON:0009847 @@ -238136,14 +234959,15 @@ name: prostate field namespace: uberon def: "A specific region of the urogenital sinus epithelium into the area in which the prostate gland will develop." [GO:0060515, GOC:dph, PMID:18977204] synonym: "prostate primordium" RELATED [] +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0006598 ! presumptive structure is_a: UBERON:0007688 ! anlage intersection_of: UBERON:0007688 ! anlage -intersection_of: has_potential_to_develop_into UBERON:0002367 ! prostate gland -relationship: developmentally_induced_by UBERON:0009845 {source="PMID:18977204"} ! urogenital sinus mesenchyme -relationship: has_potential_to_develop_into UBERON:0002367 ! prostate gland +intersection_of: RO:0002387 UBERON:0002367 ! has potential to develop into prostate gland relationship: part_of UBERON:0004902 {source="PMID:18977204"} ! urogenital sinus epithelium +relationship: RO:0002256 UBERON:0009845 {source="PMID:18977204"} ! developmentally induced by urogenital sinus mesenchyme +relationship: RO:0002387 UBERON:0002367 ! has potential to develop into prostate gland [Term] id: UBERON:0009851 @@ -238178,7 +235002,6 @@ namespace: uberon def: "Branch or outpocketing of the digestive tract." [https://orcid.org/0000-0002-6601-2165] synonym: "diverticulum of gut" RELATED [FBbt:00100316] synonym: "intestinal pouch" RELATED [] -xref: FBbt:00100316 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0004921 ! subdivision of digestive tract is_a: UBERON:0009856 ! sac intersection_of: UBERON:0009856 ! sac @@ -238193,8 +235016,8 @@ synonym: "pouch" EXACT [] xref: galen:Diverticulum is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: has_quality PATO:0001987 ! saccular -relationship: has_quality PATO:0001987 ! saccular +intersection_of: RO:0000086 PATO:0001987 ! has quality saccular +relationship: RO:0000086 PATO:0001987 ! has quality saccular [Term] id: UBERON:0009859 @@ -238209,10 +235032,9 @@ xref: UMLS:C0222658 {source="ncithesaurus:Endosteum"} xref: Wikipedia:Endosteum is_a: UBERON:0000158 ! membranous layer relationship: adjacent_to UBERON:0002484 ! bone marrow cavity -relationship: composed_primarily_of UBERON:0011825 ! loose connective tissue relationship: part_of UBERON:0002495 ! long bone -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/94/Illu_long_bone.jpg" xsd:anyURI -property_value: UBPROP:0000007 "endosteal" xsd:string +relationship: RO:0002473 UBERON:0011825 ! composed primarily of loose connective tissue +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/94/Illu_long_bone.jpg" xsd:anyURI [Term] id: UBERON:0009870 @@ -238233,8 +235055,8 @@ is_a: UBERON:0034944 ! zone of organ intersection_of: UBERON:0034944 ! zone of organ intersection_of: part_of UBERON:0000945 ! stomach relationship: part_of UBERON:0000945 ! stomach -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Regions_of_stomach.svg" xsd:anyURI -property_value: editor_note "We follow Kardong in defining stomach regions by gland, but we also include 'body of stomach'. In future we may want to have different partitions of the stomach" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Regions_of_stomach.svg" xsd:anyURI +property_value: IAO:0000116 "We follow Kardong in defining stomach regions by gland, but we also include 'body of stomach'. In future we may want to have different partitions of the stomach" xsd:string [Term] id: UBERON:0009871 @@ -238250,7 +235072,6 @@ xref: http://www.gudmap.org/Images/Organ_Summaries/Metanephros/NZ.png xref: MA:0002996 is_a: UBERON:0005423 ! developing anatomical structure relationship: part_of UBERON:0001225 ! cortex of kidney -property_value: UBPROP:0000008 "see http://www.ncbi.nlm.nih.gov/pubmed/12761251 for description of nephrogenic zone in dogfish." xsd:string [Term] id: UBERON:0009877 @@ -238267,12 +235088,11 @@ synonym: "metapodium" RELATED [] xref: SCTID:370640001 is_a: UBERON:0002529 ! limb segment intersection_of: UBERON:0002529 ! limb segment -intersection_of: has_skeleton UBERON:0010546 ! metapodial skeleton -relationship: has_skeleton UBERON:0010546 ! metapodial skeleton +intersection_of: RO:0002551 UBERON:0010546 ! has skeleton metapodial skeleton relationship: part_of UBERON:0012140 {source="PHENOSCAPE:ni"} ! digitopodium region relationship: proximally_connected_to UBERON:0006716 ! mesopodium region -property_value: editor_note "considering adding 'acropodial region'" xsd:string -property_value: UBPROP:0000013 "Naming conventions for pod terms under discussion within phenoscape group" xsd:string +relationship: RO:0002551 UBERON:0010546 ! has skeleton metapodial skeleton +property_value: IAO:0000116 "considering adding 'acropodial region'" xsd:string [Term] id: UBERON:0009878 @@ -238287,16 +235107,15 @@ synonym: "mesopodium" RELATED [VSAO:0005022, VSAO:NI] synonym: "mesopodium skeleton" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "skeletal parts of mesopodium" EXACT [https://orcid.org/0000-0002-6601-2165] xref: VSAO:0005022 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010712 ! limb skeleton subdivision intersection_of: UBERON:0010912 ! subdivision of skeleton -intersection_of: skeleton_of UBERON:0006716 ! mesopodium region +intersection_of: RO:0002576 UBERON:0006716 ! skeleton of mesopodium region relationship: distally_connected_to UBERON:0010546 ! metapodial skeleton relationship: part_of UBERON:0006716 ! mesopodium region relationship: part_of UBERON:0006717 ! autopodial skeleton relationship: proximally_connected_to UBERON:0011584 ! zeugopodial skeleton -relationship: skeleton_of UBERON:0006716 ! mesopodium region -property_value: UBPROP:0000001 "Limb skeleton subdivision consisting of endochondral bones increasing the freedom of movement of the autopodia, and located between zeugopodia and autopodia.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0005022", ontology="VSAO", source="VSAO:NI"} -property_value: UBPROP:0000002 "relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: distally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0005022", ontology="VSAO"} +relationship: RO:0002576 UBERON:0006716 ! skeleton of mesopodium region [Term] id: UBERON:0009879 @@ -238328,16 +235147,12 @@ xref: Wikipedia:Tarsus_(skeleton) xref: XAO:0003211 is_a: UBERON:0009878 ! mesopodial skeleton intersection_of: UBERON:0010912 ! subdivision of skeleton -intersection_of: skeleton_of UBERON:0004454 ! tarsal region +intersection_of: RO:0002576 UBERON:0004454 ! skeleton of tarsal region relationship: distally_connected_to UBERON:0010545 ! metatarsus skeleton relationship: part_of UBERON:0001445 ! skeleton of pes relationship: part_of UBERON:0004454 ! tarsal region relationship: proximally_connected_to UBERON:0010720 ! hindlimb zeugopod skeleton -relationship: skeleton_of UBERON:0004454 ! tarsal region -property_value: UBPROP:0000001 "Segment of the leg corresponding to the tarsus. It consists of several elements that articulate with the tibia and fibula at one end and the metatarsals at the other end.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000220", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000003 "The three main outgroup taxa of tetrapods, panderichthyids, osteolepiforms, and rhizodontids, have endoskeletal elements corresponding to the stylo- and zeugopodial elements in a tetrapod limb. In addition, there are elements that share the position and possibly the developmental derivation of the ulnare and the intermedium. From these observations, most authors have concluded that the stylo- and zeugopodial elements as well as the proximal mesopodial elements have counterparts in the fins of tetrapod ancestors, but there are no indications of wrist or ankle joints.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001160", ontology="VHOG", source="DOI:10.1002/jez.1100 Wagner GP, Chiu C, The tetrapod limb: A hypothesis on its origin. J Exp Zool (Mol Dev Evol) (2001)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "Not always associated with digits, in sarcopterygians the ulnare is present without true digits being formed, though their homologous radial elements are present" xsd:string {source="PHENOSCAPE:ad"} -property_value: UBPROP:0000012 "we assume MA:tarsus belongs here, as there is a distinct class MA:ankle, with the tarsal bone being part of the former. XAO:tarsus is part of the hindlimb skeleton. FMA set-of class lacks definition but we assume this to be equivalent." xsd:string {external_ontology="MA"} +relationship: RO:0002576 UBERON:0004454 ! skeleton of tarsal region [Term] id: UBERON:0009880 @@ -238365,18 +235180,13 @@ xref: Wikipedia:Carpus xref: XAO:0003207 is_a: UBERON:0009878 ! mesopodial skeleton intersection_of: UBERON:0010912 ! subdivision of skeleton -intersection_of: skeleton_of UBERON:0004452 ! carpal region +intersection_of: RO:0002576 UBERON:0004452 ! skeleton of carpal region relationship: distally_connected_to UBERON:0010544 ! metacarpus skeleton relationship: part_of UBERON:0001442 ! skeleton of manus relationship: part_of UBERON:0004452 ! carpal region relationship: proximally_connected_to UBERON:0010703 ! forelimb zeugopod skeleton -relationship: skeleton_of UBERON:0004452 ! carpal region -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/58/Carpus.svg" xsd:anyURI -property_value: UBPROP:0000001 "Segment of the forearm corresponding to the carpus. It consists of several elements that articulate with the radius and ulna at one end and the metacarpals at the other end.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000201", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000003 "The three main outgroup taxa of tetrapods, panderichthyids, osteolepiforms, and rhizodontids, have endoskeletal elements corresponding to the stylo- and zeugopodial elements in a tetrapod limb. In addition, there are elements that share the position and possibly the developmental derivation of the ulnare and the intermedium. From these observations, most authors have concluded that the stylo- and zeugopodial elements as well as the proximal mesopodial elements have counterparts in the fins of tetrapod ancestors, but there are no indications of wrist or ankle joints.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001161", ontology="VHOG", source="DOI:10.1002/jez.1100 Wagner GP, Chiu C, The tetrapod limb: A hypothesis on its origin. J Exp Zool (Mol Dev Evol) (2001)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "Not always associated with digits, in sarcopterygians the ulnare is present without true digits being formed, though their homologous radial elements are present[PHENOSCAPE:ad]." xsd:string {source="Wikipedia:Carpus#Evolutionary_variations"} -property_value: UBPROP:0000008 "The structure of the carpus varies widely between different groups of tetrapods, even among those that retain the full set of five digits. In primitive fossil amphibians, such as Eryops, the carpus consists of three rows of bones; a proximal row of three carpals, a second row of four bones, and a distal row of five bones. The proximal carpals are referred to as the radiale, intermediale, and ulnare, after their proximal articulations, and are homologous with the scaphoid, lunate, and triquetal bones respectively. The remaining bones are simply numbered, as the first to fourth centralia (singular: centrale), and the first to fifth distal carpals. Primitively, each of the distal bones appears to have articulated with a single metacarpal. However, the vast majority of later vertebrates, including modern amphibians, have undergone varying degrees of loss and fusion of these primitive bones, resulting in a smaller number of carpals. Almost all mammals and reptiles, for example, have lost the fifth distal carpal, and have only a single centrale - and even this is missing in humans. The pisiform bone is somewhat unusual, in that it first appears in primitive reptiles, and is never found in amphibians. Because many tetrapods have less than five digits on the forelimb, even greater degrees of fusion are common, and a huge array of different possible combinations are found. The wing of a modern bird, for example, has only two remaining carpals; the radiale (the scaphoid of mammals) and a bone formed from the fusion of four of the distal carpals. In some macropods, the scaphoid and lunar bones are fused into the scaphollunar bone" xsd:string -property_value: UBPROP:0000012 "we assume MA:carpus belongs here, as there is a distinct class MA:wrist, with the carpal bone being part of the former. XAO:carpus is part of the forelimb skeleton. FMA set-of class lacks definition but we assume this to be equivalent." xsd:string {external_ontology="MA"} +relationship: RO:0002576 UBERON:0004452 ! skeleton of carpal region +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/58/Carpus.svg" xsd:anyURI [Term] id: UBERON:0009881 @@ -238387,6 +235197,7 @@ synonym: "ALPM" EXACT [ZFA:0005041] xref: EFO:0003704 xref: TAO:0005041 xref: ZFA:0005041 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue relationship: part_of UBERON:0003081 {source="ZFA"} ! lateral plate mesoderm @@ -238402,10 +235213,11 @@ xref: NCIT:C32067 xref: SCTID:245444007 xref: UMLS:C0227428 {source="ncithesaurus:Anal_Column"} xref: Wikipedia:Anal_columns +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0034944 ! zone of organ -relationship: has_quality PATO:0001910 ! folded relationship: part_of UBERON:0000159 ! anal canal -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/0/01/Gray1078.png" xsd:anyURI +relationship: RO:0000086 PATO:0001910 ! has quality folded +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/0/01/Gray1078.png" xsd:anyURI [Term] id: UBERON:0009883 @@ -238422,12 +235234,10 @@ xref: EMAPA:37906 {source="MA:th"} xref: FMA:74299 xref: Wikipedia:Bone_marrow_of_ovaryry_ray_(anatomy) is_a: UBERON:0000064 {source="FMA"} ! organ part -relationship: contributes_to_morphology_of UBERON:0001225 ! cortex of kidney relationship: overlaps UBERON:0001231 ! nephron tubule relationship: part_of UBERON:0001225 {source="MP"} ! cortex of kidney -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000012 "FMA says parenchyma, MP says cortex" xsd:string {external_ontology="FMA"} -property_value: UBPROP:0000013 "Their name is potentially misleading -- the 'medullary' refers to their destination, not their location. They are located only in the renal cortex, and not in the renal medulla" xsd:string +relationship: RO:0002433 UBERON:0001225 ! contributes to morphology of cortex of kidney +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0009885 @@ -238449,11 +235259,10 @@ xref: SCTID:62802007 xref: Wikipedia:Interlobar_arteries is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0009913 ! renal lobe -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: supplies UBERON:0009913 ! renal lobe -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI -property_value: UBPROP:0000012 "FMA only has the set term" xsd:string {external_ontology="FMA"} +intersection_of: RO:0002178 UBERON:0009913 ! supplies renal lobe +relationship: RO:0002178 UBERON:0009913 ! supplies renal lobe +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0009887 @@ -238470,12 +235279,11 @@ xref: FMA:71631 xref: Wikipedia:Interlobar_veins is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein -intersection_of: drains UBERON:0009913 ! renal lobe -relationship: connected_to UBERON:0001140 ! renal vein -relationship: drains UBERON:0009913 ! renal lobe -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI -property_value: UBPROP:0000012 "FMA only has the set term" xsd:string {external_ontology="FMA"} +intersection_of: RO:0002179 UBERON:0009913 ! drains renal lobe +relationship: RO:0002170 UBERON:0001140 ! connected to renal vein +relationship: RO:0002179 UBERON:0009913 ! drains renal lobe +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0009889 @@ -238488,15 +235296,13 @@ synonym: "second heart field" EXACT [XAO:0004186] synonym: "SHF" RELATED [XAO:0004186] xref: XAO:0004186 is_a: UBERON:0002050 ! embryonic structure +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007688 ! anlage -relationship: anterior_to UBERON:0004140 {source="PMID:17276708"} ! primary heart field -relationship: dorsal_to UBERON:0004140 {source="PMID:17276708"} ! primary heart field -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: BSPO:0000096 UBERON:0004140 {source="PMID:17276708"} ! primary heart field +relationship: BSPO:0000098 UBERON:0004140 {source="PMID:17276708"} ! primary heart field relationship: part_of UBERON:0003081 {source="GO:0003129"} ! lateral plate mesoderm -property_value: UBPROP:0000001 "extra-cardiac population of mesodermal progenitors that gives rise to the right ventricle and outflow tract[PMID:17276708]." xsd:string {source="PMID:17276708"} -property_value: UBPROP:0000008 "In general, the two studies in chick concluded that the contribution of the SHF was to the outflow tract, whereas the mouse work suggested that the second lineage contributed more broadly to the heart, including the outflow tract and much or all of the right ventricle [11-14]. These different conclusions may represent differences in the experimental approaches used or may represent bona fide differences in the contribution of the second lineage to the hearts of birds compared to mammals [11]. Alternatively, the secondary/anterior heart fields described in the chick may represent a subset of a broader field that makes a more substantial contribution to the heart, as the mouse studies suggested" xsd:string {source="PMID:17276708"} -property_value: UBPROP:0000011 "in mouse has left ventricular identity[PMID:22855565]" xsd:string +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata [Term] id: UBERON:0009891 @@ -238526,7 +235332,7 @@ is_a: UBERON:0006843 {source="FMA"} ! root of cranial nerve intersection_of: UBERON:0002211 ! nerve root intersection_of: extends_fibers_into UBERON:0000941 ! cranial nerve II relationship: extends_fibers_into UBERON:0000941 ! cranial nerve II -property_value: editor_note "TODO - check. See comments for optic tract. FMA also has medial root." xsd:string +property_value: IAO:0000116 "TODO - check. See comments for optic tract. FMA also has medial root." xsd:string [Term] id: UBERON:0009911 @@ -238538,7 +235344,7 @@ xref: FMA:45737 xref: NCIT:C12990 xref: UMLS:C0921005 {source="ncithesaurus:Lobule"} is_a: UBERON:0000063 {source="cjm"} ! organ subunit -property_value: editor_note "todo - provide definition. Clearly distinguish between lobules, lobes and acinar parts of glands (see for example lobule of mammary gland)" xsd:string +property_value: IAO:0000116 "todo - provide definition. Clearly distinguish between lobules, lobes and acinar parts of glands (see for example lobule of mammary gland)" xsd:string [Term] id: UBERON:0009912 @@ -238569,11 +235375,10 @@ xref: Wikipedia:Renal_lobe is_a: UBERON:0009912 ! anatomical lobe intersection_of: UBERON:0009912 ! anatomical lobe intersection_of: part_of UBERON:0002113 ! kidney -relationship: contributes_to_morphology_of UBERON:0002113 ! kidney relationship: part_of UBERON:0002113 ! kidney -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI -property_value: editor_note "todo - add has_part relationships." xsd:string -property_value: UBPROP:0000008 "human kidneys have multilobar (multipyramidal) architecture while mice and rats have unilobar (unipyramidal) kidneys" xsd:string {source="MP"} +relationship: RO:0002433 UBERON:0002113 ! contributes to morphology of kidney +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI +property_value: IAO:0000116 "todo - add has_part relationships." xsd:string [Term] id: UBERON:0009914 @@ -238598,10 +235403,10 @@ xref: Wikipedia:Cortical_lobule is_a: UBERON:0009911 ! lobule intersection_of: UBERON:0009911 ! lobule intersection_of: part_of UBERON:0002113 ! kidney -relationship: contributes_to_morphology_of UBERON:0002113 ! kidney relationship: has_part UBERON:0001285 ! nephron relationship: has_part UBERON:0009883 ! medullary ray relationship: part_of UBERON:0009913 {source="FMA"} ! renal lobe +relationship: RO:0002433 UBERON:0002113 ! contributes to morphology of kidney [Term] id: UBERON:0009916 @@ -238612,6 +235417,7 @@ synonym: "ureteral wall" EXACT [FMA:15888] xref: FMA:15888 xref: SCTID:279397004 is_a: UBERON:0000060 ! anatomical wall +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0000056 ! ureter relationship: has_part UBERON:0005742 ! adventitia @@ -238631,8 +235437,8 @@ intersection_of: adjacent_to UBERON:0000362 ! renal medulla intersection_of: adjacent_to UBERON:0001225 ! cortex of kidney relationship: adjacent_to UBERON:0000362 ! renal medulla relationship: adjacent_to UBERON:0001225 ! cortex of kidney -relationship: contributes_to_morphology_of UBERON:0002113 ! kidney relationship: part_of UBERON:0002113 {source="MP"} ! kidney +relationship: RO:0002433 UBERON:0002113 ! contributes to morphology of kidney [Term] id: UBERON:0009918 @@ -238658,9 +235464,9 @@ xref: EMAPA:28811 is_a: UBERON:0001135 ! smooth muscle tissue intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0000056 ! ureter -relationship: contributes_to_morphology_of UBERON:0000056 ! ureter relationship: part_of UBERON:0006855 ! muscular coat of ureter -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002433 UBERON:0000056 ! contributes to morphology of ureter +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0009920 @@ -238668,7 +235474,7 @@ name: optic neural crest namespace: uberon xref: EHDAA2:0001315 xref: EHDAA:1122 -is_a: UBERON:0005253 ! head mesenchyme +is_a: UBERON:0007213 ! mesenchyme derived from head neural crest is_a: UBERON:0007530 {source="EHDAA2"} ! migrating mesenchyme population relationship: part_of UBERON:0007213 {source="EHDAA2"} ! mesenchyme derived from head neural crest @@ -238679,7 +235485,7 @@ namespace: uberon synonym: "plexiform layer" BROAD [NLXANAT:20090405] xref: NLXANAT:20090405 is_a: UBERON:0004001 {source="NIFSTD"} ! olfactory bulb layer -property_value: editor_note "check if the NIF class is actually a grouping class" xsd:string +property_value: IAO:0000116 "check if the NIF class is actually a grouping class" xsd:string [Term] id: UBERON:0009953 @@ -238694,8 +235500,8 @@ synonym: "TS28 mouse" NARROW [MA:0002405] xref: MA:0002405 is_a: UBERON:0000468 ! multicellular organism intersection_of: UBERON:0000468 ! multicellular organism -intersection_of: existence_starts_with UBERON:0000092 ! post-embryonic stage -relationship: existence_starts_with UBERON:0000092 ! post-embryonic stage +intersection_of: RO:0002489 UBERON:0000092 ! existence starts with post-embryonic stage +relationship: RO:0002489 UBERON:0000092 ! existence starts with post-embryonic stage property_value: seeAlso "https://github.com/obophenotype/uberon/issues/667" xsd:anyURI [Term] @@ -238705,9 +235511,9 @@ namespace: uberon def: "A vertebrate nasal chemosensory system that is responsible for detecting intraspecific pheromonal cues as well as environmental odorants." [http://orcid.org/0000-0002-6601-2165] is_a: UBERON:0001032 ! sensory system relationship: capable_of GO:0043695 {source="Wikipedia"} ! detection of pheromone -relationship: only_in_taxon NCBITaxon:8287 ! Sarcopterygii relationship: part_of UBERON:0005725 ! olfactory system -property_value: editor_note "check relationship to olfactory system. Evolution: The morphological components of the VNS are found only in tetrapods, but the genetic components of the system have been found in teleost fish, in addition to tetrapods. In tetrapods, the VNS was thought to be the olfactory system for detecting pheromones, while the main olfactory system detected general odorants (Scalia and Winans 1975). However, experimental evidence suggests that there is not such a clear functional distinction (Restrepo et al. 2004; Baxi, Dorries, and Eisthen 2006; Spehr et al. 2006; Kelliher 2007). Sea lampreys produce unique bile acids which act as pheromones both in migration and mate finding (Li, Sorensen, and Gallaher 1995; Li et al. 2002; Siefkes and Li 2004). However, bile acids in teleost fish are known to require components of the main olfactory signal transduction pathway (Hansen et al. 2003), and interruption of the VNS signal transduction pathway had no effect on bile acid olfactory response (Hansen et al. 2003)[Grus - EVOLUTION OF THE VOMERONASAL SYSTEM VIEWED THROUGH SYSTEM-SPECIFIC GENES]" xsd:string +relationship: RO:0002160 NCBITaxon:8287 ! only in taxon Sarcopterygii +property_value: IAO:0000116 "check relationship to olfactory system. Evolution: The morphological components of the VNS are found only in tetrapods, but the genetic components of the system have been found in teleost fish, in addition to tetrapods. In tetrapods, the VNS was thought to be the olfactory system for detecting pheromones, while the main olfactory system detected general odorants (Scalia and Winans 1975). However, experimental evidence suggests that there is not such a clear functional distinction (Restrepo et al. 2004; Baxi, Dorries, and Eisthen 2006; Spehr et al. 2006; Kelliher 2007). Sea lampreys produce unique bile acids which act as pheromones both in migration and mate finding (Li, Sorensen, and Gallaher 1995; Li et al. 2002; Siefkes and Li 2004). However, bile acids in teleost fish are known to require components of the main olfactory signal transduction pathway (Hansen et al. 2003), and interruption of the VNS signal transduction pathway had no effect on bile acid olfactory response (Hansen et al. 2003)[Grus - EVOLUTION OF THE VOMERONASAL SYSTEM VIEWED THROUGH SYSTEM-SPECIFIC GENES]" xsd:string [Term] id: UBERON:0009955 @@ -238724,16 +235530,14 @@ xref: XAO:0004620 xref: ZFA:0001309 is_a: UBERON:0002546 {source="cjm"} ! cranial placode intersection_of: UBERON:0005085 ! ectodermal placode -intersection_of: has_potential_to_developmentally_contribute_to CL:0000540 ! neuron -intersection_of: has_potential_to_developmentally_contribute_to UBERON:0001714 ! cranial ganglion -intersection_of: has_potential_to_developmentally_contribute_to UBERON:0001785 ! cranial nerve +intersection_of: RO:0002385 CL:0000540 ! has potential to developmentally contribute to neuron +intersection_of: RO:0002385 UBERON:0001714 ! has potential to developmentally contribute to cranial ganglion +intersection_of: RO:0002385 UBERON:0001785 ! has potential to developmentally contribute to cranial nerve disjoint_from: UBERON:0011814 ! non-neurogenic ectodermal placode -relationship: develops_from UBERON:2007013 ! preplacodal ectoderm -relationship: has_potential_to_developmentally_contribute_to CL:0000540 ! neuron -relationship: has_potential_to_developmentally_contribute_to UBERON:0001714 ! cranial ganglion -relationship: has_potential_to_developmentally_contribute_to UBERON:0001785 ! cranial nerve -property_value: IAO:0000232 "Includes: trigeminal, otic, lateral line and epibranchial placodes." xsd:string -property_value: UBPROP:0000008 "While some sensory placodes (otic and olfactory) may have homologues in basal chordates (Wada et al., 1998), the so-called neurogenenic placodes (trigeminal, otic, lateral line and epibranchial placodes) appear to have emerged at a later time (Shimeld and Holland, 2000)" xsd:string {source="NCBIBook:NBK53171"} +relationship: RO:0002202 UBERON:2007013 ! develops from preplacodal ectoderm +relationship: RO:0002385 CL:0000540 ! has potential to developmentally contribute to neuron +relationship: RO:0002385 UBERON:0001714 ! has potential to developmentally contribute to cranial ganglion +relationship: RO:0002385 UBERON:0001785 ! has potential to developmentally contribute to cranial nerve [Term] id: UBERON:0009958 @@ -238750,10 +235554,10 @@ xref: galen:UrinaryBladderCavity xref: SCTID:279405003 is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 {source="FMA"} ! anatomical space -intersection_of: luminal_space_of UBERON:0001255 {source="FMA"} ! urinary bladder -relationship: develops_from UBERON:0009844 {source="EHDAA2"} ! urogenital sinus lumen -relationship: luminal_space_of UBERON:0001255 ! urinary bladder +intersection_of: RO:0002572 UBERON:0001255 {source="FMA"} ! luminal space of urinary bladder relationship: part_of UBERON:0001255 {source="FMA"} ! urinary bladder +relationship: RO:0002202 UBERON:0009844 {source="EHDAA2"} ! develops from urogenital sinus lumen +relationship: RO:0002572 UBERON:0001255 ! luminal space of urinary bladder [Term] id: UBERON:0009960 @@ -238766,6 +235570,7 @@ synonym: "inner circular muscle layer of esophagus" EXACT [FMA:67605] xref: EMAPA:37523 {source="MA:th"} xref: FMA:67605 xref: MA:0001574 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0012368 ! circular muscle layer of muscular coat intersection_of: UBERON:0012368 ! circular muscle layer of muscular coat intersection_of: part_of UBERON:0001043 ! esophagus @@ -238784,8 +235589,7 @@ xref: FMA:9479 is_a: UBERON:0004493 ! cardiac muscle tissue of myocardium is_a: UBERON:0010131 {source="cjm"} ! conducting tissue of heart relationship: part_of UBERON:0002350 {source="FMA"} ! conducting system of heart -property_value: editor_note "include 3 subtypes?" xsd:string -property_value: IAO:0000232 "evidence is sparse [http://www.gpnotebook.co.uk/simplepage.cfm?ID=-483065798] There is some functional evidence for the existence of specialized conducting pathways within the atria (termed internodal tracts), although this is controversial" xsd:string {source="http://www.cvphysiology.com/Arrhythmias/A003.htm"} +property_value: IAO:0000116 "include 3 subtypes?" xsd:string [Term] id: UBERON:0009967 @@ -238804,8 +235608,8 @@ xref: UMLS:C1179415 {source="ncithesaurus:Splenic_Sinus"} is_a: UBERON:0003497 ! abdomen blood vessel is_a: UBERON:0006615 {source="cjm"} ! venous sinus relationship: part_of UBERON:0001250 {source="MA"} ! red pulp of spleen -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: seeAlso UBERON:0003910 ! splenic sinusoid +property_value: RO:0002175 NCBITaxon:9606 +property_value: seeAlso UBERON:0003910 [Term] id: UBERON:0009969 @@ -238831,7 +235635,7 @@ is_a: UBERON:0034969 ! epithelial layer of duct intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0007329 ! pancreatic duct relationship: part_of UBERON:0007329 ! pancreatic duct -property_value: editor_note "in EHDAA2, the embryonic pancreatic ducts (dorsal, ventral) are classified as eithelial sacs, which would render them subclasses of this" xsd:string +property_value: IAO:0000116 "in EHDAA2, the embryonic pancreatic ducts (dorsal, ventral) are classified as eithelial sacs, which would render them subclasses of this" xsd:string [Term] id: UBERON:0009971 @@ -238849,7 +235653,6 @@ synonym: "Wassman gland" RELATED [MP:0003892] xref: FMA:14921 xref: FMA:14923 is_a: UBERON:0000325 {source="FMA"} ! gastric gland -property_value: UBPROP:0000012 "FMA has this as part of both the fundus and the body, but these are largely spatially disjoint." xsd:string {external_ontology="FMA"} [Term] id: UBERON:0009972 @@ -238866,12 +235669,12 @@ xref: NCIT:C106203 xref: SCTID:264130006 is_a: UBERON:0007651 ! anatomical junction intersection_of: UBERON:0007651 ! anatomical junction -intersection_of: connects UBERON:0000056 ! ureter -intersection_of: connects UBERON:0001224 ! renal pelvis -relationship: connects UBERON:0000056 ! ureter -relationship: connects UBERON:0001224 ! renal pelvis -relationship: contributes_to_morphology_of UBERON:0001008 ! renal system +intersection_of: RO:0002176 UBERON:0000056 ! connects ureter +intersection_of: RO:0002176 UBERON:0001224 ! connects renal pelvis relationship: part_of UBERON:0001008 {source="MP"} ! renal system +relationship: RO:0002176 UBERON:0000056 ! connects ureter +relationship: RO:0002176 UBERON:0001224 ! connects renal pelvis +relationship: RO:0002433 UBERON:0001008 ! contributes to morphology of renal system [Term] id: UBERON:0009973 @@ -238890,12 +235693,12 @@ xref: SCTID:261187001 is_a: UBERON:0003978 ! valve is_a: UBERON:0007651 ! anatomical junction intersection_of: UBERON:0007651 ! anatomical junction -intersection_of: connects UBERON:0000056 ! ureter -intersection_of: connects UBERON:0001255 ! urinary bladder -relationship: connects UBERON:0000056 ! ureter -relationship: connects UBERON:0001255 ! urinary bladder -relationship: contributes_to_morphology_of UBERON:0001008 ! renal system +intersection_of: RO:0002176 UBERON:0000056 ! connects ureter +intersection_of: RO:0002176 UBERON:0001255 ! connects urinary bladder relationship: part_of UBERON:0001008 {source="MP"} ! renal system +relationship: RO:0002176 UBERON:0000056 ! connects ureter +relationship: RO:0002176 UBERON:0001255 ! connects urinary bladder +relationship: RO:0002433 UBERON:0001008 ! contributes to morphology of renal system [Term] id: UBERON:0009974 @@ -238908,10 +235711,10 @@ xref: EMAPA:25037 is_a: UBERON:0005082 {source="EHDAA2"} ! tube lumen is_a: UBERON:0007473 ! lumen of epithelial sac intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0005356 ! Rathke's pouch -relationship: luminal_space_of UBERON:0005356 ! Rathke's pouch +intersection_of: RO:0002572 UBERON:0005356 ! luminal space of Rathke's pouch relationship: part_of UBERON:0005356 ! Rathke's pouch -relationship: surrounded_by UBERON:0012287 {source="EHDAA2-modified"} ! Rathkes pouch epithelium +relationship: RO:0002219 UBERON:0012287 {source="EHDAA2-modified"} ! surrounded by Rathkes pouch epithelium +relationship: RO:0002572 UBERON:0005356 ! luminal space of Rathke's pouch [Term] id: UBERON:0010000 @@ -238922,15 +235725,14 @@ subset: common_anatomy subset: upper_level synonym: "multicellular structure" EXACT [FBbt:00100313] xref: CARO:0010000 -xref: FBbt:00100313 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: has_quality PATO:0001993 ! multicellular +intersection_of: RO:0000086 PATO:0001993 ! has quality multicellular relationship: has_part CL:0000000 ! cell -relationship: has_quality PATO:0001993 ! multicellular -relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 ! Fungi +relationship: RO:0000086 PATO:0001993 ! has quality multicellular +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0010001 @@ -238940,7 +235742,6 @@ def: "A small cluster of cells of various types which form a discrete structure, comment: Examples include arthropod sensilla. subset: upper_level xref: CARO:0010001 -xref: FBbt:00007229 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000062 {source="CARO"} ! organ is_a: UBERON:0034922 {source="CARO"} ! cell cluster disjoint_from: UBERON:0011216 {source="FBbt"} ! organ system subdivision @@ -238953,9 +235754,9 @@ def: "The vascularized and branched structures arising from the rodent trophobla subset: pheno_slim synonym: "placental labyrinth villi" RELATED OMO:0003004 [] synonym: "villous of placental labyrinth" EXACT [] -is_a: UBERON:0000061 ! anatomical structure -relationship: contributes_to_morphology_of UBERON:0003946 ! placenta labyrinth +is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0003946 {source="MP"} ! placenta labyrinth +relationship: RO:0002433 UBERON:0003946 ! contributes to morphology of placenta labyrinth [Term] id: UBERON:0010009 @@ -238964,15 +235765,14 @@ namespace: uberon def: "A regional part of brain consisting of multiple brain regions that are not related through a simple volummetric part of hierarchy, e.g., basal ganglia[NIF]." [NLXANAT:20090509] subset: non_informative synonym: "set of nuclei of neuraxis" RELATED [FMA:256381] -xref: FMA:256381 xref: NLXANAT:20090509 is_a: UBERON:0034923 ! disconnected anatomical group intersection_of: UBERON:0034923 ! disconnected anatomical group -intersection_of: has_member UBERON:0002616 ! regional part of brain intersection_of: part_of UBERON:0000955 ! brain -relationship: has_member UBERON:0002616 ! regional part of brain +intersection_of: RO:0002351 UBERON:0002616 ! has member regional part of brain relationship: part_of UBERON:0000955 ! brain -property_value: editor_note "May be obsoleted." xsd:string +relationship: RO:0002351 UBERON:0002616 ! has member regional part of brain +property_value: IAO:0000116 "May be obsoleted." xsd:string [Term] id: UBERON:0010011 @@ -238992,18 +235792,15 @@ synonym: "subcortical nuclei" RELATED [NeuroNames:2677] xref: BAMS:BG xref: BIRNLEX:826 xref: BM:Tel-BG -xref: DHBA:10331 xref: EMAPA:32673 xref: FMA:84013 xref: GAID:617 -xref: HBA:4275 xref: HBA:4276 xref: MA:0000184 xref: MBA:623 xref: MESH:D001479 xref: NCIT:C12447 xref: neuronames:2677 -xref: PBA:128012596 xref: PBA:4001 xref: UMLS:C0004781 {source="ncithesaurus:Basal_Ganglia"} xref: VHOG:0001696 @@ -239012,9 +235809,8 @@ is_a: UBERON:0010009 {source="FMA"} ! aggregate regional part of brain relationship: overlaps UBERON:0001891 ! midbrain relationship: overlaps UBERON:0001893 {source="MA", source="NIF"} ! telencephalon relationship: part_of UBERON:0000454 {source="FMA"} ! cerebral subcortex -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: editor_note "it is necessary to introduce two classes, one representing an individual basal ganglion, another representing the aggregate structure, in order to have consistent classification amongst AOs (e.g. in MA the aygdala is part of the BG, in FMA and BTO it is a subclass). Apart from achieving this consistency, the value of having two distinct classes is questionable, since the BG-plural is trivially the collection of all BGs-singular. it would be better for all AOs to decide on one single way of doing this. Do not merge until this is done." xsd:string -property_value: UBPROP:0000003 "All nuclei of the mammalian basal ganglia are also present in the oldest vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001696", ontology="VHOG", source="DOI:10.1016/j.cub.2011.05.001 Stephenson-Jones M, Samuelsson E, Ericsson J, Robertson B, Grillner S, Evolutionary conservation of the basal ganglia as a common vertebrate mechanism for action selection. Current Biology (2011)", source="http://bgee.unil.ch/"} +property_value: IAO:0000116 "it is necessary to introduce two classes, one representing an individual basal ganglion, another representing the aggregate structure, in order to have consistent classification amongst AOs (e.g. in MA the aygdala is part of the BG, in FMA and BTO it is a subclass). Apart from achieving this consistency, the value of having two distinct classes is questionable, since the BG-plural is trivially the collection of all BGs-singular. it would be better for all AOs to decide on one single way of doing this. Do not merge until this is done." xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0010020 @@ -239034,8 +235830,7 @@ is_a: UBERON:0005423 ! developing anatomical structure is_a: UBERON:0005911 ! endo-epithelium is_a: UBERON:0007499 {source="EHDAA2"} ! epithelial sac is_a: UBERON:0015813 ! middle ear epithelium -relationship: develops_from UBERON:0007122 {source="EHDAA2", source="ISBN:0073040584", source="PMID:11237469"} ! pharyngeal pouch 1 -property_value: UBPROP:0000003 "The tympanic cavity and auditory tube of an amniote develop from the first embryonic pharyngeal pouch, so they are homologous to the first gill pouch, or spiracle, of a fish. We are uncertain whether this homology strictly applies to the middle ear cavity and auditory tube of lissamphibians, which show certain peculiarities in their development.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001297", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.417", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0007122 {source="EHDAA2", source="ISBN:0073040584", source="PMID:11237469"} ! develops from pharyngeal pouch 1 [Term] id: UBERON:0010025 @@ -239050,11 +235845,9 @@ synonym: "dorsal pharyngeal pouch 3 endoderm" RELATED [] synonym: "dorsal wing of pharyngeal pouch 3" EXACT [http://orcid.org/0000-0002-6601-2165] xref: EHDAA2:0000409 xref: EMAPA:16758 -is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium +is_a: UBERON:0003258 ! endoderm of foregut is_a: UBERON:0005291 ! embryonic tissue -is_a: UBERON:0015833 ! foregut epithelium relationship: part_of UBERON:0007124 {source="EHDAA2"} ! pharyngeal pouch 3 -property_value: UBPROP:0000011 "Derivatives of the dorsal wings include the inferior parathyroid glands[WP] in mammals, the cranial dorsal aspect of the third pouch generates the inferior parathyroids (or parathyroid III)" xsd:string {source="MP"} [Term] id: UBERON:0010026 @@ -239069,11 +235862,9 @@ synonym: "ventral pharyngeal pouch 3 endoderm" RELATED [] synonym: "ventral wing of pharyngeal pouch 3" EXACT [http://orcid.org/0000-0002-6601-2165] xref: EHDAA2:0002173 xref: EMAPA:16759 -is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium +is_a: UBERON:0003258 ! endoderm of foregut is_a: UBERON:0005291 ! embryonic tissue -is_a: UBERON:0015833 ! foregut epithelium relationship: part_of UBERON:0007124 {source="EHDAA2"} ! pharyngeal pouch 3 -property_value: UBPROP:0000011 "The ventral wings fuse to form the cytoreticular cells of the thymus[WP] the caudal ventral part of the pouch gives rise to the thymus epithelium" xsd:string {source="MP"} [Term] id: UBERON:0010027 @@ -239083,9 +235874,8 @@ synonym: "dorsal 4th branchial pouch" EXACT [] synonym: "dorsal branchial pouch 4 endoderm" RELATED [] synonym: "dorsal pharyngeal pouch 4" EXACT [] synonym: "dorsal pharyngeal pouch 4 endoderm" RELATED [] -is_a: UBERON:0000490 ! unilaminar epithelium +is_a: UBERON:0003258 ! endoderm of foregut is_a: UBERON:0005291 ! embryonic tissue -is_a: UBERON:0015833 ! foregut epithelium relationship: part_of UBERON:0007125 ! pharyngeal pouch 4 [Term] @@ -239096,9 +235886,8 @@ synonym: "ventral 4th branchial pouch" EXACT [] synonym: "ventral branchial pouch 4 endoderm" RELATED [] synonym: "ventral pharyngeal pouch 4" EXACT [] synonym: "ventral pharyngeal pouch 4 endoderm" RELATED [] -is_a: UBERON:0000490 ! unilaminar epithelium +is_a: UBERON:0003258 ! endoderm of foregut is_a: UBERON:0005291 ! embryonic tissue -is_a: UBERON:0015833 ! foregut epithelium relationship: part_of UBERON:0007125 ! pharyngeal pouch 4 [Term] @@ -239138,13 +235927,11 @@ xref: UMLS:C0226946 {source="ncithesaurus:Apex_of_the_Tongue"} xref: Wikipedia:Anterior_tongue is_a: UBERON:0000064 ! organ part intersection_of: UBERON:0000064 {source="ISBN:1607950324"} ! organ part -intersection_of: develops_from UBERON:0006260 {source="ISBN:1607950324"} ! lingual swellings intersection_of: part_of UBERON:0001723 {source="ISBN:1607950324"} ! tongue -relationship: develops_from UBERON:0006260 ! lingual swellings +intersection_of: RO:0002202 UBERON:0006260 {source="ISBN:1607950324"} ! develops from lingual swellings relationship: part_of UBERON:0001723 ! tongue -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/4/4c/Illu04_tongue.jpg" xsd:anyURI -property_value: UBPROP:0000011 "The lateral lingual swellings grow and fuse with eachother, encompassing the tuberculum impar to provide the ectodermally derived mucosa of the anterior 2/3 of the tongue" xsd:string -property_value: UBPROP:0000012 "check NCIT" xsd:string {external_ontology="NCIT"} +relationship: RO:0002202 UBERON:0006260 ! develops from lingual swellings +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/4/4c/Illu04_tongue.jpg" xsd:anyURI [Term] id: UBERON:0010038 @@ -239169,8 +235956,8 @@ intersection_of: part_of UBERON:0001160 ! fundus of stomach relationship: has_part CL:0000155 {source="ISBN:0073040584"} ! peptic cell relationship: has_part CL:0000162 {source="ISBN:0073040584"} ! parietal cell relationship: part_of UBERON:0004994 ! mucosa of fundus of stomach -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/d7/Fundic_gland_polyp_%281%29.jpg" xsd:anyURI -property_value: editor_note "Consider FMA:14923 ! Principal gland of fundus of stomach. Added part_of to mucosa to be consistent with FMA pattern (note that Kardong places this in the glandular epithelium)" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d7/Fundic_gland_polyp_%281%29.jpg" xsd:anyURI +property_value: IAO:0000116 "Consider FMA:14923 ! Principal gland of fundus of stomach. Added part_of to mucosa to be consistent with FMA pattern (note that Kardong places this in the glandular epithelium)" xsd:string [Term] id: UBERON:0010039 @@ -239185,7 +235972,6 @@ xref: TGMA:0001041 is_a: UBERON:0013765 ! digestive system element relationship: part_of UBERON:0001555 ! digestive tract relationship: part_of UBERON:0005409 ! alimentary part of gastrointestinal system -property_value: IAO:0000232 "This is a very broad functionally defined grouping class that collects disparate structures from insects to vertebrates" xsd:string [Term] id: UBERON:0010042 @@ -239227,8 +236013,8 @@ xref: EMAPA:16550 xref: XAO:0004524 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue -relationship: has_developmental_contribution_from UBERON:0003099 {source="cjm"} ! cranial neural crest relationship: part_of UBERON:0008814 {source="EHDAA2"} ! pharyngeal arch system +relationship: RO:0002254 UBERON:0003099 {source="cjm"} ! has developmental contribution from cranial neural crest [Term] id: UBERON:0010047 @@ -239252,7 +236038,6 @@ is_a: UBERON:0003408 ! gland of digestive tract intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0000165 ! mouth relationship: part_of UBERON:0000165 ! mouth -property_value: UBPROP:0000012 "Note that Kardong classifies lacrimal glands here. EHDAA2 includes pituitary primordium, as this develops from oral mucosa" xsd:string {external_ontology="EHDAA2"} [Term] id: UBERON:0010052 @@ -239266,8 +236051,7 @@ is_a: UBERON:0005020 ! mucosa of tongue intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0009471 ! dorsum of tongue relationship: part_of UBERON:0009471 ! dorsum of tongue -property_value: editor_note "check surface terms" xsd:string -property_value: UBPROP:0000011 "develops fungiform papillae by WNT induction at 11 weeks pc in human. Filiform papillae develop later. ISBN:1607950324" xsd:string +property_value: IAO:0000116 "check surface terms" xsd:string [Term] id: UBERON:0010056 @@ -239280,9 +236064,9 @@ is_a: UBERON:0003103 {source="EHDAA2"} ! compound organ is_a: UBERON:0005423 ! developing anatomical structure is_a: UBERON:0013765 ! digestive system element intersection_of: UBERON:0003103 ! compound organ -intersection_of: has_potential_to_develop_into UBERON:0001723 ! tongue -relationship: has_potential_to_develop_into UBERON:0001723 ! tongue +intersection_of: RO:0002387 UBERON:0001723 ! has potential to develop into tongue relationship: part_of UBERON:0000165 ! mouth +relationship: RO:0002387 UBERON:0001723 ! has potential to develop into tongue [Term] id: UBERON:0010059 @@ -239300,8 +236084,8 @@ xref: EHDAA2:0004116 is_a: UBERON:0005911 ! endo-epithelium is_a: UBERON:0007499 {source="EHDAA2"} ! epithelial sac is_a: UBERON:0015813 ! middle ear epithelium -relationship: develops_from_part_of UBERON:0010020 {source="EHDAA2"} ! tubotympanic recess epithelium -relationship: located_in UBERON:0004114 ! tympanic cavity +relationship: RO:0001025 UBERON:0004114 ! located in tympanic cavity +relationship: RO:0002225 UBERON:0010020 {source="EHDAA2"} ! develops from part of tubotympanic recess epithelium [Term] id: UBERON:0010064 @@ -239312,9 +236096,9 @@ xref: AEO:0000221 xref: EHDAA2:0004616 is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: has_quality PATO:0000610 ! open -relationship: connected_to UBERON:0000464 {source="cjm"} ! anatomical space -relationship: has_quality PATO:0000610 ! open +intersection_of: RO:0000086 PATO:0000610 ! has quality open +relationship: RO:0000086 PATO:0000610 ! has quality open +relationship: RO:0002170 UBERON:0000464 {source="cjm"} ! connected to anatomical space [Term] id: UBERON:0010065 @@ -239322,8 +236106,10 @@ name: auditory meatus epithelium namespace: uberon xref: EHDAA2:0004114 is_a: UBERON:0003914 {source="EHDAA2"} ! epithelial tube +is_a: UBERON:0005911 ! endo-epithelium +is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0015814 ! outer ear epithelium -relationship: develops_from UBERON:0005872 {source="EHDAA2", source="PMID:16313389"} ! 1st arch pharyngeal cleft +relationship: RO:0002202 UBERON:0005872 {source="EHDAA2", source="PMID:16313389"} ! develops from 1st arch pharyngeal cleft [Term] id: UBERON:0010069 @@ -239337,7 +236123,9 @@ synonym: "outer layer of tympanic membrane" EXACT [] synonym: "tympanic membrane external acoustic meatus epithelial component" EXACT [https://orcid.org/0000-0002-6601-2165] xref: FMA:56819 xref: SCTID:39725007 +is_a: UBERON:0005911 ! endo-epithelium is_a: UBERON:0009647 ! tympanic membrane epithelium +is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0015814 ! outer ear epithelium intersection_of: UBERON:0009647 ! tympanic membrane epithelium intersection_of: part_of UBERON:0001352 ! external acoustic meatus @@ -239358,7 +236146,6 @@ xref: FMA:56830 xref: MA:0001223 xref: SCTID:44692008 is_a: UBERON:0010071 {source="FMA"} ! layer of tympanic membrane -property_value: UBPROP:0000012 "check MA" xsd:string {external_ontology="MA"} [Term] id: UBERON:0010071 @@ -239369,7 +236156,6 @@ synonym: "tympanic membrane layer" EXACT [FMA:56732] xref: FMA:56732 is_a: UBERON:0000064 ! organ part relationship: part_of UBERON:0002364 ! tympanic membrane -property_value: UBPROP:0000008 "In mammals, this class groups together the two epithelial layers plus the intermediate fibrous layer" xsd:string [Term] id: UBERON:0010074 @@ -239382,9 +236168,8 @@ xref: FMA:79645 xref: MESH:D002838 is_a: UBERON:0010313 ! neural crest-derived structure is_a: UBERON:0011216 ! organ system subdivision -relationship: composed_primarily_of CL:0000166 ! chromaffin cell relationship: part_of UBERON:0000949 {source="cjm"} ! endocrine system -property_value: UBPROP:0000008 "in adult cylostomes and teleosts, the interrenal bodies are separate from chromaffin bodies" xsd:string +relationship: RO:0002473 CL:0000166 ! composed primarily of chromaffin cell [Term] id: UBERON:0010075 @@ -239392,6 +236177,7 @@ name: sacral neural crest namespace: uberon def: "One of the 5 distinct and partially overlapping functional domains of the premigratory neural crest. The vagal and sacral neural crest cells develop into the ganglia of the enteric nervous system, also known as the parasympathetic ganglia." [http://www.ncbi.nlm.nih.gov/books/NBK10065/, XB:curator] xref: XAO:0004192 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue relationship: part_of UBERON:0002342 ! neural crest @@ -239404,8 +236190,7 @@ xref: NCIT:C32415 xref: UMLS:C0682577 {source="ncithesaurus:Cuboidal_Epithelium"} xref: Wikipedia:Cuboidal_epithelium is_a: UBERON:0000483 ! epithelium -property_value: editor_note "TODO - coordinate with CL, add cuboidal cell" xsd:string -property_value: UBPROP:0000012 "in NCIT this is glandular" xsd:string {external_ontology="NCIT"} +property_value: IAO:0000116 "TODO - coordinate with CL, add cuboidal cell" xsd:string [Term] id: UBERON:0010081 @@ -239418,9 +236203,9 @@ is_a: UBERON:0003914 ! epithelial tube is_a: UBERON:0005911 ! endo-epithelium is_a: UBERON:0034932 ! epithelium of biliary system intersection_of: UBERON:0003703 ! extrahepatic bile duct -intersection_of: has_potential_to_develop_into UBERON:0001175 ! common hepatic duct -relationship: develops_from UBERON:0005604 ! extrahepatic part of hepatic duct -relationship: has_potential_to_develop_into UBERON:0001175 ! common hepatic duct +intersection_of: RO:0002387 UBERON:0001175 ! has potential to develop into common hepatic duct +relationship: RO:0002202 UBERON:0005604 ! develops from extrahepatic part of hepatic duct +relationship: RO:0002387 UBERON:0001175 ! has potential to develop into common hepatic duct [Term] id: UBERON:0010083 @@ -239430,12 +236215,12 @@ def: "Mesenchyme that has the potential to develop into a dermis." [OBOL:automat xref: EHDAA2:0000598 is_a: UBERON:0003104 ! mesenchyme intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: has_potential_to_develop_into UBERON:0002067 ! dermis -relationship: develops_from UBERON:0003089 {source="EHDAA2"} ! sclerotome -relationship: develops_from UBERON:0004016 {source="XAO"} ! dermatome -relationship: has_potential_to_develop_into UBERON:0002067 ! dermis +intersection_of: RO:0002387 UBERON:0002067 ! has potential to develop into dermis relationship: part_of UBERON:0002199 {source="EHDAA2"} ! integument -property_value: editor_note "check development" xsd:string +relationship: RO:0002202 UBERON:0003089 {source="EHDAA2"} ! develops from sclerotome +relationship: RO:0002202 UBERON:0004016 {source="XAO"} ! develops from dermatome +relationship: RO:0002387 UBERON:0002067 ! has potential to develop into dermis +property_value: IAO:0000116 "check development" xsd:string [Term] id: UBERON:0010084 @@ -239445,11 +236230,11 @@ def: "A structure that will develop into a diaphragm." [http://orcid.org/0000-00 xref: EHDAA2:0000599 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001103 ! diaphragm -relationship: developmentally_induced_by UBERON:0009133 {source="PMID:23586979"} ! pleuroperitoneal membrane -relationship: develops_from UBERON:0005594 {source="PMID:23586979"} ! head somite -relationship: has_potential_to_develop_into UBERON:0001103 ! diaphragm -relationship: located_in UBERON:0002323 {source="EHDAA2"} ! coelemic cavity lumen +intersection_of: RO:0002387 UBERON:0001103 ! has potential to develop into diaphragm +relationship: RO:0001025 UBERON:0002323 {source="EHDAA2"} ! located in coelemic cavity lumen +relationship: RO:0002202 UBERON:0005594 {source="PMID:23586979"} ! develops from head somite +relationship: RO:0002256 UBERON:0009133 {source="PMID:23586979"} ! developmentally induced by pleuroperitoneal membrane +relationship: RO:0002387 UBERON:0001103 ! has potential to develop into diaphragm [Term] id: UBERON:0010091 @@ -239458,13 +236243,14 @@ namespace: uberon def: "A multi-tissue structure that has the potential to develop into a meninx of hindbrain." [OBOL:automatic] synonym: "future hindbrain meninges" EXACT [EHDAA2:0000610] xref: EHDAA2:0000610 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 ! dense mesenchyme tissue is_a: UBERON:0007645 ! future meninx intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0003291 ! meninx of hindbrain -relationship: has_potential_to_develop_into UBERON:0003291 ! meninx of hindbrain +intersection_of: RO:0002387 UBERON:0003291 ! has potential to develop into meninx of hindbrain relationship: part_of UBERON:0002028 ! hindbrain +relationship: RO:0002387 UBERON:0003291 ! has potential to develop into meninx of hindbrain [Term] id: UBERON:0010092 @@ -239474,9 +236260,9 @@ def: "A developing anatomical structure that has the potential to develop into a xref: EHDAA2:0000623 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001895 ! metencephalon -relationship: has_potential_to_develop_into UBERON:0001895 ! metencephalon +intersection_of: RO:0002387 UBERON:0001895 ! has potential to develop into metencephalon relationship: part_of UBERON:0002028 ! hindbrain +relationship: RO:0002387 UBERON:0001895 ! has potential to develop into metencephalon [Term] id: UBERON:0010096 @@ -239486,9 +236272,9 @@ def: "A developing anatomical structure that has the potential to develop into a xref: EHDAA2:0000640 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0005290 ! myelencephalon -relationship: has_potential_to_develop_into UBERON:0005290 ! myelencephalon +intersection_of: RO:0002387 UBERON:0005290 ! has potential to develop into myelencephalon relationship: part_of UBERON:0002028 ! hindbrain +relationship: RO:0002387 UBERON:0005290 ! has potential to develop into myelencephalon [Term] id: UBERON:0010123 @@ -239498,8 +236284,8 @@ def: "A gray matter that has the potential to develop into a facial nucleus." [O xref: EHDAA2:0004639 is_a: UBERON:0002020 ! gray matter intersection_of: UBERON:0002020 ! gray matter -intersection_of: has_potential_to_develop_into UBERON:0000127 ! facial nucleus -relationship: has_potential_to_develop_into UBERON:0000127 ! facial nucleus +intersection_of: RO:0002387 UBERON:0000127 ! has potential to develop into facial nucleus +relationship: RO:0002387 UBERON:0000127 ! has potential to develop into facial nucleus [Term] id: UBERON:0010125 @@ -239509,8 +236295,8 @@ def: "A gray matter that has the potential to develop into a superior salivatory xref: EHDAA2:0004644 is_a: UBERON:0002020 ! gray matter intersection_of: UBERON:0002020 ! gray matter -intersection_of: has_potential_to_develop_into UBERON:0002149 ! superior salivatory nucleus -relationship: has_potential_to_develop_into UBERON:0002149 ! superior salivatory nucleus +intersection_of: RO:0002387 UBERON:0002149 ! has potential to develop into superior salivatory nucleus +relationship: RO:0002387 UBERON:0002149 ! has potential to develop into superior salivatory nucleus [Term] id: UBERON:0010129 @@ -239524,11 +236310,11 @@ is_a: UBERON:0005863 ! cartilaginous condensation is_a: UBERON:0010885 ! hindlimb cartilage element is_a: UBERON:0015052 ! femur endochondral element intersection_of: UBERON:0015052 ! femur endochondral element -intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue -relationship: develops_from UBERON:0006234 ! femur pre-cartilage condensation -relationship: has_potential_to_develop_into UBERON:0000981 ! femur +intersection_of: RO:0002473 UBERON:0002418 ! composed primarily of cartilage tissue relationship: part_of UBERON:0005254 {source="EMAPA"} ! upper leg mesenchyme -property_value: editor_note "TODO - request EHDAA2" xsd:string +relationship: RO:0002202 UBERON:0006234 ! develops from femur pre-cartilage condensation +relationship: RO:0002387 UBERON:0000981 ! has potential to develop into femur +property_value: IAO:0000116 "TODO - request EHDAA2" xsd:string [Term] id: UBERON:0010130 @@ -239539,9 +236325,9 @@ synonym: "autopod plate" EXACT [] synonym: "limb plate" EXACT [] is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0002050 ! embryonic structure -intersection_of: has_potential_to_develop_into UBERON:0002470 ! autopod region -relationship: develops_from UBERON:0004347 ! limb bud -relationship: has_potential_to_develop_into UBERON:0002470 ! autopod region +intersection_of: RO:0002387 UBERON:0002470 ! has potential to develop into autopod region +relationship: RO:0002202 UBERON:0004347 ! develops from limb bud +relationship: RO:0002387 UBERON:0002470 ! has potential to develop into autopod region [Term] id: UBERON:0010131 @@ -239623,9 +236409,8 @@ is_a: UBERON:0004909 ! epithelium of gonad is_a: UBERON:0005295 ! sex cord intersection_of: UBERON:0005295 {source="EHDAA2"} ! sex cord intersection_of: part_of UBERON:0009117 {source="EHDAA2"} ! indifferent gonad -relationship: develops_from UBERON:0005891 {source="EHDAA2"} ! coelomic epithelium relationship: part_of UBERON:0009117 ! indifferent gonad -property_value: IAO:0000232 "note that this represents the indifferent structure." xsd:string +relationship: RO:0002202 UBERON:0005891 {source="EHDAA2"} ! develops from coelomic epithelium [Term] id: UBERON:0010143 @@ -239647,9 +236432,6 @@ is_a: UBERON:0006530 {source="FMA"} ! seminal fluid intersection_of: UBERON:0000456 ! secretion of exocrine gland intersection_of: produced_by UBERON:0000998 ! seminal vesicle relationship: produced_by UBERON:0000998 ! seminal vesicle -property_value: UBPROP:0000008 "constitutes 60-70 % of the ejaculate in humans[MP]" xsd:string -property_value: UBPROP:0000009 "important for semen coagulation, sperm motility, and stability of sperm chromatin and suppression of the immune activity in the female reproductive tract[MP]" xsd:string -property_value: UBPROP:0000012 "in ncit, seminal fluid is a subtype of seminal vesicle secretion" xsd:string {external_ontology="ncit"} [Term] id: UBERON:0010147 @@ -239662,7 +236444,7 @@ synonym: "male accessory gland" RELATED [BTO:0004798] synonym: "male accessory reproductive gland" RELATED [] xref: BTO:0004798 is_a: UBERON:0005399 {source="BTO"} ! male reproductive gland -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0010152 @@ -239691,11 +236473,11 @@ xref: SCTID:136349005 xref: Wikipedia:Sphenofrontal_suture is_a: UBERON:0003685 ! cranial suture intersection_of: UBERON:0003685 ! cranial suture -intersection_of: connects UBERON:0000209 ! tetrapod frontal bone -intersection_of: connects UBERON:0001677 ! sphenoid bone -relationship: connects UBERON:0000209 ! tetrapod frontal bone -relationship: connects UBERON:0001677 ! sphenoid bone -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray164.png" xsd:anyURI +intersection_of: RO:0002176 UBERON:0000209 ! connects tetrapod frontal bone +intersection_of: RO:0002176 UBERON:0001677 ! connects sphenoid bone +relationship: RO:0002176 UBERON:0000209 ! connects tetrapod frontal bone +relationship: RO:0002176 UBERON:0001677 ! connects sphenoid bone +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2d/Gray164.png" xsd:anyURI [Term] id: UBERON:0010160 @@ -239707,9 +236489,9 @@ synonym: "lymphatic vessel lumen" EXACT [FMA:59681] xref: FMA:59681 is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0001473 ! lymphatic vessel -relationship: luminal_space_of UBERON:0001473 ! lymphatic vessel +intersection_of: RO:0002572 UBERON:0001473 ! luminal space of lymphatic vessel relationship: part_of UBERON:0001473 ! lymphatic vessel +relationship: RO:0002572 UBERON:0001473 ! luminal space of lymphatic vessel [Term] id: UBERON:0010161 @@ -239721,9 +236503,9 @@ xref: FMA:312610 xref: SCTID:91747007 is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0001981 ! blood vessel -relationship: luminal_space_of UBERON:0001981 ! blood vessel +intersection_of: RO:0002572 UBERON:0001981 ! luminal space of blood vessel relationship: part_of UBERON:0001981 ! blood vessel +relationship: RO:0002572 UBERON:0001981 ! luminal space of blood vessel [Term] id: UBERON:0010162 @@ -239738,8 +236520,8 @@ xref: MA:0002848 xref: XAO:0004057 is_a: UBERON:0011676 ! subdivision of organism along main body axis intersection_of: UBERON:0011676 ! subdivision of organism along main body axis -intersection_of: distalmost_part_of UBERON:0007812 ! post-anal tail -relationship: distalmost_part_of UBERON:0007812 ! post-anal tail +intersection_of: BSPO:0001108 UBERON:0007812 ! post-anal tail +relationship: BSPO:0001108 UBERON:0007812 ! post-anal tail relationship: part_of UBERON:0007812 {source="MA"} ! post-anal tail [Term] @@ -239754,9 +236536,9 @@ synonym: "set of hairs" EXACT [FMA:70752] xref: FMA:70752 is_a: UBERON:0034925 ! anatomical collection intersection_of: UBERON:0034925 ! anatomical collection -intersection_of: has_member UBERON:0001037 ! strand of hair -relationship: has_member UBERON:0001037 ! strand of hair -relationship: has_quality PATO:0010001 ! disconnected +intersection_of: RO:0002351 UBERON:0001037 ! has member strand of hair +relationship: RO:0000086 PATO:0010001 ! has quality disconnected +relationship: RO:0002351 UBERON:0001037 ! has member strand of hair [Term] id: UBERON:0010165 @@ -239771,8 +236553,8 @@ xref: FMA:70741 is_a: UBERON:0014382 ! collection of hairs on head or neck intersection_of: UBERON:0010164 ! collection of hairs intersection_of: part_of UBERON:0001456 ! face -relationship: has_member UBERON:0010171 ! strand of hair of face relationship: part_of UBERON:0001456 ! face +relationship: RO:0002351 UBERON:0010171 ! has member strand of hair of face [Term] id: UBERON:0010171 @@ -239799,6 +236581,7 @@ def: "A trabecula that is part of a liver." [GO:0060344, OBOL:automatic] synonym: "hepatic trabecula" RELATED [] synonym: "liver trabeculae" EXACT OMO:0003004 [] is_a: UBERON:0000440 ! trabecula +is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0000440 ! trabecula intersection_of: part_of UBERON:0002107 ! liver relationship: part_of UBERON:0002107 ! liver @@ -239851,7 +236634,7 @@ xref: AEO:0000205 xref: EHDAA2:0003250 xref: FMA:82506 is_a: UBERON:0034944 {source="FMA"} ! zone of organ -property_value: editor_note "requires review" xsd:string +property_value: IAO:0000116 "requires review" xsd:string [Term] id: UBERON:0010189 @@ -239866,22 +236649,6 @@ is_a: UBERON:0005208 ! right atrium valve is_a: UBERON:0006675 ! venous valve intersection_of: UBERON:0006675 ! venous valve intersection_of: part_of UBERON:0002078 ! right cardiac atrium -property_value: UBPROP:0000012 "part_of in EHDAA2. Only child in MA." xsd:string {external_ontology="EHDAA2"} - -[Term] -id: UBERON:0010190 -name: pair of dorsal aortae -namespace: uberon -def: "The paired arterial structures of the embryo that supplies each developing somite via efferent segmental arteries; the dorsal aortae articulate with the umbilical arteries, which return mixed blood to the villi of the chorion for reoxygenation." [ISBN:0-914294-08-3, MP:0004787] -subset: pheno_slim -synonym: "paired dorsal aortae" EXACT [EHDAA2:0000410] -xref: EHDAA2:0000410 -xref: EMAPA:18606 -xref: MA:0000476 -is_a: PR:000050567 ! protein-containing material entity -is_a: UBERON:0000481 {source="EHDAA2"} ! multi-tissue structure -relationship: has_part UBERON:0005805 ! dorsal aorta -relationship: part_of UBERON:0010191 {source="EHDAA2"} ! aortic system [Term] id: UBERON:0010191 @@ -239889,8 +236656,8 @@ name: aortic system namespace: uberon xref: EHDAA2:0004512 is_a: UBERON:0011216 ! organ system subdivision -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0004571 {source="Wikipedia"} ! systemic arterial system +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata [Term] id: UBERON:0010192 @@ -239901,8 +236668,8 @@ synonym: "gonadal artery" EXACT [] xref: Wikipedia:Gonadal_artery is_a: UBERON:0012254 ! abdominal aorta artery intersection_of: UBERON:0004573 ! systemic artery -intersection_of: supplies UBERON:0000991 ! gonad -relationship: supplies UBERON:0000991 ! gonad +intersection_of: RO:0002178 UBERON:0000991 ! supplies gonad +relationship: RO:0002178 UBERON:0000991 ! supplies gonad [Term] id: UBERON:0010194 @@ -239913,9 +236680,8 @@ synonym: "hepatic-portal system" EXACT [AAO:0010225] synonym: "portal system of liver" EXACT [] xref: AAO:0010225 is_a: UBERON:0005806 ! portal system -relationship: connects UBERON:0001555 ! digestive tract -relationship: connects UBERON:0002107 ! liver -property_value: UBPROP:0000001 "Part of the circulatory system which includes the ventral abdominal vein, pelvic veins, and portal vein and collects blood from the pelvic region, liver, gall bladder and stomach.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010225", ontology="AAO", source="AAO:BJB"} +relationship: RO:0002176 UBERON:0001555 ! connects digestive tract +relationship: RO:0002176 UBERON:0002107 ! connects liver [Term] id: UBERON:0010199 @@ -239940,8 +236706,8 @@ xref: XAO:0004002 xref: ZFA:0001469 is_a: UBERON:0000479 {source="ZFA"} ! tissue is_a: UBERON:0004121 ! ectoderm-derived structure -relationship: develops_from UBERON:0009128 ! lateral line placode relationship: part_of UBERON:0002540 {source="ZFA"} ! lateral line system +relationship: RO:0002202 UBERON:0009128 ! develops from lateral line placode [Term] id: UBERON:0010204 @@ -239957,7 +236723,6 @@ is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: part_of UBERON:0007812 ! post-anal tail relationship: part_of UBERON:0007812 ! post-anal tail -property_value: UBPROP:0000012 "isa blood vessel in XAO" xsd:string {external_ontology="XAO"} [Term] id: UBERON:0010210 @@ -239976,12 +236741,12 @@ is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000463 ! organism substance intersection_of: UBERON:0000463 ! organism substance intersection_of: output_of GO:0007596 ! blood coagulation -relationship: develops_from UBERON:0000178 {source="BTO"} ! blood relationship: has_part CL:0000232 ! erythrocyte relationship: has_part CL:0000233 ! platelet relationship: has_part CL:0000738 ! leukocyte relationship: has_part GO:0005577 ! fibrinogen complex relationship: output_of GO:0007596 ! blood coagulation +relationship: RO:0002202 UBERON:0000178 {source="BTO"} ! develops from blood [Term] id: UBERON:0010212 @@ -239991,19 +236756,21 @@ def: "Apparatus located between the lungs and the buccal cavity. This apparatus synonym: "laryngeal cartilage system" EXACT [EHDAA2:0000904] xref: AAO:0000267 xref: EHDAA2:0000904 +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0034921 ! multi organ part structure -relationship: composed_primarily_of UBERON:0001739 ! laryngeal cartilage relationship: part_of UBERON:0001737 {source="EHDAA2"} ! larynx relationship: part_of UBERON:0008895 ! splanchnocranium -property_value: editor_note "check this. See also https://github.com/obophenotype/uberon/wiki/The-axial-skeleton" xsd:string +relationship: RO:0002473 UBERON:0001739 ! composed primarily of laryngeal cartilage +property_value: IAO:0000116 "check this. See also https://github.com/obophenotype/uberon/wiki/The-axial-skeleton" xsd:string [Term] id: UBERON:0010213 name: laryngeal pre-cartilage condensation namespace: uberon +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0005866 ! pre-cartilage condensation -relationship: develops_from UBERON:0010221 {source="EHDAA2-abstracted"} ! laryngeal associated mesenchyme relationship: part_of UBERON:0010212 {source="EHDAA2-abstracted"} ! laryngeal apparatus +relationship: RO:0002202 UBERON:0010221 {source="EHDAA2-abstracted"} ! develops from laryngeal associated mesenchyme [Term] id: UBERON:0010221 @@ -240011,12 +236778,13 @@ name: laryngeal associated mesenchyme namespace: uberon comment: Many sources say: thyroid cartilage from arch 4 other laryngeal cartilage (cricoid/arytenoid) from 6? xref: EHDAA2:0004085 +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue -relationship: develops_from UBERON:0002539 {source="Wikipedia"} ! pharyngeal arch -relationship: has_developmental_contribution_from UBERON:0003115 {source="Wikipedia"} ! pharyngeal arch 4 -relationship: has_developmental_contribution_from UBERON:0003117 {source="Wikipedia"} ! pharyngeal arch 6 relationship: part_of UBERON:0001737 {source="EHDAA2"} ! larynx relationship: part_of UBERON:0008895 ! splanchnocranium +relationship: RO:0002202 UBERON:0002539 {source="Wikipedia"} ! develops from pharyngeal arch +relationship: RO:0002254 UBERON:0003115 {source="Wikipedia"} ! has developmental contribution from pharyngeal arch 4 +relationship: RO:0002254 UBERON:0003117 {source="Wikipedia"} ! has developmental contribution from pharyngeal arch 6 [Term] id: UBERON:0010225 @@ -240040,8 +236808,8 @@ xref: FMA:71005 xref: TAO:0002228 xref: ZFA:0001718 is_a: UBERON:0006598 ! presumptive structure -relationship: has_potential_to_develop_into UBERON:0002081 ! cardiac atrium relationship: part_of UBERON:0004141 {source="ZFA"} ! heart tube +relationship: RO:0002387 UBERON:0002081 ! has potential to develop into cardiac atrium [Term] id: UBERON:0010230 @@ -240060,10 +236828,9 @@ xref: SCTID:244486005 xref: VHOG:0001616 xref: Wikipedia:Globe_(human_eye) is_a: UBERON:0000020 ! sense organ -relationship: contributes_to_morphology_of UBERON:0000019 ! camera-type eye +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0000019 {source="FMA"} ! camera-type eye -property_value: IAO:0000232 "See notes for camera-type eye" xsd:string -property_value: UBPROP:0000202 FMA:264089 +relationship: RO:0002433 UBERON:0000019 ! contributes to morphology of camera-type eye [Term] id: UBERON:0010233 @@ -240075,6 +236842,7 @@ synonym: "thyroid stroma" EXACT [] xref: FMA:86304 xref: SCTID:157862000 is_a: UBERON:0003891 ! stroma +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0003891 ! stroma intersection_of: part_of UBERON:0002046 ! thyroid gland @@ -240093,7 +236861,6 @@ is_a: UBERON:0002365 ! exocrine gland intersection_of: UBERON:0002365 ! exocrine gland intersection_of: capable_of GO:0006887 ! exocytosis relationship: capable_of GO:0006887 ! exocytosis -property_value: UBPROP:0000007 "merocrine" xsd:string [Term] id: UBERON:0010252 @@ -240104,11 +236871,11 @@ xref: EHDAA2:0000037 is_a: UBERON:0009584 ! 1st arch mandibular mesenchyme is_a: UBERON:0010259 {source="inferred"} ! 1st arch mesenchyme from neural crest intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: develops_from UBERON:0002342 ! neural crest intersection_of: part_of UBERON:0009584 ! 1st arch mandibular mesenchyme -relationship: develops_from UBERON:0007098 ! mandibular neural crest +intersection_of: RO:0002202 UBERON:0002342 ! develops from neural crest relationship: part_of UBERON:0009584 {source="EHDAA2"} ! 1st arch mandibular mesenchyme relationship: part_of UBERON:0010258 {source="EHDAA2"} ! mesenchyme from rhombencephalic neural crest +relationship: RO:0002202 UBERON:0007098 ! develops from mandibular neural crest [Term] id: UBERON:0010253 @@ -240119,8 +236886,8 @@ xref: EHDAA2:0000044 is_a: UBERON:0010045 ! 1st arch maxillary mesenchyme is_a: UBERON:0010259 ! 1st arch mesenchyme from neural crest intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: develops_from UBERON:0002342 ! neural crest intersection_of: part_of UBERON:0010045 ! 1st arch maxillary mesenchyme +intersection_of: RO:0002202 UBERON:0002342 ! develops from neural crest relationship: part_of UBERON:0010045 {source="EHDAA2"} ! 1st arch maxillary mesenchyme relationship: part_of UBERON:0010258 {source="EHDAA2"} ! mesenchyme from rhombencephalic neural crest @@ -240135,14 +236902,14 @@ synonym: "pharyngeal arch 2 mesenchyme from neural crest" EXACT [] xref: EHDAA2:0000068 xref: EMAPA:16281 is_a: UBERON:0005689 ! 2nd arch mesenchyme -is_a: UBERON:0007213 ! mesenchyme derived from head neural crest +is_a: UBERON:0010258 ! mesenchyme from rhombencephalic neural crest is_a: UBERON:0010359 ! pharyngeal arch mesenchyme from neural crest intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: develops_from UBERON:0002342 ! neural crest intersection_of: part_of UBERON:0005689 ! 2nd arch mesenchyme -relationship: develops_from UBERON:0007099 ! hyoid neural crest +intersection_of: RO:0002202 UBERON:0002342 ! develops from neural crest relationship: part_of UBERON:0005689 {source="EHDAA2"} ! 2nd arch mesenchyme relationship: part_of UBERON:0010258 {source="EHDAA2"} ! mesenchyme from rhombencephalic neural crest +relationship: RO:0002202 UBERON:0007099 ! develops from hyoid neural crest [Term] id: UBERON:0010255 @@ -240161,10 +236928,9 @@ is_a: UBERON:0005690 ! 3rd arch mesenchyme is_a: UBERON:0010258 ! mesenchyme from rhombencephalic neural crest is_a: UBERON:0010359 ! pharyngeal arch mesenchyme from neural crest intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: develops_from UBERON:0002342 ! neural crest intersection_of: part_of UBERON:0005690 ! 3rd arch mesenchyme +intersection_of: RO:0002202 UBERON:0002342 ! develops from neural crest relationship: part_of UBERON:0005690 {source="EHDAA2"} ! 3rd arch mesenchyme -property_value: UBPROP:0000003 "In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000571", ontology="VHOG", source="DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0010256 @@ -240183,11 +236949,10 @@ is_a: UBERON:0005691 ! 4th arch mesenchyme is_a: UBERON:0010258 ! mesenchyme from rhombencephalic neural crest is_a: UBERON:0010359 ! pharyngeal arch mesenchyme from neural crest intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: develops_from UBERON:0002342 ! neural crest intersection_of: part_of UBERON:0005691 ! 4th arch mesenchyme +intersection_of: RO:0002202 UBERON:0002342 ! develops from neural crest relationship: part_of UBERON:0005691 {source="EHDAA2"} ! 4th arch mesenchyme relationship: part_of UBERON:0010258 {source="EHDAA2"} ! mesenchyme from rhombencephalic neural crest -property_value: UBPROP:0000003 "In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000580", ontology="VHOG", source="DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0010257 @@ -240202,8 +236967,8 @@ is_a: UBERON:0010031 ! 6th arch mesenchyme is_a: UBERON:0010258 ! mesenchyme from rhombencephalic neural crest is_a: UBERON:0010359 ! pharyngeal arch mesenchyme from neural crest intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: develops_from UBERON:0002342 ! neural crest intersection_of: part_of UBERON:0010031 ! 6th arch mesenchyme +intersection_of: RO:0002202 UBERON:0002342 ! develops from neural crest relationship: part_of UBERON:0010031 {source="EHDAA2"} ! 6th arch mesenchyme relationship: part_of UBERON:0010258 {source="EHDAA2"} ! mesenchyme from rhombencephalic neural crest @@ -240214,11 +236979,10 @@ namespace: uberon def: "Mesenchyme that develops_from a rhombencephalon neural crest." [OBOL:automatic] xref: EHDAA2:0004423 is_a: UBERON:0007213 ! mesenchyme derived from head neural crest -is_a: UBERON:0014387 ! mesenchyme derived from neural crest intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: develops_from UBERON:0003852 ! rhombencephalon neural crest -relationship: develops_from UBERON:0003852 ! rhombencephalon neural crest +intersection_of: RO:0002202 UBERON:0003852 ! develops from rhombencephalon neural crest relationship: part_of UBERON:0007213 {source="EHDAA2"} ! mesenchyme derived from head neural crest +relationship: RO:0002202 UBERON:0003852 ! develops from rhombencephalon neural crest [Term] id: UBERON:0010259 @@ -240234,8 +236998,8 @@ is_a: UBERON:0010042 ! 1st arch mesenchyme is_a: UBERON:0010258 ! mesenchyme from rhombencephalic neural crest is_a: UBERON:0010359 ! pharyngeal arch mesenchyme from neural crest intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: develops_from UBERON:0002342 ! neural crest intersection_of: part_of UBERON:0010042 ! 1st arch mesenchyme +intersection_of: RO:0002202 UBERON:0002342 ! develops from neural crest relationship: part_of UBERON:0010042 ! 1st arch mesenchyme [Term] @@ -240254,8 +237018,8 @@ xref: SCTID:408728001 is_a: UBERON:0001981 ! blood vessel intersection_of: UBERON:0001981 ! blood vessel intersection_of: overlaps UBERON:0002331 ! umbilical cord -relationship: located_in UBERON:0003422 ! mesenchyme of umbilical cord relationship: overlaps UBERON:0002331 ! umbilical cord +relationship: RO:0001025 UBERON:0003422 ! located in mesenchyme of umbilical cord [Term] id: UBERON:0010272 @@ -240274,9 +237038,6 @@ xref: MA:0003037 xref: SCTID:410035009 is_a: UBERON:0000075 ! subdivision of skeletal system relationship: part_of UBERON:0005884 {source="AAO"} ! hyoid arch skeleton -property_value: UBPROP:0000001 "Apparatus located in the floor of the mouth, under the mandibular arcade. The apparatus consists of a central corpus and four pairs of processes. This apparatus serves as the site of insertion for a variety of muscles associated with movements of the tongue and as the origin of the m. hyoglossus.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000225", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000002 "relationship loss: part_of hyolaryngeal complex (AAO:0000226)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000225", ontology="AAO"} -property_value: UBPROP:0000008 "In most mammals, including humans, the hyoid apparatus is shaped like a horseshoe. However, in humans, some of the bones of the hyoid apparatus are fused into a single bone called os hyoideum. In other animals such as frogs, the hyoid apparatus has a hyoid body that is chiefly comprised of hyaline cartilage and two pairs of processes (i.e. alary process and the posteriolateral process)." xsd:string [Term] id: UBERON:0010273 @@ -240317,9 +237078,9 @@ xref: FMA:59365 xref: SCTID:263344003 xref: Wikipedia:Lacrimal_punctum is_a: UBERON:0000161 {source="FMA"} ! orifice +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001850 ! lacrimal drainage system -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/53/Gray895.png" xsd:anyURI -property_value: UBPROP:0000009 "collect tears produced by the lacrimal glands" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/53/Gray895.png" xsd:anyURI [Term] id: UBERON:0010285 @@ -240345,9 +237106,10 @@ namespace: uberon def: "Portion of neural tube that gives rise to the midbrain." [ZFA:0007039] xref: TAO:0007039 xref: ZFA:0007039 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue relationship: part_of UBERON:0003080 {source="ZFA"} ! anterior neural tube -property_value: editor_note "we follow ZFA in temporally dividing midbrain NT from presumptive midbrain, but in future this may be collapsed" xsd:string +property_value: IAO:0000116 "we follow ZFA in temporally dividing midbrain NT from presumptive midbrain, but in future this may be collapsed" xsd:string [Term] id: UBERON:0010291 @@ -240355,6 +237117,7 @@ name: layer of sclera namespace: uberon xref: Wikipedia:Sclera#Histology is_a: UBERON:0004923 ! organ component layer +is_a: UBERON:0010313 ! neural crest-derived structure relationship: part_of UBERON:0001773 {source="cjm"} ! sclera [Term] @@ -240394,10 +237157,9 @@ namespace: uberon def: "Mesenchyme surrounding the developing optic cup which develops into the sclera." [https://orcid.org/0000-0002-6601-2165, PMID:16496288] is_a: UBERON:0003104 ! mesenchyme intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: has_potential_to_develop_into UBERON:0001773 ! sclera -relationship: has_potential_to_develop_into UBERON:0001773 ! sclera -relationship: surrounds UBERON:0003072 ! optic cup -property_value: UBPROP:0000011 "The mesenchyme surrounding the developing optic cup differentiates into the sclera, the dense fibrous coat of the eye.. http://www.ncbi.nlm.nih.gov/pubmed/16496288" xsd:string +intersection_of: RO:0002387 UBERON:0001773 ! has potential to develop into sclera +relationship: RO:0002221 UBERON:0003072 ! surrounds optic cup +relationship: RO:0002387 UBERON:0001773 ! has potential to develop into sclera [Term] id: UBERON:0010302 @@ -240408,10 +237170,9 @@ subset: efo_slim synonym: "amnion-serosa" RELATED [BTO:0004800] xref: BTO:0004800 xref: EFO:0000250 -xref: FBbt:00000095 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0010303 {source="DOI:10.1073/pnas.0709145105"} ! extraembryonic epithelium -relationship: only_in_taxon NCBITaxon:6656 {notes="Cyclorrhapha", source="DOI:10.1073/pnas.0709145105"} ! Arthropoda -property_value: editor_note "May be obsoleted once added to insect ontology. Coordinate with cell type in CL" xsd:string +relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda +property_value: IAO:0000116 "May be obsoleted once added to insect ontology. Coordinate with cell type in CL" xsd:string [Term] id: UBERON:0010303 @@ -240451,6 +237212,7 @@ xref: FMA:59023 xref: SCTID:29445007 xref: Wikipedia:Conjunctiva#Gross_anatomy is_a: UBERON:0000064 ! organ part +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000064 ! organ part intersection_of: subdivision_of UBERON:0001811 ! conjunctiva relationship: part_of UBERON:0001811 ! conjunctiva @@ -240466,10 +237228,9 @@ xref: TAO:0002201 xref: ZFA:0001678 is_a: UBERON:0005423 ! developing anatomical structure intersection_of: UBERON:0005423 ! developing anatomical structure -intersection_of: has_developmental_contribution_from UBERON:0003071 ! eye primordium -relationship: develops_from UBERON:0003071 {evidence="definitional"} ! eye primordium -relationship: has_developmental_contribution_from UBERON:0003071 ! eye primordium -property_value: UBPROP:0000001 "Multi-tissue structure that consists of the structures that develop into the retina and lens.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002201", ontology="TAO", source="ZFIN:curator"} +intersection_of: RO:0002254 UBERON:0003071 ! has developmental contribution from eye primordium +relationship: RO:0002202 UBERON:0003071 ! develops from eye primordium +relationship: RO:0002254 UBERON:0003071 ! has developmental contribution from eye primordium [Term] id: UBERON:0010313 @@ -240480,9 +237241,8 @@ subset: grouping_class is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: develops_from UBERON:0002342 ! neural crest -relationship: develops_from UBERON:0002342 ! neural crest -property_value: IAO:0000232 "Grouping term for query purposes" xsd:string +intersection_of: RO:0002202 UBERON:0002342 ! develops from neural crest +relationship: RO:0002202 UBERON:0002342 ! develops from neural crest [Term] id: UBERON:0010314 @@ -240492,9 +237252,8 @@ def: "An anatomical structure that has some part that develops from the neural c subset: grouping_class is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: has_developmental_contribution_from UBERON:0002342 ! neural crest -relationship: has_developmental_contribution_from UBERON:0002342 ! neural crest -property_value: IAO:0000232 "Grouping term for query purposes" xsd:string +intersection_of: RO:0002254 UBERON:0002342 ! has developmental contribution from neural crest +relationship: RO:0002254 UBERON:0002342 ! has developmental contribution from neural crest [Term] id: UBERON:0010316 @@ -240502,7 +237261,7 @@ name: germ layer / neural crest namespace: uberon is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0005291 ! embryonic tissue -relationship: develops_from UBERON:0002532 ! epiblast (generic) +relationship: RO:0002202 UBERON:0002532 ! develops from epiblast (generic) [Term] id: UBERON:0010321 @@ -240535,12 +237294,9 @@ xref: VSAO:0000049 xref: XAO:0003075 xref: ZFA:0000737 is_a: UBERON:0000075 ! subdivision of skeletal system -relationship: only_in_taxon NCBITaxon:89593 ! Craniata relationship: part_of UBERON:0011137 ! axial skeletal system -property_value: editor_note "we use 'cranial skeletal system', so that we can include the skull, which has joints/sutures as parts (recall, we follow FMA in distinguishing between the skeleton and skeletal system - only the latter includes joints)" xsd:string -property_value: IAO:0000232 "that the cranial skeleton includes the pharyngeal arch skeleton. It is thus more inclusive that the cranium itself, and extends beyond the head in tetrapods. The AAO class called 'skull' belongs here, as it includes the whole splanchnocranium" xsd:string -property_value: UBPROP:0000001 "Bony structure that encases the central nervous system and the primary sense organs of sight, olfaction, hearing, and equilibrium.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000109", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000001 "Skeletal system which is part of the skull, including the splanchnocranium, chondrocranium, and dermatocranium.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000737", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata +property_value: IAO:0000116 "we use 'cranial skeletal system', so that we can include the skull, which has joints/sutures as parts (recall, we follow FMA in distinguishing between the skeleton and skeletal system - only the latter includes joints)" xsd:string [Term] id: UBERON:0010328 @@ -240560,8 +237316,8 @@ def: "Mesenchyme that is part of a limb/fin bud." [OBOL:automatic] is_a: UBERON:0010377 ! mesenchyme from somatopleure intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0004357 ! paired limb/fin bud -relationship: develops_from UBERON:0010377 {source="EHDAA2-abduced"} ! mesenchyme from somatopleure relationship: part_of UBERON:0004357 ! paired limb/fin bud +relationship: RO:0002202 UBERON:0010377 {source="EHDAA2-abduced"} ! develops from mesenchyme from somatopleure [Term] id: UBERON:0010330 @@ -240584,10 +237340,11 @@ xref: EHDAA2:0000730 xref: EMAPA:32630 is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0006875 ! embryonic handplate -relationship: develops_from UBERON:0003372 {source="EHDAA2"} ! pectoral appendage bud ectoderm relationship: part_of UBERON:0006875 ! embryonic handplate +relationship: RO:0002202 UBERON:0003372 {source="EHDAA2"} ! develops from pectoral appendage bud ectoderm [Term] id: UBERON:0010333 @@ -240599,8 +237356,8 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005292 ! extraembryonic tissue intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0005631 ! extraembryonic membrane -relationship: develops_from UBERON:0005728 {source="EHDAA2-abduced"} ! extraembryonic mesoderm relationship: part_of UBERON:0005631 ! extraembryonic membrane +relationship: RO:0002202 UBERON:0005728 {source="EHDAA2-abduced"} ! develops from extraembryonic mesoderm [Term] id: UBERON:0010334 @@ -240611,10 +237368,10 @@ xref: EHDAA2:0004601 is_a: UBERON:0009526 ! maxillary process mesenchyme is_a: UBERON:0010258 ! mesenchyme from rhombencephalic neural crest intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: develops_from UBERON:0002342 ! neural crest intersection_of: part_of UBERON:0009526 ! maxillary process mesenchyme -relationship: develops_from UBERON:0010253 {source="EHDAA2"} ! 1st arch maxillary mesenchyme from neural crest +intersection_of: RO:0002202 UBERON:0002342 ! develops from neural crest relationship: part_of UBERON:0009526 {source="EHDAA2"} ! maxillary process mesenchyme +relationship: RO:0002202 UBERON:0010253 {source="EHDAA2"} ! develops from 1st arch maxillary mesenchyme from neural crest [Term] id: UBERON:0010335 @@ -240625,10 +237382,10 @@ xref: EHDAA2:0004602 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0009526 ! maxillary process mesenchyme intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: develops_from UBERON:0006904 ! head mesenchyme from mesoderm intersection_of: part_of UBERON:0009526 ! maxillary process mesenchyme -relationship: develops_from UBERON:0010338 {source="EHDAA2"} ! 1st arch maxillary mesenchyme from head mesenchyme +intersection_of: RO:0002202 UBERON:0006904 ! develops from head mesenchyme from mesoderm relationship: part_of UBERON:0009526 {source="EHDAA2"} ! maxillary process mesenchyme +relationship: RO:0002202 UBERON:0010338 {source="EHDAA2"} ! develops from 1st arch maxillary mesenchyme from head mesenchyme [Term] id: UBERON:0010336 @@ -240639,10 +237396,10 @@ xref: EHDAA2:0004603 is_a: UBERON:0006905 ! mandibular process mesenchyme is_a: UBERON:0010258 ! mesenchyme from rhombencephalic neural crest intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: develops_from UBERON:0002342 ! neural crest intersection_of: part_of UBERON:0006905 ! mandibular process mesenchyme -relationship: develops_from UBERON:0010252 {source="EHDAA2"} ! 1st arch mandibular mesenchyme from neural crest +intersection_of: RO:0002202 UBERON:0002342 ! develops from neural crest relationship: part_of UBERON:0006905 {source="EHDAA2"} ! mandibular process mesenchyme +relationship: RO:0002202 UBERON:0010252 {source="EHDAA2"} ! develops from 1st arch mandibular mesenchyme from neural crest [Term] id: UBERON:0010337 @@ -240653,10 +237410,10 @@ xref: EHDAA2:0004604 is_a: UBERON:0006904 ! head mesenchyme from mesoderm is_a: UBERON:0006905 ! mandibular process mesenchyme intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: develops_from UBERON:0006904 ! head mesenchyme from mesoderm intersection_of: part_of UBERON:0006905 ! mandibular process mesenchyme -relationship: develops_from UBERON:0010339 {source="EHDAA2"} ! 1st arch mandibular mesenchyme from head mesenchyme +intersection_of: RO:0002202 UBERON:0006904 ! develops from head mesenchyme from mesoderm relationship: part_of UBERON:0006905 {source="EHDAA2"} ! mandibular process mesenchyme +relationship: RO:0002202 UBERON:0010339 {source="EHDAA2"} ! develops from 1st arch mandibular mesenchyme from head mesenchyme [Term] id: UBERON:0010338 @@ -240667,8 +237424,8 @@ xref: EHDAA2:0000043 is_a: UBERON:0010045 ! 1st arch maxillary mesenchyme is_a: UBERON:0010341 ! 1st arch mesenchyme from head mesenchyme intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: develops_from UBERON:0006904 ! head mesenchyme from mesoderm intersection_of: part_of UBERON:0010045 ! 1st arch maxillary mesenchyme +intersection_of: RO:0002202 UBERON:0006904 ! develops from head mesenchyme from mesoderm relationship: part_of UBERON:0010045 {source="EHDAA2"} ! 1st arch maxillary mesenchyme [Term] @@ -240680,8 +237437,8 @@ xref: EHDAA2:0000036 is_a: UBERON:0009584 ! 1st arch mandibular mesenchyme is_a: UBERON:0010341 ! 1st arch mesenchyme from head mesenchyme intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: develops_from UBERON:0006904 ! head mesenchyme from mesoderm intersection_of: part_of UBERON:0009584 ! 1st arch mandibular mesenchyme +intersection_of: RO:0002202 UBERON:0006904 ! develops from head mesenchyme from mesoderm relationship: part_of UBERON:0009584 {source="EHDAA2"} ! 1st arch mandibular mesenchyme [Term] @@ -240695,8 +237452,8 @@ is_a: UBERON:0006904 ! head mesenchyme from mesoderm is_a: UBERON:0010042 ! 1st arch mesenchyme is_a: UBERON:0010360 ! pharyngeal arch mesenchyme from head mesenchyme intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: develops_from UBERON:0006904 ! head mesenchyme from mesoderm intersection_of: part_of UBERON:0010042 ! 1st arch mesenchyme +intersection_of: RO:0002202 UBERON:0006904 ! develops from head mesenchyme from mesoderm relationship: part_of UBERON:0010042 {source="EMAPA"} ! 1st arch mesenchyme [Term] @@ -240714,8 +237471,8 @@ is_a: UBERON:0005689 ! 2nd arch mesenchyme is_a: UBERON:0006904 ! head mesenchyme from mesoderm is_a: UBERON:0010360 ! pharyngeal arch mesenchyme from head mesenchyme intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: develops_from UBERON:0006904 ! head mesenchyme from mesoderm intersection_of: part_of UBERON:0005689 ! 2nd arch mesenchyme +intersection_of: RO:0002202 UBERON:0006904 ! develops from head mesenchyme from mesoderm relationship: part_of UBERON:0005689 {source="EHDAA2"} ! 2nd arch mesenchyme [Term] @@ -240733,8 +237490,8 @@ is_a: UBERON:0005690 ! 3rd arch mesenchyme is_a: UBERON:0006904 ! head mesenchyme from mesoderm is_a: UBERON:0010360 ! pharyngeal arch mesenchyme from head mesenchyme intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: develops_from UBERON:0006904 ! head mesenchyme from mesoderm intersection_of: part_of UBERON:0005690 ! 3rd arch mesenchyme +intersection_of: RO:0002202 UBERON:0006904 ! develops from head mesenchyme from mesoderm relationship: part_of UBERON:0005690 {source="EHDAA2"} ! 3rd arch mesenchyme [Term] @@ -240752,8 +237509,8 @@ is_a: UBERON:0005691 ! 4th arch mesenchyme is_a: UBERON:0006904 ! head mesenchyme from mesoderm is_a: UBERON:0010360 ! pharyngeal arch mesenchyme from head mesenchyme intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: develops_from UBERON:0006904 ! head mesenchyme from mesoderm intersection_of: part_of UBERON:0005691 ! 4th arch mesenchyme +intersection_of: RO:0002202 UBERON:0006904 ! develops from head mesenchyme from mesoderm relationship: part_of UBERON:0005691 {source="EHDAA2"} ! 4th arch mesenchyme [Term] @@ -240769,8 +237526,8 @@ is_a: UBERON:0006904 ! head mesenchyme from mesoderm is_a: UBERON:0010031 ! 6th arch mesenchyme is_a: UBERON:0010360 ! pharyngeal arch mesenchyme from head mesenchyme intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: develops_from UBERON:0006904 ! head mesenchyme from mesoderm intersection_of: part_of UBERON:0010031 ! 6th arch mesenchyme +intersection_of: RO:0002202 UBERON:0006904 ! develops from head mesenchyme from mesoderm relationship: part_of UBERON:0010031 {source="EHDAA2"} ! 6th arch mesenchyme [Term] @@ -240782,8 +237539,8 @@ synonym: "otic capsule anlage" EXACT [] xref: EHDAA2:0000833 is_a: UBERON:0004637 ! otic capsule intersection_of: UBERON:0004637 ! otic capsule -intersection_of: composed_primarily_of UBERON:0005866 ! pre-cartilage condensation -relationship: composed_primarily_of UBERON:0005866 ! pre-cartilage condensation +intersection_of: RO:0002473 UBERON:0005866 ! composed primarily of pre-cartilage condensation +relationship: RO:0002473 UBERON:0005866 ! composed primarily of pre-cartilage condensation [Term] id: UBERON:0010355 @@ -240798,8 +237555,8 @@ synonym: "ossification centre" EXACT [FMA:75436] xref: FMA:75436 xref: Wikipedia:Ossification_center is_a: UBERON:0005913 {source="FMA"} ! zone of bone organ -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/fd/Gray79.png" xsd:anyURI -property_value: editor_note "currently classified as a zone of a bone organ, but exists prior to bone ossifying" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/fd/Gray79.png" xsd:anyURI +property_value: IAO:0000116 "currently classified as a zone of a bone organ, but exists prior to bone ossifying" xsd:string [Term] id: UBERON:0010358 @@ -240812,11 +237569,8 @@ synonym: "arcus vertebrae (vertebralis)" NARROW [FMA:11946] synonym: "vertebra arch" NARROW [MA:0001453] synonym: "vertebral arch" NARROW [FMA:11946] xref: EMAPA:36614 -xref: FMA:11946 is_a: UBERON:0004765 ! skeletal element relationship: part_of UBERON:0002412 {source="FMA"} ! vertebra -property_value: UBPROP:0000003 "(...) certain common components [of vertebral structure] are found in nearly all vertebrate. A representative vertebra has a vertebral arch or neural arch, which extends dorsally around the spinal cord.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001670", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.270", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "Note that humans do not have hemal arches, so VA=NA for FMA" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0010359 @@ -240830,8 +237584,8 @@ synonym: "neural crest derived arch mesenchyme" EXACT [] is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0014387 ! mesenchyme derived from neural crest intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: develops_from UBERON:0002342 ! neural crest intersection_of: part_of UBERON:0010046 ! entire pharyngeal arch associated mesenchyme +intersection_of: RO:0002202 UBERON:0002342 ! develops from neural crest relationship: part_of UBERON:0010046 ! entire pharyngeal arch associated mesenchyme [Term] @@ -240847,10 +237601,10 @@ is_a: UBERON:0003104 ! mesenchyme is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: develops_from UBERON:0006904 ! head mesenchyme from mesoderm intersection_of: part_of UBERON:0010046 ! entire pharyngeal arch associated mesenchyme -relationship: develops_from UBERON:0006904 ! head mesenchyme from mesoderm +intersection_of: RO:0002202 UBERON:0006904 ! develops from head mesenchyme from mesoderm relationship: part_of UBERON:0010046 ! entire pharyngeal arch associated mesenchyme +relationship: RO:0002202 UBERON:0006904 ! develops from head mesenchyme from mesoderm [Term] id: UBERON:0010362 @@ -240862,9 +237616,8 @@ xref: VSAO:0000037 xref: Wikipedia:Endoskeleton xref: XAO:0004026 is_a: UBERON:0010912 {source="VSAO"} ! subdivision of skeleton -relationship: composed_primarily_of UBERON:0010522 ! replacement element -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata -property_value: UBPROP:0000001 "An endoskeleton is an internal support structure of an animal, composed of mineralized tissue. Endoskeleton develops within the skin or in the deeper body tissues. The vertebrate is basically an endoskeleton made up of two types of tissues (bone and cartilage). During early embryonic development the endoskeleton is composed of notochord and cartilage. The notochord in most vertebrates is replaced by vertebral column and cartilage is replaced by bone in most adults. In three phyla and one subclass of animals, endoskeletons of various complexity are found: Chordata, Echinodermata, Porifera, and Coleoidea. An endoskeleton may function purely for support (as in the case of sponges), but often serves as an attachment site for muscle and a mechanism for transmitting muscular forces. A true endoskeleton is derived from mesodermal tissue. Such a skeleton is present in echinoderms and chordates. The poriferan 'skeleton' consists of microscopic calcareous or siliceous spicules or a spongin network. The Coleoidae do not have a true endoskeleton in the evolutionary sense; here, a mollusk exoskeleton evolved into several sorts of internal structure, the 'cuttlebone' of cuttlefish being the best-known version. Yet they do have cartilaginous tissue in their body, even if it is not mineralized, especially in the head, where it forms a primitive cranium. The endoskeleton gives shape,support and protection to the body and provides a mean of locomotion.[Wikipedia:Endoskeleton]t" xsd:string {source="Wikipedia:Endoskeleton"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002473 UBERON:0010522 ! composed primarily of replacement element [Term] id: UBERON:0010363 @@ -240891,7 +237644,7 @@ synonym: "exoskeleton" BROAD INCONSISTENT [VSAO:curator] xref: VSAO:0000035 xref: XAO:0004025 is_a: UBERON:0010912 {source="VSAO"} ! subdivision of skeleton -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata [Term] id: UBERON:0010365 @@ -240916,15 +237669,14 @@ xref: VSAO:0000063 xref: XAO:0004046 xref: ZFA:0005623 is_a: UBERON:0004755 ! skeletal tissue +is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0004755 ! skeletal tissue -intersection_of: develops_from UBERON:0001763 ! odontogenic papilla intersection_of: part_of UBERON:0010364 ! dermal skeleton -relationship: contributes_to_morphology_of UBERON:0001091 ! calcareous tooth -relationship: develops_from UBERON:0001763 ! odontogenic papilla +intersection_of: RO:0002202 UBERON:0001763 ! develops from odontogenic papilla relationship: part_of UBERON:0001091 {gci_relation="part_of", gci_filler="NCBITaxon:32524"} ! calcareous tooth relationship: part_of UBERON:0010364 ! dermal skeleton -property_value: UBPROP:0000008 "in many vertebrates, odontoid tissue is not restricted to the teeth" xsd:string -property_value: UBPROP:0000012 "Classified as a portion of organism substance in FMA" xsd:string {external_ontology="FMA"} +relationship: RO:0002202 UBERON:0001763 ! develops from odontogenic papilla +relationship: RO:0002433 UBERON:0001091 ! contributes to morphology of calcareous tooth [Term] id: UBERON:0010366 @@ -240947,10 +237699,10 @@ name: conjunctival vein namespace: uberon def: "A vein that is part of a conjunctiva." [OBOL:automatic] synonym: "conjunctival blood vessel" BROAD [] -xref: FMA:70887 xref: SCTID:149885003 is_a: UBERON:0003496 ! head blood vessel is_a: UBERON:0009141 ! craniocervical region vein +is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0001638 ! vein intersection_of: part_of UBERON:0001811 ! conjunctiva relationship: part_of UBERON:0010366 ! conjunctival vasculature @@ -240963,6 +237715,7 @@ def: "The smallest anatomical unit of the lung, measuring 0.50 to 2.00 cm in dia synonym: "lobulus pulmonis" EXACT OMO:0003011 [FMA:75739, FMA:TA] xref: FMA:75739 xref: NCIT:C33428 +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0009911 ! lobule intersection_of: UBERON:0009911 ! lobule intersection_of: part_of UBERON:0002048 ! lung @@ -240978,10 +237731,9 @@ synonym: "lobulus pulmonis secondarius" EXACT OMO:0003011 [FMA:7414, FMA:TA] synonym: "respiratory lobule" RELATED [PMID:18403324] xref: FMA:7414 is_a: UBERON:0010368 {source="FMA"} ! pulmonary lobule -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: part_of UBERON:0008946 {source="FMA"} ! lung parenchyma -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000001 "a pyramidal mass of lung tissue with sides that are bounded by the incomplete interlobular connective tissue septa and with a base, which is 1-2 cm in diameter, which usually faces the pleural surface of the lung; lobules that occupy a more central position in the lung are not well defined and are considered to consist of three to five pulmonary acini with proximate terminal bronchioles." xsd:string {source="http://medical-dictionary.thefreedictionary.com/secondary+pulmonary+lobule"} +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0010370 @@ -241006,8 +237758,8 @@ xref: FMA:69064 is_a: UBERON:0000483 ! epithelium is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000483 ! epithelium -intersection_of: develops_from UBERON:0000924 ! ectoderm -relationship: composed_primarily_of CL:0002077 ! ecto-epithelial cell +intersection_of: RO:0002202 UBERON:0000924 ! develops from ectoderm +relationship: RO:0002473 CL:0002077 ! composed primarily of ecto-epithelial cell [Term] id: UBERON:0010375 @@ -241019,10 +237771,10 @@ xref: FMA:79793 is_a: UBERON:0001048 ! primordium is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0001048 ! primordium -intersection_of: has_potential_to_develop_into UBERON:0009708 ! dorsal pancreas -relationship: has_potential_to_develop_into UBERON:0009708 ! dorsal pancreas +intersection_of: RO:0002387 UBERON:0009708 ! has potential to develop into dorsal pancreas relationship: part_of UBERON:0003921 {source="EHDAA2"} ! pancreas primordium -property_value: editor_note "consider merging with dorsal pancreatic bud. Starts at CS12 in human (EHDAA2, embryology.ch 'bud anlagen')" xsd:string +relationship: RO:0002387 UBERON:0009708 ! has potential to develop into dorsal pancreas +property_value: IAO:0000116 "consider merging with dorsal pancreatic bud. Starts at CS12 in human (EHDAA2, embryology.ch 'bud anlagen')" xsd:string [Term] id: UBERON:0010376 @@ -241034,10 +237786,9 @@ xref: FMA:79794 is_a: UBERON:0001048 ! primordium is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0001048 ! primordium -intersection_of: has_potential_to_develop_into UBERON:0009709 ! ventral pancreas -relationship: has_potential_to_develop_into UBERON:0009709 ! ventral pancreas +intersection_of: RO:0002387 UBERON:0009709 ! has potential to develop into ventral pancreas relationship: part_of UBERON:0003921 {source="EHDAA2"} ! pancreas primordium -property_value: UBPROP:0000008 "Starts at CS14 in human (EHDAA2) or CS13-14 (embryology.ch 'bud anlagen')" xsd:string +relationship: RO:0002387 UBERON:0009709 ! has potential to develop into ventral pancreas [Term] id: UBERON:0010377 @@ -241045,14 +237796,15 @@ name: mesenchyme from somatopleure namespace: uberon def: "Mesenchyme that develops_from a somatopleure." [OBOL:automatic] xref: EHDAA2:0001120 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: develops_from UBERON:0004874 ! somatopleure intersection_of: part_of UBERON:0000922 ! embryo -relationship: develops_from UBERON:0004874 ! somatopleure +intersection_of: RO:0002202 UBERON:0004874 ! develops from somatopleure relationship: part_of UBERON:0009142 {source="EHDAA2"} ! entire embryonic mesenchyme -property_value: editor_note "the way this class is defined also includes extraembryonic mesenchyme such as the amniotic mesenchyme; in future this may be restricted to embryonic derivatives" xsd:string +relationship: RO:0002202 UBERON:0004874 ! develops from somatopleure +property_value: IAO:0000116 "the way this class is defined also includes extraembryonic mesenchyme such as the amniotic mesenchyme; in future this may be restricted to embryonic derivatives" xsd:string [Term] id: UBERON:0010378 @@ -241060,13 +237812,14 @@ name: mesenchyme from splanchnopleure namespace: uberon def: "Mesenchyme that develops_from a splanchnopleure." [OBOL:automatic] xref: EHDAA2:0001122 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: develops_from UBERON:0004873 ! splanchnopleure intersection_of: part_of UBERON:0000922 ! embryo -relationship: develops_from UBERON:0004873 ! splanchnopleure +intersection_of: RO:0002202 UBERON:0004873 ! develops from splanchnopleure relationship: part_of UBERON:0009142 {source="EHDAA2"} ! entire embryonic mesenchyme +relationship: RO:0002202 UBERON:0004873 ! develops from splanchnopleure [Term] id: UBERON:0010380 @@ -241077,10 +237830,11 @@ subset: pheno_slim xref: EMAPA:37479 {source="MA:th"} xref: MA:0001145 is_a: UBERON:0001021 ! nerve +is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0001021 ! nerve intersection_of: part_of UBERON:0002005 ! enteric nervous system -relationship: contributes_to_morphology_of UBERON:0002005 ! enteric nervous system relationship: part_of UBERON:0002005 ! enteric nervous system +relationship: RO:0002433 UBERON:0002005 ! contributes to morphology of enteric nervous system [Term] id: UBERON:0010386 @@ -241093,8 +237847,8 @@ xref: MA:0000732 is_a: UBERON:0000444 ! lymphoid follicle intersection_of: UBERON:0000444 ! lymphoid follicle intersection_of: part_of UBERON:0001211 ! Peyer's patch -relationship: contributes_to_morphology_of UBERON:0001211 ! Peyer's patch relationship: part_of UBERON:0001211 ! Peyer's patch +relationship: RO:0002433 UBERON:0001211 ! contributes to morphology of Peyer's patch [Term] id: UBERON:0010387 @@ -241123,10 +237877,9 @@ synonym: "proximal rib segment" EXACT [] synonym: "vertebral part of rib" RELATED [] xref: EMAPA:37495 {source="MA:th"} xref: MA:0001400 -xref: MA:0001414 is_a: UBERON:0005913 ! zone of bone organ -relationship: connected_to UBERON:0002412 ! vertebra relationship: part_of UBERON:0002228 {source="MA"} ! rib +relationship: RO:0002170 UBERON:0002412 ! connected to vertebra [Term] id: UBERON:0010390 @@ -241138,9 +237891,9 @@ xref: FMA:19709 xref: SCTID:279432008 is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0000057 ! urethra -relationship: luminal_space_of UBERON:0000057 ! urethra +intersection_of: RO:0002572 UBERON:0000057 ! luminal space of urethra relationship: part_of UBERON:0000057 ! urethra +relationship: RO:0002572 UBERON:0000057 ! luminal space of urethra [Term] id: UBERON:0010392 @@ -241150,7 +237903,7 @@ is_a: UBERON:0010394 ! lymphocyte domain intersection_of: UBERON:0010394 ! lymphocyte domain intersection_of: has_part CL:0000236 ! B cell relationship: has_part CL:0000236 ! B cell -property_value: editor_note "TODO - check" xsd:string +property_value: IAO:0000116 "TODO - check" xsd:string [Term] id: UBERON:0010393 @@ -241160,7 +237913,7 @@ is_a: UBERON:0010394 ! lymphocyte domain intersection_of: UBERON:0010394 ! lymphocyte domain intersection_of: has_part CL:0000084 ! T cell relationship: has_part CL:0000084 ! T cell -property_value: editor_note "TODO - check" xsd:string +property_value: IAO:0000116 "TODO - check" xsd:string [Term] id: UBERON:0010394 @@ -241170,11 +237923,11 @@ is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005057 ! immune organ is_a: UBERON:0010001 ! cell cluster organ intersection_of: UBERON:0010001 ! cell cluster organ -intersection_of: composed_primarily_of CL:0000542 ! lymphocyte -relationship: composed_primarily_of CL:0000542 ! lymphocyte -relationship: only_in_taxon NCBITaxon:7711 ! Chordata +intersection_of: RO:0002473 CL:0000542 ! composed primarily of lymphocyte relationship: part_of UBERON:0002465 ! lymphoid system -property_value: editor_note "TODO - check" xsd:string +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002473 CL:0000542 ! composed primarily of lymphocyte +property_value: IAO:0000116 "TODO - check" xsd:string property_value: seeAlso "https://github.com/obophenotype/uberon/issues/513" xsd:anyURI [Term] @@ -241192,7 +237945,7 @@ is_a: UBERON:0010422 ! primary nodular lymphoid tissue is_a: UBERON:0010748 ! lymph node follicle intersection_of: UBERON:0010422 ! primary nodular lymphoid tissue intersection_of: part_of UBERON:0000029 ! lymph node -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0010397 @@ -241206,9 +237959,9 @@ synonym: "efferent lymphatic vessels" RELATED [Wikipedia:Efferent_lymph_vessel] xref: MA:0000749 xref: Wikipedia:Efferent_lymph_vessel is_a: UBERON:0001473 ! lymphatic vessel -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_F_Lymph_Node.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_M_Lymph_Node.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_F_Lymph_Node.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_M_Lymph_Node.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0010399 @@ -241226,11 +237979,10 @@ is_a: UBERON:0001637 ! artery is_a: UBERON:0003497 ! abdomen blood vessel intersection_of: UBERON:0001637 ! artery intersection_of: part_of UBERON:0001265 ! trabecula of spleen -relationship: connecting_branch_of UBERON:0001194 {source="MP"} ! splenic artery -relationship: contributes_to_morphology_of UBERON:0002106 ! spleen relationship: part_of UBERON:0001265 ! trabecula of spleen -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000001 "When the splenic artery passes into the trabecula of the spleen and branches, they become known as the trabecular arteries. When these arteries then reach the white pulp, and become covered with Periarteriolar lymphoid sheaths, the name changes again to central arteries (or central arterioles). Branches of the central arteries are given to the red pulp, and these are called penicillar arteries).[Wikipedia]" xsd:string {ontology="Wikipedia", source="Wikipedia:Trabecular_arteries"} +relationship: RO:0002252 UBERON:0001194 {source="MP"} ! connecting branch of splenic artery +relationship: RO:0002433 UBERON:0002106 ! contributes to morphology of spleen +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0010400 @@ -241247,11 +237999,10 @@ xref: Wikipedia:Trabecular_veins is_a: UBERON:0013126 ! vein of abdomen intersection_of: UBERON:0001638 ! vein intersection_of: part_of UBERON:0001265 ! trabecula of spleen -relationship: connected_to UBERON:0003713 ! splenic vein -relationship: contributes_to_morphology_of UBERON:0002106 ! spleen relationship: part_of UBERON:0001265 ! trabecula of spleen -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000001 "The trabecular veins are the largest veins inside the spleen. It drains the blood collected in the sinuses of the pulp.[Wikipedia]" xsd:string {ontology="Wikipedia", source="Wikipedia:Trabecular_veins"} +relationship: RO:0002170 UBERON:0003713 ! connected to splenic vein +relationship: RO:0002433 UBERON:0002106 ! contributes to morphology of spleen +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0010402 @@ -241264,12 +238015,13 @@ synonym: "suprabasal layer" BROAD [MP:0001233] synonym: "suprabasal layer of epidermis" EXACT [] xref: EMAPA:35315 xref: MA:0000808 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0013754 ! integumentary system layer intersection_of: UBERON:0013754 ! integumentary system layer +intersection_of: BSPO:0000108 UBERON:0002025 ! stratum basale of epidermis intersection_of: part_of UBERON:0001003 ! skin epidermis -intersection_of: superficial_to UBERON:0002025 ! stratum basale of epidermis +relationship: BSPO:0000108 UBERON:0002025 ! stratum basale of epidermis relationship: part_of UBERON:0001003 ! skin epidermis -relationship: superficial_to UBERON:0002025 ! stratum basale of epidermis [Term] id: UBERON:0010403 @@ -241282,9 +238034,8 @@ xref: DHBA:10508 xref: EMAPA:32680 xref: MA:0000812 is_a: UBERON:0005423 ! developing anatomical structure -relationship: develops_from UBERON:0004062 ! neural tube marginal layer relationship: part_of UBERON:0000955 ! brain -property_value: UBPROP:0000012 "not clear if the MA/EMAPA classes refer specifically to the cortical subset. DHBA class incldues non-neocortex derivatives so it belongs here" xsd:string {external_ontology="MA"} +relationship: RO:0002202 UBERON:0004062 ! develops from neural tube marginal layer [Term] id: UBERON:0010409 @@ -241298,8 +238049,9 @@ synonym: "ocular surface" EXACT [] xref: EMAPA:35336 xref: MA:0002486 is_a: UBERON:0000063 ! organ subunit +is_a: UBERON:0004121 ! ectoderm-derived structure +relationship: BSPO:0000108 UBERON:0022288 ! surface of eyeball relationship: part_of UBERON:0000019 ! camera-type eye -relationship: superficial_to UBERON:0022288 ! surface of eyeball [Term] id: UBERON:0010416 @@ -241335,8 +238087,8 @@ is_a: UBERON:0010393 ! T cell domain intersection_of: UBERON:0010393 ! T cell domain intersection_of: part_of UBERON:0000029 ! lymph node relationship: part_of UBERON:0002006 {source="MP"} ! cortex of lymph node -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_F_Lymph_Node.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_M_Lymph_Node.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_F_Lymph_Node.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_M_Lymph_Node.glb" xsd:anyURI [Term] id: UBERON:0010418 @@ -241374,8 +238126,8 @@ is_a: UBERON:0010755 ! secondary follicle corona intersection_of: UBERON:0010755 ! secondary follicle corona intersection_of: part_of UBERON:0000029 ! lymph node relationship: part_of UBERON:0010753 {source="MA"} ! lymph node secondary follicle -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: surrounds UBERON:0009039 ! lymph node germinal center +relationship: RO:0002221 UBERON:0009039 ! surrounds lymph node germinal center +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0010421 @@ -241395,13 +238147,14 @@ synonym: "spleen mantle zone" RELATED [CL:tm, MP:0002360] synonym: "splenic B cell corona" EXACT [MP:0002360] synonym: "splenic corona" BROAD [CL:tm] xref: EMAPA:37962 {source="MA:th"} +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010755 ! secondary follicle corona intersection_of: UBERON:0010755 ! secondary follicle corona intersection_of: part_of UBERON:0002106 ! spleen -relationship: contributes_to_morphology_of UBERON:0004042 ! spleen secondary B follicle relationship: part_of UBERON:0004042 {source="CL:tm"} ! spleen secondary B follicle -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: surrounds UBERON:0005196 ! spleen germinal center +relationship: RO:0002221 UBERON:0005196 ! surrounds spleen germinal center +relationship: RO:0002433 UBERON:0004042 ! contributes to morphology of spleen secondary B follicle +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0010422 @@ -241414,7 +238167,6 @@ synonym: "primary lymphoid nodule" EXACT [FMA:55223] xref: FMA:55223 is_a: UBERON:0000444 {source="FMA"} ! lymphoid follicle relationship: has_part CL:0000788 {source="CL:tm"} ! naive B cell -property_value: UBPROP:0000015 "The cortex of lymph nodes, the white pulp of spleen, and mucosa associated lymphoid tissue all have these primary follicles" xsd:string [Term] id: UBERON:0010423 @@ -241428,7 +238180,7 @@ is_a: UBERON:0010422 {source="FMA"} ! primary nodular lymphoid tissue intersection_of: UBERON:0010422 ! primary nodular lymphoid tissue intersection_of: part_of UBERON:0002372 ! tonsil relationship: part_of UBERON:0002372 ! tonsil -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0010425 @@ -241444,13 +238196,10 @@ synonym: "internal nostril" RELATED [] xref: NCIT:C32856 is_a: UBERON:0000003 ! naris intersection_of: UBERON:0000003 ! naris -intersection_of: connects UBERON:0001707 ! nasal cavity -intersection_of: connects UBERON:0006562 ! pharynx -relationship: connects UBERON:0006562 ! pharynx -relationship: only_in_taxon NCBITaxon:8287 ! Sarcopterygii -property_value: UBPROP:0000007 "choanal" xsd:string -property_value: UBPROP:0000008 "In humans the only internal naris is the posterior nasal aperture, which connects to the nasopharynx" xsd:string -property_value: UBPROP:0000202 FMA:76585 +intersection_of: RO:0002176 UBERON:0001707 ! connects nasal cavity +intersection_of: RO:0002176 UBERON:0006562 ! connects pharynx +relationship: RO:0002160 NCBITaxon:8287 ! only in taxon Sarcopterygii +relationship: RO:0002176 UBERON:0006562 ! connects pharynx [Term] id: UBERON:0010427 @@ -241467,12 +238216,13 @@ xref: FMA:76551 xref: SCTID:280860001 xref: Wikipedia:Ciliary_processes is_a: UBERON:0000481 ! multi-tissue structure +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001775 ! ciliary body -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/Gray875.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-l.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-r.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-l.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-r.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/Gray875.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-l.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-r.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-l.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-r.glb" xsd:anyURI [Term] id: UBERON:0010428 @@ -241488,9 +238238,7 @@ xref: SCTID:332907008 xref: UMLS:C0222649 {source="ncithesaurus:Flat_Bone"} xref: Wikipedia:Flat_bone is_a: UBERON:0001474 {source="FMA"} ! bone element -relationship: has_quality PATO:0000407 ! flat -property_value: UBPROP:0000008 "In an adult mammal, most red blood cells are formed in flat bones" xsd:string -property_value: UBPROP:0000009 "Flat bones are those bones which are found where the principal requirement is either extensive protection or the provision of broad surfaces for muscular attachment" xsd:string +relationship: RO:0000086 PATO:0000407 ! has quality flat [Term] id: UBERON:0010498 @@ -241504,8 +238252,6 @@ xref: UMLS:C0836138 {source="ncithesaurus:Pseudostratified_Columnar_Epithelium"} xref: UMLS:C1514590 {source="ncithesaurus:Pseudostratified_Epithelium"} xref: Wikipedia:Pseudostratified_columnar_epithelium is_a: UBERON:0000485 {source="FMA"} ! simple columnar epithelium -property_value: UBPROP:0000009 "Pseudostratified epithelia function in secretion or absorption. If a specimen looks stratified but has cilia, then it is a pseudostratified ciliated epithelium, since stratified epithelia do not have cilia." xsd:string -property_value: UBPROP:0000012 "glandular in NCIT; we consider the two NCIT terms synonymous" xsd:string {external_ontology="NCIT"} [Term] id: UBERON:0010499 @@ -241590,15 +238336,13 @@ xref: EHDAA2:0001143 xref: EHDAA:7007 xref: EHDAA:8105 xref: EMAPA:17953 -xref: EMAPA:27621 xref: MA:0002998 xref: VHOG:0001241 is_a: UBERON:0005423 ! developing anatomical structure -relationship: developmentally_induced_by UBERON:0000084 ! ureteric bud -relationship: develops_from UBERON:0003220 {source="EHDAA2"} ! metanephric mesenchyme relationship: has_part CL:0000354 ! blastemal cell relationship: part_of UBERON:0009871 ! nephrogenic zone -property_value: UBPROP:0000012 "different versions of EMAPA have different labels for the same classes. In vHOG this is part of metanephros cortex but this leads to a cycle in basic." xsd:string {external_ontology="EMAPA"} +relationship: RO:0002202 UBERON:0003220 {source="EHDAA2"} ! develops from metanephric mesenchyme +relationship: RO:0002256 UBERON:0000084 ! developmentally induced by ureteric bud [Term] id: UBERON:0010532 @@ -241612,10 +238356,9 @@ synonym: "primitive nephron" BROAD [] is_a: UBERON:0003914 {source="EHDAA2-inferred"} ! epithelial tube is_a: UBERON:0004819 ! kidney epithelium is_a: UBERON:0006555 ! excretory tube -relationship: develops_from UBERON:0004209 {source="EHDAA2"} ! renal vesicle -relationship: has_potential_to_develop_into UBERON:0001285 ! nephron -relationship: located_in UBERON:0003918 ! kidney mesenchyme -property_value: UBPROP:0000012 "EHDAA2 treats this as already having a tubular structure, but in the ZFA representation this is a cluster of cells" xsd:string {external_ontology="EHDAA2"} +relationship: RO:0001025 UBERON:0003918 ! located in kidney mesenchyme +relationship: RO:0002202 UBERON:0004209 {source="EHDAA2"} ! develops from renal vesicle +relationship: RO:0002387 UBERON:0001285 ! has potential to develop into nephron [Term] id: UBERON:0010533 @@ -241627,8 +238370,8 @@ is_a: UBERON:0001225 ! cortex of kidney is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0001225 ! cortex of kidney intersection_of: part_of UBERON:0000081 ! metanephros -relationship: develops_from UBERON:0005113 ! metanephric cortex mesenchyme relationship: part_of UBERON:0000081 {source="VHOG"} ! metanephros +relationship: RO:0002202 UBERON:0005113 ! develops from metanephric cortex mesenchyme [Term] id: UBERON:0010534 @@ -241663,8 +238406,8 @@ id: UBERON:0010536 name: nephron progenitor namespace: uberon is_a: UBERON:0000479 {source="ZFA"} ! tissue -relationship: has_potential_to_develop_into UBERON:0001285 ! nephron relationship: part_of UBERON:0003918 {source="cjm"} ! kidney mesenchyme +relationship: RO:0002387 UBERON:0001285 ! has potential to develop into nephron [Term] id: UBERON:0010537 @@ -241672,6 +238415,7 @@ name: mesonephric nephron progenitor namespace: uberon def: "Cluster of cells comprising a portion of tissue which gives rise to new mesonephric nephrons. The cluster contains self-renewing stem cells." [ZFA:0005587] xref: ZFA:0005587 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010536 ! nephron progenitor intersection_of: UBERON:0010536 ! nephron progenitor intersection_of: part_of UBERON:0000080 ! mesonephros @@ -241688,8 +238432,8 @@ is_a: UBERON:0010758 ! subdivision of organism along appendicular axis intersection_of: UBERON:0010758 ! subdivision of organism along appendicular axis intersection_of: part_of UBERON:0004708 ! paired limb/fin disjoint_from: UBERON:0010912 ! subdivision of skeleton -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0004708 ! paired limb/fin +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata [Term] id: UBERON:0010540 @@ -241702,10 +238446,10 @@ is_a: UBERON:0005866 ! pre-cartilage condensation is_a: UBERON:0010695 ! mesenchyme of tarsal region is_a: UBERON:0015050 ! tarsus endochondral element intersection_of: UBERON:0005866 ! pre-cartilage condensation -intersection_of: has_potential_to_develop_into UBERON:0001447 ! tarsal bone -relationship: develops_from UBERON:0010695 ! mesenchyme of tarsal region -relationship: has_potential_to_develop_into UBERON:0001447 ! tarsal bone +intersection_of: RO:0002387 UBERON:0001447 ! has potential to develop into tarsal bone relationship: part_of UBERON:0003328 ! mesenchyme of footplate +relationship: RO:0002202 UBERON:0010695 ! develops from mesenchyme of tarsal region +relationship: RO:0002387 UBERON:0001447 ! has potential to develop into tarsal bone [Term] id: UBERON:0010541 @@ -241718,10 +238462,10 @@ is_a: UBERON:0005863 ! cartilaginous condensation is_a: UBERON:0010695 ! mesenchyme of tarsal region is_a: UBERON:0015050 ! tarsus endochondral element intersection_of: UBERON:0005863 ! cartilaginous condensation -intersection_of: has_potential_to_develop_into UBERON:0001447 ! tarsal bone -relationship: develops_from UBERON:0010540 {source="EHDAA2"} ! tarsus pre-cartilage condensation -relationship: has_potential_to_develop_into UBERON:0001447 ! tarsal bone +intersection_of: RO:0002387 UBERON:0001447 ! has potential to develop into tarsal bone relationship: part_of UBERON:0003328 {source="EHDAA2"} ! mesenchyme of footplate +relationship: RO:0002202 UBERON:0010540 {source="EHDAA2"} ! develops from tarsus pre-cartilage condensation +relationship: RO:0002387 UBERON:0001447 ! has potential to develop into tarsal bone [Term] id: UBERON:0010543 @@ -241740,14 +238484,15 @@ synonym: "skeletal parts of acropodium" RELATED [] synonym: "skeleton of digits" RELATED [] xref: FMA:231315 xref: VSAO:0005028 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010712 ! limb skeleton subdivision intersection_of: UBERON:0010912 ! subdivision of skeleton -intersection_of: skeleton_of UBERON:0012354 ! acropodium region +intersection_of: RO:0002576 UBERON:0012354 ! skeleton of acropodium region relationship: has_part UBERON:0015023 ! phalanx endochondral element relationship: part_of UBERON:0012150 {source="PHENOSCAPE:ni"} ! skeleton of digitopodium relationship: part_of UBERON:0012354 ! acropodium region relationship: proximally_connected_to UBERON:0010546 ! metapodial skeleton -relationship: skeleton_of UBERON:0012354 ! acropodium region +relationship: RO:0002576 UBERON:0012354 ! skeleton of acropodium region [Term] id: UBERON:0010544 @@ -241770,7 +238515,6 @@ synonym: "set of metacarpals" EXACT [FMA:71336] synonym: "set of metacarpals [I-V]" EXACT [FMA:71336] synonym: "skeleton of metacarpus" EXACT [] xref: AAO:0000946 -xref: EMAPA:36158 xref: FMA:71336 xref: MESH:D050279 xref: VSAO:0005026 @@ -241779,13 +238523,12 @@ xref: XAO:0003208 is_a: UBERON:0010546 ! metapodial skeleton is_a: UBERON:0015042 ! manual digit metacarpus endochondral element intersection_of: UBERON:0010912 ! subdivision of skeleton -intersection_of: skeleton_of UBERON:0004453 ! metacarpus region +intersection_of: RO:0002576 UBERON:0004453 ! skeleton of metacarpus region disjoint_from: UBERON:0010545 {source="lexical"} ! metatarsus skeleton -relationship: develops_from UBERON:0010699 {notes="many to one"} ! manual digit metacarpus cartilage element relationship: proximally_connected_to UBERON:0009880 ! carpal skeleton -relationship: skeleton_of UBERON:0004453 ! metacarpus region -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/2/2f/Metacarpals_numbered-en.svg" xsd:anyURI -property_value: UBPROP:0000001 "Segment of the forearm corresponding to the metacarpus, which articulates with the carpals at one end and with the phalanges at the other end.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000946", ontology="AAO", source="AAO:LAP"} +relationship: RO:0002202 UBERON:0010699 ! develops from manual digit metacarpus cartilage element +relationship: RO:0002576 UBERON:0004453 ! skeleton of metacarpus region +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/2f/Metacarpals_numbered-en.svg" xsd:anyURI [Term] id: UBERON:0010545 @@ -241813,12 +238556,11 @@ xref: XAO:0003212 is_a: UBERON:0010546 ! metapodial skeleton is_a: UBERON:0015036 ! pedal digit metatarsal endochondral element intersection_of: UBERON:0010912 ! subdivision of skeleton -intersection_of: skeleton_of UBERON:0000983 ! metatarsus region -relationship: develops_from UBERON:0010697 {notes="many to one"} ! pedal digit metatarsal cartilage element +intersection_of: RO:0002576 UBERON:0000983 ! skeleton of metatarsus region relationship: proximally_connected_to UBERON:0009879 ! tarsal skeleton -relationship: skeleton_of UBERON:0000983 ! metatarsus region -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/52/Gray291.png" xsd:anyURI -property_value: UBPROP:0000001 "Segment of the leg corresponding to the metatarsus, which articulates with the carpals at one end and with the phalanges at the other end.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000221", ontology="AAO", source="AAO:LAP"} +relationship: RO:0002202 UBERON:0010697 ! develops from pedal digit metatarsal cartilage element +relationship: RO:0002576 UBERON:0000983 ! skeleton of metatarsus region +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/52/Gray291.png" xsd:anyURI [Term] id: UBERON:0010546 @@ -241832,17 +238574,15 @@ synonym: "metapodium skeleton" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "skeletal parts of metapodium" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "skeleton of metapodium" EXACT [] xref: VSAO:0005025 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010712 ! limb skeleton subdivision intersection_of: UBERON:0010912 ! subdivision of skeleton -intersection_of: skeleton_of UBERON:0009877 ! metapodium region +intersection_of: RO:0002576 UBERON:0009877 ! skeleton of metapodium region relationship: distally_connected_to UBERON:0010543 ! acropodial skeleton relationship: part_of UBERON:0009877 ! metapodium region relationship: part_of UBERON:0012150 {source="PHENOSCAPE:ni"} ! skeleton of digitopodium relationship: proximally_connected_to UBERON:0009878 ! mesopodial skeleton -relationship: skeleton_of UBERON:0009877 ! metapodium region -property_value: UBPROP:0000001 "Endochondral bone complex located between the mesopodium and the acropodium and consisting of the metacarpals or metatarsals.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0005025", ontology="VSAO", source="VSAO:NI"} -property_value: UBPROP:0000002 "relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: connected_to subdivision of skeleton (UBERON:0010912)[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0005025", ontology="VSAO"} -property_value: UBPROP:0000002 "relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: distally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0005025", ontology="VSAO"} +relationship: RO:0002576 UBERON:0009877 ! skeleton of metapodium region [Term] id: UBERON:0010585 @@ -241860,7 +238600,7 @@ is_a: UBERON:0010700 ! phalanx pre-cartilage condensation is_a: UBERON:0010886 ! hindlimb pre-cartilage condensation is_a: UBERON:0015030 ! pedal digit phalanx endochondral element intersection_of: UBERON:0015030 ! pedal digit phalanx endochondral element -intersection_of: composed_primarily_of UBERON:0005866 ! pre-cartilage condensation +intersection_of: RO:0002473 UBERON:0005866 ! composed primarily of pre-cartilage condensation [Term] id: UBERON:0010586 @@ -241878,7 +238618,7 @@ is_a: UBERON:0010700 ! phalanx pre-cartilage condensation is_a: UBERON:0010884 ! forelimb bone pre-cartilage condensation is_a: UBERON:0015024 ! manual digit phalanx endochondral element intersection_of: UBERON:0015024 ! manual digit phalanx endochondral element -intersection_of: composed_primarily_of UBERON:0005866 ! pre-cartilage condensation +intersection_of: RO:0002473 UBERON:0005866 ! composed primarily of pre-cartilage condensation [Term] id: UBERON:0010685 @@ -241892,8 +238632,8 @@ is_a: UBERON:0010701 ! phalanx cartilage element is_a: UBERON:0015030 ! pedal digit phalanx endochondral element is_a: UBERON:0035129 ! pes cartilage element intersection_of: UBERON:0015030 ! pedal digit phalanx endochondral element -intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue -relationship: develops_from UBERON:0010585 ! pedal digit phalanx pre-cartilage condensation +intersection_of: RO:0002473 UBERON:0002418 ! composed primarily of cartilage tissue +relationship: RO:0002202 UBERON:0010585 ! develops from pedal digit phalanx pre-cartilage condensation [Term] id: UBERON:0010686 @@ -241907,8 +238647,8 @@ is_a: UBERON:0010701 ! phalanx cartilage element is_a: UBERON:0015024 ! manual digit phalanx endochondral element is_a: UBERON:0035128 ! manus cartilage element intersection_of: UBERON:0015024 ! manual digit phalanx endochondral element -intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue -relationship: develops_from UBERON:0010586 ! manual digit phalanx pre-cartilage condensation +intersection_of: RO:0002473 UBERON:0002418 ! composed primarily of cartilage tissue +relationship: RO:0002202 UBERON:0010586 ! develops from manual digit phalanx pre-cartilage condensation [Term] id: UBERON:0010687 @@ -241927,7 +238667,7 @@ is_a: UBERON:0005866 ! pre-cartilage condensation is_a: UBERON:0010886 ! hindlimb pre-cartilage condensation is_a: UBERON:0015036 ! pedal digit metatarsal endochondral element intersection_of: UBERON:0015036 ! pedal digit metatarsal endochondral element -intersection_of: composed_primarily_of UBERON:0005866 ! pre-cartilage condensation +intersection_of: RO:0002473 UBERON:0005866 ! composed primarily of pre-cartilage condensation [Term] id: UBERON:0010688 @@ -242003,9 +238743,9 @@ xref: EMAPA:32951 is_a: UBERON:0015036 ! pedal digit metatarsal endochondral element is_a: UBERON:0035129 ! pes cartilage element intersection_of: UBERON:0015036 ! pedal digit metatarsal endochondral element -intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue -relationship: develops_from UBERON:0010687 ! pedal digit metatarsal pre-cartilage condensation -property_value: editor_note "EMAPA represents the specific child classes as being part of the digit mesenchyme - we follow this although for the fully formed structure we represent the metatarsals as adjoining rather than being part of the digit skeleton" xsd:string +intersection_of: RO:0002473 UBERON:0002418 ! composed primarily of cartilage tissue +relationship: RO:0002202 UBERON:0010687 ! develops from pedal digit metatarsal pre-cartilage condensation +property_value: IAO:0000116 "EMAPA represents the specific child classes as being part of the digit mesenchyme - we follow this although for the fully formed structure we represent the metatarsals as adjoining rather than being part of the digit skeleton" xsd:string [Term] id: UBERON:0010698 @@ -242021,7 +238761,7 @@ xref: VHOG:0000953 is_a: UBERON:0010884 ! forelimb bone pre-cartilage condensation is_a: UBERON:0015042 ! manual digit metacarpus endochondral element intersection_of: UBERON:0015042 ! manual digit metacarpus endochondral element -intersection_of: composed_primarily_of UBERON:0005866 ! pre-cartilage condensation +intersection_of: RO:0002473 UBERON:0005866 ! composed primarily of pre-cartilage condensation [Term] id: UBERON:0010699 @@ -242037,8 +238777,8 @@ xref: EMAPA:32849 is_a: UBERON:0015042 ! manual digit metacarpus endochondral element is_a: UBERON:0035128 ! manus cartilage element intersection_of: UBERON:0015042 ! manual digit metacarpus endochondral element -intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue -relationship: develops_from UBERON:0010698 ! manual digit metacarpus pre-cartilage condensation +intersection_of: RO:0002473 UBERON:0002418 ! composed primarily of cartilage tissue +relationship: RO:0002202 UBERON:0010698 ! develops from manual digit metacarpus pre-cartilage condensation [Term] id: UBERON:0010700 @@ -242048,7 +238788,7 @@ xref: EMAPA:32720 is_a: UBERON:0010882 ! limb bone pre-cartilage condensation is_a: UBERON:0015023 ! phalanx endochondral element intersection_of: UBERON:0015023 ! phalanx endochondral element -intersection_of: composed_primarily_of UBERON:0005866 ! pre-cartilage condensation +intersection_of: RO:0002473 UBERON:0005866 ! composed primarily of pre-cartilage condensation relationship: part_of UBERON:0010702 {source="EMAPA"} ! digit mesenchyme [Term] @@ -242060,8 +238800,8 @@ xref: EMAPA:32721 is_a: UBERON:0015023 ! phalanx endochondral element is_a: UBERON:0015064 ! autopod cartilage intersection_of: UBERON:0015023 ! phalanx endochondral element -intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue -relationship: develops_from UBERON:0010700 ! phalanx pre-cartilage condensation +intersection_of: RO:0002473 UBERON:0002418 ! composed primarily of cartilage tissue +relationship: RO:0002202 UBERON:0010700 ! develops from phalanx pre-cartilage condensation [Term] id: UBERON:0010702 @@ -242100,13 +238840,12 @@ xref: FMA:71199 xref: VSAO:0005011 is_a: UBERON:0011584 ! zeugopodial skeleton intersection_of: UBERON:0010912 ! subdivision of skeleton -intersection_of: skeleton_of UBERON:0002386 ! forelimb zeugopod +intersection_of: RO:0002576 UBERON:0002386 ! skeleton of forelimb zeugopod disjoint_from: UBERON:0010720 {source="lexical"} ! hindlimb zeugopod skeleton relationship: part_of UBERON:0001440 ! forelimb skeleton relationship: part_of UBERON:0002386 ! forelimb zeugopod -relationship: skeleton_of UBERON:0002386 ! forelimb zeugopod -property_value: editor_note "adding proxinally_connected_to humerus causes inconsistencies - requires investigation" xsd:string -property_value: UBPROP:0000001 "Segment of the forearm corresponding to the radius and ulna.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000200", ontology="AAO", source="AAO:LAP"} +relationship: RO:0002576 UBERON:0002386 ! skeleton of forelimb zeugopod +property_value: IAO:0000116 "adding proxinally_connected_to humerus causes inconsistencies - requires investigation" xsd:string [Term] id: UBERON:0010707 @@ -242124,14 +238863,11 @@ xref: FMA:7182 xref: VSAO:0000214 is_a: UBERON:0000475 ! organism subdivision is_a: UBERON:0015212 ! lateral structure -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 -relationship: functionally_related_to GO:0040011 ! locomotion -relationship: in_lateral_side_of UBERON:0000468 ! multicellular organism -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata -property_value: editor_note "It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO]" xsd:string -property_value: UBPROP:0000001 "Anatomical group that consists of the soft and skeletal tissues of the appendicular region of the body and the appendage proper.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000214", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070"} -property_value: UBPROP:0000005 "It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO]" xsd:string {date_retrieved="2012-09-06", external_class="VSAO:0000214", ontology="VSAO", source="Curator"} -property_value: UBPROP:0000012 "note that the FMA uses the term 'limb' to refer to the entire appendage complex (free limb plus girdle region)" xsd:string {external_ontology="FMA"} +relationship: BSPO:0000126 UBERON:0000468 ! multicellular organism +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002328 GO:0040011 ! functionally related to locomotion +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: IAO:0000116 "It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO]" xsd:string creation_date: 2012-04-23T10:46:51Z [Term] @@ -242154,10 +238890,8 @@ is_a: UBERON:0010707 ! appendage girdle complex intersection_of: UBERON:0010707 ! appendage girdle complex intersection_of: has_part UBERON:0001421 ! pectoral girdle region relationship: has_part UBERON:0001421 ! pectoral girdle region -relationship: has_skeleton UBERON:0012475 ! skeleton of pectoral complex relationship: part_of UBERON:0000153 {gci_relation="part_of", gci_filler="NCBITaxon:32523"} ! anterior region of body -property_value: UBPROP:0000001 "Appendage girdle complex that when present, encompasses the pectoral appendage and half of the pectoral girdle.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000213", ontology="VSAO", source="VSAO:MAH"} -property_value: UBPROP:0000012 "note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region)" xsd:string {external_ontology="FMA"} +relationship: RO:0002551 UBERON:0012475 ! has skeleton skeleton of pectoral complex [Term] id: UBERON:0010709 @@ -242179,11 +238913,8 @@ is_a: UBERON:0010707 ! appendage girdle complex intersection_of: UBERON:0010707 ! appendage girdle complex intersection_of: has_part UBERON:0001271 ! pelvic girdle region relationship: has_part UBERON:0001271 ! pelvic girdle region -relationship: has_skeleton UBERON:0012476 ! skeleton of pelvic complex relationship: part_of UBERON:0000154 {gci_relation="part_of", gci_filler="NCBITaxon:32523"} ! posterior region of body -property_value: RO:0002171 UBERON:0010708 -property_value: UBPROP:0000001 "Appendage girdle complex that when present, encompasses the pelvic appendage and the pelvic girdle.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000215", ontology="VSAO", source="VSAO:MAH"} -property_value: UBPROP:0000012 "note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region). Note the MA class 'hindlimb' may also belong here" xsd:string {external_ontology="FMA"} +relationship: RO:0002551 UBERON:0012476 ! has skeleton skeleton of pelvic complex [Term] id: UBERON:0010712 @@ -242196,7 +238927,7 @@ intersection_of: UBERON:0010912 ! subdivision of skeleton intersection_of: part_of UBERON:0002101 ! limb relationship: part_of UBERON:0002091 {source="VSAO"} ! appendicular skeleton relationship: part_of UBERON:0002101 ! limb -property_value: editor_note "note the distinction between this and skeleton of limb" xsd:string +property_value: IAO:0000116 "note the distinction between this and skeleton of limb" xsd:string [Term] id: UBERON:0010714 @@ -242211,8 +238942,8 @@ is_a: UBERON:0005863 {source="EHDAA2"} ! cartilaginous condensation is_a: UBERON:0007844 ! cartilage element is_a: UBERON:0015054 ! iliac endochondral element intersection_of: UBERON:0015054 ! iliac endochondral element -intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue -relationship: develops_from UBERON:0006247 {source="EHDAA2"} ! iliac pre-cartilage condensation +intersection_of: RO:0002473 UBERON:0002418 ! composed primarily of cartilage tissue +relationship: RO:0002202 UBERON:0006247 {source="EHDAA2"} ! develops from iliac pre-cartilage condensation [Term] id: UBERON:0010719 @@ -242224,14 +238955,11 @@ xref: AAO:0010686 xref: VSAO:0000302 is_a: UBERON:0010912 ! subdivision of skeleton intersection_of: UBERON:0010912 ! subdivision of skeleton -intersection_of: skeleton_of UBERON:0007823 ! appendage girdle region +intersection_of: RO:0002576 UBERON:0007823 ! skeleton of appendage girdle region relationship: part_of UBERON:0002091 ! appendicular skeleton relationship: part_of UBERON:0007823 ! appendage girdle region relationship: proximally_connected_to UBERON:0002090 ! postcranial axial skeleton -relationship: skeleton_of UBERON:0007823 ! appendage girdle region -property_value: UBPROP:0000001 "Skeletal subdivision that is part of the appendage girdle region.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000302", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070"} -property_value: UBPROP:0000002 "relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: part_of subdivision of skeleton (UBERON:0010912)[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000302", ontology="VSAO"} -property_value: UBPROP:0000002 "relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: proximally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000302", ontology="VSAO"} +relationship: RO:0002576 UBERON:0007823 ! skeleton of appendage girdle region [Term] id: UBERON:0010720 @@ -242251,11 +238979,10 @@ xref: AAO:0000216 xref: VSAO:0005014 is_a: UBERON:0011584 ! zeugopodial skeleton intersection_of: UBERON:0010912 ! subdivision of skeleton -intersection_of: skeleton_of UBERON:0003823 ! hindlimb zeugopod +intersection_of: RO:0002576 UBERON:0003823 ! skeleton of hindlimb zeugopod relationship: part_of UBERON:0003823 ! hindlimb zeugopod relationship: proximally_connected_to UBERON:0000981 ! femur -relationship: skeleton_of UBERON:0003823 ! hindlimb zeugopod -property_value: UBPROP:0000001 "Segment of the leg corresponding to the tibia and fibula.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000216", ontology="AAO", source="AAO:LAP"} +relationship: RO:0002576 UBERON:0003823 ! skeleton of hindlimb zeugopod [Term] id: UBERON:0010728 @@ -242266,12 +238993,13 @@ xref: EHDAA2:0003449 is_a: UBERON:0005866 {source="EHDAA2"} ! pre-cartilage condensation is_a: UBERON:0006904 ! head mesenchyme from mesoderm is_a: UBERON:0009891 ! facial mesenchyme +is_a: UBERON:0014387 ! mesenchyme derived from neural crest is_a: UBERON:0015059 ! orbitosphenoid endochondral element intersection_of: UBERON:0015059 ! orbitosphenoid endochondral element -intersection_of: composed_primarily_of UBERON:0005866 ! pre-cartilage condensation -relationship: composed_primarily_of UBERON:0005866 ! pre-cartilage condensation -relationship: develops_from UBERON:0006904 {source="EHDAA2"} ! head mesenchyme from mesoderm +intersection_of: RO:0002473 UBERON:0005866 ! composed primarily of pre-cartilage condensation relationship: part_of UBERON:0009191 {source="EHDAA2"} ! sphenoid bone pre-cartilage condensation +relationship: RO:0002202 UBERON:0006904 {source="EHDAA2"} ! develops from head mesenchyme from mesoderm +relationship: RO:0002473 UBERON:0005866 ! composed primarily of pre-cartilage condensation [Term] id: UBERON:0010740 @@ -242286,9 +239014,9 @@ xref: MA:0000688 is_a: UBERON:0001474 ! bone element intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0010707 ! appendage girdle complex -relationship: contributes_to_morphology_of UBERON:0002091 ! appendicular skeleton -relationship: part_of UBERON:0002091 {notes="UBERONREF:0000003"} ! appendicular skeleton +relationship: part_of UBERON:0002091 ! appendicular skeleton relationship: part_of UBERON:0010707 ! appendage girdle complex +relationship: RO:0002433 UBERON:0002091 ! contributes to morphology of appendicular skeleton [Term] id: UBERON:0010741 @@ -242299,15 +239027,13 @@ subset: pheno_slim synonym: "bone of forelimb or pectoral fin or pectoral girdle" RELATED [https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] synonym: "forelimb bone" RELATED [MA:0000612, UBERONREF:0000003] synonym: "wing bone" NARROW SENSU [UBERONREF:0000003] -xref: EMAPA:32623 xref: EMAPA:35933 xref: MA:0000612 is_a: UBERON:0010740 ! bone of appendage girdle complex intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0010708 ! pectoral complex relationship: part_of UBERON:0010708 ! pectoral complex -property_value: editor_note "considering adding pectoral and pelvic complex skeleton classes" xsd:string -property_value: UBPROP:0000012 "note that the MA class includes girdle parts so it belongs here;" xsd:string {external_ontology="MA"} +property_value: IAO:0000116 "considering adding pectoral and pelvic complex skeleton classes" xsd:string [Term] id: UBERON:0010742 @@ -242316,14 +239042,12 @@ namespace: uberon def: "A bone that is part of a pelvic complex. Examples: pubis, ischium, fot phalanx, any tarsal bone, any bone of the pelvic fin or girdle." [https://orcid.org/0000-0002-6601-2165, UBERONREF:0000003] subset: pheno_slim synonym: "hindlimb bone" RELATED [MA:0000660, UBERONREF:0000003] -xref: EMAPA:32633 xref: EMAPA:35934 xref: MA:0000660 is_a: UBERON:0010740 {source="MA"} ! bone of appendage girdle complex intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0010709 ! pelvic complex relationship: part_of UBERON:0010709 ! pelvic complex -property_value: UBPROP:0000012 "the MA class called 'hindlimb bone' belongs here, as it includes bones in the pelvic girdle" xsd:string {external_ontology="MA"} [Term] id: UBERON:0010743 @@ -242335,7 +239059,6 @@ synonym: "cerebral meninges" EXACT [] synonym: "cluster of meninges" EXACT [FMA:231572] synonym: "meninges" EXACT [FMA:231572] xref: EHDAA2:0004661 -xref: EMAPA:32660 xref: FMA:231572 xref: NCIT:C12349 xref: neuronames:1465 @@ -242346,12 +239069,10 @@ is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0034925 ! anatomical collection intersection_of: UBERON:0034925 ! anatomical collection intersection_of: bounding_layer_of UBERON:0001017 ! central nervous system -intersection_of: has_member UBERON:0002360 ! meninx +intersection_of: RO:0002351 UBERON:0002360 ! has member meninx relationship: bounding_layer_of UBERON:0001017 ! central nervous system -relationship: has_member UBERON:0002360 ! meninx relationship: part_of UBERON:0001017 ! central nervous system -property_value: UBPROP:0000007 "meningeal" xsd:string -property_value: UBPROP:0000008 "In some primitive organisms, the meningeal cluster includes only the primitive meninx" xsd:string +relationship: RO:0002351 UBERON:0002360 ! has member meninx [Term] id: UBERON:0010748 @@ -242364,9 +239085,9 @@ xref: MA:0000742 is_a: UBERON:0000444 ! lymphoid follicle intersection_of: UBERON:0000444 ! lymphoid follicle intersection_of: part_of UBERON:0000029 ! lymph node -relationship: part_of UBERON:0002006 {notes="issues/7", source="MP-def"} ! cortex of lymph node -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_F_Lymph_Node.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_M_Lymph_Node.glb" xsd:anyURI +relationship: part_of UBERON:0002006 ! cortex of lymph node +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_F_Lymph_Node.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/NIH_M_Lymph_Node.glb" xsd:anyURI [Term] id: UBERON:0010753 @@ -242382,8 +239103,8 @@ is_a: UBERON:0001745 ! secondary nodular lymphoid tissue is_a: UBERON:0010748 {source="MA"} ! lymph node follicle intersection_of: UBERON:0001745 ! secondary nodular lymphoid tissue intersection_of: part_of UBERON:0000029 ! lymph node -relationship: develops_from UBERON:0010395 ! lymph node primary follicle -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002202 UBERON:0010395 ! develops from lymph node primary follicle +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0010754 @@ -242401,13 +239122,12 @@ xref: BTO:0003671 xref: EV:0100051 xref: MESH:D018858 xref: NCIT:C13337 -xref: SCTID:64626006 xref: UMLS:C0282491 {source="ncithesaurus:Germinal_Center"} xref: Wikipedia:Germinal_center is_a: UBERON:0001744 ! lymphoid tissue relationship: part_of UBERON:0001745 ! secondary nodular lymphoid tissue -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/6/60/Germinal_center.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/60/Germinal_center.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0010755 @@ -242425,10 +239145,10 @@ xref: Wikipedia:Mantle_zone is_a: UBERON:0001744 ! lymphoid tissue intersection_of: UBERON:0001744 ! lymphoid tissue intersection_of: part_of UBERON:0001745 ! secondary nodular lymphoid tissue -intersection_of: surrounds UBERON:0010754 ! germinal center +intersection_of: RO:0002221 UBERON:0010754 ! surrounds germinal center relationship: part_of UBERON:0001745 ! secondary nodular lymphoid tissue -relationship: surrounds UBERON:0010754 ! germinal center -property_value: editor_note "consider making terminology consistent amongst subclasses - see https://github.com/obophenotype/uberon/issues/7" xsd:string +relationship: RO:0002221 UBERON:0010754 ! surrounds germinal center +property_value: IAO:0000116 "consider making terminology consistent amongst subclasses - see https://github.com/obophenotype/uberon/issues/7" xsd:string [Term] id: UBERON:0010758 @@ -242438,7 +239158,6 @@ def: "A major subdivision of an organism that divides an organism along an axis subset: upper_level synonym: "appendage segment" EXACT [FBbt:00007018] synonym: "appendicular segment" EXACT [] -xref: FBbt:00007018 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000475 ! organism subdivision relationship: part_of UBERON:0000026 ! appendage @@ -242450,11 +239169,10 @@ def: "A cartilaginous condensation that has the potential to develop into a clav xref: EMAPA:18342 is_a: UBERON:0005863 ! cartilaginous condensation intersection_of: UBERON:0005863 ! cartilaginous condensation -intersection_of: has_potential_to_develop_into UBERON:0001105 ! clavicle bone -relationship: develops_from UBERON:0010844 ! clavicle pre-cartilage condensation -relationship: has_potential_to_develop_into UBERON:0001105 ! clavicle bone +intersection_of: RO:0002387 UBERON:0001105 ! has potential to develop into clavicle bone relationship: part_of UBERON:0007831 ! pectoral girdle skeleton -property_value: UBPROP:0000008 "In most birds and mammals the clavicles are the only dermal elements in the trunk, and is the only membrane bone associated with the pectoral girdle in these taxa. However, there can be secondary cartilage, or subsequent endochondral ossification, or fusion with endochondral elements. In rodents, the lateral ends of the clavicle are endochondral but the main portion is dermal." xsd:string {source="ISBN:978-0-12-319060-4"} +relationship: RO:0002202 UBERON:0010844 ! develops from clavicle pre-cartilage condensation +relationship: RO:0002387 UBERON:0001105 ! has potential to develop into clavicle bone [Term] id: UBERON:0010844 @@ -242464,10 +239182,9 @@ def: "A pre-cartilage condensation that has the potential to develop into a clav xref: EMAPA:18026 is_a: UBERON:0005866 ! pre-cartilage condensation intersection_of: UBERON:0005866 ! pre-cartilage condensation -intersection_of: has_potential_to_develop_into UBERON:0001105 ! clavicle bone -relationship: has_potential_to_develop_into UBERON:0001105 ! clavicle bone +intersection_of: RO:0002387 UBERON:0001105 ! has potential to develop into clavicle bone relationship: part_of UBERON:0007831 ! pectoral girdle skeleton -property_value: UBPROP:0000008 "In most birds and mammals the clavicles are the only dermal elements in the trunk, and is the only membrane bone associated with the pectoral girdle in these taxa. However, there can be secondary cartilage, or subsequent endochondral ossification, or fusion with endochondral elements. In rodents, the lateral ends of the clavicle are endochondral but the main portion is dermal." xsd:string {source="ISBN:978-0-12-319060-4"} +relationship: RO:0002387 UBERON:0001105 ! has potential to develop into clavicle bone [Term] id: UBERON:0010849 @@ -242478,9 +239195,9 @@ xref: EMAPA:18155 is_a: UBERON:0010885 ! hindlimb cartilage element is_a: UBERON:0015004 ! tibia endochondral element intersection_of: UBERON:0015004 ! tibia endochondral element -intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue -relationship: develops_from UBERON:0010850 ! tibia pre-cartilage condensation +intersection_of: RO:0002473 UBERON:0002418 ! composed primarily of cartilage tissue relationship: part_of UBERON:0005259 {source="EMAPA"} ! lower leg mesenchyme +relationship: RO:0002202 UBERON:0010850 ! develops from tibia pre-cartilage condensation [Term] id: UBERON:0010850 @@ -242492,9 +239209,9 @@ is_a: UBERON:0005259 ! lower leg mesenchyme is_a: UBERON:0005866 ! pre-cartilage condensation is_a: UBERON:0015004 ! tibia endochondral element intersection_of: UBERON:0005866 ! pre-cartilage condensation -intersection_of: has_potential_to_develop_into UBERON:0000979 ! tibia -relationship: has_potential_to_develop_into UBERON:0000979 ! tibia +intersection_of: RO:0002387 UBERON:0000979 ! has potential to develop into tibia relationship: part_of UBERON:0005259 {source="EHDAA2"} ! lower leg mesenchyme +relationship: RO:0002387 UBERON:0000979 ! has potential to develop into tibia [Term] id: UBERON:0010851 @@ -242508,9 +239225,9 @@ xref: EMAPA:18154 is_a: UBERON:0010885 ! hindlimb cartilage element is_a: UBERON:0015013 ! fibula endochondral element intersection_of: UBERON:0015013 ! fibula endochondral element -intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue -relationship: develops_from UBERON:0010852 ! fibula pre-cartilage condensation +intersection_of: RO:0002473 UBERON:0002418 ! composed primarily of cartilage tissue relationship: part_of UBERON:0005259 {source="EMAPA"} ! lower leg mesenchyme +relationship: RO:0002202 UBERON:0010852 ! develops from fibula pre-cartilage condensation [Term] id: UBERON:0010852 @@ -242525,9 +239242,9 @@ is_a: UBERON:0005259 ! lower leg mesenchyme is_a: UBERON:0005866 ! pre-cartilage condensation is_a: UBERON:0015013 ! fibula endochondral element intersection_of: UBERON:0005866 ! pre-cartilage condensation -intersection_of: has_potential_to_develop_into UBERON:0001446 ! fibula -relationship: has_potential_to_develop_into UBERON:0001446 ! fibula +intersection_of: RO:0002387 UBERON:0001446 ! has potential to develop into fibula relationship: part_of UBERON:0005259 {source="EHDAA2"} ! lower leg mesenchyme +relationship: RO:0002387 UBERON:0001446 ! has potential to develop into fibula [Term] id: UBERON:0010881 @@ -242537,8 +239254,8 @@ def: "A skeletal element that is part of a limb and composed of cartilage tissue is_a: UBERON:0007844 ! cartilage element is_a: UBERON:0015061 ! limb endochondral element intersection_of: UBERON:0015061 ! limb endochondral element -intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue -relationship: develops_from UBERON:0010882 ! limb bone pre-cartilage condensation +intersection_of: RO:0002473 UBERON:0002418 ! composed primarily of cartilage tissue +relationship: RO:0002202 UBERON:0010882 ! develops from limb bone pre-cartilage condensation [Term] id: UBERON:0010882 @@ -242547,8 +239264,8 @@ namespace: uberon def: "A skeletal element that is part of a limb and composed of pre-cartilage tissue." [http://orcid.org/0000-0002-6601-2165] is_a: UBERON:0015061 ! limb endochondral element intersection_of: UBERON:0015061 ! limb endochondral element -intersection_of: composed_primarily_of UBERON:0005866 ! pre-cartilage condensation -relationship: composed_primarily_of UBERON:0005866 ! pre-cartilage condensation +intersection_of: RO:0002473 UBERON:0005866 ! composed primarily of pre-cartilage condensation +relationship: RO:0002473 UBERON:0005866 ! composed primarily of pre-cartilage condensation [Term] id: UBERON:0010883 @@ -242562,8 +239279,8 @@ xref: EMAPA:32626 is_a: UBERON:0010881 ! limb cartilage element is_a: UBERON:0015021 ! forelimb endochondral element intersection_of: UBERON:0015021 ! forelimb endochondral element -intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue -relationship: develops_from UBERON:0010884 ! forelimb bone pre-cartilage condensation +intersection_of: RO:0002473 UBERON:0002418 ! composed primarily of cartilage tissue +relationship: RO:0002202 UBERON:0010884 ! develops from forelimb bone pre-cartilage condensation [Term] id: UBERON:0010884 @@ -242576,7 +239293,7 @@ xref: EMAPA:32625 is_a: UBERON:0010882 ! limb bone pre-cartilage condensation is_a: UBERON:0015021 ! forelimb endochondral element intersection_of: UBERON:0015021 ! forelimb endochondral element -intersection_of: composed_primarily_of UBERON:0005866 ! pre-cartilage condensation +intersection_of: RO:0002473 UBERON:0005866 ! composed primarily of pre-cartilage condensation [Term] id: UBERON:0010885 @@ -242588,8 +239305,8 @@ xref: EMAPA:32632 is_a: UBERON:0010881 ! limb cartilage element is_a: UBERON:0015022 ! hindlimb endochondral element intersection_of: UBERON:0015022 ! hindlimb endochondral element -intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue -relationship: develops_from UBERON:0010886 ! hindlimb pre-cartilage condensation +intersection_of: RO:0002473 UBERON:0002418 ! composed primarily of cartilage tissue +relationship: RO:0002202 UBERON:0010886 ! develops from hindlimb pre-cartilage condensation [Term] id: UBERON:0010886 @@ -242601,7 +239318,7 @@ xref: EMAPA:32638 is_a: UBERON:0010882 ! limb bone pre-cartilage condensation is_a: UBERON:0015022 ! hindlimb endochondral element intersection_of: UBERON:0015022 ! hindlimb endochondral element -intersection_of: composed_primarily_of UBERON:0005866 ! pre-cartilage condensation +intersection_of: RO:0002473 UBERON:0005866 ! composed primarily of pre-cartilage condensation [Term] id: UBERON:0010890 @@ -242623,7 +239340,6 @@ is_a: UBERON:0014892 ! skeletal muscle organ, vertebrate intersection_of: UBERON:0014892 ! skeletal muscle organ, vertebrate intersection_of: part_of UBERON:0010709 ! pelvic complex relationship: part_of UBERON:0014792 {source="prolog"} ! musculature of pelvic complex -property_value: UBPROP:0000001 "Muscles of the pelvic girdle, thigh, leg (crus), and foot (pes).[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000218", ontology="AAO", source="AAO:EJS"} [Term] id: UBERON:0010891 @@ -242643,8 +239359,7 @@ is_a: UBERON:0014892 ! skeletal muscle organ, vertebrate intersection_of: UBERON:0014892 ! skeletal muscle organ, vertebrate intersection_of: part_of UBERON:0010708 ! pectoral complex relationship: part_of UBERON:0014793 {source="prolog"} ! musculature of pectoral complex -property_value: editor_note "the MA class belongs here, based on its current child classes" xsd:string -property_value: UBPROP:0000001 "Muscles of the pectoral girdle, arm, forearm, and hand (brachium, antebrachium, manus respectively).[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010687", ontology="AAO", source="AAO:EJS"} +property_value: IAO:0000116 "the MA class belongs here, based on its current child classes" xsd:string [Term] id: UBERON:0010893 @@ -242658,10 +239373,10 @@ synonym: "median nostril" EXACT [] synonym: "nasohypophysial opening" EXACT [http://tolweb.org/Hyperoartia] is_a: UBERON:0005928 ! external naris intersection_of: UBERON:0005928 ! external naris -intersection_of: intersects_midsagittal_plane_of UBERON:0000033 ! head -relationship: intersects_midsagittal_plane_of UBERON:0000033 ! head -relationship: never_in_taxon NCBITaxon:314146 ! Euarchontoglires -relationship: present_in_taxon NCBITaxon:7762 +intersection_of: BSPO:0005001 UBERON:0000033 ! head +relationship: BSPO:0005001 UBERON:0000033 ! head +property_value: RO:0002161 NCBITaxon:314146 +property_value: RO:0002175 NCBITaxon:7762 [Term] id: UBERON:0010894 @@ -242672,11 +239387,11 @@ subset: cyclostome_subset synonym: "horny denticle" EXACT [http://tolweb.org/Hyperoartia] is_a: UBERON:0003913 ! tooth-like structure intersection_of: UBERON:0003913 ! tooth-like structure -intersection_of: composed_primarily_of GO:0045095 ! keratin filament -relationship: composed_primarily_of GO:0045095 ! keratin filament -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata -relationship: present_in_taxon NCBITaxon:117569 -relationship: present_in_taxon NCBITaxon:7762 +intersection_of: RO:0002473 GO:0045095 ! composed primarily of keratin filament +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002473 GO:0045095 ! composed primarily of keratin filament +property_value: RO:0002175 NCBITaxon:117569 +property_value: RO:0002175 NCBITaxon:7762 [Term] id: UBERON:0010899 @@ -242707,11 +239422,11 @@ synonym: "clavicle primordium" EXACT [] xref: EHDAA2:0000254 is_a: UBERON:0001048 ! primordium intersection_of: UBERON:0001048 ! primordium -intersection_of: has_potential_to_develop_into UBERON:0001105 ! clavicle bone -relationship: develops_from UBERON:0006210 {source="EHDAA2"} ! body-wall mesenchyme -relationship: has_developmental_contribution_from UBERON:0002342 {editor="mah", notes="shown in mouse", source="PMC1352163"} ! neural crest -relationship: has_potential_to_develop_into UBERON:0001105 ! clavicle bone +intersection_of: RO:0002387 UBERON:0001105 ! has potential to develop into clavicle bone relationship: part_of UBERON:0007831 {source="EHDAA2"} ! pectoral girdle skeleton +relationship: RO:0002202 UBERON:0006210 {source="EHDAA2"} ! develops from body-wall mesenchyme +relationship: RO:0002254 UBERON:0002342 ! has developmental contribution from neural crest +relationship: RO:0002387 UBERON:0001105 ! has potential to develop into clavicle bone [Term] id: UBERON:0010911 @@ -242723,7 +239438,7 @@ subset: human_reference_atlas xref: VSAO:0000132 xref: Wikipedia:Ossicles is_a: UBERON:0004765 {source="VSAO"} ! skeletal element -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0010912 @@ -242739,7 +239454,6 @@ xref: VSAO:0000042 is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision relationship: part_of UBERON:0000075 {source="UBERONREF:0000003"} ! subdivision of skeletal system relationship: part_of UBERON:0004288 {source="VSAO"} ! skeleton -property_value: UBPROP:0000001 "Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000042", notes="incorrect", ontology="VSAO", source="VSAO:curator"} [Term] id: UBERON:0010913 @@ -242754,11 +239468,7 @@ synonym: "vertebral endochondral element" NARROW [https://github.com/obophenotyp xref: VHOG:0001143 xref: VSAO:0000184 is_a: UBERON:0004765 {source="VSAO", source="https://github.com/obophenotype/uberon/issues/82"} ! skeletal element -relationship: develops_from UBERON:0003089 {source="cjm"} ! sclerotome -property_value: IAO:0000232 "we include a distinct subclass for bony vertebra" xsd:string -property_value: UBPROP:0000003 "In contrast to lampreys and jawed vertebrates, hagfishes were thought to lack vertebrae. Now, long overlooked vertebral rudiments have been analysed in hagfish, suggesting that vertebrae existed in the last common ancestor of all vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001143", ontology="VHOG", source="DOI:10.1016/j.cub.2011.07.014 Janvier P, Comparative anatomy: all vertebrates do have vertebrae. Current Biology (2011)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "vertebral" xsd:string -property_value: UBPROP:0000008 "Typically an endochondral element, in salamanders there is an argument that vertebral development is perichondral and not preformed in cartilage" xsd:string +relationship: RO:0002202 UBERON:0003089 {source="cjm"} ! develops from sclerotome [Term] id: UBERON:0010948 @@ -242775,10 +239485,10 @@ xref: NCIT:C52895 is_a: UBERON:0000933 ! chordate pharyngeal muscle is_a: UBERON:0014892 ! skeletal muscle organ, vertebrate intersection_of: UBERON:0014892 ! skeletal muscle organ, vertebrate -intersection_of: attaches_to UBERON:0001105 ! clavicle bone -intersection_of: attaches_to UBERON:0001676 ! occipital bone -relationship: attaches_to UBERON:0001105 ! clavicle bone -relationship: attaches_to UBERON:0001676 ! occipital bone +intersection_of: RO:0002371 UBERON:0001105 ! attached to clavicle bone +intersection_of: RO:0002371 UBERON:0001676 ! attached to occipital bone +relationship: RO:0002371 UBERON:0001105 ! attached to clavicle bone +relationship: RO:0002371 UBERON:0001676 ! attached to occipital bone [Term] id: UBERON:0010949 @@ -242791,12 +239501,11 @@ xref: MA:0002385 xref: NCIT:C53069 xref: UMLS:C1710196 {source="ncithesaurus:Sternooccipital"} is_a: UBERON:0002377 ! muscle of neck -is_a: UBERON:0003897 ! axial muscle intersection_of: UBERON:0014892 ! skeletal muscle organ, vertebrate -intersection_of: has_muscle_insertion UBERON:0001676 ! occipital bone -intersection_of: has_muscle_origin UBERON:0000975 ! sternum -relationship: has_muscle_insertion UBERON:0001676 ! occipital bone -relationship: has_muscle_origin UBERON:0000975 ! sternum +intersection_of: RO:0002372 UBERON:0000975 ! has muscle origin sternum +intersection_of: RO:0002373 UBERON:0001676 ! has muscle insertion occipital bone +relationship: RO:0002372 UBERON:0000975 ! has muscle origin sternum +relationship: RO:0002373 UBERON:0001676 ! has muscle insertion occipital bone [Term] id: UBERON:0010955 @@ -242804,9 +239513,10 @@ name: trapezius pre-muscle mass namespace: uberon xref: EHDAA2:0002079 is_a: UBERON:0005865 {source="EHDAA2"} ! pre-muscle condensation +is_a: UBERON:0006904 ! head mesenchyme from mesoderm is_a: UBERON:0010258 ! mesenchyme from rhombencephalic neural crest -relationship: develops_from UBERON:0010258 {source="EHDAA2"} ! mesenchyme from rhombencephalic neural crest relationship: part_of UBERON:0008713 {source="EHDAA2"} ! pectoral girdle and thoracic body wall skeletal muscle +relationship: RO:0002202 UBERON:0010258 {source="EHDAA2"} ! develops from mesenchyme from rhombencephalic neural crest [Term] id: UBERON:0010959 @@ -242837,27 +239547,30 @@ id: UBERON:0010982 name: latissimus dorsi pre-muscle mass namespace: uberon xref: EHDAA2:0000933 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005865 {source="EHDAA2"} ! pre-muscle condensation -relationship: develops_from UBERON:0010963 {source="EHDAA2"} ! trunk and cervical myotome group relationship: part_of UBERON:0008713 {source="EHDAA2"} ! pectoral girdle and thoracic body wall skeletal muscle +relationship: RO:0002202 UBERON:0010963 {source="EHDAA2"} ! develops from trunk and cervical myotome group [Term] id: UBERON:0010983 name: levator scapulae pre-muscle mass namespace: uberon xref: EHDAA2:0000993 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005865 {source="EHDAA2"} ! pre-muscle condensation -relationship: develops_from UBERON:0010963 {source="EHDAA2"} ! trunk and cervical myotome group relationship: part_of UBERON:0008713 {source="EHDAA2"} ! pectoral girdle and thoracic body wall skeletal muscle +relationship: RO:0002202 UBERON:0010963 {source="EHDAA2"} ! develops from trunk and cervical myotome group [Term] id: UBERON:0010984 name: pectoral pre-muscle mass namespace: uberon xref: EHDAA2:0001423 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005865 {source="EHDAA2"} ! pre-muscle condensation -relationship: develops_from UBERON:0010963 {source="EHDAA2"} ! trunk and cervical myotome group relationship: part_of UBERON:0008713 {source="EHDAA2"} ! pectoral girdle and thoracic body wall skeletal muscle +relationship: RO:0002202 UBERON:0010963 {source="EHDAA2"} ! develops from trunk and cervical myotome group [Term] id: UBERON:0010986 @@ -242867,8 +239580,8 @@ synonym: "serratus anterior pre-muscle mass" EXACT [EHDAA2:0001833] xref: EHDAA2:0001833 xref: EHDAA:5992 is_a: UBERON:0005865 {source="EHDAA2"} ! pre-muscle condensation -relationship: develops_from UBERON:0010963 {source="EHDAA2"} ! trunk and cervical myotome group relationship: part_of UBERON:0003897 {source="EHDAA2"} ! axial muscle +relationship: RO:0002202 UBERON:0010963 {source="EHDAA2"} ! develops from trunk and cervical myotome group [Term] id: UBERON:0010996 @@ -242899,7 +239612,7 @@ xref: SCTID:305026006 xref: UMLS:C0007303 {source="ncithesaurus:Articular_Cartilage"} is_a: UBERON:0001994 {source="MA"} ! hyaline cartilage tissue relationship: part_of UBERON:0002217 {source="Wikipedia"} ! synovial joint -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0011004 @@ -242909,15 +239622,14 @@ def: "A cartilage element that is part of a splanchnocranium." [OBOL:automatic] subset: efo_slim synonym: "pharyngeal arch cartilages" EXACT OMO:0003004 [ZFA:0001460] synonym: "splanchnocranium cartilage" EXACT [ZFA:0001460] -xref: BTO:0006051 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: EFO:0003689 xref: TAO:0001460 xref: ZFA:0001460 is_a: UBERON:0003933 {source="ZFA"} ! cranial cartilage intersection_of: UBERON:0007844 ! cartilage element intersection_of: part_of UBERON:0008895 ! splanchnocranium -relationship: develops_from UBERON:0002539 ! pharyngeal arch relationship: part_of UBERON:0008895 {source="ZFA"} ! splanchnocranium +relationship: RO:0002202 UBERON:0002539 ! develops from pharyngeal arch [Term] id: UBERON:0011060 @@ -242936,10 +239648,10 @@ xref: SCTID:368950002 xref: Wikipedia:Perilymphatic_duct xref: ZFA:0005461 is_a: UBERON:0000025 ! tube +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001846 {source="MA"} ! internal ear -relationship: surrounds UBERON:0001845 ! perilymph -property_value: editor_note "relationship to FMA class unclear" xsd:string -property_value: UBPROP:0000001 "Duct that contains perilymph[ZFA:0005461, ZFIN:curator]." xsd:string {source="ZFA:0005461, ZFIN:curator"} +relationship: RO:0002221 UBERON:0001845 ! surrounds perilymph +property_value: IAO:0000116 "relationship to FMA class unclear" xsd:string [Term] id: UBERON:0011085 @@ -242957,13 +239669,12 @@ synonym: "upper pharyngeal jaw" EXACT [ZFA:0001272] synonym: "upper pharyngeal jaw" RELATED [VHOG:0000511] xref: EFO:0003659 xref: TAO:0001272 -xref: VHOG:0000511 xref: ZFA:0001272 +is_a: UBERON:0010313 ! neural crest-derived structure is_a: UBERON:0010912 {source="cjm"} ! subdivision of skeleton -relationship: develops_from UBERON:0004362 ! pharyngeal arch 1 relationship: part_of UBERON:0003277 ! skeleton of upper jaw relationship: part_of UBERON:0008895 {source="VHOG"} ! splanchnocranium -property_value: UBPROP:0000003 "Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000511", ontology="VHOG", source="DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0004362 ! develops from pharyngeal arch 1 [Term] id: UBERON:0011088 @@ -243009,10 +239720,9 @@ synonym: "right pelvic girdle" EXACT INCONSISTENT [FMA:16582] xref: FMA:16582 is_a: UBERON:0001271 ! pelvic girdle region intersection_of: UBERON:0001271 ! pelvic girdle region -intersection_of: in_right_side_of UBERON:0000468 ! multicellular organism -relationship: has_skeleton UBERON:0011090 ! skeleton of right pelvic girdle -relationship: in_right_side_of UBERON:0000468 ! multicellular organism -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +intersection_of: BSPO:0000121 UBERON:0000468 ! multicellular organism +relationship: BSPO:0000121 UBERON:0000468 ! multicellular organism +relationship: RO:0002551 UBERON:0011090 ! has skeleton skeleton of right pelvic girdle [Term] id: UBERON:0011093 @@ -243023,10 +239733,9 @@ synonym: "left pelvic girdle" EXACT INCONSISTENT [FMA:16583] xref: FMA:16583 is_a: UBERON:0001271 ! pelvic girdle region intersection_of: UBERON:0001271 ! pelvic girdle region -intersection_of: in_left_side_of UBERON:0000468 ! multicellular organism -relationship: has_skeleton UBERON:0011091 ! skeleton of left pelvic girdle -relationship: in_left_side_of UBERON:0000468 ! multicellular organism -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +intersection_of: BSPO:0000120 UBERON:0000468 ! multicellular organism +relationship: BSPO:0000120 UBERON:0000468 ! multicellular organism +relationship: RO:0002551 UBERON:0011091 ! has skeleton skeleton of left pelvic girdle [Term] id: UBERON:0011094 @@ -243039,11 +239748,9 @@ xref: VHOG:0000584 is_a: UBERON:0007844 ! cartilage element is_a: UBERON:0010913 ! vertebral element intersection_of: UBERON:0010913 ! vertebral element -intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue -relationship: develops_from UBERON:0011095 ! vertebra pre-cartilage condensation -relationship: has_potential_to_develop_into UBERON:0002412 ! vertebra -relationship: present_in_taxon NCBITaxon:7764 {notes="vertebra-like cartilage in hagfish are homologous to gnathostome vertebrae. mesenchymal cells express Pax1/9 and Twist", source="PMC3157150"} -property_value: UBPROP:0000012 "This class is a superclass of individual vertebral cartilage condensations. Note that EHDAA2 represents these as condensation groups" xsd:string {external_ontology="EHDAA2"} +intersection_of: RO:0002473 UBERON:0002418 ! composed primarily of cartilage tissue +relationship: RO:0002202 UBERON:0011095 ! develops from vertebra pre-cartilage condensation +relationship: RO:0002387 UBERON:0002412 ! has potential to develop into vertebra [Term] id: UBERON:0011095 @@ -243055,9 +239762,9 @@ xref: EMAPA:32671 xref: VHOG:0000582 is_a: UBERON:0010913 ! vertebral element intersection_of: UBERON:0010913 ! vertebral element -intersection_of: composed_primarily_of UBERON:0005866 ! pre-cartilage condensation -relationship: composed_primarily_of UBERON:0005866 ! pre-cartilage condensation -relationship: has_potential_to_develop_into UBERON:0002412 ! vertebra +intersection_of: RO:0002473 UBERON:0005866 ! composed primarily of pre-cartilage condensation +relationship: RO:0002387 UBERON:0002412 ! has potential to develop into vertebra +relationship: RO:0002473 UBERON:0005866 ! composed primarily of pre-cartilage condensation [Term] id: UBERON:0011096 @@ -243069,11 +239776,12 @@ xref: FMA:52628 xref: NCIT:C32908 xref: SCTID:280218007 xref: Wikipedia:Lacrimal_nerve -is_a: UBERON:0001021 ! nerve +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0011779 ! nerve of head region intersection_of: UBERON:0001021 ! nerve -intersection_of: innervates UBERON:0001817 ! lacrimal gland -relationship: branching_part_of UBERON:0000348 {source="FMA"} ! ophthalmic nerve -relationship: innervates UBERON:0001817 ! lacrimal gland +intersection_of: RO:0002134 UBERON:0001817 ! innervates lacrimal gland +relationship: RO:0002134 UBERON:0001817 ! innervates lacrimal gland +relationship: RO:0002380 UBERON:0000348 {source="FMA"} ! branching part of ophthalmic nerve [Term] id: UBERON:0011107 @@ -243089,8 +239797,8 @@ is_a: UBERON:0002217 ! synovial joint is_a: UBERON:0008114 ! joint of girdle intersection_of: UBERON:0002217 ! synovial joint intersection_of: part_of UBERON:0001271 ! pelvic girdle region -relationship: connects UBERON:0007830 ! pelvic girdle bone/zone relationship: part_of UBERON:0001271 ! pelvic girdle region +relationship: RO:0002176 UBERON:0007830 ! connects pelvic girdle bone/zone [Term] id: UBERON:0011108 @@ -243105,9 +239813,8 @@ is_a: UBERON:0002217 ! synovial joint is_a: UBERON:0008114 ! joint of girdle intersection_of: UBERON:0002217 ! synovial joint intersection_of: part_of UBERON:0001421 ! pectoral girdle region -relationship: connects UBERON:0007829 ! pectoral girdle bone relationship: part_of UBERON:0001421 ! pectoral girdle region -property_value: UBPROP:0000012 "in FMA, these are part of the bony pectoral girdle" xsd:string {external_ontology="FMA"} +relationship: RO:0002176 UBERON:0007829 ! connects pectoral girdle bone [Term] id: UBERON:0011112 @@ -243123,13 +239830,13 @@ xref: Wikipedia:Tibiofibular_joint is_a: UBERON:0002210 {source="FMA"} ! syndesmosis is_a: UBERON:0003840 ! hindlimb joint intersection_of: UBERON:0000982 ! skeletal joint -intersection_of: connects UBERON:0000979 ! tibia -intersection_of: connects UBERON:0001446 ! fibula intersection_of: part_of UBERON:0003823 ! hindlimb zeugopod -relationship: connects UBERON:0000979 ! tibia -relationship: connects UBERON:0001446 ! fibula +intersection_of: RO:0002176 UBERON:0000979 ! connects tibia +intersection_of: RO:0002176 UBERON:0001446 ! connects fibula relationship: part_of UBERON:0003823 ! hindlimb zeugopod -property_value: editor_note "we include location as part of the logical definition to prevent accidental classification of ankle joints as tibiofibular joints" xsd:string +relationship: RO:0002176 UBERON:0000979 ! connects tibia +relationship: RO:0002176 UBERON:0001446 ! connects fibula +property_value: IAO:0000116 "we include location as part of the logical definition to prevent accidental classification of ankle joints as tibiofibular joints" xsd:string [Term] id: UBERON:0011118 @@ -243148,12 +239855,12 @@ xref: SCTID:182222008 xref: Wikipedia:Tarsometatarsal_articulations is_a: UBERON:0001487 ! pes joint intersection_of: UBERON:0000982 ! skeletal joint -intersection_of: connects UBERON:0001447 ! tarsal bone -intersection_of: connects UBERON:0001448 ! metatarsal bone -relationship: connects UBERON:0001447 ! tarsal bone -relationship: connects UBERON:0001448 ! metatarsal bone -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/8e/Gray355.png" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/dc/Gray358.png" xsd:anyURI +intersection_of: RO:0002176 UBERON:0001447 ! connects tarsal bone +intersection_of: RO:0002176 UBERON:0001448 ! connects metatarsal bone +relationship: RO:0002176 UBERON:0001447 ! connects tarsal bone +relationship: RO:0002176 UBERON:0001448 ! connects metatarsal bone +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8e/Gray355.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/dc/Gray358.png" xsd:anyURI [Term] id: UBERON:0011119 @@ -243165,18 +239872,17 @@ synonym: "carpometacarpal" BROAD [Wikipedia:Carpometacarpal_joint] synonym: "carpometacarpal articulation" RELATED [Wikipedia:Carpometacarpal_joint] synonym: "CMJ" BROAD [Wikipedia:Carpometacarpal_joint] xref: FMA:35287 -xref: MESH:D052737 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C32265 xref: SCTID:361842002 xref: UMLS:C0224620 {source="ncithesaurus:Carpometacarpal_Joint"} xref: Wikipedia:Carpometacarpal_joint is_a: UBERON:0001489 ! manus joint intersection_of: UBERON:0000982 ! skeletal joint -intersection_of: connects UBERON:0001435 ! carpal bone -intersection_of: connects UBERON:0002374 ! metacarpal bone -relationship: connects UBERON:0001435 ! carpal bone -relationship: connects UBERON:0002374 ! metacarpal bone -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/7c/Gray335.png" xsd:anyURI +intersection_of: RO:0002176 UBERON:0001435 ! connects carpal bone +intersection_of: RO:0002176 UBERON:0002374 ! connects metacarpal bone +relationship: RO:0002176 UBERON:0001435 ! connects carpal bone +relationship: RO:0002176 UBERON:0002374 ! connects metacarpal bone +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7c/Gray335.png" xsd:anyURI [Term] id: UBERON:0011120 @@ -243188,9 +239894,9 @@ synonym: "laryngeal articulation" EXACT [FMA:55100] xref: FMA:55100 is_a: UBERON:0002217 {source="FMA"} ! synovial joint intersection_of: UBERON:0000982 ! skeletal joint -intersection_of: connects UBERON:0001739 ! laryngeal cartilage -relationship: connects UBERON:0001739 ! laryngeal cartilage +intersection_of: RO:0002176 UBERON:0001739 ! connects laryngeal cartilage relationship: part_of UBERON:0010323 ! cranial skeletal system +relationship: RO:0002176 UBERON:0001739 ! connects laryngeal cartilage [Term] id: UBERON:0011131 @@ -243204,9 +239910,9 @@ xref: SCTID:303065007 xref: Wikipedia:Intermetacarpal_articulations is_a: UBERON:0001489 ! manus joint intersection_of: UBERON:0000982 ! skeletal joint -intersection_of: connects UBERON:0002374 {cardinality="2"} ! metacarpal bone -relationship: connects UBERON:0002374 {notes="two adjacent metacarpals"} ! metacarpal bone +intersection_of: RO:0002176 UBERON:0002374 {cardinality="2"} ! connects metacarpal bone relationship: part_of UBERON:0004453 ! metacarpus region +relationship: RO:0002176 UBERON:0002374 ! connects metacarpal bone [Term] id: UBERON:0011132 @@ -243218,17 +239924,16 @@ synonym: "intercarpal" RELATED [Wikipedia:Intercarpal_articulations] synonym: "intercarpal articulation" RELATED [Wikipedia:Intercarpal_articulations] synonym: "midcarpal articulation" RELATED [Wikipedia:Intercarpal_articulations] xref: FMA:35292 -xref: MESH:D050824 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: NCIT:C32264 xref: SCTID:182176003 xref: UMLS:C1262468 {source="ncithesaurus:Carpal_Joint"} xref: Wikipedia:Intercarpal_articulations is_a: UBERON:0001489 ! manus joint intersection_of: UBERON:0000982 ! skeletal joint -intersection_of: connects UBERON:0001435 {cardinality="2"} ! carpal bone -relationship: connects UBERON:0001435 {notes="two adjacent carpals"} ! carpal bone +intersection_of: RO:0002176 UBERON:0001435 {cardinality="2"} ! connects carpal bone relationship: part_of UBERON:0004452 {source="FMA"} ! carpal region -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/37/Gray336.png" xsd:anyURI +relationship: RO:0002176 UBERON:0001435 ! connects carpal bone +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/37/Gray336.png" xsd:anyURI [Term] id: UBERON:0011133 @@ -243240,11 +239945,10 @@ xref: SCTID:361868009 xref: Wikipedia:Intermetatarsal_articulations is_a: UBERON:0001487 ! pes joint intersection_of: UBERON:0000982 ! skeletal joint -intersection_of: connects UBERON:0001448 {cardinality="2"} ! metatarsal bone -relationship: connects UBERON:0001448 {notes="two adjacent metatarsals"} ! metatarsal bone +intersection_of: RO:0002176 UBERON:0001448 {cardinality="2"} ! connects metatarsal bone relationship: part_of UBERON:0000983 ! metatarsus region -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/dc/Gray358.png" xsd:anyURI -property_value: UBPROP:0000008 "In humans: The base of the first metatarsal is not connected with that of the second by any ligaments; in this respect the great toe resembles the thumb" xsd:string {source="WP"} +relationship: RO:0002176 UBERON:0001448 ! connects metatarsal bone +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/dc/Gray358.png" xsd:anyURI [Term] id: UBERON:0011134 @@ -243264,9 +239968,8 @@ xref: AAO:0000795 is_a: UBERON:0007844 ! cartilage element intersection_of: UBERON:0007844 ! cartilage element intersection_of: adjacent_to UBERON:0001075 {cardinality="2"} ! bony vertebral centrum -relationship: adjacent_to UBERON:0001075 {notes="between two centra"} ! bony vertebral centrum +relationship: adjacent_to UBERON:0001075 ! bony vertebral centrum relationship: part_of UBERON:0001468 {source="FMA", source="MA"} ! intervertebral joint -property_value: UBPROP:0000001 "Block of cartilage, which usually ossifies, that lies between successive vertebral centra.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000795", ontology="AAO", source="AAO:Trueb_1973"} [Term] id: UBERON:0011136 @@ -243280,9 +239983,9 @@ xref: FMA:31892 xref: SCTID:244590009 is_a: UBERON:0008846 ! skeletal ligament intersection_of: UBERON:0008846 ! skeletal ligament -intersection_of: attaches_to UBERON:0001075 ! bony vertebral centrum -relationship: attaches_to UBERON:0001075 ! bony vertebral centrum +intersection_of: RO:0002371 UBERON:0001075 ! attached to bony vertebral centrum relationship: part_of UBERON:0001130 ! vertebral column +relationship: RO:0002371 UBERON:0001075 ! attached to bony vertebral centrum [Term] id: UBERON:0011137 @@ -243303,7 +240006,7 @@ synonym: "axial skeletal system" BROAD [https://github.com/obophenotype/uberon/w synonym: "post-cranial axial skeletal system" EXACT [] xref: FMA:302077 is_a: UBERON:0000075 {source="FMA"} ! subdivision of skeletal system -relationship: develops_from UBERON:0003089 {source="cjm"} ! sclerotome +relationship: RO:0002202 UBERON:0003089 {source="cjm"} ! develops from sclerotome property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" xsd:anyURI [Term] @@ -243361,11 +240064,11 @@ xref: NCIT:C61107 xref: SCTID:181413006 is_a: UBERON:0011216 ! organ system subdivision is_a: UBERON:0015212 ! lateral structure +relationship: BSPO:0000126 UBERON:0001008 {source="FMA-abduced-lr"} ! renal system relationship: has_part UBERON:0000056 ! ureter relationship: has_part UBERON:0002113 ! kidney -relationship: in_lateral_side_of UBERON:0001008 {source="FMA-abduced-lr"} ! renal system relationship: part_of UBERON:0001008 {source="FMA"} ! renal system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0011148 @@ -243377,9 +240080,9 @@ xref: EMAPA:37970 {source="MA:th"} xref: Wikipedia:Submucosal_glands is_a: UBERON:0000414 ! mucous gland intersection_of: UBERON:0000414 ! mucous gland -intersection_of: located_in UBERON:0000009 ! submucosa -relationship: continuous_with UBERON:0003350 {notes="perforates"} ! epithelium of mucosa -relationship: located_in UBERON:0000009 ! submucosa +intersection_of: RO:0001025 UBERON:0000009 ! located in submucosa +relationship: RO:0001025 UBERON:0000009 ! located in submucosa +relationship: RO:0002150 UBERON:0003350 ! continuous with epithelium of mucosa [Term] id: UBERON:0011156 @@ -243401,7 +240104,7 @@ xref: Wikipedia:Facial_skeleton is_a: UBERON:0010313 ! neural crest-derived structure is_a: UBERON:0011158 {source="FMA"} ! primary subdivision of skull relationship: part_of UBERON:0001456 {source="FMA"} ! face -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/77/Illu_facial_bones.jpg" xsd:anyURI [Term] id: UBERON:0011158 @@ -243445,14 +240148,12 @@ namespace: uberon def: "Synovial joint that articulates bones of upper and lower jaw." [http://evolution.berkeley.edu/evolibrary/article/evograms_05, https://orcid.org/0000-0002-6601-2165] synonym: "craniomandibular joint" NARROW [] synonym: "jaw joint" BROAD [] -xref: NCIT:C32888 is_a: UBERON:0002217 {source="abduced"} ! synovial joint intersection_of: UBERON:0000982 ! skeletal joint -intersection_of: connects UBERON:0003277 ! skeleton of upper jaw -intersection_of: connects UBERON:0003278 ! skeleton of lower jaw -relationship: connects UBERON:0003277 ! skeleton of upper jaw -relationship: connects UBERON:0003278 ! skeleton of lower jaw -property_value: UBPROP:0000008 "Some synapsids retained two pairs of jaw joints - quadrate-articular and tempero-mandibular, but this unusual paired condition did not last long" xsd:string {source="http://evolution.berkeley.edu"} +intersection_of: RO:0002176 UBERON:0003277 ! connects skeleton of upper jaw +intersection_of: RO:0002176 UBERON:0003278 ! connects skeleton of lower jaw +relationship: RO:0002176 UBERON:0003277 ! connects skeleton of upper jaw +relationship: RO:0002176 UBERON:0003278 ! connects skeleton of lower jaw [Term] id: UBERON:0011184 @@ -243468,8 +240169,7 @@ is_a: UBERON:0001277 ! intestinal epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001983 ! crypt of Lieberkuhn relationship: part_of UBERON:0001983 ! crypt of Lieberkuhn -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000012 "FMA has classes for subdivisions of this epithelium" xsd:string {external_ontology="FMA"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0011185 @@ -243500,7 +240200,7 @@ is_a: UBERON:0004780 ! gastrointestinal system lamina propria intersection_of: UBERON:0000030 ! lamina propria intersection_of: part_of UBERON:0000059 ! large intestine relationship: part_of UBERON:0001207 {source="FMA"} ! mucosa of large intestine -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0011191 @@ -243514,9 +240214,9 @@ xref: EMAPA:19313 xref: Wikipedia:Ophthalmic_veins xref: XAO:0004169 is_a: UBERON:0009141 {source="EHDAA2-modified"} ! craniocervical region vein -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray572.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray572.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI [Term] id: UBERON:0011192 @@ -243532,9 +240232,9 @@ xref: FMA:51246 xref: SCTID:149481004 xref: Wikipedia:Superior_ophthalmic_vein is_a: UBERON:0011191 ! ophthalmic vein -relationship: connected_to UBERON:0003712 ! cavernous sinus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray572.png" xsd:anyURI +relationship: RO:0002170 UBERON:0003712 ! connected to cavernous sinus +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray572.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0011197 @@ -243549,9 +240249,9 @@ is_a: UBERON:0005911 ! endo-epithelium is_a: UBERON:0006799 ! glandular epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001132 ! parathyroid gland -relationship: composed_primarily_of CL:0002260 ! epithelial cell of parathyroid gland -relationship: develops_from UBERON:0004117 ! pharyngeal pouch relationship: part_of UBERON:0001132 ! parathyroid gland +relationship: RO:0002202 UBERON:0004117 ! develops from pharyngeal pouch +relationship: RO:0002473 CL:0002260 ! composed primarily of epithelial cell of parathyroid gland [Term] id: UBERON:0011198 @@ -243610,7 +240310,6 @@ is_a: UBERON:0002211 ! nerve root intersection_of: UBERON:0002211 ! nerve root intersection_of: extends_fibers_into UBERON:0001759 ! vagus nerve relationship: extends_fibers_into UBERON:0001759 ! vagus nerve -property_value: UBPROP:0000012 "FMA distinguishes between roots and rootlets - we mix the two here" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0011214 @@ -243634,6 +240333,7 @@ subset: upper_level synonym: "cell part cluster of neuraxis" EXACT [FMA:83143] synonym: "neuraxis layer" EXACT [FMA:83143] xref: FMA:83143 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005162 ! multi cell part structure intersection_of: UBERON:0005162 ! multi cell part structure intersection_of: part_of UBERON:0001017 ! central nervous system @@ -243647,15 +240347,14 @@ def: "A subdivision of an anatomical system." [http://orcid.org/0000-0002-6601-2 subset: common_anatomy subset: human_reference_atlas subset: upper_level -xref: FBbt:00007330 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67509 xref: SCTID:91690000 is_a: UBERON:0010000 {source="FBbt"} ! multicellular anatomical structure relationship: part_of UBERON:0000467 ! anatomical system -relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 ! Fungi -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0011222 @@ -243666,9 +240365,9 @@ synonym: "intrinsic ocular muscle" EXACT [EMAPA:18808] xref: AAO:0010038 xref: EMAPA:18808 xref: FMA:49150 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004277 ! eye muscle relationship: part_of UBERON:0003386 {source="EMAPA"} ! smooth muscle of eye -property_value: UBPROP:0000001 "Muscles within the eye (bulbus oculi).[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010038", ontology="AAO", source="AAO:EJS"} [Term] id: UBERON:0011233 @@ -243694,9 +240393,9 @@ is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004923 ! organ component layer intersection_of: UBERON:0004923 ! organ component layer intersection_of: bounding_layer_of UBERON:0000304 ! tendon sheath -intersection_of: composed_primarily_of UBERON:0011824 ! fibrous connective tissue +intersection_of: RO:0002473 UBERON:0011824 ! composed primarily of fibrous connective tissue relationship: bounding_layer_of UBERON:0000304 ! tendon sheath -relationship: composed_primarily_of UBERON:0011824 ! fibrous connective tissue +relationship: RO:0002473 UBERON:0011824 ! composed primarily of fibrous connective tissue [Term] id: UBERON:0011241 @@ -243705,9 +240404,8 @@ namespace: uberon def: "The most anterior region of the braincase. Provides structural support for peripheral olfactory organ." [http://palaeos.com/vertebrates/bones/braincase/ethmoid.html, UBERONREF:0000007] xref: AAO:0000986 is_a: UBERON:0034921 ! multi organ part structure -relationship: has_developmental_contribution_from UBERON:0005945 ! neurocranial trabecula relationship: part_of UBERON:0003112 ! olfactory region -property_value: IAO:0000232 "currently this is not restricted to skeletal elements, unlike UBERONREF:0000007" xsd:string +relationship: RO:0002254 UBERON:0005945 ! has developmental contribution from neurocranial trabecula [Term] id: UBERON:0011249 @@ -243715,13 +240413,11 @@ name: appendicular skeletal system namespace: uberon def: "Subdivision of the skeletal system which consists of the appendicular skeleton plus associated joints." [https://orcid.org/0000-0002-6601-2165] xref: FMA:7484 -xref: VHOG:0001666 xref: VSAO:0000306 is_a: UBERON:0000075 ! subdivision of skeletal system relationship: has_part UBERON:0000982 ! skeletal joint relationship: has_part UBERON:0002091 ! appendicular skeleton property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton" xsd:anyURI -property_value: UBPROP:0000001 "Skeletal system which consists of the appendicular skeleton plus associated joints.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000306", ontology="VSAO", source="https://orcid.org/0000-0002-6601-2165"} [Term] id: UBERON:0011250 @@ -243731,9 +240427,8 @@ def: "A bone that is part of a autopod region. Note that this incudes the carpal is_a: UBERON:0002428 ! limb bone is_a: UBERON:0015063 ! autopod endochondral element intersection_of: UBERON:0015063 ! autopod endochondral element -intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue -relationship: develops_from UBERON:0015064 ! autopod cartilage -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern" xsd:anyURI +intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue +relationship: RO:0002202 UBERON:0015064 ! develops from autopod cartilage [Term] id: UBERON:0011270 @@ -243750,7 +240445,6 @@ xref: MA:0000020 xref: Wikipedia:Human_back is_a: UBERON:0009569 {source="FMA"} ! subdivision of trunk relationship: part_of UBERON:0001137 {source="FMA"} ! dorsum -property_value: UBPROP:0000008 "In humans, the subdivision of trunk which is demarcated from the trunk proper by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines, the external surface of the posterior abdominal wall; together with the trunk proper, it constitutes the trunk[FMA]" xsd:string [Term] id: UBERON:0011272 @@ -243760,9 +240454,10 @@ synonym: "basal cell layer of skin" RELATED [] synonym: "outer epithelium of body" RELATED [Wikipathways:WP2062] xref: EHDAA2:0001845 is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium -relationship: develops_from UBERON:0000076 {source="EHDAA2"} ! external ectoderm +is_a: UBERON:0010371 ! ecto-epithelium relationship: part_of UBERON:0002199 {source="EHDAA2"} ! integument -property_value: editor_note "compare with 'stratum basale of epidermis'. This class is the source for many adult structures - see WP2062. See also: 'enveloping layer of ectoderm'" xsd:string +relationship: RO:0002202 UBERON:0000076 {source="EHDAA2"} ! develops from external ectoderm +property_value: IAO:0000116 "compare with 'stratum basale of epidermis'. This class is the source for many adult structures - see WP2062. See also: 'enveloping layer of ectoderm'" xsd:string [Term] id: UBERON:0011289 @@ -243791,6 +240486,7 @@ synonym: "uterine submucosa" RELATED [] xref: BTO:0002116 xref: SCTID:245489008 is_a: UBERON:0000009 ! submucosa +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0000009 ! submucosa intersection_of: part_of UBERON:0003889 ! fallopian tube @@ -243817,7 +240513,6 @@ is_a: UBERON:0019261 ! white matter of forebrain intersection_of: UBERON:0002316 ! white matter intersection_of: part_of UBERON:0001893 ! telencephalon relationship: part_of UBERON:0001893 ! telencephalon -property_value: UBPROP:0000001 "CNS white matter that is part of the telencephalon[ZFA:0000597]." xsd:string {source="ZFA:0000597"} [Term] id: UBERON:0011300 @@ -243840,8 +240535,8 @@ namespace: uberon xref: EMAPA:17884 is_a: UBERON:0005865 ! pre-muscle condensation intersection_of: UBERON:0005865 ! pre-muscle condensation -intersection_of: has_potential_to_develop_into UBERON:0001575 ! extrinsic muscle of tongue -relationship: has_potential_to_develop_into UBERON:0001575 ! extrinsic muscle of tongue +intersection_of: RO:0002387 UBERON:0001575 ! has potential to develop into extrinsic muscle of tongue +relationship: RO:0002387 UBERON:0001575 ! has potential to develop into extrinsic muscle of tongue [Term] id: UBERON:0011357 @@ -243853,10 +240548,10 @@ xref: NLX:151878 xref: Wikipedia:Reissner's_fiber is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000476 ! acellular anatomical structure -relationship: composed_primarily_of PR:000015658 ! SCO-spondin +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001017 ! central nervous system -relationship: present_in_taxon NCBITaxon:7711 {source="ISBN:0471888893"} ! Chordata -property_value: UBPROP:0000008 "Reissner's fiber is present in the central canal of species in all chordate subphyla[Olsson R. (1993) Reissner's fiber mechanisms: some common denominators. In The Subcommissural Organ: An Ependymal Brain Gland ]" xsd:string +relationship: RO:0002473 PR:000015658 ! composed primarily of SCO-spondin +property_value: RO:0002175 NCBITaxon:7711 {source="ISBN:0471888893"} [Term] id: UBERON:0011362 @@ -243872,7 +240567,6 @@ is_a: UBERON:0002200 ! vasculature of head is_a: UBERON:0004537 ! blood vasculature intersection_of: UBERON:0004537 ! blood vasculature intersection_of: part_of UBERON:0000033 ! head -property_value: UBPROP:0000001 "Blood vessel part of cranial vasculature.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005297", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0011363 @@ -243904,7 +240598,7 @@ is_a: UBERON:0001077 ! transverse process of vertebra is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0001077 ! transverse process of vertebra intersection_of: part_of UBERON:0001092 ! vertebral bone 1 -relationship: in_lateral_side_of UBERON:0001092 {source="FMA-abduced-lr"} ! vertebral bone 1 +relationship: BSPO:0000126 UBERON:0001092 {source="FMA-abduced-lr"} ! vertebral bone 1 relationship: part_of UBERON:0001092 ! vertebral bone 1 [Term] @@ -243913,13 +240607,12 @@ name: prepuce namespace: uberon def: "A retractable double-layered fold of skin and mucous membrane that covers the glans penis or clitoris. Glands may also be present." [http://orcid.org/0000-0002-6601-2165] xref: NCIT:C12323 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005156 ! reproductive structure is_a: UBERON:0034929 ! external soft tissue zone relationship: has_part UBERON:0000344 ! mucosa relationship: part_of UBERON:0003133 ! reproductive organ -relationship: transformation_of UBERON:0035004 ! preputial swelling -property_value: IAO:0000232 "this is a generic sex-neutral grouping class for the male and female prepuce. Note that this structure is a combination of skin and other tissue" xsd:string -property_value: UBPROP:0000007 "preputial" xsd:string +relationship: RO:0002494 UBERON:0035004 ! transformation of preputial swelling [Term] id: UBERON:0011375 @@ -243967,10 +240660,10 @@ xref: FMA:9398 xref: SCTID:322648002 is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0001043 ! esophagus -relationship: luminal_space_of UBERON:0001043 ! esophagus +intersection_of: RO:0002572 UBERON:0001043 ! luminal space of esophagus relationship: part_of UBERON:0001043 ! esophagus relationship: part_of UBERON:0011565 {source="FMA"} ! lumen of gastrointestinal system +relationship: RO:0002572 UBERON:0001043 ! luminal space of esophagus [Term] id: UBERON:0011574 @@ -243982,8 +240675,8 @@ synonym: "nephric duct lumen" EXACT [EHDAA2:0001244] xref: EHDAA2:0001244 is_a: UBERON:0005082 ! tube lumen intersection_of: UBERON:0005082 ! tube lumen -intersection_of: luminal_space_of UBERON:0003074 ! mesonephric duct -relationship: luminal_space_of UBERON:0003074 ! mesonephric duct +intersection_of: RO:0002572 UBERON:0003074 ! luminal space of mesonephric duct +relationship: RO:0002572 UBERON:0003074 ! luminal space of mesonephric duct [Term] id: UBERON:0011582 @@ -243998,12 +240691,11 @@ xref: VSAO:0000301 is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010912 ! subdivision of skeleton intersection_of: UBERON:0010912 ! subdivision of skeleton -intersection_of: skeleton_of UBERON:0004708 ! paired limb/fin -relationship: develops_from UBERON:0003081 {source="ISBN:9780878932504"} ! lateral plate mesoderm +intersection_of: RO:0002576 UBERON:0004708 ! skeleton of paired limb/fin relationship: part_of UBERON:0002091 ! appendicular skeleton relationship: part_of UBERON:0004708 ! paired limb/fin -relationship: skeleton_of UBERON:0004708 ! paired limb/fin -property_value: UBPROP:0000001 "Skeletal subdivision that is part of the paired limb/fin.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000301", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070"} +relationship: RO:0002202 UBERON:0003081 {source="ISBN:9780878932504"} ! develops from lateral plate mesoderm +relationship: RO:0002576 UBERON:0004708 ! skeleton of paired limb/fin [Term] id: UBERON:0011583 @@ -244018,16 +240710,14 @@ synonym: "stylopod" RELATED [VSAO:0005007] synonym: "stylopodium" RELATED [] synonym: "stylopodium skeleton" EXACT [] xref: VSAO:0005007 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010712 ! limb skeleton subdivision intersection_of: UBERON:0010912 ! subdivision of skeleton -intersection_of: skeleton_of UBERON:0002472 ! stylopod +intersection_of: RO:0002576 UBERON:0002472 ! skeleton of stylopod relationship: distally_connected_to UBERON:0011584 {gci_relation="part_of", gci_filler="NCBITaxon:32523"} ! zeugopodial skeleton relationship: part_of UBERON:0002472 ! stylopod relationship: part_of UBERON:0004381 {source="VSAO"} ! skeleton of limb -relationship: skeleton_of UBERON:0002472 ! stylopod -property_value: UBPROP:0000001 "Proximal element of the limb skeleton consisting of the femur and humerus in the forelimb stylopodium and hindlimb stylopodium respectively.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0005007", ontology="VSAO", source="VSAO:NI"} -property_value: UBPROP:0000007 "propodial" xsd:string -property_value: UBPROP:0000007 "stylopodial" xsd:string +relationship: RO:0002576 UBERON:0002472 ! skeleton of stylopod [Term] id: UBERON:0011584 @@ -244042,16 +240732,15 @@ synonym: "skeleton of zeugopod" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "zeugopod skeleton" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "zygopodium" RELATED [VSAO:0005010] xref: VSAO:0005010 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010712 ! limb skeleton subdivision intersection_of: UBERON:0010912 ! subdivision of skeleton -intersection_of: skeleton_of UBERON:0002471 ! zeugopod +intersection_of: RO:0002576 UBERON:0002471 ! skeleton of zeugopod relationship: distally_connected_to UBERON:0006717 {gci_relation="part_of", gci_filler="NCBITaxon:32523"} ! autopodial skeleton relationship: part_of UBERON:0002471 ! zeugopod relationship: part_of UBERON:0004381 {source="VSAO"} ! skeleton of limb relationship: proximally_connected_to UBERON:0011583 ! stylopodial skeleton -relationship: skeleton_of UBERON:0002471 ! zeugopod -property_value: UBPROP:0000007 "zeugopodial" xsd:string -property_value: UBPROP:0000007 "zygopodial" xsd:string +relationship: RO:0002576 UBERON:0002471 ! skeleton of zeugopod [Term] id: UBERON:0011585 @@ -244061,7 +240750,7 @@ def: "Anatomical structure that is an aggregation of similar cells from which ca xref: VSAO:0000006 xref: XAO:0004021 is_a: UBERON:0000061 {source="VSAO"} ! anatomical structure -property_value: editor_note "consider obsoleting, coordinate with VSAO" xsd:string +property_value: IAO:0000116 "consider obsoleting, coordinate with VSAO" xsd:string [Term] id: UBERON:0011587 @@ -244074,7 +240763,6 @@ synonym: "predentine tissue" EXACT [VSAO:curator] xref: EMAPA:36439 xref: VSAO:0000071 xref: XAO:0004052 -is_a: UBERON:0010313 ! neural crest-derived structure is_a: UBERON:0010365 {source="VSAO"} ! odontoid tissue relationship: produced_by CL:0000060 {source="text definition"} ! odontoblast @@ -244098,7 +240786,7 @@ def: "Cartilage tissue that is not mineralized." [GO_REF:0000034, http://dx.plos xref: VSAO:0000089 xref: XAO:0004044 is_a: UBERON:0002418 {source="VSAO"} ! cartilage tissue -property_value: editor_note "add developmental relationships; add disjointness axiom" xsd:string +property_value: IAO:0000116 "add developmental relationships; add disjointness axiom" xsd:string [Term] id: UBERON:0011591 @@ -244120,8 +240808,8 @@ synonym: "upper jaw future lip" EXACT [EHDAA2:0002120] xref: EHDAA2:0002120 is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0003235 ! epithelium of upper jaw -relationship: develops_from UBERON:0004068 {notes="fusion"} ! medial nasal prominence -relationship: develops_from UBERON:0005868 {notes="fusion"} ! maxillary prominence +relationship: RO:0002202 UBERON:0004068 ! develops from medial nasal prominence +relationship: RO:0002202 UBERON:0005868 ! develops from maxillary prominence [Term] id: UBERON:0011594 @@ -244133,16 +240821,13 @@ synonym: "mandibular tooth" RELATED [] synonym: "tooth of dentary" RELATED [] xref: AAO:0000125 xref: AAO:0000641 -xref: FMA:321647 xref: SCTID:245547003 xref: TAO:0001628 is_a: UBERON:0003268 ! tooth of lower jaw intersection_of: UBERON:0001091 ! calcareous tooth -intersection_of: attaches_to UBERON:0004742 ! dentary -relationship: attaches_to UBERON:0004742 ! dentary -property_value: editor_note "Note that we treat dentary tooth and mandibular tooth as equivalent" xsd:string -property_value: UBPROP:0000001 "Tooth that is attached to the dentary.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001628", ontology="TAO", source="TAO:wd"} -property_value: UBPROP:0000002 "relationship loss: part_of dentary tooth row (TAO:0001952)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001628", ontology="TAO"} +intersection_of: RO:0002371 UBERON:0004742 ! attached to dentary +relationship: RO:0002371 UBERON:0004742 ! attached to dentary +property_value: IAO:0000116 "Note that we treat dentary tooth and mandibular tooth as equivalent" xsd:string [Term] id: UBERON:0011595 @@ -244152,11 +240837,12 @@ def: "A subdivision of the head that corresponds to the jaw skeleton, containing xref: EMAPA:32905 xref: NCIT:C114916 is_a: UBERON:0000475 ! organism subdivision +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0000475 ! organism subdivision -intersection_of: has_skeleton UBERON:0001708 ! jaw skeleton -relationship: has_skeleton UBERON:0001708 ! jaw skeleton -relationship: only_in_taxon NCBITaxon:7776 ! Gnathostomata +intersection_of: RO:0002551 UBERON:0001708 ! has skeleton jaw skeleton relationship: part_of UBERON:0000165 {source="EMAPA", source="FMA-abduced", source="ZFA-abduced"} ! mouth +relationship: RO:0002160 NCBITaxon:7776 ! only in taxon Gnathostomata +relationship: RO:0002551 UBERON:0001708 ! has skeleton jaw skeleton property_value: seeAlso "http://eol.org/collections/11578" xsd:anyURI [Term] @@ -244167,7 +240853,7 @@ synonym: "lower jaw future lip" EXACT [EHDAA2:0001020] xref: EHDAA2:0001020 is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0003236 ! epithelium of lower jaw -relationship: develops_from UBERON:0005867 {source="Wikipedia:Mandibular_prominence"} ! mandibular prominence +relationship: RO:0002202 UBERON:0005867 {source="Wikipedia:Mandibular_prominence"} ! develops from mandibular prominence [Term] id: UBERON:0011597 @@ -244180,7 +240866,7 @@ is_a: UBERON:0012360 ! bone of jaw intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0001709 ! upper jaw region relationship: part_of UBERON:0003277 ! skeleton of upper jaw -property_value: editor_note "Do not manually classify under here - bones are automatically classified" xsd:string +property_value: IAO:0000116 "Do not manually classify under here - bones are automatically classified" xsd:string [Term] id: UBERON:0011601 @@ -244237,10 +240923,10 @@ is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0002424 ! oral epithelium is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0000483 ! epithelium -intersection_of: develops_from UBERON:0000924 ! ectoderm intersection_of: part_of UBERON:0002424 ! oral epithelium -relationship: develops_from UBERON:0009479 {source="EHDAA2"} ! ectoderm of buccopharyngeal membrane +intersection_of: RO:0002202 UBERON:0000924 ! develops from ectoderm relationship: part_of UBERON:0002424 ! oral epithelium +relationship: RO:0002202 UBERON:0009479 {source="EHDAA2"} ! develops from ectoderm of buccopharyngeal membrane [Term] id: UBERON:0011645 @@ -244250,10 +240936,10 @@ def: "Limb extensor that runs from ilium to femur." [ISBN:0073040584] synonym: "iliofemoralis" EXACT [] is_a: UBERON:0001325 ! muscle of pelvis intersection_of: UBERON:0001325 ! muscle of pelvis -intersection_of: has_muscle_insertion UBERON:0000981 ! femur -intersection_of: has_muscle_origin UBERON:0001273 ! ilium -relationship: has_muscle_insertion UBERON:0000981 ! femur -relationship: has_muscle_origin UBERON:0001273 ! ilium +intersection_of: RO:0002372 UBERON:0001273 ! has muscle origin ilium +intersection_of: RO:0002373 UBERON:0000981 ! has muscle insertion femur +relationship: RO:0002372 UBERON:0001273 ! has muscle origin ilium +relationship: RO:0002373 UBERON:0000981 ! has muscle insertion femur [Term] id: UBERON:0011648 @@ -244282,7 +240968,7 @@ synonym: "body segment" RELATED [] synonym: "main body segment" RELATED [] is_a: UBERON:0000475 ! organism subdivision relationship: part_of UBERON:0013701 ! main body axis -property_value: editor_note "Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem" xsd:string +property_value: IAO:0000116 "Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem" xsd:string [Term] id: UBERON:0011677 @@ -244298,7 +240984,6 @@ is_a: UBERON:0004451 {is_inferred="true"} ! trunk or cervical vertebra intersection_of: UBERON:0002412 ! vertebra intersection_of: part_of UBERON:0009568 ! trunk region of vertebral column relationship: part_of UBERON:0009568 ! trunk region of vertebral column -property_value: UBPROP:0000202 FMA:72066 [Term] id: UBERON:0011679 @@ -244309,8 +240994,8 @@ is_a: UBERON:0001447 ! tarsal bone is_a: UBERON:0014395 ! proximal mesopodial bone is_a: UBERON:0015081 ! proximal tarsal endochondral element intersection_of: UBERON:0015081 ! proximal tarsal endochondral element -intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue -relationship: develops_from UBERON:0015082 ! proximal tarsal cartilage +intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue +relationship: RO:0002202 UBERON:0015082 ! develops from proximal tarsal cartilage [Term] id: UBERON:0011693 @@ -244320,9 +241005,9 @@ synonym: "extraembryonic umbilical artery" EXACT [VHOG:0001157] xref: VHOG:0001157 is_a: UBERON:0000478 {source="EHDAA2-abduced"} ! extraembryonic structure is_a: UBERON:0001637 ! artery -relationship: connecting_branch_of UBERON:0001309 {source="FMA"} ! internal iliac artery relationship: part_of UBERON:0001310 ! umbilical artery relationship: part_of UBERON:0007807 {source="EHDAA2-abduced"} ! connecting stalk vasculature +relationship: RO:0002252 UBERON:0001309 {source="FMA"} ! connecting branch of internal iliac artery [Term] id: UBERON:0011695 @@ -244347,7 +241032,7 @@ namespace: uberon synonym: "extraembryonic umbilical artery left" EXACT [EHDAA2:0000937] xref: EHDAA2:0000937 is_a: UBERON:0011693 ! extraembryonic portion of umbilical artery -relationship: connected_to UBERON:0011695 ! embryonic cardiovascular system +relationship: RO:0002170 UBERON:0011695 ! connected to embryonic cardiovascular system [Term] id: UBERON:0011697 @@ -244370,8 +241055,8 @@ xref: Wikipedia:Primordial_phallus is_a: UBERON:0005423 ! developing anatomical structure union_of: UBERON:0006233 ! female genital tubercle union_of: UBERON:0006261 ! male genital tubercle -relationship: develops_from UBERON:0005876 ! undifferentiated genital tubercle relationship: part_of UBERON:0004176 ! external genitalia +relationship: RO:0002202 UBERON:0005876 ! develops from undifferentiated genital tubercle [Term] id: UBERON:0011766 @@ -244385,11 +241070,11 @@ xref: FMA:14469 xref: MA:0001107 xref: SCTID:280300006 is_a: UBERON:0003716 ! recurrent laryngeal nerve +is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0003716 ! recurrent laryngeal nerve -intersection_of: in_left_side_of UBERON:0000468 ! multicellular organism -relationship: in_left_side_of UBERON:0000468 ! multicellular organism -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/6/64/Recurrent_laryngeal_nerve.svg" xsd:anyURI -property_value: UBPROP:0000008 "The left nerve is longer than the right, because it crosses under the arch of the aorta at the ligamentum arteriosum.[WP]" xsd:string +intersection_of: BSPO:0000120 UBERON:0000468 ! multicellular organism +relationship: BSPO:0000120 UBERON:0000468 ! multicellular organism +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/64/Recurrent_laryngeal_nerve.svg" xsd:anyURI [Term] id: UBERON:0011767 @@ -244403,9 +241088,10 @@ xref: FMA:14468 xref: MA:0001108 xref: SCTID:280299003 is_a: UBERON:0003716 ! recurrent laryngeal nerve +is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0003716 ! recurrent laryngeal nerve -intersection_of: in_right_side_of UBERON:0000468 ! multicellular organism -relationship: in_right_side_of UBERON:0000468 ! multicellular organism +intersection_of: BSPO:0000121 UBERON:0000468 ! multicellular organism +relationship: BSPO:0000121 UBERON:0000468 ! multicellular organism [Term] id: UBERON:0011769 @@ -244417,8 +241103,8 @@ synonym: "cartilaginous process" EXACT [] xref: FMA:284626 is_a: UBERON:0004529 ! anatomical projection intersection_of: UBERON:0004529 ! anatomical projection -intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue -relationship: composed_primarily_of UBERON:0002418 ! cartilage tissue +intersection_of: RO:0002473 UBERON:0002418 ! composed primarily of cartilage tissue +relationship: RO:0002473 UBERON:0002418 ! composed primarily of cartilage tissue [Term] id: UBERON:0011772 @@ -244428,9 +241114,9 @@ def: "An anatomical space that is part of a bone of lower jaw." [OBOL:automatic] xref: AAO:0000273 is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0004768 ! bone of lower jaw -relationship: luminal_space_of UBERON:0004768 ! bone of lower jaw +intersection_of: RO:0002572 UBERON:0004768 ! luminal space of bone of lower jaw relationship: part_of UBERON:0004768 ! bone of lower jaw +relationship: RO:0002572 UBERON:0004768 ! luminal space of bone of lower jaw [Term] id: UBERON:0011773 @@ -244440,9 +241126,9 @@ def: "An anatomical space that is part of a bone of upper jaw." [OBOL:automatic] xref: AAO:0000621 is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0011597 ! bone of upper jaw -relationship: luminal_space_of UBERON:0011597 ! bone of upper jaw +intersection_of: RO:0002572 UBERON:0011597 ! luminal space of bone of upper jaw relationship: part_of UBERON:0011597 ! bone of upper jaw +relationship: RO:0002572 UBERON:0011597 ! luminal space of bone of upper jaw [Term] id: UBERON:0011775 @@ -244509,10 +241195,10 @@ synonym: "skin follicle placode" EXACT [] is_a: UBERON:0006598 ! presumptive structure is_a: UBERON:0011814 {source="NCBIBook:NBK53175"} ! non-neurogenic ectodermal placode intersection_of: UBERON:0005085 ! ectodermal placode -intersection_of: has_potential_to_develop_into UBERON:0036150 ! skin appendage follicle -relationship: has_developmental_contribution_from UBERON:0001003 ! skin epidermis -relationship: has_developmental_contribution_from UBERON:0002067 ! dermis -relationship: has_potential_to_develop_into UBERON:0036150 ! skin appendage follicle +intersection_of: RO:0002387 UBERON:0036150 ! has potential to develop into skin appendage follicle +relationship: RO:0002254 UBERON:0001003 ! has developmental contribution from skin epidermis +relationship: RO:0002254 UBERON:0002067 ! has developmental contribution from dermis +relationship: RO:0002387 UBERON:0036150 ! has potential to develop into skin appendage follicle [Term] id: UBERON:0011820 @@ -244527,15 +241213,16 @@ synonym: "AV region" RELATED [PMID:21234997] synonym: "AV segment" RELATED [PMID:21234997] xref: EHDAA2:0004149 xref: FMA:85125 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0007651 ! anatomical junction intersection_of: UBERON:0007651 ! anatomical junction -intersection_of: connects UBERON:0002081 ! cardiac atrium -intersection_of: connects UBERON:0002082 ! cardiac ventricle intersection_of: part_of UBERON:0000948 ! heart -relationship: connects UBERON:0002081 ! cardiac atrium -relationship: connects UBERON:0002082 ! cardiac ventricle +intersection_of: RO:0002176 UBERON:0002081 ! connects cardiac atrium +intersection_of: RO:0002176 UBERON:0002082 ! connects cardiac ventricle relationship: part_of UBERON:0000948 ! heart -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002176 UBERON:0002081 ! connects cardiac atrium +relationship: RO:0002176 UBERON:0002082 ! connects cardiac ventricle +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0011821 @@ -244559,10 +241246,9 @@ xref: Wikipedia:Dense_irregular_connective_tissue is_a: UBERON:0011821 {source="FMA"} ! irregular connective tissue is_a: UBERON:0011823 ! dense connective tissue intersection_of: UBERON:0011821 ! irregular connective tissue -intersection_of: composed_primarily_of UBERON:0011860 ! collection of collagen fibrils intersection_of: has_part GO:0071953 ! elastic fiber +intersection_of: RO:0002473 UBERON:0011860 ! composed primarily of collection of collagen fibrils relationship: has_part GO:0071953 ! elastic fiber -property_value: UBPROP:0000001 "Tissue characterized by a thick, random arrangement of collagen and elastin fibers with very few cells. The majority of the cells are fibroblasts, but mast cells and macrophages may also be seen. It is found in the dermis, periosteum, perichondrium, capsules of organs and sheaths of nerves and muscles[NCIT]" xsd:string {date_retrieved="2012-08-29", external_class="ncithesaurus:Irregular_Dense_Connective_Tissue", ontology="NCIT"} [Term] id: UBERON:0011823 @@ -244576,11 +241262,10 @@ xref: Wikipedia:Dense_connective_tissue is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002384 ! connective tissue intersection_of: UBERON:0002384 ! connective tissue -intersection_of: composed_primarily_of UBERON:0011860 ! collection of collagen fibrils +intersection_of: RO:0002473 UBERON:0011860 ! composed primarily of collection of collagen fibrils disjoint_from: UBERON:0011825 ! loose connective tissue -relationship: composed_primarily_of UBERON:0011860 ! collection of collagen fibrils -property_value: editor_note "our OWL definition states that this is differentiated from other connective tissue types by virtue of the fact that the collage fiber component predominates, as opposed to cells and fluid." xsd:string -property_value: UBPROP:0000001 "Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT]" xsd:string {date_retrieved="2012-08-29", external_class="ncithesaurus:Dense_Connective_Tissue", ontology="NCIT"} +relationship: RO:0002473 UBERON:0011860 ! composed primarily of collection of collagen fibrils +property_value: IAO:0000116 "our OWL definition states that this is differentiated from other connective tissue types by virtue of the fact that the collage fiber component predominates, as opposed to cells and fluid." xsd:string [Term] id: UBERON:0011824 @@ -244612,6 +241297,7 @@ synonym: "sebaceous gland duct" EXACT [FMA:70947] xref: FMA:70947 xref: NCIT:C33520 is_a: UBERON:0000058 ! duct +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000058 ! duct intersection_of: part_of UBERON:0001821 ! sebaceous gland relationship: part_of UBERON:0001821 ! sebaceous gland @@ -244623,6 +241309,7 @@ namespace: uberon def: "An acinus that is part of a sebaceous gland." [OBOL:automatic] synonym: "sebaceous gland acinus" EXACT [FMA:59657] xref: FMA:59657 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0011858 ! acinus of exocrine gland intersection_of: UBERON:0009842 ! glandular acinus intersection_of: part_of UBERON:0001821 ! sebaceous gland @@ -244647,6 +241334,7 @@ namespace: uberon def: "An acinus that is part of a mammary gland." [OBOL:automatic] synonym: "lactiferous gland acinus" EXACT [FMA:74438] xref: FMA:74438 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0011858 ! acinus of exocrine gland intersection_of: UBERON:0009842 ! glandular acinus intersection_of: part_of UBERON:0001911 ! mammary gland @@ -244659,6 +241347,7 @@ namespace: uberon def: "An acinus that is part of a lacrimal gland." [OBOL:automatic] synonym: "lacrimal gland acinus" EXACT [FMA:85250] xref: FMA:85250 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0011858 ! acinus of exocrine gland intersection_of: UBERON:0009842 ! glandular acinus intersection_of: part_of UBERON:0001817 ! lacrimal gland @@ -244685,10 +241374,9 @@ xref: NCIT:C32339 xref: NIF_Subcellular:sao7547390221 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000476 {source="ZFA"} ! acellular anatomical structure -relationship: composed_primarily_of GO:0005581 ! collagen trimer -relationship: composed_primarily_of GO:0098643 ! banded collagen fibril -relationship: seeAlso UBERON:0007377 -property_value: UBPROP:0000012 "the FMA class specifically refers to ureter" xsd:string {external_ontology="FMA"} +relationship: RO:0002473 GO:0005581 ! composed primarily of collagen trimer +relationship: RO:0002473 GO:0098643 ! composed primarily of banded collagen fibril +property_value: seeAlso UBERON:0007377 [Term] id: UBERON:0011861 @@ -244696,11 +241384,12 @@ name: aorta collagen fibril namespace: uberon def: "The connective tissue bundles in the extracellular matrix of aorta tissue that are composed of collagen, and play a role in tissue strength and elasticity." [MP:0011640] subset: pheno_slim +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0011860 ! collection of collagen fibrils intersection_of: UBERON:0011860 ! collection of collagen fibrils intersection_of: part_of UBERON:0004664 ! aorta tunica adventitia -relationship: contributes_to_morphology_of UBERON:0004664 ! aorta tunica adventitia relationship: part_of UBERON:0004664 ! aorta tunica adventitia +relationship: RO:0002433 UBERON:0004664 ! contributes to morphology of aorta tunica adventitia [Term] id: UBERON:0011862 @@ -244708,11 +241397,12 @@ name: pulmonary collagen fibril namespace: uberon def: "The connective tissue bundles in the extracellular matrix of pulmonary tissue that are composed of collagen, and play a role in tissue strength and elasticity." [MP:0011641] subset: pheno_slim +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0011860 ! collection of collagen fibrils intersection_of: UBERON:0011860 ! collection of collagen fibrils intersection_of: part_of UBERON:0002048 ! lung -relationship: contributes_to_morphology_of UBERON:0002048 ! lung relationship: part_of UBERON:0002048 ! lung +relationship: RO:0002433 UBERON:0002048 ! contributes to morphology of lung [Term] id: UBERON:0011863 @@ -244734,8 +241424,8 @@ subset: pheno_slim is_a: UBERON:0011860 ! collection of collagen fibrils intersection_of: UBERON:0011860 ! collection of collagen fibrils intersection_of: part_of UBERON:0000043 ! tendon -relationship: contributes_to_morphology_of UBERON:0000043 ! tendon relationship: part_of UBERON:0000043 ! tendon +relationship: RO:0002433 UBERON:0000043 ! contributes to morphology of tendon [Term] id: UBERON:0011865 @@ -244743,11 +241433,12 @@ name: corneal stroma collagen fibril namespace: uberon def: "The connective tissue bundles in the extracellular matrix of corneal stroma that are composed of collagen, and play a role in tissue strength and elasticity." [MP:0011650] subset: pheno_slim +is_a: UBERON:0010313 ! neural crest-derived structure is_a: UBERON:0011860 ! collection of collagen fibrils intersection_of: UBERON:0011860 ! collection of collagen fibrils intersection_of: part_of UBERON:0001777 ! substantia propria of cornea -relationship: contributes_to_morphology_of UBERON:0001777 ! substantia propria of cornea relationship: part_of UBERON:0001777 ! substantia propria of cornea +relationship: RO:0002433 UBERON:0001777 ! contributes to morphology of substantia propria of cornea [Term] id: UBERON:0011875 @@ -244778,9 +241469,8 @@ xref: FMA:62998 is_a: UBERON:0018261 ! muscular coat of digestive tract intersection_of: UBERON:0006660 ! muscular coat intersection_of: part_of UBERON:0001043 ! esophagus -relationship: has_part UBERON:0001134 {notes="upper part", source="Wikipedia:Muscular_layer"} ! skeletal muscle tissue +relationship: has_part UBERON:0001134 ! skeletal muscle tissue relationship: part_of UBERON:0001096 ! wall of esophagus -property_value: UBPROP:0000010 "In the upper esophagus, part of the externa is skeletal muscle, rather than smooth muscle" xsd:string {source="WP"} [Term] id: UBERON:0011892 @@ -244800,11 +241490,12 @@ synonym: "ventral uveal tract" EXACT [] xref: EMAPA:37417 {source="MA:th"} xref: SCTID:280656002 is_a: UBERON:0000481 {source="ZFA"} ! multi-tissue structure -relationship: contributes_to_morphology_of UBERON:0001768 ! uvea -relationship: contributes_to_morphology_of UBERON:0001801 ! anterior segment of eyeball +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: has_part UBERON:0001769 ! iris relationship: has_part UBERON:0001775 ! ciliary body relationship: part_of UBERON:0001768 {source="MP"} ! uvea +relationship: RO:0002433 UBERON:0001768 ! contributes to morphology of uvea +relationship: RO:0002433 UBERON:0001801 ! contributes to morphology of anterior segment of eyeball [Term] id: UBERON:0011894 @@ -244829,11 +241520,11 @@ xref: FMA:9726 xref: NCIT:C32527 xref: UMLS:C0504096 {source="ncithesaurus:Epimysium"} xref: Wikipedia:Epimysium +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0011822 {source="FMA"} ! dense irregular connective tissue relationship: bounding_layer_of UBERON:0014892 ! skeletal muscle organ, vertebrate -relationship: continuous_with UBERON:0000043 ! tendon relationship: part_of UBERON:0001134 {source="FMA"} ! skeletal muscle tissue -property_value: UBPROP:0000009 "The Epimysium also protects muscles from friction against other muscles and bones" xsd:string +relationship: RO:0002150 UBERON:0000043 ! continuous with tendon [Term] id: UBERON:0011919 @@ -244849,8 +241540,8 @@ is_a: UBERON:0000478 ! extraembryonic structure is_a: UBERON:0003061 ! blood island intersection_of: UBERON:0003061 ! blood island intersection_of: part_of UBERON:0003316 ! mesenchyme of yolk sac -relationship: develops_from UBERON:0003316 {source="EHDAA2"} ! mesenchyme of yolk sac relationship: part_of UBERON:0003316 ! mesenchyme of yolk sac +relationship: RO:0002202 UBERON:0003316 {source="EHDAA2"} ! develops from mesenchyme of yolk sac [Term] id: UBERON:0011921 @@ -244862,9 +241553,8 @@ xref: EHDAA2:0003242 is_a: UBERON:0007503 {source="EHDAA2"} ! epithelial vesicle is_a: UBERON:0010303 ! extraembryonic epithelium is_a: UBERON:0012275 ! meso-epithelium -relationship: develops_from UBERON:0005667 {source="EHDAA2"} ! connecting stalk mesoderm relationship: part_of UBERON:0002331 {source="EHDAA2"} ! umbilical cord -property_value: UBPROP:0000012 "in EHDAA2 gives rise to connecting stalk blood vessels and extraembryonic umbilical vessels" xsd:string {external_ontology="EHDAA2"} +relationship: RO:0002202 UBERON:0005667 {source="EHDAA2"} ! develops from connecting stalk mesoderm [Term] id: UBERON:0011922 @@ -244875,6 +241565,7 @@ subset: pheno_slim synonym: "basement membrane of cochlear labyrinth" EXACT [] synonym: "cochlea basement membrane" EXACT [] xref: EMAPA:37830 {source="MA:th"} +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005769 ! basement membrane of epithelium intersection_of: UBERON:0005769 ! basement membrane of epithelium intersection_of: part_of UBERON:0002499 ! cochlear labyrinth @@ -244980,6 +241671,7 @@ def: "A luminal layer of epithelium that is part of a ureter." [OBOL:automatic] subset: pheno_slim xref: EMAPA:37779 {source="MA:th"} xref: MA:0002656 +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0011945 ! luminal layer of epithelium intersection_of: UBERON:0011945 ! luminal layer of epithelium intersection_of: part_of UBERON:0000056 ! ureter @@ -244993,11 +241685,12 @@ def: "A luminal layer of epithelium that is part of a endometrium epithelium." [ subset: human_reference_atlas xref: EMAPA:35309 xref: MA:0002733 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0011945 ! luminal layer of epithelium intersection_of: UBERON:0011945 ! luminal layer of epithelium intersection_of: part_of UBERON:0004811 ! endometrium epithelium relationship: part_of UBERON:0004811 ! endometrium epithelium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0011950 @@ -245007,6 +241700,7 @@ def: "The inner cell layer of the mammary epithelium bilayer that lines the lumi synonym: "lumina layer of epithelium of lactiferous gland" EXACT [FMA:74458] xref: EMAPA:37902 {source="MA:th"} xref: FMA:74458 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0011945 ! luminal layer of epithelium intersection_of: UBERON:0011945 ! luminal layer of epithelium intersection_of: part_of UBERON:0001911 ! mammary gland @@ -245019,6 +241713,7 @@ namespace: uberon def: "A luminal layer of epithelium that is part of a prostate gland." [OBOL:automatic] synonym: "subdivision of luminal layer of epithelium of prostatic gland" EXACT [FMA:74262] xref: FMA:74262 +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0011945 ! luminal layer of epithelium intersection_of: UBERON:0011945 ! luminal layer of epithelium intersection_of: part_of UBERON:0002367 ! prostate gland @@ -245041,7 +241736,7 @@ is_a: UBERON:0009870 ! zone of stomach intersection_of: UBERON:0009870 ! zone of stomach intersection_of: has_part UBERON:0006924 ! stomach glandular epithelium relationship: has_part UBERON:0006924 ! stomach glandular epithelium -property_value: editor_note "as currently defined, this would include the cardiac antrum; however, the intent may be to exclude the cardiac glands and in mice for this to be part of the region distal to the margo plicatus" xsd:string +property_value: IAO:0000116 "as currently defined, this would include the cardiac antrum; however, the intent may be to exclude the cardiac glands and in mice for this to be part of the region distal to the margo plicatus" xsd:string [Term] id: UBERON:0011955 @@ -245057,7 +241752,7 @@ is_a: UBERON:0001143 ! hepatic vein intersection_of: UBERON:0001143 ! hepatic vein intersection_of: part_of UBERON:0001115 ! left lobe of liver relationship: part_of UBERON:0001115 ! left lobe of liver -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0011956 @@ -245073,7 +241768,7 @@ is_a: UBERON:0001143 ! hepatic vein intersection_of: UBERON:0001143 ! hepatic vein intersection_of: part_of UBERON:0001114 ! right lobe of liver relationship: part_of UBERON:0001114 ! right lobe of liver -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0011960 @@ -245092,7 +241787,7 @@ is_a: UBERON:0001484 ! articular capsule intersection_of: UBERON:0001484 ! articular capsule intersection_of: part_of UBERON:0001470 ! glenohumeral joint relationship: part_of UBERON:0001470 ! glenohumeral joint -relationship: surrounds UBERON:0001470 ! glenohumeral joint +relationship: RO:0002221 UBERON:0001470 ! surrounds glenohumeral joint [Term] id: UBERON:0011965 @@ -245122,11 +241817,11 @@ xref: FMA:44055 xref: SCTID:41159004 is_a: UBERON:0008846 ! skeletal ligament intersection_of: UBERON:0008846 ! skeletal ligament -intersection_of: connects UBERON:0000979 ! tibia -intersection_of: connects UBERON:0009879 ! tarsal skeleton -relationship: connects UBERON:0000979 ! tibia -relationship: connects UBERON:0009879 ! tarsal skeleton +intersection_of: RO:0002176 UBERON:0000979 ! connects tibia +intersection_of: RO:0002176 UBERON:0009879 ! connects tarsal skeleton relationship: part_of UBERON:0001488 ! ankle joint +relationship: RO:0002176 UBERON:0000979 ! connects tibia +relationship: RO:0002176 UBERON:0009879 ! connects tarsal skeleton [Term] id: UBERON:0011973 @@ -245227,10 +241922,9 @@ synonym: "crurotarsal" RELATED [] xref: Wikipedia:Crurotarsal is_a: UBERON:0001488 ! ankle joint intersection_of: UBERON:0000982 ! skeletal joint -intersection_of: connects UBERON:0010720 ! hindlimb zeugopod skeleton -intersection_of: connects UBERON:0011679 ! proximal tarsal bone -relationship: connects UBERON:0011679 ! proximal tarsal bone -property_value: UBPROP:0000001 "an ankle joint that passes between the astragalus and calcaneum[Palaeos]." xsd:string {source="http://palaeos.com/vertebrates/glossary/glossaryCr.html#Crurotarsal%20joint"} +intersection_of: RO:0002176 UBERON:0010720 ! connects hindlimb zeugopod skeleton +intersection_of: RO:0002176 UBERON:0011679 ! connects proximal tarsal bone +relationship: RO:0002176 UBERON:0011679 ! connects proximal tarsal bone [Term] id: UBERON:0011997 @@ -245245,10 +241939,9 @@ synonym: "schizocoelom" NARROW [] xref: EHDAA2:0004731 xref: Wikipedia:Coelom is_a: UBERON:0000481 {source="EHDAA2"} ! multi-tissue structure -relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -property_value: editor_note "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." xsd:string -property_value: UBPROP:0000007 "coelomic" xsd:string +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +property_value: IAO:0000116 "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." xsd:string +property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} [Term] id: UBERON:0012054 @@ -245259,9 +241952,8 @@ xref: EMAPA:31134 xref: VHOG:0001283 is_a: UBERON:0002553 ! anatomical cavity intersection_of: UBERON:0002553 ! anatomical cavity -intersection_of: luminal_space_of UBERON:0003082 ! myotome -relationship: luminal_space_of UBERON:0003082 ! myotome -property_value: UBPROP:0000003 "The central cavity within the mesoderm is the paired primary or embryonic coelom. Parts of the embryonic coelom often become enclosed in the mesoderm, forming a myocoel within the epimere, a nephrocoel within the mesomere, and simple coelom (body cavity) within the lateral plate mesoderm.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001283", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.166 and Figure 5.6", source="http://bgee.unil.ch/"} +intersection_of: RO:0002572 UBERON:0003082 ! luminal space of myotome +relationship: RO:0002572 UBERON:0003082 ! luminal space of myotome [Term] id: UBERON:0012069 @@ -245278,8 +241970,8 @@ def: "A tooth that is on the roof of the mouth." [http://palaeos.com/vertebrates synonym: "palatal teeth" EXACT OMO:0003004 [] is_a: UBERON:0003267 ! tooth of upper jaw intersection_of: UBERON:0001091 ! calcareous tooth -intersection_of: attaches_to UBERON:0012071 ! palate bone -relationship: attaches_to UBERON:0012071 ! palate bone +intersection_of: RO:0002371 UBERON:0012071 ! attached to palate bone +relationship: RO:0002371 UBERON:0012071 ! attached to palate bone [Term] id: UBERON:0012071 @@ -245296,7 +241988,6 @@ is_a: UBERON:0008907 ! dermal bone intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0007375 ! roof of mouth relationship: part_of UBERON:0012072 ! palatal part of dermatocranium -property_value: IAO:0000232 "this is distinct (but not disjoint) from palatine bone" xsd:string [Term] id: UBERON:0012072 @@ -245319,8 +242010,6 @@ xref: TAO:0001637 xref: ZFA:0001628 is_a: UBERON:0001474 {source="ZFA"} ! bone element is_a: UBERON:0010522 {source="ZFA"} ! replacement element -property_value: UBPROP:0000001 "Bone that forms as a replacement of another structural tissue.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001637", ontology="TAO", source="TAO:wd"} -property_value: UBPROP:0000012 "This class was introduced to be consistent with the ZFA hierarchy. The corresponding TAO term was obsoleted, and never introduced into VSAO. Note that VSAO does have replacement element." xsd:string {external_ontology="ZFA"} [Term] id: UBERON:0012080 @@ -245329,14 +242018,15 @@ namespace: uberon def: "A cartilaginous condensation that has the potential to develop into a patella." [OBOL:automatic] xref: EMAPA:19140 is_a: UBERON:0003860 ! hindlimb mesenchyme +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005863 ! cartilaginous condensation intersection_of: UBERON:0005863 ! cartilaginous condensation -intersection_of: has_potential_to_develop_into UBERON:0002446 ! patella +intersection_of: RO:0002387 UBERON:0002446 ! has potential to develop into patella relationship: adjacent_to UBERON:0001485 ! knee joint -relationship: develops_from UBERON:0012081 ! patella pre-cartilage condensation -relationship: has_potential_to_develop_into UBERON:0002446 ! patella relationship: part_of UBERON:0001441 ! hindlimb skeleton -property_value: editor_note "Note some sources have this as intramembranous" xsd:string +relationship: RO:0002202 UBERON:0012081 ! develops from patella pre-cartilage condensation +relationship: RO:0002387 UBERON:0002446 ! has potential to develop into patella +property_value: IAO:0000116 "Note some sources have this as intramembranous" xsd:string [Term] id: UBERON:0012081 @@ -245345,12 +242035,13 @@ namespace: uberon def: "A pre-cartilage condensation that has the potential to develop into a patella." [OBOL:automatic] xref: EMAPA:18510 is_a: UBERON:0003321 ! mesenchyme of knee +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005866 ! pre-cartilage condensation intersection_of: UBERON:0005866 ! pre-cartilage condensation -intersection_of: has_potential_to_develop_into UBERON:0002446 ! patella -relationship: has_potential_to_develop_into UBERON:0002446 ! patella +intersection_of: RO:0002387 UBERON:0002446 ! has potential to develop into patella relationship: part_of UBERON:0001441 ! hindlimb skeleton relationship: part_of UBERON:0006256 {source="EMAPA"} ! knee joint primordium +relationship: RO:0002387 UBERON:0002446 ! has potential to develop into patella [Term] id: UBERON:0012082 @@ -245363,9 +242054,9 @@ xref: FMA:62646 xref: SCTID:199401001 is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 {source="FMA"} ! anatomical space -intersection_of: luminal_space_of UBERON:0002185 {source="FMA"} ! bronchus -relationship: luminal_space_of UBERON:0002185 ! bronchus +intersection_of: RO:0002572 UBERON:0002185 {source="FMA"} ! luminal space of bronchus relationship: part_of UBERON:0002185 {source="FMA"} ! bronchus +relationship: RO:0002572 UBERON:0002185 ! luminal space of bronchus [Term] id: UBERON:0012084 @@ -245378,9 +242069,9 @@ synonym: "secondary bronchial lumen" EXACT [] xref: FMA:62520 is_a: UBERON:0012082 ! bronchial lumen intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0002183 ! lobar bronchus -relationship: luminal_space_of UBERON:0002183 ! lobar bronchus +intersection_of: RO:0002572 UBERON:0002183 ! luminal space of lobar bronchus relationship: part_of UBERON:0002183 ! lobar bronchus +relationship: RO:0002572 UBERON:0002183 ! luminal space of lobar bronchus [Term] id: UBERON:0012085 @@ -245392,29 +242083,15 @@ synonym: "segmental bronchial lumen" EXACT [FMA:62593] xref: FMA:62593 is_a: UBERON:0012082 ! bronchial lumen intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0002184 ! segmental bronchus -relationship: luminal_space_of UBERON:0002184 ! segmental bronchus +intersection_of: RO:0002572 UBERON:0002184 ! luminal space of segmental bronchus relationship: part_of UBERON:0002184 ! segmental bronchus - -[Term] -id: UBERON:0012125 -name: dermatological-muscosal system -namespace: uberon -def: "Anatomical system that consists of the integumental system plus all mucosae and submucosae." [https://github.com/obophenotype/uberon/issues/53] -synonym: "dermatological system" RELATED [OBI:MC] -is_a: PR:000050567 ! protein-containing material entity -is_a: UBERON:0000467 ! anatomical system -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: has_part UBERON:0000009 ! submucosa -relationship: has_part UBERON:0000344 ! mucosa -relationship: has_part UBERON:0002072 ! hypodermis -relationship: has_part UBERON:0002097 ! skin of body +relationship: RO:0002572 UBERON:0002184 ! luminal space of segmental bronchus [Term] id: UBERON:0012139 name: segment of autopod namespace: uberon -is_a: UBERON:0002529 {notes="may be revised"} ! limb segment +is_a: UBERON:0002529 ! limb segment relationship: part_of UBERON:0002470 ! autopod region [Term] @@ -245425,11 +242102,10 @@ def: "A segment of the autopod consisting of both acropodial region and metapodi synonym: "acropodium (Wagner)" RELATED [] is_a: UBERON:0012139 ! segment of autopod intersection_of: UBERON:0012139 ! segment of autopod -intersection_of: has_skeleton UBERON:0012150 ! skeleton of digitopodium +intersection_of: RO:0002551 UBERON:0012150 ! has skeleton skeleton of digitopodium relationship: adjacent_to UBERON:0006716 ! mesopodium region -relationship: has_skeleton UBERON:0012150 ! skeleton of digitopodium +relationship: RO:0002551 UBERON:0012150 ! has skeleton skeleton of digitopodium property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod" xsd:anyURI -property_value: UBPROP:0000013 "some sources call this the acropodium. see https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod" xsd:string [Term] id: UBERON:0012141 @@ -245440,9 +242116,8 @@ is_a: UBERON:0005451 ! segment of manus is_a: UBERON:0012140 ! digitopodium region intersection_of: UBERON:0012140 ! digitopodium region intersection_of: part_of UBERON:0002398 ! manus -relationship: has_skeleton UBERON:0012151 ! skeleton of manual digitopodium +relationship: RO:0002551 UBERON:0012151 ! has skeleton skeleton of manual digitopodium property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod" xsd:anyURI -property_value: UBPROP:0000013 "some sources call this the acropodium. see https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod" xsd:string [Term] id: UBERON:0012142 @@ -245453,9 +242128,8 @@ is_a: UBERON:0005445 ! segment of pes is_a: UBERON:0012140 ! digitopodium region intersection_of: UBERON:0012140 ! digitopodium region intersection_of: part_of UBERON:0002387 ! pes -relationship: has_skeleton UBERON:0012152 ! skeleton of pedal digitopodium +relationship: RO:0002551 UBERON:0012152 ! has skeleton skeleton of pedal digitopodium property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod" xsd:anyURI -property_value: UBPROP:0000013 "some sources call this the acropodium. see https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod" xsd:string [Term] id: UBERON:0012150 @@ -245464,14 +242138,14 @@ namespace: uberon def: "A subdivision of the autopod skeleton consisting of both acropodial skeleon and metapodial skeleton, but excluding the mesopodial/basopodial skeleton." [PHENOSCAPE:ni] synonym: "digitopodium" RELATED [PHENOSCAPE:ni] synonym: "skeleton of digits" RELATED COMPARATIVE_PREFERRED [] +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010712 ! limb skeleton subdivision intersection_of: UBERON:0010912 ! subdivision of skeleton -intersection_of: skeleton_of UBERON:0012140 ! digitopodium region +intersection_of: RO:0002576 UBERON:0012140 ! skeleton of digitopodium region relationship: part_of UBERON:0006717 ! autopodial skeleton relationship: part_of UBERON:0012140 ! digitopodium region -relationship: skeleton_of UBERON:0012140 ! digitopodium region +relationship: RO:0002576 UBERON:0012140 ! skeleton of digitopodium region property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod" xsd:anyURI -property_value: UBPROP:0000013 "some sources call this the acropodium. see https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod" xsd:string [Term] id: UBERON:0012151 @@ -245485,7 +242159,6 @@ intersection_of: part_of UBERON:0002398 ! manus relationship: part_of UBERON:0001442 ! skeleton of manus relationship: part_of UBERON:0012141 {source="FMA"} ! manual digitopodium region property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod" xsd:anyURI -property_value: UBPROP:0000013 "some sources call this the acropodium. see https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod" xsd:string [Term] id: UBERON:0012152 @@ -245499,7 +242172,6 @@ intersection_of: part_of UBERON:0002387 ! pes relationship: part_of UBERON:0001445 ! skeleton of pes relationship: part_of UBERON:0012142 ! pedal digitopodium region property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod" xsd:anyURI -property_value: UBPROP:0000013 "some sources call this the acropodium. see https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod" xsd:string [Term] id: UBERON:0012168 @@ -245518,9 +242190,9 @@ xref: MESH:D005312 xref: Wikipedia:Cord_blood is_a: UBERON:0013755 ! arterial blood intersection_of: UBERON:0000178 ! blood -intersection_of: located_in UBERON:0001310 ! umbilical artery -relationship: located_in UBERON:0001310 ! umbilical artery +intersection_of: RO:0001025 UBERON:0001310 ! located in umbilical artery relationship: part_of UBERON:0000323 ! late embryo +relationship: RO:0001025 UBERON:0001310 ! located in umbilical artery [Term] id: UBERON:0012172 @@ -245534,9 +242206,9 @@ xref: NCIT:C34305 xref: UMLS:C1514976 {source="ncithesaurus:Stomach_Primordium"} is_a: UBERON:0001048 ! primordium intersection_of: UBERON:0001048 ! primordium -intersection_of: has_potential_to_develop_into UBERON:0000945 ! stomach -relationship: has_potential_to_develop_into UBERON:0000945 ! stomach +intersection_of: RO:0002387 UBERON:0000945 ! has potential to develop into stomach relationship: part_of UBERON:0003258 ! endoderm of foregut +relationship: RO:0002387 UBERON:0000945 ! has potential to develop into stomach [Term] id: UBERON:0012175 @@ -245550,11 +242222,10 @@ synonym: "facio-acoustic VII-VIII ganglion complex" RELATED [VHOG:0000715] xref: EHDAA2:0000494 xref: EMAPA:16794 xref: SCTID:361514006 -xref: VHOG:0000715 is_a: UBERON:0001714 {source="cjm"} ! cranial ganglion is_a: UBERON:0010313 ! neural crest-derived structure -relationship: develops_from UBERON:0003051 {source="EHDAA2"} ! ear vesicle -relationship: develops_from UBERON:0006232 {source="cjm"} ! facio-acoustic VII-VIII preganglion complex +relationship: RO:0002202 UBERON:0003051 {source="EHDAA2"} ! develops from ear vesicle +relationship: RO:0002202 UBERON:0006232 {source="cjm"} ! develops from facio-acoustic VII-VIII preganglion complex [Term] id: UBERON:0012177 @@ -245594,8 +242265,8 @@ xref: NCIT:C53062 xref: UMLS:C1709532 {source="ncithesaurus:Phrenic_Vein"} is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein -intersection_of: drains UBERON:0001103 ! diaphragm -relationship: drains UBERON:0001103 ! diaphragm +intersection_of: RO:0002179 UBERON:0001103 ! drains diaphragm +relationship: RO:0002179 UBERON:0001103 ! drains diaphragm [Term] id: UBERON:0012239 @@ -245613,9 +242284,9 @@ is_a: UBERON:0002201 ! vasculature of trunk is_a: UBERON:0006876 ! vasculature of organ intersection_of: UBERON:0002049 {source="EMAPA"} ! vasculature intersection_of: part_of UBERON:0001255 {source="EMAPA"} ! urinary bladder -relationship: contributes_to_morphology_of UBERON:0001255 ! urinary bladder relationship: part_of UBERON:0001255 ! urinary bladder -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002433 UBERON:0001255 ! contributes to morphology of urinary bladder +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0012240 @@ -245636,14 +242307,15 @@ xref: EMAPA:37977 {source="MA:th"} xref: FMA:19650 xref: SCTID:181424008 xref: Wikipedia:Urinary_meatus +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010418 ! urethral opening intersection_of: UBERON:0000161 ! orifice -intersection_of: connects UBERON:0010390 ! lumen of urethra -intersection_of: connects UBERON:0013514 ! space surrounding organism intersection_of: part_of UBERON:0000057 ! urethra -relationship: connects UBERON:0010390 ! lumen of urethra -relationship: connects UBERON:0013514 ! space surrounding organism +intersection_of: RO:0002176 UBERON:0010390 ! connects lumen of urethra +intersection_of: RO:0002176 UBERON:0013514 ! connects space surrounding organism relationship: part_of UBERON:0000057 ! urethra +relationship: RO:0002176 UBERON:0010390 ! connects lumen of urethra +relationship: RO:0002176 UBERON:0013514 ! connects space surrounding organism [Term] id: UBERON:0012241 @@ -245668,7 +242340,6 @@ intersection_of: UBERON:0012240 ! urethral meatus intersection_of: part_of UBERON:0003101 ! male organism relationship: part_of UBERON:0001299 ! glans penis relationship: part_of UBERON:0001333 ! male urethra -property_value: UBPROP:0000001 "The external urethral orifice is the external opening or meatus of the urethra, normally placed at the tip of glans penis; it presents as a vertical slit, possibly bounded on either side by two small labia-like projections, In some cases the slit may be more rounded. This occurs naturally in some males and may also be a side effect of excess skin removal during circumcision. Congenital misplacement of the urethral orifice is called hypospadias when it is located in the underside (ventral aspect) of the penis, and epispadias when located in the dorsum (upper aspect). Improper shaping of the meatus can result in meatal stenosis." xsd:string {source="Wikipedia:External_urethral_orifice_(male)"} [Term] id: UBERON:0012242 @@ -245688,14 +242359,15 @@ synonym: "vesicourethral orifice" EXACT [FMA:85263] xref: FMA:85263 xref: SCTID:362228001 xref: Wikipedia:Internal_urethral_orifice +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010418 ! urethral opening intersection_of: UBERON:0000161 ! orifice -intersection_of: connects UBERON:0009958 ! bladder lumen -intersection_of: connects UBERON:0010390 ! lumen of urethra intersection_of: part_of UBERON:0000057 ! urethra -relationship: connects UBERON:0009958 ! bladder lumen -relationship: connects UBERON:0010390 ! lumen of urethra +intersection_of: RO:0002176 UBERON:0009958 ! connects bladder lumen +intersection_of: RO:0002176 UBERON:0010390 ! connects lumen of urethra relationship: part_of UBERON:0000057 ! urethra +relationship: RO:0002176 UBERON:0009958 ! connects bladder lumen +relationship: RO:0002176 UBERON:0010390 ! connects lumen of urethra [Term] id: UBERON:0012247 @@ -245711,8 +242383,7 @@ is_a: UBERON:0002451 ! endometrial gland intersection_of: UBERON:0002365 ! exocrine gland intersection_of: part_of UBERON:0000002 ! uterine cervix relationship: part_of UBERON:0012248 ! cervical mucosa -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000202 FMA:71646 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0012248 @@ -245750,13 +242421,12 @@ is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000064 ! organ part is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0000064 ! organ part -intersection_of: distalmost_part_of UBERON:0000002 ! uterine cervix -relationship: distalmost_part_of UBERON:0000002 ! uterine cervix +intersection_of: BSPO:0001108 UBERON:0000002 ! uterine cervix +relationship: BSPO:0000100 UBERON:0000996 ! vagina +relationship: BSPO:0001108 UBERON:0000002 ! uterine cervix relationship: has_part UBERON:0010304 ! non-keratinized stratified squamous epithelium relationship: part_of UBERON:0000002 {source="BTO"} ! uterine cervix -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: proximal_to UBERON:0000996 ! vagina -property_value: UBPROP:0000012 "distinction between two FMA classes not clear - we merge them here" xsd:string {external_ontology="FMA"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0012250 @@ -245771,8 +242441,7 @@ is_a: UBERON:0004801 ! cervix epithelium is_a: UBERON:0006799 ! glandular epithelium intersection_of: UBERON:0006799 ! glandular epithelium intersection_of: part_of UBERON:0000002 ! uterine cervix -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000010 "The 'glandular' or columnar epithelium of the cervix is located cephalad to the squamocolumnar junction. It covers a variable amount of the ectocervix and lines the endocervical canal. It is comprised of a single layer of mucin-secreting cells. The epithelium is thrown into longitudinal folds and invaginations that make up the so-called endocervical glands (they are not true glands). These infolding crypts and channels make the cytologic and colposcopic detection of neoplasia less reliable and more problematic. The complex architecture of the endocervical glands gives the columnar epithelium a papillary appearance through the colposcope and a grainy appearance upon gross visual inspection. The single cell layer allows the coloration of the underlying vasculature to be seen more easily. Therefore, the columnar epithelium appears more red in comparison with the more opaque squamous epithelium." xsd:string {source="http://www.asccp.org/practicemanagement/cervix/histologyofthenormalcervix/tabid/5842/default.aspx"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0012251 @@ -245795,11 +242464,11 @@ subset: human_reference_atlas synonym: "endocervical glandular epithelium" EXACT [] xref: NCIT:C96180 xref: SCTID:362256006 -is_a: UBERON:0006799 ! glandular epithelium +is_a: UBERON:0012250 ! cervix glandular epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000458 ! endocervix relationship: part_of UBERON:0000458 ! endocervix -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0012253 @@ -245814,11 +242483,11 @@ xref: NCIT:C97148 xref: SCTID:280451001 is_a: UBERON:0004801 ! cervix epithelium intersection_of: UBERON:0000483 ! epithelium -intersection_of: continuous_with UBERON:0006922 ! cervix squamous epithelium -intersection_of: continuous_with UBERON:0012250 ! cervix glandular epithelium intersection_of: part_of UBERON:0000002 ! uterine cervix -relationship: continuous_with UBERON:0006922 ! cervix squamous epithelium -relationship: continuous_with UBERON:0012250 ! cervix glandular epithelium +intersection_of: RO:0002150 UBERON:0006922 ! continuous with cervix squamous epithelium +intersection_of: RO:0002150 UBERON:0012250 ! continuous with cervix glandular epithelium +relationship: RO:0002150 UBERON:0006922 ! continuous with cervix squamous epithelium +relationship: RO:0002150 UBERON:0012250 ! continuous with cervix glandular epithelium [Term] id: UBERON:0012254 @@ -245831,8 +242500,8 @@ synonym: "artery of abdomen" EXACT [] xref: SCTID:281470000 is_a: UBERON:0004573 ! systemic artery intersection_of: UBERON:0001637 ! artery -intersection_of: branching_part_of UBERON:0001516 ! abdominal aorta -relationship: branching_part_of UBERON:0001516 ! abdominal aorta +intersection_of: RO:0002380 UBERON:0001516 ! branching part of abdominal aorta +relationship: RO:0002380 UBERON:0001516 ! branching part of abdominal aorta [Term] id: UBERON:0012274 @@ -245854,7 +242523,7 @@ xref: FMA:86452 is_a: UBERON:0000483 ! epithelium is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000483 ! epithelium -intersection_of: develops_from UBERON:0000926 ! mesoderm +intersection_of: RO:0002202 UBERON:0000926 ! develops from mesoderm [Term] id: UBERON:0012276 @@ -245873,7 +242542,7 @@ is_a: UBERON:0007589 ! ciliated columnar oviduct epithelium intersection_of: UBERON:0006799 ! glandular epithelium intersection_of: part_of UBERON:0004811 ! endometrium epithelium relationship: part_of UBERON:0004811 ! endometrium epithelium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0012278 @@ -245891,6 +242560,8 @@ xref: SCTID:368881007 xref: UMLS:C1522269 {source="ncithesaurus:Nose_Nasal_Cavity_Nasal_Gland_MMHCC"} xref: Wikipedia:Nasal_glands is_a: UBERON:0002365 ! exocrine gland +is_a: UBERON:0004119 ! endoderm-derived structure +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0036225 ! respiratory system gland intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0001826 ! nasal cavity mucosa @@ -245911,8 +242582,8 @@ xref: MESH:D010233 xref: NCIT:C94826 xref: UMLS:C0030419 {source="ncithesaurus:Paraganglion"} is_a: UBERON:0034978 ! paraganglion (generic) -relationship: composed_primarily_of CL:0000166 ! chromaffin cell relationship: part_of UBERON:0010074 ! chromaffin system +relationship: RO:0002473 CL:0000166 ! composed primarily of chromaffin cell [Term] id: UBERON:0012287 @@ -245931,7 +242602,7 @@ intersection_of: part_of UBERON:0005356 ! Rathke's pouch relationship: adjacent_to UBERON:0009974 ! lumen of Rathke's pouch relationship: part_of UBERON:0005356 ! Rathke's pouch relationship: part_of UBERON:0011642 {source="EHDAA2"} ! oral epithelium from ectoderm -property_value: editor_note "See https://github.com/obophenotype/uberon/issues/1305" xsd:string +property_value: IAO:0000116 "See https://github.com/obophenotype/uberon/issues/1305" xsd:string [Term] id: UBERON:0012292 @@ -245958,6 +242629,7 @@ xref: EMAPA:37912 {source="MA:th"} xref: FMA:76904 xref: SCTID:362229009 is_a: UBERON:0000344 ! mucosa +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0000057 ! urethra relationship: part_of UBERON:0000057 ! urethra @@ -245971,10 +242643,11 @@ xref: EHDAA2:0000039 xref: EMAPA:16389 is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0015833 ! foregut epithelium -relationship: develops_from UBERON:0000076 {source="EHDAA2"} ! external ectoderm relationship: part_of UBERON:0000076 {source="EHDAA2"} ! external ectoderm relationship: part_of UBERON:0007238 {source="EHDAA2"} ! 1st arch maxillary component +relationship: RO:0002202 UBERON:0000076 {source="EHDAA2"} ! develops from external ectoderm [Term] id: UBERON:0012314 @@ -245987,8 +242660,8 @@ synonym: "primordium of face" RELATED [] xref: FMA:293103 xref: SCTID:89066004 is_a: UBERON:0002050 ! embryonic structure -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0000033 ! head +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata [Term] id: UBERON:0012317 @@ -246009,11 +242682,12 @@ xref: EMAPA:37983 {source="MA:th"} xref: FMA:19984 xref: Wikipedia:Vaginal_orifice is_a: UBERON:0000161 ! orifice +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0000161 ! orifice intersection_of: part_of UBERON:0000996 ! vagina -relationship: contributes_to_morphology_of UBERON:0000996 ! vagina relationship: part_of UBERON:0000996 ! vagina +relationship: RO:0002433 UBERON:0000996 ! contributes to morphology of vagina [Term] id: UBERON:0012320 @@ -246041,9 +242715,9 @@ xref: Wikipedia:Deep_cervical_artery is_a: UBERON:0012320 ! cervical artery intersection_of: UBERON:0012320 ! cervical artery intersection_of: part_of UBERON:0035551 ! deep vasculature -relationship: connecting_branch_of UBERON:0004688 {source="FMA"} ! costo-cervical trunk relationship: part_of UBERON:0035551 ! deep vasculature -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002252 UBERON:0004688 {source="FMA"} ! connecting branch of costo-cervical trunk +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0012324 @@ -246063,8 +242737,7 @@ xref: MA:0001936 xref: SCTID:244224008 xref: Wikipedia:Transverse_cervical_artery is_a: UBERON:0012320 ! cervical artery -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000012 "Unclear if MA class belongs here or in parent" xsd:string {external_ontology="MA"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0012329 @@ -246091,6 +242764,7 @@ xref: MA:0003030 xref: NCIT:C77659 xref: UMLS:C2698431 {source="ncithesaurus:Nasal-Associated_Lymphoid_Tissue"} is_a: UBERON:0001962 ! gut-associated lymphoid tissue +is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0001961 ! mucosa-associated lymphoid tissue intersection_of: part_of UBERON:0001728 ! nasopharynx relationship: overlaps UBERON:0005022 ! mucosa of nasopharynx @@ -246112,10 +242786,11 @@ xref: SCTID:362723009 xref: UMLS:C0006205 {source="ncithesaurus:Broad_Ligament"} xref: Wikipedia:Broad_ligament_of_the_uterus is_a: UBERON:0000211 {source="MESH"} ! ligament -relationship: connects UBERON:0000459 ! uterine wall -relationship: connects UBERON:0002355 ! pelvic region of trunk +is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0002095 ! mesentery -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002176 UBERON:0000459 ! connects uterine wall +relationship: RO:0002176 UBERON:0002355 ! connects pelvic region of trunk +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0012344 @@ -246139,11 +242814,10 @@ synonym: "acropodial segment of autopod" EXACT [] synonym: "set of digits" EXACT [] is_a: UBERON:0012139 ! segment of autopod intersection_of: UBERON:0012139 ! segment of autopod -intersection_of: has_skeleton UBERON:0010543 ! acropodial skeleton -relationship: distal_to UBERON:0009877 ! metapodium region -relationship: has_skeleton UBERON:0010543 ! acropodial skeleton +intersection_of: RO:0002551 UBERON:0010543 ! has skeleton acropodial skeleton +relationship: BSPO:0000097 UBERON:0009877 ! metapodium region relationship: part_of UBERON:0012140 ! digitopodium region -property_value: IAO:0000232 "class refers to an entire limb segment, not just the bones" xsd:string +relationship: RO:0002551 UBERON:0010543 ! has skeleton acropodial skeleton [Term] id: UBERON:0012355 @@ -246171,9 +242845,8 @@ is_a: UBERON:0005451 ! segment of manus is_a: UBERON:0012354 ! acropodium region intersection_of: UBERON:0012354 ! acropodium region intersection_of: part_of UBERON:0002398 ! manus -relationship: has_skeleton UBERON:0010688 ! skeleton of manual acropodium relationship: part_of UBERON:0012141 ! manual digitopodium region -property_value: IAO:0000232 "class refers to an entire limb segment, not just the bones" xsd:string +relationship: RO:0002551 UBERON:0010688 ! has skeleton skeleton of manual acropodium [Term] id: UBERON:0012356 @@ -246195,9 +242868,8 @@ is_a: UBERON:0005445 ! segment of pes is_a: UBERON:0012354 ! acropodium region intersection_of: UBERON:0012354 ! acropodium region intersection_of: part_of UBERON:0002387 ! pes -relationship: has_skeleton UBERON:0010696 ! skeleton of pedal acropodium relationship: part_of UBERON:0012142 ! pedal digitopodium region -property_value: IAO:0000232 "class refers to an entire limb segment, not just the bones" xsd:string +relationship: RO:0002551 UBERON:0010696 ! has skeleton skeleton of pedal acropodium [Term] id: UBERON:0012357 @@ -246209,7 +242881,6 @@ is_a: UBERON:0011250 ! autopod bone intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0012140 ! digitopodium region relationship: part_of UBERON:0012150 ! skeleton of digitopodium -property_value: UBPROP:0000006 https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern [Term] id: UBERON:0012358 @@ -246223,7 +242894,6 @@ is_a: UBERON:0012357 ! digitopodium bone intersection_of: UBERON:0012357 ! digitopodium bone intersection_of: part_of UBERON:0002398 ! manus relationship: part_of UBERON:0012151 ! skeleton of manual digitopodium -property_value: UBPROP:0000006 https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern [Term] id: UBERON:0012359 @@ -246236,7 +242906,6 @@ is_a: UBERON:0012357 ! digitopodium bone intersection_of: UBERON:0012357 ! digitopodium bone intersection_of: part_of UBERON:0002387 ! pes relationship: part_of UBERON:0012152 ! skeleton of pedal digitopodium -property_value: UBPROP:0000006 https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern [Term] id: UBERON:0012360 @@ -246252,7 +242921,7 @@ is_a: UBERON:0013765 ! digestive system element intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0011595 ! jaw region relationship: part_of UBERON:0001708 ! jaw skeleton -property_value: editor_note "Do not manually classify under here - bones are automatically classified" xsd:string +property_value: IAO:0000116 "Do not manually classify under here - bones are automatically classified" xsd:string [Term] id: UBERON:0012361 @@ -246316,7 +242985,7 @@ is_a: UBERON:0001816 ! autonomic nerve plexus intersection_of: UBERON:0001810 ! nerve plexus intersection_of: part_of UBERON:0000013 ! sympathetic nervous system relationship: part_of UBERON:0000013 ! sympathetic nervous system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0012375 @@ -246333,11 +243002,11 @@ xref: Wikipedia:Subserosa is_a: UBERON:0004923 ! organ component layer intersection_of: UBERON:0004923 ! organ component layer intersection_of: adjacent_to UBERON:0000042 ! serous membrane -intersection_of: composed_primarily_of UBERON:0006815 ! areolar connective tissue +intersection_of: RO:0002473 UBERON:0006815 ! composed primarily of areolar connective tissue relationship: adjacent_to UBERON:0000042 ! serous membrane -relationship: composed_primarily_of UBERON:0006815 ! areolar connective tissue -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002473 UBERON:0006815 ! composed primarily of areolar connective tissue +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0012377 @@ -246354,7 +243023,7 @@ is_a: UBERON:0011201 ! muscle layer of small intestine intersection_of: UBERON:0006660 ! muscular coat intersection_of: part_of UBERON:0002115 ! jejunum relationship: part_of UBERON:0002115 ! jejunum -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0012378 @@ -246373,12 +243042,13 @@ synonym: "tunica muscularis (vesica urinaria)" EXACT [FMA:TA] xref: FMA:15930 xref: NCIT:C32206 xref: UMLS:C1288327 {source="ncithesaurus:Bladder_Muscular_Coat"} +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0006660 ! muscular coat intersection_of: UBERON:0006660 ! muscular coat intersection_of: part_of UBERON:0001255 ! urinary bladder relationship: has_part UBERON:0004228 ! urinary bladder smooth muscle relationship: part_of UBERON:0001256 {source="FMA"} ! wall of urinary bladder -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0012398 @@ -246390,11 +243060,12 @@ synonym: "circular muscle layer of segment of large intestine" RELATED [FMA:8116 xref: EMAPA:37558 {source="MA:th"} xref: FMA:81160 xref: MA:0001548 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0012368 ! circular muscle layer of muscular coat intersection_of: UBERON:0012368 ! circular muscle layer of muscular coat intersection_of: part_of UBERON:0004220 ! large intestine smooth muscle relationship: part_of UBERON:0004220 ! large intestine smooth muscle -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0012399 @@ -246406,11 +243077,12 @@ synonym: "longitudinal muscle layer of zone of large intestine" RELATED [FMA:636 xref: EMAPA:37559 {source="MA:th"} xref: FMA:63637 xref: MA:0001549 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0012369 ! longitudinal muscle layer of muscular coat intersection_of: UBERON:0012369 ! longitudinal muscle layer of muscular coat intersection_of: part_of UBERON:0004220 ! large intestine smooth muscle relationship: part_of UBERON:0004220 ! large intestine smooth muscle -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0012401 @@ -246429,6 +243101,7 @@ xref: EMAPA:37562 {source="MA:th"} xref: FMA:14935 xref: MA:0001560 xref: SCTID:54658003 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0012368 ! circular muscle layer of muscular coat intersection_of: UBERON:0012368 ! circular muscle layer of muscular coat intersection_of: part_of UBERON:0004239 ! small intestine smooth muscle @@ -246452,6 +243125,7 @@ xref: EMAPA:37563 {source="MA:th"} xref: FMA:14936 xref: MA:0001561 xref: SCTID:59150006 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0012369 ! longitudinal muscle layer of muscular coat intersection_of: UBERON:0012369 ! longitudinal muscle layer of muscular coat intersection_of: part_of UBERON:0004239 ! small intestine smooth muscle @@ -246470,7 +243144,7 @@ is_a: UBERON:0004695 ! arterial system smooth muscle intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0003643 ! respiratory system arterial blood vessel relationship: part_of UBERON:0003643 ! respiratory system arterial blood vessel -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0012418 @@ -246484,7 +243158,7 @@ is_a: UBERON:0004696 ! venous system smooth muscle intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0003476 ! respiratory system venous blood vessel relationship: part_of UBERON:0003476 ! respiratory system venous blood vessel -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0012419 @@ -246502,7 +243176,7 @@ xref: SCTID:362160001 xref: Wikipedia:Taenia_coli is_a: UBERON:0034933 ! layer of smooth muscle tissue relationship: part_of UBERON:0011198 {source="FMA"} ! muscle layer of large intestine -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0012423 @@ -246517,10 +243191,7 @@ xref: NCIT:C33112 xref: UMLS:C0026049 {source="ncithesaurus:Microvillus"} xref: Wikipedia:Microvillus is_a: UBERON:0005162 ! multi cell part structure -relationship: composed_primarily_of GO:0005902 ! microvillus -property_value: UBPROP:0000009 "a wide variety of physiological and cellular functions including absorption, secretion, cellular adhesion, and mechanotransduction" xsd:string -property_value: UBPROP:0000009 "increases the surface area of a cell lining whilst minimizing increase in volume" xsd:string -property_value: UBPROP:0000012 "FMA class represents an individual microvillus." xsd:string {external_ontology="FMA"} +relationship: RO:0002473 GO:0005902 ! composed primarily of microvillus [Term] id: UBERON:0012425 @@ -246532,7 +243203,6 @@ xref: FMA:70978 xref: NCIT:C33634 is_a: UBERON:0012423 ! layer of microvilli relationship: part_of UBERON:0000160 ! intestine -property_value: UBPROP:0000012 "FMA class represents an individual microvillus" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0012429 @@ -246548,13 +243218,13 @@ xref: CALOHA:TS-2142 xref: FMA:14073 xref: NCIT:C13051 xref: UMLS:C0229619 {source="ncithesaurus:Hematopoietic_Tissue"} +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0034769 {source="FMA"} ! lymphomyeloid tissue intersection_of: UBERON:0000479 ! tissue intersection_of: site_of GO:0030097 ! hemopoiesis relationship: part_of UBERON:0002371 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! bone marrow relationship: part_of UBERON:0002390 {source="defitional"} ! hematopoietic system relationship: site_of GO:0030097 ! hemopoiesis -property_value: UBPROP:0000008 "Bone marrow in humans, kidney interstitium in Danio, within a stroma of reticuloendothelial tissue" xsd:string [Term] id: UBERON:0012430 @@ -246569,12 +243239,13 @@ xref: FMA:58102 xref: SCTID:361318005 xref: Wikipedia:Fibrous_tunic_of_eyeball is_a: PR:000050567 ! protein-containing material entity +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004923 {source="FMA"} ! organ component layer is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: has_part UBERON:0000964 ! cornea relationship: has_part UBERON:0001773 ! sclera relationship: part_of UBERON:0010230 ! eyeball of camera-type eye -relationship: present_in_taxon NCBITaxon:7955 {source="DOI:10.1177/0192623311409597"} +property_value: RO:0002175 NCBITaxon:7955 {source="DOI:10.1177/0192623311409597"} [Term] id: UBERON:0012441 @@ -246589,7 +243260,7 @@ is_a: UBERON:0004819 ! kidney epithelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0005272 ! peritubular capillary relationship: part_of UBERON:0005272 ! peritubular capillary -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0012463 @@ -246602,11 +243273,10 @@ xref: TAO:0000330 xref: ZFA:0000330 is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0000162 ! cloaca -relationship: luminal_space_of UBERON:0000162 ! cloaca +intersection_of: RO:0002572 UBERON:0000162 ! luminal space of cloaca relationship: part_of UBERON:0000162 ! cloaca relationship: part_of UBERON:0012465 {source="cjm"} ! lumen of terminal part of digestive tract -property_value: UBPROP:0000012 "the ZFA class belongs here as it is an anatomical space. See https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/102/" xsd:string {external_ontology="ZFA"} +relationship: RO:0002572 UBERON:0000162 ! luminal space of cloaca [Term] id: UBERON:0012464 @@ -246628,10 +243298,9 @@ namespace: uberon def: "An anatomical space that is enclosed by a terminal part of digestive tract." [OBOL:automatic] is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0006866 ! terminal part of digestive tract -relationship: luminal_space_of UBERON:0006866 ! terminal part of digestive tract +intersection_of: RO:0002572 UBERON:0006866 ! luminal space of terminal part of digestive tract relationship: part_of UBERON:0006866 ! terminal part of digestive tract -property_value: UBPROP:0000008 "includes the cloacal lumen, in species where this is present" xsd:string +relationship: RO:0002572 UBERON:0006866 ! luminal space of terminal part of digestive tract [Term] id: UBERON:0012466 @@ -246655,8 +243324,8 @@ synonym: "closed anatomical space" EXACT [] xref: AEO:0000222 is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: has_quality PATO:0000608 ! closed -relationship: has_quality PATO:0000608 ! closed +intersection_of: RO:0000086 PATO:0000608 ! has quality closed +relationship: RO:0000086 PATO:0000608 ! has quality closed [Term] id: UBERON:0012468 @@ -246670,8 +243339,8 @@ synonym: "perianal tooth" RELATED [] is_a: UBERON:0003913 ! tooth-like structure intersection_of: UBERON:0003913 ! tooth-like structure intersection_of: part_of UBERON:0001353 ! anal region -relationship: only_in_taxon NCBITaxon:7586 ! Echinodermata relationship: part_of UBERON:0001353 ! anal region +relationship: RO:0002160 NCBITaxon:7586 ! only in taxon Echinodermata [Term] id: UBERON:0012469 @@ -246696,10 +243365,10 @@ synonym: "upper limb skeleton" RELATED [FMA:24139] xref: FMA:24139 is_a: UBERON:0010912 ! subdivision of skeleton intersection_of: UBERON:0010912 ! subdivision of skeleton -intersection_of: skeleton_of UBERON:0010708 ! pectoral complex +intersection_of: RO:0002576 UBERON:0010708 ! skeleton of pectoral complex relationship: part_of UBERON:0002091 ! appendicular skeleton relationship: part_of UBERON:0010708 {source="FMA"} ! pectoral complex -relationship: skeleton_of UBERON:0010708 ! pectoral complex +relationship: RO:0002576 UBERON:0010708 ! skeleton of pectoral complex [Term] id: UBERON:0012476 @@ -246716,10 +243385,10 @@ synonym: "skeleton of posterior limb/fin and girdle" RELATED [https://orcid.org/ xref: FMA:24140 is_a: UBERON:0010912 ! subdivision of skeleton intersection_of: UBERON:0010912 ! subdivision of skeleton -intersection_of: skeleton_of UBERON:0010709 ! pelvic complex +intersection_of: RO:0002576 UBERON:0010709 ! skeleton of pelvic complex relationship: part_of UBERON:0002091 ! appendicular skeleton relationship: part_of UBERON:0010709 {source="FMA"} ! pelvic complex -relationship: skeleton_of UBERON:0010709 ! pelvic complex +relationship: RO:0002576 UBERON:0010709 ! skeleton of pelvic complex [Term] id: UBERON:0012477 @@ -246743,9 +243412,8 @@ xref: FMA:24189 xref: SCTID:182326009 xref: SCTID:304036007 is_a: UBERON:0005434 {source="FMA"} ! cervical region -relationship: in_dorsal_side_of UBERON:0000974 {source="FMA"} ! neck +relationship: BSPO:0015101 UBERON:0000974 {source="FMA"} ! neck relationship: part_of UBERON:0001137 {source="FMA"} ! dorsum -property_value: UBPROP:0000007 "nuchal" xsd:string [Term] id: UBERON:0012478 @@ -246791,7 +243459,6 @@ is_a: UBERON:0005911 ! endo-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000162 ! cloaca relationship: part_of UBERON:0000162 ! cloaca -property_value: UBPROP:0000001 "cloacal epithelium (cle) (syn: cloacal endoderm) (TS17-TS20): the cloacal epithelium is derived from endoderm and lines the cloacal cavity. It is marked by Shh and Cdh1 and lines the cloacal lumen. The cloacal epithelium gives rise to the urogenital sinus epithelium, hindgut epithelium and the urethral plate epithelium." xsd:string {source="EMAPA:27577"} [Term] id: UBERON:0012482 @@ -246848,13 +243515,14 @@ name: vaginal sphincter namespace: uberon def: "A sphincter muscle that is part of a vagina." [OBOL:automatic] synonym: "sphincter of vagina" EXACT [] +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004590 ! sphincter muscle is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0004590 ! sphincter muscle intersection_of: part_of UBERON:0000996 ! vagina -relationship: never_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: part_of UBERON:0000996 ! vagina -relationship: present_in_taxon NCBITaxon:8509 +property_value: RO:0002161 NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:8509 [Term] id: UBERON:0012488 @@ -246892,7 +243560,7 @@ is_a: UBERON:0011198 ! muscle layer of large intestine intersection_of: UBERON:0006660 ! muscular coat intersection_of: part_of UBERON:0001155 ! colon relationship: part_of UBERON:0001155 ! colon -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0012490 @@ -246907,6 +243575,7 @@ synonym: "muscularis externa of anal canal" EXACT [] synonym: "muscularis propria of anal canal" EXACT [FMA:15708] xref: FMA:15708 xref: SCTID:362171000 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0011198 ! muscle layer of large intestine intersection_of: UBERON:0006660 ! muscular coat intersection_of: part_of UBERON:0000159 ! anal canal @@ -246928,7 +243597,7 @@ is_a: UBERON:0001209 ! serosa of large intestine intersection_of: UBERON:0000042 ! serous membrane intersection_of: part_of UBERON:0001154 ! vermiform appendix relationship: part_of UBERON:0001154 ! vermiform appendix -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0012499 @@ -247003,11 +243672,11 @@ xref: FMA:17046 xref: SCTID:264014000 is_a: UBERON:1100000 ! digestive tract junction intersection_of: UBERON:0007651 ! anatomical junction -intersection_of: connects UBERON:0000945 ! stomach -intersection_of: connects UBERON:0002114 ! duodenum -relationship: connects UBERON:0000945 ! stomach -relationship: connects UBERON:0002114 ! duodenum +intersection_of: RO:0002176 UBERON:0000945 ! connects stomach +intersection_of: RO:0002176 UBERON:0002114 ! connects duodenum relationship: part_of UBERON:0000945 ! stomach +relationship: RO:0002176 UBERON:0000945 ! connects stomach +relationship: RO:0002176 UBERON:0002114 ! connects duodenum [Term] id: UBERON:0012651 @@ -247043,12 +243712,10 @@ xref: Wikipedia:Sulcus_(neuroanatomy) is_a: UBERON:0000093 ! sulcus intersection_of: UBERON:0000093 ! sulcus intersection_of: part_of UBERON:0000955 ! brain -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0000955 ! brain -relationship: surrounds UBERON:0000200 ! gyrus -property_value: editor_note "sulci are considered absent from lissencephalic mammals such as mice, but they may possess fissures. For example, the Allen mouse brain Atlas includes hippocampal, rhinal and choroid fissure. For this reason we do not place a taxon constraint on this class" xsd:string -property_value: RO:0002174 NCBITaxon:10088 -property_value: UBPROP:0000001 "Indentation on the surface of the brain or spinal cord that forms a recognizable landmark, e.g., central sulcus, sulcus limitans (CUMBO)" xsd:string {source="http://neurolex.org/wiki/Cumbo_terms"} +relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia +relationship: RO:0002221 UBERON:0000200 ! surrounds gyrus +property_value: IAO:0000116 "sulci are considered absent from lissencephalic mammals such as mice, but they may possess fissures. For example, the Allen mouse brain Atlas includes hippocampal, rhinal and choroid fissure. For this reason we do not place a taxon constraint on this class" xsd:string [Term] id: UBERON:0013121 @@ -247078,8 +243745,7 @@ is_a: UBERON:0001638 ! vein is_a: UBERON:0003497 ! abdomen blood vessel intersection_of: UBERON:0001638 ! vein intersection_of: part_of UBERON:0000916 ! abdomen -property_value: editor_note "TODO mirror representation of abdominal aorta" xsd:string -property_value: IAO:0000232 "this class groups all veins that are in the abdomen. The term 'abdominal vein' may have specific meanings in different contexts. The lateral abdominal veins are present in fishes but usually merged or absent in tetrapods; in amphibians, the L&R abdominal veins merge into the ventral abdominal vein" xsd:string +property_value: IAO:0000116 "TODO mirror representation of abdominal aorta" xsd:string [Term] id: UBERON:0013127 @@ -247091,7 +243757,6 @@ xref: Wikipedia:Pulmonary_venous_system is_a: UBERON:0002049 ! vasculature relationship: channels_from UBERON:0000102 ! lung vasculature relationship: part_of UBERON:0004582 ! venous system -property_value: UBPROP:0000001 "Pulmonary circulation is the half portion of the cardiovascular system which carries oxygen-depleted blood away from the heart, to the lungs, and returns oxygenated (oxygen-rich) blood back to the heart. The term pulmonary circulation is readily paired and contrasted with the systemic circulation. A separate system known as the bronchial circulation supplies blood to the tissue of the larger airways of the lung." xsd:string {source="Wikipedia:Pulmonary_circulation"} [Term] id: UBERON:0013136 @@ -247105,9 +243770,9 @@ synonym: "vena labialis" EXACT OMO:0003011 [] xref: SCTID:367664002 is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein -intersection_of: drains UBERON:0001833 ! lip -relationship: drains UBERON:0001833 ! lip -relationship: tributary_of UBERON:0001653 {source="FMA"} ! facial vein +intersection_of: RO:0002179 UBERON:0001833 ! drains lip +relationship: RO:0002179 UBERON:0001833 ! drains lip +relationship: RO:0002376 UBERON:0001653 {source="FMA"} ! tributary of facial vein [Term] id: UBERON:0013139 @@ -247120,6 +243785,7 @@ xref: FMA:15820 xref: NCIT:C32997 xref: SCTID:48536008 xref: UMLS:C0230238 {source="ncithesaurus:Liver_Ligament"} +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0005172 ! abdomen element is_a: UBERON:0008845 ! nonskeletal ligament is_a: UBERON:0013765 ! digestive system element @@ -247168,8 +243834,7 @@ xref: SCTID:360409004 is_a: UBERON:0010064 {source="EHDAA2"} ! open anatomical space relationship: part_of UBERON:0005281 {source="EHDAA2"} ! ventricular system of central nervous system relationship: part_of UBERON:0006238 ! future brain -property_value: editor_note "consider adding all secondary vesicles (e.g. diencephalic; my/metencephalic. See http://www.dartmouth.edu/~rswenson/NeuroSci/chapter_4.html)." xsd:string -property_value: UBPROP:0000012 "Note that some sources may treat the term vesicle as the progenitor of the whole brain region; for example 'The retina develops directly from the neural tube as an outpouching from the diencephalic vesicle'" xsd:string +property_value: IAO:0000116 "consider adding all secondary vesicles (e.g. diencephalic; my/metencephalic. See http://www.dartmouth.edu/~rswenson/NeuroSci/chapter_4.html)." xsd:string [Term] id: UBERON:0013151 @@ -247183,8 +243848,8 @@ xref: SCTID:244210009 xref: UMLS:C0226164 {source="ncithesaurus:Choroidal_Artery"} is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0001886 ! choroid plexus -relationship: supplies UBERON:0001886 ! choroid plexus +intersection_of: RO:0002178 UBERON:0001886 ! supplies choroid plexus +relationship: RO:0002178 UBERON:0001886 ! supplies choroid plexus [Term] id: UBERON:0013156 @@ -247195,9 +243860,9 @@ xref: EHDAA2:0000033 xref: EMAPA:16384 is_a: UBERON:0003258 ! endoderm of foregut is_a: UBERON:0005291 ! embryonic tissue -relationship: develops_from UBERON:0007122 {source="EHDAA2"} ! pharyngeal pouch 1 relationship: part_of UBERON:0007237 {source="EHDAA2"} ! 1st arch mandibular component relationship: part_of UBERON:0009722 {source="EHDAA2"} ! entire pharyngeal arch endoderm +relationship: RO:0002202 UBERON:0007122 {source="EHDAA2"} ! develops from pharyngeal pouch 1 [Term] id: UBERON:0013158 @@ -247225,8 +243890,8 @@ xref: VHOG:0000913 is_a: UBERON:0004061 ! neural tube mantle layer intersection_of: UBERON:0004061 ! neural tube mantle layer intersection_of: part_of UBERON:0001899 ! epithalamus -relationship: develops_from UBERON:0009580 ! diencephalon mantle layer relationship: part_of UBERON:0001899 ! epithalamus +relationship: RO:0002202 UBERON:0009580 ! develops from diencephalon mantle layer [Term] id: UBERON:0013160 @@ -247252,11 +243917,11 @@ synonym: "left telencephalic ventricle" EXACT [] xref: FMA:78450 xref: SCTID:368593005 is_a: UBERON:0002285 ! telencephalic ventricle +is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0002285 ! telencephalic ventricle -intersection_of: in_left_side_of UBERON:0001893 ! telencephalon -relationship: in_left_side_of UBERON:0001893 ! telencephalon +intersection_of: BSPO:0000120 UBERON:0001893 ! telencephalon +relationship: BSPO:0000120 UBERON:0001893 ! telencephalon relationship: part_of UBERON:0002812 {source="FMA"} ! left cerebral hemisphere -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI [Term] id: UBERON:0013162 @@ -247267,11 +243932,11 @@ synonym: "right telencephalic ventricle" EXACT [] xref: FMA:78449 xref: SCTID:368571000 is_a: UBERON:0002285 ! telencephalic ventricle +is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0002285 ! telencephalic ventricle -intersection_of: in_right_side_of UBERON:0001893 ! telencephalon -relationship: in_right_side_of UBERON:0001893 ! telencephalon +intersection_of: BSPO:0000121 UBERON:0001893 ! telencephalon +relationship: BSPO:0000121 UBERON:0001893 ! telencephalon relationship: part_of UBERON:0002813 {source="FMA"} ! right cerebral hemisphere -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI [Term] id: UBERON:0013191 @@ -247291,7 +243956,7 @@ is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0001851 ! cortex intersection_of: part_of UBERON:0000992 ! ovary relationship: part_of UBERON:0006960 ! ovary stroma -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0013192 @@ -247312,7 +243977,25 @@ is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0000958 ! medulla of organ intersection_of: part_of UBERON:0000992 ! ovary relationship: part_of UBERON:0000992 ! ovary -property_value: UBPROP:0000010 "composed of loose connective tissue that contains blood vessels, lymph vessels and nerves" xsd:string {source="NCIT"} + +[Term] +id: UBERON:0013212 +name: anal sac gland secretion +namespace: uberon +def: "A bodily secretion that is produced by a gland of anal sac." [OBOL:automatic] +synonym: "anal gland secretion" RELATED [] +synonym: "castoreum" NARROW SENSU [NCBITaxon:29132] +synonym: "civet" NARROW SENSU [NCBITaxon:9673] +synonym: "hyena butter" RELATED SENSU [Wikipedia:Hyena_butter] +synonym: "musk" RELATED [NCBITaxon:30533] +synonym: "odorous sac" RELATED [] +is_a: UBERON:0000456 ! secretion of exocrine gland +intersection_of: UBERON:0000456 ! secretion of exocrine gland +intersection_of: produced_by UBERON:0004760 ! gland of anal canal +relationship: produced_by UBERON:0004760 ! gland of anal canal +property_value: RO:0002175 NCBITaxon:119825 +property_value: RO:0002175 NCBITaxon:30533 +property_value: RO:0002175 NCBITaxon:9673 [Term] id: UBERON:0013228 @@ -247341,6 +244024,7 @@ namespace: uberon def: "Any gland that is part of an eyelid. This includes sebaceous glands (Zeis gland, tarsal gland) and sweat glands (Moll's gland)." [http://orcid.org/0000-0002-6601-2165] synonym: "gland of eyelid" EXACT [] xref: SCTID:280574000 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004859 ! eye gland is_a: UBERON:0015152 ! gland of ocular region intersection_of: UBERON:0002530 ! gland @@ -247367,8 +244051,8 @@ xref: FMA:86279 is_a: UBERON:0011858 ! acinus of exocrine gland intersection_of: UBERON:0009842 ! glandular acinus intersection_of: part_of UBERON:0000409 ! serous gland -relationship: composed_primarily_of CL:0000313 ! serous secreting cell relationship: part_of UBERON:0000409 ! serous gland +relationship: RO:0002473 CL:0000313 ! composed primarily of serous secreting cell [Term] id: UBERON:0013238 @@ -247377,8 +244061,8 @@ namespace: uberon is_a: UBERON:0005423 ! developing anatomical structure union_of: UBERON:0013239 ! future glans penis union_of: UBERON:0013240 ! future glans clitoris -relationship: has_potential_to_develop_into UBERON:0035651 ! glans relationship: part_of UBERON:0011757 ! differentiated genital tubercle +relationship: RO:0002387 UBERON:0035651 ! has potential to develop into glans [Term] id: UBERON:0013239 @@ -247415,8 +244099,7 @@ synonym: "urethral sulcus" EXACT [] xref: SCTID:361531004 xref: Wikipedia:Urethral_groove is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0004876 {source="Wikipedia"} ! urogenital fold -property_value: UBPROP:0000008 "In humans, the urethral groove is a temporary linear indentation on the underside (ventral side) of the male penis during embryonic development. It typically appears around 8 weeks of gestation and becomes closed into a normal male urethra by the 12th week" xsd:string {source="Wikipedia:Urethral_groove"} +relationship: RO:0002202 UBERON:0004876 {source="Wikipedia"} ! develops from urogenital fold [Term] id: UBERON:0013247 @@ -247431,11 +244114,11 @@ is_a: UBERON:0003914 ! epithelial tube is_a: UBERON:0005156 ! reproductive structure is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0003914 ! epithelial tube -intersection_of: develops_from UBERON:0003890 ! Mullerian duct intersection_of: part_of UBERON:0000079 ! male reproductive system -relationship: develops_from UBERON:0003890 {source="EHDAA2"} ! Mullerian duct +intersection_of: RO:0002202 UBERON:0003890 ! develops from Mullerian duct relationship: part_of UBERON:0000079 {source="EHDAA2"} ! male reproductive system -property_value: editor_note "consider separating the duct from the degenerating portion, as in EMAPA" xsd:string +relationship: RO:0002202 UBERON:0003890 {source="EHDAA2"} ! develops from Mullerian duct +property_value: IAO:0000116 "consider separating the duct from the degenerating portion, as in EMAPA" xsd:string [Term] id: UBERON:0013279 @@ -247450,11 +244133,11 @@ xref: EMAPA:37892 {source="MA:th"} xref: FMA:33738 xref: SCTID:302528006 xref: Wikipedia:Body_of_fibula +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004769 ! diaphysis intersection_of: UBERON:0004769 ! diaphysis intersection_of: part_of UBERON:0001446 ! fibula relationship: part_of UBERON:0001446 ! fibula -property_value: UBPROP:0000001 "The body of fibula presents four borders - the antero-lateral, the antero-medial, the postero-lateral, and the postero-medial; and four surfaces - anterior, posterior, medial, and lateral[Wikipedia:Body_of_fibula]." xsd:string {source="Wikipedia:Body_of_fibula"} [Term] id: UBERON:0013280 @@ -247472,11 +244155,11 @@ xref: FMA:33125 xref: MA:0003049 xref: SCTID:302525009 xref: Wikipedia:Body_of_tibia +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004769 ! diaphysis intersection_of: UBERON:0004769 ! diaphysis intersection_of: part_of UBERON:0000979 ! tibia relationship: part_of UBERON:0000979 ! tibia -property_value: UBPROP:0000001 "The body of the tibia has three borders and three surfaces[Wikipedia:Body_of_tibia]." xsd:string {source="Wikipedia:Body_of_tibia"} [Term] id: UBERON:0013411 @@ -247496,10 +244179,10 @@ xref: UMLS:C0230041 {source="ncithesaurus:Cranial_Cavity"} xref: Wikipedia:Cranial_cavity is_a: UBERON:0002553 ! anatomical cavity intersection_of: UBERON:0002553 ! anatomical cavity -intersection_of: luminal_space_of UBERON:0003129 ! skull -relationship: luminal_space_of UBERON:0003129 ! skull +intersection_of: RO:0002572 UBERON:0003129 ! luminal space of skull relationship: part_of UBERON:0003129 {source="Wikipedia"} ! skull -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI +relationship: RO:0002572 UBERON:0003129 ! luminal space of skull +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI [Term] id: UBERON:0013478 @@ -247512,9 +244195,8 @@ xref: SCTID:14239003 is_a: UBERON:0001962 ! gut-associated lymphoid tissue intersection_of: UBERON:0001961 ! mucosa-associated lymphoid tissue intersection_of: part_of UBERON:0001153 ! caecum -relationship: only_in_taxon NCBITaxon:8782 ! Aves relationship: part_of UBERON:0000314 ! cecum mucosa -property_value: UBPROP:0000008 "In avians the polycryptic cecal tissue is similar to the mammalian palatine tonsil" xsd:string +relationship: RO:0002160 NCBITaxon:8782 ! only in taxon Aves [Term] id: UBERON:0013479 @@ -247524,6 +244206,7 @@ def: "A blood vessel endothelium that is part of a lung [Automatically generated synonym: "respiratory endothelium" RELATED [BTO:0004128] xref: BTO:0004128 xref: CALOHA:TS-0573 +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0000115 ! lung epithelium is_a: UBERON:0004702 ! respiratory system blood vessel endothelium intersection_of: UBERON:0004638 ! blood vessel endothelium @@ -247588,7 +244271,7 @@ is_a: UBERON:0001984 ! crypt of Lieberkuhn of large intestine intersection_of: UBERON:0001983 ! crypt of Lieberkuhn intersection_of: part_of UBERON:0001155 ! colon relationship: part_of UBERON:0000317 ! colonic mucosa -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0013486 @@ -247616,7 +244299,7 @@ is_a: UBERON:0001714 ! cranial ganglion intersection_of: UBERON:0001714 ! cranial ganglion intersection_of: extends_fibers_into UBERON:0001648 ! vestibulocochlear nerve relationship: extends_fibers_into UBERON:0001648 ! vestibulocochlear nerve -property_value: editor_note "requires verification" xsd:string +property_value: IAO:0000116 "requires verification" xsd:string [Term] id: UBERON:0013501 @@ -247660,9 +244343,9 @@ is_a: UBERON:0011094 ! vertebra cartilage element is_a: UBERON:0018142 ! caudal vertebra endochondral element is_a: UBERON:2001457 ! postcranial axial cartilage intersection_of: UBERON:0018142 ! caudal vertebra endochondral element -intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue -relationship: develops_from UBERON:0013504 ! caudal vertebra pre-cartilage condensation -relationship: has_potential_to_develop_into UBERON:0001095 ! caudal vertebra +intersection_of: RO:0002473 UBERON:0002418 ! composed primarily of cartilage tissue +relationship: RO:0002202 UBERON:0013504 ! develops from caudal vertebra pre-cartilage condensation +relationship: RO:0002387 UBERON:0001095 ! has potential to develop into caudal vertebra [Term] id: UBERON:0013504 @@ -247676,7 +244359,7 @@ xref: EMAPA:18045 is_a: UBERON:0011095 ! vertebra pre-cartilage condensation is_a: UBERON:0018142 ! caudal vertebra endochondral element intersection_of: UBERON:0018142 ! caudal vertebra endochondral element -intersection_of: composed_primarily_of UBERON:0005866 ! pre-cartilage condensation +intersection_of: RO:0002473 UBERON:0005866 ! composed primarily of pre-cartilage condensation [Term] id: UBERON:0013505 @@ -247690,9 +244373,9 @@ is_a: UBERON:0011094 ! vertebra cartilage element is_a: UBERON:0015007 ! cervical vertebra endochondral element is_a: UBERON:2001457 ! postcranial axial cartilage intersection_of: UBERON:0015007 ! cervical vertebra endochondral element -intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue -relationship: develops_from UBERON:0013506 ! cervical vertebra pre-cartilage condensation -relationship: has_potential_to_develop_into UBERON:0002413 ! cervical vertebra +intersection_of: RO:0002473 UBERON:0002418 ! composed primarily of cartilage tissue +relationship: RO:0002202 UBERON:0013506 ! develops from cervical vertebra pre-cartilage condensation +relationship: RO:0002387 UBERON:0002413 ! has potential to develop into cervical vertebra [Term] id: UBERON:0013506 @@ -247702,7 +244385,7 @@ def: "A cervical vertebra endochondral element that is composed primarily of a p is_a: UBERON:0011095 ! vertebra pre-cartilage condensation is_a: UBERON:0015007 ! cervical vertebra endochondral element intersection_of: UBERON:0015007 ! cervical vertebra endochondral element -intersection_of: composed_primarily_of UBERON:0005866 ! pre-cartilage condensation +intersection_of: RO:0002473 UBERON:0005866 ! composed primarily of pre-cartilage condensation [Term] id: UBERON:0013507 @@ -247715,9 +244398,9 @@ is_a: UBERON:0011094 ! vertebra cartilage element is_a: UBERON:0015008 ! thoracic vertebra endochondral element is_a: UBERON:2001457 ! postcranial axial cartilage intersection_of: UBERON:0015008 ! thoracic vertebra endochondral element -intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue -relationship: develops_from UBERON:0013508 ! thoracic vertebra pre-cartilage condensation -relationship: has_potential_to_develop_into UBERON:0002347 ! thoracic vertebra +intersection_of: RO:0002473 UBERON:0002418 ! composed primarily of cartilage tissue +relationship: RO:0002202 UBERON:0013508 ! develops from thoracic vertebra pre-cartilage condensation +relationship: RO:0002387 UBERON:0002347 ! has potential to develop into thoracic vertebra [Term] id: UBERON:0013508 @@ -247727,7 +244410,7 @@ def: "A thoracic vertebra endochondral element that is composed primarily of a p is_a: UBERON:0011095 ! vertebra pre-cartilage condensation is_a: UBERON:0015008 ! thoracic vertebra endochondral element intersection_of: UBERON:0015008 ! thoracic vertebra endochondral element -intersection_of: composed_primarily_of UBERON:0005866 ! pre-cartilage condensation +intersection_of: RO:0002473 UBERON:0005866 ! composed primarily of pre-cartilage condensation [Term] id: UBERON:0013514 @@ -247738,8 +244421,8 @@ synonym: "external to organism" EXACT [] synonym: "outside of body" EXACT [] is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: surrounds UBERON:0000468 ! multicellular organism -relationship: surrounds UBERON:0000468 ! multicellular organism +intersection_of: RO:0002221 UBERON:0000468 ! surrounds multicellular organism +relationship: RO:0002221 UBERON:0000468 ! surrounds multicellular organism [Term] id: UBERON:0013515 @@ -247759,7 +244442,6 @@ intersection_of: UBERON:0013522 ! subdivision of tube intersection_of: subdivision_of UBERON:0000993 ! oviduct relationship: part_of UBERON:0000993 ! oviduct relationship: subdivision_of UBERON:0000993 ! oviduct -property_value: UBPROP:0000012 "FMA class may only represent the uterine portion" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0013522 @@ -247782,10 +244464,9 @@ xref: EMAPA:18395 xref: FMA:14585 is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0000945 ! stomach -relationship: luminal_space_of UBERON:0000945 ! stomach +intersection_of: RO:0002572 UBERON:0000945 ! luminal space of stomach relationship: part_of UBERON:0011565 {source="FMA"} ! lumen of gastrointestinal system -property_value: UBPROP:0000001 "Organ cavity which is bound by the internal surface of the wall of stomach. Examples: There is only one cavity of stomach[FMA:14585]." xsd:string {source="FMA:14585"} +relationship: RO:0002572 UBERON:0000945 ! luminal space of stomach [Term] id: UBERON:0013526 @@ -247798,10 +244479,10 @@ xref: EMAPA:25363 is_a: UBERON:0002553 ! anatomical cavity is_a: UBERON:0007473 {source="EHDAA2"} ! lumen of epithelial sac intersection_of: UBERON:0002553 ! anatomical cavity -intersection_of: luminal_space_of UBERON:0003051 ! ear vesicle -relationship: develops_from UBERON:0006273 {source="EHDAA2"} ! otic pit -relationship: luminal_space_of UBERON:0003051 ! ear vesicle +intersection_of: RO:0002572 UBERON:0003051 ! luminal space of ear vesicle relationship: part_of UBERON:0003051 {source="EHDAA2"} ! ear vesicle +relationship: RO:0002202 UBERON:0006273 {source="EHDAA2"} ! develops from otic pit +relationship: RO:0002572 UBERON:0003051 ! luminal space of ear vesicle [Term] id: UBERON:0013605 @@ -247827,9 +244508,9 @@ xref: FMA:76989 xref: PBA:128013078 is_a: UBERON:0013605 ! layer of lateral geniculate body intersection_of: UBERON:0013605 ! layer of lateral geniculate body -intersection_of: composed_primarily_of CL:0011003 ! magnocellular neurosecretory cell -relationship: composed_primarily_of CL:0011003 ! magnocellular neurosecretory cell +intersection_of: RO:0002473 CL:0011003 ! composed primarily of magnocellular neurosecretory cell relationship: part_of UBERON:0002479 ! dorsal lateral geniculate nucleus +relationship: RO:0002473 CL:0011003 ! composed primarily of magnocellular neurosecretory cell [Term] id: UBERON:0013607 @@ -247843,9 +244524,9 @@ xref: FMA:76992 xref: PBA:128013091 is_a: UBERON:0013605 ! layer of lateral geniculate body intersection_of: UBERON:0013605 ! layer of lateral geniculate body -intersection_of: composed_primarily_of CL:1001505 ! parvocellular neurosecretory cell -relationship: composed_primarily_of CL:1001505 ! parvocellular neurosecretory cell +intersection_of: RO:0002473 CL:1001505 ! composed primarily of parvocellular neurosecretory cell relationship: part_of UBERON:0002479 ! dorsal lateral geniculate nucleus +relationship: RO:0002473 CL:1001505 ! composed primarily of parvocellular neurosecretory cell [Term] id: UBERON:0013615 @@ -247868,7 +244549,7 @@ xref: NCIT:C33545 xref: SCTID:332807009 xref: Wikipedia:Short_bone is_a: UBERON:0001474 {source="NCIT"} ! bone element -property_value: editor_note "TODO - make subclass links" xsd:string +property_value: IAO:0000116 "TODO - make subclass links" xsd:string [Term] id: UBERON:0013631 @@ -247879,8 +244560,8 @@ comment: Sesamoids are often endochondral replacement elements and in addition t synonym: "sesamoid" EXACT [VSAO:0000137] xref: VSAO:0000137 is_a: UBERON:0010911 {source="VSAO"} ! ossicle -relationship: develops_in UBERON:0007846 {source="VSAO"} ! dense regular connective tissue -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002226 UBERON:0007846 {source="VSAO"} ! develops in dense regular connective tissue [Term] id: UBERON:0013632 @@ -247893,7 +244574,7 @@ xref: FMA:55379 is_a: UBERON:0007844 ! cartilage element is_a: UBERON:0013631 ! sesamoid element intersection_of: UBERON:0013631 ! sesamoid element -intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue +intersection_of: RO:0002473 UBERON:0002418 ! composed primarily of cartilage tissue [Term] id: UBERON:0013636 @@ -247926,9 +244607,8 @@ xref: NCIT:C13092 is_a: UBERON:0001328 ! lobe of prostate is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0001328 ! lobe of prostate -intersection_of: in_lateral_side_of UBERON:0002367 ! prostate gland -relationship: in_lateral_side_of UBERON:0002367 ! prostate gland -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +intersection_of: BSPO:0000126 UBERON:0002367 ! prostate gland +relationship: BSPO:0000126 UBERON:0002367 ! prostate gland [Term] id: UBERON:0013683 @@ -247939,10 +244619,10 @@ subset: pheno_slim synonym: "left thalamus" BROAD [FMA:258716] xref: FMA:258716 is_a: UBERON:0004703 ! dorsal thalamus +is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0004703 ! dorsal thalamus -intersection_of: in_left_side_of UBERON:0001894 ! diencephalon -relationship: in_left_side_of UBERON:0001894 ! diencephalon -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +intersection_of: BSPO:0000120 UBERON:0001894 ! diencephalon +relationship: BSPO:0000120 UBERON:0001894 ! diencephalon [Term] id: UBERON:0013684 @@ -247953,10 +244633,10 @@ subset: pheno_slim synonym: "right thalamus" BROAD [FMA:258714] xref: FMA:258714 is_a: UBERON:0004703 ! dorsal thalamus +is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0004703 ! dorsal thalamus -intersection_of: in_right_side_of UBERON:0001894 ! diencephalon -relationship: in_right_side_of UBERON:0001894 ! diencephalon -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +intersection_of: BSPO:0000121 UBERON:0001894 ! diencephalon +relationship: BSPO:0000121 UBERON:0001894 ! diencephalon [Term] id: UBERON:0013685 @@ -247984,11 +244664,11 @@ subset: common_anatomy synonym: "foramen space" NARROW [] xref: FMA:9338 is_a: UBERON:0000464 {source="FMA"} ! anatomical space -relationship: connects UBERON:0000464 {cardinality="2"} ! anatomical space -relationship: luminal_space_of UBERON:0004111 ! anatomical conduit -relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 ! Fungi +relationship: RO:0002176 UBERON:0000464 {cardinality="2"} ! connects anatomical space +relationship: RO:0002572 UBERON:0004111 ! luminal space of anatomical conduit +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0013687 @@ -248014,9 +244694,8 @@ is_a: UBERON:0010754 ! germinal center intersection_of: UBERON:0010754 ! germinal center intersection_of: part_of UBERON:0002372 ! tonsil relationship: part_of UBERON:0002372 ! tonsil -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: editor_note "consider adding related terms, e.g. secondary lymphoid tissue of tonsil" xsd:string -property_value: UBPROP:0000001 "The germinal center or reaction center is the activated center of a lymphoid follicle in secondary lymphoid tissue where B-lymphocytes are stimulated by antigens and helper T cells (T-lymphocytes, helper-inducer) are stimulated to generate memory cells. Here, the germinal center of a tonsil[TS-1288]." xsd:string {source="TS-1288"} +property_value: IAO:0000116 "consider adding related terms, e.g. secondary lymphoid tissue of tonsil" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0013689 @@ -248042,6 +244721,7 @@ xref: BTO:0001852 xref: BTO:0003248 xref: CALOHA:TS-0092 is_a: UBERON:0001986 ! endothelium +is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0000955 ! brain relationship: part_of UBERON:0000955 ! brain @@ -248076,7 +244756,7 @@ is_a: UBERON:0003351 ! pharyngeal epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002372 ! tonsil relationship: part_of UBERON:0002372 ! tonsil -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0013697 @@ -248086,7 +244766,7 @@ def: "Epithelium lining the exocrine pancreas." [CALOHA:TS-2108] synonym: "epithelium of exocrine pancreas" RELATED [CALOHA:TS-2108] synonym: "exocrine pancreas epithelial cell" RELATED [CALOHA:TS-2108] xref: CALOHA:TS-2108 -is_a: UBERON:0000483 ! epithelium +is_a: UBERON:0005911 ! endo-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000017 ! exocrine pancreas relationship: part_of UBERON:0000017 ! exocrine pancreas @@ -248106,7 +244786,6 @@ is_a: UBERON:0001037 ! strand of hair intersection_of: UBERON:0001037 ! strand of hair intersection_of: part_of UBERON:0009472 ! axilla relationship: part_of UBERON:0009472 ! axilla -property_value: UBPROP:0000202 FMA:70756 [Term] id: UBERON:0013700 @@ -248117,10 +244796,10 @@ xref: EHDAA2:0000159 xref: EMAPA:18166 is_a: UBERON:0001015 ! musculature intersection_of: UBERON:0001015 ! musculature -intersection_of: attaches_to UBERON:0005944 ! axial skeleton plus cranial skeleton intersection_of: part_of UBERON:0013701 ! main body axis -relationship: attaches_to UBERON:0005944 ! axial skeleton plus cranial skeleton +intersection_of: RO:0002371 UBERON:0005944 ! attached to axial skeleton plus cranial skeleton relationship: part_of UBERON:0013701 ! main body axis +relationship: RO:0002371 UBERON:0005944 ! attached to axial skeleton plus cranial skeleton [Term] id: UBERON:0013701 @@ -248129,7 +244808,7 @@ namespace: uberon def: "A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages." [https://orcid.org/0000-0002-6601-2165] subset: non_informative is_a: UBERON:0000475 ! organism subdivision -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0013702 @@ -248141,11 +244820,9 @@ synonym: "body" RELATED [AEO:0000103] synonym: "whole body" RELATED [BTO:0001489] xref: AEO:0000103 xref: BTO:0001489 -xref: EMAPA:36031 xref: FMA:231424 is_a: UBERON:0000475 {source="AEO"} ! organism subdivision relationship: part_of UBERON:0013701 ! main body axis -property_value: UBPROP:0000001 "Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]." xsd:string {source="FMA:231424"} [Term] id: UBERON:0013703 @@ -248168,6 +244845,7 @@ xref: FMA:293127 xref: NCIT:C34230 xref: UMLS:C1518428 {source="ncithesaurus:Notochordal_Canal"} is_a: UBERON:0004111 ! anatomical conduit +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0004111 ! anatomical conduit intersection_of: part_of UBERON:0006268 ! notochordal process relationship: part_of UBERON:0006268 ! notochordal process @@ -248182,10 +244860,10 @@ synonym: "notochord fluid" EXACT [] synonym: "portion of notochordal fluid" EXACT [] is_a: UBERON:0006314 ! bodily fluid intersection_of: UBERON:0006314 ! bodily fluid -intersection_of: located_in UBERON:0013704 ! notochordal canal intersection_of: part_of UBERON:0036242 ! post-embryonic notochord -relationship: located_in UBERON:0013704 ! notochordal canal +intersection_of: RO:0001025 UBERON:0013704 ! located in notochordal canal relationship: part_of UBERON:0036242 ! post-embryonic notochord +relationship: RO:0001025 UBERON:0013704 ! located in notochordal canal [Term] id: UBERON:0013749 @@ -248197,6 +244875,7 @@ synonym: "diaphyseal end of humerus" EXACT [FMA:32830] synonym: "humeral metaphysis" EXACT [FMA:32830] xref: FMA:32830 is_a: UBERON:0001438 ! metaphysis +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0001438 ! metaphysis intersection_of: part_of UBERON:0000976 ! humerus relationship: part_of UBERON:0000976 ! humerus @@ -248212,6 +244891,7 @@ xref: EMAPA:37772 {source="MA:th"} xref: FMA:33135 xref: MA:0003106 is_a: UBERON:0001438 ! metaphysis +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0001438 ! metaphysis intersection_of: part_of UBERON:0000979 ! tibia relationship: part_of UBERON:0000979 ! tibia @@ -248227,6 +244907,7 @@ synonym: "metacarpal bone diaphysis" EXACT [FMA:33804] synonym: "shaft of metacarpal" EXACT [FMA:33804] synonym: "shaft of metacarpal bone" EXACT [FMA:33804] xref: FMA:33804 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004769 ! diaphysis intersection_of: UBERON:0004769 ! diaphysis intersection_of: part_of UBERON:0002374 ! metacarpal bone @@ -248255,12 +244936,11 @@ subset: pheno_slim synonym: "arterial blood" EXACT [FMA:83066] synonym: "blood in artery" EXACT [FMA:83066] synonym: "portion of arterial blood" EXACT [FMA:83066] -xref: BTO:0006188 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: FMA:83066 is_a: UBERON:0000178 ! blood intersection_of: UBERON:0000178 ! blood -intersection_of: located_in UBERON:0001637 ! artery -relationship: located_in UBERON:0001637 ! artery +intersection_of: RO:0001025 UBERON:0001637 ! located in artery +relationship: RO:0001025 UBERON:0001637 ! located in artery [Term] id: UBERON:0013756 @@ -248270,12 +244950,11 @@ def: "A blood that is part of a vein." [OBOL:automatic] synonym: "blood in vein" EXACT [FMA:83067] synonym: "portion of venous blood" EXACT [FMA:83067] synonym: "venous blood" EXACT [FMA:83067] -xref: BTO:0006187 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: FMA:83067 is_a: UBERON:0000178 ! blood intersection_of: UBERON:0000178 ! blood -intersection_of: located_in UBERON:0001638 ! vein -relationship: located_in UBERON:0001638 ! vein +intersection_of: RO:0001025 UBERON:0001638 ! located in vein +relationship: RO:0001025 UBERON:0001638 ! located in vein [Term] id: UBERON:0013757 @@ -248289,8 +244968,8 @@ xref: FMA:263901 xref: NCIT:C32212 is_a: UBERON:0000178 ! blood intersection_of: UBERON:0000178 ! blood -intersection_of: located_in UBERON:0001982 ! capillary -relationship: located_in UBERON:0001982 ! capillary +intersection_of: RO:0001025 UBERON:0001982 ! located in capillary +relationship: RO:0001025 UBERON:0001982 ! located in capillary [Term] id: UBERON:0013758 @@ -248322,13 +245001,12 @@ xref: UMLS:C1512165 {source="ncithesaurus:Ectocervical_Os"} xref: Wikipedia:External_orifice_of_the_uterus is_a: UBERON:0013758 ! cervical os intersection_of: UBERON:0013758 ! cervical os -intersection_of: continuous_with UBERON:0000996 ! vagina -relationship: connects UBERON:0000002 ! uterine cervix -relationship: connects UBERON:0000996 ! vagina -relationship: continuous_with UBERON:0000996 ! vagina +intersection_of: RO:0002150 UBERON:0000996 ! continuous with vagina relationship: part_of UBERON:0012249 ! ectocervix -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Uterus.glb" xsd:anyURI -property_value: UBPROP:0000001 "The external orifice of the uterus (or ostium of uterus, or external os) is a small, depressed, somewhat circular aperture on the rounded extremity of the vaginal portion of the cervix. Through this aperture, the cervical cavity communicates with that of the vagina. The external orifice is bounded by two lips, an anterior and a posterior. The anterior is shorter and thicker, though it projects lower than the posterior because of the slope of the cervix. Normally, both lips are in contact with the posterior vaginal wall. Prior to pregnancy, the external orifice has a rounded shape when viewed through the vaginal canal (as through a speculum). Following parturition, the orifice takes on an appearance more like a transverse slit or is 'H-shaped'[Wikipedia:External_orifice_of_the_uterus]." xsd:string {source="Wikipedia:External_orifice_of_the_uterus"} +relationship: RO:0002150 UBERON:0000996 ! continuous with vagina +relationship: RO:0002176 UBERON:0000002 ! connects uterine cervix +relationship: RO:0002176 UBERON:0000996 ! connects vagina +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Uterus.glb" xsd:anyURI [Term] id: UBERON:0013761 @@ -248349,9 +245027,9 @@ xref: FMA:17746 xref: Wikipedia:Canal_of_the_cervix is_a: UBERON:0002553 ! anatomical cavity intersection_of: UBERON:0002553 ! anatomical cavity -intersection_of: luminal_space_of UBERON:0000002 ! uterine cervix -relationship: luminal_space_of UBERON:0000002 ! uterine cervix -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002572 UBERON:0000002 ! luminal space of uterine cervix +relationship: RO:0002572 UBERON:0000002 ! luminal space of uterine cervix +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0013765 @@ -248407,11 +245085,11 @@ def: "A nipple that is in_the_left_side_of a body proper." [OBOL:automatic] subset: pheno_slim xref: FMA:223695 is_a: UBERON:0002030 ! nipple +is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0002030 ! nipple -intersection_of: in_left_side_of UBERON:0013702 ! body proper -relationship: in_left_side_of UBERON:0013702 ! body proper -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.3/3d-vh-f-mammary-gland-l.glb" xsd:anyURI -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +intersection_of: BSPO:0000120 UBERON:0013702 ! body proper +relationship: BSPO:0000120 UBERON:0013702 ! body proper +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.3/3d-vh-f-mammary-gland-l.glb" xsd:anyURI [Term] id: UBERON:0013773 @@ -248421,11 +245099,11 @@ def: "A nipple that is in_the_right_side_of a body proper." [OBOL:automatic] subset: pheno_slim xref: FMA:223693 is_a: UBERON:0002030 ! nipple +is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0002030 ! nipple -intersection_of: in_right_side_of UBERON:0013702 ! body proper -relationship: in_right_side_of UBERON:0013702 ! body proper -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.3/3d-vh-f-mammary-gland-r.glb" xsd:anyURI -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +intersection_of: BSPO:0000121 UBERON:0013702 ! body proper +relationship: BSPO:0000121 UBERON:0013702 ! body proper +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.3/3d-vh-f-mammary-gland-r.glb" xsd:anyURI [Term] id: UBERON:0013774 @@ -248438,6 +245116,7 @@ synonym: "metatarsal bone diaphysis" EXACT [FMA:33826] synonym: "metatarsal diaphysis" EXACT [] synonym: "shaft of metatarsal bone" EXACT [FMA:33826] xref: FMA:33826 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004769 ! diaphysis intersection_of: UBERON:0004769 ! diaphysis intersection_of: part_of UBERON:0001448 ! metatarsal bone @@ -248481,9 +245160,9 @@ synonym: "piriform cortex layer 3" EXACT [NLXANAT:091009] xref: NLXANAT:091009 is_a: UBERON:0011215 ! central nervous system cell part cluster is_a: UBERON:0022303 ! nervous system cell part layer -relationship: dc-contributor https://orcid.org/0000-0002-8406-3871 relationship: has_part CL:0000598 ! pyramidal neuron relationship: part_of UBERON:0004725 {source="NIFSTD"} ! piriform cortex +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8406-3871 [Term] id: UBERON:0014371 @@ -248498,10 +245177,10 @@ xref: TAO:0000571 xref: ZFA:0000571 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001893 ! telencephalon -relationship: has_developmental_contribution_from UBERON:0003850 {evidence="definitional"} ! telencephalon neural crest -relationship: has_potential_to_develop_into UBERON:0001893 ! telencephalon +intersection_of: RO:0002387 UBERON:0001893 ! has potential to develop into telencephalon relationship: part_of UBERON:0006240 ! future forebrain +relationship: RO:0002254 UBERON:0003850 ! has developmental contribution from telencephalon neural crest +relationship: RO:0002387 UBERON:0001893 ! has potential to develop into telencephalon [Term] id: UBERON:0014382 @@ -248526,7 +245205,7 @@ xref: FMA:293883 is_a: UBERON:0003104 ! mesenchyme is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: develops_from UBERON:0002342 ! neural crest +intersection_of: RO:0002202 UBERON:0002342 ! develops from neural crest [Term] id: UBERON:0014388 @@ -248542,9 +245221,8 @@ is_a: UBERON:0000484 ! simple cuboidal epithelium is_a: UBERON:0004211 ! nephron epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001232 ! collecting duct of renal tubule -relationship: contributes_to_morphology_of UBERON:0001232 ! collecting duct of renal tubule relationship: part_of UBERON:0001232 ! collecting duct of renal tubule -property_value: UBPROP:0000008 "In mouse, the mature and differentiated CD epithelium comprises two unique cells types with principal cells responsible for vasopressin-regulated water reabsorption, and intercalated cells regulating acid-base homeostasis; injury to the epithelium is believed to cause epithelial cells to acquire mesenchymal characteristics via epithelial-mesenchymal transition (EMT), a process through which tubular epithelial cells may transform into interstitial fibroblasts and promote renal fibrosis" xsd:string +relationship: RO:0002433 UBERON:0001232 ! contributes to morphology of collecting duct of renal tubule [Term] id: UBERON:0014389 @@ -248555,7 +245233,6 @@ synonym: "gustatory papilla" EXACT [] synonym: "gustatory papillae" RELATED OMO:0003004 [] synonym: "taste papilla" EXACT [] synonym: "taste papillae" RELATED OMO:0003004 [] -xref: FMA:54822 is_a: UBERON:0001726 ! papilla of tongue intersection_of: UBERON:0001726 ! papilla of tongue intersection_of: has_part UBERON:0001727 ! taste bud @@ -248592,7 +245269,6 @@ is_a: UBERON:0000423 ! eccrine sweat gland intersection_of: UBERON:0001820 ! sweat gland intersection_of: part_of UBERON:0008837 ! palmar/plantar part of autopod relationship: part_of UBERON:0008837 ! palmar/plantar part of autopod -property_value: UBPROP:0000008 "in mice these are the only sweat glands present" xsd:string {source="MP:0000675"} [Term] id: UBERON:0014392 @@ -248606,7 +245282,6 @@ is_a: UBERON:0001089 ! sweat intersection_of: UBERON:0001089 ! sweat intersection_of: produced_by UBERON:0014391 ! palmar/plantar sweat gland relationship: produced_by UBERON:0014391 ! palmar/plantar sweat gland -property_value: UBPROP:0000009 "serves a purpose of increasing friction on the palms of hands or the pads of paws[WP]" xsd:string [Term] id: UBERON:0014393 @@ -248628,8 +245303,8 @@ def: "A proximal mesopodial endochondral element that is composed primarily of a is_a: UBERON:0003656 ! mesopodium bone is_a: UBERON:0017750 ! proximal mesopodial endochondral element intersection_of: UBERON:0017750 ! proximal mesopodial endochondral element -intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue -relationship: develops_from UBERON:0017751 ! proximal mesopodial cartilage element +intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue +relationship: RO:0002202 UBERON:0017751 ! develops from proximal mesopodial cartilage element [Term] id: UBERON:0014398 @@ -248637,13 +245312,11 @@ name: respiratory muscle namespace: uberon def: "Muscle that is part of the respiratory system." [http://orcid.org/0000-0002-6601-2165] subset: pheno_slim -xref: MESH:D012132 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} is_a: UBERON:0003831 ! respiratory system muscle intersection_of: UBERON:0001630 ! muscle organ intersection_of: capable_of_part_of GO:0007585 ! respiratory gaseous exchange by respiratory system relationship: capable_of_part_of GO:0007585 ! respiratory gaseous exchange by respiratory system -relationship: composed_primarily_of UBERON:0001134 ! skeletal muscle tissue -property_value: IAO:0000232 "this class may be merged with 'respiratory system muscle'; check intercostals" xsd:string +relationship: RO:0002473 UBERON:0001134 ! composed primarily of skeletal muscle tissue [Term] id: UBERON:0014399 @@ -248655,9 +245328,9 @@ synonym: "sinusoid lumen" EXACT [FMA:63133] xref: FMA:63133 is_a: UBERON:0010161 ! lumen of blood vessel intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0003909 ! sinusoid -relationship: luminal_space_of UBERON:0003909 ! sinusoid +intersection_of: RO:0002572 UBERON:0003909 ! luminal space of sinusoid relationship: part_of UBERON:0003909 ! sinusoid +relationship: RO:0002572 UBERON:0003909 ! luminal space of sinusoid [Term] id: UBERON:0014400 @@ -248686,7 +245359,6 @@ is_a: UBERON:0003517 ! kidney blood vessel is_a: UBERON:0003920 ! venous blood vessel intersection_of: UBERON:0003920 ! venous blood vessel intersection_of: part_of UBERON:0002113 ! kidney -property_value: UBPROP:0000012 "we follow MA and MP in distinguishing the venous blood vessel from the vein. The kidney cortex vein is not considered a renal vein, nor is the vasa recta" xsd:string {external_ontology="MA"} [Term] id: UBERON:0014402 @@ -248784,11 +245456,10 @@ xref: CALOHA:TS-2405 is_a: UBERON:0007808 ! adipose tissue of abdominal region intersection_of: UBERON:0001013 ! adipose tissue intersection_of: bounding_layer_of UBERON:0002075 ! viscus -intersection_of: located_in UBERON:0001179 ! peritoneal cavity intersection_of: part_of UBERON:0000916 ! abdomen +intersection_of: RO:0001025 UBERON:0001179 ! located in peritoneal cavity relationship: bounding_layer_of UBERON:0002075 ! viscus -relationship: located_in UBERON:0001179 ! peritoneal cavity -property_value: UBPROP:0000001 "Adipose tissue located inside the peritoneal cavity, packed in between internal organs and torso. An excess of visceral fat is known as central obesity, or belly fat, the pot belly or beer belly effect, in which the abdomen protrudes excessively[BTO:0004041]." xsd:string {source="BTO:0004041"} +relationship: RO:0001025 UBERON:0001179 ! located in peritoneal cavity [Term] id: UBERON:0014455 @@ -248824,8 +245495,7 @@ is_a: UBERON:0001808 ! parasympathetic ganglion intersection_of: UBERON:0001808 ! parasympathetic ganglion intersection_of: extends_fibers_into UBERON:0002008 ! cardiac nerve plexus relationship: extends_fibers_into UBERON:0002008 ! cardiac nerve plexus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: UBPROP:0000001 "Any of the parasympathetic ganglia of the cardiac plexus between the arch of the aorta and the bifurcation of the pulmonary artery[http://medical-dictionary.thefreedictionary.com/cardiac+ganglion]." xsd:string {source="http://medical-dictionary.thefreedictionary.com/cardiac+ganglion"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0014466 @@ -248851,7 +245521,7 @@ xref: Wikipedia:Thoracic_skeleton is_a: UBERON:0010912 ! subdivision of skeleton relationship: part_of UBERON:0000915 ! thoracic segment of trunk relationship: part_of UBERON:0002090 ! postcranial axial skeleton -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0014478 @@ -248864,10 +245534,10 @@ synonym: "set of all ribs" RELATED [FMA:265719] xref: FMA:265719 xref: TAO:0002100 is_a: UBERON:0000075 ! subdivision of skeletal system -relationship: composed_primarily_of UBERON:0015019 ! rib endochondral element relationship: has_part UBERON:0003252 ! thoracic rib cage -relationship: never_in_taxon NCBITaxon:7778 {source="Wikipedia"} relationship: part_of UBERON:0011138 ! postcranial axial skeletal system +relationship: RO:0002473 UBERON:0015019 ! composed primarily of rib endochondral element +property_value: RO:0002161 NCBITaxon:7778 {source="Wikipedia"} [Term] id: UBERON:0014530 @@ -248915,6 +245585,7 @@ subset: non_informative synonym: "regional part of spinal cord central canal" EXACT HUMAN_PREFERRED [BIRNLEX:717] xref: BIRNLEX:717 is_a: UBERON:0004111 ! anatomical conduit +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0004111 ! anatomical conduit intersection_of: subdivision_of UBERON:0002291 ! central canal of spinal cord relationship: part_of UBERON:0002291 ! central canal of spinal cord @@ -248943,7 +245614,7 @@ xref: UMLS:C0228472 {source="BIRNLEX:1105"} is_a: UBERON:0014530 ! white matter lamina of neuraxis intersection_of: UBERON:0014530 ! white matter lamina of neuraxis intersection_of: part_of UBERON:0002037 ! cerebellum -relationship: immediately_deep_to UBERON:0002956 ! granular layer of cerebellar cortex +relationship: BSPO:0001107 UBERON:0002956 ! granular layer of cerebellar cortex relationship: part_of UBERON:0002037 ! cerebellum [Term] @@ -248960,8 +245631,8 @@ xref: UMLS:C0228637 {source="BIRNLEX:1395"} is_a: UBERON:0014538 {source="NIFSTD"} ! subdivision of spinal cord central canal intersection_of: UBERON:0014538 ! subdivision of spinal cord central canal intersection_of: subdivision_of UBERON:0003038 ! thoracic spinal cord -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: subdivision_of UBERON:0003038 ! thoracic spinal cord +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0014542 @@ -248993,7 +245664,7 @@ is_a: UBERON:0002256 ! dorsal horn of spinal cord intersection_of: UBERON:0002256 ! dorsal horn of spinal cord intersection_of: part_of UBERON:0003038 ! thoracic spinal cord relationship: part_of UBERON:0003038 ! thoracic spinal cord -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0014610 @@ -249011,7 +245682,7 @@ is_a: UBERON:0002257 ! ventral horn of spinal cord intersection_of: UBERON:0002257 ! ventral horn of spinal cord intersection_of: part_of UBERON:0003038 ! thoracic spinal cord relationship: part_of UBERON:0003038 ! thoracic spinal cord -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0014613 @@ -249027,7 +245698,7 @@ is_a: UBERON:0002315 ! gray matter of spinal cord intersection_of: UBERON:0002315 ! gray matter of spinal cord intersection_of: part_of UBERON:0002726 ! cervical spinal cord relationship: part_of UBERON:0002726 ! cervical spinal cord -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0014614 @@ -249043,7 +245714,7 @@ is_a: UBERON:0002318 ! white matter of spinal cord intersection_of: UBERON:0002318 ! white matter of spinal cord intersection_of: part_of UBERON:0002726 ! cervical spinal cord relationship: part_of UBERON:0002726 ! cervical spinal cord -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0014615 @@ -249091,7 +245762,7 @@ is_a: UBERON:0002256 ! dorsal horn of spinal cord intersection_of: UBERON:0002256 ! dorsal horn of spinal cord intersection_of: part_of UBERON:0002726 ! cervical spinal cord relationship: part_of UBERON:0002726 ! cervical spinal cord -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0014621 @@ -249102,7 +245773,6 @@ subset: human_reference_atlas synonym: "cervical spinal cord anterior horn" RELATED [BIRNLEX:1680] synonym: "cervical spinal cord ventral horn" EXACT HUMAN_PREFERRED [BIRNLEX:1680] xref: BIRNLEX:1680 -xref: MESH:D066151 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: SCTID:174363005 xref: UMLS:C0228615 {source="BIRNLEX:1680"} xref: UMLS:C1278740 {source="BIRNLEX:1680"} @@ -249110,7 +245780,7 @@ is_a: UBERON:0002257 ! ventral horn of spinal cord intersection_of: UBERON:0002257 ! ventral horn of spinal cord intersection_of: part_of UBERON:0002726 ! cervical spinal cord relationship: part_of UBERON:0002726 ! cervical spinal cord -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0014635 @@ -249142,7 +245812,7 @@ is_a: UBERON:0002315 ! gray matter of spinal cord intersection_of: UBERON:0002315 ! gray matter of spinal cord intersection_of: part_of UBERON:0003038 ! thoracic spinal cord relationship: part_of UBERON:0003038 ! thoracic spinal cord -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0014637 @@ -249159,7 +245829,7 @@ is_a: UBERON:0002318 ! white matter of spinal cord intersection_of: UBERON:0002318 ! white matter of spinal cord intersection_of: part_of UBERON:0003038 ! thoracic spinal cord relationship: part_of UBERON:0003038 ! thoracic spinal cord -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0014639 @@ -249207,8 +245877,8 @@ xref: SCTID:151804007 xref: Wikipedia:Angular_vein is_a: UBERON:0003496 ! head blood vessel is_a: UBERON:0009141 ! craniocervical region vein -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: tributary_of UBERON:0001653 ! facial vein +relationship: RO:0002376 UBERON:0001653 ! tributary of facial vein +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0014687 @@ -249237,10 +245907,10 @@ xref: Wikipedia:Deep_auricular_artery is_a: UBERON:0009655 ! auricular artery intersection_of: UBERON:0009655 ! auricular artery intersection_of: part_of UBERON:0035551 ! deep vasculature -relationship: connecting_branch_of UBERON:0001616 {source="FMA"} ! maxillary artery relationship: part_of UBERON:0035551 ! deep vasculature -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: supplies UBERON:0010069 ! outer epithelial layer of tympanic membrane +relationship: RO:0002178 UBERON:0010069 ! supplies outer epithelial layer of tympanic membrane +relationship: RO:0002252 UBERON:0001616 {source="FMA"} ! connecting branch of maxillary artery +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0014699 @@ -249280,10 +245950,11 @@ xref: EHDAA2:0004108 xref: EMAPA:32918 is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0004066 ! frontonasal prominence -relationship: develops_from UBERON:0000076 {source="EHDAA2"} ! external ectoderm relationship: part_of UBERON:0004066 ! frontonasal prominence +relationship: RO:0002202 UBERON:0000076 {source="EHDAA2"} ! develops from external ectoderm [Term] id: UBERON:0014703 @@ -249295,8 +245966,8 @@ xref: EMAPA:25040 is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0000490 ! unilaminar epithelium -intersection_of: develops_from UBERON:0000924 ! ectoderm intersection_of: part_of UBERON:0001353 ! anal region +intersection_of: RO:0002202 UBERON:0000924 ! develops from ectoderm relationship: part_of UBERON:0001353 ! anal region [Term] @@ -249309,9 +245980,9 @@ xref: EHDAA2:0004736 xref: EMAPA:25034 is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0006279 ! pleuroperitoneal canal -relationship: develops_from UBERON:0002323 {source="EHDAA2"} ! coelemic cavity lumen -relationship: luminal_space_of UBERON:0006279 ! pleuroperitoneal canal +intersection_of: RO:0002572 UBERON:0006279 ! luminal space of pleuroperitoneal canal +relationship: RO:0002202 UBERON:0002323 {source="EHDAA2"} ! develops from coelemic cavity lumen +relationship: RO:0002572 UBERON:0006279 ! luminal space of pleuroperitoneal canal [Term] id: UBERON:0014705 @@ -249327,8 +245998,8 @@ is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0005911 ! endo-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0006756 ! median lingual swelling -relationship: develops_from UBERON:0013156 {source="EHDAA2"} ! 1st arch mandibular endoderm relationship: part_of UBERON:0006756 ! median lingual swelling +relationship: RO:0002202 UBERON:0013156 {source="EHDAA2"} ! develops from 1st arch mandibular endoderm [Term] id: UBERON:0014706 @@ -249340,7 +246011,7 @@ xref: EHDAA2:0001147 xref: EMAPA:17646 is_a: UBERON:0007501 {source="EHDAA2"} ! arborizing epithelial duct system is_a: UBERON:0012275 ! meso-epithelium -relationship: develops_from UBERON:0000084 {source="EHDAA2"} ! ureteric bud +relationship: RO:0002202 UBERON:0000084 {source="EHDAA2"} ! develops from ureteric bud [Term] id: UBERON:0014716 @@ -249353,11 +246024,11 @@ xref: UMLS:C1512857 xref: Wikipedia:Interlobular_ducts is_a: UBERON:0035050 ! excretory duct intersection_of: UBERON:0000058 ! duct -intersection_of: connected_to UBERON:0009911 ! lobule intersection_of: part_of UBERON:0002384 ! connective tissue -relationship: connected_to UBERON:0009911 ! lobule +intersection_of: RO:0002170 UBERON:0009911 ! connected to lobule relationship: part_of UBERON:0002384 ! connective tissue -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002170 UBERON:0009911 ! connected to lobule +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0014717 @@ -249370,8 +246041,8 @@ xref: FMA:86278 is_a: UBERON:0011858 ! acinus of exocrine gland intersection_of: UBERON:0009842 ! glandular acinus intersection_of: part_of UBERON:0000414 ! mucous gland -relationship: composed_primarily_of CL:0000319 ! mucus secreting cell relationship: part_of UBERON:0000414 ! mucous gland +relationship: RO:0002473 CL:0000319 ! composed primarily of mucus secreting cell [Term] id: UBERON:0014719 @@ -249385,7 +246056,7 @@ is_a: UBERON:0000058 ! duct intersection_of: UBERON:0000058 ! duct intersection_of: part_of UBERON:0009911 ! lobule relationship: part_of UBERON:0009911 ! lobule -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0014720 @@ -249395,67 +246066,10 @@ def: "A duct that is located between lobes, within conspicuous, thick connective synonym: "intralobular ductule" RELATED [] is_a: UBERON:0035050 ! excretory duct intersection_of: UBERON:0000058 ! duct -intersection_of: connects UBERON:0009912 ! anatomical lobe intersection_of: part_of UBERON:0002384 ! connective tissue -relationship: connects UBERON:0009912 ! anatomical lobe +intersection_of: RO:0002176 UBERON:0009912 ! connects anatomical lobe relationship: part_of UBERON:0002384 ! connective tissue - -[Term] -id: UBERON:0014765 -name: crus of diaphragm -namespace: uberon -def: "The domain of the diaphragm that is located dorsally and attaches to the vertebrae and surrounds the esophagus and aorta." [PMID:23586979] -comment: Classification notes: May be considered an external sphincter[PMID:8224664] -synonym: "crura of the diaphragm" RELATED [Wikipedia:Crus_of_diaphragm] -synonym: "crural diaphragm" EXACT [PMID:23586979] -synonym: "crus of the diaphragm" RELATED [Wikipedia:Crus_of_diaphragm] -synonym: "diaphragm crura" RELATED OMO:0003004 [] -synonym: "diaphragmatic crura" RELATED [Wikipedia:Crus_of_diaphragm] -xref: EHDAA2:0000597 -xref: EMAPA:17703 -xref: SCTID:244668003 -xref: VHOG:0001546 -xref: Wikipedia:Crus_of_diaphragm -is_a: UBERON:0000063 ! organ subunit -relationship: attaches_to UBERON:0001130 ! vertebral column -relationship: attaches_to UBERON:0006670 ! central tendon of diaphragm -relationship: intersects_midsagittal_plane_of UBERON:0001103 {source="PMID:23586979"} ! diaphragm -relationship: part_of UBERON:0001103 {source="PMID:23586979"} ! diaphragm - -[Term] -id: UBERON:0014766 -name: right crus of diaphragm -namespace: uberon -def: "A crus of diaphragm that is in_the_right_side_of a diaphragm." [OBOL:automatic] -synonym: "crus dextrum (Diaphragma)" EXACT OMO:0003011 [FMA:58286, FMA:TA] -synonym: "crus dextrum diaphragmatis" EXACT OMO:0003011 [FMA:58286, FMA:TA] -synonym: "external sphincter of esophagus" EXACT [FMA:58286] -synonym: "right crus of diaphragm" EXACT [FMA:58286] -synonym: "right crus of lumbar part of diaphragm" EXACT [FMA:58286] -xref: FMA:58286 -xref: SCTID:362690009 -is_a: UBERON:0014765 ! crus of diaphragm -intersection_of: UBERON:0014765 ! crus of diaphragm -intersection_of: in_right_side_of UBERON:0001103 ! diaphragm -relationship: in_right_side_of UBERON:0001103 ! diaphragm -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI - -[Term] -id: UBERON:0014767 -name: left crus of diaphragm -namespace: uberon -def: "A crus of diaphragm that is in_the_left_side_of a diaphragm." [OBOL:automatic] -synonym: "crus sinistrum (Diaphragma)" EXACT OMO:0003011 [FMA:58287, FMA:TA] -synonym: "crus sinistrum diaphragmatis" EXACT OMO:0003011 [FMA:58287, FMA:TA] -synonym: "left crus of diaphragm" EXACT [FMA:58287] -synonym: "left crus of lumbar part of diaphragm" EXACT [FMA:58287] -xref: FMA:58287 -xref: SCTID:244937004 -is_a: UBERON:0014765 ! crus of diaphragm -intersection_of: UBERON:0014765 ! crus of diaphragm -intersection_of: in_left_side_of UBERON:0001103 ! diaphragm -relationship: in_left_side_of UBERON:0001103 ! diaphragm -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +relationship: RO:0002176 UBERON:0009912 ! connects anatomical lobe [Term] id: UBERON:0014769 @@ -249469,9 +246083,9 @@ xref: SCTID:152208004 is_a: UBERON:0003496 ! head blood vessel is_a: UBERON:0009141 ! craniocervical region vein intersection_of: UBERON:0001638 ! vein -intersection_of: drains UBERON:0001711 ! eyelid -relationship: drains UBERON:0001711 ! eyelid -relationship: tributary_of UBERON:0014686 ! angular vein +intersection_of: RO:0002179 UBERON:0001711 ! drains eyelid +relationship: RO:0002179 UBERON:0001711 ! drains eyelid +relationship: RO:0002376 UBERON:0014686 ! tributary of angular vein [Term] id: UBERON:0014770 @@ -249482,9 +246096,8 @@ xref: SCTID:148571007 is_a: UBERON:0001637 ! artery is_a: UBERON:0003496 ! head blood vessel intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0001711 ! eyelid -relationship: supplies UBERON:0001711 ! eyelid -property_value: UBPROP:0000008 "In humans, the eyelids are supplied with blood by two arches on each upper and lower lid. The arches are formed by anastamoses of the lateral palpebral arteries and medial palpebral arteries, branching off from the lacrimal artery and ophthalmic artery, respectively. In amphibians, the eyelids may be supplied by branches of the lateral pretrosal arteries.[cjm]" xsd:string +intersection_of: RO:0002178 UBERON:0001711 ! supplies eyelid +relationship: RO:0002178 UBERON:0001711 ! supplies eyelid [Term] id: UBERON:0014775 @@ -249593,7 +246206,7 @@ is_a: UBERON:0001015 ! musculature intersection_of: UBERON:0001015 ! musculature intersection_of: part_of UBERON:0010709 ! pelvic complex relationship: part_of UBERON:0010709 ! pelvic complex -property_value: editor_note "currently defined by location rather than attachment" xsd:string +property_value: IAO:0000116 "currently defined by location rather than attachment" xsd:string [Term] id: UBERON:0014793 @@ -249611,7 +246224,7 @@ is_a: UBERON:0001015 ! musculature intersection_of: UBERON:0001015 ! musculature intersection_of: part_of UBERON:0010708 ! pectoral complex relationship: part_of UBERON:0010708 ! pectoral complex -property_value: editor_note "currently defined by location rather than attachment" xsd:string +property_value: IAO:0000116 "currently defined by location rather than attachment" xsd:string [Term] id: UBERON:0014794 @@ -249680,17 +246293,17 @@ xref: XAO:0000174 xref: ZFA:0005277 is_a: UBERON:0001630 ! muscle organ intersection_of: UBERON:0001630 ! muscle organ -intersection_of: composed_primarily_of UBERON:0001134 ! skeletal muscle tissue -intersection_of: develops_from UBERON:0003082 ! myotome -intersection_of: surrounded_by UBERON:0011899 ! epimysium -intersection_of: synapsed_by CL:0000100 ! motor neuron -relationship: composed_primarily_of UBERON:0001134 ! skeletal muscle tissue -relationship: develops_from UBERON:0003082 ! myotome -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +intersection_of: RO:0002103 CL:0000100 ! synapsed by motor neuron +intersection_of: RO:0002202 UBERON:0003082 ! develops from myotome +intersection_of: RO:0002219 UBERON:0011899 ! surrounded by epimysium +intersection_of: RO:0002473 UBERON:0001134 ! composed primarily of skeletal muscle tissue relationship: part_of UBERON:0018254 ! skeletal musculature -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: surrounded_by UBERON:0011899 ! epimysium -relationship: synapsed_by CL:0000100 ! motor neuron +relationship: RO:0002103 CL:0000100 ! synapsed by motor neuron +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002202 UBERON:0003082 ! develops from myotome +relationship: RO:0002219 UBERON:0011899 ! surrounded by epimysium +relationship: RO:0002473 UBERON:0001134 ! composed primarily of skeletal muscle tissue +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0014903 @@ -249702,9 +246315,9 @@ xref: TAO:0005076 xref: ZFA:0005076 is_a: UBERON:0001048 ! primordium intersection_of: UBERON:0001048 ! primordium -intersection_of: has_potential_to_develop_into UBERON:0002049 ! vasculature -relationship: has_potential_to_develop_into UBERON:0002049 ! vasculature +intersection_of: RO:0002387 UBERON:0002049 ! has potential to develop into vasculature relationship: part_of UBERON:0011695 ! embryonic cardiovascular system +relationship: RO:0002387 UBERON:0002049 ! has potential to develop into vasculature [Term] id: UBERON:0014907 @@ -249723,9 +246336,7 @@ xref: TAO:0001285 xref: XAO:0004075 xref: ZFA:0001285 is_a: UBERON:0001981 {source="ZFA"} ! blood vessel -is_a: UBERON:0004120 ! mesoderm-derived structure -relationship: develops_from UBERON:0005805 {source="ZFA"} ! dorsal aorta -property_value: UBPROP:0000001 "Blood vessels that connect the dorsal aorta or the posterior cardinal vein and the dorsal longitudinal anastomotic vessel. They run along the vertical myotomal boundaries. At early stages these don't have venous or arterial markers[ZFA:0001285, ZFIN:ZDB-PUB-030908-4]." xsd:string {source="ZFA:0001285, ZFIN:ZDB-PUB-030908-4"} +relationship: RO:0002202 UBERON:0005805 {source="ZFA"} ! develops from dorsal aorta [Term] id: UBERON:0014930 @@ -249748,9 +246359,9 @@ intersection_of: adjacent_to UBERON:0001981 ! blood vessel intersection_of: adjacent_to UBERON:0002361 ! pia mater relationship: adjacent_to UBERON:0001981 ! blood vessel relationship: adjacent_to UBERON:0002361 ! pia mater -relationship: location_of UBERON:0001359 ! cerebrospinal fluid relationship: part_of UBERON:0010743 ! meningeal cluster -property_value: depiction "https://static-content.springer.com/image/art%3A10.1007%2Fs11064-015-1581-6/MediaObjects/11064_2015_1581_Fig3_HTML.gif" xsd:anyURI +relationship: RO:0001015 UBERON:0001359 ! location of cerebrospinal fluid +property_value: http://xmlns.com/foaf/0.1/depiction "https://static-content.springer.com/image/art%3A10.1007%2Fs11064-015-1581-6/MediaObjects/11064_2015_1581_Fig3_HTML.gif" xsd:anyURI [Term] id: UBERON:0014935 @@ -249767,10 +246378,8 @@ xref: EMAPA:17546 xref: EMAPA:32713 xref: PBA:294021774 is_a: UBERON:0014950 ! layer of developing cerebral cortex -relationship: develops_from UBERON:0004062 ! neural tube marginal layer relationship: part_of UBERON:0010403 ! brain marginal zone -property_value: UBPROP:0000011 "in humans develops into cortical layer I" xsd:string -property_value: UBPROP:0000012 "EMAPA temporally divides this into zone and layer. TODO - unify this with marginal layers in EHDAA2" xsd:string {external_ontology="EMAPA"} +relationship: RO:0002202 UBERON:0004062 ! develops from neural tube marginal layer [Term] id: UBERON:0014950 @@ -249778,7 +246387,6 @@ name: layer of developing cerebral cortex namespace: uberon is_a: UBERON:0005423 ! developing anatomical structure relationship: part_of UBERON:0000956 {source="EMAPA"} ! cerebral cortex -property_value: IAO:0000232 "these layers primarily refer to the mammalian future neocortex" xsd:string [Term] id: UBERON:0015004 @@ -249851,7 +246459,6 @@ union_of: UBERON:0002228 ! rib union_of: UBERON:0006288 ! rib cartilage element union_of: UBERON:0006289 ! rib pre-cartilage condensation relationship: part_of UBERON:0014478 ! rib skeletal system -property_value: UBPROP:0000008 "Humans have 24 ribs (12 pairs). The first seven sets of ribs, known as 'true ribs', are directly attached to the sternum through the costal cartilage. The following five sets are known as 'false ribs', three of these sharing a common cartilaginous connection to the sternum, while the last two (eleventh and twelfth ribs) are termed floating ribs (costae fluitantes) or vertebral ribs. They are attached to the vertebrae only, and not to the sternum or cartilage coming off of the sternum. Some people are missing one of the two pairs of floating ribs, while others have a third pair. Rib removal is the surgical excision of ribs for therapeutic or cosmetic reasons. In fish, there are often two sets of ribs attached to the vertebral column. One set, the dorsal ribs, are found in the dividing septum between the upper and lower parts of the main muscle segments, projecting roughly sideways from the vertebral column. The second set, of ventral ribs arise from the vertebral column just below the dorsal ribs, and enclose the lower body, often joining at the tips. Not all species possess both types of rib, with the dorsal ribs being most commonly absent. Sharks, for example, have no dorsal ribs, and only very short ventral ribs, while lampreys have no ribs at all. In some teleosts, there may be additional rib-like bones within the muscle mass. Tetrapods, however, only ever have a single set of ribs which are probably homologous with the dorsal ribs of fishes. In the early tetrapods, every vertebra bore a pair of ribs, although those on the thoracic vertebrae are typically the longest. The sacral ribs were stout and short, since they formed part of the pelvis, connecting the backbone to the hip bones.[1] In most subsequent forms, many of these early ribs have been lost, and in living amphibians and reptiles, there is great variation in rib structure and number. For example, turtles have only eight pairs of ribs, which are developed into a bony or cartilagenous carapace and plastron, while snakes have numerous ribs running along the full length of their trunk. Frogs typically have no ribs, aside from a sacral pair, which form part of the pelvis.[1]. In birds, ribs are present as distinct bones only on the thoracic region, although small fused ribs are present on the cervical vertebrae. The thoracic ribs of birds possess a wide projection to the rear; this uncinate process is an attachment for the shoulder muscles.[1]. Mammals usually also only have distinct ribs on the thoracic vertebra, although fixed cervical ribs are also present in monotremes. In marsupials and placental mammals, the cervical and lumbar ribs are found only as tiny remnants fused to the vertebrae, where they are referred to as transverse processes. In general, the structure and number of the true ribs in humans is similar to that in other mammals. Unlike reptiles, caudal ribs are never found in mammals." xsd:string [Term] id: UBERON:0015021 @@ -250030,6 +246637,7 @@ namespace: uberon def: "An iliac bone or its cartilage or pre-cartilage precursor." [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] synonym: "iliac element" EXACT [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] synonym: "iliac skeletal element" BROAD [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005179 ! pelvic region element is_a: UBERON:0010363 ! endochondral element union_of: UBERON:0001273 ! ilium @@ -250044,6 +246652,7 @@ namespace: uberon def: "An ischial bone or its cartilage or pre-cartilage precursor." [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] synonym: "ischial element" EXACT [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] synonym: "ischial skeletal element" BROAD [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005179 ! pelvic region element is_a: UBERON:0010363 ! endochondral element union_of: UBERON:0001274 ! ischium @@ -250085,6 +246694,7 @@ namespace: uberon def: "A sphenoid bone or its cartilage or pre-cartilage precursor." [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] synonym: "sphenoid bone skeletal element" BROAD [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] synonym: "sphenoid element" EXACT [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] +is_a: UBERON:0010313 ! neural crest-derived structure is_a: UBERON:0010363 ! endochondral element union_of: UBERON:0001677 ! sphenoid bone union_of: UBERON:0009191 ! sphenoid bone pre-cartilage condensation @@ -250098,6 +246708,7 @@ namespace: uberon def: "A limb bone or its cartilage or pre-cartilage precursor." [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] synonym: "limb bone endochondral element" EXACT [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] synonym: "limb bone skeletal element" BROAD [https://github.com/obophenotype/uberon/wiki/Modeling-endochondral-elements-Design-Pattern] +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010363 ! endochondral element intersection_of: UBERON:0010363 ! endochondral element intersection_of: part_of UBERON:0002101 ! limb @@ -250115,7 +246726,6 @@ is_a: UBERON:0015061 ! limb endochondral element intersection_of: UBERON:0010363 ! endochondral element intersection_of: part_of UBERON:0002470 ! autopod region relationship: part_of UBERON:0006717 {source="cjm"} ! autopodial skeleton -property_value: UBPROP:0000006 https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern [Term] id: UBERON:0015064 @@ -250125,8 +246735,7 @@ def: "An autopod endochondral element that is composed primarily of cartilage ti is_a: UBERON:0010881 ! limb cartilage element is_a: UBERON:0015063 ! autopod endochondral element intersection_of: UBERON:0015063 ! autopod endochondral element -intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue -property_value: UBPROP:0000006 https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern +intersection_of: RO:0002473 UBERON:0002418 ! composed primarily of cartilage tissue [Term] id: UBERON:0015078 @@ -250149,8 +246758,8 @@ is_a: UBERON:0015078 ! proximal carpal endochondral element is_a: UBERON:0017751 ! proximal mesopodial cartilage element is_a: UBERON:0035128 ! manus cartilage element intersection_of: UBERON:0015078 ! proximal carpal endochondral element -intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue -relationship: develops_from UBERON:0015080 ! proximal carpal bone pre-cartilage condensation +intersection_of: RO:0002473 UBERON:0002418 ! composed primarily of cartilage tissue +relationship: RO:0002202 UBERON:0015080 ! develops from proximal carpal bone pre-cartilage condensation [Term] id: UBERON:0015080 @@ -250160,7 +246769,7 @@ def: "A proximal carpal endochondral element that is composed primarily of a pre is_a: UBERON:0010884 ! forelimb bone pre-cartilage condensation is_a: UBERON:0015078 ! proximal carpal endochondral element intersection_of: UBERON:0015078 ! proximal carpal endochondral element -intersection_of: composed_primarily_of UBERON:0005866 ! pre-cartilage condensation +intersection_of: RO:0002473 UBERON:0005866 ! composed primarily of pre-cartilage condensation [Term] id: UBERON:0015081 @@ -250182,8 +246791,8 @@ is_a: UBERON:0015081 ! proximal tarsal endochondral element is_a: UBERON:0017751 ! proximal mesopodial cartilage element is_a: UBERON:0035129 ! pes cartilage element intersection_of: UBERON:0015081 ! proximal tarsal endochondral element -intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue -relationship: develops_from UBERON:0015083 ! proximal tarsal bone pre-cartilage condensation +intersection_of: RO:0002473 UBERON:0002418 ! composed primarily of cartilage tissue +relationship: RO:0002202 UBERON:0015083 ! develops from proximal tarsal bone pre-cartilage condensation [Term] id: UBERON:0015083 @@ -250193,7 +246802,7 @@ def: "A proximal tarsal endochondral element that is composed primarily of a pre is_a: UBERON:0010886 ! hindlimb pre-cartilage condensation is_a: UBERON:0015081 ! proximal tarsal endochondral element intersection_of: UBERON:0015081 ! proximal tarsal endochondral element -intersection_of: composed_primarily_of UBERON:0005866 ! pre-cartilage condensation +intersection_of: RO:0002473 UBERON:0005866 ! composed primarily of pre-cartilage condensation [Term] id: UBERON:0015128 @@ -250204,7 +246813,7 @@ synonym: "subepicardial connective tissue" EXACT [FMA:83105] xref: FMA:83105 is_a: UBERON:0007188 ! mesothelium of serous pericardium relationship: part_of UBERON:0002348 {source="FMA"} ! epicardium -property_value: editor_note "consider merging into myocardial compact layer" xsd:string +property_value: IAO:0000116 "consider merging into myocardial compact layer" xsd:string [Term] id: UBERON:0015129 @@ -250214,17 +246823,17 @@ def: "Visceral intrapericardial fat contiguous with the myocardial surface." [DO synonym: "epicardial adipose tissue" EXACT [] synonym: "pericardial adipose tissue" EXACT [] xref: FMA:9871 -xref: SCTID:42267001 is_a: UBERON:0003837 ! thoracic segment connective tissue +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0035814 ! pericardial fat intersection_of: UBERON:0001013 ! adipose tissue intersection_of: adjacent_to UBERON:0002348 ! epicardium intersection_of: adjacent_to UBERON:0002425 ! visceral serous pericardium -intersection_of: surrounds UBERON:0000948 ! heart +intersection_of: RO:0002221 UBERON:0000948 ! surrounds heart relationship: adjacent_to UBERON:0002348 ! epicardium relationship: adjacent_to UBERON:0002425 ! visceral serous pericardium -relationship: composed_primarily_of CL:1000309 ! epicardial adipocyte relationship: part_of UBERON:0015128 ! subepicardial layer of epicardium +relationship: RO:0002473 CL:1000309 ! composed primarily of epicardial adipocyte [Term] id: UBERON:0015130 @@ -250233,6 +246842,7 @@ namespace: uberon def: "A portion of connective tissue that is part of a prostate gland." [OBOL:automatic] synonym: "connective tissue of prostate" EXACT [FMA:74165] xref: FMA:74165 +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0005156 ! reproductive structure is_a: UBERON:0011822 {source="FMA"} ! dense irregular connective tissue intersection_of: UBERON:0002384 ! connective tissue @@ -250328,8 +246938,6 @@ is_a: UBERON:0002530 ! gland intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0004088 ! orbital region relationship: part_of UBERON:0035639 {source="inferred"} ! ocular adnexa -property_value: UBPROP:0000008 "the only orbital gland found in anuran amphibians is either the Harderian or the lacrimal; if it is a lacrimal, then a progressive lateral migration of the lacrimal glands must occur through the amniotes[PMID:7559104]" xsd:string -property_value: UBPROP:0000008 "the only orbital gland found in anuran amphibians is the Harderian[PMID:8843648]" xsd:string [Term] id: UBERON:0015154 @@ -250339,7 +246947,6 @@ def: "A gland that is located in or around the ocular region, nearer the outer c synonym: "lateral ocular gland" EXACT [] synonym: "lateral orbital gland" EXACT [] is_a: UBERON:0015152 ! gland of ocular region -property_value: IAO:0000232 "The class name or definition should not be taken to mean strictly in the lateral ocular region. We place the extraocular lacrimal glands, even though they are as the name suggests outside the ocular region. The class exists as the division between lateral vs medial (Harderian, nictitans) glands is standard, e.g. http://www.ncbi.nlm.nih.gov/pubmed/7559104" xsd:string [Term] id: UBERON:0015155 @@ -250354,9 +246961,9 @@ xref: FMA:59083 xref: SCTID:280957009 is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0001811 ! conjunctiva -relationship: luminal_space_of UBERON:0001811 ! conjunctiva +intersection_of: RO:0002572 UBERON:0001811 ! luminal space of conjunctiva relationship: part_of UBERON:0005908 {source="FMA"} ! conjunctival sac +relationship: RO:0002572 UBERON:0001811 ! luminal space of conjunctiva [Term] id: UBERON:0015165 @@ -250365,12 +246972,9 @@ namespace: uberon def: "An eye consisting of multiple light-sensing organs." [http://orcid.org/0000-0002-6601-2165, PMID:21062451] is_a: UBERON:0000970 ! eye intersection_of: UBERON:0000970 ! eye -intersection_of: composed_primarily_of UBERON:0000020 ! sense organ -relationship: composed_primarily_of UBERON:0000020 ! sense organ -relationship: never_in_taxon NCBITaxon:7742 ! Vertebrata -relationship: present_in_taxon NCBITaxon:6340 {notes="present on tentacular crown", source="PMID:21062451"} -relationship: present_in_taxon NCBITaxon:6544 {notes="present on mantle edge in arcacean Bivalvia", source="PMID:21062451"} -relationship: present_in_taxon NCBITaxon:7588 {notes="The eyes (optic cushions) on the oral surface of Asteroida (Echinodermata), close to the base of the terminal tentacles, are also composed of a number of simple ocelli - as many as 80-200 in certain species", source="PMID:21062451"} +intersection_of: RO:0002473 UBERON:0000020 ! composed primarily of sense organ +relationship: RO:0002473 UBERON:0000020 ! composed primarily of sense organ +property_value: RO:0002161 NCBITaxon:7742 [Term] id: UBERON:0015172 @@ -250385,7 +246989,7 @@ is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0001295 ! endometrium relationship: part_of UBERON:0001295 ! endometrium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0015178 @@ -250438,6 +247042,7 @@ xref: FMA:55627 xref: NCIT:C32346 xref: SCTID:28638008 is_a: UBERON:0001560 ! neck of organ +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0001560 ! neck of organ intersection_of: part_of UBERON:0001091 ! calcareous tooth relationship: part_of UBERON:0001091 ! calcareous tooth @@ -250448,7 +247053,6 @@ name: non-connected functional system namespace: uberon def: "An anatomical group whose component structures share a common function." [AEO:0000093, AEO:JB, FBbt:00007278, FBC:DOS] xref: AEO:0000093 -xref: FBbt:00007278 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0034923 ! disconnected anatomical group [Term] @@ -250459,8 +247063,8 @@ def: "A non-connected functional system that is composed primarily of a gland." xref: EHDAA2:0002223 is_a: UBERON:0015203 ! non-connected functional system intersection_of: UBERON:0015203 ! non-connected functional system -intersection_of: composed_primarily_of UBERON:0002530 ! gland -relationship: composed_primarily_of UBERON:0002530 ! gland +intersection_of: RO:0002473 UBERON:0002530 ! composed primarily of gland +relationship: RO:0002473 UBERON:0002530 ! composed primarily of gland [Term] id: UBERON:0015212 @@ -250471,10 +247075,9 @@ subset: grouping_class subset: non_informative is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: in_lateral_side_of UBERON:0000465 ! material anatomical entity -relationship: in_lateral_side_of UBERON:0000465 ! material anatomical entity -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -property_value: IAO:0000232 "This class is primarily to implement taxon constraints. It may be removed in the future." xsd:string +intersection_of: BSPO:0000126 UBERON:0000465 ! material anatomical entity +relationship: BSPO:0000126 UBERON:0000465 ! material anatomical entity +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria [Term] id: UBERON:0015214 @@ -250500,10 +247103,9 @@ synonym: "cardiac structure" RELATED [] synonym: "circulatory vessel" NARROW [] synonym: "heart" BROAD [] synonym: "heart or heart like organ" EXACT [] -xref: SPD:0000130 is_a: UBERON:0003103 ! compound organ -relationship: has_quality PATO:0001690 ! contractile relationship: part_of UBERON:0001009 ! circulatory system +relationship: RO:0000086 PATO:0001690 ! has quality contractile [Term] id: UBERON:0015233 @@ -250516,7 +247118,6 @@ is_a: UBERON:0007692 ! nucleus of thalamus intersection_of: UBERON:0002308 ! nucleus of brain intersection_of: part_of UBERON:0004703 ! dorsal thalamus relationship: part_of UBERON:0004703 ! dorsal thalamus -relationship: present_in_taxon NCBITaxon:7762 {notes="Hagfish possess a habenular complex and separate nuclei in the dorsal thalamus", source="Butler, 1996, p. 303"} [Term] id: UBERON:0015238 @@ -250527,7 +247128,6 @@ xref: TAO:0001359 xref: ZFA:0001359 is_a: UBERON:0000477 ! anatomical cluster relationship: part_of UBERON:0001899 {source="ZFA"} ! epithalamus -property_value: RO:0002174 NCBITaxon:40674 [Term] id: UBERON:0015249 @@ -250550,9 +247150,10 @@ def: "A pancreatic lobule that is in_the_left_side_of a exocrine pancreas." [OBO xref: EMAPA:37711 {source="MA:th"} xref: MA:0000722 is_a: UBERON:0007324 ! pancreatic lobule +is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0007324 ! pancreatic lobule -intersection_of: in_left_side_of UBERON:0000017 ! exocrine pancreas -relationship: in_left_side_of UBERON:0000017 ! exocrine pancreas +intersection_of: BSPO:0000120 UBERON:0000017 ! exocrine pancreas +relationship: BSPO:0000120 UBERON:0000017 ! exocrine pancreas [Term] id: UBERON:0015281 @@ -250562,9 +247163,10 @@ def: "A pancreatic lobule that is in_the_right_side_of a exocrine pancreas." [OB xref: EMAPA:37712 {source="MA:th"} xref: MA:0000723 is_a: UBERON:0007324 ! pancreatic lobule +is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0007324 ! pancreatic lobule -intersection_of: in_right_side_of UBERON:0000017 ! exocrine pancreas -relationship: in_right_side_of UBERON:0000017 ! exocrine pancreas +intersection_of: BSPO:0000121 UBERON:0000017 ! exocrine pancreas +relationship: BSPO:0000121 UBERON:0000017 ! exocrine pancreas [Term] id: UBERON:0015329 @@ -250588,7 +247190,7 @@ xref: EMAPA:37597 {source="MA:th"} xref: MA:0002449 is_a: UBERON:0005178 {source="MA"} ! thoracic cavity element relationship: part_of UBERON:0004535 ! cardiovascular system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0015418 @@ -250598,6 +247200,7 @@ def: "A mesenchyme that is part of a urethra." [OBOL:automatic] xref: EMAPA:37786 {source="MA:th"} xref: MA:0002648 is_a: UBERON:0003104 ! mesenchyme +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0000057 ! urethra relationship: part_of UBERON:0000057 ! urethra @@ -250612,6 +247215,7 @@ synonym: "valve or ureter" EXACT [] xref: EMAPA:37781 {source="MA:th"} xref: MA:0002658 is_a: UBERON:0003978 ! valve +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0003978 ! valve intersection_of: part_of UBERON:0000056 ! ureter relationship: capable_of GO:0035809 ! regulation of urine volume @@ -250624,6 +247228,7 @@ namespace: uberon def: "A lymph node that is part of a hypodermis." [OBOL:automatic] xref: MA:0003028 is_a: UBERON:0000029 ! lymph node +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000029 ! lymph node intersection_of: part_of UBERON:0002072 ! hypodermis relationship: part_of UBERON:0002072 ! hypodermis @@ -250674,8 +247279,8 @@ xref: MA:0003095 xref: SCTID:244262006 xref: Wikipedia:Hepatic_artery_proper is_a: UBERON:0001193 {source="MA"} ! hepatic artery -relationship: connecting_branch_of UBERON:0005436 {source="FMA"} ! common hepatic artery -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002252 UBERON:0005436 {source="FMA"} ! connecting branch of common hepatic artery +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0015481 @@ -250693,9 +247298,9 @@ is_a: UBERON:0001193 ! hepatic artery is_a: UBERON:0015796 ! liver blood vessel intersection_of: UBERON:0001193 ! hepatic artery intersection_of: part_of UBERON:0001115 ! left lobe of liver -relationship: connected_to UBERON:0015480 ! proper hepatic artery relationship: part_of UBERON:0001115 {source="FMA"} ! left lobe of liver -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002170 UBERON:0015480 ! connected to proper hepatic artery +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0015482 @@ -250713,9 +247318,9 @@ is_a: UBERON:0001193 ! hepatic artery is_a: UBERON:0015796 ! liver blood vessel intersection_of: UBERON:0001193 ! hepatic artery intersection_of: part_of UBERON:0001114 ! right lobe of liver -relationship: connected_to UBERON:0015480 ! proper hepatic artery relationship: part_of UBERON:0001114 {source="FMA"} ! right lobe of liver -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002170 UBERON:0015480 ! connected to proper hepatic artery +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0015485 @@ -250727,10 +247332,10 @@ xref: EMAPA:37478 {source="MA:th"} xref: MA:0003108 is_a: UBERON:1100000 ! digestive tract junction intersection_of: UBERON:0007651 ! anatomical junction -intersection_of: connects UBERON:0002114 ! duodenum -intersection_of: connects UBERON:0002394 ! bile duct -relationship: connects UBERON:0002114 ! duodenum -relationship: connects UBERON:0002394 ! bile duct +intersection_of: RO:0002176 UBERON:0002114 ! connects duodenum +intersection_of: RO:0002176 UBERON:0002394 ! connects bile duct +relationship: RO:0002176 UBERON:0002114 ! connects duodenum +relationship: RO:0002176 UBERON:0002394 ! connects bile duct [Term] id: UBERON:0015593 @@ -250759,7 +247364,7 @@ is_a: UBERON:0014703 ! anal membrane ectodermal component intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000159 ! anal canal relationship: part_of UBERON:0000159 ! anal canal -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0015717 @@ -250825,7 +247430,6 @@ intersection_of: UBERON:0001826 ! nasal cavity mucosa intersection_of: has_part UBERON:0005385 ! nasal cavity respiratory epithelium intersection_of: part_of UBERON:0001004 ! respiratory system relationship: has_part UBERON:0005385 ! nasal cavity respiratory epithelium -property_value: UBPROP:0000010 "lined with ciliated pseudostratified columnar epithelium (respiratory epithelium). The respiratory segment has a very vascularized lamina propria allowing the venous plexuses of the conchal mucosa to engorge with blood, restricting airflow and causing air to be directed to the other side of the nose." xsd:string {source="Wikipedia:Nasal_cavity"} [Term] id: UBERON:0015787 @@ -250835,10 +247439,10 @@ def: "Any anatomical conduit which is part of the upper respiratory tract." [htt synonym: "respiratory conduit" RELATED [FMA:265132] xref: FMA:265132 is_a: UBERON:0004111 ! anatomical conduit +is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0004111 ! anatomical conduit intersection_of: part_of UBERON:0001557 ! upper respiratory tract relationship: part_of UBERON:0001557 ! upper respiratory tract -property_value: UBPROP:0000001 "Anatomical cluster which consists a segment of the upper respiratory tract[FMA:265132]." xsd:string {source="FMA:265132"} [Term] id: UBERON:0015788 @@ -250846,6 +247450,7 @@ name: olfactory apparatus chamber namespace: uberon def: "An anatomical chamber that is part of the olfactory apparatus, consisting of cavity walls (nasal epithelium and mucosal layers) and the space bounded anteriorly by the nares and posteriorly by the choanae, when these structures are present." [http://orcid.org/0000-0002-6601-2165] xref: FMA:265136 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0015787 ! upper respiratory conduit relationship: part_of UBERON:0000004 ! nose @@ -250862,7 +247467,6 @@ xref: EMAPA:25133 xref: MA:0000579 is_a: UBERON:0002376 ! cranial muscle relationship: part_of UBERON:0004473 ! musculature of face -property_value: IAO:0000232 "see also, 'facial nerve muscle', which is not precisely equivalent. We include this grouping to accomodate the MA class, which includes masticatory muscle as a subtype; note the masticatory muscle is noy innervated by the facial nerve, unlike the facial muscles proper" xsd:string [Term] id: UBERON:0015790 @@ -250888,7 +247492,7 @@ is_a: UBERON:0003587 ! limb connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0002544 ! digit relationship: part_of UBERON:0002544 ! digit -relationship: transformation_of UBERON:0010702 ! digit mesenchyme +relationship: RO:0002494 UBERON:0010702 ! transformation of digit mesenchyme [Term] id: UBERON:0015794 @@ -250924,6 +247528,7 @@ def: "A blood vessel that is part of a liver." [OBOL:automatic] synonym: "hepatic blood vessel" RELATED [EMAPA:35498] xref: EMAPA:35498 xref: MA:0003137 +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0003497 ! abdomen blood vessel intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0002107 ! liver @@ -250949,6 +247554,7 @@ def: "An epithelium that is part of a camera-type eye." [OBOL:automatic] xref: EMAPA:35957 xref: MA:0003162 is_a: UBERON:0007625 ! pigment epithelium of eye +is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000019 ! camera-type eye relationship: part_of UBERON:0000019 ! camera-type eye @@ -251005,7 +247611,7 @@ is_a: UBERON:0001238 ! lamina propria of small intestine intersection_of: UBERON:0000030 ! lamina propria intersection_of: part_of UBERON:0002114 ! duodenum relationship: part_of UBERON:0008342 {source="FMA"} ! intestinal villus of duodenum -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0015860 @@ -251039,7 +247645,6 @@ is_a: UBERON:0015870 ! lymph node of head intersection_of: UBERON:0000029 ! lymph node intersection_of: part_of UBERON:0001456 ! face relationship: part_of UBERON:0001456 ! face -property_value: UBPROP:0000008 "In humans, these comprise three groups: (a) infraorbital or maxillary, scattered over the infraorbital region from the groove between the nose and cheek to the zygomatic arch; (b) buccinator, one or more placed on the Buccinator opposite the angle of the mouth; (c) supramandibular, on the outer surface of the mandible, in front of the Masseter and in contact with the external maxillary artery and anterior facial vein." xsd:string [Term] id: UBERON:0015917 @@ -251101,7 +247706,7 @@ is_a: UBERON:0003512 ! lung blood vessel is_a: UBERON:0003526 ! respiratory system capillary intersection_of: UBERON:0001982 ! capillary intersection_of: part_of UBERON:0002048 ! lung -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0016410 @@ -251164,7 +247769,6 @@ def: "Subdivision of thorax which includes all structures from the skin to the c subset: pheno_slim xref: EMAPA:37233 {source="MA:th"} xref: FMA:50060 -xref: MESH:D035441 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: NCIT:C62484 xref: SCTID:181608004 is_a: UBERON:0000060 ! anatomical wall @@ -251211,10 +247815,10 @@ synonym: "oesophageal hiatus" EXACT [FMA:58289] xref: FMA:58289 is_a: UBERON:0000161 ! orifice intersection_of: UBERON:0000161 ! orifice -intersection_of: conduit_for UBERON:0001043 ! esophagus intersection_of: part_of UBERON:0001103 ! diaphragm -relationship: conduit_for UBERON:0001043 ! esophagus +intersection_of: RO:0002570 UBERON:0001043 ! conduit for esophagus relationship: part_of UBERON:0001103 ! diaphragm +relationship: RO:0002570 UBERON:0001043 ! conduit for esophagus [Term] id: UBERON:0016478 @@ -251226,10 +247830,11 @@ synonym: "hepatic stroma" EXACT [FMA:17553] synonym: "stroma of liver" EXACT [FMA:17553] xref: FMA:17553 is_a: UBERON:0003891 ! stroma +is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0003891 ! stroma intersection_of: part_of UBERON:0002107 ! liver relationship: part_of UBERON:0002107 ! liver -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0016479 @@ -251249,13 +247854,13 @@ xref: SCTID:362185005 xref: Wikipedia:Fibrous_capsule_of_Glisson is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0003893 ! capsule +is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0003893 ! capsule intersection_of: bounding_layer_of UBERON:0002107 ! liver relationship: bounding_layer_of UBERON:0002107 ! liver -relationship: composed_primarily_of UBERON:0018135 ! fibrocollagenous connective tissue -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Liver.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Liver.glb" xsd:anyURI -property_value: UBPROP:0000010 "It consists of type III collagen and extends to the stroma of endothelial sinusoids. It is covered by a single layer of mesothelial cells." xsd:string +relationship: RO:0002473 UBERON:0018135 ! composed primarily of fibrocollagenous connective tissue +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Liver.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Liver.glb" xsd:anyURI [Term] id: UBERON:0016481 @@ -251266,6 +247871,7 @@ xref: MA:0003078 xref: NCIT:C32232 xref: UMLS:C1305372 is_a: UBERON:0000029 ! lymph node +is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0000029 ! lymph node intersection_of: part_of UBERON:0002185 ! bronchus relationship: part_of UBERON:0002185 ! bronchus @@ -251288,7 +247894,6 @@ intersection_of: UBERON:0001032 ! sensory system intersection_of: capable_of GO:0007605 ! sensory perception of sound relationship: capable_of GO:0007605 ! sensory perception of sound relationship: part_of UBERON:0002105 ! vestibulo-auditory system -property_value: UBPROP:0000012 "Auditory system is general anatomical term in FMA" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0016491 @@ -251300,9 +247905,6 @@ synonym: "centrum of vertebra" EXACT [] xref: VSAO:0000183 is_a: UBERON:0004765 {source="VSAO"} ! skeletal element relationship: part_of UBERON:0010913 {source="VSAO"} ! vertebral element -property_value: UBPROP:0000001 "Skeletal element that surrounds the notochord.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000183", ontology="VSAO", source="VSAO:curator"} -property_value: UBPROP:0000001 "the main cylindrical portion of the vertebra ventral to the vertebral canal" xsd:string {source="MP:0000141,ISBN:0-683-40008-8,PMID:10572046"} -property_value: UBPROP:0000008 "The vertebral centrum may be cartilaginous, develop as cartilage but be replaced by bone or mineralized, or form directly through intramembranous ossification." xsd:string [Term] id: UBERON:0016502 @@ -251316,8 +247918,8 @@ xref: EMAPA:18382 xref: FMA:17077 is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0001160 ! fundus of stomach -relationship: luminal_space_of UBERON:0001160 ! fundus of stomach +intersection_of: RO:0002572 UBERON:0001160 ! luminal space of fundus of stomach +relationship: RO:0002572 UBERON:0001160 ! luminal space of fundus of stomach [Term] id: UBERON:0016509 @@ -251330,8 +247932,8 @@ xref: EMAPA:26047 xref: FMA:9291 is_a: UBERON:0035763 ! cavity of cardiac chamber intersection_of: UBERON:0002553 ! anatomical cavity -intersection_of: luminal_space_of UBERON:0002080 ! heart right ventricle -relationship: luminal_space_of UBERON:0002080 ! heart right ventricle +intersection_of: RO:0002572 UBERON:0002080 ! luminal space of heart right ventricle +relationship: RO:0002572 UBERON:0002080 ! luminal space of heart right ventricle [Term] id: UBERON:0016510 @@ -251385,8 +247987,8 @@ xref: EMAPA:26011 xref: FMA:9465 is_a: UBERON:0035763 ! cavity of cardiac chamber intersection_of: UBERON:0002553 ! anatomical cavity -intersection_of: luminal_space_of UBERON:0002079 ! left cardiac atrium -relationship: luminal_space_of UBERON:0002079 ! left cardiac atrium +intersection_of: RO:0002572 UBERON:0002079 ! luminal space of left cardiac atrium +relationship: RO:0002572 UBERON:0002079 ! luminal space of left cardiac atrium [Term] id: UBERON:0016514 @@ -251398,8 +248000,8 @@ xref: EMAPA:26038 xref: FMA:9466 is_a: UBERON:0035763 ! cavity of cardiac chamber intersection_of: UBERON:0002553 ! anatomical cavity -intersection_of: luminal_space_of UBERON:0002084 ! heart left ventricle -relationship: luminal_space_of UBERON:0002084 ! heart left ventricle +intersection_of: RO:0002572 UBERON:0002084 ! luminal space of heart left ventricle +relationship: RO:0002572 UBERON:0002084 ! luminal space of heart left ventricle [Term] id: UBERON:0016515 @@ -251411,6 +248013,7 @@ synonym: "muscle layer of prostatic urethra" EXACT [EMAPA:30956, FMA:FMA] synonym: "muscular coat of prostatic urethra" EXACT [FMA:FMA] xref: EMAPA:30956 xref: FMA:19699 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0006660 ! muscular coat intersection_of: UBERON:0006660 ! muscular coat intersection_of: part_of UBERON:0001335 ! prostatic urethra @@ -251468,8 +248071,8 @@ xref: EMAPA:26020 xref: FMA:11359 is_a: UBERON:0035763 ! cavity of cardiac chamber intersection_of: UBERON:0002553 ! anatomical cavity -intersection_of: luminal_space_of UBERON:0002078 ! right cardiac atrium -relationship: luminal_space_of UBERON:0002078 ! right cardiac atrium +intersection_of: RO:0002572 UBERON:0002078 ! luminal space of right cardiac atrium +relationship: RO:0002572 UBERON:0002078 ! luminal space of right cardiac atrium [Term] id: UBERON:0016525 @@ -251502,9 +248105,9 @@ xref: UMLS:C1268977 {source="BIRNLEX:928"} is_a: UBERON:0016526 {source="FMA"} ! lobe of cerebral hemisphere relationship: adjacent_to UBERON:0001871 ! temporal lobe relationship: adjacent_to UBERON:0001872 ! parietal lobe -relationship: contributes_to_morphology_of UBERON:0001893 ! telencephalon -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: editor_note "Many species don't have lobes but they do have frontal cortex. Lobe isn't a really well defined term though" xsd:string {source="MM"} +relationship: RO:0002433 UBERON:0001893 ! contributes to morphology of telencephalon +property_value: IAO:0000116 "Many species don't have lobes but they do have frontal cortex. Lobe isn't a really well defined term though" xsd:string {source="MM"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0016526 @@ -251528,8 +248131,8 @@ xref: FMA:61823 xref: neuronames:1210 xref: SCTID:272632001 is_a: UBERON:0000064 ! organ part +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001869 ! cerebral hemisphere -property_value: UBPROP:0000202 FMA:77800 [Term] id: UBERON:0016527 @@ -251539,7 +248142,7 @@ xref: FMA:256176 is_a: UBERON:0002437 ! cerebral hemisphere white matter intersection_of: UBERON:0002437 ! cerebral hemisphere white matter intersection_of: part_of UBERON:0016526 ! lobe of cerebral hemisphere -relationship: deep_to UBERON:0016529 ! cortex of cerebral lobe +relationship: BSPO:0000107 UBERON:0016529 ! cortex of cerebral lobe relationship: part_of UBERON:0016526 ! lobe of cerebral hemisphere [Term] @@ -251587,7 +248190,6 @@ xref: DMBA:16016 xref: EMAPA:35667 xref: FMA:242203 xref: MA:0000916 -xref: MESH:D010296 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: neuronames:2473 xref: NLX:79282 xref: SCTID:369217001 @@ -251645,7 +248247,6 @@ xref: DHBA:10235 xref: DMBA:16044 xref: FMA:242201 xref: MA:0000941 -xref: MESH:D013702 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: NLX:94939 xref: SCTID:362343001 is_a: UBERON:0016529 ! cortex of cerebral lobe @@ -251695,8 +248296,8 @@ synonym: "grey matter layer of neuraxis" EXACT [] xref: FMA:83142 is_a: UBERON:0022303 ! nervous system cell part layer intersection_of: UBERON:0022303 ! nervous system cell part layer -intersection_of: composed_primarily_of UBERON:0002020 ! gray matter -relationship: composed_primarily_of UBERON:0002020 ! gray matter +intersection_of: RO:0002473 UBERON:0002020 ! composed primarily of gray matter +relationship: RO:0002473 UBERON:0002020 ! composed primarily of gray matter [Term] id: UBERON:0016549 @@ -251709,8 +248310,8 @@ synonym: "white matter layer of neuraxis" EXACT [FMA:83898] xref: FMA:83898 is_a: UBERON:0022303 ! nervous system cell part layer intersection_of: UBERON:0022303 ! nervous system cell part layer -intersection_of: composed_primarily_of UBERON:0002316 ! white matter -relationship: composed_primarily_of UBERON:0002316 ! white matter +intersection_of: RO:0002473 UBERON:0002316 ! composed primarily of white matter +relationship: RO:0002473 UBERON:0002316 ! composed primarily of white matter [Term] id: UBERON:0016550 @@ -251755,7 +248356,7 @@ is_a: UBERON:0003544 ! brain white matter intersection_of: UBERON:0002316 ! white matter intersection_of: part_of UBERON:0001891 ! midbrain relationship: part_of UBERON:0001891 ! midbrain -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0016565 @@ -251797,10 +248398,10 @@ namespace: uberon def: "A collection of protruberances derived from pharyngeal arch 1 that develop into the tragus, crus of the helix, and helix." [http://php.med.unsw.edu.au/embryology/index.php?title=Hearing_-_Outer_Ear_Development#Pinna-_Auricle] is_a: UBERON:0000477 ! anatomical cluster intersection_of: UBERON:0000477 ! anatomical cluster -intersection_of: develops_from UBERON:0004362 ! pharyngeal arch 1 intersection_of: part_of UBERON:0006208 ! auditory hillocks -relationship: develops_from UBERON:0004362 ! pharyngeal arch 1 +intersection_of: RO:0002202 UBERON:0004362 ! develops from pharyngeal arch 1 relationship: part_of UBERON:0006208 ! auditory hillocks +relationship: RO:0002202 UBERON:0004362 ! develops from pharyngeal arch 1 [Term] id: UBERON:0016612 @@ -251809,10 +248410,10 @@ namespace: uberon def: "A collection of protruberances derived from pharyngeal arch 2 that develop into the concha, antihelix and antitragus." [http://php.med.unsw.edu.au/embryology/index.php?title=Hearing_-_Outer_Ear_Development#Pinna-_Auricle] is_a: UBERON:0000477 ! anatomical cluster intersection_of: UBERON:0000477 ! anatomical cluster -intersection_of: develops_from UBERON:0003066 ! pharyngeal arch 2 intersection_of: part_of UBERON:0006208 ! auditory hillocks -relationship: develops_from UBERON:0003066 ! pharyngeal arch 2 +intersection_of: RO:0002202 UBERON:0003066 ! develops from pharyngeal arch 2 relationship: part_of UBERON:0006208 ! auditory hillocks +relationship: RO:0002202 UBERON:0003066 ! develops from pharyngeal arch 2 [Term] id: UBERON:0016854 @@ -251822,9 +248423,10 @@ def: "The dorsal region of the optic cup that gives rise to the dorsal part of t synonym: "dorsal optic cup" EXACT [http://orcid.org/0000-0002-6601-2165] synonym: "dorsal region of optic cup" EXACT [http://orcid.org/0000-0002-6601-2165] is_a: UBERON:0000481 ! multi-tissue structure +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000481 ! multi-tissue structure -intersection_of: in_dorsal_side_of UBERON:0003072 ! optic cup -relationship: in_dorsal_side_of UBERON:0003072 ! optic cup +intersection_of: BSPO:0015101 UBERON:0003072 ! optic cup +relationship: BSPO:0015101 UBERON:0003072 ! optic cup relationship: part_of UBERON:0003072 ! optic cup [Term] @@ -251837,11 +248439,11 @@ synonym: "future CNS" EXACT [] synonym: "presumptive central nervous system" EXACT [] is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001017 ! central nervous system -relationship: develops_from UBERON:0000924 ! ectoderm -relationship: develops_from UBERON:0002346 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! neurectoderm -relationship: has_potential_to_develop_into UBERON:0001017 ! central nervous system +intersection_of: RO:0002387 UBERON:0001017 ! has potential to develop into central nervous system relationship: part_of UBERON:0016880 ! future nervous system +relationship: RO:0002202 UBERON:0000924 ! develops from ectoderm +relationship: RO:0002202 UBERON:0002346 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! develops from neurectoderm +relationship: RO:0002387 UBERON:0001017 ! has potential to develop into central nervous system [Term] id: UBERON:0016880 @@ -251853,9 +248455,9 @@ synonym: "presumptive nervous system" EXACT [AAO:0000477] xref: AAO:0000477 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001016 ! nervous system -relationship: existence_starts_during_or_after UBERON:0000111 ! organogenesis stage -relationship: has_potential_to_develop_into UBERON:0001016 ! nervous system +intersection_of: RO:0002387 UBERON:0001016 ! has potential to develop into nervous system +relationship: RO:0002387 UBERON:0001016 ! has potential to develop into nervous system +relationship: RO:0002496 UBERON:0000111 ! existence starts during or after organogenesis stage [Term] id: UBERON:0016884 @@ -251863,13 +248465,12 @@ name: shoulder joint namespace: uberon def: "The joint that is formed by the union of the humerus, the scapula (or shoulder blade), and the clavicle (or collarbone). Commonly thought of as a single joint, the shoulder is actually made up of two separate joints - the glenohumeral and acromioclavicular joints." [http://www.innerbody.com/image/skel17.html] synonym: "joint of shoulder region" EXACT [] -xref: MESH:D012785 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: SCTID:361835002 is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: part_of UBERON:0001467 ! shoulder -relationship: develops_from UBERON:0006292 {evidence="definitional"} ! shoulder joint primordium relationship: part_of UBERON:0001467 ! shoulder +relationship: RO:0002202 UBERON:0006292 ! develops from shoulder joint primordium [Term] id: UBERON:0016885 @@ -251908,8 +248509,8 @@ xref: EHDAA2:0000003 xref: EMAPA:16042 is_a: UBERON:0000481 {source="AEO"} ! multi-tissue structure relationship: adjacent_to UBERON:0002050 ! embryonic structure -relationship: existence_starts_and_ends_during UBERON:0000068 ! embryo stage relationship: part_of UBERON:0004716 {source="AEO"} ! conceptus +relationship: RO:0002491 UBERON:0000068 ! existence starts and ends during embryo stage [Term] id: UBERON:0016888 @@ -251940,6 +248541,7 @@ synonym: "fibula metaphysis" EXACT [FMA:33745] synonym: "fibular metaphysis" EXACT [] xref: FMA:33745 is_a: UBERON:0001438 ! metaphysis +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0001438 ! metaphysis intersection_of: part_of UBERON:0001446 ! fibula relationship: part_of UBERON:0001446 ! fibula @@ -251954,10 +248556,10 @@ synonym: "bony tubercles" RELATED OMO:0003004 [] is_a: UBERON:0005813 ! tubercle is_a: UBERON:0013703 ! integumentary projection intersection_of: UBERON:0005813 ! tubercle -intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue intersection_of: part_of UBERON:0002199 ! integument -relationship: composed_primarily_of UBERON:0002481 ! bone tissue +intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue relationship: part_of UBERON:0002199 ! integument +relationship: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue [Term] id: UBERON:0017261 @@ -251965,6 +248567,7 @@ name: intertarsal sesamoid namespace: uberon def: "A sesamoid element that is part of a tarsal skeleton." [OBOL:automatic] synonym: "tarsal sesamoid" RELATED [] +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0011141 ! appendicular ossicle is_a: UBERON:0013631 ! sesamoid element intersection_of: UBERON:0013631 ! sesamoid element @@ -251977,12 +248580,11 @@ name: vomerine dentition namespace: uberon def: "A set of teeth in which each tooth that attaches to a vomer." [OBOL:automatic] synonym: "vomerine teeth" RELATED [] -xref: AAO:0000635 is_a: UBERON:0003672 ! dentition is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0003672 ! dentition -intersection_of: attaches_to UBERON:0002396 ! vomer -relationship: attaches_to UBERON:0002396 ! vomer +intersection_of: RO:0002371 UBERON:0002396 ! attached to vomer +relationship: RO:0002371 UBERON:0002396 ! attached to vomer [Term] id: UBERON:0017635 @@ -251990,11 +248592,12 @@ name: paired venous dural sinus namespace: uberon synonym: "paired dural venous sinus" EXACT [FMA:52568] xref: FMA:52568 +is_a: UBERON:0003496 ! head blood vessel is_a: UBERON:0005486 ! venous dural sinus is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0005486 ! venous dural sinus -intersection_of: in_lateral_side_of UBERON:0000033 ! head -relationship: in_lateral_side_of UBERON:0000033 ! head +intersection_of: BSPO:0000126 UBERON:0000033 ! head +relationship: BSPO:0000126 UBERON:0000033 ! head [Term] id: UBERON:0017649 @@ -252014,8 +248617,8 @@ def: "A mesenchyme-derived anatomical entity undergoing a transtion to become an xref: AEO:0001016 is_a: UBERON:0005423 ! developing anatomical structure intersection_of: UBERON:0005423 ! developing anatomical structure -intersection_of: composed_primarily_of UBERON:0003104 ! mesenchyme -relationship: composed_primarily_of UBERON:0003104 ! mesenchyme +intersection_of: RO:0002473 UBERON:0003104 ! composed primarily of mesenchyme +relationship: RO:0002473 UBERON:0003104 ! composed primarily of mesenchyme [Term] id: UBERON:0017651 @@ -252025,8 +248628,8 @@ def: "A primordium that has the potential to develop into a saliva-secreting gla is_a: UBERON:0001048 ! primordium is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0001048 ! primordium -intersection_of: has_potential_to_develop_into UBERON:0001044 ! saliva-secreting gland -relationship: has_potential_to_develop_into UBERON:0001044 ! saliva-secreting gland +intersection_of: RO:0002387 UBERON:0001044 ! has potential to develop into saliva-secreting gland +relationship: RO:0002387 UBERON:0001044 ! has potential to develop into saliva-secreting gland [Term] id: UBERON:0017672 @@ -252051,11 +248654,11 @@ namespace: uberon def: "A mesopodial endochondral element that is in the most proximal part of the mesopodial skeleton, connected to the zeugopodial skeleton." [http://orcid.org/0000-0002-6601-2165] is_a: UBERON:0015063 ! autopod endochondral element intersection_of: UBERON:0010363 ! endochondral element -intersection_of: connected_to UBERON:0011584 ! zeugopodial skeleton intersection_of: part_of UBERON:0006716 ! mesopodium region -relationship: connected_to UBERON:0011584 ! zeugopodial skeleton +intersection_of: RO:0002170 UBERON:0011584 ! connected to zeugopodial skeleton relationship: part_of UBERON:0009878 ! mesopodial skeleton -property_value: editor_note "awaiting approval by phenoscape curators" xsd:string +relationship: RO:0002170 UBERON:0011584 ! connected to zeugopodial skeleton +property_value: IAO:0000116 "awaiting approval by phenoscape curators" xsd:string [Term] id: UBERON:0017751 @@ -252065,7 +248668,7 @@ def: "A proximal mesopodial endochondral element that is composed primarily of c is_a: UBERON:0015064 ! autopod cartilage is_a: UBERON:0017750 ! proximal mesopodial endochondral element intersection_of: UBERON:0017750 ! proximal mesopodial endochondral element -intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue +intersection_of: RO:0002473 UBERON:0002418 ! composed primarily of cartilage tissue [Term] id: UBERON:0018111 @@ -252134,6 +248737,7 @@ synonym: "renal pelvis of left kidney" EXACT [FMA:15579] xref: FMA:15579 xref: SCTID:243436005 is_a: UBERON:0001224 ! renal pelvis +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0001224 ! renal pelvis intersection_of: part_of UBERON:0001223 ! left ureter relationship: part_of UBERON:0001223 ! left ureter @@ -252148,6 +248752,7 @@ synonym: "pelvis of right ureter" EXACT [FMA:15578] xref: FMA:15578 xref: SCTID:243419002 is_a: UBERON:0001224 ! renal pelvis +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0001224 ! renal pelvis intersection_of: part_of UBERON:0001222 ! right ureter relationship: part_of UBERON:0001222 ! right ureter @@ -252203,8 +248808,8 @@ namespace: uberon xref: FMA:83521 is_a: UBERON:0011824 ! fibrous connective tissue intersection_of: UBERON:0011824 ! fibrous connective tissue -intersection_of: has_quality PATO:0002462 ! collagenous -relationship: has_quality PATO:0002462 ! collagenous +intersection_of: RO:0000086 PATO:0002462 ! has quality collagenous +relationship: RO:0000086 PATO:0002462 ! has quality collagenous [Term] id: UBERON:0018142 @@ -252237,7 +248842,6 @@ is_a: UBERON:0001077 ! transverse process of vertebra intersection_of: UBERON:0001077 ! transverse process of vertebra intersection_of: part_of UBERON:0002413 ! cervical vertebra relationship: part_of UBERON:0002413 ! cervical vertebra -property_value: UBPROP:0000008 "May be homologous with the cervical ribs of some vertebrates" xsd:string [Term] id: UBERON:0018144 @@ -252245,16 +248849,14 @@ name: cervical rib namespace: uberon def: "A rib that is attached to a cervical vertebra." [http://orcid.org/0000-0002-6601-2165] xref: EMAPA:37825 {source="MA:th"} -xref: MESH:D057070 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} is_a: UBERON:0002228 ! rib is_a: UBERON:0003458 ! neck bone intersection_of: UBERON:0002228 ! rib -intersection_of: connected_to UBERON:0002413 ! cervical vertebra -relationship: connected_to UBERON:0002413 ! cervical vertebra -relationship: never_in_taxon NCBITaxon:9606 {source="should be all Theria, see https://github.com/obophenotype/mouse-anatomy-ontology/issues/116"} ! Homo sapiens +intersection_of: RO:0002170 UBERON:0002413 ! connected to cervical vertebra relationship: part_of UBERON:0005434 ! cervical region -property_value: editor_note "Trunk, presacral and sacral ribs do not have a 'part of some region' asserted for them, we should add it to them[PHENOSCAPE:ad]" xsd:string -property_value: UBPROP:0000008 "May be homologous with the transverse processes of cervical vertebra" xsd:string +relationship: RO:0002170 UBERON:0002413 ! connected to cervical vertebra +property_value: IAO:0000116 "Trunk, presacral and sacral ribs do not have a 'part of some region' asserted for them, we should add it to them[PHENOSCAPE:ad]" xsd:string +property_value: RO:0002161 NCBITaxon:9606 {source="should be all Theria, see https://github.com/obophenotype/mouse-anatomy-ontology/issues/116"} [Term] id: UBERON:0018150 @@ -252303,6 +248905,7 @@ synonym: "pulmonary lymphatic chain" EXACT [FMA:67999] synonym: "pulmonary lymphatic vasculature" RELATED [] xref: FMA:67999 is_a: PR:000050567 ! protein-containing material entity +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0011216 ! organ system subdivision intersection_of: UBERON:0011216 ! organ system subdivision intersection_of: part_of UBERON:0002048 ! lung @@ -252322,11 +248925,12 @@ xref: FMA:234006 xref: SCTID:321862009 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0003456 ! respiratory system lymphatic vessel +is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0001473 ! lymphatic vessel intersection_of: part_of UBERON:0002048 ! lung relationship: has_part UBERON:0003529 ! respiratory system lymphatic vessel endothelium relationship: part_of UBERON:0018226 ! pulmonary part of lymphatic system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0018232 @@ -252338,8 +248942,8 @@ synonym: "sweat gland of axilla" EXACT [http://orcid.org/0000-0002-6601-2165] is_a: UBERON:0000382 {source="ISBN:0123813611"} ! apocrine sweat gland intersection_of: UBERON:0001820 ! sweat gland intersection_of: part_of UBERON:0009472 ! axilla -relationship: never_in_taxon NCBITaxon:10088 {source="ISBN:0123813611"} ! Mus relationship: part_of UBERON:0009472 ! axilla +property_value: RO:0002161 NCBITaxon:10088 {source="ISBN:0123813611"} [Term] id: UBERON:0018234 @@ -252353,7 +248957,7 @@ is_a: UBERON:0003891 ! stroma intersection_of: UBERON:0003891 ! stroma intersection_of: part_of UBERON:0001264 ! pancreas relationship: part_of UBERON:0001264 ! pancreas -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0018235 @@ -252365,7 +248969,6 @@ is_a: UBERON:0003893 ! capsule intersection_of: UBERON:0003893 ! capsule intersection_of: part_of UBERON:0001264 ! pancreas relationship: part_of UBERON:0001264 ! pancreas -property_value: UBPROP:0000010 "typically thin but can thicken with age" xsd:string [Term] id: UBERON:0018239 @@ -252373,11 +248976,12 @@ name: rhombomere boundary namespace: uberon def: "A boundary delimiting a rhombomere." [GO:0021654] synonym: "rhombomere junction" EXACT [] +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0007651 ! anatomical junction intersection_of: UBERON:0007651 ! anatomical junction -intersection_of: connects UBERON:0001892 ! rhombomere -relationship: connects UBERON:0001892 ! rhombomere +intersection_of: RO:0002176 UBERON:0001892 ! connects rhombomere relationship: part_of UBERON:0007277 ! presumptive hindbrain +relationship: RO:0002176 UBERON:0001892 ! connects rhombomere [Term] id: UBERON:0018243 @@ -252393,10 +248997,10 @@ xref: SCTID:76543001 xref: Wikipedia:Thymic_branches_of_internal_thoracic_artery is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0002370 ! thymus -relationship: connecting_branch_of UBERON:0002456 {source="FMA"} ! internal thoracic artery -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: supplies UBERON:0002370 ! thymus +intersection_of: RO:0002178 UBERON:0002370 ! supplies thymus +relationship: RO:0002178 UBERON:0002370 ! supplies thymus +relationship: RO:0002252 UBERON:0002456 {source="FMA"} ! connecting branch of internal thoracic artery +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0018246 @@ -252407,8 +249011,8 @@ xref: EMAPA:18648 xref: SCTID:303420005 is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein -intersection_of: drains UBERON:0002046 ! thyroid gland -relationship: drains UBERON:0002046 ! thyroid gland +intersection_of: RO:0002179 UBERON:0002046 ! drains thyroid gland +relationship: RO:0002179 UBERON:0002046 ! drains thyroid gland [Term] id: UBERON:0018247 @@ -252417,8 +249021,8 @@ namespace: uberon def: "An artery that supplies a cervical thymus." [http://orcid.org/0000-0002-6601-2165] is_a: UBERON:0018243 ! thymic artery intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0009114 ! cervical thymus -relationship: supplies UBERON:0009114 ! cervical thymus +intersection_of: RO:0002178 UBERON:0009114 ! supplies cervical thymus +relationship: RO:0002178 UBERON:0009114 ! supplies cervical thymus [Term] id: UBERON:0018251 @@ -252429,9 +249033,8 @@ xref: FMA:50839 xref: SCTID:84842006 is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein -intersection_of: drains UBERON:0002360 ! meninx -relationship: drains UBERON:0002360 ! meninx -property_value: UBPROP:0000008 "In humans, any of several veins that accompany the meningeal arteries, communicate with the sinuses of the dura mater and diploic veins, and drain into the regional veins outside the cranial vault." xsd:string +intersection_of: RO:0002179 UBERON:0002360 ! drains meninx +relationship: RO:0002179 UBERON:0002360 ! drains meninx [Term] id: UBERON:0018252 @@ -252445,11 +249048,10 @@ xref: FMA:18917 xref: SCTID:14885008 xref: Wikipedia:Internal_pudendal_veins is_a: UBERON:0009029 ! pudendal vein -relationship: connected_to UBERON:0001317 ! internal iliac vein -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI -property_value: UBPROP:0000008 "In humans, they begin in the deep veins of the penis which issue from the corpus cavernosum penis, accompany the internal pudendal artery, and unite to form a single vessel, which ends in the internal iliac vein. They receive the veins from the urethral bulb, and the perineal and inferior hemorrhoidal veins" xsd:string +relationship: RO:0002170 UBERON:0001317 ! connected to internal iliac vein +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0018254 @@ -252459,12 +249061,11 @@ subset: grouping_class subset: human_reference_atlas xref: EHDAA2:0001842 xref: EMAPA:35578 -xref: MA:0000165 is_a: UBERON:0000061 ! anatomical structure -relationship: composed_primarily_of UBERON:0014892 ! skeletal muscle organ, vertebrate relationship: part_of UBERON:0000383 {source="MA"} ! musculature of body -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: editor_note "Added for consistency with MA EMAPA and EHDAA2. See https://github.com/obophenotype/mouse-anatomy-ontology/issues/104" xsd:string +relationship: RO:0002473 UBERON:0014892 ! composed primarily of skeletal muscle organ, vertebrate +property_value: IAO:0000116 "Added for consistency with MA EMAPA and EHDAA2. See https://github.com/obophenotype/mouse-anatomy-ontology/issues/104" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0018255 @@ -252478,11 +249079,11 @@ xref: SCTID:265391008 xref: Wikipedia:Jejunal_arteries is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery -intersection_of: connecting_branch_of UBERON:0001182 ! superior mesenteric artery -intersection_of: supplies UBERON:0002115 ! jejunum -relationship: connecting_branch_of UBERON:0001182 ! superior mesenteric artery -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: supplies UBERON:0002115 ! jejunum +intersection_of: RO:0002178 UBERON:0002115 ! supplies jejunum +intersection_of: RO:0002252 UBERON:0001182 ! connecting branch of superior mesenteric artery +relationship: RO:0002178 UBERON:0002115 ! supplies jejunum +relationship: RO:0002252 UBERON:0001182 ! connecting branch of superior mesenteric artery +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0018256 @@ -252494,10 +249095,10 @@ xref: FMA:51779 xref: SCTID:149582008 is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein -intersection_of: drains UBERON:0001817 ! lacrimal gland -relationship: connected_to UBERON:0011192 ! superior ophthalmic vein -relationship: drains UBERON:0001817 ! lacrimal gland -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002179 UBERON:0001817 ! drains lacrimal gland +relationship: RO:0002170 UBERON:0011192 ! connected to superior ophthalmic vein +relationship: RO:0002179 UBERON:0001817 ! drains lacrimal gland +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0018257 @@ -252519,9 +249120,8 @@ xref: NCIT:C75444 xref: UMLS:C0225358 is_a: UBERON:0004923 ! organ component layer intersection_of: UBERON:0004923 ! organ component layer -intersection_of: composed_primarily_of UBERON:0002385 ! muscle tissue -relationship: composed_primarily_of UBERON:0002385 ! muscle tissue -property_value: UBPROP:0000012 "NCITA class may refer to smooth muscle only" xsd:string {external_ontology="NCIT"} +intersection_of: RO:0002473 UBERON:0002385 ! composed primarily of muscle tissue +relationship: RO:0002473 UBERON:0002385 ! composed primarily of muscle tissue [Term] id: UBERON:0018261 @@ -252537,7 +249137,6 @@ intersection_of: UBERON:0006660 ! muscular coat intersection_of: part_of UBERON:0001555 ! digestive tract relationship: capable_of_part_of GO:0030432 ! peristalsis relationship: part_of UBERON:0001555 ! digestive tract -property_value: UBPROP:0000009 "responsible for gut movement, such as peristalsis" xsd:string [Term] id: UBERON:0018303 @@ -252547,10 +249146,12 @@ def: "Tissue that is part of some adrenal gland." [PHENOSCAPE:Alex] synonym: "adrenal gland tissue" EXACT [ncithesaurus:Adrenal_Gland_Tissue] xref: NCIT:C32051 is_a: UBERON:0000479 ! tissue +is_a: UBERON:0004120 ! mesoderm-derived structure +is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0000479 ! tissue intersection_of: part_of UBERON:0002369 ! adrenal gland relationship: part_of UBERON:0002369 ! adrenal gland -property_value: editor_note "TODO - describe typology of adrenal gland tissue used in this ontology" xsd:string +property_value: IAO:0000116 "TODO - describe typology of adrenal gland tissue used in this ontology" xsd:string [Term] id: UBERON:0018321 @@ -252559,22 +249160,23 @@ namespace: uberon def: "Foramen that allows the passge of the glossopharyngeal nerve (cranial nerve IX)." [PHENOSCAPE:alex] is_a: UBERON:0013685 ! foramen of skull intersection_of: UBERON:0013685 ! foramen of skull -intersection_of: conduit_for UBERON:0001649 ! glossopharyngeal nerve -relationship: conduit_for UBERON:0001649 ! glossopharyngeal nerve +intersection_of: RO:0002570 UBERON:0001649 ! conduit for glossopharyngeal nerve relationship: part_of UBERON:0003128 ! cranium +relationship: RO:0002570 UBERON:0001649 ! conduit for glossopharyngeal nerve [Term] id: UBERON:0018326 name: ilioischiadic foramen namespace: uberon def: "Situated just caudal to the acetabulum, the foramen is bound dorsally by the illium and ventrally by the ischium. The foramen transmitts the ischiadic nerves and vessels (Baumel et al. 1993)." [PHENOSCAPE:alex] +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005744 ! bone foramen intersection_of: UBERON:0005744 ! bone foramen -intersection_of: conduit_for UBERON:0001322 ! sciatic nerve +intersection_of: RO:0002570 UBERON:0001322 ! conduit for sciatic nerve relationship: adjacent_to UBERON:0001273 ! ilium relationship: adjacent_to UBERON:0001274 ! ischium -relationship: conduit_for UBERON:0001322 ! sciatic nerve relationship: part_of UBERON:0007832 ! pelvic girdle skeleton +relationship: RO:0002570 UBERON:0001322 ! conduit for sciatic nerve [Term] id: UBERON:0018413 @@ -252588,9 +249190,9 @@ xref: FMA:54952 xref: Wikipedia:Facial_canal is_a: UBERON:0013685 ! foramen of skull intersection_of: UBERON:0013685 ! foramen of skull -intersection_of: conduit_for UBERON:0001647 ! facial nerve -relationship: conduit_for UBERON:0001647 ! facial nerve +intersection_of: RO:0002570 UBERON:0001647 ! conduit for facial nerve relationship: part_of UBERON:0001678 ! temporal bone +relationship: RO:0002570 UBERON:0001647 ! conduit for facial nerve [Term] id: UBERON:0018415 @@ -252603,11 +249205,11 @@ synonym: "ethmoidal foramen" EXACT [] synonym: "ethmoidal foramina" RELATED OMO:0003004 [] synonym: "foramina ethmoidalia" EXACT OMO:0003011 [] xref: Wikipedia:Ethmoidal_foramina +is_a: UBERON:0010313 ! neural crest-derived structure is_a: UBERON:0013685 ! foramen of skull intersection_of: UBERON:0004111 ! anatomical conduit intersection_of: part_of UBERON:0001679 ! ethmoid bone relationship: part_of UBERON:0001679 ! ethmoid bone -property_value: UBPROP:0000008 "There are usually two Foramina ethmoidalia present on each side in the dog. Sometimes one is situated rostral to the other, but often it is dorsal. They are not homologous with the Foramen ethmoidale anterius and Foramen ethmoidale posterius of man. Therefore they are not listed separately.[NOMINA ANATOMICA VETERINARIA (2005)]" xsd:string [Term] id: UBERON:0018543 @@ -252623,9 +249225,9 @@ xref: WBbt:0005791 xref: ZFA:0005807 is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0000160 ! intestine -relationship: luminal_space_of UBERON:0000160 ! intestine -property_value: editor_note "see notes in inclusivity in class 'intestine'" xsd:string +intersection_of: RO:0002572 UBERON:0000160 ! luminal space of intestine +relationship: RO:0002572 UBERON:0000160 ! luminal space of intestine +property_value: IAO:0000116 "see notes in inclusivity in class 'intestine'" xsd:string [Term] id: UBERON:0018544 @@ -252637,9 +249239,9 @@ synonym: "muscles innervated by the trigeminal nerve" EXACT OMO:0003004 [MFMO:00 xref: MFMO:0000072 is_a: UBERON:0001630 ! muscle organ intersection_of: UBERON:0001630 ! muscle organ -intersection_of: innervated_by UBERON:0001645 ! trigeminal nerve -relationship: develops_from UBERON:0004362 ! pharyngeal arch 1 -relationship: innervated_by UBERON:0001645 ! trigeminal nerve +intersection_of: RO:0002005 UBERON:0001645 ! innervated_by trigeminal nerve +relationship: RO:0002005 UBERON:0001645 ! innervated_by trigeminal nerve +relationship: RO:0002202 UBERON:0004362 ! develops from pharyngeal arch 1 [Term] id: UBERON:0018649 @@ -252662,7 +249264,7 @@ def: "The neck region of a bone organ." [http://orcid.org/0000-0002-6601-2165] synonym: "bone neck" EXACT [] synonym: "neck of bone" EXACT [] is_a: UBERON:0001560 ! neck of organ -is_a: UBERON:0005913 {notes="https://github.com/obophenotype/uberon/wiki/Hidden-GCIs"} ! zone of bone organ +is_a: UBERON:0005913 ! zone of bone organ intersection_of: UBERON:0001560 ! neck of organ intersection_of: part_of UBERON:0001474 ! bone element @@ -252689,12 +249291,13 @@ synonym: "fibula neck" EXACT [FMA:35508] synonym: "fibular neck" EXACT [] xref: EMAPA:37891 {source="MA:th"} xref: FMA:35508 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005055 ! zone of long bone is_a: UBERON:0018664 ! neck of bone element intersection_of: UBERON:0001560 ! neck of organ intersection_of: part_of UBERON:0001446 ! fibula relationship: part_of UBERON:0001446 ! fibula -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0018674 @@ -252720,9 +249323,9 @@ xref: Wikipedia:Thoracic_splanchnic_nerves is_a: UBERON:0003715 ! splanchnic nerve is_a: UBERON:0003824 ! nerve of thoracic segment intersection_of: UBERON:0003715 ! splanchnic nerve -intersection_of: connects UBERON:0004863 ! thoracic sympathetic nerve trunk -relationship: branching_part_of UBERON:0004863 {source="FMA"} ! thoracic sympathetic nerve trunk -relationship: connects UBERON:0004863 ! thoracic sympathetic nerve trunk +intersection_of: RO:0002176 UBERON:0004863 ! connects thoracic sympathetic nerve trunk +relationship: RO:0002176 UBERON:0004863 ! connects thoracic sympathetic nerve trunk +relationship: RO:0002380 UBERON:0004863 {source="FMA"} ! branching part of thoracic sympathetic nerve trunk [Term] id: UBERON:0018685 @@ -252733,8 +249336,8 @@ synonym: "suckling stage" EXACT [] is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage relationship: has_part UBERON:0007221 ! neonate stage -relationship: only_in_taxon NCBITaxon:40674 ! Mammalia relationship: part_of UBERON:0000092 ! post-embryonic stage +relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia [Term] id: UBERON:0018692 @@ -252742,8 +249345,8 @@ name: dorsal side of post-anal tail namespace: uberon is_a: UBERON:0034929 ! external soft tissue zone intersection_of: UBERON:0034929 ! external soft tissue zone -intersection_of: in_dorsal_side_of UBERON:0007812 ! post-anal tail -relationship: in_dorsal_side_of UBERON:0007812 ! post-anal tail +intersection_of: BSPO:0015101 UBERON:0007812 ! post-anal tail +relationship: BSPO:0015101 UBERON:0007812 ! post-anal tail relationship: part_of UBERON:0001137 ! dorsum relationship: part_of UBERON:0007812 ! post-anal tail @@ -252756,8 +249359,8 @@ synonym: "bladder" NARROW [BTO:0000123] xref: BTO:0000123 is_a: UBERON:0000489 ! cavitated compound organ is_a: UBERON:0009856 ! sac -relationship: has_quality PATO:0002468 ! distensible -relationship: location_of UBERON:0000463 ! organism substance +relationship: RO:0000086 PATO:0002468 ! has quality distensible +relationship: RO:0001015 UBERON:0000463 ! location of organism substance [Term] id: UBERON:0019042 @@ -252805,6 +249408,7 @@ xref: BTO:0004638 xref: FMA:13119 xref: SCTID:88410004 is_a: UBERON:0000414 ! mucous gland +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0005181 ! thoracic segment organ is_a: UBERON:0036225 ! respiratory system gland intersection_of: UBERON:0000414 ! mucous gland @@ -252827,7 +249431,7 @@ name: skin epithelium namespace: uberon def: "Any region of epithelium that is part of a skin region." [http://orcid.org/0000-0002-6601-2165] xref: BTO:0004382 -is_a: UBERON:0000483 ! epithelium +is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000014 ! zone of skin relationship: part_of UBERON:0000014 ! zone of skin @@ -252856,6 +249460,8 @@ synonym: "retinachoroid" EXACT [] synonym: "retinachoroidal region" EXACT [] xref: SCTID:110701000 is_a: UBERON:0000481 ! multi-tissue structure +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: has_part UBERON:0000966 ! retina relationship: has_part UBERON:0001776 ! optic choroid relationship: part_of UBERON:0010230 ! eyeball of camera-type eye @@ -252872,7 +249478,7 @@ is_a: UBERON:0003544 ! brain white matter intersection_of: UBERON:0002316 ! white matter intersection_of: part_of UBERON:0002028 ! hindbrain relationship: part_of UBERON:0002028 ! hindbrain -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0019261 @@ -252886,7 +249492,7 @@ is_a: UBERON:0003544 ! brain white matter intersection_of: UBERON:0002316 ! white matter intersection_of: part_of UBERON:0001890 ! forebrain relationship: part_of UBERON:0001890 ! forebrain -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0019262 @@ -252912,7 +249518,7 @@ is_a: UBERON:0003528 ! brain gray matter intersection_of: UBERON:0002020 ! gray matter intersection_of: part_of UBERON:0002028 ! hindbrain relationship: part_of UBERON:0002028 ! hindbrain -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0019264 @@ -252925,7 +249531,7 @@ is_a: UBERON:0003528 ! brain gray matter intersection_of: UBERON:0002020 ! gray matter intersection_of: part_of UBERON:0001890 ! forebrain relationship: part_of UBERON:0001890 ! forebrain -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0019267 @@ -252938,7 +249544,7 @@ is_a: UBERON:0003528 ! brain gray matter intersection_of: UBERON:0002020 ! gray matter intersection_of: part_of UBERON:0001891 ! midbrain relationship: part_of UBERON:0001891 ! midbrain -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0019269 @@ -253007,6 +249613,7 @@ name: nose epithelium namespace: uberon xref: EMAPA:35958 xref: MA:0003171 +is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0019304 ! sensory organ epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000004 ! nose @@ -253094,8 +249701,8 @@ xref: EMAPA:37386 {source="MA:th"} xref: MA:0001226 is_a: UBERON:0001981 ! blood vessel intersection_of: UBERON:0001981 ! blood vessel -intersection_of: connected_to UBERON:0001690 ! ear -relationship: connected_to UBERON:0001690 ! ear +intersection_of: RO:0002170 UBERON:0001690 ! connected to ear +relationship: RO:0002170 UBERON:0001690 ! connected to ear [Term] id: UBERON:0022248 @@ -253149,7 +249756,7 @@ is_a: UBERON:0011184 ! epithelium of crypt of Lieberkuhn intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001984 ! crypt of Lieberkuhn of large intestine relationship: part_of UBERON:0001984 ! crypt of Lieberkuhn of large intestine -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0022284 @@ -253160,7 +249767,6 @@ xref: EMAPA:35464 is_a: UBERON:0005153 ! epithelial bud is_a: UBERON:0015808 ! eye epithelium relationship: part_of UBERON:0001750 ! lacrimal apparatus -property_value: UBPROP:0000008 "in mouse, the primary bud arises around E13.5 and extends caudally into the surrounding neural-crest derived periocular mesenchyme; between E15.5 and E16.5 the bud undergoes branching morphogenesis, forming both a major extra-orbital lobe and a minor intraorbital lobe" xsd:string [Term] id: UBERON:0022288 @@ -253211,11 +249817,11 @@ synonym: "layer" BROAD [CUMBO:CUMBO] xref: NLX:149357 is_a: UBERON:0005162 ! multi cell part structure intersection_of: UBERON:0005162 ! multi cell part structure -intersection_of: has_quality PATO:0002124 ! laminar intersection_of: part_of UBERON:0001016 ! nervous system -relationship: has_quality PATO:0002124 ! laminar +intersection_of: RO:0000086 PATO:0002124 ! has quality laminar relationship: part_of UBERON:0001016 ! nervous system -property_value: editor_note "this is currently used to group some cellular layers that may not strictly conform to the CARO definition of cell-part layer. Consider genericisizing and introducing subtypes for cellular layer, fibrous layer and cell soma layer" xsd:string +relationship: RO:0000086 PATO:0002124 ! has quality laminar +property_value: IAO:0000116 "this is currently used to group some cellular layers that may not strictly conform to the CARO definition of cell-part layer. Consider genericisizing and introducing subtypes for cellular layer, fibrous layer and cell soma layer" xsd:string [Term] id: UBERON:0022315 @@ -253227,7 +249833,6 @@ xref: NLX:144263 is_a: UBERON:0002301 ! layer of neocortex relationship: part_of UBERON:0001384 {source="nlx"} ! primary motor cortex relationship: part_of UBERON:0005394 {source="nlx"} ! cortical layer V -property_value: UBPROP:0000013 "Note that in some lamination schemes, more particularly so in primates, this layer is referred to as layer IV thus resulting in some confusion when compared to the present scheme where the lamina dissecans is referred to layer IV[DOI:10.1155/2008/381243]" xsd:string [Term] id: UBERON:0022317 @@ -253256,10 +249861,10 @@ xref: NLX:152610 is_a: UBERON:0011215 ! central nervous system cell part cluster is_a: UBERON:0022303 ! nervous system cell part layer intersection_of: UBERON:0022303 ! nervous system cell part layer -intersection_of: immediately_deep_to UBERON:0022317 ! olfactory cortex layer 1 -relationship: composed_primarily_of GO:0043025 ! neuronal cell body -relationship: immediately_deep_to UBERON:0022317 ! olfactory cortex layer 1 +intersection_of: BSPO:0001107 UBERON:0022317 ! olfactory cortex layer 1 +relationship: BSPO:0001107 UBERON:0022317 ! olfactory cortex layer 1 relationship: part_of UBERON:0002894 {source="nlx"} ! olfactory cortex +relationship: RO:0002473 GO:0043025 ! composed primarily of neuronal cell body [Term] id: UBERON:0022320 @@ -253269,10 +249874,10 @@ xref: NLX:153848 is_a: UBERON:0011215 ! central nervous system cell part cluster is_a: UBERON:0022303 ! nervous system cell part layer intersection_of: UBERON:0022303 ! nervous system cell part layer -intersection_of: composed_primarily_of CL:0000598 ! pyramidal neuron intersection_of: part_of UBERON:0002829 ! dorsal cochlear nucleus -relationship: composed_primarily_of CL:0000598 ! pyramidal neuron +intersection_of: RO:0002473 CL:0000598 ! composed primarily of pyramidal neuron relationship: part_of UBERON:0002829 ! dorsal cochlear nucleus +relationship: RO:0002473 CL:0000598 ! composed primarily of pyramidal neuron [Term] id: UBERON:0022350 @@ -253281,6 +249886,7 @@ namespace: uberon def: "Serous membrane layer that is adjacent to and lines an organ." [http://orcid.org/0000-0002-6601-2165] synonym: "visceral wall of serous membrane" EXACT [FMA:15860] xref: FMA:15860 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004923 ! organ component layer intersection_of: UBERON:0004923 ! organ component layer intersection_of: adjacent_to UBERON:0000062 ! organ @@ -253297,6 +249903,7 @@ synonym: "cavity lining" BROAD [MA:0002448] synonym: "parietal wall of serous membrane" EXACT [FMA:15859] xref: FMA:15859 xref: MA:0002448 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004923 ! organ component layer intersection_of: UBERON:0004923 ! organ component layer intersection_of: adjacent_to UBERON:0002553 ! anatomical cavity @@ -253318,7 +249925,7 @@ is_a: UBERON:0004811 ! endometrium epithelium intersection_of: UBERON:0004811 ! endometrium epithelium intersection_of: adjacent_to UBERON:0013769 ! uterine lumen relationship: adjacent_to UBERON:0013769 ! uterine lumen -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0022356 @@ -253334,7 +249941,7 @@ is_a: UBERON:0004811 ! endometrium epithelium intersection_of: UBERON:0004811 ! endometrium epithelium intersection_of: adjacent_to UBERON:0001296 ! myometrium relationship: adjacent_to UBERON:0001296 ! myometrium -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0022357 @@ -253362,7 +249969,7 @@ is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0001987 ! placenta relationship: part_of UBERON:0001987 ! placenta -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0022360 @@ -253381,11 +249988,12 @@ namespace: uberon def: "A specific region of the foregut into the area in which the lung will develop." [GOC:dph, GOC:mtg_lung] synonym: "lung field" EXACT [] xref: SCTID:34922002 +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0007688 ! anlage intersection_of: UBERON:0007688 ! anlage -intersection_of: has_potential_to_develop_into UBERON:0002048 ! lung -relationship: has_potential_to_develop_into UBERON:0002048 ! lung +intersection_of: RO:0002387 UBERON:0002048 ! has potential to develop into lung relationship: part_of UBERON:0003258 ! endoderm of foregut +relationship: RO:0002387 UBERON:0002048 ! has potential to develop into lung [Term] id: UBERON:0023879 @@ -253396,7 +250004,7 @@ synonym: "neural system" EXACT [NLXANAT:090802] xref: NLXANAT:090802 is_a: UBERON:0011216 ! organ system subdivision relationship: part_of UBERON:0001016 ! nervous system -property_value: editor_note "this class was inherited from NIFSTD as part of the replacement of NIFSTD with Uberon. It may be obsoleted in the future" xsd:string +property_value: IAO:0000116 "this class was inherited from NIFSTD as part of the replacement of NIFSTD with Uberon. It may be obsoleted in the future" xsd:string [Term] id: UBERON:0024045 @@ -253574,7 +250182,6 @@ is_a: UBERON:0034709 ! hindbrain marginal layer intersection_of: UBERON:0004062 ! neural tube marginal layer intersection_of: part_of UBERON:0002037 ! cerebellum relationship: part_of UBERON:0002037 ! cerebellum -property_value: UBPROP:0000011 "In the cerebellum, some neuronal precursors enter the marginal zone to form clusters of neurons called nuclei[NBK10047]" xsd:string [Term] id: UBERON:0034709 @@ -253623,10 +250230,10 @@ synonym: "cranial nerve or tract" RELATED [http://orcid.org/0000-0002-6601-2165] synonym: "neuron projection bundle from brain" RELATED [http://orcid.org/0000-0002-6601-2165] is_a: UBERON:0000122 ! neuron projection bundle is_a: UBERON:0015212 ! lateral structure +relationship: BSPO:0000126 UBERON:0000033 ! head relationship: extends_fibers_into UBERON:0000955 ! brain -relationship: in_lateral_side_of UBERON:0000033 ! head -relationship: only_in_taxon NCBITaxon:89593 ! Craniata -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0034714 @@ -253638,9 +250245,9 @@ synonym: "epiphyseal nerve" RELATED [ISBN:0471888893] is_a: UBERON:0011215 ! central nervous system cell part cluster is_a: UBERON:0034713 ! cranial neuron projection bundle intersection_of: UBERON:0034713 ! cranial neuron projection bundle -intersection_of: innervates UBERON:0004869 ! parietal organ +intersection_of: RO:0002134 UBERON:0004869 ! innervates parietal organ relationship: extends_fibers_into UBERON:0001899 ! epithalamus -relationship: innervates UBERON:0004869 ! parietal organ +relationship: RO:0002134 UBERON:0004869 ! innervates parietal organ [Term] id: UBERON:0034715 @@ -253653,10 +250260,10 @@ xref: FMA:77600 is_a: UBERON:0011215 ! central nervous system cell part cluster is_a: UBERON:0034713 ! cranial neuron projection bundle intersection_of: UBERON:0034713 ! cranial neuron projection bundle -intersection_of: innervates UBERON:0001905 ! pineal body -relationship: branching_part_of UBERON:0034714 ! epiphyseal tract +intersection_of: RO:0002134 UBERON:0001905 ! innervates pineal body relationship: extends_fibers_into UBERON:0001899 ! epithalamus -relationship: innervates UBERON:0001905 ! pineal body +relationship: RO:0002134 UBERON:0001905 ! innervates pineal body +relationship: RO:0002380 UBERON:0034714 ! branching part of epiphyseal tract [Term] id: UBERON:0034717 @@ -253678,13 +250285,14 @@ is_a: UBERON:0013765 ! digestive system element intersection_of: UBERON:0001727 ! taste bud intersection_of: part_of UBERON:0001833 ! lip relationship: part_of UBERON:0001833 ! lip -relationship: present_in_taxon NCBITaxon:32443 ! Teleostei +property_value: RO:0002175 NCBITaxon:32443 [Term] id: UBERON:0034720 name: head taste bud namespace: uberon def: "A taste bud that is located on the skin of the head." [http://orcid.org/0000-0002-6601-2165] +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0034717 ! integumental taste bud intersection_of: UBERON:0001727 ! taste bud intersection_of: part_of UBERON:0001084 ! skin of head @@ -253700,7 +250308,7 @@ is_a: UBERON:0013765 ! digestive system element intersection_of: UBERON:0001727 ! taste bud intersection_of: part_of UBERON:0006562 ! pharynx relationship: part_of UBERON:0000355 ! pharyngeal mucosa -relationship: present_in_taxon NCBITaxon:7778 +property_value: RO:0002175 NCBITaxon:7778 [Term] id: UBERON:0034722 @@ -253711,7 +250319,7 @@ is_a: UBERON:0001727 ! taste bud intersection_of: UBERON:0001727 ! taste bud intersection_of: part_of UBERON:0007375 ! roof of mouth relationship: part_of UBERON:0007375 ! roof of mouth -relationship: present_in_taxon NCBITaxon:7778 +property_value: RO:0002175 NCBITaxon:7778 [Term] id: UBERON:0034724 @@ -253724,13 +250332,14 @@ is_a: UBERON:0013765 ! digestive system element intersection_of: UBERON:0001727 ! taste bud intersection_of: part_of UBERON:0001043 ! esophagus relationship: part_of UBERON:0001043 ! esophagus -relationship: present_in_taxon NCBITaxon:32443 ! Teleostei +property_value: RO:0002175 NCBITaxon:32443 [Term] id: UBERON:0034726 name: trunk taste bud namespace: uberon def: "A taste bud that is located on the skin of the trunk." [http://orcid.org/0000-0002-6601-2165] +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005177 ! trunk region element is_a: UBERON:0034717 ! integumental taste bud intersection_of: UBERON:0001727 ! taste bud @@ -253749,10 +250358,10 @@ xref: FMA:5866 xref: MESH:D017776 xref: SCTID:276145003 xref: Wikipedia:Autonomic_nerve -is_a: UBERON:0001021 ! nerve -relationship: branching_part_of UBERON:0036264 ! zygomaticotemporal nerve +is_a: UBERON:0011779 ! nerve of head region relationship: extends_fibers_into UBERON:0001805 ! autonomic ganglion relationship: part_of UBERON:0002410 ! autonomic nervous system +relationship: RO:0002380 UBERON:0036264 ! branching part of zygomaticotemporal nerve [Term] id: UBERON:0034729 @@ -253766,7 +250375,7 @@ intersection_of: UBERON:0001021 ! nerve intersection_of: part_of UBERON:0000013 ! sympathetic nervous system relationship: extends_fibers_into UBERON:0001806 ! sympathetic ganglion relationship: part_of UBERON:0000013 ! sympathetic nervous system -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0034730 @@ -253780,7 +250389,6 @@ is_a: UBERON:0002265 ! olfactory tract intersection_of: UBERON:0002265 ! olfactory tract intersection_of: overlaps UBERON:0000203 ! pallium relationship: overlaps UBERON:0000203 ! pallium -property_value: UBPROP:0000001 "Telencephalic white matter which extends between the olfactory bulb and the ipsilateral dorsal telencephalon and carries secondary olfactory fibers. From Neuroanatomy of the Zebrafish Brain." xsd:string {source="ZFA:0000229"} [Term] id: UBERON:0034768 @@ -253789,11 +250397,11 @@ namespace: uberon def: "A part of an organism or organ that is continuous with its surroundings and distinguished from its surroundings based on morphology." [http://orcid.org/0000-0002-6601-2165] subset: common_anatomy is_a: UBERON:0000061 ! anatomical structure -relationship: has_quality PATO:0000052 ! shape relationship: part_of UBERON:0000468 ! multicellular organism -relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 ! Fungi +relationship: RO:0000086 PATO:0000052 ! has quality shape +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0034769 @@ -253813,8 +250421,8 @@ synonym: "portion of gas in anatomical space" EXACT [FMA:84580] xref: FMA:84580 is_a: UBERON:0000463 ! organism substance intersection_of: UBERON:0000463 ! organism substance -intersection_of: has_quality PATO:0001547 ! quality of a gas -relationship: has_quality PATO:0001547 ! quality of a gas +intersection_of: RO:0000086 PATO:0001547 ! has quality quality of a gas +relationship: RO:0000086 PATO:0001547 ! has quality quality of a gas [Term] id: UBERON:0034874 @@ -253826,9 +250434,9 @@ synonym: "respiratory system air" EXACT [] xref: FMA:84581 is_a: UBERON:0034947 ! gas in respiratory system intersection_of: UBERON:0034873 ! bodily gas -intersection_of: composed_primarily_of CHEBI:25805 -intersection_of: located_in UBERON:0001004 ! respiratory system -relationship: composed_primarily_of CHEBI:25805 +intersection_of: RO:0001025 UBERON:0001004 ! located in respiratory system +intersection_of: RO:0002473 CHEBI:25805 ! composed primarily of +relationship: RO:0002473 CHEBI:25805 ! composed primarily of [Term] id: UBERON:0034875 @@ -253839,10 +250447,10 @@ xref: EHDAA2:0001472 xref: EMAPA:32796 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0000007 ! pituitary gland -relationship: develops_from UBERON:0000924 {source="Wikipedia"} ! ectoderm -relationship: has_potential_to_develop_into UBERON:0000007 ! pituitary gland +intersection_of: RO:0002387 UBERON:0000007 ! has potential to develop into pituitary gland relationship: part_of UBERON:0000033 {source="EMAPA"} ! head +relationship: RO:0002202 UBERON:0000924 {source="Wikipedia"} ! develops from ectoderm +relationship: RO:0002387 UBERON:0000007 ! has potential to develop into pituitary gland [Term] id: UBERON:0034876 @@ -253855,10 +250463,10 @@ xref: EHDAA2:0004434 xref: EMAPA:16647 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0002198 ! neurohypophysis -relationship: has_potential_to_develop_into UBERON:0002198 ! neurohypophysis +intersection_of: RO:0002387 UBERON:0002198 ! has potential to develop into neurohypophysis relationship: part_of UBERON:0001894 {source="EMAPA"} ! diencephalon relationship: part_of UBERON:0034875 {source="EMAPA"} ! future pituitary gland +relationship: RO:0002387 UBERON:0002198 ! has potential to develop into neurohypophysis [Term] id: UBERON:0034878 @@ -253868,10 +250476,10 @@ def: "The area of axial mesoderm that develops into the prechordal plate." [MGI: synonym: "prechordal mesenchyme" EXACT [] is_a: UBERON:0002050 ! embryonic structure intersection_of: UBERON:0005423 ! developing anatomical structure -intersection_of: has_potential_to_develop_into UBERON:0003063 ! prechordal plate intersection_of: part_of UBERON:0003068 ! axial mesoderm -relationship: has_potential_to_develop_into UBERON:0003063 ! prechordal plate +intersection_of: RO:0002387 UBERON:0003063 ! has potential to develop into prechordal plate relationship: part_of UBERON:0003068 ! axial mesoderm +relationship: RO:0002387 UBERON:0003063 ! has potential to develop into prechordal plate [Term] id: UBERON:0034901 @@ -253904,7 +250512,6 @@ is_a: UBERON:0002166 ! endocardium of atrium intersection_of: UBERON:0002165 ! endocardium intersection_of: part_of UBERON:0002079 ! left cardiac atrium relationship: part_of UBERON:0002079 ! left cardiac atrium -property_value: UBPROP:0000001 "Endocardium of atrium which is continuous with the tunica intima of the trunk of pulmonary vein." xsd:string {source="FMA:7286"} [Term] id: UBERON:0034905 @@ -253913,8 +250520,8 @@ namespace: uberon synonym: "lumen of gland" EXACT [] is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0002530 ! gland -relationship: luminal_space_of UBERON:0002530 ! gland +intersection_of: RO:0002572 UBERON:0002530 ! luminal space of gland +relationship: RO:0002572 UBERON:0002530 ! luminal space of gland [Term] id: UBERON:0034907 @@ -253935,8 +250542,8 @@ namespace: uberon def: "Any of the muscles that are responsible for moving the scapula. In humans these are the levator scapulae, the infraspinatus muscle, the teres major, the teres minor, and the supraspinatus muscle." [HPO:curators] is_a: UBERON:0014892 ! skeletal muscle organ, vertebrate intersection_of: UBERON:0014892 ! skeletal muscle organ, vertebrate -intersection_of: attaches_to UBERON:0006849 ! scapula -relationship: attaches_to UBERON:0006849 ! scapula +intersection_of: RO:0002371 UBERON:0006849 ! attached to scapula +relationship: RO:0002371 UBERON:0006849 ! attached to scapula [Term] id: UBERON:0034921 @@ -253947,10 +250554,10 @@ subset: common_anatomy synonym: "anatomical cluster" RELATED [CARO:0020001] xref: CARO:0020001 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure -relationship: composed_primarily_of UBERON:0000064 ! organ part -relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 ! Fungi +relationship: RO:0002473 UBERON:0000064 ! composed primarily of organ part +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0034922 @@ -253961,10 +250568,10 @@ subset: common_anatomy xref: CARO:0020002 xref: FMA:62807 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure -relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 ! Fungi -relationship: surrounded_by UBERON:0000015 ! non-material anatomical boundary +relationship: RO:0002219 UBERON:0000015 ! surrounded by non-material anatomical boundary +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0034923 @@ -253973,14 +250580,13 @@ namespace: uberon def: "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other." [CARO:0020000] subset: common_anatomy xref: CARO:0020000 -xref: FBbt:00007276 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000465 {source="CARO"} ! material anatomical entity -relationship: composed_primarily_of UBERON:0000061 ! anatomical structure relationship: has_component UBERON:0000061 {minCardinality="2"} ! anatomical structure -relationship: has_quality PATO:0010001 ! disconnected -relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 ! Fungi +relationship: RO:0000086 PATO:0010001 ! has quality disconnected +relationship: RO:0002473 UBERON:0000061 ! composed primarily of anatomical structure +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0034925 @@ -253989,11 +250595,11 @@ namespace: uberon def: "A collection of anatomical structures that are alike in terms of their morphology or developmental origin." [http://orcid.org/0000-0002-6601-2165] subset: common_anatomy is_a: UBERON:0000465 ! material anatomical entity -relationship: has_member UBERON:0000061 ! anatomical structure -relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 ! Fungi -property_value: editor_note "resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected" xsd:string +relationship: RO:0002351 UBERON:0000061 ! has member anatomical structure +property_value: IAO:0000116 "resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0034926 @@ -254001,12 +250607,11 @@ name: anatomical row namespace: uberon def: "An anatomical collection that is arranged in a line." [http://orcid.org/0000-0002-6601-2165] subset: common_anatomy -xref: FBbt:00100152 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0034925 ! anatomical collection -relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 ! Fungi -property_value: editor_note "resolve if this should be a subclass of or merged with aligned anatomical group." xsd:string +property_value: IAO:0000116 "resolve if this should be a subclass of or merged with aligned anatomical group." xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0034928 @@ -254017,8 +250622,8 @@ synonym: "dorsum penis" EXACT [FMA:TA] xref: FMA:19623 is_a: UBERON:0036215 ! anatomical surface region intersection_of: UBERON:0036215 ! anatomical surface region -intersection_of: in_dorsal_side_of UBERON:0000989 ! penis -relationship: in_dorsal_side_of UBERON:0000989 ! penis +intersection_of: BSPO:0015101 UBERON:0000989 ! penis +relationship: BSPO:0015101 UBERON:0000989 ! penis relationship: part_of UBERON:0000989 ! penis [Term] @@ -254055,8 +250660,8 @@ namespace: uberon def: "Any organ component layer that consists of smooth muscle tissue." [http://orcid.org/0000-0002-6601-2165] is_a: UBERON:0018260 ! layer of muscle tissue intersection_of: UBERON:0004923 ! organ component layer -intersection_of: composed_primarily_of UBERON:0001135 ! smooth muscle tissue -relationship: composed_primarily_of UBERON:0001135 ! smooth muscle tissue +intersection_of: RO:0002473 UBERON:0001135 ! composed primarily of smooth muscle tissue +relationship: RO:0002473 UBERON:0001135 ! composed primarily of smooth muscle tissue [Term] id: UBERON:0034940 @@ -254068,8 +250673,8 @@ synonym: "blood sinus lumen" EXACT [ZFA:0007073] xref: ZFA:0007073 is_a: UBERON:0010161 ! lumen of blood vessel intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0006615 ! venous sinus -relationship: luminal_space_of UBERON:0006615 ! venous sinus +intersection_of: RO:0002572 UBERON:0006615 ! luminal space of venous sinus +relationship: RO:0002572 UBERON:0006615 ! luminal space of venous sinus [Term] id: UBERON:0034944 @@ -254116,8 +250721,8 @@ synonym: "respiratory gas" EXACT [] synonym: "respiratory system gas" EXACT [] is_a: UBERON:0034873 ! bodily gas intersection_of: UBERON:0034873 ! bodily gas -intersection_of: located_in UBERON:0001004 ! respiratory system -relationship: located_in UBERON:0001004 ! respiratory system +intersection_of: RO:0001025 UBERON:0001004 ! located in respiratory system +relationship: RO:0001025 UBERON:0001004 ! located in respiratory system [Term] id: UBERON:0034953 @@ -254155,8 +250760,8 @@ xref: SCTID:281695005 xref: Wikipedia:Paraganglion is_a: UBERON:0010001 {source="cjm"} ! cell cluster organ is_a: UBERON:0010313 ! neural crest-derived structure -relationship: composed_primarily_of CL:0000165 {source="Wikipedia"} ! neuroendocrine cell -property_value: editor_note "corresponding portion of CL needs fixed" xsd:string +relationship: RO:0002473 CL:0000165 {source="Wikipedia"} ! composed primarily of neuroendocrine cell +property_value: IAO:0000116 "corresponding portion of CL needs fixed" xsd:string [Term] id: UBERON:0034994 @@ -254254,9 +250859,10 @@ xref: EMAPA:37798 {source="MA:th"} xref: FMA:18157 xref: MA:0001151 is_a: UBERON:0003535 ! vagus X nerve trunk +is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0003535 ! vagus X nerve trunk -intersection_of: in_left_side_of UBERON:0001016 ! nervous system -relationship: in_left_side_of UBERON:0001016 ! nervous system +intersection_of: BSPO:0000120 UBERON:0001016 ! nervous system +relationship: BSPO:0000120 UBERON:0001016 ! nervous system [Term] id: UBERON:0035021 @@ -254269,9 +250875,10 @@ xref: EMAPA:37799 {source="MA:th"} xref: FMA:18151 xref: MA:0001152 is_a: UBERON:0003535 ! vagus X nerve trunk +is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0003535 ! vagus X nerve trunk -intersection_of: in_right_side_of UBERON:0001016 ! nervous system -relationship: in_right_side_of UBERON:0001016 ! nervous system +intersection_of: BSPO:0000121 UBERON:0001016 ! nervous system +relationship: BSPO:0000121 UBERON:0001016 ! nervous system [Term] id: UBERON:0035034 @@ -254316,8 +250923,8 @@ synonym: "hemorrhoidal artery" EXACT [] xref: SCTID:277967008 is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0001052 ! rectum -relationship: supplies UBERON:0001052 ! rectum +intersection_of: RO:0002178 UBERON:0001052 ! supplies rectum +relationship: RO:0002178 UBERON:0001052 ! supplies rectum [Term] id: UBERON:0035044 @@ -254328,8 +250935,8 @@ xref: NLX:152611 is_a: UBERON:0011215 ! central nervous system cell part cluster is_a: UBERON:0022303 ! nervous system cell part layer intersection_of: UBERON:0022303 ! nervous system cell part layer -intersection_of: immediately_deep_to UBERON:0022318 ! olfactory cortex layer 2 -relationship: immediately_deep_to UBERON:0022318 ! olfactory cortex layer 2 +intersection_of: BSPO:0001107 UBERON:0022318 ! olfactory cortex layer 2 +relationship: BSPO:0001107 UBERON:0022318 ! olfactory cortex layer 2 relationship: overlaps UBERON:0014283 {source="NIFSTD"} ! piriform cortex layer 3 relationship: part_of UBERON:0002894 {source="nlx"} ! olfactory cortex @@ -254348,7 +250955,6 @@ intersection_of: part_of UBERON:0001044 ! saliva-secreting gland id: UBERON:0035050 name: excretory duct namespace: uberon -xref: BTO:0006341 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} is_a: UBERON:0000058 ! duct [Term] @@ -254369,6 +250975,7 @@ def: "A duct made up of simple tubular epithelium that is part of an eccrine swe synonym: "ductal part of eccrine sweat gland" EXACT [FMA:70617] xref: FMA:70617 is_a: UBERON:0000058 ! duct +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000058 ! duct intersection_of: part_of UBERON:0000423 ! eccrine sweat gland relationship: part_of UBERON:0000423 ! eccrine sweat gland @@ -254380,21 +250987,11 @@ namespace: uberon synonym: "ductal part of apocrine sweat gland" EXACT [FMA:70643] xref: FMA:70643 is_a: UBERON:0000058 ! duct +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000058 ! duct intersection_of: part_of UBERON:0000382 ! apocrine sweat gland relationship: part_of UBERON:0000382 ! apocrine sweat gland -[Term] -id: UBERON:0035075 -name: thymus subunit -namespace: uberon -synonym: "lobe or lobule of thymus" RELATED [] -xref: FMA:71193 -is_a: UBERON:0000063 ! organ subunit -intersection_of: UBERON:0000063 ! organ subunit -intersection_of: part_of UBERON:0002046 ! thyroid gland -relationship: part_of UBERON:0002046 ! thyroid gland - [Term] id: UBERON:0035083 name: transverse process-bearing vertebra @@ -254414,8 +251011,8 @@ namespace: uberon def: "A post-anal tail that attaches outside the tail." [http://orcid.org/0000-0002-6601-2165] is_a: UBERON:0003665 ! post-anal tail muscle intersection_of: UBERON:0003665 ! post-anal tail muscle -intersection_of: attaches_to UBERON:0010742 ! bone of pelvic complex -relationship: attaches_to UBERON:0010742 ! bone of pelvic complex +intersection_of: RO:0002371 UBERON:0010742 ! attached to bone of pelvic complex +relationship: RO:0002371 UBERON:0010742 ! attached to bone of pelvic complex [Term] id: UBERON:0035102 @@ -254441,9 +251038,9 @@ xref: UMLS:C0446824 xref: Wikipedia:Plantar_nerve is_a: UBERON:0003431 ! leg nerve intersection_of: UBERON:0001021 ! nerve -intersection_of: innervates UBERON:0008338 ! plantar part of pes -relationship: branching_part_of UBERON:0001323 ! tibial nerve -relationship: innervates UBERON:0008338 ! plantar part of pes +intersection_of: RO:0002134 UBERON:0008338 ! innervates plantar part of pes +relationship: RO:0002134 UBERON:0008338 ! innervates plantar part of pes +relationship: RO:0002380 UBERON:0001323 ! branching part of tibial nerve [Term] id: UBERON:0035118 @@ -254454,9 +251051,9 @@ synonym: "digestive tract contents" EXACT OMO:0003004 [] synonym: "ingested material entity" RELATED [] is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: located_in UBERON:0006909 ! lumen of digestive tract -relationship: located_in UBERON:0006909 ! lumen of digestive tract -property_value: editor_note "Note that we treat any material entity that is ingested as an anatomical structure by defintion, although this may be expanding the CARO usage somewhat" xsd:string +intersection_of: RO:0001025 UBERON:0006909 ! located in lumen of digestive tract +relationship: RO:0001025 UBERON:0006909 ! located in lumen of digestive tract +property_value: IAO:0000116 "Note that we treat any material entity that is ingested as an anatomical structure by defintion, although this may be expanding the CARO usage somewhat" xsd:string [Term] id: UBERON:0035128 @@ -254467,10 +251064,10 @@ xref: EMAPA:32631 is_a: UBERON:0010883 ! forelimb cartilage element is_a: UBERON:0015064 ! autopod cartilage intersection_of: UBERON:0015063 ! autopod endochondral element -intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue intersection_of: part_of UBERON:0002398 ! manus -relationship: develops_from UBERON:0009523 {source="EMAPA-modified"} ! mesenchyme of handplate +intersection_of: RO:0002473 UBERON:0002418 ! composed primarily of cartilage tissue relationship: part_of UBERON:0002398 ! manus +relationship: RO:0002202 UBERON:0009523 {source="EMAPA-modified"} ! develops from mesenchyme of handplate [Term] id: UBERON:0035129 @@ -254481,10 +251078,10 @@ xref: EMAPA:32657 is_a: UBERON:0010885 ! hindlimb cartilage element is_a: UBERON:0015064 ! autopod cartilage intersection_of: UBERON:0015063 ! autopod endochondral element -intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue intersection_of: part_of UBERON:0002387 ! pes -relationship: develops_from UBERON:0003328 {source="EMAPA-modified"} ! mesenchyme of footplate +intersection_of: RO:0002473 UBERON:0002418 ! composed primarily of cartilage tissue relationship: part_of UBERON:0002387 ! pes +relationship: RO:0002202 UBERON:0003328 {source="EMAPA-modified"} ! develops from mesenchyme of footplate [Term] id: UBERON:0035130 @@ -254499,11 +251096,12 @@ synonym: "ossicle element" BROAD [EMAPA:17824, Wikipedia:Auditory_ossicle] synonym: "ossicle element of ear" RELATED [] synonym: "ossicle element of inner ear" RELATED [] synonym: "ossicular chain element" RELATED OMO:0003004 [] +is_a: UBERON:0010313 ! neural crest-derived structure is_a: UBERON:0010363 ! endochondral element -relationship: contributes_to_morphology_of UBERON:0001756 ! middle ear -relationship: develops_from UBERON:0003099 {source="PMID:11237469", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! cranial neural crest relationship: part_of UBERON:0001756 {source="MA"} ! middle ear relationship: part_of UBERON:0008895 {source="PMID:11523816"} ! splanchnocranium +relationship: RO:0002202 UBERON:0003099 {source="PMID:11237469", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! develops from cranial neural crest +relationship: RO:0002433 UBERON:0001756 ! contributes to morphology of middle ear [Term] id: UBERON:0035131 @@ -254514,7 +251112,7 @@ xref: EMAPA:35979 is_a: UBERON:0011004 ! pharyngeal arch cartilage is_a: UBERON:0035130 ! auditory ossicle endochondral element intersection_of: UBERON:0035130 ! auditory ossicle endochondral element -intersection_of: composed_primarily_of UBERON:0002418 ! cartilage tissue +intersection_of: RO:0002473 UBERON:0002418 ! composed primarily of cartilage tissue [Term] id: UBERON:0035132 @@ -254524,8 +251122,8 @@ synonym: "ossicle pre-cartilage condensation" EXACT [EMAPA:35982] xref: EMAPA:35982 is_a: UBERON:0035130 ! auditory ossicle endochondral element intersection_of: UBERON:0035130 ! auditory ossicle endochondral element -intersection_of: composed_primarily_of UBERON:0005866 ! pre-cartilage condensation -relationship: composed_primarily_of UBERON:0005866 ! pre-cartilage condensation +intersection_of: RO:0002473 UBERON:0005866 ! composed primarily of pre-cartilage condensation +relationship: RO:0002473 UBERON:0005866 ! composed primarily of pre-cartilage condensation [Term] id: UBERON:0035159 @@ -254539,8 +251137,8 @@ xref: SCTID:261060002 xref: UMLS:C0489451 is_a: UBERON:0006984 ! anatomical surface intersection_of: UBERON:0006984 ! anatomical surface -intersection_of: surrounds UBERON:0000468 ! multicellular organism -relationship: surrounds UBERON:0000468 ! multicellular organism +intersection_of: RO:0002221 UBERON:0000468 ! surrounds multicellular organism +relationship: RO:0002221 UBERON:0000468 ! surrounds multicellular organism [Term] id: UBERON:0035165 @@ -254557,9 +251155,9 @@ xref: UMLS:C0227961 is_a: UBERON:0035480 ! surface of prostate intersection_of: UBERON:0036215 ! anatomical surface region intersection_of: bounding_layer_of UBERON:0002367 ! prostate gland -intersection_of: in_posterior_side_of UBERON:0002367 ! prostate gland +intersection_of: BSPO:0000122 UBERON:0002367 ! prostate gland disjoint_from: UBERON:0035523 {source="lexical"} ! anterior surface of prostate -relationship: in_posterior_side_of UBERON:0002367 ! prostate gland +relationship: BSPO:0000122 UBERON:0002367 ! prostate gland [Term] id: UBERON:0035174 @@ -254571,9 +251169,10 @@ xref: NCIT:C81285 xref: SCTID:368570004 xref: UMLS:C0229298 is_a: UBERON:0001690 ! ear +is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0001690 ! ear -intersection_of: in_right_side_of UBERON:0000033 ! head -relationship: in_right_side_of UBERON:0000033 ! head +intersection_of: BSPO:0000121 UBERON:0000033 ! head +relationship: BSPO:0000121 UBERON:0000033 ! head [Term] id: UBERON:0035198 @@ -254602,8 +251201,8 @@ xref: SCTID:360629008 xref: UMLS:C1182571 is_a: UBERON:0005396 ! carotid artery segment intersection_of: UBERON:0005396 ! carotid artery segment -intersection_of: connecting_branch_of UBERON:0001532 ! internal carotid artery -relationship: connecting_branch_of UBERON:0001532 ! internal carotid artery +intersection_of: RO:0002252 UBERON:0001532 ! connecting branch of internal carotid artery +relationship: RO:0002252 UBERON:0001532 ! connecting branch of internal carotid artery [Term] id: UBERON:0035267 @@ -254618,6 +251217,7 @@ xref: SCTID:245394007 xref: UMLS:C0227546 xref: Wikipedia:Neck_of_gallbladder is_a: UBERON:0001560 ! neck of organ +is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0001560 ! neck of organ intersection_of: part_of UBERON:0002110 ! gallbladder relationship: part_of UBERON:0002110 ! gallbladder @@ -254632,9 +251232,10 @@ xref: NCIT:C81259 xref: SCTID:368592000 xref: UMLS:C0229299 is_a: UBERON:0001690 ! ear +is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0001690 ! ear -intersection_of: in_left_side_of UBERON:0000033 ! head -relationship: in_left_side_of UBERON:0000033 ! head +intersection_of: BSPO:0000120 UBERON:0000033 ! head +relationship: BSPO:0000120 UBERON:0000033 ! head [Term] id: UBERON:0035316 @@ -254647,6 +251248,7 @@ xref: FMA:19583 xref: NCIT:C13086 xref: SCTID:279682007 xref: UMLS:C0227963 +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0003893 ! capsule is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0003893 ! capsule @@ -254664,10 +251266,11 @@ xref: NCIT:C33474 xref: SCTID:283392005 xref: UMLS:C0226362 is_a: UBERON:0001191 ! common iliac artery +is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0001191 ! common iliac artery -intersection_of: in_right_side_of UBERON:0000468 ! multicellular organism -relationship: in_right_side_of UBERON:0000468 ! multicellular organism -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: BSPO:0000121 UBERON:0000468 ! multicellular organism +relationship: BSPO:0000121 UBERON:0000468 ! multicellular organism +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0035383 @@ -254679,11 +251282,12 @@ xref: NCIT:C12244 xref: SCTID:361937006 xref: UMLS:C0225486 is_a: UBERON:0000328 ! gut wall +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0000060 ! anatomical wall -intersection_of: in_lateral_side_of UBERON:0001728 ! nasopharynx +intersection_of: BSPO:0000126 UBERON:0001728 ! nasopharynx intersection_of: part_of UBERON:0001728 ! nasopharynx -relationship: in_lateral_side_of UBERON:0001728 ! nasopharynx +relationship: BSPO:0000126 UBERON:0001728 ! nasopharynx relationship: part_of UBERON:0001728 ! nasopharynx [Term] @@ -254698,8 +251302,8 @@ xref: SCTID:244216003 xref: UMLS:C0447038 is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery -intersection_of: connecting_branch_of UBERON:0001070 ! external carotid artery -relationship: connecting_branch_of UBERON:0001070 ! external carotid artery +intersection_of: RO:0002252 UBERON:0001070 ! connecting branch of external carotid artery +relationship: RO:0002252 UBERON:0001070 ! connecting branch of external carotid artery [Term] id: UBERON:0035401 @@ -254711,10 +251315,11 @@ xref: NCIT:C12243 xref: SCTID:361936002 xref: UMLS:C0225484 is_a: UBERON:0000328 ! gut wall +is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0000060 ! anatomical wall -intersection_of: in_posterior_side_of UBERON:0001728 ! nasopharynx +intersection_of: BSPO:0000122 UBERON:0001728 ! nasopharynx intersection_of: part_of UBERON:0001728 ! nasopharynx -relationship: in_posterior_side_of UBERON:0001728 ! nasopharynx +relationship: BSPO:0000122 UBERON:0001728 ! nasopharynx relationship: part_of UBERON:0001728 ! nasopharynx [Term] @@ -254724,8 +251329,8 @@ namespace: uberon def: "An artery that supplies the pituitary gland." [http://orcid.org/0000-0002-6601-2165] is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0000007 ! pituitary gland -relationship: supplies UBERON:0000007 ! pituitary gland +intersection_of: RO:0002178 UBERON:0000007 ! supplies pituitary gland +relationship: RO:0002178 UBERON:0000007 ! supplies pituitary gland [Term] id: UBERON:0035428 @@ -254750,6 +251355,7 @@ xref: NCIT:C94820 xref: SCTID:362002008 xref: UMLS:C0225789 xref: Wikipedia:Mediastinal_pleura +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0034944 ! zone of organ relationship: has_part UBERON:0003728 {source="FMA"} ! mediastinum relationship: part_of UBERON:0002400 {source="FMA"} ! parietal pleura @@ -254766,11 +251372,12 @@ xref: NCIT:C53131 xref: SCTID:69354005 xref: UMLS:C0226721 is_a: UBERON:0001146 ! suprarenal vein +is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0001146 ! suprarenal vein -intersection_of: in_right_side_of UBERON:0000468 ! multicellular organism -relationship: connected_to UBERON:0001072 ! posterior vena cava -relationship: in_right_side_of UBERON:0000468 ! multicellular organism -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: BSPO:0000121 UBERON:0000468 ! multicellular organism +relationship: BSPO:0000121 UBERON:0000468 ! multicellular organism +relationship: RO:0002170 UBERON:0001072 ! connected to posterior vena cava +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0035471 @@ -254785,9 +251392,9 @@ xref: UMLS:C0227610 is_a: UBERON:0036215 ! anatomical surface region intersection_of: UBERON:0036215 ! anatomical surface region intersection_of: bounding_layer_of UBERON:0002113 ! kidney -intersection_of: in_posterior_side_of UBERON:0002113 ! kidney +intersection_of: BSPO:0000122 UBERON:0002113 ! kidney relationship: bounding_layer_of UBERON:0002113 ! kidney -relationship: in_posterior_side_of UBERON:0002113 ! kidney +relationship: BSPO:0000122 UBERON:0002113 ! kidney [Term] id: UBERON:0035480 @@ -254817,11 +251424,12 @@ xref: SCTID:85087001 xref: UMLS:C0226709 xref: Wikipedia:Suprarenal_veins is_a: UBERON:0001146 ! suprarenal vein +is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0001146 ! suprarenal vein -intersection_of: in_left_side_of UBERON:0000468 ! multicellular organism -relationship: connected_to UBERON:0001142 ! left renal vein -relationship: in_left_side_of UBERON:0000468 ! multicellular organism -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: BSPO:0000120 UBERON:0000468 ! multicellular organism +relationship: BSPO:0000120 UBERON:0000468 ! multicellular organism +relationship: RO:0002170 UBERON:0001142 ! connected to left renal vein +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0035523 @@ -254838,8 +251446,8 @@ xref: UMLS:C0227960 is_a: UBERON:0035480 ! surface of prostate intersection_of: UBERON:0036215 ! anatomical surface region intersection_of: bounding_layer_of UBERON:0002367 ! prostate gland -intersection_of: in_anterior_side_of UBERON:0002367 ! prostate gland -relationship: in_anterior_side_of UBERON:0002367 ! prostate gland +intersection_of: BSPO:0000123 UBERON:0002367 ! prostate gland +relationship: BSPO:0000123 UBERON:0002367 ! prostate gland [Term] id: UBERON:0035529 @@ -254852,10 +251460,11 @@ xref: NCIT:C32957 xref: SCTID:283493001 xref: UMLS:C0226363 is_a: UBERON:0001191 ! common iliac artery +is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0001191 ! common iliac artery -intersection_of: in_left_side_of UBERON:0000468 ! multicellular organism -relationship: in_left_side_of UBERON:0000468 ! multicellular organism -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: BSPO:0000120 UBERON:0000468 ! multicellular organism +relationship: BSPO:0000120 UBERON:0000468 ! multicellular organism +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0035539 @@ -254872,11 +251481,11 @@ xref: UMLS:C0226294 is_a: UBERON:0003834 ! thoracic segment blood vessel is_a: UBERON:0004573 {source="FMA"} ! systemic artery intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0001043 ! esophagus -relationship: branching_part_of UBERON:0001515 {source="FMA"} ! thoracic aorta -relationship: connected_to UBERON:0002345 ! descending thoracic aorta -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: supplies UBERON:0001043 ! esophagus +intersection_of: RO:0002178 UBERON:0001043 ! supplies esophagus +relationship: RO:0002170 UBERON:0002345 ! connected to descending thoracic aorta +relationship: RO:0002178 UBERON:0001043 ! supplies esophagus +relationship: RO:0002380 UBERON:0001515 {source="FMA"} ! branching part of thoracic aorta +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0035545 @@ -254902,8 +251511,8 @@ xref: FMA:51797 xref: SCTID:149683007 is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein -intersection_of: drains UBERON:0001768 ! uvea -relationship: drains UBERON:0001768 ! uvea +intersection_of: RO:0002179 UBERON:0001768 ! drains uvea +relationship: RO:0002179 UBERON:0001768 ! drains uvea [Term] id: UBERON:0035548 @@ -254912,9 +251521,9 @@ namespace: uberon xref: SCTID:77852007 is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0001155 ! colon -relationship: supplies UBERON:0001155 ! colon -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +intersection_of: RO:0002178 UBERON:0001155 ! supplies colon +relationship: RO:0002178 UBERON:0001155 ! supplies colon +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI [Term] id: UBERON:0035549 @@ -254932,10 +251541,10 @@ synonym: "vasculature of skin" RELATED [FMA:225275] xref: FMA:225275 is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature -intersection_of: located_in UBERON:0002199 ! integument +intersection_of: RO:0001025 UBERON:0002199 ! located in integument relationship: capable_of_part_of GO:0001659 ! temperature homeostasis -relationship: located_in UBERON:0002199 ! integument -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0001025 UBERON:0002199 ! located in integument +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0035550 @@ -254963,8 +251572,8 @@ def: "The part of the circulatory system that lies deep beneath the subcutaneous synonym: "deep part of circulatory system" EXACT [] is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature -intersection_of: deep_to UBERON:0002199 ! integument -relationship: deep_to UBERON:0002199 ! integument +intersection_of: BSPO:0000107 UBERON:0002199 ! integument +relationship: BSPO:0000107 UBERON:0002199 ! integument [Term] id: UBERON:0035552 @@ -254991,9 +251600,10 @@ def: "Any chamber of the left side of the heart." [http://orcid.org/0000-0002-66 xref: FMA:7166 xref: SCTID:362008007 is_a: UBERON:0004151 ! cardiac chamber +is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0004151 ! cardiac chamber -intersection_of: in_left_side_of UBERON:0000948 ! heart -relationship: in_left_side_of UBERON:0000948 ! heart +intersection_of: BSPO:0000120 UBERON:0000948 ! heart +relationship: BSPO:0000120 UBERON:0000948 ! heart [Term] id: UBERON:0035554 @@ -255003,9 +251613,10 @@ def: "Any chamber of the right side of the heart." [http://orcid.org/0000-0002-6 xref: FMA:7165 xref: SCTID:362007002 is_a: UBERON:0004151 ! cardiac chamber +is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0004151 ! cardiac chamber -intersection_of: in_right_side_of UBERON:0000948 ! heart -relationship: in_right_side_of UBERON:0000948 ! heart +intersection_of: BSPO:0000121 UBERON:0000948 ! heart +relationship: BSPO:0000121 UBERON:0000948 ! heart [Term] id: UBERON:0035555 @@ -255015,9 +251626,9 @@ is_a: UBERON:0010521 ! electroreceptor organ intersection_of: UBERON:0000062 ! organ intersection_of: capable_of GO:0050964 ! detection of electrical stimulus involved in electroception intersection_of: part_of UBERON:0002540 ! lateral line system -relationship: innervated_by UBERON:0008906 ! lateral line nerve relationship: part_of UBERON:0002540 ! lateral line system -property_value: editor_note "ensure pit organ classifies here" xsd:string +relationship: RO:0002005 UBERON:0008906 ! innervated_by lateral line nerve +property_value: IAO:0000116 "ensure pit organ classifies here" xsd:string [Term] id: UBERON:0035597 @@ -255041,6 +251652,8 @@ synonym: "cartilage of auditory canal" EXACT [FMA:61298] synonym: "cartilago meatus acustici" EXACT [FMA:TA] synonym: "external acoustic meatus cartilage" EXACT [FMA:61298] xref: FMA:61298 +is_a: UBERON:0004119 ! endoderm-derived structure +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0034944 ! zone of organ intersection_of: UBERON:0034944 ! zone of organ intersection_of: part_of UBERON:0001352 ! external acoustic meatus @@ -255057,11 +251670,11 @@ comment: Louveau et al (DOI:10.1038/nature14432) claim the discovery of lymphati synonym: "dural lymph vasculature" RELATED [] synonym: "dural lymph vessel" EXACT [] is_a: UBERON:0001473 ! lymphatic vessel +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0001473 ! lymphatic vessel -intersection_of: located_in UBERON:0002363 ! dura mater -relationship: located_in UBERON:0002363 ! dura mater +intersection_of: RO:0001025 UBERON:0002363 ! located in dura mater relationship: part_of UBERON:0010743 ! meningeal cluster -property_value: UBPROP:0000010 "while Louveau et al (DOI:10.1038/nature14432) state this is within the CNS (thus overturning dogma about the presence of lymphatics in the CNS), in this ontology the dura" xsd:string +relationship: RO:0001025 UBERON:0002363 ! located in dura mater [Term] id: UBERON:0035610 @@ -255069,14 +251682,15 @@ name: hair canal namespace: uberon def: "Tubular connection between the epidermal surface and the most distal part of the inner root sheath. Contains the hair shaft." [DOI:10.1016/j.cub.2008.12.005] is_a: UBERON:0004111 ! anatomical conduit +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0004111 ! anatomical conduit -intersection_of: conduit_for UBERON:0002074 ! hair shaft -intersection_of: connects UBERON:0001003 ! skin epidermis -intersection_of: connects UBERON:0005941 ! hair inner root sheath -relationship: conduit_for UBERON:0002074 ! hair shaft -relationship: connects UBERON:0001003 ! skin epidermis -relationship: connects UBERON:0005941 ! hair inner root sheath +intersection_of: RO:0002176 UBERON:0001003 ! connects skin epidermis +intersection_of: RO:0002176 UBERON:0005941 ! connects hair inner root sheath +intersection_of: RO:0002570 UBERON:0002074 ! conduit for hair shaft relationship: part_of UBERON:0000014 ! zone of skin +relationship: RO:0002176 UBERON:0001003 ! connects skin epidermis +relationship: RO:0002176 UBERON:0005941 ! connects hair inner root sheath +relationship: RO:0002570 UBERON:0002074 ! conduit for hair shaft [Term] id: UBERON:0035639 @@ -255110,8 +251724,8 @@ xref: MESH:D007823 xref: SCTID:307013006 is_a: UBERON:0001021 ! nerve intersection_of: UBERON:0001021 ! nerve -intersection_of: innervates UBERON:0001737 ! larynx -relationship: innervates UBERON:0001737 ! larynx +intersection_of: RO:0002134 UBERON:0001737 ! innervates larynx +relationship: RO:0002134 UBERON:0001737 ! innervates larynx [Term] id: UBERON:0035648 @@ -255121,11 +251735,11 @@ def: "Any nerve that innervates the pinna." [UBERON:cjm] synonym: "auricular nerve" EXACT [MA:0001232] xref: EMAPA:36513 xref: MA:0001232 -is_a: UBERON:0001021 ! nerve +is_a: UBERON:0011779 ! nerve of head region intersection_of: UBERON:0001021 ! nerve -intersection_of: innervates UBERON:0001757 ! pinna -relationship: branching_part_of UBERON:0001647 {source="FMA"} ! facial nerve -relationship: innervates UBERON:0001757 ! pinna +intersection_of: RO:0002134 UBERON:0001757 ! innervates pinna +relationship: RO:0002134 UBERON:0001757 ! innervates pinna +relationship: RO:0002380 UBERON:0001647 {source="FMA"} ! branching part of facial nerve [Term] id: UBERON:0035649 @@ -255137,8 +251751,8 @@ synonym: "penis nerve" EXACT [] xref: EMAPA:35057 is_a: UBERON:0001021 ! nerve intersection_of: UBERON:0001021 ! nerve -intersection_of: innervates UBERON:0000989 ! penis -relationship: innervates UBERON:0000989 ! penis +intersection_of: RO:0002134 UBERON:0000989 ! innervates penis +relationship: RO:0002134 UBERON:0000989 ! innervates penis [Term] id: UBERON:0035650 @@ -255151,9 +251765,9 @@ synonym: "clitoris nerve" EXACT [] xref: EMAPA:35044 is_a: UBERON:0001021 ! nerve intersection_of: UBERON:0001021 ! nerve -intersection_of: innervates UBERON:0002411 ! clitoris -relationship: innervates UBERON:0002411 ! clitoris -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002134 UBERON:0002411 ! innervates clitoris +relationship: RO:0002134 UBERON:0002411 ! innervates clitoris +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0035651 @@ -255161,11 +251775,12 @@ name: glans namespace: uberon xref: Wikipedia:Glans is_a: UBERON:0000063 ! organ subunit +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005156 ! reproductive structure union_of: UBERON:0001299 ! glans penis union_of: UBERON:0006653 ! glans clitoris -relationship: develops_from UBERON:0013238 ! future glans relationship: part_of UBERON:0003133 ! reproductive organ +relationship: RO:0002202 UBERON:0013238 ! develops from future glans [Term] id: UBERON:0035763 @@ -255178,9 +251793,9 @@ xref: EHDAA2:0004181 xref: FMA:9464 is_a: UBERON:0002553 ! anatomical cavity intersection_of: UBERON:0002553 ! anatomical cavity -intersection_of: luminal_space_of UBERON:0004151 ! cardiac chamber -relationship: luminal_space_of UBERON:0004151 ! cardiac chamber -relationship: surrounded_by UBERON:0002165 {source="FMA"} ! endocardium +intersection_of: RO:0002572 UBERON:0004151 ! luminal space of cardiac chamber +relationship: RO:0002219 UBERON:0002165 {source="FMA"} ! surrounded by endocardium +relationship: RO:0002572 UBERON:0004151 ! luminal space of cardiac chamber [Term] id: UBERON:0035764 @@ -255254,8 +251869,8 @@ xref: FMA:12241 xref: SCTID:304404008 is_a: UBERON:0002553 ! anatomical cavity intersection_of: UBERON:0002553 ! anatomical cavity -intersection_of: luminal_space_of UBERON:0005906 ! serous sac -relationship: luminal_space_of UBERON:0005906 ! serous sac +intersection_of: RO:0002572 UBERON:0005906 ! luminal space of serous sac +relationship: RO:0002572 UBERON:0005906 ! luminal space of serous sac [Term] id: UBERON:0035814 @@ -255266,8 +251881,8 @@ xref: SCTID:42267001 xref: ZFA:0005765 is_a: UBERON:0035818 ! visceral fat intersection_of: UBERON:0001013 ! adipose tissue -intersection_of: surrounds UBERON:0000948 ! heart -relationship: surrounds UBERON:0000948 ! heart +intersection_of: RO:0002221 UBERON:0000948 ! surrounds heart +relationship: RO:0002221 UBERON:0000948 ! surrounds heart [Term] id: UBERON:0035815 @@ -255278,7 +251893,7 @@ synonym: "intrathoracic fat" EXACT [DOI:10.5935/abc.20130138] is_a: UBERON:0035814 ! pericardial fat intersection_of: UBERON:0001013 ! adipose tissue intersection_of: adjacent_to UBERON:0002408 ! parietal serous pericardium -intersection_of: surrounds UBERON:0000948 ! heart +intersection_of: RO:0002221 UBERON:0000948 ! surrounds heart relationship: adjacent_to UBERON:0002408 ! parietal serous pericardium [Term] @@ -255288,8 +251903,8 @@ namespace: uberon def: "Any fat deposit surrounding a visceral organ." [UBERON:cjm] is_a: UBERON:0001013 ! adipose tissue intersection_of: UBERON:0001013 ! adipose tissue -intersection_of: surrounds UBERON:0000062 ! organ -relationship: surrounds UBERON:0000062 ! organ +intersection_of: RO:0002221 UBERON:0000062 ! surrounds organ +relationship: RO:0002221 UBERON:0000062 ! surrounds organ [Term] id: UBERON:0035819 @@ -255301,10 +251916,10 @@ xref: FMA:12267 xref: Wikipedia:Abdominopelvic_cavity is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0002417 ! abdominal segment of trunk intersection_of: part_of UBERON:0002323 ! coelemic cavity lumen -relationship: luminal_space_of UBERON:0002417 ! abdominal segment of trunk +intersection_of: RO:0002572 UBERON:0002417 ! luminal space of abdominal segment of trunk relationship: part_of UBERON:0002323 ! coelemic cavity lumen +relationship: RO:0002572 UBERON:0002417 ! luminal space of abdominal segment of trunk [Term] id: UBERON:0035820 @@ -255318,7 +251933,7 @@ is_a: UBERON:0002075 ! viscus is_a: UBERON:0005906 ! serous sac relationship: has_part UBERON:0001179 ! peritoneal cavity relationship: has_part UBERON:0002358 ! peritoneum -relationship: located_in UBERON:0003684 ! abdominal cavity +relationship: RO:0001025 UBERON:0003684 ! located in abdominal cavity [Term] id: UBERON:0035825 @@ -255376,21 +251991,6 @@ intersection_of: UBERON:0000958 ! medulla of organ intersection_of: part_of UBERON:0001233 ! right adrenal gland relationship: part_of UBERON:0001233 ! right adrenal gland -[Term] -id: UBERON:0035831 -name: costal diaphragm -namespace: uberon -def: "The domain of the diaphragm that is a thin domed sheet of muscle composed of a radial array of myofibers extending laterally from the ribs and medially to a central tendon." [PMID:23586979] -synonym: "costal part of diaphragm" EXACT [FMA:58277] -synonym: "pars costalis diaphragmatis" EXACT OMO:0003011 [FMA:TA] -xref: FMA:58277 -xref: SCTID:368048007 -is_a: UBERON:0000063 ! organ subunit -is_a: UBERON:0015212 ! lateral structure -relationship: attaches_to UBERON:0006670 ! central tendon of diaphragm -relationship: in_lateral_side_of UBERON:0001103 {source="PMID:23586979"} ! diaphragm -relationship: part_of UBERON:0001103 {source="PMID:23586979"} ! diaphragm - [Term] id: UBERON:0035927 name: sulcus of parietal lobe @@ -255416,9 +252016,9 @@ xref: FMA:18274 xref: SCTID:367722009 is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0001301 ! epididymis -relationship: location_of UBERON:0006530 {source="FMA"} ! seminal fluid -relationship: luminal_space_of UBERON:0001301 ! epididymis +intersection_of: RO:0002572 UBERON:0001301 ! luminal space of epididymis +relationship: RO:0001015 UBERON:0006530 {source="FMA"} ! location of seminal fluid +relationship: RO:0002572 UBERON:0001301 ! luminal space of epididymis [Term] id: UBERON:0035965 @@ -255430,10 +252030,11 @@ xref: BTO:0004378 xref: EMAPA:37987 {source="MA:th"} xref: FMA:67473 is_a: UBERON:0000060 ! anatomical wall +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0001981 ! blood vessel -relationship: composed_primarily_of UBERON:0004797 ! blood vessel layer relationship: part_of UBERON:0001981 ! blood vessel +relationship: RO:0002473 UBERON:0004797 ! composed primarily of blood vessel layer [Term] id: UBERON:0036072 @@ -255447,8 +252048,8 @@ is_a: UBERON:0009854 ! digestive tract diverticulum is_a: UBERON:0015833 ! foregut epithelium intersection_of: UBERON:0007499 ! epithelial sac intersection_of: part_of UBERON:0008947 ! respiratory primordium -relationship: develops_from UBERON:0007690 {source="EHDAA2"} ! early pharyngeal endoderm relationship: part_of UBERON:0008947 ! respiratory primordium +relationship: RO:0002202 UBERON:0007690 {source="EHDAA2"} ! develops from early pharyngeal endoderm [Term] id: UBERON:0036073 @@ -255456,11 +252057,12 @@ name: respiratory primordium mesenchyme namespace: uberon synonym: "respiratory primordium associated mesenchyme" EXACT [EHDAA2:0004071] xref: EHDAA2:0004071 +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0003104 ! mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0008947 ! respiratory primordium -relationship: develops_from UBERON:0004873 {source="EHDAA2"} ! splanchnopleure relationship: part_of UBERON:0008947 ! respiratory primordium +relationship: RO:0002202 UBERON:0004873 {source="EHDAA2"} ! develops from splanchnopleure [Term] id: UBERON:0036146 @@ -255481,15 +252083,16 @@ synonym: "cutaneous appendage follicle" EXACT [] synonym: "follicle" BROAD [] synonym: "skin follicle" EXACT [] is_a: UBERON:0000063 ! organ subunit +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000063 ! organ subunit -intersection_of: has_potential_to_develop_into UBERON:0000021 ! cutaneous appendage intersection_of: overlaps UBERON:0001003 ! skin epidermis intersection_of: overlaps UBERON:0002067 ! dermis intersection_of: part_of UBERON:0000014 ! zone of skin -relationship: has_potential_to_develop_into UBERON:0000021 ! cutaneous appendage +intersection_of: RO:0002387 UBERON:0000021 ! has potential to develop into cutaneous appendage relationship: overlaps UBERON:0001003 ! skin epidermis relationship: overlaps UBERON:0002067 ! dermis relationship: part_of UBERON:0000014 ! zone of skin +relationship: RO:0002387 UBERON:0000021 ! has potential to develop into cutaneous appendage [Term] id: UBERON:0036186 @@ -255499,7 +252102,7 @@ xref: FMA:83520 is_a: UBERON:0002521 ! elastic tissue is_a: UBERON:0011824 ! fibrous connective tissue intersection_of: UBERON:0011824 ! fibrous connective tissue -intersection_of: composed_primarily_of GO:0071953 ! elastic fiber +intersection_of: RO:0002473 GO:0071953 ! composed primarily of elastic fiber [Term] id: UBERON:0036214 @@ -255511,10 +252114,10 @@ xref: NCIT:C54188 xref: SCTID:245429006 is_a: UBERON:8410024 ! intestinal junction intersection_of: UBERON:0007651 ! anatomical junction -intersection_of: connects UBERON:0001052 ! rectum -intersection_of: connects UBERON:0001159 ! sigmoid colon -relationship: connects UBERON:0001052 ! rectum -relationship: connects UBERON:0001159 ! sigmoid colon +intersection_of: RO:0002176 UBERON:0001052 ! connects rectum +intersection_of: RO:0002176 UBERON:0001159 ! connects sigmoid colon +relationship: RO:0002176 UBERON:0001052 ! connects rectum +relationship: RO:0002176 UBERON:0001159 ! connects sigmoid colon [Term] id: UBERON:0036215 @@ -255526,9 +252129,9 @@ xref: AAO:0010270 xref: ZFA:0005594 is_a: UBERON:0000465 ! material anatomical entity relationship: bounding_layer_of UBERON:0000061 ! anatomical structure -relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 ! Fungi +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0036217 @@ -255538,9 +252141,8 @@ def: "A bodily fluid that is located in the coelom." [https://github.com/obophen xref: BTO:0001708 is_a: UBERON:0006314 ! bodily fluid intersection_of: UBERON:0006314 ! bodily fluid -intersection_of: located_in UBERON:0011997 ! coelom -relationship: located_in UBERON:0011997 ! coelom -property_value: UBPROP:0000009 "he coelomic fluid serves several functions; it acts as a hydroskeleton, it allows free movement and growth of internal organs, it serves for transport of gases, nutrients and waste products between different parts of the body, it allows storage of sperm and eggs during maturation and it acts as a reservoir for waste [Wikipedia:Coelom#Coelomic_fluid]" xsd:string +intersection_of: RO:0001025 UBERON:0011997 ! located in coelom +relationship: RO:0001025 UBERON:0011997 ! located in coelom [Term] id: UBERON:0036224 @@ -255570,13 +252172,13 @@ def: "A notochord that has persisted beyond the embryonic stage." [UBERON:cjm] is_a: UBERON:0002328 ! notochord intersection_of: UBERON:0002328 ! notochord intersection_of: part_of UBERON:0009953 ! post-embryonic organism -relationship: never_in_taxon NCBITaxon:32524 ! Amniota relationship: part_of UBERON:0009953 ! post-embryonic organism -relationship: present_in_taxon NCBITaxon:118072 -relationship: present_in_taxon NCBITaxon:7737 -relationship: present_in_taxon NCBITaxon:7746 -relationship: present_in_taxon NCBITaxon:7878 -relationship: present_in_taxon NCBITaxon:8292 +property_value: RO:0002161 NCBITaxon:32524 +property_value: RO:0002175 NCBITaxon:118072 +property_value: RO:0002175 NCBITaxon:7737 +property_value: RO:0002175 NCBITaxon:7746 +property_value: RO:0002175 NCBITaxon:7878 +property_value: RO:0002175 NCBITaxon:8292 [Term] id: UBERON:0036243 @@ -255585,11 +252187,10 @@ namespace: uberon def: "Fluid that lines the vaginal walls that consists of multiple secretions that collect in the vagina from different glands." [http://www.bumc.bu.edu/sexualmedicine/physicianinformation/female-genital-anatomy/] synonym: "vaginal discharge" RELATED [] synonym: "vaginal secretion" RELATED [] -xref: BTO:0003084 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} is_a: UBERON:0006314 ! bodily fluid intersection_of: UBERON:0006314 ! bodily fluid -intersection_of: located_in UBERON:0000996 ! vagina -relationship: located_in UBERON:0000996 ! vagina +intersection_of: RO:0001025 UBERON:0000996 ! located in vagina +relationship: RO:0001025 UBERON:0000996 ! located in vagina [Term] id: UBERON:0036244 @@ -255603,7 +252204,7 @@ is_a: UBERON:0007779 ! transudate intersection_of: UBERON:0007779 ! transudate intersection_of: filtered_through UBERON:0000042 ! serous membrane relationship: filtered_through UBERON:0000042 ! serous membrane -relationship: located_in UBERON:0005906 ! serous sac +relationship: RO:0001025 UBERON:0005906 ! located in serous sac [Term] id: UBERON:0036245 @@ -255614,6 +252215,7 @@ synonym: "lactiferous gland parenchyma" EXACT [] synonym: "mammary gland parenchyma" EXACT [] synonym: "parenchyma of lactiferous gland" EXACT [] is_a: UBERON:0000353 ! parenchyma +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000353 ! parenchyma intersection_of: part_of UBERON:0001911 ! mammary gland relationship: part_of UBERON:0001911 ! mammary gland @@ -255629,9 +252231,9 @@ synonym: "joint of auditory ossicles" EXACT [FMA:60063] xref: FMA:60063 is_a: UBERON:0002217 ! synovial joint intersection_of: UBERON:0002217 ! synovial joint -intersection_of: connects UBERON:0035130 ! auditory ossicle endochondral element -relationship: connects UBERON:0035130 ! auditory ossicle endochondral element +intersection_of: RO:0002176 UBERON:0035130 ! connects auditory ossicle endochondral element relationship: part_of UBERON:0000033 ! head +relationship: RO:0002176 UBERON:0035130 ! connects auditory ossicle endochondral element [Term] id: UBERON:0036253 @@ -255671,8 +252273,8 @@ synonym: "zygomaticotemporal branch of zygomatic nerve" EXACT [FMA:52972] xref: FMA:52972 xref: SCTID:280243001 xref: Wikipedia:Zygomaticotemporal_nerve -is_a: UBERON:0001021 ! nerve -relationship: branching_part_of UBERON:0000377 ! maxillary nerve +is_a: UBERON:0011779 ! nerve of head region +relationship: RO:0002380 UBERON:0000377 ! branching part of maxillary nerve [Term] id: UBERON:0036267 @@ -255681,8 +252283,8 @@ namespace: uberon xref: SCTID:279975006 is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein -intersection_of: drains UBERON:0000997 ! mammalian vulva -relationship: drains UBERON:0000997 ! mammalian vulva +intersection_of: RO:0002179 UBERON:0000997 ! drains mammalian vulva +relationship: RO:0002179 UBERON:0000997 ! drains mammalian vulva [Term] id: UBERON:0036268 @@ -255691,8 +252293,8 @@ namespace: uberon xref: SCTID:13152008 is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein -intersection_of: drains UBERON:0002355 ! pelvic region of trunk -relationship: drains UBERON:0002355 ! pelvic region of trunk +intersection_of: RO:0002179 UBERON:0002355 ! drains pelvic region of trunk +relationship: RO:0002179 UBERON:0002355 ! drains pelvic region of trunk [Term] id: UBERON:0036269 @@ -255704,8 +252306,8 @@ xref: EMAPA:30807 xref: SCTID:363673006 is_a: UBERON:0001981 ! blood vessel intersection_of: UBERON:0001981 ! blood vessel -intersection_of: connected_to UBERON:0000989 ! penis -relationship: connected_to UBERON:0000989 ! penis +intersection_of: RO:0002170 UBERON:0000989 ! connected to penis +relationship: RO:0002170 UBERON:0000989 ! connected to penis [Term] id: UBERON:0036285 @@ -255738,8 +252340,8 @@ namespace: uberon xref: FMA:9560 is_a: UBERON:0036285 ! wall of left ventricle intersection_of: UBERON:0004784 ! heart ventricle wall -intersection_of: in_anterior_side_of UBERON:0002084 ! heart left ventricle -relationship: in_anterior_side_of UBERON:0002084 ! heart left ventricle +intersection_of: BSPO:0000123 UBERON:0002084 ! heart left ventricle +relationship: BSPO:0000123 UBERON:0002084 ! heart left ventricle relationship: part_of UBERON:0036285 {source="FMA"} ! wall of left ventricle [Term] @@ -255748,10 +252350,10 @@ name: anterior wall of right ventricle namespace: uberon def: "Region of wall of right ventricle which is continuous with the lateral and septal walls of right ventricle." [FMA:9553] xref: FMA:9553 -is_a: UBERON:0004784 ! heart ventricle wall +is_a: UBERON:0036286 ! wall of right ventricle intersection_of: UBERON:0004784 ! heart ventricle wall -intersection_of: in_anterior_side_of UBERON:0002080 ! heart right ventricle -relationship: in_anterior_side_of UBERON:0002080 ! heart right ventricle +intersection_of: BSPO:0000123 UBERON:0002080 ! heart right ventricle +relationship: BSPO:0000123 UBERON:0002080 ! heart right ventricle [Term] id: UBERON:0036290 @@ -255768,7 +252370,7 @@ id: UBERON:0036291 name: myocardium of anterior wall of right ventricle namespace: uberon xref: FMA:260877 -is_a: UBERON:0001083 ! myocardium of ventricle +is_a: UBERON:0006567 ! right ventricle myocardium intersection_of: UBERON:0002349 ! myocardium intersection_of: part_of UBERON:0036289 ! anterior wall of right ventricle relationship: part_of UBERON:0036289 ! anterior wall of right ventricle @@ -255796,7 +252398,7 @@ synonym: "renal pelvis plus ureter" EXACT [] xref: NCIT:C54419 is_a: UBERON:0000477 ! anatomical cluster relationship: part_of UBERON:0011143 {source="NCIT"} ! upper urinary tract -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0036301 @@ -255835,9 +252437,9 @@ namespace: uberon def: "An anatomical structure that is located along the line dividing two regions of an anatomical structure." [UBERON:cjm] subset: common_anatomy is_a: UBERON:0000061 ! anatomical structure -relationship: present_in_taxon NCBITaxon:33090 ! Viridiplantae -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 ! Fungi +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0036328 @@ -255871,6 +252473,7 @@ namespace: uberon synonym: "gallbladder wall" EXACT [FMA:14657] xref: FMA:14657 is_a: UBERON:0003697 ! abdominal wall +is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0002110 ! gallbladder relationship: part_of UBERON:0002110 {source="FMA"} ! gallbladder @@ -255904,6 +252507,7 @@ namespace: uberon synonym: "anal canal wall" EXACT [FMA:15704] xref: FMA:15704 is_a: UBERON:0001169 ! wall of large intestine +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0000159 ! anal canal intersection_of: part_of UBERON:0001007 ! digestive system @@ -255931,7 +252535,7 @@ is_a: UBERON:0009916 {source="FMA"} ! wall of ureter intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0001223 ! left ureter relationship: part_of UBERON:0001223 {source="FMA"} ! left ureter -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0036422 @@ -255953,6 +252557,7 @@ synonym: "wall of fallopian tube" EXACT [FMA:18303] synonym: "wall of oviduct" EXACT [FMA:18303] xref: FMA:18303 is_a: UBERON:0000060 {source="FMA"} ! anatomical wall +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0003889 ! fallopian tube @@ -255965,6 +252570,7 @@ namespace: uberon synonym: "urethral wall" EXACT [FMA:19779] xref: FMA:19779 is_a: UBERON:0000060 {source="FMA"} ! anatomical wall +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0000057 ! urethra relationship: part_of UBERON:0000057 {source="FMA"} ! urethra @@ -255976,6 +252582,7 @@ namespace: uberon synonym: "vaginal wall" EXACT [FMA:19971] xref: FMA:19971 is_a: UBERON:0000060 {source="FMA"} ! anatomical wall +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0000996 ! vagina @@ -256019,6 +252626,7 @@ namespace: uberon synonym: "wall of central canal" EXACT [FMA:242780] xref: FMA:242780 is_a: UBERON:0000060 ! anatomical wall +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005358 {source="FMA"} ! ventricle of nervous system intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0002291 ! central canal of spinal cord @@ -256030,6 +252638,7 @@ name: wall of ventricular system of brain namespace: uberon xref: FMA:242841 is_a: UBERON:0000060 ! anatomical wall +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005358 {source="FMA"} ! ventricle of nervous system intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0005282 ! ventricular system of brain @@ -256042,6 +252651,7 @@ namespace: uberon synonym: "eyeball wall" EXACT [FMA:58098] xref: FMA:58098 is_a: UBERON:0000060 {source="FMA"} ! anatomical wall +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0010230 ! eyeball of camera-type eye relationship: part_of UBERON:0010230 {source="FMA"} ! eyeball of camera-type eye @@ -256054,6 +252664,7 @@ synonym: "orbit wall" EXACT [FMA:63144] xref: FMA:63144 is_a: UBERON:0000060 ! anatomical wall is_a: UBERON:0000075 {source="FMA"} ! subdivision of skeletal system +is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0001697 ! orbit of skull relationship: part_of UBERON:0001697 {source="FMA"} ! orbit of skull @@ -256077,11 +252688,12 @@ def: "Wall of organ which has as its parts the endocardium, myocardium , epicard synonym: "cardiac wall" EXACT [FMA:7274] xref: FMA:7274 is_a: UBERON:0000060 {source="FMA"} ! anatomical wall +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0000948 ! heart -relationship: attaches_to UBERON:0002406 {source="FMA"} ! pericardial sac -relationship: attaches_to UBERON:0004292 {source="FMA"} ! cardiac skeleton relationship: part_of UBERON:0000948 {source="FMA"} ! heart +relationship: RO:0002371 UBERON:0002406 {source="FMA"} ! attached to pericardial sac +relationship: RO:0002371 UBERON:0004292 {source="FMA"} ! attached to cardiac skeleton [Term] id: UBERON:0037191 @@ -256090,6 +252702,7 @@ namespace: uberon synonym: "membranous labyrinth wall" EXACT [FMA:79837] xref: FMA:79837 is_a: UBERON:0000060 {source="FMA"} ! anatomical wall +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0001849 ! membranous labyrinth relationship: part_of UBERON:0001849 {source="FMA"} ! membranous labyrinth @@ -256101,6 +252714,7 @@ namespace: uberon synonym: "lacrimal ductal wall" EXACT [FMA:85375] xref: FMA:85375 is_a: UBERON:0000060 {source="FMA"} ! anatomical wall +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0001850 ! lacrimal drainage system relationship: part_of UBERON:0001850 {source="FMA"} ! lacrimal drainage system @@ -256179,11 +252793,11 @@ xref: FMA:14835 is_a: UBERON:0001637 ! artery is_a: UBERON:0015796 ! liver blood vessel intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0001152 ! cystic duct +intersection_of: RO:0002178 UBERON:0001152 ! supplies cystic duct relationship: part_of UBERON:0015482 {source="FMA", source="Wikipedia"} ! right hepatic artery -relationship: supplies UBERON:0001152 ! cystic duct -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +relationship: RO:0002178 UBERON:0001152 ! supplies cystic duct +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI [Term] id: UBERON:0039228 @@ -256192,9 +252806,9 @@ namespace: uberon xref: FMA:15395 is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein -intersection_of: drains UBERON:0001159 ! sigmoid colon -relationship: drains UBERON:0001159 ! sigmoid colon -relationship: tributary_of UBERON:0001215 {source="FMA"} ! inferior mesenteric vein +intersection_of: RO:0002179 UBERON:0001159 ! drains sigmoid colon +relationship: RO:0002179 UBERON:0001159 ! drains sigmoid colon +relationship: RO:0002376 UBERON:0001215 {source="FMA"} ! tributary of inferior mesenteric vein [Term] id: UBERON:0039261 @@ -256203,9 +252817,9 @@ namespace: uberon xref: FMA:70471 is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0001264 ! pancreas -relationship: connecting_branch_of UBERON:0001194 ! splenic artery -relationship: supplies UBERON:0001264 ! pancreas +intersection_of: RO:0002178 UBERON:0001264 ! supplies pancreas +relationship: RO:0002178 UBERON:0001264 ! supplies pancreas +relationship: RO:0002252 UBERON:0001194 ! connecting branch of splenic artery [Term] id: UBERON:0039355 @@ -256215,8 +252829,8 @@ synonym: "arteria urethralis" EXACT OMO:0003011 [A12.2.15.042] xref: FMA:20903 is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0000057 ! urethra -relationship: supplies UBERON:0000057 ! urethra +intersection_of: RO:0002178 UBERON:0000057 ! supplies urethra +relationship: RO:0002178 UBERON:0000057 ! supplies urethra [Term] id: UBERON:0039377 @@ -256226,9 +252840,9 @@ def: "A vein that drains the urethra." [UBERON:cjm] xref: FMA:21270 is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein -intersection_of: drains UBERON:0000057 ! urethra -relationship: drains UBERON:0000057 ! urethra -relationship: tributary_of UBERON:0018252 {source="FMA"} ! internal pudendal vein +intersection_of: RO:0002179 UBERON:0000057 ! drains urethra +relationship: RO:0002179 UBERON:0000057 ! drains urethra +relationship: RO:0002376 UBERON:0018252 {source="FMA"} ! tributary of internal pudendal vein [Term] id: UBERON:0039856 @@ -256238,9 +252852,9 @@ def: "Ovarian vein, each instance of which is a tributary of some inferior vena xref: FMA:14342 is_a: UBERON:0001145 {source="FMA"} ! ovarian vein intersection_of: UBERON:0001145 ! ovarian vein -intersection_of: drains UBERON:0002118 ! right ovary -relationship: drains UBERON:0002118 ! right ovary -relationship: tributary_of UBERON:0001072 {source="FMA"} ! posterior vena cava +intersection_of: RO:0002179 UBERON:0002118 ! drains right ovary +relationship: RO:0002179 UBERON:0002118 ! drains right ovary +relationship: RO:0002376 UBERON:0001072 {source="FMA"} ! tributary of posterior vena cava [Term] id: UBERON:0039857 @@ -256250,8 +252864,8 @@ def: "Ovarian vein, each instance of which is a tributary of some left renal ve xref: FMA:14347 is_a: UBERON:0001145 {source="FMA"} ! ovarian vein intersection_of: UBERON:0001145 ! ovarian vein -intersection_of: drains UBERON:0002119 ! left ovary -relationship: drains UBERON:0002119 ! left ovary +intersection_of: RO:0002179 UBERON:0002119 ! drains left ovary +relationship: RO:0002179 UBERON:0002119 ! drains left ovary [Term] id: UBERON:1000004 @@ -256263,8 +252877,8 @@ synonym: "external ear hair" RELATED [] is_a: UBERON:0014382 ! collection of hairs on head or neck intersection_of: UBERON:0010164 ! collection of hairs intersection_of: part_of UBERON:0001691 ! external ear -relationship: composed_primarily_of UBERON:0022279 ! strand of hair on external ear relationship: part_of UBERON:0001691 ! external ear +relationship: RO:0002473 UBERON:0022279 ! composed primarily of strand of hair on external ear [Term] id: UBERON:1000021 @@ -256283,8 +252897,8 @@ xref: UMLS:C0222084 {source="ncithesaurus:Skin_of_the_Face"} is_a: UBERON:0001084 ! skin of head intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0001456 ! face -relationship: dc-contributor https://orcid.org/0000-0002-9611-1279 relationship: part_of UBERON:0001456 ! face +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9611-1279 creation_date: 2012-02-05T05:23:01Z [Term] @@ -256303,8 +252917,9 @@ xref: NCIT:C33603 xref: SCTID:13515001 xref: UMLS:C0229691 {source="ncithesaurus:Splenic_Pulp"} is_a: UBERON:0000064 ! organ part +is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:1000024 {source="FMA"} ! parenchyma of spleen -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:1000024 @@ -256314,6 +252929,7 @@ def: "A parenchyma that is part of a spleen." [OBOL:automatic] synonym: "splenic parenchyma" EXACT [FMA:16029] xref: FMA:16029 is_a: UBERON:0000353 ! parenchyma +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000353 ! parenchyma intersection_of: part_of UBERON:0002106 ! spleen relationship: part_of UBERON:0002106 ! spleen @@ -256325,9 +252941,9 @@ namespace: uberon def: "An anatomical junction between two parts of the digestive tract." [https://orcid.org/0000-0002-7073-9172] is_a: UBERON:0007651 ! anatomical junction intersection_of: UBERON:0007651 ! anatomical junction -intersection_of: connects UBERON:0004921 ! subdivision of digestive tract -relationship: connects UBERON:0004921 ! subdivision of digestive tract -relationship: dc-contributor https://orcid.org/0000-0002-7073-9172 +intersection_of: RO:0002176 UBERON:0004921 ! connects subdivision of digestive tract +relationship: RO:0002176 UBERON:0004921 ! connects subdivision of digestive tract +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2021-02-05T11:19:31Z [Term] @@ -256346,9 +252962,9 @@ is_a: UBERON:0001714 ! cranial ganglion is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0001714 ! cranial ganglion intersection_of: extends_fibers_into UBERON:0008906 ! lateral line nerve -relationship: develops_from UBERON:0009128 ! lateral line placode relationship: extends_fibers_into UBERON:0008906 ! lateral line nerve relationship: part_of UBERON:0002540 ! lateral line system +relationship: RO:0002202 UBERON:0009128 ! develops from lateral line placode [Term] id: UBERON:2000175 @@ -256359,7 +252975,6 @@ synonym: "caudal lateral line nerve" EXACT [TAO:0000175] xref: ZFA:0000175 is_a: UBERON:0008906 ! lateral line nerve relationship: part_of UBERON:2001471 ! posterior lateral line system -property_value: UBPROP:0000004 "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/tao.owl"} [Term] id: UBERON:2000228 @@ -256370,7 +252985,6 @@ synonym: "llp" EXACT [TAO:0000228] xref: ZFA:0000228 is_a: UBERON:0000479 ! tissue relationship: part_of UBERON:0002540 ! lateral line system -property_value: UBPROP:0000004 "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/tao.owl"} [Term] id: UBERON:2000238 @@ -256381,7 +252995,6 @@ is_a: UBERON:0002265 ! olfactory tract intersection_of: UBERON:0002265 ! olfactory tract intersection_of: overlaps UBERON:0000204 ! ventral part of telencephalon relationship: overlaps UBERON:0000204 ! ventral part of telencephalon -property_value: UBPROP:0000004 "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/tao.owl"} [Term] id: UBERON:2000425 @@ -256392,7 +253005,6 @@ synonym: "rostral lateral line nerve" EXACT [TAO:0000425] xref: ZFA:0000425 is_a: UBERON:0008906 ! lateral line nerve relationship: part_of UBERON:2001468 ! anterior lateral line system -property_value: UBPROP:0000004 "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/tao.owl"} [Term] id: UBERON:2000940 @@ -256403,9 +253015,8 @@ synonym: "neuromast posterior" EXACT [TAO:0000940] synonym: "neuromasts posterior" EXACT OMO:0003004 [TAO:0000940] xref: ZFA:0000940 is_a: UBERON:0008904 ! neuromast -relationship: develops_from UBERON:2001157 ! posterior lateral line primordium relationship: part_of UBERON:0006334 ! posterior lateral line -property_value: UBPROP:0000004 "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/tao.owl"} +relationship: RO:0002202 UBERON:2001157 ! develops from posterior lateral line primordium [Term] id: UBERON:2001053 @@ -256417,9 +253028,9 @@ xref: EFO:0003612 xref: TAO:0001053 xref: ZFA:0001053 is_a: UBERON:0004573 ! systemic artery -relationship: develops_from UBERON:0003120 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="EHDAA2"} ! pharyngeal arch artery 3 -relationship: develops_from UBERON:0004363 ! pharyngeal arch artery relationship: part_of UBERON:0001530 {source="EHDAA2"} ! common carotid artery plus branches +relationship: RO:0002202 UBERON:0003120 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="EHDAA2"} ! develops from pharyngeal arch artery 3 +relationship: RO:0002202 UBERON:0004363 ! develops from pharyngeal arch artery [Term] id: UBERON:2001073 @@ -256427,7 +253038,6 @@ name: axial vasculature namespace: uberon xref: ZFA:0001073 is_a: UBERON:0002049 ! vasculature -property_value: UBPROP:0000004 "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/tao.owl"} [Term] id: UBERON:2001156 @@ -256437,7 +253047,6 @@ xref: ZFA:0001156 is_a: UBERON:0003067 ! dorsolateral placode disjoint_from: UBERON:2001316 {source="lexical"} ! anterior lateral line placode relationship: part_of UBERON:2001471 ! posterior lateral line system -property_value: UBPROP:0000004 "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/tao.owl"} [Term] id: UBERON:2001157 @@ -256448,9 +253057,8 @@ synonym: "posterior lateral line primordia" EXACT OMO:0003004 [TAO:0001157] xref: ZFA:0001157 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:2000228 ! lateral line primordium -relationship: develops_from UBERON:2001156 ! posterior lateral line placode relationship: part_of UBERON:2001471 ! posterior lateral line system -property_value: UBPROP:0000004 "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/tao.owl"} +relationship: RO:0002202 UBERON:2001156 ! develops from posterior lateral line placode [Term] id: UBERON:2001269 @@ -256475,8 +253083,7 @@ def: "The posterior lateral line ganglion develops from a cranial ectodermal pla xref: ZFA:0001314 is_a: UBERON:2000120 ! lateral line ganglion disjoint_from: UBERON:2001391 {source="lexical"} ! anterior lateral line ganglion -relationship: develops_from UBERON:2001156 ! posterior lateral line placode -property_value: UBPROP:0000004 "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/tao.owl"} +relationship: RO:0002202 UBERON:2001156 ! develops from posterior lateral line placode [Term] id: UBERON:2001316 @@ -256494,7 +253101,6 @@ is_a: UBERON:0003067 ! dorsolateral placode intersection_of: UBERON:0003067 ! dorsolateral placode intersection_of: part_of UBERON:2001468 ! anterior lateral line system relationship: part_of UBERON:2001468 ! anterior lateral line system -property_value: UBPROP:0000001 "Lateral line placode that gives rise to the anterior lateral line nerve[XAO:0004221, XAO:EJS]." xsd:string {source="XAO:EJS"} [Term] id: UBERON:2001389 @@ -256536,10 +253142,9 @@ id: UBERON:2001431 name: primitive olfactory epithelium namespace: uberon xref: ZFA:0001431 -is_a: UBERON:0000483 ! epithelium is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010371 ! ecto-epithelium relationship: part_of UBERON:0003050 ! olfactory placode -property_value: UBPROP:0000004 "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/tao.owl"} [Term] id: UBERON:2001457 @@ -256551,7 +253156,6 @@ is_a: UBERON:0007844 ! cartilage element intersection_of: UBERON:0007844 ! cartilage element intersection_of: part_of UBERON:0002090 ! postcranial axial skeleton relationship: part_of UBERON:0002090 ! postcranial axial skeleton -property_value: UBPROP:0000004 "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/tao.owl"} [Term] id: UBERON:2001468 @@ -256575,8 +253179,8 @@ xref: ZFA:0001470 is_a: UBERON:0010202 ! lateral line intersection_of: UBERON:0010202 ! lateral line intersection_of: part_of UBERON:2001468 ! anterior lateral line system -relationship: develops_from UBERON:2005117 ! anterior lateral line primordium relationship: part_of UBERON:2001468 ! anterior lateral line system +relationship: RO:0002202 UBERON:2005117 ! develops from anterior lateral line primordium [Term] id: UBERON:2001471 @@ -256585,7 +253189,6 @@ namespace: uberon def: "The posterior lateral line system develops from cranial ectodermal placodes, situated behind the ear, that give rise to both the neuromasts and the posterior lateral line sensory nerves that innervate the neuromasts. The posterior lateral line system consists of small sensory patches (neuromasts) located superficially on the skin or just under the skin in fluid-filled canals on the head of all fishes and most amphibians. The neuromasts are innervated by several lateral line nerves, which project primarily to the hindbrain. The posterior mechanosensory lateral line system is stimulated by local water displacements and vibrations, and detects propulsion of the fish through the water, as well as facilitating shoaling, prey capture, and predator and obstacle avoidance." [ZFIN:curator] xref: ZFA:0001471 is_a: UBERON:0002540 ! lateral line system -property_value: UBPROP:0000004 "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/tao.owl"} [Term] id: UBERON:2001472 @@ -256596,7 +253199,6 @@ synonym: "neuromast anterior" EXACT [TAO:0001472] xref: ZFA:0001472 is_a: UBERON:0008904 ! neuromast relationship: part_of UBERON:2001470 ! anterior lateral line -property_value: UBPROP:0000004 "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/tao.owl"} [Term] id: UBERON:2005117 @@ -256607,7 +253209,6 @@ synonym: "anterior lateral line primordia" EXACT OMO:0003004 [TAO:0005117] xref: ZFA:0005117 is_a: UBERON:2000228 ! lateral line primordium relationship: part_of UBERON:2001468 ! anterior lateral line system -property_value: UBPROP:0000004 "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/tao.owl"} [Term] id: UBERON:2005227 @@ -256619,7 +253220,6 @@ synonym: "proto-neuromast" RELATED [TAO:0005227] xref: ZFA:0005227 is_a: UBERON:0000477 ! anatomical cluster relationship: part_of UBERON:0002540 ! lateral line system -property_value: UBPROP:0000004 "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/tao.owl"} [Term] id: UBERON:2005260 @@ -256636,8 +253236,7 @@ xref: Wikipedia:Capillary#Types xref: ZFA:0005260 is_a: UBERON:0001982 {source="FMA"} ! capillary is_a: UBERON:0004638 {source="ZFA"} ! blood vessel endothelium -property_value: editor_note "the ZFA class from which this was derived is not explicitly classified as a capillary - need to verify for taxon histology differences" xsd:string -property_value: UBPROP:0000001 "Blood vessel endothelium that has pores that allow passage small molecules and proteins[ZFA]." xsd:string +property_value: IAO:0000116 "the ZFA class from which this was derived is not explicitly classified as a capillary - need to verify for taxon histology differences" xsd:string [Term] id: UBERON:2007013 @@ -256646,7 +253245,6 @@ namespace: uberon def: "Non neural ectoderm that surrounds the presumptive neural plate and gives rise to neurogenic placodes." [ZFIN:curator] xref: ZFA:0007013 is_a: UBERON:0005497 ! non-neural ectoderm -property_value: UBPROP:0000004 "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/tao.owl"} [Term] id: UBERON:3000961 @@ -256658,7 +253256,6 @@ is_a: UBERON:0003102 ! surface structure intersection_of: UBERON:0003102 ! surface structure intersection_of: part_of UBERON:0002199 ! integument relationship: part_of UBERON:0002199 ! integument -property_value: UBPROP:0000004 "This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/aao.owl"} [Term] id: UBERON:3000972 @@ -256669,7 +253266,6 @@ is_a: UBERON:3000961 ! external integument structure intersection_of: UBERON:3000961 ! external integument structure intersection_of: part_of UBERON:0000033 ! head relationship: part_of UBERON:0000033 ! head -property_value: UBPROP:0000004 "This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/aao.owl"} [Term] id: UBERON:3000977 @@ -256680,7 +253276,6 @@ is_a: UBERON:3000961 ! external integument structure intersection_of: UBERON:3000961 ! external integument structure intersection_of: part_of UBERON:0002100 ! trunk relationship: part_of UBERON:0002100 ! trunk -property_value: UBPROP:0000004 "This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/aao.owl"} [Term] id: UBERON:3000981 @@ -256691,7 +253286,6 @@ is_a: UBERON:3000961 ! external integument structure intersection_of: UBERON:3000961 ! external integument structure intersection_of: part_of UBERON:0002101 ! limb relationship: part_of UBERON:0002101 ! limb -property_value: UBPROP:0000004 "This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/aao.owl"} [Term] id: UBERON:3000982 @@ -256702,7 +253296,6 @@ is_a: UBERON:3000961 ! external integument structure intersection_of: UBERON:3000961 ! external integument structure intersection_of: part_of UBERON:0007812 ! post-anal tail relationship: part_of UBERON:0007812 ! post-anal tail -property_value: UBPROP:0000004 "This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/aao.owl"} [Term] id: UBERON:3010200 @@ -256714,8 +253307,7 @@ intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0001004 ! respiratory system intersection_of: part_of UBERON:0002199 ! integument relationship: part_of UBERON:0002199 ! integument -property_value: editor_note "Modified from the original AAO source" xsd:string -property_value: UBPROP:0000004 "This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/aao.owl"} +property_value: IAO:0000116 "Modified from the original AAO source" xsd:string [Term] id: UBERON:3010706 @@ -256723,7 +253315,6 @@ name: lateral line nucleus namespace: uberon is_a: UBERON:0000064 ! organ part relationship: part_of UBERON:0002540 ! lateral line system -property_value: UBPROP:0000004 "This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/aao.owl"} [Term] id: UBERON:4000013 @@ -256735,8 +253326,8 @@ xref: VSAO:0000013 xref: XAO:0004039 is_a: UBERON:0004755 ! skeletal tissue intersection_of: UBERON:0004755 ! skeletal tissue -intersection_of: has_quality PATO:0002444 ! mineralized -relationship: has_quality PATO:0002444 ! mineralized +intersection_of: RO:0000086 PATO:0002444 ! has quality mineralized +relationship: RO:0000086 PATO:0002444 ! has quality mineralized [Term] id: UBERON:4000020 @@ -256745,7 +253336,6 @@ namespace: uberon def: "Extracellular matrix that is mineralized." [PSPUB:0000170] is_a: GO:0031012 ! extracellular matrix is_a: UBERON:0000479 ! tissue -property_value: UBPROP:0000004 "This class was sourced from an external ontology (vertebrate_skeletal_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/vsao.owl"} [Term] id: UBERON:4000115 @@ -256755,24 +253345,23 @@ def: "Bone tissue mineralized with hydroxyapatite." [PSPUB:0000170] is_a: UBERON:0002481 ! bone tissue is_a: UBERON:4000013 ! mineralized skeletal tissue intersection_of: UBERON:0002481 ! bone tissue -intersection_of: has_quality PATO:0002444 ! mineralized -relationship: develops_from UBERON:0008883 ! osteoid +intersection_of: RO:0000086 PATO:0002444 ! has quality mineralized relationship: has_part CHEBI:52255 relationship: has_part UBERON:4000020 ! mineralized extracellular matrix -property_value: UBPROP:0000004 "This class was sourced from an external ontology (vertebrate_skeletal_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/vsao.owl"} +relationship: RO:0002202 UBERON:0008883 ! develops from osteoid [Term] id: UBERON:4000118 name: cellular bone tissue namespace: uberon def: "Mineralized bone tissue that always includes non-terminally differentiated osteoblasts and osteocytes." [PSPUB:0000170] +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:4000115 ! mineralized bone tissue intersection_of: UBERON:4000115 ! mineralized bone tissue intersection_of: has_part CL:0000137 ! osteocyte intersection_of: has_part CL:0001040 ! non-terminally differentiated osteoblast relationship: has_part CL:0000137 ! osteocyte relationship: has_part CL:0001040 ! non-terminally differentiated osteoblast -property_value: UBPROP:0000004 "This class was sourced from an external ontology (vertebrate_skeletal_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" xsd:string {source="http://purl.obolibrary.org/obo/vsao.owl"} [Term] id: UBERON:4100000 @@ -256794,6 +253383,7 @@ synonym: "collum anatomicum humeri" EXACT OMO:0003011 [FMA:23356, FMA:TA] synonym: "humeral neck" EXACT [] xref: FMA:23356 xref: NCIT:C33164 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005055 ! zone of long bone is_a: UBERON:0018664 ! neck of bone element intersection_of: UBERON:0001560 ! neck of organ @@ -256820,8 +253410,8 @@ is_a: UBERON:0003413 ! pectoral appendage bud mesenchyme is_a: UBERON:0010328 ! limb bud mesenchyme intersection_of: UBERON:0010328 ! limb bud mesenchyme intersection_of: part_of UBERON:0005417 ! forelimb bud -relationship: dc-contributor https://orcid.org/0000-0003-3162-7490 relationship: part_of UBERON:0005417 ! forelimb bud +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3162-7490 [Term] id: UBERON:4300227 @@ -256832,8 +253422,8 @@ is_a: UBERON:0003412 ! pelvic appendage bud mesenchyme is_a: UBERON:0010328 ! limb bud mesenchyme intersection_of: UBERON:0010328 ! limb bud mesenchyme intersection_of: part_of UBERON:0005418 ! hindlimb bud -relationship: dc-contributor https://orcid.org/0000-0003-3162-7490 relationship: part_of UBERON:0005418 ! hindlimb bud +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-3162-7490 [Term] id: UBERON:5001466 @@ -256848,9 +253438,8 @@ is_a: UBERON:5002544 ! digit plus metapodial segment intersection_of: UBERON:5002544 ! digit plus metapodial segment intersection_of: part_of UBERON:0002387 ! pes relationship: has_part UBERON:0001466 ! pedal digit -relationship: has_skeleton UBERON:5101466 ! pedal digit digitopodial skeleton relationship: part_of UBERON:0002387 ! pes -property_value: IAO:0000232 "this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit." xsd:string {source="https://github.com/obophenotype/uberon/issues/458"} +relationship: RO:0002551 UBERON:5101466 ! has skeleton pedal digit digitopodial skeleton [Term] id: UBERON:5002389 @@ -256865,9 +253454,8 @@ is_a: UBERON:5002544 ! digit plus metapodial segment intersection_of: UBERON:5002544 ! digit plus metapodial segment intersection_of: part_of UBERON:0002102 ! forelimb relationship: has_part UBERON:0002389 ! manual digit -relationship: has_skeleton UBERON:5102389 ! manual digit digitopodial skeleton relationship: part_of UBERON:0002102 ! forelimb -property_value: IAO:0000232 "this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit." xsd:string {source="https://github.com/obophenotype/uberon/issues/458"} +relationship: RO:0002551 UBERON:5102389 ! has skeleton manual digit digitopodial skeleton [Term] id: UBERON:5002544 @@ -256880,11 +253468,10 @@ synonym: "digit digitopodial subdivision" EXACT [http://orcid.org/0000-0002-6601 synonym: "digit ray" EXACT [http://orcid.org/0000-0002-6601-2165] is_a: UBERON:0000475 ! organism subdivision intersection_of: UBERON:0000475 ! organism subdivision -intersection_of: has_skeleton UBERON:5102544 ! individual digit of digitopodial skeleton +intersection_of: RO:0002551 UBERON:5102544 ! has skeleton individual digit of digitopodial skeleton relationship: has_part UBERON:0002544 ! digit -relationship: has_skeleton UBERON:5102544 ! individual digit of digitopodial skeleton relationship: part_of UBERON:0012140 ! digitopodium region -property_value: IAO:0000232 "this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit." xsd:string {source="https://github.com/obophenotype/uberon/issues/458"} +relationship: RO:0002551 UBERON:5102544 ! has skeleton individual digit of digitopodial skeleton [Term] id: UBERON:5101466 @@ -256895,10 +253482,9 @@ synonym: "pedal digit" RELATED COMPARATIVE_PREFERRED [http://orcid.org/0000-0002 synonym: "pedal digit skeleton" RELATED [http://orcid.org/0000-0002-6601-2165] is_a: UBERON:5102544 ! individual digit of digitopodial skeleton intersection_of: UBERON:0010912 ! subdivision of skeleton -intersection_of: skeleton_of UBERON:5001466 ! pedal digit plus metapodial segment +intersection_of: RO:0002576 UBERON:5001466 ! skeleton of pedal digit plus metapodial segment relationship: part_of UBERON:5001466 ! pedal digit plus metapodial segment -relationship: skeleton_of UBERON:5001466 ! pedal digit plus metapodial segment -property_value: IAO:0000232 "this class represents a series of phalanges plus a metapodial element. In comparative anatomy terminology we would call this a 'digit', but the label 'digit' is sometimes used to exclude metapodials and to include soft tissue. This series of elements is hypothesized to be homologous to radials." xsd:string +relationship: RO:0002576 UBERON:5001466 ! skeleton of pedal digit plus metapodial segment [Term] id: UBERON:5102389 @@ -256909,10 +253495,9 @@ synonym: "manual digit" RELATED COMPARATIVE_PREFERRED [http://orcid.org/0000-000 synonym: "manual digit skeleton" RELATED [http://orcid.org/0000-0002-6601-2165] is_a: UBERON:5102544 ! individual digit of digitopodial skeleton intersection_of: UBERON:0010912 ! subdivision of skeleton -intersection_of: skeleton_of UBERON:5002389 ! manual digit plus metapodial segment +intersection_of: RO:0002576 UBERON:5002389 ! skeleton of manual digit plus metapodial segment relationship: part_of UBERON:5002389 ! manual digit plus metapodial segment -relationship: skeleton_of UBERON:5002389 ! manual digit plus metapodial segment -property_value: IAO:0000232 "this class represents a series of phalanges plus a metapodial element. In comparative anatomy terminology we would call this a 'digit', but the label 'digit' is sometimes used to exclude metapodials and to include soft tissue. This series of elements is hypothesized to be homologous to radials." xsd:string +relationship: RO:0002576 UBERON:5002389 ! skeleton of manual digit plus metapodial segment [Term] id: UBERON:5102544 @@ -256921,13 +253506,13 @@ namespace: uberon def: "A subdivision of the skeleton of the autopod consisting of the phalanges of a single digit plus the associated metapodial element." [http://orcid.org/0000-0002-6601-2165] synonym: "digit" RELATED COMPARATIVE_PREFERRED [http://orcid.org/0000-0002-6601-2165] synonym: "digit skeleton" RELATED [http://orcid.org/0000-0002-6601-2165] +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010712 ! limb skeleton subdivision intersection_of: UBERON:0010912 ! subdivision of skeleton -intersection_of: skeleton_of UBERON:5002544 ! digit plus metapodial segment +intersection_of: RO:0002576 UBERON:5002544 ! skeleton of digit plus metapodial segment relationship: part_of UBERON:0012150 ! skeleton of digitopodium relationship: part_of UBERON:5002544 ! digit plus metapodial segment -relationship: skeleton_of UBERON:5002544 ! digit plus metapodial segment -property_value: IAO:0000232 "this class represents a series of phalanges plus a metapodial element. In comparative anatomy terminology we would call this a 'digit', but the label 'digit' is sometimes used to exclude metapodials and to include soft tissue. This series of elements is hypothesized to be homologous to radials." xsd:string +relationship: RO:0002576 UBERON:5002544 ! skeleton of digit plus metapodial segment [Term] id: UBERON:6000002 @@ -256935,16 +253520,14 @@ name: arthropod tagma namespace: uberon def: "One of the main divisions of the whole organism of arthropods formed from groups of segments." [doi:10.1016/B978-0-12-385026-3.00024-3] comment: Strictly speaking the term "tagma" cam be used for any metameric organism, however we follow the common usage which is to restrict the term to arthropods. -xref: FBbt:00000002 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0011676 ! subdivision of organism along main body axis -relationship: never_in_taxon NCBITaxon:7742 ! Vertebrata -relationship: only_in_taxon NCBITaxon:6656 ! Arthropoda +relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda +property_value: RO:0002161 NCBITaxon:7742 [Term] id: UBERON:6000004 name: panarthropod head namespace: uberon -xref: FBbt:00000004 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000033 ! head intersection_of: UBERON:0000033 ! head intersection_of: part_of NCBITaxon:88770 ! Panarthropoda @@ -256955,7 +253538,6 @@ id: UBERON:6000137 name: embryonic tagma namespace: uberon def: "Any tagma (UBERON:6000002) that is part of some embryo (UBERON:6000052)." [FBC:auto_generated_definition] -xref: FBbt:00000137 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:6000002 ! arthropod tagma intersection_of: UBERON:6000002 ! arthropod tagma intersection_of: part_of UBERON:0000922 ! embryo @@ -256966,7 +253548,6 @@ id: UBERON:6001728 name: insect larval tagma namespace: uberon def: "Any tagma (UBERON:6000002) that is part of some larva (UBERON:6001727)." [FBC:auto_generated_definition] -xref: FBbt:00001728 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:6000002 ! arthropod tagma intersection_of: UBERON:6000002 ! arthropod tagma intersection_of: part_of UBERON:0002548 ! larva @@ -256977,13 +253558,12 @@ id: UBERON:6001730 name: insect larval head namespace: uberon def: "Any head that is part of some larva." [FBC:auto_generated_definition] -xref: FBbt:00001730 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000033 ! head intersection_of: UBERON:0000033 ! head -intersection_of: only_in_taxon NCBITaxon:50557 ! Insecta intersection_of: part_of UBERON:0002548 ! larva -relationship: only_in_taxon NCBITaxon:50557 ! Insecta +intersection_of: RO:0002160 NCBITaxon:50557 ! only in taxon Insecta relationship: part_of UBERON:0002548 ! larva +relationship: RO:0002160 NCBITaxon:50557 ! only in taxon Insecta [Term] id: UBERON:6002639 @@ -256991,20 +253571,18 @@ name: insect larval sense organ namespace: uberon def: "Any sense organ that is part of some larva." [FBC:auto_generated_definition] synonym: "larval sense organ" EXACT [] -xref: FBbt:00002639 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000020 ! sense organ intersection_of: UBERON:0000020 ! sense organ -intersection_of: only_in_taxon NCBITaxon:50557 ! Insecta intersection_of: part_of UBERON:0002548 ! larva -relationship: only_in_taxon NCBITaxon:50557 ! Insecta +intersection_of: RO:0002160 NCBITaxon:50557 ! only in taxon Insecta relationship: part_of UBERON:0002548 ! larva +relationship: RO:0002160 NCBITaxon:50557 ! only in taxon Insecta [Term] id: UBERON:6003005 name: insect adult tagma namespace: uberon def: "Any tagma (UBERON:6000002) that is part of some adult (UBERON:6003004)." [FBC:auto_generated_definition] -xref: FBbt:00003005 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:6000002 ! arthropod tagma intersection_of: UBERON:6000002 ! arthropod tagma intersection_of: part_of UBERON:0007023 ! adult organism @@ -257015,7 +253593,6 @@ id: UBERON:6003007 name: insect adult head namespace: uberon def: "Head of the adult organism." [FBC:SPR] -xref: FBbt:00003007 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:6000004 ! panarthropod head is_a: UBERON:6003005 ! insect adult tagma intersection_of: UBERON:0000033 ! head @@ -257029,7 +253606,6 @@ name: insect embryonic/larval sensillum namespace: uberon def: "Any sensillum (UBERON:6007152) that is part of some larva (UBERON:6001727)." [FBC:auto_generated_definition] synonym: "larval sensillum" EXACT [] -xref: FBbt:00007240 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0002536 ! arthropod sensillum is_a: UBERON:6002639 ! insect larval sense organ intersection_of: UBERON:0002536 ! arthropod sensillum @@ -257041,7 +253617,6 @@ name: insect embryonic/larval head sensillum namespace: uberon def: "Any sensillum (UBERON:6007152) that is part of some larval head (UBERON:6001730)." [FBC:auto_generated_definition] synonym: "larval head sensillum" NARROW [] -xref: FBbt:00007242 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000963 ! head sensillum is_a: UBERON:6007240 ! insect embryonic/larval sensillum is_a: UBERON:6007280 ! insect embryonic/larval head sense organ @@ -257054,7 +253629,6 @@ name: insect embryonic/larval head sense organ namespace: uberon def: "Any sense organ (UBERON:6005155) that is part of some larval head (UBERON:6001730)." [FBC:auto_generated_definition] synonym: "larval head sense organ" EXACT [] -xref: FBbt:00007280 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:6002639 ! insect larval sense organ intersection_of: UBERON:0000020 ! sense organ intersection_of: part_of UBERON:6001730 ! insect larval head @@ -257066,12 +253640,13 @@ name: tibial tuberosity namespace: uberon def: "The tibial tuberosity is on the anterior side of a tibia and is where a patella ligament attaches." [https://en.wikipedia.org/wiki/Tuberosity_of_the_tibia] synonym: "fossa digitalis" EXACT [] +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005813 ! tubercle is_a: UBERON:4100000 ! skeletal element projection intersection_of: UBERON:0005813 ! tubercle intersection_of: part_of UBERON:0008772 ! proximal epiphysis of tibia -relationship: dc-contributor https://orcid.org/0000-0003-2699-3066 relationship: part_of UBERON:0008772 ! proximal epiphysis of tibia +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2699-3066 [Term] id: UBERON:7500107 @@ -257080,12 +253655,12 @@ namespace: uberon def: "A suture joining a sphenoid bone with the alae of a vomer to form a schindylesis type of joint." [DOI:10.1097/SCS.0000000000002945, PMID:27483100] is_a: UBERON:0009199 ! facial suture intersection_of: UBERON:0009199 ! facial suture -intersection_of: connects UBERON:0001677 ! sphenoid bone -intersection_of: connects UBERON:0002396 ! vomer -relationship: connects UBERON:0001677 ! sphenoid bone -relationship: connects UBERON:0002396 ! vomer -relationship: dc-contributor https://orcid.org/0000-0001-8415-4848 -relationship: dc-contributor https://orcid.org/0000-0003-2699-3066 +intersection_of: RO:0002176 UBERON:0001677 ! connects sphenoid bone +intersection_of: RO:0002176 UBERON:0002396 ! connects vomer +relationship: RO:0002176 UBERON:0001677 ! connects sphenoid bone +relationship: RO:0002176 UBERON:0002396 ! connects vomer +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8415-4848 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2699-3066 [Term] id: UBERON:8000006 @@ -257093,10 +253668,11 @@ name: left side of back namespace: uberon def: "Left part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane." [https://microbiomedb.org/] is_a: UBERON:0001137 ! dorsum +is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0001137 ! dorsum -intersection_of: in_left_side_of UBERON:0000468 ! multicellular organism -relationship: dc-contributor https://orcid.org/0000-0001-5208-3432 -relationship: in_left_side_of UBERON:0000468 ! multicellular organism +intersection_of: BSPO:0000120 UBERON:0000468 ! multicellular organism +relationship: BSPO:0000120 UBERON:0000468 ! multicellular organism +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 [Term] id: UBERON:8000007 @@ -257104,10 +253680,11 @@ name: right side of back namespace: uberon def: "Right part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane." [https://microbiomedb.org/] is_a: UBERON:0001137 ! dorsum +is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0001137 ! dorsum -intersection_of: in_right_side_of UBERON:0000468 ! multicellular organism -relationship: dc-contributor https://orcid.org/0000-0001-5208-3432 -relationship: in_right_side_of UBERON:0000468 ! multicellular organism +intersection_of: BSPO:0000121 UBERON:0000468 ! multicellular organism +relationship: BSPO:0000121 UBERON:0000468 ! multicellular organism +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 [Term] id: UBERON:8000009 @@ -257117,9 +253694,9 @@ def: "A collection of Purkinje fibers that receives signals from the right and l synonym: "Purkinje fibre network" EXACT [PMID:26786210] is_a: UBERON:0010131 {source="https://github.com/obophenotype/uberon/issues/1785", source="https://orcid.org/0000-0001-5208-3432", source="https://orcid.org/0000-0002-9791-0064"} ! conducting tissue of heart is_a: UBERON:0018649 ! cardiac muscle tissue of ventricle -relationship: dc-contributor https://orcid.org/0000-0001-5208-3432 relationship: has_part UBERON:0002354 {source="https://github.com/obophenotype/uberon/issues/1785", source="https://orcid.org/0000-0001-5208-3432", source="https://orcid.org/0000-0002-9791-0064"} ! cardiac Purkinje fiber relationship: part_of UBERON:0004146 {source="https://github.com/obophenotype/uberon/issues/1785", source="https://orcid.org/0000-0001-5208-3432", source="https://orcid.org/0000-0002-9791-0064"} ! His-Purkinje system +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 [Term] id: UBERON:8300000 @@ -257135,8 +253712,8 @@ xref: FMA:24757 is_a: UBERON:0001084 ! skin of head intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0000403 ! scalp -relationship: dc-contributor https://orcid.org/0000-0001-9897-3238 relationship: part_of UBERON:0000403 ! scalp +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9897-3238 [Term] id: UBERON:8300001 @@ -257145,11 +253722,11 @@ namespace: uberon def: "A forelimb that is on the right side of a pectoral complex." [UBERONREF:0000003] xref: FMA:7185 is_a: UBERON:0002102 ! forelimb +is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0002102 ! forelimb -intersection_of: in_right_side_of UBERON:0010708 ! pectoral complex -relationship: dc-contributor https://orcid.org/0000-0001-9897-3238 -relationship: in_right_side_of UBERON:0010708 ! pectoral complex -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +intersection_of: BSPO:0000121 UBERON:0010708 ! pectoral complex +relationship: BSPO:0000121 UBERON:0010708 ! pectoral complex +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9897-3238 [Term] id: UBERON:8300002 @@ -257158,11 +253735,11 @@ namespace: uberon def: "A forelimb that is on the left side of a pectoral complex." [UBERONREF:0000003] xref: FMA:7186 is_a: UBERON:0002102 ! forelimb +is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0002102 ! forelimb -intersection_of: in_left_side_of UBERON:0010708 ! pectoral complex -relationship: dc-contributor https://orcid.org/0000-0001-9897-3238 -relationship: in_left_side_of UBERON:0010708 ! pectoral complex -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +intersection_of: BSPO:0000120 UBERON:0010708 ! pectoral complex +relationship: BSPO:0000120 UBERON:0010708 ! pectoral complex +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9897-3238 [Term] id: UBERON:8300003 @@ -257171,11 +253748,11 @@ namespace: uberon def: "A hindlimb that is on the right side of a pelvic complex." [UBERONREF:0000003] xref: FMA:7187 is_a: UBERON:0002103 ! hindlimb +is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0002103 ! hindlimb -intersection_of: in_right_side_of UBERON:0010709 ! pelvic complex -relationship: dc-contributor https://orcid.org/0000-0001-9897-3238 -relationship: in_right_side_of UBERON:0010709 ! pelvic complex -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +intersection_of: BSPO:0000121 UBERON:0010709 ! pelvic complex +relationship: BSPO:0000121 UBERON:0010709 ! pelvic complex +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9897-3238 [Term] id: UBERON:8300004 @@ -257184,11 +253761,11 @@ namespace: uberon def: "A hindlimb that is on the left side of a pelvic complex." [UBERONREF:0000003] xref: FMA:7188 is_a: UBERON:0002103 ! hindlimb +is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0002103 ! hindlimb -intersection_of: in_left_side_of UBERON:0010709 ! pelvic complex -relationship: dc-contributor https://orcid.org/0000-0001-9897-3238 -relationship: in_left_side_of UBERON:0010709 ! pelvic complex -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +intersection_of: BSPO:0000120 UBERON:0010709 ! pelvic complex +relationship: BSPO:0000120 UBERON:0010709 ! pelvic complex +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9897-3238 [Term] id: UBERON:8400001 @@ -257197,10 +253774,10 @@ namespace: uberon def: "The region of the hepatic acinus that is closest to the arterial blood supply and has the highest oxygen concentration. Zone 1 is located in the periportal region of the liver lobule, closest to the portal triad. Hepatocytes in this region are primarily involved in oxidative energy metabolism." [PMID:29763190] synonym: "hepatic acinus periportal zone" EXACT [PMID:28126520] is_a: UBERON:8400005 ! metabolic zone of liver -relationship: dc-contributor https://orcid.org/0000-0003-2034-601X relationship: overlaps UBERON:8400006 {xref="PMID:28126520"} ! liver lobule periportal region relationship: part_of UBERON:0001172 ! hepatic acinus -relationship: present_in_taxon NCBITaxon:40674 ! Mammalia +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X +property_value: RO:0002175 NCBITaxon:40674 creation_date: 2020-09-08T14:14:21Z [Term] @@ -257212,10 +253789,10 @@ synonym: "hepatic acinus centrilobular zone" EXACT [PMID:28126520] synonym: "hepatic acinus pericentral zone" EXACT [PMID:28126520] synonym: "hepatic acinus perivenous zone" EXACT [PMID:28126520] is_a: UBERON:8400005 ! metabolic zone of liver -relationship: dc-contributor https://orcid.org/0000-0003-2034-601X relationship: overlaps UBERON:8400007 {xref="PMID:28126520"} ! liver lobule centrilobular region relationship: part_of UBERON:0001172 ! hepatic acinus -relationship: present_in_taxon NCBITaxon:40674 ! Mammalia +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X +property_value: RO:0002175 NCBITaxon:40674 creation_date: 2020-09-08T15:05:03Z [Term] @@ -257227,10 +253804,10 @@ synonym: "hepatic acinus intermediary zone" EXACT [PMID:28126520] is_a: UBERON:8400005 ! metabolic zone of liver relationship: adjacent_to UBERON:8400001 ! hepatic acinus zone 1 relationship: adjacent_to UBERON:8400002 ! hepatic acinus zone 3 -relationship: dc-contributor https://orcid.org/0000-0003-2034-601X relationship: overlaps UBERON:8400008 {xref="PMID:28126520"} ! liver lobule midzonal region relationship: part_of UBERON:0001172 ! hepatic acinus -relationship: present_in_taxon NCBITaxon:40674 ! Mammalia +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X +property_value: RO:0002175 NCBITaxon:40674 creation_date: 2020-09-08T15:15:57Z [Term] @@ -257240,9 +253817,10 @@ namespace: uberon def: "Any of the metabolic zones found in the liver. Liver tissue is heterogenous at the level of morphometry and histochemistry. This heterogeneity is linked to the position of a cell within the functional unit of the tissue, which, in turn, is related to the blood supply: cells located in the upstream zone differ from those in the downstream zone with respect to subcellular structures, key enzymes, translocators, and receptors and, therefore, have different metabolic capacities. This is the basis for 'metabolic zonation', a concept first proposed in mammals for carbohydrate metabolism and later expanded to include amino acid and ammonia metabolism, xenobiotic metabolism, protective metabolism, and formation of plasma proteins." [DOI:10.1016/S0968-0004(78)91764-4, PMID:8839925] synonym: "hepatic acinus metabolic zone" EXACT [PMID:8839925] is_a: UBERON:0000063 ! organ subunit -relationship: dc-contributor https://orcid.org/0000-0003-2034-601X +is_a: UBERON:0004119 ! endoderm-derived structure relationship: part_of UBERON:0002107 ! liver -relationship: present_in_taxon NCBITaxon:40674 ! Mammalia +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X +property_value: RO:0002175 NCBITaxon:40674 creation_date: 2020-09-29T15:45:36Z [Term] @@ -257253,10 +253831,10 @@ def: "The region of the liver lobule that is closest to the portal triad. The fu synonym: "hepatic acinus zone 1" RELATED [PMID:28126520] is_a: UBERON:8400005 ! metabolic zone of liver relationship: adjacent_to UBERON:0001279 ! portal triad -relationship: dc-contributor https://orcid.org/0000-0003-2034-601X relationship: overlaps UBERON:8400001 {xref="PMID:28126520"} ! hepatic acinus zone 1 relationship: part_of UBERON:0004647 ! liver lobule -relationship: present_in_taxon NCBITaxon:40674 ! Mammalia +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X +property_value: RO:0002175 NCBITaxon:40674 creation_date: 2020-10-05T12:56:57Z [Term] @@ -257267,10 +253845,10 @@ def: "The region of the liver lobule that is closest to the central vein. The fu synonym: "hepatic acinus zone 3" RELATED [PMID:28126520] is_a: UBERON:8400005 ! metabolic zone of liver relationship: adjacent_to UBERON:0006841 ! central vein of liver -relationship: dc-contributor https://orcid.org/0000-0003-2034-601X relationship: overlaps UBERON:8400002 {xref="PMID:28126520"} ! hepatic acinus zone 3 relationship: part_of UBERON:0004647 ! liver lobule -relationship: present_in_taxon NCBITaxon:40674 ! Mammalia +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X +property_value: RO:0002175 NCBITaxon:40674 creation_date: 2020-10-05T15:43:18Z [Term] @@ -257282,10 +253860,10 @@ synonym: "hepatic acinus zone 2" RELATED [PMID:28126520] is_a: UBERON:8400005 ! metabolic zone of liver relationship: adjacent_to UBERON:0001279 ! portal triad relationship: adjacent_to UBERON:0006841 ! central vein of liver -relationship: dc-contributor https://orcid.org/0000-0003-2034-601X relationship: overlaps UBERON:8400003 {xref="PMID:28126520"} ! hepatic acinus zone 2 relationship: part_of UBERON:0004647 ! liver lobule -relationship: present_in_taxon NCBITaxon:40674 ! Mammalia +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X +property_value: RO:0002175 NCBITaxon:40674 creation_date: 2020-10-05T15:52:22Z [Term] @@ -257296,10 +253874,11 @@ def: "Hepatic serous coat; peritoneal covering of the liver, enclosing almost al synonym: "serosa of liver" EXACT [FMA:15811] synonym: "tunica serosa hepatis" EXACT OMO:0003011 [https://medical-dictionary.thefreedictionary.com/serosa+of+liver] is_a: UBERON:0000042 ! serous membrane +is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure intersection_of: UBERON:0000042 ! serous membrane intersection_of: part_of UBERON:0002107 ! liver -relationship: dc-contributor https://orcid.org/0000-0003-2034-601X relationship: part_of UBERON:0002107 ! liver +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X [Term] id: UBERON:8400023 @@ -257311,11 +253890,12 @@ synonym: "subserosal tissue of liver" EXACT [] synonym: "subserous layer of liver" EXACT [] synonym: "tela subserosa (hepar)" EXACT [FMA:15821] synonym: "tela subserosa hepatis" EXACT [https://medical-dictionary.thefreedictionary.com/subserosa+of+liver] +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0012375 ! subserosa intersection_of: UBERON:0012375 ! subserosa intersection_of: part_of UBERON:0002107 ! liver -relationship: dc-contributor https://orcid.org/0000-0003-2034-601X relationship: part_of UBERON:0002107 ! liver +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X [Term] id: UBERON:8400024 @@ -257330,7 +253910,7 @@ intersection_of: UBERON:0000353 ! parenchyma intersection_of: adjacent_to UBERON:0016479 ! capsule of liver intersection_of: part_of UBERON:0002107 ! liver relationship: adjacent_to UBERON:0016479 ! capsule of liver -relationship: dc-contributor https://orcid.org/0000-0003-2034-601X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2034-601X [Term] id: UBERON:8410000 @@ -257348,12 +253928,12 @@ xref: TA2:2952 xref: WikipediaVersioned:Duodenojejunal_flexure&oldid=937307798 is_a: UBERON:8410024 ! intestinal junction intersection_of: UBERON:0007651 ! anatomical junction -intersection_of: connects UBERON:0002114 ! duodenum -intersection_of: connects UBERON:0002115 ! jejunum -relationship: connects UBERON:0002114 ! duodenum -relationship: connects UBERON:0002115 ! jejunum +intersection_of: RO:0002176 UBERON:0002114 ! connects duodenum +intersection_of: RO:0002176 UBERON:0002115 ! connects jejunum relationship: part_of UBERON:0002108 ! small intestine -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002176 UBERON:0002114 ! connects duodenum +relationship: RO:0002176 UBERON:0002115 ! connects jejunum +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:8410001 @@ -257365,8 +253945,8 @@ synonym: "venule of small intestine" EXACT [] is_a: UBERON:0001979 ! venule intersection_of: UBERON:0001979 ! venule intersection_of: part_of UBERON:0001213 ! intestinal villus -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0001213 ! intestinal villus +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410002 @@ -257378,8 +253958,8 @@ synonym: "lymphatic vessel of small intestine" EXACT [] is_a: UBERON:0001473 ! lymphatic vessel intersection_of: UBERON:0001473 ! lymphatic vessel intersection_of: part_of UBERON:0002108 ! small intestine -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0002108 ! small intestine +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410003 @@ -257388,15 +253968,15 @@ namespace: uberon def: "In human, ductal plate is a double-layered cylindrical structure of bile duct epithelium that surrounds the portal ramifications by the eighth gestational week. After approximately the 12th gestational week, remodelling of ductal plate begins, and maturity is attained by the end of gestation or early postnatal period." [http://orcid.org/0000-0002-7073-9172, PMID:28515578] subset: added_for_HCA is_a: PR:000050567 ! protein-containing material entity +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0010000 ! multicellular anatomical structure -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 -relationship: existence_ends_during UBERON:0007220 ! late embryonic stage -relationship: existence_starts_during UBERON:0000068 ! embryo stage relationship: has_part UBERON:0004820 ! bile duct epithelium relationship: part_of UBERON:0002394 ! bile duct -relationship: present_in_taxon NCBITaxon:40674 ! Mammalia -relationship: surrounds UBERON:0002017 ! portal vein -property_value: UBPROP:0000008 "Temporal stages still need to be fully researched across species." xsd:string +relationship: RO:0002221 UBERON:0002017 ! surrounds portal vein +relationship: RO:0002488 UBERON:0000068 ! existence starts during embryo stage +relationship: RO:0002492 UBERON:0007220 ! existence ends during late embryonic stage +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: RO:0002175 NCBITaxon:40674 [Term] id: UBERON:8410004 @@ -257410,8 +253990,8 @@ synonym: "small intestine villus arteriole" EXACT [] is_a: UBERON:0001980 ! arteriole intersection_of: UBERON:0001980 ! arteriole intersection_of: part_of UBERON:0001213 ! intestinal villus -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0001213 ! intestinal villus +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410008 @@ -257422,8 +254002,8 @@ synonym: "anorectum venule" EXACT [] is_a: UBERON:0001979 ! venule intersection_of: UBERON:0001979 ! venule intersection_of: part_of UBERON:8410050 ! anorectum -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:8410050 ! anorectum +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410009 @@ -257434,8 +254014,8 @@ synonym: "anorectum arteriole" EXACT [] is_a: UBERON:0001980 ! arteriole intersection_of: UBERON:0001980 ! arteriole intersection_of: part_of UBERON:8410050 ! anorectum -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:8410050 ! anorectum +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410015 @@ -257445,8 +254025,8 @@ def: "An arteriole located in the colon." [http://orcid.org/0000-0003-3440-1876, is_a: UBERON:0001980 ! arteriole intersection_of: UBERON:0001980 ! arteriole intersection_of: part_of UBERON:0001155 ! colon -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0001155 ! colon +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410016 @@ -257458,12 +254038,12 @@ synonym: "descending-sigmoid junction" EXACT [] synonym: "sigmoid junction" BROAD [] is_a: UBERON:8410024 ! intestinal junction intersection_of: UBERON:0007651 ! anatomical junction -intersection_of: connects UBERON:0001158 ! descending colon -intersection_of: connects UBERON:0001159 ! sigmoid colon -relationship: connects UBERON:0001158 ! descending colon -relationship: connects UBERON:0001159 ! sigmoid colon -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 +intersection_of: RO:0002176 UBERON:0001158 ! connects descending colon +intersection_of: RO:0002176 UBERON:0001159 ! connects sigmoid colon relationship: part_of UBERON:0000168 ! proximal-distal subdivision of colon +relationship: RO:0002176 UBERON:0001158 ! connects descending colon +relationship: RO:0002176 UBERON:0001159 ! connects sigmoid colon +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410017 @@ -257474,12 +254054,12 @@ subset: human_reference_atlas xref: FMA:15394 is_a: UBERON:0002017 ! portal vein intersection_of: UBERON:0002017 ! portal vein -intersection_of: drains UBERON:0001158 ! descending colon -intersection_of: tributary_of UBERON:0001215 ! inferior mesenteric vein -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 -relationship: drains UBERON:0001158 ! descending colon -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: tributary_of UBERON:0001215 ! inferior mesenteric vein +intersection_of: RO:0002179 UBERON:0001158 ! drains descending colon +intersection_of: RO:0002376 UBERON:0001215 ! tributary of inferior mesenteric vein +relationship: RO:0002179 UBERON:0001158 ! drains descending colon +relationship: RO:0002376 UBERON:0001215 ! tributary of inferior mesenteric vein +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:8410018 @@ -257490,12 +254070,12 @@ subset: human_reference_atlas xref: FMA:15407 is_a: UBERON:0002017 ! portal vein intersection_of: UBERON:0002017 ! portal vein -intersection_of: drains UBERON:0001156 ! ascending colon -intersection_of: tributary_of UBERON:0001138 ! superior mesenteric vein -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 -relationship: drains UBERON:0001156 ! ascending colon -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: tributary_of UBERON:0001138 ! superior mesenteric vein +intersection_of: RO:0002179 UBERON:0001156 ! drains ascending colon +intersection_of: RO:0002376 UBERON:0001138 ! tributary of superior mesenteric vein +relationship: RO:0002179 UBERON:0001156 ! drains ascending colon +relationship: RO:0002376 UBERON:0001138 ! tributary of superior mesenteric vein +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:8410019 @@ -257505,12 +254085,12 @@ def: "The area where the jejunum ends and the ileum part of the intestine begins synonym: "jejunoileal junction" EXACT [] is_a: UBERON:8410024 ! intestinal junction intersection_of: UBERON:0007651 ! anatomical junction -intersection_of: connects UBERON:0002115 ! jejunum -intersection_of: connects UBERON:0002116 ! ileum -relationship: connects UBERON:0002115 ! jejunum -relationship: connects UBERON:0002116 ! ileum -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 +intersection_of: RO:0002176 UBERON:0002115 ! connects jejunum +intersection_of: RO:0002176 UBERON:0002116 ! connects ileum relationship: part_of UBERON:0002108 ! small intestine +relationship: RO:0002176 UBERON:0002115 ! connects jejunum +relationship: RO:0002176 UBERON:0002116 ! connects ileum +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410020 @@ -257522,8 +254102,8 @@ synonym: "vermiform appendix venule" EXACT [] is_a: UBERON:0001979 ! venule intersection_of: UBERON:0001979 ! venule intersection_of: part_of UBERON:0001154 ! vermiform appendix -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0001154 ! vermiform appendix +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410024 @@ -257533,10 +254113,10 @@ def: "An anatomical junction between two parts of the intestine." [https://orcid synonym: "junction of intestine" EXACT [] is_a: UBERON:1100000 ! digestive tract junction intersection_of: UBERON:0007651 ! anatomical junction -intersection_of: connects UBERON:0004921 ! subdivision of digestive tract intersection_of: part_of UBERON:0000160 ! intestine -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 +intersection_of: RO:0002176 UBERON:0004921 ! connects subdivision of digestive tract relationship: part_of UBERON:0000160 ! intestine +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410028 @@ -257550,8 +254130,8 @@ synonym: "vermiform appendix arteriole" EXACT [] is_a: UBERON:0001980 ! arteriole intersection_of: UBERON:0001980 ! arteriole intersection_of: part_of UBERON:0001154 ! vermiform appendix -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0001154 ! vermiform appendix +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410030 @@ -257563,8 +254143,8 @@ synonym: "lymphatic vessel of vermiform appendix" EXACT [] is_a: UBERON:0001473 ! lymphatic vessel intersection_of: UBERON:0001473 ! lymphatic vessel intersection_of: part_of UBERON:0001154 ! vermiform appendix -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0001154 ! vermiform appendix +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410032 @@ -257578,9 +254158,9 @@ intersection_of: UBERON:0000464 ! anatomical space intersection_of: adjacent_to UBERON:0002195 ! trabecula of lymph node intersection_of: part_of UBERON:0000029 ! lymph node relationship: adjacent_to UBERON:0002195 ! trabecula of lymph node -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0000029 ! lymph node -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:8410033 @@ -257592,10 +254172,10 @@ synonym: "hilar vein of lymph node" EXACT [] synonym: "vein of lymph node" EXACT [] is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein -intersection_of: drains UBERON:0000029 ! lymph node -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 -relationship: drains UBERON:0000029 ! lymph node -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +intersection_of: RO:0002179 UBERON:0000029 ! drains lymph node +relationship: RO:0002179 UBERON:0000029 ! drains lymph node +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:8410034 @@ -257607,9 +254187,9 @@ synonym: "artery of lymph node" EXACT [] synonym: "hilar artery of lymph node" EXACT [] is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0000029 ! lymph node -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -relationship: supplies UBERON:0000029 ! lymph node +intersection_of: RO:0002178 UBERON:0000029 ! supplies lymph node +relationship: RO:0002178 UBERON:0000029 ! supplies lymph node +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:8410035 @@ -257621,10 +254201,10 @@ synonym: "arteriole of medulla of lymph node" EXACT [] is_a: UBERON:8410042 ! arteriole of lymph node intersection_of: UBERON:0001980 ! arteriole intersection_of: part_of UBERON:0002007 ! medulla of lymph node -relationship: connecting_branch_of UBERON:8410034 ! lymph node artery -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0002007 ! medulla of lymph node -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +relationship: RO:0002252 UBERON:8410034 ! connecting branch of lymph node artery +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:8410036 @@ -257636,9 +254216,9 @@ synonym: "venule of medulla of lymph node" EXACT [] is_a: UBERON:8410041 ! venule of lymph node intersection_of: UBERON:0001979 ! venule intersection_of: part_of UBERON:0002007 ! medulla of lymph node -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0002007 ! medulla of lymph node -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:8410037 @@ -257649,7 +254229,7 @@ synonym: "HEV" BROAD OMO:0003000 [] xref: BTO:0004528 xref: NCIT:C32739 is_a: UBERON:0035428 ! postcapillary venule -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410038 @@ -257662,8 +254242,8 @@ is_a: UBERON:8410037 ! high endothelial venule is_a: UBERON:8410041 ! venule of lymph node intersection_of: UBERON:8410037 ! high endothelial venule intersection_of: part_of UBERON:0000029 ! lymph node -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:8410039 @@ -257677,7 +254257,7 @@ is_a: UBERON:8410020 ! venule of appendix is_a: UBERON:8410037 ! high endothelial venule intersection_of: UBERON:8410037 ! high endothelial venule intersection_of: part_of UBERON:0001154 ! vermiform appendix -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410040 @@ -257689,8 +254269,8 @@ synonym: "high endothelial venule of Peyer's patch of small intestine" EXACT [] is_a: UBERON:8410037 ! high endothelial venule intersection_of: UBERON:8410037 ! high endothelial venule intersection_of: part_of UBERON:0003454 ! small intestine Peyer's patch -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0003454 ! small intestine Peyer's patch +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410041 @@ -257702,9 +254282,9 @@ synonym: "lymph node venule" EXACT [] is_a: UBERON:0001979 ! venule intersection_of: UBERON:0001979 ! venule intersection_of: part_of UBERON:0000029 ! lymph node -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0000029 ! lymph node -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:8410042 @@ -257716,9 +254296,9 @@ synonym: "lymph node arteriole" EXACT [] is_a: UBERON:0001980 ! arteriole intersection_of: UBERON:0001980 ! arteriole intersection_of: part_of UBERON:0000029 ! lymph node -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0000029 ! lymph node -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:8410043 @@ -257733,9 +254313,9 @@ synonym: "submucosal bronchus gland" EXACT [] is_a: UBERON:8410077 ! airway submucosal gland intersection_of: UBERON:0011148 ! submucosal gland intersection_of: part_of UBERON:0002185 ! bronchus -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0002185 ! bronchus -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:8410044 @@ -257747,8 +254327,8 @@ synonym: "vein of vermiform appendix" EXACT [] is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein intersection_of: part_of UBERON:0001154 ! vermiform appendix -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0001154 ! vermiform appendix +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410045 @@ -257760,8 +254340,8 @@ synonym: "artery of vermiform appendix" EXACT [] is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery intersection_of: part_of UBERON:0001154 ! vermiform appendix -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0001154 ! vermiform appendix +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410046 @@ -257774,8 +254354,8 @@ synonym: "smooth muscle circular layer of vermiform appendix" EXACT [] is_a: UBERON:0012368 ! circular muscle layer of muscular coat intersection_of: UBERON:0012368 ! circular muscle layer of muscular coat intersection_of: part_of UBERON:0001154 ! vermiform appendix -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0001154 ! vermiform appendix +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410047 @@ -257788,8 +254368,8 @@ synonym: "smooth muscle longitudinal layer of vermiform appendix" EXACT [] is_a: UBERON:0012369 ! longitudinal muscle layer of muscular coat intersection_of: UBERON:0012369 ! longitudinal muscle layer of muscular coat intersection_of: part_of UBERON:0001154 ! vermiform appendix -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0001154 ! vermiform appendix +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410048 @@ -257799,8 +254379,8 @@ def: "A venule located in the colon." [https://orcid.org/0000-0003-3440-1876, ht is_a: UBERON:0001979 ! venule intersection_of: UBERON:0001979 ! venule intersection_of: part_of UBERON:0001155 ! colon -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0001155 ! colon +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410049 @@ -257814,11 +254394,12 @@ synonym: "serosal nerve fiber of vermiform appendix" EXACT [] synonym: "serosal nerve fibre of appendix" EXACT [] synonym: "serosal nerve fibre of appendix vermiformis" EXACT [] synonym: "serosal nerve fibre of vermiform appendix" EXACT [] +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0006134 ! nerve fiber intersection_of: UBERON:0006134 ! nerve fiber intersection_of: part_of UBERON:0012498 ! serosa of appendix -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0012498 ! serosa of appendix +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410050 @@ -257831,14 +254412,13 @@ intersection_of: UBERON:0004921 ! subdivision of digestive tract intersection_of: has_part UBERON:0000159 ! anal canal intersection_of: has_part UBERON:0001052 ! rectum intersection_of: has_part UBERON:0001245 ! anus -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: has_part UBERON:0000159 ! anal canal relationship: has_part UBERON:0001052 ! rectum relationship: has_part UBERON:0001245 ! anus relationship: part_of UBERON:0000059 ! large intestine -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: editor_note "The anatomy, pathology and medical community considers the anus to be part of the large intestine, and supports the use of 'anorectum' to include rectum, anal canal and anus. Although a few resources seem to only include the distal part of the rectum in 'anorectum', this UBERON grouping term is meant to refer more broadly to the whole of rectum." xsd:string -property_value: UBPROP:0000007 "anorectal" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: IAO:0000116 "The anatomy, pathology and medical community considers the anus to be part of the large intestine, and supports the use of 'anorectum' to include rectum, anal canal and anus. Although a few resources seem to only include the distal part of the rectum in 'anorectum', this UBERON grouping term is meant to refer more broadly to the whole of rectum." xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:8410051 @@ -257848,8 +254428,8 @@ def: "A lymphatic vessel located in the colon." [https://orcid.org/0000-0003-344 is_a: UBERON:0001473 ! lymphatic vessel intersection_of: UBERON:0001473 ! lymphatic vessel intersection_of: part_of UBERON:0001155 ! colon -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0001155 ! colon +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410052 @@ -257861,9 +254441,9 @@ synonym: "germinal center light zone" BROAD [] synonym: "light zone of germinal center" BROAD [] synonym: "light zone of lymph node germinal center" EXACT [] is_a: UBERON:0001744 ! lymphoid tissue -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0009039 ! lymph node germinal center -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:8410053 @@ -257875,9 +254455,9 @@ synonym: "dark zone of germinal center" BROAD [] synonym: "dark zone of lymph node germinal center" EXACT [] synonym: "germinal center dark zone" BROAD [] is_a: UBERON:0001744 ! lymphoid tissue -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0009039 ! lymph node germinal center -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:8410056 @@ -257888,8 +254468,8 @@ synonym: "blood vessel capillary of anorectum" EXACT [] is_a: UBERON:0001982 ! capillary intersection_of: UBERON:0001982 ! capillary intersection_of: part_of UBERON:8410050 ! anorectum -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:8410050 ! anorectum +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410057 @@ -257900,8 +254480,8 @@ synonym: "blood vessel capillary of colon" EXACT [] is_a: UBERON:0001982 ! capillary intersection_of: UBERON:0001982 ! capillary intersection_of: part_of UBERON:0001155 ! colon -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0001155 ! colon +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410060 @@ -257913,8 +254493,8 @@ is_a: UBERON:0012398 ! large intestine smooth muscle circular layer intersection_of: UBERON:0012368 ! circular muscle layer of muscular coat intersection_of: part_of UBERON:0001155 ! colon intersection_of: part_of UBERON:0004220 ! large intestine smooth muscle -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0001155 ! colon +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410061 @@ -257926,8 +254506,8 @@ is_a: UBERON:0012399 ! large intestine smooth muscle longitudinal layer intersection_of: UBERON:0012369 ! longitudinal muscle layer of muscular coat intersection_of: part_of UBERON:0001155 ! colon intersection_of: part_of UBERON:0004220 ! large intestine smooth muscle -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0001155 ! colon +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410065 @@ -257938,8 +254518,8 @@ synonym: "lymph node marginal zone" BROAD [] synonym: "marginal zone of lymph node" BROAD [] synonym: "marginal zone of lymph node follicle" EXACT [] is_a: UBERON:0001744 ! lymphoid tissue -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0000029 ! lymph node +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 [Term] id: UBERON:8410066 @@ -257948,9 +254528,9 @@ namespace: uberon def: "The lymph node paracortex is the middle layer of the lymph node and is mostly populated by T cells and dendritic cells. The paracortex also contains specialised blood vessels called high endothelial venules which allow lymphocytes to enter the node." [http://orcid.org/0000-0001-9990-8331, http://orcid.org/0000-0003-4183-8865, https://www.immunology.org/public-information/bitesized-immunology/organs-and-tissues/lymph-node] subset: human_reference_atlas is_a: UBERON:0001744 ! lymphoid tissue -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0010417 ! lymph node T cell domain -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:8410068 @@ -257963,9 +254543,9 @@ synonym: "small intestine capillary" EXACT [] is_a: UBERON:0001982 ! capillary intersection_of: UBERON:0001982 ! capillary intersection_of: part_of UBERON:0002108 ! small intestine -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0002108 ! small intestine -property_value: dcterms-date "2021-12-21T15:14:31Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/date "2021-12-21T15:14:31Z" xsd:dateTime [Term] id: UBERON:8410071 @@ -257978,10 +254558,10 @@ synonym: "floor of capsule of lymph node" EXACT [] synonym: "subcapsular sinus of lymph node ceiling" EXACT [] is_a: UBERON:0000064 ! organ part relationship: adjacent_to UBERON:0005463 ! subcapsular sinus of lymph node -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0002194 ! capsule of lymph node -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2022-02-22T17:04:49Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/date "2022-02-22T17:04:49Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:8410072 @@ -257994,10 +254574,10 @@ synonym: "floor of subcapsular sinus of lymph node" EXACT [] synonym: "subcapsular sinus of lymph node floor" EXACT [] is_a: UBERON:0000064 ! organ part relationship: adjacent_to UBERON:0005463 ! subcapsular sinus of lymph node -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0002006 ! cortex of lymph node -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2022-02-22T17:16:40Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/date "2022-02-22T17:16:40Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:8410077 @@ -258007,13 +254587,14 @@ def: "A submucosal gland found in a respiratory tract." [http://orcid.org/0000-0 synonym: "respiratory tract submucosal gland" EXACT [] synonym: "submucosal gland of respiratory tract" EXACT [] xref: EFO:0010666 +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0011148 ! submucosal gland is_a: UBERON:0036225 ! respiratory system gland intersection_of: UBERON:0011148 ! submucosal gland intersection_of: part_of UBERON:0000065 ! respiratory tract -relationship: dc-contributor https://orcid.org/0000-0002-2825-0621 relationship: part_of UBERON:0000065 ! respiratory tract -property_value: dcterms-date "2022-03-24T14:21:59Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2825-0621 +property_value: http://purl.org/dc/terms/date "2022-03-24T14:21:59Z" xsd:dateTime [Term] id: UBERON:8410080 @@ -258037,7 +254618,6 @@ synonym: "microvessel" BROAD [] is_a: UBERON:0001981 ! blood vessel is_a: UBERON:0010523 ! microcirculatory vessel property_value: seeAlso "https://github.com/obophenotype/uberon/issues/2186" xsd:string -property_value: UBPROP:0000007 "microvascular" xsd:string created_by: http://orcid.org/0000-0002-2825-0621 [Term] @@ -258049,8 +254629,8 @@ synonym: "hair" BROAD [PMID:30783333] is_a: UBERON:0016446 ! hair of head intersection_of: UBERON:0001037 ! strand of hair intersection_of: part_of UBERON:0000403 ! scalp -relationship: dc-contributor https://orcid.org/0000-0001-8314-2140 relationship: part_of UBERON:0000403 ! scalp +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8314-2140 [Term] id: UBERON:8440000 @@ -258088,8 +254668,8 @@ def: "The deepest layer of the neocortex. While layer 6b is considered part of l synonym: "cerebral cortex layer 6b" EXACT [] synonym: "neocortex layer 6b" EXACT [] is_a: UBERON:0002301 ! layer of neocortex -relationship: develops_from UBERON:0004035 ! cortical subplate relationship: part_of UBERON:0005395 ! cortical layer VI +relationship: RO:0002202 UBERON:0004035 ! develops from cortical subplate [Term] id: UBERON:8440004 @@ -258122,8 +254702,8 @@ intersection_of: UBERON:0035014 ! functional part of brain intersection_of: capable_of_part_of GO:0007601 ! visual perception intersection_of: part_of UBERON:0000956 ! cerebral cortex relationship: capable_of_part_of GO:0007601 ! visual perception -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 relationship: part_of UBERON:0000956 ! cerebral cortex +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: UBERON:8440015 @@ -258131,7 +254711,7 @@ name: noradrenergic cell groups namespace: uberon def: "Collections of neurons in the central nervous system that have been demonstrated by histochemical fluorescence to contain the neurotransmitter norepinephrine (noradrenalin)." [WikipediaVersioned:Noradrenergic_cell_groups&oldid=965992184] is_a: UBERON:0002616 ! regional part of brain -relationship: composed_primarily_of CL:0000459 ! noradrenergic cell +relationship: RO:0002473 CL:0000459 ! composed primarily of noradrenergic cell [Term] id: UBERON:8440043 @@ -258140,7 +254720,7 @@ namespace: uberon def: "A structure embedded in the superior olivary complex that is driven by input pathways from the octopus cells in the cochlear nucleus and the neurons of the medial nucleus of the trapezoid body." [DOI:10.1093/oxfordhb/9780190849061.013.11] synonym: "SPON" EXACT [DOI:10.1093/oxfordhb/9780190849061.013.11] is_a: UBERON:0007247 ! nucleus of superior olivary complex -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: UBERON:8450001 @@ -258149,9 +254729,9 @@ namespace: uberon def: "An individual reproductive unit containing a single oocyte and one or several layers of support cells (Armstrong et al., 2020)." [DOI:10.1530/REP-18-0593] is_a: UBERON:0000064 ! organ part is_a: UBERON:0005156 ! reproductive structure -relationship: dc-contributor https://orcid.org/0000-0002-6095-8718 relationship: part_of UBERON:0000992 ! ovary -property_value: dcterms-date "2022-04-19T11:08:10Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6095-8718 +property_value: http://purl.org/dc/terms/date "2022-04-19T11:08:10Z" xsd:dateTime property_value: seeAlso "https://github.com/obophenotype/uberon/issues/476" xsd:anyURI [Term] @@ -258160,12 +254740,11 @@ name: excretory system namespace: uberon def: "An anatomical system that eliminates waste products that arise as a result of metabolic activity." [GO:0007588] subset: human_reference_atlas -xref: BTO:0006338 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} is_a: UBERON:0000467 ! anatomical system intersection_of: UBERON:0000467 ! anatomical system intersection_of: capable_of GO:0046903 ! secretion relationship: capable_of GO:0046903 ! secretion -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens +property_value: RO:0002175 NCBITaxon:9606 created_by: http://orcid.org/0000-0002-6095-8718 creation_date: 2022-05-25T18:21:29Z @@ -258176,9 +254755,9 @@ namespace: uberon def: "Blood located in the placenta." [http://orcid.org/0000-0001-6595-0902, https://www.ncbi.nlm.nih.gov/books/NBK53254/] is_a: UBERON:0000178 ! blood intersection_of: UBERON:0000178 ! blood -intersection_of: located_in UBERON:0001987 ! placenta -relationship: located_in UBERON:0001987 ! placenta -property_value: dcterms-date "2022-04-04T11:06:09Z" xsd:dateTime +intersection_of: RO:0001025 UBERON:0001987 ! located in placenta +relationship: RO:0001025 UBERON:0001987 ! located in placenta +property_value: http://purl.org/dc/terms/date "2022-04-04T11:06:09Z" xsd:dateTime [Term] id: UBERON:8480000 @@ -258188,9 +254767,9 @@ def: "A portion of smooth muscle tissue that is part of an iliac vein." [https:/ is_a: UBERON:0004696 ! venous system smooth muscle intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0005610 ! iliac vein -relationship: dc-contributor https://orcid.org/0000-0002-0819-0473 relationship: part_of UBERON:0005610 ! iliac vein -property_value: dcterms-date "2022-06-17T14:34:50Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 +property_value: http://purl.org/dc/terms/date "2022-06-17T14:34:50Z" xsd:dateTime [Term] id: UBERON:8480001 @@ -258201,8 +254780,8 @@ is_a: UBERON:0001982 ! capillary is_a: UBERON:0003499 ! brain blood vessel intersection_of: UBERON:0001982 ! capillary intersection_of: part_of UBERON:0000955 ! brain -relationship: dc-contributor https://orcid.org/0000-0002-0819-0473 -property_value: dcterms-date "2022-06-24T09:28:31Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 +property_value: http://purl.org/dc/terms/date "2022-06-24T09:28:31Z" xsd:dateTime [Term] id: UBERON:8480002 @@ -258212,9 +254791,9 @@ def: "A portion of smooth muscle tissue that is part of the thoracic aorta." [ht is_a: UBERON:0004178 ! aorta smooth muscle tissue intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0001515 ! thoracic aorta -relationship: dc-contributor https://orcid.org/0000-0002-0819-0473 relationship: part_of UBERON:0001515 ! thoracic aorta -property_value: dcterms-date "2022-06-24T09:30:54Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 +property_value: http://purl.org/dc/terms/date "2022-06-24T09:30:54Z" xsd:dateTime [Term] id: UBERON:8480003 @@ -258224,9 +254803,9 @@ def: "A portion of smooth muscle tissue that is part of an iliac artery." [https is_a: UBERON:0002111 ! artery smooth muscle tissue intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0005609 ! iliac artery -relationship: dc-contributor https://orcid.org/0000-0002-0819-0473 relationship: part_of UBERON:0005609 ! iliac artery -property_value: dcterms-date "2022-06-24T09:32:07Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 +property_value: http://purl.org/dc/terms/date "2022-06-24T09:32:07Z" xsd:dateTime [Term] id: UBERON:8480004 @@ -258236,9 +254815,9 @@ def: "An endothelium that is part of an iliac vein." [https://orcid.org/0000-000 is_a: UBERON:0001919 ! endothelium of vein intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0005610 ! iliac vein -relationship: dc-contributor https://orcid.org/0000-0002-0819-0473 relationship: part_of UBERON:0005610 ! iliac vein -property_value: dcterms-date "2022-06-24T09:33:18Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 +property_value: http://purl.org/dc/terms/date "2022-06-24T09:33:18Z" xsd:dateTime [Term] id: UBERON:8480005 @@ -258250,9 +254829,9 @@ is_a: UBERON:0005156 ! reproductive structure is_a: UBERON:0005292 ! extraembryonic tissue intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:8480007 ! placental artery -relationship: dc-contributor https://orcid.org/0000-0002-0819-0473 relationship: part_of UBERON:8480007 ! placental artery -property_value: dcterms-date "2022-06-24T09:34:25Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 +property_value: http://purl.org/dc/terms/date "2022-06-24T09:34:25Z" xsd:dateTime [Term] id: UBERON:8480006 @@ -258260,11 +254839,12 @@ name: mesenteric lymphatic vessel namespace: uberon def: "Lymphatic vessel that is part of the mesentery." [https://orcid.org/0000-0002-0819-0473] is_a: UBERON:0001473 ! lymphatic vessel +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0001473 ! lymphatic vessel intersection_of: part_of UBERON:0002095 ! mesentery -relationship: dc-contributor https://orcid.org/0000-0002-0819-0473 relationship: part_of UBERON:0002095 ! mesentery -property_value: dcterms-date "2022-06-24T09:35:29Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 +property_value: http://purl.org/dc/terms/date "2022-06-24T09:35:29Z" xsd:dateTime [Term] id: UBERON:8480007 @@ -258275,8 +254855,8 @@ is_a: UBERON:0001637 ! artery is_a: UBERON:0022358 ! placenta blood vessel intersection_of: UBERON:0001637 ! artery intersection_of: part_of UBERON:0001987 ! placenta -relationship: dc-contributor https://orcid.org/0000-0002-0819-0473 -property_value: dcterms-date "2022-06-24T11:25:24Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 +property_value: http://purl.org/dc/terms/date "2022-06-24T11:25:24Z" xsd:dateTime [Term] id: UBERON:8480008 @@ -258287,8 +254867,8 @@ is_a: UBERON:0001638 ! vein is_a: UBERON:0022358 ! placenta blood vessel intersection_of: UBERON:0001638 ! vein intersection_of: part_of UBERON:0001987 ! placenta -relationship: dc-contributor https://orcid.org/0000-0002-0819-0473 -property_value: dcterms-date "2022-06-27T09:30:52Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 +property_value: http://purl.org/dc/terms/date "2022-06-27T09:30:52Z" xsd:dateTime [Term] id: UBERON:8480025 @@ -258298,9 +254878,9 @@ def: "A zone of skin that is above the clavicle zone in the pectoral girdle regi is_a: UBERON:0000014 ! zone of skin intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0001421 ! pectoral girdle region -relationship: dc-contributor https://orcid.org/0000-0002-0819-0473 relationship: part_of UBERON:0001421 ! pectoral girdle region -property_value: dcterms-date "2022-08-29T14:17:12Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 +property_value: http://purl.org/dc/terms/date "2022-08-29T14:17:12Z" xsd:dateTime [Term] id: UBERON:8480026 @@ -258309,11 +254889,12 @@ namespace: uberon def: "A zone of skin that is above the iliac crest in the pelvic girdle bone/zone." [https://orcid.org/0000-0002-0819-0473] synonym: "skin of posterior iliac crest region" BROAD [] is_a: UBERON:0001415 ! skin of pelvis +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0007830 ! pelvic girdle bone/zone -relationship: dc-contributor https://orcid.org/0000-0002-0819-0473 relationship: part_of UBERON:0007830 ! pelvic girdle bone/zone -property_value: dcterms-date "2022-08-29T14:19:16Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 +property_value: http://purl.org/dc/terms/date "2022-08-29T14:19:16Z" xsd:dateTime [Term] id: UBERON:8480029 @@ -258324,9 +254905,9 @@ is_a: UBERON:0000014 ! zone of skin is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0004176 ! external genitalia -relationship: dc-contributor https://orcid.org/0000-0002-0819-0473 relationship: part_of UBERON:0004176 ! external genitalia -property_value: dcterms-date "2022-08-30T06:55:06Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 +property_value: http://purl.org/dc/terms/date "2022-08-30T06:55:06Z" xsd:dateTime [Term] id: UBERON:8480030 @@ -258336,9 +254917,9 @@ def: "A zone of skin that is part of the breast." [https://orcid.org/0000-0002-0 is_a: UBERON:0001868 ! skin of chest intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0000310 ! breast -relationship: dc-contributor https://orcid.org/0000-0002-0819-0473 relationship: part_of UBERON:0000310 ! breast -property_value: dcterms-date "2022-08-29T14:03:54Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 +property_value: http://purl.org/dc/terms/date "2022-08-29T14:03:54Z" xsd:dateTime [Term] id: UBERON:8480037 @@ -258347,13 +254928,14 @@ namespace: uberon def: "Subserosa that is part of the uterine tube. It contains loose connective tissue, blood vessels and lymphatic tissue." [ISBN:9783662026762, PMID:30095490] synonym: "subserosa of fallopian tube" EXACT [PMID:30095490] synonym: "subserosa of oviduct" EXACT [PMID:34440264] +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005156 ! reproductive structure is_a: UBERON:0012375 ! subserosa intersection_of: UBERON:0012375 ! subserosa intersection_of: part_of UBERON:0003889 ! fallopian tube -relationship: dc-contributor https://orcid.org/0000-0002-0819-0473 relationship: part_of UBERON:0003889 ! fallopian tube -property_value: dcterms-date "2022-10-21T08:55:11Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 +property_value: http://purl.org/dc/terms/date "2022-10-21T08:55:11Z" xsd:dateTime [Term] id: UBERON:8480068 @@ -258363,9 +254945,9 @@ def: "A portion of smooth muscle tissue that is part of a saphenous vein." [http is_a: UBERON:0004696 ! venous system smooth muscle intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0007318 ! saphenous vein -relationship: dc-contributor https://orcid.org/0000-0002-0819-0473 relationship: part_of UBERON:0007318 ! saphenous vein -property_value: dcterms-date "2023-08-31T11:41:09Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 +property_value: http://purl.org/dc/terms/date "2023-08-31T11:41:09Z" xsd:dateTime [Term] id: UBERON:8480074 @@ -258376,9 +254958,9 @@ is_a: UBERON:0000014 ! zone of skin is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0000991 ! gonad -relationship: dc-contributor https://orcid.org/0000-0002-0819-0473 relationship: part_of UBERON:0000991 ! gonad -property_value: dcterms-date "2023-08-29T10:24:24Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 +property_value: http://purl.org/dc/terms/date "2023-08-29T10:24:24Z" xsd:dateTime [Term] id: UBERON:8600000 @@ -258388,9 +254970,9 @@ def: "A conductive airway that branches into terminal bronchioles." [PMID:165435 subset: human_reference_atlas synonym: "preterminal bronchiole" EXACT [PMID:16543587] is_a: UBERON:0002186 ! bronchiole -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2023-02-08T13:31:12Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-02-08T13:31:12Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:8600001 @@ -258402,9 +254984,9 @@ synonym: "lobular bronchiole epithelium" EXACT [FMA:62497] is_a: UBERON:0002051 ! epithelium of bronchiole intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:8600000 ! lobular bronchiole -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: part_of UBERON:8600000 ! lobular bronchiole -property_value: dcterms-date "2023-02-10T14:26:09Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-02-10T14:26:09Z" xsd:dateTime [Term] id: UBERON:8600002 @@ -258414,9 +254996,9 @@ def: "A mucosa that is part of a lobular bronchiole." [FMA:263230] is_a: UBERON:0005039 ! mucosa of bronchiole intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:8600000 ! lobular bronchiole -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: part_of UBERON:8600000 ! lobular bronchiole -property_value: dcterms-date "2023-02-10T14:48:35Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-02-10T14:48:35Z" xsd:dateTime [Term] id: UBERON:8600003 @@ -258426,9 +255008,9 @@ def: "A smooth muscle tissue that is part of a lobular bronchiole." [FMA:261081] is_a: UBERON:0004515 ! smooth muscle tissue of bronchiole intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:8600000 ! lobular bronchiole -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: part_of UBERON:8600000 ! lobular bronchiole -property_value: dcterms-date "2023-02-10T14:54:06Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-02-10T14:54:06Z" xsd:dateTime [Term] id: UBERON:8600004 @@ -258438,9 +255020,9 @@ def: "A muscle tissue that is associated with soft internal organs (viscera)." [ comment: It is quite common to refer to visceral muscles as smooth muscles, by analogy with vertebrates; however, most visceral muscles in arthropods are actually striated. {xref="https://en.wikipedia.org/wiki/Smooth_muscle", xref="FBbt:00005070", comment="PMID:8720463"} synonym: "visceral muscle" EXACT [] {comment="BTO:0002780"} is_a: UBERON:0002385 ! muscle tissue -relationship: composed_primarily_of CL:0008007 ! visceral muscle cell -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -property_value: dcterms-date "2023-02-16T10:17:46Z" xsd:dateTime +relationship: RO:0002473 CL:0008007 ! composed primarily of visceral muscle cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-02-16T10:17:46Z" xsd:dateTime [Term] id: UBERON:8600006 @@ -258450,8 +255032,8 @@ def: "A striated muscle tissue that is associated with soft internal organs (vis synonym: "striated visceral muscle tissue" EXACT [] is_a: UBERON:0002036 ! striated muscle tissue is_a: UBERON:8600004 ! visceral muscle tissue -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -property_value: dcterms-date "2023-02-16T10:34:43Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-02-16T10:34:43Z" xsd:dateTime [Term] id: UBERON:8600010 @@ -258459,14 +255041,15 @@ name: bronchial submucosal gland ciliated duct namespace: uberon def: "A ciliated duct part of a bronchial submucosal gland." [PMID:30864819] subset: human_reference_atlas +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:8600014 ! submucosal gland ciliated duct intersection_of: UBERON:8600014 ! submucosal gland ciliated duct intersection_of: part_of UBERON:8410043 ! bronchus submucosal gland -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: dc-contributor https://orcid.org/0000-0002-9185-3994 relationship: part_of UBERON:8410043 ! bronchus submucosal gland -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2023-05-02T08:07:56Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 +property_value: http://purl.org/dc/terms/date "2023-05-02T08:07:56Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:8600011 @@ -258474,14 +255057,15 @@ name: tracheal submucosal gland ciliated duct namespace: uberon def: "A ciliated duct part of a tracheal submucosal gland." [PMID:30864819] subset: human_reference_atlas +is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:8600014 ! submucosal gland ciliated duct intersection_of: UBERON:8600014 ! submucosal gland ciliated duct intersection_of: part_of UBERON:0005203 ! trachea gland -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: dc-contributor https://orcid.org/0000-0002-9185-3994 relationship: part_of UBERON:0005203 ! trachea gland -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2023-05-02T08:08:14Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 +property_value: http://purl.org/dc/terms/date "2023-05-02T08:08:14Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:8600012 @@ -258492,10 +255076,10 @@ subset: human_reference_atlas is_a: UBERON:0014717 ! mucous acinus intersection_of: UBERON:0009842 ! glandular acinus intersection_of: part_of UBERON:0011148 ! submucosal gland -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: part_of UBERON:0011148 ! submucosal gland -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2023-05-02T08:57:27Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-05-02T08:57:27Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:8600014 @@ -258503,10 +255087,10 @@ name: submucosal gland ciliated duct namespace: uberon def: "A ciliated tubular structure in a submucosal gland connecting the submucosal gland collecting duct with the surface epithelium." [PMID:17707699, PMID:30864819] is_a: UBERON:0000058 ! duct -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: has_part CL:0000067 ! ciliated epithelial cell relationship: part_of UBERON:0011148 ! submucosal gland -property_value: dcterms-date "2023-05-02T08:09:14Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-05-02T08:09:14Z" xsd:dateTime [Term] id: UBERON:8600017 @@ -258517,12 +255101,13 @@ comment: A bronchopulmonary segment is surrounded by connective tissue septa, wh subset: human_reference_atlas synonym: "lung segment" EXACT [PMID:33620799] is_a: UBERON:0000063 ! organ subunit -relationship: contributes_to_morphology_of UBERON:0000101 ! lobe of lung -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: dc-contributor https://orcid.org/0000-0002-9185-3994 +is_a: UBERON:0004119 ! endoderm-derived structure relationship: part_of UBERON:0000101 ! lobe of lung -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2023-07-20T12:43:29Z" xsd:dateTime +relationship: RO:0002433 UBERON:0000101 ! contributes to morphology of lobe of lung +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-9185-3994 +property_value: http://purl.org/dc/terms/date "2023-07-20T12:43:29Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:8600018 @@ -258532,10 +255117,10 @@ def: "A regulatory system of the body that integrates the nervous system and the comment: In vertebrates, the hypothalamic-pituitary-target organ axis (H-P axis), the autonomic nervous system (ANS) and the diffuse neuroendocrine or APUD system contribute to the neuroendocrine system. {xref="PMID:15481802"} synonym: "NES" RELATED OMO:0003000 [PMID:15481802] is_a: UBERON:0000467 ! anatomical system -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: overlaps UBERON:0000949 ! endocrine system relationship: overlaps UBERON:0001016 ! nervous system -property_value: dcterms-date "2023-08-29T10:49:45Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-08-29T10:49:45Z" xsd:dateTime [Term] id: UBERON:8600021 @@ -258546,10 +255131,10 @@ subset: human_reference_atlas is_a: UBERON:0022358 ! placenta blood vessel intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0004027 ! chorionic plate -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: part_of UBERON:0004027 ! chorionic plate -relationship: present_in_taxon NCBITaxon:9606 ! Homo sapiens -property_value: dcterms-date "2023-09-14T09:09:36Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-09-14T09:09:36Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:8600023 @@ -258559,12 +255144,13 @@ def: "A stroma that is part of a chorionic villus (placental villus). A placenta synonym: "chorionic villous stroma" EXACT [PMID:12624135] synonym: "CVS" RELATED OMO:0003000 [PMID:12624135] is_a: UBERON:0003891 ! stroma +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0003891 ! stroma intersection_of: part_of UBERON:0007106 ! chorionic villus -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: dc-contributor https://orcid.org/0000-0001-7655-4833 relationship: part_of UBERON:0007106 ! chorionic villus -property_value: dcterms-date "2023-07-04T10:46:17Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7655-4833 +property_value: http://purl.org/dc/terms/date "2023-07-04T10:46:17Z" xsd:dateTime [Term] id: UBERON:8600024 @@ -258576,11 +255162,11 @@ is_a: UBERON:0003512 ! lung blood vessel is_a: UBERON:0005194 ! thoracic vein intersection_of: UBERON:0001979 ! venule intersection_of: part_of UBERON:0002048 ! lung -relationship: connected_to UBERON:0002016 ! pulmonary vein -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: drains UBERON:0016405 ! pulmonary capillary relationship: part_of UBERON:0013127 ! pulmonary venous system -property_value: dcterms-date "2023-10-24T11:26:27Z" xsd:dateTime +relationship: RO:0002170 UBERON:0002016 ! connected to pulmonary vein +relationship: RO:0002179 UBERON:0016405 ! drains pulmonary capillary +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-10-24T11:26:27Z" xsd:dateTime [Term] id: UBERON:8600034 @@ -258592,10 +255178,10 @@ synonym: "lamina propria of jejunum" EXACT [PMID:22763879] is_a: UBERON:0001238 ! lamina propria of small intestine intersection_of: UBERON:0000030 ! lamina propria intersection_of: part_of UBERON:0002115 ! jejunum -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: dc-contributor https://orcid.org/0000-0001-8134-3037 relationship: part_of UBERON:0008343 ! intestinal villus of jejunum -property_value: dcterms-date "2024-01-09T16:36:35Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8134-3037 +property_value: http://purl.org/dc/terms/date "2024-01-09T16:36:35Z" xsd:dateTime [Term] id: UBERON:8600035 @@ -258607,10 +255193,10 @@ synonym: "lamina propria of ileum" EXACT [PMID:36067905] is_a: UBERON:0001238 ! lamina propria of small intestine intersection_of: UBERON:0000030 ! lamina propria intersection_of: part_of UBERON:0002116 ! ileum -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -relationship: dc-contributor https://orcid.org/0000-0001-8134-3037 relationship: part_of UBERON:0008344 ! intestinal villus of ileum -property_value: dcterms-date "2024-01-09T16:48:17Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-8134-3037 +property_value: http://purl.org/dc/terms/date "2024-01-09T16:48:17Z" xsd:dateTime [Term] id: UBERON:8600038 @@ -258618,10 +255204,10 @@ name: placental disc namespace: uberon def: "A disc-shaped structure that is part of the placenta. A placental disc supports fetal development through the exchange of nutrients between maternal and fetal bloodstreams. The placental disc is structured to keep the blood streams separate, while maximizing surface area for the transport of nutrients between them, to maintain an immunological barrier." [PMID:35496035] synonym: "placental disk" EXACT [PMID:30133439] -is_a: UBERON:0000061 ! anatomical structure -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 +is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0001987 ! placenta -property_value: dcterms-date "2024-01-16T17:50:20Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-01-16T17:50:20Z" xsd:dateTime [Term] id: UBERON:8600039 @@ -258630,12 +255216,12 @@ namespace: uberon def: "A mesenchyme that is part of a chorionic villus." [doi:10.1007/978-3-030-84725-8] is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0003265 ! chorionic mesenchyme -is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010377 ! mesenchyme from somatopleure intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0007106 ! chorionic villus -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: part_of UBERON:0007106 ! chorionic villus -property_value: dcterms-date "2024-01-16T18:13:12Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-01-16T18:13:12Z" xsd:dateTime [Term] id: UBERON:8600042 @@ -258646,9 +255232,9 @@ is_a: UBERON:0001473 ! lymphatic vessel is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0001473 ! lymphatic vessel intersection_of: part_of UBERON:0001295 ! endometrium -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: part_of UBERON:0001295 ! endometrium -property_value: dcterms-date "2024-01-16T18:18:36Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2024-01-16T18:18:36Z" xsd:dateTime [Term] id: http://purl.obolibrary.org/obo/D96882F1-8709-49AB-BCA9-772A67EA6C33 @@ -258657,6 +255243,12 @@ comment: ID was moved to the CL namespace. Use CL:0017509. is_obsolete: true replaced_by: CL:0017509 +[Typedef] +id: BFO:0000067 +name: contains process +def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] +comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant + [Typedef] id: CL:4030044 name: has_not_completed @@ -258676,11 +255268,6 @@ id: RO:0000052 name: characteristic of def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." [] comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. -property_value: IAO:0000111 "inheres in" xsd:string -property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string -property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string -property_value: IAO:0000118 "inheres_in" xsd:string -property_value: RO:0001900 RO:0001901 is_functional: true is_a: RO:0002314 ! characteristic of part of inverse_of: bearer_of ! bearer of @@ -258690,10 +255277,7 @@ id: RO:0000079 name: function of def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. -property_value: editor_note "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string -property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string -property_value: IAO:0000118 "function_of" xsd:string -property_value: IAO:0000118 "is function of" xsd:string +property_value: IAO:0000116 "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string domain: BFO:0000034 ! function is_a: RO:0000052 ! characteristic of inverse_of: RO:0000085 ! has function @@ -258703,22 +255287,16 @@ id: RO:0000080 name: quality of def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. -property_value: editor_note "A quality inheres in its bearer at all times for which the quality exists." xsd:string -property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string -property_value: IAO:0000118 "is quality of" xsd:string -property_value: IAO:0000118 "quality_of" xsd:string +property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string is_a: RO:0000052 ! characteristic of -inverse_of: has_quality ! has quality +inverse_of: RO:0000086 ! has quality [Typedef] id: RO:0000081 name: role of def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. -property_value: editor_note "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string -property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string -property_value: IAO:0000118 "is role of" xsd:string -property_value: IAO:0000118 "role_of" xsd:string +property_value: IAO:0000116 "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string is_a: RO:0000052 ! characteristic of inverse_of: RO:0000087 ! has role @@ -258726,20 +255304,24 @@ inverse_of: RO:0000087 ! has role id: RO:0000085 name: has function def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] -property_value: editor_note "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string -property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string -property_value: IAO:0000118 "has_function" xsd:string +property_value: IAO:0000116 "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000034 ! function is_a: bearer_of ! bearer of +[Typedef] +id: RO:0000086 +name: has quality +def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] +property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string +range: BFO:0000019 ! quality +is_a: bearer_of ! bearer of + [Typedef] id: RO:0000087 name: has role def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] -property_value: editor_note "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string -property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string -property_value: IAO:0000118 "has_role" xsd:string +property_value: IAO:0000116 "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000023 ! role is_a: bearer_of ! bearer of @@ -258766,12 +255348,7 @@ id: RO:0001000 name: derives from def: "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" [] subset: ro-eco -property_value: editor_note "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." xsd:string -property_value: IAO:0000112 "this cell derives from this parent cell (cell division)" xsd:string -property_value: IAO:0000112 "this nucleus derives from this parent nucleus (nuclear division)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000118 "derives_from" xsd:string -property_value: IAO:0000232 "This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations." xsd:string +property_value: IAO:0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." xsd:string inverse_of: RO:0001001 ! derives into [Typedef] @@ -258779,33 +255356,58 @@ id: RO:0001001 name: derives into def: "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" [] subset: ro-eco -property_value: editor_note "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." xsd:string -property_value: IAO:0000112 "this parent cell derives into this cell (cell division)" xsd:string -property_value: IAO:0000112 "this parent nucleus derives into this nucleus (nuclear division)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000118 "derives_into" xsd:string +property_value: IAO:0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." xsd:string + +[Typedef] +id: RO:0001015 +name: location of +def: "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" [] +property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +is_transitive: true +inverse_of: RO:0001025 ! located in + +[Typedef] +id: RO:0001025 +name: located in +def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +property_value: IAO:0000116 "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" xsd:string +property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Located_in" xsd:anyURI +domain: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +range: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +is_transitive: true +transitive_over: part_of ! part of [Typedef] id: RO:0002000 name: 2D boundary of def: "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" [] -property_value: editor_note "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string -property_value: editor_note "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string -property_value: IAO:0000112 "the surface of my skin is a 2D boundary of my body" xsd:string -property_value: IAO:0000118 "2D_boundary_of" xsd:string -property_value: IAO:0000118 "boundary of" xsd:string -property_value: IAO:0000118 "is 2D boundary of" xsd:string -property_value: IAO:0000118 "is boundary of" xsd:string -property_value: IAO:0000118 "surface of" xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string is_a: RO:0002323 ! mereotopologically related to -inverse_of: has_boundary ! has 2D boundary +inverse_of: RO:0002002 ! has 2D boundary + +[Typedef] +id: RO:0002002 +name: has 2D boundary +def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000141 ! immaterial entity +is_a: RO:0002323 ! mereotopologically related to + +[Typedef] +id: RO:0002005 +name: innervated_by +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000122 ! neuron projection bundle +inverse_of: RO:0002134 ! innervates [Typedef] id: RO:0002006 name: has synaptic terminal of -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: overlaps ! overlaps inverse_of: RO:0002130 ! has synaptic terminal in @@ -258887,16 +255489,23 @@ id: RO:0002081 name: before or simultaneous with comment: Primitive instance level timing relation between events subset: ro-eco -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000118 "<=" xsd:string is_a: RO:0002222 ! temporally related to +[Typedef] +id: RO:0002082 +name: simultaneous with +def: "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." [] +comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) +subset: ro-eco +is_symmetric: true +is_transitive: true +is_a: RO:0002081 ! before or simultaneous with + [Typedef] id: RO:0002086 name: ends after comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) subset: ro-eco -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string is_transitive: true is_a: RO:0002222 ! temporally related to @@ -258904,25 +255513,16 @@ is_a: RO:0002222 ! temporally related to id: RO:0002100 name: has soma location def: "Relation between a neuron and a material anatomical entity that its soma is part of." [] -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron range: UBERON:0000465 ! material anatomical entity is_a: overlaps ! overlaps -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] [Typedef] id: RO:0002101 name: fasciculates with def: "relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.\n" [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "fasciculates with" xsd:string -property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron range: UBERON:0000122 ! neuron projection bundle is_a: overlaps ! overlaps @@ -258932,27 +255532,23 @@ inverse_of: RO:0002132 ! has fasciculating neuron projection id: RO:0002102 name: axon synapses in def: "Relation between a neuron and some structure its axon forms (chemical) synapses in." [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: RO:0002113 ! has presynaptic terminal in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "BFO_0000051 some (\n GO_0030424 and BFO_0000051 some (\n GO_0042734 and BFO_0000050 some (\n GO_0045202 and BFO_0000050 some ?Y)))" [] +[Typedef] +id: RO:0002103 +name: synapsed by +def: "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " [] +is_a: RO:0002485 ! receives input from +inverse_of: RO:0002120 ! synapsed to +expand_expression_to: "BFO_0000051 some (GO_0045211 that part_of some (GO_0045202 that has_part some (GO_0042734 that BFO_0000050 some Y?)))" [] + [Typedef] id: RO:0002104 name: has plasma membrane part def: "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part." [] -property_value: IAO:0000112 "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9990-8331 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 -property_value: RO:0001900 RO:0001901 domain: UBERON:0000465 ! material anatomical entity range: UBERON:0000465 ! material anatomical entity is_a: has_part ! has part @@ -258962,29 +255558,19 @@ expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] id: RO:0002110 name: has postsynaptic terminal in def: "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. " [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "synapsed in" xsd:string -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: RO:0002130 ! has synaptic terminal in inverse_of: RO:0002113 ! has presynaptic terminal in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (\n http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some (\n http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))" [] [Typedef] id: RO:0002113 name: has presynaptic terminal in def: "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input." [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000118 "synapses in" xsd:string -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: RO:0002130 ! has synaptic terminal in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000050 some Y?)" [] [Typedef] @@ -258992,11 +255578,6 @@ id: RO:0002120 name: synapsed to def: " Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.\n " [] comment: N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part some (\n ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( \n ‘synapse ; GO:0045202’ that has_part some (\n ‘post-synaptic membrane ; GO:0045211’ that part_of some N2)))) -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 is_a: RO:0002486 ! sends output to expand_expression_to: "BFO_0000051 some (GO_0042734 that part_of some (GO_0045202 that BFO_0000051 some (GO_0045211 that BFO_0000050 some Y?)))" [] @@ -259004,104 +255585,272 @@ expand_expression_to: "BFO_0000051 some (GO_0042734 that part_of some (GO_004520 id: RO:0002130 name: has synaptic terminal in def: "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "has synapse in" xsd:string -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: overlaps ! overlaps -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "RO_0002131 some (GO_0045202 that BFO_0000050 some Y?)" [] [Typedef] id: RO:0002132 name: has fasciculating neuron projection def: "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "has fasciculating component" xsd:string -property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string -property_value: RO:0001900 RO:0001901 domain: UBERON:0000122 ! neuron projection bundle is_a: overlaps ! overlaps +[Typedef] +id: RO:0002134 +name: innervates +def: "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." [] +domain: UBERON:0000122 ! neuron projection bundle +transitive_over: part_of ! part of +expand_expression_to: "RO_0002132 some (GO_0043005 that (RO_0002131 some (GO_0045202 that BFO_0000050 some Y?)))" [] + +[Typedef] +id: RO:0002150 +name: continuous with +def: "X continuous_with Y if and only if X and Y share a fiat boundary." [] +property_value: seeAlso "FMA:85972" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000004 ! independent continuant +is_symmetric: true +is_a: RO:0002323 ! mereotopologically related to + +[Typedef] +id: RO:0002158 +name: shares ancestor with +def: "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." [] +comment: VBO calls this homologous_to +is_symmetric: true +is_transitive: true +is_a: RO:0002320 ! evolutionarily related to + +[Typedef] +id: RO:0002160 +name: only in taxon +def: "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." [] +property_value: IAO:0000116 "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" xsd:string +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints +is_a: RO:0002162 ! in taxon + +[Typedef] +id: RO:0002162 +name: in taxon +def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." [] +comment: Connects a biological entity to its taxon of origin. +subset: ro-eco +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints +holds_over_chain: capable_of RO:0002162 +holds_over_chain: extends_fibers_into RO:0002162 +holds_over_chain: has_part RO:0002162 +holds_over_chain: part_of RO:0002162 +holds_over_chain: results_in_developmental_progression_of RO:0002162 +holds_over_chain: RO:0002202 RO:0002162 +holds_over_chain: RO:0002206 RO:0002162 +holds_over_chain: RO:0002225 RO:0002162 +holds_over_chain: RO:0002254 RO:0002162 +is_a: RO:0002320 ! evolutionarily related to + [Typedef] id: RO:0002163 name: spatially disjoint from def: "A is spatially_disjoint_from B if and only if they have no parts in common" [] subset: ro-eco -property_value: editor_note "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" xsd:anyURI is_a: RO:0002323 ! mereotopologically related to expand_expression_to: "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" [] +[Typedef] +id: RO:0002170 +name: connected to +def: "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" [] +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI +is_a: RO:0002323 ! mereotopologically related to + +[Typedef] +id: RO:0002176 +name: connects +def: "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." [] +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI +domain: BFO:0000004 ! independent continuant +is_a: RO:0002323 ! mereotopologically related to + +[Typedef] +id: RO:0002177 +name: attached to part of +def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000061 ! anatomical structure +is_a: RO:0002323 ! mereotopologically related to +is_a: RO:0002567 ! biomechanically related to + +[Typedef] +id: RO:0002178 +name: supplies +def: "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." [] +property_value: IAO:0000116 "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" xsd:string +is_a: RO:0002170 ! connected to + +[Typedef] +id: RO:0002179 +name: drains +def: "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." [] +property_value: IAO:0000116 "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" xsd:string +is_a: RO:0002170 ! connected to + +[Typedef] +id: RO:0002202 +name: develops from +def: "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" [] +comment: This is the transitive form of the develops from relation +domain: BFO:0000004 ! independent continuant +range: BFO:0000004 ! independent continuant +is_transitive: true +is_a: RO:0002254 ! has developmental contribution from +is_a: RO:0002258 ! developmentally preceded by +inverse_of: RO:0002203 ! develops into + +[Typedef] +id: RO:0002203 +name: develops into +def: "inverse of develops from" [] +subset: RO:0002259 +is_transitive: true +is_a: RO:0002286 ! developmentally succeeded by +is_a: RO:0002387 ! has potential to develop into +is_a: RO:0002388 ! has potential to directly develop into + [Typedef] id: RO:0002206 name: expressed in def: "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" [] -property_value: IAO:0000112 "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000002 ! continuant range: UBERON:0000465 ! material anatomical entity is_a: RO:0002330 ! genomically related to inverse_of: RO:0002292 ! expresses -transitive_over: part_of ! part_of +transitive_over: part_of ! part of + +[Typedef] +id: RO:0002207 +name: directly develops from +def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] +comment: TODO - add child relations from DOS +synonym: "has developmental precursor" EXACT [] +is_a: RO:0002202 ! develops from +inverse_of: RO:0002210 ! directly develops into [Typedef] id: RO:0002210 name: directly develops into def: "inverse of directly develops from" [] subset: RO:0002259 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000118 "developmental precursor of" xsd:string -is_a: develops_into ! develops into +is_a: RO:0002203 ! develops into + +[Typedef] +id: RO:0002219 +name: surrounded by +def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" [] +is_a: adjacent_to ! adjacent to +inverse_of: RO:0002221 ! surrounds + +[Typedef] +id: RO:0002221 +name: surrounds +def: "inverse of surrounded by" [] +subset: RO:0002259 +is_a: adjacent_to ! adjacent to [Typedef] id: RO:0002222 name: temporally related to comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. subset: ro-eco -property_value: http://purl.org/dc/terms/source "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" xsd:anyURI -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent +[Typedef] +id: RO:0002223 +name: starts +def: "inverse of starts with" [] +subset: ro-eco +is_a: part_of ! part of +is_a: RO:0002222 ! temporally related to +inverse_of: starts_with ! starts with + +[Typedef] +id: RO:0002225 +name: develops from part of +def: "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" [] +holds_over_chain: RO:0002207 part_of +is_a: RO:0002202 ! develops from + +[Typedef] +id: RO:0002226 +name: develops in +def: "x develops_in y if x is located in y whilst x is developing" [] +domain: UBERON:0001062 ! anatomical entity +holds_over_chain: RO:0002207 RO:0001025 +is_a: RO:0002258 ! developmentally preceded by + +[Typedef] +id: RO:0002229 +name: ends +def: "inverse of ends with" [] +subset: ro-eco +is_a: part_of ! part of +is_a: RO:0002222 ! temporally related to +inverse_of: ends_with ! ends with + +[Typedef] +id: RO:0002252 +name: connecting branch of +def: "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." [] +property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 +is_a: RO:0002170 ! connected to +is_a: RO:0002375 ! in branching relationship with +inverse_of: RO:0002253 ! has connecting branch + [Typedef] id: RO:0002253 name: has connecting branch def: "inverse of connecting branch of" [] subset: RO:0002259 -property_value: RO:0004036 BFO:0000051 is_a: RO:0002375 ! in branching relationship with +[Typedef] +id: RO:0002254 +name: has developmental contribution from +def: "x has developmental contribution from y iff x has some part z such that z develops from y" [] +domain: UBERON:0001062 ! anatomical entity +range: UBERON:0001062 ! anatomical entity +holds_over_chain: has_part RO:0002202 +is_a: RO:0002258 ! developmentally preceded by +inverse_of: RO:0002255 ! developmentally contributes to + [Typedef] id: RO:0002255 name: developmentally contributes to def: "inverse of has developmental contribution from" [] subset: RO:0002259 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -holds_over_chain: develops_into part_of -is_a: has_potential_to_developmentally_contribute_to ! has potential to developmentally contribute to +holds_over_chain: RO:0002203 part_of is_a: RO:0002286 ! developmentally succeeded by +is_a: RO:0002385 ! has potential to developmentally contribute to + +[Typedef] +id: RO:0002256 +name: developmentally induced by +def: "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" [] +domain: UBERON:0000465 ! material anatomical entity +range: UBERON:0000465 ! material anatomical entity +is_a: RO:0002258 ! developmentally preceded by +inverse_of: RO:0002257 ! developmentally induces [Typedef] id: RO:0002257 name: developmentally induces def: "Inverse of developmentally induced by" [] -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002286 ! developmentally succeeded by is_a: RO:0002386 ! has potential to developmentally induce @@ -259110,10 +255859,7 @@ id: RO:0002258 name: developmentally preceded by def: "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p" [] comment: This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from -property_value: editor_note "false" xsd:boolean -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string +property_value: IAO:0000116 "false" xsd:boolean domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant is_a: RO:0002324 ! developmentally related to @@ -259124,7 +255870,6 @@ id: RO:0002263 name: acts upstream of def: "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: IAO:0000112 "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." xsd:string property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of holds_over_chain: RO:0002327 causally_upstream_of is_a: RO:0002264 ! acts upstream of or within @@ -259135,25 +255880,26 @@ name: acts upstream of or within def: "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term synonym: "affects" RELATED [] -property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within" xsd:anyURI holds_over_chain: RO:0002327 causally_upstream_of_or_within is_a: RO:0002500 ! causal agent in process +[Typedef] +id: RO:0002285 +name: developmentally replaces +def: "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" [] +property_value: IAO:0000116 "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" xsd:string +is_a: RO:0002258 ! developmentally preceded by + [Typedef] id: RO:0002286 name: developmentally succeeded by def: "Inverse of developmentally preceded by" [] -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002384 ! has developmental potential involving [Typedef] id: RO:0002287 name: part of developmental precursor of -property_value: IAO:0000112 "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: part_of RO:0002210 is_a: RO:0002286 ! developmentally succeeded by @@ -259161,80 +255907,58 @@ is_a: RO:0002286 ! developmentally succeeded by id: RO:0002292 name: expresses def: "y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." [] -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002330 ! genomically related to [Typedef] id: RO:0002314 name: characteristic of part of def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." [] -property_value: editor_note "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "inheres in part of" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: RO:0000052 part_of {RO:0002582="true"} is_a: RO:0002502 ! depends on -transitive_over: part_of ! part_of +transitive_over: part_of ! part of [Typedef] id: RO:0002320 name: evolutionarily related to def: "A relationship that holds via some environmental process" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." xsd:string [Typedef] id: RO:0002323 name: mereotopologically related to def: "A mereological relationship or a topological relationship" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string -property_value: RO:0001900 RO:0001901 [Typedef] id: RO:0002324 name: developmentally related to def: "A relationship that holds between entities participating in some developmental process (GO:0032502)" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" xsd:string [Typedef] id: RO:0002327 name: enables def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "catalyzes" xsd:string -property_value: IAO:0000118 "executes" xsd:string -property_value: IAO:0000118 "has" xsd:string -property_value: IAO:0000118 "is catalyzing" xsd:string -property_value: IAO:0000118 "is executing" xsd:string -property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string property_value: seeAlso "https://wiki.geneontology.org/Enables" xsd:anyURI is_a: capable_of ! capable of inverse_of: RO:0002333 ! enabled by transitive_over: has_part ! has part transitive_over: RO:0002017 ! has component activity +[Typedef] +id: RO:0002328 +name: functionally related to +def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] + [Typedef] id: RO:0002329 name: part of structure that is capable of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "false" xsd:boolean -holds_over_chain: part_of capable_of {RO:0002581="true"} -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002330 name: genomically related to def: "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant @@ -259242,31 +255966,25 @@ range: BFO:0000002 ! continuant id: RO:0002331 name: involved in def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "actively involved in" xsd:string -property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Involved_in" xsd:anyURI holds_over_chain: RO:0002327 part_of is_a: participates_in ! participates in is_a: RO:0002431 ! involved in or involved in regulation of -transitive_over: part_of ! part_of +transitive_over: part_of ! part of [Typedef] id: RO:0002333 name: enabled by def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso "https://wiki.geneontology.org/Enabled_by" xsd:anyURI -is_a: functionally_related_to ! functionally related to is_a: has_participant ! has participant +is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002337 name: related via localization to def: "A relationship that holds via some process of localization" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is a grouping relation." xsd:string domain: BFO:0000015 ! process range: BFO:0000002 ! continuant @@ -259274,84 +255992,134 @@ range: BFO:0000002 ! continuant id: RO:0002350 name: member of def: "is member of is a mereological relation between a item and a collection." [] -property_value: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string -property_value: IAO:0000118 "is member of" xsd:string -property_value: IAO:0000118 "member part of" xsd:string -property_value: IAO:0000119 "SIO" xsd:string -property_value: RO:0001900 RO:0001901 -is_a: part_of ! part_of -inverse_of: has_member ! has member +is_a: part_of ! part of +inverse_of: RO:0002351 ! has member + +[Typedef] +id: RO:0002351 +name: has member +def: "has member is a mereological relation between a collection and an item." [] +is_a: has_part ! has part + +[Typedef] +id: RO:0002352 +name: input of +def: "inverse of has input" [] +subset: ro-eco +subset: RO:0002259 +is_a: participates_in ! participates in +is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002354 name: formed as result of -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: output_of ! output of [Typedef] id: RO:0002360 name: has dendrite location -property_value: http://purl.org/dc/terms/source "http://neurolex.org/wiki/Property:DendriteLocation" xsd:anyURI -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps +[Typedef] +id: RO:0002371 +name: attached to +def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] +subset: ro-eco +is_symmetric: true +is_a: RO:0002170 ! connected to +is_a: RO:0002177 ! attached to part of + +[Typedef] +id: RO:0002372 +name: has muscle origin +def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] +property_value: seeAlso http://dbpedia.org/property/origin +domain: UBERON:0000061 {comment="We need to import uberon muscle to create a stricter domain constraint"} ! anatomical structure +is_a: RO:0002371 ! attached to +is_a: RO:0002567 ! biomechanically related to + +[Typedef] +id: RO:0002373 +name: has muscle insertion +def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] +property_value: seeAlso http://dbpedia.org/property/insertion +domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} ! anatomical structure +is_a: RO:0002371 ! attached to +is_a: RO:0002567 ! biomechanically related to + [Typedef] id: RO:0002375 name: in branching relationship with def: "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" xsd:string -property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string -property_value: RO:0004036 BFO:0000050 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png property_value: seeAlso "https://github.com/obophenotype/uberon/issues/170" xsd:anyURI domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002323 ! mereotopologically related to +[Typedef] +id: RO:0002376 +name: tributary of +def: "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." [] +subset: ro-eco +property_value: seeAlso http://dbpedia.org/ontology/drainsTo +property_value: seeAlso "http://en.wikipedia.org/wiki/Tributary" xsd:anyURI +is_a: RO:0002170 ! connected to +is_a: RO:0002375 ! in branching relationship with + [Typedef] id: RO:0002379 name: spatially coextensive with def: "x spatially_coextensive_with y if and inly if x and y have the same location" [] -property_value: IAO:0000112 "A lump of clay and a statue" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" xsd:string is_a: overlaps ! overlaps +[Typedef] +id: RO:0002380 +name: branching part of +def: "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" [] +subset: ro-eco +property_value: seeAlso "FMA:85994" xsd:string +property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 +is_a: part_of ! part of +is_a: RO:0002375 ! in branching relationship with +inverse_of: RO:0002569 ! has branching part + [Typedef] id: RO:0002384 name: has developmental potential involving def: "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: UBERON:0001062 ! anatomical entity range: UBERON:0001062 ! anatomical entity is_a: RO:0002324 ! developmentally related to +[Typedef] +id: RO:0002385 +name: has potential to developmentally contribute to +def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] +is_a: RO:0002384 ! has developmental potential involving + [Typedef] id: RO:0002386 name: has potential to developmentally induce def: "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002384 ! has developmental potential involving + +[Typedef] +id: RO:0002387 +name: has potential to develop into +def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] is_a: RO:0002384 ! has developmental potential involving [Typedef] id: RO:0002388 name: has potential to directly develop into def: "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: has_potential_to_develop_into ! has potential to develop into +is_a: RO:0002387 ! has potential to develop into [Typedef] id: RO:0002407 name: indirectly positively regulates def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "indirectly activates" xsd:string -property_value: RO:0002579 RO:0002213 property_value: seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates" xsd:anyURI holds_over_chain: directly_positively_regulates directly_positively_regulates holds_over_chain: directly_positively_regulates RO:0002407 @@ -259365,9 +256133,6 @@ transitive_over: directly_positively_regulates ! directly positively regulates id: RO:0002409 name: indirectly negatively regulates def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "indirectly inhibits" xsd:string -property_value: RO:0002579 RO:0002212 property_value: seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates" xsd:anyURI holds_over_chain: directly_negatively_regulates directly_negatively_regulates holds_over_chain: directly_negatively_regulates RO:0002409 @@ -259380,15 +256145,12 @@ transitive_over: directly_negatively_regulates ! directly negatively regulates id: RO:0002410 name: causally related to def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] -property_value: editor_note "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string [Typedef] id: RO:0002428 name: involved in regulation of def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002327 regulates holds_over_chain: RO:0002331 regulates is_a: RO:0002263 ! acts upstream of @@ -259398,8 +256160,6 @@ is_a: RO:0002431 ! involved in or involved in regulation of id: RO:0002429 name: involved in positive regulation of def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0004049 RO:0002428 holds_over_chain: RO:0002327 positively_regulates holds_over_chain: RO:0002331 positively_regulates is_a: RO:0002428 ! involved in regulation of @@ -259408,7 +256168,6 @@ is_a: RO:0002428 ! involved in regulation of id: RO:0002430 name: involved in negative regulation of def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002428 holds_over_chain: RO:0002327 negatively_regulates holds_over_chain: RO:0002331 negatively_regulates @@ -259418,11 +256177,9 @@ is_a: RO:0002428 ! involved in regulation of id: RO:0002431 name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] -property_value: editor_note "OWL does not allow defining object properties via a Union" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "involved in or reguates" xsd:string -is_a: functionally_related_to ! functionally related to +property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string is_a: RO:0002264 ! acts upstream of or within +is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process [Typedef] @@ -259430,12 +256187,14 @@ id: RO:0002432 name: is active in def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [https://orcid.org/0000-0002-6601-2165, https://orcid.org/0000-0002-7073-9172] synonym: "enables activity in" EXACT [] -property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "executes activity in" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Is_active_in" xsd:anyURI -holds_over_chain: RO:0002327 occurs_in {RO:0002581="true"} -is_a: functionally_related_to ! functionally related to +is_a: overlaps ! overlaps +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002433 +name: contributes to morphology of +def: "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." [] is_a: overlaps ! overlaps [Typedef] @@ -259444,11 +256203,8 @@ name: interacts with def: "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." [] subset: ro-eco synonym: "in pairwise interaction with" EXACT [] -property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0914" xsd:anyURI -property_value: editor_note "Considering relabeling as 'pairwise interacts with'" xsd:anyURI -property_value: editor_note "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string +property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI +property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity @@ -259458,10 +256214,6 @@ is_symmetric: true id: RO:0002436 name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] -property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0915" xsd:anyURI -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "binds" xsd:string -property_value: IAO:0000118 "molecularly binds with" xsd:string property_value: seeAlso ECO:0000353 is_symmetric: true is_a: RO:0002434 ! interacts with @@ -259469,9 +256221,7 @@ is_a: RO:0002434 ! interacts with [Typedef] id: RO:0002447 name: phosphorylates -property_value: editor_note "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string +property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string is_a: RO:0002436 ! molecularly interacts with [Typedef] @@ -259479,8 +256229,6 @@ id: RO:0002448 name: directly regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." [] synonym: "molecularly controls" EXACT [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002436 ! molecularly interacts with @@ -259491,9 +256239,6 @@ id: RO:0002449 name: directly negatively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] synonym: "molecularly decreases activity of" EXACT [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 -property_value: IAO:0000118 "directly inhibits" xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002448 ! directly regulates activity of @@ -259503,9 +256248,6 @@ id: RO:0002450 name: directly positively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] synonym: "molecularly increases activity of" EXACT [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 -property_value: IAO:0000118 "directly activates" xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002448 ! directly regulates activity of @@ -259513,61 +256255,136 @@ is_a: RO:0002448 ! directly regulates activity of [Typedef] id: RO:0002464 name: helper property (not for use in curation) -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string + +[Typedef] +id: RO:0002473 +name: composed primarily of +def: "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." [] +subset: ro-eco +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: has_part ! has part [Typedef] id: RO:0002479 name: has part that occurs in def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] subset: ro-eco -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant -holds_over_chain: has_part occurs_in {RO:0002581="true"} [Typedef] id: RO:0002481 name: is kinase activity -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002564 ! molecular interaction relation helper property [Typedef] id: RO:0002485 name: receives input from -property_value: editor_note "See notes for inverse relation" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: connected_to ! connected to +property_value: IAO:0000116 "See notes for inverse relation" xsd:string +is_a: RO:0002170 ! connected to inverse_of: RO:0002486 ! sends output to [Typedef] id: RO:0002486 name: sends output to -property_value: editor_note "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: connected_to ! connected to +property_value: IAO:0000116 "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." xsd:string +is_a: RO:0002170 ! connected to [Typedef] id: RO:0002487 name: relation between physical entity and a process or stage -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage." xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000003 ! occurrent +[Typedef] +id: RO:0002488 +name: existence starts during +def: "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." [] +is_a: RO:0002490 ! existence overlaps +is_a: RO:0002496 ! existence starts during or after +transitive_over: part_of ! part of + +[Typedef] +id: RO:0002489 +name: existence starts with +def: "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." [] +is_a: RO:0002488 ! existence starts during + [Typedef] id: RO:0002490 name: existence overlaps def: "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" [] comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002487 ! relation between physical entity and a process or stage +[Typedef] +id: RO:0002491 +name: existence starts and ends during +def: "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +synonym: "exists during" EXACT [] +is_a: RO:0002488 ! existence starts during +is_a: RO:0002492 ! existence ends during + +[Typedef] +id: RO:0002492 +name: existence ends during +def: "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +is_a: RO:0002490 ! existence overlaps +is_a: RO:0002497 ! existence ends during or before +transitive_over: part_of ! part of + +[Typedef] +id: RO:0002493 +name: existence ends with +def: "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +is_a: RO:0002492 ! existence ends during + +[Typedef] +id: RO:0002494 +name: transformation of +def: "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" [] +is_transitive: true +is_a: RO:0002202 ! develops from + +[Typedef] +id: RO:0002495 +name: immediate transformation of +def: "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" [] +is_a: RO:0002207 ! directly develops from +is_a: RO:0002494 ! transformation of + +[Typedef] +id: RO:0002496 +name: existence starts during or after +def: "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +holds_over_chain: part_of RO:0002496 +holds_over_chain: RO:0002258 RO:0002496 +is_a: RO:0002487 ! relation between physical entity and a process or stage +transitive_over: part_of ! part of +transitive_over: preceded_by ! preceded by +transitive_over: RO:0002082 ! simultaneous with + +[Typedef] +id: RO:0002497 +name: existence ends during or before +def: "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +holds_over_chain: part_of RO:0002497 +holds_over_chain: RO:0002286 RO:0002497 +is_a: RO:0002487 ! relation between physical entity and a process or stage +transitive_over: part_of ! part of +transitive_over: precedes ! precedes +transitive_over: RO:0002082 ! simultaneous with + [Typedef] id: RO:0002500 name: causal agent in process def: "A relationship between a material entity and a process where the material entity has some causal role that influences the process" [] -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_a: RO:0002595 ! causal relation between material entity and a process inverse_of: process_has_causal_agent ! process has causal agent @@ -259575,9 +256392,6 @@ inverse_of: process_has_causal_agent ! process has causal agent id: RO:0002501 name: causal relation between processes def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent is_a: RO:0002410 ! causally related to @@ -259585,33 +256399,35 @@ is_a: RO:0002410 ! causally related to [Typedef] id: RO:0002502 name: depends on -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso BFO:0000169 [Typedef] id: RO:0002506 name: causal relation between entities -property_value: editor_note "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: IAO:0000116 "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant is_a: RO:0002410 ! causally related to +[Typedef] +id: RO:0002551 +name: has skeleton +def: "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." [] +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000465 {IAO:0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} ! material anatomical entity +is_a: has_part ! has part +inverse_of: RO:0002576 ! skeleton of +is_asymmetric: true + [Typedef] id: RO:0002559 name: causally influenced by -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string is_a: RO:0002506 ! causal relation between entities inverse_of: RO:0002566 ! causally influences [Typedef] id: RO:0002563 name: interaction relation helper property -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29 property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI is_a: RO:0002464 ! helper property (not for use in curation) @@ -259619,17 +256435,12 @@ is_a: RO:0002464 ! helper property (not for use in curation) [Typedef] id: RO:0002564 name: molecular interaction relation helper property -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002563 ! interaction relation helper property [Typedef] id: RO:0002566 name: causally influences def: "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant is_a: RO:0002506 ! causal relation between entities @@ -259638,20 +256449,66 @@ is_a: RO:0002506 ! causal relation between entities id: RO:0002567 name: biomechanically related to def: "A relation that holds between elements of a musculoskeletal system or its analogs." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string domain: UBERON:0000061 ! anatomical structure range: UBERON:0000061 ! anatomical structure -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002568 +name: has muscle antagonist +def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] +is_a: RO:0002567 ! biomechanically related to + +[Typedef] +id: RO:0002569 +name: has branching part +def: "inverse of branching part of" [] +subset: ro-eco +subset: RO:0002259 +is_transitive: true +is_a: has_part ! has part +is_a: RO:0002375 ! in branching relationship with + +[Typedef] +id: RO:0002570 +name: conduit for +def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] +subset: ro-eco +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: overlaps ! overlaps + +[Typedef] +id: RO:0002571 +name: lumen of +def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] +subset: ro-eco +range: BFO:0000040 ! material entity +is_a: part_of ! part of + +[Typedef] +id: RO:0002572 +name: luminal space of +def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" [] +subset: ro-eco +domain: BFO:0000141 ! immaterial entity +is_a: RO:0002571 ! lumen of + +[Typedef] +id: RO:0002576 +name: skeleton of +def: "inverse of has skeleton" [] +subset: RO:0002259 +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000061 ! anatomical structure +is_a: part_of ! part of [Typedef] id: RO:0002584 name: has part structure that is capable of def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" [] -property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: has_part capable_of -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to is_a: RO:0002595 ! causal relation between material entity and a process [Typedef] @@ -259664,9 +256521,7 @@ is_a: has_input ! has input id: RO:0002595 name: causal relation between material entity and a process def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." [] -property_value: editor_note "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000040 ! material entity range: BFO:0000015 ! process is_a: RO:0002410 ! causally related to @@ -259675,8 +256530,6 @@ is_a: RO:0002410 ! causally related to id: RO:0002596 name: capable of regulating def: "Holds between c and p if and only if c is capable of some activity a, and a regulates p." [] -property_value: IAO:0000112 "pyrethroid -> growth" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations holds_over_chain: capable_of regulates is_a: RO:0002500 ! causal agent in process @@ -259684,7 +256537,6 @@ is_a: RO:0002500 ! causal agent in process id: RO:0002597 name: capable of negatively regulating def: "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." [] -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations holds_over_chain: capable_of negatively_regulates is_a: RO:0002596 ! capable of regulating @@ -259692,8 +256544,6 @@ is_a: RO:0002596 ! capable of regulating id: RO:0002598 name: capable of positively regulating def: "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." [] -property_value: IAO:0000112 "renin -> arteriolar smooth muscle contraction" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations holds_over_chain: capable_of positively_regulates is_a: RO:0002596 ! capable of regulating @@ -259702,7 +256552,7 @@ id: RO:0004031 name: enables subfunction def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] holds_over_chain: RO:0002327 has_part -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z @@ -259710,7 +256560,6 @@ creation_date: 2018-01-25T23:20:13Z id: RO:0004032 name: acts upstream of or within, positive effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: RO:0004049 RO:0002264 property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0004047 is_a: RO:0002264 ! acts upstream of or within @@ -259733,7 +256582,6 @@ id: RO:0004034 name: acts upstream of, positive effect def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: RO:0004049 RO:0002263 property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 causally_upstream_of,_positive_effect is_a: RO:0002263 ! acts upstream of @@ -259766,7 +256614,6 @@ creation_date: 2018-03-13T23:55:05Z [Typedef] id: RO:0004047 name: causally upstream of or within, positive effect -property_value: RO:0004049 RO:0002418 property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect is_a: causally_upstream_of_or_within ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 @@ -259776,7 +256623,6 @@ creation_date: 2018-03-13T23:55:19Z id: RO:0011002 name: regulates activity of def: "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." [] -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002566 ! causally influences @@ -259831,7 +256677,7 @@ name: has synaptic IO in region def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region." [] synonym: "has synaptic input or output in" EXACT [] is_a: RO:0002130 ! has synaptic terminal in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:26:52Z @@ -259844,7 +256690,7 @@ synonym: "has sensory terminal in" EXACT [] synonym: "has sensory terminal location" EXACT [] domain: CL:0000101 ! sensory neuron is_a: RO:0002360 ! has dendrite location -transitive_over: part_of ! part_of +transitive_over: part_of ! part of created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-20T12:10:09Z @@ -259887,9 +256733,8 @@ comment: Example: a spherical object has the quality of being spherical, and the id: RO:0015015 name: has high plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: dc-contributor https://orcid.org/0000-0003-1617-8244 -property_value: dc-contributor https://orcid.org/0000-0003-1940-6740 -property_value: IAO:0000112 "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part @@ -259897,9 +256742,8 @@ is_a: RO:0002104 ! has plasma membrane part id: RO:0015016 name: has low plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: dc-contributor https://orcid.org/0000-0003-1617-8244 -property_value: dc-contributor https://orcid.org/0000-0003-1940-6740 -property_value: IAO:0000112 "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part @@ -259908,11 +256752,6 @@ id: RO:0017001 name: device utilizes material def: "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." [] synonym: "utilizes" BROAD [] -property_value: IAO:0000112 "A diagnostic testing device utilizes a specimen." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 -property_value: IAO:0000117 https://orcid.org/0000-0003-2620-0345 -property_value: IAO:0000232 "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." xsd:string -property_value: IAO:0000232 "See github ticket https://github.com/oborel/obo-relations/issues/497" xsd:string holds_over_chain: capable_of has_input creation_date: 2021-11-08T12:00:00Z @@ -259933,65 +256772,25 @@ creation_date: 2020-06-08T17:21:33Z id: adjacent_to name: adjacent to namespace: external -namespace: uberon def: "x adjacent to y if and only if x and y share a boundary." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002220 -property_value: editor_note "This relation acts as a join point with BSPO" xsd:string -property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} -property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string -property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string -property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000004 ! independent continuant is_a: RO:0002163 ! spatially disjoint from -[Typedef] -id: anterior_to -name: anterior to -namespace: uberon -xref: BSPO:0000096 - [Typedef] id: anteriorly_connected_to name: anteriorly connected to namespace: uberon def: "x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] -is_a: connected_to ! connected to -is_a: posterior_to ! posterior to +is_a: BSPO:0000099 +is_a: RO:0002170 ! connected to is_a: transitively_anteriorly_connected_to ! transitively anteriorly connected to -[Typedef] -id: attaches_to -name: attached to -namespace: uberon -def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] -subset: ro-eco -xref: RO:0002371 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000589 "attached to (anatomical structure to anatomical structure)" xsd:string -is_symmetric: true -is_a: attaches_to_part_of ! attached to part of -is_a: connected_to ! connected to - -[Typedef] -id: attaches_to_part_of -name: attached to part of -namespace: uberon -def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] -xref: RO:0002177 -property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string -domain: UBERON:0000061 ! anatomical structure -range: UBERON:0000061 ! anatomical structure -holds_over_chain: attaches_to part_of {RO:0002582="true"} -is_a: RO:0002323 ! mereotopologically related to -is_a: RO:0002567 ! biomechanically related to - [Typedef] id: bearer_of name: bearer of @@ -259999,13 +256798,7 @@ name: has characteristic namespace: external def: "Inverse of characteristic_of" [] xref: RO:0000053 -property_value: editor_note "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string -property_value: IAO:0000111 "bearer of" xsd:string -property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string -property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string -property_value: IAO:0000118 "bearer_of" xsd:string -property_value: IAO:0000118 "is bearer of" xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string range: BFO:0000020 ! specifically dependent continuant is_inverse_functional: true @@ -260013,45 +256806,20 @@ is_inverse_functional: true id: bounding_layer_of name: bounding layer of namespace: external -namespace: uberon def: "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000" [] comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. subset: ro-eco xref: RO:0002007 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 range: BFO:0000040 ! material entity -is_a: part_of ! part_of - -[Typedef] -id: branching_part_of -name: branching part of -namespace: uberon -def: "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" [] -subset: ro-eco -xref: RO:0002380 -property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso "FMA:85994" xsd:string -property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 -is_a: part_of ! part_of -is_a: RO:0002375 ! in branching relationship with -inverse_of: has_branching_part ! has branching part +is_a: part_of ! part of [Typedef] id: capable_of name: capable of namespace: external -namespace: uberon def: "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " [] subset: ro-eco xref: RO:0002215 -property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string -property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "has function realized in" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 -property_value: IAO:0000232 "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000015 ! process is_a: capable_of_part_of ! capable of part of @@ -260060,14 +256828,10 @@ is_a: capable_of_part_of ! capable of part of id: capable_of_part_of name: capable of part of namespace: external -namespace: uberon def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] xref: RO:0002216 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "has function in" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: capable_of part_of {RO:0002582="true"} -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process [Typedef] @@ -260076,8 +256840,6 @@ name: causally downstream of namespace: external def: "inverse of upstream of" [] xref: RO:0002404 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of_or_within ! causally downstream of or within is_a: preceded_by ! preceded by inverse_of: causally_upstream_of ! causally upstream of @@ -260089,8 +256851,6 @@ namespace: external def: "inverse of causally upstream of or within" [] subset: RO:0002259 xref: RO:0002427 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_transitive: true is_a: RO:0002501 ! causal relation between processes @@ -260102,7 +256862,6 @@ def: "p is causally upstream of q iff p is causally related to q, the end of p p subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002411 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within is_a: precedes ! precedes @@ -260115,7 +256874,6 @@ def: "p is causally upstream of, negative effect q iff p is casually upstream of subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 -property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_negative_effect is_a: causally_upstream_of ! causally upstream of @@ -260130,8 +256888,6 @@ comment: holds between x and y if and only if x is causally upstream of y and th subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002304 -property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 -property_value: RO:0004049 RO:0002411 property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_positive_effect is_a: causally_upstream_of ! causally upstream of is_a: RO:0004047 ! causally upstream of or within, positive effect @@ -260143,9 +256899,7 @@ namespace: external def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] synonym: "affects" RELATED [] xref: RO:0002418 -property_value: editor_note "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "influences (processual)" xsd:string +property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string is_transitive: true is_a: RO:0002501 ! causal relation between processes inverse_of: causally_downstream_of_or_within ! causally downstream of or within @@ -260155,287 +256909,16 @@ id: channel_for name: channel for namespace: uberon synonym: "carries" BROAD [] -domain: UBERON:0004111 ! anatomical conduit -range: UBERON:0000463 ! organism substance [Typedef] id: channels_from name: channels_from namespace: uberon -is_transitive: true [Typedef] id: channels_into name: channels_into namespace: uberon -is_transitive: true - -[Typedef] -id: composed_primarily_of -name: composed primarily of -namespace: uberon -def: "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." [] -subset: ro-eco -xref: RO:0002473 -property_value: IAO:0000112 "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: RO:0001900 RO:0001901 -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: has_part ! has part - -[Typedef] -id: conduit_for -name: conduit for -namespace: uberon -def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] -subset: ro-eco -xref: RO:0002570 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "UBERON:cjm" xsd:string -property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: overlaps ! overlaps - -[Typedef] -id: connected_to -name: connected to -namespace: uberon -def: "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" [] -xref: RO:0002170 -property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI -property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: connecting_branch_of -name: connecting branch of -namespace: uberon -def: "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." [] -xref: RO:0002252 -property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." xsd:string -property_value: RO:0004036 BFO:0000050 -property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 -is_a: connected_to ! connected to -is_a: RO:0002375 ! in branching relationship with -inverse_of: RO:0002253 ! has connecting branch - -[Typedef] -id: connects -name: connects -namespace: uberon -def: "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." [] -xref: RO:0002176 -property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string -property_value: IAO:0000112 "The M8 connects Glasgow and Edinburgh" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI -property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI -domain: BFO:0000004 ! independent continuant -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: contains_process -name: contains process -namespace: uberon -def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] -comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant -xref: BFO:0000067 -property_value: IAO:0000111 "site of" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - -[Typedef] -id: continuous_with -name: continuous with -namespace: uberon -def: "X continuous_with Y if and only if X and Y share a fiat boundary." [] -xref: RO:0002150 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "connected to" xsd:string -property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string -property_value: RO:0001900 RO:0001901 -property_value: seeAlso "FMA:85972" xsd:string -domain: BFO:0000004 ! independent continuant -range: BFO:0000004 ! independent continuant -is_symmetric: true -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: contributes_to_morphology_of -name: contributes to morphology of -namespace: uberon -def: "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." [] -xref: RO:0002433 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: overlaps ! overlaps - -[Typedef] -id: dc-contributor -name: contributor -namespace: uberon -xref: http://purl.org/dc/terms/contributor -is_metadata_tag: true - -[Typedef] -id: dc-creator -name: creator -namespace: uberon -xref: http://purl.org/dc/elements/1.1/creator -is_metadata_tag: true - -[Typedef] -id: dc-description -name: description -namespace: uberon -xref: http://purl.org/dc/elements/1.1/description -is_metadata_tag: true - -[Typedef] -id: dc-title -name: title -namespace: uberon -xref: http://purl.org/dc/elements/1.1/title -is_metadata_tag: true - -[Typedef] -id: dcterms-date -name: date -namespace: uberon -xref: http://purl.org/dc/terms/date -is_metadata_tag: true - -[Typedef] -id: dcterms-license -name: license -namespace: uberon -xref: http://purl.org/dc/terms/license -is_metadata_tag: true - -[Typedef] -id: deep_to -name: deep to -namespace: uberon -xref: BSPO:0000107 - -[Typedef] -id: depiction -name: depiction -namespace: uberon -xref: http://xmlns.com/foaf/0.1/depiction -is_metadata_tag: true - -[Typedef] -id: developmentally_induced_by -name: developmentally induced by -namespace: uberon -def: "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" [] -xref: RO:0002256 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "induced by" xsd:string -property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string -property_value: IAO:0000119 "GO:0001759" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 -property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string -domain: UBERON:0000465 ! material anatomical entity -range: UBERON:0000465 ! material anatomical entity -is_a: RO:0002258 ! developmentally preceded by -inverse_of: RO:0002257 ! developmentally induces - -[Typedef] -id: developmentally_replaces -name: developmentally replaces -namespace: uberon -def: "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" [] -xref: RO:0002285 -property_value: editor_note "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "replaces" xsd:string -is_a: RO:0002258 ! developmentally preceded by - -[Typedef] -id: develops_from -name: develops from -namespace: uberon -def: "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" [] -comment: This is the transitive form of the develops from relation -xref: RO:0002202 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 -domain: BFO:0000004 ! independent continuant -range: BFO:0000004 ! independent continuant -is_transitive: true -is_a: has_developmental_contribution_from ! has developmental contribution from -is_a: RO:0002258 ! developmentally preceded by -inverse_of: develops_into ! develops into - -[Typedef] -id: develops_from_part_of -name: develops from part of -namespace: uberon -def: "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" [] -xref: RO:0002225 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -holds_over_chain: directly_develops_from part_of -is_a: develops_from ! develops from - -[Typedef] -id: develops_in -name: develops in -namespace: uberon -def: "x develops_in y if x is located in y whilst x is developing" [] -xref: RO:0002226 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "EHDAA2" xsd:string -property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string -domain: UBERON:0001062 ! anatomical entity -holds_over_chain: directly_develops_from located_in -is_a: RO:0002258 ! developmentally preceded by - -[Typedef] -id: develops_into -name: develops into -namespace: uberon -def: "inverse of develops from" [] -subset: RO:0002259 -xref: RO:0002203 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 -is_transitive: true -is_a: has_potential_to_develop_into ! has potential to develop into -is_a: RO:0002286 ! developmentally succeeded by -is_a: RO:0002388 ! has potential to directly develop into - -[Typedef] -id: directly_develops_from -name: directly develops from -namespace: uberon -def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] -comment: TODO - add child relations from DOS -synonym: "has developmental precursor" EXACT [] -xref: RO:0002207 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000119 "FBbt" xsd:string -property_value: RO:0002575 RO:0002202 -is_a: develops_from ! develops from -inverse_of: RO:0002210 ! directly develops into [Typedef] id: directly_negatively_regulates @@ -260446,8 +256929,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002630 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002578 property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates" xsd:anyURI is_a: directly_regulates ! directly regulates @@ -260462,9 +256943,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002629 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string -property_value: RO:0004049 RO:0002578 property_value: seeAlso "https://wiki.geneontology.org/Directly_positively_regulates" xsd:anyURI is_a: directly_regulates ! directly regulates is_a: positively_regulates ! positively regulates @@ -260478,188 +256956,35 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002578 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly regulates (processual)" xsd:string -property_value: RO:0002575 RO:0002211 is_a: immediately_causally_upstream_of ! immediately causally upstream of is_a: regulates ! regulates -[Typedef] -id: distal_to -name: distal to -namespace: uberon -xref: BSPO:0000097 - [Typedef] id: distally_connected_to name: distally connected to namespace: uberon def: "x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] -is_a: connected_to ! connected to -is_a: proximal_to ! proximal to +is_a: BSPO:0000100 +is_a: RO:0002170 ! connected to is_a: transitively_distally_connected_to ! transitively distally connected to -inverse_of: proximally_connected_to ! proximally connected to - -[Typedef] -id: distalmost_part_of -name: distalmost part of -namespace: uberon -xref: BSPO:0001108 - -[Typedef] -id: dorsal_to -name: dorsal to -namespace: uberon -xref: BSPO:0000098 - -[Typedef] -id: drains -name: drains -namespace: uberon -def: "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." [] -xref: RO:0002179 -property_value: editor_note "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 -domain: UBERON:0001638 ! vein -is_a: connected_to ! connected to - -[Typedef] -id: editor_note -name: editor note -namespace: uberon -def: "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology." [] -xref: IAO:0000116 -property_value: IAO:0000111 "editor note" xsd:string -property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000117 "PERSON:Daniel Schober" xsd:string -property_value: IAO:0000119 "GROUP:OBI:" xsd:string -is_metadata_tag: true - -[Typedef] -id: ends -name: ends -namespace: uberon -def: "inverse of ends with" [] -subset: ro-eco -xref: RO:0002229 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: part_of ! part_of -is_a: RO:0002222 ! temporally related to -inverse_of: ends_with ! ends with [Typedef] id: ends_with name: ends with namespace: external -namespace: uberon def: "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002230 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "finished by" xsd:string is_transitive: true is_a: has_part ! has part is_a: RO:0002222 ! temporally related to -[Typedef] -id: existence_ends_during -name: existence ends during -namespace: uberon -def: "Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely." [https://orcid.org/0000-0002-6601-2165] -def: "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -synonym: "ceases_to_exist_during" EXACT [] -xref: RO:0002492 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_ends_during_or_before ! existence ends during or before -is_a: RO:0002490 ! existence overlaps -transitive_over: part_of ! part_of - -[Typedef] -id: existence_ends_during_or_before -name: existence ends during or before -namespace: uberon -def: "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -xref: RO:0002497 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -holds_over_chain: part_of existence_ends_during_or_before -holds_over_chain: RO:0002286 existence_ends_during_or_before -is_a: RO:0002487 ! relation between physical entity and a process or stage -transitive_over: part_of ! part_of -transitive_over: precedes ! precedes -transitive_over: simultaneous_with ! simultaneous with - -[Typedef] -id: existence_ends_with -name: existence ends with -namespace: uberon -def: "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -xref: RO:0002493 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_ends_during ! existence ends during - -[Typedef] -id: existence_starts_and_ends_during -name: existence starts and ends during -namespace: uberon -def: "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -synonym: "exists during" EXACT [] -xref: RO:0002491 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_ends_during ! existence ends during -is_a: existence_starts_during ! existence starts during - -[Typedef] -id: existence_starts_during -name: existence starts during -namespace: uberon -def: "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." [] -xref: RO:0002488 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_starts_during_or_after ! existence starts during or after -is_a: RO:0002490 ! existence overlaps -transitive_over: part_of ! part_of - -[Typedef] -id: existence_starts_during_or_after -name: existence starts during or after -namespace: uberon -def: "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -xref: RO:0002496 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -holds_over_chain: part_of existence_starts_during_or_after -holds_over_chain: RO:0002258 existence_starts_during_or_after -is_a: RO:0002487 ! relation between physical entity and a process or stage -transitive_over: part_of ! part_of -transitive_over: preceded_by ! preceded by -transitive_over: simultaneous_with ! simultaneous with - -[Typedef] -id: existence_starts_with -name: existence starts with -namespace: uberon -def: "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." [] -xref: RO:0002489 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_starts_during ! existence starts during - [Typedef] id: extends_fibers_into name: extends_fibers_into namespace: uberon def: "X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y" [https://orcid.org/0000-0002-7073-9172] -holds_over_chain: RO:0002100 RO:0013001 -is_symmetric: true -is_a: connected_to ! connected to +is_a: RO:0002170 ! connected to [Typedef] id: filtered_through @@ -260668,75 +256993,17 @@ namespace: uberon def: "Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity." [] comment: Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed -[Typedef] -id: functionally_related_to -name: functionally related to -namespace: uberon -def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] -xref: RO:0002328 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string - -[Typedef] -id: has_boundary -name: has 2D boundary -namespace: uberon -def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] -xref: RO:0002002 -property_value: editor_note "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string -property_value: editor_note "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string -property_value: IAO:0000112 "my body has 2D boundary the surface of my skin" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "has boundary" xsd:string -property_value: IAO:0000118 "has_2D_boundary" xsd:string -property_value: RO:0001900 RO:0001901 -domain: BFO:0000040 ! material entity -range: BFO:0000141 ! immaterial entity -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: has_branching_part -name: has branching part -namespace: uberon -def: "inverse of branching part of" [] -subset: ro-eco -subset: RO:0002259 -xref: RO:0002569 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_transitive: true -is_a: has_part ! has part -is_a: RO:0002375 ! in branching relationship with - [Typedef] id: has_component name: has component namespace: external -namespace: uberon def: "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] subset: ro-eco xref: RO:0002180 -property_value: editor_note "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency is_a: has_part ! has part -[Typedef] -id: has_developmental_contribution_from -name: has developmental contribution from -namespace: uberon -def: "x has developmental contribution from y iff x has some part z such that z develops from y" [] -xref: RO:0002254 -property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: UBERON:0001062 ! anatomical entity -range: UBERON:0001062 ! anatomical entity -holds_over_chain: has_part develops_from -is_a: RO:0002258 ! developmentally preceded by -inverse_of: RO:0002255 ! developmentally contributes to - [Typedef] id: has_end_location name: has end location @@ -260744,9 +257011,6 @@ namespace: external def: "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" [] subset: ro-eco xref: RO:0002232 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "ends with process that occurs in" xsd:string domain: BFO:0000015 ! process range: BFO:0000004 ! independent continuant holds_over_chain: ends_with occurs_in @@ -260770,14 +257034,11 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002233 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "consumes" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Has_input" xsd:anyURI domain: BFO:0000015 ! process holds_over_chain: starts_with has_input is_a: has_participant ! has participant -inverse_of: input_of ! input of +inverse_of: RO:0002352 ! input of [Typedef] id: has_low_plasma_membrane_amount @@ -260787,52 +257048,6 @@ property_value: term_tracker_item https://github.com/obophenotype/cell-ontology/ is_obsolete: true replaced_by: RO:0015016 -[Typedef] -id: has_member -name: has member -namespace: uberon -def: "has member is a mereological relation between a collection and an item." [] -xref: RO:0002351 -property_value: IAO:0000119 "SIO" xsd:string -property_value: RO:0001900 RO:0001901 -is_a: has_part ! has part - -[Typedef] -id: has_muscle_antagonist -name: has muscle antagonist -namespace: uberon -def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] -xref: RO:0002568 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "Wikipedia:Antagonist_(muscle)" xsd:string -is_a: RO:0002567 ! biomechanically related to - -[Typedef] -id: has_muscle_insertion -name: has muscle insertion -namespace: uberon -def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] -xref: RO:0002373 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string -property_value: seeAlso http://dbpedia.org/property/insertion -domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} ! anatomical structure -is_a: attaches_to ! attached to -is_a: RO:0002567 ! biomechanically related to - -[Typedef] -id: has_muscle_origin -name: has muscle origin -namespace: uberon -def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] -xref: RO:0002372 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string -property_value: seeAlso http://dbpedia.org/property/origin -domain: UBERON:0000061 {comment="We need to import uberon muscle to create a stricter domain constraint"} ! anatomical structure -is_a: attaches_to ! attached to -is_a: RO:0002567 ! biomechanically related to - [Typedef] id: has_negative_regulatory_component_activity name: has negative regulatory component activity @@ -260850,13 +257065,9 @@ id: has_ontology_root_term name: has ontology root term name: preferred_root namespace: external -namespace: uberon def: "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root." [] xref: IAO:0000700 -property_value: IAO:0000111 "has ontology root term" xsd:string -property_value: IAO:0000117 "Nicolas Matentzoglu" xsd:string is_metadata_tag: true -is_class_level: true [Typedef] id: has_output @@ -260868,9 +257079,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002234 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "produces" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Has_output" xsd:anyURI holds_over_chain: ends_with has_output is_a: has_participant ! has participant @@ -260882,21 +257090,14 @@ name: has part name: has_part namespace: external namespace: quality -namespace: uberon def: "a core relation that holds between a whole and its part" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000051 -property_value: editor_note "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string -property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string -property_value: IAO:0000111 "has part" xsd:string -property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string -property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string -property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string -property_value: IAO:0000118 "has_part" xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string is_transitive: true is_a: overlaps ! overlaps @@ -260906,37 +257107,11 @@ name: has participant namespace: external def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] xref: RO:0000057 -property_value: editor_note "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string -property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string -property_value: IAO:0000111 "has participant" xsd:string -property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string -property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string -property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string -property_value: IAO:0000118 "has_participant" xsd:string +property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000002 ! continuant holds_over_chain: has_part has_participant -[Typedef] -id: has_potential_to_develop_into -name: has potential to develop into -namespace: uberon -def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] -xref: RO:0002387 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: RO:0002384 ! has developmental potential involving - -[Typedef] -id: has_potential_to_developmentally_contribute_to -name: has potential to developmentally contribute to -namespace: uberon -def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] -xref: RO:0002385 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: RO:0002384 ! has developmental potential involving - [Typedef] id: has_primary_input name: has primary input @@ -260972,18 +257147,6 @@ is_a: has_primary_input_or_output ! has primary input or output created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z -[Typedef] -id: has_quality -name: has quality -namespace: uberon -def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] -xref: RO:0000086 -property_value: editor_note "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string -property_value: IAO:0000112 "this apple has quality this red color" xsd:string -property_value: IAO:0000118 "has_quality" xsd:string -range: BFO:0000019 ! quality -is_a: bearer_of ! bearer of - [Typedef] id: has_regulatory_component_activity name: has regulatory component activity @@ -260995,24 +257158,6 @@ is_a: RO:0002017 ! has component activity created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z -[Typedef] -id: has_skeleton -name: has skeleton -namespace: uberon -def: "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." [] -xref: RO:0002551 -property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "has supporting framework" xsd:string -property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string -domain: UBERON:0000061 ! anatomical structure -domain: UBERON:0000475 ! organism subdivision -range: UBERON:0000465 {IAO:0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} ! material anatomical entity -range: UBERON:0010912 ! subdivision of skeleton -is_a: has_part ! has part -inverse_of: skeleton_of ! skeleton of -is_asymmetric: true - [Typedef] id: has_small_molecule_activator name: has small molecule activator @@ -261031,9 +257176,6 @@ namespace: external def: "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y" [] subset: ro-eco xref: RO:0002231 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "starts with process that occurs in" xsd:string domain: BFO:0000015 ! process range: BFO:0000004 ! independent continuant holds_over_chain: starts_with occurs_in @@ -261048,9 +257190,8 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002339 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of [Typedef] id: has_target_start_location @@ -261061,41 +257202,14 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002338 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in -transitive_over: part_of ! part_of - -[Typedef] -id: homologous_to -name: shares ancestor with -namespace: uberon -def: "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." [] -comment: VBO calls this homologous_to -xref: RO:0002158 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000232 "Consider obsoleting and merging with child relation, 'in homology relationship with'" xsd:string -is_symmetric: true -is_transitive: true -is_a: RO:0002320 ! evolutionarily related to - -[Typedef] -id: immediate_transformation_of -name: immediate transformation of -namespace: uberon -def: "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" [] -xref: RO:0002495 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0002575 RO:0002494 -is_a: directly_develops_from ! directly develops from -is_a: transformation_of ! transformation of +transitive_over: part_of ! part of [Typedef] id: immediately_causally_downstream_of name: immediately causally downstream of namespace: external xref: RO:0002405 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of ! causally downstream of is_a: immediately_preceded_by ! immediately preceded by inverse_of: immediately_causally_upstream_of ! immediately causally upstream of @@ -261106,26 +257220,15 @@ name: immediately causally upstream of namespace: external def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] xref: RO:0002412 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: immediately_precedes ! immediately precedes -[Typedef] -id: immediately_deep_to -name: immediately deep to -namespace: uberon -xref: BSPO:0001107 - [Typedef] id: immediately_preceded_by name: immediately preceded by namespace: external -namespace: uberon comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) xref: RO:0002087 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000118 "starts_at_end_of" xsd:string holds_over_chain: starts_with ends_with is_a: preceded_by ! preceded by inverse_of: immediately_precedes ! immediately precedes @@ -261137,230 +257240,22 @@ namespace: external comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) subset: ro-eco xref: RO:0002090 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "ends_at_start_of" xsd:string -property_value: IAO:0000118 "meets" xsd:string -property_value: RO:0002575 BFO:0000063 holds_over_chain: ends_with starts_with is_a: precedes ! precedes -[Typedef] -id: immediately_superficial_to -name: immediately superficial to -namespace: uberon -xref: BSPO:0015014 - -[Typedef] -id: in_anterior_side_of -name: in anterior side of -namespace: uberon -xref: BSPO:0000123 - -[Typedef] -id: in_deep_part_of -name: in deep part of -namespace: uberon -xref: BSPO:0001101 - -[Typedef] -id: in_dorsal_side_of -name: in dorsal side of -namespace: uberon -xref: BSPO:0015101 - -[Typedef] -id: in_lateral_side_of -name: in lateral side of -namespace: uberon -xref: BSPO:0000126 - -[Typedef] -id: in_left_side_of -name: in left side of -namespace: uberon -xref: BSPO:0000120 - -[Typedef] -id: in_posterior_side_of -name: in posterior side of -namespace: uberon -xref: BSPO:0000122 - -[Typedef] -id: in_proximal_side_of -name: in proximal side of -namespace: uberon -xref: BSPO:0000124 - -[Typedef] -id: in_right_side_of -name: in right side of -namespace: uberon -xref: BSPO:0000121 - -[Typedef] -id: in_superficial_part_of -name: in superficial part of -namespace: uberon -xref: BSPO:0001100 - -[Typedef] -id: in_taxon -name: in taxon -namespace: uberon -def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." [] -comment: Connects a biological entity to its taxon of origin. -subset: ro-eco -xref: RO:0002162 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9227-417X -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -holds_over_chain: attaches_to in_taxon -holds_over_chain: capable_of in_taxon -holds_over_chain: connected_to in_taxon -holds_over_chain: connects in_taxon -holds_over_chain: continuous_with in_taxon -holds_over_chain: developmentally_induced_by in_taxon -holds_over_chain: develops_from in_taxon -holds_over_chain: develops_from_part_of in_taxon -holds_over_chain: existence_ends_during in_taxon -holds_over_chain: existence_starts_during in_taxon -holds_over_chain: extends_fibers_into in_taxon -holds_over_chain: has_developmental_contribution_from in_taxon -holds_over_chain: has_part in_taxon -holds_over_chain: has_potential_to_develop_into in_taxon -holds_over_chain: innervated_by in_taxon -holds_over_chain: overlaps in_taxon -holds_over_chain: part_of in_taxon -holds_over_chain: produced_by in_taxon -holds_over_chain: produces in_taxon -holds_over_chain: results_in_developmental_progression_of in_taxon -holds_over_chain: RO:0002206 in_taxon -holds_over_chain: supplies in_taxon -is_a: RO:0002320 ! evolutionarily related to - [Typedef] id: indirectly_supplies name: indirectly_supplies namespace: uberon def: "a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s." [] -property_value: editor_note "add to RO" xsd:string -holds_over_chain: has_branching_part indirectly_supplies -holds_over_chain: has_branching_part supplies -is_transitive: true - -[Typedef] -id: innervated_by -name: innervated_by -namespace: uberon -xref: RO:0002005 -property_value: http://purl.org/spar/cito/citesAsAuthority "http://www.ncbi.nlm.nih.gov/pubmed/22402613" xsd:anyURI -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -domain: UBERON:0000061 ! anatomical structure -range: UBERON:0000122 ! neuron projection bundle -inverse_of: innervates ! innervates -transitive_over: branching_part_of ! branching part of - -[Typedef] -id: innervates -name: innervates -namespace: uberon -def: "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." [] -xref: RO:0002134 -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 -domain: UBERON:0000122 ! neuron projection bundle -transitive_over: part_of ! part_of -expand_expression_to: "RO_0002132 some (GO_0043005 that (RO_0002131 some (GO_0045202 that BFO_0000050 some Y?)))" [] - -[Typedef] -id: input_of -name: input of -namespace: uberon -def: "inverse of has input" [] -subset: ro-eco -subset: RO:0002259 -xref: RO:0002352 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: functionally_related_to ! functionally related to -is_a: participates_in ! participates in - -[Typedef] -id: intersects_midsagittal_plane_of -name: intersects midsagittal plane of -namespace: uberon -xref: BSPO:0005001 +property_value: IAO:0000116 "add to RO" xsd:string +holds_over_chain: RO:0002569 indirectly_supplies [Typedef] id: layer_part_of name: layer part of namespace: uberon -is_a: part_of ! part_of - -[Typedef] -id: located_in -name: located in -namespace: uberon -def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -xref: RO:0001025 -property_value: editor_note "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" xsd:string -property_value: editor_note "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:located_in" xsd:string -property_value: IAO:0000111 "located in" xsd:string -property_value: IAO:0000112 "my brain is located in my head" xsd:string -property_value: IAO:0000112 "this rat is located in this cage" xsd:string -property_value: IAO:0000118 "located_in" xsd:string -property_value: RO:0001900 RO:0001901 -property_value: seeAlso "https://wiki.geneontology.org/Located_in" xsd:anyURI -domain: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant -range: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant -is_transitive: true -transitive_over: part_of ! part_of - -[Typedef] -id: location_of -name: location of -namespace: uberon -def: "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" [] -xref: RO:0001015 -property_value: editor_note "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: IAO:0000111 "is location of" xsd:string -property_value: IAO:0000112 "my head is the location of my brain" xsd:string -property_value: IAO:0000112 "this cage is the location of this rat" xsd:string -property_value: IAO:0000118 "location_of" xsd:string -property_value: RO:0001900 RO:0001901 -is_transitive: true -inverse_of: located_in ! located in - -[Typedef] -id: lumen_of -name: lumen of -namespace: uberon -def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] -subset: ro-eco -xref: RO:0002571 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 https://orcid.org/0000-0002-6601-2165 -range: BFO:0000040 ! material entity -is_a: part_of ! part_of - -[Typedef] -id: luminal_space_of -name: luminal space of -namespace: uberon -def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" [] -subset: ro-eco -xref: RO:0002572 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: BFO:0000141 ! immaterial entity -is_a: lumen_of ! lumen of +is_a: part_of ! part of [Typedef] id: negatively_regulated_by @@ -261369,7 +257264,6 @@ namespace: external def: "inverse of negatively regulates" [] subset: RO:0002259 xref: RO:0002335 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -261381,9 +257275,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002212 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002211 holds_over_chain: ends_with negatively_regulates is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect @@ -261396,30 +257287,11 @@ name: negatively regulates characteristic namespace: gene_ontology def: "A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C." [] xref: RO:0019002 -property_value: dc-contributor https://orcid.org/0000-0002-8688-6599 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 holds_over_chain: negatively_regulates positively_regulates_characteristic holds_over_chain: positively_regulates negatively_regulates_characteristic is_a: regulates_characteristic ! regulates characteristic -[Typedef] -id: never_in_taxon -name: never in taxon -name: never_in_taxon -namespace: uberon -def: "S never_in_taxon T iff: S SubClassOf in_taxon only not T." [PMID:20973947] -def: "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL." [] -xref: RO:0002161 -property_value: IAO:0000112 "tooth SubClassOf 'never in taxon' value 'Aves'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 -property_value: OMO:0002000 "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" xsd:string -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -expand_assertion_to: "Class: EquivalentTo: ?X and (RO_0002162 some ?Y)" [] -expand_assertion_to: "Class: ?X DisjointWith: RO_0002162 some ?Y " [] -is_metadata_tag: true -is_class_level: true - [Typedef] id: occurs_in name: occurs in @@ -261430,64 +257302,38 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000066 -property_value: IAO:0000111 "occurs in" xsd:string -property_value: IAO:0000118 "occurs_in" xsd:string -property_value: IAO:0000118 "unfolds in" xsd:string -property_value: IAO:0000118 "unfolds_in" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl property_value: seeAlso "https://wiki.geneontology.org/Occurs_in" xsd:anyURI domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant holds_over_chain: part_of occurs_in -inverse_of: contains_process ! contains process -transitive_over: part_of ! part_of - -[Typedef] -id: only_in_taxon -name: only in taxon -namespace: uberon -def: "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." [] -xref: RO:0002160 -property_value: editor_note "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" xsd:string -property_value: IAO:0000112 "lactation SubClassOf 'only in taxon' some 'Mammalia'" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -is_a: in_taxon ! in taxon +inverse_of: BFO:0000067 ! contains process +transitive_over: part_of ! part of [Typedef] id: output_of name: output of namespace: external -namespace: uberon def: "inverse of has output" [] subset: ro-eco subset: RO:0002259 xref: RO:0002353 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: functionally_related_to ! functionally related to is_a: participates_in ! participates in +is_a: RO:0002328 ! functionally related to [Typedef] id: overlaps name: overlaps namespace: external -namespace: uberon def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002131 -property_value: IAO:0000114 IAO:0000125 -property_value: RO:0001900 RO:0001901 holds_over_chain: has_part overlaps -holds_over_chain: has_part part_of {RO:0002582="true"} holds_over_chain: part_of part_of is_symmetric: true is_a: RO:0002323 ! mereotopologically related to -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] [Typedef] @@ -261496,29 +257342,15 @@ name: part of name: part_of namespace: external namespace: quality -namespace: uberon def: "a core relation that holds between a part and its whole" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000050 -property_value: editor_note "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string -property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string -property_value: IAO:0000111 "is part of" xsd:string -property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string -property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string -property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string -property_value: IAO:0000118 "part_of" xsd:string -property_value: RO:0001900 RO:0001901 -property_value: RO:0040042 BFO:0000002 -property_value: RO:0040042 BFO:0000003 -property_value: RO:0040042 BFO:0000004 -property_value: RO:0040042 BFO:0000017 -property_value: RO:0040042 BFO:0000019 -property_value: RO:0040042 BFO:0000020 -property_value: RO:0040042 BFO:0000031 +property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string @@ -261531,14 +257363,8 @@ inverse_of: has_part ! has part id: participates_in name: participates in namespace: external -namespace: uberon def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] xref: RO:0000056 -property_value: IAO:0000111 "participates in" xsd:string -property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string -property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string -property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string -property_value: IAO:0000118 "participates_in" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000003 ! occurrent inverse_of: has_participant ! has participant @@ -261550,7 +257376,6 @@ namespace: external def: "inverse of positively regulates" [] subset: RO:0002259 xref: RO:0002336 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -261562,10 +257387,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002213 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "positively regulates (process to process)" xsd:string -property_value: RO:0004049 RO:0002211 holds_over_chain: ends_with positively_regulates holds_over_chain: negatively_regulates negatively_regulates is_transitive: true @@ -261579,49 +257400,26 @@ name: positively regulates characteristic namespace: gene_ontology def: "A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C." [] xref: RO:0019001 -property_value: dc-contributor https://orcid.org/0000-0002-8688-6599 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 holds_over_chain: positively_regulates positively_regulates_characteristic is_a: regulates_characteristic ! regulates characteristic -[Typedef] -id: postaxialmost_part_of -name: postaxialmost part of -namespace: uberon -xref: BSPO:0001115 - -[Typedef] -id: posterior_to -name: posterior to -namespace: uberon -xref: BSPO:0000099 - [Typedef] id: posteriorly_connected_to name: posteriorly connected to namespace: uberon def: "x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] -is_a: anterior_to ! anterior to -is_a: connected_to ! connected to - -[Typedef] -id: preaxialmost_part_of -name: preaxialmost part of -namespace: uberon -xref: BSPO:0001113 +is_a: BSPO:0000096 +is_a: RO:0002170 ! connected to [Typedef] id: preceded_by name: preceded by namespace: external -namespace: uberon def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000062 -property_value: editor_note "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string -property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string -property_value: IAO:0000111 "preceded by" xsd:string -property_value: IAO:0000118 "is preceded by" xsd:string -property_value: IAO:0000118 "preceded_by" xsd:string +property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent holds_over_chain: part_of preceded_by @@ -261633,53 +257431,30 @@ inverse_of: precedes ! precedes id: precedes name: precedes namespace: external -namespace: uberon def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000063 -property_value: IAO:0000111 "precedes" xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent holds_over_chain: part_of precedes is_transitive: true is_a: RO:0002222 ! temporally related to -[Typedef] -id: present_in_taxon -name: present in taxon -name: present_in_taxon -namespace: uberon -def: "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S" [] -def: "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S." [https://orcid.org/0000-0002-6601-2165] -comment: The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology. -synonym: "applicable for taxon" EXACT [] -xref: RO:0002175 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: OMO:0002000 "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" xsd:string -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -is_metadata_tag: true -is_class_level: true - [Typedef] id: process_has_causal_agent name: process has causal agent namespace: external def: "Inverse of 'causal agent in process'" [] xref: RO:0002608 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_a: RO:0002410 ! causally related to [Typedef] id: produced_by name: produced by namespace: external -namespace: uberon def: "a produced_by b iff some process that occurs_in b has_output a." [] subset: ro-eco xref: RO:0003001 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity @@ -261687,13 +257462,10 @@ range: BFO:0000040 ! material entity id: produces name: produces namespace: external -namespace: uberon def: "a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix." [] comment: Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. subset: ro-eco xref: RO:0003000 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity inverse_of: produced_by ! produced by @@ -261703,27 +257475,15 @@ id: protects name: protects namespace: uberon -[Typedef] -id: proximal_to -name: proximal to -namespace: uberon -xref: BSPO:0000100 - [Typedef] id: proximally_connected_to name: proximally connected to namespace: uberon def: "x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] -is_a: connected_to ! connected to -is_a: distal_to ! distal to +is_a: BSPO:0000097 +is_a: RO:0002170 ! connected to is_a: transitively_proximally_connected_to ! transitively proximally connected to -[Typedef] -id: proximalmost_part_of -name: proximalmost part of -namespace: uberon -xref: BSPO:0001106 - [Typedef] id: regulated_by name: regulated by @@ -261731,8 +257491,6 @@ namespace: external def: "inverse of regulates" [] subset: RO:0002259 xref: RO:0002334 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000589 "regulated by (processual)" xsd:string domain: BFO:0000015 ! process range: BFO:0000015 ! process is_transitive: true @@ -261747,14 +257505,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 -property_value: IAO:0000117 https://orcid.org/0000-0001-7476-6306 -property_value: IAO:0000117 https://orcid.org/0000-0002-3837-8864 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GO" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string -property_value: IAO:0000589 "regulates (processual)" xsd:string -property_value: IAO:0000600 "false" xsd:boolean domain: BFO:0000015 ! process range: BFO:0000015 ! process holds_over_chain: directly_regulates directly_regulates @@ -261770,7 +257520,7 @@ name: regulates characteristic namespace: gene_ontology def: "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C." [] xref: RO:0019000 -property_value: dc-contributor https://orcid.org/0000-0002-8688-6599 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 domain: BFO:0000015 ! process range: PATO:0000001 ! quality holds_over_chain: regulates regulates_characteristic @@ -261782,13 +257532,9 @@ name: regulates levels of namespace: external def: "p regulates levels of c if p regulates some amount (PATO:0000070) of c" [] xref: RO:0002332 -property_value: IAO:0000112 "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "regulates levels of (process to entity)" xsd:string domain: BFO:0000015 ! process range: BFO:0000040 ! material entity -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to [Typedef] id: results_in_acquisition_of_features_of @@ -261799,9 +257545,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002315 -property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string range: UBERON:0000061 ! anatomical structure is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -261836,10 +257579,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002296 -property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "http://www.geneontology.org/GO.doc.development.shtml" xsd:anyURI is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -261849,9 +257588,7 @@ name: results in developmental progression of namespace: external def: "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." [] xref: RO:0002295 -property_value: editor_note "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000116 "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string property_value: seeAlso Ontology:extensions domain: GO:0008150 ! biological_process range: UBERON:0001062 ! anatomical entity @@ -261883,16 +257620,12 @@ is_a: has_participant ! has participant [Typedef] id: results_in_formation_of name: results in formation of +name: results in formation of anatomical entity namespace: external subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002297 -property_value: IAO:0000112 "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." xsd:string -property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of inverse_of: RO:0002354 ! formed as result of @@ -261914,8 +257647,6 @@ id: results_in_growth_of name: results in growth of namespace: external xref: RO:0002343 -property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -261928,11 +257659,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002299 -property_value: IAO:0000112 " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" xsd:string -property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -261945,11 +257671,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002298 -property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." xsd:string -property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -261962,8 +257683,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002565 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure [Typedef] @@ -261982,7 +257701,6 @@ namespace: external def: "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002342 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in is_a: RO:0002021 ! occurs across @@ -261992,7 +257710,6 @@ name: results in transport along namespace: external def: "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " [] xref: RO:0002341 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002337 ! related via localization to [Typedef] @@ -262000,36 +257717,13 @@ id: results_in_transport_to_from_or_in name: results in transport to from or in namespace: external xref: RO:0002344 -property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002337 ! related via localization to -[Typedef] -id: seeAlso -name: see also -namespace: uberon -xref: http://www.w3.org/2000/01/rdf-schema#seeAlso -is_metadata_tag: true - [Typedef] id: sexually_homologous_to name: sexually_homologous_to namespace: uberon -is_a: homologous_to ! shares ancestor with - -[Typedef] -id: simultaneous_with -name: simultaneous with -namespace: uberon -def: "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." [] -comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) -subset: ro-eco -xref: RO:0002082 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -is_symmetric: true -is_transitive: true -is_a: RO:0002081 ! before or simultaneous with +is_a: RO:0002158 ! shares ancestor with [Typedef] id: site_of @@ -262038,46 +257732,13 @@ namespace: uberon def: "c site_of p if c is the bearer of a disposition that is realized by a process that has p as part." [] synonym: "capable_of_has_part" RELATED [] -[Typedef] -id: skeleton_of -name: skeleton of -namespace: uberon -def: "inverse of has skeleton" [] -subset: RO:0002259 -xref: RO:0002576 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: UBERON:0000061 ! anatomical structure -range: UBERON:0000061 ! anatomical structure -is_a: part_of ! part_of - -[Typedef] -id: starts -name: starts -namespace: uberon -def: "inverse of starts with" [] -subset: ro-eco -xref: RO:0002223 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "Allen" xsd:string -is_a: part_of ! part_of -is_a: RO:0002222 ! temporally related to -inverse_of: starts_with ! starts with - [Typedef] id: starts_with name: starts with namespace: external -namespace: uberon def: "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002224 -property_value: IAO:0000112 "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "started by" xsd:string is_transitive: true is_a: has_part ! has part is_a: RO:0002222 ! temporally related to @@ -262088,140 +257749,36 @@ name: subdivision of namespace: uberon comment: placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B -[Typedef] -id: superficial_to -name: superficial to -namespace: uberon -xref: BSPO:0000108 - -[Typedef] -id: supplies -name: supplies -namespace: uberon -def: "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." [] -xref: RO:0002178 -property_value: editor_note "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 -domain: UBERON:0001637 ! artery -is_a: connected_to ! connected to - -[Typedef] -id: surrounded_by -name: surrounded by -namespace: uberon -def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" [] -xref: RO:0002219 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0001900 RO:0001901 -is_a: adjacent_to ! adjacent to -inverse_of: surrounds ! surrounds - -[Typedef] -id: surrounds -name: surrounds -namespace: uberon -def: "inverse of surrounded by" [] -subset: RO:0002259 -xref: RO:0002221 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0001900 RO:0001901 -is_a: adjacent_to ! adjacent to - -[Typedef] -id: synapsed_by -name: synapsed by -namespace: uberon -def: "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " [] -xref: RO:0002103 -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 -is_a: RO:0002485 ! receives input from -inverse_of: RO:0002120 ! synapsed to -expand_expression_to: "BFO_0000051 some (GO_0045211 that part_of some (GO_0045202 that has_part some (GO_0042734 that BFO_0000050 some Y?)))" [] - [Typedef] id: term_tracker_item name: term tracker item namespace: external -namespace: uberon def: "An IRI or similar locator for a request or discussion of an ontology term." [] comment: The 'tracker item' can associate a tracker with a specific ontology term. xref: IAO:0000233 -property_value: IAO:0000111 "term tracker item" xsd:string -property_value: IAO:0000112 "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" xsd:string -property_value: IAO:0000119 "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" xsd:string is_metadata_tag: true -is_class_level: true - -[Typedef] -id: transformation_of -name: transformation of -namespace: uberon -def: "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" [] -xref: RO:0002494 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_transitive: true -is_a: develops_from ! develops from [Typedef] id: transitively_anteriorly_connected_to name: transitively anteriorly connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI -is_transitive: true [Typedef] id: transitively_distally_connected_to name: transitively distally connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI -is_transitive: true [Typedef] id: transitively_proximally_connected_to name: transitively proximally connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI -is_transitive: true - -[Typedef] -id: tributary_of -name: tributary of -namespace: uberon -def: "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." [] -subset: ro-eco -xref: RO:0002376 -property_value: IAO:0000112 "Deschutes River tributary_of Columbia River" xsd:string -property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "drains into" xsd:string -property_value: IAO:0000118 "drains to" xsd:string -property_value: IAO:0000118 "tributary channel of" xsd:string -property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Tributary" xsd:string -property_value: IAO:0000119 "http://www.medindia.net/glossary/venous_tributary.htm" xsd:string -property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" xsd:anyURI -property_value: seeAlso http://dbpedia.org/ontology/drainsTo -property_value: seeAlso "http://en.wikipedia.org/wiki/Tributary" xsd:anyURI -is_a: connected_to ! connected to -is_a: RO:0002375 ! in branching relationship with [Typedef] id: trunk_part_of name: trunk_part_of namespace: uberon -is_a: part_of ! part_of - -[Typedef] -id: ventral_to -name: ventral to -namespace: uberon -xref: BSPO:0000102 +is_a: part_of ! part of diff --git a/src/ontology/diffs/cl-diff.md b/src/ontology/diffs/cl-diff.md index 0cb2eaef3..73af8cbd1 100644 --- a/src/ontology/diffs/cl-diff.md +++ b/src/ontology/diffs/cl-diff.md @@ -2,12 +2,12 @@ ## Left - Ontology IRI: `http://purl.obolibrary.org/obo/cl.owl` -- Version IRI: `http://purl.obolibrary.org/obo/cl/releases/2024-01-04/cl.owl` +- Version IRI: `http://purl.obolibrary.org/obo/cl/releases/2024-02-13/cl.owl` - Loaded from: `http://purl.obolibrary.org/obo/cl.owl` ## Right - Ontology IRI: `http://purl.obolibrary.org/obo/cl.owl` -- Version IRI: `http://purl.obolibrary.org/obo/cl/releases/2024-02-13/cl.owl` +- Version IRI: `http://purl.obolibrary.org/obo/cl/releases/2024-04-05/cl.owl` - Loaded from: `file:/work/src/ontology/../../cl.owl` ### Ontology imports @@ -16,2755 +16,16432 @@ ### Ontology annotations #### Removed -- [versionInfo](http://www.w3.org/2002/07/owl#versionInfo) "2024-01-04" - -#### Added - [versionInfo](http://www.w3.org/2002/07/owl#versionInfo) "2024-02-13" - -### A2 amacrine cell `http://purl.obolibrary.org/obo/CL_0004219` - #### Added -- [A2 amacrine cell](http://purl.obolibrary.org/obo/CL_0004219) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [versionInfo](http://www.w3.org/2002/07/owl#versionInfo) "2024-04-05" -### Ammon's horn `http://purl.obolibrary.org/obo/UBERON_0001954` +### 1st arch mandibular component `http://purl.obolibrary.org/obo/UBERON_0007237` #### Removed -- [Ammon's horn](http://purl.obolibrary.org/obo/UBERON_0001954) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "hippocampus proprius" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:62493" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [1st arch mandibular component](http://purl.obolibrary.org/obo/UBERON_0007237) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [Ammon's horn](http://purl.obolibrary.org/obo/UBERON_0001954) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "hippocampus proprius" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000510" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:62493" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)" -### B cell `http://purl.obolibrary.org/obo/CL_0000236` -#### Added -- [B cell](http://purl.obolibrary.org/obo/CL_0000236) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### 1st arch maxillary component `http://purl.obolibrary.org/obo/UBERON_0007238` +#### Removed +- [1st arch maxillary component](http://purl.obolibrary.org/obo/UBERON_0007238) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "VHOG:0000511" +- [1st arch maxillary component](http://purl.obolibrary.org/obo/UBERON_0007238) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### B-1 B cell `http://purl.obolibrary.org/obo/CL_0000819` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [B-1 B cell](http://purl.obolibrary.org/obo/CL_0000819) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000511" -### B-1a B cell `http://purl.obolibrary.org/obo/CL_0000820` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)" -#### Added -- [B-1a B cell](http://purl.obolibrary.org/obo/CL_0000820) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### B-1b B cell `http://purl.obolibrary.org/obo/CL_0000821` +### 1st arch maxillary ectoderm `http://purl.obolibrary.org/obo/UBERON_0012313` #### Added -- [B-1b B cell](http://purl.obolibrary.org/obo/CL_0000821) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [1st arch maxillary ectoderm](http://purl.obolibrary.org/obo/UBERON_0012313) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) -### B-2 B cell `http://purl.obolibrary.org/obo/CL_0000822` +### 1st arch pharyngeal cleft `http://purl.obolibrary.org/obo/UBERON_0005872` +#### Removed +- [1st arch pharyngeal cleft](http://purl.obolibrary.org/obo/UBERON_0005872) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In all jawed vertebrates the first arch forms the jaw, while the second arch forms the hyoid apparatus. These two arches are separated by the first pharyngeal pouch and cleft.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [B-2 B cell](http://purl.obolibrary.org/obo/CL_0000822) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### BEST4+ intestinal epithelial cell, human `http://purl.obolibrary.org/obo/CL_4030026` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1016/j.semcdb.2010.01.022 Grevellec A, Tucker AS, The pharyngeal pouches and clefts: development, evolution, structure and derivatives. Seminars in Cell and Developmental Biology (2010)" -#### Added -- [BEST4+ intestinal epithelial cell, human](http://purl.obolibrary.org/obo/CL_4030026) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000969" -### Bergmann glial cell `http://purl.obolibrary.org/obo/CL_0000644` -#### Added -- [Bergmann glial cell](http://purl.obolibrary.org/obo/CL_0000644) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### 2D boundary of `http://purl.obolibrary.org/obo/RO_0002000` +#### Removed +- [2D boundary of](http://purl.obolibrary.org/obo/RO_0002000) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "2D_boundary_of"@en +- [2D boundary of](http://purl.obolibrary.org/obo/RO_0002000) [RO_0001900](http://purl.obolibrary.org/obo/RO_0001900) [RO_0001901](http://purl.obolibrary.org/obo/RO_0001901) -### CD14-low, CD16-positive monocyte `http://purl.obolibrary.org/obo/CL_0002396` +- [2D boundary of](http://purl.obolibrary.org/obo/RO_0002000) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "surface of"@en -#### Added -- [CD14-low, CD16-positive monocyte](http://purl.obolibrary.org/obo/CL_0002396) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [2D boundary of](http://purl.obolibrary.org/obo/RO_0002000) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "is boundary of"@en +- [2D boundary of](http://purl.obolibrary.org/obo/RO_0002000) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "the surface of my skin is a 2D boundary of my body"@en -### CD14-positive monocyte `http://purl.obolibrary.org/obo/CL_0001054` +- [2D boundary of](http://purl.obolibrary.org/obo/RO_0002000) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "is 2D boundary of"@en -#### Added -- [CD14-positive monocyte](http://purl.obolibrary.org/obo/CL_0001054) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [2D boundary of](http://purl.obolibrary.org/obo/RO_0002000) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "boundary of"@en -### CD14-positive, CD16-negative classical monocyte `http://purl.obolibrary.org/obo/CL_0002057` -#### Added -- [CD14-positive, CD16-negative classical monocyte](http://purl.obolibrary.org/obo/CL_0002057) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### 2nd arch ectoderm `http://purl.obolibrary.org/obo/UBERON_0005660` +#### Removed +- [2nd arch ectoderm](http://purl.obolibrary.org/obo/UBERON_0005660) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001062" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### CD14-positive, CD16-positive monocyte `http://purl.obolibrary.org/obo/CL_0002397` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [CD14-positive, CD16-positive monocyte](http://purl.obolibrary.org/obo/CL_0002397) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)" -### CD141-positive myeloid dendritic cell `http://purl.obolibrary.org/obo/CL_0002394` -#### Added -- [CD141-positive myeloid dendritic cell](http://purl.obolibrary.org/obo/CL_0002394) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### 2nd arch endoderm `http://purl.obolibrary.org/obo/UBERON_0005664` +#### Removed +- [2nd arch endoderm](http://purl.obolibrary.org/obo/UBERON_0005664) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001108" -### CD16-negative, CD56-bright natural killer cell, human `http://purl.obolibrary.org/obo/CL_0000938` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [CD16-negative, CD56-bright natural killer cell, human](http://purl.obolibrary.org/obo/CL_0000938) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### CD16-positive, CD56-dim natural killer cell, human `http://purl.obolibrary.org/obo/CL_0000939` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)" -#### Added -- [CD16-positive, CD56-dim natural killer cell, human](http://purl.obolibrary.org/obo/CL_0000939) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### CD1c-positive myeloid dendritic cell `http://purl.obolibrary.org/obo/CL_0002399` +### 2nd arch mesenchyme `http://purl.obolibrary.org/obo/UBERON_0005689` +#### Removed +- [2nd arch mesenchyme](http://purl.obolibrary.org/obo/UBERON_0005689) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [CD1c-positive myeloid dendritic cell](http://purl.obolibrary.org/obo/CL_0002399) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### CD34-positive, CD38-negative hematopoietic stem cell `http://purl.obolibrary.org/obo/CL_0001024` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)" -#### Added -- [CD34-positive, CD38-negative hematopoietic stem cell](http://purl.obolibrary.org/obo/CL_0001024) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001102" -### CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human `http://purl.obolibrary.org/obo/CL_0001074` -#### Added -- [CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human](http://purl.obolibrary.org/obo/CL_0001074) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### 2nd arch mesenchyme from neural crest `http://purl.obolibrary.org/obo/UBERON_0010254` +#### Removed +- [2nd arch mesenchyme from neural crest](http://purl.obolibrary.org/obo/UBERON_0010254) SubClassOf [mesenchyme derived from head neural crest](http://purl.obolibrary.org/obo/UBERON_0007213) +#### Added +- [2nd arch mesenchyme from neural crest](http://purl.obolibrary.org/obo/UBERON_0010254) SubClassOf [mesenchyme from rhombencephalic neural crest](http://purl.obolibrary.org/obo/UBERON_0010258) -### CD4-positive helper T cell `http://purl.obolibrary.org/obo/CL_0000492` -#### Added -- [CD4-positive helper T cell](http://purl.obolibrary.org/obo/CL_0000492) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### 3rd arch ectoderm `http://purl.obolibrary.org/obo/UBERON_0005661` +#### Removed +- [3rd arch ectoderm](http://purl.obolibrary.org/obo/UBERON_0005661) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### CD4-positive, CD25-positive, alpha-beta regulatory T cell `http://purl.obolibrary.org/obo/CL_0000792` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [CD4-positive, CD25-positive, alpha-beta regulatory T cell](http://purl.obolibrary.org/obo/CL_0000792) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000946" -### CD4-positive, alpha-beta T cell `http://purl.obolibrary.org/obo/CL_0000624` -#### Added -- [CD4-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_0000624) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### 3rd arch endoderm `http://purl.obolibrary.org/obo/UBERON_0005665` +#### Removed +- [3rd arch endoderm](http://purl.obolibrary.org/obo/UBERON_0005665) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### CD4-positive, alpha-beta cytotoxic T cell `http://purl.obolibrary.org/obo/CL_0000934` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [CD4-positive, alpha-beta cytotoxic T cell](http://purl.obolibrary.org/obo/CL_0000934) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)" -### CD4-positive, alpha-beta memory T cell `http://purl.obolibrary.org/obo/CL_0000897` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001081" -#### Added -- [CD4-positive, alpha-beta memory T cell](http://purl.obolibrary.org/obo/CL_0000897) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### CD4-positive, alpha-beta thymocyte `http://purl.obolibrary.org/obo/CL_0000810` +### 3rd arch mesenchyme `http://purl.obolibrary.org/obo/UBERON_0005690` +#### Removed +- [3rd arch mesenchyme](http://purl.obolibrary.org/obo/UBERON_0005690) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [CD4-positive, alpha-beta thymocyte](http://purl.obolibrary.org/obo/CL_0000810) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### CD56-positive, CD161-positive immature natural killer cell, human `http://purl.obolibrary.org/obo/CL_0002338` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001083" -#### Added -- [CD56-positive, CD161-positive immature natural killer cell, human](http://purl.obolibrary.org/obo/CL_0002338) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)" -### CD8-alpha alpha positive, gamma-delta intraepithelial T cell `http://purl.obolibrary.org/obo/CL_0000802` -#### Added -- [CD8-alpha alpha positive, gamma-delta intraepithelial T cell](http://purl.obolibrary.org/obo/CL_0000802) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### 3rd arch mesenchyme from neural crest `http://purl.obolibrary.org/obo/UBERON_0010255` +#### Removed +- [3rd arch mesenchyme from neural crest](http://purl.obolibrary.org/obo/UBERON_0010255) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### CD8-alpha-alpha-positive, alpha-beta intraepithelial T cell `http://purl.obolibrary.org/obo/CL_0000915` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000571" -#### Added -- [CD8-alpha-alpha-positive, alpha-beta intraepithelial T cell](http://purl.obolibrary.org/obo/CL_0000915) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)" -### CD8-alpha-beta-positive, alpha-beta intraepithelial T cell `http://purl.obolibrary.org/obo/CL_0000796` -#### Added -- [CD8-alpha-beta-positive, alpha-beta intraepithelial T cell](http://purl.obolibrary.org/obo/CL_0000796) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### 4th arch ectoderm `http://purl.obolibrary.org/obo/UBERON_0005662` +#### Removed +- [4th arch ectoderm](http://purl.obolibrary.org/obo/UBERON_0005662) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### CD8-positive, alpha-beta T cell `http://purl.obolibrary.org/obo/CL_0000625` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [CD8-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_0000625) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001095" -### CD8-positive, alpha-beta cytokine secreting effector T cell `http://purl.obolibrary.org/obo/CL_0000908` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)" -#### Added -- [CD8-positive, alpha-beta cytokine secreting effector T cell](http://purl.obolibrary.org/obo/CL_0000908) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### CD8-positive, alpha-beta cytotoxic T cell `http://purl.obolibrary.org/obo/CL_0000794` +### 4th arch endoderm `http://purl.obolibrary.org/obo/UBERON_0005666` +#### Removed +- [4th arch endoderm](http://purl.obolibrary.org/obo/UBERON_0005666) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [CD8-positive, alpha-beta cytotoxic T cell](http://purl.obolibrary.org/obo/CL_0000794) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### CD8-positive, alpha-beta memory T cell `http://purl.obolibrary.org/obo/CL_0000909` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)" -#### Added -- [CD8-positive, alpha-beta memory T cell](http://purl.obolibrary.org/obo/CL_0000909) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001092" -### CD8-positive, alpha-beta memory T cell, CD45RO-positive `http://purl.obolibrary.org/obo/CL_0001203` -#### Added -- [CD8-positive, alpha-beta memory T cell, CD45RO-positive](http://purl.obolibrary.org/obo/CL_0001203) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### 4th arch mesenchyme `http://purl.obolibrary.org/obo/UBERON_0005691` +#### Removed +- [4th arch mesenchyme](http://purl.obolibrary.org/obo/UBERON_0005691) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### CD8-positive, alpha-beta thymocyte `http://purl.obolibrary.org/obo/CL_0000811` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [CD8-positive, alpha-beta thymocyte](http://purl.obolibrary.org/obo/CL_0000811) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001052" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)" -### CHEBI_16480 `http://purl.obolibrary.org/obo/CHEBI_16480` -#### Removed -- Class: [CHEBI_16480](http://purl.obolibrary.org/obo/CHEBI_16480) +### 4th arch mesenchyme from neural crest `http://purl.obolibrary.org/obo/UBERON_0010256` +#### Removed +- [4th arch mesenchyme from neural crest](http://purl.obolibrary.org/obo/UBERON_0010256) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In all vertebrates, the pharyngeal apparatus develops from a series of bulges found on the lateral surface of the head, the pharyngeal arches, which consist of a number of different embryonic cell types. Each arch has an external covering of ectoderm and inner covering of endoderm, and between these a mesenchymal filling of neural crest with a central core of mesoderm.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### CHEBI_35238 `http://purl.obolibrary.org/obo/CHEBI_35238` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- Class: [CHEBI_35238](http://purl.obolibrary.org/obo/CHEBI_35238) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000580" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### CHEBI_37022 `http://purl.obolibrary.org/obo/CHEBI_37022` -#### Removed -- Class: [CHEBI_37022](http://purl.obolibrary.org/obo/CHEBI_37022) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)" -### Cajal-Retzius cell `http://purl.obolibrary.org/obo/CL_0000695` +### ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 `http://purl.obolibrary.org/obo/PR_000001408` +#### Removed +- [ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1](http://purl.obolibrary.org/obo/PR_000001408) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 (human)](http://purl.obolibrary.org/obo/PR_P28907) -#### Added -- [Cajal-Retzius cell](http://purl.obolibrary.org/obo/CL_0000695) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### DN1 thymic pro-T cell `http://purl.obolibrary.org/obo/CL_0000894` +### Acrogymnospermae `http://purl.obolibrary.org/obo/NCBITaxon_1437180` +#### Removed +- [Acrogymnospermae](http://purl.obolibrary.org/obo/NCBITaxon_1437180) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) -#### Added -- [DN1 thymic pro-T cell](http://purl.obolibrary.org/obo/CL_0000894) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### DN3 thymocyte `http://purl.obolibrary.org/obo/CL_0000807` +### Actinopteri `http://purl.obolibrary.org/obo/NCBITaxon_186623` +#### Removed +- [Actinopteri](http://purl.obolibrary.org/obo/NCBITaxon_186623) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_class](http://purl.obolibrary.org/obo/NCBITaxon_class) -#### Added -- [DN3 thymocyte](http://purl.obolibrary.org/obo/CL_0000807) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### DN4 thymocyte `http://purl.obolibrary.org/obo/CL_0000808` +### Actinopterygii `http://purl.obolibrary.org/obo/NCBITaxon_7898` +#### Removed +- [Actinopterygii](http://purl.obolibrary.org/obo/NCBITaxon_7898) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_superclass](http://purl.obolibrary.org/obo/NCBITaxon_superclass) -#### Added -- [DN4 thymocyte](http://purl.obolibrary.org/obo/CL_0000808) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### DNA binding `http://purl.obolibrary.org/obo/GO_0003677` +### Alveolata `http://purl.obolibrary.org/obo/NCBITaxon_33630` #### Removed -- [DNA binding](http://purl.obolibrary.org/obo/GO_0003677) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) +- [Alveolata](http://purl.obolibrary.org/obo/NCBITaxon_33630) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) -#### Added -- [DNA binding](http://purl.obolibrary.org/obo/GO_0003677) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) -### DNA recombination `http://purl.obolibrary.org/obo/GO_0006310` +### Ammon's horn `http://purl.obolibrary.org/obo/UBERON_0001954` #### Removed -- [DNA recombination](http://purl.obolibrary.org/obo/GO_0006310) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) +- [Ammon's horn](http://purl.obolibrary.org/obo/UBERON_0001954) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002601](http://purl.obolibrary.org/obo/UBERON_0002601) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" -#### Added -- [DNA recombination](http://purl.obolibrary.org/obo/GO_0006310) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) +- [Ammon's horn](http://purl.obolibrary.org/obo/UBERON_0001954) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "hippocampal" +- [Ammon's horn](http://purl.obolibrary.org/obo/UBERON_0001954) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [dentate gyrus of hippocampal formation](http://purl.obolibrary.org/obo/UBERON_0001885) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" -### DUBIOUS `http://purl.obolibrary.org/obo/uberon/core#DUBIOUS` -#### Removed -- AnnotationProperty: [DUBIOUS](http://purl.obolibrary.org/obo/uberon/core#DUBIOUS) +- [Ammon's horn](http://purl.obolibrary.org/obo/UBERON_0001954) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "Non-mammalian species do not have a brain structure that looks like the mammalian hippocampus, but they have one that is considered homologous to it. The hippocampus, as pointed out above, is essentially the medial edge of the cortex. Only mammals have a fully developed cortex, but the structure it evolved from, called the pallium, is present in all vertebrates, even the most primitive ones such as the lamprey or hagfish. The pallium is usually divided into three zones: medial, lateral, and dorsal. The medial pallium forms the precursor of the hippocampus. It does not resemble the hippocampus visually, because the layers are not warped into an S shape or enwrapped by the dentate gyrus, but the homology is indicated by strong chemical and functional affinities. There is now evidence that these hippocampal-like structures are involved in spatial cognition in birds, reptiles, and fish. In birds, the correspondence is sufficiently well established that most anatomists refer to the medial pallial zone as the 'avian hippocampus'. The story for fish is more complex. In teleost fish (which make up the great majority of existing species), the forebrain is distorted in comparison to other types of vertebrates: most neuroanatomists believe that the teleost forebrain is essentially everted, like a sock turned inside-out, so that structures that lie in the interior, next to the ventricles, for most vertebrates, are found on the outside in teleost fish, and vice versa. One of the consequences of this is that the medial pallium ('hippocampal' zone) of a typical vertebrate is thought to correspond to the lateral pallium of a typical fish. Several types of fish (particularly goldfish) have been shown experimentally to have strong spatial memory abilities, even forming 'cognitive maps' of the areas they inhabit.[WP]" -- [DUBIOUS](http://purl.obolibrary.org/obo/uberon/core#DUBIOUS) SubPropertyOf: [synonym_type_property](http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty) +- [Ammon's horn](http://purl.obolibrary.org/obo/UBERON_0001954) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:32772" -### Descemet's membrane `http://purl.obolibrary.org/obo/UBERON_0004367` +### Amniota `http://purl.obolibrary.org/obo/NCBITaxon_32524` #### Removed -- [Descemet's membrane](http://purl.obolibrary.org/obo/UBERON_0004367) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lamina limitans posterior corneae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58309" +- [Amniota](http://purl.obolibrary.org/obo/NCBITaxon_32524) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [Descemet's membrane](http://purl.obolibrary.org/obo/UBERON_0004367) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lamina limitans posterior corneae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### Amoebozoa `http://purl.obolibrary.org/obo/NCBITaxon_554915` +#### Removed +- [Amoebozoa](http://purl.obolibrary.org/obo/NCBITaxon_554915) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58309" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### Archaea `http://purl.obolibrary.org/obo/NCBITaxon_2157` +#### Removed +- [Archaea](http://purl.obolibrary.org/obo/NCBITaxon_2157) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_superkingdom](http://purl.obolibrary.org/obo/NCBITaxon_superkingdom) -### GABAergic amacrine cell `http://purl.obolibrary.org/obo/CL_4030027` -#### Added -- [GABAergic amacrine cell](http://purl.obolibrary.org/obo/CL_4030027) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### Archelosauria `http://purl.obolibrary.org/obo/NCBITaxon_1329799` +#### Removed +- [Archelosauria](http://purl.obolibrary.org/obo/NCBITaxon_1329799) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) -### GABAergic neuron `http://purl.obolibrary.org/obo/CL_0000617` -#### Added -- [GABAergic neuron](http://purl.obolibrary.org/obo/CL_0000617) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### Archosauria `http://purl.obolibrary.org/obo/NCBITaxon_8492` +#### Removed +- [Archosauria](http://purl.obolibrary.org/obo/NCBITaxon_8492) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) -### GCIs -#### Added -- [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [embryo stage](http://purl.obolibrary.org/obo/UBERON_0000068) DisjointWith [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [post-embryonic stage](http://purl.obolibrary.org/obo/UBERON_0000092) -- [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [hypodermis](http://purl.obolibrary.org/obo/UBERON_0002072) DisjointWith [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [skin of body](http://purl.obolibrary.org/obo/UBERON_0002097) +### Arthropoda `http://purl.obolibrary.org/obo/NCBITaxon_6656` +#### Removed +- [Arthropoda](http://purl.obolibrary.org/obo/NCBITaxon_6656) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_phylum](http://purl.obolibrary.org/obo/NCBITaxon_phylum) -- [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [respiratory primordium epithelium](http://purl.obolibrary.org/obo/UBERON_0036072) DisjointWith [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [respiratory primordium mesenchyme](http://purl.obolibrary.org/obo/UBERON_0036073) -- DisjointClasses: [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [sebaceous gland](http://purl.obolibrary.org/obo/UBERON_0001821), [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [arrector muscle of hair](http://purl.obolibrary.org/obo/UBERON_0002033), [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [hair follicle](http://purl.obolibrary.org/obo/UBERON_0002073) -- DisjointClasses: [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [central tendon of diaphragm](http://purl.obolibrary.org/obo/UBERON_0006670), [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765), [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [costal diaphragm](http://purl.obolibrary.org/obo/UBERON_0035831) +### Ascomycota `http://purl.obolibrary.org/obo/NCBITaxon_4890` +#### Removed +- [Ascomycota](http://purl.obolibrary.org/obo/NCBITaxon_4890) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_phylum](http://purl.obolibrary.org/obo/NCBITaxon_phylum) -- [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [parietal pleura](http://purl.obolibrary.org/obo/UBERON_0002400) DisjointWith [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [visceral pleura](http://purl.obolibrary.org/obo/UBERON_0002401) -- DisjointClasses: [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [dentate gyrus of hippocampal formation](http://purl.obolibrary.org/obo/UBERON_0001885), [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [Ammon's horn](http://purl.obolibrary.org/obo/UBERON_0001954), [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) -- [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [right lung](http://purl.obolibrary.org/obo/UBERON_0002167) DisjointWith [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [left lung](http://purl.obolibrary.org/obo/UBERON_0002168) +### Aves `http://purl.obolibrary.org/obo/NCBITaxon_8782` +#### Removed +- [Aves](http://purl.obolibrary.org/obo/NCBITaxon_8782) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_class](http://purl.obolibrary.org/obo/NCBITaxon_class) -- [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [eyeball of camera-type eye](http://purl.obolibrary.org/obo/UBERON_0010230) DisjointWith [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [ocular adnexa](http://purl.obolibrary.org/obo/UBERON_0035639) -- [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [cortex of hair](http://purl.obolibrary.org/obo/UBERON_0002077) DisjointWith [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [hair medulla](http://purl.obolibrary.org/obo/UBERON_0005184) -- [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [peritoneal cavity](http://purl.obolibrary.org/obo/UBERON_0001179) DisjointWith [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [peritoneum](http://purl.obolibrary.org/obo/UBERON_0002358) +### B-cell lymphoma 6 protein `http://purl.obolibrary.org/obo/PR_000003450` +#### Removed +- [B-cell lymphoma 6 protein](http://purl.obolibrary.org/obo/PR_000003450) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [B-cell lymphoma 6 protein (human)](http://purl.obolibrary.org/obo/PR_P41182) -- [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [parietal serous pericardium](http://purl.obolibrary.org/obo/UBERON_0002408) DisjointWith [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [visceral serous pericardium](http://purl.obolibrary.org/obo/UBERON_0002425) -- [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [pleura](http://purl.obolibrary.org/obo/UBERON_0000977) DisjointWith [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [pleural cavity](http://purl.obolibrary.org/obo/UBERON_0002402) -- [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [peripheral nervous system](http://purl.obolibrary.org/obo/UBERON_0000010) DisjointWith [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [central nervous system](http://purl.obolibrary.org/obo/UBERON_0001017) +### B-cell receptor CD22 `http://purl.obolibrary.org/obo/PR_000001288` +#### Removed +- [B-cell receptor CD22](http://purl.obolibrary.org/obo/PR_000001288) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [B-cell receptor CD22 (human)](http://purl.obolibrary.org/obo/PR_P20273) -- [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [abdominal cavity](http://purl.obolibrary.org/obo/UBERON_0003684) DisjointWith [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [pelvic cavity](http://purl.obolibrary.org/obo/UBERON_0008203) -- [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [left dorsal aorta](http://purl.obolibrary.org/obo/UBERON_0005613) DisjointWith [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [right dorsal aorta](http://purl.obolibrary.org/obo/UBERON_0005622) -- DisjointClasses: [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [submucosa](http://purl.obolibrary.org/obo/UBERON_0000009), [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [mucosa](http://purl.obolibrary.org/obo/UBERON_0000344), [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [hypodermis](http://purl.obolibrary.org/obo/UBERON_0002072), [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [skin of body](http://purl.obolibrary.org/obo/UBERON_0002097) +### Bacteria `http://purl.obolibrary.org/obo/NCBITaxon_2` +#### Removed +- [Bacteria](http://purl.obolibrary.org/obo/NCBITaxon_2) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_superkingdom](http://purl.obolibrary.org/obo/NCBITaxon_superkingdom) -- ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [peritoneal cavity](http://purl.obolibrary.org/obo/UBERON_0001179)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [peritoneum](http://purl.obolibrary.org/obo/UBERON_0002358)) EquivalentTo [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [peritoneal sac](http://purl.obolibrary.org/obo/UBERON_0035820) -- ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [submucosa](http://purl.obolibrary.org/obo/UBERON_0000009)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [mucosa](http://purl.obolibrary.org/obo/UBERON_0000344)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [hypodermis](http://purl.obolibrary.org/obo/UBERON_0002072)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [skin of body](http://purl.obolibrary.org/obo/UBERON_0002097)) EquivalentTo [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [dermatological-muscosal system](http://purl.obolibrary.org/obo/UBERON_0012125) -- ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [cortex of hair](http://purl.obolibrary.org/obo/UBERON_0002077)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [hair medulla](http://purl.obolibrary.org/obo/UBERON_0005184)) EquivalentTo [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [hair shaft](http://purl.obolibrary.org/obo/UBERON_0002074) +### Bilateria `http://purl.obolibrary.org/obo/NCBITaxon_33213` +#### Removed +- [Bilateria](http://purl.obolibrary.org/obo/NCBITaxon_33213) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) -- ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [left dorsal aorta](http://purl.obolibrary.org/obo/UBERON_0005613)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [right dorsal aorta](http://purl.obolibrary.org/obo/UBERON_0005622)) EquivalentTo [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [pair of dorsal aortae](http://purl.obolibrary.org/obo/UBERON_0010190) -- ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [respiratory primordium epithelium](http://purl.obolibrary.org/obo/UBERON_0036072)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [respiratory primordium mesenchyme](http://purl.obolibrary.org/obo/UBERON_0036073)) EquivalentTo [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [respiratory primordium](http://purl.obolibrary.org/obo/UBERON_0008947) -- ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [abdominal cavity](http://purl.obolibrary.org/obo/UBERON_0003684)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [pelvic cavity](http://purl.obolibrary.org/obo/UBERON_0008203)) EquivalentTo [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [abdominopelvic cavity](http://purl.obolibrary.org/obo/UBERON_0035819) +### Boreoeutheria `http://purl.obolibrary.org/obo/NCBITaxon_1437010` +#### Removed +- [Boreoeutheria](http://purl.obolibrary.org/obo/NCBITaxon_1437010) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) -- ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [eyeball of camera-type eye](http://purl.obolibrary.org/obo/UBERON_0010230)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [ocular adnexa](http://purl.obolibrary.org/obo/UBERON_0035639)) EquivalentTo [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [orbital region](http://purl.obolibrary.org/obo/UBERON_0004088) -- ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [peripheral nervous system](http://purl.obolibrary.org/obo/UBERON_0000010)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [central nervous system](http://purl.obolibrary.org/obo/UBERON_0001017)) EquivalentTo [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [nervous system](http://purl.obolibrary.org/obo/UBERON_0001016) -- ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [central tendon of diaphragm](http://purl.obolibrary.org/obo/UBERON_0006670)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [costal diaphragm](http://purl.obolibrary.org/obo/UBERON_0035831)) EquivalentTo [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [diaphragm](http://purl.obolibrary.org/obo/UBERON_0001103) +### Bowman's space `http://purl.obolibrary.org/obo/UBERON_0001286` +#### Removed +- [Bowman's space](http://purl.obolibrary.org/obo/UBERON_0001286) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Space between the renal glomerulus and the glomerular capsule. Renal filtrate collects here then passes into the renal tubule.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005312" -- ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [parietal pleura](http://purl.obolibrary.org/obo/UBERON_0002400)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [visceral pleura](http://purl.obolibrary.org/obo/UBERON_0002401)) EquivalentTo [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [pleura](http://purl.obolibrary.org/obo/UBERON_0000977) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -- ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [hypodermis](http://purl.obolibrary.org/obo/UBERON_0002072)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [skin of body](http://purl.obolibrary.org/obo/UBERON_0002097)) EquivalentTo [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [integument](http://purl.obolibrary.org/obo/UBERON_0002199) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005283" -- ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [right lung](http://purl.obolibrary.org/obo/UBERON_0002167)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [left lung](http://purl.obolibrary.org/obo/UBERON_0002168)) EquivalentTo [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [pair of lungs](http://purl.obolibrary.org/obo/UBERON_0000170) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -- ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [pleura](http://purl.obolibrary.org/obo/UBERON_0000977)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [pleural cavity](http://purl.obolibrary.org/obo/UBERON_0002402)) EquivalentTo [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [pleural sac](http://purl.obolibrary.org/obo/UBERON_0009778) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -- ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [parietal serous pericardium](http://purl.obolibrary.org/obo/UBERON_0002408)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [visceral serous pericardium](http://purl.obolibrary.org/obo/UBERON_0002425)) EquivalentTo [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [serous pericardium](http://purl.obolibrary.org/obo/UBERON_0002357) -- ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [dentate gyrus of hippocampal formation](http://purl.obolibrary.org/obo/UBERON_0001885)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [Ammon's horn](http://purl.obolibrary.org/obo/UBERON_0001954)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191)) EquivalentTo [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [hippocampal formation](http://purl.obolibrary.org/obo/UBERON_0002421) -- ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [embryo stage](http://purl.obolibrary.org/obo/UBERON_0000068)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [post-embryonic stage](http://purl.obolibrary.org/obo/UBERON_0000092)) EquivalentTo [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [life cycle](http://purl.obolibrary.org/obo/UBERON_0000104) +### C-C chemokine receptor type 1 `http://purl.obolibrary.org/obo/PR_000001254` +#### Removed +- [C-C chemokine receptor type 1](http://purl.obolibrary.org/obo/PR_000001254) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [C-C chemokine receptor type 1 (human)](http://purl.obolibrary.org/obo/PR_P32246) -- ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [sebaceous gland](http://purl.obolibrary.org/obo/UBERON_0001821)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [arrector muscle of hair](http://purl.obolibrary.org/obo/UBERON_0002033)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [hair follicle](http://purl.obolibrary.org/obo/UBERON_0002073)) EquivalentTo [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [pilosebaceous unit](http://purl.obolibrary.org/obo/UBERON_0011932) -### GIP cell `http://purl.obolibrary.org/obo/CL_0002278` +### C-C chemokine receptor type 2 `http://purl.obolibrary.org/obo/PR_000001199` +#### Removed +- [C-C chemokine receptor type 2](http://purl.obolibrary.org/obo/PR_000001199) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [C-C chemokine receptor type 2 (human)](http://purl.obolibrary.org/obo/PR_P41597) -#### Added -- [GIP cell](http://purl.obolibrary.org/obo/CL_0002278) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### Hofbauer cell `http://purl.obolibrary.org/obo/CL_3000001` +### C-C chemokine receptor type 3 `http://purl.obolibrary.org/obo/PR_000001255` +#### Removed +- [C-C chemokine receptor type 3](http://purl.obolibrary.org/obo/PR_000001255) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [C-C chemokine receptor type 3 (human)](http://purl.obolibrary.org/obo/PR_P51677) -#### Added -- [Hofbauer cell](http://purl.obolibrary.org/obo/CL_3000001) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### ILC1, human `http://purl.obolibrary.org/obo/CL_0001077` +### C-C chemokine receptor type 4 `http://purl.obolibrary.org/obo/PR_000001200` +#### Removed +- [C-C chemokine receptor type 4](http://purl.obolibrary.org/obo/PR_000001200) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [C-C chemokine receptor type 4 (human)](http://purl.obolibrary.org/obo/PR_P51679) -#### Added -- [ILC1, human](http://purl.obolibrary.org/obo/CL_0001077) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### IgA plasma cell `http://purl.obolibrary.org/obo/CL_0000987` +### C-C chemokine receptor type 5 `http://purl.obolibrary.org/obo/PR_000001201` +#### Removed +- [C-C chemokine receptor type 5](http://purl.obolibrary.org/obo/PR_000001201) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [C-C chemokine receptor type 5 (human)](http://purl.obolibrary.org/obo/PR_P51681) -#### Added -- [IgA plasma cell](http://purl.obolibrary.org/obo/CL_0000987) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### IgA plasmablast `http://purl.obolibrary.org/obo/CL_0000984` +### C-C chemokine receptor type 6 `http://purl.obolibrary.org/obo/PR_000001202` +#### Removed +- [C-C chemokine receptor type 6](http://purl.obolibrary.org/obo/PR_000001202) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [C-C chemokine receptor type 6 (human)](http://purl.obolibrary.org/obo/PR_P51684) -#### Added -- [IgA plasmablast](http://purl.obolibrary.org/obo/CL_0000984) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### IgG memory B cell `http://purl.obolibrary.org/obo/CL_0000979` +### C-C chemokine receptor type 7 `http://purl.obolibrary.org/obo/PR_000001203` +#### Removed +- [C-C chemokine receptor type 7](http://purl.obolibrary.org/obo/PR_000001203) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [C-C chemokine receptor type 7 (human)](http://purl.obolibrary.org/obo/PR_P32248) -#### Added -- [IgG memory B cell](http://purl.obolibrary.org/obo/CL_0000979) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### IgG plasma cell `http://purl.obolibrary.org/obo/CL_0000985` +### C-C motif chemokine 3 `http://purl.obolibrary.org/obo/PR_000002123` +#### Removed +- [C-C motif chemokine 3](http://purl.obolibrary.org/obo/PR_000002123) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [C-C motif chemokine 3 (human)](http://purl.obolibrary.org/obo/PR_P10147) -#### Added -- [IgG plasma cell](http://purl.obolibrary.org/obo/CL_0000985) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### IgG plasmablast `http://purl.obolibrary.org/obo/CL_0000982` +### C-X-C chemokine receptor type 1 `http://purl.obolibrary.org/obo/PR_000001256` +#### Removed +- [C-X-C chemokine receptor type 1](http://purl.obolibrary.org/obo/PR_000001256) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [C-X-C chemokine receptor type 1 (human)](http://purl.obolibrary.org/obo/PR_P25024) -#### Added -- [IgG plasmablast](http://purl.obolibrary.org/obo/CL_0000982) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### IgG-negative class switched memory B cell `http://purl.obolibrary.org/obo/CL_0002117` +### C-X-C chemokine receptor type 2 `http://purl.obolibrary.org/obo/PR_000001257` +#### Removed +- [C-X-C chemokine receptor type 2](http://purl.obolibrary.org/obo/PR_000001257) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [C-X-C chemokine receptor type 2 (human)](http://purl.obolibrary.org/obo/PR_P25025) -#### Added -- [IgG-negative class switched memory B cell](http://purl.obolibrary.org/obo/CL_0002117) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### IgM plasma cell `http://purl.obolibrary.org/obo/CL_0000986` +### C-X-C chemokine receptor type 3 `http://purl.obolibrary.org/obo/PR_000001207` +#### Removed +- [C-X-C chemokine receptor type 3](http://purl.obolibrary.org/obo/PR_000001207) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [C-X-C chemokine receptor type 3 (human)](http://purl.obolibrary.org/obo/PR_P49682) -#### Added -- [IgM plasma cell](http://purl.obolibrary.org/obo/CL_0000986) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### Kupffer cell `http://purl.obolibrary.org/obo/CL_0000091` +### C-X-C chemokine receptor type 4 `http://purl.obolibrary.org/obo/PR_000001208` +#### Removed +- [C-X-C chemokine receptor type 4](http://purl.obolibrary.org/obo/PR_000001208) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [C-X-C chemokine receptor type 4 (human)](http://purl.obolibrary.org/obo/PR_P61073) -#### Added -- [Kupffer cell](http://purl.obolibrary.org/obo/CL_0000091) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### L2/3 intratelencephalic projecting glutamatergic neuron of the primary motor cortex `http://purl.obolibrary.org/obo/CL_4023047` +### C-X-C chemokine receptor type 5 `http://purl.obolibrary.org/obo/PR_000001209` +#### Removed +- [C-X-C chemokine receptor type 5](http://purl.obolibrary.org/obo/PR_000001209) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [C-X-C chemokine receptor type 5 (human)](http://purl.obolibrary.org/obo/PR_P32302) -#### Added -- [L2/3 intratelencephalic projecting glutamatergic neuron of the primary motor cortex](http://purl.obolibrary.org/obo/CL_4023047) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### L2/3-6 intratelencephalic projecting glutamatergic neuron `http://purl.obolibrary.org/obo/CL_4023040` +### C-type lectin domain family 4 member C `http://purl.obolibrary.org/obo/PR_000001292` +#### Removed +- [C-type lectin domain family 4 member C](http://purl.obolibrary.org/obo/PR_000001292) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [C-type lectin domain family 4 member C (human)](http://purl.obolibrary.org/obo/PR_Q8WTT0) -#### Added -- [L2/3-6 intratelencephalic projecting glutamatergic neuron](http://purl.obolibrary.org/obo/CL_4023040) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### L4/5 intratelencephalic projecting glutamatergic neuron of the primary motor cortex `http://purl.obolibrary.org/obo/CL_4023048` +### C-type lectin domain family 4 member K `http://purl.obolibrary.org/obo/PR_000001293` +#### Removed +- [C-type lectin domain family 4 member K](http://purl.obolibrary.org/obo/PR_000001293) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [C-type lectin domain family 4 member K (human)](http://purl.obolibrary.org/obo/PR_Q9UJ71) -#### Added -- [L4/5 intratelencephalic projecting glutamatergic neuron of the primary motor cortex](http://purl.obolibrary.org/obo/CL_4023048) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### L5 extratelencephalic projecting glutamatergic cortical neuron `http://purl.obolibrary.org/obo/CL_4023041` +### C-type lectin domain family 6 member A `http://purl.obolibrary.org/obo/PR_000001806` +#### Removed +- [C-type lectin domain family 6 member A](http://purl.obolibrary.org/obo/PR_000001806) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [C-type lectin domain family 6 member A (human)](http://purl.obolibrary.org/obo/PR_Q6EIG7) -#### Added -- [L5 extratelencephalic projecting glutamatergic cortical neuron](http://purl.obolibrary.org/obo/CL_4023041) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### L5/6 near-projecting glutamatergic neuron of the primary motor cortex `http://purl.obolibrary.org/obo/CL_4023043` +### C-type lectin domain family 7 member A `http://purl.obolibrary.org/obo/PR_000001807` +#### Removed +- [C-type lectin domain family 7 member A](http://purl.obolibrary.org/obo/PR_000001807) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [C-type lectin domain family 7 member A (human)](http://purl.obolibrary.org/obo/PR_Q9BXN2) -#### Added -- [L5/6 near-projecting glutamatergic neuron of the primary motor cortex](http://purl.obolibrary.org/obo/CL_4023043) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### L6 corticothalamic-projecting glutamatergic cortical neuron `http://purl.obolibrary.org/obo/CL_4023042` +### CCAAT/enhancer-binding protein alpha `http://purl.obolibrary.org/obo/PR_000005307` +#### Removed +- [CCAAT/enhancer-binding protein alpha](http://purl.obolibrary.org/obo/PR_000005307) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [CCAAT/enhancer-binding protein alpha (human)](http://purl.obolibrary.org/obo/PR_P49715) -#### Added -- [L6 corticothalamic-projecting glutamatergic cortical neuron](http://purl.obolibrary.org/obo/CL_4023042) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex `http://purl.obolibrary.org/obo/CL_4023050` +### CCAAT/enhancer-binding protein epsilon `http://purl.obolibrary.org/obo/PR_000005310` +#### Removed +- [CCAAT/enhancer-binding protein epsilon](http://purl.obolibrary.org/obo/PR_000005310) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [CCAAT/enhancer-binding protein epsilon (human)](http://purl.obolibrary.org/obo/PR_Q15744) -#### Added -- [L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex](http://purl.obolibrary.org/obo/CL_4023050) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### L6b glutamatergic cortical neuron `http://purl.obolibrary.org/obo/CL_4023038` +### CX3C chemokine receptor 1 `http://purl.obolibrary.org/obo/PR_000001206` +#### Removed +- [CX3C chemokine receptor 1](http://purl.obolibrary.org/obo/PR_000001206) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [CX3C chemokine receptor 1 (human)](http://purl.obolibrary.org/obo/PR_P49238) -#### Added -- [L6b glutamatergic cortical neuron](http://purl.obolibrary.org/obo/CL_4023038) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### LATIN `http://purl.obolibrary.org/obo/uberon/core#LATIN` +### Caenorhabditis `http://purl.obolibrary.org/obo/NCBITaxon_6237` #### Removed -- AnnotationProperty: [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [Caenorhabditis](http://purl.obolibrary.org/obo/NCBITaxon_6237) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_genus](http://purl.obolibrary.org/obo/NCBITaxon_genus) -- [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) SubPropertyOf: [synonym_type_property](http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty) +### Callithrix `http://purl.obolibrary.org/obo/NCBITaxon_9481` +#### Removed +- [Callithrix ](http://purl.obolibrary.org/obo/NCBITaxon_9481) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_genus](http://purl.obolibrary.org/obo/NCBITaxon_genus) -### Langerhans cell `http://purl.obolibrary.org/obo/CL_0000453` - -#### Added -- [Langerhans cell](http://purl.obolibrary.org/obo/CL_0000453) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### Leydig cell `http://purl.obolibrary.org/obo/CL_0000178` +### Callithrix `http://purl.obolibrary.org/obo/NCBITaxon_1965096` +#### Removed +- [Callithrix ](http://purl.obolibrary.org/obo/NCBITaxon_1965096) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_subgenus](http://purl.obolibrary.org/obo/NCBITaxon_subgenus) -#### Added -- [Leydig cell](http://purl.obolibrary.org/obo/CL_0000178) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### M cell of gut `http://purl.obolibrary.org/obo/CL_0000682` +### Callithrix jacchus `http://purl.obolibrary.org/obo/NCBITaxon_9483` +#### Removed +- [Callithrix jacchus](http://purl.obolibrary.org/obo/NCBITaxon_9483) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_species](http://purl.obolibrary.org/obo/NCBITaxon_species) -#### Added -- [M cell of gut](http://purl.obolibrary.org/obo/CL_0000682) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### MHC-II-positive classical monocyte `http://purl.obolibrary.org/obo/CL_0002470` +### Callitrichinae `http://purl.obolibrary.org/obo/NCBITaxon_9480` +#### Removed +- [Callitrichinae](http://purl.obolibrary.org/obo/NCBITaxon_9480) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_subfamily](http://purl.obolibrary.org/obo/NCBITaxon_subfamily) -#### Added -- [MHC-II-positive classical monocyte](http://purl.obolibrary.org/obo/CL_0002470) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### Malpighian tubule `http://purl.obolibrary.org/obo/UBERON_0001054` +### Carnivora `http://purl.obolibrary.org/obo/NCBITaxon_33554` #### Removed -- [Malpighian tubule](http://purl.obolibrary.org/obo/UBERON_0001054) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005786" - -#### Added -- [Malpighian tubule](http://purl.obolibrary.org/obo/UBERON_0001054) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005786" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [Carnivora](http://purl.obolibrary.org/obo/NCBITaxon_33554) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_order](http://purl.obolibrary.org/obo/NCBITaxon_order) -### Merkel cell `http://purl.obolibrary.org/obo/CL_0000242` -#### Added -- [Merkel cell](http://purl.obolibrary.org/obo/CL_0000242) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### Catarrhini `http://purl.obolibrary.org/obo/NCBITaxon_9526` +#### Removed +- [Catarrhini](http://purl.obolibrary.org/obo/NCBITaxon_9526) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_parvorder](http://purl.obolibrary.org/obo/NCBITaxon_parvorder) -### Mueller cell `http://purl.obolibrary.org/obo/CL_0000636` -#### Added -- [Mueller cell](http://purl.obolibrary.org/obo/CL_0000636) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### Cebidae `http://purl.obolibrary.org/obo/NCBITaxon_9498` +#### Removed +- [Cebidae](http://purl.obolibrary.org/obo/NCBITaxon_9498) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_family](http://purl.obolibrary.org/obo/NCBITaxon_family) -### NKp44-negative group 3 innate lymphoid cell, human `http://purl.obolibrary.org/obo/CL_0001080` -#### Added -- [NKp44-negative group 3 innate lymphoid cell, human](http://purl.obolibrary.org/obo/CL_0001080) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### Chordata `http://purl.obolibrary.org/obo/NCBITaxon_7711` +#### Removed +- [Chordata](http://purl.obolibrary.org/obo/NCBITaxon_7711) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_phylum](http://purl.obolibrary.org/obo/NCBITaxon_phylum) -### NKp44-positive group 3 innate lymphoid cell, human `http://purl.obolibrary.org/obo/CL_0001079` -#### Added -- [NKp44-positive group 3 innate lymphoid cell, human](http://purl.obolibrary.org/obo/CL_0001079) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### Chromadorea `http://purl.obolibrary.org/obo/NCBITaxon_119089` +#### Removed +- [Chromadorea](http://purl.obolibrary.org/obo/NCBITaxon_119089) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_class](http://purl.obolibrary.org/obo/NCBITaxon_class) -### NKp46-positive innate lymphoid cell, human `http://purl.obolibrary.org/obo/CL_0001076` -#### Added -- [NKp46-positive innate lymphoid cell, human](http://purl.obolibrary.org/obo/CL_0001076) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### Cnidaria `http://purl.obolibrary.org/obo/NCBITaxon_6073` +#### Removed +- [Cnidaria](http://purl.obolibrary.org/obo/NCBITaxon_6073) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_phylum](http://purl.obolibrary.org/obo/NCBITaxon_phylum) -### OFF retinal ganglion cell `http://purl.obolibrary.org/obo/CL_4023033` -#### Added -- [OFF retinal ganglion cell](http://purl.obolibrary.org/obo/CL_4023033) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### Coelurosauria `http://purl.obolibrary.org/obo/NCBITaxon_436492` +#### Removed +- [Coelurosauria](http://purl.obolibrary.org/obo/NCBITaxon_436492) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) -### OFF-bipolar cell `http://purl.obolibrary.org/obo/CL_0000750` -#### Added -- [OFF-bipolar cell](http://purl.obolibrary.org/obo/CL_0000750) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### Coniferophyta `http://purl.obolibrary.org/obo/NCBITaxon_3312` +#### Removed +- [Coniferophyta](http://purl.obolibrary.org/obo/NCBITaxon_3312) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) -### OMO_0003002 `http://purl.obolibrary.org/obo/OMO_0003002` -#### Added -- AnnotationProperty: [OMO_0003002](http://purl.obolibrary.org/obo/OMO_0003002) +### Craniata `http://purl.obolibrary.org/obo/NCBITaxon_89593` +#### Removed +- [Craniata ](http://purl.obolibrary.org/obo/NCBITaxon_89593) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_subphylum](http://purl.obolibrary.org/obo/NCBITaxon_subphylum) -- [OMO_0003002](http://purl.obolibrary.org/obo/OMO_0003002) SubPropertyOf: [synonym_type_property](http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty) -### OMO_0003011 `http://purl.obolibrary.org/obo/OMO_0003011` +### D(1A) dopamine receptor `http://purl.obolibrary.org/obo/PR_000001175` +#### Removed +- [D(1A) dopamine receptor](http://purl.obolibrary.org/obo/PR_000001175) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [D(1A) dopamine receptor (human)](http://purl.obolibrary.org/obo/PR_P21728) -#### Added -- AnnotationProperty: [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -- [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) SubPropertyOf: [synonym_type_property](http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty) +### D(2) dopamine receptor `http://purl.obolibrary.org/obo/PR_000001177` +#### Removed +- [D(2) dopamine receptor](http://purl.obolibrary.org/obo/PR_000001177) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [D(2) dopamine receptor (human)](http://purl.obolibrary.org/obo/PR_P14416) -### ON retinal ganglion cell `http://purl.obolibrary.org/obo/CL_4023032` -#### Added -- [ON retinal ganglion cell](http://purl.obolibrary.org/obo/CL_4023032) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### DNA nucleotidylexotransferase `http://purl.obolibrary.org/obo/PR_000006611` +#### Removed +- [DNA nucleotidylexotransferase](http://purl.obolibrary.org/obo/PR_000006611) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [DNA nucleotidylexotransferase (human)](http://purl.obolibrary.org/obo/PR_P04053) -### ON-bipolar cell `http://purl.obolibrary.org/obo/CL_0000749` -#### Added -- [ON-bipolar cell](http://purl.obolibrary.org/obo/CL_0000749) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### Descemet's membrane `http://purl.obolibrary.org/obo/UBERON_0004367` +#### Removed +- [Descemet's membrane](http://purl.obolibrary.org/obo/UBERON_0004367) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Acellular anatomical structure composed of collagen, Descemet's membrane is secreted as a basement membrane of the corneal endothelium. Located between the stroma and the corneal endothelium, it is approximately 0.15 micrometer thick at 6 months post-fertilization.[ZFIN]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0002157" -### P/D1 enteroendocrine cell `http://purl.obolibrary.org/obo/CL_0002268` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2016-05-01" -#### Added -- [P/D1 enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0002268) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:ZDB-PUB-061010-3" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "https://orcid.org/0000-0001-9114-8737" -### PP cell `http://purl.obolibrary.org/obo/CL_0000696` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "ZFIN" #### Added -- [PP cell](http://purl.obolibrary.org/obo/CL_0000696) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [Descemet's membrane](http://purl.obolibrary.org/obo/UBERON_0004367) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) -### Peyer's patch `http://purl.obolibrary.org/obo/UBERON_0001211` +### Deuterostomia `http://purl.obolibrary.org/obo/NCBITaxon_33511` #### Removed -- [Peyer's patch](http://purl.obolibrary.org/obo/UBERON_0001211) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "noduli lymphoidei aggregati" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [Deuterostomia](http://purl.obolibrary.org/obo/NCBITaxon_33511) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) -#### Added -- [Peyer's patch](http://purl.obolibrary.org/obo/UBERON_0001211) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "noduli lymphoidei aggregati" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### Purkinje cell `http://purl.obolibrary.org/obo/CL_0000121` +### Dictyostelia `http://purl.obolibrary.org/obo/NCBITaxon_33083` +#### Removed +- [Dictyostelia](http://purl.obolibrary.org/obo/NCBITaxon_33083) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) -#### Added -- [Purkinje cell](http://purl.obolibrary.org/obo/CL_0000121) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### Purkinje cell layer of cerebellar cortex `http://purl.obolibrary.org/obo/UBERON_0002979` +### Dictyosteliaceae `http://purl.obolibrary.org/obo/NCBITaxon_2058185` #### Removed -- [Purkinje cell layer of cerebellar cortex](http://purl.obolibrary.org/obo/UBERON_0002979) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus thalamicus reticularis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:365" +- [Dictyosteliaceae](http://purl.obolibrary.org/obo/NCBITaxon_2058185) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_family](http://purl.obolibrary.org/obo/NCBITaxon_family) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [Purkinje cell layer of cerebellar cortex](http://purl.obolibrary.org/obo/UBERON_0002979) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus reticularis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:365" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### Dictyosteliales `http://purl.obolibrary.org/obo/NCBITaxon_2058949` +#### Removed +- [Dictyosteliales](http://purl.obolibrary.org/obo/NCBITaxon_2058949) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_order](http://purl.obolibrary.org/obo/NCBITaxon_order) -- [Purkinje cell layer of cerebellar cortex](http://purl.obolibrary.org/obo/UBERON_0002979) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "reticulatum thalami (Hassler)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:365" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [Purkinje cell layer of cerebellar cortex](http://purl.obolibrary.org/obo/UBERON_0002979) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nuclei reticulares (thalami)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:365" +### Dictyostelium `http://purl.obolibrary.org/obo/NCBITaxon_5782` +#### Removed +- [Dictyostelium](http://purl.obolibrary.org/obo/NCBITaxon_5782) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_genus](http://purl.obolibrary.org/obo/NCBITaxon_genus) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [Purkinje cell layer of cerebellar cortex](http://purl.obolibrary.org/obo/UBERON_0002979) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus reticulatus (thalami)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:365" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### Dikarya `http://purl.obolibrary.org/obo/NCBITaxon_451864` +#### Removed +- [Dikarya](http://purl.obolibrary.org/obo/NCBITaxon_451864) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_subkingdom](http://purl.obolibrary.org/obo/NCBITaxon_subkingdom) -#### Added -- [Purkinje cell layer of cerebellar cortex](http://purl.obolibrary.org/obo/UBERON_0002979) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus thalamicus reticularis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:365" -- [Purkinje cell layer of cerebellar cortex](http://purl.obolibrary.org/obo/UBERON_0002979) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus reticularis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### Dinosauria `http://purl.obolibrary.org/obo/NCBITaxon_436486` +#### Removed +- [Dinosauria](http://purl.obolibrary.org/obo/NCBITaxon_436486) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:365" -- [Purkinje cell layer of cerebellar cortex](http://purl.obolibrary.org/obo/UBERON_0002979) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nuclei reticulares (thalami)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:365" +### Dipnotetrapodomorpha `http://purl.obolibrary.org/obo/NCBITaxon_1338369` +#### Removed +- [Dipnotetrapodomorpha](http://purl.obolibrary.org/obo/NCBITaxon_1338369) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) -- [Purkinje cell layer of cerebellar cortex](http://purl.obolibrary.org/obo/UBERON_0002979) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus reticulatus (thalami)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:365" -- [Purkinje cell layer of cerebellar cortex](http://purl.obolibrary.org/obo/UBERON_0002979) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "reticulatum thalami (Hassler)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### Discoba `http://purl.obolibrary.org/obo/NCBITaxon_2611352` +#### Removed +- [Discoba](http://purl.obolibrary.org/obo/NCBITaxon_2611352) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:365" -### RNA binding `http://purl.obolibrary.org/obo/GO_0003723` +### Ecdysozoa `http://purl.obolibrary.org/obo/NCBITaxon_1206794` #### Removed -- [RNA binding](http://purl.obolibrary.org/obo/GO_0003723) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) +- [Ecdysozoa](http://purl.obolibrary.org/obo/NCBITaxon_1206794) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) -#### Added -- [RNA binding](http://purl.obolibrary.org/obo/GO_0003723) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) -### RNA metabolic process `http://purl.obolibrary.org/obo/GO_0016070` +### Echinodermata `http://purl.obolibrary.org/obo/NCBITaxon_7586` #### Removed -- [RNA metabolic process](http://purl.obolibrary.org/obo/GO_0016070) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) +- [Echinodermata](http://purl.obolibrary.org/obo/NCBITaxon_7586) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_phylum](http://purl.obolibrary.org/obo/NCBITaxon_phylum) -#### Added -- [RNA metabolic process](http://purl.obolibrary.org/obo/GO_0016070) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) -### S cone cell `http://purl.obolibrary.org/obo/CL_0003050` +### Embryophyta `http://purl.obolibrary.org/obo/NCBITaxon_3193` +#### Removed +- [Embryophyta](http://purl.obolibrary.org/obo/NCBITaxon_3193) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) -#### Added -- [S cone cell](http://purl.obolibrary.org/obo/CL_0003050) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### S-shaped body `http://purl.obolibrary.org/obo/UBERON_0004199` +### Equidae `http://purl.obolibrary.org/obo/NCBITaxon_9788` +#### Removed +- [Equidae](http://purl.obolibrary.org/obo/NCBITaxon_9788) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_family](http://purl.obolibrary.org/obo/NCBITaxon_family) -#### Added -- [S-shaped body](http://purl.obolibrary.org/obo/UBERON_0004199) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "VO:0010896" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" - - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) +### Equus `http://purl.obolibrary.org/obo/NCBITaxon_9789` +#### Removed +- [Equus](http://purl.obolibrary.org/obo/NCBITaxon_9789) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_genus](http://purl.obolibrary.org/obo/NCBITaxon_genus) -### Schwann cell `http://purl.obolibrary.org/obo/CL_0002573` -#### Added -- [Schwann cell](http://purl.obolibrary.org/obo/CL_0002573) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### Euarchontoglires `http://purl.obolibrary.org/obo/NCBITaxon_314146` +#### Removed +- [Euarchontoglires](http://purl.obolibrary.org/obo/NCBITaxon_314146) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_superorder](http://purl.obolibrary.org/obo/NCBITaxon_superorder) -### Schwann cell precursor `http://purl.obolibrary.org/obo/CL_0002375` -#### Added -- [Schwann cell precursor](http://purl.obolibrary.org/obo/CL_0002375) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### Euglenozoa `http://purl.obolibrary.org/obo/NCBITaxon_33682` +#### Removed +- [Euglenozoa](http://purl.obolibrary.org/obo/NCBITaxon_33682) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_phylum](http://purl.obolibrary.org/obo/NCBITaxon_phylum) -### Sertoli cell `http://purl.obolibrary.org/obo/CL_0000216` -#### Added -- [Sertoli cell](http://purl.obolibrary.org/obo/CL_0000216) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### Eukaryota `http://purl.obolibrary.org/obo/NCBITaxon_2759` +#### Removed +- [Eukaryota](http://purl.obolibrary.org/obo/NCBITaxon_2759) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_superkingdom](http://purl.obolibrary.org/obo/NCBITaxon_superkingdom) -### T cell `http://purl.obolibrary.org/obo/CL_0000084` -#### Added -- [T cell](http://purl.obolibrary.org/obo/CL_0000084) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### Eumetazoa `http://purl.obolibrary.org/obo/NCBITaxon_6072` +#### Removed +- [Eumetazoa](http://purl.obolibrary.org/obo/NCBITaxon_6072) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) -### T follicular helper cell `http://purl.obolibrary.org/obo/CL_0002038` -#### Added -- [T follicular helper cell](http://purl.obolibrary.org/obo/CL_0002038) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### Eumycetozoa `http://purl.obolibrary.org/obo/NCBITaxon_142796` +#### Removed +- [Eumycetozoa](http://purl.obolibrary.org/obo/NCBITaxon_142796) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_class](http://purl.obolibrary.org/obo/NCBITaxon_class) -### T follicular regulatory cell `http://purl.obolibrary.org/obo/CL_0009113` -#### Added -- [T follicular regulatory cell](http://purl.obolibrary.org/obo/CL_0009113) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### Euphyllophyta `http://purl.obolibrary.org/obo/NCBITaxon_78536` +#### Removed +- [Euphyllophyta](http://purl.obolibrary.org/obo/NCBITaxon_78536) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) -### T-helper 1 cell `http://purl.obolibrary.org/obo/CL_0000545` -#### Added -- [T-helper 1 cell](http://purl.obolibrary.org/obo/CL_0000545) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### Euteleostomi `http://purl.obolibrary.org/obo/NCBITaxon_117571` +#### Removed +- [Euteleostomi](http://purl.obolibrary.org/obo/NCBITaxon_117571) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) -### T-helper 17 cell `http://purl.obolibrary.org/obo/CL_0000899` -#### Added -- [T-helper 17 cell](http://purl.obolibrary.org/obo/CL_0000899) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### Eutheria `http://purl.obolibrary.org/obo/NCBITaxon_9347` +#### Removed +- [Eutheria](http://purl.obolibrary.org/obo/NCBITaxon_9347) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) -### T-helper 2 cell `http://purl.obolibrary.org/obo/CL_0000546` -#### Added -- [T-helper 2 cell](http://purl.obolibrary.org/obo/CL_0000546) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### Evosea `http://purl.obolibrary.org/obo/NCBITaxon_2605435` +#### Removed +- [Evosea](http://purl.obolibrary.org/obo/NCBITaxon_2605435) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_phylum](http://purl.obolibrary.org/obo/NCBITaxon_phylum) -### T-helper 22 cell `http://purl.obolibrary.org/obo/CL_0001042` -#### Added -- [T-helper 22 cell](http://purl.obolibrary.org/obo/CL_0001042) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### Felidae `http://purl.obolibrary.org/obo/NCBITaxon_9681` +#### Removed +- [Felidae](http://purl.obolibrary.org/obo/NCBITaxon_9681) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_family](http://purl.obolibrary.org/obo/NCBITaxon_family) -### abdominal aorta `http://purl.obolibrary.org/obo/UBERON_0001516` -#### Removed -- [abdominal aorta](http://purl.obolibrary.org/obo/UBERON_0001516) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pars abdominalis aortae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Abdominal_aorta" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0002976" +### Feliformia `http://purl.obolibrary.org/obo/NCBITaxon_379583` +#### Removed +- [Feliformia](http://purl.obolibrary.org/obo/NCBITaxon_379583) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_suborder](http://purl.obolibrary.org/obo/NCBITaxon_suborder) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [abdominal aorta](http://purl.obolibrary.org/obo/UBERON_0001516) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "aorta abdominalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Abdominal_aorta" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0002976" +### Felinae `http://purl.obolibrary.org/obo/NCBITaxon_338152` +#### Removed +- [Felinae](http://purl.obolibrary.org/obo/NCBITaxon_338152) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_subfamily](http://purl.obolibrary.org/obo/NCBITaxon_subfamily) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [abdominal aorta](http://purl.obolibrary.org/obo/UBERON_0001516) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "aorta abdominalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Abdominal_aorta" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### Felis `http://purl.obolibrary.org/obo/NCBITaxon_9682` +#### Removed +- [Felis](http://purl.obolibrary.org/obo/NCBITaxon_9682) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_genus](http://purl.obolibrary.org/obo/NCBITaxon_genus) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0002976" -- [abdominal aorta](http://purl.obolibrary.org/obo/UBERON_0001516) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pars abdominalis aortae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Abdominal_aorta" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### Felis catus `http://purl.obolibrary.org/obo/NCBITaxon_9685` +#### Removed +- [Felis catus](http://purl.obolibrary.org/obo/NCBITaxon_9685) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_species](http://purl.obolibrary.org/obo/NCBITaxon_species) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0002976" -### abdominal cavity `http://purl.obolibrary.org/obo/UBERON_0003684` +### Fungi `http://purl.obolibrary.org/obo/NCBITaxon_4751` #### Removed -- [abdominal cavity](http://purl.obolibrary.org/obo/UBERON_0003684) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cavitas abdominis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GAID:17" +- [Fungi](http://purl.obolibrary.org/obo/NCBITaxon_4751) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_kingdom](http://purl.obolibrary.org/obo/NCBITaxon_kingdom) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Abdominal_cavity" -#### Added -- [abdominal cavity](http://purl.obolibrary.org/obo/UBERON_0003684) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cavitas abdominis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### GCIs +#### Removed +- DisjointClasses: [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [central tendon of diaphragm](http://purl.obolibrary.org/obo/UBERON_0006670), [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765), [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [costal diaphragm](http://purl.obolibrary.org/obo/UBERON_0035831) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GAID:17" +- ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [parietal pleura](http://purl.obolibrary.org/obo/UBERON_0002400)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [visceral pleura](http://purl.obolibrary.org/obo/UBERON_0002401)) EquivalentTo [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [pleura](http://purl.obolibrary.org/obo/UBERON_0000977) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Abdominal_cavity" +- ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [peritoneal cavity](http://purl.obolibrary.org/obo/UBERON_0001179)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [peritoneum](http://purl.obolibrary.org/obo/UBERON_0002358)) EquivalentTo [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [peritoneal sac](http://purl.obolibrary.org/obo/UBERON_0035820) +- ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [pleura](http://purl.obolibrary.org/obo/UBERON_0000977)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [pleural cavity](http://purl.obolibrary.org/obo/UBERON_0002402)) EquivalentTo [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [pleural sac](http://purl.obolibrary.org/obo/UBERON_0009778) -### abdominal wall `http://purl.obolibrary.org/obo/UBERON_0003697` -#### Removed -- [abdominal wall](http://purl.obolibrary.org/obo/UBERON_0003697) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "paries abdominalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Abdominal_wall" +- ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [eyeball of camera-type eye](http://purl.obolibrary.org/obo/UBERON_0010230)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [ocular adnexa](http://purl.obolibrary.org/obo/UBERON_0035639)) EquivalentTo [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [orbital region](http://purl.obolibrary.org/obo/UBERON_0004088) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [right lung](http://purl.obolibrary.org/obo/UBERON_0002167)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [left lung](http://purl.obolibrary.org/obo/UBERON_0002168)) EquivalentTo [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [pair of lungs](http://purl.obolibrary.org/obo/UBERON_0000170) -#### Added -- [abdominal wall](http://purl.obolibrary.org/obo/UBERON_0003697) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "paries abdominalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Abdominal_wall" +- ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [central tendon of diaphragm](http://purl.obolibrary.org/obo/UBERON_0006670)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [costal diaphragm](http://purl.obolibrary.org/obo/UBERON_0035831)) EquivalentTo [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [diaphragm](http://purl.obolibrary.org/obo/UBERON_0001103) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [submucosa](http://purl.obolibrary.org/obo/UBERON_0000009)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [mucosa](http://purl.obolibrary.org/obo/UBERON_0000344)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [hypodermis](http://purl.obolibrary.org/obo/UBERON_0002072)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [skin of body](http://purl.obolibrary.org/obo/UBERON_0002097)) EquivalentTo [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [dermatological-muscosal system](http://purl.obolibrary.org/obo/UBERON_0012125) +- ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [dentate gyrus of hippocampal formation](http://purl.obolibrary.org/obo/UBERON_0001885)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [Ammon's horn](http://purl.obolibrary.org/obo/UBERON_0001954)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191)) EquivalentTo [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [hippocampal formation](http://purl.obolibrary.org/obo/UBERON_0002421) -### abdominopelvic cavity `http://purl.obolibrary.org/obo/UBERON_0035819` -#### Removed -- [abdominopelvic cavity](http://purl.obolibrary.org/obo/UBERON_0035819) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cavitas abdominis et pelvis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [abdominal cavity](http://purl.obolibrary.org/obo/UBERON_0003684)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [pelvic cavity](http://purl.obolibrary.org/obo/UBERON_0008203)) EquivalentTo [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [abdominopelvic cavity](http://purl.obolibrary.org/obo/UBERON_0035819) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [sebaceous gland](http://purl.obolibrary.org/obo/UBERON_0001821)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [arrector muscle of hair](http://purl.obolibrary.org/obo/UBERON_0002033)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [hair follicle](http://purl.obolibrary.org/obo/UBERON_0002073)) EquivalentTo [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [pilosebaceous unit](http://purl.obolibrary.org/obo/UBERON_0011932) -#### Added -- [abdominopelvic cavity](http://purl.obolibrary.org/obo/UBERON_0035819) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cavitas abdominis et pelvis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [left dorsal aorta](http://purl.obolibrary.org/obo/UBERON_0005613)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [right dorsal aorta](http://purl.obolibrary.org/obo/UBERON_0005622)) EquivalentTo [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [pair of dorsal aortae](http://purl.obolibrary.org/obo/UBERON_0010190) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [cortex of hair](http://purl.obolibrary.org/obo/UBERON_0002077)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [hair medulla](http://purl.obolibrary.org/obo/UBERON_0005184)) EquivalentTo [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [hair shaft](http://purl.obolibrary.org/obo/UBERON_0002074) +- ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [parietal serous pericardium](http://purl.obolibrary.org/obo/UBERON_0002408)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [visceral serous pericardium](http://purl.obolibrary.org/obo/UBERON_0002425)) EquivalentTo [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [serous pericardium](http://purl.obolibrary.org/obo/UBERON_0002357) -### abnormal cell `http://purl.obolibrary.org/obo/CL_0001061` +- ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [respiratory primordium epithelium](http://purl.obolibrary.org/obo/UBERON_0036072)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [respiratory primordium mesenchyme](http://purl.obolibrary.org/obo/UBERON_0036073)) EquivalentTo [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [respiratory primordium](http://purl.obolibrary.org/obo/UBERON_0008947) -#### Added -- [abnormal cell](http://purl.obolibrary.org/obo/CL_0001061) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [hypodermis](http://purl.obolibrary.org/obo/UBERON_0002072)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [skin of body](http://purl.obolibrary.org/obo/UBERON_0002097)) EquivalentTo [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [integument](http://purl.obolibrary.org/obo/UBERON_0002199) +- ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [embryo stage](http://purl.obolibrary.org/obo/UBERON_0000068)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [post-embryonic stage](http://purl.obolibrary.org/obo/UBERON_0000092)) EquivalentTo [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [life cycle](http://purl.obolibrary.org/obo/UBERON_0000104) -### accessory XI nerve `http://purl.obolibrary.org/obo/UBERON_0002019` -#### Removed -- [accessory XI nerve](http://purl.obolibrary.org/obo/UBERON_0002019) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus accessorius [XI]" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [peripheral nervous system](http://purl.obolibrary.org/obo/UBERON_0000010)) or ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [central nervous system](http://purl.obolibrary.org/obo/UBERON_0001017)) EquivalentTo [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [nervous system](http://purl.obolibrary.org/obo/UBERON_0001016) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [common iliac artery](http://purl.obolibrary.org/obo/UBERON_0001191) and ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [Homo sapiens](http://purl.obolibrary.org/obo/NCBITaxon_9606)) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [right umbilical artery](http://purl.obolibrary.org/obo/UBERON_0005470) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "requires review" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:6720" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "EHDAA2" -- [accessory XI nerve](http://purl.obolibrary.org/obo/UBERON_0002019) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pars spinalis nervus accessorius" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [thymus primordium](http://purl.obolibrary.org/obo/UBERON_0005562) and ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [Aves](http://purl.obolibrary.org/obo/NCBITaxon_8782)) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [dorsal part of pharyngeal pouch 3](http://purl.obolibrary.org/obo/UBERON_0010025) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "Aves" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0073040584-table13.1" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:6720" +- [telencephalic ventricle](http://purl.obolibrary.org/obo/UBERON_0002285) and ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [Tetrapoda](http://purl.obolibrary.org/obo/NCBITaxon_32523)) SubClassOf [in lateral side of](http://purl.obolibrary.org/obo/BSPO_0000126) some [telencephalon](http://purl.obolibrary.org/obo/UBERON_0001893) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "evaginated" -- [accessory XI nerve](http://purl.obolibrary.org/obo/UBERON_0002019) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "radix spinalis nervus accessorius" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [thymus primordium](http://purl.obolibrary.org/obo/UBERON_0005562) and ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [Mammalia](http://purl.obolibrary.org/obo/NCBITaxon_40674)) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [ventral part of pharyngeal pouch 4](http://purl.obolibrary.org/obo/UBERON_0010028) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "Mammals" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0073040584-table13.1" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:6720" +- [naris](http://purl.obolibrary.org/obo/UBERON_0000003) and ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [Gnathostomata ](http://purl.obolibrary.org/obo/NCBITaxon_7776)) SubClassOf [in lateral side of](http://purl.obolibrary.org/obo/BSPO_0000126) some [head](http://purl.obolibrary.org/obo/UBERON_0000033) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "hagfish have median nostril" -#### Added -- [accessory XI nerve](http://purl.obolibrary.org/obo/UBERON_0002019) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pars spinalis nervus accessorius" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [nose](http://purl.obolibrary.org/obo/UBERON_0000004) and ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [Gnathostomata ](http://purl.obolibrary.org/obo/NCBITaxon_7776)) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [midface](http://purl.obolibrary.org/obo/UBERON_0004089) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "midface division only makes sense for gnathostomes" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [thymus primordium](http://purl.obolibrary.org/obo/UBERON_0005562) and ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [Aves](http://purl.obolibrary.org/obo/NCBITaxon_8782)) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [dorsal part of pharyngeal pouch 4](http://purl.obolibrary.org/obo/UBERON_0010027) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "Aves" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:6720" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0073040584-table13.1" -- [accessory XI nerve](http://purl.obolibrary.org/obo/UBERON_0002019) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "radix spinalis nervus accessorius" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [lens vesicle](http://purl.obolibrary.org/obo/UBERON_0005426) and ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [Mammalia](http://purl.obolibrary.org/obo/NCBITaxon_40674)) SubClassOf [has quality](http://purl.obolibrary.org/obo/RO_0000086) some [hollow](http://purl.obolibrary.org/obo/PATO_0002078) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "Mammals" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [adenohypophysis](http://purl.obolibrary.org/obo/UBERON_0002196) and ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [Tetrapoda](http://purl.obolibrary.org/obo/NCBITaxon_32523)) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [Rathke's pouch](http://purl.obolibrary.org/obo/UBERON_0005356) + - [exception](http://www.geneontology.org/formats/oboInOwl#exception) "teleost" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:6720" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "NCBIBook:NBK53175" -- [accessory XI nerve](http://purl.obolibrary.org/obo/UBERON_0002019) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus accessorius [XI]" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [intestinal villus](http://purl.obolibrary.org/obo/UBERON_0001213) and ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [Homo sapiens](http://purl.obolibrary.org/obo/NCBITaxon_9606)) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [mucosa of small intestine](http://purl.obolibrary.org/obo/UBERON_0001204) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "may be present in other parts in other species" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:6720" +- [parathyroid gland](http://purl.obolibrary.org/obo/UBERON_0001132) and ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [Aves](http://purl.obolibrary.org/obo/NCBITaxon_8782)) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [ventral part of pharyngeal pouch 4](http://purl.obolibrary.org/obo/UBERON_0010028) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "Aves" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0073040584-table13.1" -### accessory XI nerve nucleus `http://purl.obolibrary.org/obo/UBERON_0020358` -#### Removed -- [accessory XI nerve nucleus](http://purl.obolibrary.org/obo/UBERON_0020358) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus nervi accessorii" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:2003" +- [parathyroid gland](http://purl.obolibrary.org/obo/UBERON_0001132) and ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [Mammalia](http://purl.obolibrary.org/obo/NCBITaxon_40674)) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [dorsal part of pharyngeal pouch 4](http://purl.obolibrary.org/obo/UBERON_0010027) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "Mammals" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0073040584-table13.1" -- [accessory XI nerve nucleus](http://purl.obolibrary.org/obo/UBERON_0020358) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus accessorius columnae anterioris medullae spinalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:2003" +- [testis](http://purl.obolibrary.org/obo/UBERON_0000473) and ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [Vertebrata ](http://purl.obolibrary.org/obo/NCBITaxon_7742)) SubClassOf [in lateral side of](http://purl.obolibrary.org/obo/BSPO_0000126) some [multicellular organism](http://purl.obolibrary.org/obo/UBERON_0000468) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "vertebrates" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [parathyroid gland](http://purl.obolibrary.org/obo/UBERON_0001132) and ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [Mammalia](http://purl.obolibrary.org/obo/NCBITaxon_40674)) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [dorsal part of pharyngeal pouch 3](http://purl.obolibrary.org/obo/UBERON_0010025) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "Mammals" -#### Added -- [accessory XI nerve nucleus](http://purl.obolibrary.org/obo/UBERON_0020358) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus nervi accessorii" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0073040584-table13.1" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:2003" +- [thymus primordium](http://purl.obolibrary.org/obo/UBERON_0005562) and ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [Mammalia](http://purl.obolibrary.org/obo/NCBITaxon_40674)) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [ventral part of pharyngeal pouch 3](http://purl.obolibrary.org/obo/UBERON_0010026) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "EHDAA2" -- [accessory XI nerve nucleus](http://purl.obolibrary.org/obo/UBERON_0020358) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus accessorius columnae anterioris medullae spinalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "Mammals" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:2003" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0073040584-table13.1" +- [parathyroid gland](http://purl.obolibrary.org/obo/UBERON_0001132) and ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [Homo sapiens](http://purl.obolibrary.org/obo/NCBITaxon_9606)) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [pharyngeal pouch 4](http://purl.obolibrary.org/obo/UBERON_0007125) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "pouches 3 and 4 in human" -### accessory nerve root `http://purl.obolibrary.org/obo/UBERON_0014615` -#### Removed -- [accessory nerve root](http://purl.obolibrary.org/obo/UBERON_0014615) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pars vagalis of nervus accessorius" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:703" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:16313389" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [gonad primordium](http://purl.obolibrary.org/obo/UBERON_0005564) and ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [Deuterostomia](http://purl.obolibrary.org/obo/NCBITaxon_33511)) SubClassOf [located in](http://purl.obolibrary.org/obo/RO_0001025) some [coelemic cavity lumen](http://purl.obolibrary.org/obo/UBERON_0002323) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "conservatively place at deuterostome, excluding acoelomates" -- [accessory nerve root](http://purl.obolibrary.org/obo/UBERON_0014615) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "radices craniales nervi accessorii" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:703" +- [central nervous system](http://purl.obolibrary.org/obo/UBERON_0001017) and ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [Vertebrata ](http://purl.obolibrary.org/obo/NCBITaxon_7742)) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [neural tube](http://purl.obolibrary.org/obo/UBERON_0001049) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [parathyroid gland](http://purl.obolibrary.org/obo/UBERON_0001132) and ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [Aves](http://purl.obolibrary.org/obo/NCBITaxon_8782)) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [ventral part of pharyngeal pouch 3](http://purl.obolibrary.org/obo/UBERON_0010026) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "Aves" -#### Added -- [accessory nerve root](http://purl.obolibrary.org/obo/UBERON_0014615) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pars vagalis of nervus accessorius" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0073040584-table13.1" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:703" +- [telencephalic ventricle](http://purl.obolibrary.org/obo/UBERON_0002285) and ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [Tetrapoda](http://purl.obolibrary.org/obo/NCBITaxon_32523)) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [cerebral hemisphere](http://purl.obolibrary.org/obo/UBERON_0001869) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "evaginated" -- [accessory nerve root](http://purl.obolibrary.org/obo/UBERON_0014615) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "radices craniales nervi accessorii" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [lens vesicle](http://purl.obolibrary.org/obo/UBERON_0005426) and ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [Teleostei](http://purl.obolibrary.org/obo/NCBITaxon_32443)) SubClassOf [has quality](http://purl.obolibrary.org/obo/RO_0000086) some [solid configuration](http://purl.obolibrary.org/obo/PATO_0001736) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "teleosts" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:703" +- [common iliac artery](http://purl.obolibrary.org/obo/UBERON_0001191) and ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [Homo sapiens](http://purl.obolibrary.org/obo/NCBITaxon_9606)) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [left umbilical artery](http://purl.obolibrary.org/obo/UBERON_0005458) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "requires review" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "EHDAA2" -### acellular anatomical structure `http://purl.obolibrary.org/obo/UBERON_0000476` -#### Removed -- [acellular anatomical structure](http://purl.obolibrary.org/obo/UBERON_0000476) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007013" +- [rib](http://purl.obolibrary.org/obo/UBERON_0002228) and ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [Euarchontoglires](http://purl.obolibrary.org/obo/NCBITaxon_314146)) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [thoracic rib cage](http://purl.obolibrary.org/obo/UBERON_0003252) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "Euarchontoglires" -#### Added -- [acellular anatomical structure](http://purl.obolibrary.org/obo/UBERON_0000476) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007013" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [esophagus](http://purl.obolibrary.org/obo/UBERON_0001043) and ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [Mammalia](http://purl.obolibrary.org/obo/NCBITaxon_40674)) SubClassOf [distally connected to](http://purl.obolibrary.org/obo/uberon/core#distally_connected_to) some [stomach](http://purl.obolibrary.org/obo/UBERON_0000945) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "only in species that have a stomach" +- [right subclavian artery](http://purl.obolibrary.org/obo/UBERON_0001534) and ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [Mammalia](http://purl.obolibrary.org/obo/NCBITaxon_40674)) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [pharyngeal arch artery 4](http://purl.obolibrary.org/obo/UBERON_0003121) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "embryology.ch" -### acinar cell `http://purl.obolibrary.org/obo/CL_0000622` + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "right arch 4 in human" -#### Added -- [acinar cell](http://purl.obolibrary.org/obo/CL_0000622) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### acinar cell of salivary gland `http://purl.obolibrary.org/obo/CL_0002623` +### Glaucocystophyceae `http://purl.obolibrary.org/obo/NCBITaxon_38254` +#### Removed +- [Glaucocystophyceae](http://purl.obolibrary.org/obo/NCBITaxon_38254) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_class](http://purl.obolibrary.org/obo/NCBITaxon_class) -#### Added -- [acinar cell of salivary gland](http://purl.obolibrary.org/obo/CL_0002623) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### acromioclavicular joint `http://purl.obolibrary.org/obo/UBERON_0003692` +### Glires `http://purl.obolibrary.org/obo/NCBITaxon_314147` #### Removed -- [acromioclavicular joint](http://purl.obolibrary.org/obo/UBERON_0003692) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "articulatio acromioclavicularis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Acromioclavicular_joint" +- [Glires](http://purl.obolibrary.org/obo/NCBITaxon_314147) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [acromioclavicular joint](http://purl.obolibrary.org/obo/UBERON_0003692) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "articulatio acromioclavicularis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Acromioclavicular_joint" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### Gnathostomata `http://purl.obolibrary.org/obo/NCBITaxon_7776` +#### Removed +- [Gnathostomata ](http://purl.obolibrary.org/obo/NCBITaxon_7776) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) -### activated CD4-positive, alpha-beta T cell `http://purl.obolibrary.org/obo/CL_0000896` -#### Added -- [activated CD4-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_0000896) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### Gnetales `http://purl.obolibrary.org/obo/NCBITaxon_3378` +#### Removed +- [Gnetales](http://purl.obolibrary.org/obo/NCBITaxon_3378) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_order](http://purl.obolibrary.org/obo/NCBITaxon_order) -### activated CD4-positive, alpha-beta T cell, human `http://purl.obolibrary.org/obo/CL_0001043` -#### Added -- [activated CD4-positive, alpha-beta T cell, human](http://purl.obolibrary.org/obo/CL_0001043) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### Gnetidae `http://purl.obolibrary.org/obo/NCBITaxon_1445966` +#### Removed +- [Gnetidae](http://purl.obolibrary.org/obo/NCBITaxon_1445966) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_subclass](http://purl.obolibrary.org/obo/NCBITaxon_subclass) -### activated CD8-positive, alpha-beta T cell `http://purl.obolibrary.org/obo/CL_0000906` -#### Added -- [activated CD8-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_0000906) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### Gnetopsida `http://purl.obolibrary.org/obo/NCBITaxon_3372` +#### Removed +- [Gnetopsida](http://purl.obolibrary.org/obo/NCBITaxon_3372) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_class](http://purl.obolibrary.org/obo/NCBITaxon_class) -### activated CD8-positive, alpha-beta T cell, human `http://purl.obolibrary.org/obo/CL_0001049` -#### Added -- [activated CD8-positive, alpha-beta T cell, human](http://purl.obolibrary.org/obo/CL_0001049) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### Haplorrhini `http://purl.obolibrary.org/obo/NCBITaxon_376913` +#### Removed +- [Haplorrhini](http://purl.obolibrary.org/obo/NCBITaxon_376913) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_suborder](http://purl.obolibrary.org/obo/NCBITaxon_suborder) -### activated type II NK T cell `http://purl.obolibrary.org/obo/CL_0000931` -#### Added -- [activated type II NK T cell](http://purl.obolibrary.org/obo/CL_0000931) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### Hexapoda `http://purl.obolibrary.org/obo/NCBITaxon_6960` +#### Removed +- [Hexapoda](http://purl.obolibrary.org/obo/NCBITaxon_6960) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_subphylum](http://purl.obolibrary.org/obo/NCBITaxon_subphylum) -### adenohypophysis `http://purl.obolibrary.org/obo/UBERON_0002196` + +### His-Purkinje system `http://purl.obolibrary.org/obo/UBERON_0004146` #### Removed -- [adenohypophysis](http://purl.obolibrary.org/obo/UBERON_0002196) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lobus anterior hypophysis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:74627" +- [His-Purkinje system](http://purl.obolibrary.org/obo/UBERON_0004146) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "the intraventricular conduction system from the bundle of His to the distal Purkinje fibers, which carries the impulse to the ventricles." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/His-Purkinje+system" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [adenohypophysis](http://purl.obolibrary.org/obo/UBERON_0002196) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lobus anterior (glandula pituitaria)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:74627" +### Hominidae `http://purl.obolibrary.org/obo/NCBITaxon_9604` +#### Removed +- [Hominidae](http://purl.obolibrary.org/obo/NCBITaxon_9604) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_family](http://purl.obolibrary.org/obo/NCBITaxon_family) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [adenohypophysis](http://purl.obolibrary.org/obo/UBERON_0002196) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lobus anterior" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:407" +### Homininae `http://purl.obolibrary.org/obo/NCBITaxon_207598` +#### Removed +- [Homininae](http://purl.obolibrary.org/obo/NCBITaxon_207598) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_subfamily](http://purl.obolibrary.org/obo/NCBITaxon_subfamily) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [adenohypophysis](http://purl.obolibrary.org/obo/UBERON_0002196) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lobus anterior hypophysis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:74627" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### Hominoidea `http://purl.obolibrary.org/obo/NCBITaxon_314295` +#### Removed +- [Hominoidea](http://purl.obolibrary.org/obo/NCBITaxon_314295) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_superfamily](http://purl.obolibrary.org/obo/NCBITaxon_superfamily) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [adenohypophysis](http://purl.obolibrary.org/obo/UBERON_0002196) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lobus anterior" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:407" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### Homo `http://purl.obolibrary.org/obo/NCBITaxon_9605` +#### Removed +- [Homo](http://purl.obolibrary.org/obo/NCBITaxon_9605) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_genus](http://purl.obolibrary.org/obo/NCBITaxon_genus) -- [adenohypophysis](http://purl.obolibrary.org/obo/UBERON_0002196) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lobus anterior (glandula pituitaria)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:74627" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### Homo sapiens `http://purl.obolibrary.org/obo/NCBITaxon_9606` +#### Removed +- [Homo sapiens](http://purl.obolibrary.org/obo/NCBITaxon_9606) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_species](http://purl.obolibrary.org/obo/NCBITaxon_species) -### adipocyte `http://purl.obolibrary.org/obo/CL_0000136` -#### Added -- [adipocyte](http://purl.obolibrary.org/obo/CL_0000136) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### IAO_0000111 `http://purl.obolibrary.org/obo/IAO_0000111` +#### Removed +- AnnotationProperty: [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) -### adipocyte of breast `http://purl.obolibrary.org/obo/CL_0002617` -#### Added -- [adipocyte of breast](http://purl.obolibrary.org/obo/CL_0002617) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### IAO_0000112 `http://purl.obolibrary.org/obo/IAO_0000112` +#### Removed +- AnnotationProperty: [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) -### adipocyte of epicardial fat of left ventricle `http://purl.obolibrary.org/obo/CL_1000311` -#### Added -- [adipocyte of epicardial fat of left ventricle](http://purl.obolibrary.org/obo/CL_1000311) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### IAO_0000114 `http://purl.obolibrary.org/obo/IAO_0000114` +#### Removed +- AnnotationProperty: [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) -### adrenal cortex `http://purl.obolibrary.org/obo/UBERON_0001235` + +### IAO_0000117 `http://purl.obolibrary.org/obo/IAO_0000117` #### Removed -- [adrenal cortex](http://purl.obolibrary.org/obo/UBERON_0001235) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cortex glandulae suprarenalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0000045" +- AnnotationProperty: [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Adrenal_cortex" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [adrenal cortex](http://purl.obolibrary.org/obo/UBERON_0001235) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cortex glandulae suprarenalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0000045" +### IAO_0000118 `http://purl.obolibrary.org/obo/IAO_0000118` +#### Removed +- AnnotationProperty: [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Adrenal_cortex" +### IAO_0000119 `http://purl.obolibrary.org/obo/IAO_0000119` +#### Removed +- AnnotationProperty: [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) -### adrenal gland `http://purl.obolibrary.org/obo/UBERON_0002369` + + +### IAO_0000232 `http://purl.obolibrary.org/obo/IAO_0000232` #### Removed -- [adrenal gland](http://purl.obolibrary.org/obo/UBERON_0002369) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "glandula suprarenalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Adrenal_gland" +- AnnotationProperty: [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [adrenal gland](http://purl.obolibrary.org/obo/UBERON_0002369) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "glandula adrenalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Adrenal_gland" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### IAO_0000233 `http://www.geneontology.org/formats/oboInOwl#http://purl.obolibrary.org/obo/IAO_0000233` +#### Removed +- AnnotationProperty: [IAO_0000233](http://www.geneontology.org/formats/oboInOwl#http://purl.obolibrary.org/obo/IAO_0000233) -#### Added -- [adrenal gland](http://purl.obolibrary.org/obo/UBERON_0002369) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "glandula adrenalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Adrenal_gland" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -- [adrenal gland](http://purl.obolibrary.org/obo/UBERON_0002369) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "glandula suprarenalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Adrenal_gland" +### IAO_0000234 `http://purl.obolibrary.org/obo/IAO_0000234` +#### Removed +- AnnotationProperty: [IAO_0000234](http://purl.obolibrary.org/obo/IAO_0000234) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### adrenal medulla `http://purl.obolibrary.org/obo/UBERON_0001236` +### IAO_0000425 `http://purl.obolibrary.org/obo/IAO_0000425` #### Removed -- [adrenal medulla](http://purl.obolibrary.org/obo/UBERON_0001236) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "medulla glandulae suprarenalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15633" +- AnnotationProperty: [IAO_0000425](http://purl.obolibrary.org/obo/IAO_0000425) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [adrenal medulla](http://purl.obolibrary.org/obo/UBERON_0001236) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "medulla glandulae suprarenalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15633" +### IAO_0000426 `http://purl.obolibrary.org/obo/IAO_0000426` +#### Removed +- AnnotationProperty: [IAO_0000426](http://purl.obolibrary.org/obo/IAO_0000426) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + +### IAO_0000589 `http://purl.obolibrary.org/obo/IAO_0000589` +#### Removed +- AnnotationProperty: [IAO_0000589](http://purl.obolibrary.org/obo/IAO_0000589) -### adult organism `http://purl.obolibrary.org/obo/UBERON_0007023` + +### IAO_0000600 `http://purl.obolibrary.org/obo/IAO_0000600` #### Removed -- [adult organism](http://purl.obolibrary.org/obo/UBERON_0007023) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00003004" +- AnnotationProperty: [IAO_0000600](http://purl.obolibrary.org/obo/IAO_0000600) -#### Added -- [adult organism](http://purl.obolibrary.org/obo/UBERON_0007023) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00003004" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### adventitia `http://purl.obolibrary.org/obo/UBERON_0005742` +### IAO_0006012 `http://purl.obolibrary.org/obo/IAO_0006012` #### Removed -- [adventitia](http://purl.obolibrary.org/obo/UBERON_0005742) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D063194" +- AnnotationProperty: [IAO_0006012](http://purl.obolibrary.org/obo/IAO_0006012) -#### Added -- [adventitia](http://purl.obolibrary.org/obo/UBERON_0005742) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D063194" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +### Insecta `http://purl.obolibrary.org/obo/NCBITaxon_50557` +#### Removed +- [Insecta](http://purl.obolibrary.org/obo/NCBITaxon_50557) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_class](http://purl.obolibrary.org/obo/NCBITaxon_class) + -### adventitia of ductus deferens `http://purl.obolibrary.org/obo/UBERON_0006647` +### L-selectin `http://purl.obolibrary.org/obo/PR_000001318` #### Removed -- [adventitia of ductus deferens](http://purl.obolibrary.org/obo/UBERON_0006647) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica adventitia ductus deferentis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:19238" +- [L-selectin](http://purl.obolibrary.org/obo/PR_000001318) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [L-selectin (human)](http://purl.obolibrary.org/obo/PR_P14151) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [adventitia of ductus deferens](http://purl.obolibrary.org/obo/UBERON_0006647) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica adventitia ductus deferentis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### Laurasiatheria `http://purl.obolibrary.org/obo/NCBITaxon_314145` +#### Removed +- [Laurasiatheria](http://purl.obolibrary.org/obo/NCBITaxon_314145) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_superorder](http://purl.obolibrary.org/obo/NCBITaxon_superorder) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:19238" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + +### Lophotrochozoa `http://purl.obolibrary.org/obo/NCBITaxon_1206795` +#### Removed +- [Lophotrochozoa](http://purl.obolibrary.org/obo/NCBITaxon_1206795) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) -### adventitia of seminal vesicle `http://purl.obolibrary.org/obo/UBERON_0006648` + +### Magnoliopsida `http://purl.obolibrary.org/obo/NCBITaxon_3398` #### Removed -- [adventitia of seminal vesicle](http://purl.obolibrary.org/obo/UBERON_0006648) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica adventitia glandulae vesiculosae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:19403" +- [Magnoliopsida](http://purl.obolibrary.org/obo/NCBITaxon_3398) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_class](http://purl.obolibrary.org/obo/NCBITaxon_class) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [adventitia of seminal vesicle](http://purl.obolibrary.org/obo/UBERON_0006648) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica adventitia glandulae vesiculosae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### Malpighian tubule `http://purl.obolibrary.org/obo/UBERON_0001054` +#### Removed +- [Malpighian tubule](http://purl.obolibrary.org/obo/UBERON_0001054) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "It is unclear as to whether the Malpighian tubules of arachnids and those of the Uniramia are homologous or the result of convergent evolution.[Wikipedia:Malpighian_tubule_system]" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:19403" +- [Malpighian tubule](http://purl.obolibrary.org/obo/UBERON_0001054) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005786" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### adventitia of ureter `http://purl.obolibrary.org/obo/UBERON_0001252` +### Mammalia `http://purl.obolibrary.org/obo/NCBITaxon_40674` #### Removed -- [adventitia of ureter](http://purl.obolibrary.org/obo/UBERON_0001252) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica adventitia ureteris" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15892" +- [Mammalia](http://purl.obolibrary.org/obo/NCBITaxon_40674) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_class](http://purl.obolibrary.org/obo/NCBITaxon_class) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [adventitia of ureter](http://purl.obolibrary.org/obo/UBERON_0001252) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica adventitia (ureter)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15892" +### Mandibulata `http://purl.obolibrary.org/obo/NCBITaxon_197563` +#### Removed +- [Mandibulata](http://purl.obolibrary.org/obo/NCBITaxon_197563) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [adventitia of ureter](http://purl.obolibrary.org/obo/UBERON_0001252) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica adventitia (ureter)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### Metazoa `http://purl.obolibrary.org/obo/NCBITaxon_33208` +#### Removed +- [Metazoa](http://purl.obolibrary.org/obo/NCBITaxon_33208) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_kingdom](http://purl.obolibrary.org/obo/NCBITaxon_kingdom) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15892" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [adventitia of ureter](http://purl.obolibrary.org/obo/UBERON_0001252) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica adventitia ureteris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### Mullerian duct `http://purl.obolibrary.org/obo/UBERON_0003890` +#### Removed +- [Mullerian duct](http://purl.obolibrary.org/obo/UBERON_0003890) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Either of the paired embryonic ducts developing into the uterine tubes, uterus, and vagina in the female and becoming largely obliterated in the male. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/paramesonephric+duct" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15892" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### adventitial cell `http://purl.obolibrary.org/obo/CL_0002503` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001199" -#### Added -- [adventitial cell](http://purl.obolibrary.org/obo/CL_0002503) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [Mullerian duct](http://purl.obolibrary.org/obo/UBERON_0003890) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In females, the archinephric (mesonephric) ducts tend to function only within the urinary systems. The muellerian duct arises embryologically next to the archinephric (wolffian) duct. In males, the muellerian duct regresses if it appears at all, but in females, the muellerian ducts become the oviducts of the reproductive system.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.559" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### alpha-amino acid biosynthetic process `http://purl.obolibrary.org/obo/GO_1901607` -#### Removed -- [alpha-amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_1901607) SubClassOf [amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_0008652) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [alpha-amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_1901607) SubClassOf [biosynthetic process](http://purl.obolibrary.org/obo/GO_0009058) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001199" -### alpha-amino acid metabolic process `http://purl.obolibrary.org/obo/GO_1901605` -#### Removed -- [alpha-amino acid metabolic process](http://purl.obolibrary.org/obo/GO_1901605) SubClassOf [amino acid metabolic process](http://purl.obolibrary.org/obo/GO_0006520) +- [Mullerian duct](http://purl.obolibrary.org/obo/UBERON_0003890) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Transient developmental organ which gives rise to oviducts in female (documented to persist in some male frogs).[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -#### Added -- [alpha-amino acid metabolic process](http://purl.obolibrary.org/obo/GO_1901605) SubClassOf [metabolic process](http://purl.obolibrary.org/obo/GO_0008152) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010141" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### alpha-beta T cell `http://purl.obolibrary.org/obo/CL_0000789` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:RED" -#### Added -- [alpha-beta T cell](http://purl.obolibrary.org/obo/CL_0000789) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [Mullerian duct](http://purl.obolibrary.org/obo/UBERON_0003890) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "Sertoli cells secrete anti-Mullerian hormone (AMH) inducing the demise of this duct" -### alternatively activated macrophage `http://purl.obolibrary.org/obo/CL_0000890` -#### Added -- [alternatively activated macrophage](http://purl.obolibrary.org/obo/CL_0000890) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### Muridae `http://purl.obolibrary.org/obo/NCBITaxon_10066` +#### Removed +- [Muridae](http://purl.obolibrary.org/obo/NCBITaxon_10066) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_family](http://purl.obolibrary.org/obo/NCBITaxon_family) -### alveolar macrophage `http://purl.obolibrary.org/obo/CL_0000583` -#### Added -- [alveolar macrophage](http://purl.obolibrary.org/obo/CL_0000583) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### Murinae `http://purl.obolibrary.org/obo/NCBITaxon_39107` +#### Removed +- [Murinae](http://purl.obolibrary.org/obo/NCBITaxon_39107) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_subfamily](http://purl.obolibrary.org/obo/NCBITaxon_subfamily) -### alveolar ridge `http://purl.obolibrary.org/obo/UBERON_0004103` + +### Muroidea `http://purl.obolibrary.org/obo/NCBITaxon_337687` #### Removed -- [alveolar ridge](http://purl.obolibrary.org/obo/UBERON_0004103) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "margo alveolaris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [Muroidea](http://purl.obolibrary.org/obo/NCBITaxon_337687) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) -#### Added -- [alveolar ridge](http://purl.obolibrary.org/obo/UBERON_0004103) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "margo alveolaris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### alveolar type 1 fibroblast cell `http://purl.obolibrary.org/obo/CL_4028004` +### Mus `http://purl.obolibrary.org/obo/NCBITaxon_10088` +#### Removed +- [Mus ](http://purl.obolibrary.org/obo/NCBITaxon_10088) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "mice" + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003003](http://purl.obolibrary.org/obo/OMO_0003003) + +- [Mus ](http://purl.obolibrary.org/obo/NCBITaxon_10088) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_genus](http://purl.obolibrary.org/obo/NCBITaxon_genus) #### Added -- [alveolar type 1 fibroblast cell](http://purl.obolibrary.org/obo/CL_4028004) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [Mus ](http://purl.obolibrary.org/obo/NCBITaxon_10088) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "mice" + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [genbank_common_name](http://purl.obolibrary.org/obo/ncbitaxon#genbank_common_name) -### alveolar type 2 fibroblast cell `http://purl.obolibrary.org/obo/CL_4028006` +### Mus `http://purl.obolibrary.org/obo/NCBITaxon_862507` +#### Removed +- [Mus ](http://purl.obolibrary.org/obo/NCBITaxon_862507) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_subgenus](http://purl.obolibrary.org/obo/NCBITaxon_subgenus) -#### Added -- [alveolar type 2 fibroblast cell](http://purl.obolibrary.org/obo/CL_4028006) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### alveolus of lung `http://purl.obolibrary.org/obo/UBERON_0002299` +### Mus musculus `http://purl.obolibrary.org/obo/NCBITaxon_10090` #### Removed -- [alveolus of lung](http://purl.obolibrary.org/obo/UBERON_0002299) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "alveolus pulmonis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pulmonary_alveolus" +- [Mus musculus](http://purl.obolibrary.org/obo/NCBITaxon_10090) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_species](http://purl.obolibrary.org/obo/NCBITaxon_species) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [alveolus of lung](http://purl.obolibrary.org/obo/UBERON_0002299) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "alveolus pulmonis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pulmonary_alveolus" +### Myomorpha `http://purl.obolibrary.org/obo/NCBITaxon_1963758` +#### Removed +- [Myomorpha](http://purl.obolibrary.org/obo/NCBITaxon_1963758) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_suborder](http://purl.obolibrary.org/obo/NCBITaxon_suborder) + -### amacrine cell `http://purl.obolibrary.org/obo/CL_0000561` +### NKG2-A/NKG2-B type II integral membrane protein `http://purl.obolibrary.org/obo/PR_000002023` +#### Removed +- [NKG2-A/NKG2-B type II integral membrane protein](http://purl.obolibrary.org/obo/PR_000002023) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [NKG2-A/NKG2-B type II integral membrane protein (human)](http://purl.obolibrary.org/obo/PR_P26715) -#### Added -- [amacrine cell](http://purl.obolibrary.org/obo/CL_0000561) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### amino acid biosynthetic process `http://purl.obolibrary.org/obo/GO_0008652` +### Nematoda `http://purl.obolibrary.org/obo/NCBITaxon_6231` #### Removed -- [amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_0008652) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "amino acid synthesis" +- [Nematoda](http://purl.obolibrary.org/obo/NCBITaxon_6231) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_phylum](http://purl.obolibrary.org/obo/NCBITaxon_phylum) -- [amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_0008652) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Amino_acid_synthesis" -- [amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_0008652) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cellular amino acid biosynthetic process" -- [amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_0008652) [label](http://www.w3.org/2000/01/rdf-schema#label) "amino acid biosynthetic process" +### Neopterygii `http://purl.obolibrary.org/obo/NCBITaxon_41665` +#### Removed +- [Neopterygii](http://purl.obolibrary.org/obo/NCBITaxon_41665) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_subclass](http://purl.obolibrary.org/obo/NCBITaxon_subclass) -- [amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_0008652) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/geneontology/go-ontology/issues/17904"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) -- [amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_0008652) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0198506732" -- [amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_0008652) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" +### Opisthokonta `http://purl.obolibrary.org/obo/NCBITaxon_33154` +#### Removed +- [Opisthokonta](http://purl.obolibrary.org/obo/NCBITaxon_33154) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) -- [amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_0008652) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "amino acid anabolism" -- [amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_0008652) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:0008652" -- [amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_0008652) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "amino acid biosynthesis" +### Panarthropoda `http://purl.obolibrary.org/obo/NCBITaxon_88770` +#### Removed +- [Panarthropoda](http://purl.obolibrary.org/obo/NCBITaxon_88770) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) -- [amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_0008652) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "amino acid formation" -- Class: [amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_0008652) -- [amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_0008652) EquivalentTo [biosynthetic process](http://purl.obolibrary.org/obo/GO_0009058) and ([has primary output](http://purl.obolibrary.org/obo/RO_0004008) some [CHEBI_37022](http://purl.obolibrary.org/obo/CHEBI_37022)) +### Pancrustacea `http://purl.obolibrary.org/obo/NCBITaxon_197562` +#### Removed +- [Pancrustacea](http://purl.obolibrary.org/obo/NCBITaxon_197562) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) -- [amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_0008652) SubClassOf [biosynthetic process](http://purl.obolibrary.org/obo/GO_0009058) -- [amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_0008652) SubClassOf [has primary output](http://purl.obolibrary.org/obo/RO_0004008) some [CHEBI_37022](http://purl.obolibrary.org/obo/CHEBI_37022) -- [amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_0008652) SubClassOf [amino acid metabolic process](http://purl.obolibrary.org/obo/GO_0006520) +### Peloderinae `http://purl.obolibrary.org/obo/NCBITaxon_55885` +#### Removed +- [Peloderinae](http://purl.obolibrary.org/obo/NCBITaxon_55885) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_subfamily](http://purl.obolibrary.org/obo/NCBITaxon_subfamily) -### amino acid catabolic process `http://purl.obolibrary.org/obo/GO_0009063` +### Perissodactyla `http://purl.obolibrary.org/obo/NCBITaxon_9787` #### Removed -- [amino acid catabolic process](http://purl.obolibrary.org/obo/GO_0009063) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/geneontology/go-ontology/issues/17904"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) +- [Perissodactyla](http://purl.obolibrary.org/obo/NCBITaxon_9787) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_order](http://purl.obolibrary.org/obo/NCBITaxon_order) -- [amino acid catabolic process](http://purl.obolibrary.org/obo/GO_0009063) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cellular amino acid catabolic process" -- [amino acid catabolic process](http://purl.obolibrary.org/obo/GO_0009063) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "amino acid degradation" -- [amino acid catabolic process](http://purl.obolibrary.org/obo/GO_0009063) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" +### Peyer's patch `http://purl.obolibrary.org/obo/UBERON_0001211` +#### Removed +- [Peyer's patch](http://purl.obolibrary.org/obo/UBERON_0001211) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Reptiles have accumulations of lymphocytes in their guts that may be primitive Peyer's patches (Zapata and Solas)." -- [amino acid catabolic process](http://purl.obolibrary.org/obo/GO_0009063) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:0009063" +- [Peyer's patch](http://purl.obolibrary.org/obo/UBERON_0001211) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA has [set of?] [aggregated,small] lymphoid [follice,nodule] of [colon, SI, I, etc]" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" -- [amino acid catabolic process](http://purl.obolibrary.org/obo/GO_0009063) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "amino acid breakdown" +- [Peyer's patch](http://purl.obolibrary.org/obo/UBERON_0001211) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "Pp is a syn for Aggregated lymphoid follicle of small intestine; but MA uses Pp as covering both SI and LI. MA also includes follicle as a part. WP says duodenum and jejunum lack PPs" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" -- [amino acid catabolic process](http://purl.obolibrary.org/obo/GO_0009063) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "The chemical reactions and pathways resulting in the breakdown of amino acids, organic acids containing one or more amino substituents." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:ai" -- [amino acid catabolic process](http://purl.obolibrary.org/obo/GO_0009063) [label](http://www.w3.org/2000/01/rdf-schema#label) "amino acid catabolic process" -- [amino acid catabolic process](http://purl.obolibrary.org/obo/GO_0009063) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "amino acid catabolism" +### Platyhelminthes `http://purl.obolibrary.org/obo/NCBITaxon_6157` +#### Removed +- [Platyhelminthes](http://purl.obolibrary.org/obo/NCBITaxon_6157) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_phylum](http://purl.obolibrary.org/obo/NCBITaxon_phylum) + -- Class: [amino acid catabolic process](http://purl.obolibrary.org/obo/GO_0009063) -- [amino acid catabolic process](http://purl.obolibrary.org/obo/GO_0009063) EquivalentTo [catabolic process](http://purl.obolibrary.org/obo/GO_0009056) and ([has primary input](http://purl.obolibrary.org/obo/RO_0004009) some [CHEBI_37022](http://purl.obolibrary.org/obo/CHEBI_37022)) +### Platyrrhini `http://purl.obolibrary.org/obo/NCBITaxon_9479` +#### Removed +- [Platyrrhini](http://purl.obolibrary.org/obo/NCBITaxon_9479) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_parvorder](http://purl.obolibrary.org/obo/NCBITaxon_parvorder) -- [amino acid catabolic process](http://purl.obolibrary.org/obo/GO_0009063) SubClassOf [has primary input](http://purl.obolibrary.org/obo/RO_0004009) some [CHEBI_37022](http://purl.obolibrary.org/obo/CHEBI_37022) -- [amino acid catabolic process](http://purl.obolibrary.org/obo/GO_0009063) SubClassOf [catabolic process](http://purl.obolibrary.org/obo/GO_0009056) -- [amino acid catabolic process](http://purl.obolibrary.org/obo/GO_0009063) SubClassOf [amino acid metabolic process](http://purl.obolibrary.org/obo/GO_0006520) +### Primates `http://purl.obolibrary.org/obo/NCBITaxon_9443` +#### Removed +- [Primates](http://purl.obolibrary.org/obo/NCBITaxon_9443) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_order](http://purl.obolibrary.org/obo/NCBITaxon_order) -### amino acid metabolic process `http://purl.obolibrary.org/obo/GO_0006520` +### Protostomia `http://purl.obolibrary.org/obo/NCBITaxon_33317` #### Removed -- [amino acid metabolic process](http://purl.obolibrary.org/obo/GO_0006520) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) +- [Protostomia](http://purl.obolibrary.org/obo/NCBITaxon_33317) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) -- [amino acid metabolic process](http://purl.obolibrary.org/obo/GO_0006520) EquivalentTo [metabolic process](http://purl.obolibrary.org/obo/GO_0008152) and ([has primary input or output](http://purl.obolibrary.org/obo/RO_0004007) some [CHEBI_37022](http://purl.obolibrary.org/obo/CHEBI_37022)) -- [amino acid metabolic process](http://purl.obolibrary.org/obo/GO_0006520) SubClassOf [carboxylic acid metabolic process](http://purl.obolibrary.org/obo/GO_0019752) -- [amino acid metabolic process](http://purl.obolibrary.org/obo/GO_0006520) SubClassOf [has primary input or output](http://purl.obolibrary.org/obo/RO_0004007) some [CHEBI_37022](http://purl.obolibrary.org/obo/CHEBI_37022) +### Purkinje cell layer of cerebellar cortex `http://purl.obolibrary.org/obo/UBERON_0002979` +#### Removed +- [Purkinje cell layer of cerebellar cortex](http://purl.obolibrary.org/obo/UBERON_0002979) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [granular layer of cerebellar cortex](http://purl.obolibrary.org/obo/UBERON_0002956) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" -- [amino acid metabolic process](http://purl.obolibrary.org/obo/GO_0006520) SubClassOf [organonitrogen compound metabolic process](http://purl.obolibrary.org/obo/GO_1901564) -#### Added -- [amino acid metabolic process](http://purl.obolibrary.org/obo/GO_0006520) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) -- [amino acid metabolic process](http://purl.obolibrary.org/obo/GO_0006520) EquivalentTo [metabolic process](http://purl.obolibrary.org/obo/GO_0008152) and ([has primary input or output](http://purl.obolibrary.org/obo/RO_0004007) some [CHEBI_35238](http://purl.obolibrary.org/obo/CHEBI_35238)) +### RO_0001900 `http://purl.obolibrary.org/obo/RO_0001900` +#### Removed +- AnnotationProperty: [RO_0001900](http://purl.obolibrary.org/obo/RO_0001900) -- [amino acid metabolic process](http://purl.obolibrary.org/obo/GO_0006520) SubClassOf [has primary input or output](http://purl.obolibrary.org/obo/RO_0004007) some [CHEBI_35238](http://purl.obolibrary.org/obo/CHEBI_35238) -### amnioserosa `http://purl.obolibrary.org/obo/UBERON_0010302` +### RO_0002171 `http://purl.obolibrary.org/obo/RO_0002171` #### Removed -- [amnioserosa](http://purl.obolibrary.org/obo/UBERON_0010302) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000095" +- AnnotationProperty: [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) -#### Added -- [amnioserosa](http://purl.obolibrary.org/obo/UBERON_0010302) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000095" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### amniotic fluid `http://purl.obolibrary.org/obo/UBERON_0000173` +### RO_0002174 `http://purl.obolibrary.org/obo/RO_0002174` #### Removed -- [amniotic fluid](http://purl.obolibrary.org/obo/UBERON_0000173) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "acqua amnii" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0000068" +- AnnotationProperty: [RO_0002174](http://purl.obolibrary.org/obo/RO_0002174) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [amniotic fluid](http://purl.obolibrary.org/obo/UBERON_0000173) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "liquor amnii" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0000068" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### RO_0002475 `http://purl.obolibrary.org/obo/RO_0002475` +#### Removed +- AnnotationProperty: [RO_0002475](http://purl.obolibrary.org/obo/RO_0002475) -#### Added -- [amniotic fluid](http://purl.obolibrary.org/obo/UBERON_0000173) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "acqua amnii" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0000068" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -- [amniotic fluid](http://purl.obolibrary.org/obo/UBERON_0000173) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "liquor amnii" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0000068" +### RO_0002575 `http://purl.obolibrary.org/obo/RO_0002575` +#### Removed +- AnnotationProperty: [RO_0002575](http://purl.obolibrary.org/obo/RO_0002575) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### amygdala `http://purl.obolibrary.org/obo/UBERON_0001876` +### RO_0002579 `http://purl.obolibrary.org/obo/RO_0002579` #### Removed -- [amygdala](http://purl.obolibrary.org/obo/UBERON_0001876) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "corpus amygdaloideum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001042" +- AnnotationProperty: [RO_0002579](http://purl.obolibrary.org/obo/RO_0002579) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Amygdala" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [amygdala](http://purl.obolibrary.org/obo/UBERON_0001876) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "corpus amygdalae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:237" +### RO_0002604 `http://purl.obolibrary.org/obo/RO_0002604` +#### Removed +- AnnotationProperty: [RO_0002604](http://purl.obolibrary.org/obo/RO_0002604) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [amygdala](http://purl.obolibrary.org/obo/UBERON_0001876) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "corpus amygdalae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:237" +### RO_0004036 `http://purl.obolibrary.org/obo/RO_0004036` +#### Removed +- AnnotationProperty: [RO_0004036](http://purl.obolibrary.org/obo/RO_0004036) -- [amygdala](http://purl.obolibrary.org/obo/UBERON_0001876) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "corpus amygdaloideum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001042" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Amygdala" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### RO_0004049 `http://purl.obolibrary.org/obo/RO_0004049` +#### Removed +- AnnotationProperty: [RO_0004049](http://purl.obolibrary.org/obo/RO_0004049) -### anal canal `http://purl.obolibrary.org/obo/UBERON_0000159` + +### RO_0040042 `http://purl.obolibrary.org/obo/RO_0040042` #### Removed -- [anal canal](http://purl.obolibrary.org/obo/UBERON_0000159) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D001003" +- AnnotationProperty: [RO_0040042](http://purl.obolibrary.org/obo/RO_0040042) + -- [anal canal](http://purl.obolibrary.org/obo/UBERON_0000159) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "canalis analis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Anal_canal" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001978" +### Rathke's pouch `http://purl.obolibrary.org/obo/UBERON_0005356` +#### Removed +- [Rathke's pouch](http://purl.obolibrary.org/obo/UBERON_0005356) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "median funnel­-shaped invagination of ectoderm, the nasohypophyseal pouch. It will contribute to the formation of the pituitary gland of the adult lamprey and is homologous to Rathke's pouch and perhaps to Hatschek 's pit (amphioxus)." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://webs.lander.edu/rsfox/invertebrates/ammocoetes.html" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [Rathke's pouch](http://purl.obolibrary.org/obo/UBERON_0005356) [RO_0002174](http://purl.obolibrary.org/obo/RO_0002174) [NCBITaxon_7955](http://purl.obolibrary.org/obo/NCBITaxon_7955) -#### Added -- [anal canal](http://purl.obolibrary.org/obo/UBERON_0000159) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "canalis analis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Anal_canal" +- [Rathke's pouch](http://purl.obolibrary.org/obo/UBERON_0005356) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "EHDAA2 distinguishes between the adenohypophyseal pouch and it's precursor Rathke's pouch epithelium." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EHDAA2" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [Rathke's pouch](http://purl.obolibrary.org/obo/UBERON_0005356) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. An infundibulum grows ventrally from the diencephalon of the brain, and Rathke's pouch extends dorsally from the roof of the developing mouth, or stomodaeum. The infundibulum remains connected to the floor of the diencephalon, which becomes the hypothalamus, and gives rise to the part of the gland known as the neurohypophysis. (...) Rathke's pouch loses its connection with the stomodaeum in most adult vertebrates and gives rise to the rest of the gland, the adenohypophysis. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001978" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [anal canal](http://purl.obolibrary.org/obo/UBERON_0000159) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D001003" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510 and Figure 15-5" - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000674" +- [Rathke's pouch](http://purl.obolibrary.org/obo/UBERON_0005356) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A depression that forms in the roof of the mouth of an embryo, anterior to the buccopharyngeal membrane. The walls of the diverticulum develop into the anterior lobe of the pituitary gland. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### anal column `http://purl.obolibrary.org/obo/UBERON_0009882` -#### Removed -- [anal column](http://purl.obolibrary.org/obo/UBERON_0009882) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "columnae anales" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Anal_columns" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [anal column](http://purl.obolibrary.org/obo/UBERON_0009882) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "columnae anales" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/rathke's+pouch" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Anal_columns" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000674" -### anatomical cluster `http://purl.obolibrary.org/obo/UBERON_0000477` -#### Removed -- [anatomical cluster](http://purl.obolibrary.org/obo/UBERON_0000477) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "IDOMAL:0002461" - - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0003-4423-4370" -- [anatomical cluster](http://purl.obolibrary.org/obo/UBERON_0000477) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007277" +### Reissner's fiber `http://purl.obolibrary.org/obo/UBERON_0011357` +#### Removed +- [Reissner's fiber](http://purl.obolibrary.org/obo/UBERON_0011357) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Reissner's fiber is present in the central canal of species in all chordate subphyla[Olsson R. (1993) Reissner's fiber mechanisms: some common denominators. In The Subcommissural Organ: An Ependymal Brain Gland ]" #### Added -- [anatomical cluster](http://purl.obolibrary.org/obo/UBERON_0000477) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007277" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [Reissner's fiber](http://purl.obolibrary.org/obo/UBERON_0011357) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### anatomical entity `http://purl.obolibrary.org/obo/UBERON_0001062` +### Rhabditida `http://purl.obolibrary.org/obo/NCBITaxon_6236` #### Removed -- [anatomical entity](http://purl.obolibrary.org/obo/UBERON_0001062) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:10000000" +- [Rhabditida](http://purl.obolibrary.org/obo/NCBITaxon_6236) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_order](http://purl.obolibrary.org/obo/NCBITaxon_order) -#### Added -- [anatomical entity](http://purl.obolibrary.org/obo/UBERON_0001062) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:10000000" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### anatomical lobe `http://purl.obolibrary.org/obo/UBERON_0009912` +### Rhabditidae `http://purl.obolibrary.org/obo/NCBITaxon_6243` #### Removed -- [anatomical lobe](http://purl.obolibrary.org/obo/UBERON_0009912) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lobus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:45728" +- [Rhabditidae](http://purl.obolibrary.org/obo/NCBITaxon_6243) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_family](http://purl.obolibrary.org/obo/NCBITaxon_family) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [anatomical lobe](http://purl.obolibrary.org/obo/UBERON_0009912) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lobus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### Rhabditina `http://purl.obolibrary.org/obo/NCBITaxon_2301116` +#### Removed +- [Rhabditina](http://purl.obolibrary.org/obo/NCBITaxon_2301116) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_suborder](http://purl.obolibrary.org/obo/NCBITaxon_suborder) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:45728" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + +### Rhabditoidea `http://purl.obolibrary.org/obo/NCBITaxon_55879` +#### Removed +- [Rhabditoidea](http://purl.obolibrary.org/obo/NCBITaxon_55879) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_superfamily](http://purl.obolibrary.org/obo/NCBITaxon_superfamily) -### anatomical projection `http://purl.obolibrary.org/obo/UBERON_0004529` + +### Rhabditomorpha `http://purl.obolibrary.org/obo/NCBITaxon_2301119` #### Removed -- [anatomical projection](http://purl.obolibrary.org/obo/UBERON_0004529) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "processus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:67601" +- [Rhabditomorpha](http://purl.obolibrary.org/obo/NCBITaxon_2301119) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_infraorder](http://purl.obolibrary.org/obo/NCBITaxon_infraorder) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + +### Rodentia `http://purl.obolibrary.org/obo/NCBITaxon_9989` +#### Removed +- [Rodentia](http://purl.obolibrary.org/obo/NCBITaxon_9989) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_order](http://purl.obolibrary.org/obo/NCBITaxon_order) + + + +### Rules +#### Removed +- [directly positively regulates](http://purl.obolibrary.org/obo/RO_0002629)(?mf, ?mf2), [has effector activity](http://purl.obolibrary.org/obo/RO_0002025)(?mf, ?eff) -> [directly positively regulates](http://purl.obolibrary.org/obo/RO_0002629)(?eff, ?mf2) + - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "if effector directly positively regulates X, its parent MF directly positively regulates X" + +- [causally upstream of](http://purl.obolibrary.org/obo/RO_0002411)(?x, ?y), [overlaps](http://purl.obolibrary.org/obo/RO_0002131)(?x, ?y) -> [Nothing](http://www.w3.org/2002/07/owl#Nothing)(?x), [Nothing](http://www.w3.org/2002/07/owl#Nothing)(?y) + - [label](http://www.w3.org/2000/01/rdf-schema#label) "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties)." + +- [input of](http://purl.obolibrary.org/obo/RO_0002352)(?B, ?C), [enabled by](http://purl.obolibrary.org/obo/RO_0002333)(?A, ?B), [has regulatory component activity](http://purl.obolibrary.org/obo/RO_0002013)(?D, ?C) -> [directly regulates](http://purl.obolibrary.org/obo/RO_0002578)(?A, ?D) + - [label](http://www.w3.org/2000/01/rdf-schema#label) "inferring direct reg edge from input to regulatory subfunction" + + - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this." + +- [input of](http://purl.obolibrary.org/obo/RO_0002352)(?B, ?C), [enabled by](http://purl.obolibrary.org/obo/RO_0002333)(?A, ?B), [has negative regulatory component activity](http://purl.obolibrary.org/obo/RO_0002014)(?D, ?C) -> [directly negatively regulates](http://purl.obolibrary.org/obo/RO_0002630)(?A, ?D) + - [label](http://www.w3.org/2000/01/rdf-schema#label) "inferring direct neg reg edge from input to regulatory subfunction" + +- [biological_process](http://purl.obolibrary.org/obo/GO_0008150)(?z), [part_of](http://purl.obolibrary.org/obo/BFO_0000050)(?y, ?z), [enables](http://purl.obolibrary.org/obo/RO_0002327)(?x, ?y) -> [involved in](http://purl.obolibrary.org/obo/RO_0002331)(?x, ?z) + - [label](http://www.w3.org/2000/01/rdf-schema#label) "involved in BP" + + - [isRuleEnabled](http://swrl.stanford.edu/ontologies/3.3/swrla.owl#isRuleEnabled) true + + - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction'" + +- [molecular_function](http://purl.obolibrary.org/obo/GO_0003674)(?y), [enables](http://purl.obolibrary.org/obo/RO_0002327)(?x, ?y), [has part](http://purl.obolibrary.org/obo/BFO_0000051)(?y, ?z) -> [enables](http://purl.obolibrary.org/obo/RO_0002327)(?x, ?z) + - [label](http://www.w3.org/2000/01/rdf-schema#label) "enabling an MF enables its parts" + + - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), +e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'" + +- [has input](http://purl.obolibrary.org/obo/RO_0002233)(?mf, ?in), [has effector activity](http://purl.obolibrary.org/obo/RO_0002025)(?mf, ?eff) -> [has input](http://purl.obolibrary.org/obo/RO_0002233)(?eff, ?in) + - [label](http://www.w3.org/2000/01/rdf-schema#label) "Input of effector is input of its parent MF" + +- [directly regulates](http://purl.obolibrary.org/obo/RO_0002578)(?a1, ?a2), [kinase activity](http://purl.obolibrary.org/obo/GO_0016301)(?a1), [enabled by](http://purl.obolibrary.org/obo/RO_0002333)(?a1, ?g1), [enabled by](http://purl.obolibrary.org/obo/RO_0002333)(?a2, ?g2) -> [phosphorylates](http://purl.obolibrary.org/obo/RO_0002447)(?g1, ?g2) + +- [has input](http://purl.obolibrary.org/obo/RO_0002233)(?eff, ?in), [has effector activity](http://purl.obolibrary.org/obo/RO_0002025)(?mf, ?eff) -> [has input](http://purl.obolibrary.org/obo/RO_0002233)(?mf, ?in) + - [label](http://www.w3.org/2000/01/rdf-schema#label) "effector input is compound function input" + +- [causally downstream of](http://purl.obolibrary.org/obo/RO_0002404)(?x, ?y), [overlaps](http://purl.obolibrary.org/obo/RO_0002131)(?x, ?y) -> [Nothing](http://www.w3.org/2002/07/owl#Nothing)(?x), [Nothing](http://www.w3.org/2002/07/owl#Nothing)(?y) + - [label](http://www.w3.org/2000/01/rdf-schema#label) "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties)." + +- [has effector activity](http://purl.obolibrary.org/obo/RO_0002025)(?mf, ?eff), [directly regulates](http://purl.obolibrary.org/obo/RO_0002578)(?mf, ?mf2) -> [directly regulates](http://purl.obolibrary.org/obo/RO_0002578)(?eff, ?mf2) + - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "if effector directly regulates X, its parent MF directly regulates X" + +- [positively regulates](http://purl.obolibrary.org/obo/RO_0002213)(?y, ?z), [negatively regulates](http://purl.obolibrary.org/obo/RO_0002212)(?x, ?y) -> [negatively regulates](http://purl.obolibrary.org/obo/RO_0002212)(?x, ?z) + +- [positively regulates](http://purl.obolibrary.org/obo/RO_0002213)(?x, ?y), [negatively regulates](http://purl.obolibrary.org/obo/RO_0002212)(?y, ?z) -> [negatively regulates](http://purl.obolibrary.org/obo/RO_0002212)(?x, ?z) + +- [input of](http://purl.obolibrary.org/obo/RO_0002352)(?B, ?C), [enabled by](http://purl.obolibrary.org/obo/RO_0002333)(?A, ?B), [has positive regulatory component activity](http://purl.obolibrary.org/obo/RO_0002015)(?D, ?C) -> [directly positively regulates](http://purl.obolibrary.org/obo/RO_0002629)(?A, ?D) + - [label](http://www.w3.org/2000/01/rdf-schema#label) "inferring direct positive reg edge from input to regulatory subfunction" + +- [enables](http://purl.obolibrary.org/obo/RO_0002327)(?, ?), [directly regulates](http://purl.obolibrary.org/obo/RO_0002578)(?, ?), [molecular_function](http://purl.obolibrary.org/obo/GO_0003674)(?), [molecular_function](http://purl.obolibrary.org/obo/GO_0003674)(?) -> [has input](http://purl.obolibrary.org/obo/RO_0002233)(?, ?) + - [isRuleEnabled](http://swrl.stanford.edu/ontologies/3.3/swrla.owl#isRuleEnabled) true + + - [label](http://www.w3.org/2000/01/rdf-schema#label) "infer input from direct reg" + + - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z" + +- [has effector activity](http://purl.obolibrary.org/obo/RO_0002025)(?mf, ?eff), [directly negatively regulates](http://purl.obolibrary.org/obo/RO_0002630)(?mf, ?mf2) -> [directly negatively regulates](http://purl.obolibrary.org/obo/RO_0002630)(?eff, ?mf2) + - [label](http://www.w3.org/2000/01/rdf-schema#label) "if effector directly negatively regulates X, its parent MF directly negatively regulates X" + +- [has component](http://purl.obolibrary.org/obo/RO_0002180)(?w, ?p), [process](http://purl.obolibrary.org/obo/BFO_0000015)(?w), [process](http://purl.obolibrary.org/obo/BFO_0000015)(?p) -> [has component process](http://purl.obolibrary.org/obo/RO_0002018)(?w, ?p) #### Added -- [anatomical projection](http://purl.obolibrary.org/obo/UBERON_0004529) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "processus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [directly regulates](http://purl.obolibrary.org/obo/RO_0002578)(?a1, ?a2), [kinase activity](http://purl.obolibrary.org/obo/GO_0016301)(?a1), [enabled by](http://purl.obolibrary.org/obo/RO_0002333)(?a1, ?g1), [enabled by](http://purl.obolibrary.org/obo/RO_0002333)(?a2, ?g2) -> [phosphorylates](http://purl.obolibrary.org/obo/RO_0002447)(?g1, ?g2) + +- [causally upstream of](http://purl.obolibrary.org/obo/RO_0002411)(?x, ?y), [overlaps](http://purl.obolibrary.org/obo/RO_0002131)(?x, ?y) -> [Nothing](http://www.w3.org/2002/07/owl#Nothing)(?x), [Nothing](http://www.w3.org/2002/07/owl#Nothing)(?y) + - [label](http://www.w3.org/2000/01/rdf-schema#label) "'causally upstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties)." + +- [input of](http://purl.obolibrary.org/obo/RO_0002352)(?B, ?C), [enabled by](http://purl.obolibrary.org/obo/RO_0002333)(?A, ?B), [has regulatory component activity](http://purl.obolibrary.org/obo/RO_0002013)(?D, ?C) -> [directly regulates](http://purl.obolibrary.org/obo/RO_0002578)(?A, ?D) + - [label](http://www.w3.org/2000/01/rdf-schema#label) "inferring direct reg edge from input to regulatory subfunction" + + - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "If a molecular function (X) has a regulatory subfunction, then any gene product which is an input to that subfunction has an activity that directly_regulates X. Note: this is intended for cases where the regaultory subfunction is protein binding, so it could be tightened with an additional clause to specify this." + +- [input of](http://purl.obolibrary.org/obo/RO_0002352)(?B, ?C), [enabled by](http://purl.obolibrary.org/obo/RO_0002333)(?A, ?B), [has negative regulatory component activity](http://purl.obolibrary.org/obo/RO_0002014)(?D, ?C) -> [directly negatively regulates](http://purl.obolibrary.org/obo/RO_0002630)(?A, ?D) + - [label](http://www.w3.org/2000/01/rdf-schema#label) "inferring direct neg reg edge from input to regulatory subfunction" + +- [has input](http://purl.obolibrary.org/obo/RO_0002233)(?eff, ?in), [has effector activity](http://purl.obolibrary.org/obo/RO_0002025)(?mf, ?eff) -> [has input](http://purl.obolibrary.org/obo/RO_0002233)(?mf, ?in) + - [label](http://www.w3.org/2000/01/rdf-schema#label) "effector input is compound function input" + +- [molecular_function](http://purl.obolibrary.org/obo/GO_0003674)(?y), [enables](http://purl.obolibrary.org/obo/RO_0002327)(?x, ?y), [has part](http://purl.obolibrary.org/obo/BFO_0000051)(?y, ?z) -> [enables](http://purl.obolibrary.org/obo/RO_0002327)(?x, ?z) + - [label](http://www.w3.org/2000/01/rdf-schema#label) "enabling an MF enables its parts" + + - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "GP(X)-enables->MF(Y)-has_part->MF(Z) => GP(X) enables MF(Z), +e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'" + +- [has effector activity](http://purl.obolibrary.org/obo/RO_0002025)(?mf, ?eff), [directly regulates](http://purl.obolibrary.org/obo/RO_0002578)(?mf, ?mf2) -> [directly regulates](http://purl.obolibrary.org/obo/RO_0002578)(?eff, ?mf2) + - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "if effector directly regulates X, its parent MF directly regulates X" + +- [has effector activity](http://purl.obolibrary.org/obo/RO_0002025)(?mf, ?eff), [directly negatively regulates](http://purl.obolibrary.org/obo/RO_0002630)(?mf, ?mf2) -> [directly negatively regulates](http://purl.obolibrary.org/obo/RO_0002630)(?eff, ?mf2) + - [label](http://www.w3.org/2000/01/rdf-schema#label) "if effector directly negatively regulates X, its parent MF directly negatively regulates X" + +- [has input](http://purl.obolibrary.org/obo/RO_0002233)(?mf, ?in), [has effector activity](http://purl.obolibrary.org/obo/RO_0002025)(?mf, ?eff) -> [has input](http://purl.obolibrary.org/obo/RO_0002233)(?eff, ?in) + - [label](http://www.w3.org/2000/01/rdf-schema#label) "Input of effector is input of its parent MF" + +- [causally downstream of](http://purl.obolibrary.org/obo/RO_0002404)(?x, ?y), [overlaps](http://purl.obolibrary.org/obo/RO_0002131)(?x, ?y) -> [Nothing](http://www.w3.org/2002/07/owl#Nothing)(?x), [Nothing](http://www.w3.org/2002/07/owl#Nothing)(?y) + - [label](http://www.w3.org/2000/01/rdf-schema#label) "'causally downstream of' and 'overlaps' should be disjoint properties (a SWRL rule is required because these are non-simple properties)." + +- [has component](http://purl.obolibrary.org/obo/RO_0002180)(?w, ?p), [process](http://purl.obolibrary.org/obo/BFO_0000015)(?w), [process](http://purl.obolibrary.org/obo/BFO_0000015)(?p) -> [has component process](http://purl.obolibrary.org/obo/RO_0002018)(?w, ?p) + +- [positively regulates](http://purl.obolibrary.org/obo/RO_0002213)(?y, ?z), [negatively regulates](http://purl.obolibrary.org/obo/RO_0002212)(?x, ?y) -> [negatively regulates](http://purl.obolibrary.org/obo/RO_0002212)(?x, ?z) + +- [positively regulates](http://purl.obolibrary.org/obo/RO_0002213)(?x, ?y), [negatively regulates](http://purl.obolibrary.org/obo/RO_0002212)(?y, ?z) -> [negatively regulates](http://purl.obolibrary.org/obo/RO_0002212)(?x, ?z) + +- [input of](http://purl.obolibrary.org/obo/RO_0002352)(?B, ?C), [enabled by](http://purl.obolibrary.org/obo/RO_0002333)(?A, ?B), [has positive regulatory component activity](http://purl.obolibrary.org/obo/RO_0002015)(?D, ?C) -> [directly positively regulates](http://purl.obolibrary.org/obo/RO_0002629)(?A, ?D) + - [label](http://www.w3.org/2000/01/rdf-schema#label) "inferring direct positive reg edge from input to regulatory subfunction" + +- [directly positively regulates](http://purl.obolibrary.org/obo/RO_0002629)(?mf, ?mf2), [has effector activity](http://purl.obolibrary.org/obo/RO_0002025)(?mf, ?eff) -> [directly positively regulates](http://purl.obolibrary.org/obo/RO_0002629)(?eff, ?mf2) + - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "if effector directly positively regulates X, its parent MF directly positively regulates X" + + +### S-shaped body `http://purl.obolibrary.org/obo/UBERON_0004199` +#### Removed +- [S-shaped body](http://purl.obolibrary.org/obo/UBERON_0004199) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "VO:0010896" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + + - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) + + + +### SCO-spondin `http://purl.obolibrary.org/obo/PR_000015658` +#### Removed +- [SCO-spondin](http://purl.obolibrary.org/obo/PR_000015658) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [SCO-spondin (human)](http://purl.obolibrary.org/obo/PR_A2VEC9) + + + +### SLAM family member 5 `http://purl.obolibrary.org/obo/PR_000001319` +#### Removed +- [SLAM family member 5](http://purl.obolibrary.org/obo/PR_000001319) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [SLAM family member 5 (human)](http://purl.obolibrary.org/obo/PR_Q9UIB8) + + + +### Saccharomyces `http://purl.obolibrary.org/obo/NCBITaxon_4930` +#### Removed +- [Saccharomyces](http://purl.obolibrary.org/obo/NCBITaxon_4930) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_genus](http://purl.obolibrary.org/obo/NCBITaxon_genus) + + + +### Saccharomyces cerevisiae `http://purl.obolibrary.org/obo/NCBITaxon_4932` +#### Removed +- [Saccharomyces cerevisiae](http://purl.obolibrary.org/obo/NCBITaxon_4932) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_species](http://purl.obolibrary.org/obo/NCBITaxon_species) + + + +### Saccharomycetaceae `http://purl.obolibrary.org/obo/NCBITaxon_4893` +#### Removed +- [Saccharomycetaceae](http://purl.obolibrary.org/obo/NCBITaxon_4893) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_family](http://purl.obolibrary.org/obo/NCBITaxon_family) + + + +### Saccharomycetales `http://purl.obolibrary.org/obo/NCBITaxon_4892` +#### Removed +- [Saccharomycetales](http://purl.obolibrary.org/obo/NCBITaxon_4892) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_order](http://purl.obolibrary.org/obo/NCBITaxon_order) + + + +### Saccharomycetes `http://purl.obolibrary.org/obo/NCBITaxon_4891` +#### Removed +- [Saccharomycetes](http://purl.obolibrary.org/obo/NCBITaxon_4891) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_class](http://purl.obolibrary.org/obo/NCBITaxon_class) + + + +### Saccharomycotina `http://purl.obolibrary.org/obo/NCBITaxon_147537` +#### Removed +- [Saccharomycotina](http://purl.obolibrary.org/obo/NCBITaxon_147537) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_subphylum](http://purl.obolibrary.org/obo/NCBITaxon_subphylum) + + + +### Sar `http://purl.obolibrary.org/obo/NCBITaxon_2698737` +#### Removed +- [Sar](http://purl.obolibrary.org/obo/NCBITaxon_2698737) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) + + + +### Sarcopterygii `http://purl.obolibrary.org/obo/NCBITaxon_8287` +#### Removed +- [Sarcopterygii](http://purl.obolibrary.org/obo/NCBITaxon_8287) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_superclass](http://purl.obolibrary.org/obo/NCBITaxon_superclass) + + + +### Sauria `http://purl.obolibrary.org/obo/NCBITaxon_32561` +#### Removed +- [Sauria](http://purl.obolibrary.org/obo/NCBITaxon_32561) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) + + + +### Saurischia `http://purl.obolibrary.org/obo/NCBITaxon_436489` +#### Removed +- [Saurischia](http://purl.obolibrary.org/obo/NCBITaxon_436489) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) + + + +### Sauropsida `http://purl.obolibrary.org/obo/NCBITaxon_8457` +#### Removed +- [Sauropsida](http://purl.obolibrary.org/obo/NCBITaxon_8457) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) + + + +### Schizosaccharomyces `http://purl.obolibrary.org/obo/NCBITaxon_4895` +#### Removed +- [Schizosaccharomyces](http://purl.obolibrary.org/obo/NCBITaxon_4895) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_genus](http://purl.obolibrary.org/obo/NCBITaxon_genus) + + + +### Schizosaccharomyces pombe `http://purl.obolibrary.org/obo/NCBITaxon_4896` +#### Removed +- [Schizosaccharomyces pombe](http://purl.obolibrary.org/obo/NCBITaxon_4896) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_species](http://purl.obolibrary.org/obo/NCBITaxon_species) + + + +### Schizosaccharomycetaceae `http://purl.obolibrary.org/obo/NCBITaxon_4894` +#### Removed +- [Schizosaccharomycetaceae](http://purl.obolibrary.org/obo/NCBITaxon_4894) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_family](http://purl.obolibrary.org/obo/NCBITaxon_family) + + + +### Schizosaccharomycetales `http://purl.obolibrary.org/obo/NCBITaxon_34346` +#### Removed +- [Schizosaccharomycetales](http://purl.obolibrary.org/obo/NCBITaxon_34346) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_order](http://purl.obolibrary.org/obo/NCBITaxon_order) + + + +### Schizosaccharomycetes `http://purl.obolibrary.org/obo/NCBITaxon_147554` +#### Removed +- [Schizosaccharomycetes](http://purl.obolibrary.org/obo/NCBITaxon_147554) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_class](http://purl.obolibrary.org/obo/NCBITaxon_class) + + + +### Simiiformes `http://purl.obolibrary.org/obo/NCBITaxon_314293` +#### Removed +- [Simiiformes](http://purl.obolibrary.org/obo/NCBITaxon_314293) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_infraorder](http://purl.obolibrary.org/obo/NCBITaxon_infraorder) + + + +### Spermatophyta `http://purl.obolibrary.org/obo/NCBITaxon_58024` +#### Removed +- [Spermatophyta](http://purl.obolibrary.org/obo/NCBITaxon_58024) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) + + + +### Spiralia `http://purl.obolibrary.org/obo/NCBITaxon_2697495` +#### Removed +- [Spiralia](http://purl.obolibrary.org/obo/NCBITaxon_2697495) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) + + + +### Streptophyta `http://purl.obolibrary.org/obo/NCBITaxon_35493` +#### Removed +- [Streptophyta](http://purl.obolibrary.org/obo/NCBITaxon_35493) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_phylum](http://purl.obolibrary.org/obo/NCBITaxon_phylum) + + + +### Streptophytina `http://purl.obolibrary.org/obo/NCBITaxon_131221` +#### Removed +- [Streptophytina](http://purl.obolibrary.org/obo/NCBITaxon_131221) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_subphylum](http://purl.obolibrary.org/obo/NCBITaxon_subphylum) + + + +### T-box transcription factor TBX21 `http://purl.obolibrary.org/obo/PR_000001835` +#### Removed +- [T-box transcription factor TBX21](http://purl.obolibrary.org/obo/PR_000001835) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [T-box transcription factor TBX21 (human)](http://purl.obolibrary.org/obo/PR_Q9UL17) + + + +### T-cell acute lymphocytic leukemia protein 1 `http://purl.obolibrary.org/obo/PR_000016043` +#### Removed +- [T-cell acute lymphocytic leukemia protein 1](http://purl.obolibrary.org/obo/PR_000016043) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [T-cell acute lymphocytic leukemia protein 1 (human)](http://purl.obolibrary.org/obo/PR_P17542) + + + +### T-cell surface glycoprotein CD1a `http://purl.obolibrary.org/obo/PR_000002025` +#### Removed +- [T-cell surface glycoprotein CD1a](http://purl.obolibrary.org/obo/PR_000002025) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [T-cell surface glycoprotein CD1a (human)](http://purl.obolibrary.org/obo/PR_P06126) + + + +### T-cell surface glycoprotein CD1c `http://purl.obolibrary.org/obo/PR_000002027` +#### Removed +- [T-cell surface glycoprotein CD1c](http://purl.obolibrary.org/obo/PR_000002027) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [T-cell surface glycoprotein CD1c (human)](http://purl.obolibrary.org/obo/PR_P29017) + + + +### T-cell surface glycoprotein CD5 `http://purl.obolibrary.org/obo/PR_000001839` +#### Removed +- [T-cell surface glycoprotein CD5](http://purl.obolibrary.org/obo/PR_000001839) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [T-cell surface glycoprotein CD5 (human)](http://purl.obolibrary.org/obo/PR_P06127) + + + +### T-cell surface glycoprotein CD8 alpha chain `http://purl.obolibrary.org/obo/PR_000001084` +#### Removed +- [T-cell surface glycoprotein CD8 alpha chain](http://purl.obolibrary.org/obo/PR_000001084) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [T-cell surface glycoprotein CD8 alpha chain (human)](http://purl.obolibrary.org/obo/PR_P01732) + + + +### T-cell surface glycoprotein CD8 alpha chain isoform 1 `http://purl.obolibrary.org/obo/PR_000025403` +#### Removed +- [T-cell surface glycoprotein CD8 alpha chain isoform 1](http://purl.obolibrary.org/obo/PR_000025403) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [T-cell surface glycoprotein CD8 alpha chain isoform 1 (human)](http://purl.obolibrary.org/obo/PR_P01732-1) + + + +### T-cell surface glycoprotein CD8 beta chain `http://purl.obolibrary.org/obo/PR_000001085` +#### Removed +- [T-cell surface glycoprotein CD8 beta chain](http://purl.obolibrary.org/obo/PR_000001085) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [T-cell surface glycoprotein CD8 beta chain (human)](http://purl.obolibrary.org/obo/PR_P10966) + + + +### T-cell-specific surface glycoprotein CD28 `http://purl.obolibrary.org/obo/PR_000001841` +#### Removed +- [T-cell-specific surface glycoprotein CD28](http://purl.obolibrary.org/obo/PR_000001841) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [T-cell-specific surface glycoprotein CD28 (human)](http://purl.obolibrary.org/obo/PR_P10747) + + + +### TAC3-positive medium spiny neuron `http://purl.obolibrary.org/obo/CL_4042002` + +#### Added +- [TAC3-positive medium spiny neuron](http://purl.obolibrary.org/obo/CL_4042002) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "A TAC3-positive medium spiny neuron has its soma in a cluster in the medial shell region of the nucleus accumbens. In Rhesus Macaque, this medium spiny neuron has an enriched expression of the genes MPPED1, HPCAL1, MEIS3." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34727523" + +- [TAC3-positive medium spiny neuron](http://purl.obolibrary.org/obo/CL_4042002) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "TAC3-positive D1Sh-MSN" + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [abbreviation](http://purl.obolibrary.org/obo/OMO_0003000) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34727523" + +- [TAC3-positive medium spiny neuron](http://purl.obolibrary.org/obo/CL_4042002) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) + +- [TAC3-positive medium spiny neuron](http://purl.obolibrary.org/obo/CL_4042002) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "TAC3-positive MSN" + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [abbreviation](http://purl.obolibrary.org/obo/OMO_0003000) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34727523" + +- [TAC3-positive medium spiny neuron](http://purl.obolibrary.org/obo/CL_4042002) [date](http://purl.org/dc/terms/date) "2024-03-05T13:36:54Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- [TAC3-positive medium spiny neuron](http://purl.obolibrary.org/obo/CL_4042002) [label](http://www.w3.org/2000/01/rdf-schema#label) "TAC3-positive medium spiny neuron"@en + +- [TAC3-positive medium spiny neuron](http://purl.obolibrary.org/obo/CL_4042002) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A nucleus accumbens shell and olfactory tubercle D1 medium spiny neuron that co-expresses TAC3 and the DRD1 receptor." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34727523" + +- [TAC3-positive medium spiny neuron](http://purl.obolibrary.org/obo/CL_4042002) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "D1Sh TAC3 archetype" + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [abbreviation](http://purl.obolibrary.org/obo/OMO_0003000) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34727523" + +- Class: [TAC3-positive medium spiny neuron](http://purl.obolibrary.org/obo/CL_4042002) + +- [TAC3-positive medium spiny neuron](http://purl.obolibrary.org/obo/CL_4042002) SubClassOf [has plasma membrane part](http://purl.obolibrary.org/obo/RO_0002104) some [tachykinin-3](http://purl.obolibrary.org/obo/PR_000016004) + +- [TAC3-positive medium spiny neuron](http://purl.obolibrary.org/obo/CL_4042002) SubClassOf [nucleus accumbens shell and olfactory tubercle D1 medium spiny neuron](http://purl.obolibrary.org/obo/CL_4030051) + +- [TAC3-positive medium spiny neuron](http://purl.obolibrary.org/obo/CL_4042002) SubClassOf [protein-containing material entity](http://purl.obolibrary.org/obo/PR_000050567) + + +### TAC3-positive striatal interneuron `http://purl.obolibrary.org/obo/CL_4042001` + +#### Added +- [TAC3-positive striatal interneuron](http://purl.obolibrary.org/obo/CL_4042001) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) + +- [TAC3-positive striatal interneuron](http://purl.obolibrary.org/obo/CL_4042001) [label](http://www.w3.org/2000/01/rdf-schema#label) "TAC3-positive striatal interneuron"@en + +- [TAC3-positive striatal interneuron](http://purl.obolibrary.org/obo/CL_4042001) [date](http://purl.org/dc/terms/date) "2024-03-05T14:29:32Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- [TAC3-positive striatal interneuron](http://purl.obolibrary.org/obo/CL_4042001) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A GABAergic interneuron that has its soma located in the striatum and that has an enriched expression of the gene TAC3." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34727523" + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32999462" + +- [TAC3-positive striatal interneuron](http://purl.obolibrary.org/obo/CL_4042001) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "TAC3 interneuron" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34727523" + +- Class: [TAC3-positive striatal interneuron](http://purl.obolibrary.org/obo/CL_4042001) + +- [TAC3-positive striatal interneuron](http://purl.obolibrary.org/obo/CL_4042001) SubClassOf [protein-containing material entity](http://purl.obolibrary.org/obo/PR_000050567) + +- [TAC3-positive striatal interneuron](http://purl.obolibrary.org/obo/CL_4042001) SubClassOf [GABAergic interneuron](http://purl.obolibrary.org/obo/CL_0011005) + +- [TAC3-positive striatal interneuron](http://purl.obolibrary.org/obo/CL_4042001) SubClassOf [has plasma membrane part](http://purl.obolibrary.org/obo/RO_0002104) some [tachykinin-3](http://purl.obolibrary.org/obo/PR_000016004) + +- [TAC3-positive striatal interneuron](http://purl.obolibrary.org/obo/CL_4042001) SubClassOf [has soma location](http://purl.obolibrary.org/obo/RO_0002100) some [striatum](http://purl.obolibrary.org/obo/UBERON_0002435) + +- [TAC3-positive striatal interneuron](http://purl.obolibrary.org/obo/CL_4042001) SubClassOf [CNS interneuron](http://purl.obolibrary.org/obo/CL_0000402) + + +### Taphrinomycotina `http://purl.obolibrary.org/obo/NCBITaxon_451866` +#### Removed +- [Taphrinomycotina](http://purl.obolibrary.org/obo/NCBITaxon_451866) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_subphylum](http://purl.obolibrary.org/obo/NCBITaxon_subphylum) + + + +### Teleostei `http://purl.obolibrary.org/obo/NCBITaxon_32443` +#### Removed +- [Teleostei](http://purl.obolibrary.org/obo/NCBITaxon_32443) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_infraclass](http://purl.obolibrary.org/obo/NCBITaxon_infraclass) + + + +### Teleostomi `http://purl.obolibrary.org/obo/NCBITaxon_117570` +#### Removed +- [Teleostomi](http://purl.obolibrary.org/obo/NCBITaxon_117570) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) + + + +### Tetrapoda `http://purl.obolibrary.org/obo/NCBITaxon_32523` +#### Removed +- [Tetrapoda](http://purl.obolibrary.org/obo/NCBITaxon_32523) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) + + + +### Theria `http://purl.obolibrary.org/obo/NCBITaxon_32525` +#### Removed +- [Theria ](http://purl.obolibrary.org/obo/NCBITaxon_32525) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) + + + +### Theropoda `http://purl.obolibrary.org/obo/NCBITaxon_436491` +#### Removed +- [Theropoda](http://purl.obolibrary.org/obo/NCBITaxon_436491) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) + + + +### Thy-1 membrane glycoprotein `http://purl.obolibrary.org/obo/PR_000001843` +#### Removed +- [Thy-1 membrane glycoprotein](http://purl.obolibrary.org/obo/PR_000001843) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [Thy-1 membrane glycoprotein (human)](http://purl.obolibrary.org/obo/PR_P04216) + + + +### Tracheophyta `http://purl.obolibrary.org/obo/NCBITaxon_58023` +#### Removed +- [Tracheophyta](http://purl.obolibrary.org/obo/NCBITaxon_58023) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) + + + +### UBPROP_0000001 `http://purl.obolibrary.org/obo/UBPROP_0000001` +#### Removed +- AnnotationProperty: [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) + + + +### UBPROP_0000002 `http://purl.obolibrary.org/obo/UBPROP_0000002` +#### Removed +- AnnotationProperty: [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) + + + +### UBPROP_0000003 `http://purl.obolibrary.org/obo/UBPROP_0000003` +#### Removed +- AnnotationProperty: [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) + + + +### UBPROP_0000004 `http://purl.obolibrary.org/obo/UBPROP_0000004` +#### Removed +- AnnotationProperty: [UBPROP_0000004](http://purl.obolibrary.org/obo/UBPROP_0000004) + + + +### UBPROP_0000005 `http://purl.obolibrary.org/obo/UBPROP_0000005` +#### Removed +- AnnotationProperty: [UBPROP_0000005](http://purl.obolibrary.org/obo/UBPROP_0000005) + + + +### UBPROP_0000006 `http://purl.obolibrary.org/obo/UBPROP_0000006` +#### Removed +- AnnotationProperty: [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) + + + +### UBPROP_0000007 `http://purl.obolibrary.org/obo/UBPROP_0000007` +#### Removed +- AnnotationProperty: [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) + + + +### UBPROP_0000008 `http://purl.obolibrary.org/obo/UBPROP_0000008` +#### Removed +- AnnotationProperty: [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) + + + +### UBPROP_0000009 `http://purl.obolibrary.org/obo/UBPROP_0000009` +#### Removed +- AnnotationProperty: [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) + + + +### UBPROP_0000010 `http://purl.obolibrary.org/obo/UBPROP_0000010` +#### Removed +- AnnotationProperty: [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) + + + +### UBPROP_0000011 `http://purl.obolibrary.org/obo/UBPROP_0000011` +#### Removed +- AnnotationProperty: [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) + + + +### UBPROP_0000012 `http://purl.obolibrary.org/obo/UBPROP_0000012` +#### Removed +- AnnotationProperty: [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) + + + +### UBPROP_0000013 `http://purl.obolibrary.org/obo/UBPROP_0000013` +#### Removed +- AnnotationProperty: [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) + + + +### UBPROP_0000015 `http://purl.obolibrary.org/obo/UBPROP_0000015` +#### Removed +- AnnotationProperty: [UBPROP_0000015](http://purl.obolibrary.org/obo/UBPROP_0000015) + + + +### UBPROP_0000103 `http://purl.obolibrary.org/obo/UBPROP_0000103` +#### Removed +- AnnotationProperty: [UBPROP_0000103](http://purl.obolibrary.org/obo/UBPROP_0000103) + + + +### UBPROP_0000105 `http://purl.obolibrary.org/obo/UBPROP_0000105` +#### Removed +- AnnotationProperty: [UBPROP_0000105](http://purl.obolibrary.org/obo/UBPROP_0000105) + + + +### UBPROP_0000107 `http://purl.obolibrary.org/obo/UBPROP_0000107` +#### Removed +- AnnotationProperty: [UBPROP_0000107](http://purl.obolibrary.org/obo/UBPROP_0000107) + + + +### UBPROP_0000111 `http://purl.obolibrary.org/obo/UBPROP_0000111` +#### Removed +- AnnotationProperty: [UBPROP_0000111](http://purl.obolibrary.org/obo/UBPROP_0000111) + + + +### UBPROP_0000202 `http://purl.obolibrary.org/obo/UBPROP_0000202` +#### Removed +- AnnotationProperty: [UBPROP_0000202](http://purl.obolibrary.org/obo/UBPROP_0000202) + + + +### V(D)J recombination-activating protein 1 `http://purl.obolibrary.org/obo/PR_000003457` +#### Removed +- [V(D)J recombination-activating protein 1](http://purl.obolibrary.org/obo/PR_000003457) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [V(D)J recombination-activating protein 1 (human)](http://purl.obolibrary.org/obo/PR_P15918) + + + +### V(D)J recombination-activating protein 2 `http://purl.obolibrary.org/obo/PR_000003460` +#### Removed +- [V(D)J recombination-activating protein 2](http://purl.obolibrary.org/obo/PR_000003460) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [V(D)J recombination-activating protein 2 (human)](http://purl.obolibrary.org/obo/PR_P55895) + + + +### VIP peptides `http://purl.obolibrary.org/obo/PR_000017299` +#### Removed +- [VIP peptides](http://purl.obolibrary.org/obo/PR_000017299) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [VIP peptides (human)](http://purl.obolibrary.org/obo/PR_P01282) + + + +### Vertebrata `http://purl.obolibrary.org/obo/NCBITaxon_7742` +#### Removed +- [Vertebrata ](http://purl.obolibrary.org/obo/NCBITaxon_7742) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) + + + +### Viridiplantae `http://purl.obolibrary.org/obo/NCBITaxon_33090` +#### Removed +- [Viridiplantae](http://purl.obolibrary.org/obo/NCBITaxon_33090) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_kingdom](http://purl.obolibrary.org/obo/NCBITaxon_kingdom) + + + +### Zygnematales `http://purl.obolibrary.org/obo/NCBITaxon_3176` +#### Removed +- [Zygnematales](http://purl.obolibrary.org/obo/NCBITaxon_3176) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_order](http://purl.obolibrary.org/obo/NCBITaxon_order) + + + +### Zygnematophycidae `http://purl.obolibrary.org/obo/NCBITaxon_2684882` +#### Removed +- [Zygnematophycidae](http://purl.obolibrary.org/obo/NCBITaxon_2684882) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_subclass](http://purl.obolibrary.org/obo/NCBITaxon_subclass) + + + +### Zygnemophyceae `http://purl.obolibrary.org/obo/NCBITaxon_131209` +#### Removed +- [Zygnemophyceae](http://purl.obolibrary.org/obo/NCBITaxon_131209) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_class](http://purl.obolibrary.org/obo/NCBITaxon_class) + + + +### abbreviation `http://purl.obolibrary.org/obo/OMO_0003000` +#### Removed +- [abbreviation](http://purl.obolibrary.org/obo/OMO_0003000) [created](http://purl.org/dc/terms/created) "2023-03-03"^^[date](http://www.w3.org/2001/XMLSchema#date) + +- [abbreviation](http://purl.obolibrary.org/obo/OMO_0003000) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation)" + + + +### abdomen `http://purl.obolibrary.org/obo/UBERON_0000916` +#### Removed +- [abdomen](http://purl.obolibrary.org/obo/UBERON_0000916) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "celiac" + +- [abdomen](http://purl.obolibrary.org/obo/UBERON_0000916) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "abdominal" + + + +### abdomen blood vessel `http://purl.obolibrary.org/obo/UBERON_0003497` +#### Removed +- [abdomen blood vessel](http://purl.obolibrary.org/obo/UBERON_0003497) [see also](http://www.w3.org/2000/01/rdf-schema#seeAlso) "UBERON:0012254" + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "abdominal aorta artery" + + + +### abdomen musculature `http://purl.obolibrary.org/obo/UBERON_0002343` +#### Removed +- [abdomen musculature](http://purl.obolibrary.org/obo/UBERON_0002343) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "distinction between abdomen muscle and abdomen musculature" + + + +### abdominal cavity `http://purl.obolibrary.org/obo/UBERON_0003684` +#### Removed +- [abdominal cavity](http://purl.obolibrary.org/obo/UBERON_0003684) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in FMA this contains the pelvic cavity, but this is inconsistent with the concept of abdominopelvic cavity" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + + + +### abdominal mammary gland `http://purl.obolibrary.org/obo/UBERON_0003488` +#### Removed +- [abdominal mammary gland](http://purl.obolibrary.org/obo/UBERON_0003488) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Female mice normally have five pairs of nipples and mammary glands, three in the thoracic and two in the abdominal region. (There is an additional abdominal pair in female rats.) http://www.informatics.jax.org/greenbook/chapters/chapter13.shtml" + + + +### abnormal `http://purl.obolibrary.org/obo/PATO_0000460` +#### Removed +- [abnormal](http://purl.obolibrary.org/obo/PATO_0000460) [RO_0002604](http://purl.obolibrary.org/obo/RO_0002604) [normal](http://purl.obolibrary.org/obo/PATO_0000461) + + + +### accessory XI nerve `http://purl.obolibrary.org/obo/UBERON_0002019` +#### Removed +- [accessory XI nerve](http://purl.obolibrary.org/obo/UBERON_0002019) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Small motor nerve which innervates a single pectoral suspensory muscle, the m. cucullaris.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010476" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + +- [accessory XI nerve](http://purl.obolibrary.org/obo/UBERON_0002019) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA has distinct cranial and spinal parts - WP says 'Traditional descriptions of the accessory nerve divide it into two parts: a spinal part and a cranial part.[1] However, because the cranial component rapidly joins the vagus nerve, becoming an integral part of said nerve, modern descriptions often consider the cranial component to be part of the vagus nerve and not part of the accessory nerve proper.[2]" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + +- [accessory XI nerve](http://purl.obolibrary.org/obo/UBERON_0002019) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A small motor nerve which emerges from the lateral wall of the medulla with the roots of the vagus nerve, and innervates a single pectoral suspensory muscle, the m.cucullaris." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "XAO:0004214" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:080184780X" + +- [accessory XI nerve](http://purl.obolibrary.org/obo/UBERON_0002019) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Cranial nerve that innervates the sternocleidomastoid and trapezius complex of muscles. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-1, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000699" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + +- [accessory XI nerve](http://purl.obolibrary.org/obo/UBERON_0002019) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In mice, the spinal branch of this motor nerve innervates the trapezius and the sternocleidomastoid muscles. The cranial branch joins the vagus nerve and innervates the same targets as the vagus nerve" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GO" + +- [accessory XI nerve](http://purl.obolibrary.org/obo/UBERON_0002019) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Cranial nerves XI and XII evolved in the common ancestor to amniotes (non-amphibian tetrapods) thus totalling twelve pairs.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000699" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Cranial_nerves" + +- [accessory XI nerve](http://purl.obolibrary.org/obo/UBERON_0002019) [RO_0002174](http://purl.obolibrary.org/obo/RO_0002174) [NCBITaxon_8292](http://purl.obolibrary.org/obo/NCBITaxon_8292) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "VHOG" + + - [see also](http://www.w3.org/2000/01/rdf-schema#seeAlso) "http://code.google.com/p/xenopus-anatomy-ontology/issues/detail?id=7" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia" + + + +### acellular anatomical structure `http://purl.obolibrary.org/obo/UBERON_0000476` +#### Removed +- [acellular anatomical structure](http://purl.obolibrary.org/obo/UBERON_0000476) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007013" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + + +### acinus of lacrimal gland `http://purl.obolibrary.org/obo/UBERON_0011857` + +#### Added +- [acinus of lacrimal gland](http://purl.obolibrary.org/obo/UBERON_0011857) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### acinus of lactiferous gland `http://purl.obolibrary.org/obo/UBERON_0011856` + +#### Added +- [acinus of lactiferous gland](http://purl.obolibrary.org/obo/UBERON_0011856) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### acinus of sebaceous gland `http://purl.obolibrary.org/obo/UBERON_0011846` + +#### Added +- [acinus of sebaceous gland](http://purl.obolibrary.org/obo/UBERON_0011846) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### acoustico-facial VII-VIII ganglion complex `http://purl.obolibrary.org/obo/UBERON_0012175` +#### Removed +- [acoustico-facial VII-VIII ganglion complex](http://purl.obolibrary.org/obo/UBERON_0012175) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "VHOG:0000715" + + + +### acromioclavicular joint `http://purl.obolibrary.org/obo/UBERON_0003692` +#### Removed +- [acromioclavicular joint](http://purl.obolibrary.org/obo/UBERON_0003692) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The gliding joint formed by the outer extremity of the clavicle and the inner margin of the acromion process of the scapula." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "MESH:A02.835.583.032" + + + +### acromion `http://purl.obolibrary.org/obo/UBERON_0002497` +#### Removed +- [acromion](http://purl.obolibrary.org/obo/UBERON_0002497) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: part_of pars acromialis (AAO:0000752)[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000826" + +- [acromion](http://purl.obolibrary.org/obo/UBERON_0002497) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anterior rounded projection of the pars acromialis of the scapula.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000826" + + + +### acropodial skeleton `http://purl.obolibrary.org/obo/UBERON_0010543` + +#### Added +- [acropodial skeleton](http://purl.obolibrary.org/obo/UBERON_0010543) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### acropodium region `http://purl.obolibrary.org/obo/UBERON_0012354` +#### Removed +- [acropodium region](http://purl.obolibrary.org/obo/UBERON_0012354) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "class refers to an entire limb segment, not just the bones" + + + +### acts upstream of `http://purl.obolibrary.org/obo/RO_0002263` +#### Removed +- [acts upstream of](http://purl.obolibrary.org/obo/RO_0002263) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." + + + +### acts upstream of or within `http://purl.obolibrary.org/obo/RO_0002264` +#### Removed +- [acts upstream of or within](http://purl.obolibrary.org/obo/RO_0002264) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." + + + +### acts upstream of or within, positive effect `http://purl.obolibrary.org/obo/RO_0004032` +#### Removed +- [acts upstream of or within, positive effect](http://purl.obolibrary.org/obo/RO_0004032) [RO_0004049](http://purl.obolibrary.org/obo/RO_0004049) [acts upstream of or within](http://purl.obolibrary.org/obo/RO_0002264) + + + +### acts upstream of, positive effect `http://purl.obolibrary.org/obo/RO_0004034` +#### Removed +- [acts upstream of, positive effect](http://purl.obolibrary.org/obo/RO_0004034) [RO_0004049](http://purl.obolibrary.org/obo/RO_0004049) [acts upstream of](http://purl.obolibrary.org/obo/RO_0002263) + + + +### adenohypophyseal placode `http://purl.obolibrary.org/obo/UBERON_0009122` +#### Removed +- [adenohypophyseal placode](http://purl.obolibrary.org/obo/UBERON_0009122) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "Fate-mapping studies in amphibian, chick and mouse embryos (Eagleson et al., 1986; 1995; Couly and Le Douarin, 1985; Cobos et al., 2001; Osumi-Yamachita et al., 1994; Kawamura et al., 2002) have shown that the cells contributing to the adenohypophysis develop at the midline of the anterior neural ridge, which delineates the rostral boundary of the neural plate, a region devoid of neural crest. The anterior neural ridge also gives rise to the olfactory placodes and some forebrain tissues including the olfactory bulbs (reviewed in Papalopulu, 1995). Ablation of this region in chick embryos at the 2-4 somite stage confirmed these lineage analyses as it prevented formation of Rathke's pouch and any further pituitary development (elAmraoui and Dubois, 1993). Upon head folding, the oral ectoderm cells of the adenohypophyseal placode invaginate towards the prospective ventral diencephalon to form Rathke's pouch, the anlage of the adenohypophysis. Rathke's pouch starts as an invagination of the oral ectoderm in response to inductive signals from the prospective diencephalon. The region of the diencephalon above the pouch is known as the infundibulum and forms the posterior lobe of the pituitary or neurohypohysis (Figure 3). While in most basal fish and tetrapods the adenohypophyseal anlagen invaginates to form Rathke's pouch, in teleost fish the adenohypophyseal placode does not invaginate but rather maintains its initial organization forming a solid structure in the head (reviewed in Pogoda and Hammerschmidt; 2009)" + + + +### adenohypophysis `http://purl.obolibrary.org/obo/UBERON_0002196` +#### Removed +- [adenohypophysis](http://purl.obolibrary.org/obo/UBERON_0002196) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. An infundibulum grows ventrally from the diencephalon of the brain, and Rathke's pouch extends dorsally from the roof of the developing mouth, or stomodaeum. The infundibulum remains connected to the floor of the diencephalon, which becomes the hypothalamus, and gives rise to the part of the gland known as the neurohypophysis. (...) Rathke's pouch loses its connection with the stomodaeum in most adult vertebrates and gives rise to the rest of the gland, the adenohypophysis. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510 and Figure 15-5" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000141" + +- [adenohypophysis](http://purl.obolibrary.org/obo/UBERON_0002196) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The anterior lobe of the hypophysis (pituitary gland). This lobe contains cells that produce prolactin, growth hormone, thyroid-stimulating hormone, follicle-stimulating hormone and proopiomelanocortin. In contrast to mamalian vertebrates, the adenohypophysis remains in a subepithelial position and there exists no equivalent of Rathke's pouch in zebrafish. Herzog et al, 2004.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001282" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [adenohypophysis](http://purl.obolibrary.org/obo/UBERON_0002196) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "While in most basal fish and tetrapods the adenohypophyseal anlagen invaginates to form Rathke's pouch, in teleost fish the adenohypophyseal placode does not invaginate but rather maintains its initial organization forming a solid structure in the head[NCBIBook:NBK53175]." + +- [adenohypophysis](http://purl.obolibrary.org/obo/UBERON_0002196) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Region of the pituitary gland derived from the buccal protrusion consisting of three regions.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010540" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + +- [adenohypophysis](http://purl.obolibrary.org/obo/UBERON_0002196) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In contrast to mammalian vertebrates, the adenohypophysis remains in a subepithelial position and there exists no equivalent of Rathke's pouch in zebrafish" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFA" + +#### Added +- [adenohypophysis](http://purl.obolibrary.org/obo/UBERON_0002196) SubClassOf [structure with developmental contribution from neural crest](http://purl.obolibrary.org/obo/UBERON_0010314) + + +### adhesion G protein-coupled receptor E1 `http://purl.obolibrary.org/obo/PR_000001813` +#### Removed +- [adhesion G protein-coupled receptor E1](http://purl.obolibrary.org/obo/PR_000001813) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [adhesion G protein-coupled receptor E1 (human)](http://purl.obolibrary.org/obo/PR_Q14246) + + + +### adipose tissue `http://purl.obolibrary.org/obo/UBERON_0001013` +#### Removed +- [adipose tissue](http://purl.obolibrary.org/obo/UBERON_0001013) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in FMA this is dense irregular connective tissue" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + +- [adipose tissue](http://purl.obolibrary.org/obo/UBERON_0001013) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In humans, adipose tissue is located beneath the skin (subcutaneous fat), around internal organs (visceral fat), in bone marrow (yellow bone marrow) and in breast tissue. Adipose tissue is found in specific locations, which are referred to as adipose depots. Adipose tissue contains several cell types, with the highest percentage of cells being adipocytes, which contain fat droplets. Other cell types include fibroblasts, macrophages, and endothelial cells. Adipose tissue contains many small blood vessels.; Mice have eight major adipose depots, four of which are within the abdominal cavity. The paired gonadal depots are attached to the uterus and ovaries in females and the epididymis and testes in males; the paired retroperitoneal depots are found along the dorsal wall of the abdomen, surrounding the kidney, and, when massive, extend into the pelvis. The mesenteric depot forms a glue-like web that supports the intestines, and the omental depot, which originates near the stomach and spleen, and, when massive, extends into the ventral abdomen." + +- [adipose tissue](http://purl.obolibrary.org/obo/UBERON_0001013) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Adipose tissue is unique to vertebrates. It is found in mostmammals, birds, reptiles and amphibians, and a variety is found in some species of fish. Furthermore, in insects the fat body found in larvae as well as in adults shares some homology with adipose tissue.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1017/S0029665107005423 Haugen F, Drevon CA, The interplay between nutrients and the adipose tissue. The Proceedings of the Nutrition Society (2007)" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001284" + +- [adipose tissue](http://purl.obolibrary.org/obo/UBERON_0001013) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Connective tissue in which fat is stored.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0002134" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [adipose tissue](http://purl.obolibrary.org/obo/UBERON_0001013) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "adipose" + +- [adipose tissue](http://purl.obolibrary.org/obo/UBERON_0001013) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Tissue that contains adipocytes, used for cushioning, thermal insulation, lubrication (primarily in the pericardium) and energy storage.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000001" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + +- [adipose tissue](http://purl.obolibrary.org/obo/UBERON_0001013) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: subclass connective tissue proper (AAO:0000099)[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000001" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + + +### adjacent to `http://purl.obolibrary.org/obo/RO_0002220` +#### Removed +- [adjacent to](http://purl.obolibrary.org/obo/RO_0002220) [RO_0001900](http://purl.obolibrary.org/obo/RO_0001900) [RO_0001901](http://purl.obolibrary.org/obo/RO_0001901) + +- [adjacent to](http://purl.obolibrary.org/obo/RO_0002220) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." + - [see also](http://www.w3.org/2000/01/rdf-schema#seeAlso) [issuecomment-218584934](https://github.com/jhpoelen/eol-globi-data/issues/225#issuecomment-218584934) + +- [adjacent to](http://purl.obolibrary.org/obo/RO_0002220) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) + +- [adjacent to](http://purl.obolibrary.org/obo/RO_0002220) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." + +- [adjacent to](http://purl.obolibrary.org/obo/RO_0002220) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "The epidermis layer of a vertebrate is adjacent to the dermis." + +- [adjacent to](http://purl.obolibrary.org/obo/RO_0002220) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [adjacent to](http://purl.obolibrary.org/obo/RO_0002220) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [adjacent to](http://purl.obolibrary.org/obo/RO_0002220) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." + + + +### adrenal cortex `http://purl.obolibrary.org/obo/UBERON_0001235` +#### Removed +- [adrenal cortex](http://purl.obolibrary.org/obo/UBERON_0001235) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Kardong states that mammals are the first to have distinct cortext and medulla, but this contradicts XAO" + +- [adrenal cortex](http://purl.obolibrary.org/obo/UBERON_0001235) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues (medulla), but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001481" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9" + +#### Added +- [adrenal cortex](http://purl.obolibrary.org/obo/UBERON_0001235) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) + + +### adrenal gland `http://purl.obolibrary.org/obo/UBERON_0002369` +#### Removed +- [adrenal gland](http://purl.obolibrary.org/obo/UBERON_0002369) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "suprarenal cortex manufactures corticosteroids; suprarenal medulla manufactures epinephrine and norepinephrine; suprarenal medulla receives preganglionic sympathetic innervation from the greater thoracic splanchnic n." + +- [adrenal gland](http://purl.obolibrary.org/obo/UBERON_0002369) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "VHOG:0001141" + +- [adrenal gland](http://purl.obolibrary.org/obo/UBERON_0002369) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The origin of the adrenal gland is still controversial. It is thought to share the same origin as the kidney and gonads, derived from coelomic epithelium of the urogenital ridge and/or the underlying mesenchyme (Keegan and Hammer, 2002; Morohashi, 1997). We follow Kardong and state homology at the level of the cortex and medulla rather than gland as a whole" + +- [adrenal gland](http://purl.obolibrary.org/obo/UBERON_0002369) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001141" + +- [adrenal gland](http://purl.obolibrary.org/obo/UBERON_0002369) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical structure which is found on the surface of the kidney and secretes various hormones including epinephrine, norephinephrine, aldosterone, corticosterone, and cortisol.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010551" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + +- [adrenal gland](http://purl.obolibrary.org/obo/UBERON_0002369) SubClassOf [structure with developmental contribution from neural crest](http://purl.obolibrary.org/obo/UBERON_0010314) + + + +### adrenal gland capsule `http://purl.obolibrary.org/obo/UBERON_0002052` + +#### Added +- [adrenal gland capsule](http://purl.obolibrary.org/obo/UBERON_0002052) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) + +- [adrenal gland capsule](http://purl.obolibrary.org/obo/UBERON_0002052) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### adrenal gland cortex zone `http://purl.obolibrary.org/obo/UBERON_0009753` + +#### Added +- [adrenal gland cortex zone](http://purl.obolibrary.org/obo/UBERON_0009753) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) + +- [adrenal gland cortex zone](http://purl.obolibrary.org/obo/UBERON_0009753) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### adrenal medulla `http://purl.obolibrary.org/obo/UBERON_0001236` +#### Removed +- [adrenal medulla](http://purl.obolibrary.org/obo/UBERON_0001236) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues (medulla), but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001378" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9" + +#### Added +- [adrenal medulla](http://purl.obolibrary.org/obo/UBERON_0001236) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### adrenal tissue `http://purl.obolibrary.org/obo/UBERON_0018303` + +#### Added +- [adrenal tissue](http://purl.obolibrary.org/obo/UBERON_0018303) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + +- [adrenal tissue](http://purl.obolibrary.org/obo/UBERON_0018303) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) + + +### adrenal/interrenal gland `http://purl.obolibrary.org/obo/UBERON_0006858` +#### Removed +- [adrenal/interrenal gland](http://purl.obolibrary.org/obo/UBERON_0006858) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "VHOG:0001141" + +- [adrenal/interrenal gland](http://purl.obolibrary.org/obo/UBERON_0006858) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "All craniates have groups of cells homologous to the mammalian adrenocortical and chromaffin tissues, but they are scattered in and near the kidneys in fishes. (...) The cortical and chromaffin tissues come together to form adrenal glands in tetrapods.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.518 and Figure 15-9" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001141" + +#### Added +- [adrenal/interrenal gland](http://purl.obolibrary.org/obo/UBERON_0006858) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) + + +### adult organism `http://purl.obolibrary.org/obo/UBERON_0007023` +#### Removed +- [adult organism](http://purl.obolibrary.org/obo/UBERON_0007023) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Whole organism that is fully grown or sexually mature.[TAO]" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0002046" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TAO:wd" + +- [adult organism](http://purl.obolibrary.org/obo/UBERON_0007023) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00003004" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + + +### adventitia `http://purl.obolibrary.org/obo/UBERON_0005742` +#### Removed +- [adventitia](http://purl.obolibrary.org/obo/UBERON_0005742) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D063194" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + + + +### adventitia of epididymis `http://purl.obolibrary.org/obo/UBERON_0006645` + +#### Added +- [adventitia of epididymis](http://purl.obolibrary.org/obo/UBERON_0006645) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### adventitia of seminal vesicle `http://purl.obolibrary.org/obo/UBERON_0006648` + +#### Added +- [adventitia of seminal vesicle](http://purl.obolibrary.org/obo/UBERON_0006648) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### adventitia of ureter `http://purl.obolibrary.org/obo/UBERON_0001252` + +#### Added +- [adventitia of ureter](http://purl.obolibrary.org/obo/UBERON_0001252) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### aggregate regional part of brain `http://purl.obolibrary.org/obo/UBERON_0010009` +#### Removed +- [aggregate regional part of brain](http://purl.obolibrary.org/obo/UBERON_0010009) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:256381" + + + +### airway submucosal gland `http://purl.obolibrary.org/obo/UBERON_8410077` + +#### Added +- [airway submucosal gland](http://purl.obolibrary.org/obo/UBERON_8410077) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) + + +### alimentary part of gastrointestinal system `http://purl.obolibrary.org/obo/UBERON_0005409` +#### Removed +- [alimentary part of gastrointestinal system](http://purl.obolibrary.org/obo/UBERON_0005409) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "that many anatomy ontologies consider this synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class. We have one entity that is part of both gastrointestinal and hepatobiliary systems: hepatopancreatic ampulla." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" + +- [alimentary part of gastrointestinal system](http://purl.obolibrary.org/obo/UBERON_0005409) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The system that includes the esophagus, stomach, small and large intestine, anus, liver, biliary tract, and pancreas[ncithesaurus:Gastrointestinal_System]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ncithesaurus:Gastrointestinal_System" + +- [alimentary part of gastrointestinal system](http://purl.obolibrary.org/obo/UBERON_0005409) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EV:0100056" + +- [alimentary part of gastrointestinal system](http://purl.obolibrary.org/obo/UBERON_0005409) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "All metazoans (with degenerate exceptions) have some sort of digestive cavity with a means of entrance to and exit from it.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000412" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0721676685 Sherwood Romer A and Parsons T, Vertebrate body (1977) p.3" + + + +### allantois `http://purl.obolibrary.org/obo/UBERON_0004340` +#### Removed +- [allantois](http://purl.obolibrary.org/obo/UBERON_0004340) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "allantoic" + +- [allantois](http://purl.obolibrary.org/obo/UBERON_0004340) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "a diverticulum of the hindgut endoderm [ISBN:0073040584 (Vertebrates, Kardong)]" + +- [allantois](http://purl.obolibrary.org/obo/UBERON_0004340) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A membranous sac that develops from the posterior part of the alimentary canal in the embryos of mammals, birds, and reptiles, and it is important in the formation of the umbilical cord and placenta in mammals. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/allantois" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000738" + +- [allantois](http://purl.obolibrary.org/obo/UBERON_0004340) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "part_of embryo in EHDAA2 - note differences in humans" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EHDAA2" + +- [allantois](http://purl.obolibrary.org/obo/UBERON_0004340) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.187" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000738" + +- [allantois](http://purl.obolibrary.org/obo/UBERON_0004340) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [endoderm](http://purl.obolibrary.org/obo/UBERON_0000925) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0073040584" + + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "hindgut diverticulum endoderm" + +#### Added +- [allantois](http://purl.obolibrary.org/obo/UBERON_0004340) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [endoderm](http://purl.obolibrary.org/obo/UBERON_0000925) + + +### alpha-(1,3)-fucosyltransferase 4 `http://purl.obolibrary.org/obo/PR_000001456` +#### Removed +- [alpha-(1,3)-fucosyltransferase 4](http://purl.obolibrary.org/obo/PR_000001456) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [alpha-(1,3)-fucosyltransferase 4 (human)](http://purl.obolibrary.org/obo/PR_P22083) + + + +### alveolar ridge `http://purl.obolibrary.org/obo/UBERON_0004103` +#### Removed +- [alveolar ridge](http://purl.obolibrary.org/obo/UBERON_0004103) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in BTO, this is part of an embryo" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "BTO" + +#### Added +- [alveolar ridge](http://purl.obolibrary.org/obo/UBERON_0004103) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) + + +### alveolar system `http://purl.obolibrary.org/obo/UBERON_0006524` + +#### Added +- [alveolar system](http://purl.obolibrary.org/obo/UBERON_0006524) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) + + +### alveolar wall `http://purl.obolibrary.org/obo/UBERON_0004894` +#### Removed +- [alveolar wall](http://purl.obolibrary.org/obo/UBERON_0004894) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "part of wall in FMA" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + +#### Added +- [alveolar wall](http://purl.obolibrary.org/obo/UBERON_0004894) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) + + +### alveolus `http://purl.obolibrary.org/obo/UBERON_0003215` +#### Removed +- [alveolus](http://purl.obolibrary.org/obo/UBERON_0003215) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EV:0100043" + +- [alveolus](http://purl.obolibrary.org/obo/UBERON_0003215) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "alveolar" + + + +### alveolus of lung `http://purl.obolibrary.org/obo/UBERON_0002299` +#### Removed +- [alveolus of lung](http://purl.obolibrary.org/obo/UBERON_0002299) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EV:0100043" + +#### Added +- [alveolus of lung](http://purl.obolibrary.org/obo/UBERON_0002299) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) + + +### amino acid transmembrane transporter activity `http://purl.obolibrary.org/obo/GO_0015171` +#### Removed +- [amino acid transmembrane transporter activity](http://purl.obolibrary.org/obo/GO_0015171) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [amino acid transmembrane transport](http://purl.obolibrary.org/obo/GO_0003333) + - [source](http://www.geneontology.org/formats/oboInOwl#http://purl.org/dc/terms/source) "GO_REF:0000090" + +#### Added +- [amino acid transmembrane transporter activity](http://purl.obolibrary.org/obo/GO_0015171) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [amino acid transmembrane transport](http://purl.obolibrary.org/obo/GO_0003333) + + +### aminopeptidase N `http://purl.obolibrary.org/obo/PR_000002031` +#### Removed +- [aminopeptidase N](http://purl.obolibrary.org/obo/PR_000002031) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [aminopeptidase N (human)](http://purl.obolibrary.org/obo/PR_P15144) + + + +### ammonium transmembrane transporter activity `http://purl.obolibrary.org/obo/GO_0008519` +#### Removed +- [ammonium transmembrane transporter activity](http://purl.obolibrary.org/obo/GO_0008519) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "TC:1.A.11" + - [IAO_0000233](http://www.geneontology.org/formats/oboInOwl#http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/geneontology/go-ontology/issues/23129" + +- [ammonium transmembrane transporter activity](http://purl.obolibrary.org/obo/GO_0008519) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [ammonium transmembrane transport](http://purl.obolibrary.org/obo/GO_0072488) + - [source](http://www.geneontology.org/formats/oboInOwl#http://purl.org/dc/terms/source) "GO_REF:0000090" + +#### Added +- [ammonium transmembrane transporter activity](http://purl.obolibrary.org/obo/GO_0008519) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [ammonium transmembrane transport](http://purl.obolibrary.org/obo/GO_0072488) + + +### amnion `http://purl.obolibrary.org/obo/UBERON_0000305` +#### Removed +- [amnion](http://purl.obolibrary.org/obo/UBERON_0000305) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.187" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000721" + +- [amnion](http://purl.obolibrary.org/obo/UBERON_0000305) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "amniotic" + +- [amnion](http://purl.obolibrary.org/obo/UBERON_0000305) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A thin but tough extraembryonic membrane of reptiles, birds and mammals that lines the chorion and contains the fEtus and the amniotic fluid around it. [Biology_Online][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000721" + +#### Added +- [amnion](http://purl.obolibrary.org/obo/UBERON_0000305) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### amnioserosa `http://purl.obolibrary.org/obo/UBERON_0010302` +#### Removed +- [amnioserosa](http://purl.obolibrary.org/obo/UBERON_0010302) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000095" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + +- [amnioserosa](http://purl.obolibrary.org/obo/UBERON_0010302) SubClassOf [only in taxon](http://purl.obolibrary.org/obo/RO_0002160) some [Arthropoda](http://purl.obolibrary.org/obo/NCBITaxon_6656) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1073/pnas.0709145105" + + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "Cyclorrhapha" + +#### Added +- [amnioserosa](http://purl.obolibrary.org/obo/UBERON_0010302) SubClassOf [only in taxon](http://purl.obolibrary.org/obo/RO_0002160) some [Arthropoda](http://purl.obolibrary.org/obo/NCBITaxon_6656) + + +### amniotic ectoderm `http://purl.obolibrary.org/obo/UBERON_0003254` +#### Removed +- [amniotic ectoderm](http://purl.obolibrary.org/obo/UBERON_0003254) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [epiblast (generic)](http://purl.obolibrary.org/obo/UBERON_0002532) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:9780878932504" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "EHDAA2-via-amnioblasts" + +#### Added +- [amniotic ectoderm](http://purl.obolibrary.org/obo/UBERON_0003254) SubClassOf [meso-epithelium](http://purl.obolibrary.org/obo/UBERON_0012275) + + +### amygdala `http://purl.obolibrary.org/obo/UBERON_0001876` +#### Removed +- [amygdala](http://purl.obolibrary.org/obo/UBERON_0001876) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "One part of the striatum is called the archistriatum. (...) The archistriatum of fishes consists of several indistinctly segregated nuclei called the amygdaloid (...) complex. Tetrapods retain the structure, and in mammals the corresponding amygdala is a globular mass that tends to be ventral to the other basal nuclei.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001277" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.342" + +- [amygdala](http://purl.obolibrary.org/obo/UBERON_0001876) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Subdivision of basal ganglion of telencephalon which is an almond-shaped gray mass in the dorsomedial part of the temporal lobe[FMA:61841]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:61841" + +- [amygdala](http://purl.obolibrary.org/obo/UBERON_0001876) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "MA and FMA differ on relationship to basal ganglion. The FMA text def suggests a subdivision, but it is classified as a subtype" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" + +- [amygdala](http://purl.obolibrary.org/obo/UBERON_0001876) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "amygdalar" + + + +### anal canal `http://purl.obolibrary.org/obo/UBERON_0000159` +#### Removed +- [anal canal](http://purl.obolibrary.org/obo/UBERON_0000159) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D001003" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + +#### Added +- [anal canal](http://purl.obolibrary.org/obo/UBERON_0000159) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### anal column `http://purl.obolibrary.org/obo/UBERON_0009882` + +#### Added +- [anal column](http://purl.obolibrary.org/obo/UBERON_0009882) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### anal region `http://purl.obolibrary.org/obo/UBERON_0001353` +#### Removed +- [anal region](http://purl.obolibrary.org/obo/UBERON_0001353) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000395" + +- [anal region](http://purl.obolibrary.org/obo/UBERON_0001353) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [proctodeum](http://purl.obolibrary.org/obo/UBERON_0000931) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "cjm" + +#### Added +- [anal region](http://purl.obolibrary.org/obo/UBERON_0001353) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [proctodeum](http://purl.obolibrary.org/obo/UBERON_0000931) + + +### anal sac gland secretion `http://purl.obolibrary.org/obo/UBERON_0013212` + +#### Added +- [anal sac gland secretion](http://purl.obolibrary.org/obo/UBERON_0013212) [id](http://www.geneontology.org/formats/oboInOwl#id) "UBERON:0013212" + +- [anal sac gland secretion](http://purl.obolibrary.org/obo/UBERON_0013212) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "hyena butter" + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [SENSU](http://purl.obolibrary.org/obo/uberon/core#SENSU) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Hyena_butter" + +- [anal sac gland secretion](http://purl.obolibrary.org/obo/UBERON_0013212) [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_119825](http://purl.obolibrary.org/obo/NCBITaxon_119825) + +- [anal sac gland secretion](http://purl.obolibrary.org/obo/UBERON_0013212) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "civet" + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [SENSU](http://purl.obolibrary.org/obo/uberon/core#SENSU) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NCBITaxon:9673" + +- [anal sac gland secretion](http://purl.obolibrary.org/obo/UBERON_0013212) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A bodily secretion that is produced by a gland of anal sac." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "OBOL:automatic" + +- [anal sac gland secretion](http://purl.obolibrary.org/obo/UBERON_0013212) [label](http://www.w3.org/2000/01/rdf-schema#label) "anal sac gland secretion" + +- [anal sac gland secretion](http://purl.obolibrary.org/obo/UBERON_0013212) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [anal sac gland secretion](http://purl.obolibrary.org/obo/UBERON_0013212) [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_30533](http://purl.obolibrary.org/obo/NCBITaxon_30533) + +- [anal sac gland secretion](http://purl.obolibrary.org/obo/UBERON_0013212) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "musk" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NCBITaxon:30533" + +- [anal sac gland secretion](http://purl.obolibrary.org/obo/UBERON_0013212) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "odorous sac" + +- [anal sac gland secretion](http://purl.obolibrary.org/obo/UBERON_0013212) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "anal gland secretion" + +- [anal sac gland secretion](http://purl.obolibrary.org/obo/UBERON_0013212) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "castoreum" + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [SENSU](http://purl.obolibrary.org/obo/uberon/core#SENSU) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NCBITaxon:29132" + +- [anal sac gland secretion](http://purl.obolibrary.org/obo/UBERON_0013212) [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9673](http://purl.obolibrary.org/obo/NCBITaxon_9673) + +- Class: [anal sac gland secretion](http://purl.obolibrary.org/obo/UBERON_0013212) + +- [anal sac gland secretion](http://purl.obolibrary.org/obo/UBERON_0013212) EquivalentTo [secretion of exocrine gland](http://purl.obolibrary.org/obo/UBERON_0000456) and ([produced by](http://purl.obolibrary.org/obo/RO_0003001) some [gland of anal canal](http://purl.obolibrary.org/obo/UBERON_0004760)) + +- [anal sac gland secretion](http://purl.obolibrary.org/obo/UBERON_0013212) SubClassOf [produced by](http://purl.obolibrary.org/obo/RO_0003001) some [gland of anal canal](http://purl.obolibrary.org/obo/UBERON_0004760) + +- [anal sac gland secretion](http://purl.obolibrary.org/obo/UBERON_0013212) SubClassOf [secretion of exocrine gland](http://purl.obolibrary.org/obo/UBERON_0000456) + + +### anatomical cluster `http://purl.obolibrary.org/obo/UBERON_0000477` +#### Removed +- [anatomical cluster](http://purl.obolibrary.org/obo/UBERON_0000477) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007277" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + + +### anatomical conduit `http://purl.obolibrary.org/obo/UBERON_0004111` +#### Removed +- [anatomical conduit](http://purl.obolibrary.org/obo/UBERON_0004111) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA has both conduit and conduit space. In EHDAA2 this is a surface feature" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + + + +### anatomical entity `http://purl.obolibrary.org/obo/UBERON_0001062` +#### Removed +- [anatomical entity](http://purl.obolibrary.org/obo/UBERON_0001062) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:10000000" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + + +### anatomical projection `http://purl.obolibrary.org/obo/UBERON_0004529` +#### Removed +- [anatomical projection](http://purl.obolibrary.org/obo/UBERON_0004529) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, or tissue.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010278" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + +- [anatomical projection](http://purl.obolibrary.org/obo/UBERON_0004529) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, tissue, fin, scale, etc.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001834" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TAO:wd" + +- [anatomical projection](http://purl.obolibrary.org/obo/UBERON_0004529) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical structure that is a natural outgrowth, projection, or appendage. A process can be part of a bone, cartilage, tissue, fin, scale, etc.[VSAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TAO:curator" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000180" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" + + + +### anatomical row `http://purl.obolibrary.org/obo/UBERON_0034926` +#### Removed +- [anatomical row](http://purl.obolibrary.org/obo/UBERON_0034926) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00100152" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + + +### anatomical space `http://purl.obolibrary.org/obo/UBERON_0000464` +#### Removed +- [anatomical space](http://purl.obolibrary.org/obo/UBERON_0000464) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007017" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + + +### anatomical structure `http://purl.obolibrary.org/obo/UBERON_0000061` +#### Removed +- [anatomical structure](http://purl.obolibrary.org/obo/UBERON_0000061) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007001" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + + +### anatomical surface `http://purl.obolibrary.org/obo/UBERON_0006984` +#### Removed +- [anatomical surface](http://purl.obolibrary.org/obo/UBERON_0006984) SubClassOf [bona-fide anatomical boundary](http://purl.obolibrary.org/obo/UBERON_0010199) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "via morphological boundary in CARO" + +#### Added +- [anatomical surface](http://purl.obolibrary.org/obo/UBERON_0006984) SubClassOf [bona-fide anatomical boundary](http://purl.obolibrary.org/obo/UBERON_0010199) + + +### anatomical system `http://purl.obolibrary.org/obo/UBERON_0000467` +#### Removed +- [anatomical system](http://purl.obolibrary.org/obo/UBERON_0000467) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004856" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + +- [anatomical system](http://purl.obolibrary.org/obo/UBERON_0000467) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "IDOMAL:0002460" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + + - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) + + + +### anatomical wall `http://purl.obolibrary.org/obo/UBERON_0000060` +#### Removed +- [anatomical wall](http://purl.obolibrary.org/obo/UBERON_0000060) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:25036" + +- [anatomical wall](http://purl.obolibrary.org/obo/UBERON_0000060) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in FMA, serosa is a wall" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + + + +### ankle joint `http://purl.obolibrary.org/obo/UBERON_0001488` +#### Removed +- [ankle joint](http://purl.obolibrary.org/obo/UBERON_0001488) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "todo - accurately represent different types of ankle joint" + + + +### ankle nerve `http://purl.obolibrary.org/obo/UBERON_0003446` +#### Removed +- [ankle nerve](http://purl.obolibrary.org/obo/UBERON_0003446) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA placement dubious" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + + + +### anlage `http://purl.obolibrary.org/obo/UBERON_0007688` +#### Removed +- [anlage](http://purl.obolibrary.org/obo/UBERON_0007688) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005426" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + + +### annulus fibrosus `http://purl.obolibrary.org/obo/UBERON_0006444` +#### Removed +- [annulus fibrosus](http://purl.obolibrary.org/obo/UBERON_0006444) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D000070616" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + +- [annulus fibrosus](http://purl.obolibrary.org/obo/UBERON_0006444) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:32670" + + + +### anorectum `http://purl.obolibrary.org/obo/UBERON_8410050` +#### Removed +- [anorectum](http://purl.obolibrary.org/obo/UBERON_8410050) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "anorectal" + + + +### anterior chamber of eyeball `http://purl.obolibrary.org/obo/UBERON_0001766` +#### Removed +- [anterior chamber of eyeball](http://purl.obolibrary.org/obo/UBERON_0001766) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The part of the eyeball between the cornea and the iris, filled with aqueous humor. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001431" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/anterior+chamber" + +- [anterior chamber of eyeball](http://purl.obolibrary.org/obo/UBERON_0001766) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "space in EHDAA2 - consider adding Cavity of anterior chamber of eyeball" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EHDAA2" + + + +### anterior lateral line nerve `http://purl.obolibrary.org/obo/UBERON_2000425` +#### Removed +- [anterior lateral line nerve](http://purl.obolibrary.org/obo/UBERON_2000425) [UBPROP_0000004](http://purl.obolibrary.org/obo/UBPROP_0000004) "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://purl.obolibrary.org/obo/tao.owl" + + + +### anterior lateral line neuromast `http://purl.obolibrary.org/obo/UBERON_2001472` +#### Removed +- [anterior lateral line neuromast](http://purl.obolibrary.org/obo/UBERON_2001472) [UBPROP_0000004](http://purl.obolibrary.org/obo/UBPROP_0000004) "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://purl.obolibrary.org/obo/tao.owl" + + + +### anterior lateral line placode `http://purl.obolibrary.org/obo/UBERON_2001316` +#### Removed +- [anterior lateral line placode](http://purl.obolibrary.org/obo/UBERON_2001316) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Lateral line placode that gives rise to the anterior lateral line nerve[XAO:0004221, XAO:EJS]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "XAO:EJS" + + + +### anterior lateral line primordium `http://purl.obolibrary.org/obo/UBERON_2005117` +#### Removed +- [anterior lateral line primordium](http://purl.obolibrary.org/obo/UBERON_2005117) [UBPROP_0000004](http://purl.obolibrary.org/obo/UBPROP_0000004) "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://purl.obolibrary.org/obo/tao.owl" + + + +### anterior lateral plate mesoderm `http://purl.obolibrary.org/obo/UBERON_0009881` + +#### Added +- [anterior lateral plate mesoderm](http://purl.obolibrary.org/obo/UBERON_0009881) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### anterior limiting lamina of cornea `http://purl.obolibrary.org/obo/UBERON_0004370` +#### Removed +- [anterior limiting lamina of cornea](http://purl.obolibrary.org/obo/UBERON_0004370) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Acellular anatomical structure that is the zone of collagen fibers adjacent the basement membrane of the corneal epithelium.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0002155" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:ZDB-PUB-061010-3" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [anterior limiting lamina of cornea](http://purl.obolibrary.org/obo/UBERON_0004370) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals" + +#### Added +- [anterior limiting lamina of cornea](http://purl.obolibrary.org/obo/UBERON_0004370) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) + + +### anterior neural tube `http://purl.obolibrary.org/obo/UBERON_0003080` +#### Removed +- [anterior neural tube](http://purl.obolibrary.org/obo/UBERON_0003080) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001384" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28" + + + +### anterior part of tongue `http://purl.obolibrary.org/obo/UBERON_0010032` +#### Removed +- [anterior part of tongue](http://purl.obolibrary.org/obo/UBERON_0010032) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "check NCIT" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "NCIT" + +- [anterior part of tongue](http://purl.obolibrary.org/obo/UBERON_0010032) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "The lateral lingual swellings grow and fuse with eachother, encompassing the tuberculum impar to provide the ectodermally derived mucosa of the anterior 2/3 of the tongue" + + + +### anterior segment of eyeball `http://purl.obolibrary.org/obo/UBERON_0001801` +#### Removed +- [anterior segment of eyeball](http://purl.obolibrary.org/obo/UBERON_0001801) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [posterior segment of eyeball](http://purl.obolibrary.org/obo/UBERON_0001802) + - [exceptions](http://www.geneontology.org/formats/oboInOwl#exceptions) "ZFA" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "https://github.com/obophenotype/uberon/issues/378" + + - [status](http://www.geneontology.org/formats/oboInOwl#status) "pending" + +#### Added +- [anterior segment of eyeball](http://purl.obolibrary.org/obo/UBERON_0001801) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### anterior stroma of cornea `http://purl.obolibrary.org/obo/UBERON_0003952` + +#### Added +- [anterior stroma of cornea](http://purl.obolibrary.org/obo/UBERON_0003952) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) + + +### anterior to `http://purl.obolibrary.org/obo/BSPO_0000096` +#### Removed +- [anterior to](http://purl.obolibrary.org/obo/BSPO_0000096) [id](http://www.geneontology.org/formats/oboInOwl#id) "anterior_to" + +- [anterior to](http://purl.obolibrary.org/obo/BSPO_0000096) [label](http://www.w3.org/2000/01/rdf-schema#label) "anterior to" + +- [anterior to](http://purl.obolibrary.org/obo/BSPO_0000096) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BSPO:0000096" + +- [anterior to](http://purl.obolibrary.org/obo/BSPO_0000096) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [anterior to](http://purl.obolibrary.org/obo/BSPO_0000096) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "anterior_to" + + + +### anterior uvea `http://purl.obolibrary.org/obo/UBERON_0011892` + +#### Added +- [anterior uvea](http://purl.obolibrary.org/obo/UBERON_0011892) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### anterior vena cava `http://purl.obolibrary.org/obo/UBERON_0001585` +#### Removed +- [anterior vena cava](http://purl.obolibrary.org/obo/UBERON_0001585) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The mouse has both left and right anterior vena cava. adult humans only have a right. Postnatally the left regresses and becomes non-functional (Wessels and Sedmera 2003). In the mouse, The right pulmonary vein passes dorsal to the right superior vena cava, the left pulmonary dorsal to the left superior vena cava (Biology of the Laboratory Mouse, Green)." + +- [anterior vena cava](http://purl.obolibrary.org/obo/UBERON_0001585) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Phylogenetic modifications within this basic pattern of arteries and veins are largely correlated with functional changes. In the transition from water to land, gills gave way to lungs, accompanied by the establishment of a pulmonary circulation. In some fishes and certainly in tetrapods, the cardinal veins become less involved in blood return. Instead, the composite, prominent postcava (posterior vena cava) arose to drain the posterior part of the body and the precava (anterior vena cava) developed to drain the anterior part of the body.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001195" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.454-455" + + + +### anterior wall of right ventricle `http://purl.obolibrary.org/obo/UBERON_0036289` +#### Removed +- [anterior wall of right ventricle](http://purl.obolibrary.org/obo/UBERON_0036289) SubClassOf [heart ventricle wall](http://purl.obolibrary.org/obo/UBERON_0004784) + +#### Added +- [anterior wall of right ventricle](http://purl.obolibrary.org/obo/UBERON_0036289) SubClassOf [wall of right ventricle](http://purl.obolibrary.org/obo/UBERON_0036286) + + +### anteroventral periventricular nucleus `http://purl.obolibrary.org/obo/UBERON_0002690` +#### Removed +- [anteroventral periventricular nucleus](http://purl.obolibrary.org/obo/UBERON_0002690) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0001934](http://purl.obolibrary.org/obo/UBERON_0001934) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" + +- [anteroventral periventricular nucleus](http://purl.obolibrary.org/obo/UBERON_0002690) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002034](http://purl.obolibrary.org/obo/UBERON_0002034) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" + +- [anteroventral periventricular nucleus](http://purl.obolibrary.org/obo/UBERON_0002690) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0007626](http://purl.obolibrary.org/obo/UBERON_0007626) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" + +- [anteroventral periventricular nucleus](http://purl.obolibrary.org/obo/UBERON_0002690) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [median preoptic nucleus](http://purl.obolibrary.org/obo/UBERON_0002625) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" + +- [anteroventral periventricular nucleus](http://purl.obolibrary.org/obo/UBERON_0002690) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002219](http://purl.obolibrary.org/obo/UBERON_0002219) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" + +- [anteroventral periventricular nucleus](http://purl.obolibrary.org/obo/UBERON_0002690) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002689](http://purl.obolibrary.org/obo/UBERON_0002689) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" + + + +### antigen-presenting glycoprotein CD1d `http://purl.obolibrary.org/obo/PR_000002028` +#### Removed +- [antigen-presenting glycoprotein CD1d](http://purl.obolibrary.org/obo/PR_000002028) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [antigen-presenting glycoprotein CD1d (human)](http://purl.obolibrary.org/obo/PR_P15813) + + + +### anus `http://purl.obolibrary.org/obo/UBERON_0001245` +#### Removed +- [anus](http://purl.obolibrary.org/obo/UBERON_0001245) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "anal" + +- [anus](http://purl.obolibrary.org/obo/UBERON_0001245) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00047153" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + +- [anus](http://purl.obolibrary.org/obo/UBERON_0001245) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html" + + + +### aorta `http://purl.obolibrary.org/obo/UBERON_0000947` +#### Removed +- [aorta](http://purl.obolibrary.org/obo/UBERON_0000947) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "All amniotes have a broadly similar arrangement to that of humans, albeit with a number of individual variations. In fish, however, there are two separate vessels referred to as aortas. The ventral aorta carries de-oxygenated blood from the heart to the gills; part of this vessel forms the ascending aorta in tetrapods (the remainder forms the pulmonary artery). A second, dorsal aorta carries oxygenated blood from the gills to the rest of the body, and is homologous with the descending aorta of tetrapods. The two aortas are connected by a number of vessels, one passing through each of the gills. Amphibians also retain the fifth connecting vessel, so that the aorta has two parallel arches" + +- [aorta](http://purl.obolibrary.org/obo/UBERON_0000947) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The main artery of the circulatory system which carries oxygenated blood from the heart to all the arteries of the body except those of the lungs.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010213" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + +- [aorta](http://purl.obolibrary.org/obo/UBERON_0000947) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001523" + +- [aorta](http://purl.obolibrary.org/obo/UBERON_0000947) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "aortic" + + + +### aorta collagen fibril `http://purl.obolibrary.org/obo/UBERON_0011861` + +#### Added +- [aorta collagen fibril](http://purl.obolibrary.org/obo/UBERON_0011861) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### aortic sac `http://purl.obolibrary.org/obo/UBERON_0005432` +#### Removed +- [aortic sac](http://purl.obolibrary.org/obo/UBERON_0005432) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "the merged ventral aortae of the embryo which supplies blood to the aortic arches[TMD][http://medical-dictionary.thefreedictionary.com/aortic+sac]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/aortic+sac" + + + +### aortico-pulmonary spiral septum `http://purl.obolibrary.org/obo/UBERON_0006207` + +#### Added +- [aortico-pulmonary spiral septum](http://purl.obolibrary.org/obo/UBERON_0006207) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) + + +### apical ectodermal ridge `http://purl.obolibrary.org/obo/UBERON_0004356` +#### Removed +- [apical ectodermal ridge](http://purl.obolibrary.org/obo/UBERON_0004356) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: subclass proliferative region (TAO:0000098)[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0002146" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [apical ectodermal ridge](http://purl.obolibrary.org/obo/UBERON_0004356) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Proliferative region that is part of the developing fin fold or fin.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0002146" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [apical ectodermal ridge](http://purl.obolibrary.org/obo/UBERON_0004356) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Distal ectodermal thickening which forms along the anterior-posterior limb axis. Signaling from this region influences proximal-distal patterning of the limb. Structure is missing in some lineages (salamanders, Eleutherodactylus coqui) however morphologically their indistinct distal ectoderm may still be involved in signaling.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010760" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + +- [apical ectodermal ridge](http://purl.obolibrary.org/obo/UBERON_0004356) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "note that media, dorsal fins etc have AERs." + +- [apical ectodermal ridge](http://purl.obolibrary.org/obo/UBERON_0004356) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "maintaining mesenchyme in plastic proliferating state; maintaining expression of A-P axis genes; interacting with D-V proteins. Genes: AER induced by Fgf10 in mesenchyme. AER secretes Fgf8, which stimulates mitosis in the mesenchyme causing Fgf10 production - positive feedback loop" + +- [apical ectodermal ridge](http://purl.obolibrary.org/obo/UBERON_0004356) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The AER of tetrapods regresses after specification of skeletal progenitors, the AER of teleosts form an elongating fin fold" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:20574421" + + + +### apocrine gland `http://purl.obolibrary.org/obo/UBERON_0008974` +#### Removed +- [apocrine gland](http://purl.obolibrary.org/obo/UBERON_0008974) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D001050" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + +- [apocrine gland](http://purl.obolibrary.org/obo/UBERON_0008974) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "apocrine" + +- [apocrine gland](http://purl.obolibrary.org/obo/UBERON_0008974) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Mammary glands are modified apocrine glands present in both humans and mice; unlike humans, mice do not have axillary apocrine sweat glands[MGI:anna]" + + + +### apocrine sweat gland `http://purl.obolibrary.org/obo/UBERON_0000382` +#### Removed +- [apocrine sweat gland](http://purl.obolibrary.org/obo/UBERON_0000382) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In humans, apocrine sweat glands are found only in certain locations of the body: the axillae (armpits), the areola of the nipples, and the genitoanal region." + + + +### aponeurosis `http://purl.obolibrary.org/obo/UBERON_0006614` +#### Removed +- [aponeurosis](http://purl.obolibrary.org/obo/UBERON_0006614) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in ZFA, aponeuroses are subtypes of tendons, but this is inconsistent with tendons being muscle-bone connections" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "ZFA" + +- [aponeurosis](http://purl.obolibrary.org/obo/UBERON_0006614) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Aponeuroses are layers of flat broad tendons. They have a shiny, whitish-silvery color, and are histologically similar to tendons, but are very sparingly supplied with blood vessels and nerves. When dissected, aponeuroses are papery, and peel off by sections. The primary regions with thick aponeurosis is in the ventral abdominal region, the dorsal lumbar region, and in the palmar region. Their primary function is to join muscles and the body parts the muscles act upon[Wikipedia:Aponeurosis]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Aponeurosis" + +- [aponeurosis](http://purl.obolibrary.org/obo/UBERON_0006614) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D000070606" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + + + +### appendage `http://purl.obolibrary.org/obo/UBERON_0000026` +#### Removed +- [appendage](http://purl.obolibrary.org/obo/UBERON_0000026) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "this is currently a subtype of organism subdivision - which would exclude feathers" + +- [appendage](http://purl.obolibrary.org/obo/UBERON_0000026) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007000" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + +- [appendage](http://purl.obolibrary.org/obo/UBERON_0000026) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Organ or organ part that is attached to the body of an organism. For example a limb[GO, modified][GO:0048736]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GO:0048736" + +- [appendage](http://purl.obolibrary.org/obo/UBERON_0000026) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "appendicular" + +- [appendage](http://purl.obolibrary.org/obo/UBERON_0000026) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "An appendage is an external body part, or natural prolongation, that protrudes from an organism's body, such as a vertebrate's limbs[BILA][BILA:0000018]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "BILA:0000018" + + + +### appendage girdle complex `http://purl.obolibrary.org/obo/UBERON_0010707` +#### Removed +- [appendage girdle complex](http://purl.obolibrary.org/obo/UBERON_0010707) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical group that consists of the soft and skeletal tissues of the appendicular region of the body and the appendage proper.[VSAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000214" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" + +- [appendage girdle complex](http://purl.obolibrary.org/obo/UBERON_0010707) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "note that the FMA uses the term 'limb' to refer to the entire appendage complex (free limb plus girdle region)" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + +- [appendage girdle complex](http://purl.obolibrary.org/obo/UBERON_0010707) [UBPROP_0000005](http://purl.obolibrary.org/obo/UBPROP_0000005) "It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000214" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-06" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Curator" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" + + + +### appendage girdle region `http://purl.obolibrary.org/obo/UBERON_0007823` +#### Removed +- [appendage girdle region](http://purl.obolibrary.org/obo/UBERON_0007823) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There are only two instances of appendage girdle regions per organism.[VSAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "https://orcid.org/0000-0002-6601-2165" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000303" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" + +- [appendage girdle region](http://purl.obolibrary.org/obo/UBERON_0007823) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "this encompasses non-skeletal tissue" + + + +### appendicular skeletal system `http://purl.obolibrary.org/obo/UBERON_0011249` +#### Removed +- [appendicular skeletal system](http://purl.obolibrary.org/obo/UBERON_0011249) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "VHOG:0001666" + +- [appendicular skeletal system](http://purl.obolibrary.org/obo/UBERON_0011249) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Skeletal system which consists of the appendicular skeleton plus associated joints.[VSAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000306" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "https://orcid.org/0000-0002-6601-2165" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" + + + +### appendicular skeleton `http://purl.obolibrary.org/obo/UBERON_0002091` +#### Removed +- [appendicular skeleton](http://purl.obolibrary.org/obo/UBERON_0002091) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "VHOG:0001666" + +- [appendicular skeleton](http://purl.obolibrary.org/obo/UBERON_0002091) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "ontologies differ in whether they treat the term appendicular skeleton as being the entire set of bones in the limbs, or whether the fore and hind limbs/fins are treated as seperate appendicular skeletons. Here we follow FMA, and treat the appendicular skeleton as the sum total of skeletal elements in the organism (this is evidenced by the fact that in FMA, skeleton of left/right upper/lower limb is part_of a appendicular skeleton, and subtypes of 'subdivision of appendicular skeleton'). We have separate classes such as 'skeleton of limb', and 'skeleton of hindlimb' for the 4 parts of the appendicular skeleton. In future the ZFA/TAO classes may be moved." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + +- [appendicular skeleton](http://purl.obolibrary.org/obo/UBERON_0002091) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The pectoral and pelvic girdles, which articulate with the axial skeleton, together with their associated limbs, the forelimbs and hind limbs, form the appendicular skeleton.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000747" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + +- [appendicular skeleton](http://purl.obolibrary.org/obo/UBERON_0002091) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Skeletal subdivision consisting of all the skeletal elements in the pectoral and pelvic appendage complexes.[VSAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "https://orcid.org/0000-0002-6601-2165" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000076" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PSPUB:0000170" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" + +- [appendicular skeleton](http://purl.obolibrary.org/obo/UBERON_0002091) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Skeletal system that consists of the paired fins (pectoral or pelvic fins).[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000027" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TAO:wd" + + + +### aqueous drainage system `http://purl.obolibrary.org/obo/UBERON_0003956` + +#### Added +- [aqueous drainage system](http://purl.obolibrary.org/obo/UBERON_0003956) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### aqueous humor of eyeball `http://purl.obolibrary.org/obo/UBERON_0001796` +#### Removed +- [aqueous humor of eyeball](http://purl.obolibrary.org/obo/UBERON_0001796) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424 and p.426 and p.429 and Figure 12-24" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000548" + +- [aqueous humor of eyeball](http://purl.obolibrary.org/obo/UBERON_0001796) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA says A+P chambers, and MA states A chamber. ZFA states A chamber and tha it is produced primarily by dorsal ciliary epithelial cells.To be investigated across taxa." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + +- [aqueous humor of eyeball](http://purl.obolibrary.org/obo/UBERON_0001796) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The fluid produced by the ciliary process in the eye and occupying the anterior and posterior chambers. It provides nourishment for the lens and cornea and maintains the ocular pressure, and hence the optical integrity of the eyeball. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000548" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/aqueous+humour" + +- [aqueous humor of eyeball](http://purl.obolibrary.org/obo/UBERON_0001796) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [anterior chamber of eyeball](http://purl.obolibrary.org/obo/UBERON_0001766) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "FMA def states A and P" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "VHOG" + + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "located_in in EHDAA2" + +#### Added +- [aqueous humor of eyeball](http://purl.obolibrary.org/obo/UBERON_0001796) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [anterior chamber of eyeball](http://purl.obolibrary.org/obo/UBERON_0001766) + + +### arachnoid barrier layer `http://purl.obolibrary.org/obo/UBERON_0000437` + +#### Added +- [arachnoid barrier layer](http://purl.obolibrary.org/obo/UBERON_0000437) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + +- [arachnoid barrier layer](http://purl.obolibrary.org/obo/UBERON_0000437) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) + + +### arachnoid mater `http://purl.obolibrary.org/obo/UBERON_0002362` +#### Removed +- [arachnoid mater](http://purl.obolibrary.org/obo/UBERON_0002362) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [vasculature](http://purl.obolibrary.org/obo/UBERON_0002049) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0471888893" + + + +### arachnoid trabecula `http://purl.obolibrary.org/obo/UBERON_0000439` + +#### Added +- [arachnoid trabecula](http://purl.obolibrary.org/obo/UBERON_0000439) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) + + +### arch of aorta `http://purl.obolibrary.org/obo/UBERON_0001508` +#### Removed +- [arch of aorta](http://purl.obolibrary.org/obo/UBERON_0001508) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "birds have right aortic arch, mammals left." + +- [arch of aorta](http://purl.obolibrary.org/obo/UBERON_0001508) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The curving portion between the ascending aorta and the descending aorta, giving rise to the brachiocephalic trunk, the left common carotid artery, and the left subclavian artery. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/arch+of+aorta" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001196" + +- [arch of aorta](http://purl.obolibrary.org/obo/UBERON_0001508) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "Do not confuse with aortic arch" + +- [arch of aorta](http://purl.obolibrary.org/obo/UBERON_0001508) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The double systemic arch arches (left and right) present in amphibians and reptiles become reduced to a single systemic arch - the right in birds, the left in mammals.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001196" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.460 and p.461 Figure 12.20" + +- [arch of aorta](http://purl.obolibrary.org/obo/UBERON_0001508) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [pharyngeal arch artery 4](http://purl.obolibrary.org/obo/UBERON_0003121) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "embryology.ch" + + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "left arch 4 in human" + +#### Added +- [arch of aorta](http://purl.obolibrary.org/obo/UBERON_0001508) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [pharyngeal arch artery 4](http://purl.obolibrary.org/obo/UBERON_0003121) + + +### arch of centrum of vertebra `http://purl.obolibrary.org/obo/UBERON_0010358` +#### Removed +- [arch of centrum of vertebra](http://purl.obolibrary.org/obo/UBERON_0010358) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "Note that humans do not have hemal arches, so VA=NA for FMA" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + +- [arch of centrum of vertebra](http://purl.obolibrary.org/obo/UBERON_0010358) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) certain common components [of vertebral structure] are found in nearly all vertebrate. A representative vertebra has a vertebral arch or neural arch, which extends dorsally around the spinal cord.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.270" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001670" + +- [arch of centrum of vertebra](http://purl.obolibrary.org/obo/UBERON_0010358) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:11946" + + + +### arcuate nucleus of hypothalamus `http://purl.obolibrary.org/obo/UBERON_0001932` +#### Removed +- [arcuate nucleus of hypothalamus](http://purl.obolibrary.org/obo/UBERON_0001932) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "the semantics of the BTO class arcuate nucleus are not clear" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "BTO" + +- [arcuate nucleus of hypothalamus](http://purl.obolibrary.org/obo/UBERON_0001932) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0001929](http://purl.obolibrary.org/obo/UBERON_0001929) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" + +- [arcuate nucleus of hypothalamus](http://purl.obolibrary.org/obo/UBERON_0001932) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [paraventricular nucleus of hypothalamus](http://purl.obolibrary.org/obo/UBERON_0001930) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" + + + +### areolar connective tissue `http://purl.obolibrary.org/obo/UBERON_0006815` +#### Removed +- [areolar connective tissue](http://purl.obolibrary.org/obo/UBERON_0006815) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "cushions body organs" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO" + +- [areolar connective tissue](http://purl.obolibrary.org/obo/UBERON_0006815) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Also known as loose connective tissue. A pliable, mesh-like tissue with a fluid matrix that functions to cushion and protect body organs.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000027" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + +- [areolar connective tissue](http://purl.obolibrary.org/obo/UBERON_0006815) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: subclass connective tissue proper (AAO:0000099)[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000027" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + + +### arginase-1 `http://purl.obolibrary.org/obo/PR_000001844` +#### Removed +- [arginase-1](http://purl.obolibrary.org/obo/PR_000001844) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [arginase-1 (human)](http://purl.obolibrary.org/obo/PR_P05089) + + + +### arm `http://purl.obolibrary.org/obo/UBERON_0001460` +#### Removed +- [arm](http://purl.obolibrary.org/obo/UBERON_0001460) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "this class refers to the combination of the stylopod and zeugopod of a forelimb. Sometimes (cf FMA), 'arm' denotes the stylopod only; sometimes (cf MA), 'arm' denotes the part of the forelimb covering both (i.e. shoulder to hand). Also note distinction between arm and forelimb: hand is part of forelimb, but not part of arm" + +- [arm](http://purl.obolibrary.org/obo/UBERON_0001460) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000339" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268" + + + +### arm bone `http://purl.obolibrary.org/obo/UBERON_0003460` +#### Removed +- [arm bone](http://purl.obolibrary.org/obo/UBERON_0003460) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D050280" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + + + +### arrector muscle of hair `http://purl.obolibrary.org/obo/UBERON_0002033` +#### Removed +- [arrector muscle of hair](http://purl.obolibrary.org/obo/UBERON_0002033) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "When contracted the arrector pili causes the raising of the hair" + + + +### arterial blood `http://purl.obolibrary.org/obo/UBERON_0013755` +#### Removed +- [arterial blood](http://purl.obolibrary.org/obo/UBERON_0013755) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006188" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + + - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) + + + +### arterial system `http://purl.obolibrary.org/obo/UBERON_0004572` +#### Removed +- [arterial system](http://purl.obolibrary.org/obo/UBERON_0004572) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000273" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005)" + + + +### arteriole `http://purl.obolibrary.org/obo/UBERON_0001980` +#### Removed +- [arteriole](http://purl.obolibrary.org/obo/UBERON_0001980) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Multi-tissue structure part of the blood vasculature, feeds into capillaries. Arterioles carry blood away from the heart.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0002138" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [arteriole](http://purl.obolibrary.org/obo/UBERON_0001980) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Small, terminal branch of an artery which generally connects to capillaries.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010253" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + + + +### artery `http://purl.obolibrary.org/obo/UBERON_0001637` +#### Removed +- [artery](http://purl.obolibrary.org/obo/UBERON_0001637) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "arterial" + +- [artery](http://purl.obolibrary.org/obo/UBERON_0001637) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "Some arthropods have primitive arterial systems but this term refers to arteries in a true closed circulatory system." + +- [artery](http://purl.obolibrary.org/obo/UBERON_0001637) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EHDAA2:0000143" + +- [artery](http://purl.obolibrary.org/obo/UBERON_0001637) [UBPROP_0000202](http://purl.obolibrary.org/obo/UBPROP_0000202) [FMA_63812](http://purl.obolibrary.org/obo/FMA_63812) + +- [artery](http://purl.obolibrary.org/obo/UBERON_0001637) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Part of the circulatory system composed of blood vessels which carry oxygenated blood away from the heart to the rest of the body.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010211" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + +- [artery](http://purl.obolibrary.org/obo/UBERON_0001637) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001251" + + + +### arthropod sensillum `http://purl.obolibrary.org/obo/UBERON_0002536` +#### Removed +- [arthropod sensillum](http://purl.obolibrary.org/obo/UBERON_0002536) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007152" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + + +### arthropod tagma `http://purl.obolibrary.org/obo/UBERON_6000002` +#### Removed +- [arthropod tagma](http://purl.obolibrary.org/obo/UBERON_6000002) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000002" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + + +### articular capsule `http://purl.obolibrary.org/obo/UBERON_0001484` +#### Removed +- [articular capsule](http://purl.obolibrary.org/obo/UBERON_0001484) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "check ncita" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "ncit" + + + +### articulation `http://purl.obolibrary.org/obo/UBERON_0004905` +#### Removed +- [articulation](http://purl.obolibrary.org/obo/UBERON_0004905) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005811" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + + +### ascending colon `http://purl.obolibrary.org/obo/UBERON_0001156` +#### Removed +- [ascending colon](http://purl.obolibrary.org/obo/UBERON_0001156) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in MA, this is a subclass of colon" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" + +- [ascending colon](http://purl.obolibrary.org/obo/UBERON_0001156) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D044682" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + + + +### atlanto-occipital joint `http://purl.obolibrary.org/obo/UBERON_0000220` +#### Removed +- [atlanto-occipital joint](http://purl.obolibrary.org/obo/UBERON_0000220) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D001269" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + + + +### atrioventricular node `http://purl.obolibrary.org/obo/UBERON_0002352` +#### Removed +- [atrioventricular node](http://purl.obolibrary.org/obo/UBERON_0002352) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Three major adaptations, or 'novel cardiac components', that were not present in the ancestor chordate heart tube can be distinguished in the lower vertebrate heart: the atrium, ventricle, and possibly the muscular sinus venosus. Furthermore, within the ventricular component a compact outer myocardial component and an interiorly localized extensive trabecular component can be distinguished. The specific activation of the ventricle adds to its complexity as follows. The depolarizing impulse travels rapidly from the atrioventricular node toward the apex and then toward the conal region, achieving activation from apex to base.[uncertain][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001474" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1152/physrev.00006.2003 Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003)" + + + +### atrioventricular region `http://purl.obolibrary.org/obo/UBERON_0011820` + +#### Added +- [atrioventricular region](http://purl.obolibrary.org/obo/UBERON_0011820) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### atrium myocardial trabecula `http://purl.obolibrary.org/obo/UBERON_0005988` + +#### Added +- [atrium myocardial trabecula](http://purl.obolibrary.org/obo/UBERON_0005988) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### attached to `http://purl.obolibrary.org/obo/RO_0002371` +#### Removed +- [attached to](http://purl.obolibrary.org/obo/RO_0002371) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "attaches_to" + +- [attached to](http://purl.obolibrary.org/obo/RO_0002371) [label](http://www.w3.org/2000/01/rdf-schema#label) "attached to" + +- [attached to](http://purl.obolibrary.org/obo/RO_0002371) [id](http://www.geneontology.org/formats/oboInOwl#id) "attaches_to" + +- [attached to](http://purl.obolibrary.org/obo/RO_0002371) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [attached to](http://purl.obolibrary.org/obo/RO_0002371) [IAO_0000589](http://purl.obolibrary.org/obo/IAO_0000589) "attached to (anatomical structure to anatomical structure)" + +- [attached to](http://purl.obolibrary.org/obo/RO_0002371) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002371" + +- [attached to](http://purl.obolibrary.org/obo/RO_0002371) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + + + +### attached to part of `http://purl.obolibrary.org/obo/RO_0002177` +#### Removed +- [attached to part of](http://purl.obolibrary.org/obo/RO_0002177) [IAO_0000589](http://purl.obolibrary.org/obo/IAO_0000589) "attached to part of (anatomical structure to anatomical structure)" + +- [attached to part of](http://purl.obolibrary.org/obo/RO_0002177) [id](http://www.geneontology.org/formats/oboInOwl#id) "attaches_to_part_of" + +- [attached to part of](http://purl.obolibrary.org/obo/RO_0002177) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "attaches_to_part_of" + +- [attached to part of](http://purl.obolibrary.org/obo/RO_0002177) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002177" + +- [attached to part of](http://purl.obolibrary.org/obo/RO_0002177) [label](http://www.w3.org/2000/01/rdf-schema#label) "attached to part of" + +- [attached to part of](http://purl.obolibrary.org/obo/RO_0002177) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [attached to](http://purl.obolibrary.org/obo/RO_0002371) o [part_of](http://purl.obolibrary.org/obo/BFO_0000050) SubPropertyOf: [attached to part of](http://purl.obolibrary.org/obo/RO_0002177) + - [is a defining property chain axiom where second argument is reflexive](http://purl.obolibrary.org/obo/RO_0002582) true + + + +### auditory meatus epithelium `http://purl.obolibrary.org/obo/UBERON_0010065` + +#### Added +- [auditory meatus epithelium](http://purl.obolibrary.org/obo/UBERON_0010065) SubClassOf [endo-epithelium](http://purl.obolibrary.org/obo/UBERON_0005911) + +- [auditory meatus epithelium](http://purl.obolibrary.org/obo/UBERON_0010065) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) + + +### auditory ossicle bone `http://purl.obolibrary.org/obo/UBERON_0001686` +#### Removed +- [auditory ossicle bone](http://purl.obolibrary.org/obo/UBERON_0001686) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The small bones of the middle ear: incus, malleus, and stapes. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/auditory+ossicles" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000461" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + +- [auditory ossicle bone](http://purl.obolibrary.org/obo/UBERON_0001686) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Additional structural analysis within a phylogenetic context has led to the remarkable discovery that in synapsids, thought to be ancestral to mammals, both the quadrate and articular have become reduced and less firmly articulated with their surrounding bones, reducing their jaw-joint-bearing role. This trend culminated with the incorporation of the quadrate, the columella (which remains articulated with the quadrate), and the articular into the expanded middle ear in mammals.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.695" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000461" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + +- [auditory ossicle bone](http://purl.obolibrary.org/obo/UBERON_0001686) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "Studies have shown that ear bones in mammal embryos are attached to the dentary, which is part of the jaw. These are ossified portions of cartilage -- called Meckel's cartilage -- that are attached to the jaw. As the embryo develops, the cartilage hardens to form bone. Later in development, the bone structure breaks loose from the jaw and migrates to the inner ear area. The structure is known as the middle ear, and is made up of the incus, stapes, malleus, and tympanic membrane. These correspond to the quadrate, prearticular, articular, and angular structures in the reptile jaw. For this reason, researchers believe the similarity of the results shows that mammals and reptiles have a common ancestry." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" + + + +### auditory ossicle endochondral element `http://purl.obolibrary.org/obo/UBERON_0035130` + +#### Added +- [auditory ossicle endochondral element](http://purl.obolibrary.org/obo/UBERON_0035130) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) + + +### auditory system `http://purl.obolibrary.org/obo/UBERON_0016490` +#### Removed +- [auditory system](http://purl.obolibrary.org/obo/UBERON_0016490) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "Auditory system is general anatomical term in FMA" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + + + +### author_id `https://w3id.org/sssom/author_id` +#### Removed +- AnnotationProperty: [author_id](https://w3id.org/sssom/author_id) + + + +### autonomic ganglion `http://purl.obolibrary.org/obo/UBERON_0001805` +#### Removed +- [autonomic ganglion](http://purl.obolibrary.org/obo/UBERON_0001805) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:17157" + + + +### autonomic nerve `http://purl.obolibrary.org/obo/UBERON_0034728` +#### Removed +- [autonomic nerve](http://purl.obolibrary.org/obo/UBERON_0034728) SubClassOf [nerve](http://purl.obolibrary.org/obo/UBERON_0001021) + +#### Added +- [autonomic nerve](http://purl.obolibrary.org/obo/UBERON_0034728) SubClassOf [nerve of head region](http://purl.obolibrary.org/obo/UBERON_0011779) + + +### autonomic nervous system `http://purl.obolibrary.org/obo/UBERON_0002410` +#### Removed +- [autonomic nervous system](http://purl.obolibrary.org/obo/UBERON_0002410) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Nervous system including a portion of the central and peripheral systems and presiding over the control and coordination of the vegetative functions of the organism. It innervates smooth and cardiac muscles and glandular tissues and is responsible for many actions which are more or less automatic (e.g. secretion, vasoconstriction etc.). It consists of the sympathetic and parasympathetic nervous systems. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000396" + +- [autonomic nervous system](http://purl.obolibrary.org/obo/UBERON_0002410) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "From comparative analyses of craniate brains, a morphotype of the brain in the earliest craniate stock can be constructed. In marked contrast to cephalochordates, the ancestral craniate morphotype had a plethora of unique features, which included a telencephalon with pallial and subpallial parts, paired olfactory bulbs with substantial projections to most or all of the telencephalic pallium, paired lateral eyes and ears, a lateral line system for both electroreception and mechanoreception, spinal cord dorsal root ganglia, and an autonomic nervous system.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000396" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1002/1097-0185(20000615)261:3<111::AID-AR6>3.0.CO;2-F Butler AB, Chordate evolution and the origin of craniates: An old brain in a new head. AnaT Rec (New Anat) (2000)" + +- [autonomic nervous system](http://purl.obolibrary.org/obo/UBERON_0002410) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Part of the peripheral nervous system which regulates involuntary functions of the body and consists of the sympathetic and parasympathetic system.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000033" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + +- [autonomic nervous system](http://purl.obolibrary.org/obo/UBERON_0002410) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA splits this into peripheral and nervous parts; GO has ANS directly under NS; PNS is a sib" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + +- [autonomic nervous system](http://purl.obolibrary.org/obo/UBERON_0002410) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "IDOMAL:0002126" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + + + +### autopod bone `http://purl.obolibrary.org/obo/UBERON_0011250` +#### Removed +- [autopod bone](http://purl.obolibrary.org/obo/UBERON_0011250) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) + + + +### autopod cartilage `http://purl.obolibrary.org/obo/UBERON_0015064` +#### Removed +- [autopod cartilage](http://purl.obolibrary.org/obo/UBERON_0015064) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) [Skeleton-partonomy-Design-Pattern](https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern) + + + +### autopod endochondral element `http://purl.obolibrary.org/obo/UBERON_0015063` +#### Removed +- [autopod endochondral element](http://purl.obolibrary.org/obo/UBERON_0015063) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) [Skeleton-partonomy-Design-Pattern](https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern) + + + +### autopod region `http://purl.obolibrary.org/obo/UBERON_0002470` +#### Removed +- [autopod region](http://purl.obolibrary.org/obo/UBERON_0002470) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "Naming conventions for pod terms under discussion within phenoscape group; note that this refers to the limb segment, not just the skeleton." + +- [autopod region](http://purl.obolibrary.org/obo/UBERON_0002470) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [embryonic autopod plate](http://purl.obolibrary.org/obo/UBERON_0010130) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" + +#### Added +- [autopod region](http://purl.obolibrary.org/obo/UBERON_0002470) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [embryonic autopod plate](http://purl.obolibrary.org/obo/UBERON_0010130) + + +### autopodial skeleton `http://purl.obolibrary.org/obo/UBERON_0006717` +#### Removed +- [autopodial skeleton](http://purl.obolibrary.org/obo/UBERON_0006717) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "Naming conventions for pod terms under discussion within phenoscape group" + +- [autopodial skeleton](http://purl.obolibrary.org/obo/UBERON_0006717) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Distal section of the limb skeleton, consisting of the anterior autopodium or posterior autopodium.[VSAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "VSAO:NI" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0005019" + +#### Added +- [autopodial skeleton](http://purl.obolibrary.org/obo/UBERON_0006717) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### axial mesoderm `http://purl.obolibrary.org/obo/UBERON_0003068` +#### Removed +- [axial mesoderm](http://purl.obolibrary.org/obo/UBERON_0003068) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000107" + + + +### axial skeleton plus cranial skeleton `http://purl.obolibrary.org/obo/UBERON_0005944` +#### Removed +- [axial skeleton plus cranial skeleton](http://purl.obolibrary.org/obo/UBERON_0005944) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:18043" + +- [axial skeleton plus cranial skeleton](http://purl.obolibrary.org/obo/UBERON_0005944) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000056" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PSPUB:0000170" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" + + + +### axial vasculature `http://purl.obolibrary.org/obo/UBERON_2001073` +#### Removed +- [axial vasculature](http://purl.obolibrary.org/obo/UBERON_2001073) [UBPROP_0000004](http://purl.obolibrary.org/obo/UBPROP_0000004) "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://purl.obolibrary.org/obo/tao.owl" + + + +### axilla `http://purl.obolibrary.org/obo/UBERON_0009472` +#### Removed +- [axilla](http://purl.obolibrary.org/obo/UBERON_0009472) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "axillary" + + + +### axillary artery `http://purl.obolibrary.org/obo/UBERON_0001394` +#### Removed +- [axillary artery](http://purl.obolibrary.org/obo/UBERON_0001394) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In human anatomy, the axillary artery is a large blood vessel that conveys oxygenated blood to the lateral aspect of the thorax, the axilla (armpit) and the upper limb. Its origin is at the lateral margin of the first rib, before which it is called the subclavian artery. After passing the lower margin of teres major it becomes the brachial artery." + + + +### axillary vein `http://purl.obolibrary.org/obo/UBERON_0000985` +#### Removed +- [axillary vein](http://purl.obolibrary.org/obo/UBERON_0000985) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In human anatomy, the axillary vein is a large blood vessel that conveys blood from the lateral aspect of the thorax, axilla (armpit) and upper limb toward the heart. There is one axillary vein on each side of the body. Its origin is at the lower margin of the teres major muscle and a continuation of the brachial vein. Its tributaries include the basilic vein and cephalic vein, which are both superficial veins. It terminates at the lateral margin of the first rib, at which it becomes the subclavian vein. It is accompanied along its course by a similarly named artery, the axillary artery" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" + + + +### axon synapses in `http://purl.obolibrary.org/obo/RO_0002102` +#### Removed +- [axon synapses in](http://purl.obolibrary.org/obo/RO_0002102) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) + +- [axon synapses in](http://purl.obolibrary.org/obo/RO_0002102) [citesAsAuthority](http://purl.org/spar/cito/citesAsAuthority) [22402613](http://www.ncbi.nlm.nih.gov/pubmed/22402613) + +- [axon synapses in](http://purl.obolibrary.org/obo/RO_0002102) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [axon synapses in](http://purl.obolibrary.org/obo/RO_0002102) [RO_0001900](http://purl.obolibrary.org/obo/RO_0001900) [RO_0001901](http://purl.obolibrary.org/obo/RO_0001901) + +- [axon synapses in](http://purl.obolibrary.org/obo/RO_0002102) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-7073-9172](https://orcid.org/0000-0002-7073-9172) + + + +### axon tract `http://purl.obolibrary.org/obo/UBERON_0001018` +#### Removed +- [axon tract](http://purl.obolibrary.org/obo/UBERON_0001018) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "White matter structure of CNS that contains axons that arise predominantly in one central nervous system part and terminate in another. Tracts are generally named by their region or origin followed by their region of primary termination, e.g., mammillothalamic tract contains axons that arise from neurons in the mammillary bodies and terminate in the thalamus. (CUMBO)" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://neurolex.org/wiki/Cumbo_terms" + +- [axon tract](http://purl.obolibrary.org/obo/UBERON_0001018) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005100" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + + +### basal forebrain `http://purl.obolibrary.org/obo/UBERON_0002743` +#### Removed +- [basal forebrain](http://purl.obolibrary.org/obo/UBERON_0002743) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D066187" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + + + +### basal nuclear complex `http://purl.obolibrary.org/obo/UBERON_0006098` +#### Removed +- [basal nuclear complex](http://purl.obolibrary.org/obo/UBERON_0006098) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D001479" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + + + +### basal plate metencephalon `http://purl.obolibrary.org/obo/UBERON_0005239` +#### Removed +- [basal plate metencephalon](http://purl.obolibrary.org/obo/UBERON_0005239) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The ventral half of the developing neural tube that is the metencephalon. [Chordate_evolution_and_the_origin_of_craniates:_An_old_brain_in_a_new_head._AnaT_Rec_(New_Anat)_(2000)_261(3):_111-125, See_Butler_AB][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000320" + + + +### basement membrane of epithelium `http://purl.obolibrary.org/obo/UBERON_0005769` +#### Removed +- [basement membrane of epithelium](http://purl.obolibrary.org/obo/UBERON_0005769) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell." + + + +### basicranium `http://purl.obolibrary.org/obo/UBERON_0002517` +#### Removed +- [basicranium](http://purl.obolibrary.org/obo/UBERON_0002517) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "basicranial" + + + +### bearer of `http://purl.obolibrary.org/obo/RO_0000053` +#### Removed +- [bearer of](http://purl.obolibrary.org/obo/RO_0000053) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "this apple is bearer of this red color"@en + +- [bearer of](http://purl.obolibrary.org/obo/RO_0000053) [RO_0001900](http://purl.obolibrary.org/obo/RO_0001900) [RO_0001901](http://purl.obolibrary.org/obo/RO_0001901) + +- [bearer of](http://purl.obolibrary.org/obo/RO_0000053) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "this vase is bearer of this fragility"@en + +- [bearer of](http://purl.obolibrary.org/obo/RO_0000053) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "bearer_of"@en + +- [bearer of](http://purl.obolibrary.org/obo/RO_0000053) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "bearer of"@en + +- [bearer of](http://purl.obolibrary.org/obo/RO_0000053) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "is bearer of"@en + + + +### before or simultaneous with `http://purl.obolibrary.org/obo/RO_0002081` +#### Removed +- [before or simultaneous with](http://purl.obolibrary.org/obo/RO_0002081) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) "David Osumi-Sutherland" + +- [before or simultaneous with](http://purl.obolibrary.org/obo/RO_0002081) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "<="@en + + + +### bestrophin-4 `http://purl.obolibrary.org/obo/PR_000004724` +#### Removed +- [bestrophin-4](http://purl.obolibrary.org/obo/PR_000004724) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [bestrophin-4 (human)](http://purl.obolibrary.org/obo/PR_Q8NFU0) + + + +### biconcave `http://purl.obolibrary.org/obo/PATO_0002039` +#### Removed +- [biconcave](http://purl.obolibrary.org/obo/PATO_0002039) [RO_0002604](http://purl.obolibrary.org/obo/RO_0002604) [PATO_0002040](http://purl.obolibrary.org/obo/PATO_0002040) + + + +### bile `http://purl.obolibrary.org/obo/UBERON_0001970` +#### Removed +- [bile](http://purl.obolibrary.org/obo/UBERON_0001970) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "elimination of cholesterol" + +- [bile](http://purl.obolibrary.org/obo/UBERON_0001970) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "major excretory route for potentially harmful exogenous lipophilic substances" + +- [bile](http://purl.obolibrary.org/obo/UBERON_0001970) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "protects the organism from enteric infections by excreting immune globulin A (IgA), inflammatory cytokines, and stimulating the innate immune system in the intestine" + +- [bile](http://purl.obolibrary.org/obo/UBERON_0001970) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "many hormones and pheromones are excreted in bile, and contribute to growth and development of the intestine in some species and provide attractants for the weaning of non-human vertebrates" + +- [bile](http://purl.obolibrary.org/obo/UBERON_0001970) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "aids the process of digestion of lipids in the small intestine" + +- [bile](http://purl.obolibrary.org/obo/UBERON_0001970) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In many species, bile is stored in the gallbladder and upon eating is discharged into the duodenum." + +- [bile](http://purl.obolibrary.org/obo/UBERON_0001970) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "bile salts function to emulsify dietary fats and facilitate their intestinal absorption" + +- [bile](http://purl.obolibrary.org/obo/UBERON_0001970) SubClassOf [has part](http://purl.obolibrary.org/obo/BFO_0000051) some [CHEBI_16990](http://purl.obolibrary.org/obo/CHEBI_16990) + - [composition](http://www.geneontology.org/formats/oboInOwl#composition) "0.3% in humans" + +#### Added +- [bile](http://purl.obolibrary.org/obo/UBERON_0001970) SubClassOf [has part](http://purl.obolibrary.org/obo/BFO_0000051) some [CHEBI_16990](http://purl.obolibrary.org/obo/CHEBI_16990) + + +### bile duct `http://purl.obolibrary.org/obo/UBERON_0002394` +#### Removed +- [bile duct](http://purl.obolibrary.org/obo/UBERON_0002394) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "we place the ZFA class here as this fits its textual definition and child nodes. We may recommend a label change for ZFA" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "ZFA" + +- [bile duct](http://purl.obolibrary.org/obo/UBERON_0002394) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A duct that carries bile from the liver to the intestine." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFA:0001100, ZFA:curator" + +- [bile duct](http://purl.obolibrary.org/obo/UBERON_0002394) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EHDAA2:0000741" + +- [bile duct](http://purl.obolibrary.org/obo/UBERON_0002394) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) the amphibian liver has characteristics in common with both fish and terrestrial vertebrates. (...) The histological structure of the liver is similar to that in other vertebrates, with hepatocytes arranged in clusters and cords separated by a meshwork of sinusoids and the presence of the traditional triad of portal venule, hepatic arteriole, and bile duct.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1053/ax.2000.7133 Crawshaw GJ, Weinkle TK, Clinical and pathological aspects of the amphibian liver. Seminars in Avian and Exotic Pet Medicine (2000)" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000212" + +- [bile duct](http://purl.obolibrary.org/obo/UBERON_0002394) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Any of the excretory ducts in the liver that convey bile between the liver and the intestine. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/bile+duct" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000212" + + + +### bile duct epithelium `http://purl.obolibrary.org/obo/UBERON_0004820` +#### Removed +- [bile duct epithelium](http://purl.obolibrary.org/obo/UBERON_0004820) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The irregularly shaped proliferating bile ducts are lined by normal cuboidal epithelium." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "BTO:0000417" + +#### Added +- [bile duct epithelium](http://purl.obolibrary.org/obo/UBERON_0004820) SubClassOf [endo-epithelium](http://purl.obolibrary.org/obo/UBERON_0005911) + + +### biliary ductule `http://purl.obolibrary.org/obo/UBERON_0004058` +#### Removed +- [biliary ductule](http://purl.obolibrary.org/obo/UBERON_0004058) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "In ZFA, Digestive system duct that collects bile from the canaliculus and transports bile through the liver -- (check if the same) // The smallest and the most peripheral branches of the biliary tree consist of a portal part (portal ductule) and an intralobular part (intralobular ductule)" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "ZFA" + +#### Added +- [biliary ductule](http://purl.obolibrary.org/obo/UBERON_0004058) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) + + +### biliary system `http://purl.obolibrary.org/obo/UBERON_0002294` +#### Removed +- [biliary system](http://purl.obolibrary.org/obo/UBERON_0002294) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [liver stroma](http://purl.obolibrary.org/obo/UBERON_0016478) + + + +### biliary tree `http://purl.obolibrary.org/obo/UBERON_0001173` +#### Removed +- [biliary tree](http://purl.obolibrary.org/obo/UBERON_0001173) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D001659" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + +- [biliary tree](http://purl.obolibrary.org/obo/UBERON_0001173) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [gallbladder](http://purl.obolibrary.org/obo/UBERON_0002110) + +- [biliary tree](http://purl.obolibrary.org/obo/UBERON_0001173) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Hollow tree organ, the organ parts of which consist of the bile ducts.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0011020" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "UBERON:0001173" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + + +### biomechanically related to `http://purl.obolibrary.org/obo/RO_0002567` +#### Removed +- [biomechanically related to](http://purl.obolibrary.org/obo/RO_0002567) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [biomechanically related to](http://purl.obolibrary.org/obo/RO_0002567) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." + + + +### blood `http://purl.obolibrary.org/obo/UBERON_0000178` +#### Removed +- [blood](http://purl.obolibrary.org/obo/UBERON_0000178) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid." + +- [blood](http://purl.obolibrary.org/obo/UBERON_0000178) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000046" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + +- [blood](http://purl.obolibrary.org/obo/UBERON_0000178) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006) " + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000224" + +- [blood](http://purl.obolibrary.org/obo/UBERON_0000178) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000046" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + +- [blood](http://purl.obolibrary.org/obo/UBERON_0000178) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000007" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + + +### blood brain barrier `http://purl.obolibrary.org/obo/UBERON_0000120` +#### Removed +- [blood brain barrier](http://purl.obolibrary.org/obo/UBERON_0000120) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D001812" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + + + +### blood island `http://purl.obolibrary.org/obo/UBERON_0003061` +#### Removed +- [blood island](http://purl.obolibrary.org/obo/UBERON_0003061) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EHDAA2" + +- [blood island](http://purl.obolibrary.org/obo/UBERON_0003061) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0011006" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + +- [blood island](http://purl.obolibrary.org/obo/UBERON_0003061) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000094" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [blood island](http://purl.obolibrary.org/obo/UBERON_0003061) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450, DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual Review of Cell and Developmental Biology (2006)" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000085" + +- [blood island](http://purl.obolibrary.org/obo/UBERON_0003061) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000094" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + + +### blood microvessel `http://purl.obolibrary.org/obo/UBERON_8410081` +#### Removed +- [blood microvessel](http://purl.obolibrary.org/obo/UBERON_8410081) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "microvascular" + + + +### blood nerve barrier `http://purl.obolibrary.org/obo/UBERON_0003209` +#### Removed +- [blood nerve barrier](http://purl.obolibrary.org/obo/UBERON_0003209) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D049428" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + + + +### blood vessel `http://purl.obolibrary.org/obo/UBERON_0001981` +#### Removed +- [blood vessel](http://purl.obolibrary.org/obo/UBERON_0001981) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001250" + +- [blood vessel](http://purl.obolibrary.org/obo/UBERON_0001981) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001250" + +- [blood vessel](http://purl.obolibrary.org/obo/UBERON_0001981) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "annelids have blood vessels, but this class is not applicable to annelids." + +- [blood vessel](http://purl.obolibrary.org/obo/UBERON_0001981) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + +- [blood vessel](http://purl.obolibrary.org/obo/UBERON_0001981) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Any of the vessels through which blood circulates in the body.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0011004" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + +#### Added +- [blood vessel](http://purl.obolibrary.org/obo/UBERON_0001981) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### blood vessel elastic tissue `http://purl.obolibrary.org/obo/UBERON_0003614` + +#### Added +- [blood vessel elastic tissue](http://purl.obolibrary.org/obo/UBERON_0003614) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### blood vessel layer `http://purl.obolibrary.org/obo/UBERON_0004797` + +#### Added +- [blood vessel layer](http://purl.obolibrary.org/obo/UBERON_0004797) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### blood vessel smooth muscle `http://purl.obolibrary.org/obo/UBERON_0004237` +#### Removed +- [blood vessel smooth muscle](http://purl.obolibrary.org/obo/UBERON_0004237) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "Vascular smooth muscle contracts or relaxes to both change the volume of blood vessels and the local blood pressure, a mechanism that is responsible for the redistribution of the blood within the body to areas where it is needed (i.e. areas with temporarily enhanced oxygen consumption). Thus the main function of vascular smooth muscle tonus is to regulate the caliber of the blood vessels in the body. Excessive vasoconstriction leads to hypertension, while excessive vasodilation as in shock leads to hypotension." + + + +### blood-cerebrospinal fluid barrier `http://purl.obolibrary.org/obo/UBERON_0003210` + +#### Added +- [blood-cerebrospinal fluid barrier](http://purl.obolibrary.org/obo/UBERON_0003210) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### body external integument structure `http://purl.obolibrary.org/obo/UBERON_3000977` +#### Removed +- [body external integument structure](http://purl.obolibrary.org/obo/UBERON_3000977) [UBPROP_0000004](http://purl.obolibrary.org/obo/UBPROP_0000004) "This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://purl.obolibrary.org/obo/aao.owl" + + + +### body proper `http://purl.obolibrary.org/obo/UBERON_0013702` +#### Removed +- [body proper](http://purl.obolibrary.org/obo/UBERON_0013702) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:36031" + +- [body proper](http://purl.obolibrary.org/obo/UBERON_0013702) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:231424" + + + +### body wall `http://purl.obolibrary.org/obo/UBERON_0000309` +#### Removed +- [body wall](http://purl.obolibrary.org/obo/UBERON_0000309) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "the BTO class refers to earthworms." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "BTO" + +- [body wall](http://purl.obolibrary.org/obo/UBERON_0000309) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "defined generically to encompass both vertebrates and invertebrates" + + + +### bone element `http://purl.obolibrary.org/obo/UBERON_0001474` +#### Removed +- [bone element](http://purl.obolibrary.org/obo/UBERON_0001474) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000047" + +- [bone element](http://purl.obolibrary.org/obo/UBERON_0001474) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [muscle tissue](http://purl.obolibrary.org/obo/UBERON_0002385) + +- [bone element](http://purl.obolibrary.org/obo/UBERON_0001474) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000047" + +- [bone element](http://purl.obolibrary.org/obo/UBERON_0001474) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001514" + +- [bone element](http://purl.obolibrary.org/obo/UBERON_0001474) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Skeletal element that is composed of bone tissue.[VSAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000057" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PSPUB:0000170" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" + +- [bone element](http://purl.obolibrary.org/obo/UBERON_0001474) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [muscle organ](http://purl.obolibrary.org/obo/UBERON_0001630) + +- [bone element](http://purl.obolibrary.org/obo/UBERON_0001474) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [musculature](http://purl.obolibrary.org/obo/UBERON_0001015) + +- [bone element](http://purl.obolibrary.org/obo/UBERON_0001474) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001190" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1159/000324245 Murdock DJ, Donoghue PC, Evolutionary Origins of Animal Skeletal Biomineralization. Cells Tissues Organs (2011)" + + + +### bone foramen `http://purl.obolibrary.org/obo/UBERON_0005744` +#### Removed +- [bone foramen](http://purl.obolibrary.org/obo/UBERON_0005744) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in FMA and ZFA this is a conduit space, not a conduit. Note there may be some additional disambiguation required: foramen is used loosely in the sense of any opening (e.g. foramen primum). FMA appears to use cranial conduit (undefined) in the sense of any foramen of the skull (includes mental foramen, which is not in the cranium proper)." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + + + +### bone fossa `http://purl.obolibrary.org/obo/UBERON_0004704` +#### Removed +- [bone fossa](http://purl.obolibrary.org/obo/UBERON_0004704) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical space that is a concavity, shallow depression, or groove on a bone.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001743" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TAO:wd" + +- [bone fossa](http://purl.obolibrary.org/obo/UBERON_0004704) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "General Anatomical term in FMA; not restricted to bone in ncit; surface feature in VSAO; note that entities named 'fossa' are cavities in FMA, hence placement here" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + + + +### bone marrow `http://purl.obolibrary.org/obo/UBERON_0002371` +#### Removed +- [bone marrow](http://purl.obolibrary.org/obo/UBERON_0002371) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "In adults, marrow in large bones produces new blood cells[Wikipedia:Bone_marrow]" + +- [bone marrow](http://purl.obolibrary.org/obo/UBERON_0002371) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood Cells and Blood Cell Development in the Animal Kingdom. Annual Review of Cell and Developmental Biology (2006)" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001218" + +#### Added +- [bone marrow](http://purl.obolibrary.org/obo/UBERON_0002371) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### bone marrow cavity `http://purl.obolibrary.org/obo/UBERON_0002484` +#### Removed +- [bone marrow cavity](http://purl.obolibrary.org/obo/UBERON_0002484) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "not clear if the FMA intends to have two classes. MP:0000065: 'the medullary cavities of the bones.'. NCITA also has 'medullary bone'" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + +- [bone marrow cavity](http://purl.obolibrary.org/obo/UBERON_0002484) [RO_0002174](http://purl.obolibrary.org/obo/RO_0002174) [NCBITaxon_7955](http://purl.obolibrary.org/obo/NCBITaxon_7955) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1177/0192623311409597" + +- [bone marrow cavity](http://purl.obolibrary.org/obo/UBERON_0002484) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "Located in the main shaft (cortical bone) of a long bone (diaphysis) (consisting mostly of compact bone), the medullary cavity has walls composed of spongy bone (cancellous bone) and is lined with a thin, vascular membrane (endosteum)[Wikipedia:Bone_marrow_of_ovaryry_cavity]" + + + +### bone marrow proteoglycan `http://purl.obolibrary.org/obo/PR_000013206` +#### Removed +- [bone marrow proteoglycan](http://purl.obolibrary.org/obo/PR_000013206) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [bone marrow proteoglycan (human)](http://purl.obolibrary.org/obo/PR_P13727) + + + +### bone marrow stromal antigen 2 `http://purl.obolibrary.org/obo/PR_000001326` +#### Removed +- [bone marrow stromal antigen 2](http://purl.obolibrary.org/obo/PR_000001326) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [bone marrow stromal antigen 2 (human)](http://purl.obolibrary.org/obo/PR_Q10589) + + + +### bone of appendage girdle complex `http://purl.obolibrary.org/obo/UBERON_0010740` +#### Removed +- [bone of appendage girdle complex](http://purl.obolibrary.org/obo/UBERON_0010740) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [appendicular skeleton](http://purl.obolibrary.org/obo/UBERON_0002091) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "UBERONREF:0000003" + +#### Added +- [bone of appendage girdle complex](http://purl.obolibrary.org/obo/UBERON_0010740) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [appendicular skeleton](http://purl.obolibrary.org/obo/UBERON_0002091) + + +### bone of dorsum `http://purl.obolibrary.org/obo/UBERON_0004247` +#### Removed +- [bone of dorsum](http://purl.obolibrary.org/obo/UBERON_0004247) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "this class may be obsoleted. See: https://github.com/obophenotype/mouse-anatomy-ontology/issues/93" + +- [bone of dorsum](http://purl.obolibrary.org/obo/UBERON_0004247) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) + + + +### bone of free limb or fin `http://purl.obolibrary.org/obo/UBERON_0004375` + +#### Added +- [bone of free limb or fin](http://purl.obolibrary.org/obo/UBERON_0004375) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### bone of hip region `http://purl.obolibrary.org/obo/UBERON_0008202` +#### Removed +- [bone of hip region](http://purl.obolibrary.org/obo/UBERON_0008202) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in MA, this includes the femur. i.e. pelvic girdle bone or femur; note that this makes the ilium etc in MA hindlimb bones. in MA this is a hindlimb bone" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" + + + +### bone of lower jaw `http://purl.obolibrary.org/obo/UBERON_0004768` +#### Removed +- [bone of lower jaw](http://purl.obolibrary.org/obo/UBERON_0004768) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) + + + +### bone of pectoral complex `http://purl.obolibrary.org/obo/UBERON_0010741` +#### Removed +- [bone of pectoral complex](http://purl.obolibrary.org/obo/UBERON_0010741) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "note that the MA class includes girdle parts so it belongs here;" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" + +- [bone of pectoral complex](http://purl.obolibrary.org/obo/UBERON_0010741) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:32623" + + + +### bone of pelvic complex `http://purl.obolibrary.org/obo/UBERON_0010742` +#### Removed +- [bone of pelvic complex](http://purl.obolibrary.org/obo/UBERON_0010742) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:32633" + +- [bone of pelvic complex](http://purl.obolibrary.org/obo/UBERON_0010742) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "the MA class called 'hindlimb bone' belongs here, as it includes bones in the pelvic girdle" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" + + + +### bone of tail `http://purl.obolibrary.org/obo/UBERON_0006068` +#### Removed +- [bone of tail](http://purl.obolibrary.org/obo/UBERON_0006068) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "MA has distinct classes for 'tail bone', 'caudal vertebra' and 'coccygeal vertebra' but these may all be equivalent. This class may be obsoleted in future." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" + + + +### bone tissue `http://purl.obolibrary.org/obo/UBERON_0002481` +#### Removed +- [bone tissue](http://purl.obolibrary.org/obo/UBERON_0002481) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000047" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PSPUB:0000170" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" + + + +### bony labyrinth `http://purl.obolibrary.org/obo/UBERON_0001839` + +#### Added +- [bony labyrinth](http://purl.obolibrary.org/obo/UBERON_0001839) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### bony otic capsule `http://purl.obolibrary.org/obo/UBERON_0005411` +#### Removed +- [bony otic capsule](http://purl.obolibrary.org/obo/UBERON_0005411) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In elasmobranchs, the otic capsule remains cartilaginous in the adult; in the embryos of higher vertebrates, it is cartilaginous at first but later becomes bony (at approximately 23 weeks in humans)" + +- [bony otic capsule](http://purl.obolibrary.org/obo/UBERON_0005411) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:17596" + + + +### bony vertebral centrum `http://purl.obolibrary.org/obo/UBERON_0001075` +#### Removed +- [bony vertebral centrum](http://purl.obolibrary.org/obo/UBERON_0001075) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "VSAO definition states it surrounds notochord but not applicable to post-natal." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "VSAO" + +- [bony vertebral centrum](http://purl.obolibrary.org/obo/UBERON_0001075) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The body is the largest part of a vertebra, and is more or less cylindrical in shape. Its upper and lower surfaces are flattened and rough, and give attachment to the intervertebral fibrocartilages, and each presents a rim around its circumference. In front, the body is convex from side to side and concave from above downward. Behind, it is flat from above downward and slightly concave from side to side. Its anterior surface presents a few small apertures, for the passage of nutrient vessels. On the posterior surface is a single large, irregular aperture, or occasionally more than one, for the exit of the basi-vertebral veins from the body of the vertebra. [WP,unvetted][Wikipedia:Body_of_vertebra]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Body_of_vertebra" + +- [bony vertebral centrum](http://purl.obolibrary.org/obo/UBERON_0001075) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Cylindrical body of bone, round or oval in cross section, which functionally replaces the notochord.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:Duellman_and_Trueb_2008" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000697" + +- [bony vertebral centrum](http://purl.obolibrary.org/obo/UBERON_0001075) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Centra are represented by mineralized, calcified, or ossified portions that surround the notochord. The autocentrum, present in Danio and all other living teleosts, is formed by direct ossification outside the elastica externa of the notochord (Arratia, 1999).[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000126" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [bony vertebral centrum](http://purl.obolibrary.org/obo/UBERON_0001075) [UBPROP_0000005](http://purl.obolibrary.org/obo/UBPROP_0000005) "The vertebral centrum may be cartilaginous, develop as cartilage but be replaced by bone or mineralized, or form directly through intramembranous ossification.[VSAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000183" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-06" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Curator" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" + +- [bony vertebral centrum](http://purl.obolibrary.org/obo/UBERON_0001075) SubClassOf [bone element](http://purl.obolibrary.org/obo/UBERON_0001474) + +#### Added +- [bony vertebral centrum](http://purl.obolibrary.org/obo/UBERON_0001075) SubClassOf [endochondral bone](http://purl.obolibrary.org/obo/UBERON_0002513) + + +### border associated macrophage `http://purl.obolibrary.org/obo/CL_4042003` + +#### Added +- [border associated macrophage](http://purl.obolibrary.org/obo/CL_4042003) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "In humans, a border associate macrophage expresses CD45 and CD11B. This cell is also known to have the following molecular signature: CD206, CD38, LYVE1, CD163, CD169." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29426702" + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37232741" + +- [border associated macrophage](http://purl.obolibrary.org/obo/CL_4042003) [label](http://www.w3.org/2000/01/rdf-schema#label) "border associated macrophage"@en + +- [border associated macrophage](http://purl.obolibrary.org/obo/CL_4042003) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "BAM" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36945367" + + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [abbreviation](http://purl.obolibrary.org/obo/OMO_0003000) + +- [border associated macrophage](http://purl.obolibrary.org/obo/CL_4042003) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "CAM" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33556248" + + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [abbreviation](http://purl.obolibrary.org/obo/OMO_0003000) + +- [border associated macrophage](http://purl.obolibrary.org/obo/CL_4042003) [date](http://purl.org/dc/terms/date) "2024-03-26T16:39:56Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- [border associated macrophage](http://purl.obolibrary.org/obo/CL_4042003) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) + +- [border associated macrophage](http://purl.obolibrary.org/obo/CL_4042003) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A central nervous system macrophage that is part of a choroid plexus, a meninx and a perivascular space. A border associated macrophage interacts with various components of the CNS vasculature and meninges, it participates in immune surveillance and in the regulation of the blood brain barrier." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37626977" + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37232741" + +- [border associated macrophage](http://purl.obolibrary.org/obo/CL_4042003) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "CNS-associated macrophage" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37232741" + +- Class: [border associated macrophage](http://purl.obolibrary.org/obo/CL_4042003) + +- [border associated macrophage](http://purl.obolibrary.org/obo/CL_4042003) SubClassOf [central nervous system macrophage](http://purl.obolibrary.org/obo/CL_0000878) + + +### border between sublaminar layers `http://purl.obolibrary.org/obo/UBERON_0009740` + +#### Added +- [border between sublaminar layers](http://purl.obolibrary.org/obo/UBERON_0009740) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### bounding layer of `http://purl.obolibrary.org/obo/RO_0002007` +#### Removed +- [bounding layer of](http://purl.obolibrary.org/obo/RO_0002007) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-7073-9172](https://orcid.org/0000-0002-7073-9172) + +- [bounding layer of](http://purl.obolibrary.org/obo/RO_0002007) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + + + +### brachial nerve plexus `http://purl.obolibrary.org/obo/UBERON_0001814` +#### Removed +- [brachial nerve plexus](http://purl.obolibrary.org/obo/UBERON_0001814) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A nerve plexus originating from the anterior branches of the last four cervical and the first thoracic spinal nerves, giving off many of the principal nerves of the shoulder, chest, and arms. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000372" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/brachial+plexus" + +- [brachial nerve plexus](http://purl.obolibrary.org/obo/UBERON_0001814) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "To reach the muscles, dermatomes, and other structures of the limbs, some of the neurons in the spinal nerves come together in the plexus at the base of the limb. Such plexuses occur in all gnathostomes, and they reach their highest complexity among mammals and birds in which the cervical plexus supplies many ventral neck muscles, the brachial plexus supplies the pectoral appendage, a lumbosacral plexus supplies the pelvic appendage, and a coccygeal plexus supplies some of the pelvic muscles.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000372" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.436" + + + +### brain `http://purl.obolibrary.org/obo/UBERON_0000955` +#### Removed +- [brain](http://purl.obolibrary.org/obo/UBERON_0000955) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO)" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://neurolex.org/wiki/Cumbo_terms" + +- [brain](http://purl.obolibrary.org/obo/UBERON_0000955) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000157" + +- [brain](http://purl.obolibrary.org/obo/UBERON_0000955) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010478" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + +- [brain](http://purl.obolibrary.org/obo/UBERON_0000955) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005095" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + +- [brain](http://purl.obolibrary.org/obo/UBERON_0000955) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000008" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + + +### brain arachnoid mater `http://purl.obolibrary.org/obo/UBERON_0005397` +#### Removed +- [brain arachnoid mater](http://purl.obolibrary.org/obo/UBERON_0005397) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000230" + +- [brain arachnoid mater](http://purl.obolibrary.org/obo/UBERON_0005397) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The middle membrane of the three mammalian meninges covering the brain and spinal cord. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/arachnoid+mater" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000230" + + + +### brain blood vessel `http://purl.obolibrary.org/obo/UBERON_0003499` + +#### Added +- [brain blood vessel](http://purl.obolibrary.org/obo/UBERON_0003499) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### brain dura mater `http://purl.obolibrary.org/obo/UBERON_0002092` +#### Removed +- [brain dura mater](http://purl.obolibrary.org/obo/UBERON_0002092) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EV:0100313" + +- [brain dura mater](http://purl.obolibrary.org/obo/UBERON_0002092) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000270" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + +- [brain dura mater](http://purl.obolibrary.org/obo/UBERON_0002092) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The outermost and densest membrane of the three mammalian meninges covering the brain and spinal cord. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000270" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + + +### brain endothelium `http://purl.obolibrary.org/obo/UBERON_0013694` + +#### Added +- [brain endothelium](http://purl.obolibrary.org/obo/UBERON_0013694) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) + + +### brain ependyma `http://purl.obolibrary.org/obo/UBERON_0005357` +#### Removed +- [brain ependyma](http://purl.obolibrary.org/obo/UBERON_0005357) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in FMA this is treated as part of the ependyma, but here we treat ependyma as a portion" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + + + +### brain marginal zone `http://purl.obolibrary.org/obo/UBERON_0010403` +#### Removed +- [brain marginal zone](http://purl.obolibrary.org/obo/UBERON_0010403) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "not clear if the MA/EMAPA classes refer specifically to the cortical subset. DHBA class incldues non-neocortex derivatives so it belongs here" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" + + + +### brain meninx `http://purl.obolibrary.org/obo/UBERON_0003547` +#### Removed +- [brain meninx](http://purl.obolibrary.org/obo/UBERON_0003547) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000013" + +- [brain meninx](http://purl.obolibrary.org/obo/UBERON_0003547) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Meninges that are part of the brain. [Bgee_curator][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000013" + +- [brain meninx](http://purl.obolibrary.org/obo/UBERON_0003547) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EV:0100312" + + + +### brain pia mater `http://purl.obolibrary.org/obo/UBERON_0003549` +#### Removed +- [brain pia mater](http://purl.obolibrary.org/obo/UBERON_0003549) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The innermost of the three mammalian meninges covering the brain and spinal cord. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/pia+mater" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000470" + +- [brain pia mater](http://purl.obolibrary.org/obo/UBERON_0003549) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EV:0100315" + +- [brain pia mater](http://purl.obolibrary.org/obo/UBERON_0003549) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000470" + + + +### brain ventricle `http://purl.obolibrary.org/obo/UBERON_0004086` +#### Removed +- [brain ventricle](http://purl.obolibrary.org/obo/UBERON_0004086) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Organ cavity of the brain which consists of the lateral ventricles, the third and fourth ventricles and the cerebral aqueduct[BIRNLEX:1356]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "BIRNLEX:1356" + +- [brain ventricle](http://purl.obolibrary.org/obo/UBERON_0004086) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA draws the distinction between e.g. 'fourth ventricle' and 'cavity of fourth ventricle'. The latter is a cavity, and part of the former, which is a region. The superclass of 'fourth ventricle' is_a 'region of ventricular system of the brain'. We place this class here, although it is not equivalent to ventricles, as it includes ventricle bodies." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + + + +### brain ventricle/choroid plexus `http://purl.obolibrary.org/obo/UBERON_0003947` + +#### Added +- [brain ventricle/choroid plexus](http://purl.obolibrary.org/obo/UBERON_0003947) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### brain white matter `http://purl.obolibrary.org/obo/UBERON_0003544` +#### Removed +- [brain white matter](http://purl.obolibrary.org/obo/UBERON_0003544) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "HBA:9218" + + + +### brainstem `http://purl.obolibrary.org/obo/UBERON_0002298` +#### Removed +- [brainstem](http://purl.obolibrary.org/obo/UBERON_0002298) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [forebrain](http://purl.obolibrary.org/obo/UBERON_0001890) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "we apply a strict definition" + +- [brainstem](http://purl.obolibrary.org/obo/UBERON_0002298) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [midbrain tectum](http://purl.obolibrary.org/obo/UBERON_0002314) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "we apply a strict definition" + +- [brainstem](http://purl.obolibrary.org/obo/UBERON_0002298) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,adopted][ZFA:0001707]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFA:0001707" + +- [brainstem](http://purl.obolibrary.org/obo/UBERON_0002298) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "the stalk-like part of the brain that comprises the midbrain (aka mesencephalon), the pons (aka pons Varolii), and the medulla oblongata, and connects the cerebral hemispheres with the cervical spinal cord[MP]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "MP:0005277" + +- [brainstem](http://purl.obolibrary.org/obo/UBERON_0002298) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [cerebellum](http://purl.obolibrary.org/obo/UBERON_0002037) + - [exceptions](http://www.geneontology.org/formats/oboInOwl#exceptions) "ZFA" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "https://github.com/obophenotype/uberon/issues/378" + + - [status](http://www.geneontology.org/formats/oboInOwl#status) "pending" + +- [brainstem](http://purl.obolibrary.org/obo/UBERON_0002298) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:3764351209" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0002156" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + + +### branched `http://purl.obolibrary.org/obo/PATO_0000402` +#### Removed +- [branched](http://purl.obolibrary.org/obo/PATO_0000402) [RO_0002604](http://purl.obolibrary.org/obo/RO_0002604) [PATO_0000414](http://purl.obolibrary.org/obo/PATO_0000414) + + + +### branching part of `http://purl.obolibrary.org/obo/RO_0002380` +#### Removed +- [branching part of](http://purl.obolibrary.org/obo/RO_0002380) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [branching part of](http://purl.obolibrary.org/obo/RO_0002380) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "branching_part_of" + +- [branching part of](http://purl.obolibrary.org/obo/RO_0002380) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [branching part of](http://purl.obolibrary.org/obo/RO_0002380) [id](http://www.geneontology.org/formats/oboInOwl#id) "branching_part_of" + +- [branching part of](http://purl.obolibrary.org/obo/RO_0002380) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002380" + +- [branching part of](http://purl.obolibrary.org/obo/RO_0002380) [label](http://www.w3.org/2000/01/rdf-schema#label) "branching part of" + +- [branching part of](http://purl.obolibrary.org/obo/RO_0002380) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" + + + +### branchiomeric muscle `http://purl.obolibrary.org/obo/UBERON_0004164` +#### Removed +- [branchiomeric muscle](http://purl.obolibrary.org/obo/UBERON_0004164) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The branchiomeric muscle is derived from cranial mesoderm and controls facial expression, pharyngeal and laryngeal function, operating the jaw. Branchiomeric muscles of mammals correspond to the musculature of fish[GO][GO:0014707]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GO:0014707" + +- [branchiomeric muscle](http://purl.obolibrary.org/obo/UBERON_0004164) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "It has been hypothesized that Haikouella must have been powered by branchiomeric muscles, as in living craniates, rather than by water moving through the pharynx via ciliary currents, as in lancelets[http://icb.oxfordjournals.org/content/42/4/743.full]" + + + +### breast `http://purl.obolibrary.org/obo/UBERON_0000310` +#### Removed +- [breast](http://purl.obolibrary.org/obo/UBERON_0000310) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The breasts of a female primate's body contain the mammary glands, which secrete milk used to feed infants. Both men and women develop breasts from the same embryological tissues. However, at puberty female sex hormones, mainly estrogens, promote breast development, which does not happen with men. As a result women's breasts become more prominent than men's." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP,unvetted" + + + +### broad ligament of uterus `http://purl.obolibrary.org/obo/UBERON_0012332` + +#### Added +- [broad ligament of uterus](http://purl.obolibrary.org/obo/UBERON_0012332) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### bronchial lymph node `http://purl.obolibrary.org/obo/UBERON_0016481` + +#### Added +- [bronchial lymph node](http://purl.obolibrary.org/obo/UBERON_0016481) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) + + +### bronchial mucosa `http://purl.obolibrary.org/obo/UBERON_0000410` + +#### Added +- [bronchial mucosa](http://purl.obolibrary.org/obo/UBERON_0000410) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) + + +### bronchial submucosal gland ciliated duct `http://purl.obolibrary.org/obo/UBERON_8600010` + +#### Added +- [bronchial submucosal gland ciliated duct](http://purl.obolibrary.org/obo/UBERON_8600010) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) + + +### bronchial-associated lymphoid tissue `http://purl.obolibrary.org/obo/UBERON_0001963` + +#### Added +- [bronchial-associated lymphoid tissue](http://purl.obolibrary.org/obo/UBERON_0001963) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) + + +### bronchiole `http://purl.obolibrary.org/obo/UBERON_0002186` +#### Removed +- [bronchiole](http://purl.obolibrary.org/obo/UBERON_0002186) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "bronchiolar" + +- [bronchiole](http://purl.obolibrary.org/obo/UBERON_0002186) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D055745" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + +- [bronchiole](http://purl.obolibrary.org/obo/UBERON_0002186) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "In FMA2 and FMA3, lobular bronchiole is an exact synonym of bronchiole; however, there are two distinct terms for the corresponding epithelium." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + +- [bronchiole](http://purl.obolibrary.org/obo/UBERON_0002186) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "lacks submucosa and cartilage plates; they have 3 layers: mucosa, muscular layer and outer layer" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0123813611" + + + +### bronchopulmonary segment `http://purl.obolibrary.org/obo/UBERON_8600017` + +#### Added +- [bronchopulmonary segment](http://purl.obolibrary.org/obo/UBERON_8600017) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) + + +### bronchus `http://purl.obolibrary.org/obo/UBERON_0002185` +#### Removed +- [bronchus](http://purl.obolibrary.org/obo/UBERON_0002185) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In humans, the main bronchus is histologically identical to trachea; 2ary and 3ary bronchi are not; epithelium becomes simple columnar, goblet cell number decreases, elastic fibers in lamina propria increases, distribution more uniform. Muscular layer between mucosa and submucosa appears. cartilage rings become discontinuous plates connected by fibrous connective tissue" + +- [bronchus](http://purl.obolibrary.org/obo/UBERON_0002185) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "bronchial" + +- [bronchus](http://purl.obolibrary.org/obo/UBERON_0002185) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Each of the two primary divisions of the trachea leading respectively into the right and the left lung. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000262" + + + +### bronchus basement membrane `http://purl.obolibrary.org/obo/UBERON_0009652` +#### Removed +- [bronchus basement membrane](http://purl.obolibrary.org/obo/UBERON_0009652) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "MA classifies as type of connective tissue: https://github.com/obophenotype/mouse-anatomy-ontology/issues/108" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" + +#### Added +- [bronchus basement membrane](http://purl.obolibrary.org/obo/UBERON_0009652) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) + + +### brown adipose tissue `http://purl.obolibrary.org/obo/UBERON_0001348` +#### Removed +- [brown adipose tissue](http://purl.obolibrary.org/obo/UBERON_0001348) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Adipose tissue, cells of which contain multiple small lipid droplets.[FMA]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA" + +- [brown adipose tissue](http://purl.obolibrary.org/obo/UBERON_0001348) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "thermogenesis" + +- [brown adipose tissue](http://purl.obolibrary.org/obo/UBERON_0001348) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "especially abundant in newborns and in hibernating mammals" + + + +### bulb of hair follicle `http://purl.obolibrary.org/obo/UBERON_0005932` + +#### Added +- [bulb of hair follicle](http://purl.obolibrary.org/obo/UBERON_0005932) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### bulbus cordis `http://purl.obolibrary.org/obo/UBERON_0004706` +#### Removed +- [bulbus cordis](http://purl.obolibrary.org/obo/UBERON_0004706) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A pear shaped chamber that functions as a capacitor, maintaining continuous blood flow into the gill arches. The bulbus arteriosus has three distinct layers. Hu et al. 2000.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000173" + + + +### cadherin-1 `http://purl.obolibrary.org/obo/PR_000001447` +#### Removed +- [cadherin-1](http://purl.obolibrary.org/obo/PR_000001447) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [cadherin-1 (human)](http://purl.obolibrary.org/obo/PR_P12830) + + + +### cadherin-5 `http://purl.obolibrary.org/obo/PR_000001444` +#### Removed +- [cadherin-5](http://purl.obolibrary.org/obo/PR_000001444) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [cadherin-5 (human)](http://purl.obolibrary.org/obo/PR_P33151) + + + +### caecum `http://purl.obolibrary.org/obo/UBERON_0001153` +#### Removed +- [caecum](http://purl.obolibrary.org/obo/UBERON_0001153) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "A cecum is present in most amniote species, and also in lungfish, but not in any living species of amphibian. In reptiles, it is usually a single median structure, arising from the dorsal side of the large intestine. Birds typically have two paired ceca, as, unlike other mammals, do hyraxes. Most mammalian herbivores have a relatively large cecum, hosting a large number of bacteria, which aid in the enzymatic breakdown of plant materials such as cellulose; in many species, it is considerably wider than the colon. In contrast, obligatory carnivores, whose diets contain little or no plant material, have a reduced cecum, which is often partially or wholly replaced by the vermiform appendix. Many fish have a number of small outpocketings, called pyloric ceca, along their intestine; despite the name they are not homologous with the cecum of amniotes, and their purpose is to increase the overall area of the digestive epithelium.[2] Some invertebrates, such as squid,[3] may also have structures with the same name, but these have no relationship with those of vertebrates." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" + +- [caecum](http://purl.obolibrary.org/obo/UBERON_0001153) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "caecal" + + + +### calcareous tooth `http://purl.obolibrary.org/obo/UBERON_0001091` +#### Removed +- [calcareous tooth](http://purl.obolibrary.org/obo/UBERON_0001091) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0000694" + +- [calcareous tooth](http://purl.obolibrary.org/obo/UBERON_0001091) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The ancestor of recent vertebrate teeth was a tooth-like structure on the outer body surface of jawless fishes.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001733" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:19266065 Koussoulakou DS, Margaritis LH, Koussoulakos SL, A curriculum vitae of teeth: evolution, generation, regeneration. International Journal of Biological Sciences (2009)" + +- [calcareous tooth](http://purl.obolibrary.org/obo/UBERON_0001091) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "absent in living platypus, present in toothed Miocene platypus Obduron dicksoni" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:10210685" + +- [calcareous tooth](http://purl.obolibrary.org/obo/UBERON_0001091) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "dental" + +#### Added +- [calcareous tooth](http://purl.obolibrary.org/obo/UBERON_0001091) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### camera-type eye `http://purl.obolibrary.org/obo/UBERON_0000019` +#### Removed +- [camera-type eye](http://purl.obolibrary.org/obo/UBERON_0000019) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000275" + +- [camera-type eye](http://purl.obolibrary.org/obo/UBERON_0000019) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA distinguishes Eye (subdivision of face) which has its parts an Eyeball (organ), as well as other structures, and the orbit of skull. MA includes eyelid, conjunctiva and lacrimal apparatus as part of MA:eye - consistent with FMA - so we can infer that MA:eye is more like FMA:eye than FMA:eyeball. For other AOs this distinction is less meaningful - e.g. ZFA has no eyelid; XAO has no eyelid, but it has conjuctiva, which is considered part of the xao:eye. GO considers eyelid development part of eye development. See also notes on optic nerve - XAO, AAO and BTO consider this part of the eye. MA considers the eye muscles part of the eye, whereas FMA has a class 'orbital content' for this" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + +- [camera-type eye](http://purl.obolibrary.org/obo/UBERON_0000019) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A cavitated compound organ that transduces light waves into neural signals.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000107" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TAO:wd" + +- [camera-type eye](http://purl.obolibrary.org/obo/UBERON_0000019) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [optic cup](http://purl.obolibrary.org/obo/UBERON_0003072) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" + +#### Added +- [camera-type eye](http://purl.obolibrary.org/obo/UBERON_0000019) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [optic cup](http://purl.obolibrary.org/obo/UBERON_0003072) + + +### camera-type eye photoreceptor cell `http://purl.obolibrary.org/obo/CL_0010009` +#### Removed +- [camera-type eye photoreceptor cell](http://purl.obolibrary.org/obo/CL_0010009) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [camera-type eye](http://purl.obolibrary.org/obo/UBERON_0000019) + +#### Added +- [camera-type eye photoreceptor cell](http://purl.obolibrary.org/obo/CL_0010009) SubClassOf [retinal cell](http://purl.obolibrary.org/obo/CL_0009004) + +- [camera-type eye photoreceptor cell](http://purl.obolibrary.org/obo/CL_0010009) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [retina](http://purl.obolibrary.org/obo/UBERON_0000966) + - [see also](http://www.w3.org/2000/01/rdf-schema#seeAlso) "https://github.com/obophenotype/cell-ontology/issues/2245" + + +### capable of `http://purl.obolibrary.org/obo/RO_0002215` +#### Removed +- [capable of](http://purl.obolibrary.org/obo/RO_0002215) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "has function realized in" + +- [capable of](http://purl.obolibrary.org/obo/RO_0002215) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [capable of](http://purl.obolibrary.org/obo/RO_0002215) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) [20123131](http://www.ncbi.nlm.nih.gov/pubmed/20123131) + +- [capable of](http://purl.obolibrary.org/obo/RO_0002215) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "osteoclast SubClassOf 'capable of' some 'bone resorption'" + +- [capable of](http://purl.obolibrary.org/obo/RO_0002215) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) [21208450](http://www.ncbi.nlm.nih.gov/pubmed/21208450) + +- [capable of](http://purl.obolibrary.org/obo/RO_0002215) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [capable of](http://purl.obolibrary.org/obo/RO_0002215) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" + +- [capable of](http://purl.obolibrary.org/obo/RO_0002215) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)"." + + + +### capable of negatively regulating `http://purl.obolibrary.org/obo/RO_0002597` +#### Removed +- [capable of negatively regulating](http://purl.obolibrary.org/obo/RO_0002597) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) [causal-relations](http://purl.obolibrary.org/obo/ro/docs/causal-relations) + + + +### capable of part of `http://purl.obolibrary.org/obo/RO_0002216` +#### Removed +- [capable of part of](http://purl.obolibrary.org/obo/RO_0002216) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [capable of part of](http://purl.obolibrary.org/obo/RO_0002216) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [capable of part of](http://purl.obolibrary.org/obo/RO_0002216) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "has function in" + +- [capable of](http://purl.obolibrary.org/obo/RO_0002215) o [part_of](http://purl.obolibrary.org/obo/BFO_0000050) SubPropertyOf: [capable of part of](http://purl.obolibrary.org/obo/RO_0002216) + - [is a defining property chain axiom where second argument is reflexive](http://purl.obolibrary.org/obo/RO_0002582) true + + + +### capable of positively regulating `http://purl.obolibrary.org/obo/RO_0002598` +#### Removed +- [capable of positively regulating](http://purl.obolibrary.org/obo/RO_0002598) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "renin -> arteriolar smooth muscle contraction" + +- [capable of positively regulating](http://purl.obolibrary.org/obo/RO_0002598) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) [causal-relations](http://purl.obolibrary.org/obo/ro/docs/causal-relations) + + + +### capable of regulating `http://purl.obolibrary.org/obo/RO_0002596` +#### Removed +- [capable of regulating](http://purl.obolibrary.org/obo/RO_0002596) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "pyrethroid -> growth" + +- [capable of regulating](http://purl.obolibrary.org/obo/RO_0002596) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) [causal-relations](http://purl.obolibrary.org/obo/ro/docs/causal-relations) + + + +### capillary `http://purl.obolibrary.org/obo/UBERON_0001982` +#### Removed +- [capillary](http://purl.obolibrary.org/obo/UBERON_0001982) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001253" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)" + +- [capillary](http://purl.obolibrary.org/obo/UBERON_0001982) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Any of the tiny blood vessels connecting the arterioles to the venules.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010252" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + +- [capillary](http://purl.obolibrary.org/obo/UBERON_0001982) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "capillaries lack tunica media and tunica adventitia; only the endothelial wall of the tunica intima belongs" + + + +### capsule `http://purl.obolibrary.org/obo/UBERON_0003893` +#### Removed +- [capsule](http://purl.obolibrary.org/obo/UBERON_0003893) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "capsular" + + + +### capsule of lens `http://purl.obolibrary.org/obo/UBERON_0001804` +#### Removed +- [capsule of lens](http://purl.obolibrary.org/obo/UBERON_0001804) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424 and p.426 and p.429 and Figure 12-24" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000550" + +- [capsule of lens](http://purl.obolibrary.org/obo/UBERON_0001804) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The transparent membrane which surrounds the lens of the eye. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000550" + +- [capsule of lens](http://purl.obolibrary.org/obo/UBERON_0001804) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "synthesized by the lens epithelium and its main components are Type IV collagen and sulfated glycosaminoglycans (GAGs). [Wikipedia:Capsule_of_lens" + +- [capsule of lens](http://purl.obolibrary.org/obo/UBERON_0001804) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA classifies this is a capsule and hence an organ part. In contrast we classify this as acellular" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + + + +### capsule of liver `http://purl.obolibrary.org/obo/UBERON_0016479` +#### Removed +- [capsule of liver](http://purl.obolibrary.org/obo/UBERON_0016479) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "It consists of type III collagen and extends to the stroma of endothelial sinusoids. It is covered by a single layer of mesothelial cells." + +#### Added +- [capsule of liver](http://purl.obolibrary.org/obo/UBERON_0016479) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) + + +### capsule of lymph node `http://purl.obolibrary.org/obo/UBERON_0002194` +#### Removed +- [capsule of lymph node](http://purl.obolibrary.org/obo/UBERON_0002194) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "from its internal surface are given off a number of membranous processes or trabeculae, consisting, in man, of connective tissue, with a small admixture of plain muscle fibers; but in many of the lower animals composed almost entirely of involuntary muscle[WP]" + + + +### capsule of pancreas `http://purl.obolibrary.org/obo/UBERON_0018235` +#### Removed +- [capsule of pancreas](http://purl.obolibrary.org/obo/UBERON_0018235) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "typically thin but can thicken with age" + + + +### capsule of thymus `http://purl.obolibrary.org/obo/UBERON_0002122` + +#### Added +- [capsule of thymus](http://purl.obolibrary.org/obo/UBERON_0002122) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) + + +### capsule of thyroid gland `http://purl.obolibrary.org/obo/UBERON_0001746` + +#### Added +- [capsule of thyroid gland](http://purl.obolibrary.org/obo/UBERON_0001746) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) + + +### carbohydrate derivative transmembrane transporter activity `http://purl.obolibrary.org/obo/GO_1901505` +#### Removed +- [carbohydrate derivative transmembrane transporter activity](http://purl.obolibrary.org/obo/GO_1901505) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [carbohydrate derivative transport](http://purl.obolibrary.org/obo/GO_1901264) + - [source](http://www.geneontology.org/formats/oboInOwl#http://purl.org/dc/terms/source) "GO_REF:0000090" + +#### Added +- [carbohydrate derivative transmembrane transporter activity](http://purl.obolibrary.org/obo/GO_1901505) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [carbohydrate derivative transport](http://purl.obolibrary.org/obo/GO_1901264) + + +### carbohydrate transmembrane transporter activity `http://purl.obolibrary.org/obo/GO_0015144` +#### Removed +- [carbohydrate transmembrane transporter activity](http://purl.obolibrary.org/obo/GO_0015144) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [carbohydrate transmembrane transport](http://purl.obolibrary.org/obo/GO_0034219) + - [source](http://www.geneontology.org/formats/oboInOwl#http://purl.org/dc/terms/source) "GO_REF:0000090" + +#### Added +- [carbohydrate transmembrane transporter activity](http://purl.obolibrary.org/obo/GO_0015144) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [carbohydrate transmembrane transport](http://purl.obolibrary.org/obo/GO_0034219) + + +### carcinoembryonic antigen-related cell adhesion molecule 8 `http://purl.obolibrary.org/obo/PR_000001332` +#### Removed +- [carcinoembryonic antigen-related cell adhesion molecule 8](http://purl.obolibrary.org/obo/PR_000001332) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [carcinoembryonic antigen-related cell adhesion molecule 8 (human)](http://purl.obolibrary.org/obo/PR_P31997) + + + +### cardiac atrium `http://purl.obolibrary.org/obo/UBERON_0002081` +#### Removed +- [cardiac atrium](http://purl.obolibrary.org/obo/UBERON_0002081) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "One of two chambers of the heart which receive blood from the veins and forces it by muscular contration to the ventricle.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010246" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + +- [cardiac atrium](http://purl.obolibrary.org/obo/UBERON_0002081) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "One of four heart chambers.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000471" + +- [cardiac atrium](http://purl.obolibrary.org/obo/UBERON_0002081) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000175" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.428" + +- [cardiac atrium](http://purl.obolibrary.org/obo/UBERON_0002081) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + + +### cardiac chamber `http://purl.obolibrary.org/obo/UBERON_0004151` + +#### Added +- [cardiac chamber](http://purl.obolibrary.org/obo/UBERON_0004151) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### cardiac ganglion `http://purl.obolibrary.org/obo/UBERON_0014463` +#### Removed +- [cardiac ganglion](http://purl.obolibrary.org/obo/UBERON_0014463) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Any of the parasympathetic ganglia of the cardiac plexus between the arch of the aorta and the bifurcation of the pulmonary artery[http://medical-dictionary.thefreedictionary.com/cardiac+ganglion]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/cardiac+ganglion" + + + +### cardiac gastric gland `http://purl.obolibrary.org/obo/UBERON_0008859` +#### Removed +- [cardiac gastric gland](http://purl.obolibrary.org/obo/UBERON_0008859) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The cardiac glands of the stomach secrete primarily mucus. They are few in number and occur close to the cardiac orifice where the esophagus joins the stomach. In general, they are more shallow than those in the other parts of the stomach. They are of two kinds: (1) simple tubular glands resembling those of the pyloric end of the stomach, but with short ducts. (2) compound racemose glands resembling the duodenal glands. The cardiac gland is both innervated by the parasympathetic and symapthetic nerve fibres of the autonomic nervous system[Wikipedia:Cardiac_glands]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Cardiac_glands" + +- [cardiac gastric gland](http://purl.obolibrary.org/obo/UBERON_0008859) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "Kardong places this in the glandular epithelium, FMA more generally in the mucosa" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + + + +### cardiac mesenchyme `http://purl.obolibrary.org/obo/UBERON_0009751` + +#### Added +- [cardiac mesenchyme](http://purl.obolibrary.org/obo/UBERON_0009751) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### cardiac muscle tissue of atrium `http://purl.obolibrary.org/obo/UBERON_0004490` +#### Removed +- [cardiac muscle tissue of atrium](http://purl.obolibrary.org/obo/UBERON_0004490) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in GO, this is equivalent to the atrial myocardium, but FMA distinguishes these two. Consider merging." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "GO" + + + +### cardiac muscle tissue of myocardium `http://purl.obolibrary.org/obo/UBERON_0004493` +#### Removed +- [cardiac muscle tissue of myocardium](http://purl.obolibrary.org/obo/UBERON_0004493) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:32688" + + + +### cardiac neural crest `http://purl.obolibrary.org/obo/UBERON_0000095` +#### Removed +- [cardiac neural crest](http://purl.obolibrary.org/obo/UBERON_0000095) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "ZFA treats this as a subtype of NC." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "ZFA" + +- [cardiac neural crest](http://purl.obolibrary.org/obo/UBERON_0000095) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A subpopulation of the cephalic neural crest that emerges from the otic level to the anterior limit of somite 4. It migrates to the heart and is essential for the septation of the outflow track[DOI:10.1242/dev.091751]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1242/dev.091751" + +#### Added +- [cardiac neural crest](http://purl.obolibrary.org/obo/UBERON_0000095) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### cardiac septum `http://purl.obolibrary.org/obo/UBERON_0002099` +#### Removed +- [cardiac septum](http://purl.obolibrary.org/obo/UBERON_0002099) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in GO, septum morphogenesis is part of cardiac chamber morphogenesis; need to add axioms to infer this" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "GO" + +- [cardiac septum](http://purl.obolibrary.org/obo/UBERON_0002099) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "'Terrestrial vertebrates have divided hearts in which septae separate the oxygenated and deoxygenated blood within the pulmonary and systemic circulations'" + +#### Added +- [cardiac septum](http://purl.obolibrary.org/obo/UBERON_0002099) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### cardiac skeleton `http://purl.obolibrary.org/obo/UBERON_0004292` +#### Removed +- [cardiac skeleton](http://purl.obolibrary.org/obo/UBERON_0004292) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "It is not a true skeleton, but it does provide structure and support for the heart, as well as isolating the atria from the ventricles. This allows the AV node and AV bundle to delay the wave of depolarisation such that the atria can contract and assist in ventricular filling before the ventricles themselves depolarise and contract (the AV bundle is the only part of the conduction system that passes from the atria to the ventricles in a normal heart). It also allows the valves (bicuspid, tricuspid, semilunar) to keep open by giving them structural support[WP]" + +#### Added +- [cardiac skeleton](http://purl.obolibrary.org/obo/UBERON_0004292) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### cardiac valve `http://purl.obolibrary.org/obo/UBERON_0000946` +#### Removed +- [cardiac valve](http://purl.obolibrary.org/obo/UBERON_0000946) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Extensive conservation of valve developmental mechanisms also has been observed among vertebrate species including chicken, mouse, and human.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1161/CIRCRESAHA.109.201566 Combs MD, Yutzey KE, Heart valve development. Circulatory Research (2009)" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000818" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + +- [cardiac valve](http://purl.obolibrary.org/obo/UBERON_0000946) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "Rector et al: One might be tempted to define 'heart valve' equivalently to 'valve in the heart', and 'valve' as a 'structure which functions as a valve'. But this combination results in the 'foramen ovale' being classified as a kind of 'heart valve', since it is undoubtedly located in the heart and functions as a valve" + +- [cardiac valve](http://purl.obolibrary.org/obo/UBERON_0000946) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "One of the four structures within the heart that prevent backflow of blood by opening and closing with each heartbeat. The valves include two semilunar valves, the aortic and pulmonary; the mitral or bicuspid valve; and the tricuspid valve. The valves permit blood flow in only one direction. [TFD][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000818" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/heart+valve" + +#### Added +- [cardiac valve](http://purl.obolibrary.org/obo/UBERON_0000946) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### cardiac ventricle `http://purl.obolibrary.org/obo/UBERON_0002082` +#### Removed +- [cardiac ventricle](http://purl.obolibrary.org/obo/UBERON_0002082) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "One of four heart chambers.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000009" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [cardiac ventricle](http://purl.obolibrary.org/obo/UBERON_0002082) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A chamber of the heart that receives blood from one or more atria and pumps it by muscular contraction into the arteries.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010249" + +- [cardiac ventricle](http://purl.obolibrary.org/obo/UBERON_0002082) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...)[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000435" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.428" + +- [cardiac ventricle](http://purl.obolibrary.org/obo/UBERON_0002082) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + + +### cardiogenic plate `http://purl.obolibrary.org/obo/UBERON_0004139` +#### Removed +- [cardiogenic plate](http://purl.obolibrary.org/obo/UBERON_0004139) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000975" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:15611355 Gittenberger-de Groot AC, Bartelings MM, Deruiter MC, Poelmann RE, Basics of cardiac development for the understanding of congenital heart malformations. Pediatric Research (2005)" + + + +### cardiogenic splanchnic mesoderm `http://purl.obolibrary.org/obo/UBERON_0007005` + +#### Added +- [cardiogenic splanchnic mesoderm](http://purl.obolibrary.org/obo/UBERON_0007005) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### cardiovascular system `http://purl.obolibrary.org/obo/UBERON_0004535` +#### Removed +- [cardiovascular system](http://purl.obolibrary.org/obo/UBERON_0004535) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph." + +- [cardiovascular system](http://purl.obolibrary.org/obo/UBERON_0004535) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EHDAA2:0000216" + +- [cardiovascular system](http://purl.obolibrary.org/obo/UBERON_0004535) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:16370" + +- [cardiovascular system](http://purl.obolibrary.org/obo/UBERON_0004535) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.451" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000302" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + + +### cardiovascular system endothelium `http://purl.obolibrary.org/obo/UBERON_0004852` +#### Removed +- [cardiovascular system endothelium](http://purl.obolibrary.org/obo/UBERON_0004852) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001217" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207" + + + +### carotid artery segment `http://purl.obolibrary.org/obo/UBERON_0005396` +#### Removed +- [carotid artery segment](http://purl.obolibrary.org/obo/UBERON_0005396) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Artery originating at the junction of the first two aortic arches and supplying the anterior brain. Kimmel et al, 1995.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000097" + + + +### carpal bone `http://purl.obolibrary.org/obo/UBERON_0001435` +#### Removed +- [carpal bone](http://purl.obolibrary.org/obo/UBERON_0001435) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In tetrapods, the carpals is the sole cluster of the bones in the wrist between the radius and ulna and the metacarpus. The bones of the carpus do not belong to individual fingers (or toes in quadrupeds), whereas those of the metacarpus do. The corresponding part of the foot is the tarsus. The carpal bones allow the wrist to move and rotate vertically, horizontally and laterally. In human anatomy, the main role of the carpus is to facilitate effective positioning of the hand and powerful use of the extensors and flexors of the forearm, but the mobility of individual carpal bones increase the freedom of movements at the wrist." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Carpus" + + + +### carpal skeleton `http://purl.obolibrary.org/obo/UBERON_0009880` +#### Removed +- [carpal skeleton](http://purl.obolibrary.org/obo/UBERON_0009880) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The three main outgroup taxa of tetrapods, panderichthyids, osteolepiforms, and rhizodontids, have endoskeletal elements corresponding to the stylo- and zeugopodial elements in a tetrapod limb. In addition, there are elements that share the position and possibly the developmental derivation of the ulnare and the intermedium. From these observations, most authors have concluded that the stylo- and zeugopodial elements as well as the proximal mesopodial elements have counterparts in the fins of tetrapod ancestors, but there are no indications of wrist or ankle joints.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1002/jez.1100 Wagner GP, Chiu C, The tetrapod limb: A hypothesis on its origin. J Exp Zool (Mol Dev Evol) (2001)" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001161" + +- [carpal skeleton](http://purl.obolibrary.org/obo/UBERON_0009880) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "we assume MA:carpus belongs here, as there is a distinct class MA:wrist, with the carpal bone being part of the former. XAO:carpus is part of the forelimb skeleton. FMA set-of class lacks definition but we assume this to be equivalent." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" + +- [carpal skeleton](http://purl.obolibrary.org/obo/UBERON_0009880) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Segment of the forearm corresponding to the carpus. It consists of several elements that articulate with the radius and ulna at one end and the metacarpals at the other end.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000201" + +- [carpal skeleton](http://purl.obolibrary.org/obo/UBERON_0009880) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The structure of the carpus varies widely between different groups of tetrapods, even among those that retain the full set of five digits. In primitive fossil amphibians, such as Eryops, the carpus consists of three rows of bones; a proximal row of three carpals, a second row of four bones, and a distal row of five bones. The proximal carpals are referred to as the radiale, intermediale, and ulnare, after their proximal articulations, and are homologous with the scaphoid, lunate, and triquetal bones respectively. The remaining bones are simply numbered, as the first to fourth centralia (singular: centrale), and the first to fifth distal carpals. Primitively, each of the distal bones appears to have articulated with a single metacarpal. However, the vast majority of later vertebrates, including modern amphibians, have undergone varying degrees of loss and fusion of these primitive bones, resulting in a smaller number of carpals. Almost all mammals and reptiles, for example, have lost the fifth distal carpal, and have only a single centrale - and even this is missing in humans. The pisiform bone is somewhat unusual, in that it first appears in primitive reptiles, and is never found in amphibians. Because many tetrapods have less than five digits on the forelimb, even greater degrees of fusion are common, and a huge array of different possible combinations are found. The wing of a modern bird, for example, has only two remaining carpals; the radiale (the scaphoid of mammals) and a bone formed from the fusion of four of the distal carpals. In some macropods, the scaphoid and lunar bones are fused into the scaphollunar bone" + +- [carpal skeleton](http://purl.obolibrary.org/obo/UBERON_0009880) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Not always associated with digits, in sarcopterygians the ulnare is present without true digits being formed, though their homologous radial elements are present[PHENOSCAPE:ad]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Carpus#Evolutionary_variations" + + + +### carpometacarpal joint `http://purl.obolibrary.org/obo/UBERON_0011119` +#### Removed +- [carpometacarpal joint](http://purl.obolibrary.org/obo/UBERON_0011119) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D052737" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + + + +### cartilage element `http://purl.obolibrary.org/obo/UBERON_0007844` +#### Removed +- [cartilage element](http://purl.obolibrary.org/obo/UBERON_0007844) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:32730" + +- [cartilage element](http://purl.obolibrary.org/obo/UBERON_0007844) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "TAO still mixes tissue and element" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "TAO" + + + +### cartilage of external acoustic meatus `http://purl.obolibrary.org/obo/UBERON_0035606` + +#### Added +- [cartilage of external acoustic meatus](http://purl.obolibrary.org/obo/UBERON_0035606) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + +- [cartilage of external acoustic meatus](http://purl.obolibrary.org/obo/UBERON_0035606) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) + + +### cartilage tissue `http://purl.obolibrary.org/obo/UBERON_0002418` +#### Removed +- [cartilage tissue](http://purl.obolibrary.org/obo/UBERON_0002418) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000060" + +- [cartilage tissue](http://purl.obolibrary.org/obo/UBERON_0002418) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts.[VSAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000040" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PSPUB:0000170" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" + +- [cartilage tissue](http://purl.obolibrary.org/obo/UBERON_0002418) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Phylogenetic analysis suggests that cartilage arose independently in cnidarians, hemichordates, vertebrates, arthropods, annelids, brachiopods, and molluscs - or a common ancestor of brachiopods and molluscs (...). Analyses of cartilage as a tissue and of the development of invertebrate cartilages are consistent with homology between invertebrate and vertebrate cartilage. From the discussion above, it will be clear that understanding genetic changes underlying cartilage evolution is key to determining whether the multiple origins of cartilage represent parallel evolution.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1111/j.1525-142X.2011.00520.x Hall BK, Parallelism, deep homology, and evo-devo. Evolution and Development (2012)" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001207" + +- [cartilage tissue](http://purl.obolibrary.org/obo/UBERON_0002418) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A type of dense connective tissue. It is composed of cells called chondrocytes which are dispersed in a firm gel-like ground substance, called the matrix. Cartilage is avascular (contains no blood vessels) and nutrients are diffused through the matrix. Cartilage is found in the joints, the rib cage, the ear, the nose, in the throat and between intervertebral disks. It makes up virtually the entire skeleton in chondrichthyes.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000060" + +- [cartilage tissue](http://purl.obolibrary.org/obo/UBERON_0002418) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Portion of tissue which is connective tissue composed of collagen and/or elastin fibers and chondrocytes. Cartilage is avascular and provides both skeletal functions and a framework upon which bone is deposited.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001501" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + + +### cartilaginous condensation `http://purl.obolibrary.org/obo/UBERON_0005863` +#### Removed +- [cartilaginous condensation](http://purl.obolibrary.org/obo/UBERON_0005863) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "isa cell condensation in VSAO; has_part chondroblast in AEO" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "VSAO" + + + +### cartilaginous neurocranium `http://purl.obolibrary.org/obo/UBERON_0004761` +#### Removed +- [cartilaginous neurocranium](http://purl.obolibrary.org/obo/UBERON_0004761) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "AAO:0010153" + +- [cartilaginous neurocranium](http://purl.obolibrary.org/obo/UBERON_0004761) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in contrast to chondrocranium, this structure is entirely cartiliginous. In Chondricthyes this is the same as the neurocranium. FMA:76621 is an undefined fetal structure, so we assume the correct placement is here. Note that this is distinct from MA:0000317 which is the uberon:neurocranium (the part of the cranium that encloses the brain)" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + + + +### cartilaginous otic capsule `http://purl.obolibrary.org/obo/UBERON_0005410` +#### Removed +- [cartilaginous otic capsule](http://purl.obolibrary.org/obo/UBERON_0005410) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Bilaterally paired cartilage encasing the semicircular canals of the inner ear.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001500" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [cartilaginous otic capsule](http://purl.obolibrary.org/obo/UBERON_0005410) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In elasmobranchs, the otic capsule remains cartilaginous in the adult; in the embryos of higher vertebrates, it is cartilaginous at first but later becomes bony (at approximately 23 weeks in humans). todo - check EMAPA" + +- [cartilaginous otic capsule](http://purl.obolibrary.org/obo/UBERON_0005410) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:17596" + +- [cartilaginous otic capsule](http://purl.obolibrary.org/obo/UBERON_0005410) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship type change: overlaps neurocranium (TAO:0001580) CHANGED TO: part_of neurocranium (UBERON:0001703)[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001500" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [cartilaginous otic capsule](http://purl.obolibrary.org/obo/UBERON_0005410) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship type change: overlaps neurocranium (TAO:0001580) CHANGED TO: develops_from neurocranium (UBERON:0001703)[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001500" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + + +### cathepsin K `http://purl.obolibrary.org/obo/PR_000001850` +#### Removed +- [cathepsin K](http://purl.obolibrary.org/obo/PR_000001850) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [cathepsin K (human)](http://purl.obolibrary.org/obo/PR_P43235) + + + +### caudal artery `http://purl.obolibrary.org/obo/UBERON_0003086` +#### Removed +- [caudal artery](http://purl.obolibrary.org/obo/UBERON_0003086) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The posterior extension of the dorsal aorta to the tail region, which degenerates at metamorphosis.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0-226-55763-4" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0011023" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + +- [caudal artery](http://purl.obolibrary.org/obo/UBERON_0003086) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Extension of the dorsal aorta in the tail. Kimmel et al, 1995.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000011" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + + +### caudal region `http://purl.obolibrary.org/obo/UBERON_0006071` +#### Removed +- [caudal region](http://purl.obolibrary.org/obo/UBERON_0006071) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "This region is reduced in humans and corresponds to the coccyx" + +- [caudal region](http://purl.obolibrary.org/obo/UBERON_0006071) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "We follow XAO is distinguishing the tail region from the tail; the tail bud is part of the tail region; the tail starts after the tail bud" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "XAO" + + + +### caudal region of vertebral column `http://purl.obolibrary.org/obo/UBERON_0006076` +#### Removed +- [caudal region of vertebral column](http://purl.obolibrary.org/obo/UBERON_0006076) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Region of the vertebral column posterior to the caudal-sacral region, that may consists of two or three to more than 100 vertebrae. These vertebrae exhibit a gradual reduction in the sizes of their transverse processes and zygapophyses, but these structures are never entirely absent. All caudal vertebrae bear haemal arches.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000082" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:Duellman_and_Trueb_1994" + +- [caudal region of vertebral column](http://purl.obolibrary.org/obo/UBERON_0006076) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in AAO, this is posterior to the caudal-sacral region" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "AAO" + + + +### caudal vertebra `http://purl.obolibrary.org/obo/UBERON_0001095` +#### Removed +- [caudal vertebra](http://purl.obolibrary.org/obo/UBERON_0001095) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "we deliberately merge the MA classes as we believe them equivalent" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" + +- [caudal vertebra](http://purl.obolibrary.org/obo/UBERON_0001095) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Vertebrae bearing a hemal arch and spine. The most posterior caudal vertebrae support the caudal fin and are referred to as preural vertebrae.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000326" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + + +### caudate nucleus `http://purl.obolibrary.org/obo/UBERON_0001873` +#### Removed +- [caudate nucleus](http://purl.obolibrary.org/obo/UBERON_0001873) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Nucleus of brain which is an elongated crescent-shaped mass lying parallel and adjacent to the lateral ventricle throughout its extent[FMA:61833]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:61833" + + + +### caudate-putamen `http://purl.obolibrary.org/obo/UBERON_0005383` +#### Removed +- [caudate-putamen](http://purl.obolibrary.org/obo/UBERON_0005383) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "In the human, histologically the caudate nucleus and putamen are identically and share a common embryological origin[ISBN:0123813611]" + + + +### causal agent in process `http://purl.obolibrary.org/obo/RO_0002500` +#### Removed +- [causal agent in process](http://purl.obolibrary.org/obo/RO_0002500) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) [causal-relations](http://purl.obolibrary.org/obo/ro/docs/causal-relations) + + + +### causal relation between entities `http://purl.obolibrary.org/obo/RO_0002506` +#### Removed +- [causal relation between entities](http://purl.obolibrary.org/obo/RO_0002506) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [causal relation between entities](http://purl.obolibrary.org/obo/RO_0002506) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) [causal-relations](http://purl.obolibrary.org/obo/ro/docs/causal-relations) + +- [causal relation between entities](http://purl.obolibrary.org/obo/RO_0002506) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + + + +### causal relation between material entity and a process `http://purl.obolibrary.org/obo/RO_0002595` +#### Removed +- [causal relation between material entity and a process](http://purl.obolibrary.org/obo/RO_0002595) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [causal relation between material entity and a process](http://purl.obolibrary.org/obo/RO_0002595) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) [causal-relations](http://purl.obolibrary.org/obo/ro/docs/causal-relations) + + + +### causal relation between processes `http://purl.obolibrary.org/obo/RO_0002501` +#### Removed +- [causal relation between processes](http://purl.obolibrary.org/obo/RO_0002501) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + +- [causal relation between processes](http://purl.obolibrary.org/obo/RO_0002501) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) [causal-relations](http://purl.obolibrary.org/obo/ro/docs/causal-relations) + +- [causal relation between processes](http://purl.obolibrary.org/obo/RO_0002501) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + + + +### causally downstream of `http://purl.obolibrary.org/obo/RO_0002404` +#### Removed +- [causally downstream of](http://purl.obolibrary.org/obo/RO_0002404) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [causally downstream of](http://purl.obolibrary.org/obo/RO_0002404) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [requires discussion](http://purl.obolibrary.org/obo/IAO_0000428) + + + +### causally downstream of or within `http://purl.obolibrary.org/obo/RO_0002427` +#### Removed +- [causally downstream of or within](http://purl.obolibrary.org/obo/RO_0002427) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [causally downstream of or within](http://purl.obolibrary.org/obo/RO_0002427) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) [causal-relations](http://purl.obolibrary.org/obo/ro/docs/causal-relations) + + + +### causally influenced by `http://purl.obolibrary.org/obo/RO_0002559` +#### Removed +- [causally influenced by](http://purl.obolibrary.org/obo/RO_0002559) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [causally influenced by](http://purl.obolibrary.org/obo/RO_0002559) [IAO_0000589](http://purl.obolibrary.org/obo/IAO_0000589) "causally influenced by (entity-centric)" + +- [causally influenced by](http://purl.obolibrary.org/obo/RO_0002559) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) [causal-relations](http://purl.obolibrary.org/obo/ro/docs/causal-relations) + + + +### causally influences `http://purl.obolibrary.org/obo/RO_0002566` +#### Removed +- [causally influences](http://purl.obolibrary.org/obo/RO_0002566) [IAO_0000589](http://purl.obolibrary.org/obo/IAO_0000589) "causally influences (entity-centric)" + +- [causally influences](http://purl.obolibrary.org/obo/RO_0002566) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [causally influences](http://purl.obolibrary.org/obo/RO_0002566) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0003-4639-4431](https://orcid.org/0000-0003-4639-4431) + +- [causally influences](http://purl.obolibrary.org/obo/RO_0002566) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) [causal-relations](http://purl.obolibrary.org/obo/ro/docs/causal-relations) + + + +### causally related to `http://purl.obolibrary.org/obo/RO_0002410` +#### Removed +- [causally related to](http://purl.obolibrary.org/obo/RO_0002410) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." + +- [causally related to](http://purl.obolibrary.org/obo/RO_0002410) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + + + +### causally upstream of `http://purl.obolibrary.org/obo/RO_0002411` +#### Removed +- [causally upstream of](http://purl.obolibrary.org/obo/RO_0002411) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + + + +### causally upstream of or within `http://purl.obolibrary.org/obo/RO_0002418` +#### Removed +- [causally upstream of or within](http://purl.obolibrary.org/obo/RO_0002418) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [causally upstream of or within](http://purl.obolibrary.org/obo/RO_0002418) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "influences (processual)" + + + +### causally upstream of or within, positive effect `http://purl.obolibrary.org/obo/RO_0004047` +#### Removed +- [causally upstream of or within, positive effect](http://purl.obolibrary.org/obo/RO_0004047) [RO_0004049](http://purl.obolibrary.org/obo/RO_0004049) [causally upstream of or within](http://purl.obolibrary.org/obo/RO_0002418) + + + +### causally upstream of, negative effect `http://purl.obolibrary.org/obo/RO_0002305` +#### Removed +- [causally upstream of, negative effect](http://purl.obolibrary.org/obo/RO_0002305) [creator](http://purl.org/dc/terms/creator) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + + + +### causally upstream of, positive effect `http://purl.obolibrary.org/obo/RO_0002304` +#### Removed +- [causally upstream of, positive effect](http://purl.obolibrary.org/obo/RO_0002304) [RO_0004049](http://purl.obolibrary.org/obo/RO_0004049) [causally upstream of](http://purl.obolibrary.org/obo/RO_0002411) + +- [causally upstream of, positive effect](http://purl.obolibrary.org/obo/RO_0002304) [creator](http://purl.org/dc/terms/creator) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + + + +### cavernous sinus `http://purl.obolibrary.org/obo/UBERON_0003712` +#### Removed +- [cavernous sinus](http://purl.obolibrary.org/obo/UBERON_0003712) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "An irregularly shaped venous space in the dura mater at either side of the sphenoid bone[MESH:A07.231.908.224.334]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "MESH:A07.231.908.224.334" + + + +### cavitated compound organ `http://purl.obolibrary.org/obo/UBERON_0000489` +#### Removed +- [cavitated compound organ](http://purl.obolibrary.org/obo/UBERON_0000489) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future" + + + +### cavity of pharynx `http://purl.obolibrary.org/obo/UBERON_0001731` +#### Removed +- [cavity of pharynx](http://purl.obolibrary.org/obo/UBERON_0001731) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "See notes for pharynx - as a grouping class this is probably too bad. We exclude WBbt:0005790 (pharyngeal lumen) because of the developmental relationship" + +- [cavity of pharynx](http://purl.obolibrary.org/obo/UBERON_0001731) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "TOODO check" + + + +### cecal tonsil `http://purl.obolibrary.org/obo/UBERON_0013478` +#### Removed +- [cecal tonsil](http://purl.obolibrary.org/obo/UBERON_0013478) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In avians the polycryptic cecal tissue is similar to the mammalian palatine tonsil" + + + +### cell cluster organ `http://purl.obolibrary.org/obo/UBERON_0010001` +#### Removed +- [cell cluster organ](http://purl.obolibrary.org/obo/UBERON_0010001) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007229" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + + +### cellular bone tissue `http://purl.obolibrary.org/obo/UBERON_4000118` +#### Removed +- [cellular bone tissue](http://purl.obolibrary.org/obo/UBERON_4000118) [UBPROP_0000004](http://purl.obolibrary.org/obo/UBPROP_0000004) "This class was sourced from an external ontology (vertebrate_skeletal_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://purl.obolibrary.org/obo/vsao.owl" + +#### Added +- [cellular bone tissue](http://purl.obolibrary.org/obo/UBERON_4000118) SubClassOf [structure with developmental contribution from neural crest](http://purl.obolibrary.org/obo/UBERON_0010314) + + +### cementum `http://purl.obolibrary.org/obo/UBERON_0001753` +#### Removed +- [cementum](http://purl.obolibrary.org/obo/UBERON_0001753) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Odontoid tissue that is deposited by cementoblasts onto dentine tissue and functions to attach teeth, odontodes and other odontogenic derivatives to bone tissue and the integument.[VSAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000062" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PSPUB:0000170" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" + +- [cementum](http://purl.obolibrary.org/obo/UBERON_0001753) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Substance of tooth produced by cementoblasts; surrounds the dentine of the root of the tooth[FMA:55630]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:55630" + +- [cementum](http://purl.obolibrary.org/obo/UBERON_0001753) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Cementum, the supporting tissue that anchors mammalian and crocodylian teeth into their sockets, differs among species and can have features of dentine, of bone, and of calcified cartilage, as well as unique features. Cementum is deposited by cementoblasts onto existing dentine. As in bone and dentine, cementoblasts produce an organic matrix, the main constituent of which is collagen type I (Bosshardt, 2005), but cementum, dentine, and bone also share a number of important noncollagenous matrix components such as osteopontin, osteocalcin, bone sialoprotein, a2-HS- glycoprotein, dentine matrix protein, dentine sialoprotein, and den- tine phosphoprotein (McKee et al., 1996; Bosshardt, 2005). it has been argued that in all rodents and ruminants, cementum is a form of calcified cartilage[H&W]" + + + +### central nervous system `http://purl.obolibrary.org/obo/UBERON_0001017` +#### Removed +- [central nervous system](http://purl.obolibrary.org/obo/UBERON_0001017) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The brain and spinal cord. Kimmel et al, 1995.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000012" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [central nervous system](http://purl.obolibrary.org/obo/UBERON_0001017) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO)." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "BIRNLEX:1099" + +- [central nervous system](http://purl.obolibrary.org/obo/UBERON_0001017) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Part of the nervous system which includes the brain and spinal cord.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000090" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + +- [central nervous system](http://purl.obolibrary.org/obo/UBERON_0001017) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000293" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 (reference 1), ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 (reference 2), DOI:10.1016/j.cell.2007.02.040 Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud'homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007) (reference 3)" + +- [central nervous system](http://purl.obolibrary.org/obo/UBERON_0001017) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005094" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + + +### central nervous system cell part cluster `http://purl.obolibrary.org/obo/UBERON_0011215` + +#### Added +- [central nervous system cell part cluster](http://purl.obolibrary.org/obo/UBERON_0011215) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### central tendon of diaphragm `http://purl.obolibrary.org/obo/UBERON_0006670` +#### Removed +- [central tendon of diaphragm](http://purl.obolibrary.org/obo/UBERON_0006670) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In mammals, the diaphragm muscle divides the thoracoabdominal cavity into thorax and abdomen. In most mammals, the diaphragm is a flat sheet with muscle fibers radiating outward from a central tendon, and the diaphragm's apposition to the cranial surface of the liver gives it a dome-shape. Muscle fiber contraction reduces the curvature of the dome, thereby expanding the thoracic cavity and aspirating air into the lungs.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1016/j.resp.2006.06.003" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001399" + +- [central tendon of diaphragm](http://purl.obolibrary.org/obo/UBERON_0006670) SubClassOf [immediate transformation of](http://purl.obolibrary.org/obo/RO_0002495) some [future central tendon](http://purl.obolibrary.org/obo/UBERON_0006239) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" + +#### Added +- [central tendon of diaphragm](http://purl.obolibrary.org/obo/UBERON_0006670) SubClassOf [immediate transformation of](http://purl.obolibrary.org/obo/RO_0002495) some [future central tendon](http://purl.obolibrary.org/obo/UBERON_0006239) + + +### cerebellar cortex `http://purl.obolibrary.org/obo/UBERON_0002129` +#### Removed +- [cerebellar cortex](http://purl.obolibrary.org/obo/UBERON_0002129) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002130](http://purl.obolibrary.org/obo/UBERON_0002130) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" + +- [cerebellar cortex](http://purl.obolibrary.org/obo/UBERON_0002129) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The cerebellar cortex is a thin mantle of gray matter that covers the surface of each cerebral hemisphere. It has a characteristic morphology with convolutions (gyri) and crevices (sulci) that have specific functions. Six layers of nerve cells and the nerve pathways that connect them comprise the cerebellar cortex. Together, these regions are responsible for the processes of conscious thought, perception, emotion and memory as well as advanced motor function[GO][GO:0021695]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GO:0021695" + + + +### cerebellum `http://purl.obolibrary.org/obo/UBERON_0002037` +#### Removed +- [cerebellum](http://purl.obolibrary.org/obo/UBERON_0002037) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Dorsal part of the hindbrain that coordinates muscle movement, posture, and balance.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010485" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + +- [cerebellum](http://purl.obolibrary.org/obo/UBERON_0002037) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "almost all AOs agree that the cerebellum is part of the hindbrain (sometimes specifically part of the metencephalon, which, when present, is part of the hindbrain). However, ABA has cerebellum and brain stem as partof siblings, with the hindbrain part of the brainstem" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "ABA" + +- [cerebellum](http://purl.obolibrary.org/obo/UBERON_0002037) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [telencephalon](http://purl.obolibrary.org/obo/UBERON_0001893) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" + +- [cerebellum](http://purl.obolibrary.org/obo/UBERON_0002037) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "However, although the lamprey possesses a region comparable to the cerebellum and display expression of LjFgf8/17 at the MHB (midbrain hindbrain boundary), it does not have Purkinje cells and cerebellar nuclei, as well as components of the rhombic lip-derived cerebellar and pre-cerebellar systems. It is noteworthy that the latter structures require specific expression of Pax6 in the rhombic lip of the gnathostome hindbrain. Interestingly, the lamprey rhombic lip does not express Pax6. Thus, it is tempting to speculate that in vertebrate evolution the rostral hindbrain is incapable of differentiating into the cerebellum before the co-option of Pax6 in that region. In other words, cerebellum has been brought about as an evolutionary innovation in gnathostomes, based on exaptation of MHB, rhombic lip, and some regulatory gene expression already present in the vertebrate common ancestor.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1016/j.ydbio.2005.02.008 Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005)" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000024" + +- [cerebellum](http://purl.obolibrary.org/obo/UBERON_0002037) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Specialized brain region derived from the dorsal metencephalon (anterior hindbrain, and perhaps including posterior midbrain) and becoming distinctive late in the segmentation period. Kimmel et al, 1995.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000100" + +- [cerebellum](http://purl.obolibrary.org/obo/UBERON_0002037) [RO_0002174](http://purl.obolibrary.org/obo/RO_0002174) [NCBITaxon_117569](http://purl.obolibrary.org/obo/NCBITaxon_117569) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://icb.oxfordjournals.org/content/42/4/743.full" + +- [cerebellum](http://purl.obolibrary.org/obo/UBERON_0002037) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The absence of a cerebellum in hagfishes and lampreys appears to be the only exception [to the rule that vertebrates possess the same number of brain divisions]. Both hagfishes and lampreys do possess a thin band of cells located medial to the lateral line centers of the medulla (Ronan and Northcutt, 1998), which has been interpreted as a primitive cerebellum (Larsell, 1967), but more recent experimental studies (Kishida et al., 1987; Weigle and Northcutt, 1998) fail to support Larsell's claim[http://icb.oxfordjournals.org/content/42/4/743.full]" + +- [cerebellum](http://purl.obolibrary.org/obo/UBERON_0002037) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [brainstem](http://purl.obolibrary.org/obo/UBERON_0002298) + - [exceptions](http://www.geneontology.org/formats/oboInOwl#exceptions) "ZFA" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "https://github.com/obophenotype/uberon/issues/378" + + - [status](http://www.geneontology.org/formats/oboInOwl#status) "pending" + +- [cerebellum](http://purl.obolibrary.org/obo/UBERON_0002037) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "cerebellar" + +- [cerebellum](http://purl.obolibrary.org/obo/UBERON_0002037) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [rhombic lip](http://purl.obolibrary.org/obo/UBERON_0006215) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" + +#### Added +- [cerebellum](http://purl.obolibrary.org/obo/UBERON_0002037) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [rhombic lip](http://purl.obolibrary.org/obo/UBERON_0006215) + + +### cerebellum fissure `http://purl.obolibrary.org/obo/UBERON_0003980` +#### Removed +- [cerebellum fissure](http://purl.obolibrary.org/obo/UBERON_0003980) [UBPROP_0000202](http://purl.obolibrary.org/obo/UBPROP_0000202) [FMA_77789](http://purl.obolibrary.org/obo/FMA_77789) + + + +### cerebellum marginal layer `http://purl.obolibrary.org/obo/UBERON_0034708` +#### Removed +- [cerebellum marginal layer](http://purl.obolibrary.org/obo/UBERON_0034708) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "In the cerebellum, some neuronal precursors enter the marginal zone to form clusters of neurons called nuclei[NBK10047]" + + + +### cerebral artery `http://purl.obolibrary.org/obo/UBERON_0004449` +#### Removed +- [cerebral artery](http://purl.obolibrary.org/obo/UBERON_0004449) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in AAO this is part_of the internal carotid, but in humans the PCA intervenes for some cerebral arteries. Proper comparative review required" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "AAO" + +- [cerebral artery](http://purl.obolibrary.org/obo/UBERON_0004449) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Part of the internal carotid containing many branches supplying blood to the chorioid plexuses of the brain.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010493" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + +- [cerebral artery](http://purl.obolibrary.org/obo/UBERON_0004449) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: part_of internal carotid (AAO:0010219)[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010493" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + + +### cerebral cortex `http://purl.obolibrary.org/obo/UBERON_0000956` +#### Removed +- [cerebral cortex](http://purl.obolibrary.org/obo/UBERON_0000956) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "We follow NIFSTD in defining cerebral cortex and including both neocortex and hippocampal formation (DG+hippocampus)." + +- [cerebral cortex](http://purl.obolibrary.org/obo/UBERON_0000956) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "hagfishes have independently evolved a highly laminated cerebral cortex, comparable in many ways to the cerebral cortex of mammals [http://icb.oxfordjournals.org/content/42/4/743]" + +- [cerebral cortex](http://purl.obolibrary.org/obo/UBERON_0000956) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Migration of neurons from the basal or striatal portions of the anterior part of the neural tube occurs to varying degrees in different vertebrate classes, but a true cerebral cortex is generally acknowledged to have made its first appearance in reptiles. The definition can be unambiguous, since 'cortex' simply implies the existence of a surface neuronal layer with an overlying 'zonal lamina' or 'molecular' layer containing dendrites and axons, which is separated from the underlying basal 'matrix' by white matter. Although reptilian cerebral cortex does indeed fulfill these conditions in certain locations, the separation from striatal structures is often indistinct, so that it may even be argued that some primitive dipnoans possess a pallium or cortex. Nevertheless, an extensive laminated layer separated by underlying white matter is well represented only in reptiles and mammals.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000722" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1111/j.1749-6632.1969.tb20437.x Kruger L, Experimental analyses of the reptilian nervous system. Annals of the New York Academy of Sciences (1969)" + +- [cerebral cortex](http://purl.obolibrary.org/obo/UBERON_0000956) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The cerebral cortex is a structure within the brain that plays a key role in memory, attention, perceptual awareness, thought, language, and consciousness. It constitutes the outermost layer of the cerebrum. In preserved brains, it has a grey color, hence the name 'grey matter'. Grey matter is formed by neurons and their unmyelinated fibers, whereas the white matter below the grey matter of the cortex is formed predominantly by myelinated axons interconnecting different regions of the central nervous system. The human cerebral cortex is 2-4 mm (0.08-0.16 inches) thick. The surface of the cerebral cortex is folded in large mammals, such that more than two-thirds of the cortical surface is buried in the grooves, called 'sulci. ' The phylogenetically most recent part of the cerebral cortex, the neocortex, also called isocortex, is differentiated into six horizontal layers; the more ancient part of the cerebral cortex, the hippocampus (also called archicortex), has at most three cellular layers, and is divided into subfields. Relative variations in thickness or cell type (among other parameters) allow us to distinguish between different neocortical architectonic fields. The geometry of at least some of these fields seems to be related to the anatomy of the cortical folds, and, for example, layers in the upper part of the cortical ridges seem to be more clearly differentiated than in its deeper parts. [WP,unvetted][Wikipedia:Cerebral_cortex]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Cerebral_cortex" + + + +### cerebral cortex marginal layer `http://purl.obolibrary.org/obo/UBERON_0014935` +#### Removed +- [cerebral cortex marginal layer](http://purl.obolibrary.org/obo/UBERON_0014935) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "EMAPA temporally divides this into zone and layer. TODO - unify this with marginal layers in EHDAA2" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EMAPA" + +- [cerebral cortex marginal layer](http://purl.obolibrary.org/obo/UBERON_0014935) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "in humans develops into cortical layer I" + + + +### cerebral hemisphere `http://purl.obolibrary.org/obo/UBERON_0001869` +#### Removed +- [cerebral hemisphere](http://purl.obolibrary.org/obo/UBERON_0001869) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Part of the telencephalon consisting of either of the two smooth, elongated halves of the cerebrum.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010480" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + +- [cerebral hemisphere](http://purl.obolibrary.org/obo/UBERON_0001869) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The presence of paired evaginated hemispheres and olfactory bulbs in both agnathan and gnathostome radiations suggests that such hemispheres were also present in the common ancestor.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1146/annurev.ne.04.030181.001505 Northcutt RG, Evolution of the telencephalon in nonmammals. Ann. Rev. Neurosci. (1981)" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001639" + +#### Added +- [cerebral hemisphere](http://purl.obolibrary.org/obo/UBERON_0001869) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### cerebral hemisphere gray matter `http://purl.obolibrary.org/obo/UBERON_0005401` +#### Removed +- [cerebral hemisphere gray matter](http://purl.obolibrary.org/obo/UBERON_0005401) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "BTO may actually be a more generic structure; FMA may represent a more specific structure. Consider merging with gray matter of telencephalon" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "BTO" + + + +### cerebral hemisphere white matter `http://purl.obolibrary.org/obo/UBERON_0002437` +#### Removed +- [cerebral hemisphere white matter](http://purl.obolibrary.org/obo/UBERON_0002437) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "sometimes the term 'cerebral white matter' may be used generically but here is refers specifically to the white matter in a hemisphere" + +- [cerebral hemisphere white matter](http://purl.obolibrary.org/obo/UBERON_0002437) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "The BTO class is inconsistent as it is part of the brain and spinal cord." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "BTO" + + + +### cerebral subcortex `http://purl.obolibrary.org/obo/UBERON_0000454` + +#### Added +- [cerebral subcortex](http://purl.obolibrary.org/obo/UBERON_0000454) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### cerebral vein `http://purl.obolibrary.org/obo/UBERON_0001663` +#### Removed +- [cerebral vein](http://purl.obolibrary.org/obo/UBERON_0001663) [UBPROP_0000202](http://purl.obolibrary.org/obo/UBPROP_0000202) [FMA_70861](http://purl.obolibrary.org/obo/FMA_70861) + + + +### cerebrospinal fluid `http://purl.obolibrary.org/obo/UBERON_0001359` +#### Removed +- [cerebrospinal fluid](http://purl.obolibrary.org/obo/UBERON_0001359) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "the FMA def states that this is subarachnoid spaces only. ZFA def states subarachnoid spaces and brain ventricles, but not SC (and has part_of to brain). Circulation: It circulates from the lateral ventricles to the foramen of Monro (Interventricular foramen), third ventricle, aqueduct of Sylvius (Cerebral aqueduct), fourth ventricle, foramen of Magendie (Median aperture) and foramina of Luschka (Lateral apertures), subarachnoid space over brain and spinal cord. It should be noted that the CSF moves in a pulsatile manner throughout the CSF system with nearly zero net flow. CSF is reabsorbed into venous sinus blood via arachnoid granulations." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + +- [cerebrospinal fluid](http://purl.obolibrary.org/obo/UBERON_0001359) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In vertebrates, at early stages of Central Nervous System (CNS) development, the architecture of the brain primordium reveals the presence of the cavity of brain vesicles, which is filled by Embryonic Cerebro-Spinal Fluid (E-CSF). (...) Rat and chick E-CSF proteomes are similar, although rat is more complex in certain groups of proteins, e.g., apolipoproteins, which may be involved in the control of neural diversity, and has soluble enzymes present, just like adult human CSF, but unlike chick E-CSF, revealing phylogenetic brain differences between these groups of vertebrates.[uncertain][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001278" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1021/pr050213t Parada C, Gato A, Bueno D, Mammalian embryonic cerebrospinal fluid proteome has greater apolipoprotein and enzyme pattern complexity than the avian proteome. Journal of Proteome Research (2005)" + +- [cerebrospinal fluid](http://purl.obolibrary.org/obo/UBERON_0001359) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "EHDAA2 models this as developing from CP, which is wrong" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EHDAA2" + +- [cerebrospinal fluid](http://purl.obolibrary.org/obo/UBERON_0001359) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Portion of organism substance that is a clear fluid that occupies the subarachnoid space and the ventricular system around and inside the brain.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0002184" + +- [cerebrospinal fluid](http://purl.obolibrary.org/obo/UBERON_0001359) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [choroid plexus of lateral ventricle](http://purl.obolibrary.org/obo/UBERON_0002307) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "EHDAA2" + + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "see notes" + +#### Added +- [cerebrospinal fluid](http://purl.obolibrary.org/obo/UBERON_0001359) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [choroid plexus of lateral ventricle](http://purl.obolibrary.org/obo/UBERON_0002307) + + +### cervical gland `http://purl.obolibrary.org/obo/UBERON_0012247` +#### Removed +- [cervical gland](http://purl.obolibrary.org/obo/UBERON_0012247) [UBPROP_0000202](http://purl.obolibrary.org/obo/UBPROP_0000202) [FMA_71646](http://purl.obolibrary.org/obo/FMA_71646) + + + +### cervical mammary gland `http://purl.obolibrary.org/obo/UBERON_0005199` +#### Removed +- [cervical mammary gland](http://purl.obolibrary.org/obo/UBERON_0005199) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "mice have a single pair of cervical mammary glands" + + + +### cervical region of vertebral column `http://purl.obolibrary.org/obo/UBERON_0006072` +#### Removed +- [cervical region of vertebral column](http://purl.obolibrary.org/obo/UBERON_0006072) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anterior region of the vertebral column consisting of one to 19 or 20 vertebrae.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000092" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:Duellman_and_Trueb_1994" + + + +### cervical rib `http://purl.obolibrary.org/obo/UBERON_0018144` +#### Removed +- [cervical rib](http://purl.obolibrary.org/obo/UBERON_0018144) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D057070" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + +- [cervical rib](http://purl.obolibrary.org/obo/UBERON_0018144) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "May be homologous with the transverse processes of cervical vertebra" + + + +### cervical spinal cord `http://purl.obolibrary.org/obo/UBERON_0002726` +#### Removed +- [cervical spinal cord](http://purl.obolibrary.org/obo/UBERON_0002726) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D066193" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + + + +### cervical spinal cord ventral horn `http://purl.obolibrary.org/obo/UBERON_0014621` +#### Removed +- [cervical spinal cord ventral horn](http://purl.obolibrary.org/obo/UBERON_0014621) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D066151" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + + + +### cervical thymus `http://purl.obolibrary.org/obo/UBERON_0009114` +#### Removed +- [cervical thymus](http://purl.obolibrary.org/obo/UBERON_0009114) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "A cervical thymus is a pathological structure in a human - it can form during the migration of the thymus to its location in the mediastinum. Some mice have a cervical thymus. There are examples of cervical thymi in marsupials and prosimians[ISBN:0781714125]" + + + +### cervical vertebra `http://purl.obolibrary.org/obo/UBERON_0002413` +#### Removed +- [cervical vertebra](http://purl.obolibrary.org/obo/UBERON_0002413) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In some species, some parts of the skull may be composed of vertebra-like elements, e.g. the occipital bone in humans is composed of four vertebra-like segments. In many vertebrate species, cervical vertebrae are variable in number; however, almost all mammals have seven (including those with very short necks relative to body size, such as elephants or whales, and those with very long necks, such as giraffes). The few exceptions include the manatee and the sloths, of which the two-toed sloth has six cervical vertebrae and the three-toed sloth has up to nine cervical vertebrae. In many species, though not in mammals, the cervical vertebrae bear ribs. In many other groups, such as lizards and saurischian dinosaurs, the cervical ribs are large; in birds they are small and completely fused to the vertebrae. The transverse processes of mammals are homologous to the cervical ribs of other amniotes. Thoracic vertebrae in all species are defined as those vertebrae which also carry a pair of ribs, and lie caudal to the cervical vertebrae. In humans, cervical vertebrae are the smallest of the true vertebrae, and can be readily distinguished from those of the thoracic or lumbar regions by the presence of a foramen (hole) in each transverse process, through which passes the vertebral artery." + + + +### cervix epithelium `http://purl.obolibrary.org/obo/UBERON_0004801` +#### Removed +- [cervix epithelium](http://purl.obolibrary.org/obo/UBERON_0004801) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "The epithelium of the cervix is varied. The ectocervix (more distal, by the vagina) is composed of nonkeratinized stratified squamous epithelium. The endocervix (more proximal, within the uterus) is composed of simple columnar epithelium" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Cervix#Histology" + + + +### cervix glandular epithelium `http://purl.obolibrary.org/obo/UBERON_0012250` +#### Removed +- [cervix glandular epithelium](http://purl.obolibrary.org/obo/UBERON_0012250) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "The 'glandular' or columnar epithelium of the cervix is located cephalad to the squamocolumnar junction. It covers a variable amount of the ectocervix and lines the endocervical canal. It is comprised of a single layer of mucin-secreting cells. The epithelium is thrown into longitudinal folds and invaginations that make up the so-called endocervical glands (they are not true glands). These infolding crypts and channels make the cytologic and colposcopic detection of neoplasia less reliable and more problematic. The complex architecture of the endocervical glands gives the columnar epithelium a papillary appearance through the colposcope and a grainy appearance upon gross visual inspection. The single cell layer allows the coloration of the underlying vasculature to be seen more easily. Therefore, the columnar epithelium appears more red in comparison with the more opaque squamous epithelium." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://www.asccp.org/practicemanagement/cervix/histologyofthenormalcervix/tabid/5842/default.aspx" + + + +### chamber of eyeball `http://purl.obolibrary.org/obo/UBERON_0006311` + +#### Added +- [chamber of eyeball](http://purl.obolibrary.org/obo/UBERON_0006311) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### channel for `http://purl.obolibrary.org/obo/uberon/core#channel_for` +#### Removed +- [channel for](http://purl.obolibrary.org/obo/uberon/core#channel_for) Domain [anatomical conduit](http://purl.obolibrary.org/obo/UBERON_0004111) + +- [channel for](http://purl.obolibrary.org/obo/uberon/core#channel_for) Range [organism substance](http://purl.obolibrary.org/obo/UBERON_0000463) + + + +### channels_from `http://purl.obolibrary.org/obo/uberon/core#channels_from` +#### Removed +- Transitive: [channels_from](http://purl.obolibrary.org/obo/uberon/core#channels_from) + + + +### channels_into `http://purl.obolibrary.org/obo/uberon/core#channels_into` +#### Removed +- Transitive: [channels_into](http://purl.obolibrary.org/obo/uberon/core#channels_into) + + + +### characteristic of `http://purl.obolibrary.org/obo/RO_0000052` +#### Removed +- [characteristic of](http://purl.obolibrary.org/obo/RO_0000052) [RO_0001900](http://purl.obolibrary.org/obo/RO_0001900) [RO_0001901](http://purl.obolibrary.org/obo/RO_0001901) + +- [characteristic of](http://purl.obolibrary.org/obo/RO_0000052) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "inheres in"@en + +- [characteristic of](http://purl.obolibrary.org/obo/RO_0000052) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "this red color is a characteristic of this apple"@en + +- [characteristic of](http://purl.obolibrary.org/obo/RO_0000052) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "this fragility is a characteristic of this vase"@en + +- [characteristic of](http://purl.obolibrary.org/obo/RO_0000052) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "inheres_in"@en + + + +### characteristic of part of `http://purl.obolibrary.org/obo/RO_0002314` +#### Removed +- [characteristic of part of](http://purl.obolibrary.org/obo/RO_0002314) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) [20064205](http://www.ncbi.nlm.nih.gov/pubmed/20064205) + +- [characteristic of part of](http://purl.obolibrary.org/obo/RO_0002314) [RO_0001900](http://purl.obolibrary.org/obo/RO_0001900) [RO_0001901](http://purl.obolibrary.org/obo/RO_0001901) + +- [characteristic of part of](http://purl.obolibrary.org/obo/RO_0002314) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [characteristic of part of](http://purl.obolibrary.org/obo/RO_0002314) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "inheres in part of" + +- [characteristic of](http://purl.obolibrary.org/obo/RO_0000052) o [part_of](http://purl.obolibrary.org/obo/BFO_0000050) SubPropertyOf: [characteristic of part of](http://purl.obolibrary.org/obo/RO_0002314) + - [is a defining property chain axiom where second argument is reflexive](http://purl.obolibrary.org/obo/RO_0002582) true + + + +### chemosensory organ `http://purl.obolibrary.org/obo/UBERON_0000005` +#### Removed +- [chemosensory organ](http://purl.obolibrary.org/obo/UBERON_0000005) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005157" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + + +### chest `http://purl.obolibrary.org/obo/UBERON_0001443` +#### Removed +- [chest](http://purl.obolibrary.org/obo/UBERON_0001443) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "pectoral" + +- [chest](http://purl.obolibrary.org/obo/UBERON_0001443) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [abdomen](http://purl.obolibrary.org/obo/UBERON_0000916) + +- [chest](http://purl.obolibrary.org/obo/UBERON_0001443) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "thoracic" + + + +### chest muscle `http://purl.obolibrary.org/obo/UBERON_0002426` +#### Removed +- [chest muscle](http://purl.obolibrary.org/obo/UBERON_0002426) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:17748" + + + +### chest wall `http://purl.obolibrary.org/obo/UBERON_0016435` +#### Removed +- [chest wall](http://purl.obolibrary.org/obo/UBERON_0016435) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D035441" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + + + +### cholecystokinin `http://purl.obolibrary.org/obo/PR_000005110` +#### Removed +- [cholecystokinin](http://purl.obolibrary.org/obo/PR_000005110) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [cholecystokinin (human)](http://purl.obolibrary.org/obo/PR_P06307) + + + +### chondrocranium `http://purl.obolibrary.org/obo/UBERON_0002241` +#### Removed +- [chondrocranium](http://purl.obolibrary.org/obo/UBERON_0002241) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010169" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + +- [chondrocranium](http://purl.obolibrary.org/obo/UBERON_0002241) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "covers the brain dorsally in chondrichthyans" + +- [chondrocranium](http://purl.obolibrary.org/obo/UBERON_0002241) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "chondrocranial" + +- [chondrocranium](http://purl.obolibrary.org/obo/UBERON_0002241) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical cluster that is part of the cranium and composed of cartilage and cartilage replacement bones.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001424" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + + +### chondrolectin `http://purl.obolibrary.org/obo/PR_000005444` +#### Removed +- [chondrolectin](http://purl.obolibrary.org/obo/PR_000005444) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [chondrolectin (human)](http://purl.obolibrary.org/obo/PR_Q9H9P2) + + + +### chordal neural plate `http://purl.obolibrary.org/obo/UBERON_0003057` +#### Removed +- [chordal neural plate](http://purl.obolibrary.org/obo/UBERON_0003057) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001201" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28" + + + +### chordamesoderm `http://purl.obolibrary.org/obo/UBERON_0004880` +#### Removed +- [chordamesoderm](http://purl.obolibrary.org/obo/UBERON_0004880) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Notochord rudiment[ZFIN:ZDB-PUB-961014-576]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:ZDB-PUB-961014-576" + +- [chordamesoderm](http://purl.obolibrary.org/obo/UBERON_0004880) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord." + + + +### chordate pharyngeal muscle `http://purl.obolibrary.org/obo/UBERON_0000933` +#### Removed +- [chordate pharyngeal muscle](http://purl.obolibrary.org/obo/UBERON_0000933) [UBPROP_0000202](http://purl.obolibrary.org/obo/UBPROP_0000202) [FMA_67169](http://purl.obolibrary.org/obo/FMA_67169) + +- [chordate pharyngeal muscle](http://purl.obolibrary.org/obo/UBERON_0000933) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:18963" + +- [chordate pharyngeal muscle](http://purl.obolibrary.org/obo/UBERON_0000933) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A pharyngeal muscle is any muscle that forms part of the pharynx[GO]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GOC:go_curators" + + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "does not quite work for some muscles such as stylopharyngeus" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-30" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "GO:0043282" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "GO" + + + +### chordate pharynx `http://purl.obolibrary.org/obo/UBERON_0001042` +#### Removed +- [chordate pharynx](http://purl.obolibrary.org/obo/UBERON_0001042) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills[ZFA:0000056, ZFIN:ZDB-PUB-961014-576]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:ZDB-PUB-961014-576" + +- [chordate pharynx](http://purl.obolibrary.org/obo/UBERON_0001042) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A funnel-shaped fibromuscular tube that conducts food to the ESOPHAGUS, and air to the LARYNYX and LUNGS. It is located posterior to the NASAL CAVITY; ORAL CAVITY; and LARYNX, and extends from the SKULL BASE to the inferior border of the CRICOID CARTILAGE anteriorly and to the inferior border of the C6 vertebra posteriorly. It is divided into the NASOPHARYNX; OROPHARYNX; and HYPOPHARYNX (laryngopharynx)[MESH:A03.867]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "MESH:A03.867" + +- [chordate pharynx](http://purl.obolibrary.org/obo/UBERON_0001042) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Swollen region of the anterior foregut, posterior to the mouth and anterior to the liver; its walls form the jaws and gills. Kimmel et al, 1995.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000056" + +- [chordate pharynx](http://purl.obolibrary.org/obo/UBERON_0001042) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: part_of respiratory system (UBERON:0001004)[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000967" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + +- [chordate pharynx](http://purl.obolibrary.org/obo/UBERON_0001042) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The portion of the alimentary canal between the mouth and the oesophagus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000462" + +- [chordate pharynx](http://purl.obolibrary.org/obo/UBERON_0001042) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "MA/FMA pharynx not part of digestive/alimentary system, we are consistent with this scheme" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" + +- [chordate pharynx](http://purl.obolibrary.org/obo/UBERON_0001042) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship type change: part_of_proxy respiratory system (AAO:0000541) CHANGED TO: develops_from respiratory system (UBERON:0001004)[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000967" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + +- [chordate pharynx](http://purl.obolibrary.org/obo/UBERON_0001042) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical cavity bounded by the derivatives of the branchial arches.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000967" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + +- [chordate pharynx](http://purl.obolibrary.org/obo/UBERON_0001042) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) the earliest vertebrates possessed unjointed internal and external branchial arches, and musculature encircling the pharynx.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) Box essay 13.1 and Box figure I, p.502-503" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000462" + + + +### chordotonal organ `http://purl.obolibrary.org/obo/UBERON_0001038` +#### Removed +- [chordotonal organ](http://purl.obolibrary.org/obo/UBERON_0001038) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005215" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + + +### chorion membrane `http://purl.obolibrary.org/obo/UBERON_0003124` +#### Removed +- [chorion membrane](http://purl.obolibrary.org/obo/UBERON_0003124) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.187" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000200" + +- [chorion membrane](http://purl.obolibrary.org/obo/UBERON_0003124) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "Extra-embryonic ectoderm" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:19829370" + +- [chorion membrane](http://purl.obolibrary.org/obo/UBERON_0003124) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The outer membrane of the two membranes enclosing the embryo in reptiles, birds, and mammals. In placental mammals it contributes to the development of the placenta[BTO:0000252]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "BTO:0000252" + +- [chorion membrane](http://purl.obolibrary.org/obo/UBERON_0003124) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The chorion of placentals is bilaminar as in reptiles and birds, but forms from the trophoblast and includes the ajdacent mesodermal layer [ISBN:0073040584]" + +- [chorion membrane](http://purl.obolibrary.org/obo/UBERON_0003124) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The outer membrane enclosing the embryo in reptiles, birds, and mammals. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/chorion" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000200" + +- [chorion membrane](http://purl.obolibrary.org/obo/UBERON_0003124) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "chorionic" + +#### Added +- [chorion membrane](http://purl.obolibrary.org/obo/UBERON_0003124) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### chorion syncytiotrophoblast `http://purl.obolibrary.org/obo/UBERON_0003224` +#### Removed +- [chorion syncytiotrophoblast](http://purl.obolibrary.org/obo/UBERON_0003224) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [syncytiotrophoblast](http://purl.obolibrary.org/obo/UBERON_0000371) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "polar trophectoderm syncytiotrophoblast" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "EHDAA2" + +#### Added +- [chorion syncytiotrophoblast](http://purl.obolibrary.org/obo/UBERON_0003224) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [syncytiotrophoblast](http://purl.obolibrary.org/obo/UBERON_0000371) + + +### chorionic plate `http://purl.obolibrary.org/obo/UBERON_0004027` + +#### Added +- [chorionic plate](http://purl.obolibrary.org/obo/UBERON_0004027) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### chorionic villous mesenchyme `http://purl.obolibrary.org/obo/UBERON_8600039` +#### Removed +- [chorionic villous mesenchyme](http://purl.obolibrary.org/obo/UBERON_8600039) SubClassOf [embryonic tissue](http://purl.obolibrary.org/obo/UBERON_0005291) + +#### Added +- [chorionic villous mesenchyme](http://purl.obolibrary.org/obo/UBERON_8600039) SubClassOf [mesenchyme from somatopleure](http://purl.obolibrary.org/obo/UBERON_0010377) + + +### chorionic villus `http://purl.obolibrary.org/obo/UBERON_0007106` +#### Removed +- [chorionic villus](http://purl.obolibrary.org/obo/UBERON_0007106) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The mouse and human placentas have labyrinthine and villous types of interdigitation between maternal and fetal tissues, respectively" + +- [chorionic villus](http://purl.obolibrary.org/obo/UBERON_0007106) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "The bulk of the villi consist of connective tissues in which blood vessels are found. Most of the cells in the connective tissue core of the villi are fibroblasts. Macrophages known as Hofbauer cells are also present." + + + +### chorioretinal region `http://purl.obolibrary.org/obo/UBERON_0019207` + +#### Added +- [chorioretinal region](http://purl.obolibrary.org/obo/UBERON_0019207) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + +- [chorioretinal region](http://purl.obolibrary.org/obo/UBERON_0019207) SubClassOf [structure with developmental contribution from neural crest](http://purl.obolibrary.org/obo/UBERON_0010314) + + +### choroid epiplexus macrophage `http://purl.obolibrary.org/obo/CL_4042004` + +#### Added +- [choroid epiplexus macrophage](http://purl.obolibrary.org/obo/CL_4042004) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A choroid plexus macrophage that is part of the apical surface of some choroid plexus epithelium. This macrophage has a star-like shaped body." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31061494" + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37232741" + +- [choroid epiplexus macrophage](http://purl.obolibrary.org/obo/CL_4042004) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "epiplexus cpMΦ" + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [abbreviation](http://purl.obolibrary.org/obo/OMO_0003000) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38347231" + +- [choroid epiplexus macrophage](http://purl.obolibrary.org/obo/CL_4042004) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) + +- [choroid epiplexus macrophage](http://purl.obolibrary.org/obo/CL_4042004) [label](http://www.w3.org/2000/01/rdf-schema#label) "choroid epiplexus macrophage"@en + +- [choroid epiplexus macrophage](http://purl.obolibrary.org/obo/CL_4042004) [date](http://purl.org/dc/terms/date) "2024-03-26T19:14:58Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- [choroid epiplexus macrophage](http://purl.obolibrary.org/obo/CL_4042004) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "Kolmer’s cell" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31433571" + +- [choroid epiplexus macrophage](http://purl.obolibrary.org/obo/CL_4042004) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cpepiMΦ" + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [abbreviation](http://purl.obolibrary.org/obo/OMO_0003000) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38347231" + +- Class: [choroid epiplexus macrophage](http://purl.obolibrary.org/obo/CL_4042004) + +- [choroid epiplexus macrophage](http://purl.obolibrary.org/obo/CL_4042004) SubClassOf [choroid-plexus macrophage](http://purl.obolibrary.org/obo/CL_0000880) + +- [choroid epiplexus macrophage](http://purl.obolibrary.org/obo/CL_4042004) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [choroid plexus epithelium](http://purl.obolibrary.org/obo/UBERON_0003911) + + +### choroid plexus `http://purl.obolibrary.org/obo/UBERON_0001886` +#### Removed +- [choroid plexus](http://purl.obolibrary.org/obo/UBERON_0001886) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "choroidal" + +- [choroid plexus](http://purl.obolibrary.org/obo/UBERON_0001886) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Fringe of the tela choroidea of the brain ventricles[MP]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "MP:0000820" + +- [choroid plexus](http://purl.obolibrary.org/obo/UBERON_0001886) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A tuft of capillaries that project into the ventricles of the brain and secretes cerebral spinal fluid. The choroid plexus is covered by a cuboidal epithelium which maintains the integrity of the blood-brain barrier.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001443" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + + +### choroid plexus epithelium `http://purl.obolibrary.org/obo/UBERON_0003911` +#### Removed +- [choroid plexus epithelium](http://purl.obolibrary.org/obo/UBERON_0003911) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "The CP epithelial layer is continuous with the ependymal cell layer that lines the ventricles, but unlike the ependyma, the epithelial layer has tight gap junctions between the cells on the side facing the ventricle (apical surface). These gap junctions prevent the majority of substances from crossing the cell layer into the CSF; thus the CP acts as a blood-CSF barrier" + +- [choroid plexus epithelium](http://purl.obolibrary.org/obo/UBERON_0003911) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006008" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + + - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) + +- [choroid plexus epithelium](http://purl.obolibrary.org/obo/UBERON_0003911) SubClassOf [epithelium](http://purl.obolibrary.org/obo/UBERON_0000483) + +#### Added +- [choroid plexus epithelium](http://purl.obolibrary.org/obo/UBERON_0003911) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) + + +### choroid plexus stroma `http://purl.obolibrary.org/obo/UBERON_0005206` + +#### Added +- [choroid plexus stroma](http://purl.obolibrary.org/obo/UBERON_0005206) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### choroid-plexus macrophage `http://purl.obolibrary.org/obo/CL_0000880` +#### Removed +- [choroid-plexus macrophage](http://purl.obolibrary.org/obo/CL_0000880) [label](http://www.w3.org/2000/01/rdf-schema#label) "choroid-plexus macrophage" + +- [choroid-plexus macrophage](http://purl.obolibrary.org/obo/CL_0000880) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A central nervous system macrophage found at the interface between the blood and the cerebrospinal fluid in the brain. This cell expresses scavenger receptors." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:9550136" + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO_REF:0000031" + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:ana" + +- [choroid-plexus macrophage](http://purl.obolibrary.org/obo/CL_0000880) EquivalentTo [central nervous system macrophage](http://purl.obolibrary.org/obo/CL_0000878) and ([located in](http://purl.obolibrary.org/obo/RO_0001025) some [choroid plexus](http://purl.obolibrary.org/obo/UBERON_0001886)) and ([capable of](http://purl.obolibrary.org/obo/RO_0002215) some [scavenger receptor activity](http://purl.obolibrary.org/obo/GO_0005044)) + +- [choroid-plexus macrophage](http://purl.obolibrary.org/obo/CL_0000880) SubClassOf [central nervous system macrophage](http://purl.obolibrary.org/obo/CL_0000878) + - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true" + +- [choroid-plexus macrophage](http://purl.obolibrary.org/obo/CL_0000880) SubClassOf [located in](http://purl.obolibrary.org/obo/RO_0001025) some [choroid plexus](http://purl.obolibrary.org/obo/UBERON_0001886) + +#### Added +- [choroid-plexus macrophage](http://purl.obolibrary.org/obo/CL_0000880) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cpMΦ" + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [abbreviation](http://purl.obolibrary.org/obo/OMO_0003000) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37232741" + +- [choroid-plexus macrophage](http://purl.obolibrary.org/obo/CL_0000880) [label](http://www.w3.org/2000/01/rdf-schema#label) "choroid plexus macrophage" + +- [choroid-plexus macrophage](http://purl.obolibrary.org/obo/CL_0000880) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A border associated macrophage found at the interface between the blood and the cerebrospinal fluid in the brain. This central nervous system macrophage has a star-like shaped body and expresses scavenger receptors." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:9550136" + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO_REF:0000031" + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:ana" + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37232741" + +- [choroid-plexus macrophage](http://purl.obolibrary.org/obo/CL_0000880) EquivalentTo [border associated macrophage](http://purl.obolibrary.org/obo/CL_4042003) and ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [choroid plexus](http://purl.obolibrary.org/obo/UBERON_0001886)) and ([capable of](http://purl.obolibrary.org/obo/RO_0002215) some [scavenger receptor activity](http://purl.obolibrary.org/obo/GO_0005044)) + +- [choroid-plexus macrophage](http://purl.obolibrary.org/obo/CL_0000880) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [choroid plexus](http://purl.obolibrary.org/obo/UBERON_0001886) + +- [choroid-plexus macrophage](http://purl.obolibrary.org/obo/CL_0000880) SubClassOf [border associated macrophage](http://purl.obolibrary.org/obo/CL_4042003) + + +### choroidal blood vessel `http://purl.obolibrary.org/obo/UBERON_0002443` + +#### Added +- [choroidal blood vessel](http://purl.obolibrary.org/obo/UBERON_0002443) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) + + +### chromaffin system `http://purl.obolibrary.org/obo/UBERON_0010074` +#### Removed +- [chromaffin system](http://purl.obolibrary.org/obo/UBERON_0010074) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "in adult cylostomes and teleosts, the interrenal bodies are separate from chromaffin bodies" + + + +### ciliary body `http://purl.obolibrary.org/obo/UBERON_0001775` +#### Removed +- [ciliary body](http://purl.obolibrary.org/obo/UBERON_0001775) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000102" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + + +### ciliary processes `http://purl.obolibrary.org/obo/UBERON_0010427` + +#### Added +- [ciliary processes](http://purl.obolibrary.org/obo/UBERON_0010427) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### ciliated columnar epithelium `http://purl.obolibrary.org/obo/UBERON_0007592` +#### Removed +- [ciliated columnar epithelium](http://purl.obolibrary.org/obo/UBERON_0007592) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "Ciliated columnar epithelium in the pulmonary system is interspersed with goblet cells that secrete mucous to form a mucosal layer apical to the epithelial layer. The rowing-like action of epithelial cilia work in tandem with goblet cells to propel mucus away from the lungs, preventing particulate matter from causing infection[http://www.bio.davidson.edu/people/kabernd/berndcv/lab/epithelialinfoweb/ciliated%20columnar%20epithelium.html]" + +- [ciliated columnar epithelium](http://purl.obolibrary.org/obo/UBERON_0007592) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In humans, Ciliated columnar epithelial cells are found mainly in the tracheal and bronchial regions of the pulmonary system and also in the fallopian tubes of the female reproductive system" + + + +### ciliated columnar oviduct epithelium `http://purl.obolibrary.org/obo/UBERON_0007589` +#### Removed +- [ciliated columnar oviduct epithelium](http://purl.obolibrary.org/obo/UBERON_0007589) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in FMA, epithelium of uterine tube is a subclass of ciliated columnar epithelium. MA introduces subtypes: ciliated columnar and cuboidal. We map the FMA type according to its relationships, not its label" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + + + +### circle of Willis `http://purl.obolibrary.org/obo/UBERON_0003709` +#### Removed +- [circle of Willis](http://purl.obolibrary.org/obo/UBERON_0003709) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In zebrafish, the circle of vessels comprised of the basal communicating artery (BCA) and posterior communicating segments (PCS) superficially resemble but are not homologous to the human circle of Willis" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://zfish.nichd.nih.gov/zfatlas/Intro%20Page/comparative.html" + + + +### circulatory organ `http://purl.obolibrary.org/obo/UBERON_0015228` +#### Removed +- [circulatory organ](http://purl.obolibrary.org/obo/UBERON_0015228) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "SPD:0000130" + + + +### circulatory system `http://purl.obolibrary.org/obo/UBERON_0001009` +#### Removed +- [circulatory system](http://purl.obolibrary.org/obo/UBERON_0001009) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.493" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001248" + +- [circulatory system](http://purl.obolibrary.org/obo/UBERON_0001009) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000959" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + +- [circulatory system](http://purl.obolibrary.org/obo/UBERON_0001009) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D002319" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + +- [circulatory system](http://purl.obolibrary.org/obo/UBERON_0001009) [RO_0002174](http://purl.obolibrary.org/obo/RO_0002174) [Nematoda](http://purl.obolibrary.org/obo/NCBITaxon_6231) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "WBbt coelomocyte currently classified as circulating cell" + +- [circulatory system](http://purl.obolibrary.org/obo/UBERON_0001009) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "the cardiovascular system and the lymphatic system are parts of the circulatory system" + + + +### circumventricular organ `http://purl.obolibrary.org/obo/UBERON_0005408` +#### Removed +- [circumventricular organ](http://purl.obolibrary.org/obo/UBERON_0005408) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006267" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + + - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) + +- [circumventricular organ](http://purl.obolibrary.org/obo/UBERON_0005408) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "CVOs contain neural tissue and are an integral part of neuroendocrine function; all of the CVOs, besides the subcommissural organ, contain extensive vasculature and fenestrated capillaries which leads to a leaky BBB at the site of the organs; the lack of a BBB allows CVOs to act as an alternative route for peptides and hormones in the neural tissue to the peripheral blood stream, while still protecting it from toxic substances" + +- [circumventricular organ](http://purl.obolibrary.org/obo/UBERON_0005408) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "All vertebrates possess at least 4 circumventricular organs (including the hypothalamus) which can monitor the contents of the cerebrospinal fluid and secrete additional substances into it. (Butler, 1996, p. 330)" + +- [circumventricular organ](http://purl.obolibrary.org/obo/UBERON_0005408) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D066280" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + + + +### citesAsAuthority `http://purl.org/spar/cito/citesAsAuthority` +#### Removed +- AnnotationProperty: [citesAsAuthority](http://purl.org/spar/cito/citesAsAuthority) + + + +### clavicle bone `http://purl.obolibrary.org/obo/UBERON_0001105` +#### Removed +- [clavicle bone](http://purl.obolibrary.org/obo/UBERON_0001105) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA and MA differ in whether they consider this part of the shoulder" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + +- [clavicle bone](http://purl.obolibrary.org/obo/UBERON_0001105) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "clavicular" + +- [clavicle bone](http://purl.obolibrary.org/obo/UBERON_0001105) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Slender, paired bones of intramembranous origin that invest the anterior margins of the procoracoids.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000761" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + +- [clavicle bone](http://purl.obolibrary.org/obo/UBERON_0001105) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: part_of zonal element (AAO:0000936)[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000761" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + +- [clavicle bone](http://purl.obolibrary.org/obo/UBERON_0001105) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "In most birds and mammals the clavicles are the only dermal elements in the trunk, and is the only membrane bone associated with the pectoral girdle in these taxa. However, there can be secondary cartilage, or subsequent endochondral ossification, or fusion with endochondral elements. In rodents, the lateral ends of the clavicle are endochondral but the main portion is dermal." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0-12-319060-4" + +- [clavicle bone](http://purl.obolibrary.org/obo/UBERON_0001105) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The clavicle first appears as part of the skeleton in primitive bony fish, where it is associated with the pectoral fin; they also have a bone called the cleithrum. In such fish, the paired clavicles run behind and below the gills on each side, and are joined by a solid symphysis on the fish's underside. They are, however, absent in cartilagenous fish and in the vast majority of living bony fish, including all of the teleosts[ISBN 0-03-910284-X]." + +- [clavicle bone](http://purl.obolibrary.org/obo/UBERON_0001105) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In early tetrapods, the connecting skull bone, the posttemporal, and adjoining shoulder bones, supracleithrum and postcleithrum (=anocleithrum), are absent, leaving a dermal shoulder girdle composed of the remaining ventral elements: the paired cleithrum and clavicle, and an unpaired midventral interclavicle that joins both halves of the girdle across the midline. (...) Several dermal elements of the shoulder persist in early synapsids. The clavicle and interclavicle are present in therapsids and monotremes, but in marsupials and placentals, the interclavicle is absent, the clavicle often is reduced in size, and the scapula becomes the predominant shoulder element.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.330-333 and Figure 9.18" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000849" + +- [clavicle bone](http://purl.obolibrary.org/obo/UBERON_0001105) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [clavicle cartilage element](http://purl.obolibrary.org/obo/UBERON_0010843) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0-12-319060-4" + + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "from secondary cartilage of fusion" + +- [clavicle bone](http://purl.obolibrary.org/obo/UBERON_0001105) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [clavicle bone primordium](http://purl.obolibrary.org/obo/UBERON_0010905) + - [editor](http://www.geneontology.org/formats/oboInOwl#editor) "mah" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0-12-319060-4" + +#### Added +- [clavicle bone](http://purl.obolibrary.org/obo/UBERON_0001105) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [clavicle bone primordium](http://purl.obolibrary.org/obo/UBERON_0010905) + +- [clavicle bone](http://purl.obolibrary.org/obo/UBERON_0001105) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [clavicle cartilage element](http://purl.obolibrary.org/obo/UBERON_0010843) + + +### clavicle bone primordium `http://purl.obolibrary.org/obo/UBERON_0010905` +#### Removed +- [clavicle bone primordium](http://purl.obolibrary.org/obo/UBERON_0010905) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [neural crest](http://purl.obolibrary.org/obo/UBERON_0002342) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMC1352163" + + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "shown in mouse" + + - [editor](http://www.geneontology.org/formats/oboInOwl#editor) "mah" + +#### Added +- [clavicle bone primordium](http://purl.obolibrary.org/obo/UBERON_0010905) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [neural crest](http://purl.obolibrary.org/obo/UBERON_0002342) + + +### clavicle cartilage element `http://purl.obolibrary.org/obo/UBERON_0010843` +#### Removed +- [clavicle cartilage element](http://purl.obolibrary.org/obo/UBERON_0010843) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In most birds and mammals the clavicles are the only dermal elements in the trunk, and is the only membrane bone associated with the pectoral girdle in these taxa. However, there can be secondary cartilage, or subsequent endochondral ossification, or fusion with endochondral elements. In rodents, the lateral ends of the clavicle are endochondral but the main portion is dermal." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0-12-319060-4" + + + +### clavicle pre-cartilage condensation `http://purl.obolibrary.org/obo/UBERON_0010844` +#### Removed +- [clavicle pre-cartilage condensation](http://purl.obolibrary.org/obo/UBERON_0010844) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In most birds and mammals the clavicles are the only dermal elements in the trunk, and is the only membrane bone associated with the pectoral girdle in these taxa. However, there can be secondary cartilage, or subsequent endochondral ossification, or fusion with endochondral elements. In rodents, the lateral ends of the clavicle are endochondral but the main portion is dermal." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0-12-319060-4" + + + +### clitoris `http://purl.obolibrary.org/obo/UBERON_0002411` +#### Removed +- [clitoris](http://purl.obolibrary.org/obo/UBERON_0002411) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "clitoral" + +#### Added +- [clitoris](http://purl.obolibrary.org/obo/UBERON_0002411) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### cloaca `http://purl.obolibrary.org/obo/UBERON_0000162` +#### Removed +- [cloaca](http://purl.obolibrary.org/obo/UBERON_0000162) [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9369](http://purl.obolibrary.org/obo/NCBITaxon_9369) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "most adult placentals have no trace of a cloaca. However, the tenrecs and golden moles, small placental mammals native to Africa, retain a cloaca as adults." + +- [cloaca](http://purl.obolibrary.org/obo/UBERON_0000162) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A common passage for fecal, urinary, and reproductive discharge in most lower vertebrates as well as the terminal end of the hindgut before division into rectum, bladder, and genital primordia in mammalian embryos. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/cloaca" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001186" + +- [cloaca](http://purl.obolibrary.org/obo/UBERON_0000162) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "cloacal" + +- [cloaca](http://purl.obolibrary.org/obo/UBERON_0000162) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Human beings only have an embryonic cloaca, which is split up into separate tracts during the development of the urinary and reproductive organs" + +- [cloaca](http://purl.obolibrary.org/obo/UBERON_0000162) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical structure which is the common receptacle for the alimentary canal, Wolffian ducts, oviducts, and the bladder.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000095" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + +- [cloaca](http://purl.obolibrary.org/obo/UBERON_0000162) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "hindgut endoderm and proctodeal ectoderm." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" + +- [cloaca](http://purl.obolibrary.org/obo/UBERON_0000162) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "A cloaca is apparently a primitive vertebrate feature because it occurs in most primitive gnathostomes and persists in the embryos of almost all vertebrates.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001186" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.572" + + + +### cloacal epithelium `http://purl.obolibrary.org/obo/UBERON_0012481` +#### Removed +- [cloacal epithelium](http://purl.obolibrary.org/obo/UBERON_0012481) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "cloacal epithelium (cle) (syn: cloacal endoderm) (TS17-TS20): the cloacal epithelium is derived from endoderm and lines the cloacal cavity. It is marked by Shh and Cdh1 and lines the cloacal lumen. The cloacal epithelium gives rise to the urogenital sinus epithelium, hindgut epithelium and the urethral plate epithelium." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "EMAPA:27577" + + + +### cloacal lumen `http://purl.obolibrary.org/obo/UBERON_0012463` +#### Removed +- [cloacal lumen](http://purl.obolibrary.org/obo/UBERON_0012463) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "the ZFA class belongs here as it is an anatomical space. See https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/102/" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "ZFA" + + + +### cloacal membrane `http://purl.obolibrary.org/obo/UBERON_0006217` +#### Removed +- [cloacal membrane](http://purl.obolibrary.org/obo/UBERON_0006217) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In mammals, the cloaca exists as an embryonic structure that undergoes septation to become distinct urethral, anal, and genital orifices.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001198" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:11830557 De Santa Barbara P, Roberts DJ, Tail gut endoderm and gut/genitourinary/tail development: a new tissue-specific role for Hoxa13. Development (2002)" + +- [cloacal membrane](http://purl.obolibrary.org/obo/UBERON_0006217) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A membrane that separates the proctodeum and the hindgut in the early embryo. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.497, see_Kardong_KV][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001198" + + + +### closeMatch `http://www.w3.org/2004/02/skos/core#closeMatch` +#### Removed +- AnnotationProperty: [closeMatch](http://www.w3.org/2004/02/skos/core#closeMatch) + + + +### closed `http://purl.obolibrary.org/obo/PATO_0000608` +#### Removed +- [closed](http://purl.obolibrary.org/obo/PATO_0000608) [RO_0002604](http://purl.obolibrary.org/obo/RO_0002604) [open](http://purl.obolibrary.org/obo/PATO_0000610) + + + +### cochlea `http://purl.obolibrary.org/obo/UBERON_0001844` +#### Removed +- [cochlea](http://purl.obolibrary.org/obo/UBERON_0001844) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A spiral-shaped cavity in the petrous portion of the temporal bone of the inner ear, containing the nerve endings essential for hearing and forming one of the divisions of the labyrinth. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000691" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/cochlea" + +- [cochlea](http://purl.obolibrary.org/obo/UBERON_0001844) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "cochlear" + +- [cochlea](http://purl.obolibrary.org/obo/UBERON_0001844) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "sources vary in connection to bony labyrinth" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "XAO" + +- [cochlea](http://purl.obolibrary.org/obo/UBERON_0001844) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Because achieving high sensitivity is generally advantageous for auditory organs, it is not surprising that evidence for cochlear amplification is also seen in nonmammals. Spontaneous otoacoustic emissions (SOAEs) are narrow-band sound signals emitted from the inner ear, and it is generally assumed that their energy derives from the hair-cell molecular motors underlying cochlear amplification. However, all terrestrial vertebrates studied so far (including amphibians) show very similar SOAEs. The most parsimonious explanation for the universality of this phenomena is that some kind of amplifying mechanism is at least as old as land vertebrates themselves.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1016/S0959-4388(98)80033-0 Manley GA, Koeppl C, Phylogenetic development of the cochlea and its innervation. Current Opinion in Neurobiology (1998)" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000691" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + +- [cochlea](http://purl.obolibrary.org/obo/UBERON_0001844) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "the cochlea is coiled in most mammals, monotremes being the exceptions." + +- [cochlea](http://purl.obolibrary.org/obo/UBERON_0001844) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The association with 'lagena' in frog and fish comes from HOG, although HOG is inconsistent here, associating lagena with XAO cochlea and ZFA cochlear duct. NBK53175 says: 'In contrast, the ventrally located auditory chambers have undergone more extensive evolutionary modifications. The saccule and lagena are prominent auditory organs in fish but the saccule has a vestibular role in mammals and birds, and the lagena is absent in mammals. The primary au- ditory organ in mammals and birds is the cochlea, which has no known counterpart in amphibians and fish (Riley and Phillips, 2003)'" + +#### Added +- [cochlea](http://purl.obolibrary.org/obo/UBERON_0001844) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### cochlear basement membrane `http://purl.obolibrary.org/obo/UBERON_0011922` + +#### Added +- [cochlear basement membrane](http://purl.obolibrary.org/obo/UBERON_0011922) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### cochlear canal `http://purl.obolibrary.org/obo/UBERON_0006106` + +#### Added +- [cochlear canal](http://purl.obolibrary.org/obo/UBERON_0006106) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### cochlear duct of membranous labyrinth `http://purl.obolibrary.org/obo/UBERON_0001855` +#### Removed +- [cochlear duct of membranous labyrinth](http://purl.obolibrary.org/obo/UBERON_0001855) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In gnathostomes, each membranous labyrinth has three semicircular ducts that connect with a chamber known as the utriculus. (...) In all gnathostomes, the utriculus connects ventrally with a larger sac, called the sacculus (...) In most groups of gnathostomes, the caudoventral evagination of the sacculus forms a small lagena, and in some diapsids and mammals the lagena develops into a longer duct. The lagena becomes greatly elongated in therians and coils to form the cochlear duct.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000507" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.413-414" + +- [cochlear duct of membranous labyrinth](http://purl.obolibrary.org/obo/UBERON_0001855) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The coiled portion of the membranous labyrinth located inside the cochlea. It contains endolymph. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000507" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/cochlear+duct" + +#### Added +- [cochlear duct of membranous labyrinth](http://purl.obolibrary.org/obo/UBERON_0001855) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### cochlear ganglion `http://purl.obolibrary.org/obo/UBERON_0000395` +#### Removed +- [cochlear ganglion](http://purl.obolibrary.org/obo/UBERON_0000395) SubClassOf [located in](http://purl.obolibrary.org/obo/RO_0001025) some [cochlear modiolus](http://purl.obolibrary.org/obo/UBERON_0006723) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "cell bodies" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "BTO-modified" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia" + +#### Added +- [cochlear ganglion](http://purl.obolibrary.org/obo/UBERON_0000395) SubClassOf [located in](http://purl.obolibrary.org/obo/RO_0001025) some [cochlear modiolus](http://purl.obolibrary.org/obo/UBERON_0006723) + +- [cochlear ganglion](http://purl.obolibrary.org/obo/UBERON_0000395) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) + + +### cochlear labyrinth `http://purl.obolibrary.org/obo/UBERON_0002499` + +#### Added +- [cochlear labyrinth](http://purl.obolibrary.org/obo/UBERON_0002499) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### cochlear modiolus `http://purl.obolibrary.org/obo/UBERON_0006723` + +#### Added +- [cochlear modiolus](http://purl.obolibrary.org/obo/UBERON_0006723) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### cochlear nerve `http://purl.obolibrary.org/obo/UBERON_0004727` +#### Removed +- [cochlear nerve](http://purl.obolibrary.org/obo/UBERON_0004727) SubClassOf [nerve](http://purl.obolibrary.org/obo/UBERON_0001021) + +#### Added +- [cochlear nerve](http://purl.obolibrary.org/obo/UBERON_0004727) SubClassOf [nerve of head region](http://purl.obolibrary.org/obo/UBERON_0011779) + +- [cochlear nerve](http://purl.obolibrary.org/obo/UBERON_0004727) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### cochlear nuclear complex `http://purl.obolibrary.org/obo/UBERON_0002610` +#### Removed +- [cochlear nuclear complex](http://purl.obolibrary.org/obo/UBERON_0002610) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002864](http://purl.obolibrary.org/obo/UBERON_0002864) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" + +- [cochlear nuclear complex](http://purl.obolibrary.org/obo/UBERON_0002610) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002591](http://purl.obolibrary.org/obo/UBERON_0002591) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" + +- [cochlear nuclear complex](http://purl.obolibrary.org/obo/UBERON_0002610) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002126](http://purl.obolibrary.org/obo/UBERON_0002126) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" + +- [cochlear nuclear complex](http://purl.obolibrary.org/obo/UBERON_0002610) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0007633](http://purl.obolibrary.org/obo/UBERON_0007633) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" + +- [cochlear nuclear complex](http://purl.obolibrary.org/obo/UBERON_0002610) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002162](http://purl.obolibrary.org/obo/UBERON_0002162) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" + +- [cochlear nuclear complex](http://purl.obolibrary.org/obo/UBERON_0002610) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002866](http://purl.obolibrary.org/obo/UBERON_0002866) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" + +- [cochlear nuclear complex](http://purl.obolibrary.org/obo/UBERON_0002610) [UBPROP_0000015](http://purl.obolibrary.org/obo/UBPROP_0000015) "WP says 'The CN is located at the dorso-lateral side of the brainstem, spanning the junction of the pons and medulla.'. MA places this in pons, other sources the medulla" + +- [cochlear nuclear complex](http://purl.obolibrary.org/obo/UBERON_0002610) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002873](http://purl.obolibrary.org/obo/UBERON_0002873) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" + +- [cochlear nuclear complex](http://purl.obolibrary.org/obo/UBERON_0002610) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [medulla oblongata](http://purl.obolibrary.org/obo/UBERON_0001896) + - [inconsistent_with](http://www.geneontology.org/formats/oboInOwl#inconsistent_with) "MA" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA" + +#### Added +- [cochlear nuclear complex](http://purl.obolibrary.org/obo/UBERON_0002610) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [medulla oblongata](http://purl.obolibrary.org/obo/UBERON_0001896) + + +### coelemic cavity lumen `http://purl.obolibrary.org/obo/UBERON_0002323` +#### Removed +- [coelemic cavity lumen](http://purl.obolibrary.org/obo/UBERON_0002323) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005060" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + +- [coelemic cavity lumen](http://purl.obolibrary.org/obo/UBERON_0002323) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In mammals it forms the peritoneal, pleural, and pericardial cavities" + +- [coelemic cavity lumen](http://purl.obolibrary.org/obo/UBERON_0002323) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-12" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "ZFA" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "ZFA:0001438" + +- [coelemic cavity lumen](http://purl.obolibrary.org/obo/UBERON_0002323) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "BTO" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "BTO:0001707" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "BTO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-12" + +- [coelemic cavity lumen](http://purl.obolibrary.org/obo/UBERON_0002323) SubClassOf [transformation of](http://purl.obolibrary.org/obo/RO_0002494) some [future coelemic cavity lumen](http://purl.obolibrary.org/obo/UBERON_0003886) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" + +#### Added +- [coelemic cavity lumen](http://purl.obolibrary.org/obo/UBERON_0002323) SubClassOf [transformation of](http://purl.obolibrary.org/obo/RO_0002494) some [future coelemic cavity lumen](http://purl.obolibrary.org/obo/UBERON_0003886) + + +### coelom `http://purl.obolibrary.org/obo/UBERON_0011997` +#### Removed +- [coelom](http://purl.obolibrary.org/obo/UBERON_0011997) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "coelomic" + + + +### coelomic epithelium `http://purl.obolibrary.org/obo/UBERON_0005891` +#### Removed +- [coelomic epithelium](http://purl.obolibrary.org/obo/UBERON_0005891) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "EHDAA2:0004049 used to be called 'coelomic epithelium' but is now 'gonadal ridge mesothelium'" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EHDAA2" + + + +### coelomic fluid `http://purl.obolibrary.org/obo/UBERON_0036217` +#### Removed +- [coelomic fluid](http://purl.obolibrary.org/obo/UBERON_0036217) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "he coelomic fluid serves several functions; it acts as a hydroskeleton, it allows free movement and growth of internal organs, it serves for transport of gases, nutrients and waste products between different parts of the body, it allows storage of sperm and eggs during maturation and it acts as a reservoir for waste [Wikipedia:Coelom#Coelomic_fluid]" + + + +### coiled `http://purl.obolibrary.org/obo/PATO_0000404` +#### Removed +- [coiled](http://purl.obolibrary.org/obo/PATO_0000404) [RO_0002604](http://purl.obolibrary.org/obo/RO_0002604) [PATO_0000415](http://purl.obolibrary.org/obo/PATO_0000415) + + + +### collagen alpha-1(I) chain `http://purl.obolibrary.org/obo/PR_000003264` +#### Removed +- [collagen alpha-1(I) chain](http://purl.obolibrary.org/obo/PR_000003264) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [collagen alpha-1(I) chain (human)](http://purl.obolibrary.org/obo/PR_P02452) + + + +### collecting duct of renal tubule `http://purl.obolibrary.org/obo/UBERON_0001232` +#### Removed +- [collecting duct of renal tubule](http://purl.obolibrary.org/obo/UBERON_0001232) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in ISBN:0073040584 (Vertebrates, Kardong), the nephron is adjacent to the collecting tubule, consistent with FMA, but not GO. Wikipedia says: Many sources include the connecting tubule as part of the collecting duct system. However, the embryological origin is more similar to the nephron than it is to the rest of the collecting duct (which derives from the ureteric bud), and other sources therefore classify the connecting tubule with the nephron" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + +- [collecting duct of renal tubule](http://purl.obolibrary.org/obo/UBERON_0001232) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Renal duct that collects the output from renal tubules.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005294" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [collecting duct of renal tubule](http://purl.obolibrary.org/obo/UBERON_0001232) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [nephron](http://purl.obolibrary.org/obo/UBERON_0001285) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "checkme" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GO" + +#### Added +- [collecting duct of renal tubule](http://purl.obolibrary.org/obo/UBERON_0001232) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [nephron](http://purl.obolibrary.org/obo/UBERON_0001285) + + +### collection of basal ganglia `http://purl.obolibrary.org/obo/UBERON_0010011` +#### Removed +- [collection of basal ganglia](http://purl.obolibrary.org/obo/UBERON_0010011) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "HBA:4275" + +- [collection of basal ganglia](http://purl.obolibrary.org/obo/UBERON_0010011) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "All nuclei of the mammalian basal ganglia are also present in the oldest vertebrates.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001696" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1016/j.cub.2011.05.001 Stephenson-Jones M, Samuelsson E, Ericsson J, Robertson B, Grillner S, Evolutionary conservation of the basal ganglia as a common vertebrate mechanism for action selection. Current Biology (2011)" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + +- [collection of basal ganglia](http://purl.obolibrary.org/obo/UBERON_0010011) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DHBA:10331" + +- [collection of basal ganglia](http://purl.obolibrary.org/obo/UBERON_0010011) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PBA:128012596" + + + +### collection of collagen fibrils `http://purl.obolibrary.org/obo/UBERON_0011860` +#### Removed +- [collection of collagen fibrils](http://purl.obolibrary.org/obo/UBERON_0011860) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "the FMA class specifically refers to ureter" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + + + +### colon `http://purl.obolibrary.org/obo/UBERON_0001155` +#### Removed +- [colon](http://purl.obolibrary.org/obo/UBERON_0001155) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "colonic" + +- [colon](http://purl.obolibrary.org/obo/UBERON_0001155) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "it extracts water and salt from solid wastes before they are eliminated from the body[WP]" + +- [colon](http://purl.obolibrary.org/obo/UBERON_0001155) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In mammals, the colon consists of four sections: the ascending colon, the transverse colon, the descending colon, and the sigmoid colon[WP]" + +- [colon](http://purl.obolibrary.org/obo/UBERON_0001155) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The last portion of the digestive system, it extracts water and salt from solid wastes before they are eliminated from the body.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "UBERON:0001155" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010400" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + +- [colon](http://purl.obolibrary.org/obo/UBERON_0001155) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000648" + +- [colon](http://purl.obolibrary.org/obo/UBERON_0001155) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In zebrafish, the posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates[ZFIN]" + +- [colon](http://purl.obolibrary.org/obo/UBERON_0001155) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates. Wallace et al, 2005.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000706" + +- [colon](http://purl.obolibrary.org/obo/UBERON_0001155) SubClassOf [subdivision of digestive tract](http://purl.obolibrary.org/obo/UBERON_0004921) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "cjm" + + - [order](http://www.geneontology.org/formats/oboInOwl#order) "3" + +#### Added +- [colon](http://purl.obolibrary.org/obo/UBERON_0001155) SubClassOf [subdivision of digestive tract](http://purl.obolibrary.org/obo/UBERON_0004921) + + +### colonic epithelium `http://purl.obolibrary.org/obo/UBERON_0000397` +#### Removed +- [colonic epithelium](http://purl.obolibrary.org/obo/UBERON_0000397) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Intestinal epithelium which lines the lumen of the posterior intestine.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005128" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + + +### common bile duct `http://purl.obolibrary.org/obo/UBERON_0001174` +#### Removed +- [common bile duct](http://purl.obolibrary.org/obo/UBERON_0001174) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Digestive system duct that collects bile from the hepatic bile duct and the cystic duct.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005165" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:Curator" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [common bile duct](http://purl.obolibrary.org/obo/UBERON_0001174) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The duct formed by the union of the common hepatic and cystic ducts. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000214" + + + +### common carotid artery plus branches `http://purl.obolibrary.org/obo/UBERON_0001530` +#### Removed +- [common carotid artery plus branches](http://purl.obolibrary.org/obo/UBERON_0001530) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "in birds and reptiles, develops from arch III and parts of ventral and dorsal aortae" + +- [common carotid artery plus branches](http://purl.obolibrary.org/obo/UBERON_0001530) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "This class represents the adult and developing structures'" + + + +### common hepatic duct `http://purl.obolibrary.org/obo/UBERON_0001175` +#### Removed +- [common hepatic duct](http://purl.obolibrary.org/obo/UBERON_0001175) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The duct which conveys the bile from the liver and unites with the cystic duct to form the common bile duct. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000220" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + +- [common hepatic duct](http://purl.obolibrary.org/obo/UBERON_0001175) SubClassOf [immediate transformation of](http://purl.obolibrary.org/obo/RO_0002495) some [future common hepatic duct](http://purl.obolibrary.org/obo/UBERON_0010081) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" + +#### Added +- [common hepatic duct](http://purl.obolibrary.org/obo/UBERON_0001175) SubClassOf [immediate transformation of](http://purl.obolibrary.org/obo/RO_0002495) some [future common hepatic duct](http://purl.obolibrary.org/obo/UBERON_0010081) + + +### common iliac vein `http://purl.obolibrary.org/obo/UBERON_0001139` +#### Removed +- [common iliac vein](http://purl.obolibrary.org/obo/UBERON_0001139) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In human anatomy, the common iliac veins are formed by the external iliac veins and internal iliac veins and together, in the abdomen at the level of the fifth lumbar vertebrae, form the inferior vena cava. They drain blood from the pelvis and lower limbs. Both common iliac veins are accompanied along their course by common iliac arteries." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Common_iliac_vein" + + + +### compact bone tissue `http://purl.obolibrary.org/obo/UBERON_0001439` +#### Removed +- [compact bone tissue](http://purl.obolibrary.org/obo/UBERON_0001439) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D000071538" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + + + +### complement component C1q receptor `http://purl.obolibrary.org/obo/PR_000002037` +#### Removed +- [complement component C1q receptor](http://purl.obolibrary.org/obo/PR_000002037) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [complement component C1q receptor (human)](http://purl.obolibrary.org/obo/PR_Q9NPY3) + + + +### complement receptor type 1 `http://purl.obolibrary.org/obo/PR_000001337` +#### Removed +- [complement receptor type 1](http://purl.obolibrary.org/obo/PR_000001337) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [complement receptor type 1 (human)](http://purl.obolibrary.org/obo/PR_P17927) + + + +### complement receptor type 2 `http://purl.obolibrary.org/obo/PR_000001338` +#### Removed +- [complement receptor type 2](http://purl.obolibrary.org/obo/PR_000001338) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [complement receptor type 2 (human)](http://purl.obolibrary.org/obo/PR_P20023) + + + +### component `http://www.geneontology.org/formats/oboInOwl#component` +#### Removed +- AnnotationProperty: [component](http://www.geneontology.org/formats/oboInOwl#component) + + + +### composed primarily of `http://purl.obolibrary.org/obo/RO_0002473` +#### Removed +- [composed primarily of](http://purl.obolibrary.org/obo/RO_0002473) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [composed primarily of](http://purl.obolibrary.org/obo/RO_0002473) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) [22293552](http://www.ncbi.nlm.nih.gov/pubmed/22293552) + +- [composed primarily of](http://purl.obolibrary.org/obo/RO_0002473) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [composed primarily of](http://purl.obolibrary.org/obo/RO_0002473) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "composed_primarily_of" + +- [composed primarily of](http://purl.obolibrary.org/obo/RO_0002473) [RO_0001900](http://purl.obolibrary.org/obo/RO_0001900) [RO_0001901](http://purl.obolibrary.org/obo/RO_0001901) + +- [composed primarily of](http://purl.obolibrary.org/obo/RO_0002473) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002473" + +- [composed primarily of](http://purl.obolibrary.org/obo/RO_0002473) [id](http://www.geneontology.org/formats/oboInOwl#id) "composed_primarily_of" + +- [composed primarily of](http://purl.obolibrary.org/obo/RO_0002473) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" + + + +### composition `http://www.geneontology.org/formats/oboInOwl#composition` +#### Removed +- AnnotationProperty: [composition](http://www.geneontology.org/formats/oboInOwl#composition) + + + +### compound eye `http://purl.obolibrary.org/obo/UBERON_0000018` +#### Removed +- [compound eye](http://purl.obolibrary.org/obo/UBERON_0000018) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The term compound eye is sometimes used for the multi-unit eyes of annelids, bivalves, echinoderms. We follow Richter et al and restrict this class to the arthropod structure for these structures" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:21062451" + +- [compound eye](http://purl.obolibrary.org/obo/UBERON_0000018) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "IDOMAL:0002421" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + + - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) + +- [compound eye](http://purl.obolibrary.org/obo/UBERON_0000018) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004508" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + + +### compound organ `http://purl.obolibrary.org/obo/UBERON_0003103` +#### Removed +- [compound organ](http://purl.obolibrary.org/obo/UBERON_0003103) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs" + + + +### compound organ component `http://purl.obolibrary.org/obo/UBERON_0000471` +#### Removed +- [compound organ component](http://purl.obolibrary.org/obo/UBERON_0000471) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future" + + + +### concave `http://purl.obolibrary.org/obo/PATO_0001857` +#### Removed +- [concave](http://purl.obolibrary.org/obo/PATO_0001857) [RO_0002604](http://purl.obolibrary.org/obo/RO_0002604) [PATO_0001355](http://purl.obolibrary.org/obo/PATO_0001355) + + + +### concave 3-D shape `http://purl.obolibrary.org/obo/PATO_0002008` +#### Removed +- [concave 3-D shape](http://purl.obolibrary.org/obo/PATO_0002008) [RO_0002604](http://purl.obolibrary.org/obo/RO_0002604) [convex 3-D shape](http://purl.obolibrary.org/obo/PATO_0002007) + + + +### conducting system of heart `http://purl.obolibrary.org/obo/UBERON_0002350` +#### Removed +- [conducting system of heart](http://purl.obolibrary.org/obo/UBERON_0002350) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The fish heart displays clear polarity of contraction in a posterior-to-anterior direction. The contraction waves originate in the sinus venosus and terminate in the conus arteriosus. The nodal phenotype persists in the inflow region of the heart, varying from the venosinus to the sinoatrial junctional areas in different species . Similar to the mammalian situation, pacemaker tissue with a lower intrinsic rhythmicity is also found at the atrioventricular junction.[uncertain][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001271" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1152/physrev.00006.2003 Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003)" + + + +### conduit for `http://purl.obolibrary.org/obo/RO_0002570` +#### Removed +- [conduit for](http://purl.obolibrary.org/obo/RO_0002570) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "conduit_for" + +- [conduit for](http://purl.obolibrary.org/obo/RO_0002570) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." + +- [conduit for](http://purl.obolibrary.org/obo/RO_0002570) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [conduit for](http://purl.obolibrary.org/obo/RO_0002570) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) "UBERON:cjm" + +- [conduit for](http://purl.obolibrary.org/obo/RO_0002570) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [conduit for](http://purl.obolibrary.org/obo/RO_0002570) [id](http://www.geneontology.org/formats/oboInOwl#id) "conduit_for" + +- [conduit for](http://purl.obolibrary.org/obo/RO_0002570) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002570" + + + +### conjunctiva `http://purl.obolibrary.org/obo/UBERON_0001811` +#### Removed +- [conjunctiva](http://purl.obolibrary.org/obo/UBERON_0001811) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "conjunctival" + +- [conjunctiva](http://purl.obolibrary.org/obo/UBERON_0001811) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:18233" + +#### Added +- [conjunctiva](http://purl.obolibrary.org/obo/UBERON_0001811) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### conjunctival sac `http://purl.obolibrary.org/obo/UBERON_0005908` +#### Removed +- [conjunctival sac](http://purl.obolibrary.org/obo/UBERON_0005908) SubClassOf [adjacent to](http://purl.obolibrary.org/obo/RO_0002220) some [anterior segment of eyeball](http://purl.obolibrary.org/obo/UBERON_0001801) + - [modified_from](http://www.geneontology.org/formats/oboInOwl#modified_from) "MA" + +#### Added +- [conjunctival sac](http://purl.obolibrary.org/obo/UBERON_0005908) SubClassOf [adjacent to](http://purl.obolibrary.org/obo/RO_0002220) some [anterior segment of eyeball](http://purl.obolibrary.org/obo/UBERON_0001801) + +- [conjunctival sac](http://purl.obolibrary.org/obo/UBERON_0005908) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### conjunctival vein `http://purl.obolibrary.org/obo/UBERON_0010367` +#### Removed +- [conjunctival vein](http://purl.obolibrary.org/obo/UBERON_0010367) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:70887" + +#### Added +- [conjunctival vein](http://purl.obolibrary.org/obo/UBERON_0010367) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) + + +### connected to `http://purl.obolibrary.org/obo/RO_0002170` +#### Removed +- [connected to](http://purl.obolibrary.org/obo/RO_0002170) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) [22293552](http://www.ncbi.nlm.nih.gov/pubmed/22293552) + +- [connected to](http://purl.obolibrary.org/obo/RO_0002170) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002170" + +- [connected to](http://purl.obolibrary.org/obo/RO_0002170) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." + +- [connected to](http://purl.obolibrary.org/obo/RO_0002170) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [connected to](http://purl.obolibrary.org/obo/RO_0002170) [label](http://www.w3.org/2000/01/rdf-schema#label) "connected to" + +- [connected to](http://purl.obolibrary.org/obo/RO_0002170) [id](http://www.geneontology.org/formats/oboInOwl#id) "connected_to" + +- [connected to](http://purl.obolibrary.org/obo/RO_0002170) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "connected_to" + + + +### connecting branch of `http://purl.obolibrary.org/obo/RO_0002252` +#### Removed +- [connecting branch of](http://purl.obolibrary.org/obo/RO_0002252) [id](http://www.geneontology.org/formats/oboInOwl#id) "connecting_branch_of" + +- [connecting branch of](http://purl.obolibrary.org/obo/RO_0002252) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [connecting branch of](http://purl.obolibrary.org/obo/RO_0002252) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002252" + +- [connecting branch of](http://purl.obolibrary.org/obo/RO_0002252) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "connecting_branch_of" + +- [connecting branch of](http://purl.obolibrary.org/obo/RO_0002252) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." + +- [connecting branch of](http://purl.obolibrary.org/obo/RO_0002252) [RO_0004036](http://purl.obolibrary.org/obo/RO_0004036) [part_of](http://purl.obolibrary.org/obo/BFO_0000050) + + + +### connecting stalk blood islands `http://purl.obolibrary.org/obo/UBERON_0011921` +#### Removed +- [connecting stalk blood islands](http://purl.obolibrary.org/obo/UBERON_0011921) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in EHDAA2 gives rise to connecting stalk blood vessels and extraembryonic umbilical vessels" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EHDAA2" + + + +### connecting stalk mesoderm `http://purl.obolibrary.org/obo/UBERON_0005667` +#### Removed +- [connecting stalk mesoderm](http://purl.obolibrary.org/obo/UBERON_0005667) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + + +### connective tissue `http://purl.obolibrary.org/obo/UBERON_0002384` +#### Removed +- [connective tissue](http://purl.obolibrary.org/obo/UBERON_0002384) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO]" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001641" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TAO:wd" + +- [connective tissue](http://purl.obolibrary.org/obo/UBERON_0002384) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PSPUB:0000170" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000017" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" + +- [connective tissue](http://purl.obolibrary.org/obo/UBERON_0002384) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000098" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + +- [connective tissue](http://purl.obolibrary.org/obo/UBERON_0002384) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "MA also has set of connective tissues" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" + + + +### connective tissue of prostate gland `http://purl.obolibrary.org/obo/UBERON_0015130` + +#### Added +- [connective tissue of prostate gland](http://purl.obolibrary.org/obo/UBERON_0015130) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) + + +### connects `http://purl.obolibrary.org/obo/RO_0002176` +#### Removed +- [connects](http://purl.obolibrary.org/obo/RO_0002176) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) [22293552](http://www.ncbi.nlm.nih.gov/pubmed/22293552) + +- [connects](http://purl.obolibrary.org/obo/RO_0002176) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002176" + +- [connects](http://purl.obolibrary.org/obo/RO_0002176) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [connects](http://purl.obolibrary.org/obo/RO_0002176) [id](http://www.geneontology.org/formats/oboInOwl#id) "connects" + +- [connects](http://purl.obolibrary.org/obo/RO_0002176) [label](http://www.w3.org/2000/01/rdf-schema#label) "connects" + +- [connects](http://purl.obolibrary.org/obo/RO_0002176) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "connects" + +- [connects](http://purl.obolibrary.org/obo/RO_0002176) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "The M8 connects Glasgow and Edinburgh" + +- [connects](http://purl.obolibrary.org/obo/RO_0002176) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." + + + +### consistent_with `http://www.geneontology.org/formats/oboInOwl#consistent_with` +#### Removed +- AnnotationProperty: [consistent_with](http://www.geneontology.org/formats/oboInOwl#consistent_with) + + + +### contains process `http://purl.obolibrary.org/obo/BFO_0000067` +#### Removed +- [contains process](http://purl.obolibrary.org/obo/BFO_0000067) [isDefinedBy](http://www.w3.org/2000/01/rdf-schema#isDefinedBy) [bfo.owl](http://purl.obolibrary.org/obo/bfo.owl) + +- [contains process](http://purl.obolibrary.org/obo/BFO_0000067) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "site of"@en + +- [contains process](http://purl.obolibrary.org/obo/BFO_0000067) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "contains_process" + +- [contains process](http://purl.obolibrary.org/obo/BFO_0000067) [label](http://www.w3.org/2000/01/rdf-schema#label) "contains process" + +- [contains process](http://purl.obolibrary.org/obo/BFO_0000067) [id](http://www.geneontology.org/formats/oboInOwl#id) "contains_process" + +- [contains process](http://purl.obolibrary.org/obo/BFO_0000067) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [contains process](http://purl.obolibrary.org/obo/BFO_0000067) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BFO:0000067" + + + +### continuous with `http://purl.obolibrary.org/obo/RO_0002150` +#### Removed +- [continuous with](http://purl.obolibrary.org/obo/RO_0002150) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" + +- [continuous with](http://purl.obolibrary.org/obo/RO_0002150) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) + +- [continuous with](http://purl.obolibrary.org/obo/RO_0002150) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "connected to" + +- [continuous with](http://purl.obolibrary.org/obo/RO_0002150) [RO_0001900](http://purl.obolibrary.org/obo/RO_0001900) [RO_0001901](http://purl.obolibrary.org/obo/RO_0001901) + +- [continuous with](http://purl.obolibrary.org/obo/RO_0002150) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [continuous with](http://purl.obolibrary.org/obo/RO_0002150) [id](http://www.geneontology.org/formats/oboInOwl#id) "continuous_with" + +- [continuous with](http://purl.obolibrary.org/obo/RO_0002150) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-7073-9172](https://orcid.org/0000-0002-7073-9172) + +- [continuous with](http://purl.obolibrary.org/obo/RO_0002150) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002150" + +- [continuous with](http://purl.obolibrary.org/obo/RO_0002150) [label](http://www.w3.org/2000/01/rdf-schema#label) "continuous with" + +- [continuous with](http://purl.obolibrary.org/obo/RO_0002150) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "continuous_with" + + + +### contractile `http://purl.obolibrary.org/obo/PATO_0001690` +#### Removed +- [contractile](http://purl.obolibrary.org/obo/PATO_0001690) [RO_0002604](http://purl.obolibrary.org/obo/RO_0002604) [PATO_0001691](http://purl.obolibrary.org/obo/PATO_0001691) + + + +### contradicted_by `http://www.geneontology.org/formats/oboInOwl#contradicted_by` +#### Removed +- AnnotationProperty: [contradicted_by](http://www.geneontology.org/formats/oboInOwl#contradicted_by) + + + +### contributes to morphology of `http://purl.obolibrary.org/obo/RO_0002433` +#### Removed +- [contributes to morphology of](http://purl.obolibrary.org/obo/RO_0002433) [id](http://www.geneontology.org/formats/oboInOwl#id) "contributes_to_morphology_of" + +- [contributes to morphology of](http://purl.obolibrary.org/obo/RO_0002433) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002433" + +- [contributes to morphology of](http://purl.obolibrary.org/obo/RO_0002433) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [contributes to morphology of](http://purl.obolibrary.org/obo/RO_0002433) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "contributes_to_morphology_of" + +- [contributes to morphology of](http://purl.obolibrary.org/obo/RO_0002433) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + + + +### contributor `http://purl.org/dc/terms/contributor` +#### Removed +- [contributor](http://purl.org/dc/terms/contributor) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://purl.org/dc/terms/contributor" + +- [contributor](http://purl.org/dc/terms/contributor) [label](http://www.w3.org/2000/01/rdf-schema#label) "contributor" + +- [contributor](http://purl.org/dc/terms/contributor) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "dc-contributor" + +- [contributor](http://purl.org/dc/terms/contributor) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [contributor](http://purl.org/dc/terms/contributor) [id](http://www.geneontology.org/formats/oboInOwl#id) "dc-contributor" + +- [contributor](http://purl.org/dc/terms/contributor) [is_metadata_tag](http://www.geneontology.org/formats/oboInOwl#is_metadata_tag) true + + + +### conus arteriosus `http://purl.obolibrary.org/obo/UBERON_0003983` +#### Removed +- [conus arteriosus](http://purl.obolibrary.org/obo/UBERON_0003983) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Kardong says absent in adult tetrapods, check AAO" + +- [conus arteriosus](http://purl.obolibrary.org/obo/UBERON_0003983) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Receives blood from the left atrium and becomes the median truncus arteriosus.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010250" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + +- [conus arteriosus](http://purl.obolibrary.org/obo/UBERON_0003983) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "we use the term CA for the anterior chamber if it is composed of cardiac muscle, contractile, and contains conal valves internally" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0073040584" + + + +### convex 3-D shape `http://purl.obolibrary.org/obo/PATO_0002007` +#### Removed +- [convex 3-D shape](http://purl.obolibrary.org/obo/PATO_0002007) [RO_0002604](http://purl.obolibrary.org/obo/RO_0002604) [concave 3-D shape](http://purl.obolibrary.org/obo/PATO_0002008) + + + +### cornea `http://purl.obolibrary.org/obo/UBERON_0000964` +#### Removed +- [cornea](http://purl.obolibrary.org/obo/UBERON_0000964) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "corneal" + +- [cornea](http://purl.obolibrary.org/obo/UBERON_0000964) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals. In fish, and aquatic vertebrates in general, the cornea plays no role in focusing light, since it has virtually the same refractive index as water" + +- [cornea](http://purl.obolibrary.org/obo/UBERON_0000964) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [optic eminence](http://purl.obolibrary.org/obo/UBERON_0004348) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" + +#### Added +- [cornea](http://purl.obolibrary.org/obo/UBERON_0000964) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [optic eminence](http://purl.obolibrary.org/obo/UBERON_0004348) + + +### corneal blood vessel `http://purl.obolibrary.org/obo/UBERON_0003500` + +#### Added +- [corneal blood vessel](http://purl.obolibrary.org/obo/UBERON_0003500) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) + + +### corneal endothelium `http://purl.obolibrary.org/obo/UBERON_0001985` +#### Removed +- [corneal endothelium](http://purl.obolibrary.org/obo/UBERON_0001985) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) + + + +### corneal epithelium `http://purl.obolibrary.org/obo/UBERON_0001772` +#### Removed +- [corneal epithelium](http://purl.obolibrary.org/obo/UBERON_0001772) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In Humans: It consists of several layers of cells. The cells of the deepest layer are columnar; then follow two or three layers of polyhedral cells, the majority of which are prickle cells similar to those found in the stratum mucosum of the cuticle. Lastly, there are three or four layers of squamous cells, with flattened nuclei" + +- [corneal epithelium](http://purl.obolibrary.org/obo/UBERON_0001772) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Portion of tissue comprised of four to six layers of nonkeratinized, stratified squamous cells and represents approximately 60% of the thickness of the cornea.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:ZDB-PUB-061010-3" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0002187" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [corneal epithelium](http://purl.obolibrary.org/obo/UBERON_0001772) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In zebrafish: nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals" + +#### Added +- [corneal epithelium](http://purl.obolibrary.org/obo/UBERON_0001772) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) + + +### corneal primordium `http://purl.obolibrary.org/obo/UBERON_0005427` + +#### Added +- [corneal primordium](http://purl.obolibrary.org/obo/UBERON_0005427) SubClassOf [immature eye](http://purl.obolibrary.org/obo/UBERON_0010312) + + +### corneal stroma collagen fibril `http://purl.obolibrary.org/obo/UBERON_0011865` + +#### Added +- [corneal stroma collagen fibril](http://purl.obolibrary.org/obo/UBERON_0011865) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) + + +### corneo-scleral junction `http://purl.obolibrary.org/obo/UBERON_0006761` + +#### Added +- [corneo-scleral junction](http://purl.obolibrary.org/obo/UBERON_0006761) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### coronary vessel `http://purl.obolibrary.org/obo/UBERON_0005985` + +#### Added +- [coronary vessel](http://purl.obolibrary.org/obo/UBERON_0005985) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### corpus luteum `http://purl.obolibrary.org/obo/UBERON_0002512` +#### Removed +- [corpus luteum](http://purl.obolibrary.org/obo/UBERON_0002512) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "maintains the endometrium in mammals[WP]. A corpus luteum is known in hagfish (100), Squalus (101), and salamander (100) but not lamprey (102). There are no data for Branchiostoma and Ciona, and given that they are multiple spawners, there is no a priori reason to conclude that they lack a corpus luteum" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:20959416" + +- [corpus luteum](http://purl.obolibrary.org/obo/UBERON_0002512) SubClassOf [female reproductive organ](http://purl.obolibrary.org/obo/UBERON_0003134) + + + +### corpus striatum `http://purl.obolibrary.org/obo/UBERON_0000369` +#### Removed +- [corpus striatum](http://purl.obolibrary.org/obo/UBERON_0000369) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Thus, certain telencephalic characters - such as the presence of a pallium divided into lateral, dorsal, and medial formations and a subpallium divided into striatum and septum - appear to characterize all vertebrates. They are primitive characters and are homologous among all vertebrates.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1146/annurev.ne.04.030181.001505, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.487 Figure 14-10" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001175" + +- [corpus striatum](http://purl.obolibrary.org/obo/UBERON_0000369) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "The term has been used in a few different ways: * It is a pair of nuclear masses which form the basal ganglia, along with the subthalamic nucleus and the substantia nigra. * It may also refer to both the basal ganglia and internal capsule collectively.[2]" + + + +### cortex `http://purl.obolibrary.org/obo/UBERON_0001851` +#### Removed +- [cortex](http://purl.obolibrary.org/obo/UBERON_0001851) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "cortical" + +- [cortex](http://purl.obolibrary.org/obo/UBERON_0001851) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "this class is used more generically than in FMA, and includes e.g. cortex of hair" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + + + +### cortex of hair `http://purl.obolibrary.org/obo/UBERON_0002077` + +#### Added +- [cortex of hair](http://purl.obolibrary.org/obo/UBERON_0002077) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### cortex of humerus `http://purl.obolibrary.org/obo/UBERON_0004109` + +#### Added +- [cortex of humerus](http://purl.obolibrary.org/obo/UBERON_0004109) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### cortex of kidney `http://purl.obolibrary.org/obo/UBERON_0001225` +#### Removed +- [cortex of kidney](http://purl.obolibrary.org/obo/UBERON_0001225) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "In the adult metanephros, it forms a continuous smooth outer zone with a number of projections that extend down between the pyramids. It contains the renal corpuscles and the renal tubules except for parts of the loop of Henle which descend into the renal medulla. It also contains blood vessels and cortical collecting ducts. The renal cortex is the part of the kidney where ultrafiltration occurs.[WP]" + + + +### cortex of thymus `http://purl.obolibrary.org/obo/UBERON_0002123` +#### Removed +- [cortex of thymus](http://purl.obolibrary.org/obo/UBERON_0002123) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "Histologically, the thymus can be divided into a central medulla and a peripheral cortex which is surrounded by an outer capsule. The cortex and medulla play different roles in the development of T cells. Cells in the thymus can be divided into thymic stromal cells and cells of hematopoietic origin[WP]" + +#### Added +- [cortex of thymus](http://purl.obolibrary.org/obo/UBERON_0002123) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) + + +### cortical layer IV `http://purl.obolibrary.org/obo/UBERON_0005393` +#### Removed +- [cortical layer IV](http://purl.obolibrary.org/obo/UBERON_0005393) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "..." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:23027930" + +- [cortical layer IV](http://purl.obolibrary.org/obo/UBERON_0005393) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Relatively undeveloped in some mammals such as the tenrec." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0471888893" + + + +### cortical plate `http://purl.obolibrary.org/obo/UBERON_0005343` +#### Removed +- [cortical plate](http://purl.obolibrary.org/obo/UBERON_0005343) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "A single stem cell in the ventricular layer can give rise to neurons (and glial cells) in any of the cortical layers (Walsh and Cepko 1988)[NCBIBook:NBK10047]" + +- [cortical plate](http://purl.obolibrary.org/obo/UBERON_0005343) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "in humans develops into cortical layers II-VI" + +- [cortical plate](http://purl.obolibrary.org/obo/UBERON_0005343) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D002540" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + + + +### cortical subplate `http://purl.obolibrary.org/obo/UBERON_0004035` +#### Removed +- [cortical subplate](http://purl.obolibrary.org/obo/UBERON_0004035) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "The transient fetal subplate zone, together with the marginal zone and the cortical plate, represents the developmental anlage of the mammalian cerebral cortex. It serves as a waiting compartment for growing cortical afferents; its cells are involved in the establishment of pioneering cortical efferent projections and transient fetal circuitry, and apparently have a number of other developmental roles. The subplate zone is a phylogenetically recent structure and it is most developed in the human brain. Subplate neurons are among the first generated neurons in the mammalian cerebral cortex [1]. These neurons disappear during postnatal development and are important in establishing the correct wiring [2][3] and functional maturation [4] of the cerebral cortex. Subplate neurons appear to be selectively sensitive to injury (such as hypoxia) which in humans are associated with motor and cognitive defects" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" + +- [cortical subplate](http://purl.obolibrary.org/obo/UBERON_0004035) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "VO:0011276" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + + - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) + + + +### corticospinal tract `http://purl.obolibrary.org/obo/UBERON_0002707` +#### Removed +- [corticospinal tract](http://purl.obolibrary.org/obo/UBERON_0002707) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006132" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + + - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) + +- [corticospinal tract](http://purl.obolibrary.org/obo/UBERON_0002707) SubClassOf [axon tract](http://purl.obolibrary.org/obo/UBERON_0001018) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "In NIFSTD this is a tract of brain but this leads to issues due to its overlap with the spinal cord" + +#### Added +- [corticospinal tract](http://purl.obolibrary.org/obo/UBERON_0002707) SubClassOf [axon tract](http://purl.obolibrary.org/obo/UBERON_0001018) + + +### costal diaphragm `http://purl.obolibrary.org/obo/UBERON_0035831` +#### Removed +- [costal diaphragm](http://purl.obolibrary.org/obo/UBERON_0035831) [id](http://www.geneontology.org/formats/oboInOwl#id) "UBERON:0035831" + +- [costal diaphragm](http://purl.obolibrary.org/obo/UBERON_0035831) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58277" + +- [costal diaphragm](http://purl.obolibrary.org/obo/UBERON_0035831) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "The domain of the diaphragm that is a thin domed sheet of muscle composed of a radial array of myofibers extending laterally from the ribs and medially to a central tendon." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:23586979" + +- [costal diaphragm](http://purl.obolibrary.org/obo/UBERON_0035831) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "SCTID:368048007" + +- [costal diaphragm](http://purl.obolibrary.org/obo/UBERON_0035831) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [costal diaphragm](http://purl.obolibrary.org/obo/UBERON_0035831) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pars costalis diaphragmatis" + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + +- [costal diaphragm](http://purl.obolibrary.org/obo/UBERON_0035831) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "costal part of diaphragm" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58277" + +- [costal diaphragm](http://purl.obolibrary.org/obo/UBERON_0035831) [label](http://www.w3.org/2000/01/rdf-schema#label) "costal diaphragm" + +- Class: [costal diaphragm](http://purl.obolibrary.org/obo/UBERON_0035831) + +- [costal diaphragm](http://purl.obolibrary.org/obo/UBERON_0035831) SubClassOf [in lateral side of](http://purl.obolibrary.org/obo/BSPO_0000126) some [diaphragm](http://purl.obolibrary.org/obo/UBERON_0001103) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:23586979" + +- [costal diaphragm](http://purl.obolibrary.org/obo/UBERON_0035831) SubClassOf [organ subunit](http://purl.obolibrary.org/obo/UBERON_0000063) + +- [costal diaphragm](http://purl.obolibrary.org/obo/UBERON_0035831) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [diaphragm](http://purl.obolibrary.org/obo/UBERON_0001103) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:23586979" + +- [costal diaphragm](http://purl.obolibrary.org/obo/UBERON_0035831) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) + +- [costal diaphragm](http://purl.obolibrary.org/obo/UBERON_0035831) SubClassOf [attached to](http://purl.obolibrary.org/obo/RO_0002371) some [central tendon of diaphragm](http://purl.obolibrary.org/obo/UBERON_0006670) + + + +### cranial blood vasculature `http://purl.obolibrary.org/obo/UBERON_0011362` +#### Removed +- [cranial blood vasculature](http://purl.obolibrary.org/obo/UBERON_0011362) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Blood vessel part of cranial vasculature.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005297" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + + +### cranial bone `http://purl.obolibrary.org/obo/UBERON_0004766` +#### Removed +- [cranial bone](http://purl.obolibrary.org/obo/UBERON_0004766) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "here cranium = skull - mandible" + + + +### cranial cartilage `http://purl.obolibrary.org/obo/UBERON_0003933` +#### Removed +- [cranial cartilage](http://purl.obolibrary.org/obo/UBERON_0003933) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Cartilage which is part of the cranium.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001458" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + + +### cranial ganglion `http://purl.obolibrary.org/obo/UBERON_0001714` +#### Removed +- [cranial ganglion](http://purl.obolibrary.org/obo/UBERON_0001714) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Ganglion which is located in the head.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000013" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + + +### cranial nerve `http://purl.obolibrary.org/obo/UBERON_0001785` +#### Removed +- [cranial nerve](http://purl.obolibrary.org/obo/UBERON_0001785) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "See https://github.com/obophenotype/mouse-anatomy-ontology/issues/6" + +- [cranial nerve](http://purl.obolibrary.org/obo/UBERON_0001785) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Twelve pairs of cranial nerves exit/enter the cranium through openings in the skull. The nerves contain efferent axons with motor and glandular functions, as well as afferent axons from cranial ganglia with sensory functions. The nerves are numbered in a rostral to caudal sequence, with the exception of the lateral line nerves.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000641" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [cranial nerve](http://purl.obolibrary.org/obo/UBERON_0001785) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...).[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000279" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" + +- [cranial nerve](http://purl.obolibrary.org/obo/UBERON_0001785) SubClassOf [nerve](http://purl.obolibrary.org/obo/UBERON_0001021) + +#### Added +- [cranial nerve](http://purl.obolibrary.org/obo/UBERON_0001785) SubClassOf [nerve of head region](http://purl.obolibrary.org/obo/UBERON_0011779) + + +### cranial nerve II `http://purl.obolibrary.org/obo/UBERON_0000941` +#### Removed +- [cranial nerve II](http://purl.obolibrary.org/obo/UBERON_0000941) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup (reference 1); The (optic) stalk persists as the optic nerve (reference 2).[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000543" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429, http://medical-dictionary.thefreedictionary.com/optic+stalk" + +- [cranial nerve II](http://purl.obolibrary.org/obo/UBERON_0000941) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A collection of nerve cells that project visual information from the eyes to the brain. (Source: BioGlossary, www.Biology-Text.com)[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000435" + +- [cranial nerve II](http://purl.obolibrary.org/obo/UBERON_0000941) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "(relaion to eye): MA, XAO, AAO and BTO consider this part of the eye. This is in contrast to GO, FMA, EHDAA2 (FMA has a class 'intra-ocular part of optic nerve' which represents the region of overlap). Relation to brain: part of diencephalon in EHDAA2, ZFA. In NIF, has the optic nerve root as part, which is a feature part of the diencphalon" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" + +- [cranial nerve II](http://purl.obolibrary.org/obo/UBERON_0000941) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Fibrous, somatic sensory element covered by a fibrous connective-tissue sheath and is continuous with the layer of nerve cells on the inner surface of the eye.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010345" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + +- [cranial nerve II](http://purl.obolibrary.org/obo/UBERON_0000941) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + + +### cranial neural crest `http://purl.obolibrary.org/obo/UBERON_0003099` +#### Removed +- [cranial neural crest](http://purl.obolibrary.org/obo/UBERON_0003099) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anterior most portion of the neural crest. Migrates in three highly conserved streams: mandibular, hyoid and branchial.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010580" + +- [cranial neural crest](http://purl.obolibrary.org/obo/UBERON_0003099) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Neural crest that is part of the head.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001194" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [cranial neural crest](http://purl.obolibrary.org/obo/UBERON_0003099) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000063" + +#### Added +- [cranial neural crest](http://purl.obolibrary.org/obo/UBERON_0003099) SubClassOf [structure with developmental contribution from neural crest](http://purl.obolibrary.org/obo/UBERON_0010314) + +- [cranial neural crest](http://purl.obolibrary.org/obo/UBERON_0003099) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### cranial or facial muscle `http://purl.obolibrary.org/obo/UBERON_0015789` +#### Removed +- [cranial or facial muscle](http://purl.obolibrary.org/obo/UBERON_0015789) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "see also, 'facial nerve muscle', which is not precisely equivalent. We include this grouping to accomodate the MA class, which includes masticatory muscle as a subtype; note the masticatory muscle is noy innervated by the facial nerve, unlike the facial muscles proper" + + + +### cranial placode `http://purl.obolibrary.org/obo/UBERON_0002546` +#### Removed +- [cranial placode](http://purl.obolibrary.org/obo/UBERON_0002546) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:293966" + +- [cranial placode](http://purl.obolibrary.org/obo/UBERON_0002546) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "The term placode or placodes also applies to developing organs such as teeth, mammary glands, hair follicles, feathers and scales. We include a separate parent class for this. to avoid confusion, we include neurogenic placode as a subclass" + +- [cranial placode](http://purl.obolibrary.org/obo/UBERON_0002546) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:11523831" + + + +### cranial skeletal system `http://purl.obolibrary.org/obo/UBERON_0010323` +#### Removed +- [cranial skeletal system](http://purl.obolibrary.org/obo/UBERON_0010323) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Skeletal system which is part of the skull, including the splanchnocranium, chondrocranium, and dermatocranium.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000737" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [cranial skeletal system](http://purl.obolibrary.org/obo/UBERON_0010323) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "that the cranial skeleton includes the pharyngeal arch skeleton. It is thus more inclusive that the cranium itself, and extends beyond the head in tetrapods. The AAO class called 'skull' belongs here, as it includes the whole splanchnocranium" + +- [cranial skeletal system](http://purl.obolibrary.org/obo/UBERON_0010323) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Bony structure that encases the central nervous system and the primary sense organs of sight, olfaction, hearing, and equilibrium.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000109" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + + +### cranial suture `http://purl.obolibrary.org/obo/UBERON_0003685` +#### Removed +- [cranial suture](http://purl.obolibrary.org/obo/UBERON_0003685) [UBPROP_0000202](http://purl.obolibrary.org/obo/UBPROP_0000202) [FMA_71385](http://purl.obolibrary.org/obo/FMA_71385) + + + +### craniocervical region musculature `http://purl.obolibrary.org/obo/UBERON_0008229` +#### Removed +- [craniocervical region musculature](http://purl.obolibrary.org/obo/UBERON_0008229) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in MA this is restricted to skeletal muscles" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" + + + +### cranium `http://purl.obolibrary.org/obo/UBERON_0003128` +#### Removed +- [cranium](http://purl.obolibrary.org/obo/UBERON_0003128) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D012886" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + +- [cranium](http://purl.obolibrary.org/obo/UBERON_0003128) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" + +- [cranium](http://purl.obolibrary.org/obo/UBERON_0003128) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:17680" + +- [cranium](http://purl.obolibrary.org/obo/UBERON_0003128) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "cranial" + +- [cranium](http://purl.obolibrary.org/obo/UBERON_0003128) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "the inclusion of the FMA class here is probably not quite correct, as this class includes as parts sutures, whereas this is not part of the bones of the cranium" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + +- [cranium](http://purl.obolibrary.org/obo/UBERON_0003128) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [skeleton of lower jaw](http://purl.obolibrary.org/obo/UBERON_0003278) + + + +### created `http://purl.org/dc/terms/created` +#### Removed +- AnnotationProperty: [created](http://purl.org/dc/terms/created) + + + +### creator `http://purl.org/dc/terms/creator` +#### Removed +- AnnotationProperty: [creator](http://purl.org/dc/terms/creator) + + + +### creator `http://purl.org/dc/elements/1.1/creator` +#### Removed +- [creator](http://purl.org/dc/elements/1.1/creator) [id](http://www.geneontology.org/formats/oboInOwl#id) "dc-creator" + +- [creator](http://purl.org/dc/elements/1.1/creator) [is_metadata_tag](http://www.geneontology.org/formats/oboInOwl#is_metadata_tag) true + +- [creator](http://purl.org/dc/elements/1.1/creator) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "dc-creator" + +- [creator](http://purl.org/dc/elements/1.1/creator) [label](http://www.w3.org/2000/01/rdf-schema#label) "creator" + +- [creator](http://purl.org/dc/elements/1.1/creator) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://purl.org/dc/elements/1.1/creator" + +- [creator](http://purl.org/dc/elements/1.1/creator) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + + + +### crista ampullaris `http://purl.obolibrary.org/obo/UBERON_0004721` + +#### Added +- [crista ampullaris](http://purl.obolibrary.org/obo/UBERON_0004721) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### crista terminalis `http://purl.obolibrary.org/obo/UBERON_0005979` + +#### Added +- [crista terminalis](http://purl.obolibrary.org/obo/UBERON_0005979) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### crossSpeciesExactMatch `https://w3id.org/semapv/vocab/crossSpeciesExactMatch` +#### Removed +- AnnotationProperty: [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) + + + +### crurotarsal joint `http://purl.obolibrary.org/obo/UBERON_0011980` +#### Removed +- [crurotarsal joint](http://purl.obolibrary.org/obo/UBERON_0011980) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "an ankle joint that passes between the astragalus and calcaneum[Palaeos]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://palaeos.com/vertebrates/glossary/glossaryCr.html#Crurotarsal%20joint" + + + +### crus of diaphragm `http://purl.obolibrary.org/obo/UBERON_0014765` +#### Removed +- [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Crus_of_diaphragm" + +- [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "diaphragmatic crura" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Crus_of_diaphragm" + +- [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:17703" + +- [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "crus of the diaphragm" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Crus_of_diaphragm" + +- [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "diaphragm crura" + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [plural form](http://purl.obolibrary.org/obo/OMO_0003004) + +- [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "SCTID:244668003" + +- [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "crural diaphragm" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:23586979" + +- [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "The domain of the diaphragm that is located dorsally and attaches to the vertebrae and surrounds the esophagus and aorta." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:23586979" + +- [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EHDAA2:0000597" + +- [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "VHOG:0001546" + +- [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Classification notes: May be considered an external sphincter[PMID:8224664]" + +- [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) [id](http://www.geneontology.org/formats/oboInOwl#id) "UBERON:0014765" + +- [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) [label](http://www.w3.org/2000/01/rdf-schema#label) "crus of diaphragm" + +- [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "crura of the diaphragm" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Crus_of_diaphragm" + +- Class: [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) + +- [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) SubClassOf [intersects midsagittal plane of](http://purl.obolibrary.org/obo/BSPO_0005001) some [diaphragm](http://purl.obolibrary.org/obo/UBERON_0001103) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:23586979" + +- [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) SubClassOf [organ subunit](http://purl.obolibrary.org/obo/UBERON_0000063) + +- [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [diaphragm](http://purl.obolibrary.org/obo/UBERON_0001103) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:23586979" + +- [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) SubClassOf [attached to](http://purl.obolibrary.org/obo/RO_0002371) some [central tendon of diaphragm](http://purl.obolibrary.org/obo/UBERON_0006670) + +- [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) SubClassOf [attached to](http://purl.obolibrary.org/obo/RO_0002371) some [vertebral column](http://purl.obolibrary.org/obo/UBERON_0001130) + + + +### crypt of Lieberkuhn `http://purl.obolibrary.org/obo/UBERON_0001983` +#### Removed +- [crypt of Lieberkuhn](http://purl.obolibrary.org/obo/UBERON_0001983) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "In histology, an intestinal crypt, also crypt of LieberkC<hn and intestinal gland, is a gland found in the epithelial lining of the small intestine and colon. The crypts secrete various enzymes, including sucrase and maltase, along with endopeptidases and exopeptidases. Also new epithelium is formed here, keeping in mind that the epithelium at this site is frequently worn away by the passing food. Loss of proliferation control in the crypts is thought to lead to colorectal cancer. The basal portion of the Crypt contains multipotent stem cells. At each mitosis one daughter remains a stem cell while the other differentiates and migrates up the side of the crypt and eventually the villus. Goblet cells are among the cells produced in this fashion[Wikipedia:Intestinal_crypt]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Intestinal_crypt" + +- [crypt of Lieberkuhn](http://purl.obolibrary.org/obo/UBERON_0001983) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Most fish lack intestinal glands that extend into the mucosa, Gadidae (Jacobshagen 1937) and Macrouridae (Geisterdoerfer 1973( have glands at the base of surface folds throughout intestine - these have been called crypts, but cell types are the same as for surface epithelium. Crypts have been described in salamander midguts (Reeder 1964) some reptiles (Luppa 1977) and some birds (Ziswiler and Farner 1972). Reptile crypts are less developed than birds and mammals, with epithelium similar to the surface. Avian crypts vary from those with absorprive and goblet cells to those that have cells with basophilic granules" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:9780521617147" + +- [crypt of Lieberkuhn](http://purl.obolibrary.org/obo/UBERON_0001983) SubClassOf [only in taxon](http://purl.obolibrary.org/obo/RO_0002160) some [Tetrapoda](http://purl.obolibrary.org/obo/NCBITaxon_32523) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:9780521617147" + + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "further investigation required" + +#### Added +- [crypt of Lieberkuhn](http://purl.obolibrary.org/obo/UBERON_0001983) SubClassOf [only in taxon](http://purl.obolibrary.org/obo/RO_0002160) some [Tetrapoda](http://purl.obolibrary.org/obo/NCBITaxon_32523) + + +### cuboidal epithelium `http://purl.obolibrary.org/obo/UBERON_0010077` +#### Removed +- [cuboidal epithelium](http://purl.obolibrary.org/obo/UBERON_0010077) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in NCIT this is glandular" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "NCIT" + + + +### curation status specification `http://purl.obolibrary.org/obo/IAO_0000078` +#### Removed +- [curation status specification](http://purl.obolibrary.org/obo/IAO_0000078) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "curation status specification"@en + +- [curation status specification](http://purl.obolibrary.org/obo/IAO_0000078) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) + +- [curation status specification](http://purl.obolibrary.org/obo/IAO_0000078) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) "GROUP:OBI:<http://purl.obolibrary.org/obo/obi>"@en + +- [curation status specification](http://purl.obolibrary.org/obo/IAO_0000078) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) "PERSON:Bill Bug"@en + +- [curation status specification](http://purl.obolibrary.org/obo/IAO_0000078) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) "OBI_0000266"@en + + + +### cutaneous elastic tissue `http://purl.obolibrary.org/obo/UBERON_0003967` + +#### Added +- [cutaneous elastic tissue](http://purl.obolibrary.org/obo/UBERON_0003967) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### cuticle of hair `http://purl.obolibrary.org/obo/UBERON_0002076` + +#### Added +- [cuticle of hair](http://purl.obolibrary.org/obo/UBERON_0002076) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### cystic duct `http://purl.obolibrary.org/obo/UBERON_0001152` +#### Removed +- [cystic duct](http://purl.obolibrary.org/obo/UBERON_0001152) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Duct that connects the gall bladder and the common bile duct.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005166" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:Curator" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [cystic duct](http://purl.obolibrary.org/obo/UBERON_0001152) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The duct of the gallbladder which joins the common hepatic duct, thus forming the common biliary duct. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000213" + + + +### cytotoxic T-lymphocyte protein 4 `http://purl.obolibrary.org/obo/PR_000001852` +#### Removed +- [cytotoxic T-lymphocyte protein 4](http://purl.obolibrary.org/obo/PR_000001852) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [cytotoxic T-lymphocyte protein 4 (human)](http://purl.obolibrary.org/obo/PR_P16410) + + + +### data about an ontology part `http://purl.obolibrary.org/obo/IAO_0000102` +#### Removed +- [data about an ontology part](http://purl.obolibrary.org/obo/IAO_0000102) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "data about an ontology part"@en + +- [data about an ontology part](http://purl.obolibrary.org/obo/IAO_0000102) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) "Person:Alan Ruttenberg"@en + + + +### data item `http://purl.obolibrary.org/obo/IAO_0000027` +#### Removed +- [data item](http://purl.obolibrary.org/obo/IAO_0000027) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "data item"@en + + + +### date `http://purl.org/dc/terms/date` +#### Removed +- [date](http://purl.org/dc/terms/date) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://purl.org/dc/terms/date" + +- [date](http://purl.org/dc/terms/date) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [date](http://purl.org/dc/terms/date) [is_metadata_tag](http://www.geneontology.org/formats/oboInOwl#is_metadata_tag) true + +- [date](http://purl.org/dc/terms/date) [label](http://www.w3.org/2000/01/rdf-schema#label) "date" + +- [date](http://purl.org/dc/terms/date) [id](http://www.geneontology.org/formats/oboInOwl#id) "dcterms-date" + +- [date](http://purl.org/dc/terms/date) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "dcterms-date" + + + +### date `http://www.w3.org/2001/XMLSchema#date` +#### Removed +- [date](http://www.w3.org/2001/XMLSchema#date) + + + +### date_retrieved `http://www.geneontology.org/formats/oboInOwl#date_retrieved` +#### Removed +- AnnotationProperty: [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) + + + +### death stage `http://purl.obolibrary.org/obo/UBERON_0000071` +#### Removed +- [death stage](http://purl.obolibrary.org/obo/UBERON_0000071) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "ncit:Death is an outcome" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "ncit" + + + +### decidua `http://purl.obolibrary.org/obo/UBERON_0002450` +#### Removed +- [decidua](http://purl.obolibrary.org/obo/UBERON_0002450) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "formed under the influence of progesterone and forms highly-characteristic cells. [Wikipedia:Decidua]" + +- [decidua](http://purl.obolibrary.org/obo/UBERON_0002450) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [placenta](http://purl.obolibrary.org/obo/UBERON_0001987) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "MA" + + - [component](http://www.geneontology.org/formats/oboInOwl#component) "maternal" + +#### Added +- [decidua](http://purl.obolibrary.org/obo/UBERON_0002450) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [placenta](http://purl.obolibrary.org/obo/UBERON_0001987) + + +### decreased coiling `http://purl.obolibrary.org/obo/PATO_0001796` +#### Removed +- [decreased coiling](http://purl.obolibrary.org/obo/PATO_0001796) [RO_0002604](http://purl.obolibrary.org/obo/RO_0002604) [increased coiling](http://purl.obolibrary.org/obo/PATO_0001795) + + + +### decreased contractility `http://purl.obolibrary.org/obo/PATO_0001581` +#### Removed +- [decreased contractility](http://purl.obolibrary.org/obo/PATO_0001581) [RO_0002604](http://purl.obolibrary.org/obo/RO_0002604) [increased contractility](http://purl.obolibrary.org/obo/PATO_0001580) + + + +### decreased elasticity `http://purl.obolibrary.org/obo/PATO_0002288` +#### Removed +- [decreased elasticity](http://purl.obolibrary.org/obo/PATO_0002288) [RO_0002604](http://purl.obolibrary.org/obo/RO_0002604) [increased elasticity](http://purl.obolibrary.org/obo/PATO_0002287) + + + +### decreased flexibility `http://purl.obolibrary.org/obo/PATO_0001777` +#### Removed +- [decreased flexibility](http://purl.obolibrary.org/obo/PATO_0001777) [RO_0002604](http://purl.obolibrary.org/obo/RO_0002604) [increased flexibility](http://purl.obolibrary.org/obo/PATO_0001776) + + + +### decreased life span `http://purl.obolibrary.org/obo/PATO_0001604` +#### Removed +- [decreased life span](http://purl.obolibrary.org/obo/PATO_0001604) [RO_0002604](http://purl.obolibrary.org/obo/RO_0002604) [increased life span](http://purl.obolibrary.org/obo/PATO_0001603) + + + +### decreased object quality `http://purl.obolibrary.org/obo/PATO_0002303` +#### Removed +- [decreased object quality](http://purl.obolibrary.org/obo/PATO_0002303) [RO_0002604](http://purl.obolibrary.org/obo/RO_0002604) [increased object quality](http://purl.obolibrary.org/obo/PATO_0002305) + + + +### decreased quality `http://purl.obolibrary.org/obo/PATO_0002301` +#### Removed +- [decreased quality](http://purl.obolibrary.org/obo/PATO_0002301) [RO_0002604](http://purl.obolibrary.org/obo/RO_0002604) [increased quality](http://purl.obolibrary.org/obo/PATO_0002300) + + + +### decreased size `http://purl.obolibrary.org/obo/PATO_0000587` +#### Removed +- [decreased size](http://purl.obolibrary.org/obo/PATO_0000587) [RO_0002604](http://purl.obolibrary.org/obo/RO_0002604) [increased size](http://purl.obolibrary.org/obo/PATO_0000586) + + + +### decreased viscosity `http://purl.obolibrary.org/obo/PATO_0001694` +#### Removed +- [decreased viscosity](http://purl.obolibrary.org/obo/PATO_0001694) [RO_0002604](http://purl.obolibrary.org/obo/RO_0002604) [increased viscosity](http://purl.obolibrary.org/obo/PATO_0001693) + + + +### deep to `http://purl.obolibrary.org/obo/BSPO_0000107` +#### Removed +- [deep to](http://purl.obolibrary.org/obo/BSPO_0000107) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [deep to](http://purl.obolibrary.org/obo/BSPO_0000107) [label](http://www.w3.org/2000/01/rdf-schema#label) "deep to" + +- [deep to](http://purl.obolibrary.org/obo/BSPO_0000107) [id](http://www.geneontology.org/formats/oboInOwl#id) "deep_to" + +- [deep to](http://purl.obolibrary.org/obo/BSPO_0000107) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BSPO:0000107" + +- [deep to](http://purl.obolibrary.org/obo/BSPO_0000107) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "deep_to" + + + +### defined by construct `http://purl.obolibrary.org/obo/OMO_0002000` +#### Removed +- [defined by construct](http://purl.obolibrary.org/obo/OMO_0002000) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "'part disjoint with' 'defined by construct' """ + PREFIX owl: <http://www.w3.org/2002/07/owl#> + PREFIX : <http://example.org/ + CONSTRUCT { + [ + a owl:Restriction ; + owl:onProperty :part_of ; + owl:someValuesFrom ?a ; + owl:disjointWith [ + a owl:Restriction ; + owl:onProperty :part_of ; + owl:someValuesFrom ?b + ] + ] + } + WHERE { + ?a :part_disjoint_with ?b . + }" + + + +### defined class `http://purl.obolibrary.org/obo/IAO_0000420` +#### Removed +- [defined class](http://purl.obolibrary.org/obo/IAO_0000420) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "defined class"@en + +- [defined class](http://purl.obolibrary.org/obo/IAO_0000420) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) "Alan Ruttenberg"@en + + + +### definition `http://purl.obolibrary.org/obo/IAO_0000115` +#### Removed +- [definition](http://purl.obolibrary.org/obo/IAO_0000115) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [ready for release](http://purl.obolibrary.org/obo/IAO_0000122) + +- [definition](http://purl.obolibrary.org/obo/IAO_0000115) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) "PERSON:Daniel Schober"@en + +- [definition](http://purl.obolibrary.org/obo/IAO_0000115) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "definition"@en + +- [definition](http://purl.obolibrary.org/obo/IAO_0000115) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) "GROUP:OBI:<http://purl.obolibrary.org/obo/obi>"@en + + + +### deltoid `http://purl.obolibrary.org/obo/UBERON_0001476` +#### Removed +- [deltoid](http://purl.obolibrary.org/obo/UBERON_0001476) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Muscle which originates as three heads, the pars externalis, pars clavicularis, and pars scapularis. The pars externalis originates from the lateral border of the omosternum and inserts on the distal portion of the humerus. The pars clavicularis originates from the ventro-lateral surface of the clavicle and inserts on the deltoid crest of the humerus. The pars scapularis originates from the lateral surface of the clavicle and inserts on the deltoid crest of the humerus.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:MEJ" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010716" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + +- [deltoid](http://purl.obolibrary.org/obo/UBERON_0001476) SubClassOf [has muscle origin](http://purl.obolibrary.org/obo/RO_0002372) some [acromion](http://purl.obolibrary.org/obo/UBERON_0002497) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "the anterior border and upper surface of the lateral third of the clavicle acromion spine of the scapula" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "dbpedia" + +- [deltoid](http://purl.obolibrary.org/obo/UBERON_0001476) SubClassOf [has muscle origin](http://purl.obolibrary.org/obo/RO_0002372) some [scapula](http://purl.obolibrary.org/obo/UBERON_0006849) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "the anterior border and upper surface of the lateral third of the clavicle acromion spine of the scapula" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "dbpedia" + +- [deltoid](http://purl.obolibrary.org/obo/UBERON_0001476) SubClassOf [has muscle insertion](http://purl.obolibrary.org/obo/RO_0002373) some [deltopectoral crest](http://purl.obolibrary.org/obo/UBERON_0002498) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "dbpedia" + + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "deltoid tuberosity of humerus" + +- [deltoid](http://purl.obolibrary.org/obo/UBERON_0001476) SubClassOf [has muscle origin](http://purl.obolibrary.org/obo/RO_0002372) some [clavicle bone](http://purl.obolibrary.org/obo/UBERON_0001105) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "the anterior border and upper surface of the lateral third of the clavicle acromion spine of the scapula" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "dbpedia" + +#### Added +- [deltoid](http://purl.obolibrary.org/obo/UBERON_0001476) SubClassOf [has muscle origin](http://purl.obolibrary.org/obo/RO_0002372) some [scapula](http://purl.obolibrary.org/obo/UBERON_0006849) + +- [deltoid](http://purl.obolibrary.org/obo/UBERON_0001476) SubClassOf [has muscle origin](http://purl.obolibrary.org/obo/RO_0002372) some [clavicle bone](http://purl.obolibrary.org/obo/UBERON_0001105) + +- [deltoid](http://purl.obolibrary.org/obo/UBERON_0001476) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + +- [deltoid](http://purl.obolibrary.org/obo/UBERON_0001476) SubClassOf [has muscle insertion](http://purl.obolibrary.org/obo/RO_0002373) some [deltopectoral crest](http://purl.obolibrary.org/obo/UBERON_0002498) + +- [deltoid](http://purl.obolibrary.org/obo/UBERON_0001476) SubClassOf [has muscle origin](http://purl.obolibrary.org/obo/RO_0002372) some [acromion](http://purl.obolibrary.org/obo/UBERON_0002497) + + +### deltoid pre-muscle mass `http://purl.obolibrary.org/obo/UBERON_0006219` + +#### Added +- [deltoid pre-muscle mass](http://purl.obolibrary.org/obo/UBERON_0006219) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### deltopectoral crest `http://purl.obolibrary.org/obo/UBERON_0002498` +#### Removed +- [deltopectoral crest](http://purl.obolibrary.org/obo/UBERON_0002498) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In basal Tetrapodomorph lineages often the deltoid process and the pectoral processes are separate and thus should not be made exact synonyms to the deltopectoral crest.[PHENOSCAPE:ad]" + +#### Added +- [deltopectoral crest](http://purl.obolibrary.org/obo/UBERON_0002498) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### denotator type `http://purl.obolibrary.org/obo/IAO_0000409` +#### Removed +- [denotator type](http://purl.obolibrary.org/obo/IAO_0000409) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) "Barry Smith, Werner Ceusters"@en + +- [denotator type](http://purl.obolibrary.org/obo/IAO_0000409) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) "Alan Ruttenberg"@en + +- [denotator type](http://purl.obolibrary.org/obo/IAO_0000409) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "denotator type"@en + +- [denotator type](http://purl.obolibrary.org/obo/IAO_0000409) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are "natural kinds" and the latter arbitrary collections of entities."@en + + + +### dense connective tissue `http://purl.obolibrary.org/obo/UBERON_0011823` +#### Removed +- [dense connective tissue](http://purl.obolibrary.org/obo/UBERON_0011823) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "ncithesaurus:Dense_Connective_Tissue" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-29" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "NCIT" + + + +### dense irregular connective tissue `http://purl.obolibrary.org/obo/UBERON_0011822` +#### Removed +- [dense irregular connective tissue](http://purl.obolibrary.org/obo/UBERON_0011822) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Tissue characterized by a thick, random arrangement of collagen and elastin fibers with very few cells. The majority of the cells are fibroblasts, but mast cells and macrophages may also be seen. It is found in the dermis, periosteum, perichondrium, capsules of organs and sheaths of nerves and muscles[NCIT]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-29" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "NCIT" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "ncithesaurus:Irregular_Dense_Connective_Tissue" + + + +### dense regular connective tissue `http://purl.obolibrary.org/obo/UBERON_0007846` +#### Removed +- [dense regular connective tissue](http://purl.obolibrary.org/obo/UBERON_0007846) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).[VSAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000050" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PSPUB:0000170" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" + +- [dense regular connective tissue](http://purl.obolibrary.org/obo/UBERON_0007846) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Regular connective tissue, the intercellular matrix of which consists predominantly of collagen fiber bundles arranged in parallel arrays.[FMA]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-29" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "FMA" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "FMA:64781" + + + +### dental epithelium `http://purl.obolibrary.org/obo/UBERON_0003843` +#### Removed +- [dental epithelium](http://purl.obolibrary.org/obo/UBERON_0003843) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "In the developing molar dentition of the mouse, tooth inductive po- tential resides in the dental epithelium until embryonic day (E)12.5 (3). Thereafter, tooth inductive potential shifts to neural crest-derived dental mesenchyme, which acquires the ability to direct tooth formation in nonodontogenic tissues (3, 4)" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:10954731" + +- [dental epithelium](http://purl.obolibrary.org/obo/UBERON_0003843) SubClassOf [epithelium](http://purl.obolibrary.org/obo/UBERON_0000483) + +- [dental epithelium](http://purl.obolibrary.org/obo/UBERON_0003843) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [pharyngeal arch 1](http://purl.obolibrary.org/obo/UBERON_0004362) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "JB" + + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "epithelium" + +#### Added +- [dental epithelium](http://purl.obolibrary.org/obo/UBERON_0003843) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [pharyngeal arch 1](http://purl.obolibrary.org/obo/UBERON_0004362) + +- [dental epithelium](http://purl.obolibrary.org/obo/UBERON_0003843) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) + + +### dental follicle `http://purl.obolibrary.org/obo/UBERON_0008969` +#### Removed +- [dental follicle](http://purl.obolibrary.org/obo/UBERON_0008969) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D003795" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + + + +### dental pulp `http://purl.obolibrary.org/obo/UBERON_0001754` +#### Removed +- [dental pulp](http://purl.obolibrary.org/obo/UBERON_0001754) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Material in the center of the dentine of the mature tooth. In secondary teeth the pulp contains blood vessels and odontoblast.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005141" + +- [dental pulp](http://purl.obolibrary.org/obo/UBERON_0001754) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The oral cavity of vertebrates is generally thought to arise as an ectodermal invagination. Consistent with this, oral teeth are proposed to arise exclusively from ectoderm, contributing to tooth enamel epithelium, and from neural crest derived mesenchyme, contributing to dentin and pulp (reference 1); Teeth and tooth-like structures, together named odontodes, are repeated organs thought to share a common evolutionary origin. These structures can be found in gnathostomes at different locations along the body: oral teeth in the jaws, teeth and denticles in the oral-pharyngeal cavity, and dermal denticles on elasmobranch skin (reference 2).[uncertain][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001469" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1038/nature07304 Soukup V, Epperlein HH, Horacek I, Cerny R, Dual epithelial origin of vertebrate oral teeth. Nature (2008), DOI:10.1186/1471-2148-11-307 The homology of odontodes in gnathostomes: insights from Dlx gene expression in the dogfish, Scyliorhinus canicula. BMC Evolutionary Biology (2011)" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + +#### Added +- [dental pulp](http://purl.obolibrary.org/obo/UBERON_0001754) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) + + +### dentary `http://purl.obolibrary.org/obo/UBERON_0004742` +#### Removed +- [dentary](http://purl.obolibrary.org/obo/UBERON_0004742) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Dermal bone that is usually the anteriormost bone of the lower jaw, and that articulates with the angular, or anguloarticular bone, posteriorly, and carries part of the mandibular sensory canal and pore openings of the mandibular sensory canal on its lateral surface. The dentary is a paired bone.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000191" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TAO:GA_TG" + +- [dentary](http://purl.obolibrary.org/obo/UBERON_0004742) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Ossified element of intramembranous origin that invests the lateral margin of Meckel's cartilage thereby forming the lateral side of the mandible in anurans and salamanders (Duellman & Trueb, 1994:293). In caecilians, the dentary is part of a compound bone termed the pseudodentary.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000124" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + +- [dentary](http://purl.obolibrary.org/obo/UBERON_0004742) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In lobe-finned fishes and the early fossil tetrapods, the bone homologous to the mandible of mammals is merely the largest of several bones in the lower jaw. In such animals, it is referred to as the dentary bone, and forms the body of the outer surface of the jaw. It is bordered below by a number of splenial bones, while the angle of the jaw is formed by a lower angular bone and a suprangular bone just above it. The inner surface of the jaw is lined by a prearticular bone, while the articular bone forms the articulation with the skull proper. Finally a set of three narrow coronoid bones lie above the prearticular bone. As the name implies, the majority of the teeth are attached to the dentary, but there are commonly also teeth on the coronoid bones, and sometimes on the prearticular as well. This complex primitive pattern has, however, been simplified to various degrees in the great majority of vertebrates, as bones have either fused or vanished entirely. In teleosts, only the dentary, articular, and angular bones remain, while in living amphibians, the dentary is accompanied only by the prearticular, and, in salamanders, one of the coronoids. The lower jaw of reptiles has only a single coronoid and splenial, but retains all the other primitive bones except the prearticular." + +- [dentary](http://purl.obolibrary.org/obo/UBERON_0004742) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Of all these bones [dentary, splenials, coronoids, angular, surangular and prearticular], only the dentary remains in the lower jaw of a mammal.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.248" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001022" + +- [dentary](http://purl.obolibrary.org/obo/UBERON_0004742) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: overlaps dentary-anguloarticular joint (TAO:0001749)[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000191" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [dentary](http://purl.obolibrary.org/obo/UBERON_0004742) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The dentary is a dermal bone that forms the antero-lateral part of the lower jaw in fishes and amphibians. In mammals the lower jaw consists entirely of the dentary bone. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, ZFA:0000191_and_Liem_KF, p.248][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001022" + +- [dentary](http://purl.obolibrary.org/obo/UBERON_0004742) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [dermatocranium](http://purl.obolibrary.org/obo/UBERON_0003113) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0073040584" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFA" + + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "mandibular series" + +#### Added +- [dentary](http://purl.obolibrary.org/obo/UBERON_0004742) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [dermatocranium](http://purl.obolibrary.org/obo/UBERON_0003113) + + +### dentary tooth `http://purl.obolibrary.org/obo/UBERON_0011594` +#### Removed +- [dentary tooth](http://purl.obolibrary.org/obo/UBERON_0011594) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:321647" + +- [dentary tooth](http://purl.obolibrary.org/obo/UBERON_0011594) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Tooth that is attached to the dentary.[TAO]" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TAO:wd" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001628" + +- [dentary tooth](http://purl.obolibrary.org/obo/UBERON_0011594) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: part_of dentary tooth row (TAO:0001952)[TAO]" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001628" + + + +### dentate gyrus of hippocampal formation `http://purl.obolibrary.org/obo/UBERON_0001885` +#### Removed +- [dentate gyrus of hippocampal formation](http://purl.obolibrary.org/obo/UBERON_0001885) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [Ammon's horn](http://purl.obolibrary.org/obo/UBERON_0001954) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" + +- [dentate gyrus of hippocampal formation](http://purl.obolibrary.org/obo/UBERON_0001885) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The dentate gyrus is one of two interlocking gyri of the hippocampus. It contains granule cells, which project to the pyramidal cells and interneurons of the CA3 region of the ammon gyrus[GO][GO:0021542]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GO:0021542" + +- [dentate gyrus of hippocampal formation](http://purl.obolibrary.org/obo/UBERON_0001885) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002601](http://purl.obolibrary.org/obo/UBERON_0002601) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" + + + +### dentine `http://purl.obolibrary.org/obo/UBERON_0001751` +#### Removed +- [dentine](http://purl.obolibrary.org/obo/UBERON_0001751) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Mineralized collagen containing substance that forms the tooth structure.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005143" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [dentine](http://purl.obolibrary.org/obo/UBERON_0001751) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Dentine is a bona fide vertebrate novelty, and dentine-secreting odontoblasts represent a cell type that is exclusively derived from the neural crest.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001589" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1111/j.1469-7580.2012.01495.x Hall BK, Gillis JA, Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues. J Anat (2012)" + +- [dentine](http://purl.obolibrary.org/obo/UBERON_0001751) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "dentinal" + +- [dentine](http://purl.obolibrary.org/obo/UBERON_0001751) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Dentine is found in the fossil record as early as the late Cambrian, in fish, where it may have had a role in electrochemical sensing of the environment as well as assisting in defense[WP]" + +- [dentine](http://purl.obolibrary.org/obo/UBERON_0001751) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) + + + +### dentition `http://purl.obolibrary.org/obo/UBERON_0003672` +#### Removed +- [dentition](http://purl.obolibrary.org/obo/UBERON_0003672) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The teeth collectively in the dental arch. Dentition ordinarily refers to the natural teeth in position in their alveoli. (MeSH[ncithesaurus:Dentition])" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ncithesaurus:Dentition" + +- [dentition](http://purl.obolibrary.org/obo/UBERON_0003672) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "In FMA this is an anatomical set" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + +- [dentition](http://purl.obolibrary.org/obo/UBERON_0003672) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Dentition refers to set of teeth, especially with regard to their number, kind, and arrangement, in the mouth.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000126" + + + +### depends on `http://purl.obolibrary.org/obo/RO_0002502` +#### Removed +- [depends on](http://purl.obolibrary.org/obo/RO_0002502) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + + + +### depiction `http://xmlns.com/foaf/0.1/depiction` +#### Removed +- [depiction](http://xmlns.com/foaf/0.1/depiction) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://xmlns.com/foaf/0.1/depiction" + +- [depiction](http://xmlns.com/foaf/0.1/depiction) [id](http://www.geneontology.org/formats/oboInOwl#id) "depiction" + +- [depiction](http://xmlns.com/foaf/0.1/depiction) [is_metadata_tag](http://www.geneontology.org/formats/oboInOwl#is_metadata_tag) true + +- [depiction](http://xmlns.com/foaf/0.1/depiction) [label](http://www.w3.org/2000/01/rdf-schema#label) "depiction" + +- [depiction](http://xmlns.com/foaf/0.1/depiction) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "depiction" + +- [depiction](http://xmlns.com/foaf/0.1/depiction) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + + + +### derives from `http://purl.obolibrary.org/obo/RO_0001000` +#### Removed +- [derives from](http://purl.obolibrary.org/obo/RO_0001000) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) + +- [derives from](http://purl.obolibrary.org/obo/RO_0001000) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "derives_from"@en + +- [derives from](http://purl.obolibrary.org/obo/RO_0001000) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations." + +- [derives from](http://purl.obolibrary.org/obo/RO_0001000) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "this cell derives from this parent cell (cell division)"@en + +- [derives from](http://purl.obolibrary.org/obo/RO_0001000) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "this nucleus derives from this parent nucleus (nuclear division)"@en + + + +### derives into `http://purl.obolibrary.org/obo/RO_0001001` +#### Removed +- [derives into](http://purl.obolibrary.org/obo/RO_0001001) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) + +- [derives into](http://purl.obolibrary.org/obo/RO_0001001) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "derives_into"@en + +- [derives into](http://purl.obolibrary.org/obo/RO_0001001) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "this parent nucleus derives into this nucleus (nuclear division)"@en + +- [derives into](http://purl.obolibrary.org/obo/RO_0001001) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "this parent cell derives into this cell (cell division)"@en + + + +### dermal bone `http://purl.obolibrary.org/obo/UBERON_0008907` +#### Removed +- [dermal bone](http://purl.obolibrary.org/obo/UBERON_0008907) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Intramembranous bone that forms superficially in the organism.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001590" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TAO:wd" + +- [dermal bone](http://purl.obolibrary.org/obo/UBERON_0008907) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "other AOs are not yet in sync with this classification" + + + +### dermal chromatophore `http://purl.obolibrary.org/obo/CL_4040006` + +#### Added +- [dermal chromatophore](http://purl.obolibrary.org/obo/CL_4040006) [label](http://www.w3.org/2000/01/rdf-schema#label) "dermal chromatophore" + +- [dermal chromatophore](http://purl.obolibrary.org/obo/CL_4040006) [date](http://purl.org/dc/terms/date) "2024-03-07T09:37:14Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- [dermal chromatophore](http://purl.obolibrary.org/obo/CL_4040006) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0819-0473](https://orcid.org/0000-0002-0819-0473) + +- [dermal chromatophore](http://purl.obolibrary.org/obo/CL_4040006) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A chromatophore that is part of the dermis." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:28553007" + +- Class: [dermal chromatophore](http://purl.obolibrary.org/obo/CL_4040006) + +- [dermal chromatophore](http://purl.obolibrary.org/obo/CL_4040006) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [dermis](http://purl.obolibrary.org/obo/UBERON_0002067) + +- [dermal chromatophore](http://purl.obolibrary.org/obo/CL_4040006) SubClassOf [pigment cell](http://purl.obolibrary.org/obo/CL_0000147) + + +### dermal papilla `http://purl.obolibrary.org/obo/UBERON_0000412` +#### Removed +- [dermal papilla](http://purl.obolibrary.org/obo/UBERON_0000412) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "ncit has 'hair papilla' as part of hypodermis" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "ncit" + +- [dermal papilla](http://purl.obolibrary.org/obo/UBERON_0000412) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "Blood vessels in the dermal papillae nourish all hair follicles and bring nutrients and oxygen to the lower layers of epidermal cells." + +- [dermal papilla](http://purl.obolibrary.org/obo/UBERON_0000412) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In humans, at the surface of the skin in hands and feet, they appear as epidermal or papillary ridges (colloquially known as fingerprints)" + +#### Added +- [dermal papilla](http://purl.obolibrary.org/obo/UBERON_0000412) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### dermal skeletal element `http://purl.obolibrary.org/obo/UBERON_0004756` + +#### Added +- [dermal skeletal element](http://purl.obolibrary.org/obo/UBERON_0004756) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### dermatocranium `http://purl.obolibrary.org/obo/UBERON_0003113` +#### Removed +- [dermatocranium](http://purl.obolibrary.org/obo/UBERON_0003113) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical cluster that is part of the cranium and composed of dermally derived bones.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000863" + +- [dermatocranium](http://purl.obolibrary.org/obo/UBERON_0003113) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical cluster that is part of the cranium which consists of dermally derived bones.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010154" + + + +### dermatological-muscosal system `http://purl.obolibrary.org/obo/UBERON_0012125` +#### Removed +- [dermatological-muscosal system](http://purl.obolibrary.org/obo/UBERON_0012125) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Anatomical system that consists of the integumental system plus all mucosae and submucosae." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://github.com/obophenotype/uberon/issues/53" + +- [dermatological-muscosal system](http://purl.obolibrary.org/obo/UBERON_0012125) [label](http://www.w3.org/2000/01/rdf-schema#label) "dermatological-muscosal system" + +- [dermatological-muscosal system](http://purl.obolibrary.org/obo/UBERON_0012125) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "dermatological system" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "OBI:MC" + +- [dermatological-muscosal system](http://purl.obolibrary.org/obo/UBERON_0012125) [id](http://www.geneontology.org/formats/oboInOwl#id) "UBERON:0012125" + +- [dermatological-muscosal system](http://purl.obolibrary.org/obo/UBERON_0012125) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- Class: [dermatological-muscosal system](http://purl.obolibrary.org/obo/UBERON_0012125) + +- [dermatological-muscosal system](http://purl.obolibrary.org/obo/UBERON_0012125) SubClassOf [anatomical system](http://purl.obolibrary.org/obo/UBERON_0000467) + +- [dermatological-muscosal system](http://purl.obolibrary.org/obo/UBERON_0012125) SubClassOf [has part](http://purl.obolibrary.org/obo/BFO_0000051) some [hypodermis](http://purl.obolibrary.org/obo/UBERON_0002072) + +- [dermatological-muscosal system](http://purl.obolibrary.org/obo/UBERON_0012125) SubClassOf [existence ends during](http://purl.obolibrary.org/obo/RO_0002492) some [fully formed stage](http://purl.obolibrary.org/obo/UBERON_0000066) + +- [dermatological-muscosal system](http://purl.obolibrary.org/obo/UBERON_0012125) SubClassOf [has part](http://purl.obolibrary.org/obo/BFO_0000051) some [submucosa](http://purl.obolibrary.org/obo/UBERON_0000009) + +- [dermatological-muscosal system](http://purl.obolibrary.org/obo/UBERON_0012125) SubClassOf [protein-containing material entity](http://purl.obolibrary.org/obo/PR_000050567) + +- [dermatological-muscosal system](http://purl.obolibrary.org/obo/UBERON_0012125) SubClassOf [has part](http://purl.obolibrary.org/obo/BFO_0000051) some [skin of body](http://purl.obolibrary.org/obo/UBERON_0002097) + +- [dermatological-muscosal system](http://purl.obolibrary.org/obo/UBERON_0012125) SubClassOf [has part](http://purl.obolibrary.org/obo/BFO_0000051) some [mucosa](http://purl.obolibrary.org/obo/UBERON_0000344) + + + +### dermatome `http://purl.obolibrary.org/obo/UBERON_0004016` +#### Removed +- [dermatome](http://purl.obolibrary.org/obo/UBERON_0004016) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006248" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + + - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) + +- [dermatome](http://purl.obolibrary.org/obo/UBERON_0004016) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "Not to be confused with 'dermatome segment of skin'." + + + +### dermis `http://purl.obolibrary.org/obo/UBERON_0002067` +#### Removed +- [dermis](http://purl.obolibrary.org/obo/UBERON_0002067) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A collagenous layer of the skin subjacent to the epidermis and covering the hypodermis. It contains various types of cells (e.g. fibroblasts, pigment cells, nerve, blood vessels and scales. Le Guellec et al, 2004.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001119" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [dermis](http://purl.obolibrary.org/obo/UBERON_0002067) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "dermal" + +- [dermis](http://purl.obolibrary.org/obo/UBERON_0002067) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "When approaching controversies surrounding skin evolution, we need to remember that the skin consists of two layers, an epidermis and a dermis, not a single evolving structure. (...) It is little wonder that controversies about homology exist. If we think of the epidermis, the dermis, and their interactions as an evolving unit, then their specialized products (hair, feathers, and reptilian scales) are broadly homologous.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000108" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.231-232 see also p.209 and p.228 and Figure 6-1" + +- [dermis](http://purl.obolibrary.org/obo/UBERON_0002067) SubClassOf [immediate transformation of](http://purl.obolibrary.org/obo/RO_0002495) some [future dermis](http://purl.obolibrary.org/obo/UBERON_0010083) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" + +#### Added +- [dermis](http://purl.obolibrary.org/obo/UBERON_0002067) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + +- [dermis](http://purl.obolibrary.org/obo/UBERON_0002067) SubClassOf [immediate transformation of](http://purl.obolibrary.org/obo/RO_0002495) some [future dermis](http://purl.obolibrary.org/obo/UBERON_0010083) + + +### dermomyotome `http://purl.obolibrary.org/obo/UBERON_0004290` +#### Removed +- [dermomyotome](http://purl.obolibrary.org/obo/UBERON_0004290) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768" + +- [dermomyotome](http://purl.obolibrary.org/obo/UBERON_0004290) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "all but the sclerotome of a mesodermal somite; the primordium of skeletal muscle and, perhaps, of the dermis." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/dermomyotome" + +- [dermomyotome](http://purl.obolibrary.org/obo/UBERON_0004290) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000676" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1111/j.1525-142X.2006.05079.x Devoto SH, Stoiber W, Hammond CL, Steinbacher P, Haslett JR, Barresi MJF, Patterson SE, Adiarte EG and Hughes SM, Generality of vertebrate developmental patterns: evidence for a dermomyotome in fish. Evolution and Development (2006)" + +- [dermomyotome](http://purl.obolibrary.org/obo/UBERON_0004290) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001513" + +- [dermomyotome](http://purl.obolibrary.org/obo/UBERON_0004290) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Portion of somites that gives rise to dermis and muscles.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010572" + + + +### descending aorta `http://purl.obolibrary.org/obo/UBERON_0001514` +#### Removed +- [descending aorta](http://purl.obolibrary.org/obo/UBERON_0001514) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "results from fusion of left and right dorsal aortae" + +- [descending aorta](http://purl.obolibrary.org/obo/UBERON_0001514) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + + +### descending colon `http://purl.obolibrary.org/obo/UBERON_0001158` +#### Removed +- [descending colon](http://purl.obolibrary.org/obo/UBERON_0001158) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D044683" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + + + +### descending thoracic aorta `http://purl.obolibrary.org/obo/UBERON_0002345` + +#### Added +- [descending thoracic aorta](http://purl.obolibrary.org/obo/UBERON_0002345) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### description `http://purl.org/dc/elements/1.1/description` +#### Removed +- [description](http://purl.org/dc/elements/1.1/description) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://purl.org/dc/elements/1.1/description" + +- [description](http://purl.org/dc/elements/1.1/description) [label](http://www.w3.org/2000/01/rdf-schema#label) "description" + +- [description](http://purl.org/dc/elements/1.1/description) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "dc-description" + +- [description](http://purl.org/dc/elements/1.1/description) [is_metadata_tag](http://www.geneontology.org/formats/oboInOwl#is_metadata_tag) true + +- [description](http://purl.org/dc/elements/1.1/description) [id](http://www.geneontology.org/formats/oboInOwl#id) "dc-description" + +- [description](http://purl.org/dc/elements/1.1/description) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + + + +### developing anatomical structure `http://purl.obolibrary.org/obo/UBERON_0005423` +#### Removed +- [developing anatomical structure](http://purl.obolibrary.org/obo/UBERON_0005423) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007006" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + + +### developmentally contributes to `http://purl.obolibrary.org/obo/RO_0002255` +#### Removed +- [developmentally contributes to](http://purl.obolibrary.org/obo/RO_0002255) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [developmentally contributes to](http://purl.obolibrary.org/obo/RO_0002255) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) + + + +### developmentally induced by `http://purl.obolibrary.org/obo/RO_0002256` +#### Removed +- [developmentally induced by](http://purl.obolibrary.org/obo/RO_0002256) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "induced by" + +- [developmentally induced by](http://purl.obolibrary.org/obo/RO_0002256) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-7073-9172](https://orcid.org/0000-0002-7073-9172) + +- [developmentally induced by](http://purl.obolibrary.org/obo/RO_0002256) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0001-9114-8737](https://orcid.org/0000-0001-9114-8737) + +- [developmentally induced by](http://purl.obolibrary.org/obo/RO_0002256) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" + +- [developmentally induced by](http://purl.obolibrary.org/obo/RO_0002256) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "developmentally_induced_by" + +- [developmentally induced by](http://purl.obolibrary.org/obo/RO_0002256) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) + +- [developmentally induced by](http://purl.obolibrary.org/obo/RO_0002256) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [developmentally induced by](http://purl.obolibrary.org/obo/RO_0002256) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [developmentally induced by](http://purl.obolibrary.org/obo/RO_0002256) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) "GO:0001759" + +- [developmentally induced by](http://purl.obolibrary.org/obo/RO_0002256) [id](http://www.geneontology.org/formats/oboInOwl#id) "developmentally_induced_by" + +- [developmentally induced by](http://purl.obolibrary.org/obo/RO_0002256) [label](http://www.w3.org/2000/01/rdf-schema#label) "developmentally induced by" + +- [developmentally induced by](http://purl.obolibrary.org/obo/RO_0002256) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" + +- [developmentally induced by](http://purl.obolibrary.org/obo/RO_0002256) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002256" + +- [developmentally induced by](http://purl.obolibrary.org/obo/RO_0002256) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) [20064205](http://www.ncbi.nlm.nih.gov/pubmed/20064205) + + + +### developmentally induces `http://purl.obolibrary.org/obo/RO_0002257` +#### Removed +- [developmentally induces](http://purl.obolibrary.org/obo/RO_0002257) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) + +- [developmentally induces](http://purl.obolibrary.org/obo/RO_0002257) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + + + +### developmentally preceded by `http://purl.obolibrary.org/obo/RO_0002258` +#### Removed +- [developmentally preceded by](http://purl.obolibrary.org/obo/RO_0002258) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [developmentally preceded by](http://purl.obolibrary.org/obo/RO_0002258) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) + +- [developmentally preceded by](http://purl.obolibrary.org/obo/RO_0002258) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "In general you should not use this relation to make assertions - use one of the more specific relations below this one" + + + +### developmentally related to `http://purl.obolibrary.org/obo/RO_0002324` +#### Removed +- [developmentally related to](http://purl.obolibrary.org/obo/RO_0002324) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" + +- [developmentally related to](http://purl.obolibrary.org/obo/RO_0002324) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + + + +### developmentally replaces `http://purl.obolibrary.org/obo/RO_0002285` +#### Removed +- [developmentally replaces](http://purl.obolibrary.org/obo/RO_0002285) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) + +- [developmentally replaces](http://purl.obolibrary.org/obo/RO_0002285) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002285" + +- [developmentally replaces](http://purl.obolibrary.org/obo/RO_0002285) [label](http://www.w3.org/2000/01/rdf-schema#label) "developmentally replaces" + +- [developmentally replaces](http://purl.obolibrary.org/obo/RO_0002285) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "developmentally_replaces" + +- [developmentally replaces](http://purl.obolibrary.org/obo/RO_0002285) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "replaces" + +- [developmentally replaces](http://purl.obolibrary.org/obo/RO_0002285) [id](http://www.geneontology.org/formats/oboInOwl#id) "developmentally_replaces" + +- [developmentally replaces](http://purl.obolibrary.org/obo/RO_0002285) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [developmentally replaces](http://purl.obolibrary.org/obo/RO_0002285) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + + + +### developmentally succeeded by `http://purl.obolibrary.org/obo/RO_0002286` +#### Removed +- [developmentally succeeded by](http://purl.obolibrary.org/obo/RO_0002286) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) + +- [developmentally succeeded by](http://purl.obolibrary.org/obo/RO_0002286) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + + + +### develops from `http://purl.obolibrary.org/obo/RO_0002202` +#### Removed +- [develops from](http://purl.obolibrary.org/obo/RO_0002202) [id](http://www.geneontology.org/formats/oboInOwl#id) "develops_from" + +- [develops from](http://purl.obolibrary.org/obo/RO_0002202) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [develops from](http://purl.obolibrary.org/obo/RO_0002202) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-7073-9172](https://orcid.org/0000-0002-7073-9172) + +- [develops from](http://purl.obolibrary.org/obo/RO_0002202) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "develops_from" + +- [develops from](http://purl.obolibrary.org/obo/RO_0002202) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [develops from](http://purl.obolibrary.org/obo/RO_0002202) [label](http://www.w3.org/2000/01/rdf-schema#label) "develops from" + +- [develops from](http://purl.obolibrary.org/obo/RO_0002202) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002202" + +- [develops from](http://purl.obolibrary.org/obo/RO_0002202) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0001-9114-8737](https://orcid.org/0000-0001-9114-8737) + +- [develops from](http://purl.obolibrary.org/obo/RO_0002202) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0003-1980-3228](https://orcid.org/0000-0003-1980-3228) + +- [develops from](http://purl.obolibrary.org/obo/RO_0002202) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) + + + +### develops from part of `http://purl.obolibrary.org/obo/RO_0002225` +#### Removed +- [develops from part of](http://purl.obolibrary.org/obo/RO_0002225) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) + +- [develops from part of](http://purl.obolibrary.org/obo/RO_0002225) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "develops_from_part_of" + +- [develops from part of](http://purl.obolibrary.org/obo/RO_0002225) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [develops from part of](http://purl.obolibrary.org/obo/RO_0002225) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [develops from part of](http://purl.obolibrary.org/obo/RO_0002225) [label](http://www.w3.org/2000/01/rdf-schema#label) "develops from part of" + +- [develops from part of](http://purl.obolibrary.org/obo/RO_0002225) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002225" + +- [develops from part of](http://purl.obolibrary.org/obo/RO_0002225) [id](http://www.geneontology.org/formats/oboInOwl#id) "develops_from_part_of" + + + +### develops in `http://purl.obolibrary.org/obo/RO_0002226` +#### Removed +- [develops in](http://purl.obolibrary.org/obo/RO_0002226) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) "EHDAA2" + +- [develops in](http://purl.obolibrary.org/obo/RO_0002226) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) + +- [develops in](http://purl.obolibrary.org/obo/RO_0002226) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [develops in](http://purl.obolibrary.org/obo/RO_0002226) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002226" + +- [develops in](http://purl.obolibrary.org/obo/RO_0002226) [label](http://www.w3.org/2000/01/rdf-schema#label) "develops in" + +- [develops in](http://purl.obolibrary.org/obo/RO_0002226) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "develops_in" + +- [develops in](http://purl.obolibrary.org/obo/RO_0002226) [id](http://www.geneontology.org/formats/oboInOwl#id) "develops_in" + +- [develops in](http://purl.obolibrary.org/obo/RO_0002226) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [develops in](http://purl.obolibrary.org/obo/RO_0002226) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) "Jonathan Bard, EHDAA2" + + + +### develops into `http://purl.obolibrary.org/obo/RO_0002203` +#### Removed +- [develops into](http://purl.obolibrary.org/obo/RO_0002203) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002203" + +- [develops into](http://purl.obolibrary.org/obo/RO_0002203) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [develops into](http://purl.obolibrary.org/obo/RO_0002203) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [develops into](http://purl.obolibrary.org/obo/RO_0002203) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0003-1980-3228](https://orcid.org/0000-0003-1980-3228) + +- [develops into](http://purl.obolibrary.org/obo/RO_0002203) [label](http://www.w3.org/2000/01/rdf-schema#label) "develops into" + +- [develops into](http://purl.obolibrary.org/obo/RO_0002203) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-7073-9172](https://orcid.org/0000-0002-7073-9172) + +- [develops into](http://purl.obolibrary.org/obo/RO_0002203) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) + +- [develops into](http://purl.obolibrary.org/obo/RO_0002203) [id](http://www.geneontology.org/formats/oboInOwl#id) "develops_into" + +- [develops into](http://purl.obolibrary.org/obo/RO_0002203) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "develops_into" + + + +### device utilizes material `http://purl.obolibrary.org/obo/RO_0017001` +#### Removed +- [device utilizes material](http://purl.obolibrary.org/obo/RO_0017001) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "See github ticket https://github.com/oborel/obo-relations/issues/497" + +- [device utilizes material](http://purl.obolibrary.org/obo/RO_0017001) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0001-9625-1899](https://orcid.org/0000-0001-9625-1899) + +- [device utilizes material](http://purl.obolibrary.org/obo/RO_0017001) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0003-2620-0345](https://orcid.org/0000-0003-2620-0345) + +- [device utilizes material](http://purl.obolibrary.org/obo/RO_0017001) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "A diagnostic testing device utilizes a specimen." + +- [device utilizes material](http://purl.obolibrary.org/obo/RO_0017001) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." + + + +### diaphragm `http://purl.obolibrary.org/obo/UBERON_0001103` +#### Removed +- [diaphragm](http://purl.obolibrary.org/obo/UBERON_0001103) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "breathing control" + +- [diaphragm](http://purl.obolibrary.org/obo/UBERON_0001103) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The urochordate epicardium separates digestive organs from the pharynx and heart, but the anus returns to the upper compartment to discharge wastes through an outgoing siphon (Thoracic_diaphragm#Comparative_anatomy_and_evolution)" + +- [diaphragm](http://purl.obolibrary.org/obo/UBERON_0001103) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "phrenic" + +- [diaphragm](http://purl.obolibrary.org/obo/UBERON_0001103) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The mammals are characterized by a diaphragm, which separates the thoracic portion of the body cavity from the abdominal region and assists in drawing air into the lungs and forcing it out. Modern reptiles lack a muscular diaphragm and it is reasonable to suppose that the diaphragm developed as a new device that made possible a large degree of oxygen intake for active animals. The change may have taken place during the transition from reptile to mammal (...).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0471384618 Colbert EH, Evolution of the vertebrates: a history of the backboned animals through time (2001) p.278" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000713" + +- [diaphragm](http://purl.obolibrary.org/obo/UBERON_0001103) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The diaphragm is a skeletal muscle that is responsible for contraction and expansion of the lungs[GO]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GO:0060539" + +- [diaphragm](http://purl.obolibrary.org/obo/UBERON_0001103) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "barrier between thoracic and abdominal cavities; stop gastric contents from refluxing into the oesophagus" + +- [diaphragm](http://purl.obolibrary.org/obo/UBERON_0001103) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The existence of some membrane separating the pharynx from the stomach can be traced widely among the chordates. Thus amphioxus possesses an atrium by which water exits the pharynx, which has been argued (and disputed) to be homologous to structures in ascidians and hagfishes.[3]" + +- [diaphragm](http://purl.obolibrary.org/obo/UBERON_0001103) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "originate from the cervical somites, likely C3-C5[PMID:23586979]" + +- [diaphragm](http://purl.obolibrary.org/obo/UBERON_0001103) SubClassOf [immediate transformation of](http://purl.obolibrary.org/obo/RO_0002495) some [future diaphragm](http://purl.obolibrary.org/obo/UBERON_0010084) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" + +#### Added +- [diaphragm](http://purl.obolibrary.org/obo/UBERON_0001103) SubClassOf [immediate transformation of](http://purl.obolibrary.org/obo/RO_0002495) some [future diaphragm](http://purl.obolibrary.org/obo/UBERON_0010084) + + +### diaphysis `http://purl.obolibrary.org/obo/UBERON_0004769` +#### Removed +- [diaphysis](http://purl.obolibrary.org/obo/UBERON_0004769) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Subdivision of long bone which forms the part of the bone between the two epiphyses; together with other the subdivisions of long bone, it constitutes the long bone. Examples: diaphysis of humerus, diaphysis of femur[FMA]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:24013" + +- [diaphysis](http://purl.obolibrary.org/obo/UBERON_0004769) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The main or mid section (shaft) of a long bone. It is made up of cortical bone and usually contains bone marrow and adipose tissue (fat)[WP][FMA:24013, Wikipedia:Diaphysis]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:24013, Wikipedia:Diaphysis" + + + +### diaphysis of femur `http://purl.obolibrary.org/obo/UBERON_0006862` +#### Removed +- [diaphysis of femur](http://purl.obolibrary.org/obo/UBERON_0006862) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The body of the femur (or shaft), almost cylindrical in form, is a little broader above than in the center, broadest and somewhat flattened from before backward below. It is slightly arched, so as to be convex in front, and concave behind, where it is strengthened by a prominent longitudinal ridge, the linea aspera. It presents for examination three borders, separating three surfaces. Of the borders, one, the linea aspera, is posterior, one is medial, and the other, lateral[Wikipedia:Body_of_femur]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Body_of_femur" + +#### Added +- [diaphysis of femur](http://purl.obolibrary.org/obo/UBERON_0006862) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### diaphysis of fibula `http://purl.obolibrary.org/obo/UBERON_0013279` +#### Removed +- [diaphysis of fibula](http://purl.obolibrary.org/obo/UBERON_0013279) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The body of fibula presents four borders - the antero-lateral, the antero-medial, the postero-lateral, and the postero-medial; and four surfaces - anterior, posterior, medial, and lateral[Wikipedia:Body_of_fibula]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Body_of_fibula" + +#### Added +- [diaphysis of fibula](http://purl.obolibrary.org/obo/UBERON_0013279) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### diaphysis of metacarpal bone `http://purl.obolibrary.org/obo/UBERON_0013752` + +#### Added +- [diaphysis of metacarpal bone](http://purl.obolibrary.org/obo/UBERON_0013752) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### diaphysis of metatarsal bone `http://purl.obolibrary.org/obo/UBERON_0013774` + +#### Added +- [diaphysis of metatarsal bone](http://purl.obolibrary.org/obo/UBERON_0013774) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### diaphysis of tibia `http://purl.obolibrary.org/obo/UBERON_0013280` +#### Removed +- [diaphysis of tibia](http://purl.obolibrary.org/obo/UBERON_0013280) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The body of the tibia has three borders and three surfaces[Wikipedia:Body_of_tibia]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Body_of_tibia" + +#### Added +- [diaphysis of tibia](http://purl.obolibrary.org/obo/UBERON_0013280) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### diaphysis proper `http://purl.obolibrary.org/obo/UBERON_0006861` +#### Removed +- [diaphysis proper](http://purl.obolibrary.org/obo/UBERON_0006861) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [metaphysis](http://purl.obolibrary.org/obo/UBERON_0001438) + +- [diaphysis proper](http://purl.obolibrary.org/obo/UBERON_0006861) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "The MA class is associated with EMAPA:35505 but we associate this with the more precise concept of diaphyseal plate" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" + + + +### diencephalon `http://purl.obolibrary.org/obo/UBERON_0001894` +#### Removed +- [diencephalon](http://purl.obolibrary.org/obo/UBERON_0001894) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000318" + +- [diencephalon](http://purl.obolibrary.org/obo/UBERON_0001894) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Unpaired part of the forebrain comprised of three major parts; the epithalamus, thalamus, and hypothalamus.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010481" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + +- [diencephalon](http://purl.obolibrary.org/obo/UBERON_0001894) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The more posterior and ventral of two forebrain neuromeres, the other being the telencephalon; major derivatives are the eye cups, the brain pretectal region, the thalamus, hypothalamus, and epithalamus (including the habenula and epiphysis). Kimmel et al, 1995.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000101" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [diencephalon](http://purl.obolibrary.org/obo/UBERON_0001894) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "diencephalic" + +- [diencephalon](http://purl.obolibrary.org/obo/UBERON_0001894) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [midbrain](http://purl.obolibrary.org/obo/UBERON_0001891) + - [exceptions](http://www.geneontology.org/formats/oboInOwl#exceptions) "ZFA" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "https://github.com/obophenotype/uberon/issues/378" + + - [status](http://www.geneontology.org/formats/oboInOwl#status) "pending" + +- [diencephalon](http://purl.obolibrary.org/obo/UBERON_0001894) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in ABA, this is part of the brain stem" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "ABA" + +- [diencephalon](http://purl.obolibrary.org/obo/UBERON_0001894) [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_7762](http://purl.obolibrary.org/obo/NCBITaxon_7762) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "not well differentiated from the cerebrum. (Ariens, p. 868)" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:8932866" + +- [diencephalon](http://purl.obolibrary.org/obo/UBERON_0001894) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [hindbrain](http://purl.obolibrary.org/obo/UBERON_0002028) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" + +- [diencephalon](http://purl.obolibrary.org/obo/UBERON_0001894) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + +- [diencephalon](http://purl.obolibrary.org/obo/UBERON_0001894) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [diencephalon neural crest](http://purl.obolibrary.org/obo/UBERON_0003851) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" + +- [diencephalon](http://purl.obolibrary.org/obo/UBERON_0001894) SubClassOf [immediate transformation of](http://purl.obolibrary.org/obo/RO_0002495) some [future diencephalon](http://purl.obolibrary.org/obo/UBERON_0006222) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" + +#### Added +- [diencephalon](http://purl.obolibrary.org/obo/UBERON_0001894) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [diencephalon neural crest](http://purl.obolibrary.org/obo/UBERON_0003851) + +- [diencephalon](http://purl.obolibrary.org/obo/UBERON_0001894) SubClassOf [immediate transformation of](http://purl.obolibrary.org/obo/RO_0002495) some [future diencephalon](http://purl.obolibrary.org/obo/UBERON_0006222) + + +### diencephalon arachnoid mater `http://purl.obolibrary.org/obo/UBERON_0003558` +#### Removed +- [diencephalon arachnoid mater](http://purl.obolibrary.org/obo/UBERON_0003558) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Arachnoid mater that is part of the diencephalon. [Bgee_curator][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000231" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + +- [diencephalon arachnoid mater](http://purl.obolibrary.org/obo/UBERON_0003558) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000231" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + + +### diencephalon dura mater `http://purl.obolibrary.org/obo/UBERON_0003564` +#### Removed +- [diencephalon dura mater](http://purl.obolibrary.org/obo/UBERON_0003564) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000258" + +- [diencephalon dura mater](http://purl.obolibrary.org/obo/UBERON_0003564) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Dura mater that is part of the diencephalon. [Bgee_curator][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000258" + + + +### diencephalon neural crest `http://purl.obolibrary.org/obo/UBERON_0003851` +#### Removed +- [diencephalon neural crest](http://purl.obolibrary.org/obo/UBERON_0003851) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000798" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" + + + +### diencephalon pia mater `http://purl.obolibrary.org/obo/UBERON_0003553` +#### Removed +- [diencephalon pia mater](http://purl.obolibrary.org/obo/UBERON_0003553) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Pia mater that is part of the diencephalon. [Bgee_curator][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000475" + +- [diencephalon pia mater](http://purl.obolibrary.org/obo/UBERON_0003553) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000475" + + + +### diencephalon subarachnoid space `http://purl.obolibrary.org/obo/UBERON_0005218` +#### Removed +- [diencephalon subarachnoid space](http://purl.obolibrary.org/obo/UBERON_0005218) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Subarachnoid space that is part of the diencephalon. [Bgee_curator][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001302" + + + +### digestive system `http://purl.obolibrary.org/obo/UBERON_0001007` +#### Removed +- [digestive system](http://purl.obolibrary.org/obo/UBERON_0001007) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" + +- [digestive system](http://purl.obolibrary.org/obo/UBERON_0001007) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005055" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + +- [digestive system](http://purl.obolibrary.org/obo/UBERON_0001007) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "digestive" + +- [digestive system](http://purl.obolibrary.org/obo/UBERON_0001007) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EV:0100056" + +- [digestive system](http://purl.obolibrary.org/obo/UBERON_0001007) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000129" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + + + +### digestive tract `http://purl.obolibrary.org/obo/UBERON_0001555` +#### Removed +- [digestive tract](http://purl.obolibrary.org/obo/UBERON_0001555) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The alimentary or digestive tract, and associated organs.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000112" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [digestive tract](http://purl.obolibrary.org/obo/UBERON_0001555) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA also has a term 'gastrointestinal tract', but this includes the liver." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + +- [digestive tract](http://purl.obolibrary.org/obo/UBERON_0001555) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D041981" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + +- [digestive tract](http://purl.obolibrary.org/obo/UBERON_0001555) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this" + +- [digestive tract](http://purl.obolibrary.org/obo/UBERON_0001555) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000309" + +- [digestive tract](http://purl.obolibrary.org/obo/UBERON_0001555) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" + +- [digestive tract](http://purl.obolibrary.org/obo/UBERON_0001555) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00003125" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + + +### digestive tract diverticulum `http://purl.obolibrary.org/obo/UBERON_0009854` +#### Removed +- [digestive tract diverticulum](http://purl.obolibrary.org/obo/UBERON_0009854) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00100316" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + + +### digestive tract epithelium `http://purl.obolibrary.org/obo/UBERON_0003929` +#### Removed +- [digestive tract epithelium](http://purl.obolibrary.org/obo/UBERON_0003929) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00047166" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + +- [digestive tract epithelium](http://purl.obolibrary.org/obo/UBERON_0003929) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Epithelium lining the lumen of the gut.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005123" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [digestive tract epithelium](http://purl.obolibrary.org/obo/UBERON_0003929) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "" + + + +### digit `http://purl.obolibrary.org/obo/UBERON_0002544` +#### Removed +- [digit](http://purl.obolibrary.org/obo/UBERON_0002544) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:85518" + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "GAT" + +- [digit](http://purl.obolibrary.org/obo/UBERON_0002544) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Our reinterpretation of the distal fin endoskeleton of Panderichthys removes the final piece of evidence supporting the formerly popular hypothesis that tetrapod digits are wholly new structures without homologues in sarcopterygian fish fins. This hypothesis, which was based partly on the complete absence of plausible digit homologues in Panderichthys (then the closest known relative of tetrapods), has already been called into question by the discovery of digit-like radials in Tiktaalik and the fact that Hox gene expression patterns closely resembling those associated with digit formation in tetrapods occur in the distal fin skeletons of paddlefish and Australian lungfish. Our new data show that Panderichthys is not an anomaly: like Tiktaalik and other fish members of the Tetrapodomorpha, it has distal radials that can be interpreted as digit homologues.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1038/nature07339 Boisvert CA, Mark-Kurik E and Ahlberg PE, The pectoral fin of Panderichthys and the origin of digits. Nature (2008)" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000944" + +- [digit](http://purl.obolibrary.org/obo/UBERON_0002544) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "this class represents the entire organism subdivision encompassing soft tissue as well as the underlying skeletal framework. The class represents the phalangeal part only - historically the term 'digit' has also been used to represent the unit consisting of a series of phalanges together with a metapodial bone. We may in future relabel this class to avoid confusion with this concept, but the class will continue to represent the phalangeal portion" + +- [digit](http://purl.obolibrary.org/obo/UBERON_0002544) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "digital" + +- [digit](http://purl.obolibrary.org/obo/UBERON_0002544) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [metapodium region](http://purl.obolibrary.org/obo/UBERON_0009877) + + + +### digit plus metapodial segment `http://purl.obolibrary.org/obo/UBERON_5002544` +#### Removed +- [digit plus metapodial segment](http://purl.obolibrary.org/obo/UBERON_5002544) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "https://github.com/obophenotype/uberon/issues/458" + + + +### digitopodium bone `http://purl.obolibrary.org/obo/UBERON_0012357` +#### Removed +- [digitopodium bone](http://purl.obolibrary.org/obo/UBERON_0012357) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) [Skeleton-partonomy-Design-Pattern](https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern) + + + +### digitopodium region `http://purl.obolibrary.org/obo/UBERON_0012140` +#### Removed +- [digitopodium region](http://purl.obolibrary.org/obo/UBERON_0012140) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "some sources call this the acropodium. see https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod" + + + +### dilatator pupillae `http://purl.obolibrary.org/obo/UBERON_0001608` +#### Removed +- [dilatator pupillae](http://purl.obolibrary.org/obo/UBERON_0001608) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "It is innervated by the sympathetic system, which acts by releasing noradrenaline, which acts on alpha1-receptors. Thus, when presented with a threatening stimuli that activates the fight-or-flight response, this innervation dilates the iris, thus temporarily letting more light reach the retina" + +- [dilatator pupillae](http://purl.obolibrary.org/obo/UBERON_0001608) SubClassOf [has muscle insertion](http://purl.obolibrary.org/obo/RO_0002373) some [iris](http://purl.obolibrary.org/obo/UBERON_0001769) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "dbpedia" + + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "inner margins of iris" + +- [dilatator pupillae](http://purl.obolibrary.org/obo/UBERON_0001608) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + +- [dilatator pupillae](http://purl.obolibrary.org/obo/UBERON_0001608) SubClassOf [has muscle origin](http://purl.obolibrary.org/obo/RO_0002372) some [iris](http://purl.obolibrary.org/obo/UBERON_0001769) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "outer margins of iris" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "dbpedia" + +#### Added +- [dilatator pupillae](http://purl.obolibrary.org/obo/UBERON_0001608) SubClassOf [has muscle origin](http://purl.obolibrary.org/obo/RO_0002372) some [iris](http://purl.obolibrary.org/obo/UBERON_0001769) + +- [dilatator pupillae](http://purl.obolibrary.org/obo/UBERON_0001608) SubClassOf [has muscle insertion](http://purl.obolibrary.org/obo/RO_0002373) some [iris](http://purl.obolibrary.org/obo/UBERON_0001769) + + +### directly develops from `http://purl.obolibrary.org/obo/RO_0002207` +#### Removed +- [directly develops from](http://purl.obolibrary.org/obo/RO_0002207) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-7073-9172](https://orcid.org/0000-0002-7073-9172) + +- [directly develops from](http://purl.obolibrary.org/obo/RO_0002207) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [directly develops from](http://purl.obolibrary.org/obo/RO_0002207) [id](http://www.geneontology.org/formats/oboInOwl#id) "directly_develops_from" + +- [directly develops from](http://purl.obolibrary.org/obo/RO_0002207) [RO_0002575](http://purl.obolibrary.org/obo/RO_0002575) [develops from](http://purl.obolibrary.org/obo/RO_0002202) + +- [directly develops from](http://purl.obolibrary.org/obo/RO_0002207) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002207" + +- [directly develops from](http://purl.obolibrary.org/obo/RO_0002207) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [directly develops from](http://purl.obolibrary.org/obo/RO_0002207) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) + +- [directly develops from](http://purl.obolibrary.org/obo/RO_0002207) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "directly_develops_from" + +- [directly develops from](http://purl.obolibrary.org/obo/RO_0002207) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) "FBbt" + +- [directly develops from](http://purl.obolibrary.org/obo/RO_0002207) [label](http://www.w3.org/2000/01/rdf-schema#label) "directly develops from" + + + +### directly develops into `http://purl.obolibrary.org/obo/RO_0002210` +#### Removed +- [directly develops into](http://purl.obolibrary.org/obo/RO_0002210) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) + +- [directly develops into](http://purl.obolibrary.org/obo/RO_0002210) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "developmental precursor of" + + + +### directly negatively regulates `http://purl.obolibrary.org/obo/RO_0002630` +#### Removed +- [directly negatively regulates](http://purl.obolibrary.org/obo/RO_0002630) [IAO_0000589](http://purl.obolibrary.org/obo/IAO_0000589) "directly negatively regulates (process to process)" + +- [directly negatively regulates](http://purl.obolibrary.org/obo/RO_0002630) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) [causal-relations](http://purl.obolibrary.org/obo/ro/docs/causal-relations) + + + +### directly negatively regulates activity of `http://purl.obolibrary.org/obo/RO_0002449` +#### Removed +- [directly negatively regulates activity of](http://purl.obolibrary.org/obo/RO_0002449) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [directly negatively regulates activity of](http://purl.obolibrary.org/obo/RO_0002449) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "directly inhibits" + +- [directly negatively regulates activity of](http://purl.obolibrary.org/obo/RO_0002449) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0003-4639-4431](https://orcid.org/0000-0003-4639-4431) + + + +### directly positively regulates `http://purl.obolibrary.org/obo/RO_0002629` +#### Removed +- [directly positively regulates](http://purl.obolibrary.org/obo/RO_0002629) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) [causal-relations](http://purl.obolibrary.org/obo/ro/docs/causal-relations) + +- [directly positively regulates](http://purl.obolibrary.org/obo/RO_0002629) [RO_0004049](http://purl.obolibrary.org/obo/RO_0004049) [directly regulates](http://purl.obolibrary.org/obo/RO_0002578) + +- [directly positively regulates](http://purl.obolibrary.org/obo/RO_0002629) [IAO_0000589](http://purl.obolibrary.org/obo/IAO_0000589) "directly positively regulates (process to process)" + + + +### directly positively regulates activity of `http://purl.obolibrary.org/obo/RO_0002450` +#### Removed +- [directly positively regulates activity of](http://purl.obolibrary.org/obo/RO_0002450) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "directly activates" + +- [directly positively regulates activity of](http://purl.obolibrary.org/obo/RO_0002450) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0003-4639-4431](https://orcid.org/0000-0003-4639-4431) + +- [directly positively regulates activity of](http://purl.obolibrary.org/obo/RO_0002450) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + + + +### directly regulates `http://purl.obolibrary.org/obo/RO_0002578` +#### Removed +- [directly regulates](http://purl.obolibrary.org/obo/RO_0002578) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) [causal-relations](http://purl.obolibrary.org/obo/ro/docs/causal-relations) + +- [directly regulates](http://purl.obolibrary.org/obo/RO_0002578) [IAO_0000589](http://purl.obolibrary.org/obo/IAO_0000589) "directly regulates (processual)" + +- [directly regulates](http://purl.obolibrary.org/obo/RO_0002578) [RO_0002575](http://purl.obolibrary.org/obo/RO_0002575) [regulates](http://purl.obolibrary.org/obo/RO_0002211) + +- [directly regulates](http://purl.obolibrary.org/obo/RO_0002578) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + + + +### directly regulates activity of `http://purl.obolibrary.org/obo/RO_0002448` +#### Removed +- [directly regulates activity of](http://purl.obolibrary.org/obo/RO_0002448) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [directly regulates activity of](http://purl.obolibrary.org/obo/RO_0002448) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0003-4639-4431](https://orcid.org/0000-0003-4639-4431) + + + +### disconnected anatomical group `http://purl.obolibrary.org/obo/UBERON_0034923` +#### Removed +- [disconnected anatomical group](http://purl.obolibrary.org/obo/UBERON_0034923) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007276" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + + +### distal convoluted tubule `http://purl.obolibrary.org/obo/UBERON_0001292` +#### Removed +- [distal convoluted tubule](http://purl.obolibrary.org/obo/UBERON_0001292) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "in humans it is responsible for the reabsorption of about 5% of filtered sodium via the thiazide-sensitive Na-Cl symporter." + +- [distal convoluted tubule](http://purl.obolibrary.org/obo/UBERON_0001292) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "a portion of kidney nephron between the loop of Henle and the collecting duct system[Wikipedia:Distal_convoluted_tubule]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Distal_convoluted_tubule" + + + +### distal convoluted tubule macula densa `http://purl.obolibrary.org/obo/UBERON_0003546` + +#### Added +- [distal convoluted tubule macula densa](http://purl.obolibrary.org/obo/UBERON_0003546) SubClassOf [meso-epithelium](http://purl.obolibrary.org/obo/UBERON_0012275) + + +### distal limb integumentary appendage `http://purl.obolibrary.org/obo/UBERON_0009564` + +#### Added +- [distal limb integumentary appendage](http://purl.obolibrary.org/obo/UBERON_0009564) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### distal phalanx `http://purl.obolibrary.org/obo/UBERON_0004300` +#### Removed +- [distal phalanx](http://purl.obolibrary.org/obo/UBERON_0004300) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In human anatomy, the distal phalanges of the four fingers and toes articulate proximally with the intermediate phalanges at the distal interphalangeal joints (DIP); in the thumb and big toe, with only two phalanges, the distal phalanges articulate proximally with the proximal phalanges. The distal phalanges carry and shape nails and claws and are therefore occasionally referred to as the ungual phalanges. The distal phalanges are cone-shaped in most mammals, including most primates, but relatively wide and flat in humans." + + + +### distal segment of digit `http://purl.obolibrary.org/obo/UBERON_0009551` +#### Removed +- [distal segment of digit](http://purl.obolibrary.org/obo/UBERON_0009551) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "Newborn and adult mice are able to regrow forelimb (finger) and hindlimb (toe) digit tips after their amputation through the distal interphalangeal joint. Regeneration of the digit tip involves the integrated regrowth of multiple tissues within 2-3 months, reaching an external morphology that is cosmetically and functionally similar to normal digits. Most importantly, regeneration of the mouse distal digit shares morphological similarities with clinical cases documenting regrowth of missing distal portions of fingers in both children and adults" + + + +### distal straight tubule macula densa `http://purl.obolibrary.org/obo/UBERON_0005202` +#### Removed +- [distal straight tubule macula densa](http://purl.obolibrary.org/obo/UBERON_0005202) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:28399" + + + +### distal to `http://purl.obolibrary.org/obo/BSPO_0000097` +#### Removed +- [distal to](http://purl.obolibrary.org/obo/BSPO_0000097) [id](http://www.geneontology.org/formats/oboInOwl#id) "distal_to" + +- [distal to](http://purl.obolibrary.org/obo/BSPO_0000097) [label](http://www.w3.org/2000/01/rdf-schema#label) "distal to" + +- [distal to](http://purl.obolibrary.org/obo/BSPO_0000097) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "distal_to" + +- [distal to](http://purl.obolibrary.org/obo/BSPO_0000097) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BSPO:0000097" + +- [distal to](http://purl.obolibrary.org/obo/BSPO_0000097) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + + + +### distal tubule `http://purl.obolibrary.org/obo/UBERON_0004135` +#### Removed +- [distal tubule](http://purl.obolibrary.org/obo/UBERON_0004135) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0012424](http://purl.obolibrary.org/obo/UBERON_0012424) + + + +### distally connected to `http://purl.obolibrary.org/obo/uberon/core#distally_connected_to` +#### Removed +- [distally connected to](http://purl.obolibrary.org/obo/uberon/core#distally_connected_to) InverseOf [proximally connected to](http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to) + + + +### distalmost part of `http://purl.obolibrary.org/obo/BSPO_0001108` +#### Removed +- [distalmost part of](http://purl.obolibrary.org/obo/BSPO_0001108) [id](http://www.geneontology.org/formats/oboInOwl#id) "distalmost_part_of" + +- [distalmost part of](http://purl.obolibrary.org/obo/BSPO_0001108) [label](http://www.w3.org/2000/01/rdf-schema#label) "distalmost part of" + +- [distalmost part of](http://purl.obolibrary.org/obo/BSPO_0001108) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "distalmost_part_of" + +- [distalmost part of](http://purl.obolibrary.org/obo/BSPO_0001108) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [distalmost part of](http://purl.obolibrary.org/obo/BSPO_0001108) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BSPO:0001108" + + + +### dorsal aorta `http://purl.obolibrary.org/obo/UBERON_0005805` +#### Removed +- [dorsal aorta](http://purl.obolibrary.org/obo/UBERON_0005805) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: part_of axial vasculature (TAO:0001073)[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000014" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [dorsal aorta](http://purl.obolibrary.org/obo/UBERON_0005805) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Principal unpaired, median artery of the trunk, leading from the paired roots (radices) of the dorsal aorta to the caudal artery. Kimmel et al, 1995.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000014" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [dorsal aorta](http://purl.obolibrary.org/obo/UBERON_0005805) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000264" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620" + +- [dorsal aorta](http://purl.obolibrary.org/obo/UBERON_0005805) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The artery in vertebrate embryos that transports blood from the aortic arches to the trunk and limbs. In adult fish it is a major artery that carries oxygenated blood from the efferent branchial arteries to branches that supply the body organ. In adult tetrapods it arises from the systemic arch" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "BTO:0004673" + +- [dorsal aorta](http://purl.obolibrary.org/obo/UBERON_0005805) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Each primitive aorta receives anteriorly a vein 'the vitelline vein' from the yolk-sac, and is prolonged backward on the lateral aspect of the notochord under the name of the dorsal aorta. The dorsal aortae give branches to the yolk-sac, and are continued backward through the body-stalk as the umbilical arteries to the villi of the chorion. The two dorsal aortae combine to become the descending aorta in later development[WP]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Dorsal_aorta" + +- [dorsal aorta](http://purl.obolibrary.org/obo/UBERON_0005805) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + + +### dorsal lateral geniculate nucleus `http://purl.obolibrary.org/obo/UBERON_0002479` +#### Removed +- [dorsal lateral geniculate nucleus](http://purl.obolibrary.org/obo/UBERON_0002479) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0001927](http://purl.obolibrary.org/obo/UBERON_0001927) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" + + + +### dorsal mesentery `http://purl.obolibrary.org/obo/UBERON_0002296` +#### Removed +- [dorsal mesentery](http://purl.obolibrary.org/obo/UBERON_0002296) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The mesentery that originates from the dorsal side of the peritoneal cavity.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005130" + + + +### dorsal mesogastrium `http://purl.obolibrary.org/obo/UBERON_0005602` +#### Removed +- [dorsal mesogastrium](http://purl.obolibrary.org/obo/UBERON_0005602) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The dorsal sheet of the primitive mesentery that encloses the stomach. The greater omentum develops from the dorsal mesogastrium. [TFD][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000352" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/mesogastrium" + + + +### dorsal pancreas `http://purl.obolibrary.org/obo/UBERON_0009708` + +#### Added +- [dorsal pancreas](http://purl.obolibrary.org/obo/UBERON_0009708) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) + + +### dorsal pancreatic bud `http://purl.obolibrary.org/obo/UBERON_0003923` +#### Removed +- [dorsal pancreatic bud](http://purl.obolibrary.org/obo/UBERON_0003923) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The pancreatic bud that gives rise to the accessory pancreatic duct.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "XAO:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0011031" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + +- [dorsal pancreatic bud](http://purl.obolibrary.org/obo/UBERON_0003923) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In chick, Xenopus laevis, and the teleost fish Medaka, the pancreas develops from three buds that emerge from the gut tube, two from its ventral aspect, and one from its dorsal aspect. In mouse, although there are initially three buds that arise from the gut tube at the point of contact between the endoderm and the vasculature, the pancreas develops from only two of these buds, one dorsal and one ventral. (...) In this study, we use a transgenic zebrafish line (...). We provide evidence for the existence of two distinct pancreatic anlagen - a ventral anterior bud and a dorsal posterior bud - that join to form the definitive pancreas (reference 1); The pancreas develops from the fusion of distinct endoderm-derived dorsal and ventral diverticula. In humans, by day 35 of development, the ventral pancreatic bud begins to migrate backwards and comes into contact and eventually fuses with the dorsal pancreatic bud during the sixth week of development (reference 2).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001428" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1016/S0012-1606(03)00308-7 Field HA, Dong PD, Beis D, Stainier DY, Formation of the digestive system in zebrafish. II. Pancreas morphogenesis. Developmental Biology (2003), DOI:10.2337/diabetes.49.2.225 Polak M, Bouchareb-Banaei L, Scharfmann R, Czernichow P, Early pattern of differentiation in the human pancreas. Diabetes (2000)" + + + +### dorsal part of neck `http://purl.obolibrary.org/obo/UBERON_0012477` +#### Removed +- [dorsal part of neck](http://purl.obolibrary.org/obo/UBERON_0012477) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "nuchal" + + + +### dorsal part of optic cup `http://purl.obolibrary.org/obo/UBERON_0016854` + +#### Added +- [dorsal part of optic cup](http://purl.obolibrary.org/obo/UBERON_0016854) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### dorsal part of pharyngeal pouch 3 `http://purl.obolibrary.org/obo/UBERON_0010025` +#### Removed +- [dorsal part of pharyngeal pouch 3](http://purl.obolibrary.org/obo/UBERON_0010025) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "Derivatives of the dorsal wings include the inferior parathyroid glands[WP] in mammals, the cranial dorsal aspect of the third pouch generates the inferior parathyroids (or parathyroid III)" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "MP" + +- [dorsal part of pharyngeal pouch 3](http://purl.obolibrary.org/obo/UBERON_0010025) SubClassOf [foregut epithelium](http://purl.obolibrary.org/obo/UBERON_0015833) + +- [dorsal part of pharyngeal pouch 3](http://purl.obolibrary.org/obo/UBERON_0010025) SubClassOf [unilaminar epithelium](http://purl.obolibrary.org/obo/UBERON_0000490) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "EHDAA2" + +#### Added +- [dorsal part of pharyngeal pouch 3](http://purl.obolibrary.org/obo/UBERON_0010025) SubClassOf [endoderm of foregut](http://purl.obolibrary.org/obo/UBERON_0003258) + + +### dorsal part of pharyngeal pouch 4 `http://purl.obolibrary.org/obo/UBERON_0010027` +#### Removed +- [dorsal part of pharyngeal pouch 4](http://purl.obolibrary.org/obo/UBERON_0010027) SubClassOf [unilaminar epithelium](http://purl.obolibrary.org/obo/UBERON_0000490) + +- [dorsal part of pharyngeal pouch 4](http://purl.obolibrary.org/obo/UBERON_0010027) SubClassOf [foregut epithelium](http://purl.obolibrary.org/obo/UBERON_0015833) + +#### Added +- [dorsal part of pharyngeal pouch 4](http://purl.obolibrary.org/obo/UBERON_0010027) SubClassOf [endoderm of foregut](http://purl.obolibrary.org/obo/UBERON_0003258) + + +### dorsal plus ventral thalamus `http://purl.obolibrary.org/obo/UBERON_0001897` +#### Removed +- [dorsal plus ventral thalamus](http://purl.obolibrary.org/obo/UBERON_0001897) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "One of a pair of large oval nervous structures made of gray matter and forming most of the lateral walls of the third ventricle of the brain and part of the diencephalon. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000657" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/thalamus" + +- [dorsal plus ventral thalamus](http://purl.obolibrary.org/obo/UBERON_0001897) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "thalamic" + +- [dorsal plus ventral thalamus](http://purl.obolibrary.org/obo/UBERON_0001897) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [hypothalamus](http://purl.obolibrary.org/obo/UBERON_0001898) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" + +- [dorsal plus ventral thalamus](http://purl.obolibrary.org/obo/UBERON_0001897) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) the brain regions of tetrapods, the structures they contain, and their basic organizational features are the same as in fishes.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.484" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000657" + +- [dorsal plus ventral thalamus](http://purl.obolibrary.org/obo/UBERON_0001897) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Part of the diencephalon consisting of a mass of connecting fibers which relay sensory information to the cerebral cortex.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010483" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + + + +### dorsal root ganglion `http://purl.obolibrary.org/obo/UBERON_0000044` +#### Removed +- [dorsal root ganglion](http://purl.obolibrary.org/obo/UBERON_0000044) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Trunk ganglion which is located adjacent to the spine on a dorsal root and contains the cell bodies of afferent sensory nerves.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000200" + +- [dorsal root ganglion](http://purl.obolibrary.org/obo/UBERON_0000044) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "The sensory ganglia of spinal nerves arise only from the neural crest, whereas many sensory ganglia of the 'dorsal' cranial nerves arise from epibranchial placodes as well as the neural crest[DOI:10.1093/icb/icn065]" + +- [dorsal root ganglion](http://purl.obolibrary.org/obo/UBERON_0000044) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "From comparative analyses of craniate brains, a morphotype of the brain in the earliest craniate stock can be constructed. In marked contrast to cephalochordates, the ancestral craniate morphotype had a plethora of unique features, which included a telencephalon with pallial and subpallial parts, paired olfactory bulbs with substantial projections to most or all of the telencephalic pallium, paired lateral eyes and ears, a lateral line system for both electroreception and mechanoreception, spinal cord dorsal root ganglia, and an autonomic nervous system.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000222" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1002/1097-0185(20000615)261:3<111::AID-AR6>3.0.CO;2-F Butler AB, Chordate evolution and the origin of craniates: An old brain in a new head. AnaT Rec (New Anat) (2000)" + +- [dorsal root ganglion](http://purl.obolibrary.org/obo/UBERON_0000044) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D005727" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + +- [dorsal root ganglion](http://purl.obolibrary.org/obo/UBERON_0000044) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "MA and EMAPA introduce distinct classes for what appears to be the same thing" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + +#### Added +- [dorsal root ganglion](http://purl.obolibrary.org/obo/UBERON_0000044) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) + + +### dorsal root of spinal cord `http://purl.obolibrary.org/obo/UBERON_0002261` +#### Removed +- [dorsal root of spinal cord](http://purl.obolibrary.org/obo/UBERON_0002261) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "In anatomy and neurology, the dorsal root (or posterior root) is the afferent sensory root of a spinal nerve. At the distal end of the dorsal root is the dorsal root ganglion, which contains the neuron cell bodies of the nerve fibres conveyed by the root. If the dorsal root of a spinal nerve were severed it would lead to numbness in certain areas of the body. The lateral division of the dorsal root contains lightly myelinated and unmyelinated axons of small diameter. These transmit pain and temperature sensation from the body. These fibers cross through the anterior white commissure to form the Anterior lateral system in the lateral funiculus. The medial division of the dorsal root contains myelinated axons of larger diameter. These transmit information of discriminative touch, pressure, vibration, and conscious proprioception originating from spinal levels C2 through S5. These fibers are pushed in towards the posterior medial sulcus to form the fasciculus gracilis and the fasciculus cuneatus. [WP,unvetted][Wikipedia:Posterior_root_of_spinal_nerve]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Posterior_root_of_spinal_nerve" + + + +### dorsal skin of finger `http://purl.obolibrary.org/obo/UBERON_0005276` +#### Removed +- [dorsal skin of finger](http://purl.obolibrary.org/obo/UBERON_0005276) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "this class is explicitly the union of the two FMA classes" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + + + +### dorsal skin of toe `http://purl.obolibrary.org/obo/UBERON_0005277` +#### Removed +- [dorsal skin of toe](http://purl.obolibrary.org/obo/UBERON_0005277) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "this class is explicitly the union of the two FMA classes" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + + + +### dorsal striatum `http://purl.obolibrary.org/obo/UBERON_0005382` +#### Removed +- [dorsal striatum](http://purl.obolibrary.org/obo/UBERON_0005382) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "It may also refer to both the basal ganglia and the internal capsule collectively." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Dorsal_striatum" + +- [dorsal striatum](http://purl.obolibrary.org/obo/UBERON_0005382) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The term dorsal striatum refers to a composite structure of the endbrain that is defined in the striatopallidal system by connectivity and neurochemical staining. It includes most of the striatum ( Heimer-1995 ). The boundary between this structure and the ventral striatum is indistinct in sections stained for Nissl substance." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "neuronames:2340" + +- [dorsal striatum](http://purl.obolibrary.org/obo/UBERON_0005382) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "It may also refer to the putamen and caudate collectively." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Dorsal_striatum" + +- [dorsal striatum](http://purl.obolibrary.org/obo/UBERON_0005382) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "According to the 1917 version of Gray's Anatomy, it is the combination of the lentiform nucleus (putamen and the globus pallidus) and the caudate nucleus" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Dorsal_striatum" + +- [dorsal striatum](http://purl.obolibrary.org/obo/UBERON_0005382) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "According to BrainInfo it is a part of the basal ganglia comprising the globus pallidus and striatum" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Dorsal_striatum" + + + +### dorsal thalamus `http://purl.obolibrary.org/obo/UBERON_0004703` +#### Removed +- [dorsal thalamus](http://purl.obolibrary.org/obo/UBERON_0004703) [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [Gnathostomata ](http://purl.obolibrary.org/obo/NCBITaxon_7776) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:8167659" + + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "http://neurolex.org/wiki/Category_talk:Thalamus" + + + +### dorsal to `http://purl.obolibrary.org/obo/BSPO_0000098` +#### Removed +- [dorsal to](http://purl.obolibrary.org/obo/BSPO_0000098) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [dorsal to](http://purl.obolibrary.org/obo/BSPO_0000098) [label](http://www.w3.org/2000/01/rdf-schema#label) "dorsal to" + +- [dorsal to](http://purl.obolibrary.org/obo/BSPO_0000098) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BSPO:0000098" + +- [dorsal to](http://purl.obolibrary.org/obo/BSPO_0000098) [id](http://www.geneontology.org/formats/oboInOwl#id) "dorsal_to" + +- [dorsal to](http://purl.obolibrary.org/obo/BSPO_0000098) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "dorsal_to" + + + +### dorsal trunk `http://purl.obolibrary.org/obo/UBERON_0011270` +#### Removed +- [dorsal trunk](http://purl.obolibrary.org/obo/UBERON_0011270) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In humans, the subdivision of trunk which is demarcated from the trunk proper by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines, the external surface of the posterior abdominal wall; together with the trunk proper, it constitutes the trunk[FMA]" + + + +### dorsolateral placode `http://purl.obolibrary.org/obo/UBERON_0003067` +#### Removed +- [dorsolateral placode](http://purl.obolibrary.org/obo/UBERON_0003067) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000103" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + + +### dorsum `http://purl.obolibrary.org/obo/UBERON_0001137` +#### Removed +- [dorsum](http://purl.obolibrary.org/obo/UBERON_0001137) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "dorsal" + +- [dorsum](http://purl.obolibrary.org/obo/UBERON_0001137) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In humans, called the back, a large posterior area of the human body, rising from the top of the buttocks to the back of the neck and the shoulders. It is the surface opposite to the chest, its height being defined by the vertebral column (commonly referred to as the spine or backbone) and its breadth being supported by the ribcage and shoulders. The spinal canal runs through the spine and provides nerves to the rest of the body" + + + +### drains `http://purl.obolibrary.org/obo/RO_0002179` +#### Removed +- [drains](http://purl.obolibrary.org/obo/RO_0002179) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "drains" + +- [drains](http://purl.obolibrary.org/obo/RO_0002179) [label](http://www.w3.org/2000/01/rdf-schema#label) "drains" + +- [drains](http://purl.obolibrary.org/obo/RO_0002179) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002179" + +- [drains](http://purl.obolibrary.org/obo/RO_0002179) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [drains](http://purl.obolibrary.org/obo/RO_0002179) [id](http://www.geneontology.org/formats/oboInOwl#id) "drains" + +- [drains](http://purl.obolibrary.org/obo/RO_0002179) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) [20064205](http://www.ncbi.nlm.nih.gov/pubmed/20064205) + +- [drains](http://purl.obolibrary.org/obo/RO_0002179) Domain [vein](http://purl.obolibrary.org/obo/UBERON_0001638) + + + +### duct `http://purl.obolibrary.org/obo/UBERON_0000058` +#### Removed +- [duct](http://purl.obolibrary.org/obo/UBERON_0000058) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00100314" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + +- [duct](http://purl.obolibrary.org/obo/UBERON_0000058) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here." + +- [duct](http://purl.obolibrary.org/obo/UBERON_0000058) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFA:0005171" + + + +### duct of apocrine sweat gland `http://purl.obolibrary.org/obo/UBERON_0035074` + +#### Added +- [duct of apocrine sweat gland](http://purl.obolibrary.org/obo/UBERON_0035074) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### duct of eccrine sweat gland `http://purl.obolibrary.org/obo/UBERON_0035073` + +#### Added +- [duct of eccrine sweat gland](http://purl.obolibrary.org/obo/UBERON_0035073) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### duct of epididymis `http://purl.obolibrary.org/obo/UBERON_0008824` + +#### Added +- [duct of epididymis](http://purl.obolibrary.org/obo/UBERON_0008824) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### duct of male reproductive system `http://purl.obolibrary.org/obo/UBERON_0005904` +#### Removed +- [duct of male reproductive system](http://purl.obolibrary.org/obo/UBERON_0005904) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "this class groups the individual ducts in a variety of species" + + + +### duct of sebaceous gland `http://purl.obolibrary.org/obo/UBERON_0011845` + +#### Added +- [duct of sebaceous gland](http://purl.obolibrary.org/obo/UBERON_0011845) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### duct of seminal vesicle `http://purl.obolibrary.org/obo/UBERON_0005903` + +#### Added +- [duct of seminal vesicle](http://purl.obolibrary.org/obo/UBERON_0005903) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### ductal plate `http://purl.obolibrary.org/obo/UBERON_8410003` +#### Removed +- [ductal plate](http://purl.obolibrary.org/obo/UBERON_8410003) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Temporal stages still need to be fully researched across species." + +#### Added +- [ductal plate](http://purl.obolibrary.org/obo/UBERON_8410003) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) + + +### duodenal gland `http://purl.obolibrary.org/obo/UBERON_0001212` +#### Removed +- [duodenal gland](http://purl.obolibrary.org/obo/UBERON_0001212) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Said to be absent outside mammlian (Andrew 1959) but Ziswiler and Farner (1972) noted similar glands at the gastroduodenal junction of some birds" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:9780521617147" + +- [duodenal gland](http://purl.obolibrary.org/obo/UBERON_0001212) SubClassOf [submucosal gland](http://purl.obolibrary.org/obo/UBERON_0011148) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "compound tubular" + +- [duodenal gland](http://purl.obolibrary.org/obo/UBERON_0001212) SubClassOf [only in taxon](http://purl.obolibrary.org/obo/RO_0002160) some [Mammalia](http://purl.obolibrary.org/obo/NCBITaxon_40674) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:9780521617147" + + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "unclear for Aves" + +#### Added +- [duodenal gland](http://purl.obolibrary.org/obo/UBERON_0001212) SubClassOf [only in taxon](http://purl.obolibrary.org/obo/RO_0002160) some [Mammalia](http://purl.obolibrary.org/obo/NCBITaxon_40674) + +- [duodenal gland](http://purl.obolibrary.org/obo/UBERON_0001212) SubClassOf [submucosal gland](http://purl.obolibrary.org/obo/UBERON_0011148) + + +### duodenum `http://purl.obolibrary.org/obo/UBERON_0002114` +#### Removed +- [duodenum](http://purl.obolibrary.org/obo/UBERON_0002114) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The fixed portion of the small intestine deeply lodged in the posterior wall of the abdomen and extending from the pylorus to the beginning of the jejunum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000052" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + +- [duodenum](http://purl.obolibrary.org/obo/UBERON_0002114) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In fish, the divisions of the small intestine are not as clear, and the terms anterior intestine or proximal intestine may be used instead of duodenum." + - [hasScope](http://www.geneontology.org/formats/oboInOwl#hasScope) "NCBITaxon:32443" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Duodenum" + +- [duodenum](http://purl.obolibrary.org/obo/UBERON_0002114) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "duodenal" + +- [duodenum](http://purl.obolibrary.org/obo/UBERON_0002114) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In humans, the duodenum is a hollow jointed tube about 10-15 inches (25-38 centimetres) long connecting the stomach to the jejunum. It begins with the duodenal bulb and ends at the ligament of Treitz." + - [hasScope](http://www.geneontology.org/formats/oboInOwl#hasScope) "NCBITaxon:9606" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Duodenum" + +- [duodenum](http://purl.obolibrary.org/obo/UBERON_0002114) SubClassOf [subdivision of digestive tract](http://purl.obolibrary.org/obo/UBERON_0004921) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "cjm" + + - [order](http://www.geneontology.org/formats/oboInOwl#order) "3" + +#### Added +- [duodenum](http://purl.obolibrary.org/obo/UBERON_0002114) SubClassOf [subdivision of digestive tract](http://purl.obolibrary.org/obo/UBERON_0004921) + + +### dura mater `http://purl.obolibrary.org/obo/UBERON_0002363` +#### Removed +- [dura mater](http://purl.obolibrary.org/obo/UBERON_0002363) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "some ontologies consider dura mater part of the CNS, others dispute this and claim it surrounds it (e.g. DOI:10.1111/joa.12381)[https://github.com/obophenotype/uberon/issues/1261]" + +- [dura mater](http://purl.obolibrary.org/obo/UBERON_0002363) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "the outermost of the three layers of the meninges surrounding the brain and spinal cord. The other two meningeal layers are the pia mater and the arachnoid mater. The dura surrounds the brain and the spinal cord and is responsible for keeping in the cerebrospinal fluid[Wikipedia:Dura_mater]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Dura_mater" + +- [dura mater](http://purl.obolibrary.org/obo/UBERON_0002363) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EV:0100313" + +- [dura mater](http://purl.obolibrary.org/obo/UBERON_0002363) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "capable of inducing chondrogenesis - requires contact with an epithelium - http://www.ncbi.nlm.nih.gov/pubmed/16496288" + +- [dura mater](http://purl.obolibrary.org/obo/UBERON_0002363) SubClassOf [immediate transformation of](http://purl.obolibrary.org/obo/RO_0002495) some [ectomeninx](http://purl.obolibrary.org/obo/UBERON_0007647) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" + +#### Added +- [dura mater](http://purl.obolibrary.org/obo/UBERON_0002363) SubClassOf [immediate transformation of](http://purl.obolibrary.org/obo/RO_0002495) some [ectomeninx](http://purl.obolibrary.org/obo/UBERON_0007647) + + +### dura mater lymph vessel `http://purl.obolibrary.org/obo/UBERON_0035608` +#### Removed +- [dura mater lymph vessel](http://purl.obolibrary.org/obo/UBERON_0035608) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "while Louveau et al (DOI:10.1038/nature14432) state this is within the CNS (thus overturning dogma about the presence of lymphatics in the CNS), in this ontology the dura" + +#### Added +- [dura mater lymph vessel](http://purl.obolibrary.org/obo/UBERON_0035608) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### dural macrophage `http://purl.obolibrary.org/obo/CL_4042006` + +#### Added +- [dural macrophage](http://purl.obolibrary.org/obo/CL_4042006) [label](http://www.w3.org/2000/01/rdf-schema#label) "dural macrophage"@en + +- [dural macrophage](http://purl.obolibrary.org/obo/CL_4042006) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A border associated macrophage which is part of a dura matter. This macrophage phagocytoses intruding pathogens and foreign molecules detected in the bloodstream or in the cerebrospinal fluid. This cell has an amoeboid body with dynamic protrusions in homeostasis." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31061494" + +- [dural macrophage](http://purl.obolibrary.org/obo/CL_4042006) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) + +- [dural macrophage](http://purl.obolibrary.org/obo/CL_4042006) [date](http://purl.org/dc/terms/date) "2024-03-26T19:27:03Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- [dural macrophage](http://purl.obolibrary.org/obo/CL_4042006) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "dmMΦ" + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [abbreviation](http://purl.obolibrary.org/obo/OMO_0003000) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37232741" + +- Class: [dural macrophage](http://purl.obolibrary.org/obo/CL_4042006) + +- [dural macrophage](http://purl.obolibrary.org/obo/CL_4042006) SubClassOf [border associated macrophage](http://purl.obolibrary.org/obo/CL_4042003) + +- [dural macrophage](http://purl.obolibrary.org/obo/CL_4042006) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [brain dura mater](http://purl.obolibrary.org/obo/UBERON_0002092) + + +### ear `http://purl.obolibrary.org/obo/UBERON_0001690` +#### Removed +- [ear](http://purl.obolibrary.org/obo/UBERON_0001690) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Both vertebrate and invertebrate auditory organs are thought to have evolved from primitive mechanosensors, but the nature of the ancestral structure and the evolutionary trajectories followed in distinct animal lineages remain unknown. In particular, we do not know how many types of mechanosensor existed in the protostome-deuterostome ancestor from which insects and vertebrates evolved or whether the PDA had an auditory organ.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1002/dvdy.20207 Boekhoff-Falk G, Hearing in Drosophila: Development of Johnston's organ and emerging parallels to vertebrate ear development. Developmental Dynamics (2005)" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000330" + +- [ear](http://purl.obolibrary.org/obo/UBERON_0001690) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The organ of hearing and of equilibrium. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/ear" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000330" + +- [ear](http://purl.obolibrary.org/obo/UBERON_0001690) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "auricular" + + + +### ear vesicle `http://purl.obolibrary.org/obo/UBERON_0003051` +#### Removed +- [ear vesicle](http://purl.obolibrary.org/obo/UBERON_0003051) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "One of the paired sacs of invaginated ectoderm that develop into the membranous labyrinth of the internal ear. [Biology_online][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001148" + +- [ear vesicle](http://purl.obolibrary.org/obo/UBERON_0003051) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The inner ear develops embryonically in all vertebrates as an invagination of the ectodermal otic placode to form an otic vesicle.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001148" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.413" + +- [ear vesicle](http://purl.obolibrary.org/obo/UBERON_0003051) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Epithelial sac present beside the fifth rhombomere; forms the semicircular canals dorsally and the otolith organs ventrally, and houses the acoustico-vestibular sensory epithelia (maculae) of hair cells. Kimmel et al, 1995. (Also see Anatomical Atlas entry for ear by T. Whitfield.)[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000051" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [ear vesicle](http://purl.obolibrary.org/obo/UBERON_0003051) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "MP defines as epithelial sac, but EHDAA defines as multi-tissue; See https://github.com/obophenotype/uberon/issues/1305" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MP" + +#### Added +- [ear vesicle](http://purl.obolibrary.org/obo/UBERON_0003051) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) + + +### early distal convoluted tubule `http://purl.obolibrary.org/obo/UBERON_0005101` +#### Removed +- [early distal convoluted tubule](http://purl.obolibrary.org/obo/UBERON_0005101) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:28393" + +#### Added +- [early distal convoluted tubule](http://purl.obolibrary.org/obo/UBERON_0005101) SubClassOf [meso-epithelium](http://purl.obolibrary.org/obo/UBERON_0012275) + + +### early pharyngeal endoderm `http://purl.obolibrary.org/obo/UBERON_0007690` +#### Removed +- [early pharyngeal endoderm](http://purl.obolibrary.org/obo/UBERON_0007690) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:32754" + +- [early pharyngeal endoderm](http://purl.obolibrary.org/obo/UBERON_0007690) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:293087" + + + +### early prosencephalic vesicle `http://purl.obolibrary.org/obo/UBERON_0006284` +#### Removed +- [early prosencephalic vesicle](http://purl.obolibrary.org/obo/UBERON_0006284) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000644" + + + +### eccrine sweat gland `http://purl.obolibrary.org/obo/UBERON_0000423` +#### Removed +- [eccrine sweat gland](http://purl.obolibrary.org/obo/UBERON_0000423) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "in mice, found only on footpads; in humans, entire body including soles and palms" + + + +### ectocervix `http://purl.obolibrary.org/obo/UBERON_0012249` +#### Removed +- [ectocervix](http://purl.obolibrary.org/obo/UBERON_0012249) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "distinction between two FMA classes not clear - we merge them here" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + + + +### ectoderm `http://purl.obolibrary.org/obo/UBERON_0000924` +#### Removed +- [ectoderm](http://purl.obolibrary.org/obo/UBERON_0000924) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000153" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722" + +- [ectoderm](http://purl.obolibrary.org/obo/UBERON_0000924) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000111" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + +- [ectoderm](http://purl.obolibrary.org/obo/UBERON_0000924) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "ectodermal" + +- [ectoderm](http://purl.obolibrary.org/obo/UBERON_0000924) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000137" + + + +### ectoderm-derived structure `http://purl.obolibrary.org/obo/UBERON_0004121` +#### Removed +- [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "Grouping term for query purposes" + + + +### ectodermal placode `http://purl.obolibrary.org/obo/UBERON_0005085` +#### Removed +- [ectodermal placode](http://purl.obolibrary.org/obo/UBERON_0005085) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in GO, covers optic, otic, olfactory, mammary, hair, tooth, sebaceous - and also insect structures" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "https://github.com/geneontology/go-ontology/issues/12223#issuecomment-215692347" + + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "GO" + +- [ectodermal placode](http://purl.obolibrary.org/obo/UBERON_0005085) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "With the exception of the adenohypophysis, homologues of the nonneurogenic placodes (e.g. placodes giving rise to the teeth, hair follicles and lens), appear to be lacking in invertebrate chordates." + + + +### ectonucleotide pyrophosphatase/phosphodiesterase family member 3 `http://purl.obolibrary.org/obo/PR_000001344` +#### Removed +- [ectonucleotide pyrophosphatase/phosphodiesterase family member 3](http://purl.obolibrary.org/obo/PR_000001344) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [ectonucleotide pyrophosphatase/phosphodiesterase family member 3 (human)](http://purl.obolibrary.org/obo/PR_O14638) + + + +### ectoplacental cone `http://purl.obolibrary.org/obo/UBERON_0004364` +#### Removed +- [ectoplacental cone](http://purl.obolibrary.org/obo/UBERON_0004364) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "derivative of the early postimplantation trophoblast, which probably gives rise to the spongiotrophoblast." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:19829370" + + + +### editor `http://www.geneontology.org/formats/oboInOwl#editor` +#### Removed +- AnnotationProperty: [editor](http://www.geneontology.org/formats/oboInOwl#editor) + + + +### editor note `http://purl.obolibrary.org/obo/IAO_0000116` +#### Removed +- [editor note](http://purl.obolibrary.org/obo/IAO_0000116) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [ready for release](http://purl.obolibrary.org/obo/IAO_0000122) + +- [editor note](http://purl.obolibrary.org/obo/IAO_0000116) [label](http://www.w3.org/2000/01/rdf-schema#label) "editor note" + +- [editor note](http://purl.obolibrary.org/obo/IAO_0000116) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "IAO:0000116" + +- [editor note](http://purl.obolibrary.org/obo/IAO_0000116) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "editor note"@en + +- [editor note](http://purl.obolibrary.org/obo/IAO_0000116) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) "PERSON:Daniel Schober"@en + +- [editor note](http://purl.obolibrary.org/obo/IAO_0000116) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) "GROUP:OBI:<http://purl.obofoundry.org/obo/obi>"@en + +- [editor note](http://purl.obolibrary.org/obo/IAO_0000116) [is_metadata_tag](http://www.geneontology.org/formats/oboInOwl#is_metadata_tag) true + +- [editor note](http://purl.obolibrary.org/obo/IAO_0000116) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [editor note](http://purl.obolibrary.org/obo/IAO_0000116) [id](http://www.geneontology.org/formats/oboInOwl#id) "editor_note" + +- [editor note](http://purl.obolibrary.org/obo/IAO_0000116) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "editor_note" + + + +### efferent duct `http://purl.obolibrary.org/obo/UBERON_0006946` +#### Removed +- [efferent duct](http://purl.obolibrary.org/obo/UBERON_0006946) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Any of a group ranging from one to twelve (varies in species) small seminal ducts per testis which transport sperm from the testes to the kidney.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010532" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + +- [efferent duct](http://purl.obolibrary.org/obo/UBERON_0006946) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "There are two basic designs for efferent ductule structure: a) multiple entries into the epididymis, as seen in most large mammals. In humans and other large mammals, there are approximately 15-20 efferent ducts, which also occupy nearly one third of the head of the epididymis. b) single entry, as seen in most small animals such as rodents, whereby the 3-6 ductules merge into a single small ductule prior to entering the epididymis" + +- [efferent duct](http://purl.obolibrary.org/obo/UBERON_0006946) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "Check EMAPA" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EMAPA" + + + +### elastic `http://purl.obolibrary.org/obo/PATO_0001171` +#### Removed +- [elastic](http://purl.obolibrary.org/obo/PATO_0001171) [RO_0002604](http://purl.obolibrary.org/obo/RO_0002604) [PATO_0001172](http://purl.obolibrary.org/obo/PATO_0001172) + + + +### elastic cartilage tissue `http://purl.obolibrary.org/obo/UBERON_0001996` +#### Removed +- [elastic cartilage tissue](http://purl.obolibrary.org/obo/UBERON_0001996) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Cartilage (tissue) which consists of chondrocytes and collagen, the intercellular matrix of which consists of elastic fibers[FMA:64785]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:64785" + +- [elastic cartilage tissue](http://purl.obolibrary.org/obo/UBERON_0001996) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Cartilage tissue that is flexible and contains abundant elastic fibers.[VSAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000091" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PSPUB:0000170" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" + +- [elastic cartilage tissue](http://purl.obolibrary.org/obo/UBERON_0001996) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "MA has a distinct class for yellow" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" + + + +### elbow `http://purl.obolibrary.org/obo/UBERON_0001461` +#### Removed +- [elbow](http://purl.obolibrary.org/obo/UBERON_0001461) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "Naming conventions for pod terms under discussion within phenoscape group" + +- [elbow](http://purl.obolibrary.org/obo/UBERON_0001461) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "cubital" + + + +### elbow joint `http://purl.obolibrary.org/obo/UBERON_0001490` +#### Removed +- [elbow joint](http://purl.obolibrary.org/obo/UBERON_0001490) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In human anatomy, the elbow joint is a compound joint that actually comprises three separate joints: the joints connecting the upper and lower arm: 1) Articulatio humero-ulnaris and 2) Articulatio humero-radialis as well as the proximal joint connecting the forarm bones: 3) Articulatio radio-ulnaris proximalis" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "HP" + +- [elbow joint](http://purl.obolibrary.org/obo/UBERON_0001490) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [elbow joint primordium](http://purl.obolibrary.org/obo/UBERON_0006224) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" + +#### Added +- [elbow joint](http://purl.obolibrary.org/obo/UBERON_0001490) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [elbow joint primordium](http://purl.obolibrary.org/obo/UBERON_0006224) + + +### embryo `http://purl.obolibrary.org/obo/UBERON_0000922` +#### Removed +- [embryo](http://purl.obolibrary.org/obo/UBERON_0000922) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "IDOMAL:0000646" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + + - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) + +- [embryo](http://purl.obolibrary.org/obo/UBERON_0000922) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "ZFA" + +- [embryo](http://purl.obolibrary.org/obo/UBERON_0000922) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000052" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + +- [embryo](http://purl.obolibrary.org/obo/UBERON_0000922) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "embryonic" + + + +### embryonic cloaca `http://purl.obolibrary.org/obo/UBERON_0000163` +#### Removed +- [embryonic cloaca](http://purl.obolibrary.org/obo/UBERON_0000163) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "this class represents the embryonic form of the cloaca, as found in both mammals and non-mammals." + + + +### embryonic footplate `http://purl.obolibrary.org/obo/UBERON_0006871` +#### Removed +- [embryonic footplate](http://purl.obolibrary.org/obo/UBERON_0006871) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "EHDAA2 does not have a single class for footplate, but includes epithelium, mesenchyme and AER" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EHDAA2" + + + +### embryonic head `http://purl.obolibrary.org/obo/UBERON_0008816` +#### Removed +- [embryonic head](http://purl.obolibrary.org/obo/UBERON_0008816) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000155" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + + +### embryonic nasal process `http://purl.obolibrary.org/obo/UBERON_0009292` +#### Removed +- [embryonic nasal process](http://purl.obolibrary.org/obo/UBERON_0009292) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:293971" + +- [embryonic nasal process](http://purl.obolibrary.org/obo/UBERON_0009292) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "medial or lateral; in EHDAA2 also frontonasal or intermaxillary" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EHDAA2" + + + +### embryonic post-anal tail `http://purl.obolibrary.org/obo/UBERON_0007144` +#### Removed +- [embryonic post-anal tail](http://purl.obolibrary.org/obo/UBERON_0007144) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "By the fourth week a clear tail is seen in the human embryo. It recedes after a few weeks and these tissues form what is commonly known as the tailbone (coccyx)." + + + +### embryonic skin basal layer `http://purl.obolibrary.org/obo/UBERON_0011272` + +#### Added +- [embryonic skin basal layer](http://purl.obolibrary.org/obo/UBERON_0011272) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) + + +### embryonic structure `http://purl.obolibrary.org/obo/UBERON_0002050` +#### Removed +- [embryonic structure](http://purl.obolibrary.org/obo/UBERON_0002050) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in FMA embryo is_a embryonic structure" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + +- [embryonic structure](http://purl.obolibrary.org/obo/UBERON_0002050) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004208" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + +- [embryonic structure](http://purl.obolibrary.org/obo/UBERON_0002050) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000178" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" + +- [embryonic structure](http://purl.obolibrary.org/obo/UBERON_0002050) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000138" + +- [embryonic structure](http://purl.obolibrary.org/obo/UBERON_0002050) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001105" + + + +### embryonic tagma `http://purl.obolibrary.org/obo/UBERON_6000137` +#### Removed +- [embryonic tagma](http://purl.obolibrary.org/obo/UBERON_6000137) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000137" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + + +### embryonic urethral groove `http://purl.obolibrary.org/obo/UBERON_0013241` +#### Removed +- [embryonic urethral groove](http://purl.obolibrary.org/obo/UBERON_0013241) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In humans, the urethral groove is a temporary linear indentation on the underside (ventral side) of the male penis during embryonic development. It typically appears around 8 weeks of gestation and becomes closed into a normal male urethra by the 12th week" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Urethral_groove" + + + +### enabled by `http://purl.obolibrary.org/obo/RO_0002333` +#### Removed +- [enabled by](http://purl.obolibrary.org/obo/RO_0002333) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + + + +### enables `http://purl.obolibrary.org/obo/RO_0002327` +#### Removed +- [enables](http://purl.obolibrary.org/obo/RO_0002327) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "catalyzes" + +- [enables](http://purl.obolibrary.org/obo/RO_0002327) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "is executing" + +- [enables](http://purl.obolibrary.org/obo/RO_0002327) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [enables](http://purl.obolibrary.org/obo/RO_0002327) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "a particular instances of akt-2 enables some instance of protein kinase activity" + +- [enables](http://purl.obolibrary.org/obo/RO_0002327) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "has" + +- [enables](http://purl.obolibrary.org/obo/RO_0002327) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "is catalyzing" + +- [enables](http://purl.obolibrary.org/obo/RO_0002327) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." + +- [enables](http://purl.obolibrary.org/obo/RO_0002327) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "executes" + + + +### enamel `http://purl.obolibrary.org/obo/UBERON_0001752` +#### Removed +- [enamel](http://purl.obolibrary.org/obo/UBERON_0001752) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "part_of tooth enamel organ in MA" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" + +- [enamel](http://purl.obolibrary.org/obo/UBERON_0001752) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Skeletal tissue that consists of an avascular, noncollagenous, hypermineralized matrix that is deposited by ameloblasts that are excluded from the matrix. Enamel develops from organic pre-enamel tissue that is replaced by a largely inorganic matrix.[VSAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000065" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PSPUB:0000170" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" + +- [enamel](http://purl.obolibrary.org/obo/UBERON_0001752) SubClassOf [composed primarily of](http://purl.obolibrary.org/obo/RO_0002473) some [CHEBI_52255](http://purl.obolibrary.org/obo/CHEBI_52255) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:ENAM" + + - [proportion](http://www.geneontology.org/formats/oboInOwl#proportion) "85" + +#### Added +- [enamel](http://purl.obolibrary.org/obo/UBERON_0001752) SubClassOf [composed primarily of](http://purl.obolibrary.org/obo/RO_0002473) some [CHEBI_52255](http://purl.obolibrary.org/obo/CHEBI_52255) + + +### endocardial cushion `http://purl.obolibrary.org/obo/UBERON_0002062` +#### Removed +- [endocardial cushion](http://purl.obolibrary.org/obo/UBERON_0002062) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(Cardiac valve formation in vertebrates) In response to a myocardial signal, endocardial cells at chamber boundaries take on a mesenchymal character, delaminate and migrate into the cardiac jelly. There, they form an endocardial cushion that is later remodelled into a valve.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1038/35047564 Stainier DYR, Zebrafish genetics and vertebrate heart formation. Nature Reviews Genetics (2001) Figure 3" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000932" + +- [endocardial cushion](http://purl.obolibrary.org/obo/UBERON_0002062) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001317" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [endocardial cushion](http://purl.obolibrary.org/obo/UBERON_0002062) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: develops_from endocardial ring (TAO:0005072)[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001317" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [endocardial cushion](http://purl.obolibrary.org/obo/UBERON_0002062) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D054089" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + + + +### endocardium `http://purl.obolibrary.org/obo/UBERON_0002165` +#### Removed +- [endocardium](http://purl.obolibrary.org/obo/UBERON_0002165) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Layer that lines the lumen of the heart.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001320" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [endocardium](http://purl.obolibrary.org/obo/UBERON_0002165) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Part of the heart comprised of thin serous membrane, composed of endothelial tissue, that lines the interior of the heart.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010408" + +- [endocardium](http://purl.obolibrary.org/obo/UBERON_0002165) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Tunica intima which has as its parts the endothelium of endocardium and the fibroelastic connective tissue that surrounds the cavity of a cardiac chamber." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:7280" + +- [endocardium](http://purl.obolibrary.org/obo/UBERON_0002165) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + + +### endocardium of left ventricle `http://purl.obolibrary.org/obo/UBERON_0009713` +#### Removed +- [endocardium of left ventricle](http://purl.obolibrary.org/obo/UBERON_0009713) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Endocardium of ventricle which is continuous with mitral valve, aortic valve, atrioventricular septum and the tunica intima of the aorta." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:9559" + + + +### endocardium of right ventricle `http://purl.obolibrary.org/obo/UBERON_0009712` +#### Removed +- [endocardium of right ventricle](http://purl.obolibrary.org/obo/UBERON_0009712) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Endocardium of ventricle which is continuous tricuspid valve, pulmonary valve and with the tunica intima of the pulmonary trunk." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:9536" + + + +### endocervical epithelium `http://purl.obolibrary.org/obo/UBERON_0012252` +#### Removed +- [endocervical epithelium](http://purl.obolibrary.org/obo/UBERON_0012252) SubClassOf [glandular epithelium](http://purl.obolibrary.org/obo/UBERON_0006799) + +#### Added +- [endocervical epithelium](http://purl.obolibrary.org/obo/UBERON_0012252) SubClassOf [cervix glandular epithelium](http://purl.obolibrary.org/obo/UBERON_0012250) + + +### endocervix `http://purl.obolibrary.org/obo/UBERON_0000458` + +#### Added +- [endocervix](http://purl.obolibrary.org/obo/UBERON_0000458) SubClassOf [reproductive structure](http://purl.obolibrary.org/obo/UBERON_0005156) + + +### endochondral bone `http://purl.obolibrary.org/obo/UBERON_0002513` +#### Removed +- [endochondral bone](http://purl.obolibrary.org/obo/UBERON_0002513) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Replacement bone that forms within cartilage.[VSAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PSPUB:0000170" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000145" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" + +- [endochondral bone](http://purl.obolibrary.org/obo/UBERON_0002513) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "some structures, e.g. in ZFA are both intramembrane and endochondral" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "ZFA" + + + +### endochondral bone tissue `http://purl.obolibrary.org/obo/UBERON_0004763` +#### Removed +- [endochondral bone tissue](http://purl.obolibrary.org/obo/UBERON_0004763) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "the distinction between endochondral bone and endochondral bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" + + + +### endocrine pancreas `http://purl.obolibrary.org/obo/UBERON_0000016` +#### Removed +- [endocrine pancreas](http://purl.obolibrary.org/obo/UBERON_0000016) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The zebrafish endocrine pancreas is composed of small groups of islet cells that are distributed throughout the exocrine pancreas. The islet cells produce insulin, glucagon and somatostatin.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001260" + +- [endocrine pancreas](http://purl.obolibrary.org/obo/UBERON_0000016) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D007515" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + +- [endocrine pancreas](http://purl.obolibrary.org/obo/UBERON_0000016) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The part of the pancreas that acts as an endocrine gland, consisting of the islets of Langerhans, which secrete insulin and other hormones. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/Pancreas" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000049" + +- [endocrine pancreas](http://purl.obolibrary.org/obo/UBERON_0000016) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1016/j.crvi.2007.03.006 Madsen OD, Pancreas phylogeny and ontogeny in relation to a 'pancreatic stem cell'. C.R. Biologies (2007)" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000049" + +- [endocrine pancreas](http://purl.obolibrary.org/obo/UBERON_0000016) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "endocrine and exocrine pancreas are not co-associated in hagfishes or lampreys" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:20959416" + + + +### endocrine system `http://purl.obolibrary.org/obo/UBERON_0000949` +#### Removed +- [endocrine system](http://purl.obolibrary.org/obo/UBERON_0000949) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "endocrine" + +- [endocrine system](http://purl.obolibrary.org/obo/UBERON_0000949) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010279" + +- [endocrine system](http://purl.obolibrary.org/obo/UBERON_0000949) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1073/pnas.0812138106 Markov GV, Tavares R, Dauphin-Villemant C, Demeneix BA, Baker ME, Laudet V, Independent elaboration of steroid hormone signaling pathways in metazoans. PNAS (2009)" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000098" + +- [endocrine system](http://purl.obolibrary.org/obo/UBERON_0000949) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005068" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + + +### endoderm `http://purl.obolibrary.org/obo/UBERON_0000925` +#### Removed +- [endoderm](http://purl.obolibrary.org/obo/UBERON_0000925) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "endodermal" + +- [endoderm](http://purl.obolibrary.org/obo/UBERON_0000925) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000154" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722" + +- [endoderm](http://purl.obolibrary.org/obo/UBERON_0000925) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000125" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + + +### endoderm-derived structure `http://purl.obolibrary.org/obo/UBERON_0004119` +#### Removed +- [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "Grouping term for query purposes" + + + +### endoglin `http://purl.obolibrary.org/obo/PR_000001345` +#### Removed +- [endoglin](http://purl.obolibrary.org/obo/PR_000001345) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [endoglin (human)](http://purl.obolibrary.org/obo/PR_P17813) + + + +### endometrial gland `http://purl.obolibrary.org/obo/UBERON_0002451` +#### Removed +- [endometrial gland](http://purl.obolibrary.org/obo/UBERON_0002451) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "simple or branched tubular" + +- [endometrial gland](http://purl.obolibrary.org/obo/UBERON_0002451) [UBPROP_0000202](http://purl.obolibrary.org/obo/UBPROP_0000202) [FMA_71647](http://purl.obolibrary.org/obo/FMA_71647) + +#### Added +- [endometrial gland](http://purl.obolibrary.org/obo/UBERON_0002451) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### endometrium `http://purl.obolibrary.org/obo/UBERON_0001295` +#### Removed +- [endometrium](http://purl.obolibrary.org/obo/UBERON_0001295) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The maternal part of the placenta (of eutherian mammals) is the vascularized and glandular uterine lining, or endometrium.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.144" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001285" + +- [endometrium](http://purl.obolibrary.org/obo/UBERON_0001295) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in FMA this is subdivided into basal and outer" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + +- [endometrium](http://purl.obolibrary.org/obo/UBERON_0001295) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The mucous membrane lining the uterus. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/Endometrium" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001285" + +- [endometrium](http://purl.obolibrary.org/obo/UBERON_0001295) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "endometrial" + +- [endometrium](http://purl.obolibrary.org/obo/UBERON_0001295) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Animals that have estrous cycles reabsorb the endometrium if conception does not occur during that cycle. Animals that have menstrual cycles shed the endometrium through menstruation instead" + + + +### endometrium epithelium `http://purl.obolibrary.org/obo/UBERON_0004811` +#### Removed +- [endometrium epithelium](http://purl.obolibrary.org/obo/UBERON_0004811) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In rodents and primates, the uterine epithelium (the endometrium) is eroded away so that maternal blood comes into direct contact with the trophoblast surface (called haemochorial)" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:19829370" + + + +### endometrium luminal epithelium `http://purl.obolibrary.org/obo/UBERON_0011949` + +#### Added +- [endometrium luminal epithelium](http://purl.obolibrary.org/obo/UBERON_0011949) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### endoskeleton `http://purl.obolibrary.org/obo/UBERON_0010362` +#### Removed +- [endoskeleton](http://purl.obolibrary.org/obo/UBERON_0010362) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "An endoskeleton is an internal support structure of an animal, composed of mineralized tissue. Endoskeleton develops within the skin or in the deeper body tissues. The vertebrate is basically an endoskeleton made up of two types of tissues (bone and cartilage). During early embryonic development the endoskeleton is composed of notochord and cartilage. The notochord in most vertebrates is replaced by vertebral column and cartilage is replaced by bone in most adults. In three phyla and one subclass of animals, endoskeletons of various complexity are found: Chordata, Echinodermata, Porifera, and Coleoidea. An endoskeleton may function purely for support (as in the case of sponges), but often serves as an attachment site for muscle and a mechanism for transmitting muscular forces. A true endoskeleton is derived from mesodermal tissue. Such a skeleton is present in echinoderms and chordates. The poriferan 'skeleton' consists of microscopic calcareous or siliceous spicules or a spongin network. The Coleoidae do not have a true endoskeleton in the evolutionary sense; here, a mollusk exoskeleton evolved into several sorts of internal structure, the 'cuttlebone' of cuttlefish being the best-known version. Yet they do have cartilaginous tissue in their body, even if it is not mineralized, especially in the head, where it forms a primitive cranium. The endoskeleton gives shape,support and protection to the body and provides a mean of locomotion.[Wikipedia:Endoskeleton]t" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Endoskeleton" + + + +### endosteum `http://purl.obolibrary.org/obo/UBERON_0009859` +#### Removed +- [endosteum](http://purl.obolibrary.org/obo/UBERON_0009859) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "endosteal" + + + +### endothelial transcription factor GATA-2 `http://purl.obolibrary.org/obo/PR_000007858` +#### Removed +- [endothelial transcription factor GATA-2](http://purl.obolibrary.org/obo/PR_000007858) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [endothelial transcription factor GATA-2 (human)](http://purl.obolibrary.org/obo/PR_P23769) + + + +### endothelium `http://purl.obolibrary.org/obo/UBERON_0001986` +#### Removed +- [endothelium](http://purl.obolibrary.org/obo/UBERON_0001986) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "endothelial" + + + +### endothelium of artery `http://purl.obolibrary.org/obo/UBERON_0001917` +#### Removed +- [endothelium of artery](http://purl.obolibrary.org/obo/UBERON_0001917) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001215" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207" + +- [endothelium of artery](http://purl.obolibrary.org/obo/UBERON_0001917) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The endothelium is the thin layer of cells that lines the interior surface of blood vessels, forming an interface between circulating blood in the lumen and the rest of the vessel wall.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "XAO:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0011013" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + + +### endothelium of vein `http://purl.obolibrary.org/obo/UBERON_0001919` +#### Removed +- [endothelium of vein](http://purl.obolibrary.org/obo/UBERON_0001919) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001216" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207" + + + +### ends `http://purl.obolibrary.org/obo/RO_0002229` +#### Removed +- [ends](http://purl.obolibrary.org/obo/RO_0002229) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [ends](http://purl.obolibrary.org/obo/RO_0002229) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [ends](http://purl.obolibrary.org/obo/RO_0002229) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "ends" + +- [ends](http://purl.obolibrary.org/obo/RO_0002229) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) + +- [ends](http://purl.obolibrary.org/obo/RO_0002229) [id](http://www.geneontology.org/formats/oboInOwl#id) "ends" + +- [ends](http://purl.obolibrary.org/obo/RO_0002229) [label](http://www.w3.org/2000/01/rdf-schema#label) "ends" + +- [ends](http://purl.obolibrary.org/obo/RO_0002229) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) "Chris Mungall" + +- [ends](http://purl.obolibrary.org/obo/RO_0002229) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002229" + + + +### ends after `http://purl.obolibrary.org/obo/RO_0002086` +#### Removed +- [ends after](http://purl.obolibrary.org/obo/RO_0002086) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) "David Osumi-Sutherland" + + + +### ends with `http://purl.obolibrary.org/obo/RO_0002230` +#### Removed +- [ends with](http://purl.obolibrary.org/obo/RO_0002230) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) "Chris Mungall" + +- [ends with](http://purl.obolibrary.org/obo/RO_0002230) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) + +- [ends with](http://purl.obolibrary.org/obo/RO_0002230) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [ends with](http://purl.obolibrary.org/obo/RO_0002230) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [ends with](http://purl.obolibrary.org/obo/RO_0002230) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "finished by" + + + +### enteric nerve `http://purl.obolibrary.org/obo/UBERON_0010380` + +#### Added +- [enteric nerve](http://purl.obolibrary.org/obo/UBERON_0010380) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) + + +### enteric nervous system `http://purl.obolibrary.org/obo/UBERON_0002005` +#### Removed +- [enteric nervous system](http://purl.obolibrary.org/obo/UBERON_0002005) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "most sources classify this as autonomic, but in FMA it is placed directly under nervous system." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + +#### Added +- [enteric nervous system](http://purl.obolibrary.org/obo/UBERON_0002005) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) + + +### enteric plexus `http://purl.obolibrary.org/obo/UBERON_0000429` + +#### Added +- [enteric plexus](http://purl.obolibrary.org/obo/UBERON_0000429) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) + + +### entire sense organ system `http://purl.obolibrary.org/obo/UBERON_0004456` +#### Removed +- [entire sense organ system](http://purl.obolibrary.org/obo/UBERON_0004456) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs" + + + +### enveloping layer of ectoderm `http://purl.obolibrary.org/obo/UBERON_0007383` +#### Removed +- [enveloping layer of ectoderm](http://purl.obolibrary.org/obo/UBERON_0007383) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Originally this tissue is one cell layer thick but in most vertebrates it soon becomes a two layered structure. The outer layer gives rise to the periderm." + +- [enveloping layer of ectoderm](http://purl.obolibrary.org/obo/UBERON_0007383) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: develops_from superficial blastomere (TAO:0001484)[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000086" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [enveloping layer of ectoderm](http://purl.obolibrary.org/obo/UBERON_0007383) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Outermost monolayer of cells surrounding the embryo that become very flattened in the blastula and give rise to the periderm. Sometimes used synonymously with periderm. Kimmel et al, 1995.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000086" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +#### Added +- [enveloping layer of ectoderm](http://purl.obolibrary.org/obo/UBERON_0007383) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) + + +### eosinophil cationic protein `http://purl.obolibrary.org/obo/PR_000014047` +#### Removed +- [eosinophil cationic protein](http://purl.obolibrary.org/obo/PR_000014047) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [eosinophil cationic protein (human)](http://purl.obolibrary.org/obo/PR_P12724) + + + +### eosinophil peroxidase `http://purl.obolibrary.org/obo/PR_000007152` +#### Removed +- [eosinophil peroxidase](http://purl.obolibrary.org/obo/PR_000007152) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [eosinophil peroxidase (human)](http://purl.obolibrary.org/obo/PR_P11678) + + + +### ependyma `http://purl.obolibrary.org/obo/UBERON_0004670` +#### Removed +- [ependyma](http://purl.obolibrary.org/obo/UBERON_0004670) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "unlike other epithelia, there is no basement membrane under the ependymal epithelium[ISBN:0387949542]" + +- [ependyma](http://purl.obolibrary.org/obo/UBERON_0004670) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "ependymal" + +- [ependyma](http://purl.obolibrary.org/obo/UBERON_0004670) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [basement membrane](http://purl.obolibrary.org/obo/GO_0005604) + +- [ependyma](http://purl.obolibrary.org/obo/UBERON_0004670) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA breaks ependyma into ependyma proper (a subdivsion of epithelium) and epithelium of choroid plexus" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + + + +### epiblast (generic) `http://purl.obolibrary.org/obo/UBERON_0002532` +#### Removed +- [epiblast (generic)](http://purl.obolibrary.org/obo/UBERON_0002532) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000243" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1146/annurev.cellbio.042308.113344 Zorn AM, Wells JM, Vertebrate endoderm development and organ formation. Annual Review of Cell Developmental Biology (2009)" + + + +### epibranchial ganglion `http://purl.obolibrary.org/obo/UBERON_0009127` +#### Removed +- [epibranchial ganglion](http://purl.obolibrary.org/obo/UBERON_0009127) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006250" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + + - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) + + + +### epibranchial placode `http://purl.obolibrary.org/obo/UBERON_0003078` +#### Removed +- [epibranchial placode](http://purl.obolibrary.org/obo/UBERON_0003078) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "Epibranchial placodes-derived neurons innervate internal organs to transmit information such as heart rate, blood pressure, and visceral distension from the periphery to the central nervous system (Baker and Bronner-Fraser, 2001). From rostral to caudal the epibranchial placodes comprise the geniculate, petrosal, and nodose placodes, each associated in sequence with the first, second and third branchial clefts. Each placode contributes sensory neurons to cranial nerves VII (facial nerve), IX (glossopharyngeal nerve), and X (vagal nerve), respectively" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "NCBIBook:NBK53175" + +- [epibranchial placode](http://purl.obolibrary.org/obo/UBERON_0003078) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches and that produce the neuroblasts that migrate and condense to form the distal cranial ganglia. [Graham_A, The_development_and_evolution_of_the_pharyngeal_arches._J_Anat_(2001)_199:_133-141][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000117" + +- [epibranchial placode](http://purl.obolibrary.org/obo/UBERON_0003078) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia. (...) The one substantial difference between the vertebrate pharyngeal arches and those of the protochordates is the presence of the epibranchial placodes but the evolution of these structures was undoubtedly driven by the endoderm.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A, The development and evolution of the pharyngeal arches. J Anat (2001)" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000117" + +- [epibranchial placode](http://purl.obolibrary.org/obo/UBERON_0003078) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in XAO this develops_from dorsolateral placode, but in NBK53175, this is a separate group" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "XAO" + + + +### epicardial fat `http://purl.obolibrary.org/obo/UBERON_0015129` +#### Removed +- [epicardial fat](http://purl.obolibrary.org/obo/UBERON_0015129) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "SCTID:42267001" + +#### Added +- [epicardial fat](http://purl.obolibrary.org/obo/UBERON_0015129) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### epicardium `http://purl.obolibrary.org/obo/UBERON_0002348` +#### Removed +- [epicardium](http://purl.obolibrary.org/obo/UBERON_0002348) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The inner layer of the pericardium that is in contact with the surface of the heart.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010409" + +- [epicardium](http://purl.obolibrary.org/obo/UBERON_0002348) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "External layer of the heart.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005057" + +- [epicardium](http://purl.obolibrary.org/obo/UBERON_0002348) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "The visceral pericardium apparently produces the pericardial fluid, which lubricates motion between the inner and outer layers of the pericardium. During ventricular contraction, the wave of depolarization moves from endocardial to epicardial surface. [Wikipedia:Epicardium]" + +#### Added +- [epicardium](http://purl.obolibrary.org/obo/UBERON_0002348) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### epicardium of ventricle `http://purl.obolibrary.org/obo/UBERON_0001082` +#### Removed +- [epicardium of ventricle](http://purl.obolibrary.org/obo/UBERON_0001082) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The external layer of the ventricle bounding the ventricular myocardium. It is formed by a single layer of mesothelial cells supported by a basal lamina, and imbricated with collagen, fibroblasts, and vascular structures in the subepicardial space. Hu et al. 2001.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005058" + + + +### epidermal-dermal junction `http://purl.obolibrary.org/obo/UBERON_0008877` + +#### Added +- [epidermal-dermal junction](http://purl.obolibrary.org/obo/UBERON_0008877) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### epidermis suprabasal layer `http://purl.obolibrary.org/obo/UBERON_0010402` + +#### Added +- [epidermis suprabasal layer](http://purl.obolibrary.org/obo/UBERON_0010402) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### epididymis `http://purl.obolibrary.org/obo/UBERON_0001301` +#### Removed +- [epididymis](http://purl.obolibrary.org/obo/UBERON_0001301) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "Typically divided into three main regions. In reptiles, there is an additional canal between the testis and the head of the epididymis, which receives the various efferent ducts. This is, however, absent in all birds and mammals. The epididymis is covered by a two layered pseudostratified epithelium. The epithelium is separated by a basement membrane from the connective tissue wall which has smooth muscle cells." + +- [epididymis](http://purl.obolibrary.org/obo/UBERON_0001301) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "epididymal" + +- [epididymis](http://purl.obolibrary.org/obo/UBERON_0001301) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "A similar, but probably non-homologous, structure is found in cartilaginous fishes" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" + + + +### epididymis epithelium `http://purl.obolibrary.org/obo/UBERON_0004544` + +#### Added +- [epididymis epithelium](http://purl.obolibrary.org/obo/UBERON_0004544) SubClassOf [meso-epithelium](http://purl.obolibrary.org/obo/UBERON_0012275) + + +### epididymis smooth muscle `http://purl.obolibrary.org/obo/UBERON_0004835` +#### Removed +- [epididymis smooth muscle](http://purl.obolibrary.org/obo/UBERON_0004835) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:30747" + + + +### epidural space `http://purl.obolibrary.org/obo/UBERON_0003691` +#### Removed +- [epidural space](http://purl.obolibrary.org/obo/UBERON_0003691) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In humans the epidural space contains lymphatics, spinal nerve roots, loose fatty tissue, small arteries, and a network of large, thin-walled blood vessels called the epidural venous plexus" + +- [epidural space](http://purl.obolibrary.org/obo/UBERON_0003691) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "extradural" + +- [epidural space](http://purl.obolibrary.org/obo/UBERON_0003691) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "epidural" + +- [epidural space](http://purl.obolibrary.org/obo/UBERON_0003691) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in the FMA this is treated as a space of the head, but this ontology covers non-humans, where the space may continue into the tail" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + + + +### epimysium `http://purl.obolibrary.org/obo/UBERON_0011899` +#### Removed +- [epimysium](http://purl.obolibrary.org/obo/UBERON_0011899) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "The Epimysium also protects muscles from friction against other muscles and bones" + +#### Added +- [epimysium](http://purl.obolibrary.org/obo/UBERON_0011899) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### epineurium `http://purl.obolibrary.org/obo/UBERON_0000124` +#### Removed +- [epineurium](http://purl.obolibrary.org/obo/UBERON_0000124) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "outermost layer of connective tissue surrounding a peripheral nerve. It includes the blood vessels supplying the nerve. It consists of adipose tissue and fibrocollagenous tissues[Wikipedia:Epineurium]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Epineurium" + + + +### epiphysis `http://purl.obolibrary.org/obo/UBERON_0001437` +#### Removed +- [epiphysis](http://purl.obolibrary.org/obo/UBERON_0001437) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "epiphysial" + +- [epiphysis](http://purl.obolibrary.org/obo/UBERON_0001437) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "epiphyseal" + +- [epiphysis](http://purl.obolibrary.org/obo/UBERON_0001437) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Cartilaginous expansion at the distal end of an anterior rib or transverse process that serves for the attachment of muscles suspending the pectoral girdle to the vertebral column.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000742" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:Pugener_2002" + +- [epiphysis](http://purl.obolibrary.org/obo/UBERON_0001437) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Subdivision of long bone which forms its expanded proximal or distal articular end; together with other the subdivisions of long bone, it constitutes the long bone. Examples: proximal epiphysis of humerus, distal epiphysis of femur." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:24012" + + + +### epiphysis of femur `http://purl.obolibrary.org/obo/UBERON_0004384` + +#### Added +- [epiphysis of femur](http://purl.obolibrary.org/obo/UBERON_0004384) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### epiphysis of fibula `http://purl.obolibrary.org/obo/UBERON_0004388` + +#### Added +- [epiphysis of fibula](http://purl.obolibrary.org/obo/UBERON_0004388) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### epiphysis of humerus `http://purl.obolibrary.org/obo/UBERON_0004382` + +#### Added +- [epiphysis of humerus](http://purl.obolibrary.org/obo/UBERON_0004382) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### epiphysis of metacarpal bone `http://purl.obolibrary.org/obo/UBERON_0004390` + +#### Added +- [epiphysis of metacarpal bone](http://purl.obolibrary.org/obo/UBERON_0004390) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### epiphysis of metatarsal bone `http://purl.obolibrary.org/obo/UBERON_0004389` + +#### Added +- [epiphysis of metatarsal bone](http://purl.obolibrary.org/obo/UBERON_0004389) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### epiphysis of phalanx `http://purl.obolibrary.org/obo/UBERON_0004446` + +#### Added +- [epiphysis of phalanx](http://purl.obolibrary.org/obo/UBERON_0004446) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### epiphysis of tibia `http://purl.obolibrary.org/obo/UBERON_0004383` + +#### Added +- [epiphysis of tibia](http://purl.obolibrary.org/obo/UBERON_0004383) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### epithalamus `http://purl.obolibrary.org/obo/UBERON_0001899` +#### Removed +- [epithalamus](http://purl.obolibrary.org/obo/UBERON_0001899) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Dorsal segment of the diencephalon containing the habenular ganglia, a choroid plexus, and the pineal organ.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010482" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + +- [epithalamus](http://purl.obolibrary.org/obo/UBERON_0001899) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The roof of the diencephalon lying above the thalamus. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-11, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000178" + +- [epithalamus](http://purl.obolibrary.org/obo/UBERON_0001899) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002736](http://purl.obolibrary.org/obo/UBERON_0002736) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" + +- [epithalamus](http://purl.obolibrary.org/obo/UBERON_0001899) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The epithalamus has been historically conceived as a distinct neuroanatomical moiety within the diencephalon of all vertebrates. (...) The evolutionary origins of epithalamic structures are uncertain but asymmetry in this region is likely to have existed at the origin of the vertebrate, perhaps even the chordate, lineage.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1046/j.1469-7580.2001.19910063.x Concha ML and Wilson SW, Asymmetry in the epithalamus of vertebrates. J Anat (2001)" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000178" + +- [epithalamus](http://purl.obolibrary.org/obo/UBERON_0001899) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002733](http://purl.obolibrary.org/obo/UBERON_0002733) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" + +- [epithalamus](http://purl.obolibrary.org/obo/UBERON_0001899) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0001903](http://purl.obolibrary.org/obo/UBERON_0001903) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" + +- [epithalamus](http://purl.obolibrary.org/obo/UBERON_0001899) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "epithalamic" + + + +### epithelial tube `http://purl.obolibrary.org/obo/UBERON_0003914` +#### Removed +- [epithelial tube](http://purl.obolibrary.org/obo/UBERON_0003914) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007474" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + +- [epithelial tube](http://purl.obolibrary.org/obo/UBERON_0003914) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers" + + + +### epithelium `http://purl.obolibrary.org/obo/UBERON_0000483` +#### Removed +- [epithelium](http://purl.obolibrary.org/obo/UBERON_0000483) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "epithelial" + +- [epithelium](http://purl.obolibrary.org/obo/UBERON_0000483) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.59" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000387" + +- [epithelium](http://purl.obolibrary.org/obo/UBERON_0000483) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007005" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + + +### epithelium of carpal region `http://purl.obolibrary.org/obo/UBERON_0003230` + +#### Added +- [epithelium of carpal region](http://purl.obolibrary.org/obo/UBERON_0003230) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) + + +### epithelium of crypt of Lieberkuhn `http://purl.obolibrary.org/obo/UBERON_0011184` +#### Removed +- [epithelium of crypt of Lieberkuhn](http://purl.obolibrary.org/obo/UBERON_0011184) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA has classes for subdivisions of this epithelium" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + + + +### epithelium of elbow `http://purl.obolibrary.org/obo/UBERON_0003229` +#### Removed +- [epithelium of elbow](http://purl.obolibrary.org/obo/UBERON_0003229) SubClassOf [epithelium](http://purl.obolibrary.org/obo/UBERON_0000483) + +#### Added +- [epithelium of elbow](http://purl.obolibrary.org/obo/UBERON_0003229) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) + + +### epithelium of esophagus `http://purl.obolibrary.org/obo/UBERON_0001976` +#### Removed +- [epithelium of esophagus](http://purl.obolibrary.org/obo/UBERON_0001976) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Simple columnar epithelium that lines the esophagus. Chen et al, 2007.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001499" + + + +### epithelium of footplate `http://purl.obolibrary.org/obo/UBERON_0003248` + +#### Added +- [epithelium of footplate](http://purl.obolibrary.org/obo/UBERON_0003248) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) + + +### epithelium of forearm `http://purl.obolibrary.org/obo/UBERON_0003247` +#### Removed +- [epithelium of forearm](http://purl.obolibrary.org/obo/UBERON_0003247) SubClassOf [epithelium](http://purl.obolibrary.org/obo/UBERON_0000483) + +#### Added +- [epithelium of forearm](http://purl.obolibrary.org/obo/UBERON_0003247) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) + + +### epithelium of gall bladder `http://purl.obolibrary.org/obo/UBERON_0002029` + +#### Added +- [epithelium of gall bladder](http://purl.obolibrary.org/obo/UBERON_0002029) SubClassOf [endo-epithelium](http://purl.obolibrary.org/obo/UBERON_0005911) + + +### epithelium of handplate `http://purl.obolibrary.org/obo/UBERON_0010332` + +#### Added +- [epithelium of handplate](http://purl.obolibrary.org/obo/UBERON_0010332) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) + + +### epithelium of hip `http://purl.obolibrary.org/obo/UBERON_0003231` +#### Removed +- [epithelium of hip](http://purl.obolibrary.org/obo/UBERON_0003231) SubClassOf [epithelium](http://purl.obolibrary.org/obo/UBERON_0000483) + +#### Added +- [epithelium of hip](http://purl.obolibrary.org/obo/UBERON_0003231) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) + + +### epithelium of knee `http://purl.obolibrary.org/obo/UBERON_0003232` +#### Removed +- [epithelium of knee](http://purl.obolibrary.org/obo/UBERON_0003232) SubClassOf [epithelium](http://purl.obolibrary.org/obo/UBERON_0000483) + +#### Added +- [epithelium of knee](http://purl.obolibrary.org/obo/UBERON_0003232) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) + + +### epithelium of lens `http://purl.obolibrary.org/obo/UBERON_0001803` +#### Removed +- [epithelium of lens](http://purl.obolibrary.org/obo/UBERON_0001803) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "this class is the superclass of the anterior epithelium and equatorial epithlium, although the term 'lens epithelium' may refer specifically to the former" + + + +### epithelium of mammary gland `http://purl.obolibrary.org/obo/UBERON_0003244` +#### Removed +- [epithelium of mammary gland](http://purl.obolibrary.org/obo/UBERON_0003244) SubClassOf [epithelium](http://purl.obolibrary.org/obo/UBERON_0000483) + +#### Added +- [epithelium of mammary gland](http://purl.obolibrary.org/obo/UBERON_0003244) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) + + +### epithelium of otic placode `http://purl.obolibrary.org/obo/UBERON_0003249` + +#### Added +- [epithelium of otic placode](http://purl.obolibrary.org/obo/UBERON_0003249) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) + + +### epithelium of shoulder `http://purl.obolibrary.org/obo/UBERON_0003233` +#### Removed +- [epithelium of shoulder](http://purl.obolibrary.org/obo/UBERON_0003233) SubClassOf [epithelium](http://purl.obolibrary.org/obo/UBERON_0000483) + +#### Added +- [epithelium of shoulder](http://purl.obolibrary.org/obo/UBERON_0003233) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) + + +### epithelium of small intestine `http://purl.obolibrary.org/obo/UBERON_0001902` +#### Removed +- [epithelium of small intestine](http://purl.obolibrary.org/obo/UBERON_0001902) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Intestinal epithelium which lines the lumen of the mid intestine.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005127" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + + +### epithelium of stomach `http://purl.obolibrary.org/obo/UBERON_0001276` +#### Removed +- [epithelium of stomach](http://purl.obolibrary.org/obo/UBERON_0001276) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in FMA this is classified as simple columnar, MA divides this into squamous and glandular" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + + + +### epithelium of trachea `http://purl.obolibrary.org/obo/UBERON_0001901` +#### Removed +- [epithelium of trachea](http://purl.obolibrary.org/obo/UBERON_0001901) SubClassOf [endo-epithelium](http://purl.obolibrary.org/obo/UBERON_0005911) + + + +### epithelium of upper jaw `http://purl.obolibrary.org/obo/UBERON_0003235` +#### Removed +- [epithelium of upper jaw](http://purl.obolibrary.org/obo/UBERON_0003235) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:17943" + + + +### epithelium of urethra `http://purl.obolibrary.org/obo/UBERON_0002325` + +#### Added +- [epithelium of urethra](http://purl.obolibrary.org/obo/UBERON_0002325) SubClassOf [meso-epithelium](http://purl.obolibrary.org/obo/UBERON_0012275) + +- [epithelium of urethra](http://purl.obolibrary.org/obo/UBERON_0002325) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) + + +### epithelium of utricle `http://purl.obolibrary.org/obo/UBERON_0003241` +#### Removed +- [epithelium of utricle](http://purl.obolibrary.org/obo/UBERON_0003241) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:17820" + +- [epithelium of utricle](http://purl.obolibrary.org/obo/UBERON_0003241) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:17301" + +- [epithelium of utricle](http://purl.obolibrary.org/obo/UBERON_0003241) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:17298" + +- [epithelium of utricle](http://purl.obolibrary.org/obo/UBERON_0003241) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:17823" + + + +### epithelium of vagina `http://purl.obolibrary.org/obo/UBERON_0001344` +#### Removed +- [epithelium of vagina](http://purl.obolibrary.org/obo/UBERON_0001344) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA: nonkeratinizing stratified squamous epithelium; BTO: Vaginal epithelium is stratified squamous epithelium having a thickness of 15-200 microns; MA has single subclass (squamous)" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + + + +### epithelium of vomeronasal organ `http://purl.obolibrary.org/obo/UBERON_0003367` +#### Removed +- [epithelium of vomeronasal organ](http://purl.obolibrary.org/obo/UBERON_0003367) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) + +#### Added +- [epithelium of vomeronasal organ](http://purl.obolibrary.org/obo/UBERON_0003367) SubClassOf [endo-epithelium](http://purl.obolibrary.org/obo/UBERON_0005911) + + +### erythroid transcription factor `http://purl.obolibrary.org/obo/PR_000007857` +#### Removed +- [erythroid transcription factor](http://purl.obolibrary.org/obo/PR_000007857) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [erythroid transcription factor (human)](http://purl.obolibrary.org/obo/PR_P15976) + + + +### esophagus `http://purl.obolibrary.org/obo/UBERON_0001043` +#### Removed +- [esophagus](http://purl.obolibrary.org/obo/UBERON_0001043) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "esophageal" + +- [esophagus](http://purl.obolibrary.org/obo/UBERON_0001043) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The few structural specializations in (adult lampreys) pharynx include complex valves on the external gill openings that direct the tidal flow, and the division of the ancestral pharynx into an oesophagus and a respiratory pharynx.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000450" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1111/j.1096-3642.1996.tb01658.x Mallatt J, Ventilation and the origin of jawed vertebrates: a new mouth. Zoological Journal of the Linnean Society (1996)" + +- [esophagus](http://purl.obolibrary.org/obo/UBERON_0001043) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anterior end of the alimentary canal lined with smooth muscle. Bounded anteriorly by a constriction in the pharynx. Bounded posteriorly by and increase in circular and/or longitudinal smooth muscle associated with the stomach.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000145" + +- [esophagus](http://purl.obolibrary.org/obo/UBERON_0001043) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "esophagus NOT part of gut in MA. part of gut in ZFA. part_of gut (via UGIT) in FMA. Consider splitting. Interspecies: The human oesophagus is 25 cm long and has a diameter of ca. 2 cm. Only little information was found on the oesophagus in rat, rabbit and pig. The oesophagus of rat (75 x 2 mm) and rabbit has no mucous glands and the cardia of the stomach has a well-developed sphincter, which prevents them from vomiting (Hebel and Stromberg, 1988; Manning et al., 1994). Morphologically the oesophagus is similar in man and pig; both are omnivores and have a non-keratinised epithelium, submucous glands and similar membrane enzymes. Like in humans, pigs can suffer from reflux oesophagitis and stress ulceration of the oesophagus. The pig oesophagus may therefore be a good model for investigation compared to the human oesophagus (Christie et al., 1995)" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" + + + +### esophagus mucosa `http://purl.obolibrary.org/obo/UBERON_0002469` +#### Removed +- [esophagus mucosa](http://purl.obolibrary.org/obo/UBERON_0002469) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D000071041" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + + + +### esophagus smooth muscle circular layer `http://purl.obolibrary.org/obo/UBERON_0009960` + +#### Added +- [esophagus smooth muscle circular layer](http://purl.obolibrary.org/obo/UBERON_0009960) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### esophagus squamous epithelium `http://purl.obolibrary.org/obo/UBERON_0006920` +#### Removed +- [esophagus squamous epithelium](http://purl.obolibrary.org/obo/UBERON_0006920) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "MA introduces basal and squamous subtypes of esophagus epithelium; consider adding the FMA class 'epithelium of esophagus' here, because it is classified as squamous. BTO also has a singleton subclass" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" + + + +### estrogen receptor `http://purl.obolibrary.org/obo/PR_000007204` +#### Removed +- [estrogen receptor](http://purl.obolibrary.org/obo/PR_000007204) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [estrogen receptor (human)](http://purl.obolibrary.org/obo/PR_P03372) + + + +### ethmoid bone `http://purl.obolibrary.org/obo/UBERON_0001679` +#### Removed +- [ethmoid bone](http://purl.obolibrary.org/obo/UBERON_0001679) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A light spongy bone located between the eye sockets, forming part of the walls and septum of the superior nasal cavity, and containing perforations for the passage of olfactory nerve fibers. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/ethmoid+bone" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001317" + +- [ethmoid bone](http://purl.obolibrary.org/obo/UBERON_0001679) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "todo - homology e.g. mesethmoid of teleost" + +- [ethmoid bone](http://purl.obolibrary.org/obo/UBERON_0001679) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "Note the WP states the Neurocranium contains the ethmoid bone, both MA and FMA place the ethmoid as part of the viscerocranium. FMA also has it in neurocranium (via basicranium). Ideally we would have non-overlapping divisions of the skull, but for now we follow FMA" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" + +- [ethmoid bone](http://purl.obolibrary.org/obo/UBERON_0001679) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "ethmoidal" + +- [ethmoid bone](http://purl.obolibrary.org/obo/UBERON_0001679) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The ethmoid region of the chondrocranium and the nasal capsules, which were largely unossified in early tetrapods and ancestral amniotes, are represented in mammals by the ethmoid and turbinates bones, respectively.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001317" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.259" + +- [ethmoid bone](http://purl.obolibrary.org/obo/UBERON_0001679) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [ethmoid bone primordium](http://purl.obolibrary.org/obo/UBERON_0006227) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" + +#### Added +- [ethmoid bone](http://purl.obolibrary.org/obo/UBERON_0001679) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [ethmoid bone primordium](http://purl.obolibrary.org/obo/UBERON_0006227) + + +### ethmoid foramen `http://purl.obolibrary.org/obo/UBERON_0018415` +#### Removed +- [ethmoid foramen](http://purl.obolibrary.org/obo/UBERON_0018415) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "There are usually two Foramina ethmoidalia present on each side in the dog. Sometimes one is situated rostral to the other, but often it is dorsal. They are not homologous with the Foramen ethmoidale anterius and Foramen ethmoidale posterius of man. Therefore they are not listed separately.[NOMINA ANATOMICA VETERINARIA (2005)]" + +#### Added +- [ethmoid foramen](http://purl.obolibrary.org/obo/UBERON_0018415) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) + + +### ethmoid region `http://purl.obolibrary.org/obo/UBERON_0011241` +#### Removed +- [ethmoid region](http://purl.obolibrary.org/obo/UBERON_0011241) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "currently this is not restricted to skeletal elements, unlike UBERONREF:0000007" + + + +### evidence `http://www.geneontology.org/formats/oboInOwl#evidence` +#### Removed +- AnnotationProperty: [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) + + + +### evolutionarily related to `http://purl.obolibrary.org/obo/RO_0002320` +#### Removed +- [evolutionarily related to](http://purl.obolibrary.org/obo/RO_0002320) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." + +- [evolutionarily related to](http://purl.obolibrary.org/obo/RO_0002320) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + + + +### example to be eventually removed `http://purl.obolibrary.org/obo/IAO_0000002` +#### Removed +- [example to be eventually removed](http://purl.obolibrary.org/obo/IAO_0000002) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "example to be eventually removed"@en + + + +### exception `http://www.geneontology.org/formats/oboInOwl#exception` +#### Removed +- AnnotationProperty: [exception](http://www.geneontology.org/formats/oboInOwl#exception) + + + +### exceptions `http://www.geneontology.org/formats/oboInOwl#exceptions` +#### Removed +- AnnotationProperty: [exceptions](http://www.geneontology.org/formats/oboInOwl#exceptions) + + + +### exceptions_url `http://www.geneontology.org/formats/oboInOwl#exceptions_url` +#### Removed +- AnnotationProperty: [exceptions_url](http://www.geneontology.org/formats/oboInOwl#exceptions_url) + + + +### excretory duct `http://purl.obolibrary.org/obo/UBERON_0035050` +#### Removed +- [excretory duct](http://purl.obolibrary.org/obo/UBERON_0035050) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006341" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + + - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) + + + +### excretory system `http://purl.obolibrary.org/obo/UBERON_8450002` +#### Removed +- [excretory system](http://purl.obolibrary.org/obo/UBERON_8450002) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006338" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + + - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) + + + +### existence ends during `http://purl.obolibrary.org/obo/RO_0002492` +#### Removed +- [existence ends during](http://purl.obolibrary.org/obo/RO_0002492) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ceases_to_exist_during" + +- [existence ends during](http://purl.obolibrary.org/obo/RO_0002492) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "existence_ends_during" + +- [existence ends during](http://purl.obolibrary.org/obo/RO_0002492) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [existence ends during](http://purl.obolibrary.org/obo/RO_0002492) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://orcid.org/0000-0002-6601-2165" + +- [existence ends during](http://purl.obolibrary.org/obo/RO_0002492) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [existence ends during](http://purl.obolibrary.org/obo/RO_0002492) [id](http://www.geneontology.org/formats/oboInOwl#id) "existence_ends_during" + +- [existence ends during](http://purl.obolibrary.org/obo/RO_0002492) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002492" + + + +### existence ends during or before `http://purl.obolibrary.org/obo/RO_0002497` +#### Removed +- [existence ends during or before](http://purl.obolibrary.org/obo/RO_0002497) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [existence ends during or before](http://purl.obolibrary.org/obo/RO_0002497) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "existence_ends_during_or_before" + +- [existence ends during or before](http://purl.obolibrary.org/obo/RO_0002497) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [existence ends during or before](http://purl.obolibrary.org/obo/RO_0002497) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002497" + +- [existence ends during or before](http://purl.obolibrary.org/obo/RO_0002497) [id](http://www.geneontology.org/formats/oboInOwl#id) "existence_ends_during_or_before" + + + +### existence ends with `http://purl.obolibrary.org/obo/RO_0002493` +#### Removed +- [existence ends with](http://purl.obolibrary.org/obo/RO_0002493) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "existence_ends_with" + +- [existence ends with](http://purl.obolibrary.org/obo/RO_0002493) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [existence ends with](http://purl.obolibrary.org/obo/RO_0002493) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [existence ends with](http://purl.obolibrary.org/obo/RO_0002493) [id](http://www.geneontology.org/formats/oboInOwl#id) "existence_ends_with" + +- [existence ends with](http://purl.obolibrary.org/obo/RO_0002493) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002493" + + + +### existence overlaps `http://purl.obolibrary.org/obo/RO_0002490` +#### Removed +- [existence overlaps](http://purl.obolibrary.org/obo/RO_0002490) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + + + +### existence starts and ends during `http://purl.obolibrary.org/obo/RO_0002491` +#### Removed +- [existence starts and ends during](http://purl.obolibrary.org/obo/RO_0002491) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "existence_starts_and_ends_during" + +- [existence starts and ends during](http://purl.obolibrary.org/obo/RO_0002491) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002491" + +- [existence starts and ends during](http://purl.obolibrary.org/obo/RO_0002491) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [existence starts and ends during](http://purl.obolibrary.org/obo/RO_0002491) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [existence starts and ends during](http://purl.obolibrary.org/obo/RO_0002491) [id](http://www.geneontology.org/formats/oboInOwl#id) "existence_starts_and_ends_during" + + + +### existence starts during `http://purl.obolibrary.org/obo/RO_0002488` +#### Removed +- [existence starts during](http://purl.obolibrary.org/obo/RO_0002488) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002488" + +- [existence starts during](http://purl.obolibrary.org/obo/RO_0002488) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "existence_starts_during" + +- [existence starts during](http://purl.obolibrary.org/obo/RO_0002488) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [existence starts during](http://purl.obolibrary.org/obo/RO_0002488) [id](http://www.geneontology.org/formats/oboInOwl#id) "existence_starts_during" + +- [existence starts during](http://purl.obolibrary.org/obo/RO_0002488) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + + + +### existence starts during or after `http://purl.obolibrary.org/obo/RO_0002496` +#### Removed +- [existence starts during or after](http://purl.obolibrary.org/obo/RO_0002496) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [existence starts during or after](http://purl.obolibrary.org/obo/RO_0002496) [id](http://www.geneontology.org/formats/oboInOwl#id) "existence_starts_during_or_after" + +- [existence starts during or after](http://purl.obolibrary.org/obo/RO_0002496) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "existence_starts_during_or_after" + +- [existence starts during or after](http://purl.obolibrary.org/obo/RO_0002496) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [existence starts during or after](http://purl.obolibrary.org/obo/RO_0002496) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002496" + + + +### existence starts with `http://purl.obolibrary.org/obo/RO_0002489` +#### Removed +- [existence starts with](http://purl.obolibrary.org/obo/RO_0002489) [id](http://www.geneontology.org/formats/oboInOwl#id) "existence_starts_with" + +- [existence starts with](http://purl.obolibrary.org/obo/RO_0002489) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [existence starts with](http://purl.obolibrary.org/obo/RO_0002489) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002489" + +- [existence starts with](http://purl.obolibrary.org/obo/RO_0002489) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "existence_starts_with" + +- [existence starts with](http://purl.obolibrary.org/obo/RO_0002489) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + + + +### exocrine pancreas `http://purl.obolibrary.org/obo/UBERON_0000017` +#### Removed +- [exocrine pancreas](http://purl.obolibrary.org/obo/UBERON_0000017) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The exocrine pancreas is composed of acinar epithelial cells and ductal epithelium that manufacture the proteolytic enzymes and bicarbonate required for digestion.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001249" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [exocrine pancreas](http://purl.obolibrary.org/obo/UBERON_0000017) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D046790" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + +- [exocrine pancreas](http://purl.obolibrary.org/obo/UBERON_0000017) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The part of the pancreas that acts as an exocrine gland, consisting of the pancreatic acini, which produce pancreatic juice and secrete it into the intestine to aid in protein digestion. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/Pancreas" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000048" + +- [exocrine pancreas](http://purl.obolibrary.org/obo/UBERON_0000017) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1016/j.crvi.2007.03.006 Madsen OD, Pancreas phylogeny and ontogeny in relation to a 'pancreatic stem cell'. C.R. Biologies (2007)" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000048" + +#### Added +- [exocrine pancreas](http://purl.obolibrary.org/obo/UBERON_0000017) SubClassOf [digestive system element](http://purl.obolibrary.org/obo/UBERON_0013765) + + +### exocrine pancreas epithelium `http://purl.obolibrary.org/obo/UBERON_0013697` +#### Removed +- [exocrine pancreas epithelium](http://purl.obolibrary.org/obo/UBERON_0013697) SubClassOf [epithelium](http://purl.obolibrary.org/obo/UBERON_0000483) + +#### Added +- [exocrine pancreas epithelium](http://purl.obolibrary.org/obo/UBERON_0013697) SubClassOf [endo-epithelium](http://purl.obolibrary.org/obo/UBERON_0005911) + + +### expand expression to `http://purl.obolibrary.org/obo/IAO_0000424` +#### Removed +- [expand expression to](http://purl.obolibrary.org/obo/IAO_0000424) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "ObjectProperty: RO_0002104 +Label: has plasma membrane part +Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" +"@en + +- [expand expression to](http://purl.obolibrary.org/obo/IAO_0000424) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) "Chris Mungall"@en + +- [expand expression to](http://purl.obolibrary.org/obo/IAO_0000424) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "expand expression to"@en + + + +### expressed in `http://purl.obolibrary.org/obo/RO_0002206` +#### Removed +- [expressed in](http://purl.obolibrary.org/obo/RO_0002206) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" + +- [expressed in](http://purl.obolibrary.org/obo/RO_0002206) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [expressed in](http://purl.obolibrary.org/obo/RO_0002206) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) + + + +### expresses `http://purl.obolibrary.org/obo/RO_0002292` +#### Removed +- [expresses](http://purl.obolibrary.org/obo/RO_0002292) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [expresses](http://purl.obolibrary.org/obo/RO_0002292) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) + + + +### extends_fibers_into `http://purl.obolibrary.org/obo/uberon/core#extends_fibers_into` +#### Removed +- [has soma location](http://purl.obolibrary.org/obo/RO_0002100) o [has synaptic IO in region](http://purl.obolibrary.org/obo/RO_0013001) SubPropertyOf: [extends_fibers_into](http://purl.obolibrary.org/obo/uberon/core#extends_fibers_into) + +- Symmetric: [extends_fibers_into](http://purl.obolibrary.org/obo/uberon/core#extends_fibers_into) + + + +### external acoustic meatus `http://purl.obolibrary.org/obo/UBERON_0001352` +#### Removed +- [external acoustic meatus](http://purl.obolibrary.org/obo/UBERON_0001352) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "tympanic ring, which serves as support for the tympanic membrane, directs invagination of the first pharingeal cleft ectoderm to form the external acoustic meatus (EAM), which provides the outer layer of the membrane[PMID 11237469]" + +- [external acoustic meatus](http://purl.obolibrary.org/obo/UBERON_0001352) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "subdivision of head in FMA." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + +#### Added +- [external acoustic meatus](http://purl.obolibrary.org/obo/UBERON_0001352) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + +- [external acoustic meatus](http://purl.obolibrary.org/obo/UBERON_0001352) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) + + +### external carotid artery `http://purl.obolibrary.org/obo/UBERON_0001070` +#### Removed +- [external carotid artery](http://purl.obolibrary.org/obo/UBERON_0001070) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "not homologous to the external carotid of zebrafish (Goodrich, 1958) - http://zfish.nichd.nih.gov/zfatlas/Intro%20Page/comparative.html; check XAO" + + + +### external cervical os `http://purl.obolibrary.org/obo/UBERON_0013760` +#### Removed +- [external cervical os](http://purl.obolibrary.org/obo/UBERON_0013760) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The external orifice of the uterus (or ostium of uterus, or external os) is a small, depressed, somewhat circular aperture on the rounded extremity of the vaginal portion of the cervix. Through this aperture, the cervical cavity communicates with that of the vagina. The external orifice is bounded by two lips, an anterior and a posterior. The anterior is shorter and thicker, though it projects lower than the posterior because of the slope of the cervix. Normally, both lips are in contact with the posterior vaginal wall. Prior to pregnancy, the external orifice has a rounded shape when viewed through the vaginal canal (as through a speculum). Following parturition, the orifice takes on an appearance more like a transverse slit or is 'H-shaped'[Wikipedia:External_orifice_of_the_uterus]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:External_orifice_of_the_uterus" + + + +### external ear `http://purl.obolibrary.org/obo/UBERON_0001691` +#### Removed +- [external ear](http://purl.obolibrary.org/obo/UBERON_0001691) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The external part of the organ, which consists of an outer portion (external auditory meatus) which leads to the tympanum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000311" + +- [external ear](http://purl.obolibrary.org/obo/UBERON_0001691) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in XAO this includes and is only the tympanum" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "XAO" + +- [external ear](http://purl.obolibrary.org/obo/UBERON_0001691) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Some species, like Amolops tormotus (Feng et al. 2006), have a cavity in front of the tympanic membrane which is considered to be an ear canal and thus an outer ear. (...) The ancestral lineage of amphibians separated from the mammalian lineage, approximately 350 million years ago, in the paleozoic era. Many of the important developments in the auditory systems emerged after the ancestral paths separated (Manley and Clack 2003). This implies that shared features, like the tympanic middle ear, developed independently in different vertebrate lineages.[uncertain][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000311" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1007/s00359-008-0327-1 Schoffelen RLM, Segenhout JM, Van Dijk P, Mechanics of the exceptional anuran ear. Journal of Comparative Physiology A (2008)" + + + +### external ectoderm `http://purl.obolibrary.org/obo/UBERON_0000076` +#### Removed +- [external ectoderm](http://purl.obolibrary.org/obo/UBERON_0000076) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "(or external ectoderm) forms the following structures: Skin Epithelium of the mouth and nasal cavity saliavary glands, and glands of mouth and nasal cavity Enamel - as a side note dentin and dental pulp are formed from ectomesenchyme which is derived from ectoderm Epithelium of pineal and pituitary glands Lens and cornea of the eye Apical ectodermal ridge inducing development of the limb buds of the embryo. Sensory receptors in epidermis" + +- [external ectoderm](http://purl.obolibrary.org/obo/UBERON_0000076) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [neurectoderm](http://purl.obolibrary.org/obo/UBERON_0002346) + +- [external ectoderm](http://purl.obolibrary.org/obo/UBERON_0000076) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006242" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + + - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) + + + +### external female genitalia `http://purl.obolibrary.org/obo/UBERON_0005056` +#### Removed +- [external female genitalia](http://purl.obolibrary.org/obo/UBERON_0005056) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "in eutherians, this is known as the vulva in and composed of the mons pubis, the labia majora and minora, the clitoris, the vestibule of the vagina and its glands, and the opening of the urethra and of the vagina [MP:0003126]" + + + +### external integument structure `http://purl.obolibrary.org/obo/UBERON_3000961` +#### Removed +- [external integument structure](http://purl.obolibrary.org/obo/UBERON_3000961) [UBPROP_0000004](http://purl.obolibrary.org/obo/UBPROP_0000004) "This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://purl.obolibrary.org/obo/aao.owl" + + + +### external naris `http://purl.obolibrary.org/obo/UBERON_0005928` +#### Removed +- [external naris](http://purl.obolibrary.org/obo/UBERON_0005928) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Fish have two pairs of external nostrils." + +- [external naris](http://purl.obolibrary.org/obo/UBERON_0005928) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In a tetrapod, the nasal sac has an external naris (homologous with the anterior naris of the fish) (...).[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000544" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.257 and Figure 7.27" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + +- [external naris](http://purl.obolibrary.org/obo/UBERON_0005928) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Hole on the nasal capsule that connects the nasal cavity with the exterior.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000024" + +- [external naris](http://purl.obolibrary.org/obo/UBERON_0005928) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: subclass nasal opening (AAO:0000316)[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000024" + +#### Added +- [external naris](http://purl.obolibrary.org/obo/UBERON_0005928) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### external nose `http://purl.obolibrary.org/obo/UBERON_0007827` +#### Removed +- [external nose](http://purl.obolibrary.org/obo/UBERON_0007827) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Subdivision of face, the exterior of the nose, which consists of a root, dorsum, tip, columella, and right and left alae[FMA:59515]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:59515" + +#### Added +- [external nose](http://purl.obolibrary.org/obo/UBERON_0007827) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### external_class `http://www.geneontology.org/formats/oboInOwl#external_class` +#### Removed +- AnnotationProperty: [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) + + + +### external_class_label `http://www.geneontology.org/formats/oboInOwl#external_class_label` +#### Removed +- AnnotationProperty: [external_class_label](http://www.geneontology.org/formats/oboInOwl#external_class_label) + + + +### external_ontology `http://www.geneontology.org/formats/oboInOwl#external_ontology` +#### Removed +- AnnotationProperty: [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) + + + +### extraembryonic membrane `http://purl.obolibrary.org/obo/UBERON_0005631` +#### Removed +- [extraembryonic membrane](http://purl.obolibrary.org/obo/UBERON_0005631) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "stuctures homologous to the four extraembryonic membranes appear in mammals [ISBN:0073040584 (Vertebrates, Kardong)]" + +- [extraembryonic membrane](http://purl.obolibrary.org/obo/UBERON_0005631) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "EHDAA2 is a mereological sum." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EHDAA2" + +- [extraembryonic membrane](http://purl.obolibrary.org/obo/UBERON_0005631) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D005321" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + + + +### extraembryonic structure `http://purl.obolibrary.org/obo/UBERON_0000478` +#### Removed +- [extraembryonic structure](http://purl.obolibrary.org/obo/UBERON_0000478) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005835" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + + +### extraglomerular mesangium `http://purl.obolibrary.org/obo/UBERON_0002321` + +#### Added +- [extraglomerular mesangium](http://purl.obolibrary.org/obo/UBERON_0002321) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### extrahepatic bile duct `http://purl.obolibrary.org/obo/UBERON_0003703` +#### Removed +- [extrahepatic bile duct](http://purl.obolibrary.org/obo/UBERON_0003703) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [liver](http://purl.obolibrary.org/obo/UBERON_0002107) + + + +### extrinsic muscle of tongue `http://purl.obolibrary.org/obo/UBERON_0001575` +#### Removed +- [extrinsic muscle of tongue](http://purl.obolibrary.org/obo/UBERON_0001575) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1002/dvdy.20587 Kusakabe R, Kuratani S, Evolution and developmental patterning of the vertebrate skeletal muscles: perspectives from the lamprey. Developmental Dynamics (2005)" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000825" + +- [extrinsic muscle of tongue](http://purl.obolibrary.org/obo/UBERON_0001575) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "main functions are altering the tongue's position allowing for protrusion, retraction, and side-to-side movement" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" + +- [extrinsic muscle of tongue](http://purl.obolibrary.org/obo/UBERON_0001575) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "All intrinsic and extrinsic muscles of the tongue are supplied by the hypoglossal nerve (CN XII), except for one of the extrinsic muscles, palatoglossus, which is innervated by the Vagus nerve CN X of the pharyngeal plexus." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" + +- [extrinsic muscle of tongue](http://purl.obolibrary.org/obo/UBERON_0001575) SubClassOf [innervated_by](http://purl.obolibrary.org/obo/RO_0002005) some [hypoglossal nerve](http://purl.obolibrary.org/obo/UBERON_0001650) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "check palatoglossus" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia" + +#### Added +- [extrinsic muscle of tongue](http://purl.obolibrary.org/obo/UBERON_0001575) SubClassOf [innervated_by](http://purl.obolibrary.org/obo/RO_0002005) some [hypoglossal nerve](http://purl.obolibrary.org/obo/UBERON_0001650) + + +### eye `http://purl.obolibrary.org/obo/UBERON_0000970` +#### Removed +- [eye](http://purl.obolibrary.org/obo/UBERON_0000970) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "This class encompasses a variety of light-detecting structures from different phyla with no implication of homology, from the compound insect eye to the vertebrate camera-type eye (distinct classes are provided for each)" + +- [eye](http://purl.obolibrary.org/obo/UBERON_0000970) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005162" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + +- [eye](http://purl.obolibrary.org/obo/UBERON_0000970) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "Note that whilst this is classified as an organ, it is in fact more of a unit composed of different structures: in Drosophila, it includes the interommatidial bristle as a part; we consider here the vertebrate eye to include the eyeball/eye proper as a part, with the eye having as parts (when present): eyelids, conjuctiva," + +- [eye](http://purl.obolibrary.org/obo/UBERON_0000970) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "ocular" + +- [eye](http://purl.obolibrary.org/obo/UBERON_0000970) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "optic" + + + +### eye epithelium `http://purl.obolibrary.org/obo/UBERON_0015808` + +#### Added +- [eye epithelium](http://purl.obolibrary.org/obo/UBERON_0015808) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) + + +### eye mesenchyme `http://purl.obolibrary.org/obo/UBERON_0003314` + +#### Added +- [eye mesenchyme](http://purl.obolibrary.org/obo/UBERON_0003314) SubClassOf [mesenchyme derived from head neural crest](http://purl.obolibrary.org/obo/UBERON_0007213) + + +### eye muscle `http://purl.obolibrary.org/obo/UBERON_0004277` + +#### Added +- [eye muscle](http://purl.obolibrary.org/obo/UBERON_0004277) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### eye primordium `http://purl.obolibrary.org/obo/UBERON_0003071` +#### Removed +- [eye primordium](http://purl.obolibrary.org/obo/UBERON_0003071) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "TODO - check that GO's optic placode is the same as ZFA's eye primordium; we may want to have separate term for ocular primordium precursor. XAO has both optic field and eye primordium." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "GO" + +#### Added +- [eye primordium](http://purl.obolibrary.org/obo/UBERON_0003071) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) + + +### eye trabecular meshwork `http://purl.obolibrary.org/obo/UBERON_0005969` + +#### Added +- [eye trabecular meshwork](http://purl.obolibrary.org/obo/UBERON_0005969) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### eyeball of camera-type eye `http://purl.obolibrary.org/obo/UBERON_0010230` +#### Removed +- [eyeball of camera-type eye](http://purl.obolibrary.org/obo/UBERON_0010230) [UBPROP_0000202](http://purl.obolibrary.org/obo/UBPROP_0000202) [FMA_264089](http://purl.obolibrary.org/obo/FMA_264089) + +- [eyeball of camera-type eye](http://purl.obolibrary.org/obo/UBERON_0010230) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "See notes for camera-type eye" + +#### Added +- [eyeball of camera-type eye](http://purl.obolibrary.org/obo/UBERON_0010230) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### eyelid `http://purl.obolibrary.org/obo/UBERON_0001711` +#### Removed +- [eyelid](http://purl.obolibrary.org/obo/UBERON_0001711) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "palpebral" + +- [eyelid](http://purl.obolibrary.org/obo/UBERON_0001711) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In humans the upper and lower eyelid consists of the following layers, starting anteriorly: (1) skin, (2) a layer of subcutaneous connective tissue, (3) a layer of striated muscle fibres of the orbicularis muscle, (4) a layer of submuscular connective tissue, (5) a fibrous layer, including the tarsal plates, (6) a layer of smooth muscle, (7) the palpebral conjunctiva." + +- [eyelid](http://purl.obolibrary.org/obo/UBERON_0001711) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "Consider adding 'eye surface', like MA" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" + +- [eyelid](http://purl.obolibrary.org/obo/UBERON_0001711) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "blepharic" + +- [eyelid](http://purl.obolibrary.org/obo/UBERON_0001711) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA divides this into skin, fascia, conjunctiva" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + +- [eyelid](http://purl.obolibrary.org/obo/UBERON_0001711) [UBPROP_0000202](http://purl.obolibrary.org/obo/UBPROP_0000202) [FMA_75178](http://purl.obolibrary.org/obo/FMA_75178) + +#### Added +- [eyelid](http://purl.obolibrary.org/obo/UBERON_0001711) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### eyelid blood vessel `http://purl.obolibrary.org/obo/UBERON_0003510` + +#### Added +- [eyelid blood vessel](http://purl.obolibrary.org/obo/UBERON_0003510) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### eyelid connective tissue `http://purl.obolibrary.org/obo/UBERON_0003581` + +#### Added +- [eyelid connective tissue](http://purl.obolibrary.org/obo/UBERON_0003581) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) + + +### eyelid gland `http://purl.obolibrary.org/obo/UBERON_0013229` + +#### Added +- [eyelid gland](http://purl.obolibrary.org/obo/UBERON_0013229) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### eyelid muscle `http://purl.obolibrary.org/obo/UBERON_0003660` +#### Removed +- [eyelid muscle](http://purl.obolibrary.org/obo/UBERON_0003660) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The muscle in the orbit of the eye that lifts the upper eyelid[ncithesaurus:Eyelid_Muscle]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ncithesaurus:Eyelid_Muscle" + + + +### eyelid subcutaneous connective tissue `http://purl.obolibrary.org/obo/UBERON_0009648` + +#### Added +- [eyelid subcutaneous connective tissue](http://purl.obolibrary.org/obo/UBERON_0009648) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### fMet-Leu-Phe receptor `http://purl.obolibrary.org/obo/PR_000001580` +#### Removed +- [fMet-Leu-Phe receptor](http://purl.obolibrary.org/obo/PR_000001580) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [fMet-Leu-Phe receptor (human)](http://purl.obolibrary.org/obo/PR_P21462) + + + +### face `http://purl.obolibrary.org/obo/UBERON_0001456` +#### Removed +- [face](http://purl.obolibrary.org/obo/UBERON_0001456) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "The face develops from outward growth of tissue located rostral to the cranium & pharynx. The lower jaw and most of the upper jaw are formed by growth of the first pharyngeal (branchial) arch. The upper incisor region and the nose and forehead (frontal region) are formed from tissue located rostral to the neural tube (frontonasal prominence)" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "vanat.cvm.umn.edu/TFFlectPDFs/LectFaceDevelop.pdf" + +- [face](http://purl.obolibrary.org/obo/UBERON_0001456) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:24728" + +- [face](http://purl.obolibrary.org/obo/UBERON_0001456) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The area that extends from the median ocellus to the oral foramen[HAO]." + - [taxon](http://www.geneontology.org/formats/oboInOwl#taxon) "NCBITaxon:7399" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "HAO:0000316" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://api.hymao.org/api/ref/67791" + +- [face](http://purl.obolibrary.org/obo/UBERON_0001456) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "facial" + + + +### facial bone `http://purl.obolibrary.org/obo/UBERON_0003462` +#### Removed +- [facial bone](http://purl.obolibrary.org/obo/UBERON_0003462) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D005147" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + +#### Added +- [facial bone](http://purl.obolibrary.org/obo/UBERON_0003462) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) + + +### facial lymph node `http://purl.obolibrary.org/obo/UBERON_0015871` +#### Removed +- [facial lymph node](http://purl.obolibrary.org/obo/UBERON_0015871) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In humans, these comprise three groups: (a) infraorbital or maxillary, scattered over the infraorbital region from the groove between the nose and cheek to the zygomatic arch; (b) buccinator, one or more placed on the Buccinator opposite the angle of the mouth; (c) supramandibular, on the outer surface of the mandible, in front of the Masseter and in contact with the external maxillary artery and anterior facial vein." + + + +### facial nerve `http://purl.obolibrary.org/obo/UBERON_0001647` +#### Removed +- [facial nerve](http://purl.obolibrary.org/obo/UBERON_0001647) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000706" + +- [facial nerve](http://purl.obolibrary.org/obo/UBERON_0001647) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Slender nerve composed of branchiomotor and visceral efferent fibers innervating the mouth and various muscles within the jaw. Sensory components innervate the bucccal roof and somatomotor components innervate the depressor musculature and muscle interhyoideus.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:DSM" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010472" + + + +### facial nucleus `http://purl.obolibrary.org/obo/UBERON_0000127` +#### Removed +- [facial nucleus](http://purl.obolibrary.org/obo/UBERON_0000127) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA has 3 subclasses - left, right and motor nucleus of facial nerve, but no defs. It's not clear how facial nucleus is distinct from facial motor nucleus." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + +- [facial nucleus](http://purl.obolibrary.org/obo/UBERON_0000127) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + +- [facial nucleus](http://purl.obolibrary.org/obo/UBERON_0000127) SubClassOf [immediate transformation of](http://purl.obolibrary.org/obo/RO_0002495) some [future facial nucleus](http://purl.obolibrary.org/obo/UBERON_0010123) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" + +#### Added +- [facial nucleus](http://purl.obolibrary.org/obo/UBERON_0000127) SubClassOf [immediate transformation of](http://purl.obolibrary.org/obo/RO_0002495) some [future facial nucleus](http://purl.obolibrary.org/obo/UBERON_0010123) + + +### facial suture `http://purl.obolibrary.org/obo/UBERON_0009199` +#### Removed +- [facial suture](http://purl.obolibrary.org/obo/UBERON_0009199) SubClassOf [connects](http://purl.obolibrary.org/obo/RO_0002176) some [facial bone](http://purl.obolibrary.org/obo/UBERON_0003462) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "between two adjacent facial bones" + +#### Added +- [facial suture](http://purl.obolibrary.org/obo/UBERON_0009199) SubClassOf [connects](http://purl.obolibrary.org/obo/RO_0002176) some [facial bone](http://purl.obolibrary.org/obo/UBERON_0003462) + + +### facial vein `http://purl.obolibrary.org/obo/UBERON_0001653` +#### Removed +- [facial vein](http://purl.obolibrary.org/obo/UBERON_0001653) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "MA and NCITA also has 'anterior facial vein'" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" + +- [facial vein](http://purl.obolibrary.org/obo/UBERON_0001653) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Vein which collects blood from muscles of the head and drains into the external jugular vein.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010513" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + + + +### facio-acoustic VII-VIII preganglion complex `http://purl.obolibrary.org/obo/UBERON_0006232` +#### Removed +- [facio-acoustic VII-VIII preganglion complex](http://purl.obolibrary.org/obo/UBERON_0006232) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "VHOG:0000715" + + + +### facio-acoustic neural crest `http://purl.obolibrary.org/obo/UBERON_0005565` +#### Removed +- [facio-acoustic neural crest](http://purl.obolibrary.org/obo/UBERON_0005565) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000268" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" + +- [facio-acoustic neural crest](http://purl.obolibrary.org/obo/UBERON_0005565) SubClassOf [mesenchyme derived from neural crest](http://purl.obolibrary.org/obo/UBERON_0014387) + + + +### failed exploratory term `http://purl.obolibrary.org/obo/IAO_0000103` +#### Removed +- [failed exploratory term](http://purl.obolibrary.org/obo/IAO_0000103) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "failed exploratory term"@en + +- [failed exploratory term](http://purl.obolibrary.org/obo/IAO_0000103) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) "Person:Alan Ruttenberg"@en + + + +### falciform ligament `http://purl.obolibrary.org/obo/UBERON_0001247` +#### Removed +- [falciform ligament](http://purl.obolibrary.org/obo/UBERON_0001247) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in FMA this is a subclass of mesentery. In MA it is a subclass of ligament, we infer and assert this is a nonskeletal ligament" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + +#### Added +- [falciform ligament](http://purl.obolibrary.org/obo/UBERON_0001247) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) + + +### fallopian tube `http://purl.obolibrary.org/obo/UBERON_0003889` +#### Removed +- [fallopian tube](http://purl.obolibrary.org/obo/UBERON_0003889) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:18984" + +- [fallopian tube](http://purl.obolibrary.org/obo/UBERON_0003889) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Homologous to appendix testis" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Talk:Fallopian_tube#Homology" + + + +### fasciculates with `http://purl.obolibrary.org/obo/RO_0002101` +#### Removed +- [fasciculates with](http://purl.obolibrary.org/obo/RO_0002101) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-7073-9172](https://orcid.org/0000-0002-7073-9172) + +- [fasciculates with](http://purl.obolibrary.org/obo/RO_0002101) [RO_0001900](http://purl.obolibrary.org/obo/RO_0001900) [RO_0001901](http://purl.obolibrary.org/obo/RO_0001901) + +- [fasciculates with](http://purl.obolibrary.org/obo/RO_0002101) [IAO_0000426](http://purl.obolibrary.org/obo/IAO_0000426) "(forall (?x ?y) + (iff + (fasciculates_with ?x ?y) + (exists (?nps ?npbs) + (and + ("neuron ; CL_0000540" ?x) + ("neuron projection bundle ; CARO_0001001" ?y) + ("neuron projection segment ; CARO_0001502" ?nps) + ("neuron projection bundle segment ; CARO_0001500' " ?npbs) + (part_of ?npbs ?y) + (part_of ?nps ?x) + (part_of ?nps ?npbs) + (forall (?npbss) + (if + (and + ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) + (part_of ?npbss ?npbs) + ) + (overlaps ?nps ?npbss) + ))))))" + +- [fasciculates with](http://purl.obolibrary.org/obo/RO_0002101) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "fasciculates with" + +- [fasciculates with](http://purl.obolibrary.org/obo/RO_0002101) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) + +- [fasciculates with](http://purl.obolibrary.org/obo/RO_0002101) [citesAsAuthority](http://purl.org/spar/cito/citesAsAuthority) [22402613](http://www.ncbi.nlm.nih.gov/pubmed/22402613) + + + +### feces `http://purl.obolibrary.org/obo/UBERON_0001988` +#### Removed +- [feces](http://purl.obolibrary.org/obo/UBERON_0001988) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Excretion in semisolid state processed by the intestine.[FMA]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:64183" + +- [feces](http://purl.obolibrary.org/obo/UBERON_0001988) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "fecal" + + + +### female organism `http://purl.obolibrary.org/obo/UBERON_0003100` +#### Removed +- [female organism](http://purl.obolibrary.org/obo/UBERON_0003100) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [male organism](http://purl.obolibrary.org/obo/UBERON_0003101) + +- [female organism](http://purl.obolibrary.org/obo/UBERON_0003100) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007011" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + + +### female reproductive system `http://purl.obolibrary.org/obo/UBERON_0000474` +#### Removed +- [female reproductive system](http://purl.obolibrary.org/obo/UBERON_0000474) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0792383369 Lombardi J, Comparative vertebrate reproduction (1998) p.43" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000726" + +- [female reproductive system](http://purl.obolibrary.org/obo/UBERON_0000474) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004864" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + + +### female urethral meatus `http://purl.obolibrary.org/obo/UBERON_0006565` +#### Removed +- [female urethral meatus](http://purl.obolibrary.org/obo/UBERON_0006565) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The external urethral orifice (urinary meatus) is the external opening of the urethra, from which urine is ejected during urination. It is placed about 2.5 cm behind the glans clitoridis and immediately in front of that of the vagina; it usually assumes the form of a short, sagittal cleft with slightly raised margins. To its left and right are the openings of the Skene's ducts." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:External_urethral_orifice_(female)" + + + +### femoral artery `http://purl.obolibrary.org/obo/UBERON_0002060` +#### Removed +- [femoral artery](http://purl.obolibrary.org/obo/UBERON_0002060) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Artery which supplies blood via branches to the hindlimbs.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010222" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + + + +### femoral vein `http://purl.obolibrary.org/obo/UBERON_0001361` +#### Removed +- [femoral vein](http://purl.obolibrary.org/obo/UBERON_0001361) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Either of the primary veins in the hindlimbs which collect blood from the hindlimb region.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010237" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + + + +### femur `http://purl.obolibrary.org/obo/UBERON_0000981` +#### Removed +- [femur](http://purl.obolibrary.org/obo/UBERON_0000981) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001159" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268" + +- [femur](http://purl.obolibrary.org/obo/UBERON_0000981) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "femoral" + +- [femur](http://purl.obolibrary.org/obo/UBERON_0000981) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Endochondral longbone connecting the pelvic girdle with posterior zeugopodium.[VSAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "VSAO:NI" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000186" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" + +- [femur](http://purl.obolibrary.org/obo/UBERON_0000981) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Paired, elongate, cylindrical bones of endochondral origin that form the thighs, extending from the pelvic girdles to the knees.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000889" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + +- [femur](http://purl.obolibrary.org/obo/UBERON_0000981) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [femur cartilage element](http://purl.obolibrary.org/obo/UBERON_0010129) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" + +#### Added +- [femur](http://purl.obolibrary.org/obo/UBERON_0000981) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [femur cartilage element](http://purl.obolibrary.org/obo/UBERON_0010129) + + +### fenestrated capillary `http://purl.obolibrary.org/obo/UBERON_2005260` +#### Removed +- [fenestrated capillary](http://purl.obolibrary.org/obo/UBERON_2005260) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Blood vessel endothelium that has pores that allow passage small molecules and proteins[ZFA]." + + + +### fibroblast growth factor 8 `http://purl.obolibrary.org/obo/PR_000007499` +#### Removed +- [fibroblast growth factor 8](http://purl.obolibrary.org/obo/PR_000007499) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [fibroblast growth factor 8 (human)](http://purl.obolibrary.org/obo/PR_P55075) + + + +### fibroblast neural crest derived `http://purl.obolibrary.org/obo/CL_0000005` +#### Removed +- [fibroblast neural crest derived](http://purl.obolibrary.org/obo/CL_0000005) [label](http://www.w3.org/2000/01/rdf-schema#label) "fibroblast neural crest derived" + +- [fibroblast neural crest derived](http://purl.obolibrary.org/obo/CL_0000005) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any fibroblast that is deriived from the neural crest." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://orcid.org/0000-0001-5208-3432" + +#### Added +- [fibroblast neural crest derived](http://purl.obolibrary.org/obo/CL_0000005) [label](http://www.w3.org/2000/01/rdf-schema#label) "neural crest derived fibroblast" + +- [fibroblast neural crest derived](http://purl.obolibrary.org/obo/CL_0000005) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any fibroblast that is derived from the neural crest." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://orcid.org/0000-0001-5208-3432" + +- [fibroblast neural crest derived](http://purl.obolibrary.org/obo/CL_0000005) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "fibroblast neural crest derived" + + +### fibrocartilage `http://purl.obolibrary.org/obo/UBERON_0001995` +#### Removed +- [fibrocartilage](http://purl.obolibrary.org/obo/UBERON_0001995) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Cartilage tissue intermediate between hyaline cartilage and dense connective tissue; contains of abundant collagen fibers; chondrocytes often arranged in columns.[VSAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000103" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PSPUB:0000170" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" + +- [fibrocartilage](http://purl.obolibrary.org/obo/UBERON_0001995) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "fibrocartilaginous" + +- [fibrocartilage](http://purl.obolibrary.org/obo/UBERON_0001995) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Cartilage (tissue) which consists of chondrocytes and collagen, the intercellular matrix of which is an amorphous gel without a well-defined perichondrium[FMA:64784]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:64784" + +- [fibrocartilage](http://purl.obolibrary.org/obo/UBERON_0001995) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D051445" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + +- [fibrocartilage](http://purl.obolibrary.org/obo/UBERON_0001995) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A mixture of white fibrous tissue and cartilaginous tissue in various proportions. It owes its flexibility and toughness to the former of these constituents, and its elasticity to the latter. It is the only type of cartilage that contains type I collagen in addition to the normal type I[Wikipedia:Fibrocartilage]I" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Fibrocartilage" + + + +### fibrous joint `http://purl.obolibrary.org/obo/UBERON_0002209` +#### Removed +- [fibrous joint](http://purl.obolibrary.org/obo/UBERON_0002209) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A joint where fibrous tissue such as ligament connects two calcified tissues.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005156" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + + +### fibrous pericardium `http://purl.obolibrary.org/obo/UBERON_0002359` +#### Removed +- [fibrous pericardium](http://purl.obolibrary.org/obo/UBERON_0002359) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "most superficial part of pericardium; continuous with the outer adventitial layer of the neighboring great blood vessels. [Wikipedia:Pericardium]" + + + +### fibrous ring of heart `http://purl.obolibrary.org/obo/UBERON_0006008` + +#### Added +- [fibrous ring of heart](http://purl.obolibrary.org/obo/UBERON_0006008) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### fibula `http://purl.obolibrary.org/obo/UBERON_0001446` +#### Removed +- [fibula](http://purl.obolibrary.org/obo/UBERON_0001446) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "One of the two long bones of endochondral origin of the hind-epipodium; it is a rather more slender bone than the tibia but of about the same length.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000891" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + +- [fibula](http://purl.obolibrary.org/obo/UBERON_0001446) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "fibular" + + + +### flat bone `http://purl.obolibrary.org/obo/UBERON_0010428` +#### Removed +- [flat bone](http://purl.obolibrary.org/obo/UBERON_0010428) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "Flat bones are those bones which are found where the principal requirement is either extensive protection or the provision of broad surfaces for muscular attachment" + +- [flat bone](http://purl.obolibrary.org/obo/UBERON_0010428) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In an adult mammal, most red blood cells are formed in flat bones" + + + +### flexible `http://purl.obolibrary.org/obo/PATO_0001544` +#### Removed +- [flexible](http://purl.obolibrary.org/obo/PATO_0001544) [RO_0002604](http://purl.obolibrary.org/obo/RO_0002604) [PATO_0001545](http://purl.obolibrary.org/obo/PATO_0001545) + + + +### follicular fluid `http://purl.obolibrary.org/obo/UBERON_0000038` +#### Removed +- [follicular fluid](http://purl.obolibrary.org/obo/UBERON_0000038) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Generally, larger species such as ovine, equine, porcine, human, and bovine have larger follicles, with the fluid comprising a substantial proportion of the volume of the follicles at ovulation (estimated at >95% in bovine [3]). Smaller species such as rats and mice have smaller follicles with fractionally less follicular fluid[20164441]" + +- [follicular fluid](http://purl.obolibrary.org/obo/UBERON_0000038) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "The follicular fluid contains sex steroids, glycoprotein hormones, plasma proteins, mucopolysaccharides, and enzymes and is rich in hyaluronic acid." + + + +### food storage organ `http://purl.obolibrary.org/obo/UBERON_0010039` +#### Removed +- [food storage organ](http://purl.obolibrary.org/obo/UBERON_0010039) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "This is a very broad functionally defined grouping class that collects disparate structures from insects to vertebrates" + + + +### foramen magnum `http://purl.obolibrary.org/obo/UBERON_0003687` +#### Removed +- [foramen magnum](http://purl.obolibrary.org/obo/UBERON_0003687) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Foramen in the occipital region of neurocranium to allow passage of spinal cord.[TAO]" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TAO:wd" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0002045" + +- [foramen magnum](http://purl.obolibrary.org/obo/UBERON_0003687) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006035" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + + - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) + + + +### foramen rotundum `http://purl.obolibrary.org/obo/UBERON_0005446` +#### Removed +- [foramen rotundum](http://purl.obolibrary.org/obo/UBERON_0005446) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A circular hole in the sphenoid bone that connects the middle cranial fossa and the pterygopalatine fossa.vity. [Wikipedia:Foramen_rotundum][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001543" + +- [foramen rotundum](http://purl.obolibrary.org/obo/UBERON_0005446) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "todo - check placement of AAO class" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "AAO" + +- [foramen rotundum](http://purl.obolibrary.org/obo/UBERON_0005446) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "It is suggested that the mammalian lamina ascendens arose from an upgrowth of the root of the quadrate ramus of the epipterygoid in cynodonts, separating foramen rotundum from foramen ovale.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:1018003 Presley R, Steel FLD, On the homology of the alisphenoid. Journal of Anatomy (1976)" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001543" + +#### Added +- [foramen rotundum](http://purl.obolibrary.org/obo/UBERON_0005446) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) + + +### forebrain `http://purl.obolibrary.org/obo/UBERON_0001890` +#### Removed +- [forebrain](http://purl.obolibrary.org/obo/UBERON_0001890) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In craniate embryos, neural expression of Distal-less-related genes is exclusively in the forebrain (...). Because the major neural expression domain of amphioxus AmphiDll is in the anterior three-fourths of the cerebral vesicle, we suggest that this region of the neural tube is homologous to parts of the craniate forebrain. This conclusion is strongly supported by three-dimensional, computer-assisted reconstruction of the neural tube of amphioxus based on serial transmission electron microscopy. At the neuroanatomical level, a number of detailed homologies are indicated between the anterior three-fourths of the amphioxus cerebral vesicle and the diencephalic region of the craniate forebrain. If one assumes that the amphioxus condition fairly represents the nervous system of the proximate ancestor of the craniates, one can suggest that they evolved from a creature that had the beginnings of a forebrain.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:8787764 Holland ND, Panganiban G, Henyey EL, Holland LZ, Sequence and developmental expression of AmphiDll, an amphioxus Distal-less gene transcribed in the ectoderm, epidermis and nervous system: insights into evolution of craniate forebrain and neural crest. Development (1996)" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000383" + +- [forebrain](http://purl.obolibrary.org/obo/UBERON_0001890) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "prosencephalic" + +- [forebrain](http://purl.obolibrary.org/obo/UBERON_0001890) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Most anterior of the three regions of the brain consisting of the telencephalon and diencephalon.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010147" + +- [forebrain](http://purl.obolibrary.org/obo/UBERON_0001890) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The most anterior region the brain including both the telencephalon and diencephalon. Kimmel et al, 1995.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000109" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [forebrain](http://purl.obolibrary.org/obo/UBERON_0001890) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: develops_from forebrain neural tube (TAO:0007041)[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000109" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [forebrain](http://purl.obolibrary.org/obo/UBERON_0001890) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + +- [forebrain](http://purl.obolibrary.org/obo/UBERON_0001890) SubClassOf [immediate transformation of](http://purl.obolibrary.org/obo/RO_0002495) some [future forebrain](http://purl.obolibrary.org/obo/UBERON_0006240) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" + +#### Added +- [forebrain](http://purl.obolibrary.org/obo/UBERON_0001890) SubClassOf [immediate transformation of](http://purl.obolibrary.org/obo/RO_0002495) some [future forebrain](http://purl.obolibrary.org/obo/UBERON_0006240) + + +### forebrain arachnoid mater `http://purl.obolibrary.org/obo/UBERON_0003556` +#### Removed +- [forebrain arachnoid mater](http://purl.obolibrary.org/obo/UBERON_0003556) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:17775" + +- [forebrain arachnoid mater](http://purl.obolibrary.org/obo/UBERON_0003556) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:17765" + + + +### forebrain dura mater `http://purl.obolibrary.org/obo/UBERON_0003561` +#### Removed +- [forebrain dura mater](http://purl.obolibrary.org/obo/UBERON_0003561) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:17766" + + + +### forebrain meninges `http://purl.obolibrary.org/obo/UBERON_0003548` +#### Removed +- [forebrain meninges](http://purl.obolibrary.org/obo/UBERON_0003548) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:17764" + +- [forebrain meninges](http://purl.obolibrary.org/obo/UBERON_0003548) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:17774" + + + +### forebrain pia mater `http://purl.obolibrary.org/obo/UBERON_0003550` +#### Removed +- [forebrain pia mater](http://purl.obolibrary.org/obo/UBERON_0003550) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:17777" + +- [forebrain pia mater](http://purl.obolibrary.org/obo/UBERON_0003550) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:17767" + + + +### forebrain-midbrain boundary `http://purl.obolibrary.org/obo/UBERON_0005075` +#### Removed +- [forebrain-midbrain boundary](http://purl.obolibrary.org/obo/UBERON_0005075) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The boundary between the diencephalon and the mesencephalon.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001367" + +- [forebrain-midbrain boundary](http://purl.obolibrary.org/obo/UBERON_0005075) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: develops_from forebrain midbrain boundary neural tube (TAO:0007040)[TAO]" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001367" + +- [forebrain-midbrain boundary](http://purl.obolibrary.org/obo/UBERON_0005075) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [presumptive forebrain midbrain boundary](http://purl.obolibrary.org/obo/UBERON_0007288) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" + +#### Added +- [forebrain-midbrain boundary](http://purl.obolibrary.org/obo/UBERON_0005075) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + +- [forebrain-midbrain boundary](http://purl.obolibrary.org/obo/UBERON_0005075) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [presumptive forebrain midbrain boundary](http://purl.obolibrary.org/obo/UBERON_0007288) + + +### foregut `http://purl.obolibrary.org/obo/UBERON_0001041` +#### Removed +- [foregut](http://purl.obolibrary.org/obo/UBERON_0001041) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The anterior portion of the primitive digestive tube of the embryo that lies cephalic to the junction of the yolk stalk, consists of endodermal tissue, and gives rise to the the pharynx, lower respiratory system, esophagus, stomach, duodenum proximal to the biliary tract, liver, pancreas, biliary tract, and gall bladder." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "MP:0000474" + +- [foregut](http://purl.obolibrary.org/obo/UBERON_0001041) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000285" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11" + +- [foregut](http://purl.obolibrary.org/obo/UBERON_0001041) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005379" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + + +### foregut-midgut junction `http://purl.obolibrary.org/obo/UBERON_0006235` +#### Removed +- [foregut-midgut junction](http://purl.obolibrary.org/obo/UBERON_0006235) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000291" + + + +### forelimb `http://purl.obolibrary.org/obo/UBERON_0002102` +#### Removed +- [forelimb](http://purl.obolibrary.org/obo/UBERON_0002102) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Upper limb, which connects the manus with the pectoral girdle.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000205" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + +- [forelimb](http://purl.obolibrary.org/obo/UBERON_0002102) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "note that this corresponds to FMA:'free upper limb' (a limb segment), NOT FMA:'upper limb'. Both MA and FMA consider shoulder (and shoulder bones) part of upper limb" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + +- [forelimb](http://purl.obolibrary.org/obo/UBERON_0002102) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "Note distinction between arm and forelimb. hand is part of forelimb, but not part of arm" + +- [forelimb](http://purl.obolibrary.org/obo/UBERON_0002102) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [hindlimb](http://purl.obolibrary.org/obo/UBERON_0002103) + + + +### forelimb joint `http://purl.obolibrary.org/obo/UBERON_0003839` +#### Removed +- [forelimb joint](http://purl.obolibrary.org/obo/UBERON_0003839) [UBPROP_0000202](http://purl.obolibrary.org/obo/UBPROP_0000202) [FMA_71344](http://purl.obolibrary.org/obo/FMA_71344) + + + +### forelimb muscle `http://purl.obolibrary.org/obo/UBERON_0003662` +#### Removed +- [forelimb muscle](http://purl.obolibrary.org/obo/UBERON_0003662) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA and MA class actually refer to muscles of entire pectoral complex" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + + + +### forelimb skeleton `http://purl.obolibrary.org/obo/UBERON_0001440` +#### Removed +- [forelimb skeleton](http://purl.obolibrary.org/obo/UBERON_0001440) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001256" + +- [forelimb skeleton](http://purl.obolibrary.org/obo/UBERON_0001440) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000202" + +- [forelimb skeleton](http://purl.obolibrary.org/obo/UBERON_0001440) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Skeletal structure of the paired, anterior appendages.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000202" + +- [forelimb skeleton](http://purl.obolibrary.org/obo/UBERON_0001440) [RO_0002475](http://purl.obolibrary.org/obo/RO_0002475) [hindlimb skeleton](http://purl.obolibrary.org/obo/UBERON_0001441) + + + +### forelimb stylopod `http://purl.obolibrary.org/obo/UBERON_0003822` +#### Removed +- [forelimb stylopod](http://purl.obolibrary.org/obo/UBERON_0003822) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Segment of the hindleg corresponding to the humerus.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000887" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + +- [forelimb stylopod](http://purl.obolibrary.org/obo/UBERON_0003822) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "anatomical usage, the term arm refers specifically to the segment between the shoulder and the elbow, while the segment between the elbow and wrist is the forearm. However, in common, literary, and historical usage, arm refers to the entire upper limb from shoulder to wrist. FMA uses the term Arm for this class, so we place it here. Naming conventions for pod terms under discussion within phenoscape group." + +- [forelimb stylopod](http://purl.obolibrary.org/obo/UBERON_0003822) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000343" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268" + + + +### forelimb stylopod muscle `http://purl.obolibrary.org/obo/UBERON_0004255` +#### Removed +- [forelimb stylopod muscle](http://purl.obolibrary.org/obo/UBERON_0004255) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "See notes on UBERON:0001460 for possible terminological confusion over term 'arm'" + + + +### forelimb zeugopod `http://purl.obolibrary.org/obo/UBERON_0002386` +#### Removed +- [forelimb zeugopod](http://purl.obolibrary.org/obo/UBERON_0002386) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "Naming conventions for pod terms under discussion within phenoscape group. TODO - add distinct term for skeleton and place AAO class here" + +- [forelimb zeugopod](http://purl.obolibrary.org/obo/UBERON_0002386) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000341" + +- [forelimb zeugopod](http://purl.obolibrary.org/obo/UBERON_0002386) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The middle forelimb region. [Evolution, Fourth_Edition_(2006)_Boston_etc.:_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.321, see_Kardong_KV][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000341" + + + +### forelimb zeugopod skeleton `http://purl.obolibrary.org/obo/UBERON_0010703` +#### Removed +- [forelimb zeugopod skeleton](http://purl.obolibrary.org/obo/UBERON_0010703) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Segment of the forearm corresponding to the radius and ulna.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000200" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + + +### forkhead box protein N1 `http://purl.obolibrary.org/obo/PR_000007636` +#### Removed +- [forkhead box protein N1](http://purl.obolibrary.org/obo/PR_000007636) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [forkhead box protein N1 (human)](http://purl.obolibrary.org/obo/PR_O15353) + + + +### forkhead box protein P3 `http://purl.obolibrary.org/obo/PR_000001350` +#### Removed +- [forkhead box protein P3](http://purl.obolibrary.org/obo/PR_000001350) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [forkhead box protein P3 (human)](http://purl.obolibrary.org/obo/PR_Q9BZS1) + + + +### formed as result of `http://purl.obolibrary.org/obo/RO_0002354` +#### Removed +- [formed as result of](http://purl.obolibrary.org/obo/RO_0002354) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + + + +### fornix of brain `http://purl.obolibrary.org/obo/UBERON_0000052` +#### Removed +- [fornix of brain](http://purl.obolibrary.org/obo/UBERON_0000052) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:61965" + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "inferred" + + + +### fourth ventricle `http://purl.obolibrary.org/obo/UBERON_0002422` +#### Removed +- [fourth ventricle](http://purl.obolibrary.org/obo/UBERON_0002422) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The fourth ventricle is an irregularly shaped cavity in the rhombencephalon, between the medulla oblongata, the pons, and the isthmus in front, and the cerebellum behind. It is continuous with the central canal of the cord below and with the cerebral aqueduct above, and through its lateral and median apertures it communicates with the subarachnoid space[GO][GO:0021592]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GO:0021592" + +- [fourth ventricle](http://purl.obolibrary.org/obo/UBERON_0002422) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Irregularly shaped cavity in the rhombencephalon, between the medulla oblongata, the pons, and the isthmus in front, and the cerebellum behind. It is continuous with the central canal of the cord below and with the cerebral aqueduct above, and through its lateral and median apertures it communicates with the subarachnoid space.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "UBERON:0002422" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0011043" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + +- [fourth ventricle](http://purl.obolibrary.org/obo/UBERON_0002422) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Fluid-filled brain cavity. Kimmel et al, 1995.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000110" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [fourth ventricle](http://purl.obolibrary.org/obo/UBERON_0002422) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000006" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500" + + + +### fourth ventricle aperture `http://purl.obolibrary.org/obo/UBERON_0004668` + +#### Added +- [fourth ventricle aperture](http://purl.obolibrary.org/obo/UBERON_0004668) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### fovea centralis `http://purl.obolibrary.org/obo/UBERON_0001786` +#### Removed +- [fovea centralis](http://purl.obolibrary.org/obo/UBERON_0001786) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "high acuity vision" + +- [fovea centralis](http://purl.obolibrary.org/obo/UBERON_0001786) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The fovea is also a pit in the surface of the retinas of many types of fish, reptiles, and birds. Among mammals, it is found only in simian primates. The retinal fovea takes slightly different forms in different types of animals. For example, in primates, cone photoreceptors line the base of the foveal pit, the cells that elsewhere in the retina form more superficial layers having been displaced away from the foveal region during late fetal and early postnatal life. Other foveae may show only a reduced thickness in the inner cell layers, rather than an almost complete absence" + +- [fovea centralis](http://purl.obolibrary.org/obo/UBERON_0001786) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "foveal" + +- [fovea centralis](http://purl.obolibrary.org/obo/UBERON_0001786) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Definition of fovea centralis should be considered here as 'an area centralis at the visual axis' (reference 1). There is an uncertaincy of the relation, because: 1.-The fovea first appeared in evolution in the temporal retina of fishes. Then, in birds, the nasal fovea and bifoveal system with nasal and temporal foveas developed. The fovea disappeared in primitive mammals, and reappeared in primates. A residue of the fovea is conserved in the visual streak, and the disappearance and reappearance of the fovea, in primitive mammals and primates respectively, correlates with degeneration and restoration of cone pigment genes in photoreceptors (reference 2). 2.-Many retinal features (foveas, trichromacy, midget pathways and associated cell types) appear specific to primates. This has led to investigations in parallel with other mammalian models such as cat or rabbit. Correlation of the results often proves to be difficult, since an evolutionary scenario with transitions between the mammalian models is largely lacking (reference 3).[uncertain][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1017/S095252380623342X Ahnelt PK, Schubert C, Kübber-Heiss A, Schiviz A, Anger E, Independent variation of retinal S and M cone photoreceptor topographies: A survey of four families of mammals. Visual neuroscience (2006), http://www.ncbi.nlm.nih.gov/pubmed/11193946 Azuma N, Molecular cell biology on morphogenesis of the fovea and evolution of the central vision. Nihon Ganka Gakkai Zasshi (2000), DOI:10.1016/S1350-9462(00)00012-4 Ahnelt PK, Kolb H, The mammalian photoreceptor mosaic-adaptive design. Progress in Retinal and Eye Research (2000)" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001572" + +- [fovea centralis](http://purl.obolibrary.org/obo/UBERON_0001786) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A small pit in the center of the macula lutea, the area of clearest vision, where the retinal layers are spread aside, and light falls directly on the cones. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/fovea" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001572" + +#### Added +- [fovea centralis](http://purl.obolibrary.org/obo/UBERON_0001786) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### frontal cortex `http://purl.obolibrary.org/obo/UBERON_0001870` +#### Removed +- [frontal cortex](http://purl.obolibrary.org/obo/UBERON_0001870) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D005625" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + +- [frontal cortex](http://purl.obolibrary.org/obo/UBERON_0001870) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anterior portion of the frontal cortex, lying anterior to the central sulcus. It is bounded by the parietal cortex posteriorly and the temporal cortex laterally." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "NLXANAT:20090601" + + + +### frontal suture `http://purl.obolibrary.org/obo/UBERON_0002490` +#### Removed +- [frontal suture](http://purl.obolibrary.org/obo/UBERON_0002490) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "in humans, the frontal suture is a dense connective tissue structure that divides the two halves of the frontal bone of the skull in infants and children. It usually disappears by the age of six, with the two halves of the frontal bone being fused together. If it does not disappear it may be called a 'metopic suture' or 'sutura frontalis persistens. ' If the suture is not present at birth (craniosynostosis) it will cause a keel-shaped deformity of the skull called 'trigonocephaly. ' It is present in a fetal skull so that the skull can bend and is very elastic at the time of birth. The baby's head literally bends when coming out of the mother's womb. The space is filled as the child grows older. [WP,unvetted]" + +- [frontal suture](http://purl.obolibrary.org/obo/UBERON_0002490) SubClassOf [connects](http://purl.obolibrary.org/obo/RO_0002176) some [tetrapod frontal bone](http://purl.obolibrary.org/obo/UBERON_0000209) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "two halves of the frontal bone" + +#### Added +- [frontal suture](http://purl.obolibrary.org/obo/UBERON_0002490) SubClassOf [connects](http://purl.obolibrary.org/obo/RO_0002176) some [tetrapod frontal bone](http://purl.obolibrary.org/obo/UBERON_0000209) + + +### frontonasal process epithelium `http://purl.obolibrary.org/obo/UBERON_0014702` + +#### Added +- [frontonasal process epithelium](http://purl.obolibrary.org/obo/UBERON_0014702) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) + + +### function of `http://purl.obolibrary.org/obo/RO_0000079` +#### Removed +- [function of](http://purl.obolibrary.org/obo/RO_0000079) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "this catalysis function is a function of this enzyme"@en + +- [function of](http://purl.obolibrary.org/obo/RO_0000079) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "is function of"@en + +- [function of](http://purl.obolibrary.org/obo/RO_0000079) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "function_of"@en + + + +### functionally related to `http://purl.obolibrary.org/obo/RO_0002328` +#### Removed +- [functionally related to](http://purl.obolibrary.org/obo/RO_0002328) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002328" + +- [functionally related to](http://purl.obolibrary.org/obo/RO_0002328) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [functionally related to](http://purl.obolibrary.org/obo/RO_0002328) [id](http://www.geneontology.org/formats/oboInOwl#id) "functionally_related_to" + +- [functionally related to](http://purl.obolibrary.org/obo/RO_0002328) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [functionally related to](http://purl.obolibrary.org/obo/RO_0002328) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "This is a grouping relation that collects relations used for the purpose of connecting structure and function" + +- [functionally related to](http://purl.obolibrary.org/obo/RO_0002328) [label](http://www.w3.org/2000/01/rdf-schema#label) "functionally related to" + +- [functionally related to](http://purl.obolibrary.org/obo/RO_0002328) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "functionally_related_to" + + + +### fundus of stomach `http://purl.obolibrary.org/obo/UBERON_0001160` +#### Removed +- [fundus of stomach](http://purl.obolibrary.org/obo/UBERON_0001160) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000421" + +- [fundus of stomach](http://purl.obolibrary.org/obo/UBERON_0001160) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The greater curvature of the stomach. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000421" + + + +### fundus of urinary bladder `http://purl.obolibrary.org/obo/UBERON_0006082` + +#### Added +- [fundus of urinary bladder](http://purl.obolibrary.org/obo/UBERON_0006082) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### future brain `http://purl.obolibrary.org/obo/UBERON_0006238` +#### Removed +- [future brain](http://purl.obolibrary.org/obo/UBERON_0006238) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO)" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://neurolex.org/wiki/Cumbo_terms" + + + +### future brain vesicle `http://purl.obolibrary.org/obo/UBERON_0013150` +#### Removed +- [future brain vesicle](http://purl.obolibrary.org/obo/UBERON_0013150) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "Note that some sources may treat the term vesicle as the progenitor of the whole brain region; for example 'The retina develops directly from the neural tube as an outpouching from the diencephalic vesicle'" + + + +### future central tendon `http://purl.obolibrary.org/obo/UBERON_0006239` +#### Removed +- [future central tendon](http://purl.obolibrary.org/obo/UBERON_0006239) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "The cranial part of the septum transversum gives rise to the central tendon of the diaphragm and is the origin of the myoblasts that invade the pleuroperitoneal folds resulting in the formation of the muscular diaphragm." + +- [future central tendon](http://purl.obolibrary.org/obo/UBERON_0006239) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [septum transversum](http://purl.obolibrary.org/obo/UBERON_0004161) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "mesenchyme" + + - [region](http://www.geneontology.org/formats/oboInOwl#region) "cranial part" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia" + +#### Added +- [future central tendon](http://purl.obolibrary.org/obo/UBERON_0006239) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [septum transversum](http://purl.obolibrary.org/obo/UBERON_0004161) + + +### future hindbrain meninx `http://purl.obolibrary.org/obo/UBERON_0010091` + +#### Added +- [future hindbrain meninx](http://purl.obolibrary.org/obo/UBERON_0010091) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### future meninx `http://purl.obolibrary.org/obo/UBERON_0007645` +#### Removed +- [future meninx](http://purl.obolibrary.org/obo/UBERON_0007645) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "the outermost mesenchymal covering of the developing brain and spinal cord that is composed of tough fibrous connective tissue from which the arachnoid mater, pia mater and dura mater are formed[MP:0009726]d" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "MP:0009726" + + + +### future telencephalon `http://purl.obolibrary.org/obo/UBERON_0014371` +#### Removed +- [future telencephalon](http://purl.obolibrary.org/obo/UBERON_0014371) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [telencephalon neural crest](http://purl.obolibrary.org/obo/UBERON_0003850) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" + +#### Added +- [future telencephalon](http://purl.obolibrary.org/obo/UBERON_0014371) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [telencephalon neural crest](http://purl.obolibrary.org/obo/UBERON_0003850) + + +### future upper lip `http://purl.obolibrary.org/obo/UBERON_0011592` +#### Removed +- [future upper lip](http://purl.obolibrary.org/obo/UBERON_0011592) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [medial nasal prominence](http://purl.obolibrary.org/obo/UBERON_0004068) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "fusion" + +- [future upper lip](http://purl.obolibrary.org/obo/UBERON_0011592) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [maxillary prominence](http://purl.obolibrary.org/obo/UBERON_0005868) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "fusion" + +#### Added +- [future upper lip](http://purl.obolibrary.org/obo/UBERON_0011592) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [maxillary prominence](http://purl.obolibrary.org/obo/UBERON_0005868) + +- [future upper lip](http://purl.obolibrary.org/obo/UBERON_0011592) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [medial nasal prominence](http://purl.obolibrary.org/obo/UBERON_0004068) + + +### galectin-1 `http://purl.obolibrary.org/obo/PR_000009766` +#### Removed +- [galectin-1](http://purl.obolibrary.org/obo/PR_000009766) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [galectin-1 (human)](http://purl.obolibrary.org/obo/PR_P09382) + + + +### gallbladder `http://purl.obolibrary.org/obo/UBERON_0002110` +#### Removed +- [gallbladder](http://purl.obolibrary.org/obo/UBERON_0002110) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The presence of a gallbladder appears to be a primitive trait. It is found in most fish and all adult reptiles and amphibians and has been well conserved in mammals, for the most part.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000221" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1002/(SICI)1097-0029(19970915)38:6<571::AID-JEMT3>3.0.CO;2-I Oldham-Ott CK, Gilloteaux J, Comparative morphology of the gallbladder and biliary tract in vertebrates: Variation in structure, homology in function and gallstones. Microscopy research and technique (1997)" + +- [gallbladder](http://purl.obolibrary.org/obo/UBERON_0002110) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010114" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + +- [gallbladder](http://purl.obolibrary.org/obo/UBERON_0002110) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Organ attached to the liver which stores bile and empties into the duodenum via the bile duct as needed for digestion.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010114" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + +- [gallbladder](http://purl.obolibrary.org/obo/UBERON_0002110) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Membranous muscular sac in which the bile from the liver remains stored until it is required. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000221" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + +- [gallbladder](http://purl.obolibrary.org/obo/UBERON_0002110) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [gallbladder primordium](http://purl.obolibrary.org/obo/UBERON_0006242) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" + +#### Added +- [gallbladder](http://purl.obolibrary.org/obo/UBERON_0002110) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [gallbladder primordium](http://purl.obolibrary.org/obo/UBERON_0006242) + + +### gallbladder lamina propria `http://purl.obolibrary.org/obo/UBERON_0004781` + +#### Added +- [gallbladder lamina propria](http://purl.obolibrary.org/obo/UBERON_0004781) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) + + +### gallbladder serosa `http://purl.obolibrary.org/obo/UBERON_0004783` + +#### Added +- [gallbladder serosa](http://purl.obolibrary.org/obo/UBERON_0004783) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) + + +### gallbladder smooth muscle `http://purl.obolibrary.org/obo/UBERON_0004240` + +#### Added +- [gallbladder smooth muscle](http://purl.obolibrary.org/obo/UBERON_0004240) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) + + +### gamma-synuclein `http://purl.obolibrary.org/obo/PR_000015325` +#### Removed +- [gamma-synuclein](http://purl.obolibrary.org/obo/PR_000015325) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [gamma-synuclein (human)](http://purl.obolibrary.org/obo/PR_O76070) + + + +### ganglion `http://purl.obolibrary.org/obo/UBERON_0000045` +#### Removed +- [ganglion](http://purl.obolibrary.org/obo/UBERON_0000045) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Portion of tissue that contains cell bodies of neurons and is located outside the central nervous system.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010426" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + +- [ganglion](http://purl.obolibrary.org/obo/UBERON_0000045) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "ganglionic" + +- [ganglion](http://purl.obolibrary.org/obo/UBERON_0000045) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A ganglion is a cluster of neurons. It is part of a nervous system. It may include glial cells. The neurons are arranged in a specific constellation: neuronal somata are concentrated at the surface, thus forming a cell cortex, and neurites are concentrated in the centre of the ganglion to form the neuropil. A ganglion is a distinct unit but several ganglia may be anterio-posteriorly joined by connectives or transversally by commissures" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:21062451" + +- [ganglion](http://purl.obolibrary.org/obo/UBERON_0000045) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Structures containing a collection of nerve cell bodies. (Source: BioGlossary, www.Biology-Text.com)[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000190" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [ganglion](http://purl.obolibrary.org/obo/UBERON_0000045) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Cranial sensory placodes are focused areas of the head ectoderm of vertebrates that contribute to the development of the cranial sense organs and their associated ganglia. Placodes have long been considered a key character of vertebrates, and their evolution is proposed to have been essential for the evolution of an active predatory lifestyle by early vertebrates.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1016/j.ydbio.2005.02.021 Mazet F, Hutt JA, Milloz J, Millard J, Graham A, Shimeld SM, Molecular evidence from Ciona intestinalis for the evolutionary origin of vertebrate sensory placodes. Developmental Biology (2005)" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000156" + +- [ganglion](http://purl.obolibrary.org/obo/UBERON_0000045) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Subdivision of nervous system which primarily consists of cell bodies of neurons located outside the neuraxis (brain and spinal cord. Examples: spinal ganglion, trigeminal ganglion, superior cervical ganglion, celiac ganglion, inferior hypogastric (pelvic) ganglion (adapted from Foundational Model of Anatomy)[NLXANAT:100302]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "NLXANAT:100302" + +- [ganglion](http://purl.obolibrary.org/obo/UBERON_0000045) DisjointWith [basal ganglion](http://purl.obolibrary.org/obo/UBERON_0002420) + - [inconsistent_with](http://www.geneontology.org/formats/oboInOwl#inconsistent_with) "BTO" + + + +### ganglion of central nervous system `http://purl.obolibrary.org/obo/UBERON_0003339` +#### Removed +- [ganglion of central nervous system](http://purl.obolibrary.org/obo/UBERON_0003339) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "this has no subclasses in FMA. In EHDAA2 and EMAPA it has only the cranial ganglia" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + +#### Added +- [ganglion of central nervous system](http://purl.obolibrary.org/obo/UBERON_0003339) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### ganglion of peripheral nervous system `http://purl.obolibrary.org/obo/UBERON_0003338` +#### Removed +- [ganglion of peripheral nervous system](http://purl.obolibrary.org/obo/UBERON_0003338) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "we follow MA in including separate classes for ganglion and peripheral nervous system, even though for vertebrates gangia are always in the PNS" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" + + + +### ganglionic eminence `http://purl.obolibrary.org/obo/UBERON_0004023` +#### Removed +- [ganglionic eminence](http://purl.obolibrary.org/obo/UBERON_0004023) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "contributes significantly in building up the GABAergic cortical cell population[WP]" + + + +### ganglionic layer of retina `http://purl.obolibrary.org/obo/UBERON_0001792` +#### Removed +- [ganglionic layer of retina](http://purl.obolibrary.org/obo/UBERON_0001792) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "a layer of the retina that consists of retinal ganglion cells[WP]. innermost nuclear layer of the retina, which contains neurons that project axons through the optic nerve to the brain[Wikipedia:Ganglion_cell_layer]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Ganglion_cell_layer" + +- [ganglionic layer of retina](http://purl.obolibrary.org/obo/UBERON_0001792) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "NIFSTD class appears to be retired in nlx[http://neurolex.org/wiki/Nlx_anat_1005030]" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "NIF" + +- [ganglionic layer of retina](http://purl.obolibrary.org/obo/UBERON_0001792) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001166" + + + +### gastroesophageal sphincter `http://purl.obolibrary.org/obo/UBERON_0004550` +#### Removed +- [gastroesophageal sphincter](http://purl.obolibrary.org/obo/UBERON_0004550) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D049630" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + + + +### gastrula `http://purl.obolibrary.org/obo/UBERON_0004734` +#### Removed +- [gastrula](http://purl.obolibrary.org/obo/UBERON_0004734) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "We explicitly merge the NCITA terms here" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "NCIT" + +- [gastrula](http://purl.obolibrary.org/obo/UBERON_0004734) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005317" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + + +### gene `http://www.geneontology.org/formats/oboInOwl#gene` +#### Removed +- AnnotationProperty: [gene](http://www.geneontology.org/formats/oboInOwl#gene) + + + +### geniculate ganglion `http://purl.obolibrary.org/obo/UBERON_0001700` +#### Removed +- [geniculate ganglion](http://purl.obolibrary.org/obo/UBERON_0001700) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia. (...) The one substantial difference between the vertebrate pharyngeal arches and those of the protochordates is the presence of the epibranchial placodes but the evolution of these structures was undoubtedly driven by the endoderm.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000707" + + + +### genioglossus muscle `http://purl.obolibrary.org/obo/UBERON_0001571` +#### Removed +- [genioglossus muscle](http://purl.obolibrary.org/obo/UBERON_0001571) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Makes up bulk of tongue in frogs and salamanders; makes up entire tongue in caecilians.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010660" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BMZ" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + +- [genioglossus muscle](http://purl.obolibrary.org/obo/UBERON_0001571) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "see Intrinsic Tongue.[FEED]" + - [url](http://www.geneontology.org/formats/oboInOwl#url) "http://www.feedexp.org" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "FEED" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-07-02" + +- [genioglossus muscle](http://purl.obolibrary.org/obo/UBERON_0001571) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Makes up bulk of tongue in frogs and salamanders; makes up entire tongue in caecilians." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:0010660" + +- [genioglossus muscle](http://purl.obolibrary.org/obo/UBERON_0001571) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1002/dvdy.20587, DOI:10.1186/1471-213X-8-24 Table 7" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000847" + +- [genioglossus muscle](http://purl.obolibrary.org/obo/UBERON_0001571) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: subclass hyobranchial muscles (AAO:0000224)[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010660" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + +- [genioglossus muscle](http://purl.obolibrary.org/obo/UBERON_0001571) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Either of a pair of lingual muscles with origin in the mandible, with insertion to the lingual fascia below the mucous membrane and epiglottis, with nerve supply from the hypoglossal nerve, and whose action depresses and protrudes the tongue. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/genioglossus" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000847" + + + +### genitourinary system `http://purl.obolibrary.org/obo/UBERON_0004122` +#### Removed +- [genitourinary system](http://purl.obolibrary.org/obo/UBERON_0004122) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "urogenital" + +- [genitourinary system](http://purl.obolibrary.org/obo/UBERON_0004122) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Kidneys and gonads (of vertebrates) develop from adjacent tissues, and after the excretory or urinary ducts have developed, the reproductive system usually taps into them or their derivatives.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.633" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000286" + +- [genitourinary system](http://purl.obolibrary.org/obo/UBERON_0004122) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship type change: differentiates_from intermediate mesoderm (AAO:0010575) CHANGED TO: develops_from intermediate mesoderm (UBERON:0003064)[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000624" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + +- [genitourinary system](http://purl.obolibrary.org/obo/UBERON_0004122) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "genitourinary" + +- [genitourinary system](http://purl.obolibrary.org/obo/UBERON_0004122) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000624" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + + +### genomically related to `http://purl.obolibrary.org/obo/RO_0002330` +#### Removed +- [genomically related to](http://purl.obolibrary.org/obo/RO_0002330) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [genomically related to](http://purl.obolibrary.org/obo/RO_0002330) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism" + + + +### germ layer `http://purl.obolibrary.org/obo/UBERON_0000923` +#### Removed +- [germ layer](http://purl.obolibrary.org/obo/UBERON_0000923) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001223" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722" + +- [germ layer](http://purl.obolibrary.org/obo/UBERON_0000923) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000110" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + + +### germinal center `http://purl.obolibrary.org/obo/UBERON_0010754` +#### Removed +- [germinal center](http://purl.obolibrary.org/obo/UBERON_0010754) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "SCTID:64626006" + + + +### germinal neuroepithelium `http://purl.obolibrary.org/obo/UBERON_0004022` +#### Removed +- [germinal neuroepithelium](http://purl.obolibrary.org/obo/UBERON_0004022) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "As the cells adjacent to the lumen continue to divide, the migrating cells form a second layer around the original neural tube. This layer becomes progressively thicker as more cells are added to it from the germinal neuroepithelium. This new layer is called the mantle (or intermediate) zone, and the germinal epithelium is now called the ventricular zone (and, later, the ependyma)[NCBIBook:NBK10047]" + +#### Added +- [germinal neuroepithelium](http://purl.obolibrary.org/obo/UBERON_0004022) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) + + +### gingiva `http://purl.obolibrary.org/obo/UBERON_0001828` +#### Removed +- [gingiva](http://purl.obolibrary.org/obo/UBERON_0001828) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "gingival" + + + +### gingival epithelium `http://purl.obolibrary.org/obo/UBERON_0001949` +#### Removed +- [gingival epithelium](http://purl.obolibrary.org/obo/UBERON_0001949) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In humans: 15% orthokeratinized, 75% parakeratinized, 10% non-keratinized; diurnal; decreased keratinization with age. Note that in FMA this is classified as keratinized squamous - this perhaps refers to the epithelium of the attached or free gingiva" + + + +### girdle skeleton `http://purl.obolibrary.org/obo/UBERON_0010719` +#### Removed +- [girdle skeleton](http://purl.obolibrary.org/obo/UBERON_0010719) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: part_of subdivision of skeleton (UBERON:0010912)[VSAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000302" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" + +- [girdle skeleton](http://purl.obolibrary.org/obo/UBERON_0010719) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Skeletal subdivision that is part of the appendage girdle region.[VSAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000302" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" + +- [girdle skeleton](http://purl.obolibrary.org/obo/UBERON_0010719) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: proximally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000302" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" + + + +### gland `http://purl.obolibrary.org/obo/UBERON_0002530` +#### Removed +- [gland](http://purl.obolibrary.org/obo/UBERON_0002530) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EHDAA:6522" + +- [gland](http://purl.obolibrary.org/obo/UBERON_0002530) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00100317" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + +- [gland](http://purl.obolibrary.org/obo/UBERON_0002530) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "glandular" + +- [gland](http://purl.obolibrary.org/obo/UBERON_0002530) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [skeletal system](http://purl.obolibrary.org/obo/UBERON_0001434) + +- [gland](http://purl.obolibrary.org/obo/UBERON_0002530) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EHDAA:4475" + + + +### gland of anal canal `http://purl.obolibrary.org/obo/UBERON_0004760` +#### Removed +- [gland of anal canal](http://purl.obolibrary.org/obo/UBERON_0004760) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "gland of anal canal" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "OBOL:automatic" + +#### Added +- [gland of anal canal](http://purl.obolibrary.org/obo/UBERON_0004760) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "gland of anal sac" + +- [gland of anal canal](http://purl.obolibrary.org/obo/UBERON_0004760) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### gland of diencephalon `http://purl.obolibrary.org/obo/UBERON_0003296` +#### Removed +- [gland of diencephalon](http://purl.obolibrary.org/obo/UBERON_0003296) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EHDAA:4475" + +#### Added +- [gland of diencephalon](http://purl.obolibrary.org/obo/UBERON_0003296) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### gland of integumental system `http://purl.obolibrary.org/obo/UBERON_0003297` +#### Removed +- [gland of integumental system](http://purl.obolibrary.org/obo/UBERON_0003297) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EHDAA:6522" + + + +### gland of nasal mucosa `http://purl.obolibrary.org/obo/UBERON_0012278` + +#### Added +- [gland of nasal mucosa](http://purl.obolibrary.org/obo/UBERON_0012278) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + +- [gland of nasal mucosa](http://purl.obolibrary.org/obo/UBERON_0012278) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) + + +### gland of ocular region `http://purl.obolibrary.org/obo/UBERON_0015152` +#### Removed +- [gland of ocular region](http://purl.obolibrary.org/obo/UBERON_0015152) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "the only orbital gland found in anuran amphibians is the Harderian[PMID:8843648]" + +- [gland of ocular region](http://purl.obolibrary.org/obo/UBERON_0015152) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "the only orbital gland found in anuran amphibians is either the Harderian or the lacrimal; if it is a lacrimal, then a progressive lateral migration of the lacrimal glands must occur through the amniotes[PMID:7559104]" + + + +### glandular acinus `http://purl.obolibrary.org/obo/UBERON_0009842` +#### Removed +- [glandular acinus](http://purl.obolibrary.org/obo/UBERON_0009842) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "acinar" + + + +### glans `http://purl.obolibrary.org/obo/UBERON_0035651` + +#### Added +- [glans](http://purl.obolibrary.org/obo/UBERON_0035651) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### glans clitoris `http://purl.obolibrary.org/obo/UBERON_0006653` +#### Removed +- [glans clitoris](http://purl.obolibrary.org/obo/UBERON_0006653) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:19170" + + + +### glenohumeral joint `http://purl.obolibrary.org/obo/UBERON_0001470` +#### Removed +- [glenohumeral joint](http://purl.obolibrary.org/obo/UBERON_0001470) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in FMA, this is part of the bony pectoral girdle, alongside the skeleton of pectoral girdle" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + + + +### glenoid fossa `http://purl.obolibrary.org/obo/UBERON_0006657` +#### Removed +- [glenoid fossa](http://purl.obolibrary.org/obo/UBERON_0006657) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D061165" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + +- [glenoid fossa](http://purl.obolibrary.org/obo/UBERON_0006657) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA also has classes for the bony parts around the cavity - these may be more useful than the cavity term itself" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + +- [glenoid fossa](http://purl.obolibrary.org/obo/UBERON_0006657) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: part_of scapular area (AAO:0000935)[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000749" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + +- [glenoid fossa](http://purl.obolibrary.org/obo/UBERON_0006657) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Cavity for the articulation of the forelimb formed by the scapula, coracoid, and clavicle.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000749" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + +- [glenoid fossa](http://purl.obolibrary.org/obo/UBERON_0006657) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The glenoid fossa can be associated with the metapterygium in sarcopterygians, or either the meso- or propterygium in basal gnathostomes such as Chondrichthyans" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ad" + +- [glenoid fossa](http://purl.obolibrary.org/obo/UBERON_0006657) SubClassOf [adjacent to](http://purl.obolibrary.org/obo/RO_0002220) some [scapula](http://purl.obolibrary.org/obo/UBERON_0006849) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "to be revised after scapulocoracoid fixes" + +#### Added +- [glenoid fossa](http://purl.obolibrary.org/obo/UBERON_0006657) SubClassOf [adjacent to](http://purl.obolibrary.org/obo/RO_0002220) some [scapula](http://purl.obolibrary.org/obo/UBERON_0006849) + + +### glial blood brain barrier `http://purl.obolibrary.org/obo/UBERON_0000202` +#### Removed +- [glial blood brain barrier](http://purl.obolibrary.org/obo/UBERON_0000202) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007091" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + + +### glial fibrillary acidic protein `http://purl.obolibrary.org/obo/PR_000007939` +#### Removed +- [glial fibrillary acidic protein](http://purl.obolibrary.org/obo/PR_000007939) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [glial fibrillary acidic protein (human)](http://purl.obolibrary.org/obo/PR_P14136) + + + +### glomerular basement membrane `http://purl.obolibrary.org/obo/UBERON_0005777` +#### Removed +- [glomerular basement membrane](http://purl.obolibrary.org/obo/UBERON_0005777) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D050533" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + +- [glomerular basement membrane](http://purl.obolibrary.org/obo/UBERON_0005777) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Membrane between the mesonephric podocytes and the renal glomerular capillaries. It is a trilaminar structure composed of the fused basement membranes of the glomerular capillaries and basement membrane of the podocytes. The capillary membranes touch the GBM at contact points that are separated by pores. The membrane is semi-permeable allowing water and small molecules to pass into the renal capsular space.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:ZDB-PUB-000824-1" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005285" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +#### Added +- [glomerular basement membrane](http://purl.obolibrary.org/obo/UBERON_0005777) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### glomerular capillary `http://purl.obolibrary.org/obo/UBERON_0004212` +#### Removed +- [glomerular capillary](http://purl.obolibrary.org/obo/UBERON_0004212) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Capillary that is part of the renal glomerulus. Glomerular capillary endothelial membranes in zebrafish normally have a fenestrated morphology that is visible at the ultrastructural level.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:ZDB-PUB-000824-1" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005284" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + + +### glomerular capsule `http://purl.obolibrary.org/obo/UBERON_0001230` +#### Removed +- [glomerular capsule](http://purl.obolibrary.org/obo/UBERON_0001230) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "One fold of the S-shaped body gives rise to Bowman's capsule[GUDMAP]" + +- [glomerular capsule](http://purl.obolibrary.org/obo/UBERON_0001230) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "Fluids from blood in the glomerulus are collected in the Bowman's capsule and further processed along the nephron to form urine. This process is known as ultrafiltration[WP]." + +- [glomerular capsule](http://purl.obolibrary.org/obo/UBERON_0001230) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical structure found in the kidney consisting of an expanded end of a kidney tubule surrounding a glomerulus and is the major site of filtration.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010526" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + + + +### glomerular epithelium `http://purl.obolibrary.org/obo/UBERON_0004188` + +#### Added +- [glomerular epithelium](http://purl.obolibrary.org/obo/UBERON_0004188) SubClassOf [meso-epithelium](http://purl.obolibrary.org/obo/UBERON_0012275) + + +### glomerular mesangium `http://purl.obolibrary.org/obo/UBERON_0002320` +#### Removed +- [glomerular mesangium](http://purl.obolibrary.org/obo/UBERON_0002320) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:28248" + +#### Added +- [glomerular mesangium](http://purl.obolibrary.org/obo/UBERON_0002320) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### glomerular parietal epithelium `http://purl.obolibrary.org/obo/UBERON_0005750` +#### Removed +- [glomerular parietal epithelium](http://purl.obolibrary.org/obo/UBERON_0005750) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Simple squamous epithelium that lines the capsule of the renal glomerulus.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005253" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + + +### glomerular tuft `http://purl.obolibrary.org/obo/UBERON_0005749` +#### Removed +- [glomerular tuft](http://purl.obolibrary.org/obo/UBERON_0005749) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "...Soon afterwards, endothelial cells invade to make a capillary knot-like outgrowth, the glomerular tuft, which goes on to form the glomerulus" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GudMap" + +- [glomerular tuft](http://purl.obolibrary.org/obo/UBERON_0005749) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "SCTID:362217000" + + + +### glossopharyngeal ganglion `http://purl.obolibrary.org/obo/UBERON_0001701` +#### Removed +- [glossopharyngeal ganglion](http://purl.obolibrary.org/obo/UBERON_0001701) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "These (the epibranchial placodes) are focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches in all vertebrates, and they produce the neuroblasts which migrate and condense to form the distal cranial ganglia: the geniculate, petrosal and nodose ganglia. (...) The one substantial difference between the vertebrate pharyngeal arches and those of the protochordates is the presence of the epibranchial placodes but the evolution of these structures was undoubtedly driven by the endoderm.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000702" + +- [glossopharyngeal ganglion](http://purl.obolibrary.org/obo/UBERON_0001701) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [petrosal placode](http://purl.obolibrary.org/obo/UBERON_0009125) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFA" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0471888893" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "EHDAA2" + + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "ventrolateral" + +- [glossopharyngeal ganglion](http://purl.obolibrary.org/obo/UBERON_0001701) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [glossopharyngeal neural crest](http://purl.obolibrary.org/obo/UBERON_0005491) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFA" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0471888893" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "EHDAA2" + + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "dorsal" + +#### Added +- [glossopharyngeal ganglion](http://purl.obolibrary.org/obo/UBERON_0001701) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [petrosal placode](http://purl.obolibrary.org/obo/UBERON_0009125) + +- [glossopharyngeal ganglion](http://purl.obolibrary.org/obo/UBERON_0001701) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [glossopharyngeal neural crest](http://purl.obolibrary.org/obo/UBERON_0005491) + + +### glossopharyngeal nerve `http://purl.obolibrary.org/obo/UBERON_0001649` +#### Removed +- [glossopharyngeal nerve](http://purl.obolibrary.org/obo/UBERON_0001649) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Small nerve consisting of branchiomotor and visceral efferent and afferent fibers which innervate the m. subarculais rectus I, dorsal buccal mucosa, and the tongue.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010474" + +- [glossopharyngeal nerve](http://purl.obolibrary.org/obo/UBERON_0001649) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000701" + +- [glossopharyngeal nerve](http://purl.obolibrary.org/obo/UBERON_0001649) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [basal plate metencephalon](http://purl.obolibrary.org/obo/UBERON_0005239) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "motor" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia" + +#### Added +- [glossopharyngeal nerve](http://purl.obolibrary.org/obo/UBERON_0001649) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [basal plate metencephalon](http://purl.obolibrary.org/obo/UBERON_0005239) + + +### glutamate decarboxylase 1 `http://purl.obolibrary.org/obo/PR_000007785` +#### Removed +- [glutamate decarboxylase 1](http://purl.obolibrary.org/obo/PR_000007785) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [glutamate decarboxylase 1 (human)](http://purl.obolibrary.org/obo/PR_Q99259) + + + +### glutamyl aminopeptidase `http://purl.obolibrary.org/obo/PR_000002039` +#### Removed +- [glutamyl aminopeptidase](http://purl.obolibrary.org/obo/PR_000002039) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [glutamyl aminopeptidase (human)](http://purl.obolibrary.org/obo/PR_Q07075) + + + +### glycophorin-A `http://purl.obolibrary.org/obo/PR_000001460` +#### Removed +- [glycophorin-A](http://purl.obolibrary.org/obo/PR_000001460) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [glycophorin-A (human)](http://purl.obolibrary.org/obo/PR_P02724) + + + +### gonad `http://purl.obolibrary.org/obo/UBERON_0000991` +#### Removed +- [gonad](http://purl.obolibrary.org/obo/UBERON_0000991) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004858" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + +- [gonad](http://purl.obolibrary.org/obo/UBERON_0000991) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA xref is a 'general anatomical term'" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + +- [gonad](http://purl.obolibrary.org/obo/UBERON_0000991) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T, Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000397" + +- [gonad](http://purl.obolibrary.org/obo/UBERON_0000991) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000213" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + +- [gonad](http://purl.obolibrary.org/obo/UBERON_0000991) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000413" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [gonad](http://purl.obolibrary.org/obo/UBERON_0000991) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "gonadal" + + + +### gonad primordium `http://purl.obolibrary.org/obo/UBERON_0005564` +#### Removed +- [gonad primordium](http://purl.obolibrary.org/obo/UBERON_0005564) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "this is a very broad grouping class" + +- [gonad primordium](http://purl.obolibrary.org/obo/UBERON_0005564) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Immature reproductive tissue that has not undergone final maturation into either testis or ovary.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001262" + + + +### gonadal ridge `http://purl.obolibrary.org/obo/UBERON_0005294` +#### Removed +- [gonadal ridge](http://purl.obolibrary.org/obo/UBERON_0005294) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "in eutherians, SRY transforms the indifferent gonad into testes" + + + +### granular layer of cerebellar cortex `http://purl.obolibrary.org/obo/UBERON_0002956` +#### Removed +- [granular layer of cerebellar cortex](http://purl.obolibrary.org/obo/UBERON_0002956) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [Purkinje cell layer of cerebellar cortex](http://purl.obolibrary.org/obo/UBERON_0002979) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" + + + +### granulosa cell layer `http://purl.obolibrary.org/obo/UBERON_0005170` +#### Removed +- [granulosa cell layer](http://purl.obolibrary.org/obo/UBERON_0005170) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "At one part of the mature follicle the cells of the membrana granulosa are collected into a mass which projects into the cavity of the follicle. This is termed the discus proligerus. [Wikipedia:Membrana_granulosa, Wikipedia:Membrana_granulosa]" + +#### Added +- [granulosa cell layer](http://purl.obolibrary.org/obo/UBERON_0005170) SubClassOf [meso-epithelium](http://purl.obolibrary.org/obo/UBERON_0012275) + + +### granzyme B `http://purl.obolibrary.org/obo/PR_000003499` +#### Removed +- [granzyme B](http://purl.obolibrary.org/obo/PR_000003499) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [granzyme B (human)](http://purl.obolibrary.org/obo/PR_P10144) + + + +### gravid organism `http://purl.obolibrary.org/obo/UBERON_0009097` +#### Removed +- [gravid organism](http://purl.obolibrary.org/obo/UBERON_0009097) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "IDOMAL:0000443" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + + + +### gray matter `http://purl.obolibrary.org/obo/UBERON_0002020` +#### Removed +- [gray matter](http://purl.obolibrary.org/obo/UBERON_0002020) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Multi-tissue comprised of neurons, dendrites, axon terminals, glial cells, and capillaries.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0002197" + +- [gray matter](http://purl.obolibrary.org/obo/UBERON_0002020) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D066128" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + + + +### gustatory organ `http://purl.obolibrary.org/obo/UBERON_0003212` +#### Removed +- [gustatory organ](http://purl.obolibrary.org/obo/UBERON_0003212) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005159" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + + +### gustatory papilla of tongue `http://purl.obolibrary.org/obo/UBERON_0014389` +#### Removed +- [gustatory papilla of tongue](http://purl.obolibrary.org/obo/UBERON_0014389) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:54822" + + + +### gustatory pore `http://purl.obolibrary.org/obo/UBERON_0007691` + +#### Added +- [gustatory pore](http://purl.obolibrary.org/obo/UBERON_0007691) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) + + +### gustatory system `http://purl.obolibrary.org/obo/UBERON_0001033` +#### Removed +- [gustatory system](http://purl.obolibrary.org/obo/UBERON_0001033) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in ZFA and MA this is a subtype of sensory system. we should change sensory system to disambiguate parts and wholes" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "ZFA" + +- [gustatory system](http://purl.obolibrary.org/obo/UBERON_0001033) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The sensory system for the sense of taste[NLXANAT:090803]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "NLXANAT:090803" + +- [gustatory system](http://purl.obolibrary.org/obo/UBERON_0001033) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "gustatory" + +- [gustatory system](http://purl.obolibrary.org/obo/UBERON_0001033) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The sensory system used for the sense of taste.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010577" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + + +### gut wall `http://purl.obolibrary.org/obo/UBERON_0000328` +#### Removed +- [gut wall](http://purl.obolibrary.org/obo/UBERON_0000328) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "We model the digestive tract as consisting of two parts: the wall and the lumen." + + + +### gut-associated lymphoid tissue `http://purl.obolibrary.org/obo/UBERON_0001962` +#### Removed +- [gut-associated lymphoid tissue](http://purl.obolibrary.org/obo/UBERON_0001962) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "guts of jawless fish contains cells with lymphocyte-like morphology (Mayer 2002)." + + + +### gyrus `http://purl.obolibrary.org/obo/UBERON_0000200` +#### Removed +- [gyrus](http://purl.obolibrary.org/obo/UBERON_0000200) [UBPROP_0000202](http://purl.obolibrary.org/obo/UBPROP_0000202) [FMA_72015](http://purl.obolibrary.org/obo/FMA_72015) + +- [gyrus](http://purl.obolibrary.org/obo/UBERON_0000200) [RO_0002174](http://purl.obolibrary.org/obo/RO_0002174) [Mus ](http://purl.obolibrary.org/obo/NCBITaxon_10088) + +#### Added +- [gyrus](http://purl.obolibrary.org/obo/UBERON_0000200) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### hair canal `http://purl.obolibrary.org/obo/UBERON_0035610` + +#### Added +- [hair canal](http://purl.obolibrary.org/obo/UBERON_0035610) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### hair follicle `http://purl.obolibrary.org/obo/UBERON_0002073` +#### Removed +- [hair follicle](http://purl.obolibrary.org/obo/UBERON_0002073) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The earliest reliable record of hair is found in a fossil of the Paleocene period, in which the structure of hair cuticles is preserved. Its appearance suggests that the complicated structure of the hair follicle, closely similar to that of present-day mammals, had already appeared at this time.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-4431998051 Morioka K, Hair follicle: differentiation under the electron microscope, An atlas (2005) p.3" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001268" + + + +### hair follicle matrix region `http://purl.obolibrary.org/obo/UBERON_0006004` + +#### Added +- [hair follicle matrix region](http://purl.obolibrary.org/obo/UBERON_0006004) SubClassOf [structure with developmental contribution from neural crest](http://purl.obolibrary.org/obo/UBERON_0010314) + + +### hair follicle placode `http://purl.obolibrary.org/obo/UBERON_0005086` +#### Removed +- [hair follicle placode](http://purl.obolibrary.org/obo/UBERON_0005086) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "An hair follicle placode is a thickening of the ectoderm that will give rise to the hair follicle bud[GO]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GO:0060789" + + + +### hair medulla `http://purl.obolibrary.org/obo/UBERON_0005184` + +#### Added +- [hair medulla](http://purl.obolibrary.org/obo/UBERON_0005184) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### hair root sheath `http://purl.obolibrary.org/obo/UBERON_0005933` + +#### Added +- [hair root sheath](http://purl.obolibrary.org/obo/UBERON_0005933) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### hair shaft `http://purl.obolibrary.org/obo/UBERON_0002074` + +#### Added +- [hair shaft](http://purl.obolibrary.org/obo/UBERON_0002074) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### has 2D boundary `http://purl.obolibrary.org/obo/RO_0002002` +#### Removed +- [has 2D boundary](http://purl.obolibrary.org/obo/RO_0002002) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002002" + +- [has 2D boundary](http://purl.obolibrary.org/obo/RO_0002002) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [has 2D boundary](http://purl.obolibrary.org/obo/RO_0002002) [label](http://www.w3.org/2000/01/rdf-schema#label) "has 2D boundary" + +- [has 2D boundary](http://purl.obolibrary.org/obo/RO_0002002) [id](http://www.geneontology.org/formats/oboInOwl#id) "has_boundary" + +- [has 2D boundary](http://purl.obolibrary.org/obo/RO_0002002) [RO_0001900](http://purl.obolibrary.org/obo/RO_0001900) [RO_0001901](http://purl.obolibrary.org/obo/RO_0001901) + +- [has 2D boundary](http://purl.obolibrary.org/obo/RO_0002002) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-7073-9172](https://orcid.org/0000-0002-7073-9172) + +- [has 2D boundary](http://purl.obolibrary.org/obo/RO_0002002) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "has boundary"@en + +- [has 2D boundary](http://purl.obolibrary.org/obo/RO_0002002) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "has_2D_boundary"@en + +- [has 2D boundary](http://purl.obolibrary.org/obo/RO_0002002) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "my body has 2D boundary the surface of my skin"@en + +- [has 2D boundary](http://purl.obolibrary.org/obo/RO_0002002) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "has_boundary" + + + +### has branching part `http://purl.obolibrary.org/obo/RO_0002569` +#### Removed +- [has branching part](http://purl.obolibrary.org/obo/RO_0002569) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "has_branching_part" + +- [has branching part](http://purl.obolibrary.org/obo/RO_0002569) [id](http://www.geneontology.org/formats/oboInOwl#id) "has_branching_part" + +- [has branching part](http://purl.obolibrary.org/obo/RO_0002569) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [has branching part](http://purl.obolibrary.org/obo/RO_0002569) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [has branching part](http://purl.obolibrary.org/obo/RO_0002569) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002569" + + + +### has component `http://purl.obolibrary.org/obo/RO_0002180` +#### Removed +- [has component](http://purl.obolibrary.org/obo/RO_0002180) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) + +- [has component](http://purl.obolibrary.org/obo/RO_0002180) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [has component](http://purl.obolibrary.org/obo/RO_0002180) [RO_0001900](http://purl.obolibrary.org/obo/RO_0001900) [RO_0001901](http://purl.obolibrary.org/obo/RO_0001901) + +- [has component](http://purl.obolibrary.org/obo/RO_0002180) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit."@en + + + +### has connecting branch `http://purl.obolibrary.org/obo/RO_0002253` +#### Removed +- [has connecting branch](http://purl.obolibrary.org/obo/RO_0002253) [RO_0004036](http://purl.obolibrary.org/obo/RO_0004036) [has part](http://purl.obolibrary.org/obo/BFO_0000051) + + + +### has dendrite location `http://purl.obolibrary.org/obo/RO_0002360` +#### Removed +- [has dendrite location](http://purl.obolibrary.org/obo/RO_0002360) [source](http://purl.org/dc/terms/source) "http://neurolex.org/wiki/Property:DendriteLocation"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) + +- [has dendrite location](http://purl.obolibrary.org/obo/RO_0002360) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + + + +### has developmental contribution from `http://purl.obolibrary.org/obo/RO_0002254` +#### Removed +- [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) + +- [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "has_developmental_contribution_from" + +- [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) [id](http://www.geneontology.org/formats/oboInOwl#id) "has_developmental_contribution_from" + +- [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002254" + +- [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) [label](http://www.w3.org/2000/01/rdf-schema#label) "has developmental contribution from" + +- [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" + + + +### has developmental potential involving `http://purl.obolibrary.org/obo/RO_0002384` +#### Removed +- [has developmental potential involving](http://purl.obolibrary.org/obo/RO_0002384) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [has developmental potential involving](http://purl.obolibrary.org/obo/RO_0002384) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [requires discussion](http://purl.obolibrary.org/obo/IAO_0000428) + + + +### has end location `http://purl.obolibrary.org/obo/RO_0002232` +#### Removed +- [has end location](http://purl.obolibrary.org/obo/RO_0002232) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) + +- [has end location](http://purl.obolibrary.org/obo/RO_0002232) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [has end location](http://purl.obolibrary.org/obo/RO_0002232) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "ends with process that occurs in" + + + +### has exact synonym `http://www.geneontology.org/formats/oboInOwl#hasExactSynonym` +#### Removed +- [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0001-5208-3432](http://orcid.org/0000-0001-5208-3432) + + + +### has fasciculating neuron projection `http://purl.obolibrary.org/obo/RO_0002132` +#### Removed +- [has fasciculating neuron projection](http://purl.obolibrary.org/obo/RO_0002132) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) + +- [has fasciculating neuron projection](http://purl.obolibrary.org/obo/RO_0002132) [RO_0001900](http://purl.obolibrary.org/obo/RO_0001900) [RO_0001901](http://purl.obolibrary.org/obo/RO_0001901) + +- [has fasciculating neuron projection](http://purl.obolibrary.org/obo/RO_0002132) [citesAsAuthority](http://purl.org/spar/cito/citesAsAuthority) [22402613](http://www.ncbi.nlm.nih.gov/pubmed/22402613) + +- [has fasciculating neuron projection](http://purl.obolibrary.org/obo/RO_0002132) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "has fasciculating component"@en + +- [has fasciculating neuron projection](http://purl.obolibrary.org/obo/RO_0002132) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-7073-9172](https://orcid.org/0000-0002-7073-9172) + +- [has fasciculating neuron projection](http://purl.obolibrary.org/obo/RO_0002132) [IAO_0000426](http://purl.obolibrary.org/obo/IAO_0000426) "(forall (?x ?y) + (iff + (has_fasciculating_neuron_projection ?x ?y) + (exists (?nps ?npbs) + (and + ("neuron projection bundle ; CARO_0001001" ?x) + ("neuron projection ; GO0043005" ?y) + ("neuron projection segment ; CARO_0001502" ?nps) + ("neuron projection bundle segment ; CARO_0001500" ?npbs) + (part_of ?nps ?y) + (part_of ?npbs ?x) + (part_of ?nps ?npbs) + (forall (?npbss) + (if + (and + ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) + (part_of ?npbss ?npbs) + ) + (overlaps ?nps ?npbss) + )))))) + + +" + + + +### has function `http://purl.obolibrary.org/obo/RO_0000085` +#### Removed +- [has function](http://purl.obolibrary.org/obo/RO_0000085) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "has_function"@en + +- [has function](http://purl.obolibrary.org/obo/RO_0000085) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)"@en + + + +### has high plasma membrane amount `http://purl.obolibrary.org/obo/RO_0015015` +#### Removed +- [has high plasma membrane amount](http://purl.obolibrary.org/obo/RO_0015015) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" + + + +### has input `http://purl.obolibrary.org/obo/RO_0002233` +#### Removed +- [has input](http://purl.obolibrary.org/obo/RO_0002233) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "consumes" + +- [has input](http://purl.obolibrary.org/obo/RO_0002233) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) + +- [has input](http://purl.obolibrary.org/obo/RO_0002233) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + + + +### has low plasma membrane amount `http://purl.obolibrary.org/obo/RO_0015016` +#### Removed +- [has low plasma membrane amount](http://purl.obolibrary.org/obo/RO_0015016) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" + + + +### has member `http://purl.obolibrary.org/obo/RO_0002351` +#### Removed +- [has member](http://purl.obolibrary.org/obo/RO_0002351) [label](http://www.w3.org/2000/01/rdf-schema#label) "has member" + +- [has member](http://purl.obolibrary.org/obo/RO_0002351) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) "SIO" + +- [has member](http://purl.obolibrary.org/obo/RO_0002351) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "has_member" + +- [has member](http://purl.obolibrary.org/obo/RO_0002351) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002351" + +- [has member](http://purl.obolibrary.org/obo/RO_0002351) [RO_0001900](http://purl.obolibrary.org/obo/RO_0001900) [RO_0001901](http://purl.obolibrary.org/obo/RO_0001901) + +- [has member](http://purl.obolibrary.org/obo/RO_0002351) [id](http://www.geneontology.org/formats/oboInOwl#id) "has_member" + +- [has member](http://purl.obolibrary.org/obo/RO_0002351) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + + + +### has muscle antagonist `http://purl.obolibrary.org/obo/RO_0002568` +#### Removed +- [has muscle antagonist](http://purl.obolibrary.org/obo/RO_0002568) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002568" + +- [has muscle antagonist](http://purl.obolibrary.org/obo/RO_0002568) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) "Wikipedia:Antagonist_(muscle)" + +- [has muscle antagonist](http://purl.obolibrary.org/obo/RO_0002568) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [has muscle antagonist](http://purl.obolibrary.org/obo/RO_0002568) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [has muscle antagonist](http://purl.obolibrary.org/obo/RO_0002568) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "has_muscle_antagonist" + +- [has muscle antagonist](http://purl.obolibrary.org/obo/RO_0002568) [id](http://www.geneontology.org/formats/oboInOwl#id) "has_muscle_antagonist" + + + +### has muscle insertion `http://purl.obolibrary.org/obo/RO_0002373` +#### Removed +- [has muscle insertion](http://purl.obolibrary.org/obo/RO_0002373) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "has_muscle_insertion" + +- [has muscle insertion](http://purl.obolibrary.org/obo/RO_0002373) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002373" + +- [has muscle insertion](http://purl.obolibrary.org/obo/RO_0002373) [label](http://www.w3.org/2000/01/rdf-schema#label) "has muscle insertion" + +- [has muscle insertion](http://purl.obolibrary.org/obo/RO_0002373) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) "Wikipedia:Insertion_(anatomy)"@en + +- [has muscle insertion](http://purl.obolibrary.org/obo/RO_0002373) [id](http://www.geneontology.org/formats/oboInOwl#id) "has_muscle_insertion" + +- [has muscle insertion](http://purl.obolibrary.org/obo/RO_0002373) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [has muscle insertion](http://purl.obolibrary.org/obo/RO_0002373) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + + + +### has muscle origin `http://purl.obolibrary.org/obo/RO_0002372` +#### Removed +- [has muscle origin](http://purl.obolibrary.org/obo/RO_0002372) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [has muscle origin](http://purl.obolibrary.org/obo/RO_0002372) [label](http://www.w3.org/2000/01/rdf-schema#label) "has muscle origin" + +- [has muscle origin](http://purl.obolibrary.org/obo/RO_0002372) [id](http://www.geneontology.org/formats/oboInOwl#id) "has_muscle_origin" + +- [has muscle origin](http://purl.obolibrary.org/obo/RO_0002372) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "has_muscle_origin" + +- [has muscle origin](http://purl.obolibrary.org/obo/RO_0002372) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) "Wikipedia:Insertion_(anatomy)"@en + +- [has muscle origin](http://purl.obolibrary.org/obo/RO_0002372) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [has muscle origin](http://purl.obolibrary.org/obo/RO_0002372) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002372" + + + +### has narrow synonym `http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym` +#### Removed +- [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0001-5208-3432](http://orcid.org/0000-0001-5208-3432) + + + +### has obsolescence reason `http://purl.obolibrary.org/obo/IAO_0000231` +#### Removed +- [has obsolescence reason](http://purl.obolibrary.org/obo/IAO_0000231) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) "PERSON:Alan Ruttenberg"@en + +- [has obsolescence reason](http://purl.obolibrary.org/obo/IAO_0000231) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "has obsolescence reason"@en + +- [has obsolescence reason](http://purl.obolibrary.org/obo/IAO_0000231) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) "PERSON:Melanie Courtot"@en + + + +### has ontology root term `http://purl.obolibrary.org/obo/IAO_0000700` +#### Removed +- [has ontology root term](http://purl.obolibrary.org/obo/IAO_0000700) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) "Nicolas Matentzoglu"@en + +- [has ontology root term](http://purl.obolibrary.org/obo/IAO_0000700) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "has ontology root term"@en + +- [has ontology root term](http://purl.obolibrary.org/obo/IAO_0000700) [is_class_level](http://www.geneontology.org/formats/oboInOwl#is_class_level) true + +- [has ontology root term](http://purl.obolibrary.org/obo/IAO_0000700) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + + + +### has output `http://purl.obolibrary.org/obo/RO_0002234` +#### Removed +- [has output](http://purl.obolibrary.org/obo/RO_0002234) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) + +- [has output](http://purl.obolibrary.org/obo/RO_0002234) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [has output](http://purl.obolibrary.org/obo/RO_0002234) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "produces" + + + +### has part `http://purl.obolibrary.org/obo/BFO_0000051` +#### Removed +- [has part](http://purl.obolibrary.org/obo/BFO_0000051) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [has part](http://purl.obolibrary.org/obo/BFO_0000051) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "this year has part this day (occurrent parthood)"@en + +- [has part](http://purl.obolibrary.org/obo/BFO_0000051) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)"@en + +- [has part](http://purl.obolibrary.org/obo/BFO_0000051) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "has part"@en + +- [has part](http://purl.obolibrary.org/obo/BFO_0000051) [RO_0001900](http://purl.obolibrary.org/obo/RO_0001900) [RO_0001901](http://purl.obolibrary.org/obo/RO_0001901) + +- [has part](http://purl.obolibrary.org/obo/BFO_0000051) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "has_part"@en + +- [has part](http://purl.obolibrary.org/obo/BFO_0000051) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "my body has part my brain (continuant parthood, two material entities)"@en + + + +### has part structure that is capable of `http://purl.obolibrary.org/obo/RO_0002584` +#### Removed +- [has part structure that is capable of](http://purl.obolibrary.org/obo/RO_0002584) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" + +- [has part structure that is capable of](http://purl.obolibrary.org/obo/RO_0002584) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + + + +### has part that occurs in `http://purl.obolibrary.org/obo/RO_0002479` +#### Removed +- [has part that occurs in](http://purl.obolibrary.org/obo/RO_0002479) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [has part](http://purl.obolibrary.org/obo/BFO_0000051) o [occurs in](http://purl.obolibrary.org/obo/BFO_0000066) SubPropertyOf: [has part that occurs in](http://purl.obolibrary.org/obo/RO_0002479) + - [is a defining property chain axiom](http://purl.obolibrary.org/obo/RO_0002581) true + + + +### has participant `http://purl.obolibrary.org/obo/RO_0000057` +#### Removed +- [has participant](http://purl.obolibrary.org/obo/RO_0000057) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "this investigation has participant this investigator"@en + +- [has participant](http://purl.obolibrary.org/obo/RO_0000057) [source](http://purl.org/dc/terms/source) "http://www.obofoundry.org/ro/#OBO_REL:has_participant" + +- [has participant](http://purl.obolibrary.org/obo/RO_0000057) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "has participant"@en + +- [has participant](http://purl.obolibrary.org/obo/RO_0000057) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "this process has participant this input material (or this output material)"@en + +- [has participant](http://purl.obolibrary.org/obo/RO_0000057) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "this blood coagulation has participant this blood clot"@en + +- [has participant](http://purl.obolibrary.org/obo/RO_0000057) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "has_participant"@en + + + +### has plasma membrane part `http://purl.obolibrary.org/obo/RO_0002104` +#### Removed +- [has plasma membrane part](http://purl.obolibrary.org/obo/RO_0002104) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0003-1617-8244](https://orcid.org/0000-0003-1617-8244) + +- [has plasma membrane part](http://purl.obolibrary.org/obo/RO_0002104) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [has plasma membrane part](http://purl.obolibrary.org/obo/RO_0002104) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]"@en + +- [has plasma membrane part](http://purl.obolibrary.org/obo/RO_0002104) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) [19243617](http://www.ncbi.nlm.nih.gov/pubmed/19243617) + +- [has plasma membrane part](http://purl.obolibrary.org/obo/RO_0002104) [RO_0001900](http://purl.obolibrary.org/obo/RO_0001900) [RO_0001901](http://purl.obolibrary.org/obo/RO_0001901) + +- [has plasma membrane part](http://purl.obolibrary.org/obo/RO_0002104) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) + +- [has plasma membrane part](http://purl.obolibrary.org/obo/RO_0002104) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0001-9990-8331](https://orcid.org/0000-0001-9990-8331) + + + +### has postsynaptic terminal in `http://purl.obolibrary.org/obo/RO_0002110` +#### Removed +- [has postsynaptic terminal in](http://purl.obolibrary.org/obo/RO_0002110) [citesAsAuthority](http://purl.org/spar/cito/citesAsAuthority) [22402613](http://www.ncbi.nlm.nih.gov/pubmed/22402613) + +- [has postsynaptic terminal in](http://purl.obolibrary.org/obo/RO_0002110) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) + +- [has postsynaptic terminal in](http://purl.obolibrary.org/obo/RO_0002110) [RO_0001900](http://purl.obolibrary.org/obo/RO_0001900) [RO_0001901](http://purl.obolibrary.org/obo/RO_0001901) + +- [has postsynaptic terminal in](http://purl.obolibrary.org/obo/RO_0002110) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "synapsed in"@en + +- [has postsynaptic terminal in](http://purl.obolibrary.org/obo/RO_0002110) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-7073-9172](https://orcid.org/0000-0002-7073-9172) + +- [has postsynaptic terminal in](http://purl.obolibrary.org/obo/RO_0002110) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + + + +### has potential to develop into `http://purl.obolibrary.org/obo/RO_0002387` +#### Removed +- [has potential to develop into](http://purl.obolibrary.org/obo/RO_0002387) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [has potential to develop into](http://purl.obolibrary.org/obo/RO_0002387) [label](http://www.w3.org/2000/01/rdf-schema#label) "has potential to develop into" + +- [has potential to develop into](http://purl.obolibrary.org/obo/RO_0002387) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "has_potential_to_develop_into" + +- [has potential to develop into](http://purl.obolibrary.org/obo/RO_0002387) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002387" + +- [has potential to develop into](http://purl.obolibrary.org/obo/RO_0002387) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [has potential to develop into](http://purl.obolibrary.org/obo/RO_0002387) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [requires discussion](http://purl.obolibrary.org/obo/IAO_0000428) + +- [has potential to develop into](http://purl.obolibrary.org/obo/RO_0002387) [id](http://www.geneontology.org/formats/oboInOwl#id) "has_potential_to_develop_into" + + + +### has potential to developmentally contribute to `http://purl.obolibrary.org/obo/RO_0002385` +#### Removed +- [has potential to developmentally contribute to](http://purl.obolibrary.org/obo/RO_0002385) [id](http://www.geneontology.org/formats/oboInOwl#id) "has_potential_to_developmentally_contribute_to" + +- [has potential to developmentally contribute to](http://purl.obolibrary.org/obo/RO_0002385) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [requires discussion](http://purl.obolibrary.org/obo/IAO_0000428) + +- [has potential to developmentally contribute to](http://purl.obolibrary.org/obo/RO_0002385) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "has_potential_to_developmentally_contribute_to" + +- [has potential to developmentally contribute to](http://purl.obolibrary.org/obo/RO_0002385) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002385" + +- [has potential to developmentally contribute to](http://purl.obolibrary.org/obo/RO_0002385) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [has potential to developmentally contribute to](http://purl.obolibrary.org/obo/RO_0002385) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [has potential to developmentally contribute to](http://purl.obolibrary.org/obo/RO_0002385) [label](http://www.w3.org/2000/01/rdf-schema#label) "has potential to developmentally contribute to" + + + +### has potential to developmentally induce `http://purl.obolibrary.org/obo/RO_0002386` +#### Removed +- [has potential to developmentally induce](http://purl.obolibrary.org/obo/RO_0002386) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [requires discussion](http://purl.obolibrary.org/obo/IAO_0000428) + +- [has potential to developmentally induce](http://purl.obolibrary.org/obo/RO_0002386) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + + + +### has potential to directly develop into `http://purl.obolibrary.org/obo/RO_0002388` +#### Removed +- [has potential to directly develop into](http://purl.obolibrary.org/obo/RO_0002388) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [requires discussion](http://purl.obolibrary.org/obo/IAO_0000428) + +- [has potential to directly develop into](http://purl.obolibrary.org/obo/RO_0002388) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + + + +### has presynaptic terminal in `http://purl.obolibrary.org/obo/RO_0002113` +#### Removed +- [has presynaptic terminal in](http://purl.obolibrary.org/obo/RO_0002113) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "synapses in"@en + +- [has presynaptic terminal in](http://purl.obolibrary.org/obo/RO_0002113) [citesAsAuthority](http://purl.org/spar/cito/citesAsAuthority) [22402613](http://www.ncbi.nlm.nih.gov/pubmed/22402613) + +- [has presynaptic terminal in](http://purl.obolibrary.org/obo/RO_0002113) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) + +- [has presynaptic terminal in](http://purl.obolibrary.org/obo/RO_0002113) [RO_0001900](http://purl.obolibrary.org/obo/RO_0001900) [RO_0001901](http://purl.obolibrary.org/obo/RO_0001901) + + + +### has quality `http://purl.obolibrary.org/obo/RO_0000086` +#### Removed +- [has quality](http://purl.obolibrary.org/obo/RO_0000086) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "has_quality"@en + +- [has quality](http://purl.obolibrary.org/obo/RO_0000086) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0000086" + +- [has quality](http://purl.obolibrary.org/obo/RO_0000086) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "this apple has quality this red color"@en + +- [has quality](http://purl.obolibrary.org/obo/RO_0000086) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [has quality](http://purl.obolibrary.org/obo/RO_0000086) [label](http://www.w3.org/2000/01/rdf-schema#label) "has quality" + +- [has quality](http://purl.obolibrary.org/obo/RO_0000086) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "has_quality" + +- [has quality](http://purl.obolibrary.org/obo/RO_0000086) [id](http://www.geneontology.org/formats/oboInOwl#id) "has_quality" + + + +### has role `http://purl.obolibrary.org/obo/RO_0000087` +#### Removed +- [has role](http://purl.obolibrary.org/obo/RO_0000087) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "this person has role this investigator role (more colloquially: this person has this role of investigator)"@en + +- [has role](http://purl.obolibrary.org/obo/RO_0000087) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "has_role"@en + + + +### has skeleton `http://purl.obolibrary.org/obo/RO_0002551` +#### Removed +- [has skeleton](http://purl.obolibrary.org/obo/RO_0002551) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" + +- [has skeleton](http://purl.obolibrary.org/obo/RO_0002551) [id](http://www.geneontology.org/formats/oboInOwl#id) "has_skeleton" + +- [has skeleton](http://purl.obolibrary.org/obo/RO_0002551) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [has skeleton](http://purl.obolibrary.org/obo/RO_0002551) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "has supporting framework" + +- [has skeleton](http://purl.obolibrary.org/obo/RO_0002551) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002551" + +- [has skeleton](http://purl.obolibrary.org/obo/RO_0002551) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." + +- [has skeleton](http://purl.obolibrary.org/obo/RO_0002551) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "has_skeleton" + +- [has skeleton](http://purl.obolibrary.org/obo/RO_0002551) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [has skeleton](http://purl.obolibrary.org/obo/RO_0002551) Domain [organism subdivision](http://purl.obolibrary.org/obo/UBERON_0000475) + +- [has skeleton](http://purl.obolibrary.org/obo/RO_0002551) Range [subdivision of skeleton](http://purl.obolibrary.org/obo/UBERON_0010912) + + + +### has soma location `http://purl.obolibrary.org/obo/RO_0002100` +#### Removed +- [has soma location](http://purl.obolibrary.org/obo/RO_0002100) [RO_0001900](http://purl.obolibrary.org/obo/RO_0001900) [RO_0001901](http://purl.obolibrary.org/obo/RO_0001901) + +- [has soma location](http://purl.obolibrary.org/obo/RO_0002100) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-7073-9172](https://orcid.org/0000-0002-7073-9172) + +- [has soma location](http://purl.obolibrary.org/obo/RO_0002100) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) + + + +### has start location `http://purl.obolibrary.org/obo/RO_0002231` +#### Removed +- [has start location](http://purl.obolibrary.org/obo/RO_0002231) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) + +- [has start location](http://purl.obolibrary.org/obo/RO_0002231) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "starts with process that occurs in" + +- [has start location](http://purl.obolibrary.org/obo/RO_0002231) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + + + +### has synaptic terminal in `http://purl.obolibrary.org/obo/RO_0002130` +#### Removed +- [has synaptic terminal in](http://purl.obolibrary.org/obo/RO_0002130) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-7073-9172](https://orcid.org/0000-0002-7073-9172) + +- [has synaptic terminal in](http://purl.obolibrary.org/obo/RO_0002130) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "has synapse in" + +- [has synaptic terminal in](http://purl.obolibrary.org/obo/RO_0002130) [RO_0001900](http://purl.obolibrary.org/obo/RO_0001900) [RO_0001901](http://purl.obolibrary.org/obo/RO_0001901) + +- [has synaptic terminal in](http://purl.obolibrary.org/obo/RO_0002130) [citesAsAuthority](http://purl.org/spar/cito/citesAsAuthority) [22402613](http://www.ncbi.nlm.nih.gov/pubmed/22402613) + +- [has synaptic terminal in](http://purl.obolibrary.org/obo/RO_0002130) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) + + + +### has synaptic terminal of `http://purl.obolibrary.org/obo/RO_0002006` +#### Removed +- [has synaptic terminal of](http://purl.obolibrary.org/obo/RO_0002006) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-7073-9172](https://orcid.org/0000-0002-7073-9172) + +- [has synaptic terminal of](http://purl.obolibrary.org/obo/RO_0002006) [citesAsAuthority](http://purl.org/spar/cito/citesAsAuthority) [22402613](http://www.ncbi.nlm.nih.gov/pubmed/22402613) + + + +### has target end location `http://purl.obolibrary.org/obo/RO_0002339` +#### Removed +- [has target end location](http://purl.obolibrary.org/obo/RO_0002339) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + + + +### has target start location `http://purl.obolibrary.org/obo/RO_0002338` +#### Removed +- [has target start location](http://purl.obolibrary.org/obo/RO_0002338) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + + + +### hasScope `http://www.geneontology.org/formats/oboInOwl#hasScope` +#### Removed +- AnnotationProperty: [hasScope](http://www.geneontology.org/formats/oboInOwl#hasScope) + + + +### has_broad_synonym `http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym` +#### Removed +- [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0001-5208-3432](http://orcid.org/0000-0001-5208-3432) + + + +### has_rank `http://purl.obolibrary.org/obo/ncbitaxon#has_rank` +#### Removed +- AnnotationProperty: [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) + - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:67601" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### has_related_synonym `http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym` +#### Removed +- [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0001-5208-3432](http://orcid.org/0000-0001-5208-3432) -### anatomical row `http://purl.obolibrary.org/obo/UBERON_0034926` + +### head `http://purl.obolibrary.org/obo/UBERON_0000033` #### Removed -- [anatomical row](http://purl.obolibrary.org/obo/UBERON_0034926) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00100152" +- [head](http://purl.obolibrary.org/obo/UBERON_0000033) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010335" -#### Added -- [anatomical row](http://purl.obolibrary.org/obo/UBERON_0034926) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00100152" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### anatomical space `http://purl.obolibrary.org/obo/UBERON_0000464` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + +- [head](http://purl.obolibrary.org/obo/UBERON_0000033) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001114" + +- [head](http://purl.obolibrary.org/obo/UBERON_0000033) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.82" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001644" + +- [head](http://purl.obolibrary.org/obo/UBERON_0000033) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [heart](http://purl.obolibrary.org/obo/UBERON_0000948) + + + +### head connective tissue `http://purl.obolibrary.org/obo/UBERON_0003566` #### Removed -- [anatomical space](http://purl.obolibrary.org/obo/UBERON_0000464) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007017" +- [head connective tissue](http://purl.obolibrary.org/obo/UBERON_0003566) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:16098" -#### Added -- [anatomical space](http://purl.obolibrary.org/obo/UBERON_0000464) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007017" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### anatomical structure `http://purl.obolibrary.org/obo/UBERON_0000061` +### head external integument structure `http://purl.obolibrary.org/obo/UBERON_3000972` #### Removed -- [anatomical structure](http://purl.obolibrary.org/obo/UBERON_0000061) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007001" +- [head external integument structure](http://purl.obolibrary.org/obo/UBERON_3000972) [UBPROP_0000004](http://purl.obolibrary.org/obo/UBPROP_0000004) "This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://purl.obolibrary.org/obo/aao.owl" + -#### Added -- [anatomical structure](http://purl.obolibrary.org/obo/UBERON_0000061) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007001" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +### head mesenchyme `http://purl.obolibrary.org/obo/UBERON_0005253` +#### Removed +- [head mesenchyme](http://purl.obolibrary.org/obo/UBERON_0005253) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Mesoderm that will give rise, along with cranial neural crest cells, to connective tissue, bone and musculature in the head. (Source: BioGlossary, www.Biology-Text.com)[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -### anatomical structure development `http://purl.obolibrary.org/obo/GO_0048856` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000113" -#### Added -- [anatomical structure development](http://purl.obolibrary.org/obo/GO_0048856) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/geneontology/go-ontology/issues/26424"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -- [anatomical structure development](http://purl.obolibrary.org/obo/GO_0048856) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [gocheck_do_not_annotate](http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -### anatomical system `http://purl.obolibrary.org/obo/UBERON_0000467` + +### head paraxial mesoderm `http://purl.obolibrary.org/obo/UBERON_0009617` #### Removed -- [anatomical system](http://purl.obolibrary.org/obo/UBERON_0000467) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "IDOMAL:0002460" - - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0003-4423-4370" +- [head paraxial mesoderm](http://purl.obolibrary.org/obo/UBERON_0009617) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "A major contributor to neurocranium [PMID:16313393]" -- [anatomical system](http://purl.obolibrary.org/obo/UBERON_0000467) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004856" -#### Added -- [anatomical system](http://purl.obolibrary.org/obo/UBERON_0000467) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "IDOMAL:0002460" + +### head sensillum `http://purl.obolibrary.org/obo/UBERON_0000963` +#### Removed +- [head sensillum](http://purl.obolibrary.org/obo/UBERON_0000963) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004114" - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" - - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) -- [anatomical system](http://purl.obolibrary.org/obo/UBERON_0000467) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004856" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +### head somite `http://purl.obolibrary.org/obo/UBERON_0005594` +#### Removed +- [head somite](http://purl.obolibrary.org/obo/UBERON_0005594) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "in humans this includes somites 1-4" +- [head somite](http://purl.obolibrary.org/obo/UBERON_0005594) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "EHDAA2 has both 'head somite' and 'head somite group', with part_of and develops_from for latter" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EHDAA2" -### anlage `http://purl.obolibrary.org/obo/UBERON_0007688` -#### Removed -- [anlage](http://purl.obolibrary.org/obo/UBERON_0007688) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005426" +- [head somite](http://purl.obolibrary.org/obo/UBERON_0005594) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "They provide the epaxial and hypaxial muscles of the neck, the pharyngeal and laryngeal muscles that develop in the caudal branchial arches and the musculature of the tongue. Despite their localisation in the head, myogenic precursors from occipital somites essentially follow the trunk programmes (E. H. Walters and S. D., unpublished). during evolution, have been secondarily incorporated into the head (Gans and Northcutt, 1983)" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:11830559" + + + +### head taste bud `http://purl.obolibrary.org/obo/UBERON_0034720` #### Added -- [anlage](http://purl.obolibrary.org/obo/UBERON_0007688) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005426" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [head taste bud](http://purl.obolibrary.org/obo/UBERON_0034720) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### annulus fibrosus `http://purl.obolibrary.org/obo/UBERON_0006444` +### heart `http://purl.obolibrary.org/obo/UBERON_0000948` #### Removed -- [annulus fibrosus](http://purl.obolibrary.org/obo/UBERON_0006444) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D000070616" +- [heart](http://purl.obolibrary.org/obo/UBERON_0000948) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -#### Added -- [annulus fibrosus](http://purl.obolibrary.org/obo/UBERON_0006444) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D000070616" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010210" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +- [heart](http://purl.obolibrary.org/obo/UBERON_0000948) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000114" -### anterior chamber of eyeball `http://purl.obolibrary.org/obo/UBERON_0001766` -#### Removed -- [anterior chamber of eyeball](http://purl.obolibrary.org/obo/UBERON_0001766) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "camera anterior bulbi oculi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Anterior_chamber_of_eyeball" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -#### Added -- [anterior chamber of eyeball](http://purl.obolibrary.org/obo/UBERON_0001766) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "camera anterior bulbi oculi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [heart](http://purl.obolibrary.org/obo/UBERON_0000948) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Anterior_chamber_of_eyeball" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### anterior lens cell `http://purl.obolibrary.org/obo/CL_0002223` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000276" -#### Added -- [anterior lens cell](http://purl.obolibrary.org/obo/CL_0002223) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481" +- [heart](http://purl.obolibrary.org/obo/UBERON_0000948) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "cardiac" -### anterior limiting lamina of cornea `http://purl.obolibrary.org/obo/UBERON_0004370` -#### Removed -- [anterior limiting lamina of cornea](http://purl.obolibrary.org/obo/UBERON_0004370) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lamina limitans anterior corneae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58273" +- [heart](http://purl.obolibrary.org/obo/UBERON_0000948) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" -- [anterior limiting lamina of cornea](http://purl.obolibrary.org/obo/UBERON_0004370) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "Reichert's membrane" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [DUBIOUS](http://purl.obolibrary.org/obo/uberon/core#DUBIOUS) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010210" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://sourceforge.net/tracker/?func=detail&aid=2956371&group_id=76834&atid=974957" + + +### heart elastic tissue `http://purl.obolibrary.org/obo/UBERON_0003610` #### Added -- [anterior limiting lamina of cornea](http://purl.obolibrary.org/obo/UBERON_0004370) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lamina limitans anterior corneae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [heart elastic tissue](http://purl.obolibrary.org/obo/UBERON_0003610) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58273" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### heart endothelium `http://purl.obolibrary.org/obo/UBERON_0008307` +#### Removed +- [heart endothelium](http://purl.obolibrary.org/obo/UBERON_0008307) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "this class includes any endothelia that are part of the heart. This might include the endocardial epithelia, as well as endothelia of vessels that are considered strictly part of the heart (e.g. outflow tract). As a grouping class, this may lack utility, and pending review this class may be obsoleted. For annotation consider a more specific class." -- [anterior limiting lamina of cornea](http://purl.obolibrary.org/obo/UBERON_0004370) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "Reichert's membrane" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003002](http://purl.obolibrary.org/obo/OMO_0003002) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://sourceforge.net/tracker/?func=detail&aid=2956371&group_id=76834&atid=974957" +### heart layer `http://purl.obolibrary.org/obo/UBERON_0005983` -### anterior part of tongue `http://purl.obolibrary.org/obo/UBERON_0010032` +#### Added +- [heart layer](http://purl.obolibrary.org/obo/UBERON_0005983) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### heart left ventricle `http://purl.obolibrary.org/obo/UBERON_0002084` #### Removed -- [anterior part of tongue](http://purl.obolibrary.org/obo/UBERON_0010032) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pars anterior dorsi linguae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Anterior_tongue" +- [heart left ventricle](http://purl.obolibrary.org/obo/UBERON_0002084) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [heart left ventricle](http://purl.obolibrary.org/obo/UBERON_0002084) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Thick-walled muscular chamber constituting the left border and apex of the heart. It receives oxygenated blood from the left atrium through the mitral orifice and send it off into the aorta. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [anterior part of tongue](http://purl.obolibrary.org/obo/UBERON_0010032) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pars anterior dorsi linguae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Anterior_tongue" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000718" -### anterior segment of eyeball `http://purl.obolibrary.org/obo/UBERON_0001801` -#### Removed -- [anterior segment of eyeball](http://purl.obolibrary.org/obo/UBERON_0001801) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "segmentum anterius bulbi oculi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Anterior_segment_of_eyeball" +- [heart left ventricle](http://purl.obolibrary.org/obo/UBERON_0002084) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The vertebrate heart initially forms as a tube from a population of precursor cells termed the first heart field (FHF). Cells from the adjacent second heart field (SHF) are then progressively added to the developing heart. In avian and mammalian hearts, the FHF contributes mainly to the left ventricle, whereas the SHF gives rise to the outflow tract and large portions of the right ventricle and atria. Both fields arise from common mesodermal progenitors, although the detailed lineage relationships between FHF and SHF remain uncertain.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [anterior segment of eyeball](http://purl.obolibrary.org/obo/UBERON_0001801) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "segmentum anterius bulbi oculi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Anterior_segment_of_eyeball" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000718" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1126/science.1190181 Stolfi A, Gainous TB, Young JJ, Mori A, Levine M, Christiaen L, Early chordate origins of the vertebrate second heart field. Science (2010)" -### anterior surface of prostate `http://purl.obolibrary.org/obo/UBERON_0035523` +- [heart left ventricle](http://purl.obolibrary.org/obo/UBERON_0002084) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In mammals continuous with aorta" + + + +### heart primordium `http://purl.obolibrary.org/obo/UBERON_0003084` #### Removed -- [anterior surface of prostate](http://purl.obolibrary.org/obo/UBERON_0035523) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "facies anterior prostatae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:19591" +- [heart primordium](http://purl.obolibrary.org/obo/UBERON_0003084) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -#### Added -- [anterior surface of prostate](http://purl.obolibrary.org/obo/UBERON_0035523) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "facies anterior prostatae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000028" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:19591" +- [heart primordium](http://purl.obolibrary.org/obo/UBERON_0003084) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "XAO:curator" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0011044" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### anterior tibial vein `http://purl.obolibrary.org/obo/UBERON_0001545` +- [heart primordium](http://purl.obolibrary.org/obo/UBERON_0003084) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO]" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000028" + + + +### heart right ventricle `http://purl.obolibrary.org/obo/UBERON_0002080` #### Removed -- [anterior tibial vein](http://purl.obolibrary.org/obo/UBERON_0001545) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "venae tibiales anteriores" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Anterior_tibial_vein" +- [heart right ventricle](http://purl.obolibrary.org/obo/UBERON_0002080) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [heart right ventricle](http://purl.obolibrary.org/obo/UBERON_0002080) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The muscular chamber on the right and in front of the left ventricle. It generally receives venous blood from the right atrium and conveys it into the pulmonary artery. [(1988)_Dorian_AF, Amsterdam, Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B._Anatomy, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier's_Encyclopaedic_Dictionary_of_Medicine][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [anterior tibial vein](http://purl.obolibrary.org/obo/UBERON_0001545) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "venae tibiales anteriores" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Anterior_tibial_vein" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000717" -### anterior vena cava `http://purl.obolibrary.org/obo/UBERON_0001585` +- [heart right ventricle](http://purl.obolibrary.org/obo/UBERON_0002080) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In mammals continuous with the pulmonary arteries" + + + +### heart rudiment `http://purl.obolibrary.org/obo/UBERON_0004291` #### Removed -- [anterior vena cava](http://purl.obolibrary.org/obo/UBERON_0001585) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena cava superior" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Superior_vena_cava" +- [heart rudiment](http://purl.obolibrary.org/obo/UBERON_0004291) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000115" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0002683" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -- [anterior vena cava](http://purl.obolibrary.org/obo/UBERON_0001585) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena maxima" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Superior_vena_cava" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [anterior vena cava](http://purl.obolibrary.org/obo/UBERON_0001585) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena cava superior" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Superior_vena_cava" +### heart tube `http://purl.obolibrary.org/obo/UBERON_0004141` +#### Removed +- [heart tube](http://purl.obolibrary.org/obo/UBERON_0004141) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "MP:0012700" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0002683" -- [anterior vena cava](http://purl.obolibrary.org/obo/UBERON_0001585) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena maxima" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Superior_vena_cava" +### helper property (not for use in curation) `http://purl.obolibrary.org/obo/RO_0002464` +#### Removed +- [helper property (not for use in curation)](http://purl.obolibrary.org/obo/RO_0002464) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) + +- [helper property (not for use in curation)](http://purl.obolibrary.org/obo/RO_0002464) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." -### anterograde trans-synaptic signaling by nitric oxide `http://purl.obolibrary.org/obo/GO_0098940` + +### hematopoietic system `http://purl.obolibrary.org/obo/UBERON_0002390` #### Removed -- [anterograde trans-synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0098940) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_synapse](http://purl.obolibrary.org/obo/go#goslim_synapse) +- [hematopoietic system](http://purl.obolibrary.org/obo/UBERON_0002390) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" -- [anterograde trans-synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0098940) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Cell-cell signaling from presynapse to postynapse, across the synaptic cleft, mediated by nitric oxide." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:dos" +- [hematopoietic system](http://purl.obolibrary.org/obo/UBERON_0002390) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical system that consists of the blood and blood forming tissues.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" -- [anterograde trans-synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0098940) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:0098940" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -- [anterograde trans-synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0098940) [label](http://www.w3.org/2000/01/rdf-schema#label) "anterograde trans-synaptic signaling by nitric oxide" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0011002" -- [anterograde trans-synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0098940) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -- Class: [anterograde trans-synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0098940) +- [hematopoietic system](http://purl.obolibrary.org/obo/UBERON_0002390) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001624" -- [anterograde trans-synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0098940) EquivalentTo [trans-synaptic signaling](http://purl.obolibrary.org/obo/GO_0099537) and ([has start location](http://purl.obolibrary.org/obo/RO_0002231) some [presynapse](http://purl.obolibrary.org/obo/GO_0098793)) and ([has end location](http://purl.obolibrary.org/obo/RO_0002232) some [postsynapse](http://purl.obolibrary.org/obo/GO_0098794)) and ([process has causal agent](http://purl.obolibrary.org/obo/RO_0002608) some [CHEBI_16480](http://purl.obolibrary.org/obo/CHEBI_16480)) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [anterograde trans-synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0098940) SubClassOf [anterograde trans-synaptic signaling](http://purl.obolibrary.org/obo/GO_0098916) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [anterograde trans-synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0098940) SubClassOf [trans-synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0099548) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1016/j.coph.2010.05.004 Ellett F, Lieschke GJ, Zebrafish as a model for vertebrate hematopoiesis. Current Opinion in Pharmacology (2010)" +- [hematopoietic system](http://purl.obolibrary.org/obo/UBERON_0002390) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "hematopoietic" -### anteroventral cochlear nucleus `http://purl.obolibrary.org/obo/UBERON_0002830` -#### Removed -- [anteroventral cochlear nucleus](http://purl.obolibrary.org/obo/UBERON_0002830) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus cochlearis anteroventralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:723" +- [hematopoietic system](http://purl.obolibrary.org/obo/UBERON_0002390) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [blood island](http://purl.obolibrary.org/obo/UBERON_0003061) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +#### Added +- [hematopoietic system](http://purl.obolibrary.org/obo/UBERON_0002390) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [blood island](http://purl.obolibrary.org/obo/UBERON_0003061) + + +### hematopoietic tissue `http://purl.obolibrary.org/obo/UBERON_0012429` +#### Removed +- [hematopoietic tissue](http://purl.obolibrary.org/obo/UBERON_0012429) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Bone marrow in humans, kidney interstitium in Danio, within a stroma of reticuloendothelial tissue" #### Added -- [anteroventral cochlear nucleus](http://purl.obolibrary.org/obo/UBERON_0002830) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus cochlearis anteroventralis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [hematopoietic tissue](http://purl.obolibrary.org/obo/UBERON_0012429) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:723" +### hemoglobin subunit zeta `http://purl.obolibrary.org/obo/PR_000008467` +#### Removed +- [hemoglobin subunit zeta](http://purl.obolibrary.org/obo/PR_000008467) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [hemoglobin subunit zeta (human)](http://purl.obolibrary.org/obo/PR_P02008) -### anteroventral periventricular nucleus `http://purl.obolibrary.org/obo/UBERON_0002690` + +### hemopoietic organ `http://purl.obolibrary.org/obo/UBERON_0004177` #### Removed -- [anteroventral periventricular nucleus](http://purl.obolibrary.org/obo/UBERON_0002690) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus periventricularis anteroventralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:382" +- [hemopoietic organ](http://purl.obolibrary.org/obo/UBERON_0004177) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "the FMA class 'lymphoid organ' is a general anatomical term" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [hemopoietic organ](http://purl.obolibrary.org/obo/UBERON_0004177) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "the organs in which the formed elements of the blood and lymph are produced[http://encyclopedia2.thefreedictionary.com/Hematopoietic+Organs]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://encyclopedia2.thefreedictionary.com/Hematopoietic+Organs" #### Added -- [anteroventral periventricular nucleus](http://purl.obolibrary.org/obo/UBERON_0002690) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus periventricularis anteroventralis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [hemopoietic organ](http://purl.obolibrary.org/obo/UBERON_0004177) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### hepatic acinus `http://purl.obolibrary.org/obo/UBERON_0001172` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:382" +#### Added +- [hepatic acinus](http://purl.obolibrary.org/obo/UBERON_0001172) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -### antimicrobial humoral response `http://purl.obolibrary.org/obo/GO_0019730` +### hepatic artery `http://purl.obolibrary.org/obo/UBERON_0001193` #### Removed -- [antimicrobial humoral response](http://purl.obolibrary.org/obo/GO_0019730) SubClassOf [defense response to other organism](http://purl.obolibrary.org/obo/GO_0098542) +- [hepatic artery](http://purl.obolibrary.org/obo/UBERON_0001193) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Artery that supplies blood to the liver.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -#### Added -- [antimicrobial humoral response](http://purl.obolibrary.org/obo/GO_0019730) SubClassOf [defense response to symbiont](http://purl.obolibrary.org/obo/GO_0140546) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005161" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -### anus `http://purl.obolibrary.org/obo/UBERON_0001245` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [hepatic artery](http://purl.obolibrary.org/obo/UBERON_0001193) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "currently defined in a generic fashion." + + + +### hepatic diverticulum `http://purl.obolibrary.org/obo/UBERON_0008835` #### Removed -- [anus](http://purl.obolibrary.org/obo/UBERON_0001245) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00047153" +- [hepatic diverticulum](http://purl.obolibrary.org/obo/UBERON_0008835) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "in mice, the hepatic diverticulum forms by E9 and expands into an obvious liver bud by E10" + +- [hepatic diverticulum](http://purl.obolibrary.org/obo/UBERON_0008835) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "The caudal part of the septum transversum is invaded by the hepatic diverticulum which divides within it to form the liver and thus gives rise to the ventral mesentery of the foregut." + +- [hepatic diverticulum](http://purl.obolibrary.org/obo/UBERON_0008835) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [septum transversum](http://purl.obolibrary.org/obo/UBERON_0004161) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "EHDAA2" + + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "caudal part" #### Added -- [anus](http://purl.obolibrary.org/obo/UBERON_0001245) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00047153" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [hepatic diverticulum](http://purl.obolibrary.org/obo/UBERON_0008835) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [septum transversum](http://purl.obolibrary.org/obo/UBERON_0004161) -### aorta `http://purl.obolibrary.org/obo/UBERON_0000947` +### hepatic duct `http://purl.obolibrary.org/obo/UBERON_0005171` #### Removed -- [aorta](http://purl.obolibrary.org/obo/UBERON_0000947) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria maxima" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Aorta" +- [hepatic duct](http://purl.obolibrary.org/obo/UBERON_0005171) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A duct that carries bile from the liver to the small intestine.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001100" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -#### Added -- [aorta](http://purl.obolibrary.org/obo/UBERON_0000947) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria maxima" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Aorta" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" +- [hepatic duct](http://purl.obolibrary.org/obo/UBERON_0005171) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The excretory duct of the liver or one of its branches in the lobes of the liver. [TFD][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000219" -### aortic endothelial cell `http://purl.obolibrary.org/obo/CL_0002544` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [aortic endothelial cell](http://purl.obolibrary.org/obo/CL_0002544) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### aortic sac `http://purl.obolibrary.org/obo/UBERON_0005432` -#### Removed -- [aortic sac](http://purl.obolibrary.org/obo/UBERON_0005432) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "saccus aorticus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/hepatic+duct" -#### Added -- [aortic sac](http://purl.obolibrary.org/obo/UBERON_0005432) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "saccus aorticus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [hepatic duct](http://purl.obolibrary.org/obo/UBERON_0005171) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The hepatic duct is the duct that leads from the liver to the bile duct[GO]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GO:0061011" -### aortic smooth muscle cell `http://purl.obolibrary.org/obo/CL_0002539` + +### hepatic duct smooth muscle `http://purl.obolibrary.org/obo/UBERON_0004834` #### Added -- [aortic smooth muscle cell](http://purl.obolibrary.org/obo/CL_0002539) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [hepatic duct smooth muscle](http://purl.obolibrary.org/obo/UBERON_0004834) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) -### aortico-pulmonary spiral septum `http://purl.obolibrary.org/obo/UBERON_0006207` +### hepatic portal system `http://purl.obolibrary.org/obo/UBERON_0010194` #### Removed -- [aortico-pulmonary spiral septum](http://purl.obolibrary.org/obo/UBERON_0006207) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "septum aorticopulmonale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Aorticopulmonary_septum" +- [hepatic portal system](http://purl.obolibrary.org/obo/UBERON_0010194) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Part of the circulatory system which includes the ventral abdominal vein, pelvic veins, and portal vein and collects blood from the pelvic region, liver, gall bladder and stomach.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010225" -#### Added -- [aortico-pulmonary spiral septum](http://purl.obolibrary.org/obo/UBERON_0006207) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "septum aorticopulmonale" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Aorticopulmonary_septum" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" -### apical ectodermal ridge `http://purl.obolibrary.org/obo/UBERON_0004356` + +### hepatic portal vein `http://purl.obolibrary.org/obo/UBERON_0001639` #### Removed -- [apical ectodermal ridge](http://purl.obolibrary.org/obo/UBERON_0004356) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "crista ectodermalis apicalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Apical_ectodermal_ridge" +- [hepatic portal vein](http://purl.obolibrary.org/obo/UBERON_0001639) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Adults of all vertebrates lose the vitelline veins and establish a single large hepatic portal vein (...) by the selective retention of parts of the left and right subintestinals and of several anastomoses that occur between them within and just posterior to the liver.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [apical ectodermal ridge](http://purl.obolibrary.org/obo/UBERON_0004356) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "crista ectodermalis apicalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000642" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Apical_ectodermal_ridge" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.265" -### apocrine gland `http://purl.obolibrary.org/obo/UBERON_0008974` +- [hepatic portal vein](http://purl.obolibrary.org/obo/UBERON_0001639) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In humans A vein in the abdominal cavity that drains blood from the gastrointestinal tract and spleen. It is usually formed by the confluence of the superior mesenteric and splenic veins, and also receives blood from the inferior mesenteric, gastric, and cystic veins. The hepatic portal vein is a major component of the hepatic portal system, one of the main portal venous systems in the body. Conditions involving the hepatic portal vein cause considerable illness and death. An important example of such a condition is elevated blood pressure in the hepatic portal vein. This condition, called portal hypertension, is a major complication of cirrhosis worldwide. [WP,unvetted]" + + + +### hepatic sinusoid `http://purl.obolibrary.org/obo/UBERON_0001281` #### Removed -- [apocrine gland](http://purl.obolibrary.org/obo/UBERON_0008974) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D001050" +- [hepatic sinusoid](http://purl.obolibrary.org/obo/UBERON_0001281) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) the amphibian liver has characteristics in common with both fish and terrestrial vertebrates. (...) The histological structure of the liver is similar to that in other vertebrates, with hepatocytes arranged in clusters and cords separated by a meshwork of sinusoids and the presence of the traditional triad of portal venule, hepatic arteriole, and bile duct.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1053/ax.2000.7133 Crawshaw GJ, Weinkle TK, Clinical and pathological aspects of the amphibian liver. Seminars in Avian and Exotic Pet Medicine (2000)" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000708" #### Added -- [apocrine gland](http://purl.obolibrary.org/obo/UBERON_0008974) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D001050" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [hepatic sinusoid](http://purl.obolibrary.org/obo/UBERON_0001281) SubClassOf [endo-epithelium](http://purl.obolibrary.org/obo/UBERON_0005911) - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +### hepatobiliary system `http://purl.obolibrary.org/obo/UBERON_0002423` +#### Removed +- [hepatobiliary system](http://purl.obolibrary.org/obo/UBERON_0002423) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "System responsible for the production and movement of bile[ZFIN:curator]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" +- [hepatobiliary system](http://purl.obolibrary.org/obo/UBERON_0002423) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "The hepaticobiliary system is responsible for metabolic and catabolic processing of small molecules absorbed from the blood or gut, hormones and serum proteins, detoxification, storage of glycogen, triglycerides, metals and lipid soluble vitamins and excretion of bile. Included are the synthesis of albumin, blood coagulation factors, complement, and specific binding proteins. The parts are: liver, bile duct, gall bladder and hepatic duct [GO:0061008]" -### apocrine sweat gland `http://purl.obolibrary.org/obo/UBERON_0000382` + + +### hepatopancreatic ampulla `http://purl.obolibrary.org/obo/UBERON_0004913` #### Removed -- [apocrine sweat gland](http://purl.obolibrary.org/obo/UBERON_0000382) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "glandula sudorifera apocrina" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Apocrine_sweat_gland" +- [hepatopancreatic ampulla](http://purl.obolibrary.org/obo/UBERON_0004913) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Ampulla formed by the union of the pancreatic duct and the common bile duct where they enter the intestine.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:ZDB-PUB-080414-12" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005167" -#### Added -- [apocrine sweat gland](http://purl.obolibrary.org/obo/UBERON_0000382) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "glandula sudorifera apocrina" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:ZDB-PUB-070212-11" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Apocrine_sweat_gland" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -### aponeurosis `http://purl.obolibrary.org/obo/UBERON_0006614` + + +### hexose transmembrane transporter activity `http://purl.obolibrary.org/obo/GO_0015149` #### Removed -- [aponeurosis](http://purl.obolibrary.org/obo/UBERON_0006614) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D000070606" +- [hexose transmembrane transporter activity](http://purl.obolibrary.org/obo/GO_0015149) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [hexose transmembrane transport](http://purl.obolibrary.org/obo/GO_0008645) + - [source](http://www.geneontology.org/formats/oboInOwl#http://purl.org/dc/terms/source) "GO_REF:0000090" #### Added -- [aponeurosis](http://purl.obolibrary.org/obo/UBERON_0006614) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D000070606" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [hexose transmembrane transporter activity](http://purl.obolibrary.org/obo/GO_0015149) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [hexose transmembrane transport](http://purl.obolibrary.org/obo/GO_0008645) - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +### high affinity immunoglobulin epsilon receptor subunit alpha `http://purl.obolibrary.org/obo/PR_000007431` +#### Removed +- [high affinity immunoglobulin epsilon receptor subunit alpha](http://purl.obolibrary.org/obo/PR_000007431) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [high affinity immunoglobulin epsilon receptor subunit alpha (human)](http://purl.obolibrary.org/obo/PR_P12319) -### appendage `http://purl.obolibrary.org/obo/UBERON_0000026` + +### high affinity immunoglobulin gamma Fc receptor I `http://purl.obolibrary.org/obo/PR_000001465` #### Removed -- [appendage](http://purl.obolibrary.org/obo/UBERON_0000026) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007000" +- [high affinity immunoglobulin gamma Fc receptor I](http://purl.obolibrary.org/obo/PR_000001465) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [high affinity immunoglobulin gamma Fc receptor I (human)](http://purl.obolibrary.org/obo/PR_P12314) -#### Added -- [appendage](http://purl.obolibrary.org/obo/UBERON_0000026) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007000" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### appendicular skeleton `http://purl.obolibrary.org/obo/UBERON_0002091` +### hindbrain `http://purl.obolibrary.org/obo/UBERON_0002028` #### Removed -- [appendicular skeleton](http://purl.obolibrary.org/obo/UBERON_0002091) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "skeleton appendiculare" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [hindbrain](http://purl.obolibrary.org/obo/UBERON_0002028) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The most posterior of the three principal regions of the brain, forming the rhombencephalon and all or most of the metencephalon. Kimmel et al, 1995.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Appendicular_skeleton" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -#### Added -- [appendicular skeleton](http://purl.obolibrary.org/obo/UBERON_0002091) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "skeleton appendiculare" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Appendicular_skeleton" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000029" +- [hindbrain](http://purl.obolibrary.org/obo/UBERON_0002028) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in MA, brainstem and hindbrain and part-of siblings under brain, consistent with FMA and NIF. See also notes for cerebellum. We weaken the relation in ABA to overlaps" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" -### aqueous humor of eyeball `http://purl.obolibrary.org/obo/UBERON_0001796` -#### Removed -- [aqueous humor of eyeball](http://purl.obolibrary.org/obo/UBERON_0001796) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "humor aquosus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58819" +- [hindbrain](http://purl.obolibrary.org/obo/UBERON_0002028) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [diencephalon](http://purl.obolibrary.org/obo/UBERON_0001894) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [hindbrain](http://purl.obolibrary.org/obo/UBERON_0002028) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: develops_from hindbrain neural tube (TAO:0007043)[TAO]" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000029" + +- [hindbrain](http://purl.obolibrary.org/obo/UBERON_0002028) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [midbrain](http://purl.obolibrary.org/obo/UBERON_0001891) + - [exceptions](http://www.geneontology.org/formats/oboInOwl#exceptions) "ZFA" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "https://github.com/obophenotype/uberon/issues/378" + + - [status](http://www.geneontology.org/formats/oboInOwl#status) "pending" + +- [hindbrain](http://purl.obolibrary.org/obo/UBERON_0002028) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Posterior part of the brain consisting of the cerebellum and medulla oblongata.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010150" + +- [hindbrain](http://purl.obolibrary.org/obo/UBERON_0002028) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000070" + +- [hindbrain](http://purl.obolibrary.org/obo/UBERON_0002028) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "rhombencephalic" + +- [hindbrain](http://purl.obolibrary.org/obo/UBERON_0002028) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + +- [hindbrain](http://purl.obolibrary.org/obo/UBERON_0002028) SubClassOf [overlaps](http://purl.obolibrary.org/obo/RO_0002131) some [brainstem](http://purl.obolibrary.org/obo/UBERON_0002298) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "modified-source-relation" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" #### Added -- [aqueous humor of eyeball](http://purl.obolibrary.org/obo/UBERON_0001796) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "humor aquosus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [hindbrain](http://purl.obolibrary.org/obo/UBERON_0002028) SubClassOf [overlaps](http://purl.obolibrary.org/obo/RO_0002131) some [brainstem](http://purl.obolibrary.org/obo/UBERON_0002298) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58819" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### hindbrain arachnoid mater `http://purl.obolibrary.org/obo/UBERON_0003559` +#### Removed +- [hindbrain arachnoid mater](http://purl.obolibrary.org/obo/UBERON_0003559) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### arachnoid trabecula `http://purl.obolibrary.org/obo/UBERON_0000439` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000236" + +- [hindbrain arachnoid mater](http://purl.obolibrary.org/obo/UBERON_0003559) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Arachnoid mater that is part of the hindbrain. [Bgee_curator][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000236" + + + +### hindbrain dura mater `http://purl.obolibrary.org/obo/UBERON_0003565` #### Removed -- [arachnoid trabecula](http://purl.obolibrary.org/obo/UBERON_0000439) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "trabecula arachnoideum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [hindbrain dura mater](http://purl.obolibrary.org/obo/UBERON_0003565) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Dura mater that is part of the hindbrain. [Bgee_curator][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000409" -#### Added -- [arachnoid trabecula](http://purl.obolibrary.org/obo/UBERON_0000439) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "trabecula arachnoideum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### arch of aorta `http://purl.obolibrary.org/obo/UBERON_0001508` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + +- [hindbrain dura mater](http://purl.obolibrary.org/obo/UBERON_0003565) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000409" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + + +### hindbrain pia mater `http://purl.obolibrary.org/obo/UBERON_0003554` #### Removed -- [arch of aorta](http://purl.obolibrary.org/obo/UBERON_0001508) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arcus aortae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:3768" +- [hindbrain pia mater](http://purl.obolibrary.org/obo/UBERON_0003554) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [arch of aorta](http://purl.obolibrary.org/obo/UBERON_0001508) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arcus aortae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:3768" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000466" + +- [hindbrain pia mater](http://purl.obolibrary.org/obo/UBERON_0003554) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Pia mater that is part of the hindbrain. [Bgee_curator][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000466" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### arcuate nucleus of hypothalamus `http://purl.obolibrary.org/obo/UBERON_0001932` +### hindbrain subarachnoid space `http://purl.obolibrary.org/obo/UBERON_0005219` #### Removed -- [arcuate nucleus of hypothalamus](http://purl.obolibrary.org/obo/UBERON_0001932) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus arcuatus (hypothalamus)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:395" +- [hindbrain subarachnoid space](http://purl.obolibrary.org/obo/UBERON_0005219) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Subarachnoid space that is part of the hindbrain. [Bgee_curator][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [arcuate nucleus of hypothalamus](http://purl.obolibrary.org/obo/UBERON_0001932) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus arcuatus hypothalami" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Arcuate_nucleus" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001303" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [arcuate nucleus of hypothalamus](http://purl.obolibrary.org/obo/UBERON_0001932) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus infundibularis hypothalami" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:395" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### hindbrain venous system `http://purl.obolibrary.org/obo/UBERON_0005720` -- [arcuate nucleus of hypothalamus](http://purl.obolibrary.org/obo/UBERON_0001932) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nucleus arcuatus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:62329" +#### Added +- [hindbrain venous system](http://purl.obolibrary.org/obo/UBERON_0005720) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### hindbrain-spinal cord boundary `http://purl.obolibrary.org/obo/UBERON_0005076` #### Added -- [arcuate nucleus of hypothalamus](http://purl.obolibrary.org/obo/UBERON_0001932) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nucleus arcuatus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [hindbrain-spinal cord boundary](http://purl.obolibrary.org/obo/UBERON_0005076) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:62329" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### hindgut `http://purl.obolibrary.org/obo/UBERON_0001046` +#### Removed +- [hindgut](http://purl.obolibrary.org/obo/UBERON_0001046) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "the caudal portion of the primitive digestive tube of the embryo" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "MP:0008786" -- [arcuate nucleus of hypothalamus](http://purl.obolibrary.org/obo/UBERON_0001932) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus infundibularis hypothalami" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [hindgut](http://purl.obolibrary.org/obo/UBERON_0001046) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000459" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:395" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [arcuate nucleus of hypothalamus](http://purl.obolibrary.org/obo/UBERON_0001932) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus arcuatus hypothalami" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Arcuate_nucleus" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [arcuate nucleus of hypothalamus](http://purl.obolibrary.org/obo/UBERON_0001932) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus arcuatus (hypothalamus)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11" + +- [hindgut](http://purl.obolibrary.org/obo/UBERON_0001046) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005384" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:395" +- [hindgut](http://purl.obolibrary.org/obo/UBERON_0001046) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in FMA this class has no children. In MA it has a single child hindgut epithelium" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" -### arm `http://purl.obolibrary.org/obo/UBERON_0001460` + +### hindlimb `http://purl.obolibrary.org/obo/UBERON_0002103` #### Removed -- [arm](http://purl.obolibrary.org/obo/UBERON_0001460) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "brachium" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Arm" +- [hindlimb](http://purl.obolibrary.org/obo/UBERON_0002103) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "crural" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [hindlimb](http://purl.obolibrary.org/obo/UBERON_0002103) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Lower limb, which connects the pes with the pelvic girdle.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" -#### Added -- [arm](http://purl.obolibrary.org/obo/UBERON_0001460) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "brachium" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000219" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Arm" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### arm bone `http://purl.obolibrary.org/obo/UBERON_0003460` -#### Removed -- [arm bone](http://purl.obolibrary.org/obo/UBERON_0003460) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D050280" +- [hindlimb](http://purl.obolibrary.org/obo/UBERON_0002103) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [arm bone](http://purl.obolibrary.org/obo/UBERON_0003460) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D050280" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000337" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268" -### arterial blood `http://purl.obolibrary.org/obo/UBERON_0013755` -#### Removed -- [arterial blood](http://purl.obolibrary.org/obo/UBERON_0013755) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006188" - - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0003-4423-4370" +- [hindlimb](http://purl.obolibrary.org/obo/UBERON_0002103) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "note that this corresponds to FMA:'free lower limb' (a limb segment), NOT 'lower limb'. Both MA and FMA consider shoulder (and shoulder bones) part of upper limb. Note that AAO class probably refers to skeleton" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" -#### Added -- [arterial blood](http://purl.obolibrary.org/obo/UBERON_0013755) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006188" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" - - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) +### hindlimb bone `http://purl.obolibrary.org/obo/UBERON_0003464` +#### Removed +- [hindlimb bone](http://purl.obolibrary.org/obo/UBERON_0003464) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "the MA class is actually bone of pelvic complex; in contrast the NCIT class excludes ilium etc" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" -### arteriole `http://purl.obolibrary.org/obo/UBERON_0001980` + +### hindlimb bud `http://purl.obolibrary.org/obo/UBERON_0005418` #### Removed -- [arteriole](http://purl.obolibrary.org/obo/UBERON_0001980) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteriola" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Arteriole" +- [hindlimb bud](http://purl.obolibrary.org/obo/UBERON_0005418) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The bilateral thickening of the ectoderm in the region of the first noticeable at NF stage 47, and innervated by NF stage 51. The hind limb buds develop before the forelimb buds.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "XAO:curator" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -#### Added -- [arteriole](http://purl.obolibrary.org/obo/UBERON_0001980) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteriola" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010382" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Arteriole" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### artery of lower lip `http://purl.obolibrary.org/obo/UBERON_0003471` -#### Removed -- [artery of lower lip](http://purl.obolibrary.org/obo/UBERON_0003471) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ramus labialis inferior arteriae facialis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Inferior_labial_artery" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### hindlimb joint `http://purl.obolibrary.org/obo/UBERON_0003840` +#### Removed +- [hindlimb joint](http://purl.obolibrary.org/obo/UBERON_0003840) [UBPROP_0000202](http://purl.obolibrary.org/obo/UBPROP_0000202) [FMA_71348](http://purl.obolibrary.org/obo/FMA_71348) -- [artery of lower lip](http://purl.obolibrary.org/obo/UBERON_0003471) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arteria labialis inferior" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Inferior_labial_artery" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [artery of lower lip](http://purl.obolibrary.org/obo/UBERON_0003471) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ramus labialis inferior arteriae facialis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### hindlimb skeleton `http://purl.obolibrary.org/obo/UBERON_0001441` +#### Removed +- [hindlimb skeleton](http://purl.obolibrary.org/obo/UBERON_0001441) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Skeletal structure of the paired, posterior appendages.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Inferior_labial_artery" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -- [artery of lower lip](http://purl.obolibrary.org/obo/UBERON_0003471) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arteria labialis inferior" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000217" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Inferior_labial_artery" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" +- [hindlimb skeleton](http://purl.obolibrary.org/obo/UBERON_0001441) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### artery of upper lip `http://purl.obolibrary.org/obo/UBERON_0003470` -#### Removed -- [artery of upper lip](http://purl.obolibrary.org/obo/UBERON_0003470) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arteria labialis superior" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Superior_labial_artery" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [artery of upper lip](http://purl.obolibrary.org/obo/UBERON_0003470) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ramus labialis superior arteriae facialis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Superior_labial_artery" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001255" -#### Added -- [artery of upper lip](http://purl.obolibrary.org/obo/UBERON_0003470) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ramus labialis superior arteriae facialis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Superior_labial_artery" +- [hindlimb skeleton](http://purl.obolibrary.org/obo/UBERON_0001441) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000217" -- [artery of upper lip](http://purl.obolibrary.org/obo/UBERON_0003470) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arteria labialis superior" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Superior_labial_artery" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### arthropod sensillum `http://purl.obolibrary.org/obo/UBERON_0002536` +### hindlimb stylopod `http://purl.obolibrary.org/obo/UBERON_0000376` #### Removed -- [arthropod sensillum](http://purl.obolibrary.org/obo/UBERON_0002536) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007152" +- [hindlimb stylopod](http://purl.obolibrary.org/obo/UBERON_0000376) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "Naming conventions for pod terms under discussion within phenoscape group." + - [see also](http://www.w3.org/2000/01/rdf-schema#seeAlso) "https://github.com/obophenotype/uberon/issues/61" -#### Added -- [arthropod sensillum](http://purl.obolibrary.org/obo/UBERON_0002536) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007152" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [hindlimb stylopod](http://purl.obolibrary.org/obo/UBERON_0000376) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### arthropod tagma `http://purl.obolibrary.org/obo/UBERON_6000002` -#### Removed -- [arthropod tagma](http://purl.obolibrary.org/obo/UBERON_6000002) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000002" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000349" -#### Added -- [arthropod tagma](http://purl.obolibrary.org/obo/UBERON_6000002) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000002" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268" -### articular capsule `http://purl.obolibrary.org/obo/UBERON_0001484` + + +### hindlimb zeugopod `http://purl.obolibrary.org/obo/UBERON_0003823` #### Removed -- [articular capsule](http://purl.obolibrary.org/obo/UBERON_0001484) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "capsulae articulares" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Articular_capsule" +- [hindlimb zeugopod](http://purl.obolibrary.org/obo/UBERON_0003823) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "Naming conventions for pod terms under discussion within phenoscape group. TODO - add distinct term for skeleton and place AAO class here" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [hindlimb zeugopod](http://purl.obolibrary.org/obo/UBERON_0003823) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA:24979 denotes the middle segment (zeugopod), its placement here is correct. See obo-anatomy archives for discussion" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" -- [articular capsule](http://purl.obolibrary.org/obo/UBERON_0001484) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "capsula articularis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [hindlimb zeugopod](http://purl.obolibrary.org/obo/UBERON_0003823) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "sural" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [hindlimb zeugopod](http://purl.obolibrary.org/obo/UBERON_0003823) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:34836" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [articular capsule](http://purl.obolibrary.org/obo/UBERON_0001484) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "capsula articularis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000348" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:34836" +- [hindlimb zeugopod](http://purl.obolibrary.org/obo/UBERON_0003823) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "VO:0010971" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -- [articular capsule](http://purl.obolibrary.org/obo/UBERON_0001484) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "capsulae articulares" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Articular_capsule" + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) -### articulation `http://purl.obolibrary.org/obo/UBERON_0004905` + +### hindlimb zeugopod bone `http://purl.obolibrary.org/obo/UBERON_0004251` #### Removed -- [articulation](http://purl.obolibrary.org/obo/UBERON_0004905) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005811" +- [hindlimb zeugopod bone](http://purl.obolibrary.org/obo/UBERON_0004251) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) -#### Added -- [articulation](http://purl.obolibrary.org/obo/UBERON_0004905) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005811" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### ascending aorta `http://purl.obolibrary.org/obo/UBERON_0001496` +### hindlimb zeugopod muscle `http://purl.obolibrary.org/obo/UBERON_0004256` #### Removed -- [ascending aorta](http://purl.obolibrary.org/obo/UBERON_0001496) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "aorta ascendens" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ascending_aorta" +- [hindlimb zeugopod muscle](http://purl.obolibrary.org/obo/UBERON_0004256) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "See notes on UBERON:0000978 for possible terminological confusion over term 'leg'" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [ascending aorta](http://purl.obolibrary.org/obo/UBERON_0001496) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pars ascendens aortae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ascending_aorta" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### hindlimb zeugopod skeleton `http://purl.obolibrary.org/obo/UBERON_0010720` +#### Removed +- [hindlimb zeugopod skeleton](http://purl.obolibrary.org/obo/UBERON_0010720) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Segment of the leg corresponding to the tibia and fibula.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" -#### Added -- [ascending aorta](http://purl.obolibrary.org/obo/UBERON_0001496) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "aorta ascendens" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ascending_aorta" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000216" -- [ascending aorta](http://purl.obolibrary.org/obo/UBERON_0001496) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pars ascendens aortae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ascending_aorta" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### ascending colon `http://purl.obolibrary.org/obo/UBERON_0001156` +### hip `http://purl.obolibrary.org/obo/UBERON_0001464` #### Removed -- [ascending colon](http://purl.obolibrary.org/obo/UBERON_0001156) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D044682" +- [hip](http://purl.obolibrary.org/obo/UBERON_0001464) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [ascending colon](http://purl.obolibrary.org/obo/UBERON_0001156) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "colon ascendens" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ascending_colon" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.333" -#### Added -- [ascending colon](http://purl.obolibrary.org/obo/UBERON_0001156) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "colon ascendens" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ascending_colon" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000346" -- [ascending colon](http://purl.obolibrary.org/obo/UBERON_0001156) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D044682" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [hip](http://purl.obolibrary.org/obo/UBERON_0001464) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "See notes for shoulder. in BTO this is part of the abdomen - this creates an inconsistency if limb and abdomen are spatially disjoint" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "BTO" - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) +- [hip](http://purl.obolibrary.org/obo/UBERON_0001464) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "coxal" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -### astrocyte `http://purl.obolibrary.org/obo/CL_0000127` +### hippocampal formation `http://purl.obolibrary.org/obo/UBERON_0002421` +#### Removed +- [hippocampal formation](http://purl.obolibrary.org/obo/UBERON_0002421) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "BTO:0000601 is placed here since it includes the DG. GO also includes dentate gyrus development as part of hippocampus development, so we assume when GO says 'hippocampus' it means 'hippocampal formation'. In ABA HPF = (.. subiculum) + HIP, HIP = DG + AH." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "BTO" -#### Added -- [astrocyte](http://purl.obolibrary.org/obo/CL_0000127) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [hippocampal formation](http://purl.obolibrary.org/obo/UBERON_0002421) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [olfactory bulb](http://purl.obolibrary.org/obo/UBERON_0002264) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" +- [hippocampal formation](http://purl.obolibrary.org/obo/UBERON_0002421) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "The term hippocampus is often used synonymously with hippocampal formation which consists of the hippocampus proper or Cornu Ammonis, the dentate gyrus and the subiculum" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "NIF" -### astrocyte of the cerebellum `http://purl.obolibrary.org/obo/CL_0002603` -#### Added -- [astrocyte of the cerebellum](http://purl.obolibrary.org/obo/CL_0002603) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### hippocampus fimbria `http://purl.obolibrary.org/obo/UBERON_0002310` +#### Removed +- [hippocampus fimbria](http://purl.obolibrary.org/obo/UBERON_0002310) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [fornix of brain](http://purl.obolibrary.org/obo/UBERON_0000052) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "Need to determine whether the fimbria is part of the fornix. Sometimes the language suggests it isn't always thought of that way, but I see no useful reason why it should be separate; it all forms one continuous white matter tract. Neuronames and others include this as part of the hippocampal formation (MM)" -### astrocyte of the cerebral cortex `http://purl.obolibrary.org/obo/CL_0002605` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "NIFSTD" #### Added -- [astrocyte of the cerebral cortex](http://purl.obolibrary.org/obo/CL_0002605) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [hippocampus fimbria](http://purl.obolibrary.org/obo/UBERON_0002310) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [fornix of brain](http://purl.obolibrary.org/obo/UBERON_0000052) -### atlanto-occipital joint `http://purl.obolibrary.org/obo/UBERON_0000220` +### hippocampus stratum lucidum `http://purl.obolibrary.org/obo/UBERON_0007637` #### Removed -- [atlanto-occipital joint](http://purl.obolibrary.org/obo/UBERON_0000220) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D001269" +- [hippocampus stratum lucidum](http://purl.obolibrary.org/obo/UBERON_0007637) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NCIT:C33629" -- [atlanto-occipital joint](http://purl.obolibrary.org/obo/UBERON_0000220) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "articulatio atlantooccipitalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Atlanto-occipital_joint" +- [hippocampus stratum lucidum](http://purl.obolibrary.org/obo/UBERON_0007637) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "SCTID:419156002" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [atlanto-occipital joint](http://purl.obolibrary.org/obo/UBERON_0000220) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D001269" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) +### hippocampus stratum radiatum `http://purl.obolibrary.org/obo/UBERON_0005372` +#### Removed +- [hippocampus stratum radiatum](http://purl.obolibrary.org/obo/UBERON_0005372) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "contains septal and commissural fibers. It also contains Schaffer collateral fibers, which are the projection forward from CA3 to CA1. Some interneurons that can be found in more superficial layers can also be found here, including basket cells, bistratified cells, and radial trilaminar cells" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -- [atlanto-occipital joint](http://purl.obolibrary.org/obo/UBERON_0000220) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "articulatio atlantooccipitalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Atlanto-occipital_joint" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### homeobox protein Meis2 `http://purl.obolibrary.org/obo/PR_000010317` +#### Removed +- [homeobox protein Meis2](http://purl.obolibrary.org/obo/PR_000010317) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [homeobox protein Meis2 (human)](http://purl.obolibrary.org/obo/PR_O14770) -### atrioventricular node `http://purl.obolibrary.org/obo/UBERON_0002352` + +### humerus `http://purl.obolibrary.org/obo/UBERON_0000976` #### Removed -- [atrioventricular node](http://purl.obolibrary.org/obo/UBERON_0002352) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nodus atrioventricularis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Atrioventricular_node" +- [humerus](http://purl.obolibrary.org/obo/UBERON_0000976) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "humeral" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [humerus](http://purl.obolibrary.org/obo/UBERON_0000976) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001158" -- [atrioventricular node](http://purl.obolibrary.org/obo/UBERON_0002352) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nodus atrioventricularis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [atrioventricular node](http://purl.obolibrary.org/obo/UBERON_0002352) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nodus atrioventricularis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268" -- [atrioventricular node](http://purl.obolibrary.org/obo/UBERON_0002352) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nodus atrioventricularis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [humerus](http://purl.obolibrary.org/obo/UBERON_0000976) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Paired, elongate, cylindrical bones of endochondral origin that extend from the pectoral girdle to the elbows.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Atrioventricular_node" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000679" -### author_id `https://w3id.org/sssom/author_id` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -#### Added -- AnnotationProperty: [author_id](https://w3id.org/sssom/author_id) +- [humerus](http://purl.obolibrary.org/obo/UBERON_0000976) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [humerus cartilage element](http://purl.obolibrary.org/obo/UBERON_0006245) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" +#### Added +- [humerus](http://purl.obolibrary.org/obo/UBERON_0000976) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [humerus cartilage element](http://purl.obolibrary.org/obo/UBERON_0006245) -### autonomic ganglion `http://purl.obolibrary.org/obo/UBERON_0001805` -#### Removed -- [autonomic ganglion](http://purl.obolibrary.org/obo/UBERON_0001805) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ganglion autonomicum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Autonomic_ganglion" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### humerus diaphysis `http://purl.obolibrary.org/obo/UBERON_0004652` #### Added -- [autonomic ganglion](http://purl.obolibrary.org/obo/UBERON_0001805) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ganglion autonomicum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Autonomic_ganglion" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [humerus diaphysis](http://purl.obolibrary.org/obo/UBERON_0004652) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### autonomic nerve plexus `http://purl.obolibrary.org/obo/UBERON_0001816` +### hyaline cartilage tissue `http://purl.obolibrary.org/obo/UBERON_0001994` #### Removed -- [autonomic nerve plexus](http://purl.obolibrary.org/obo/UBERON_0001816) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "plexus visceralis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [hyaline cartilage tissue](http://purl.obolibrary.org/obo/UBERON_0001994) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Cartilage tissue primarily composed of type II collagen (thin fibrils) and a glassy appearance.[VSAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000094" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:5910" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PSPUB:0000170" -- [autonomic nerve plexus](http://purl.obolibrary.org/obo/UBERON_0001816) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "plexus autonomicus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:5910" +- [hyaline cartilage tissue](http://purl.obolibrary.org/obo/UBERON_0001994) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Cartilage (tissue) which consists of chondrocytes and collagen, the intercellular matrix of which is an amorphous gel with a perichondrium[FMA:64783]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:64783" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [autonomic nerve plexus](http://purl.obolibrary.org/obo/UBERON_0001816) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "plexus nervosus visceralis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:5910" +### hyaloid cavity `http://purl.obolibrary.org/obo/UBERON_0005606` +#### Removed +- [hyaloid cavity](http://purl.obolibrary.org/obo/UBERON_0005606) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A depression in the front of the vitreous body, lodging the lens. [adapted_from_the_definition_of_the_hyaloid_fossa]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [autonomic nerve plexus](http://purl.obolibrary.org/obo/UBERON_0001816) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "plexus nervosus visceralis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:5910" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001477" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/hyaloid+fossa" -- [autonomic nerve plexus](http://purl.obolibrary.org/obo/UBERON_0001816) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "plexus visceralis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:5910" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### hyoglossus muscle `http://purl.obolibrary.org/obo/UBERON_0001572` +#### Removed +- [hyoglossus muscle](http://purl.obolibrary.org/obo/UBERON_0001572) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The hyoglossus is a muscle that attaches to the hyoid and tongue and is innervated by Cranial Nerve XII.[FEED]" + - [url](http://www.geneontology.org/formats/oboInOwl#url) "http://www.feedexp.org" -- [autonomic nerve plexus](http://purl.obolibrary.org/obo/UBERON_0001816) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "plexus autonomicus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "FEED" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:5910" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-07-02" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [hyoglossus muscle](http://purl.obolibrary.org/obo/UBERON_0001572) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: subclass hyobranchial muscles (AAO:0000224)[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010663" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -### autonomic nervous system `http://purl.obolibrary.org/obo/UBERON_0002410` -#### Removed -- [autonomic nervous system](http://purl.obolibrary.org/obo/UBERON_0002410) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "divisio autonomica systematis nervosi peripherici" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Autonomic_nervous_system" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [hyoglossus muscle](http://purl.obolibrary.org/obo/UBERON_0001572) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Makes up part of the tongue in frogs and salamanders.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BMZ" -#### Added -- [autonomic nervous system](http://purl.obolibrary.org/obo/UBERON_0002410) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "divisio autonomica systematis nervosi peripherici" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010663" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Autonomic_nervous_system" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -- [autonomic nervous system](http://purl.obolibrary.org/obo/UBERON_0002410) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "IDOMAL:0002126" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +- [hyoglossus muscle](http://purl.obolibrary.org/obo/UBERON_0001572) SubClassOf [has muscle origin](http://purl.obolibrary.org/obo/RO_0002372) some [hyoid bone](http://purl.obolibrary.org/obo/UBERON_0001685) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "dbpedia" + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "lingual process in horse" -### axial skeleton plus cranial skeleton `http://purl.obolibrary.org/obo/UBERON_0005944` -#### Removed -- [axial skeleton plus cranial skeleton](http://purl.obolibrary.org/obo/UBERON_0005944) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "skeleton axiale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Axial_skeleton" +#### Added +- [hyoglossus muscle](http://purl.obolibrary.org/obo/UBERON_0001572) SubClassOf [has muscle origin](http://purl.obolibrary.org/obo/RO_0002372) some [hyoid bone](http://purl.obolibrary.org/obo/UBERON_0001685) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [axial skeleton plus cranial skeleton](http://purl.obolibrary.org/obo/UBERON_0005944) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "skeleton axiale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Axial_skeleton" +### hyoid apparatus `http://purl.obolibrary.org/obo/UBERON_0010272` +#### Removed +- [hyoid apparatus](http://purl.obolibrary.org/obo/UBERON_0010272) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: part_of hyolaryngeal complex (AAO:0000226)[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000225" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### axilla `http://purl.obolibrary.org/obo/UBERON_0009472` -#### Removed -- [axilla](http://purl.obolibrary.org/obo/UBERON_0009472) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "axilla" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [hyoid apparatus](http://purl.obolibrary.org/obo/UBERON_0010272) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In most mammals, including humans, the hyoid apparatus is shaped like a horseshoe. However, in humans, some of the bones of the hyoid apparatus are fused into a single bone called os hyoideum. In other animals such as frogs, the hyoid apparatus has a hyoid body that is chiefly comprised of hyaline cartilage and two pairs of processes (i.e. alary process and the posteriolateral process)." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Axilla" +- [hyoid apparatus](http://purl.obolibrary.org/obo/UBERON_0010272) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Apparatus located in the floor of the mouth, under the mandibular arcade. The apparatus consists of a central corpus and four pairs of processes. This apparatus serves as the site of insertion for a variety of muscles associated with movements of the tongue and as the origin of the m. hyoglossus.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" -- [axilla](http://purl.obolibrary.org/obo/UBERON_0009472) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "regio axillaris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000225" -#### Added -- [axilla](http://purl.obolibrary.org/obo/UBERON_0009472) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "axilla" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Axilla" -- [axilla](http://purl.obolibrary.org/obo/UBERON_0009472) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "regio axillaris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### hyoid arch skeleton `http://purl.obolibrary.org/obo/UBERON_0005884` +#### Removed +- [hyoid arch skeleton](http://purl.obolibrary.org/obo/UBERON_0005884) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "it's not clear where AAO:'hyobranchial skeleton' belongs" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "AAO" -### axillary artery `http://purl.obolibrary.org/obo/UBERON_0001394` + +### hyoid bone `http://purl.obolibrary.org/obo/UBERON_0001685` #### Removed -- [axillary artery](http://purl.obolibrary.org/obo/UBERON_0001394) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arteria axillaris" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Axillary_artery" +- [hyoid bone](http://purl.obolibrary.org/obo/UBERON_0001685) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The hyoid bone is derived from the lower half of the second gill arch in fish, which separates the first gill slit from the spiracle. In many animals, it also incorporates elements of other gill arches, and has a correspondingly greater number of cornua. Amphibians and reptiles may have many cornua, while mammals (including humans) have two pairs, and birds only one. In birds, and some reptiles, the body of the hyoid is greatly extended forward, creating a solid bony support for the tongue. The howler monkey Alouatta has a pneumatized hyoid bone, one of the few cases of postcranial pneumatization of bones outside Saurischia." + - [see also](http://www.w3.org/2000/01/rdf-schema#seeAlso) "https://github.com/obophenotype/uberon/issues/548" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" -#### Added -- [axillary artery](http://purl.obolibrary.org/obo/UBERON_0001394) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arteria axillaris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [hyoid bone](http://purl.obolibrary.org/obo/UBERON_0001685) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: part_of hyoid plate (AAO:0000664)[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000684" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Axillary_artery" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### axillary nerve `http://purl.obolibrary.org/obo/UBERON_0001493` -#### Removed -- [axillary nerve](http://purl.obolibrary.org/obo/UBERON_0001493) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nervus axillaris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [hyoid bone](http://purl.obolibrary.org/obo/UBERON_0001685) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Paired processes that extend posterolaterally from the posterior margin of the hyoid plate. These processes are the ossified posteromedial processes and invest the laryngeal apparatus.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Axillary_nerve" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000684" -#### Added -- [axillary nerve](http://purl.obolibrary.org/obo/UBERON_0001493) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nervus axillaris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Axillary_nerve" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### axillary vein `http://purl.obolibrary.org/obo/UBERON_0000985` -#### Removed -- [axillary vein](http://purl.obolibrary.org/obo/UBERON_0000985) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vena axillaris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Axillary_vein" +### hypodermis `http://purl.obolibrary.org/obo/UBERON_0002072` +#### Removed +- [hypodermis](http://purl.obolibrary.org/obo/UBERON_0002072) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "hypodermal" -#### Added -- [axillary vein](http://purl.obolibrary.org/obo/UBERON_0000985) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vena axillaris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [hypodermis](http://purl.obolibrary.org/obo/UBERON_0002072) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D040521" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Axillary_vein" + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +- [hypodermis](http://purl.obolibrary.org/obo/UBERON_0002072) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "BTO has 'subcutis', as part of dermis. We follow FMA in having distinct classes for hypodermis and superficial fascia, and including these as part of the non-skin intgeument." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "BTO" -### axon tract `http://purl.obolibrary.org/obo/UBERON_0001018` -#### Removed -- [axon tract](http://purl.obolibrary.org/obo/UBERON_0001018) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005100" +- [hypodermis](http://purl.obolibrary.org/obo/UBERON_0002072) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells. Le Guellec et al, 2004.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001136" -#### Added -- [axon tract](http://purl.obolibrary.org/obo/UBERON_0001018) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005100" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -### basal cell `http://purl.obolibrary.org/obo/CL_0000646` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -#### Added -- [basal cell](http://purl.obolibrary.org/obo/CL_0000646) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [hypodermis](http://purl.obolibrary.org/obo/UBERON_0002072) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A layer separating the inner face of the dermis from the subjacent muscle cells. It is covered on both sides by a basement membrane. It contains pigment cells[FMA:70544]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:70544" +- [hypodermis](http://purl.obolibrary.org/obo/UBERON_0002072) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "subcutaneus" -### basal cell of epidermis `http://purl.obolibrary.org/obo/CL_0002187` +- [hypodermis](http://purl.obolibrary.org/obo/UBERON_0002072) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "subcutaneous" -#### Added -- [basal cell of epidermis](http://purl.obolibrary.org/obo/CL_0002187) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### basal cell of epithelium of trachea `http://purl.obolibrary.org/obo/CL_1000348` +### hypodermis skeletal muscle layer `http://purl.obolibrary.org/obo/UBERON_0008876` #### Added -- [basal cell of epithelium of trachea](http://purl.obolibrary.org/obo/CL_1000348) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [hypodermis skeletal muscle layer](http://purl.obolibrary.org/obo/UBERON_0008876) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### basal cell of prostate epithelium `http://purl.obolibrary.org/obo/CL_0002341` +### hypoglossal nerve `http://purl.obolibrary.org/obo/UBERON_0001650` +#### Removed +- [hypoglossal nerve](http://purl.obolibrary.org/obo/UBERON_0001650) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "In amphibians, represents the hypoglossal nerve in amniotes. Innverates mm. geniohyoideus, genioglossus, hyoglossus, rectus cervicis" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:080184780X" -#### Added -- [basal cell of prostate epithelium](http://purl.obolibrary.org/obo/CL_0002341) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [hypoglossal nerve](http://purl.obolibrary.org/obo/UBERON_0001650) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "we use a broad definition of this cranial nerve that encompasses the amphibian predecessor of true amniote hypoglossal nerves" +- [hypoglossal nerve](http://purl.obolibrary.org/obo/UBERON_0001650) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Nerve which innervates the muscles associated with the tongue including mm geniohyoideus, genioglossus, hyoglossus and rectus cervicis.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" -### basal epithelial cell of prostatic duct `http://purl.obolibrary.org/obo/CL_0002236` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010477" -#### Added -- [basal epithelial cell of prostatic duct](http://purl.obolibrary.org/obo/CL_0002236) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### basal epithelial cell of tracheobronchial tree `http://purl.obolibrary.org/obo/CL_0002329` +- [hypoglossal nerve](http://purl.obolibrary.org/obo/UBERON_0001650) [RO_0002174](http://purl.obolibrary.org/obo/RO_0002174) [NCBITaxon_8292](http://purl.obolibrary.org/obo/NCBITaxon_8292) -#### Added -- [basal epithelial cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002329) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [hypoglossal nerve](http://purl.obolibrary.org/obo/UBERON_0001650) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Cranial nerves XI and XII evolved in the common ancestor to amniotes (non-amphibian tetrapods) thus totalling twelve pairs.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### basal forebrain `http://purl.obolibrary.org/obo/UBERON_0002743` -#### Removed -- [basal forebrain](http://purl.obolibrary.org/obo/UBERON_0002743) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pars basalis telencephali" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Basal_forebrain" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000693" -- [basal forebrain](http://purl.obolibrary.org/obo/UBERON_0002743) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D066187" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Cranial_nerves" -#### Added -- [basal forebrain](http://purl.obolibrary.org/obo/UBERON_0002743) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pars basalis telencephali" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Basal_forebrain" +- [hypoglossal nerve](http://purl.obolibrary.org/obo/UBERON_0001650) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Cranial nerve that innervates muscles in the tongue. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-14, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [basal forebrain](http://purl.obolibrary.org/obo/UBERON_0002743) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D066187" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000693" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -### basal ganglion `http://purl.obolibrary.org/obo/UBERON_0002420` +### hypoglossal nucleus `http://purl.obolibrary.org/obo/UBERON_0002871` #### Removed -- [basal ganglion](http://purl.obolibrary.org/obo/UBERON_0002420) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nuclei basales" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Basal_ganglia" +- [hypoglossal nucleus](http://purl.obolibrary.org/obo/UBERON_0002871) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002872](http://purl.obolibrary.org/obo/UBERON_0002872) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [hypoglossal nucleus](http://purl.obolibrary.org/obo/UBERON_0002871) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002877](http://purl.obolibrary.org/obo/UBERON_0002877) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" -#### Added -- [basal ganglion](http://purl.obolibrary.org/obo/UBERON_0002420) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nuclei basales" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Basal_ganglia" +- [hypoglossal nucleus](http://purl.obolibrary.org/obo/UBERON_0002871) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0001719](http://purl.obolibrary.org/obo/UBERON_0001719) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [hypoglossal nucleus](http://purl.obolibrary.org/obo/UBERON_0002871) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002559](http://purl.obolibrary.org/obo/UBERON_0002559) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" +- [hypoglossal nucleus](http://purl.obolibrary.org/obo/UBERON_0002871) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002870](http://purl.obolibrary.org/obo/UBERON_0002870) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" -### basal nuclear complex `http://purl.obolibrary.org/obo/UBERON_0006098` -#### Removed -- [basal nuclear complex](http://purl.obolibrary.org/obo/UBERON_0006098) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "corpus striatum (Savel'ev)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:224" +- [hypoglossal nucleus](http://purl.obolibrary.org/obo/UBERON_0002871) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002127](http://purl.obolibrary.org/obo/UBERON_0002127) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [hypoglossal nucleus](http://purl.obolibrary.org/obo/UBERON_0002871) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002673](http://purl.obolibrary.org/obo/UBERON_0002673) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" -- [basal nuclear complex](http://purl.obolibrary.org/obo/UBERON_0006098) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ganglia basales" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:224" +- [hypoglossal nucleus](http://purl.obolibrary.org/obo/UBERON_0002871) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002155](http://purl.obolibrary.org/obo/UBERON_0002155) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [hypoglossal nucleus](http://purl.obolibrary.org/obo/UBERON_0002871) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002154](http://purl.obolibrary.org/obo/UBERON_0002154) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" -#### Added -- [basal nuclear complex](http://purl.obolibrary.org/obo/UBERON_0006098) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D001479" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -- [basal nuclear complex](http://purl.obolibrary.org/obo/UBERON_0006098) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "corpus striatum (Savel'ev)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### hypothalamus `http://purl.obolibrary.org/obo/UBERON_0001898` +#### Removed +- [hypothalamus](http://purl.obolibrary.org/obo/UBERON_0001898) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "For instance, the vertebrate ventral diencephalon generates the hypothalamus which functions as a major endocrine center in cooperation with the hypophysis, the anterior part of the pituitary gland, located just ventral to the hypothalamus. In the amphioxus brain, the presence of a hypothalamus-like structure has been reported associated with the ventrally located Hatschek's pit, the hypothetical hypophysial homologue. It is thus conceivable that a hypothalamus-like structure originally involved in endocrine functions may have already been present before the establishment of vertebrates.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:224" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [basal nuclear complex](http://purl.obolibrary.org/obo/UBERON_0006098) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ganglia basales" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:224" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1016/j.ydbio.2005.02.008 Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005)" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000179" -### basement membrane of epithelium `http://purl.obolibrary.org/obo/UBERON_0005769` -#### Removed -- [basement membrane of epithelium](http://purl.obolibrary.org/obo/UBERON_0005769) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "membrana basalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Basement_membrane" +- [hypothalamus](http://purl.obolibrary.org/obo/UBERON_0001898) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [dorsal plus ventral thalamus](http://purl.obolibrary.org/obo/UBERON_0001897) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [hypothalamus](http://purl.obolibrary.org/obo/UBERON_0001898) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "hypothalamic" -#### Added -- [basement membrane of epithelium](http://purl.obolibrary.org/obo/UBERON_0005769) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "membrana basalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [hypothalamus](http://purl.obolibrary.org/obo/UBERON_0001898) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A specialized brain region of the ventral diencephalon arising near the end of the segmentation period; the embryonic hypothalamic region will give rise to the posterior pituitary gland as well as a number of brain nuclei. Kimmel et al, 1995.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Basement_membrane" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000032" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -### basicranium `http://purl.obolibrary.org/obo/UBERON_0002517` -#### Removed -- [basicranium](http://purl.obolibrary.org/obo/UBERON_0002517) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "basis cranii" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:52801" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Base_of_skull" +- [hypothalamus](http://purl.obolibrary.org/obo/UBERON_0001898) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Part of the diencephalon ventral to the thalamus consisting of connecting fibers and is a center for control of the autonomous nervous system.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010484" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -#### Added -- [basicranium](http://purl.obolibrary.org/obo/UBERON_0002517) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "basis cranii" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:52801" +- [hypothalamus](http://purl.obolibrary.org/obo/UBERON_0001898) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "all vertebrates contain a hypothalamus" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Base_of_skull" +- [hypothalamus](http://purl.obolibrary.org/obo/UBERON_0001898) [RO_0002174](http://purl.obolibrary.org/obo/RO_0002174) [NCBITaxon_7737](http://purl.obolibrary.org/obo/NCBITaxon_7737) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "Lancelets possess a region similar to the hypothalamus (Murakami, 2005)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [hypothalamus](http://purl.obolibrary.org/obo/UBERON_0001898) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [thalamic complex](http://purl.obolibrary.org/obo/UBERON_0010225) + - [missing_from](http://www.geneontology.org/formats/oboInOwl#missing_from) "FMA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "EHDAA2" -### basophil `http://purl.obolibrary.org/obo/CL_0000767` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia" #### Added -- [basophil](http://purl.obolibrary.org/obo/CL_0000767) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [hypothalamus](http://purl.obolibrary.org/obo/UBERON_0001898) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [thalamic complex](http://purl.obolibrary.org/obo/UBERON_0010225) -### basophil mast progenitor cell `http://purl.obolibrary.org/obo/CL_0002028` - -#### Added -- [basophil mast progenitor cell](http://purl.obolibrary.org/obo/CL_0002028) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### ileum `http://purl.obolibrary.org/obo/UBERON_0002116` +#### Removed +- [ileum](http://purl.obolibrary.org/obo/UBERON_0002116) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "ileal" +- [ileum](http://purl.obolibrary.org/obo/UBERON_0002116) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The ileum is the final section of the small intestine in most higher vertebrates, including mammals, reptiles, and birds. In fish, the divisions of the small intestine are not as clear and the terms posterior intestine or distal intestine may be used instead of ileum.[Wikipedia:Ileum]" -### bicarbonate channel activity `http://purl.obolibrary.org/obo/GO_0160133` +- [ileum](http://purl.obolibrary.org/obo/UBERON_0002116) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11" -#### Added -- [bicarbonate channel activity](http://purl.obolibrary.org/obo/GO_0160133) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/geneontology/go-ontology/issues/26601"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [bicarbonate channel activity](http://purl.obolibrary.org/obo/GO_0160133) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "molecular_function" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [bicarbonate channel activity](http://purl.obolibrary.org/obo/GO_0160133) [creation date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2023-12-13T00:09:44Z" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [bicarbonate channel activity](http://purl.obolibrary.org/obo/GO_0160133) [created by](http://www.geneontology.org/formats/oboInOwl#created_by) "rynl" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000647" -- [bicarbonate channel activity](http://purl.obolibrary.org/obo/GO_0160133) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:0160133" +- [ileum](http://purl.obolibrary.org/obo/UBERON_0002116) SubClassOf [subdivision of digestive tract](http://purl.obolibrary.org/obo/UBERON_0004921) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "cjm" -- [bicarbonate channel activity](http://purl.obolibrary.org/obo/GO_0160133) [label](http://www.w3.org/2000/01/rdf-schema#label) "bicarbonate channel activity" + - [order](http://www.geneontology.org/formats/oboInOwl#order) "3" -- [bicarbonate channel activity](http://purl.obolibrary.org/obo/GO_0160133) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Enables the facilitated diffusion of a bicarbonate (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:18400985" +#### Added +- [ileum](http://purl.obolibrary.org/obo/UBERON_0002116) SubClassOf [subdivision of digestive tract](http://purl.obolibrary.org/obo/UBERON_0004921) -- Class: [bicarbonate channel activity](http://purl.obolibrary.org/obo/GO_0160133) -- [bicarbonate channel activity](http://purl.obolibrary.org/obo/GO_0160133) EquivalentTo [channel activity](http://purl.obolibrary.org/obo/GO_0015267) and ([has primary input](http://purl.obolibrary.org/obo/RO_0004009) some [CHEBI_17544](http://purl.obolibrary.org/obo/CHEBI_17544)) +### iliac artery `http://purl.obolibrary.org/obo/UBERON_0005609` +#### Removed +- [iliac artery](http://purl.obolibrary.org/obo/UBERON_0005609) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "we place the XAO structure here for now. In terms of analagy, it is more closely related to common iliac, but the relationships currently attached to this class are mammal specific" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "XAO" -- [bicarbonate channel activity](http://purl.obolibrary.org/obo/GO_0160133) SubClassOf [bicarbonate transmembrane transporter activity](http://purl.obolibrary.org/obo/GO_0015106) +- [iliac artery](http://purl.obolibrary.org/obo/UBERON_0005609) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "this is an extremely loose and flexible grouping class that is the superclass of the mammalian common iliac and its main brahces, together with analagous structures in other tetrapods" -- [bicarbonate channel activity](http://purl.obolibrary.org/obo/GO_0160133) SubClassOf [channel activity](http://purl.obolibrary.org/obo/GO_0015267) -### biliary tree `http://purl.obolibrary.org/obo/UBERON_0001173` +### iliac endochondral element `http://purl.obolibrary.org/obo/UBERON_0015054` #### Added -- [biliary tree](http://purl.obolibrary.org/obo/UBERON_0001173) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D001659" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) - - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +- [iliac endochondral element](http://purl.obolibrary.org/obo/UBERON_0015054) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### bipolar neuron `http://purl.obolibrary.org/obo/CL_0000103` +### iliac pre-cartilage condensation `http://purl.obolibrary.org/obo/UBERON_0006247` #### Added -- [bipolar neuron](http://purl.obolibrary.org/obo/CL_0000103) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [iliac pre-cartilage condensation](http://purl.obolibrary.org/obo/UBERON_0006247) SubClassOf [mesenchyme from somatopleure](http://purl.obolibrary.org/obo/UBERON_0010377) + +### ilioischiadic foramen `http://purl.obolibrary.org/obo/UBERON_0018326` + +#### Added +- [ilioischiadic foramen](http://purl.obolibrary.org/obo/UBERON_0018326) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### bladder cell `http://purl.obolibrary.org/obo/CL_1001319` -#### Added -- [bladder cell](http://purl.obolibrary.org/obo/CL_1001319) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### ilium `http://purl.obolibrary.org/obo/UBERON_0001273` +#### Removed +- [ilium](http://purl.obolibrary.org/obo/UBERON_0001273) [RO_0002174](http://purl.obolibrary.org/obo/RO_0002174) [NCBITaxon_8570](http://purl.obolibrary.org/obo/NCBITaxon_8570) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia" +- [ilium](http://purl.obolibrary.org/obo/UBERON_0001273) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "All reptiles have an ilium except snakes, although some snake species have a tiny bone which is considered to be an ilium" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" -### bladder urothelial cell `http://purl.obolibrary.org/obo/CL_1001428` +- [ilium](http://purl.obolibrary.org/obo/UBERON_0001273) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "this is_a hip bone in MA." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" -#### Added -- [bladder urothelial cell](http://purl.obolibrary.org/obo/CL_1001428) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [ilium](http://purl.obolibrary.org/obo/UBERON_0001273) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Paired, rodlike endochondral bones that constitute the anterior pelvic girdle.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -### blastocyst `http://purl.obolibrary.org/obo/UBERON_0000358` -#### Removed -- [blastocyst](http://purl.obolibrary.org/obo/UBERON_0000358) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "blastocystis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Blastocyst" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000772" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -#### Added -- [blastocyst](http://purl.obolibrary.org/obo/UBERON_0000358) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "blastocystis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [ilium](http://purl.obolibrary.org/obo/UBERON_0001273) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "iliac" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Blastocyst" -### blood brain barrier `http://purl.obolibrary.org/obo/UBERON_0000120` +### imaginal disc `http://purl.obolibrary.org/obo/UBERON_0000939` #### Removed -- [blood brain barrier](http://purl.obolibrary.org/obo/UBERON_0000120) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D001812" +- [imaginal disc](http://purl.obolibrary.org/obo/UBERON_0000939) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001761" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -#### Added -- [blood brain barrier](http://purl.obolibrary.org/obo/UBERON_0000120) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D001812" +- [imaginal disc](http://purl.obolibrary.org/obo/UBERON_0000939) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D060227" - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) @@ -2772,24624 +16449,22424 @@ - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -### blood cell `http://purl.obolibrary.org/obo/CL_0000081` -#### Added -- [blood cell](http://purl.obolibrary.org/obo/CL_0000081) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### immaterial anatomical entity `http://purl.obolibrary.org/obo/UBERON_0000466` +#### Removed +- [immaterial anatomical entity](http://purl.obolibrary.org/obo/UBERON_0000466) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007015" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + -### blood coagulation `http://purl.obolibrary.org/obo/GO_0007596` +### immature `http://purl.obolibrary.org/obo/PATO_0001501` #### Removed -- [blood coagulation](http://purl.obolibrary.org/obo/GO_0007596) EquivalentTo [coagulation](http://purl.obolibrary.org/obo/GO_0050817) and ([has primary output](http://purl.obolibrary.org/obo/RO_0004008) some [blood clot](http://purl.obolibrary.org/obo/UBERON_0010210)) +- [immature](http://purl.obolibrary.org/obo/PATO_0001501) [RO_0002604](http://purl.obolibrary.org/obo/RO_0002604) [PATO_0001701](http://purl.obolibrary.org/obo/PATO_0001701) -- [blood coagulation](http://purl.obolibrary.org/obo/GO_0007596) SubClassOf [has primary output](http://purl.obolibrary.org/obo/RO_0004008) some [blood clot](http://purl.obolibrary.org/obo/UBERON_0010210) -#### Added -- [blood coagulation](http://purl.obolibrary.org/obo/GO_0007596) EquivalentTo [coagulation](http://purl.obolibrary.org/obo/GO_0050817) and ([results in assembly of](http://purl.obolibrary.org/obo/RO_0002588) some [blood clot](http://purl.obolibrary.org/obo/UBERON_0010210)) -- [blood coagulation](http://purl.obolibrary.org/obo/GO_0007596) SubClassOf [results in assembly of](http://purl.obolibrary.org/obo/RO_0002588) some [blood clot](http://purl.obolibrary.org/obo/UBERON_0010210) +### immature eye `http://purl.obolibrary.org/obo/UBERON_0010312` +#### Removed +- [immature eye](http://purl.obolibrary.org/obo/UBERON_0010312) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Multi-tissue structure that consists of the structures that develop into the retina and lens.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -### blood nerve barrier `http://purl.obolibrary.org/obo/UBERON_0003209` -#### Removed -- [blood nerve barrier](http://purl.obolibrary.org/obo/UBERON_0003209) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D049428" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -#### Added -- [blood nerve barrier](http://purl.obolibrary.org/obo/UBERON_0003209) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D049428" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0002201" - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) +- [immature eye](http://purl.obolibrary.org/obo/UBERON_0010312) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [eye primordium](http://purl.obolibrary.org/obo/UBERON_0003071) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +#### Added +- [immature eye](http://purl.obolibrary.org/obo/UBERON_0010312) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [eye primordium](http://purl.obolibrary.org/obo/UBERON_0003071) -### blood vessel `http://purl.obolibrary.org/obo/UBERON_0001981` +### immediate transformation of `http://purl.obolibrary.org/obo/RO_0002495` #### Removed -- [blood vessel](http://purl.obolibrary.org/obo/UBERON_0001981) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vas sanguineum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Blood_vessel" +- [immediate transformation of](http://purl.obolibrary.org/obo/RO_0002495) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [immediate transformation of](http://purl.obolibrary.org/obo/RO_0002495) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "immediate_transformation_of" -#### Added -- [blood vessel](http://purl.obolibrary.org/obo/UBERON_0001981) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vas sanguineum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Blood_vessel" +- [immediate transformation of](http://purl.obolibrary.org/obo/RO_0002495) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002495" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [immediate transformation of](http://purl.obolibrary.org/obo/RO_0002495) [id](http://www.geneontology.org/formats/oboInOwl#id) "immediate_transformation_of" +- [immediate transformation of](http://purl.obolibrary.org/obo/RO_0002495) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) -### blood vessel endothelial cell `http://purl.obolibrary.org/obo/CL_0000071` +- [immediate transformation of](http://purl.obolibrary.org/obo/RO_0002495) [RO_0002575](http://purl.obolibrary.org/obo/RO_0002575) [transformation of](http://purl.obolibrary.org/obo/RO_0002494) -#### Added -- [blood vessel endothelial cell](http://purl.obolibrary.org/obo/CL_0000071) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### blood vessel endothelium `http://purl.obolibrary.org/obo/UBERON_0004638` +### immediately causally downstream of `http://purl.obolibrary.org/obo/RO_0002405` +#### Removed +- [immediately causally downstream of](http://purl.obolibrary.org/obo/RO_0002405) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [requires discussion](http://purl.obolibrary.org/obo/IAO_0000428) -#### Added -- [blood vessel endothelium](http://purl.obolibrary.org/obo/UBERON_0004638) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas) +- [immediately causally downstream of](http://purl.obolibrary.org/obo/RO_0002405) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) -- [blood vessel endothelium](http://purl.obolibrary.org/obo/UBERON_0004638) [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [Homo sapiens](http://purl.obolibrary.org/obo/NCBITaxon_9606) -### body of stomach `http://purl.obolibrary.org/obo/UBERON_0001161` +### immediately causally upstream of `http://purl.obolibrary.org/obo/RO_0002412` #### Removed -- [body of stomach](http://purl.obolibrary.org/obo/UBERON_0001161) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "corpus gastricum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0000505" +- [immediately causally upstream of](http://purl.obolibrary.org/obo/RO_0002412) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Body_of_stomach" +- [immediately causally upstream of](http://purl.obolibrary.org/obo/RO_0002412) [RO_0002575](http://purl.obolibrary.org/obo/RO_0002575) [causally upstream of](http://purl.obolibrary.org/obo/RO_0002411) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [body of stomach](http://purl.obolibrary.org/obo/UBERON_0001161) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "corpus gastricum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0000505" +### immediately deep to `http://purl.obolibrary.org/obo/BSPO_0001107` +#### Removed +- [immediately deep to](http://purl.obolibrary.org/obo/BSPO_0001107) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "immediately_deep_to" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Body_of_stomach" +- [immediately deep to](http://purl.obolibrary.org/obo/BSPO_0001107) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BSPO:0001107" +- [immediately deep to](http://purl.obolibrary.org/obo/BSPO_0001107) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" -### body proper `http://purl.obolibrary.org/obo/UBERON_0013702` -#### Removed -- [body proper](http://purl.obolibrary.org/obo/UBERON_0013702) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas) +- [immediately deep to](http://purl.obolibrary.org/obo/BSPO_0001107) [id](http://www.geneontology.org/formats/oboInOwl#id) "immediately_deep_to" -- [body proper](http://purl.obolibrary.org/obo/UBERON_0013702) [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [Homo sapiens](http://purl.obolibrary.org/obo/NCBITaxon_9606) +- [immediately deep to](http://purl.obolibrary.org/obo/BSPO_0001107) [label](http://www.w3.org/2000/01/rdf-schema#label) "immediately deep to" -### bone marrow `http://purl.obolibrary.org/obo/UBERON_0002371` +### immediately preceded by `http://purl.obolibrary.org/obo/RO_0002087` #### Removed -- [bone marrow](http://purl.obolibrary.org/obo/UBERON_0002371) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "medulla ossea" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0000141" +- [immediately preceded by](http://purl.obolibrary.org/obo/RO_0002087) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9608" +- [immediately preceded by](http://purl.obolibrary.org/obo/RO_0002087) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "starts_at_end_of" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [immediately preceded by](http://purl.obolibrary.org/obo/RO_0002087) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) "David Osumi-Sutherland" -- [bone marrow](http://purl.obolibrary.org/obo/UBERON_0002371) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "medulla ossium" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0000141" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Bone_marrow" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### immediately precedes `http://purl.obolibrary.org/obo/RO_0002090` +#### Removed +- [immediately precedes](http://purl.obolibrary.org/obo/RO_0002090) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "meets" -#### Added -- [bone marrow](http://purl.obolibrary.org/obo/UBERON_0002371) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "medulla ossea" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0000141" +- [immediately precedes](http://purl.obolibrary.org/obo/RO_0002090) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-7073-9172](https://orcid.org/0000-0002-7073-9172) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [immediately precedes](http://purl.obolibrary.org/obo/RO_0002090) [RO_0002575](http://purl.obolibrary.org/obo/RO_0002575) [precedes](http://purl.obolibrary.org/obo/BFO_0000063) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9608" +- [immediately precedes](http://purl.obolibrary.org/obo/RO_0002090) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "ends_at_start_of" -- [bone marrow](http://purl.obolibrary.org/obo/UBERON_0002371) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "medulla ossium" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0000141" +- [immediately precedes](http://purl.obolibrary.org/obo/RO_0002090) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) "David Osumi-Sutherland" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Bone_marrow" +### immediately superficial to `http://purl.obolibrary.org/obo/BSPO_0015014` +#### Removed +- [immediately superficial to](http://purl.obolibrary.org/obo/BSPO_0015014) [label](http://www.w3.org/2000/01/rdf-schema#label) "immediately superficial to" -### bone marrow cell `http://purl.obolibrary.org/obo/CL_0002092` +- [immediately superficial to](http://purl.obolibrary.org/obo/BSPO_0015014) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" -#### Added -- [bone marrow cell](http://purl.obolibrary.org/obo/CL_0002092) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [immediately superficial to](http://purl.obolibrary.org/obo/BSPO_0015014) [id](http://www.geneontology.org/formats/oboInOwl#id) "immediately_superficial_to" +- [immediately superficial to](http://purl.obolibrary.org/obo/BSPO_0015014) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "immediately_superficial_to" -### bony labyrinth `http://purl.obolibrary.org/obo/UBERON_0001839` +- [immediately superficial to](http://purl.obolibrary.org/obo/BSPO_0015014) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BSPO:0015014" + + + +### immune system `http://purl.obolibrary.org/obo/UBERON_0002405` #### Removed -- [bony labyrinth](http://purl.obolibrary.org/obo/UBERON_0001839) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "labyrinthus osseus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Bony_labyrinth" +- [immune system](http://purl.obolibrary.org/obo/UBERON_0002405) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [bony labyrinth](http://purl.obolibrary.org/obo/UBERON_0001839) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "labyrinthus osseus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:21046016 Dzik JM, The ancestry and cumulative evolution of immune reactions. Acta biochimica Polonica (2010)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Bony_labyrinth" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001247" -### bony vertebral centrum `http://purl.obolibrary.org/obo/UBERON_0001075` + + +### immunoglobulin iota chain `http://purl.obolibrary.org/obo/PR_000001858` #### Removed -- [bony vertebral centrum](http://purl.obolibrary.org/obo/UBERON_0001075) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "corpus vertebra" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [immunoglobulin iota chain](http://purl.obolibrary.org/obo/PR_000001858) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [immunoglobulin iota chain (human)](http://purl.obolibrary.org/obo/PR_P12018) -#### Added -- [bony vertebral centrum](http://purl.obolibrary.org/obo/UBERON_0001075) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "corpus vertebra" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### brachial nerve plexus `http://purl.obolibrary.org/obo/UBERON_0001814` +### immunoglobulin lambda-like polypeptide 1 `http://purl.obolibrary.org/obo/PR_000001859` #### Removed -- [brachial nerve plexus](http://purl.obolibrary.org/obo/UBERON_0001814) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "plexus brachialis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Brachial_plexus" +- [immunoglobulin lambda-like polypeptide 1](http://purl.obolibrary.org/obo/PR_000001859) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [immunoglobulin lambda-like polypeptide 1 (human)](http://purl.obolibrary.org/obo/PR_P15814) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [brachial nerve plexus](http://purl.obolibrary.org/obo/UBERON_0001814) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "plexus brachialis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Brachial_plexus" +### in anterior side of `http://purl.obolibrary.org/obo/BSPO_0000123` +#### Removed +- [in anterior side of](http://purl.obolibrary.org/obo/BSPO_0000123) [id](http://www.geneontology.org/formats/oboInOwl#id) "in_anterior_side_of" +- [in anterior side of](http://purl.obolibrary.org/obo/BSPO_0000123) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "in_anterior_side_of" -### brachiocephalic artery `http://purl.obolibrary.org/obo/UBERON_0001529` -#### Removed -- [brachiocephalic artery](http://purl.obolibrary.org/obo/UBERON_0001529) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "truncus brachiocephalicus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [in anterior side of](http://purl.obolibrary.org/obo/BSPO_0000123) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BSPO:0000123" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [in anterior side of](http://purl.obolibrary.org/obo/BSPO_0000123) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:3932" +- [in anterior side of](http://purl.obolibrary.org/obo/BSPO_0000123) [label](http://www.w3.org/2000/01/rdf-schema#label) "in anterior side of" -- [brachiocephalic artery](http://purl.obolibrary.org/obo/UBERON_0001529) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "truncus brachiocephalicus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Brachiocephalic_artery" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [brachiocephalic artery](http://purl.obolibrary.org/obo/UBERON_0001529) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "truncus brachiocephalicus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### in branching relationship with `http://purl.obolibrary.org/obo/RO_0002375` +#### Removed +- [in branching relationship with](http://purl.obolibrary.org/obo/RO_0002375) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Brachiocephalic_artery" +- [in branching relationship with](http://purl.obolibrary.org/obo/RO_0002375) [RO_0004036](http://purl.obolibrary.org/obo/RO_0004036) [part_of](http://purl.obolibrary.org/obo/BFO_0000050) -- [brachiocephalic artery](http://purl.obolibrary.org/obo/UBERON_0001529) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "truncus brachiocephalicus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [in branching relationship with](http://purl.obolibrary.org/obo/RO_0002375) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [in branching relationship with](http://purl.obolibrary.org/obo/RO_0002375) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [requires discussion](http://purl.obolibrary.org/obo/IAO_0000428) + +- [in branching relationship with](http://purl.obolibrary.org/obo/RO_0002375) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:3932" -### brachiocephalic vein `http://purl.obolibrary.org/obo/UBERON_0003711` +### in deep part of `http://purl.obolibrary.org/obo/BSPO_0001101` #### Removed -- [brachiocephalic vein](http://purl.obolibrary.org/obo/UBERON_0003711) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena brachiocephalica" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Brachiocephalic_vein" +- [in deep part of](http://purl.obolibrary.org/obo/BSPO_0001101) [id](http://www.geneontology.org/formats/oboInOwl#id) "in_deep_part_of" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [in deep part of](http://purl.obolibrary.org/obo/BSPO_0001101) [label](http://www.w3.org/2000/01/rdf-schema#label) "in deep part of" -- [brachiocephalic vein](http://purl.obolibrary.org/obo/UBERON_0003711) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "venae anonyma" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Brachiocephalic_vein" +- [in deep part of](http://purl.obolibrary.org/obo/BSPO_0001101) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [in deep part of](http://purl.obolibrary.org/obo/BSPO_0001101) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BSPO:0001101" -#### Added -- [brachiocephalic vein](http://purl.obolibrary.org/obo/UBERON_0003711) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "venae anonyma" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Brachiocephalic_vein" +- [in deep part of](http://purl.obolibrary.org/obo/BSPO_0001101) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "in_deep_part_of" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -- [brachiocephalic vein](http://purl.obolibrary.org/obo/UBERON_0003711) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena brachiocephalica" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Brachiocephalic_vein" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### in dorsal side of `http://purl.obolibrary.org/obo/BSPO_0015101` +#### Removed +- [in dorsal side of](http://purl.obolibrary.org/obo/BSPO_0015101) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" +- [in dorsal side of](http://purl.obolibrary.org/obo/BSPO_0015101) [id](http://www.geneontology.org/formats/oboInOwl#id) "in_dorsal_side_of" -### brain `http://purl.obolibrary.org/obo/UBERON_0000955` -#### Removed -- [brain](http://purl.obolibrary.org/obo/UBERON_0000955) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005095" +- [in dorsal side of](http://purl.obolibrary.org/obo/BSPO_0015101) [label](http://www.w3.org/2000/01/rdf-schema#label) "in dorsal side of" -#### Added -- [brain](http://purl.obolibrary.org/obo/UBERON_0000955) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005095" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [in dorsal side of](http://purl.obolibrary.org/obo/BSPO_0015101) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "in_dorsal_side_of" +- [in dorsal side of](http://purl.obolibrary.org/obo/BSPO_0015101) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BSPO:0015101" -### brain arachnoid mater `http://purl.obolibrary.org/obo/UBERON_0005397` + + +### in lateral side of `http://purl.obolibrary.org/obo/BSPO_0000126` #### Removed -- [brain arachnoid mater](http://purl.obolibrary.org/obo/UBERON_0005397) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arachnoidea mater encephali" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:83981" +- [in lateral side of](http://purl.obolibrary.org/obo/BSPO_0000126) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "in_lateral_side_of" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [in lateral side of](http://purl.obolibrary.org/obo/BSPO_0000126) [label](http://www.w3.org/2000/01/rdf-schema#label) "in lateral side of" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [in lateral side of](http://purl.obolibrary.org/obo/BSPO_0000126) [id](http://www.geneontology.org/formats/oboInOwl#id) "in_lateral_side_of" -- [brain arachnoid mater](http://purl.obolibrary.org/obo/UBERON_0005397) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arachnoidea mater cranialis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:83981" +- [in lateral side of](http://purl.obolibrary.org/obo/BSPO_0000126) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [in lateral side of](http://purl.obolibrary.org/obo/BSPO_0000126) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BSPO:0000126" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [brain arachnoid mater](http://purl.obolibrary.org/obo/UBERON_0005397) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arachnoidea mater cranialis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:83981" +### in left side of `http://purl.obolibrary.org/obo/BSPO_0000120` +#### Removed +- [in left side of](http://purl.obolibrary.org/obo/BSPO_0000120) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BSPO:0000120" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [in left side of](http://purl.obolibrary.org/obo/BSPO_0000120) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "in_left_side_of" -- [brain arachnoid mater](http://purl.obolibrary.org/obo/UBERON_0005397) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arachnoidea mater encephali" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [in left side of](http://purl.obolibrary.org/obo/BSPO_0000120) [id](http://www.geneontology.org/formats/oboInOwl#id) "in_left_side_of" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:83981" +- [in left side of](http://purl.obolibrary.org/obo/BSPO_0000120) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [in left side of](http://purl.obolibrary.org/obo/BSPO_0000120) [label](http://www.w3.org/2000/01/rdf-schema#label) "in left side of" -### brain dura mater `http://purl.obolibrary.org/obo/UBERON_0002092` + +### in posterior side of `http://purl.obolibrary.org/obo/BSPO_0000122` #### Removed -- [brain dura mater](http://purl.obolibrary.org/obo/UBERON_0002092) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "dura mater cranialis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71236" +- [in posterior side of](http://purl.obolibrary.org/obo/BSPO_0000122) [label](http://www.w3.org/2000/01/rdf-schema#label) "in posterior side of" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [in posterior side of](http://purl.obolibrary.org/obo/BSPO_0000122) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [in posterior side of](http://purl.obolibrary.org/obo/BSPO_0000122) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BSPO:0000122" -#### Added -- [brain dura mater](http://purl.obolibrary.org/obo/UBERON_0002092) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "dura mater cranialis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [in posterior side of](http://purl.obolibrary.org/obo/BSPO_0000122) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "in_posterior_side_of" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71236" +- [in posterior side of](http://purl.obolibrary.org/obo/BSPO_0000122) [id](http://www.geneontology.org/formats/oboInOwl#id) "in_posterior_side_of" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### brain pericyte `http://purl.obolibrary.org/obo/CL_2000043` +### in proximal side of `http://purl.obolibrary.org/obo/BSPO_0000124` +#### Removed +- [in proximal side of](http://purl.obolibrary.org/obo/BSPO_0000124) [id](http://www.geneontology.org/formats/oboInOwl#id) "in_proximal_side_of" -#### Added -- [brain pericyte](http://purl.obolibrary.org/obo/CL_2000043) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [in proximal side of](http://purl.obolibrary.org/obo/BSPO_0000124) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" +- [in proximal side of](http://purl.obolibrary.org/obo/BSPO_0000124) [label](http://www.w3.org/2000/01/rdf-schema#label) "in proximal side of" -### brainstem `http://purl.obolibrary.org/obo/UBERON_0002298` -#### Removed -- [brainstem](http://purl.obolibrary.org/obo/UBERON_0002298) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lamina medullaris accessoria" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:236" +- [in proximal side of](http://purl.obolibrary.org/obo/BSPO_0000124) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BSPO:0000124" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [in proximal side of](http://purl.obolibrary.org/obo/BSPO_0000124) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "in_proximal_side_of" -- [brainstem](http://purl.obolibrary.org/obo/UBERON_0002298) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "truncus encephalicus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0000146" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [brainstem](http://purl.obolibrary.org/obo/UBERON_0002298) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lamina medullaris incompleta pallidi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:236" +### in right side of `http://purl.obolibrary.org/obo/BSPO_0000121` +#### Removed +- [in right side of](http://purl.obolibrary.org/obo/BSPO_0000121) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [in right side of](http://purl.obolibrary.org/obo/BSPO_0000121) [id](http://www.geneontology.org/formats/oboInOwl#id) "in_right_side_of" -- [brainstem](http://purl.obolibrary.org/obo/UBERON_0002298) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lamina pallidi incompleta" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:236" +- [in right side of](http://purl.obolibrary.org/obo/BSPO_0000121) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BSPO:0000121" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [in right side of](http://purl.obolibrary.org/obo/BSPO_0000121) [label](http://www.w3.org/2000/01/rdf-schema#label) "in right side of" -- [brainstem](http://purl.obolibrary.org/obo/UBERON_0002298) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lamella pallidi incompleta" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:236" +- [in right side of](http://purl.obolibrary.org/obo/BSPO_0000121) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "in_right_side_of" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [brainstem](http://purl.obolibrary.org/obo/UBERON_0002298) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "truncus encephali" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Brainstem" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### in superficial part of `http://purl.obolibrary.org/obo/BSPO_0001100` +#### Removed +- [in superficial part of](http://purl.obolibrary.org/obo/BSPO_0001100) [label](http://www.w3.org/2000/01/rdf-schema#label) "in superficial part of" -#### Added -- [brainstem](http://purl.obolibrary.org/obo/UBERON_0002298) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "truncus encephalicus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [in superficial part of](http://purl.obolibrary.org/obo/BSPO_0001100) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BSPO:0001100" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0000146" +- [in superficial part of](http://purl.obolibrary.org/obo/BSPO_0001100) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" -- [brainstem](http://purl.obolibrary.org/obo/UBERON_0002298) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lamina medullaris incompleta pallidi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [in superficial part of](http://purl.obolibrary.org/obo/BSPO_0001100) [id](http://www.geneontology.org/formats/oboInOwl#id) "in_superficial_part_of" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:236" +- [in superficial part of](http://purl.obolibrary.org/obo/BSPO_0001100) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "in_superficial_part_of" -- [brainstem](http://purl.obolibrary.org/obo/UBERON_0002298) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lamella pallidi incompleta" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:236" -- [brainstem](http://purl.obolibrary.org/obo/UBERON_0002298) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lamina medullaris accessoria" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### in taxon `http://purl.obolibrary.org/obo/RO_0002162` +#### Removed +- [in taxon](http://purl.obolibrary.org/obo/RO_0002162) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:236" +- [in taxon](http://purl.obolibrary.org/obo/RO_0002162) [id](http://www.geneontology.org/formats/oboInOwl#id) "in_taxon" -- [brainstem](http://purl.obolibrary.org/obo/UBERON_0002298) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "truncus encephali" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Brainstem" +- [in taxon](http://purl.obolibrary.org/obo/RO_0002162) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) [20973947](http://www.ncbi.nlm.nih.gov/pubmed/20973947) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [in taxon](http://purl.obolibrary.org/obo/RO_0002162) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "in_taxon" -- [brainstem](http://purl.obolibrary.org/obo/UBERON_0002298) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lamina pallidi incompleta" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [in taxon](http://purl.obolibrary.org/obo/RO_0002162) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) [17921072](http://www.ncbi.nlm.nih.gov/pubmed/17921072) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:236" +- [in taxon](http://purl.obolibrary.org/obo/RO_0002162) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002162" +- [in taxon](http://purl.obolibrary.org/obo/RO_0002162) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) -### breast `http://purl.obolibrary.org/obo/UBERON_0000310` -#### Removed -- [breast](http://purl.obolibrary.org/obo/UBERON_0000310) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "mamma" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Breast" +- [in taxon](http://purl.obolibrary.org/obo/RO_0002162) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [in taxon](http://purl.obolibrary.org/obo/RO_0002162) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [X](https://orcid.org/0000-0001-9227-417X) -#### Added -- [breast](http://purl.obolibrary.org/obo/UBERON_0000310) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "mamma" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Breast" +- [existence ends during](http://purl.obolibrary.org/obo/RO_0002492) o [in taxon](http://purl.obolibrary.org/obo/RO_0002162) SubPropertyOf: [in taxon](http://purl.obolibrary.org/obo/RO_0002162) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [connected to](http://purl.obolibrary.org/obo/RO_0002170) o [in taxon](http://purl.obolibrary.org/obo/RO_0002162) SubPropertyOf: [in taxon](http://purl.obolibrary.org/obo/RO_0002162) +- [produces](http://purl.obolibrary.org/obo/RO_0003000) o [in taxon](http://purl.obolibrary.org/obo/RO_0002162) SubPropertyOf: [in taxon](http://purl.obolibrary.org/obo/RO_0002162) -### broad ligament of uterus `http://purl.obolibrary.org/obo/UBERON_0012332` -#### Removed -- [broad ligament of uterus](http://purl.obolibrary.org/obo/UBERON_0012332) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ligamentum latum uteri" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [continuous with](http://purl.obolibrary.org/obo/RO_0002150) o [in taxon](http://purl.obolibrary.org/obo/RO_0002162) SubPropertyOf: [in taxon](http://purl.obolibrary.org/obo/RO_0002162) -#### Added -- [broad ligament of uterus](http://purl.obolibrary.org/obo/UBERON_0012332) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ligamentum latum uteri" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [produced by](http://purl.obolibrary.org/obo/RO_0003001) o [in taxon](http://purl.obolibrary.org/obo/RO_0002162) SubPropertyOf: [in taxon](http://purl.obolibrary.org/obo/RO_0002162) +- [connects](http://purl.obolibrary.org/obo/RO_0002176) o [in taxon](http://purl.obolibrary.org/obo/RO_0002162) SubPropertyOf: [in taxon](http://purl.obolibrary.org/obo/RO_0002162) -### bronchial artery `http://purl.obolibrary.org/obo/UBERON_0002040` -#### Removed -- [bronchial artery](http://purl.obolibrary.org/obo/UBERON_0002040) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "rami bronchiales partis thoracicae aortae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Bronchial_artery" +- [supplies](http://purl.obolibrary.org/obo/RO_0002178) o [in taxon](http://purl.obolibrary.org/obo/RO_0002162) SubPropertyOf: [in taxon](http://purl.obolibrary.org/obo/RO_0002162) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [existence starts during](http://purl.obolibrary.org/obo/RO_0002488) o [in taxon](http://purl.obolibrary.org/obo/RO_0002162) SubPropertyOf: [in taxon](http://purl.obolibrary.org/obo/RO_0002162) -- [bronchial artery](http://purl.obolibrary.org/obo/UBERON_0002040) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteriae bronchiales" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Bronchial_artery" +- [attached to](http://purl.obolibrary.org/obo/RO_0002371) o [in taxon](http://purl.obolibrary.org/obo/RO_0002162) SubPropertyOf: [in taxon](http://purl.obolibrary.org/obo/RO_0002162) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [developmentally induced by](http://purl.obolibrary.org/obo/RO_0002256) o [in taxon](http://purl.obolibrary.org/obo/RO_0002162) SubPropertyOf: [in taxon](http://purl.obolibrary.org/obo/RO_0002162) -#### Added -- [bronchial artery](http://purl.obolibrary.org/obo/UBERON_0002040) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteriae bronchiales" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [overlaps](http://purl.obolibrary.org/obo/RO_0002131) o [in taxon](http://purl.obolibrary.org/obo/RO_0002162) SubPropertyOf: [in taxon](http://purl.obolibrary.org/obo/RO_0002162) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Bronchial_artery" +- [has potential to develop into](http://purl.obolibrary.org/obo/RO_0002387) o [in taxon](http://purl.obolibrary.org/obo/RO_0002162) SubPropertyOf: [in taxon](http://purl.obolibrary.org/obo/RO_0002162) -- [bronchial artery](http://purl.obolibrary.org/obo/UBERON_0002040) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "rami bronchiales partis thoracicae aortae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [innervated_by](http://purl.obolibrary.org/obo/RO_0002005) o [in taxon](http://purl.obolibrary.org/obo/RO_0002162) SubPropertyOf: [in taxon](http://purl.obolibrary.org/obo/RO_0002162) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Bronchial_artery" -### bronchial epithelial cell `http://purl.obolibrary.org/obo/CL_0002328` +### inconsistent_with `http://www.geneontology.org/formats/oboInOwl#inconsistent_with` +#### Removed +- AnnotationProperty: [inconsistent_with](http://www.geneontology.org/formats/oboInOwl#inconsistent_with) -#### Added -- [bronchial epithelial cell](http://purl.obolibrary.org/obo/CL_0002328) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### bronchial goblet cell `http://purl.obolibrary.org/obo/CL_1000312` +### increased coiling `http://purl.obolibrary.org/obo/PATO_0001795` +#### Removed +- [increased coiling](http://purl.obolibrary.org/obo/PATO_0001795) [RO_0002604](http://purl.obolibrary.org/obo/RO_0002604) [decreased coiling](http://purl.obolibrary.org/obo/PATO_0001796) -#### Added -- [bronchial goblet cell](http://purl.obolibrary.org/obo/CL_1000312) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### bronchial mucosa `http://purl.obolibrary.org/obo/UBERON_0000410` +### increased contractility `http://purl.obolibrary.org/obo/PATO_0001580` #### Removed -- [bronchial mucosa](http://purl.obolibrary.org/obo/UBERON_0000410) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa bronchi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:62652" +- [increased contractility](http://purl.obolibrary.org/obo/PATO_0001580) [RO_0002604](http://purl.obolibrary.org/obo/RO_0002604) [decreased contractility](http://purl.obolibrary.org/obo/PATO_0001581) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [bronchial mucosa](http://purl.obolibrary.org/obo/UBERON_0000410) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa bronchi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:62652" +### increased elasticity `http://purl.obolibrary.org/obo/PATO_0002287` +#### Removed +- [increased elasticity](http://purl.obolibrary.org/obo/PATO_0002287) [RO_0002604](http://purl.obolibrary.org/obo/RO_0002604) [decreased elasticity](http://purl.obolibrary.org/obo/PATO_0002288) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + +### increased flexibility `http://purl.obolibrary.org/obo/PATO_0001776` +#### Removed +- [increased flexibility](http://purl.obolibrary.org/obo/PATO_0001776) [RO_0002604](http://purl.obolibrary.org/obo/RO_0002604) [decreased flexibility](http://purl.obolibrary.org/obo/PATO_0001777) -### bronchial smooth muscle cell `http://purl.obolibrary.org/obo/CL_0002598` -#### Added -- [bronchial smooth muscle cell](http://purl.obolibrary.org/obo/CL_0002598) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### increased life span `http://purl.obolibrary.org/obo/PATO_0001603` +#### Removed +- [increased life span](http://purl.obolibrary.org/obo/PATO_0001603) [RO_0002604](http://purl.obolibrary.org/obo/RO_0002604) [decreased life span](http://purl.obolibrary.org/obo/PATO_0001604) -### bronchiole `http://purl.obolibrary.org/obo/UBERON_0002186` + +### increased object quality `http://purl.obolibrary.org/obo/PATO_0002305` #### Removed -- [bronchiole](http://purl.obolibrary.org/obo/UBERON_0002186) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D055745" +- [increased object quality](http://purl.obolibrary.org/obo/PATO_0002305) [RO_0002604](http://purl.obolibrary.org/obo/RO_0002604) [decreased object quality](http://purl.obolibrary.org/obo/PATO_0002303) -#### Added -- [bronchiole](http://purl.obolibrary.org/obo/UBERON_0002186) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D055745" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +### increased quality `http://purl.obolibrary.org/obo/PATO_0002300` +#### Removed +- [increased quality](http://purl.obolibrary.org/obo/PATO_0002300) [RO_0002604](http://purl.obolibrary.org/obo/RO_0002604) [decreased quality](http://purl.obolibrary.org/obo/PATO_0002301) -### bronchus `http://purl.obolibrary.org/obo/UBERON_0002185` -#### Added -- [bronchus](http://purl.obolibrary.org/obo/UBERON_0002185) [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [Homo sapiens](http://purl.obolibrary.org/obo/NCBITaxon_9606) +### increased size `http://purl.obolibrary.org/obo/PATO_0000586` +#### Removed +- [increased size](http://purl.obolibrary.org/obo/PATO_0000586) [RO_0002604](http://purl.obolibrary.org/obo/RO_0002604) [decreased size](http://purl.obolibrary.org/obo/PATO_0000587) -- [bronchus](http://purl.obolibrary.org/obo/UBERON_0002185) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas) -### bronchus fibroblast of lung `http://purl.obolibrary.org/obo/CL_2000093` +### increased viscosity `http://purl.obolibrary.org/obo/PATO_0001693` +#### Removed +- [increased viscosity](http://purl.obolibrary.org/obo/PATO_0001693) [RO_0002604](http://purl.obolibrary.org/obo/RO_0002604) [decreased viscosity](http://purl.obolibrary.org/obo/PATO_0001694) -#### Added -- [bronchus fibroblast of lung](http://purl.obolibrary.org/obo/CL_2000093) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### brown adipose tissue `http://purl.obolibrary.org/obo/UBERON_0001348` +### indirectly negatively regulates `http://purl.obolibrary.org/obo/RO_0002409` #### Removed -- [brown adipose tissue](http://purl.obolibrary.org/obo/UBERON_0001348) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "textus adiposus fuscus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Brown_adipose_tissue" +- [indirectly negatively regulates](http://purl.obolibrary.org/obo/RO_0002409) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [indirectly negatively regulates](http://purl.obolibrary.org/obo/RO_0002409) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "indirectly inhibits" -#### Added -- [brown adipose tissue](http://purl.obolibrary.org/obo/UBERON_0001348) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "textus adiposus fuscus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Brown_adipose_tissue" +- [indirectly negatively regulates](http://purl.obolibrary.org/obo/RO_0002409) [RO_0002579](http://purl.obolibrary.org/obo/RO_0002579) [negatively regulates](http://purl.obolibrary.org/obo/RO_0002212) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### brush cell `http://purl.obolibrary.org/obo/CL_0002204` +### indirectly positively regulates `http://purl.obolibrary.org/obo/RO_0002407` +#### Removed +- [indirectly positively regulates](http://purl.obolibrary.org/obo/RO_0002407) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) -#### Added -- [brush cell](http://purl.obolibrary.org/obo/CL_0002204) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [indirectly positively regulates](http://purl.obolibrary.org/obo/RO_0002407) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "indirectly activates" +- [indirectly positively regulates](http://purl.obolibrary.org/obo/RO_0002407) [RO_0002579](http://purl.obolibrary.org/obo/RO_0002579) [positively regulates](http://purl.obolibrary.org/obo/RO_0002213) -### brush cell of epithelium proper of large intestine `http://purl.obolibrary.org/obo/CL_0002203` -#### Added -- [brush cell of epithelium proper of large intestine](http://purl.obolibrary.org/obo/CL_0002203) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### indirectly_supplies `http://purl.obolibrary.org/obo/uberon/core#indirectly_supplies` +#### Removed +- [has branching part](http://purl.obolibrary.org/obo/RO_0002569) o [supplies](http://purl.obolibrary.org/obo/RO_0002178) SubPropertyOf: [indirectly_supplies](http://purl.obolibrary.org/obo/uberon/core#indirectly_supplies) -### brush cell of trachea `http://purl.obolibrary.org/obo/CL_0002207` +- Transitive: [indirectly_supplies](http://purl.obolibrary.org/obo/uberon/core#indirectly_supplies) -#### Added -- [brush cell of trachea](http://purl.obolibrary.org/obo/CL_0002207) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### brush cell of trachebronchial tree `http://purl.obolibrary.org/obo/CL_0002075` +### individual digit of digitopodial skeleton `http://purl.obolibrary.org/obo/UBERON_5102544` +#### Removed +- [individual digit of digitopodial skeleton](http://purl.obolibrary.org/obo/UBERON_5102544) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "this class represents a series of phalanges plus a metapodial element. In comparative anatomy terminology we would call this a 'digit', but the label 'digit' is sometimes used to exclude metapodials and to include soft tissue. This series of elements is hypothesized to be homologous to radials." #### Added -- [brush cell of trachebronchial tree](http://purl.obolibrary.org/obo/CL_0002075) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [individual digit of digitopodial skeleton](http://purl.obolibrary.org/obo/UBERON_5102544) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### bundle of His `http://purl.obolibrary.org/obo/UBERON_0002353` +### inducible T-cell costimulator `http://purl.obolibrary.org/obo/PR_000001860` #### Removed -- [bundle of His](http://purl.obolibrary.org/obo/UBERON_0002353) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "fasciculus atrioventricularis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Bundle_of_His" +- [inducible T-cell costimulator](http://purl.obolibrary.org/obo/PR_000001860) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [inducible T-cell costimulator (human)](http://purl.obolibrary.org/obo/PR_Q9Y6W8) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [bundle of His](http://purl.obolibrary.org/obo/UBERON_0002353) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "fasciculus atrioventricularis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Bundle_of_His" +### inferred_by `http://www.geneontology.org/formats/oboInOwl#inferred_by` +#### Removed +- AnnotationProperty: [inferred_by](http://www.geneontology.org/formats/oboInOwl#inferred_by) -### calcium ion import `http://purl.obolibrary.org/obo/GO_0070509` -#### Added -- [calcium ion import](http://purl.obolibrary.org/obo/GO_0070509) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/geneontology/go-ontology/issues/23015"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) +### information content entity `http://purl.obolibrary.org/obo/IAO_0000030` +#### Removed +- [information content entity](http://purl.obolibrary.org/obo/IAO_0000030) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "information content entity"@en -- [calcium ion import](http://purl.obolibrary.org/obo/GO_0070509) [label](http://www.w3.org/2000/01/rdf-schema#label) "calcium ion import" -- [calcium ion import](http://purl.obolibrary.org/obo/GO_0070509) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "calcium ion uptake" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:mah" -- [calcium ion import](http://purl.obolibrary.org/obo/GO_0070509) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" +### inner cell mass `http://purl.obolibrary.org/obo/UBERON_0000087` +#### Removed +- [inner cell mass](http://purl.obolibrary.org/obo/UBERON_0000087) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "This structure forms in the earliest steps of development, before implantation into the endometrium of the uterus has occurred.The ICM lies within the blastocyst cavity and is entirely surrounded by the single layer of cells called trophoblast. [Wikipedia:Inner_cell_mass]" -- [calcium ion import](http://purl.obolibrary.org/obo/GO_0070509) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "The directed movement of calcium ions into a cell or organelle." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:mah" +- [inner cell mass](http://purl.obolibrary.org/obo/UBERON_0000087) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "A small sphere of cells known as the inner cell mass lies within the trophoblast (of all eutherian mammals).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.144" -- [calcium ion import](http://purl.obolibrary.org/obo/GO_0070509) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "transmembrane calcium influx" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tb" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [calcium ion import](http://purl.obolibrary.org/obo/GO_0070509) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:0070509" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- Class: [calcium ion import](http://purl.obolibrary.org/obo/GO_0070509) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [calcium ion import](http://purl.obolibrary.org/obo/GO_0070509) SubClassOf [calcium ion transport](http://purl.obolibrary.org/obo/GO_0006816) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000742" +- [inner cell mass](http://purl.obolibrary.org/obo/UBERON_0000087) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A group of cells found in the mammalian blastocyst that give rise to the embryo. [Biology_Online][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### calcium ion import across plasma membrane `http://purl.obolibrary.org/obo/GO_0098703` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [calcium ion import across plasma membrane](http://purl.obolibrary.org/obo/GO_0098703) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/geneontology/go-ontology/issues/24965"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [calcium ion import across plasma membrane](http://purl.obolibrary.org/obo/GO_0098703) SubClassOf [calcium ion import](http://purl.obolibrary.org/obo/GO_0070509) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000742" -- [calcium ion import across plasma membrane](http://purl.obolibrary.org/obo/GO_0098703) SubClassOf [calcium ion import into cytosol](http://purl.obolibrary.org/obo/GO_1902656) -### calcium ion import into cytosol `http://purl.obolibrary.org/obo/GO_1902656` +### inner ear epithelium `http://purl.obolibrary.org/obo/UBERON_0006937` #### Added -- [calcium ion import into cytosol](http://purl.obolibrary.org/obo/GO_1902656) [creation date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2014-01-22T13:41:11Z" +- [inner ear epithelium](http://purl.obolibrary.org/obo/UBERON_0006937) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) -- [calcium ion import into cytosol](http://purl.obolibrary.org/obo/GO_1902656) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "The directed movement of calcium ion into a cytosol." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:vw" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" +### inner epithelial layer of tympanic membrane `http://purl.obolibrary.org/obo/UBERON_0005042` +#### Removed +- [inner epithelial layer of tympanic membrane](http://purl.obolibrary.org/obo/UBERON_0005042) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in FMA this is classified as a mucosa" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + +#### Added +- [inner epithelial layer of tympanic membrane](http://purl.obolibrary.org/obo/UBERON_0005042) SubClassOf [endo-epithelium](http://purl.obolibrary.org/obo/UBERON_0005911) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO_REF:0000075" -- [calcium ion import into cytosol](http://purl.obolibrary.org/obo/GO_1902656) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" +### inner limiting layer of retina `http://purl.obolibrary.org/obo/UBERON_0001794` +#### Removed +- [inner limiting layer of retina](http://purl.obolibrary.org/obo/UBERON_0001794) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Membrane on the apical surface of the retina. The retinal vasculature becomes adhered to the apical surface of the ILM by 30dpf[ZFIN:ZDB-PUB-071023-7, ZFIN:ZDB-PUB-120529-3]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:ZDB-PUB-071023-7, ZFIN:ZDB-PUB-120529-3" -- [calcium ion import into cytosol](http://purl.obolibrary.org/obo/GO_1902656) [label](http://www.w3.org/2000/01/rdf-schema#label) "calcium ion import into cytosol" +#### Added +- [inner limiting layer of retina](http://purl.obolibrary.org/obo/UBERON_0001794) SubClassOf [structure with developmental contribution from neural crest](http://purl.obolibrary.org/obo/UBERON_0010314) -- [calcium ion import into cytosol](http://purl.obolibrary.org/obo/GO_1902656) [created by](http://www.geneontology.org/formats/oboInOwl#created_by) "pr" -- [calcium ion import into cytosol](http://purl.obolibrary.org/obo/GO_1902656) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "calcium import into cytosol" +### inner medulla of kidney `http://purl.obolibrary.org/obo/UBERON_0001294` +#### Removed +- [inner medulla of kidney](http://purl.obolibrary.org/obo/UBERON_0001294) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "unique to mammals" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GO:0072053" -- [calcium ion import into cytosol](http://purl.obolibrary.org/obo/GO_1902656) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:1902656" -- Class: [calcium ion import into cytosol](http://purl.obolibrary.org/obo/GO_1902656) -- [calcium ion import into cytosol](http://purl.obolibrary.org/obo/GO_1902656) SubClassOf [calcium ion transport](http://purl.obolibrary.org/obo/GO_0006816) +### inner medulla vasa recta ascending limb `http://purl.obolibrary.org/obo/UBERON_0009092` +#### Removed +- [inner medulla vasa recta ascending limb](http://purl.obolibrary.org/obo/UBERON_0009092) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta in the inner medulla parallel to the ascending limb" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "CL" -- [calcium ion import into cytosol](http://purl.obolibrary.org/obo/GO_1902656) SubClassOf [has target end location](http://purl.obolibrary.org/obo/RO_0002339) some [cytosol](http://purl.obolibrary.org/obo/GO_0005829) +#### Added +- [inner medulla vasa recta ascending limb](http://purl.obolibrary.org/obo/UBERON_0009092) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### calcium-mediated signaling `http://purl.obolibrary.org/obo/GO_0019722` +### inner medulla vasa recta descending limb `http://purl.obolibrary.org/obo/UBERON_0009089` #### Removed -- [calcium-mediated signaling](http://purl.obolibrary.org/obo/GO_0019722) SubClassOf [second-messenger-mediated signaling](http://purl.obolibrary.org/obo/GO_0019932) +- [inner medulla vasa recta descending limb](http://purl.obolibrary.org/obo/UBERON_0009089) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta in the inner medullar parallel to the descending limb" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "CL" #### Added -- [calcium-mediated signaling](http://purl.obolibrary.org/obo/GO_0019722) SubClassOf [intracellular signaling cassette](http://purl.obolibrary.org/obo/GO_0141124) +- [inner medulla vasa recta descending limb](http://purl.obolibrary.org/obo/UBERON_0009089) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### camera-type eye `http://purl.obolibrary.org/obo/UBERON_0000019` +### inner nuclear layer of retina `http://purl.obolibrary.org/obo/UBERON_0001791` #### Removed -- [camera-type eye](http://purl.obolibrary.org/obo/UBERON_0000019) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "regio orbitalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:54448" +- [inner nuclear layer of retina](http://purl.obolibrary.org/obo/UBERON_0001791) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [camera-type eye](http://purl.obolibrary.org/obo/UBERON_0000019) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "regio orbitalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:54448" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001167" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [inner nuclear layer of retina](http://purl.obolibrary.org/obo/UBERON_0001791) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The layer of the retina composed of the cell bodies of bipolar cells, horizontal cells, and some of the cell bodies of amacrine cells[BTO:0003176]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "BTO:0003176" -### capillary endothelial cell `http://purl.obolibrary.org/obo/CL_0002144` -#### Added -- [capillary endothelial cell](http://purl.obolibrary.org/obo/CL_0002144) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### inner plexiform layer of retina `http://purl.obolibrary.org/obo/UBERON_0001795` +#### Removed +- [inner plexiform layer of retina](http://purl.obolibrary.org/obo/UBERON_0001795) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001168" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429" -### capsule of lens `http://purl.obolibrary.org/obo/UBERON_0001804` -#### Removed -- [capsule of lens](http://purl.obolibrary.org/obo/UBERON_0001804) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "capsula lentis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [capsule of lens](http://purl.obolibrary.org/obo/UBERON_0001804) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "capsula lentis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### capsule of liver `http://purl.obolibrary.org/obo/UBERON_0016479` -#### Removed -- [capsule of liver](http://purl.obolibrary.org/obo/UBERON_0016479) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "capsula fibrosa perivascularis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Fibrous_capsule_of_Glisson" +- [inner plexiform layer of retina](http://purl.obolibrary.org/obo/UBERON_0001795) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The layer within the retina where the bipolar cells synapse with the dendrites of the ganglion cells.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001329" -- [capsule of liver](http://purl.obolibrary.org/obo/UBERON_0016479) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica fibrosa hepatis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15813" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [inner plexiform layer of retina](http://purl.obolibrary.org/obo/UBERON_0001795) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The inner plexiform layer (IPL) is positioned between the INL and the ganglion cell layer and contains the dendrites of RGCs and processes of bipolar and amacrine cells[GO][GO:0010842]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GO:0010842" -#### Added -- [capsule of liver](http://purl.obolibrary.org/obo/UBERON_0016479) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "capsula fibrosa perivascularis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [inner plexiform layer of retina](http://purl.obolibrary.org/obo/UBERON_0001795) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "http://neurolex.org/wiki/Nlx_anat_1005032 appears to be retired" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Fibrous_capsule_of_Glisson" -- [capsule of liver](http://purl.obolibrary.org/obo/UBERON_0016479) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica fibrosa hepatis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15813" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### innervated_by `http://purl.obolibrary.org/obo/RO_0002005` +#### Removed +- [innervated_by](http://purl.obolibrary.org/obo/RO_0002005) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "innervated_by" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [innervated_by](http://purl.obolibrary.org/obo/RO_0002005) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" +- [innervated_by](http://purl.obolibrary.org/obo/RO_0002005) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-7073-9172](https://orcid.org/0000-0002-7073-9172) -### capsule of lymph node `http://purl.obolibrary.org/obo/UBERON_0002194` -#### Removed -- [capsule of lymph node](http://purl.obolibrary.org/obo/UBERON_0002194) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "capsula nodi lymphoidei" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:74604" +- [innervated_by](http://purl.obolibrary.org/obo/RO_0002005) [label](http://www.w3.org/2000/01/rdf-schema#label) "innervated_by" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [innervated_by](http://purl.obolibrary.org/obo/RO_0002005) [citesAsAuthority](http://purl.org/spar/cito/citesAsAuthority) "http://www.ncbi.nlm.nih.gov/pubmed/22402613"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [innervated_by](http://purl.obolibrary.org/obo/RO_0002005) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002005" -#### Added -- [capsule of lymph node](http://purl.obolibrary.org/obo/UBERON_0002194) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "capsula nodi lymphoidei" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:74604" +- [innervated_by](http://purl.obolibrary.org/obo/RO_0002005) [id](http://www.geneontology.org/formats/oboInOwl#id) "innervated_by" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [innervated_by](http://purl.obolibrary.org/obo/RO_0002005) o [branching part of](http://purl.obolibrary.org/obo/RO_0002380) SubPropertyOf: [innervated_by](http://purl.obolibrary.org/obo/RO_0002005) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### capsule of thyroid gland `http://purl.obolibrary.org/obo/UBERON_0001746` +### innervates `http://purl.obolibrary.org/obo/RO_0002134` #### Removed -- [capsule of thyroid gland](http://purl.obolibrary.org/obo/UBERON_0001746) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "capsula fibrosa glandulae thyroideae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [innervates](http://purl.obolibrary.org/obo/RO_0002134) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-7073-9172](https://orcid.org/0000-0002-7073-9172) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [innervates](http://purl.obolibrary.org/obo/RO_0002134) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "innervates" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:55513" +- [innervates](http://purl.obolibrary.org/obo/RO_0002134) [id](http://www.geneontology.org/formats/oboInOwl#id) "innervates" -#### Added -- [capsule of thyroid gland](http://purl.obolibrary.org/obo/UBERON_0001746) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "capsula fibrosa glandulae thyroideae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [innervates](http://purl.obolibrary.org/obo/RO_0002134) [citesAsAuthority](http://purl.org/spar/cito/citesAsAuthority) [22402613](http://www.ncbi.nlm.nih.gov/pubmed/22402613) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [innervates](http://purl.obolibrary.org/obo/RO_0002134) [label](http://www.w3.org/2000/01/rdf-schema#label) "innervates" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:55513" +- [innervates](http://purl.obolibrary.org/obo/RO_0002134) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002134" +- [innervates](http://purl.obolibrary.org/obo/RO_0002134) [RO_0001900](http://purl.obolibrary.org/obo/RO_0001900) [RO_0001901](http://purl.obolibrary.org/obo/RO_0001901) -### carbohydrate derivative metabolic process `http://purl.obolibrary.org/obo/GO_1901135` -#### Removed -- [carbohydrate derivative metabolic process](http://purl.obolibrary.org/obo/GO_1901135) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) +- [innervates](http://purl.obolibrary.org/obo/RO_0002134) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" -#### Added -- [carbohydrate derivative metabolic process](http://purl.obolibrary.org/obo/GO_1901135) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) +- [innervates](http://purl.obolibrary.org/obo/RO_0002134) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) -### carbohydrate metabolic process `http://purl.obolibrary.org/obo/GO_0005975` + +### innominate bone `http://purl.obolibrary.org/obo/UBERON_0001272` #### Removed -- [carbohydrate metabolic process](http://purl.obolibrary.org/obo/GO_0005975) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) +- [innominate bone](http://purl.obolibrary.org/obo/UBERON_0001272) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in FMA this is a paired structure. NCITA has 'pelvic bone' but this is the *superclass* of ilium/ischium/pubis. The MA class 'pelvis bone' is actually a superclass of 'pelvic girdle bone' and caudal/sacral vertebra." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + +- [innominate bone](http://purl.obolibrary.org/obo/UBERON_0001272) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The hip/pelvic bone/basipterygium first appears in fishes, where it consists of a simple, usually triangular bone, to which the pelvic fin articulates. The hip bones on each side usually connect with each other at the forward end, and are even solidly fused in lungfishes and sharks, but they never attach to the vertebral column" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" -#### Added -- [carbohydrate metabolic process](http://purl.obolibrary.org/obo/GO_0005975) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) -### cardia of stomach `http://purl.obolibrary.org/obo/UBERON_0001162` +### input of `http://purl.obolibrary.org/obo/RO_0002352` #### Removed -- [cardia of stomach](http://purl.obolibrary.org/obo/UBERON_0001162) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pars cardiaca gastricae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:14561" +- [input of](http://purl.obolibrary.org/obo/RO_0002352) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [input of](http://purl.obolibrary.org/obo/RO_0002352) [label](http://www.w3.org/2000/01/rdf-schema#label) "input of" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [input of](http://purl.obolibrary.org/obo/RO_0002352) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "input_of" -- [cardia of stomach](http://purl.obolibrary.org/obo/UBERON_0001162) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "antrum cardiacum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cardia" +- [input of](http://purl.obolibrary.org/obo/RO_0002352) [id](http://www.geneontology.org/formats/oboInOwl#id) "input_of" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [input of](http://purl.obolibrary.org/obo/RO_0002352) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" -#### Added -- [cardia of stomach](http://purl.obolibrary.org/obo/UBERON_0001162) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "antrum cardiacum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [input of](http://purl.obolibrary.org/obo/RO_0002352) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002352" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cardia" -- [cardia of stomach](http://purl.obolibrary.org/obo/UBERON_0001162) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pars cardiaca gastricae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:14561" +### insect adult head `http://purl.obolibrary.org/obo/UBERON_6003007` +#### Removed +- [insect adult head](http://purl.obolibrary.org/obo/UBERON_6003007) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00003007" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### cardiac Purkinje fiber `http://purl.obolibrary.org/obo/UBERON_0002354` +### insect adult tagma `http://purl.obolibrary.org/obo/UBERON_6003005` #### Removed -- [cardiac Purkinje fiber](http://purl.obolibrary.org/obo/UBERON_0002354) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "myofibra conducens cardiacus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - -#### Added -- [cardiac Purkinje fiber](http://purl.obolibrary.org/obo/UBERON_0002354) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "myofibra conducens cardiacus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - +- [insect adult tagma](http://purl.obolibrary.org/obo/UBERON_6003005) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00003005" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### cardiac endothelial cell `http://purl.obolibrary.org/obo/CL_0010008` -#### Added -- [cardiac endothelial cell](http://purl.obolibrary.org/obo/CL_0010008) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### insect embryonic/larval head sense organ `http://purl.obolibrary.org/obo/UBERON_6007280` +#### Removed +- [insect embryonic/larval head sense organ](http://purl.obolibrary.org/obo/UBERON_6007280) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007280" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### cardiac mesenchymal cell `http://purl.obolibrary.org/obo/CL_0000569` -#### Added -- [cardiac mesenchymal cell](http://purl.obolibrary.org/obo/CL_0000569) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### insect embryonic/larval head sensillum `http://purl.obolibrary.org/obo/UBERON_6007242` +#### Removed +- [insect embryonic/larval head sensillum](http://purl.obolibrary.org/obo/UBERON_6007242) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007242" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### cardiac muscle cell `http://purl.obolibrary.org/obo/CL_0000746` -#### Added -- [cardiac muscle cell](http://purl.obolibrary.org/obo/CL_0000746) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### insect embryonic/larval sensillum `http://purl.obolibrary.org/obo/UBERON_6007240` +#### Removed +- [insect embryonic/larval sensillum](http://purl.obolibrary.org/obo/UBERON_6007240) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007240" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### cardiac muscle myoblast `http://purl.obolibrary.org/obo/CL_0000513` -#### Added -- [cardiac muscle myoblast](http://purl.obolibrary.org/obo/CL_0000513) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### insect larval head `http://purl.obolibrary.org/obo/UBERON_6001730` +#### Removed +- [insect larval head](http://purl.obolibrary.org/obo/UBERON_6001730) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001730" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### cardiac nerve plexus `http://purl.obolibrary.org/obo/UBERON_0002008` -#### Removed -- [cardiac nerve plexus](http://purl.obolibrary.org/obo/UBERON_0002008) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "plexus cardiacus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cardiac_plexus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [cardiac nerve plexus](http://purl.obolibrary.org/obo/UBERON_0002008) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "plexus cardiacus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### insect larval sense organ `http://purl.obolibrary.org/obo/UBERON_6002639` +#### Removed +- [insect larval sense organ](http://purl.obolibrary.org/obo/UBERON_6002639) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00002639" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cardiac_plexus" -### cardiac neuron `http://purl.obolibrary.org/obo/CL_0010022` +### insect larval tagma `http://purl.obolibrary.org/obo/UBERON_6001728` +#### Removed +- [insect larval tagma](http://purl.obolibrary.org/obo/UBERON_6001728) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001728" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -#### Added -- [cardiac neuron](http://purl.obolibrary.org/obo/CL_0010022) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### cardiac skeleton `http://purl.obolibrary.org/obo/UBERON_0004292` +### insulin gene translation product `http://purl.obolibrary.org/obo/PR_000009054` #### Removed -- [cardiac skeleton](http://purl.obolibrary.org/obo/UBERON_0004292) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "anulus fibrosus sinister cordis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cardiac_skeleton" +- [insulin gene translation product](http://purl.obolibrary.org/obo/PR_000009054) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [insulin gene translation product (human)](http://purl.obolibrary.org/obo/PR_P01308) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [cardiac skeleton](http://purl.obolibrary.org/obo/UBERON_0004292) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "trigona fibrosa" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cardiac_skeleton" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### integrin alpha-2 `http://purl.obolibrary.org/obo/PR_000001008` +#### Removed +- [integrin alpha-2](http://purl.obolibrary.org/obo/PR_000001008) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [integrin alpha-2 (human)](http://purl.obolibrary.org/obo/PR_P17301) -- [cardiac skeleton](http://purl.obolibrary.org/obo/UBERON_0004292) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "anulus fibrosus dexter cordis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cardiac_skeleton" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [cardiac skeleton](http://purl.obolibrary.org/obo/UBERON_0004292) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "trigonum fibrosum dextrum cordis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cardiac_skeleton" +### integrin alpha-4 `http://purl.obolibrary.org/obo/PR_000009129` +#### Removed +- [integrin alpha-4](http://purl.obolibrary.org/obo/PR_000009129) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [integrin alpha-4 (human)](http://purl.obolibrary.org/obo/PR_P13612) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [cardiac skeleton](http://purl.obolibrary.org/obo/UBERON_0004292) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "trigonum fibrosum sinistrum cordis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cardiac_skeleton" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### integrin alpha-E `http://purl.obolibrary.org/obo/PR_000001010` +#### Removed +- [integrin alpha-E](http://purl.obolibrary.org/obo/PR_000001010) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [integrin alpha-E (human)](http://purl.obolibrary.org/obo/PR_P38570) -#### Added -- [cardiac skeleton](http://purl.obolibrary.org/obo/UBERON_0004292) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "anulus fibrosus sinister cordis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cardiac_skeleton" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -- [cardiac skeleton](http://purl.obolibrary.org/obo/UBERON_0004292) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "anulus fibrosus dexter cordis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cardiac_skeleton" +### integrin alpha-IIb `http://purl.obolibrary.org/obo/PR_000009127` +#### Removed +- [integrin alpha-IIb](http://purl.obolibrary.org/obo/PR_000009127) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [integrin alpha-IIb (human)](http://purl.obolibrary.org/obo/PR_P08514) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -- [cardiac skeleton](http://purl.obolibrary.org/obo/UBERON_0004292) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "trigonum fibrosum dextrum cordis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cardiac_skeleton" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### integrin alpha-M `http://purl.obolibrary.org/obo/PR_000001012` +#### Removed +- [integrin alpha-M](http://purl.obolibrary.org/obo/PR_000001012) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [integrin alpha-M (human)](http://purl.obolibrary.org/obo/PR_P11215) -- [cardiac skeleton](http://purl.obolibrary.org/obo/UBERON_0004292) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "trigona fibrosa" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cardiac_skeleton" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -- [cardiac skeleton](http://purl.obolibrary.org/obo/UBERON_0004292) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "trigonum fibrosum sinistrum cordis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cardiac_skeleton" +### integrin alpha-X `http://purl.obolibrary.org/obo/PR_000001013` +#### Removed +- [integrin alpha-X](http://purl.obolibrary.org/obo/PR_000001013) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [integrin alpha-X (human)](http://purl.obolibrary.org/obo/PR_P20702) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### cardiac valve cell `http://purl.obolibrary.org/obo/CL_1000147` +### integrin beta-7 `http://purl.obolibrary.org/obo/PR_000009143` +#### Removed +- [integrin beta-7](http://purl.obolibrary.org/obo/PR_000009143) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [integrin beta-7 (human)](http://purl.obolibrary.org/obo/PR_P26010) -#### Added -- [cardiac valve cell](http://purl.obolibrary.org/obo/CL_1000147) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### carotid canal `http://purl.obolibrary.org/obo/UBERON_0006668` +### integument `http://purl.obolibrary.org/obo/UBERON_0002199` #### Removed -- [carotid canal](http://purl.obolibrary.org/obo/UBERON_0006668) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "canalis caroticus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Carotid_canal" +- [integument](http://purl.obolibrary.org/obo/UBERON_0002199) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Surface structure that is the outer protective covering of the body.[VSAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000029" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -#### Added -- [carotid canal](http://purl.obolibrary.org/obo/UBERON_0006668) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "canalis caroticus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PSPUB:0000170" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Carotid_canal" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" +- [integument](http://purl.obolibrary.org/obo/UBERON_0002199) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical system that protects the body from damage, comprising the skin and its appendages.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" -### carpal region `http://purl.obolibrary.org/obo/UBERON_0004452` -#### Removed -- [carpal region](http://purl.obolibrary.org/obo/UBERON_0004452) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "articulatio radiocarpea" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Wrist" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000239" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -- [carpal region](http://purl.obolibrary.org/obo/UBERON_0004452) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "regio carpalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:24922" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [integument](http://purl.obolibrary.org/obo/UBERON_0002199) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "integumental" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [integument](http://purl.obolibrary.org/obo/UBERON_0002199) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "integumentary" -#### Added -- [carpal region](http://purl.obolibrary.org/obo/UBERON_0004452) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "articulatio radiocarpea" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [integument](http://purl.obolibrary.org/obo/UBERON_0002199) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "in FMA intergument = skin+superficial fascia(hypodermis), skin=dermis+epidermis+hair_nail. Note that the definition provided here excludes the more general sense of the term 'integument' used in invertebrates; consider 'integumental system'. Note that the VSAO class appears to include adnexa by its definition." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Wrist" +- [integument](http://purl.obolibrary.org/obo/UBERON_0002199) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The outer protective barrier that separates the animal from its aquatic environment. Le Guellec et al, 2004.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000368" -- [carpal region](http://purl.obolibrary.org/obo/UBERON_0004452) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "regio carpalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:24922" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -### carpal skeleton `http://purl.obolibrary.org/obo/UBERON_0009880` + +### integumental system `http://purl.obolibrary.org/obo/UBERON_0002416` #### Removed -- [carpal skeleton](http://purl.obolibrary.org/obo/UBERON_0009880) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ossa carpi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Carpus" +- [integumental system](http://purl.obolibrary.org/obo/UBERON_0002416) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004969" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [integumental system](http://purl.obolibrary.org/obo/UBERON_0002416) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes (...).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [carpal skeleton](http://purl.obolibrary.org/obo/UBERON_0009880) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ossa carpi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Carpus" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000403" -### carpometacarpal joint `http://purl.obolibrary.org/obo/UBERON_0011119` -#### Removed -- [carpometacarpal joint](http://purl.obolibrary.org/obo/UBERON_0011119) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D052737" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1111/j.1469-7580.2008.01043.x Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009)" -- [carpometacarpal joint](http://purl.obolibrary.org/obo/UBERON_0011119) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "articulationes carpometacarpeæ" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Carpometacarpal_joint" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [carpometacarpal joint](http://purl.obolibrary.org/obo/UBERON_0011119) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "articulationes carpometacarpeæ" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Carpometacarpal_joint" +### integumentary adnexa `http://purl.obolibrary.org/obo/UBERON_0006003` +#### Removed +- [integumentary adnexa](http://purl.obolibrary.org/obo/UBERON_0006003) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "the tissue or structures associated with or embedded in the skin such as hair and hair follicles, sweat glands, sebaceous glands and claws or nails[MP:0010678]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "MP:0010678" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -- [carpometacarpal joint](http://purl.obolibrary.org/obo/UBERON_0011119) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D052737" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) +### interaction relation helper property `http://purl.obolibrary.org/obo/RO_0002563` +#### Removed +- [interaction relation helper property](http://purl.obolibrary.org/obo/RO_0002563) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -### cartilaginous joint `http://purl.obolibrary.org/obo/UBERON_0002213` +### interacts with `http://purl.obolibrary.org/obo/RO_0002434` #### Removed -- [cartilaginous joint](http://purl.obolibrary.org/obo/UBERON_0002213) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "junctura cartilaginea" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cartilaginous_joint" +- [interacts with](http://purl.obolibrary.org/obo/RO_0002434) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [interacts with](http://purl.obolibrary.org/obo/RO_0002434) [closeMatch](http://www.w3.org/2004/02/skos/core#closeMatch) "http://purl.obolibrary.org/obo/MI_0914"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) -#### Added -- [cartilaginous joint](http://purl.obolibrary.org/obo/UBERON_0002213) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "junctura cartilaginea" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cartilaginous_joint" +- [interacts with](http://purl.obolibrary.org/obo/RO_0002434) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### catalytic activity, acting on DNA `http://purl.obolibrary.org/obo/GO_0140097` -#### Removed -- [catalytic activity, acting on DNA](http://purl.obolibrary.org/obo/GO_0140097) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) +### interalveolar septum `http://purl.obolibrary.org/obo/UBERON_0004893` #### Added -- [catalytic activity, acting on DNA](http://purl.obolibrary.org/obo/GO_0140097) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) +- [interalveolar septum](http://purl.obolibrary.org/obo/UBERON_0004893) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -### catalytic activity, acting on RNA `http://purl.obolibrary.org/obo/GO_0140098` +### interatrial septum `http://purl.obolibrary.org/obo/UBERON_0002085` #### Removed -- [catalytic activity, acting on RNA](http://purl.obolibrary.org/obo/GO_0140098) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) +- [interatrial septum](http://purl.obolibrary.org/obo/UBERON_0002085) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The partition separating the right and left atria of the heart. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/interatrial+septum" -#### Added -- [catalytic activity, acting on RNA](http://purl.obolibrary.org/obo/GO_0140098) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### catalytic activity, acting on a protein `http://purl.obolibrary.org/obo/GO_0140096` -#### Removed -- [catalytic activity, acting on a protein](http://purl.obolibrary.org/obo/GO_0140096) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [catalytic activity, acting on a protein](http://purl.obolibrary.org/obo/GO_0140096) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000385" +- [interatrial septum](http://purl.obolibrary.org/obo/UBERON_0002085) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### caudal ganglionic eminence derived GABAergic cortical interneuron `http://purl.obolibrary.org/obo/CL_4023070` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [caudal ganglionic eminence derived GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023070) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000385" -### caudal segment of spinal cord `http://purl.obolibrary.org/obo/UBERON_0005845` -#### Removed -- [caudal segment of spinal cord](http://purl.obolibrary.org/obo/UBERON_0005845) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pars coccygea medullae spinalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:256635" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [caudal segment of spinal cord](http://purl.obolibrary.org/obo/UBERON_0005845) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "segmenta coccygea" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:1656" +### intercarpal joint `http://purl.obolibrary.org/obo/UBERON_0011132` +#### Removed +- [intercarpal joint](http://purl.obolibrary.org/obo/UBERON_0011132) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D050824" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -- [caudal segment of spinal cord](http://purl.obolibrary.org/obo/UBERON_0005845) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "segmenta coccygea medullae spinalis [1-3]" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:256635" +- [intercarpal joint](http://purl.obolibrary.org/obo/UBERON_0011132) SubClassOf [connects](http://purl.obolibrary.org/obo/RO_0002176) some [carpal bone](http://purl.obolibrary.org/obo/UBERON_0001435) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "two adjacent carpals" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +#### Added +- [intercarpal joint](http://purl.obolibrary.org/obo/UBERON_0011132) SubClassOf [connects](http://purl.obolibrary.org/obo/RO_0002176) some [carpal bone](http://purl.obolibrary.org/obo/UBERON_0001435) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [caudal segment of spinal cord](http://purl.obolibrary.org/obo/UBERON_0005845) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "segmenta coccygea medullae spinalis [1-3]" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:256635" +### interleukin-1 receptor-like 1 `http://purl.obolibrary.org/obo/PR_000008994` +#### Removed +- [interleukin-1 receptor-like 1](http://purl.obolibrary.org/obo/PR_000008994) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [interleukin-1 receptor-like 1 (human)](http://purl.obolibrary.org/obo/PR_Q01638) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [caudal segment of spinal cord](http://purl.obolibrary.org/obo/UBERON_0005845) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pars coccygea medullae spinalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:256635" +### interleukin-17 receptor B `http://purl.obolibrary.org/obo/PR_000008982` +#### Removed +- [interleukin-17 receptor B](http://purl.obolibrary.org/obo/PR_000008982) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [interleukin-17 receptor B (human)](http://purl.obolibrary.org/obo/PR_Q9NRM6) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [caudal segment of spinal cord](http://purl.obolibrary.org/obo/UBERON_0005845) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "segmenta coccygea" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### interleukin-2 receptor subunit alpha `http://purl.obolibrary.org/obo/PR_000001380` +#### Removed +- [interleukin-2 receptor subunit alpha](http://purl.obolibrary.org/obo/PR_000001380) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [interleukin-2 receptor subunit alpha (human)](http://purl.obolibrary.org/obo/PR_P01589) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:1656" -### caudate nucleus `http://purl.obolibrary.org/obo/UBERON_0001873` +### interleukin-2 receptor subunit beta `http://purl.obolibrary.org/obo/PR_000001381` #### Removed -- [caudate nucleus](http://purl.obolibrary.org/obo/UBERON_0001873) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus caudatus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Caudate_nucleus" - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0000211" +- [interleukin-2 receptor subunit beta](http://purl.obolibrary.org/obo/PR_000001381) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [interleukin-2 receptor subunit beta (human)](http://purl.obolibrary.org/obo/PR_P14784) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [caudate nucleus](http://purl.obolibrary.org/obo/UBERON_0001873) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus caudatus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Caudate_nucleus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0000211" +### interleukin-5 receptor subunit alpha `http://purl.obolibrary.org/obo/PR_000001867` +#### Removed +- [interleukin-5 receptor subunit alpha](http://purl.obolibrary.org/obo/PR_000001867) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [interleukin-5 receptor subunit alpha (human)](http://purl.obolibrary.org/obo/PR_Q01344) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### cavernous artery `http://purl.obolibrary.org/obo/UBERON_0000457` +### interleukin-7 receptor subunit alpha `http://purl.obolibrary.org/obo/PR_000001869` #### Removed -- [cavernous artery](http://purl.obolibrary.org/obo/UBERON_0000457) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ramus sinus cavernosi (pars cavernosa) (arteria carotis interna)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:70527" +- [interleukin-7 receptor subunit alpha](http://purl.obolibrary.org/obo/PR_000001869) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [interleukin-7 receptor subunit alpha (human)](http://purl.obolibrary.org/obo/PR_P16871) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [cavernous artery](http://purl.obolibrary.org/obo/UBERON_0000457) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ramus sinus cavernosi (pars cavernosa) (arteria carotis interna)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### interlobar artery `http://purl.obolibrary.org/obo/UBERON_0009885` +#### Removed +- [interlobar artery](http://purl.obolibrary.org/obo/UBERON_0009885) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA only has the set term" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:70527" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + +### interlobar vein `http://purl.obolibrary.org/obo/UBERON_0009887` +#### Removed +- [interlobar vein](http://purl.obolibrary.org/obo/UBERON_0009887) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA only has the set term" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" -### cavity of pharynx `http://purl.obolibrary.org/obo/UBERON_0001731` + +### intermaxillary process `http://purl.obolibrary.org/obo/UBERON_0009714` #### Removed -- [cavity of pharynx](http://purl.obolibrary.org/obo/UBERON_0001731) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cavitas pharyngealis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [intermaxillary process](http://purl.obolibrary.org/obo/UBERON_0009714) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [lateral nasal prominence](http://purl.obolibrary.org/obo/UBERON_0004067) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "EHDAA2" + + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "inconsistent" #### Added -- [cavity of pharynx](http://purl.obolibrary.org/obo/UBERON_0001731) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cavitas pharyngealis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [intermaxillary process](http://purl.obolibrary.org/obo/UBERON_0009714) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [lateral nasal prominence](http://purl.obolibrary.org/obo/UBERON_0004067) -### celiac artery `http://purl.obolibrary.org/obo/UBERON_0001640` +### intermediate hypothalamic region `http://purl.obolibrary.org/obo/UBERON_0002555` #### Removed -- [celiac artery](http://purl.obolibrary.org/obo/UBERON_0001640) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria coeliaca" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Celiac_artery" +- [intermediate hypothalamic region](http://purl.obolibrary.org/obo/UBERON_0002555) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In humans it contains the following nuclei: dorsal nucleus [TA] (nucleus dorsalis hypothalami [TA]), parts of the dorsomedial nucleus [TA] (nucleus dorsomedialis [TA]), arcuate nucleus [TA] (nucleus arcuatus [TA]), posterior periventricular nucleus [TA] (nucleus periventricularis posterior [TA]), retrochiasmatic area [TA] (area retrochiasmatica [TA]), lateral tuberal nuclei [TA] (nuclei tuberales laterales [TA]), and ventromedial nucleus [TA] (nucleus ventromedialis hypothalami" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TA" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [intermediate hypothalamic region](http://purl.obolibrary.org/obo/UBERON_0002555) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "See notes for pars intermedia of adenohypophysis." -- [celiac artery](http://purl.obolibrary.org/obo/UBERON_0001640) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "truncus cœliacus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Celiac_artery" +- [intermediate hypothalamic region](http://purl.obolibrary.org/obo/UBERON_0002555) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Brain structure that lies perpendicular to the longitudinal axis of the embryonic neural tube, is continuous with the rostral hypothalamic proliferation and whose most lateral extent is deflected dorsally within the inferior lobe.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:ZDB-PUB-081114-19" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:ZDB-PUB-001018-1" -- [celiac artery](http://purl.obolibrary.org/obo/UBERON_0001640) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "truncus coeliacus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Celiac_artery" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:ZDB-PUB-020730-6" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -- [celiac artery](http://purl.obolibrary.org/obo/UBERON_0001640) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria cœliaca" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Celiac_artery" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0006000" -#### Added -- [celiac artery](http://purl.obolibrary.org/obo/UBERON_0001640) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "truncus cœliacus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Celiac_artery" - -- [celiac artery](http://purl.obolibrary.org/obo/UBERON_0001640) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "truncus coeliacus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Celiac_artery" +### intermediate layer of tympanic membrane `http://purl.obolibrary.org/obo/UBERON_0010070` +#### Removed +- [intermediate layer of tympanic membrane](http://purl.obolibrary.org/obo/UBERON_0010070) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "check MA" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" -- [celiac artery](http://purl.obolibrary.org/obo/UBERON_0001640) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria cœliaca" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Celiac_artery" -- [celiac artery](http://purl.obolibrary.org/obo/UBERON_0001640) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria coeliaca" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### intermediate mesoderm `http://purl.obolibrary.org/obo/UBERON_0003064` +#### Removed +- [intermediate mesoderm](http://purl.obolibrary.org/obo/UBERON_0003064) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Mesoderm between somite and lateral plate. Traditionally thought to give rise to the urogenital system.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Celiac_artery" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### cell `http://purl.obolibrary.org/obo/CL_0000000` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010575" -#### Added -- [cell](http://purl.obolibrary.org/obo/CL_0000000) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [intermediate mesoderm](http://purl.obolibrary.org/obo/UBERON_0003064) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm')." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "ZFA" +- [intermediate mesoderm](http://purl.obolibrary.org/obo/UBERON_0003064) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...)the mesoderm of a developing vertebrate transitionally differentiates into the following sub-types: Chordamesoderm (also known as axial mesoderm) which later on gives rise to notochord in all chordates, Paraxial mesoderm, Intermediate mesoderm, Lateral plate mesoderm (reference 1); The mesoderm is present in Bilateria, therefore they are sometimes called triploblasts. Ectoderm and endoderm are usually organized as epithelial layers, while mesoderm can be epithelial or a compact, three-dimensional tissue.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### cell adhesion `http://purl.obolibrary.org/obo/GO_0007155` -#### Removed -- [cell adhesion](http://purl.obolibrary.org/obo/GO_0007155) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [cell adhesion](http://purl.obolibrary.org/obo/GO_0007155) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000087" -### cell adhesion mediator activity `http://purl.obolibrary.org/obo/GO_0098631` -#### Removed -- [cell adhesion mediator activity](http://purl.obolibrary.org/obo/GO_0098631) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Mesoderm, ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.43" -#### Added -- [cell adhesion mediator activity](http://purl.obolibrary.org/obo/GO_0098631) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) -### cell cluster organ `http://purl.obolibrary.org/obo/UBERON_0010001` +### intermetacarpal joint `http://purl.obolibrary.org/obo/UBERON_0011131` #### Removed -- [cell cluster organ](http://purl.obolibrary.org/obo/UBERON_0010001) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007229" +- [intermetacarpal joint](http://purl.obolibrary.org/obo/UBERON_0011131) SubClassOf [connects](http://purl.obolibrary.org/obo/RO_0002176) some [metacarpal bone](http://purl.obolibrary.org/obo/UBERON_0002374) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "two adjacent metacarpals" #### Added -- [cell cluster organ](http://purl.obolibrary.org/obo/UBERON_0010001) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007229" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [intermetacarpal joint](http://purl.obolibrary.org/obo/UBERON_0011131) SubClassOf [connects](http://purl.obolibrary.org/obo/RO_0002176) some [metacarpal bone](http://purl.obolibrary.org/obo/UBERON_0002374) -### cell death `http://purl.obolibrary.org/obo/GO_0008219` +### intermetatarsal joint `http://purl.obolibrary.org/obo/UBERON_0011133` #### Removed -- [cell death](http://purl.obolibrary.org/obo/GO_0008219) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "This term should not be used for direct annotation, it is currently kept in GO as a placeholder for describing cell death phenotypes in uPHENO. When information is provided on a programmed cell death mechanism, annotations should be made to the appropriate descendant of 'cell death' (such as, but not limited to, GO:0097300 'programmed necrotic cell death' or GO:0006915 'apoptotic process'). Unintentional cell death, i.e. cell death caused by injury, ageing, or cell phenotypes observed as a result of a pathological mutation in an essential gene should NOT be annotated using GO terms." +- [intermetatarsal joint](http://purl.obolibrary.org/obo/UBERON_0011133) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In humans: The base of the first metatarsal is not connected with that of the second by any ligaments; in this respect the great toe resembles the thumb" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" + +- [intermetatarsal joint](http://purl.obolibrary.org/obo/UBERON_0011133) SubClassOf [connects](http://purl.obolibrary.org/obo/RO_0002176) some [metatarsal bone](http://purl.obolibrary.org/obo/UBERON_0001448) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "two adjacent metatarsals" #### Added -- [cell death](http://purl.obolibrary.org/obo/GO_0008219) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "This term should not be used for direct annotation, it is currently kept in GO as a placeholder for describing cell death phenotypes in uPHENO. When information is provided on a programmed cell death mechanism, annotations should be made to the appropriate descendant of 'cell death' (such as, but not limited to, GO:0097300 'programmed necrotic cell death' or GO:0006915 'apoptotic process'). Unintentional cell death, i.e. cell death caused by injury, ageing, or cell phenotypes observed as a result of a pathological mutation in an essential gene should NOT be annotated using GO terms." +- [intermetatarsal joint](http://purl.obolibrary.org/obo/UBERON_0011133) SubClassOf [connects](http://purl.obolibrary.org/obo/RO_0002176) some [metatarsal bone](http://purl.obolibrary.org/obo/UBERON_0001448) -### cell motility `http://purl.obolibrary.org/obo/GO_0048870` +### internal carotid artery `http://purl.obolibrary.org/obo/UBERON_0001532` #### Removed -- [cell motility](http://purl.obolibrary.org/obo/GO_0048870) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) - -#### Added -- [cell motility](http://purl.obolibrary.org/obo/GO_0048870) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) +- [internal carotid artery](http://purl.obolibrary.org/obo/UBERON_0001532) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "One of the major arteries of the head, it is the as the cranial continuation of the aortic arches and the dorsal aorta. It curves ventrally before resuming a dorsal course as it enters the head proper, and it lies ventral to the internal jugular vein. The internal carotid artery gives off palatine, ophthalmic, and cerebral branches by stage NF stage 41.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0011054" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -### cell of skeletal muscle `http://purl.obolibrary.org/obo/CL_0000188` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -#### Added -- [cell of skeletal muscle](http://purl.obolibrary.org/obo/CL_0000188) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:12606281" +- [internal carotid artery](http://purl.obolibrary.org/obo/UBERON_0001532) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Each of two arteries starting at the bifurcation of the common carotid arteries through which blood circulates to many structures and organs in the head. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### cell periphery `http://purl.obolibrary.org/obo/GO_0071944` -#### Removed -- [cell periphery](http://purl.obolibrary.org/obo/GO_0071944) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:pdt" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [cell periphery](http://purl.obolibrary.org/obo/GO_0071944) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:pdt" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000267" -### cell projection `http://purl.obolibrary.org/obo/GO_0042995` -#### Removed -- [cell projection](http://purl.obolibrary.org/obo/GO_0042995) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/Internal+carotid+artery" -#### Added -- [cell projection](http://purl.obolibrary.org/obo/GO_0042995) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) -### cell projection organization `http://purl.obolibrary.org/obo/GO_0030030` +### internal ear `http://purl.obolibrary.org/obo/UBERON_0001846` #### Removed -- [cell projection organization](http://purl.obolibrary.org/obo/GO_0030030) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) +- [internal ear](http://purl.obolibrary.org/obo/UBERON_0001846) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The auditory (hearing) and vestibular (balance) organ of the fish, equivalent to the inner ear of amniotes. (See Anatomical Atlas entry for ear by T. Whitfield.)[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -#### Added -- [cell projection organization](http://purl.obolibrary.org/obo/GO_0030030) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000217" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -### cellular anatomical entity `http://purl.obolibrary.org/obo/GO_0110165` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -#### Added -- [cellular anatomical entity](http://purl.obolibrary.org/obo/GO_0110165) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/geneontology/go-ontology/issues/26424"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) +- [internal ear](http://purl.obolibrary.org/obo/UBERON_0001846) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The labyrinth, or inner ear, evolved very early in vertebrate history and, with many variations in configuration but none of basic design and function, has been retained by all vertebrates.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### cellular modified amino acid metabolic process `http://purl.obolibrary.org/obo/GO_0006575` -#### Removed -- [cellular modified amino acid metabolic process](http://purl.obolibrary.org/obo/GO_0006575) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000284" -#### Added -- [cellular modified amino acid metabolic process](http://purl.obolibrary.org/obo/GO_0006575) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.366" -### cellular nitrogen compound metabolic process `http://purl.obolibrary.org/obo/GO_0034641` +- [internal ear](http://purl.obolibrary.org/obo/UBERON_0001846) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [ear vesicle](http://purl.obolibrary.org/obo/UBERON_0003051) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" #### Added -- [cellular nitrogen compound metabolic process](http://purl.obolibrary.org/obo/GO_0034641) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/geneontology/go-ontology/issues/26424"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) +- [internal ear](http://purl.obolibrary.org/obo/UBERON_0001846) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -- [cellular nitrogen compound metabolic process](http://purl.obolibrary.org/obo/GO_0034641) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [gocheck_do_not_annotate](http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate) +- [internal ear](http://purl.obolibrary.org/obo/UBERON_0001846) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [ear vesicle](http://purl.obolibrary.org/obo/UBERON_0003051) -### cellular response to inorganic substance `http://purl.obolibrary.org/obo/GO_0071241` +### internal jugular vein `http://purl.obolibrary.org/obo/UBERON_0001586` #### Removed -- [cellular response to inorganic substance](http://purl.obolibrary.org/obo/GO_0071241) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" +- [internal jugular vein](http://purl.obolibrary.org/obo/UBERON_0001586) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Vein which receives many veins draining the palate, brain, and the orbital, nasal, and auditory regions.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010236" -- [cellular response to inorganic substance](http://purl.obolibrary.org/obo/GO_0071241) [creation date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2009-12-03T02:35:49Z" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -- [cellular response to inorganic substance](http://purl.obolibrary.org/obo/GO_0071241) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:0071241" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -- [cellular response to inorganic substance](http://purl.obolibrary.org/obo/GO_0071241) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an inorganic substance stimulus." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:mah" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" -- [cellular response to inorganic substance](http://purl.obolibrary.org/obo/GO_0071241) [created by](http://www.geneontology.org/formats/oboInOwl#created_by) "mah" -- [cellular response to inorganic substance](http://purl.obolibrary.org/obo/GO_0071241) [label](http://www.w3.org/2000/01/rdf-schema#label) "cellular response to inorganic substance" -- Class: [cellular response to inorganic substance](http://purl.obolibrary.org/obo/GO_0071241) +### internal naris `http://purl.obolibrary.org/obo/UBERON_0010425` +#### Removed +- [internal naris](http://purl.obolibrary.org/obo/UBERON_0010425) [UBPROP_0000202](http://purl.obolibrary.org/obo/UBPROP_0000202) [FMA_76585](http://purl.obolibrary.org/obo/FMA_76585) -- [cellular response to inorganic substance](http://purl.obolibrary.org/obo/GO_0071241) SubClassOf [response to inorganic substance](http://purl.obolibrary.org/obo/GO_0010035) +- [internal naris](http://purl.obolibrary.org/obo/UBERON_0010425) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In humans the only internal naris is the posterior nasal aperture, which connects to the nasopharynx" -- [cellular response to inorganic substance](http://purl.obolibrary.org/obo/GO_0071241) SubClassOf [cellular response to chemical stimulus](http://purl.obolibrary.org/obo/GO_0070887) +- [internal naris](http://purl.obolibrary.org/obo/UBERON_0010425) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "choanal" -### cellular response to nitric oxide `http://purl.obolibrary.org/obo/GO_0071732` +### internal pudendal vein `http://purl.obolibrary.org/obo/UBERON_0018252` #### Removed -- [cellular response to nitric oxide](http://purl.obolibrary.org/obo/GO_0071732) [creation date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2010-03-17T04:12:52Z" +- [internal pudendal vein](http://purl.obolibrary.org/obo/UBERON_0018252) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In humans, they begin in the deep veins of the penis which issue from the corpus cavernosum penis, accompany the internal pudendal artery, and unite to form a single vessel, which ends in the internal iliac vein. They receive the veins from the urethral bulb, and the perineal and inferior hemorrhoidal veins" -- [cellular response to nitric oxide](http://purl.obolibrary.org/obo/GO_0071732) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" -- [cellular response to nitric oxide](http://purl.obolibrary.org/obo/GO_0071732) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:0071732" -- [cellular response to nitric oxide](http://purl.obolibrary.org/obo/GO_0071732) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitric oxide stimulus." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:mah" - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:yaf" +### internal thoracic artery `http://purl.obolibrary.org/obo/UBERON_0002456` +#### Removed +- [internal thoracic artery](http://purl.obolibrary.org/obo/UBERON_0002456) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "MA has both mammary and thoracic" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" -- [cellular response to nitric oxide](http://purl.obolibrary.org/obo/GO_0071732) [created by](http://www.geneontology.org/formats/oboInOwl#created_by) "mah" -- [cellular response to nitric oxide](http://purl.obolibrary.org/obo/GO_0071732) [label](http://www.w3.org/2000/01/rdf-schema#label) "cellular response to nitric oxide" -- Class: [cellular response to nitric oxide](http://purl.obolibrary.org/obo/GO_0071732) +### internal urethral orifice `http://purl.obolibrary.org/obo/UBERON_0012242` -- [cellular response to nitric oxide](http://purl.obolibrary.org/obo/GO_0071732) EquivalentTo [cellular response to chemical stimulus](http://purl.obolibrary.org/obo/GO_0070887) and ([has primary input](http://purl.obolibrary.org/obo/RO_0004009) some [CHEBI_16480](http://purl.obolibrary.org/obo/CHEBI_16480)) +#### Added +- [internal urethral orifice](http://purl.obolibrary.org/obo/UBERON_0012242) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -- [cellular response to nitric oxide](http://purl.obolibrary.org/obo/GO_0071732) SubClassOf [response to nitric oxide](http://purl.obolibrary.org/obo/GO_0071731) -- [cellular response to nitric oxide](http://purl.obolibrary.org/obo/GO_0071732) SubClassOf [cellular response to inorganic substance](http://purl.obolibrary.org/obo/GO_0071241) +### internodal tract `http://purl.obolibrary.org/obo/UBERON_0009966` +#### Removed +- [internodal tract](http://purl.obolibrary.org/obo/UBERON_0009966) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "evidence is sparse [http://www.gpnotebook.co.uk/simplepage.cfm?ID=-483065798] There is some functional evidence for the existence of specialized conducting pathways within the atria (termed internodal tracts), although this is controversial" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://www.cvphysiology.com/Arrhythmias/A003.htm" -### cellular_component `http://purl.obolibrary.org/obo/GO_0005575` +### interphalangeal joint `http://purl.obolibrary.org/obo/UBERON_0006658` #### Removed -- [cellular_component](http://purl.obolibrary.org/obo/GO_0005575) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex)." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:pdt" +- [interphalangeal joint](http://purl.obolibrary.org/obo/UBERON_0006658) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Hinge joints between the phalanges of the hand or foot[ncithesaurus:Interphalangeal_Joint]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ncithesaurus:Interphalangeal_Joint" + +- [interphalangeal joint](http://purl.obolibrary.org/obo/UBERON_0006658) SubClassOf [connects](http://purl.obolibrary.org/obo/RO_0002176) some [phalanx](http://purl.obolibrary.org/obo/UBERON_0003221) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "two phalanges in series" #### Added -- [cellular_component](http://purl.obolibrary.org/obo/GO_0005575) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex)." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:pdt" +- [interphalangeal joint](http://purl.obolibrary.org/obo/UBERON_0006658) SubClassOf [connects](http://purl.obolibrary.org/obo/RO_0002176) some [phalanx](http://purl.obolibrary.org/obo/UBERON_0003221) -### central memory CD4-positive, alpha-beta T cell `http://purl.obolibrary.org/obo/CL_0000904` +### interphalangeal joint of manus `http://purl.obolibrary.org/obo/UBERON_0007722` +#### Removed +- [interphalangeal joint of manus](http://purl.obolibrary.org/obo/UBERON_0007722) SubClassOf [connects](http://purl.obolibrary.org/obo/RO_0002176) some [phalanx of manus](http://purl.obolibrary.org/obo/UBERON_0001436) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "two in series" #### Added -- [central memory CD4-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_0000904) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [interphalangeal joint of manus](http://purl.obolibrary.org/obo/UBERON_0007722) SubClassOf [connects](http://purl.obolibrary.org/obo/RO_0002176) some [phalanx of manus](http://purl.obolibrary.org/obo/UBERON_0001436) -### central memory CD8-positive, alpha-beta T cell `http://purl.obolibrary.org/obo/CL_0000907` +### interphalangeal joint of pes `http://purl.obolibrary.org/obo/UBERON_0007721` +#### Removed +- [interphalangeal joint of pes](http://purl.obolibrary.org/obo/UBERON_0007721) SubClassOf [connects](http://purl.obolibrary.org/obo/RO_0002176) some [phalanx of pes](http://purl.obolibrary.org/obo/UBERON_0001449) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "two in series" #### Added -- [central memory CD8-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_0000907) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [interphalangeal joint of pes](http://purl.obolibrary.org/obo/UBERON_0007721) SubClassOf [connects](http://purl.obolibrary.org/obo/RO_0002176) some [phalanx of pes](http://purl.obolibrary.org/obo/UBERON_0001449) -### central nervous system `http://purl.obolibrary.org/obo/UBERON_0001017` +### intersects midsagittal plane of `http://purl.obolibrary.org/obo/BSPO_0005001` #### Removed -- [central nervous system](http://purl.obolibrary.org/obo/UBERON_0001017) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005094" +- [intersects midsagittal plane of](http://purl.obolibrary.org/obo/BSPO_0005001) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" -- [central nervous system](http://purl.obolibrary.org/obo/UBERON_0001017) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "systema nervosum centrale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:55675" +- [intersects midsagittal plane of](http://purl.obolibrary.org/obo/BSPO_0005001) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BSPO:0005001" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [intersects midsagittal plane of](http://purl.obolibrary.org/obo/BSPO_0005001) [id](http://www.geneontology.org/formats/oboInOwl#id) "intersects_midsagittal_plane_of" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [intersects midsagittal plane of](http://purl.obolibrary.org/obo/BSPO_0005001) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "intersects_midsagittal_plane_of" -#### Added -- [central nervous system](http://purl.obolibrary.org/obo/UBERON_0001017) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005094" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [intersects midsagittal plane of](http://purl.obolibrary.org/obo/BSPO_0005001) [label](http://www.w3.org/2000/01/rdf-schema#label) "intersects midsagittal plane of" -- [central nervous system](http://purl.obolibrary.org/obo/UBERON_0001017) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas) -- [central nervous system](http://purl.obolibrary.org/obo/UBERON_0001017) [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [Homo sapiens](http://purl.obolibrary.org/obo/NCBITaxon_9606) -- [central nervous system](http://purl.obolibrary.org/obo/UBERON_0001017) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "systema nervosum centrale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:55675" +### intersomitic artery `http://purl.obolibrary.org/obo/UBERON_0002457` +#### Removed +- [intersomitic artery](http://purl.obolibrary.org/obo/UBERON_0002457) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Arteries that connect the dorsal aorta and the dorsal longitudinal anastomotic vessel. They run along the vertical myotomal boundaries. At early stages these vessels don't have venous or arteriproperty_value external_definitionmarkers. They form from the primary sprouts from the dorsal aorta[ZFA:0001061]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFA:0001061" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [intersomitic artery](http://purl.obolibrary.org/obo/UBERON_0002457) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Few changes of evolutionary significance occur in the branching pattern of the dorsal aorta. All vertebrates have (...) paired intersegmental arteries to the trunk, tail, and paired appendages.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### central nervous system macrophage `http://purl.obolibrary.org/obo/CL_0000878` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.612" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000225" -#### Added -- [central nervous system macrophage](http://purl.obolibrary.org/obo/CL_0000878) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### central sulcus `http://purl.obolibrary.org/obo/UBERON_0002916` +### intersomitic vessel `http://purl.obolibrary.org/obo/UBERON_0014907` #### Removed -- [central sulcus](http://purl.obolibrary.org/obo/UBERON_0002916) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "sulcus centralis cerebri" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Central_sulcus" +- [intersomitic vessel](http://purl.obolibrary.org/obo/UBERON_0014907) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Blood vessels that connect the dorsal aorta or the posterior cardinal vein and the dorsal longitudinal anastomotic vessel. They run along the vertical myotomal boundaries. At early stages these don't have venous or arterial markers[ZFA:0001285, ZFIN:ZDB-PUB-030908-4]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFA:0001285, ZFIN:ZDB-PUB-030908-4" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BIRNLEX:4035" +- [intersomitic vessel](http://purl.obolibrary.org/obo/UBERON_0014907) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [central sulcus](http://purl.obolibrary.org/obo/UBERON_0002916) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "sulcus centralis cerebri" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Central_sulcus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### interstitial fluid `http://purl.obolibrary.org/obo/UBERON_0000913` +#### Removed +- [interstitial fluid](http://purl.obolibrary.org/obo/UBERON_0000913) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [blood plasma](http://purl.obolibrary.org/obo/UBERON_0001969) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BIRNLEX:4035" -### central tendon of diaphragm `http://purl.obolibrary.org/obo/UBERON_0006670` +### interstitial tissue `http://purl.obolibrary.org/obo/UBERON_0005169` #### Removed -- [central tendon of diaphragm](http://purl.obolibrary.org/obo/UBERON_0006670) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "centrum tendineum diaphragmatis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [interstitial tissue](http://purl.obolibrary.org/obo/UBERON_0005169) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "interstital" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58279" -#### Added -- [central tendon of diaphragm](http://purl.obolibrary.org/obo/UBERON_0006670) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "centrum tendineum diaphragmatis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### intertarsal joint `http://purl.obolibrary.org/obo/UBERON_0008447` +#### Removed +- [intertarsal joint](http://purl.obolibrary.org/obo/UBERON_0008447) SubClassOf [connects](http://purl.obolibrary.org/obo/RO_0002176) some [tarsal bone](http://purl.obolibrary.org/obo/UBERON_0001447) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "two adjacent tarsals" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58279" +#### Added +- [intertarsal joint](http://purl.obolibrary.org/obo/UBERON_0008447) SubClassOf [connects](http://purl.obolibrary.org/obo/RO_0002176) some [tarsal bone](http://purl.obolibrary.org/obo/UBERON_0001447) -### centrilobular region hepatocyte `http://purl.obolibrary.org/obo/CL_0019029` +### intertarsal sesamoid `http://purl.obolibrary.org/obo/UBERON_0017261` #### Added -- [centrilobular region hepatocyte](http://purl.obolibrary.org/obo/CL_0019029) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [intertarsal sesamoid](http://purl.obolibrary.org/obo/UBERON_0017261) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### centroblast `http://purl.obolibrary.org/obo/CL_0009112` - -#### Added -- [centroblast](http://purl.obolibrary.org/obo/CL_0009112) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### interventricular septum `http://purl.obolibrary.org/obo/UBERON_0002094` +#### Removed +- [interventricular septum](http://purl.obolibrary.org/obo/UBERON_0002094) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The partition separating the right and left ventricles of the heart. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### centrocyte `http://purl.obolibrary.org/obo/CL_0009111` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/interventricular+septum" -#### Added -- [centrocyte](http://purl.obolibrary.org/obo/CL_0009111) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000386" -### cerebellar Golgi cell `http://purl.obolibrary.org/obo/CL_0000119` +- [interventricular septum](http://purl.obolibrary.org/obo/UBERON_0002094) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "involves the recruitment of myocardial cells as well as of non- muscular mesenchymal cells (Kaufman and Bard, 1999)" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0124020607" -#### Added -- [cerebellar Golgi cell](http://purl.obolibrary.org/obo/CL_0000119) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [interventricular septum](http://purl.obolibrary.org/obo/UBERON_0002094) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The two most progressive vertebrate classes, the birds and mammals, have completed the ventricular septum and at long last have completely separated the two blood streams along the length of the major heart chambers. This development has obviously been brought about independently in the two cases, since mammals and birds have evolved independently from primitive reptiles.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### cerebellar cortex `http://purl.obolibrary.org/obo/UBERON_0002129` -#### Removed -- [cerebellar cortex](http://purl.obolibrary.org/obo/UBERON_0002129) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cortex cerebelli" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:647" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.430" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [cerebellar cortex](http://purl.obolibrary.org/obo/UBERON_0002129) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cortex cerebelli" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:647" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000386" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### cerebellar granule cell `http://purl.obolibrary.org/obo/CL_0001031` +### interventricular septum membranous part `http://purl.obolibrary.org/obo/UBERON_0004666` +#### Removed +- [interventricular septum membranous part](http://purl.obolibrary.org/obo/UBERON_0004666) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The membranous septum is the upper part of ventricular septum[GO:0003149]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GO:0003149" #### Added -- [cerebellar granule cell](http://purl.obolibrary.org/obo/CL_0001031) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [interventricular septum membranous part](http://purl.obolibrary.org/obo/UBERON_0004666) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) -### cerebellum `http://purl.obolibrary.org/obo/UBERON_0002037` +### interventricular septum muscular part `http://purl.obolibrary.org/obo/UBERON_0004667` #### Removed -- [cerebellum](http://purl.obolibrary.org/obo/UBERON_0002037) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "parencephalon" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:643" +- [interventricular septum muscular part](http://purl.obolibrary.org/obo/UBERON_0004667) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The muscular septum is the lower part of the ventricular septum[GO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GO:0003150" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [cerebellum](http://purl.obolibrary.org/obo/UBERON_0002037) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "corpus cerebelli" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:643" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### intervertebral cartilage `http://purl.obolibrary.org/obo/UBERON_0011135` +#### Removed +- [intervertebral cartilage](http://purl.obolibrary.org/obo/UBERON_0011135) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Block of cartilage, which usually ossifies, that lies between successive vertebral centra.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000795" -#### Added -- [cerebellum](http://purl.obolibrary.org/obo/UBERON_0002037) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "parencephalon" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:643" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:Trueb_1973" -- [cerebellum](http://purl.obolibrary.org/obo/UBERON_0002037) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "corpus cerebelli" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:643" +- [intervertebral cartilage](http://purl.obolibrary.org/obo/UBERON_0011135) SubClassOf [adjacent to](http://purl.obolibrary.org/obo/RO_0002220) some [bony vertebral centrum](http://purl.obolibrary.org/obo/UBERON_0001075) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "between two centra" +#### Added +- [intervertebral cartilage](http://purl.obolibrary.org/obo/UBERON_0011135) SubClassOf [adjacent to](http://purl.obolibrary.org/obo/RO_0002220) some [bony vertebral centrum](http://purl.obolibrary.org/obo/UBERON_0001075) -### cerebellum fissure `http://purl.obolibrary.org/obo/UBERON_0003980` + +### intervertebral disk `http://purl.obolibrary.org/obo/UBERON_0001066` #### Removed -- [cerebellum fissure](http://purl.obolibrary.org/obo/UBERON_0003980) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "fissurae cerebelli" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:77789" +- [intervertebral disk](http://purl.obolibrary.org/obo/UBERON_0001066) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "strictly speaking the term intervertebral disk [applies to intervertebral cartilage]" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [cerebellum fissure](http://purl.obolibrary.org/obo/UBERON_0003980) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "fissurae cerebelli" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### intervertebral joint `http://purl.obolibrary.org/obo/UBERON_0001468` +#### Removed +- [intervertebral joint](http://purl.obolibrary.org/obo/UBERON_0001468) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA has 'intervertebral joint' as a GAT, and has two distinct classes 'intervertebral symphysis' and 'intervertebral syndesmosis', but note that the latter do not connect the centra" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:77789" +- [intervertebral joint](http://purl.obolibrary.org/obo/UBERON_0001468) SubClassOf [connects](http://purl.obolibrary.org/obo/RO_0002176) some [bony vertebral centrum](http://purl.obolibrary.org/obo/UBERON_0001075) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "connects successive pairs of centra" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +#### Added +- [intervertebral joint](http://purl.obolibrary.org/obo/UBERON_0001468) SubClassOf [connects](http://purl.obolibrary.org/obo/RO_0002176) some [bony vertebral centrum](http://purl.obolibrary.org/obo/UBERON_0001075) -### cerebral cortex `http://purl.obolibrary.org/obo/UBERON_0000956` +### intestinal epithelium `http://purl.obolibrary.org/obo/UBERON_0001277` #### Removed -- [cerebral cortex](http://purl.obolibrary.org/obo/UBERON_0000956) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cortex cerebralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:39" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [intestinal epithelium](http://purl.obolibrary.org/obo/UBERON_0001277) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Simple columnar epithelium that lines the intestine, sometimes pseudostratified, with absorptive brush-border cells and mucous goblet cells clearly visible. Crosnier et al. 2005[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -- [cerebral cortex](http://purl.obolibrary.org/obo/UBERON_0000956) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cortex cerebri" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cerebral_cortex" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -#### Added -- [cerebral cortex](http://purl.obolibrary.org/obo/UBERON_0000956) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cortex cerebralis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005124" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:39" - -- [cerebral cortex](http://purl.obolibrary.org/obo/UBERON_0000956) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cortex cerebri" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cerebral_cortex" +### intestinal gland `http://purl.obolibrary.org/obo/UBERON_0000333` +#### Removed +- [intestinal gland](http://purl.obolibrary.org/obo/UBERON_0000333) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "Note that some sources treat 'intestinal gland' as synonymous with crypts" -### cerebral cortex GABAergic interneuron `http://purl.obolibrary.org/obo/CL_0010011` -#### Added -- [cerebral cortex GABAergic interneuron](http://purl.obolibrary.org/obo/CL_0010011) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### intestinal villus `http://purl.obolibrary.org/obo/UBERON_0001213` +#### Removed +- [intestinal villus](http://purl.obolibrary.org/obo/UBERON_0001213) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The entire digestive tract is lined by well developed villi, which are longest in the intestinal bulb and decrease progressively in size towards the caudal end of the intestine. No crypts are present, but, the regions between the villi, the intervillus pockets, have a crypt-like function. Cells are produced in the intervillus pockets and shed from the villus tips. Crosnier et al. 2005[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -### cerebral cortex endothelial cell `http://purl.obolibrary.org/obo/CL_1001602` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005125" -#### Added -- [cerebral cortex endothelial cell](http://purl.obolibrary.org/obo/CL_1001602) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -### cerebral cortex neuron `http://purl.obolibrary.org/obo/CL_0010012` +- [intestinal villus](http://purl.obolibrary.org/obo/UBERON_0001213) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "the BTO class refers to a generic villous" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "BTO" -#### Added -- [cerebral cortex neuron](http://purl.obolibrary.org/obo/CL_0010012) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### cerebral hemisphere `http://purl.obolibrary.org/obo/UBERON_0001869` +### intestine `http://purl.obolibrary.org/obo/UBERON_0000160` #### Removed -- [cerebral hemisphere](http://purl.obolibrary.org/obo/UBERON_0001869) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "hemispherium cerebri" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cerebral_hemisphere" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [intestine](http://purl.obolibrary.org/obo/UBERON_0000160) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The tract of the alimentary canal. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [cerebral hemisphere](http://purl.obolibrary.org/obo/UBERON_0001869) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus medialis amygdalae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:241" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [cerebral hemisphere](http://purl.obolibrary.org/obo/UBERON_0001869) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus amygdaloideus medialis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:241" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000056" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [intestine](http://purl.obolibrary.org/obo/UBERON_0000160) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Portion of the alimentary canal bounded anteriorly by the pyloric sphincter and posteriorly by the cloacal sphincter.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" -#### Added -- [cerebral hemisphere](http://purl.obolibrary.org/obo/UBERON_0001869) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus medialis amygdalae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:241" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000246" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -- [cerebral hemisphere](http://purl.obolibrary.org/obo/UBERON_0001869) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus amygdaloideus medialis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:241" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [intestine](http://purl.obolibrary.org/obo/UBERON_0000160) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "intestinal" -- [cerebral hemisphere](http://purl.obolibrary.org/obo/UBERON_0001869) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "hemispherium cerebri" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [intestine](http://purl.obolibrary.org/obo/UBERON_0000160) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In zebrafish, No stomach, small intestine, or large intestine can be distinguished. However, differences can be found in the morphology of the mucosa columnar epithelial cells and the number of goblet cells, suggesting functional differentiation. The intestine has numerous folds that become progressively shorter in a rostral-to-caudal direction. Proportionally, these folds are significantly larger than the finger-like intestinal villi of mammals and other amniotes (Wallace et al. 2005). Columnar-shaped absorptive enterocytes are the most numerous in the zebrafish intestinal epithelium. Goblet cells are the second most populous epithelial cell type." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cerebral_hemisphere" -### cerebral hemisphere white matter `http://purl.obolibrary.org/obo/UBERON_0002437` +### intestine smooth muscle `http://purl.obolibrary.org/obo/UBERON_0004221` #### Removed -- [cerebral hemisphere white matter](http://purl.obolibrary.org/obo/UBERON_0002437) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "substantia medullaris cerebri" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:189" +- [intestine smooth muscle](http://purl.obolibrary.org/obo/UBERON_0004221) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [intestine smooth muscle](http://purl.obolibrary.org/obo/UBERON_0004221) SubClassOf [overlaps](http://purl.obolibrary.org/obo/RO_0002131) some [muscle layer of intestine](http://purl.obolibrary.org/obo/UBERON_0012367) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "consider merging" #### Added -- [cerebral hemisphere white matter](http://purl.obolibrary.org/obo/UBERON_0002437) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "substantia medullaris cerebri" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [intestine smooth muscle](http://purl.obolibrary.org/obo/UBERON_0004221) SubClassOf [overlaps](http://purl.obolibrary.org/obo/RO_0002131) some [muscle layer of intestine](http://purl.obolibrary.org/obo/UBERON_0012367) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:189" - -### cerebral vein `http://purl.obolibrary.org/obo/UBERON_0001663` +### intra-ocular muscle `http://purl.obolibrary.org/obo/UBERON_0011222` #### Removed -- [cerebral vein](http://purl.obolibrary.org/obo/UBERON_0001663) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "venae cerebri" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cerebral_veins" +- [intra-ocular muscle](http://purl.obolibrary.org/obo/UBERON_0011222) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Muscles within the eye (bulbus oculi).[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010038" -- [cerebral vein](http://purl.obolibrary.org/obo/UBERON_0001663) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "venae encephali" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cerebral_veins" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" #### Added -- [cerebral vein](http://purl.obolibrary.org/obo/UBERON_0001663) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "venae encephali" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cerebral_veins" +- [intra-ocular muscle](http://purl.obolibrary.org/obo/UBERON_0011222) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -- [cerebral vein](http://purl.obolibrary.org/obo/UBERON_0001663) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "venae cerebri" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cerebral_veins" +### intraembryonic coelom `http://purl.obolibrary.org/obo/UBERON_0003887` +#### Removed +- [intraembryonic coelom](http://purl.obolibrary.org/obo/UBERON_0003887) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### cervical rib `http://purl.obolibrary.org/obo/UBERON_0018144` -#### Removed -- [cervical rib](http://purl.obolibrary.org/obo/UBERON_0018144) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D057070" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.166" -#### Added -- [cervical rib](http://purl.obolibrary.org/obo/UBERON_0018144) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D057070" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000316" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -### cervical spinal cord `http://purl.obolibrary.org/obo/UBERON_0002726` +### intrahepatic bile duct `http://purl.obolibrary.org/obo/UBERON_0003704` #### Removed -- [cervical spinal cord](http://purl.obolibrary.org/obo/UBERON_0002726) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "segmenta cervicalia medullae spinalis [1-8" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71166" +- [intrahepatic bile duct](http://purl.obolibrary.org/obo/UBERON_0003704) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Duct that collects bile from the bile ductules and connects to the extrahepatic bile duct.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005169" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -- [cervical spinal cord](http://purl.obolibrary.org/obo/UBERON_0002726) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pars cervicalis medullae spinalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71166" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [cervical spinal cord](http://purl.obolibrary.org/obo/UBERON_0002726) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pars cervicalis medullae spinalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### intramembranous bone `http://purl.obolibrary.org/obo/UBERON_0002514` +#### Removed +- [intramembranous bone](http://purl.obolibrary.org/obo/UBERON_0002514) [UBPROP_0000005](http://purl.obolibrary.org/obo/UBPROP_0000005) "[In TAO], This term was made obsolete because it is considered a synonym of membrane bone (VSAO:0000023).[TAO]" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71166" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-06" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Curator" -- [cervical spinal cord](http://purl.obolibrary.org/obo/UBERON_0002726) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D066193" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001644" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +- [intramembranous bone](http://purl.obolibrary.org/obo/UBERON_0002514) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Bone that forms directly within mesenchyme, and does not replace other tissues.[TAO]" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -- [cervical spinal cord](http://purl.obolibrary.org/obo/UBERON_0002726) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "segmenta cervicalia medullae spinalis [1-8" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71166" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TAO:wd" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001644" -### cervical spinal cord ventral horn `http://purl.obolibrary.org/obo/UBERON_0014621` -#### Added -- [cervical spinal cord ventral horn](http://purl.obolibrary.org/obo/UBERON_0014621) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D066151" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) +### intramembranous bone tissue `http://purl.obolibrary.org/obo/UBERON_0004764` +#### Removed +- [intramembranous bone tissue](http://purl.obolibrary.org/obo/UBERON_0004764) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "note the distinction between intramembranous bone and intramembranous bone tissue. Some bones may be a mixture of both tissue types. The MA class most likely refers to a tissue type (it is under bone tissue and connective tissue; there are no child classes)" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -### cervical vertebra `http://purl.obolibrary.org/obo/UBERON_0002413` +### intrinsic muscle of tongue `http://purl.obolibrary.org/obo/UBERON_0001576` #### Removed -- [cervical vertebra](http://purl.obolibrary.org/obo/UBERON_0002413) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vertebrae cervicales" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cervical_vertebrae" +- [intrinsic muscle of tongue](http://purl.obolibrary.org/obo/UBERON_0001576) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The intrinsic tongue muscles are an integral part of the tongue that are innervated by Cranial Nerve XII.[FEED]" + - [url](http://www.geneontology.org/formats/oboInOwl#url) "http://www.feedexp.org" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "FEED" -#### Added -- [cervical vertebra](http://purl.obolibrary.org/obo/UBERON_0002413) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vertebrae cervicales" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cervical_vertebrae" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-07-02" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [intrinsic muscle of tongue](http://purl.obolibrary.org/obo/UBERON_0001576) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals).[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000748" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### chandelier pvalb GABAergic cortical interneuron `http://purl.obolibrary.org/obo/CL_4023036` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [chandelier pvalb GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023036) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1002/dvdy.20587 Kusakabe R, Kuratani S, Evolution and developmental patterning of the vertebrate skeletal muscles: perspectives from the lamprey. Developmental Dynamics (2005)" -### chemosensory organ `http://purl.obolibrary.org/obo/UBERON_0000005` -#### Removed -- [chemosensory organ](http://purl.obolibrary.org/obo/UBERON_0000005) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005157" +- [intrinsic muscle of tongue](http://purl.obolibrary.org/obo/UBERON_0001576) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "The main function of the intrinsic muscles is to provide shape. They are not involved with changing the position of the tongue and are not attached to bone" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" -#### Added -- [chemosensory organ](http://purl.obolibrary.org/obo/UBERON_0000005) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005157" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### chest `http://purl.obolibrary.org/obo/UBERON_0001443` +### intromittent organ `http://purl.obolibrary.org/obo/UBERON_0008811` #### Removed -- [chest](http://purl.obolibrary.org/obo/UBERON_0001443) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pectus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:24816" +- [intromittent organ](http://purl.obolibrary.org/obo/UBERON_0008811) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Surface structure that is an external structure of a male organism through which sperm is transferred to a female organism during mating.[TAO]" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TAO:wd" -- [chest](http://purl.obolibrary.org/obo/UBERON_0001443) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "thorax" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9576" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0002036" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Chest" +- [intromittent organ](http://purl.obolibrary.org/obo/UBERON_0008811) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "this is a broad grouping class connecting a number of different analagous organs by their function. We place the insect aedeagus here rather than penis, although this is somewhat arbitrary given the broadness of the current definition" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [intromittent organ](http://purl.obolibrary.org/obo/UBERON_0008811) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004850" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -#### Added -- [chest](http://purl.obolibrary.org/obo/UBERON_0001443) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pectus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:24816" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### involved in `http://purl.obolibrary.org/obo/RO_0002331` +#### Removed +- [involved in](http://purl.obolibrary.org/obo/RO_0002331) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "actively involved in" -- [chest](http://purl.obolibrary.org/obo/UBERON_0001443) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "thorax" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9576" +- [involved in](http://purl.obolibrary.org/obo/RO_0002331) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "enables part of" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [involved in](http://purl.obolibrary.org/obo/RO_0002331) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Chest" -### chest wall `http://purl.obolibrary.org/obo/UBERON_0016435` +### involved in negative regulation of `http://purl.obolibrary.org/obo/RO_0002430` +#### Removed +- [involved in negative regulation of](http://purl.obolibrary.org/obo/RO_0002430) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) -#### Added -- [chest wall](http://purl.obolibrary.org/obo/UBERON_0016435) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D035441" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +### involved in or involved in regulation of `http://purl.obolibrary.org/obo/RO_0002431` +#### Removed +- [involved in or involved in regulation of](http://purl.obolibrary.org/obo/RO_0002431) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) -### cholangiocyte `http://purl.obolibrary.org/obo/CL_1000488` +- [involved in or involved in regulation of](http://purl.obolibrary.org/obo/RO_0002431) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "involved in or reguates" -#### Added -- [cholangiocyte](http://purl.obolibrary.org/obo/CL_1000488) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### chondrocyte `http://purl.obolibrary.org/obo/CL_0000138` +### involved in positive regulation of `http://purl.obolibrary.org/obo/RO_0002429` +#### Removed +- [involved in positive regulation of](http://purl.obolibrary.org/obo/RO_0002429) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) -#### Added -- [chondrocyte](http://purl.obolibrary.org/obo/CL_0000138) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [involved in positive regulation of](http://purl.obolibrary.org/obo/RO_0002429) [RO_0004049](http://purl.obolibrary.org/obo/RO_0004049) [involved in regulation of](http://purl.obolibrary.org/obo/RO_0002428) -### chordate pharyngeal muscle `http://purl.obolibrary.org/obo/UBERON_0000933` + +### involved in regulation of `http://purl.obolibrary.org/obo/RO_0002428` #### Removed -- [chordate pharyngeal muscle](http://purl.obolibrary.org/obo/UBERON_0000933) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "musculi pharyngis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pharyngeal_muscles" +- [involved in regulation of](http://purl.obolibrary.org/obo/RO_0002428) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [chordate pharyngeal muscle](http://purl.obolibrary.org/obo/UBERON_0000933) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tunica muscularis pharyngis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pharyngeal_muscles" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### iris `http://purl.obolibrary.org/obo/UBERON_0001769` +#### Removed +- [iris](http://purl.obolibrary.org/obo/UBERON_0001769) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The opaque muscular contractile diaphragm suspended in the aqueous humour in front of the lens of the eye. The organ is perforated by the pupil and continues peripherally with the ciliary body. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [chordate pharyngeal muscle](http://purl.obolibrary.org/obo/UBERON_0000933) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tunica muscularis pharyngis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pharyngeal_muscles" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000101" -- [chordate pharyngeal muscle](http://purl.obolibrary.org/obo/UBERON_0000933) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "musculi pharyngis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pharyngeal_muscles" +- [iris](http://purl.obolibrary.org/obo/UBERON_0001769) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The avian iris and ciliary body undergoes a transition from smooth-to-striated muscle during embryonic development [DOI:dx.doi.org/10.1006/dbio.1998.9019]" +- [iris](http://purl.obolibrary.org/obo/UBERON_0001769) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)" -### chordotonal organ `http://purl.obolibrary.org/obo/UBERON_0001038` -#### Removed -- [chordotonal organ](http://purl.obolibrary.org/obo/UBERON_0001038) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005215" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [chordotonal organ](http://purl.obolibrary.org/obo/UBERON_0001038) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005215" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000101" -### chorionic plate `http://purl.obolibrary.org/obo/UBERON_0004027` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [chorionic plate](http://purl.obolibrary.org/obo/UBERON_0004027) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [placental disc](http://purl.obolibrary.org/obo/UBERON_8600038) +- [iris](http://purl.obolibrary.org/obo/UBERON_0001769) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "iridial" -- [chorionic plate](http://purl.obolibrary.org/obo/UBERON_0004027) SubClassOf [reproductive structure](http://purl.obolibrary.org/obo/UBERON_0005156) -### chorionic plate blood vessel `http://purl.obolibrary.org/obo/UBERON_8600021` +### iris blood vessel `http://purl.obolibrary.org/obo/UBERON_0003511` #### Removed -- [chorionic plate blood vessel](http://purl.obolibrary.org/obo/UBERON_8600021) SubClassOf [blood vessel](http://purl.obolibrary.org/obo/UBERON_0001981) +- [iris blood vessel](http://purl.obolibrary.org/obo/UBERON_0003511) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005568" #### Added -- [chorionic plate blood vessel](http://purl.obolibrary.org/obo/UBERON_8600021) SubClassOf [placenta blood vessel](http://purl.obolibrary.org/obo/UBERON_0022358) +- [iris blood vessel](http://purl.obolibrary.org/obo/UBERON_0003511) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) -### chorionic trophoblast cell `http://purl.obolibrary.org/obo/CL_0011101` +### iris stroma `http://purl.obolibrary.org/obo/UBERON_0001779` #### Added -- [chorionic trophoblast cell](http://purl.obolibrary.org/obo/CL_0011101) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [iris stroma](http://purl.obolibrary.org/obo/UBERON_0001779) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### chorionic villous mesenchyme `http://purl.obolibrary.org/obo/UBERON_8600039` +### is a defining property chain axiom `http://purl.obolibrary.org/obo/RO_0002581` +#### Removed +- [is a defining property chain axiom](http://purl.obolibrary.org/obo/RO_0002581) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL" -#### Added -- [chorionic villous mesenchyme](http://purl.obolibrary.org/obo/UBERON_8600039) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A mesenchyme that is part of a chorionic villus." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.1007/978-3-030-84725-8" +- [is a defining property chain axiom](http://purl.obolibrary.org/obo/RO_0002581) [label](http://www.w3.org/2000/01/rdf-schema#label) "is a defining property chain axiom" -- [chorionic villous mesenchyme](http://purl.obolibrary.org/obo/UBERON_8600039) [id](http://www.geneontology.org/formats/oboInOwl#id) "UBERON:8600039" +- AnnotationProperty: [is a defining property chain axiom](http://purl.obolibrary.org/obo/RO_0002581) -- [chorionic villous mesenchyme](http://purl.obolibrary.org/obo/UBERON_8600039) [label](http://www.w3.org/2000/01/rdf-schema#label) "chorionic villous mesenchyme" -- [chorionic villous mesenchyme](http://purl.obolibrary.org/obo/UBERON_8600039) [date](http://purl.org/dc/terms/date) "2024-01-16T18:13:12Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -- [chorionic villous mesenchyme](http://purl.obolibrary.org/obo/UBERON_8600039) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) +### is a defining property chain axiom where second argument is reflexive `http://purl.obolibrary.org/obo/RO_0002582` +#### Removed +- [is a defining property chain axiom where second argument is reflexive](http://purl.obolibrary.org/obo/RO_0002582) [label](http://www.w3.org/2000/01/rdf-schema#label) "is a defining property chain axiom where second argument is reflexive" -- [chorionic villous mesenchyme](http://purl.obolibrary.org/obo/UBERON_8600039) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" +- [is a defining property chain axiom where second argument is reflexive](http://purl.obolibrary.org/obo/RO_0002582) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R." -- Class: [chorionic villous mesenchyme](http://purl.obolibrary.org/obo/UBERON_8600039) +- AnnotationProperty: [is a defining property chain axiom where second argument is reflexive](http://purl.obolibrary.org/obo/RO_0002582) -- [chorionic villous mesenchyme](http://purl.obolibrary.org/obo/UBERON_8600039) EquivalentTo [mesenchyme](http://purl.obolibrary.org/obo/UBERON_0003104) and ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [chorionic villus](http://purl.obolibrary.org/obo/UBERON_0007106)) -- [chorionic villous mesenchyme](http://purl.obolibrary.org/obo/UBERON_8600039) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [chorionic villus](http://purl.obolibrary.org/obo/UBERON_0007106) -- [chorionic villous mesenchyme](http://purl.obolibrary.org/obo/UBERON_8600039) SubClassOf [embryonic tissue](http://purl.obolibrary.org/obo/UBERON_0005291) +### is active in `http://purl.obolibrary.org/obo/RO_0002432` +#### Removed +- [is active in](http://purl.obolibrary.org/obo/RO_0002432) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "executes activity in" -- [chorionic villous mesenchyme](http://purl.obolibrary.org/obo/UBERON_8600039) SubClassOf [chorionic mesenchyme](http://purl.obolibrary.org/obo/UBERON_0003265) +- [is active in](http://purl.obolibrary.org/obo/RO_0002432) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "A protein that enables activity in a cytosol." -- [chorionic villous mesenchyme](http://purl.obolibrary.org/obo/UBERON_8600039) SubClassOf [embryonic structure](http://purl.obolibrary.org/obo/UBERON_0002050) +- [is active in](http://purl.obolibrary.org/obo/RO_0002432) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) +- [enables](http://purl.obolibrary.org/obo/RO_0002327) o [occurs in](http://purl.obolibrary.org/obo/BFO_0000066) SubPropertyOf: [is active in](http://purl.obolibrary.org/obo/RO_0002432) + - [is a defining property chain axiom](http://purl.obolibrary.org/obo/RO_0002581) true -### choroid plexus `http://purl.obolibrary.org/obo/UBERON_0001886` -#### Removed -- [choroid plexus](http://purl.obolibrary.org/obo/UBERON_0001886) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "plexus choroideus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:61934" +### is kinase activity `http://purl.obolibrary.org/obo/RO_0002481` +#### Removed +- [is kinase activity](http://purl.obolibrary.org/obo/RO_0002481) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) -- [choroid plexus](http://purl.obolibrary.org/obo/UBERON_0001886) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "plexus choroideus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Choroid_plexus" -#### Added -- [choroid plexus](http://purl.obolibrary.org/obo/UBERON_0001886) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "plexus choroideus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### isRuleEnabled `http://swrl.stanford.edu/ontologies/3.3/swrla.owl#isRuleEnabled` +#### Removed +- AnnotationProperty: [isRuleEnabled](http://swrl.stanford.edu/ontologies/3.3/swrla.owl#isRuleEnabled) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:61934" -- [choroid plexus](http://purl.obolibrary.org/obo/UBERON_0001886) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "plexus choroideus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### is_class_level `http://www.geneontology.org/formats/oboInOwl#is_class_level` +#### Removed +- AnnotationProperty: [is_class_level](http://www.geneontology.org/formats/oboInOwl#is_class_level) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Choroid_plexus" -### choroid plexus epithelial cell `http://purl.obolibrary.org/obo/CL_0000706` +### is_entailed `http://www.geneontology.org/formats/oboInOwl#is_entailed` +#### Removed +- AnnotationProperty: [is_entailed](http://www.geneontology.org/formats/oboInOwl#is_entailed) -#### Added -- [choroid plexus epithelial cell](http://purl.obolibrary.org/obo/CL_0000706) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### choroid plexus epithelium `http://purl.obolibrary.org/obo/UBERON_0003911` +### is_redundant `http://www.geneontology.org/formats/oboInOwl#is_redundant` #### Removed -- [choroid plexus epithelium](http://purl.obolibrary.org/obo/UBERON_0003911) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006008" - - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0003-4423-4370" - -#### Added -- [choroid plexus epithelium](http://purl.obolibrary.org/obo/UBERON_0003911) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006008" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- AnnotationProperty: [is_redundant](http://www.geneontology.org/formats/oboInOwl#is_redundant) - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" - - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) +### ischial endochondral element `http://purl.obolibrary.org/obo/UBERON_0015056` -### choroidal blood vessel `http://purl.obolibrary.org/obo/UBERON_0002443` -#### Removed -- [choroidal blood vessel](http://purl.obolibrary.org/obo/UBERON_0002443) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vasa sanguinea choroideae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:76550" +#### Added +- [ischial endochondral element](http://purl.obolibrary.org/obo/UBERON_0015056) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### ischial pre-cartilage condensation `http://purl.obolibrary.org/obo/UBERON_0006255` #### Added -- [choroidal blood vessel](http://purl.obolibrary.org/obo/UBERON_0002443) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vasa sanguinea choroideae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:76550" +- [ischial pre-cartilage condensation](http://purl.obolibrary.org/obo/UBERON_0006255) SubClassOf [mesenchyme from somatopleure](http://purl.obolibrary.org/obo/UBERON_0010377) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### ischium `http://purl.obolibrary.org/obo/UBERON_0001274` +#### Removed +- [ischium](http://purl.obolibrary.org/obo/UBERON_0001274) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "this is_a hip bone in MA; in FMA it is a zone of bone organ." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" +- [ischium](http://purl.obolibrary.org/obo/UBERON_0001274) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Paired bones of endochondral origin that constitute the posterior elements of the pelvic girdle. They are synostotically fused to each other and form the posterior part of the acetabulum.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" -### chromaffin cell `http://purl.obolibrary.org/obo/CL_0000166` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -#### Added -- [chromaffin cell](http://purl.obolibrary.org/obo/CL_0000166) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000860" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### chromosome `http://purl.obolibrary.org/obo/GO_0005694` -#### Removed -- [chromosome](http://purl.obolibrary.org/obo/GO_0005694) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) +- [ischium](http://purl.obolibrary.org/obo/UBERON_0001274) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "ischial" -#### Added -- [chromosome](http://purl.obolibrary.org/obo/GO_0005694) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) -### chromosome segregation `http://purl.obolibrary.org/obo/GO_0007059` +### island of Calleja `http://purl.obolibrary.org/obo/UBERON_0001881` #### Removed -- [chromosome segregation](http://purl.obolibrary.org/obo/GO_0007059) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) +- [island of Calleja](http://purl.obolibrary.org/obo/UBERON_0001881) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The islands of Calleja are located within the olfactory tubercle in most species; however, in primates these islands are located within the nucleus accumbens, since the olfactory tubercle is absent or extremely rudimentary in the brains of primates" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "MP:0010010" -#### Added -- [chromosome segregation](http://purl.obolibrary.org/obo/GO_0007059) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) -### ciliary body `http://purl.obolibrary.org/obo/UBERON_0001775` +### islet of Langerhans `http://purl.obolibrary.org/obo/UBERON_0000006` #### Removed -- [ciliary body](http://purl.obolibrary.org/obo/UBERON_0001775) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "corpus ciliare" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ciliary_body" +- [islet of Langerhans](http://purl.obolibrary.org/obo/UBERON_0000006) [UBPROP_0000202](http://purl.obolibrary.org/obo/UBPROP_0000202) [FMA_76489](http://purl.obolibrary.org/obo/FMA_76489) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [islet of Langerhans](http://purl.obolibrary.org/obo/UBERON_0000006) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical structure which consists of glands developed from pancreatic ducts in the larvae and secrete insulin.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -#### Added -- [ciliary body](http://purl.obolibrary.org/obo/UBERON_0001775) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "corpus ciliare" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ciliary_body" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010406" -### ciliary muscle `http://purl.obolibrary.org/obo/UBERON_0001605` -#### Removed -- [ciliary muscle](http://purl.obolibrary.org/obo/UBERON_0001605) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "musculus ciliaris" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ciliary_muscle" +- [islet of Langerhans](http://purl.obolibrary.org/obo/UBERON_0000006) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Mammals, birds, reptiles and amphibians have a pancreas with similar histology and mode of development, while in some fish, the islet cells are segregated as Brockmann bodies.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [ciliary muscle](http://purl.obolibrary.org/obo/UBERON_0001605) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "musculus ciliaris" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ciliary_muscle" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000646" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:7600975 Slack JMW, Developmental biology of the pancreas. Development (1995)" -### ciliary muscle cell `http://purl.obolibrary.org/obo/CL_1000443` +- [islet of Langerhans](http://purl.obolibrary.org/obo/UBERON_0000006) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "A primitive exocrine pancreas can be found in holocephalan cartilaginous fish; a pancreatic duct directly ending in the gut lumen is connected to a glandular structure made of exocrine cells and associated with cell islets, which comprises three different hormone-producing cell types: insulin, somatostatin and glucagon (Yui and Fujita, 1986)" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:16417468" #### Added -- [ciliary muscle cell](http://purl.obolibrary.org/obo/CL_1000443) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [islet of Langerhans](http://purl.obolibrary.org/obo/UBERON_0000006) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -### ciliary processes `http://purl.obolibrary.org/obo/UBERON_0010427` -#### Removed -- [ciliary processes](http://purl.obolibrary.org/obo/UBERON_0010427) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "processus ciliares" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### jaw region `http://purl.obolibrary.org/obo/UBERON_0011595` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +#### Added +- [jaw region](http://purl.obolibrary.org/obo/UBERON_0011595) SubClassOf [structure with developmental contribution from neural crest](http://purl.obolibrary.org/obo/UBERON_0010314) -- [ciliary processes](http://purl.obolibrary.org/obo/UBERON_0010427) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "processus ciliares" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ciliary_processes" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### jaw skeleton `http://purl.obolibrary.org/obo/UBERON_0001708` +#### Removed +- [jaw skeleton](http://purl.obolibrary.org/obo/UBERON_0001708) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "There are cellular contributions from all three embryonic germ layers: pharyngeal mesoderm, endoderm and neural crest that migrates out of the ectoderm (Noden, 1983)." -#### Added -- [ciliary processes](http://purl.obolibrary.org/obo/UBERON_0010427) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "processus ciliares" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [jaw skeleton](http://purl.obolibrary.org/obo/UBERON_0001708) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Skeletal and cartilage elements of the first pharyngeal arch.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -- [ciliary processes](http://purl.obolibrary.org/obo/UBERON_0010427) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "processus ciliares" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ciliary_processes" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001227" +- [jaw skeleton](http://purl.obolibrary.org/obo/UBERON_0001708) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in FMA, the jaw is an organism subdivision cluster, and includes mucosal tissue such as the gingiva as parts. It appears to be skeletal in MA (and has teeth as parts). It is reasonable to assume that ZFA and XAO consider the upper and lower jaws to be skeletal elements or clusters. EHDAA2 also considers these clusters. TODO - follow EHDAA2 model. These arbitrary differences in terminology and classification have to be reconciled with the genuine well-known biological differences in the skeletal elements across vertebrates" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" -### ciliated cell `http://purl.obolibrary.org/obo/CL_0000064` +- [jaw skeleton](http://purl.obolibrary.org/obo/UBERON_0001708) SubClassOf [structure with developmental contribution from neural crest](http://purl.obolibrary.org/obo/UBERON_0010314) #### Added -- [ciliated cell](http://purl.obolibrary.org/obo/CL_0000064) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [jaw skeleton](http://purl.obolibrary.org/obo/UBERON_0001708) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) -### ciliated cell of the bronchus `http://purl.obolibrary.org/obo/CL_0002332` +### jejunum `http://purl.obolibrary.org/obo/UBERON_0002115` +#### Removed +- [jejunum](http://purl.obolibrary.org/obo/UBERON_0002115) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The jejunum is the middle section of the small intestine in most higher vertebrates, including mammals, reptiles, and birds. In fish, the divisions of the small intestine are not as clear and the terms middle intestine or mid-gut may be used instead of jejunum.[Wikipedia:Jejunum]" -#### Added -- [ciliated cell of the bronchus](http://purl.obolibrary.org/obo/CL_0002332) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [jejunum](http://purl.obolibrary.org/obo/UBERON_0002115) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The first two fifth of the small intestine beyond the duodenum. It extends from the end of the duodenum to the ileum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000053" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### ciliated columnar cell of tracheobronchial tree `http://purl.obolibrary.org/obo/CL_0002145` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [ciliated columnar cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002145) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + +- [jejunum](http://purl.obolibrary.org/obo/UBERON_0002115) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "jejunal" +- [jejunum](http://purl.obolibrary.org/obo/UBERON_0002115) SubClassOf [subdivision of digestive tract](http://purl.obolibrary.org/obo/UBERON_0004921) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "cjm" -### ciliated epithelial cell `http://purl.obolibrary.org/obo/CL_0000067` + - [order](http://www.geneontology.org/formats/oboInOwl#order) "3" #### Added -- [ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0000067) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [jejunum](http://purl.obolibrary.org/obo/UBERON_0002115) SubClassOf [subdivision of digestive tract](http://purl.obolibrary.org/obo/UBERON_0004921) -### circle of Willis `http://purl.obolibrary.org/obo/UBERON_0003709` +### joint connecting upper and lower jaws `http://purl.obolibrary.org/obo/UBERON_0011171` #### Removed -- [circle of Willis](http://purl.obolibrary.org/obo/UBERON_0003709) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "circulus arteriosus cerebri" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Circle_of_Willis" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [joint connecting upper and lower jaws](http://purl.obolibrary.org/obo/UBERON_0011171) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NCIT:C32888" -#### Added -- [circle of Willis](http://purl.obolibrary.org/obo/UBERON_0003709) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "circulus arteriosus cerebri" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [joint connecting upper and lower jaws](http://purl.obolibrary.org/obo/UBERON_0011171) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Some synapsids retained two pairs of jaw joints - quadrate-articular and tempero-mandibular, but this unusual paired condition did not last long" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://evolution.berkeley.edu" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Circle_of_Willis" -### circulatory system `http://purl.obolibrary.org/obo/UBERON_0001009` +### jugular foramen `http://purl.obolibrary.org/obo/UBERON_0005456` #### Removed -- [circulatory system](http://purl.obolibrary.org/obo/UBERON_0001009) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "systema cardiovasculare" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Circulatory_system" +- [jugular foramen](http://purl.obolibrary.org/obo/UBERON_0005456) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "One of a pair of openings between the lateral part of the occipital bone and the petrous part of the temporal bones in the skull. The foramen contains the inferior petrosal sinus; the transverse sinus; some meningeal branches of the occipital and ascending pharyngeal arteries; and the glossopharyngeal, vagus, and accessory nerves. [Free_Online_Medical_Dictionary]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - -#### Added -- [circulatory system](http://purl.obolibrary.org/obo/UBERON_0001009) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D002319" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [circulatory system](http://purl.obolibrary.org/obo/UBERON_0001009) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "systema cardiovasculare" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001113" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Circulatory_system" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/jugular+foramen" +- [jugular foramen](http://purl.obolibrary.org/obo/UBERON_0005456) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: subclass braincase and otic capsule opening (AAO:0000051)[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -### circumventricular organ `http://purl.obolibrary.org/obo/UBERON_0005408` -#### Removed -- [circumventricular organ](http://purl.obolibrary.org/obo/UBERON_0005408) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D066280" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -- [circumventricular organ](http://purl.obolibrary.org/obo/UBERON_0005408) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006267" - - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0003-4423-4370" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000249" -#### Added -- [circumventricular organ](http://purl.obolibrary.org/obo/UBERON_0005408) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D066280" +- [jugular foramen](http://purl.obolibrary.org/obo/UBERON_0005456) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D000080869" - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -- [circumventricular organ](http://purl.obolibrary.org/obo/UBERON_0005408) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006267" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [jugular foramen](http://purl.obolibrary.org/obo/UBERON_0005456) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Large foramen that houses the glossopharyngeal and vagus nerves and is located inside the condyloid fossa.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000249" -### class switched memory B cell `http://purl.obolibrary.org/obo/CL_0000972` -#### Added -- [class switched memory B cell](http://purl.obolibrary.org/obo/CL_0000972) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### kidney `http://purl.obolibrary.org/obo/UBERON_0002113` +#### Removed +- [kidney](http://purl.obolibrary.org/obo/UBERON_0002113) [UBPROP_0000202](http://purl.obolibrary.org/obo/UBPROP_0000202) [FMA_264815](http://purl.obolibrary.org/obo/FMA_264815) -### classical monocyte `http://purl.obolibrary.org/obo/CL_0000860` +- [kidney](http://purl.obolibrary.org/obo/UBERON_0002113) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [intestine](http://purl.obolibrary.org/obo/UBERON_0000160) -#### Added -- [classical monocyte](http://purl.obolibrary.org/obo/CL_0000860) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [kidney](http://purl.obolibrary.org/obo/UBERON_0002113) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "One of either of a pair of structures lying on either side of the dorsal aorta in which fluid balance is regulated and waste is excreted out in the form of urine.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000250" -### cloacal membrane `http://purl.obolibrary.org/obo/UBERON_0006217` -#### Removed -- [cloacal membrane](http://purl.obolibrary.org/obo/UBERON_0006217) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "membrana cloacalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cloacal_membrane" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" -#### Added -- [cloacal membrane](http://purl.obolibrary.org/obo/UBERON_0006217) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "membrana cloacalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [kidney](http://purl.obolibrary.org/obo/UBERON_0002113) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A paired organ of the urinary tract which has the production of urine as its primary function." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://anatomy.uams.edu/anatomyhtml/kidney.html" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cloacal_membrane" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Kidney" +- [kidney](http://purl.obolibrary.org/obo/UBERON_0002113) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NCIT:C12415" -### club cell `http://purl.obolibrary.org/obo/CL_0000158` +- [kidney](http://purl.obolibrary.org/obo/UBERON_0002113) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:17373" -#### Added -- [club cell](http://purl.obolibrary.org/obo/CL_0000158) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [kidney](http://purl.obolibrary.org/obo/UBERON_0002113) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:7203" +- [kidney](http://purl.obolibrary.org/obo/UBERON_0002113) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MA:0000368" -### cochlear duct of membranous labyrinth `http://purl.obolibrary.org/obo/UBERON_0001855` -#### Removed -- [cochlear duct of membranous labyrinth](http://purl.obolibrary.org/obo/UBERON_0001855) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ductus cochlearis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001692" +- [kidney](http://purl.obolibrary.org/obo/UBERON_0002113) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EV:0100096" + +- [kidney](http://purl.obolibrary.org/obo/UBERON_0002113) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "renal" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cochlear_duct" +- [kidney](http://purl.obolibrary.org/obo/UBERON_0002113) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EFO:0000929" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [kidney](http://purl.obolibrary.org/obo/UBERON_0002113) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "SCTID:181414000" + +- [kidney](http://purl.obolibrary.org/obo/UBERON_0002113) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [kidney mesenchyme](http://purl.obolibrary.org/obo/UBERON_0003918) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" #### Added -- [cochlear duct of membranous labyrinth](http://purl.obolibrary.org/obo/UBERON_0001855) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ductus cochlearis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [kidney](http://purl.obolibrary.org/obo/UBERON_0002113) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-7655-4833](https://orcid.org/0000-0001-7655-4833) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001692" +- [kidney](http://purl.obolibrary.org/obo/UBERON_0002113) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A paired organ of the urinary tract that produces urine and maintains bodily fluid homeostasis, blood pressure, pH levels, red blood cell production and skeleton mineralization." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://anatomy.uams.edu/anatomyhtml/kidney.html" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cochlear_duct" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.kidney.org/kidneydisease/top-5-jobs-kidneys-do" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:25140012" -### cochlear ganglion `http://purl.obolibrary.org/obo/UBERON_0000395` -#### Removed -- [cochlear ganglion](http://purl.obolibrary.org/obo/UBERON_0000395) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ganglion spirale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Spiral_ganglion" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35003210" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Kidney" -#### Added -- [cochlear ganglion](http://purl.obolibrary.org/obo/UBERON_0000395) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ganglion spirale" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [kidney](http://purl.obolibrary.org/obo/UBERON_0002113) [contributor](http://purl.org/dc/terms/contributor) [X](https://orcid.org/0000-0003-2804-127X) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Spiral_ganglion" +- [kidney](http://purl.obolibrary.org/obo/UBERON_0002113) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [kidney mesenchyme](http://purl.obolibrary.org/obo/UBERON_0003918) -### cochlear modiolus `http://purl.obolibrary.org/obo/UBERON_0006723` +### kidney arcuate vein `http://purl.obolibrary.org/obo/UBERON_0004719` #### Removed -- [cochlear modiolus](http://purl.obolibrary.org/obo/UBERON_0006723) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "modiolus cochleae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [kidney arcuate vein](http://purl.obolibrary.org/obo/UBERON_0004719) [UBPROP_0000202](http://purl.obolibrary.org/obo/UBPROP_0000202) [FMA_71632](http://purl.obolibrary.org/obo/FMA_71632) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:61278" -#### Added -- [cochlear modiolus](http://purl.obolibrary.org/obo/UBERON_0006723) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "modiolus cochleae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### kidney blood vessel `http://purl.obolibrary.org/obo/UBERON_0003517` +#### Removed +- [kidney blood vessel](http://purl.obolibrary.org/obo/UBERON_0003517) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:28457" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:61278" -### cochlear nuclear complex `http://purl.obolibrary.org/obo/UBERON_0002610` +### kidney blood vessel cell `http://purl.obolibrary.org/obo/CL_1000854` #### Removed -- [cochlear nuclear complex](http://purl.obolibrary.org/obo/UBERON_0002610) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nuclei cochleares" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cochlear_nuclei" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [kidney blood vessel cell](http://purl.obolibrary.org/obo/CL_1000854) EquivalentTo [kidney medulla cell](http://purl.obolibrary.org/obo/CL_1000504) and ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [kidney blood vessel](http://purl.obolibrary.org/obo/UBERON_0003517)) #### Added -- [cochlear nuclear complex](http://purl.obolibrary.org/obo/UBERON_0002610) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nuclei cochleares" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cochlear_nuclei" +- [kidney blood vessel cell](http://purl.obolibrary.org/obo/CL_1000854) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A blood vessel cell that is part of a kidney." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34843404" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [kidney blood vessel cell](http://purl.obolibrary.org/obo/CL_1000854) EquivalentTo [cell](http://purl.obolibrary.org/obo/CL_0000000) and ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [kidney blood vessel](http://purl.obolibrary.org/obo/UBERON_0003517)) -### coelemic cavity lumen `http://purl.obolibrary.org/obo/UBERON_0002323` +### kidney capsule `http://purl.obolibrary.org/obo/UBERON_0002015` #### Removed -- [coelemic cavity lumen](http://purl.obolibrary.org/obo/UBERON_0002323) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005060" +- [kidney capsule](http://purl.obolibrary.org/obo/UBERON_0002015) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "The renal capsule relates to the other layers in the following order (moving from innermost to outermost): renal medulla renal cortex renal capsule perinephric fat (or 'perirenal fat') renal fascia paranephric fat (or 'pararenal fat') peritoneum (anteriorly), and transversalis fascia (posteriorly).[Wikipedia:Kidney_capsule]" + +- [kidney capsule](http://purl.obolibrary.org/obo/UBERON_0002015) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "provides some protection from trauma and damage." -#### Added -- [coelemic cavity lumen](http://purl.obolibrary.org/obo/UBERON_0002323) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005060" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### collagen fibril binding `http://purl.obolibrary.org/obo/GO_0098633` +### kidney collecting duct epithelium `http://purl.obolibrary.org/obo/UBERON_0014388` #### Removed -- [collagen fibril binding](http://purl.obolibrary.org/obo/GO_0098633) SubClassOf [binding](http://purl.obolibrary.org/obo/GO_0005488) +- [kidney collecting duct epithelium](http://purl.obolibrary.org/obo/UBERON_0014388) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In mouse, the mature and differentiated CD epithelium comprises two unique cells types with principal cells responsible for vasopressin-regulated water reabsorption, and intercalated cells regulating acid-base homeostasis; injury to the epithelium is believed to cause epithelial cells to acquire mesenchymal characteristics via epithelial-mesenchymal transition (EMT), a process through which tubular epithelial cells may transform into interstitial fibroblasts and promote renal fibrosis" + + + +### kidney cortex interstitial cell `http://purl.obolibrary.org/obo/CL_1000681` #### Added -- [collagen fibril binding](http://purl.obolibrary.org/obo/GO_0098633) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/geneontology/go-ontology/issues/21211"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) +- [kidney cortex interstitial cell](http://purl.obolibrary.org/obo/CL_1000681) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cell that is part of an interstitial compartment of a renal cortex." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:18575881" + -- [collagen fibril binding](http://purl.obolibrary.org/obo/GO_0098633) SubClassOf [extracellular matrix binding](http://purl.obolibrary.org/obo/GO_0050840) +### kidney inner medulla interstitial cell `http://purl.obolibrary.org/obo/CL_1000803` + +#### Added +- [kidney inner medulla interstitial cell](http://purl.obolibrary.org/obo/CL_1000803) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cell that is part of an interstitial compartment of an inner renal medulla." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:21359760" -### collagen secreting cell `http://purl.obolibrary.org/obo/CL_0000667` +### kidney interstitial fibroblast `http://purl.obolibrary.org/obo/CL_1000692` #### Added -- [collagen secreting cell](http://purl.obolibrary.org/obo/CL_0000667) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [kidney interstitial fibroblast](http://purl.obolibrary.org/obo/CL_1000692) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A fibroblast that is part of an interstitial compartment of a kidney." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:10559635" -### collecting duct of renal tubule `http://purl.obolibrary.org/obo/UBERON_0001232` +### kidney interstitium `http://purl.obolibrary.org/obo/UBERON_0005215` #### Removed -- [collecting duct of renal tubule](http://purl.obolibrary.org/obo/UBERON_0001232) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tubulus renalis arcuatus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Connecting_tubule" +- [kidney interstitium](http://purl.obolibrary.org/obo/UBERON_0005215) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "The interstitium is necessarily involved in all intrarenal exchange processes since the reabsorption and secretion of fluid and solutes implicates a transit across the interstitial compartment." - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - -#### Added -- [collecting duct of renal tubule](http://purl.obolibrary.org/obo/UBERON_0001232) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tubulus renalis arcuatus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [kidney interstitium](http://purl.obolibrary.org/obo/UBERON_0005215) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "The fibroblasts in the interstitium provide the 'skeleton' of the tissue and maintain the three-dimensional architecture of the tissue." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Connecting_tubule" -### collection of hairs `http://purl.obolibrary.org/obo/UBERON_0010164` +### kidney medulla cell `http://purl.obolibrary.org/obo/CL_1000504` #### Removed -- [collection of hairs](http://purl.obolibrary.org/obo/UBERON_0010164) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pili" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [kidney medulla cell](http://purl.obolibrary.org/obo/CL_1000504) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cell that is part of a renal medulla." #### Added -- [collection of hairs](http://purl.obolibrary.org/obo/UBERON_0010164) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pili" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [kidney medulla cell](http://purl.obolibrary.org/obo/CL_1000504) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cell that is part of a renal medulla." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:22343825" -### colon epithelial cell `http://purl.obolibrary.org/obo/CL_0011108` +### kidney medulla interstitial cell `http://purl.obolibrary.org/obo/CL_1000682` #### Added -- [colon epithelial cell](http://purl.obolibrary.org/obo/CL_0011108) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [kidney medulla interstitial cell](http://purl.obolibrary.org/obo/CL_1000682) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cell that is part of an interstitum of a renal medulla." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:21359760" -### colon goblet cell `http://purl.obolibrary.org/obo/CL_0009039` +### kidney outer medulla interstitial cell `http://purl.obolibrary.org/obo/CL_1000804` #### Added -- [colon goblet cell](http://purl.obolibrary.org/obo/CL_0009039) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [kidney outer medulla interstitial cell](http://purl.obolibrary.org/obo/CL_1000804) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A kidney cell that is part of an interstitial compartment of an outer renal medulla." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:8694267" -### colon macrophage `http://purl.obolibrary.org/obo/CL_0009038` +### kidney pyramid `http://purl.obolibrary.org/obo/UBERON_0004200` +#### Removed +- [kidney pyramid](http://purl.obolibrary.org/obo/UBERON_0004200) [UBPROP_0000202](http://purl.obolibrary.org/obo/UBPROP_0000202) [FMA_74268](http://purl.obolibrary.org/obo/FMA_74268) + +- [kidney pyramid](http://purl.obolibrary.org/obo/UBERON_0004200) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "not the same as FMA:50609 Pyramid (which is a volume / dimensional entity)" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" -#### Added -- [colon macrophage](http://purl.obolibrary.org/obo/CL_0009038) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### columnar/cuboidal epithelial cell `http://purl.obolibrary.org/obo/CL_0000075` +### kidney resident dendritic cell `http://purl.obolibrary.org/obo/CL_1000699` #### Added -- [columnar/cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000075) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [kidney resident dendritic cell](http://purl.obolibrary.org/obo/CL_1000699) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A resident-dendritic cell that is part of a kidney." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:25266210" -### common bile duct `http://purl.obolibrary.org/obo/UBERON_0001174` +### killer cell lectin-like receptor subfamily B member 1 `http://purl.obolibrary.org/obo/PR_000025670` #### Removed -- [common bile duct](http://purl.obolibrary.org/obo/UBERON_0001174) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ductus choledochus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Common_bile_duct" +- [killer cell lectin-like receptor subfamily B member 1](http://purl.obolibrary.org/obo/PR_000025670) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [killer cell lectin-like receptor subfamily B member 1 (human)](http://purl.obolibrary.org/obo/PR_Q12918) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [common bile duct](http://purl.obolibrary.org/obo/UBERON_0001174) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ductus choledochus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Common_bile_duct" +### killer cell lectin-like receptor subfamily G member 1 `http://purl.obolibrary.org/obo/PR_000009426` +#### Removed +- [killer cell lectin-like receptor subfamily G member 1](http://purl.obolibrary.org/obo/PR_000009426) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [killer cell lectin-like receptor subfamily G member 1 (human)](http://purl.obolibrary.org/obo/PR_Q96E93) -### common carotid artery plus branches `http://purl.obolibrary.org/obo/UBERON_0001530` -#### Removed -- [common carotid artery plus branches](http://purl.obolibrary.org/obo/UBERON_0001530) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "a. carotis communis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Common_carotid_artery" +### knee joint `http://purl.obolibrary.org/obo/UBERON_0001485` +#### Removed +- [knee joint](http://purl.obolibrary.org/obo/UBERON_0001485) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [knee joint primordium](http://purl.obolibrary.org/obo/UBERON_0006256) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" #### Added -- [common carotid artery plus branches](http://purl.obolibrary.org/obo/UBERON_0001530) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "a. carotis communis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [knee joint](http://purl.obolibrary.org/obo/UBERON_0001485) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [knee joint primordium](http://purl.obolibrary.org/obo/UBERON_0006256) + - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Common_carotid_artery" +### lacrimal apparatus `http://purl.obolibrary.org/obo/UBERON_0001750` +#### Removed +- [lacrimal apparatus](http://purl.obolibrary.org/obo/UBERON_0001750) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "this is an eye appendage in ncit, along with eyelid and eyebrow. in MA, part of eye surface part_of eye" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "ncit" + +#### Added +- [lacrimal apparatus](http://purl.obolibrary.org/obo/UBERON_0001750) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### common dendritic progenitor `http://purl.obolibrary.org/obo/CL_0001029` +### lacrimal canaliculus `http://purl.obolibrary.org/obo/UBERON_0001770` #### Added -- [common dendritic progenitor](http://purl.obolibrary.org/obo/CL_0001029) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [lacrimal canaliculus](http://purl.obolibrary.org/obo/UBERON_0001770) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### common hepatic artery `http://purl.obolibrary.org/obo/UBERON_0005436` +### lacrimal drainage system `http://purl.obolibrary.org/obo/UBERON_0001850` #### Removed -- [common hepatic artery](http://purl.obolibrary.org/obo/UBERON_0005436) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria hepatica communis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Common_hepatic_artery" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [lacrimal drainage system](http://purl.obolibrary.org/obo/UBERON_0001850) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "chelonians lack a lacrimal duct, and lacrimal/harderian secretions remain in or spill from the conjunctival sac[PMID:7559104]" #### Added -- [common hepatic artery](http://purl.obolibrary.org/obo/UBERON_0005436) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria hepatica communis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Common_hepatic_artery" +- [lacrimal drainage system](http://purl.obolibrary.org/obo/UBERON_0001850) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### common hepatic duct `http://purl.obolibrary.org/obo/UBERON_0001175` +### lacrimal gland `http://purl.obolibrary.org/obo/UBERON_0001817` #### Removed -- [common hepatic duct](http://purl.obolibrary.org/obo/UBERON_0001175) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ductus hepaticus communis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Common_hepatic_duct" +- [lacrimal gland](http://purl.obolibrary.org/obo/UBERON_0001817) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The preorbital gland is a paired exocrine gland found in many species of hoofed animals, which is homologous to the lacrimal gland found in humans. These glands are trenchlike slits of dark blue to black, nearly bare skin extending from the medial canthus of each eye. They are lined by a combination of sebaceous and sudoriferous glands, and they produce secretions which contain pheromones and other semiochemical compounds. Ungulates frequently deposit these secretions on twigs and grass as a means of communication with other animals. The preorbital gland serves different roles in different species. Pheromone-containing secretions from the preorbital gland may serve to establish an animal's dominance (especially in preparation for breeding), mark its territory, or simply to produce a pleasurable sensation to the animal. Because of its critical role in scent marking, the preorbital gland is usually considered as a type of scent gland. A further function of these glands may be to produce antimicrobial compounds against skin pathogens. Antimicrobial compounds found in these glands may be biosynthesized by the animal itself, or by microorganisms that live in these glands[Wikipedia:Preorbital_gland]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Preorbital_gland" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [lacrimal gland](http://purl.obolibrary.org/obo/UBERON_0001817) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In humans, they are situated in the upper, outer portion of each orbit" -#### Added -- [common hepatic duct](http://purl.obolibrary.org/obo/UBERON_0001175) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ductus hepaticus communis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Common_hepatic_duct" +- [lacrimal gland](http://purl.obolibrary.org/obo/UBERON_0001817) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [lacrimal gland](http://purl.obolibrary.org/obo/UBERON_0001817) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Lobular organ the parenchyma of which consists of glandular acini which communicate the lacrimal sac. Examples: There only two instances, right lacrimal and left lacrimal glands." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:59101" +- [lacrimal gland](http://purl.obolibrary.org/obo/UBERON_0001817) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Innervation is highly complex and species-specific" -### common iliac artery `http://purl.obolibrary.org/obo/UBERON_0001191` -#### Removed -- [common iliac artery](http://purl.obolibrary.org/obo/UBERON_0001191) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria iliaca communis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Common_iliac_artery" +#### Added +- [lacrimal gland](http://purl.obolibrary.org/obo/UBERON_0001817) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [common iliac artery](http://purl.obolibrary.org/obo/UBERON_0001191) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria iliaca communis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Common_iliac_artery" +### lacrimal gland bud `http://purl.obolibrary.org/obo/UBERON_0022284` +#### Removed +- [lacrimal gland bud](http://purl.obolibrary.org/obo/UBERON_0022284) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "in mouse, the primary bud arises around E13.5 and extends caudally into the surrounding neural-crest derived periocular mesenchyme; between E15.5 and E16.5 the bud undergoes branching morphogenesis, forming both a major extra-orbital lobe and a minor intraorbital lobe" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### common iliac vein `http://purl.obolibrary.org/obo/UBERON_0001139` +### lacrimal nerve `http://purl.obolibrary.org/obo/UBERON_0011096` #### Removed -- [common iliac vein](http://purl.obolibrary.org/obo/UBERON_0001139) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena iliaca communis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Common_iliac_vein" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [lacrimal nerve](http://purl.obolibrary.org/obo/UBERON_0011096) SubClassOf [nerve](http://purl.obolibrary.org/obo/UBERON_0001021) #### Added -- [common iliac vein](http://purl.obolibrary.org/obo/UBERON_0001139) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena iliaca communis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [lacrimal nerve](http://purl.obolibrary.org/obo/UBERON_0011096) SubClassOf [nerve of head region](http://purl.obolibrary.org/obo/UBERON_0011779) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Common_iliac_vein" +- [lacrimal nerve](http://purl.obolibrary.org/obo/UBERON_0011096) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### common lymphoid progenitor `http://purl.obolibrary.org/obo/CL_0000051` +### lacrimal punctum `http://purl.obolibrary.org/obo/UBERON_0010284` +#### Removed +- [lacrimal punctum](http://purl.obolibrary.org/obo/UBERON_0010284) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "collect tears produced by the lacrimal glands" #### Added -- [common lymphoid progenitor](http://purl.obolibrary.org/obo/CL_0000051) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [lacrimal punctum](http://purl.obolibrary.org/obo/UBERON_0010284) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### common myeloid progenitor `http://purl.obolibrary.org/obo/CL_0000049` +### lacrimal sac `http://purl.obolibrary.org/obo/UBERON_0001351` #### Added -- [common myeloid progenitor](http://purl.obolibrary.org/obo/CL_0000049) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [lacrimal sac](http://purl.obolibrary.org/obo/UBERON_0001351) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### compact bone tissue `http://purl.obolibrary.org/obo/UBERON_0001439` +### lactosylceramide 4-alpha-galactosyltransferase `http://purl.obolibrary.org/obo/PR_000003516` #### Removed -- [compact bone tissue](http://purl.obolibrary.org/obo/UBERON_0001439) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "substantia compacta" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:24018" +- [lactosylceramide 4-alpha-galactosyltransferase](http://purl.obolibrary.org/obo/PR_000003516) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [lactosylceramide 4-alpha-galactosyltransferase (human)](http://purl.obolibrary.org/obo/PR_Q9NPC4) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [compact bone tissue](http://purl.obolibrary.org/obo/UBERON_0001439) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "substantia corticalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:24018" +### lactotransferrin `http://purl.obolibrary.org/obo/PR_000009978` +#### Removed +- [lactotransferrin](http://purl.obolibrary.org/obo/PR_000009978) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [lactotransferrin (human)](http://purl.obolibrary.org/obo/PR_P02788) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [compact bone tissue](http://purl.obolibrary.org/obo/UBERON_0001439) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "substantia compacta" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### lamina `http://purl.obolibrary.org/obo/UBERON_0000957` +#### Removed +- [lamina](http://purl.obolibrary.org/obo/UBERON_0000957) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "laminar" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:24018" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [compact bone tissue](http://purl.obolibrary.org/obo/UBERON_0001439) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D000071538" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) +### lamina densa of glomerular basement membrane `http://purl.obolibrary.org/obo/UBERON_0005787` - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +#### Added +- [lamina densa of glomerular basement membrane](http://purl.obolibrary.org/obo/UBERON_0005787) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -- [compact bone tissue](http://purl.obolibrary.org/obo/UBERON_0001439) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "substantia corticalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:24018" +### lamina of spiral limbus `http://purl.obolibrary.org/obo/UBERON_0002276` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +#### Added +- [lamina of spiral limbus](http://purl.obolibrary.org/obo/UBERON_0002276) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### compound eye `http://purl.obolibrary.org/obo/UBERON_0000018` -#### Removed -- [compound eye](http://purl.obolibrary.org/obo/UBERON_0000018) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004508" +### lamina propria of bronchus `http://purl.obolibrary.org/obo/UBERON_0002338` -- [compound eye](http://purl.obolibrary.org/obo/UBERON_0000018) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "IDOMAL:0002421" - - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0003-4423-4370" +#### Added +- [lamina propria of bronchus](http://purl.obolibrary.org/obo/UBERON_0002338) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) + + +### lamina propria of ureter `http://purl.obolibrary.org/obo/UBERON_0001253` #### Added -- [compound eye](http://purl.obolibrary.org/obo/UBERON_0000018) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004508" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [lamina propria of ureter](http://purl.obolibrary.org/obo/UBERON_0001253) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -- [compound eye](http://purl.obolibrary.org/obo/UBERON_0000018) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "IDOMAL:0002421" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +### lamina propria of urethra `http://purl.obolibrary.org/obo/UBERON_0002326` - - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) +#### Added +- [lamina propria of urethra](http://purl.obolibrary.org/obo/UBERON_0002326) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### conducting system of heart `http://purl.obolibrary.org/obo/UBERON_0002350` +### lamina propria of urinary bladder `http://purl.obolibrary.org/obo/UBERON_0001261` #### Removed -- [conducting system of heart](http://purl.obolibrary.org/obo/UBERON_0002350) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "complexus stimulans cordis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9476" +- [lamina propria of urinary bladder](http://purl.obolibrary.org/obo/UBERON_0001261) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "Contains loose to dense connective tissue, variably sized blood vessels that may be close to epithelium, lymphatics, variable adipose tissue" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +#### Added +- [lamina propria of urinary bladder](http://purl.obolibrary.org/obo/UBERON_0001261) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [conducting system of heart](http://purl.obolibrary.org/obo/UBERON_0002350) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "systema conducente cordis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9476" +### lamina propria of vagina `http://purl.obolibrary.org/obo/UBERON_0005205` - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +#### Added +- [lamina propria of vagina](http://purl.obolibrary.org/obo/UBERON_0005205) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + +### lamina rara externa `http://purl.obolibrary.org/obo/UBERON_0005789` #### Added -- [conducting system of heart](http://purl.obolibrary.org/obo/UBERON_0002350) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "systema conducente cordis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [lamina rara externa](http://purl.obolibrary.org/obo/UBERON_0005789) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9476" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### lamina rara interna `http://purl.obolibrary.org/obo/UBERON_0005788` -- [conducting system of heart](http://purl.obolibrary.org/obo/UBERON_0002350) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "complexus stimulans cordis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +#### Added +- [lamina rara interna](http://purl.obolibrary.org/obo/UBERON_0005788) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9476" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### large intestine `http://purl.obolibrary.org/obo/UBERON_0000059` +#### Removed +- [large intestine](http://purl.obolibrary.org/obo/UBERON_0000059) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000054" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### conjunctiva `http://purl.obolibrary.org/obo/UBERON_0001811` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.566" + + + +### large intestine smooth muscle `http://purl.obolibrary.org/obo/UBERON_0004220` #### Removed -- [conjunctiva](http://purl.obolibrary.org/obo/UBERON_0001811) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica conjunctiva" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [large intestine smooth muscle](http://purl.obolibrary.org/obo/UBERON_0004220) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [large intestine smooth muscle](http://purl.obolibrary.org/obo/UBERON_0004220) SubClassOf [overlaps](http://purl.obolibrary.org/obo/RO_0002131) some [muscle layer of large intestine](http://purl.obolibrary.org/obo/UBERON_0011198) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "consider merging" + +#### Added +- [large intestine smooth muscle](http://purl.obolibrary.org/obo/UBERON_0004220) SubClassOf [overlaps](http://purl.obolibrary.org/obo/RO_0002131) some [muscle layer of large intestine](http://purl.obolibrary.org/obo/UBERON_0011198) + + +### large intestine smooth muscle circular layer `http://purl.obolibrary.org/obo/UBERON_0012398` #### Added -- [conjunctiva](http://purl.obolibrary.org/obo/UBERON_0001811) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica conjunctiva" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [large intestine smooth muscle circular layer](http://purl.obolibrary.org/obo/UBERON_0012398) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### conjunctival epithelial cell `http://purl.obolibrary.org/obo/CL_1000432` +### large intestine smooth muscle longitudinal layer `http://purl.obolibrary.org/obo/UBERON_0012399` #### Added -- [conjunctival epithelial cell](http://purl.obolibrary.org/obo/CL_1000432) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [large intestine smooth muscle longitudinal layer](http://purl.obolibrary.org/obo/UBERON_0012399) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### conjunctival vasculature `http://purl.obolibrary.org/obo/UBERON_0010366` +### larva `http://purl.obolibrary.org/obo/UBERON_0002548` #### Removed -- [conjunctival vasculature](http://purl.obolibrary.org/obo/UBERON_0010366) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "venae conjunctivales" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [larva](http://purl.obolibrary.org/obo/UBERON_0002548) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001727" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -#### Added -- [conjunctival vasculature](http://purl.obolibrary.org/obo/UBERON_0010366) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "venae conjunctivales" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [larva](http://purl.obolibrary.org/obo/UBERON_0002548) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Whole organism that is premetamorphic or a very immature individual.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0002048" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -### connective tissue cell `http://purl.obolibrary.org/obo/CL_0002320` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TAO:wd" -#### Added -- [connective tissue cell](http://purl.obolibrary.org/obo/CL_0002320) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [larva](http://purl.obolibrary.org/obo/UBERON_0002548) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "larval" +- [larva](http://purl.obolibrary.org/obo/UBERON_0002548) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D007814" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### contractile cell `http://purl.obolibrary.org/obo/CL_0000183` + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) -#### Added -- [contractile cell](http://purl.obolibrary.org/obo/CL_0000183) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -### conventional dendritic cell `http://purl.obolibrary.org/obo/CL_0000990` -#### Added -- [conventional dendritic cell](http://purl.obolibrary.org/obo/CL_0000990) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### larval stage `http://purl.obolibrary.org/obo/UBERON_0000069` +#### Removed +- [larval stage](http://purl.obolibrary.org/obo/UBERON_0000069) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "It is a misunderstanding that the larval form always reflects the group's evolutionary history. It could be the case, but often the larval stage has evolved secondarily, as in insects. In these cases the larval form might differ more from the group's common origin than the adult form" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" +- [larval stage](http://purl.obolibrary.org/obo/UBERON_0000069) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBdv:00005336" -### cord blood hematopoietic stem cell `http://purl.obolibrary.org/obo/CL_2000095` +- [larval stage](http://purl.obolibrary.org/obo/UBERON_0000069) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "Uberon includes clade-specific subclasses, e.g. nematod larva" -#### Added -- [cord blood hematopoietic stem cell](http://purl.obolibrary.org/obo/CL_2000095) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### corneal endothelial cell `http://purl.obolibrary.org/obo/CL_0000132` +### laryngeal apparatus `http://purl.obolibrary.org/obo/UBERON_0010212` #### Added -- [corneal endothelial cell](http://purl.obolibrary.org/obo/CL_0000132) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [laryngeal apparatus](http://purl.obolibrary.org/obo/UBERON_0010212) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -### corneal endothelium `http://purl.obolibrary.org/obo/UBERON_0001985` -#### Removed -- [corneal endothelium](http://purl.obolibrary.org/obo/UBERON_0001985) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "epithelium posterius corneae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Corneal_endothelium" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### laryngeal associated mesenchyme `http://purl.obolibrary.org/obo/UBERON_0010221` #### Added -- [corneal endothelium](http://purl.obolibrary.org/obo/UBERON_0001985) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "epithelium posterius corneae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [laryngeal associated mesenchyme](http://purl.obolibrary.org/obo/UBERON_0010221) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Corneal_endothelium" +### laryngeal cartilage `http://purl.obolibrary.org/obo/UBERON_0001739` +#### Removed +- [laryngeal cartilage](http://purl.obolibrary.org/obo/UBERON_0001739) [UBPROP_0000202](http://purl.obolibrary.org/obo/UBPROP_0000202) [FMA_64159](http://purl.obolibrary.org/obo/FMA_64159) -### corneal epithelial cell `http://purl.obolibrary.org/obo/CL_0000575` +- [laryngeal cartilage](http://purl.obolibrary.org/obo/UBERON_0001739) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(In anura) a dorsal pair of arytenoid cartilages (...), which support vocal cords, and a ventral pair (often fused) of cricoid cartilage (...). These cartilages are regarded as derivatives of posterior visceral arches of ancestors. Together they constitute the larynx, a structure characteristic of tetrapods. (...) (In mammals) Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (...) and a cartilage in the epiglottis.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.239-241" -#### Added -- [corneal epithelial cell](http://purl.obolibrary.org/obo/CL_0000575) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### corneal epithelium `http://purl.obolibrary.org/obo/UBERON_0001772` -#### Removed -- [corneal epithelium](http://purl.obolibrary.org/obo/UBERON_0001772) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "e. anterius corneae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Corneal_epithelium" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001550" -- [corneal epithelium](http://purl.obolibrary.org/obo/UBERON_0001772) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "epithelium anterius corneae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58263" +#### Added +- [laryngeal cartilage](http://purl.obolibrary.org/obo/UBERON_0001739) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### laryngeal pre-cartilage condensation `http://purl.obolibrary.org/obo/UBERON_0010213` #### Added -- [corneal epithelium](http://purl.obolibrary.org/obo/UBERON_0001772) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "e. anterius corneae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [laryngeal pre-cartilage condensation](http://purl.obolibrary.org/obo/UBERON_0010213) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Corneal_epithelium" -- [corneal epithelium](http://purl.obolibrary.org/obo/UBERON_0001772) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "epithelium anterius corneae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### larynx `http://purl.obolibrary.org/obo/UBERON_0001737` +#### Removed +- [larynx](http://purl.obolibrary.org/obo/UBERON_0001737) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "An anatomical cluster consisting of the epiglottus, the arytenoid cartilages, the thyroid cartilage, the cricoid cartilage and the muscles, membranes, and ligaments connecting them, and also of the mucosal covering these structures.[FEED]" + - [url](http://www.geneontology.org/formats/oboInOwl#url) "http://www.feedexp.org" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58263" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "FEED" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-07-02" +- [larynx](http://purl.obolibrary.org/obo/UBERON_0001737) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical structure consisting of a narrowly triangular chamber supported by a series of semicircular cartilages in which part of the sound-production system is located.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000268" -### corneo-scleral junction `http://purl.obolibrary.org/obo/UBERON_0006761` -#### Removed -- [corneo-scleral junction](http://purl.obolibrary.org/obo/UBERON_0006761) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "limbus corneae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Corneal_limbus" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -- [corneo-scleral junction](http://purl.obolibrary.org/obo/UBERON_0006761) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "limbus corneae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Corneal_limbus" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [larynx](http://purl.obolibrary.org/obo/UBERON_0001737) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(In anura) a dorsal pair of arytenoid cartilages (...), which support vocal cords, and a ventral pair (often fused) of cricoid cartilage (...). These cartilages are regarded as derivatives of posterior visceral arches of ancestors. Together they constitute the larynx, a structure characteristic of tetrapods. (...) (In mammals) Paired arytenoid cartilages help support and control the vocal cords. The cricoid cartilage is single. Two additional cartilages are present that are lacking in other vertebrates: a large ventral thyroid cartilage (...) and a cartilage in the epiglottis.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.239-241" -#### Added -- [corneo-scleral junction](http://purl.obolibrary.org/obo/UBERON_0006761) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "limbus corneae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Corneal_limbus" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [corneo-scleral junction](http://purl.obolibrary.org/obo/UBERON_0006761) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "limbus corneae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001279" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Corneal_limbus" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" +- [larynx](http://purl.obolibrary.org/obo/UBERON_0001737) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "laryngeal" -### cortex of kidney `http://purl.obolibrary.org/obo/UBERON_0001225` -#### Removed -- [cortex of kidney](http://purl.obolibrary.org/obo/UBERON_0001225) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cortex renalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15581" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### larynx connective tissue `http://purl.obolibrary.org/obo/UBERON_0003583` #### Added -- [cortex of kidney](http://purl.obolibrary.org/obo/UBERON_0001225) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cortex renalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [larynx connective tissue](http://purl.obolibrary.org/obo/UBERON_0003583) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15581" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### larynx epithelium `http://purl.obolibrary.org/obo/UBERON_0004816` +#### Removed +- [larynx epithelium](http://purl.obolibrary.org/obo/UBERON_0004816) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "composed of squamous epithelium in the upper larynx and ciliated columnar epithelium in the lower larynx [ISBN:0-397-51047-0]" -### cortex of lymph node `http://purl.obolibrary.org/obo/UBERON_0002006` -#### Removed -- [cortex of lymph node](http://purl.obolibrary.org/obo/UBERON_0002006) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cortex nodi lymphoidei" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cortex_of_lymph_node" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### larynx mucous gland `http://purl.obolibrary.org/obo/UBERON_0004789` #### Added -- [cortex of lymph node](http://purl.obolibrary.org/obo/UBERON_0002006) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cortex nodi lymphoidei" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cortex_of_lymph_node" +- [larynx mucous gland](http://purl.obolibrary.org/obo/UBERON_0004789) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -### cortical cell of adrenal gland `http://purl.obolibrary.org/obo/CL_0002097` +### larynx submucosa `http://purl.obolibrary.org/obo/UBERON_0004778` #### Added -- [cortical cell of adrenal gland](http://purl.obolibrary.org/obo/CL_0002097) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [larynx submucosa](http://purl.obolibrary.org/obo/UBERON_0004778) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -### cortical interneuron `http://purl.obolibrary.org/obo/CL_0008031` +### larynx submucosa gland `http://purl.obolibrary.org/obo/UBERON_0005204` #### Added -- [cortical interneuron](http://purl.obolibrary.org/obo/CL_0008031) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [larynx submucosa gland](http://purl.obolibrary.org/obo/UBERON_0005204) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -### cortical layer I `http://purl.obolibrary.org/obo/UBERON_0005390` +### late distal convoluted tubule `http://purl.obolibrary.org/obo/UBERON_0005102` #### Removed -- [cortical layer I](http://purl.obolibrary.org/obo/UBERON_0005390) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lamina molecularis isocorticis [lamina I]" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:83900" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [late distal convoluted tubule](http://purl.obolibrary.org/obo/UBERON_0005102) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:28393" #### Added -- [cortical layer I](http://purl.obolibrary.org/obo/UBERON_0005390) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lamina molecularis isocorticis [lamina I]" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [late distal convoluted tubule](http://purl.obolibrary.org/obo/UBERON_0005102) SubClassOf [meso-epithelium](http://purl.obolibrary.org/obo/UBERON_0012275) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:83900" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" - - -### cortical layer II `http://purl.obolibrary.org/obo/UBERON_0005391` +### late embryo `http://purl.obolibrary.org/obo/UBERON_0000323` #### Removed -- [cortical layer II](http://purl.obolibrary.org/obo/UBERON_0005391) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lamina granularis externa isocorticis [lamina ii]" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:77804" +- [late embryo](http://purl.obolibrary.org/obo/UBERON_0000323) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005333" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [late embryo](http://purl.obolibrary.org/obo/UBERON_0000323) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Fetal structure, which is a developmental form of a vertebrate animal at any given time point from 8 weeks of gestation to birth (or hatching). Examples: There is only one fetus[FMA:63919]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:63919" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [cortical layer II](http://purl.obolibrary.org/obo/UBERON_0005391) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lamina granularis externa isocorticis [lamina ii]" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:77804" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### lateral geniculate body `http://purl.obolibrary.org/obo/UBERON_0001926` +#### Removed +- [lateral geniculate body](http://purl.obolibrary.org/obo/UBERON_0001926) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "BTO has distinct classes for body and nucleus, but other sources treat as identical" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "BTO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### cortical layer III `http://purl.obolibrary.org/obo/UBERON_0005392` +### lateral gland of orbital region `http://purl.obolibrary.org/obo/UBERON_0015154` #### Removed -- [cortical layer III](http://purl.obolibrary.org/obo/UBERON_0005392) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lamina pyramidalis externa" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:2448" +- [lateral gland of orbital region](http://purl.obolibrary.org/obo/UBERON_0015154) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "The class name or definition should not be taken to mean strictly in the lateral ocular region. We place the extraocular lacrimal glands, even though they are as the name suggests outside the ocular region. The class exists as the division between lateral vs medial (Harderian, nictitans) glands is standard, e.g. http://www.ncbi.nlm.nih.gov/pubmed/7559104" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [cortical layer III](http://purl.obolibrary.org/obo/UBERON_0005392) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lamina pyramidalis externa isocorticis [lamina iii]" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:77810" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### lateral line nerve `http://purl.obolibrary.org/obo/UBERON_0008906` +#### Removed +- [lateral line nerve](http://purl.obolibrary.org/obo/UBERON_0008906) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Any of the sensory nerves that innervate mechano- and electroreceptors of the lateral line system. The lateral line nerves may be separated in two components, anterior and posterior, in relation to the position of its roots with respect to the otic capsule. These nerves develop from lateral line placodes.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010077" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:SIQ" -#### Added -- [cortical layer III](http://purl.obolibrary.org/obo/UBERON_0005392) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lamina pyramidalis externa isocorticis [lamina iii]" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:77810" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [lateral line nerve](http://purl.obolibrary.org/obo/UBERON_0008906) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship type change: part_of_proxy lateral line system (AAO:0000975) CHANGED TO: part_of lateral line system (UBERON:0002540)[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010077" -- [cortical layer III](http://purl.obolibrary.org/obo/UBERON_0005392) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lamina pyramidalis externa" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:2448" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" +- [lateral line nerve](http://purl.obolibrary.org/obo/UBERON_0008906) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: innervates lateral line receptor organ (AAO:0001001)[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010077" -### cortical layer IV `http://purl.obolibrary.org/obo/UBERON_0005393` -#### Removed -- [cortical layer IV](http://purl.obolibrary.org/obo/UBERON_0005393) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lamina granularis interna isocorticis [lamina iv]" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:77811" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [cortical layer IV](http://purl.obolibrary.org/obo/UBERON_0005393) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lamina granularis interna isocorticis [lamina iv]" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:77811" +### lateral line nucleus `http://purl.obolibrary.org/obo/UBERON_3010706` +#### Removed +- [lateral line nucleus](http://purl.obolibrary.org/obo/UBERON_3010706) [UBPROP_0000004](http://purl.obolibrary.org/obo/UBPROP_0000004) "This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://purl.obolibrary.org/obo/aao.owl" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### cortical layer V `http://purl.obolibrary.org/obo/UBERON_0005394` +### lateral line placode `http://purl.obolibrary.org/obo/UBERON_0009128` #### Removed -- [cortical layer V](http://purl.obolibrary.org/obo/UBERON_0005394) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lamina ganglionaris" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:2450" +- [lateral line placode](http://purl.obolibrary.org/obo/UBERON_0009128) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Specialized series of dorsolateral ectodermal placodes.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010718" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:SIQ" -- [cortical layer V](http://purl.obolibrary.org/obo/UBERON_0005394) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lamina pyramidalis interna" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:2450" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -- [cortical layer V](http://purl.obolibrary.org/obo/UBERON_0005394) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lamina pyramidalis interna isocorticis [lamina v]" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:77812" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### lateral line primordium `http://purl.obolibrary.org/obo/UBERON_2000228` +#### Removed +- [lateral line primordium](http://purl.obolibrary.org/obo/UBERON_2000228) [UBPROP_0000004](http://purl.obolibrary.org/obo/UBPROP_0000004) "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://purl.obolibrary.org/obo/tao.owl" -#### Added -- [cortical layer V](http://purl.obolibrary.org/obo/UBERON_0005394) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lamina pyramidalis interna isocorticis [lamina v]" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:77812" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### lateral line system `http://purl.obolibrary.org/obo/UBERON_0002540` +#### Removed +- [lateral line system](http://purl.obolibrary.org/obo/UBERON_0002540) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: is_formed_by lateral line receptor organ (AAO:0001001)[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -- [cortical layer V](http://purl.obolibrary.org/obo/UBERON_0005394) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lamina ganglionaris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:2450" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000975" -- [cortical layer V](http://purl.obolibrary.org/obo/UBERON_0005394) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lamina pyramidalis interna" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [lateral line system](http://purl.obolibrary.org/obo/UBERON_0002540) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Sensory system which develops from a specialized series of dorsolateral ectodermal placodes named lateral line placodes.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:2450" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### cortical layer VI `http://purl.obolibrary.org/obo/UBERON_0005395` -#### Removed -- [cortical layer VI](http://purl.obolibrary.org/obo/UBERON_0005395) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lamina multiformis isocorticis [lamina vi]" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:77805" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000975" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [lateral line system](http://purl.obolibrary.org/obo/UBERON_0002540) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The mechanosensory lateral line system is widely distributed in aquatic anamniotes. It was apparently present in the earliest vertebrates, as it has been identified in agnathans, cartilaginous fishes, bony fishes, lungfishes, the crossopterygian Latimeria, and aquatic amphibians.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.195" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [cortical layer VI](http://purl.obolibrary.org/obo/UBERON_0005395) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lamina multiformis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:2451" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [cortical layer VI](http://purl.obolibrary.org/obo/UBERON_0005395) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lamina multiformis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:2451" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001243" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [lateral line system](http://purl.obolibrary.org/obo/UBERON_0002540) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D053403" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -- [cortical layer VI](http://purl.obolibrary.org/obo/UBERON_0005395) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lamina multiformis isocorticis [lamina vi]" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:77805" + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [lateral line system](http://purl.obolibrary.org/obo/UBERON_0002540) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A sensory system on the surface of the fish, consisting of small sensory patches (neuromasts) distributed in discrete lines over the body surface. The lateral line system is stimulated by local water displacements and vibrations, and detects propulsion of the fish through the water, as well as facilitating shoaling, prey capture, and predator and obstacle avoidance. (See Anatomical Atlas entry for lateral line by T. Whitfield.)[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000034" -### cortical plate `http://purl.obolibrary.org/obo/UBERON_0005343` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -#### Added -- [cortical plate](http://purl.obolibrary.org/obo/UBERON_0005343) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D002540" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -### cortical subplate `http://purl.obolibrary.org/obo/UBERON_0004035` +### lateral lingual swelling `http://purl.obolibrary.org/obo/UBERON_0006757` +#### Removed +- [lateral lingual swelling](http://purl.obolibrary.org/obo/UBERON_0006757) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [cortical subplate](http://purl.obolibrary.org/obo/UBERON_0004035) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "VO:0011276" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1046/j.1469-7580.2002.00073.x Iwasaki S, Evolution of the structure and function of the vertebrate tongue. J Anat (2002)" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000731" -### cortical thymic epithelial cell `http://purl.obolibrary.org/obo/CL_0002364` +- [lateral lingual swelling](http://purl.obolibrary.org/obo/UBERON_0006757) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "paired" -#### Added -- [cortical thymic epithelial cell](http://purl.obolibrary.org/obo/CL_0002364) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### corticospinal tract `http://purl.obolibrary.org/obo/UBERON_0002707` +### lateral olfactory stria `http://purl.obolibrary.org/obo/UBERON_0001888` #### Removed -- [corticospinal tract](http://purl.obolibrary.org/obo/UBERON_0002707) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tractus cortico-spinalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:1320" +- [lateral olfactory stria](http://purl.obolibrary.org/obo/UBERON_0001888) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In mammals the fibers of the dorsal lateral olfactory tract either pass under the accessory olfactory formation, or they penetrate through it separating the internal granule cells from the output cells." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:7437895" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [corticospinal tract](http://purl.obolibrary.org/obo/UBERON_0002707) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tractus corticospinalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Corticospinal_tract" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:1320" +### lateral plate mesoderm `http://purl.obolibrary.org/obo/UBERON_0003081` +#### Removed +- [lateral plate mesoderm](http://purl.obolibrary.org/obo/UBERON_0003081) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [corticospinal tract](http://purl.obolibrary.org/obo/UBERON_0002707) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006132" - - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0003-4423-4370" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [corticospinal tract](http://purl.obolibrary.org/obo/UBERON_0002707) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "fasciculus pyramidalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:800" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000118" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [lateral plate mesoderm](http://purl.obolibrary.org/obo/UBERON_0003081) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)" -- [corticospinal tract](http://purl.obolibrary.org/obo/UBERON_0002707) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "fibrae corticospinales" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:1320" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [corticospinal tract](http://purl.obolibrary.org/obo/UBERON_0002707) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tractus pyramidalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:800" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000118" -- [corticospinal tract](http://purl.obolibrary.org/obo/UBERON_0002707) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "fasciculus cerebro-spinalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:1320" +- [lateral plate mesoderm](http://purl.obolibrary.org/obo/UBERON_0003081) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "subclass of mesoderm in ZFA." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "ZFA" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [lateral plate mesoderm](http://purl.obolibrary.org/obo/UBERON_0003081) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" -#### Added -- [corticospinal tract](http://purl.obolibrary.org/obo/UBERON_0002707) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "fasciculus cerebro-spinalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:1320" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -- [corticospinal tract](http://purl.obolibrary.org/obo/UBERON_0002707) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tractus corticospinalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Corticospinal_tract" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010574" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:1320" -- [corticospinal tract](http://purl.obolibrary.org/obo/UBERON_0002707) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "fasciculus pyramidalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:800" +### lateral structure `http://purl.obolibrary.org/obo/UBERON_0015212` +#### Removed +- [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "This class is primarily to implement taxon constraints. It may be removed in the future." - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -- [corticospinal tract](http://purl.obolibrary.org/obo/UBERON_0002707) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tractus cortico-spinalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:1320" +### lateral wall of nasopharynx `http://purl.obolibrary.org/obo/UBERON_0035383` -- [corticospinal tract](http://purl.obolibrary.org/obo/UBERON_0002707) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tractus pyramidalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:800" +#### Added +- [lateral wall of nasopharynx](http://purl.obolibrary.org/obo/UBERON_0035383) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -- [corticospinal tract](http://purl.obolibrary.org/obo/UBERON_0002707) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006132" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +### latissimus dorsi muscle `http://purl.obolibrary.org/obo/UBERON_0001112` +#### Removed +- [latissimus dorsi muscle](http://purl.obolibrary.org/obo/UBERON_0001112) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In humans it inserts along a roughened line deep in the groove. In other mammals (most, I believe) it is an actual projection, the latissimus dorsi process [FEED:rd] [https://github.com/obophenotype/uberon/issues/1192]" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +- [latissimus dorsi muscle](http://purl.obolibrary.org/obo/UBERON_0001112) SubClassOf [has muscle origin](http://purl.obolibrary.org/obo/RO_0002372) some [inferior angle of scapula](http://purl.obolibrary.org/obo/UBERON_0007175) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "spinous processes of thoracic T7-T12 thoracolumbar fascia iliac crest and inferior 3 or 4 ribs inferior angle of scapula" - - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "dbpedia" -- [corticospinal tract](http://purl.obolibrary.org/obo/UBERON_0002707) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "fibrae corticospinales" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [latissimus dorsi muscle](http://purl.obolibrary.org/obo/UBERON_0001112) SubClassOf [has muscle insertion](http://purl.obolibrary.org/obo/RO_0002373) some [humerus](http://purl.obolibrary.org/obo/UBERON_0000976) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "dbpedia" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:1320" + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "floor of intertubercular groove of the humerus" +#### Added +- [latissimus dorsi muscle](http://purl.obolibrary.org/obo/UBERON_0001112) SubClassOf [has muscle insertion](http://purl.obolibrary.org/obo/RO_0002373) some [humerus](http://purl.obolibrary.org/obo/UBERON_0000976) -### corticothalamic-projecting glutamatergic cortical neuron `http://purl.obolibrary.org/obo/CL_4023013` +- [latissimus dorsi muscle](http://purl.obolibrary.org/obo/UBERON_0001112) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -#### Added -- [corticothalamic-projecting glutamatergic cortical neuron](http://purl.obolibrary.org/obo/CL_4023013) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [latissimus dorsi muscle](http://purl.obolibrary.org/obo/UBERON_0001112) SubClassOf [has muscle origin](http://purl.obolibrary.org/obo/RO_0002372) some [inferior angle of scapula](http://purl.obolibrary.org/obo/UBERON_0007175) -### costal diaphragm `http://purl.obolibrary.org/obo/UBERON_0035831` +### latissimus dorsi pre-muscle mass `http://purl.obolibrary.org/obo/UBERON_0010982` #### Added -- [costal diaphragm](http://purl.obolibrary.org/obo/UBERON_0035831) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" +- [latissimus dorsi pre-muscle mass](http://purl.obolibrary.org/obo/UBERON_0010982) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -- [costal diaphragm](http://purl.obolibrary.org/obo/UBERON_0035831) [id](http://www.geneontology.org/formats/oboInOwl#id) "UBERON:0035831" -- [costal diaphragm](http://purl.obolibrary.org/obo/UBERON_0035831) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "SCTID:368048007" +### layer of dentate gyrus `http://purl.obolibrary.org/obo/UBERON_0002304` +#### Removed +- [layer of dentate gyrus](http://purl.obolibrary.org/obo/UBERON_0002304) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "the basic trilaminar structure of the dentate gyrus is common across all species studied, with relatively minimal phylogenetic variation[PMC2492885]" -- [costal diaphragm](http://purl.obolibrary.org/obo/UBERON_0035831) [label](http://www.w3.org/2000/01/rdf-schema#label) "costal diaphragm" -- [costal diaphragm](http://purl.obolibrary.org/obo/UBERON_0035831) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "costal part of diaphragm" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58277" -- [costal diaphragm](http://purl.obolibrary.org/obo/UBERON_0035831) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "The domain of the diaphragm that is a thin domed sheet of muscle composed of a radial array of myofibers extending laterally from the ribs and medially to a central tendon." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:23586979" +### layer of developing cerebral cortex `http://purl.obolibrary.org/obo/UBERON_0014950` +#### Removed +- [layer of developing cerebral cortex](http://purl.obolibrary.org/obo/UBERON_0014950) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "these layers primarily refer to the mammalian future neocortex" -- [costal diaphragm](http://purl.obolibrary.org/obo/UBERON_0035831) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pars costalis diaphragmatis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [costal diaphragm](http://purl.obolibrary.org/obo/UBERON_0035831) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58277" +### layer of microvilli `http://purl.obolibrary.org/obo/UBERON_0012423` +#### Removed +- [layer of microvilli](http://purl.obolibrary.org/obo/UBERON_0012423) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA class represents an individual microvillus." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" -- Class: [costal diaphragm](http://purl.obolibrary.org/obo/UBERON_0035831) +- [layer of microvilli](http://purl.obolibrary.org/obo/UBERON_0012423) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "a wide variety of physiological and cellular functions including absorption, secretion, cellular adhesion, and mechanotransduction" -- [costal diaphragm](http://purl.obolibrary.org/obo/UBERON_0035831) SubClassOf [organ subunit](http://purl.obolibrary.org/obo/UBERON_0000063) +- [layer of microvilli](http://purl.obolibrary.org/obo/UBERON_0012423) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "increases the surface area of a cell lining whilst minimizing increase in volume" -- [costal diaphragm](http://purl.obolibrary.org/obo/UBERON_0035831) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) -- [costal diaphragm](http://purl.obolibrary.org/obo/UBERON_0035831) SubClassOf [attached to](http://purl.obolibrary.org/obo/RO_0002371) some [central tendon of diaphragm](http://purl.obolibrary.org/obo/UBERON_0006670) -- [costal diaphragm](http://purl.obolibrary.org/obo/UBERON_0035831) SubClassOf [in lateral side of](http://purl.obolibrary.org/obo/BSPO_0000126) some [diaphragm](http://purl.obolibrary.org/obo/UBERON_0001103) - - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:23586979" +### layer of muscle tissue `http://purl.obolibrary.org/obo/UBERON_0018260` +#### Removed +- [layer of muscle tissue](http://purl.obolibrary.org/obo/UBERON_0018260) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "NCITA class may refer to smooth muscle only" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "NCIT" -- [costal diaphragm](http://purl.obolibrary.org/obo/UBERON_0035831) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [diaphragm](http://purl.obolibrary.org/obo/UBERON_0001103) - - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:23586979" -### costo-cervical trunk `http://purl.obolibrary.org/obo/UBERON_0004688` +### layer of retina `http://purl.obolibrary.org/obo/UBERON_0001781` #### Removed -- [costo-cervical trunk](http://purl.obolibrary.org/obo/UBERON_0004688) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "truncus costocervicalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Costocervical_trunk" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [layer of retina](http://purl.obolibrary.org/obo/UBERON_0001781) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "MA does not treat internal/external limiting memranes as layers - these are classified as laminae. Here we follow other ontologies in grouping with other layers. MA also treats retinal pigment epithelium and neural retina epithelium as distinct from the layers. We follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers - these are also classified as layers, giving us over the usual 10 layers" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" #### Added -- [costo-cervical trunk](http://purl.obolibrary.org/obo/UBERON_0004688) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "truncus costocervicalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [layer of retina](http://purl.obolibrary.org/obo/UBERON_0001781) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Costocervical_trunk" +### layer of sclera `http://purl.obolibrary.org/obo/UBERON_0010291` + +#### Added +- [layer of sclera](http://purl.obolibrary.org/obo/UBERON_0010291) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) -### cranial cavity `http://purl.obolibrary.org/obo/UBERON_0013411` +### layer of tympanic membrane `http://purl.obolibrary.org/obo/UBERON_0010071` #### Removed -- [cranial cavity](http://purl.obolibrary.org/obo/UBERON_0013411) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cavitas cranii" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9644" +- [layer of tympanic membrane](http://purl.obolibrary.org/obo/UBERON_0010071) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In mammals, this class groups together the two epithelial layers plus the intermediate fibrous layer" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [cranial cavity](http://purl.obolibrary.org/obo/UBERON_0013411) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cavitas cranii" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### left adrenal gland `http://purl.obolibrary.org/obo/UBERON_0001234` +#### Removed +- [left adrenal gland](http://purl.obolibrary.org/obo/UBERON_0001234) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9644" +- [left adrenal gland](http://purl.obolibrary.org/obo/UBERON_0001234) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In humans, the left adrenal gland is semilunar shaped" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### cranial nerve `http://purl.obolibrary.org/obo/UBERON_0001785` +### left atrium endocardium `http://purl.obolibrary.org/obo/UBERON_0034903` #### Removed -- [cranial nerve](http://purl.obolibrary.org/obo/UBERON_0001785) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nervus cranialis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cranial_nerve" +- [left atrium endocardium](http://purl.obolibrary.org/obo/UBERON_0034903) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Endocardium of atrium which is continuous with the tunica intima of the trunk of pulmonary vein." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:7286" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [cranial nerve](http://purl.obolibrary.org/obo/UBERON_0001785) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nervus cranialis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cranial_nerve" +### left bundle branch `http://purl.obolibrary.org/obo/UBERON_0005986` + +#### Added +- [left bundle branch](http://purl.obolibrary.org/obo/UBERON_0005986) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) -### cranial nerve II `http://purl.obolibrary.org/obo/UBERON_0000941` +### left cardiac atrium `http://purl.obolibrary.org/obo/UBERON_0002079` #### Removed -- [cranial nerve II](http://purl.obolibrary.org/obo/UBERON_0000941) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus opticus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [left cardiac atrium](http://purl.obolibrary.org/obo/UBERON_0002079) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [cranial nerve II](http://purl.obolibrary.org/obo/UBERON_0000941) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus opticus [II]" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:50863" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620" -#### Added -- [cranial nerve II](http://purl.obolibrary.org/obo/UBERON_0000941) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus opticus [II]" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:50863" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000369" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [left cardiac atrium](http://purl.obolibrary.org/obo/UBERON_0002079) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Left cardiac chamber which is continuous with the pulmonary venous trunk.[FMA]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:7097" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [left cardiac atrium](http://purl.obolibrary.org/obo/UBERON_0002079) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The chamber of the heart that receives blood from the lungs[XAO:EJS]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "XAO:EJS" -- [cranial nerve II](http://purl.obolibrary.org/obo/UBERON_0000941) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus opticus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [left cardiac atrium](http://purl.obolibrary.org/obo/UBERON_0002079) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) -### cranial nerve nucleus `http://purl.obolibrary.org/obo/UBERON_0000126` -#### Removed -- [cranial nerve nucleus](http://purl.obolibrary.org/obo/UBERON_0000126) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus nervi cranialis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cranial_nerve_nucleus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### left cardiac chamber `http://purl.obolibrary.org/obo/UBERON_0035553` #### Added -- [cranial nerve nucleus](http://purl.obolibrary.org/obo/UBERON_0000126) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus nervi cranialis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cranial_nerve_nucleus" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [left cardiac chamber](http://purl.obolibrary.org/obo/UBERON_0035553) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) -### cranial neural crest `http://purl.obolibrary.org/obo/UBERON_0003099` +### left cerebral hemisphere `http://purl.obolibrary.org/obo/UBERON_0002812` #### Removed -- [cranial neural crest](http://purl.obolibrary.org/obo/UBERON_0003099) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "crista neuralis cranialis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [left cerebral hemisphere](http://purl.obolibrary.org/obo/UBERON_0002812) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cranial_neural_crest" -#### Added -- [cranial neural crest](http://purl.obolibrary.org/obo/UBERON_0003099) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "crista neuralis cranialis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cranial_neural_crest" +### left clavicle `http://purl.obolibrary.org/obo/UBERON_0008256` +#### Removed +- [left clavicle](http://purl.obolibrary.org/obo/UBERON_0008256) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) -### cranium `http://purl.obolibrary.org/obo/UBERON_0003128` + +### left common carotid artery plus branches `http://purl.obolibrary.org/obo/UBERON_0001536` #### Removed -- [cranium](http://purl.obolibrary.org/obo/UBERON_0003128) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ossa cranii" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71325" +- [left common carotid artery plus branches](http://purl.obolibrary.org/obo/UBERON_0001536) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "placement of the MA class here is not strictly correct, as the MA class does not include the branches" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + +### left common iliac artery `http://purl.obolibrary.org/obo/UBERON_0035529` #### Added -- [cranium](http://purl.obolibrary.org/obo/UBERON_0003128) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D012886" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) +- [left common iliac artery](http://purl.obolibrary.org/obo/UBERON_0035529) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -- [cranium](http://purl.obolibrary.org/obo/UBERON_0003128) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ossa cranii" +### left crus of diaphragm `http://purl.obolibrary.org/obo/UBERON_0014767` +#### Removed +- [left crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014767) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "crus sinistrum diaphragmatis" - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71325" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58287" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [left crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014767) [id](http://www.geneontology.org/formats/oboInOwl#id) "UBERON:0014767" -### crista terminalis `http://purl.obolibrary.org/obo/UBERON_0005979` -#### Removed -- [crista terminalis](http://purl.obolibrary.org/obo/UBERON_0005979) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "crista terminalis atrii dextri" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9236" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [left crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014767) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "left crus of diaphragm" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58287" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [left crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014767) [label](http://www.w3.org/2000/01/rdf-schema#label) "left crus of diaphragm" -#### Added -- [crista terminalis](http://purl.obolibrary.org/obo/UBERON_0005979) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "crista terminalis atrii dextri" +- [left crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014767) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "crus sinistrum (Diaphragma)" - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9236" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58287" - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [left crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014767) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) -### crus of diaphragm `http://purl.obolibrary.org/obo/UBERON_0014765` - -#### Added -- [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Classification notes: May be considered an external sphincter[PMID:8224664]" - -- [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "crural diaphragm" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:23586979" - -- [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "crus of the diaphragm" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Crus_of_diaphragm" - -- [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "diaphragm crura" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [plural form](http://purl.obolibrary.org/obo/OMO_0003004) +- [left crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014767) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58287" -- [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) [label](http://www.w3.org/2000/01/rdf-schema#label) "crus of diaphragm" +- [left crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014767) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A crus of diaphragm that is in_the_left_side_of a diaphragm." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "OBOL:automatic" -- [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:17703" +- [left crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014767) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "left crus of lumbar part of diaphragm" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58287" -- [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "VHOG:0001546" +- [left crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014767) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "SCTID:244937004" -- [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "SCTID:244668003" +- [left crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014767) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" -- [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "The domain of the diaphragm that is located dorsally and attaches to the vertebrae and surrounds the esophagus and aorta." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:23586979" +- Class: [left crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014767) -- [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EHDAA2:0000597" +- [left crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014767) EquivalentTo [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) and ([in left side of](http://purl.obolibrary.org/obo/BSPO_0000120) some [diaphragm](http://purl.obolibrary.org/obo/UBERON_0001103)) -- [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Crus_of_diaphragm" +- [left crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014767) SubClassOf [in left side of](http://purl.obolibrary.org/obo/BSPO_0000120) some [diaphragm](http://purl.obolibrary.org/obo/UBERON_0001103) -- [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "diaphragmatic crura" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Crus_of_diaphragm" +- [left crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014767) SubClassOf [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) -- [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "crura of the diaphragm" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Crus_of_diaphragm" -- [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" -- [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) [id](http://www.geneontology.org/formats/oboInOwl#id) "UBERON:0014765" +### left dorsal aorta `http://purl.obolibrary.org/obo/UBERON_0005613` +#### Removed +- [left dorsal aorta](http://purl.obolibrary.org/obo/UBERON_0005613) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "A study of embryos shows that in all vertebrates six arterial arches link the ventral aorta with a pair of lateral dorsal aortae on each side of the body. The latter unite posteriorly to form a single median dorsal aorta wich takes blood to the body.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000484" -- Class: [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) SubClassOf [attached to](http://purl.obolibrary.org/obo/RO_0002371) some [vertebral column](http://purl.obolibrary.org/obo/UBERON_0001130) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) SubClassOf [intersects midsagittal plane of](http://purl.obolibrary.org/obo/BSPO_0005001) some [diaphragm](http://purl.obolibrary.org/obo/UBERON_0001103) - - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:23586979" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) SubClassOf [attached to](http://purl.obolibrary.org/obo/RO_0002371) some [central tendon of diaphragm](http://purl.obolibrary.org/obo/UBERON_0006670) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0174480198 Roberts MBV, Biology: a functional approach (1986) p.572" -- [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) SubClassOf [organ subunit](http://purl.obolibrary.org/obo/UBERON_0000063) +- [left dorsal aorta](http://purl.obolibrary.org/obo/UBERON_0005613) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Contributes to the arch of aorta in humans" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://emedicine.medscape.com/article/899609-overview" -- [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [diaphragm](http://purl.obolibrary.org/obo/UBERON_0001103) - - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:23586979" -### cystic duct `http://purl.obolibrary.org/obo/UBERON_0001152` +### left dorsal thalamus `http://purl.obolibrary.org/obo/UBERON_0013683` #### Removed -- [cystic duct](http://purl.obolibrary.org/obo/UBERON_0001152) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ductus cysticus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cystic_duct" +- [left dorsal thalamus](http://purl.obolibrary.org/obo/UBERON_0013683) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) + +#### Added +- [left dorsal thalamus](http://purl.obolibrary.org/obo/UBERON_0013683) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + +### left ear `http://purl.obolibrary.org/obo/UBERON_0035295` #### Added -- [cystic duct](http://purl.obolibrary.org/obo/UBERON_0001152) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ductus cysticus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [left ear](http://purl.obolibrary.org/obo/UBERON_0035295) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cystic_duct" + +### left external ear `http://purl.obolibrary.org/obo/UBERON_0006617` +#### Removed +- [left external ear](http://purl.obolibrary.org/obo/UBERON_0006617) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) -### cytoplasm `http://purl.obolibrary.org/obo/GO_0005737` + +### left eye `http://purl.obolibrary.org/obo/UBERON_0004548` #### Removed -- [cytoplasm](http://purl.obolibrary.org/obo/GO_0005737) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) +- [left eye](http://purl.obolibrary.org/obo/UBERON_0004548) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) #### Added -- [cytoplasm](http://purl.obolibrary.org/obo/GO_0005737) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) +- [left eye](http://purl.obolibrary.org/obo/UBERON_0004548) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) -### cytoplasmic transport, nurse cell to oocyte `http://purl.obolibrary.org/obo/GO_0007303` +### left forelimb `http://purl.obolibrary.org/obo/UBERON_8300002` #### Removed -- [cytoplasmic transport, nurse cell to oocyte](http://purl.obolibrary.org/obo/GO_0007303) [label](http://www.w3.org/2000/01/rdf-schema#label) "cytoplasmic transport, nurse cell to oocyte" - -- [cytoplasmic transport, nurse cell to oocyte](http://purl.obolibrary.org/obo/GO_0007303) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:0007303" +- [left forelimb](http://purl.obolibrary.org/obo/UBERON_8300002) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) -- [cytoplasmic transport, nurse cell to oocyte](http://purl.obolibrary.org/obo/GO_0007303) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "The directed movement of cytoplasmic constituents synthesized in the nurse cells to the oocyte." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0879694238" +#### Added +- [left forelimb](http://purl.obolibrary.org/obo/UBERON_8300002) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) -- [cytoplasmic transport, nurse cell to oocyte](http://purl.obolibrary.org/obo/GO_0007303) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" -- Class: [cytoplasmic transport, nurse cell to oocyte](http://purl.obolibrary.org/obo/GO_0007303) +### left frontal lobe `http://purl.obolibrary.org/obo/UBERON_0002811` +#### Removed +- [left frontal lobe](http://purl.obolibrary.org/obo/UBERON_0002811) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [right frontal lobe](http://purl.obolibrary.org/obo/UBERON_0002810) -- [cytoplasmic transport, nurse cell to oocyte](http://purl.obolibrary.org/obo/GO_0007303) EquivalentTo [cytosolic transport](http://purl.obolibrary.org/obo/GO_0016482) and ([has target start location](http://purl.obolibrary.org/obo/RO_0002338) some [invertebrate nurse cell](http://purl.obolibrary.org/obo/CL_0000026)) and ([has target end location](http://purl.obolibrary.org/obo/RO_0002339) some [oocyte](http://purl.obolibrary.org/obo/CL_0000023)) -- [cytoplasmic transport, nurse cell to oocyte](http://purl.obolibrary.org/obo/GO_0007303) SubClassOf [has target end location](http://purl.obolibrary.org/obo/RO_0002339) some [oocyte](http://purl.obolibrary.org/obo/CL_0000023) -- [cytoplasmic transport, nurse cell to oocyte](http://purl.obolibrary.org/obo/GO_0007303) SubClassOf [has target start location](http://purl.obolibrary.org/obo/RO_0002338) some [invertebrate nurse cell](http://purl.obolibrary.org/obo/CL_0000026) +### left hepatic duct `http://purl.obolibrary.org/obo/UBERON_0001177` +#### Removed +- [left hepatic duct](http://purl.obolibrary.org/obo/UBERON_0001177) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The duct which drains bile from the left half of the liver and unites with the right hepatic duct to form the common hepatic duct. [adapted_from_http://www.medterms.com/script/main/art.asp?articlekey=26032][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000218" -- [cytoplasmic transport, nurse cell to oocyte](http://purl.obolibrary.org/obo/GO_0007303) SubClassOf [cytosolic transport](http://purl.obolibrary.org/obo/GO_0016482) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [cytoplasmic transport, nurse cell to oocyte](http://purl.obolibrary.org/obo/GO_0007303) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [ovarian nurse cell to oocyte transport](http://purl.obolibrary.org/obo/GO_0007300) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [cytoplasmic transport, nurse cell to oocyte](http://purl.obolibrary.org/obo/GO_0007303) SubClassOf [cellular process involved in reproduction in multicellular organism](http://purl.obolibrary.org/obo/GO_0022412) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### cytoskeletal protein binding `http://purl.obolibrary.org/obo/GO_0008092` +### left hindlimb `http://purl.obolibrary.org/obo/UBERON_8300004` #### Removed -- [cytoskeletal protein binding](http://purl.obolibrary.org/obo/GO_0008092) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) +- [left hindlimb](http://purl.obolibrary.org/obo/UBERON_8300004) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) #### Added -- [cytoskeletal protein binding](http://purl.obolibrary.org/obo/GO_0008092) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) +- [left hindlimb](http://purl.obolibrary.org/obo/UBERON_8300004) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) -### cytoskeleton `http://purl.obolibrary.org/obo/GO_0005856` +### left kidney `http://purl.obolibrary.org/obo/UBERON_0004538` #### Removed -- [cytoskeleton](http://purl.obolibrary.org/obo/GO_0005856) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) +- [left kidney](http://purl.obolibrary.org/obo/UBERON_0004538) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) -#### Added -- [cytoskeleton](http://purl.obolibrary.org/obo/GO_0005856) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) -### cytoskeleton organization `http://purl.obolibrary.org/obo/GO_0007010` +### left lateral ventricle `http://purl.obolibrary.org/obo/UBERON_0013161` #### Removed -- [cytoskeleton organization](http://purl.obolibrary.org/obo/GO_0007010) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) +- [left lateral ventricle](http://purl.obolibrary.org/obo/UBERON_0013161) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) #### Added -- [cytoskeleton organization](http://purl.obolibrary.org/obo/GO_0007010) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) +- [left lateral ventricle](http://purl.obolibrary.org/obo/UBERON_0013161) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) -### cytoskeleton-dependent cytoplasmic transport, nurse cell to oocyte `http://purl.obolibrary.org/obo/GO_0019749` +### left lobe of liver `http://purl.obolibrary.org/obo/UBERON_0001115` #### Removed -- [cytoskeleton-dependent cytoplasmic transport, nurse cell to oocyte](http://purl.obolibrary.org/obo/GO_0019749) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" +- [left lobe of liver](http://purl.obolibrary.org/obo/UBERON_0001115) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Portion of the liver which develops on the fish's left side.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -- [cytoskeleton-dependent cytoplasmic transport, nurse cell to oocyte](http://purl.obolibrary.org/obo/GO_0019749) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:0019749" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005172" -- [cytoskeleton-dependent cytoplasmic transport, nurse cell to oocyte](http://purl.obolibrary.org/obo/GO_0019749) [label](http://www.w3.org/2000/01/rdf-schema#label) "cytoskeleton-dependent cytoplasmic transport, nurse cell to oocyte" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -- [cytoskeleton-dependent cytoplasmic transport, nurse cell to oocyte](http://purl.obolibrary.org/obo/GO_0019749) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "The directed movement of substances along cytoskeletal elements, such as microfilaments or microtubules, from a nurse cell to an oocyte." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:ai" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -- Class: [cytoskeleton-dependent cytoplasmic transport, nurse cell to oocyte](http://purl.obolibrary.org/obo/GO_0019749) -- [cytoskeleton-dependent cytoplasmic transport, nurse cell to oocyte](http://purl.obolibrary.org/obo/GO_0019749) EquivalentTo [cytoplasmic transport, nurse cell to oocyte](http://purl.obolibrary.org/obo/GO_0007303) and [cytoskeleton-dependent intracellular transport](http://purl.obolibrary.org/obo/GO_0030705) -- [cytoskeleton-dependent cytoplasmic transport, nurse cell to oocyte](http://purl.obolibrary.org/obo/GO_0019749) SubClassOf [cytoplasmic transport, nurse cell to oocyte](http://purl.obolibrary.org/obo/GO_0007303) +### left lobe of thyroid gland `http://purl.obolibrary.org/obo/UBERON_0001120` +#### Removed +- [left lobe of thyroid gland](http://purl.obolibrary.org/obo/UBERON_0001120) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Thus, a thyroid capable of forming iodotyrosines and iodothyronines is present in all vertebrates. (...) Certain morphologic changes occur after the biochemical evolution of the thyroid has ceased. In the adult lamprey and in most bony fishes, the gland is not encapsulated. (...) In cartilaginous fish, the thyroid is encapsulated. In the higher vertebrate forms, the thyroid is a one- or two-lobed encapsulated structure.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000734" -- [cytoskeleton-dependent cytoplasmic transport, nurse cell to oocyte](http://purl.obolibrary.org/obo/GO_0019749) SubClassOf [cytoskeleton-dependent intracellular transport](http://purl.obolibrary.org/obo/GO_0030705) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### cytosolic transport `http://purl.obolibrary.org/obo/GO_0016482` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://www.thyroidmanager.org/Chapter1/chapter01.htm" -#### Added -- [cytosolic transport](http://purl.obolibrary.org/obo/GO_0016482) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/geneontology/go-ontology/issues/26386"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) +- [left lobe of thyroid gland](http://purl.obolibrary.org/obo/UBERON_0001120) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) -### cytotoxic T cell `http://purl.obolibrary.org/obo/CL_0000910` -#### Added -- [cytotoxic T cell](http://purl.obolibrary.org/obo/CL_0000910) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### left lung `http://purl.obolibrary.org/obo/UBERON_0002168` +#### Removed +- [left lung](http://purl.obolibrary.org/obo/UBERON_0002168) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### decidual cell `http://purl.obolibrary.org/obo/CL_2000002` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210" -#### Added -- [decidual cell](http://purl.obolibrary.org/obo/CL_2000002) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000618" -### decidual natural killer cell, human `http://purl.obolibrary.org/obo/CL_0002343` +- [left lung](http://purl.obolibrary.org/obo/UBERON_0002168) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) -#### Added -- [decidual natural killer cell, human](http://purl.obolibrary.org/obo/CL_0002343) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### defense response to other organism `http://purl.obolibrary.org/obo/GO_0098542` -#### Removed -- [defense response to other organism](http://purl.obolibrary.org/obo/GO_0098542) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) +### left lung alveolar system `http://purl.obolibrary.org/obo/UBERON_0006525` #### Added -- [defense response to other organism](http://purl.obolibrary.org/obo/GO_0098542) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) +- [left lung alveolar system](http://purl.obolibrary.org/obo/UBERON_0006525) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -### defense response to symbiont `http://purl.obolibrary.org/obo/GO_0140546` +### left lung endothelium `http://purl.obolibrary.org/obo/UBERON_0005673` #### Added -- [defense response to symbiont](http://purl.obolibrary.org/obo/GO_0140546) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/geneontology/go-ontology/issues/20261"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) - -- [defense response to symbiont](http://purl.obolibrary.org/obo/GO_0140546) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Reactions triggered in response to the presence of a symbiont that act to protect or prevent damage to the host." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:pg" - -- [defense response to symbiont](http://purl.obolibrary.org/obo/GO_0140546) [created by](http://www.geneontology.org/formats/oboInOwl#created_by) "pg" - -- [defense response to symbiont](http://purl.obolibrary.org/obo/GO_0140546) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" +- [left lung endothelium](http://purl.obolibrary.org/obo/UBERON_0005673) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) -- [defense response to symbiont](http://purl.obolibrary.org/obo/GO_0140546) [creation date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2020-11-11T17:19:06Z" -- [defense response to symbiont](http://purl.obolibrary.org/obo/GO_0140546) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:0140546" - -- [defense response to symbiont](http://purl.obolibrary.org/obo/GO_0140546) [label](http://www.w3.org/2000/01/rdf-schema#label) "defense response to symbiont" - -- Class: [defense response to symbiont](http://purl.obolibrary.org/obo/GO_0140546) +### left lung lobe `http://purl.obolibrary.org/obo/UBERON_0008951` +#### Removed +- [left lung lobe](http://purl.obolibrary.org/obo/UBERON_0008951) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "1 in mice, divided into 2 in human by a single interlobar fissure, the oblqiue fissure" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0123813611" -- [defense response to symbiont](http://purl.obolibrary.org/obo/GO_0140546) SubClassOf [defense response to other organism](http://purl.obolibrary.org/obo/GO_0098542) -### deferent duct artery `http://purl.obolibrary.org/obo/UBERON_0005192` +### left nipple `http://purl.obolibrary.org/obo/UBERON_0013772` #### Removed -- [deferent duct artery](http://purl.obolibrary.org/obo/UBERON_0005192) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arteria ductus deferentis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Artery_to_the_ductus_deferens" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [left nipple](http://purl.obolibrary.org/obo/UBERON_0013772) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) #### Added -- [deferent duct artery](http://purl.obolibrary.org/obo/UBERON_0005192) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arteria ductus deferentis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Artery_to_the_ductus_deferens" +- [left nipple](http://purl.obolibrary.org/obo/UBERON_0013772) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) -### deltoid `http://purl.obolibrary.org/obo/UBERON_0001476` +### left ovary `http://purl.obolibrary.org/obo/UBERON_0002119` #### Removed -- [deltoid](http://purl.obolibrary.org/obo/UBERON_0001476) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "musculus deltoideus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Deltoid_muscle" +- [left ovary](http://purl.obolibrary.org/obo/UBERON_0002119) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In some elasmobranchs, the left ovary does not mature, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Ovary#In_other_animals" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [left ovary](http://purl.obolibrary.org/obo/UBERON_0002119) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) #### Added -- [deltoid](http://purl.obolibrary.org/obo/UBERON_0001476) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "musculus deltoideus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [left ovary](http://purl.obolibrary.org/obo/UBERON_0002119) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Deltoid_muscle" - -### deltopectoral crest `http://purl.obolibrary.org/obo/UBERON_0002498` +### left parietal lobe `http://purl.obolibrary.org/obo/UBERON_0002802` #### Removed -- [deltopectoral crest](http://purl.obolibrary.org/obo/UBERON_0002498) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tuberositas deltoidea humeri" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [left parietal lobe](http://purl.obolibrary.org/obo/UBERON_0002802) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [right parietal lobe](http://purl.obolibrary.org/obo/UBERON_0002803) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Deltoid_tuberosity" -- [deltopectoral crest](http://purl.obolibrary.org/obo/UBERON_0002498) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tuberositas deltoidea" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:23418" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### left pelvic girdle region `http://purl.obolibrary.org/obo/UBERON_0011093` +#### Removed +- [left pelvic girdle region](http://purl.obolibrary.org/obo/UBERON_0011093) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [deltopectoral crest](http://purl.obolibrary.org/obo/UBERON_0002498) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tuberositas deltoidea humeri" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Deltoid_tuberosity" +### left pulmonary vein `http://purl.obolibrary.org/obo/UBERON_0009030` +#### Removed +- [left pulmonary vein](http://purl.obolibrary.org/obo/UBERON_0009030) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A vein that returns oxygenated blood from the left lung to the left atrium of the heart[ncithesaurus:Left_Pulmonary_Vein]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ncithesaurus:Left_Pulmonary_Vein" -- [deltopectoral crest](http://purl.obolibrary.org/obo/UBERON_0002498) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tuberositas deltoidea" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:23418" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### left recurrent laryngeal nerve `http://purl.obolibrary.org/obo/UBERON_0011766` +#### Removed +- [left recurrent laryngeal nerve](http://purl.obolibrary.org/obo/UBERON_0011766) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The left nerve is longer than the right, because it crosses under the arch of the aorta at the ligamentum arteriosum.[WP]" + +#### Added +- [left recurrent laryngeal nerve](http://purl.obolibrary.org/obo/UBERON_0011766) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) -### dendritic cell `http://purl.obolibrary.org/obo/CL_0000451` +### left renal pelvis `http://purl.obolibrary.org/obo/UBERON_0018115` #### Added -- [dendritic cell](http://purl.obolibrary.org/obo/CL_0000451) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [left renal pelvis](http://purl.obolibrary.org/obo/UBERON_0018115) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### dendritic cell, human `http://purl.obolibrary.org/obo/CL_0001056` +### left renal vein `http://purl.obolibrary.org/obo/UBERON_0001142` +#### Removed +- [left renal vein](http://purl.obolibrary.org/obo/UBERON_0001142) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A vein that drains blood from the left kidney into the inferior vena cava[ncithesaurus]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ncithesaurus:Left_Renal_Vein" -#### Added -- [dendritic cell, human](http://purl.obolibrary.org/obo/CL_0001056) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### dental follicle `http://purl.obolibrary.org/obo/UBERON_0008969` +### left side of back `http://purl.obolibrary.org/obo/UBERON_8000006` #### Added -- [dental follicle](http://purl.obolibrary.org/obo/UBERON_0008969) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D003795" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) - - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +- [left side of back](http://purl.obolibrary.org/obo/UBERON_8000006) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) -### dentate gyrus granule cell layer `http://purl.obolibrary.org/obo/UBERON_0005381` +### left subclavian artery `http://purl.obolibrary.org/obo/UBERON_0001584` #### Removed -- [dentate gyrus granule cell layer](http://purl.obolibrary.org/obo/UBERON_0005381) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum granulare gyri dentati" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:83146" +- [left subclavian artery](http://purl.obolibrary.org/obo/UBERON_0001584) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "in humans, branches off the arch of aorta" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [left subclavian artery](http://purl.obolibrary.org/obo/UBERON_0001584) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "arises from left intersegmental 6th artery in the region of the 6th -7th cervical segment in humans" #### Added -- [dentate gyrus granule cell layer](http://purl.obolibrary.org/obo/UBERON_0005381) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum granulare gyri dentati" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:83146" +- [left subclavian artery](http://purl.obolibrary.org/obo/UBERON_0001584) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### left suprarenal vein `http://purl.obolibrary.org/obo/UBERON_0035483` -### dentate gyrus molecular layer `http://purl.obolibrary.org/obo/UBERON_0004679` -#### Removed -- [dentate gyrus molecular layer](http://purl.obolibrary.org/obo/UBERON_0004679) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum moleculare gyri dentati" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:83677" +#### Added +- [left suprarenal vein](http://purl.obolibrary.org/obo/UBERON_0035483) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### left testis `http://purl.obolibrary.org/obo/UBERON_0004533` +#### Removed +- [left testis](http://purl.obolibrary.org/obo/UBERON_0004533) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) #### Added -- [dentate gyrus molecular layer](http://purl.obolibrary.org/obo/UBERON_0004679) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum moleculare gyri dentati" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:83677" +- [left testis](http://purl.obolibrary.org/obo/UBERON_0004533) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### left thymus lobe `http://purl.obolibrary.org/obo/UBERON_0005457` +#### Removed +- [left thymus lobe](http://purl.obolibrary.org/obo/UBERON_0005457) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) -### dentate gyrus of hippocampal formation `http://purl.obolibrary.org/obo/UBERON_0001885` + +### left umbilical artery `http://purl.obolibrary.org/obo/UBERON_0005458` #### Removed -- [dentate gyrus of hippocampal formation](http://purl.obolibrary.org/obo/UBERON_0001885) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "gyrus dentatus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0002496" +- [left umbilical artery](http://purl.obolibrary.org/obo/UBERON_0005458) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [left dorsal aorta](http://purl.obolibrary.org/obo/UBERON_0005613) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "EHDAA2" + + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "check this" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Dentate_gyrus" +- [left umbilical artery](http://purl.obolibrary.org/obo/UBERON_0005458) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [left extraembryonic umbilical artery](http://purl.obolibrary.org/obo/UBERON_0011696) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "EHDAA2" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "check this" #### Added -- [dentate gyrus of hippocampal formation](http://purl.obolibrary.org/obo/UBERON_0001885) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "gyrus dentatus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [left umbilical artery](http://purl.obolibrary.org/obo/UBERON_0005458) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [left extraembryonic umbilical artery](http://purl.obolibrary.org/obo/UBERON_0011696) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0002496" +- [left umbilical artery](http://purl.obolibrary.org/obo/UBERON_0005458) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [left dorsal aorta](http://purl.obolibrary.org/obo/UBERON_0005613) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Dentate_gyrus" - -### dentate gyrus polymorphic layer `http://purl.obolibrary.org/obo/UBERON_0002928` +### left umbilical vein `http://purl.obolibrary.org/obo/UBERON_0005459` #### Removed -- [dentate gyrus polymorphic layer](http://purl.obolibrary.org/obo/UBERON_0002928) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "CA4" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [DUBIOUS](http://purl.obolibrary.org/obo/uberon/core#DUBIOUS) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:17765709" +- [left umbilical vein](http://purl.obolibrary.org/obo/UBERON_0005459) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) #### Added -- [dentate gyrus polymorphic layer](http://purl.obolibrary.org/obo/UBERON_0002928) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "CA4" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:17765709" +- [left umbilical vein](http://purl.obolibrary.org/obo/UBERON_0005459) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003002](http://purl.obolibrary.org/obo/OMO_0003002) - -### dentition `http://purl.obolibrary.org/obo/UBERON_0003672` +### left ureter `http://purl.obolibrary.org/obo/UBERON_0001223` #### Removed -- [dentition](http://purl.obolibrary.org/obo/UBERON_0003672) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "dentes" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:75150" +- [left ureter](http://purl.obolibrary.org/obo/UBERON_0001223) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [dentition](http://purl.obolibrary.org/obo/UBERON_0003672) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "dentes" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### left uterine tube `http://purl.obolibrary.org/obo/UBERON_0001303` +#### Removed +- [left uterine tube](http://purl.obolibrary.org/obo/UBERON_0001303) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:75150" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### left vagus X nerve trunk `http://purl.obolibrary.org/obo/UBERON_0035020` -### dermal papilla `http://purl.obolibrary.org/obo/UBERON_0000412` -#### Removed -- [dermal papilla](http://purl.obolibrary.org/obo/UBERON_0000412) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "papillae dermis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Dermal_papillae" +#### Added +- [left vagus X nerve trunk](http://purl.obolibrary.org/obo/UBERON_0035020) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [dermal papilla](http://purl.obolibrary.org/obo/UBERON_0000412) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "papillae dermis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Dermal_papillae" +### left ventricle myocardium `http://purl.obolibrary.org/obo/UBERON_0006566` +#### Removed +- [left ventricle myocardium](http://purl.obolibrary.org/obo/UBERON_0006566) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:17339" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [left ventricle myocardium](http://purl.obolibrary.org/obo/UBERON_0006566) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Myocardium of ventricle which is continuous with the tunica media of aorta." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:9558" -### dermatological-muscosal system `http://purl.obolibrary.org/obo/UBERON_0012125` + +### left vitelline vein `http://purl.obolibrary.org/obo/UBERON_0005460` +#### Removed +- [left vitelline vein](http://purl.obolibrary.org/obo/UBERON_0005460) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) #### Added -- [dermatological-muscosal system](http://purl.obolibrary.org/obo/UBERON_0012125) [id](http://www.geneontology.org/formats/oboInOwl#id) "UBERON:0012125" +- [left vitelline vein](http://purl.obolibrary.org/obo/UBERON_0005460) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) -- [dermatological-muscosal system](http://purl.obolibrary.org/obo/UBERON_0012125) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Anatomical system that consists of the integumental system plus all mucosae and submucosae." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://github.com/obophenotype/uberon/issues/53" -- [dermatological-muscosal system](http://purl.obolibrary.org/obo/UBERON_0012125) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" +### leg `http://purl.obolibrary.org/obo/UBERON_0000978` +#### Removed +- [leg](http://purl.obolibrary.org/obo/UBERON_0000978) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "The term leg can mean: [1] an appendage on which an animal walks [2] the entire hindlimb of a tetrapod [3] the segment of a human leg between knee and ankle (cf FMA) [4] the region of a hindlimb include the stylopod and zeugopod, but excluding the autopod. We define this class as [4], and thus 'leg' is compltely analagous to 'arm'. For [1], see the class 'locomotive weight-bearing appendage'. For [2] we use 'hindlimb'. For" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "3" -- [dermatological-muscosal system](http://purl.obolibrary.org/obo/UBERON_0012125) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "dermatological system" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "OBI:MC" +- [leg](http://purl.obolibrary.org/obo/UBERON_0000978) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [dermatological-muscosal system](http://purl.obolibrary.org/obo/UBERON_0012125) [label](http://www.w3.org/2000/01/rdf-schema#label) "dermatological-muscosal system" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- Class: [dermatological-muscosal system](http://purl.obolibrary.org/obo/UBERON_0012125) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [dermatological-muscosal system](http://purl.obolibrary.org/obo/UBERON_0012125) SubClassOf [has part](http://purl.obolibrary.org/obo/BFO_0000051) some [hypodermis](http://purl.obolibrary.org/obo/UBERON_0002072) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000345" -- [dermatological-muscosal system](http://purl.obolibrary.org/obo/UBERON_0012125) SubClassOf [protein-containing material entity](http://purl.obolibrary.org/obo/PR_000050567) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268" -- [dermatological-muscosal system](http://purl.obolibrary.org/obo/UBERON_0012125) SubClassOf [has part](http://purl.obolibrary.org/obo/BFO_0000051) some [skin of body](http://purl.obolibrary.org/obo/UBERON_0002097) -- [dermatological-muscosal system](http://purl.obolibrary.org/obo/UBERON_0012125) SubClassOf [anatomical system](http://purl.obolibrary.org/obo/UBERON_0000467) -- [dermatological-muscosal system](http://purl.obolibrary.org/obo/UBERON_0012125) SubClassOf [has part](http://purl.obolibrary.org/obo/BFO_0000051) some [submucosa](http://purl.obolibrary.org/obo/UBERON_0000009) +### lens anterior epithelium `http://purl.obolibrary.org/obo/UBERON_0005614` +#### Removed +- [lens anterior epithelium](http://purl.obolibrary.org/obo/UBERON_0005614) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "Cells of the subcapsular epithelium (or anterior lens cells) are mitotically active. In adult individuals they only cover the anterior 'hemisphere' of the lens. As they divide, cells gradually move towards the equator of the lens where they tranform into lens fibres. The apical part of the gradually elongating cell extends between the subcapsular epithelium and adjacent lens fibres towards the anterior pole of the lens. The basal part extends towards the posterior pole. The nucleus remains close to the equatorial plane of the lens - http://www.lab.anhb.uwa.edu.au/mb140/corepages/eye/eye.htm" -- [dermatological-muscosal system](http://purl.obolibrary.org/obo/UBERON_0012125) SubClassOf [existence ends during](http://purl.obolibrary.org/obo/RO_0002492) some [fully formed stage](http://purl.obolibrary.org/obo/UBERON_0000066) +- [lens anterior epithelium](http://purl.obolibrary.org/obo/UBERON_0005614) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) -- [dermatological-muscosal system](http://purl.obolibrary.org/obo/UBERON_0012125) SubClassOf [has part](http://purl.obolibrary.org/obo/BFO_0000051) some [mucosa](http://purl.obolibrary.org/obo/UBERON_0000344) -### dermatome `http://purl.obolibrary.org/obo/UBERON_0004016` +### lens fiber `http://purl.obolibrary.org/obo/UBERON_0002444` #### Removed -- [dermatome](http://purl.obolibrary.org/obo/UBERON_0004016) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006248" - - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0003-4423-4370" +- [lens fiber](http://purl.obolibrary.org/obo/UBERON_0002444) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) the line, or Y, or star sutures common to mammalian lenses, including those of primates. In the case of line or Y sutures, the overlapping of lens fibers in each successive shell is coincident and results in the formation of four or six three-dimensional suture planes that extend from the lens nucleus to the periphery.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [dermatome](http://purl.obolibrary.org/obo/UBERON_0004016) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "mesenchyma dermatomiale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Dermatomal_mesenchyme" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [dermatome](http://purl.obolibrary.org/obo/UBERON_0004016) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006248" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000444" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1167/iovs.03-0466 Sivak JG, Through the lens clearly: phylogeny and development, The Proctor lecture. Investigative ophthalmology and visual science (2004)" - - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) +- [lens fiber](http://purl.obolibrary.org/obo/UBERON_0002444) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Fibres resembling a ribbon and arranged in very thin plates in the lens. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [dermatome](http://purl.obolibrary.org/obo/UBERON_0004016) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "mesenchyma dermatomiale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Dermatomal_mesenchyme" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000444" -### dermis `http://purl.obolibrary.org/obo/UBERON_0002067` -#### Removed -- [dermis](http://purl.obolibrary.org/obo/UBERON_0002067) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "corium" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Dermis" +#### Added +- [lens fiber](http://purl.obolibrary.org/obo/UBERON_0002444) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0000294" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### lens of camera-type eye `http://purl.obolibrary.org/obo/UBERON_0000965` +#### Removed +- [lens of camera-type eye](http://purl.obolibrary.org/obo/UBERON_0000965) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)" -#### Added -- [dermis](http://purl.obolibrary.org/obo/UBERON_0002067) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "corium" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Dermis" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0000294" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000169" -### dermis microvascular lymphatic vessel endothelial cell `http://purl.obolibrary.org/obo/CL_2000041` +- [lens of camera-type eye](http://purl.obolibrary.org/obo/UBERON_0000965) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "This class excludes compound eye corneal lenses." + +- [lens of camera-type eye](http://purl.obolibrary.org/obo/UBERON_0000965) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [vasculature](http://purl.obolibrary.org/obo/UBERON_0002049) #### Added -- [dermis microvascular lymphatic vessel endothelial cell](http://purl.obolibrary.org/obo/CL_2000041) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [lens of camera-type eye](http://purl.obolibrary.org/obo/UBERON_0000965) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### descending aorta `http://purl.obolibrary.org/obo/UBERON_0001514` +### lens placode `http://purl.obolibrary.org/obo/UBERON_0003073` #### Removed -- [descending aorta](http://purl.obolibrary.org/obo/UBERON_0001514) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pars descendens aortae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Descending_aorta" +- [lens placode](http://purl.obolibrary.org/obo/UBERON_0003073) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "Classical transplantation experiments using amphibian embryos suggested that the optic vesicle is the source of lens-inducing signals sufficient to generate lens tissues in competent ectoderm (reviewed in Grainger et al., 1996). More recent findings suggest a multistep model for lens induction. There is now good evidence that lens specification occurs at the neurula stage, before the optic vesicle contact the surface ectoderm, and that neural crest cell migration in the frontonasal region is required to restrict the position of the lens placode (Bailey et al., 2006)" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "NCBIBook:NBK53175" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [lens placode](http://purl.obolibrary.org/obo/UBERON_0003073) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Ectodermal primordium of the lens of the eye. Kimmel et al, 1995.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -- [descending aorta](http://purl.obolibrary.org/obo/UBERON_0001514) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "aorta descendens" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Descending_aorta" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000122" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -#### Added -- [descending aorta](http://purl.obolibrary.org/obo/UBERON_0001514) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "aorta descendens" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Descending_aorta" +- [lens placode](http://purl.obolibrary.org/obo/UBERON_0003073) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429" -- [descending aorta](http://purl.obolibrary.org/obo/UBERON_0001514) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pars descendens aortae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Descending_aorta" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### descending colon `http://purl.obolibrary.org/obo/UBERON_0001158` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000166" + +#### Added +- [lens placode](http://purl.obolibrary.org/obo/UBERON_0003073) SubClassOf [immature eye](http://purl.obolibrary.org/obo/UBERON_0010312) + + +### lens vesicle `http://purl.obolibrary.org/obo/UBERON_0005426` #### Removed -- [descending colon](http://purl.obolibrary.org/obo/UBERON_0001158) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D044683" +- [lens vesicle](http://purl.obolibrary.org/obo/UBERON_0005426) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "the lens of zebrafish (and other teleosts) forms from delamination of cells from the lens placode; thus, there is no formation of a hollow lens vesicle, in contrast to the situation in mammals and birds (Glass and Dahm, 2004) [PMID:16496288] The lens of the zebrafish forms by delamination of lens placodal cells and not through invagination. This results in a solid spherical mass as opposed to a hollow lens vesicle. Detachment of the solid lens vesicle of zebrafish at 24b26 hpf is accomplished in part by apoptosis, similar to mammals" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFA" -- [descending colon](http://purl.obolibrary.org/obo/UBERON_0001158) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "colon descendens" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Descending_colon" +- [lens vesicle](http://purl.obolibrary.org/obo/UBERON_0005426) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [descending colon](http://purl.obolibrary.org/obo/UBERON_0001158) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D044683" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001163" -- [descending colon](http://purl.obolibrary.org/obo/UBERON_0001158) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "colon descendens" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Descending_colon" +- [lens vesicle](http://purl.obolibrary.org/obo/UBERON_0005426) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A vesicle formed from the lens pit of the embryo, developing into the crystalline lens. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### detoxification `http://purl.obolibrary.org/obo/GO_0098754` -#### Removed -- [detoxification](http://purl.obolibrary.org/obo/GO_0098754) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001163" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/lens+vesicle" #### Added -- [detoxification](http://purl.obolibrary.org/obo/GO_0098754) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) +- [lens vesicle](http://purl.obolibrary.org/obo/UBERON_0005426) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### developing anatomical structure `http://purl.obolibrary.org/obo/UBERON_0005423` +### lens vesicle cavity `http://purl.obolibrary.org/obo/UBERON_0005688` #### Removed -- [developing anatomical structure](http://purl.obolibrary.org/obo/UBERON_0005423) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007006" +- [lens vesicle cavity](http://purl.obolibrary.org/obo/UBERON_0005688) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429" -#### Added -- [developing anatomical structure](http://purl.obolibrary.org/obo/UBERON_0005423) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007006" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### developmental cell growth `http://purl.obolibrary.org/obo/GO_0048588` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [developmental cell growth](http://purl.obolibrary.org/obo/GO_0048588) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [gocheck_do_not_annotate](http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000531" -- [developmental cell growth](http://purl.obolibrary.org/obo/GO_0048588) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/geneontology/go-ontology/issues/26424"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) -### develops into `http://purl.obolibrary.org/obo/RO_0002203` +### lens vesicle epithelium `http://purl.obolibrary.org/obo/UBERON_0005656` +#### Removed +- [lens vesicle epithelium](http://purl.obolibrary.org/obo/UBERON_0005656) SubClassOf [epithelium](http://purl.obolibrary.org/obo/UBERON_0000483) #### Added -- [develops into](http://purl.obolibrary.org/obo/RO_0002203) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" - -- [develops into](http://purl.obolibrary.org/obo/RO_0002203) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "develops_into" +- [lens vesicle epithelium](http://purl.obolibrary.org/obo/UBERON_0005656) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) -- [develops into](http://purl.obolibrary.org/obo/RO_0002203) [id](http://www.geneontology.org/formats/oboInOwl#id) "develops_into" -- [develops into](http://purl.obolibrary.org/obo/RO_0002203) [label](http://www.w3.org/2000/01/rdf-schema#label) "develops into" +### leptomeninx `http://purl.obolibrary.org/obo/UBERON_0000391` +#### Removed +- [leptomeninx](http://purl.obolibrary.org/obo/UBERON_0000391) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in FMA/NIF this is a superclass of PM/AM - in BTO it is the mereological sum. We go with superclass here, as we are naming the class in the singular" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" -- [develops into](http://purl.obolibrary.org/obo/RO_0002203) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002203" +#### Added +- [leptomeninx](http://purl.obolibrary.org/obo/UBERON_0000391) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) -### diaphysis of femur `http://purl.obolibrary.org/obo/UBERON_0006862` +### leukocyte immunoglobulin-like receptor subfamily A member 4 `http://purl.obolibrary.org/obo/PR_000001398` #### Removed -- [diaphysis of femur](http://purl.obolibrary.org/obo/UBERON_0006862) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "corpus femoris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [leukocyte immunoglobulin-like receptor subfamily A member 4](http://purl.obolibrary.org/obo/PR_000001398) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [leukocyte immunoglobulin-like receptor subfamily A member 4 (human)](http://purl.obolibrary.org/obo/PR_P59901) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:32847" -#### Added -- [diaphysis of femur](http://purl.obolibrary.org/obo/UBERON_0006862) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "corpus femoris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### leukosialin `http://purl.obolibrary.org/obo/PR_000001879` +#### Removed +- [leukosialin](http://purl.obolibrary.org/obo/PR_000001879) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [leukosialin (human)](http://purl.obolibrary.org/obo/PR_P16150) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:32847" -### diencephalon `http://purl.obolibrary.org/obo/UBERON_0001894` +### levator scapulae muscle `http://purl.obolibrary.org/obo/UBERON_0005461` #### Removed -- [diencephalon](http://purl.obolibrary.org/obo/UBERON_0001894) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "diencephalon" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Diencephalon" +- [levator scapulae muscle](http://purl.obolibrary.org/obo/UBERON_0005461) SubClassOf [axial muscle](http://purl.obolibrary.org/obo/UBERON_0003897) -#### Added -- [diencephalon](http://purl.obolibrary.org/obo/UBERON_0001894) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "diencephalon" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [levator scapulae muscle](http://purl.obolibrary.org/obo/UBERON_0005461) SubClassOf [has muscle insertion](http://purl.obolibrary.org/obo/RO_0002373) some [medial border of scapula](http://purl.obolibrary.org/obo/UBERON_0007174) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "Superior part of medial border of scapula" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Diencephalon" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "dbpedia" +- [levator scapulae muscle](http://purl.obolibrary.org/obo/UBERON_0005461) SubClassOf [innervated_by](http://purl.obolibrary.org/obo/RO_0002005) some [nerve of cervical vertebra](http://purl.obolibrary.org/obo/UBERON_0000962) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "dbpedia" -### differentiated genital tubercle `http://purl.obolibrary.org/obo/UBERON_0011757` -#### Removed -- [differentiated genital tubercle](http://purl.obolibrary.org/obo/UBERON_0011757) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "phallus primordialis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Primordial_phallus" + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "cervical nerve and dorsal scapular nerve" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [levator scapulae muscle](http://purl.obolibrary.org/obo/UBERON_0005461) SubClassOf [has muscle origin](http://purl.obolibrary.org/obo/RO_0002372) some [transverse process of vertebra](http://purl.obolibrary.org/obo/UBERON_0001077) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "Posterior tubercles of transverse processes of C1 - C4 vertebrae" -- [differentiated genital tubercle](http://purl.obolibrary.org/obo/UBERON_0011757) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Primordial_phallus" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "dbpedia" #### Added -- [differentiated genital tubercle](http://purl.obolibrary.org/obo/UBERON_0011757) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "phallus primordialis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [levator scapulae muscle](http://purl.obolibrary.org/obo/UBERON_0005461) SubClassOf [has muscle origin](http://purl.obolibrary.org/obo/RO_0002372) some [transverse process of vertebra](http://purl.obolibrary.org/obo/UBERON_0001077) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Primordial_phallus" +- [levator scapulae muscle](http://purl.obolibrary.org/obo/UBERON_0005461) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [axial musculature](http://purl.obolibrary.org/obo/UBERON_0013700) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Kardong" +- [levator scapulae muscle](http://purl.obolibrary.org/obo/UBERON_0005461) SubClassOf [innervated_by](http://purl.obolibrary.org/obo/RO_0002005) some [nerve of cervical vertebra](http://purl.obolibrary.org/obo/UBERON_0000962) -### differentiation-committed oligodendrocyte precursor `http://purl.obolibrary.org/obo/CL_4023059` +- [levator scapulae muscle](http://purl.obolibrary.org/obo/UBERON_0005461) SubClassOf [has muscle insertion](http://purl.obolibrary.org/obo/RO_0002373) some [medial border of scapula](http://purl.obolibrary.org/obo/UBERON_0007174) -#### Added -- [differentiation-committed oligodendrocyte precursor](http://purl.obolibrary.org/obo/CL_4023059) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [levator scapulae muscle](http://purl.obolibrary.org/obo/UBERON_0005461) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### digestive system `http://purl.obolibrary.org/obo/UBERON_0001007` -#### Removed -- [digestive system](http://purl.obolibrary.org/obo/UBERON_0001007) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005055" +### levator scapulae pre-muscle mass `http://purl.obolibrary.org/obo/UBERON_0010983` #### Added -- [digestive system](http://purl.obolibrary.org/obo/UBERON_0001007) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005055" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [levator scapulae pre-muscle mass](http://purl.obolibrary.org/obo/UBERON_0010983) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### digestive tract `http://purl.obolibrary.org/obo/UBERON_0001555` +### license `http://purl.org/dc/terms/license` #### Removed -- [digestive tract](http://purl.obolibrary.org/obo/UBERON_0001555) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00003125" +- [license](http://purl.org/dc/terms/license) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" -#### Added -- [digestive tract](http://purl.obolibrary.org/obo/UBERON_0001555) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00003125" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [license](http://purl.org/dc/terms/license) [is_metadata_tag](http://www.geneontology.org/formats/oboInOwl#is_metadata_tag) true -- [digestive tract](http://purl.obolibrary.org/obo/UBERON_0001555) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D041981" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) +- [license](http://purl.org/dc/terms/license) [label](http://www.w3.org/2000/01/rdf-schema#label) "license" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +- [license](http://purl.org/dc/terms/license) [id](http://www.geneontology.org/formats/oboInOwl#id) "dcterms-license" +- [license](http://purl.org/dc/terms/license) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://purl.org/dc/terms/license" -### digestive tract diverticulum `http://purl.obolibrary.org/obo/UBERON_0009854` -#### Removed -- [digestive tract diverticulum](http://purl.obolibrary.org/obo/UBERON_0009854) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00100316" +- [license](http://purl.org/dc/terms/license) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "dcterms-license" -#### Added -- [digestive tract diverticulum](http://purl.obolibrary.org/obo/UBERON_0009854) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00100316" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### digestive tract epithelium `http://purl.obolibrary.org/obo/UBERON_0003929` +### life cycle stage `http://purl.obolibrary.org/obo/UBERON_0000105` #### Removed -- [digestive tract epithelium](http://purl.obolibrary.org/obo/UBERON_0003929) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00047166" +- [life cycle stage](http://purl.obolibrary.org/obo/UBERON_0000105) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "the WBls class 'all stages' belongs here as it is the superclass of other WBls stages" -#### Added -- [digestive tract epithelium](http://purl.obolibrary.org/obo/UBERON_0003929) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00047166" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [life cycle stage](http://purl.obolibrary.org/obo/UBERON_0000105) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage" -### dilatator pupillae `http://purl.obolibrary.org/obo/UBERON_0001608` + +### ligament `http://purl.obolibrary.org/obo/UBERON_0000211` #### Removed -- [dilatator pupillae](http://purl.obolibrary.org/obo/UBERON_0001608) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "musculus dilatator pupillae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:49158" +- [ligament](http://purl.obolibrary.org/obo/UBERON_0000211) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Compared with their Ediacarian predecessor, Cambrian animals in general were characterized by their much stouter bodies. The stoutness of the body is likely due to the formation of ligaments and tendons, which in turn requires the crosslinking of collagen triple helices.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:8710894 Ohno S, The notion of the Cambrian pananimalia genome. PNAS (1996)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [dilatator pupillae](http://purl.obolibrary.org/obo/UBERON_0001608) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "musculus dilatator pupillae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Iris_dilator_muscle" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001272" -#### Added -- [dilatator pupillae](http://purl.obolibrary.org/obo/UBERON_0001608) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "musculus dilatator pupillae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:49158" +- [ligament](http://purl.obolibrary.org/obo/UBERON_0000211) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Portion of connective tissue that connects bone or cartilage.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001682" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -- [dilatator pupillae](http://purl.obolibrary.org/obo/UBERON_0001608) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "musculus dilatator pupillae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TAO:wd" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Iris_dilator_muscle" +- [ligament](http://purl.obolibrary.org/obo/UBERON_0000211) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "this groups both skeletal and non-skeletal ligaments. What is called a 'ligament' in many AOs is actually a skeletal ligament" +- [ligament](http://purl.obolibrary.org/obo/UBERON_0000211) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Nonparenchymatous organ that primarily consists of dense connective tissue aggregated into fasciculi by connective tissue. Examples: sutural ligament, radiate sternocostal ligament, ligament of liver, ovarian ligament[FMA][FMA:21496]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:21496" -### disconnected anatomical group `http://purl.obolibrary.org/obo/UBERON_0034923` -#### Removed -- [disconnected anatomical group](http://purl.obolibrary.org/obo/UBERON_0034923) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007276" -#### Added -- [disconnected anatomical group](http://purl.obolibrary.org/obo/UBERON_0034923) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007276" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +### ligament of larynx `http://purl.obolibrary.org/obo/UBERON_0001743` -### distal convoluted tubule `http://purl.obolibrary.org/obo/UBERON_0001292` -#### Removed -- [distal convoluted tubule](http://purl.obolibrary.org/obo/UBERON_0001292) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tubulus contortus distalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Distal_convoluted_tubule" +#### Added +- [ligament of larynx](http://purl.obolibrary.org/obo/UBERON_0001743) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [distal convoluted tubule](http://purl.obolibrary.org/obo/UBERON_0001292) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tubulus convolutus distalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### ligament of liver `http://purl.obolibrary.org/obo/UBERON_0013139` #### Added -- [distal convoluted tubule](http://purl.obolibrary.org/obo/UBERON_0001292) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tubulus convolutus distalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [ligament of liver](http://purl.obolibrary.org/obo/UBERON_0013139) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -- [distal convoluted tubule](http://purl.obolibrary.org/obo/UBERON_0001292) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tubulus contortus distalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Distal_convoluted_tubule" +### limb `http://purl.obolibrary.org/obo/UBERON_0002101` +#### Removed +- [limb](http://purl.obolibrary.org/obo/UBERON_0002101) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D005121" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -### distal phalanx `http://purl.obolibrary.org/obo/UBERON_0004300` -#### Removed -- [distal phalanx](http://purl.obolibrary.org/obo/UBERON_0004300) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "phalanx distalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Distal_phalanges" +- [limb](http://purl.obolibrary.org/obo/UBERON_0002101) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Organism subdivision that has as its parts the jointed appendages used for locomotion and manipulation.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010336" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -#### Added -- [distal phalanx](http://purl.obolibrary.org/obo/UBERON_0004300) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "phalanx distalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Distal_phalanges" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" +- [limb](http://purl.obolibrary.org/obo/UBERON_0002101) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### distal phalanx of manus `http://purl.obolibrary.org/obo/UBERON_0003865` -#### Removed -- [distal phalanx of manus](http://purl.obolibrary.org/obo/UBERON_0003865) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "phalanx distalis manus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:75818" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000336" -#### Added -- [distal phalanx of manus](http://purl.obolibrary.org/obo/UBERON_0003865) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "phalanx distalis manus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:75818" +- [limb](http://purl.obolibrary.org/obo/UBERON_0002101) SubClassOf [paired limb/fin](http://purl.obolibrary.org/obo/UBERON_0004708) + - [specialization_within](http://www.geneontology.org/formats/oboInOwl#specialization_within) "Sarcopterygians" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +#### Added +- [limb](http://purl.obolibrary.org/obo/UBERON_0002101) SubClassOf [paired limb/fin](http://purl.obolibrary.org/obo/UBERON_0004708) -### distal phalanx of pes `http://purl.obolibrary.org/obo/UBERON_0003867` +### limb bone `http://purl.obolibrary.org/obo/UBERON_0002428` #### Removed -- [distal phalanx of pes](http://purl.obolibrary.org/obo/UBERON_0003867) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "phalanx distalis pedis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:75830" +- [limb bone](http://purl.obolibrary.org/obo/UBERON_0002428) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "NCITA includes clavicle. MA:'limb bone' is actually a bone of limb or girdle" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "NCIT" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [limb bone](http://purl.obolibrary.org/obo/UBERON_0002428) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "the formal definition is very inclusive, and includes sesamoids" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [distal phalanx of pes](http://purl.obolibrary.org/obo/UBERON_0003867) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "phalanx distalis pedis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:75830" +### limb bud `http://purl.obolibrary.org/obo/UBERON_0004347` +#### Removed +- [limb bud](http://purl.obolibrary.org/obo/UBERON_0004347) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Early outgrowth of presumptive limb.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010375" -### distal straight tubule postmacula segment `http://purl.obolibrary.org/obo/UBERON_0006854` -#### Removed -- [distal straight tubule postmacula segment](http://purl.obolibrary.org/obo/UBERON_0006854) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://sourceforge.net/tracker/?func=detail&aid=3123598&group_id=76834&atid=1205376" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -#### Added -- [distal straight tubule postmacula segment](http://purl.obolibrary.org/obo/UBERON_0006854) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) "https://sourceforge.net/tracker/?func=detail&aid=3123598&group_id=76834&atid=1205376"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) -### dopaminergic neuron `http://purl.obolibrary.org/obo/CL_0000700` +### limb endochondral element `http://purl.obolibrary.org/obo/UBERON_0015061` #### Added -- [dopaminergic neuron](http://purl.obolibrary.org/obo/CL_0000700) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [limb endochondral element](http://purl.obolibrary.org/obo/UBERON_0015061) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### dorsal aorta `http://purl.obolibrary.org/obo/UBERON_0005805` +### limb external integument structure `http://purl.obolibrary.org/obo/UBERON_3000981` #### Removed -- [dorsal aorta](http://purl.obolibrary.org/obo/UBERON_0005805) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "aorta dorsalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "XAO:0000051" +- [limb external integument structure](http://purl.obolibrary.org/obo/UBERON_3000981) [UBPROP_0000004](http://purl.obolibrary.org/obo/UBPROP_0000004) "This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://purl.obolibrary.org/obo/aao.owl" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [dorsal aorta](http://purl.obolibrary.org/obo/UBERON_0005805) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "aortae dorsales" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Dorsal_aorta" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### limb mesenchyme `http://purl.obolibrary.org/obo/UBERON_0009749` +#### Removed +- [limb mesenchyme](http://purl.obolibrary.org/obo/UBERON_0009749) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "EMAPA mapping from TH" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EMAPA" -#### Added -- [dorsal aorta](http://purl.obolibrary.org/obo/UBERON_0005805) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "aortae dorsales" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Dorsal_aorta" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -- [dorsal aorta](http://purl.obolibrary.org/obo/UBERON_0005805) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "aorta dorsalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### limb muscle `http://purl.obolibrary.org/obo/UBERON_0003661` +#### Removed +- [limb muscle](http://purl.obolibrary.org/obo/UBERON_0003661) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:32700" + - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "XAO:0000051" +### limb segment `http://purl.obolibrary.org/obo/UBERON_0002529` +#### Removed +- [limb segment](http://purl.obolibrary.org/obo/UBERON_0002529) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA has both limb segment and free limb segment, the former includes the girdles. Note that MA uses the term more generally and includes A,S,Z,S+Z(arm/leg), whereas FMA is just A,S,Z" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + + + +### limbic lobe `http://purl.obolibrary.org/obo/UBERON_0002600` +#### Removed +- [limbic lobe](http://purl.obolibrary.org/obo/UBERON_0002600) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D065726" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) -### dorsal cochlear nucleus `http://purl.obolibrary.org/obo/UBERON_0002829` -#### Removed -- [dorsal cochlear nucleus](http://purl.obolibrary.org/obo/UBERON_0002829) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus cochlearis posterior" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Dorsal_cochlear_nucleus" + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [dorsal cochlear nucleus](http://purl.obolibrary.org/obo/UBERON_0002829) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus cochlearis dorsalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:721" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### limbic system `http://purl.obolibrary.org/obo/UBERON_0000349` #### Added -- [dorsal cochlear nucleus](http://purl.obolibrary.org/obo/UBERON_0002829) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus cochlearis posterior" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [limbic system](http://purl.obolibrary.org/obo/UBERON_0000349) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Dorsal_cochlear_nucleus" -- [dorsal cochlear nucleus](http://purl.obolibrary.org/obo/UBERON_0002829) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus cochlearis dorsalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### limiting membrane of retina `http://purl.obolibrary.org/obo/UBERON_0007619` +#### Removed +- [limiting membrane of retina](http://purl.obolibrary.org/obo/UBERON_0007619) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "MA does treat internal/external limiting membranes as layers - these are classified as laminae. We do not follow this convention. However, we do following MA is grouping these terms together" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:721" -### dorsal horn of spinal cord `http://purl.obolibrary.org/obo/UBERON_0002256` +### lingual artery `http://purl.obolibrary.org/obo/UBERON_0001610` #### Removed -- [dorsal horn of spinal cord](http://purl.obolibrary.org/obo/UBERON_0002256) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cornu posterius medullae spinalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Posterior_horn_of_spinal_cord" +- [lingual artery](http://purl.obolibrary.org/obo/UBERON_0001610) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: part_of external carotid (AAO:0010218)[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010492" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -- [dorsal horn of spinal cord](http://purl.obolibrary.org/obo/UBERON_0002256) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "columna grisea posterior medullae spinalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:256530" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [lingual artery](http://purl.obolibrary.org/obo/UBERON_0001610) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Part of the external carotid which supplies blood to the tongue.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010492" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -#### Added -- [dorsal horn of spinal cord](http://purl.obolibrary.org/obo/UBERON_0002256) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "columna grisea posterior medullae spinalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:256530" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [dorsal horn of spinal cord](http://purl.obolibrary.org/obo/UBERON_0002256) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cornu posterius medullae spinalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Posterior_horn_of_spinal_cord" +### lingual nerve `http://purl.obolibrary.org/obo/UBERON_0003721` +#### Removed +- [lingual nerve](http://purl.obolibrary.org/obo/UBERON_0003721) SubClassOf [nerve](http://purl.obolibrary.org/obo/UBERON_0001021) +#### Added +- [lingual nerve](http://purl.obolibrary.org/obo/UBERON_0003721) SubClassOf [nerve of head region](http://purl.obolibrary.org/obo/UBERON_0011779) -### dorsal lateral geniculate nucleus `http://purl.obolibrary.org/obo/UBERON_0002479` + +### lingual swellings `http://purl.obolibrary.org/obo/UBERON_0006260` #### Removed -- [dorsal lateral geniculate nucleus](http://purl.obolibrary.org/obo/UBERON_0002479) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nucleus dorsalis corporis geniculati lateralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:62214" +- [lingual swellings](http://purl.obolibrary.org/obo/UBERON_0006260) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [dorsal lateral geniculate nucleus](http://purl.obolibrary.org/obo/UBERON_0002479) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus corporis geniculati lateralis, pars dorsalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:353" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1046/j.1469-7580.2002.00073.x Iwasaki S, Evolution of the structure and function of the vertebrate tongue. J Anat (2002)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000449" -- [dorsal lateral geniculate nucleus](http://purl.obolibrary.org/obo/UBERON_0002479) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "corpus geniculatum laterale (Hassler)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:353" +- [lingual swellings](http://purl.obolibrary.org/obo/UBERON_0006260) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Primordium of the tongue; the median swelling and the distal and proximal swellings arise from the ventral aspect of the stomodeum. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [dorsal lateral geniculate nucleus](http://purl.obolibrary.org/obo/UBERON_0002479) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus geniculatus lateralis dorsalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:353" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/lingual+swellings" -#### Added -- [dorsal lateral geniculate nucleus](http://purl.obolibrary.org/obo/UBERON_0002479) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "corpus geniculatum laterale (Hassler)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000449" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:353" -- [dorsal lateral geniculate nucleus](http://purl.obolibrary.org/obo/UBERON_0002479) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nucleus dorsalis corporis geniculati lateralis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:62214" +### lip `http://purl.obolibrary.org/obo/UBERON_0001833` +#### Removed +- [lip](http://purl.obolibrary.org/obo/UBERON_0001833) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "labial" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [lip](http://purl.obolibrary.org/obo/UBERON_0001833) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Surface structure that is one of the two fleshy folds surrounding the opening of the mouth.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -- [dorsal lateral geniculate nucleus](http://purl.obolibrary.org/obo/UBERON_0002479) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus corporis geniculati lateralis, pars dorsalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0007006" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:353" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -- [dorsal lateral geniculate nucleus](http://purl.obolibrary.org/obo/UBERON_0002479) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus geniculatus lateralis dorsalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:353" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http//:www.medterms.com/script/main/art.asp?articlekey=9458" -### dorsal mesentery `http://purl.obolibrary.org/obo/UBERON_0002296` + +### lip epithelium `http://purl.obolibrary.org/obo/UBERON_0006913` #### Removed -- [dorsal mesentery](http://purl.obolibrary.org/obo/UBERON_0002296) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "mesenterium dorsale commune" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Dorsal_mesentery" +- [lip epithelium](http://purl.obolibrary.org/obo/UBERON_0006913) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The thick, high squamous-stratified epithelium that covers the lips. It contains abundant melanocytes, many mucous cells and has well differentiated taste buds.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005334" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -#### Added -- [dorsal mesentery](http://purl.obolibrary.org/obo/UBERON_0002296) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "mesenterium dorsale commune" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Dorsal_mesentery" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:ZDB-PUB-060921-12" -### dorsal metatarsal vein `http://purl.obolibrary.org/obo/UBERON_0001549` -#### Removed -- [dorsal metatarsal vein](http://purl.obolibrary.org/obo/UBERON_0001549) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "venae metatarsales dorsales" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Dorsal_metatarsal_veins" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### lipid transporter activity `http://purl.obolibrary.org/obo/GO_0005319` +#### Removed +- [lipid transporter activity](http://purl.obolibrary.org/obo/GO_0005319) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [lipid transport](http://purl.obolibrary.org/obo/GO_0006869) + - [source](http://www.geneontology.org/formats/oboInOwl#http://purl.org/dc/terms/source) "GO_REF:0000090" #### Added -- [dorsal metatarsal vein](http://purl.obolibrary.org/obo/UBERON_0001549) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "venae metatarsales dorsales" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Dorsal_metatarsal_veins" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [lipid transporter activity](http://purl.obolibrary.org/obo/GO_0005319) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [lipid transport](http://purl.obolibrary.org/obo/GO_0006869) -### dorsal plus ventral thalamus `http://purl.obolibrary.org/obo/UBERON_0001897` +### liver `http://purl.obolibrary.org/obo/UBERON_0002107` #### Removed -- [dorsal plus ventral thalamus](http://purl.obolibrary.org/obo/UBERON_0001897) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "thalamencephalon" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:300" +- [liver](http://purl.obolibrary.org/obo/UBERON_0002107) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The liver is found in all vertebrates, and is typically the largest visceral organ. Its form varies considerably in different species, and is largely determined by the shape and arrangement of the surrounding organs. Nonetheless, in most species it is divided into right and left lobes; exceptions to this general rule include snakes, where the shape of the body necessitates a simple cigar-like form. The internal structure of the liver is broadly similar in all vertebrates." - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [liver](http://purl.obolibrary.org/obo/UBERON_0002107) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "All vertebrates possess a liver (reference 1); Later in craniate evolution, an anterior gill arch was transformed into jaws, and many new types of feeding subsequently evolved.(...) A liver evolved that, among its many functions, stores considerable energy as glycogen or lipid (reference 2).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [dorsal plus ventral thalamus](http://purl.obolibrary.org/obo/UBERON_0001897) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "thalamus opticus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:300" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [dorsal plus ventral thalamus](http://purl.obolibrary.org/obo/UBERON_0001897) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "thalamus opticus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:300" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000257" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.526, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" -- [dorsal plus ventral thalamus](http://purl.obolibrary.org/obo/UBERON_0001897) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "thalamencephalon" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:300" +- [liver](http://purl.obolibrary.org/obo/UBERON_0002107) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "Only ZFA considers this part_of immune system - we weaken this to an overlaps relation, as in general it's only a subset of cells that have clear immune function." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "ZFA" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [liver](http://purl.obolibrary.org/obo/UBERON_0002107) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Organ which secretes bile and participates in formation of certain blood proteins.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010111" -### dorsal root ganglion `http://purl.obolibrary.org/obo/UBERON_0000044` -#### Removed -- [dorsal root ganglion](http://purl.obolibrary.org/obo/UBERON_0000044) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ganglion sensorium nervi spinalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001264" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Dorsal_root_ganglion" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [liver](http://purl.obolibrary.org/obo/UBERON_0002107) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "An organ sometimes referred to as a liver is found associated with the digestive tract of the primitive chordate Amphioxus. However, this is an enzyme secreting gland, not a metabolic organ, and it is unclear how truly homologous it is to the vertebrate liver. The zebrafish liver differs from the mammalian liver in that the hepatocytes are not clearly organized in cords or lobules and the typical portal triads are not apparent. In addition, the zebrafish liver does not have Kuppfer cells. Furthermore, a clear distinction can be made between the male and female liver in the adult zebrafish. The female hepatocytes are very basophilic (Figure 15c) as a result of the production of vitellogenin (Van der Ven et al. 2003)." -#### Added -- [dorsal root ganglion](http://purl.obolibrary.org/obo/UBERON_0000044) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D005727" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) +- [liver](http://purl.obolibrary.org/obo/UBERON_0002107) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010111" -- [dorsal root ganglion](http://purl.obolibrary.org/obo/UBERON_0000044) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ganglion sensorium nervi spinalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001264" +- [liver](http://purl.obolibrary.org/obo/UBERON_0002107) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "hepatic" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Dorsal_root_ganglion" +- [liver](http://purl.obolibrary.org/obo/UBERON_0002107) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]." -### dorsal root of spinal cord `http://purl.obolibrary.org/obo/UBERON_0002261` -#### Removed -- [dorsal root of spinal cord](http://purl.obolibrary.org/obo/UBERON_0002261) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "radix posterior" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Posterior_root_of_spinal_nerve" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### liver blood vessel `http://purl.obolibrary.org/obo/UBERON_0015796` #### Added -- [dorsal root of spinal cord](http://purl.obolibrary.org/obo/UBERON_0002261) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "radix posterior" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Posterior_root_of_spinal_nerve" +- [liver blood vessel](http://purl.obolibrary.org/obo/UBERON_0015796) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) -### dorsal thalamus `http://purl.obolibrary.org/obo/UBERON_0004703` +### liver lobule `http://purl.obolibrary.org/obo/UBERON_0004647` #### Removed -- [dorsal thalamus](http://purl.obolibrary.org/obo/UBERON_0004703) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "thalamus dorsalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001365" - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Thalamus" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [liver lobule](http://purl.obolibrary.org/obo/UBERON_0004647) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "should not be confused with the anatomic lobes of the liver (caudate lobe, quadrate lobe, left lobe, and right lobe), or any of the functional lobe classification systems.[WP]" #### Added -- [dorsal thalamus](http://purl.obolibrary.org/obo/UBERON_0004703) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "thalamus dorsalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001365" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [liver lobule](http://purl.obolibrary.org/obo/UBERON_0004647) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Thalamus" - -### dorsal venous arch `http://purl.obolibrary.org/obo/UBERON_0008783` +### liver parenchyma `http://purl.obolibrary.org/obo/UBERON_0001280` #### Removed -- [dorsal venous arch](http://purl.obolibrary.org/obo/UBERON_0008783) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arcus venosus dorsalis pedis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Dorsal_venous_arch_of_the_foot" +- [liver parenchyma](http://purl.obolibrary.org/obo/UBERON_0001280) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "the (liver) tubular structure (dual layered parenchyma) appears to be conserved among all embryonic vertebrates (...) it is not unlikely that all vertebrate livers share the same fundamental functional unit.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [dorsal venous arch](http://purl.obolibrary.org/obo/UBERON_0008783) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arcus venosus dorsalis pedis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Dorsal_venous_arch_of_the_foot" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000539" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1002/ar.20524 Hardman RC, Volz DC, Kullman SW, Hinton DE, An in vivo look at vertebrate liver architecture: three-dimensional reconstruction from Medaka (Oryzias latipes). The Anatomical Record (2007)" -### double negative T regulatory cell `http://purl.obolibrary.org/obo/CL_0011024` -#### Added -- [double negative T regulatory cell](http://purl.obolibrary.org/obo/CL_0011024) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### liver primordium `http://purl.obolibrary.org/obo/UBERON_0003894` +#### Removed +- [liver primordium](http://purl.obolibrary.org/obo/UBERON_0003894) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [foregut](http://purl.obolibrary.org/obo/UBERON_0001041) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Zaret 1996" -### double negative thymocyte `http://purl.obolibrary.org/obo/CL_0002489` + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "ventral foregut endoderm" #### Added -- [double negative thymocyte](http://purl.obolibrary.org/obo/CL_0002489) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [liver primordium](http://purl.obolibrary.org/obo/UBERON_0003894) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [foregut](http://purl.obolibrary.org/obo/UBERON_0001041) -### double-positive, alpha-beta thymocyte `http://purl.obolibrary.org/obo/CL_0000809` +### liver serosa `http://purl.obolibrary.org/obo/UBERON_8400021` #### Added -- [double-positive, alpha-beta thymocyte](http://purl.obolibrary.org/obo/CL_0000809) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [liver serosa](http://purl.obolibrary.org/obo/UBERON_8400021) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) -### duct `http://purl.obolibrary.org/obo/UBERON_0000058` -#### Removed -- [duct](http://purl.obolibrary.org/obo/UBERON_0000058) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00100314" +### liver stroma `http://purl.obolibrary.org/obo/UBERON_0016478` #### Added -- [duct](http://purl.obolibrary.org/obo/UBERON_0000058) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00100314" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [liver stroma](http://purl.obolibrary.org/obo/UBERON_0016478) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -### duct epithelial cell `http://purl.obolibrary.org/obo/CL_0000068` +### liver subserosa `http://purl.obolibrary.org/obo/UBERON_8400023` #### Added -- [duct epithelial cell](http://purl.obolibrary.org/obo/CL_0000068) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) - - -### duct of seminal vesicle `http://purl.obolibrary.org/obo/UBERON_0005903` -#### Removed -- [duct of seminal vesicle](http://purl.obolibrary.org/obo/UBERON_0005903) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ductus excretorius glandulae vesiculosae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:19473" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [liver subserosa](http://purl.obolibrary.org/obo/UBERON_8400023) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" - -- [duct of seminal vesicle](http://purl.obolibrary.org/obo/UBERON_0005903) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ductus excretorius glandulae vesiculosae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Excretory_duct_of_seminal_gland" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### liver trabecula `http://purl.obolibrary.org/obo/UBERON_0010183` #### Added -- [duct of seminal vesicle](http://purl.obolibrary.org/obo/UBERON_0005903) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ductus excretorius glandulae vesiculosae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:19473" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [liver trabecula](http://purl.obolibrary.org/obo/UBERON_0010183) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [duct of seminal vesicle](http://purl.obolibrary.org/obo/UBERON_0005903) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ductus excretorius glandulae vesiculosae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### lobar bronchus `http://purl.obolibrary.org/obo/UBERON_0002183` +#### Removed +- [lobar bronchus](http://purl.obolibrary.org/obo/UBERON_0002183) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "They have relatively large lumens that are lined by respiratory epithelium. There is a smooth muscle layer below the epithelium arranged as two ribbons of muscle that spiral in opposite directions. This smooth muscle layer contains seromucous glands. Irregularly arranged plates of hyaline cartilage surround the smooth muscle. These plates give structural support to the bronchus and maintain the patency of the lumen." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Excretory_duct_of_seminal_gland" -### duodenal gland `http://purl.obolibrary.org/obo/UBERON_0001212` +### lobe of cerebral hemisphere `http://purl.obolibrary.org/obo/UBERON_0016526` #### Removed -- [duodenal gland](http://purl.obolibrary.org/obo/UBERON_0001212) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "glandula duodenales Brunneri" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0002376" +- [lobe of cerebral hemisphere](http://purl.obolibrary.org/obo/UBERON_0016526) [UBPROP_0000202](http://purl.obolibrary.org/obo/UBPROP_0000202) [FMA_77800](http://purl.obolibrary.org/obo/FMA_77800) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +#### Added +- [lobe of cerebral hemisphere](http://purl.obolibrary.org/obo/UBERON_0016526) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -- [duodenal gland](http://purl.obolibrary.org/obo/UBERON_0001212) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "glandula duodenales" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0002376" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### lobe of liver `http://purl.obolibrary.org/obo/UBERON_0001113` #### Added -- [duodenal gland](http://purl.obolibrary.org/obo/UBERON_0001212) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "glandula duodenales Brunneri" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [lobe of liver](http://purl.obolibrary.org/obo/UBERON_0001113) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0002376" -- [duodenal gland](http://purl.obolibrary.org/obo/UBERON_0001212) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "glandula duodenales" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### lobe of lung `http://purl.obolibrary.org/obo/UBERON_0000101` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0002376" +#### Added +- [lobe of lung](http://purl.obolibrary.org/obo/UBERON_0000101) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -### duodenal papilla `http://purl.obolibrary.org/obo/UBERON_0004914` +### lobe of prostate `http://purl.obolibrary.org/obo/UBERON_0001328` #### Removed -- [duodenal papilla](http://purl.obolibrary.org/obo/UBERON_0004914) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "papilla duodeni" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Major_duodenal_papilla" +- [lobe of prostate](http://purl.obolibrary.org/obo/UBERON_0001328) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Anatomically, the human prostate gland is located between the base of the bladder and the rectum, and it completely surrounds the proximal urethra (Fig. 1A). It is a single alobular structure with central (CZ), peripheral (PZ) and transitional (TZ) zones. In contrast, the mouse prostate is not merged into one compact anatomical structure. It comprises four paired lobes situated circumferentially around the urethra, immediately caudal to the urinary bladder-namely, anterior (AP), dorsal (DP), lateral (LP), and ventral (VP) prostate (Fig. 1B). Often, the dorsal and the lateral lobes are thought of in combination and referred to as the dorsolateral (DLP) lobe as they share a ductal system. The mouse AP is considered analogous to the human CZ, which is rarely a site of neoplastic transformation in humans. The mouse DLP is considered most similar to the human PZ, which is the zone in which most carcinomas arise (Xue et al. 1997). These analogies, however, are limited as they are based solely on descriptive data and need to be re-evaluated using molecular techniques before the relationship between specific mouse prostate lobes and the human prostate zones is definitively asserted (Abate-Shen & Shen 2000). The mouse VP does not have a human homologue, and the human TZ does not have a murine homologue" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "https://github.com/obophenotype/uberon/issues/665" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:15163300" #### Added -- [duodenal papilla](http://purl.obolibrary.org/obo/UBERON_0004914) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "papilla duodeni" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Major_duodenal_papilla" +- [lobe of prostate](http://purl.obolibrary.org/obo/UBERON_0001328) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) -### duodeno-jejunal junction `http://purl.obolibrary.org/obo/UBERON_8410000` +### lobe of thyroid gland `http://purl.obolibrary.org/obo/UBERON_0001118` #### Removed -- [duodeno-jejunal junction](http://purl.obolibrary.org/obo/UBERON_8410000) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "flexura duodenojejunalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Duodenojejunal_flexure" +- [lobe of thyroid gland](http://purl.obolibrary.org/obo/UBERON_0001118) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Thus, a thyroid capable of forming iodotyrosines and iodothyronines is present in all vertebrates. (...) Certain morphologic changes occur after the biochemical evolution of the thyroid has ceased. In the adult lamprey and in most bony fishes, the gland is not encapsulated. (...) In cartilaginous fish, the thyroid is encapsulated. In the higher vertebrate forms, the thyroid is a one- or two-lobed encapsulated structure.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [duodeno-jejunal junction](http://purl.obolibrary.org/obo/UBERON_8410000) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "flexura duodenojejunalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Duodenojejunal_flexure" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://www.thyroidmanager.org/Chapter1/chapter01.htm" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000732" -### duodenum glandular cell `http://purl.obolibrary.org/obo/CL_1001589` +- [lobe of thyroid gland](http://purl.obolibrary.org/obo/UBERON_0001118) SubClassOf [thymus subunit](http://purl.obolibrary.org/obo/UBERON_0035075) #### Added -- [duodenum glandular cell](http://purl.obolibrary.org/obo/CL_1001589) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) - +- [lobe of thyroid gland](http://purl.obolibrary.org/obo/UBERON_0001118) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [thyroid gland](http://purl.obolibrary.org/obo/UBERON_0002046) -### early T lineage precursor `http://purl.obolibrary.org/obo/CL_0002425` - -#### Added -- [early T lineage precursor](http://purl.obolibrary.org/obo/CL_0002425) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [lobe of thyroid gland](http://purl.obolibrary.org/obo/UBERON_0001118) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -### early lymphoid progenitor `http://purl.obolibrary.org/obo/CL_0000936` +### lobule of mammary gland `http://purl.obolibrary.org/obo/UBERON_0001912` #### Added -- [early lymphoid progenitor](http://purl.obolibrary.org/obo/CL_0000936) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [lobule of mammary gland](http://purl.obolibrary.org/obo/UBERON_0001912) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### early pharyngeal endoderm `http://purl.obolibrary.org/obo/UBERON_0007690` +### located in `http://purl.obolibrary.org/obo/RO_0001025` #### Removed -- [early pharyngeal endoderm](http://purl.obolibrary.org/obo/UBERON_0007690) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://dev.biologists.org/content/128/22/4573.full" - -#### Added -- [early pharyngeal endoderm](http://purl.obolibrary.org/obo/UBERON_0007690) [see also](http://www.w3.org/2000/01/rdf-schema#seeAlso) "http://dev.biologists.org/content/128/22/4573.full"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) - - -### early pro-B cell `http://purl.obolibrary.org/obo/CL_0002046` - -#### Added -- [early pro-B cell](http://purl.obolibrary.org/obo/CL_0002046) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) - +- [located in](http://purl.obolibrary.org/obo/RO_0001025) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "located_in"@en -### early promyelocyte `http://purl.obolibrary.org/obo/CL_0002154` +- [located in](http://purl.obolibrary.org/obo/RO_0001025) [RO_0001900](http://purl.obolibrary.org/obo/RO_0001900) [RO_0001901](http://purl.obolibrary.org/obo/RO_0001901) -#### Added -- [early promyelocyte](http://purl.obolibrary.org/obo/CL_0002154) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [located in](http://purl.obolibrary.org/obo/RO_0001025) [label](http://www.w3.org/2000/01/rdf-schema#label) "located in" +- [located in](http://purl.obolibrary.org/obo/RO_0001025) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "this rat is located in this cage"@en -### eccrine sweat gland `http://purl.obolibrary.org/obo/UBERON_0000423` -#### Removed -- [eccrine sweat gland](http://purl.obolibrary.org/obo/UBERON_0000423) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "glandula sudorifera merocrina" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Eccrine_sweat_gland" +- [located in](http://purl.obolibrary.org/obo/RO_0001025) [source](http://purl.org/dc/terms/source) "http://www.obofoundry.org/ro/#OBO_REL:located_in" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [located in](http://purl.obolibrary.org/obo/RO_0001025) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0001025" -- [eccrine sweat gland](http://purl.obolibrary.org/obo/UBERON_0000423) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "glandula sudorifera eccrina" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Eccrine_sweat_gland" +- [located in](http://purl.obolibrary.org/obo/RO_0001025) [id](http://www.geneontology.org/formats/oboInOwl#id) "located_in" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [located in](http://purl.obolibrary.org/obo/RO_0001025) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "my brain is located in my head"@en -#### Added -- [eccrine sweat gland](http://purl.obolibrary.org/obo/UBERON_0000423) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "glandula sudorifera eccrina" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [located in](http://purl.obolibrary.org/obo/RO_0001025) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "located in"@en - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Eccrine_sweat_gland" +- [located in](http://purl.obolibrary.org/obo/RO_0001025) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "located_in" -- [eccrine sweat gland](http://purl.obolibrary.org/obo/UBERON_0000423) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "glandula sudorifera merocrina" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [located in](http://purl.obolibrary.org/obo/RO_0001025) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Eccrine_sweat_gland" -### ectocervix `http://purl.obolibrary.org/obo/UBERON_0012249` +### location of `http://purl.obolibrary.org/obo/RO_0001015` #### Removed -- [ectocervix](http://purl.obolibrary.org/obo/UBERON_0012249) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "portio vaginalis cervicis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001850" +- [location of](http://purl.obolibrary.org/obo/RO_0001015) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [location of](http://purl.obolibrary.org/obo/RO_0001015) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "location_of" -#### Added -- [ectocervix](http://purl.obolibrary.org/obo/UBERON_0012249) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "portio vaginalis cervicis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [location of](http://purl.obolibrary.org/obo/RO_0001015) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0001015" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001850" +- [location of](http://purl.obolibrary.org/obo/RO_0001015) [RO_0001900](http://purl.obolibrary.org/obo/RO_0001900) [RO_0001901](http://purl.obolibrary.org/obo/RO_0001901) +- [location of](http://purl.obolibrary.org/obo/RO_0001015) [label](http://www.w3.org/2000/01/rdf-schema#label) "location of" -### ectoderm `http://purl.obolibrary.org/obo/UBERON_0000924` -#### Removed -- [ectoderm](http://purl.obolibrary.org/obo/UBERON_0000924) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000111" +- [location of](http://purl.obolibrary.org/obo/RO_0001015) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "my head is the location of my brain"@en -#### Added -- [ectoderm](http://purl.obolibrary.org/obo/UBERON_0000924) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000111" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [location of](http://purl.obolibrary.org/obo/RO_0001015) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "this cage is the location of this rat"@en +- [location of](http://purl.obolibrary.org/obo/RO_0001015) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "is location of"@en -### effector CD4-positive, alpha-beta T cell `http://purl.obolibrary.org/obo/CL_0001044` +- [location of](http://purl.obolibrary.org/obo/RO_0001015) [id](http://www.geneontology.org/formats/oboInOwl#id) "location_of" -#### Added -- [effector CD4-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_0001044) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [location of](http://purl.obolibrary.org/obo/RO_0001015) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "location_of"@en -### effector CD8-positive, alpha-beta T cell `http://purl.obolibrary.org/obo/CL_0001050` -#### Added -- [effector CD8-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_0001050) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### locus ceruleus `http://purl.obolibrary.org/obo/UBERON_0002148` +#### Removed +- [locus ceruleus](http://purl.obolibrary.org/obo/UBERON_0002148) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0003004](http://purl.obolibrary.org/obo/UBERON_0003004) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" +- [locus ceruleus](http://purl.obolibrary.org/obo/UBERON_0002148) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [pontine raphe nucleus](http://purl.obolibrary.org/obo/UBERON_0002047) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" -### effector memory CD4-positive, alpha-beta T cell `http://purl.obolibrary.org/obo/CL_0000905` +- [locus ceruleus](http://purl.obolibrary.org/obo/UBERON_0002148) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002587](http://purl.obolibrary.org/obo/UBERON_0002587) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" -#### Added -- [effector memory CD4-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_0000905) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [locus ceruleus](http://purl.obolibrary.org/obo/UBERON_0002148) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002267](http://purl.obolibrary.org/obo/UBERON_0002267) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" +- [locus ceruleus](http://purl.obolibrary.org/obo/UBERON_0002148) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [pontine tegmentum](http://purl.obolibrary.org/obo/UBERON_0003023) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "check ZFA" -### effector memory CD8-positive, alpha-beta T cell `http://purl.obolibrary.org/obo/CL_0000913` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "NIFSTD" #### Added -- [effector memory CD8-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_0000913) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [locus ceruleus](http://purl.obolibrary.org/obo/UBERON_0002148) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [pontine tegmentum](http://purl.obolibrary.org/obo/UBERON_0003023) -### effector memory CD8-positive, alpha-beta T cell, terminally differentiated `http://purl.obolibrary.org/obo/CL_0001062` +### long-wave-sensitive opsin 1 `http://purl.obolibrary.org/obo/PR_000001244` +#### Removed +- [long-wave-sensitive opsin 1](http://purl.obolibrary.org/obo/PR_000001244) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [long-wave-sensitive opsin 1 (human)](http://purl.obolibrary.org/obo/PR_P04000) -#### Added -- [effector memory CD8-positive, alpha-beta T cell, terminally differentiated](http://purl.obolibrary.org/obo/CL_0001062) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### efferent duct `http://purl.obolibrary.org/obo/UBERON_0006946` +### loop of Henle `http://purl.obolibrary.org/obo/UBERON_0001288` #### Removed -- [efferent duct](http://purl.obolibrary.org/obo/UBERON_0006946) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ductuli efferentes testis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Efferent_ducts" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [loop of Henle](http://purl.obolibrary.org/obo/UBERON_0001288) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The structure differs considerably between species; there is a definite physical loop of Henle in the mammalian and avian renal systems but this seems to be absent in Xenopus. However, homologs of some, but not all, molecular markers (e.g. cldn8 and clcnk) of the mammalian loop of Henle were found to be present in the pronephros of the frog larva ." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1371/journal.pone.0099864" -#### Added -- [efferent duct](http://purl.obolibrary.org/obo/UBERON_0006946) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ductuli efferentes testis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [loop of Henle](http://purl.obolibrary.org/obo/UBERON_0001288) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "The loop of Henle plays an important role in creating a concentration gradient in the medulla of the kidney. It is involved in reabsorption of filtered water and ions including sodium, potassium and calcium, and independently regulates both the volume and osmolarity of body fluids." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1371/journal.pone.0099864" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Efferent_ducts" +- [loop of Henle](http://purl.obolibrary.org/obo/UBERON_0001288) [RO_0002174](http://purl.obolibrary.org/obo/RO_0002174) [NCBITaxon_8353](http://purl.obolibrary.org/obo/NCBITaxon_8353) +- [loop of Henle](http://purl.obolibrary.org/obo/UBERON_0001288) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A highly specialized segment of the mammalian kidney tubules, that dips into the medulla. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, p.648, see_Liem_KF][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### ejaculatory duct `http://purl.obolibrary.org/obo/UBERON_0000999` -#### Removed -- [ejaculatory duct](http://purl.obolibrary.org/obo/UBERON_0000999) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ductus ejaculatorii" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ejaculatory_duct" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [ejaculatory duct](http://purl.obolibrary.org/obo/UBERON_0000999) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ductus ejaculatorii" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001270" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ejaculatory_duct" -### elastic tissue `http://purl.obolibrary.org/obo/UBERON_0002521` +### low affinity immunoglobulin epsilon Fc receptor `http://purl.obolibrary.org/obo/PR_000001880` #### Removed -- [elastic tissue](http://purl.obolibrary.org/obo/UBERON_0002521) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "textus connectivus elasticus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [low affinity immunoglobulin epsilon Fc receptor](http://purl.obolibrary.org/obo/PR_000001880) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [low affinity immunoglobulin epsilon Fc receptor (human)](http://purl.obolibrary.org/obo/PR_P06734) -#### Added -- [elastic tissue](http://purl.obolibrary.org/obo/UBERON_0002521) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "textus connectivus elasticus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### elbow `http://purl.obolibrary.org/obo/UBERON_0001461` +### low affinity immunoglobulin gamma Fc region receptor II-b `http://purl.obolibrary.org/obo/PR_000001481` #### Removed -- [elbow](http://purl.obolibrary.org/obo/UBERON_0001461) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "articulatio cubiti" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Elbow" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - -#### Added -- [elbow](http://purl.obolibrary.org/obo/UBERON_0001461) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "articulatio cubiti" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [low affinity immunoglobulin gamma Fc region receptor II-b](http://purl.obolibrary.org/obo/PR_000001481) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [low affinity immunoglobulin gamma Fc region receptor II-b (human)](http://purl.obolibrary.org/obo/PR_P31994) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Elbow" -### elbow joint `http://purl.obolibrary.org/obo/UBERON_0001490` +### lower digestive tract `http://purl.obolibrary.org/obo/UBERON_0004907` #### Removed -- [elbow joint](http://purl.obolibrary.org/obo/UBERON_0001490) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "articulatio cubiti" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - -#### Added -- [elbow joint](http://purl.obolibrary.org/obo/UBERON_0001490) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "articulatio cubiti" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [lower digestive tract](http://purl.obolibrary.org/obo/UBERON_0004907) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "WP: small intestine, large intestine, anus. Anal canal not part of LGIT according to FMA, but anus is considered part of LGIT according to WP. Duodenum overlaps both U/L" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" +- [lower digestive tract](http://purl.obolibrary.org/obo/UBERON_0004907) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "MA class was moved from here. See https://github.com/obophenotype/uberon/issues/509" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" -### elicited macrophage `http://purl.obolibrary.org/obo/CL_0000861` - -#### Added -- [elicited macrophage](http://purl.obolibrary.org/obo/CL_0000861) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### embryo `http://purl.obolibrary.org/obo/UBERON_0000922` +### lower jaw region `http://purl.obolibrary.org/obo/UBERON_0001710` #### Removed -- [embryo](http://purl.obolibrary.org/obo/UBERON_0000922) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000052" - -- [embryo](http://purl.obolibrary.org/obo/UBERON_0000922) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "IDOMAL:0000646" - - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0003-4423-4370" - -#### Added -- [embryo](http://purl.obolibrary.org/obo/UBERON_0000922) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "IDOMAL:0000646" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +- [lower jaw region](http://purl.obolibrary.org/obo/UBERON_0001710) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Inferior mandibular arch located on the anterior and lateral sides of the skull.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" - - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -- [embryo](http://purl.obolibrary.org/obo/UBERON_0000922) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000052" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000272" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### embryonic fibroblast `http://purl.obolibrary.org/obo/CL_2000042` +- [lower jaw region](http://purl.obolibrary.org/obo/UBERON_0001710) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "Note isa/partof difference MA/FMA" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" -#### Added -- [embryonic fibroblast](http://purl.obolibrary.org/obo/CL_2000042) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [lower jaw region](http://purl.obolibrary.org/obo/UBERON_0001710) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### embryonic head `http://purl.obolibrary.org/obo/UBERON_0008816` -#### Removed -- [embryonic head](http://purl.obolibrary.org/obo/UBERON_0008816) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000155" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [embryonic head](http://purl.obolibrary.org/obo/UBERON_0008816) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000155" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000453" -### embryonic stem cell `http://purl.obolibrary.org/obo/CL_0002322` +- [lower jaw region](http://purl.obolibrary.org/obo/UBERON_0001710) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [upper jaw region](http://purl.obolibrary.org/obo/UBERON_0001709) #### Added -- [embryonic stem cell](http://purl.obolibrary.org/obo/CL_0002322) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [lower jaw region](http://purl.obolibrary.org/obo/UBERON_0001710) SubClassOf [structure with developmental contribution from neural crest](http://purl.obolibrary.org/obo/UBERON_0010314) -### embryonic structure `http://purl.obolibrary.org/obo/UBERON_0002050` +### lower leg epithelium `http://purl.obolibrary.org/obo/UBERON_0005229` #### Removed -- [embryonic structure](http://purl.obolibrary.org/obo/UBERON_0002050) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004208" +- [lower leg epithelium](http://purl.obolibrary.org/obo/UBERON_0005229) SubClassOf [epithelium](http://purl.obolibrary.org/obo/UBERON_0000483) #### Added -- [embryonic structure](http://purl.obolibrary.org/obo/UBERON_0002050) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004208" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [lower leg epithelium](http://purl.obolibrary.org/obo/UBERON_0005229) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) -### embryonic tagma `http://purl.obolibrary.org/obo/UBERON_6000137` +### lower lip `http://purl.obolibrary.org/obo/UBERON_0001835` #### Removed -- [embryonic tagma](http://purl.obolibrary.org/obo/UBERON_6000137) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000137" - -#### Added -- [embryonic tagma](http://purl.obolibrary.org/obo/UBERON_6000137) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000137" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [lower lip](http://purl.obolibrary.org/obo/UBERON_0001835) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EHDAA2:0001020" +- [lower lip](http://purl.obolibrary.org/obo/UBERON_0001835) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Lip that covers the lower portion of the mouth.[TAO]" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -### embryonic urethral groove `http://purl.obolibrary.org/obo/UBERON_0013241` -#### Removed -- [embryonic urethral groove](http://purl.obolibrary.org/obo/UBERON_0013241) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "sulcus urethralis primarius" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Urethral_groove" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TAO:wd" -#### Added -- [embryonic urethral groove](http://purl.obolibrary.org/obo/UBERON_0013241) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "sulcus urethralis primarius" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0002060" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Urethral_groove" -### endocardial cell `http://purl.obolibrary.org/obo/CL_0002350` +### lower respiratory tract cartilage `http://purl.obolibrary.org/obo/UBERON_0003603` #### Added -- [endocardial cell](http://purl.obolibrary.org/obo/CL_0002350) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [lower respiratory tract cartilage](http://purl.obolibrary.org/obo/UBERON_0003603) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -### endocardial cushion `http://purl.obolibrary.org/obo/UBERON_0002062` -#### Removed -- [endocardial cushion](http://purl.obolibrary.org/obo/UBERON_0002062) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D054089" +### lower respiratory tract connective tissue `http://purl.obolibrary.org/obo/UBERON_0003580` #### Added -- [endocardial cushion](http://purl.obolibrary.org/obo/UBERON_0002062) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D054089" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) - - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +- [lower respiratory tract connective tissue](http://purl.obolibrary.org/obo/UBERON_0003580) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -### endocrine cell `http://purl.obolibrary.org/obo/CL_0000163` +### lower respiratory tract smooth muscle `http://purl.obolibrary.org/obo/UBERON_0004233` #### Added -- [endocrine cell](http://purl.obolibrary.org/obo/CL_0000163) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [lower respiratory tract smooth muscle](http://purl.obolibrary.org/obo/UBERON_0004233) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) -### endocrine gland `http://purl.obolibrary.org/obo/UBERON_0002368` +### lumen of `http://purl.obolibrary.org/obo/RO_0002571` #### Removed -- [endocrine gland](http://purl.obolibrary.org/obo/UBERON_0002368) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "glandulae endocrinae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Endocrine_gland" +- [lumen of](http://purl.obolibrary.org/obo/RO_0002571) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - -#### Added -- [endocrine gland](http://purl.obolibrary.org/obo/UBERON_0002368) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "glandulae endocrinae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [lumen of](http://purl.obolibrary.org/obo/RO_0002571) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Endocrine_gland" +- [lumen of](http://purl.obolibrary.org/obo/RO_0002571) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002571" +- [lumen of](http://purl.obolibrary.org/obo/RO_0002571) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) -### endocrine pancreas `http://purl.obolibrary.org/obo/UBERON_0000016` +- [lumen of](http://purl.obolibrary.org/obo/RO_0002571) [id](http://www.geneontology.org/formats/oboInOwl#id) "lumen_of" -#### Added -- [endocrine pancreas](http://purl.obolibrary.org/obo/UBERON_0000016) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D007515" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) +- [lumen of](http://purl.obolibrary.org/obo/RO_0002571) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "lumen_of" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -### endocrine system `http://purl.obolibrary.org/obo/UBERON_0000949` +### lumen of open tracheal system trachea `http://purl.obolibrary.org/obo/UBERON_0006832` #### Removed -- [endocrine system](http://purl.obolibrary.org/obo/UBERON_0000949) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005068" - -#### Added -- [endocrine system](http://purl.obolibrary.org/obo/UBERON_0000949) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005068" +- [lumen of open tracheal system trachea](http://purl.obolibrary.org/obo/UBERON_0006832) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007410" - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### endoderm `http://purl.obolibrary.org/obo/UBERON_0000925` + +### lumen of terminal part of digestive tract `http://purl.obolibrary.org/obo/UBERON_0012465` #### Removed -- [endoderm](http://purl.obolibrary.org/obo/UBERON_0000925) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000125" +- [lumen of terminal part of digestive tract](http://purl.obolibrary.org/obo/UBERON_0012465) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "includes the cloacal lumen, in species where this is present" -#### Added -- [endoderm](http://purl.obolibrary.org/obo/UBERON_0000925) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000125" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### endometrial gland `http://purl.obolibrary.org/obo/UBERON_0002451` +### lumican `http://purl.obolibrary.org/obo/PR_000009981` #### Removed -- [endometrial gland](http://purl.obolibrary.org/obo/UBERON_0002451) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "glandulae uterinae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71647" +- [lumican](http://purl.obolibrary.org/obo/PR_000009981) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [lumican (human)](http://purl.obolibrary.org/obo/PR_P51884) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [endometrial gland](http://purl.obolibrary.org/obo/UBERON_0002451) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "glandulae uterinae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Uterine_glands" +### luminal space of `http://purl.obolibrary.org/obo/RO_0002572` +#### Removed +- [luminal space of](http://purl.obolibrary.org/obo/RO_0002572) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [luminal space of](http://purl.obolibrary.org/obo/RO_0002572) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "luminal_space_of" -#### Added -- [endometrial gland](http://purl.obolibrary.org/obo/UBERON_0002451) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "glandulae uterinae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Uterine_glands" +- [luminal space of](http://purl.obolibrary.org/obo/RO_0002572) [id](http://www.geneontology.org/formats/oboInOwl#id) "luminal_space_of" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [luminal space of](http://purl.obolibrary.org/obo/RO_0002572) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" -- [endometrial gland](http://purl.obolibrary.org/obo/UBERON_0002451) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "glandulae uterinae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [luminal space of](http://purl.obolibrary.org/obo/RO_0002572) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002572" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71647" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### lung `http://purl.obolibrary.org/obo/UBERON_0002048` +#### Removed +- [lung](http://purl.obolibrary.org/obo/UBERON_0002048) [never_in_taxon](http://purl.obolibrary.org/obo/RO_0002161) [NCBITaxon_7777](http://purl.obolibrary.org/obo/NCBITaxon_7777) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "https://github.com/obophenotype/uberon/issues/701" -### endometrial lymphatic vessel `http://purl.obolibrary.org/obo/UBERON_8600042` + - [editor](http://www.geneontology.org/formats/oboInOwl#editor) "https://orcid.org/0000-0002-9415-5104" -#### Added -- [endometrial lymphatic vessel](http://purl.obolibrary.org/obo/UBERON_8600042) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" +- [lung](http://purl.obolibrary.org/obo/UBERON_0002048) [never_in_taxon](http://purl.obolibrary.org/obo/RO_0002161) [Teleostei](http://purl.obolibrary.org/obo/NCBITaxon_32443) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "https://github.com/obophenotype/uberon/issues/701" -- [endometrial lymphatic vessel](http://purl.obolibrary.org/obo/UBERON_8600042) [id](http://www.geneontology.org/formats/oboInOwl#id) "UBERON:8600042" + - [editor](http://www.geneontology.org/formats/oboInOwl#editor) "https://orcid.org/0000-0002-9415-5104" -- [endometrial lymphatic vessel](http://purl.obolibrary.org/obo/UBERON_8600042) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A lymphatic vessel that is part of an endometrium." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:23054374" +- [lung](http://purl.obolibrary.org/obo/UBERON_0002048) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "respiration organ in all air-breathing animals, including most tetrapods, a few fish and a few snails. In mammals and the more complex life forms, the two lungs are located in the chest on either side of the heart. Their principal function is to transport oxygen from the atmosphere into the bloodstream, and to release carbon dioxide from the bloodstream into the atmosphere. This exchange of gases is accomplished in the mosaic of specialized cells that form millions of tiny, exceptionally thin-walled air sacs called alveoli. // Avian lungs do not have alveoli as mammalian lungs do, they have Faveolar lungs. They contain millions of tiny passages known as para-bronchi, connected at both ends by the dorsobronchi" -- [endometrial lymphatic vessel](http://purl.obolibrary.org/obo/UBERON_8600042) [date](http://purl.org/dc/terms/date) "2024-01-16T18:18:36Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +- [lung](http://purl.obolibrary.org/obo/UBERON_0002048) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "pulmonary" -- [endometrial lymphatic vessel](http://purl.obolibrary.org/obo/UBERON_8600042) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) +- [lung](http://purl.obolibrary.org/obo/UBERON_0002048) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "VHOG:0000310" -- [endometrial lymphatic vessel](http://purl.obolibrary.org/obo/UBERON_8600042) [label](http://www.w3.org/2000/01/rdf-schema#label) "endometrial lymphatic vessel" +- [lung](http://purl.obolibrary.org/obo/UBERON_0002048) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -- Class: [endometrial lymphatic vessel](http://purl.obolibrary.org/obo/UBERON_8600042) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -- [endometrial lymphatic vessel](http://purl.obolibrary.org/obo/UBERON_8600042) EquivalentTo [lymphatic vessel](http://purl.obolibrary.org/obo/UBERON_0001473) and ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [endometrium](http://purl.obolibrary.org/obo/UBERON_0001295)) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010567" -- [endometrial lymphatic vessel](http://purl.obolibrary.org/obo/UBERON_8600042) SubClassOf [reproductive structure](http://purl.obolibrary.org/obo/UBERON_0005156) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:SBH" -- [endometrial lymphatic vessel](http://purl.obolibrary.org/obo/UBERON_8600042) SubClassOf [lymphatic vessel](http://purl.obolibrary.org/obo/UBERON_0001473) +- [lung](http://purl.obolibrary.org/obo/UBERON_0002048) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata. (...) In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ (reference 1); Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung (reference 2).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [endometrial lymphatic vessel](http://purl.obolibrary.org/obo/UBERON_8600042) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [endometrium](http://purl.obolibrary.org/obo/UBERON_0001295) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### endometrium `http://purl.obolibrary.org/obo/UBERON_0001295` -#### Removed -- [endometrium](http://purl.obolibrary.org/obo/UBERON_0001295) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa uteri" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Endometrium" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000310" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210, DOI:10.1371/journal.pone.0024019 Zheng W, Wang Z, Collins JE, Andrews RM, Stemple D, Gong Z, Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung. PLoS One (2011)" #### Added -- [endometrium](http://purl.obolibrary.org/obo/UBERON_0001295) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa uteri" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [lung](http://purl.obolibrary.org/obo/UBERON_0002048) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Endometrium" - -### endosteal cell `http://purl.obolibrary.org/obo/CL_0002157` +### lung blood vessel `http://purl.obolibrary.org/obo/UBERON_0003512` #### Added -- [endosteal cell](http://purl.obolibrary.org/obo/CL_0002157) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [lung blood vessel](http://purl.obolibrary.org/obo/UBERON_0003512) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) -### endothelial cell `http://purl.obolibrary.org/obo/CL_0000115` +### lung bud `http://purl.obolibrary.org/obo/UBERON_0000118` #### Added -- [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [lung bud](http://purl.obolibrary.org/obo/UBERON_0000118) SubClassOf [endo-epithelium](http://purl.obolibrary.org/obo/UBERON_0005911) -### endothelial cell of artery `http://purl.obolibrary.org/obo/CL_1000413` +### lung connective tissue `http://purl.obolibrary.org/obo/UBERON_0000114` +#### Removed +- [lung connective tissue](http://purl.obolibrary.org/obo/UBERON_0000114) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "it functions in the mechanical behavior of the lung, and forms a barrier to regulate the flow of plasma constituents from the capillaries to the airway and alveolar spaces" + +- [lung connective tissue](http://purl.obolibrary.org/obo/UBERON_0000114) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) #### Added -- [endothelial cell of artery](http://purl.obolibrary.org/obo/CL_1000413) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [lung connective tissue](http://purl.obolibrary.org/obo/UBERON_0000114) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) -### endothelial cell of coronary artery `http://purl.obolibrary.org/obo/CL_2000018` +### lung endothelium `http://purl.obolibrary.org/obo/UBERON_0013479` #### Added -- [endothelial cell of coronary artery](http://purl.obolibrary.org/obo/CL_2000018) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [lung endothelium](http://purl.obolibrary.org/obo/UBERON_0013479) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) -### endothelial cell of hepatic sinusoid `http://purl.obolibrary.org/obo/CL_1000398` +### lung epithelium `http://purl.obolibrary.org/obo/UBERON_0000115` +#### Removed +- [lung epithelium](http://purl.obolibrary.org/obo/UBERON_0000115) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "A pseudostratified epithelium, containing basal cells, stem cells of the airway, submucosal glands and cartilage rings, is limited to the trachea and large lobar airways in the mouse (Morrisey and Hogan, 2010). This more complex epithelium extends to terminal bronchioles in the human[DOI:10.1242/dev.115469]" -#### Added -- [endothelial cell of hepatic sinusoid](http://purl.obolibrary.org/obo/CL_1000398) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### endothelial cell of lymphatic vessel `http://purl.obolibrary.org/obo/CL_0002138` +### lung field `http://purl.obolibrary.org/obo/UBERON_0022361` #### Added -- [endothelial cell of lymphatic vessel](http://purl.obolibrary.org/obo/CL_0002138) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [lung field](http://purl.obolibrary.org/obo/UBERON_0022361) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -### endothelial cell of pericentral hepatic sinusoid `http://purl.obolibrary.org/obo/CL_0019022` +### lung mesenchyme `http://purl.obolibrary.org/obo/UBERON_0004883` +#### Removed +- [lung mesenchyme](http://purl.obolibrary.org/obo/UBERON_0004883) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) #### Added -- [endothelial cell of pericentral hepatic sinusoid](http://purl.obolibrary.org/obo/CL_0019022) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [lung mesenchyme](http://purl.obolibrary.org/obo/UBERON_0004883) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) -### endothelial cell of periportal hepatic sinusoid `http://purl.obolibrary.org/obo/CL_0019021` +### lung parenchyma `http://purl.obolibrary.org/obo/UBERON_0008946` #### Added -- [endothelial cell of periportal hepatic sinusoid](http://purl.obolibrary.org/obo/CL_0019021) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [lung parenchyma](http://purl.obolibrary.org/obo/UBERON_0008946) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) + +### lymph node `http://purl.obolibrary.org/obo/UBERON_0000029` +#### Removed +- [lymph node](http://purl.obolibrary.org/obo/UBERON_0000029) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Lymph nodes that are associated with the lymphatic system have evolved in mammals.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### endothelial cell of placenta `http://purl.obolibrary.org/obo/CL_0009092` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [endothelial cell of placenta](http://purl.obolibrary.org/obo/CL_0009092) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.630" -### endothelial cell of sinusoid `http://purl.obolibrary.org/obo/CL_0002262` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001273" -#### Added -- [endothelial cell of sinusoid](http://purl.obolibrary.org/obo/CL_0002262) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### endothelial cell of uterus `http://purl.obolibrary.org/obo/CL_0009095` +### lymph node follicle `http://purl.obolibrary.org/obo/UBERON_0010748` +#### Removed +- [lymph node follicle](http://purl.obolibrary.org/obo/UBERON_0010748) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [cortex of lymph node](http://purl.obolibrary.org/obo/UBERON_0002006) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "MP-def" + + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "issues/7" #### Added -- [endothelial cell of uterus](http://purl.obolibrary.org/obo/CL_0009095) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [lymph node follicle](http://purl.obolibrary.org/obo/UBERON_0010748) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [cortex of lymph node](http://purl.obolibrary.org/obo/UBERON_0002006) -### endothelial cell of vascular tree `http://purl.obolibrary.org/obo/CL_0002139` +### lymph vasculature `http://purl.obolibrary.org/obo/UBERON_0004536` +#### Removed +- [lymph vasculature](http://purl.obolibrary.org/obo/UBERON_0004536) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "TAO:0005105" -#### Added -- [endothelial cell of vascular tree](http://purl.obolibrary.org/obo/CL_0002139) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [lymph vasculature](http://purl.obolibrary.org/obo/UBERON_0004536) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A network of blunt ended vessels lacking direct connection to the blood vascular system. These vessels collect and drain fluids and macromolecules from interstitial spaces throughout the animal. They derive from a subpopulation of endothelial cells and have walls that are much thinner than the blood carrying vessels. Lymphatic vessels are usually classified as either superficial or deep.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -### endothelial cell of venule `http://purl.obolibrary.org/obo/CL_1000414` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -#### Added -- [endothelial cell of venule](http://purl.obolibrary.org/obo/CL_1000414) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005105" -### endothelial stalk cell `http://purl.obolibrary.org/obo/CL_0002671` -#### Added -- [endothelial stalk cell](http://purl.obolibrary.org/obo/CL_0002671) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### lymphatic part of lymphoid system `http://purl.obolibrary.org/obo/UBERON_0006558` +#### Removed +- [lymphatic part of lymphoid system](http://purl.obolibrary.org/obo/UBERON_0006558) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "lymporeticular" +- [lymphatic part of lymphoid system](http://purl.obolibrary.org/obo/UBERON_0006558) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in FMA this is part of the cardiovascular system, but here we treat the CV system as a separate component of the circulatory system from the lymphatic system" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" -### endothelial tip cell `http://purl.obolibrary.org/obo/CL_0000704` +- [lymphatic part of lymphoid system](http://purl.obolibrary.org/obo/UBERON_0006558) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Part of the circulatory system which consists of a series of vessels which collect blood (exclusive of erythrocytes) which seep through capillary walls and return it to the veins.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -#### Added -- [endothelial tip cell](http://purl.obolibrary.org/obo/CL_0000704) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010522" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### endovascular extravillous trophoblast cell `http://purl.obolibrary.org/obo/CL_4033063` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" -#### Added -- [endovascular extravillous trophoblast cell](http://purl.obolibrary.org/obo/CL_4033063) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "endovascular extravillous trophoblast" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37630754" -- [endovascular extravillous trophoblast cell](http://purl.obolibrary.org/obo/CL_4033063) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) -- [endovascular extravillous trophoblast cell](http://purl.obolibrary.org/obo/CL_4033063) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Shortly after implantation, the endovascular extravillous trophoblast cells occlude the maternal spiral arteries, preventing premature oxygen delivery to the placental villi and reducing fetal oxidative stress." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37630754" +### lymphatic vessel `http://purl.obolibrary.org/obo/UBERON_0001473` +#### Removed +- [lymphatic vessel](http://purl.obolibrary.org/obo/UBERON_0001473) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D042601" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -- [endovascular extravillous trophoblast cell](http://purl.obolibrary.org/obo/CL_4033063) [date](http://purl.org/dc/terms/date) "2024-01-08T15:43:32Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +- [lymphatic vessel](http://purl.obolibrary.org/obo/UBERON_0001473) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A network of blunt ended vessels lacking direct connection to the blood vascular system. These vessels collect and drain fluids and macromolecules from interstitial spaces throughout the animal. They derive from a subpopulation of endothelial cells and have walls that are much thinner than the blood carrying vessels. Lymphatic vessels are usually classified as either superficial or deep.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -- [endovascular extravillous trophoblast cell](http://purl.obolibrary.org/obo/CL_4033063) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A trophoblast cell that invades the maternal spiral arteries and replace the endothelial lining, remodeling the vessels and allowing for adequate blood transport into the placenta. An endovascular extravillous trophoblast cell differentiates from an extravillous trophoblast cell. In humans, this cell can be distinguished by the expression of CD56." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37630754" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.1007/978-3-030-84725-8" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -- [endovascular extravillous trophoblast cell](http://purl.obolibrary.org/obo/CL_4033063) [label](http://www.w3.org/2000/01/rdf-schema#label) "endovascular extravillous trophoblast cell" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005105" -- [endovascular extravillous trophoblast cell](http://purl.obolibrary.org/obo/CL_4033063) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "endovascular trophoblast" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:11337369" +- [lymphatic vessel](http://purl.obolibrary.org/obo/UBERON_0001473) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A vessel that contains or conveys lymph.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" -- [endovascular extravillous trophoblast cell](http://purl.obolibrary.org/obo/CL_4033063) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "eEVT" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37630754" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0011005" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [abbreviation](http://purl.obolibrary.org/obo/OMO_0003000) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -- Class: [endovascular extravillous trophoblast cell](http://purl.obolibrary.org/obo/CL_4033063) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -- [endovascular extravillous trophoblast cell](http://purl.obolibrary.org/obo/CL_4033063) SubClassOf [trophoblast cell](http://purl.obolibrary.org/obo/CL_0000351) +- [lymphatic vessel](http://purl.obolibrary.org/obo/UBERON_0001473) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "TAO:0005105" -- [endovascular extravillous trophoblast cell](http://purl.obolibrary.org/obo/CL_4033063) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [extravillous trophoblast](http://purl.obolibrary.org/obo/CL_0008036) +- [lymphatic vessel](http://purl.obolibrary.org/obo/UBERON_0001473) [RO_0002174](http://purl.obolibrary.org/obo/RO_0002174) [NCBITaxon_8342](http://purl.obolibrary.org/obo/NCBITaxon_8342) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1152/japplphysiol.00201.2013" +- [lymphatic vessel](http://purl.obolibrary.org/obo/UBERON_0001473) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Tetrapods have evolved distinct lymphatic systems, in which lymphatic capillaries help drain most of the tissues of the body.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### enteric ganglion `http://purl.obolibrary.org/obo/UBERON_0001809` -#### Removed -- [enteric ganglion](http://purl.obolibrary.org/obo/UBERON_0001809) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Enteric_ganglia" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.627" -### enteric neuron `http://purl.obolibrary.org/obo/CL_0007011` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001249" -#### Added -- [enteric neuron](http://purl.obolibrary.org/obo/CL_0007011) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### enteric plexus `http://purl.obolibrary.org/obo/UBERON_0000429` +### lymphatic vessel endothelium `http://purl.obolibrary.org/obo/UBERON_0002042` #### Removed -- [enteric plexus](http://purl.obolibrary.org/obo/UBERON_0000429) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "plexus nervosus entericus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:77597" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" - -#### Added -- [enteric plexus](http://purl.obolibrary.org/obo/UBERON_0000429) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "plexus nervosus entericus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [lymphatic vessel endothelium](http://purl.obolibrary.org/obo/UBERON_0002042) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The vascular endothelium that lines the lymph vessels.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:77597" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005258" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -### enteric smooth muscle cell `http://purl.obolibrary.org/obo/CL_0002504` -#### Added -- [enteric smooth muscle cell](http://purl.obolibrary.org/obo/CL_0002504) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### lymphocyte antigen 75 `http://purl.obolibrary.org/obo/PR_000001026` +#### Removed +- [lymphocyte antigen 75](http://purl.obolibrary.org/obo/PR_000001026) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [lymphocyte antigen 75 (human)](http://purl.obolibrary.org/obo/PR_000034294) -### enterocyte `http://purl.obolibrary.org/obo/CL_0000584` -#### Added -- [enterocyte](http://purl.obolibrary.org/obo/CL_0000584) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### lymphoid system `http://purl.obolibrary.org/obo/UBERON_0002465` +#### Removed +- [lymphoid system](http://purl.obolibrary.org/obo/UBERON_0002465) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "We follow FMA and MA in distinguishing between lymphatic system and lymphoid system, with lymhoid tissue part of the non-lymphatic component, although these terms are often used interchangeably. We assume the ZFA term lymphatic tissue actually corresponds to the broader class (e.g. ZFA lymph node in the ZFA lymphatic system). See tracker for more comments." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "https://github.com/obophenotype/mouse-anatomy-ontology/issues/51" -### enterocyte of colon `http://purl.obolibrary.org/obo/CL_1000347` +- [lymphoid system](http://purl.obolibrary.org/obo/UBERON_0002465) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "lymphoid" -#### Added -- [enterocyte of colon](http://purl.obolibrary.org/obo/CL_1000347) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [lymphoid system](http://purl.obolibrary.org/obo/UBERON_0002465) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Part of the circulatory system which consists of a series of vessels which collect blood (exclusive of erythrocytes) which seep through capillary walls and return it to the veins.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010522" -### enterocyte of epithelium of large intestine `http://purl.obolibrary.org/obo/CL_0002071` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -#### Added -- [enterocyte of epithelium of large intestine](http://purl.obolibrary.org/obo/CL_0002071) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" +- [lymphoid system](http://purl.obolibrary.org/obo/UBERON_0002465) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The lymphatic systems of reptiles and some birds have lymph hearts, and both groups have extensive lymph vessels, but their functional role in both lymph movement and plasma volume homeostasis is almost completely unknown [10.1152/japplphysiol.00201.2013]" -### enterocyte of epithelium of small intestine `http://purl.obolibrary.org/obo/CL_1000334` +- [lymphoid system](http://purl.obolibrary.org/obo/UBERON_0002465) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The lymphatic system of anuran amphibians is characterized by large lymphatic sacs and two pairs of lymph hearts that return lymph into the venous circulation but no lymph vessels per se [10.1152/japplphysiol.00201.2013]" -#### Added -- [enterocyte of epithelium of small intestine](http://purl.obolibrary.org/obo/CL_1000334) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [lymphoid system](http://purl.obolibrary.org/obo/UBERON_0002465) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Tetrapods have evolved distinct lymphatic systems, in which lymphatic capillaries help drain most of the tissues of the body.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000842" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### enterocyte of epithelium proper of ileum `http://purl.obolibrary.org/obo/CL_1000342` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [enterocyte of epithelium proper of ileum](http://purl.obolibrary.org/obo/CL_1000342) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.627" -### enteroendocrine cell `http://purl.obolibrary.org/obo/CL_0000164` -#### Added -- [enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000164) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### lymphoid tissue `http://purl.obolibrary.org/obo/UBERON_0001744` +#### Removed +- [lymphoid tissue](http://purl.obolibrary.org/obo/UBERON_0001744) [RO_0002174](http://purl.obolibrary.org/obo/RO_0002174) [Gnathostomata ](http://purl.obolibrary.org/obo/NCBITaxon_7776) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "lampreys lack organized lymphoid tissue" -### enteroendocrine cell of colon `http://purl.obolibrary.org/obo/CL_0009042` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "NCBIBook:NBK27108" -#### Added -- [enteroendocrine cell of colon](http://purl.obolibrary.org/obo/CL_0009042) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### enteroendocrine cell of small intestine `http://purl.obolibrary.org/obo/CL_0009006` +### lysosome-associated membrane glycoprotein 5 `http://purl.obolibrary.org/obo/PR_000032148` +#### Removed +- [lysosome-associated membrane glycoprotein 5](http://purl.obolibrary.org/obo/PR_000032148) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [lysosome-associated membrane glycoprotein 5 (human)](http://purl.obolibrary.org/obo/PR_Q9UJQ1) -#### Added -- [enteroendocrine cell of small intestine](http://purl.obolibrary.org/obo/CL_0009006) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### enucleate erythrocyte `http://purl.obolibrary.org/obo/CL_0000595` +### macrophage colony-stimulating factor 1 receptor `http://purl.obolibrary.org/obo/PR_000002062` +#### Removed +- [macrophage colony-stimulating factor 1 receptor](http://purl.obolibrary.org/obo/PR_000002062) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [macrophage colony-stimulating factor 1 receptor (human)](http://purl.obolibrary.org/obo/PR_P07333) -#### Added -- [enucleate erythrocyte](http://purl.obolibrary.org/obo/CL_0000595) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### enucleated reticulocyte `http://purl.obolibrary.org/obo/CL_0002422` +### macrophage mannose receptor 1 `http://purl.obolibrary.org/obo/PR_000002972` +#### Removed +- [macrophage mannose receptor 1](http://purl.obolibrary.org/obo/PR_000002972) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [macrophage mannose receptor 1 (human)](http://purl.obolibrary.org/obo/PR_P22897) -#### Added -- [enucleated reticulocyte](http://purl.obolibrary.org/obo/CL_0002422) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### eosinophil `http://purl.obolibrary.org/obo/CL_0000771` +### macrophage receptor MARCO `http://purl.obolibrary.org/obo/PR_000001884` +#### Removed +- [macrophage receptor MARCO](http://purl.obolibrary.org/obo/PR_000001884) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [macrophage receptor MARCO (human)](http://purl.obolibrary.org/obo/PR_Q9UEW3) -#### Added -- [eosinophil](http://purl.obolibrary.org/obo/CL_0000771) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### ependymal cell `http://purl.obolibrary.org/obo/CL_0000065` +### macrophage scavenger receptor types I and II `http://purl.obolibrary.org/obo/PR_000001885` +#### Removed +- [macrophage scavenger receptor types I and II](http://purl.obolibrary.org/obo/PR_000001885) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [macrophage scavenger receptor types I and II (human)](http://purl.obolibrary.org/obo/PR_P21757) -#### Added -- [ependymal cell](http://purl.obolibrary.org/obo/CL_0000065) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### epiblast (generic) `http://purl.obolibrary.org/obo/UBERON_0002532` +### macrosialin `http://purl.obolibrary.org/obo/PR_000002064` #### Removed -- [epiblast (generic)](http://purl.obolibrary.org/obo/UBERON_0002532) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "epiblastus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Epiblast" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - -#### Added -- [epiblast (generic)](http://purl.obolibrary.org/obo/UBERON_0002532) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "epiblastus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [macrosialin](http://purl.obolibrary.org/obo/PR_000002064) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [macrosialin (human)](http://purl.obolibrary.org/obo/PR_P34810) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Epiblast" -### epibranchial ganglion `http://purl.obolibrary.org/obo/UBERON_0009127` +### macula `http://purl.obolibrary.org/obo/UBERON_0000054` #### Removed -- [epibranchial ganglion](http://purl.obolibrary.org/obo/UBERON_0009127) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006250" - - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0003-4423-4370" +- [macula](http://purl.obolibrary.org/obo/UBERON_0000054) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "macular" -#### Added -- [epibranchial ganglion](http://purl.obolibrary.org/obo/UBERON_0009127) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006250" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [macula](http://purl.obolibrary.org/obo/UBERON_0000054) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Patches of thickened, pseudostratified epithelium of the inner ear, consisting of regular arrays of sensory hair cells interspersed with supporting cells. Each patch has its own charcteristic shape and polarity pattern. (See Anatomical Atlas entry for sensory patches of the ear by T. Whitfield.)[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000386" - - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -### epicardial adipocyte `http://purl.obolibrary.org/obo/CL_1000309` +- [macula](http://purl.obolibrary.org/obo/UBERON_0000054) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "this refers to the inner ear structure, not the macula of the retina. We follow ZFA in including a grouping class for the macula of utricle and sacule" #### Added -- [epicardial adipocyte](http://purl.obolibrary.org/obo/CL_1000309) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [macula](http://purl.obolibrary.org/obo/UBERON_0000054) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### epicranial aponeurosis `http://purl.obolibrary.org/obo/UBERON_0006661` +### macula densa `http://purl.obolibrary.org/obo/UBERON_0002335` #### Removed -- [epicranial aponeurosis](http://purl.obolibrary.org/obo/UBERON_0006661) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "galea aponeurotica; aponeurosis epicranialis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Galea_aponeurotica" +- [macula densa](http://purl.obolibrary.org/obo/UBERON_0002335) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "not part of a nephron or distal tubule in MA and FMA" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [epicranial aponeurosis](http://purl.obolibrary.org/obo/UBERON_0006661) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "aponeurosis epicranialis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:46768" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### macula lutea `http://purl.obolibrary.org/obo/UBERON_0000053` #### Added -- [epicranial aponeurosis](http://purl.obolibrary.org/obo/UBERON_0006661) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "aponeurosis epicranialis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:46768" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" - -- [epicranial aponeurosis](http://purl.obolibrary.org/obo/UBERON_0006661) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "galea aponeurotica; aponeurosis epicranialis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [macula lutea](http://purl.obolibrary.org/obo/UBERON_0000053) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Galea_aponeurotica" +### male genital duct `http://purl.obolibrary.org/obo/UBERON_0006947` +#### Removed +- [male genital duct](http://purl.obolibrary.org/obo/UBERON_0006947) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in FMA includes as parts: seminal vesicle, efferent ductule (vas efferentia), epididymis, deferent duct (vas deferens), ejaculatory duct" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" -### epidermal Langerhans cell `http://purl.obolibrary.org/obo/CL_0002457` +- [male genital duct](http://purl.obolibrary.org/obo/UBERON_0006947) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "we use this as a generic grouping class for a number of taxa" -#### Added -- [epidermal Langerhans cell](http://purl.obolibrary.org/obo/CL_0002457) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### epidermal cell `http://purl.obolibrary.org/obo/CL_0000362` +### male organism `http://purl.obolibrary.org/obo/UBERON_0003101` +#### Removed +- [male organism](http://purl.obolibrary.org/obo/UBERON_0003101) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007004" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -#### Added -- [epidermal cell](http://purl.obolibrary.org/obo/CL_0000362) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### epidural space `http://purl.obolibrary.org/obo/UBERON_0003691` +### male reproductive system `http://purl.obolibrary.org/obo/UBERON_0000079` #### Removed -- [epidural space](http://purl.obolibrary.org/obo/UBERON_0003691) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "spatium epidurale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Epidural_space" +- [male reproductive system](http://purl.obolibrary.org/obo/UBERON_0000079) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004927" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [male reproductive system](http://purl.obolibrary.org/obo/UBERON_0000079) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [epidural space](http://purl.obolibrary.org/obo/UBERON_0003691) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "spatium extradurale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71228" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0792383369 Lombardi J, Comparative vertebrate reproduction (1998) p.43" -- [epidural space](http://purl.obolibrary.org/obo/UBERON_0003691) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cavum epidurale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Epidural_space" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000725" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [epidural space](http://purl.obolibrary.org/obo/UBERON_0003691) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cavum extradurale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Epidural_space" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### male urethral meatus `http://purl.obolibrary.org/obo/UBERON_0012241` +#### Removed +- [male urethral meatus](http://purl.obolibrary.org/obo/UBERON_0012241) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The external urethral orifice is the external opening or meatus of the urethra, normally placed at the tip of glans penis; it presents as a vertical slit, possibly bounded on either side by two small labia-like projections, In some cases the slit may be more rounded. This occurs naturally in some males and may also be a side effect of excess skin removal during circumcision. Congenital misplacement of the urethral orifice is called hypospadias when it is located in the underside (ventral aspect) of the penis, and epispadias when located in the dorsum (upper aspect). Improper shaping of the meatus can result in meatal stenosis." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:External_urethral_orifice_(male)" -#### Added -- [epidural space](http://purl.obolibrary.org/obo/UBERON_0003691) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "spatium extradurale" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71228" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### mammalian vulva `http://purl.obolibrary.org/obo/UBERON_0000997` +#### Removed +- [mammalian vulva](http://purl.obolibrary.org/obo/UBERON_0000997) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The external genital organs of the female, including the labia majora, labia minora, clitoris, and vestibule of the vagina. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [epidural space](http://purl.obolibrary.org/obo/UBERON_0003691) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "spatium epidurale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Epidural_space" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [epidural space](http://purl.obolibrary.org/obo/UBERON_0003691) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cavum extradurale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Epidural_space" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001458" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/vulva" -- [epidural space](http://purl.obolibrary.org/obo/UBERON_0003691) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cavum epidurale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Epidural_space" +- [mammalian vulva](http://purl.obolibrary.org/obo/UBERON_0000997) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "vulval" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### epinephrine binding `http://purl.obolibrary.org/obo/GO_0051379` +### mammary bud `http://purl.obolibrary.org/obo/UBERON_0005333` #### Removed -- [epinephrine binding](http://purl.obolibrary.org/obo/GO_0051379) SubClassOf [binding](http://purl.obolibrary.org/obo/GO_0005488) - -#### Added -- [epinephrine binding](http://purl.obolibrary.org/obo/GO_0051379) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/geneontology/go-ontology/issues/21211"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) +- [mammary bud](http://purl.obolibrary.org/obo/UBERON_0005333) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "produced along the length of the embryonic mammary ridge these buds represent the future locations of the mammary glands. Invagination of ectoderm at each bud leads to the development of epithelial diverticula, later maturing as lactiferous ducts" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/mammary+bud" -- [epinephrine binding](http://purl.obolibrary.org/obo/GO_0051379) SubClassOf [hormone binding](http://purl.obolibrary.org/obo/GO_0042562) -### epithalamus `http://purl.obolibrary.org/obo/UBERON_0001899` +### mammary gland `http://purl.obolibrary.org/obo/UBERON_0001911` #### Removed -- [epithalamus](http://purl.obolibrary.org/obo/UBERON_0001899) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "epithalamus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Epithalamus" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [mammary gland](http://purl.obolibrary.org/obo/UBERON_0001911) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The detailed similarities of mammary glands in living monotremes, marsupials, and eutherians argue for a monophyletic origin of these glands, perhaps by the combination of parts of preexisting sebaceous and sweat glands.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [epithalamus](http://purl.obolibrary.org/obo/UBERON_0001899) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "epithalamus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Epithalamus" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.224" -### epithelial cell `http://purl.obolibrary.org/obo/CL_0000066` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000398" -#### Added -- [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [mammary gland](http://purl.obolibrary.org/obo/UBERON_0001911) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The mammary glands of humans are in the thoracid/breast region. In other mammals they may be located elsewhere on the mammary ridges." +- [mammary gland](http://purl.obolibrary.org/obo/UBERON_0001911) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "The BTO class represents the combination of nipple plus lobe" -### epithelial cell of alveolus of lung `http://purl.obolibrary.org/obo/CL_0010003` +- [mammary gland](http://purl.obolibrary.org/obo/UBERON_0001911) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "The MA class represents a composite structure, including the nipple, fat, connective tissue, smooth muscle as parts" -#### Added -- [epithelial cell of alveolus of lung](http://purl.obolibrary.org/obo/CL_0010003) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [mammary gland](http://purl.obolibrary.org/obo/UBERON_0001911) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "A mouse mammary gland contains a single duct or sinus, forming 5-10 secondary ducts" +- [mammary gland](http://purl.obolibrary.org/obo/UBERON_0001911) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "mammary" -### epithelial cell of esophagus `http://purl.obolibrary.org/obo/CL_0002252` +- [mammary gland](http://purl.obolibrary.org/obo/UBERON_0001911) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "The FMA class represents an individule lobe. The nipple is not a part" -#### Added -- [epithelial cell of esophagus](http://purl.obolibrary.org/obo/CL_0002252) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [mammary gland](http://purl.obolibrary.org/obo/UBERON_0001911) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Any of the milk-producing apocrine glands typically occurring in pairs in female mammals and consisting of lobes containing clusters of alveoli with a system of ducts to convey the milk to an external nipple or teat. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/mammary+gland" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### epithelial cell of exocrine pancreas `http://purl.obolibrary.org/obo/CL_1001433` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [epithelial cell of exocrine pancreas](http://purl.obolibrary.org/obo/CL_1001433) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000398" -### epithelial cell of glomerular capsule `http://purl.obolibrary.org/obo/CL_1000450` +- [mammary gland](http://purl.obolibrary.org/obo/UBERON_0001911) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The male Dayak fruit bat has lactating mammary glands" -#### Added -- [epithelial cell of glomerular capsule](http://purl.obolibrary.org/obo/CL_1000450) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### epithelial cell of lacrimal sac `http://purl.obolibrary.org/obo/CL_1000436` +### mammary gland alveolus `http://purl.obolibrary.org/obo/UBERON_0003214` #### Added -- [epithelial cell of lacrimal sac](http://purl.obolibrary.org/obo/CL_1000436) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [mammary gland alveolus](http://purl.obolibrary.org/obo/UBERON_0003214) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### epithelial cell of large intestine `http://purl.obolibrary.org/obo/CL_0002253` +### mammary gland connective tissue `http://purl.obolibrary.org/obo/UBERON_0003584` #### Added -- [epithelial cell of large intestine](http://purl.obolibrary.org/obo/CL_0002253) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [mammary gland connective tissue](http://purl.obolibrary.org/obo/UBERON_0003584) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + +### mammary gland cord `http://purl.obolibrary.org/obo/UBERON_0004182` +#### Removed +- [mammary gland cord](http://purl.obolibrary.org/obo/UBERON_0004182) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "in female mouse embryos, the primary mammary cord (aka 'mammary sprout') is formed between E15.5 and E16.5; once the primary cord reaches the adipocytes of the fat pad (around E16), it begins to branch in a characteristic dichotomous fashion to form the initial ductal tree" -### epithelial cell of lower respiratory tract `http://purl.obolibrary.org/obo/CL_0002632` +- [mammary gland cord](http://purl.obolibrary.org/obo/UBERON_0004182) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) -#### Added -- [epithelial cell of lower respiratory tract](http://purl.obolibrary.org/obo/CL_0002632) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### epithelial cell of lung `http://purl.obolibrary.org/obo/CL_0000082` +### mammary gland luminal epithelium `http://purl.obolibrary.org/obo/UBERON_0011950` #### Added -- [epithelial cell of lung](http://purl.obolibrary.org/obo/CL_0000082) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [mammary gland luminal epithelium](http://purl.obolibrary.org/obo/UBERON_0011950) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### epithelial cell of nephron `http://purl.obolibrary.org/obo/CL_1000449` +### mammary gland myoepithelium `http://purl.obolibrary.org/obo/UBERON_0006954` +#### Removed +- [mammary gland myoepithelium](http://purl.obolibrary.org/obo/UBERON_0006954) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "The cells of this structure are specialized epithelial cells that express smooth muscle-specific contractile and cytoskeletal properties; during lactation, MECs contract in response to oxytocin to generate the contractile force required for milk ejection; MECs are involved in all developmental stages of mammary gland morphogenesis, modulating proliferation and differentiation of luminal cells; they take part in the formation of extracellular matrix, synthesizing its components and secreting proteinases and their inhibitors; in addition, MECs are regarded as natural cancer suppressors: they secrete suppressor proteins limiting cancer growth, invasiveness, and neoangiogenesis; MECs are markedly resistant to malignant transformation and they are able to suppress the transformation of neighboring luminal cells[MP]" -#### Added -- [epithelial cell of nephron](http://purl.obolibrary.org/obo/CL_1000449) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### epithelial cell of prostate `http://purl.obolibrary.org/obo/CL_0002231` +### mammary gland smooth muscle `http://purl.obolibrary.org/obo/UBERON_0004235` #### Added -- [epithelial cell of prostate](http://purl.obolibrary.org/obo/CL_0002231) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [mammary gland smooth muscle](http://purl.obolibrary.org/obo/UBERON_0004235) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### epithelial cell of proximal tubule `http://purl.obolibrary.org/obo/CL_0002306` - -#### Added -- [epithelial cell of proximal tubule](http://purl.obolibrary.org/obo/CL_0002306) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### mammary placode `http://purl.obolibrary.org/obo/UBERON_0005311` +#### Removed +- [mammary placode](http://purl.obolibrary.org/obo/UBERON_0005311) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "in mouse, five pairs of symmetrically positioned mammary placodes (three thoracic and two inguinal) form at reproducible locations along the mammary line at E11.5; the individual pairs develop asynchronously and in a distinct order; pair 3 is first, followed by pair 4, then by pairs 1 and 5 (which develop together), and finally by pair 2; the orientation of placodal cells is not uniform, suggesting that placodes are formed by migration of cells from the mammary line; between E11.5 and E12.5, each mammary placode expands and invaginates into the underlying mesenchyme to form an early bulb-shaped mammary bud[MP]" -### epithelial cell of proximal tubule segment 1 `http://purl.obolibrary.org/obo/CL_4030009` -#### Added -- [epithelial cell of proximal tubule segment 1](http://purl.obolibrary.org/obo/CL_4030009) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### mammary ridge `http://purl.obolibrary.org/obo/UBERON_0008425` +#### Removed +- [mammary ridge](http://purl.obolibrary.org/obo/UBERON_0008425) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "The first manifestation of the mammary gland in many mammals is an elevated ridge or milk line, which then fragments into individual buds in specific regions lateral of the dorsal midline. After initial development of the milk lines they go into remission." +- [mammary ridge](http://purl.obolibrary.org/obo/UBERON_0008425) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "in mouse, mammary gland development begins shortly after mid-gestation (about E10.5); epidermal cells within the milk line become columnar and multilayered, defining a ridge that protrudes above and below the plane of the single-layered primitive epidermis or periderm; by E11.5, five pairs of lens-shaped placodes form along the mammary line at the site of each future nipple.[MP]" -### epithelial cell of proximal tubule segment 3 `http://purl.obolibrary.org/obo/CL_4030011` +- [mammary ridge](http://purl.obolibrary.org/obo/UBERON_0008425) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "These buds are either located in the thoracic region in primates, in the inguinal area in ungulates or along the entire length of the trunk in rodents and pigs. In humans, milk lines appear in the seventh week of embryonic development" -#### Added -- [epithelial cell of proximal tubule segment 3](http://purl.obolibrary.org/obo/CL_4030011) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### epithelial cell of small intestine `http://purl.obolibrary.org/obo/CL_0002254` +### mammillary body `http://purl.obolibrary.org/obo/UBERON_0002206` +#### Removed +- [mammillary body](http://purl.obolibrary.org/obo/UBERON_0002206) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002035](http://purl.obolibrary.org/obo/UBERON_0002035) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" -#### Added -- [epithelial cell of small intestine](http://purl.obolibrary.org/obo/CL_0002254) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [mammillary body](http://purl.obolibrary.org/obo/UBERON_0002206) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002706](http://purl.obolibrary.org/obo/UBERON_0002706) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" +- [mammillary body](http://purl.obolibrary.org/obo/UBERON_0002206) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0001935](http://purl.obolibrary.org/obo/UBERON_0001935) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" -### epithelial cell of stratum germinativum of esophagus `http://purl.obolibrary.org/obo/CL_1000447` +- [mammillary body](http://purl.obolibrary.org/obo/UBERON_0002206) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002634](http://purl.obolibrary.org/obo/UBERON_0002634) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" #### Added -- [epithelial cell of stratum germinativum of esophagus](http://purl.obolibrary.org/obo/CL_1000447) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [mammillary body](http://purl.obolibrary.org/obo/UBERON_0002206) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### epithelial cell of sweat gland `http://purl.obolibrary.org/obo/CL_1000448` +### mandibular nerve `http://purl.obolibrary.org/obo/UBERON_0000375` +#### Removed +- [mandibular nerve](http://purl.obolibrary.org/obo/UBERON_0000375) SubClassOf [nerve](http://purl.obolibrary.org/obo/UBERON_0001021) #### Added -- [epithelial cell of sweat gland](http://purl.obolibrary.org/obo/CL_1000448) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) - +- [mandibular nerve](http://purl.obolibrary.org/obo/UBERON_0000375) SubClassOf [nerve of head region](http://purl.obolibrary.org/obo/UBERON_0011779) -### epithelial cell of thymus `http://purl.obolibrary.org/obo/CL_0002293` -#### Added -- [epithelial cell of thymus](http://purl.obolibrary.org/obo/CL_0002293) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### mandibular symphysis `http://purl.obolibrary.org/obo/UBERON_0006606` +#### Removed +- [mandibular symphysis](http://purl.obolibrary.org/obo/UBERON_0006606) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "in snakes, the mandibular symphysis is composed of soft tissues, allowing independent movement of each mandible" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0073040584" +- [mandibular symphysis](http://purl.obolibrary.org/obo/UBERON_0006606) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Joint that articulates the left and right dentary bones. Mandibular symphysis is unpaired.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001851" -### epithelial cell of urethra `http://purl.obolibrary.org/obo/CL_1000296` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -#### Added -- [epithelial cell of urethra](http://purl.obolibrary.org/obo/CL_1000296) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TAO:wd" -### epithelial cell of uterus `http://purl.obolibrary.org/obo/CL_0002149` +- [mandibular symphysis](http://purl.obolibrary.org/obo/UBERON_0006606) SubClassOf [connects](http://purl.obolibrary.org/obo/RO_0002176) some [dentary](http://purl.obolibrary.org/obo/UBERON_0004742) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "connects adjacent mandibles" #### Added -- [epithelial cell of uterus](http://purl.obolibrary.org/obo/CL_0002149) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [mandibular symphysis](http://purl.obolibrary.org/obo/UBERON_0006606) SubClassOf [connects](http://purl.obolibrary.org/obo/RO_0002176) some [dentary](http://purl.obolibrary.org/obo/UBERON_0004742) -### epithelial fate stem cell `http://purl.obolibrary.org/obo/CL_0000036` +### manual acropodium region `http://purl.obolibrary.org/obo/UBERON_0012355` +#### Removed +- [manual acropodium region](http://purl.obolibrary.org/obo/UBERON_0012355) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "class refers to an entire limb segment, not just the bones" -#### Added -- [epithelial fate stem cell](http://purl.obolibrary.org/obo/CL_0000036) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### epithelial tube `http://purl.obolibrary.org/obo/UBERON_0003914` +### manual digit `http://purl.obolibrary.org/obo/UBERON_0002389` #### Removed -- [epithelial tube](http://purl.obolibrary.org/obo/UBERON_0003914) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007474" +- [manual digit](http://purl.obolibrary.org/obo/UBERON_0002389) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "One of the fingers of the manus.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" -#### Added -- [epithelial tube](http://purl.obolibrary.org/obo/UBERON_0003914) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007474" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000857" -### epithelium `http://purl.obolibrary.org/obo/UBERON_0000483` -#### Removed -- [epithelium](http://purl.obolibrary.org/obo/UBERON_0000483) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007005" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -#### Added -- [epithelium](http://purl.obolibrary.org/obo/UBERON_0000483) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007005" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### epithelium of lens `http://purl.obolibrary.org/obo/UBERON_0001803` +### manual digit bone `http://purl.obolibrary.org/obo/UBERON_0004249` #### Removed -- [epithelium of lens](http://purl.obolibrary.org/obo/UBERON_0001803) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "epithelium lentis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58871" +- [manual digit bone](http://purl.obolibrary.org/obo/UBERON_0004249) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" - -#### Added -- [epithelium of lens](http://purl.obolibrary.org/obo/UBERON_0001803) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "epithelium lentis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58871" +### manual digit digitopodial skeleton `http://purl.obolibrary.org/obo/UBERON_5102389` +#### Removed +- [manual digit digitopodial skeleton](http://purl.obolibrary.org/obo/UBERON_5102389) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "this class represents a series of phalanges plus a metapodial element. In comparative anatomy terminology we would call this a 'digit', but the label 'digit' is sometimes used to exclude metapodials and to include soft tissue. This series of elements is hypothesized to be homologous to radials." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### erythroblast `http://purl.obolibrary.org/obo/CL_0000765` +### manual digit epithelium `http://purl.obolibrary.org/obo/UBERON_0005227` #### Added -- [erythroblast](http://purl.obolibrary.org/obo/CL_0000765) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [manual digit epithelium](http://purl.obolibrary.org/obo/UBERON_0005227) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) -### erythrocyte `http://purl.obolibrary.org/obo/CL_0000232` +### manual digit mesenchyme `http://purl.obolibrary.org/obo/UBERON_0005257` #### Added -- [erythrocyte](http://purl.obolibrary.org/obo/CL_0000232) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [manual digit mesenchyme](http://purl.obolibrary.org/obo/UBERON_0005257) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### erythroid lineage cell `http://purl.obolibrary.org/obo/CL_0000764` +### manual digit plus metapodial segment `http://purl.obolibrary.org/obo/UBERON_5002389` +#### Removed +- [manual digit plus metapodial segment](http://purl.obolibrary.org/obo/UBERON_5002389) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "https://github.com/obophenotype/uberon/issues/458" -#### Added -- [erythroid lineage cell](http://purl.obolibrary.org/obo/CL_0000764) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### erythroid progenitor cell `http://purl.obolibrary.org/obo/CL_0000038` +### manual digitopodium bone `http://purl.obolibrary.org/obo/UBERON_0012358` +#### Removed +- [manual digitopodium bone](http://purl.obolibrary.org/obo/UBERON_0012358) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) [Skeleton-partonomy-Design-Pattern](https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern) -#### Added -- [erythroid progenitor cell](http://purl.obolibrary.org/obo/CL_0000038) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### erythroid progenitor cell, mammalian `http://purl.obolibrary.org/obo/CL_0001066` +### manual digitopodium region `http://purl.obolibrary.org/obo/UBERON_0012141` +#### Removed +- [manual digitopodium region](http://purl.obolibrary.org/obo/UBERON_0012141) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "some sources call this the acropodium. see https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod" -#### Added -- [erythroid progenitor cell, mammalian](http://purl.obolibrary.org/obo/CL_0001066) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### esophagus mucosa `http://purl.obolibrary.org/obo/UBERON_0002469` +### manus `http://purl.obolibrary.org/obo/UBERON_0002398` #### Removed -- [esophagus mucosa](http://purl.obolibrary.org/obo/UBERON_0002469) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D000071041" +- [manus](http://purl.obolibrary.org/obo/UBERON_0002398) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "manual" -- [esophagus mucosa](http://purl.obolibrary.org/obo/UBERON_0002469) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lamina muscularis mucosae oesophageae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:62996" +- [manus](http://purl.obolibrary.org/obo/UBERON_0002398) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "like all limb segments, this class encompasses both the unformed hand region of the embryo to the fully formed structure complete with skeleton" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [esophagus mucosa](http://purl.obolibrary.org/obo/UBERON_0002469) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa oesophageae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:62996" +### manus bone `http://purl.obolibrary.org/obo/UBERON_0005897` +#### Removed +- [manus bone](http://purl.obolibrary.org/obo/UBERON_0005897) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) + - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### manus connective tissue `http://purl.obolibrary.org/obo/UBERON_0003598` #### Added -- [esophagus mucosa](http://purl.obolibrary.org/obo/UBERON_0002469) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lamina muscularis mucosae oesophageae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:62996" +- [manus connective tissue](http://purl.obolibrary.org/obo/UBERON_0003598) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### manus joint `http://purl.obolibrary.org/obo/UBERON_0001489` +#### Removed +- [manus joint](http://purl.obolibrary.org/obo/UBERON_0001489) [UBPROP_0000202](http://purl.obolibrary.org/obo/UBPROP_0000202) [FMA_71345](http://purl.obolibrary.org/obo/FMA_71345) -- [esophagus mucosa](http://purl.obolibrary.org/obo/UBERON_0002469) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D000071041" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +### mapping_justification `https://w3id.org/sssom/mapping_justification` +#### Removed +- AnnotationProperty: [mapping_justification](https://w3id.org/sssom/mapping_justification) -- [esophagus mucosa](http://purl.obolibrary.org/obo/UBERON_0002469) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa oesophageae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:62996" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### mapping_provider `https://w3id.org/sssom/mapping_provider` +#### Removed +- AnnotationProperty: [mapping_provider](https://w3id.org/sssom/mapping_provider) -### establishment or maintenance of cell polarity `http://purl.obolibrary.org/obo/GO_0007163` + +### marginal zone of spleen `http://purl.obolibrary.org/obo/UBERON_0001251` #### Removed -- [establishment or maintenance of cell polarity](http://purl.obolibrary.org/obo/GO_0007163) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) +- [marginal zone of spleen](http://purl.obolibrary.org/obo/UBERON_0001251) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "WP says - (Some sources consider it to be the part of red pulp which borders on the white pulp, while other sources consider it to be neither red pulp nor white pulp.) - we use the adjacency relation here so it overlaps neither. FMA considers this an anatomical line." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" #### Added -- [establishment or maintenance of cell polarity](http://purl.obolibrary.org/obo/GO_0007163) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) +- [marginal zone of spleen](http://purl.obolibrary.org/obo/UBERON_0001251) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### ethmoid bone `http://purl.obolibrary.org/obo/UBERON_0001679` +### material anatomical entity `http://purl.obolibrary.org/obo/UBERON_0000465` #### Removed -- [ethmoid bone](http://purl.obolibrary.org/obo/UBERON_0001679) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "os ethmoidale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ethmoid" +- [material anatomical entity](http://purl.obolibrary.org/obo/UBERON_0000465) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007016" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:52740" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### maxillary artery `http://purl.obolibrary.org/obo/UBERON_0001616` +#### Removed +- [maxillary artery](http://purl.obolibrary.org/obo/UBERON_0001616) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "...1st pair undergoes partial regression, the remnants of which becomes part of the maxillary arteries" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://download.videohelp.com/vitualis/med/Vascular_Devt.html" -#### Added -- [ethmoid bone](http://purl.obolibrary.org/obo/UBERON_0001679) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "os ethmoidale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ethmoid" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:52740" +### maxillary nerve `http://purl.obolibrary.org/obo/UBERON_0000377` +#### Removed +- [maxillary nerve](http://purl.obolibrary.org/obo/UBERON_0000377) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: part_of trunk maxillary-mandibularis (AAO:0010669)[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010670" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### ethmoid foramen `http://purl.obolibrary.org/obo/UBERON_0018415` -#### Removed -- [ethmoid foramen](http://purl.obolibrary.org/obo/UBERON_0018415) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "foramina ethmoidalia" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [maxillary nerve](http://purl.obolibrary.org/obo/UBERON_0000377) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Medial ramus (sensory) of the trigeminal nerve.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" -#### Added -- [ethmoid foramen](http://purl.obolibrary.org/obo/UBERON_0018415) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "foramina ethmoidalia" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010670" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### eukaryotic cell `http://purl.obolibrary.org/obo/CL_0000255` +- [maxillary nerve](http://purl.obolibrary.org/obo/UBERON_0000377) SubClassOf [nerve](http://purl.obolibrary.org/obo/UBERON_0001021) #### Added -- [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [maxillary nerve](http://purl.obolibrary.org/obo/UBERON_0000377) SubClassOf [nerve of head region](http://purl.obolibrary.org/obo/UBERON_0011779) -### eurydendroid cell `http://purl.obolibrary.org/obo/CL_0000253` +### medial nasal prominence `http://purl.obolibrary.org/obo/UBERON_0004068` +#### Removed +- [medial nasal prominence](http://purl.obolibrary.org/obo/UBERON_0004068) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "Fusion of right and left medial nasal processes forms a primary palate rostrally and the nasal septum caudally. The incisive bone, including upper incisor teeth and the rostral up- per lip, are derived from the primary palate. The nasal septum consists of bone, cartilage, and a patch of soft tissue membrane that separates right & left halves of the nasal cavity." -#### Added -- [eurydendroid cell](http://purl.obolibrary.org/obo/CL_0000253) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### excretory duct `http://purl.obolibrary.org/obo/UBERON_0035050` +### medial zone of hypothalamus `http://purl.obolibrary.org/obo/UBERON_0002272` #### Added -- [excretory duct](http://purl.obolibrary.org/obo/UBERON_0035050) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006341" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" - - - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) +- [medial zone of hypothalamus](http://purl.obolibrary.org/obo/UBERON_0002272) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### excretory system `http://purl.obolibrary.org/obo/UBERON_8450002` +### median lingual swelling `http://purl.obolibrary.org/obo/UBERON_0006756` #### Removed -- [excretory system](http://purl.obolibrary.org/obo/UBERON_8450002) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006338" - - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0003-4423-4370" - -#### Added -- [excretory system](http://purl.obolibrary.org/obo/UBERON_8450002) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006338" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [median lingual swelling](http://purl.obolibrary.org/obo/UBERON_0006756) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1046/j.1469-7580.2002.00073.x" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### exhausted T cell `http://purl.obolibrary.org/obo/CL_0011025` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000730" -#### Added -- [exhausted T cell](http://purl.obolibrary.org/obo/CL_0011025) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### exocrine gland `http://purl.obolibrary.org/obo/UBERON_0002365` +### median preoptic nucleus `http://purl.obolibrary.org/obo/UBERON_0002625` #### Removed -- [exocrine gland](http://purl.obolibrary.org/obo/UBERON_0002365) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "glandula exocrina" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Exocrine_gland" +- [median preoptic nucleus](http://purl.obolibrary.org/obo/UBERON_0002625) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0007626](http://purl.obolibrary.org/obo/UBERON_0007626) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [median preoptic nucleus](http://purl.obolibrary.org/obo/UBERON_0002625) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002034](http://purl.obolibrary.org/obo/UBERON_0002034) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" -#### Added -- [exocrine gland](http://purl.obolibrary.org/obo/UBERON_0002365) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "glandula exocrina" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Exocrine_gland" +- [median preoptic nucleus](http://purl.obolibrary.org/obo/UBERON_0002625) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006168" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) -### exocrine pancreas `http://purl.obolibrary.org/obo/UBERON_0000017` -#### Removed -- [exocrine pancreas](http://purl.obolibrary.org/obo/UBERON_0000017) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D046790" +- [median preoptic nucleus](http://purl.obolibrary.org/obo/UBERON_0002625) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002689](http://purl.obolibrary.org/obo/UBERON_0002689) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" -#### Added -- [exocrine pancreas](http://purl.obolibrary.org/obo/UBERON_0000017) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D046790" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [median preoptic nucleus](http://purl.obolibrary.org/obo/UBERON_0002625) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [anteroventral periventricular nucleus](http://purl.obolibrary.org/obo/UBERON_0002690) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) +- [median preoptic nucleus](http://purl.obolibrary.org/obo/UBERON_0002625) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002219](http://purl.obolibrary.org/obo/UBERON_0002219) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +- [median preoptic nucleus](http://purl.obolibrary.org/obo/UBERON_0002625) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0001934](http://purl.obolibrary.org/obo/UBERON_0001934) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" -### external carotid artery `http://purl.obolibrary.org/obo/UBERON_0001070` -#### Removed -- [external carotid artery](http://purl.obolibrary.org/obo/UBERON_0001070) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria carotis externa" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:External_carotid_artery" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### mediastinal pleura `http://purl.obolibrary.org/obo/UBERON_0035431` #### Added -- [external carotid artery](http://purl.obolibrary.org/obo/UBERON_0001070) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria carotis externa" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:External_carotid_artery" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [mediastinal pleura](http://purl.obolibrary.org/obo/UBERON_0035431) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) -### external ectoderm `http://purl.obolibrary.org/obo/UBERON_0000076` +### mediastinum `http://purl.obolibrary.org/obo/UBERON_0003728` #### Removed -- [external ectoderm](http://purl.obolibrary.org/obo/UBERON_0000076) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006242" - - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0003-4423-4370" +- [mediastinum](http://purl.obolibrary.org/obo/UBERON_0003728) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "mediastinal" -#### Added -- [external ectoderm](http://purl.obolibrary.org/obo/UBERON_0000076) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006242" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" - - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) +### medium-wave-sensitive opsin `http://purl.obolibrary.org/obo/PR_000001224` +#### Removed +- [medium-wave-sensitive opsin](http://purl.obolibrary.org/obo/PR_000001224) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [medium-wave-sensitive opsin (human)](http://purl.obolibrary.org/obo/PR_000050522) -### external iliac artery `http://purl.obolibrary.org/obo/UBERON_0001308` -#### Removed -- [external iliac artery](http://purl.obolibrary.org/obo/UBERON_0001308) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria iliaca externa" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:External_iliac_artery" +### medulla oblongata `http://purl.obolibrary.org/obo/UBERON_0001896` +#### Removed +- [medulla oblongata](http://purl.obolibrary.org/obo/UBERON_0001896) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The posterior region of the brain that is continuous with the spinal cord. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-17, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [external iliac artery](http://purl.obolibrary.org/obo/UBERON_0001308) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria iliaca externa" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:External_iliac_artery" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000181" -### external iliac vein `http://purl.obolibrary.org/obo/UBERON_0001316` -#### Removed -- [external iliac vein](http://purl.obolibrary.org/obo/UBERON_0001316) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena iliaca externa" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:External_iliac_vein" +- [medulla oblongata](http://purl.obolibrary.org/obo/UBERON_0001896) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Posterior portion of the hindbrain which controls respiration, heartbeat, digestion, and swallowing as well as some locomotor responses.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010486" -#### Added -- [external iliac vein](http://purl.obolibrary.org/obo/UBERON_0001316) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena iliaca externa" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:External_iliac_vein" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" +- [medulla oblongata](http://purl.obolibrary.org/obo/UBERON_0001896) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Classical anatomical studies subdivided the vertebrate rhombencephalon into pons and medulla oblongata. (...) The medulla oblongata appears therefore as a tagma, that is, a group of segmental units (pseudorhombomeres, in this case) sharing some morphological and molecular characteristics, and in some aspects different from the segmental units present in adjoining brain regions, pons and spinal cord.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1016/j.ydbio.2008.08.017 Marin F, Aroca P, Puelles L, Hox gene colinear expression in the avian medulla oblongata is correlated with pseudorhombomeric domains. Developmental Biology (2008)" -### extracellular matrix `http://purl.obolibrary.org/obo/GO_0031012` -#### Removed -- [extracellular matrix](http://purl.obolibrary.org/obo/GO_0031012) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [extracellular matrix](http://purl.obolibrary.org/obo/GO_0031012) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### extracellular region `http://purl.obolibrary.org/obo/GO_0005576` -#### Removed -- [extracellular region](http://purl.obolibrary.org/obo/GO_0005576) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000181" #### Added -- [extracellular region](http://purl.obolibrary.org/obo/GO_0005576) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) +- [medulla oblongata](http://purl.obolibrary.org/obo/UBERON_0001896) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### extracellular space `http://purl.obolibrary.org/obo/GO_0005615` +### medulla of organ `http://purl.obolibrary.org/obo/UBERON_0000958` #### Removed -- [extracellular space](http://purl.obolibrary.org/obo/GO_0005615) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) +- [medulla of organ](http://purl.obolibrary.org/obo/UBERON_0000958) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "medullary" -#### Added -- [extracellular space](http://purl.obolibrary.org/obo/GO_0005615) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) +- [medulla of organ](http://purl.obolibrary.org/obo/UBERON_0000958) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "this class is used in a very general sense" -### extracellular structure organization `http://purl.obolibrary.org/obo/GO_0043062` -#### Removed -- [extracellular structure organization](http://purl.obolibrary.org/obo/GO_0043062) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) + +### medulla of thymus `http://purl.obolibrary.org/obo/UBERON_0002124` #### Added -- [extracellular structure organization](http://purl.obolibrary.org/obo/GO_0043062) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) +- [medulla of thymus](http://purl.obolibrary.org/obo/UBERON_0002124) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) -### extraembryonic membrane `http://purl.obolibrary.org/obo/UBERON_0005631` +### medullary ray `http://purl.obolibrary.org/obo/UBERON_0009883` #### Removed -- [extraembryonic membrane](http://purl.obolibrary.org/obo/UBERON_0005631) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D005321" - -#### Added -- [extraembryonic membrane](http://purl.obolibrary.org/obo/UBERON_0005631) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D005321" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [medullary ray](http://purl.obolibrary.org/obo/UBERON_0009883) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA says parenchyma, MP says cortex" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) +- [medullary ray](http://purl.obolibrary.org/obo/UBERON_0009883) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "Their name is potentially misleading -- the 'medullary' refers to their destination, not their location. They are located only in the renal cortex, and not in the renal medulla" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -### extraembryonic mesoderm `http://purl.obolibrary.org/obo/UBERON_0005728` +### melanopsin `http://purl.obolibrary.org/obo/PR_000001243` #### Removed -- [extraembryonic mesoderm](http://purl.obolibrary.org/obo/UBERON_0005728) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://www.ana.ed.ac.uk/database/humat/notes/extraemb/mesoder.htm" +- [melanopsin](http://purl.obolibrary.org/obo/PR_000001243) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [melanopsin (human)](http://purl.obolibrary.org/obo/PR_Q9UHM6) -### extraembryonic structure `http://purl.obolibrary.org/obo/UBERON_0000478` +### member of `http://purl.obolibrary.org/obo/RO_0002350` #### Removed -- [extraembryonic structure](http://purl.obolibrary.org/obo/UBERON_0000478) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005835" +- [member of](http://purl.obolibrary.org/obo/RO_0002350) [RO_0001900](http://purl.obolibrary.org/obo/RO_0001900) [RO_0001901](http://purl.obolibrary.org/obo/RO_0001901) -#### Added -- [extraembryonic structure](http://purl.obolibrary.org/obo/UBERON_0000478) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005835" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [member of](http://purl.obolibrary.org/obo/RO_0002350) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "is member of" +- [member of](http://purl.obolibrary.org/obo/RO_0002350) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) "SIO" -### extravillous trophoblast `http://purl.obolibrary.org/obo/CL_0008036` +- [member of](http://purl.obolibrary.org/obo/RO_0002350) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "member part of" -#### Added -- [extravillous trophoblast](http://purl.obolibrary.org/obo/CL_0008036) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [member of](http://purl.obolibrary.org/obo/RO_0002350) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "An organism that is a member of a population of organisms" -### eye `http://purl.obolibrary.org/obo/UBERON_0000970` + +### membrane bone `http://purl.obolibrary.org/obo/UBERON_0007842` #### Removed -- [eye](http://purl.obolibrary.org/obo/UBERON_0000970) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005162" +- [membrane bone](http://purl.obolibrary.org/obo/UBERON_0007842) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Bone element that arises as a result of intramembranous ossification.[VSAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070" -#### Added -- [eye](http://purl.obolibrary.org/obo/UBERON_0000970) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005162" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PSPUB:0000170" -### eye photoreceptor cell `http://purl.obolibrary.org/obo/CL_0000287` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000023" -#### Added -- [eye photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000287) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" +- [membrane bone](http://purl.obolibrary.org/obo/UBERON_0007842) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Intramembranous bone that forms deep in the organism.[TAO]" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -### eye trabecular meshwork `http://purl.obolibrary.org/obo/UBERON_0005969` -#### Removed -- [eye trabecular meshwork](http://purl.obolibrary.org/obo/UBERON_0005969) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "reticulum trabeculare sclerae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Trabecular_meshwork" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TAO:wd" -#### Added -- [eye trabecular meshwork](http://purl.obolibrary.org/obo/UBERON_0005969) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "reticulum trabeculare sclerae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001645" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Trabecular_meshwork" -### face `http://purl.obolibrary.org/obo/UBERON_0001456` +### membranous labyrinth `http://purl.obolibrary.org/obo/UBERON_0001849` #### Removed -- [face](http://purl.obolibrary.org/obo/UBERON_0001456) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "facia/facies" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Face" +- [membranous labyrinth](http://purl.obolibrary.org/obo/UBERON_0001849) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:17815" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [membranous labyrinth](http://purl.obolibrary.org/obo/UBERON_0001849) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The labyrinth, or inner ear, evolved very early in vertebrate history and, with many variations in configuration but none of basic design and function, has been retained by all vertebrates.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [face](http://purl.obolibrary.org/obo/UBERON_0001456) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "facia/facies" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Face" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000729" -### facial artery `http://purl.obolibrary.org/obo/UBERON_0001612` -#### Removed -- [facial artery](http://purl.obolibrary.org/obo/UBERON_0001612) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria maxillaris externa" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Facial_artery" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.366" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [membranous labyrinth](http://purl.obolibrary.org/obo/UBERON_0001849) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A system of communicating epithelial sacs and ducts within the bony labyrinth, containing the endolymph. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [facial artery](http://purl.obolibrary.org/obo/UBERON_0001612) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria maxillaris externa" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Facial_artery" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/membranous+labyrinth" -### facial bone `http://purl.obolibrary.org/obo/UBERON_0003462` -#### Removed -- [facial bone](http://purl.obolibrary.org/obo/UBERON_0003462) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D005147" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000729" + +- [membranous labyrinth](http://purl.obolibrary.org/obo/UBERON_0001849) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "inner ear has parts membranous and osseuous/bony labyrinth. it's not clear where the EMAPA term 'labyrinth' belong, we place them here for now" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EMAPA" #### Added -- [facial bone](http://purl.obolibrary.org/obo/UBERON_0003462) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D005147" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [membranous labyrinth](http://purl.obolibrary.org/obo/UBERON_0001849) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +### membranous layer `http://purl.obolibrary.org/obo/UBERON_0000158` +#### Removed +- [membranous layer](http://purl.obolibrary.org/obo/UBERON_0000158) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A thin sheet or layer of pliable tissue, serving as a covering or envelope of a part, as the lining of a cavity, as a partition or septum, or to connect two structures." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ncithesaurus:Membrane" + -### facial muscle `http://purl.obolibrary.org/obo/UBERON_0001577` +### meningeal cluster `http://purl.obolibrary.org/obo/UBERON_0010743` #### Removed -- [facial muscle](http://purl.obolibrary.org/obo/UBERON_0001577) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "musculi faciei" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Facial_muscles" +- [meningeal cluster](http://purl.obolibrary.org/obo/UBERON_0010743) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:32660" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [meningeal cluster](http://purl.obolibrary.org/obo/UBERON_0010743) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "meningeal" -#### Added -- [facial muscle](http://purl.obolibrary.org/obo/UBERON_0001577) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "musculi faciei" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Facial_muscles" +- [meningeal cluster](http://purl.obolibrary.org/obo/UBERON_0010743) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In some primitive organisms, the meningeal cluster includes only the primitive meninx" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### facial nerve `http://purl.obolibrary.org/obo/UBERON_0001647` +### meningeal macrophage `http://purl.obolibrary.org/obo/CL_0000879` #### Removed -- [facial nerve](http://purl.obolibrary.org/obo/UBERON_0001647) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus facialis [vii]" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [meningeal macrophage](http://purl.obolibrary.org/obo/CL_0000879) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A central nervous system macrophage found in the meninges (the three membranes that surround the brain). This macrophage types is highly phagocytic and expresses scavenger receptors." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:11591794" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO_REF:0000031" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:50868" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:ana" -- [facial nerve](http://purl.obolibrary.org/obo/UBERON_0001647) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nervus facialis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Facial_nerve" +- [meningeal macrophage](http://purl.obolibrary.org/obo/CL_0000879) EquivalentTo [central nervous system macrophage](http://purl.obolibrary.org/obo/CL_0000878) and ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [meninx](http://purl.obolibrary.org/obo/UBERON_0002360)) and ([capable of](http://purl.obolibrary.org/obo/RO_0002215) some [scavenger receptor activity](http://purl.obolibrary.org/obo/GO_0005044)) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [meningeal macrophage](http://purl.obolibrary.org/obo/CL_0000879) SubClassOf [central nervous system macrophage](http://purl.obolibrary.org/obo/CL_0000878) + - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true" #### Added -- [facial nerve](http://purl.obolibrary.org/obo/UBERON_0001647) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus facialis [vii]" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [meningeal macrophage](http://purl.obolibrary.org/obo/CL_0000879) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "MnMΦ" + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [abbreviation](http://purl.obolibrary.org/obo/OMO_0003000) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:50868" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38347231" -- [facial nerve](http://purl.obolibrary.org/obo/UBERON_0001647) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nervus facialis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [meningeal macrophage](http://purl.obolibrary.org/obo/CL_0000879) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "subdural leptomeningeal macrophage" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33556248" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Facial_nerve" +- [meningeal macrophage](http://purl.obolibrary.org/obo/CL_0000879) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "sdΜΦ" + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [abbreviation](http://purl.obolibrary.org/obo/OMO_0003000) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37232741" -### facial nerve canal `http://purl.obolibrary.org/obo/UBERON_0018413` -#### Removed -- [facial nerve canal](http://purl.obolibrary.org/obo/UBERON_0018413) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "canalis nervi facialis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:54952" +- [meningeal macrophage](http://purl.obolibrary.org/obo/CL_0000879) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A border associated macrophage that is part of a meninx. This macrophage type is elongated and amoeboid spindle-shaped with limited mobility. This macrophage is highly phagocytic, expresses scavenger receptors, has dynamic protrusions and extends its processes during inflammation." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:24078900" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:11591794" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO_REF:0000031" -#### Added -- [facial nerve canal](http://purl.obolibrary.org/obo/UBERON_0018413) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "canalis nervi facialis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:54952" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:ana" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37232741" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [meningeal macrophage](http://purl.obolibrary.org/obo/CL_0000879) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "subdural meningeal macrophage" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:28323268" +- [meningeal macrophage](http://purl.obolibrary.org/obo/CL_0000879) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "MM" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33556248" -### facial nerve root `http://purl.obolibrary.org/obo/UBERON_0004674` -#### Removed -- [facial nerve root](http://purl.obolibrary.org/obo/UBERON_0004674) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "fibrae nervi facialis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:53418" + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [abbreviation](http://purl.obolibrary.org/obo/OMO_0003000) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [meningeal macrophage](http://purl.obolibrary.org/obo/CL_0000879) EquivalentTo [border associated macrophage](http://purl.obolibrary.org/obo/CL_4042003) and ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [meninx](http://purl.obolibrary.org/obo/UBERON_0002360)) and ([capable of](http://purl.obolibrary.org/obo/RO_0002215) some [scavenger receptor activity](http://purl.obolibrary.org/obo/GO_0005044)) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [meningeal macrophage](http://purl.obolibrary.org/obo/CL_0000879) SubClassOf [border associated macrophage](http://purl.obolibrary.org/obo/CL_4042003) -#### Added -- [facial nerve root](http://purl.obolibrary.org/obo/UBERON_0004674) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "fibrae nervi facialis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:53418" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### meningeal vein `http://purl.obolibrary.org/obo/UBERON_0018251` +#### Removed +- [meningeal vein](http://purl.obolibrary.org/obo/UBERON_0018251) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In humans, any of several veins that accompany the meningeal arteries, communicate with the sinuses of the dura mater and diploic veins, and drain into the regional veins outside the cranial vault." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### facial skeleton `http://purl.obolibrary.org/obo/UBERON_0011156` +### meninx `http://purl.obolibrary.org/obo/UBERON_0002360` #### Removed -- [facial skeleton](http://purl.obolibrary.org/obo/UBERON_0011156) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ossa faciei" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Facial_skeleton" +- [meninx](http://purl.obolibrary.org/obo/UBERON_0002360) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EV:0100312" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [meninx](http://purl.obolibrary.org/obo/UBERON_0002360) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Whereas cyclostomes and fishes only have a single envelope called the primitive meninx, amphibians have two layers, consisting of an outer dura mater which is extremely dense and protective, and a pia-arachnoid or secondary meninx which is more delicate and vascular. Mammals have three meninges: pia mater (which follows all the convolutions of the brain and is the most interior), the arachnoid layer (which is delicate and sends strands to the pia mater), and the dura mater (the outer, more protective meninx)." -- [facial skeleton](http://purl.obolibrary.org/obo/UBERON_0011156) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ossa facialia" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Facial_skeleton" +- [meninx](http://purl.obolibrary.org/obo/UBERON_0002360) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "Not consider part of the CNS/neuraxis in FMA" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [see also](http://www.w3.org/2000/01/rdf-schema#seeAlso) "https://github.com/obophenotype/uberon/issues/1261" -#### Added -- [facial skeleton](http://purl.obolibrary.org/obo/UBERON_0011156) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ossa faciei" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Facial_skeleton" +- [meninx](http://purl.obolibrary.org/obo/UBERON_0002360) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Membrane covering the brain and spinal cord. It is represented by a single layer in fishes, two in amphibians, reptiles and birds and three in mammals (named dura mater, arachnoid and pia mater). [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [facial skeleton](http://purl.obolibrary.org/obo/UBERON_0011156) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ossa facialia" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Facial_skeleton" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001295" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/meninges" -### facial vein `http://purl.obolibrary.org/obo/UBERON_0001653` -#### Removed -- [facial vein](http://purl.obolibrary.org/obo/UBERON_0001653) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena facialis anterior" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [meninx](http://purl.obolibrary.org/obo/UBERON_0002360) [UBPROP_0000202](http://purl.obolibrary.org/obo/UBPROP_0000202) [FMA_76821](http://purl.obolibrary.org/obo/FMA_76821) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Facial_vein" +- [meninx](http://purl.obolibrary.org/obo/UBERON_0002360) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "meningeal" -#### Added -- [facial vein](http://purl.obolibrary.org/obo/UBERON_0001653) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena facialis anterior" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [meninx](http://purl.obolibrary.org/obo/UBERON_0002360) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Facial_vein" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### falciform ligament `http://purl.obolibrary.org/obo/UBERON_0001247` -#### Removed -- [falciform ligament](http://purl.obolibrary.org/obo/UBERON_0001247) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ligamentum falciforme hepatis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15823" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001295" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [falciform ligament](http://purl.obolibrary.org/obo/UBERON_0001247) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ligamentum falciforme hepatis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15823" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### meninx of diencephalon `http://purl.obolibrary.org/obo/UBERON_0003290` +#### Removed +- [meninx of diencephalon](http://purl.obolibrary.org/obo/UBERON_0003290) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Meninges that are part of the diencephalon. [Bgee_curator][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### fallopian tube `http://purl.obolibrary.org/obo/UBERON_0003889` -#### Removed -- [fallopian tube](http://purl.obolibrary.org/obo/UBERON_0003889) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tuba uterina" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Fallopian_tube" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000009" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [meninx of diencephalon](http://purl.obolibrary.org/obo/UBERON_0003290) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639" -#### Added -- [fallopian tube](http://purl.obolibrary.org/obo/UBERON_0003889) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tuba uterina" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Fallopian_tube" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### fast muscle cell `http://purl.obolibrary.org/obo/CL_0000190` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000009" -#### Added -- [fast muscle cell](http://purl.obolibrary.org/obo/CL_0000190) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### feces `http://purl.obolibrary.org/obo/UBERON_0001988` +### meninx of hindbrain `http://purl.obolibrary.org/obo/UBERON_0003291` #### Removed -- [feces](http://purl.obolibrary.org/obo/UBERON_0001988) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "portionem cacas" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [meninx of hindbrain](http://purl.obolibrary.org/obo/UBERON_0003291) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Meninges that are part of the hindbrain. [Bgee_curator][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [feces](http://purl.obolibrary.org/obo/UBERON_0001988) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "portionem cacas" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### female germ cell `http://purl.obolibrary.org/obo/CL_0000021` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000011" -#### Added -- [female germ cell](http://purl.obolibrary.org/obo/CL_0000021) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [meninx of hindbrain](http://purl.obolibrary.org/obo/UBERON_0003291) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### female organism `http://purl.obolibrary.org/obo/UBERON_0003100` -#### Removed -- [female organism](http://purl.obolibrary.org/obo/UBERON_0003100) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007011" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [female organism](http://purl.obolibrary.org/obo/UBERON_0003100) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007011" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000011" -### female reproductive system `http://purl.obolibrary.org/obo/UBERON_0000474` -#### Removed -- [female reproductive system](http://purl.obolibrary.org/obo/UBERON_0000474) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004864" +- [meninx of hindbrain](http://purl.obolibrary.org/obo/UBERON_0003291) SubClassOf [immediate transformation of](http://purl.obolibrary.org/obo/RO_0002495) some [future hindbrain meninx](http://purl.obolibrary.org/obo/UBERON_0010091) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" #### Added -- [female reproductive system](http://purl.obolibrary.org/obo/UBERON_0000474) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas) +- [meninx of hindbrain](http://purl.obolibrary.org/obo/UBERON_0003291) SubClassOf [immediate transformation of](http://purl.obolibrary.org/obo/RO_0002495) some [future hindbrain meninx](http://purl.obolibrary.org/obo/UBERON_0010091) -- [female reproductive system](http://purl.obolibrary.org/obo/UBERON_0000474) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004864" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -- [female reproductive system](http://purl.obolibrary.org/obo/UBERON_0000474) [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [Homo sapiens](http://purl.obolibrary.org/obo/NCBITaxon_9606) +### meninx of midbrain `http://purl.obolibrary.org/obo/UBERON_0003288` +#### Removed +- [meninx of midbrain](http://purl.obolibrary.org/obo/UBERON_0003288) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Meninges that are part of the midbrain. [Bgee_curator][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### female urethral meatus `http://purl.obolibrary.org/obo/UBERON_0006565` -#### Removed -- [female urethral meatus](http://purl.obolibrary.org/obo/UBERON_0006565) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ostium urethrae externum (urethra feminina)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:85266" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000012" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [meninx of midbrain](http://purl.obolibrary.org/obo/UBERON_0003288) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639" -#### Added -- [female urethral meatus](http://purl.obolibrary.org/obo/UBERON_0006565) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ostium urethrae externum (urethra feminina)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:85266" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000012" -### femoral artery `http://purl.obolibrary.org/obo/UBERON_0002060` + + +### meninx of spinal cord `http://purl.obolibrary.org/obo/UBERON_0003292` #### Removed -- [femoral artery](http://purl.obolibrary.org/obo/UBERON_0002060) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria femoralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Femoral_artery" +- [meninx of spinal cord](http://purl.obolibrary.org/obo/UBERON_0003292) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Meninges that are part of the spinal cord. [Bgee_curator][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [femoral artery](http://purl.obolibrary.org/obo/UBERON_0002060) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria femoralis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Femoral_artery" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000443" +- [meninx of spinal cord](http://purl.obolibrary.org/obo/UBERON_0003292) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639" -### femoral vein `http://purl.obolibrary.org/obo/UBERON_0001361` -#### Removed -- [femoral vein](http://purl.obolibrary.org/obo/UBERON_0001361) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena femoralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Femoral_vein" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [femoral vein](http://purl.obolibrary.org/obo/UBERON_0001361) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena femoralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Femoral_vein" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000443" -### femur `http://purl.obolibrary.org/obo/UBERON_0000981` + +### meninx of telencephalon `http://purl.obolibrary.org/obo/UBERON_0003289` #### Removed -- [femur](http://purl.obolibrary.org/obo/UBERON_0000981) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "os femorale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001284" +- [meninx of telencephalon](http://purl.obolibrary.org/obo/UBERON_0003289) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [femur](http://purl.obolibrary.org/obo/UBERON_0000981) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "os femoris" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001284" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [femur](http://purl.obolibrary.org/obo/UBERON_0000981) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "os longissimum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Femur" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000010" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [meninx of telencephalon](http://purl.obolibrary.org/obo/UBERON_0003289) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Meninges that are part of the telencephalon. [Bgee_curator][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [femur](http://purl.obolibrary.org/obo/UBERON_0000981) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "os femoris" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001284" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [femur](http://purl.obolibrary.org/obo/UBERON_0000981) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "os femorale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001284" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000010" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -- [femur](http://purl.obolibrary.org/obo/UBERON_0000981) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "os longissimum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Femur" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### mereotopologically related to `http://purl.obolibrary.org/obo/RO_0002323` +#### Removed +- [mereotopologically related to](http://purl.obolibrary.org/obo/RO_0002323) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) +- [mereotopologically related to](http://purl.obolibrary.org/obo/RO_0002323) [RO_0001900](http://purl.obolibrary.org/obo/RO_0001900) [RO_0001901](http://purl.obolibrary.org/obo/RO_0001901) -### fenestrated cell `http://purl.obolibrary.org/obo/CL_0000666` +- [mereotopologically related to](http://purl.obolibrary.org/obo/RO_0002323) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" -#### Added -- [fenestrated cell](http://purl.obolibrary.org/obo/CL_0000666) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### fetal cardiomyocyte `http://purl.obolibrary.org/obo/CL_0002495` +### merocrine gland `http://purl.obolibrary.org/obo/UBERON_0010243` +#### Removed +- [merocrine gland](http://purl.obolibrary.org/obo/UBERON_0010243) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "merocrine" -#### Added -- [fetal cardiomyocyte](http://purl.obolibrary.org/obo/CL_0002495) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### fibro/adipogenic progenitor cell `http://purl.obolibrary.org/obo/CL_0009099` +### mesangium `http://purl.obolibrary.org/obo/UBERON_0002319` +#### Removed +- [mesangium](http://purl.obolibrary.org/obo/UBERON_0002319) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "mesangial" + +- [mesangium](http://purl.obolibrary.org/obo/UBERON_0002319) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:28248" + +- [mesangium](http://purl.obolibrary.org/obo/UBERON_0002319) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "WP considers this the same as glomerular mesangium. In MA, glomerular and extraglomerular are distingsuished. FMA class has no definition and is a type of stroma, which is inconsistent with our classification of this here." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" #### Added -- [fibro/adipogenic progenitor cell](http://purl.obolibrary.org/obo/CL_0009099) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [mesangium](http://purl.obolibrary.org/obo/UBERON_0002319) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### fibroblast `http://purl.obolibrary.org/obo/CL_0000057` +### mesencephalic neural crest `http://purl.obolibrary.org/obo/UBERON_0003849` +#### Removed +- [mesencephalic neural crest](http://purl.obolibrary.org/obo/UBERON_0003849) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [fibroblast](http://purl.obolibrary.org/obo/CL_0000057) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### fibroblast of breast `http://purl.obolibrary.org/obo/CL_4006000` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" -#### Added -- [fibroblast of breast](http://purl.obolibrary.org/obo/CL_4006000) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000796" -### fibroblast of cardiac tissue `http://purl.obolibrary.org/obo/CL_0002548` -#### Added -- [fibroblast of cardiac tissue](http://purl.obolibrary.org/obo/CL_0002548) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### mesenchyme `http://purl.obolibrary.org/obo/UBERON_0003104` +#### Removed +- [mesenchyme](http://purl.obolibrary.org/obo/UBERON_0003104) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -### fibroblast of connective tissue of glandular part of prostate `http://purl.obolibrary.org/obo/CL_1000305` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -#### Added -- [fibroblast of connective tissue of glandular part of prostate](http://purl.obolibrary.org/obo/CL_1000305) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010427" +- [mesenchyme](http://purl.obolibrary.org/obo/UBERON_0003104) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "mesenchymal" -### fibroblast of connective tissue of nonglandular part of prostate `http://purl.obolibrary.org/obo/CL_1000304` +- [mesenchyme](http://purl.obolibrary.org/obo/UBERON_0003104) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000393" -#### Added -- [fibroblast of connective tissue of nonglandular part of prostate](http://purl.obolibrary.org/obo/CL_1000304) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -### fibroblast of connective tissue of prostate `http://purl.obolibrary.org/obo/CL_1000299` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -#### Added -- [fibroblast of connective tissue of prostate](http://purl.obolibrary.org/obo/CL_1000299) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### fibroblast of lung `http://purl.obolibrary.org/obo/CL_0002553` +### mesenchyme derived from head neural crest `http://purl.obolibrary.org/obo/UBERON_0007213` #### Added -- [fibroblast of lung](http://purl.obolibrary.org/obo/CL_0002553) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [mesenchyme derived from head neural crest](http://purl.obolibrary.org/obo/UBERON_0007213) SubClassOf [mesenchyme derived from neural crest](http://purl.obolibrary.org/obo/UBERON_0014387) -### fibroblast of mammary gland `http://purl.obolibrary.org/obo/CL_0002555` +### mesenchyme derived from trunk neural crest `http://purl.obolibrary.org/obo/UBERON_0007214` #### Added -- [fibroblast of mammary gland](http://purl.obolibrary.org/obo/CL_0002555) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [mesenchyme derived from trunk neural crest](http://purl.obolibrary.org/obo/UBERON_0007214) SubClassOf [mesenchyme derived from neural crest](http://purl.obolibrary.org/obo/UBERON_0014387) -### fibrocartilage `http://purl.obolibrary.org/obo/UBERON_0001995` +### mesenchyme from rhombencephalic neural crest `http://purl.obolibrary.org/obo/UBERON_0010258` #### Removed -- [fibrocartilage](http://purl.obolibrary.org/obo/UBERON_0001995) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D051445" +- [mesenchyme from rhombencephalic neural crest](http://purl.obolibrary.org/obo/UBERON_0010258) SubClassOf [mesenchyme derived from neural crest](http://purl.obolibrary.org/obo/UBERON_0014387) -#### Added -- [fibrocartilage](http://purl.obolibrary.org/obo/UBERON_0001995) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D051445" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +### mesenchyme from somatopleure `http://purl.obolibrary.org/obo/UBERON_0010377` + +#### Added +- [mesenchyme from somatopleure](http://purl.obolibrary.org/obo/UBERON_0010377) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### fibrocyte `http://purl.obolibrary.org/obo/CL_0000135` +### mesenchyme from splanchnopleure `http://purl.obolibrary.org/obo/UBERON_0010378` #### Added -- [fibrocyte](http://purl.obolibrary.org/obo/CL_0000135) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [mesenchyme from splanchnopleure](http://purl.obolibrary.org/obo/UBERON_0010378) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### fibrous joint `http://purl.obolibrary.org/obo/UBERON_0002209` +### mesenchyme of carpal region `http://purl.obolibrary.org/obo/UBERON_0003319` #### Removed -- [fibrous joint](http://purl.obolibrary.org/obo/UBERON_0002209) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "junctura fibrosa" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [mesenchyme of carpal region](http://purl.obolibrary.org/obo/UBERON_0003319) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:19122" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Fibrous_joint" -#### Added -- [fibrous joint](http://purl.obolibrary.org/obo/UBERON_0002209) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "junctura fibrosa" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Fibrous_joint" +### mesenchyme of footplate `http://purl.obolibrary.org/obo/UBERON_0003328` +#### Removed +- [mesenchyme of footplate](http://purl.obolibrary.org/obo/UBERON_0003328) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "We group two EMAPA classes here but these may need to be separated" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EMAPA" -### fibrous pericardium `http://purl.obolibrary.org/obo/UBERON_0002359` + +### mesenchyme of handplate `http://purl.obolibrary.org/obo/UBERON_0009523` #### Removed -- [fibrous pericardium](http://purl.obolibrary.org/obo/UBERON_0002359) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pericardium fibrosum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Fibrous_pericardium" +- [mesenchyme of handplate](http://purl.obolibrary.org/obo/UBERON_0009523) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "We group two EMAPA classes here but these may need to be separated" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EMAPA" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [fibrous pericardium](http://purl.obolibrary.org/obo/UBERON_0002359) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pericardium fibrosum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Fibrous_pericardium" +### mesenchyme of mammary gland `http://purl.obolibrary.org/obo/UBERON_0003326` + +#### Added +- [mesenchyme of mammary gland](http://purl.obolibrary.org/obo/UBERON_0003326) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### fibrous ring of heart `http://purl.obolibrary.org/obo/UBERON_0006008` +### mesenchyme of middle ear `http://purl.obolibrary.org/obo/UBERON_0009506` #### Removed -- [fibrous ring of heart](http://purl.obolibrary.org/obo/UBERON_0006008) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "annulus fibrosus cordis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Fibrous_rings_of_heart" +- [mesenchyme of middle ear](http://purl.obolibrary.org/obo/UBERON_0009506) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "Also 1st arch maxillary mesenchyme in EHDAA2" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EHDAA2" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [fibrous ring of heart](http://purl.obolibrary.org/obo/UBERON_0006008) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "annulus fibrosus cordis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Fibrous_rings_of_heart" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### mesenchyme of pinna `http://purl.obolibrary.org/obo/UBERON_0003325` +#### Removed +- [mesenchyme of pinna](http://purl.obolibrary.org/obo/UBERON_0003325) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "EMAPA divides this spatially into condensation + rest, and temporally into mesenchyme and cartilage condensation" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EMAPA" -### flat bone `http://purl.obolibrary.org/obo/UBERON_0010428` -#### Removed -- [flat bone](http://purl.obolibrary.org/obo/UBERON_0010428) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "os planum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Flat_bone" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### mesenchyme of trachea `http://purl.obolibrary.org/obo/UBERON_0009505` #### Added -- [flat bone](http://purl.obolibrary.org/obo/UBERON_0010428) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "os planum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [mesenchyme of trachea](http://purl.obolibrary.org/obo/UBERON_0009505) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Flat_bone" - -### follicular B cell `http://purl.obolibrary.org/obo/CL_0000843` +### mesenchyme of umbilical cord `http://purl.obolibrary.org/obo/UBERON_0003422` #### Added -- [follicular B cell](http://purl.obolibrary.org/obo/CL_0000843) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) - +- [mesenchyme of umbilical cord](http://purl.obolibrary.org/obo/UBERON_0003422) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### follicular antrum `http://purl.obolibrary.org/obo/UBERON_0000039` -#### Removed -- [follicular antrum](http://purl.obolibrary.org/obo/UBERON_0000039) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "antrum follicularum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Follicular_antrum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### mesenteric lymph node `http://purl.obolibrary.org/obo/UBERON_0002509` #### Added -- [follicular antrum](http://purl.obolibrary.org/obo/UBERON_0000039) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "antrum follicularum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Follicular_antrum" +- [mesenteric lymph node](http://purl.obolibrary.org/obo/UBERON_0002509) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### follicular dendritic cell `http://purl.obolibrary.org/obo/CL_0000442` +### mesenteric lymphatic vessel `http://purl.obolibrary.org/obo/UBERON_8480006` #### Added -- [follicular dendritic cell](http://purl.obolibrary.org/obo/CL_0000442) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [mesenteric lymphatic vessel](http://purl.obolibrary.org/obo/UBERON_8480006) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### follicular fluid `http://purl.obolibrary.org/obo/UBERON_0000038` +### mesenteric vein `http://purl.obolibrary.org/obo/UBERON_0005617` #### Removed -- [follicular fluid](http://purl.obolibrary.org/obo/UBERON_0000038) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "liquor folliculi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [mesenteric vein](http://purl.obolibrary.org/obo/UBERON_0005617) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In humans the inferior mesenteric vein empties into the splenic vein, the superior mesenteric vein joins the splenic vein to form the portal vein" -- [follicular fluid](http://purl.obolibrary.org/obo/UBERON_0000038) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "liquor folliculi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Follicular_fluid" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [follicular fluid](http://purl.obolibrary.org/obo/UBERON_0000038) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "liquor folliculi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### mesentery `http://purl.obolibrary.org/obo/UBERON_0002095` +#### Removed +- [mesentery](http://purl.obolibrary.org/obo/UBERON_0002095) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "mesenteric" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Follicular_fluid" +- [mesentery](http://purl.obolibrary.org/obo/UBERON_0002095) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in Uberon, this term is used in the generic sense, not necessarily restricted to the peritoneum, consistent with FMA. WP: 'In anatomy, the mesentery is the double layer of peritoneum that suspends the jejunum and ileum from the posterior wall of the abdomen. Its meaning, however, is frequently extended to include double layers of peritoneum connecting various components of the abdominal cavity.'. TODO - check. Consider FMA:259286 - Region of mesentery." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" -- [follicular fluid](http://purl.obolibrary.org/obo/UBERON_0000038) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "liquor folliculi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### foramen magnum `http://purl.obolibrary.org/obo/UBERON_0003687` +### mesentery of foregut-midgut junction `http://purl.obolibrary.org/obo/UBERON_0009483` #### Removed -- [foramen magnum](http://purl.obolibrary.org/obo/UBERON_0003687) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006035" - - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0003-4423-4370" +- [mesentery of foregut-midgut junction](http://purl.obolibrary.org/obo/UBERON_0009483) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11" -#### Added -- [foramen magnum](http://purl.obolibrary.org/obo/UBERON_0003687) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006035" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000430" -### foramen rotundum `http://purl.obolibrary.org/obo/UBERON_0005446` -#### Removed -- [foramen rotundum](http://purl.obolibrary.org/obo/UBERON_0005446) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "foramen rotundum ossis sphenoidalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Foramen_rotundum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [foramen rotundum](http://purl.obolibrary.org/obo/UBERON_0005446) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "foramen rotundum ossis sphenoidalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Foramen_rotundum" +### mesentery of midgut `http://purl.obolibrary.org/obo/UBERON_0003284` +#### Removed +- [mesentery of midgut](http://purl.obolibrary.org/obo/UBERON_0003284) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000413" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### forebrain radial glial cell `http://purl.obolibrary.org/obo/CL_0013000` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [forebrain radial glial cell](http://purl.obolibrary.org/obo/CL_0013000) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### foregut `http://purl.obolibrary.org/obo/UBERON_0001041` + +### mesentery of oesophagus `http://purl.obolibrary.org/obo/UBERON_0003283` #### Removed -- [foregut](http://purl.obolibrary.org/obo/UBERON_0001041) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "praeenteron" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Foregut" +- [mesentery of oesophagus](http://purl.obolibrary.org/obo/UBERON_0003283) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [foregut](http://purl.obolibrary.org/obo/UBERON_0001041) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "proenteron" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Foregut" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [foregut](http://purl.obolibrary.org/obo/UBERON_0001041) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005379" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000415" -#### Added -- [foregut](http://purl.obolibrary.org/obo/UBERON_0001041) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005379" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -- [foregut](http://purl.obolibrary.org/obo/UBERON_0001041) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "proenteron" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Foregut" +### mesentery of stomach `http://purl.obolibrary.org/obo/UBERON_0003281` +#### Removed +- [mesentery of stomach](http://purl.obolibrary.org/obo/UBERON_0003281) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The portion of the primitive mesentery that encloses the stomach; from its dorsal sheet, the greater omentum develops, and from its ventral sheet, the lesser omentum. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [foregut](http://purl.obolibrary.org/obo/UBERON_0001041) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "praeenteron" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Foregut" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/mesogastrium" -### forelimb `http://purl.obolibrary.org/obo/UBERON_0002102` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000358" + + + +### mesoderm `http://purl.obolibrary.org/obo/UBERON_0000926` #### Removed -- [forelimb](http://purl.obolibrary.org/obo/UBERON_0002102) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "membrum superius" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:7183" +- [mesoderm](http://purl.obolibrary.org/obo/UBERON_0000926) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "mesodermal" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [mesoderm](http://purl.obolibrary.org/obo/UBERON_0000926) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "https://github.com/obophenotype/uberon/wiki/The-neural-crest" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [mesoderm](http://purl.obolibrary.org/obo/UBERON_0000926) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Primary germ layer that is the middle of the embryonic germ layers.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" -#### Added -- [forelimb](http://purl.obolibrary.org/obo/UBERON_0002102) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "membrum superius" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:7183" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000304" +- [mesoderm](http://purl.obolibrary.org/obo/UBERON_0000926) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### forelimb skeleton `http://purl.obolibrary.org/obo/UBERON_0001440` -#### Removed -- [forelimb skeleton](http://purl.obolibrary.org/obo/UBERON_0001440) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ossa membri superioris" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:24139" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000152" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722" + +- [mesoderm](http://purl.obolibrary.org/obo/UBERON_0000926) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000126" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + +- [mesoderm](http://purl.obolibrary.org/obo/UBERON_0000926) SubClassOf [germ layer](http://purl.obolibrary.org/obo/UBERON_0000923) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "sometimes not considered primary" #### Added -- [forelimb skeleton](http://purl.obolibrary.org/obo/UBERON_0001440) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ossa membri superioris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [mesoderm](http://purl.obolibrary.org/obo/UBERON_0000926) SubClassOf [germ layer](http://purl.obolibrary.org/obo/UBERON_0000923) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:24139" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### mesoderm blood island `http://purl.obolibrary.org/obo/UBERON_0003304` +#### Removed +- [mesoderm blood island](http://purl.obolibrary.org/obo/UBERON_0003304) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:16115" +- [mesoderm blood island](http://purl.obolibrary.org/obo/UBERON_0003304) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in EHDAA2, gives rise to blood and dorsal aorta" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EHDAA2" -### forelimb stylopod `http://purl.obolibrary.org/obo/UBERON_0003822` + + +### mesoderm-derived structure `http://purl.obolibrary.org/obo/UBERON_0004120` #### Removed -- [forelimb stylopod](http://purl.obolibrary.org/obo/UBERON_0003822) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "regio brachialis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:24890" +- [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "Grouping term for query purposes" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + +### mesonephric capsule `http://purl.obolibrary.org/obo/UBERON_0006170` #### Added -- [forelimb stylopod](http://purl.obolibrary.org/obo/UBERON_0003822) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "regio brachialis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [mesonephric capsule](http://purl.obolibrary.org/obo/UBERON_0006170) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:24890" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### mesonephric collecting duct `http://purl.obolibrary.org/obo/UBERON_0005319` +#### Added +- [mesonephric collecting duct](http://purl.obolibrary.org/obo/UBERON_0005319) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### forelimb zeugopod `http://purl.obolibrary.org/obo/UBERON_0002386` + +### mesonephric distal tubule `http://purl.obolibrary.org/obo/UBERON_0006190` #### Removed -- [forelimb zeugopod](http://purl.obolibrary.org/obo/UBERON_0002386) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "regio antebrachialis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9663" +- [mesonephric distal tubule](http://purl.obolibrary.org/obo/UBERON_0006190) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "ZFA has terms for developing tubule" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "ZFA" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [forelimb zeugopod](http://purl.obolibrary.org/obo/UBERON_0002386) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "antebrachium" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Forearm" +### mesonephric duct `http://purl.obolibrary.org/obo/UBERON_0003074` +#### Removed +- [mesonephric duct](http://purl.obolibrary.org/obo/UBERON_0003074) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "In the male the Wolffian duct persists, and forms for example the epididymis, the ductus deferens, the ejaculatory duct, seminal vesicle and efferent ducts." - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [mesonephric duct](http://purl.obolibrary.org/obo/UBERON_0003074) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "VHOG:0000082" -#### Added -- [forelimb zeugopod](http://purl.obolibrary.org/obo/UBERON_0002386) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "regio antebrachialis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9663" +- [mesonephric duct](http://purl.obolibrary.org/obo/UBERON_0003074) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [forelimb zeugopod](http://purl.obolibrary.org/obo/UBERON_0002386) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "antebrachium" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.686" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Forearm" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000082" +- [mesonephric duct](http://purl.obolibrary.org/obo/UBERON_0003074) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0005990" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### fornix of brain `http://purl.obolibrary.org/obo/UBERON_0000052` -#### Removed -- [fornix of brain](http://purl.obolibrary.org/obo/UBERON_0000052) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "fornix cerebri" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:268" + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) -#### Added -- [fornix of brain](http://purl.obolibrary.org/obo/UBERON_0000052) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "fornix cerebri" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [mesonephric duct](http://purl.obolibrary.org/obo/UBERON_0003074) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:268" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### fourth ventricle `http://purl.obolibrary.org/obo/UBERON_0002422` -#### Removed -- [fourth ventricle](http://purl.obolibrary.org/obo/UBERON_0002422) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ventriculus quartus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Fourth_ventricle" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000082" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [mesonephric duct](http://purl.obolibrary.org/obo/UBERON_0003074) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical structure consisting of either of a pair of longitudinal ducts which carry urine and in males, sperm, to the cloaca.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000637" -#### Added -- [fourth ventricle](http://purl.obolibrary.org/obo/UBERON_0002422) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ventriculus quartus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Fourth_ventricle" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" -### foveolar cell of stomach `http://purl.obolibrary.org/obo/CL_0002179` +- [mesonephric duct](http://purl.obolibrary.org/obo/UBERON_0003074) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:16577" + +- [mesonephric duct](http://purl.obolibrary.org/obo/UBERON_0003074) SubClassOf [meso-epithelium](http://purl.obolibrary.org/obo/UBERON_0012275) -#### Added -- [foveolar cell of stomach](http://purl.obolibrary.org/obo/CL_0002179) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### fraction A pre-pro B cell `http://purl.obolibrary.org/obo/CL_0002045` +### mesonephric epithelium `http://purl.obolibrary.org/obo/UBERON_0005103` #### Added -- [fraction A pre-pro B cell](http://purl.obolibrary.org/obo/CL_0002045) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [mesonephric epithelium](http://purl.obolibrary.org/obo/UBERON_0005103) SubClassOf [meso-epithelium](http://purl.obolibrary.org/obo/UBERON_0012275) -### frontal cortex `http://purl.obolibrary.org/obo/UBERON_0001870` +### mesonephric glomerulus `http://purl.obolibrary.org/obo/UBERON_0005325` +#### Removed +- [mesonephric glomerulus](http://purl.obolibrary.org/obo/UBERON_0005325) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "SCTID:362217000" -#### Added -- [frontal cortex](http://purl.obolibrary.org/obo/UBERON_0001870) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D005625" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) +- [mesonephric glomerulus](http://purl.obolibrary.org/obo/UBERON_0005325) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In animals in which the mesonephros is the terminal kidney, such as amphibians and fish, the final organ is very complex, containing a large number of nephrons, most of which have an internal glomerulus.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0127224411 Vize PD, Woolf AS, Bard JBL, The kidney: From normal development to congenital disease (2003) p.3" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### frontal lobe `http://purl.obolibrary.org/obo/UBERON_0016525` -#### Removed -- [frontal lobe](http://purl.obolibrary.org/obo/UBERON_0016525) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lobi frontales" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:56" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001238" -- [frontal lobe](http://purl.obolibrary.org/obo/UBERON_0016525) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "regio frontalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:61824" +- [mesonephric glomerulus](http://purl.obolibrary.org/obo/UBERON_0005325) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A tuft of capillaries found in a Bowman's capsule in which waste products are filtered from the blood and urine formation is initiated.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010388" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -- [frontal lobe](http://purl.obolibrary.org/obo/UBERON_0016525) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lobus frontalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Frontal_lobe" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [mesonephric glomerulus](http://purl.obolibrary.org/obo/UBERON_0005325) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "XAO/AAO class belongs here, as it refers to mesonephric structure" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "XAO" -#### Added -- [frontal lobe](http://purl.obolibrary.org/obo/UBERON_0016525) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lobi frontales" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:56" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -- [frontal lobe](http://purl.obolibrary.org/obo/UBERON_0016525) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "regio frontalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### mesonephric juxtaglomerular apparatus `http://purl.obolibrary.org/obo/UBERON_0005320` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:61824" +#### Added +- [mesonephric juxtaglomerular apparatus](http://purl.obolibrary.org/obo/UBERON_0005320) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [frontal lobe](http://purl.obolibrary.org/obo/UBERON_0016525) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lobus frontalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### mesonephric mesenchyme `http://purl.obolibrary.org/obo/UBERON_0005323` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Frontal_lobe" +#### Added +- [mesonephric mesenchyme](http://purl.obolibrary.org/obo/UBERON_0005323) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### frontal suture `http://purl.obolibrary.org/obo/UBERON_0002490` +### mesonephric nephron `http://purl.obolibrary.org/obo/UBERON_0005322` #### Removed -- [frontal suture](http://purl.obolibrary.org/obo/UBERON_0002490) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "sutura frontalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [mesonephric nephron](http://purl.obolibrary.org/obo/UBERON_0005322) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The structure that is the basic functional unit of the kidney.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:9268568" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010387" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Frontal_suture" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -- [frontal suture](http://purl.obolibrary.org/obo/UBERON_0002490) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "sutura metopica" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +#### Added +- [mesonephric nephron](http://purl.obolibrary.org/obo/UBERON_0005322) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:52989" +### mesonephric nephron progenitor `http://purl.obolibrary.org/obo/UBERON_0010537` #### Added -- [frontal suture](http://purl.obolibrary.org/obo/UBERON_0002490) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "sutura metopica" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [mesonephric nephron progenitor](http://purl.obolibrary.org/obo/UBERON_0010537) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:52989" -- [frontal suture](http://purl.obolibrary.org/obo/UBERON_0002490) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "sutura frontalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### mesonephric proximal tubule `http://purl.obolibrary.org/obo/UBERON_0006192` +#### Removed +- [mesonephric proximal tubule](http://purl.obolibrary.org/obo/UBERON_0006192) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "ZFA has terms for developing tubule" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "ZFA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Frontal_suture" -### frontonasal prominence `http://purl.obolibrary.org/obo/UBERON_0004066` +### mesonephric tubule `http://purl.obolibrary.org/obo/UBERON_0000083` #### Removed -- [frontonasal prominence](http://purl.obolibrary.org/obo/UBERON_0004066) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "prominentia frontonasalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Frontonasal_prominence" +- [mesonephric tubule](http://purl.obolibrary.org/obo/UBERON_0000083) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Any of the renal tubules composing the mesonephros. In mammals they function as excretory structures during the early embryonic development but are later incorporated into the reproductive system. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [frontonasal prominence](http://purl.obolibrary.org/obo/UBERON_0004066) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "prominentia frontonasalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Frontonasal_prominence" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/mesonephric+tubule" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000500" -### fundic gastric gland `http://purl.obolibrary.org/obo/UBERON_0010038` -#### Removed -- [fundic gastric gland](http://purl.obolibrary.org/obo/UBERON_0010038) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "glandulae gastricae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Fundic_glands" +- [mesonephric tubule](http://purl.obolibrary.org/obo/UBERON_0000083) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [fundic gastric gland](http://purl.obolibrary.org/obo/UBERON_0010038) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "glandulae gastricae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Fundic_glands" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000500" -### fundus of urinary bladder `http://purl.obolibrary.org/obo/UBERON_0006082` -#### Removed -- [fundus of urinary bladder](http://purl.obolibrary.org/obo/UBERON_0006082) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "fundus vesicae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15908" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### mesonephros `http://purl.obolibrary.org/obo/UBERON_0000080` +#### Removed +- [mesonephros](http://purl.obolibrary.org/obo/UBERON_0000080) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A kidney formed of nephric tubules arising in the middle region of the nephric ridge; a transient embryonic stage that replaces the pronephros, but is itself replaced by the adult metanephros [in mammals; in fishes and amphibians it is the adult kidney]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [fundus of urinary bladder](http://purl.obolibrary.org/obo/UBERON_0006082) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "fundus vesicae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15908" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000038" +- [mesonephros](http://purl.obolibrary.org/obo/UBERON_0000080) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In mammals, the mesonephros is the second of the three embryonic kidneys to be established and exists only transiently. In fish and amphibians, the mesonephros will form the mature kidney" -### gallbladder `http://purl.obolibrary.org/obo/UBERON_0002110` -#### Removed -- [gallbladder](http://purl.obolibrary.org/obo/UBERON_0002110) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vesica fellea" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Gallbladder" +- [mesonephros](http://purl.obolibrary.org/obo/UBERON_0000080) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates. (...) In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [gallbladder](http://purl.obolibrary.org/obo/UBERON_0002110) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vesica biliaris" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Gallbladder" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639" -#### Added -- [gallbladder](http://purl.obolibrary.org/obo/UBERON_0002110) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vesica fellea" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Gallbladder" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000038" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [mesonephros](http://purl.obolibrary.org/obo/UBERON_0000080) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "By contrast to the pronephros, the histological features of the mammalian mesonephros, with its primitive glomeruli, suggest that it probably functions as a primitive kidney, and is involved in the production of much of the amniotic fluid. Within the two mesonephroi, one located on either side of the dorsal mesentery of the hindgut, a substantial number (in the region of about 40 or more) of cranio-caudally segmented mesonephric tubules are formed. It has, however, been suggested that only the most rostrally located 4-6 pairs of mesonephric tubules drain into the mesonephric portion of the nephric duct. This is now seen to extend along the length of the mesonephroi, being located towards their lateral sides. The mesonephros is also retained over a considerably longer period than the pronephros, but gradually undergoes regression in a cranio-caudal direction. While the rostral part displays clear evidence of regression its more caudal part appears to display evidence of functional activity. Within the medial part of the mesonephros, vesicles are formed, although no glomeruli are formed there in this species. It is, however, difficult to believe that the relatively enormous mesonephroi do not have an excretory role in the mouse, only serving as a base for gonadal differentiation. In the human embryo, the medial part of the mesonephric tubules enlarges, become invaginated by capillaries, and form glomeruli. These then take on an excretory role. In the mouse, the mesonephric ducts appear to be patent throughout their length[GUDMAP, modified]" -- [gallbladder](http://purl.obolibrary.org/obo/UBERON_0002110) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vesica biliaris" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Gallbladder" +- [mesonephros](http://purl.obolibrary.org/obo/UBERON_0000080) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Organ that is the definitive adult kidney. It replaces the earlier pronephros, which degenerates as the mesonephros becomes functional in feeding stage tadpoles.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010384" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### gallbladder serosa `http://purl.obolibrary.org/obo/UBERON_0004783` -#### Removed -- [gallbladder serosa](http://purl.obolibrary.org/obo/UBERON_0004783) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica serosa vesicae biliaris" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:14659" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [mesonephros](http://purl.obolibrary.org/obo/UBERON_0000080) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "mesonephric" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [gallbladder serosa](http://purl.obolibrary.org/obo/UBERON_0004783) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica serosa vesicae biliaris" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:14659" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### mesopodial skeleton `http://purl.obolibrary.org/obo/UBERON_0009878` +#### Removed +- [mesopodial skeleton](http://purl.obolibrary.org/obo/UBERON_0009878) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Limb skeleton subdivision consisting of endochondral bones increasing the freedom of movement of the autopodia, and located between zeugopodia and autopodia.[VSAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "VSAO:NI" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0005022" -### gamma-delta T cell `http://purl.obolibrary.org/obo/CL_0000798` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" -#### Added -- [gamma-delta T cell](http://purl.obolibrary.org/obo/CL_0000798) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [mesopodial skeleton](http://purl.obolibrary.org/obo/UBERON_0009878) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: distally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0005022" -### ganglion interneuron `http://purl.obolibrary.org/obo/CL_0000397` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" #### Added -- [ganglion interneuron](http://purl.obolibrary.org/obo/CL_0000397) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [mesopodial skeleton](http://purl.obolibrary.org/obo/UBERON_0009878) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### ganglionic layer of retina `http://purl.obolibrary.org/obo/UBERON_0001792` +### mesopodium bone `http://purl.obolibrary.org/obo/UBERON_0003656` #### Removed -- [ganglionic layer of retina](http://purl.obolibrary.org/obo/UBERON_0001792) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "stratum ganglionicum retinae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ganglion_cell_layer" +- [mesopodium bone](http://purl.obolibrary.org/obo/UBERON_0003656) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The carpus (wrist) and tarsus (ankle) of land vertebrates primitively had three rows of carpal or tarsal bones. Often some of these have become lost or fused in evolution. Three proximals. In the hand humans has all three. In the foot the middle proximal appears in 5-15% of people as an os trigonum. Centrale or os centrale, on the medial side. In humans and our closest relatives the African apes (chimpanzees and gorillas) it fuses to the scaphoid where it forms the articulation with the trapezoid bone; occasionally it stays separate. In Man's foot it is the navicular. Some early land vertebrates had more than one (up to three) os centrale per hand or foot. Distals, one per finger / toe at the base of each metacarpal or metatarsal. In mammals the 4th and 5th fuse. In the horse the 1st is lost" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Carpus_and_tarsus_of_land_vertebrates" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [mesopodium bone](http://purl.obolibrary.org/obo/UBERON_0003656) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [mesopodial skeleton](http://purl.obolibrary.org/obo/UBERON_0009878) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern" #### Added -- [ganglionic layer of retina](http://purl.obolibrary.org/obo/UBERON_0001792) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "stratum ganglionicum retinae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ganglion_cell_layer" +- [mesopodium bone](http://purl.obolibrary.org/obo/UBERON_0003656) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [mesopodial skeleton](http://purl.obolibrary.org/obo/UBERON_0009878) -### gas excreted from digestive tract `http://purl.obolibrary.org/obo/UBERON_0034946` +### mesopodium region `http://purl.obolibrary.org/obo/UBERON_0006716` #### Removed -- [gas excreted from digestive tract](http://purl.obolibrary.org/obo/UBERON_0034946) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "flatus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Flatulence" +- [mesopodium region](http://purl.obolibrary.org/obo/UBERON_0006716) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "Naming conventions for pod terms under discussion within phenoscape group" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [gas excreted from digestive tract](http://purl.obolibrary.org/obo/UBERON_0034946) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "flatus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Flatulence" +### metabolic zone of liver `http://purl.obolibrary.org/obo/UBERON_8400005` + +#### Added +- [metabolic zone of liver](http://purl.obolibrary.org/obo/UBERON_8400005) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -### gastric juice `http://purl.obolibrary.org/obo/UBERON_0001971` +### metacarpophalangeal joint `http://purl.obolibrary.org/obo/UBERON_0003695` #### Removed -- [gastric juice](http://purl.obolibrary.org/obo/UBERON_0001971) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Gastric_juice" +- [metacarpophalangeal joint](http://purl.obolibrary.org/obo/UBERON_0003695) [UBPROP_0000202](http://purl.obolibrary.org/obo/UBPROP_0000202) [FMA_71364](http://purl.obolibrary.org/obo/FMA_71364) -### gastroesophageal sphincter `http://purl.obolibrary.org/obo/UBERON_0004550` +### metacarpus region `http://purl.obolibrary.org/obo/UBERON_0004453` #### Removed -- [gastroesophageal sphincter](http://purl.obolibrary.org/obo/UBERON_0004550) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "constrictor cardiae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MP:0010153" +- [metacarpus region](http://purl.obolibrary.org/obo/UBERON_0004453) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "Note that mammalian and non-mammalian AOs differ in whether they consider this a part of the skeleton" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [metacarpus region](http://purl.obolibrary.org/obo/UBERON_0004453) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "metacarpal" -#### Added -- [gastroesophageal sphincter](http://purl.obolibrary.org/obo/UBERON_0004550) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "constrictor cardiae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MP:0010153" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -- [gastroesophageal sphincter](http://purl.obolibrary.org/obo/UBERON_0004550) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D049630" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) +### metacarpus skeleton `http://purl.obolibrary.org/obo/UBERON_0010544` +#### Removed +- [metacarpus skeleton](http://purl.obolibrary.org/obo/UBERON_0010544) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:36158" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +- [metacarpus skeleton](http://purl.obolibrary.org/obo/UBERON_0010544) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Segment of the forearm corresponding to the metacarpus, which articulates with the carpals at one end and with the phalanges at the other end.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -### gastrula `http://purl.obolibrary.org/obo/UBERON_0004734` -#### Removed -- [gastrula](http://purl.obolibrary.org/obo/UBERON_0004734) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005317" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000946" + +- [metacarpus skeleton](http://purl.obolibrary.org/obo/UBERON_0010544) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [manual digit metacarpus cartilage element](http://purl.obolibrary.org/obo/UBERON_0010699) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "many to one" #### Added -- [gastrula](http://purl.obolibrary.org/obo/UBERON_0004734) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005317" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [metacarpus skeleton](http://purl.obolibrary.org/obo/UBERON_0010544) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [manual digit metacarpus cartilage element](http://purl.obolibrary.org/obo/UBERON_0010699) -### generation of precursor metabolites and energy `http://purl.obolibrary.org/obo/GO_0006091` +### metadata complete `http://purl.obolibrary.org/obo/IAO_0000120` #### Removed -- [generation of precursor metabolites and energy](http://purl.obolibrary.org/obo/GO_0006091) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) +- [metadata complete](http://purl.obolibrary.org/obo/IAO_0000120) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "metadata complete"@en -#### Added -- [generation of precursor metabolites and energy](http://purl.obolibrary.org/obo/GO_0006091) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) -### geniculate ganglion `http://purl.obolibrary.org/obo/UBERON_0001700` +### metadata incomplete `http://purl.obolibrary.org/obo/IAO_0000123` #### Removed -- [geniculate ganglion](http://purl.obolibrary.org/obo/UBERON_0001700) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ganglion geniculi nervi facialis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [metadata incomplete](http://purl.obolibrary.org/obo/IAO_0000123) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "metadata incomplete"@en + + - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Geniculate_ganglion" +### metanephric capsule `http://purl.obolibrary.org/obo/UBERON_0005137` #### Added -- [geniculate ganglion](http://purl.obolibrary.org/obo/UBERON_0001700) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ganglion geniculi nervi facialis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [metanephric capsule](http://purl.obolibrary.org/obo/UBERON_0005137) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Geniculate_ganglion" +### metanephric cortical collecting duct `http://purl.obolibrary.org/obo/UBERON_0005115` + +#### Added +- [metanephric cortical collecting duct](http://purl.obolibrary.org/obo/UBERON_0005115) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### germ cell `http://purl.obolibrary.org/obo/CL_0000586` +### metanephric descending thin limb `http://purl.obolibrary.org/obo/UBERON_0005116` #### Added -- [germ cell](http://purl.obolibrary.org/obo/CL_0000586) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [metanephric descending thin limb](http://purl.obolibrary.org/obo/UBERON_0005116) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### germ layer `http://purl.obolibrary.org/obo/UBERON_0000923` -#### Removed -- [germ layer](http://purl.obolibrary.org/obo/UBERON_0000923) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000110" +### metanephric epithelium `http://purl.obolibrary.org/obo/UBERON_0005108` #### Added -- [germ layer](http://purl.obolibrary.org/obo/UBERON_0000923) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000110" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [metanephric epithelium](http://purl.obolibrary.org/obo/UBERON_0005108) SubClassOf [meso-epithelium](http://purl.obolibrary.org/obo/UBERON_0012275) -### germinal center B cell `http://purl.obolibrary.org/obo/CL_0000844` +### metanephric juxtaglomerular apparatus `http://purl.obolibrary.org/obo/UBERON_0004738` #### Added -- [germinal center B cell](http://purl.obolibrary.org/obo/CL_0000844) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [metanephric juxtaglomerular apparatus](http://purl.obolibrary.org/obo/UBERON_0004738) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### germline ring canal `http://purl.obolibrary.org/obo/GO_0045172` +### metanephric mesenchyme `http://purl.obolibrary.org/obo/UBERON_0003220` #### Removed -- [germline ring canal](http://purl.obolibrary.org/obo/GO_0045172) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:0045172" +- [metanephric mesenchyme](http://purl.obolibrary.org/obo/UBERON_0003220) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A mass of intermediate mesodermal cells around the distal end of the ureteric bud that gives rise to nephrons in the metanephric kidney. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/metanephric+mesenchyme" -- [germline ring canal](http://purl.obolibrary.org/obo/GO_0045172) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "cellular_component" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [germline ring canal](http://purl.obolibrary.org/obo/GO_0045172) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Germline specific intercellular bridge. During cyst formation in insects, ring canals interconnect the cells of the cyst, facilitating the passage of cytoplasmic components between cells." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:9635420" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:mtg_sensu" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:9655801" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000540" -- [germline ring canal](http://purl.obolibrary.org/obo/GO_0045172) [label](http://www.w3.org/2000/01/rdf-schema#label) "germline ring canal" +- [metanephric mesenchyme](http://purl.obolibrary.org/obo/UBERON_0003220) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "When the ureteric buds emerge from the nephric duct, they enter the metanephrogenic mesenchyme. The ureteric buds induce this mesenchymal tissue to condense around them and differentiate into the nephrons of the mammalian kidney. As this mesenchyme differentiates, it tells the ureteric bud to branch and grow.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- Class: [germline ring canal](http://purl.obolibrary.org/obo/GO_0045172) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [germline ring canal](http://purl.obolibrary.org/obo/GO_0045172) SubClassOf [intercellular bridge](http://purl.obolibrary.org/obo/GO_0045171) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [germline ring canal](http://purl.obolibrary.org/obo/GO_0045172) SubClassOf [only in taxon](http://purl.obolibrary.org/obo/RO_0002160) some [Arthropoda](http://purl.obolibrary.org/obo/NCBITaxon_6656) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000540" -- [germline ring canal](http://purl.obolibrary.org/obo/GO_0045172) SubClassOf [in taxon](http://purl.obolibrary.org/obo/RO_0002162) only [Arthropoda](http://purl.obolibrary.org/obo/NCBITaxon_6656) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.462" -### gingival groove `http://purl.obolibrary.org/obo/UBERON_0008805` +### metanephric nephron `http://purl.obolibrary.org/obo/UBERON_0005110` #### Removed -- [gingival groove](http://purl.obolibrary.org/obo/UBERON_0008805) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "sulcus gingivalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" - -- [gingival groove](http://purl.obolibrary.org/obo/UBERON_0008805) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "sulcus gingivalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Gingival_sulcus" +- [metanephric nephron](http://purl.obolibrary.org/obo/UBERON_0005110) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The primitive form of the vertebrate nephron consists of a vascular filtration surface overlain with podocytes, a specialized coelomic cavity to receive the ultrafiltrate, and a tubule for modification to final urine. Although previously thought to be unique to the vertebrates, this design is now known to be widespread among invertebrates, including most of the protochordates, and especially their larvae.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [gingival groove](http://purl.obolibrary.org/obo/UBERON_0008805) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "sulcus gingivalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1093/icb/34.4.542 Ruppert EE, Evolutionary Origin of the Vertebrate Nephron. Integrative and Comparative Biology (1994)" -- [gingival groove](http://purl.obolibrary.org/obo/UBERON_0008805) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "sulcus gingivalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000719" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Gingival_sulcus" -### gland `http://purl.obolibrary.org/obo/UBERON_0002530` +### metanephric nephron tubule `http://purl.obolibrary.org/obo/UBERON_0005146` #### Removed -- [gland](http://purl.obolibrary.org/obo/UBERON_0002530) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "glandula" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0000522" +- [metanephric nephron tubule](http://purl.obolibrary.org/obo/UBERON_0005146) SubClassOf [meso-epithelium](http://purl.obolibrary.org/obo/UBERON_0012275) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Gland" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [gland](http://purl.obolibrary.org/obo/UBERON_0002530) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00100317" +### metanephric pyramid `http://purl.obolibrary.org/obo/UBERON_0005111` #### Added -- [gland](http://purl.obolibrary.org/obo/UBERON_0002530) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00100317" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [metanephric pyramid](http://purl.obolibrary.org/obo/UBERON_0005111) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -- [gland](http://purl.obolibrary.org/obo/UBERON_0002530) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "glandula" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0000522" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### metanephric renal pelvis `http://purl.obolibrary.org/obo/UBERON_0005249` +#### Removed +- [metanephric renal pelvis](http://purl.obolibrary.org/obo/UBERON_0005249) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The ureteric bud itself forms the collecting tubules and the ureter that drain the adult kidney. This type of kidney, called the metanephros, occurs in all adult amniotes.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Gland" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### gland of nasal mucosa `http://purl.obolibrary.org/obo/UBERON_0012278` -#### Removed -- [gland of nasal mucosa](http://purl.obolibrary.org/obo/UBERON_0012278) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "glandula nasalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639" -- [gland of nasal mucosa](http://purl.obolibrary.org/obo/UBERON_0012278) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "glandulae nasales" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000945" #### Added -- [gland of nasal mucosa](http://purl.obolibrary.org/obo/UBERON_0012278) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "glandulae nasales" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [metanephric renal pelvis](http://purl.obolibrary.org/obo/UBERON_0005249) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -- [gland of nasal mucosa](http://purl.obolibrary.org/obo/UBERON_0012278) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "glandula nasalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### metanephric renal vesicle `http://purl.obolibrary.org/obo/UBERON_0005147` +#### Removed +- [metanephric renal vesicle](http://purl.obolibrary.org/obo/UBERON_0005147) SubClassOf [meso-epithelium](http://purl.obolibrary.org/obo/UBERON_0012275) -### glandular cell of esophagus `http://purl.obolibrary.org/obo/CL_0002657` -#### Added -- [glandular cell of esophagus](http://purl.obolibrary.org/obo/CL_0002657) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### metanephric tubule `http://purl.obolibrary.org/obo/UBERON_0005106` +#### Removed +- [metanephric tubule](http://purl.obolibrary.org/obo/UBERON_0005106) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001526" -### glandular epithelial cell `http://purl.obolibrary.org/obo/CL_0000150` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [glandular epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### glenohumeral joint `http://purl.obolibrary.org/obo/UBERON_0001470` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543" + + + +### metanephros `http://purl.obolibrary.org/obo/UBERON_0000081` #### Removed -- [glenohumeral joint](http://purl.obolibrary.org/obo/UBERON_0001470) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "articulatio humeri" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:25912" +- [metanephros](http://purl.obolibrary.org/obo/UBERON_0000081) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A kidney formed of nephric tubules arising in the posterior region of the nephric ridge and drained by a ureter; replaces the embryonic pronephros and mesonephros [in mammals]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [glenohumeral joint](http://purl.obolibrary.org/obo/UBERON_0001470) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "articulatio humeri" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000039" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:25912" +- [metanephros](http://purl.obolibrary.org/obo/UBERON_0000081) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### glenoid fossa `http://purl.obolibrary.org/obo/UBERON_0006657` -#### Removed -- [glenoid fossa](http://purl.obolibrary.org/obo/UBERON_0006657) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cavitas glenoidalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Glenoid_cavity" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000039" -- [glenoid fossa](http://purl.obolibrary.org/obo/UBERON_0006657) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cavitas glenoidalis scapulae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:23275" +- [metanephros](http://purl.obolibrary.org/obo/UBERON_0000081) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "metanephric" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [metanephros](http://purl.obolibrary.org/obo/UBERON_0000081) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "During the fifth week of gestation, the mesonephric duct develops an outpouching, the ureteric bud, near its attachment to the cloaca. This bud, also called the metanephrogenic diverticulum, grows posteriorly and towards the head of the embryo. The elongated stalk of the ureteric bud, the metanephric duct, later forms the ureter. As the cranial end of the bud extends into the intermediate mesoderm, it undergoes a series of branchings to form the collecting duct system of the kidney. It also forms the major and minor calyces and the renal pelvis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [metanephros](http://purl.obolibrary.org/obo/UBERON_0000081) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [metanephric mesenchyme](http://purl.obolibrary.org/obo/UBERON_0003220) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" #### Added -- [glenoid fossa](http://purl.obolibrary.org/obo/UBERON_0006657) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cavitas glenoidalis scapulae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [metanephros](http://purl.obolibrary.org/obo/UBERON_0000081) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [metanephric mesenchyme](http://purl.obolibrary.org/obo/UBERON_0003220) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:23275" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### metanephros induced blastemal cells `http://purl.obolibrary.org/obo/UBERON_0010531` +#### Removed +- [metanephros induced blastemal cells](http://purl.obolibrary.org/obo/UBERON_0010531) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:27621" -- [glenoid fossa](http://purl.obolibrary.org/obo/UBERON_0006657) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D061165" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) +- [metanephros induced blastemal cells](http://purl.obolibrary.org/obo/UBERON_0010531) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "different versions of EMAPA have different labels for the same classes. In vHOG this is part of metanephros cortex but this leads to a cycle in basic." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EMAPA" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -- [glenoid fossa](http://purl.obolibrary.org/obo/UBERON_0006657) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cavitas glenoidalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Glenoid_cavity" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### metaphysis `http://purl.obolibrary.org/obo/UBERON_0001438` +#### Removed +- [metaphysis](http://purl.obolibrary.org/obo/UBERON_0001438) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Subdivision of diaphysis which forms the proximal or distal end of diaphysis next to the epiphysis; together with diaphysis proper, it constitutes the diaphysis. Examples: proximal metaphysis of humerus, distal metaphysis of femur.[FMA]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:24014" -### glial blood brain barrier `http://purl.obolibrary.org/obo/UBERON_0000202` + +### metaphysis of femur `http://purl.obolibrary.org/obo/UBERON_0006865` #### Added -- [glial blood brain barrier](http://purl.obolibrary.org/obo/UBERON_0000202) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007091" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [metaphysis of femur](http://purl.obolibrary.org/obo/UBERON_0006865) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### glial cell `http://purl.obolibrary.org/obo/CL_0000125` +### metaphysis of fibula `http://purl.obolibrary.org/obo/UBERON_0016928` #### Added -- [glial cell](http://purl.obolibrary.org/obo/CL_0000125) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [metaphysis of fibula](http://purl.obolibrary.org/obo/UBERON_0016928) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### glioblast `http://purl.obolibrary.org/obo/CL_0000030` +### metaphysis of humerus `http://purl.obolibrary.org/obo/UBERON_0013749` #### Added -- [glioblast](http://purl.obolibrary.org/obo/CL_0000030) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [metaphysis of humerus](http://purl.obolibrary.org/obo/UBERON_0013749) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### glomerular basement membrane `http://purl.obolibrary.org/obo/UBERON_0005777` -#### Removed -- [glomerular basement membrane](http://purl.obolibrary.org/obo/UBERON_0005777) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D050533" +### metaphysis of tibia `http://purl.obolibrary.org/obo/UBERON_0013750` #### Added -- [glomerular basement membrane](http://purl.obolibrary.org/obo/UBERON_0005777) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D050533" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [metaphysis of tibia](http://purl.obolibrary.org/obo/UBERON_0013750) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +### metapodial skeleton `http://purl.obolibrary.org/obo/UBERON_0010546` +#### Removed +- [metapodial skeleton](http://purl.obolibrary.org/obo/UBERON_0010546) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: connected_to subdivision of skeleton (UBERON:0010912)[VSAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0005025" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -### glomerular capillary endothelial cell `http://purl.obolibrary.org/obo/CL_1001005` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" -#### Added -- [glomerular capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1001005) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [metapodial skeleton](http://purl.obolibrary.org/obo/UBERON_0010546) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: distally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0005025" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -### glomerular capsule `http://purl.obolibrary.org/obo/UBERON_0001230` -#### Removed -- [glomerular capsule](http://purl.obolibrary.org/obo/UBERON_0001230) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "capsula glomeruli" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" -- [glomerular capsule](http://purl.obolibrary.org/obo/UBERON_0001230) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "capsula glomerularis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [metapodial skeleton](http://purl.obolibrary.org/obo/UBERON_0010546) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Endochondral bone complex located between the mesopodium and the acropodium and consisting of the metacarpals or metatarsals.[VSAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0005025" -#### Added -- [glomerular capsule](http://purl.obolibrary.org/obo/UBERON_0001230) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "capsula glomerularis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "VSAO:NI" -- [glomerular capsule](http://purl.obolibrary.org/obo/UBERON_0001230) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "capsula glomeruli" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" -### glomerular endothelial cell `http://purl.obolibrary.org/obo/CL_0002188` +#### Added +- [metapodial skeleton](http://purl.obolibrary.org/obo/UBERON_0010546) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### metapodium bone `http://purl.obolibrary.org/obo/UBERON_0003821` +#### Removed +- [metapodium bone](http://purl.obolibrary.org/obo/UBERON_0003821) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [metapodial skeleton](http://purl.obolibrary.org/obo/UBERON_0010546) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern" #### Added -- [glomerular endothelial cell](http://purl.obolibrary.org/obo/CL_0002188) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [metapodium bone](http://purl.obolibrary.org/obo/UBERON_0003821) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [metapodial skeleton](http://purl.obolibrary.org/obo/UBERON_0010546) -### glossopharyngeal nerve `http://purl.obolibrary.org/obo/UBERON_0001649` +### metapodium region `http://purl.obolibrary.org/obo/UBERON_0009877` #### Removed -- [glossopharyngeal nerve](http://purl.obolibrary.org/obo/UBERON_0001649) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus glossopharyngeus [ix]" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:50870" +- [metapodium region](http://purl.obolibrary.org/obo/UBERON_0009877) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "Naming conventions for pod terms under discussion within phenoscape group" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [glossopharyngeal nerve](http://purl.obolibrary.org/obo/UBERON_0001649) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nervus glossopharyngeus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Glossopharyngeal_nerve" +### metastasis-suppressor KiSS-1 `http://purl.obolibrary.org/obo/PR_000009344` +#### Removed +- [metastasis-suppressor KiSS-1](http://purl.obolibrary.org/obo/PR_000009344) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [metastasis-suppressor KiSS-1 (human)](http://purl.obolibrary.org/obo/PR_Q15726) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [glossopharyngeal nerve](http://purl.obolibrary.org/obo/UBERON_0001649) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus glossopharyngeus [ix]" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:50870" +### metatarsus region `http://purl.obolibrary.org/obo/UBERON_0000983` +#### Removed +- [metatarsus region](http://purl.obolibrary.org/obo/UBERON_0000983) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "mammalian and non-mammalian AOs differ in whether they consider this a part of the skeleton" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [glossopharyngeal nerve](http://purl.obolibrary.org/obo/UBERON_0001649) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nervus glossopharyngeus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Glossopharyngeal_nerve" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### metatarsus skeleton `http://purl.obolibrary.org/obo/UBERON_0010545` +#### Removed +- [metatarsus skeleton](http://purl.obolibrary.org/obo/UBERON_0010545) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Segment of the leg corresponding to the metatarsus, which articulates with the carpals at one end and with the phalanges at the other end.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000221" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -### glutamatergic neuron `http://purl.obolibrary.org/obo/CL_0000679` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + +- [metatarsus skeleton](http://purl.obolibrary.org/obo/UBERON_0010545) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [pedal digit metatarsal cartilage element](http://purl.obolibrary.org/obo/UBERON_0010697) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "many to one" #### Added -- [glutamatergic neuron](http://purl.obolibrary.org/obo/CL_0000679) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [metatarsus skeleton](http://purl.obolibrary.org/obo/UBERON_0010545) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [pedal digit metatarsal cartilage element](http://purl.obolibrary.org/obo/UBERON_0010697) + +### metathalamus `http://purl.obolibrary.org/obo/UBERON_0002704` +#### Removed +- [metathalamus](http://purl.obolibrary.org/obo/UBERON_0002704) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D005829" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) -### glycinergic amacrine cell `http://purl.obolibrary.org/obo/CL_4030028` + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -#### Added -- [glycinergic amacrine cell](http://purl.obolibrary.org/obo/CL_4030028) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [metathalamus](http://purl.obolibrary.org/obo/UBERON_0002704) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002776](http://purl.obolibrary.org/obo/UBERON_0002776) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" +- [metathalamus](http://purl.obolibrary.org/obo/UBERON_0002704) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "we follow FMA in making this a subtype of nucleus, but in fact it is a group containing two nuclei" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" -### goblet cell `http://purl.obolibrary.org/obo/CL_0000160` +- [metathalamus](http://purl.obolibrary.org/obo/UBERON_0002704) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002144](http://purl.obolibrary.org/obo/UBERON_0002144) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" -#### Added -- [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### gonad `http://purl.obolibrary.org/obo/UBERON_0000991` +### metencephalon `http://purl.obolibrary.org/obo/UBERON_0001895` #### Removed -- [gonad](http://purl.obolibrary.org/obo/UBERON_0000991) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004858" +- [metencephalon](http://purl.obolibrary.org/obo/UBERON_0001895) [RO_0002174](http://purl.obolibrary.org/obo/RO_0002174) [NCBITaxon_7955](http://purl.obolibrary.org/obo/NCBITaxon_7955) -#### Added -- [gonad](http://purl.obolibrary.org/obo/UBERON_0000991) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004858" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [metencephalon](http://purl.obolibrary.org/obo/UBERON_0001895) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### gonadal ridge `http://purl.obolibrary.org/obo/UBERON_0005294` -#### Removed -- [gonadal ridge](http://purl.obolibrary.org/obo/UBERON_0005294) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "crista gonadalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Gonadal_ridge" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500" -#### Added -- [gonadal ridge](http://purl.obolibrary.org/obo/UBERON_0005294) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "crista gonadalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Gonadal_ridge" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000741" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [metencephalon](http://purl.obolibrary.org/obo/UBERON_0001895) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The anterior of two brain vesicles formed by specialization of the rhombencephalon in the developing embryo. It gives rise to cerebellum and pons. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### goslim_prokaryote `http://purl.obolibrary.org/obo/go#goslim_prokaryote` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- AnnotationProperty: [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000741" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/metencephalon" -- [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) SubPropertyOf: [subset_property](http://www.geneontology.org/formats/oboInOwl#SubsetProperty) +- [metencephalon](http://purl.obolibrary.org/obo/UBERON_0001895) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anterior part of the hindbrain ventral to the cerebellum[BIRNLEX:965]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "BIRNLEX:965" +- [metencephalon](http://purl.obolibrary.org/obo/UBERON_0001895) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### granular cell of epidermis `http://purl.obolibrary.org/obo/CL_0002189` +- [metencephalon](http://purl.obolibrary.org/obo/UBERON_0001895) SubClassOf [immediate transformation of](http://purl.obolibrary.org/obo/RO_0002495) some [future metencephalon](http://purl.obolibrary.org/obo/UBERON_0010092) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" #### Added -- [granular cell of epidermis](http://purl.obolibrary.org/obo/CL_0002189) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [metencephalon](http://purl.obolibrary.org/obo/UBERON_0001895) SubClassOf [immediate transformation of](http://purl.obolibrary.org/obo/RO_0002495) some [future metencephalon](http://purl.obolibrary.org/obo/UBERON_0010092) -### granular layer of cerebellar cortex `http://purl.obolibrary.org/obo/UBERON_0002956` +### midbrain `http://purl.obolibrary.org/obo/UBERON_0001891` #### Removed -- [granular layer of cerebellar cortex](http://purl.obolibrary.org/obo/UBERON_0002956) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum granulosum corticis cerebelli" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:83140" +- [midbrain](http://purl.obolibrary.org/obo/UBERON_0001891) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "part of brainstem in ABA - we reject this in favor of ISBN:0471888893 which has an implicit overlaps relationships" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "ABA" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [midbrain](http://purl.obolibrary.org/obo/UBERON_0001891) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Middle part of the brain composed of the optic tectum and penducular region.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -#### Added -- [granular layer of cerebellar cortex](http://purl.obolibrary.org/obo/UBERON_0002956) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum granulosum corticis cerebelli" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:83140" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010149" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [midbrain](http://purl.obolibrary.org/obo/UBERON_0001891) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally. Kimmel et al, 1995.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000128" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -### granule cell `http://purl.obolibrary.org/obo/CL_0000120` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -#### Added -- [granule cell](http://purl.obolibrary.org/obo/CL_0000120) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" +- [midbrain](http://purl.obolibrary.org/obo/UBERON_0001891) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [hindbrain](http://purl.obolibrary.org/obo/UBERON_0002028) + - [exceptions](http://www.geneontology.org/formats/oboInOwl#exceptions) "ZFA" -### granulocyte `http://purl.obolibrary.org/obo/CL_0000094` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" -#### Added -- [granulocyte](http://purl.obolibrary.org/obo/CL_0000094) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [status](http://www.geneontology.org/formats/oboInOwl#status) "pending" +- [midbrain](http://purl.obolibrary.org/obo/UBERON_0001891) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)" -### granulocyte monocyte progenitor cell `http://purl.obolibrary.org/obo/CL_0000557` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [granulocyte monocyte progenitor cell](http://purl.obolibrary.org/obo/CL_0000557) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### granulocytopoietic cell `http://purl.obolibrary.org/obo/CL_0002191` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000069" -#### Added -- [granulocytopoietic cell](http://purl.obolibrary.org/obo/CL_0002191) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [midbrain](http://purl.obolibrary.org/obo/UBERON_0001891) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [diencephalon](http://purl.obolibrary.org/obo/UBERON_0001894) + - [exceptions](http://www.geneontology.org/formats/oboInOwl#exceptions) "ZFA" + - [exceptions_url](http://www.geneontology.org/formats/oboInOwl#exceptions_url) "https://github.com/obophenotype/uberon/issues/378" -### granulosa cell `http://purl.obolibrary.org/obo/CL_0000501` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" -#### Added -- [granulosa cell](http://purl.obolibrary.org/obo/CL_0000501) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [status](http://www.geneontology.org/formats/oboInOwl#status) "pending" +- [midbrain](http://purl.obolibrary.org/obo/UBERON_0001891) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "mesencephalic" -### gravid organism `http://purl.obolibrary.org/obo/UBERON_0009097` +- [midbrain](http://purl.obolibrary.org/obo/UBERON_0001891) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -#### Added -- [gravid organism](http://purl.obolibrary.org/obo/UBERON_0009097) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "IDOMAL:0000443" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) +- [midbrain](http://purl.obolibrary.org/obo/UBERON_0001891) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [mesencephalic neural crest](http://purl.obolibrary.org/obo/UBERON_0003849) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +#### Added +- [midbrain](http://purl.obolibrary.org/obo/UBERON_0001891) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [mesencephalic neural crest](http://purl.obolibrary.org/obo/UBERON_0003849) -### gray matter `http://purl.obolibrary.org/obo/UBERON_0002020` +### midbrain arachnoid mater `http://purl.obolibrary.org/obo/UBERON_0003557` #### Removed -- [gray matter](http://purl.obolibrary.org/obo/UBERON_0002020) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D066128" +- [midbrain arachnoid mater](http://purl.obolibrary.org/obo/UBERON_0003557) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Arachnoid mater that is part of the midbrain. [Bgee_curator][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [gray matter](http://purl.obolibrary.org/obo/UBERON_0002020) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "substantia grisea" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:67242" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000233" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" - -- [gray matter](http://purl.obolibrary.org/obo/UBERON_0002020) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "grisea" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - -#### Added -- [gray matter](http://purl.obolibrary.org/obo/UBERON_0002020) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D066128" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) +- [midbrain arachnoid mater](http://purl.obolibrary.org/obo/UBERON_0003557) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [gray matter](http://purl.obolibrary.org/obo/UBERON_0002020) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "substantia grisea" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:67242" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000233" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [gray matter](http://purl.obolibrary.org/obo/UBERON_0002020) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "grisea" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### gray matter of spinal cord `http://purl.obolibrary.org/obo/UBERON_0002315` +### midbrain dura mater `http://purl.obolibrary.org/obo/UBERON_0003562` #### Removed -- [gray matter of spinal cord](http://purl.obolibrary.org/obo/UBERON_0002315) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "substantia grisea medullae spinalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:256580" +- [midbrain dura mater](http://purl.obolibrary.org/obo/UBERON_0003562) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Dura mater that is part of the midbrain. [Bgee_curator][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [gray matter of spinal cord](http://purl.obolibrary.org/obo/UBERON_0002315) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "substantia grisea medullae spinalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000410" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:256580" +- [midbrain dura mater](http://purl.obolibrary.org/obo/UBERON_0003562) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### great saphenous vein `http://purl.obolibrary.org/obo/UBERON_0001363` -#### Removed -- [great saphenous vein](http://purl.obolibrary.org/obo/UBERON_0001363) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena saphena magna" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Great_saphenous_vein" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000410" -#### Added -- [great saphenous vein](http://purl.obolibrary.org/obo/UBERON_0001363) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena saphena magna" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Great_saphenous_vein" +### midbrain hindbrain boundary neural plate `http://purl.obolibrary.org/obo/UBERON_0009615` +#### Removed +- [midbrain hindbrain boundary neural plate](http://purl.obolibrary.org/obo/UBERON_0009615) SubClassOf [immediate transformation of](http://purl.obolibrary.org/obo/RO_0002495) some [presumptive midbrain hindbrain boundary](http://purl.obolibrary.org/obo/UBERON_0007281) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "https://github.com/obophenotype/uberon/issues/438" -### group 2 innate lymphoid cell `http://purl.obolibrary.org/obo/CL_0001069` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Bgee:AN" #### Added -- [group 2 innate lymphoid cell](http://purl.obolibrary.org/obo/CL_0001069) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [midbrain hindbrain boundary neural plate](http://purl.obolibrary.org/obo/UBERON_0009615) SubClassOf [immediate transformation of](http://purl.obolibrary.org/obo/RO_0002495) some [presumptive midbrain hindbrain boundary](http://purl.obolibrary.org/obo/UBERON_0007281) -### group 2 innate lymphoid cell, human `http://purl.obolibrary.org/obo/CL_0001081` +### midbrain neural tube `http://purl.obolibrary.org/obo/UBERON_0010286` #### Added -- [group 2 innate lymphoid cell, human](http://purl.obolibrary.org/obo/CL_0001081) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [midbrain neural tube](http://purl.obolibrary.org/obo/UBERON_0010286) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + +### midbrain pia mater `http://purl.obolibrary.org/obo/UBERON_0003551` +#### Removed +- [midbrain pia mater](http://purl.obolibrary.org/obo/UBERON_0003551) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Pia mater that is part of the midbrain. [Bgee_curator][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### group 3 innate lymphoid cell `http://purl.obolibrary.org/obo/CL_0001071` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [group 3 innate lymphoid cell](http://purl.obolibrary.org/obo/CL_0001071) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000467" -### group 3 innate lymphoid cell, human `http://purl.obolibrary.org/obo/CL_0001078` +- [midbrain pia mater](http://purl.obolibrary.org/obo/UBERON_0003551) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639" -#### Added -- [group 3 innate lymphoid cell, human](http://purl.obolibrary.org/obo/CL_0001078) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### gustatory organ `http://purl.obolibrary.org/obo/UBERON_0003212` -#### Removed -- [gustatory organ](http://purl.obolibrary.org/obo/UBERON_0003212) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005159" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [gustatory organ](http://purl.obolibrary.org/obo/UBERON_0003212) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005159" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000467" -### gut absorptive cell `http://purl.obolibrary.org/obo/CL_0000677` -#### Added -- [gut absorptive cell](http://purl.obolibrary.org/obo/CL_0000677) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### midbrain subarachnoid space `http://purl.obolibrary.org/obo/UBERON_0005217` +#### Removed +- [midbrain subarachnoid space](http://purl.obolibrary.org/obo/UBERON_0005217) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Subarachnoid space that is part of the midbrain. [Bgee_curator][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### gut endothelial cell `http://purl.obolibrary.org/obo/CL_0000131` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [gut endothelial cell](http://purl.obolibrary.org/obo/CL_0000131) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001304" -### hair follicle `http://purl.obolibrary.org/obo/UBERON_0002073` + +### midbrain tectum `http://purl.obolibrary.org/obo/UBERON_0002314` #### Removed -- [hair follicle](http://purl.obolibrary.org/obo/UBERON_0002073) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "folliculus pili" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Hair_follicle" +- [midbrain tectum](http://purl.obolibrary.org/obo/UBERON_0002314) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In adult humans it is present only in the mesencephalon as the inferior and the superior colliculi" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [midbrain tectum](http://purl.obolibrary.org/obo/UBERON_0002314) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The tectum - a multisensory, topologically mapped structure in the roof of the midbrain presents a remarkable degree of conservation in all vertebrate radiations; although it varies in the extent of its development in different vertebrate classes, there is considerable evidence now to deem its layered structure, its cell types, and its hodological pattern as homologous in all vertebrates.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [hair follicle](http://purl.obolibrary.org/obo/UBERON_0002073) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "folliculus pili" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Hair_follicle" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1371/journal.pone.0003582 Maximino C, Evolutionary Changes in the Complexity of the Tectum of Nontetrapods: A Cladistic Approach. PLoS ONE (2008)" -### hair follicular keratinocyte `http://purl.obolibrary.org/obo/CL_2000092` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001388" -#### Added -- [hair follicular keratinocyte](http://purl.obolibrary.org/obo/CL_2000092) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### hair root sheath `http://purl.obolibrary.org/obo/UBERON_0005933` +### midbrain tegmentum `http://purl.obolibrary.org/obo/UBERON_0001943` #### Removed -- [hair root sheath](http://purl.obolibrary.org/obo/UBERON_0005933) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://github.com/obophenotype/mouse-anatomy-ontology/issues/56" +- [midbrain tegmentum](http://purl.obolibrary.org/obo/UBERON_0001943) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D013681" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) -#### Added -- [hair root sheath](http://purl.obolibrary.org/obo/UBERON_0005933) [see also](http://www.w3.org/2000/01/rdf-schema#seeAlso) "https://github.com/obophenotype/mouse-anatomy-ontology/issues/56"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +- [midbrain tegmentum](http://purl.obolibrary.org/obo/UBERON_0001943) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### head sensillum `http://purl.obolibrary.org/obo/UBERON_0000963` -#### Removed -- [head sensillum](http://purl.obolibrary.org/obo/UBERON_0000963) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004114" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [head sensillum](http://purl.obolibrary.org/obo/UBERON_0000963) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004114" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1016/j.brainresbull.2005.05.001 Villar-Cheda B, Abalo XM, Anadon R, Rodicio MC, The tegmental proliferation region in the sea lamprey. Brain Research Bulletin (2005)" -### heart left ventricle `http://purl.obolibrary.org/obo/UBERON_0002084` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001367" + + + +### midbrain-hindbrain boundary `http://purl.obolibrary.org/obo/UBERON_0003052` #### Removed -- [heart left ventricle](http://purl.obolibrary.org/obo/UBERON_0002084) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ventriculus sinister cordis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Left_ventricle" +- [midbrain-hindbrain boundary](http://purl.obolibrary.org/obo/UBERON_0003052) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [heart left ventricle](http://purl.obolibrary.org/obo/UBERON_0002084) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ventriculus sinister cordis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Left_ventricle" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000649" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1016/j.ydbio.2005.02.008 Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005)" -### heart right ventricle `http://purl.obolibrary.org/obo/UBERON_0002080` -#### Removed -- [heart right ventricle](http://purl.obolibrary.org/obo/UBERON_0002080) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ventriculus dexter" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [midbrain-hindbrain boundary](http://purl.obolibrary.org/obo/UBERON_0003052) SubClassOf [anatomical junction](http://purl.obolibrary.org/obo/UBERON_0007651) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/106/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Right_ventricle" + - [inconsistent_with](http://www.geneontology.org/formats/oboInOwl#inconsistent_with) "ZFA" #### Added -- [heart right ventricle](http://purl.obolibrary.org/obo/UBERON_0002080) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ventriculus dexter" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Right_ventricle" +- [midbrain-hindbrain boundary](http://purl.obolibrary.org/obo/UBERON_0003052) SubClassOf [anatomical junction](http://purl.obolibrary.org/obo/UBERON_0007651) -### helper T cell `http://purl.obolibrary.org/obo/CL_0000912` +### middle ear `http://purl.obolibrary.org/obo/UBERON_0001756` +#### Removed +- [middle ear](http://purl.obolibrary.org/obo/UBERON_0001756) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The tympanic cavity and auditory tube of an amniote develop from the first embryonic pharyngeal pouch, so they are homologous to the first gill pouch, or spiracle, of a fish. We are uncertain whether this homology strictly applies to the middle ear cavity and auditory tube of lissamphibians, which show certain peculiarities in their development.[uncertain][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.417" -#### Added -- [helper T cell](http://purl.obolibrary.org/obo/CL_0000912) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### hematopoietic cell `http://purl.obolibrary.org/obo/CL_0000988` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [hematopoietic cell](http://purl.obolibrary.org/obo/CL_0000988) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000312" +- [middle ear](http://purl.obolibrary.org/obo/UBERON_0001756) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The intermediate portion of the ear which consists of a small air-filled and membrane-lined chamber. It is lodged in the temporal bone and continues with the nasopharynx through the Eustachian tube. It is separated from the external ear by the tympanic membrane and from the inner ear by the fenestrae. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### hematopoietic multipotent progenitor cell `http://purl.obolibrary.org/obo/CL_0000837` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [hematopoietic multipotent progenitor cell](http://purl.obolibrary.org/obo/CL_0000837) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000312" -### hematopoietic precursor cell `http://purl.obolibrary.org/obo/CL_0008001` -#### Added -- [hematopoietic precursor cell](http://purl.obolibrary.org/obo/CL_0008001) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### middle phalanx `http://purl.obolibrary.org/obo/UBERON_0004301` +#### Removed +- [middle phalanx](http://purl.obolibrary.org/obo/UBERON_0004301) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Intermediate phalanges are bones found in the limbs of most vertebrates. In humans, they are the bones of the finger and toe which lie in the middle, between the two wrinkly joints. The thumb and big toe do not have intermediate phalanges. In most other vertebrates, they have a corresponding place in their limbs, whether they be paw, wing, hoof or fin" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" -### hematopoietic stem cell `http://purl.obolibrary.org/obo/CL_0000037` +- [middle phalanx](http://purl.obolibrary.org/obo/UBERON_0004301) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "in some groups such as whales, there are multiple intermediate phalanges" -#### Added -- [hematopoietic stem cell](http://purl.obolibrary.org/obo/CL_0000037) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### hepatic artery `http://purl.obolibrary.org/obo/UBERON_0001193` +### midface `http://purl.obolibrary.org/obo/UBERON_0004089` #### Removed -- [hepatic artery](http://purl.obolibrary.org/obo/UBERON_0001193) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arteria hepatica propria" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [midface](http://purl.obolibrary.org/obo/UBERON_0004089) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "midfacial" -#### Added -- [hepatic artery](http://purl.obolibrary.org/obo/UBERON_0001193) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arteria hepatica propria" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [midface](http://purl.obolibrary.org/obo/UBERON_0004089) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:32806" -### hepatic diverticulum `http://purl.obolibrary.org/obo/UBERON_0008835` + +### midgut `http://purl.obolibrary.org/obo/UBERON_0001045` #### Removed -- [hepatic diverticulum](http://purl.obolibrary.org/obo/UBERON_0008835) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "diverticulum hepaticum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Hepatic_diverticulum" +- [midgut](http://purl.obolibrary.org/obo/UBERON_0001045) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [hepatic diverticulum](http://purl.obolibrary.org/obo/UBERON_0008835) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "diverticulum hepaticum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Hepatic_diverticulum" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000290" -### hepatic portal vein `http://purl.obolibrary.org/obo/UBERON_0001639` -#### Removed -- [hepatic portal vein](http://purl.obolibrary.org/obo/UBERON_0001639) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena portae hepatis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Hepatic_portal_vein" +- [midgut](http://purl.obolibrary.org/obo/UBERON_0001045) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in FMA this represents an embryonic region." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [midgut](http://purl.obolibrary.org/obo/UBERON_0001045) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In humans: originates from the foregut at the opening of the bile duct into the duodenum and continues through the small intestine and much of the large intestine until the transition to the hindgut about two-thirds of the way through the transverse colon" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" -#### Added -- [hepatic portal vein](http://purl.obolibrary.org/obo/UBERON_0001639) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena portae hepatis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [midgut](http://purl.obolibrary.org/obo/UBERON_0001045) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005383" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Hepatic_portal_vein" -### hepatic sinusoid `http://purl.obolibrary.org/obo/UBERON_0001281` +### milk `http://purl.obolibrary.org/obo/UBERON_0001913` #### Removed -- [hepatic sinusoid](http://purl.obolibrary.org/obo/UBERON_0001281) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vas sinusoideum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Hepatic_sinusoid" +- [milk](http://purl.obolibrary.org/obo/UBERON_0001913) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The detailed similarities of mammary glands in living monotremes, marsupials, and eutherians argue for a monophyletic origin of these glands, perhaps by the combination of parts of preexisting sebaceous and sweat glands.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [hepatic sinusoid](http://purl.obolibrary.org/obo/UBERON_0001281) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vas sinusoideum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Hepatic_sinusoid" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.224" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001263" -### hepatic stellate cell `http://purl.obolibrary.org/obo/CL_0000632` +- [milk](http://purl.obolibrary.org/obo/UBERON_0001913) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "ncit:Milk refers specifically to cow milk" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "ncit" -#### Added -- [hepatic stellate cell](http://purl.obolibrary.org/obo/CL_0000632) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### hepatic vein `http://purl.obolibrary.org/obo/UBERON_0001143` +### mineralized bone tissue `http://purl.obolibrary.org/obo/UBERON_4000115` #### Removed -- [hepatic vein](http://purl.obolibrary.org/obo/UBERON_0001143) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vena hepatica" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [mineralized bone tissue](http://purl.obolibrary.org/obo/UBERON_4000115) [UBPROP_0000004](http://purl.obolibrary.org/obo/UBPROP_0000004) "This class was sourced from an external ontology (vertebrate_skeletal_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://purl.obolibrary.org/obo/vsao.owl" -- [hepatic vein](http://purl.obolibrary.org/obo/UBERON_0001143) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "venae hepaticae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Hepatic_vein" -#### Added -- [hepatic vein](http://purl.obolibrary.org/obo/UBERON_0001143) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "venae hepaticae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### mineralized extracellular matrix `http://purl.obolibrary.org/obo/UBERON_4000020` +#### Removed +- [mineralized extracellular matrix](http://purl.obolibrary.org/obo/UBERON_4000020) [UBPROP_0000004](http://purl.obolibrary.org/obo/UBPROP_0000004) "This class was sourced from an external ontology (vertebrate_skeletal_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://purl.obolibrary.org/obo/vsao.owl" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Hepatic_vein" -- [hepatic vein](http://purl.obolibrary.org/obo/UBERON_0001143) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vena hepatica" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### missing_from `http://www.geneontology.org/formats/oboInOwl#missing_from` +#### Removed +- AnnotationProperty: [missing_from](http://www.geneontology.org/formats/oboInOwl#missing_from) -### hepatoblast `http://purl.obolibrary.org/obo/CL_0005026` -#### Added -- [hepatoblast](http://purl.obolibrary.org/obo/CL_0005026) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### mixed ectoderm/mesoderm/endoderm-derived structure `http://purl.obolibrary.org/obo/UBERON_0000078` +#### Removed +- [mixed ectoderm/mesoderm/endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000078) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple" -### hepatocyte `http://purl.obolibrary.org/obo/CL_0000182` -#### Added -- [hepatocyte](http://purl.obolibrary.org/obo/CL_0000182) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### mixed endoderm/mesoderm-derived structure `http://purl.obolibrary.org/obo/UBERON_0000077` +#### Removed +- [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple" -### hepatopancreatic ampulla `http://purl.obolibrary.org/obo/UBERON_0004913` + + +### modified_from `http://www.geneontology.org/formats/oboInOwl#modified_from` #### Removed -- [hepatopancreatic ampulla](http://purl.obolibrary.org/obo/UBERON_0004913) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ampulla Vaterii" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ampulla_of_Vater" +- AnnotationProperty: [modified_from](http://www.geneontology.org/formats/oboInOwl#modified_from) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [hepatopancreatic ampulla](http://purl.obolibrary.org/obo/UBERON_0004913) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ampulla hepatopancreatica" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ampulla_of_Vater" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### molecular interaction relation helper property `http://purl.obolibrary.org/obo/RO_0002564` +#### Removed +- [molecular interaction relation helper property](http://purl.obolibrary.org/obo/RO_0002564) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) -- [hepatopancreatic ampulla](http://purl.obolibrary.org/obo/UBERON_0004913) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ampulla biliaropancreatica" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15076" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### molecular layer of cerebellar cortex `http://purl.obolibrary.org/obo/UBERON_0002974` +#### Removed +- [molecular layer of cerebellar cortex](http://purl.obolibrary.org/obo/UBERON_0002974) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Compare with ZFA:0000636 - cerebellar crest, which is also composed of parallel fibers but located in a more restricted nucleus within the cerebellum" -#### Added -- [hepatopancreatic ampulla](http://purl.obolibrary.org/obo/UBERON_0004913) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ampulla hepatopancreatica" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ampulla_of_Vater" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -- [hepatopancreatic ampulla](http://purl.obolibrary.org/obo/UBERON_0004913) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ampulla Vaterii" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ampulla_of_Vater" +### molecularly interacts with `http://purl.obolibrary.org/obo/RO_0002436` +#### Removed +- [molecularly interacts with](http://purl.obolibrary.org/obo/RO_0002436) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "molecularly binds with" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [molecularly interacts with](http://purl.obolibrary.org/obo/RO_0002436) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "binds" -- [hepatopancreatic ampulla](http://purl.obolibrary.org/obo/UBERON_0004913) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ampulla biliaropancreatica" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [molecularly interacts with](http://purl.obolibrary.org/obo/RO_0002436) [closeMatch](http://www.w3.org/2004/02/skos/core#closeMatch) "http://purl.obolibrary.org/obo/MI_0915"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15076" +- [molecularly interacts with](http://purl.obolibrary.org/obo/RO_0002436) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### high nuclear/cytoplasmic ratio `http://purl.obolibrary.org/obo/PATO_0040072` +### monoatomic ion transmembrane transporter activity `http://purl.obolibrary.org/obo/GO_0015075` +#### Removed +- [monoatomic ion transmembrane transporter activity](http://purl.obolibrary.org/obo/GO_0015075) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [monoatomic ion transmembrane transport](http://purl.obolibrary.org/obo/GO_0034220) + - [source](http://www.geneontology.org/formats/oboInOwl#http://purl.org/dc/terms/source) "GO_REF:0000090" #### Added -- [high nuclear/cytoplasmic ratio](http://purl.obolibrary.org/obo/PATO_0040072) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "high N:C ratio" +- [monoatomic ion transmembrane transporter activity](http://purl.obolibrary.org/obo/GO_0015075) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [monoatomic ion transmembrane transport](http://purl.obolibrary.org/obo/GO_0034220) -- [high nuclear/cytoplasmic ratio](http://purl.obolibrary.org/obo/PATO_0040072) [created by](http://www.geneontology.org/formats/oboInOwl#created_by) "http://orcid.org/0000-0001-5208-3432" -- [high nuclear/cytoplasmic ratio](http://purl.obolibrary.org/obo/PATO_0040072) [label](http://www.w3.org/2000/01/rdf-schema#label) "high nuclear/cytoplasmic ratio" +### morula `http://purl.obolibrary.org/obo/UBERON_0000085` +#### Removed +- [morula](http://purl.obolibrary.org/obo/UBERON_0000085) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "EHDAA2 has embryo starting later" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EHDAA2" -- [high nuclear/cytoplasmic ratio](http://purl.obolibrary.org/obo/PATO_0040072) [id](http://www.geneontology.org/formats/oboInOwl#id) "PATO:0040072" -- [high nuclear/cytoplasmic ratio](http://purl.obolibrary.org/obo/PATO_0040072) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "A high nuclear/cytolasmic ratio is 70% or higher." -- [high nuclear/cytoplasmic ratio](http://purl.obolibrary.org/obo/PATO_0040072) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A quality inhering in a cell by virtue of the cell having a high nuclear/cytoplasmic ratio." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://lymerick.net/blood-cells.pdf" +### mouth `http://purl.obolibrary.org/obo/UBERON_0000165` +#### Removed +- [mouth](http://purl.obolibrary.org/obo/UBERON_0000165) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:NC_ratio&oldid=931936284" +- [mouth](http://purl.obolibrary.org/obo/UBERON_0000165) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "oral" -- [high nuclear/cytoplasmic ratio](http://purl.obolibrary.org/obo/PATO_0040072) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "quality" +- [mouth](http://purl.obolibrary.org/obo/UBERON_0000165) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -- Class: [high nuclear/cytoplasmic ratio](http://purl.obolibrary.org/obo/PATO_0040072) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010355" -- [high nuclear/cytoplasmic ratio](http://purl.obolibrary.org/obo/PATO_0040072) SubClassOf [cellular quality](http://purl.obolibrary.org/obo/PATO_0001396) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" -### hindgut `http://purl.obolibrary.org/obo/UBERON_0001046` -#### Removed -- [hindgut](http://purl.obolibrary.org/obo/UBERON_0001046) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "metenteron" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Hindgut" +- [mouth](http://purl.obolibrary.org/obo/UBERON_0000165) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [hindgut](http://purl.obolibrary.org/obo/UBERON_0001046) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005384" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [hindgut](http://purl.obolibrary.org/obo/UBERON_0001046) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "metenteron" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Hindgut" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000812" -- [hindgut](http://purl.obolibrary.org/obo/UBERON_0001046) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005384" +- [mouth](http://purl.obolibrary.org/obo/UBERON_0000165) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + +- [mouth](http://purl.obolibrary.org/obo/UBERON_0000165) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00003126" - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [mouth](http://purl.obolibrary.org/obo/UBERON_0000165) SubClassOf [subdivision of digestive tract](http://purl.obolibrary.org/obo/UBERON_0004921) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts" -### hindlimb `http://purl.obolibrary.org/obo/UBERON_0002103` -#### Removed -- [hindlimb](http://purl.obolibrary.org/obo/UBERON_0002103) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "membrum inferius" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:7184" +#### Added +- [mouth](http://purl.obolibrary.org/obo/UBERON_0000165) SubClassOf [subdivision of digestive tract](http://purl.obolibrary.org/obo/UBERON_0004921) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### mouth mucosa `http://purl.obolibrary.org/obo/UBERON_0003729` +#### Removed +- [mouth mucosa](http://purl.obolibrary.org/obo/UBERON_0003729) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "this is defined as any mucous membrane of the mouth - including palate, lips, uvula, etc. ncit split mouth/oral mucosa into lip and buccal. In future we may split into masticatory/keratinized (gingiva + hard palate) vs lining/non-keratinized (lips, cheeks, floor of mouth, soft palate). FMA distinguishes between mucosa of mouth and region of mouth (the latter including the buccal mucosa)" -- [hindlimb](http://purl.obolibrary.org/obo/UBERON_0002103) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "membrum inferius" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lower_limb" +- [mouth mucosa](http://purl.obolibrary.org/obo/UBERON_0003729) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "the mucous membrane epithelium of the mouth. It can be divided into three categories: masticatory, lining, and specialized[Wikipedia:Oral_mucosa]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Oral_mucosa" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [hindlimb](http://purl.obolibrary.org/obo/UBERON_0002103) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "membrum inferius" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lower_limb" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### mucosa `http://purl.obolibrary.org/obo/UBERON_0000344` +#### Removed +- [mucosa](http://purl.obolibrary.org/obo/UBERON_0000344) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA has mucosa vs region of mucosa; these are subtypes of Mucosa: Mucosa of gallbladder, tongue, .... The following are subtypes of Region of mucosa: Mucosa of zone of stomach, trachea, bronchus, dorsum of tongue.... Depends on whether the covered area is an organ or organ component. Uberon does not regard organ vs organ component as crucial distinction and thus collapses these into a single class deliberately" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" -- [hindlimb](http://purl.obolibrary.org/obo/UBERON_0002103) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "membrum inferius" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [mucosa](http://purl.obolibrary.org/obo/UBERON_0000344) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "mucosal" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:7184" +- [mucosa](http://purl.obolibrary.org/obo/UBERON_0000344) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [submucosa](http://purl.obolibrary.org/obo/UBERON_0000009) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### hindlimb muscle `http://purl.obolibrary.org/obo/UBERON_0003663` +### mucosa of anal canal `http://purl.obolibrary.org/obo/UBERON_0003342` #### Added -- [hindlimb muscle](http://purl.obolibrary.org/obo/UBERON_0003663) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas) +- [mucosa of anal canal](http://purl.obolibrary.org/obo/UBERON_0003342) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -- [hindlimb muscle](http://purl.obolibrary.org/obo/UBERON_0003663) [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [Homo sapiens](http://purl.obolibrary.org/obo/NCBITaxon_9606) +### mucosa of biliary tree `http://purl.obolibrary.org/obo/UBERON_0004999` -### hindlimb skeleton `http://purl.obolibrary.org/obo/UBERON_0001441` -#### Removed -- [hindlimb skeleton](http://purl.obolibrary.org/obo/UBERON_0001441) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ossa membri inferioris" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:24140" +#### Added +- [mucosa of biliary tree](http://purl.obolibrary.org/obo/UBERON_0004999) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### mucosa of bronchiole `http://purl.obolibrary.org/obo/UBERON_0005039` #### Added -- [hindlimb skeleton](http://purl.obolibrary.org/obo/UBERON_0001441) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ossa membri inferioris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [mucosa of bronchiole](http://purl.obolibrary.org/obo/UBERON_0005039) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:24140" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### mucosa of dorsum of tongue `http://purl.obolibrary.org/obo/UBERON_0010052` +#### Removed +- [mucosa of dorsum of tongue](http://purl.obolibrary.org/obo/UBERON_0010052) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "develops fungiform papillae by WNT induction at 11 weeks pc in human. Filiform papillae develop later. ISBN:1607950324" -### hindlimb stylopod `http://purl.obolibrary.org/obo/UBERON_0000376` -#### Removed -- [hindlimb stylopod](http://purl.obolibrary.org/obo/UBERON_0000376) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "femur" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Thigh" +### mucosa of gallbladder `http://purl.obolibrary.org/obo/UBERON_0005033` #### Added -- [hindlimb stylopod](http://purl.obolibrary.org/obo/UBERON_0000376) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "femur" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Thigh" +- [mucosa of gallbladder](http://purl.obolibrary.org/obo/UBERON_0005033) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -### hindlimb zeugopod `http://purl.obolibrary.org/obo/UBERON_0003823` +### mucosa of lacrimal canaliculus `http://purl.obolibrary.org/obo/UBERON_0005029` #### Added -- [hindlimb zeugopod](http://purl.obolibrary.org/obo/UBERON_0003823) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "VO:0010971" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" - - - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) +- [mucosa of lacrimal canaliculus](http://purl.obolibrary.org/obo/UBERON_0005029) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### hindlimb zeugopod muscle `http://purl.obolibrary.org/obo/UBERON_0004256` +### mucosa of larynx `http://purl.obolibrary.org/obo/UBERON_0001824` #### Added -- [hindlimb zeugopod muscle](http://purl.obolibrary.org/obo/UBERON_0004256) [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [Homo sapiens](http://purl.obolibrary.org/obo/NCBITaxon_9606) - -- [hindlimb zeugopod muscle](http://purl.obolibrary.org/obo/UBERON_0004256) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas) +- [mucosa of larynx](http://purl.obolibrary.org/obo/UBERON_0001824) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -### hindlimb zeugopod skeleton `http://purl.obolibrary.org/obo/UBERON_0010720` -#### Removed -- [hindlimb zeugopod skeleton](http://purl.obolibrary.org/obo/UBERON_0010720) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "skeleton cruris" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NominaAnatomicaVeterinaria:2005" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### mucosa of nasolacrimal duct `http://purl.obolibrary.org/obo/UBERON_0005043` #### Added -- [hindlimb zeugopod skeleton](http://purl.obolibrary.org/obo/UBERON_0010720) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "skeleton cruris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NominaAnatomicaVeterinaria:2005" - +- [mucosa of nasolacrimal duct](http://purl.obolibrary.org/obo/UBERON_0005043) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### hip `http://purl.obolibrary.org/obo/UBERON_0001464` -#### Removed -- [hip](http://purl.obolibrary.org/obo/UBERON_0001464) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "coxa" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Hip" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### mucosa of nasopharynx `http://purl.obolibrary.org/obo/UBERON_0005022` #### Added -- [hip](http://purl.obolibrary.org/obo/UBERON_0001464) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "coxa" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Hip" +- [mucosa of nasopharynx](http://purl.obolibrary.org/obo/UBERON_0005022) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -### hippocampal formation `http://purl.obolibrary.org/obo/UBERON_0002421` +### mucosa of oral region `http://purl.obolibrary.org/obo/UBERON_0003343` #### Removed -- [hippocampal formation](http://purl.obolibrary.org/obo/UBERON_0002421) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "formatio hippocampi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:177" - -#### Added -- [hippocampal formation](http://purl.obolibrary.org/obo/UBERON_0002421) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "formatio hippocampi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [mucosa of oral region](http://purl.obolibrary.org/obo/UBERON_0003343) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:26937" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:177" -### hippocampal neuron `http://purl.obolibrary.org/obo/CL_0002608` +### mucosa of seminal vesicle `http://purl.obolibrary.org/obo/UBERON_0004984` #### Added -- [hippocampal neuron](http://purl.obolibrary.org/obo/CL_0002608) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [mucosa of seminal vesicle](http://purl.obolibrary.org/obo/UBERON_0004984) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### hippocampus alveus `http://purl.obolibrary.org/obo/UBERON_0007639` +### mucosa of stomach `http://purl.obolibrary.org/obo/UBERON_0001199` #### Removed -- [hippocampus alveus](http://purl.obolibrary.org/obo/UBERON_0007639) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "alveus hippocampi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [mucosa of stomach](http://purl.obolibrary.org/obo/UBERON_0001199) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The gastric mucosa is the mucous membrane layer of the stomach which contains the glands and the gastric pits. In men it is about 1 mm thick and its surface is smooth, soft, and velvety. It consists of epithelium, lamina propria, and the muscularis mucosae. In its fresh state, it is of a pinkish tinge at the pyloric end and of a red or reddish-brown color over the rest of its surface. In infancy it is of a brighter hue, the vascular redness being more marked. It is thin at the cardiac extremity, but thicker toward the pylorus. During the contracted state of the organ it is thrown into numerous plaits or rugae, which, for the most part, have a longitudinal direction, and are most marked toward the pyloric end of the stomach, and along the greater curvature. These folds are entirely obliterated when the organ becomes distended. When examined with a lens, the inner surface of the mucous membrane presents a peculiar honeycomb appearance from being covered with funnel-like depressions or foveolae of a polygonal or hexagonal form, which vary from 0.12 to 0.25 mm. in diameter. These are the ducts of the gastric glands, and at the bottom of each may be seen one or more minute orifices, the openings of the gland tubes. Gastric glands are simple or branched tubular glands that emerge on the deeper part of the gastric foveola, inside the gastric areas and outlined by the folds of the mucosa. There are three types of glands: cardiac glands (in the proximal part of the stomach), oxyntic glands (the dominating type of gland), and pyloric glands. The cardiac glands mainly contain mucus producing cells. The bottom part of the oxyntic glands is dominated by zymogen (chief) cells that produce pepsinogen (an inactive precursor of the pepsin enzyme). Parietal cells, which secrete hydrochloric acid are scattered in the glands, with most of them in the middle part. The upper part of the glands consist of mucous neck cells; in this part the dividing cells are seen. The pyloric glands contain mucus-secreting cells. Several types of endocrine cells are found in all regions of the gastric mucosa. In the pyloric glands contain gastrin producing cells (G cells); this hormone stimulates acid production from the parietal cells. ECL (enterochromaffine-like) cells, found in the oxyntic glands release histamine, which also is a powerful stimulant of the acid secretion. The A cells produce glucagon, which mobilizes the hepatic glycogen, and the enterochromaffin cells that produce serotonin, which stimulates the contraction of the smooth muscles. The surface of the mucous membrane is covered by a single layer of columnar epithelium . This epithelium commences very abruptly at the cardiac orifice, where there is a sudden transition from the stratified epithelium of the esophagus. The epithelial lining of the gland ducts is of the same character and is continuous with the general lining of the stomach. [WP,unvetted][Wikipedia:Gastric_mucosa]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Gastric_mucosa" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:186" -#### Added -- [hippocampus alveus](http://purl.obolibrary.org/obo/UBERON_0007639) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "alveus hippocampi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:186" +### mucosa of ureter `http://purl.obolibrary.org/obo/UBERON_0004980` +#### Added +- [mucosa of ureter](http://purl.obolibrary.org/obo/UBERON_0004980) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### hippocampus fimbria `http://purl.obolibrary.org/obo/UBERON_0002310` -#### Removed -- [hippocampus fimbria](http://purl.obolibrary.org/obo/UBERON_0002310) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "fimbria fornicis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:187" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### mucosa of urethra `http://purl.obolibrary.org/obo/UBERON_0012299` -- [hippocampus fimbria](http://purl.obolibrary.org/obo/UBERON_0002310) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "fimbria hippocampi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Fimbria_of_hippocampus" +#### Added +- [mucosa of urethra](http://purl.obolibrary.org/obo/UBERON_0012299) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:187" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### mucosa of urinary bladder `http://purl.obolibrary.org/obo/UBERON_0001259` #### Added -- [hippocampus fimbria](http://purl.obolibrary.org/obo/UBERON_0002310) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "fimbria fornicis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [mucosa of urinary bladder](http://purl.obolibrary.org/obo/UBERON_0001259) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:187" -- [hippocampus fimbria](http://purl.obolibrary.org/obo/UBERON_0002310) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "fimbria hippocampi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### mucosa of uterine tube `http://purl.obolibrary.org/obo/UBERON_0005048` + +#### Added +- [mucosa of uterine tube](http://purl.obolibrary.org/obo/UBERON_0005048) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Fimbria_of_hippocampus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:187" +### mucosa of vagina `http://purl.obolibrary.org/obo/UBERON_0004983` + +#### Added +- [mucosa of vagina](http://purl.obolibrary.org/obo/UBERON_0004983) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### hippocampus pyramidal layer `http://purl.obolibrary.org/obo/UBERON_0002313` +### mucous gland `http://purl.obolibrary.org/obo/UBERON_0000414` #### Removed -- [hippocampus pyramidal layer](http://purl.obolibrary.org/obo/UBERON_0002313) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "gyrus occipitalis tertius" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:156" +- [mucous gland](http://purl.obolibrary.org/obo/UBERON_0000414) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In frogs and salamanders, this is the smaller of the two types of gland, the other being the granular (poison) gland. In these species the mucous gland is a cluster of cells that release secretion into a common duct[Kardong]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0073040584" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [hasScope](http://www.geneontology.org/formats/oboInOwl#hasScope) "NCBITaxon:8292" -- [hippocampus pyramidal layer](http://purl.obolibrary.org/obo/UBERON_0002313) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "gyrus occipitalis inferior" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:156" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + +### mucous gland of lung `http://purl.obolibrary.org/obo/UBERON_0019190` #### Added -- [hippocampus pyramidal layer](http://purl.obolibrary.org/obo/UBERON_0002313) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "gyrus occipitalis inferior" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:156" +- [mucous gland of lung](http://purl.obolibrary.org/obo/UBERON_0019190) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -- [hippocampus pyramidal layer](http://purl.obolibrary.org/obo/UBERON_0002313) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "gyrus occipitalis tertius" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:156" +### mucus `http://purl.obolibrary.org/obo/UBERON_0000912` +#### Removed +- [mucus](http://purl.obolibrary.org/obo/UBERON_0000912) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "mucous" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [mucus](http://purl.obolibrary.org/obo/UBERON_0000912) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "mucoid" -### hippocampus stratum lucidum `http://purl.obolibrary.org/obo/UBERON_0007637` + +### multi cell part structure `http://purl.obolibrary.org/obo/UBERON_0005162` #### Removed -- [hippocampus stratum lucidum](http://purl.obolibrary.org/obo/UBERON_0007637) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "stratum lucidum hippocampi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Stratum_lucidum_of_hippocampus" +- [multi cell part structure](http://purl.obolibrary.org/obo/UBERON_0005162) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "we go with the FMA classification rather than the CARO one. FMA def: 'Anatomical cluster which has as direct parts cell parts from two or more cells.'" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "CARO" -#### Added -- [hippocampus stratum lucidum](http://purl.obolibrary.org/obo/UBERON_0007637) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "stratum lucidum hippocampi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Stratum_lucidum_of_hippocampus" +- [multi cell part structure](http://purl.obolibrary.org/obo/UBERON_0005162) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007060" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### hippocampus stratum oriens `http://purl.obolibrary.org/obo/UBERON_0005371` +### multi-tissue structure `http://purl.obolibrary.org/obo/UBERON_0000481` #### Removed -- [hippocampus stratum oriens](http://purl.obolibrary.org/obo/UBERON_0005371) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "gyrus cuneus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:157" +- [multi-tissue structure](http://purl.obolibrary.org/obo/UBERON_0000481) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007010" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [hippocampus stratum oriens](http://purl.obolibrary.org/obo/UBERON_0005371) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum oriens hippocampi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:83893" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### multi-unit eye `http://purl.obolibrary.org/obo/UBERON_0015165` +#### Removed +- [multi-unit eye](http://purl.obolibrary.org/obo/UBERON_0015165) [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_6544](http://purl.obolibrary.org/obo/NCBITaxon_6544) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "present on mantle edge in arcacean Bivalvia" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:21062451" -#### Added -- [hippocampus stratum oriens](http://purl.obolibrary.org/obo/UBERON_0005371) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum oriens hippocampi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:83893" +- [multi-unit eye](http://purl.obolibrary.org/obo/UBERON_0015165) [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_6340](http://purl.obolibrary.org/obo/NCBITaxon_6340) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "present on tentacular crown" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:21062451" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [multi-unit eye](http://purl.obolibrary.org/obo/UBERON_0015165) [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_7588](http://purl.obolibrary.org/obo/NCBITaxon_7588) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "The eyes (optic cushions) on the oral surface of Asteroida (Echinodermata), close to the base of the terminal tentacles, are also composed of a number of simple ocelli - as many as 80-200 in certain species" -- [hippocampus stratum oriens](http://purl.obolibrary.org/obo/UBERON_0005371) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "gyrus cuneus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:157" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:21062451" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### hippocampus stratum radiatum `http://purl.obolibrary.org/obo/UBERON_0005372` +### multicellular anatomical structure `http://purl.obolibrary.org/obo/UBERON_0010000` #### Removed -- [hippocampus stratum radiatum](http://purl.obolibrary.org/obo/UBERON_0005372) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum radiatum hippocampi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:83894" +- [multicellular anatomical structure](http://purl.obolibrary.org/obo/UBERON_0010000) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00100313" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [hippocampus stratum radiatum](http://purl.obolibrary.org/obo/UBERON_0005372) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum radiatum hippocampi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:83894" +### multicellular organism `http://purl.obolibrary.org/obo/UBERON_0000468` +#### Removed +- [multicellular organism](http://purl.obolibrary.org/obo/UBERON_0000468) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000001" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [multicellular organism](http://purl.obolibrary.org/obo/UBERON_0000468) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "organismal" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### humerus diaphysis `http://purl.obolibrary.org/obo/UBERON_0004652` +### multilaminar epithelium `http://purl.obolibrary.org/obo/UBERON_0000486` #### Removed -- [humerus diaphysis](http://purl.obolibrary.org/obo/UBERON_0004652) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "corpus humeri" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:13305" +- [multilaminar epithelium](http://purl.obolibrary.org/obo/UBERON_0000486) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Epithelium that consists of more than one layer of epithelial cells.[CARO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://orcid.org/0000-0001-9114-8737" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "CARO:0000069" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -#### Added -- [humerus diaphysis](http://purl.obolibrary.org/obo/UBERON_0004652) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "corpus humeri" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:13305" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "CARO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:45562" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### hydrolase activity `http://purl.obolibrary.org/obo/GO_0016787` -#### Removed -- [hydrolase activity](http://purl.obolibrary.org/obo/GO_0016787) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) +### muscle layer of anal canal `http://purl.obolibrary.org/obo/UBERON_0012490` #### Added -- [hydrolase activity](http://purl.obolibrary.org/obo/GO_0016787) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) +- [muscle layer of anal canal](http://purl.obolibrary.org/obo/UBERON_0012490) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### hydroxyapatite binding `http://purl.obolibrary.org/obo/GO_0046848` -#### Removed -- [hydroxyapatite binding](http://purl.obolibrary.org/obo/GO_0046848) SubClassOf [binding](http://purl.obolibrary.org/obo/GO_0005488) +### muscle layer of epididymis `http://purl.obolibrary.org/obo/UBERON_0006646` #### Added -- [hydroxyapatite binding](http://purl.obolibrary.org/obo/GO_0046848) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/geneontology/go-ontology/issues/21211"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) - -- [hydroxyapatite binding](http://purl.obolibrary.org/obo/GO_0046848) SubClassOf [small molecule binding](http://purl.obolibrary.org/obo/GO_0036094) +- [muscle layer of epididymis](http://purl.obolibrary.org/obo/UBERON_0006646) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### hyoid apparatus `http://purl.obolibrary.org/obo/UBERON_0010272` +### muscle layer of esophagus `http://purl.obolibrary.org/obo/UBERON_0011878` #### Removed -- [hyoid apparatus](http://purl.obolibrary.org/obo/UBERON_0010272) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "apparatus hyobranchialis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [muscle layer of esophagus](http://purl.obolibrary.org/obo/UBERON_0011878) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "In the upper esophagus, part of the externa is skeletal muscle, rather than smooth muscle" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" -#### Added -- [hyoid apparatus](http://purl.obolibrary.org/obo/UBERON_0010272) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "apparatus hyobranchialis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [muscle layer of esophagus](http://purl.obolibrary.org/obo/UBERON_0011878) SubClassOf [has part](http://purl.obolibrary.org/obo/BFO_0000051) some [skeletal muscle tissue](http://purl.obolibrary.org/obo/UBERON_0001134) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "upper part" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Muscular_layer" -### hyoid bone `http://purl.obolibrary.org/obo/UBERON_0001685` -#### Removed -- [hyoid bone](http://purl.obolibrary.org/obo/UBERON_0001685) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "os hyoideum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Hyoid_bone" +#### Added +- [muscle layer of esophagus](http://purl.obolibrary.org/obo/UBERON_0011878) SubClassOf [has part](http://purl.obolibrary.org/obo/BFO_0000051) some [skeletal muscle tissue](http://purl.obolibrary.org/obo/UBERON_0001134) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [hyoid bone](http://purl.obolibrary.org/obo/UBERON_0001685) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "os hyoideum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Hyoid_bone" +### muscle layer of oviduct `http://purl.obolibrary.org/obo/UBERON_0006642` - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +#### Added +- [muscle layer of oviduct](http://purl.obolibrary.org/obo/UBERON_0006642) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### hypendymal cell `http://purl.obolibrary.org/obo/CL_4023181` +### muscle layer of urinary bladder `http://purl.obolibrary.org/obo/UBERON_0012378` #### Added -- [hypendymal cell](http://purl.obolibrary.org/obo/CL_4023181) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [muscle layer of urinary bladder](http://purl.obolibrary.org/obo/UBERON_0012378) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### hypodermis `http://purl.obolibrary.org/obo/UBERON_0002072` +### muscle of arm `http://purl.obolibrary.org/obo/UBERON_0001499` #### Removed -- [hypodermis](http://purl.obolibrary.org/obo/UBERON_0002072) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tela subcutanea" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Hypodermis" +- [muscle of arm](http://purl.obolibrary.org/obo/UBERON_0001499) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "See notes on UBERON:0001460 for possible terminological confusion over term 'arm'. MA uses this consistent with uberon (forelimb muscle is subdivided into shoulder, arm and hand)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - -#### Added -- [hypodermis](http://purl.obolibrary.org/obo/UBERON_0002072) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D040521" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -- [hypodermis](http://purl.obolibrary.org/obo/UBERON_0002072) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tela subcutanea" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### muscle of auditory ossicle `http://purl.obolibrary.org/obo/UBERON_0004113` +#### Removed +- [muscle of auditory ossicle](http://purl.obolibrary.org/obo/UBERON_0004113) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "attenuate low-frequency sounds, reduce masking of high-frequency sounds by low-frequency sounds, frequency-selection filter" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Hypodermis" -### hypoglossal canal `http://purl.obolibrary.org/obo/UBERON_0006682` +### muscle of iris `http://purl.obolibrary.org/obo/UBERON_0001606` #### Removed -- [hypoglossal canal](http://purl.obolibrary.org/obo/UBERON_0006682) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "canalis nervi hypoglossi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [muscle of iris](http://purl.obolibrary.org/obo/UBERON_0001606) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:35448" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Hypoglossal_canal" +- [muscle of iris](http://purl.obolibrary.org/obo/UBERON_0001606) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "in aves, stromal mesenchymal cells may migrate to the iris and become skeletal" -#### Added -- [hypoglossal canal](http://purl.obolibrary.org/obo/UBERON_0006682) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "canalis nervi hypoglossi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [muscle of iris](http://purl.obolibrary.org/obo/UBERON_0001606) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The muscle cells of the iris are smooth muscle in mammals and amphibians, but are striated muscle in birds and reptiles. Many fish have neither, and, as a result, their irides are unable to dilate and contract, so that the pupil always remains of a fixed size[Romer, via WP]" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Hypoglossal_canal" -### hypoglossal nerve `http://purl.obolibrary.org/obo/UBERON_0001650` -#### Removed -- [hypoglossal nerve](http://purl.obolibrary.org/obo/UBERON_0001650) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nervus hypoglossus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Hypoglossal_nerve" +### muscle of larynx `http://purl.obolibrary.org/obo/UBERON_0001568` - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +#### Added +- [muscle of larynx](http://purl.obolibrary.org/obo/UBERON_0001568) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -- [hypoglossal nerve](http://purl.obolibrary.org/obo/UBERON_0001650) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus hypoglossus [xii]" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:50871" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### muscle of leg `http://purl.obolibrary.org/obo/UBERON_0001383` +#### Removed +- [muscle of leg](http://purl.obolibrary.org/obo/UBERON_0001383) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:19318" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [muscle of leg](http://purl.obolibrary.org/obo/UBERON_0001383) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:19144" -- [hypoglossal nerve](http://purl.obolibrary.org/obo/UBERON_0001650) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nervi hypoglossalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [muscle of leg](http://purl.obolibrary.org/obo/UBERON_0001383) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "see notes on UBERON:0000978 for possible confusion over the term 'leg'." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:704" -#### Added -- [hypoglossal nerve](http://purl.obolibrary.org/obo/UBERON_0001650) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nervus hypoglossus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Hypoglossal_nerve" +### muscle of neck `http://purl.obolibrary.org/obo/UBERON_0002377` +#### Removed +- [muscle of neck](http://purl.obolibrary.org/obo/UBERON_0002377) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:36050" -- [hypoglossal nerve](http://purl.obolibrary.org/obo/UBERON_0001650) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nervi hypoglossalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:704" -- [hypoglossal nerve](http://purl.obolibrary.org/obo/UBERON_0001650) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus hypoglossus [xii]" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### muscle of pectoral girdle `http://purl.obolibrary.org/obo/UBERON_0008196` +#### Removed +- [muscle of pectoral girdle](http://purl.obolibrary.org/obo/UBERON_0008196) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:17748" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:50871" +- [muscle of pectoral girdle](http://purl.obolibrary.org/obo/UBERON_0008196) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "EMAPA has both non-skeletal and skeletal types, with the non-skeletal also including a chest muscle, so we place the skeletal class here as the most accurate" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EMAPA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### hypoglossal nerve root `http://purl.obolibrary.org/obo/UBERON_0004675` +### muscle of pelvic girdle `http://purl.obolibrary.org/obo/UBERON_0001497` #### Removed -- [hypoglossal nerve root](http://purl.obolibrary.org/obo/UBERON_0004675) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "fibrae nervi hypoglossi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:72632" +- [muscle of pelvic girdle](http://purl.obolibrary.org/obo/UBERON_0001497) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:18184" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [muscle of pelvic girdle](http://purl.obolibrary.org/obo/UBERON_0001497) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "Note that in MA, this is a subclass of pelvis muscle; in FMA this is a hindlimb muscle, but recall in FMA hindlimb includes the girdle." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [hypoglossal nerve root](http://purl.obolibrary.org/obo/UBERON_0004675) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "fibrae nervi hypoglossi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:72632" +### muscle of pelvis `http://purl.obolibrary.org/obo/UBERON_0001325` +#### Removed +- [muscle of pelvis](http://purl.obolibrary.org/obo/UBERON_0001325) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:18184" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### hypoglossal nucleus `http://purl.obolibrary.org/obo/UBERON_0002871` +### muscle organ `http://purl.obolibrary.org/obo/UBERON_0001630` #### Removed -- [hypoglossal nucleus](http://purl.obolibrary.org/obo/UBERON_0002871) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nucleus nervi hypoglossi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:54505" +- [muscle organ](http://purl.obolibrary.org/obo/UBERON_0001630) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [hypoglossal nucleus](http://purl.obolibrary.org/obo/UBERON_0002871) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus hypoglossalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:757" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.75" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001245" -- [hypoglossal nucleus](http://purl.obolibrary.org/obo/UBERON_0002871) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus nervi hypoglossi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [muscle organ](http://purl.obolibrary.org/obo/UBERON_0001630) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "AAO:0011066" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Hypoglossal_nucleus" +- [muscle organ](http://purl.obolibrary.org/obo/UBERON_0001630) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "muscular" -#### Added -- [hypoglossal nucleus](http://purl.obolibrary.org/obo/UBERON_0002871) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nucleus nervi hypoglossi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [muscle organ](http://purl.obolibrary.org/obo/UBERON_0001630) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:32715" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:54505" +- [muscle organ](http://purl.obolibrary.org/obo/UBERON_0001630) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Portion of tissue composed of contractile fibers.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005145" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -- [hypoglossal nucleus](http://purl.obolibrary.org/obo/UBERON_0002871) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus nervi hypoglossi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Hypoglossal_nucleus" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -- [hypoglossal nucleus](http://purl.obolibrary.org/obo/UBERON_0002871) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus hypoglossalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:757" +### muscle structure `http://purl.obolibrary.org/obo/UBERON_0005090` +#### Removed +- [muscle structure](http://purl.obolibrary.org/obo/UBERON_0005090) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila" -### hypothalamus `http://purl.obolibrary.org/obo/UBERON_0001898` +- [muscle structure](http://purl.obolibrary.org/obo/UBERON_0005090) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:32715" + + + +### muscle tissue `http://purl.obolibrary.org/obo/UBERON_0002385` #### Removed -- [hypothalamus](http://purl.obolibrary.org/obo/UBERON_0001898) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "hypothalamus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [muscle tissue](http://purl.obolibrary.org/obo/UBERON_0002385) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Hypothalamus" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -#### Added -- [hypothalamus](http://purl.obolibrary.org/obo/UBERON_0001898) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "hypothalamus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000306" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Hypothalamus" +- [muscle tissue](http://purl.obolibrary.org/obo/UBERON_0002385) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [neural tissue](http://purl.obolibrary.org/obo/UBERON_0003714) -### ileal goblet cell `http://purl.obolibrary.org/obo/CL_1000326` + +### muscle tissue of prostate `http://purl.obolibrary.org/obo/UBERON_0008715` #### Added -- [ileal goblet cell](http://purl.obolibrary.org/obo/CL_1000326) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [muscle tissue of prostate](http://purl.obolibrary.org/obo/UBERON_0008715) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) -### ileocolic artery `http://purl.obolibrary.org/obo/UBERON_0001197` +### muscular coat `http://purl.obolibrary.org/obo/UBERON_0006660` #### Removed -- [ileocolic artery](http://purl.obolibrary.org/obo/UBERON_0001197) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria ileocolica" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ileocolic_artery" +- [muscular coat](http://purl.obolibrary.org/obo/UBERON_0006660) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "An outer layer of smooth muscle surrounding a hollow or tubular organ as the bladder, esophagus, large intestine, small intestine, stomach, ureter, uterus, and vagina that often consists of an inner layer of circular fibers serving to narrow the lumen of the organ and an outer layer of longitudinal fibers serving to shorten its length[BTO]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "BTO:0004838" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [muscular coat](http://purl.obolibrary.org/obo/UBERON_0006660) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0006676](http://purl.obolibrary.org/obo/UBERON_0006676) -#### Added -- [ileocolic artery](http://purl.obolibrary.org/obo/UBERON_0001197) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria ileocolica" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ileocolic_artery" +- [muscular coat](http://purl.obolibrary.org/obo/UBERON_0006660) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [submucosa](http://purl.obolibrary.org/obo/UBERON_0000009) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [muscular coat](http://purl.obolibrary.org/obo/UBERON_0006660) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "typically smooth muscle, but there may be exceptions - in the upper esophagus, part of the externa is skeletal muscle, rather than smooth muscle." -### ileocolic vein `http://purl.obolibrary.org/obo/UBERON_0001219` + +### muscular coat of digestive tract `http://purl.obolibrary.org/obo/UBERON_0018261` #### Removed -- [ileocolic vein](http://purl.obolibrary.org/obo/UBERON_0001219) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena ileocolica" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ileocolic_vein" +- [muscular coat of digestive tract](http://purl.obolibrary.org/obo/UBERON_0018261) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "responsible for gut movement, such as peristalsis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [ileocolic vein](http://purl.obolibrary.org/obo/UBERON_0001219) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena ileocolica" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ileocolic_vein" +### muscular coat of seminal vesicle `http://purl.obolibrary.org/obo/UBERON_0004665` + +#### Added +- [muscular coat of seminal vesicle](http://purl.obolibrary.org/obo/UBERON_0004665) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### ileum lamina propria `http://purl.obolibrary.org/obo/UBERON_8600035` +### muscular coat of ureter `http://purl.obolibrary.org/obo/UBERON_0006855` +#### Removed +- [muscular coat of ureter](http://purl.obolibrary.org/obo/UBERON_0006855) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:28811" #### Added -- [ileum lamina propria](http://purl.obolibrary.org/obo/UBERON_8600035) [label](http://www.w3.org/2000/01/rdf-schema#label) "ileum lamina propria" +- [muscular coat of ureter](http://purl.obolibrary.org/obo/UBERON_0006855) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -- [ileum lamina propria](http://purl.obolibrary.org/obo/UBERON_8600035) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" -- [ileum lamina propria](http://purl.obolibrary.org/obo/UBERON_8600035) [id](http://www.geneontology.org/formats/oboInOwl#id) "UBERON:8600035" +### muscular layer of prostatic urethra `http://purl.obolibrary.org/obo/UBERON_0016515` -- [ileum lamina propria](http://purl.obolibrary.org/obo/UBERON_8600035) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lamina propria of ileum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36067905" +#### Added +- [muscular layer of prostatic urethra](http://purl.obolibrary.org/obo/UBERON_0016515) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -- [ileum lamina propria](http://purl.obolibrary.org/obo/UBERON_8600035) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A lamina propria that is part of an ileum." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29316348" -- [ileum lamina propria](http://purl.obolibrary.org/obo/UBERON_8600035) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ileal lamina propria" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37467267" +### muscular layer of vagina `http://purl.obolibrary.org/obo/UBERON_0006652` -- [ileum lamina propria](http://purl.obolibrary.org/obo/UBERON_8600035) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-8134-3037](https://orcid.org/0000-0001-8134-3037) +#### Added +- [muscular layer of vagina](http://purl.obolibrary.org/obo/UBERON_0006652) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -- [ileum lamina propria](http://purl.obolibrary.org/obo/UBERON_8600035) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) -- [ileum lamina propria](http://purl.obolibrary.org/obo/UBERON_8600035) [date](http://purl.org/dc/terms/date) "2024-01-09T16:48:17Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +### musculature `http://purl.obolibrary.org/obo/UBERON_0001015` +#### Removed +- [musculature](http://purl.obolibrary.org/obo/UBERON_0001015) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "AAO:0011066" -- Class: [ileum lamina propria](http://purl.obolibrary.org/obo/UBERON_8600035) +- [musculature](http://purl.obolibrary.org/obo/UBERON_0001015) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:32715" -- [ileum lamina propria](http://purl.obolibrary.org/obo/UBERON_8600035) EquivalentTo [lamina propria](http://purl.obolibrary.org/obo/UBERON_0000030) and ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [ileum](http://purl.obolibrary.org/obo/UBERON_0002116)) +- [musculature](http://purl.obolibrary.org/obo/UBERON_0001015) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" -- [ileum lamina propria](http://purl.obolibrary.org/obo/UBERON_8600035) SubClassOf [lamina propria of small intestine](http://purl.obolibrary.org/obo/UBERON_0001238) +- [musculature](http://purl.obolibrary.org/obo/UBERON_0001015) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [bone element](http://purl.obolibrary.org/obo/UBERON_0001474) -- [ileum lamina propria](http://purl.obolibrary.org/obo/UBERON_8600035) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [intestinal villus of ileum](http://purl.obolibrary.org/obo/UBERON_0008344) -### ilium `http://purl.obolibrary.org/obo/UBERON_0001273` +### musculature of body `http://purl.obolibrary.org/obo/UBERON_0000383` #### Removed -- [ilium](http://purl.obolibrary.org/obo/UBERON_0001273) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "os ilium" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:16589" +- [musculature of body](http://purl.obolibrary.org/obo/UBERON_0000383) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical system that consists of the muscles of the body.[VSAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000033" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "VSAO:curator" -#### Added -- [ilium](http://purl.obolibrary.org/obo/UBERON_0001273) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "os ilium" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:16589" +- [musculature of body](http://purl.obolibrary.org/obo/UBERON_0000383) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [musculature of body](http://purl.obolibrary.org/obo/UBERON_0000383) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:35578" -### imaginal disc `http://purl.obolibrary.org/obo/UBERON_0000939` -#### Removed -- [imaginal disc](http://purl.obolibrary.org/obo/UBERON_0000939) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001761" -- [imaginal disc](http://purl.obolibrary.org/obo/UBERON_0000939) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D060227" +### musculature of body wall `http://purl.obolibrary.org/obo/UBERON_0004462` +#### Removed +- [musculature of body wall](http://purl.obolibrary.org/obo/UBERON_0004462) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "define generically to encompass both vertebrates and invertebrates" -#### Added -- [imaginal disc](http://purl.obolibrary.org/obo/UBERON_0000939) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001761" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -- [imaginal disc](http://purl.obolibrary.org/obo/UBERON_0000939) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D060227" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) +### musculature of larynx `http://purl.obolibrary.org/obo/UBERON_0004478` - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +#### Added +- [musculature of larynx](http://purl.obolibrary.org/obo/UBERON_0004478) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -### immaterial anatomical entity `http://purl.obolibrary.org/obo/UBERON_0000466` +### musculature of leg `http://purl.obolibrary.org/obo/UBERON_0004466` #### Removed -- [immaterial anatomical entity](http://purl.obolibrary.org/obo/UBERON_0000466) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007015" - -#### Added -- [immaterial anatomical entity](http://purl.obolibrary.org/obo/UBERON_0000466) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007015" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - +- [musculature of leg](http://purl.obolibrary.org/obo/UBERON_0004466) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "see notes on UBERON:0000978 for possible confusion over the term 'leg'. This class represents the class-union of upper leg musculature and lower leg musculature (and thus may not mean precisely the same thing as the EHDAA2 class)" -### immature B cell `http://purl.obolibrary.org/obo/CL_0000816` -#### Added -- [immature B cell](http://purl.obolibrary.org/obo/CL_0000816) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### musculature of pelvic girdle `http://purl.obolibrary.org/obo/UBERON_0004470` +#### Removed +- [musculature of pelvic girdle](http://purl.obolibrary.org/obo/UBERON_0004470) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "we merge two FMA classes here" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" -### immature NK T cell `http://purl.obolibrary.org/obo/CL_0000914` -#### Added -- [immature NK T cell](http://purl.obolibrary.org/obo/CL_0000914) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### musculature of thorax `http://purl.obolibrary.org/obo/UBERON_0004464` +#### Removed +- [musculature of thorax](http://purl.obolibrary.org/obo/UBERON_0004464) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "BTO and FMA do not mean precisely the same thing here. BTO thorax muscle is a pectoral muscle or diaphragm" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "BTO" -### immature Schwann cell `http://purl.obolibrary.org/obo/CL_0002377` -#### Added -- [immature Schwann cell](http://purl.obolibrary.org/obo/CL_0002377) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### musculoskeletal system `http://purl.obolibrary.org/obo/UBERON_0002204` +#### Removed +- [musculoskeletal system](http://purl.obolibrary.org/obo/UBERON_0002204) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "musculoskeletal" -### immature T cell `http://purl.obolibrary.org/obo/CL_0002420` +- [musculoskeletal system](http://purl.obolibrary.org/obo/UBERON_0002204) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [immature T cell](http://purl.obolibrary.org/obo/CL_0002420) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### immature alpha-beta T cell `http://purl.obolibrary.org/obo/CL_0000790` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1002/jez.b.21246 Shearman RM, Burke AC, The lateral somitic frontier in ontogeny and phylogeny. Journal of Experimental Zoology (2009)" -#### Added -- [immature alpha-beta T cell](http://purl.obolibrary.org/obo/CL_0000790) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001275" +- [musculoskeletal system](http://purl.obolibrary.org/obo/UBERON_0002204) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical system that provides locomotion and physical support to the organism.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" -### immature innate lymphoid cell `http://purl.obolibrary.org/obo/CL_0001082` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -#### Added -- [immature innate lymphoid cell](http://purl.obolibrary.org/obo/CL_0001082) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010546" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### immature natural killer cell `http://purl.obolibrary.org/obo/CL_0000823` +- [musculoskeletal system](http://purl.obolibrary.org/obo/UBERON_0002204) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [mesoderm](http://purl.obolibrary.org/obo/UBERON_0000926) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "check ctenophore" #### Added -- [immature natural killer cell](http://purl.obolibrary.org/obo/CL_0000823) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [musculoskeletal system](http://purl.obolibrary.org/obo/UBERON_0002204) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [mesoderm](http://purl.obolibrary.org/obo/UBERON_0000926) + + +### mushroom body `http://purl.obolibrary.org/obo/UBERON_0001058` +#### Removed +- [mushroom body](http://purl.obolibrary.org/obo/UBERON_0001058) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Also in annelids. 'Comparison to the vertebrate pallium reveals that the annelid mushroom bodies develop from similar molecular coordinates within a conserved overall molecular brain topology and that their development involves conserved patterning mechanisms and produces conserved neuron types that existed already in the proto- stome-deuterostome ancestors. These data indicate deep homology of pallium and mushroom bodies and date back the origin of higher brain centers to prebilaterian times'" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:20813265" +- [mushroom body](http://purl.obolibrary.org/obo/UBERON_0001058) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005801" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### immature neutrophil `http://purl.obolibrary.org/obo/CL_0000776` +- [mushroom body](http://purl.obolibrary.org/obo/UBERON_0001058) SubClassOf [only in taxon](http://purl.obolibrary.org/obo/RO_0002160) some [Protostomia](http://purl.obolibrary.org/obo/NCBITaxon_33317) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "annelids and arthropods" #### Added -- [immature neutrophil](http://purl.obolibrary.org/obo/CL_0000776) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [mushroom body](http://purl.obolibrary.org/obo/UBERON_0001058) SubClassOf [only in taxon](http://purl.obolibrary.org/obo/RO_0002160) some [Protostomia](http://purl.obolibrary.org/obo/NCBITaxon_33317) -### import across plasma membrane `http://purl.obolibrary.org/obo/GO_0098739` +### myelencephalon `http://purl.obolibrary.org/obo/UBERON_0005290` #### Removed -- [import across plasma membrane](http://purl.obolibrary.org/obo/GO_0098739) SubClassOf [has target start location](http://purl.obolibrary.org/obo/RO_0002338) some [extracellular region](http://purl.obolibrary.org/obo/GO_0005576) +- [myelencephalon](http://purl.obolibrary.org/obo/UBERON_0005290) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D054024" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -#### Added -- [import across plasma membrane](http://purl.obolibrary.org/obo/GO_0098739) SubClassOf [import into cell](http://purl.obolibrary.org/obo/GO_0098657) + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -### inferior angle of scapula `http://purl.obolibrary.org/obo/UBERON_0007175` -#### Removed -- [inferior angle of scapula](http://purl.obolibrary.org/obo/UBERON_0007175) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "angulus inferior scapulae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [myelencephalon](http://purl.obolibrary.org/obo/UBERON_0005290) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Inferior_angle_of_scapula" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [inferior angle of scapula](http://purl.obolibrary.org/obo/UBERON_0007175) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "angulus inferior scapulae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Inferior_angle_of_scapula" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/myelencephalon" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000456" -### inferior mesenteric artery `http://purl.obolibrary.org/obo/UBERON_0001183` -#### Removed -- [inferior mesenteric artery](http://purl.obolibrary.org/obo/UBERON_0001183) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria mesenterica inferior" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Inferior_mesenteric_artery" +- [myelencephalon](http://purl.obolibrary.org/obo/UBERON_0005290) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0002302" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [inferior mesenteric artery](http://purl.obolibrary.org/obo/UBERON_0001183) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria mesenterica inferior" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Inferior_mesenteric_artery" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000456" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0002302" +- [myelencephalon](http://purl.obolibrary.org/obo/UBERON_0005290) [RO_0002174](http://purl.obolibrary.org/obo/RO_0002174) [NCBITaxon_7955](http://purl.obolibrary.org/obo/NCBITaxon_7955) +- [myelencephalon](http://purl.obolibrary.org/obo/UBERON_0005290) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "the terms metencephalon and myelencephalon are only meaningful in mammals and birds - Neuroanatomy of the Zebrafish Brain. Note that its not clear if this refers to the developing medulla oblongata - MA (adult) has two distinct classes" -### inferior mesenteric vein `http://purl.obolibrary.org/obo/UBERON_0001215` -#### Removed -- [inferior mesenteric vein](http://purl.obolibrary.org/obo/UBERON_0001215) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena mesenterica inferior" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Inferior_mesenteric_vein" +- [myelencephalon](http://purl.obolibrary.org/obo/UBERON_0005290) SubClassOf [immediate transformation of](http://purl.obolibrary.org/obo/RO_0002495) some [future myelencephalon](http://purl.obolibrary.org/obo/UBERON_0010096) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [myelencephalon](http://purl.obolibrary.org/obo/UBERON_0005290) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) #### Added -- [inferior mesenteric vein](http://purl.obolibrary.org/obo/UBERON_0001215) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena mesenterica inferior" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Inferior_mesenteric_vein" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [myelencephalon](http://purl.obolibrary.org/obo/UBERON_0005290) SubClassOf [immediate transformation of](http://purl.obolibrary.org/obo/RO_0002495) some [future myelencephalon](http://purl.obolibrary.org/obo/UBERON_0010096) -### inferior suprarenal artery `http://purl.obolibrary.org/obo/UBERON_0002056` +### myelinated nerve fiber `http://purl.obolibrary.org/obo/UBERON_0006135` #### Removed -- [inferior suprarenal artery](http://purl.obolibrary.org/obo/UBERON_0002056) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria suprarenalis inferior" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Inferior_suprarenal_artery" +- [myelinated nerve fiber](http://purl.obolibrary.org/obo/UBERON_0006135) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "http://www1.pbrc.hawaii.edu/~danh/MyelinEvolution/evolution.html, http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=6134604, Wikipedia:Myelin#Invertebrate_myelin" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [inferior suprarenal artery](http://purl.obolibrary.org/obo/UBERON_0002056) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria suprarenalis inferior" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Inferior_suprarenal_artery" +### myeloperoxidase `http://purl.obolibrary.org/obo/PR_000010543` +#### Removed +- [myeloperoxidase](http://purl.obolibrary.org/obo/PR_000010543) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [myeloperoxidase (human)](http://purl.obolibrary.org/obo/PR_P05164) + -### inferior vesical artery `http://purl.obolibrary.org/obo/UBERON_0001311` +### myocardium `http://purl.obolibrary.org/obo/UBERON_0002349` #### Removed -- [inferior vesical artery](http://purl.obolibrary.org/obo/UBERON_0001311) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria vesicalis inferior" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Inferior_vesical_artery" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [myocardium](http://purl.obolibrary.org/obo/UBERON_0002349) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The middle layer of the heart, consisting of cardiac muscle.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010410" -- [inferior vesical artery](http://purl.obolibrary.org/obo/UBERON_0001311) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arteria vesicali inferior" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Inferior_vesical_artery" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -- [inferior vesical artery](http://purl.obolibrary.org/obo/UBERON_0001311) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arteria vesicalis inferior" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Inferior_vesical_artery" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [myocardium](http://purl.obolibrary.org/obo/UBERON_0002349) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "myocardial" -#### Added -- [inferior vesical artery](http://purl.obolibrary.org/obo/UBERON_0001311) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arteria vesicali inferior" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Inferior_vesical_artery" +- [myocardium](http://purl.obolibrary.org/obo/UBERON_0002349) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:32688" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [myocardium](http://purl.obolibrary.org/obo/UBERON_0002349) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Robust muscular tunic of the heart which forms the basic part of its walls. Its external surface is covered by the pericardium and its internal one by the endocardium. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [inferior vesical artery](http://purl.obolibrary.org/obo/UBERON_0001311) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arteria vesicalis inferior" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Inferior_vesical_artery" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [inferior vesical artery](http://purl.obolibrary.org/obo/UBERON_0001311) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria vesicalis inferior" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Inferior_vesical_artery" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000083" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### inflammatory cell `http://purl.obolibrary.org/obo/CL_0009002` +### myocardium of anterior wall of right ventricle `http://purl.obolibrary.org/obo/UBERON_0036291` +#### Removed +- [myocardium of anterior wall of right ventricle](http://purl.obolibrary.org/obo/UBERON_0036291) SubClassOf [myocardium of ventricle](http://purl.obolibrary.org/obo/UBERON_0001083) #### Added -- [inflammatory cell](http://purl.obolibrary.org/obo/CL_0009002) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [myocardium of anterior wall of right ventricle](http://purl.obolibrary.org/obo/UBERON_0036291) SubClassOf [right ventricle myocardium](http://purl.obolibrary.org/obo/UBERON_0006567) -### inflammatory macrophage `http://purl.obolibrary.org/obo/CL_0000863` +### myocardium of atrium `http://purl.obolibrary.org/obo/UBERON_0002302` +#### Removed +- [myocardium of atrium](http://purl.obolibrary.org/obo/UBERON_0002302) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[uncertain][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000602" -#### Added -- [inflammatory macrophage](http://purl.obolibrary.org/obo/CL_0000863) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### inhibitory interneuron `http://purl.obolibrary.org/obo/CL_0000498` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [inhibitory interneuron](http://purl.obolibrary.org/obo/CL_0000498) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481" -### inhibitory motor neuron `http://purl.obolibrary.org/obo/CL_0008015` -#### Added -- [inhibitory motor neuron](http://purl.obolibrary.org/obo/CL_0008015) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### myocardium of ventricle `http://purl.obolibrary.org/obo/UBERON_0001083` +#### Removed +- [myocardium of ventricle](http://purl.obolibrary.org/obo/UBERON_0001083) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[uncertain][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000604" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### innate immune response `http://purl.obolibrary.org/obo/GO_0045087` -#### Removed -- [innate immune response](http://purl.obolibrary.org/obo/GO_0045087) SubClassOf [defense response to other organism](http://purl.obolibrary.org/obo/GO_0098542) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [innate immune response](http://purl.obolibrary.org/obo/GO_0045087) SubClassOf [defense response to symbiont](http://purl.obolibrary.org/obo/GO_0140546) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481" -### innate lymphoid cell `http://purl.obolibrary.org/obo/CL_0001065` +- [myocardium of ventricle](http://purl.obolibrary.org/obo/UBERON_0001083) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer Hu et al. 2001.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005061" -#### Added -- [innate lymphoid cell](http://purl.obolibrary.org/obo/CL_0001065) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -### inner cell mass `http://purl.obolibrary.org/obo/UBERON_0000087` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + + +### myocardium trabecular layer `http://purl.obolibrary.org/obo/UBERON_0004124` #### Removed -- [inner cell mass](http://purl.obolibrary.org/obo/UBERON_0000087) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "embryoblastus; massa cellularis interna; pluriblastus senior" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [myocardium trabecular layer](http://purl.obolibrary.org/obo/UBERON_0004124) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The layer of the myocardium composed of projections of contractile myocytes. The trabecular layer is bounded internally by the the endocardium. Unlike the trabeculations of higher vertebrates, both atrial and ventricular trabeculae of the zebrafish have more strut-like character, and are more uniform without apparent regional differences Hu et al. 2001.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Inner_cell_mass" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005059" -#### Added -- [inner cell mass](http://purl.obolibrary.org/obo/UBERON_0000087) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "embryoblastus; massa cellularis interna; pluriblastus senior" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Inner_cell_mass" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -### inner limiting layer of retina `http://purl.obolibrary.org/obo/UBERON_0001794` + +### myocoele `http://purl.obolibrary.org/obo/UBERON_0012054` #### Removed -- [inner limiting layer of retina](http://purl.obolibrary.org/obo/UBERON_0001794) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum limitans internum retinae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [myocoele](http://purl.obolibrary.org/obo/UBERON_0012054) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The central cavity within the mesoderm is the paired primary or embryonic coelom. Parts of the embryonic coelom often become enclosed in the mesoderm, forming a myocoel within the epimere, a nephrocoel within the mesomere, and simple coelom (body cavity) within the lateral plate mesoderm.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58689" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [inner limiting layer of retina](http://purl.obolibrary.org/obo/UBERON_0001794) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum limitans internum retinae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001283" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.166 and Figure 5.6" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58689" -### inner medulla of kidney `http://purl.obolibrary.org/obo/UBERON_0001294` +### myoepithelial cell of mammary gland `http://purl.obolibrary.org/obo/CL_0002324` #### Removed -- [inner medulla of kidney](http://purl.obolibrary.org/obo/UBERON_0001294) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "zona interna medullae renalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:17734" +- [myoepithelial cell of mammary gland](http://purl.obolibrary.org/obo/CL_0002324) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "basal cell of lactiferous duct" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:67800" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [myoepithelial cell of mammary gland](http://purl.obolibrary.org/obo/CL_0002324) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "myoepithelial cell of lactiferous gland" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [myoepithelial cell of mammary gland](http://purl.obolibrary.org/obo/CL_0002324) [label](http://www.w3.org/2000/01/rdf-schema#label) "myoepithelial cell of mammary gland" -- [inner medulla of kidney](http://purl.obolibrary.org/obo/UBERON_0001294) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "zona interna (medullaris renalis)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:17734" +- [myoepithelial cell of mammary gland](http://purl.obolibrary.org/obo/CL_0002324) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A myoepithelial cell that surrounds milk-secreting luminal epithelial cells. This cell type contracts under the stimulation of oxytocin and is attached to the basement membrane by hemidesmosomes and to the adjacent luminal cells by desmosomes. This cell type expresses high level of keratin-14 and is estrogen receptor alpha negative." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:19022771" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:11250738" #### Added -- [inner medulla of kidney](http://purl.obolibrary.org/obo/UBERON_0001294) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "zona interna medullae renalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:17734" +- [myoepithelial cell of mammary gland](http://purl.obolibrary.org/obo/CL_0002324) [contributor](http://purl.org/dc/terms/contributor) [X](https://orcid.org/0000-0003-4969-670X) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [myoepithelial cell of mammary gland](http://purl.obolibrary.org/obo/CL_0002324) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A myoepithelial cell that is part of a mammary gland and is located in the basal layer. During lactation, a basal-myoepithelial cell of mammary gland contracts under the stimulation of oxytocin. In humans, a basal-myoepithelial cell of mammary gland can be identified by high levels of CD49f and low levels of EpCAM." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38059556" -- [inner medulla of kidney](http://purl.obolibrary.org/obo/UBERON_0001294) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "zona interna (medullaris renalis)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:17734" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:19022771" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:11250738" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [myoepithelial cell of mammary gland](http://purl.obolibrary.org/obo/CL_0002324) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Due inconsistencies in naming this and other mammary gland epithelial cell types, several mammary gland experts gathered for a breast atlas annotation jamboree organized by Chan-Zuckerberg initiative. They agreed to label this cell type as basal-myoepithelial cell (and abbreviated: B-Myo cell)." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38059556" +- [myoepithelial cell of mammary gland](http://purl.obolibrary.org/obo/CL_0002324) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "basal-myoepithelial cell" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37380767" -### inner nuclear layer of retina `http://purl.obolibrary.org/obo/UBERON_0001791` -#### Removed -- [inner nuclear layer of retina](http://purl.obolibrary.org/obo/UBERON_0001791) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum nucleare internum retinae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [myoepithelial cell of mammary gland](http://purl.obolibrary.org/obo/CL_0002324) [label](http://www.w3.org/2000/01/rdf-schema#label) "basal-myoepithelial cell of mammary gland" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [myoepithelial cell of mammary gland](http://purl.obolibrary.org/obo/CL_0002324) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "B-Myo cell" + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [abbreviation](http://purl.obolibrary.org/obo/OMO_0003000) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58686" +- [myoepithelial cell of mammary gland](http://purl.obolibrary.org/obo/CL_0002324) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "BM" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38059556" -#### Added -- [inner nuclear layer of retina](http://purl.obolibrary.org/obo/UBERON_0001791) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum nucleare internum retinae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [abbreviation](http://purl.obolibrary.org/obo/OMO_0003000) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [myoepithelial cell of mammary gland](http://purl.obolibrary.org/obo/CL_0002324) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58686" +- [myoepithelial cell of mammary gland](http://purl.obolibrary.org/obo/CL_0002324) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "myoepithelial cell of mammary gland" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:11250738" +- [myoepithelial cell of mammary gland](http://purl.obolibrary.org/obo/CL_0002324) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "myoepithelial cell of lactiferous gland" -### inner plexiform layer of retina `http://purl.obolibrary.org/obo/UBERON_0001795` -#### Removed -- [inner plexiform layer of retina](http://purl.obolibrary.org/obo/UBERON_0001795) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "stratum plexiforme internum retinae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Inner_plexiform_layer" +- [myoepithelial cell of mammary gland](http://purl.obolibrary.org/obo/CL_0002324) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "basal myoepithelial cell" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37694522" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [myoepithelial cell of mammary gland](http://purl.obolibrary.org/obo/CL_0002324) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "basal cell of lactiferous duct" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:67800" -#### Added -- [inner plexiform layer of retina](http://purl.obolibrary.org/obo/UBERON_0001795) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "stratum plexiforme internum retinae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Inner_plexiform_layer" +- [myoepithelial cell of mammary gland](http://purl.obolibrary.org/obo/CL_0002324) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "basal" + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [abbreviation](http://purl.obolibrary.org/obo/OMO_0003000) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37380767" -### innominate bone `http://purl.obolibrary.org/obo/UBERON_0001272` +### myometrium `http://purl.obolibrary.org/obo/UBERON_0001296` #### Removed -- [innominate bone](http://purl.obolibrary.org/obo/UBERON_0001272) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "os coxa" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [myometrium](http://purl.obolibrary.org/obo/UBERON_0001296) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "The myometrium stretches (the smooth muscle cells expand in both size and number) during pregnancy to allow for the harboring of the pregnancy, and contracts in a coordinated fashion during the process of labor. After delivery the myometrium contracts to expel the placenta and reduce blood loss." -- [innominate bone](http://purl.obolibrary.org/obo/UBERON_0001272) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "os innominatum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Hip_bone" +- [myometrium](http://purl.obolibrary.org/obo/UBERON_0001296) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The muscular wall of the uterus. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/myometrium" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [innominate bone](http://purl.obolibrary.org/obo/UBERON_0001272) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "os coxae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:16585" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001281" -#### Added -- [innominate bone](http://purl.obolibrary.org/obo/UBERON_0001272) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "os coxae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [myometrium](http://purl.obolibrary.org/obo/UBERON_0001296) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "myometrial" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:16585" +- [myometrium](http://purl.obolibrary.org/obo/UBERON_0001296) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In all mammals, the uterus develops as a specialization of the paramesonephric or Müllerian ducts, which gives rise to the infundibula, oviducts, uterus, cervix, and anterior vagina. Morphogenetic events common to development of all uteri include: 1) differentiation and growth of the myometrium, 2) differentiation and morphogenesis of the endometrial glands, and 3) organization and stratification of endometrial stroma. Uterine development is initiated in the fetus, but is only completed postnatally with differentiation and development of the endometrial glands.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [innominate bone](http://purl.obolibrary.org/obo/UBERON_0001272) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "os innominatum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Hip_bone" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:15471813 Spencer TE, Bazer FW, Uterine and placental factors regulating conceptus growth in domestic animals. Journal of Animal Science (2004)" -- [innominate bone](http://purl.obolibrary.org/obo/UBERON_0001272) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "os coxa" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001281" -### insect adult head `http://purl.obolibrary.org/obo/UBERON_6003007` -#### Removed -- [insect adult head](http://purl.obolibrary.org/obo/UBERON_6003007) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00003007" -#### Added -- [insect adult head](http://purl.obolibrary.org/obo/UBERON_6003007) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00003007" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +### myotome `http://purl.obolibrary.org/obo/UBERON_0003082` +#### Removed +- [myotome](http://purl.obolibrary.org/obo/UBERON_0003082) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In all vertebrates, the skeletal muscle of the body axis is chiefly derived from an early embryonic compartment, known as the myotome.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### insect adult tagma `http://purl.obolibrary.org/obo/UBERON_6003005` -#### Removed -- [insect adult tagma](http://purl.obolibrary.org/obo/UBERON_6003005) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00003005" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [insect adult tagma](http://purl.obolibrary.org/obo/UBERON_6003005) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00003005" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1038/sj.embor.embor920 Hollway GE, Currie PD, Myotome meanderings. Cellular morphogenesis and the making of muscle. EMBO Rep.(2003)" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001244" -### insect embryonic/larval head sense organ `http://purl.obolibrary.org/obo/UBERON_6007280` -#### Removed -- [insect embryonic/larval head sense organ](http://purl.obolibrary.org/obo/UBERON_6007280) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007280" +- [myotome](http://purl.obolibrary.org/obo/UBERON_0003082) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Portion of the somites giving rise to body wall muscle masses. Kimmel et al, 1995.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -#### Added -- [insect embryonic/larval head sense organ](http://purl.obolibrary.org/obo/UBERON_6007280) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007280" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001056" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -### insect embryonic/larval head sensillum `http://purl.obolibrary.org/obo/UBERON_6007242` -#### Removed -- [insect embryonic/larval head sensillum](http://purl.obolibrary.org/obo/UBERON_6007242) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007242" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -#### Added -- [insect embryonic/larval head sensillum](http://purl.obolibrary.org/obo/UBERON_6007242) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007242" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### insect embryonic/larval sensillum `http://purl.obolibrary.org/obo/UBERON_6007240` +### nail `http://purl.obolibrary.org/obo/UBERON_0001705` #### Removed -- [insect embryonic/larval sensillum](http://purl.obolibrary.org/obo/UBERON_6007240) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007240" +- [nail](http://purl.obolibrary.org/obo/UBERON_0001705) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "A primate's nail consists of the unguis alone; the subunguis has disappeared" -#### Added -- [insect embryonic/larval sensillum](http://purl.obolibrary.org/obo/UBERON_6007240) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007240" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [nail](http://purl.obolibrary.org/obo/UBERON_0001705) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "Use this class for both the nails of primates and the homologous claws of mammals such as mouse." -### insect larval head `http://purl.obolibrary.org/obo/UBERON_6001730` + +### nail plate `http://purl.obolibrary.org/obo/UBERON_0008198` #### Removed -- [insect larval head](http://purl.obolibrary.org/obo/UBERON_6001730) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001730" +- [nail plate](http://purl.obolibrary.org/obo/UBERON_0008198) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in FMA, the nail is the nail plate" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" #### Added -- [insect larval head](http://purl.obolibrary.org/obo/UBERON_6001730) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001730" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [nail plate](http://purl.obolibrary.org/obo/UBERON_0008198) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### insect larval sense organ `http://purl.obolibrary.org/obo/UBERON_6002639` +### named class expression `http://purl.obolibrary.org/obo/IAO_0000421` #### Removed -- [insect larval sense organ](http://purl.obolibrary.org/obo/UBERON_6002639) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00002639" +- [named class expression](http://purl.obolibrary.org/obo/IAO_0000421) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "named class expression"@en -#### Added -- [insect larval sense organ](http://purl.obolibrary.org/obo/UBERON_6002639) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00002639" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [named class expression](http://purl.obolibrary.org/obo/IAO_0000421) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) "Alan Ruttenberg"@en -### insect larval tagma `http://purl.obolibrary.org/obo/UBERON_6001728` + +### naris `http://purl.obolibrary.org/obo/UBERON_0000003` #### Removed -- [insect larval tagma](http://purl.obolibrary.org/obo/UBERON_6001728) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001728" +- [naris](http://purl.obolibrary.org/obo/UBERON_0000003) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "we have classified this as an orifice, according to FMA. Note that in FMA, orifices are immaterial entities, but in ZFA this is a surface structure" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" -#### Added -- [insect larval tagma](http://purl.obolibrary.org/obo/UBERON_6001728) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001728" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [naris](http://purl.obolibrary.org/obo/UBERON_0000003) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "in actinopterygians, both pairs of nares are external. In tetrapods, the exhalant empties into the buccal cavity" +- [naris](http://purl.obolibrary.org/obo/UBERON_0000003) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Naris refer to the external and interior naris (choana) of tetrapods, and to anterior and posterior naris of zebrafish. It seems now accepted that the structure is homologous: The choana, a unique 'internal nostril' opening from the nasal sac into the roof of the mouth, is a key part of the tetrapod (land vertebrate) respiratory system. It was the first component of the tetrapod body plan to evolve, well before the origin of limbs, and is therefore crucial to our understanding of the beginning of the fish-tetrapod transition. (...) Here we present new material of Kenichthys, a 395-million-year-old fossil fish from China, that provides direct evidence for the origin of the choana and establishes its homology: it is indeed a displaced posterior external nostril that, during a brief transitional stage illustrated by Kenichthys, separated the maxilla from the premaxilla.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000663" -### integument `http://purl.obolibrary.org/obo/UBERON_0002199` -#### Removed -- [integument](http://purl.obolibrary.org/obo/UBERON_0002199) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "integumentum commune" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:74657" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [integument](http://purl.obolibrary.org/obo/UBERON_0002199) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "integumentum commune" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1038/nature02843 Zhu M, Ahlberg PE, The origin of the internal nostril in tetrapodes. Nature (2004)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:74657" +- [naris](http://purl.obolibrary.org/obo/UBERON_0000003) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "One of paired external openings of the nasal chamber.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### integumental system `http://purl.obolibrary.org/obo/UBERON_0002416` -#### Removed -- [integumental system](http://purl.obolibrary.org/obo/UBERON_0002416) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "integumentum commune" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Integumentary_system" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000311" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [integumental system](http://purl.obolibrary.org/obo/UBERON_0002416) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004969" -#### Added -- [integumental system](http://purl.obolibrary.org/obo/UBERON_0002416) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004969" +### nasal cartilage `http://purl.obolibrary.org/obo/UBERON_0001823` +#### Removed +- [nasal cartilage](http://purl.obolibrary.org/obo/UBERON_0001823) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D055171" - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -- [integumental system](http://purl.obolibrary.org/obo/UBERON_0002416) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "integumentum commune" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Integumentary_system" + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + +#### Added +- [nasal cartilage](http://purl.obolibrary.org/obo/UBERON_0001823) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### integumentary adnexa `http://purl.obolibrary.org/obo/UBERON_0006003` +### nasal cavity `http://purl.obolibrary.org/obo/UBERON_0001707` #### Removed -- [integumentary adnexa](http://purl.obolibrary.org/obo/UBERON_0006003) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "adnexae cutis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Skin_appendage" +- [nasal cavity](http://purl.obolibrary.org/obo/UBERON_0001707) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "a large air filled space above and behind the nose in the middle of the face[WP][Wikipedia:Nasal_cavity]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Nasal_cavity" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [nasal cavity](http://purl.obolibrary.org/obo/UBERON_0001707) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Saclike space internal to the nasal capsule lined by respiratory and sensory epithelium and glandular tissue.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000314" -#### Added -- [integumentary adnexa](http://purl.obolibrary.org/obo/UBERON_0006003) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "adnexae cutis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Skin_appendage" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### intercarpal joint `http://purl.obolibrary.org/obo/UBERON_0011132` +- [nasal cavity](http://purl.obolibrary.org/obo/UBERON_0001707) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Despite significant modification to the nasal cavity within Archosauria and its extreme hypertrophy and supraorbital development in Lambeosaurinae, the neural olfactory system and the olfactory region of the nasal cavity proper retain their plesiomorphic positions and associations, suggesting that this system is highly conserved in vertebrate evolution.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [intercarpal joint](http://purl.obolibrary.org/obo/UBERON_0011132) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D050824" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000271" -### intercellular bridge `http://purl.obolibrary.org/obo/GO_0045171` -#### Removed -- [intercellular bridge](http://purl.obolibrary.org/obo/GO_0045171) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "cellular_component" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1666/0094-8373(2006)032[0109:NCHACC]2.0.CO;2 Evans DC, Nasal cavity homologies and cranial crest function in lambeosaurine dinosaurs. Paleobiology (2006)" -- [intercellular bridge](http://purl.obolibrary.org/obo/GO_0045171) [label](http://www.w3.org/2000/01/rdf-schema#label) "intercellular bridge" +- [nasal cavity](http://purl.obolibrary.org/obo/UBERON_0001707) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "in humans, the cavity includes and starts at the nares and reaches all the way through to the and includes the choanae, the posterior nasal apertures" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "HP" -- [intercellular bridge](http://purl.obolibrary.org/obo/GO_0045171) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:0045171" -- [intercellular bridge](http://purl.obolibrary.org/obo/GO_0045171) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A direct connection between the cytoplasm of two cells that is formed following the completion of cleavage furrow ingression during cell division. They are usually present only briefly prior to completion of cytokinesis. However, in some cases, such as the bridges between germ cells during their development, they become stabilised." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:9635420" -- Class: [intercellular bridge](http://purl.obolibrary.org/obo/GO_0045171) +### nasal cavity mucosa `http://purl.obolibrary.org/obo/UBERON_0001826` -- [intercellular bridge](http://purl.obolibrary.org/obo/GO_0045171) SubClassOf [cellular anatomical entity](http://purl.obolibrary.org/obo/GO_0110165) +#### Added +- [nasal cavity mucosa](http://purl.obolibrary.org/obo/UBERON_0001826) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) +- [nasal cavity mucosa](http://purl.obolibrary.org/obo/UBERON_0001826) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -### intercellular bridge organization `http://purl.obolibrary.org/obo/GO_0043063` +### nasal mucus `http://purl.obolibrary.org/obo/UBERON_0002306` #### Removed -- [intercellular bridge organization](http://purl.obolibrary.org/obo/GO_0043063) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" +- [nasal mucus](http://purl.obolibrary.org/obo/UBERON_0002306) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "protects the olfactory epithelium and allows odors to dissolve so that they can be detected by olfactory receptor neurons" -- [intercellular bridge organization](http://purl.obolibrary.org/obo/GO_0043063) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the intracellular bridge. An intracellular bridge is a direct link between the cytoplasms of sister cells that allows cells to communicate with one another." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:jid" -- [intercellular bridge organization](http://purl.obolibrary.org/obo/GO_0043063) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:0043063" -- [intercellular bridge organization](http://purl.obolibrary.org/obo/GO_0043063) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "intercellular bridge organisation" +### nasal muscle `http://purl.obolibrary.org/obo/UBERON_0008522` -- [intercellular bridge organization](http://purl.obolibrary.org/obo/GO_0043063) [label](http://www.w3.org/2000/01/rdf-schema#label) "intercellular bridge organization" +#### Added +- [nasal muscle](http://purl.obolibrary.org/obo/UBERON_0008522) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -- [intercellular bridge organization](http://purl.obolibrary.org/obo/GO_0043063) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "intercellular bridge organization and biogenesis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:mah" -- Class: [intercellular bridge organization](http://purl.obolibrary.org/obo/GO_0043063) +### nasal skeleton `http://purl.obolibrary.org/obo/UBERON_0006813` +#### Removed +- [nasal skeleton](http://purl.obolibrary.org/obo/UBERON_0006813) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [dermatocranium](http://purl.obolibrary.org/obo/UBERON_0003113) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Kardong-abduced" -- [intercellular bridge organization](http://purl.obolibrary.org/obo/GO_0043063) EquivalentTo [cellular component organization](http://purl.obolibrary.org/obo/GO_0016043) and ([results in organization of](http://purl.obolibrary.org/obo/RO_0002592) some [intercellular bridge](http://purl.obolibrary.org/obo/GO_0045171)) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "facial series" -- [intercellular bridge organization](http://purl.obolibrary.org/obo/GO_0043063) SubClassOf [results in organization of](http://purl.obolibrary.org/obo/RO_0002592) some [intercellular bridge](http://purl.obolibrary.org/obo/GO_0045171) +#### Added +- [nasal skeleton](http://purl.obolibrary.org/obo/UBERON_0006813) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [dermatocranium](http://purl.obolibrary.org/obo/UBERON_0003113) -- [intercellular bridge organization](http://purl.obolibrary.org/obo/GO_0043063) SubClassOf [extracellular structure organization](http://purl.obolibrary.org/obo/GO_0043062) +- [nasal skeleton](http://purl.obolibrary.org/obo/UBERON_0006813) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) +### nasal-associated lymphoid tissue `http://purl.obolibrary.org/obo/UBERON_0012330` -### intercostal nerve `http://purl.obolibrary.org/obo/UBERON_0003727` -#### Removed -- [intercostal nerve](http://purl.obolibrary.org/obo/UBERON_0003727) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nervi intercostales" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Intercostal_nerves" +#### Added +- [nasal-associated lymphoid tissue](http://purl.obolibrary.org/obo/UBERON_0012330) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [intercostal nerve](http://purl.obolibrary.org/obo/UBERON_0003727) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nervi intercostales" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### nasolacrimal duct `http://purl.obolibrary.org/obo/UBERON_0002392` +#### Removed +- [nasolacrimal duct](http://purl.obolibrary.org/obo/UBERON_0002392) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The nasolacrimal duct is probably homologous to the posterior (excurrent) naris of actinopterygian fishes.[uncertain][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Intercostal_nerves" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### interlobar artery `http://purl.obolibrary.org/obo/UBERON_0009885` -#### Removed -- [interlobar artery](http://purl.obolibrary.org/obo/UBERON_0009885) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteriae interlobares renis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Interlobar_arteries" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000664" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.256" + +- [nasolacrimal duct](http://purl.obolibrary.org/obo/UBERON_0002392) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "the nasolacrimal duct, the sac is lined by stratified columnar epithelium with mucus-secreting goblet cells, and is surrounded by connective tissue" #### Added -- [interlobar artery](http://purl.obolibrary.org/obo/UBERON_0009885) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteriae interlobares renis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Interlobar_arteries" +- [nasolacrimal duct](http://purl.obolibrary.org/obo/UBERON_0002392) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### nasopharyngeal gland `http://purl.obolibrary.org/obo/UBERON_0008310` -### interlobar vein `http://purl.obolibrary.org/obo/UBERON_0009887` -#### Removed -- [interlobar vein](http://purl.obolibrary.org/obo/UBERON_0009887) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "venae interlobares renis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Interlobar_veins" +#### Added +- [nasopharyngeal gland](http://purl.obolibrary.org/obo/UBERON_0008310) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [interlobar vein](http://purl.obolibrary.org/obo/UBERON_0009887) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "venae interlobares renis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### nasopharynx `http://purl.obolibrary.org/obo/UBERON_0001728` +#### Removed +- [nasopharynx](http://purl.obolibrary.org/obo/UBERON_0001728) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "nasopharyngeal" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Interlobar_veins" +- [nasopharynx](http://purl.obolibrary.org/obo/UBERON_0001728) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In humans - in front it communicates through the choanae with the nasal cavities. On its lateral wall is the pharyngeal ostium of the auditory tube, somewhat triangular in shape, and bounded behind by a firm prominence, the torus tubarius or cushion, caused by the medial end of the cartilage of the tube which elevates the mucous membrane" +- [nasopharynx](http://purl.obolibrary.org/obo/UBERON_0001728) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The uppermost of the three regions of the throat (pharynx), situated behind the nasal cavity and extending from the posterior nares to the level above the soft palate. [TFD][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000375" -### interlobular artery `http://purl.obolibrary.org/obo/UBERON_0004723` -#### Removed -- [interlobular artery](http://purl.obolibrary.org/obo/UBERON_0004723) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteriae interlobulares renis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Interlobular_arteries" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [interlobular artery](http://purl.obolibrary.org/obo/UBERON_0004723) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteriae corticales radiatae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Interlobular_arteries" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/nasopharynx" -#### Added -- [interlobular artery](http://purl.obolibrary.org/obo/UBERON_0004723) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteriae interlobulares renis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Interlobular_arteries" -- [interlobular artery](http://purl.obolibrary.org/obo/UBERON_0004723) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteriae corticales radiatae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### nasopharynx connective tissue `http://purl.obolibrary.org/obo/UBERON_0003582` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Interlobular_arteries" +#### Added +- [nasopharynx connective tissue](http://purl.obolibrary.org/obo/UBERON_0003582) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -### interlobular duct of salivary gland `http://purl.obolibrary.org/obo/UBERON_0035053` +### natural cytotoxicity triggering receptor 1 `http://purl.obolibrary.org/obo/PR_000001893` #### Removed -- [interlobular duct of salivary gland](http://purl.obolibrary.org/obo/UBERON_0035053) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006341" - - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0003-4423-4370" +- [natural cytotoxicity triggering receptor 1](http://purl.obolibrary.org/obo/PR_000001893) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [natural cytotoxicity triggering receptor 1 (human)](http://purl.obolibrary.org/obo/PR_O76036) -### intermediate hypothalamic region `http://purl.obolibrary.org/obo/UBERON_0002555` +### natural cytotoxicity triggering receptor 2 `http://purl.obolibrary.org/obo/PR_000001894` #### Removed -- [intermediate hypothalamic region](http://purl.obolibrary.org/obo/UBERON_0002555) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "area hypothalamica intermedia" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:62028" +- [natural cytotoxicity triggering receptor 2](http://purl.obolibrary.org/obo/PR_000001894) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [natural cytotoxicity triggering receptor 2 (human)](http://purl.obolibrary.org/obo/PR_O95944) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [intermediate hypothalamic region](http://purl.obolibrary.org/obo/UBERON_0002555) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "regio hypothalamica intermedia" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:392" +### natural killer cell receptor 2B4 `http://purl.obolibrary.org/obo/PR_000001896` +#### Removed +- [natural killer cell receptor 2B4](http://purl.obolibrary.org/obo/PR_000001896) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [natural killer cell receptor 2B4 (human)](http://purl.obolibrary.org/obo/PR_Q9BZW8) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [intermediate hypothalamic region](http://purl.obolibrary.org/obo/UBERON_0002555) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "regio hypothalamica intermedia" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:392" +### neck `http://purl.obolibrary.org/obo/UBERON_0000974` +#### Removed +- [neck](http://purl.obolibrary.org/obo/UBERON_0000974) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "cervical" -- [intermediate hypothalamic region](http://purl.obolibrary.org/obo/UBERON_0002555) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "area hypothalamica intermedia" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:62028" +- [neck](http://purl.obolibrary.org/obo/UBERON_0000974) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "true necks are considered to be present when the pectoral girdle is separate from the skull - Tiktaalik is the earliest known fish to have a true neck." - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [neck](http://purl.obolibrary.org/obo/UBERON_0000974) [RO_0002174](http://purl.obolibrary.org/obo/RO_0002174) [Teleostei](http://purl.obolibrary.org/obo/NCBITaxon_32443) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:9780674021839" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### intermediate mesoderm `http://purl.obolibrary.org/obo/UBERON_0003064` +### neck of bone element `http://purl.obolibrary.org/obo/UBERON_0018664` #### Removed -- [intermediate mesoderm](http://purl.obolibrary.org/obo/UBERON_0003064) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "mesenchyma intermedium" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Intermediate_mesoderm" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [neck of bone element](http://purl.obolibrary.org/obo/UBERON_0018664) SubClassOf [zone of bone organ](http://purl.obolibrary.org/obo/UBERON_0005913) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "https://github.com/obophenotype/uberon/wiki/Hidden-GCIs" #### Added -- [intermediate mesoderm](http://purl.obolibrary.org/obo/UBERON_0003064) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "mesenchyma intermedium" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [neck of bone element](http://purl.obolibrary.org/obo/UBERON_0018664) SubClassOf [zone of bone organ](http://purl.obolibrary.org/obo/UBERON_0005913) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Intermediate_mesoderm" - -### intermediate monocyte `http://purl.obolibrary.org/obo/CL_0002393` +### neck of femur `http://purl.obolibrary.org/obo/UBERON_0007119` #### Added -- [intermediate monocyte](http://purl.obolibrary.org/obo/CL_0002393) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [neck of femur](http://purl.obolibrary.org/obo/UBERON_0007119) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### internal carotid artery `http://purl.obolibrary.org/obo/UBERON_0001532` -#### Removed -- [internal carotid artery](http://purl.obolibrary.org/obo/UBERON_0001532) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria carotis interna" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Internal_carotid_artery" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### neck of fibula `http://purl.obolibrary.org/obo/UBERON_0018673` #### Added -- [internal carotid artery](http://purl.obolibrary.org/obo/UBERON_0001532) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria carotis interna" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Internal_carotid_artery" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [neck of fibula](http://purl.obolibrary.org/obo/UBERON_0018673) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### internal female genitalia `http://purl.obolibrary.org/obo/UBERON_0003975` +### neck of gallbladder `http://purl.obolibrary.org/obo/UBERON_0035267` #### Added -- [internal female genitalia](http://purl.obolibrary.org/obo/UBERON_0003975) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas) - -- [internal female genitalia](http://purl.obolibrary.org/obo/UBERON_0003975) [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [Homo sapiens](http://purl.obolibrary.org/obo/NCBITaxon_9606) +- [neck of gallbladder](http://purl.obolibrary.org/obo/UBERON_0035267) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -### internal genitalia `http://purl.obolibrary.org/obo/UBERON_0004175` +### neck of humerus `http://purl.obolibrary.org/obo/UBERON_4200172` #### Added -- [internal genitalia](http://purl.obolibrary.org/obo/UBERON_0004175) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas) +- [neck of humerus](http://purl.obolibrary.org/obo/UBERON_4200172) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -- [internal genitalia](http://purl.obolibrary.org/obo/UBERON_0004175) [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [Homo sapiens](http://purl.obolibrary.org/obo/NCBITaxon_9606) +### neck of tooth `http://purl.obolibrary.org/obo/UBERON_0015181` -### internal iliac artery `http://purl.obolibrary.org/obo/UBERON_0001309` -#### Removed -- [internal iliac artery](http://purl.obolibrary.org/obo/UBERON_0001309) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria iliaca interna" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Internal_iliac_artery" +#### Added +- [neck of tooth](http://purl.obolibrary.org/obo/UBERON_0015181) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [internal iliac artery](http://purl.obolibrary.org/obo/UBERON_0001309) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria iliaca interna" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### neck of urinary bladder `http://purl.obolibrary.org/obo/UBERON_0001258` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Internal_iliac_artery" +#### Added +- [neck of urinary bladder](http://purl.obolibrary.org/obo/UBERON_0001258) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### internal iliac vein `http://purl.obolibrary.org/obo/UBERON_0001317` +### negatively regulated by `http://purl.obolibrary.org/obo/RO_0002335` #### Removed -- [internal iliac vein](http://purl.obolibrary.org/obo/UBERON_0001317) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "v. iliaca interna" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Internal_iliac_vein" +- [negatively regulated by](http://purl.obolibrary.org/obo/RO_0002335) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [internal iliac vein](http://purl.obolibrary.org/obo/UBERON_0001317) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "v. hypogastrica" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Internal_iliac_vein" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - -#### Added -- [internal iliac vein](http://purl.obolibrary.org/obo/UBERON_0001317) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "v. hypogastrica" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Internal_iliac_vein" +### negatively regulates `http://purl.obolibrary.org/obo/RO_0002212` +#### Removed +- [negatively regulates](http://purl.obolibrary.org/obo/RO_0002212) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) [causal-relations](http://purl.obolibrary.org/obo/ro/docs/causal-relations) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [negatively regulates](http://purl.obolibrary.org/obo/RO_0002212) [IAO_0000589](http://purl.obolibrary.org/obo/IAO_0000589) "negatively regulates (process to process)" -- [internal iliac vein](http://purl.obolibrary.org/obo/UBERON_0001317) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "v. iliaca interna" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Internal_iliac_vein" +- [negatively regulates](http://purl.obolibrary.org/obo/RO_0002212) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### internal jugular vein `http://purl.obolibrary.org/obo/UBERON_0001586` +### neocortex `http://purl.obolibrary.org/obo/UBERON_0001950` #### Removed -- [internal jugular vein](http://purl.obolibrary.org/obo/UBERON_0001586) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena jugularis interna" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Internal_jugular_vein" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [neocortex](http://purl.obolibrary.org/obo/UBERON_0001950) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [olfactory bulb](http://purl.obolibrary.org/obo/UBERON_0002264) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" -#### Added -- [internal jugular vein](http://purl.obolibrary.org/obo/UBERON_0001586) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena jugularis interna" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [neocortex](http://purl.obolibrary.org/obo/UBERON_0001950) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The 6-layer neocortex is well conserved in all extant mammals, but not present in birds or reptils" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:23027930" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Internal_jugular_vein" -### internal pudendal vein `http://purl.obolibrary.org/obo/UBERON_0018252` +### nephrogenic zone `http://purl.obolibrary.org/obo/UBERON_0009871` #### Removed -- [internal pudendal vein](http://purl.obolibrary.org/obo/UBERON_0018252) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vena pudenda interna" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [nephrogenic zone](http://purl.obolibrary.org/obo/UBERON_0009871) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "see http://www.ncbi.nlm.nih.gov/pubmed/12761251 for description of nephrogenic zone in dogfish." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Internal_pudendal_veins" -#### Added -- [internal pudendal vein](http://purl.obolibrary.org/obo/UBERON_0018252) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vena pudenda interna" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Internal_pudendal_veins" +### nephron `http://purl.obolibrary.org/obo/UBERON_0001285` +#### Removed +- [nephron](http://purl.obolibrary.org/obo/UBERON_0001285) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Functional unit of the kidney that filters waste.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -### internal thoracic artery `http://purl.obolibrary.org/obo/UBERON_0002456` -#### Removed -- [internal thoracic artery](http://purl.obolibrary.org/obo/UBERON_0002456) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria mammaria interna" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Internal_thoracic_artery" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0002153" -- [internal thoracic artery](http://purl.obolibrary.org/obo/UBERON_0002456) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria thoracica interna" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Internal_thoracic_artery" +- [nephron](http://purl.obolibrary.org/obo/UBERON_0001285) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In the avian kidney, three types of nephron are identified: mammalian-type nephrons with long and short loops of Henle, and reptilian type nephrons (Gambaryan, 1992)" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [nephron](http://purl.obolibrary.org/obo/UBERON_0001285) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [nephrogenic mesenchyme](http://purl.obolibrary.org/obo/UBERON_0004208) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" #### Added -- [internal thoracic artery](http://purl.obolibrary.org/obo/UBERON_0002456) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria mammaria interna" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Internal_thoracic_artery" +- [nephron](http://purl.obolibrary.org/obo/UBERON_0001285) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [nephrogenic mesenchyme](http://purl.obolibrary.org/obo/UBERON_0004208) -- [internal thoracic artery](http://purl.obolibrary.org/obo/UBERON_0002456) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria thoracica interna" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Internal_thoracic_artery" +### nephron tubule `http://purl.obolibrary.org/obo/UBERON_0001231` +#### Removed +- [nephron tubule](http://purl.obolibrary.org/obo/UBERON_0001231) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "note that in ISBN:0073040584 (Vertebrates, Kardong), the uriniferous tubule contains the nephron, so we have a separate class, rather than using a synonym, as in MA" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" +- [nephron tubule](http://purl.obolibrary.org/obo/UBERON_0001231) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [kidney mesenchyme](http://purl.obolibrary.org/obo/UBERON_0003918) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "checkme" -### internal urethral orifice `http://purl.obolibrary.org/obo/UBERON_0012242` -#### Removed -- [internal urethral orifice](http://purl.obolibrary.org/obo/UBERON_0012242) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ostium orificium internum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +#### Added +- [nephron tubule](http://purl.obolibrary.org/obo/UBERON_0001231) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [kidney mesenchyme](http://purl.obolibrary.org/obo/UBERON_0003918) -- [internal urethral orifice](http://purl.obolibrary.org/obo/UBERON_0012242) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "orificium urethrae internum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MP:0011782" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### neprilysin `http://purl.obolibrary.org/obo/PR_000001898` +#### Removed +- [neprilysin](http://purl.obolibrary.org/obo/PR_000001898) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [neprilysin (human)](http://purl.obolibrary.org/obo/PR_P08473) -- [internal urethral orifice](http://purl.obolibrary.org/obo/UBERON_0012242) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ostium urethrae internum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Internal_urethral_orifice" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [internal urethral orifice](http://purl.obolibrary.org/obo/UBERON_0012242) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "orificium urethrae internum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### nerve `http://purl.obolibrary.org/obo/UBERON_0001021` +#### Removed +- [nerve](http://purl.obolibrary.org/obo/UBERON_0001021) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005105" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MP:0011782" +- [nerve](http://purl.obolibrary.org/obo/UBERON_0001021) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A portion of tissue which is a fasiculated group of axons.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -- [internal urethral orifice](http://purl.obolibrary.org/obo/UBERON_0012242) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ostium orificium internum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0007009" -- [internal urethral orifice](http://purl.obolibrary.org/obo/UBERON_0012242) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ostium urethrae internum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Internal_urethral_orifice" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" +- [nerve](http://purl.obolibrary.org/obo/UBERON_0001021) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "nervous" -### interneuron `http://purl.obolibrary.org/obo/CL_0000099` -#### Added -- [interneuron](http://purl.obolibrary.org/obo/CL_0000099) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + +### nerve fiber `http://purl.obolibrary.org/obo/UBERON_0006134` +#### Removed +- [nerve fiber](http://purl.obolibrary.org/obo/UBERON_0006134) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "neurofibrous" -### interstitial cell of Cajal `http://purl.obolibrary.org/obo/CL_0002088` -#### Added -- [interstitial cell of Cajal](http://purl.obolibrary.org/obo/CL_0002088) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### nerve fiber layer of retina `http://purl.obolibrary.org/obo/UBERON_0001793` +#### Removed +- [nerve fiber layer of retina](http://purl.obolibrary.org/obo/UBERON_0001793) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001169" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429" -### interstitial cell of ovary `http://purl.obolibrary.org/obo/CL_0002094` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [interstitial cell of ovary](http://purl.obolibrary.org/obo/CL_0002094) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### interstitial extravillous trophoblast cell `http://purl.obolibrary.org/obo/CL_4033062` -#### Added -- [interstitial extravillous trophoblast cell](http://purl.obolibrary.org/obo/CL_4033062) [label](http://www.w3.org/2000/01/rdf-schema#label) "interstitial extravillous trophoblast cell" -- [interstitial extravillous trophoblast cell](http://purl.obolibrary.org/obo/CL_4033062) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A trophoblast cell that invades the uterine wall to anchor the placenta to the uterus. An interstitial extravillous trophoblast cell differentiates from an extravillous trophoblast cell, becoming hyperchromatic and changing its morphology to a fibroblast-like spindle-shaped cell. In humans, this cell can be distinguished by the expression of placental-specific protein 8, which stimulates migration." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37630754" +### nerve innervating pinna `http://purl.obolibrary.org/obo/UBERON_0035648` +#### Removed +- [nerve innervating pinna](http://purl.obolibrary.org/obo/UBERON_0035648) SubClassOf [nerve](http://purl.obolibrary.org/obo/UBERON_0001021) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.1007/978-3-030-84725-8" +#### Added +- [nerve innervating pinna](http://purl.obolibrary.org/obo/UBERON_0035648) SubClassOf [nerve of head region](http://purl.obolibrary.org/obo/UBERON_0011779) -- [interstitial extravillous trophoblast cell](http://purl.obolibrary.org/obo/CL_4033062) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) -- [interstitial extravillous trophoblast cell](http://purl.obolibrary.org/obo/CL_4033062) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "iEVT" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37630754" +### nerve plexus `http://purl.obolibrary.org/obo/UBERON_0001810` +#### Removed +- [nerve plexus](http://purl.obolibrary.org/obo/UBERON_0001810) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "Made to be a subtype of junction rather than tissue to be consistent with FMA" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [abbreviation](http://purl.obolibrary.org/obo/OMO_0003000) -- [interstitial extravillous trophoblast cell](http://purl.obolibrary.org/obo/CL_4033062) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "interstitial extravillous trophoblast" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37630754" -- [interstitial extravillous trophoblast cell](http://purl.obolibrary.org/obo/CL_4033062) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "invasive interstitial extravillous trophoblast cell" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.1007/978-3-030-84725-8" +### nerve root `http://purl.obolibrary.org/obo/UBERON_0002211` +#### Removed +- [nerve root](http://purl.obolibrary.org/obo/UBERON_0002211) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The continuation of the neurite bundle and associated glia of a nerve, inside the central nervous system[FBbt:00007602, FBC:DOS]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FBbt:00007602, FBC:DOS" -- [interstitial extravillous trophoblast cell](http://purl.obolibrary.org/obo/CL_4033062) [date](http://purl.org/dc/terms/date) "2024-01-08T15:43:15Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +- [nerve root](http://purl.obolibrary.org/obo/UBERON_0002211) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA has 'central zone of nerve' which is the superclass of cranial nerve tracts, which the FMA sometimes calls roots" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" -- [interstitial extravillous trophoblast cell](http://purl.obolibrary.org/obo/CL_4033062) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "interstitial trophoblast" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:11337369" -- Class: [interstitial extravillous trophoblast cell](http://purl.obolibrary.org/obo/CL_4033062) -- [interstitial extravillous trophoblast cell](http://purl.obolibrary.org/obo/CL_4033062) SubClassOf [trophoblast cell](http://purl.obolibrary.org/obo/CL_0000351) +### nerve trunk `http://purl.obolibrary.org/obo/UBERON_0002464` +#### Removed +- [nerve trunk](http://purl.obolibrary.org/obo/UBERON_0002464) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Segment of neural tree organ which consists of nerve fiber bundles aggregated to form a cable-like structure that branches off to different nerves; together with all nerves of the same tree. Example: trunk of cranial nerve, trunk of spinal nerve, trunk of peripheral nerve[FMA:5913]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:5913" -- [interstitial extravillous trophoblast cell](http://purl.obolibrary.org/obo/CL_4033062) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [extravillous trophoblast](http://purl.obolibrary.org/obo/CL_0008036) -### intertarsal joint `http://purl.obolibrary.org/obo/UBERON_0008447` +### nervous system `http://purl.obolibrary.org/obo/UBERON_0001016` #### Removed -- [intertarsal joint](http://purl.obolibrary.org/obo/UBERON_0008447) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "articulationes intertarsales" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Intertarsal_articulations" +- [nervous system](http://purl.obolibrary.org/obo/UBERON_0001016) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000324" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -#### Added -- [intertarsal joint](http://purl.obolibrary.org/obo/UBERON_0008447) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "articulationes intertarsales" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Intertarsal_articulations" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" +- [nervous system](http://purl.obolibrary.org/obo/UBERON_0001016) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### interventricular septum `http://purl.obolibrary.org/obo/UBERON_0002094` -#### Removed -- [interventricular septum](http://purl.obolibrary.org/obo/UBERON_0002094) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "s. interventriculare cordis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Interventricular_septum" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000402" -#### Added -- [interventricular septum](http://purl.obolibrary.org/obo/UBERON_0002094) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "s. interventriculare cordis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Interventricular_septum" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.117" +- [nervous system](http://purl.obolibrary.org/obo/UBERON_0001016) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "neural" -### interventricular septum membranous part `http://purl.obolibrary.org/obo/UBERON_0004666` -#### Removed -- [interventricular septum membranous part](http://purl.obolibrary.org/obo/UBERON_0004666) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pars membranacea septi interventricularis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:7135" +- [nervous system](http://purl.obolibrary.org/obo/UBERON_0001016) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000396" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -#### Added -- [interventricular septum membranous part](http://purl.obolibrary.org/obo/UBERON_0004666) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pars membranacea septi interventricularis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:7135" +- [nervous system](http://purl.obolibrary.org/obo/UBERON_0001016) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "nervous" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [nervous system](http://purl.obolibrary.org/obo/UBERON_0001016) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005093" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### interventricular septum muscular part `http://purl.obolibrary.org/obo/UBERON_0004667` -#### Removed -- [interventricular septum muscular part](http://purl.obolibrary.org/obo/UBERON_0004667) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pars muscularis septi interventricularis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:7134" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### netrin-G1 `http://purl.obolibrary.org/obo/PR_000011467` +#### Removed +- [netrin-G1](http://purl.obolibrary.org/obo/PR_000011467) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [netrin-G1 (human)](http://purl.obolibrary.org/obo/PR_Q9Y2I2) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [interventricular septum muscular part](http://purl.obolibrary.org/obo/UBERON_0004667) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "septum membranaceum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [interventricular septum muscular part](http://purl.obolibrary.org/obo/UBERON_0004667) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "septum membranaceum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### neural arch `http://purl.obolibrary.org/obo/UBERON_0003861` +#### Removed +- [neural arch](http://purl.obolibrary.org/obo/UBERON_0003861) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "the dorsal bony and/or cartilaginous part of a vertebra, consisting of a pair of pedicles, a pair of laminae, and seven processes (four articular processes, two transverse processes, and one spinous process)" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "MP:0004599:csmith" -- [interventricular septum muscular part](http://purl.obolibrary.org/obo/UBERON_0004667) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pars muscularis septi interventricularis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [neural arch](http://purl.obolibrary.org/obo/UBERON_0003861) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) certain common components [of vertebral structure] are found in nearly all vertebrate. A representative vertebra has a vertebral arch or neural arch, which extends dorsally around the spinal cord.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:7134" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.270" -### intervertebral disk `http://purl.obolibrary.org/obo/UBERON_0001066` -#### Removed -- [intervertebral disk](http://purl.obolibrary.org/obo/UBERON_0001066) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "discus intervertebralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:10446" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001670" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [neural arch](http://purl.obolibrary.org/obo/UBERON_0003861) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "tiny neural arches present in Hagfish (which lack a true vertebraal column)." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [neural arch](http://purl.obolibrary.org/obo/UBERON_0003861) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A neural arch encloses the neural canal and typically meets its partner to form a neural spine. The neural arch can be a replacement ossification of the basidorsal cartilage or can form directly in membrane bone.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -#### Added -- [intervertebral disk](http://purl.obolibrary.org/obo/UBERON_0001066) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "discus intervertebralis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001066" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:10446" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" +- [neural arch](http://purl.obolibrary.org/obo/UBERON_0003861) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Bony arch perched on the vertebral centrum; successive arches enclose the neural canal that surrounds and protects the spinal cord dorsally.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -### intestinal crypt stem cell `http://purl.obolibrary.org/obo/CL_0002250` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000725" -#### Added -- [intestinal crypt stem cell](http://purl.obolibrary.org/obo/CL_0002250) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:Pugener_2002" -### intestinal crypt stem cell of colon `http://purl.obolibrary.org/obo/CL_0009043` +- [neural arch](http://purl.obolibrary.org/obo/UBERON_0003861) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "The neural arch can be a replacement ossification of the basidorsal cartilage or can form directly in membrane bone" -#### Added -- [intestinal crypt stem cell of colon](http://purl.obolibrary.org/obo/CL_0009043) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [neural arch](http://purl.obolibrary.org/obo/UBERON_0003861) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: develops_from basidorsal (TAO:0001060)[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001066" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -### intestinal crypt stem cell of large intestine `http://purl.obolibrary.org/obo/CL_0009016` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -#### Added -- [intestinal crypt stem cell of large intestine](http://purl.obolibrary.org/obo/CL_0009016) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### intestinal crypt stem cell of small intestine `http://purl.obolibrary.org/obo/CL_0009017` +### neural cell adhesion molecule 1 `http://purl.obolibrary.org/obo/PR_000001024` +#### Removed +- [neural cell adhesion molecule 1](http://purl.obolibrary.org/obo/PR_000001024) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [neural cell adhesion molecule 1 (human)](http://purl.obolibrary.org/obo/PR_P13591) -#### Added -- [intestinal crypt stem cell of small intestine](http://purl.obolibrary.org/obo/CL_0009017) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### intestinal enteroendocrine cell `http://purl.obolibrary.org/obo/CL_1001516` +### neural crest `http://purl.obolibrary.org/obo/UBERON_0002342` +#### Removed +- [neural crest](http://purl.obolibrary.org/obo/UBERON_0002342) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" -#### Added -- [intestinal enteroendocrine cell](http://purl.obolibrary.org/obo/CL_1001516) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### intestinal epithelial cell `http://purl.obolibrary.org/obo/CL_0002563` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010578" -#### Added -- [intestinal epithelial cell](http://purl.obolibrary.org/obo/CL_0002563) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [neural crest](http://purl.obolibrary.org/obo/UBERON_0002342) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000045" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -### intestinal tuft cell `http://purl.obolibrary.org/obo/CL_0019032` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -#### Added -- [intestinal tuft cell](http://purl.obolibrary.org/obo/CL_0019032) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" +- [neural crest](http://purl.obolibrary.org/obo/UBERON_0002342) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:11523831" -### intestinal villus `http://purl.obolibrary.org/obo/UBERON_0001213` -#### Removed -- [intestinal villus](http://purl.obolibrary.org/obo/UBERON_0001213) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "villi intestinales" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Intestinal_villus" +- [neural crest](http://purl.obolibrary.org/obo/UBERON_0002342) [RO_0002174](http://purl.obolibrary.org/obo/RO_0002174) [NCBITaxon_117565](http://purl.obolibrary.org/obo/NCBITaxon_117565) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0073040584" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:17377535" -#### Added -- [intestinal villus](http://purl.obolibrary.org/obo/UBERON_0001213) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "villi intestinales" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Intestinal_villus" +- [neural crest](http://purl.obolibrary.org/obo/UBERON_0002342) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "EDITOR_NOTE consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams)." - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [neural crest](http://purl.obolibrary.org/obo/UBERON_0002342) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "TAO:0000045" +- [neural crest](http://purl.obolibrary.org/obo/UBERON_0002342) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### intestine goblet cell `http://purl.obolibrary.org/obo/CL_0019031` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [intestine goblet cell](http://purl.obolibrary.org/obo/CL_0019031) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1111/j.1469-7580.2012.01495.x Hall BK, Gillis JA, Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues. J Anat (2012)" -### intracellular nitric oxide homeostasis `http://purl.obolibrary.org/obo/GO_0033484` -#### Removed -- [intracellular nitric oxide homeostasis](http://purl.obolibrary.org/obo/GO_0033484) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:0033484" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000057" -- [intracellular nitric oxide homeostasis](http://purl.obolibrary.org/obo/GO_0033484) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/geneontology/go-ontology/issues/24224"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) +- [neural crest](http://purl.obolibrary.org/obo/UBERON_0002342) SubClassOf [composed primarily of](http://purl.obolibrary.org/obo/RO_0002473) some [migratory neural crest cell](http://purl.obolibrary.org/obo/CL_0000333) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest" -- [intracellular nitric oxide homeostasis](http://purl.obolibrary.org/obo/GO_0033484) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "NO homeostasis" +- [neural crest](http://purl.obolibrary.org/obo/UBERON_0002342) SubClassOf [only in taxon](http://purl.obolibrary.org/obo/RO_0002160) some [Craniata ](http://purl.obolibrary.org/obo/NCBITaxon_89593) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0073040584" -- [intracellular nitric oxide homeostasis](http://purl.obolibrary.org/obo/GO_0033484) [label](http://www.w3.org/2000/01/rdf-schema#label) "intracellular nitric oxide homeostasis" + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells" -- [intracellular nitric oxide homeostasis](http://purl.obolibrary.org/obo/GO_0033484) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cellular nitric oxide homeostasis" +#### Added +- [neural crest](http://purl.obolibrary.org/obo/UBERON_0002342) SubClassOf [only in taxon](http://purl.obolibrary.org/obo/RO_0002160) some [Craniata ](http://purl.obolibrary.org/obo/NCBITaxon_89593) -- [intracellular nitric oxide homeostasis](http://purl.obolibrary.org/obo/GO_0033484) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A homeostatic process involved in the maintenance of a steady state level of nitric oxide within a cell." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:mah" +- [neural crest](http://purl.obolibrary.org/obo/UBERON_0002342) SubClassOf [composed primarily of](http://purl.obolibrary.org/obo/RO_0002473) some [migratory neural crest cell](http://purl.obolibrary.org/obo/CL_0000333) -- [intracellular nitric oxide homeostasis](http://purl.obolibrary.org/obo/GO_0033484) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" +- [neural crest](http://purl.obolibrary.org/obo/UBERON_0002342) SubClassOf [structure with developmental contribution from neural crest](http://purl.obolibrary.org/obo/UBERON_0010314) -- [intracellular nitric oxide homeostasis](http://purl.obolibrary.org/obo/GO_0033484) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "nitric oxide homeostasis" -- Class: [intracellular nitric oxide homeostasis](http://purl.obolibrary.org/obo/GO_0033484) +### neural crest-derived structure `http://purl.obolibrary.org/obo/UBERON_0010313` +#### Removed +- [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "Grouping term for query purposes" -- [intracellular nitric oxide homeostasis](http://purl.obolibrary.org/obo/GO_0033484) EquivalentTo [intracellular chemical homeostasis](http://purl.obolibrary.org/obo/GO_0055082) and ([regulates levels of](http://purl.obolibrary.org/obo/RO_0002332) some [CHEBI_16480](http://purl.obolibrary.org/obo/CHEBI_16480)) -- [intracellular nitric oxide homeostasis](http://purl.obolibrary.org/obo/GO_0033484) SubClassOf [intracellular chemical homeostasis](http://purl.obolibrary.org/obo/GO_0055082) -- [intracellular nitric oxide homeostasis](http://purl.obolibrary.org/obo/GO_0033484) SubClassOf [regulates levels of](http://purl.obolibrary.org/obo/RO_0002332) some [CHEBI_16480](http://purl.obolibrary.org/obo/CHEBI_16480) +### neural fold `http://purl.obolibrary.org/obo/UBERON_0005062` +#### Removed +- [neural fold](http://purl.obolibrary.org/obo/UBERON_0005062) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Neural_fold" +#### Added +- [neural fold](http://purl.obolibrary.org/obo/UBERON_0005062) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) -### intracellular protein transport `http://purl.obolibrary.org/obo/GO_0006886` +### neural groove `http://purl.obolibrary.org/obo/UBERON_0005061` #### Removed -- [intracellular protein transport](http://purl.obolibrary.org/obo/GO_0006886) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) +- [neural groove](http://purl.obolibrary.org/obo/UBERON_0005061) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Neural_groove" -#### Added -- [intracellular protein transport](http://purl.obolibrary.org/obo/GO_0006886) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) -### intracellular signal transduction `http://purl.obolibrary.org/obo/GO_0035556` +### neural keel `http://purl.obolibrary.org/obo/UBERON_0007135` #### Removed -- [intracellular signal transduction](http://purl.obolibrary.org/obo/GO_0035556) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "intracellular protein kinase cascade" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:signaling" +- [neural keel](http://purl.obolibrary.org/obo/UBERON_0007135) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -- [intracellular signal transduction](http://purl.obolibrary.org/obo/GO_0035556) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "intracellular signaling chain" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:3527303782" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000131" -- [intracellular signal transduction](http://purl.obolibrary.org/obo/GO_0035556) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "protein kinase cascade" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:signaling" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -- [intracellular signal transduction](http://purl.obolibrary.org/obo/GO_0035556) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "signal transduction via intracellular signaling cascade" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -### intracellular signal transduction involved in positive regulation of cell growth `http://purl.obolibrary.org/obo/GO_1905427` +### neural nucleus `http://purl.obolibrary.org/obo/UBERON_0000125` #### Removed -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "intracellular signal transduction pathway involved in upregulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" +- [neural nucleus](http://purl.obolibrary.org/obo/UBERON_0000125) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical structure consisting of a discrete aggregate of neuronal soma[GO][GO_REF:0000021]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GO_REF:0000021" + +- [neural nucleus](http://purl.obolibrary.org/obo/UBERON_0000125) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "Proposed CUMBO def from MM: A subcortical part of the nervous system consisting of a relatively compact group of cells that is distinguishable histologically that share a commonality of cytoarchitecture, chemoarchitecturel and connectivity. (comments: I put in 'subcortical' because I don't think we consider either the cerebellar cortex or cerebral cortex to be nuclei. Some people distinguish between a nucleus and a laminar structure (see Wikipedia definition). However, there are structures identified as nuclei that are laminar, e.g., lateral geniculate nucleus, although they are not laminated in all species. Also, I put in 'relatively compact' and 'distiguishable by histology' because we have groups of cells, e.g., cholinergic cell groups, doparminergic cell groups that are related on the 3 criteria but which we don't tend to consider nuclei because they don't occupy an easily defined territory. But all is open to debate." -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "intracellular signaling cascade involved in positive regulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" +- [neural nucleus](http://purl.obolibrary.org/obo/UBERON_0000125) SubClassOf [only in taxon](http://purl.obolibrary.org/obo/RO_0002160) some [Chordata](http://purl.obolibrary.org/obo/NCBITaxon_7711) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "we limit this structure by definition to chordate and vertebrate nervous systems" + +#### Added +- [neural nucleus](http://purl.obolibrary.org/obo/UBERON_0000125) SubClassOf [only in taxon](http://purl.obolibrary.org/obo/RO_0002160) some [Chordata](http://purl.obolibrary.org/obo/NCBITaxon_7711) -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "intracellular protein kinase cascade involved in stimulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [creation date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2016-09-07T18:15:01Z" +### neural plate `http://purl.obolibrary.org/obo/UBERON_0003075` +#### Removed +- [neural plate](http://purl.obolibrary.org/obo/UBERON_0003075) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D054258" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "signal transmission via intracellular cascade involved in up regulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "intracellular signal transduction involved in activation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "intracellular signal transduction pathway involved in up regulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" +- [neural plate](http://purl.obolibrary.org/obo/UBERON_0003075) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "intracellular signal transduction involved in up-regulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "intracellular signaling chain involved in up-regulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "intracellular signal transduction involved in up regulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000068" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "intracellular signaling pathway involved in up-regulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" +- [neural plate](http://purl.obolibrary.org/obo/UBERON_0003075) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "intracellular protein kinase cascade involved in up-regulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000132" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "intracellular signaling chain involved in stimulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "intracellular protein kinase cascade involved in up regulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "protein kinase cascade involved in up regulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "intracellular signaling chain involved in activation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "signal transduction via intracellular signaling cascade involved in up regulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" +### neural rod `http://purl.obolibrary.org/obo/UBERON_0005068` +#### Removed +- [neural rod](http://purl.obolibrary.org/obo/UBERON_0005068) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "intracellular signaling cascade involved in up-regulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000133" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "intracellular signal transduction pathway involved in positive regulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "intracellular protein kinase cascade involved in upregulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "intracellular signal transduction pathway involved in up-regulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:1905427" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "intracellular protein kinase cascade involved in activation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" +### neural spine `http://purl.obolibrary.org/obo/UBERON_0001076` +#### Removed +- [neural spine](http://purl.obolibrary.org/obo/UBERON_0001076) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The spinous process of a vertebra is directed backward and downward from the junction of the laminae (in humans), and serves for the attachment of muscles and ligaments. In animals without an erect stance, the process points upward and may slant forward or backward. Spinous processes are exaggerated in some animals, such as the extinct Dimetrodon and Spinosaurus, where they form a sail- or finback. [Wikipedia:Spinous_process]" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "intracellular signaling pathway involved in activation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" +- [neural spine](http://purl.obolibrary.org/obo/UBERON_0001076) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Elaboration of the mid-dorsal keel into a posterior or posterolateral process.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [label](http://www.w3.org/2000/01/rdf-schema#label) "intracellular signal transduction involved in positive regulation of cell growth" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:Pugener_and_Maglia_2008" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any intracellular signal transduction that is involved in positive regulation of cell growth." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO_REF:0000060" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:15917811" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000705" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:vw" +- [neural spine](http://purl.obolibrary.org/obo/UBERON_0001076) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Small, posteriorly directed process at the posterior margin of each neural arch lamina; it is not a neural spine.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000739" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:al" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "signal transduction via intracellular signaling cascade involved in positive regulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:Pugener_2002" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "intracellular signaling cascade involved in stimulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" +- [neural spine](http://purl.obolibrary.org/obo/UBERON_0001076) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Neural spines are extensions of neural arches dorsal to the neural canal in the median skeletogenous septum. Neural spines are typically unpaired median structures but can be paired in some instances, e.g., in the abdominal region of basal teleosts such as Leptolepis, Elops, Megalops, and Hiodon).[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "protein kinase cascade involved in upregulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001336" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "intracellular signaling cascade involved in activation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "intracellular signal transduction pathway involved in activation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "intracellular protein kinase cascade involved in positive regulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" +- [neural spine](http://purl.obolibrary.org/obo/UBERON_0001076) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: part_of mid-dorsal keel (AAO:0000735)[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "protein kinase cascade involved in activation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "intracellular signaling pathway involved in stimulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000705" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "intracellular signaling chain involved in upregulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "protein kinase cascade involved in stimulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "signal transmission via intracellular cascade involved in upregulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" +### neural tissue `http://purl.obolibrary.org/obo/UBERON_0003714` +#### Removed +- [neural tissue](http://purl.obolibrary.org/obo/UBERON_0003714) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [created by](http://www.geneontology.org/formats/oboInOwl#created_by) "dph" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000325" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "protein kinase cascade involved in positive regulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "intracellular signaling chain involved in positive regulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "intracellular signaling cascade involved in up regulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" +- [neural tissue](http://purl.obolibrary.org/obo/UBERON_0003714) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA definition includes vasculature" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "intracellular signaling cascade involved in upregulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "signal transduction via intracellular signaling cascade involved in activation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "intracellular signal transduction involved in upregulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" +### neural tube `http://purl.obolibrary.org/obo/UBERON_0001049` +#### Removed +- [neural tube](http://purl.obolibrary.org/obo/UBERON_0001049) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:JOR" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "signal transmission via intracellular cascade involved in activation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "intracellular signal transduction pathway involved in stimulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010617" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "signal transmission via intracellular cascade involved in positive regulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "intracellular signaling pathway involved in up regulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" +- [neural tube](http://purl.obolibrary.org/obo/UBERON_0001049) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D054259" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "signal transmission via intracellular cascade involved in up-regulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "protein kinase cascade involved in up-regulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "signal transduction via intracellular signaling cascade involved in upregulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" +- [neural tube](http://purl.obolibrary.org/obo/UBERON_0001049) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "intracellular signal transduction involved in stimulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "intracellular signaling chain involved in up regulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "intracellular signaling pathway involved in upregulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/neural+tube" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "signal transduction via intracellular signaling cascade involved in up-regulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000307" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "intracellular signaling pathway involved in positive regulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" +- [neural tube](http://purl.obolibrary.org/obo/UBERON_0001049) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GO:0021915" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "signal transduction via intracellular signaling cascade involved in stimulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" +- [neural tube](http://purl.obolibrary.org/obo/UBERON_0001049) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "signal transmission via intracellular cascade involved in stimulation of cell growth" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- Class: [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) EquivalentTo [intracellular signal transduction](http://purl.obolibrary.org/obo/GO_0035556) and ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_0030307)) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) SubClassOf [intracellular signal transduction](http://purl.obolibrary.org/obo/GO_0035556) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000307" -- [intracellular signal transduction involved in positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_1905427) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [positive regulation of cell growth](http://purl.obolibrary.org/obo/GO_0030307) +### neural tube basal plate `http://purl.obolibrary.org/obo/UBERON_0004064` +#### Removed +- [neural tube basal plate](http://purl.obolibrary.org/obo/UBERON_0004064) SubClassOf [developmentally induced by](http://purl.obolibrary.org/obo/RO_0002256) some [notochord](http://purl.obolibrary.org/obo/UBERON_0002328) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Swenson" -### intracellular signaling cassette `http://purl.obolibrary.org/obo/GO_0141124` + - [gene](http://www.geneontology.org/formats/oboInOwl#gene) "Shh" #### Added -- [intracellular signaling cassette](http://purl.obolibrary.org/obo/GO_0141124) [label](http://www.w3.org/2000/01/rdf-schema#label) "intracellular signaling cassette" +- [neural tube basal plate](http://purl.obolibrary.org/obo/UBERON_0004064) SubClassOf [developmentally induced by](http://purl.obolibrary.org/obo/RO_0002256) some [notochord](http://purl.obolibrary.org/obo/UBERON_0002328) -- [intracellular signaling cassette](http://purl.obolibrary.org/obo/GO_0141124) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/geneontology/go-ontology/issues/26557"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) +- [neural tube basal plate](http://purl.obolibrary.org/obo/UBERON_0004064) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -- [intracellular signaling cassette](http://purl.obolibrary.org/obo/GO_0141124) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" -- [intracellular signaling cassette](http://purl.obolibrary.org/obo/GO_0141124) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An intracellular signaling module that is part of larger signaling pathways that can be initiated either intracellularly or by cell surface receptors. Intracellular signaling cassettes are discrete signaling units that are often shared by multiple signaling pathways." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:pg" +### neural tube lateral wall `http://purl.obolibrary.org/obo/UBERON_0005496` +#### Removed +- [neural tube lateral wall](http://purl.obolibrary.org/obo/UBERON_0005496) SubClassOf [anatomical structure](http://purl.obolibrary.org/obo/UBERON_0000061) + +#### Added +- [neural tube lateral wall](http://purl.obolibrary.org/obo/UBERON_0005496) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:ha" -- [intracellular signaling cassette](http://purl.obolibrary.org/obo/GO_0141124) [creation date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2023-12-04T14:13:20Z" +### neural tube lumen `http://purl.obolibrary.org/obo/UBERON_0003842` +#### Removed +- [neural tube lumen](http://purl.obolibrary.org/obo/UBERON_0003842) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001119" -- [intracellular signaling cassette](http://purl.obolibrary.org/obo/GO_0141124) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:0141124" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [intracellular signaling cassette](http://purl.obolibrary.org/obo/GO_0141124) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "intracellular signaling module" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [intracellular signaling cassette](http://purl.obolibrary.org/obo/GO_0141124) [created by](http://www.geneontology.org/formats/oboInOwl#created_by) "pg" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [intracellular signaling cassette](http://purl.obolibrary.org/obo/GO_0141124) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "intracellular signaling cascade" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28" -- Class: [intracellular signaling cassette](http://purl.obolibrary.org/obo/GO_0141124) -- [intracellular signaling cassette](http://purl.obolibrary.org/obo/GO_0141124) SubClassOf [intracellular signal transduction](http://purl.obolibrary.org/obo/GO_0035556) +### neural tube mantle layer `http://purl.obolibrary.org/obo/UBERON_0004061` +#### Removed +- [neural tube mantle layer](http://purl.obolibrary.org/obo/UBERON_0004061) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [germinal neuroepithelium](http://purl.obolibrary.org/obo/UBERON_0004022) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "by division" -### intraepithelial lymphocyte `http://purl.obolibrary.org/obo/CL_0002496` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "NCBIBook:NBK10047" #### Added -- [intraepithelial lymphocyte](http://purl.obolibrary.org/obo/CL_0002496) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [neural tube mantle layer](http://purl.obolibrary.org/obo/UBERON_0004061) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [germinal neuroepithelium](http://purl.obolibrary.org/obo/UBERON_0004022) + +- [neural tube mantle layer](http://purl.obolibrary.org/obo/UBERON_0004061) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) -### intrahepatic cholangiocyte `http://purl.obolibrary.org/obo/CL_0002538` +### neural tube marginal layer `http://purl.obolibrary.org/obo/UBERON_0004062` +#### Removed +- [neural tube marginal layer](http://purl.obolibrary.org/obo/UBERON_0004062) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [neural tube mantle layer](http://purl.obolibrary.org/obo/UBERON_0004061) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "forms from axons" #### Added -- [intrahepatic cholangiocyte](http://purl.obolibrary.org/obo/CL_0002538) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [neural tube marginal layer](http://purl.obolibrary.org/obo/UBERON_0004062) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [neural tube mantle layer](http://purl.obolibrary.org/obo/UBERON_0004061) + +- [neural tube marginal layer](http://purl.obolibrary.org/obo/UBERON_0004062) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### intralobular bile duct `http://purl.obolibrary.org/obo/UBERON_0001282` +### neural tube ventricular layer `http://purl.obolibrary.org/obo/UBERON_0004060` #### Removed -- [intralobular bile duct](http://purl.obolibrary.org/obo/UBERON_0001282) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ductus interlobularis bilifer" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:17545" +- [neural tube ventricular layer](http://purl.obolibrary.org/obo/UBERON_0004060) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The layer of undifferentiated, proliferating cells that line the neural tube lumen" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "MP:0009689" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [intralobular bile duct](http://purl.obolibrary.org/obo/UBERON_0001282) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ductus interlobularis bilifer" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### neurectoderm `http://purl.obolibrary.org/obo/UBERON_0002346` +#### Removed +- [neurectoderm](http://purl.obolibrary.org/obo/UBERON_0002346) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:17545" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000150" -### intromittent organ `http://purl.obolibrary.org/obo/UBERON_0008811` -#### Removed -- [intromittent organ](http://purl.obolibrary.org/obo/UBERON_0008811) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004850" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)" -#### Added -- [intromittent organ](http://purl.obolibrary.org/obo/UBERON_0008811) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004850" +- [neurectoderm](http://purl.obolibrary.org/obo/UBERON_0002346) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001057" - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [neurectoderm](http://purl.obolibrary.org/obo/UBERON_0002346) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "neurectodermal" -### ionocyte `http://purl.obolibrary.org/obo/CL_0005006` +- [neurectoderm](http://purl.obolibrary.org/obo/UBERON_0002346) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here" -#### Added -- [ionocyte](http://purl.obolibrary.org/obo/CL_0005006) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### iris epithelium `http://purl.obolibrary.org/obo/UBERON_0002506` +### neurocranium `http://purl.obolibrary.org/obo/UBERON_0001703` #### Removed -- [iris epithelium](http://purl.obolibrary.org/obo/UBERON_0002506) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "epithelium pigmentosum iridis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58517" +- [neurocranium](http://purl.obolibrary.org/obo/UBERON_0001703) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical cluster that consists of the cartilages and bones that surround the brain.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001580" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TAO:MAH" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -#### Added -- [iris epithelium](http://purl.obolibrary.org/obo/UBERON_0002506) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "epithelium pigmentosum iridis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58517" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [neurocranium](http://purl.obolibrary.org/obo/UBERON_0001703) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "It includes the following bones: Ethmoid bone, Frontal bone, Occipital bone, Parietal bone, Sphenoid bone, Temporal bone. The term cranium can be ambiguous, in that it can refer to the neurocranium, or the neurocranium and the Facial skeleton" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [neurocranium](http://purl.obolibrary.org/obo/UBERON_0001703) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "The cartilaginous parts of the neurocranium undergo endochondral ossification in most species; ossification has been lost in cartilaginous fishes, but the cartilaginous condition of the skull of lampreys is considered to be primitive (Kardong, 1995)[PMID:11523816]. The neurocranium arises from paraxial mesoderm in the head (first five somites and the unsegmented somitomeres rostral to the first somite) and from ectoderm via the neural crest. In Chondrichthyes and other cartilaginous vertebrates this portion of the cranium does not ossify; it is not replaced via endochondral ossification[WP]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" +- [neurocranium](http://purl.obolibrary.org/obo/UBERON_0001703) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:17681" -### irregular bone `http://purl.obolibrary.org/obo/UBERON_0008001` -#### Removed -- [irregular bone](http://purl.obolibrary.org/obo/UBERON_0008001) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "os irregulare" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Irregular_bone" +- [neurocranium](http://purl.obolibrary.org/obo/UBERON_0001703) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "It seems MA uses 'neurocranium' as a synonym for chondrocranium. Note there are currently some structures part of both viscero and neurocranium - ethmoid, zyogomatic, ..." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [neurocranium](http://purl.obolibrary.org/obo/UBERON_0001703) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "AAO:0010153" -#### Added -- [irregular bone](http://purl.obolibrary.org/obo/UBERON_0008001) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "os irregulare" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [neurocranium](http://purl.obolibrary.org/obo/UBERON_0001703) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "neurocranial" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Irregular_bone" +- [neurocranium](http://purl.obolibrary.org/obo/UBERON_0001703) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EHDAA2:0000243" -### ischium `http://purl.obolibrary.org/obo/UBERON_0001274` + +### neurogenic placode `http://purl.obolibrary.org/obo/UBERON_0009955` #### Removed -- [ischium](http://purl.obolibrary.org/obo/UBERON_0001274) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "os ischii" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "AAO:0000860" +- [neurogenic placode](http://purl.obolibrary.org/obo/UBERON_0009955) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "While some sensory placodes (otic and olfactory) may have homologues in basal chordates (Wada et al., 1998), the so-called neurogenenic placodes (trigeminal, otic, lateral line and epibranchial placodes) appear to have emerged at a later time (Shimeld and Holland, 2000)" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "NCBIBook:NBK53171" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ischium" +- [neurogenic placode](http://purl.obolibrary.org/obo/UBERON_0009955) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "Includes: trigeminal, otic, lateral line and epibranchial placodes." - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [ischium](http://purl.obolibrary.org/obo/UBERON_0001274) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "os ischii" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "AAO:0000860" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### neurohypophysis `http://purl.obolibrary.org/obo/UBERON_0002198` +#### Removed +- [neurohypophysis](http://purl.obolibrary.org/obo/UBERON_0002198) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. An infundibulum grows ventrally from the diencephalon of the brain, and Rathke's pouch extends dorsally from the roof of the developing mouth, or stomodaeum. The infundibulum remains connected to the floor of the diencephalon, which becomes the hypothalamus, and gives rise to the part of the gland known as the neurohypophysis. (...) Rathke's pouch loses its connection with the stomodaeum in most adult vertebrates and gives rise to the rest of the gland, the adenohypophysis. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ischium" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510 and Figure 15-5" -### island of Calleja `http://purl.obolibrary.org/obo/UBERON_0001881` -#### Removed -- [island of Calleja](http://purl.obolibrary.org/obo/UBERON_0001881) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "insula callejae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Islands_of_Calleja" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000142" -- [island of Calleja](http://purl.obolibrary.org/obo/UBERON_0001881) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "insulae olfactoriae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Islands_of_Calleja" +- [neurohypophysis](http://purl.obolibrary.org/obo/UBERON_0002198) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "todo - resolve EMAPA and EHDAA2 models, include future neurohypophysis (TS15-19)? relationship to infundibular recess of 3rd ventricle (TS15-19)" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EMAPA" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [neurohypophysis](http://purl.obolibrary.org/obo/UBERON_0002198) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The infundibular part of the pituitary gland consisting of two regions.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -#### Added -- [island of Calleja](http://purl.obolibrary.org/obo/UBERON_0001881) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "insula callejae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Islands_of_Calleja" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" -- [island of Calleja](http://purl.obolibrary.org/obo/UBERON_0001881) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "insulae olfactoriae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010537" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Islands_of_Calleja" +- [neurohypophysis](http://purl.obolibrary.org/obo/UBERON_0002198) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### jejunal vein `http://purl.obolibrary.org/obo/UBERON_0001216` -#### Removed -- [jejunal vein](http://purl.obolibrary.org/obo/UBERON_0001216) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "venae jejunales" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Jejunal_veins" +### neuromast `http://purl.obolibrary.org/obo/UBERON_0008904` +#### Removed +- [neuromast](http://purl.obolibrary.org/obo/UBERON_0008904) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Type of mechanoreceptive organ of the lateral line which are arranged in lines on the body surface. These organs are constituted by hair cells and supporting cells and it is located in the epidermis with its hair cells exposed to the surface. Absent in some caecilians. These receptors receive afferent and efferent innervations.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" -#### Added -- [jejunal vein](http://purl.obolibrary.org/obo/UBERON_0001216) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "venae jejunales" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Jejunal_veins" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0001004" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### jejunum lamina propria `http://purl.obolibrary.org/obo/UBERON_8600034` +- [neuromast](http://purl.obolibrary.org/obo/UBERON_0008904) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Volcano-shaped lateral line sensory organ located in characteristic positions within the skin epithelium and containing hair cells and their support elements. Kimmel et al, 1995. (Also see Anatomical Atlas entry for lateral line by T. Whitfield.)[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -#### Added -- [jejunum lamina propria](http://purl.obolibrary.org/obo/UBERON_8600034) [id](http://www.geneontology.org/formats/oboInOwl#id) "UBERON:8600034" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000243" -- [jejunum lamina propria](http://purl.obolibrary.org/obo/UBERON_8600034) [date](http://purl.org/dc/terms/date) "2024-01-09T16:36:35Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -- [jejunum lamina propria](http://purl.obolibrary.org/obo/UBERON_8600034) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -- [jejunum lamina propria](http://purl.obolibrary.org/obo/UBERON_8600034) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A lamina propria that is part of a jejunum." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:9394954" +- [neuromast](http://purl.obolibrary.org/obo/UBERON_0008904) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006219" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -- [jejunum lamina propria](http://purl.obolibrary.org/obo/UBERON_8600034) [label](http://www.w3.org/2000/01/rdf-schema#label) "jejunum lamina propria" + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -- [jejunum lamina propria](http://purl.obolibrary.org/obo/UBERON_8600034) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "jejunal lamina propria" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:1556433" + - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) -- [jejunum lamina propria](http://purl.obolibrary.org/obo/UBERON_8600034) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) +- [neuromast](http://purl.obolibrary.org/obo/UBERON_0008904) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: part_of lateral line receptor organ (AAO:0001001)[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -- [jejunum lamina propria](http://purl.obolibrary.org/obo/UBERON_8600034) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lamina propria of jejunum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:22763879" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0001004" -- [jejunum lamina propria](http://purl.obolibrary.org/obo/UBERON_8600034) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-8134-3037](https://orcid.org/0000-0001-8134-3037) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -- Class: [jejunum lamina propria](http://purl.obolibrary.org/obo/UBERON_8600034) +- [neuromast](http://purl.obolibrary.org/obo/UBERON_0008904) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: subclass lateral line receptor (AAO:0010705)[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -- [jejunum lamina propria](http://purl.obolibrary.org/obo/UBERON_8600034) EquivalentTo [lamina propria](http://purl.obolibrary.org/obo/UBERON_0000030) and ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [jejunum](http://purl.obolibrary.org/obo/UBERON_0002115)) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0001004" -- [jejunum lamina propria](http://purl.obolibrary.org/obo/UBERON_8600034) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [intestinal villus of jejunum](http://purl.obolibrary.org/obo/UBERON_0008343) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -- [jejunum lamina propria](http://purl.obolibrary.org/obo/UBERON_8600034) SubClassOf [lamina propria of small intestine](http://purl.obolibrary.org/obo/UBERON_0001238) -### jugular foramen `http://purl.obolibrary.org/obo/UBERON_0005456` +### neuromere `http://purl.obolibrary.org/obo/UBERON_0004731` #### Removed -- [jugular foramen](http://purl.obolibrary.org/obo/UBERON_0005456) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D000080869" +- [neuromere](http://purl.obolibrary.org/obo/UBERON_0004731) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A metameric segment of the central nervous system.[ZFA]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -#### Added -- [jugular foramen](http://purl.obolibrary.org/obo/UBERON_0005456) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D000080869" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001328" - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +#### Added +- [neuromere](http://purl.obolibrary.org/obo/UBERON_0004731) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### juxtaglomerular apparatus `http://purl.obolibrary.org/obo/UBERON_0002303` +### neuron projection bundle `http://purl.obolibrary.org/obo/UBERON_0000122` #### Removed -- [juxtaglomerular apparatus](http://purl.obolibrary.org/obo/UBERON_0002303) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "complexus juxtaglomerularis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [neuron projection bundle](http://purl.obolibrary.org/obo/UBERON_0000122) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005099" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -#### Added -- [juxtaglomerular apparatus](http://purl.obolibrary.org/obo/UBERON_0002303) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "complexus juxtaglomerularis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### keratinized stratified squamous epithelium `http://purl.obolibrary.org/obo/UBERON_0012329` +### neuron projection bundle connecting eye with brain `http://purl.obolibrary.org/obo/UBERON_0004904` #### Removed -- [keratinized stratified squamous epithelium](http://purl.obolibrary.org/obo/UBERON_0012329) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "epithelium stratificatum squamosum cornificatum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:45568" +- [neuron projection bundle connecting eye with brain](http://purl.obolibrary.org/obo/UBERON_0004904) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001956" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [keratinized stratified squamous epithelium](http://purl.obolibrary.org/obo/UBERON_0012329) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "epithelium stratificatum squamosum cornificatum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:45568" +### neuronal acetylcholine receptor subunit alpha-7 `http://purl.obolibrary.org/obo/PR_000005460` +#### Removed +- [neuronal acetylcholine receptor subunit alpha-7](http://purl.obolibrary.org/obo/PR_000005460) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [neuronal acetylcholine receptor subunit alpha-7 (human)](http://purl.obolibrary.org/obo/PR_P36544) + -### keratinocyte `http://purl.obolibrary.org/obo/CL_0000312` +### neuropilin and tolloid-like protein 1 `http://purl.obolibrary.org/obo/PR_000011143` +#### Removed +- [neuropilin and tolloid-like protein 1](http://purl.obolibrary.org/obo/PR_000011143) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [neuropilin and tolloid-like protein 1 (human)](http://purl.obolibrary.org/obo/PR_Q8TDF5) -#### Added -- [keratinocyte](http://purl.obolibrary.org/obo/CL_0000312) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### keratinocyte stem cell `http://purl.obolibrary.org/obo/CL_0002337` +### neurotransmitter transmembrane transporter activity `http://purl.obolibrary.org/obo/GO_0005326` +#### Removed +- [neurotransmitter transmembrane transporter activity](http://purl.obolibrary.org/obo/GO_0005326) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [neurotransmitter transport](http://purl.obolibrary.org/obo/GO_0006836) + - [source](http://www.geneontology.org/formats/oboInOwl#http://purl.org/dc/terms/source) "GO_REF:0000090" #### Added -- [keratinocyte stem cell](http://purl.obolibrary.org/obo/CL_0002337) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [neurotransmitter transmembrane transporter activity](http://purl.obolibrary.org/obo/GO_0005326) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [neurotransmitter transport](http://purl.obolibrary.org/obo/GO_0006836) -### keratocyte `http://purl.obolibrary.org/obo/CL_0002363` +### neurula stage `http://purl.obolibrary.org/obo/UBERON_0000110` +#### Removed +- [neurula stage](http://purl.obolibrary.org/obo/UBERON_0000110) [RO_0002174](http://purl.obolibrary.org/obo/RO_0002174) [NCBITaxon_7955](http://purl.obolibrary.org/obo/NCBITaxon_7955) -#### Added -- [keratocyte](http://purl.obolibrary.org/obo/CL_0002363) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [neurula stage](http://purl.obolibrary.org/obo/UBERON_0000110) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In zebrafish, the times of neurulation and segmentation overlap so extensively there is no distinct neurula period of development, such as occurs largely before segmentation in amphibian embryos." -### kidney afferent arteriole endothelial cell `http://purl.obolibrary.org/obo/CL_1001096` -#### Added -- [kidney afferent arteriole endothelial cell](http://purl.obolibrary.org/obo/CL_1001096) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### neutrophil gelatinase-associated lipocalin `http://purl.obolibrary.org/obo/PR_000009725` +#### Removed +- [neutrophil gelatinase-associated lipocalin](http://purl.obolibrary.org/obo/PR_000009725) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [neutrophil gelatinase-associated lipocalin (human)](http://purl.obolibrary.org/obo/PR_P80188) -### kidney arcuate vein `http://purl.obolibrary.org/obo/UBERON_0004719` + +### never_in_taxon `http://purl.obolibrary.org/obo/RO_0002161` #### Removed -- [kidney arcuate vein](http://purl.obolibrary.org/obo/UBERON_0004719) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "venae arcuatae renis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Arcuate_vein" +- [never_in_taxon](http://purl.obolibrary.org/obo/RO_0002161) [id](http://www.geneontology.org/formats/oboInOwl#id) "never_in_taxon" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [never_in_taxon](http://purl.obolibrary.org/obo/RO_0002161) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "tooth SubClassOf 'never in taxon' value 'Aves'" -#### Added -- [kidney arcuate vein](http://purl.obolibrary.org/obo/UBERON_0004719) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "venae arcuatae renis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [never_in_taxon](http://purl.obolibrary.org/obo/RO_0002161) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) [17921072](http://www.ncbi.nlm.nih.gov/pubmed/17921072) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Arcuate_vein" +- [never_in_taxon](http://purl.obolibrary.org/obo/RO_0002161) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "S never_in_taxon T iff: S SubClassOf in_taxon only not T." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20973947" +- [never_in_taxon](http://purl.obolibrary.org/obo/RO_0002161) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002161" -### kidney capillary endothelial cell `http://purl.obolibrary.org/obo/CL_1000892` +- [never_in_taxon](http://purl.obolibrary.org/obo/RO_0002161) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "never_in_taxon" -#### Added -- [kidney capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1000892) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [never_in_taxon](http://purl.obolibrary.org/obo/RO_0002161) [is_metadata_tag](http://www.geneontology.org/formats/oboInOwl#is_metadata_tag) true +- [never_in_taxon](http://purl.obolibrary.org/obo/RO_0002161) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" -### kidney capsule `http://purl.obolibrary.org/obo/UBERON_0002015` -#### Removed -- [kidney capsule](http://purl.obolibrary.org/obo/UBERON_0002015) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "capsula fibrosa renis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:66610" +- [never_in_taxon](http://purl.obolibrary.org/obo/RO_0002161) [is_class_level](http://www.geneontology.org/formats/oboInOwl#is_class_level) true - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [never_in_taxon](http://purl.obolibrary.org/obo/RO_0002161) [label](http://www.w3.org/2000/01/rdf-schema#label) "never_in_taxon" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [never_in_taxon](http://purl.obolibrary.org/obo/RO_0002161) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) -#### Added -- [kidney capsule](http://purl.obolibrary.org/obo/UBERON_0002015) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "capsula fibrosa renis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:66610" +- [never_in_taxon](http://purl.obolibrary.org/obo/RO_0002161) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) [20973947](http://www.ncbi.nlm.nih.gov/pubmed/20973947) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [never_in_taxon](http://purl.obolibrary.org/obo/RO_0002161) [IAO_0000425](http://purl.obolibrary.org/obo/IAO_0000425) "Class: ?X DisjointWith: RO_0002162 some ?Y " - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [never_in_taxon](http://purl.obolibrary.org/obo/RO_0002161) [IAO_0000425](http://purl.obolibrary.org/obo/IAO_0000425) "Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: ?X and (RO_0002162 some ?Y)" -### kidney cell `http://purl.obolibrary.org/obo/CL_1000497` -#### Added -- [kidney cell](http://purl.obolibrary.org/obo/CL_1000497) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### nipple `http://purl.obolibrary.org/obo/UBERON_0002030` +#### Removed +- [nipple](http://purl.obolibrary.org/obo/UBERON_0002030) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA makes this part of the breast, whereas in MA it is part of the mammary gland -" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" +- [nipple](http://purl.obolibrary.org/obo/UBERON_0002030) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "a male mouse has no nipples - mammary tissue regresses during embryonic development" -### kidney collecting duct cell `http://purl.obolibrary.org/obo/CL_1001225` -#### Added -- [kidney collecting duct cell](http://purl.obolibrary.org/obo/CL_1001225) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### non-connected functional system `http://purl.obolibrary.org/obo/UBERON_0015203` +#### Removed +- [non-connected functional system](http://purl.obolibrary.org/obo/UBERON_0015203) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007278" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### kidney collecting duct epithelial cell `http://purl.obolibrary.org/obo/CL_1000454` -#### Added -- [kidney collecting duct epithelial cell](http://purl.obolibrary.org/obo/CL_1000454) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### non-neural ectoderm `http://purl.obolibrary.org/obo/UBERON_0005497` +#### Removed +- [non-neural ectoderm](http://purl.obolibrary.org/obo/UBERON_0005497) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In the early gastrula of vertebrates, factors from the organizer (e.g. noggin, chordin, and follistatin in Xenopus) antagonize the epidermalizing factor bone morphogenetic protein 4 (BMP4), thus dividing the epiblast into neuroectoderm. In Drosophila, decapentaplegic, the homologue of BMP4, interacts similarly with the protein short gastrulation, the homologue of chordin. Thus, a comparable molecular mechanism for distinguishing non-neural ectoderm from neural ectoderm was probably present in the common ancestor of all bilaterally symmetrical animals.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)" -### kidney collecting duct intercalated cell `http://purl.obolibrary.org/obo/CL_1001432` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [kidney collecting duct intercalated cell](http://purl.obolibrary.org/obo/CL_1001432) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001372" -### kidney collecting duct principal cell `http://purl.obolibrary.org/obo/CL_1001431` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [kidney collecting duct principal cell](http://purl.obolibrary.org/obo/CL_1001431) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [non-neural ectoderm](http://purl.obolibrary.org/obo/UBERON_0005497) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "After gastrulation, neural crest cells are specified at the border of the neural plate and the non-neural ectoderm." +- [non-neural ectoderm](http://purl.obolibrary.org/obo/UBERON_0005497) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [neurectoderm](http://purl.obolibrary.org/obo/UBERON_0002346) -### kidney connecting tubule epithelial cell `http://purl.obolibrary.org/obo/CL_1000768` -#### Added -- [kidney connecting tubule epithelial cell](http://purl.obolibrary.org/obo/CL_1000768) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### non-secretory ribonuclease `http://purl.obolibrary.org/obo/PR_000014046` +#### Removed +- [non-secretory ribonuclease](http://purl.obolibrary.org/obo/PR_000014046) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [non-secretory ribonuclease (human)](http://purl.obolibrary.org/obo/PR_P10153) -### kidney connecting tubule principal cell `http://purl.obolibrary.org/obo/CL_4030018` -#### Added -- [kidney connecting tubule principal cell](http://purl.obolibrary.org/obo/CL_4030018) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### nonskeletal ligament `http://purl.obolibrary.org/obo/UBERON_0008845` +#### Removed +- [nonskeletal ligament](http://purl.obolibrary.org/obo/UBERON_0008845) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Ligament organ that primarily consists of dense connective tissue aggregated into fasciculi which may be admixed with smooth muscle. Examples: ligament of liver, ovarian ligament[FMA:25625]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:25625" -### kidney cortex artery cell `http://purl.obolibrary.org/obo/CL_1001045` +- [nonskeletal ligament](http://purl.obolibrary.org/obo/UBERON_0008845) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "this class is used more generally than the FMA class, to include for example folds of mesentery such as the broad ligament of the uterus." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" -#### Added -- [kidney cortex artery cell](http://purl.obolibrary.org/obo/CL_1001045) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### kidney cortex tubule cell `http://purl.obolibrary.org/obo/CL_1000615` +### normal `http://purl.obolibrary.org/obo/PATO_0000461` +#### Removed +- [normal](http://purl.obolibrary.org/obo/PATO_0000461) [RO_0002604](http://purl.obolibrary.org/obo/RO_0002604) [abnormal](http://purl.obolibrary.org/obo/PATO_0000460) -#### Added -- [kidney cortex tubule cell](http://purl.obolibrary.org/obo/CL_1000615) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### kidney distal convoluted tubule epithelial cell `http://purl.obolibrary.org/obo/CL_1000849` +### nose `http://purl.obolibrary.org/obo/UBERON_0000004` +#### Removed +- [nose](http://purl.obolibrary.org/obo/UBERON_0000004) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Organ that is the specialized structure of the face that contains olfactory neurons. The peripheral olfactory organ is paired[ZFA:0000047]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFA:0000047" -#### Added -- [kidney distal convoluted tubule epithelial cell](http://purl.obolibrary.org/obo/CL_1000849) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [nose](http://purl.obolibrary.org/obo/UBERON_0000004) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "the organ that is specialized for smell and is part of the respiratory system" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "MP:0002233" +- [nose](http://purl.obolibrary.org/obo/UBERON_0000004) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "the structure of the nose varies across vertebrates. In tetrapods the nose is part of the respiratory system.[PMID:25312359]" -### kidney efferent arteriole endothelial cell `http://purl.obolibrary.org/obo/CL_1001099` +- [nose](http://purl.obolibrary.org/obo/UBERON_0000004) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "a protuberance in vertebrates that houses the nostrils, or nares, which admit and expel air for respiration in conjunction with the mouth. Behind the nose are the olfactory mucosa and the sinuses. Behind the nasal cavity, air next passes through the pharynx, shared with the digestive system, and then into the rest of the respiratory system. In humans, the nose is located centrally on the face; on most other mammals, it is on the upper tip of the snout[WP]. GO: The nose is the specialized structure of the face that serves as the organ of the sense of smell and as part of the respiratory system. Includes the nasi externus (external nose) and cavitas nasi (nasal cavity)[Wikipedia:Nose]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Nose" -#### Added -- [kidney efferent arteriole endothelial cell](http://purl.obolibrary.org/obo/CL_1001099) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### kidney epithelial cell `http://purl.obolibrary.org/obo/CL_0002518` +### nose epithelium `http://purl.obolibrary.org/obo/UBERON_0019306` #### Added -- [kidney epithelial cell](http://purl.obolibrary.org/obo/CL_0002518) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [nose epithelium](http://purl.obolibrary.org/obo/UBERON_0019306) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) -### kidney glomerular epithelial cell `http://purl.obolibrary.org/obo/CL_1000510` +### notes `http://www.geneontology.org/formats/oboInOwl#notes` +#### Removed +- AnnotationProperty: [notes](http://www.geneontology.org/formats/oboInOwl#notes) -#### Added -- [kidney glomerular epithelial cell](http://purl.obolibrary.org/obo/CL_1000510) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### kidney interstitial cell `http://purl.obolibrary.org/obo/CL_1000500` +### notochord `http://purl.obolibrary.org/obo/UBERON_0002328` +#### Removed +- [notochord](http://purl.obolibrary.org/obo/UBERON_0002328) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "notochordal" -#### Added -- [kidney interstitial cell](http://purl.obolibrary.org/obo/CL_1000500) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [notochord](http://purl.obolibrary.org/obo/UBERON_0002328) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord." +- [notochord](http://purl.obolibrary.org/obo/UBERON_0002328) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" -### kidney interstitial fibroblast `http://purl.obolibrary.org/obo/CL_1000692` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000327" -#### Added -- [kidney interstitial fibroblast](http://purl.obolibrary.org/obo/CL_1000692) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### kidney loop of Henle ascending limb epithelial cell `http://purl.obolibrary.org/obo/CL_1001016` +- [notochord](http://purl.obolibrary.org/obo/UBERON_0002328) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000032" -#### Added -- [kidney loop of Henle ascending limb epithelial cell](http://purl.obolibrary.org/obo/CL_1001016) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PSPUB:0000170" -### kidney loop of Henle cortical thick ascending limb epithelial cell `http://purl.obolibrary.org/obo/CL_1001109` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" -#### Added -- [kidney loop of Henle cortical thick ascending limb epithelial cell](http://purl.obolibrary.org/obo/CL_1001109) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [notochord](http://purl.obolibrary.org/obo/UBERON_0002328) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000135" -### kidney loop of Henle epithelial cell `http://purl.obolibrary.org/obo/CL_1000909` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -#### Added -- [kidney loop of Henle epithelial cell](http://purl.obolibrary.org/obo/CL_1000909) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" +- [notochord](http://purl.obolibrary.org/obo/UBERON_0002328) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000327" -### kidney loop of Henle medullary thick ascending limb epithelial cell `http://purl.obolibrary.org/obo/CL_1001108` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -#### Added -- [kidney loop of Henle medullary thick ascending limb epithelial cell](http://purl.obolibrary.org/obo/CL_1001108) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" +- [notochord](http://purl.obolibrary.org/obo/UBERON_0002328) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### kidney loop of Henle thick ascending limb epithelial cell `http://purl.obolibrary.org/obo/CL_1001106` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [kidney loop of Henle thick ascending limb epithelial cell](http://purl.obolibrary.org/obo/CL_1001106) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28" -### kidney loop of Henle thin ascending limb epithelial cell `http://purl.obolibrary.org/obo/CL_1001107` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000199" #### Added -- [kidney loop of Henle thin ascending limb epithelial cell](http://purl.obolibrary.org/obo/CL_1001107) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [notochord](http://purl.obolibrary.org/obo/UBERON_0002328) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### kidney loop of Henle thin descending limb epithelial cell `http://purl.obolibrary.org/obo/CL_1001111` +### notochordal canal `http://purl.obolibrary.org/obo/UBERON_0013704` #### Added -- [kidney loop of Henle thin descending limb epithelial cell](http://purl.obolibrary.org/obo/CL_1001111) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [notochordal canal](http://purl.obolibrary.org/obo/UBERON_0013704) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### kidney outer medulla inner stripe `http://purl.obolibrary.org/obo/UBERON_0004201` +### notochordal plate `http://purl.obolibrary.org/obo/UBERON_0006267` #### Removed -- [kidney outer medulla inner stripe](http://purl.obolibrary.org/obo/UBERON_0004201) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stria interna medullae renalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:76663" +- [notochordal plate](http://purl.obolibrary.org/obo/UBERON_0006267) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [kidney outer medulla inner stripe](http://purl.obolibrary.org/obo/UBERON_0004201) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stria interna medullae renalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:76663" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001212" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### kidney outer medulla outer stripe `http://purl.obolibrary.org/obo/UBERON_0004202` +### nuchal ligament `http://purl.obolibrary.org/obo/UBERON_0000351` #### Removed -- [kidney outer medulla outer stripe](http://purl.obolibrary.org/obo/UBERON_0004202) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stria externa medullae renalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:76662" +- [nuchal ligament](http://purl.obolibrary.org/obo/UBERON_0000351) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In humans it is a tendon-like structure that has developed independently in humans and other animals well adapted for running. In some four legged animals, particularly ungulates, the nuchal ligament serves to sustain the weight of the head" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [nuchal ligament](http://purl.obolibrary.org/obo/UBERON_0000351) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "As it is required for running, not all animals have a nuchal ligament" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [nuchal ligament](http://purl.obolibrary.org/obo/UBERON_0000351) SubClassOf [attached to](http://purl.obolibrary.org/obo/RO_0002371) some [cervical vertebra](http://purl.obolibrary.org/obo/UBERON_0002413) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "C7 in humans" #### Added -- [kidney outer medulla outer stripe](http://purl.obolibrary.org/obo/UBERON_0004202) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stria externa medullae renalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [nuchal ligament](http://purl.obolibrary.org/obo/UBERON_0000351) SubClassOf [attached to](http://purl.obolibrary.org/obo/RO_0002371) some [cervical vertebra](http://purl.obolibrary.org/obo/UBERON_0002413) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:76662" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### nuclear factor NF-kappa-B p100 subunit `http://purl.obolibrary.org/obo/PR_000011178` +#### Removed +- [nuclear factor NF-kappa-B p100 subunit](http://purl.obolibrary.org/obo/PR_000011178) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [nuclear factor NF-kappa-B p100 subunit (human)](http://purl.obolibrary.org/obo/PR_Q00653) -### kidney pelvis urothelial cell `http://purl.obolibrary.org/obo/CL_1000703` -#### Added -- [kidney pelvis urothelial cell](http://purl.obolibrary.org/obo/CL_1000703) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### nuclear receptor ROR-gamma `http://purl.obolibrary.org/obo/PR_000001902` +#### Removed +- [nuclear receptor ROR-gamma](http://purl.obolibrary.org/obo/PR_000001902) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [nuclear receptor ROR-gamma (human)](http://purl.obolibrary.org/obo/PR_P51449) -### kidney proximal convoluted tubule epithelial cell `http://purl.obolibrary.org/obo/CL_1000838` -#### Added -- [kidney proximal convoluted tubule epithelial cell](http://purl.obolibrary.org/obo/CL_1000838) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### nucleus accumbens `http://purl.obolibrary.org/obo/UBERON_0001882` +#### Removed +- [nucleus accumbens](http://purl.obolibrary.org/obo/UBERON_0001882) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [olfactory tubercle](http://purl.obolibrary.org/obo/UBERON_0001883) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" +- [nucleus accumbens](http://purl.obolibrary.org/obo/UBERON_0001882) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "a collection of pleomorphic cells in the caudal part of the anterior horn of the lateral ventricle, in the region of the olfactory tubercle, lying between the head of the caudate nucleus and the anterior perforated substance. It is part of the ventral striatum, a composite structure considered part of the basal ganglia[GO][GO:0021768]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GO:0021768" -### kidney proximal straight tubule epithelial cell `http://purl.obolibrary.org/obo/CL_1000839` +- [nucleus accumbens](http://purl.obolibrary.org/obo/UBERON_0001882) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The ventral striatopallidal complex in birds corresponds closely to its counterpart in mammals, with a nucleus accumbes present in the rostral telenceaphalon. Note that in birds, a region previously called the nucleus accumbens is now recognized as the lateral part of the bed nucleus of stria terminalis.[ISBN:0471888893]" -#### Added -- [kidney proximal straight tubule epithelial cell](http://purl.obolibrary.org/obo/CL_1000839) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### kidney pyramid `http://purl.obolibrary.org/obo/UBERON_0004200` +### nucleus of dorsal thalamus `http://purl.obolibrary.org/obo/UBERON_0015233` #### Removed -- [kidney pyramid](http://purl.obolibrary.org/obo/UBERON_0004200) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pyramides renales" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [nucleus of dorsal thalamus](http://purl.obolibrary.org/obo/UBERON_0015233) [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_7762](http://purl.obolibrary.org/obo/NCBITaxon_7762) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "Hagfish possess a habenular complex and separate nuclei in the dorsal thalamus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Renal_pyramids" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Butler, 1996, p. 303" -#### Added -- [kidney pyramid](http://purl.obolibrary.org/obo/UBERON_0004200) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pyramides renales" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Renal_pyramids" +### nucleus of lateral olfactory tract `http://purl.obolibrary.org/obo/UBERON_0002893` +#### Removed +- [nucleus of lateral olfactory tract](http://purl.obolibrary.org/obo/UBERON_0002893) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0004069](http://purl.obolibrary.org/obo/UBERON_0004069) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" -### kidney resident macrophage `http://purl.obolibrary.org/obo/CL_1000698` +- [nucleus of lateral olfactory tract](http://purl.obolibrary.org/obo/UBERON_0002893) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002590](http://purl.obolibrary.org/obo/UBERON_0002590) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" -#### Added -- [kidney resident macrophage](http://purl.obolibrary.org/obo/CL_1000698) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [nucleus of lateral olfactory tract](http://purl.obolibrary.org/obo/UBERON_0002893) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002266](http://purl.obolibrary.org/obo/UBERON_0002266) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" -### kidney rudiment `http://purl.obolibrary.org/obo/UBERON_0005095` + +### nucleus of midbrain tegmentum `http://purl.obolibrary.org/obo/UBERON_0007414` #### Removed -- [kidney rudiment](http://purl.obolibrary.org/obo/UBERON_0005095) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO:0072003" +- [nucleus of midbrain tegmentum](http://purl.obolibrary.org/obo/UBERON_0007414) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "this class groups together any nuclei in the tegmentum region, possibly including disparate structures across species" -#### Added -- [kidney rudiment](http://purl.obolibrary.org/obo/UBERON_0005095) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Missing definition for term UBERON:0005095. Please replace it using linked reference." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO:0072003" -### knee joint `http://purl.obolibrary.org/obo/UBERON_0001485` +### nucleus of superior olivary complex `http://purl.obolibrary.org/obo/UBERON_0007247` #### Removed -- [knee joint](http://purl.obolibrary.org/obo/UBERON_0001485) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "articulatio genus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Knee" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [nucleus of superior olivary complex](http://purl.obolibrary.org/obo/UBERON_0007247) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "this class exists largely for consistency with the FMA. It is defined trivially with respect to the SOC. The class may be removed in future." -#### Added -- [knee joint](http://purl.obolibrary.org/obo/UBERON_0001485) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "articulatio genus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Knee" - -### koniocellular layer of dorsal nucleus of lateral geniculate body `http://purl.obolibrary.org/obo/UBERON_0013615` +### nucleus pulposus `http://purl.obolibrary.org/obo/UBERON_0002242` #### Removed -- [koniocellular layer of dorsal nucleus of lateral geniculate body](http://purl.obolibrary.org/obo/UBERON_0013615) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum koniocellulare nuclei dorsalis corporis geniculati lateralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:76988" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [nucleus pulposus](http://purl.obolibrary.org/obo/UBERON_0002242) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D000070614" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -#### Added -- [koniocellular layer of dorsal nucleus of lateral geniculate body](http://purl.obolibrary.org/obo/UBERON_0013615) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum koniocellulare nuclei dorsalis corporis geniculati lateralis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:76988" + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [nucleus pulposus](http://purl.obolibrary.org/obo/UBERON_0002242) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "The nucleus pulposus consists of chondrocytes, collagen fibrils, and proteoglycan aggrecans that have hyaluronic long chains which attract water. Attached to each hyaluronic chain are side chains of chondroitin sulfate and keratan sulfate[Wikipedia:Nucleus_pulposus]" +- [nucleus pulposus](http://purl.obolibrary.org/obo/UBERON_0002242) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "we group two FMA classes together" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" -### lacrimal apparatus `http://purl.obolibrary.org/obo/UBERON_0001750` -#### Removed -- [lacrimal apparatus](http://purl.obolibrary.org/obo/UBERON_0001750) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "apparatus lacrimalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lacrimal_apparatus" +- [nucleus pulposus](http://purl.obolibrary.org/obo/UBERON_0002242) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [notochord](http://purl.obolibrary.org/obo/UBERON_0002328) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0073040584" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [editor](http://www.geneontology.org/formats/oboInOwl#editor) "mah" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia" #### Added -- [lacrimal apparatus](http://purl.obolibrary.org/obo/UBERON_0001750) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "apparatus lacrimalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [nucleus pulposus](http://purl.obolibrary.org/obo/UBERON_0002242) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lacrimal_apparatus" +- [nucleus pulposus](http://purl.obolibrary.org/obo/UBERON_0002242) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [notochord](http://purl.obolibrary.org/obo/UBERON_0002328) -### lacrimal artery `http://purl.obolibrary.org/obo/UBERON_0001622` +### obsolescence reason specification `http://purl.obolibrary.org/obo/IAO_0000225` #### Removed -- [lacrimal artery](http://purl.obolibrary.org/obo/UBERON_0001622) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "a. lacrimalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lacrimal_artery" +- [obsolescence reason specification](http://purl.obolibrary.org/obo/IAO_0000225) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "obsolescence reason specification"@en - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [obsolescence reason specification](http://purl.obolibrary.org/obo/IAO_0000225) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) -#### Added -- [lacrimal artery](http://purl.obolibrary.org/obo/UBERON_0001622) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "a. lacrimalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lacrimal_artery" +- [obsolescence reason specification](http://purl.obolibrary.org/obo/IAO_0000225) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) "PERSON: Alan Ruttenberg"@en - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [obsolescence reason specification](http://purl.obolibrary.org/obo/IAO_0000225) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) "PERSON: Melanie Courtot"@en -### lacrimal canaliculus `http://purl.obolibrary.org/obo/UBERON_0001770` + +### occipital bone `http://purl.obolibrary.org/obo/UBERON_0001676` #### Removed -- [lacrimal canaliculus](http://purl.obolibrary.org/obo/UBERON_0001770) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "canaliculus lacrimalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lacrimal_canaliculi" +- [occipital bone](http://purl.obolibrary.org/obo/UBERON_0001676) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "formed from the sclerotome of the occipital somites. It is not present in living or fossil agnathans or cartilaginous fishes, but appears to have arisen in parallel in many bony fishes. Incorporation of the occipital ver- tebrae into the skull was associated with the annexation of the upper part of the spinal cord into the brain, together with the first 2 spinal nerves as cranial nerves XI and XII" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:11523816" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [occipital bone](http://purl.obolibrary.org/obo/UBERON_0001676) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "fusion of basi-, exo- and supra-occipitals (and maybe tabular)" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Kardong" + +- [occipital bone](http://purl.obolibrary.org/obo/UBERON_0001676) SubClassOf [overlaps](http://purl.obolibrary.org/obo/RO_0002131) some [chondrocranium](http://purl.obolibrary.org/obo/UBERON_0002241) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "MA-modified" + + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "basi paired exo and supra occipital bones" + +- [occipital bone](http://purl.obolibrary.org/obo/UBERON_0001676) SubClassOf [overlaps](http://purl.obolibrary.org/obo/RO_0002131) some [dermatocranium](http://purl.obolibrary.org/obo/UBERON_0003113) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "interparietal (postparietal)" #### Added -- [lacrimal canaliculus](http://purl.obolibrary.org/obo/UBERON_0001770) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "canaliculus lacrimalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [occipital bone](http://purl.obolibrary.org/obo/UBERON_0001676) SubClassOf [overlaps](http://purl.obolibrary.org/obo/RO_0002131) some [chondrocranium](http://purl.obolibrary.org/obo/UBERON_0002241) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lacrimal_canaliculi" +- [occipital bone](http://purl.obolibrary.org/obo/UBERON_0001676) SubClassOf [overlaps](http://purl.obolibrary.org/obo/RO_0002131) some [dermatocranium](http://purl.obolibrary.org/obo/UBERON_0003113) -### lacrimal gland `http://purl.obolibrary.org/obo/UBERON_0001817` +### occipital region `http://purl.obolibrary.org/obo/UBERON_0005902` #### Removed -- [lacrimal gland](http://purl.obolibrary.org/obo/UBERON_0001817) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "glandula lacrimalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lacrimal_gland" +- [occipital region](http://purl.obolibrary.org/obo/UBERON_0005902) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D009778" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -#### Added -- [lacrimal gland](http://purl.obolibrary.org/obo/UBERON_0001817) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "glandula lacrimalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lacrimal_gland" +- [occipital region](http://purl.obolibrary.org/obo/UBERON_0005902) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "An anatomical cluster that is located in the posterior region of the neurocranium and forms the margin of the foramen margin and occipital condyles.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### lacrimal nerve `http://purl.obolibrary.org/obo/UBERON_0011096` -#### Removed -- [lacrimal nerve](http://purl.obolibrary.org/obo/UBERON_0011096) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus lacrimalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lacrimal_nerve" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010199" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [occipital region](http://purl.obolibrary.org/obo/UBERON_0005902) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occiptal condyle.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TAO:MAH" -#### Added -- [lacrimal nerve](http://purl.obolibrary.org/obo/UBERON_0011096) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus lacrimalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001414" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lacrimal_nerve" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -### lacrimal punctum `http://purl.obolibrary.org/obo/UBERON_0010284` + + +### occurs in `http://purl.obolibrary.org/obo/BFO_0000066` #### Removed -- [lacrimal punctum](http://purl.obolibrary.org/obo/UBERON_0010284) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "puncta lacrimalia" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lacrimal_punctum" +- [occurs in](http://purl.obolibrary.org/obo/BFO_0000066) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "occurs_in"@en - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [occurs in](http://purl.obolibrary.org/obo/BFO_0000066) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "unfolds_in"@en -#### Added -- [lacrimal punctum](http://purl.obolibrary.org/obo/UBERON_0010284) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "puncta lacrimalia" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [occurs in](http://purl.obolibrary.org/obo/BFO_0000066) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "occurs in"@en - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lacrimal_punctum" +- [occurs in](http://purl.obolibrary.org/obo/BFO_0000066) [isDefinedBy](http://www.w3.org/2000/01/rdf-schema#isDefinedBy) [bfo.owl](http://purl.obolibrary.org/obo/bfo.owl) +- [occurs in](http://purl.obolibrary.org/obo/BFO_0000066) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "unfolds in"@en -### lacrimal sac `http://purl.obolibrary.org/obo/UBERON_0001351` -#### Removed -- [lacrimal sac](http://purl.obolibrary.org/obo/UBERON_0001351) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "saccus lacrimalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lacrimal_sac" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [lacrimal sac](http://purl.obolibrary.org/obo/UBERON_0001351) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "saccus lacrimalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### ocular refractive media `http://purl.obolibrary.org/obo/UBERON_0006312` +#### Removed +- [ocular refractive media](http://purl.obolibrary.org/obo/UBERON_0006312) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "ocular refraction" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lacrimal_sac" -### lactocyte `http://purl.obolibrary.org/obo/CL_0002325` +### ocular surface region `http://purl.obolibrary.org/obo/UBERON_0010409` #### Added -- [lactocyte](http://purl.obolibrary.org/obo/CL_0002325) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [ocular surface region](http://purl.obolibrary.org/obo/UBERON_0010409) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### lamp5 GABAergic cortical interneuron `http://purl.obolibrary.org/obo/CL_4023011` +### odontogenic papilla `http://purl.obolibrary.org/obo/UBERON_0001763` +#### Removed +- [odontogenic papilla](http://purl.obolibrary.org/obo/UBERON_0001763) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "In humans, the dental papilla appears after 8-10 weeks intra uteral life" -#### Added -- [lamp5 GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023011) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [odontogenic papilla](http://purl.obolibrary.org/obo/UBERON_0001763) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Teeth and tooth-like structures, together named odontodes, are repeated organs thought to share a common evolutionary origin. These structures can be found in gnathostomes at different locations along the body: oral teeth in the jaws, teeth and denticles in the oral-pharyngeal cavity, and dermal denticles on elasmobranch skin.[uncertain][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1186/1471-2148-11-307 The homology of odontodes in gnathostomes: insights from Dlx gene expression in the dogfish, Scyliorhinus canicula. BMC Evolutionary Biology (2011)" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### large intestine goblet cell `http://purl.obolibrary.org/obo/CL_1000320` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [large intestine goblet cell](http://purl.obolibrary.org/obo/CL_1000320) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001465" -### large pre-B-II cell `http://purl.obolibrary.org/obo/CL_0000957` +- [odontogenic papilla](http://purl.obolibrary.org/obo/UBERON_0001763) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Cell condensation that is a well-defined population of densely organized mesenchymal cells that aggregates adjacent to an epithelium.[VSAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -#### Added -- [large pre-B-II cell](http://purl.obolibrary.org/obo/CL_0000957) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000025" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PSPUB:0000170" -### larva `http://purl.obolibrary.org/obo/UBERON_0002548` -#### Removed -- [larva](http://purl.obolibrary.org/obo/UBERON_0002548) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D007814" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" -- [larva](http://purl.obolibrary.org/obo/UBERON_0002548) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001727" +- [odontogenic papilla](http://purl.obolibrary.org/obo/UBERON_0001763) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Tissue of the developing tooth. It is composed of pre-odontoblast and undiffentiated mesnchyme cells and connects to the basal lamina.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -#### Added -- [larva](http://purl.obolibrary.org/obo/UBERON_0002548) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D007814" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005140" -- [larva](http://purl.obolibrary.org/obo/UBERON_0002548) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001727" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### late embryo `http://purl.obolibrary.org/obo/UBERON_0000323` +### odontoid tissue `http://purl.obolibrary.org/obo/UBERON_0010365` #### Removed -- [late embryo](http://purl.obolibrary.org/obo/UBERON_0000323) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005333" - -#### Added -- [late embryo](http://purl.obolibrary.org/obo/UBERON_0000323) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005333" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - +- [odontoid tissue](http://purl.obolibrary.org/obo/UBERON_0010365) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "Classified as a portion of organism substance in FMA" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" -### late pro-B cell `http://purl.obolibrary.org/obo/CL_0002048` +- [odontoid tissue](http://purl.obolibrary.org/obo/UBERON_0010365) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "in many vertebrates, odontoid tissue is not restricted to the teeth" #### Added -- [late pro-B cell](http://purl.obolibrary.org/obo/CL_0002048) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [odontoid tissue](http://purl.obolibrary.org/obo/UBERON_0010365) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) -### late promyelocyte `http://purl.obolibrary.org/obo/CL_0002151` +### olfactory apparatus chamber `http://purl.obolibrary.org/obo/UBERON_0015788` #### Added -- [late promyelocyte](http://purl.obolibrary.org/obo/CL_0002151) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [olfactory apparatus chamber](http://purl.obolibrary.org/obo/UBERON_0015788) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### lateral border of scapula `http://purl.obolibrary.org/obo/UBERON_0007173` +### olfactory bulb `http://purl.obolibrary.org/obo/UBERON_0002264` #### Removed -- [lateral border of scapula](http://purl.obolibrary.org/obo/UBERON_0007173) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "margo lateralis scapulae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [olfactory bulb](http://purl.obolibrary.org/obo/UBERON_0002264) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In most vertebrates, the olfactory bulb is the most rostral (forward) part of the brain. In humans, however, the olfactory bulb is on the inferior (bottom) side of the brain. The olfactory bulb is supported and protected by the cribriform plate which in mammals, separates it from the olfactory epithelium, and which is perforated by olfactory nerve axons. The bulb is divided into two distinct structures, the main olfactory bulb, and the accessory olfactory bulb" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [olfactory bulb](http://purl.obolibrary.org/obo/UBERON_0002264) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [hippocampal formation](http://purl.obolibrary.org/obo/UBERON_0002421) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:23239" +- [olfactory bulb](http://purl.obolibrary.org/obo/UBERON_0002264) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Segment of neural tree organ which is continuous with a set of olfactory nerves and an olfactory tract[FMA:77624]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:77624" -#### Added -- [lateral border of scapula](http://purl.obolibrary.org/obo/UBERON_0007173) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "margo lateralis scapulae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [olfactory bulb](http://purl.obolibrary.org/obo/UBERON_0002264) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [neocortex](http://purl.obolibrary.org/obo/UBERON_0001950) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [olfactory bulb](http://purl.obolibrary.org/obo/UBERON_0002264) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The part of the forebrain in which the olfactory nerves end and the olfactory tracts originate. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:23239" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### lateral ganglionic eminence `http://purl.obolibrary.org/obo/UBERON_0004025` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000033" -#### Added -- [lateral ganglionic eminence](http://purl.obolibrary.org/obo/UBERON_0004025) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" +- [olfactory bulb](http://purl.obolibrary.org/obo/UBERON_0002264) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Note that in uberon 'main olfactory bulb' is a separate class, but some ontologies may treat this as partially synonymous. The distinction may only make sense in tetrapods with a vomeronasal organ (olfactory nerves terminate in OB in fishes and in main OB in tetrapods - Butler and Hodos)" -- [lateral ganglionic eminence](http://purl.obolibrary.org/obo/UBERON_0004025) [label](http://www.w3.org/2000/01/rdf-schema#label) "lateral ganglionic eminence" +- [olfactory bulb](http://purl.obolibrary.org/obo/UBERON_0002264) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Part of the rostral part of the cerebrum where axons of olfactory cells from the nasal mucosa terminate. Projects onto olfactory parts of pallium via olfactory tracts" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0471888893" -- [lateral ganglionic eminence](http://purl.obolibrary.org/obo/UBERON_0004025) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DHBA:10551" +- [olfactory bulb](http://purl.obolibrary.org/obo/UBERON_0002264) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "the olfactory bulbs develop as bilateral evaginations from a region of the prosencephalic neural plate intercalated between the septal and the cortical anlagen (Cobos et al. 2001b, Rubenstein et al. 1998). Comparing the structure of the olfactory bulb among vertebrate species, such as the leopard frog and the lab mouse, reveals that they all share the same fundamental layout(WP)." -- [lateral ganglionic eminence](http://purl.obolibrary.org/obo/UBERON_0004025) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "LGE" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [abbreviation](http://purl.obolibrary.org/obo/OMO_0003000) +- [olfactory bulb](http://purl.obolibrary.org/obo/UBERON_0002264) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The presence of paired evaginated hemispheres and olfactory bulbs in both agnathan and gnathostome radiations suggests that such hemispheres were also present in the common ancestor.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1146/annurev.ne.04.030181.001505 Northcutt RG, Evolution of the telencephalon in nonmammals. Ann. Rev. Neurosci. (1981)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:23375746" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [lateral ganglionic eminence](http://purl.obolibrary.org/obo/UBERON_0004025) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A distinct elevation of a transient proliferating cell mass of the fetal subventricular zone; this mass contributes most of its cells to the striatum; however, neocortex, thalamus, septum and olfactory bulb neurons are also partly derived from the LGE." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MP:0004277" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [lateral ganglionic eminence](http://purl.obolibrary.org/obo/UBERON_0004025) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PBA:128012822" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [lateral ganglionic eminence](http://purl.obolibrary.org/obo/UBERON_0004025) [id](http://www.geneontology.org/formats/oboInOwl#id) "UBERON:0004025" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000033" -- [lateral ganglionic eminence](http://purl.obolibrary.org/obo/UBERON_0004025) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:37470" - - [source](http://www.geneontology.org/formats/oboInOwl#source) "MA:th" +- [olfactory bulb](http://purl.obolibrary.org/obo/UBERON_0002264) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Part of the telencephalon comprised of anterior outgrowths of either of the cerebral hemispheres in which the olfactory nerve exits.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -- [lateral ganglionic eminence](http://purl.obolibrary.org/obo/UBERON_0004025) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [pheno_slim](http://purl.obolibrary.org/obo/uberon/core#pheno_slim) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -- Class: [lateral ganglionic eminence](http://purl.obolibrary.org/obo/UBERON_0004025) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" -- [lateral ganglionic eminence](http://purl.obolibrary.org/obo/UBERON_0004025) SubClassOf [embryonic structure](http://purl.obolibrary.org/obo/UBERON_0002050) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010165" -- [lateral ganglionic eminence](http://purl.obolibrary.org/obo/UBERON_0004025) SubClassOf [contributes to morphology of](http://purl.obolibrary.org/obo/RO_0002433) some [ganglionic eminence](http://purl.obolibrary.org/obo/UBERON_0004023) -- [lateral ganglionic eminence](http://purl.obolibrary.org/obo/UBERON_0004025) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [ganglionic eminence](http://purl.obolibrary.org/obo/UBERON_0004023) +### olfactory bulb mitral cell layer `http://purl.obolibrary.org/obo/UBERON_0004186` +#### Removed +- [olfactory bulb mitral cell layer](http://purl.obolibrary.org/obo/UBERON_0004186) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "NIF divides this into main and accessory" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "NIF" -### lateral ganglionic eminence derived neuron `http://purl.obolibrary.org/obo/CL_4023035` -#### Added -- [lateral ganglionic eminence derived neuron](http://purl.obolibrary.org/obo/CL_4023035) [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0001-7258-9596" -- [lateral ganglionic eminence derived neuron](http://purl.obolibrary.org/obo/CL_4023035) [label](http://www.w3.org/2000/01/rdf-schema#label) "lateral ganglionic eminence derived neuron"@en +### olfactory cortex `http://purl.obolibrary.org/obo/UBERON_0002894` +#### Removed +- [olfactory cortex](http://purl.obolibrary.org/obo/UBERON_0002894) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "That portion of the cerebral cortex that, with the palaeocortex, develops in association with the olfactory system, and which is phylogenetically older than the neocortex and lacks its layered structure. The embryonic archaeocortex corresponds to the cortex of the dentate gyrus and hippocampus in mature mammals[BTO:0001446]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "BTO:0001446" -- [lateral ganglionic eminence derived neuron](http://purl.obolibrary.org/obo/CL_4023035) [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0002-7073-9172" +- [olfactory cortex](http://purl.obolibrary.org/obo/UBERON_0002894) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The olfactory cortex is involved in the perception of smell. It receives input from the olfactory bulb and is responsible for the identification of odors[GO][GO:0021989]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GO:0021989" -- [lateral ganglionic eminence derived neuron](http://purl.obolibrary.org/obo/CL_4023035) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "LGE-derived neuron" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:10377350" +- [olfactory cortex](http://purl.obolibrary.org/obo/UBERON_0002894) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(In mammals) Odorant detection is mediated by millions of olfactory sensory neurons located in the olfactory epithelium lining the nasal cavity. These neurons transmit sensory signals to the olfactory bulb of the brain, which in turn sends signals to the olfactory cortex.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1111/j.1753-4887.2004.tb00097.x Buck LB, Olfactory receptors and odor coding in mammals. Nutrition Reviews (2008)" -- [lateral ganglionic eminence derived neuron](http://purl.obolibrary.org/obo/CL_4023035) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A neuron that is derived from a precursor cell in the lateral ganglion eminence." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "wikipediaversioned:Ganglionic_eminence&oldid=1186824360" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- Class: [lateral ganglionic eminence derived neuron](http://purl.obolibrary.org/obo/CL_4023035) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [lateral ganglionic eminence derived neuron](http://purl.obolibrary.org/obo/CL_4023035) EquivalentTo [neuron](http://purl.obolibrary.org/obo/CL_0000540) and ([develops from](http://purl.obolibrary.org/obo/RO_0002202) some [lateral ganglionic eminence](http://purl.obolibrary.org/obo/UBERON_0004025)) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [lateral ganglionic eminence derived neuron](http://purl.obolibrary.org/obo/CL_4023035) SubClassOf [neuron](http://purl.obolibrary.org/obo/CL_0000540) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000325" -- [lateral ganglionic eminence derived neuron](http://purl.obolibrary.org/obo/CL_4023035) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [lateral ganglionic eminence](http://purl.obolibrary.org/obo/UBERON_0004025) -### lateral geniculate body `http://purl.obolibrary.org/obo/UBERON_0001926` +### olfactory epithelium `http://purl.obolibrary.org/obo/UBERON_0001997` #### Removed -- [lateral geniculate body](http://purl.obolibrary.org/obo/UBERON_0001926) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus corporis geniculati lateralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BAMS:LG" - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:352" +- [olfactory epithelium](http://purl.obolibrary.org/obo/UBERON_0001997) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: part_of principal cavity (AAO:0000992)[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -- [lateral geniculate body](http://purl.obolibrary.org/obo/UBERON_0001926) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "corpus geniculatus lateralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:352" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010158" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [olfactory epithelium](http://purl.obolibrary.org/obo/UBERON_0001997) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Sensory lining of the medial wall, roof and anterior aspects of the main olfactory cavity (cavum principale).[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -#### Added -- [lateral geniculate body](http://purl.obolibrary.org/obo/UBERON_0001926) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "corpus geniculatus lateralis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:DSM" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:352" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -- [lateral geniculate body](http://purl.obolibrary.org/obo/UBERON_0001926) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus corporis geniculati lateralis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010158" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BAMS:LG" +- [olfactory epithelium](http://purl.obolibrary.org/obo/UBERON_0001997) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:352" -### lateral line system `http://purl.obolibrary.org/obo/UBERON_0002540` +### olfactory lobe `http://purl.obolibrary.org/obo/UBERON_0005366` #### Removed -- [lateral line system](http://purl.obolibrary.org/obo/UBERON_0002540) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D053403" - -#### Added -- [lateral line system](http://purl.obolibrary.org/obo/UBERON_0002540) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D053403" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) +- [olfactory lobe](http://purl.obolibrary.org/obo/UBERON_0005366) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(In mammals) Odorant detection is mediated by millions of olfactory sensory neurons located in the olfactory epithelium lining the nasal cavity. These neurons transmit sensory signals to the olfactory bulb of the brain, which in turn sends signals to the olfactory cortex.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1111/j.1753-4887.2004.tb00097.x Buck LB, Olfactory receptors and odor coding in mammals. Nutrition Reviews (2008)" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### lateral lingual swelling `http://purl.obolibrary.org/obo/UBERON_0006757` -#### Removed -- [lateral lingual swelling](http://purl.obolibrary.org/obo/UBERON_0006757) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tuberculum linguale laterale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lateral_lingual_swelling" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000833" -#### Added -- [lateral lingual swelling](http://purl.obolibrary.org/obo/UBERON_0006757) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tuberculum linguale laterale" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [olfactory lobe](http://purl.obolibrary.org/obo/UBERON_0005366) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Part of the telencephalon, comprised of paired anterior outgrowths of either of the cerebral hemispheres in which the olfactory nerve exits. In Xenopus,the olfactory bulbs begin to fuse at NF stage 50, fusion is complete around NF stage 58. The cerebral vein loops around the olfactory bulb by NF stage 43[XAO:0004180]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "XAO:0004180" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lateral_lingual_swelling" -### lateral nasal prominence `http://purl.obolibrary.org/obo/UBERON_0004067` +### olfactory nerve `http://purl.obolibrary.org/obo/UBERON_0001579` #### Removed -- [lateral nasal prominence](http://purl.obolibrary.org/obo/UBERON_0004067) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "prominentia nasalis lateralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lateral_nasal_prominence" +- [olfactory nerve](http://purl.obolibrary.org/obo/UBERON_0001579) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Segment of neural tree organ which is continuous with the olfactory epithelium and an olfactory bulb[FMA:46787]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:46787" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [olfactory nerve](http://purl.obolibrary.org/obo/UBERON_0001579) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "connects to main OB (in taxa where main/accessory distinction is important)" -#### Added -- [lateral nasal prominence](http://purl.obolibrary.org/obo/UBERON_0004067) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "prominentia nasalis lateralis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [olfactory nerve](http://purl.obolibrary.org/obo/UBERON_0001579) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The 1st cranial nerve. The olfactory nerve conveys the sense of smell. It is formed by the axons of OLFACTORY RECEPTOR NEURONS which project from the olfactory epithelium (in the nasal epithelium) to the OLFACTORY BULB[MESH:A08.800.800.120.640]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "MESH:A08.800.800.120.640" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lateral_nasal_prominence" +- [olfactory nerve](http://purl.obolibrary.org/obo/UBERON_0001579) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### lateral olfactory stria `http://purl.obolibrary.org/obo/UBERON_0001888` -#### Removed -- [lateral olfactory stria](http://purl.obolibrary.org/obo/UBERON_0001888) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tractus olfactorius lateralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:284" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [lateral olfactory stria](http://purl.obolibrary.org/obo/UBERON_0001888) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "stria olfactoria lateralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lateral_olfactory_stria" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000703" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:284" +- [olfactory nerve](http://purl.obolibrary.org/obo/UBERON_0001579) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Nerve that carries information from the olfactory epithelium through the olfactory bulb to the olfactory cortex of the telencephalon.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010088" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -- [lateral olfactory stria](http://purl.obolibrary.org/obo/UBERON_0001888) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tractus olfactorius lateralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0000229" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:DSM" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -#### Added -- [lateral olfactory stria](http://purl.obolibrary.org/obo/UBERON_0001888) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "stria olfactoria lateralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lateral_olfactory_stria" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:284" +### olfactory organ `http://purl.obolibrary.org/obo/UBERON_0002268` +#### Removed +- [olfactory organ](http://purl.obolibrary.org/obo/UBERON_0002268) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "fma general anatomical term. xao has no subtypes (but Johnstons organ develops from this). An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint" -- [lateral olfactory stria](http://purl.obolibrary.org/obo/UBERON_0001888) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tractus olfactorius lateralis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [olfactory organ](http://purl.obolibrary.org/obo/UBERON_0002268) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005158" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:284" -- [lateral olfactory stria](http://purl.obolibrary.org/obo/UBERON_0001888) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tractus olfactorius lateralis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0000229" +### olfactory pit `http://purl.obolibrary.org/obo/UBERON_0005870` +#### Removed +- [olfactory pit](http://purl.obolibrary.org/obo/UBERON_0005870) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "By the upgrowth of the surrounding parts the olfactory areas are converted into pits, the nasal pits or olfactory pits, which indent the fronto-nasal process and divide it into a medial and two lateral nasal processes[Wikipedia:Nasal_pit]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Nasal_pit" + -### lateral plate mesoderm `http://purl.obolibrary.org/obo/UBERON_0003081` +### olfactory placode `http://purl.obolibrary.org/obo/UBERON_0003050` #### Removed -- [lateral plate mesoderm](http://purl.obolibrary.org/obo/UBERON_0003081) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "mesoderma laminae lateralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lateral_plate_mesoderm" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [olfactory placode](http://purl.obolibrary.org/obo/UBERON_0003050) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (2) neurogenic placodes (...).[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000186" -#### Added -- [lateral plate mesoderm](http://purl.obolibrary.org/obo/UBERON_0003081) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "mesoderma laminae lateralis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lateral_plate_mesoderm" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### latissimus dorsi muscle `http://purl.obolibrary.org/obo/UBERON_0001112` -#### Removed -- [latissimus dorsi muscle](http://purl.obolibrary.org/obo/UBERON_0001112) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "musculus latissimus dorsi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Latissimus_dorsi_muscle" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [olfactory placode](http://purl.obolibrary.org/obo/UBERON_0003050) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006222" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -#### Added -- [latissimus dorsi muscle](http://purl.obolibrary.org/obo/UBERON_0001112) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "musculus latissimus dorsi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Latissimus_dorsi_muscle" + - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) +- [olfactory placode](http://purl.obolibrary.org/obo/UBERON_0003050) SubClassOf [neurogenic placode](http://purl.obolibrary.org/obo/UBERON_0009955) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFA" -### layer of sclera `http://purl.obolibrary.org/obo/UBERON_0010291` -#### Removed -- [layer of sclera](http://purl.obolibrary.org/obo/UBERON_0010291) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Sclera#Histology" + - [contradicted_by](http://www.geneontology.org/formats/oboInOwl#contradicted_by) "NCBIBook:NBK53171" +#### Added +- [olfactory placode](http://purl.obolibrary.org/obo/UBERON_0003050) SubClassOf [neurogenic placode](http://purl.obolibrary.org/obo/UBERON_0009955) -### left adrenal gland `http://purl.obolibrary.org/obo/UBERON_0001234` +### olfactory region `http://purl.obolibrary.org/obo/UBERON_0003112` #### Removed -- [left adrenal gland](http://purl.obolibrary.org/obo/UBERON_0001234) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "glandula suprarenalis sinister" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [olfactory region](http://purl.obolibrary.org/obo/UBERON_0003112) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical cluster that is located in the anterior region of the cranium and provides structural support for the peripheral olfactory organ.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TAO:MAH" -#### Added -- [left adrenal gland](http://purl.obolibrary.org/obo/UBERON_0001234) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "glandula suprarenalis sinister" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000351" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -### left bundle branch `http://purl.obolibrary.org/obo/UBERON_0005986` -#### Removed -- [left bundle branch](http://purl.obolibrary.org/obo/UBERON_0005986) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "crus sinistrum fasciculi atrioventricularis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9487" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [olfactory region](http://purl.obolibrary.org/obo/UBERON_0003112) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical cluster that is located in the anterior region of the neurocranium and provides structural support for the olfactory organs.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010206" -#### Added -- [left bundle branch](http://purl.obolibrary.org/obo/UBERON_0005986) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "crus sinistrum fasciculi atrioventricularis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9487" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### left cardiac atrium `http://purl.obolibrary.org/obo/UBERON_0002079` +### olfactory segment of nasal mucosa `http://purl.obolibrary.org/obo/UBERON_0005386` #### Removed -- [left cardiac atrium](http://purl.obolibrary.org/obo/UBERON_0002079) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "atrium sinistrum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Left_atrium" +- [olfactory segment of nasal mucosa](http://purl.obolibrary.org/obo/UBERON_0005386) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The olfactory mucosa is located in the upper region of the nasal cavity and is made up of the olfactory epithelium and the underlying lamina propria, connective tissue containing fibroblasts, blood vessels, Bowman's glands and bundles of fine axons from the olfactory neurons. The mucus protects the olfactory epithelium and allows odors to dissolve so that they can be detected by olfactory receptor neurons. Electron microscopy studies show that Bowman's glands contain cells with large secretory vesicles. The exact composition of the secretions from Bowman's glands is unclear, but there is evidence that Bowman's glands do not produce odorant binding protein[WP][Wikipedia:Olfactory_mucosa]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Olfactory_mucosa" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [left cardiac atrium](http://purl.obolibrary.org/obo/UBERON_0002079) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "atrium sinistrum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Left_atrium" +### olfactory system `http://purl.obolibrary.org/obo/UBERON_0005725` +#### Removed +- [olfactory system](http://purl.obolibrary.org/obo/UBERON_0005725) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The sensory system used for olfaction (the sense of smell).[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -### left crus of diaphragm `http://purl.obolibrary.org/obo/UBERON_0014767` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000978" -#### Added -- [left crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014767) [label](http://www.w3.org/2000/01/rdf-schema#label) "left crus of diaphragm" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -- [left crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014767) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "SCTID:244937004" +- [olfactory system](http://purl.obolibrary.org/obo/UBERON_0005725) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In mammals, the main olfactory system detects odorants that are inhaled through the nose, where they contact the main olfactory epithelium, which contains various olfactory receptors. These olfactory receptors are membrane proteins of bipolar olfactory receptor neurons in the olfactory epithelium. Rather than binding specific ligands like most receptors, olfactory receptors display affinity for a range of odor molecules. Olfactory neurons transduce receptor activation into electrical signals in neurons. The signals travel along the olfactory nerve, which belongs to the peripheral nervous system. This nerve terminates in the olfactory bulb, which belongs to the central nervous system. The complex set of olfactory receptors on different olfactory neurons can distinguish a new odor from the background environmental odors and determine the concentration of the odor[WP]." -- [left crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014767) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "left crus of diaphragm" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58287" +- [olfactory system](http://purl.obolibrary.org/obo/UBERON_0005725) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The olfactory system is the sensory system used for olfaction, or the sense of smell. Most mammals and reptiles have two distinct parts to their olfactory system: a main olfactory system and an accessory olfactory system. The main olfactory system detects volatile, airborne substances, while the accessory olfactory system senses fluid-phase stimuli. Behavioral evidence indicates that most often, the stimuli detected by the accessory olfactory system are pheromones. The olfactory system is often spoken of along with the gustatory system as the chemosensory senses because both transduce chemical signals into perception[WP][Wikipedia:Olfactory_system]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Olfactory_system" -- [left crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014767) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A crus of diaphragm that is in_the_left_side_of a diaphragm." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "OBOL:automatic" -- [left crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014767) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) -- [left crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014767) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" +### olfactory tract `http://purl.obolibrary.org/obo/UBERON_0002265` +#### Removed +- [olfactory tract](http://purl.obolibrary.org/obo/UBERON_0002265) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The olfactory tract is a bundle of axons connecting the mitral and tufted cells of the olfactory bulb to several target regions in the brain, including piriform cortex, amygdala, and entorhinal cortex. It is a narrow white band, triangular on coronal section, the apex being directed upward. It lies in the olfactory sulcus on the inferior surface of the frontal lobe, and divides posteriorly into two striæ, a medial olfactory stria and a lateral olfactory stria.[Wikipedia]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Olfactory_tract" -- [left crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014767) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "left crus of lumbar part of diaphragm" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58287" +- [olfactory tract](http://purl.obolibrary.org/obo/UBERON_0002265) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "The definition was adapted from the NIFSTD class which has been retired. It has been generalized so it is applicable to various different kinds of olfactory tracts found in different taxa." + - [editor](http://www.geneontology.org/formats/oboInOwl#editor) "cjm" -- [left crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014767) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "crus sinistrum diaphragmatis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0471888893" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58287" +- [olfactory tract](http://purl.obolibrary.org/obo/UBERON_0002265) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A nervelike, white band composed primarily of nerve fibres originating from the mitral cells and tufted cells of the olfactory bulb but also containing the scattered cells of the anterior olfactory nucleus[BTO:0003647]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "BTO:0003647" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [olfactory tract](http://purl.obolibrary.org/obo/UBERON_0002265) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Tract of brain which is continuous with olfactory bulb and the cerebral cortex.[FMA]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA" -- [left crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014767) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58287" +- [olfactory tract](http://purl.obolibrary.org/obo/UBERON_0002265) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "White matter tract that contains projections from the olfactory bulb to the olfactory cortex (Maryann Martone)" + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "deprecated class" -- [left crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014767) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "crus sinistrum (Diaphragma)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "BIRNLEX:1663" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58287" +- [olfactory tract](http://purl.obolibrary.org/obo/UBERON_0002265) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "in animals with a long snout, the olfactory tract is long, whereas it is short in short-snouted animals such as primates. In some birds the tract per se does not exist as the bulb is connected directly to the cerebral hemisphere.[ISBN:0471888893]" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [left crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014767) [id](http://www.geneontology.org/formats/oboInOwl#id) "UBERON:0014767" -- Class: [left crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014767) +### olfactory tract linking bulb to ipsilateral dorsal telencephalon `http://purl.obolibrary.org/obo/UBERON_0034730` +#### Removed +- [olfactory tract linking bulb to ipsilateral dorsal telencephalon](http://purl.obolibrary.org/obo/UBERON_0034730) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Telencephalic white matter which extends between the olfactory bulb and the ipsilateral dorsal telencephalon and carries secondary olfactory fibers. From Neuroanatomy of the Zebrafish Brain." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFA:0000229" -- [left crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014767) EquivalentTo [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) and ([in left side of](http://purl.obolibrary.org/obo/BSPO_0000120) some [diaphragm](http://purl.obolibrary.org/obo/UBERON_0001103)) -- [left crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014767) SubClassOf [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) -- [left crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014767) SubClassOf [in left side of](http://purl.obolibrary.org/obo/BSPO_0000120) some [diaphragm](http://purl.obolibrary.org/obo/UBERON_0001103) +### olfactory tract linking bulb to ipsilateral ventral telencephalon `http://purl.obolibrary.org/obo/UBERON_2000238` +#### Removed +- [olfactory tract linking bulb to ipsilateral ventral telencephalon](http://purl.obolibrary.org/obo/UBERON_2000238) [UBPROP_0000004](http://purl.obolibrary.org/obo/UBPROP_0000004) "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://purl.obolibrary.org/obo/tao.owl" + -### left hepatic artery `http://purl.obolibrary.org/obo/UBERON_0015481` +### olfactory tubercle `http://purl.obolibrary.org/obo/UBERON_0001883` #### Removed -- [left hepatic artery](http://purl.obolibrary.org/obo/UBERON_0015481) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ramus sinister (arteria hepatica propria)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:14779" +- [olfactory tubercle](http://purl.obolibrary.org/obo/UBERON_0001883) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The olfactory tubercle is a structure involved in Olfaction. It is present in humans, but much smaller than it is in some other animals. It is a frequent subject of research." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Olfactory_tubercle" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [olfactory tubercle](http://purl.obolibrary.org/obo/UBERON_0001883) [RO_0002174](http://purl.obolibrary.org/obo/RO_0002174) [Primates](http://purl.obolibrary.org/obo/NCBITaxon_9443) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "MP" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "EDITOR_NOTE check EHDAA2" -#### Added -- [left hepatic artery](http://purl.obolibrary.org/obo/UBERON_0015481) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ramus sinister (arteria hepatica propria)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [olfactory tubercle](http://purl.obolibrary.org/obo/UBERON_0001883) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Absent in primates" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "MP" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:14779" +- [olfactory tubercle](http://purl.obolibrary.org/obo/UBERON_0001883) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [nucleus accumbens](http://purl.obolibrary.org/obo/UBERON_0001882) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### left hepatic duct `http://purl.obolibrary.org/obo/UBERON_0001177` +### omentum `http://purl.obolibrary.org/obo/UBERON_0003688` #### Removed -- [left hepatic duct](http://purl.obolibrary.org/obo/UBERON_0001177) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ductus hepaticus sinister" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [omentum](http://purl.obolibrary.org/obo/UBERON_0003688) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "omental" #### Added -- [left hepatic duct](http://purl.obolibrary.org/obo/UBERON_0001177) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ductus hepaticus sinister" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [omentum](http://purl.obolibrary.org/obo/UBERON_0003688) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### left lobe of liver `http://purl.obolibrary.org/obo/UBERON_0001115` -#### Removed -- [left lobe of liver](http://purl.obolibrary.org/obo/UBERON_0001115) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lobus hepatis sinister" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Left_lobe_of_liver" +### omentum preadipocyte `http://purl.obolibrary.org/obo/CL_0002579` - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +#### Added +- [omentum preadipocyte](http://purl.obolibrary.org/obo/CL_0002579) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A preadipocyte that is part of an omentum." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:21484051" -- [left lobe of liver](http://purl.obolibrary.org/obo/UBERON_0001115) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lobus hepaticus sinister" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [left lobe of liver](http://purl.obolibrary.org/obo/UBERON_0001115) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lobus hepaticus sinister" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### ommatidium `http://purl.obolibrary.org/obo/UBERON_0000971` +#### Removed +- [ommatidium](http://purl.obolibrary.org/obo/UBERON_0000971) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004510" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -- [left lobe of liver](http://purl.obolibrary.org/obo/UBERON_0001115) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lobus hepatis sinister" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Left_lobe_of_liver" +- [ommatidium](http://purl.obolibrary.org/obo/UBERON_0000971) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "ommatidial" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### left pulmonary artery `http://purl.obolibrary.org/obo/UBERON_0001652` +### only in taxon `http://purl.obolibrary.org/obo/RO_0002160` #### Removed -- [left pulmonary artery](http://purl.obolibrary.org/obo/UBERON_0001652) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria pulmonalis sinistra" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Left_pulmonary_artery" +- [only in taxon](http://purl.obolibrary.org/obo/RO_0002160) [id](http://www.geneontology.org/formats/oboInOwl#id) "only_in_taxon" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [only in taxon](http://purl.obolibrary.org/obo/RO_0002160) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) -#### Added -- [left pulmonary artery](http://purl.obolibrary.org/obo/UBERON_0001652) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria pulmonalis sinistra" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [only in taxon](http://purl.obolibrary.org/obo/RO_0002160) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002160" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Left_pulmonary_artery" +- [only in taxon](http://purl.obolibrary.org/obo/RO_0002160) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) [17921072](http://www.ncbi.nlm.nih.gov/pubmed/17921072) +- [only in taxon](http://purl.obolibrary.org/obo/RO_0002160) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) -### left subclavian artery `http://purl.obolibrary.org/obo/UBERON_0001584` -#### Removed -- [left subclavian artery](http://purl.obolibrary.org/obo/UBERON_0001584) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arteria subclavia (sinistra)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:4694" +- [only in taxon](http://purl.obolibrary.org/obo/RO_0002160) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [only in taxon](http://purl.obolibrary.org/obo/RO_0002160) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "lactation SubClassOf 'only in taxon' some 'Mammalia'" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [only in taxon](http://purl.obolibrary.org/obo/RO_0002160) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "only_in_taxon" -#### Added -- [left subclavian artery](http://purl.obolibrary.org/obo/UBERON_0001584) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arteria subclavia (sinistra)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:4694" +- [only in taxon](http://purl.obolibrary.org/obo/RO_0002160) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) [20973947](http://www.ncbi.nlm.nih.gov/pubmed/20973947) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + +### ontology `http://www.geneontology.org/formats/oboInOwl#ontology` +#### Removed +- AnnotationProperty: [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) -### left ventricular trabecular myocardium `http://purl.obolibrary.org/obo/UBERON_0005064` + +### opaque `http://purl.obolibrary.org/obo/PATO_0000963` #### Removed -- [left ventricular trabecular myocardium](http://purl.obolibrary.org/obo/UBERON_0005064) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO:0003225" +- [opaque](http://purl.obolibrary.org/obo/PATO_0000963) [RO_0002604](http://purl.obolibrary.org/obo/RO_0002604) [transparent](http://purl.obolibrary.org/obo/PATO_0000964) -#### Added -- [left ventricular trabecular myocardium](http://purl.obolibrary.org/obo/UBERON_0005064) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Missing definition for term UBERON:0005064. Please replace it using linked reference." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO:0003225" -### lens epithelial cell `http://purl.obolibrary.org/obo/CL_0002224` +### open `http://purl.obolibrary.org/obo/PATO_0000610` +#### Removed +- [open](http://purl.obolibrary.org/obo/PATO_0000610) [RO_0002604](http://purl.obolibrary.org/obo/RO_0002604) [closed](http://purl.obolibrary.org/obo/PATO_0000608) -#### Added -- [lens epithelial cell](http://purl.obolibrary.org/obo/CL_0002224) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### lens fiber `http://purl.obolibrary.org/obo/UBERON_0002444` +### open tracheal system `http://purl.obolibrary.org/obo/UBERON_0005155` #### Removed -- [lens fiber](http://purl.obolibrary.org/obo/UBERON_0002444) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "fibrae lentis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [open tracheal system](http://purl.obolibrary.org/obo/UBERON_0005155) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005024" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:76827" -#### Added -- [lens fiber](http://purl.obolibrary.org/obo/UBERON_0002444) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "fibrae lentis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### ophthalmic artery `http://purl.obolibrary.org/obo/UBERON_0001619` +#### Removed +- [ophthalmic artery](http://purl.obolibrary.org/obo/UBERON_0001619) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: part_of internal carotid (AAO:0010219)[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010497" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:76827" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" +- [ophthalmic artery](http://purl.obolibrary.org/obo/UBERON_0001619) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Part of internal carotid which carries blood via branches to the eye, the eye muscles, and eyelids.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010497" -### lens fiber cell `http://purl.obolibrary.org/obo/CL_0011004` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -#### Added -- [lens fiber cell](http://purl.obolibrary.org/obo/CL_0011004) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" -### lens placode `http://purl.obolibrary.org/obo/UBERON_0003073` -#### Removed -- [lens placode](http://purl.obolibrary.org/obo/UBERON_0003073) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "placoda lentis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lens_placode" -#### Added -- [lens placode](http://purl.obolibrary.org/obo/UBERON_0003073) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "placoda lentis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### ophthalmic nerve `http://purl.obolibrary.org/obo/UBERON_0000348` +#### Removed +- [ophthalmic nerve](http://purl.obolibrary.org/obo/UBERON_0000348) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The profundus nerve is a distinct nerve only in fishes. (...) In mammals, the profundus nerve is the same as the most rostral (ophthalmic) branch of the trigeminal nerve.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001349" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lens_placode" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### leptomeningeal cell `http://purl.obolibrary.org/obo/CL_0000708` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [leptomeningeal cell](http://purl.obolibrary.org/obo/CL_0000708) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.177" +- [ophthalmic nerve](http://purl.obolibrary.org/obo/UBERON_0000348) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Sensory medial ramus of the trigeminal nerve.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" -### leukocyte `http://purl.obolibrary.org/obo/CL_0000738` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010648" -#### Added -- [leukocyte](http://purl.obolibrary.org/obo/CL_0000738) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### levator scapulae muscle `http://purl.obolibrary.org/obo/UBERON_0005461` -#### Removed -- [levator scapulae muscle](http://purl.obolibrary.org/obo/UBERON_0005461) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "musculus levator scapulae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Levator_scapulae_muscle" +- [ophthalmic nerve](http://purl.obolibrary.org/obo/UBERON_0000348) SubClassOf [branching part of](http://purl.obolibrary.org/obo/RO_0002380) some [trigeminal nerve](http://purl.obolibrary.org/obo/UBERON_0001645) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "multiple" + + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "may be a distinct nerve in teleosts" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [ophthalmic nerve](http://purl.obolibrary.org/obo/UBERON_0000348) SubClassOf [nerve](http://purl.obolibrary.org/obo/UBERON_0001021) #### Added -- [levator scapulae muscle](http://purl.obolibrary.org/obo/UBERON_0005461) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "musculus levator scapulae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [ophthalmic nerve](http://purl.obolibrary.org/obo/UBERON_0000348) SubClassOf [nerve of head region](http://purl.obolibrary.org/obo/UBERON_0011779) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Levator_scapulae_muscle" +- [ophthalmic nerve](http://purl.obolibrary.org/obo/UBERON_0000348) SubClassOf [branching part of](http://purl.obolibrary.org/obo/RO_0002380) some [trigeminal nerve](http://purl.obolibrary.org/obo/UBERON_0001645) -### ligament of sternoclavicular joint `http://purl.obolibrary.org/obo/UBERON_0011875` +### optic chiasma `http://purl.obolibrary.org/obo/UBERON_0000959` #### Removed -- [ligament of sternoclavicular joint](http://purl.obolibrary.org/obo/UBERON_0011875) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ligamentum sternoclavicularis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [optic chiasma](http://purl.obolibrary.org/obo/UBERON_0000959) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The point at which fibers of the optic nerves cross.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010622" -#### Added -- [ligament of sternoclavicular joint](http://purl.obolibrary.org/obo/UBERON_0011875) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ligamentum sternoclavicularis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:DSM" -### limb `http://purl.obolibrary.org/obo/UBERON_0002101` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -#### Added -- [limb](http://purl.obolibrary.org/obo/UBERON_0002101) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D005121" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) +- [optic chiasma](http://purl.obolibrary.org/obo/UBERON_0000959) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The chiasm has been studied in great detail in some animals, while in others relatively little or nothing is known. Although there are some gross architectural features that are conserved within some animals, such as birds and fish, the general picture is one of diversity. This review will attempt to consider the key features of such diversity of chiasmatic organisation in vertebrates and the mechanisms that sculpt them from the limited literature that is available. However, as so much research has been undertaken on the structure and development of the chiasm in laboratory animals, any review must consider the information that has been gleaned from them and hope that future studies will determine whether the features revealed in these animals, and the underlying mechanisms that generate them, have a common vertebrate plan.[uncertain][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1016/j.preteyeres.2005.04.005 Jeffery G, Erskine L, Variations in the architecture and development of the vertebrate optic chiasm. Progress in retinal and eye research (2005)" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### limb bud `http://purl.obolibrary.org/obo/UBERON_0004347` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000190" + + + +### optic choroid `http://purl.obolibrary.org/obo/UBERON_0001776` #### Removed -- [limb bud](http://purl.obolibrary.org/obo/UBERON_0004347) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "gemmae membrorum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Limb_bud" +- [optic choroid](http://purl.obolibrary.org/obo/UBERON_0001776) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "MP treats posterior uvea and optic choroid as distinct" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MP" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [optic choroid](http://purl.obolibrary.org/obo/UBERON_0001776) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "choroidal" -#### Added -- [limb bud](http://purl.obolibrary.org/obo/UBERON_0004347) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "gemmae membrorum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Limb_bud" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### optic cup `http://purl.obolibrary.org/obo/UBERON_0003072` +#### Removed +- [optic cup](http://purl.obolibrary.org/obo/UBERON_0003072) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429" -### limb muscle `http://purl.obolibrary.org/obo/UBERON_0003661` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [limb muscle](http://purl.obolibrary.org/obo/UBERON_0003661) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [limb muscle](http://purl.obolibrary.org/obo/UBERON_0003661) [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [Homo sapiens](http://purl.obolibrary.org/obo/NCBITaxon_9606) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000167" -### limbic lobe `http://purl.obolibrary.org/obo/UBERON_0002600` + + +### optic eminence surface ectoderm `http://purl.obolibrary.org/obo/UBERON_0005216` #### Removed -- [limbic lobe](http://purl.obolibrary.org/obo/UBERON_0002600) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D065726" +- [optic eminence surface ectoderm](http://purl.obolibrary.org/obo/UBERON_0005216) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "VHOG:0000520" -- [limbic lobe](http://purl.obolibrary.org/obo/UBERON_0002600) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "gyrus fornicatus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [optic eminence surface ectoderm](http://purl.obolibrary.org/obo/UBERON_0005216) [id](http://www.geneontology.org/formats/oboInOwl#id) "UBERON:0005216" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:834" +- [optic eminence surface ectoderm](http://purl.obolibrary.org/obo/UBERON_0005216) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:16539" -- [limbic lobe](http://purl.obolibrary.org/obo/UBERON_0002600) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lobus limbicus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Limbic_lobe" +- [optic eminence surface ectoderm](http://purl.obolibrary.org/obo/UBERON_0005216) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RETIRED_EHDAA2:0001311" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [optic eminence surface ectoderm](http://purl.obolibrary.org/obo/UBERON_0005216) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" -#### Added -- [limbic lobe](http://purl.obolibrary.org/obo/UBERON_0002600) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lobus limbicus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [optic eminence surface ectoderm](http://purl.obolibrary.org/obo/UBERON_0005216) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An external ectoderm that is part of a optic eminence [Automatically generated definition]." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "OBOL:automatic" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Limbic_lobe" +- [optic eminence surface ectoderm](http://purl.obolibrary.org/obo/UBERON_0005216) [label](http://www.w3.org/2000/01/rdf-schema#label) "optic eminence surface ectoderm" -- [limbic lobe](http://purl.obolibrary.org/obo/UBERON_0002600) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D065726" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- Class: [optic eminence surface ectoderm](http://purl.obolibrary.org/obo/UBERON_0005216) - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) +- [optic eminence surface ectoderm](http://purl.obolibrary.org/obo/UBERON_0005216) EquivalentTo [external ectoderm](http://purl.obolibrary.org/obo/UBERON_0000076) and ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [optic eminence](http://purl.obolibrary.org/obo/UBERON_0004348)) - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +- [optic eminence surface ectoderm](http://purl.obolibrary.org/obo/UBERON_0005216) SubClassOf [external ectoderm](http://purl.obolibrary.org/obo/UBERON_0000076) -- [limbic lobe](http://purl.obolibrary.org/obo/UBERON_0002600) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "gyrus fornicatus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [optic eminence surface ectoderm](http://purl.obolibrary.org/obo/UBERON_0005216) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [optic eminence ectoderm](http://purl.obolibrary.org/obo/UBERON_0005234) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:834" + - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true" -### lingual artery `http://purl.obolibrary.org/obo/UBERON_0001610` + +### optic foramen `http://purl.obolibrary.org/obo/UBERON_0005745` #### Removed -- [lingual artery](http://purl.obolibrary.org/obo/UBERON_0001610) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria lingualis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lingual_artery" +- [optic foramen](http://purl.obolibrary.org/obo/UBERON_0005745) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "An aperture in the root of the lesser wing of the sphenoid bone transmitting the optic nerve. [TFD][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001408" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [lingual artery](http://purl.obolibrary.org/obo/UBERON_0001610) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria lingualis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lingual_artery" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/optic+foramen" -### lip `http://purl.obolibrary.org/obo/UBERON_0001833` -#### Removed -- [lip](http://purl.obolibrary.org/obo/UBERON_0001833) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "labia oris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [optic foramen](http://purl.obolibrary.org/obo/UBERON_0005745) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Foramen in the orbital region of the neurocranium for the passage of the optic nerve (cranial nerve II).[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0002025" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lip" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -#### Added -- [lip](http://purl.obolibrary.org/obo/UBERON_0001833) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "labia oris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lip" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TAO:wd" +- [optic foramen](http://purl.obolibrary.org/obo/UBERON_0005745) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The short canal through the orbitosphenoid bone at the apex of the orbit that gives passage to the optic nerve and the opthalmic artery" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "MP" -### lipid binding `http://purl.obolibrary.org/obo/GO_0008289` -#### Removed -- [lipid binding](http://purl.obolibrary.org/obo/GO_0008289) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "MP:0010704" #### Added -- [lipid binding](http://purl.obolibrary.org/obo/GO_0008289) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) +- [optic foramen](http://purl.obolibrary.org/obo/UBERON_0005745) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) +- [optic foramen](http://purl.obolibrary.org/obo/UBERON_0005745) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### lipid metabolic process `http://purl.obolibrary.org/obo/GO_0006629` + +### optic neural crest `http://purl.obolibrary.org/obo/UBERON_0009920` #### Removed -- [lipid metabolic process](http://purl.obolibrary.org/obo/GO_0006629) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) +- [optic neural crest](http://purl.obolibrary.org/obo/UBERON_0009920) SubClassOf [head mesenchyme](http://purl.obolibrary.org/obo/UBERON_0005253) #### Added -- [lipid metabolic process](http://purl.obolibrary.org/obo/GO_0006629) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) +- [optic neural crest](http://purl.obolibrary.org/obo/UBERON_0009920) SubClassOf [mesenchyme derived from head neural crest](http://purl.obolibrary.org/obo/UBERON_0007213) -### liver `http://purl.obolibrary.org/obo/UBERON_0002107` +### optic stalk `http://purl.obolibrary.org/obo/UBERON_0003098` #### Removed -- [liver](http://purl.obolibrary.org/obo/UBERON_0002107) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "jecur" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Liver" +- [optic stalk](http://purl.obolibrary.org/obo/UBERON_0003098) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [liver](http://purl.obolibrary.org/obo/UBERON_0002107) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "iecur" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Liver" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [liver](http://purl.obolibrary.org/obo/UBERON_0002107) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "iecur" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000223" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Liver" +- [optic stalk](http://purl.obolibrary.org/obo/UBERON_0003098) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The evagination from the neural tube of the developing embryo which develops the optic cup at its extremity; the stalk persists as the optic nerve. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/optic+stalk" -- [liver](http://purl.obolibrary.org/obo/UBERON_0002107) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "jecur" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Liver" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### liver dendritic cell `http://purl.obolibrary.org/obo/CL_2000055` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000223" -#### Added -- [liver dendritic cell](http://purl.obolibrary.org/obo/CL_2000055) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### liver lobule `http://purl.obolibrary.org/obo/UBERON_0004647` +### optic tract `http://purl.obolibrary.org/obo/UBERON_0001908` #### Removed -- [liver lobule](http://purl.obolibrary.org/obo/UBERON_0004647) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lobuli hepatis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lobules_of_liver" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [optic tract](http://purl.obolibrary.org/obo/UBERON_0001908) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:16678" -- [liver lobule](http://purl.obolibrary.org/obo/UBERON_0004647) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lobulus hepaticus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:14471" -#### Added -- [liver lobule](http://purl.obolibrary.org/obo/UBERON_0004647) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lobuli hepatis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lobules_of_liver" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### optic vesicle `http://purl.obolibrary.org/obo/UBERON_0004128` +#### Removed +- [optic vesicle](http://purl.obolibrary.org/obo/UBERON_0004128) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429" -- [liver lobule](http://purl.obolibrary.org/obo/UBERON_0004647) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lobulus hepaticus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:14471" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### liver serosa `http://purl.obolibrary.org/obo/UBERON_8400021` -#### Removed -- [liver serosa](http://purl.obolibrary.org/obo/UBERON_8400021) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica serosa hepatis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://medical-dictionary.thefreedictionary.com/serosa+of+liver" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000165" - - [synonym_type_property](http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty) "LATIN" -#### Added -- [liver serosa](http://purl.obolibrary.org/obo/UBERON_8400021) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica serosa hepatis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://medical-dictionary.thefreedictionary.com/serosa+of+liver" +### oral cavity `http://purl.obolibrary.org/obo/UBERON_0000167` +#### Removed +- [oral cavity](http://purl.obolibrary.org/obo/UBERON_0000167) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D009055" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -### lobar bronchus `http://purl.obolibrary.org/obo/UBERON_0002183` -#### Removed -- [lobar bronchus](http://purl.obolibrary.org/obo/UBERON_0002183) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "bronchi lobaris" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Secondary_bronchus" +- [oral cavity](http://purl.obolibrary.org/obo/UBERON_0000167) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The cavity of the mouth, bounded by the jaw bones and associated structures (muscles and mucosa). [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/oral+cavity" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [lobar bronchus](http://purl.obolibrary.org/obo/UBERON_0002183) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "bronchi lobaris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Secondary_bronchus" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000188" -### lobe of cerebral hemisphere `http://purl.obolibrary.org/obo/UBERON_0016526` -#### Removed -- [lobe of cerebral hemisphere](http://purl.obolibrary.org/obo/UBERON_0016526) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lobi cerebri" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:77800" +- [oral cavity](http://purl.obolibrary.org/obo/UBERON_0000167) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical cavity bounded anteriorly by the mouth and posteriorly by the derivatives of the branchial arches.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000960" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -#### Added -- [lobe of cerebral hemisphere](http://purl.obolibrary.org/obo/UBERON_0016526) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lobi cerebri" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:77800" +- [oral cavity](http://purl.obolibrary.org/obo/UBERON_0000167) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Echinoderms, hemichordates, and chordates are called deuterostomes because the mouth arises not from the blastopore but from a second invagination at the anterior end of the larva that pushes in to connect with the archenteron.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### lobe of thyroid gland `http://purl.obolibrary.org/obo/UBERON_0001118` -#### Removed -- [lobe of thyroid gland](http://purl.obolibrary.org/obo/UBERON_0001118) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lobuli glandulae thyroideae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lobes_of_thyroid_gland" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.32" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000188" -- [lobe of thyroid gland](http://purl.obolibrary.org/obo/UBERON_0001118) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lobus glandulae thyroideae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:13367" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### oral epithelium `http://purl.obolibrary.org/obo/UBERON_0002424` +#### Removed +- [oral epithelium](http://purl.obolibrary.org/obo/UBERON_0002424) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The epithelium that lines the oral cavity. The oral epithelium epithelial cells with many short microvilli as well as mucous cells, rodlet cells and taste buds[ZFIN:ZDB-PUB-060921-12, ZFIN:ZDB-PUB-091204-24]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFA:0000816" -#### Added -- [lobe of thyroid gland](http://purl.obolibrary.org/obo/UBERON_0001118) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lobus glandulae thyroideae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:13367" +- [oral epithelium](http://purl.obolibrary.org/obo/UBERON_0002424) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "the avian oral epithelium has the developmental capacity to initiate tooth developmental programs with underlying grafts of non-avian oral ectomesenchyme" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:16488870" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [lobe of thyroid gland](http://purl.obolibrary.org/obo/UBERON_0001118) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lobuli glandulae thyroideae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### oral gland `http://purl.obolibrary.org/obo/UBERON_0010047` +#### Removed +- [oral gland](http://purl.obolibrary.org/obo/UBERON_0010047) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "Note that Kardong classifies lacrimal glands here. EHDAA2 includes pituitary primordium, as this develops from oral mucosa" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EHDAA2" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lobes_of_thyroid_gland" -### lobule `http://purl.obolibrary.org/obo/UBERON_0009911` +### oral opening `http://purl.obolibrary.org/obo/UBERON_0000166` #### Removed -- [lobule](http://purl.obolibrary.org/obo/UBERON_0009911) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lobulus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:45737" +- [oral opening](http://purl.obolibrary.org/obo/UBERON_0000166) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) mouth development is very similar in protostomes and 'basal' deuterostomes, whereas the chordate mouth seems to develop at a new position. Recent data for echinoderms and hemichordates further suggest that this change in mouth position may result from change in the influence of a conserved ectodermal patterning system on mouth development. It has been suggested that the mouths of vertebrates and urochordates may constitute a 'new' mouth.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [lobule](http://purl.obolibrary.org/obo/UBERON_0009911) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lobulus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:45737" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000280" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1016/j.semcdb.2007.06.002 Christiaen L, Jaszczyszyn Y, Kerfant M, Kanob S, Thermes V, Joly JS, Evolutionary modification of mouth position in deuterostomes. Seminars in Cell and Developmental Biology (2007)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### locus ceruleus `http://purl.obolibrary.org/obo/UBERON_0002148` +### orbit of skull `http://purl.obolibrary.org/obo/UBERON_0001697` #### Removed -- [locus ceruleus](http://purl.obolibrary.org/obo/UBERON_0002148) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nucleus caeruleus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [orbit of skull](http://purl.obolibrary.org/obo/UBERON_0001697) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in FMA, this overlaps with bones such as the maxilla and sphenoid; in ZFA, individual bones are part of the orbit" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:72478" +- [orbit of skull](http://purl.obolibrary.org/obo/UBERON_0001697) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical cluster that is a anterolateral part of the cranium and structurally supports the eye.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TAO:MAH" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001410" -- [locus ceruleus](http://purl.obolibrary.org/obo/UBERON_0002148) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus loci caerulei" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:583" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" #### Added -- [locus ceruleus](http://purl.obolibrary.org/obo/UBERON_0002148) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nucleus caeruleus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [orbit of skull](http://purl.obolibrary.org/obo/UBERON_0001697) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:72478" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" - -- [locus ceruleus](http://purl.obolibrary.org/obo/UBERON_0002148) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus loci caerulei" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### orbital cavity `http://purl.obolibrary.org/obo/UBERON_0004867` +#### Removed +- [orbital cavity](http://purl.obolibrary.org/obo/UBERON_0004867) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "note that the AAO and ZFA class is a cavity" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "AAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:583" + - [see also](http://www.w3.org/2000/01/rdf-schema#seeAlso) "https://github.com/obophenotype/uberon/issues/462" -### loop of Henle `http://purl.obolibrary.org/obo/UBERON_0001288` -#### Removed -- [loop of Henle](http://purl.obolibrary.org/obo/UBERON_0001288) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ansa nephroni" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Loop_of_Henle" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### orbital fissure `http://purl.obolibrary.org/obo/UBERON_0006271` #### Added -- [loop of Henle](http://purl.obolibrary.org/obo/UBERON_0001288) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ansa nephroni" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Loop_of_Henle" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [orbital fissure](http://purl.obolibrary.org/obo/UBERON_0006271) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) -### loose connective tissue `http://purl.obolibrary.org/obo/UBERON_0011825` +### orbital region `http://purl.obolibrary.org/obo/UBERON_0004088` #### Removed -- [loose connective tissue](http://purl.obolibrary.org/obo/UBERON_0011825) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "textus connectivus collagenosus laxus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:19783" +- [orbital region](http://purl.obolibrary.org/obo/UBERON_0004088) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in HP covers eyelid, eyebrow." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "HP:0000284" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" - -- [loose connective tissue](http://purl.obolibrary.org/obo/UBERON_0011825) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "textus connectivus laxus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:19783" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### orbitosphenoid `http://purl.obolibrary.org/obo/UBERON_0002478` +#### Removed +- [orbitosphenoid](http://purl.obolibrary.org/obo/UBERON_0002478) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: overlaps orbitosphenoid-lateral ethmoid joint (TAO:0001941)[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000253" -#### Added -- [loose connective tissue](http://purl.obolibrary.org/obo/UBERON_0011825) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "textus connectivus laxus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:19783" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [orbitosphenoid](http://purl.obolibrary.org/obo/UBERON_0002478) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship type change: overlaps neurocranium (TAO:0001580) CHANGED TO: part_of neurocranium (UBERON:0001703)[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000253" -- [loose connective tissue](http://purl.obolibrary.org/obo/UBERON_0011825) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "textus connectivus collagenosus laxus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:19783" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [orbitosphenoid](http://purl.obolibrary.org/obo/UBERON_0002478) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Large median unpaired cartilage bone consisting of two diverging plates. Positioned medial to the eye. The orbitosphenoid develops from the Trabeculae communis and forms the anterior and anterolateral boundary of the orbital foramen and constitutes a significant part of the sidewalls and floor of the cranial cavity. Bordered by the lateral ethmoid anteriorly, and the pterosphenoid posteriorly, The orbitosphenoid may extend ventrally to meet the parasphenoid. In the adult, the orbitosphenoid is fused ventrally to the parasphenoid via a thin sheet of bone.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000253" -### lower lip `http://purl.obolibrary.org/obo/UBERON_0001835` -#### Removed -- [lower lip](http://purl.obolibrary.org/obo/UBERON_0001835) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "labium inferius oris" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lower_lip" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -#### Added -- [lower lip](http://purl.obolibrary.org/obo/UBERON_0001835) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "labium inferius oris" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lower_lip" +- [orbitosphenoid](http://purl.obolibrary.org/obo/UBERON_0002478) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship type change: overlaps neurocranium (TAO:0001580) CHANGED TO: develops_from neurocranium (UBERON:0001703)[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000253" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -### lower urinary tract `http://purl.obolibrary.org/obo/UBERON_0001556` +- [orbitosphenoid](http://purl.obolibrary.org/obo/UBERON_0002478) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: overlaps orbitosphenoid-prootic joint (TAO:0001794)[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000253" -#### Added -- [lower urinary tract](http://purl.obolibrary.org/obo/UBERON_0001556) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -- [lower urinary tract](http://purl.obolibrary.org/obo/UBERON_0001556) [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [Homo sapiens](http://purl.obolibrary.org/obo/NCBITaxon_9606) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" +- [orbitosphenoid](http://purl.obolibrary.org/obo/UBERON_0002478) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: overlaps pterosphenoid-orbitosphenoid joint (TAO:0001831)[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000253" -### lumbosacral nerve plexus `http://purl.obolibrary.org/obo/UBERON_0001815` -#### Removed -- [lumbosacral nerve plexus](http://purl.obolibrary.org/obo/UBERON_0001815) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "plexus lumbosacralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lumbosacral_plexus" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -- [lumbosacral nerve plexus](http://purl.obolibrary.org/obo/UBERON_0001815) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "plexus lumbosacralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:5907" +- [orbitosphenoid](http://purl.obolibrary.org/obo/UBERON_0002478) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: part_of braincase and otic capsule skeleton (AAO:0000052)[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000345" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -#### Added -- [lumbosacral nerve plexus](http://purl.obolibrary.org/obo/UBERON_0001815) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "plexus lumbosacralis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [orbitosphenoid](http://purl.obolibrary.org/obo/UBERON_0002478) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Endochondral ossification of the lateral sides of the braincase.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:5907" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000345" -- [lumbosacral nerve plexus](http://purl.obolibrary.org/obo/UBERON_0001815) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "plexus lumbosacralis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lumbosacral_plexus" +- [orbitosphenoid](http://purl.obolibrary.org/obo/UBERON_0002478) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: develops_from taenia marginalis anterior (TAO:0001505)[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000253" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -### lumen of open tracheal system trachea `http://purl.obolibrary.org/obo/UBERON_0006832` -#### Removed -- [lumen of open tracheal system trachea](http://purl.obolibrary.org/obo/UBERON_0006832) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007410" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -#### Added -- [lumen of open tracheal system trachea](http://purl.obolibrary.org/obo/UBERON_0006832) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007410" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### luminal cell of prostate epithelium `http://purl.obolibrary.org/obo/CL_0002340` +### orbitosphenoid cartilage element `http://purl.obolibrary.org/obo/UBERON_0005687` #### Added -- [luminal cell of prostate epithelium](http://purl.obolibrary.org/obo/CL_0002340) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [orbitosphenoid cartilage element](http://purl.obolibrary.org/obo/UBERON_0005687) SubClassOf [mesenchyme derived from neural crest](http://purl.obolibrary.org/obo/UBERON_0014387) -### luminal epithelial cell of mammary gland `http://purl.obolibrary.org/obo/CL_0002326` +### order `http://www.geneontology.org/formats/oboInOwl#order` +#### Removed +- AnnotationProperty: [order](http://www.geneontology.org/formats/oboInOwl#order) -#### Added -- [luminal epithelial cell of mammary gland](http://purl.obolibrary.org/obo/CL_0002326) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### luminal layer of epithelium `http://purl.obolibrary.org/obo/UBERON_0011945` +### organ `http://purl.obolibrary.org/obo/UBERON_0000062` #### Removed -- [luminal layer of epithelium](http://purl.obolibrary.org/obo/UBERON_0011945) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas) +- [organ](http://purl.obolibrary.org/obo/UBERON_0000062) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4" -- [luminal layer of epithelium](http://purl.obolibrary.org/obo/UBERON_0011945) [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [Homo sapiens](http://purl.obolibrary.org/obo/NCBITaxon_9606) +- [organ](http://purl.obolibrary.org/obo/UBERON_0000062) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GO:0048513" -### lung `http://purl.obolibrary.org/obo/UBERON_0002048` +### organ part `http://purl.obolibrary.org/obo/UBERON_0000064` #### Removed -- [lung](http://purl.obolibrary.org/obo/UBERON_0002048) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pulmo" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [organ part](http://purl.obolibrary.org/obo/UBERON_0000064) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "currently defined in a very broad sense, may be replaced by more specific classes in the future" -#### Added -- [lung](http://purl.obolibrary.org/obo/UBERON_0002048) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pulmo" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### lung bud `http://purl.obolibrary.org/obo/UBERON_0000118` +### organ subunit `http://purl.obolibrary.org/obo/UBERON_0000063` #### Removed -- [lung bud](http://purl.obolibrary.org/obo/UBERON_0000118) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "gemma pulmonalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lung_buds" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - -- [lung bud](http://purl.obolibrary.org/obo/UBERON_0000118) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "gemma respiratoria" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lung_buds" +- [organ subunit](http://purl.obolibrary.org/obo/UBERON_0000063) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:86140" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [version](http://www.geneontology.org/formats/oboInOwl#version) "3" -#### Added -- [lung bud](http://purl.obolibrary.org/obo/UBERON_0000118) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "gemma respiratoria" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [organ subunit](http://purl.obolibrary.org/obo/UBERON_0000063) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:86140" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lung_buds" + - [version](http://www.geneontology.org/formats/oboInOwl#version) "1" -- [lung bud](http://purl.obolibrary.org/obo/UBERON_0000118) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "gemma pulmonalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lung_buds" +### organ system subdivision `http://purl.obolibrary.org/obo/UBERON_0011216` +#### Removed +- [organ system subdivision](http://purl.obolibrary.org/obo/UBERON_0011216) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007330" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### lung ciliated cell `http://purl.obolibrary.org/obo/CL_1000271` -#### Added -- [lung ciliated cell](http://purl.obolibrary.org/obo/CL_1000271) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### organism subdivision `http://purl.obolibrary.org/obo/UBERON_0000475` +#### Removed +- [organism subdivision](http://purl.obolibrary.org/obo/UBERON_0000475) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007009" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### lung goblet cell `http://purl.obolibrary.org/obo/CL_1000143` -#### Added -- [lung goblet cell](http://purl.obolibrary.org/obo/CL_1000143) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### organism substance `http://purl.obolibrary.org/obo/UBERON_0000463` +#### Removed +- [organism substance](http://purl.obolibrary.org/obo/UBERON_0000463) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007019" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### lung macrophage `http://purl.obolibrary.org/obo/CL_1001603` +- [organism substance](http://purl.obolibrary.org/obo/UBERON_0000463) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [multicellular organism](http://purl.obolibrary.org/obo/UBERON_0000468) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "this relationship may be too strong and may be weakened in future" #### Added -- [lung macrophage](http://purl.obolibrary.org/obo/CL_1001603) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [organism substance](http://purl.obolibrary.org/obo/UBERON_0000463) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [multicellular organism](http://purl.obolibrary.org/obo/UBERON_0000468) -### lung microvascular endothelial cell `http://purl.obolibrary.org/obo/CL_2000016` +### organizational term `http://purl.obolibrary.org/obo/IAO_0000121` +#### Removed +- [organizational term](http://purl.obolibrary.org/obo/IAO_0000121) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "organizational term"@en -#### Added -- [lung microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000016) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### lung neuroendocrine cell `http://purl.obolibrary.org/obo/CL_1000223` +### orifice `http://purl.obolibrary.org/obo/UBERON_0000161` +#### Removed +- [orifice](http://purl.obolibrary.org/obo/UBERON_0000161) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in FMA, this is an anatomical conduit *space*, rather than anatomical conduit" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" -#### Added -- [lung neuroendocrine cell](http://purl.obolibrary.org/obo/CL_1000223) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### lung pericyte `http://purl.obolibrary.org/obo/CL_0009089` +### os clitoris `http://purl.obolibrary.org/obo/UBERON_0006440` #### Added -- [lung pericyte](http://purl.obolibrary.org/obo/CL_0009089) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [os clitoris](http://purl.obolibrary.org/obo/UBERON_0006440) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### lung secretory cell `http://purl.obolibrary.org/obo/CL_1000272` +### os penis `http://purl.obolibrary.org/obo/UBERON_0006435` +#### Removed +- [os penis](http://purl.obolibrary.org/obo/UBERON_0006435) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "found in most mammals, with the exception of humans" #### Added -- [lung secretory cell](http://purl.obolibrary.org/obo/CL_1000272) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [os penis](http://purl.obolibrary.org/obo/UBERON_0006435) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### lymph `http://purl.obolibrary.org/obo/UBERON_0002391` +### osseus cochlea `http://purl.obolibrary.org/obo/UBERON_0007223` #### Removed -- [lymph](http://purl.obolibrary.org/obo/UBERON_0002391) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lympha" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lymph" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [osseus cochlea](http://purl.obolibrary.org/obo/UBERON_0007223) SubClassOf [anatomical structure](http://purl.obolibrary.org/obo/UBERON_0000061) #### Added -- [lymph](http://purl.obolibrary.org/obo/UBERON_0002391) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lympha" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [osseus cochlea](http://purl.obolibrary.org/obo/UBERON_0007223) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lymph" - -### lymph node `http://purl.obolibrary.org/obo/UBERON_0000029` +### osteoid `http://purl.obolibrary.org/obo/UBERON_0008883` #### Removed -- [lymph node](http://purl.obolibrary.org/obo/UBERON_0000029) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nodus lymphaticus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lymph_node" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - -#### Added -- [lymph node](http://purl.obolibrary.org/obo/UBERON_0000029) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nodus lymphaticus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [osteoid](http://purl.obolibrary.org/obo/UBERON_0008883) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "Note that in VSAO this was classified both as tissue and acellular extracellular matrix. Consider also the AEO class 'bone condensation'. is_a intercellular matrix in FMA." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "VSAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lymph_node" +- [osteoid](http://purl.obolibrary.org/obo/UBERON_0008883) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Newly formed organic bone matrix secreted by osteoblasts, that exists prior to calcification; it is comprised mainly of type I collagen fibers, chondroitin sulfate and osteocalci[ISBN:0-683-40008-8]n" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "MP:0010924" + - [reference](http://www.geneontology.org/formats/oboInOwl#reference) "ISBN:0-683-40008-8" -### lymph vasculature `http://purl.obolibrary.org/obo/UBERON_0004536` -#### Removed -- [lymph vasculature](http://purl.obolibrary.org/obo/UBERON_0004536) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "trunci et ductus lymphatici" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:63815" +- [osteoid](http://purl.obolibrary.org/obo/UBERON_0008883) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Bone tissue that is an unmineralized bone matrix deposited by osteoblasts prior to the mineralization of bone tissue.[VSAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000046" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -#### Added -- [lymph vasculature](http://purl.obolibrary.org/obo/UBERON_0004536) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "trunci et ductus lymphatici" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PSPUB:0000170" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:63815" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### lymphatic vessel `http://purl.obolibrary.org/obo/UBERON_0001473` +### otic capsule `http://purl.obolibrary.org/obo/UBERON_0004637` #### Removed -- [lymphatic vessel](http://purl.obolibrary.org/obo/UBERON_0001473) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D042601" +- [otic capsule](http://purl.obolibrary.org/obo/UBERON_0004637) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: part_of occipito-petrosal (AAO:0010831)[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010143" -- [lymphatic vessel](http://purl.obolibrary.org/obo/UBERON_0001473) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vas lymphaticum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lymphatic_vessel" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -#### Added -- [lymphatic vessel](http://purl.obolibrary.org/obo/UBERON_0001473) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D042601" +- [otic capsule](http://purl.obolibrary.org/obo/UBERON_0004637) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0005981" - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -- [lymphatic vessel](http://purl.obolibrary.org/obo/UBERON_0001473) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vas lymphaticum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lymphatic_vessel" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) +- [otic capsule](http://purl.obolibrary.org/obo/UBERON_0004637) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "in elasmobranchs, it remains cartilaginous in the adult; in the embryos of higher vertebrates, it is cartilaginous at first but later becomes bony (at approximately 23 weeks in humans)" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Biology-Online" -### lymphocyte `http://purl.obolibrary.org/obo/CL_0000542` -#### Removed -- [lymphocyte](http://purl.obolibrary.org/obo/CL_0000542) EquivalentTo [leukocyte](http://purl.obolibrary.org/obo/CL_0000738) and ([has part](http://purl.obolibrary.org/obo/BFO_0000051) some [neutrophillic cytoplasm](http://purl.obolibrary.org/obo/CL_0017500)) and ([has part](http://purl.obolibrary.org/obo/BFO_0000051) some [obsolete increased nucleus size](http://purl.obolibrary.org/obo/CL_0017505)) and ([has part](http://purl.obolibrary.org/obo/BFO_0000051) some [heterochromatin](http://purl.obolibrary.org/obo/GO_0000792)) and ([bearer of](http://purl.obolibrary.org/obo/RO_0000053) some [mononucleate](http://purl.obolibrary.org/obo/PATO_0001407)) +- [otic capsule](http://purl.obolibrary.org/obo/UBERON_0004637) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: part_of otic and occipital (AAO:0000993)[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010143" -- [lymphocyte](http://purl.obolibrary.org/obo/CL_0000542) SubClassOf [has part](http://purl.obolibrary.org/obo/BFO_0000051) some [obsolete increased nucleus size](http://purl.obolibrary.org/obo/CL_0017505) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -#### Added -- [lymphocyte](http://purl.obolibrary.org/obo/CL_0000542) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -- [lymphocyte](http://purl.obolibrary.org/obo/CL_0000542) EquivalentTo [leukocyte](http://purl.obolibrary.org/obo/CL_0000738) and ([has part](http://purl.obolibrary.org/obo/BFO_0000051) some [neutrophillic cytoplasm](http://purl.obolibrary.org/obo/CL_0017500)) and ([has part](http://purl.obolibrary.org/obo/BFO_0000051) some [heterochromatin](http://purl.obolibrary.org/obo/GO_0000792)) and ([bearer of](http://purl.obolibrary.org/obo/RO_0000053) some [mononucleate](http://purl.obolibrary.org/obo/PATO_0001407)) and ([bearer of](http://purl.obolibrary.org/obo/RO_0000053) some [high nuclear/cytoplasmic ratio](http://purl.obolibrary.org/obo/PATO_0040072)) +- [otic capsule](http://purl.obolibrary.org/obo/UBERON_0004637) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Otic capsules develop around the parts of the ear that lie within the chondrocranium. This part of the ear, known as the inner ear, is composed of the semicircular ducts and associated sacs that contain the receptive cells for equilibrium and hearing (reference 1); (...) considerations have led to our rethinking issues related to the origin of several aspects of vertebrate hearing, and to the view that many basic auditory functions evolved very early in vertebrate history, and that the functions observed in more `advanced' vertebrates, such as birds and mammals, are frequently modifications of themes first encountered in fishes, and perhaps even more ancestral animals.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000854" -- [lymphocyte](http://purl.obolibrary.org/obo/CL_0000542) SubClassOf [bearer of](http://purl.obolibrary.org/obo/RO_0000053) some [high nuclear/cytoplasmic ratio](http://purl.obolibrary.org/obo/PATO_0040072) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.235, DOI:10.1016/S0378-5955(00)00168-4 Fay RR, Popper AN, Evolution of hearing in vertebrates: the inner ears and processing. Hearing research (2000)" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### lymphoid follicle `http://purl.obolibrary.org/obo/UBERON_0000444` -#### Removed -- [lymphoid follicle](http://purl.obolibrary.org/obo/UBERON_0000444) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://github.com/obophenotype/uberon/issues/7" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://github.com/obophenotype/uberon/issues/6" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [lymphoid follicle](http://purl.obolibrary.org/obo/UBERON_0000444) [see also](http://www.w3.org/2000/01/rdf-schema#seeAlso) "https://github.com/obophenotype/uberon/issues/6"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) +- [otic capsule](http://purl.obolibrary.org/obo/UBERON_0004637) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Skeletal elements surrounding the membranous labyrinth of the inner ear. Sensory capsules anterolateral to and confluent with occipital arch.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" -- [lymphoid follicle](http://purl.obolibrary.org/obo/UBERON_0000444) [see also](http://www.w3.org/2000/01/rdf-schema#seeAlso) "https://github.com/obophenotype/uberon/issues/7"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010143" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -### lymphoid lineage restricted progenitor cell `http://purl.obolibrary.org/obo/CL_0000838` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -#### Added -- [lymphoid lineage restricted progenitor cell](http://purl.obolibrary.org/obo/CL_0000838) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [otic capsule](http://purl.obolibrary.org/obo/UBERON_0004637) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The cartilage capsule surrounding the inner ear mechanism; in the embryos of higher vertebrates, it is cartilaginous at first but later becomes bony. [Biology_online][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000854" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### lymphoid system `http://purl.obolibrary.org/obo/UBERON_0002465` -#### Removed -- [lymphoid system](http://purl.obolibrary.org/obo/UBERON_0002465) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "systema lymphoideum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lymphoid_system" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" #### Added -- [lymphoid system](http://purl.obolibrary.org/obo/UBERON_0002465) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "systema lymphoideum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lymphoid_system" +- [otic capsule](http://purl.obolibrary.org/obo/UBERON_0004637) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:17596" + +- [otic capsule](http://purl.obolibrary.org/obo/UBERON_0004637) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### otic pit `http://purl.obolibrary.org/obo/UBERON_0006273` +#### Removed +- [otic pit](http://purl.obolibrary.org/obo/UBERON_0006273) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A depression appearing in each otic placode, marking the beginnning of embryonic development of the internal ear. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/Otic+pit" -### macroglial cell `http://purl.obolibrary.org/obo/CL_0000126` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [macroglial cell](http://purl.obolibrary.org/obo/CL_0000126) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001147" -### macromolecule metabolic process `http://purl.obolibrary.org/obo/GO_0043170` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [macromolecule metabolic process](http://purl.obolibrary.org/obo/GO_0043170) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/geneontology/go-ontology/issues/26424"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) -- [macromolecule metabolic process](http://purl.obolibrary.org/obo/GO_0043170) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [gocheck_do_not_annotate](http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate) +### otic placode `http://purl.obolibrary.org/obo/UBERON_0003069` +#### Removed +- [otic placode](http://purl.obolibrary.org/obo/UBERON_0003069) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Primordium of the ear epithelium before it hollows into the otic vesicle, present beside the hindbrain rudiment in the midsegmentation period. Kimmel et al, 1995. (Also see Anatomical Atlas entry for ear by T. Whitfield.)[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -### macrophage `http://purl.obolibrary.org/obo/CL_0000235` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000138" -#### Added -- [macrophage](http://purl.obolibrary.org/obo/CL_0000235) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -### macrophage dendritic cell progenitor `http://purl.obolibrary.org/obo/CL_0002009` +- [otic placode](http://purl.obolibrary.org/obo/UBERON_0003069) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "With the exception of the pigment cells of the stria vascularis and the secretory epithelium of the cochlea, which are of neural crest origin, all compo- nents of the inner ear derive from the otic placode. In most species the thickening of the ectoderm into a placode occurs in a region adjacent to rhombomere 5 (reviewed in Ohyama et al., 2007), while in amphibians the otic placode is centered onto rhombomere 4 (Ruiz i Altaba and Jessell, 1991)." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "NCBIBook:NBK53175" -#### Added -- [macrophage dendritic cell progenitor](http://purl.obolibrary.org/obo/CL_0002009) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [otic placode](http://purl.obolibrary.org/obo/UBERON_0003069) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (2) neurogenic placodes (...).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### macula `http://purl.obolibrary.org/obo/UBERON_0000054` -#### Removed -- [macula](http://purl.obolibrary.org/obo/UBERON_0000054) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000235" -- [macula](http://purl.obolibrary.org/obo/UBERON_0000054) [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [Homo sapiens](http://purl.obolibrary.org/obo/NCBITaxon_9606) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" +- [otic placode](http://purl.obolibrary.org/obo/UBERON_0003069) SubClassOf [dorsolateral placode](http://purl.obolibrary.org/obo/UBERON_0003067) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "invaginates" -### macula densa epithelial cell `http://purl.obolibrary.org/obo/CL_1000850` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "NCBIBook:NBK53175" #### Added -- [macula densa epithelial cell](http://purl.obolibrary.org/obo/CL_1000850) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [otic placode](http://purl.obolibrary.org/obo/UBERON_0003069) SubClassOf [dorsolateral placode](http://purl.obolibrary.org/obo/UBERON_0003067) -### macula of saccule of membranous labyrinth `http://purl.obolibrary.org/obo/UBERON_0002212` +### otic region `http://purl.obolibrary.org/obo/UBERON_0003110` #### Removed -- [macula of saccule of membranous labyrinth](http://purl.obolibrary.org/obo/UBERON_0002212) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "macula sacculi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:74944" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [otic region](http://purl.obolibrary.org/obo/UBERON_0003110) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical cluster that is a posterolateral part of the cranium and structurally supports the vestibuloauditory system.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TAO:MAH" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -- [macula of saccule of membranous labyrinth](http://purl.obolibrary.org/obo/UBERON_0002212) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "macula sacculi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Macula_of_saccule" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000189" -#### Added -- [macula of saccule of membranous labyrinth](http://purl.obolibrary.org/obo/UBERON_0002212) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "macula sacculi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [otic region](http://purl.obolibrary.org/obo/UBERON_0003110) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: overlaps hyomandibular-otic region joint (TAO:0001947)[TAO]" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:74944" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000189" -- [macula of saccule of membranous labyrinth](http://purl.obolibrary.org/obo/UBERON_0002212) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "macula sacculi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [otic region](http://purl.obolibrary.org/obo/UBERON_0003110) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "UBERONREF:0000007 has this as a syn for otic capsule" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Macula_of_saccule" +- [otic region](http://purl.obolibrary.org/obo/UBERON_0003110) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical cluster that is a posterolateral part of the neurocranium and structurally supports the vestibuloauditory system.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -### macula of utricle of membranous labyrinth `http://purl.obolibrary.org/obo/UBERON_0002214` -#### Removed -- [macula of utricle of membranous labyrinth](http://purl.obolibrary.org/obo/UBERON_0002214) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "macula utriculi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:74960" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010208" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [macula of utricle of membranous labyrinth](http://purl.obolibrary.org/obo/UBERON_0002214) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "macula utriculi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Macula_of_utricle" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### otolith organ `http://purl.obolibrary.org/obo/UBERON_0002518` +#### Removed +- [otolith organ](http://purl.obolibrary.org/obo/UBERON_0002518) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In fishes, as in other vertebrates, the vestibular end-organs are divided into a gravity receptor system, with three subdivisions and an angular acceleration receptor system. The gravity receptor system on each side consists of utricular, saccular, and lagenar maculae, each covered by an otolith (reference 1); (...)considerations have led to our rethinking issues related to the origin of several aspects of vertebrate hearing, and to the view that many basic auditory functions evolved very early in vertebrate history, and that the functions observed in more `advanced' vertebrates, such as birds and mammals, are frequently modifications of themes first encountered in fishes, and perhaps even more ancestral animals (reference 2).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [macula of utricle of membranous labyrinth](http://purl.obolibrary.org/obo/UBERON_0002214) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "macula utriculi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:74960" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001676" -- [macula of utricle of membranous labyrinth](http://purl.obolibrary.org/obo/UBERON_0002214) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "macula utriculi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:11581521 Moorman SJ, Development of sensory systems in zebrafish (Danio rerio). ILAR Journal (2001), DOI:10.1016/S0378-5955(00)00168-4 Fay RR, Popper AN, Evolution of hearing in vertebrates: the inner ears and processing. Hearing research (2000)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Macula_of_utricle" +#### Added +- [otolith organ](http://purl.obolibrary.org/obo/UBERON_0002518) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### magnocellular layer of dorsal nucleus of lateral geniculate body `http://purl.obolibrary.org/obo/UBERON_0013606` +### otolymph `http://purl.obolibrary.org/obo/UBERON_0006586` #### Removed -- [magnocellular layer of dorsal nucleus of lateral geniculate body](http://purl.obolibrary.org/obo/UBERON_0013606) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "strata magnocellularia nuclei dorsalis corporis geniculati lateralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:76989" +- [otolymph](http://purl.obolibrary.org/obo/UBERON_0006586) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Fluids found within the osseous labyrinth (PERILYMPH) and the membranous labyrinth (ENDOLYMPH) of the inner ear. (From Gray's Anatomy, 30th American ed, p1328, 1332[MESH:A12.207.571])" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "MESH:A12.207.571" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [magnocellular layer of dorsal nucleus of lateral geniculate body](http://purl.obolibrary.org/obo/UBERON_0013606) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "strata magnocellularia nuclei dorsalis corporis geniculati lateralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:76989" +### out of scope `http://purl.obolibrary.org/obo/OMO_0001000` +#### Removed +- [out of scope](http://purl.obolibrary.org/obo/OMO_0001000) [IAO_0000234](http://purl.obolibrary.org/obo/IAO_0000234) "https://orcid.org/0000-0001-5208-3432" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [out of scope](http://purl.obolibrary.org/obo/OMO_0001000) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0001-5208-3432](http://orcid.org/0000-0001-5208-3432) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### male accessory sex gland `http://purl.obolibrary.org/obo/UBERON_0010147` +### outer epithelial layer of tympanic membrane `http://purl.obolibrary.org/obo/UBERON_0010069` #### Added -- [male accessory sex gland](http://purl.obolibrary.org/obo/UBERON_0010147) [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [Homo sapiens](http://purl.obolibrary.org/obo/NCBITaxon_9606) +- [outer epithelial layer of tympanic membrane](http://purl.obolibrary.org/obo/UBERON_0010069) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) -- [male accessory sex gland](http://purl.obolibrary.org/obo/UBERON_0010147) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas) +- [outer epithelial layer of tympanic membrane](http://purl.obolibrary.org/obo/UBERON_0010069) SubClassOf [endo-epithelium](http://purl.obolibrary.org/obo/UBERON_0005911) -### male germ cell `http://purl.obolibrary.org/obo/CL_0000015` - -#### Added -- [male germ cell](http://purl.obolibrary.org/obo/CL_0000015) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) - - -### male organism `http://purl.obolibrary.org/obo/UBERON_0003101` +### outer epithelium `http://purl.obolibrary.org/obo/UBERON_0007376` #### Removed -- [male organism](http://purl.obolibrary.org/obo/UBERON_0003101) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007004" - -#### Added -- [male organism](http://purl.obolibrary.org/obo/UBERON_0003101) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007004" +- [outer epithelium](http://purl.obolibrary.org/obo/UBERON_0007376) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004993" - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - -### male reproductive system `http://purl.obolibrary.org/obo/UBERON_0000079` -#### Removed -- [male reproductive system](http://purl.obolibrary.org/obo/UBERON_0000079) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004927" +- [outer epithelium](http://purl.obolibrary.org/obo/UBERON_0007376) SubClassOf [epithelium](http://purl.obolibrary.org/obo/UBERON_0000483) #### Added -- [male reproductive system](http://purl.obolibrary.org/obo/UBERON_0000079) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas) - -- [male reproductive system](http://purl.obolibrary.org/obo/UBERON_0000079) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004927" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [outer epithelium](http://purl.obolibrary.org/obo/UBERON_0007376) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) -- [male reproductive system](http://purl.obolibrary.org/obo/UBERON_0000079) [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [Homo sapiens](http://purl.obolibrary.org/obo/NCBITaxon_9606) - -### male urethral gland `http://purl.obolibrary.org/obo/UBERON_0010186` +### outer medulla vasa recta ascending limb `http://purl.obolibrary.org/obo/UBERON_0009093` #### Removed -- [male urethral gland](http://purl.obolibrary.org/obo/UBERON_0010186) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "glandulae urethrales urethrae masculinae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Urethral_gland" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [outer medulla vasa recta ascending limb](http://purl.obolibrary.org/obo/UBERON_0009093) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta in the outer medulla parallel to the ascending limb" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "CL" #### Added -- [male urethral gland](http://purl.obolibrary.org/obo/UBERON_0010186) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "glandulae urethrales urethrae masculinae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Urethral_gland" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [outer medulla vasa recta ascending limb](http://purl.obolibrary.org/obo/UBERON_0009093) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### male urethral meatus `http://purl.obolibrary.org/obo/UBERON_0012241` +### outer medulla vasa recta descending limb `http://purl.obolibrary.org/obo/UBERON_0009090` #### Removed -- [male urethral meatus](http://purl.obolibrary.org/obo/UBERON_0012241) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ostium urethrae externum (urethra masculina)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [outer medulla vasa recta descending limb](http://purl.obolibrary.org/obo/UBERON_0009090) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta in the outer medullar parallel to the descending limb" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "CL" #### Added -- [male urethral meatus](http://purl.obolibrary.org/obo/UBERON_0012241) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ostium urethrae externum (urethra masculina)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [outer medulla vasa recta descending limb](http://purl.obolibrary.org/obo/UBERON_0009090) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### outer nuclear layer of retina `http://purl.obolibrary.org/obo/UBERON_0001789` +#### Removed +- [outer nuclear layer of retina](http://purl.obolibrary.org/obo/UBERON_0001789) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001170" -### malignant cell `http://purl.obolibrary.org/obo/CL_0001064` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429" -#### Added -- [malignant cell](http://purl.obolibrary.org/obo/CL_0001064) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### mammary duct `http://purl.obolibrary.org/obo/UBERON_0001765` -#### Removed -- [mammary duct](http://purl.obolibrary.org/obo/UBERON_0001765) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ductus lactiferi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0002845" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lactiferous_duct" +- [outer nuclear layer of retina](http://purl.obolibrary.org/obo/UBERON_0001789) SubClassOf [overlaps](http://purl.obolibrary.org/obo/RO_0002131) some [eye photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000287) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "soma" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFA" #### Added -- [mammary duct](http://purl.obolibrary.org/obo/UBERON_0001765) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ductus lactiferi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [outer nuclear layer of retina](http://purl.obolibrary.org/obo/UBERON_0001789) SubClassOf [overlaps](http://purl.obolibrary.org/obo/RO_0002131) some [eye photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000287) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0002845" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lactiferous_duct" - - -### mammary gland `http://purl.obolibrary.org/obo/UBERON_0001911` +### outer plexiform layer of retina `http://purl.obolibrary.org/obo/UBERON_0001790` #### Removed -- [mammary gland](http://purl.obolibrary.org/obo/UBERON_0001911) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "glandula mammaria" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Mammary_gland" +- [outer plexiform layer of retina](http://purl.obolibrary.org/obo/UBERON_0001790) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The layer within the retina where the bipolar cells synapse with the photoreceptor cells.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001330" -- [mammary gland](http://purl.obolibrary.org/obo/UBERON_0001911) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "glandula mammaria" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:57983" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [outer plexiform layer of retina](http://purl.obolibrary.org/obo/UBERON_0001790) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429" -#### Added -- [mammary gland](http://purl.obolibrary.org/obo/UBERON_0001911) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "glandula mammaria" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001171" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:57983" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [mammary gland](http://purl.obolibrary.org/obo/UBERON_0001911) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "glandula mammaria" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Mammary_gland" -### mammary gland epithelial cell `http://purl.obolibrary.org/obo/CL_0002327` +### outflow tract `http://purl.obolibrary.org/obo/UBERON_0004145` +#### Removed +- [outflow tract](http://purl.obolibrary.org/obo/UBERON_0004145) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Depending on the species, attached at the cardiac outflow are described the conus arteriosus, the truncus arteriosus and, or the bulbus arteriosus. At the distal limit of these outflow structures, but lying outside the pericardial cavity, is the ventral aorta[PMID:20735616]" #### Added -- [mammary gland epithelial cell](http://purl.obolibrary.org/obo/CL_0002327) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [outflow tract](http://purl.obolibrary.org/obo/UBERON_0004145) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### mammillary body `http://purl.obolibrary.org/obo/UBERON_0002206` +### outflow tract endothelium `http://purl.obolibrary.org/obo/UBERON_0004699` #### Removed -- [mammillary body](http://purl.obolibrary.org/obo/UBERON_0002206) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "corpus mammillare" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:412" +- [outflow tract endothelium](http://purl.obolibrary.org/obo/UBERON_0004699) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "It is assumed that during evolution, a circulatory system composed of the heart and endothelial tubular system first formed in vertebrates, medial smooth muscle then appeared for regulation of the system, and innervation of the muscle tissue took place. This sequence of development assumed for phylogenesis is actually realized in the ontogenetic processes.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1254/jjp.87.253 Shigei T, Tsuru H, Ishikawa N, Yoshioka K, Absence of endothelium in invertebrate blood vessels: significance of endothelium and sympathetic nerve/medial smooth muscle in the vertebrate vascular system. Japanese Journal of Pharmacology (2001)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [mammillary body](http://purl.obolibrary.org/obo/UBERON_0002206) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "corpora mamillaria" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:412" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [mammillary body](http://purl.obolibrary.org/obo/UBERON_0002206) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "corpus mamillaris" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:412" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001524" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [mammillary body](http://purl.obolibrary.org/obo/UBERON_0002206) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "corpus mamillare" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Mammillary_body" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### outflow tract myocardium `http://purl.obolibrary.org/obo/UBERON_0004265` +#### Removed +- [outflow tract myocardium](http://purl.obolibrary.org/obo/UBERON_0004265) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) (theme) is how the vertebrate cardiovascular system differs from that of the presumptive evolutionary chordate ancestor. (...) At best we can tell there are two essential new ingredients: (1) vertebrates all have a continuous endothelial lining to the heart and vessels and (2) vertebrates have developed a second chamber in the heart, one designed for generating high systemic blood pressure.[uncertain][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:9187138 Fishman MC, Chien KR, Fashioning the vertebrate heart: earliest embryonic decisions. Development (1997)" -- [mammillary body](http://purl.obolibrary.org/obo/UBERON_0002206) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "corpora mammillaria" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:412" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000603" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [mammillary body](http://purl.obolibrary.org/obo/UBERON_0002206) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "corpus mammillare" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:412" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [mammillary body](http://purl.obolibrary.org/obo/UBERON_0002206) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "corpus mamillare" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Mammillary_body" -- [mammillary body](http://purl.obolibrary.org/obo/UBERON_0002206) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "corpora mamillaria" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### outflow tract pericardium `http://purl.obolibrary.org/obo/UBERON_0004271` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:412" +#### Added +- [outflow tract pericardium](http://purl.obolibrary.org/obo/UBERON_0004271) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -- [mammillary body](http://purl.obolibrary.org/obo/UBERON_0002206) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "corpora mammillaria" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:412" +### output of `http://purl.obolibrary.org/obo/RO_0002353` +#### Removed +- [output of](http://purl.obolibrary.org/obo/RO_0002353) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) -- [mammillary body](http://purl.obolibrary.org/obo/UBERON_0002206) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "corpus mamillaris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [output of](http://purl.obolibrary.org/obo/RO_0002353) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:412" -### mandibular nerve `http://purl.obolibrary.org/obo/UBERON_0000375` +### ovarian artery `http://purl.obolibrary.org/obo/UBERON_0001190` #### Removed -- [mandibular nerve](http://purl.obolibrary.org/obo/UBERON_0000375) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus mandibularis [v3]" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [ovarian artery](http://purl.obolibrary.org/obo/UBERON_0001190) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "In human anatomy, the ovarian artery is a blood vessel that supplies oxygenated blood to the ovary. It arises from the abdominal aorta below the renal artery, and does not pass out of the abdomiproperty_value external_definitioncavity. It can be found in the suspensory ligament of the ovary. [WP]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Ovarian_artery" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:52996" -- [mandibular nerve](http://purl.obolibrary.org/obo/UBERON_0000375) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus mandibularis [vc]" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### ovarian follicle `http://purl.obolibrary.org/obo/UBERON_0001305` +#### Removed +- [ovarian follicle](http://purl.obolibrary.org/obo/UBERON_0001305) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "The somatic cell component of the follicle produces hormones important for oocyte development and proper endocrine function" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:52996" +- [ovarian follicle](http://purl.obolibrary.org/obo/UBERON_0001305) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [mandibular nerve](http://purl.obolibrary.org/obo/UBERON_0000375) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "n. mandibularis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Mandibular_nerve" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [mandibular nerve](http://purl.obolibrary.org/obo/UBERON_0000375) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "n. mandibularis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T, Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Mandibular_nerve" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001536" -- [mandibular nerve](http://purl.obolibrary.org/obo/UBERON_0000375) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus mandibularis [v3]" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [ovarian follicle](http://purl.obolibrary.org/obo/UBERON_0001305) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Oocyte development of zebrafish has been divided into five stages based on morphological criteria and on physiological and biochemical events. Stage I follicles (less than 140 microns) are primary growth stage, stage II follicles (140-340 microns) are cortical alveolus stage, stage III (340-690 microns) are vitellogenesis, stage IV (690-730 microns) are oocyte maturation, and stage V follicles are matured egg. Selman et al, 1993.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:52996" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -- [mandibular nerve](http://purl.obolibrary.org/obo/UBERON_0000375) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus mandibularis [vc]" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001110" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [ovarian follicle](http://purl.obolibrary.org/obo/UBERON_0001305) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "These structures are periodically initiated to grow and develop, culminating in ovulation of usually a single competent oocyte in humans. These eggs/ova are only developed once every menstrual cycle (e.g. once a month in humans)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:52996" -### mandibular prominence `http://purl.obolibrary.org/obo/UBERON_0005867` +### ovarian medulla `http://purl.obolibrary.org/obo/UBERON_0013192` #### Removed -- [mandibular prominence](http://purl.obolibrary.org/obo/UBERON_0005867) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "prominentia mandibularis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Mandibular_prominence" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - -#### Added -- [mandibular prominence](http://purl.obolibrary.org/obo/UBERON_0005867) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "prominentia mandibularis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [ovarian medulla](http://purl.obolibrary.org/obo/UBERON_0013192) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "composed of loose connective tissue that contains blood vessels, lymph vessels and nerves" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "NCIT" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Mandibular_prominence" -### mandibular symphysis `http://purl.obolibrary.org/obo/UBERON_0006606` +### ovary `http://purl.obolibrary.org/obo/UBERON_0000992` #### Removed -- [mandibular symphysis](http://purl.obolibrary.org/obo/UBERON_0006606) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "symphysis mandibulae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Symphysis_menti" +- [ovary](http://purl.obolibrary.org/obo/UBERON_0000992) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "ovarian" + +- [ovary](http://purl.obolibrary.org/obo/UBERON_0000992) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Female reproductive organ.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000403" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -#### Added -- [mandibular symphysis](http://purl.obolibrary.org/obo/UBERON_0006606) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "symphysis mandibulae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Symphysis_menti" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" +- [ovary](http://purl.obolibrary.org/obo/UBERON_0000992) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004865" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### manus joint `http://purl.obolibrary.org/obo/UBERON_0001489` -#### Removed -- [manus joint](http://purl.obolibrary.org/obo/UBERON_0001489) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "articulationes manus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71345" +- [ovary](http://purl.obolibrary.org/obo/UBERON_0000992) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Either of paired female reproductive organs involved in production of ova and female sex hormones.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000371" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -#### Added -- [manus joint](http://purl.obolibrary.org/obo/UBERON_0001489) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "articulationes manus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71345" +- [ovary](http://purl.obolibrary.org/obo/UBERON_0000992) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Ovaries of some kind are found in the female reproductive system of many animals that employ sexual reproduction, including invertebrates. However, they develop in a very different way in most invertebrates than they do in vertebrates, and are not truly homologous. Many of the features found in human ovaries are common to all vertebrates, including the presence of follicular cells, tunica albuginea, and so on. However, many species produce a far greater number of eggs during their lifetime than do humans, so that, in fish and amphibians, there may be hundreds, or even millions of fertile eggs present in the ovary at any given time. In these species, fresh eggs may be developing from the germinal epithelium throughout life. Corpora lutea are found only in mammals, and in some elasmobranch fish; in other species, the remnants of the follicle are quickly resorbed by the ovary. In birds, reptiles, and monotremes, the egg is relatively large, filling the follicle, and distorting the shape of the ovary at maturity. Amphibians and reptiles have no ovarian medulla; the central part of the ovary is a hollow, lymph-filled space. The ovary of teleosts is also often hollow, but in this case, the eggs are shed into the cavity, which opens into the oviduct. Although most normal female vertebrates have two ovaries, this is not the case in all species. In birds and platypuses, the right ovary never matures, so that only the left is functional. In some elasmobranchs, the reverse is true, with only the right ovary fully developing. In the primitive jawless fish, and some teleosts, there is only one ovary, formed by the fusion of the paired organs in the embryo" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [ovary](http://purl.obolibrary.org/obo/UBERON_0000992) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### mapping_justification `https://w3id.org/sssom/mapping_justification` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- AnnotationProperty: [mapping_justification](https://w3id.org/sssom/mapping_justification) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000251" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1093/icb/icm052 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across the Bilateria. Integrative and Comparative Biology (2007), DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T and Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)" -### mapping_provider `https://w3id.org/sssom/mapping_provider` -#### Added -- AnnotationProperty: [mapping_provider](https://w3id.org/sssom/mapping_provider) +### overlaps `http://purl.obolibrary.org/obo/RO_0002131` +#### Removed +- [overlaps](http://purl.obolibrary.org/obo/RO_0002131) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) -### mast cell `http://purl.obolibrary.org/obo/CL_0000097` +- [overlaps](http://purl.obolibrary.org/obo/RO_0002131) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" -#### Added -- [mast cell](http://purl.obolibrary.org/obo/CL_0000097) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [overlaps](http://purl.obolibrary.org/obo/RO_0002131) [RO_0001900](http://purl.obolibrary.org/obo/RO_0001900) [RO_0001901](http://purl.obolibrary.org/obo/RO_0001901) +- [has part](http://purl.obolibrary.org/obo/BFO_0000051) o [part_of](http://purl.obolibrary.org/obo/BFO_0000050) SubPropertyOf: [overlaps](http://purl.obolibrary.org/obo/RO_0002131) + - [is a defining property chain axiom where second argument is reflexive](http://purl.obolibrary.org/obo/RO_0002582) true -### material anatomical entity `http://purl.obolibrary.org/obo/UBERON_0000465` -#### Removed -- [material anatomical entity](http://purl.obolibrary.org/obo/UBERON_0000465) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007016" -#### Added -- [material anatomical entity](http://purl.obolibrary.org/obo/UBERON_0000465) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007016" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +### oviduct `http://purl.obolibrary.org/obo/UBERON_0000993` +#### Removed +- [oviduct](http://purl.obolibrary.org/obo/UBERON_0000993) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "sometimes oviduct is used interchangeably with follaopian tube. Here they are different - the oviduct connects the gonad to the outside in a variety of animals. The mammal-class fallopian tube is derived from the mullerian duct and connects the gonads/infubdibulum to the uterus" -### mature B cell `http://purl.obolibrary.org/obo/CL_0000785` +- [oviduct](http://purl.obolibrary.org/obo/UBERON_0000993) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In all remaining vertebrates (i.e., coelacanths, lungfishes, amphibians, reptiles, birds, and mammals), the oviduct arises in ontogeny as a longitudinal, groovelike invagination of the coelomic epithelium on the lateral surface of the mesonephros.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.687-688" -#### Added -- [mature B cell](http://purl.obolibrary.org/obo/CL_0000785) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### mature NK T cell `http://purl.obolibrary.org/obo/CL_0000814` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [mature NK T cell](http://purl.obolibrary.org/obo/CL_0000814) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001136" +- [oviduct](http://purl.obolibrary.org/obo/UBERON_0000993) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "in birds divided into infundibulum, magnum, isthmus, uterus, and vagina" -### mature T cell `http://purl.obolibrary.org/obo/CL_0002419` +- [oviduct](http://purl.obolibrary.org/obo/UBERON_0000993) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A passage through which ova leave the maternal body or pass to an organ communicating with the exterior of the body. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [mature T cell](http://purl.obolibrary.org/obo/CL_0002419) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### mature alpha-beta T cell `http://purl.obolibrary.org/obo/CL_0000791` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001136" -#### Added -- [mature alpha-beta T cell](http://purl.obolibrary.org/obo/CL_0000791) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/oviduct" +- [oviduct](http://purl.obolibrary.org/obo/UBERON_0000993) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The only female vertebrates to lack oviducts are the jawless fishes. In these species, the single fused ovary releases eggs directly into the body cavity. The fish eventually extrudes the eggs through small genital pores towards the rear of the body[WP]" -### mature astrocyte `http://purl.obolibrary.org/obo/CL_0002627` -#### Added -- [mature astrocyte](http://purl.obolibrary.org/obo/CL_0002627) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### oviduct epithelium `http://purl.obolibrary.org/obo/UBERON_0004804` +#### Removed +- [oviduct epithelium](http://purl.obolibrary.org/obo/UBERON_0004804) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in FMA, epithelium of uterine tube is a subclass of ciliated columnar epithelium. MA introduces subtypes: ciliated columnar and cuboidal. We map the FMA type according to its relationships, not its label" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" -### mature conventional dendritic cell `http://purl.obolibrary.org/obo/CL_0000841` +- [oviduct epithelium](http://purl.obolibrary.org/obo/UBERON_0004804) SubClassOf [epithelium](http://purl.obolibrary.org/obo/UBERON_0000483) #### Added -- [mature conventional dendritic cell](http://purl.obolibrary.org/obo/CL_0000841) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [oviduct epithelium](http://purl.obolibrary.org/obo/UBERON_0004804) SubClassOf [meso-epithelium](http://purl.obolibrary.org/obo/UBERON_0012275) -### mature gamma-delta T cell `http://purl.obolibrary.org/obo/CL_0000800` +### oviduct smooth muscle `http://purl.obolibrary.org/obo/UBERON_0004245` +#### Removed +- [oviduct smooth muscle](http://purl.obolibrary.org/obo/UBERON_0004245) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:29046" -#### Added -- [mature gamma-delta T cell](http://purl.obolibrary.org/obo/CL_0000800) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### mature microglial cell `http://purl.obolibrary.org/obo/CL_0002629` +### oxytocin receptor `http://purl.obolibrary.org/obo/PR_000001635` +#### Removed +- [oxytocin receptor](http://purl.obolibrary.org/obo/PR_000001635) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [oxytocin receptor (human)](http://purl.obolibrary.org/obo/PR_P30559) -#### Added -- [mature microglial cell](http://purl.obolibrary.org/obo/CL_0002629) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### maxillary artery `http://purl.obolibrary.org/obo/UBERON_0001616` +### pair of dorsal aortae `http://purl.obolibrary.org/obo/UBERON_0010190` #### Removed -- [maxillary artery](http://purl.obolibrary.org/obo/UBERON_0001616) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria maxillaris" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Maxillary_artery" +- [pair of dorsal aortae](http://purl.obolibrary.org/obo/UBERON_0010190) [label](http://www.w3.org/2000/01/rdf-schema#label) "pair of dorsal aortae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [pair of dorsal aortae](http://purl.obolibrary.org/obo/UBERON_0010190) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MA:0000476" -#### Added -- [maxillary artery](http://purl.obolibrary.org/obo/UBERON_0001616) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria maxillaris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [pair of dorsal aortae](http://purl.obolibrary.org/obo/UBERON_0010190) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "The paired arterial structures of the embryo that supplies each developing somite via efferent segmental arteries; the dorsal aortae articulate with the umbilical arteries, which return mixed blood to the villi of the chorion for reoxygenation." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MP:0004787" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Maxillary_artery" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0-914294-08-3" +- [pair of dorsal aortae](http://purl.obolibrary.org/obo/UBERON_0010190) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EHDAA2:0000410" -### maxillary nerve `http://purl.obolibrary.org/obo/UBERON_0000377` -#### Removed -- [maxillary nerve](http://purl.obolibrary.org/obo/UBERON_0000377) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus maxillaris [v2]" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [pair of dorsal aortae](http://purl.obolibrary.org/obo/UBERON_0010190) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:18606" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [pair of dorsal aortae](http://purl.obolibrary.org/obo/UBERON_0010190) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "paired dorsal aortae" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EHDAA2:0000410" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:52724" +- [pair of dorsal aortae](http://purl.obolibrary.org/obo/UBERON_0010190) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" -- [maxillary nerve](http://purl.obolibrary.org/obo/UBERON_0000377) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus maxillaris [vb]" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [pair of dorsal aortae](http://purl.obolibrary.org/obo/UBERON_0010190) [id](http://www.geneontology.org/formats/oboInOwl#id) "UBERON:0010190" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [pair of dorsal aortae](http://purl.obolibrary.org/obo/UBERON_0010190) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [pheno_slim](http://purl.obolibrary.org/obo/uberon/core#pheno_slim) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:52724" +- Class: [pair of dorsal aortae](http://purl.obolibrary.org/obo/UBERON_0010190) -- [maxillary nerve](http://purl.obolibrary.org/obo/UBERON_0000377) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "n. maxillaris" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Maxillary_nerve" +- [pair of dorsal aortae](http://purl.obolibrary.org/obo/UBERON_0010190) SubClassOf [multi-tissue structure](http://purl.obolibrary.org/obo/UBERON_0000481) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "EHDAA2" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [pair of dorsal aortae](http://purl.obolibrary.org/obo/UBERON_0010190) SubClassOf [protein-containing material entity](http://purl.obolibrary.org/obo/PR_000050567) -#### Added -- [maxillary nerve](http://purl.obolibrary.org/obo/UBERON_0000377) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus maxillaris [vb]" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [pair of dorsal aortae](http://purl.obolibrary.org/obo/UBERON_0010190) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [aortic system](http://purl.obolibrary.org/obo/UBERON_0010191) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "EHDAA2" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [pair of dorsal aortae](http://purl.obolibrary.org/obo/UBERON_0010190) SubClassOf [has part](http://purl.obolibrary.org/obo/BFO_0000051) some [dorsal aorta](http://purl.obolibrary.org/obo/UBERON_0005805) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:52724" -- [maxillary nerve](http://purl.obolibrary.org/obo/UBERON_0000377) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus maxillaris [v2]" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### pair of nares `http://purl.obolibrary.org/obo/UBERON_0002109` +#### Removed +- [pair of nares](http://purl.obolibrary.org/obo/UBERON_0002109) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "this is a 'set of anatomical planes' in FMA" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:52724" -- [maxillary nerve](http://purl.obolibrary.org/obo/UBERON_0000377) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "n. maxillaris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Maxillary_nerve" +### paired box protein PAX-5 `http://purl.obolibrary.org/obo/PR_000001903` +#### Removed +- [paired box protein PAX-5](http://purl.obolibrary.org/obo/PR_000001903) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [paired box protein Pax-5 (human)](http://purl.obolibrary.org/obo/PR_Q02548) + -### maxillary prominence `http://purl.obolibrary.org/obo/UBERON_0005868` +### paired limb/fin `http://purl.obolibrary.org/obo/UBERON_0004708` #### Removed -- [maxillary prominence](http://purl.obolibrary.org/obo/UBERON_0005868) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "prominentia maxilaris" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Maxillary_prominence" +- [paired limb/fin](http://purl.obolibrary.org/obo/UBERON_0004708) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "this class is the union of the classes limb, pectoral fin and pelvic fin." - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [paired limb/fin](http://purl.obolibrary.org/obo/UBERON_0004708) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [paired limb/fin bud](http://purl.obolibrary.org/obo/UBERON_0004357) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" #### Added -- [maxillary prominence](http://purl.obolibrary.org/obo/UBERON_0005868) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "prominentia maxilaris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [paired limb/fin](http://purl.obolibrary.org/obo/UBERON_0004708) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [paired limb/fin bud](http://purl.obolibrary.org/obo/UBERON_0004357) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Maxillary_prominence" - -### medial border of scapula `http://purl.obolibrary.org/obo/UBERON_0007174` +### paired limb/fin bud `http://purl.obolibrary.org/obo/UBERON_0004357` #### Removed -- [medial border of scapula](http://purl.obolibrary.org/obo/UBERON_0007174) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "margo medialis scapulae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:23242" +- [paired limb/fin bud](http://purl.obolibrary.org/obo/UBERON_0004357) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The tetrapod limb is derived from a posterior part of the fin endoskeleton of elasmobranchs and basal bony fish, the so-called metapterygium, a series of endoskeletal elements that is the first to form in the developing paired fins. (...) In addition, there is an independent endoskeletal element called the protopterygium that develops anterior to the metapterygium in many basal fishes (e.g., the bichir and sturgeon). Teleosts have lost the metapterygium whereas the sarcopterygians, on the other hand, have lost the protopterygium. Sarcopterygians thus develop all their endoskeletal structures from the metapterygium and consequently the tetrapod limb skeleton is derived from the metapterygium.[uncertain][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1002/jez.1100 Wagner GP, Chiu C, The tetrapod limb: A hypothesis on its origin. J Exp Zool (Mol Dev Evol) (2001)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [medial border of scapula](http://purl.obolibrary.org/obo/UBERON_0007174) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "margo medialis scapulae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:23242" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001258" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### medial circumflex femoral artery `http://purl.obolibrary.org/obo/UBERON_0001356` +### paired limb/fin cartilage `http://purl.obolibrary.org/obo/UBERON_0007389` #### Removed -- [medial circumflex femoral artery](http://purl.obolibrary.org/obo/UBERON_0001356) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria circumflexa femoris medialis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Medial_circumflex_femoral_artery" +- [paired limb/fin cartilage](http://purl.obolibrary.org/obo/UBERON_0007389) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Cartilage which is part of one of the paired fins.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001543" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -#### Added -- [medial circumflex femoral artery](http://purl.obolibrary.org/obo/UBERON_0001356) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria circumflexa femoris medialis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Medial_circumflex_femoral_artery" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### medial ganglionic eminence `http://purl.obolibrary.org/obo/UBERON_0004024` +### paired limb/fin field `http://purl.obolibrary.org/obo/UBERON_0005732` #### Added -- [medial ganglionic eminence](http://purl.obolibrary.org/obo/UBERON_0004024) DisjointWith [lateral ganglionic eminence](http://purl.obolibrary.org/obo/UBERON_0004025) - - [source](http://www.geneontology.org/formats/oboInOwl#source) "lexical" +- [paired limb/fin field](http://purl.obolibrary.org/obo/UBERON_0005732) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### medial ligament of ankle joint `http://purl.obolibrary.org/obo/UBERON_0011972` +### paired limb/fin skeleton `http://purl.obolibrary.org/obo/UBERON_0011582` #### Removed -- [medial ligament of ankle joint](http://purl.obolibrary.org/obo/UBERON_0011972) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ligamentum collaterale mediale articulationis talocruralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:44055" +- [paired limb/fin skeleton](http://purl.obolibrary.org/obo/UBERON_0011582) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Skeletal subdivision that is part of the paired limb/fin.[VSAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000301" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -#### Added -- [medial ligament of ankle joint](http://purl.obolibrary.org/obo/UBERON_0011972) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ligamentum collaterale mediale articulationis talocruralis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:44055" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### paired venous dural sinus `http://purl.obolibrary.org/obo/UBERON_0017635` -### medial marginal vein `http://purl.obolibrary.org/obo/UBERON_0001550` +#### Added +- [paired venous dural sinus](http://purl.obolibrary.org/obo/UBERON_0017635) SubClassOf [head blood vessel](http://purl.obolibrary.org/obo/UBERON_0003496) + + +### palate bone `http://purl.obolibrary.org/obo/UBERON_0012071` #### Removed -- [medial marginal vein](http://purl.obolibrary.org/obo/UBERON_0001550) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vena marginalis medialis pedis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:44420" +- [palate bone](http://purl.obolibrary.org/obo/UBERON_0012071) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "this is distinct (but not disjoint) from palatine bone" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [medial marginal vein](http://purl.obolibrary.org/obo/UBERON_0001550) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vena marginalis medialis pedis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### palatoquadrate arch `http://purl.obolibrary.org/obo/UBERON_0011085` +#### Removed +- [palatoquadrate arch](http://purl.obolibrary.org/obo/UBERON_0011085) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "VHOG:0000511" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:44420" +- [palatoquadrate arch](http://purl.obolibrary.org/obo/UBERON_0011085) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### medial nasal prominence `http://purl.obolibrary.org/obo/UBERON_0004068` -#### Removed -- [medial nasal prominence](http://purl.obolibrary.org/obo/UBERON_0004068) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "prominentia nasalis medialis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Medial_nasal_prominence" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000511" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)" #### Added -- [medial nasal prominence](http://purl.obolibrary.org/obo/UBERON_0004068) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "prominentia nasalis medialis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Medial_nasal_prominence" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [palatoquadrate arch](http://purl.obolibrary.org/obo/UBERON_0011085) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) -### medial zone of hypothalamus `http://purl.obolibrary.org/obo/UBERON_0002272` +### pallium `http://purl.obolibrary.org/obo/UBERON_0000203` #### Removed -- [medial zone of hypothalamus](http://purl.obolibrary.org/obo/UBERON_0002272) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "zona medialis hypothalamicae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:77683" +- [pallium](http://purl.obolibrary.org/obo/UBERON_0000203) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In the anatomy of animals, an avian pallium is the dorsal telencephalon of a bird's brain. Pallium of avian species tend to be relatively large, comprising ~75% of the telencephalic volume." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Avian_pallium" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [taxon](http://www.geneontology.org/formats/oboInOwl#taxon) "NCBITaxon:8782" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [pallium](http://purl.obolibrary.org/obo/UBERON_0000203) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In humans the cerebrum has three parts: the archipallium, the paleopallium and the neopallium. The developing telencephalon or forebrain is divided into pallium and subpallium. In amphibians, the cerebrum includes archipallium, paleopallium and some of the basal nuclei. Reptiles first developed a neopallium, which continued to develop in the brains of more recent species to become the neocortex of humans and Old World monkeys. In fish, the archipallium is the largest part of the cerebrum. Some researchers suggest the early archipallium gave rise to the human hippocampus" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" -#### Added -- [medial zone of hypothalamus](http://purl.obolibrary.org/obo/UBERON_0002272) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "zona medialis hypothalamicae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:77683" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### palmar/plantar sweat gland `http://purl.obolibrary.org/obo/UBERON_0014391` +#### Removed +- [palmar/plantar sweat gland](http://purl.obolibrary.org/obo/UBERON_0014391) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "in mice these are the only sweat glands present" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "MP:0000675" -### median preoptic nucleus `http://purl.obolibrary.org/obo/UBERON_0002625` + +### palpebral artery `http://purl.obolibrary.org/obo/UBERON_0014770` #### Removed -- [median preoptic nucleus](http://purl.obolibrary.org/obo/UBERON_0002625) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus praeopticus medianus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:378" +- [palpebral artery](http://purl.obolibrary.org/obo/UBERON_0014770) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In humans, the eyelids are supplied with blood by two arches on each upper and lower lid. The arches are formed by anastamoses of the lateral palpebral arteries and medial palpebral arteries, branching off from the lacrimal artery and ophthalmic artery, respectively. In amphibians, the eyelids may be supplied by branches of the lateral pretrosal arteries.[cjm]" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [median preoptic nucleus](http://purl.obolibrary.org/obo/UBERON_0002625) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus preopticus medianus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:378" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### panarthropod head `http://purl.obolibrary.org/obo/UBERON_6000004` +#### Removed +- [panarthropod head](http://purl.obolibrary.org/obo/UBERON_6000004) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000004" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -- [median preoptic nucleus](http://purl.obolibrary.org/obo/UBERON_0002625) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006168" - - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0003-4423-4370" -#### Added -- [median preoptic nucleus](http://purl.obolibrary.org/obo/UBERON_0002625) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006168" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +### pancreas `http://purl.obolibrary.org/obo/UBERON_0001264` +#### Removed +- [pancreas](http://purl.obolibrary.org/obo/UBERON_0001264) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [median preoptic nucleus](http://purl.obolibrary.org/obo/UBERON_0002625) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus preopticus medianus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:378" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000050" -- [median preoptic nucleus](http://purl.obolibrary.org/obo/UBERON_0002625) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus praeopticus medianus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1016/j.crvi.2007.03.006 Madsen OD, Pancreas phylogeny and ontogeny in relation to a 'pancreatic stem cell'. C.R. Biologies (2007)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:378" +- [pancreas](http://purl.obolibrary.org/obo/UBERON_0001264) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The zebrafish does not have a discrete pancreas. Exocrine pancreatic tissue can be found scattered along the intestinal tract. The acinar structure of the exocrine pancreas is very similar to that of mammals and comprises cells with a very dark, basophilic cytoplasm" +- [pancreas](http://purl.obolibrary.org/obo/UBERON_0001264) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "The mature pancreas of higher vertebrates and mammals comprises two major functional units: the exocrine pancreas, which is responsible for the production of digestive enzymes to be secreted into the gut lumen, and the endocrine pancreas, which has its role in the synthesis of several hormones with key regulatory functions in food uptake and metabolism. The exocrine portion constitutes the majority of the mass of the pancreas, and contains only two different cell types, the secretory acinar cells and the ductular cells. The endocrine portion, which comprises only 1-2% of the total mass, contains five different cell types, which are organized into mixed functional assemblies referred to as the islets of Langerhans" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:16417468" -### mediastinal pleura `http://purl.obolibrary.org/obo/UBERON_0035431` -#### Removed -- [mediastinal pleura](http://purl.obolibrary.org/obo/UBERON_0035431) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pars mediastinalis pleurae parietalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [pancreas](http://purl.obolibrary.org/obo/UBERON_0001264) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "pancreatic" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9736" +- [pancreas](http://purl.obolibrary.org/obo/UBERON_0001264) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Organ which secretes a fluid containing enzymes that aid in the digestion of food.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010112" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -#### Added -- [mediastinal pleura](http://purl.obolibrary.org/obo/UBERON_0035431) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pars mediastinalis pleurae parietalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9736" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + +- [pancreas](http://purl.obolibrary.org/obo/UBERON_0001264) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "As a secretory organ serving exocrine and endocrine functions, the pancreas is specific to the vertebrates[PMID:16417468] Hagfishes and lampreys are unique in the complete separation of their endocrine pancreas (islet or- gan) and their exocrine pancreas (50). The endocrine and exocrine pancreas are coassociated in crown gnathostomes (50). In Branchiostoma and Ciona, there is no diverticulum as there is in hagfishes, lampreys, and gnathostomes, only dispersed insulin-secreting cells in the walls of the gastrointestinal tract (51, 52)" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:20959416" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### medium spiny neuron `http://purl.obolibrary.org/obo/CL_1001474` +### pancreas left lobe `http://purl.obolibrary.org/obo/UBERON_0015280` #### Added -- [medium spiny neuron](http://purl.obolibrary.org/obo/CL_1001474) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [pancreas left lobe](http://purl.obolibrary.org/obo/UBERON_0015280) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) -### medulla oblongata `http://purl.obolibrary.org/obo/UBERON_0001896` +### pancreas primordium `http://purl.obolibrary.org/obo/UBERON_0003921` #### Removed -- [medulla oblongata](http://purl.obolibrary.org/obo/UBERON_0001896) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "bulbus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:62004" +- [pancreas primordium](http://purl.obolibrary.org/obo/UBERON_0003921) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "revisit after standardizing terms 'primordium', 'anlagen', 'bud'" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [pancreas primordium](http://purl.obolibrary.org/obo/UBERON_0003921) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in EHDAA2 this has dorsal and ventral primordia as parts. the buds are part of the primordium, with the ducts developing from the buds; only parenchyma and ducts have contribution from buds" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EHDAA2" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [medulla oblongata](http://purl.obolibrary.org/obo/UBERON_0001896) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "medulla oblonzata" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Medulla_oblongata" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### pancreas right lobe `http://purl.obolibrary.org/obo/UBERON_0015281` #### Added -- [medulla oblongata](http://purl.obolibrary.org/obo/UBERON_0001896) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "medulla oblonzata" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Medulla_oblongata" +- [pancreas right lobe](http://purl.obolibrary.org/obo/UBERON_0015281) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) -- [medulla oblongata](http://purl.obolibrary.org/obo/UBERON_0001896) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "bulbus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:62004" +### pancreas ventral primordium `http://purl.obolibrary.org/obo/UBERON_0010376` +#### Removed +- [pancreas ventral primordium](http://purl.obolibrary.org/obo/UBERON_0010376) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Starts at CS14 in human (EHDAA2) or CS13-14 (embryology.ch 'bud anlagen')" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### medulla of lymph node `http://purl.obolibrary.org/obo/UBERON_0002007` +### pancreatic acinus `http://purl.obolibrary.org/obo/UBERON_0001263` #### Removed -- [medulla of lymph node](http://purl.obolibrary.org/obo/UBERON_0002007) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "medulla nodi lymphoidei" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Medulla_of_lymph_node" +- [pancreatic acinus](http://purl.obolibrary.org/obo/UBERON_0001263) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0000028" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) #### Added -- [medulla of lymph node](http://purl.obolibrary.org/obo/UBERON_0002007) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "medulla nodi lymphoidei" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Medulla_of_lymph_node" +- [pancreatic acinus](http://purl.obolibrary.org/obo/UBERON_0001263) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### pancreatic duct `http://purl.obolibrary.org/obo/UBERON_0007329` +#### Removed +- [pancreatic duct](http://purl.obolibrary.org/obo/UBERON_0007329) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "this class groups together accessory (dorsal) and main (ventral) pancreatic ducts" + +- [pancreatic duct](http://purl.obolibrary.org/obo/UBERON_0007329) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "These data show that ducts within the zebrafish pancreas originally arise in situ from isolated progenitor cells rather than arising from reiterative branching of the pancreatic epithelium. This process of pancreatic duct formation in zebrafish may be analogous to the mechanism of duct formation in the mammalian mammary and salivary glands. (...) A related mechanism of duct formation has also been proposed to occur within the mammalian pancreatic epithelium.[uncertain][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### medullary thymic epithelial cell `http://purl.obolibrary.org/obo/CL_0002365` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [medullary thymic epithelial cell](http://purl.obolibrary.org/obo/CL_0002365) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000254" -### megakaryocyte `http://purl.obolibrary.org/obo/CL_0000556` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1016/j.ydbio.2005.04.035 Yee NS, Lorent K, Pack M, Exocrine pancreas development in zebrafish. Developmental Biology (2005)" -#### Added -- [megakaryocyte](http://purl.obolibrary.org/obo/CL_0000556) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [pancreatic duct](http://purl.obolibrary.org/obo/UBERON_0007329) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in EHDAA2, the dorsal and ventral ducts are classified as epithelial sacs - review after overhaul of duct/epithelia terms" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EHDAA2" +- [pancreatic duct](http://purl.obolibrary.org/obo/UBERON_0007329) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D010183" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### megakaryocyte progenitor cell `http://purl.obolibrary.org/obo/CL_0000553` + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) -#### Added -- [megakaryocyte progenitor cell](http://purl.obolibrary.org/obo/CL_0000553) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +- [pancreatic duct](http://purl.obolibrary.org/obo/UBERON_0007329) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Duct connecting the pancreas with the intestine. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### megakaryocyte-erythroid progenitor cell `http://purl.obolibrary.org/obo/CL_0000050` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [megakaryocyte-erythroid progenitor cell](http://purl.obolibrary.org/obo/CL_0000050) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000254" -### meis2 expressing cortical GABAergic cell `http://purl.obolibrary.org/obo/CL_4023065` -#### Added -- [meis2 expressing cortical GABAergic cell](http://purl.obolibrary.org/obo/CL_4023065) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### pancreatic epithelial bud `http://purl.obolibrary.org/obo/UBERON_0003922` +#### Removed +- [pancreatic epithelial bud](http://purl.obolibrary.org/obo/UBERON_0003922) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [duodenum](http://purl.obolibrary.org/obo/UBERON_0002114) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Pancreatic_bud" -### melanocyte `http://purl.obolibrary.org/obo/CL_0000148` + - [exception](http://www.geneontology.org/formats/oboInOwl#exception) "zebrafish" #### Added -- [melanocyte](http://purl.obolibrary.org/obo/CL_0000148) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [pancreatic epithelial bud](http://purl.obolibrary.org/obo/UBERON_0003922) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [duodenum](http://purl.obolibrary.org/obo/UBERON_0002114) -### melanocyte of skin `http://purl.obolibrary.org/obo/CL_1000458` +### pancreatic lobule `http://purl.obolibrary.org/obo/UBERON_0007324` +#### Removed +- [pancreatic lobule](http://purl.obolibrary.org/obo/UBERON_0007324) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In mice many lobules lack islets, in contrast to other mammals including humans" #### Added -- [melanocyte of skin](http://purl.obolibrary.org/obo/CL_1000458) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [pancreatic lobule](http://purl.obolibrary.org/obo/UBERON_0007324) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -### membrane organization `http://purl.obolibrary.org/obo/GO_0061024` +### papillary layer of dermis `http://purl.obolibrary.org/obo/UBERON_0001992` #### Removed -- [membrane organization](http://purl.obolibrary.org/obo/GO_0061024) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) +- [papillary layer of dermis](http://purl.obolibrary.org/obo/UBERON_0001992) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Dense irregular connective tissue of the skin that consists of fibroblasts, various connective tissue cell types, and collagen, predominantly type III." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:64776" #### Added -- [membrane organization](http://purl.obolibrary.org/obo/GO_0061024) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) +- [papillary layer of dermis](http://purl.obolibrary.org/obo/UBERON_0001992) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### membranous labyrinth `http://purl.obolibrary.org/obo/UBERON_0001849` +### parasympathetic ganglion `http://purl.obolibrary.org/obo/UBERON_0001808` #### Removed -- [membranous labyrinth](http://purl.obolibrary.org/obo/UBERON_0001849) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "labyrinthus membranaceus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Membranous_labyrinth" +- [parasympathetic ganglion](http://purl.obolibrary.org/obo/UBERON_0001808) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D005726" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) -#### Added -- [membranous labyrinth](http://purl.obolibrary.org/obo/UBERON_0001849) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "labyrinthus membranaceus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Membranous_labyrinth" + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### memory B cell `http://purl.obolibrary.org/obo/CL_0000787` +### parasympathetic nervous system `http://purl.obolibrary.org/obo/UBERON_0000011` +#### Removed +- [parasympathetic nervous system](http://purl.obolibrary.org/obo/UBERON_0000011) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Part of the autonomic nervous system which has opposing physiological effects of the sympathetic nervous system. Examples include decreasing the heart rate or dilating the blood vessels.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010488" -#### Added -- [memory B cell](http://purl.obolibrary.org/obo/CL_0000787) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### memory T cell `http://purl.obolibrary.org/obo/CL_0000813` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" -#### Added -- [memory T cell](http://purl.obolibrary.org/obo/CL_0000813) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [parasympathetic nervous system](http://purl.obolibrary.org/obo/UBERON_0000011) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In mammals, the autonomic nervous system is divided into two contrasting, antagonistic systems of control over visceral activity: the sympathetic system and the parasympathetic system (reference 1); In general, the teleosts may be considered phylogenetically the first class of vertebrates in which the heart is regulated by both sympathetic and parasympathetic neural pathways (reference 2).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### memory regulatory T cell `http://purl.obolibrary.org/obo/CL_0002678` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [memory regulatory T cell](http://purl.obolibrary.org/obo/CL_0002678) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.634, DOI:10.1016/S0306-4530(98)00057-2 Porges SW, Love: an emergent property of the mammalian autonomic nervous system. Psychoneuroendocrinology (1998)" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000755" -### mesangial cell `http://purl.obolibrary.org/obo/CL_0000650` -#### Added -- [mesangial cell](http://purl.obolibrary.org/obo/CL_0000650) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### parathyroid gland `http://purl.obolibrary.org/obo/UBERON_0001132` +#### Removed +- [parathyroid gland](http://purl.obolibrary.org/obo/UBERON_0001132) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Either of the two pairs of small, spherical, encapsulated glands which develop from ventral growths of the third and fourth pharyngeal pouches and are closely associated with the external jugular veins. Calcitonin and parathyroid hormone are secreted by these glands.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -### mesenchymal cell `http://purl.obolibrary.org/obo/CL_0008019` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010545" -#### Added -- [mesenchymal cell](http://purl.obolibrary.org/obo/CL_0008019) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" -### mesenchymal lymphangioblast `http://purl.obolibrary.org/obo/CL_0005021` +- [parathyroid gland](http://purl.obolibrary.org/obo/UBERON_0001132) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Any one of several small structures, usually four, attached to the dorsal surfaces of the lateral lobes of the thyroid gland. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [mesenchymal lymphangioblast](http://purl.obolibrary.org/obo/CL_0005021) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### mesenchymal stem cell `http://purl.obolibrary.org/obo/CL_0000134` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/parathyroid+gland" -#### Added -- [mesenchymal stem cell](http://purl.obolibrary.org/obo/CL_0000134) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001188" +- [parathyroid gland](http://purl.obolibrary.org/obo/UBERON_0001132) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "In humans and chick it emerges from pouches 3 and 4, but in mice it is exclusively generated by the third pouch" -### mesenchymal stem cell of adipose tissue `http://purl.obolibrary.org/obo/CL_0002570` +- [parathyroid gland](http://purl.obolibrary.org/obo/UBERON_0001132) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "table 13.1 of Kardong is used to create the taxon-specific developmental relationships here, although some omissions are made for simplicity." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:16313389" -#### Added -- [mesenchymal stem cell of adipose tissue](http://purl.obolibrary.org/obo/CL_0002570) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [parathyroid gland](http://purl.obolibrary.org/obo/UBERON_0001132) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The evolution of the tetrapods, and the shift from an aquatic to a terrestrial environment, was believed to have required new controls for regulating calcium homeostasis, and thus the evolution of parathyroid glands (...) both the tetrapod parathyroid and the gills of fish contribute to the regulation of extracellular calcium levels. It is therefore reasonable to suggest that the parathyroid gland evolved as a result of the transformation of the gills into the parathyroid glands of tetrapods and the transition from an aquatic to a terrestrial environment. This interpretation would also explain the positioning of the parathyroid gland within the pharynx in the tetrapod body. Were the parathyroid gland to have emerged de novo with the evolution of the tetrapods it could, as an endocrine organ, have been placed anywhere in the body and still exert its effect.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### mesenchyme `http://purl.obolibrary.org/obo/UBERON_0003104` -#### Removed -- [mesenchyme](http://purl.obolibrary.org/obo/UBERON_0003104) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "mesenchyma" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Mesenchyme" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M, Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)" -#### Added -- [mesenchyme](http://purl.obolibrary.org/obo/UBERON_0003104) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "mesenchyma" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001188" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Mesenchyme" +- [parathyroid gland](http://purl.obolibrary.org/obo/UBERON_0001132) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Parathyroid glands are found in all adult tetrapods, although they vary in their number, and in their exact position. Mammals typically have four parathyroids, while other groups typically have six. Fish do not possess parathyroid glands, although the ultimobranchial glands, which are found close to the oesophagus, may have a similar function and could even be homologous with the tetrapod parathyroids. Even these glands are absent in the most primitive vertebrates, the jawless fish, but as these species have no bone in their skeletons, only cartilage, it may be that they have less need to regulate calcium metabolism. The conserved homology of genes and calcium-sensing receptors in fish gills with those in the parathryroid glands of birds and mammals is recognized by evolutionary developmental biology as evolution-using genes and gene networks in novel ways to generate new structures with some similar functions and novel functions[WP]" -### mesenteric lymph node `http://purl.obolibrary.org/obo/UBERON_0002509` -#### Removed -- [mesenteric lymph node](http://purl.obolibrary.org/obo/UBERON_0002509) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nodi lymphoidei mesenterici" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0000767" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### paraventricular nucleus of hypothalamus `http://purl.obolibrary.org/obo/UBERON_0001930` +#### Removed +- [paraventricular nucleus of hypothalamus](http://purl.obolibrary.org/obo/UBERON_0001930) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [arcuate nucleus of hypothalamus](http://purl.obolibrary.org/obo/UBERON_0001932) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" -#### Added -- [mesenteric lymph node](http://purl.obolibrary.org/obo/UBERON_0002509) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nodi lymphoidei mesenterici" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [paraventricular nucleus of hypothalamus](http://purl.obolibrary.org/obo/UBERON_0001930) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0001929](http://purl.obolibrary.org/obo/UBERON_0001929) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0000767" -### mesoderm `http://purl.obolibrary.org/obo/UBERON_0000926` +### paravertebral ganglion `http://purl.obolibrary.org/obo/UBERON_0001807` #### Removed -- [mesoderm](http://purl.obolibrary.org/obo/UBERON_0000926) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000126" +- [paravertebral ganglion](http://purl.obolibrary.org/obo/UBERON_0001807) [UBPROP_0000202](http://purl.obolibrary.org/obo/UBPROP_0000202) [FMA_80128](http://purl.obolibrary.org/obo/FMA_80128) -#### Added -- [mesoderm](http://purl.obolibrary.org/obo/UBERON_0000926) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000126" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### mesodermal cell `http://purl.obolibrary.org/obo/CL_0000222` +### paraxial mesoderm `http://purl.obolibrary.org/obo/UBERON_0003077` +#### Removed +- [paraxial mesoderm](http://purl.obolibrary.org/obo/UBERON_0003077) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" -#### Added -- [mesodermal cell](http://purl.obolibrary.org/obo/CL_0000222) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### mesonephric duct `http://purl.obolibrary.org/obo/UBERON_0003074` -#### Removed -- [mesonephric duct](http://purl.obolibrary.org/obo/UBERON_0003074) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ductus mesonephricus; ductus Wolffi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Mesonephric_duct" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010568" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [paraxial mesoderm](http://purl.obolibrary.org/obo/UBERON_0003077) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here)" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "ZFA" -- [mesonephric duct](http://purl.obolibrary.org/obo/UBERON_0003074) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0005990" - - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0003-4423-4370" +- [paraxial mesoderm](http://purl.obolibrary.org/obo/UBERON_0003077) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1002/dvdy.21177 Kusakabe R and Kuratani S. Evolutionary perspectives from development of mesodermal components in the lamprey. Developmental dynamics (2007)" -#### Added -- [mesonephric duct](http://purl.obolibrary.org/obo/UBERON_0003074) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ductus mesonephricus; ductus Wolffi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Mesonephric_duct" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [mesonephric duct](http://purl.obolibrary.org/obo/UBERON_0003074) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0005990" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000114" - - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) -### mesonephric glomerular capillary `http://purl.obolibrary.org/obo/UBERON_0006183` +### parenchyma `http://purl.obolibrary.org/obo/UBERON_0000353` #### Removed -- [mesonephric glomerular capillary](http://purl.obolibrary.org/obo/UBERON_0006183) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO:0061249" +- [parenchyma](http://purl.obolibrary.org/obo/UBERON_0000353) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "Early in development the mammalian embryo has three distinct layers: ectoderm (external layer), endoderm (internal layer) and in between those two layers the middle layer or mesoderm. The parenchyma of most organs is of ectodermal (brain, skin) or endodermal origin (lungs, gastrointestinal tract, liver, pancreas). The parenchyma of a few organs (spleen, kidneys, heart) is of mesodermal origin. The stroma of all organs is of mesodermal origin" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" -#### Added -- [mesonephric glomerular capillary](http://purl.obolibrary.org/obo/UBERON_0006183) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Missing definition for term UBERON:0006183. Please replace it using linked reference." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO:0061249" +- [parenchyma](http://purl.obolibrary.org/obo/UBERON_0000353) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "parenchymal" +- [parenchyma](http://purl.obolibrary.org/obo/UBERON_0000353) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "the FMA definition is more restrictive, and limits this to solid organs. This would seem to cause problems for the lung parenchyma, except FMA classifies Lung as solid rather than cavitated" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" -### mesonephric smooth muscle tissue `http://purl.obolibrary.org/obo/UBERON_0005321` -#### Removed -- [mesonephric smooth muscle tissue](http://purl.obolibrary.org/obo/UBERON_0005321) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO:0061214" +- [parenchyma](http://purl.obolibrary.org/obo/UBERON_0000353) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001539" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -#### Added -- [mesonephric smooth muscle tissue](http://purl.obolibrary.org/obo/UBERON_0005321) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Missing definition for term UBERON:0005321. Please replace it using linked reference." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO:0061214" + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) -### mesonephric tubule `http://purl.obolibrary.org/obo/UBERON_0000083` -#### Removed -- [mesonephric tubule](http://purl.obolibrary.org/obo/UBERON_0000083) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tubuli mesonephrici" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Mesonephric_tubules" +- [parenchyma](http://purl.obolibrary.org/obo/UBERON_0000353) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0000999" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -#### Added -- [mesonephric tubule](http://purl.obolibrary.org/obo/UBERON_0000083) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tubuli mesonephrici" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Mesonephric_tubules" -### mesothelial cell `http://purl.obolibrary.org/obo/CL_0000077` +### parenchyma of central nervous system `http://purl.obolibrary.org/obo/UBERON_0005158` #### Added -- [mesothelial cell](http://purl.obolibrary.org/obo/CL_0000077) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [parenchyma of central nervous system](http://purl.obolibrary.org/obo/UBERON_0005158) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### mesothelial cell of epicardium `http://purl.obolibrary.org/obo/CL_0011019` +### parenchyma of mammary gland `http://purl.obolibrary.org/obo/UBERON_0036245` #### Added -- [mesothelial cell of epicardium](http://purl.obolibrary.org/obo/CL_0011019) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [parenchyma of mammary gland](http://purl.obolibrary.org/obo/UBERON_0036245) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### mesothelial cell of pleura `http://purl.obolibrary.org/obo/CL_1000491` +### parenchyma of spleen `http://purl.obolibrary.org/obo/UBERON_1000024` #### Added -- [mesothelial cell of pleura](http://purl.obolibrary.org/obo/CL_1000491) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [parenchyma of spleen](http://purl.obolibrary.org/obo/UBERON_1000024) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### mesothelial cell of visceral pleura `http://purl.obolibrary.org/obo/CL_1000493` +### parenchyma of thyroid gland `http://purl.obolibrary.org/obo/UBERON_0001747` #### Added -- [mesothelial cell of visceral pleura](http://purl.obolibrary.org/obo/CL_1000493) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [parenchyma of thyroid gland](http://purl.obolibrary.org/obo/UBERON_0001747) SubClassOf [structure with developmental contribution from neural crest](http://purl.obolibrary.org/obo/UBERON_0010314) +- [parenchyma of thyroid gland](http://purl.obolibrary.org/obo/UBERON_0001747) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -### mesothelial fibroblast `http://purl.obolibrary.org/obo/CL_4023054` -#### Added -- [mesothelial fibroblast](http://purl.obolibrary.org/obo/CL_4023054) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### parietal cortex `http://purl.obolibrary.org/obo/UBERON_0016530` +#### Removed +- [parietal cortex](http://purl.obolibrary.org/obo/UBERON_0016530) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D010296" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -### metacarpophalangeal joint `http://purl.obolibrary.org/obo/UBERON_0003695` -#### Removed -- [metacarpophalangeal joint](http://purl.obolibrary.org/obo/UBERON_0003695) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "articulationes metacarpophalangeae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Metacarpophalangeal_joint" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### parietal organ `http://purl.obolibrary.org/obo/UBERON_0004869` #### Added -- [metacarpophalangeal joint](http://purl.obolibrary.org/obo/UBERON_0003695) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "articulationes metacarpophalangeae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Metacarpophalangeal_joint" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [parietal organ](http://purl.obolibrary.org/obo/UBERON_0004869) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### metacarpus skeleton `http://purl.obolibrary.org/obo/UBERON_0010544` +### parietal peritoneum `http://purl.obolibrary.org/obo/UBERON_0001366` #### Removed -- [metacarpus skeleton](http://purl.obolibrary.org/obo/UBERON_0010544) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ossa metacarpi [I-V]" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71336" +- [parietal peritoneum](http://purl.obolibrary.org/obo/UBERON_0001366) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Peritoneum attached to the abdominal wall.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:JMG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -- [metacarpus skeleton](http://purl.obolibrary.org/obo/UBERON_0010544) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "metacarpalia" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Metacarpus" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010816" -- [metacarpus skeleton](http://purl.obolibrary.org/obo/UBERON_0010544) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ossa metacarpalia [I-V]" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71336" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### parietal pleura `http://purl.obolibrary.org/obo/UBERON_0002400` #### Added -- [metacarpus skeleton](http://purl.obolibrary.org/obo/UBERON_0010544) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ossa metacarpi [I-V]" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [parietal pleura](http://purl.obolibrary.org/obo/UBERON_0002400) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71336" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### parietal serous membrane `http://purl.obolibrary.org/obo/UBERON_0022351` -- [metacarpus skeleton](http://purl.obolibrary.org/obo/UBERON_0010544) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ossa metacarpalia [I-V]" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +#### Added +- [parietal serous membrane](http://purl.obolibrary.org/obo/UBERON_0022351) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71336" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### pars distalis of adenohypophysis `http://purl.obolibrary.org/obo/UBERON_0006964` +#### Removed +- [pars distalis of adenohypophysis](http://purl.obolibrary.org/obo/UBERON_0006964) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The anterior part of the adenohypophysis. [TFD][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000244" -- [metacarpus skeleton](http://purl.obolibrary.org/obo/UBERON_0010544) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "metacarpalia" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Metacarpus" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### metanephros induced blastemal cells `http://purl.obolibrary.org/obo/UBERON_0010531` -#### Removed -- [metanephros induced blastemal cells](http://purl.obolibrary.org/obo/UBERON_0010531) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://www.embryology.ch/anglais/turinary/urinhaute03.html" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://www.thefreedictionary.com/pars+anterior" +- [pars distalis of adenohypophysis](http://purl.obolibrary.org/obo/UBERON_0006964) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. An infundibulum grows ventrally from the diencephalon of the brain, and Rathke's pouch extends dorsally from the roof of the developing mouth, or stomodaeum. The infundibulum remains connected to the floor of the diencephalon, which becomes the hypothalamus, and gives rise to the part of the gland known as the neurohypophysis. (...) Rathke's pouch loses its connection with the stomodaeum in most adult vertebrates and gives rise to the rest of the gland, the adenohypophysis. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000244" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### metatarsophalangeal joint `http://purl.obolibrary.org/obo/UBERON_0003696` -#### Removed -- [metatarsophalangeal joint](http://purl.obolibrary.org/obo/UBERON_0003696) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "articulationes metatarsophalangeae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Metatarsophalangeal_articulations" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510 and Figure 15-5" -#### Added -- [metatarsophalangeal joint](http://purl.obolibrary.org/obo/UBERON_0003696) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "articulationes metatarsophalangeae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Metatarsophalangeal_articulations" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [pars distalis of adenohypophysis](http://purl.obolibrary.org/obo/UBERON_0006964) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Region of the adenohypophysis which produces the follicle-stimulating hormone, luteinizing hormone, prolactin, thyrotropin, and adrenocorticotropin.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010542" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -### metatarsus region `http://purl.obolibrary.org/obo/UBERON_0000983` -#### Removed -- [metatarsus region](http://purl.obolibrary.org/obo/UBERON_0000983) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "regio metatarsalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:24997" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [pars distalis of adenohypophysis](http://purl.obolibrary.org/obo/UBERON_0006964) SubClassOf [epithelium](http://purl.obolibrary.org/obo/UBERON_0000483) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "EHDAA2" #### Added -- [metatarsus region](http://purl.obolibrary.org/obo/UBERON_0000983) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "regio metatarsalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [pars distalis of adenohypophysis](http://purl.obolibrary.org/obo/UBERON_0006964) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) + + +### part of developmental precursor of `http://purl.obolibrary.org/obo/RO_0002287` +#### Removed +- [part of developmental precursor of](http://purl.obolibrary.org/obo/RO_0002287) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" + +- [part of developmental precursor of](http://purl.obolibrary.org/obo/RO_0002287) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:24997" +- [part of developmental precursor of](http://purl.obolibrary.org/obo/RO_0002287) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### metatarsus skeleton `http://purl.obolibrary.org/obo/UBERON_0010545` +### part of structure that is capable of `http://purl.obolibrary.org/obo/RO_0002329` #### Removed -- [metatarsus skeleton](http://purl.obolibrary.org/obo/UBERON_0010545) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ossa metatarsalia" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Metatarsus" +- [part of structure that is capable of](http://purl.obolibrary.org/obo/RO_0002329) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [part of structure that is capable of](http://purl.obolibrary.org/obo/RO_0002329) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) false -- [metatarsus skeleton](http://purl.obolibrary.org/obo/UBERON_0010545) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ossa metatarsalia [I-V]" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71340" +- [part_of](http://purl.obolibrary.org/obo/BFO_0000050) o [capable of](http://purl.obolibrary.org/obo/RO_0002215) SubPropertyOf: [part of structure that is capable of](http://purl.obolibrary.org/obo/RO_0002329) + - [is a defining property chain axiom](http://purl.obolibrary.org/obo/RO_0002581) true - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [metatarsus skeleton](http://purl.obolibrary.org/obo/UBERON_0010545) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ossa metatarsi[I-V]" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71340" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### part_of `http://purl.obolibrary.org/obo/BFO_0000050` +#### Removed +- [part_of](http://purl.obolibrary.org/obo/BFO_0000050) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "is part of"@en - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [part_of](http://purl.obolibrary.org/obo/BFO_0000050) [RO_0040042](http://purl.obolibrary.org/obo/RO_0040042) [specifically dependent continuant](http://purl.obolibrary.org/obo/BFO_0000020) -#### Added -- [metatarsus skeleton](http://purl.obolibrary.org/obo/UBERON_0010545) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ossa metatarsi[I-V]" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71340" +- [part_of](http://purl.obolibrary.org/obo/BFO_0000050) [RO_0040042](http://purl.obolibrary.org/obo/RO_0040042) [realizable entity](http://purl.obolibrary.org/obo/BFO_0000017) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [part_of](http://purl.obolibrary.org/obo/BFO_0000050) [RO_0001900](http://purl.obolibrary.org/obo/RO_0001900) [RO_0001901](http://purl.obolibrary.org/obo/RO_0001901) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [part_of](http://purl.obolibrary.org/obo/BFO_0000050) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "this day is part of this year (occurrent parthood)"@en -- [metatarsus skeleton](http://purl.obolibrary.org/obo/UBERON_0010545) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ossa metatarsalia" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [part_of](http://purl.obolibrary.org/obo/BFO_0000050) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Metatarsus" +- [part_of](http://purl.obolibrary.org/obo/BFO_0000050) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "my brain is part of my body (continuant parthood, two material entities)"@en -- [metatarsus skeleton](http://purl.obolibrary.org/obo/UBERON_0010545) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ossa metatarsalia [I-V]" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71340" +- [part_of](http://purl.obolibrary.org/obo/BFO_0000050) [RO_0040042](http://purl.obolibrary.org/obo/RO_0040042) [quality](http://purl.obolibrary.org/obo/BFO_0000019) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [part_of](http://purl.obolibrary.org/obo/BFO_0000050) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "part_of"@en - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [part_of](http://purl.obolibrary.org/obo/BFO_0000050) [RO_0040042](http://purl.obolibrary.org/obo/RO_0040042) [generically dependent continuant](http://purl.obolibrary.org/obo/BFO_0000031) +- [part_of](http://purl.obolibrary.org/obo/BFO_0000050) [RO_0040042](http://purl.obolibrary.org/obo/RO_0040042) [occurrent](http://purl.obolibrary.org/obo/BFO_0000003) -### metathalamus `http://purl.obolibrary.org/obo/UBERON_0002704` -#### Removed -- [metathalamus](http://purl.obolibrary.org/obo/UBERON_0002704) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "corpora geniculata" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Metathalamus" +- [part_of](http://purl.obolibrary.org/obo/BFO_0000050) [RO_0040042](http://purl.obolibrary.org/obo/RO_0040042) [independent continuant](http://purl.obolibrary.org/obo/BFO_0000004) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [part_of](http://purl.obolibrary.org/obo/BFO_0000050) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)"@en -#### Added -- [metathalamus](http://purl.obolibrary.org/obo/UBERON_0002704) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "corpora geniculata" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [part_of](http://purl.obolibrary.org/obo/BFO_0000050) [RO_0040042](http://purl.obolibrary.org/obo/RO_0040042) [continuant](http://purl.obolibrary.org/obo/BFO_0000002) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Metathalamus" -- [metathalamus](http://purl.obolibrary.org/obo/UBERON_0002704) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D005829" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +### participates in `http://purl.obolibrary.org/obo/RO_0000056` +#### Removed +- [participates in](http://purl.obolibrary.org/obo/RO_0000056) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "participates in"@en +- [participates in](http://purl.obolibrary.org/obo/RO_0000056) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "this input material (or this output material) participates in this process"@en -### microfold cell of epithelium of small intestine `http://purl.obolibrary.org/obo/CL_1000353` +- [participates in](http://purl.obolibrary.org/obo/RO_0000056) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "this investigator participates in this investigation"@en -#### Added -- [microfold cell of epithelium of small intestine](http://purl.obolibrary.org/obo/CL_1000353) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [participates in](http://purl.obolibrary.org/obo/RO_0000056) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" +- [participates in](http://purl.obolibrary.org/obo/RO_0000056) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "this blood clot participates in this blood coagulation"@en -### microglial cell `http://purl.obolibrary.org/obo/CL_0000129` +- [participates in](http://purl.obolibrary.org/obo/RO_0000056) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "participates_in"@en -#### Added -- [microglial cell](http://purl.obolibrary.org/obo/CL_0000129) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### midbrain `http://purl.obolibrary.org/obo/UBERON_0001891` +### parvalbumin alpha `http://purl.obolibrary.org/obo/PR_000013502` #### Removed -- [midbrain](http://purl.obolibrary.org/obo/UBERON_0001891) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "mesencephalon" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Midbrain" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [parvalbumin alpha](http://purl.obolibrary.org/obo/PR_000013502) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [parvalbumin alpha (human)](http://purl.obolibrary.org/obo/PR_P20472) -#### Added -- [midbrain](http://purl.obolibrary.org/obo/UBERON_0001891) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "mesencephalon" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Midbrain" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### midbrain tectum `http://purl.obolibrary.org/obo/UBERON_0002314` +### patella `http://purl.obolibrary.org/obo/UBERON_0002446` #### Removed -- [midbrain tectum](http://purl.obolibrary.org/obo/UBERON_0002314) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "t. mesencephali" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [patella](http://purl.obolibrary.org/obo/UBERON_0002446) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "patellar" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Midbrain_tectum" -- [midbrain tectum](http://purl.obolibrary.org/obo/UBERON_0002314) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tectum mesencephalicum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:465" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### patella cartilage element `http://purl.obolibrary.org/obo/UBERON_0012080` #### Added -- [midbrain tectum](http://purl.obolibrary.org/obo/UBERON_0002314) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "t. mesencephali" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [patella cartilage element](http://purl.obolibrary.org/obo/UBERON_0012080) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Midbrain_tectum" -- [midbrain tectum](http://purl.obolibrary.org/obo/UBERON_0002314) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tectum mesencephalicum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### patella pre-cartilage condensation `http://purl.obolibrary.org/obo/UBERON_0012081` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:465" +#### Added +- [patella pre-cartilage condensation](http://purl.obolibrary.org/obo/UBERON_0012081) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### midbrain tegmentum `http://purl.obolibrary.org/obo/UBERON_0001943` +### pectinate line `http://purl.obolibrary.org/obo/UBERON_0006574` #### Removed -- [midbrain tegmentum](http://purl.obolibrary.org/obo/UBERON_0001943) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tegmentum mesencephalicum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:491" +- [pectinate line](http://purl.obolibrary.org/obo/UBERON_0006574) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA also has FMA:29321 but it's not clear how this differs" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +#### Added +- [pectinate line](http://purl.obolibrary.org/obo/UBERON_0006574) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -- [midbrain tegmentum](http://purl.obolibrary.org/obo/UBERON_0001943) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tegmentum mesencephali" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Midbrain_tegmentum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### pectoral appendage `http://purl.obolibrary.org/obo/UBERON_0004710` +#### Removed +- [pectoral appendage](http://purl.obolibrary.org/obo/UBERON_0004710) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "While the skeletons of teleost pectoral fins and tetrapod forelimbs are homologous at the level of endoskeletal radials, teleosts and tetrapods do not share homologous skeletal elements at the level of 'individuated' pro-, meso-, and metapterygia. Among osteichthyans, only basal actinopterygians retain the full complement of elements present in non-osteichthyan gnathostomes.[uncertain][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001753" -#### Added -- [midbrain tegmentum](http://purl.obolibrary.org/obo/UBERON_0001943) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tegmentum mesencephalicum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:491" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [midbrain tegmentum](http://purl.obolibrary.org/obo/UBERON_0001943) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tegmentum mesencephali" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Midbrain_tegmentum" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1002/jmor.10264 Davis MC, Shubin NH, Force A, Pectoral fin and girdle development in the basal actinopterygians Polyodon spathula and Acipenser transmontanus. Journal of Morphology (2004)" -- [midbrain tegmentum](http://purl.obolibrary.org/obo/UBERON_0001943) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D013681" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) +- [pectoral appendage](http://purl.obolibrary.org/obo/UBERON_0004710) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [pectoral appendage bud](http://purl.obolibrary.org/obo/UBERON_0005419) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +#### Added +- [pectoral appendage](http://purl.obolibrary.org/obo/UBERON_0004710) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [pectoral appendage bud](http://purl.obolibrary.org/obo/UBERON_0005419) -### middle colic artery `http://purl.obolibrary.org/obo/UBERON_0001196` +### pectoral appendage apical ectodermal ridge `http://purl.obolibrary.org/obo/UBERON_0005421` #### Removed -- [middle colic artery](http://purl.obolibrary.org/obo/UBERON_0001196) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria colica media" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Middle_colic_artery" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [pectoral appendage apical ectodermal ridge](http://purl.obolibrary.org/obo/UBERON_0005421) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Pectoral and pelvic fins are homologous to the tetrapod fore and hindlimb, respectively. (...) The zebrafish AER [apical ectodermal ridge] is an apical ectodermal thickening at the distal tip of the fin bud and consists of wedge-shaped cells of the basal stratum. The AER is observed only transiently, and from 36 hpf onwards the cells of this region form the apical fold (AF), which consists of a dorsal and a ventral layer of cylindrically-shaped ectodermal cells extending from the anterior to the posterior fin margin. Despite the change in shape, the AF still carries out the same functions as the AER. Indeed, although the AER receives its name from its characteristic shape, being composed of a pseudostratified ectoderm in the chicken and a polystratified ectoderm in the mouse, this independence of AER morphology from its function is also observed in tetrapods. The AF also expresses similar molecular markers to the tetrapod AER, suggesting that it fulfills similar functions in the fin as the AER does in tetrapod limbs.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1111/j.1440-169X.2007.00942.x" -#### Added -- [middle colic artery](http://purl.obolibrary.org/obo/UBERON_0001196) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria colica media" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Middle_colic_artery" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### middle colic vein `http://purl.obolibrary.org/obo/UBERON_0001218` -#### Removed -- [middle colic vein](http://purl.obolibrary.org/obo/UBERON_0001218) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena colica media" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Middle_colic_vein" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001064" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [pectoral appendage apical ectodermal ridge](http://purl.obolibrary.org/obo/UBERON_0005421) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "An ectodermal thickening at the end of the forelimb bud in the developing embryo. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [middle colic vein](http://purl.obolibrary.org/obo/UBERON_0001218) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena colica media" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Middle_colic_vein" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001064" -### middle ear `http://purl.obolibrary.org/obo/UBERON_0001756` -#### Removed -- [middle ear](http://purl.obolibrary.org/obo/UBERON_0001756) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "auris media" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0002099" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/apical+ectodermal+ridge" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Middle_ear" +- [pectoral appendage apical ectodermal ridge](http://purl.obolibrary.org/obo/UBERON_0005421) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Apical ectodermal ridge that is part of the pectoral fin bud.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -#### Added -- [middle ear](http://purl.obolibrary.org/obo/UBERON_0001756) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "auris media" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0002099" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Middle_ear" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000085" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### middle phalanx of manus `http://purl.obolibrary.org/obo/UBERON_0003864` +### pectoral appendage bud `http://purl.obolibrary.org/obo/UBERON_0005419` #### Removed -- [middle phalanx of manus](http://purl.obolibrary.org/obo/UBERON_0003864) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "phalanx media manus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:75817" +- [pectoral appendage bud](http://purl.obolibrary.org/obo/UBERON_0005419) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "While the skeletons of teleost pectoral fins and tetrapod forelimbs are homologous at the level of endoskeletal radials, teleosts and tetrapods do not share homologous skeletal elements at the level of 'individuated' pro-, meso-, and metapterygia. Among osteichthyans, only basal actinopterygians retain the full complement of elements present in non-osteichthyan gnathostomes.[uncertain][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001754" -#### Added -- [middle phalanx of manus](http://purl.obolibrary.org/obo/UBERON_0003864) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "phalanx media manus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:75817" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1002/jmor.10264 Davis MC, Shubin NH, Force A, Pectoral fin and girdle development in the basal actinopterygians Polyodon spathula and Acipenser transmontanus. Journal of Morphology (2004)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [pectoral appendage bud](http://purl.obolibrary.org/obo/UBERON_0005419) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Fin bud that develops into the pectoral fin.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000141" -### middle phalanx of pes `http://purl.obolibrary.org/obo/UBERON_0003866` -#### Removed -- [middle phalanx of pes](http://purl.obolibrary.org/obo/UBERON_0003866) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "phalanx media pedis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:75829" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [middle phalanx of pes](http://purl.obolibrary.org/obo/UBERON_0003866) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "phalanx media pedis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:75829" +### pectoral appendage bud ectoderm `http://purl.obolibrary.org/obo/UBERON_0003372` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +#### Added +- [pectoral appendage bud ectoderm](http://purl.obolibrary.org/obo/UBERON_0003372) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) -### midgut `http://purl.obolibrary.org/obo/UBERON_0001045` +### pectoral appendage bud mesenchyme `http://purl.obolibrary.org/obo/UBERON_0003413` #### Removed -- [midgut](http://purl.obolibrary.org/obo/UBERON_0001045) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005383" - -- [midgut](http://purl.obolibrary.org/obo/UBERON_0001045) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "mesenteron" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Midgut" +- [pectoral appendage bud mesenchyme](http://purl.obolibrary.org/obo/UBERON_0003413) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Mesoderm that is part of the pectoral fin bud.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000789" -#### Added -- [midgut](http://purl.obolibrary.org/obo/UBERON_0001045) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005383" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -- [midgut](http://purl.obolibrary.org/obo/UBERON_0001045) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "mesenteron" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Midgut" -### midzonal region hepatocyte `http://purl.obolibrary.org/obo/CL_0019028` +### pectoral appendage cartilage tissue `http://purl.obolibrary.org/obo/UBERON_0007390` +#### Removed +- [pectoral appendage cartilage tissue](http://purl.obolibrary.org/obo/UBERON_0007390) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Cartilage which is part of the pectoral fin.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -#### Added -- [midzonal region hepatocyte](http://purl.obolibrary.org/obo/CL_0019028) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000257" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -### migratory enteric neural crest cell `http://purl.obolibrary.org/obo/CL_0002607` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" #### Added -- [migratory enteric neural crest cell](http://purl.obolibrary.org/obo/CL_0002607) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [pectoral appendage cartilage tissue](http://purl.obolibrary.org/obo/UBERON_0007390) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### molecular adaptor activity `http://purl.obolibrary.org/obo/GO_0060090` +### pectoral appendage field `http://purl.obolibrary.org/obo/UBERON_0005729` #### Removed -- [molecular adaptor activity](http://purl.obolibrary.org/obo/GO_0060090) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) - -#### Added -- [molecular adaptor activity](http://purl.obolibrary.org/obo/GO_0060090) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) +- [pectoral appendage field](http://purl.obolibrary.org/obo/UBERON_0005729) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Embryonic region that develops into the pectoral fin bud.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001453" -### molecular layer of cerebellar cortex `http://purl.obolibrary.org/obo/UBERON_0002974` -#### Removed -- [molecular layer of cerebellar cortex](http://purl.obolibrary.org/obo/UBERON_0002974) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum moleculare corticis cerebelli" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:83897" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [molecular layer of cerebellar cortex](http://purl.obolibrary.org/obo/UBERON_0002974) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "fasciculi thalami" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:366" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### pectoral appendage skeleton `http://purl.obolibrary.org/obo/UBERON_0007272` +#### Removed +- [pectoral appendage skeleton](http://purl.obolibrary.org/obo/UBERON_0007272) [RO_0002475](http://purl.obolibrary.org/obo/RO_0002475) [pelvic appendage skeleton](http://purl.obolibrary.org/obo/UBERON_0007273) -#### Added -- [molecular layer of cerebellar cortex](http://purl.obolibrary.org/obo/UBERON_0002974) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "fasciculi thalami" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:366" -- [molecular layer of cerebellar cortex](http://purl.obolibrary.org/obo/UBERON_0002974) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum moleculare corticis cerebelli" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### pectoral complex `http://purl.obolibrary.org/obo/UBERON_0010708` +#### Removed +- [pectoral complex](http://purl.obolibrary.org/obo/UBERON_0010708) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region)" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:83897" +- [pectoral complex](http://purl.obolibrary.org/obo/UBERON_0010708) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Appendage girdle complex that when present, encompasses the pectoral appendage and half of the pectoral girdle.[VSAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000213" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "VSAO:MAH" -### molecular transducer activity `http://purl.obolibrary.org/obo/GO_0060089` -#### Removed -- [molecular transducer activity](http://purl.obolibrary.org/obo/GO_0060089) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" -#### Added -- [molecular transducer activity](http://purl.obolibrary.org/obo/GO_0060089) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) -### monocyte `http://purl.obolibrary.org/obo/CL_0000576` +### pectoral complex muscle `http://purl.obolibrary.org/obo/UBERON_0010891` +#### Removed +- [pectoral complex muscle](http://purl.obolibrary.org/obo/UBERON_0010891) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Muscles of the pectoral girdle, arm, forearm, and hand (brachium, antebrachium, manus respectively).[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" -#### Added -- [monocyte](http://purl.obolibrary.org/obo/CL_0000576) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### mononuclear cell `http://purl.obolibrary.org/obo/CL_0000842` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010687" -#### Added -- [mononuclear cell](http://purl.obolibrary.org/obo/CL_0000842) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### mononuclear phagocyte `http://purl.obolibrary.org/obo/CL_0000113` +### pectoral girdle region `http://purl.obolibrary.org/obo/UBERON_0001421` +#### Removed +- [pectoral girdle region](http://purl.obolibrary.org/obo/UBERON_0001421) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "An organism subdivision that includes the pectoral girdle skeleton. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There is only one instance of the pectoral girdle region per organism.[VSAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000305" -#### Added -- [mononuclear phagocyte](http://purl.obolibrary.org/obo/CL_0000113) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "https://orcid.org/0000-0002-6601-2165" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -### motor neuron `http://purl.obolibrary.org/obo/CL_0000100` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" -#### Added -- [motor neuron](http://purl.obolibrary.org/obo/CL_0000100) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [pectoral girdle region](http://purl.obolibrary.org/obo/UBERON_0001421) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [pelvic girdle region](http://purl.obolibrary.org/obo/UBERON_0001271) +- [pectoral girdle region](http://purl.obolibrary.org/obo/UBERON_0001421) [UBPROP_0000005](http://purl.obolibrary.org/obo/UBPROP_0000005) "Note that this class describes the central subdivision of the pectoral girdle complex, NOT the skeleton within.[VSAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000305" -### mouth `http://purl.obolibrary.org/obo/UBERON_0000165` -#### Removed -- [mouth](http://purl.obolibrary.org/obo/UBERON_0000165) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cavital oralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Mouth" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-06" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Curator" -- [mouth](http://purl.obolibrary.org/obo/UBERON_0000165) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "regio oralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:49184" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0004698" +- [pectoral girdle region](http://purl.obolibrary.org/obo/UBERON_0001421) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "this class describes the organism subdivision, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831)." - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [mouth](http://purl.obolibrary.org/obo/UBERON_0000165) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00003126" +### pectoral girdle skeleton `http://purl.obolibrary.org/obo/UBERON_0007831` +#### Removed +- [pectoral girdle skeleton](http://purl.obolibrary.org/obo/UBERON_0007831) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Girdle skeleton consisting of a set of bones linking the axial series to the forelimb/fin skeleton and offering anchoring areas for forelimb/fin and caudal musculature.[VSAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "https://orcid.org/0000-0002-6601-2165" -#### Added -- [mouth](http://purl.obolibrary.org/obo/UBERON_0000165) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "regio oralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:49184" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0004698" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000156" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [pectoral girdle skeleton](http://purl.obolibrary.org/obo/UBERON_0007831) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Skeletal structure immediately behind the head attached to the vertebral column by muscles and supporting the forelimbs.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000422" -- [mouth](http://purl.obolibrary.org/obo/UBERON_0000165) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00003126" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" -- [mouth](http://purl.obolibrary.org/obo/UBERON_0000165) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cavital oralis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Mouth" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" +- [pectoral girdle skeleton](http://purl.obolibrary.org/obo/UBERON_0007831) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The pectoral girdle is clearly of dual origin, composed of dermal as well as endochondral bones. The endochondral component, the scapulocoracoid, evolved by fusion or enlargment of several basal fin elements. (...) The dermal component of the shoulder girdle evolved from dermal bones of the body's surface. (...) Like endochondral bones, these dermal bones were passed along to tetrapods (...).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.336 and Figure 9.18" -### mouth mucosa `http://purl.obolibrary.org/obo/UBERON_0003729` -#### Removed -- [mouth mucosa](http://purl.obolibrary.org/obo/UBERON_0003729) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tunica mucosa oris" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Oral_mucosa" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [mouth mucosa](http://purl.obolibrary.org/obo/UBERON_0003729) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa oris" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:59660" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001156" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [pectoral girdle skeleton](http://purl.obolibrary.org/obo/UBERON_0007831) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "Note that the VSAO and many ontologies use the label 'pectoral girdle' to denote the skeletal region specifically." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "VSAO" -#### Added -- [mouth mucosa](http://purl.obolibrary.org/obo/UBERON_0003729) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa oris" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:59660" +- [pectoral girdle skeleton](http://purl.obolibrary.org/obo/UBERON_0007831) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical cluster of paired dermal and endochondral bones that attaches to the dorso-posterior part of the cranium, and support the radials and pectoral fin. It consists of two components: the primary pectoral girdle consisting of the endochondral coracoid, scapula and mesocoracoid bones, and the secondary pectoral girdle consisting of the dermal posttemporal, supracleithrum, cleithrum and poscleithrum(thra) bones.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000407" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -- [mouth mucosa](http://purl.obolibrary.org/obo/UBERON_0003729) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tunica mucosa oris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TAO:wd" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Oral_mucosa" -### mucosa `http://purl.obolibrary.org/obo/UBERON_0000344` +### pectoral muscle `http://purl.obolibrary.org/obo/UBERON_0001495` #### Removed -- [mucosa](http://purl.obolibrary.org/obo/UBERON_0000344) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tunica mucosa" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0000886" +- [pectoral muscle](http://purl.obolibrary.org/obo/UBERON_0001495) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Muscle which is comprised of three heads. The anterior head is the portio epicoracoidea that originates on the epicoracoid cartilage and inserts on the deltoid crest of the humerus. The next more posterior head, portio sternalis, originates on the sternum and inserts in the groove next to the deltoid crest of the humerus. The most posterior head, portio abdominalis, arises from the M. rectus abdominis and inserts on the deltoid crest of the humerus.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:MEJ" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Mucous_membrane" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010727" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" #### Added -- [mucosa](http://purl.obolibrary.org/obo/UBERON_0000344) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tunica mucosa" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [pectoral muscle](http://purl.obolibrary.org/obo/UBERON_0001495) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0000886" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Mucous_membrane" +### pectoral pre-muscle mass `http://purl.obolibrary.org/obo/UBERON_0010984` +#### Added +- [pectoral pre-muscle mass](http://purl.obolibrary.org/obo/UBERON_0010984) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### mucosa of deferent duct `http://purl.obolibrary.org/obo/UBERON_0004986` -#### Removed -- [mucosa of deferent duct](http://purl.obolibrary.org/obo/UBERON_0004986) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa ductus deferentis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:19240" +### pectoralis major `http://purl.obolibrary.org/obo/UBERON_0002381` +#### Removed +- [pectoralis major](http://purl.obolibrary.org/obo/UBERON_0002381) SubClassOf [axial muscle](http://purl.obolibrary.org/obo/UBERON_0003897) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [pectoralis major](http://purl.obolibrary.org/obo/UBERON_0002381) SubClassOf [innervated_by](http://purl.obolibrary.org/obo/RO_0002005) some [thoracic nerve](http://purl.obolibrary.org/obo/UBERON_0003726) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "lateral pectoral nerve and medial pectoral nerveClavicular head: C5 and C6Sternocostal head: C7 C8 and T1" -#### Added -- [mucosa of deferent duct](http://purl.obolibrary.org/obo/UBERON_0004986) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa ductus deferentis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "dbpedia" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:19240" +- [pectoralis major](http://purl.obolibrary.org/obo/UBERON_0002381) SubClassOf [has muscle origin](http://purl.obolibrary.org/obo/RO_0002372) some [sternum](http://purl.obolibrary.org/obo/UBERON_0000975) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "anterior surface of the sternum and the superior six costal cartilages and the aponeurosis of the external oblique muscle" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "dbpedia" +- [pectoralis major](http://purl.obolibrary.org/obo/UBERON_0002381) SubClassOf [has muscle origin](http://purl.obolibrary.org/obo/RO_0002372) some [clavicle bone](http://purl.obolibrary.org/obo/UBERON_0001105) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "anterior surface of the medial half of the clavicle" -### mucosa of gallbladder `http://purl.obolibrary.org/obo/UBERON_0005033` -#### Removed -- [mucosa of gallbladder](http://purl.obolibrary.org/obo/UBERON_0005033) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa vesicae biliaris" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:14662" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "dbpedia" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [pectoralis major](http://purl.obolibrary.org/obo/UBERON_0002381) SubClassOf [has muscle insertion](http://purl.obolibrary.org/obo/RO_0002373) some [humerus](http://purl.obolibrary.org/obo/UBERON_0000976) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "Lateral lip of intertubercular groove of the humerus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "dbpedia" #### Added -- [mucosa of gallbladder](http://purl.obolibrary.org/obo/UBERON_0005033) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa vesicae biliaris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [pectoralis major](http://purl.obolibrary.org/obo/UBERON_0002381) SubClassOf [has muscle insertion](http://purl.obolibrary.org/obo/RO_0002373) some [humerus](http://purl.obolibrary.org/obo/UBERON_0000976) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:14662" +- [pectoralis major](http://purl.obolibrary.org/obo/UBERON_0002381) SubClassOf [has muscle origin](http://purl.obolibrary.org/obo/RO_0002372) some [sternum](http://purl.obolibrary.org/obo/UBERON_0000975) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [pectoralis major](http://purl.obolibrary.org/obo/UBERON_0002381) SubClassOf [innervated_by](http://purl.obolibrary.org/obo/RO_0002005) some [thoracic nerve](http://purl.obolibrary.org/obo/UBERON_0003726) + +- [pectoralis major](http://purl.obolibrary.org/obo/UBERON_0002381) SubClassOf [has muscle origin](http://purl.obolibrary.org/obo/RO_0002372) some [clavicle bone](http://purl.obolibrary.org/obo/UBERON_0001105) -### mucosa of large intestine `http://purl.obolibrary.org/obo/UBERON_0001207` +### pectoralis minor `http://purl.obolibrary.org/obo/UBERON_0001100` #### Removed -- [mucosa of large intestine](http://purl.obolibrary.org/obo/UBERON_0001207) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa intestini crassi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [pectoralis minor](http://purl.obolibrary.org/obo/UBERON_0001100) SubClassOf [has muscle insertion](http://purl.obolibrary.org/obo/RO_0002373) some [medial border of scapula](http://purl.obolibrary.org/obo/UBERON_0007174) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "medial border and superior surface of the coracoid process of the scapula" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "dbpedia" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:14969" +- [pectoralis minor](http://purl.obolibrary.org/obo/UBERON_0001100) SubClassOf [has muscle origin](http://purl.obolibrary.org/obo/RO_0002372) some [rib](http://purl.obolibrary.org/obo/UBERON_0002228) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "third to fifth ribs near their costal cartilages" -#### Added -- [mucosa of large intestine](http://purl.obolibrary.org/obo/UBERON_0001207) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa intestini crassi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "dbpedia" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +#### Added +- [pectoralis minor](http://purl.obolibrary.org/obo/UBERON_0001100) SubClassOf [has muscle origin](http://purl.obolibrary.org/obo/RO_0002372) some [rib](http://purl.obolibrary.org/obo/UBERON_0002228) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:14969" +- [pectoralis minor](http://purl.obolibrary.org/obo/UBERON_0001100) SubClassOf [has muscle insertion](http://purl.obolibrary.org/obo/RO_0002373) some [medial border of scapula](http://purl.obolibrary.org/obo/UBERON_0007174) -### mucosa of larynx `http://purl.obolibrary.org/obo/UBERON_0001824` +### pedal acropodium region `http://purl.obolibrary.org/obo/UBERON_0012356` #### Removed -- [mucosa of larynx](http://purl.obolibrary.org/obo/UBERON_0001824) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa laryngis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:59662" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [pedal acropodium region](http://purl.obolibrary.org/obo/UBERON_0012356) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "class refers to an entire limb segment, not just the bones" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [mucosa of larynx](http://purl.obolibrary.org/obo/UBERON_0001824) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa laryngis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:59662" +### pedal digit bone `http://purl.obolibrary.org/obo/UBERON_0004248` +#### Removed +- [pedal digit bone](http://purl.obolibrary.org/obo/UBERON_0004248) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### mucosa of middle ear `http://purl.obolibrary.org/obo/UBERON_0005026` +### pedal digit digitopodial skeleton `http://purl.obolibrary.org/obo/UBERON_5101466` #### Removed -- [mucosa of middle ear](http://purl.obolibrary.org/obo/UBERON_0005026) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa cavitatis tympanicae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:59663" +- [pedal digit digitopodial skeleton](http://purl.obolibrary.org/obo/UBERON_5101466) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "this class represents a series of phalanges plus a metapodial element. In comparative anatomy terminology we would call this a 'digit', but the label 'digit' is sometimes used to exclude metapodials and to include soft tissue. This series of elements is hypothesized to be homologous to radials." - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + +### pedal digit epithelium `http://purl.obolibrary.org/obo/UBERON_0005226` #### Added -- [mucosa of middle ear](http://purl.obolibrary.org/obo/UBERON_0005026) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa cavitatis tympanicae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [pedal digit epithelium](http://purl.obolibrary.org/obo/UBERON_0005226) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:59663" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### pedal digit mesenchyme `http://purl.obolibrary.org/obo/UBERON_0005255` + +#### Added +- [pedal digit mesenchyme](http://purl.obolibrary.org/obo/UBERON_0005255) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### mucosa of prostatic urethra `http://purl.obolibrary.org/obo/UBERON_0005015` +### pedal digit plus metapodial segment `http://purl.obolibrary.org/obo/UBERON_5001466` #### Removed -- [mucosa of prostatic urethra](http://purl.obolibrary.org/obo/UBERON_0005015) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa urethrae prosticae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:77079" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [pedal digit plus metapodial segment](http://purl.obolibrary.org/obo/UBERON_5001466) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "this class represents a series of phalanges plus a metapodial element plus associated soft tissues. Instances of this class typically do not form a distinct unit." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "https://github.com/obophenotype/uberon/issues/458" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [mucosa of prostatic urethra](http://purl.obolibrary.org/obo/UBERON_0005015) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa urethrae prosticae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:77079" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### pedal digitopodium bone `http://purl.obolibrary.org/obo/UBERON_0012359` +#### Removed +- [pedal digitopodium bone](http://purl.obolibrary.org/obo/UBERON_0012359) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) [Skeleton-partonomy-Design-Pattern](https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### mucosa of renal pelvis `http://purl.obolibrary.org/obo/UBERON_0005006` +### pedal digitopodium region `http://purl.obolibrary.org/obo/UBERON_0012142` #### Removed -- [mucosa of renal pelvis](http://purl.obolibrary.org/obo/UBERON_0005006) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa pelvis renalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:17931" +- [pedal digitopodium region](http://purl.obolibrary.org/obo/UBERON_0012142) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "some sources call this the acropodium. see https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + +### pelvic appendage `http://purl.obolibrary.org/obo/UBERON_0004709` +#### Removed +- [pelvic appendage](http://purl.obolibrary.org/obo/UBERON_0004709) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [pelvic appendage bud](http://purl.obolibrary.org/obo/UBERON_0005420) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" #### Added -- [mucosa of renal pelvis](http://purl.obolibrary.org/obo/UBERON_0005006) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa pelvis renalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [pelvic appendage](http://purl.obolibrary.org/obo/UBERON_0004709) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [pelvic appendage bud](http://purl.obolibrary.org/obo/UBERON_0005420) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:17931" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### pelvic appendage apical ectodermal ridge `http://purl.obolibrary.org/obo/UBERON_0005422` +#### Removed +- [pelvic appendage apical ectodermal ridge](http://purl.obolibrary.org/obo/UBERON_0005422) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "An ectodermal thickening at the end of the hindlimb bud in the developing embryo. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### mucosa of seminal vesicle `http://purl.obolibrary.org/obo/UBERON_0004984` -#### Removed -- [mucosa of seminal vesicle](http://purl.obolibrary.org/obo/UBERON_0004984) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa glandulae vesiculosae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:19405" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001066" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/apical+ectodermal+ridge" -#### Added -- [mucosa of seminal vesicle](http://purl.obolibrary.org/obo/UBERON_0004984) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa glandulae vesiculosae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [pelvic appendage apical ectodermal ridge](http://purl.obolibrary.org/obo/UBERON_0005422) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Apical ectodermal ridge that is part of the pelvic fin bud.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZIFIN:curator" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:19405" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001385" -### mucosa of small intestine `http://purl.obolibrary.org/obo/UBERON_0001204` -#### Removed -- [mucosa of small intestine](http://purl.obolibrary.org/obo/UBERON_0001204) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa intestini tenuis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:14933" +- [pelvic appendage apical ectodermal ridge](http://purl.obolibrary.org/obo/UBERON_0005422) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Pectoral and pelvic fins are homologous to the tetrapod fore and hindlimb, respectively. (...) The zebrafish AER [apical ectodermal ridge] is an apical ectodermal thickening at the distal tip of the fin bud and consists of wedge-shaped cells of the basal stratum. The AER is observed only transiently, and from 36 hpf onwards the cells of this region form the apical fold (AF), which consists of a dorsal and a ventral layer of cylindrically-shaped ectodermal cells extending from the anterior to the posterior fin margin. Despite the change in shape, the AF still carries out the same functions as the AER. Indeed, although the AER receives its name from its characteristic shape, being composed of a pseudostratified ectoderm in the chicken and a polystratified ectoderm in the mouse, this independence of AER morphology from its function is also observed in tetrapods. The AF also expresses similar molecular markers to the tetrapod AER, suggesting that it fulfills similar functions in the fin as the AER does in tetrapod limbs.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1111/j.1440-169X.2007.00942.x" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [mucosa of small intestine](http://purl.obolibrary.org/obo/UBERON_0001204) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa intestini tenuis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:14933" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001066" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### mucosa of stomach `http://purl.obolibrary.org/obo/UBERON_0001199` +### pelvic appendage bud `http://purl.obolibrary.org/obo/UBERON_0005420` #### Removed -- [mucosa of stomach](http://purl.obolibrary.org/obo/UBERON_0001199) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa gastricae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:14907" +- [pelvic appendage bud](http://purl.obolibrary.org/obo/UBERON_0005420) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [mucosa of stomach](http://purl.obolibrary.org/obo/UBERON_0001199) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tunica mucosa gastris" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001308" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001260" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Gastric_mucosa" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0198540472 Janvier P, Early vertebrates (1996) p.268" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [pelvic appendage bud](http://purl.obolibrary.org/obo/UBERON_0005420) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Fin bud that develops into the pelvic fin.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -#### Added -- [mucosa of stomach](http://purl.obolibrary.org/obo/UBERON_0001199) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa gastricae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:14907" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001384" -- [mucosa of stomach](http://purl.obolibrary.org/obo/UBERON_0001199) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tunica mucosa gastris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001308" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Gastric_mucosa" +### pelvic appendage bud ectoderm `http://purl.obolibrary.org/obo/UBERON_0003371` +#### Added +- [pelvic appendage bud ectoderm](http://purl.obolibrary.org/obo/UBERON_0003371) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) -### mucosa of tongue `http://purl.obolibrary.org/obo/UBERON_0005020` -#### Removed -- [mucosa of tongue](http://purl.obolibrary.org/obo/UBERON_0005020) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa linguae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:54807" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### pelvic appendage bud mesenchyme `http://purl.obolibrary.org/obo/UBERON_0003412` +#### Removed +- [pelvic appendage bud mesenchyme](http://purl.obolibrary.org/obo/UBERON_0003412) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Mesoderm part of pelvic fin bud.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -#### Added -- [mucosa of tongue](http://purl.obolibrary.org/obo/UBERON_0005020) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa linguae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:54807" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001386" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### mucosa of ureter `http://purl.obolibrary.org/obo/UBERON_0004980` +### pelvic appendage cartilage tissue `http://purl.obolibrary.org/obo/UBERON_0007391` #### Removed -- [mucosa of ureter](http://purl.obolibrary.org/obo/UBERON_0004980) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa ureteris" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15894" +- [pelvic appendage cartilage tissue](http://purl.obolibrary.org/obo/UBERON_0007391) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Cartilage which is part of the pelvic fin.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001459" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" - -#### Added -- [mucosa of ureter](http://purl.obolibrary.org/obo/UBERON_0004980) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa ureteris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15894" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +#### Added +- [pelvic appendage cartilage tissue](http://purl.obolibrary.org/obo/UBERON_0007391) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### mucosa of urinary bladder `http://purl.obolibrary.org/obo/UBERON_0001259` +### pelvic appendage field `http://purl.obolibrary.org/obo/UBERON_0005730` #### Removed -- [mucosa of urinary bladder](http://purl.obolibrary.org/obo/UBERON_0001259) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa (vesica urinaria)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15928" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [pelvic appendage field](http://purl.obolibrary.org/obo/UBERON_0005730) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Embryonic region that develops into the pelvic fin bud.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001454" -- [mucosa of urinary bladder](http://purl.obolibrary.org/obo/UBERON_0001259) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa vesicae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15928" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [mucosa of urinary bladder](http://purl.obolibrary.org/obo/UBERON_0001259) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa (vesica urinaria)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15928" +### pelvic appendage musculature `http://purl.obolibrary.org/obo/UBERON_0007270` +#### Removed +- [pelvic appendage musculature](http://purl.obolibrary.org/obo/UBERON_0007270) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Musculature that is part of the pelvic fin.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000258" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TAO:curator" -- [mucosa of urinary bladder](http://purl.obolibrary.org/obo/UBERON_0001259) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa vesicae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15928" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### mucosa of uterine tube `http://purl.obolibrary.org/obo/UBERON_0005048` +### pelvic complex `http://purl.obolibrary.org/obo/UBERON_0010709` #### Removed -- [mucosa of uterine tube](http://purl.obolibrary.org/obo/UBERON_0005048) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa tubae uterinae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:18319" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [pelvic complex](http://purl.obolibrary.org/obo/UBERON_0010709) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [pectoral complex](http://purl.obolibrary.org/obo/UBERON_0010708) -#### Added -- [mucosa of uterine tube](http://purl.obolibrary.org/obo/UBERON_0005048) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa tubae uterinae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [pelvic complex](http://purl.obolibrary.org/obo/UBERON_0010709) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Appendage girdle complex that when present, encompasses the pelvic appendage and the pelvic girdle.[VSAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000215" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:18319" - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "VSAO:MAH" -### mucosa of vagina `http://purl.obolibrary.org/obo/UBERON_0004983` -#### Removed -- [mucosa of vagina](http://purl.obolibrary.org/obo/UBERON_0004983) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa vaginae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:19975" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [pelvic complex](http://purl.obolibrary.org/obo/UBERON_0010709) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region). Note the MA class 'hindlimb' may also belong here" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [mucosa of vagina](http://purl.obolibrary.org/obo/UBERON_0004983) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa vaginae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:19975" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### pelvic complex muscle `http://purl.obolibrary.org/obo/UBERON_0010890` +#### Removed +- [pelvic complex muscle](http://purl.obolibrary.org/obo/UBERON_0010890) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Muscles of the pelvic girdle, thigh, leg (crus), and foot (pes).[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000218" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -### mucosal invariant T cell `http://purl.obolibrary.org/obo/CL_0000940` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -#### Added -- [mucosal invariant T cell](http://purl.obolibrary.org/obo/CL_0000940) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### mucous gland `http://purl.obolibrary.org/obo/UBERON_0000414` +### pelvic girdle bone/zone `http://purl.obolibrary.org/obo/UBERON_0007830` #### Removed -- [mucous gland](http://purl.obolibrary.org/obo/UBERON_0000414) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "glandula mucosa" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Mucous_gland" +- [pelvic girdle bone/zone](http://purl.obolibrary.org/obo/UBERON_0007830) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "typically the ilium, ischium and pubis. These can alternately be considered individual bones, or zones of a single fused bone" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [pelvic girdle bone/zone](http://purl.obolibrary.org/obo/UBERON_0007830) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:18028" #### Added -- [mucous gland](http://purl.obolibrary.org/obo/UBERON_0000414) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "glandula mucosa" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Mucous_gland" +- [pelvic girdle bone/zone](http://purl.obolibrary.org/obo/UBERON_0007830) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### pelvic girdle region `http://purl.obolibrary.org/obo/UBERON_0001271` +#### Removed +- [pelvic girdle region](http://purl.obolibrary.org/obo/UBERON_0001271) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "this class describes the subdivision of the limb/fin, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831). See also comments on obo-anatomy mail list. Note that even though the class includes soft tissue it is more restrictive than 'pelvis' which also includes structures in cavities etc. TODO this needs to be better documented" -### mucous neck cell `http://purl.obolibrary.org/obo/CL_0000651` +- [pelvic girdle region](http://purl.obolibrary.org/obo/UBERON_0001271) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Subdivision of lower limb or fin which links the limb/fin to the body[FMA,modified]. There is only one instance of the pelvic girdle region per organism.[VSAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "https://orcid.org/0000-0002-6601-2165" -#### Added -- [mucous neck cell](http://purl.obolibrary.org/obo/CL_0000651) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000304" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -### mucus secreting cell `http://purl.obolibrary.org/obo/CL_0000319` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" -#### Added -- [mucus secreting cell](http://purl.obolibrary.org/obo/CL_0000319) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### multi cell part structure `http://purl.obolibrary.org/obo/UBERON_0005162` +### pelvic girdle skeleton `http://purl.obolibrary.org/obo/UBERON_0007832` #### Removed -- [multi cell part structure](http://purl.obolibrary.org/obo/UBERON_0005162) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007060" - -#### Added -- [multi cell part structure](http://purl.obolibrary.org/obo/UBERON_0005162) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007060" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [pelvic girdle skeleton](http://purl.obolibrary.org/obo/UBERON_0007832) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Girdle skeleton consisting of a set of bones linking the axial series to the hindlimb/fin skeleton and offering anchoring areas for hindlimb/fin and caudal musculature.[VSAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "https://orcid.org/0000-0002-6601-2165" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -### multi-ciliated epithelial cell `http://purl.obolibrary.org/obo/CL_0005012` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000155" -#### Added -- [multi-ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" +- [pelvic girdle skeleton](http://purl.obolibrary.org/obo/UBERON_0007832) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical cluster by which the hind limbs are supported and attached to the vertebral column.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" -### multi-tissue structure `http://purl.obolibrary.org/obo/UBERON_0000481` -#### Removed -- [multi-tissue structure](http://purl.obolibrary.org/obo/UBERON_0000481) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007010" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -#### Added -- [multi-tissue structure](http://purl.obolibrary.org/obo/UBERON_0000481) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007010" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000426" -### multicellular anatomical structure `http://purl.obolibrary.org/obo/UBERON_0010000` -#### Removed -- [multicellular anatomical structure](http://purl.obolibrary.org/obo/UBERON_0010000) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00100313" +- [pelvic girdle skeleton](http://purl.obolibrary.org/obo/UBERON_0007832) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [multicellular anatomical structure](http://purl.obolibrary.org/obo/UBERON_0010000) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00100313" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.333" -### multicellular organism `http://purl.obolibrary.org/obo/UBERON_0000468` -#### Removed -- [multicellular organism](http://purl.obolibrary.org/obo/UBERON_0000468) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000001" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [multicellular organism](http://purl.obolibrary.org/obo/UBERON_0000468) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000001" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000305" +- [pelvic girdle skeleton](http://purl.obolibrary.org/obo/UBERON_0007832) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical cluster that consists of the paired basipterygia which support the pelvic fin.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000565" -### mural cell `http://purl.obolibrary.org/obo/CL_0008034` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -#### Added -- [mural cell](http://purl.obolibrary.org/obo/CL_0008034) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TAO:wd" -### muscle cell `http://purl.obolibrary.org/obo/CL_0000187` +- [pelvic girdle skeleton](http://purl.obolibrary.org/obo/UBERON_0007832) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "Note that the VSAO and many ontologies use the label 'pelvic girdle' to denote the skeletal region specifically. We place the EHDAA2 class here, note that this includes the pre-cartilage condensation as parts" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "VSAO" #### Added -- [muscle cell](http://purl.obolibrary.org/obo/CL_0000187) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [pelvic girdle skeleton](http://purl.obolibrary.org/obo/UBERON_0007832) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### muscle layer of esophagus `http://purl.obolibrary.org/obo/UBERON_0011878` +### pelvic region of trunk `http://purl.obolibrary.org/obo/UBERON_0002355` #### Removed -- [muscle layer of esophagus](http://purl.obolibrary.org/obo/UBERON_0011878) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica muscularis oesophageae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [pelvic region of trunk](http://purl.obolibrary.org/obo/UBERON_0002355) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "pelvic" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" - -- [muscle layer of esophagus](http://purl.obolibrary.org/obo/UBERON_0011878) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tela muscularis (oesophagus)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [pelvic region of trunk](http://purl.obolibrary.org/obo/UBERON_0002355) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "MA and FMA differ in what they consider to be parts of the pelvis. MA includes ureter, urethra, urinary bladder, reproductive organs" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:62998" -- [muscle layer of esophagus](http://purl.obolibrary.org/obo/UBERON_0011878) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica muscularis esophagi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### pending final vetting `http://purl.obolibrary.org/obo/IAO_0000125` +#### Removed +- [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "pending final vetting"@en -#### Added -- [muscle layer of esophagus](http://purl.obolibrary.org/obo/UBERON_0011878) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica muscularis oesophageae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [muscle layer of esophagus](http://purl.obolibrary.org/obo/UBERON_0011878) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica muscularis esophagi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### penis `http://purl.obolibrary.org/obo/UBERON_0000989` +#### Removed +- [penis](http://purl.obolibrary.org/obo/UBERON_0000989) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "phallic" -- [muscle layer of esophagus](http://purl.obolibrary.org/obo/UBERON_0011878) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tela muscularis (oesophagus)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [penis](http://purl.obolibrary.org/obo/UBERON_0000989) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Most male birds (e.g., roosters and turkeys) have a cloaca (also present on the female), but not a penis. Among bird species with a penis are paleognathes (tinamous and ratites), Anatidae (ducks, geese and swans), and a very few other species (such as flamingoes). A bird penis is different in structure from mammal penises, being an erectile expansion of the cloacal wall and being erected by lymph, not blood. It is usually partially feathered and in some species features spines and brush-like filaments, and in flaccid state curls up inside the cloaca" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [penis](http://purl.obolibrary.org/obo/UBERON_0000989) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "penile" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:62998" -### muscle layer of large intestine `http://purl.obolibrary.org/obo/UBERON_0011198` +### penis epithelium `http://purl.obolibrary.org/obo/UBERON_0004803` #### Removed -- [muscle layer of large intestine](http://purl.obolibrary.org/obo/UBERON_0011198) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica muscularis intestini crassi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [penis epithelium](http://purl.obolibrary.org/obo/UBERON_0004803) SubClassOf [epithelium](http://purl.obolibrary.org/obo/UBERON_0000483) #### Added -- [muscle layer of large intestine](http://purl.obolibrary.org/obo/UBERON_0011198) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica muscularis intestini crassi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [penis epithelium](http://purl.obolibrary.org/obo/UBERON_0004803) SubClassOf [meso-epithelium](http://purl.obolibrary.org/obo/UBERON_0012275) -### muscle layer of oviduct `http://purl.obolibrary.org/obo/UBERON_0006642` +### perforin-1 `http://purl.obolibrary.org/obo/PR_000003466` #### Removed -- [muscle layer of oviduct](http://purl.obolibrary.org/obo/UBERON_0006642) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica muscularis tubae uterinae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:18318" +- [perforin-1](http://purl.obolibrary.org/obo/PR_000003466) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [perforin-1 (human)](http://purl.obolibrary.org/obo/PR_P14222) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [muscle layer of oviduct](http://purl.obolibrary.org/obo/UBERON_0006642) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica muscularis tubae uterinae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### periarterial lymphatic sheath `http://purl.obolibrary.org/obo/UBERON_0001960` +#### Removed +- [periarterial lymphatic sheath](http://purl.obolibrary.org/obo/UBERON_0001960) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA distinguishes periarterial (PALS) from periarteriolar (FMA:62806)" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:18318" +- [periarterial lymphatic sheath](http://purl.obolibrary.org/obo/UBERON_0001960) SubClassOf [digestive system element](http://purl.obolibrary.org/obo/UBERON_0013765) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### muscle layer of small intestine `http://purl.obolibrary.org/obo/UBERON_0011201` +### pericardial cavity `http://purl.obolibrary.org/obo/UBERON_0001074` #### Removed -- [muscle layer of small intestine](http://purl.obolibrary.org/obo/UBERON_0011201) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica muscularis intestini tenuis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [pericardial cavity](http://purl.obolibrary.org/obo/UBERON_0001074) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart (of other tetrapods) is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [muscle layer of small intestine](http://purl.obolibrary.org/obo/UBERON_0011201) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica muscularis intestini tenuis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000556" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### muscle of iris `http://purl.obolibrary.org/obo/UBERON_0001606` -#### Removed -- [muscle of iris](http://purl.obolibrary.org/obo/UBERON_0001606) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Iris_muscle" +- [pericardial cavity](http://purl.obolibrary.org/obo/UBERON_0001074) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "check ZFA, should actually be thoracic cavity. Note that Hyman defines the cavity as the space between the heart and the sac (but defines the sac as parietal)" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "ZFA" +- [pericardial cavity](http://purl.obolibrary.org/obo/UBERON_0001074) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical space in which the heart is located and is surrounded by the pericardium.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -### muscle precursor cell `http://purl.obolibrary.org/obo/CL_0000680` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -#### Added -- [muscle precursor cell](http://purl.obolibrary.org/obo/CL_0000680) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0002220" -### muscular coat `http://purl.obolibrary.org/obo/UBERON_0006660` + +### pericardial fluid `http://purl.obolibrary.org/obo/UBERON_0002409` #### Removed -- [muscular coat](http://purl.obolibrary.org/obo/UBERON_0006660) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica muscularis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0004838" +- [pericardial fluid](http://purl.obolibrary.org/obo/UBERON_0002409) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D000069236" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) -#### Added -- [muscular coat](http://purl.obolibrary.org/obo/UBERON_0006660) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica muscularis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0004838" -### muscular coat of seminal vesicle `http://purl.obolibrary.org/obo/UBERON_0004665` +### pericardial sac `http://purl.obolibrary.org/obo/UBERON_0002406` #### Removed -- [muscular coat of seminal vesicle](http://purl.obolibrary.org/obo/UBERON_0004665) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica muscularis glandulae vesiculosae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:19404" +- [pericardial sac](http://purl.obolibrary.org/obo/UBERON_0002406) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "TAO:0000054" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" - -#### Added -- [muscular coat of seminal vesicle](http://purl.obolibrary.org/obo/UBERON_0004665) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica muscularis glandulae vesiculosae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:19404" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### pericardium `http://purl.obolibrary.org/obo/UBERON_0002407` +#### Removed +- [pericardium](http://purl.obolibrary.org/obo/UBERON_0002407) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:16133" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [pericardium](http://purl.obolibrary.org/obo/UBERON_0002407) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "TAO:0000054" +- [pericardium](http://purl.obolibrary.org/obo/UBERON_0002407) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Peritoneum that surrounds the heart.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:JMG" -### muscular coat of ureter `http://purl.obolibrary.org/obo/UBERON_0006855` -#### Removed -- [muscular coat of ureter](http://purl.obolibrary.org/obo/UBERON_0006855) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica muscularis ureteris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -- [muscular coat of ureter](http://purl.obolibrary.org/obo/UBERON_0006855) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica muscularis (ureter)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010817" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [pericardium](http://purl.obolibrary.org/obo/UBERON_0002407) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "this class denotes a combination of fibrous PC + PC sac (itself a combination of cavity, epithelium and connective tissue). Many sources use the term 'pericardium' to denote either just the serous membrane (ZFA) or the epithelium (GO)" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "ZFA" -#### Added -- [muscular coat of ureter](http://purl.obolibrary.org/obo/UBERON_0006855) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica muscularis ureteris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [pericardium](http://purl.obolibrary.org/obo/UBERON_0002407) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "we follow FMA in dividing pericardium into pericardial sac and fibrous pericardium" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [pericardium](http://purl.obolibrary.org/obo/UBERON_0002407) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "pericardial" -- [muscular coat of ureter](http://purl.obolibrary.org/obo/UBERON_0006855) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica muscularis (ureter)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [pericardium](http://purl.obolibrary.org/obo/UBERON_0002407) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "In GO the concept of pericardium is developmental implicitly epithelial, but here it represents a multi-tissue structure encompassing the sac (epithelium plus connective) and cavity" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### muscular coat of vas deferens `http://purl.obolibrary.org/obo/UBERON_0004224` +### perichondrium `http://purl.obolibrary.org/obo/UBERON_0002222` #### Removed -- [muscular coat of vas deferens](http://purl.obolibrary.org/obo/UBERON_0004224) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica muscularis ductus deferentis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:19239" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [perichondrium](http://purl.obolibrary.org/obo/UBERON_0002222) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Portion of connective tissue which surrounds cartilage.[TAO]" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -#### Added -- [muscular coat of vas deferens](http://purl.obolibrary.org/obo/UBERON_0004224) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica muscularis ductus deferentis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TAO:wd" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:19239" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001643" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### muscular layer of vagina `http://purl.obolibrary.org/obo/UBERON_0006652` +### perichordal bone `http://purl.obolibrary.org/obo/UBERON_0008909` #### Removed -- [muscular layer of vagina](http://purl.obolibrary.org/obo/UBERON_0006652) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica muscularis vaginae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:19976" +- [perichordal bone](http://purl.obolibrary.org/obo/UBERON_0008909) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Replacement bone that forms within the connective tissue surrounding the notochord.[TAO]" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TAO:wd" -#### Added -- [muscular layer of vagina](http://purl.obolibrary.org/obo/UBERON_0006652) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica muscularis vaginae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:19976" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001639" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [perichordal bone](http://purl.obolibrary.org/obo/UBERON_0008909) SubClassOf [replacement bone](http://purl.obolibrary.org/obo/UBERON_0012075) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "not in VSAO" +#### Added +- [perichordal bone](http://purl.obolibrary.org/obo/UBERON_0008909) SubClassOf [replacement bone](http://purl.obolibrary.org/obo/UBERON_0012075) -### musculature `http://purl.obolibrary.org/obo/UBERON_0001015` -#### Removed -- [musculature](http://purl.obolibrary.org/obo/UBERON_0001015) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "musculi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:32558" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### periderm `http://purl.obolibrary.org/obo/UBERON_0003055` +#### Removed +- [periderm](http://purl.obolibrary.org/obo/UBERON_0003055) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "Originally the epidermis is one layer thick, in most vertebrates it soon becomes a two-layered structure. The outer layer gives rise to the periderm. The periderm goes through distinct developmental phases and is ultimately sloughed into the amniotic fluid when differentiation of the underlying epidermal layers is complete. The function of the periderm is not known, but is thought to be related to transport/exchange between the fetus and the amniotic fluid (http://courses.washington.edu/hubio567/devbio/periderm.html)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [periderm](http://purl.obolibrary.org/obo/UBERON_0003055) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The outermost epidermal layer covering the fish at embryonic stages; derived from the EVL and thought to eventually be replaced by the superficial stratum of the epidermis. Sometimes used synonymously with EVL. Le Guellec et al, 2004.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001185" -#### Added -- [musculature](http://purl.obolibrary.org/obo/UBERON_0001015) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "musculi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:32558" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" +- [periderm](http://purl.obolibrary.org/obo/UBERON_0003055) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0003377" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### musculature of back `http://purl.obolibrary.org/obo/UBERON_0004469` -#### Removed -- [musculature of back](http://purl.obolibrary.org/obo/UBERON_0004469) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "musculi dorsi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71291" + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [periderm](http://purl.obolibrary.org/obo/UBERON_0003055) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship type change: OBO_REL:part_of ectoderm (TAO:0000016) CHANGED TO: develops_from ectoderm (UBERON:0000924)[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001185" -#### Added -- [musculature of back](http://purl.obolibrary.org/obo/UBERON_0004469) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "musculi dorsi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71291" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [periderm](http://purl.obolibrary.org/obo/UBERON_0003055) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "periderm" +- [periderm](http://purl.obolibrary.org/obo/UBERON_0003055) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "epidermis outer layer" -### musculature of face `http://purl.obolibrary.org/obo/UBERON_0004473` -#### Removed -- [musculature of face](http://purl.obolibrary.org/obo/UBERON_0004473) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "musculi faciei" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [periderm](http://purl.obolibrary.org/obo/UBERON_0003055) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "skin periderm" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EHDAA2:0001846" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71288" +- [periderm](http://purl.obolibrary.org/obo/UBERON_0003055) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In mice, the first non-basal layer formed at ~E9.5; it is a temporary structure composed of simple squamous epithelium that serves as the first barrier to the embryo's physical environment, exists throughout the entire keratinocyte stratification process, and sheds off at ~E17, when it is replaced by corneocytes[MP]" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [periderm](http://purl.obolibrary.org/obo/UBERON_0003055) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "EVL" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0001185" -#### Added -- [musculature of face](http://purl.obolibrary.org/obo/UBERON_0004473) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "musculi faciei" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [periderm](http://purl.obolibrary.org/obo/UBERON_0003055) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A temporary epithelium that derives from the outer layer of the ectdoerm and is shed once the inner layer differentiates to form a true epidermis." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:9780878932504" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71288" +- [periderm](http://purl.obolibrary.org/obo/UBERON_0003055) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "In some mammals, Eyelid Fusion is thought to be driven by a population of cells which are derived from the periderm, the outermost layer of the developing epidermis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [periderm](http://purl.obolibrary.org/obo/UBERON_0003055) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "epitrichium" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MP:0013530" +- [periderm](http://purl.obolibrary.org/obo/UBERON_0003055) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "epidermis epithelial layer" -### musculature of neck `http://purl.obolibrary.org/obo/UBERON_0004465` -#### Removed -- [musculature of neck](http://purl.obolibrary.org/obo/UBERON_0004465) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "musculi colli" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71290" +- [periderm](http://purl.obolibrary.org/obo/UBERON_0003055) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [integument](http://purl.obolibrary.org/obo/UBERON_0002199) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "EHDAA2" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [periderm](http://purl.obolibrary.org/obo/UBERON_0003055) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [enveloping layer of ectoderm](http://purl.obolibrary.org/obo/UBERON_0007383) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +#### Added +- [periderm](http://purl.obolibrary.org/obo/UBERON_0003055) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "epitrichium" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:28722897" -- [musculature of neck](http://purl.obolibrary.org/obo/UBERON_0004465) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "musculi cervicis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71290" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MP:0013530" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [periderm](http://purl.obolibrary.org/obo/UBERON_0003055) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "EVL" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0001185" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [abbreviation](http://purl.obolibrary.org/obo/OMO_0003000) -#### Added -- [musculature of neck](http://purl.obolibrary.org/obo/UBERON_0004465) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "musculi colli" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [periderm](http://purl.obolibrary.org/obo/UBERON_0003055) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "The outermost layer (or layers, depending on the species) of embryonic skin, essential for the development of the epidermis and establishment of the barrier functions. The periderm derives from the outer layer of the ectoderm." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:25133425" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71290" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35582825" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:9780878932504" -- [musculature of neck](http://purl.obolibrary.org/obo/UBERON_0004465) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "musculi cervicis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [periderm](http://purl.obolibrary.org/obo/UBERON_0003055) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "enveloping layer" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0001185" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71290" +- [periderm](http://purl.obolibrary.org/obo/UBERON_0003055) SubClassOf [outer epithelium](http://purl.obolibrary.org/obo/UBERON_0007376) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [periderm](http://purl.obolibrary.org/obo/UBERON_0003055) SubClassOf [external integument structure](http://purl.obolibrary.org/obo/UBERON_3000961) -### musculature of thorax `http://purl.obolibrary.org/obo/UBERON_0004464` +### perilymphatic channel `http://purl.obolibrary.org/obo/UBERON_0011060` #### Removed -- [musculature of thorax](http://purl.obolibrary.org/obo/UBERON_0004464) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "musculi thoracis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71293" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [perilymphatic channel](http://purl.obolibrary.org/obo/UBERON_0011060) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Duct that contains perilymph[ZFA:0005461, ZFIN:curator]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFA:0005461, ZFIN:curator" #### Added -- [musculature of thorax](http://purl.obolibrary.org/obo/UBERON_0004464) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "musculi thoracis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71293" +- [perilymphatic channel](http://purl.obolibrary.org/obo/UBERON_0011060) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### perineurium `http://purl.obolibrary.org/obo/UBERON_0000121` +#### Removed +- [perineurium](http://purl.obolibrary.org/obo/UBERON_0000121) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Connective tissue surrounding a fascicle[Wikipedia:Perineurium]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Perineurium" +- [perineurium](http://purl.obolibrary.org/obo/UBERON_0000121) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "perineurial" -### mushroom body `http://purl.obolibrary.org/obo/UBERON_0001058` -#### Removed -- [mushroom body](http://purl.obolibrary.org/obo/UBERON_0001058) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005801" +- [perineurium](http://purl.obolibrary.org/obo/UBERON_0000121) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "consider FBbt:00007090 (perineurium): The outer two layers of glial cells that cover the central nervous system and the nerves. The outer layer is the perineurial sheath (sometimes referred to as the perineurial sheath outer layer); the inner layer is the sub-perineural glial sheath (sometimes referred to as the perineurial sheath inner layer)" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FBbt" -#### Added -- [mushroom body](http://purl.obolibrary.org/obo/UBERON_0001058) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005801" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### myelencephalon `http://purl.obolibrary.org/obo/UBERON_0005290` +### periodontal ligament `http://purl.obolibrary.org/obo/UBERON_0008266` #### Removed -- [myelencephalon](http://purl.obolibrary.org/obo/UBERON_0005290) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D054024" +- [periodontal ligament](http://purl.obolibrary.org/obo/UBERON_0008266) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The collagen fibers, running from the cementum to the alveolar bone, that suspend a tooth in its socket; they include apical, oblique, horizontal, and alveolar crest fibers, indicating that the orientation of the fibers varies at different levels[http://www.drugs.com/dict/desmodentium.html]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://www.drugs.com/dict/desmodentium.html" -#### Added -- [myelencephalon](http://purl.obolibrary.org/obo/UBERON_0005290) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D054024" +- [periodontal ligament](http://purl.obolibrary.org/obo/UBERON_0008266) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The fibrous connective tissue that surrounds the root of a tooth, separating it from and attaching it to the alveolar bone. It extends from the base of the gingival mucosa to the fundus of the bony socket, and its main function is to hold the tooth in its socket[BTO]. It consist of cells, extracellular compartment of fibers. The cells are fibroblast, epithelial, undifferentiated mesenchymal cells, bone and cementum cells. The extracellular compartment consists of collagen fibers bundles embedded in ground substance. The PDL substance has been estimated to be 70% water and is thought to have a significant effect on the tooth's ability to withstand stress loads[WP][BTO:0001020, Wikipedia:Periodontal_fiber, https://github.com/obophenotype/uberon/issues/21]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Periodontal_fiber" + +- [periodontal ligament](http://purl.obolibrary.org/obo/UBERON_0008266) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D010513" - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +- [periodontal ligament](http://purl.obolibrary.org/obo/UBERON_0008266) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA treats periodontium and periodontal ligament as the same; it has a separate class desmodentium, which we place here even though it is classified as fetal in FMA" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" -### myeloblast `http://purl.obolibrary.org/obo/CL_0000835` -#### Removed -- [myeloblast](http://purl.obolibrary.org/obo/CL_0000835) EquivalentTo [granulocytopoietic cell](http://purl.obolibrary.org/obo/CL_0002191) and ([has part](http://purl.obolibrary.org/obo/BFO_0000051) some [basophilic cytoplasm](http://purl.obolibrary.org/obo/CL_0017503)) and ([has part](http://purl.obolibrary.org/obo/BFO_0000051) some [obsolete increased nucleus size](http://purl.obolibrary.org/obo/CL_0017505)) and ([has part](http://purl.obolibrary.org/obo/BFO_0000051) some [euchromatin](http://purl.obolibrary.org/obo/GO_0000791)) and ([lacks_part](http://purl.obolibrary.org/obo/CL_4030045) some [azurophil granule](http://purl.obolibrary.org/obo/GO_0042582)) - -- [myeloblast](http://purl.obolibrary.org/obo/CL_0000835) SubClassOf [has part](http://purl.obolibrary.org/obo/BFO_0000051) some [obsolete increased nucleus size](http://purl.obolibrary.org/obo/CL_0017505) -#### Added -- [myeloblast](http://purl.obolibrary.org/obo/CL_0000835) EquivalentTo [granulocytopoietic cell](http://purl.obolibrary.org/obo/CL_0002191) and ([has part](http://purl.obolibrary.org/obo/BFO_0000051) some [basophilic cytoplasm](http://purl.obolibrary.org/obo/CL_0017503)) and ([has part](http://purl.obolibrary.org/obo/BFO_0000051) some [euchromatin](http://purl.obolibrary.org/obo/GO_0000791)) and ([lacks_part](http://purl.obolibrary.org/obo/CL_4030045) some [azurophil granule](http://purl.obolibrary.org/obo/GO_0042582)) and ([bearer of](http://purl.obolibrary.org/obo/RO_0000053) some [high nuclear/cytoplasmic ratio](http://purl.obolibrary.org/obo/PATO_0040072)) -- [myeloblast](http://purl.obolibrary.org/obo/CL_0000835) SubClassOf [bearer of](http://purl.obolibrary.org/obo/RO_0000053) some [high nuclear/cytoplasmic ratio](http://purl.obolibrary.org/obo/PATO_0040072) +### periodontium `http://purl.obolibrary.org/obo/UBERON_0001758` +#### Removed +- [periodontium](http://purl.obolibrary.org/obo/UBERON_0001758) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA treats periodontium and periodontal ligament as the same" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" -### myelocyte `http://purl.obolibrary.org/obo/CL_0002193` -#### Added -- [myelocyte](http://purl.obolibrary.org/obo/CL_0002193) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### periosteum `http://purl.obolibrary.org/obo/UBERON_0002515` +#### Removed +- [periosteum](http://purl.obolibrary.org/obo/UBERON_0002515) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "periosteal" -### myeloid cell `http://purl.obolibrary.org/obo/CL_0000763` -#### Added -- [myeloid cell](http://purl.obolibrary.org/obo/CL_0000763) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### peripheral nervous system `http://purl.obolibrary.org/obo/UBERON_0000010` +#### Removed +- [peripheral nervous system](http://purl.obolibrary.org/obo/UBERON_0000010) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) specific vertebrate traits within the chordate phylum such as skeletal tissues, PNS, and spectacular head and brain development, are linked to the NC (neural crest) and its derivatives.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### myeloid dendritic cell `http://purl.obolibrary.org/obo/CL_0000782` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [myeloid dendritic cell](http://purl.obolibrary.org/obo/CL_0000782) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000399" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1007/978-0-387-46954-6_6 Dupin E, Creuzet S, Le Douarin NM, The contribution of the neural crest to the vertebrate body. Advances in experimental medicine and biology (2006)" -### myeloid dendritic cell, human `http://purl.obolibrary.org/obo/CL_0001057` +- [peripheral nervous system](http://purl.obolibrary.org/obo/UBERON_0000010) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Part of nervous system in which nerves extend throughout the body outside of the brain and spinal cord.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -#### Added -- [myeloid dendritic cell, human](http://purl.obolibrary.org/obo/CL_0001057) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" -### myeloid leukocyte `http://purl.obolibrary.org/obo/CL_0000766` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000429" -#### Added -- [myeloid leukocyte](http://purl.obolibrary.org/obo/CL_0000766) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [peripheral nervous system](http://purl.obolibrary.org/obo/UBERON_0000010) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The peripheral nervous system (PNS) is the part of the nervous system connected to the CNS which contains cranial nerves III - XII, spinal, peripheral and autonomic nerves. (CUMBO)" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://neurolex.org/wiki/Cumbo_terms" +- [peripheral nervous system](http://purl.obolibrary.org/obo/UBERON_0000010) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005098" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### myeloid lineage restricted progenitor cell `http://purl.obolibrary.org/obo/CL_0000839` +- [peripheral nervous system](http://purl.obolibrary.org/obo/UBERON_0000010) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Nervous structures including ganglia outside of the central nervous system. Kimmel et al, 1995.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -#### Added -- [myeloid lineage restricted progenitor cell](http://purl.obolibrary.org/obo/CL_0000839) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000142" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -### myoepithelial cell `http://purl.obolibrary.org/obo/CL_0000185` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -#### Added -- [myoepithelial cell](http://purl.obolibrary.org/obo/CL_0000185) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### myoepithelial cell of mammary gland `http://purl.obolibrary.org/obo/CL_0002324` +### perirenal preadipocyte `http://purl.obolibrary.org/obo/CL_0002581` #### Added -- [myoepithelial cell of mammary gland](http://purl.obolibrary.org/obo/CL_0002324) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [perirenal preadipocyte](http://purl.obolibrary.org/obo/CL_0002581) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A preadipocyte that is part of a perirenal fat tissue." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20106964" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31079959" -### myoepithelium `http://purl.obolibrary.org/obo/UBERON_0000420` + +### peritoneal cavity `http://purl.obolibrary.org/obo/UBERON_0001179` #### Removed -- [myoepithelium](http://purl.obolibrary.org/obo/UBERON_0000420) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "myoepitheliocytus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [peritoneal cavity](http://purl.obolibrary.org/obo/UBERON_0001179) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes) Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Myoepithelial_cell" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [myoepithelium](http://purl.obolibrary.org/obo/UBERON_0000420) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "myoepitheliocytus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Myoepithelial_cell" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000852" -### myofibroblast cell `http://purl.obolibrary.org/obo/CL_0000186` +- [peritoneal cavity](http://purl.obolibrary.org/obo/UBERON_0001179) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The potential space between the parietal and visceral layers of the peritoneum, which are normally in contact. The peritoneal cavity is divided into the greater and lesser sac. The greater sac is the peritoneal cavity, and the lesser sac is the omental bursa. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/peritoneal+cavity" -#### Added -- [myofibroblast cell](http://purl.obolibrary.org/obo/CL_0000186) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### myometrial cell `http://purl.obolibrary.org/obo/CL_0002366` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [myometrial cell](http://purl.obolibrary.org/obo/CL_0002366) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000852" -### myometrium `http://purl.obolibrary.org/obo/UBERON_0001296` + +### peritoneal cavity mesothelium `http://purl.obolibrary.org/obo/UBERON_0005669` #### Removed -- [myometrium](http://purl.obolibrary.org/obo/UBERON_0001296) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tunica muscularis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Myometrium" +- [peritoneal cavity mesothelium](http://purl.obolibrary.org/obo/UBERON_0005669) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "we believe that this corresponds to EMAPA:16139 based on synonyms and parenthood" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EMAPA" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [myometrium](http://purl.obolibrary.org/obo/UBERON_0001296) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tunica muscularis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Myometrium" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### peritoneal fluid `http://purl.obolibrary.org/obo/UBERON_0001268` +#### Removed +- [peritoneal fluid](http://purl.obolibrary.org/obo/UBERON_0001268) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D001202" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -### myotome `http://purl.obolibrary.org/obo/UBERON_0003082` + + +### peritoneum `http://purl.obolibrary.org/obo/UBERON_0002358` #### Removed -- [myotome](http://purl.obolibrary.org/obo/UBERON_0003082) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "myotomus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Myotome" +- [peritoneum](http://purl.obolibrary.org/obo/UBERON_0002358) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "An epithelium that lines the peritoneal cavity.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005120" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -#### Added -- [myotome](http://purl.obolibrary.org/obo/UBERON_0003082) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "myotomus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Myotome" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" +- [peritoneum](http://purl.obolibrary.org/obo/UBERON_0002358) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "todo: check MA/EMAPA." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" -### nail plate `http://purl.obolibrary.org/obo/UBERON_0008198` -#### Removed -- [nail plate](http://purl.obolibrary.org/obo/UBERON_0008198) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lamina unguis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Nail_plate" +- [peritoneum](http://purl.obolibrary.org/obo/UBERON_0002358) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Serous membrane that forms the lining of the abdominal cavity or the coelom. It covers most of the intra-abdominal organs, supports the abdominal organs, and serves as a conduit for their blood and lymph vessels and nerves. It is composed of a layer of mesothelium.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010814" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:JMG" -#### Added -- [nail plate](http://purl.obolibrary.org/obo/UBERON_0008198) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lamina unguis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Nail_plate" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" +- [peritoneum](http://purl.obolibrary.org/obo/UBERON_0002358) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "peritoneal" -### naive B cell `http://purl.obolibrary.org/obo/CL_0000788` -#### Added -- [naive B cell](http://purl.obolibrary.org/obo/CL_0000788) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### perivascular macrophage `http://purl.obolibrary.org/obo/CL_0000881` +#### Removed +- [perivascular macrophage](http://purl.obolibrary.org/obo/CL_0000881) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A central nervous system macrophage found in small blood vessels in the brain. Markers include CD14+CD16+CD163+." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm" -### naive T cell `http://purl.obolibrary.org/obo/CL_0000898` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO_REF:0000031" -#### Added -- [naive T cell](http://purl.obolibrary.org/obo/CL_0000898) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:16507898" +- [perivascular macrophage](http://purl.obolibrary.org/obo/CL_0000881) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Markers: Human/monkey, mice: CD163. Human: CD14+CD16+CD163+." -### naive regulatory T cell `http://purl.obolibrary.org/obo/CL_0002677` +- [perivascular macrophage](http://purl.obolibrary.org/obo/CL_0000881) EquivalentTo [central nervous system macrophage](http://purl.obolibrary.org/obo/CL_0000878) and ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [blood vessel](http://purl.obolibrary.org/obo/UBERON_0001981)) and ([has plasma membrane part](http://purl.obolibrary.org/obo/RO_0002104) some [low affinity immunoglobulin gamma Fc region receptor III](http://purl.obolibrary.org/obo/PR_000001483)) and ([has plasma membrane part](http://purl.obolibrary.org/obo/RO_0002104) some [CD14 molecule](http://purl.obolibrary.org/obo/PR_000001889)) and ([has plasma membrane part](http://purl.obolibrary.org/obo/RO_0002104) some [scavenger receptor cysteine-rich type 1 protein M130](http://purl.obolibrary.org/obo/PR_000001925)) + +- [perivascular macrophage](http://purl.obolibrary.org/obo/CL_0000881) SubClassOf [central nervous system macrophage](http://purl.obolibrary.org/obo/CL_0000878) + - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true" #### Added -- [naive regulatory T cell](http://purl.obolibrary.org/obo/CL_0002677) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [perivascular macrophage](http://purl.obolibrary.org/obo/CL_0000881) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pvMΦ" + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [abbreviation](http://purl.obolibrary.org/obo/OMO_0003000) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37232741" -### naive thymus-derived CD4-positive, alpha-beta T cell `http://purl.obolibrary.org/obo/CL_0000895` +- [perivascular macrophage](http://purl.obolibrary.org/obo/CL_0000881) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A border associated macrophage that is adjacent to a small blood vessel of a brain. A perivascular macrophage expresses the markers CD14, CD16 and CD163. In homeostatic conditions, this central nervous system macrophage has a non-motile cell body with extending and retracting projections through the blood vessel wall." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm" -#### Added -- [naive thymus-derived CD4-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_0000895) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO_REF:0000031" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:16507898" -### naive thymus-derived CD8-positive, alpha-beta T cell `http://purl.obolibrary.org/obo/CL_0000900` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37232741" -#### Added -- [naive thymus-derived CD8-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_0000900) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [perivascular macrophage](http://purl.obolibrary.org/obo/CL_0000881) EquivalentTo [border associated macrophage](http://purl.obolibrary.org/obo/CL_4042003) and ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [blood vessel](http://purl.obolibrary.org/obo/UBERON_0001981)) and ([has plasma membrane part](http://purl.obolibrary.org/obo/RO_0002104) some [low affinity immunoglobulin gamma Fc region receptor III](http://purl.obolibrary.org/obo/PR_000001483)) and ([has plasma membrane part](http://purl.obolibrary.org/obo/RO_0002104) some [CD14 molecule](http://purl.obolibrary.org/obo/PR_000001889)) and ([has plasma membrane part](http://purl.obolibrary.org/obo/RO_0002104) some [scavenger receptor cysteine-rich type 1 protein M130](http://purl.obolibrary.org/obo/PR_000001925)) +- [perivascular macrophage](http://purl.obolibrary.org/obo/CL_0000881) SubClassOf [border associated macrophage](http://purl.obolibrary.org/obo/CL_4042003) + - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true" -### nasal cartilage `http://purl.obolibrary.org/obo/UBERON_0001823` + +### periventricular nucleus `http://purl.obolibrary.org/obo/UBERON_0002322` #### Removed -- [nasal cartilage](http://purl.obolibrary.org/obo/UBERON_0001823) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D055171" +- [periventricular nucleus](http://purl.obolibrary.org/obo/UBERON_0002322) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Diencephalic nucleus which is the periventricular part of the ventral hypothalamic zone. From Neuroanatomy of the Zebrafish Brain." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFA:0000260, GOC:MAH, ISBN:3764351209" -#### Added -- [nasal cartilage](http://purl.obolibrary.org/obo/UBERON_0001823) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D055171" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +### periventricular zone of hypothalamus `http://purl.obolibrary.org/obo/UBERON_0002271` +#### Added +- [periventricular zone of hypothalamus](http://purl.obolibrary.org/obo/UBERON_0002271) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### nasal cavity `http://purl.obolibrary.org/obo/UBERON_0001707` + +### pes `http://purl.obolibrary.org/obo/UBERON_0002387` #### Removed -- [nasal cavity](http://purl.obolibrary.org/obo/UBERON_0001707) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cavitas nasi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0002096" +- [pes](http://purl.obolibrary.org/obo/UBERON_0002387) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "pedal" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Nasal_cavity" -- [nasal cavity](http://purl.obolibrary.org/obo/UBERON_0001707) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cavum nasi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### pes bone `http://purl.obolibrary.org/obo/UBERON_0005899` +#### Removed +- [pes bone](http://purl.obolibrary.org/obo/UBERON_0005899) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Nasal_cavity" -#### Added -- [nasal cavity](http://purl.obolibrary.org/obo/UBERON_0001707) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cavum nasi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Nasal_cavity" +### pes connective tissue `http://purl.obolibrary.org/obo/UBERON_0003595` + +#### Added +- [pes connective tissue](http://purl.obolibrary.org/obo/UBERON_0003595) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -- [nasal cavity](http://purl.obolibrary.org/obo/UBERON_0001707) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cavitas nasi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0002096" +### pes joint `http://purl.obolibrary.org/obo/UBERON_0001487` +#### Removed +- [pes joint](http://purl.obolibrary.org/obo/UBERON_0001487) [UBPROP_0000202](http://purl.obolibrary.org/obo/UBPROP_0000202) [FMA_71349](http://purl.obolibrary.org/obo/FMA_71349) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Nasal_cavity" -### nasal cavity mucosa `http://purl.obolibrary.org/obo/UBERON_0001826` +### petrous part of temporal bone `http://purl.obolibrary.org/obo/UBERON_0001694` #### Removed -- [nasal cavity mucosa](http://purl.obolibrary.org/obo/UBERON_0001826) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa nasi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:59684" +- [petrous part of temporal bone](http://purl.obolibrary.org/obo/UBERON_0001694) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "derivative of prootic and opisthotic" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [petrous part of temporal bone](http://purl.obolibrary.org/obo/UBERON_0001694) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The petrosal bone arises from the two otic bones on the lateral wall of the chondrocranium and encases the inner ear of mammals. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, p.258, see_Liem_KF][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001553" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [nasal cavity mucosa](http://purl.obolibrary.org/obo/UBERON_0001826) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa nasi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:59684" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### phalanx `http://purl.obolibrary.org/obo/UBERON_0003221` +#### Removed +- [phalanx](http://purl.obolibrary.org/obo/UBERON_0003221) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In primates such as humans and monkeys, the thumb and big toe have two phalanges, while the other fingers and toes consist of three" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" -### nasal mucosa goblet cell `http://purl.obolibrary.org/obo/CL_0002480` +- [phalanx](http://purl.obolibrary.org/obo/UBERON_0003221) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "phalangeal" -#### Added -- [nasal mucosa goblet cell](http://purl.obolibrary.org/obo/CL_0002480) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### nasal vestibule `http://purl.obolibrary.org/obo/UBERON_0000402` +### phalanx of manus `http://purl.obolibrary.org/obo/UBERON_0001436` #### Removed -- [nasal vestibule](http://purl.obolibrary.org/obo/UBERON_0000402) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vestibulum nasi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Nasal_vestibule" +- [phalanx of manus](http://purl.obolibrary.org/obo/UBERON_0001436) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Dumb-bell shaped bones of endochondral origin with cartilaginous epiphyses that make the four digits of the manus. The terminal phalanges are much smaller than the proximal and penultimate phalanges. The typical phalangeal formula of the manus, in a medial to lateral sequence, is 2-2-3-3.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001761" - -#### Added -- [nasal vestibule](http://purl.obolibrary.org/obo/UBERON_0000402) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vestibulum nasi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Nasal_vestibule" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000947" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001761" -### nasolacrimal duct `http://purl.obolibrary.org/obo/UBERON_0002392` +### phalanx of pes `http://purl.obolibrary.org/obo/UBERON_0001449` #### Removed -- [nasolacrimal duct](http://purl.obolibrary.org/obo/UBERON_0002392) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "d. nasolacrimalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Nasolacrimal_duct" +- [phalanx of pes](http://purl.obolibrary.org/obo/UBERON_0001449) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Dumb-bell shaped bones of endochondral origin with cartilaginous epiphyses that make the five digits of the pes. The terminal phalanges are much smaller than the proximal and penultimate phalanges. The typical phalangeal formula of the pes, in a medial to lateral sequence, is 2(1)-2-3-4(3)-3(2).[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -#### Added -- [nasolacrimal duct](http://purl.obolibrary.org/obo/UBERON_0002392) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "d. nasolacrimalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000930" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Nasolacrimal_duct" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### nasolacrimal groove `http://purl.obolibrary.org/obo/UBERON_0006266` + +### pharyngeal arch `http://purl.obolibrary.org/obo/UBERON_0002539` #### Removed -- [nasolacrimal groove](http://purl.obolibrary.org/obo/UBERON_0006266) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "s. lacrimalis maxillae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lacrimal_groove" +- [pharyngeal arch](http://purl.obolibrary.org/obo/UBERON_0002539) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "Numbered cranial to caudal. different in mammals. branchial arch = ZFA:0001613 pharyngeal arch 3-7. generally gill arch 1 = pharyngeal arch 3. terminology varies as to whether branchial arch follows gill or pharyngeal numbering" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [pharyngeal arch](http://purl.obolibrary.org/obo/UBERON_0002539) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [nasolacrimal groove](http://purl.obolibrary.org/obo/UBERON_0006266) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "s. lacrimalis maxillae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lacrimal_groove" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### nasopharynx `http://purl.obolibrary.org/obo/UBERON_0001728` -#### Removed -- [nasopharynx](http://purl.obolibrary.org/obo/UBERON_0001728) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pars nasalis pharyngis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Nasopharynx" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000155" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [pharyngeal arch](http://purl.obolibrary.org/obo/UBERON_0002539) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "One of a series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "NLM:branchial+arch" -#### Added -- [nasopharynx](http://purl.obolibrary.org/obo/UBERON_0001728) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pars nasalis pharyngis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010359" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Nasopharynx" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### natural T-regulatory cell `http://purl.obolibrary.org/obo/CL_0000903` -#### Added -- [natural T-regulatory cell](http://purl.obolibrary.org/obo/CL_0000903) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### pharyngeal arch 1 `http://purl.obolibrary.org/obo/UBERON_0004362` +#### Removed +- [pharyngeal arch 1](http://purl.obolibrary.org/obo/UBERON_0004362) [UBPROP_0000103](http://purl.obolibrary.org/obo/UBPROP_0000103) "1"^^[nonNegativeInteger](http://www.w3.org/2001/XMLSchema#nonNegativeInteger) -### natural killer cell `http://purl.obolibrary.org/obo/CL_0000623` +- [pharyngeal arch 1](http://purl.obolibrary.org/obo/UBERON_0004362) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "the first arch which contributes to development of mastication muscles, maxilla, mandible, incus, malleus, Meckel's cartilage, trigeminal nerve, and maxillary artery" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "MP:0006337,MGI:smb" -#### Added -- [natural killer cell](http://purl.obolibrary.org/obo/CL_0000623) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [pharyngeal arch 1](http://purl.obolibrary.org/obo/UBERON_0004362) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### near-projecting glutamatergic cortical neuron `http://purl.obolibrary.org/obo/CL_4023012` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)" -#### Added -- [near-projecting glutamatergic cortical neuron](http://purl.obolibrary.org/obo/CL_4023012) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000296" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### neck `http://purl.obolibrary.org/obo/UBERON_0000974` -#### Removed -- [neck](http://purl.obolibrary.org/obo/UBERON_0000974) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "collum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Neck" +- [pharyngeal arch 1](http://purl.obolibrary.org/obo/UBERON_0004362) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The first of the series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010364" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -#### Added -- [neck](http://purl.obolibrary.org/obo/UBERON_0000974) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "collum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Neck" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "XAO:EJS" -### neck of femur `http://purl.obolibrary.org/obo/UBERON_0007119` + +### pharyngeal arch 2 `http://purl.obolibrary.org/obo/UBERON_0003066` #### Removed -- [neck of femur](http://purl.obolibrary.org/obo/UBERON_0007119) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "collum femoris" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Femur_neck" +- [pharyngeal arch 2](http://purl.obolibrary.org/obo/UBERON_0003066) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [neck of femur](http://purl.obolibrary.org/obo/UBERON_0007119) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "collum femoris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Femur_neck" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000297" -### neck of humerus `http://purl.obolibrary.org/obo/UBERON_4200172` -#### Removed -- [neck of humerus](http://purl.obolibrary.org/obo/UBERON_4200172) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "collum anatomicum humeri" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:23356" +- [pharyngeal arch 2](http://purl.obolibrary.org/obo/UBERON_0003066) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The second of the series of bony or cartilaginous arches that develop in the walls of the mouth cavity and pharynx of the embryo.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010363" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -#### Added -- [neck of humerus](http://purl.obolibrary.org/obo/UBERON_4200172) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "collum anatomicum humeri" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "XAO:EJS" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:23356" +- [pharyngeal arch 2](http://purl.obolibrary.org/obo/UBERON_0003066) [UBPROP_0000103](http://purl.obolibrary.org/obo/UBPROP_0000103) "2"^^[nonNegativeInteger](http://www.w3.org/2001/XMLSchema#nonNegativeInteger) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [pharyngeal arch 2](http://purl.obolibrary.org/obo/UBERON_0003066) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in XAO, develops from visceral pouch 2" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "XAO" -### neck of rib `http://purl.obolibrary.org/obo/UBERON_0003253` + +### pharyngeal arch 3 `http://purl.obolibrary.org/obo/UBERON_0003114` #### Removed -- [neck of rib](http://purl.obolibrary.org/obo/UBERON_0003253) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "collum costae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Neck_of_rib" +- [pharyngeal arch 3](http://purl.obolibrary.org/obo/UBERON_0003114) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in XAO, called branchial arch 1 and df VP3" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "XAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [pharyngeal arch 3](http://purl.obolibrary.org/obo/UBERON_0003114) [UBPROP_0000103](http://purl.obolibrary.org/obo/UBPROP_0000103) "3"^^[nonNegativeInteger](http://www.w3.org/2001/XMLSchema#nonNegativeInteger) -- [neck of rib](http://purl.obolibrary.org/obo/UBERON_0003253) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "collum costae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Neck_of_rib" +- [pharyngeal arch 3](http://purl.obolibrary.org/obo/UBERON_0003114) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The most anterior, or first, pharygeal/branchial arch, composed of the mandibular process, forming the posterior border of the stomodeum, and the maxillary process anterior to the stomodeum, contains the first aortic arch.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0-02-377110-0" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -#### Added -- [neck of rib](http://purl.obolibrary.org/obo/UBERON_0003253) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "collum costae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Neck_of_rib" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010365" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -- [neck of rib](http://purl.obolibrary.org/obo/UBERON_0003253) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "collum costae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Neck_of_rib" +- [pharyngeal arch 3](http://purl.obolibrary.org/obo/UBERON_0003114) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)" -### neck of tooth `http://purl.obolibrary.org/obo/UBERON_0015181` -#### Removed -- [neck of tooth](http://purl.obolibrary.org/obo/UBERON_0015181) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cervix dentis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000298" -- [neck of tooth](http://purl.obolibrary.org/obo/UBERON_0015181) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "collumn dentis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ncithesaurus:Collum_Dentis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [neck of tooth](http://purl.obolibrary.org/obo/UBERON_0015181) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cervix dentis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### pharyngeal arch 4 `http://purl.obolibrary.org/obo/UBERON_0003115` +#### Removed +- [pharyngeal arch 4](http://purl.obolibrary.org/obo/UBERON_0003115) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The second pharyngeal/branchial arch; arises as a thickening of the pharygeal wall between the first and second branchial clefts; contains the second aortic arch; forms part of the hyoid bone, tongue and facial musculature.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0-02-377110-0" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -- [neck of tooth](http://purl.obolibrary.org/obo/UBERON_0015181) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "collumn dentis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010366" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ncithesaurus:Collum_Dentis" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" +- [pharyngeal arch 4](http://purl.obolibrary.org/obo/UBERON_0003115) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in XAO, called branchial arch 2 and df VP4" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "XAO" -### neck of urinary bladder `http://purl.obolibrary.org/obo/UBERON_0001258` -#### Removed -- [neck of urinary bladder](http://purl.obolibrary.org/obo/UBERON_0001258) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cervix vesicae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [pharyngeal arch 4](http://purl.obolibrary.org/obo/UBERON_0003115) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15912" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)" -- [neck of urinary bladder](http://purl.obolibrary.org/obo/UBERON_0001258) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "collum vesicae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000299" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15912" +- [pharyngeal arch 4](http://purl.obolibrary.org/obo/UBERON_0003115) [UBPROP_0000103](http://purl.obolibrary.org/obo/UBPROP_0000103) "4"^^[nonNegativeInteger](http://www.w3.org/2001/XMLSchema#nonNegativeInteger) -- [neck of urinary bladder](http://purl.obolibrary.org/obo/UBERON_0001258) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cervix vesicae urinariae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Neck_of_urinary_bladder" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [neck of urinary bladder](http://purl.obolibrary.org/obo/UBERON_0001258) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cervix vesicae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### pharyngeal arch 5 `http://purl.obolibrary.org/obo/UBERON_0003116` +#### Removed +- [pharyngeal arch 5](http://purl.obolibrary.org/obo/UBERON_0003116) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The third in a series of paired bars in the wall of the pharynx, within which are formed the third aortic arch and the cartilage bar of the visceral skeleton, forms and supports the gills.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0-02-377110-0" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15912" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010367" -- [neck of urinary bladder](http://purl.obolibrary.org/obo/UBERON_0001258) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cervix vesicae urinariae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Neck_of_urinary_bladder" +- [pharyngeal arch 5](http://purl.obolibrary.org/obo/UBERON_0003116) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in XAO, called branchial arch 3 and df VP5" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "XAO" -- [neck of urinary bladder](http://purl.obolibrary.org/obo/UBERON_0001258) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "collum vesicae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [pharyngeal arch 5](http://purl.obolibrary.org/obo/UBERON_0003116) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "A fifth arch never establishes itself in amniotes" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [pharyngeal arch 5](http://purl.obolibrary.org/obo/UBERON_0003116) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001204" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15912" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### negative regulation of amino acid biosynthetic process `http://purl.obolibrary.org/obo/GO_2000283` -#### Removed -- [negative regulation of amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000283) [created by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [negative regulation of amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000283) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "negative regulation of amino acid biosynthesis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:obol" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M, Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)" -- [negative regulation of amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000283) [creation date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2010-12-10T11:54:23Z" +- [pharyngeal arch 5](http://purl.obolibrary.org/obo/UBERON_0003116) [UBPROP_0000103](http://purl.obolibrary.org/obo/UBPROP_0000103) "5"^^[nonNegativeInteger](http://www.w3.org/2001/XMLSchema#nonNegativeInteger) -- [negative regulation of amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000283) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "negative regulation of amino acid formation" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:obol" -- [negative regulation of amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000283) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any process that stops, prevents or reduces the frequency, rate or extent of an amino acid biosynthetic process." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:obol" -- [negative regulation of amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000283) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "negative regulation of cellular amino acid biosynthetic process" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:obol" +### pharyngeal arch 6 `http://purl.obolibrary.org/obo/UBERON_0003117` +#### Removed +- [pharyngeal arch 6](http://purl.obolibrary.org/obo/UBERON_0003117) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The forth in a series of paired bars in the wall of the pharynx, within which are formed the forth aortic arch and the cartilage bar of the visceral skeleton, forms and supports the gills.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0-02-377110-0" -- [negative regulation of amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000283) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010368" -- [negative regulation of amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000283) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:2000283" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -- [negative regulation of amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000283) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "negative regulation of amino acid anabolism" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:obol" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -- [negative regulation of amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000283) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "negative regulation of amino acid synthesis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:obol" +- [pharyngeal arch 6](http://purl.obolibrary.org/obo/UBERON_0003117) [UBPROP_0000103](http://purl.obolibrary.org/obo/UBPROP_0000103) "6"^^[nonNegativeInteger](http://www.w3.org/2001/XMLSchema#nonNegativeInteger) -- [negative regulation of amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000283) [label](http://www.w3.org/2000/01/rdf-schema#label) "negative regulation of amino acid biosynthetic process" +- [pharyngeal arch 6](http://purl.obolibrary.org/obo/UBERON_0003117) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001205" -- Class: [negative regulation of amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000283) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [negative regulation of amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000283) EquivalentTo [biological regulation](http://purl.obolibrary.org/obo/GO_0065007) and ([negatively regulates](http://purl.obolibrary.org/obo/RO_0002212) some [amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_0008652)) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [negative regulation of amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000283) SubClassOf [negatively regulates](http://purl.obolibrary.org/obo/RO_0002212) some [amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_0008652) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [negative regulation of amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000283) SubClassOf [negative regulation of cellular amino acid metabolic process](http://purl.obolibrary.org/obo/GO_0045763) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M, Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)" -- [negative regulation of amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000283) SubClassOf [negative regulation of biosynthetic process](http://purl.obolibrary.org/obo/GO_0009890) -- [negative regulation of amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000283) SubClassOf [regulation of cellular amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000282) +### pharyngeal arch artery `http://purl.obolibrary.org/obo/UBERON_0004363` +#### Removed +- [pharyngeal arch artery](http://purl.obolibrary.org/obo/UBERON_0004363) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "When vertebrates first appeared, they must have possessed a ventral and dorsal aorta with aortic arches between them.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### negative regulation of calcium ion import `http://purl.obolibrary.org/obo/GO_0090281` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000122" -#### Added -- [negative regulation of calcium ion import](http://purl.obolibrary.org/obo/GO_0090281) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "negative regulation of transmembrane calcium influx" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tb" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [negative regulation of calcium ion import](http://purl.obolibrary.org/obo/GO_0090281) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any process that decreases the rate, frequency, or extent of the directed movement of calcium ions into a cell or organelle." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:BHF" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620" -- [negative regulation of calcium ion import](http://purl.obolibrary.org/obo/GO_0090281) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:0090281" +- [pharyngeal arch artery](http://purl.obolibrary.org/obo/UBERON_0004363) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "The third, fourth, and sixth arches, along with the seventh intersegmental arteries and the left dorsal aorta, are the primary contributors to the normal aortic arch and its major thoracic branches" -- [negative regulation of calcium ion import](http://purl.obolibrary.org/obo/GO_0090281) [label](http://www.w3.org/2000/01/rdf-schema#label) "negative regulation of calcium ion import" +- [pharyngeal arch artery](http://purl.obolibrary.org/obo/UBERON_0004363) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Paired vessels arching from the ventral to the dorsal aorta through the pharyngeal arches. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [negative regulation of calcium ion import](http://purl.obolibrary.org/obo/GO_0090281) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [negative regulation of calcium ion import](http://purl.obolibrary.org/obo/GO_0090281) [creation date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2010-02-08T05:11:20Z" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000122" -- [negative regulation of calcium ion import](http://purl.obolibrary.org/obo/GO_0090281) [created by](http://www.geneontology.org/formats/oboInOwl#created_by) "tb" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- Class: [negative regulation of calcium ion import](http://purl.obolibrary.org/obo/GO_0090281) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/aortic+arches" -- [negative regulation of calcium ion import](http://purl.obolibrary.org/obo/GO_0090281) EquivalentTo [biological regulation](http://purl.obolibrary.org/obo/GO_0065007) and ([negatively regulates](http://purl.obolibrary.org/obo/RO_0002212) some [calcium ion import](http://purl.obolibrary.org/obo/GO_0070509)) +- [pharyngeal arch artery](http://purl.obolibrary.org/obo/UBERON_0004363) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "Do not confuse with arch of aorta." -- [negative regulation of calcium ion import](http://purl.obolibrary.org/obo/GO_0090281) SubClassOf [negatively regulates](http://purl.obolibrary.org/obo/RO_0002212) some [calcium ion import](http://purl.obolibrary.org/obo/GO_0070509) +- [pharyngeal arch artery](http://purl.obolibrary.org/obo/UBERON_0004363) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Number varies - Lampreys have 8, hagfishes 15; only up to 6 appear in embryonic development in most gnathostome fishes and all tetrapods" -- [negative regulation of calcium ion import](http://purl.obolibrary.org/obo/GO_0090281) SubClassOf [negative regulation of calcium ion transport](http://purl.obolibrary.org/obo/GO_0051926) -- [negative regulation of calcium ion import](http://purl.obolibrary.org/obo/GO_0090281) SubClassOf [regulation of calcium ion import](http://purl.obolibrary.org/obo/GO_0090279) +### pharyngeal arch artery 1 `http://purl.obolibrary.org/obo/UBERON_0003118` +#### Removed +- [pharyngeal arch artery 1](http://purl.obolibrary.org/obo/UBERON_0003118) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "ZFA states that The paired aortic arch 1 arteries branch off of the ventral aorta, and empty into the right and left lateral dorsal aortas" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "ZFA" -### negative regulation of calcium ion import across plasma membrane `http://purl.obolibrary.org/obo/GO_1905949` +- [pharyngeal arch artery 1](http://purl.obolibrary.org/obo/UBERON_0003118) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Disappears early in development in tetrapods" -#### Added -- [negative regulation of calcium ion import across plasma membrane](http://purl.obolibrary.org/obo/GO_1905949) SubClassOf [negative regulation of calcium ion import](http://purl.obolibrary.org/obo/GO_0090281) -### negative regulation of cellular amino acid metabolic process `http://purl.obolibrary.org/obo/GO_0045763` +### pharyngeal arch artery 2 `http://purl.obolibrary.org/obo/UBERON_0003119` #### Removed -- [negative regulation of cellular amino acid metabolic process](http://purl.obolibrary.org/obo/GO_0045763) SubClassOf [negative regulation of nitrogen compound metabolic process](http://purl.obolibrary.org/obo/GO_0051172) +- [pharyngeal arch artery 2](http://purl.obolibrary.org/obo/UBERON_0003119) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The second in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 2 that is part of hyoid arch.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0-02-377110-0" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -- [negative regulation of cellular amino acid metabolic process](http://purl.obolibrary.org/obo/GO_0045763) SubClassOf [negative regulation of small molecule metabolic process](http://purl.obolibrary.org/obo/GO_0062014) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010418" -- [negative regulation of cellular amino acid metabolic process](http://purl.obolibrary.org/obo/GO_0045763) SubClassOf [negative regulation of cellular metabolic process](http://purl.obolibrary.org/obo/GO_0031324) +- [pharyngeal arch artery 2](http://purl.obolibrary.org/obo/UBERON_0003119) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The first and second arches disappear early, but the dorsal end of the second gives origin to the stapedial artery, a vessel which atrophies in humans but persists in some mammals. It passes through the ring of the stapes and divides into supraorbital, infraorbital, and mandibular branches which follow the three divisions of the trigeminal nerve. The infraorbital and mandibular arise from a common stem, the terminal part of which anastomoses with the external carotid. On the obliteration of the stapedial artery this anastomosis enlarges and forms the internal maxillary artery, and the branches of the stapedial artery are now branches of this vessel. The common stem of the infraorbital and mandibular branches passes between the two roots of the auriculotemporal nerve and becomes the middle meningeal artery; the original supraorbital branch of the stapedial is represented by the orbital twigs of the middle meningeal[WP][Wikipedia:Aortic_arches#Arches_1_and_2]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Aortic_arches#Arches_1_and_2" -### negative regulation of cytoplasmic transport `http://purl.obolibrary.org/obo/GO_1903650` +### pharyngeal arch artery 3 `http://purl.obolibrary.org/obo/UBERON_0003120` #### Removed -- [negative regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903650) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "down-regulation of cytoplasmic transport" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" +- [pharyngeal arch artery 3](http://purl.obolibrary.org/obo/UBERON_0003120) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The third in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 3 lies within the 3rd branchial arch and branches directly from the ventral aorta to the lateral dorsal aorta, and are retained as the branchial arteries providing circulation through the gills in the adult.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010419" -- [negative regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903650) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any process that stops, prevents or reduces the frequency, rate or extent of cytoplasmic transport." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0-02-377110-0" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:25049409" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO_REF:0000058" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -- [negative regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903650) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" +- [pharyngeal arch artery 3](http://purl.obolibrary.org/obo/UBERON_0003120) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The third aortic arch constitutes the commencement of the internal carotid artery, and is therefore named the carotid arch[WP][Wikipedia:Aortic_arches#Arch_3]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Aortic_arches#Arch_3" -- [negative regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903650) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "down regulation of cytoplasmic streaming" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" +- [pharyngeal arch artery 3](http://purl.obolibrary.org/obo/UBERON_0003120) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Aortic arches 3 and 4 are not remodeled but are retained largely intact as the branchial arteries providing circulation through the gills. These areches are direct branches from the ventral aorta to the lateral dorsal aorta. Isogai et al. 2001.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -- [negative regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903650) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "inhibition of cytoplasmic streaming" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005007" -- [negative regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903650) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "down regulation of cytoplasmic transport" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -- [negative regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903650) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "negative regulation of cytoplasmic streaming" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -- [negative regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903650) [label](http://www.w3.org/2000/01/rdf-schema#label) "negative regulation of cytoplasmic transport" -- [negative regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903650) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "down-regulation of cytoplasmic streaming" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" -- [negative regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903650) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "inhibition of cytoplasmic transport" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" - -- [negative regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903650) [creation date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2014-11-24T13:38:26Z" +### pharyngeal arch artery 4 `http://purl.obolibrary.org/obo/UBERON_0003121` +#### Removed +- [pharyngeal arch artery 4](http://purl.obolibrary.org/obo/UBERON_0003121) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The fourth right arch forms the right subclavian as far as the origin of its internal mammary branch; while the fourth left arch constitutes the arch of the aorta between the origin of the left carotid artery and the termination of the ductus arteriosus[WP][Wikipedia:Aortic_arches#Arch_4]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Aortic_arches#Arch_4" -- [negative regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903650) [created by](http://www.geneontology.org/formats/oboInOwl#created_by) "jl" +- [pharyngeal arch artery 4](http://purl.obolibrary.org/obo/UBERON_0003121) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Aortic arches 3 and 4 are not remodeled but are retained largely intact as the branchial arteries providing circulation through the gills. These areches are direct branches from the ventral aorta to the lateral dorsal aorta. Isogai et al. 2001.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -- [negative regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903650) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "downregulation of cytoplasmic streaming" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005008" -- [negative regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903650) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "downregulation of cytoplasmic transport" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -- [negative regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903650) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:1903650" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -- Class: [negative regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903650) +- [pharyngeal arch artery 4](http://purl.obolibrary.org/obo/UBERON_0003121) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The forth in a series paired arterial connections between the dorsal and ventral aortae, lies within the 4th branchial arch. The paired aortic arch 4 arteries branch directly from the ventral aorta to the lateral dorsal aorta, and are retained as the branchial arteries providing circulation through the gills in the adult.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010420" -- [negative regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903650) EquivalentTo [biological regulation](http://purl.obolibrary.org/obo/GO_0065007) and ([negatively regulates](http://purl.obolibrary.org/obo/RO_0002212) some [cytosolic transport](http://purl.obolibrary.org/obo/GO_0016482)) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0-02-377110-0" -- [negative regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903650) SubClassOf [regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903649) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -- [negative regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903650) SubClassOf [negatively regulates](http://purl.obolibrary.org/obo/RO_0002212) some [cytosolic transport](http://purl.obolibrary.org/obo/GO_0016482) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -- [negative regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903650) SubClassOf [negative regulation of intracellular transport](http://purl.obolibrary.org/obo/GO_0032387) +- [pharyngeal arch artery 4](http://purl.obolibrary.org/obo/UBERON_0003121) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "Normally, the left fourth arch becomes the aortic arch, the right fourth arch contributes to the innominate artery[http://emedicine.medscape.com/article/899609-overview] in birds it is the right fourth arch which forms the permanent aorta" -### negative regulation of dense core granule transport `http://purl.obolibrary.org/obo/GO_1904810` +### pharyngeal arch artery 5 `http://purl.obolibrary.org/obo/UBERON_0003122` #### Removed -- [negative regulation of dense core granule transport](http://purl.obolibrary.org/obo/GO_1904810) SubClassOf [negative regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903650) +- [pharyngeal arch artery 5](http://purl.obolibrary.org/obo/UBERON_0003122) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In humans the 5th arch disappears on both sides" -#### Added -- [negative regulation of dense core granule transport](http://purl.obolibrary.org/obo/GO_1904810) SubClassOf [negative regulation of intracellular transport](http://purl.obolibrary.org/obo/GO_0032387) +- [pharyngeal arch artery 5](http://purl.obolibrary.org/obo/UBERON_0003122) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The fifth and sixth arches, which come on-line at approximately 2.5 dpf, have a common trunk from the ventral aorta and drain to the midline dorsal aorta via an independent route. The fifth and sixth aortic arches supply the trunk and tail with oxigenated blood. Isogai et al. 2001.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005009" -### negative regulation of gamma-aminobutyric acid catabolic process `http://purl.obolibrary.org/obo/GO_1901716` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -#### Added -- [negative regulation of gamma-aminobutyric acid catabolic process](http://purl.obolibrary.org/obo/GO_1901716) SubClassOf [negative regulation of cellular metabolic process](http://purl.obolibrary.org/obo/GO_0031324) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -- [negative regulation of gamma-aminobutyric acid catabolic process](http://purl.obolibrary.org/obo/GO_1901716) SubClassOf [negative regulation of small molecule metabolic process](http://purl.obolibrary.org/obo/GO_0062014) +- [pharyngeal arch artery 5](http://purl.obolibrary.org/obo/UBERON_0003122) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The fifth arch disappears on both sides[WP][Wikipedia:Aortic_arches#Arch_5]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Aortic_arches#Arch_5" +- [pharyngeal arch artery 5](http://purl.obolibrary.org/obo/UBERON_0003122) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The fifth in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 5 artery is paired and has a common trunk with aortic arch 6 from the ventral aorta, and drains via a separate branch of the lateral dorsal aorta. Aortic arches 5 and 6 supply the trunk and tail with oxygenated blood.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010421" -### negative regulation of glutamate metabolic process `http://purl.obolibrary.org/obo/GO_2000212` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0-02-377110-0" -#### Added -- [negative regulation of glutamate metabolic process](http://purl.obolibrary.org/obo/GO_2000212) SubClassOf [negative regulation of small molecule metabolic process](http://purl.obolibrary.org/obo/GO_0062014) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -- [negative regulation of glutamate metabolic process](http://purl.obolibrary.org/obo/GO_2000212) SubClassOf [negative regulation of cellular metabolic process](http://purl.obolibrary.org/obo/GO_0031324) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### negative regulation of nitric oxide biosynthetic process `http://purl.obolibrary.org/obo/GO_0045019` -#### Removed -- [negative regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045019) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "negative regulation of nitric oxide synthesis" -- [negative regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045019) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "downregulation of nitric oxide biosynthetic process" +### pharyngeal arch artery 6 `http://purl.obolibrary.org/obo/UBERON_0003123` +#### Removed +- [pharyngeal arch artery 6](http://purl.obolibrary.org/obo/UBERON_0003123) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The sixth right arch disappears; the sixth left arch gives off the pulmonary arteries and forms the ductus arteriosus; this duct remains pervious during the whole of fetal life, but then closes within the first few days after birth due to increased O2 concentration. Oxygen concentration causes the production of bradykinin which causes the ductus to constrict occluding all flow. Within 1-3 months, the ductus is obliterated and becomes the ligamentum arteriosus. His showed that in the early embryo the right and left arches each gives a branch to the lungs, but that later both pulmonary arteries take origin from the left arch[WP][Wikipedia:Aortic_arches#Arch_6]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Aortic_arches#Arch_6" -- [negative regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045019) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "negative regulation of nitric oxide anabolism" +- [pharyngeal arch artery 6](http://purl.obolibrary.org/obo/UBERON_0003123) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "the distal left sixth arch becomes the ductus arteriosus, the proximal sixth arches bilaterally contribute to the proximal branch pulmonary arteries" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://emedicine.medscape.com/article/899609-overview" -- [negative regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045019) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:0045019" +- [pharyngeal arch artery 6](http://purl.obolibrary.org/obo/UBERON_0003123) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The sixth in a series paired arterial connections between the dorsal and ventral aortae. Aortic arch 6 artery is paired and has a common trunk with aortic arch 5 from the ventral aorta, and drains via a separate branch of the lateral dorsal aorta. It forms part of the pulmonary arteries, and in the later embryo, the ductus arteriosis. Aortic arches 5 and 6 together supply the trunk and tail with oxygenated blood.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0-02-377110-0" -- [negative regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045019) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "down-regulation of nitric oxide biosynthetic process" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -- [negative regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045019) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "negative regulation of nitric oxide biosynthesis" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -- [negative regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045019) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "down regulation of nitric oxide biosynthetic process" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010422" -- [negative regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045019) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" +- [pharyngeal arch artery 6](http://purl.obolibrary.org/obo/UBERON_0003123) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The fifth and sixth arches, which come on-line at approximately 2.5 dpf, have a common trunk from the ventral aorta and drain to the midline dorsal aorta via an independent route. The fifth and sixth aortic arches supply the trunk and tail with oxigenated blood. Isogai et al. 2001.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -- [negative regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045019) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "inhibition of nitric oxide biosynthetic process" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005016" -- [negative regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045019) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of nitric oxide." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:go_curators" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -- [negative regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045019) [label](http://www.w3.org/2000/01/rdf-schema#label) "negative regulation of nitric oxide biosynthetic process" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -- [negative regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045019) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "negative regulation of nitric oxide formation" -- Class: [negative regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045019) -- [negative regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045019) EquivalentTo [biological regulation](http://purl.obolibrary.org/obo/GO_0065007) and ([negatively regulates](http://purl.obolibrary.org/obo/RO_0002212) some [nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0006809)) +### pharyngeal arch cartilage `http://purl.obolibrary.org/obo/UBERON_0011004` +#### Removed +- [pharyngeal arch cartilage](http://purl.obolibrary.org/obo/UBERON_0011004) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006051" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -- [negative regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045019) SubClassOf [negative regulation of cellular biosynthetic process](http://purl.obolibrary.org/obo/GO_0031327) + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -- [negative regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045019) SubClassOf [regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045428) + - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) -- [negative regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045019) SubClassOf [negatively regulates](http://purl.obolibrary.org/obo/RO_0002212) some [nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0006809) -- [negative regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045019) SubClassOf [negative regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904406) -- [negative regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045019) SubClassOf [negative regulation of nitrogen compound metabolic process](http://purl.obolibrary.org/obo/GO_0051172) +### pharyngeal cleft `http://purl.obolibrary.org/obo/UBERON_0005879` +#### Removed +- [pharyngeal cleft](http://purl.obolibrary.org/obo/UBERON_0005879) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "EMAPA distinguishes between the groove ectoderm and epithelium, with the latter arising after the former" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EMAPA" -### negative regulation of nitric oxide metabolic process `http://purl.obolibrary.org/obo/GO_1904406` +### pharyngeal epithelium `http://purl.obolibrary.org/obo/UBERON_0003351` #### Removed -- [negative regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904406) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "downregulation of nitric oxide metabolism" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" +- [pharyngeal epithelium](http://purl.obolibrary.org/obo/UBERON_0003351) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Epithelium lining the pharynx consisting largely of simple columnar epithelium with a short segment (1mm) of stratified squamous epithelium on the ventral side. Chen et al, 2007.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001174" -- [negative regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904406) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "inhibition of nitric oxide metabolism" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -- [negative regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904406) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "down regulation of nitric oxide metabolism" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -- [negative regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904406) [created by](http://www.geneontology.org/formats/oboInOwl#created_by) "sl" -- [negative regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904406) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" -- [negative regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904406) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "inhibition of nitric oxide metabolic process" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" +### pharyngeal membrane `http://purl.obolibrary.org/obo/UBERON_0009210` +#### Removed +- [pharyngeal membrane](http://purl.obolibrary.org/obo/UBERON_0009210) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In all vertebrates, the endodermal epithelium lining each pouch contacts the surface ectoderm of the clefts to form a series of bilayered branchial membranes, that break down in fish to form the gill openings.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0124020603 Kaufman MH, Bard JBL, The anatomical basis of mouse development (1999) p.72" -- [negative regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904406) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:1904406" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [negative regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904406) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any process that stops, prevents or reduces the frequency, rate or extent of nitric oxide metabolic process." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:11991626" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO_REF:0000058" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001427" -- [negative regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904406) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "down-regulation of nitric oxide metabolism" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" -- [negative regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904406) [label](http://www.w3.org/2000/01/rdf-schema#label) "negative regulation of nitric oxide metabolic process" -- [negative regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904406) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "downregulation of nitric oxide metabolic process" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" +### pharyngeal pouch `http://purl.obolibrary.org/obo/UBERON_0004117` +#### Removed +- [pharyngeal pouch](http://purl.obolibrary.org/obo/UBERON_0004117) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Outpocketings of pharyngeal endoderm that interdigitate with the neural crest derived pharyngeal arches. The pouches later fuse with the surface ectoderm to form the gill slits. Crump et al, 2004.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -- [negative regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904406) [creation date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2015-06-24T20:56:41Z" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -- [negative regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904406) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "down-regulation of nitric oxide metabolic process" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -- [negative regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904406) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "negative regulation of nitric oxide metabolism" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001106" -- [negative regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904406) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "down regulation of nitric oxide metabolic process" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" +- [pharyngeal pouch](http://purl.obolibrary.org/obo/UBERON_0004117) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "EMAPA also includes a distinct pouch endoderm" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EMAPA" -- Class: [negative regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904406) +- [pharyngeal pouch](http://purl.obolibrary.org/obo/UBERON_0004117) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001203" -- [negative regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904406) EquivalentTo [biological regulation](http://purl.obolibrary.org/obo/GO_0065007) and ([negatively regulates](http://purl.obolibrary.org/obo/RO_0002212) some [nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_0046209)) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [negative regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904406) SubClassOf [negatively regulates](http://purl.obolibrary.org/obo/RO_0002212) some [nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_0046209) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [negative regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904406) SubClassOf [negative regulation of metabolic process](http://purl.obolibrary.org/obo/GO_0009892) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [negative regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904406) SubClassOf [regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_0080164) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M, Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)" -### neocortex `http://purl.obolibrary.org/obo/UBERON_0001950` +### pharyngeal pouch 1 `http://purl.obolibrary.org/obo/UBERON_0007122` #### Removed -- [neocortex](http://purl.obolibrary.org/obo/UBERON_0001950) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus hypoglossalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:757" +- [pharyngeal pouch 1](http://purl.obolibrary.org/obo/UBERON_0007122) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "The endoderm lines the future auditory tube (Pharyngotympanic Eustachian tube) , middle ear, mastoid antrum, and inner layer of the tympanic membrane. & origin of Mandibular nerve & Maxillary artery" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [pharyngeal pouch 1](http://purl.obolibrary.org/obo/UBERON_0007122) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In all jawed vertebrates the first arch forms the jaw, while the second arch forms the hyoid apparatus. These two arches are separated by the first pharyngeal pouch and cleft.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [neocortex](http://purl.obolibrary.org/obo/UBERON_0001950) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus hypoglossalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:757" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000970" -### neoplastic cell `http://purl.obolibrary.org/obo/CL_0001063` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1016/j.semcdb.2010.01.022 Grevellec A, Tucker AS, The pharyngeal pouches and clefts: development, evolution, structure and derivatives. Seminars in Cell and Developmental Biology (2010)" -#### Added -- [neoplastic cell](http://purl.obolibrary.org/obo/CL_0001063) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [pharyngeal pouch 1](http://purl.obolibrary.org/obo/UBERON_0007122) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) ". [][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### nephrogenic cord `http://purl.obolibrary.org/obo/UBERON_0004875` -#### Removed -- [nephrogenic cord](http://purl.obolibrary.org/obo/UBERON_0004875) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "chorda nephrogenica" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Nephrogenic_cord" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000970" -#### Added -- [nephrogenic cord](http://purl.obolibrary.org/obo/UBERON_0004875) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "chorda nephrogenica" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [pharyngeal pouch 1](http://purl.obolibrary.org/obo/UBERON_0007122) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "we use adjacency relations rather than part_of, as in EHDAA2." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EHDAA2" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Nephrogenic_cord" -### nephron `http://purl.obolibrary.org/obo/UBERON_0001285` +### pharyngeal pouch 2 `http://purl.obolibrary.org/obo/UBERON_0007123` #### Removed -- [nephron](http://purl.obolibrary.org/obo/UBERON_0001285) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tubulus renalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Nephron" +- [pharyngeal pouch 2](http://purl.obolibrary.org/obo/UBERON_0007123) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A pouch that is situated between the 2nd and 3rd pharyngeal arch. [ISBN:0124020607][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [nephron](http://purl.obolibrary.org/obo/UBERON_0001285) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nephroneum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Nephron" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000967" -#### Added -- [nephron](http://purl.obolibrary.org/obo/UBERON_0001285) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tubulus renalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Nephron" +- [pharyngeal pouch 2](http://purl.obolibrary.org/obo/UBERON_0007123) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Second of the pharyngeal (endodermal) evaginations between the visceral arches from which the Eustachian tube is derived; pouches 2-4 open as gill slits.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0011115" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0-226-55763-4" -- [nephron](http://purl.obolibrary.org/obo/UBERON_0001285) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nephroneum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Nephron" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" +- [pharyngeal pouch 2](http://purl.obolibrary.org/obo/UBERON_0007123) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "Contributes to the middle ear, epithelial lining of Crypts (spaces) of the palatine tonsils, supplied by the facial nerve" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" -### nephron tubule epithelial cell `http://purl.obolibrary.org/obo/CL_1000494` +- [pharyngeal pouch 2](http://purl.obolibrary.org/obo/UBERON_0007123) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:16276" -#### Added -- [nephron tubule epithelial cell](http://purl.obolibrary.org/obo/CL_1000494) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [pharyngeal pouch 2](http://purl.obolibrary.org/obo/UBERON_0007123) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### nerve `http://purl.obolibrary.org/obo/UBERON_0001021` -#### Removed -- [nerve](http://purl.obolibrary.org/obo/UBERON_0001021) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005105" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)" -#### Added -- [nerve](http://purl.obolibrary.org/obo/UBERON_0001021) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005105" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000967" -### nerve fasciculus `http://purl.obolibrary.org/obo/UBERON_0001019` -#### Removed -- [nerve fasciculus](http://purl.obolibrary.org/obo/UBERON_0001019) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "fasciculus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [pharyngeal pouch 2](http://purl.obolibrary.org/obo/UBERON_0007123) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "the dorsal elongation of the second pouch endoderm of all mammals, with the exception of rodents, gives rise to the epithelial lining of palatine tonsils; in rodents, the ventral portion of the second pouch appears to degenerate whereas the remaining part is incorporated into the lateral border of the pharynx; it appears that rodents no longer require tonsils as their function is carried out by the NALT (Nose/Nasal-Associated Lymphoid Tissue) system in the upper respiratory tract." -#### Added -- [nerve fasciculus](http://purl.obolibrary.org/obo/UBERON_0001019) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "fasciculus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### nerve fiber `http://purl.obolibrary.org/obo/UBERON_0006134` +### pharyngeal pouch 3 `http://purl.obolibrary.org/obo/UBERON_0007124` #### Removed -- [nerve fiber](http://purl.obolibrary.org/obo/UBERON_0006134) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "neurofibra" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Nerve_fiber" +- [pharyngeal pouch 3](http://purl.obolibrary.org/obo/UBERON_0007124) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [nerve fiber](http://purl.obolibrary.org/obo/UBERON_0006134) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "neurofibra" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:5914" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000966" -#### Added -- [nerve fiber](http://purl.obolibrary.org/obo/UBERON_0006134) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "neurofibra" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Nerve_fiber" +- [pharyngeal pouch 3](http://purl.obolibrary.org/obo/UBERON_0007124) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "The third pouch possesses Dorsal and Ventral wings. Derivatives of the dorsal wings include the inferior parathyroid glands, while the ventral wings fuse to form the cytoreticular cells of the thymus. The main nerve supply to the derivatives of this pouch is Cranial Nerve IX, glossopharyngeal nerve" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [pharyngeal pouch 3](http://purl.obolibrary.org/obo/UBERON_0007124) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A pouch that is situated between the 3rd and 4th pharyngeal arch. [ISBN:0124020607][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [nerve fiber](http://purl.obolibrary.org/obo/UBERON_0006134) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "neurofibra" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:5914" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000966" +- [pharyngeal pouch 3](http://purl.obolibrary.org/obo/UBERON_0007124) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Third of the pharyngeal (endodermal) evaginations between the visceral arches from which the Eustachian tube is derived; pouches 2-4 open as gill slits.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0011116" -### nerve fiber layer of retina `http://purl.obolibrary.org/obo/UBERON_0001793` -#### Removed -- [nerve fiber layer of retina](http://purl.obolibrary.org/obo/UBERON_0001793) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "stratum neurofibrum retinae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Nerve_fiber_layer" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0-226-55763-4" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -- [nerve fiber layer of retina](http://purl.obolibrary.org/obo/UBERON_0001793) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum neurofibrarum retinae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58688" -#### Added -- [nerve fiber layer of retina](http://purl.obolibrary.org/obo/UBERON_0001793) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "stratum neurofibrum retinae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### pharyngeal pouch 4 `http://purl.obolibrary.org/obo/UBERON_0007125` +#### Removed +- [pharyngeal pouch 4](http://purl.obolibrary.org/obo/UBERON_0007125) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A pouch that is situated between the 4th and 5th pharyngeal arch. [ISBN:0124020607][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Nerve_fiber_layer" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [nerve fiber layer of retina](http://purl.obolibrary.org/obo/UBERON_0001793) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum neurofibrarum retinae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000971" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58688" +- [pharyngeal pouch 4](http://purl.obolibrary.org/obo/UBERON_0007125) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "A conserved feature of all vertebrate embryos is the presence of a series of bulges on the lateral surface of the head, the pharyngeal arches; it is within these structures that the nerves, muscles and skeletal components of the pharyngeal apparatus are laid down. The pharyngeal arches are separated by endodermal outpocketings, the pharyngeal pouches.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### nerve of cervical vertebra `http://purl.obolibrary.org/obo/UBERON_0000962` -#### Removed -- [nerve of cervical vertebra](http://purl.obolibrary.org/obo/UBERON_0000962) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus cervicalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:5859" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1111/j.1469-7580.2005.00472.x Graham A, Okabe M and Quinlan R, The role of the endoderm in the development and evolution of the pharyngeal arches. J Anat (2005)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000971" -#### Added -- [nerve of cervical vertebra](http://purl.obolibrary.org/obo/UBERON_0000962) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus cervicalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [pharyngeal pouch 4](http://purl.obolibrary.org/obo/UBERON_0007125) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Fourth of the pharyngeal (endodermal) evaginations between the visceral arches from which the Eustachian tube is derived; pouches 2-4 open as gill slits.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0011117" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:5859" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0-226-55763-4" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### nerve root `http://purl.obolibrary.org/obo/UBERON_0002211` -#### Removed -- [nerve root](http://purl.obolibrary.org/obo/UBERON_0002211) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "radix nervi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [pharyngeal pouch 4](http://purl.obolibrary.org/obo/UBERON_0007125) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "Derivatives include: superior parathyroid glands and ultimobranchial body which forms the parafollicular C-Cells of the thyroid gland. Musculature and cartilage of larynx (along with the sixth pharyngeal pouch)[WP] in most mammals, excluding rodents, the dorsal part of each fourth pouch develops into a superior parathyroid gland (parathyroid IV), which lies on the dorsal surface of the thyroid gland (the parathyroid glands derived from the third pouches descend with the thymus and are carried to a more inferior position than the parathyroid glands that are derived from the fourth pouches); the elongated ventral part of each fourth pouch develops into the ultimopharyngeal body, which fuses with the thyroid gland, giving rise to the calcitonin-producing parafollicular or C-cells of the thyroid gland. In the mouse, but also in the rat and hamster, the dorsal fourth pouch does not generate a parathyroid. Thus, rodents develop only one pair of parathyroid glands." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "MP" -#### Added -- [nerve root](http://purl.obolibrary.org/obo/UBERON_0002211) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "radix nervi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### nervous system `http://purl.obolibrary.org/obo/UBERON_0001016` +### pharyngula stage `http://purl.obolibrary.org/obo/UBERON_0004707` #### Removed -- [nervous system](http://purl.obolibrary.org/obo/UBERON_0001016) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "systema nervosum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Nervous_system" +- [pharyngula stage](http://purl.obolibrary.org/obo/UBERON_0004707) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Corresponds to E7-E11 in Mouse (Galis et al, TREE, 2001)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [nervous system](http://purl.obolibrary.org/obo/UBERON_0001016) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005093" -#### Added -- [nervous system](http://purl.obolibrary.org/obo/UBERON_0001016) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "systema nervosum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### pharynx `http://purl.obolibrary.org/obo/UBERON_0006562` +#### Removed +- [pharynx](http://purl.obolibrary.org/obo/UBERON_0006562) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "currently this is an extremely generic class, encompassing both protostomes and deuterostomes." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Nervous_system" +- [pharynx](http://purl.obolibrary.org/obo/UBERON_0006562) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "pharyngeal" -- [nervous system](http://purl.obolibrary.org/obo/UBERON_0001016) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005093" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [pharynx](http://purl.obolibrary.org/obo/UBERON_0006562) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "branchial" -- [nervous system](http://purl.obolibrary.org/obo/UBERON_0001016) [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [Homo sapiens](http://purl.obolibrary.org/obo/NCBITaxon_9606) +- [pharynx](http://purl.obolibrary.org/obo/UBERON_0006562) [IAO_0006012](http://purl.obolibrary.org/obo/IAO_0006012) "2023-04-20" -- [nervous system](http://purl.obolibrary.org/obo/UBERON_0001016) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas) -### neural arch `http://purl.obolibrary.org/obo/UBERON_0003861` +### phosphorylates `http://purl.obolibrary.org/obo/RO_0002447` #### Removed -- [neural arch](http://purl.obolibrary.org/obo/UBERON_0003861) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arcus vertebrae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Vertebral_arch" +- [phosphorylates](http://purl.obolibrary.org/obo/RO_0002447) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - -#### Added -- [neural arch](http://purl.obolibrary.org/obo/UBERON_0003861) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arcus vertebrae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [phosphorylates](http://purl.obolibrary.org/obo/RO_0002447) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Vertebral_arch" -### neural cell `http://purl.obolibrary.org/obo/CL_0002319` +### photoreceptor array `http://purl.obolibrary.org/obo/UBERON_0005388` +#### Removed +- [photoreceptor array](http://purl.obolibrary.org/obo/UBERON_0005388) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004200" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -#### Added -- [neural cell](http://purl.obolibrary.org/obo/CL_0002319) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### neural crest `http://purl.obolibrary.org/obo/UBERON_0002342` +### photoreceptor layer of retina `http://purl.obolibrary.org/obo/UBERON_0001787` #### Removed -- [neural crest](http://purl.obolibrary.org/obo/UBERON_0002342) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "crista neuralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Neural_crest" +- [photoreceptor layer of retina](http://purl.obolibrary.org/obo/UBERON_0001787) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [neural crest](http://purl.obolibrary.org/obo/UBERON_0002342) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "crista neuralis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Neural_crest" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001165" -### neural crest cell `http://purl.obolibrary.org/obo/CL_0011012` +- [photoreceptor layer of retina](http://purl.obolibrary.org/obo/UBERON_0001787) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "we follow MA and ZFA in subdividing this into inner and outer segments" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" -#### Added -- [neural crest cell](http://purl.obolibrary.org/obo/CL_0011012) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### neural plate `http://purl.obolibrary.org/obo/UBERON_0003075` +### phrenic artery `http://purl.obolibrary.org/obo/UBERON_0002057` #### Removed -- [neural plate](http://purl.obolibrary.org/obo/UBERON_0003075) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D054258" +- [phrenic artery](http://purl.obolibrary.org/obo/UBERON_0002057) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In humans this includes the superior and inferior phrenic arteries" -- [neural plate](http://purl.obolibrary.org/obo/UBERON_0003075) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lamina neuralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Neural_plate" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [neural plate](http://purl.obolibrary.org/obo/UBERON_0003075) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lamina neuralis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### phrenic nerve `http://purl.obolibrary.org/obo/UBERON_0001884` +#### Removed +- [phrenic nerve](http://purl.obolibrary.org/obo/UBERON_0001884) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A nerve that arises from the caudal cervical nerves and is primarily the motor nerve of the diaphragm but also sends sensory fibers to the pericardium. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Neural_plate" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [neural plate](http://purl.obolibrary.org/obo/UBERON_0003075) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D054258" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000728" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/phrenic+nerve" -### neural progenitor cell `http://purl.obolibrary.org/obo/CL_0011020` -#### Added -- [neural progenitor cell](http://purl.obolibrary.org/obo/CL_0011020) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### pia mater `http://purl.obolibrary.org/obo/UBERON_0002361` +#### Removed +- [pia mater](http://purl.obolibrary.org/obo/UBERON_0002361) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "delicate innermost layer of the meninges-the membranes surrounding the brain and spinal cord. The thin, mesh-like pia mater closely envelops the entire surface of the brain, running down into the fissures of the cortex. It joins with the ependyma which lines the ventricles to form choroid plexuses that produce cerebrospinal fluid. In the spinal cord, the pia mater attaches to the dura mater by the denticular ligaments through the arachnoid membrane. The pia mater is a neural crest derivative[Wikipedia:Pia_mater]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Pia_mater" + +- [pia mater](http://purl.obolibrary.org/obo/UBERON_0002361) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EV:0100315" +- [pia mater](http://purl.obolibrary.org/obo/UBERON_0002361) SubClassOf [only in taxon](http://purl.obolibrary.org/obo/RO_0002160) some [Mammalia](http://purl.obolibrary.org/obo/NCBITaxon_40674) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0073040584" -### neural stem cell `http://purl.obolibrary.org/obo/CL_0000047` + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "check-aves" #### Added -- [neural stem cell](http://purl.obolibrary.org/obo/CL_0000047) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [pia mater](http://purl.obolibrary.org/obo/UBERON_0002361) SubClassOf [only in taxon](http://purl.obolibrary.org/obo/RO_0002160) some [Mammalia](http://purl.obolibrary.org/obo/NCBITaxon_40674) -### neural tube `http://purl.obolibrary.org/obo/UBERON_0001049` +### pigmented layer of retina `http://purl.obolibrary.org/obo/UBERON_0001782` #### Removed -- [neural tube](http://purl.obolibrary.org/obo/UBERON_0001049) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D054259" +- [pigmented layer of retina](http://purl.obolibrary.org/obo/UBERON_0001782) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429" -- [neural tube](http://purl.obolibrary.org/obo/UBERON_0001049) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tubus neuralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Neural_tube" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [neural tube](http://purl.obolibrary.org/obo/UBERON_0001049) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tubus neuralis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Neural_tube" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000536" -- [neural tube](http://purl.obolibrary.org/obo/UBERON_0001049) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D054259" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [pigmented layer of retina](http://purl.obolibrary.org/obo/UBERON_0001782) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A monolayer of pigmented epithelium covering the neural retina; develops from the outer of the two layers of the optic cup. Kimmel et al, 1995.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000144" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -### neural tube alar plate `http://purl.obolibrary.org/obo/UBERON_0005882` -#### Removed -- [neural tube alar plate](http://purl.obolibrary.org/obo/UBERON_0005882) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lamina dorsolateralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Alar_plate" +- [pigmented layer of retina](http://purl.obolibrary.org/obo/UBERON_0001782) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The monolayer of pigmented epithelium covering the neural retina.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFA:0000144" -- [neural tube alar plate](http://purl.obolibrary.org/obo/UBERON_0005882) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lamina alaris" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Alar_plate" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0011096" -#### Added -- [neural tube alar plate](http://purl.obolibrary.org/obo/UBERON_0005882) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lamina alaris" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Alar_plate" +- [pigmented layer of retina](http://purl.obolibrary.org/obo/UBERON_0001782) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -- [neural tube alar plate](http://purl.obolibrary.org/obo/UBERON_0005882) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lamina dorsolateralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Alar_plate" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### pineal body `http://purl.obolibrary.org/obo/UBERON_0001905` +#### Removed +- [pineal body](http://purl.obolibrary.org/obo/UBERON_0001905) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "epiphysial" +- [pineal body](http://purl.obolibrary.org/obo/UBERON_0001905) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0001942](http://purl.obolibrary.org/obo/UBERON_0001942) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" -### neurectoderm `http://purl.obolibrary.org/obo/UBERON_0002346` -#### Removed -- [neurectoderm](http://purl.obolibrary.org/obo/UBERON_0002346) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "epithelium tubi neuralis; neuroectoderma" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Neuroectoderm" +- [pineal body](http://purl.obolibrary.org/obo/UBERON_0001905) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The pineal gland has evolved from a part of the epiphyseal complex of anamniotes, which includes a median light-receptive pineal eye, parietal eye, or both.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [neurectoderm](http://purl.obolibrary.org/obo/UBERON_0002346) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001057" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [neurectoderm](http://purl.obolibrary.org/obo/UBERON_0002346) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001057" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000051" -- [neurectoderm](http://purl.obolibrary.org/obo/UBERON_0002346) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "epithelium tubi neuralis; neuroectoderma" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.516" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Neuroectoderm" +- [pineal body](http://purl.obolibrary.org/obo/UBERON_0001905) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A circumscribed swelling, includes the pineal primordium that appears late in the segmentation period in the dorsal midline of the diencephalon. Kimmel et al, 1995.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000019" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -### neuroblast (sensu Vertebrata) `http://purl.obolibrary.org/obo/CL_0000031` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -#### Added -- [neuroblast (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000031) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" +- [pineal body](http://purl.obolibrary.org/obo/UBERON_0001905) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "epiphyseal" -### neuroendocrine cell `http://purl.obolibrary.org/obo/CL_0000165` +- [pineal body](http://purl.obolibrary.org/obo/UBERON_0001905) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "lobulated in humans, homogeneous in mouse. Calcifies with age in humans." -#### Added -- [neuroendocrine cell](http://purl.obolibrary.org/obo/CL_0000165) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [pineal body](http://purl.obolibrary.org/obo/UBERON_0001905) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical structure which is a medial outgrowth of the thalamus on the dorsal surface of the brain. This structure is light sensitive and secretes melatonin when exposed to prolonged darkness.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### neuroepithelial stem cell `http://purl.obolibrary.org/obo/CL_0002259` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" -#### Added -- [neuroepithelial stem cell](http://purl.obolibrary.org/obo/CL_0002259) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010549" +- [pineal body](http://purl.obolibrary.org/obo/UBERON_0001905) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: part_of pineal complex (TAO:0001359)[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000019" -### neurogenic placode `http://purl.obolibrary.org/obo/UBERON_0009955` -#### Removed -- [neurogenic placode](http://purl.obolibrary.org/obo/UBERON_0009955) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "placodae neurogenicae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Neurogenic_placodes" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -#### Added -- [neurogenic placode](http://purl.obolibrary.org/obo/UBERON_0009955) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "placodae neurogenicae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [pineal body](http://purl.obolibrary.org/obo/UBERON_0001905) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0001941](http://purl.obolibrary.org/obo/UBERON_0001941) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Neurogenic_placodes" -### neurohypophysis `http://purl.obolibrary.org/obo/UBERON_0002198` +### pineal complex `http://purl.obolibrary.org/obo/UBERON_0015238` #### Removed -- [neurohypophysis](http://purl.obolibrary.org/obo/UBERON_0002198) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lobus posterior (glandula pituitaria)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:74628" +- [pineal complex](http://purl.obolibrary.org/obo/UBERON_0015238) [RO_0002174](http://purl.obolibrary.org/obo/RO_0002174) [Mammalia](http://purl.obolibrary.org/obo/NCBITaxon_40674) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [neurohypophysis](http://purl.obolibrary.org/obo/UBERON_0002198) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lobus nervosus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:401" +### pinna `http://purl.obolibrary.org/obo/UBERON_0001757` +#### Removed +- [pinna](http://purl.obolibrary.org/obo/UBERON_0001757) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Mammals have a third type of tympanic ear. An external flap, the auricle or pinna, helps funnel sound waves down the external acoustic meatus to the tympanic membrane.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000460" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [neurohypophysis](http://purl.obolibrary.org/obo/UBERON_0002198) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lobus nervosus neurohypophysis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:74628" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.420" -- [neurohypophysis](http://purl.obolibrary.org/obo/UBERON_0002198) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lobus posterior hypophysis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:74628" +- [pinna](http://purl.obolibrary.org/obo/UBERON_0001757) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The external expanded part of the ear characterized by a funnel-shaped structure through which the sound vibrations are received. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000460" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [neurohypophysis](http://purl.obolibrary.org/obo/UBERON_0002198) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lobus posterior" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:401" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [pinna](http://purl.obolibrary.org/obo/UBERON_0001757) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "The purpose of the pinna is to collect sound. It does so by acting as a funnel, amplifying the sound and directing it to the ear canal. While reflecting from the pinna, sound also goes through a filtering process which adds directional information to the sound (see sound localization, head-related transfer function, pinna notch)." -#### Added -- [neurohypophysis](http://purl.obolibrary.org/obo/UBERON_0002198) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lobus posterior (glandula pituitaria)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [pinna](http://purl.obolibrary.org/obo/UBERON_0001757) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In various species, the pinna can also signal mood and radiate heat" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:74628" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [neurohypophysis](http://purl.obolibrary.org/obo/UBERON_0002198) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lobus nervosus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### piriform cortex `http://purl.obolibrary.org/obo/UBERON_0004725` +#### Removed +- [piriform cortex](http://purl.obolibrary.org/obo/UBERON_0004725) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Piriform cortical regions are present in the brains of amphibians, reptiles and mammals. The piriform cortex is among three areas that emerge in the telencephalon of amphibians, situated caudally to a dorsal area, which is caudal to a hippocampal area. Farther along the phylogenic timeline, the telencephalic bulb of reptiles as viewed in a cross section of the transverse plane extends with the archipallial hippocampus folding toward the midline and down as the dorsal area begins to form a recognizable cortex. As mammalian cerebrums developed, volume of the dorsal cortex increased in slightly greater proportion, as compared proportionally with increased overall brain volume, until it enveloped the hippocampal regions. Recognized as neopallium or neocortex, enlarged dorsal areas envelop the paleopallial piriform cortex in humans and Old World monkeys. Among taxonomic groupings of mammals, the piriform cortex and the olfactory bulb become proportionally smaller in the brains of phylogenically younger species. The piriform cortex occupies a greater proportion of the overall brain and of the telencephalic brains of insectivores than in primates. The piriform cortex continues to occupy a consistent albeit small and declining proportion of the increasingly large telencephalon in the most recent primate species while the volume of the olfactory bulb becomes less in proportion" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:401" -- [neurohypophysis](http://purl.obolibrary.org/obo/UBERON_0002198) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lobus nervosus neurohypophysis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:74628" +### pituitary gland `http://purl.obolibrary.org/obo/UBERON_0000007` +#### Removed +- [pituitary gland](http://purl.obolibrary.org/obo/UBERON_0000007) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000118" -- [neurohypophysis](http://purl.obolibrary.org/obo/UBERON_0002198) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lobus posterior hypophysis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:74628" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [pituitary gland](http://purl.obolibrary.org/obo/UBERON_0000007) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "It (the hypophysis) develops embryonically in all vertebrates from two ectodermal evaginations that meet and unite. (...) A well-developed hypophyseal system with functional connections to the hypothalamus is unique to craniates.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [neurohypophysis](http://purl.obolibrary.org/obo/UBERON_0002198) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lobus posterior" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:401" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000143" -### neuromast `http://purl.obolibrary.org/obo/UBERON_0008904` -#### Removed -- [neuromast](http://purl.obolibrary.org/obo/UBERON_0008904) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006219" - - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0003-4423-4370" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.510" -#### Added -- [neuromast](http://purl.obolibrary.org/obo/UBERON_0008904) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006219" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [pituitary gland](http://purl.obolibrary.org/obo/UBERON_0000007) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The lamprey possesses a distinct pituitary organ and hormones, the ascidian does not show distinct evidence of them [Sower S, Freamat M, Kavanaugh S. The origins of the vertebrate hypothalamic-pituitary-gonadal (HPG) and hypothalamic-pituitary-thyroid (HPT) endocrine systems: new insights from lampreys. Gen Comp Endocrinol 2009;161:20-9]" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +- [pituitary gland](http://purl.obolibrary.org/obo/UBERON_0000007) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "An endocrine gland derived from infundibulum of the floor of the diencephalon and an ectodermal dorsal protrusion from the buccal cavity which controls the secretion of many hormones influencing the function of various organs of the body.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010536" -### neuron `http://purl.obolibrary.org/obo/CL_0000540` +- [pituitary gland](http://purl.obolibrary.org/obo/UBERON_0000007) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) #### Added -- [neuron](http://purl.obolibrary.org/obo/CL_0000540) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [pituitary gland](http://purl.obolibrary.org/obo/UBERON_0000007) SubClassOf [structure with developmental contribution from neural crest](http://purl.obolibrary.org/obo/UBERON_0010314) -### neuron associated cell `http://purl.obolibrary.org/obo/CL_0000095` +### placeholder removed `http://purl.obolibrary.org/obo/IAO_0000226` +#### Removed +- [placeholder removed](http://purl.obolibrary.org/obo/IAO_0000226) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "placeholder removed"@en -#### Added -- [neuron associated cell](http://purl.obolibrary.org/obo/CL_0000095) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### neuron associated cell (sensu Vertebrata) `http://purl.obolibrary.org/obo/CL_0000123` +### placenta `http://purl.obolibrary.org/obo/UBERON_0001987` +#### Removed +- [placenta](http://purl.obolibrary.org/obo/UBERON_0001987) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Eutherians: In eutherians, the chorioallantoic membrane of the fetus establishes intimate contact with the adjacent vascular wall of the mother's uterus to produce the placenta, a composite structure formed in part from tissues of the fetus and in part from tissues of the mother [ISBN:0073040584 (Vertebrates, Kardong)]. TODO - is taxon restriction too strict, even if we restrict def to allantoic placenta? - WP says: also found in some snakes and lizards with varying levels of development up to mammalian levels. Pough et al. 1992. Herpetology: Third Edition. Pearson Prentice Hall:Pearson Education, Inc., 2002. // See also: DOI:10.1002/jmor.11011" -#### Added -- [neuron associated cell (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000123) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [placenta](http://purl.obolibrary.org/obo/UBERON_0001987) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Phylogenetic analyses of the concatenated data set using maximum parsimony, maximum likelihood and distance based (neighbour joining) methods all converged on a nearly identical, well supported topology defining four principal eutherian lineages. The results affirm monophyly of traditional placental orders (except Artiodactyla and Insectivora), and also support some previously proposed, as well as new, superordinal clades.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### neuron projection bundle `http://purl.obolibrary.org/obo/UBERON_0000122` -#### Removed -- [neuron projection bundle](http://purl.obolibrary.org/obo/UBERON_0000122) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005099" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1038/35054550 Murphy WJ, Eizirik E, Johnson WE, Zhang YP, Ryder OA, O'Brien SJ, Molecular phylogenetics and the origins of placental mammals. Nature (2001)" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001266" + +- [placenta](http://purl.obolibrary.org/obo/UBERON_0001987) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "placental" #### Added -- [neuron projection bundle](http://purl.obolibrary.org/obo/UBERON_0000122) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005099" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [placenta](http://purl.obolibrary.org/obo/UBERON_0001987) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### neuron projection bundle connecting eye with brain `http://purl.obolibrary.org/obo/UBERON_0004904` +### placenta labyrinth `http://purl.obolibrary.org/obo/UBERON_0003946` #### Removed -- [neuron projection bundle connecting eye with brain](http://purl.obolibrary.org/obo/UBERON_0004904) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001956" +- [placenta labyrinth](http://purl.obolibrary.org/obo/UBERON_0003946) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Mouse-human differences: The mouse and human placentas have labyrinthine and villous types of interdigitation between maternal and fetal tissues, respectively ... The mouse placental labyrinth is composed of an intricate network of maternal blood spaces and embryonal blood vessels. Maternal and embryonal blood is separated by a placental barrier that consists of four cellular layers: layer I trophoblasts line the maternal lacunae, trophoblasts in layers II and III form syncytial-like layers, and endothelial cells line the embryonic vessels[DOI: 10.1073/pnas.96.14.8138 ]" #### Added -- [neuron projection bundle connecting eye with brain](http://purl.obolibrary.org/obo/UBERON_0004904) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001956" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [placenta labyrinth](http://purl.obolibrary.org/obo/UBERON_0003946) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### neuronal brush cell `http://purl.obolibrary.org/obo/CL_0000555` +### placental disc `http://purl.obolibrary.org/obo/UBERON_8600038` +#### Removed +- [placental disc](http://purl.obolibrary.org/obo/UBERON_8600038) SubClassOf [anatomical structure](http://purl.obolibrary.org/obo/UBERON_0000061) #### Added -- [neuronal brush cell](http://purl.obolibrary.org/obo/CL_0000555) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [placental disc](http://purl.obolibrary.org/obo/UBERON_8600038) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### neuronal receptor cell `http://purl.obolibrary.org/obo/CL_0000006` +### placental labyrinth villous `http://purl.obolibrary.org/obo/UBERON_0010005` +#### Removed +- [placental labyrinth villous](http://purl.obolibrary.org/obo/UBERON_0010005) SubClassOf [anatomical structure](http://purl.obolibrary.org/obo/UBERON_0000061) #### Added -- [neuronal receptor cell](http://purl.obolibrary.org/obo/CL_0000006) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [placental labyrinth villous](http://purl.obolibrary.org/obo/UBERON_0010005) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### neutrophil `http://purl.obolibrary.org/obo/CL_0000775` +### placental villous stroma `http://purl.obolibrary.org/obo/UBERON_8600023` #### Added -- [neutrophil](http://purl.obolibrary.org/obo/CL_0000775) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [placental villous stroma](http://purl.obolibrary.org/obo/UBERON_8600023) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### neutrophil progenitor cell `http://purl.obolibrary.org/obo/CL_0000834` +### plantar part of pes `http://purl.obolibrary.org/obo/UBERON_0008338` +#### Removed +- [plantar part of pes](http://purl.obolibrary.org/obo/UBERON_0008338) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In humans is the sole of the foot anatomically referred to as the plantar aspect. The equivalent surface in ungulates is the hoof" -#### Added -- [neutrophil progenitor cell](http://purl.obolibrary.org/obo/CL_0000834) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### nipple `http://purl.obolibrary.org/obo/UBERON_0002030` +### platelet glycoprotein 4 `http://purl.obolibrary.org/obo/PR_000001905` #### Removed -- [nipple](http://purl.obolibrary.org/obo/UBERON_0002030) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "papilla mammaria" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Nipple" +- [platelet glycoprotein 4](http://purl.obolibrary.org/obo/PR_000001905) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [platelet glycoprotein 4 (human)](http://purl.obolibrary.org/obo/PR_P16671) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [nipple](http://purl.obolibrary.org/obo/UBERON_0002030) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "papilla mammaria" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Nipple" +### platelet glycoprotein Ib alpha chain `http://purl.obolibrary.org/obo/PR_000001907` +#### Removed +- [platelet glycoprotein Ib alpha chain](http://purl.obolibrary.org/obo/PR_000001907) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [platelet glycoprotein Ib alpha chain (human)](http://purl.obolibrary.org/obo/PR_P07359) + -### nitric oxide biosynthetic process `http://purl.obolibrary.org/obo/GO_0006809` +### pleura `http://purl.obolibrary.org/obo/UBERON_0000977` #### Removed -- [nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0006809) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nitric oxide formation" +- [pleura](http://purl.obolibrary.org/obo/UBERON_0000977) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "pleural" -- [nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0006809) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" +- [pleura](http://purl.obolibrary.org/obo/UBERON_0000977) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "In MA, is_a cavity lining (which we equate to parietal). In FMA, is_a (viscous) serous membrane (which includes mesothelium plus connective tissue). Note the MA structure should probably be associated with the mesothelium of pleura in FMA. JB/EHDAA2 argues the term 'pleura' is best used for the mesothelial lining (thus excluding connective tissue). See https://github.com/obophenotype/uberon/issues/86" -- [nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0006809) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nitric oxide anabolism" +- [pleura](http://purl.obolibrary.org/obo/UBERON_0000977) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The serous membrane that covers the lungs and lines the pleural cavity. [Kaufman_MH_and_Bard_JBL, The_anatomical_basis_of_mouse_development_(1999)_San_Diego:_Academic_Press, p.264][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0006809) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:0006809" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0006809) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "The chemical reactions and pathways resulting in the formation of nitric oxide, nitrogen monoxide (NO), a colorless gas only slightly soluble in water." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:ai" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0006809) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nitric oxide biosynthesis" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0124020607" -- [nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0006809) [label](http://www.w3.org/2000/01/rdf-schema#label) "nitric oxide biosynthetic process" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000394" -- [nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0006809) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nitric oxide synthesis" +- [pleura](http://purl.obolibrary.org/obo/UBERON_0000977) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:16775" -- Class: [nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0006809) +#### Added +- [pleura](http://purl.obolibrary.org/obo/UBERON_0000977) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) -- [nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0006809) EquivalentTo [biosynthetic process](http://purl.obolibrary.org/obo/GO_0009058) and ([has primary output](http://purl.obolibrary.org/obo/RO_0004008) some [CHEBI_16480](http://purl.obolibrary.org/obo/CHEBI_16480)) -- [nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0006809) SubClassOf [nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_0046209) +### pleural cavity `http://purl.obolibrary.org/obo/UBERON_0002402` +#### Removed +- [pleural cavity](http://purl.obolibrary.org/obo/UBERON_0002402) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206" -- [nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0006809) SubClassOf [cellular nitrogen compound biosynthetic process](http://purl.obolibrary.org/obo/GO_0044271) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0006809) SubClassOf [has primary output](http://purl.obolibrary.org/obo/RO_0004008) some [CHEBI_16480](http://purl.obolibrary.org/obo/CHEBI_16480) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000581" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### nitric oxide catabolic process `http://purl.obolibrary.org/obo/GO_0046210` -#### Removed -- [nitric oxide catabolic process](http://purl.obolibrary.org/obo/GO_0046210) [label](http://www.w3.org/2000/01/rdf-schema#label) "nitric oxide catabolic process" +- [pleural cavity](http://purl.obolibrary.org/obo/UBERON_0002402) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "the EHDAA2 class of the same is not equivalent. See https://github.com/obophenotype/uberon/issues/86" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EHDAA2" -- [nitric oxide catabolic process](http://purl.obolibrary.org/obo/GO_0046210) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" +- [pleural cavity](http://purl.obolibrary.org/obo/UBERON_0002402) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "The contraction of the diaphragm creates a negative pressure within the pleural cavity which forces the lungs to expand resulting in passive exhalation and active inhalation. This breathing process can be made forceful through the contraction of the external intercostal muscles which forces the rib cage to expand and add to the negative pressure in the pleural cavity causing the lungs to fill with air. The fluid in the cavity provides lubrication and cushioning" -- [nitric oxide catabolic process](http://purl.obolibrary.org/obo/GO_0046210) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nitric oxide degradation" -- [nitric oxide catabolic process](http://purl.obolibrary.org/obo/GO_0046210) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nitric oxide breakdown" -- [nitric oxide catabolic process](http://purl.obolibrary.org/obo/GO_0046210) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:0046210" +### pleural sac `http://purl.obolibrary.org/obo/UBERON_0009778` +#### Removed +- [pleural sac](http://purl.obolibrary.org/obo/UBERON_0009778) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "despite its name the class EHDAA2:0004737 is not a true cavity, it corresponds to what we call the sac" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EHDAA2" -- [nitric oxide catabolic process](http://purl.obolibrary.org/obo/GO_0046210) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nitric oxide catabolism" +#### Added +- [pleural sac](http://purl.obolibrary.org/obo/UBERON_0009778) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -- [nitric oxide catabolic process](http://purl.obolibrary.org/obo/GO_0046210) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "The chemical reactions and pathways resulting in the breakdown of nitric oxide, nitrogen monoxide (NO), a colorless gas only slightly soluble in water." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:ai" -- Class: [nitric oxide catabolic process](http://purl.obolibrary.org/obo/GO_0046210) +### pleuroperitoneal canal `http://purl.obolibrary.org/obo/UBERON_0006279` +#### Removed +- [pleuroperitoneal canal](http://purl.obolibrary.org/obo/UBERON_0006279) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Each of the canal that links the peritoneal cavity and the caudal part of a pleural cavity. [ISBN:0124020607][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [nitric oxide catabolic process](http://purl.obolibrary.org/obo/GO_0046210) EquivalentTo [catabolic process](http://purl.obolibrary.org/obo/GO_0009056) and ([has primary input](http://purl.obolibrary.org/obo/RO_0004009) some [CHEBI_16480](http://purl.obolibrary.org/obo/CHEBI_16480)) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [nitric oxide catabolic process](http://purl.obolibrary.org/obo/GO_0046210) SubClassOf [nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_0046209) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [nitric oxide catabolic process](http://purl.obolibrary.org/obo/GO_0046210) SubClassOf [cellular nitrogen compound catabolic process](http://purl.obolibrary.org/obo/GO_0044270) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001505" -- [nitric oxide catabolic process](http://purl.obolibrary.org/obo/GO_0046210) SubClassOf [has primary input](http://purl.obolibrary.org/obo/RO_0004009) some [CHEBI_16480](http://purl.obolibrary.org/obo/CHEBI_16480) +- [pleuroperitoneal canal](http://purl.obolibrary.org/obo/UBERON_0006279) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:17704" -### nitric oxide metabolic process `http://purl.obolibrary.org/obo/GO_0046209` +### pleuroperitoneal membrane `http://purl.obolibrary.org/obo/UBERON_0009133` #### Removed -- [nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_0046209) [label](http://www.w3.org/2000/01/rdf-schema#label) "nitric oxide metabolic process" +- [pleuroperitoneal membrane](http://purl.obolibrary.org/obo/UBERON_0009133) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart [of other tetrapods] is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes). Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206" -- [nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_0046209) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000757" -- [nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_0046209) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "The chemical reactions and pathways involving nitric oxide, nitrogen monoxide (NO), a colorless gas only slightly soluble in water." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:ai" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_0046209) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:0046209" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_0046209) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nitric oxide metabolism" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- Class: [nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_0046209) -- [nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_0046209) EquivalentTo [metabolic process](http://purl.obolibrary.org/obo/GO_0008152) and ([has primary input or output](http://purl.obolibrary.org/obo/RO_0004007) some [CHEBI_16480](http://purl.obolibrary.org/obo/CHEBI_16480)) -- [nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_0046209) SubClassOf [metabolic process](http://purl.obolibrary.org/obo/GO_0008152) +### plural form `http://purl.obolibrary.org/obo/OMO_0003004` +#### Removed +- [plural form](http://purl.obolibrary.org/obo/OMO_0003004) [created](http://purl.org/dc/terms/created) "2023-03-03"^^[date](http://www.w3.org/2001/XMLSchema#date) -- [nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_0046209) SubClassOf [has primary input or output](http://purl.obolibrary.org/obo/RO_0004007) some [CHEBI_16480](http://purl.obolibrary.org/obo/CHEBI_16480) +- [plural form](http://purl.obolibrary.org/obo/OMO_0003004) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form)" -### nitric oxide production involved in inflammatory response `http://purl.obolibrary.org/obo/GO_0002537` +### pneumatized bone `http://purl.obolibrary.org/obo/UBERON_0008193` #### Removed -- [nitric oxide production involved in inflammatory response](http://purl.obolibrary.org/obo/GO_0002537) SubClassOf [has primary output](http://purl.obolibrary.org/obo/RO_0004008) some [CHEBI_16480](http://purl.obolibrary.org/obo/CHEBI_16480) +- [pneumatized bone](http://purl.obolibrary.org/obo/UBERON_0008193) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Skeletal pneumaticity is the presence of air spaces within bones. Skeletal pneumaticity exists only in synapsids and archosaurs. It is generally produced during development by excavation of bone by pneumatic diverticula (air sacs) from an air-filled space such as the lungs or nasal cavity. Pneumatization is highly variable between individuals, and bones not normally pneumatized can become pneumatized in pathological development. Pneumatization occurs in the skulls of mammals, crocodilians and birds among extant groups, as well as extinct archosaurs including the dinosaurs and pterosaurs. Pneumatic spaces include the paranasal sinuses and some of the mastoid cells[WP]. [Wikipedia:Skeletal_pneumaticity]" -### nitric oxide transmembrane transporter activity `http://purl.obolibrary.org/obo/GO_0030184` +### pons `http://purl.obolibrary.org/obo/UBERON_0000988` #### Removed -- [nitric oxide transmembrane transporter activity](http://purl.obolibrary.org/obo/GO_0030184) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Enables the transfer of nitric oxide, nitrogen monoxide, from one side of a membrane to the other." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:mah" +- [pons](http://purl.obolibrary.org/obo/UBERON_0000988) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "During the embryonic development of birds and mammals, neuroblasts migrate from the cerebellum into the ventral part of the rhombencephalon and differentiate into pontine and other nuclei, which relay information from between the cerebrum and cerebellum, and a conspicuous band of transverse fibers. This region is known as the pons. A pons does not differentiate in reptiles and anamniotes (...).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [nitric oxide transmembrane transporter activity](http://purl.obolibrary.org/obo/GO_0030184) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "molecular_function" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [nitric oxide transmembrane transporter activity](http://purl.obolibrary.org/obo/GO_0030184) [label](http://www.w3.org/2000/01/rdf-schema#label) "nitric oxide transmembrane transporter activity" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [nitric oxide transmembrane transporter activity](http://purl.obolibrary.org/obo/GO_0030184) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:0030184" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.474" -- Class: [nitric oxide transmembrane transporter activity](http://purl.obolibrary.org/obo/GO_0030184) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001176" -- [nitric oxide transmembrane transporter activity](http://purl.obolibrary.org/obo/GO_0030184) EquivalentTo [transmembrane transporter activity](http://purl.obolibrary.org/obo/GO_0022857) and ([has primary input](http://purl.obolibrary.org/obo/RO_0004009) some [CHEBI_16480](http://purl.obolibrary.org/obo/CHEBI_16480)) +- [pons](http://purl.obolibrary.org/obo/UBERON_0000988) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/pons" -- [nitric oxide transmembrane transporter activity](http://purl.obolibrary.org/obo/GO_0030184) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [nitric oxide transport](http://purl.obolibrary.org/obo/GO_0030185) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [nitric oxide transmembrane transporter activity](http://purl.obolibrary.org/obo/GO_0030184) SubClassOf [has primary input](http://purl.obolibrary.org/obo/RO_0004009) some [CHEBI_16480](http://purl.obolibrary.org/obo/CHEBI_16480) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [nitric oxide transmembrane transporter activity](http://purl.obolibrary.org/obo/GO_0030184) SubClassOf [transmembrane transporter activity](http://purl.obolibrary.org/obo/GO_0022857) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001176" + +- [pons](http://purl.obolibrary.org/obo/UBERON_0000988) [RO_0002174](http://purl.obolibrary.org/obo/RO_0002174) [NCBITaxon_7955](http://purl.obolibrary.org/obo/NCBITaxon_7955) -### nitric oxide transport `http://purl.obolibrary.org/obo/GO_0030185` -#### Removed -- [nitric oxide transport](http://purl.obolibrary.org/obo/GO_0030185) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" -- [nitric oxide transport](http://purl.obolibrary.org/obo/GO_0030185) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:0030185" +### pontine raphe nucleus `http://purl.obolibrary.org/obo/UBERON_0002047` +#### Removed +- [pontine raphe nucleus](http://purl.obolibrary.org/obo/UBERON_0002047) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002267](http://purl.obolibrary.org/obo/UBERON_0002267) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" -- [nitric oxide transport](http://purl.obolibrary.org/obo/GO_0030185) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "The directed movement of nitric oxide, nitrogen monoxide, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:mah" +- [pontine raphe nucleus](http://purl.obolibrary.org/obo/UBERON_0002047) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0003004](http://purl.obolibrary.org/obo/UBERON_0003004) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" -- [nitric oxide transport](http://purl.obolibrary.org/obo/GO_0030185) [label](http://www.w3.org/2000/01/rdf-schema#label) "nitric oxide transport" +- [pontine raphe nucleus](http://purl.obolibrary.org/obo/UBERON_0002047) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002587](http://purl.obolibrary.org/obo/UBERON_0002587) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" -- Class: [nitric oxide transport](http://purl.obolibrary.org/obo/GO_0030185) +- [pontine raphe nucleus](http://purl.obolibrary.org/obo/UBERON_0002047) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [locus ceruleus](http://purl.obolibrary.org/obo/UBERON_0002148) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" -- [nitric oxide transport](http://purl.obolibrary.org/obo/GO_0030185) EquivalentTo [transport](http://purl.obolibrary.org/obo/GO_0006810) and ([has primary input](http://purl.obolibrary.org/obo/RO_0004009) some [CHEBI_16480](http://purl.obolibrary.org/obo/CHEBI_16480)) -- [nitric oxide transport](http://purl.obolibrary.org/obo/GO_0030185) SubClassOf [has primary input](http://purl.obolibrary.org/obo/RO_0004009) some [CHEBI_16480](http://purl.obolibrary.org/obo/CHEBI_16480) -- [nitric oxide transport](http://purl.obolibrary.org/obo/GO_0030185) SubClassOf [transport](http://purl.obolibrary.org/obo/GO_0006810) +### pontine tegmentum `http://purl.obolibrary.org/obo/UBERON_0003023` +#### Removed +- [pontine tegmentum](http://purl.obolibrary.org/obo/UBERON_0003023) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "involved in the initiation of REM sleep [Wikipedia:Pontine_tegmentum]" +- [pontine tegmentum](http://purl.obolibrary.org/obo/UBERON_0003023) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D065821" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) -### nitrogen compound metabolic process `http://purl.obolibrary.org/obo/GO_0006807` + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" #### Added -- [nitrogen compound metabolic process](http://purl.obolibrary.org/obo/GO_0006807) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/geneontology/go-ontology/issues/26424"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) +- [pontine tegmentum](http://purl.obolibrary.org/obo/UBERON_0003023) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### portal lobule `http://purl.obolibrary.org/obo/UBERON_0001171` -- [nitrogen compound metabolic process](http://purl.obolibrary.org/obo/GO_0006807) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [gocheck_do_not_annotate](http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate) +#### Added +- [portal lobule](http://purl.obolibrary.org/obo/UBERON_0001171) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -### nitrogen cycle metabolic process `http://purl.obolibrary.org/obo/GO_0071941` +### portal triad `http://purl.obolibrary.org/obo/UBERON_0001279` #### Removed -- [nitrogen cycle metabolic process](http://purl.obolibrary.org/obo/GO_0071941) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) +- [portal triad](http://purl.obolibrary.org/obo/UBERON_0001279) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "The misnomer 'portal triad' traditionally has included only the first three structures, and was named before lymphatic vessels were discovered in the structure. It can refer both to the largest branch of each of these vessels running inside the hepatoduodenal ligament, and to the smaller branches of these vessels inside the liver." #### Added -- [nitrogen cycle metabolic process](http://purl.obolibrary.org/obo/GO_0071941) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) +- [portal triad](http://purl.obolibrary.org/obo/UBERON_0001279) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -### non-classical monocyte `http://purl.obolibrary.org/obo/CL_0000875` +### portion of cartilage tissue in tibia `http://purl.obolibrary.org/obo/UBERON_0000313` +#### Removed +- [portion of cartilage tissue in tibia](http://purl.obolibrary.org/obo/UBERON_0000313) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "This class represents a portion of cartilage tissue located in the tibia, *not* the cartilaginous condensation of an emrbyonic tibia" -#### Added -- [non-classical monocyte](http://purl.obolibrary.org/obo/CL_0000875) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### non-connected functional system `http://purl.obolibrary.org/obo/UBERON_0015203` +### positively regulated by `http://purl.obolibrary.org/obo/RO_0002336` #### Removed -- [non-connected functional system](http://purl.obolibrary.org/obo/UBERON_0015203) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007278" +- [positively regulated by](http://purl.obolibrary.org/obo/RO_0002336) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) -#### Added -- [non-connected functional system](http://purl.obolibrary.org/obo/UBERON_0015203) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007278" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### non-pigmented ciliary epithelial cell `http://purl.obolibrary.org/obo/CL_0002304` +### positively regulates `http://purl.obolibrary.org/obo/RO_0002213` +#### Removed +- [positively regulates](http://purl.obolibrary.org/obo/RO_0002213) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) [causal-relations](http://purl.obolibrary.org/obo/ro/docs/causal-relations) -#### Added -- [non-pigmented ciliary epithelial cell](http://purl.obolibrary.org/obo/CL_0002304) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [positively regulates](http://purl.obolibrary.org/obo/RO_0002213) [RO_0004049](http://purl.obolibrary.org/obo/RO_0004049) [regulates](http://purl.obolibrary.org/obo/RO_0002211) +- [positively regulates](http://purl.obolibrary.org/obo/RO_0002213) [IAO_0000589](http://purl.obolibrary.org/obo/IAO_0000589) "positively regulates (process to process)" -### non-terminally differentiated cell `http://purl.obolibrary.org/obo/CL_0000055` +- [positively regulates](http://purl.obolibrary.org/obo/RO_0002213) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) -#### Added -- [non-terminally differentiated cell](http://purl.obolibrary.org/obo/CL_0000055) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### nose `http://purl.obolibrary.org/obo/UBERON_0000004` +### possible_exception `http://www.geneontology.org/formats/oboInOwl#possible_exception` #### Removed -- [nose](http://purl.obolibrary.org/obo/UBERON_0000004) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nasus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Nose" +- AnnotationProperty: [possible_exception](http://www.geneontology.org/formats/oboInOwl#possible_exception) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [nose](http://purl.obolibrary.org/obo/UBERON_0000004) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nasus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Nose" +### post-anal tail `http://purl.obolibrary.org/obo/UBERON_0007812` +#### Removed +- [post-anal tail](http://purl.obolibrary.org/obo/UBERON_0007812) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Organism subdivision which is the part of the body posterior to the vent which includes the anal and caudal fins.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001117" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -### notochord `http://purl.obolibrary.org/obo/UBERON_0002328` -#### Removed -- [notochord](http://purl.obolibrary.org/obo/UBERON_0002328) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "notochorda" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Notochord" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [post-anal tail](http://purl.obolibrary.org/obo/UBERON_0007812) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical structure that is the terminal, flexible posterior appendage of the organism.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" -#### Added -- [notochord](http://purl.obolibrary.org/obo/UBERON_0002328) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "notochorda" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Notochord" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010338" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### nuchal ligament `http://purl.obolibrary.org/obo/UBERON_0000351` -#### Removed -- [nuchal ligament](http://purl.obolibrary.org/obo/UBERON_0000351) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ligamentum nuchae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:13427" +- [post-anal tail](http://purl.obolibrary.org/obo/UBERON_0007812) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "present at some time in chordate life history (eg in Urochordates, present only in free-swimming larvae). Function: propellor locomotion (in some species)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [post-anal tail](http://purl.obolibrary.org/obo/UBERON_0007812) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:16748" -#### Added -- [nuchal ligament](http://purl.obolibrary.org/obo/UBERON_0000351) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ligamentum nuchae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [post-anal tail](http://purl.obolibrary.org/obo/UBERON_0007812) SubClassOf [only in taxon](http://purl.obolibrary.org/obo/RO_0002160) some [Chordata](http://purl.obolibrary.org/obo/NCBITaxon_7711) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "cjm" + + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "possible exception in hemichordates" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:13427" +#### Added +- [post-anal tail](http://purl.obolibrary.org/obo/UBERON_0007812) SubClassOf [only in taxon](http://purl.obolibrary.org/obo/RO_0002160) some [Chordata](http://purl.obolibrary.org/obo/NCBITaxon_7711) -### nucleus accumbens `http://purl.obolibrary.org/obo/UBERON_0001882` +### post-anal tail bud `http://purl.obolibrary.org/obo/UBERON_0002533` #### Removed -- [nucleus accumbens](http://purl.obolibrary.org/obo/UBERON_0001882) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "colliculus nuclei caudati" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:277" +- [post-anal tail bud](http://purl.obolibrary.org/obo/UBERON_0002533) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (5) a larva or embryo with a postanal tail.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [nucleus accumbens](http://purl.obolibrary.org/obo/UBERON_0001882) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "colliculus nuclei caudati" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:277" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000201" -### nucleus of lateral olfactory tract `http://purl.obolibrary.org/obo/UBERON_0002893` -#### Removed -- [nucleus of lateral olfactory tract](http://purl.obolibrary.org/obo/UBERON_0002893) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus striae olfactoriae lateralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:242" +- [post-anal tail bud](http://purl.obolibrary.org/obo/UBERON_0002533) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Rapidly proliferating mass of cells at the caudal extremity of the embryo. Its formation is reflected in a caudal carving of the posterior portion of the archenteric canal at NF stage 22. With its further outgrowth, the postanal gut primordium becomes stretched. Its lumen is in broad communication with the hindgut at NF stage 25.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0011104" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -- [nucleus of lateral olfactory tract](http://purl.obolibrary.org/obo/UBERON_0002893) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus of tractus olfactorius lateralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:242" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0815318960" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -#### Added -- [nucleus of lateral olfactory tract](http://purl.obolibrary.org/obo/UBERON_0002893) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus striae olfactoriae lateralis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "OMD:tail+bud" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:242" -- [nucleus of lateral olfactory tract](http://purl.obolibrary.org/obo/UBERON_0002893) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus of tractus olfactorius lateralis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:242" +### post-anal tail muscle `http://purl.obolibrary.org/obo/UBERON_0003665` +#### Removed +- [post-anal tail muscle](http://purl.obolibrary.org/obo/UBERON_0003665) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "the BTO class may possibly refer to an invertebrate structure" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "BTO" + -### nucleus pulposus `http://purl.obolibrary.org/obo/UBERON_0002242` +### post-embryonic stage `http://purl.obolibrary.org/obo/UBERON_0000092` #### Removed -- [nucleus pulposus](http://purl.obolibrary.org/obo/UBERON_0002242) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D000070614" +- [post-embryonic stage](http://purl.obolibrary.org/obo/UBERON_0000092) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)" -#### Added -- [nucleus pulposus](http://purl.obolibrary.org/obo/UBERON_0002242) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D000070614" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +### post-hyoid pharyngeal arch `http://purl.obolibrary.org/obo/UBERON_0008896` +#### Removed +- [post-hyoid pharyngeal arch](http://purl.obolibrary.org/obo/UBERON_0008896) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Posterior-most stream of cranial neural crest, which sub-divides during migration.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010362" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + +- [post-hyoid pharyngeal arch](http://purl.obolibrary.org/obo/UBERON_0008896) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "SCTID:308766004" + -### obsolete L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus) `http://purl.obolibrary.org/obo/CL_4023034` +### postaxialmost part of `http://purl.obolibrary.org/obo/BSPO_0001115` #### Removed -- [obsolete L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus)](http://purl.obolibrary.org/obo/CL_4023034) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Moved to PCL - see https://github.com/obophenotype/brain_data_standards_ontologies/issues/231. Use PCL:1000002 instead." - -#### Added -- [obsolete L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus)](http://purl.obolibrary.org/obo/CL_4023034) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Moved to PCL. Use PCL:1000002 instead." +- [postaxialmost part of](http://purl.obolibrary.org/obo/BSPO_0001115) [label](http://www.w3.org/2000/01/rdf-schema#label) "postaxialmost part of" -- [obsolete L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus)](http://purl.obolibrary.org/obo/CL_4023034) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [231](https://github.com/obophenotype/brain_data_standards_ontologies/issues/231) +- [postaxialmost part of](http://purl.obolibrary.org/obo/BSPO_0001115) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" +- [postaxialmost part of](http://purl.obolibrary.org/obo/BSPO_0001115) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BSPO:0001115" -### obsolete Martinotti morphology L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus) `http://purl.obolibrary.org/obo/CL_4023067` -#### Removed -- [obsolete Martinotti morphology L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus)](http://purl.obolibrary.org/obo/CL_4023067) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Moved to PCL - see https://github.com/obophenotype/brain_data_standards_ontologies/issues/231. Use PCL:1000004 instead." +- [postaxialmost part of](http://purl.obolibrary.org/obo/BSPO_0001115) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "postaxialmost_part_of" -#### Added -- [obsolete Martinotti morphology L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus)](http://purl.obolibrary.org/obo/CL_4023067) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Moved to PCL. Use PCL:1000004 instead." +- [postaxialmost part of](http://purl.obolibrary.org/obo/BSPO_0001115) [id](http://www.geneontology.org/formats/oboInOwl#id) "postaxialmost_part_of" -- [obsolete Martinotti morphology L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus)](http://purl.obolibrary.org/obo/CL_4023067) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [231](https://github.com/obophenotype/brain_data_standards_ontologies/issues/231) -### obsolete acid secreting cell `http://purl.obolibrary.org/obo/CL_0000161` +### postcranial axial cartilage `http://purl.obolibrary.org/obo/UBERON_2001457` #### Removed -- [obsolete acid secreting cell](http://purl.obolibrary.org/obo/CL_0000161) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "https://github.com/obophenotype/cell-ontology/issues/427" +- [postcranial axial cartilage](http://purl.obolibrary.org/obo/UBERON_2001457) [UBPROP_0000004](http://purl.obolibrary.org/obo/UBPROP_0000004) "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://purl.obolibrary.org/obo/tao.owl" -#### Added -- [obsolete acid secreting cell](http://purl.obolibrary.org/obo/CL_0000161) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [427](https://github.com/obophenotype/cell-ontology/issues/427) -### obsolete animal cell `http://purl.obolibrary.org/obo/CL_0000548` +### postcranial axial skeleton `http://purl.obolibrary.org/obo/UBERON_0002090` #### Removed -- [obsolete animal cell](http://purl.obolibrary.org/obo/CL_0000548) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "https://github.com/obophenotype/cell-ontology/issues/2124" +- [postcranial axial skeleton](http://purl.obolibrary.org/obo/UBERON_0002090) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" -#### Added -- [obsolete animal cell](http://purl.obolibrary.org/obo/CL_0000548) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -- [obsolete animal cell](http://purl.obolibrary.org/obo/CL_0000548) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [2124](https://github.com/obophenotype/cell-ontology/issues/2124) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000034" -### obsolete barrier epithelial cell `http://purl.obolibrary.org/obo/CL_0000073` -#### Removed -- [obsolete barrier epithelial cell](http://purl.obolibrary.org/obo/CL_0000073) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "https://github.com/obophenotype/cell-ontology/issues/1149" +- [postcranial axial skeleton](http://purl.obolibrary.org/obo/UBERON_0002090) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D013131" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) -#### Added -- [obsolete barrier epithelial cell](http://purl.obolibrary.org/obo/CL_0000073) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [1149](https://github.com/obophenotype/cell-ontology/issues/1149) + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +- [postcranial axial skeleton](http://purl.obolibrary.org/obo/UBERON_0002090) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000093" -### obsolete basket morphology L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus) `http://purl.obolibrary.org/obo/CL_4023078` -#### Removed -- [obsolete basket morphology L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus)](http://purl.obolibrary.org/obo/CL_4023078) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Moved to PCL - see https://github.com/obophenotype/brain_data_standards_ontologies/issues/231. Use PCL:1000003 instead." + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -#### Added -- [obsolete basket morphology L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus)](http://purl.obolibrary.org/obo/CL_4023078) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Moved to PCL. Use PCL:1000003 instead." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PSPUB:0000170" -- [obsolete basket morphology L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus)](http://purl.obolibrary.org/obo/CL_4023078) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [231](https://github.com/obophenotype/brain_data_standards_ontologies/issues/231) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" +- [postcranial axial skeleton](http://purl.obolibrary.org/obo/UBERON_0002090) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -### obsolete bronchioalveolar stem cells `http://purl.obolibrary.org/obo/CL_1001566` -#### Removed -- [obsolete bronchioalveolar stem cells](http://purl.obolibrary.org/obo/CL_1001566) [see also](http://www.w3.org/2000/01/rdf-schema#seeAlso) "https://github.com/obophenotype/cell-ontology/issues/1443" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -#### Added -- [obsolete bronchioalveolar stem cells](http://purl.obolibrary.org/obo/CL_1001566) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [1443](https://github.com/obophenotype/cell-ontology/issues/1443) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000317" -### obsolete choroid plexus cell `http://purl.obolibrary.org/obo/CL_4023073` -#### Removed -- [obsolete choroid plexus cell](http://purl.obolibrary.org/obo/CL_4023073) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "https://github.com/obophenotype/cell-ontology/issues/2043" +- [postcranial axial skeleton](http://purl.obolibrary.org/obo/UBERON_0002090) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:17214" -#### Added -- [obsolete choroid plexus cell](http://purl.obolibrary.org/obo/CL_4023073) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [2043](https://github.com/obophenotype/cell-ontology/issues/2043) +- [postcranial axial skeleton](http://purl.obolibrary.org/obo/UBERON_0002090) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### obsolete closable valve cell `http://purl.obolibrary.org/obo/CL_0000664` -#### Removed -- [obsolete closable valve cell](http://purl.obolibrary.org/obo/CL_0000664) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "https://github.com/obophenotype/cell-ontology/issues/726" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1186/1742-9994-8-4 Schilling N, Evolution of the axial system in craniates: morphology and function of the perivertebral musculature. Frontiers in Zoology (2011)" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000317" -#### Added -- [obsolete closable valve cell](http://purl.obolibrary.org/obo/CL_0000664) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [726](https://github.com/obophenotype/cell-ontology/issues/726) -### obsolete excitatory neuron `http://purl.obolibrary.org/obo/CL_0008030` +### posterior communicating artery `http://purl.obolibrary.org/obo/UBERON_0001628` #### Removed -- [obsolete excitatory neuron](http://purl.obolibrary.org/obo/CL_0008030) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "See https://github.com/obophenotype/cell-ontology/issues/1540. Consider using glutamatergic neuron instead. Do note that not all glutamatergic neurons are excitatory and replacing excitatory neuron with glutamatergic neuron should be done with caution." +- [posterior communicating artery](http://purl.obolibrary.org/obo/UBERON_0001628) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "todo - verify ZFA link: An artery that connects caudal division of the internal carotid artery and the basal communicating artery to the basilar artery" -#### Added -- [obsolete excitatory neuron](http://purl.obolibrary.org/obo/CL_0008030) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [1540](https://github.com/obophenotype/cell-ontology/issues/1540) +- [posterior communicating artery](http://purl.obolibrary.org/obo/UBERON_0001628) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "An artery that connects caudal division of the internal carotid artery and the basal communicating artery to the basilar artery. Isogai et al. 2001.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -- [obsolete excitatory neuron](http://purl.obolibrary.org/obo/CL_0008030) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Consider using glutamatergic neuron instead. Do note that not all glutamatergic neurons are excitatory and replacing excitatory neuron with glutamatergic neuron should be done with caution." + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005001" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -### obsolete female germ line stem cell (sensu Nematoda and Protostomia) `http://purl.obolibrary.org/obo/CL_0000088` -#### Removed -- [obsolete female germ line stem cell (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000088) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/obophenotype/cell-ontology/issues/1935" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -#### Added -- [obsolete female germ line stem cell (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000088) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [1935](https://github.com/obophenotype/cell-ontology/issues/1935) -### obsolete female germ line stem cell (sensu Vertebrata) `http://purl.obolibrary.org/obo/CL_0000090` +### posterior lateral line `http://purl.obolibrary.org/obo/UBERON_0006334` #### Removed -- [obsolete female germ line stem cell (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000090) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/obophenotype/cell-ontology/issues/1935" +- [posterior lateral line](http://purl.obolibrary.org/obo/UBERON_0006334) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "One of eight distinct lateral lines in the 4-day larva. A sensory system on the surface of the fish, consisting of small sensory patches (neuromasts) distributed in discrete lines over the body surface. The lateral line system is stimulated by local water displacements and vibrations, and detects propulsion of the fish through the water, as well as facilitating shoaling, prey capture, and predator and obstacle avoidance. (See Anatomical Atlas entry for lateral line by T. Whitfield.)[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -#### Added -- [obsolete female germ line stem cell (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000090) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [1935](https://github.com/obophenotype/cell-ontology/issues/1935) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000944" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -### obsolete fusimotor neuron `http://purl.obolibrary.org/obo/CL_0000717` -#### Removed -- [obsolete fusimotor neuron](http://purl.obolibrary.org/obo/CL_0000717) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Term merged into CL:0008037. Refer to https://github.com/obophenotype/cell-ontology/issues/1364" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -#### Added -- [obsolete fusimotor neuron](http://purl.obolibrary.org/obo/CL_0000717) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [1364](https://github.com/obophenotype/cell-ontology/issues/1364) +- [posterior lateral line](http://purl.obolibrary.org/obo/UBERON_0006334) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: part_of posterior lateral line system (TAO:0001471)[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000944" -- [obsolete fusimotor neuron](http://purl.obolibrary.org/obo/CL_0000717) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Term merged into CL:0008037." + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -### obsolete germ line stem cell (sensu Nematoda and Protostomia) `http://purl.obolibrary.org/obo/CL_0000086` -#### Removed -- [obsolete germ line stem cell (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000086) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/obophenotype/cell-ontology/issues/1935" +- [posterior lateral line](http://purl.obolibrary.org/obo/UBERON_0006334) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: develops_from posterior lateral line primordium (TAO:0001157)[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000944" -#### Added -- [obsolete germ line stem cell (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000086) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [1935](https://github.com/obophenotype/cell-ontology/issues/1935) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -### obsolete germ line stem cell (sensu Vertebrata) `http://purl.obolibrary.org/obo/CL_0000085` + +### posterior lateral line ganglion `http://purl.obolibrary.org/obo/UBERON_2001314` #### Removed -- [obsolete germ line stem cell (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000085) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/obophenotype/cell-ontology/issues/1935" +- [posterior lateral line ganglion](http://purl.obolibrary.org/obo/UBERON_2001314) [UBPROP_0000004](http://purl.obolibrary.org/obo/UBPROP_0000004) "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://purl.obolibrary.org/obo/tao.owl" -#### Added -- [obsolete germ line stem cell (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000085) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [1935](https://github.com/obophenotype/cell-ontology/issues/1935) -### obsolete glial cell (sensu Nematoda and Protostomia) `http://purl.obolibrary.org/obo/CL_0000124` +### posterior lateral line nerve `http://purl.obolibrary.org/obo/UBERON_2000175` #### Removed -- [obsolete glial cell (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000124) [see also](http://www.w3.org/2000/01/rdf-schema#seeAlso) "https://github.com/obophenotype/cell-ontology/issues/715" +- [posterior lateral line nerve](http://purl.obolibrary.org/obo/UBERON_2000175) [UBPROP_0000004](http://purl.obolibrary.org/obo/UBPROP_0000004) "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://purl.obolibrary.org/obo/tao.owl" -#### Added -- [obsolete glial cell (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000124) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [715](https://github.com/obophenotype/cell-ontology/issues/715) -### obsolete glial cell (sensu Vertebrata) `http://purl.obolibrary.org/obo/CL_0000243` +### posterior lateral line neuromast `http://purl.obolibrary.org/obo/UBERON_2000940` #### Removed -- [obsolete glial cell (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000243) [see also](http://www.w3.org/2000/01/rdf-schema#seeAlso) "https://github.com/obophenotype/cell-ontology/issues/715" +- [posterior lateral line neuromast](http://purl.obolibrary.org/obo/UBERON_2000940) [UBPROP_0000004](http://purl.obolibrary.org/obo/UBPROP_0000004) "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://purl.obolibrary.org/obo/tao.owl" -#### Added -- [obsolete glial cell (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000243) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [715](https://github.com/obophenotype/cell-ontology/issues/715) -### obsolete has_high_plasma_membrane_amount `http://purl.obolibrary.org/obo/cl#has_high_plasma_membrane_amount` +### posterior lateral line placode `http://purl.obolibrary.org/obo/UBERON_2001156` #### Removed -- [obsolete has_high_plasma_membrane_amount](http://purl.obolibrary.org/obo/cl#has_high_plasma_membrane_amount) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Replaced with RO:0015015, see https://github.com/obophenotype/cell-ontology/issues/1481" +- [posterior lateral line placode](http://purl.obolibrary.org/obo/UBERON_2001156) [UBPROP_0000004](http://purl.obolibrary.org/obo/UBPROP_0000004) "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://purl.obolibrary.org/obo/tao.owl" -#### Added -- [obsolete has_high_plasma_membrane_amount](http://purl.obolibrary.org/obo/cl#has_high_plasma_membrane_amount) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [1481](https://github.com/obophenotype/cell-ontology/issues/1481) -### obsolete has_low_plasma_membrane_amount `http://purl.obolibrary.org/obo/cl#has_low_plasma_membrane_amount` +### posterior lateral line primordium `http://purl.obolibrary.org/obo/UBERON_2001157` #### Removed -- [obsolete has_low_plasma_membrane_amount](http://purl.obolibrary.org/obo/cl#has_low_plasma_membrane_amount) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Replaced with RO:0015016, see https://github.com/obophenotype/cell-ontology/issues/1481" +- [posterior lateral line primordium](http://purl.obolibrary.org/obo/UBERON_2001157) [UBPROP_0000004](http://purl.obolibrary.org/obo/UBPROP_0000004) "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://purl.obolibrary.org/obo/tao.owl" -#### Added -- [obsolete has_low_plasma_membrane_amount](http://purl.obolibrary.org/obo/cl#has_low_plasma_membrane_amount) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [1481](https://github.com/obophenotype/cell-ontology/issues/1481) -### obsolete increased nucleus size `http://purl.obolibrary.org/obo/CL_0017505` +### posterior lateral line system `http://purl.obolibrary.org/obo/UBERON_2001471` #### Removed -- [obsolete increased nucleus size](http://purl.obolibrary.org/obo/CL_0017505) [label](http://www.w3.org/2000/01/rdf-schema#label) "increased nucleus size" +- [posterior lateral line system](http://purl.obolibrary.org/obo/UBERON_2001471) [UBPROP_0000004](http://purl.obolibrary.org/obo/UBPROP_0000004) "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://purl.obolibrary.org/obo/tao.owl" -- [obsolete increased nucleus size](http://purl.obolibrary.org/obo/CL_0017505) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm" -- [obsolete increased nucleus size](http://purl.obolibrary.org/obo/CL_0017505) EquivalentTo [nucleus](http://purl.obolibrary.org/obo/GO_0005634) and ([bearer of](http://purl.obolibrary.org/obo/RO_0000053) some [increased size](http://purl.obolibrary.org/obo/PATO_0000586)) -- [obsolete increased nucleus size](http://purl.obolibrary.org/obo/CL_0017505) SubClassOf [bearer of](http://purl.obolibrary.org/obo/RO_0000053) some [increased size](http://purl.obolibrary.org/obo/PATO_0000586) +### posterior nasal aperture `http://purl.obolibrary.org/obo/UBERON_0004771` +#### Removed +- [posterior nasal aperture](http://purl.obolibrary.org/obo/UBERON_0004771) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Fish don't have choanae, instead they have two pairs of external nostrils" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" -- [obsolete increased nucleus size](http://purl.obolibrary.org/obo/CL_0017505) SubClassOf [nucleus](http://purl.obolibrary.org/obo/GO_0005634) +- [posterior nasal aperture](http://purl.obolibrary.org/obo/UBERON_0004771) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In addition to tetrapods, the lungfish has internal nostrils too. In tetrapods the exhalant nostril (choana) empties into the buccal cavity." -#### Added -- [obsolete increased nucleus size](http://purl.obolibrary.org/obo/CL_0017505) [deprecated](http://www.w3.org/2002/07/owl#deprecated) true +- [posterior nasal aperture](http://purl.obolibrary.org/obo/UBERON_0004771) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "One of the paired openings from the nasal cavities into the pharynx. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-6, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000545" -- [obsolete increased nucleus size](http://purl.obolibrary.org/obo/CL_0017505) [term replaced by](http://purl.obolibrary.org/obo/IAO_0100001) [high nuclear/cytoplasmic ratio](http://purl.obolibrary.org/obo/PATO_0040072) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [obsolete increased nucleus size](http://purl.obolibrary.org/obo/CL_0017505) [label](http://www.w3.org/2000/01/rdf-schema#label) "obsolete increased nucleus size" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [obsolete increased nucleus size](http://purl.obolibrary.org/obo/CL_0017505) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "OBSOLETE. A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [obsolete increased nucleus size](http://purl.obolibrary.org/obo/CL_0017505) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [2251](https://github.com/obophenotype/cell-ontology/issues/2251) +- [posterior nasal aperture](http://purl.obolibrary.org/obo/UBERON_0004771) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Opening between the nasal cavity and the nasopharynx.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" -- [obsolete increased nucleus size](http://purl.obolibrary.org/obo/CL_0017505) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "This class was a phenotype, not a cell type." + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000093" -### obsolete inhibitory neuron `http://purl.obolibrary.org/obo/CL_0008029` -#### Removed -- [obsolete inhibitory neuron](http://purl.obolibrary.org/obo/CL_0008029) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "See https://github.com/obophenotype/cell-ontology/issues/1540. Consider GABAergic neuron or inhibitory interneuron instead. Do note that not all GABAergic neurons are inhibitory (see PMID:12209121) and replacing inhibitory neuron with GABAergic neuron should be done with caution." + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -#### Added -- [obsolete inhibitory neuron](http://purl.obolibrary.org/obo/CL_0008029) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Consider GABAergic neuron or inhibitory interneuron instead. Do note that not all GABAergic neurons are inhibitory (see PMID:12209121) and replacing inhibitory neuron with GABAergic neuron should be done with caution." +- [posterior nasal aperture](http://purl.obolibrary.org/obo/UBERON_0004771) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The choana, a unique 'internal nostril' opening from the nasal sac into the roof of the mouth, is a key part of the tetrapod (land vertebrate) respiratory system. It was the first component of the tetrapod body plan to evolve, well before the origin of limbs, and is therefore crucial to our understanding of the beginning of the fish-tetrapod transition. (...) Here we present new material of Kenichthys, a 395-million-year-old fossil fish from China, that provides direct evidence for the origin of the choana and establishes its homology: it is indeed a displaced posterior external nostril that, during a brief transitional stage illustrated by Kenichthys, separated the maxilla from the premaxilla.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000545" -- [obsolete inhibitory neuron](http://purl.obolibrary.org/obo/CL_0008029) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [1540](https://github.com/obophenotype/cell-ontology/issues/1540) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### obsolete lobed nucleus `http://purl.obolibrary.org/obo/CL_0017501` -#### Removed -- [obsolete lobed nucleus](http://purl.obolibrary.org/obo/CL_0017501) [see also](http://www.w3.org/2000/01/rdf-schema#seeAlso) "https://github.com/obophenotype/cell-ontology/issues/734" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [obsolete lobed nucleus](http://purl.obolibrary.org/obo/CL_0017501) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [734](https://github.com/obophenotype/cell-ontology/issues/734) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1038/nature02843 Zhu M, Ahlberg PE, The origin of the internal nostril in tetrapodes. Nature (2004)" -### obsolete macrophage (sensu Diptera) `http://purl.obolibrary.org/obo/CL_0000401` + +### posterior neural tube `http://purl.obolibrary.org/obo/UBERON_0003076` #### Removed -- [obsolete macrophage (sensu Diptera)](http://purl.obolibrary.org/obo/CL_0000401) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/obophenotype/cell-ontology/issues/1949" +- [posterior neural tube](http://purl.obolibrary.org/obo/UBERON_0003076) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [obsolete macrophage (sensu Diptera)](http://purl.obolibrary.org/obo/CL_0000401) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [1949](https://github.com/obophenotype/cell-ontology/issues/1949) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### obsolete male germ line stem cell (sensu Nematoda and Protostomia) `http://purl.obolibrary.org/obo/CL_0000087` -#### Removed -- [obsolete male germ line stem cell (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000087) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/obophenotype/cell-ontology/issues/1935" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28" -#### Added -- [obsolete male germ line stem cell (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000087) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [1935](https://github.com/obophenotype/cell-ontology/issues/1935) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001383" -### obsolete male germ line stem cell (sensu Vertebrata) `http://purl.obolibrary.org/obo/CL_0000089` -#### Removed -- [obsolete male germ line stem cell (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000089) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/obophenotype/cell-ontology/issues/1935" + +### posterior segment of eyeball `http://purl.obolibrary.org/obo/UBERON_0001802` #### Added -- [obsolete male germ line stem cell (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000089) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [1935](https://github.com/obophenotype/cell-ontology/issues/1935) +- [posterior segment of eyeball](http://purl.obolibrary.org/obo/UBERON_0001802) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### obsolete metabolising cell `http://purl.obolibrary.org/obo/CL_0000181` -#### Removed -- [obsolete metabolising cell](http://purl.obolibrary.org/obo/CL_0000181) [see also](http://www.w3.org/2000/01/rdf-schema#seeAlso) "https://github.com/obophenotype/cell-ontology/issues/720" +### posterior stroma of cornea `http://purl.obolibrary.org/obo/UBERON_0003953` #### Added -- [obsolete metabolising cell](http://purl.obolibrary.org/obo/CL_0000181) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [720](https://github.com/obophenotype/cell-ontology/issues/720) +- [posterior stroma of cornea](http://purl.obolibrary.org/obo/UBERON_0003953) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) -### obsolete native cell `http://purl.obolibrary.org/obo/CL_0000003` +### posterior to `http://purl.obolibrary.org/obo/BSPO_0000099` #### Removed -- [obsolete native cell](http://purl.obolibrary.org/obo/CL_0000003) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "https://github.com/obophenotype/cell-ontology/issues/2124" +- [posterior to](http://purl.obolibrary.org/obo/BSPO_0000099) [label](http://www.w3.org/2000/01/rdf-schema#label) "posterior to" -#### Added -- [obsolete native cell](http://purl.obolibrary.org/obo/CL_0000003) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [2124](https://github.com/obophenotype/cell-ontology/issues/2124) +- [posterior to](http://purl.obolibrary.org/obo/BSPO_0000099) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BSPO:0000099" -- [obsolete native cell](http://purl.obolibrary.org/obo/CL_0000003) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [posterior to](http://purl.obolibrary.org/obo/BSPO_0000099) [id](http://www.geneontology.org/formats/oboInOwl#id) "posterior_to" +- [posterior to](http://purl.obolibrary.org/obo/BSPO_0000099) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "posterior_to" -### obsolete neuroepidermoblast `http://purl.obolibrary.org/obo/CL_0000405` -#### Removed -- [obsolete neuroepidermoblast](http://purl.obolibrary.org/obo/CL_0000405) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/FlyBase/drosophila-anatomy-developmental-ontology/issues/1621" +- [posterior to](http://purl.obolibrary.org/obo/BSPO_0000099) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" -#### Added -- [obsolete neuroepidermoblast](http://purl.obolibrary.org/obo/CL_0000405) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [1621](https://github.com/FlyBase/drosophila-anatomy-developmental-ontology/issues/1621) -### obsolete neurosecretory neuron `http://purl.obolibrary.org/obo/CL_0000381` +### posterior vena cava `http://purl.obolibrary.org/obo/UBERON_0001072` #### Removed -- [obsolete neurosecretory neuron](http://purl.obolibrary.org/obo/CL_0000381) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "https://github.com/obophenotype/cell-ontology/issues/1784 -'neuroendocrine cell' (which has exact synonym "neurosecretory cell") and 'neurosecretory neuron' may all refer to the same cell type." +- [posterior vena cava](http://purl.obolibrary.org/obo/UBERON_0001072) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Phylogenetic modifications within this basic pattern of arteries and veins are largely correlated with functional changes. In the transition from water to land, gills gave way to lungs, accompanied by the establishment of a pulmonary circulation. In some fishes and certainly in tetrapods, the cardinal veins become less involved in blood return. Instead, the composite, prominent postcava (posterior vena cava) arose to drain the posterior part of the body and the precava (anterior vena cava) developed to drain the anterior part of the body.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001194" -#### Added -- [obsolete neurosecretory neuron](http://purl.obolibrary.org/obo/CL_0000381) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [1784](https://github.com/obophenotype/cell-ontology/issues/1784) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [obsolete neurosecretory neuron](http://purl.obolibrary.org/obo/CL_0000381) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "'neuroendocrine cell' (which has exact synonym "neurosecretory cell") and 'neurosecretory neuron' may all refer to the same cell type." + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### obsolete peripheral neuron `http://purl.obolibrary.org/obo/CL_0000111` -#### Removed -- [obsolete peripheral neuron](http://purl.obolibrary.org/obo/CL_0000111) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Merging into CL:2000032, see https://github.com/obophenotype/cell-ontology/issues/1069" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.454-455" -#### Added -- [obsolete peripheral neuron](http://purl.obolibrary.org/obo/CL_0000111) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Merging into CL:2000032." +- [posterior vena cava](http://purl.obolibrary.org/obo/UBERON_0001072) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Trunk of systemic vein which is formed by the union of the right common iliac vein and the left common iliac vein and terminates in the right atrium[FMA]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:10951" -- [obsolete peripheral neuron](http://purl.obolibrary.org/obo/CL_0000111) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [1069](https://github.com/obophenotype/cell-ontology/issues/1069) -### obsolete permanently open valve cell `http://purl.obolibrary.org/obo/CL_0000665` -#### Removed -- [obsolete permanently open valve cell](http://purl.obolibrary.org/obo/CL_0000665) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "https://github.com/obophenotype/cell-ontology/issues/726" +### posterior wall of nasopharynx `http://purl.obolibrary.org/obo/UBERON_0035401` #### Added -- [obsolete permanently open valve cell](http://purl.obolibrary.org/obo/CL_0000665) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [726](https://github.com/obophenotype/cell-ontology/issues/726) +- [posterior wall of nasopharynx](http://purl.obolibrary.org/obo/UBERON_0035401) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -### obsolete podocyte (sensu Diptera) `http://purl.obolibrary.org/obo/CL_0000391` +### pre-cartilage condensation `http://purl.obolibrary.org/obo/UBERON_0005866` #### Removed -- [obsolete podocyte (sensu Diptera)](http://purl.obolibrary.org/obo/CL_0000391) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/obophenotype/cell-ontology/issues/1949" +- [pre-cartilage condensation](http://purl.obolibrary.org/obo/UBERON_0005866) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A closely packed aggregation of mesenchymal cells just prior to their differentiation into embryonic cartilage." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://dictionary.reference.com/browse/precartilage" -#### Added -- [obsolete podocyte (sensu Diptera)](http://purl.obolibrary.org/obo/CL_0000391) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [1949](https://github.com/obophenotype/cell-ontology/issues/1949) -### obsolete polygonal cell `http://purl.obolibrary.org/obo/CL_0000398` +### pre-chordal neural plate `http://purl.obolibrary.org/obo/UBERON_0003056` #### Removed -- [obsolete polygonal cell](http://purl.obolibrary.org/obo/CL_0000398) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/obophenotype/cell-ontology/issues/1949" +- [pre-chordal neural plate](http://purl.obolibrary.org/obo/UBERON_0003056) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [obsolete polygonal cell](http://purl.obolibrary.org/obo/CL_0000398) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [1949](https://github.com/obophenotype/cell-ontology/issues/1949) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### obsolete primary pigment cell `http://purl.obolibrary.org/obo/CL_0000727` -#### Removed -- [obsolete primary pigment cell](http://purl.obolibrary.org/obo/CL_0000727) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/obophenotype/cell-ontology/issues/1930" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001200" #### Added -- [obsolete primary pigment cell](http://purl.obolibrary.org/obo/CL_0000727) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [1930](https://github.com/obophenotype/cell-ontology/issues/1930) +- [pre-chordal neural plate](http://purl.obolibrary.org/obo/UBERON_0003056) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### obsolete scaffold cell `http://purl.obolibrary.org/obo/CL_0000426` +### pre-dentine `http://purl.obolibrary.org/obo/UBERON_0011587` #### Removed -- [obsolete scaffold cell](http://purl.obolibrary.org/obo/CL_0000426) [see also](http://www.w3.org/2000/01/rdf-schema#seeAlso) "https://github.com/obophenotype/cell-ontology/issues/708" +- [pre-dentine](http://purl.obolibrary.org/obo/UBERON_0011587) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) -#### Added -- [obsolete scaffold cell](http://purl.obolibrary.org/obo/CL_0000426) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [708](https://github.com/obophenotype/cell-ontology/issues/708) -### obsolete secondary pigment cell `http://purl.obolibrary.org/obo/CL_0000728` +### preaxialmost part of `http://purl.obolibrary.org/obo/BSPO_0001113` #### Removed -- [obsolete secondary pigment cell](http://purl.obolibrary.org/obo/CL_0000728) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/obophenotype/cell-ontology/issues/1930" +- [preaxialmost part of](http://purl.obolibrary.org/obo/BSPO_0001113) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "preaxialmost_part_of" -#### Added -- [obsolete secondary pigment cell](http://purl.obolibrary.org/obo/CL_0000728) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [1930](https://github.com/obophenotype/cell-ontology/issues/1930) +- [preaxialmost part of](http://purl.obolibrary.org/obo/BSPO_0001113) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BSPO:0001113" +- [preaxialmost part of](http://purl.obolibrary.org/obo/BSPO_0001113) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" -### obsolete seminal fluid secreting cell `http://purl.obolibrary.org/obo/CL_0000321` -#### Removed -- [obsolete seminal fluid secreting cell](http://purl.obolibrary.org/obo/CL_0000321) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "https://github.com/obophenotype/cell-ontology/issues/1149" +- [preaxialmost part of](http://purl.obolibrary.org/obo/BSPO_0001113) [id](http://www.geneontology.org/formats/oboInOwl#id) "preaxialmost_part_of" -#### Added -- [obsolete seminal fluid secreting cell](http://purl.obolibrary.org/obo/CL_0000321) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [1149](https://github.com/obophenotype/cell-ontology/issues/1149) +- [preaxialmost part of](http://purl.obolibrary.org/obo/BSPO_0001113) [label](http://www.w3.org/2000/01/rdf-schema#label) "preaxialmost part of" -### obsolete somatic cell `http://purl.obolibrary.org/obo/CL_0002371` + +### preceded by `http://purl.obolibrary.org/obo/BFO_0000062` #### Removed -- [obsolete somatic cell](http://purl.obolibrary.org/obo/CL_0002371) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "https://github.com/obophenotype/cell-ontology/issues/1150" +- [preceded by](http://purl.obolibrary.org/obo/BFO_0000062) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "preceded_by"@en -#### Added -- [obsolete somatic cell](http://purl.obolibrary.org/obo/CL_0002371) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [1150](https://github.com/obophenotype/cell-ontology/issues/1150) +- [preceded by](http://purl.obolibrary.org/obo/BFO_0000062) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "is preceded by"@en -- [obsolete somatic cell](http://purl.obolibrary.org/obo/CL_0002371) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [preceded by](http://purl.obolibrary.org/obo/BFO_0000062) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "preceded by"@en +- [preceded by](http://purl.obolibrary.org/obo/BFO_0000062) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" -### obsolete tertiary pigment cell `http://purl.obolibrary.org/obo/CL_0000729` -#### Removed -- [obsolete tertiary pigment cell](http://purl.obolibrary.org/obo/CL_0000729) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/obophenotype/cell-ontology/issues/1930" +- [preceded by](http://purl.obolibrary.org/obo/BFO_0000062) [source](http://purl.org/dc/terms/source) "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" -#### Added -- [obsolete tertiary pigment cell](http://purl.obolibrary.org/obo/CL_0000729) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [1930](https://github.com/obophenotype/cell-ontology/issues/1930) -### obsolete valve cell `http://purl.obolibrary.org/obo/CL_0000663` +### precedes `http://purl.obolibrary.org/obo/BFO_0000063` #### Removed -- [obsolete valve cell](http://purl.obolibrary.org/obo/CL_0000663) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "https://github.com/obophenotype/cell-ontology/issues/726" +- [precedes](http://purl.obolibrary.org/obo/BFO_0000063) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [precedes](http://purl.obolibrary.org/obo/BFO_0000063) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "precedes"@en -#### Added -- [obsolete valve cell](http://purl.obolibrary.org/obo/CL_0000663) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [726](https://github.com/obophenotype/cell-ontology/issues/726) -### occipital artery `http://purl.obolibrary.org/obo/UBERON_0001613` +### prechordal plate `http://purl.obolibrary.org/obo/UBERON_0003063` #### Removed -- [occipital artery](http://purl.obolibrary.org/obo/UBERON_0001613) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria occipitalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Occipital_artery" +- [prechordal plate](http://purl.obolibrary.org/obo/UBERON_0003063) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Axial mesoderm that lies anterior to the notochord and that underlies the forebrain. [Amphioxus_goosecoid_and_the_evolution_of_the_head_organizer_and_prechordal_plate._Evolution_and_Development_(2008)_2(6):303-310, Neidert_AH, Panopoulou_G_and_Langeland_JA][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [occipital artery](http://purl.obolibrary.org/obo/UBERON_0001613) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria occipitalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Occipital_artery" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000086" +- [prechordal plate](http://purl.obolibrary.org/obo/UBERON_0003063) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "There are two opposing models that can potentially explain the differences in gsc (goosecoid) expression between amphioxus and vertebrates. In one model, the vertebrate gsc expression pattern more closely resembles the common ancestral state and the amphioxus gsc expression pattern is a derivation associated with its unique morphology. (...) In an alternate model, the amphioxus gsc expression pattern most closely represents the common ancestral state and the vertebrate pattern is derived. This model suggests that the evolution of vertebrates was accompanied by the segregation of gsc expression, from a more general domain underlying the entire brain anlage to a distinct forebrain organizer domain and subsequent prechordal plate. We feel this second model is more parsimonious than the first model in that what would be novel anterior gsc expression in vertebrates directly correlates with a novel vertebrate anterior structure, the prechordal plate.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### occipital bone `http://purl.obolibrary.org/obo/UBERON_0001676` -#### Removed -- [occipital bone](http://purl.obolibrary.org/obo/UBERON_0001676) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "os occipitale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Occipital_bone" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1046/j.1525-142x.2000.00073.x Neidert AH, Panopoulou G and Langeland JA, Amphioxus goosecoid and the evolution of the head organizer and prechordal plate. Evolution and Development (2008)" -#### Added -- [occipital bone](http://purl.obolibrary.org/obo/UBERON_0001676) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "os occipitale" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Occipital_bone" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000086" +- [prechordal plate](http://purl.obolibrary.org/obo/UBERON_0003063) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Axial hypoblast located anterior to the chorda mesoderm; the polster is its most anterior region. Kimmel et al, 1995.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -### occipital region `http://purl.obolibrary.org/obo/UBERON_0005902` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -#### Added -- [occipital region](http://purl.obolibrary.org/obo/UBERON_0005902) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D009778" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000060" +- [prechordal plate](http://purl.obolibrary.org/obo/UBERON_0003063) SubClassOf [transformation of](http://purl.obolibrary.org/obo/RO_0002494) some [prechordal mesoderm](http://purl.obolibrary.org/obo/UBERON_0034878) + - [todo](http://www.geneontology.org/formats/oboInOwl#todo) "PMID:16313393" -### ocular adnexa `http://purl.obolibrary.org/obo/UBERON_0035639` -#### Removed -- [ocular adnexa](http://purl.obolibrary.org/obo/UBERON_0035639) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "adnexa oculi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://medical-dictionary.thefreedictionary.com/ocular+adnexa" +#### Added +- [prechordal plate](http://purl.obolibrary.org/obo/UBERON_0003063) SubClassOf [transformation of](http://purl.obolibrary.org/obo/RO_0002494) some [prechordal mesoderm](http://purl.obolibrary.org/obo/UBERON_0034878) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [ocular adnexa](http://purl.obolibrary.org/obo/UBERON_0035639) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "structurae oculi accessoriae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Accessory_visual_structures" +### preoptic area `http://purl.obolibrary.org/obo/UBERON_0001928` +#### Removed +- [preoptic area](http://purl.obolibrary.org/obo/UBERON_0001928) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Area of the forebrain anterior to the posterior tuberculum and the hypothalamus and ventral to the ventral thalamus. See Figure 7, Atlas of Early Zebrafish Brain Development.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000470" -#### Added -- [ocular adnexa](http://purl.obolibrary.org/obo/UBERON_0035639) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "structurae oculi accessoriae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Accessory_visual_structures" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -- [ocular adnexa](http://purl.obolibrary.org/obo/UBERON_0035639) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "adnexa oculi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://medical-dictionary.thefreedictionary.com/ocular+adnexa" +- [preoptic area](http://purl.obolibrary.org/obo/UBERON_0001928) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Located in the hypothalamus in amniotes[PMC4038951]" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### odontogenic papilla `http://purl.obolibrary.org/obo/UBERON_0001763` +### preoptic nucleus `http://purl.obolibrary.org/obo/UBERON_0007251` #### Removed -- [odontogenic papilla](http://purl.obolibrary.org/obo/UBERON_0001763) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "papilla dentis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Dental_papilla" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [preoptic nucleus](http://purl.obolibrary.org/obo/UBERON_0007251) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D011301" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) -#### Added -- [odontogenic papilla](http://purl.obolibrary.org/obo/UBERON_0001763) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "papilla dentis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Dental_papilla" + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### olfactory bulb `http://purl.obolibrary.org/obo/UBERON_0002264` +### preplacodal ectoderm `http://purl.obolibrary.org/obo/UBERON_2007013` #### Removed -- [olfactory bulb](http://purl.obolibrary.org/obo/UBERON_0002264) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "bulbus olfactorius (Morgagni)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:279" +- [preplacodal ectoderm](http://purl.obolibrary.org/obo/UBERON_2007013) [UBPROP_0000004](http://purl.obolibrary.org/obo/UBPROP_0000004) "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://purl.obolibrary.org/obo/tao.owl" + - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [olfactory bulb](http://purl.obolibrary.org/obo/UBERON_0002264) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "bulbus olfactorius" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Olfactory_bulb" +### prepuce `http://purl.obolibrary.org/obo/UBERON_0011374` +#### Removed +- [prepuce](http://purl.obolibrary.org/obo/UBERON_0011374) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "preputial" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [prepuce](http://purl.obolibrary.org/obo/UBERON_0011374) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "this is a generic sex-neutral grouping class for the male and female prepuce. Note that this structure is a combination of skin and other tissue" #### Added -- [olfactory bulb](http://purl.obolibrary.org/obo/UBERON_0002264) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "bulbus olfactorius (Morgagni)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [prepuce](http://purl.obolibrary.org/obo/UBERON_0011374) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:279" -- [olfactory bulb](http://purl.obolibrary.org/obo/UBERON_0002264) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "bulbus olfactorius" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Olfactory_bulb" +### prepuce of clitoris `http://purl.obolibrary.org/obo/UBERON_0005299` +#### Removed +- [prepuce of clitoris](http://purl.obolibrary.org/obo/UBERON_0005299) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "FMA has FMA:27886 skin of prepuce of clitoris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### olfactory bulb layer `http://purl.obolibrary.org/obo/UBERON_0004001` +### prepuce of penis `http://purl.obolibrary.org/obo/UBERON_0001332` #### Removed -- [olfactory bulb layer](http://purl.obolibrary.org/obo/UBERON_0004001) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MP:0009946" +- [prepuce of penis](http://purl.obolibrary.org/obo/UBERON_0001332) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EV:0100109" -#### Added -- [olfactory bulb layer](http://purl.obolibrary.org/obo/UBERON_0004001) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Missing definition for term UBERON:0004001. Please replace it using linked reference." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MP:0009946" -### olfactory nerve `http://purl.obolibrary.org/obo/UBERON_0001579` +### present_in_taxon `http://purl.obolibrary.org/obo/RO_0002175` #### Removed -- [olfactory nerve](http://purl.obolibrary.org/obo/UBERON_0001579) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nervus olfactorius" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0003648" +- [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Olfactory_nerve" +- [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "present_in_taxon" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://orcid.org/0000-0002-6601-2165" -- [olfactory nerve](http://purl.obolibrary.org/obo/UBERON_0001579) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus olfactorius [i]" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:46787" +- [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [is_metadata_tag](http://www.geneontology.org/formats/oboInOwl#is_metadata_tag) true - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [id](http://www.geneontology.org/formats/oboInOwl#id) "present_in_taxon" -#### Added -- [olfactory nerve](http://purl.obolibrary.org/obo/UBERON_0001579) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nervus olfactorius" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "applicable for taxon" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0003648" +- [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [label](http://www.w3.org/2000/01/rdf-schema#label) "present_in_taxon" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Olfactory_nerve" +- [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002175" -- [olfactory nerve](http://purl.obolibrary.org/obo/UBERON_0001579) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus olfactorius [i]" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [is_class_level](http://www.geneontology.org/formats/oboInOwl#is_class_level) true - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:46787" +- [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) [22293552](http://www.ncbi.nlm.nih.gov/pubmed/22293552) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### olfactory organ `http://purl.obolibrary.org/obo/UBERON_0002268` +### presomitic mesoderm `http://purl.obolibrary.org/obo/UBERON_0003059` #### Removed -- [olfactory organ](http://purl.obolibrary.org/obo/UBERON_0002268) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005158" - -#### Added -- [olfactory organ](http://purl.obolibrary.org/obo/UBERON_0002268) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005158" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [presomitic mesoderm](http://purl.obolibrary.org/obo/UBERON_0003059) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### olfactory placode `http://purl.obolibrary.org/obo/UBERON_0003050` -#### Removed -- [olfactory placode](http://purl.obolibrary.org/obo/UBERON_0003050) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "placoda nasalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [olfactory placode](http://purl.obolibrary.org/obo/UBERON_0003050) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "placoda olfactoria" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1006/dbio.2001.0460 Schubert M, Holland LZ, Dale Stokes M and Holland ND, Three Amphoxius Wnt Genes (AmphiWnt3, AmphiWnt5, and AmphiWnt6) Associated with the Tail Bud: the Evolution of Somitogenesis in Chordates. Developmental Biology (2001)" -- [olfactory placode](http://purl.obolibrary.org/obo/UBERON_0003050) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006222" - - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0003-4423-4370" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000559" -#### Added -- [olfactory placode](http://purl.obolibrary.org/obo/UBERON_0003050) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006222" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [presomitic mesoderm](http://purl.obolibrary.org/obo/UBERON_0003059) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -- [olfactory placode](http://purl.obolibrary.org/obo/UBERON_0003050) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "placoda olfactoria" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000279" -- [olfactory placode](http://purl.obolibrary.org/obo/UBERON_0003050) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "placoda nasalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### olfactory segment of nasal mucosa `http://purl.obolibrary.org/obo/UBERON_0005386` +### presumptive endocardium `http://purl.obolibrary.org/obo/UBERON_0007280` #### Removed -- [olfactory segment of nasal mucosa](http://purl.obolibrary.org/obo/UBERON_0005386) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pars olfactoria tunicae mucosae nasi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:77199" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [presumptive endocardium](http://purl.obolibrary.org/obo/UBERON_0007280) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Portion of tissue that is part of the heart tube and will become the endocardium.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" - -- [olfactory segment of nasal mucosa](http://purl.obolibrary.org/obo/UBERON_0005386) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pars olfactoria tunicae mucosae nasi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0002233" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Olfactory_mucosa" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -#### Added -- [olfactory segment of nasal mucosa](http://purl.obolibrary.org/obo/UBERON_0005386) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pars olfactoria tunicae mucosae nasi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Olfactory_mucosa" -- [olfactory segment of nasal mucosa](http://purl.obolibrary.org/obo/UBERON_0005386) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pars olfactoria tunicae mucosae nasi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:77199" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### presumptive gut `http://purl.obolibrary.org/obo/UBERON_0007026` +#### Removed +- [presumptive gut](http://purl.obolibrary.org/obo/UBERON_0007026) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "NCBIBook:NBK10107" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### olfactory tract `http://purl.obolibrary.org/obo/UBERON_0002265` +### presumptive hindbrain `http://purl.obolibrary.org/obo/UBERON_0007277` #### Removed -- [olfactory tract](http://purl.obolibrary.org/obo/UBERON_0002265) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tractus olfactorium" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:283" +- [presumptive hindbrain](http://purl.obolibrary.org/obo/UBERON_0007277) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The embryonic rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. Rhombomeres Rh7-Rh4 form the myelencephalon that will give the medulla oblongata. Rhombomeres Rh3-Rh1 form the metencephalon that will form the pons and the cerebellum[NPX:PDR]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "NPX:PDR" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [olfactory tract](http://purl.obolibrary.org/obo/UBERON_0002265) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tractus olfactorius" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Olfactory_tract" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0003647" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - -- [olfactory tract](http://purl.obolibrary.org/obo/UBERON_0002265) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pedunclulus olfactorius" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:283" +### presumptive neural plate `http://purl.obolibrary.org/obo/UBERON_0007284` +#### Removed +- [presumptive neural plate](http://purl.obolibrary.org/obo/UBERON_0007284) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Region of the gastrula which gives rise to the neural plate.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000063" -#### Added -- [olfactory tract](http://purl.obolibrary.org/obo/UBERON_0002265) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pedunclulus olfactorius" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:283" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -- [olfactory tract](http://purl.obolibrary.org/obo/UBERON_0002265) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tractus olfactorius" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Olfactory_tract" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0003647" +### presumptive neural retina `http://purl.obolibrary.org/obo/UBERON_0005425` +#### Removed +- [presumptive neural retina](http://purl.obolibrary.org/obo/UBERON_0005425) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429" -- [olfactory tract](http://purl.obolibrary.org/obo/UBERON_0002265) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tractus olfactorium" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:283" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### olfactory tubercle `http://purl.obolibrary.org/obo/UBERON_0001883` -#### Removed -- [olfactory tubercle](http://purl.obolibrary.org/obo/UBERON_0001883) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tuberculum olfactorium" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000490" #### Added -- [olfactory tubercle](http://purl.obolibrary.org/obo/UBERON_0001883) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tuberculum olfactorium" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [presumptive neural retina](http://purl.obolibrary.org/obo/UBERON_0005425) SubClassOf [immature eye](http://purl.obolibrary.org/obo/UBERON_0010312) + +### presumptive retinal pigmented epithelium `http://purl.obolibrary.org/obo/UBERON_0005424` +#### Removed +- [presumptive retinal pigmented epithelium](http://purl.obolibrary.org/obo/UBERON_0005424) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429" -### oligodendrocyte `http://purl.obolibrary.org/obo/CL_0000128` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [oligodendrocyte](http://purl.obolibrary.org/obo/CL_0000128) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### oligodendrocyte precursor cell `http://purl.obolibrary.org/obo/CL_0002453` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000492" #### Added -- [oligodendrocyte precursor cell](http://purl.obolibrary.org/obo/CL_0002453) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [presumptive retinal pigmented epithelium](http://purl.obolibrary.org/obo/UBERON_0005424) SubClassOf [immature eye](http://purl.obolibrary.org/obo/UBERON_0010312) -### ommatidium `http://purl.obolibrary.org/obo/UBERON_0000971` +### presumptive segmental plate `http://purl.obolibrary.org/obo/UBERON_0007282` #### Removed -- [ommatidium](http://purl.obolibrary.org/obo/UBERON_0000971) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004510" +- [presumptive segmental plate](http://purl.obolibrary.org/obo/UBERON_0007282) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [trunk paraxial mesoderm](http://purl.obolibrary.org/obo/UBERON_0009618) + - [consistent_with](http://www.geneontology.org/formats/oboInOwl#consistent_with) "https://github.com/obophenotype/uberon/wiki/The-neural-crest" -#### Added -- [ommatidium](http://purl.obolibrary.org/obo/UBERON_0000971) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004510" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "EDHAA2" +#### Added +- [presumptive segmental plate](http://purl.obolibrary.org/obo/UBERON_0007282) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [trunk paraxial mesoderm](http://purl.obolibrary.org/obo/UBERON_0009618) -### oocyte `http://purl.obolibrary.org/obo/CL_0000023` -#### Added -- [oocyte](http://purl.obolibrary.org/obo/CL_0000023) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### primary circulatory organ `http://purl.obolibrary.org/obo/UBERON_0007100` +#### Removed +- [primary circulatory organ](http://purl.obolibrary.org/obo/UBERON_0007100) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis" +- [primary circulatory organ](http://purl.obolibrary.org/obo/UBERON_0007100) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "SPD:0000130" -### oogonial cell `http://purl.obolibrary.org/obo/CL_0000024` +- [primary circulatory organ](http://purl.obolibrary.org/obo/UBERON_0007100) SubClassOf [capable of](http://purl.obolibrary.org/obo/RO_0002215) some [blood circulation](http://purl.obolibrary.org/obo/GO_0008015) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "GO uses blood circulation generically to include the haemolymphatic fluid of arthropods" #### Added -- [oogonial cell](http://purl.obolibrary.org/obo/CL_0000024) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [primary circulatory organ](http://purl.obolibrary.org/obo/UBERON_0007100) SubClassOf [capable of](http://purl.obolibrary.org/obo/RO_0002215) some [blood circulation](http://purl.obolibrary.org/obo/GO_0008015) -### open tracheal system `http://purl.obolibrary.org/obo/UBERON_0005155` +### primary heart field `http://purl.obolibrary.org/obo/UBERON_0004140` #### Removed -- [open tracheal system](http://purl.obolibrary.org/obo/UBERON_0005155) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005024" +- [primary heart field](http://purl.obolibrary.org/obo/UBERON_0004140) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138]" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "GO" #### Added -- [open tracheal system](http://purl.obolibrary.org/obo/UBERON_0005155) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005024" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [primary heart field](http://purl.obolibrary.org/obo/UBERON_0004140) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### ophthalmic artery `http://purl.obolibrary.org/obo/UBERON_0001619` +### primary motor cortex `http://purl.obolibrary.org/obo/UBERON_0001384` #### Removed -- [ophthalmic artery](http://purl.obolibrary.org/obo/UBERON_0001619) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria ophthalmica" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ophthalmic_artery" +- [primary motor cortex](http://purl.obolibrary.org/obo/UBERON_0001384) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The part of the cerebral cortex that receives projections from the motor thalamus and which projects to motor neurons in the brainstem and spinal cord. The motor cortex corresponds to Brodmann's area 4 (MM). The primary motor cortex, or M1, is located on the precentral gyrus and on the anterior paracentral lobule on the medial surface of the brain. Of the three motor cortex areas, stimulation of the primary motor cortex requires the least amount of electrical current to elicit a movement. http://neuroscience.uth.tmc.edu/s3/chapter03.html" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "NLX:143555" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [primary motor cortex](http://purl.obolibrary.org/obo/UBERON_0001384) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "the area of the frontal lobe that is involved with integration of voluntary movements and with speech.[MP]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "MGI:csmith" -#### Added -- [ophthalmic artery](http://purl.obolibrary.org/obo/UBERON_0001619) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria ophthalmica" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ophthalmic_artery" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-31" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "MP" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "MP:0000800" -### ophthalmic nerve `http://purl.obolibrary.org/obo/UBERON_0000348` + + +### primary motor cortex layer 5 `http://purl.obolibrary.org/obo/UBERON_0022315` #### Removed -- [ophthalmic nerve](http://purl.obolibrary.org/obo/UBERON_0000348) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus ophthalmicus [va]" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:52621" +- [primary motor cortex layer 5](http://purl.obolibrary.org/obo/UBERON_0022315) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "Note that in some lamination schemes, more particularly so in primates, this layer is referred to as layer IV thus resulting in some confusion when compared to the present scheme where the lamina dissecans is referred to layer IV[DOI:10.1155/2008/381243]" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [ophthalmic nerve](http://purl.obolibrary.org/obo/UBERON_0000348) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus ophthalmicus [v1]" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:52621" +### primary nodular lymphoid tissue `http://purl.obolibrary.org/obo/UBERON_0010422` +#### Removed +- [primary nodular lymphoid tissue](http://purl.obolibrary.org/obo/UBERON_0010422) [UBPROP_0000015](http://purl.obolibrary.org/obo/UBPROP_0000015) "The cortex of lymph nodes, the white pulp of spleen, and mucosa associated lymphoid tissue all have these primary follicles" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + +### primary ovarian follicle `http://purl.obolibrary.org/obo/UBERON_0000035` #### Added -- [ophthalmic nerve](http://purl.obolibrary.org/obo/UBERON_0000348) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus ophthalmicus [v1]" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [primary ovarian follicle](http://purl.obolibrary.org/obo/UBERON_0000035) SubClassOf [protein-containing material entity](http://purl.obolibrary.org/obo/PR_000050567) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:52621" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### primitive heart tube `http://purl.obolibrary.org/obo/UBERON_0005498` +#### Removed +- [primitive heart tube](http://purl.obolibrary.org/obo/UBERON_0005498) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006179" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -- [ophthalmic nerve](http://purl.obolibrary.org/obo/UBERON_0000348) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus ophthalmicus [va]" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:52621" + - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### optic chiasma `http://purl.obolibrary.org/obo/UBERON_0000959` +### primitive nephron `http://purl.obolibrary.org/obo/UBERON_0010532` #### Removed -- [optic chiasma](http://purl.obolibrary.org/obo/UBERON_0000959) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "chiasma opticum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Optic_chiasm" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [primitive nephron](http://purl.obolibrary.org/obo/UBERON_0010532) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "EHDAA2 treats this as already having a tubular structure, but in the ZFA representation this is a cluster of cells" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EHDAA2" -- [optic chiasma](http://purl.obolibrary.org/obo/UBERON_0000959) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "chiasma" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:459" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [optic chiasma](http://purl.obolibrary.org/obo/UBERON_0000959) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "chiasma nervorum opticorum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:459" +### primitive olfactory epithelium `http://purl.obolibrary.org/obo/UBERON_2001431` +#### Removed +- [primitive olfactory epithelium](http://purl.obolibrary.org/obo/UBERON_2001431) [UBPROP_0000004](http://purl.obolibrary.org/obo/UBPROP_0000004) "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://purl.obolibrary.org/obo/tao.owl" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [primitive olfactory epithelium](http://purl.obolibrary.org/obo/UBERON_2001431) SubClassOf [epithelium](http://purl.obolibrary.org/obo/UBERON_0000483) #### Added -- [optic chiasma](http://purl.obolibrary.org/obo/UBERON_0000959) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "chiasma nervorum opticorum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [primitive olfactory epithelium](http://purl.obolibrary.org/obo/UBERON_2001431) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:459" -- [optic chiasma](http://purl.obolibrary.org/obo/UBERON_0000959) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "chiasma" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### primitive sex cord of indifferent gonad `http://purl.obolibrary.org/obo/UBERON_0010141` +#### Removed +- [primitive sex cord of indifferent gonad](http://purl.obolibrary.org/obo/UBERON_0010141) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "note that this represents the indifferent structure." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:459" -- [optic chiasma](http://purl.obolibrary.org/obo/UBERON_0000959) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "chiasma opticum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Optic_chiasm" +### primitive streak `http://purl.obolibrary.org/obo/UBERON_0004341` +#### Removed +- [primitive streak](http://purl.obolibrary.org/obo/UBERON_0004341) [RO_0002174](http://purl.obolibrary.org/obo/RO_0002174) [Teleostei](http://purl.obolibrary.org/obo/NCBITaxon_32443) +- [primitive streak](http://purl.obolibrary.org/obo/UBERON_0004341) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D054240" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### optic choroid `http://purl.obolibrary.org/obo/UBERON_0001776` -#### Removed -- [optic choroid](http://purl.obolibrary.org/obo/UBERON_0001776) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "choroidea" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Choroid" + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -#### Added -- [optic choroid](http://purl.obolibrary.org/obo/UBERON_0001776) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "choroidea" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [primitive streak](http://purl.obolibrary.org/obo/UBERON_0004341) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "VHOG includes a very broad grouping here based on http://www.ncbi.nlm.nih.gov/pubmed/9609826" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Choroid" +- [primitive streak](http://purl.obolibrary.org/obo/UBERON_0004341) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) the blastopore equivalent of chordates (germ ring in fish, marginal zone/blastopore lip in frog and node/primitive streak in chick and mouse) (...) (reference 1); Indeed, the primitive streak has been considered the homologue of the blastopore since the 1870s (reference 2).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### optic foramen `http://purl.obolibrary.org/obo/UBERON_0005745` -#### Removed -- [optic foramen](http://purl.obolibrary.org/obo/UBERON_0005745) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "foramen opticum ossis sphenoidalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Optic_canal" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001202" -- [optic foramen](http://purl.obolibrary.org/obo/UBERON_0005745) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "canalis opticus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Optic_canal" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:9609826 Wu LH, Lengyel JA, Role of caudal in hindgut specification and gastrulation suggests homology between Drosophila amnioproctodeal invagination and vertebrate blastopore. Development (1998), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.139" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [optic foramen](http://purl.obolibrary.org/obo/UBERON_0005745) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "foramen opticum ossis sphenoidalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Optic_canal" +### primitive urogenital sinus `http://purl.obolibrary.org/obo/UBERON_0000164` +#### Removed +- [primitive urogenital sinus](http://purl.obolibrary.org/obo/UBERON_0000164) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In mammals the lowly monotremes still have a cloaca. Higher types have done away with this structure and have a separate anal outlet for the rectum. The monotreme cloaca shows the initiation of this subdivision. The cloaca has such includes only the distal part, roughly comparable to the proctodeum. The more proximal part is divided into (1) a large dorsal passage into which the intestine opens, the coprodeum, and (2) a ventral portion, the urodeum with which the bladder connects. (...) the development of the placental mammals recapitulates in many respects the phylogenetic story. In the sexually indifferent stage of placental mammal there is a cloaca. While the indifferent stage still persists, a septum develops, and extends out to the closing membrane. This divides the cloaca into two chambers: a coprodeum continuous with the gut above, and a urodeum or urogenital sinus below.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [optic foramen](http://purl.obolibrary.org/obo/UBERON_0005745) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "canalis opticus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Optic_canal" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000414" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### optic stalk `http://purl.obolibrary.org/obo/UBERON_0003098` -#### Removed -- [optic stalk](http://purl.obolibrary.org/obo/UBERON_0003098) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pedunculus opticus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Optic_stalk" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0721676678 Romer AS, Vertebrate body (1970)p.388-89 and Figure 300" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [primitive urogenital sinus](http://purl.obolibrary.org/obo/UBERON_0000164) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "the term 'urogenital sinus' may refer to the primitive urogenital sinus present as a transient developmental structure in most mammals or it may refer to a condition in which an unseptated cloaca persists in animals longer than normal" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "MP" -#### Added -- [optic stalk](http://purl.obolibrary.org/obo/UBERON_0003098) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pedunculus opticus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [primitive urogenital sinus](http://purl.obolibrary.org/obo/UBERON_0000164) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The ventral part of the cloaca after its separation from the rectum, giving rise to the lower part of the bladder in both sexes, to the prostatic portion of the male urethra, and to the urethra and vestibule in the female. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/urogenital+sinus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Optic_stalk" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### optic tract `http://purl.obolibrary.org/obo/UBERON_0001908` -#### Removed -- [optic tract](http://purl.obolibrary.org/obo/UBERON_0001908) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tractus opticus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Optic_tract" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000414" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [optic tract](http://purl.obolibrary.org/obo/UBERON_0001908) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tractus optici" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:460" -#### Added -- [optic tract](http://purl.obolibrary.org/obo/UBERON_0001908) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tractus optici" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### primordium `http://purl.obolibrary.org/obo/UBERON_0001048` +#### Removed +- [primordium](http://purl.obolibrary.org/obo/UBERON_0001048) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005495" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:460" -- [optic tract](http://purl.obolibrary.org/obo/UBERON_0001908) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tractus opticus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Optic_tract" +### principal gastric gland `http://purl.obolibrary.org/obo/UBERON_0009971` +#### Removed +- [principal gastric gland](http://purl.obolibrary.org/obo/UBERON_0009971) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA has this as part of both the fundus and the body, but these are largely spatially disjoint." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" -### oral cavity `http://purl.obolibrary.org/obo/UBERON_0000167` -#### Added -- [oral cavity](http://purl.obolibrary.org/obo/UBERON_0000167) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D009055" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) +### process has causal agent `http://purl.obolibrary.org/obo/RO_0002608` +#### Removed +- [process has causal agent](http://purl.obolibrary.org/obo/RO_0002608) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) [causal-relations](http://purl.obolibrary.org/obo/ro/docs/causal-relations) - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -### orbitosphenoid `http://purl.obolibrary.org/obo/UBERON_0002478` +### process of vertebra `http://purl.obolibrary.org/obo/UBERON_0006061` #### Removed -- [orbitosphenoid](http://purl.obolibrary.org/obo/UBERON_0002478) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ala minor ossis sphenoidalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:52869" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [process of vertebra](http://purl.obolibrary.org/obo/UBERON_0006061) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NCIT:C116112" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [orbitosphenoid](http://purl.obolibrary.org/obo/UBERON_0002478) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "alae parvae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lesser_wing_of_sphenoid_bone" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### proctodeum `http://purl.obolibrary.org/obo/UBERON_0000931` +#### Removed +- [proctodeum](http://purl.obolibrary.org/obo/UBERON_0000931) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "proctodeal" -#### Added -- [orbitosphenoid](http://purl.obolibrary.org/obo/UBERON_0002478) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ala minor ossis sphenoidalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [proctodeum](http://purl.obolibrary.org/obo/UBERON_0000931) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000123" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:52869" +- [proctodeum](http://purl.obolibrary.org/obo/UBERON_0000931) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "An inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -- [orbitosphenoid](http://purl.obolibrary.org/obo/UBERON_0002478) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "alae parvae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Lesser_wing_of_sphenoid_bone" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000066" +- [proctodeum](http://purl.obolibrary.org/obo/UBERON_0000931) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFA:0000066" -### organ system subdivision `http://purl.obolibrary.org/obo/UBERON_0011216` -#### Removed -- [organ system subdivision](http://purl.obolibrary.org/obo/UBERON_0011216) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007330" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -#### Added -- [organ system subdivision](http://purl.obolibrary.org/obo/UBERON_0011216) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007330" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -- [organ system subdivision](http://purl.obolibrary.org/obo/UBERON_0011216) [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [Homo sapiens](http://purl.obolibrary.org/obo/NCBITaxon_9606) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0011087" -- [organ system subdivision](http://purl.obolibrary.org/obo/UBERON_0011216) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas) -### organelle `http://purl.obolibrary.org/obo/GO_0043226` +### produced by `http://purl.obolibrary.org/obo/RO_0003001` #### Removed -- [organelle](http://purl.obolibrary.org/obo/GO_0043226) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) +- [produced by](http://purl.obolibrary.org/obo/RO_0003001) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) + +- [produced by](http://purl.obolibrary.org/obo/RO_0003001) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0001-9114-8737](https://orcid.org/0000-0001-9114-8737) + +- [produced by](http://purl.obolibrary.org/obo/RO_0003001) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + -#### Added -- [organelle](http://purl.obolibrary.org/obo/GO_0043226) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) +### produces `http://purl.obolibrary.org/obo/RO_0003000` +#### Removed +- [produces](http://purl.obolibrary.org/obo/RO_0003000) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0001-9114-8737](https://orcid.org/0000-0001-9114-8737) -### organic substance metabolic process `http://purl.obolibrary.org/obo/GO_0071704` +- [produces](http://purl.obolibrary.org/obo/RO_0003000) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" -#### Added -- [organic substance metabolic process](http://purl.obolibrary.org/obo/GO_0071704) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [gocheck_do_not_annotate](http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate) +- [produces](http://purl.obolibrary.org/obo/RO_0003000) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) -- [organic substance metabolic process](http://purl.obolibrary.org/obo/GO_0071704) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/geneontology/go-ontology/issues/26424"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) -### organism subdivision `http://purl.obolibrary.org/obo/UBERON_0000475` +### proenkephalin-B `http://purl.obolibrary.org/obo/PR_000012526` #### Removed -- [organism subdivision](http://purl.obolibrary.org/obo/UBERON_0000475) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007009" +- [proenkephalin-B](http://purl.obolibrary.org/obo/PR_000012526) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [proenkephalin-B (human)](http://purl.obolibrary.org/obo/PR_P01213) -#### Added -- [organism subdivision](http://purl.obolibrary.org/obo/UBERON_0000475) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007009" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### organism substance `http://purl.obolibrary.org/obo/UBERON_0000463` +### proepicardium `http://purl.obolibrary.org/obo/UBERON_0004160` #### Removed -- [organism substance](http://purl.obolibrary.org/obo/UBERON_0000463) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007019" - -#### Added -- [organism substance](http://purl.obolibrary.org/obo/UBERON_0000463) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007019" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [proepicardium](http://purl.obolibrary.org/obo/UBERON_0004160) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Proepicardial clusters in Zebrafish form on the pericardial wall, adjacent to the atrioventricular (AV) junction and near the venous pole[ZFA]" +- [proepicardium](http://purl.obolibrary.org/obo/UBERON_0004160) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "propepicardial" -### organonitrogen compound metabolic process `http://purl.obolibrary.org/obo/GO_1901564` +- [proepicardium](http://purl.obolibrary.org/obo/UBERON_0004160) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [septum transversum](http://purl.obolibrary.org/obo/UBERON_0004161) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "todo check other taxa" #### Added -- [organonitrogen compound metabolic process](http://purl.obolibrary.org/obo/GO_1901564) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/geneontology/go-ontology/issues/26424"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) +- [proepicardium](http://purl.obolibrary.org/obo/UBERON_0004160) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [septum transversum](http://purl.obolibrary.org/obo/UBERON_0004161) -- [organonitrogen compound metabolic process](http://purl.obolibrary.org/obo/GO_1901564) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [gocheck_do_not_annotate](http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate) - -### ossification center `http://purl.obolibrary.org/obo/UBERON_0010355` +### programmed cell death protein 1 `http://purl.obolibrary.org/obo/PR_000001919` #### Removed -- [ossification center](http://purl.obolibrary.org/obo/UBERON_0010355) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "centrum ossificationis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [programmed cell death protein 1](http://purl.obolibrary.org/obo/PR_000001919) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [programmed cell death protein 1 (human)](http://purl.obolibrary.org/obo/PR_Q15116) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [ossification center](http://purl.obolibrary.org/obo/UBERON_0010355) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "centrum ossificationis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ossification_center" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### prolactin `http://purl.obolibrary.org/obo/PR_000013246` +#### Removed +- [prolactin](http://purl.obolibrary.org/obo/PR_000013246) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [prolactin (human)](http://purl.obolibrary.org/obo/PR_P01236) -#### Added -- [ossification center](http://purl.obolibrary.org/obo/UBERON_0010355) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "centrum ossificationis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [ossification center](http://purl.obolibrary.org/obo/UBERON_0010355) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "centrum ossificationis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ossification_center" +### prominin-1 `http://purl.obolibrary.org/obo/PR_000001786` +#### Removed +- [prominin-1](http://purl.obolibrary.org/obo/PR_000001786) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [prominin-1 (human)](http://purl.obolibrary.org/obo/PR_O43490) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### osteoblast `http://purl.obolibrary.org/obo/CL_0000062` +### pronephric duct `http://purl.obolibrary.org/obo/UBERON_0003060` +#### Removed +- [pronephric duct](http://purl.obolibrary.org/obo/UBERON_0003060) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Duct of the embryonic kidney, present bilaterally ventral to the somites and leading to the anal region where it empties separately from, and just posterior to the anus. Kimmel et al, 1995.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000150" -#### Added -- [osteoblast](http://purl.obolibrary.org/obo/CL_0000062) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -### osteoclast `http://purl.obolibrary.org/obo/CL_0000092` +- [pronephric duct](http://purl.obolibrary.org/obo/UBERON_0003060) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [osteoclast](http://purl.obolibrary.org/obo/CL_0000092) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### otic capsule `http://purl.obolibrary.org/obo/UBERON_0004637` -#### Removed -- [otic capsule](http://purl.obolibrary.org/obo/UBERON_0004637) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0005981" - - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0003-4423-4370" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.686" -#### Added -- [otic capsule](http://purl.obolibrary.org/obo/UBERON_0004637) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0005981" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000082" + +- [pronephric duct](http://purl.obolibrary.org/obo/UBERON_0003060) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0005991" - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) +- [pronephric duct](http://purl.obolibrary.org/obo/UBERON_0003060) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### otic placode `http://purl.obolibrary.org/obo/UBERON_0003069` -#### Removed -- [otic placode](http://purl.obolibrary.org/obo/UBERON_0003069) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "placoda otica" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [otic placode](http://purl.obolibrary.org/obo/UBERON_0003069) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "placoda otica" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000082" -### outer epithelium `http://purl.obolibrary.org/obo/UBERON_0007376` -#### Removed -- [outer epithelium](http://purl.obolibrary.org/obo/UBERON_0007376) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004993" +- [pronephric duct](http://purl.obolibrary.org/obo/UBERON_0003060) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "VHOG:0000082" -#### Added -- [outer epithelium](http://purl.obolibrary.org/obo/UBERON_0007376) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004993" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### outer limiting layer of retina `http://purl.obolibrary.org/obo/UBERON_0001788` +### pronephric glomerulus `http://purl.obolibrary.org/obo/UBERON_0004739` #### Removed -- [outer limiting layer of retina](http://purl.obolibrary.org/obo/UBERON_0001788) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum limitans externum retinae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58683" +- [pronephric glomerulus](http://purl.obolibrary.org/obo/UBERON_0004739) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "a glomus differs from a glomerulus in that each vascular glomus services several tubules" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0073040584" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [pronephric glomerulus](http://purl.obolibrary.org/obo/UBERON_0004739) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "GO treats glomus and pronephric glomerulus differently" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "GO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" - -#### Added -- [outer limiting layer of retina](http://purl.obolibrary.org/obo/UBERON_0001788) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum limitans externum retinae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [pronephric glomerulus](http://purl.obolibrary.org/obo/UBERON_0004739) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Paired highly vascularized portion of the pronephros. Left and right glomeruli are fused at the midline. Begins to function between 40 and 48hpf. Drummond, 2000.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58683" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001557" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -### outer medulla of kidney `http://purl.obolibrary.org/obo/UBERON_0001293` -#### Removed -- [outer medulla of kidney](http://purl.obolibrary.org/obo/UBERON_0001293) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "zona externa medullae renalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:17733" +- [pronephric glomerulus](http://purl.obolibrary.org/obo/UBERON_0004739) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The teleost pronephros shares many essential features with the amphibian pronephros including its derivation from mesoderm associated with the coelom and the derivation of the glomerular blood supply from the medial dorsal aorta. However, unlike the pronephros of amphibians, which have an external glomus and tubules with nephrostomes open to the coelom, the mature teleost pronephros has no connection to the body cavity and instead functions as a closed system (reference 1); This variation in nephron types [with external glomeruli that open into the coelom and with internal glomeruli that do not connect with the coelom] and their pattern of distribution suggest an evolutionary sequence. Ancestral craniates probably had an external glomerulus and nephrostomes, as do the first few to develop in very primitive craniates. (...) The mechanism would become more efficient as the coelomic recess into which each glomerulus discharged became a part of the tubule, that is, grew around the glomerulus as a renal capsule. The glomerulus becomes internal. The nephrostomes were lost during subsequent evolution, leaving the type of renal tubule found in most vertebrates (reference 2).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [outer medulla of kidney](http://purl.obolibrary.org/obo/UBERON_0001293) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "zona externa (medullaris renalis)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:17733" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:9806915 Drummond IA, Majumdar A, Hentschel H, Elger M, Solnica-Krezel L, Schier AF, Neuhauss SCF, Stemple DL, Zwartkruis F, Rangini Z, Driever W, Fishman MC, Early development of the zebrafish pronephros and analysis of mutations affecting pronephric function. Development (1998), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.636" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001237" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [outer medulla of kidney](http://purl.obolibrary.org/obo/UBERON_0001293) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "zona externa (medullaris renalis)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:17733" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### pronephric mesoderm `http://purl.obolibrary.org/obo/UBERON_0005721` +#### Removed +- [pronephric mesoderm](http://purl.obolibrary.org/obo/UBERON_0005721) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Portion of tissue that consists of the mesenchymal precursor to the pronephric kidney and that begins to separate from the intermediate mesoderm at NF stage 21 and epithelializes by NF stage 30.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "XAO:curator" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -- [outer medulla of kidney](http://purl.obolibrary.org/obo/UBERON_0001293) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "zona externa medullae renalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:17733" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0011090" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +#### Added +- [pronephric mesoderm](http://purl.obolibrary.org/obo/UBERON_0005721) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### outer nuclear layer of retina `http://purl.obolibrary.org/obo/UBERON_0001789` +### pronephric nephron `http://purl.obolibrary.org/obo/UBERON_0005309` #### Removed -- [outer nuclear layer of retina](http://purl.obolibrary.org/obo/UBERON_0001789) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum nucleare externum retinae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58684" +- [pronephric nephron](http://purl.obolibrary.org/obo/UBERON_0005309) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The structure that is the basic functional unit of the pronephros.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "UBERON:0005309" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0011091" #### Added -- [outer nuclear layer of retina](http://purl.obolibrary.org/obo/UBERON_0001789) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum nucleare externum retinae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [pronephric nephron](http://purl.obolibrary.org/obo/UBERON_0005309) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58684" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### pronephric nephron tubule `http://purl.obolibrary.org/obo/UBERON_0005310` +#### Removed +- [pronephric nephron tubule](http://purl.obolibrary.org/obo/UBERON_0005310) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Bilaterally paired tubes connecting the pronephric glomeruli to the pronephric ducts. In zebrafish and other teleosts, the pronephric nephron and tubules form after the pronephric duct, connecting to the anterior-most tip of the pronephric ducts. Drummond, 2000.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001558" -### outer plexiform layer of retina `http://purl.obolibrary.org/obo/UBERON_0001790` -#### Removed -- [outer plexiform layer of retina](http://purl.obolibrary.org/obo/UBERON_0001790) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum plexiforme externum retinae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58685" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [pronephric nephron tubule](http://purl.obolibrary.org/obo/UBERON_0005310) [RO_0002174](http://purl.obolibrary.org/obo/RO_0002174) [Amniota](http://purl.obolibrary.org/obo/NCBITaxon_32524) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0073040584" #### Added -- [outer plexiform layer of retina](http://purl.obolibrary.org/obo/UBERON_0001790) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum plexiforme externum retinae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [pronephric nephron tubule](http://purl.obolibrary.org/obo/UBERON_0005310) SubClassOf [meso-epithelium](http://purl.obolibrary.org/obo/UBERON_0012275) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58685" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### pronephros `http://purl.obolibrary.org/obo/UBERON_0002120` +#### Removed +- [pronephros](http://purl.obolibrary.org/obo/UBERON_0002120) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Organ that serves as a transient kidney, providing osmoregulation during early developmental stages and then degenerating during metamorphosis.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "XAO:curator" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -### outflow part of left ventricle `http://purl.obolibrary.org/obo/UBERON_0005956` -#### Removed -- [outflow part of left ventricle](http://purl.obolibrary.org/obo/UBERON_0005956) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vestibulum aortae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9473" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0011089" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [pronephros](http://purl.obolibrary.org/obo/UBERON_0002120) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A kidney formed of nephric tubules arising in the anterior region of the nephric ridge; forms only as a transient embryonic structure. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.748][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [outflow part of left ventricle](http://purl.obolibrary.org/obo/UBERON_0005956) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vestibulum aortae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9473" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000037" +- [pronephros](http://purl.obolibrary.org/obo/UBERON_0002120) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "pronephric" -### ovarian artery `http://purl.obolibrary.org/obo/UBERON_0001190` -#### Removed -- [ovarian artery](http://purl.obolibrary.org/obo/UBERON_0001190) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria ovarica" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ovarian_artery" +- [pronephros](http://purl.obolibrary.org/obo/UBERON_0002120) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D060910" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) -#### Added -- [ovarian artery](http://purl.obolibrary.org/obo/UBERON_0001190) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria ovarica" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ovarian_artery" +- [pronephros](http://purl.obolibrary.org/obo/UBERON_0002120) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### ovarian follicle `http://purl.obolibrary.org/obo/UBERON_0001305` -#### Removed -- [ovarian follicle](http://purl.obolibrary.org/obo/UBERON_0001305) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "folliculi ovarici primarii" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ovarian_follicle" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.637" -- [ovarian follicle](http://purl.obolibrary.org/obo/UBERON_0001305) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "folliculi ovarici vesiculosi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000037" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ovarian_follicle" +- [pronephros](http://purl.obolibrary.org/obo/UBERON_0002120) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The embryonic kidney, present at the level of the third somite, is composed of two glomeruli fused at the midline, two pronephric tubules, and paired bilateral pronephric ducts that modify the composition of the blood filtrate before delivering it to the cloaca for excretion.Kimmel et al, 1995.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -#### Added -- [ovarian follicle](http://purl.obolibrary.org/obo/UBERON_0001305) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "folliculi ovarici vesiculosi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000151" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ovarian_follicle" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -- [ovarian follicle](http://purl.obolibrary.org/obo/UBERON_0001305) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "folliculi ovarici primarii" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ovarian_follicle" -### ovarian nurse cell to oocyte transport `http://purl.obolibrary.org/obo/GO_0007300` +### proportion `http://www.geneontology.org/formats/oboInOwl#proportion` #### Removed -- [ovarian nurse cell to oocyte transport](http://purl.obolibrary.org/obo/GO_0007300) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "nurse cell to oocyte transport" +- AnnotationProperty: [proportion](http://www.geneontology.org/formats/oboInOwl#proportion) -- [ovarian nurse cell to oocyte transport](http://purl.obolibrary.org/obo/GO_0007300) [label](http://www.w3.org/2000/01/rdf-schema#label) "ovarian nurse cell to oocyte transport" -- [ovarian nurse cell to oocyte transport](http://purl.obolibrary.org/obo/GO_0007300) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:0007300" -- [ovarian nurse cell to oocyte transport](http://purl.obolibrary.org/obo/GO_0007300) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" - -- [ovarian nurse cell to oocyte transport](http://purl.obolibrary.org/obo/GO_0007300) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Transfer of constituents synthesized in the ovarian nurse cells to the oocyte, through the ring canals, as the egg chamber is growing. An example of this is found in Drosophila melanogaster." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:mtg_sensu" +### prostate bud `http://purl.obolibrary.org/obo/UBERON_0003820` +#### Removed +- [prostate bud](http://purl.obolibrary.org/obo/UBERON_0003820) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "AR activation releases instructive signals from UGM that acts on UGS epithelium (UGE) to stimulate cell proliferation, form prostate ductal progenitors (prostatic buds), and regulate cell adhesion dynamics to permit prostatic bud outgrowth. There are three phases of prostatic budding: (1) the specification phase, when instructive developmental cues define where buds will form in the UGS, (2) the initiation phase, when prostatic buds begin to form, and (3) the elongation phase, when proliferation, cell adhesion, and cell migration coordinate outgrowth of prostatic buds into UGM. Timing of prostatic bud formation and the quantity and pattern of buds that are formed in the UGS are strictly regulated [3, 4]. The position of prostatic buds as they emerge from the UGS in utero determines the arrangement of prostate ducts in adulthood.[PMID:18977204]" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0879694238" -- Class: [ovarian nurse cell to oocyte transport](http://purl.obolibrary.org/obo/GO_0007300) -- [ovarian nurse cell to oocyte transport](http://purl.obolibrary.org/obo/GO_0007300) EquivalentTo [transport](http://purl.obolibrary.org/obo/GO_0006810) and ([has target start location](http://purl.obolibrary.org/obo/RO_0002338) some [invertebrate nurse cell](http://purl.obolibrary.org/obo/CL_0000026)) and ([has target end location](http://purl.obolibrary.org/obo/RO_0002339) some [oocyte](http://purl.obolibrary.org/obo/CL_0000023)) and ([results in transport along](http://purl.obolibrary.org/obo/RO_0002341) some [germline ring canal](http://purl.obolibrary.org/obo/GO_0045172)) +### prostate duct `http://purl.obolibrary.org/obo/UBERON_0002485` +#### Removed +- [prostate duct](http://purl.obolibrary.org/obo/UBERON_0002485) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -- [ovarian nurse cell to oocyte transport](http://purl.obolibrary.org/obo/GO_0007300) SubClassOf [results in transport along](http://purl.obolibrary.org/obo/RO_0002341) some [germline ring canal](http://purl.obolibrary.org/obo/GO_0045172) +#### Added +- [prostate duct](http://purl.obolibrary.org/obo/UBERON_0002485) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) -- [ovarian nurse cell to oocyte transport](http://purl.obolibrary.org/obo/GO_0007300) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [oogenesis](http://purl.obolibrary.org/obo/GO_0048477) -- [ovarian nurse cell to oocyte transport](http://purl.obolibrary.org/obo/GO_0007300) SubClassOf [has target start location](http://purl.obolibrary.org/obo/RO_0002338) some [invertebrate nurse cell](http://purl.obolibrary.org/obo/CL_0000026) +### prostate epithelium `http://purl.obolibrary.org/obo/UBERON_0000428` -- [ovarian nurse cell to oocyte transport](http://purl.obolibrary.org/obo/GO_0007300) SubClassOf [only in taxon](http://purl.obolibrary.org/obo/RO_0002160) some [Insecta](http://purl.obolibrary.org/obo/NCBITaxon_50557) +#### Added +- [prostate epithelium](http://purl.obolibrary.org/obo/UBERON_0000428) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) -- [ovarian nurse cell to oocyte transport](http://purl.obolibrary.org/obo/GO_0007300) SubClassOf [in taxon](http://purl.obolibrary.org/obo/RO_0002162) only [Insecta](http://purl.obolibrary.org/obo/NCBITaxon_50557) +- [prostate epithelium](http://purl.obolibrary.org/obo/UBERON_0000428) SubClassOf [meso-epithelium](http://purl.obolibrary.org/obo/UBERON_0012275) -- [ovarian nurse cell to oocyte transport](http://purl.obolibrary.org/obo/GO_0007300) SubClassOf [has target end location](http://purl.obolibrary.org/obo/RO_0002339) some [oocyte](http://purl.obolibrary.org/obo/CL_0000023) -- [ovarian nurse cell to oocyte transport](http://purl.obolibrary.org/obo/GO_0007300) SubClassOf [reproductive process](http://purl.obolibrary.org/obo/GO_0022414) +### prostate field `http://purl.obolibrary.org/obo/UBERON_0009847` -- [ovarian nurse cell to oocyte transport](http://purl.obolibrary.org/obo/GO_0007300) SubClassOf [transport](http://purl.obolibrary.org/obo/GO_0006810) +#### Added +- [prostate field](http://purl.obolibrary.org/obo/UBERON_0009847) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) +### prostate gland `http://purl.obolibrary.org/obo/UBERON_0002367` +#### Removed +- [prostate gland](http://purl.obolibrary.org/obo/UBERON_0002367) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "prostatic" -### ovarian surface epithelial cell `http://purl.obolibrary.org/obo/CL_2000064` +- [prostate gland](http://purl.obolibrary.org/obo/UBERON_0002367) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) #### Added -- [ovarian surface epithelial cell](http://purl.obolibrary.org/obo/CL_2000064) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [prostate gland](http://purl.obolibrary.org/obo/UBERON_0002367) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) -### ovarian vein `http://purl.obolibrary.org/obo/UBERON_0001145` +### prostate gland lateral lobe `http://purl.obolibrary.org/obo/UBERON_0013637` #### Removed -- [ovarian vein](http://purl.obolibrary.org/obo/UBERON_0001145) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena ovarica sinistra" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ovarian_vein" +- [prostate gland lateral lobe](http://purl.obolibrary.org/obo/UBERON_0013637) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [ovarian vein](http://purl.obolibrary.org/obo/UBERON_0001145) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena ovarica dextra" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ovarian_vein" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### prostate gland secretion `http://purl.obolibrary.org/obo/UBERON_0004796` +#### Removed +- [prostate gland secretion](http://purl.obolibrary.org/obo/UBERON_0004796) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Prostatic secretions vary among species. They are generally composed of simple sugars and are often slightly alkaline." -#### Added -- [ovarian vein](http://purl.obolibrary.org/obo/UBERON_0001145) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena ovarica sinistra" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [prostate gland secretion](http://purl.obolibrary.org/obo/UBERON_0004796) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "A secretion of the prostate this is slightly alkaline fluid, milky or white in appearance. Usually constitutes 20-30% of the volume of the semen along with spermatozoa and seminal vesicle fluid [Wikipedia:Prostate#Secretions]" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ovarian_vein" -- [ovarian vein](http://purl.obolibrary.org/obo/UBERON_0001145) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena ovarica dextra" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ovarian_vein" +### prostate gland stroma `http://purl.obolibrary.org/obo/UBERON_0004184` +#### Added +- [prostate gland stroma](http://purl.obolibrary.org/obo/UBERON_0004184) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) -### ovary `http://purl.obolibrary.org/obo/UBERON_0000992` + +### prostate glandular acinus `http://purl.obolibrary.org/obo/UBERON_0004179` #### Removed -- [ovary](http://purl.obolibrary.org/obo/UBERON_0000992) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004865" +- [prostate glandular acinus](http://purl.obolibrary.org/obo/UBERON_0004179) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "Concurrent with branching morphogenesis, the solid cords of epithelium formed by budding arborize and differentiate postnatally into glandular acin. The basic prostate architecture is established by puberty and acquires secretory function thereafter[PMID:18977204]" + +#### Added +- [prostate glandular acinus](http://purl.obolibrary.org/obo/UBERON_0004179) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) -- [ovary](http://purl.obolibrary.org/obo/UBERON_0000992) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ovarium" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ovary" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### prostate luminal epithelium `http://purl.obolibrary.org/obo/UBERON_0011951` #### Added -- [ovary](http://purl.obolibrary.org/obo/UBERON_0000992) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004865" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [prostate luminal epithelium](http://purl.obolibrary.org/obo/UBERON_0011951) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) -- [ovary](http://purl.obolibrary.org/obo/UBERON_0000992) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ovarium" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ovary" +### prostatic capsule `http://purl.obolibrary.org/obo/UBERON_0035316` +#### Added +- [prostatic capsule](http://purl.obolibrary.org/obo/UBERON_0035316) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) -### ovary stroma `http://purl.obolibrary.org/obo/UBERON_0006960` -#### Removed -- [ovary stroma](http://purl.obolibrary.org/obo/UBERON_0006960) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "stroma ovarii" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Stroma_of_ovary" +### prostatic urethra `http://purl.obolibrary.org/obo/UBERON_0001335` #### Added -- [ovary stroma](http://purl.obolibrary.org/obo/UBERON_0006960) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "stroma ovarii" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Stroma_of_ovary" +- [prostatic urethra](http://purl.obolibrary.org/obo/UBERON_0001335) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### pair of dorsal aortae `http://purl.obolibrary.org/obo/UBERON_0010190` +### protein c-Fos `http://purl.obolibrary.org/obo/PR_000007597` +#### Removed +- [protein c-Fos](http://purl.obolibrary.org/obo/PR_000007597) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [protein c-Fos (human)](http://purl.obolibrary.org/obo/PR_P01100) -#### Added -- [pair of dorsal aortae](http://purl.obolibrary.org/obo/UBERON_0010190) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MA:0000476" -- [pair of dorsal aortae](http://purl.obolibrary.org/obo/UBERON_0010190) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" -- [pair of dorsal aortae](http://purl.obolibrary.org/obo/UBERON_0010190) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "paired dorsal aortae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EHDAA2:0000410" +### protein transmembrane transporter activity `http://purl.obolibrary.org/obo/GO_0008320` +#### Removed +- [protein transmembrane transporter activity](http://purl.obolibrary.org/obo/GO_0008320) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [protein transmembrane transport](http://purl.obolibrary.org/obo/GO_0071806) + - [source](http://www.geneontology.org/formats/oboInOwl#http://purl.org/dc/terms/source) "GO_REF:0000090" -- [pair of dorsal aortae](http://purl.obolibrary.org/obo/UBERON_0010190) [label](http://www.w3.org/2000/01/rdf-schema#label) "pair of dorsal aortae" +#### Added +- [protein transmembrane transporter activity](http://purl.obolibrary.org/obo/GO_0008320) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [protein transmembrane transport](http://purl.obolibrary.org/obo/GO_0071806) -- [pair of dorsal aortae](http://purl.obolibrary.org/obo/UBERON_0010190) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EHDAA2:0000410" -- [pair of dorsal aortae](http://purl.obolibrary.org/obo/UBERON_0010190) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [pheno_slim](http://purl.obolibrary.org/obo/uberon/core#pheno_slim) +### protoneuromast `http://purl.obolibrary.org/obo/UBERON_2005227` +#### Removed +- [protoneuromast](http://purl.obolibrary.org/obo/UBERON_2005227) [UBPROP_0000004](http://purl.obolibrary.org/obo/UBPROP_0000004) "This class was sourced from an external ontology (teleost_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://purl.obolibrary.org/obo/tao.owl" -- [pair of dorsal aortae](http://purl.obolibrary.org/obo/UBERON_0010190) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "The paired arterial structures of the embryo that supplies each developing somite via efferent segmental arteries; the dorsal aortae articulate with the umbilical arteries, which return mixed blood to the villi of the chorion for reoxygenation." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MP:0004787" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0-914294-08-3" -- [pair of dorsal aortae](http://purl.obolibrary.org/obo/UBERON_0010190) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:18606" +### proximal convoluted tubule `http://purl.obolibrary.org/obo/UBERON_0001287` +#### Removed +- [proximal convoluted tubule](http://purl.obolibrary.org/obo/UBERON_0001287) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Renal tubule that connects to the renal corpuscle.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -- [pair of dorsal aortae](http://purl.obolibrary.org/obo/UBERON_0010190) [id](http://www.geneontology.org/formats/oboInOwl#id) "UBERON:0010190" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005290" -- Class: [pair of dorsal aortae](http://purl.obolibrary.org/obo/UBERON_0010190) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -- [pair of dorsal aortae](http://purl.obolibrary.org/obo/UBERON_0010190) SubClassOf [has part](http://purl.obolibrary.org/obo/BFO_0000051) some [dorsal aorta](http://purl.obolibrary.org/obo/UBERON_0005805) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -- [pair of dorsal aortae](http://purl.obolibrary.org/obo/UBERON_0010190) SubClassOf [protein-containing material entity](http://purl.obolibrary.org/obo/PR_000050567) +- [proximal convoluted tubule](http://purl.obolibrary.org/obo/UBERON_0001287) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [proximal tubule](http://purl.obolibrary.org/obo/UBERON_0004134) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GOC:mtg_kidney_jan10" -- [pair of dorsal aortae](http://purl.obolibrary.org/obo/UBERON_0010190) SubClassOf [multi-tissue structure](http://purl.obolibrary.org/obo/UBERON_0000481) - - [source](http://www.geneontology.org/formats/oboInOwl#source) "EHDAA2" + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "MA uses subclass" -- [pair of dorsal aortae](http://purl.obolibrary.org/obo/UBERON_0010190) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [aortic system](http://purl.obolibrary.org/obo/UBERON_0010191) - - [source](http://www.geneontology.org/formats/oboInOwl#source) "EHDAA2" +#### Added +- [proximal convoluted tubule](http://purl.obolibrary.org/obo/UBERON_0001287) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [proximal tubule](http://purl.obolibrary.org/obo/UBERON_0004134) -### pair of lungs `http://purl.obolibrary.org/obo/UBERON_0000170` +### proximal epiphysis of fibula `http://purl.obolibrary.org/obo/UBERON_0008775` #### Removed -- [pair of lungs](http://purl.obolibrary.org/obo/UBERON_0000170) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pulmones" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:68877" +- [proximal epiphysis of fibula](http://purl.obolibrary.org/obo/UBERON_0008775) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The upper extremity or head of the fibula is of an irregular quadrate form, presenting above a flattened articular surface, directed upward, forward, and medialward, for articulation with a corresponding surface on the lateral condyle of the tibia. On the lateral side is a thick and rough prominence continued behind into a pointed eminence, the apex, which projects upward from the posterior part of the head. The prominence, at its upper and lateral part, gives attachment to the tendon of the Biceps femoris and to the fibular collateral ligament of the knee-joint, the ligament dividing the tendon into two parts. The remaining part of the circumference of the head is rough, for the attachment of muscles and ligaments. It presents in front a tubercle for the origin of the upper and anterior fibers of the Peronæus longus, and a surface for the attachment of the anterior ligament of the head; and behind, another tubercle, for the attachment of the posterior ligament of the head and the origin of the upper fibers of the Soleus[Wikipedia:Head_of_fibula]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Head_of_fibula" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [pair of lungs](http://purl.obolibrary.org/obo/UBERON_0000170) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas) +### proximal phalanx `http://purl.obolibrary.org/obo/UBERON_0004302` +#### Removed +- [proximal phalanx](http://purl.obolibrary.org/obo/UBERON_0004302) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Proximal phalanges are bones found in the limbs of most vertebrates. In humans, they are the bones at the base of a toe or finger, the prominent, knobby ends of which are often called the knuckles. In other vertebrates, proximal phalanges have a similar placement in the corresponding limbs, be they paw, wing or fin. In many species, they are the longest and thickest phalanx ('finger' bone)" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" -- [pair of lungs](http://purl.obolibrary.org/obo/UBERON_0000170) [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [Homo sapiens](http://purl.obolibrary.org/obo/NCBITaxon_9606) +- [proximal phalanx](http://purl.obolibrary.org/obo/UBERON_0004302) [UBPROP_0000105](http://purl.obolibrary.org/obo/UBPROP_0000105) "1"^^[nonNegativeInteger](http://www.w3.org/2001/XMLSchema#nonNegativeInteger) -- [pair of lungs](http://purl.obolibrary.org/obo/UBERON_0000170) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pulmones" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:68877" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### proximal segment of rib `http://purl.obolibrary.org/obo/UBERON_0010388` +#### Removed +- [proximal segment of rib](http://purl.obolibrary.org/obo/UBERON_0010388) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MA:0001414" + -### palpebral vein `http://purl.obolibrary.org/obo/UBERON_0014769` +### proximal straight tubule `http://purl.obolibrary.org/obo/UBERON_0001290` #### Removed -- [palpebral vein](http://purl.obolibrary.org/obo/UBERON_0014769) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "venae palpebrales" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [proximal straight tubule](http://purl.obolibrary.org/obo/UBERON_0001290) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Portion of the renal tubule which is just posterior to the proximal convoluted tubule.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -#### Added -- [palpebral vein](http://purl.obolibrary.org/obo/UBERON_0014769) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "venae palpebrales" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005291" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -### pampiniform plexus `http://purl.obolibrary.org/obo/UBERON_0001330` -#### Removed -- [pampiniform plexus](http://purl.obolibrary.org/obo/UBERON_0001330) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "plexus venosus pampiniformis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:19607" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [proximal straight tubule](http://purl.obolibrary.org/obo/UBERON_0001290) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [proximal tubule](http://purl.obolibrary.org/obo/UBERON_0004134) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GOC:mtg_kidney_jan10" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "MA uses subclass" #### Added -- [pampiniform plexus](http://purl.obolibrary.org/obo/UBERON_0001330) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "plexus venosus pampiniformis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [proximal straight tubule](http://purl.obolibrary.org/obo/UBERON_0001290) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [proximal tubule](http://purl.obolibrary.org/obo/UBERON_0004134) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:19607" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### proximal to `http://purl.obolibrary.org/obo/BSPO_0000100` +#### Removed +- [proximal to](http://purl.obolibrary.org/obo/BSPO_0000100) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BSPO:0000100" +- [proximal to](http://purl.obolibrary.org/obo/BSPO_0000100) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "proximal_to" -### panarthropod head `http://purl.obolibrary.org/obo/UBERON_6000004` -#### Removed -- [panarthropod head](http://purl.obolibrary.org/obo/UBERON_6000004) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000004" +- [proximal to](http://purl.obolibrary.org/obo/BSPO_0000100) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" -#### Added -- [panarthropod head](http://purl.obolibrary.org/obo/UBERON_6000004) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000004" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [proximal to](http://purl.obolibrary.org/obo/BSPO_0000100) [id](http://www.geneontology.org/formats/oboInOwl#id) "proximal_to" +- [proximal to](http://purl.obolibrary.org/obo/BSPO_0000100) [label](http://www.w3.org/2000/01/rdf-schema#label) "proximal to" -### pancreatic A cell `http://purl.obolibrary.org/obo/CL_0000171` -#### Added -- [pancreatic A cell](http://purl.obolibrary.org/obo/CL_0000171) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### proximal-distal subdivision of colon `http://purl.obolibrary.org/obo/UBERON_0000168` +#### Removed +- [proximal-distal subdivision of colon](http://purl.obolibrary.org/obo/UBERON_0000168) SubClassOf [subdivision of digestive tract](http://purl.obolibrary.org/obo/UBERON_0004921) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "cjm" -### pancreatic D cell `http://purl.obolibrary.org/obo/CL_0000173` + - [order](http://www.geneontology.org/formats/oboInOwl#order) "4" #### Added -- [pancreatic D cell](http://purl.obolibrary.org/obo/CL_0000173) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [proximal-distal subdivision of colon](http://purl.obolibrary.org/obo/UBERON_0000168) SubClassOf [subdivision of digestive tract](http://purl.obolibrary.org/obo/UBERON_0004921) + +### proximalmost part of `http://purl.obolibrary.org/obo/BSPO_0001106` +#### Removed +- [proximalmost part of](http://purl.obolibrary.org/obo/BSPO_0001106) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" -### pancreatic PP cell `http://purl.obolibrary.org/obo/CL_0002275` +- [proximalmost part of](http://purl.obolibrary.org/obo/BSPO_0001106) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BSPO:0001106" -#### Added -- [pancreatic PP cell](http://purl.obolibrary.org/obo/CL_0002275) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [proximalmost part of](http://purl.obolibrary.org/obo/BSPO_0001106) [label](http://www.w3.org/2000/01/rdf-schema#label) "proximalmost part of" +- [proximalmost part of](http://purl.obolibrary.org/obo/BSPO_0001106) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "proximalmost_part_of" -### pancreatic acinar cell `http://purl.obolibrary.org/obo/CL_0002064` +- [proximalmost part of](http://purl.obolibrary.org/obo/BSPO_0001106) [id](http://www.geneontology.org/formats/oboInOwl#id) "proximalmost_part_of" -#### Added -- [pancreatic acinar cell](http://purl.obolibrary.org/obo/CL_0002064) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### pancreatic acinus `http://purl.obolibrary.org/obo/UBERON_0001263` +### proximo-distal subdivision of respiratory tract `http://purl.obolibrary.org/obo/UBERON_0000072` #### Removed -- [pancreatic acinus](http://purl.obolibrary.org/obo/UBERON_0001263) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "acinus pancreaticus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:16011" +- [proximo-distal subdivision of respiratory tract](http://purl.obolibrary.org/obo/UBERON_0000072) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:16737" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [proximo-distal subdivision of respiratory tract](http://purl.obolibrary.org/obo/UBERON_0000072) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "MA:0000434 has subclasses upper and lower, so it corresponds to a segment of the tract, rather than the tract as a whole" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" #### Added -- [pancreatic acinus](http://purl.obolibrary.org/obo/UBERON_0001263) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0000028" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [proximo-distal subdivision of respiratory tract](http://purl.obolibrary.org/obo/UBERON_0000072) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" - - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) +### pseudostratified columnar epithelium `http://purl.obolibrary.org/obo/UBERON_0010498` +#### Removed +- [pseudostratified columnar epithelium](http://purl.obolibrary.org/obo/UBERON_0010498) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "Pseudostratified epithelia function in secretion or absorption. If a specimen looks stratified but has cilia, then it is a pseudostratified ciliated epithelium, since stratified epithelia do not have cilia." -- [pancreatic acinus](http://purl.obolibrary.org/obo/UBERON_0001263) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "acinus pancreaticus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [pseudostratified columnar epithelium](http://purl.obolibrary.org/obo/UBERON_0010498) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "glandular in NCIT; we consider the two NCIT terms synonymous" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "NCIT" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:16011" -### pancreatic duct `http://purl.obolibrary.org/obo/UBERON_0007329` +### pulmonary alveolar duct `http://purl.obolibrary.org/obo/UBERON_0002173` #### Removed -- [pancreatic duct](http://purl.obolibrary.org/obo/UBERON_0007329) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D010183" +- [pulmonary alveolar duct](http://purl.obolibrary.org/obo/UBERON_0002173) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In human anatomy, respiratory bronchioles exists proximal to the alveolar ducts. The epithelial lining consists of smooth muscle knobs covered by nonciliated, simple cuboidal cells. The smooth muscle constricts under parasympathetic innervation and relax under sympathetic innervation" -- [pancreatic duct](http://purl.obolibrary.org/obo/UBERON_0007329) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ductus pancreaticus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pancreatic_duct" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [pancreatic duct](http://purl.obolibrary.org/obo/UBERON_0007329) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D010183" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +### pulmonary artery `http://purl.obolibrary.org/obo/UBERON_0002012` +#### Removed +- [pulmonary artery](http://purl.obolibrary.org/obo/UBERON_0002012) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In the human heart, the pulmonary trunk (pulmonary artery or main pulmonary artery) begins at the base of the right ventricle. It is short and wide - approximately 5 cm (2 inches) in length and 3 cm (1.2 inches) in diameter. It then branches into two pulmonary arteries (left and right), which deliver deoxygenated blood to the corresponding lung[WP]" - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) +- [pulmonary artery](http://purl.obolibrary.org/obo/UBERON_0002012) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [pancreatic duct](http://purl.obolibrary.org/obo/UBERON_0007329) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ductus pancreaticus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pancreatic_duct" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000982" -### pancreatic ductal cell `http://purl.obolibrary.org/obo/CL_0002079` +- [pulmonary artery](http://purl.obolibrary.org/obo/UBERON_0002012) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Major artery which supplies blood to the lungs.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010221" -#### Added -- [pancreatic ductal cell](http://purl.obolibrary.org/obo/CL_0002079) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### pancreatic endocrine cell `http://purl.obolibrary.org/obo/CL_0008024` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" -#### Added -- [pancreatic endocrine cell](http://purl.obolibrary.org/obo/CL_0008024) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [pulmonary artery](http://purl.obolibrary.org/obo/UBERON_0002012) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "One of two arteries, leaving from the heart, the left one supplying the left lung and the right one supplying the right lung. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### pancreatic epsilon cell `http://purl.obolibrary.org/obo/CL_0005019` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [pancreatic epsilon cell](http://purl.obolibrary.org/obo/CL_0005019) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/pulmonary+artery" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000982" -### pancreatic stellate cell `http://purl.obolibrary.org/obo/CL_0002410` + + +### pulmonary collagen fibril `http://purl.obolibrary.org/obo/UBERON_0011862` #### Added -- [pancreatic stellate cell](http://purl.obolibrary.org/obo/CL_0002410) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [pulmonary collagen fibril](http://purl.obolibrary.org/obo/UBERON_0011862) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -### paneth cell `http://purl.obolibrary.org/obo/CL_0000510` +### pulmonary lobule `http://purl.obolibrary.org/obo/UBERON_0010368` #### Added -- [paneth cell](http://purl.obolibrary.org/obo/CL_0000510) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [pulmonary lobule](http://purl.obolibrary.org/obo/UBERON_0010368) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -### paneth cell of colon `http://purl.obolibrary.org/obo/CL_0009009` +### pulmonary lymphatic vessel `http://purl.obolibrary.org/obo/UBERON_0018227` #### Added -- [paneth cell of colon](http://purl.obolibrary.org/obo/CL_0009009) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [pulmonary lymphatic vessel](http://purl.obolibrary.org/obo/UBERON_0018227) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -### paneth cell of epithelium of small intestine `http://purl.obolibrary.org/obo/CL_1000343` +### pulmonary part of lymphatic system `http://purl.obolibrary.org/obo/UBERON_0018226` #### Added -- [paneth cell of epithelium of small intestine](http://purl.obolibrary.org/obo/CL_1000343) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [pulmonary part of lymphatic system](http://purl.obolibrary.org/obo/UBERON_0018226) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -### papillary layer of dermis `http://purl.obolibrary.org/obo/UBERON_0001992` +### pulmonary surfactant `http://purl.obolibrary.org/obo/UBERON_0008826` #### Removed -- [papillary layer of dermis](http://purl.obolibrary.org/obo/UBERON_0001992) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum papillare dermis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:64776" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [pulmonary surfactant](http://purl.obolibrary.org/obo/UBERON_0008826) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "surfactant" -- [papillary layer of dermis](http://purl.obolibrary.org/obo/UBERON_0001992) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum papillare (dermis)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:64776" +- [pulmonary surfactant](http://purl.obolibrary.org/obo/UBERON_0008826) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D011663" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -- [papillary layer of dermis](http://purl.obolibrary.org/obo/UBERON_0001992) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "stratum papillare" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Papillary_dermis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [papillary layer of dermis](http://purl.obolibrary.org/obo/UBERON_0001992) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum papillare (dermis)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:64776" +### pulmonary trunk `http://purl.obolibrary.org/obo/UBERON_0002333` +#### Removed +- [pulmonary trunk](http://purl.obolibrary.org/obo/UBERON_0002333) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "As in birds, the conus arteriosus split during embryonic development in mammals to produce the pulmonary trunk and single aortic trunk of the adult.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [papillary layer of dermis](http://purl.obolibrary.org/obo/UBERON_0001992) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum papillare dermis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:64776" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001134" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [pulmonary trunk](http://purl.obolibrary.org/obo/UBERON_0002333) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "An arterial trunk with origin from the right ventricle of the heart, and dividing into the right and left pulmonary arteries, which enter the corresponding lungs and branch with the bronchi. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [papillary layer of dermis](http://purl.obolibrary.org/obo/UBERON_0001992) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "stratum papillare" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Papillary_dermis" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/pulmonary+trunk" -### papillary tips cell `http://purl.obolibrary.org/obo/CL_1000597` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001134" -#### Added -- [papillary tips cell](http://purl.obolibrary.org/obo/CL_1000597) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### parasympathetic ganglion `http://purl.obolibrary.org/obo/UBERON_0001808` +### pulmonary vascular system `http://purl.obolibrary.org/obo/UBERON_0008886` #### Removed -- [parasympathetic ganglion](http://purl.obolibrary.org/obo/UBERON_0001808) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D005726" +- [pulmonary vascular system](http://purl.obolibrary.org/obo/UBERON_0008886) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Subdivision of cardiovascular system which has as its parts the pulmonary arterial and venous tree organs.[FMA]" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "FMA" -- [parasympathetic ganglion](http://purl.obolibrary.org/obo/UBERON_0001808) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ganglion parasympathicum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001256" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:45621" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Parasympathetic_ganglion" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [parasympathetic ganglion](http://purl.obolibrary.org/obo/UBERON_0001808) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ganglion parasympathicum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001256" +### pulmonary vein `http://purl.obolibrary.org/obo/UBERON_0002016` +#### Removed +- [pulmonary vein](http://purl.obolibrary.org/obo/UBERON_0002016) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "One of two pairs of large vessels that return oxygenated blood from each lung to the left atrium of the heart. [TFD][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001133" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/pulmonary+vein" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Parasympathetic_ganglion" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [parasympathetic ganglion](http://purl.obolibrary.org/obo/UBERON_0001808) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D005726" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +- [pulmonary vein](http://purl.obolibrary.org/obo/UBERON_0002016) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "the veins that return oxygenated blood from the lungs to the left atrium of the heart" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "MP:0002726,MGI:cwg" +- [pulmonary vein](http://purl.obolibrary.org/obo/UBERON_0002016) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Any of the veins which collect blood from the lungs and some small vesicles received from the esophagus.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -### parasympathetic nervous system `http://purl.obolibrary.org/obo/UBERON_0000011` -#### Removed -- [parasympathetic nervous system](http://purl.obolibrary.org/obo/UBERON_0000011) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pars parasympathica divisionis autonomici systematis nervosi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9907" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010521" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" -- [parasympathetic nervous system](http://purl.obolibrary.org/obo/UBERON_0000011) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pars parasympathica divisionis autonomici systematis nervosi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Parasympathetic_nervous_system" +- [pulmonary vein](http://purl.obolibrary.org/obo/UBERON_0002016) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "On the other hand, in the sister clade of the actinopterygians, the sarcopterygians, the gill circulation is supplemented with lung ventilation. As a result, the pulmonary artery and vein and a functional ductus arteriosus arose as a major evolutionary innovation from the sixth arch, giving the organism a flexible shunt to balance blood supply to and from gills and lungs according to environmental conditions.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001133" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [parasympathetic nervous system](http://purl.obolibrary.org/obo/UBERON_0000011) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pars parasympathica divisionis autonomici systematis nervosi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Parasympathetic_nervous_system" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [parasympathetic nervous system](http://purl.obolibrary.org/obo/UBERON_0000011) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pars parasympathica divisionis autonomici systematis nervosi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9907" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [pulmonary vein](http://purl.obolibrary.org/obo/UBERON_0002016) [UBPROP_0000202](http://purl.obolibrary.org/obo/UBPROP_0000202) [FMA_70827](http://purl.obolibrary.org/obo/FMA_70827) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### paraventricular nucleus of hypothalamus `http://purl.obolibrary.org/obo/UBERON_0001930` +### pulmonary venous system `http://purl.obolibrary.org/obo/UBERON_0013127` #### Removed -- [paraventricular nucleus of hypothalamus](http://purl.obolibrary.org/obo/UBERON_0001930) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nuclei paraventriculares" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:387" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [pulmonary venous system](http://purl.obolibrary.org/obo/UBERON_0013127) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Pulmonary circulation is the half portion of the cardiovascular system which carries oxygen-depleted blood away from the heart, to the lungs, and returns oxygenated (oxygen-rich) blood back to the heart. The term pulmonary circulation is readily paired and contrasted with the systemic circulation. A separate system known as the bronchial circulation supplies blood to the tissue of the larger airways of the lung." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Pulmonary_circulation" -- [paraventricular nucleus of hypothalamus](http://purl.obolibrary.org/obo/UBERON_0001930) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus hypothalami paraventricularis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:387" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [paraventricular nucleus of hypothalamus](http://purl.obolibrary.org/obo/UBERON_0001930) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus hypothalami filiformis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:387" +### putamen `http://purl.obolibrary.org/obo/UBERON_0001874` +#### Removed +- [putamen](http://purl.obolibrary.org/obo/UBERON_0001874) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "All nuclei of the mammalian basal ganglia are also present in the oldest vertebrates.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001456" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [paraventricular nucleus of hypothalamus](http://purl.obolibrary.org/obo/UBERON_0001930) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nuclei paraventricularis hypothalami" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Paraventricular_nucleus_of_hypothalamus" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1016/j.cub.2011.05.001 Stephenson-Jones M, Samuelsson E, Ericsson J, Robertson B, Grillner S, Evolutionary conservation of the basal ganglia as a common vertebrate mechanism for action selection. Current Biology (2011)" -- [paraventricular nucleus of hypothalamus](http://purl.obolibrary.org/obo/UBERON_0001930) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus filiformis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:387" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [putamen](http://purl.obolibrary.org/obo/UBERON_0001874) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Nucleus of brain which lies ventral to the caudate nucleus and internal capsule and medial to the external capsule. The putamen and caudate nucleus together form the dorsal striatum. It is also one of the structures that comprises the basal ganglia. Through various pathways, the putamen is connected to the substantia nigra and globus pallidus. The main function of the putamen is to regulate movements and influence various types of learning. It employs dopamine to perform its functions. The putamen also plays a role in degenerative neurological disorders, such as Parkinson's disease[Wikipedia:Putamen]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Putamen" -#### Added -- [paraventricular nucleus of hypothalamus](http://purl.obolibrary.org/obo/UBERON_0001930) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus filiformis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:387" -- [paraventricular nucleus of hypothalamus](http://purl.obolibrary.org/obo/UBERON_0001930) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nuclei paraventricularis hypothalami" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### pyloric sphincter `http://purl.obolibrary.org/obo/UBERON_0001202` +#### Removed +- [pyloric sphincter](http://purl.obolibrary.org/obo/UBERON_0001202) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) the adult Xenopus stomach exhibits both glandular and aglandular regions and a distinct pyloric sphincter similar to that of the amniotic vertebrates (...).[uncertain][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Paraventricular_nucleus_of_hypothalamus" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [paraventricular nucleus of hypothalamus](http://purl.obolibrary.org/obo/UBERON_0001930) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus hypothalami filiformis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1046/j.1525-142x.2000.00076.x" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:387" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [paraventricular nucleus of hypothalamus](http://purl.obolibrary.org/obo/UBERON_0001930) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nuclei paraventriculares" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001466" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:387" -- [paraventricular nucleus of hypothalamus](http://purl.obolibrary.org/obo/UBERON_0001930) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus hypothalami paraventricularis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:387" +### pylorus `http://purl.obolibrary.org/obo/UBERON_0001166` +#### Removed +- [pylorus](http://purl.obolibrary.org/obo/UBERON_0001166) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### paravertebral ganglion `http://purl.obolibrary.org/obo/UBERON_0001807` -#### Removed -- [paravertebral ganglion](http://purl.obolibrary.org/obo/UBERON_0001807) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ganglia trunci sympathici" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Paravertebral_ganglia" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [paravertebral ganglion](http://purl.obolibrary.org/obo/UBERON_0001807) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ganglion trunci sympathici" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:5891" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000420" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [pylorus](http://purl.obolibrary.org/obo/UBERON_0001166) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The orifice which allows the passage from the stomach into the intestine. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [paravertebral ganglion](http://purl.obolibrary.org/obo/UBERON_0001807) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ganglion trunci sympathetici" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [paravertebral ganglion](http://purl.obolibrary.org/obo/UBERON_0001807) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ganglion trunci sympathetici" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000420" -- [paravertebral ganglion](http://purl.obolibrary.org/obo/UBERON_0001807) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ganglion trunci sympathici" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:5891" +- [pylorus](http://purl.obolibrary.org/obo/UBERON_0001166) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "pyloric" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [paravertebral ganglion](http://purl.obolibrary.org/obo/UBERON_0001807) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ganglia trunci sympathici" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### quality of `http://purl.obolibrary.org/obo/RO_0000080` +#### Removed +- [quality of](http://purl.obolibrary.org/obo/RO_0000080) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "this red color is a quality of this apple"@en - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Paravertebral_ganglia" +- [quality of](http://purl.obolibrary.org/obo/RO_0000080) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "quality_of"@en +- [quality of](http://purl.obolibrary.org/obo/RO_0000080) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "is quality of"@en -### paraxial mesoderm `http://purl.obolibrary.org/obo/UBERON_0003077` -#### Removed -- [paraxial mesoderm](http://purl.obolibrary.org/obo/UBERON_0003077) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "mesoderma paraxiale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Paraxial_mesoderm" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [paraxial mesoderm](http://purl.obolibrary.org/obo/UBERON_0003077) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "mesoderma paraxiale" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### ready for release `http://purl.obolibrary.org/obo/IAO_0000122` +#### Removed +- [ready for release](http://purl.obolibrary.org/obo/IAO_0000122) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "ready for release"@en - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Paraxial_mesoderm" -### parenchyma `http://purl.obolibrary.org/obo/UBERON_0000353` +### receives input from `http://purl.obolibrary.org/obo/RO_0002485` #### Removed -- [parenchyma](http://purl.obolibrary.org/obo/UBERON_0000353) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001539" - - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0003-4423-4370" +- [receives input from](http://purl.obolibrary.org/obo/RO_0002485) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) -#### Added -- [parenchyma](http://purl.obolibrary.org/obo/UBERON_0000353) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001539" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" - - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) +### receptor-type tyrosine-protein kinase FLT3 `http://purl.obolibrary.org/obo/PR_000002001` +#### Removed +- [receptor-type tyrosine-protein kinase FLT3](http://purl.obolibrary.org/obo/PR_000002001) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [receptor-type tyrosine-protein kinase FLT3 (human)](http://purl.obolibrary.org/obo/PR_P36888) -- [parenchyma](http://purl.obolibrary.org/obo/UBERON_0000353) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0000999" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" - - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) +### receptor-type tyrosine-protein phosphatase C `http://purl.obolibrary.org/obo/PR_000001006` +#### Removed +- [receptor-type tyrosine-protein phosphatase C](http://purl.obolibrary.org/obo/PR_000001006) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [receptor-type tyrosine-protein phosphatase C (human)](http://purl.obolibrary.org/obo/PR_P08575) -### parietal cell `http://purl.obolibrary.org/obo/CL_0000162` -#### Added -- [parietal cell](http://purl.obolibrary.org/obo/CL_0000162) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### receptor-type tyrosine-protein phosphatase C isoform CD45RA `http://purl.obolibrary.org/obo/PR_000001015` +#### Removed +- [receptor-type tyrosine-protein phosphatase C isoform CD45RA](http://purl.obolibrary.org/obo/PR_000001015) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [receptor-type tyrosine-protein phosphatase C isoform CD45RA (human)](http://purl.obolibrary.org/obo/PR_P08575-8) -### parietal cortex `http://purl.obolibrary.org/obo/UBERON_0016530` -#### Added -- [parietal cortex](http://purl.obolibrary.org/obo/UBERON_0016530) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D010296" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) +### receptor-type tyrosine-protein phosphatase C isoform CD45RABC `http://purl.obolibrary.org/obo/PR_000001014` +#### Removed +- [receptor-type tyrosine-protein phosphatase C isoform CD45RABC](http://purl.obolibrary.org/obo/PR_000001014) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [receptor-type tyrosine-protein phosphatase C isoform CD45RABC (human)](http://purl.obolibrary.org/obo/PR_P08575-3) - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -### parietal epithelial cell `http://purl.obolibrary.org/obo/CL_1000452` +### receptor-type tyrosine-protein phosphatase C isoform CD45RO `http://purl.obolibrary.org/obo/PR_000001017` +#### Removed +- [receptor-type tyrosine-protein phosphatase C isoform CD45RO](http://purl.obolibrary.org/obo/PR_000001017) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [receptor-type tyrosine-protein phosphatase C isoform CD45RO (human)](http://purl.obolibrary.org/obo/PR_P08575-4) -#### Added -- [parietal epithelial cell](http://purl.obolibrary.org/obo/CL_1000452) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### parietal lobe `http://purl.obolibrary.org/obo/UBERON_0001872` +### rectum `http://purl.obolibrary.org/obo/UBERON_0001052` #### Removed -- [parietal lobe](http://purl.obolibrary.org/obo/UBERON_0001872) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "regio parietalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:61826" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [rectum](http://purl.obolibrary.org/obo/UBERON_0001052) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "rectal" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [rectum](http://purl.obolibrary.org/obo/UBERON_0001052) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html" -- [parietal lobe](http://purl.obolibrary.org/obo/UBERON_0001872) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lobus parietalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Parietal_lobe" +- [rectum](http://purl.obolibrary.org/obo/UBERON_0001052) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The terminal portion of the large intestine between the ileo-pelvic colon and the anus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [parietal lobe](http://purl.obolibrary.org/obo/UBERON_0001872) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "regio parietalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:61826" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001751" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [rectum](http://purl.obolibrary.org/obo/UBERON_0001052) SubClassOf [subdivision of digestive tract](http://purl.obolibrary.org/obo/UBERON_0004921) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "cjm" -- [parietal lobe](http://purl.obolibrary.org/obo/UBERON_0001872) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lobus parietalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [order](http://www.geneontology.org/formats/oboInOwl#order) "4" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Parietal_lobe" +#### Added +- [rectum](http://purl.obolibrary.org/obo/UBERON_0001052) SubClassOf [subdivision of digestive tract](http://purl.obolibrary.org/obo/UBERON_0004921) -### parietal pleura `http://purl.obolibrary.org/obo/UBERON_0002400` +### recurrent laryngeal nerve `http://purl.obolibrary.org/obo/UBERON_0003716` #### Removed -- [parietal pleura](http://purl.obolibrary.org/obo/UBERON_0002400) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pleura parietalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Parietal_pleura" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [recurrent laryngeal nerve](http://purl.obolibrary.org/obo/UBERON_0003716) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Branch of the vagus nerve that separates from the vagus well postcranially, then continues anteriorly to innervate the larynx[AAO:0010754]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:0010754" #### Added -- [parietal pleura](http://purl.obolibrary.org/obo/UBERON_0002400) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pleura parietalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Parietal_pleura" +- [recurrent laryngeal nerve](http://purl.obolibrary.org/obo/UBERON_0003716) SubClassOf [nerve of head region](http://purl.obolibrary.org/obo/UBERON_0011779) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + +### reelin `http://purl.obolibrary.org/obo/PR_000013879` +#### Removed +- [reelin](http://purl.obolibrary.org/obo/PR_000013879) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [reelin (human)](http://purl.obolibrary.org/obo/PR_P78509) -### parietal serous pericardium `http://purl.obolibrary.org/obo/UBERON_0002408` + +### reference `http://www.geneontology.org/formats/oboInOwl#reference` #### Removed -- [parietal serous pericardium](http://purl.obolibrary.org/obo/UBERON_0002408) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lamina parietalis pericardii" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9870" +- AnnotationProperty: [reference](http://www.geneontology.org/formats/oboInOwl#reference) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [parietal serous pericardium](http://purl.obolibrary.org/obo/UBERON_0002408) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lamina parietalis pericardii" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### regenerating anatomical structure `http://purl.obolibrary.org/obo/UBERON_0007567` +#### Removed +- [regenerating anatomical structure](http://purl.obolibrary.org/obo/UBERON_0007567) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A portion of tissue that is regrowing after damage or amputation.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9870" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005147" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -### pars distalis of adenohypophysis `http://purl.obolibrary.org/obo/UBERON_0006964` -#### Removed -- [pars distalis of adenohypophysis](http://purl.obolibrary.org/obo/UBERON_0006964) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pars distalis adenohypophysis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:74630" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### region `http://www.geneontology.org/formats/oboInOwl#region` +#### Removed +- AnnotationProperty: [region](http://www.geneontology.org/formats/oboInOwl#region) -- [pars distalis of adenohypophysis](http://purl.obolibrary.org/obo/UBERON_0006964) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pars distalis (hypophysis)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:410" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [pars distalis of adenohypophysis](http://purl.obolibrary.org/obo/UBERON_0006964) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pars distalis (glandula pituitaria)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:74630" +### region of nephron tubule `http://purl.obolibrary.org/obo/UBERON_0007685` +#### Removed +- [region of nephron tubule](http://purl.obolibrary.org/obo/UBERON_0007685) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "consider moving MA:0000377 renal tubule here, as it includes the various segments (proximal etc) as subclasses, not parts" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + +### regional part of brain `http://purl.obolibrary.org/obo/UBERON_0002616` #### Added -- [pars distalis of adenohypophysis](http://purl.obolibrary.org/obo/UBERON_0006964) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pars distalis adenohypophysis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [regional part of brain](http://purl.obolibrary.org/obo/UBERON_0002616) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:74630" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### regional part of spinal cord `http://purl.obolibrary.org/obo/UBERON_0001948` -- [pars distalis of adenohypophysis](http://purl.obolibrary.org/obo/UBERON_0006964) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pars distalis (hypophysis)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:410" +#### Added +- [regional part of spinal cord](http://purl.obolibrary.org/obo/UBERON_0001948) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -- [pars distalis of adenohypophysis](http://purl.obolibrary.org/obo/UBERON_0006964) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pars distalis (glandula pituitaria)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### regulated by `http://purl.obolibrary.org/obo/RO_0002334` +#### Removed +- [regulated by](http://purl.obolibrary.org/obo/RO_0002334) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:74630" +- [regulated by](http://purl.obolibrary.org/obo/RO_0002334) [IAO_0000589](http://purl.obolibrary.org/obo/IAO_0000589) "regulated by (processual)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### parvocellular layer of dorsal nucleus of lateral geniculate body `http://purl.obolibrary.org/obo/UBERON_0013607` +### regulates `http://purl.obolibrary.org/obo/RO_0002211` #### Removed -- [parvocellular layer of dorsal nucleus of lateral geniculate body](http://purl.obolibrary.org/obo/UBERON_0013607) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "strata parvocellularia nuclei dorsalis corporis geniculati lateralis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [regulates](http://purl.obolibrary.org/obo/RO_0002211) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-3837-8864](https://orcid.org/0000-0002-3837-8864) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [regulates](http://purl.obolibrary.org/obo/RO_0002211) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:76992" +- [regulates](http://purl.obolibrary.org/obo/RO_0002211) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) [causal-relations](http://purl.obolibrary.org/obo/ro/docs/causal-relations) -#### Added -- [parvocellular layer of dorsal nucleus of lateral geniculate body](http://purl.obolibrary.org/obo/UBERON_0013607) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "strata parvocellularia nuclei dorsalis corporis geniculati lateralis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [regulates](http://purl.obolibrary.org/obo/RO_0002211) [IAO_0000600](http://purl.obolibrary.org/obo/IAO_0000600) false - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [regulates](http://purl.obolibrary.org/obo/RO_0002211) [IAO_0000589](http://purl.obolibrary.org/obo/IAO_0000589) "regulates (processual)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:76992" +- [regulates](http://purl.obolibrary.org/obo/RO_0002211) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0001-7476-6306](https://orcid.org/0000-0001-7476-6306) +- [regulates](http://purl.obolibrary.org/obo/RO_0002211) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "Regulation precludes parthood; the regulatory process may not be within the regulated process." -### patella `http://purl.obolibrary.org/obo/UBERON_0002446` -#### Removed -- [patella](http://purl.obolibrary.org/obo/UBERON_0002446) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "patella" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Patella" +- [regulates](http://purl.obolibrary.org/obo/RO_0002211) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) "GO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [patella](http://purl.obolibrary.org/obo/UBERON_0002446) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "patella" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Patella" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### regulates activity of `http://purl.obolibrary.org/obo/RO_0011002` +#### Removed +- [regulates activity of](http://purl.obolibrary.org/obo/RO_0011002) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0003-4639-4431](https://orcid.org/0000-0003-4639-4431) -### pectinate line `http://purl.obolibrary.org/obo/UBERON_0006574` -#### Removed -- [pectinate line](http://purl.obolibrary.org/obo/UBERON_0006574) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "linea pectinata canalis analis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:75383" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### regulates levels of `http://purl.obolibrary.org/obo/RO_0002332` +#### Removed +- [regulates levels of](http://purl.obolibrary.org/obo/RO_0002332) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) [causal-relations](http://purl.obolibrary.org/obo/ro/docs/causal-relations) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [regulates levels of](http://purl.obolibrary.org/obo/RO_0002332) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" -- [pectinate line](http://purl.obolibrary.org/obo/UBERON_0006574) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "linea anocutanea" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pectinate_line" +- [regulates levels of](http://purl.obolibrary.org/obo/RO_0002332) [IAO_0000589](http://purl.obolibrary.org/obo/IAO_0000589) "regulates levels of (process to entity)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [regulates levels of](http://purl.obolibrary.org/obo/RO_0002332) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) -#### Added -- [pectinate line](http://purl.obolibrary.org/obo/UBERON_0006574) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "linea pectinata canalis analis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:75383" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### related via localization to `http://purl.obolibrary.org/obo/RO_0002337` +#### Removed +- [related via localization to](http://purl.obolibrary.org/obo/RO_0002337) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "Do not use this relation directly. It is a grouping relation." -- [pectinate line](http://purl.obolibrary.org/obo/UBERON_0006574) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "linea anocutanea" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [related via localization to](http://purl.obolibrary.org/obo/RO_0002337) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pectinate_line" -### pectoral girdle region `http://purl.obolibrary.org/obo/UBERON_0001421` +### relation between physical entity and a process or stage `http://purl.obolibrary.org/obo/RO_0002487` #### Removed -- [pectoral girdle region](http://purl.obolibrary.org/obo/UBERON_0001421) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cingulum membri superioris" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:23217" +- [relation between physical entity and a process or stage](http://purl.obolibrary.org/obo/RO_0002487) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [relation between physical entity and a process or stage](http://purl.obolibrary.org/obo/RO_0002487) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [pectoral girdle region](http://purl.obolibrary.org/obo/UBERON_0001421) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cingulum membri superioris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:23217" +### relaxin receptor 1 `http://purl.obolibrary.org/obo/PR_000001666` +#### Removed +- [relaxin receptor 1](http://purl.obolibrary.org/obo/PR_000001666) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [relaxin receptor 1 (human)](http://purl.obolibrary.org/obo/PR_Q9HBX9) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### pectoral girdle skeleton `http://purl.obolibrary.org/obo/UBERON_0007831` +### renal artery `http://purl.obolibrary.org/obo/UBERON_0001184` #### Removed -- [pectoral girdle skeleton](http://purl.obolibrary.org/obo/UBERON_0007831) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cingulum pectorale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pectoral_girdle" +- [renal artery](http://purl.obolibrary.org/obo/UBERON_0001184) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Artery which supplies blood via branches to the gonads, oviducts, and kidneys.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010223" -#### Added -- [pectoral girdle skeleton](http://purl.obolibrary.org/obo/UBERON_0007831) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cingulum pectorale" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pectoral_girdle" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" +- [renal artery](http://purl.obolibrary.org/obo/UBERON_0001184) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The renal arteries normally arise off the side of the abdominal aorta, immediately below the superior mesenteric artery, and supply the kidneys with blood. Each is directed across the crus of the diaphragm, so as to form nearly a right angle with the aorta. The renal arteries carry a large portion of total blood flow to the kidneys. Up to a third of total cardiac output can pass through the renal arteries to be filtered by the kidneys. The arterial supply of the kidneys is variable and there may be one or more renal arteries supplying each kidney. It is located above the renal vein. It has a radius of approximately 0.25cm, 0.26 cm at the root. The measured mean diameter can differ depending on the imaging method used. For example, the diameter was found to be 5.04 ± 0.74 mm using ultrasound, but 5.68 ± 1.19 mm using angiography. [WP,unvetted].[Wikipedia]" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "Wikipedia" -### pectoralis major `http://purl.obolibrary.org/obo/UBERON_0002381` -#### Removed -- [pectoralis major](http://purl.obolibrary.org/obo/UBERON_0002381) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "musculus pectoralis major" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pectoralis_major_muscle" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Renal_artery" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [pectoralis major](http://purl.obolibrary.org/obo/UBERON_0002381) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "musculus pectoralis major" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pectoralis_major_muscle" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### renal corpuscle `http://purl.obolibrary.org/obo/UBERON_0001229` +#### Removed +- [renal corpuscle](http://purl.obolibrary.org/obo/UBERON_0001229) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A mass of arterial capillaries enveloped in a capsule and attached to a tubule in the kidney[BTO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "BTO:0000333" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "BTO" -### pectoralis minor `http://purl.obolibrary.org/obo/UBERON_0001100` -#### Removed -- [pectoralis minor](http://purl.obolibrary.org/obo/UBERON_0001100) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "musculus pectoralis minor" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pectoralis_minor_muscle" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "BTO:curator" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-11-28" -#### Added -- [pectoralis minor](http://purl.obolibrary.org/obo/UBERON_0001100) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "musculus pectoralis minor" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [renal corpuscle](http://purl.obolibrary.org/obo/UBERON_0001229) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A tuft of capillaries found in a Bowman's capsule in which waste products are filtered from the blood and urine formation is initiated. Paired highly vascularized structures of the pronephros, responsible for blood filtration.[XAO]" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "XAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pectoralis_minor_muscle" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "XAO:curator" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "XAO:0000146" -### pedal digit `http://purl.obolibrary.org/obo/UBERON_0001466` -#### Removed -- [pedal digit](http://purl.obolibrary.org/obo/UBERON_0001466) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "digiti pedis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Toe" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-11-28" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [renal corpuscle](http://purl.obolibrary.org/obo/UBERON_0001229) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The part of the nephron that filters blood.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -#### Added -- [pedal digit](http://purl.obolibrary.org/obo/UBERON_0001466) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "digiti pedis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Toe" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005281" -### pelvic cavity `http://purl.obolibrary.org/obo/UBERON_0008203` -#### Removed -- [pelvic cavity](http://purl.obolibrary.org/obo/UBERON_0008203) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cavitas pelvis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pelvic_cavity" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [pelvic cavity](http://purl.obolibrary.org/obo/UBERON_0008203) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cavitas pelvis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### renal cortex interstitium `http://purl.obolibrary.org/obo/UBERON_0005270` +#### Removed +- [renal cortex interstitium](http://purl.obolibrary.org/obo/UBERON_0005270) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "In the renal cortex, interstitial fibroblasts produce erythropoietin and are distinguished from other interstitial cells by their prominent F-actin cytoskeleton, abundance of rough endoplasmic reticulum, and by ecto-5'-nucleotidase expression in their plasma membrane. The resident dendritic cells belong to the mononuclear phagocyte system and fulfil a sentinel function. They are characterized by their expression of MHC class II and CD11c." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:18575881" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pelvic_cavity" -### peptic cell `http://purl.obolibrary.org/obo/CL_0000155` +### renal duct `http://purl.obolibrary.org/obo/UBERON_0006553` +#### Removed +- [renal duct](http://purl.obolibrary.org/obo/UBERON_0006553) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in ZFA this is defined as part of mesonephros" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "ZFA" -#### Added -- [peptic cell](http://purl.obolibrary.org/obo/CL_0000155) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### pericardial cavity `http://purl.obolibrary.org/obo/UBERON_0001074` +### renal glomerulus `http://purl.obolibrary.org/obo/UBERON_0000074` #### Removed -- [pericardial cavity](http://purl.obolibrary.org/obo/UBERON_0001074) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cavitas pericardiaca" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pericardial_cavity" +- [renal glomerulus](http://purl.obolibrary.org/obo/UBERON_0000074) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "ZFA - The multi-tissue structure where the glomerular basement membrane supported by mesonephric podocytes filters blood from the glomerular capillaries. GUDMAP: 'Together, the Bowman's capsule and the glomerulus comprise the definitive renal corpuscle.' - here the glomerulus is part of the capsule?" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "ZFA" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [pericardial cavity](http://purl.obolibrary.org/obo/UBERON_0001074) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cavitas pericardiaca" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pericardial_cavity" +### renal lobe `http://purl.obolibrary.org/obo/UBERON_0009913` +#### Removed +- [renal lobe](http://purl.obolibrary.org/obo/UBERON_0009913) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "human kidneys have multilobar (multipyramidal) architecture while mice and rats have unilobar (unipyramidal) kidneys" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "MP" -### pericardial fluid `http://purl.obolibrary.org/obo/UBERON_0002409` -#### Removed -- [pericardial fluid](http://purl.obolibrary.org/obo/UBERON_0002409) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D000069236" -#### Added -- [pericardial fluid](http://purl.obolibrary.org/obo/UBERON_0002409) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D000069236" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +### renal lymph node `http://purl.obolibrary.org/obo/UBERON_0003425` +#### Removed +- [renal lymph node](http://purl.obolibrary.org/obo/UBERON_0003425) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Dorsal to the ipsilateral kidney nearby the renal blood vessels, caudal to the adrenal gland" + - [taxon](http://www.geneontology.org/formats/oboInOwl#taxon) "NCBITaxon:10090" - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:16624319" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -### pericranium `http://purl.obolibrary.org/obo/UBERON_0013687` +### renal medulla `http://purl.obolibrary.org/obo/UBERON_0000362` #### Removed -- [pericranium](http://purl.obolibrary.org/obo/UBERON_0013687) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "periosteum externum cranii" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:76623" +- [renal medulla](http://purl.obolibrary.org/obo/UBERON_0000362) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "The renal medulla is split up into a number of sections, known as the renal pyramids. Blood enters into the kidney via the renal artery, which then splits up to form the arcuate arterioles. The arcuate arterioles each in turn branch into interlobular arterioles, which finally reach the glomeruli. At the glomerulus the blood reaches a highly disfavourable pressure gradient and a large exchange surface area, which forces the serum portion of the blood out of the vessel into the renal tubules. Flow continues through the renal tubules, including the proximal tubule, the Loop of Henle, and finally leaves the kidney by means of the collecting duct, leading to the renal ureter. The renal medulla contains the structures of the nephrons responsible for maintaining the salt and water balance of the blood. The renal medulla is hypertonic to the filtrate in the nephron and aids in the reabsorption of water" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [pericranium](http://purl.obolibrary.org/obo/UBERON_0013687) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "periosteum externum cranii" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### renal medulla interstitium `http://purl.obolibrary.org/obo/UBERON_0005211` +#### Removed +- [renal medulla interstitium](http://purl.obolibrary.org/obo/UBERON_0005211) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "It functions in renal water reabsorption by building up a high hypertonicity, which draws water out of the thin descending limb of the loop of Henle and the collecting duct system. This hypertonicity, in turn, is created by an efflux of urea from the inner medullary collecting duct." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:76623" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### renal system `http://purl.obolibrary.org/obo/UBERON_0001008` +#### Removed +- [renal system](http://purl.obolibrary.org/obo/UBERON_0001008) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Evolution of vertebrate renal anatomy appears quite conservative when compared, for example, to evolution of respiratory and cardiovascular systems in vertebrates. Major anatomical changes in vertebrates kidneys separate those of birds and mammals from kidneys of lower vertebrates. General increase in animal size from fish to mammals is reflected by an increase in total number of nephrons per kidney, rather than by constant change in tubular dimensions.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### pericyte `http://purl.obolibrary.org/obo/CL_0000669` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [pericyte](http://purl.obolibrary.org/obo/CL_0000669) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-3540428541 Kapoor BG, Bhavna Khanna, Ichthyology Handbook (2004) p.406" -### periderm `http://purl.obolibrary.org/obo/UBERON_0003055` -#### Removed -- [periderm](http://purl.obolibrary.org/obo/UBERON_0003055) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0003377" - - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0003-4423-4370" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000723" -#### Added -- [periderm](http://purl.obolibrary.org/obo/UBERON_0003055) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0003377" +- [renal system](http://purl.obolibrary.org/obo/UBERON_0001008) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005056" - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +- [renal system](http://purl.obolibrary.org/obo/UBERON_0001008) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "This definition is inclusive of the organs of the vertebrate renal system, as well as the Malpighian tubules of insects, and allows for future incorporation of structures such as the antennal glands of crustaceans" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1371/journal.pone.0099864" - - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) +- [renal system](http://purl.obolibrary.org/obo/UBERON_0001008) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### perilymph `http://purl.obolibrary.org/obo/UBERON_0001845` -#### Removed -- [perilymph](http://purl.obolibrary.org/obo/UBERON_0001845) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "liquor cotunnii" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Perilymph" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010257" -#### Added -- [perilymph](http://purl.obolibrary.org/obo/UBERON_0001845) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "liquor cotunnii" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Perilymph" +- [renal system](http://purl.obolibrary.org/obo/UBERON_0001008) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### periodontal ligament `http://purl.obolibrary.org/obo/UBERON_0008266` +### renal tubule `http://purl.obolibrary.org/obo/UBERON_0009773` #### Removed -- [periodontal ligament](http://purl.obolibrary.org/obo/UBERON_0008266) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D010513" +- [renal tubule](http://purl.obolibrary.org/obo/UBERON_0009773) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "this class groups vertebrate nephron tubules with analagous structures such as insect Malpighian tubules" -- [periodontal ligament](http://purl.obolibrary.org/obo/UBERON_0008266) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "periodontal fiber" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Periodontal_ligament" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [periodontal ligament](http://purl.obolibrary.org/obo/UBERON_0008266) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "periodontal fibre" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Periodontal_ligament" +### renal vein `http://purl.obolibrary.org/obo/UBERON_0001140` +#### Removed +- [renal vein](http://purl.obolibrary.org/obo/UBERON_0001140) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in EHDAA2, the renal vein is part of the kidney" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EHDAA2" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [renal vein](http://purl.obolibrary.org/obo/UBERON_0001140) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The renal veins are veins that drain the kidney. They connect the kidney to the inferior vena cava. It is usually singular to each kidney, except in the condition 'multiple renal veins'. It also divides into 2 divisions upon entering the kidney: the anterior branch which receives blood from the anterior portion of the kidney and, the posterior branch which receives blood from the posterior portion. Often, each renal vein will have a branch that receives blood from the ureter. [WP,unvetted][Wikipedia:Renal_vein]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Renal_vein" -- [periodontal ligament](http://purl.obolibrary.org/obo/UBERON_0008266) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "fibra periodontalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Periodontal_ligament" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [periodontal ligament](http://purl.obolibrary.org/obo/UBERON_0008266) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "fibra periodontalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### renal venous blood vessel `http://purl.obolibrary.org/obo/UBERON_0014401` +#### Removed +- [renal venous blood vessel](http://purl.obolibrary.org/obo/UBERON_0014401) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "we follow MA and MP in distinguishing the venous blood vessel from the vein. The kidney cortex vein is not considered a renal vein, nor is the vasa recta" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Periodontal_ligament" -- [periodontal ligament](http://purl.obolibrary.org/obo/UBERON_0008266) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "periodontal fibre" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Periodontal_ligament" +### renin `http://purl.obolibrary.org/obo/PR_000013883` +#### Removed +- [renin](http://purl.obolibrary.org/obo/PR_000013883) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [renin (human)](http://purl.obolibrary.org/obo/PR_P00797) -- [periodontal ligament](http://purl.obolibrary.org/obo/UBERON_0008266) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "periodontal fiber" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Periodontal_ligament" -- [periodontal ligament](http://purl.obolibrary.org/obo/UBERON_0008266) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D010513" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +### replacement bone `http://purl.obolibrary.org/obo/UBERON_0012075` +#### Removed +- [replacement bone](http://purl.obolibrary.org/obo/UBERON_0012075) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "This class was introduced to be consistent with the ZFA hierarchy. The corresponding TAO term was obsoleted, and never introduced into VSAO. Note that VSAO does have replacement element." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "ZFA" - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) +- [replacement bone](http://purl.obolibrary.org/obo/UBERON_0012075) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Bone that forms as a replacement of another structural tissue.[TAO]" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TAO:wd" -### peripheral blood mononuclear cell `http://purl.obolibrary.org/obo/CL_2000001` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001637" -#### Added -- [peripheral blood mononuclear cell](http://purl.obolibrary.org/obo/CL_2000001) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### peripheral nervous system `http://purl.obolibrary.org/obo/UBERON_0000010` +### reproductive gland `http://purl.obolibrary.org/obo/UBERON_0003937` #### Removed -- [peripheral nervous system](http://purl.obolibrary.org/obo/UBERON_0000010) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pars peripherica" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Peripheral_nervous_system" - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9903" +- [reproductive gland](http://purl.obolibrary.org/obo/UBERON_0003937) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006162" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) -- [peripheral nervous system](http://purl.obolibrary.org/obo/UBERON_0000010) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005098" -- [peripheral nervous system](http://purl.obolibrary.org/obo/UBERON_0000010) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "systema nervosum periphericum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Peripheral_nervous_system" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9903" +### reproductive organ `http://purl.obolibrary.org/obo/UBERON_0003133` +#### Removed +- [reproductive organ](http://purl.obolibrary.org/obo/UBERON_0003133) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "GO uses genitalia for the singular organ" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "GO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [reproductive organ](http://purl.obolibrary.org/obo/UBERON_0003133) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:17381" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [peripheral nervous system](http://purl.obolibrary.org/obo/UBERON_0000010) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pars peripherica" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Peripheral_nervous_system" +### reproductive system `http://purl.obolibrary.org/obo/UBERON_0000990` +#### Removed +- [reproductive system](http://purl.obolibrary.org/obo/UBERON_0000990) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004857" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9903" +- [reproductive system](http://purl.obolibrary.org/obo/UBERON_0000990) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D005835" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -- [peripheral nervous system](http://purl.obolibrary.org/obo/UBERON_0000010) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "systema nervosum periphericum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [reproductive system](http://purl.obolibrary.org/obo/UBERON_0000990) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Arguably, one of the most important aspects of urbilaterian organogenesis would have been gonadogenesis, since Urbilateria must have successfully generated gametes and developed a strategy for extrusion and fertilization, in order to be the ancestor of all living Bilateria.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Peripheral_nervous_system" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9903" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:21672850 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across Bilateria. Integrative and Comparative Biology (2007)" -- [peripheral nervous system](http://purl.obolibrary.org/obo/UBERON_0000010) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005098" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000182" +- [reproductive system](http://purl.obolibrary.org/obo/UBERON_0000990) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical system which consists of organs and tissues associated with sexual reproduction of the organism.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -### peripheral nervous system neuron `http://purl.obolibrary.org/obo/CL_2000032` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -#### Added -- [peripheral nervous system neuron](http://purl.obolibrary.org/obo/CL_2000032) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010258" -### periportal region hepatocyte `http://purl.obolibrary.org/obo/CL_0019026` +- [reproductive system](http://purl.obolibrary.org/obo/UBERON_0000990) [UBPROP_0000202](http://purl.obolibrary.org/obo/UBPROP_0000202) [FMA_75572](http://purl.obolibrary.org/obo/FMA_75572) -#### Added -- [periportal region hepatocyte](http://purl.obolibrary.org/obo/CL_0019026) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### perirenal fat `http://purl.obolibrary.org/obo/UBERON_0005406` +### requires discussion `http://purl.obolibrary.org/obo/IAO_0000428` #### Removed -- [perirenal fat](http://purl.obolibrary.org/obo/UBERON_0005406) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "capsula adiposa renis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Adipose_capsule_of_kidney" +- [requires discussion](http://purl.obolibrary.org/obo/IAO_0000428) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) "group:OBI"@en - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [requires discussion](http://purl.obolibrary.org/obo/IAO_0000428) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) "Alan Ruttenberg"@en -#### Added -- [perirenal fat](http://purl.obolibrary.org/obo/UBERON_0005406) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "capsula adiposa renis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [requires discussion](http://purl.obolibrary.org/obo/IAO_0000428) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "requires discussion"@en - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Adipose_capsule_of_kidney" -### peritoneal cavity `http://purl.obolibrary.org/obo/UBERON_0001179` +### respiration organ `http://purl.obolibrary.org/obo/UBERON_0000171` #### Removed -- [peritoneal cavity](http://purl.obolibrary.org/obo/UBERON_0001179) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cavitas peritonealis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001782" +- [respiration organ](http://purl.obolibrary.org/obo/UBERON_0000171) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:17607" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Peritoneal_cavity" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [peritoneal cavity](http://purl.obolibrary.org/obo/UBERON_0001179) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "saccus serosus peritonei" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Peritoneal_cavity" +### respiratory airway `http://purl.obolibrary.org/obo/UBERON_0001005` +#### Removed +- [respiratory airway](http://purl.obolibrary.org/obo/UBERON_0001005) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "This class generically groups trachea and analagous structures throughout metazoa. Consider renaming, as the term could be taken to mean lumen of tracheal system (e.g. in SNOMED). As a grouping class this is quite vague, as it is not clear where the airway begins and ends" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [respiratory airway](http://purl.obolibrary.org/obo/UBERON_0001005) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:265130" -#### Added -- [peritoneal cavity](http://purl.obolibrary.org/obo/UBERON_0001179) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "saccus serosus peritonei" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Peritoneal_cavity" -- [peritoneal cavity](http://purl.obolibrary.org/obo/UBERON_0001179) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cavitas peritonealis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001782" +### respiratory bronchiole `http://purl.obolibrary.org/obo/UBERON_0002188` +#### Removed +- [respiratory bronchiole](http://purl.obolibrary.org/obo/UBERON_0002188) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "mice have few or none of these structures, with the terminal bronchioles transitioning directly to the alveolary ducts" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0123813611" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Peritoneal_cavity" +### respiratory muscle `http://purl.obolibrary.org/obo/UBERON_0014398` +#### Removed +- [respiratory muscle](http://purl.obolibrary.org/obo/UBERON_0014398) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "this class may be merged with 'respiratory system muscle'; check intercostals" -### peritoneal fluid `http://purl.obolibrary.org/obo/UBERON_0001268` +- [respiratory muscle](http://purl.obolibrary.org/obo/UBERON_0014398) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D012132" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -#### Added -- [peritoneal fluid](http://purl.obolibrary.org/obo/UBERON_0001268) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D001202" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -### peritubular capillary endothelial cell `http://purl.obolibrary.org/obo/CL_1001033` + +### respiratory primordium mesenchyme `http://purl.obolibrary.org/obo/UBERON_0036073` #### Added -- [peritubular capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1001033) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [respiratory primordium mesenchyme](http://purl.obolibrary.org/obo/UBERON_0036073) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) -### periventricular zone of hypothalamus `http://purl.obolibrary.org/obo/UBERON_0002271` +### respiratory segment of nasal mucosa `http://purl.obolibrary.org/obo/UBERON_0015786` #### Removed -- [periventricular zone of hypothalamus](http://purl.obolibrary.org/obo/UBERON_0002271) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "zona periventricularis hypothalamicae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:77682" +- [respiratory segment of nasal mucosa](http://purl.obolibrary.org/obo/UBERON_0015786) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "lined with ciliated pseudostratified columnar epithelium (respiratory epithelium). The respiratory segment has a very vascularized lamina propria allowing the venous plexuses of the conchal mucosa to engorge with blood, restricting airflow and causing air to be directed to the other side of the nose." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Nasal_cavity" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [periventricular zone of hypothalamus](http://purl.obolibrary.org/obo/UBERON_0002271) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "zona periventricularis hypothalamicae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### respiratory system `http://purl.obolibrary.org/obo/UBERON_0001004` +#### Removed +- [respiratory system](http://purl.obolibrary.org/obo/UBERON_0001004) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The anatomical system in which the exchange of oxygen and carbon dioxide between the organism and its environment.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000541" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:77682" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" -### pes connective tissue `http://purl.obolibrary.org/obo/UBERON_0003595` -#### Removed -- [pes connective tissue](http://purl.obolibrary.org/obo/UBERON_0003595) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "textus connectivus of pes" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "OBOL:automatic" +- [respiratory system](http://purl.obolibrary.org/obo/UBERON_0001004) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "There is no doubt that the primitive pattern of vertebrate air-breathing is the buccal pulse pump found in actinopterygian fishes.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.599 and Figure 18-23" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [pes connective tissue](http://purl.obolibrary.org/obo/UBERON_0003595) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "textus connectivus of pes" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "OBOL:automatic" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000202" -### pes joint `http://purl.obolibrary.org/obo/UBERON_0001487` -#### Removed -- [pes joint](http://purl.obolibrary.org/obo/UBERON_0001487) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "articulationes pedis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71349" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### respiratory system epithelium `http://purl.obolibrary.org/obo/UBERON_0004807` +#### Removed +- [respiratory system epithelium](http://purl.obolibrary.org/obo/UBERON_0004807) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "VHOG:0000981" -#### Added -- [pes joint](http://purl.obolibrary.org/obo/UBERON_0001487) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "articulationes pedis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71349" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### respiratory system mucosa `http://purl.obolibrary.org/obo/UBERON_0004785` +#### Removed +- [respiratory system mucosa](http://purl.obolibrary.org/obo/UBERON_0004785) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:18334" -### phagocyte `http://purl.obolibrary.org/obo/CL_0000234` + +### respiratory tract `http://purl.obolibrary.org/obo/UBERON_0000065` #### Added -- [phagocyte](http://purl.obolibrary.org/obo/CL_0000234) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [respiratory tract](http://purl.obolibrary.org/obo/UBERON_0000065) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -### pharyngeal arch `http://purl.obolibrary.org/obo/UBERON_0002539` +### respiratory tract epithelium `http://purl.obolibrary.org/obo/UBERON_0004802` #### Removed -- [pharyngeal arch](http://purl.obolibrary.org/obo/UBERON_0002539) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arcus pharyngei" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pharyngeal_arch" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [respiratory tract epithelium](http://purl.obolibrary.org/obo/UBERON_0004802) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "VHOG:0000981" #### Added -- [pharyngeal arch](http://purl.obolibrary.org/obo/UBERON_0002539) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arcus pharyngei" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [respiratory tract epithelium](http://purl.obolibrary.org/obo/UBERON_0004802) SubClassOf [endo-epithelium](http://purl.obolibrary.org/obo/UBERON_0005911) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pharyngeal_arch" +### respiratory tube `http://purl.obolibrary.org/obo/UBERON_0000117` +#### Removed +- [respiratory tube](http://purl.obolibrary.org/obo/UBERON_0000117) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in GO lung development is part of respiratory tube development. This can lead to inconsistencies with other ontologies, e.g. VT. The GO structure may be better represented by a tree of tubes (see the FMA class)" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "GO" -### pharyngeal arch 1 `http://purl.obolibrary.org/obo/UBERON_0004362` +#### Added +- [respiratory tube](http://purl.obolibrary.org/obo/UBERON_0000117) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) + + +### results in acquisition of features of `http://purl.obolibrary.org/obo/RO_0002315` #### Removed -- [pharyngeal arch 1](http://purl.obolibrary.org/obo/UBERON_0004362) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arcus pharyngeus primus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:First_pharyngeal_arch" +- [results in acquisition of features of](http://purl.obolibrary.org/obo/RO_0002315) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) "GOC:mtg_berkeley_2013" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [results in acquisition of features of](http://purl.obolibrary.org/obo/RO_0002315) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) -#### Added -- [pharyngeal arch 1](http://purl.obolibrary.org/obo/UBERON_0004362) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arcus pharyngeus primus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [results in acquisition of features of](http://purl.obolibrary.org/obo/RO_0002315) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:First_pharyngeal_arch" -### pharyngeal arch 2 `http://purl.obolibrary.org/obo/UBERON_0003066` +### results in development of `http://purl.obolibrary.org/obo/RO_0002296` #### Removed -- [pharyngeal arch 2](http://purl.obolibrary.org/obo/UBERON_0003066) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arcus pharyngeus secundus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [results in development of](http://purl.obolibrary.org/obo/RO_0002296) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Second_pharyngeal_arch" +- [results in development of](http://purl.obolibrary.org/obo/RO_0002296) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "every flower development (GO:0009908) results in development of some flower (PO:0009046)"@en -#### Added -- [pharyngeal arch 2](http://purl.obolibrary.org/obo/UBERON_0003066) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arcus pharyngeus secundus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [results in development of](http://purl.obolibrary.org/obo/RO_0002296) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) "http://www.geneontology.org/GO.doc.development.shtml"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Second_pharyngeal_arch" +- [results in development of](http://purl.obolibrary.org/obo/RO_0002296) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) -### pharyngeal arch artery `http://purl.obolibrary.org/obo/UBERON_0004363` + +### results in developmental progression of `http://purl.obolibrary.org/obo/RO_0002295` #### Removed -- [pharyngeal arch artery](http://purl.obolibrary.org/obo/UBERON_0004363) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "a. arcuum pharyngeorum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Aortic_arches" +- [results in developmental progression of](http://purl.obolibrary.org/obo/RO_0002295) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [results in developmental progression of](http://purl.obolibrary.org/obo/RO_0002295) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) -- [pharyngeal arch artery](http://purl.obolibrary.org/obo/UBERON_0004363) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteriae arcuum pharyngeorum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Aortic_arches" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [pharyngeal arch artery](http://purl.obolibrary.org/obo/UBERON_0004363) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "a. arcuum pharyngeorum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### results in formation of `http://purl.obolibrary.org/obo/RO_0002297` +#### Removed +- [results in formation of](http://purl.obolibrary.org/obo/RO_0002297) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062)"@en - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Aortic_arches" +- [results in formation of](http://purl.obolibrary.org/obo/RO_0002297) [label](http://www.w3.org/2000/01/rdf-schema#label) "results in formation of"@en -- [pharyngeal arch artery](http://purl.obolibrary.org/obo/UBERON_0004363) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteriae arcuum pharyngeorum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [results in formation of](http://purl.obolibrary.org/obo/RO_0002297) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) "GOC:mtg_berkeley_2013" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Aortic_arches" +- [results in formation of](http://purl.obolibrary.org/obo/RO_0002297) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." +- [results in formation of](http://purl.obolibrary.org/obo/RO_0002297) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) -### pharyngeal arch cartilage `http://purl.obolibrary.org/obo/UBERON_0011004` -#### Removed -- [pharyngeal arch cartilage](http://purl.obolibrary.org/obo/UBERON_0011004) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006051" - - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0003-4423-4370" +- [results in formation of](http://purl.obolibrary.org/obo/RO_0002297) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) #### Added -- [pharyngeal arch cartilage](http://purl.obolibrary.org/obo/UBERON_0011004) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006051" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [results in formation of](http://purl.obolibrary.org/obo/RO_0002297) [label](http://www.w3.org/2000/01/rdf-schema#label) "results in formation of anatomical entity"@en - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" - - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) +### results in growth of `http://purl.obolibrary.org/obo/RO_0002343` +#### Removed +- [results in growth of](http://purl.obolibrary.org/obo/RO_0002343) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) +- [results in growth of](http://purl.obolibrary.org/obo/RO_0002343) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "'pollen tube growth' results_in growth_of some 'pollen tube'" -### pharyngeal cleft `http://purl.obolibrary.org/obo/UBERON_0005879` + + +### results in maturation of `http://purl.obolibrary.org/obo/RO_0002299` #### Removed -- [pharyngeal cleft](http://purl.obolibrary.org/obo/UBERON_0005879) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "sulcus pharyngei" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pharyngeal_groove" +- [results in maturation of](http://purl.obolibrary.org/obo/RO_0002299) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [results in maturation of](http://purl.obolibrary.org/obo/RO_0002299) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) "GOC:mtg_berkeley_2013" -#### Added -- [pharyngeal cleft](http://purl.obolibrary.org/obo/UBERON_0005879) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "sulcus pharyngei" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [results in maturation of](http://purl.obolibrary.org/obo/RO_0002299) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) + +- [results in maturation of](http://purl.obolibrary.org/obo/RO_0002299) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pharyngeal_groove" +- [results in maturation of](http://purl.obolibrary.org/obo/RO_0002299) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)"@en -### pharyngeal mucosa `http://purl.obolibrary.org/obo/UBERON_0000355` + +### results in morphogenesis of `http://purl.obolibrary.org/obo/RO_0002298` #### Removed -- [pharyngeal mucosa](http://purl.obolibrary.org/obo/UBERON_0000355) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa pharyngea" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:55031" +- [results in morphogenesis of](http://purl.obolibrary.org/obo/RO_0002298) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [results in morphogenesis of](http://purl.obolibrary.org/obo/RO_0002298) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [results in morphogenesis of](http://purl.obolibrary.org/obo/RO_0002298) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)"@en -#### Added -- [pharyngeal mucosa](http://purl.obolibrary.org/obo/UBERON_0000355) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa pharyngea" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:55031" +- [results in morphogenesis of](http://purl.obolibrary.org/obo/RO_0002298) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [results in morphogenesis of](http://purl.obolibrary.org/obo/RO_0002298) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) "GOC:mtg_berkeley_2013" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### photoreceptor array `http://purl.obolibrary.org/obo/UBERON_0005388` +### results in movement of `http://purl.obolibrary.org/obo/RO_0002565` #### Removed -- [photoreceptor array](http://purl.obolibrary.org/obo/UBERON_0005388) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004200" +- [results in movement of](http://purl.obolibrary.org/obo/RO_0002565) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) -#### Added -- [photoreceptor array](http://purl.obolibrary.org/obo/UBERON_0005388) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004200" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [results in movement of](http://purl.obolibrary.org/obo/RO_0002565) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "" -### photoreceptor cell `http://purl.obolibrary.org/obo/CL_0000210` -#### Added -- [photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000210) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### results in transport across `http://purl.obolibrary.org/obo/RO_0002342` +#### Removed +- [results in transport across](http://purl.obolibrary.org/obo/RO_0002342) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) -### photoreceptor layer of retina `http://purl.obolibrary.org/obo/UBERON_0001787` + +### results in transport along `http://purl.obolibrary.org/obo/RO_0002341` #### Removed -- [photoreceptor layer of retina](http://purl.obolibrary.org/obo/UBERON_0001787) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum segmentorum externorum et internorum retinae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58680" +- [results in transport along](http://purl.obolibrary.org/obo/RO_0002341) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [photoreceptor layer of retina](http://purl.obolibrary.org/obo/UBERON_0001787) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum segmentorum externorum et internorum retinae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### results in transport to from or in `http://purl.obolibrary.org/obo/RO_0002344` +#### Removed +- [results in transport to from or in](http://purl.obolibrary.org/obo/RO_0002344) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58680" +- [results in transport to from or in](http://purl.obolibrary.org/obo/RO_0002344) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### photosynthesis `http://purl.obolibrary.org/obo/GO_0015979` +### reticular formation `http://purl.obolibrary.org/obo/UBERON_0002275` #### Removed -- [photosynthesis](http://purl.obolibrary.org/obo/GO_0015979) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) +- [reticular formation](http://purl.obolibrary.org/obo/UBERON_0002275) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "this class denotes the generic structure, and not a specific one such as medullary or pontine reticular formation." -#### Added -- [photosynthesis](http://purl.obolibrary.org/obo/GO_0015979) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) +- [reticular formation](http://purl.obolibrary.org/obo/UBERON_0002275) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA has a spinal cord reticular formation but we follow NNs (classical) to restrict this to brainstem structures. This means we also include the MA class for brainstem reticular formation here. FMA has subtypes of reticular formation but we treat this as a composite structure" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" +- [reticular formation](http://purl.obolibrary.org/obo/UBERON_0002275) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "It is essential for governing some of the basic functions of higher organisms, and is one of the phylogenetically oldest portions of the brain." -### phrenic nerve `http://purl.obolibrary.org/obo/UBERON_0001884` -#### Removed -- [phrenic nerve](http://purl.obolibrary.org/obo/UBERON_0001884) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nervus phrenicus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001063" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Phrenic_nerve" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### reticular layer of dermis `http://purl.obolibrary.org/obo/UBERON_0001993` #### Added -- [phrenic nerve](http://purl.obolibrary.org/obo/UBERON_0001884) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nervus phrenicus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001063" +- [reticular layer of dermis](http://purl.obolibrary.org/obo/UBERON_0001993) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Phrenic_nerve" +### retina `http://purl.obolibrary.org/obo/UBERON_0000966` +#### Removed +- [retina](http://purl.obolibrary.org/obo/UBERON_0000966) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### pigmented ciliary epithelial cell `http://purl.obolibrary.org/obo/CL_0002303` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [pigmented ciliary epithelial cell](http://purl.obolibrary.org/obo/CL_0002303) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000229" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### pigmented epithelial cell `http://purl.obolibrary.org/obo/CL_0000529` +- [retina](http://purl.obolibrary.org/obo/UBERON_0000966) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The portion of the eye developing from the optic primordium and including the neural retina and the retinal pigment layer. Kimmel et al, 1995.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000152" -#### Added -- [pigmented epithelial cell](http://purl.obolibrary.org/obo/CL_0000529) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -### pigmented layer of retina `http://purl.obolibrary.org/obo/UBERON_0001782` -#### Removed -- [pigmented layer of retina](http://purl.obolibrary.org/obo/UBERON_0001782) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum pigmentosum retinae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58627" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [retina](http://purl.obolibrary.org/obo/UBERON_0000966) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "retinal" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [pigmented layer of retina](http://purl.obolibrary.org/obo/UBERON_0001782) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "p. pigmentosa retinae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Retinal_pigment_epithelium" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### retina blood vessel `http://purl.obolibrary.org/obo/UBERON_0003501` -- [pigmented layer of retina](http://purl.obolibrary.org/obo/UBERON_0001782) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "stratum pigmentosa retinae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Retinal_pigment_epithelium" +#### Added +- [retina blood vessel](http://purl.obolibrary.org/obo/UBERON_0003501) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [pigmented layer of retina](http://purl.obolibrary.org/obo/UBERON_0001782) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum pigmentosum retinae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58627" +### retinal neural layer `http://purl.obolibrary.org/obo/UBERON_0003902` +#### Removed +- [retinal neural layer](http://purl.obolibrary.org/obo/UBERON_0003902) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [pigmented layer of retina](http://purl.obolibrary.org/obo/UBERON_0001782) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "p. pigmentosa retinae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Retinal_pigment_epithelium" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000535" -- [pigmented layer of retina](http://purl.obolibrary.org/obo/UBERON_0001782) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "stratum pigmentosa retinae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [retinal neural layer](http://purl.obolibrary.org/obo/UBERON_0003902) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Retinal_pigment_epithelium" -### pineal body `http://purl.obolibrary.org/obo/UBERON_0001905` +### rhombencephalon neural crest `http://purl.obolibrary.org/obo/UBERON_0003852` #### Removed -- [pineal body](http://purl.obolibrary.org/obo/UBERON_0001905) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "glandula pinealis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:62033" +- [rhombencephalon neural crest](http://purl.obolibrary.org/obo/UBERON_0003852) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [pineal body](http://purl.obolibrary.org/obo/UBERON_0001905) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "glandula pinealis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:62033" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001210" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [rhombencephalon neural crest](http://purl.obolibrary.org/obo/UBERON_0003852) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Cranial neural crest that is part of the hindbrain.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -### piriform cortex `http://purl.obolibrary.org/obo/UBERON_0004725` -#### Removed -- [piriform cortex](http://purl.obolibrary.org/obo/UBERON_0004725) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cortex piriformis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Piriform_cortex" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0007063" -- [piriform cortex](http://purl.obolibrary.org/obo/UBERON_0004725) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "eupalaeocortex" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:165" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [piriform cortex](http://purl.obolibrary.org/obo/UBERON_0004725) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "regio praepiriformis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:165" +### rhombic lip `http://purl.obolibrary.org/obo/UBERON_0006215` +#### Removed +- [rhombic lip](http://purl.obolibrary.org/obo/UBERON_0006215) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The interface between the dorsal neuroepithelium and the roofplate of the fourth ventricle. The source of a number of migratory neuron populations of the hindbrain.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -- [piriform cortex](http://purl.obolibrary.org/obo/UBERON_0004725) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "area prepiriformis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:165" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001440" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -- [piriform cortex](http://purl.obolibrary.org/obo/UBERON_0004725) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "palaeocortex II" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:165" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [piriform cortex](http://purl.obolibrary.org/obo/UBERON_0004725) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "eupalaeocortex" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### rhombomere `http://purl.obolibrary.org/obo/UBERON_0001892` +#### Removed +- [rhombomere](http://purl.obolibrary.org/obo/UBERON_0001892) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "DHBA divides this into A(1-3),B(4),C(5-7) and D(8)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:165" +- [rhombomere](http://purl.obolibrary.org/obo/UBERON_0001892) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A segment of the developing hindbrain. Kimmel et al, 1995.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -- [piriform cortex](http://purl.obolibrary.org/obo/UBERON_0004725) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "regio praepiriformis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001064" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:165" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -- [piriform cortex](http://purl.obolibrary.org/obo/UBERON_0004725) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cortex piriformis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Piriform_cortex" +- [rhombomere](http://purl.obolibrary.org/obo/UBERON_0001892) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Rhombomeric segmentation is found in all living vertebrates and is of fundamental importance to the development of the vertebrate head.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [piriform cortex](http://purl.obolibrary.org/obo/UBERON_0004725) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "area prepiriformis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:165" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [piriform cortex](http://purl.obolibrary.org/obo/UBERON_0004725) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "palaeocortex II" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000672" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:165" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1006/dbio.2002.0831 Mazet F, Shimeld SM, The Evolution of Chordate Neural Segmentation. Developmental Biology (2002)" +- [rhombomere](http://purl.obolibrary.org/obo/UBERON_0001892) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In human embryonic development, the rhombomeres are present by day 29" -### pituitary gland `http://purl.obolibrary.org/obo/UBERON_0000007` + + +### rhombomere 1 `http://purl.obolibrary.org/obo/UBERON_0005499` #### Removed -- [pituitary gland](http://purl.obolibrary.org/obo/UBERON_0000007) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "glandula pituitaria" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pituitary_gland" +- [rhombomere 1](http://purl.obolibrary.org/obo/UBERON_0005499) [UBPROP_0000111](http://purl.obolibrary.org/obo/UBPROP_0000111) "1"^^[nonNegativeInteger](http://www.w3.org/2001/XMLSchema#nonNegativeInteger) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [rhombomere 1](http://purl.obolibrary.org/obo/UBERON_0005499) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Hindbrain segment or neuromere. Kimmel et al, 1995.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -#### Added -- [pituitary gland](http://purl.obolibrary.org/obo/UBERON_0000007) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "glandula pituitaria" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001031" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pituitary_gland" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -### pituitary gland cell `http://purl.obolibrary.org/obo/CL_2000004` +- [rhombomere 1](http://purl.obolibrary.org/obo/UBERON_0005499) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [presumptive rhombomere 1](http://purl.obolibrary.org/obo/UBERON_0007289) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" #### Added -- [pituitary gland cell](http://purl.obolibrary.org/obo/CL_2000004) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [rhombomere 1](http://purl.obolibrary.org/obo/UBERON_0005499) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [presumptive rhombomere 1](http://purl.obolibrary.org/obo/UBERON_0007289) -### placental disc `http://purl.obolibrary.org/obo/UBERON_8600038` +### rhombomere boundary `http://purl.obolibrary.org/obo/UBERON_0018239` #### Added -- [placental disc](http://purl.obolibrary.org/obo/UBERON_8600038) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A disc-shaped structure that is part of the placenta. A placental disc supports fetal development through the exchange of nutrients between maternal and fetal bloodstreams. The placental disc is structured to keep the blood streams separate, while maximizing surface area for the transport of nutrients between them, to maintain an immunological barrier." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35496035" - -- [placental disc](http://purl.obolibrary.org/obo/UBERON_8600038) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) +- [rhombomere boundary](http://purl.obolibrary.org/obo/UBERON_0018239) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -- [placental disc](http://purl.obolibrary.org/obo/UBERON_8600038) [label](http://www.w3.org/2000/01/rdf-schema#label) "placental disc" -- [placental disc](http://purl.obolibrary.org/obo/UBERON_8600038) [date](http://purl.org/dc/terms/date) "2024-01-16T17:50:20Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +### rib `http://purl.obolibrary.org/obo/UBERON_0002228` +#### Removed +- [rib](http://purl.obolibrary.org/obo/UBERON_0002228) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In most vertebrates, ribs surround the chest. In some species, especially snakes, ribs may provide support and protection for the entire body" -- [placental disc](http://purl.obolibrary.org/obo/UBERON_8600038) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "placental disk" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30133439" +- [rib](http://purl.obolibrary.org/obo/UBERON_0002228) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Endochondral, rodlike element that articulates with the transverse process and parapophysis (double-headed rib), or with the transverse process only (single-headed rib); it extends into the body wall and provides a site for muscle attachment.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -- [placental disc](http://purl.obolibrary.org/obo/UBERON_8600038) [id](http://www.geneontology.org/formats/oboInOwl#id) "UBERON:8600038" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -- [placental disc](http://purl.obolibrary.org/obo/UBERON_8600038) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:Pugener_2002" -- Class: [placental disc](http://purl.obolibrary.org/obo/UBERON_8600038) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000545" -- [placental disc](http://purl.obolibrary.org/obo/UBERON_8600038) SubClassOf [anatomical structure](http://purl.obolibrary.org/obo/UBERON_0000061) +- [rib](http://purl.obolibrary.org/obo/UBERON_0002228) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Endochondral bone that is intersegmental and rod-shaped, forming in the peritoneal membrane and attached to the vertebral parapophyses. Ribs protect and support internal organs.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -- [placental disc](http://purl.obolibrary.org/obo/UBERON_8600038) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [placenta](http://purl.obolibrary.org/obo/UBERON_0001987) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -### placental villous stroma `http://purl.obolibrary.org/obo/UBERON_8600023` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000538" -#### Added -- [placental villous stroma](http://purl.obolibrary.org/obo/UBERON_8600023) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" +- [rib](http://purl.obolibrary.org/obo/UBERON_0002228) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "costal" -- [placental villous stroma](http://purl.obolibrary.org/obo/UBERON_8600023) [date](http://purl.org/dc/terms/date) "2023-07-04T10:46:17Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +- [rib](http://purl.obolibrary.org/obo/UBERON_0002228) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "They protect and support internal organs and enable lungs to expand by expanding the chest." -- [placental villous stroma](http://purl.obolibrary.org/obo/UBERON_8600023) [label](http://www.w3.org/2000/01/rdf-schema#label) "placental villous stroma" +- [rib](http://purl.obolibrary.org/obo/UBERON_0002228) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "VO:0012403" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -- [placental villous stroma](http://purl.obolibrary.org/obo/UBERON_8600023) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -- [placental villous stroma](http://purl.obolibrary.org/obo/UBERON_8600023) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "chorionic villous stroma" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:12624135" + - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) -- [placental villous stroma](http://purl.obolibrary.org/obo/UBERON_8600023) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-7655-4833](https://orcid.org/0000-0001-7655-4833) +- [rib](http://purl.obolibrary.org/obo/UBERON_0002228) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [rib cartilage element](http://purl.obolibrary.org/obo/UBERON_0006288) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" -- [placental villous stroma](http://purl.obolibrary.org/obo/UBERON_8600023) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "CVS" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:12624135" +#### Added +- [rib](http://purl.obolibrary.org/obo/UBERON_0002228) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [rib cartilage element](http://purl.obolibrary.org/obo/UBERON_0006288) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [abbreviation](http://purl.obolibrary.org/obo/OMO_0003000) -- [placental villous stroma](http://purl.obolibrary.org/obo/UBERON_8600023) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A stroma that is part of a chorionic villus (placental villus). A placental villous stroma supports the fetal capillaries and villous trophoblast." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31512233" +### rib endochondral element `http://purl.obolibrary.org/obo/UBERON_0015019` +#### Removed +- [rib endochondral element](http://purl.obolibrary.org/obo/UBERON_0015019) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Humans have 24 ribs (12 pairs). The first seven sets of ribs, known as 'true ribs', are directly attached to the sternum through the costal cartilage. The following five sets are known as 'false ribs', three of these sharing a common cartilaginous connection to the sternum, while the last two (eleventh and twelfth ribs) are termed floating ribs (costae fluitantes) or vertebral ribs. They are attached to the vertebrae only, and not to the sternum or cartilage coming off of the sternum. Some people are missing one of the two pairs of floating ribs, while others have a third pair. Rib removal is the surgical excision of ribs for therapeutic or cosmetic reasons. In fish, there are often two sets of ribs attached to the vertebral column. One set, the dorsal ribs, are found in the dividing septum between the upper and lower parts of the main muscle segments, projecting roughly sideways from the vertebral column. The second set, of ventral ribs arise from the vertebral column just below the dorsal ribs, and enclose the lower body, often joining at the tips. Not all species possess both types of rib, with the dorsal ribs being most commonly absent. Sharks, for example, have no dorsal ribs, and only very short ventral ribs, while lampreys have no ribs at all. In some teleosts, there may be additional rib-like bones within the muscle mass. Tetrapods, however, only ever have a single set of ribs which are probably homologous with the dorsal ribs of fishes. In the early tetrapods, every vertebra bore a pair of ribs, although those on the thoracic vertebrae are typically the longest. The sacral ribs were stout and short, since they formed part of the pelvis, connecting the backbone to the hip bones.[1] In most subsequent forms, many of these early ribs have been lost, and in living amphibians and reptiles, there is great variation in rib structure and number. For example, turtles have only eight pairs of ribs, which are developed into a bony or cartilagenous carapace and plastron, while snakes have numerous ribs running along the full length of their trunk. Frogs typically have no ribs, aside from a sacral pair, which form part of the pelvis.[1]. In birds, ribs are present as distinct bones only on the thoracic region, although small fused ribs are present on the cervical vertebrae. The thoracic ribs of birds possess a wide projection to the rear; this uncinate process is an attachment for the shoulder muscles.[1]. Mammals usually also only have distinct ribs on the thoracic vertebra, although fixed cervical ribs are also present in monotremes. In marsupials and placental mammals, the cervical and lumbar ribs are found only as tiny remnants fused to the vertebrae, where they are referred to as transverse processes. In general, the structure and number of the true ribs in humans is similar to that in other mammals. Unlike reptiles, caudal ribs are never found in mammals." -- [placental villous stroma](http://purl.obolibrary.org/obo/UBERON_8600023) [id](http://www.geneontology.org/formats/oboInOwl#id) "UBERON:8600023" -- Class: [placental villous stroma](http://purl.obolibrary.org/obo/UBERON_8600023) -- [placental villous stroma](http://purl.obolibrary.org/obo/UBERON_8600023) EquivalentTo [stroma](http://purl.obolibrary.org/obo/UBERON_0003891) and ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [chorionic villus](http://purl.obolibrary.org/obo/UBERON_0007106)) +### right adrenal gland `http://purl.obolibrary.org/obo/UBERON_0001233` +#### Removed +- [right adrenal gland](http://purl.obolibrary.org/obo/UBERON_0001233) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In humans, the right adrenal gland is triangular shaped" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" -- [placental villous stroma](http://purl.obolibrary.org/obo/UBERON_8600023) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [chorionic villus](http://purl.obolibrary.org/obo/UBERON_0007106) +- [right adrenal gland](http://purl.obolibrary.org/obo/UBERON_0001233) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) -- [placental villous stroma](http://purl.obolibrary.org/obo/UBERON_8600023) SubClassOf [stroma](http://purl.obolibrary.org/obo/UBERON_0003891) -### placental villous trophoblast `http://purl.obolibrary.org/obo/CL_2000060` +### right atrium valve `http://purl.obolibrary.org/obo/UBERON_0005208` #### Added -- [placental villous trophoblast](http://purl.obolibrary.org/obo/CL_2000060) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [right atrium valve](http://purl.obolibrary.org/obo/UBERON_0005208) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### plantar part of pes `http://purl.obolibrary.org/obo/UBERON_0008338` +### right atrium venous valve `http://purl.obolibrary.org/obo/UBERON_0010189` #### Removed -- [plantar part of pes](http://purl.obolibrary.org/obo/UBERON_0008338) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "regio plantaris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" - -- [plantar part of pes](http://purl.obolibrary.org/obo/UBERON_0008338) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "planta" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Sole_(foot)" +- [right atrium venous valve](http://purl.obolibrary.org/obo/UBERON_0010189) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "part_of in EHDAA2. Only child in MA." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EHDAA2" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [plantar part of pes](http://purl.obolibrary.org/obo/UBERON_0008338) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "planta" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### right bundle branch `http://purl.obolibrary.org/obo/UBERON_0005987` #### Added -- [plantar part of pes](http://purl.obolibrary.org/obo/UBERON_0008338) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "planta" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" - -- [plantar part of pes](http://purl.obolibrary.org/obo/UBERON_0008338) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "planta" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [right bundle branch](http://purl.obolibrary.org/obo/UBERON_0005987) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Sole_(foot)" -- [plantar part of pes](http://purl.obolibrary.org/obo/UBERON_0008338) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "regio plantaris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### right cardiac atrium `http://purl.obolibrary.org/obo/UBERON_0002078` +#### Removed +- [right cardiac atrium](http://purl.obolibrary.org/obo/UBERON_0002078) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Right cardiac chamber which is continuous with the superior vena cava and inferior vena cava.[FMA]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:7096" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [right cardiac atrium](http://purl.obolibrary.org/obo/UBERON_0002078) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) +- [right cardiac atrium](http://purl.obolibrary.org/obo/UBERON_0002078) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000328" -### plasma cell `http://purl.obolibrary.org/obo/CL_0000786` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [plasma cell](http://purl.obolibrary.org/obo/CL_0000786) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### plasma membrane `http://purl.obolibrary.org/obo/GO_0005886` -#### Removed -- [plasma membrane](http://purl.obolibrary.org/obo/GO_0005886) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620" -#### Added -- [plasma membrane](http://purl.obolibrary.org/obo/GO_0005886) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) -### plasmablast `http://purl.obolibrary.org/obo/CL_0000980` +### right cardiac chamber `http://purl.obolibrary.org/obo/UBERON_0035554` #### Added -- [plasmablast](http://purl.obolibrary.org/obo/CL_0000980) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [right cardiac chamber](http://purl.obolibrary.org/obo/UBERON_0035554) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) -### plasmacytoid dendritic cell `http://purl.obolibrary.org/obo/CL_0000784` +### right cerebral hemisphere `http://purl.obolibrary.org/obo/UBERON_0002813` +#### Removed +- [right cerebral hemisphere](http://purl.obolibrary.org/obo/UBERON_0002813) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) -#### Added -- [plasmacytoid dendritic cell](http://purl.obolibrary.org/obo/CL_0000784) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### plasmacytoid dendritic cell, human `http://purl.obolibrary.org/obo/CL_0001058` +### right clavicle `http://purl.obolibrary.org/obo/UBERON_0008255` +#### Removed +- [right clavicle](http://purl.obolibrary.org/obo/UBERON_0008255) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) -#### Added -- [plasmacytoid dendritic cell, human](http://purl.obolibrary.org/obo/CL_0001058) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### plasmatocyte `http://purl.obolibrary.org/obo/CL_0000394` +### right common carotid artery plus branches `http://purl.obolibrary.org/obo/UBERON_0001531` +#### Removed +- [right common carotid artery plus branches](http://purl.obolibrary.org/obo/UBERON_0001531) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "placement of the MA class here is not strictly correct, as the MA class does not include the branches" -#### Added -- [plasmatocyte](http://purl.obolibrary.org/obo/CL_0000394) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### platelet `http://purl.obolibrary.org/obo/CL_0000233` +### right common iliac artery `http://purl.obolibrary.org/obo/UBERON_0035322` #### Added -- [platelet](http://purl.obolibrary.org/obo/CL_0000233) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [right common iliac artery](http://purl.obolibrary.org/obo/UBERON_0035322) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) -### pleural cavity `http://purl.obolibrary.org/obo/UBERON_0002402` +### right crus of diaphragm `http://purl.obolibrary.org/obo/UBERON_0014766` #### Removed -- [pleural cavity](http://purl.obolibrary.org/obo/UBERON_0002402) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cavitum pleurale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pleural_cavity" +- [right crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014766) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "external sphincter of esophagus" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58286" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [right crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014766) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "right crus of lumbar part of diaphragm" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58286" -- [pleural cavity](http://purl.obolibrary.org/obo/UBERON_0002402) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cavitas pleuralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pleural_cavity" +- [right crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014766) [id](http://www.geneontology.org/formats/oboInOwl#id) "UBERON:0014766" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [right crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014766) [label](http://www.w3.org/2000/01/rdf-schema#label) "right crus of diaphragm" -- [pleural cavity](http://purl.obolibrary.org/obo/UBERON_0002402) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cavitum pleuralae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pleural_cavity" +- [right crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014766) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [right crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014766) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "SCTID:362690009" -#### Added -- [pleural cavity](http://purl.obolibrary.org/obo/UBERON_0002402) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cavitum pleuralae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [right crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014766) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pleural_cavity" +- [right crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014766) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A crus of diaphragm that is in_the_right_side_of a diaphragm." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "OBOL:automatic" -- [pleural cavity](http://purl.obolibrary.org/obo/UBERON_0002402) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cavitum pleurale" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [right crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014766) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "right crus of diaphragm" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58286" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pleural_cavity" +- [right crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014766) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58286" -- [pleural cavity](http://purl.obolibrary.org/obo/UBERON_0002402) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cavitas pleuralis" +- [right crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014766) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "crus dextrum diaphragmatis" - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pleural_cavity" - - -### pneumocyte `http://purl.obolibrary.org/obo/CL_0000322` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58286" -#### Added -- [pneumocyte](http://purl.obolibrary.org/obo/CL_0000322) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [right crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014766) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "crus dextrum (Diaphragma)" + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### podocyte `http://purl.obolibrary.org/obo/CL_0000653` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58286" -#### Added -- [podocyte](http://purl.obolibrary.org/obo/CL_0000653) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- Class: [right crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014766) -### pons `http://purl.obolibrary.org/obo/UBERON_0000988` -#### Removed -- [pons](http://purl.obolibrary.org/obo/UBERON_0000988) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pons cerebri" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:547" +- [right crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014766) EquivalentTo [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) and ([in right side of](http://purl.obolibrary.org/obo/BSPO_0000121) some [diaphragm](http://purl.obolibrary.org/obo/UBERON_0001103)) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [right crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014766) SubClassOf [in right side of](http://purl.obolibrary.org/obo/BSPO_0000121) some [diaphragm](http://purl.obolibrary.org/obo/UBERON_0001103) -#### Added -- [pons](http://purl.obolibrary.org/obo/UBERON_0000988) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pons cerebri" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [right crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014766) SubClassOf [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:547" -### pontine raphe nucleus `http://purl.obolibrary.org/obo/UBERON_0002047` +### right dorsal aorta `http://purl.obolibrary.org/obo/UBERON_0005622` #### Removed -- [pontine raphe nucleus](http://purl.obolibrary.org/obo/UBERON_0002047) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus raphe pontis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:589" +- [right dorsal aorta](http://purl.obolibrary.org/obo/UBERON_0005622) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Normally regresses in humans" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://emedicine.medscape.com/article/899609-overview" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [right dorsal aorta](http://purl.obolibrary.org/obo/UBERON_0005622) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "A study of embryos shows that in all vertebrates six arterial arches link the ventral aorta with a pair of lateral dorsal aortae on each side of the body. The latter unite posteriorly to form a single median dorsal aorta wich takes blood to the body.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000485" -- [pontine raphe nucleus](http://purl.obolibrary.org/obo/UBERON_0002047) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus raphes pontis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pontine_raphe_nucleus" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [pontine raphe nucleus](http://purl.obolibrary.org/obo/UBERON_0002047) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "raphe (mediana pontina)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:589" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0174480198 Roberts MBV, Biology: a functional approach (1986) p.572" -- [pontine raphe nucleus](http://purl.obolibrary.org/obo/UBERON_0002047) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "raphe pontis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:68875" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### right dorsal thalamus `http://purl.obolibrary.org/obo/UBERON_0013684` +#### Removed +- [right dorsal thalamus](http://purl.obolibrary.org/obo/UBERON_0013684) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) #### Added -- [pontine raphe nucleus](http://purl.obolibrary.org/obo/UBERON_0002047) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus raphe pontis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:589" +- [right dorsal thalamus](http://purl.obolibrary.org/obo/UBERON_0013684) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -- [pontine raphe nucleus](http://purl.obolibrary.org/obo/UBERON_0002047) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "raphe pontis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:68875" +### right ear `http://purl.obolibrary.org/obo/UBERON_0035174` - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +#### Added +- [right ear](http://purl.obolibrary.org/obo/UBERON_0035174) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [pontine raphe nucleus](http://purl.obolibrary.org/obo/UBERON_0002047) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "raphe (mediana pontina)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:589" +### right external ear `http://purl.obolibrary.org/obo/UBERON_0006616` +#### Removed +- [right external ear](http://purl.obolibrary.org/obo/UBERON_0006616) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) + - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -- [pontine raphe nucleus](http://purl.obolibrary.org/obo/UBERON_0002047) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus raphes pontis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pontine_raphe_nucleus" +### right eye `http://purl.obolibrary.org/obo/UBERON_0004549` +#### Removed +- [right eye](http://purl.obolibrary.org/obo/UBERON_0004549) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +#### Added +- [right eye](http://purl.obolibrary.org/obo/UBERON_0004549) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) -### pontine tegmentum `http://purl.obolibrary.org/obo/UBERON_0003023` +### right forelimb `http://purl.obolibrary.org/obo/UBERON_8300001` #### Removed -- [pontine tegmentum](http://purl.obolibrary.org/obo/UBERON_0003023) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pars posterior pontis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:557" +- [right forelimb](http://purl.obolibrary.org/obo/UBERON_8300001) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +#### Added +- [right forelimb](http://purl.obolibrary.org/obo/UBERON_8300001) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) -- [pontine tegmentum](http://purl.obolibrary.org/obo/UBERON_0003023) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tegmentum pontis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pontine_tegmentum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### right hepatic duct `http://purl.obolibrary.org/obo/UBERON_0001176` +#### Removed +- [right hepatic duct](http://purl.obolibrary.org/obo/UBERON_0001176) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The duct which drains bile from the right half of the liver and unites with the left hepatic duct to form the common hepatic duct. [adapted_from_http://www.medterms.com/script/main/art.asp?articlekey=26032][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [pontine tegmentum](http://purl.obolibrary.org/obo/UBERON_0003023) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tegmentum pontis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71108" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000217" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [pontine tegmentum](http://purl.obolibrary.org/obo/UBERON_0003023) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pars dorsalis pontis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:557" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [pontine tegmentum](http://purl.obolibrary.org/obo/UBERON_0003023) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D065821" +### right hindlimb `http://purl.obolibrary.org/obo/UBERON_8300003` +#### Removed +- [right hindlimb](http://purl.obolibrary.org/obo/UBERON_8300003) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) #### Added -- [pontine tegmentum](http://purl.obolibrary.org/obo/UBERON_0003023) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tegmentum pontis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pontine_tegmentum" +- [right hindlimb](http://purl.obolibrary.org/obo/UBERON_8300003) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) -- [pontine tegmentum](http://purl.obolibrary.org/obo/UBERON_0003023) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pars dorsalis pontis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:557" +### right horn of sinus venosus `http://purl.obolibrary.org/obo/UBERON_0005092` +#### Removed +- [right horn of sinus venosus](http://purl.obolibrary.org/obo/UBERON_0005092) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Three major adaptations, or 'novel cardiac components', that were not present in the ancestor chordate heart tube can be distinguished in the lower vertebrate heart: the atrium, ventricle, and possibly the muscular sinus venosus.[uncertain][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [pontine tegmentum](http://purl.obolibrary.org/obo/UBERON_0003023) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tegmentum pontis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71108" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1152/physrev.00006.2003 Moorman AFM, Christoffels VM, Cardiac Chamber Formation: Development, Genes, and Evolution. Physiological Reviews (2003" -- [pontine tegmentum](http://purl.obolibrary.org/obo/UBERON_0003023) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pars posterior pontis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000489" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:557" -- [pontine tegmentum](http://purl.obolibrary.org/obo/UBERON_0003023) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D065821" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) +### right kidney `http://purl.obolibrary.org/obo/UBERON_0004539` +#### Removed +- [right kidney](http://purl.obolibrary.org/obo/UBERON_0004539) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -### popliteal vein `http://purl.obolibrary.org/obo/UBERON_0001544` +### right lateral ventricle `http://purl.obolibrary.org/obo/UBERON_0013162` #### Removed -- [popliteal vein](http://purl.obolibrary.org/obo/UBERON_0001544) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena poplitea" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Popliteal_vein" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [right lateral ventricle](http://purl.obolibrary.org/obo/UBERON_0013162) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) #### Added -- [popliteal vein](http://purl.obolibrary.org/obo/UBERON_0001544) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena poplitea" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [right lateral ventricle](http://purl.obolibrary.org/obo/UBERON_0013162) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Popliteal_vein" - -### portal triad `http://purl.obolibrary.org/obo/UBERON_0001279` +### right lobe of liver `http://purl.obolibrary.org/obo/UBERON_0001114` #### Removed -- [portal triad](http://purl.obolibrary.org/obo/UBERON_0001279) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "trias hepatica" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Portal_triad" +- [right lobe of liver](http://purl.obolibrary.org/obo/UBERON_0001114) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Portion of the liver which develops on the fish's right side adjacent to the gall bladder.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005173" -#### Added -- [portal triad](http://purl.obolibrary.org/obo/UBERON_0001279) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "trias hepatica" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Portal_triad" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### positive regulation of amino acid biosynthetic process `http://purl.obolibrary.org/obo/GO_2000284` +### right lobe of thyroid gland `http://purl.obolibrary.org/obo/UBERON_0001119` #### Removed -- [positive regulation of amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000284) [created by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" +- [right lobe of thyroid gland](http://purl.obolibrary.org/obo/UBERON_0001119) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) -- [positive regulation of amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000284) [label](http://www.w3.org/2000/01/rdf-schema#label) "positive regulation of amino acid biosynthetic process" +- [right lobe of thyroid gland](http://purl.obolibrary.org/obo/UBERON_0001119) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Thus, a thyroid capable of forming iodotyrosines and iodothyronines is present in all vertebrates. (...) Certain morphologic changes occur after the biochemical evolution of the thyroid has ceased. In the adult lamprey and in most bony fishes, the gland is not encapsulated. (...) In cartilaginous fish, the thyroid is encapsulated. In the higher vertebrate forms, the thyroid is a one- or two-lobed encapsulated structure.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [positive regulation of amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000284) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any process that activates or increases the frequency, rate or extent of cellular amino acid biosynthetic process." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:obol" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [positive regulation of amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000284) [creation date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2010-12-10T11:54:27Z" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [positive regulation of amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000284) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:2000284" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000733" -- [positive regulation of amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000284) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "positive regulation of amino acid anabolism" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:obol" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://www.thyroidmanager.org/Chapter1/chapter01.htm" -- [positive regulation of amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000284) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "positive regulation of cellular amino acid biosynthetic process" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:obol" -- [positive regulation of amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000284) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "positive regulation of amino acid formation" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:obol" -- [positive regulation of amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000284) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "positive regulation of amino acid biosynthesis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:obol" +### right lung `http://purl.obolibrary.org/obo/UBERON_0002167` +#### Removed +- [right lung](http://purl.obolibrary.org/obo/UBERON_0002167) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) + +- [right lung](http://purl.obolibrary.org/obo/UBERON_0002167) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [positive regulation of amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000284) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "positive regulation of amino acid synthesis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:obol" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [positive regulation of amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000284) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000301" -- Class: [positive regulation of amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000284) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.210" -- [positive regulation of amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000284) EquivalentTo [biological regulation](http://purl.obolibrary.org/obo/GO_0065007) and ([positively regulates](http://purl.obolibrary.org/obo/RO_0002213) some [amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_0008652)) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [positive regulation of amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000284) SubClassOf [positively regulates](http://purl.obolibrary.org/obo/RO_0002213) some [amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_0008652) -- [positive regulation of amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000284) SubClassOf [regulation of cellular amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000282) -- [positive regulation of amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000284) SubClassOf [positive regulation of amino acid metabolic process](http://purl.obolibrary.org/obo/GO_0045764) +### right lung alveolar system `http://purl.obolibrary.org/obo/UBERON_0006526` -- [positive regulation of amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000284) SubClassOf [positive regulation of biosynthetic process](http://purl.obolibrary.org/obo/GO_0009891) +#### Added +- [right lung alveolar system](http://purl.obolibrary.org/obo/UBERON_0006526) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) +### right lung endothelium `http://purl.obolibrary.org/obo/UBERON_0005672` -### positive regulation of amino acid metabolic process `http://purl.obolibrary.org/obo/GO_0045764` -#### Removed -- [positive regulation of amino acid metabolic process](http://purl.obolibrary.org/obo/GO_0045764) SubClassOf [positive regulation of nitrogen compound metabolic process](http://purl.obolibrary.org/obo/GO_0051173) +#### Added +- [right lung endothelium](http://purl.obolibrary.org/obo/UBERON_0005672) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) -- [positive regulation of amino acid metabolic process](http://purl.obolibrary.org/obo/GO_0045764) SubClassOf [positive regulation of cellular metabolic process](http://purl.obolibrary.org/obo/GO_0031325) -- [positive regulation of amino acid metabolic process](http://purl.obolibrary.org/obo/GO_0045764) SubClassOf [positive regulation of small molecule metabolic process](http://purl.obolibrary.org/obo/GO_0062013) +### right lung lobe `http://purl.obolibrary.org/obo/UBERON_0006518` +#### Removed +- [right lung lobe](http://purl.obolibrary.org/obo/UBERON_0006518) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "4 in mice, divided into 3 in human by two interlobal fissures" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0123813611" -### positive regulation of calcium ion import `http://purl.obolibrary.org/obo/GO_0090280` +### right nipple `http://purl.obolibrary.org/obo/UBERON_0013773` +#### Removed +- [right nipple](http://purl.obolibrary.org/obo/UBERON_0013773) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) #### Added -- [positive regulation of calcium ion import](http://purl.obolibrary.org/obo/GO_0090280) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any process that increases the rate, frequency, or extent of the directed movement of calcium ions into a cell or organelle." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:BHF" +- [right nipple](http://purl.obolibrary.org/obo/UBERON_0013773) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) + -- [positive regulation of calcium ion import](http://purl.obolibrary.org/obo/GO_0090280) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:0090280" +### right ovary `http://purl.obolibrary.org/obo/UBERON_0002118` +#### Removed +- [right ovary](http://purl.obolibrary.org/obo/UBERON_0002118) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) -- [positive regulation of calcium ion import](http://purl.obolibrary.org/obo/GO_0090280) [label](http://www.w3.org/2000/01/rdf-schema#label) "positive regulation of calcium ion import" +#### Added +- [right ovary](http://purl.obolibrary.org/obo/UBERON_0002118) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) -- [positive regulation of calcium ion import](http://purl.obolibrary.org/obo/GO_0090280) [creation date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2010-02-08T05:11:20Z" -- [positive regulation of calcium ion import](http://purl.obolibrary.org/obo/GO_0090280) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "positive regulation of transmembrane calcium influx" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tb" +### right pelvic girdle region `http://purl.obolibrary.org/obo/UBERON_0011092` +#### Removed +- [right pelvic girdle region](http://purl.obolibrary.org/obo/UBERON_0011092) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) -- [positive regulation of calcium ion import](http://purl.obolibrary.org/obo/GO_0090280) [created by](http://www.geneontology.org/formats/oboInOwl#created_by) "tb" -- [positive regulation of calcium ion import](http://purl.obolibrary.org/obo/GO_0090280) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" -- Class: [positive regulation of calcium ion import](http://purl.obolibrary.org/obo/GO_0090280) +### right pulmonary vein `http://purl.obolibrary.org/obo/UBERON_0009032` +#### Removed +- [right pulmonary vein](http://purl.obolibrary.org/obo/UBERON_0009032) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A vein that returns oxygenated blood from the right lung to the left atrium of the heart[ncithesaurus:Right_Pulmonary_Vein]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ncithesaurus:Right_Pulmonary_Vein" -- [positive regulation of calcium ion import](http://purl.obolibrary.org/obo/GO_0090280) EquivalentTo [biological regulation](http://purl.obolibrary.org/obo/GO_0065007) and ([positively regulates](http://purl.obolibrary.org/obo/RO_0002213) some [calcium ion import](http://purl.obolibrary.org/obo/GO_0070509)) -- [positive regulation of calcium ion import](http://purl.obolibrary.org/obo/GO_0090280) SubClassOf [positive regulation of calcium ion transport](http://purl.obolibrary.org/obo/GO_0051928) -- [positive regulation of calcium ion import](http://purl.obolibrary.org/obo/GO_0090280) SubClassOf [regulation of calcium ion import](http://purl.obolibrary.org/obo/GO_0090279) +### right recurrent laryngeal nerve `http://purl.obolibrary.org/obo/UBERON_0011767` -- [positive regulation of calcium ion import](http://purl.obolibrary.org/obo/GO_0090280) SubClassOf [positively regulates](http://purl.obolibrary.org/obo/RO_0002213) some [calcium ion import](http://purl.obolibrary.org/obo/GO_0070509) +#### Added +- [right recurrent laryngeal nerve](http://purl.obolibrary.org/obo/UBERON_0011767) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) -### positive regulation of calcium ion import across plasma membrane `http://purl.obolibrary.org/obo/GO_1905665` +### right renal pelvis `http://purl.obolibrary.org/obo/UBERON_0018116` #### Added -- [positive regulation of calcium ion import across plasma membrane](http://purl.obolibrary.org/obo/GO_1905665) SubClassOf [positive regulation of calcium ion import](http://purl.obolibrary.org/obo/GO_0090280) +- [right renal pelvis](http://purl.obolibrary.org/obo/UBERON_0018116) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### positive regulation of cytoplasmic transport `http://purl.obolibrary.org/obo/GO_1903651` +### right renal vein `http://purl.obolibrary.org/obo/UBERON_0001141` #### Removed -- [positive regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903651) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "up regulation of cytoplasmic streaming" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" +- [right renal vein](http://purl.obolibrary.org/obo/UBERON_0001141) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A vein that drains blood from the right kidney into the inferior vena cava[ncithesaurus]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ncithesaurus:Right_Renal_Vein" + -- [positive regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903651) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "activation of cytoplasmic transport" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" -- [positive regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903651) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any process that activates or increases the frequency, rate or extent of cytoplasmic transport." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" +### right side of back `http://purl.obolibrary.org/obo/UBERON_8000007` + +#### Added +- [right side of back](http://purl.obolibrary.org/obo/UBERON_8000007) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:25049409" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO_REF:0000058" +### right subclavian artery `http://purl.obolibrary.org/obo/UBERON_0001534` +#### Removed +- [right subclavian artery](http://purl.obolibrary.org/obo/UBERON_0001534) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "proximal part arises from right 4th aortic arch in humans" -- [positive regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903651) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "up regulation of cytoplasmic transport" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" +- [right subclavian artery](http://purl.obolibrary.org/obo/UBERON_0001534) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "in humans, arises from the relatively short brachiocephalic artery (trunk) when it bifurcates into the subclavian and the right common carotid artery" -- [positive regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903651) [created by](http://www.geneontology.org/formats/oboInOwl#created_by) "jl" +#### Added +- [right subclavian artery](http://purl.obolibrary.org/obo/UBERON_0001534) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) -- [positive regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903651) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "activation of cytoplasmic streaming" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" -- [positive regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903651) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "up-regulation of cytoplasmic transport" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" +### right suprarenal vein `http://purl.obolibrary.org/obo/UBERON_0035435` -- [positive regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903651) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" +#### Added +- [right suprarenal vein](http://purl.obolibrary.org/obo/UBERON_0035435) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) -- [positive regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903651) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "upregulation of cytoplasmic transport" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" -- [positive regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903651) [creation date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2014-11-24T13:38:34Z" +### right testis `http://purl.obolibrary.org/obo/UBERON_0004534` +#### Removed +- [right testis](http://purl.obolibrary.org/obo/UBERON_0004534) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) -- [positive regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903651) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:1903651" +#### Added +- [right testis](http://purl.obolibrary.org/obo/UBERON_0004534) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) -- [positive regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903651) [label](http://www.w3.org/2000/01/rdf-schema#label) "positive regulation of cytoplasmic transport" -- [positive regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903651) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "upregulation of cytoplasmic streaming" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" +### right thymus lobe `http://purl.obolibrary.org/obo/UBERON_0005469` +#### Removed +- [right thymus lobe](http://purl.obolibrary.org/obo/UBERON_0005469) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) -- [positive regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903651) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "positive regulation of cytoplasmic streaming" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" -- [positive regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903651) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "up-regulation of cytoplasmic streaming" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" -- Class: [positive regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903651) +### right umbilical artery `http://purl.obolibrary.org/obo/UBERON_0005470` +#### Removed +- [right umbilical artery](http://purl.obolibrary.org/obo/UBERON_0005470) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [right dorsal aorta](http://purl.obolibrary.org/obo/UBERON_0005622) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "EHDAA2" -- [positive regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903651) EquivalentTo [biological regulation](http://purl.obolibrary.org/obo/GO_0065007) and ([positively regulates](http://purl.obolibrary.org/obo/RO_0002213) some [cytosolic transport](http://purl.obolibrary.org/obo/GO_0016482)) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "check this" -- [positive regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903651) SubClassOf [regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903649) +- [right umbilical artery](http://purl.obolibrary.org/obo/UBERON_0005470) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [right extraembryonic umbilical artery](http://purl.obolibrary.org/obo/UBERON_0011697) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "EHDAA2" -- [positive regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903651) SubClassOf [positive regulation of intracellular transport](http://purl.obolibrary.org/obo/GO_0032388) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "check this" -- [positive regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903651) SubClassOf [positively regulates](http://purl.obolibrary.org/obo/RO_0002213) some [cytosolic transport](http://purl.obolibrary.org/obo/GO_0016482) +#### Added +- [right umbilical artery](http://purl.obolibrary.org/obo/UBERON_0005470) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [right dorsal aorta](http://purl.obolibrary.org/obo/UBERON_0005622) +- [right umbilical artery](http://purl.obolibrary.org/obo/UBERON_0005470) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [right extraembryonic umbilical artery](http://purl.obolibrary.org/obo/UBERON_0011697) -### positive regulation of dense core granule transport `http://purl.obolibrary.org/obo/GO_1904811` +### right umbilical vein `http://purl.obolibrary.org/obo/UBERON_0005471` #### Removed -- [positive regulation of dense core granule transport](http://purl.obolibrary.org/obo/GO_1904811) SubClassOf [positive regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903651) +- [right umbilical vein](http://purl.obolibrary.org/obo/UBERON_0005471) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) #### Added -- [positive regulation of dense core granule transport](http://purl.obolibrary.org/obo/GO_1904811) SubClassOf [positive regulation of intracellular transport](http://purl.obolibrary.org/obo/GO_0032388) +- [right umbilical vein](http://purl.obolibrary.org/obo/UBERON_0005471) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) + +### right ureter `http://purl.obolibrary.org/obo/UBERON_0001222` +#### Removed +- [right ureter](http://purl.obolibrary.org/obo/UBERON_0001222) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) -### positive regulation of gamma-aminobutyric acid catabolic process `http://purl.obolibrary.org/obo/GO_1901717` -#### Added -- [positive regulation of gamma-aminobutyric acid catabolic process](http://purl.obolibrary.org/obo/GO_1901717) SubClassOf [positive regulation of cellular metabolic process](http://purl.obolibrary.org/obo/GO_0031325) -- [positive regulation of gamma-aminobutyric acid catabolic process](http://purl.obolibrary.org/obo/GO_1901717) SubClassOf [positive regulation of small molecule metabolic process](http://purl.obolibrary.org/obo/GO_0062013) +### right uterine tube `http://purl.obolibrary.org/obo/UBERON_0001302` +#### Removed +- [right uterine tube](http://purl.obolibrary.org/obo/UBERON_0001302) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) + +- [right uterine tube](http://purl.obolibrary.org/obo/UBERON_0001302) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "non-functional in monotremes[ISBN:978-0226870137]" -### positive regulation of glutamate metabolic process `http://purl.obolibrary.org/obo/GO_2000213` + +### right vagus X nerve trunk `http://purl.obolibrary.org/obo/UBERON_0035021` #### Added -- [positive regulation of glutamate metabolic process](http://purl.obolibrary.org/obo/GO_2000213) SubClassOf [positive regulation of small molecule metabolic process](http://purl.obolibrary.org/obo/GO_0062013) +- [right vagus X nerve trunk](http://purl.obolibrary.org/obo/UBERON_0035021) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) + + +### right ventricle myocardium `http://purl.obolibrary.org/obo/UBERON_0006567` +#### Removed +- [right ventricle myocardium](http://purl.obolibrary.org/obo/UBERON_0006567) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:17342" -- [positive regulation of glutamate metabolic process](http://purl.obolibrary.org/obo/GO_2000213) SubClassOf [positive regulation of cellular metabolic process](http://purl.obolibrary.org/obo/GO_0031325) +- [right ventricle myocardium](http://purl.obolibrary.org/obo/UBERON_0006567) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Myocardium of ventricle which is continuous with the tunica media of the pulmonary trunk." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:9535" -### positive regulation of nitric oxide biosynthetic process `http://purl.obolibrary.org/obo/GO_0045429` + +### right vitelline vein `http://purl.obolibrary.org/obo/UBERON_0005472` #### Removed -- [positive regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045429) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "up-regulation of nitric oxide biosynthetic process" +- [right vitelline vein](http://purl.obolibrary.org/obo/UBERON_0005472) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) + +#### Added +- [right vitelline vein](http://purl.obolibrary.org/obo/UBERON_0005472) SubClassOf [lateral structure](http://purl.obolibrary.org/obo/UBERON_0015212) + -- [positive regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045429) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of nitric oxide." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:go_curators" +### role of `http://purl.obolibrary.org/obo/RO_0000081` +#### Removed +- [role of](http://purl.obolibrary.org/obo/RO_0000081) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "role_of"@en -- [positive regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045429) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:0045429" +- [role of](http://purl.obolibrary.org/obo/RO_0000081) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "this investigator role is a role of this person"@en -- [positive regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045429) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "positive regulation of nitric oxide biosynthesis" +- [role of](http://purl.obolibrary.org/obo/RO_0000081) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "is role of"@en -- [positive regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045429) [label](http://www.w3.org/2000/01/rdf-schema#label) "positive regulation of nitric oxide biosynthetic process" -- [positive regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045429) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" -- [positive regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045429) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "positive regulation of nitric oxide formation" +### root of vagus nerve `http://purl.obolibrary.org/obo/UBERON_0011213` +#### Removed +- [root of vagus nerve](http://purl.obolibrary.org/obo/UBERON_0011213) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA distinguishes between roots and rootlets - we mix the two here" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" -- [positive regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045429) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "stimulation of nitric oxide biosynthetic process" -- [positive regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045429) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "positive regulation of nitric oxide anabolism" -- [positive regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045429) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "positive regulation of nitric oxide synthesis" +### runt-related transcription factor 1 `http://purl.obolibrary.org/obo/PR_000014362` +#### Removed +- [runt-related transcription factor 1](http://purl.obolibrary.org/obo/PR_000014362) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [runt-related transcription factor 1 (human)](http://purl.obolibrary.org/obo/PR_Q01196) -- [positive regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045429) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "activation of nitric oxide biosynthetic process" -- [positive regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045429) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "up regulation of nitric oxide biosynthetic process" -- [positive regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045429) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "upregulation of nitric oxide biosynthetic process" +### saccharomyceta `http://purl.obolibrary.org/obo/NCBITaxon_716545` +#### Removed +- [saccharomyceta](http://purl.obolibrary.org/obo/NCBITaxon_716545) [has_rank](http://purl.obolibrary.org/obo/ncbitaxon#has_rank) [NCBITaxon_clade](http://purl.obolibrary.org/obo/NCBITaxon_clade) -- Class: [positive regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045429) -- [positive regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045429) EquivalentTo [biological regulation](http://purl.obolibrary.org/obo/GO_0065007) and ([positively regulates](http://purl.obolibrary.org/obo/RO_0002213) some [nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0006809)) -- [positive regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045429) SubClassOf [positive regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904407) +### saccule of membranous labyrinth `http://purl.obolibrary.org/obo/UBERON_0001854` +#### Removed +- [saccule of membranous labyrinth](http://purl.obolibrary.org/obo/UBERON_0001854) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The most ventral chamber of the membranous labyrinth. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-25, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [positive regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045429) SubClassOf [positive regulation of nitrogen compound metabolic process](http://purl.obolibrary.org/obo/GO_0051173) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [positive regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045429) SubClassOf [positively regulates](http://purl.obolibrary.org/obo/RO_0002213) some [nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0006809) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000374" -- [positive regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045429) SubClassOf [regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045428) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [positive regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045429) SubClassOf [positive regulation of cellular biosynthetic process](http://purl.obolibrary.org/obo/GO_0031328) +- [saccule of membranous labyrinth](http://purl.obolibrary.org/obo/UBERON_0001854) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In gnathostomes, each membranous labyrinth has three semicircular ducts that connect with a chamber known as the utriculus. (...) In all gnathostomes, the utriculus connects ventrally with a larger sac, called the sacculus (...) .[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000374" -### positive regulation of nitric oxide metabolic process `http://purl.obolibrary.org/obo/GO_1904407` -#### Removed -- [positive regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904407) [created by](http://www.geneontology.org/formats/oboInOwl#created_by) "sl" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [positive regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904407) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "up-regulation of nitric oxide metabolic process" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.413-414" -- [positive regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904407) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" -- [positive regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904407) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "up regulation of nitric oxide metabolic process" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" -- [positive regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904407) [creation date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2015-06-24T20:56:47Z" +### sacral neural crest `http://purl.obolibrary.org/obo/UBERON_0010075` -- [positive regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904407) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "upregulation of nitric oxide metabolic process" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" +#### Added +- [sacral neural crest](http://purl.obolibrary.org/obo/UBERON_0010075) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -- [positive regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904407) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "activation of nitric oxide metabolism" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" -- [positive regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904407) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:1904407" +### saliva `http://purl.obolibrary.org/obo/UBERON_0001836` +#### Removed +- [saliva](http://purl.obolibrary.org/obo/UBERON_0001836) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "salivary" -- [positive regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904407) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any process that activates or increases the frequency, rate or extent of nitric oxide metabolic process." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:11991626" +- [saliva](http://purl.obolibrary.org/obo/UBERON_0001836) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "We classify a wide variety of not necessarily homologous fluids here. In humans, the saliva is a turbid and slightly viscous fluid, generally of an alkaline reaction, and is secreted by the parotid, submaxillary, and sublingual glands. In the mouth the saliva is mixed with the secretion from the buccal glands. In man and many animals, saliva is an important digestive fluid on account of the presence of the peculiar enzyme, ptyalin" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO_REF:0000058" -- [positive regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904407) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "activation of nitric oxide metabolic process" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" +### saliva-secreting gland `http://purl.obolibrary.org/obo/UBERON_0001044` +#### Removed +- [saliva-secreting gland](http://purl.obolibrary.org/obo/UBERON_0001044) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In air-feeding animals, the lack of water column to lubricate the food has been compensated for by the evolution of the salivary glands. These glands are present only in amniotes and are controlled by the parasympathetic system.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000376" -- [positive regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904407) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "upregulation of nitric oxide metabolism" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptationm(2005) p.211" -- [positive regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904407) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "up-regulation of nitric oxide metabolism" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [positive regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904407) [label](http://www.w3.org/2000/01/rdf-schema#label) "positive regulation of nitric oxide metabolic process" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [positive regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904407) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "up regulation of nitric oxide metabolism" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [positive regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904407) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "positive regulation of nitric oxide metabolism" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" +- [saliva-secreting gland](http://purl.obolibrary.org/obo/UBERON_0001044) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "currently we define saliva and salivary glands very generally in functional terms but it may be more appropriate to split this class. From WP: In most vertebrates, saliva does not contain any enzymes, consisting of mucus and water only, and its primary function is to moisten food while eating. As a result, true salivary glands are rarely found in fish or aquatic tetrapods, although there are often individual mucus-secreting cells. Amphibians have a single salivary gland, the intermaxillary gland, located in the forward part of the palate. Reptiles and birds normally have only very small glands on the lips, palate, and base of the mouth, although there are some birds with large glands, which produce a sticky saliva that helps in nest-building. The distinct parotid, submandibular, and sublingual glands are only developed in mammals." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "3" -- Class: [positive regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904407) +- [saliva-secreting gland](http://purl.obolibrary.org/obo/UBERON_0001044) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A gland that produces the saliva. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-25, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000376" -- [positive regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904407) EquivalentTo [biological regulation](http://purl.obolibrary.org/obo/GO_0065007) and ([positively regulates](http://purl.obolibrary.org/obo/RO_0002213) some [nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_0046209)) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [positive regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904407) SubClassOf [regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_0080164) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [positive regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904407) SubClassOf [positively regulates](http://purl.obolibrary.org/obo/RO_0002213) some [nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_0046209) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [positive regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_1904407) SubClassOf [positive regulation of metabolic process](http://purl.obolibrary.org/obo/GO_0009893) +- [saliva-secreting gland](http://purl.obolibrary.org/obo/UBERON_0001044) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005382" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [saliva-secreting gland](http://purl.obolibrary.org/obo/UBERON_0001044) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The salivary glands in mammals are exocrine glands, glands with ducts, that produce saliva. They also secrete amylase, an enzyme that breaks down starch into maltose. In other organisms such as insects, salivary glands are often used to produce biologically important proteins like silk or glues, and fly salivary glands contain polytene chromosomes that have been useful in genetic research. The salivary glands of some species are modified to produce enzymes; salivary amylase is found in many, but by no means all, bird and mammal species (including humans, as noted above). Furthermore, the venom glands of poisonous snakes, Gila monsters, and some shrews, are modified salivary glands" -### postcranial axial skeleton `http://purl.obolibrary.org/obo/UBERON_0002090` -#### Added -- [postcranial axial skeleton](http://purl.obolibrary.org/obo/UBERON_0002090) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D013131" +### scala media `http://purl.obolibrary.org/obo/UBERON_0002295` +#### Removed +- [scala media](http://purl.obolibrary.org/obo/UBERON_0002295) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D003053" - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +- [scala media](http://purl.obolibrary.org/obo/UBERON_0002295) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EHDAA2:0000262" -### posterior communicating artery `http://purl.obolibrary.org/obo/UBERON_0001628` -#### Removed -- [posterior communicating artery](http://purl.obolibrary.org/obo/UBERON_0001628) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria cerebri communicans posterior" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Posterior_communicating_artery" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [posterior communicating artery](http://purl.obolibrary.org/obo/UBERON_0001628) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria cerebri communicans posterior" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### scapula `http://purl.obolibrary.org/obo/UBERON_0006849` +#### Removed +- [scapula](http://purl.obolibrary.org/obo/UBERON_0006849) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "scapular" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Posterior_communicating_artery" +- [scapula](http://purl.obolibrary.org/obo/UBERON_0006849) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "present in all tetrapods with even vestiges of anterior limbs, e.g., turtles & birds & mammals." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0-12-319060-4" +- [scapula](http://purl.obolibrary.org/obo/UBERON_0006849) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "chick scapula is of dual origin and segmentally organized" -### posterior hypothalamic region `http://purl.obolibrary.org/obo/UBERON_0002770` -#### Removed -- [posterior hypothalamic region](http://purl.obolibrary.org/obo/UBERON_0002770) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "regio hypothalamica posterior" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:411" +- [scapula](http://purl.obolibrary.org/obo/UBERON_0006849) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Paired bony elements of endochondral origin. They are situated at the level of the jaw articulation, in a vertical position, with the suprascapular margin being dorsal and the glenoid end being ventral.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -- [posterior hypothalamic region](http://purl.obolibrary.org/obo/UBERON_0002770) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "hypothalamus posterior" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:411" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000751" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -#### Added -- [posterior hypothalamic region](http://purl.obolibrary.org/obo/UBERON_0002770) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "regio hypothalamica posterior" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [scapula](http://purl.obolibrary.org/obo/UBERON_0006849) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Endochondral bone that is located medial to the cleithrum, and articulates ventrally with the coracoid, medially with the mesocoracoid when the later is present and posteriorly with the upper one to three proximal radials. The scapula develops from the scapulocoracoid cartilage and belongs to the primary pectoral girdle. It may be perforated by the scapular foramen or it may be notched ventr and forms together with a similar notch of the coracoid the scapulocoracoid foramen[TAO:0000583]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TAO:0000583" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:411" +- [scapula](http://purl.obolibrary.org/obo/UBERON_0006849) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: has pars glenoidalis of scapula (AAO:0000753)[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -- [posterior hypothalamic region](http://purl.obolibrary.org/obo/UBERON_0002770) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "hypothalamus posterior" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000751" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:411" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" +- [scapula](http://purl.obolibrary.org/obo/UBERON_0006849) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: part_of scapular area (AAO:0000935)[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -### posterior segment of eyeball `http://purl.obolibrary.org/obo/UBERON_0001802` -#### Removed -- [posterior segment of eyeball](http://purl.obolibrary.org/obo/UBERON_0001802) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "segmentum posterius bulbi oculi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Posterior_segment_of_eyeball" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000751" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -#### Added -- [posterior segment of eyeball](http://purl.obolibrary.org/obo/UBERON_0001802) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "segmentum posterius bulbi oculi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [scapula](http://purl.obolibrary.org/obo/UBERON_0006849) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [scapula cartilage element](http://purl.obolibrary.org/obo/UBERON_0006290) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Posterior_segment_of_eyeball" +#### Added +- [scapula](http://purl.obolibrary.org/obo/UBERON_0006849) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [scapula cartilage element](http://purl.obolibrary.org/obo/UBERON_0006290) -### posterior surface of kidney `http://purl.obolibrary.org/obo/UBERON_0035471` +### scapula pre-cartilage condensation `http://purl.obolibrary.org/obo/UBERON_0006291` #### Removed -- [posterior surface of kidney](http://purl.obolibrary.org/obo/UBERON_0035471) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "facies posterior renis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15590" +- [scapula pre-cartilage condensation](http://purl.obolibrary.org/obo/UBERON_0006291) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "the scapula has been shown to develop from multiple tissues, such as the dermomyotome of the somites, the mesodermal portion of the soma- topleure (a domain of the lateral plate mesoderm or LPM) and neural crest cell-derived mesenchyme (Huang et al., 2000; Matsuoka et al., 2005; Wang et al., 2005)." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:21455939" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [posterior surface of kidney](http://purl.obolibrary.org/obo/UBERON_0035471) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "facies posterior renis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### scapulocoracoid `http://purl.obolibrary.org/obo/UBERON_0004753` +#### Removed +- [scapulocoracoid](http://purl.obolibrary.org/obo/UBERON_0004753) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "either a fusion of the scapula and coracoid (the two main bones of the shoulder girdle), or the scapula & coracoid considered as a single structural unit.[Palaeos]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://palaeos.com/vertebrates/glossary/glossaryS.html" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-10" + +- [scapulocoracoid](http://purl.obolibrary.org/obo/UBERON_0004753) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: part_of scapular area (AAO:0000935)[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15590" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000781" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" +- [scapulocoracoid](http://purl.obolibrary.org/obo/UBERON_0004753) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "ZFA defines as precursor to scapula and coracoid. Cartilage in TAO" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "ZFA" -### posterior surface of prostate `http://purl.obolibrary.org/obo/UBERON_0035165` -#### Removed -- [posterior surface of prostate](http://purl.obolibrary.org/obo/UBERON_0035165) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "facies posterior prostatae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:19592" +- [scapulocoracoid](http://purl.obolibrary.org/obo/UBERON_0004753) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Fused, ossified portions of the scapula, procoracoid, and coracoid.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000781" -#### Added -- [posterior surface of prostate](http://purl.obolibrary.org/obo/UBERON_0035165) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "facies posterior prostatae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:19592" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [scapulocoracoid](http://purl.obolibrary.org/obo/UBERON_0004753) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Pectoral fin cartilage that consists of a paired cartilaginous plate of the embryonic primary pectoral girdle and from which the scapular and coracaoid bones ossify.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001455" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -### posterior vena cava `http://purl.obolibrary.org/obo/UBERON_0001072` -#### Removed -- [posterior vena cava](http://purl.obolibrary.org/obo/UBERON_0001072) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena cava inferior" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Inferior_vena_cava" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TAO:GA_TG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0002682" -#### Added -- [posterior vena cava](http://purl.obolibrary.org/obo/UBERON_0001072) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena cava inferior" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Inferior_vena_cava" +### scavenger receptor cysteine-rich type 1 protein M130 `http://purl.obolibrary.org/obo/PR_000001925` +#### Removed +- [scavenger receptor cysteine-rich type 1 protein M130](http://purl.obolibrary.org/obo/PR_000001925) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [scavenger receptor cysteine-rich type 1 protein M130 (human)](http://purl.obolibrary.org/obo/PR_Q86VB7) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0002682" -### posteroventral cochlear nucleus `http://purl.obolibrary.org/obo/UBERON_0002831` +### sciatic nerve `http://purl.obolibrary.org/obo/UBERON_0001322` #### Removed -- [posteroventral cochlear nucleus](http://purl.obolibrary.org/obo/UBERON_0002831) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus cochlearis posteroventralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:724" +- [sciatic nerve](http://purl.obolibrary.org/obo/UBERON_0001322) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "mouse sciatic nerve origins predominantly from the third lumbar (L3) and L4 spinal nerves, unlike the L4 and L5 in rats - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2700063/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [posteroventral cochlear nucleus](http://purl.obolibrary.org/obo/UBERON_0002831) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus cochlearis posteroventralis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:724" +### sclera `http://purl.obolibrary.org/obo/UBERON_0001773` +#### Removed +- [sclera](http://purl.obolibrary.org/obo/UBERON_0001773) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The sclera, also known as the white part of the eye, is the opaque (usually white, though certain animals, such as horses and lizards, can have black sclera), fibrous, protective, outer layer of the eye containing collagen and elastic fiber. It is derived from the neural crest. In children, it is thinner and shows some of the underlying pigment, appearing slightly blue. In the elderly, however, fatty deposits on the sclera can make it appear slightly yellow. The sclera forms the posterior five sixths of the connective tissue coat of the globe. It is continuous with the dura mater and the cornea, and maintains the shape of the globe, offering resistance to internal and external forces, and provides an attachment for the extraocular muscle insertions. The sclera is perforated by plenty of nerves and vessels passing through the posterior scleral foramen, the hole that is formed by the optic nerve. At the optic disk the outer two-thirds of the sclera continues with the dura mater (outer coat of the brain) via the dural sheath of the optic nerve. The inner third joins with some choroidal tissue to form a plate (lamina cribrosa) across the optic nerve with perforations through which the optic fibers (fasciculi). The thickness of the sclera varies from 1mm at the posterior pole to 0.3 mm just behind the rectus muscle insertions. The sclera's blood vessels are mainly on the surface, and together with the conjunctiva (which lies on top) This is a thin layer covering the sclera. Along with the vessels of the conjunctiva, those of the sclera renders the inflamed eye bright red. [WP,unvetted][Wikipedia:Sclera]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Sclera" -### pre-B-I cell `http://purl.obolibrary.org/obo/CL_0000956` +- [sclera](http://purl.obolibrary.org/obo/UBERON_0001773) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "Majority derives from NC that surrounds optic cup of neurectoderm; a small temporal portion develops from the mesoderm that contributes to striated extra-ocular muscles and vascular endothelia[Rada&Johnson]." -#### Added -- [pre-B-I cell](http://purl.obolibrary.org/obo/CL_0000956) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [sclera](http://purl.obolibrary.org/obo/UBERON_0001773) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "scleral" +- [sclera](http://purl.obolibrary.org/obo/UBERON_0001773) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The tough, usually white, outer coat of the eyeball, covering all the posterior surface and continuous anteriorly with the cornea. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/sclera" -### pre-conventional dendritic cell `http://purl.obolibrary.org/obo/CL_0002010` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [pre-conventional dendritic cell](http://purl.obolibrary.org/obo/CL_0002010) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### pre-natural killer cell `http://purl.obolibrary.org/obo/CL_0000937` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001274" -#### Added -- [pre-natural killer cell](http://purl.obolibrary.org/obo/CL_0000937) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [sclera](http://purl.obolibrary.org/obo/UBERON_0001773) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "Seko et al demonstrate chondrogenic potential and identify this as connective tissue[DOI:10.1371/journal.pone.0003709]." +- [sclera](http://purl.obolibrary.org/obo/UBERON_0001773) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "continuous with the dura mater and the cornea; The sclera forms the posterior five-sixths of the connective tissue coat of the globe." -### precursor B cell `http://purl.obolibrary.org/obo/CL_0000817` +- [sclera](http://purl.obolibrary.org/obo/UBERON_0001773) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "in fish, reptiles and monotremes the connective tissue of the sclera is skeletal" -#### Added -- [precursor B cell](http://purl.obolibrary.org/obo/CL_0000817) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [sclera](http://purl.obolibrary.org/obo/UBERON_0001773) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [mesenchyme derived from head neural crest](http://purl.obolibrary.org/obo/UBERON_0007213) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0781772214" + - [inferred_by](http://www.geneontology.org/formats/oboInOwl#inferred_by) "cjm" -### precursor cell `http://purl.obolibrary.org/obo/CL_0011115` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia" #### Added -- [precursor cell](http://purl.obolibrary.org/obo/CL_0011115) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [sclera](http://purl.obolibrary.org/obo/UBERON_0001773) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) -### premacula segment of distal straight tubule `http://purl.obolibrary.org/obo/UBERON_0006376` +### scleral mesenchyme `http://purl.obolibrary.org/obo/UBERON_0010299` #### Removed -- [premacula segment of distal straight tubule](http://purl.obolibrary.org/obo/UBERON_0006376) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://sourceforge.net/tracker/?func=detail&aid=3123600&group_id=76834&atid=1205376" +- [scleral mesenchyme](http://purl.obolibrary.org/obo/UBERON_0010299) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "The mesenchyme surrounding the developing optic cup differentiates into the sclera, the dense fibrous coat of the eye.. http://www.ncbi.nlm.nih.gov/pubmed/16496288" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:14595018" -#### Added -- [premacula segment of distal straight tubule](http://purl.obolibrary.org/obo/UBERON_0006376) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Missing definition for term UBERON:0006376. Please replace it using linked reference." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:14595018" -- [premacula segment of distal straight tubule](http://purl.obolibrary.org/obo/UBERON_0006376) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) "https://sourceforge.net/tracker/?func=detail&aid=3123600&group_id=76834&atid=1205376"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) +### sclerotome `http://purl.obolibrary.org/obo/UBERON_0003089` +#### Removed +- [sclerotome](http://purl.obolibrary.org/obo/UBERON_0003089) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Skeletogenic portion of somites.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -### preoptic area `http://purl.obolibrary.org/obo/UBERON_0001928` -#### Removed -- [preoptic area](http://purl.obolibrary.org/obo/UBERON_0001928) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "area preoptica" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Preoptic_area" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010571" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -- [preoptic area](http://purl.obolibrary.org/obo/UBERON_0001928) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nuclei preoptici" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:377" +- [sclerotome](http://purl.obolibrary.org/obo/UBERON_0003089) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "part_of somite in XAO" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "XAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [sclerotome](http://purl.obolibrary.org/obo/UBERON_0003089) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006255" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -#### Added -- [preoptic area](http://purl.obolibrary.org/obo/UBERON_0001928) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "area preoptica" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Preoptic_area" + - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) -- [preoptic area](http://purl.obolibrary.org/obo/UBERON_0001928) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nuclei preoptici" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [sclerotome](http://purl.obolibrary.org/obo/UBERON_0003089) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:377" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### preoptic nucleus `http://purl.obolibrary.org/obo/UBERON_0007251` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [preoptic nucleus](http://purl.obolibrary.org/obo/UBERON_0007251) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D011301" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000680" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -### preoptic periventricular nucleus `http://purl.obolibrary.org/obo/UBERON_0002622` +### sebaceous gland `http://purl.obolibrary.org/obo/UBERON_0001821` #### Removed -- [preoptic periventricular nucleus](http://purl.obolibrary.org/obo/UBERON_0002622) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus periventricularis preopticus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:379" +- [sebaceous gland](http://purl.obolibrary.org/obo/UBERON_0001821) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Sebaceous glands are also limited to mammals.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001468" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [preoptic periventricular nucleus](http://purl.obolibrary.org/obo/UBERON_0002622) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus periventricularis praeopticus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:379" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [preoptic periventricular nucleus](http://purl.obolibrary.org/obo/UBERON_0002622) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus periventricularis hypothalami, pars dorsalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:379" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.102" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [sebaceous gland](http://purl.obolibrary.org/obo/UBERON_0001821) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Any of the numerous holocrine glands in the dermis that empty into a hair follicle and produce and secrete sebum. [TFD][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001468" -- [preoptic periventricular nucleus](http://purl.obolibrary.org/obo/UBERON_0002622) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nucleus preopticus periventricularis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:62324" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/sebaceous+gland" + +- [sebaceous gland](http://purl.obolibrary.org/obo/UBERON_0001821) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "sebaceous glands are also found in glabrous areas of eyelids, nose, penis, labia minora and nipples, and do not always secrete into hair follices. This causes some confusion in classification. In addition some structures, such as preputial glands are sometimes called 'modified' sebaceous glands, implying a non-subclass relationship. we follow MP and MA in keeping this class generic and creating a distinct subclass for sebaceuous glands of the skin. The FMA class may be better placed under this subclass." + +- [sebaceous gland](http://purl.obolibrary.org/obo/UBERON_0001821) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [sebaceous gland placode](http://purl.obolibrary.org/obo/UBERON_0005088) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" #### Added -- [preoptic periventricular nucleus](http://purl.obolibrary.org/obo/UBERON_0002622) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus periventricularis hypothalami, pars dorsalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [sebaceous gland](http://purl.obolibrary.org/obo/UBERON_0001821) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [sebaceous gland placode](http://purl.obolibrary.org/obo/UBERON_0005088) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:379" -- [preoptic periventricular nucleus](http://purl.obolibrary.org/obo/UBERON_0002622) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus periventricularis praeopticus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### sebum `http://purl.obolibrary.org/obo/UBERON_0001866` +#### Removed +- [sebum](http://purl.obolibrary.org/obo/UBERON_0001866) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "waterproofs skin" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:379" +- [sebum](http://purl.obolibrary.org/obo/UBERON_0001866) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The composition of sebum varies across species. In humans, the lipid content is as follows: 25% wax monoesters, 41% triglycerides, 16% free fatty acids, 12% squalene; Sapienic acid is a sebum fatty acid that is unique to humans." -- [preoptic periventricular nucleus](http://purl.obolibrary.org/obo/UBERON_0002622) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus periventricularis preopticus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:379" -- [preoptic periventricular nucleus](http://purl.obolibrary.org/obo/UBERON_0002622) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nucleus preopticus periventricularis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### secondary heart field `http://purl.obolibrary.org/obo/UBERON_0009889` +#### Removed +- [secondary heart field](http://purl.obolibrary.org/obo/UBERON_0009889) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "extra-cardiac population of mesodermal progenitors that gives rise to the right ventricle and outflow tract[PMID:17276708]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:17276708" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:62324" +- [secondary heart field](http://purl.obolibrary.org/obo/UBERON_0009889) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "in mouse has left ventricular identity[PMID:22855565]" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [secondary heart field](http://purl.obolibrary.org/obo/UBERON_0009889) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In general, the two studies in chick concluded that the contribution of the SHF was to the outflow tract, whereas the mouse work suggested that the second lineage contributed more broadly to the heart, including the outflow tract and much or all of the right ventricle [11-14]. These different conclusions may represent differences in the experimental approaches used or may represent bona fide differences in the contribution of the second lineage to the hearts of birds compared to mammals [11]. Alternatively, the secondary/anterior heart fields described in the chick may represent a subset of a broader field that makes a more substantial contribution to the heart, as the mouse studies suggested" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:17276708" + +#### Added +- [secondary heart field](http://purl.obolibrary.org/obo/UBERON_0009889) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### preosteoblast `http://purl.obolibrary.org/obo/CL_0007010` +### secondary ovarian follicle `http://purl.obolibrary.org/obo/UBERON_0000036` #### Added -- [preosteoblast](http://purl.obolibrary.org/obo/CL_0007010) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [secondary ovarian follicle](http://purl.obolibrary.org/obo/UBERON_0000036) SubClassOf [protein-containing material entity](http://purl.obolibrary.org/obo/PR_000050567) -### prepuce of penis `http://purl.obolibrary.org/obo/UBERON_0001332` +### secondary pulmonary lobule `http://purl.obolibrary.org/obo/UBERON_0010369` #### Removed -- [prepuce of penis](http://purl.obolibrary.org/obo/UBERON_0001332) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "prepucium" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Foreskin" +- [secondary pulmonary lobule](http://purl.obolibrary.org/obo/UBERON_0010369) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "a pyramidal mass of lung tissue with sides that are bounded by the incomplete interlobular connective tissue septa and with a base, which is 1-2 cm in diameter, which usually faces the pleural surface of the lung; lobules that occupy a more central position in the lung are not well defined and are considered to consist of three to five pulmonary acini with proximate terminal bronchioles." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/secondary+pulmonary+lobule" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [prepuce of penis](http://purl.obolibrary.org/obo/UBERON_0001332) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "praeputium" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Foreskin" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### secretion of exocrine gland `http://purl.obolibrary.org/obo/UBERON_0000456` +#### Removed +- [secretion of exocrine gland](http://purl.obolibrary.org/obo/UBERON_0000456) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "BTO has two distunct classes, with exocrine glandular secretion a subtype of secretion - however, all examples in BTO directly under secretion appear to be exocrine gland secretions" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "BTO" -- [prepuce of penis](http://purl.obolibrary.org/obo/UBERON_0001332) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "preputium penis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:19639" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### section of aorta `http://purl.obolibrary.org/obo/UBERON_0005800` #### Added -- [prepuce of penis](http://purl.obolibrary.org/obo/UBERON_0001332) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "praeputium" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Foreskin" +- [section of aorta](http://purl.obolibrary.org/obo/UBERON_0005800) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -- [prepuce of penis](http://purl.obolibrary.org/obo/UBERON_0001332) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "preputium penis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:19639" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### see also `http://www.w3.org/2000/01/rdf-schema#seeAlso` +#### Removed +- [see also](http://www.w3.org/2000/01/rdf-schema#seeAlso) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [see also](http://www.w3.org/2000/01/rdf-schema#seeAlso) [id](http://www.geneontology.org/formats/oboInOwl#id) "seeAlso" -- [prepuce of penis](http://purl.obolibrary.org/obo/UBERON_0001332) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "prepucium" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [see also](http://www.w3.org/2000/01/rdf-schema#seeAlso) [is_metadata_tag](http://www.geneontology.org/formats/oboInOwl#is_metadata_tag) true - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Foreskin" -### prickle cell `http://purl.obolibrary.org/obo/CL_0000649` +### segment of autopod `http://purl.obolibrary.org/obo/UBERON_0012139` +#### Removed +- [segment of autopod](http://purl.obolibrary.org/obo/UBERON_0012139) SubClassOf [limb segment](http://purl.obolibrary.org/obo/UBERON_0002529) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "may be revised" #### Added -- [prickle cell](http://purl.obolibrary.org/obo/CL_0000649) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [segment of autopod](http://purl.obolibrary.org/obo/UBERON_0012139) SubClassOf [limb segment](http://purl.obolibrary.org/obo/UBERON_0002529) -### primary cultured cell `http://purl.obolibrary.org/obo/CL_0000001` +### segmental subdivision of hindbrain `http://purl.obolibrary.org/obo/UBERON_0004733` #### Added -- [primary cultured cell](http://purl.obolibrary.org/obo/CL_0000001) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [segmental subdivision of hindbrain](http://purl.obolibrary.org/obo/UBERON_0004733) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### primary metabolic process `http://purl.obolibrary.org/obo/GO_0044238` +### semen `http://purl.obolibrary.org/obo/UBERON_0001968` +#### Removed +- [semen](http://purl.obolibrary.org/obo/UBERON_0001968) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Note that in this ontology, semen is defined as the sum of sperm and seminal fluid, where seminal fluid is defined in taxonomically generic way (see comments for UBERON:0006530)." -#### Added -- [primary metabolic process](http://purl.obolibrary.org/obo/GO_0044238) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [gocheck_do_not_annotate](http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate) +- [semen](http://purl.obolibrary.org/obo/UBERON_0001968) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "seminal" -- [primary metabolic process](http://purl.obolibrary.org/obo/GO_0044238) [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/geneontology/go-ontology/issues/26424"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) -### primary motor cortex `http://purl.obolibrary.org/obo/UBERON_0001384` +### semicircular canal `http://purl.obolibrary.org/obo/UBERON_0001840` #### Removed -- [primary motor cortex](http://purl.obolibrary.org/obo/UBERON_0001384) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "gyrus precentralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Primary_motor_cortex" +- [semicircular canal](http://purl.obolibrary.org/obo/UBERON_0001840) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In gnathostomes, each membranous labyrinth has three semicircular ducts that connect with a chamber known as the utriculus. These ducts are sometimes called canals, but technically the term semicircular canal applies to the spaces in the osseus labyrinth in which the semicircular ducts lie.[uncertain][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001144" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [primary motor cortex](http://purl.obolibrary.org/obo/UBERON_0001384) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "gyrus precentralis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Primary_motor_cortex" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.414" -### primary ovarian follicle `http://purl.obolibrary.org/obo/UBERON_0000035` -#### Removed -- [primary ovarian follicle](http://purl.obolibrary.org/obo/UBERON_0000035) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "folliculus ovaricus primarius" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:18634" +- [semicircular canal](http://purl.obolibrary.org/obo/UBERON_0001840) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Fluid-filled toroidal spaces, arranged orthogonally to each other in the ear, that detect angular accelerations. (See Anatomical Atlas entry for semicircular canals by T. Whitfield.)[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -#### Added -- [primary ovarian follicle](http://purl.obolibrary.org/obo/UBERON_0000035) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "folliculus ovaricus primarius" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:18634" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000431" +- [semicircular canal](http://purl.obolibrary.org/obo/UBERON_0001840) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "detects angular acceleration" -### primary sensory neuron (sensu Teleostei) `http://purl.obolibrary.org/obo/CL_0000531` +- [semicircular canal](http://purl.obolibrary.org/obo/UBERON_0001840) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "MA divides this into osseous and duct. In FMA, this is systemically part of the bony labyrinth. Note this is an anatomical space in ZFA. The MA treatment has advantages for representing the neuroepithelium, which should not be part of bone. Also check duct vs canal" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" #### Added -- [primary sensory neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000531) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [semicircular canal](http://purl.obolibrary.org/obo/UBERON_0001840) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### primitive heart tube `http://purl.obolibrary.org/obo/UBERON_0005498` -#### Removed -- [primitive heart tube](http://purl.obolibrary.org/obo/UBERON_0005498) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006179" - - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0003-4423-4370" +### semicircular canal ampulla `http://purl.obolibrary.org/obo/UBERON_0004043` #### Added -- [primitive heart tube](http://purl.obolibrary.org/obo/UBERON_0005498) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006179" +- [semicircular canal ampulla](http://purl.obolibrary.org/obo/UBERON_0004043) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### semicircular duct `http://purl.obolibrary.org/obo/UBERON_0001856` +#### Removed +- [semicircular duct](http://purl.obolibrary.org/obo/UBERON_0001856) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D054776" - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" - - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) +- [semicircular duct](http://purl.obolibrary.org/obo/UBERON_0001856) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In gnathostomes, each membranous labyrinth has three semicircular ducts that connect with a chamber known as the utriculus (...); Gnathostome ears have a horizontal semicircular duct. This brings their complement to three semicircular ducts, a pattern retained throughout gnathostome evolution.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.413-414 and p.58" -### primitive red blood cell `http://purl.obolibrary.org/obo/CL_0002355` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000238" #### Added -- [primitive red blood cell](http://purl.obolibrary.org/obo/CL_0002355) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [semicircular duct](http://purl.obolibrary.org/obo/UBERON_0001856) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### primitive streak `http://purl.obolibrary.org/obo/UBERON_0004341` +### seminal fluid `http://purl.obolibrary.org/obo/UBERON_0006530` #### Removed -- [primitive streak](http://purl.obolibrary.org/obo/UBERON_0004341) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D054240" +- [seminal fluid](http://purl.obolibrary.org/obo/UBERON_0006530) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "we follow FMA and make this class a generic superclass of the secretions of different glands (prostate, bulbo-urethreal, seminal vesicle). MA (and ncit) follows a mixture model, where these secretions are part of the seminal fluid" -#### Added -- [primitive streak](http://purl.obolibrary.org/obo/UBERON_0004341) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D054240" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [seminal fluid](http://purl.obolibrary.org/obo/UBERON_0006530) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "This term covers a variety of species. Example: In D. melanogaster, seminal fluid proteins affect female receptivity, ovulation, oogenesis, sperm storage, sperm competition and mating plug formation" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1046/j.1365-2540.2001.00961.x" - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) +- [seminal fluid](http://purl.obolibrary.org/obo/UBERON_0006530) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "seminal fluid may have a role in sperm capacitation, sperm motility" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +- [seminal fluid](http://purl.obolibrary.org/obo/UBERON_0006530) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "this ontology contains a number of subtypes of seminal fluid, defined according to glands (which are more taxonomically restricted)" -### primitive urogenital sinus `http://purl.obolibrary.org/obo/UBERON_0000164` + +### seminal fluid secreting gland `http://purl.obolibrary.org/obo/UBERON_0006868` #### Removed -- [primitive urogenital sinus](http://purl.obolibrary.org/obo/UBERON_0000164) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "sinus urogenitalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [seminal fluid secreting gland](http://purl.obolibrary.org/obo/UBERON_0006868) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004958" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -#### Added -- [primitive urogenital sinus](http://purl.obolibrary.org/obo/UBERON_0000164) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "sinus urogenitalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### primordial germ cell `http://purl.obolibrary.org/obo/CL_0000670` +### seminal vesicle `http://purl.obolibrary.org/obo/UBERON_0000998` +#### Removed +- [seminal vesicle](http://purl.obolibrary.org/obo/UBERON_0000998) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Either of a pair of pouchlike glands situated on each side of the male urinary bladder that secrete seminal fluid and nourish and promote the movement of spermatozoa through the urethra. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [primordial germ cell](http://purl.obolibrary.org/obo/CL_0000670) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### primordium `http://purl.obolibrary.org/obo/UBERON_0001048` -#### Removed -- [primordium](http://purl.obolibrary.org/obo/UBERON_0001048) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005495" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/prominence" -#### Added -- [primordium](http://purl.obolibrary.org/obo/UBERON_0001048) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005495" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001379" +- [seminal vesicle](http://purl.obolibrary.org/obo/UBERON_0000998) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "The seminal vesicles secrete a significant proportion of the fluid that ultimately becomes semen. Lipofuscin granules from dead epithelial cells give the secretion its yellowish color. About 50-70% of the seminal fluid in humans originates from the seminal vesicles, but is not expelled in the first ejaculate fractions which are dominated by spermatozoa and zinc-rich prostatic fluid." -### pro-B cell `http://purl.obolibrary.org/obo/CL_0000826` +- [seminal vesicle](http://purl.obolibrary.org/obo/UBERON_0000998) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(In mammalian testis) Along the way (the sperm travel), three accessory sex glands, the seminal vesicle, prostate, and bulbourethral (Cowper's) gland, respectively, add their secretions as sperm move from the testes to the urethra.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [pro-B cell](http://purl.obolibrary.org/obo/CL_0000826) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### pro-T cell `http://purl.obolibrary.org/obo/CL_0000827` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.556" -#### Added -- [pro-T cell](http://purl.obolibrary.org/obo/CL_0000827) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001379" -### proctodeum `http://purl.obolibrary.org/obo/UBERON_0000931` -#### Removed -- [proctodeum](http://purl.obolibrary.org/obo/UBERON_0000931) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000123" + +### seminal vesicle epithelium `http://purl.obolibrary.org/obo/UBERON_0004805` #### Added -- [proctodeum](http://purl.obolibrary.org/obo/UBERON_0000931) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000123" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [seminal vesicle epithelium](http://purl.obolibrary.org/obo/UBERON_0004805) SubClassOf [meso-epithelium](http://purl.obolibrary.org/obo/UBERON_0012275) -### proerythroblast `http://purl.obolibrary.org/obo/CL_0000547` +### seminal vesicle fluid `http://purl.obolibrary.org/obo/UBERON_0010143` #### Removed -- [proerythroblast](http://purl.obolibrary.org/obo/CL_0000547) EquivalentTo [erythroid lineage cell](http://purl.obolibrary.org/obo/CL_0000764) and ([has part](http://purl.obolibrary.org/obo/BFO_0000051) some [basophilic cytoplasm](http://purl.obolibrary.org/obo/CL_0017503)) and ([has part](http://purl.obolibrary.org/obo/BFO_0000051) some [obsolete increased nucleus size](http://purl.obolibrary.org/obo/CL_0017505)) and ([has part](http://purl.obolibrary.org/obo/BFO_0000051) some [nucleolus](http://purl.obolibrary.org/obo/GO_0005730)) and ([lacks_plasma_membrane_part](http://purl.obolibrary.org/obo/CL_4030046) some [CD19 molecule](http://purl.obolibrary.org/obo/PR_000001002)) and ([lacks_plasma_membrane_part](http://purl.obolibrary.org/obo/CL_4030046) some [CD4 molecule](http://purl.obolibrary.org/obo/PR_000001004)) and ([lacks_plasma_membrane_part](http://purl.obolibrary.org/obo/CL_4030046) some [integrin alpha-M](http://purl.obolibrary.org/obo/PR_000001012)) and ([lacks_plasma_membrane_part](http://purl.obolibrary.org/obo/CL_4030046) some [CD3 epsilon](http://purl.obolibrary.org/obo/PR_000001020)) and ([lacks_plasma_membrane_part](http://purl.obolibrary.org/obo/CL_4030046) some [neural cell adhesion molecule 1](http://purl.obolibrary.org/obo/PR_000001024)) and ([lacks_plasma_membrane_part](http://purl.obolibrary.org/obo/CL_4030046) some [CD2 molecule](http://purl.obolibrary.org/obo/PR_000001083)) and ([lacks_plasma_membrane_part](http://purl.obolibrary.org/obo/CL_4030046) some [T-cell surface glycoprotein CD8 alpha chain](http://purl.obolibrary.org/obo/PR_000001084)) and ([lacks_plasma_membrane_part](http://purl.obolibrary.org/obo/CL_4030046) some [membrane-spanning 4-domains subfamily A member 1](http://purl.obolibrary.org/obo/PR_000001289)) and ([lacks_plasma_membrane_part](http://purl.obolibrary.org/obo/CL_4030046) some [T-cell surface glycoprotein CD5](http://purl.obolibrary.org/obo/PR_000001839)) and ([lacks_plasma_membrane_part](http://purl.obolibrary.org/obo/CL_4030046) some [CD14 molecule](http://purl.obolibrary.org/obo/PR_000001889)) and ([lacks_plasma_membrane_part](http://purl.obolibrary.org/obo/CL_4030046) some [lymphocyte antigen 6G](http://purl.obolibrary.org/obo/PR_000002978)) and ([bearer of](http://purl.obolibrary.org/obo/RO_0000053) some [nucleated](http://purl.obolibrary.org/obo/PATO_0002505)) and ([has plasma membrane part](http://purl.obolibrary.org/obo/RO_0002104) some [transferrin receptor protein 1](http://purl.obolibrary.org/obo/PR_000001945)) +- [seminal vesicle fluid](http://purl.obolibrary.org/obo/UBERON_0010143) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "constitutes 60-70 % of the ejaculate in humans[MP]" -- [proerythroblast](http://purl.obolibrary.org/obo/CL_0000547) SubClassOf [has part](http://purl.obolibrary.org/obo/BFO_0000051) some [obsolete increased nucleus size](http://purl.obolibrary.org/obo/CL_0017505) +- [seminal vesicle fluid](http://purl.obolibrary.org/obo/UBERON_0010143) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "important for semen coagulation, sperm motility, and stability of sperm chromatin and suppression of the immune activity in the female reproductive tract[MP]" -#### Added -- [proerythroblast](http://purl.obolibrary.org/obo/CL_0000547) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [seminal vesicle fluid](http://purl.obolibrary.org/obo/UBERON_0010143) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in ncit, seminal fluid is a subtype of seminal vesicle secretion" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "ncit" -- [proerythroblast](http://purl.obolibrary.org/obo/CL_0000547) EquivalentTo [erythroid lineage cell](http://purl.obolibrary.org/obo/CL_0000764) and ([has part](http://purl.obolibrary.org/obo/BFO_0000051) some [basophilic cytoplasm](http://purl.obolibrary.org/obo/CL_0017503)) and ([has part](http://purl.obolibrary.org/obo/BFO_0000051) some [nucleolus](http://purl.obolibrary.org/obo/GO_0005730)) and ([lacks_plasma_membrane_part](http://purl.obolibrary.org/obo/CL_4030046) some [CD19 molecule](http://purl.obolibrary.org/obo/PR_000001002)) and ([lacks_plasma_membrane_part](http://purl.obolibrary.org/obo/CL_4030046) some [CD4 molecule](http://purl.obolibrary.org/obo/PR_000001004)) and ([lacks_plasma_membrane_part](http://purl.obolibrary.org/obo/CL_4030046) some [integrin alpha-M](http://purl.obolibrary.org/obo/PR_000001012)) and ([lacks_plasma_membrane_part](http://purl.obolibrary.org/obo/CL_4030046) some [CD3 epsilon](http://purl.obolibrary.org/obo/PR_000001020)) and ([lacks_plasma_membrane_part](http://purl.obolibrary.org/obo/CL_4030046) some [neural cell adhesion molecule 1](http://purl.obolibrary.org/obo/PR_000001024)) and ([lacks_plasma_membrane_part](http://purl.obolibrary.org/obo/CL_4030046) some [CD2 molecule](http://purl.obolibrary.org/obo/PR_000001083)) and ([lacks_plasma_membrane_part](http://purl.obolibrary.org/obo/CL_4030046) some [T-cell surface glycoprotein CD8 alpha chain](http://purl.obolibrary.org/obo/PR_000001084)) and ([lacks_plasma_membrane_part](http://purl.obolibrary.org/obo/CL_4030046) some [membrane-spanning 4-domains subfamily A member 1](http://purl.obolibrary.org/obo/PR_000001289)) and ([lacks_plasma_membrane_part](http://purl.obolibrary.org/obo/CL_4030046) some [T-cell surface glycoprotein CD5](http://purl.obolibrary.org/obo/PR_000001839)) and ([lacks_plasma_membrane_part](http://purl.obolibrary.org/obo/CL_4030046) some [CD14 molecule](http://purl.obolibrary.org/obo/PR_000001889)) and ([lacks_plasma_membrane_part](http://purl.obolibrary.org/obo/CL_4030046) some [lymphocyte antigen 6G](http://purl.obolibrary.org/obo/PR_000002978)) and ([bearer of](http://purl.obolibrary.org/obo/RO_0000053) some [nucleated](http://purl.obolibrary.org/obo/PATO_0002505)) and ([bearer of](http://purl.obolibrary.org/obo/RO_0000053) some [high nuclear/cytoplasmic ratio](http://purl.obolibrary.org/obo/PATO_0040072)) and ([has plasma membrane part](http://purl.obolibrary.org/obo/RO_0002104) some [transferrin receptor protein 1](http://purl.obolibrary.org/obo/PR_000001945)) -- [proerythroblast](http://purl.obolibrary.org/obo/CL_0000547) SubClassOf [bearer of](http://purl.obolibrary.org/obo/RO_0000053) some [high nuclear/cytoplasmic ratio](http://purl.obolibrary.org/obo/PATO_0040072) +### seminiferous tubule of testis `http://purl.obolibrary.org/obo/UBERON_0001343` +#### Removed +- [seminiferous tubule of testis](http://purl.obolibrary.org/obo/UBERON_0001343) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Any of the coiled tubules located in the testes in which spermatozoa are produced.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010399" -### professional antigen presenting cell `http://purl.obolibrary.org/obo/CL_0000145` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -#### Added -- [professional antigen presenting cell](http://purl.obolibrary.org/obo/CL_0000145) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" -### progenitor cell `http://purl.obolibrary.org/obo/CL_0011026` +- [seminiferous tubule of testis](http://purl.obolibrary.org/obo/UBERON_0001343) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Frogs among amphibians and the amniotes have males with testes that are composed of seminiferous tubules, which differ from ampullae in being long, highly convoluted ductules.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [progenitor cell](http://purl.obolibrary.org/obo/CL_0011026) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001363" -### progenitor cell of endocrine pancreas `http://purl.obolibrary.org/obo/CL_0002351` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [progenitor cell of endocrine pancreas](http://purl.obolibrary.org/obo/CL_0002351) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.688 and Figure 21-28" +- [seminiferous tubule of testis](http://purl.obolibrary.org/obo/UBERON_0001343) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "One of two or three twisted curved tubules in each lobule of the testis in which spermatogenesis occurs. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### progenitor cell of mammary luminal epithelium `http://purl.obolibrary.org/obo/CL_0009116` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [progenitor cell of mammary luminal epithelium](http://purl.obolibrary.org/obo/CL_0009116) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001363" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### programmed cell death `http://purl.obolibrary.org/obo/GO_0012501` -#### Removed -- [programmed cell death](http://purl.obolibrary.org/obo/GO_0012501) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/SEMINIFEROUS+TUBULE" -#### Added -- [programmed cell death](http://purl.obolibrary.org/obo/GO_0012501) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) -### prokaryote_subset `http://purl.obolibrary.org/obo/go#prokaryote_subset` +### sends output to `http://purl.obolibrary.org/obo/RO_0002486` #### Removed -- AnnotationProperty: [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) +- [sends output to](http://purl.obolibrary.org/obo/RO_0002486) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) -- [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) SubPropertyOf: [subset_property](http://www.geneontology.org/formats/oboInOwl#SubsetProperty) +### sense organ `http://purl.obolibrary.org/obo/UBERON_0000020` +#### Removed +- [sense organ](http://purl.obolibrary.org/obo/UBERON_0000020) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005155" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### promonocyte `http://purl.obolibrary.org/obo/CL_0000559` - -#### Added -- [promonocyte](http://purl.obolibrary.org/obo/CL_0000559) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### promyelocyte `http://purl.obolibrary.org/obo/CL_0000836` +### sensory epithelium `http://purl.obolibrary.org/obo/UBERON_0006934` #### Removed -- [promyelocyte](http://purl.obolibrary.org/obo/CL_0000836) EquivalentTo [myeloid lineage restricted progenitor cell](http://purl.obolibrary.org/obo/CL_0000839) and ([has part](http://purl.obolibrary.org/obo/BFO_0000051) some [basophilic cytoplasm](http://purl.obolibrary.org/obo/CL_0017503)) and ([has part](http://purl.obolibrary.org/obo/BFO_0000051) some [obsolete increased nucleus size](http://purl.obolibrary.org/obo/CL_0017505)) and ([has part](http://purl.obolibrary.org/obo/BFO_0000051) some [nucleolus](http://purl.obolibrary.org/obo/GO_0005730)) and ([has part](http://purl.obolibrary.org/obo/BFO_0000051) some [azurophil granule](http://purl.obolibrary.org/obo/GO_0042582)) and ([lacks_plasma_membrane_part](http://purl.obolibrary.org/obo/CL_4030046) some [integrin alpha-M](http://purl.obolibrary.org/obo/PR_000001012)) and ([lacks_plasma_membrane_part](http://purl.obolibrary.org/obo/CL_4030046) some [low affinity immunoglobulin gamma Fc region receptor III](http://purl.obolibrary.org/obo/PR_000001483)) and ([lacks_plasma_membrane_part](http://purl.obolibrary.org/obo/CL_4030046) some [signal transducer CD24](http://purl.obolibrary.org/obo/PR_000001932)) and ([has plasma membrane part](http://purl.obolibrary.org/obo/RO_0002104) some [alpha-(1,3)-fucosyltransferase 4](http://purl.obolibrary.org/obo/PR_000001456)) and ([has plasma membrane part](http://purl.obolibrary.org/obo/RO_0002104) some [CD33 molecule](http://purl.obolibrary.org/obo/PR_000001892)) +- [sensory epithelium](http://purl.obolibrary.org/obo/UBERON_0006934) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "note that the definition sourced from Dorlands say 'simple columnar', but FMA says atypical" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" -- [promyelocyte](http://purl.obolibrary.org/obo/CL_0000836) SubClassOf [has part](http://purl.obolibrary.org/obo/BFO_0000051) some [obsolete increased nucleus size](http://purl.obolibrary.org/obo/CL_0017505) -#### Added -- [promyelocyte](http://purl.obolibrary.org/obo/CL_0000836) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -- [promyelocyte](http://purl.obolibrary.org/obo/CL_0000836) EquivalentTo [myeloid lineage restricted progenitor cell](http://purl.obolibrary.org/obo/CL_0000839) and ([has part](http://purl.obolibrary.org/obo/BFO_0000051) some [basophilic cytoplasm](http://purl.obolibrary.org/obo/CL_0017503)) and ([has part](http://purl.obolibrary.org/obo/BFO_0000051) some [nucleolus](http://purl.obolibrary.org/obo/GO_0005730)) and ([has part](http://purl.obolibrary.org/obo/BFO_0000051) some [azurophil granule](http://purl.obolibrary.org/obo/GO_0042582)) and ([lacks_plasma_membrane_part](http://purl.obolibrary.org/obo/CL_4030046) some [integrin alpha-M](http://purl.obolibrary.org/obo/PR_000001012)) and ([lacks_plasma_membrane_part](http://purl.obolibrary.org/obo/CL_4030046) some [low affinity immunoglobulin gamma Fc region receptor III](http://purl.obolibrary.org/obo/PR_000001483)) and ([lacks_plasma_membrane_part](http://purl.obolibrary.org/obo/CL_4030046) some [signal transducer CD24](http://purl.obolibrary.org/obo/PR_000001932)) and ([bearer of](http://purl.obolibrary.org/obo/RO_0000053) some [high nuclear/cytoplasmic ratio](http://purl.obolibrary.org/obo/PATO_0040072)) and ([has plasma membrane part](http://purl.obolibrary.org/obo/RO_0002104) some [alpha-(1,3)-fucosyltransferase 4](http://purl.obolibrary.org/obo/PR_000001456)) and ([has plasma membrane part](http://purl.obolibrary.org/obo/RO_0002104) some [CD33 molecule](http://purl.obolibrary.org/obo/PR_000001892)) +### sensory nerve `http://purl.obolibrary.org/obo/UBERON_0001027` +#### Removed +- [sensory nerve](http://purl.obolibrary.org/obo/UBERON_0001027) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005136" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -- [promyelocyte](http://purl.obolibrary.org/obo/CL_0000836) SubClassOf [bearer of](http://purl.obolibrary.org/obo/RO_0000053) some [high nuclear/cytoplasmic ratio](http://purl.obolibrary.org/obo/PATO_0040072) -### pronephric duct `http://purl.obolibrary.org/obo/UBERON_0003060` +### sensory system `http://purl.obolibrary.org/obo/UBERON_0001032` #### Removed -- [pronephric duct](http://purl.obolibrary.org/obo/UBERON_0003060) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ductus pronephricus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pronephric_duct" +- [sensory system](http://purl.obolibrary.org/obo/UBERON_0001032) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [pronephric duct](http://purl.obolibrary.org/obo/UBERON_0003060) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0005991" - - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0003-4423-4370" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [pronephric duct](http://purl.obolibrary.org/obo/UBERON_0003060) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ductus pronephricus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pronephric_duct" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001674" -- [pronephric duct](http://purl.obolibrary.org/obo/UBERON_0003060) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0005991" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [sensory system](http://purl.obolibrary.org/obo/UBERON_0001032) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +- [sensory system](http://purl.obolibrary.org/obo/UBERON_0001032) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007692" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) -### pronephros `http://purl.obolibrary.org/obo/UBERON_0002120` +### septal nuclear complex `http://purl.obolibrary.org/obo/UBERON_0002663` #### Removed -- [pronephros](http://purl.obolibrary.org/obo/UBERON_0002120) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D060910" +- [septal nuclear complex](http://purl.obolibrary.org/obo/UBERON_0002663) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The septal nuclei are structures in the middle anteroventral cerebrum that are composed of medium-size neurons grouped into medial, lateral, and posterior groups. The septal nuclei receive reciprocal connections from the olfactory bulb, hippocampus, amygdala, hypothalamus, midbrain, habenula, cingulate gyrus, and thalamus. The septal nuclei play a role in reward and reinforcement along with the nucleus accumbens. In the 1950s, Olds &amp; Milner showed that rats with electrodes implanted in this area will self-stimulate repeatedly in order to experience a euphoric feeling (i.e. press a bar to receive electrical current that will stimulate the neurons). [WP,unvetted][Wikipedia:Septal_nuclei]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Septal_nuclei" -#### Added -- [pronephros](http://purl.obolibrary.org/obo/UBERON_0002120) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D060910" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [septal nuclear complex](http://purl.obolibrary.org/obo/UBERON_0002663) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in NIFSTD this is the mereological sum of the individual complexes - in MA it is the superclass" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "NIF" - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) +- [septal nuclear complex](http://purl.obolibrary.org/obo/UBERON_0002663) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Any of the groups of neural nuclei situated in the septal region which have afferent and cholinergic efferent connections with a variety of forebrain and brainstem areas including the hippocampus, the lateral hypothalamus, the tegmentum, and the amygdala." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "MP:0012682" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -### prostate gland `http://purl.obolibrary.org/obo/UBERON_0002367` +### septum `http://purl.obolibrary.org/obo/UBERON_0003037` #### Removed -- [prostate gland](http://purl.obolibrary.org/obo/UBERON_0002367) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "prostata" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Prostate" +- [septum](http://purl.obolibrary.org/obo/UBERON_0003037) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "septal" -#### Added -- [prostate gland](http://purl.obolibrary.org/obo/UBERON_0002367) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "prostata" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Prostate" +### septum of telencephalon `http://purl.obolibrary.org/obo/UBERON_0000446` +#### Removed +- [septum of telencephalon](http://purl.obolibrary.org/obo/UBERON_0000446) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Subdivision of the telencephalon on the midline between the lateral ventricles which contains the septum pellucidum and the septal nuclei[FMA][FMA:61842]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:61842" -### prostate gland microvascular endothelial cell `http://purl.obolibrary.org/obo/CL_2000059` - -#### Added -- [prostate gland microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000059) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### prostate gland smooth muscle `http://purl.obolibrary.org/obo/UBERON_0004243` +### septum transversum `http://purl.obolibrary.org/obo/UBERON_0004161` #### Removed -- [prostate gland smooth muscle](http://purl.obolibrary.org/obo/UBERON_0004243) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "substantia muscularis prostatae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:74245" +- [septum transversum](http://purl.obolibrary.org/obo/UBERON_0004161) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/transverse+septum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [prostate gland smooth muscle](http://purl.obolibrary.org/obo/UBERON_0004243) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "substantia muscularis prostatae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:74245" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000019" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [septum transversum](http://purl.obolibrary.org/obo/UBERON_0004161) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "The cranial part of the septum transversum gives rise to the central tendon of the diaphragm and is the origin of the myoblasts that invade the pleuroperitoneal folds resulting in the formation of the muscular diaphragm. The caudal part of the septum transversum is invaded by the hepatic diverticulum which divides within it to form the liver and thus gives rise to the ventral mesentery of the foregut." +- [septum transversum](http://purl.obolibrary.org/obo/UBERON_0004161) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In hagfishes a transverse septum extends upward from the ventral body wall posterior to the heart, partly separating an anterior pericardial cavity from a larger peritoneal cavity. (...) These basic relationships have not been modified by urodeles. The small pericardial cavity remains far forward where it is separated by a transverse septum from the principal coelom, which may now be called a pleuroperitoneal cavity because slender lungs are present. (...) The heart (of other tetrapods) is separated from the lungs (and liver if present) by more or less horizontal partitions that have their origin in the embryo as folds on the serous membrane of the right and left lateral body walls. These grow out to join in the midline of the body. They are called lateral mesocardia (birds) or pleuropericardial membranes. Posteriorly they join the transverse septum to form the adult pericardial membrane, or pericardium. (...) In their partitioning of their coelom, embryonic mammals resemble first early fishes (incomplete partition, posterior to heart, consisting of the transverse septum) and then reptiles (pericardium derived from transverse septum and pleuropericardial membranes) Mammals then separate paired pleural cavities from the peritoneal cavity by a diaphragm. The ventral portion of this organ comes from the transverse septum. The dorsal portion is derived from the dorsal mesentery and from still another pair of outgrowths from the lateral body wall, the pleuroperitoneal membranes.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.205-206" -### prostate stromal cell `http://purl.obolibrary.org/obo/CL_0002622` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [prostate stromal cell](http://purl.obolibrary.org/obo/CL_0002622) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### prostatic urethra `http://purl.obolibrary.org/obo/UBERON_0001335` -#### Removed -- [prostatic urethra](http://purl.obolibrary.org/obo/UBERON_0001335) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pars prostatica urethrae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MP:0011777" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000019" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Prostatic_urethra" +- [septum transversum](http://purl.obolibrary.org/obo/UBERON_0004161) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in EHDAA2 this is divided into mesenchymal portion and hepatic diverticulum" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EHDAA2" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [prostatic urethra](http://purl.obolibrary.org/obo/UBERON_0001335) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pars prostatica urethrae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MP:0011777" +### serosa of duodenum `http://purl.obolibrary.org/obo/UBERON_0003336` +#### Removed +- [serosa of duodenum](http://purl.obolibrary.org/obo/UBERON_0003336) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "1st part serosa, 2nd - 4th adventitia" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Prostatic_urethra" -### prostatic venous plexus `http://purl.obolibrary.org/obo/UBERON_0009042` +### serosa of small intestine `http://purl.obolibrary.org/obo/UBERON_0001206` #### Removed -- [prostatic venous plexus](http://purl.obolibrary.org/obo/UBERON_0009042) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "plexus venosus prostaticus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Prostatic_venous_plexus" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - -#### Added -- [prostatic venous plexus](http://purl.obolibrary.org/obo/UBERON_0009042) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "plexus venosus prostaticus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [serosa of small intestine](http://purl.obolibrary.org/obo/UBERON_0001206) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "duodenum, 1st part serosa, 2nd - 4th adventitia" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Prostatic_venous_plexus" -### protein catabolic process `http://purl.obolibrary.org/obo/GO_0030163` -#### Removed -- [protein catabolic process](http://purl.obolibrary.org/obo/GO_0030163) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) +### serosal nerve fiber of appendix `http://purl.obolibrary.org/obo/UBERON_8410049` #### Added -- [protein catabolic process](http://purl.obolibrary.org/obo/GO_0030163) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) +- [serosal nerve fiber of appendix](http://purl.obolibrary.org/obo/UBERON_8410049) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### protein localization to membrane `http://purl.obolibrary.org/obo/GO_0072657` +### serous gland `http://purl.obolibrary.org/obo/UBERON_0000409` #### Removed -- [protein localization to membrane](http://purl.obolibrary.org/obo/GO_0072657) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) +- [serous gland](http://purl.obolibrary.org/obo/UBERON_0000409) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "glands that secrete watery albuminous material that often contains enzymes[MP:0008052]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "MP:0008052" -#### Added -- [protein localization to membrane](http://purl.obolibrary.org/obo/GO_0072657) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) -### protein maturation `http://purl.obolibrary.org/obo/GO_0051604` +### serous membrane `http://purl.obolibrary.org/obo/UBERON_0000042` #### Removed -- [protein maturation](http://purl.obolibrary.org/obo/GO_0051604) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) +- [serous membrane](http://purl.obolibrary.org/obo/UBERON_0000042) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Serous_membrane" -#### Added -- [protein maturation](http://purl.obolibrary.org/obo/GO_0051604) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005425" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -### protein modification process `http://purl.obolibrary.org/obo/GO_0036211` -#### Removed -- [protein modification process](http://purl.obolibrary.org/obo/GO_0036211) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -#### Added -- [protein modification process](http://purl.obolibrary.org/obo/GO_0036211) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) +- [serous membrane](http://purl.obolibrary.org/obo/UBERON_0000042) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Serous_membrane" + +- [serous membrane](http://purl.obolibrary.org/obo/UBERON_0000042) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" -### protein-containing complex assembly `http://purl.obolibrary.org/obo/GO_0065003` + +### serratus ventralis `http://purl.obolibrary.org/obo/UBERON_0001125` #### Removed -- [protein-containing complex assembly](http://purl.obolibrary.org/obo/GO_0065003) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) +- [serratus ventralis](http://purl.obolibrary.org/obo/UBERON_0001125) SubClassOf [innervated_by](http://purl.obolibrary.org/obo/RO_0002005) some [thoracic nerve](http://purl.obolibrary.org/obo/UBERON_0003726) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "dbpedia" -#### Added -- [protein-containing complex assembly](http://purl.obolibrary.org/obo/GO_0065003) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "long thoracic nerve" +- [serratus ventralis](http://purl.obolibrary.org/obo/UBERON_0001125) SubClassOf [has muscle origin](http://purl.obolibrary.org/obo/RO_0002372) some [rib](http://purl.obolibrary.org/obo/UBERON_0002228) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "dbpedia" -### proximal convoluted tubule `http://purl.obolibrary.org/obo/UBERON_0001287` -#### Removed -- [proximal convoluted tubule](http://purl.obolibrary.org/obo/UBERON_0001287) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tubulus contortus proximalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Proximal_convoluted_tubule" + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "fleshy slips from the outer surface of upper 8 or 9 ribs" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [serratus ventralis](http://purl.obolibrary.org/obo/UBERON_0001125) SubClassOf [has muscle insertion](http://purl.obolibrary.org/obo/RO_0002373) some [scapula](http://purl.obolibrary.org/obo/UBERON_0006849) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "dbpedia" -- [proximal convoluted tubule](http://purl.obolibrary.org/obo/UBERON_0001287) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tubulus convolutus proximalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "costal aspect of medial margin of the scapula" #### Added -- [proximal convoluted tubule](http://purl.obolibrary.org/obo/UBERON_0001287) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tubulus convolutus proximalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [serratus ventralis](http://purl.obolibrary.org/obo/UBERON_0001125) SubClassOf [has muscle insertion](http://purl.obolibrary.org/obo/RO_0002373) some [scapula](http://purl.obolibrary.org/obo/UBERON_0006849) -- [proximal convoluted tubule](http://purl.obolibrary.org/obo/UBERON_0001287) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tubulus contortus proximalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [serratus ventralis](http://purl.obolibrary.org/obo/UBERON_0001125) SubClassOf [innervated_by](http://purl.obolibrary.org/obo/RO_0002005) some [thoracic nerve](http://purl.obolibrary.org/obo/UBERON_0003726) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Proximal_convoluted_tubule" +- [serratus ventralis](http://purl.obolibrary.org/obo/UBERON_0001125) SubClassOf [has muscle origin](http://purl.obolibrary.org/obo/RO_0002372) some [rib](http://purl.obolibrary.org/obo/UBERON_0002228) -### proximal epiphysis of fibula `http://purl.obolibrary.org/obo/UBERON_0008775` +### sex cord `http://purl.obolibrary.org/obo/UBERON_0005295` #### Removed -- [proximal epiphysis of fibula](http://purl.obolibrary.org/obo/UBERON_0008775) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "caput fibulae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Head_of_fibula" +- [sex cord](http://purl.obolibrary.org/obo/UBERON_0005295) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EHDAA2:0004051" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [proximal epiphysis of fibula](http://purl.obolibrary.org/obo/UBERON_0008775) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "caput fibulae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Head_of_fibula" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### sexually immature organism `http://purl.obolibrary.org/obo/UBERON_0007021` +#### Removed +- [sexually immature organism](http://purl.obolibrary.org/obo/UBERON_0007021) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Whole organism that is not fully grown or sexually mature.[TAO]" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -### proximal epiphysis of metacarpal bone `http://purl.obolibrary.org/obo/UBERON_0004416` -#### Removed -- [proximal epiphysis of metacarpal bone](http://purl.obolibrary.org/obo/UBERON_0004416) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "basis ossis metacarpi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TAO:wd" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0002047" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:33795" -#### Added -- [proximal epiphysis of metacarpal bone](http://purl.obolibrary.org/obo/UBERON_0004416) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "basis ossis metacarpi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### sexually immature stage `http://purl.obolibrary.org/obo/UBERON_0000112` +#### Removed +- [sexually immature stage](http://purl.obolibrary.org/obo/UBERON_0000112) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In mammals this would include infant (nourishment from lactation) and juvenile (prepubertal no longer dependent on mother)" + +- [sexually immature stage](http://purl.obolibrary.org/obo/UBERON_0000112) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The stage of being a sexually immature adult animal[XAO:1000010]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "XAO:1000010" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:33795" -### proximal epiphysis of metatarsal bone `http://purl.obolibrary.org/obo/UBERON_0004415` +### shares ancestor with `http://purl.obolibrary.org/obo/RO_0002158` #### Removed -- [proximal epiphysis of metatarsal bone](http://purl.obolibrary.org/obo/UBERON_0004415) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "basis ossis metatarsi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:33817" +- [shares ancestor with](http://purl.obolibrary.org/obo/RO_0002158) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "Consider obsoleting and merging with child relation, 'in homology relationship with'" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [shares ancestor with](http://purl.obolibrary.org/obo/RO_0002158) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002158" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [shares ancestor with](http://purl.obolibrary.org/obo/RO_0002158) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "homologous_to" -#### Added -- [proximal epiphysis of metatarsal bone](http://purl.obolibrary.org/obo/UBERON_0004415) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "basis ossis metatarsi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:33817" +- [shares ancestor with](http://purl.obolibrary.org/obo/RO_0002158) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [shares ancestor with](http://purl.obolibrary.org/obo/RO_0002158) [id](http://www.geneontology.org/formats/oboInOwl#id) "homologous_to" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [shares ancestor with](http://purl.obolibrary.org/obo/RO_0002158) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" -### proximal epiphysis of phalanx of manus `http://purl.obolibrary.org/obo/UBERON_0004414` + +### shoulder `http://purl.obolibrary.org/obo/UBERON_0001467` #### Removed -- [proximal epiphysis of phalanx of manus](http://purl.obolibrary.org/obo/UBERON_0004414) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "basis phalangis manus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:226482" +- [shoulder](http://purl.obolibrary.org/obo/UBERON_0001467) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) endochondral elements of the early tetrapod shoulder develop from two centers of ossification, giving rise to a scapula and a 'coracoid'.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.332" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [proximal epiphysis of phalanx of manus](http://purl.obolibrary.org/obo/UBERON_0004414) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "basis phalangis manus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:226482" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000342" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [shoulder](http://purl.obolibrary.org/obo/UBERON_0001467) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "In FMA, the shoulder is part of the pectoral girdle region. in MA, shoulder structures like shoulder joints, bones, nerves etc are part of the shoulder and the forelimb. E.g. humerus is a shoulder bone" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" -### proximal phalanx of manus `http://purl.obolibrary.org/obo/UBERON_0002234` + +### shoulder bone `http://purl.obolibrary.org/obo/UBERON_0003461` #### Removed -- [proximal phalanx of manus](http://purl.obolibrary.org/obo/UBERON_0002234) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "phalanx proximalis manus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:75816" +- [shoulder bone](http://purl.obolibrary.org/obo/UBERON_0003461) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "this is a forelimb bone in MA, but this would lead to part-disjointness violations." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [shoulder bone](http://purl.obolibrary.org/obo/UBERON_0003461) SubClassOf [bone of pectoral complex](http://purl.obolibrary.org/obo/UBERON_0010741) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "MA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "UBERONREF:0000003" #### Added -- [proximal phalanx of manus](http://purl.obolibrary.org/obo/UBERON_0002234) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "phalanx proximalis manus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:75816" - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [shoulder bone](http://purl.obolibrary.org/obo/UBERON_0003461) SubClassOf [bone of pectoral complex](http://purl.obolibrary.org/obo/UBERON_0010741) -### proximal phalanx of pes `http://purl.obolibrary.org/obo/UBERON_0003868` +### shoulder joint `http://purl.obolibrary.org/obo/UBERON_0016884` #### Removed -- [proximal phalanx of pes](http://purl.obolibrary.org/obo/UBERON_0003868) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "phalanx proximalis pedis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:75828" +- [shoulder joint](http://purl.obolibrary.org/obo/UBERON_0016884) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D012785" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + +- [shoulder joint](http://purl.obolibrary.org/obo/UBERON_0016884) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [shoulder joint primordium](http://purl.obolibrary.org/obo/UBERON_0006292) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" #### Added -- [proximal phalanx of pes](http://purl.obolibrary.org/obo/UBERON_0003868) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "phalanx proximalis pedis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [shoulder joint](http://purl.obolibrary.org/obo/UBERON_0016884) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [shoulder joint primordium](http://purl.obolibrary.org/obo/UBERON_0006292) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:75828" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### shoulder joint primordium `http://purl.obolibrary.org/obo/UBERON_0006292` +#### Removed +- [shoulder joint primordium](http://purl.obolibrary.org/obo/UBERON_0006292) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "this is part of the forelimb skeleton in EHDAA2, but this violates part-disjointness" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EHDAA2" -### pudendal vein `http://purl.obolibrary.org/obo/UBERON_0009029` + +### sialic acid-binding Ig-like lectin 5 `http://purl.obolibrary.org/obo/PR_000001927` #### Removed -- [pudendal vein](http://purl.obolibrary.org/obo/UBERON_0009029) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vena pudendales" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.1002/ca.23705" +- [sialic acid-binding Ig-like lectin 5](http://purl.obolibrary.org/obo/PR_000001927) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [sialic acid-binding Ig-like lectin 5 (human)](http://purl.obolibrary.org/obo/PR_O15389) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [pudendal vein](http://purl.obolibrary.org/obo/UBERON_0009029) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vena pudendae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.1002/ca.23705" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### sialic acid-binding Ig-like lectin 6 `http://purl.obolibrary.org/obo/PR_000001928` +#### Removed +- [sialic acid-binding Ig-like lectin 6](http://purl.obolibrary.org/obo/PR_000001928) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [sialic acid-binding Ig-like lectin 6 (human)](http://purl.obolibrary.org/obo/PR_O43699) -#### Added -- [pudendal vein](http://purl.obolibrary.org/obo/UBERON_0009029) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vena pudendales" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.1002/ca.23705" -- [pudendal vein](http://purl.obolibrary.org/obo/UBERON_0009029) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vena pudendae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### sialoadhesin `http://purl.obolibrary.org/obo/PR_000001931` +#### Removed +- [sialoadhesin](http://purl.obolibrary.org/obo/PR_000001931) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [sialoadhesin (human)](http://purl.obolibrary.org/obo/PR_Q9BZZ2) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.1002/ca.23705" -### pulmonary acinus `http://purl.obolibrary.org/obo/UBERON_0008874` +### signal transducer CD24 `http://purl.obolibrary.org/obo/PR_000001932` #### Removed -- [pulmonary acinus](http://purl.obolibrary.org/obo/UBERON_0008874) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "acinus pulmonaris" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:7313" +- [signal transducer CD24](http://purl.obolibrary.org/obo/PR_000001932) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [signal transducer CD24 (human)](http://purl.obolibrary.org/obo/PR_P25063) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [pulmonary acinus](http://purl.obolibrary.org/obo/UBERON_0008874) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arbor alveolaris" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:7313" +### simple columnar epithelium `http://purl.obolibrary.org/obo/UBERON_0000485` +#### Removed +- [simple columnar epithelium](http://purl.obolibrary.org/obo/UBERON_0000485) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007027" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [pulmonary acinus](http://purl.obolibrary.org/obo/UBERON_0008874) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arbor alveolaris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### simple squamous epithelium `http://purl.obolibrary.org/obo/UBERON_0000487` +#### Removed +- [simple squamous epithelium](http://purl.obolibrary.org/obo/UBERON_0000487) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Unilaminar epithelium that consists of a single layer of squamous cells.[CARO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:45565" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:7313" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://orcid.org/0000-0001-9114-8737" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -- [pulmonary acinus](http://purl.obolibrary.org/obo/UBERON_0008874) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "acinus pulmonaris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "CARO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:7313" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "CARO:0000070" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### pulmonary alveolar duct `http://purl.obolibrary.org/obo/UBERON_0002173` +### simultaneous with `http://purl.obolibrary.org/obo/RO_0002082` #### Removed -- [pulmonary alveolar duct](http://purl.obolibrary.org/obo/UBERON_0002173) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ductus alveolaris" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:7341" +- [simultaneous with](http://purl.obolibrary.org/obo/RO_0002082) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) "David Osumi-Sutherland" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [simultaneous with](http://purl.obolibrary.org/obo/RO_0002082) [id](http://www.geneontology.org/formats/oboInOwl#id) "simultaneous_with" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [simultaneous with](http://purl.obolibrary.org/obo/RO_0002082) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" -#### Added -- [pulmonary alveolar duct](http://purl.obolibrary.org/obo/UBERON_0002173) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ductus alveolaris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [simultaneous with](http://purl.obolibrary.org/obo/RO_0002082) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002082" + +- [simultaneous with](http://purl.obolibrary.org/obo/RO_0002082) [label](http://www.w3.org/2000/01/rdf-schema#label) "simultaneous with" + +- [simultaneous with](http://purl.obolibrary.org/obo/RO_0002082) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-7073-9172](https://orcid.org/0000-0002-7073-9172) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:7341" +- [simultaneous with](http://purl.obolibrary.org/obo/RO_0002082) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "simultaneous_with" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### pulmonary artery `http://purl.obolibrary.org/obo/UBERON_0002012` +### sinus venosus `http://purl.obolibrary.org/obo/UBERON_0002063` #### Removed -- [pulmonary artery](http://purl.obolibrary.org/obo/UBERON_0002012) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria pulmonalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pulmonary_artery" +- [sinus venosus](http://purl.obolibrary.org/obo/UBERON_0002063) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Part of the circulatory system which receives blood from the systemic veins and contracts to pump the blood into the atrium of the heart.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010505" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -- [pulmonary artery](http://purl.obolibrary.org/obo/UBERON_0002012) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "truncus pulmonalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pulmonary_artery" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" -#### Added -- [pulmonary artery](http://purl.obolibrary.org/obo/UBERON_0002012) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria pulmonalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [sinus venosus](http://purl.obolibrary.org/obo/UBERON_0002063) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In humans, it exists distinctly only in the embryonic heart, where it is found between the two venae cavae. In the adult, it is incorporated into the wall of the right atrium to form a smooth part called the sinus venarum, also known as the venarum sinus, which is separated from the rest of the atrium by a ridge of fibres called the crista terminalis. The sinus venosus also forms the SA node and the coronary sinus. In the embryo, the thin walls of the sinus venosus are connected below with the right ventricle, and medially with the left atrium, but are free in the rest of their extent. It receives blood from the vitelline vein, umbilical vein and common cardinal vein. It originally starts as a paired structure but shifts towards associating only with the right atrium as the embryonic heart develops. The left portion shrinks in size and eventually forms the coronary sinus and oblique vein of the left atrium, whereas the right part becomes incorporated into the right atrium to form the sinus venarmu" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pulmonary_artery" +- [sinus venosus](http://purl.obolibrary.org/obo/UBERON_0002063) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In zebrafish, the sinus venosus also acts as a pacemaker and is the first to contract" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFA:0000154" -- [pulmonary artery](http://purl.obolibrary.org/obo/UBERON_0002012) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "truncus pulmonalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [sinus venosus](http://purl.obolibrary.org/obo/UBERON_0002063) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Heart region collecting blood from the paired common cardinal veins and delivering to the atrium. One of four components of the heart. The sinus venosus also acts as a pacemaker and is the first to contract. Kimmel et al, 1995.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pulmonary_artery" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000154" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -### pulmonary artery endothelial cell `http://purl.obolibrary.org/obo/CL_1001568` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -#### Added -- [pulmonary artery endothelial cell](http://purl.obolibrary.org/obo/CL_1001568) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [sinus venosus](http://purl.obolibrary.org/obo/UBERON_0002063) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### pulmonary interstitial fibroblast `http://purl.obolibrary.org/obo/CL_0002241` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [pulmonary interstitial fibroblast](http://purl.obolibrary.org/obo/CL_0002241) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.428" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000177" -### pulmonary ionocyte `http://purl.obolibrary.org/obo/CL_0017000` +- [sinus venosus](http://purl.obolibrary.org/obo/UBERON_0002063) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In fish, receives venous blood from the systemic circulation through paired hepatic veins, anterior jugular veins and Cuvierian ducts[PMID:20735616]" -#### Added -- [pulmonary ionocyte](http://purl.obolibrary.org/obo/CL_0017000) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [sinus venosus](http://purl.obolibrary.org/obo/UBERON_0002063) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### pulmonary lobule `http://purl.obolibrary.org/obo/UBERON_0010368` + +### sinusoid `http://purl.obolibrary.org/obo/UBERON_0003909` #### Removed -- [pulmonary lobule](http://purl.obolibrary.org/obo/UBERON_0010368) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lobulus pulmonis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:75739" +- [sinusoid](http://purl.obolibrary.org/obo/UBERON_0003909) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "some sources give discontinuous capillary as synonym but this may be a subtype - see FMA:63198 discontinuous sinusoid (undefined)." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [sinusoid](http://purl.obolibrary.org/obo/UBERON_0003909) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Fenestrated blood vessel endothelium with pores that are large enough for blood cells to pass. The basal lamina and gap junctions may be discontinuous.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -#### Added -- [pulmonary lobule](http://purl.obolibrary.org/obo/UBERON_0010368) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lobulus pulmonis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:75739" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005261" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [sinusoid](http://purl.obolibrary.org/obo/UBERON_0003909) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "sinusoidal" -### pulmonary surfactant `http://purl.obolibrary.org/obo/UBERON_0008826` + +### skeletal element `http://purl.obolibrary.org/obo/UBERON_0004765` #### Removed -- [pulmonary surfactant](http://purl.obolibrary.org/obo/UBERON_0008826) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D011663" +- [skeletal element](http://purl.obolibrary.org/obo/UBERON_0004765) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -#### Added -- [pulmonary surfactant](http://purl.obolibrary.org/obo/UBERON_0008826) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D011663" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PSPUB:0000170" - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000128" +- [skeletal element](http://purl.obolibrary.org/obo/UBERON_0004765) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001890" -### pulmonary vein `http://purl.obolibrary.org/obo/UBERON_0002016` -#### Removed -- [pulmonary vein](http://purl.obolibrary.org/obo/UBERON_0002016) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "venae pulmonales" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pulmonary_vein" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TAO:VSAO_workshop" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -#### Added -- [pulmonary vein](http://purl.obolibrary.org/obo/UBERON_0002016) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "venae pulmonales" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pulmonary_vein" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### pvalb GABAergic cortical interneuron `http://purl.obolibrary.org/obo/CL_4023018` +### skeletal joint `http://purl.obolibrary.org/obo/UBERON_0000982` +#### Removed +- [skeletal joint](http://purl.obolibrary.org/obo/UBERON_0000982) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000367" -#### Added -- [pvalb GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023018) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TAO:pem" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -### pyloric antrum `http://purl.obolibrary.org/obo/UBERON_0001165` -#### Removed -- [pyloric antrum](http://purl.obolibrary.org/obo/UBERON_0001165) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "antrum pyloricum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pyloric_antrum" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001732" +- [skeletal joint](http://purl.obolibrary.org/obo/UBERON_0000982) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000101" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -#### Added -- [pyloric antrum](http://purl.obolibrary.org/obo/UBERON_0001165) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "antrum pyloricum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PSPUB:0000170" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pyloric_antrum" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001732" -### pyloric canal `http://purl.obolibrary.org/obo/UBERON_0008858` +### skeletal ligament `http://purl.obolibrary.org/obo/UBERON_0008846` #### Removed -- [pyloric canal](http://purl.obolibrary.org/obo/UBERON_0008858) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "canalis pyloricus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pyloric_canal" +- [skeletal ligament](http://purl.obolibrary.org/obo/UBERON_0008846) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Ligament organ that primarily consists of regular dense connective tissue aggregated into fasciculi; connects bone and cartilage organs. Examples: sutural ligament, ligament of pinna, tarsal ligament[FMA:25624]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:25624" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [skeletal ligament](http://purl.obolibrary.org/obo/UBERON_0008846) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Dense regular connective tissue connecting two or more adjacent skeletal elements or supporting an organ.[VSAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000072" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PSPUB:0000170" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" + +- [skeletal ligament](http://purl.obolibrary.org/obo/UBERON_0008846) SubClassOf [connects](http://purl.obolibrary.org/obo/RO_0002176) some [skeletal element](http://purl.obolibrary.org/obo/UBERON_0004765) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "bones or cartilage organs" #### Added -- [pyloric canal](http://purl.obolibrary.org/obo/UBERON_0008858) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "canalis pyloricus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pyloric_canal" +- [skeletal ligament](http://purl.obolibrary.org/obo/UBERON_0008846) SubClassOf [connects](http://purl.obolibrary.org/obo/RO_0002176) some [skeletal element](http://purl.obolibrary.org/obo/UBERON_0004765) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + +### skeletal muscle of trunk `http://purl.obolibrary.org/obo/UBERON_0001774` +#### Removed +- [skeletal muscle of trunk](http://purl.obolibrary.org/obo/UBERON_0001774) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "Many ontologies do not appear to have a coherent distinction between an individual muscle and the musculature (i.e. the set of muscles in a region), so we group all together here." -### pylorus `http://purl.obolibrary.org/obo/UBERON_0001166` + +### skeletal muscle tissue `http://purl.obolibrary.org/obo/UBERON_0001134` #### Removed -- [pylorus](http://purl.obolibrary.org/obo/UBERON_0001166) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "valvula pylori" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pylorus" +- [skeletal muscle tissue](http://purl.obolibrary.org/obo/UBERON_0001134) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "This result implies the following views in terms of evolutionary differentiation: (1) Arthropod striated muscle and vertebrate skeletal and cardiac muscles share a common ancestor. In other words, they did not evolve independently (...) (5) The divergence of vertebrate skeletal and cardiac muscles/vertebrate smooth muscle and nonmuscle is at least before that of vertebrates/arthropods. In other words, emergence of skeletal and cardiac musle type tissues preceded the vertebrate/arthropod divergence (ca. 700 MYA).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [pylorus](http://purl.obolibrary.org/obo/UBERON_0001166) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pars pylorica" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [pylorus](http://purl.obolibrary.org/obo/UBERON_0001166) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pars pylorica gastricae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:14581" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000319" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:10368962 Oota S, Saitou N, Phylogenetic relationship of muscle tissues deduced from superimposition of gene trees. Mol Biol Evol (1999)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [skeletal muscle tissue](http://purl.obolibrary.org/obo/UBERON_0001134) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005277" -#### Added -- [pylorus](http://purl.obolibrary.org/obo/UBERON_0001166) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "valvula pylori" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Pylorus" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -- [pylorus](http://purl.obolibrary.org/obo/UBERON_0001166) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pars pylorica" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -- [pylorus](http://purl.obolibrary.org/obo/UBERON_0001166) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pars pylorica gastricae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [skeletal muscle tissue](http://purl.obolibrary.org/obo/UBERON_0001134) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA]" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "FMA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:14581" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "FMA:14069" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### pyramidal neuron `http://purl.obolibrary.org/obo/CL_0000598` +### skeletal muscle tissue of eye `http://purl.obolibrary.org/obo/UBERON_0003269` #### Added -- [pyramidal neuron](http://purl.obolibrary.org/obo/CL_0000598) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [skeletal muscle tissue of eye](http://purl.obolibrary.org/obo/UBERON_0003269) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### radial glial cell `http://purl.obolibrary.org/obo/CL_0000681` +### skeletal muscle tissue of trapezius `http://purl.obolibrary.org/obo/UBERON_0004509` #### Added -- [radial glial cell](http://purl.obolibrary.org/obo/CL_0000681) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [skeletal muscle tissue of trapezius](http://purl.obolibrary.org/obo/UBERON_0004509) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) -### raphe nuclei `http://purl.obolibrary.org/obo/UBERON_0004684` +### skeletal musculature `http://purl.obolibrary.org/obo/UBERON_0018254` #### Removed -- [raphe nuclei](http://purl.obolibrary.org/obo/UBERON_0004684) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nuclei raphes" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Raphe_nuclei" +- [skeletal musculature](http://purl.obolibrary.org/obo/UBERON_0018254) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MA:0000165" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [raphe nuclei](http://purl.obolibrary.org/obo/UBERON_0004684) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nuclei raphes" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:84017" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### skeletal system `http://purl.obolibrary.org/obo/UBERON_0001434` +#### Removed +- [skeletal system](http://purl.obolibrary.org/obo/UBERON_0001434) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [nervous system](http://purl.obolibrary.org/obo/UBERON_0001016) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [skeletal system](http://purl.obolibrary.org/obo/UBERON_0001434) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "skeletal" -#### Added -- [raphe nuclei](http://purl.obolibrary.org/obo/UBERON_0004684) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nuclei raphes" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:84017" +- [skeletal system](http://purl.obolibrary.org/obo/UBERON_0001434) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1159/000324245 Donoghue PCJ, Sansom IJ, Origin and early evolution of vertebrate skeletonization. Microscopy research and technique (2002)" -- [raphe nuclei](http://purl.obolibrary.org/obo/UBERON_0004684) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nuclei raphes" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Raphe_nuclei" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001254" +- [skeletal system](http://purl.obolibrary.org/obo/UBERON_0001434) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000434" -### rectal venous plexus `http://purl.obolibrary.org/obo/UBERON_0008887` -#### Removed -- [rectal venous plexus](http://purl.obolibrary.org/obo/UBERON_0008887) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "plexus venosus rectalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Rectal_venous_plexus" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -- [rectal venous plexus](http://purl.obolibrary.org/obo/UBERON_0008887) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "plexus haemorrhoidalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Rectal_venous_plexus" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TAO:wd" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [skeletal system](http://purl.obolibrary.org/obo/UBERON_0001434) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "GO" -#### Added -- [rectal venous plexus](http://purl.obolibrary.org/obo/UBERON_0008887) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "plexus venosus rectalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [skeletal system](http://purl.obolibrary.org/obo/UBERON_0001434) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "System that provides physical support to the organism.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000566" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Rectal_venous_plexus" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" -- [rectal venous plexus](http://purl.obolibrary.org/obo/UBERON_0008887) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "plexus haemorrhoidalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Rectal_venous_plexus" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" +- [skeletal system](http://purl.obolibrary.org/obo/UBERON_0001434) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070" -### recurrent laryngeal nerve `http://purl.obolibrary.org/obo/UBERON_0003716` -#### Removed -- [recurrent laryngeal nerve](http://purl.obolibrary.org/obo/UBERON_0003716) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus laryngeus recurrens" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Recurrent_laryngeal_nerve" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PSPUB:0000170" -#### Added -- [recurrent laryngeal nerve](http://purl.obolibrary.org/obo/UBERON_0003716) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus laryngeus recurrens" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Recurrent_laryngeal_nerve" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000027" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" -### red bone marrow `http://purl.obolibrary.org/obo/UBERON_0000361` -#### Removed -- [red bone marrow](http://purl.obolibrary.org/obo/UBERON_0000361) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "medulla ossium rubra" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001160" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### skeletal tissue `http://purl.obolibrary.org/obo/UBERON_0004755` +#### Removed +- [skeletal tissue](http://purl.obolibrary.org/obo/UBERON_0004755) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]" + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "taken from version of VSAO used in TAO and used directly in Uberon" -#### Added -- [red bone marrow](http://purl.obolibrary.org/obo/UBERON_0000361) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "medulla ossium rubra" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001160" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000015" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -### red pulp of spleen `http://purl.obolibrary.org/obo/UBERON_0001250` -#### Removed -- [red pulp of spleen](http://purl.obolibrary.org/obo/UBERON_0001250) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pulpa rubra" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15844" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PSPUB:0000170" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [skeletal tissue](http://purl.obolibrary.org/obo/UBERON_0004755) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [skeletogenic cell](http://purl.obolibrary.org/obo/CL_0007001) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "VSAO" -- [red pulp of spleen](http://purl.obolibrary.org/obo/UBERON_0001250) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pulpa splenica" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Red_pulp" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000015" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" #### Added -- [red pulp of spleen](http://purl.obolibrary.org/obo/UBERON_0001250) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pulpa splenica" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Red_pulp" +- [skeletal tissue](http://purl.obolibrary.org/obo/UBERON_0004755) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [skeletogenic cell](http://purl.obolibrary.org/obo/CL_0007001) -- [red pulp of spleen](http://purl.obolibrary.org/obo/UBERON_0001250) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pulpa rubra" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15844" +### skeleton `http://purl.obolibrary.org/obo/UBERON_0004288` +#### Removed +- [skeleton](http://purl.obolibrary.org/obo/UBERON_0004288) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000026" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -### regular atrial cardiac myocyte `http://purl.obolibrary.org/obo/CL_0002129` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" -#### Added -- [regular atrial cardiac myocyte](http://purl.obolibrary.org/obo/CL_0002129) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [skeleton](http://purl.obolibrary.org/obo/UBERON_0004288) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [musculature of body](http://purl.obolibrary.org/obo/UBERON_0000383) +- [skeleton](http://purl.obolibrary.org/obo/UBERON_0004288) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "skeletal" -### regular ventricular cardiac myocyte `http://purl.obolibrary.org/obo/CL_0002131` -#### Added -- [regular ventricular cardiac myocyte](http://purl.obolibrary.org/obo/CL_0002131) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### skeleton of `http://purl.obolibrary.org/obo/RO_0002576` +#### Removed +- [skeleton of](http://purl.obolibrary.org/obo/RO_0002576) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "skeleton_of" -### regulation of calcium ion import `http://purl.obolibrary.org/obo/GO_0090279` +- [skeleton of](http://purl.obolibrary.org/obo/RO_0002576) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) -#### Added -- [regulation of calcium ion import](http://purl.obolibrary.org/obo/GO_0090279) [label](http://www.w3.org/2000/01/rdf-schema#label) "regulation of calcium ion import" +- [skeleton of](http://purl.obolibrary.org/obo/RO_0002576) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002576" -- [regulation of calcium ion import](http://purl.obolibrary.org/obo/GO_0090279) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" +- [skeleton of](http://purl.obolibrary.org/obo/RO_0002576) [id](http://www.geneontology.org/formats/oboInOwl#id) "skeleton_of" -- [regulation of calcium ion import](http://purl.obolibrary.org/obo/GO_0090279) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:0090279" +- [skeleton of](http://purl.obolibrary.org/obo/RO_0002576) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" -- [regulation of calcium ion import](http://purl.obolibrary.org/obo/GO_0090279) [creation date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2010-02-08T05:11:20Z" -- [regulation of calcium ion import](http://purl.obolibrary.org/obo/GO_0090279) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any process that modulates the rate, frequency, or extent of the directed movement of calcium ions into a cell or organelle." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:BHF" -- [regulation of calcium ion import](http://purl.obolibrary.org/obo/GO_0090279) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "regulation of transmembrane calcium influx" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tb" +### skeleton of digitopodium `http://purl.obolibrary.org/obo/UBERON_0012150` +#### Removed +- [skeleton of digitopodium](http://purl.obolibrary.org/obo/UBERON_0012150) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "some sources call this the acropodium. see https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod" -- [regulation of calcium ion import](http://purl.obolibrary.org/obo/GO_0090279) [created by](http://www.geneontology.org/formats/oboInOwl#created_by) "tb" +#### Added +- [skeleton of digitopodium](http://purl.obolibrary.org/obo/UBERON_0012150) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -- Class: [regulation of calcium ion import](http://purl.obolibrary.org/obo/GO_0090279) -- [regulation of calcium ion import](http://purl.obolibrary.org/obo/GO_0090279) EquivalentTo [biological regulation](http://purl.obolibrary.org/obo/GO_0065007) and ([regulates](http://purl.obolibrary.org/obo/RO_0002211) some [calcium ion import](http://purl.obolibrary.org/obo/GO_0070509)) +### skeleton of limb `http://purl.obolibrary.org/obo/UBERON_0004381` +#### Removed +- [skeleton of limb](http://purl.obolibrary.org/obo/UBERON_0004381) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "EHDAA2 considers hip and shoulder joints part of limb skeleton." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EHDAA2" -- [regulation of calcium ion import](http://purl.obolibrary.org/obo/GO_0090279) SubClassOf [regulation of calcium ion transport](http://purl.obolibrary.org/obo/GO_0051924) +- [skeleton of limb](http://purl.obolibrary.org/obo/UBERON_0004381) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Skeletal subdivision that is part of the limb.[VSAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070" -- [regulation of calcium ion import](http://purl.obolibrary.org/obo/GO_0090279) SubClassOf [regulates](http://purl.obolibrary.org/obo/RO_0002211) some [calcium ion import](http://purl.obolibrary.org/obo/GO_0070509) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000300" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -### regulation of calcium ion import across plasma membrane `http://purl.obolibrary.org/obo/GO_1905664` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" -#### Added -- [regulation of calcium ion import across plasma membrane](http://purl.obolibrary.org/obo/GO_1905664) SubClassOf [regulation of calcium ion import](http://purl.obolibrary.org/obo/GO_0090279) -### regulation of cellular amino acid biosynthetic process `http://purl.obolibrary.org/obo/GO_2000282` +### skeleton of lower jaw `http://purl.obolibrary.org/obo/UBERON_0003278` #### Removed -- [regulation of cellular amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000282) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" - -- [regulation of cellular amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000282) [label](http://www.w3.org/2000/01/rdf-schema#label) "regulation of cellular amino acid biosynthetic process" +- [skeleton of lower jaw](http://purl.obolibrary.org/obo/UBERON_0003278) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The jaw joint of all jawed vertebrates, except for mammals, involves the quadrate and articular bones, or the posterior ends of the palatoquadrate and mandibular cartilages; A correlate of the conversion of the articular and quadrate bones to the malleus and incus is that all adult mammals have a jaw joint that lies between the dentary of the lower jaw and the squamosal bone of the skull roof.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [regulation of cellular amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000282) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:2000282" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [regulation of cellular amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000282) [creation date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2010-12-10T11:54:19Z" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [regulation of cellular amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000282) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "regulation of cellular amino acid anabolism" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:obol" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.241 and p.101" -- [regulation of cellular amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000282) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "regulation of cellular amino acid biosynthesis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:obol" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000428" -- [regulation of cellular amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000282) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "regulation of cellular amino acid synthesis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:obol" +- [skeleton of lower jaw](http://purl.obolibrary.org/obo/UBERON_0003278) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The ventral portion of the first pharyngeal arch, comprising the lower jaw.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -- [regulation of cellular amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000282) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "regulation of cellular amino acid formation" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:obol" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -- [regulation of cellular amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000282) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "regulation of amino acid biosynthetic process" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:obol" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -- [regulation of cellular amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000282) [created by](http://www.geneontology.org/formats/oboInOwl#created_by) "vw" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001273" -- [regulation of cellular amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000282) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any process that modulates the frequency, rate or extent of cellular amino acid biosynthetic process." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:obol" +- [skeleton of lower jaw](http://purl.obolibrary.org/obo/UBERON_0003278) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:17906" -- Class: [regulation of cellular amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000282) +- [skeleton of lower jaw](http://purl.obolibrary.org/obo/UBERON_0003278) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "Inclusion of the FMA class 'lower jaw' is debatable - this mostly corresponds to the lower jaw skeleton (with 'maxillary part of mouth' corresponding to the upper jaw region); however, the FMA class also includes gingiva. See also: https://github.com/obophenotype/mouse-anatomy-ontology/issues/102" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" -- [regulation of cellular amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000282) EquivalentTo [biological regulation](http://purl.obolibrary.org/obo/GO_0065007) and ([regulates](http://purl.obolibrary.org/obo/RO_0002211) some [amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_0008652)) - -- [regulation of cellular amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000282) SubClassOf [regulation of cellular amino acid metabolic process](http://purl.obolibrary.org/obo/GO_0006521) +#### Added +- [skeleton of lower jaw](http://purl.obolibrary.org/obo/UBERON_0003278) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) -- [regulation of cellular amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000282) SubClassOf [regulation of biosynthetic process](http://purl.obolibrary.org/obo/GO_0009889) -- [regulation of cellular amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_2000282) SubClassOf [regulates](http://purl.obolibrary.org/obo/RO_0002211) some [amino acid biosynthetic process](http://purl.obolibrary.org/obo/GO_0008652) +### skeleton of manual digitopodium `http://purl.obolibrary.org/obo/UBERON_0012151` +#### Removed +- [skeleton of manual digitopodium](http://purl.obolibrary.org/obo/UBERON_0012151) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "some sources call this the acropodium. see https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod" -### regulation of cellular amino acid metabolic process `http://purl.obolibrary.org/obo/GO_0006521` +### skeleton of manus `http://purl.obolibrary.org/obo/UBERON_0001442` #### Removed -- [regulation of cellular amino acid metabolic process](http://purl.obolibrary.org/obo/GO_0006521) SubClassOf [regulation of nitrogen compound metabolic process](http://purl.obolibrary.org/obo/GO_0051171) +- [skeleton of manus](http://purl.obolibrary.org/obo/UBERON_0001442) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) -### regulation of cytoplasmic transport `http://purl.obolibrary.org/obo/GO_1903649` +### skeleton of pedal digitopodium `http://purl.obolibrary.org/obo/UBERON_0012152` #### Removed -- [regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903649) [created by](http://www.geneontology.org/formats/oboInOwl#created_by) "jl" +- [skeleton of pedal digitopodium](http://purl.obolibrary.org/obo/UBERON_0012152) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "some sources call this the acropodium. see https://github.com/obophenotype/uberon/wiki/Subdivisions-of-the-autopod" -- [regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903649) [label](http://www.w3.org/2000/01/rdf-schema#label) "regulation of cytoplasmic transport" -- [regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903649) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any process that modulates the frequency, rate or extent of cytoplasmic transport." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:25049409" - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO_REF:0000058" +### skeleton of pes `http://purl.obolibrary.org/obo/UBERON_0001445` +#### Removed +- [skeleton of pes](http://purl.obolibrary.org/obo/UBERON_0001445) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) -- [regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903649) [has narrow synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "regulation of cytoplasmic streaming" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:TermGenie" -- [regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903649) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:1903649" -- [regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903649) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" +### skeleton of upper jaw `http://purl.obolibrary.org/obo/UBERON_0003277` +#### Removed +- [skeleton of upper jaw](http://purl.obolibrary.org/obo/UBERON_0003277) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "EMAPA/MA placement unclear. See https://github.com/obophenotype/mouse-anatomy-ontology/issues/102" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EMAPA" -- [regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903649) [creation date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2014-11-24T13:38:17Z" +- [skeleton of upper jaw](http://purl.obolibrary.org/obo/UBERON_0003277) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The jaw joint of all jawed vertebrates, except for mammals, involves the quadrate and articular bones, or the posterior ends of the palatoquadrate and mandibular cartilages; A correlate of the conversion of the articular and quadrate bones to the malleus and incus is that all adult mammals have a jaw joint that lies between the dentary of the lower jaw and the squamosal bone of the skull roof.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- Class: [regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903649) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903649) EquivalentTo [biological regulation](http://purl.obolibrary.org/obo/GO_0065007) and ([regulates](http://purl.obolibrary.org/obo/RO_0002211) some [cytosolic transport](http://purl.obolibrary.org/obo/GO_0016482)) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903649) SubClassOf [regulates](http://purl.obolibrary.org/obo/RO_0002211) some [cytosolic transport](http://purl.obolibrary.org/obo/GO_0016482) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.241 and p.101" -- [regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903649) SubClassOf [regulation of intracellular transport](http://purl.obolibrary.org/obo/GO_0032386) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000429" +#### Added +- [skeleton of upper jaw](http://purl.obolibrary.org/obo/UBERON_0003277) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) -### regulation of dense core granule transport `http://purl.obolibrary.org/obo/GO_1904809` -#### Removed -- [regulation of dense core granule transport](http://purl.obolibrary.org/obo/GO_1904809) SubClassOf [regulation of cytoplasmic transport](http://purl.obolibrary.org/obo/GO_1903649) +### skin appendage follicle `http://purl.obolibrary.org/obo/UBERON_0036150` #### Added -- [regulation of dense core granule transport](http://purl.obolibrary.org/obo/GO_1904809) SubClassOf [regulation of intracellular transport](http://purl.obolibrary.org/obo/GO_0032386) +- [skin appendage follicle](http://purl.obolibrary.org/obo/UBERON_0036150) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### regulation of nitric oxide biosynthetic process `http://purl.obolibrary.org/obo/GO_0045428` +### skin epidermis `http://purl.obolibrary.org/obo/UBERON_0001003` #### Removed -- [regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045428) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "regulation of nitric oxide biosynthesis" +- [skin epidermis](http://purl.obolibrary.org/obo/UBERON_0001003) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) outer epithelia in all metazoan animals are homologous. (...) The ancestor of all metazoans likely had an epidermis with a basal extracellular matrix (ECM), an apical extracellular glycocalyx, and one cilium with a striated rootlet per cell.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000077" -- [regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045428) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "regulation of nitric oxide synthesis" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045428) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of nitric oxide." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:go_curators" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045428) [label](http://www.w3.org/2000/01/rdf-schema#label) "regulation of nitric oxide biosynthetic process" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045428) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "regulation of nitric oxide anabolism" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.71-72" -- [regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045428) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "regulation of nitric oxide formation" +- [skin epidermis](http://purl.obolibrary.org/obo/UBERON_0001003) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A cellular, multilayered epithelium derived from the ectoderm. Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. Le Guellec et al, 2004.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -- [regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045428) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000105" -- [regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045428) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:0045428" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -- Class: [regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045428) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -- [regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045428) EquivalentTo [biological regulation](http://purl.obolibrary.org/obo/GO_0065007) and ([regulates](http://purl.obolibrary.org/obo/RO_0002211) some [nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0006809)) +- [skin epidermis](http://purl.obolibrary.org/obo/UBERON_0001003) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Zebrafish epidermis consists only of living cells unlike terrestrial vertebrates in which dead, keratinized cells are present. In terrestrial vertebrates the epidermis often forms an outer keratinized or cornified layer, the stratum corneum. Interaction between the epideris and dermis gives rise to feathers (birds), hair and mammary glands (mammals), teeth and scales (placoid: chondrichthyans; cosmoids, ganoid, cycloid in bony fishes)." -- [regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045428) SubClassOf [regulation of nitrogen compound metabolic process](http://purl.obolibrary.org/obo/GO_0051171) +- [skin epidermis](http://purl.obolibrary.org/obo/UBERON_0001003) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: subclass external integument structures (AAO:0000961)[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -- [regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045428) SubClassOf [regulates](http://purl.obolibrary.org/obo/RO_0002211) some [nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0006809) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -- [regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045428) SubClassOf [regulation of cellular biosynthetic process](http://purl.obolibrary.org/obo/GO_0031326) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000143" -- [regulation of nitric oxide biosynthetic process](http://purl.obolibrary.org/obo/GO_0045428) SubClassOf [regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_0080164) +- [skin epidermis](http://purl.obolibrary.org/obo/UBERON_0001003) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The outer epithelial layer of the external integument of the body that is derived from the embryonic epiblast.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000143" -### regulation of nitric oxide metabolic process `http://purl.obolibrary.org/obo/GO_0080164` -#### Removed -- [regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_0080164) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" -- [regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_0080164) [created by](http://www.geneontology.org/formats/oboInOwl#created_by) "dhl" +- [skin epidermis](http://purl.obolibrary.org/obo/UBERON_0001003) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "epidermal" -- [regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_0080164) [label](http://www.w3.org/2000/01/rdf-schema#label) "regulation of nitric oxide metabolic process" -- [regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_0080164) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:0080164" -- [regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_0080164) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitric oxide, nitrogen monoxide (NO), a colorless gas only slightly soluble in water." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:DHL" +### skin epithelium `http://purl.obolibrary.org/obo/UBERON_0019204` +#### Removed +- [skin epithelium](http://purl.obolibrary.org/obo/UBERON_0019204) SubClassOf [epithelium](http://purl.obolibrary.org/obo/UBERON_0000483) + +#### Added +- [skin epithelium](http://purl.obolibrary.org/obo/UBERON_0019204) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) -- [regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_0080164) [creation date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2010-09-23T04:02:50Z" -- Class: [regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_0080164) +### skin gland `http://purl.obolibrary.org/obo/UBERON_0002419` -- [regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_0080164) EquivalentTo [biological regulation](http://purl.obolibrary.org/obo/GO_0065007) and ([regulates](http://purl.obolibrary.org/obo/RO_0002211) some [nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_0046209)) +#### Added +- [skin gland](http://purl.obolibrary.org/obo/UBERON_0002419) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -- [regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_0080164) SubClassOf [regulates](http://purl.obolibrary.org/obo/RO_0002211) some [nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_0046209) -- [regulation of nitric oxide metabolic process](http://purl.obolibrary.org/obo/GO_0080164) SubClassOf [regulation of metabolic process](http://purl.obolibrary.org/obo/GO_0019222) +### skin muscle `http://purl.obolibrary.org/obo/UBERON_0004253` +#### Removed +- [skin muscle](http://purl.obolibrary.org/obo/UBERON_0004253) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in MA, the only skin muscle is arrector pili. The only integumental muscle is panniculus carnosus. In EMAPA, the arrector pili only" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" -### regulation of synaptic signaling by nitric oxide `http://purl.obolibrary.org/obo/GO_0150045` +### skin of body `http://purl.obolibrary.org/obo/UBERON_0002097` #### Removed -- [regulation of synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0150045) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:0150045" +- [skin of body](http://purl.obolibrary.org/obo/UBERON_0002097) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "consider 'integumentary system' for invertebrates" -- [regulation of synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0150045) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any process that modulates the frequency, rate or extent of synaptic signaling by nitric oxide." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:26311509" +- [skin of body](http://purl.obolibrary.org/obo/UBERON_0002097) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "MA uses the term skin to refer to what is called here: zone of skin" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + +#### Added +- [skin of body](http://purl.obolibrary.org/obo/UBERON_0002097) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:bc" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:aruk" +### skin of clitoris `http://purl.obolibrary.org/obo/UBERON_0005298` -- [regulation of synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0150045) [label](http://www.w3.org/2000/01/rdf-schema#label) "regulation of synaptic signaling by nitric oxide" +#### Added +- [skin of clitoris](http://purl.obolibrary.org/obo/UBERON_0005298) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -- [regulation of synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0150045) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_synapse](http://purl.obolibrary.org/obo/go#goslim_synapse) -- [regulation of synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0150045) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" +### skin of hip `http://purl.obolibrary.org/obo/UBERON_0001554` +#### Removed +- [skin of hip](http://purl.obolibrary.org/obo/UBERON_0001554) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in MA this isa hindlimb skin" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" -- [regulation of synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0150045) [created by](http://www.geneontology.org/formats/oboInOwl#created_by) "bc" -- [regulation of synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0150045) [creation date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2018-04-23T09:42:25Z" -- Class: [regulation of synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0150045) +### skin of iliac crest region `http://purl.obolibrary.org/obo/UBERON_8480026` -- [regulation of synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0150045) EquivalentTo [biological regulation](http://purl.obolibrary.org/obo/GO_0065007) and ([regulates](http://purl.obolibrary.org/obo/RO_0002211) some [synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0099163)) +#### Added +- [skin of iliac crest region](http://purl.obolibrary.org/obo/UBERON_8480026) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -- [regulation of synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0150045) SubClassOf [regulation of cell communication](http://purl.obolibrary.org/obo/GO_0010646) -- [regulation of synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0150045) SubClassOf [regulates](http://purl.obolibrary.org/obo/RO_0002211) some [synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0099163) +### skin of leg `http://purl.obolibrary.org/obo/UBERON_0001511` +#### Removed +- [skin of leg](http://purl.obolibrary.org/obo/UBERON_0001511) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:18156" -- [regulation of synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0150045) SubClassOf [regulation of signaling](http://purl.obolibrary.org/obo/GO_0023051) +- [skin of leg](http://purl.obolibrary.org/obo/UBERON_0001511) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:18159" -### regulatory T cell `http://purl.obolibrary.org/obo/CL_0000815` +### skin of penis `http://purl.obolibrary.org/obo/UBERON_0001331` #### Added -- [regulatory T cell](http://purl.obolibrary.org/obo/CL_0000815) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [skin of penis](http://purl.obolibrary.org/obo/UBERON_0001331) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### renal afferent arteriole `http://purl.obolibrary.org/obo/UBERON_0004639` +### skin of prepuce of penis `http://purl.obolibrary.org/obo/UBERON_0001471` #### Removed -- [renal afferent arteriole](http://purl.obolibrary.org/obo/UBERON_0004639) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteriola glomerularis afferens" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [skin of prepuce of penis](http://purl.obolibrary.org/obo/UBERON_0001471) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EV:0100109" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Afferent_arterioles" -- [renal afferent arteriole](http://purl.obolibrary.org/obo/UBERON_0004639) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arteriola glomerularis afferens renis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:77042" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" - -#### Added -- [renal afferent arteriole](http://purl.obolibrary.org/obo/UBERON_0004639) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arteriola glomerularis afferens renis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:77042" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### skin of shoulder `http://purl.obolibrary.org/obo/UBERON_0001483` +#### Removed +- [skin of shoulder](http://purl.obolibrary.org/obo/UBERON_0001483) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in MA this is a subclass of forelimb skin, but this violates part-disjointness in Uberon" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [renal afferent arteriole](http://purl.obolibrary.org/obo/UBERON_0004639) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteriola glomerularis afferens" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Afferent_arterioles" +### skull `http://purl.obolibrary.org/obo/UBERON_0003129` +#### Removed +- [skull](http://purl.obolibrary.org/obo/UBERON_0003129) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in FMA the skull is divided into orbit, neurocranium (8 parts), viscerocranium (26 parts). Here we have a separate overlapping division into cranium and mandible." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" +- [skull](http://purl.obolibrary.org/obo/UBERON_0003129) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "A skull that is missing a mandible is only a cranium; this is the source of a very commonly made error in terminology. Those animals having skulls are called craniates" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" -### renal alpha-intercalated cell `http://purl.obolibrary.org/obo/CL_0005011` +- [skull](http://purl.obolibrary.org/obo/UBERON_0003129) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in many ontologies, the structure called the cranium is inclusive of the mandible/lower jaw skeleton" #### Added -- [renal alpha-intercalated cell](http://purl.obolibrary.org/obo/CL_0005011) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [skull](http://purl.obolibrary.org/obo/UBERON_0003129) SubClassOf [structure with developmental contribution from neural crest](http://purl.obolibrary.org/obo/UBERON_0010314) -### renal artery `http://purl.obolibrary.org/obo/UBERON_0001184` +### slow muscle tissue `http://purl.obolibrary.org/obo/UBERON_0006907` #### Removed -- [renal artery](http://purl.obolibrary.org/obo/UBERON_0001184) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria renalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Renal_artery" +- [slow muscle tissue](http://purl.obolibrary.org/obo/UBERON_0006907) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "The fast and slow skeletal muscles are different in terms of twitching speed (Fitts 1994), and they are believed to be derived from distinct myogenic precursors (Stockdale 1992)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [slow muscle tissue](http://purl.obolibrary.org/obo/UBERON_0006907) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "check if CALOHA term is for fiber or tissue." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "CALOHA" -#### Added -- [renal artery](http://purl.obolibrary.org/obo/UBERON_0001184) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria renalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Renal_artery" +### small intestine `http://purl.obolibrary.org/obo/UBERON_0002108` +#### Removed +- [small intestine](http://purl.obolibrary.org/obo/UBERON_0002108) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### renal beta-intercalated cell `http://purl.obolibrary.org/obo/CL_0002201` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [renal beta-intercalated cell](http://purl.obolibrary.org/obo/CL_0002201) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.566" -### renal collecting system `http://purl.obolibrary.org/obo/UBERON_0004100` -#### Removed -- [renal collecting system](http://purl.obolibrary.org/obo/UBERON_0004100) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tubulus renalis colligens" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Collecting_duct_system" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000055" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [small intestine](http://purl.obolibrary.org/obo/UBERON_0002108) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The terminal region of the mid intestine is comprised of specialized enterocytes that appear to play a role in mucosal immunity. Wallace et al, 2005.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -#### Added -- [renal collecting system](http://purl.obolibrary.org/obo/UBERON_0004100) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tubulus renalis colligens" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001323" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Collecting_duct_system" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -### renal connecting tubule `http://purl.obolibrary.org/obo/UBERON_0005097` -#### Removed -- [renal connecting tubule](http://purl.obolibrary.org/obo/UBERON_0005097) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tubulus renalis arcuatus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Connecting_tubule" +- [small intestine](http://purl.obolibrary.org/obo/UBERON_0002108) SubClassOf [subdivision of digestive tract](http://purl.obolibrary.org/obo/UBERON_0004921) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "cjm" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [order](http://www.geneontology.org/formats/oboInOwl#order) "2" #### Added -- [renal connecting tubule](http://purl.obolibrary.org/obo/UBERON_0005097) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tubulus renalis arcuatus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Connecting_tubule" +- [small intestine](http://purl.obolibrary.org/obo/UBERON_0002108) SubClassOf [subdivision of digestive tract](http://purl.obolibrary.org/obo/UBERON_0004921) -### renal corpuscle `http://purl.obolibrary.org/obo/UBERON_0001229` +### small intestine Peyer's patch `http://purl.obolibrary.org/obo/UBERON_0003454` #### Removed -- [renal corpuscle](http://purl.obolibrary.org/obo/UBERON_0001229) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "corpusculum renis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Renal_corpuscle" +- [small intestine Peyer's patch](http://purl.obolibrary.org/obo/UBERON_0003454) [UBPROP_0000202](http://purl.obolibrary.org/obo/UBPROP_0000202) [FMA_76466](http://purl.obolibrary.org/obo/FMA_76466) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [renal corpuscle](http://purl.obolibrary.org/obo/UBERON_0001229) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "corpusculum renale" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + +### small intestine smooth muscle `http://purl.obolibrary.org/obo/UBERON_0004239` +#### Removed +- [small intestine smooth muscle](http://purl.obolibrary.org/obo/UBERON_0004239) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "MA class may specifically mean muscle layer, but we treat as the sum of smooth muscle in both muscle layer and muscularis mucosa" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" + +- [small intestine smooth muscle](http://purl.obolibrary.org/obo/UBERON_0004239) SubClassOf [overlaps](http://purl.obolibrary.org/obo/RO_0002131) some [muscle layer of small intestine](http://purl.obolibrary.org/obo/UBERON_0011201) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "consider merging" #### Added -- [renal corpuscle](http://purl.obolibrary.org/obo/UBERON_0001229) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "corpusculum renale" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [small intestine smooth muscle](http://purl.obolibrary.org/obo/UBERON_0004239) SubClassOf [overlaps](http://purl.obolibrary.org/obo/RO_0002131) some [muscle layer of small intestine](http://purl.obolibrary.org/obo/UBERON_0011201) -- [renal corpuscle](http://purl.obolibrary.org/obo/UBERON_0001229) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "corpusculum renis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Renal_corpuscle" +### small intestine smooth muscle circular layer `http://purl.obolibrary.org/obo/UBERON_0012401` +#### Added +- [small intestine smooth muscle circular layer](http://purl.obolibrary.org/obo/UBERON_0012401) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### renal efferent arteriole `http://purl.obolibrary.org/obo/UBERON_0004640` -#### Removed -- [renal efferent arteriole](http://purl.obolibrary.org/obo/UBERON_0004640) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteriola glomerularis efferens capsulae renalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Efferent_arteriole" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### small intestine smooth muscle longitudinal layer `http://purl.obolibrary.org/obo/UBERON_0012402` -- [renal efferent arteriole](http://purl.obolibrary.org/obo/UBERON_0004640) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arteriola glomerularis efferens renis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:77043" +#### Added +- [small intestine smooth muscle longitudinal layer](http://purl.obolibrary.org/obo/UBERON_0012402) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### smooth muscle of eye `http://purl.obolibrary.org/obo/UBERON_0003386` #### Added -- [renal efferent arteriole](http://purl.obolibrary.org/obo/UBERON_0004640) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteriola glomerularis efferens capsulae renalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Efferent_arteriole" +- [smooth muscle of eye](http://purl.obolibrary.org/obo/UBERON_0003386) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -- [renal efferent arteriole](http://purl.obolibrary.org/obo/UBERON_0004640) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arteriola glomerularis efferens renis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### smooth muscle tissue `http://purl.obolibrary.org/obo/UBERON_0001135` +#### Removed +- [smooth muscle tissue](http://purl.obolibrary.org/obo/UBERON_0001135) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) the first bilateral animals possessed only smooth muscles with the molecular repertoire necessary to build a striated muscle. (...) it is more parsimonious to regard striated muscle cells as a sister cell type to the smooth muscle cells. In this scenario, striated and smooth muscles would have arisen in the stem lineage that led to the Nephrozoa (i.e. all Bilateria exclusive the acoelomorphs) (Hejnol et al., 2009), from an 'acoel-like' smooth muscle, by segregation and divergence of functions and through differential recruitment of additional genes[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:77043" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001246" -### renal glomerulus `http://purl.obolibrary.org/obo/UBERON_0000074` -#### Removed -- [renal glomerulus](http://purl.obolibrary.org/obo/UBERON_0000074) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "glomerulus renis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Glomerulus" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1002/jez.b.21416 Chiodin M, Achatz JG, Wanninger A, Martinez P, Molecular architecture of muscles in an acoel and its evolutionary implications. Journal of Experimental Zoology (2011)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [smooth muscle tissue](http://purl.obolibrary.org/obo/UBERON_0001135) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -#### Added -- [renal glomerulus](http://purl.obolibrary.org/obo/UBERON_0000074) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "glomerulus renis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005274" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Glomerulus" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -### renal intercalated cell `http://purl.obolibrary.org/obo/CL_0005010` +- [smooth muscle tissue](http://purl.obolibrary.org/obo/UBERON_0001135) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "GO uses visceral and smooth interchangeably. However visceral can also be used in the sense of the viscera. Many fly annotations to smooth muscle terms. If we want to be inclusive of insects have to have a general definition of tissue that includes cells." -#### Added -- [renal intercalated cell](http://purl.obolibrary.org/obo/CL_0005010) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [smooth muscle tissue](http://purl.obolibrary.org/obo/UBERON_0001135) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010244" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -### renal interlobular vein `http://purl.obolibrary.org/obo/UBERON_0005168` -#### Removed -- [renal interlobular vein](http://purl.obolibrary.org/obo/UBERON_0005168) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "venae interlobulares renis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Interlobular_veins" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:CAM" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -- [renal interlobular vein](http://purl.obolibrary.org/obo/UBERON_0005168) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "venae interlobulares renis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71634" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### somatopleure `http://purl.obolibrary.org/obo/UBERON_0004874` +#### Removed +- [somatopleure](http://purl.obolibrary.org/obo/UBERON_0004874) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "Gives rise to the paired appendages in jawed vertebrates. a persistent somatopleure through the redistribution and expansion of the lateral plate mesoderm is a synapomorphy for gnathostomes and a critical step in generating a novel developmental module with dramatic evolutionary potentia (Tulenko et al. 2012) http://burkelab.research.wesleyan.edu/current-projects/lamprey/" -#### Added -- [renal interlobular vein](http://purl.obolibrary.org/obo/UBERON_0005168) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "venae interlobulares renis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [somatopleure](http://purl.obolibrary.org/obo/UBERON_0004874) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "sources differ as to whether this is part-of or develops-from the LPM" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Interlobular_veins" -- [renal interlobular vein](http://purl.obolibrary.org/obo/UBERON_0005168) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "venae interlobulares renis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71634" +### somatosensory system `http://purl.obolibrary.org/obo/UBERON_0003942` +#### Removed +- [somatosensory system](http://purl.obolibrary.org/obo/UBERON_0003942) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The neural tissue involved in the transmission of sensory signals" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "MP:0000959" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [somatosensory system](http://purl.obolibrary.org/obo/UBERON_0003942) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "MP defines this in a may more appropriate to somatosensory cortex" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MP" -### renal interstitial pericyte `http://purl.obolibrary.org/obo/CL_1001318` -#### Added -- [renal interstitial pericyte](http://purl.obolibrary.org/obo/CL_1001318) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### somatostatin `http://purl.obolibrary.org/obo/PR_000015665` +#### Removed +- [somatostatin](http://purl.obolibrary.org/obo/PR_000015665) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [somatostatin (human)](http://purl.obolibrary.org/obo/PR_P61278) -### renal lobe `http://purl.obolibrary.org/obo/UBERON_0009913` + +### somite `http://purl.obolibrary.org/obo/UBERON_0002329` #### Removed -- [renal lobe](http://purl.obolibrary.org/obo/UBERON_0009913) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lobi renales" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Renal_lobe" +- [somite](http://purl.obolibrary.org/obo/UBERON_0002329) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000155" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -#### Added -- [renal lobe](http://purl.obolibrary.org/obo/UBERON_0009913) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lobi renales" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Renal_lobe" +- [somite](http://purl.obolibrary.org/obo/UBERON_0002329) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "EDITOR_NOTE currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk" +- [somite](http://purl.obolibrary.org/obo/UBERON_0002329) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Post-cranial axial segments which form sclerotome and dermomyotome.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" -### renal lobule `http://purl.obolibrary.org/obo/UBERON_0009914` -#### Removed -- [renal lobule](http://purl.obolibrary.org/obo/UBERON_0009914) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lobuli corticales renis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cortical_lobule" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010569" -#### Added -- [renal lobule](http://purl.obolibrary.org/obo/UBERON_0009914) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lobuli corticales renis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Cortical_lobule" +- [somite](http://purl.obolibrary.org/obo/UBERON_0002329) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### renal medulla `http://purl.obolibrary.org/obo/UBERON_0000362` -#### Removed -- [renal medulla](http://purl.obolibrary.org/obo/UBERON_0000362) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "medulla renalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:74268" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.40, DOI:10.1093/icb/43.1.137 Balavoine G, Adoutte A, The segmented urbilateria: a testable scenario. Integrative and Comparative Biology (2003)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000191" -- [renal medulla](http://purl.obolibrary.org/obo/UBERON_0000362) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pyramides renales" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:74268" +- [somite](http://purl.obolibrary.org/obo/UBERON_0002329) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000155" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -#### Added -- [renal medulla](http://purl.obolibrary.org/obo/UBERON_0000362) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pyramides renales" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:74268" +- [somite](http://purl.obolibrary.org/obo/UBERON_0002329) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000155" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -- [renal medulla](http://purl.obolibrary.org/obo/UBERON_0000362) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "medulla renalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:74268" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [somite](http://purl.obolibrary.org/obo/UBERON_0002329) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010569" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### renal pelvis `http://purl.obolibrary.org/obo/UBERON_0001224` -#### Removed -- [renal pelvis](http://purl.obolibrary.org/obo/UBERON_0001224) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "p. renallis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Renal_pelvis" +- [somite](http://purl.obolibrary.org/obo/UBERON_0002329) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "somitic" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [renal pelvis](http://purl.obolibrary.org/obo/UBERON_0001224) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "p. renallis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Renal_pelvis" +### sonic hedgehog protein `http://purl.obolibrary.org/obo/PR_000014841` +#### Removed +- [sonic hedgehog protein](http://purl.obolibrary.org/obo/PR_000014841) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [sonic hedgehog protein (human)](http://purl.obolibrary.org/obo/PR_Q15465) -### renal pelvis/ureter `http://purl.obolibrary.org/obo/UBERON_0036295` -#### Added -- [renal pelvis/ureter](http://purl.obolibrary.org/obo/UBERON_0036295) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas) +### source `http://purl.org/dc/terms/source` +#### Removed +- AnnotationProperty: [source](http://purl.org/dc/terms/source) -- [renal pelvis/ureter](http://purl.obolibrary.org/obo/UBERON_0036295) [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [Homo sapiens](http://purl.obolibrary.org/obo/NCBITaxon_9606) -### renal principal cell `http://purl.obolibrary.org/obo/CL_0005009` +### source `http://www.geneontology.org/formats/oboInOwl#http://purl.org/dc/terms/source` +#### Removed +- AnnotationProperty: [source](http://www.geneontology.org/formats/oboInOwl#http://purl.org/dc/terms/source) -#### Added -- [renal principal cell](http://purl.obolibrary.org/obo/CL_0005009) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### renal system `http://purl.obolibrary.org/obo/UBERON_0001008` +### spatially coextensive with `http://purl.obolibrary.org/obo/RO_0002379` #### Removed -- [renal system](http://purl.obolibrary.org/obo/UBERON_0001008) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005056" +- [spatially coextensive with](http://purl.obolibrary.org/obo/RO_0002379) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) -#### Added -- [renal system](http://purl.obolibrary.org/obo/UBERON_0001008) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005056" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [spatially coextensive with](http://purl.obolibrary.org/obo/RO_0002379) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" +- [spatially coextensive with](http://purl.obolibrary.org/obo/RO_0002379) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "A lump of clay and a statue" -### renal vein `http://purl.obolibrary.org/obo/UBERON_0001140` + + +### spatially disjoint from `http://purl.obolibrary.org/obo/RO_0002163` #### Removed -- [renal vein](http://purl.obolibrary.org/obo/UBERON_0001140) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "venae renales" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Renal_vein" +- [spatially disjoint from](http://purl.obolibrary.org/obo/RO_0002163) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [spatially disjoint from](http://purl.obolibrary.org/obo/RO_0002163) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) [22293552](http://www.ncbi.nlm.nih.gov/pubmed/22293552) -#### Added -- [renal vein](http://purl.obolibrary.org/obo/UBERON_0001140) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "venae renales" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Renal_vein" +- [spatially disjoint from](http://purl.obolibrary.org/obo/RO_0002163) [RO_0001900](http://purl.obolibrary.org/obo/RO_0001900) [RO_0001901](http://purl.obolibrary.org/obo/RO_0001901) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [spatially disjoint from](http://purl.obolibrary.org/obo/RO_0002163) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) +- [spatially disjoint from](http://purl.obolibrary.org/obo/RO_0002163) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" -### reproductive gland `http://purl.obolibrary.org/obo/UBERON_0003937` -#### Removed -- [reproductive gland](http://purl.obolibrary.org/obo/UBERON_0003937) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006162" - - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0003-4423-4370" -#### Added -- [reproductive gland](http://purl.obolibrary.org/obo/UBERON_0003937) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006162" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +### specialization_within `http://www.geneontology.org/formats/oboInOwl#specialization_within` +#### Removed +- AnnotationProperty: [specialization_within](http://www.geneontology.org/formats/oboInOwl#specialization_within) - - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) -### reproductive system `http://purl.obolibrary.org/obo/UBERON_0000990` +### sphenoid bone `http://purl.obolibrary.org/obo/UBERON_0001677` #### Removed -- [reproductive system](http://purl.obolibrary.org/obo/UBERON_0000990) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004857" +- [sphenoid bone](http://purl.obolibrary.org/obo/UBERON_0001677) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "part of viscerocranium (facial skeleton) in FMA" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" -- [reproductive system](http://purl.obolibrary.org/obo/UBERON_0000990) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "systemata genitalia" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Reproductive_system" +- [sphenoid bone](http://purl.obolibrary.org/obo/UBERON_0001677) SubClassOf [overlaps](http://purl.obolibrary.org/obo/RO_0002131) some [splanchnocranium](http://purl.obolibrary.org/obo/UBERON_0008895) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "alisphenoid" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [sphenoid bone](http://purl.obolibrary.org/obo/UBERON_0001677) SubClassOf [overlaps](http://purl.obolibrary.org/obo/RO_0002131) some [chondrocranium](http://purl.obolibrary.org/obo/UBERON_0002241) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "orbito pre and basi sphenoid" -#### Added -- [reproductive system](http://purl.obolibrary.org/obo/UBERON_0000990) [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [Homo sapiens](http://purl.obolibrary.org/obo/NCBITaxon_9606) +- [sphenoid bone](http://purl.obolibrary.org/obo/UBERON_0001677) SubClassOf [overlaps](http://purl.obolibrary.org/obo/RO_0002131) some [dermatocranium](http://purl.obolibrary.org/obo/UBERON_0003113) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "pterygoid process" -- [reproductive system](http://purl.obolibrary.org/obo/UBERON_0000990) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004857" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +#### Added +- [sphenoid bone](http://purl.obolibrary.org/obo/UBERON_0001677) SubClassOf [overlaps](http://purl.obolibrary.org/obo/RO_0002131) some [chondrocranium](http://purl.obolibrary.org/obo/UBERON_0002241) -- [reproductive system](http://purl.obolibrary.org/obo/UBERON_0000990) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas) +- [sphenoid bone](http://purl.obolibrary.org/obo/UBERON_0001677) SubClassOf [overlaps](http://purl.obolibrary.org/obo/RO_0002131) some [dermatocranium](http://purl.obolibrary.org/obo/UBERON_0003113) -- [reproductive system](http://purl.obolibrary.org/obo/UBERON_0000990) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D005835" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) +- [sphenoid bone](http://purl.obolibrary.org/obo/UBERON_0001677) SubClassOf [overlaps](http://purl.obolibrary.org/obo/RO_0002131) some [splanchnocranium](http://purl.obolibrary.org/obo/UBERON_0008895) - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -- [reproductive system](http://purl.obolibrary.org/obo/UBERON_0000990) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "systemata genitalia" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Reproductive_system" +### sphenoid bone pre-cartilage condensation `http://purl.obolibrary.org/obo/UBERON_0009191` - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +#### Added +- [sphenoid bone pre-cartilage condensation](http://purl.obolibrary.org/obo/UBERON_0009191) SubClassOf [mesenchyme derived from neural crest](http://purl.obolibrary.org/obo/UBERON_0014387) -### respiratory basal cell `http://purl.obolibrary.org/obo/CL_0002633` +### sphenoid cartilage element `http://purl.obolibrary.org/obo/UBERON_0009193` #### Added -- [respiratory basal cell](http://purl.obolibrary.org/obo/CL_0002633) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [sphenoid cartilage element](http://purl.obolibrary.org/obo/UBERON_0009193) SubClassOf [mesenchyme derived from neural crest](http://purl.obolibrary.org/obo/UBERON_0014387) -### respiratory bronchiole `http://purl.obolibrary.org/obo/UBERON_0002188` -#### Removed -- [respiratory bronchiole](http://purl.obolibrary.org/obo/UBERON_0002188) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "bronchiolus respiratorii" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Respiratory_bronchiole" +### sphenoid endochondral element `http://purl.obolibrary.org/obo/UBERON_0015060` - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +#### Added +- [sphenoid endochondral element](http://purl.obolibrary.org/obo/UBERON_0015060) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) -- [respiratory bronchiole](http://purl.obolibrary.org/obo/UBERON_0002188) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "bronchiolus respiratorius" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:7412" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### sphenoid lesser wing pre-cartilage condensation `http://purl.obolibrary.org/obo/UBERON_0010728` #### Added -- [respiratory bronchiole](http://purl.obolibrary.org/obo/UBERON_0002188) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "bronchiolus respiratorii" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [sphenoid lesser wing pre-cartilage condensation](http://purl.obolibrary.org/obo/UBERON_0010728) SubClassOf [mesenchyme derived from neural crest](http://purl.obolibrary.org/obo/UBERON_0014387) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Respiratory_bronchiole" -- [respiratory bronchiole](http://purl.obolibrary.org/obo/UBERON_0002188) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "bronchiolus respiratorius" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### sphenoid region `http://purl.obolibrary.org/obo/UBERON_0003111` +#### Removed +- [sphenoid region](http://purl.obolibrary.org/obo/UBERON_0003111) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical cluster that forms the floor and sidewalls of the middle part of the neurocranium.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:7412" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010207" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -### respiratory epithelial cell `http://purl.obolibrary.org/obo/CL_0002368` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -#### Added -- [respiratory epithelial cell](http://purl.obolibrary.org/obo/CL_0002368) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### respiratory goblet cell `http://purl.obolibrary.org/obo/CL_0002370` +### sphincter muscle `http://purl.obolibrary.org/obo/UBERON_0004590` +#### Removed +- [sphincter muscle](http://purl.obolibrary.org/obo/UBERON_0004590) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA class is not a subtype of muscle" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" -#### Added -- [respiratory goblet cell](http://purl.obolibrary.org/obo/CL_0002370) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### respiratory hillock cell `http://purl.obolibrary.org/obo/CL_4030023` +### sphincter of hepatopancreatic ampulla `http://purl.obolibrary.org/obo/UBERON_0004915` #### Added -- [respiratory hillock cell](http://purl.obolibrary.org/obo/CL_4030023) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [sphincter of hepatopancreatic ampulla](http://purl.obolibrary.org/obo/UBERON_0004915) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -### respiratory muscle `http://purl.obolibrary.org/obo/UBERON_0014398` +### sphincter pupillae `http://purl.obolibrary.org/obo/UBERON_0001607` #### Removed -- [respiratory muscle](http://purl.obolibrary.org/obo/UBERON_0014398) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D012132" +- [sphincter pupillae](http://purl.obolibrary.org/obo/UBERON_0001607) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "constricts iris" -#### Added -- [respiratory muscle](http://purl.obolibrary.org/obo/UBERON_0014398) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D012132" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [sphincter pupillae](http://purl.obolibrary.org/obo/UBERON_0001607) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "WP says: It is found in vertebrates and some cephalopods; this class refers to the vertebrate structure" - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) +- [sphincter pupillae](http://purl.obolibrary.org/obo/UBERON_0001607) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In humans, it functions to constrict the pupil in bright light or during accommodation. Its dimensions are about 0.75 mm wide by 0.15 mm thick. It is controlled by parasympathetic fibers that originate from the Edinger-Westphal nucleus, travel along the oculomotor nerve (CN III), synapse in the ciliary ganglion, and then enter the eye via the short ciliary nerves. Initially, all the myocytes are of the smooth muscle type, but much later in life, so that ultimately most cells are of the striated muscle type. [WP,unvetted]" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +- [sphincter pupillae](http://purl.obolibrary.org/obo/UBERON_0001607) SubClassOf [has muscle origin](http://purl.obolibrary.org/obo/RO_0002372) some [iris](http://purl.obolibrary.org/obo/UBERON_0001769) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "dbpedia" + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "encircles iris" -### respiratory segment of nasal mucosa `http://purl.obolibrary.org/obo/UBERON_0015786` -#### Removed -- [respiratory segment of nasal mucosa](http://purl.obolibrary.org/obo/UBERON_0015786) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pars respiratoria tunicae mucosae nasi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:77198" +- [sphincter pupillae](http://purl.obolibrary.org/obo/UBERON_0001607) SubClassOf [has muscle insertion](http://purl.obolibrary.org/obo/RO_0002373) some [iris](http://purl.obolibrary.org/obo/UBERON_0001769) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "dbpedia" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "encircles iris" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [sphincter pupillae](http://purl.obolibrary.org/obo/UBERON_0001607) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) #### Added -- [respiratory segment of nasal mucosa](http://purl.obolibrary.org/obo/UBERON_0015786) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pars respiratoria tunicae mucosae nasi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:77198" +- [sphincter pupillae](http://purl.obolibrary.org/obo/UBERON_0001607) SubClassOf [has muscle origin](http://purl.obolibrary.org/obo/RO_0002372) some [iris](http://purl.obolibrary.org/obo/UBERON_0001769) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [sphincter pupillae](http://purl.obolibrary.org/obo/UBERON_0001607) SubClassOf [has muscle insertion](http://purl.obolibrary.org/obo/RO_0002373) some [iris](http://purl.obolibrary.org/obo/UBERON_0001769) -### respiratory system `http://purl.obolibrary.org/obo/UBERON_0001004` +### spinal cord `http://purl.obolibrary.org/obo/UBERON_0002240` #### Removed -- [respiratory system](http://purl.obolibrary.org/obo/UBERON_0001004) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "systema respiratorium" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Respiratory_system" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [spinal cord](http://purl.obolibrary.org/obo/UBERON_0002240) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [respiratory system](http://purl.obolibrary.org/obo/UBERON_0001004) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "systema respiratorium" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Respiratory_system" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165" -### response to nitric oxide `http://purl.obolibrary.org/obo/GO_0071731` -#### Removed -- [response to nitric oxide](http://purl.obolibrary.org/obo/GO_0071731) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:0071731" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000601" -- [response to nitric oxide](http://purl.obolibrary.org/obo/GO_0071731) [created by](http://www.geneontology.org/formats/oboInOwl#created_by) "mah" +- [spinal cord](http://purl.obolibrary.org/obo/UBERON_0002240) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [brain](http://purl.obolibrary.org/obo/UBERON_0000955) + - [exceptions](http://www.geneontology.org/formats/oboInOwl#exceptions) "ZFA" -- [response to nitric oxide](http://purl.obolibrary.org/obo/GO_0071731) [creation date](http://www.geneontology.org/formats/oboInOwl#creation_date) "2010-03-17T04:03:38Z" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "https://github.com/obophenotype/uberon/issues/378" -- [response to nitric oxide](http://purl.obolibrary.org/obo/GO_0071731) [label](http://www.w3.org/2000/01/rdf-schema#label) "response to nitric oxide" + - [status](http://www.geneontology.org/formats/oboInOwl#status) "pending" -- [response to nitric oxide](http://purl.obolibrary.org/obo/GO_0071731) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitric oxide stimulus." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:mah" +- [spinal cord](http://purl.obolibrary.org/obo/UBERON_0002240) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Part of the central nervous system which descends from the hindbrain within the vertebral column.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:yaf" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -- [response to nitric oxide](http://purl.obolibrary.org/obo/GO_0071731) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" -- Class: [response to nitric oxide](http://purl.obolibrary.org/obo/GO_0071731) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010151" -- [response to nitric oxide](http://purl.obolibrary.org/obo/GO_0071731) EquivalentTo [response to stimulus](http://purl.obolibrary.org/obo/GO_0050896) and ([has primary input](http://purl.obolibrary.org/obo/RO_0004009) some [CHEBI_16480](http://purl.obolibrary.org/obo/CHEBI_16480)) +- [spinal cord](http://purl.obolibrary.org/obo/UBERON_0002240) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [spinal cord neural crest](http://purl.obolibrary.org/obo/UBERON_0003853) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" -- [response to nitric oxide](http://purl.obolibrary.org/obo/GO_0071731) SubClassOf [has primary input](http://purl.obolibrary.org/obo/RO_0004009) some [CHEBI_16480](http://purl.obolibrary.org/obo/CHEBI_16480) +- [spinal cord](http://purl.obolibrary.org/obo/UBERON_0002240) SubClassOf [immediate transformation of](http://purl.obolibrary.org/obo/RO_0002495) some [future spinal cord](http://purl.obolibrary.org/obo/UBERON_0006241) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" -- [response to nitric oxide](http://purl.obolibrary.org/obo/GO_0071731) SubClassOf [response to stimulus](http://purl.obolibrary.org/obo/GO_0050896) +#### Added +- [spinal cord](http://purl.obolibrary.org/obo/UBERON_0002240) SubClassOf [immediate transformation of](http://purl.obolibrary.org/obo/RO_0002495) some [future spinal cord](http://purl.obolibrary.org/obo/UBERON_0006241) +- [spinal cord](http://purl.obolibrary.org/obo/UBERON_0002240) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [spinal cord neural crest](http://purl.obolibrary.org/obo/UBERON_0003853) -### response to stimulus `http://purl.obolibrary.org/obo/GO_0050896` +### spinal cord arachnoid mater `http://purl.obolibrary.org/obo/UBERON_0003560` #### Removed -- [response to stimulus](http://purl.obolibrary.org/obo/GO_0050896) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) +- [spinal cord arachnoid mater](http://purl.obolibrary.org/obo/UBERON_0003560) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The middle membrane of the three mammalian meninges covering the brain and spinal cord. [TFD][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000234" -#### Added -- [response to stimulus](http://purl.obolibrary.org/obo/GO_0050896) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### reticular cell `http://purl.obolibrary.org/obo/CL_0000432` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [reticular cell](http://purl.obolibrary.org/obo/CL_0000432) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/arachnoid+mater" +- [spinal cord arachnoid mater](http://purl.obolibrary.org/obo/UBERON_0003560) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639" -### reticular layer of dermis `http://purl.obolibrary.org/obo/UBERON_0001993` -#### Removed -- [reticular layer of dermis](http://purl.obolibrary.org/obo/UBERON_0001993) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "stratum reticulare" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Reticular_dermis" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000234" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + + +### spinal cord ependyma `http://purl.obolibrary.org/obo/UBERON_0005359` +#### Removed +- [spinal cord ependyma](http://purl.obolibrary.org/obo/UBERON_0005359) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in FMA this is treated as part of the ependyma, but here we treat ependyma as a portion" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" -- [reticular layer of dermis](http://purl.obolibrary.org/obo/UBERON_0001993) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum reticulare dermis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:64778" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### spinal cord neural crest `http://purl.obolibrary.org/obo/UBERON_0003853` +#### Removed +- [spinal cord neural crest](http://purl.obolibrary.org/obo/UBERON_0003853) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [reticular layer of dermis](http://purl.obolibrary.org/obo/UBERON_0001993) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum reticulare dermis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:64778" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" -- [reticular layer of dermis](http://purl.obolibrary.org/obo/UBERON_0001993) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "stratum reticulare" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001006" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Reticular_dermis" -### reticulocyte `http://purl.obolibrary.org/obo/CL_0000558` +### spinal cord neural plate `http://purl.obolibrary.org/obo/UBERON_0003854` +#### Removed +- [spinal cord neural plate](http://purl.obolibrary.org/obo/UBERON_0003854) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Neural plate that is part of the spinal cord. [Bgee_curator][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [reticulocyte](http://purl.obolibrary.org/obo/CL_0000558) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### retina horizontal cell `http://purl.obolibrary.org/obo/CL_0000745` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000439" -#### Added -- [retina horizontal cell](http://purl.obolibrary.org/obo/CL_0000745) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [spinal cord neural plate](http://purl.obolibrary.org/obo/UBERON_0003854) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...)[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### retinal bipolar neuron `http://purl.obolibrary.org/obo/CL_0000748` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [retinal bipolar neuron](http://purl.obolibrary.org/obo/CL_0000748) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000439" -### retinal blood vessel endothelial cell `http://purl.obolibrary.org/obo/CL_0002585` -#### Added -- [retinal blood vessel endothelial cell](http://purl.obolibrary.org/obo/CL_0002585) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### spinal cord pia mater `http://purl.obolibrary.org/obo/UBERON_0003555` +#### Removed +- [spinal cord pia mater](http://purl.obolibrary.org/obo/UBERON_0003555) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The innermost of the three mammalian meninges covering the brain and spinal cord. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### retinal cone cell `http://purl.obolibrary.org/obo/CL_0000573` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [retinal cone cell](http://purl.obolibrary.org/obo/CL_0000573) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/pia+mater" -### retinal ganglion cell `http://purl.obolibrary.org/obo/CL_0000740` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000468" -#### Added -- [retinal ganglion cell](http://purl.obolibrary.org/obo/CL_0000740) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [spinal cord pia mater](http://purl.obolibrary.org/obo/UBERON_0003555) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### retinal neural layer `http://purl.obolibrary.org/obo/UBERON_0003902` -#### Removed -- [retinal neural layer](http://purl.obolibrary.org/obo/UBERON_0003902) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum nervosum retinae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58628" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000468" -#### Added -- [retinal neural layer](http://purl.obolibrary.org/obo/UBERON_0003902) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum nervosum retinae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58628" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### spinal cord ventral column `http://purl.obolibrary.org/obo/UBERON_0005375` +#### Removed +- [spinal cord ventral column](http://purl.obolibrary.org/obo/UBERON_0005375) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in MA, this is a subclass of white matter, but in WP/Gray's, the anterior column is a synonym of the grey matter section. is this the same as funiculus? See lateral column." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" +- [spinal cord ventral column](http://purl.obolibrary.org/obo/UBERON_0005375) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The ventral ridge of gray matter in each half of the spinal cord. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### retinal pigment epithelial cell `http://purl.obolibrary.org/obo/CL_0002586` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [retinal pigment epithelial cell](http://purl.obolibrary.org/obo/CL_0002586) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001622" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### retinal rod cell `http://purl.obolibrary.org/obo/CL_0000604` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/anterior+column+of+spinal+cord" -#### Added -- [retinal rod cell](http://purl.obolibrary.org/obo/CL_0000604) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### retrograde trans-synaptic signaling by nitric oxide `http://purl.obolibrary.org/obo/GO_0098924` +### spinal dura mater `http://purl.obolibrary.org/obo/UBERON_0002093` #### Removed -- [retrograde trans-synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0098924) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:0098924" +- [spinal dura mater](http://purl.obolibrary.org/obo/UBERON_0002093) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The outermost and densest membrane of the three mammalian meninges covering the brain and spinal cord. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000411" -- [retrograde trans-synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0098924) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [retrograde trans-synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0098924) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Cell-cell signaling from postsynapse to presynapse, across the synaptic cleft, mediated by nitric oxide." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:dos" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [retrograde trans-synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0098924) [label](http://www.w3.org/2000/01/rdf-schema#label) "retrograde trans-synaptic signaling by nitric oxide" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [retrograde trans-synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0098924) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_synapse](http://purl.obolibrary.org/obo/go#goslim_synapse) +- [spinal dura mater](http://purl.obolibrary.org/obo/UBERON_0002093) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000411" -- Class: [retrograde trans-synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0098924) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639" -- [retrograde trans-synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0098924) EquivalentTo [trans-synaptic signaling](http://purl.obolibrary.org/obo/GO_0099537) and ([has start location](http://purl.obolibrary.org/obo/RO_0002231) some [postsynapse](http://purl.obolibrary.org/obo/GO_0098794)) and ([has end location](http://purl.obolibrary.org/obo/RO_0002232) some [presynapse](http://purl.obolibrary.org/obo/GO_0098793)) and ([process has causal agent](http://purl.obolibrary.org/obo/RO_0002608) some [CHEBI_16480](http://purl.obolibrary.org/obo/CHEBI_16480)) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [retrograde trans-synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0098924) SubClassOf [trans-synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0099548) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [retrograde trans-synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0098924) SubClassOf [retrograde trans-synaptic signaling by soluble gas](http://purl.obolibrary.org/obo/GO_0098923) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### retrograde trans-synaptic signaling by nitric oxide, modulating synaptic transmission `http://purl.obolibrary.org/obo/GO_0098925` +### spinal nerve `http://purl.obolibrary.org/obo/UBERON_0001780` #### Removed -- [retrograde trans-synaptic signaling by nitric oxide, modulating synaptic transmission](http://purl.obolibrary.org/obo/GO_0098925) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_synapse](http://purl.obolibrary.org/obo/go#goslim_synapse) +- [spinal nerve](http://purl.obolibrary.org/obo/UBERON_0001780) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Any of the paired nerves emerging from the spinal cord, each attached to the cord by two roots: ventral and dorsal, and passing out between the vertebrae. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/spinal+nerve" -- [retrograde trans-synaptic signaling by nitric oxide, modulating synaptic transmission](http://purl.obolibrary.org/obo/GO_0098925) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [retrograde trans-synaptic signaling by nitric oxide, modulating synaptic transmission](http://purl.obolibrary.org/obo/GO_0098925) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [retrograde trans-synaptic signaling by nitric oxide, modulating synaptic transmission](http://purl.obolibrary.org/obo/GO_0098925) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:0098925" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [retrograde trans-synaptic signaling by nitric oxide, modulating synaptic transmission](http://purl.obolibrary.org/obo/GO_0098925) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Modulation of synaptic transmission by cell-cell signaling from postsynapse to presynapse, across the synaptic cleft, mediated by nitric oxide." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:dos" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000824" -- [retrograde trans-synaptic signaling by nitric oxide, modulating synaptic transmission](http://purl.obolibrary.org/obo/GO_0098925) [label](http://www.w3.org/2000/01/rdf-schema#label) "retrograde trans-synaptic signaling by nitric oxide, modulating synaptic transmission" -- Class: [retrograde trans-synaptic signaling by nitric oxide, modulating synaptic transmission](http://purl.obolibrary.org/obo/GO_0098925) -- [retrograde trans-synaptic signaling by nitric oxide, modulating synaptic transmission](http://purl.obolibrary.org/obo/GO_0098925) EquivalentTo [trans-synaptic signaling](http://purl.obolibrary.org/obo/GO_0099537) and ([regulates](http://purl.obolibrary.org/obo/RO_0002211) some [chemical synaptic transmission](http://purl.obolibrary.org/obo/GO_0007268)) and ([has start location](http://purl.obolibrary.org/obo/RO_0002231) some [postsynapse](http://purl.obolibrary.org/obo/GO_0098794)) and ([has end location](http://purl.obolibrary.org/obo/RO_0002232) some [presynapse](http://purl.obolibrary.org/obo/GO_0098793)) and ([process has causal agent](http://purl.obolibrary.org/obo/RO_0002608) some [CHEBI_16480](http://purl.obolibrary.org/obo/CHEBI_16480)) +### spinal nerve plexus `http://purl.obolibrary.org/obo/UBERON_0001813` +#### Removed +- [spinal nerve plexus](http://purl.obolibrary.org/obo/UBERON_0001813) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "To reach the muscles, dermatomes, and other structures of the limbs, some of the neurons in the spinal nerves come together in the plexus at the base of the limb. Such plexuses occur in all gnathostomes, and they reach their highest complexity among mammals and birds in which the cervical plexus supplies many ventral neck muscles, the brachial plexus supplies the pectoral appendage, a lumbosacral plexus supplies the pelvic appendage, and a coccygeal plexus supplies some of the pelvic muscles.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000926" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [retrograde trans-synaptic signaling by nitric oxide, modulating synaptic transmission](http://purl.obolibrary.org/obo/GO_0098925) SubClassOf [trans-synaptic signaling by nitric oxide, modulating synaptic transmission](http://purl.obolibrary.org/obo/GO_0099555) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [retrograde trans-synaptic signaling by nitric oxide, modulating synaptic transmission](http://purl.obolibrary.org/obo/GO_0098925) SubClassOf [retrograde trans-synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0098924) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.436" -### retrograde trans-synaptic signaling by soluble gas `http://purl.obolibrary.org/obo/GO_0098923` +### spinal nerve root `http://purl.obolibrary.org/obo/UBERON_0009623` #### Removed -- [retrograde trans-synaptic signaling by soluble gas](http://purl.obolibrary.org/obo/GO_0098923) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Cell-cell signaling from postsynapse to presynapse, across the synaptic cleft, mediated by an soluble gas ligand." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:dos" +- [spinal nerve root](http://purl.obolibrary.org/obo/UBERON_0009623) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "SCTID:362436008" -- [retrograde trans-synaptic signaling by soluble gas](http://purl.obolibrary.org/obo/GO_0098923) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:0098923" +- [spinal nerve root](http://purl.obolibrary.org/obo/UBERON_0009623) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "ZFA has part_of to spinal cord but this causes spatial disjointness violations (CNS/PNS)" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "ZFA" -- [retrograde trans-synaptic signaling by soluble gas](http://purl.obolibrary.org/obo/GO_0098923) [label](http://www.w3.org/2000/01/rdf-schema#label) "retrograde trans-synaptic signaling by soluble gas" -- [retrograde trans-synaptic signaling by soluble gas](http://purl.obolibrary.org/obo/GO_0098923) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_synapse](http://purl.obolibrary.org/obo/go#goslim_synapse) -- [retrograde trans-synaptic signaling by soluble gas](http://purl.obolibrary.org/obo/GO_0098923) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" +### spiral ligament `http://purl.obolibrary.org/obo/UBERON_0006725` +#### Removed +- [spiral ligament](http://purl.obolibrary.org/obo/UBERON_0006725) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "this is not classified as a ligament in FMA" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" -- Class: [retrograde trans-synaptic signaling by soluble gas](http://purl.obolibrary.org/obo/GO_0098923) +#### Added +- [spiral ligament](http://purl.obolibrary.org/obo/UBERON_0006725) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -- [retrograde trans-synaptic signaling by soluble gas](http://purl.obolibrary.org/obo/GO_0098923) EquivalentTo [trans-synaptic signaling by soluble gas](http://purl.obolibrary.org/obo/GO_0099543) and ([has start location](http://purl.obolibrary.org/obo/RO_0002231) some [postsynapse](http://purl.obolibrary.org/obo/GO_0098794)) and ([has end location](http://purl.obolibrary.org/obo/RO_0002232) some [presynapse](http://purl.obolibrary.org/obo/GO_0098793)) -- [retrograde trans-synaptic signaling by soluble gas](http://purl.obolibrary.org/obo/GO_0098923) SubClassOf [trans-synaptic signaling by soluble gas](http://purl.obolibrary.org/obo/GO_0099543) +### spiral organ of cochlea `http://purl.obolibrary.org/obo/UBERON_0002227` +#### Removed +- [spiral organ of cochlea](http://purl.obolibrary.org/obo/UBERON_0002227) [RO_0002174](http://purl.obolibrary.org/obo/RO_0002174) [Sauropsida](http://purl.obolibrary.org/obo/NCBITaxon_8457) -- [retrograde trans-synaptic signaling by soluble gas](http://purl.obolibrary.org/obo/GO_0098923) SubClassOf [retrograde trans-synaptic signaling](http://purl.obolibrary.org/obo/GO_0098917) +- [spiral organ of cochlea](http://purl.obolibrary.org/obo/UBERON_0002227) [RO_0002174](http://purl.obolibrary.org/obo/RO_0002174) [NCBITaxon_8292](http://purl.obolibrary.org/obo/NCBITaxon_8292) +- [spiral organ of cochlea](http://purl.obolibrary.org/obo/UBERON_0002227) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The auditory hair cells in tetrapods are located in the inner ear in a structure known as the basilar papilla. In mammals this structure (along with some related structure) is called the organ of Corti.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### rib `http://purl.obolibrary.org/obo/UBERON_0002228` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [rib](http://purl.obolibrary.org/obo/UBERON_0002228) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "VO:0012403" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001567" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.33" - - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) +- [spiral organ of cochlea](http://purl.obolibrary.org/obo/UBERON_0002227) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "VHOG:0001567" +- [spiral organ of cochlea](http://purl.obolibrary.org/obo/UBERON_0002227) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "in basal early lizards, organized into 3 tonotopically organized areas, the outer areas lack a tectorial membrane[ISBN:9780387714691]" -### ribosome `http://purl.obolibrary.org/obo/GO_0005840` -#### Removed -- [ribosome](http://purl.obolibrary.org/obo/GO_0005840) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) +- [spiral organ of cochlea](http://purl.obolibrary.org/obo/UBERON_0002227) SubClassOf [only in taxon](http://purl.obolibrary.org/obo/RO_0002160) some [Tetrapoda](http://purl.obolibrary.org/obo/NCBITaxon_32523) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "https://github.com/obophenotype/uberon/issues/387" #### Added -- [ribosome](http://purl.obolibrary.org/obo/GO_0005840) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) +- [spiral organ of cochlea](http://purl.obolibrary.org/obo/UBERON_0002227) SubClassOf [only in taxon](http://purl.obolibrary.org/obo/RO_0002160) some [Tetrapoda](http://purl.obolibrary.org/obo/NCBITaxon_32523) +- [spiral organ of cochlea](http://purl.obolibrary.org/obo/UBERON_0002227) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### ribosome biogenesis `http://purl.obolibrary.org/obo/GO_0042254` + +### splanchnic layer of lateral plate mesoderm `http://purl.obolibrary.org/obo/UBERON_0004872` #### Removed -- [ribosome biogenesis](http://purl.obolibrary.org/obo/GO_0042254) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) +- [splanchnic layer of lateral plate mesoderm](http://purl.obolibrary.org/obo/UBERON_0004872) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "BILA" -#### Added -- [ribosome biogenesis](http://purl.obolibrary.org/obo/GO_0042254) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) -### right adrenal gland `http://purl.obolibrary.org/obo/UBERON_0001233` +### splanchnic nerve `http://purl.obolibrary.org/obo/UBERON_0003715` #### Removed -- [right adrenal gland](http://purl.obolibrary.org/obo/UBERON_0001233) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "glandula suprarenalis dexter" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [splanchnic nerve](http://purl.obolibrary.org/obo/UBERON_0003715) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "All carry sympathetic fibers except for the pelvic splanchnic nerves, which carry parasympathetic fibers" -#### Added -- [right adrenal gland](http://purl.obolibrary.org/obo/UBERON_0001233) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "glandula suprarenalis dexter" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### right bundle branch `http://purl.obolibrary.org/obo/UBERON_0005987` +### splanchnocranium `http://purl.obolibrary.org/obo/UBERON_0008895` #### Removed -- [right bundle branch](http://purl.obolibrary.org/obo/UBERON_0005987) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "crus dextrum fasciculi atrioventricularis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [splanchnocranium](http://purl.obolibrary.org/obo/UBERON_0008895) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The part of the skull derived from the embryonic pharyngeal arches. [Biology_Online][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9486" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [right bundle branch](http://purl.obolibrary.org/obo/UBERON_0005987) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "crus dextrum fasciculi atrioventricularis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000315" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9486" +- [splanchnocranium](http://purl.obolibrary.org/obo/UBERON_0008895) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical cluster that is part of the cranium and consists of the jaws, hyoid, and branchial arches.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010157" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -### right cardiac atrium `http://purl.obolibrary.org/obo/UBERON_0002078` -#### Removed -- [right cardiac atrium](http://purl.obolibrary.org/obo/UBERON_0002078) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "atrium dextrum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Right_atrium" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [splanchnocranium](http://purl.obolibrary.org/obo/UBERON_0008895) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical cluster that is part of the cranium and consists of the jaws, hyoid and branchial arches.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -#### Added -- [right cardiac atrium](http://purl.obolibrary.org/obo/UBERON_0002078) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "atrium dextrum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Right_atrium" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001216" -### right crus of diaphragm `http://purl.obolibrary.org/obo/UBERON_0014766` +- [splanchnocranium](http://purl.obolibrary.org/obo/UBERON_0008895) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The skull of ancestral tetrapods has the three basic components that we have been considering: (1) chondrocranium, (2) splanchnocranium, and (3) dermatocranium (reference 1); Each part of the skull arises from a separate phylogenetic source. The most ancient part is the splanchnocranium (visceral cranium), which first arose to support pharyngeal slits in protochordates (reference 2).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.242, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.235" -#### Added -- [right crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014766) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "right crus of diaphragm" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58286" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [right crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014766) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "crus dextrum diaphragmatis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58286" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000315" -- [right crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014766) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" +- [splanchnocranium](http://purl.obolibrary.org/obo/UBERON_0008895) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "VSAO labels this term 'pharyngeal arch' (2012-06-01) - however, it clearly means pharyngeal arch skeleton." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "VSAO" -- [right crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014766) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) +- [splanchnocranium](http://purl.obolibrary.org/obo/UBERON_0008895) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "many sources define this as the part of the endoskeletal that is from pharyngeal arches - this would make it part-disjoint from dermatocranium. However, there are many bones in AOs that have part-paths to both" -- [right crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014766) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "SCTID:362690009" +- [splanchnocranium](http://purl.obolibrary.org/obo/UBERON_0008895) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [cranial neural crest](http://purl.obolibrary.org/obo/UBERON_0003099) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Grays" -- [right crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014766) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "crus dextrum (Diaphragma)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "redundant" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58286" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:11237469" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +#### Added +- [splanchnocranium](http://purl.obolibrary.org/obo/UBERON_0008895) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [cranial neural crest](http://purl.obolibrary.org/obo/UBERON_0003099) -- [right crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014766) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "external sphincter of esophagus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58286" -- [right crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014766) [label](http://www.w3.org/2000/01/rdf-schema#label) "right crus of diaphragm" +### spleen `http://purl.obolibrary.org/obo/UBERON_0002106` +#### Removed +- [spleen](http://purl.obolibrary.org/obo/UBERON_0002106) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "It synthesizes antibodies in its white pulp and removes, from blood and lymph node circulation, antibody-coated bacteria along with antibody-coated blood cells" -- [right crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014766) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A crus of diaphragm that is in_the_right_side_of a diaphragm." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "OBOL:automatic" +- [spleen](http://purl.obolibrary.org/obo/UBERON_0002106) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Neither hagfish nor lampreys possess what might be considered a discrete and condensed spleen. Hagfish possess dispersed lymphoid tissue within the submucosa of the intestine (96) associated with the portal vein (97), whereas lymphoid tissue is associated with the typhlosole portion of the intestine in lampreys (96)" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:20959416" -- [right crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014766) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "right crus of lumbar part of diaphragm" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58286" +- [spleen](http://purl.obolibrary.org/obo/UBERON_0002106) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In humans, it is located in the left upper quadrant of the abdomen. It removes old red blood cells and holds a reserve in case of hemorrhagic shock, especially in animals like horses (not in humans), while recycling iron" -- [right crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014766) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58286" +- [spleen](http://purl.obolibrary.org/obo/UBERON_0002106) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "With the advent of clonal selection, the accumulation and segregation of T and B cells in specialized organs for antigen presentation became necessary, and indeed the spleen is found in all jawed vertebrates, but not in agnathans or invertebrates.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [right crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014766) [id](http://www.geneontology.org/formats/oboInOwl#id) "UBERON:0014766" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- Class: [right crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014766) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [right crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014766) EquivalentTo [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) and ([in right side of](http://purl.obolibrary.org/obo/BSPO_0000121) some [diaphragm](http://purl.obolibrary.org/obo/UBERON_0001103)) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0781765190 Paul WE, Fundamental Immunology (2008) p.94" -- [right crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014766) SubClassOf [crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014765) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000120" -- [right crus of diaphragm](http://purl.obolibrary.org/obo/UBERON_0014766) SubClassOf [in right side of](http://purl.obolibrary.org/obo/BSPO_0000121) some [diaphragm](http://purl.obolibrary.org/obo/UBERON_0001103) +- [spleen](http://purl.obolibrary.org/obo/UBERON_0002106) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "lienal" +- [spleen](http://purl.obolibrary.org/obo/UBERON_0002106) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "An organ involved in red blood cell filtration and immune response.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BMZ" -### right hepatic artery `http://purl.obolibrary.org/obo/UBERON_0015482` -#### Removed -- [right hepatic artery](http://purl.obolibrary.org/obo/UBERON_0015482) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ramus dexter (arteria hepatica propria)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:14778" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010395" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -#### Added -- [right hepatic artery](http://purl.obolibrary.org/obo/UBERON_0015482) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ramus dexter (arteria hepatica propria)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:14778" +- [spleen](http://purl.obolibrary.org/obo/UBERON_0002106) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "splenic" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [spleen](http://purl.obolibrary.org/obo/UBERON_0002106) SubClassOf [digestive system element](http://purl.obolibrary.org/obo/UBERON_0013765) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### right hepatic duct `http://purl.obolibrary.org/obo/UBERON_0001176` -#### Removed -- [right hepatic duct](http://purl.obolibrary.org/obo/UBERON_0001176) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ductus hepaticus dexter" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### spleen B cell corona `http://purl.obolibrary.org/obo/UBERON_0010421` #### Added -- [right hepatic duct](http://purl.obolibrary.org/obo/UBERON_0001176) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ductus hepaticus dexter" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [spleen B cell corona](http://purl.obolibrary.org/obo/UBERON_0010421) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### right lobe of liver `http://purl.obolibrary.org/obo/UBERON_0001114` -#### Removed -- [right lobe of liver](http://purl.obolibrary.org/obo/UBERON_0001114) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lobus hepatis dexter" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Right_lobe_of_liver" +### spleen capsule `http://purl.obolibrary.org/obo/UBERON_0004641` + +#### Added +- [spleen capsule](http://purl.obolibrary.org/obo/UBERON_0004641) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [right lobe of liver](http://purl.obolibrary.org/obo/UBERON_0001114) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lobus hepaticus dexter" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### spleen germinal center `http://purl.obolibrary.org/obo/UBERON_0005196` #### Added -- [right lobe of liver](http://purl.obolibrary.org/obo/UBERON_0001114) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lobus hepatis dexter" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [spleen germinal center](http://purl.obolibrary.org/obo/UBERON_0005196) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Right_lobe_of_liver" -- [right lobe of liver](http://purl.obolibrary.org/obo/UBERON_0001114) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lobus hepaticus dexter" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### spleen lymphoid follicle `http://purl.obolibrary.org/obo/UBERON_0001249` + +#### Added +- [spleen lymphoid follicle](http://purl.obolibrary.org/obo/UBERON_0001249) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### right pulmonary artery `http://purl.obolibrary.org/obo/UBERON_0001651` +### spleen primary B follicle `http://purl.obolibrary.org/obo/UBERON_0004041` #### Removed -- [right pulmonary artery](http://purl.obolibrary.org/obo/UBERON_0001651) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria pulmonalis dextra" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Right_pulmonary_artery" +- [spleen primary B follicle](http://purl.obolibrary.org/obo/UBERON_0004041) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA:15843 is classified as primary follicle so it belongs here" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" + + - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### spleen primordium `http://purl.obolibrary.org/obo/UBERON_0006293` +#### Removed +- [spleen primordium](http://purl.obolibrary.org/obo/UBERON_0006293) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "check difference between splenic and spleen in EMAPA; note that in EHDAA2 the class 'spleen' refers to the mesenchyme" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EMAPA" #### Added -- [right pulmonary artery](http://purl.obolibrary.org/obo/UBERON_0001651) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria pulmonalis dextra" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Right_pulmonary_artery" +- [spleen primordium](http://purl.obolibrary.org/obo/UBERON_0006293) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### spleen pulp `http://purl.obolibrary.org/obo/UBERON_1000023` -### right subclavian artery `http://purl.obolibrary.org/obo/UBERON_0001534` +#### Added +- [spleen pulp](http://purl.obolibrary.org/obo/UBERON_1000023) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + + +### spleen trabecular artery `http://purl.obolibrary.org/obo/UBERON_0010399` #### Removed -- [right subclavian artery](http://purl.obolibrary.org/obo/UBERON_0001534) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arteria subclavia dextra" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:3953" +- [spleen trabecular artery](http://purl.obolibrary.org/obo/UBERON_0010399) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "When the splenic artery passes into the trabecula of the spleen and branches, they become known as the trabecular arteries. When these arteries then reach the white pulp, and become covered with Periarteriolar lymphoid sheaths, the name changes again to central arteries (or central arterioles). Branches of the central arteries are given to the red pulp, and these are called penicillar arteries).[Wikipedia]" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "Wikipedia" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Trabecular_arteries" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [right subclavian artery](http://purl.obolibrary.org/obo/UBERON_0001534) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arteria subclavia dextra" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:3953" +### spleen trabecular vein `http://purl.obolibrary.org/obo/UBERON_0010400` +#### Removed +- [spleen trabecular vein](http://purl.obolibrary.org/obo/UBERON_0010400) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The trabecular veins are the largest veins inside the spleen. It drains the blood collected in the sinuses of the pulp.[Wikipedia]" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "Wikipedia" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Trabecular_veins" -### right ventricular trabecular myocardium `http://purl.obolibrary.org/obo/UBERON_0005066` -#### Removed -- [right ventricular trabecular myocardium](http://purl.obolibrary.org/obo/UBERON_0005066) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO:0003227" + +### splenic cord `http://purl.obolibrary.org/obo/UBERON_0001266` #### Added -- [right ventricular trabecular myocardium](http://purl.obolibrary.org/obo/UBERON_0005066) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Missing definition for term UBERON:0005066. Please replace it using linked reference." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO:0003227" +- [splenic cord](http://purl.obolibrary.org/obo/UBERON_0001266) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### rod bipolar cell `http://purl.obolibrary.org/obo/CL_0000751` +### splenic sinusoid `http://purl.obolibrary.org/obo/UBERON_0003910` +#### Removed +- [splenic sinusoid](http://purl.obolibrary.org/obo/UBERON_0003910) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Whereas man and the rat are in the 'sinusal' group, the mouse belongs in the 'nonsinusal' group. The red pulp of spleens of rat, dog, man, and many other mammals contains an elaborate plexus of sinuses; that of mouse, cat, pig and others has no true sinuses and relatively few veins leading from the meshes into collecting veins - http://www.informatics.jax.org/greenbook/chapters/chapter13.shtml" -#### Added -- [rod bipolar cell](http://purl.obolibrary.org/obo/CL_0000751) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### saccule of membranous labyrinth `http://purl.obolibrary.org/obo/UBERON_0001854` +### spongiotrophoblast layer `http://purl.obolibrary.org/obo/UBERON_0004021` #### Removed -- [saccule of membranous labyrinth](http://purl.obolibrary.org/obo/UBERON_0001854) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "sacculus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Saccule" +- [spongiotrophoblast layer](http://purl.obolibrary.org/obo/UBERON_0004021) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "In the absence of direct lineage analysis, it has been assumed, from histological studies and from the continuity of marker gene expression, that the spongiotrophoblast largely derives from the cells of the ectoplacental cone" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:19829370" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [spongiotrophoblast layer](http://purl.obolibrary.org/obo/UBERON_0004021) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "restriction to Rodentia may be too strong - we apply it for now as we are inheriting the MP definition" -#### Added -- [saccule of membranous labyrinth](http://purl.obolibrary.org/obo/UBERON_0001854) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "sacculus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [spongiotrophoblast layer](http://purl.obolibrary.org/obo/UBERON_0004021) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "Forms a compact layer of non-syncytial cells between the labyrinth and the outer giant cells" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Saccule" +#### Added +- [spongiotrophoblast layer](http://purl.obolibrary.org/obo/UBERON_0004021) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### saliva `http://purl.obolibrary.org/obo/UBERON_0001836` +### squamous epithelium `http://purl.obolibrary.org/obo/UBERON_0006914` #### Removed -- [saliva](http://purl.obolibrary.org/obo/UBERON_0001836) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "saliva molecularis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Saliva" +- [squamous epithelium](http://purl.obolibrary.org/obo/UBERON_0006914) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FBbt" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [saliva](http://purl.obolibrary.org/obo/UBERON_0001836) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "saliva atomaris" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Saliva" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - -- [saliva](http://purl.obolibrary.org/obo/UBERON_0001836) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "sailva normalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Saliva" +### starts `http://purl.obolibrary.org/obo/RO_0002223` +#### Removed +- [starts](http://purl.obolibrary.org/obo/RO_0002223) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002223" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [starts](http://purl.obolibrary.org/obo/RO_0002223) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) "Allen" -#### Added -- [saliva](http://purl.obolibrary.org/obo/UBERON_0001836) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "saliva molecularis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [starts](http://purl.obolibrary.org/obo/RO_0002223) [label](http://www.w3.org/2000/01/rdf-schema#label) "starts" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Saliva" +- [starts](http://purl.obolibrary.org/obo/RO_0002223) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" -- [saliva](http://purl.obolibrary.org/obo/UBERON_0001836) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "sailva normalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [starts](http://purl.obolibrary.org/obo/RO_0002223) [id](http://www.geneontology.org/formats/oboInOwl#id) "starts" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Saliva" +- [starts](http://purl.obolibrary.org/obo/RO_0002223) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) -- [saliva](http://purl.obolibrary.org/obo/UBERON_0001836) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "saliva atomaris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [starts](http://purl.obolibrary.org/obo/RO_0002223) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) "Chris Mungall" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Saliva" +- [starts](http://purl.obolibrary.org/obo/RO_0002223) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "starts" +- [starts](http://purl.obolibrary.org/obo/RO_0002223) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) -### saliva-secreting gland `http://purl.obolibrary.org/obo/UBERON_0001044` -#### Removed -- [saliva-secreting gland](http://purl.obolibrary.org/obo/UBERON_0001044) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "glandulae salivariae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Salivary_gland" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [saliva-secreting gland](http://purl.obolibrary.org/obo/UBERON_0001044) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005382" +### starts with `http://purl.obolibrary.org/obo/RO_0002224` +#### Removed +- [starts with](http://purl.obolibrary.org/obo/RO_0002224) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) -#### Added -- [saliva-secreting gland](http://purl.obolibrary.org/obo/UBERON_0001044) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005382" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [starts with](http://purl.obolibrary.org/obo/RO_0002224) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) "Chris Mungall" -- [saliva-secreting gland](http://purl.obolibrary.org/obo/UBERON_0001044) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "glandulae salivariae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [starts with](http://purl.obolibrary.org/obo/RO_0002224) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Salivary_gland" +- [starts with](http://purl.obolibrary.org/obo/RO_0002224) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" +- [starts with](http://purl.obolibrary.org/obo/RO_0002224) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) -### salivary gland cell `http://purl.obolibrary.org/obo/CL_0009005` +- [starts with](http://purl.obolibrary.org/obo/RO_0002224) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "started by" -#### Added -- [salivary gland cell](http://purl.obolibrary.org/obo/CL_0009005) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### salivatory nucleus `http://purl.obolibrary.org/obo/UBERON_0004133` +### status `http://www.geneontology.org/formats/oboInOwl#status` #### Removed -- [salivatory nucleus](http://purl.obolibrary.org/obo/UBERON_0004133) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO:0021751" +- AnnotationProperty: [status](http://www.geneontology.org/formats/oboInOwl#status) -#### Added -- [salivatory nucleus](http://purl.obolibrary.org/obo/UBERON_0004133) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Missing definition for term UBERON:0004133. Please replace it using linked reference." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO:0021751" -### scala media `http://purl.obolibrary.org/obo/UBERON_0002295` +### sternoclavicular joint `http://purl.obolibrary.org/obo/UBERON_0001469` +#### Removed +- [sternoclavicular joint](http://purl.obolibrary.org/obo/UBERON_0001469) SubClassOf [connects](http://purl.obolibrary.org/obo/RO_0002176) some [clavicle bone](http://purl.obolibrary.org/obo/UBERON_0001105) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "sternal end of the clavicle and first rib" + +- [sternoclavicular joint](http://purl.obolibrary.org/obo/UBERON_0001469) SubClassOf [connects](http://purl.obolibrary.org/obo/RO_0002176) some [sternum](http://purl.obolibrary.org/obo/UBERON_0000975) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "clavicular notch of the manubrium sterni" #### Added -- [scala media](http://purl.obolibrary.org/obo/UBERON_0002295) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D003053" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) +- [sternoclavicular joint](http://purl.obolibrary.org/obo/UBERON_0001469) SubClassOf [connects](http://purl.obolibrary.org/obo/RO_0002176) some [clavicle bone](http://purl.obolibrary.org/obo/UBERON_0001105) - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +- [sternoclavicular joint](http://purl.obolibrary.org/obo/UBERON_0001469) SubClassOf [connects](http://purl.obolibrary.org/obo/RO_0002176) some [sternum](http://purl.obolibrary.org/obo/UBERON_0000975) -### scalp `http://purl.obolibrary.org/obo/UBERON_0000403` +### sternooccipital muscle `http://purl.obolibrary.org/obo/UBERON_0010949` #### Removed -- [scalp](http://purl.obolibrary.org/obo/UBERON_0000403) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "scalpus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Scalp" +- [sternooccipital muscle](http://purl.obolibrary.org/obo/UBERON_0010949) SubClassOf [axial muscle](http://purl.obolibrary.org/obo/UBERON_0003897) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [scalp](http://purl.obolibrary.org/obo/UBERON_0000403) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "scalpus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Scalp" +### sternum `http://purl.obolibrary.org/obo/UBERON_0000975` +#### Removed +- [sternum](http://purl.obolibrary.org/obo/UBERON_0000975) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: part_of postzonal element (AAO:0000938)[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000765" -### sciatic nerve `http://purl.obolibrary.org/obo/UBERON_0001322` -#### Removed -- [sciatic nerve](http://purl.obolibrary.org/obo/UBERON_0001322) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nervus ischiadicus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Sciatic_nerve" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [sternum](http://purl.obolibrary.org/obo/UBERON_0000975) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Single element that constitutes the postzonal area of the pectoral girdle.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001221" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -#### Added -- [sciatic nerve](http://purl.obolibrary.org/obo/UBERON_0001322) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nervus ischiadicus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000765" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Sciatic_nerve" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001221" +- [sternum](http://purl.obolibrary.org/obo/UBERON_0000975) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Fishes lack a sternum. (...) A sternum is absent in the first fossil tetrapods, but it is present in modern amphibians. (...) Thus, a sternum occurs in some modern amphibians, birds, mammals and archosaurs. However, its absence in the common ancestors to these groups means that it has arisen independently several times within the field of the midventral connective tissue.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### sclerotome `http://purl.obolibrary.org/obo/UBERON_0003089` -#### Removed -- [sclerotome](http://purl.obolibrary.org/obo/UBERON_0003089) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "sclerotomus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Sclerotome" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.294" -- [sclerotome](http://purl.obolibrary.org/obo/UBERON_0003089) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006255" - - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0003-4423-4370" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000856" -#### Added -- [sclerotome](http://purl.obolibrary.org/obo/UBERON_0003089) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006255" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [sternum](http://purl.obolibrary.org/obo/UBERON_0000975) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "in birds, either ratite (no keel or carina) or carinate (keel and carina present)" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +- [sternum](http://purl.obolibrary.org/obo/UBERON_0000975) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "sternal" - - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) +- [sternum](http://purl.obolibrary.org/obo/UBERON_0000975) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "While its developmental origins are similar to the ribs (from the myospetum and septum of the trunk region), it is often associated with the pectoral skeleton, due to both function and physical connections (i.e. the coracoid of archosaurs). It may be a single element or a series of smaller structure (sternebrae). Based on Kardong 2012. [PHENOSCAPE:ad]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" -- [sclerotome](http://purl.obolibrary.org/obo/UBERON_0003089) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "sclerotomus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Sclerotome" +- [sternum](http://purl.obolibrary.org/obo/UBERON_0000975) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "It probably first evolved in early tetrapods as an extension of the pectoral girdle; it is not found in fish. In amphibians and reptiles it is typically a shield-shaped structure, often composed entirely of cartilage. It is absent in both turtles and snakes. In birds it is a relatively large bone and typically bears an enormous projecting keel to which the flight muscles are attached. Only in mammals does the sternum take on the elongated, segmented form seen in humans. In some mammals, such as opossums, the individual segments never fuse and remain separated by cartilagenous plates throughout life" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### sebaceous gland `http://purl.obolibrary.org/obo/UBERON_0001821` +### stomach `http://purl.obolibrary.org/obo/UBERON_0000945` #### Removed -- [sebaceous gland](http://purl.obolibrary.org/obo/UBERON_0001821) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "glandula sebacea" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Sebaceous_gland" +- [stomach](http://purl.obolibrary.org/obo/UBERON_0000945) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000579" -#### Added -- [sebaceous gland](http://purl.obolibrary.org/obo/UBERON_0001821) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "glandula sebacea" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Sebaceous_gland" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" +- [stomach](http://purl.obolibrary.org/obo/UBERON_0000945) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "It appears that the stomach has an ancient origin. The stomach first appears in the fish lineage. The prevertebrate chordates do not have a true stomach, whereas the cartilaginous and bony fish do. Although most fish do have a true stomach, some fish species appear to have lost the stomach secondarily. The remaining vertebrate lineages do have a true stomach (at least in the adult animal), although there is great variation in the size and shape of the stomach.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### sebaceous gland cell `http://purl.obolibrary.org/obo/CL_2000021` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [sebaceous gland cell](http://purl.obolibrary.org/obo/CL_2000021) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000408" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### second-messenger-mediated signaling `http://purl.obolibrary.org/obo/GO_0019932` -#### Removed -- [second-messenger-mediated signaling](http://purl.obolibrary.org/obo/GO_0019932) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "second-messenger-mediated signalling" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1046/j.1525-142x.2000.00076.x Smith DM, Grasty RC, Theodosiou NA, Tabin CJ, Nascone-Yoder NM, Evolutionary relationships between the amphibian, avian, and mammalian stomachs. Evolution and development (2000)" + +- [stomach](http://purl.obolibrary.org/obo/UBERON_0000945) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "We restrict this to the vertebrate specific structure - see the grouping class 'food storage organ' for analogous structures in other species. Teleosts: Zebrafish is functionally stomach-less, but may retain ontogenic footprint. Although the precise shape and size of the stomach varies widely among different vertebrates, the relative positions of the oesophageal and duodenal openings remain relatively constant. As a result, the organ always curves somewhat to the left before curving back to meet the pyloric sphincter. However, lampreys, hagfishes, chimaeras, lungfishes, and some teleost fish have no stomach at all, with the oesophagus opening directly into the intestine. The gastric lining is usually divided into two regions, an anterior portion lined by fundic glands, and a posterior with pyloric glands. Cardiac glands are unique to mammals, and even then are absent in a number of species. The distributions of these glands vary between species, and do not always correspond with the same regions as in man. Furthermore, in many non-human mammals, a portion of the stomach anterior to the cardiac glands is lined with epithelium essentially identical to that of the oesophagus. Ruminants, in particular, have a complex stomach, the first three chambers of which are all lined with oesophageal mucosa" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP:Stomach#In_other_animals" -- [second-messenger-mediated signaling](http://purl.obolibrary.org/obo/GO_0019932) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "second messenger-mediated signalling" +- [stomach](http://purl.obolibrary.org/obo/UBERON_0000945) SubClassOf [capable of](http://purl.obolibrary.org/obo/RO_0002215) some [gastric acid secretion](http://purl.obolibrary.org/obo/GO_0001696) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "ISBN:0486692132" -- [second-messenger-mediated signaling](http://purl.obolibrary.org/obo/GO_0019932) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "second messenger mediated signalling" +- [stomach](http://purl.obolibrary.org/obo/UBERON_0000945) SubClassOf [only in taxon](http://purl.obolibrary.org/obo/RO_0002160) some [Gnathostomata ](http://purl.obolibrary.org/obo/NCBITaxon_7776) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0073040584" -- [second-messenger-mediated signaling](http://purl.obolibrary.org/obo/GO_0019932) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:0019932" + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "absent in lampreys and hagfishes" -- [second-messenger-mediated signaling](http://purl.obolibrary.org/obo/GO_0019932) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" +#### Added +- [stomach](http://purl.obolibrary.org/obo/UBERON_0000945) SubClassOf [only in taxon](http://purl.obolibrary.org/obo/RO_0002160) some [Gnathostomata ](http://purl.obolibrary.org/obo/NCBITaxon_7776) -- [second-messenger-mediated signaling](http://purl.obolibrary.org/obo/GO_0019932) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "second messenger-mediated signaling" +- [stomach](http://purl.obolibrary.org/obo/UBERON_0000945) SubClassOf [capable of](http://purl.obolibrary.org/obo/RO_0002215) some [gastric acid secretion](http://purl.obolibrary.org/obo/GO_0001696) -- [second-messenger-mediated signaling](http://purl.obolibrary.org/obo/GO_0019932) [label](http://www.w3.org/2000/01/rdf-schema#label) "second-messenger-mediated signaling" -- [second-messenger-mediated signaling](http://purl.obolibrary.org/obo/GO_0019932) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any intracellular signal transduction in which the signal is passed on within the cell via a second messenger; a small molecule or ion that can be quickly generated or released from intracellular stores, and can diffuse within the cell. Second-messenger signaling includes production or release of the second messenger, and effectors downstream of the second messenger that further transmit the signal within the cell." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Second_messenger_system" +### stomach glandular epithelium `http://purl.obolibrary.org/obo/UBERON_0006924` +#### Removed +- [stomach glandular epithelium](http://purl.obolibrary.org/obo/UBERON_0006924) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:17623" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:15221855" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:signaling" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0815316194" +### stomach lumen `http://purl.obolibrary.org/obo/UBERON_0013525` +#### Removed +- [stomach lumen](http://purl.obolibrary.org/obo/UBERON_0013525) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Organ cavity which is bound by the internal surface of the wall of stomach. Examples: There is only one cavity of stomach[FMA:14585]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:14585" -- [second-messenger-mediated signaling](http://purl.obolibrary.org/obo/GO_0019932) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "second-messenger-mediated signal transduction" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:signaling" -- [second-messenger-mediated signaling](http://purl.obolibrary.org/obo/GO_0019932) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "second messenger mediated signaling" -- Class: [second-messenger-mediated signaling](http://purl.obolibrary.org/obo/GO_0019932) +### stomach muscularis externa `http://purl.obolibrary.org/obo/UBERON_0008856` +#### Removed +- [stomach muscularis externa](http://purl.obolibrary.org/obo/UBERON_0008856) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "the muscularis externa in the stomach differs from that of other GI organs in that it has three layers of smooth muscle instead of two" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" -- [second-messenger-mediated signaling](http://purl.obolibrary.org/obo/GO_0019932) SubClassOf [intracellular signal transduction](http://purl.obolibrary.org/obo/GO_0035556) +#### Added +- [stomach muscularis externa](http://purl.obolibrary.org/obo/UBERON_0008856) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) +### stomodeum `http://purl.obolibrary.org/obo/UBERON_0000930` +#### Removed +- [stomodeum](http://purl.obolibrary.org/obo/UBERON_0000930) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "MP:0012522" -### secondary lens fiber `http://purl.obolibrary.org/obo/CL_0002225` + - [taxon](http://www.geneontology.org/formats/oboInOwl#taxon) "NCBITaxon:40674" -#### Added -- [secondary lens fiber](http://purl.obolibrary.org/obo/CL_0002225) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [stomodeum](http://purl.obolibrary.org/obo/UBERON_0000930) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "stomodeal" +- [stomodeum](http://purl.obolibrary.org/obo/UBERON_0000930) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -### secondary pulmonary lobule `http://purl.obolibrary.org/obo/UBERON_0010369` -#### Removed -- [secondary pulmonary lobule](http://purl.obolibrary.org/obo/UBERON_0010369) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lobulus pulmonis secondarius" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:7414" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001290" -#### Added -- [secondary pulmonary lobule](http://purl.obolibrary.org/obo/UBERON_0010369) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lobulus pulmonis secondarius" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [stomodeum](http://purl.obolibrary.org/obo/UBERON_0000930) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:7414" +- [stomodeum](http://purl.obolibrary.org/obo/UBERON_0000930) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000439" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### secretory cell `http://purl.obolibrary.org/obo/CL_0000151` +### strand of axillary hair `http://purl.obolibrary.org/obo/UBERON_0013699` +#### Removed +- [strand of axillary hair](http://purl.obolibrary.org/obo/UBERON_0013699) [UBPROP_0000202](http://purl.obolibrary.org/obo/UBPROP_0000202) [FMA_70756](http://purl.obolibrary.org/obo/FMA_70756) -#### Added -- [secretory cell](http://purl.obolibrary.org/obo/CL_0000151) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### segment of manus `http://purl.obolibrary.org/obo/UBERON_0005451` +### strand of hair `http://purl.obolibrary.org/obo/UBERON_0001037` #### Removed -- [segment of manus](http://purl.obolibrary.org/obo/UBERON_0005451) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "regio manus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [strand of hair](http://purl.obolibrary.org/obo/UBERON_0001037) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "this class defines an individual hair" #### Added -- [segment of manus](http://purl.obolibrary.org/obo/UBERON_0005451) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "regio manus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [strand of hair](http://purl.obolibrary.org/obo/UBERON_0001037) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### segment of pes `http://purl.obolibrary.org/obo/UBERON_0005445` +### stratum basale of epidermis `http://purl.obolibrary.org/obo/UBERON_0002025` #### Removed -- [segment of pes](http://purl.obolibrary.org/obo/UBERON_0005445) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "regio pedis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [stratum basale of epidermis](http://purl.obolibrary.org/obo/UBERON_0002025) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "consisting of non-keratinized, viable cells, in contrast to the outer (upper) layer of epidermis made up of keratinized, anucleated, non-viable cells" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:24993" +- [stratum basale of epidermis](http://purl.obolibrary.org/obo/UBERON_0002025) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "replaces damaged cells on outside of body" #### Added -- [segment of pes](http://purl.obolibrary.org/obo/UBERON_0005445) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "regio pedis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [stratum basale of epidermis](http://purl.obolibrary.org/obo/UBERON_0002025) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:24993" +- [stratum basale of epidermis](http://purl.obolibrary.org/obo/UBERON_0002025) SubClassOf [structure with developmental contribution from neural crest](http://purl.obolibrary.org/obo/UBERON_0010314) -### semicircular canal `http://purl.obolibrary.org/obo/UBERON_0001840` +### stratum corneum of epidermis `http://purl.obolibrary.org/obo/UBERON_0002027` #### Removed -- [semicircular canal](http://purl.obolibrary.org/obo/UBERON_0001840) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "canalis semicircularis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Semicircular_canal" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [stratum corneum of epidermis](http://purl.obolibrary.org/obo/UBERON_0002027) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "some oral epitehlium also has cornified layer / stratum corneum" -#### Added -- [semicircular canal](http://purl.obolibrary.org/obo/UBERON_0001840) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "canalis semicircularis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [stratum corneum of epidermis](http://purl.obolibrary.org/obo/UBERON_0002027) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The keratinized outermost layer of the epidermis, which is periodically shed.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Semicircular_canal" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:CAM" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### semicircular canal ampulla `http://purl.obolibrary.org/obo/UBERON_0004043` -#### Removed -- [semicircular canal ampulla](http://purl.obolibrary.org/obo/UBERON_0004043) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ampullae osseae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010597" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Osseous_ampullae" +- [stratum corneum of epidermis](http://purl.obolibrary.org/obo/UBERON_0002027) SubClassOf [periderm](http://purl.obolibrary.org/obo/UBERON_0003055) #### Added -- [semicircular canal ampulla](http://purl.obolibrary.org/obo/UBERON_0004043) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ampullae osseae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [stratum corneum of epidermis](http://purl.obolibrary.org/obo/UBERON_0002027) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Osseous_ampullae" +- [stratum corneum of epidermis](http://purl.obolibrary.org/obo/UBERON_0002027) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [skin epidermis](http://purl.obolibrary.org/obo/UBERON_0001003) -### semicircular duct `http://purl.obolibrary.org/obo/UBERON_0001856` -#### Removed -- [semicircular duct](http://purl.obolibrary.org/obo/UBERON_0001856) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D054776" +### stratum granulosum of epidermis `http://purl.obolibrary.org/obo/UBERON_0002069` #### Added -- [semicircular duct](http://purl.obolibrary.org/obo/UBERON_0001856) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D054776" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [stratum granulosum of epidermis](http://purl.obolibrary.org/obo/UBERON_0002069) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +### stratum spinosum of epidermis `http://purl.obolibrary.org/obo/UBERON_0002026` +#### Removed +- [stratum spinosum of epidermis](http://purl.obolibrary.org/obo/UBERON_0002026) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "Has cells that produce and secrete bipolar lipids which prevent evaporation, helping to 'water-proof' the skin. Keratinization begins in the stratum spinosum. [Wikipedia:Stratum_spinosum]" +#### Added +- [stratum spinosum of epidermis](http://purl.obolibrary.org/obo/UBERON_0002026) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### seminal fluid secreting gland `http://purl.obolibrary.org/obo/UBERON_0006868` + +### stria vascularis of cochlear duct `http://purl.obolibrary.org/obo/UBERON_0002282` #### Removed -- [seminal fluid secreting gland](http://purl.obolibrary.org/obo/UBERON_0006868) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004958" +- [stria vascularis of cochlear duct](http://purl.obolibrary.org/obo/UBERON_0002282) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "represented as a wall in FMA. MESH def implies part of spiral ligament but better represented as adjacency / overlaps" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" #### Added -- [seminal fluid secreting gland](http://purl.obolibrary.org/obo/UBERON_0006868) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004958" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [stria vascularis of cochlear duct](http://purl.obolibrary.org/obo/UBERON_0002282) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### seminal vesicle `http://purl.obolibrary.org/obo/UBERON_0000998` +### striated border microvillus layer `http://purl.obolibrary.org/obo/UBERON_0012425` #### Removed -- [seminal vesicle](http://purl.obolibrary.org/obo/UBERON_0000998) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vesiculae seminales" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Seminal_vesicle" +- [striated border microvillus layer](http://purl.obolibrary.org/obo/UBERON_0012425) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA class represents an individual microvillus" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [seminal vesicle](http://purl.obolibrary.org/obo/UBERON_0000998) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vesiculae seminales" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Seminal_vesicle" +### striated muscle tissue `http://purl.obolibrary.org/obo/UBERON_0002036` +#### Removed +- [striated muscle tissue](http://purl.obolibrary.org/obo/UBERON_0002036) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Voluntary muscle tissue arranged in bundles of fibers.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:CAM" -### seminal vesicle glandular cell `http://purl.obolibrary.org/obo/CL_1001597` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010762" -#### Added -- [seminal vesicle glandular cell](http://purl.obolibrary.org/obo/CL_1001597) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### seminiferous tubule of testis `http://purl.obolibrary.org/obo/UBERON_0001343` + +### striatum `http://purl.obolibrary.org/obo/UBERON_0002435` #### Removed -- [seminiferous tubule of testis](http://purl.obolibrary.org/obo/UBERON_0001343) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tubuli seminiferi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Seminiferous_tubule" +- [striatum](http://purl.obolibrary.org/obo/UBERON_0002435) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA divides 'striatum of neuraxis' into 4, neostriatum is seperate class. In NIF these are synonyms. TODO - check striatum vs corpus striatum see Wikipedia:Striatum#History. Check caudoputamen" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [striatum](http://purl.obolibrary.org/obo/UBERON_0002435) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "striatal" -#### Added -- [seminiferous tubule of testis](http://purl.obolibrary.org/obo/UBERON_0001343) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tubuli seminiferi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [striatum](http://purl.obolibrary.org/obo/UBERON_0002435) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0006514](http://purl.obolibrary.org/obo/UBERON_0006514) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Seminiferous_tubule" -### sense organ `http://purl.obolibrary.org/obo/UBERON_0000020` +### stroma `http://purl.obolibrary.org/obo/UBERON_0003891` #### Removed -- [sense organ](http://purl.obolibrary.org/obo/UBERON_0000020) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005155" +- [stroma](http://purl.obolibrary.org/obo/UBERON_0003891) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "stromal" -#### Added -- [sense organ](http://purl.obolibrary.org/obo/UBERON_0000020) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005155" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### sensory ganglion `http://purl.obolibrary.org/obo/UBERON_0001800` -#### Removed -- [sensory ganglion](http://purl.obolibrary.org/obo/UBERON_0001800) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ganglion sensorium" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### stroma of bone marrow `http://purl.obolibrary.org/obo/UBERON_0007195` #### Added -- [sensory ganglion](http://purl.obolibrary.org/obo/UBERON_0001800) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ganglion sensorium" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [stroma of bone marrow](http://purl.obolibrary.org/obo/UBERON_0007195) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### sensory nerve `http://purl.obolibrary.org/obo/UBERON_0001027` -#### Removed -- [sensory nerve](http://purl.obolibrary.org/obo/UBERON_0001027) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005136" +### stroma of thyroid gland `http://purl.obolibrary.org/obo/UBERON_0010233` + +#### Added +- [stroma of thyroid gland](http://purl.obolibrary.org/obo/UBERON_0010233) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -- [sensory nerve](http://purl.obolibrary.org/obo/UBERON_0001027) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus sensorius" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Sensory_nerve" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### stromal choroid plexus macrophage `http://purl.obolibrary.org/obo/CL_4042005` #### Added -- [sensory nerve](http://purl.obolibrary.org/obo/UBERON_0001027) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005136" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [stromal choroid plexus macrophage](http://purl.obolibrary.org/obo/CL_4042005) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A choroid plexus macrophage that is part of a choroid plexus stroma." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38347231" -- [sensory nerve](http://purl.obolibrary.org/obo/UBERON_0001027) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus sensorius" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [stromal choroid plexus macrophage](http://purl.obolibrary.org/obo/CL_4042005) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "stromal cpMΦ" + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [abbreviation](http://purl.obolibrary.org/obo/OMO_0003000) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38347231" + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37232741" + +- [stromal choroid plexus macrophage](http://purl.obolibrary.org/obo/CL_4042005) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) + +- [stromal choroid plexus macrophage](http://purl.obolibrary.org/obo/CL_4042005) [date](http://purl.org/dc/terms/date) "2024-03-26T19:21:51Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- [stromal choroid plexus macrophage](http://purl.obolibrary.org/obo/CL_4042005) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cpstMΦ" + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [abbreviation](http://purl.obolibrary.org/obo/OMO_0003000) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37626977" + +- [stromal choroid plexus macrophage](http://purl.obolibrary.org/obo/CL_4042005) [label](http://www.w3.org/2000/01/rdf-schema#label) "stromal choroid plexus macrophage"@en + +- Class: [stromal choroid plexus macrophage](http://purl.obolibrary.org/obo/CL_4042005) + +- [stromal choroid plexus macrophage](http://purl.obolibrary.org/obo/CL_4042005) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [choroid plexus stroma](http://purl.obolibrary.org/obo/UBERON_0005206) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Sensory_nerve" +- [stromal choroid plexus macrophage](http://purl.obolibrary.org/obo/CL_4042005) SubClassOf [choroid-plexus macrophage](http://purl.obolibrary.org/obo/CL_0000880) -### sensory system `http://purl.obolibrary.org/obo/UBERON_0001032` +### structure with developmental contribution from neural crest `http://purl.obolibrary.org/obo/UBERON_0010314` #### Removed -- [sensory system](http://purl.obolibrary.org/obo/UBERON_0001032) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007692" +- [structure with developmental contribution from neural crest](http://purl.obolibrary.org/obo/UBERON_0010314) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "Grouping term for query purposes" -- [sensory system](http://purl.obolibrary.org/obo/UBERON_0001032) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "organa sensuum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Sensory_system" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [sensory system](http://purl.obolibrary.org/obo/UBERON_0001032) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "organa sensuum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:75259" +### stylopod `http://purl.obolibrary.org/obo/UBERON_0002472` +#### Removed +- [stylopod](http://purl.obolibrary.org/obo/UBERON_0002472) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "Naming conventions for pod terms under discussion within phenoscape group" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [stylopod](http://purl.obolibrary.org/obo/UBERON_0002472) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [zeugopod](http://purl.obolibrary.org/obo/UBERON_0002471) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [stylopod](http://purl.obolibrary.org/obo/UBERON_0002472) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "stylopodial" -#### Added -- [sensory system](http://purl.obolibrary.org/obo/UBERON_0001032) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "organa sensuum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [stylopod](http://purl.obolibrary.org/obo/UBERON_0002472) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [autopod region](http://purl.obolibrary.org/obo/UBERON_0002470) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:75259" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [sensory system](http://purl.obolibrary.org/obo/UBERON_0001032) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007692" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +### stylopodial skeleton `http://purl.obolibrary.org/obo/UBERON_0011583` +#### Removed +- [stylopodial skeleton](http://purl.obolibrary.org/obo/UBERON_0011583) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Proximal element of the limb skeleton consisting of the femur and humerus in the forelimb stylopodium and hindlimb stylopodium respectively.[VSAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "VSAO:NI" -- [sensory system](http://purl.obolibrary.org/obo/UBERON_0001032) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "organa sensuum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0005007" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Sensory_system" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" -### septal nuclear complex `http://purl.obolibrary.org/obo/UBERON_0002663` -#### Removed -- [septal nuclear complex](http://purl.obolibrary.org/obo/UBERON_0002663) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nuclei septales" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Septal_nuclei" +- [stylopodial skeleton](http://purl.obolibrary.org/obo/UBERON_0011583) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "stylopodial" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [stylopodial skeleton](http://purl.obolibrary.org/obo/UBERON_0011583) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "propodial" #### Added -- [septal nuclear complex](http://purl.obolibrary.org/obo/UBERON_0002663) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nuclei septales" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Septal_nuclei" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [stylopodial skeleton](http://purl.obolibrary.org/obo/UBERON_0011583) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### septum of telencephalon `http://purl.obolibrary.org/obo/UBERON_0000446` +### subclavian artery `http://purl.obolibrary.org/obo/UBERON_0001533` #### Removed -- [septum of telencephalon](http://purl.obolibrary.org/obo/UBERON_0000446) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "massa praecommissuralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:255" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [subclavian artery](http://purl.obolibrary.org/obo/UBERON_0001533) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "In human anatomy, the subclavian artery is a major artery of the upper thorax that mainly supplies blood to the head and arms. It is located below the clavicle, hence the name. There is a left subclavian and a right subclavian. On the left side of the body, the subclavian comes directly off the arch of aorta. On the right side of the body, the subclavian arises from the relatively short brachiocephalic artery (trunk) when it bifurcates into the subclavian and the right common carotid artery. The usual branches of the subclavian on both sides of the body are the vertebral artery, the internal thoracic artery, the thyrocervical trunk, the costocervical trunk and the dorsal scapular artery. The subclavian becomes the axillary artery at the lateral border of the first rib[WP]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Subclavian_artery" -- [septum of telencephalon](http://purl.obolibrary.org/obo/UBERON_0000446) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "septum pellucidum (BNA,PNA)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:255" +- [subclavian artery](http://purl.obolibrary.org/obo/UBERON_0001533) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The pectoral (subclavian) arteries originate from the dorsal aorta and takes the blood outward into the fin from the paired portion of the dorsal aorta posterior to the last aortic arch. Kimmel et al. 1993[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005086" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -- [septum of telencephalon](http://purl.obolibrary.org/obo/UBERON_0000446) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "septum telencephali" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:255" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -- [septum of telencephalon](http://purl.obolibrary.org/obo/UBERON_0000446) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "area septalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:61842" +- [subclavian artery](http://purl.obolibrary.org/obo/UBERON_0001533) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Artery which supplies blood via branches to the various muscles of the shoulder region and to the forelimb.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010232" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -#### Added -- [septum of telencephalon](http://purl.obolibrary.org/obo/UBERON_0000446) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "area septalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:61842" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [subclavian artery](http://purl.obolibrary.org/obo/UBERON_0001533) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [septum of telencephalon](http://purl.obolibrary.org/obo/UBERON_0000446) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "massa praecommissuralis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:255" +### subclavian vein `http://purl.obolibrary.org/obo/UBERON_0001587` +#### Removed +- [subclavian vein](http://purl.obolibrary.org/obo/UBERON_0001587) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Vein which collects blood from the forelimb via the brachial veins and from the muscles and skin of the trunk via the anterior epigastric and lateral veins.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -- [septum of telencephalon](http://purl.obolibrary.org/obo/UBERON_0000446) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "septum pellucidum (BNA,PNA)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010510" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:255" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -- [septum of telencephalon](http://purl.obolibrary.org/obo/UBERON_0000446) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "septum telencephali" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:255" -### serosa of esophagus `http://purl.obolibrary.org/obo/UBERON_0001975` +### subcommissural organ `http://purl.obolibrary.org/obo/UBERON_0002139` #### Removed -- [serosa of esophagus](http://purl.obolibrary.org/obo/UBERON_0001975) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica serosa oesophageae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:63057" +- [subcommissural organ](http://purl.obolibrary.org/obo/UBERON_0002139) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "Hypendymal cells being part of the subcommissural organ is not axiomatized as it is rare in non-mammals. Consider using GCIs if this axiom needs to be added." - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" - -#### Added -- [serosa of esophagus](http://purl.obolibrary.org/obo/UBERON_0001975) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica serosa oesophageae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:63057" +### subcutaneous adipose tissue `http://purl.obolibrary.org/obo/UBERON_0002190` +#### Removed +- [subcutaneous adipose tissue](http://purl.obolibrary.org/obo/UBERON_0002190) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D015434" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +- [subcutaneous adipose tissue](http://purl.obolibrary.org/obo/UBERON_0002190) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "the superficial portion of the subcutaneous tissue which is specialized for fat storage[MP:0011156]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "MP:0011156" -### serosa of large intestine `http://purl.obolibrary.org/obo/UBERON_0001209` -#### Removed -- [serosa of large intestine](http://purl.obolibrary.org/obo/UBERON_0001209) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica serosa intestini crassi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:14975" +#### Added +- [subcutaneous adipose tissue](http://purl.obolibrary.org/obo/UBERON_0002190) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### subcutaneous lymph node `http://purl.obolibrary.org/obo/UBERON_0015453` #### Added -- [serosa of large intestine](http://purl.obolibrary.org/obo/UBERON_0001209) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica serosa intestini crassi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [subcutaneous lymph node](http://purl.obolibrary.org/obo/UBERON_0015453) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:14975" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### subdivision of conjunctiva `http://purl.obolibrary.org/obo/UBERON_0010305` + +#### Added +- [subdivision of conjunctiva](http://purl.obolibrary.org/obo/UBERON_0010305) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### serosa of small intestine `http://purl.obolibrary.org/obo/UBERON_0001206` +### subdivision of digestive tract `http://purl.obolibrary.org/obo/UBERON_0004921` #### Removed -- [serosa of small intestine](http://purl.obolibrary.org/obo/UBERON_0001206) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica serosa intestini tenuis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:14938" +- [subdivision of digestive tract](http://purl.obolibrary.org/obo/UBERON_0004921) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct." - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [subdivision of digestive tract](http://purl.obolibrary.org/obo/UBERON_0004921) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00100315" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [serosa of small intestine](http://purl.obolibrary.org/obo/UBERON_0001206) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica serosa intestini tenuis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:14938" +### subdivision of organism along appendicular axis `http://purl.obolibrary.org/obo/UBERON_0010758` +#### Removed +- [subdivision of organism along appendicular axis](http://purl.obolibrary.org/obo/UBERON_0010758) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007018" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### serosa of stomach `http://purl.obolibrary.org/obo/UBERON_0001201` +### subdivision of oviduct `http://purl.obolibrary.org/obo/UBERON_0013515` #### Removed -- [serosa of stomach](http://purl.obolibrary.org/obo/UBERON_0001201) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica serosa gastricae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:14914" +- [subdivision of oviduct](http://purl.obolibrary.org/obo/UBERON_0013515) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA class may only represent the uterine portion" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [serosa of stomach](http://purl.obolibrary.org/obo/UBERON_0001201) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica serosa gastricae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:14914" +### subdivision of skeleton `http://purl.obolibrary.org/obo/UBERON_0010912` +#### Removed +- [subdivision of skeleton](http://purl.obolibrary.org/obo/UBERON_0010912) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO]" + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "incorrect" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "VSAO:curator" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000042" -### serosa of urinary bladder `http://purl.obolibrary.org/obo/UBERON_0001260` -#### Removed -- [serosa of urinary bladder](http://purl.obolibrary.org/obo/UBERON_0001260) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica serosa (vesica urinaria)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15932" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [serosa of urinary bladder](http://purl.obolibrary.org/obo/UBERON_0001260) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica serosa vesicae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15932" +### subdivision of spinal cord central canal `http://purl.obolibrary.org/obo/UBERON_0014538` - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +#### Added +- [subdivision of spinal cord central canal](http://purl.obolibrary.org/obo/UBERON_0014538) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [serosa of urinary bladder](http://purl.obolibrary.org/obo/UBERON_0001260) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica serosa (vesica urinaria)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15932" +### subiculum `http://purl.obolibrary.org/obo/UBERON_0002191` +#### Removed +- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0004683](http://purl.obolibrary.org/obo/UBERON_0004683) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in DHBA subicular cortex is divided into subiculum, prosubiculum and supracallosal subiculum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002728](http://purl.obolibrary.org/obo/UBERON_0002728) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" -- [serosa of urinary bladder](http://purl.obolibrary.org/obo/UBERON_0001260) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica serosa vesicae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15932" +- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "The pyramidal neurons in the subiculum exhibit transitions between two modes of action potential output: bursting and single spiking. The transitions between these two modes is thought to be important for routing information out of the hippocampus. It is the site responsible for ictal activity in some cases of human epilepsy. It has also been implicated in working memory and drug addiction.[Wikipedia:Subiculum]" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "subicular" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0001953](http://purl.obolibrary.org/obo/UBERON_0001953) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" +- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "In ABA SUB is part of the retrohippocampal region, along with the entorhinal area. this is in the hippocampal formation but not the hippocampal region" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "ABA" -### serosa of uterus `http://purl.obolibrary.org/obo/UBERON_0001297` -#### Removed -- [serosa of uterus](http://purl.obolibrary.org/obo/UBERON_0001297) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica serosa uteri" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:17744" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### submitter `http://www.geneontology.org/formats/oboInOwl#submitter` +#### Removed +- AnnotationProperty: [submitter](http://www.geneontology.org/formats/oboInOwl#submitter) -#### Added -- [serosa of uterus](http://purl.obolibrary.org/obo/UBERON_0001297) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica serosa uteri" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:17744" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### submucosa `http://purl.obolibrary.org/obo/UBERON_0000009` +#### Removed +- [submucosa](http://purl.obolibrary.org/obo/UBERON_0000009) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "submucosal" + -### serous cell of epithelium of bronchus `http://purl.obolibrary.org/obo/CL_1000331` +### submucosa of anal canal `http://purl.obolibrary.org/obo/UBERON_0003329` #### Added -- [serous cell of epithelium of bronchus](http://purl.obolibrary.org/obo/CL_1000331) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [submucosa of anal canal](http://purl.obolibrary.org/obo/UBERON_0003329) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### serous cell of epithelium of trachea `http://purl.obolibrary.org/obo/CL_1000330` +### submucosa of biliary tree `http://purl.obolibrary.org/obo/UBERON_0004938` #### Added -- [serous cell of epithelium of trachea](http://purl.obolibrary.org/obo/CL_1000330) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [submucosa of biliary tree](http://purl.obolibrary.org/obo/UBERON_0004938) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -### serous membrane `http://purl.obolibrary.org/obo/UBERON_0000042` -#### Removed -- [serous membrane](http://purl.obolibrary.org/obo/UBERON_0000042) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica serosa" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9581" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### submucosa of bronchiole `http://purl.obolibrary.org/obo/UBERON_0004952` #### Added -- [serous membrane](http://purl.obolibrary.org/obo/UBERON_0000042) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica serosa" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [submucosa of bronchiole](http://purl.obolibrary.org/obo/UBERON_0004952) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9581" +### submucosa of bronchus `http://purl.obolibrary.org/obo/UBERON_0001957` + +#### Added +- [submucosa of bronchus](http://purl.obolibrary.org/obo/UBERON_0001957) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -### serous pericardium `http://purl.obolibrary.org/obo/UBERON_0002357` -#### Removed -- [serous pericardium](http://purl.obolibrary.org/obo/UBERON_0002357) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pericardium serosum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Serous_pericardium" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### submucosa of trachea `http://purl.obolibrary.org/obo/UBERON_0002202` #### Added -- [serous pericardium](http://purl.obolibrary.org/obo/UBERON_0002357) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pericardium serosum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Serous_pericardium" +- [submucosa of trachea](http://purl.obolibrary.org/obo/UBERON_0002202) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + +### submucosa of urinary bladder `http://purl.obolibrary.org/obo/UBERON_0004943` + +#### Added +- [submucosa of urinary bladder](http://purl.obolibrary.org/obo/UBERON_0004943) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### serous secreting cell `http://purl.obolibrary.org/obo/CL_0000313` +### submucosa of uterine tube `http://purl.obolibrary.org/obo/UBERON_0011298` #### Added -- [serous secreting cell](http://purl.obolibrary.org/obo/CL_0000313) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [submucosa of uterine tube](http://purl.obolibrary.org/obo/UBERON_0011298) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### serratus ventralis `http://purl.obolibrary.org/obo/UBERON_0001125` +### submucosal gland `http://purl.obolibrary.org/obo/UBERON_0011148` #### Removed -- [serratus ventralis](http://purl.obolibrary.org/obo/UBERON_0001125) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "serratus lateralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Serratus_anterior_muscle" +- [submucosal gland](http://purl.obolibrary.org/obo/UBERON_0011148) SubClassOf [continuous with](http://purl.obolibrary.org/obo/RO_0002150) some [epithelium of mucosa](http://purl.obolibrary.org/obo/UBERON_0003350) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "perforates" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +#### Added +- [submucosal gland](http://purl.obolibrary.org/obo/UBERON_0011148) SubClassOf [continuous with](http://purl.obolibrary.org/obo/RO_0002150) some [epithelium of mucosa](http://purl.obolibrary.org/obo/UBERON_0003350) -- [serratus ventralis](http://purl.obolibrary.org/obo/UBERON_0001125) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "musculus serratus anterior" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Serratus_anterior_muscle" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### subserosa of uterine tube `http://purl.obolibrary.org/obo/UBERON_8480037` #### Added -- [serratus ventralis](http://purl.obolibrary.org/obo/UBERON_0001125) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "musculus serratus anterior" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [subserosa of uterine tube](http://purl.obolibrary.org/obo/UBERON_8480037) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Serratus_anterior_muscle" -- [serratus ventralis](http://purl.obolibrary.org/obo/UBERON_0001125) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "serratus lateralis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### substantia nigra `http://purl.obolibrary.org/obo/UBERON_0002038` +#### Removed +- [substantia nigra](http://purl.obolibrary.org/obo/UBERON_0002038) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) the substantia nigra first appears in reptiles and is best developed in primates.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Serratus_anterior_muscle" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### sesamoid bone `http://purl.obolibrary.org/obo/UBERON_0001479` -#### Removed -- [sesamoid bone](http://purl.obolibrary.org/obo/UBERON_0001479) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ossa sesamoidea" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001573" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Sesamoid_bone" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.336" -#### Added -- [sesamoid bone](http://purl.obolibrary.org/obo/UBERON_0001479) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ossa sesamoidea" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [substantia nigra](http://purl.obolibrary.org/obo/UBERON_0002038) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Subdivision of the midbrain anterior to the midbrain tegmentum which contains darkly pigmented neurons[FMA][FMA:67947]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:67947" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Sesamoid_bone" -### set of lower jaw teeth `http://purl.obolibrary.org/obo/UBERON_0009679` +### substantia propria of cornea `http://purl.obolibrary.org/obo/UBERON_0001777` #### Removed -- [set of lower jaw teeth](http://purl.obolibrary.org/obo/UBERON_0009679) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arcus dentalis inferior" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [substantia propria of cornea](http://purl.obolibrary.org/obo/UBERON_0001777) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Portion of tissue that is located basal to Bowman's layer and distal to Descemet's membrane and is comprised largely of connective tissue.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:ZDB-PUB-061010-3" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -#### Added -- [set of lower jaw teeth](http://purl.obolibrary.org/obo/UBERON_0009679) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arcus dentalis inferior" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0002189" +- [substantia propria of cornea](http://purl.obolibrary.org/obo/UBERON_0001777) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship type change: subclass tissue (CARO:0000043) CHANGED TO: has_developmental_contribution_from tissue (UBERON:0000479)[TAO]" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -### set of upper jaw teeth `http://purl.obolibrary.org/obo/UBERON_0009680` -#### Removed -- [set of upper jaw teeth](http://purl.obolibrary.org/obo/UBERON_0009680) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arcus dentalis superior" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0002189" -#### Added -- [set of upper jaw teeth](http://purl.obolibrary.org/obo/UBERON_0009680) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arcus dentalis superior" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [substantia propria of cornea](http://purl.obolibrary.org/obo/UBERON_0001777) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship type change: subclass tissue (CARO:0000043) CHANGED TO: develops_from tissue (UBERON:0000479)[TAO]" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0002189" -### shoulder `http://purl.obolibrary.org/obo/UBERON_0001467` -#### Removed -- [shoulder](http://purl.obolibrary.org/obo/UBERON_0001467) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "articulatio humeri" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Shoulder" +- [substantia propria of cornea](http://purl.obolibrary.org/obo/UBERON_0001777) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [mesenchyme derived from head neural crest](http://purl.obolibrary.org/obo/UBERON_0007213) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0781772214" + + - [inferred_by](http://www.geneontology.org/formats/oboInOwl#inferred_by) "cjm" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia" #### Added -- [shoulder](http://purl.obolibrary.org/obo/UBERON_0001467) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "articulatio humeri" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Shoulder" +- [substantia propria of cornea](http://purl.obolibrary.org/obo/UBERON_0001777) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [mesenchyme derived from head neural crest](http://purl.obolibrary.org/obo/UBERON_0007213) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [substantia propria of cornea](http://purl.obolibrary.org/obo/UBERON_0001777) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) -### shoulder joint `http://purl.obolibrary.org/obo/UBERON_0016884` -#### Removed -- [shoulder joint](http://purl.obolibrary.org/obo/UBERON_0016884) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D012785" +### substratum of layer of retina `http://purl.obolibrary.org/obo/UBERON_0008921` #### Added -- [shoulder joint](http://purl.obolibrary.org/obo/UBERON_0016884) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D012785" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [substratum of layer of retina](http://purl.obolibrary.org/obo/UBERON_0008921) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +### sulcus of brain `http://purl.obolibrary.org/obo/UBERON_0013118` +#### Removed +- [sulcus of brain](http://purl.obolibrary.org/obo/UBERON_0013118) [RO_0002174](http://purl.obolibrary.org/obo/RO_0002174) [Mus ](http://purl.obolibrary.org/obo/NCBITaxon_10088) +- [sulcus of brain](http://purl.obolibrary.org/obo/UBERON_0013118) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Indentation on the surface of the brain or spinal cord that forms a recognizable landmark, e.g., central sulcus, sulcus limitans (CUMBO)" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://neurolex.org/wiki/Cumbo_terms" -### sigmoid colon `http://purl.obolibrary.org/obo/UBERON_0001159` -#### Removed -- [sigmoid colon](http://purl.obolibrary.org/obo/UBERON_0001159) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "colon sigmoideum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Sigmoid_colon" -#### Added -- [sigmoid colon](http://purl.obolibrary.org/obo/UBERON_0001159) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "colon sigmoideum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### superficial to `http://purl.obolibrary.org/obo/BSPO_0000108` +#### Removed +- [superficial to](http://purl.obolibrary.org/obo/BSPO_0000108) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Sigmoid_colon" +- [superficial to](http://purl.obolibrary.org/obo/BSPO_0000108) [id](http://www.geneontology.org/formats/oboInOwl#id) "superficial_to" +- [superficial to](http://purl.obolibrary.org/obo/BSPO_0000108) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BSPO:0000108" -### signaling `http://purl.obolibrary.org/obo/GO_0023052` -#### Removed -- [signaling](http://purl.obolibrary.org/obo/GO_0023052) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) +- [superficial to](http://purl.obolibrary.org/obo/BSPO_0000108) [label](http://www.w3.org/2000/01/rdf-schema#label) "superficial to" -#### Added -- [signaling](http://purl.obolibrary.org/obo/GO_0023052) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) +- [superficial to](http://purl.obolibrary.org/obo/BSPO_0000108) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "superficial_to" -### simple columnar epithelium `http://purl.obolibrary.org/obo/UBERON_0000485` + +### superior mesenteric artery `http://purl.obolibrary.org/obo/UBERON_0001182` #### Removed -- [simple columnar epithelium](http://purl.obolibrary.org/obo/UBERON_0000485) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007027" +- [superior mesenteric artery](http://purl.obolibrary.org/obo/UBERON_0001182) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "Origin: abdominal aorta; branches, inferior pancreaticoduodenal, jejunal, ileal, ileocolic, right colic, and middle colic arteries; distribution: small intestine, proximal half of colon" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "BTO" -#### Added -- [simple columnar epithelium](http://purl.obolibrary.org/obo/UBERON_0000485) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007027" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### sinoatrial node `http://purl.obolibrary.org/obo/UBERON_0002351` +### superior olivary complex `http://purl.obolibrary.org/obo/UBERON_0002128` #### Removed -- [sinoatrial node](http://purl.obolibrary.org/obo/UBERON_0002351) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nodus sinuatrialis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Sinoatrial_node" +- [superior olivary complex](http://purl.obolibrary.org/obo/UBERON_0002128) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D065832" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -- [sinoatrial node](http://purl.obolibrary.org/obo/UBERON_0002351) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nodus sinuatrialis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9477" + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [superior olivary complex](http://purl.obolibrary.org/obo/UBERON_0002128) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In mice, the superior olivary nucleus is a small cylindrical mass on the dorsal surface of the lateral part of the trapezoid body of the pons, and it is situated immediately above the inferior olivary nucleus. It receives projections from the cochlear nucleus and thus is involved in the perception of sound[GO:0021718]" -#### Added -- [sinoatrial node](http://purl.obolibrary.org/obo/UBERON_0002351) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nodus sinuatrialis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [superior olivary complex](http://purl.obolibrary.org/obo/UBERON_0002128) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The SOC displays a significant interspecies variation, being largest in bats and rodents and smaller in primates." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Sinoatrial_node" +- [superior olivary complex](http://purl.obolibrary.org/obo/UBERON_0002128) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0006840](http://purl.obolibrary.org/obo/UBERON_0006840) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" -- [sinoatrial node](http://purl.obolibrary.org/obo/UBERON_0002351) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nodus sinuatrialis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [superior olivary complex](http://purl.obolibrary.org/obo/UBERON_0002128) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0007634](http://purl.obolibrary.org/obo/UBERON_0007634) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9477" +- [superior olivary complex](http://purl.obolibrary.org/obo/UBERON_0002128) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002597](http://purl.obolibrary.org/obo/UBERON_0002597) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### sinus venosus `http://purl.obolibrary.org/obo/UBERON_0002063` +### superior salivatory nucleus `http://purl.obolibrary.org/obo/UBERON_0002149` #### Removed -- [sinus venosus](http://purl.obolibrary.org/obo/UBERON_0002063) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "sinus venosus cordis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Sinus_venosus" +- [superior salivatory nucleus](http://purl.obolibrary.org/obo/UBERON_0002149) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002151](http://purl.obolibrary.org/obo/UBERON_0002151) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" -#### Added -- [sinus venosus](http://purl.obolibrary.org/obo/UBERON_0002063) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "sinus venosus cordis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [superior salivatory nucleus](http://purl.obolibrary.org/obo/UBERON_0002149) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002968](http://purl.obolibrary.org/obo/UBERON_0002968) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Sinus_venosus" +- [superior salivatory nucleus](http://purl.obolibrary.org/obo/UBERON_0002149) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002147](http://purl.obolibrary.org/obo/UBERON_0002147) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" +- [superior salivatory nucleus](http://purl.obolibrary.org/obo/UBERON_0002149) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0007632](http://purl.obolibrary.org/obo/UBERON_0007632) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" -### skeletal muscle fiber `http://purl.obolibrary.org/obo/CL_0008002` +- [superior salivatory nucleus](http://purl.obolibrary.org/obo/UBERON_0002149) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002963](http://purl.obolibrary.org/obo/UBERON_0002963) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" -#### Added -- [skeletal muscle fiber](http://purl.obolibrary.org/obo/CL_0008002) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [superior salivatory nucleus](http://purl.obolibrary.org/obo/UBERON_0002149) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002682](http://purl.obolibrary.org/obo/UBERON_0002682) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" +- [superior salivatory nucleus](http://purl.obolibrary.org/obo/UBERON_0002149) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0003011](http://purl.obolibrary.org/obo/UBERON_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" -### skeletal muscle fibroblast `http://purl.obolibrary.org/obo/CL_0011027` +- [superior salivatory nucleus](http://purl.obolibrary.org/obo/UBERON_0002149) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002633](http://purl.obolibrary.org/obo/UBERON_0002633) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" -#### Added -- [skeletal muscle fibroblast](http://purl.obolibrary.org/obo/CL_0011027) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [superior salivatory nucleus](http://purl.obolibrary.org/obo/UBERON_0002149) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002143](http://purl.obolibrary.org/obo/UBERON_0002143) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" +- [superior salivatory nucleus](http://purl.obolibrary.org/obo/UBERON_0002149) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### skeletal muscle organ, vertebrate `http://purl.obolibrary.org/obo/UBERON_0014892` +- [superior salivatory nucleus](http://purl.obolibrary.org/obo/UBERON_0002149) SubClassOf [immediate transformation of](http://purl.obolibrary.org/obo/RO_0002495) some [future superior salivatory nucleus](http://purl.obolibrary.org/obo/UBERON_0010125) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" #### Added -- [skeletal muscle organ, vertebrate](http://purl.obolibrary.org/obo/UBERON_0014892) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas) +- [superior salivatory nucleus](http://purl.obolibrary.org/obo/UBERON_0002149) SubClassOf [immediate transformation of](http://purl.obolibrary.org/obo/RO_0002495) some [future superior salivatory nucleus](http://purl.obolibrary.org/obo/UBERON_0010125) -- [skeletal muscle organ, vertebrate](http://purl.obolibrary.org/obo/UBERON_0014892) [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [Homo sapiens](http://purl.obolibrary.org/obo/NCBITaxon_9606) + +### superior vesical artery `http://purl.obolibrary.org/obo/UBERON_0001312` +#### Removed +- [superior vesical artery](http://purl.obolibrary.org/obo/UBERON_0001312) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "The first part of the superior vesical artery represents the terminal section of the previous portion of the umbilical artery (fetal hypogastric artery)[WP]" -### skeletal muscle satellite cell `http://purl.obolibrary.org/obo/CL_0000594` -#### Added -- [skeletal muscle satellite cell](http://purl.obolibrary.org/obo/CL_0000594) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### supplies `http://purl.obolibrary.org/obo/RO_0002178` +#### Removed +- [supplies](http://purl.obolibrary.org/obo/RO_0002178) [label](http://www.w3.org/2000/01/rdf-schema#label) "supplies" +- [supplies](http://purl.obolibrary.org/obo/RO_0002178) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) [20064205](http://www.ncbi.nlm.nih.gov/pubmed/20064205) -### skeletal muscle satellite stem cell `http://purl.obolibrary.org/obo/CL_0008011` +- [supplies](http://purl.obolibrary.org/obo/RO_0002178) [id](http://www.geneontology.org/formats/oboInOwl#id) "supplies" -#### Added -- [skeletal muscle satellite stem cell](http://purl.obolibrary.org/obo/CL_0008011) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [supplies](http://purl.obolibrary.org/obo/RO_0002178) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002178" +- [supplies](http://purl.obolibrary.org/obo/RO_0002178) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" -### skeletal musculature `http://purl.obolibrary.org/obo/UBERON_0018254` +- [supplies](http://purl.obolibrary.org/obo/RO_0002178) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "supplies" -#### Added -- [skeletal musculature](http://purl.obolibrary.org/obo/UBERON_0018254) [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [Homo sapiens](http://purl.obolibrary.org/obo/NCBITaxon_9606) +- [supplies](http://purl.obolibrary.org/obo/RO_0002178) Domain [artery](http://purl.obolibrary.org/obo/UBERON_0001637) -- [skeletal musculature](http://purl.obolibrary.org/obo/UBERON_0018254) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas) -### skeletal musculature of head `http://purl.obolibrary.org/obo/UBERON_0004461` +### surface structure `http://purl.obolibrary.org/obo/UBERON_0003102` #### Removed -- [skeletal musculature of head](http://purl.obolibrary.org/obo/UBERON_0004461) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "musculi capitis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71287" +- [surface structure](http://purl.obolibrary.org/obo/UBERON_0003102) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Organism subdivision which is the collection of anatomical structures on the body surface.[ZFA]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000292" -#### Added -- [skeletal musculature of head](http://purl.obolibrary.org/obo/UBERON_0004461) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "musculi capitis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71287" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### skeleton of manus `http://purl.obolibrary.org/obo/UBERON_0001442` +### surrounded by `http://purl.obolibrary.org/obo/RO_0002219` #### Removed -- [skeleton of manus](http://purl.obolibrary.org/obo/UBERON_0001442) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ossa manus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:24159" +- [surrounded by](http://purl.obolibrary.org/obo/RO_0002219) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [surrounded by](http://purl.obolibrary.org/obo/RO_0002219) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "surrounded_by" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [surrounded by](http://purl.obolibrary.org/obo/RO_0002219) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" -#### Added -- [skeleton of manus](http://purl.obolibrary.org/obo/UBERON_0001442) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ossa manus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [surrounded by](http://purl.obolibrary.org/obo/RO_0002219) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:24159" +- [surrounded by](http://purl.obolibrary.org/obo/RO_0002219) [id](http://www.geneontology.org/formats/oboInOwl#id) "surrounded_by" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [surrounded by](http://purl.obolibrary.org/obo/RO_0002219) [RO_0001900](http://purl.obolibrary.org/obo/RO_0001900) [RO_0001901](http://purl.obolibrary.org/obo/RO_0001901) +- [surrounded by](http://purl.obolibrary.org/obo/RO_0002219) [label](http://www.w3.org/2000/01/rdf-schema#label) "surrounded by" -### skin fibroblast `http://purl.obolibrary.org/obo/CL_0002620` +- [surrounded by](http://purl.obolibrary.org/obo/RO_0002219) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002219" -#### Added -- [skin fibroblast](http://purl.obolibrary.org/obo/CL_0002620) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### skin gland `http://purl.obolibrary.org/obo/UBERON_0002419` +### surrounds `http://purl.obolibrary.org/obo/RO_0002221` #### Removed -- [skin gland](http://purl.obolibrary.org/obo/UBERON_0002419) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "glandulae cutis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71878" +- [surrounds](http://purl.obolibrary.org/obo/RO_0002221) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "surrounds" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [surrounds](http://purl.obolibrary.org/obo/RO_0002221) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [surrounds](http://purl.obolibrary.org/obo/RO_0002221) [id](http://www.geneontology.org/formats/oboInOwl#id) "surrounds" -#### Added -- [skin gland](http://purl.obolibrary.org/obo/UBERON_0002419) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "glandulae cutis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71878" +- [surrounds](http://purl.obolibrary.org/obo/RO_0002221) [label](http://www.w3.org/2000/01/rdf-schema#label) "surrounds" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [surrounds](http://purl.obolibrary.org/obo/RO_0002221) [RO_0001900](http://purl.obolibrary.org/obo/RO_0001900) [RO_0001901](http://purl.obolibrary.org/obo/RO_0001901) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [surrounds](http://purl.obolibrary.org/obo/RO_0002221) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) + +- [surrounds](http://purl.obolibrary.org/obo/RO_0002221) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" + +- [surrounds](http://purl.obolibrary.org/obo/RO_0002221) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002221" -### skin of trunk `http://purl.obolibrary.org/obo/UBERON_0001085` + +### sweat gland `http://purl.obolibrary.org/obo/UBERON_0001820` #### Removed -- [skin of trunk](http://purl.obolibrary.org/obo/UBERON_0001085) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas) +- [sweat gland](http://purl.obolibrary.org/obo/UBERON_0001820) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A gland that secretes sweat, found in the dermis or subcutaneous tissue, opening by a duct on the body surface. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/sweat+gland" -- [skin of trunk](http://purl.obolibrary.org/obo/UBERON_0001085) [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [Homo sapiens](http://purl.obolibrary.org/obo/NCBITaxon_9606) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001467" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### slow muscle cell `http://purl.obolibrary.org/obo/CL_0000189` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [slow muscle cell](http://purl.obolibrary.org/obo/CL_0000189) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [sweat gland](http://purl.obolibrary.org/obo/UBERON_0001820) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In humans a system of apocrine - and merocrine sweat glands is the main method of cooling. Many other mammals rely on panting or other means as a primary source of cooling, but still use sweat glands to aid in body temperature regulation" +- [sweat gland](http://purl.obolibrary.org/obo/UBERON_0001820) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Sweat glands (also called sudoriferous glands) are unique to mammals.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001467" -### small intestine `http://purl.obolibrary.org/obo/UBERON_0002108` -#### Removed -- [small intestine](http://purl.obolibrary.org/obo/UBERON_0002108) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "intestinum tenue" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0000651" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Small_intestine" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [small intestine](http://purl.obolibrary.org/obo/UBERON_0002108) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "intestinum tenue" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0471090588 Hildebrand M, Analysis of vertebrate structure (1983) p.101" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0000651" +- [sweat gland](http://purl.obolibrary.org/obo/UBERON_0001820) SubClassOf [has quality](http://purl.obolibrary.org/obo/RO_0000086) some [tubular](http://purl.obolibrary.org/obo/PATO_0002299) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "coiled tubular" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Small_intestine" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Tubular_gland" +- [sweat gland](http://purl.obolibrary.org/obo/UBERON_0001820) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [sweat gland placode](http://purl.obolibrary.org/obo/UBERON_0005089) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" -### small intestine Peyer's patch `http://purl.obolibrary.org/obo/UBERON_0003454` +#### Added +- [sweat gland](http://purl.obolibrary.org/obo/UBERON_0001820) SubClassOf [has quality](http://purl.obolibrary.org/obo/RO_0000086) some [tubular](http://purl.obolibrary.org/obo/PATO_0002299) + +- [sweat gland](http://purl.obolibrary.org/obo/UBERON_0001820) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [sweat gland placode](http://purl.obolibrary.org/obo/UBERON_0005089) + + +### sweat of palm `http://purl.obolibrary.org/obo/UBERON_0014392` #### Removed -- [small intestine Peyer's patch](http://purl.obolibrary.org/obo/UBERON_0003454) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "noduli lymphoidei aggregati intestini tenuis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:76466" +- [sweat of palm](http://purl.obolibrary.org/obo/UBERON_0014392) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "serves a purpose of increasing friction on the palms of hands or the pads of paws[WP]" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [small intestine Peyer's patch](http://purl.obolibrary.org/obo/UBERON_0003454) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "noduli lymphoidei aggregati intestini tenuis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:76466" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### sympathetic ganglion `http://purl.obolibrary.org/obo/UBERON_0001806` +#### Removed +- [sympathetic ganglion](http://purl.obolibrary.org/obo/UBERON_0001806) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D005728" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) -### small intestine goblet cell `http://purl.obolibrary.org/obo/CL_1000495` + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" #### Added -- [small intestine goblet cell](http://purl.obolibrary.org/obo/CL_1000495) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [sympathetic ganglion](http://purl.obolibrary.org/obo/UBERON_0001806) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) -### small intestine smooth muscle circular layer `http://purl.obolibrary.org/obo/UBERON_0012401` +### sympathetic nervous system `http://purl.obolibrary.org/obo/UBERON_0000013` #### Removed -- [small intestine smooth muscle circular layer](http://purl.obolibrary.org/obo/UBERON_0012401) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum circulare tunicae muscularis intestini tenuis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:14935" +- [sympathetic nervous system](http://purl.obolibrary.org/obo/UBERON_0000013) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Part of the autonomic nervous system which has opposing physiological effects of the parasympathetic nervous system. Examples include increasing the heart rate or constricting the blood vessels.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010487" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -#### Added -- [small intestine smooth muscle circular layer](http://purl.obolibrary.org/obo/UBERON_0012401) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum circulare tunicae muscularis intestini tenuis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:14935" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [sympathetic nervous system](http://purl.obolibrary.org/obo/UBERON_0000013) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "has developmental contribution from NC in verteberates (https://github.com/obophenotype/uberon/wiki/The-neural-crest)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [sympathetic nervous system](http://purl.obolibrary.org/obo/UBERON_0000013) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The autonomic nervous system is composed of three divisions: the sympathetic division, the parasympathetic division, and the enteric division. (...) In ray-finned teleost fishes, a sympathetic chain is present, and dual innervation of additional organs can be observed. A similar pattern can be found in amphibians (...). The evolution of the autonomic nervous system has been quite conservative, especially in the tetrapod lineage.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### small intestine smooth muscle longitudinal layer `http://purl.obolibrary.org/obo/UBERON_0012402` -#### Removed -- [small intestine smooth muscle longitudinal layer](http://purl.obolibrary.org/obo/UBERON_0012402) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum longitudinale tunicae muscularis intestini tenuis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:14936" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000384" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0471210054 Butler AB and Hodos W, Comparative vertebrate neuroanatomy: Evolution and Adaptation (2005) p.461-463" -#### Added -- [small intestine smooth muscle longitudinal layer](http://purl.obolibrary.org/obo/UBERON_0012402) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum longitudinale tunicae muscularis intestini tenuis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:14936" +- [sympathetic nervous system](http://purl.obolibrary.org/obo/UBERON_0000013) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The part of the autonomic nervous system which chiefly contains adrenergic fibres and tends to control and reduce secretions, decrease the contractility and hence the tone of smooth muscles and provoke the contraction of blood vessels. Essentially, it consists of preganglionic fibres from the thoracic and upper lumbar parts of the spinal cord. These fibres, by means of delicate rami communicantes, cross over to ganglia sited in a pair of ganglionated cords on each side of the vertebral column or to more peripheral ganglia. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000384" -### small molecule biosynthetic process `http://purl.obolibrary.org/obo/GO_0044283` + +### synapsed by `http://purl.obolibrary.org/obo/RO_0002103` #### Removed -- [small molecule biosynthetic process](http://purl.obolibrary.org/obo/GO_0044283) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) +- [synapsed by](http://purl.obolibrary.org/obo/RO_0002103) [id](http://www.geneontology.org/formats/oboInOwl#id) "synapsed_by" -#### Added -- [small molecule biosynthetic process](http://purl.obolibrary.org/obo/GO_0044283) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) +- [synapsed by](http://purl.obolibrary.org/obo/RO_0002103) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-7073-9172](https://orcid.org/0000-0002-7073-9172) +- [synapsed by](http://purl.obolibrary.org/obo/RO_0002103) [label](http://www.w3.org/2000/01/rdf-schema#label) "synapsed by" -### small pre-B-II cell `http://purl.obolibrary.org/obo/CL_0000954` +- [synapsed by](http://purl.obolibrary.org/obo/RO_0002103) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002103" -#### Added -- [small pre-B-II cell](http://purl.obolibrary.org/obo/CL_0000954) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [synapsed by](http://purl.obolibrary.org/obo/RO_0002103) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) +- [synapsed by](http://purl.obolibrary.org/obo/RO_0002103) [RO_0001900](http://purl.obolibrary.org/obo/RO_0001900) [RO_0001901](http://purl.obolibrary.org/obo/RO_0001901) -### small saphenous vein `http://purl.obolibrary.org/obo/UBERON_0001547` -#### Removed -- [small saphenous vein](http://purl.obolibrary.org/obo/UBERON_0001547) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vena saphena parva" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Small_saphenous_vein" +- [synapsed by](http://purl.obolibrary.org/obo/RO_0002103) [citesAsAuthority](http://purl.org/spar/cito/citesAsAuthority) [22402613](http://www.ncbi.nlm.nih.gov/pubmed/22402613) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [synapsed by](http://purl.obolibrary.org/obo/RO_0002103) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" -#### Added -- [small saphenous vein](http://purl.obolibrary.org/obo/UBERON_0001547) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vena saphena parva" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Small_saphenous_vein" +- [synapsed by](http://purl.obolibrary.org/obo/RO_0002103) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [synapsed by](http://purl.obolibrary.org/obo/RO_0002103) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "synapsed_by" -### smooth muscle cell `http://purl.obolibrary.org/obo/CL_0000192` -#### Added -- [smooth muscle cell](http://purl.obolibrary.org/obo/CL_0000192) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### synapsed to `http://purl.obolibrary.org/obo/RO_0002120` +#### Removed +- [synapsed to](http://purl.obolibrary.org/obo/RO_0002120) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) +- [synapsed to](http://purl.obolibrary.org/obo/RO_0002120) [citesAsAuthority](http://purl.org/spar/cito/citesAsAuthority) [22402613](http://www.ncbi.nlm.nih.gov/pubmed/22402613) -### smooth muscle cell of large intestine `http://purl.obolibrary.org/obo/CL_1000279` +- [synapsed to](http://purl.obolibrary.org/obo/RO_0002120) [RO_0001900](http://purl.obolibrary.org/obo/RO_0001900) [RO_0001901](http://purl.obolibrary.org/obo/RO_0001901) -#### Added -- [smooth muscle cell of large intestine](http://purl.obolibrary.org/obo/CL_1000279) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [synapsed to](http://purl.obolibrary.org/obo/RO_0002120) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-7073-9172](https://orcid.org/0000-0002-7073-9172) +- [synapsed to](http://purl.obolibrary.org/obo/RO_0002120) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) -### smooth muscle cell of prostate `http://purl.obolibrary.org/obo/CL_1000487` -#### Added -- [smooth muscle cell of prostate](http://purl.obolibrary.org/obo/CL_1000487) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### syndecan-1 `http://purl.obolibrary.org/obo/PR_000001935` +#### Removed +- [syndecan-1](http://purl.obolibrary.org/obo/PR_000001935) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [syndecan-1 (human)](http://purl.obolibrary.org/obo/PR_P18827) -### smooth muscle cell of small intestine `http://purl.obolibrary.org/obo/CL_1000275` -#### Added -- [smooth muscle cell of small intestine](http://purl.obolibrary.org/obo/CL_1000275) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### synovial fluid `http://purl.obolibrary.org/obo/UBERON_0001090` +#### Removed +- [synovial fluid](http://purl.obolibrary.org/obo/UBERON_0001090) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "It provides nutrients and lubrication for articular cartilage" -### smooth muscle cell of sphincter of pupil `http://purl.obolibrary.org/obo/CL_0002243` +- [synovial fluid](http://purl.obolibrary.org/obo/UBERON_0001090) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Portion of organism substance that is a clear fluid that occupies the space in synovial joints.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -#### Added -- [smooth muscle cell of sphincter of pupil](http://purl.obolibrary.org/obo/CL_0002243) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005154" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -### smooth muscle cell of the pulmonary artery `http://purl.obolibrary.org/obo/CL_0002591` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [synovial fluid](http://purl.obolibrary.org/obo/UBERON_0001090) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "The fluid contains hyaluronan secreted by fibroblast-like cells in the synovial membrane, lubricin (proteoglycan 4; PRG4) secreted by the surface chondrocytes of the articular cartilage and interstitial fluid filtered from the blood plasma" -#### Added -- [smooth muscle cell of the pulmonary artery](http://purl.obolibrary.org/obo/CL_0002591) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### smooth muscle cell of trachea `http://purl.obolibrary.org/obo/CL_0002600` +### synovial joint `http://purl.obolibrary.org/obo/UBERON_0002217` +#### Removed +- [synovial joint](http://purl.obolibrary.org/obo/UBERON_0002217) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Is a joint that is located at the point of contact of articulating bones allowing movement. The joint has a capsule containing synovial fluid surrounding the articulating bone surfaces.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005153" -#### Added -- [smooth muscle cell of trachea](http://purl.obolibrary.org/obo/CL_0002600) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:Curator" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -### smooth muscle fiber of ileum `http://purl.obolibrary.org/obo/CL_1000278` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -#### Added -- [smooth muscle fiber of ileum](http://purl.obolibrary.org/obo/CL_1000278) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### smooth muscle layer in fatty layer of subcutaneous tissue `http://purl.obolibrary.org/obo/UBERON_0015783` +### synovial joint of pectoral girdle `http://purl.obolibrary.org/obo/UBERON_0011108` #### Removed -- [smooth muscle layer in fatty layer of subcutaneous tissue](http://purl.obolibrary.org/obo/UBERON_0015783) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum musculosum panniculi adiposi telae subcutaneae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:77862" +- [synovial joint of pectoral girdle](http://purl.obolibrary.org/obo/UBERON_0011108) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in FMA, these are part of the bony pectoral girdle" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [smooth muscle layer in fatty layer of subcutaneous tissue](http://purl.obolibrary.org/obo/UBERON_0015783) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum musculosum panniculi adiposi telae subcutaneae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### synovial membrane of synovial joint `http://purl.obolibrary.org/obo/UBERON_0002018` +#### Removed +- [synovial membrane of synovial joint](http://purl.obolibrary.org/obo/UBERON_0002018) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Phylogenetically, synovium is one of the newer attributes of the vertebrate locomotor apparatus. The first synovial joints developed in the piscine jaw of ancestors of modern lungfish by an evolutionary process that modified preexisting fibrous and cartilaginous joints, which were the predominant articulation of the early sea- and land-dwelling vertebrates.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:77862" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:11068553 O'Connel JX, Pathology of the synovium. American Journal of Clinical Pathology (2000)" -### smooth muscle myoblast `http://purl.obolibrary.org/obo/CL_0000514` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001282" -#### Added -- [smooth muscle myoblast](http://purl.obolibrary.org/obo/CL_0000514) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### smooth muscle tissue `http://purl.obolibrary.org/obo/UBERON_0001135` +### system `http://purl.obolibrary.org/obo/RO_0002577` #### Removed -- [smooth muscle tissue](http://purl.obolibrary.org/obo/UBERON_0001135) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "textus muscularis levis; textus muscularis nonstriatus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Smooth_muscle_tissue" +- [system](http://purl.obolibrary.org/obo/RO_0002577) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) "http://www.jbiomedsem.com/content/4/1/43" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [system](http://purl.obolibrary.org/obo/RO_0002577) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) -- [smooth muscle tissue](http://purl.obolibrary.org/obo/UBERON_0001135) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "textus muscularis nonstriatus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:14070" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### systemic venous system `http://purl.obolibrary.org/obo/UBERON_0004581` +#### Removed +- [systemic venous system](http://purl.obolibrary.org/obo/UBERON_0004581) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Subdivision of cardiovascular system which has as its parts the right side of heart, the superior vena cava and the inferior vena cava[FMA]" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "FMA" -#### Added -- [smooth muscle tissue](http://purl.obolibrary.org/obo/UBERON_0001135) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "textus muscularis levis; textus muscularis nonstriatus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:45626" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Smooth_muscle_tissue" +- [systemic venous system](http://purl.obolibrary.org/obo/UBERON_0004581) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "In human anatomy, the systemic venous system refers to veins that drain into the right atrium without passing through two vascular beds (i.e. they originate from a set of capillaries and do not pass through a second set of capillaries before reaching the right side of the heart). The term systemic venous system is often used to differentiate veins from veins that drain the pulmonary system (the pulmonary venous system) and veins that drain the digestive tract (the portal venous system). Large veins that are considered part of the systemic venous system are the: Superior vena cava; Inferior vena cava[WP]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Systemic_venous_system" -- [smooth muscle tissue](http://purl.obolibrary.org/obo/UBERON_0001135) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "textus muscularis nonstriatus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [systemic venous system](http://purl.obolibrary.org/obo/UBERON_0004581) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:14070" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000277" -### sncg GABAergic cortical interneuron `http://purl.obolibrary.org/obo/CL_4023015` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005)" -#### Added -- [sncg GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023015) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### somite `http://purl.obolibrary.org/obo/UBERON_0002329` +### tachykinin-3 `http://purl.obolibrary.org/obo/PR_000016004` #### Removed -- [somite](http://purl.obolibrary.org/obo/UBERON_0002329) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "somitus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Somite" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [tachykinin-3](http://purl.obolibrary.org/obo/PR_000016004) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [tachykinin-3 (human)](http://purl.obolibrary.org/obo/PR_Q9UHF0) -#### Added -- [somite](http://purl.obolibrary.org/obo/UBERON_0002329) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "somitus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Somite" +### tail external integument structure `http://purl.obolibrary.org/obo/UBERON_3000982` +#### Removed +- [tail external integument structure](http://purl.obolibrary.org/obo/UBERON_3000982) [UBPROP_0000004](http://purl.obolibrary.org/obo/UBPROP_0000004) "This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://purl.obolibrary.org/obo/aao.owl" -### sperm `http://purl.obolibrary.org/obo/CL_0000019` - -#### Added -- [sperm](http://purl.obolibrary.org/obo/CL_0000019) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### spermatic cord `http://purl.obolibrary.org/obo/UBERON_0005352` +### tail vasculature `http://purl.obolibrary.org/obo/UBERON_0010204` #### Removed -- [spermatic cord](http://purl.obolibrary.org/obo/UBERON_0005352) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "funiculus spermaticus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Spermatic_cord" +- [tail vasculature](http://purl.obolibrary.org/obo/UBERON_0010204) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "isa blood vessel in XAO" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "XAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [spermatic cord](http://purl.obolibrary.org/obo/UBERON_0005352) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "funiculus spermaticus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Spermatic_cord" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### tarsal bone `http://purl.obolibrary.org/obo/UBERON_0001447` +#### Removed +- [tarsal bone](http://purl.obolibrary.org/obo/UBERON_0001447) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In primitive tetrapods, such as Trematops, the tarsus consists of three rows of bones. There are three proximal tarsals, the tibiale, intermedium, and fibulare, named for their points of articulation with the bones of the lower limb. These are followed by a second row of four bones, referred to as the centralia (singular: centrale), and then a row of five distal tarsals, each articulating with a single metatarsal. In the great majority of tetrapods, including all of those alive today, this simple pattern is modified by the loss and fusion of various of the bones.[3] In reptiles and mammals, there are normally just two proximal tarsals, the calcaneus (equivalent to the amphibian fibulare) and the talus (probably derived from a fusion of multiple bones). In mammals, including humans, the talus forms a hinge joint with the tibia, a feature especially well developed in the artiodactyls. The calcaneus is also modified, forming a heel for the attachment of the Achilles tendon. Neither of these adaptations is found in reptiles, which have a relatively simple structure to both bones.[3] The fifth distal tarsal disappears relatively early in evolution, with the remainder becoming the cuneiform and cuboid bones. Reptiles usually retain two centralia, while mammals typically have only one (the navicular).[3] In birds, the tarsus has disappeared, with the proximal tarsals having fused with the tibia, the centralia having disappeared, and the distal bones having fused with the metatarsals to form a single tarsometatarsus bone, effectively giving the leg a third segment" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Tarsus_(skeleton)" -### sphenofrontal suture `http://purl.obolibrary.org/obo/UBERON_0010156` -#### Removed -- [sphenofrontal suture](http://purl.obolibrary.org/obo/UBERON_0010156) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "sutura sphenofrontalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Sphenofrontal_suture" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### tarsal region `http://purl.obolibrary.org/obo/UBERON_0004454` +#### Removed +- [tarsal region](http://purl.obolibrary.org/obo/UBERON_0004454) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "MA has both tarsus (part of foot, has tarsal bone) and ankle (part of hindlimb, has joint, nerve, skin)." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" -#### Added -- [sphenofrontal suture](http://purl.obolibrary.org/obo/UBERON_0010156) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "sutura sphenofrontalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [tarsal region](http://purl.obolibrary.org/obo/UBERON_0004454) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "this term refers to the limb segment. See also: tarsal bones and tarsal skeleton" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Sphenofrontal_suture" -### sphenoid bone `http://purl.obolibrary.org/obo/UBERON_0001677` +### tarsal skeleton `http://purl.obolibrary.org/obo/UBERON_0009879` #### Removed -- [sphenoid bone](http://purl.obolibrary.org/obo/UBERON_0001677) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "os sphenoidale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:52736" +- [tarsal skeleton](http://purl.obolibrary.org/obo/UBERON_0009879) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "we assume MA:tarsus belongs here, as there is a distinct class MA:ankle, with the tarsal bone being part of the former. XAO:tarsus is part of the hindlimb skeleton. FMA set-of class lacks definition but we assume this to be equivalent." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [tarsal skeleton](http://purl.obolibrary.org/obo/UBERON_0009879) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The three main outgroup taxa of tetrapods, panderichthyids, osteolepiforms, and rhizodontids, have endoskeletal elements corresponding to the stylo- and zeugopodial elements in a tetrapod limb. In addition, there are elements that share the position and possibly the developmental derivation of the ulnare and the intermedium. From these observations, most authors have concluded that the stylo- and zeugopodial elements as well as the proximal mesopodial elements have counterparts in the fins of tetrapod ancestors, but there are no indications of wrist or ankle joints.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1002/jez.1100 Wagner GP, Chiu C, The tetrapod limb: A hypothesis on its origin. J Exp Zool (Mol Dev Evol) (2001)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [sphenoid bone](http://purl.obolibrary.org/obo/UBERON_0001677) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "os sphenoidale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Sphenoid_bone" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [sphenoid bone](http://purl.obolibrary.org/obo/UBERON_0001677) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "os sphenoidale" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001160" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Sphenoid_bone" +- [tarsal skeleton](http://purl.obolibrary.org/obo/UBERON_0009879) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Not always associated with digits, in sarcopterygians the ulnare is present without true digits being formed, though their homologous radial elements are present" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PHENOSCAPE:ad" -- [sphenoid bone](http://purl.obolibrary.org/obo/UBERON_0001677) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "os sphenoidale" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [tarsal skeleton](http://purl.obolibrary.org/obo/UBERON_0009879) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Segment of the leg corresponding to the tarsus. It consists of several elements that articulate with the tibia and fibula at one end and the metatarsals at the other end.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:52736" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000220" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### sphincter of hepatopancreatic ampulla `http://purl.obolibrary.org/obo/UBERON_0004915` -#### Removed -- [sphincter of hepatopancreatic ampulla](http://purl.obolibrary.org/obo/UBERON_0004915) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "musculus sphincter ampullae hepatopancreatica" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15077" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### tartrate-resistant acid phosphatase type 5 `http://purl.obolibrary.org/obo/PR_000001937` +#### Removed +- [tartrate-resistant acid phosphatase type 5](http://purl.obolibrary.org/obo/PR_000001937) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [tartrate-resistant acid phosphatase type 5 (human)](http://purl.obolibrary.org/obo/PR_P13686) -#### Added -- [sphincter of hepatopancreatic ampulla](http://purl.obolibrary.org/obo/UBERON_0004915) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "musculus sphincter ampullae hepatopancreatica" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15077" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### taste bud `http://purl.obolibrary.org/obo/UBERON_0001727` +#### Removed +- [taste bud](http://purl.obolibrary.org/obo/UBERON_0001727) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "One of a number of receptor cell nests located in the epithelium of the papillae of the tongue and in the soft palate, epiglottis, and pharynx that mediate the sense of taste. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### sphincter pupillae `http://purl.obolibrary.org/obo/UBERON_0001607` -#### Removed -- [sphincter pupillae](http://purl.obolibrary.org/obo/UBERON_0001607) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "m. sphincter pupillae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Iris_sphincter_muscle" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000130" -#### Added -- [sphincter pupillae](http://purl.obolibrary.org/obo/UBERON_0001607) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "m. sphincter pupillae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/taste+bud" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Iris_sphincter_muscle" +- [taste bud](http://purl.obolibrary.org/obo/UBERON_0001727) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A chemoreceptive organ.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -### spinal cord `http://purl.obolibrary.org/obo/UBERON_0002240` -#### Removed -- [spinal cord](http://purl.obolibrary.org/obo/UBERON_0002240) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "fissura cerebro-cerebellaris" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:22" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010573" -- [spinal cord](http://purl.obolibrary.org/obo/UBERON_0002240) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "fissura cerebrocerebellaris" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:22" +- [taste bud](http://purl.obolibrary.org/obo/UBERON_0001727) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002467](http://purl.obolibrary.org/obo/UBERON_0002467) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://periowiki.wikispot.org/Taste_bud_histology" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [taste bud](http://purl.obolibrary.org/obo/UBERON_0001727) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "arise by inductive interactions between epithelial cells and invading gustatory cells from chorda tympani (facial), glossophrayngeal and vagues nerves ISBN:1607950324 (todo - request cell terms from CL)" -- [spinal cord](http://purl.obolibrary.org/obo/UBERON_0002240) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "medulla spinalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Spinal_cord" +- [taste bud](http://purl.obolibrary.org/obo/UBERON_0001727) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In humans, saste buds may be found on the tongue, soft palatte, epiglottis and upper pharynx. In other species they may be found in more unusual places, such as the trunk, or on the barbels or fins of fish." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001279" +- [taste bud](http://purl.obolibrary.org/obo/UBERON_0001727) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Experients in amphibia have shown that an intrinsic feature of the pharyngeal endoderm is its ability to generate taste buds and this capacity must have been acquired by the endoderm at the origin of the vertebrates.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [spinal cord](http://purl.obolibrary.org/obo/UBERON_0002240) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "fissura cerebrocerebellaris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:22" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)" -- [spinal cord](http://purl.obolibrary.org/obo/UBERON_0002240) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "medulla spinalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Spinal_cord" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000130" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001279" -- [spinal cord](http://purl.obolibrary.org/obo/UBERON_0002240) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "fissura cerebro-cerebellaris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### taxon `http://www.geneontology.org/formats/oboInOwl#taxon` +#### Removed +- AnnotationProperty: [taxon](http://www.geneontology.org/formats/oboInOwl#taxon) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:22" -### spinal nerve `http://purl.obolibrary.org/obo/UBERON_0001780` +### tela choroidea `http://purl.obolibrary.org/obo/UBERON_0005283` #### Removed -- [spinal nerve](http://purl.obolibrary.org/obo/UBERON_0001780) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nervi spinales" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Spinal_nerve" +- [tela choroidea](http://purl.obolibrary.org/obo/UBERON_0005283) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Portion of tissue that is part of the primitive meninx which forms a fold, roofing a ventricle of the brain and supporting the choroid plexus[ZFA:0000447]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFA:0000447" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [tela choroidea](http://purl.obolibrary.org/obo/UBERON_0005283) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "Note that the structure in ZFA may be different" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "ZFA" -#### Added -- [spinal nerve](http://purl.obolibrary.org/obo/UBERON_0001780) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nervi spinales" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [tela choroidea](http://purl.obolibrary.org/obo/UBERON_0005283) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "Vascularized tela choroidea is choroid plexus." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Spinal_nerve" -### spinal nerve plexus `http://purl.obolibrary.org/obo/UBERON_0001813` +### tela choroidea of fourth ventricle `http://purl.obolibrary.org/obo/UBERON_0005287` #### Removed -- [spinal nerve plexus](http://purl.obolibrary.org/obo/UBERON_0001813) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "plexus nervorum spinalium" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [tela choroidea of fourth ventricle](http://purl.obolibrary.org/obo/UBERON_0005287) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Tela chorioidea that lines the fourth ventricle.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005158" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:5903" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" #### Added -- [spinal nerve plexus](http://purl.obolibrary.org/obo/UBERON_0001813) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "plexus nervorum spinalium" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [tela choroidea of fourth ventricle](http://purl.obolibrary.org/obo/UBERON_0005287) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:5903" +### tela choroidea of telencephalic ventricle `http://purl.obolibrary.org/obo/UBERON_0005289` + +#### Added +- [tela choroidea of telencephalic ventricle](http://purl.obolibrary.org/obo/UBERON_0005289) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### spinal vein `http://purl.obolibrary.org/obo/UBERON_0006686` +### telencephalic ventricle `http://purl.obolibrary.org/obo/UBERON_0002285` #### Removed -- [spinal vein](http://purl.obolibrary.org/obo/UBERON_0006686) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vena spinalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:76735" +- [telencephalic ventricle](http://purl.obolibrary.org/obo/UBERON_0002285) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [spinal vein](http://purl.obolibrary.org/obo/UBERON_0006686) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vena spinalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000643" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:76735" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [telencephalic ventricle](http://purl.obolibrary.org/obo/UBERON_0002285) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The lateral ventricles are part of the ventricular system of the brain. Classified as part of the telencephalon, they are the largest of the ventricles. The lateral ventricles connect to the central third ventricle through the interventricular foramina of Monro[WP]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Lateral_ventricle" +- [telencephalic ventricle](http://purl.obolibrary.org/obo/UBERON_0002285) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The two lateral ventricles are a cavity in each of the cerebral hemispheres derived from the cavity of the embryonic neural tube. They are separated from each other by the septum pellucidum, and each communicates with the third ventricle by the foramen of Monro, through which also the choroid plexuses of the lateral ventricles become continuous with that of the third ventricle[GO]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GO:0021670" -### spiral ligament `http://purl.obolibrary.org/obo/UBERON_0006725` +- [telencephalic ventricle](http://purl.obolibrary.org/obo/UBERON_0002285) SubClassOf [transformation of](http://purl.obolibrary.org/obo/RO_0002494) some [early telencephalic vesicle](http://purl.obolibrary.org/obo/UBERON_0009676) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "material to immaterial" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "EHDAA2" + +#### Added +- [telencephalic ventricle](http://purl.obolibrary.org/obo/UBERON_0002285) SubClassOf [transformation of](http://purl.obolibrary.org/obo/RO_0002494) some [early telencephalic vesicle](http://purl.obolibrary.org/obo/UBERON_0009676) + + +### telencephalon `http://purl.obolibrary.org/obo/UBERON_0001893` #### Removed -- [spiral ligament](http://purl.obolibrary.org/obo/UBERON_0006725) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ligamentum spirale ductus cochlearis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Spiral_ligament" +- [telencephalon](http://purl.obolibrary.org/obo/UBERON_0001893) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In mammals the cortex covers almost the whole of the cerebral hemispheres." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Telencephalon#Variation_among_species" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [telencephalon](http://purl.obolibrary.org/obo/UBERON_0001893) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "From an evolutionary standpoint, the telencephalon is the most recent brain structure: the amphioxus does not have this structure as a morphological entity. Overt telencephalon is present in the hagfish and lamprey to receive numerous input fibers from various parts of the CNS, similar to gnathostomes.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [spiral ligament](http://purl.obolibrary.org/obo/UBERON_0006725) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "spiral cochlear ligament" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [spiral ligament](http://purl.obolibrary.org/obo/UBERON_0006725) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ligamentum spirale ductus cochlearis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Spiral_ligament" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000283" -- [spiral ligament](http://purl.obolibrary.org/obo/UBERON_0006725) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "spiral cochlear ligament" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1016/j.ydbio.2005.02.008 Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005)" +- [telencephalon](http://purl.obolibrary.org/obo/UBERON_0001893) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "dolphins are the only species (other than humans) to have cerebra accounting for as much as 2 percent of their body weight." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Telencephalon#Variation_among_species" -### spiral organ of cochlea `http://purl.obolibrary.org/obo/UBERON_0002227` -#### Removed -- [spiral organ of cochlea](http://purl.obolibrary.org/obo/UBERON_0002227) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "organum spirale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Organ_of_Corti" +- [telencephalon](http://purl.obolibrary.org/obo/UBERON_0001893) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In ray-finned fishes and most pronounced in teleosts the roof plate of the embryonic telencephalon extends laterally with the effect that the paired alar plates forming the hemispheric walls roll out lateroventrally in a process called eversion. This is unlike the development in other vertebrate groups. [ZFA:0000079, ISBN:3764351209]" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [telencephalon](http://purl.obolibrary.org/obo/UBERON_0001893) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "telencephalic" -#### Added -- [spiral organ of cochlea](http://purl.obolibrary.org/obo/UBERON_0002227) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "organum spirale" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [telencephalon](http://purl.obolibrary.org/obo/UBERON_0001893) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In the amniotes, the cerebrum becomes increasingly large and complex. In reptiles, the paleopallium is much larger than in amphibians, and its growth has pushed the basal nuclei into the central regions of the cerebrum." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Telencephalon#Variation_among_species" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Organ_of_Corti" +- [telencephalon](http://purl.obolibrary.org/obo/UBERON_0001893) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010479" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -### spleen `http://purl.obolibrary.org/obo/UBERON_0002106` -#### Removed -- [spleen](http://purl.obolibrary.org/obo/UBERON_0002106) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lien" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Spleen" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" -#### Added -- [spleen](http://purl.obolibrary.org/obo/UBERON_0002106) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lien" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Spleen" +- [telencephalon](http://purl.obolibrary.org/obo/UBERON_0001893) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "telenencephalic" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [telencephalon](http://purl.obolibrary.org/obo/UBERON_0001893) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [cerebellum](http://purl.obolibrary.org/obo/UBERON_0002037) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" +- [telencephalon](http://purl.obolibrary.org/obo/UBERON_0001893) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In the most primitive living vertebrates, the hagfishes and lampreys, the cerebrum is a relatively simple structure receiving nerve impulses from the olfactory bulb." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Telencephalon#Variation_among_species" -### spleen capsule `http://purl.obolibrary.org/obo/UBERON_0004641` -#### Removed -- [spleen capsule](http://purl.obolibrary.org/obo/UBERON_0004641) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "capsula splenica" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15849" +- [telencephalon](http://purl.obolibrary.org/obo/UBERON_0001893) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In ray-finned fishes the inner surfaces of the lateral and ventral regions of the cerebrum bulge up into the ventricles." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Telencephalon#Variation_among_species" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [telencephalon](http://purl.obolibrary.org/obo/UBERON_0001893) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Organ component of neuraxis that has as its parts the cerebral cortex, cerebral white matter, basal ganglia, septum and fornix, as well as subcortical gray and white matter structures[FMA:62000]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:62000" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [telencephalon](http://purl.obolibrary.org/obo/UBERON_0001893) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "cerebral" -- [spleen capsule](http://purl.obolibrary.org/obo/UBERON_0004641) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica fibrosa splenica" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15849" +- [telencephalon](http://purl.obolibrary.org/obo/UBERON_0001893) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The anterior and dorsal forebrain neuromere, includes the olfactory bulb. Kimmel et al, 1995.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000079" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -#### Added -- [spleen capsule](http://purl.obolibrary.org/obo/UBERON_0004641) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica fibrosa splenica" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15849" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [telencephalon](http://purl.obolibrary.org/obo/UBERON_0001893) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: develops_from presumptive telencephalon (TAO:0000571)[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000079" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -- [spleen capsule](http://purl.obolibrary.org/obo/UBERON_0004641) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "capsula splenica" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15849" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [telencephalon](http://purl.obolibrary.org/obo/UBERON_0001893) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The cerebrum of birds has evolved along different lines to that of mammals, although they are similarly enlarged, by comparison with reptiles. However, this enlargement is largely due to the basal ganglia, with the other areas remaining relatively primitive in structure." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Telencephalon#Variation_among_species" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [telencephalon](http://purl.obolibrary.org/obo/UBERON_0001893) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### spleen venous sinus `http://purl.obolibrary.org/obo/UBERON_0009967` + +### telencephalon neural crest `http://purl.obolibrary.org/obo/UBERON_0003850` #### Removed -- [spleen venous sinus](http://purl.obolibrary.org/obo/UBERON_0009967) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "sinus lienalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [telencephalon neural crest](http://purl.obolibrary.org/obo/UBERON_0003850) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [spleen venous sinus](http://purl.obolibrary.org/obo/UBERON_0009967) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "sinus splenicus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000799" -#### Added -- [spleen venous sinus](http://purl.obolibrary.org/obo/UBERON_0009967) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "sinus lienalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [telencephalon neural crest](http://purl.obolibrary.org/obo/UBERON_0003850) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Cranial neural crest that is part of the telencephalon.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -- [spleen venous sinus](http://purl.obolibrary.org/obo/UBERON_0009967) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "sinus splenicus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000812" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -### splenic artery `http://purl.obolibrary.org/obo/UBERON_0001194` -#### Removed -- [splenic artery](http://purl.obolibrary.org/obo/UBERON_0001194) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria lienalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Splenic_artery" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [splenic artery](http://purl.obolibrary.org/obo/UBERON_0001194) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arteria splenica" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Splenic_artery" +### telencephalon pia mater `http://purl.obolibrary.org/obo/UBERON_0003552` +#### Removed +- [telencephalon pia mater](http://purl.obolibrary.org/obo/UBERON_0003552) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In fishes, the meninges consist of a single membrane, the primitive meninx, wrapped around the brain and spinal cord. With the adoption of terrestrial life, the meninges doubled. In amphibians, reptiles, and birds, the meninges include a thick outer dura mater derived from mesoderm and a thin inner secondary meninx. (...) In mammals, the dura mater persists, but division of the secondary meninx yields both the arachnoid and the pia mater from ectomesoderm.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.639" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [splenic artery](http://purl.obolibrary.org/obo/UBERON_0001194) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria lienalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Splenic_artery" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [splenic artery](http://purl.obolibrary.org/obo/UBERON_0001194) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arteria splenica" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000476" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Splenic_artery" +- [telencephalon pia mater](http://purl.obolibrary.org/obo/UBERON_0003552) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Pia mater that is part of the telencephalon. [Bgee_curator][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### splenic vein `http://purl.obolibrary.org/obo/UBERON_0003713` -#### Removed -- [splenic vein](http://purl.obolibrary.org/obo/UBERON_0003713) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena lienalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Splenic_vein" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000476" -- [splenic vein](http://purl.obolibrary.org/obo/UBERON_0003713) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vena splenica" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:14331" +### temporal bone `http://purl.obolibrary.org/obo/UBERON_0001678` +#### Removed +- [temporal bone](http://purl.obolibrary.org/obo/UBERON_0001678) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "fusion of squamosal + angular (tympanic annulus) [derm.] + petrosal (prootic + opisthotic)" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "chond." -#### Added -- [splenic vein](http://purl.obolibrary.org/obo/UBERON_0003713) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena lienalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Splenic_vein" +- [temporal bone](http://purl.obolibrary.org/obo/UBERON_0001678) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "The temporal bone consists of four parts: * Squama temporalis * Mastoid portion * Petrous portion (Petrosal ridge) * Tympanic part[WP]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "[WP]" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [temporal bone](http://purl.obolibrary.org/obo/UBERON_0001678) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In many mammals, as in humans, the petrosal, ectotympanic and squamosal bones synostose to form the temporal bone + styloid process" -- [splenic vein](http://purl.obolibrary.org/obo/UBERON_0003713) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vena splenica" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [temporal bone](http://purl.obolibrary.org/obo/UBERON_0001678) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "Note the Temporal bone is not explicitly categorized to a part of the cranium in FMA" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [temporal bone](http://purl.obolibrary.org/obo/UBERON_0001678) SubClassOf [overlaps](http://purl.obolibrary.org/obo/RO_0002131) some [chondrocranium](http://purl.obolibrary.org/obo/UBERON_0002241) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "petrosal" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:14331" +- [temporal bone](http://purl.obolibrary.org/obo/UBERON_0001678) SubClassOf [overlaps](http://purl.obolibrary.org/obo/RO_0002131) some [dermatocranium](http://purl.obolibrary.org/obo/UBERON_0003113) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "squamosal plus angular" + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "temporal series" -### squamous epithelial cell `http://purl.obolibrary.org/obo/CL_0000076` +- [temporal bone](http://purl.obolibrary.org/obo/UBERON_0001678) SubClassOf [overlaps](http://purl.obolibrary.org/obo/RO_0002131) some [splanchnocranium](http://purl.obolibrary.org/obo/UBERON_0008895) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "styloid process" #### Added -- [squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000076) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [temporal bone](http://purl.obolibrary.org/obo/UBERON_0001678) SubClassOf [overlaps](http://purl.obolibrary.org/obo/RO_0002131) some [splanchnocranium](http://purl.obolibrary.org/obo/UBERON_0008895) +- [temporal bone](http://purl.obolibrary.org/obo/UBERON_0001678) SubClassOf [overlaps](http://purl.obolibrary.org/obo/RO_0002131) some [dermatocranium](http://purl.obolibrary.org/obo/UBERON_0003113) -### sst GABAergic cortical interneuron `http://purl.obolibrary.org/obo/CL_4023017` +- [temporal bone](http://purl.obolibrary.org/obo/UBERON_0001678) SubClassOf [overlaps](http://purl.obolibrary.org/obo/RO_0002131) some [chondrocranium](http://purl.obolibrary.org/obo/UBERON_0002241) -#### Added -- [sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023017) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### temporal cortex `http://purl.obolibrary.org/obo/UBERON_0016538` +#### Removed +- [temporal cortex](http://purl.obolibrary.org/obo/UBERON_0016538) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D013702" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) -### sst chodl GABAergic cortical interneuron `http://purl.obolibrary.org/obo/CL_4023121` + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -#### Added -- [sst chodl GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023121) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### starburst amacrine cell `http://purl.obolibrary.org/obo/CL_0004232` +### temporally related to `http://purl.obolibrary.org/obo/RO_0002222` +#### Removed +- [temporally related to](http://purl.obolibrary.org/obo/RO_0002222) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) -#### Added -- [starburst amacrine cell](http://purl.obolibrary.org/obo/CL_0004232) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [temporally related to](http://purl.obolibrary.org/obo/RO_0002222) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) [s_interval_algebra](https://en.wikipedia.org/wiki/Allen%27s_interval_algebra) +- [temporally related to](http://purl.obolibrary.org/obo/RO_0002222) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) -### stellate neuron `http://purl.obolibrary.org/obo/CL_0000122` +- [temporally related to](http://purl.obolibrary.org/obo/RO_0002222) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." -#### Added -- [stellate neuron](http://purl.obolibrary.org/obo/CL_0000122) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [temporally related to](http://purl.obolibrary.org/obo/RO_0002222) [source](http://purl.org/dc/terms/source) "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) -### stem cell `http://purl.obolibrary.org/obo/CL_0000034` -#### Added -- [stem cell](http://purl.obolibrary.org/obo/CL_0000034) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### tendon `http://purl.obolibrary.org/obo/UBERON_0000043` +#### Removed +- [tendon](http://purl.obolibrary.org/obo/UBERON_0000043) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Phylogenetically, tendinous tissue first appears in the invertebrate chordate Branchiostoma as myosepta. This two-dimensional array of collagen fibers is highly organized, with fibers running along two primary axes. In hagfish the first linear tendons appear and the myosepta have developed specialized regions with unidirectional fiber orientation - a linear tendon within the flat sheet of myoseptum.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### stem cell of epidermis `http://purl.obolibrary.org/obo/CL_1000428` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [stem cell of epidermis](http://purl.obolibrary.org/obo/CL_1000428) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1016/S1095-6433(02)00241-6 Summers AP, Koob TJ, The evolution of tendon - morphology and material properties. Comparative Biochemistry and Physiology-Part A: Molecular and Integrative Physiology (2002)" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001286" -### sternoclavicular joint `http://purl.obolibrary.org/obo/UBERON_0001469` -#### Removed -- [sternoclavicular joint](http://purl.obolibrary.org/obo/UBERON_0001469) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "articulatio sternoclavicularis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Sternoclavicular_articulation" +- [tendon](http://purl.obolibrary.org/obo/UBERON_0000043) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in FMA, tendon is an organ component that with parts dense-irregular-connective-tissue of tendon and dense-irregular-connective-tissue of tendon sheath; we follow VSAO in making it a subtype of the former. In VSAO tendons connect muscle to bone; in WP the def states integument (e.g. auricular muscles) - but JB confirms this is not actually tendon but aponeurosis" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [tendon](http://purl.obolibrary.org/obo/UBERON_0000043) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Dense regular connective tissue that connects muscle to bone.[VSAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000073" -#### Added -- [sternoclavicular joint](http://purl.obolibrary.org/obo/UBERON_0001469) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "articulatio sternoclavicularis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Sternoclavicular_articulation" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PSPUB:0000170" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" -### stomach `http://purl.obolibrary.org/obo/UBERON_0000945` -#### Removed -- [stomach](http://purl.obolibrary.org/obo/UBERON_0000945) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ventriculus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Stomach" -#### Added -- [stomach](http://purl.obolibrary.org/obo/UBERON_0000945) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ventriculus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### term imported `http://purl.obolibrary.org/obo/IAO_0000228` +#### Removed +- [term imported](http://purl.obolibrary.org/obo/IAO_0000228) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "term imported"@en - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Stomach" -### stomodeum `http://purl.obolibrary.org/obo/UBERON_0000930` +### term replaced by `http://purl.obolibrary.org/obo/IAO_0100001` #### Removed -- [stomodeum](http://purl.obolibrary.org/obo/UBERON_0000930) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000439" +- [term replaced by](http://purl.obolibrary.org/obo/IAO_0100001) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) "Person:Alan Ruttenberg"@en -#### Added -- [stomodeum](http://purl.obolibrary.org/obo/UBERON_0000930) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000439" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [term replaced by](http://purl.obolibrary.org/obo/IAO_0100001) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) +- [term replaced by](http://purl.obolibrary.org/obo/IAO_0100001) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) "Person:Alan Ruttenberg"@en -### stratified epithelial cell `http://purl.obolibrary.org/obo/CL_0000079` +- [term replaced by](http://purl.obolibrary.org/obo/IAO_0100001) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "term replaced by"@en -#### Added -- [stratified epithelial cell](http://purl.obolibrary.org/obo/CL_0000079) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### stratum basale of epidermis `http://purl.obolibrary.org/obo/UBERON_0002025` +### term split `http://purl.obolibrary.org/obo/IAO_0000229` #### Removed -- [stratum basale of epidermis](http://purl.obolibrary.org/obo/UBERON_0002025) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "stratum Malpighi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Malpighian_layer" +- [term split](http://purl.obolibrary.org/obo/IAO_0000229) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "term split"@en - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [stratum basale of epidermis](http://purl.obolibrary.org/obo/UBERON_0002025) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "stratum Malpighi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Malpighian_layer" +### term tracker item `http://purl.obolibrary.org/obo/IAO_0000233` +#### Removed +- [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg"@en +- [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" -### stratum corneum of epidermis `http://purl.obolibrary.org/obo/UBERON_0002027` -#### Removed -- [stratum corneum of epidermis](http://purl.obolibrary.org/obo/UBERON_0002027) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "stratum corneum epidermidis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Stratum_corneum" +- [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [pending final vetting](http://purl.obolibrary.org/obo/IAO_0000125) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/"@en -#### Added -- [stratum corneum of epidermis](http://purl.obolibrary.org/obo/UBERON_0002027) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "stratum corneum epidermidis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "term tracker item"@en - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Stratum_corneum" +- [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg"@en +- [term tracker item](http://purl.obolibrary.org/obo/IAO_0000233) [is_class_level](http://www.geneontology.org/formats/oboInOwl#is_class_level) true -### stratum spinosum of epidermis `http://purl.obolibrary.org/obo/UBERON_0002026` -#### Removed -- [stratum spinosum of epidermis](http://purl.obolibrary.org/obo/UBERON_0002026) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "stratum Malpighii" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Malpighian" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [stratum spinosum of epidermis](http://purl.obolibrary.org/obo/UBERON_0002026) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "stratum Malpighii" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Malpighian" +### terminal bronchiole epithelium `http://purl.obolibrary.org/obo/UBERON_0001958` +#### Removed +- [terminal bronchiole epithelium](http://purl.obolibrary.org/obo/UBERON_0001958) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "A pseudostratified epithelium, containing basal cells, stem cells of the airway, submucosal glands and cartilage rings, is limited to the trachea and large lobar airways in the mouse (Morrisey and Hogan, 2010). This more complex epithelium extends to terminal bronchioles in the human[DOI:10.1242/dev.115469]" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### stria vascularis of cochlear duct `http://purl.obolibrary.org/obo/UBERON_0002282` +### terminal part of digestive tract `http://purl.obolibrary.org/obo/UBERON_0006866` #### Removed -- [stria vascularis of cochlear duct](http://purl.obolibrary.org/obo/UBERON_0002282) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "stria vascularis ductus cochlearis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001819" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [terminal part of digestive tract](http://purl.obolibrary.org/obo/UBERON_0006866) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005756" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -#### Added -- [stria vascularis of cochlear duct](http://purl.obolibrary.org/obo/UBERON_0002282) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "stria vascularis ductus cochlearis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001819" +- [terminal part of digestive tract](http://purl.obolibrary.org/obo/UBERON_0006866) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "this class is the superclass of 'rectum', which is currently reserved for the vertebrate structure. May be merged in future." - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### striatum `http://purl.obolibrary.org/obo/UBERON_0002435` +### terms merged `http://purl.obolibrary.org/obo/IAO_0000227` #### Removed -- [striatum](http://purl.obolibrary.org/obo/UBERON_0002435) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "corpus striatum (Zilles)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:225" +- [terms merged](http://purl.obolibrary.org/obo/IAO_0000227) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "terms merged"@en + - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + +### tertiary ovarian follicle `http://purl.obolibrary.org/obo/UBERON_0000037` #### Added -- [striatum](http://purl.obolibrary.org/obo/UBERON_0002435) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "corpus striatum (Zilles)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [tertiary ovarian follicle](http://purl.obolibrary.org/obo/UBERON_0000037) SubClassOf [protein-containing material entity](http://purl.obolibrary.org/obo/PR_000050567) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:225" +### testicular vein `http://purl.obolibrary.org/obo/UBERON_0001144` +#### Removed +- [testicular vein](http://purl.obolibrary.org/obo/UBERON_0001144) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In humans, the right testicular vein generally joins the inferior vena cava; the left testicular vein, unlike the right, often joins the left renal vein instead of the inferior vena cava. The veins emerge from the back of the testis, and receive tributaries from the epididymis; they unite and form a convoluted plexus, called the pampiniform plexus, which constitutes the greater mass of the spermatic cord; the vessels composing this plexus are very numerous, and ascend along the cord, in front of the ductus deferens. Below the subcutaneous inguinal ring, they unite to form three or four veins, which pass along the inguinal canal, and, entering the abdomen through the abdominal inguinal ring, coalesce to form two veins, which ascend on the Psoas major, behind the peritoneum, lying one on either side of the internal spermatic artery. These unite to form a single vein, which opens, on the right side, into the inferior vena cava (at an acute angle), on the left side into the left renal vein (at a right angle). The spermatic veins are provided with valves. The left spermatic vein passes behind the iliac colon and is thus exposed to pressure from the contents of that part of the bowel" -### stromal cell `http://purl.obolibrary.org/obo/CL_0000499` -#### Added -- [stromal cell](http://purl.obolibrary.org/obo/CL_0000499) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### testis `http://purl.obolibrary.org/obo/UBERON_0000473` +#### Removed +- [testis](http://purl.obolibrary.org/obo/UBERON_0000473) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The testes are descended in metatherian and eutherian mammals, first transabdominally, then inguinoscrotally" + - [taxon](http://www.geneontology.org/formats/oboInOwl#taxon) "NCBITaxon:40674" -### stromal cell of lamina propria of small intestine `http://purl.obolibrary.org/obo/CL_0009022` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0123971756" -#### Added -- [stromal cell of lamina propria of small intestine](http://purl.obolibrary.org/obo/CL_0009022) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [testis](http://purl.obolibrary.org/obo/UBERON_0000473) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "testicular" +- [testis](http://purl.obolibrary.org/obo/UBERON_0000473) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) while it is likely that Urbilateria lacked a complex somatic reproductive system, it is at present impossible to speculate on whether or not it possessed a true gonad, let alone any other somatic adaptations for reproduction (reference 1); Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved (reference 2).[uncertain][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### stromal cell of ovary `http://purl.obolibrary.org/obo/CL_0002132` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [stromal cell of ovary](http://purl.obolibrary.org/obo/CL_0002132) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1093/icb/icm052 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across the Bilateria. Integrative and Comparative Biology (2007), DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T and Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)" -### subarachnoid space `http://purl.obolibrary.org/obo/UBERON_0000315` -#### Removed -- [subarachnoid space](http://purl.obolibrary.org/obo/UBERON_0000315) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "spatium leptomeningeum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0000230" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000252" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [testis](http://purl.obolibrary.org/obo/UBERON_0000473) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Male reproductive organ.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -- [subarachnoid space](http://purl.obolibrary.org/obo/UBERON_0000315) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "spatium subarachnoideum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Subarachnoid_space" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0000230" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000598" -- [subarachnoid space](http://purl.obolibrary.org/obo/UBERON_0000315) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cavitas subarachnoidea" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0000230" +- [testis](http://purl.obolibrary.org/obo/UBERON_0000473) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004928" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [subarachnoid space](http://purl.obolibrary.org/obo/UBERON_0000315) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cavum subarachnoideale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Subarachnoid_space" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### tetrapod frontal bone `http://purl.obolibrary.org/obo/UBERON_0000209` +#### Removed +- [tetrapod frontal bone](http://purl.obolibrary.org/obo/UBERON_0000209) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "VHOG:0001324" -#### Added -- [subarachnoid space](http://purl.obolibrary.org/obo/UBERON_0000315) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cavum subarachnoideale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Subarachnoid_space" +- [tetrapod frontal bone](http://purl.obolibrary.org/obo/UBERON_0000209) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "In the mouse the parietal originates from cephalic paraxial mesoderm (Jiang 2000; Morriss-Kay 2001), whereas in the chicken it is traced back to either mesodermal (Noden 1978) or neural crest (Couly 1992, 1993)." - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [tetrapod frontal bone](http://purl.obolibrary.org/obo/UBERON_0000209) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "fused in humans, paired in other animals" -- [subarachnoid space](http://purl.obolibrary.org/obo/UBERON_0000315) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "spatium subarachnoideum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Subarachnoid_space" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0000230" +### theca cell layer `http://purl.obolibrary.org/obo/UBERON_0000155` +#### Removed +- [theca cell layer](http://purl.obolibrary.org/obo/UBERON_0000155) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "The theca folliculi are responsible for the production of testosterone from androstenedione in females, and indirectly the production of estrogens by supplying the neighboring granulosa cells with androstenedione that can then be used as a substrate for aromatase. [Wikipedia:Theca_of_follicle]" -- [subarachnoid space](http://purl.obolibrary.org/obo/UBERON_0000315) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cavitas subarachnoidea" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +#### Added +- [theca cell layer](http://purl.obolibrary.org/obo/UBERON_0000155) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0000230" -- [subarachnoid space](http://purl.obolibrary.org/obo/UBERON_0000315) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "spatium leptomeningeum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### thoracic cavity `http://purl.obolibrary.org/obo/UBERON_0002224` +#### Removed +- [thoracic cavity](http://purl.obolibrary.org/obo/UBERON_0002224) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In many species, the diaphragm separates thoracic and abdominal cavities" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0000230" -### subclavian artery `http://purl.obolibrary.org/obo/UBERON_0001533` +### thoracic cavity artery `http://purl.obolibrary.org/obo/UBERON_0003473` #### Removed -- [subclavian artery](http://purl.obolibrary.org/obo/UBERON_0001533) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria subclavia" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Subclavian_artery" +- [thoracic cavity artery](http://purl.obolibrary.org/obo/UBERON_0003473) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in MA, aorta is classified here - but this is problematic because the abdominal aorta is not in the thoracic cavity" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [subclavian artery](http://purl.obolibrary.org/obo/UBERON_0001533) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arteria subclavia" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "XAO:0000365" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### thoracic mammary gland `http://purl.obolibrary.org/obo/UBERON_0005200` +#### Removed +- [thoracic mammary gland](http://purl.obolibrary.org/obo/UBERON_0005200) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Most primates have one pair of mammary glands, which are thoracic." -#### Added -- [subclavian artery](http://purl.obolibrary.org/obo/UBERON_0001533) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arteria subclavia" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [thoracic mammary gland](http://purl.obolibrary.org/obo/UBERON_0005200) [UBPROP_0000202](http://purl.obolibrary.org/obo/UBPROP_0000202) [FMA_57983](http://purl.obolibrary.org/obo/FMA_57983) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "XAO:0000365" -- [subclavian artery](http://purl.obolibrary.org/obo/UBERON_0001533) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria subclavia" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Subclavian_artery" +### thoracic region of vertebral column `http://purl.obolibrary.org/obo/UBERON_0006073` +#### Removed +- [thoracic region of vertebral column](http://purl.obolibrary.org/obo/UBERON_0006073) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Region of the vertebral column between the atlas and the sacrum consisting of seven to 285 vertebrae.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000612" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -### subclavian vein `http://purl.obolibrary.org/obo/UBERON_0001587` -#### Removed -- [subclavian vein](http://purl.obolibrary.org/obo/UBERON_0001587) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vena subclavia" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Subclavian_vein" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:Duellman_and_Trueb_1994" -#### Added -- [subclavian vein](http://purl.obolibrary.org/obo/UBERON_0001587) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vena subclavia" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [thoracic region of vertebral column](http://purl.obolibrary.org/obo/UBERON_0006073) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "AAO:0000612" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Subclavian_vein" -### subcommissural organ `http://purl.obolibrary.org/obo/UBERON_0002139` +### thoracic rib cage `http://purl.obolibrary.org/obo/UBERON_0003252` #### Removed -- [subcommissural organ](http://purl.obolibrary.org/obo/UBERON_0002139) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "organum subcommissurale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Subcommissural_organ" +- [thoracic rib cage](http://purl.obolibrary.org/obo/UBERON_0003252) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical cluster that consists of more than one rib in an individual.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0002100" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -- [subcommissural organ](http://purl.obolibrary.org/obo/UBERON_0002139) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "corpus subcommissurale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:483" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TAO:wd" -#### Added -- [subcommissural organ](http://purl.obolibrary.org/obo/UBERON_0002139) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "organum subcommissurale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Subcommissural_organ" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -- [subcommissural organ](http://purl.obolibrary.org/obo/UBERON_0002139) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "corpus subcommissurale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:483" +### thoracic segment of trunk `http://purl.obolibrary.org/obo/UBERON_0000915` +#### Removed +- [thoracic segment of trunk](http://purl.obolibrary.org/obo/UBERON_0000915) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [appendage](http://purl.obolibrary.org/obo/UBERON_0000026) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [thoracic segment of trunk](http://purl.obolibrary.org/obo/UBERON_0000915) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [abdominal segment of trunk](http://purl.obolibrary.org/obo/UBERON_0002417) +- [thoracic segment of trunk](http://purl.obolibrary.org/obo/UBERON_0000915) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest" -### subcutaneous adipocyte `http://purl.obolibrary.org/obo/CL_0002521` +- [thoracic segment of trunk](http://purl.obolibrary.org/obo/UBERON_0000915) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [head](http://purl.obolibrary.org/obo/UBERON_0000033) -#### Added -- [subcutaneous adipocyte](http://purl.obolibrary.org/obo/CL_0002521) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### subcutaneous adipose tissue `http://purl.obolibrary.org/obo/UBERON_0002190` +### thoracic vertebra `http://purl.obolibrary.org/obo/UBERON_0002347` #### Removed -- [subcutaneous adipose tissue](http://purl.obolibrary.org/obo/UBERON_0002190) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "panniculus adiposus (tela subcutanea)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [thoracic vertebra](http://purl.obolibrary.org/obo/UBERON_0002347) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Thoracic vertebrae in all species are defined as those vertebrae which also carry a pair of ribs, and lie caudal to the cervical vertebrae. In humans, they are distinguished by the presence of facets on the sides of the bodies for articulation with the heads of the ribs, and facets on the transverse processes of all, except the eleventh and twelfth, for articulation with the tubercles of the ribs" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:74315" -- [subcutaneous adipose tissue](http://purl.obolibrary.org/obo/UBERON_0002190) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "panniculus adiposus telae subcutaneae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### thrombomodulin `http://purl.obolibrary.org/obo/PR_000002105` +#### Removed +- [thrombomodulin](http://purl.obolibrary.org/obo/PR_000002105) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [thrombomodulin (human)](http://purl.obolibrary.org/obo/PR_P07204) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:74315" -#### Added -- [subcutaneous adipose tissue](http://purl.obolibrary.org/obo/UBERON_0002190) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "panniculus adiposus (tela subcutanea)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### thymus `http://purl.obolibrary.org/obo/UBERON_0002370` +#### Removed +- [thymus](http://purl.obolibrary.org/obo/UBERON_0002370) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical structure which originates as several paired thickenings on the dorsal side of the pharyngeal pouches and secretes thymosin.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:74315" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" -- [subcutaneous adipose tissue](http://purl.obolibrary.org/obo/UBERON_0002190) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "panniculus adiposus telae subcutaneae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010548" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [thymus](http://purl.obolibrary.org/obo/UBERON_0002370) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "thymic" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:74315" +- [thymus](http://purl.obolibrary.org/obo/UBERON_0002370) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "A thymus develops in all vertebrates from the endodermal epithelium of certain pharyngeal pouches and from the adjacent ectodermal epithelium. In fishes, all the pouches, or the first four, contribute to thymus formation, but in tetrapods, the number is more restricted. In mammals, only the third and fourth are involved, and the contribution of the third is by far the greater.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [subcutaneous adipose tissue](http://purl.obolibrary.org/obo/UBERON_0002190) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D015434" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000253" -### subdivision of digestive tract `http://purl.obolibrary.org/obo/UBERON_0004921` -#### Removed -- [subdivision of digestive tract](http://purl.obolibrary.org/obo/UBERON_0004921) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00100315" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.558" + +- [thymus](http://purl.obolibrary.org/obo/UBERON_0002370) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) #### Added -- [subdivision of digestive tract](http://purl.obolibrary.org/obo/UBERON_0004921) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00100315" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [thymus](http://purl.obolibrary.org/obo/UBERON_0002370) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) -### subdivision of organism along appendicular axis `http://purl.obolibrary.org/obo/UBERON_0010758` -#### Removed -- [subdivision of organism along appendicular axis](http://purl.obolibrary.org/obo/UBERON_0010758) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007018" +### thymus corticomedullary boundary `http://purl.obolibrary.org/obo/UBERON_0003988` #### Added -- [subdivision of organism along appendicular axis](http://purl.obolibrary.org/obo/UBERON_0010758) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007018" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [thymus corticomedullary boundary](http://purl.obolibrary.org/obo/UBERON_0003988) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) -### subiculum `http://purl.obolibrary.org/obo/UBERON_0002191` +### thymus epithelium `http://purl.obolibrary.org/obo/UBERON_0003846` +#### Removed +- [thymus epithelium](http://purl.obolibrary.org/obo/UBERON_0003846) SubClassOf [epithelium](http://purl.obolibrary.org/obo/UBERON_0000483) #### Added -- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Subiculum" - -- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0004683](http://purl.obolibrary.org/obo/UBERON_0004683) - - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" +- [thymus epithelium](http://purl.obolibrary.org/obo/UBERON_0003846) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) -- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DMBA:16163" +- [thymus epithelium](http://purl.obolibrary.org/obo/UBERON_0003846) SubClassOf [meso-epithelium](http://purl.obolibrary.org/obo/UBERON_0012275) -- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PBA:128012354" +- [thymus epithelium](http://purl.obolibrary.org/obo/UBERON_0003846) SubClassOf [endo-epithelium](http://purl.obolibrary.org/obo/UBERON_0005911) -- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BAMS:S" -- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "UMLS:C0152316" - - [source](http://www.geneontology.org/formats/oboInOwl#source) "ncithesaurus:Subiculum" +### thymus lobe `http://purl.obolibrary.org/obo/UBERON_0005483` +#### Removed +- [thymus lobe](http://purl.obolibrary.org/obo/UBERON_0005483) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "each lobe of the thymus can be divided into a central medulla and a peripheral cortex which is surrounded by an outer capsule. Each lobe is composed of numerous lobules held together by delicate areolar tissue; the entire organ being enclosed in an investing capsule of a similar but denser structure. The primary lobules vary in size from that of a pin's head to that of a small pea, and are made up of a number of small nodules or follicles.[WP]" -- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PBA:10054" +#### Added +- [thymus lobe](http://purl.obolibrary.org/obo/UBERON_0005483) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "thymus subunit" -- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "SCTID:369097009" +- [thymus lobe](http://purl.obolibrary.org/obo/UBERON_0005483) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) -- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BM:Tel-Cx-SB" -- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "subiculum cornu ammonis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0003087" +### thymus lobule `http://purl.obolibrary.org/obo/UBERON_0002125` +#### Removed +- [thymus lobule](http://purl.obolibrary.org/obo/UBERON_0002125) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "in the mouse, the lobes of the thymus are not subdivided into lobules but only in the central medulla and a peripheral cortex (i.e. there is no distinct sublobulation). In humans, the two thymus lobes are composed of many lobules of various sizes which contain follicles, each comprising a medulla and a cortex. in the rat, the thymus is partially subdivided into lobules separated by thin bands of connective tissue which are continuous with the thin connective tissue capsule.[MP]" -- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BIRNLEX:1305" +- [thymus lobule](http://purl.obolibrary.org/obo/UBERON_0002125) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "Lymphocytes, reticular cells and macrophages are found in the lobules" -- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:35832" +#### Added +- [thymus lobule](http://purl.obolibrary.org/obo/UBERON_0002125) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) -- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "HBA:12896" -- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0002728](http://purl.obolibrary.org/obo/UBERON_0002728) - - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" +### thymus lymphoid tissue `http://purl.obolibrary.org/obo/UBERON_0003483` -- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [UBERON_0001953](http://purl.obolibrary.org/obo/UBERON_0001953) - - [source](http://www.geneontology.org/formats/oboInOwl#source) "ABA" +#### Added +- [thymus lymphoid tissue](http://purl.obolibrary.org/obo/UBERON_0003483) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) -- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "The pyramidal neurons in the subiculum exhibit transitions between two modes of action potential output: bursting and single spiking. The transitions between these two modes is thought to be important for routing information out of the hippocampus. It is the site responsible for ictal activity in some cases of human epilepsy. It has also been implicated in working memory and drug addiction.[Wikipedia:Subiculum]" -- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MA:0000960" +### thymus primordium `http://purl.obolibrary.org/obo/UBERON_0005562` +#### Removed +- [thymus primordium](http://purl.obolibrary.org/obo/UBERON_0005562) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A small outgrowth of the pharyngeal epithelium that is the site of lymphocyte cell production. Willett et al, 1999.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001077" -- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [label](http://www.w3.org/2000/01/rdf-schema#label) "subiculum" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [pheno_slim](http://purl.obolibrary.org/obo/uberon/core#pheno_slim) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "gyrus parahippocampalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0003087" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DHBA:10301" +- [thymus primordium](http://purl.obolibrary.org/obo/UBERON_0005562) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "variability of developmental origin: In fish, thymic primordia are generated by all the pouches except the first. However, in avians the thymus arises from pouches 3 and 4, whereas in humans it is only generated by the third pouch[PMID:16313389] The thymus arises from the second pouch in frogs, 2-6 in cartilaginous fish, 2-3 in reptiles, 3 or 4 in bony fish, birds and mammals. The final number is variable - 5 paired organs in sharks, 4 in caecilians, 3 in urodeles, 1 in many teleost, anurans and many mammals" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0781714125" -- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [depiction](http://xmlns.com/foaf/0.1/depiction) "https://upload.wikimedia.org/wikipedia/commons/9/99/Hippocampus.gif"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) +- [thymus primordium](http://purl.obolibrary.org/obo/UBERON_0005562) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [vagal neural crest](http://purl.obolibrary.org/obo/UBERON_0005428) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFA" -- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0003087" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "https://github.com/obophenotype/uberon/wiki/The-neural-crest" -- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MBA:502" + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "mesenchymal" -- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "subiculum hippocampi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:74414" +#### Added +- [thymus primordium](http://purl.obolibrary.org/obo/UBERON_0005562) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [vagal neural crest](http://purl.obolibrary.org/obo/UBERON_0005428) -- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "neuronames:188" -- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Part of the hippocampal formation that is bounded by the entorhinal cortex and area CA1. It is characterized on the CA1 border by an abrupt widening of the pyramidal cell layer. A molecular layer is present that is continuous with that of CA1, although the stratum radiatum is no longer present. The stratum oriens is also not present. adapted from Paxinos, G. The rat central nervous system, 2nd ed, Academic Press, San Diego, 1995, pg. 468)." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BIRNLEX:1305" +### thymus primordium endoderm `http://purl.obolibrary.org/obo/UBERON_0008817` -- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DHBA:10302" +#### Added +- [thymus primordium endoderm](http://purl.obolibrary.org/obo/UBERON_0008817) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [uberon_slim](http://purl.obolibrary.org/obo/uberon/core#uberon_slim) -- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NCIT:C33648" +### thymus subunit `http://purl.obolibrary.org/obo/UBERON_0035075` +#### Removed +- [thymus subunit](http://purl.obolibrary.org/obo/UBERON_0035075) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "lobe or lobule of thymus" -- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [id](http://www.geneontology.org/formats/oboInOwl#id) "UBERON:0002191" +- [thymus subunit](http://purl.obolibrary.org/obo/UBERON_0035075) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" -- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:74414" +- [thymus subunit](http://purl.obolibrary.org/obo/UBERON_0035075) [id](http://www.geneontology.org/formats/oboInOwl#id) "UBERON:0035075" -- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "In ABA SUB is part of the retrohippocampal region, along with the entorhinal area. this is in the hippocampal formation but not the hippocampal region" - - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "ABA" +- [thymus subunit](http://purl.obolibrary.org/obo/UBERON_0035075) [label](http://www.w3.org/2000/01/rdf-schema#label) "thymus subunit" -- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "subicular cortex" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BIRNLEX:1305" +- [thymus subunit](http://purl.obolibrary.org/obo/UBERON_0035075) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71193" -- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BAMS:SUB" +- Class: [thymus subunit](http://purl.obolibrary.org/obo/UBERON_0035075) -- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" +- [thymus subunit](http://purl.obolibrary.org/obo/UBERON_0035075) EquivalentTo [organ subunit](http://purl.obolibrary.org/obo/UBERON_0000063) and ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [thyroid gland](http://purl.obolibrary.org/obo/UBERON_0002046)) -- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in DHBA subicular cortex is divided into subiculum, prosubiculum and supracallosal subiculum" +- [thymus subunit](http://purl.obolibrary.org/obo/UBERON_0035075) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [thyroid gland](http://purl.obolibrary.org/obo/UBERON_0002046) -- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "subicular" +- [thymus subunit](http://purl.obolibrary.org/obo/UBERON_0035075) SubClassOf [organ subunit](http://purl.obolibrary.org/obo/UBERON_0000063) -- Class: [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) -- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) SubClassOf [regional part of brain](http://purl.obolibrary.org/obo/UBERON_0002616) -- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) SubClassOf [capable of part of](http://purl.obolibrary.org/obo/RO_0002216) some [memory](http://purl.obolibrary.org/obo/GO_0007613) - - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia" +### thymus trabecula `http://purl.obolibrary.org/obo/UBERON_0004791` -- [subiculum](http://purl.obolibrary.org/obo/UBERON_0002191) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [hippocampal formation](http://purl.obolibrary.org/obo/UBERON_0002421) - - [source](http://www.geneontology.org/formats/oboInOwl#source) "NIFSTD" +#### Added +- [thymus trabecula](http://purl.obolibrary.org/obo/UBERON_0004791) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) -### submucosa of bronchus `http://purl.obolibrary.org/obo/UBERON_0001957` +### thyroid artery `http://purl.obolibrary.org/obo/UBERON_0003847` #### Removed -- [submucosa of bronchus](http://purl.obolibrary.org/obo/UBERON_0001957) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tela submucosa bronchi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:62653" +- [thyroid artery](http://purl.obolibrary.org/obo/UBERON_0003847) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Part of the external carotid which supplies blood to the thyroid gland.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" -#### Added -- [submucosa of bronchus](http://purl.obolibrary.org/obo/UBERON_0001957) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tela submucosa bronchi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010490" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:62653" +- [thyroid artery](http://purl.obolibrary.org/obo/UBERON_0003847) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: part_of external carotid (AAO:0010218)[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010490" -### submucosa of esophagus `http://purl.obolibrary.org/obo/UBERON_0001972` + +### thyroid gland `http://purl.obolibrary.org/obo/UBERON_0002046` #### Removed -- [submucosa of esophagus](http://purl.obolibrary.org/obo/UBERON_0001972) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tela submucosa (oesophagus)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [thyroid gland](http://purl.obolibrary.org/obo/UBERON_0002046) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In larval lampreys, the thyroid originates as an exocrine gland, secreting its hormones into the gut, and associated with the larva's filter-feeding apparatus. In the adult lamprey, the gland separates from the gut, and becomes endocrine, but this path of development may reflect the evolutionary origin of the thyroid. For instance, the closest living relatives of vertebrates, the tunicates and Amphioxus, have a structure very similar to that of larval lampreys, and this also secretes iodine-containing compounds (albeit not thyroxine)" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Romer" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [hasScope](http://www.geneontology.org/formats/oboInOwl#hasScope) "NCBITaxon:7746" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:62997" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Thyroid_gland#Other_animals" -- [submucosa of esophagus](http://purl.obolibrary.org/obo/UBERON_0001972) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tela submucosa oesophageae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [thyroid gland](http://purl.obolibrary.org/obo/UBERON_0002046) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (2) a groove in the pharyngeal floor known as the endostyle, or a thyroid gland derived from part of the endostyle (...).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:62997" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [submucosa of esophagus](http://purl.obolibrary.org/obo/UBERON_0001972) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tela submucosa esophagi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0002109" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000418" -#### Added -- [submucosa of esophagus](http://purl.obolibrary.org/obo/UBERON_0001972) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tela submucosa esophagi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [thyroid gland](http://purl.obolibrary.org/obo/UBERON_0002046) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Either of paired structures located in the throat which develop from the ventral wall of the pharynx and excretes hormones involved in the morphological and functional changes during metamorphosis as well as influencing other tissues.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0002109" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010544" -- [submucosa of esophagus](http://purl.obolibrary.org/obo/UBERON_0001972) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tela submucosa oesophageae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:62997" +- [thyroid gland](http://purl.obolibrary.org/obo/UBERON_0002046) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In tetrapods, the thyroid is always found somewhere in the neck region. In most tetrapod species, there are two paired thyroid glands - that is, the right and left lobes are not joined together. However, there is only ever a single thyroid gland in most mammals, and the shape found in humans is common to many other species" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Romer" -- [submucosa of esophagus](http://purl.obolibrary.org/obo/UBERON_0001972) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tela submucosa (oesophagus)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [hasScope](http://www.geneontology.org/formats/oboInOwl#hasScope) "NCBITaxon:32523" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Thyroid_gland#Other_animals" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:62997" +- [thyroid gland](http://purl.obolibrary.org/obo/UBERON_0002046) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In fish, it is usually located below the gills and is not always divided into distinct lobes. However, in some teleosts, patches of thyroid tissue are found elsewhere in the body, associated with the kidneys, spleen, heart, or eyes" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Romer" + - [hasScope](http://www.geneontology.org/formats/oboInOwl#hasScope) "NCBITaxon:32443" -### submucosa of large intestine `http://purl.obolibrary.org/obo/UBERON_0001208` -#### Removed -- [submucosa of large intestine](http://purl.obolibrary.org/obo/UBERON_0001208) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tela submucosa intestini crassi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:14970" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Thyroid_gland#Other_animals" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + +### thyroid gland medulla `http://purl.obolibrary.org/obo/UBERON_0004827` #### Added -- [submucosa of large intestine](http://purl.obolibrary.org/obo/UBERON_0001208) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tela submucosa intestini crassi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:14970" +- [thyroid gland medulla](http://purl.obolibrary.org/obo/UBERON_0004827) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### thyroid primordium `http://purl.obolibrary.org/obo/UBERON_0003091` +#### Removed +- [thyroid primordium](http://purl.obolibrary.org/obo/UBERON_0003091) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "Note that we follow EHDAA2 in dividing this into endoderm and mesenchyme. In this ontology we place the broad developmental relationship at this level, and include specific relationships to the pharyngeal endoderm at the level of the endoderm" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EHDAA2" +- [thyroid primordium](http://purl.obolibrary.org/obo/UBERON_0003091) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Portion of tissue part of the pharyngeal endoderm that is fated to become thyroid follicle[ZFIN:curator]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -### submucosa of pharynx `http://purl.obolibrary.org/obo/UBERON_0004924` -#### Removed -- [submucosa of pharynx](http://purl.obolibrary.org/obo/UBERON_0004924) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tela submucosa pharyngea" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:75144" +- [thyroid primordium](http://purl.obolibrary.org/obo/UBERON_0003091) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In all vertebrates the thyroid arises from the ventral aspect of the second pouch" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:16313389" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [submucosa of pharynx](http://purl.obolibrary.org/obo/UBERON_0004924) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tela submucosa pharyngis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0002113" +### tibia `http://purl.obolibrary.org/obo/UBERON_0000979` +#### Removed +- [tibia](http://purl.obolibrary.org/obo/UBERON_0000979) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "One of the two long bones of endochondral origin of the hind-epipodium; it is a straight, simple bone whose section is more or less rectangular at the ends and circular at its central portion.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000890" -#### Added -- [submucosa of pharynx](http://purl.obolibrary.org/obo/UBERON_0004924) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tela submucosa pharyngea" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:75144" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [submucosa of pharynx](http://purl.obolibrary.org/obo/UBERON_0004924) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tela submucosa pharyngis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0002113" +### tibial tuberosity `http://purl.obolibrary.org/obo/UBERON_7500062` + +#### Added +- [tibial tuberosity](http://purl.obolibrary.org/obo/UBERON_7500062) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### submucosa of rectum `http://purl.obolibrary.org/obo/UBERON_0003330` +### tissue `http://purl.obolibrary.org/obo/UBERON_0000479` #### Removed -- [submucosa of rectum](http://purl.obolibrary.org/obo/UBERON_0003330) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tela submucosa recti" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0002114" +- [tissue](http://purl.obolibrary.org/obo/UBERON_0000479) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007003" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [submucosa of rectum](http://purl.obolibrary.org/obo/UBERON_0003330) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tela submucosa recti" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0002114" +### title `http://purl.org/dc/elements/1.1/title` +#### Removed +- [title](http://purl.org/dc/elements/1.1/title) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "dc-title" +- [title](http://purl.org/dc/elements/1.1/title) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" -### submucosa of small intestine `http://purl.obolibrary.org/obo/UBERON_0001205` -#### Removed -- [submucosa of small intestine](http://purl.obolibrary.org/obo/UBERON_0001205) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tela submucosa intestini tenuis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0002112" +- [title](http://purl.org/dc/elements/1.1/title) [is_metadata_tag](http://www.geneontology.org/formats/oboInOwl#is_metadata_tag) true - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [title](http://purl.org/dc/elements/1.1/title) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://purl.org/dc/elements/1.1/title" -#### Added -- [submucosa of small intestine](http://purl.obolibrary.org/obo/UBERON_0001205) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tela submucosa intestini tenuis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [title](http://purl.org/dc/elements/1.1/title) [id](http://www.geneontology.org/formats/oboInOwl#id) "dc-title" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0002112" +- [title](http://purl.org/dc/elements/1.1/title) [label](http://www.w3.org/2000/01/rdf-schema#label) "title" -### submucosa of stomach `http://purl.obolibrary.org/obo/UBERON_0001200` + +### to be replaced with external ontology term `http://purl.obolibrary.org/obo/IAO_0000423` #### Removed -- [submucosa of stomach](http://purl.obolibrary.org/obo/UBERON_0001200) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tela submucosa gastricae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:14908" +- [to be replaced with external ontology term](http://purl.obolibrary.org/obo/IAO_0000423) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "to be replaced with external ontology term"@en - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [to be replaced with external ontology term](http://purl.obolibrary.org/obo/IAO_0000423) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) "group:OBI"@en - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [to be replaced with external ontology term](http://purl.obolibrary.org/obo/IAO_0000423) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) "Alan Ruttenberg"@en -#### Added -- [submucosa of stomach](http://purl.obolibrary.org/obo/UBERON_0001200) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tela submucosa gastricae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:14908" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### todo `http://www.geneontology.org/formats/oboInOwl#todo` +#### Removed +- AnnotationProperty: [todo](http://www.geneontology.org/formats/oboInOwl#todo) -### submucosa of urinary bladder `http://purl.obolibrary.org/obo/UBERON_0004943` + +### tongue `http://purl.obolibrary.org/obo/UBERON_0001723` #### Removed -- [submucosa of urinary bladder](http://purl.obolibrary.org/obo/UBERON_0004943) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tela submucosa vesicae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15929" +- [tongue](http://purl.obolibrary.org/obo/UBERON_0001723) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "The tongue has contributions from all pharyngeal arches which changes with time. The tongue initially begins as swelling rostral to foramen cecum, the median tongue bud.. tongue muscles derive from the somites - http://php.med.unsw.edu.au/embryology/index.php?title=Tongue_Development#Pharyngeal_Arch_Contributions" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [tongue](http://purl.obolibrary.org/obo/UBERON_0001723) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "lingual" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [tongue](http://purl.obolibrary.org/obo/UBERON_0001723) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "glossal" -- [submucosa of urinary bladder](http://purl.obolibrary.org/obo/UBERON_0004943) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tela submucosa (vesica urinaria)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15929" +- [tongue](http://purl.obolibrary.org/obo/UBERON_0001723) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The tongue is the movable, muscular organ on the floor of the mouth of most vertebrates, in many other mammals is the principal organ of taste, aids in the prehension of food, in swallowing, and in modifying the voice as in speech[GO][GO:0043586]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "GO:0043586" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [tongue](http://purl.obolibrary.org/obo/UBERON_0001723) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A mobile mass of muscular tissue that is covered with mucous membrane, occupies much of the cavity of the mouth, forms part of its floor, bears the organ of taste, and assists in chewing and swallowing. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/tongue" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [submucosa of urinary bladder](http://purl.obolibrary.org/obo/UBERON_0004943) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tela submucosa vesicae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15929" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000419" -- [submucosa of urinary bladder](http://purl.obolibrary.org/obo/UBERON_0004943) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tela submucosa (vesica urinaria)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [tongue](http://purl.obolibrary.org/obo/UBERON_0001723) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Muscular organ in the floor of the mouth.[FEED]" + - [url](http://www.geneontology.org/formats/oboInOwl#url) "http://www.feedexp.org" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15929" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "FEED" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-07-02" +- [tongue](http://purl.obolibrary.org/obo/UBERON_0001723) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Most adult amphibians have a tongue, as do all known reptiles, birds and mammals. Thus it is likely that the tongue appeared with the establishment of tetrapods and this structure seems to be related, to some extant, to the terrestrial lifestyle.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### submucosa of uterine tube `http://purl.obolibrary.org/obo/UBERON_0011298` -#### Removed -- [submucosa of uterine tube](http://purl.obolibrary.org/obo/UBERON_0011298) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tela submucosa tubae uterinae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0002116" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [submucosa of uterine tube](http://purl.obolibrary.org/obo/UBERON_0011298) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tela submucosa tubae uterinae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1046/j.1469-7580.2002.00073.x Iwasaki S, Evolution of the structure and function of the vertebrate tongue. J Anat (2002)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0002116" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000419" +- [tongue](http://purl.obolibrary.org/obo/UBERON_0001723) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Many species of fish have small folds at the base of their mouths that might informally be called tongues, but they lack a muscular structure like the true tongues found in most tetrapods" -### subscapular artery `http://purl.obolibrary.org/obo/UBERON_0001397` -#### Removed -- [subscapular artery](http://purl.obolibrary.org/obo/UBERON_0001397) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria subscapularis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [tongue](http://purl.obolibrary.org/obo/UBERON_0001723) SubClassOf [immediate transformation of](http://purl.obolibrary.org/obo/RO_0002495) some [future tongue](http://purl.obolibrary.org/obo/UBERON_0010056) + - [evidence](http://www.geneontology.org/formats/oboInOwl#evidence) "definitional" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Subscapular_artery" +- [tongue](http://purl.obolibrary.org/obo/UBERON_0001723) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [lingual swellings](http://purl.obolibrary.org/obo/UBERON_0006260) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "anterior 2/3" #### Added -- [subscapular artery](http://purl.obolibrary.org/obo/UBERON_0001397) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria subscapularis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [tongue](http://purl.obolibrary.org/obo/UBERON_0001723) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [lingual swellings](http://purl.obolibrary.org/obo/UBERON_0006260) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Subscapular_artery" +- [tongue](http://purl.obolibrary.org/obo/UBERON_0001723) SubClassOf [immediate transformation of](http://purl.obolibrary.org/obo/RO_0002495) some [future tongue](http://purl.obolibrary.org/obo/UBERON_0010056) -### substantia nigra `http://purl.obolibrary.org/obo/UBERON_0002038` +### tongue muscle `http://purl.obolibrary.org/obo/UBERON_0000378` #### Removed -- [substantia nigra](http://purl.obolibrary.org/obo/UBERON_0002038) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "substantia nigra (Soemmerringi)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:536" +- [tongue muscle](http://purl.obolibrary.org/obo/UBERON_0000378) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The lamprey head contains another group of muscles, the epi- and hypo-branchial muscles (EBM and HBM), derivatives of anterior trunk myotomes. (...) The origin and the migration pattern of HBM precursors are very similar to that of the gnathostome MPP, especially to that of the tongue muscle precursors. Other evidence of homology of lamprey HBM to the gnathostome tongue muscle is that HBM is innervated by the nerve termed the hypoglossal nerve based on its morphological position associated with the head/trunk interface. (...) The HBM-specific expression of the LampPax3/7 gene is consistent with the homology of this muscle to the gnathostome tongue muscle, or to the hypobranchial series as a whole (including the infrahyoid and possibly the diaphragm in mammals).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [substantia nigra](http://purl.obolibrary.org/obo/UBERON_0002038) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus pigmentosus subthalamo-peduncularis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:536" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1002/dvdy.20587 Kusakabe R, Kuratani S, Evolution and developmental patterning of the vertebrate skeletal muscles: perspectives from the lamprey. Developmental Dynamics (2005)" -#### Added -- [substantia nigra](http://purl.obolibrary.org/obo/UBERON_0002038) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "substantia nigra (Soemmerringi)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001390" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:536" -- [substantia nigra](http://purl.obolibrary.org/obo/UBERON_0002038) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus pigmentosus subthalamo-peduncularis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:536" +### tongue squamous epithelium `http://purl.obolibrary.org/obo/UBERON_0006919` +#### Removed +- [tongue squamous epithelium](http://purl.obolibrary.org/obo/UBERON_0006919) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "this is a singleton subclass of tongue epithelium in MA" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" -### substantia propria of cornea `http://purl.obolibrary.org/obo/UBERON_0001777` -#### Removed -- [substantia propria of cornea](http://purl.obolibrary.org/obo/UBERON_0001777) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "substantia propria corneae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58306" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### tonsil `http://purl.obolibrary.org/obo/UBERON_0002372` +#### Removed +- [tonsil](http://purl.obolibrary.org/obo/UBERON_0002372) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "the term 'tonsil' can be ambiguous, sometimes refering specifically to the palatine tonsil, sometimes generically to include the cecal tonsils of avians. This class represents lymphoid tissue that is part of the tonsillar ring, in the mouth/throat region" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [substantia propria of cornea](http://purl.obolibrary.org/obo/UBERON_0001777) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "substantia propria corneae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58306" +### tonsil germinal center `http://purl.obolibrary.org/obo/UBERON_0013688` +#### Removed +- [tonsil germinal center](http://purl.obolibrary.org/obo/UBERON_0013688) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The germinal center or reaction center is the activated center of a lymphoid follicle in secondary lymphoid tissue where B-lymphocytes are stimulated by antigens and helper T cells (T-lymphocytes, helper-inducer) are stimulated to generate memory cells. Here, the germinal center of a tonsil[TS-1288]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TS-1288" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### substantia propria of sclera `http://purl.obolibrary.org/obo/UBERON_0010295` +### tonsillar ring `http://purl.obolibrary.org/obo/UBERON_0001735` #### Removed -- [substantia propria of sclera](http://purl.obolibrary.org/obo/UBERON_0010295) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "substantia propria sclerae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58365" +- [tonsillar ring](http://purl.obolibrary.org/obo/UBERON_0001735) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "The circular lymphoid tissue formed by the lingual, pharyngeal, and facial tonsils." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MGI:cwg" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MP:0002379" #### Added -- [substantia propria of sclera](http://purl.obolibrary.org/obo/UBERON_0010295) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "substantia propria sclerae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58365" +- [tonsillar ring](http://purl.obolibrary.org/obo/UBERON_0001735) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "The circular lymphoid tissue formed by the lingual, pharyngeal, and faucial tonsils." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MGI:cwg" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MP:0002379" -### substratum of layer of retina `http://purl.obolibrary.org/obo/UBERON_0008921` +### tooth enamel organ `http://purl.obolibrary.org/obo/UBERON_0005176` #### Removed -- [substratum of layer of retina](http://purl.obolibrary.org/obo/UBERON_0008921) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://retina.anatomy.upenn.edu/~lance/eye/retina_gross.html" - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "UBERON:CL_meeting_20110725" +- [tooth enamel organ](http://purl.obolibrary.org/obo/UBERON_0005176) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "NOT develops_from NC[https://github.com/obophenotype/uberon/wiki/The-neural-crest]" -#### Added -- [substratum of layer of retina](http://purl.obolibrary.org/obo/UBERON_0008921) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Missing definition for term UBERON:0008921. Please replace it using linked reference." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "UBERON:CL_meeting_20110725" +- [tooth enamel organ](http://purl.obolibrary.org/obo/UBERON_0005176) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A structure that is involved in tooth formation. A bell shape two layer epithelial structure that descends toward the ceratobranchial 5 bone, enclosing the dental mesenchyme. At later times in tooth development the cells at the apex of the bell may be involved in enameloid formation. This structure remains at the base of the erupted tooth and is the source of replacement teeth.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005138" -### superior mesenteric artery `http://purl.obolibrary.org/obo/UBERON_0001182` -#### Removed -- [superior mesenteric artery](http://purl.obolibrary.org/obo/UBERON_0001182) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria mesenterica superior" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Superior_mesenteric_artery" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0002303" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [tooth enamel organ](http://purl.obolibrary.org/obo/UBERON_0005176) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "Historically, enamel organ has been the term to describe this structure, but it was attempted unsuccessfully in recent years to change the name to dental organ in order to better represent its multiple functions apart from enamel formation" -#### Added -- [superior mesenteric artery](http://purl.obolibrary.org/obo/UBERON_0001182) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria mesenterica superior" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Superior_mesenteric_artery" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0002303" +### tooth of lower jaw `http://purl.obolibrary.org/obo/UBERON_0003268` +#### Removed +- [tooth of lower jaw](http://purl.obolibrary.org/obo/UBERON_0003268) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EHDAA2:0001029" +#### Added +- [tooth of lower jaw](http://purl.obolibrary.org/obo/UBERON_0003268) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) -### superior mesenteric vein `http://purl.obolibrary.org/obo/UBERON_0001138` -#### Removed -- [superior mesenteric vein](http://purl.obolibrary.org/obo/UBERON_0001138) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena mesenterica superior" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Superior_mesenteric_vein" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### tooth of upper jaw `http://purl.obolibrary.org/obo/UBERON_0003267` #### Added -- [superior mesenteric vein](http://purl.obolibrary.org/obo/UBERON_0001138) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena mesenterica superior" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Superior_mesenteric_vein" +- [tooth of upper jaw](http://purl.obolibrary.org/obo/UBERON_0003267) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) -### superior olivary complex `http://purl.obolibrary.org/obo/UBERON_0002128` +### tooth placode `http://purl.obolibrary.org/obo/UBERON_0005087` #### Removed -- [superior olivary complex](http://purl.obolibrary.org/obo/UBERON_0002128) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D065832" +- [tooth placode](http://purl.obolibrary.org/obo/UBERON_0005087) [UBPROP_0000015](http://purl.obolibrary.org/obo/UBPROP_0000015) "In mammals this may be located in the alveolar ridges, but note that some species such as zebrafish have ceratobranchial teeth. Sharks have dermal denticles that share developmental origins. Currently we don't include location information due to this diversity, but in future we may include specific subclasses and/or taxon GCIs." -- [superior olivary complex](http://purl.obolibrary.org/obo/UBERON_0002128) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "regio olivaris superioris" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:569" +- [tooth placode](http://purl.obolibrary.org/obo/UBERON_0005087) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Placode that develops into a tooth. The placode is a thickening of the pharyngeal epithelium.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -- [superior olivary complex](http://purl.obolibrary.org/obo/UBERON_0002128) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nucleus olivaris superior" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:72247" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001153" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [tooth placode](http://purl.obolibrary.org/obo/UBERON_0005087) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [pharyngeal arch 1](http://purl.obolibrary.org/obo/UBERON_0004362) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "check for other species" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Tooth_development" #### Added -- [superior olivary complex](http://purl.obolibrary.org/obo/UBERON_0002128) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nucleus olivaris superior" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [tooth placode](http://purl.obolibrary.org/obo/UBERON_0005087) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [pharyngeal arch 1](http://purl.obolibrary.org/obo/UBERON_0004362) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:72247" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### tooth root `http://purl.obolibrary.org/obo/UBERON_0003677` -- [superior olivary complex](http://purl.obolibrary.org/obo/UBERON_0002128) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "regio olivaris superioris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +#### Added +- [tooth root](http://purl.obolibrary.org/obo/UBERON_0003677) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:569" -- [superior olivary complex](http://purl.obolibrary.org/obo/UBERON_0002128) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D065832" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +### touch receptor cell `http://purl.obolibrary.org/obo/CL_0000200` +#### Removed +- [touch receptor cell](http://purl.obolibrary.org/obo/CL_0000200) SubClassOf [neuronal receptor cell](http://purl.obolibrary.org/obo/CL_0000006) - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) +- [touch receptor cell](http://purl.obolibrary.org/obo/CL_0000200) SubClassOf [somatosensory neuron](http://purl.obolibrary.org/obo/CL_4023168) - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -### superior salivatory nucleus `http://purl.obolibrary.org/obo/UBERON_0002149` +### trabecula `http://purl.obolibrary.org/obo/UBERON_0000440` #### Removed -- [superior salivatory nucleus](http://purl.obolibrary.org/obo/UBERON_0002149) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus salivatorius cranialis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [trabecula](http://purl.obolibrary.org/obo/UBERON_0000440) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "trabecular" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:590" -- [superior salivatory nucleus](http://purl.obolibrary.org/obo/UBERON_0002149) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus salivatorius superior" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:590" +### trabecula carnea `http://purl.obolibrary.org/obo/UBERON_0002511` +#### Removed +- [trabecula carnea](http://purl.obolibrary.org/obo/UBERON_0002511) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "The purpose of the trabeculae carneae is most likely to prevent suction that would occur with a flat surfaced membrane and thus impair the heart's ability to pump efficiently. The trabeculae carneae also serve a similar function to papillary muscles in that their contraction pulls on the chordae tendineae, preventing inversion of the mitral (bicuspid) and tricuspid valves, that is, their bulging towards the atrial chambers, which would lead to subsequent leakage of the blood into the atria. So by the action of papillary muscles on the atrioventricular valves, backflow of the blood from the ventricles into the atria is prevented" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" -- [superior salivatory nucleus](http://purl.obolibrary.org/obo/UBERON_0002149) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus salivatorius rostralis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [trabecula carnea](http://purl.obolibrary.org/obo/UBERON_0002511) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "Note that WP states they are ventricular, but MP has classes for atrial ventricular carnea." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MP" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:590" +#### Added +- [trabecula carnea](http://purl.obolibrary.org/obo/UBERON_0002511) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -- [superior salivatory nucleus](http://purl.obolibrary.org/obo/UBERON_0002149) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus salivarius superior" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:590" +### trabecula of spleen `http://purl.obolibrary.org/obo/UBERON_0001265` #### Added -- [superior salivatory nucleus](http://purl.obolibrary.org/obo/UBERON_0002149) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus salivarius superior" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [trabecula of spleen](http://purl.obolibrary.org/obo/UBERON_0001265) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:590" -- [superior salivatory nucleus](http://purl.obolibrary.org/obo/UBERON_0002149) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus salivatorius cranialis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### trachea `http://purl.obolibrary.org/obo/UBERON_0003126` +#### Removed +- [trachea](http://purl.obolibrary.org/obo/UBERON_0003126) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In primitive fishes and most tetrapods, the lungs of adults are usually paired. They lie ventral to the digestive tract and are connected to the outside environment through the trachea.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:590" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [superior salivatory nucleus](http://purl.obolibrary.org/obo/UBERON_0002149) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus salivatorius rostralis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:590" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000371" -- [superior salivatory nucleus](http://purl.obolibrary.org/obo/UBERON_0002149) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus salivatorius superior" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.409" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:590" +- [trachea](http://purl.obolibrary.org/obo/UBERON_0003126) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The respiratory tube between the larynx and the bronchi. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### superior vesical artery `http://purl.obolibrary.org/obo/UBERON_0001312` -#### Removed -- [superior vesical artery](http://purl.obolibrary.org/obo/UBERON_0001312) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arteria vesicalis superior" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Superior_vesical_artery" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000371" -- [superior vesical artery](http://purl.obolibrary.org/obo/UBERON_0001312) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arteria vesicali superior" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Superior_vesical_artery" +- [trachea](http://purl.obolibrary.org/obo/UBERON_0003126) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "An elongated tube which carries air to and from the lungs.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010140" -- [superior vesical artery](http://purl.obolibrary.org/obo/UBERON_0001312) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteriae vesicales superiores" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Superior_vesical_artery" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" -#### Added -- [superior vesical artery](http://purl.obolibrary.org/obo/UBERON_0001312) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteriae vesicales superiores" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [trachea](http://purl.obolibrary.org/obo/UBERON_0003126) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "in mouse 15-18 C-rings, 15-20 in human." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0123813611" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Superior_vesical_artery" +- [trachea](http://purl.obolibrary.org/obo/UBERON_0003126) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In birds, the trachea runs from the pharynx to the syrinx, from which the primary bronchi diverge. Swans have an unusually elongated trachea, part of which is coiled beneath the sternum; this may act as a resonator to amplify sound. In some birds, the cartilagenous rings are complete, and may even be ossified. In amphibians, the trachea is normally extremely short, and leads directly into the lungs, without clear primary bronchi. A longer trachea is, however found in some long-necked salamanders, and in caecilians. While there are irregular cartilagenous nodules on the amphibian trachea, these do not form the rings found in amniotes. The only vertebrate to have lungs, but no trachea, is Polypterus, in which the lungs arise directly from the pharynx." -- [superior vesical artery](http://purl.obolibrary.org/obo/UBERON_0001312) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arteria vesicali superior" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [trachea](http://purl.obolibrary.org/obo/UBERON_0003126) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "tracheal" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Superior_vesical_artery" -- [superior vesical artery](http://purl.obolibrary.org/obo/UBERON_0001312) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arteria vesicalis superior" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Superior_vesical_artery" +### trachea basement membrane `http://purl.obolibrary.org/obo/UBERON_0009653` + +#### Added +- [trachea basement membrane](http://purl.obolibrary.org/obo/UBERON_0009653) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -### supporting cell `http://purl.obolibrary.org/obo/CL_0000630` +### trachea blood vessel `http://purl.obolibrary.org/obo/UBERON_0003505` #### Added -- [supporting cell](http://purl.obolibrary.org/obo/CL_0000630) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [trachea blood vessel](http://purl.obolibrary.org/obo/UBERON_0003505) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) -### surface ectodermal cell `http://purl.obolibrary.org/obo/CL_0000114` +### trachea cartilage `http://purl.obolibrary.org/obo/UBERON_0003604` +#### Removed +- [trachea cartilage](http://purl.obolibrary.org/obo/UBERON_0003604) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "in mammals the rings are incomplete, in avians the rings are complete." -#### Added -- [surface ectodermal cell](http://purl.obolibrary.org/obo/CL_0000114) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### sympathetic ganglion `http://purl.obolibrary.org/obo/UBERON_0001806` +### trachea gland `http://purl.obolibrary.org/obo/UBERON_0005203` #### Removed -- [sympathetic ganglion](http://purl.obolibrary.org/obo/UBERON_0001806) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D005728" +- [trachea gland](http://purl.obolibrary.org/obo/UBERON_0005203) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "These glands secrete mucus, lysozyme, defensins, and other agents that help protect the lungs from particles and infectious agents." -- [sympathetic ganglion](http://purl.obolibrary.org/obo/UBERON_0001806) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ganglion sympathicum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001333" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Sympathetic_ganglion" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### tracheal submucosal gland ciliated duct `http://purl.obolibrary.org/obo/UBERON_8600011` #### Added -- [sympathetic ganglion](http://purl.obolibrary.org/obo/UBERON_0001806) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ganglion sympathicum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [tracheal submucosal gland ciliated duct](http://purl.obolibrary.org/obo/UBERON_8600011) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001333" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Sympathetic_ganglion" +### tracheobronchial tree `http://purl.obolibrary.org/obo/UBERON_0007196` -- [sympathetic ganglion](http://purl.obolibrary.org/obo/UBERON_0001806) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D005728" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +#### Added +- [tracheobronchial tree](http://purl.obolibrary.org/obo/UBERON_0007196) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +### trans-acting T-cell-specific transcription factor GATA-3 `http://purl.obolibrary.org/obo/PR_000001941` +#### Removed +- [trans-acting T-cell-specific transcription factor GATA-3](http://purl.obolibrary.org/obo/PR_000001941) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [trans-acting T-cell-specific transcription factor GATA-3 (human)](http://purl.obolibrary.org/obo/PR_P23771) -### sympathetic nervous system `http://purl.obolibrary.org/obo/UBERON_0000013` + +### transcription factor PU.1 `http://purl.obolibrary.org/obo/PR_000001944` #### Removed -- [sympathetic nervous system](http://purl.obolibrary.org/obo/UBERON_0000013) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pars sympathica divisionis autonomici systematis nervosi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9906" +- [transcription factor PU.1](http://purl.obolibrary.org/obo/PR_000001944) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [transcription factor PU.1 (human)](http://purl.obolibrary.org/obo/PR_P17947) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [sympathetic nervous system](http://purl.obolibrary.org/obo/UBERON_0000013) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pars sympathica divisionis autonomici systematis nervosi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Sympathetic_nervous_system" +### transcription factor SOX-2 `http://purl.obolibrary.org/obo/PR_000015426` +#### Removed +- [transcription factor SOX-2](http://purl.obolibrary.org/obo/PR_000015426) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [transcription factor SOX-2 (human)](http://purl.obolibrary.org/obo/PR_P48431) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [sympathetic nervous system](http://purl.obolibrary.org/obo/UBERON_0000013) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pars sympathica divisionis autonomici systematis nervosi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Sympathetic_nervous_system" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### transferrin receptor protein 1 `http://purl.obolibrary.org/obo/PR_000001945` +#### Removed +- [transferrin receptor protein 1](http://purl.obolibrary.org/obo/PR_000001945) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [transferrin receptor protein 1 (human)](http://purl.obolibrary.org/obo/PR_P02786) -- [sympathetic nervous system](http://purl.obolibrary.org/obo/UBERON_0000013) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pars sympathica divisionis autonomici systematis nervosi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9906" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### transformation of `http://purl.obolibrary.org/obo/RO_0002494` +#### Removed +- [transformation of](http://purl.obolibrary.org/obo/RO_0002494) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "transformation_of" +- [transformation of](http://purl.obolibrary.org/obo/RO_0002494) [id](http://www.geneontology.org/formats/oboInOwl#id) "transformation_of" -### sympathetic neuron `http://purl.obolibrary.org/obo/CL_0011103` +- [transformation of](http://purl.obolibrary.org/obo/RO_0002494) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" -#### Added -- [sympathetic neuron](http://purl.obolibrary.org/obo/CL_0011103) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [transformation of](http://purl.obolibrary.org/obo/RO_0002494) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) +- [transformation of](http://purl.obolibrary.org/obo/RO_0002494) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002494" -### sympathetic trunk `http://purl.obolibrary.org/obo/UBERON_0000407` -#### Removed -- [sympathetic trunk](http://purl.obolibrary.org/obo/UBERON_0000407) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "truncus sympathicus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Sympathetic_trunk" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [sympathetic trunk](http://purl.obolibrary.org/obo/UBERON_0000407) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "truncus sympathicus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### transitively anteriorly connected to `http://purl.obolibrary.org/obo/uberon/core#transitively_anteriorly_connected_to` +#### Removed +- Transitive: [transitively anteriorly connected to](http://purl.obolibrary.org/obo/uberon/core#transitively_anteriorly_connected_to) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Sympathetic_trunk" -### synaptic signaling by nitric oxide `http://purl.obolibrary.org/obo/GO_0099163` +### transitively distally connected to `http://purl.obolibrary.org/obo/uberon/core#transitively_distally_connected_to` #### Removed -- [synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0099163) [label](http://www.w3.org/2000/01/rdf-schema#label) "synaptic signaling by nitric oxide" +- Transitive: [transitively distally connected to](http://purl.obolibrary.org/obo/uberon/core#transitively_distally_connected_to) -- [synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0099163) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Cell-cell signaling to or from a synapse, mediated by nitric oxide." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:dos" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:19038221" -- [synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0099163) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" +### transitively proximally connected to `http://purl.obolibrary.org/obo/uberon/core#transitively_proximally_connected_to` +#### Removed +- Transitive: [transitively proximally connected to](http://purl.obolibrary.org/obo/uberon/core#transitively_proximally_connected_to) -- [synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0099163) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:0099163" -- [synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0099163) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_synapse](http://purl.obolibrary.org/obo/go#goslim_synapse) -- Class: [synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0099163) +### transmembrane emp24 domain-containing protein 1 `http://purl.obolibrary.org/obo/PR_000016401` +#### Removed +- [transmembrane emp24 domain-containing protein 1](http://purl.obolibrary.org/obo/PR_000016401) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [transmembrane emp24 domain-containing protein 1 (human)](http://purl.obolibrary.org/obo/PR_Q13445) -- [synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0099163) EquivalentTo [synaptic signaling](http://purl.obolibrary.org/obo/GO_0099536) and ([process has causal agent](http://purl.obolibrary.org/obo/RO_0002608) some [CHEBI_16480](http://purl.obolibrary.org/obo/CHEBI_16480)) -- [synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0099163) SubClassOf [process has causal agent](http://purl.obolibrary.org/obo/RO_0002608) some [CHEBI_16480](http://purl.obolibrary.org/obo/CHEBI_16480) -- [synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0099163) SubClassOf [synaptic signaling](http://purl.obolibrary.org/obo/GO_0099536) +### transparent `http://purl.obolibrary.org/obo/PATO_0000964` +#### Removed +- [transparent](http://purl.obolibrary.org/obo/PATO_0000964) [RO_0002604](http://purl.obolibrary.org/obo/RO_0002604) [opaque](http://purl.obolibrary.org/obo/PATO_0000963) -### synchondrosis `http://purl.obolibrary.org/obo/UBERON_0002215` +### transparent eye structure `http://purl.obolibrary.org/obo/UBERON_0005389` #### Removed -- [synchondrosis](http://purl.obolibrary.org/obo/UBERON_0002215) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cartilago epiphysialis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [transparent eye structure](http://purl.obolibrary.org/obo/UBERON_0005389) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "directing or focusing light onto light receptors" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:7497" -#### Added -- [synchondrosis](http://purl.obolibrary.org/obo/UBERON_0002215) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cartilago epiphysialis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### transudate `http://purl.obolibrary.org/obo/UBERON_0007779` +#### Removed +- [transudate](http://purl.obolibrary.org/obo/UBERON_0007779) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "characteristically low in protein and cellular content (unless there has been secondary concentration)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [transudate](http://purl.obolibrary.org/obo/UBERON_0007779) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "transudative" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:7497" -### syncytiotrophoblast `http://purl.obolibrary.org/obo/UBERON_0000371` +### transverse cervical artery `http://purl.obolibrary.org/obo/UBERON_0012324` #### Removed -- [syncytiotrophoblast](http://purl.obolibrary.org/obo/UBERON_0000371) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "syncitiotrophoblastus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Syncytiotrophoblast" +- [transverse cervical artery](http://purl.obolibrary.org/obo/UBERON_0012324) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "Unclear if MA class belongs here or in parent" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [syncytiotrophoblast](http://purl.obolibrary.org/obo/UBERON_0000371) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "syncitiotrophoblastus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Syncytiotrophoblast" +### transverse colon `http://purl.obolibrary.org/obo/UBERON_0001157` +#### Removed +- [transverse colon](http://purl.obolibrary.org/obo/UBERON_0001157) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D044684" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) -### syncytiotrophoblast cell `http://purl.obolibrary.org/obo/CL_0000525` + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -#### Added -- [syncytiotrophoblast cell](http://purl.obolibrary.org/obo/CL_0000525) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### synovial membrane of synovial joint `http://purl.obolibrary.org/obo/UBERON_0002018` +### transverse process of cervical vertebra `http://purl.obolibrary.org/obo/UBERON_0018143` #### Removed -- [synovial membrane of synovial joint](http://purl.obolibrary.org/obo/UBERON_0002018) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum synoviale (capsula articularis)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9865" +- [transverse process of cervical vertebra](http://purl.obolibrary.org/obo/UBERON_0018143) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "May be homologous with the cervical ribs of some vertebrates" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [synovial membrane of synovial joint](http://purl.obolibrary.org/obo/UBERON_0002018) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "membrana synovialis capsulae articularis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Synovial_membrane" +### transverse process of vertebra `http://purl.obolibrary.org/obo/UBERON_0001077` +#### Removed +- [transverse process of vertebra](http://purl.obolibrary.org/obo/UBERON_0001077) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Projections on each side of the vertebra from the point where the neural arch lamina joins the pedicel for the articulation with the head of a single-headed rib or the upper head of a double-headed rib. Also called diapophyses. They provide surfaces for the attachment of muscles. In anurans, the term transverse process is used in reference to the processes associated with the presacral and postsacral vertebrae." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:0000698" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [synovial membrane of synovial joint](http://purl.obolibrary.org/obo/UBERON_0002018) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum synoviale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:66762" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### trapezius muscle `http://purl.obolibrary.org/obo/UBERON_0002380` +#### Removed +- [trapezius muscle](http://purl.obolibrary.org/obo/UBERON_0002380) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The sternomastoid and the three parts of the trapezius are branchiomeric muscles that have secondarily acquired an attachment to the pectoral girdle. They evolved from the fish cucullaris.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [synovial membrane of synovial joint](http://purl.obolibrary.org/obo/UBERON_0002018) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "membrana synovialis (capsula articularis)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9865" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.345" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000834" -#### Added -- [synovial membrane of synovial joint](http://purl.obolibrary.org/obo/UBERON_0002018) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "membrana synovialis capsulae articularis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [trapezius muscle](http://purl.obolibrary.org/obo/UBERON_0002380) SubClassOf [has muscle insertion](http://purl.obolibrary.org/obo/RO_0002373) some [acromion](http://purl.obolibrary.org/obo/UBERON_0002497) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "posterior border of the lateral third of the clavicle acromion process and spine of scapula" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Synovial_membrane" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "dbpedia" -- [synovial membrane of synovial joint](http://purl.obolibrary.org/obo/UBERON_0002018) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "membrana synovialis (capsula articularis)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9865" +- [trapezius muscle](http://purl.obolibrary.org/obo/UBERON_0002380) SubClassOf [has muscle insertion](http://purl.obolibrary.org/obo/RO_0002373) some [lateral border of scapula](http://purl.obolibrary.org/obo/UBERON_0007173) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "posterior border of the lateral third of the clavicle acromion process and spine of scapula" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "dbpedia" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [trapezius muscle](http://purl.obolibrary.org/obo/UBERON_0002380) SubClassOf [has muscle origin](http://purl.obolibrary.org/obo/RO_0002372) some [neural spine](http://purl.obolibrary.org/obo/UBERON_0001076) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "dbpedia" -- [synovial membrane of synovial joint](http://purl.obolibrary.org/obo/UBERON_0002018) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum synoviale" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "external occipital protuberance nuchal ligament medial superior nuchal line spinous processes of vertebrae C7-T12" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:66762" +- [trapezius muscle](http://purl.obolibrary.org/obo/UBERON_0002380) SubClassOf [has muscle origin](http://purl.obolibrary.org/obo/RO_0002372) some [nuchal ligament](http://purl.obolibrary.org/obo/UBERON_0000351) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "dbpedia" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "external occipital protuberance nuchal ligament medial superior nuchal line spinous processes of vertebrae C7-T12" + +#### Added +- [trapezius muscle](http://purl.obolibrary.org/obo/UBERON_0002380) SubClassOf [has muscle origin](http://purl.obolibrary.org/obo/RO_0002372) some [neural spine](http://purl.obolibrary.org/obo/UBERON_0001076) -- [synovial membrane of synovial joint](http://purl.obolibrary.org/obo/UBERON_0002018) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stratum synoviale (capsula articularis)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9865" +- [trapezius muscle](http://purl.obolibrary.org/obo/UBERON_0002380) SubClassOf [has muscle insertion](http://purl.obolibrary.org/obo/RO_0002373) some [acromion](http://purl.obolibrary.org/obo/UBERON_0002497) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [trapezius muscle](http://purl.obolibrary.org/obo/UBERON_0002380) SubClassOf [has muscle origin](http://purl.obolibrary.org/obo/RO_0002372) some [nuchal ligament](http://purl.obolibrary.org/obo/UBERON_0000351) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [trapezius muscle](http://purl.obolibrary.org/obo/UBERON_0002380) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) + +- [trapezius muscle](http://purl.obolibrary.org/obo/UBERON_0002380) SubClassOf [has muscle insertion](http://purl.obolibrary.org/obo/RO_0002373) some [lateral border of scapula](http://purl.obolibrary.org/obo/UBERON_0007173) -### tanycyte `http://purl.obolibrary.org/obo/CL_0002085` +### trapezius pre-muscle mass `http://purl.obolibrary.org/obo/UBERON_0010955` #### Added -- [tanycyte](http://purl.obolibrary.org/obo/CL_0002085) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [trapezius pre-muscle mass](http://purl.obolibrary.org/obo/UBERON_0010955) SubClassOf [head mesenchyme from mesoderm](http://purl.obolibrary.org/obo/UBERON_0006904) -### tarsal region `http://purl.obolibrary.org/obo/UBERON_0004454` +### tributary of `http://purl.obolibrary.org/obo/RO_0002376` #### Removed -- [tarsal region](http://purl.obolibrary.org/obo/UBERON_0004454) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "articulatio talocruralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ankle" +- [tributary of](http://purl.obolibrary.org/obo/RO_0002376) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "drains into" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [tributary of](http://purl.obolibrary.org/obo/RO_0002376) [label](http://www.w3.org/2000/01/rdf-schema#label) "tributary of" -#### Added -- [tarsal region](http://purl.obolibrary.org/obo/UBERON_0004454) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "articulatio talocruralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ankle" +- [tributary of](http://purl.obolibrary.org/obo/RO_0002376) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [tributary of](http://purl.obolibrary.org/obo/RO_0002376) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" +- [tributary of](http://purl.obolibrary.org/obo/RO_0002376) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "inferior epigastric vein tributary_of external iliac vein" -### tarsometatarsal joint `http://purl.obolibrary.org/obo/UBERON_0011118` -#### Removed -- [tarsometatarsal joint](http://purl.obolibrary.org/obo/UBERON_0011118) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "articulationes tarsometatarsales" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Tarsometatarsal_articulations" +- [tributary of](http://purl.obolibrary.org/obo/RO_0002376) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "tributary_of" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [tributary of](http://purl.obolibrary.org/obo/RO_0002376) [IAO_0000112](http://purl.obolibrary.org/obo/IAO_0000112) "Deschutes River tributary_of Columbia River" -#### Added -- [tarsometatarsal joint](http://purl.obolibrary.org/obo/UBERON_0011118) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "articulationes tarsometatarsales" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Tarsometatarsal_articulations" +- [tributary of](http://purl.obolibrary.org/obo/RO_0002376) [id](http://www.geneontology.org/formats/oboInOwl#id) "tributary_of" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [tributary of](http://purl.obolibrary.org/obo/RO_0002376) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) "http://www.medindia.net/glossary/venous_tributary.htm" +- [tributary of](http://purl.obolibrary.org/obo/RO_0002376) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) "http://en.wikipedia.org/wiki/Tributary" -### taste receptor cell `http://purl.obolibrary.org/obo/CL_0000209` +- [tributary of](http://purl.obolibrary.org/obo/RO_0002376) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "drains to" -#### Added -- [taste receptor cell](http://purl.obolibrary.org/obo/CL_0000209) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [tributary of](http://purl.obolibrary.org/obo/RO_0002376) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) [0000-0002-6601-2165](https://orcid.org/0000-0002-6601-2165) +- [tributary of](http://purl.obolibrary.org/obo/RO_0002376) [IAO_0000118](http://purl.obolibrary.org/obo/IAO_0000118) "tributary channel of" -### tela choroidea of fourth ventricle `http://purl.obolibrary.org/obo/UBERON_0005287` +- [tributary of](http://purl.obolibrary.org/obo/RO_0002376) [IAO_0000114](http://purl.obolibrary.org/obo/IAO_0000114) [requires discussion](http://purl.obolibrary.org/obo/IAO_0000428) + +- [tributary of](http://purl.obolibrary.org/obo/RO_0002376) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "RO:0002376" + + + +### trigeminal ganglion `http://purl.obolibrary.org/obo/UBERON_0001675` #### Removed -- [tela choroidea of fourth ventricle](http://purl.obolibrary.org/obo/UBERON_0005287) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tela choroidea ventriculi quarti" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Tela_chorioidea_of_fourth_ventricle" +- [trigeminal ganglion](http://purl.obolibrary.org/obo/UBERON_0001675) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In Xenopus, the profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:21452441" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "XAO:0004093" -- [tela choroidea of fourth ventricle](http://purl.obolibrary.org/obo/UBERON_0005287) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tela choroidea ventriculi quarti" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:78493" +- [trigeminal ganglion](http://purl.obolibrary.org/obo/UBERON_0001675) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A prominent collection of touch-sensory neurons of the trigeminal or fifth cranial nerve, positioned beside the brain between the eye and the ear. Kimmel et al, 1995.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000295" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [trigeminal ganglion](http://purl.obolibrary.org/obo/UBERON_0001675) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) #### Added -- [tela choroidea of fourth ventricle](http://purl.obolibrary.org/obo/UBERON_0005287) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tela choroidea ventriculi quarti" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:78493" +- [trigeminal ganglion](http://purl.obolibrary.org/obo/UBERON_0001675) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### trigeminal nerve `http://purl.obolibrary.org/obo/UBERON_0001645` +#### Removed +- [trigeminal nerve](http://purl.obolibrary.org/obo/UBERON_0001645) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Nerve consists of motor and sensory components. Ganglion cells of the sensory component form the proximal part of the trigeminal (Gasserian) ganglion. From the ganglion 3 major rami innervate jaws, snout, and buccal roof.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" -- [tela choroidea of fourth ventricle](http://purl.obolibrary.org/obo/UBERON_0005287) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tela choroidea ventriculi quarti" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010470" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Tela_chorioidea_of_fourth_ventricle" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### tela choroidea of telencephalic ventricle `http://purl.obolibrary.org/obo/UBERON_0005289` -#### Removed -- [tela choroidea of telencephalic ventricle](http://purl.obolibrary.org/obo/UBERON_0005289) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tela choroidea (ventriculi lateralis)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:83712" +- [trigeminal nerve](http://purl.obolibrary.org/obo/UBERON_0001645) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625" -#### Added -- [tela choroidea of telencephalic ventricle](http://purl.obolibrary.org/obo/UBERON_0005289) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tela choroidea (ventriculi lateralis)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:83712" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000704" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [trigeminal nerve](http://purl.obolibrary.org/obo/UBERON_0001645) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "the ophthalmic usually usually merges with the other two. In some vertebrates, the ophthalmic emerges from the brain separately[Kardong] The trigeminal nerve has 3 branches in mammals - similar branches are present in nonmammalian vertebrates, but in some a separate profundus nerve that corresponds to opthalmic branch in mammls" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0471888893" -### temporal bone `http://purl.obolibrary.org/obo/UBERON_0001678` + +### trigeminal neural crest `http://purl.obolibrary.org/obo/UBERON_0005563` #### Removed -- [temporal bone](http://purl.obolibrary.org/obo/UBERON_0001678) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "os temporale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Temporal_bone" +- [trigeminal neural crest](http://purl.obolibrary.org/obo/UBERON_0005563) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000269" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [temporal bone](http://purl.obolibrary.org/obo/UBERON_0001678) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "os temporale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Temporal_bone" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" -### temporal cortex `http://purl.obolibrary.org/obo/UBERON_0016538` +- [trigeminal neural crest](http://purl.obolibrary.org/obo/UBERON_0005563) SubClassOf [head mesenchyme](http://purl.obolibrary.org/obo/UBERON_0005253) #### Added -- [temporal cortex](http://purl.obolibrary.org/obo/UBERON_0016538) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D013702" +- [trigeminal neural crest](http://purl.obolibrary.org/obo/UBERON_0005563) SubClassOf [mesenchyme derived from head neural crest](http://purl.obolibrary.org/obo/UBERON_0007213) + + +### trigeminal nuclear complex `http://purl.obolibrary.org/obo/UBERON_0007641` +#### Removed +- [trigeminal nuclear complex](http://purl.obolibrary.org/obo/UBERON_0007641) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D014278" - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +- [trigeminal nuclear complex](http://purl.obolibrary.org/obo/UBERON_0007641) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in MA and FMA this is part of the pons / pontime tegmentum. We weaken this to overlaps to avoid inconsistency. In NIF this is a composite structure spanning multiple regions, which is more appropriate." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" -### temporal lobe `http://purl.obolibrary.org/obo/UBERON_0001871` -#### Removed -- [temporal lobe](http://purl.obolibrary.org/obo/UBERON_0001871) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lobus temporalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Temporal_lobe" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [temporal lobe](http://purl.obolibrary.org/obo/UBERON_0001871) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lobus temporalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### trigeminal nucleus `http://purl.obolibrary.org/obo/UBERON_0002925` +#### Removed +- [trigeminal nucleus](http://purl.obolibrary.org/obo/UBERON_0002925) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "massive inconsistencies between GO, MA, wikipedia. Part of pons in MA, but this leads to inconsistencies with ABA." + - [url](http://www.geneontology.org/formats/oboInOwl#url) "https://github.com/obophenotype/mouse-anatomy-ontology/issues/58" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Temporal_lobe" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "GO" -### tendon `http://purl.obolibrary.org/obo/UBERON_0000043` + +### trigeminal placode complex `http://purl.obolibrary.org/obo/UBERON_0003070` #### Removed -- [tendon](http://purl.obolibrary.org/obo/UBERON_0000043) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tendo" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [trigeminal placode complex](http://purl.obolibrary.org/obo/UBERON_0003070) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The ectodermal rudiment of the trigeminal ganglion, distinguishable during much of the segmentation period. Kimmel et al, 1995.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Tendon" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000162" -#### Added -- [tendon](http://purl.obolibrary.org/obo/UBERON_0000043) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tendo" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Tendon" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" +- [trigeminal placode complex](http://purl.obolibrary.org/obo/UBERON_0003070) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The dorsolateral placodes (trigeminal and vestibular) develop from ectoderm lateral to the brain (...). In summary, the collective term 'placodes' refers to some rather different structures, probably with different evolutionary origins. Some sensory placodes (at least the otic and olfactory) may have homologues in basal chordates. Even if this is so, it is apparent that they were elaborated considerably during early vertebrate evolution. Epibranchial and dorsolateral placodes appear to be new; we infer that their origin depended on the evolution of specific inductive signals.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)" -### tendon cell `http://purl.obolibrary.org/obo/CL_0000388` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [tendon cell](http://purl.obolibrary.org/obo/CL_0000388) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000109" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### tendon sheath `http://purl.obolibrary.org/obo/UBERON_0000304` +- [trigeminal placode complex](http://purl.obolibrary.org/obo/UBERON_0003070) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "Consider naming this 'trigeminal placode complex'. Also, Fig9-5 of ISBN:0471888893 calls this the profundus placode; XAO says 'profundal and the trigeminal ganglia are separate distally but fused at their proximal end...'" + +- [trigeminal placode complex](http://purl.obolibrary.org/obo/UBERON_0003070) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The ectodermal precursor of the trigeminal ganglion. The profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24.[XAO]" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "XAO" + + + +### trigone of urinary bladder `http://purl.obolibrary.org/obo/UBERON_0001257` #### Removed -- [tendon sheath](http://purl.obolibrary.org/obo/UBERON_0000304) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vagina tendinis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [trigone of urinary bladder](http://purl.obolibrary.org/obo/UBERON_0001257) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "Embryologically, the trigone of the bladder is derived from the caudal end of mesonephric ducts, which is of mesodermal origin (the rest of the bladder is endodermal). In the female the mesonephric ducts regresses, causing the trigone to be less prominent, but still present" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" + +- [trigone of urinary bladder](http://purl.obolibrary.org/obo/UBERON_0001257) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "The area is very sensitive to expansion and once stretched to a certain degree, the urinary bladder signals the brain of its need to empty. The signals become stronger as the bladder continues to fill." + +#### Added +- [trigone of urinary bladder](http://purl.obolibrary.org/obo/UBERON_0001257) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Tendon_sheath" -#### Added -- [tendon sheath](http://purl.obolibrary.org/obo/UBERON_0000304) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vagina tendinis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### trophectoderm `http://purl.obolibrary.org/obo/UBERON_0004345` +#### Removed +- [trophectoderm](http://purl.obolibrary.org/obo/UBERON_0004345) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The outer cellular layer of the mammalian blastocyst. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.750, see_Kardong_KV][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Tendon_sheath" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### terminal bronchiole `http://purl.obolibrary.org/obo/UBERON_0002187` -#### Removed -- [terminal bronchiole](http://purl.obolibrary.org/obo/UBERON_0002187) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "bronchioli terminalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Terminal_bronchiole" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000979" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [trophectoderm](http://purl.obolibrary.org/obo/UBERON_0004345) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "BTO has this has part of the trophoblast" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "BTO" -- [terminal bronchiole](http://purl.obolibrary.org/obo/UBERON_0002187) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "bronchiolus terminalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [trophectoderm](http://purl.obolibrary.org/obo/UBERON_0004345) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) the trophoblast develops rapidly so that contact may be made with the maternal uterine tissues when conditions are appropriate. We have here an excellent example of an embryonic adaptation, the development of a structure never present in either adult or embryo of 'lower' vertebrates.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0721676685 Romer AS, Parsons TS, Vertebrate body (1977) p.105-106" -#### Added -- [terminal bronchiole](http://purl.obolibrary.org/obo/UBERON_0002187) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "bronchiolus terminalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [terminal bronchiole](http://purl.obolibrary.org/obo/UBERON_0002187) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "bronchioli terminalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Terminal_bronchiole" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000979" -### terminal part of digestive tract `http://purl.obolibrary.org/obo/UBERON_0006866` -#### Removed -- [terminal part of digestive tract](http://purl.obolibrary.org/obo/UBERON_0006866) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005756" +- [trophectoderm](http://purl.obolibrary.org/obo/UBERON_0004345) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "trophectodermal" -#### Added -- [terminal part of digestive tract](http://purl.obolibrary.org/obo/UBERON_0006866) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005756" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### tertiary ovarian follicle `http://purl.obolibrary.org/obo/UBERON_0000037` +### trophoblast `http://purl.obolibrary.org/obo/UBERON_0000088` #### Removed -- [tertiary ovarian follicle](http://purl.obolibrary.org/obo/UBERON_0000037) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "folliculi ovarici vesiculosi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:18641" +- [trophoblast](http://purl.obolibrary.org/obo/UBERON_0000088) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "The postimplantation derivatives of the trophectoderm, which make up most of the fetal part of the placenta" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:19829370" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [trophoblast](http://purl.obolibrary.org/obo/UBERON_0000088) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "the mesectodermal cell layer arising from the trophectoderm that erodes the uterine mucosa and contributes to the formation of the placenta[MP]" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "MP" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0-683-40008-8" -#### Added -- [tertiary ovarian follicle](http://purl.obolibrary.org/obo/UBERON_0000037) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "folliculi ovarici vesiculosi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class_label](http://www.geneontology.org/formats/oboInOwl#external_class_label) "trophoblast layer" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:18641" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "MP:0005031" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-23" +- [trophoblast](http://purl.obolibrary.org/obo/UBERON_0000088) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "trophoblastic" -### testicular artery `http://purl.obolibrary.org/obo/UBERON_0001187` -#### Removed -- [testicular artery](http://purl.obolibrary.org/obo/UBERON_0001187) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria testicularis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Testicular_artery" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [testicular artery](http://purl.obolibrary.org/obo/UBERON_0001187) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria testicularis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Testicular_artery" +### truncus arteriosus `http://purl.obolibrary.org/obo/UBERON_0002061` +#### Removed +- [truncus arteriosus](http://purl.obolibrary.org/obo/UBERON_0002061) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "assume spelling error for ncit" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "ncit" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### testicular vein `http://purl.obolibrary.org/obo/UBERON_0001144` +### trunk `http://purl.obolibrary.org/obo/UBERON_0002100` #### Removed -- [testicular vein](http://purl.obolibrary.org/obo/UBERON_0001144) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena testicularis sinistra" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Testicular_vein" +- [trunk](http://purl.obolibrary.org/obo/UBERON_0002100) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [head](http://purl.obolibrary.org/obo/UBERON_0000033) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [trunk](http://purl.obolibrary.org/obo/UBERON_0002100) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -- [testicular vein](http://purl.obolibrary.org/obo/UBERON_0001144) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena testicularis dextra" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Testicular_vein" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -- [testicular vein](http://purl.obolibrary.org/obo/UBERON_0001144) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "venae spermaticae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Testicular_vein" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001115" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [trunk](http://purl.obolibrary.org/obo/UBERON_0002100) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [appendage](http://purl.obolibrary.org/obo/UBERON_0000026) + - [exceptions](http://www.geneontology.org/formats/oboInOwl#exceptions) "ZFA" -#### Added -- [testicular vein](http://purl.obolibrary.org/obo/UBERON_0001144) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena testicularis dextra" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "https://github.com/obophenotype/uberon/issues/378" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Testicular_vein" + - [status](http://www.geneontology.org/formats/oboInOwl#status) "pending" -- [testicular vein](http://purl.obolibrary.org/obo/UBERON_0001144) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena testicularis sinistra" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [trunk](http://purl.obolibrary.org/obo/UBERON_0002100) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010339" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Testicular_vein" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -- [testicular vein](http://purl.obolibrary.org/obo/UBERON_0001144) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "venae spermaticae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Testicular_vein" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" -### testis `http://purl.obolibrary.org/obo/UBERON_0000473` + +### trunk neural crest `http://purl.obolibrary.org/obo/UBERON_0003083` #### Removed -- [testis](http://purl.obolibrary.org/obo/UBERON_0000473) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "testiculus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001363" +- [trunk neural crest](http://purl.obolibrary.org/obo/UBERON_0003083) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [testis](http://purl.obolibrary.org/obo/UBERON_0000473) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004928" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [testis](http://purl.obolibrary.org/obo/UBERON_0000473) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004928" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" -- [testis](http://purl.obolibrary.org/obo/UBERON_0000473) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "testiculus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000062" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001363" +- [trunk neural crest](http://purl.obolibrary.org/obo/UBERON_0003083) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Post-cranial portion of the neural crest. Exact anatomical derivations not experimentally resolved in amphibians.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -### tetrapod frontal bone `http://purl.obolibrary.org/obo/UBERON_0000209` -#### Removed -- [tetrapod frontal bone](http://purl.obolibrary.org/obo/UBERON_0000209) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "os frontale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Frontal_bone" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010582" #### Added -- [tetrapod frontal bone](http://purl.obolibrary.org/obo/UBERON_0000209) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "os frontale" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [trunk neural crest](http://purl.obolibrary.org/obo/UBERON_0003083) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Frontal_bone" +- [trunk neural crest](http://purl.obolibrary.org/obo/UBERON_0003083) SubClassOf [structure with developmental contribution from neural crest](http://purl.obolibrary.org/obo/UBERON_0010314) -### theca cell `http://purl.obolibrary.org/obo/CL_0000503` +### trunk of intercostal nerve `http://purl.obolibrary.org/obo/UBERON_0002327` +#### Removed +- [trunk of intercostal nerve](http://purl.obolibrary.org/obo/UBERON_0002327) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:18227" -#### Added -- [theca cell](http://purl.obolibrary.org/obo/CL_0000503) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### theca cell layer `http://purl.obolibrary.org/obo/UBERON_0000155` +### trunk of sciatic nerve `http://purl.obolibrary.org/obo/UBERON_0002004` #### Removed -- [theca cell layer](http://purl.obolibrary.org/obo/UBERON_0000155) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "theca folliculi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Theca_of_follicle" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - -#### Added -- [theca cell layer](http://purl.obolibrary.org/obo/UBERON_0000155) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "theca folliculi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [trunk of sciatic nerve](http://purl.obolibrary.org/obo/UBERON_0002004) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:18577" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Theca_of_follicle" -### thick ascending limb of loop of Henle `http://purl.obolibrary.org/obo/UBERON_0001291` +### trunk or cervical vertebra `http://purl.obolibrary.org/obo/UBERON_0004451` #### Removed -- [thick ascending limb of loop of Henle](http://purl.obolibrary.org/obo/UBERON_0001291) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tubulus rectus distalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Thick_ascending_limb_of_loop_of_Henle" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [trunk or cervical vertebra](http://purl.obolibrary.org/obo/UBERON_0004451) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "it's not clear if the XAO class belongs here or below" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "XAO" -#### Added -- [thick ascending limb of loop of Henle](http://purl.obolibrary.org/obo/UBERON_0001291) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tubulus rectus distalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [trunk or cervical vertebra](http://purl.obolibrary.org/obo/UBERON_0004451) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In humans, there are 24 presacral vertebrae (7 cervical, 12 thoracic, and 5 lumbar)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Thick_ascending_limb_of_loop_of_Henle" -### thoracic aorta `http://purl.obolibrary.org/obo/UBERON_0001515` +### trunk region of vertebral column `http://purl.obolibrary.org/obo/UBERON_0009568` #### Removed -- [thoracic aorta](http://purl.obolibrary.org/obo/UBERON_0001515) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "aorta thoracica" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:3786" +- [trunk region of vertebral column](http://purl.obolibrary.org/obo/UBERON_0009568) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "AAO:0000612" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [trunk region of vertebral column](http://purl.obolibrary.org/obo/UBERON_0009568) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Region of the vertebral column between the atlas and the sacrum consisting of seven to 285 vertebrae.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000612" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" - -- [thoracic aorta](http://purl.obolibrary.org/obo/UBERON_0001515) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "aorta thoracalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Thoracic_aorta" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -- [thoracic aorta](http://purl.obolibrary.org/obo/UBERON_0001515) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pars thoracica aortae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Thoracic_aorta" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:Duellman_and_Trueb_1994" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - -#### Added -- [thoracic aorta](http://purl.obolibrary.org/obo/UBERON_0001515) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "aorta thoracica" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:3786" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### trunk taste bud `http://purl.obolibrary.org/obo/UBERON_0034726` -- [thoracic aorta](http://purl.obolibrary.org/obo/UBERON_0001515) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "aorta thoracalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Thoracic_aorta" +#### Added +- [trunk taste bud](http://purl.obolibrary.org/obo/UBERON_0034726) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -- [thoracic aorta](http://purl.obolibrary.org/obo/UBERON_0001515) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pars thoracica aortae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Thoracic_aorta" +### trunk vertebra `http://purl.obolibrary.org/obo/UBERON_0011677` +#### Removed +- [trunk vertebra](http://purl.obolibrary.org/obo/UBERON_0011677) [UBPROP_0000202](http://purl.obolibrary.org/obo/UBPROP_0000202) [FMA_72066](http://purl.obolibrary.org/obo/FMA_72066) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### thoracic cavity `http://purl.obolibrary.org/obo/UBERON_0002224` +### tube `http://purl.obolibrary.org/obo/UBERON_0000025` #### Removed -- [thoracic cavity](http://purl.obolibrary.org/obo/UBERON_0002224) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cavitas thoracis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Thoracic_cavity" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [tube](http://purl.obolibrary.org/obo/UBERON_0000025) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "tubular" -#### Added -- [thoracic cavity](http://purl.obolibrary.org/obo/UBERON_0002224) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cavitas thoracis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Thoracic_cavity" +- [tube](http://purl.obolibrary.org/obo/UBERON_0000025) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### thoracic ganglion `http://purl.obolibrary.org/obo/UBERON_0000961` +### tubotympanic recess epithelium `http://purl.obolibrary.org/obo/UBERON_0010020` #### Removed -- [thoracic ganglion](http://purl.obolibrary.org/obo/UBERON_0000961) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ganglion thoracicum splanchnicum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [tubotympanic recess epithelium](http://purl.obolibrary.org/obo/UBERON_0010020) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The tympanic cavity and auditory tube of an amniote develop from the first embryonic pharyngeal pouch, so they are homologous to the first gill pouch, or spiracle, of a fish. We are uncertain whether this homology strictly applies to the middle ear cavity and auditory tube of lissamphibians, which show certain peculiarities in their development.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.417" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:6471" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [thoracic ganglion](http://purl.obolibrary.org/obo/UBERON_0000961) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ganglion thoracicum splanchnicum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001297" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:6471" -### thoracic nerve `http://purl.obolibrary.org/obo/UBERON_0003726` +### tumor necrosis factor receptor superfamily member 11A `http://purl.obolibrary.org/obo/PR_000001954` #### Removed -- [thoracic nerve](http://purl.obolibrary.org/obo/UBERON_0003726) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus thoracis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:5860" +- [tumor necrosis factor receptor superfamily member 11A](http://purl.obolibrary.org/obo/PR_000001954) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [tumor necrosis factor receptor superfamily member 11A (human)](http://purl.obolibrary.org/obo/PR_Q9Y6Q6) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [thoracic nerve](http://purl.obolibrary.org/obo/UBERON_0003726) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nervi thoracici" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Thoracic_nerves" +### tunica adventitia of blood vessel `http://purl.obolibrary.org/obo/UBERON_0005734` +#### Removed +- [tunica adventitia of blood vessel](http://purl.obolibrary.org/obo/UBERON_0005734) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The outermost layer of a blood vessel, surrounding the tunica media. It is mainly composed of collagen. The collagen serves to anchor the blood vessel to nearby organs, giving it stability[Wikipedia:Tunica_externa_(vessels)]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Tunica_externa_(vessels)" + - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + +### tunica fibrosa of eyeball `http://purl.obolibrary.org/obo/UBERON_0012430` #### Added -- [thoracic nerve](http://purl.obolibrary.org/obo/UBERON_0003726) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nervi thoracici" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [tunica fibrosa of eyeball](http://purl.obolibrary.org/obo/UBERON_0012430) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Thoracic_nerves" -- [thoracic nerve](http://purl.obolibrary.org/obo/UBERON_0003726) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus thoracis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### tunica intima `http://purl.obolibrary.org/obo/UBERON_0002523` +#### Removed +- [tunica intima](http://purl.obolibrary.org/obo/UBERON_0002523) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The tunica intima (or just intima) is the innermost layer of an artery or vein. It is made up of one layer of endothelial cells and is supported by an internal elastic lamina. The endothelial cells are in direct contact with the blood flow. The inner coat (tunica intima) can be separated from the middle by a little maceration, or it may be stripped off in small pieces; but, on account of its friability, it cannot be separated as a complete membrane. It is a fine, transparent, colorless structure which is highly elastic, and, after death, is commonly corrugated into longitudinal wrinkles. The inner coat consists of: A layer of pavement endothelium, the cells of which are polygonal, oval, or fusiform, and have very distinct round or oval nuclei. This endothelium is brought into view most distinctly by staining with silver nitrate. A subendothelial layer, consisting of delicate connective tissue with branched cells lying in the interspaces of the tissue; in arteries of less than 2 mm. in diameter the subendothelial layer consists of a single stratum of stellate cells, and the connective tissue is only largely developed in vessels of a considerable size. An elastic or fenestrated layer, which consists of a membrane containing a net-work of elastic fibers, having principally a longitudinal direction, and in which, under the microscope, small elongated apertures or perforations may be seen, giving it a fenestrated appearance. It was therefore called by Henle the fenestrated membrane. This membrane forms the chief thickness of the inner coat, and can be separated into several layers, some of which present the appearance of a network of longitudinal elastic fibers, and others a more membranous character, marked by pale lines having a longitudinal direction. In minute arteries the fenestrated membrane is a very thin layer; but in the larger arteries, and especially in the aorta, it has a very considerable thickness. [WP,unvetted].[Wikipedia]" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "Wikipedia" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:5860" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Tunica_intima" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [tunica intima](http://purl.obolibrary.org/obo/UBERON_0002523) SubClassOf [surrounded by](http://purl.obolibrary.org/obo/RO_0002219) some [tunica media](http://purl.obolibrary.org/obo/UBERON_0002522) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "check for exceptions, e.g. capillaries" + +#### Added +- [tunica intima](http://purl.obolibrary.org/obo/UBERON_0002523) SubClassOf [surrounded by](http://purl.obolibrary.org/obo/RO_0002219) some [tunica media](http://purl.obolibrary.org/obo/UBERON_0002522) -### thoracic rib cage `http://purl.obolibrary.org/obo/UBERON_0003252` +### tympanic membrane `http://purl.obolibrary.org/obo/UBERON_0002364` #### Removed -- [thoracic rib cage](http://purl.obolibrary.org/obo/UBERON_0003252) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cavea thoracis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:7480" +- [tympanic membrane](http://purl.obolibrary.org/obo/UBERON_0002364) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "most AOs consider this part of the middle ear, so we go with this and place it in the middle ear as a border to the external, although it could be considered to overlap the external ear in that it has an EAM layer as part - for this reason we do not consider middle and external ear to be spatially disjoint." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:11237469" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [tympanic membrane](http://purl.obolibrary.org/obo/UBERON_0002364) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "The tympanic membrane (TM) has three layers, two epithelia provided by the external acoustic meatus (EAM) and the MEC, derived respectively from the first pharyngeal cleft and pouch, and a mesenchymally derived fibrous stratum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [tympanic membrane](http://purl.obolibrary.org/obo/UBERON_0002364) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The thin membrane which closes externally the cavity of the middle ear and is deeply sited at the bottom of the external auditory meatus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001146" -- [thoracic rib cage](http://purl.obolibrary.org/obo/UBERON_0003252) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cavea thoracis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Human_rib_cage" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [thoracic rib cage](http://purl.obolibrary.org/obo/UBERON_0003252) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cavea thoracis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:7480" +- [tympanic membrane](http://purl.obolibrary.org/obo/UBERON_0002364) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In particular, a tympanic membrane was not present in the earliest tetrapods (...). An ear utilizing a tympanic membrane evolved independently at least three times in tetrapods: (1) in the lineage that leads to anurans (frogs), (2) in the line of evolution to turtles and diapsids, and (3) in the late synapsid lineage that gave rise to mammals.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.418" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001146" -- [thoracic rib cage](http://purl.obolibrary.org/obo/UBERON_0003252) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cavea thoracis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Human_rib_cage" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### thoracic spinal cord `http://purl.obolibrary.org/obo/UBERON_0003038` + + +### tyrosine-protein kinase Mer `http://purl.obolibrary.org/obo/PR_000010329` #### Removed -- [thoracic spinal cord](http://purl.obolibrary.org/obo/UBERON_0003038) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pars thoracica medullae spinalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71167" +- [tyrosine-protein kinase Mer](http://purl.obolibrary.org/obo/PR_000010329) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [tyrosine-protein kinase Mer (human)](http://purl.obolibrary.org/obo/PR_Q12866) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [thoracic spinal cord](http://purl.obolibrary.org/obo/UBERON_0003038) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "segmenta thoracica medullae spinalis [1-12]" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71167" +### tyrosine-protein kinase receptor UFO `http://purl.obolibrary.org/obo/PR_000004528` +#### Removed +- [tyrosine-protein kinase receptor UFO](http://purl.obolibrary.org/obo/PR_000004528) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [tyrosine-protein kinase receptor UFO (human)](http://purl.obolibrary.org/obo/PR_P30530) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [thoracic spinal cord](http://purl.obolibrary.org/obo/UBERON_0003038) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "segmenta thoracica medullae spinalis [1-12]" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### tyrosine-protein phosphatase non-receptor type substrate 1 `http://purl.obolibrary.org/obo/PR_000001968` +#### Removed +- [tyrosine-protein phosphatase non-receptor type substrate 1](http://purl.obolibrary.org/obo/PR_000001968) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [tyrosine-protein phosphatase non-receptor type substrate 1 (human)](http://purl.obolibrary.org/obo/PR_P78324) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71167" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [thoracic spinal cord](http://purl.obolibrary.org/obo/UBERON_0003038) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pars thoracica medullae spinalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### umbilical cord `http://purl.obolibrary.org/obo/UBERON_0002331` +#### Removed +- [umbilical cord](http://purl.obolibrary.org/obo/UBERON_0002331) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "umbilical" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:71167" +- [umbilical cord](http://purl.obolibrary.org/obo/UBERON_0002331) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The connecting cord from the developing embryo or fetus to the placenta. During prenatal development, the umbilical cord comes from the same zygote as the fetus and (in humans) normally contains two arteries (the umbilical arteries) and one vein (the umbilical vein), buried within Wharton's jelly. The umbilical vein supplies the fetus with oxygenated, nutrient-rich blood from the placenta.property_value, external_definition the umbilical arteries return the deoxygenated, nutrient-depleted blood[WP]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Umbilical_cord" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### thoracodorsal artery `http://purl.obolibrary.org/obo/UBERON_0002011` +### uncondensed odontogenic mesenchyme `http://purl.obolibrary.org/obo/UBERON_0003856` #### Removed -- [thoracodorsal artery](http://purl.obolibrary.org/obo/UBERON_0002011) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria thoracodorsalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Thoracodorsal_artery" +- [uncondensed odontogenic mesenchyme](http://purl.obolibrary.org/obo/UBERON_0003856) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Mesenchyme enclosed by dental organ.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005139" -#### Added -- [thoracodorsal artery](http://purl.obolibrary.org/obo/UBERON_0002011) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteria thoracodorsalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Thoracodorsal_artery" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" +- [uncondensed odontogenic mesenchyme](http://purl.obolibrary.org/obo/UBERON_0003856) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Mesenchyme enclosed by dental organ.[MP]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "J:153554" -### thymic vein `http://purl.obolibrary.org/obo/UBERON_0001591` -#### Removed -- [thymic vein](http://purl.obolibrary.org/obo/UBERON_0001591) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "venae thymicae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "MP" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Thymic_veins" +- [uncondensed odontogenic mesenchyme](http://purl.obolibrary.org/obo/UBERON_0003856) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [mesenchyme derived from head neural crest](http://purl.obolibrary.org/obo/UBERON_0007213) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "see comments" -- [thymic vein](http://purl.obolibrary.org/obo/UBERON_0001591) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vena thymica" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +#### Added +- [uncondensed odontogenic mesenchyme](http://purl.obolibrary.org/obo/UBERON_0003856) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [mesenchyme derived from head neural crest](http://purl.obolibrary.org/obo/UBERON_0007213) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Thymic_veins" -#### Added -- [thymic vein](http://purl.obolibrary.org/obo/UBERON_0001591) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "venae thymicae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### uncurated `http://purl.obolibrary.org/obo/IAO_0000124` +#### Removed +- [uncurated](http://purl.obolibrary.org/obo/IAO_0000124) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "uncurated"@en - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Thymic_veins" -- [thymic vein](http://purl.obolibrary.org/obo/UBERON_0001591) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vena thymica" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Thymic_veins" +### undifferentiated genital tubercle `http://purl.obolibrary.org/obo/UBERON_0005876` +#### Removed +- [undifferentiated genital tubercle](http://purl.obolibrary.org/obo/UBERON_0005876) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In mammalian embryos, male and female external genitalia develop from the genital tubercle.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### thymocyte `http://purl.obolibrary.org/obo/CL_0000893` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [thymocyte](http://purl.obolibrary.org/obo/CL_0000893) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1242/dev.036830 Seifert AW, Yamaguchi T, Cohn MJ, Functional and phylogenetic analysis shows that Fgf8 is a marker of genital induction in mammals but is not required for external genital development. Development (2009)" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000583" -### thyroid diverticulum `http://purl.obolibrary.org/obo/UBERON_0007689` -#### Removed -- [thyroid diverticulum](http://purl.obolibrary.org/obo/UBERON_0007689) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "diverticulum thyroideum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Thyroid_diverticulum" +- [undifferentiated genital tubercle](http://purl.obolibrary.org/obo/UBERON_0005876) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "embryonic anlage of the external genitalia, which emerges as paired swellings ventral to the cloacal membrane, is proposed to be derived from all three germ layers, and gives rise to the penis, clitoris, scrotum, labia, and foreskin; GT development is indistinguishable in male and female mouse embryos until ~E16, when the urethral plate begins to be masculinized to form the penile urethra, marking the beginning of an androgen-dependent phase of sexual differentiation[MP]" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "MP" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [undifferentiated genital tubercle](http://purl.obolibrary.org/obo/UBERON_0005876) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "GT development is indistinguishable in male and female mouse embryos until approximately E16, when the urethral plate begins to be masculinized to form the penile urethra, marking the beginning of an androgen-dependent phase of sexual differentiation[MP:0011771]" -- [thyroid diverticulum](http://purl.obolibrary.org/obo/UBERON_0007689) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "saccus thyroideus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Thyroid_diverticulum" +- [undifferentiated genital tubercle](http://purl.obolibrary.org/obo/UBERON_0005876) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "todo - add taxon constraints" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [undifferentiated genital tubercle](http://purl.obolibrary.org/obo/UBERON_0005876) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "All amniotes studied to date initiate external genital development with the formation of paired genital swellings. In mammals, archosaurs, and turtles, these swellings merge to form a single genital tubercle, the precursor of the penis and clitoris[PMID:24960313]" -#### Added -- [thyroid diverticulum](http://purl.obolibrary.org/obo/UBERON_0007689) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "saccus thyroideus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Thyroid_diverticulum" +- [undifferentiated genital tubercle](http://purl.obolibrary.org/obo/UBERON_0005876) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The eminence in the embryo which develops into the clitoris or penis. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [thyroid diverticulum](http://purl.obolibrary.org/obo/UBERON_0007689) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "diverticulum thyroideum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Thyroid_diverticulum" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000583" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/genital+tubercle" -### thyroid follicular cell `http://purl.obolibrary.org/obo/CL_0002258` +- [undifferentiated genital tubercle](http://purl.obolibrary.org/obo/UBERON_0005876) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "we assume the EMAPA class is the undifferentiated form based on TS timings" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EMAPA" -#### Added -- [thyroid follicular cell](http://purl.obolibrary.org/obo/CL_0002258) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### thyroid gland `http://purl.obolibrary.org/obo/UBERON_0002046` +### unilaminar epithelium `http://purl.obolibrary.org/obo/UBERON_0000490` #### Removed -- [thyroid gland](http://purl.obolibrary.org/obo/UBERON_0002046) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "glandula thyroidea" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [unilaminar epithelium](http://purl.obolibrary.org/obo/UBERON_0000490) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Epithelium that consists of a single layer of epithelial cells.[CARO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://orcid.org/0000-0001-9114-8737" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Thyroid" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -#### Added -- [thyroid gland](http://purl.obolibrary.org/obo/UBERON_0002046) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "glandula thyroidea" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "CARO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Thyroid" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "CARO:0000073" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:45561" -### tibial nerve `http://purl.obolibrary.org/obo/UBERON_0001323` + + +### universal `http://purl.obolibrary.org/obo/IAO_0000410` #### Removed -- [tibial nerve](http://purl.obolibrary.org/obo/UBERON_0001323) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "n. tibialis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Tibial_nerve" +- [universal](http://purl.obolibrary.org/obo/IAO_0000410) [IAO_0000117](http://purl.obolibrary.org/obo/IAO_0000117) "Alan Ruttenberg"@en - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [universal](http://purl.obolibrary.org/obo/IAO_0000410) [IAO_0000119](http://purl.obolibrary.org/obo/IAO_0000119) "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf"@en -#### Added -- [tibial nerve](http://purl.obolibrary.org/obo/UBERON_0001323) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "n. tibialis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [universal](http://purl.obolibrary.org/obo/IAO_0000410) [IAO_0000111](http://purl.obolibrary.org/obo/IAO_0000111) "universal"@en - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Tibial_nerve" -### tissue `http://purl.obolibrary.org/obo/UBERON_0000479` +### upper arm bone `http://purl.obolibrary.org/obo/UBERON_0004250` #### Removed -- [tissue](http://purl.obolibrary.org/obo/UBERON_0000479) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007003" +- [upper arm bone](http://purl.obolibrary.org/obo/UBERON_0004250) [UBPROP_0000006](http://purl.obolibrary.org/obo/UBPROP_0000006) "https://github.com/obophenotype/uberon/wiki/Skeleton-partonomy-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) -#### Added -- [tissue](http://purl.obolibrary.org/obo/UBERON_0000479) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007003" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### tissue-resident macrophage `http://purl.obolibrary.org/obo/CL_0000864` +### upper arm epithelium `http://purl.obolibrary.org/obo/UBERON_0005228` +#### Removed +- [upper arm epithelium](http://purl.obolibrary.org/obo/UBERON_0005228) SubClassOf [epithelium](http://purl.obolibrary.org/obo/UBERON_0000483) #### Added -- [tissue-resident macrophage](http://purl.obolibrary.org/obo/CL_0000864) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [upper arm epithelium](http://purl.obolibrary.org/obo/UBERON_0005228) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) -### tongue muscle `http://purl.obolibrary.org/obo/UBERON_0000378` +### upper digestive tract `http://purl.obolibrary.org/obo/UBERON_0004908` #### Removed -- [tongue muscle](http://purl.obolibrary.org/obo/UBERON_0000378) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "musculi linguae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Muscles_of_tongue" +- [upper digestive tract](http://purl.obolibrary.org/obo/UBERON_0004908) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "WP: small intestine, large intestine, anus. Anal canal not part of LGIT according to FMA, but anus is considered part of LGIT according to WP. Duodenum overlaps both U/L. In Galen, entire GI tract excludes esophagus" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [tongue muscle](http://purl.obolibrary.org/obo/UBERON_0000378) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "musculi linguae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Muscles_of_tongue" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### upper jaw region `http://purl.obolibrary.org/obo/UBERON_0001709` +#### Removed +- [upper jaw region](http://purl.obolibrary.org/obo/UBERON_0001709) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Subsequent vertebrate evolution has also involved major alterations to the pharynx; perhaps the most notable occurred with the evolution of the gnathostomes. This involved substantial modifications to the most anterior pharyngeal segments, with the jaw forming from the first, anterior, pharyngeal segment, while the second formed its supporting apparatus, the hyoid.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### tongue muscle cell `http://purl.obolibrary.org/obo/CL_0002673` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [tongue muscle cell](http://purl.obolibrary.org/obo/CL_0002673) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000454" -### tonsil germinal center B cell `http://purl.obolibrary.org/obo/CL_2000006` +- [upper jaw region](http://purl.obolibrary.org/obo/UBERON_0001709) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "Note isa/partof difference MA/FMA" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" -#### Added -- [tonsil germinal center B cell](http://purl.obolibrary.org/obo/CL_2000006) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [upper jaw region](http://purl.obolibrary.org/obo/UBERON_0001709) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [lower jaw region](http://purl.obolibrary.org/obo/UBERON_0001710) +- [upper jaw region](http://purl.obolibrary.org/obo/UBERON_0001709) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Superior maxillary arch located on the anterior and lateral sides of the skull.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" -### tonsillar ring `http://purl.obolibrary.org/obo/UBERON_0001735` -#### Removed -- [tonsillar ring](http://purl.obolibrary.org/obo/UBERON_0001735) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "anulus lymphoideus pharyngis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:55070" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000620" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" #### Added -- [tonsillar ring](http://purl.obolibrary.org/obo/UBERON_0001735) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "anulus lymphoideus pharyngis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [upper jaw region](http://purl.obolibrary.org/obo/UBERON_0001709) SubClassOf [structure with developmental contribution from neural crest](http://purl.obolibrary.org/obo/UBERON_0010314) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:55070" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" - - -### tooth enamel organ `http://purl.obolibrary.org/obo/UBERON_0005176` +### upper leg epithelium `http://purl.obolibrary.org/obo/UBERON_0005225` #### Removed -- [tooth enamel organ](http://purl.obolibrary.org/obo/UBERON_0005176) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "organum enameleum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Enamel_organ" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [upper leg epithelium](http://purl.obolibrary.org/obo/UBERON_0005225) SubClassOf [epithelium](http://purl.obolibrary.org/obo/UBERON_0000483) #### Added -- [tooth enamel organ](http://purl.obolibrary.org/obo/UBERON_0005176) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "organum enameleum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Enamel_organ" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [upper leg epithelium](http://purl.obolibrary.org/obo/UBERON_0005225) SubClassOf [ecto-epithelium](http://purl.obolibrary.org/obo/UBERON_0010371) -### trabecula carnea `http://purl.obolibrary.org/obo/UBERON_0002511` +### upper lip `http://purl.obolibrary.org/obo/UBERON_0001834` #### Removed -- [trabecula carnea](http://purl.obolibrary.org/obo/UBERON_0002511) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "columnae carneae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Trabeculae_carneae" +- [upper lip](http://purl.obolibrary.org/obo/UBERON_0001834) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Lip that covers the lower portion of the mouth. [ZFIN:Curator][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [trabecula carnea](http://purl.obolibrary.org/obo/UBERON_0002511) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "trabeculae carneae cordis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Trabeculae_carneae" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001750" -#### Added -- [trabecula carnea](http://purl.obolibrary.org/obo/UBERON_0002511) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "trabeculae carneae cordis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [upper lip](http://purl.obolibrary.org/obo/UBERON_0001834) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Lip that covers the upper portion of the mouth.[TAO]" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Trabeculae_carneae" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001970" -- [trabecula carnea](http://purl.obolibrary.org/obo/UBERON_0002511) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "columnae carneae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Trabeculae_carneae" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TAO:wd" -### trachea cartilage `http://purl.obolibrary.org/obo/UBERON_0003604` -#### Removed -- [trachea cartilage](http://purl.obolibrary.org/obo/UBERON_0003604) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cartilagines tracheales" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Tracheal_rings" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### upper respiratory conduit `http://purl.obolibrary.org/obo/UBERON_0015787` +#### Removed +- [upper respiratory conduit](http://purl.obolibrary.org/obo/UBERON_0015787) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical cluster which consists a segment of the upper respiratory tract[FMA:265132]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:265132" #### Added -- [trachea cartilage](http://purl.obolibrary.org/obo/UBERON_0003604) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cartilagines tracheales" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [upper respiratory conduit](http://purl.obolibrary.org/obo/UBERON_0015787) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Tracheal_rings" +### upper respiratory tract `http://purl.obolibrary.org/obo/UBERON_0001557` +#### Removed +- [upper respiratory tract](http://purl.obolibrary.org/obo/UBERON_0001557) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "Some specify that the glottis (vocal cords) is the defining line between the upper and lower respiratory tracts;[2] yet even others make the line at the cricoid cartilage. The FMA includes nose, nasopharynx, oropharynx and larynx[WP]" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" -### tracheal goblet cell `http://purl.obolibrary.org/obo/CL_1000329` +- [upper respiratory tract](http://purl.obolibrary.org/obo/UBERON_0001557) [RO_0002171](http://purl.obolibrary.org/obo/RO_0002171) [lower respiratory tract](http://purl.obolibrary.org/obo/UBERON_0001558) -#### Added -- [tracheal goblet cell](http://purl.obolibrary.org/obo/CL_1000329) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### tracheal mucosa `http://purl.obolibrary.org/obo/UBERON_0000379` +### ureter `http://purl.obolibrary.org/obo/UBERON_0000056` #### Removed -- [tracheal mucosa](http://purl.obolibrary.org/obo/UBERON_0000379) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa tracheae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:7471" +- [ureter](http://purl.obolibrary.org/obo/UBERON_0000056) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "in humans, consists of adventitial, muscular and mucoa layers" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [ureter](http://purl.obolibrary.org/obo/UBERON_0000056) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [tracheal mucosa](http://purl.obolibrary.org/obo/UBERON_0000379) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica mucosa tracheae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:7471" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000605" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543" +- [ureter](http://purl.obolibrary.org/obo/UBERON_0000056) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical structure consisting of long narrow duct which carries urine from the kidney to the urinary bladder.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010254" -### tracheobronchial goblet cell `http://purl.obolibrary.org/obo/CL_0019003` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -#### Added -- [tracheobronchial goblet cell](http://purl.obolibrary.org/obo/CL_0019003) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" -### tracheobronchial serous cell `http://purl.obolibrary.org/obo/CL_0019001` +- [ureter](http://purl.obolibrary.org/obo/UBERON_0000056) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "ureteric" -#### Added -- [tracheobronchial serous cell](http://purl.obolibrary.org/obo/CL_0019001) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [ureter](http://purl.obolibrary.org/obo/UBERON_0000056) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "ureteral" +- [ureter](http://purl.obolibrary.org/obo/UBERON_0000056) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The duct of amniotes that carries urine from a metanephric kidney to the urinary bladder. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### tracheobronchial smooth muscle cell `http://purl.obolibrary.org/obo/CL_0019019` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [tracheobronchial smooth muscle cell](http://purl.obolibrary.org/obo/CL_0019019) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000605" -### tracheobronchial tree `http://purl.obolibrary.org/obo/UBERON_0007196` -#### Removed -- [tracheobronchial tree](http://purl.obolibrary.org/obo/UBERON_0007196) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arbor tracheobronchialis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:7393" +### ureter luminal urothelium `http://purl.obolibrary.org/obo/UBERON_0011947` #### Added -- [tracheobronchial tree](http://purl.obolibrary.org/obo/UBERON_0007196) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arbor tracheobronchialis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [ureter luminal urothelium](http://purl.obolibrary.org/obo/UBERON_0011947) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:7393" +### ureteral valve `http://purl.obolibrary.org/obo/UBERON_0015420` +#### Added +- [ureteral valve](http://purl.obolibrary.org/obo/UBERON_0015420) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### trans-synaptic signaling by nitric oxide `http://purl.obolibrary.org/obo/GO_0099548` -#### Removed -- [trans-synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0099548) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Cell-cell signaling between presynapse and postsynapse mediated by nitric oxide." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:dos" -- [trans-synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0099548) [label](http://www.w3.org/2000/01/rdf-schema#label) "trans-synaptic signaling by nitric oxide" +### ureteric bud `http://purl.obolibrary.org/obo/UBERON_0000084` +#### Removed +- [ureteric bud](http://purl.obolibrary.org/obo/UBERON_0000084) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts[VHOG:0000541]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "VHOG:0000541" -- [trans-synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0099548) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" +- [ureteric bud](http://purl.obolibrary.org/obo/UBERON_0000084) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts. [Embryology, See_Dudek_RW_and_Fix_JD, Third_Edition_(2004)_Philadelphia:_Lippincott_William_and_Wilkins, p.137][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [trans-synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0099548) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_synapse](http://purl.obolibrary.org/obo/go#goslim_synapse) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [trans-synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0099548) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:0099548" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- Class: [trans-synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0099548) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000541" -- [trans-synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0099548) EquivalentTo [trans-synaptic signaling](http://purl.obolibrary.org/obo/GO_0099537) and ([process has causal agent](http://purl.obolibrary.org/obo/RO_0002608) some [CHEBI_16480](http://purl.obolibrary.org/obo/CHEBI_16480)) +- [ureteric bud](http://purl.obolibrary.org/obo/UBERON_0000084) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [trans-synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0099548) SubClassOf [trans-synaptic signaling by soluble gas](http://purl.obolibrary.org/obo/GO_0099543) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [trans-synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0099548) SubClassOf [synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0099163) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000541" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543" -### trans-synaptic signaling by nitric oxide, modulating synaptic transmission `http://purl.obolibrary.org/obo/GO_0099555` -#### Removed -- [trans-synaptic signaling by nitric oxide, modulating synaptic transmission](http://purl.obolibrary.org/obo/GO_0099555) [label](http://www.w3.org/2000/01/rdf-schema#label) "trans-synaptic signaling by nitric oxide, modulating synaptic transmission" +- [ureteric bud](http://purl.obolibrary.org/obo/UBERON_0000084) SubClassOf [meso-epithelium](http://purl.obolibrary.org/obo/UBERON_0012275) -- [trans-synaptic signaling by nitric oxide, modulating synaptic transmission](http://purl.obolibrary.org/obo/GO_0099555) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_synapse](http://purl.obolibrary.org/obo/go#goslim_synapse) -- [trans-synaptic signaling by nitric oxide, modulating synaptic transmission](http://purl.obolibrary.org/obo/GO_0099555) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua." -- [trans-synaptic signaling by nitric oxide, modulating synaptic transmission](http://purl.obolibrary.org/obo/GO_0099555) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" +### urethra `http://purl.obolibrary.org/obo/UBERON_0000057` +#### Removed +- [urethra](http://purl.obolibrary.org/obo/UBERON_0000057) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "urethral" -- [trans-synaptic signaling by nitric oxide, modulating synaptic transmission](http://purl.obolibrary.org/obo/GO_0099555) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Cell-cell signaling between presynapse and postsynapse, via the release and reception of nitric oxide molecules, that modulates the synaptic transmission properties of the synapse." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:dos" +- [urethra](http://purl.obolibrary.org/obo/UBERON_0000057) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In human males, the urethra travels through the penis, and carries semen as well as urine. In females, the urethra is shorter and emerges above the vaginal opening." -- [trans-synaptic signaling by nitric oxide, modulating synaptic transmission](http://purl.obolibrary.org/obo/GO_0099555) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:0099555" +- [urethra](http://purl.obolibrary.org/obo/UBERON_0000057) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [primitive urogenital sinus](http://purl.obolibrary.org/obo/UBERON_0000164) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "pelvic part of UG sinus gives rise to prostatic and membranous parts of urethra" -- Class: [trans-synaptic signaling by nitric oxide, modulating synaptic transmission](http://purl.obolibrary.org/obo/GO_0099555) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia" -- [trans-synaptic signaling by nitric oxide, modulating synaptic transmission](http://purl.obolibrary.org/obo/GO_0099555) EquivalentTo [trans-synaptic signaling](http://purl.obolibrary.org/obo/GO_0099537) and ([regulates](http://purl.obolibrary.org/obo/RO_0002211) some [chemical synaptic transmission](http://purl.obolibrary.org/obo/GO_0007268)) and ([process has causal agent](http://purl.obolibrary.org/obo/RO_0002608) some [CHEBI_16480](http://purl.obolibrary.org/obo/CHEBI_16480)) +#### Added +- [urethra](http://purl.obolibrary.org/obo/UBERON_0000057) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [primitive urogenital sinus](http://purl.obolibrary.org/obo/UBERON_0000164) -- [trans-synaptic signaling by nitric oxide, modulating synaptic transmission](http://purl.obolibrary.org/obo/GO_0099555) SubClassOf [trans-synaptic signaling by nitric oxide](http://purl.obolibrary.org/obo/GO_0099548) -- [trans-synaptic signaling by nitric oxide, modulating synaptic transmission](http://purl.obolibrary.org/obo/GO_0099555) SubClassOf [trans-synaptic signaling by soluble gas, modulating synaptic transmission](http://purl.obolibrary.org/obo/GO_0099554) +### urethra mesenchymal layer `http://purl.obolibrary.org/obo/UBERON_0015418` +#### Added +- [urethra mesenchymal layer](http://purl.obolibrary.org/obo/UBERON_0015418) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### trans-synaptic signaling by soluble gas `http://purl.obolibrary.org/obo/GO_0099543` -#### Removed -- [trans-synaptic signaling by soluble gas](http://purl.obolibrary.org/obo/GO_0099543) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" +### urethra muscle tissue `http://purl.obolibrary.org/obo/UBERON_0003829` -- [trans-synaptic signaling by soluble gas](http://purl.obolibrary.org/obo/GO_0099543) [label](http://www.w3.org/2000/01/rdf-schema#label) "trans-synaptic signaling by soluble gas" +#### Added +- [urethra muscle tissue](http://purl.obolibrary.org/obo/UBERON_0003829) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -- [trans-synaptic signaling by soluble gas](http://purl.obolibrary.org/obo/GO_0099543) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Cell-cell signaling between presynapse and postsynapse mediated by a soluble gas ligand crossing the synaptic cleft." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:dos" -- [trans-synaptic signaling by soluble gas](http://purl.obolibrary.org/obo/GO_0099543) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:0099543" +### urethral gland `http://purl.obolibrary.org/obo/UBERON_0001338` +#### Removed +- [urethral gland](http://purl.obolibrary.org/obo/UBERON_0001338) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "NCIT:C12339 paraurethral gland belongs here" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "NCIT" -- [trans-synaptic signaling by soluble gas](http://purl.obolibrary.org/obo/GO_0099543) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_synapse](http://purl.obolibrary.org/obo/go#goslim_synapse) +#### Added +- [urethral gland](http://purl.obolibrary.org/obo/UBERON_0001338) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -- Class: [trans-synaptic signaling by soluble gas](http://purl.obolibrary.org/obo/GO_0099543) -- [trans-synaptic signaling by soluble gas](http://purl.obolibrary.org/obo/GO_0099543) SubClassOf [trans-synaptic signaling](http://purl.obolibrary.org/obo/GO_0099537) +### urethral meatus `http://purl.obolibrary.org/obo/UBERON_0012240` +#### Added +- [urethral meatus](http://purl.obolibrary.org/obo/UBERON_0012240) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### trans-synaptic signaling by soluble gas, modulating synaptic transmission `http://purl.obolibrary.org/obo/GO_0099554` +### urinary bladder `http://purl.obolibrary.org/obo/UBERON_0001255` #### Removed -- [trans-synaptic signaling by soluble gas, modulating synaptic transmission](http://purl.obolibrary.org/obo/GO_0099554) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_synapse](http://purl.obolibrary.org/obo/go#goslim_synapse) - -- [trans-synaptic signaling by soluble gas, modulating synaptic transmission](http://purl.obolibrary.org/obo/GO_0099554) [id](http://www.geneontology.org/formats/oboInOwl#id) "GO:0099554" - -- [trans-synaptic signaling by soluble gas, modulating synaptic transmission](http://purl.obolibrary.org/obo/GO_0099554) [label](http://www.w3.org/2000/01/rdf-schema#label) "trans-synaptic signaling by soluble gas, modulating synaptic transmission" +- [urinary bladder](http://purl.obolibrary.org/obo/UBERON_0001255) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The urinary bladder evolved in tetrapods. Birds to not possess a true urinary bladder, although Palaeognathae have an undifferentiated cloacal outpocketing that serves a similar function[https://github.com/obophenotype/uberon/issues/454]" -- [trans-synaptic signaling by soluble gas, modulating synaptic transmission](http://purl.obolibrary.org/obo/GO_0099554) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Note that this term was created for the SynGO project, and will be obsoleted when the SynGO annotations are made in Noctua." +- [urinary bladder](http://purl.obolibrary.org/obo/UBERON_0001255) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A saccular organ in which urine accumulates before discharge from the body. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [trans-synaptic signaling by soluble gas, modulating synaptic transmission](http://purl.obolibrary.org/obo/GO_0099554) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "biological_process" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [trans-synaptic signaling by soluble gas, modulating synaptic transmission](http://purl.obolibrary.org/obo/GO_0099554) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Cell-cell signaling between presynapse and postsynapse, via the release and reception of gaseous molecules, that modulates the synaptic transmission properties of the synapse." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:dos" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- Class: [trans-synaptic signaling by soluble gas, modulating synaptic transmission](http://purl.obolibrary.org/obo/GO_0099554) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000740" -- [trans-synaptic signaling by soluble gas, modulating synaptic transmission](http://purl.obolibrary.org/obo/GO_0099554) SubClassOf [trans-synaptic signaling by soluble gas](http://purl.obolibrary.org/obo/GO_0099543) +- [urinary bladder](http://purl.obolibrary.org/obo/UBERON_0001255) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical structure which consists of a membranous sac used to temporarily store urine until it is excreted from the body.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000623" -- [trans-synaptic signaling by soluble gas, modulating synaptic transmission](http://purl.obolibrary.org/obo/GO_0099554) SubClassOf [trans-synaptic signaling, modulating synaptic transmission](http://purl.obolibrary.org/obo/GO_0099550) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" -### transferase activity `http://purl.obolibrary.org/obo/GO_0016740` -#### Removed -- [transferase activity](http://purl.obolibrary.org/obo/GO_0016740) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) +- [urinary bladder](http://purl.obolibrary.org/obo/UBERON_0001255) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In tetrapods, the urinary bladder arises as an outpocketing of the cloaca. (...) The tetrapod urinary bladder appears first among amphibians and is present in Sphenodon, turtles, most lizards, ostriches among birds, and all mammals.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [transferase activity](http://purl.obolibrary.org/obo/GO_0016740) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### transit amplifying cell `http://purl.obolibrary.org/obo/CL_0009010` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.577-78" -#### Added -- [transit amplifying cell](http://purl.obolibrary.org/obo/CL_0009010) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000740" +- [urinary bladder](http://purl.obolibrary.org/obo/UBERON_0001255) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "vesical" -### transit amplifying cell of colon `http://purl.obolibrary.org/obo/CL_0009011` +- [urinary bladder](http://purl.obolibrary.org/obo/UBERON_0001255) [never_in_taxon](http://purl.obolibrary.org/obo/RO_0002161) [Aves](http://purl.obolibrary.org/obo/NCBITaxon_8782) + - [editor](http://www.geneontology.org/formats/oboInOwl#editor) "https://orcid.org/0000-0003-3308-6245" -#### Added -- [transit amplifying cell of colon](http://purl.obolibrary.org/obo/CL_0009011) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "https://github.com/obophenotype/uberon/issues/454" + - [id](http://www.geneontology.org/formats/oboInOwl#id) "GOTAX:0010073" -### transit amplifying cell of small intestine `http://purl.obolibrary.org/obo/CL_0009012` +- [urinary bladder](http://purl.obolibrary.org/obo/UBERON_0001255) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [primitive urogenital sinus](http://purl.obolibrary.org/obo/UBERON_0000164) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "upper part of UG sinus" #### Added -- [transit amplifying cell of small intestine](http://purl.obolibrary.org/obo/CL_0009012) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [urinary bladder](http://purl.obolibrary.org/obo/UBERON_0001255) SubClassOf [develops from](http://purl.obolibrary.org/obo/RO_0002202) some [primitive urogenital sinus](http://purl.obolibrary.org/obo/UBERON_0000164) -### transitional stage B cell `http://purl.obolibrary.org/obo/CL_0000818` +### urinary bladder urothelium `http://purl.obolibrary.org/obo/UBERON_0004645` +#### Removed +- [urinary bladder urothelium](http://purl.obolibrary.org/obo/UBERON_0004645) [UBPROP_0000010](http://purl.obolibrary.org/obo/UBPROP_0000010) "5-7 cell layers thick in contracted bladder, 2-3 cells thick in distended bladder; lines renal pelvis, ureters, bladder, most of urethra but not distal urethra" + +- [urinary bladder urothelium](http://purl.obolibrary.org/obo/UBERON_0004645) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NCIT:C13318" #### Added -- [transitional stage B cell](http://purl.obolibrary.org/obo/CL_0000818) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [urinary bladder urothelium](http://purl.obolibrary.org/obo/UBERON_0004645) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) +- [urinary bladder urothelium](http://purl.obolibrary.org/obo/UBERON_0004645) SubClassOf [meso-epithelium](http://purl.obolibrary.org/obo/UBERON_0012275) -### transitively anteriorly connected to `http://purl.obolibrary.org/obo/uberon/core#transitively_anteriorly_connected_to` + +### urine `http://purl.obolibrary.org/obo/UBERON_0001088` #### Removed -- [transitively anteriorly connected to](http://purl.obolibrary.org/obo/uberon/core#transitively_anteriorly_connected_to) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" +- [urine](http://purl.obolibrary.org/obo/UBERON_0001088) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "kidney excreta from some taxa (e.g. in aves) may not be liquid" -#### Added -- [transitively anteriorly connected to](http://purl.obolibrary.org/obo/uberon/core#transitively_anteriorly_connected_to) [see also](http://www.w3.org/2000/01/rdf-schema#seeAlso) "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) -### transitively distally connected to `http://purl.obolibrary.org/obo/uberon/core#transitively_distally_connected_to` +### url `http://www.geneontology.org/formats/oboInOwl#url` #### Removed -- [transitively distally connected to](http://purl.obolibrary.org/obo/uberon/core#transitively_distally_connected_to) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" +- AnnotationProperty: [url](http://www.geneontology.org/formats/oboInOwl#url) -#### Added -- [transitively distally connected to](http://purl.obolibrary.org/obo/uberon/core#transitively_distally_connected_to) [see also](http://www.w3.org/2000/01/rdf-schema#seeAlso) "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) -### transitively proximally connected to `http://purl.obolibrary.org/obo/uberon/core#transitively_proximally_connected_to` +### urogenital fold `http://purl.obolibrary.org/obo/UBERON_0004876` #### Removed -- [transitively proximally connected to](http://purl.obolibrary.org/obo/uberon/core#transitively_proximally_connected_to) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" +- [urogenital fold](http://purl.obolibrary.org/obo/UBERON_0004876) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "Less commonly, urogenital fold refers to the fold in the mesonephros which is the precursor of e.g. the suspensory ligament of the ovary. This is the case in older versions of Gray's anatomy[WP]" -#### Added -- [transitively proximally connected to](http://purl.obolibrary.org/obo/uberon/core#transitively_proximally_connected_to) [see also](http://www.w3.org/2000/01/rdf-schema#seeAlso) "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern"^^[anyURI](http://www.w3.org/2001/XMLSchema#anyURI) -### translation `http://purl.obolibrary.org/obo/GO_0006412` +### urogenital sinus epithelium `http://purl.obolibrary.org/obo/UBERON_0004902` #### Removed -- [translation](http://purl.obolibrary.org/obo/GO_0006412) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) +- [urogenital sinus epithelium](http://purl.obolibrary.org/obo/UBERON_0004902) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "we follow EHDAA2 in dividing the UGS into epithelium and lumen" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EHDAA2" #### Added -- [translation](http://purl.obolibrary.org/obo/GO_0006412) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) +- [urogenital sinus epithelium](http://purl.obolibrary.org/obo/UBERON_0004902) SubClassOf [meso-epithelium](http://purl.obolibrary.org/obo/UBERON_0012275) + +- [urogenital sinus epithelium](http://purl.obolibrary.org/obo/UBERON_0004902) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) -### transport `http://purl.obolibrary.org/obo/GO_0006810` +### urogenital sinus mesenchyme `http://purl.obolibrary.org/obo/UBERON_0009845` #### Removed -- [transport](http://purl.obolibrary.org/obo/GO_0006810) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) +- [urogenital sinus mesenchyme](http://purl.obolibrary.org/obo/UBERON_0009845) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "Androgen receptor (AR) activation releases instructive signals from UGM that acts on UGS epithelium (UGE) to stimulate cell proliferation, form prostate ductal progenitors (prostatic buds), and regulate cell adhesion dynamics to permit prostatic bud outgrowth" -#### Added -- [transport](http://purl.obolibrary.org/obo/GO_0006810) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) -### transporter activity `http://purl.obolibrary.org/obo/GO_0005215` +### urokinase plasminogen activator surface receptor `http://purl.obolibrary.org/obo/PR_000001969` #### Removed -- [transporter activity](http://purl.obolibrary.org/obo/GO_0005215) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [prokaryote_subset](http://purl.obolibrary.org/obo/go#prokaryote_subset) +- [urokinase plasminogen activator surface receptor](http://purl.obolibrary.org/obo/PR_000001969) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [urokinase plasminogen activator surface receptor (human)](http://purl.obolibrary.org/obo/PR_Q03405) -#### Added -- [transporter activity](http://purl.obolibrary.org/obo/GO_0005215) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [goslim_prokaryote](http://purl.obolibrary.org/obo/go#goslim_prokaryote) -### transverse colon `http://purl.obolibrary.org/obo/UBERON_0001157` +### urorectal septum `http://purl.obolibrary.org/obo/UBERON_0005760` #### Removed -- [transverse colon](http://purl.obolibrary.org/obo/UBERON_0001157) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D044684" - -- [transverse colon](http://purl.obolibrary.org/obo/UBERON_0001157) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "colon transversum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Transverse_colon" +- [urorectal septum](http://purl.obolibrary.org/obo/UBERON_0005760) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In mammals the lowly monotremes still have a cloaca. Higher types have done away with this structure and have a separate anal outlet for the rectum. The monotreme cloaca shows the initiation of this subdivision. The cloaca has such includes only the distal part, roughly comparable to the proctodeum. The more proximal part is divided into (1) a large dorsal passage into which the intestine opens, the coprodeum, and (2) a ventral portion, the urodeum with which the bladder connects. (...) the development of the placental mammals recapitulates in many respects the phylogenetic story. In the sexually indifferent stage of placental mammal there is a cloaca. While the indifferent stage still persists, a septum develops, and extends out to the closing membrane. This divides the cloaca into two chambers: a coprodeum continuous with the gut above, and a urodeum or urogenital sinus below.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000018" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [transverse colon](http://purl.obolibrary.org/obo/UBERON_0001157) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "colon transversum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Transverse_colon" - -- [transverse colon](http://purl.obolibrary.org/obo/UBERON_0001157) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D044684" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.388-89 and Figure 300" - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +- [urorectal septum](http://purl.obolibrary.org/obo/UBERON_0005760) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "A ridge of mesoderm covered with endoderm that in the early developing embryo divides the endodermal cloaca into the urogenital sinus and the rectum. [TFD][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000018" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### trapezius muscle `http://purl.obolibrary.org/obo/UBERON_0002380` -#### Removed -- [trapezius muscle](http://purl.obolibrary.org/obo/UBERON_0002380) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "musculus trapezius" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Trapezius_muscle" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [trapezius muscle](http://purl.obolibrary.org/obo/UBERON_0002380) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "musculus trapezius" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/urorectal+septum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Trapezius_muscle" -### trigeminal ganglion `http://purl.obolibrary.org/obo/UBERON_0001675` +### urothelium `http://purl.obolibrary.org/obo/UBERON_0000365` #### Removed -- [trigeminal ganglion](http://purl.obolibrary.org/obo/UBERON_0001675) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ganglion semilunare" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Trigeminal_ganglion" +- [urothelium](http://purl.obolibrary.org/obo/UBERON_0000365) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NCIT:C13318" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [urothelium](http://purl.obolibrary.org/obo/UBERON_0000365) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "urothelial" -- [trigeminal ganglion](http://purl.obolibrary.org/obo/UBERON_0001675) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ganglion trigeminale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Trigeminal_ganglion" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001231" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### urothelium of ureter `http://purl.obolibrary.org/obo/UBERON_0001254` +#### Removed +- [urothelium of ureter](http://purl.obolibrary.org/obo/UBERON_0001254) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "MP treats ureter urothelium and ureter luminal urothelium as exact synonyms, yes MA treats these as distinct; see also: transitional epithelium vs urothelium" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MP" #### Added -- [trigeminal ganglion](http://purl.obolibrary.org/obo/UBERON_0001675) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ganglion semilunare" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Trigeminal_ganglion" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [urothelium of ureter](http://purl.obolibrary.org/obo/UBERON_0001254) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) -- [trigeminal ganglion](http://purl.obolibrary.org/obo/UBERON_0001675) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ganglion trigeminale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Trigeminal_ganglion" +- [urothelium of ureter](http://purl.obolibrary.org/obo/UBERON_0001254) SubClassOf [meso-epithelium](http://purl.obolibrary.org/obo/UBERON_0012275) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0001231" +### uterine cervix `http://purl.obolibrary.org/obo/UBERON_0000002` +#### Removed +- [uterine cervix](http://purl.obolibrary.org/obo/UBERON_0000002) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The evolution of mammals is associated with radical changes in their reproductive biology, particularly the structure and function of the female reproductive organs. These changes include the evolution of the uterus, cervix, vagina, placenta and specialized cell types associated with each of those structures.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001359" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### trigeminal nerve `http://purl.obolibrary.org/obo/UBERON_0001645` -#### Removed -- [trigeminal nerve](http://purl.obolibrary.org/obo/UBERON_0001645) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus trigeminus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Trigeminal_nerve" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [trigeminal nerve](http://purl.obolibrary.org/obo/UBERON_0001645) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus trigeminus [v]" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1098/rspb.2004.2848 Lynch VJ, Roth JJ, Takahashi K, Dunn CW, Nonaka DF, Stopper GF, Wagner GP, Adaptive evolution of HoxA-11 and HoxA-13 at the origin of the uterus in mammals. Proceedings of the Royal Society of London, Series B (2004)" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:50866" +- [uterine cervix](http://purl.obolibrary.org/obo/UBERON_0000002) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The narrow caudal end of the uterus that opens into the vagina. [TFD][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001359" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [trigeminal nerve](http://purl.obolibrary.org/obo/UBERON_0001645) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus trigeminus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Trigeminal_nerve" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [trigeminal nerve](http://purl.obolibrary.org/obo/UBERON_0001645) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus trigeminus [v]" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/uterine+cervix" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:50866" +- [uterine cervix](http://purl.obolibrary.org/obo/UBERON_0000002) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "cervical" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### trigeminal nerve fibers `http://purl.obolibrary.org/obo/UBERON_0003041` +### uterine tube infundibulum `http://purl.obolibrary.org/obo/UBERON_0003984` #### Removed -- [trigeminal nerve fibers](http://purl.obolibrary.org/obo/UBERON_0003041) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "fibrae nervi trigemini" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:607" +- [uterine tube infundibulum](http://purl.obolibrary.org/obo/UBERON_0003984) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The third part of the uterine tube is the infundibulum. It terminates with the ostium of Fallopian tube, surrounded by fimbriae, one of which is attached to the ovary[Wikipedia:Infundibulum_of_uterine_tube]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Infundibulum_of_uterine_tube" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - -#### Added -- [trigeminal nerve fibers](http://purl.obolibrary.org/obo/UBERON_0003041) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "fibrae nervi trigemini" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [uterine tube infundibulum](http://purl.obolibrary.org/obo/UBERON_0003984) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In mammals, the uterine tube infundibulum is part of the fallopian tube. In birds, where there is no fallopian tube, the uterine tube infundibulum is part of the oviduct." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://orcid.org/0000-0002-2825-0621" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:607" -### trigeminal nerve root `http://purl.obolibrary.org/obo/UBERON_0004673` +### uteroglobin `http://purl.obolibrary.org/obo/PR_000014505` #### Removed -- [trigeminal nerve root](http://purl.obolibrary.org/obo/UBERON_0004673) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "radix descendens nervi trigemini" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [uteroglobin](http://purl.obolibrary.org/obo/PR_000014505) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [uteroglobin (human)](http://purl.obolibrary.org/obo/PR_P11684) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0000192" -#### Added -- [trigeminal nerve root](http://purl.obolibrary.org/obo/UBERON_0004673) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "radix descendens nervi trigemini" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0000192" +### uterus `http://purl.obolibrary.org/obo/UBERON_0000995` +#### Removed +- [uterus](http://purl.obolibrary.org/obo/UBERON_0000995) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The hollow muscular organ in female mammals in which the blastocyst normally becomes embedded and in which the developing embryo and fetus is nourished. Its cavity opens into the vagina below and into a uterine tube on either side. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### trigeminal nuclear complex `http://purl.obolibrary.org/obo/UBERON_0007641` -#### Removed -- [trigeminal nuclear complex](http://purl.obolibrary.org/obo/UBERON_0007641) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nuclei trigemini" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Trigeminal_nerve_nuclei" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/uterus" -#### Added -- [trigeminal nuclear complex](http://purl.obolibrary.org/obo/UBERON_0007641) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D014278" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001137" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +- [uterus](http://purl.obolibrary.org/obo/UBERON_0000995) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "An infundibulum, uterine tube, uterus, and vagina also differentiate along the oviducts of eutherian mammals.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [trigeminal nuclear complex](http://purl.obolibrary.org/obo/UBERON_0007641) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nuclei trigemini" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Trigeminal_nerve_nuclei" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001137" -### trigone of urinary bladder `http://purl.obolibrary.org/obo/UBERON_0001257` -#### Removed -- [trigone of urinary bladder](http://purl.obolibrary.org/obo/UBERON_0001257) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "musculus trigoni vesicae profundus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.678" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [uterus](http://purl.obolibrary.org/obo/UBERON_0000995) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Most animals that lay eggs, such as birds and reptiles, have an oviduct instead of a uterus. In monotremes, mammals which lay eggs and include the platypus, either the term uterus or oviduct is used to describe the same organ, but the egg does not develop a placenta within the mother and thus does not receive further nourishment after formation and fertilization. Marsupials have two uteruses, each of which connect to a lateral vagina and which both use a third, middle 'vagina' which functions as the birth canal. Marsupial embryos form a choriovitelline 'placenta' (which can be thought of as something between a monotreme egg and a 'true' placenta), in which the egg's yolk sac supplies a large part of the embryo's nutrition but also attaches to the uterine wall and takes nutrients from the mother's bloodstream." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15910" +- [uterus](http://purl.obolibrary.org/obo/UBERON_0000995) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "Two uteruses usually form initially in a female fetus, and in placental mammals they may partially or completely fuse into a single uterus depending on the species. In many species with two uteruses, only one is functional. Humans and other higher primates such as chimpanzees, along with horses, usually have a single completely fused uterus, although in some individuals the uteruses may not have completely fused [Wikipedia:Uterus]" -- [trigone of urinary bladder](http://purl.obolibrary.org/obo/UBERON_0001257) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "trigonum vesicae urinariae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Trigone_of_urinary_bladder" +- [uterus](http://purl.obolibrary.org/obo/UBERON_0000995) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "uterine" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [trigone of urinary bladder](http://purl.obolibrary.org/obo/UBERON_0001257) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "trigonum vesicae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### uterus or analog `http://purl.obolibrary.org/obo/UBERON_0006834` +#### Removed +- [uterus or analog](http://purl.obolibrary.org/obo/UBERON_0006834) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004924" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15910" -#### Added -- [trigone of urinary bladder](http://purl.obolibrary.org/obo/UBERON_0001257) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "trigonum vesicae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### utricle of membranous labyrinth `http://purl.obolibrary.org/obo/UBERON_0001853` +#### Removed +- [utricle of membranous labyrinth](http://purl.obolibrary.org/obo/UBERON_0001853) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In gnathostomes, each membranous labyrinth has three semicircular ducts that connect with a chamber known as the utriculus.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15910" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.413-414" -- [trigone of urinary bladder](http://purl.obolibrary.org/obo/UBERON_0001257) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "trigonum vesicae urinariae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Trigone_of_urinary_bladder" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000289" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [utricle of membranous labyrinth](http://purl.obolibrary.org/obo/UBERON_0001853) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The portion of the membranous labyrinth of the ear into which the semicircular ducts find their outlet. [Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier, adapted_from_Dorian_AF][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [trigone of urinary bladder](http://purl.obolibrary.org/obo/UBERON_0001257) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "musculus trigoni vesicae profundus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:15910" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000289" -### trophoblast `http://purl.obolibrary.org/obo/UBERON_0000088` + +### uvea `http://purl.obolibrary.org/obo/UBERON_0001768` #### Removed -- [trophoblast](http://purl.obolibrary.org/obo/UBERON_0000088) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "trophoblastus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Trophoblast" +- [uvea](http://purl.obolibrary.org/obo/UBERON_0001768) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "uveal" + +#### Added +- [uvea](http://purl.obolibrary.org/obo/UBERON_0001768) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [uvea](http://purl.obolibrary.org/obo/UBERON_0001768) SubClassOf [structure with developmental contribution from neural crest](http://purl.obolibrary.org/obo/UBERON_0010314) -- [trophoblast](http://purl.obolibrary.org/obo/UBERON_0000088) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "massa cellularis externa" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Trophoblast" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### vagal neural crest `http://purl.obolibrary.org/obo/UBERON_0005428` +#### Removed +- [vagal neural crest](http://purl.obolibrary.org/obo/UBERON_0005428) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [trophoblast](http://purl.obolibrary.org/obo/UBERON_0000088) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "massa cellularis externa" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Trophoblast" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [trophoblast](http://purl.obolibrary.org/obo/UBERON_0000088) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "trophoblastus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Trophoblast" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001208" +- [vagal neural crest](http://purl.obolibrary.org/obo/UBERON_0005428) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -### trophoblast giant cell `http://purl.obolibrary.org/obo/CL_0002488` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -#### Added -- [trophoblast giant cell](http://purl.obolibrary.org/obo/CL_0002488) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000818" -### tuft cell of colon `http://purl.obolibrary.org/obo/CL_0009041` +- [vagal neural crest](http://purl.obolibrary.org/obo/UBERON_0005428) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In chicken fate mapping studies it was found to originate from neural crest residing between Somite 1-7 (S1-7); In mouse it is considered to be derived from rhombencephalic (post otic) neural crest cells and trunk neural crest cells (anterior to S5)" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "filemaps.com" #### Added -- [tuft cell of colon](http://purl.obolibrary.org/obo/CL_0009041) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [vagal neural crest](http://purl.obolibrary.org/obo/UBERON_0005428) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### tunica adventitia of blood vessel `http://purl.obolibrary.org/obo/UBERON_0005734` +### vagina `http://purl.obolibrary.org/obo/UBERON_0000996` #### Removed -- [tunica adventitia of blood vessel](http://purl.obolibrary.org/obo/UBERON_0005734) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tunica externa vasorum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Tunica_externa_(vessels)" +- [vagina](http://purl.obolibrary.org/obo/UBERON_0000996) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "vaginal" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [vagina](http://purl.obolibrary.org/obo/UBERON_0000996) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The genital canal in the female, leading from the opening of the vulva to the cervix of the uterus. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/vagina" -- [tunica adventitia of blood vessel](http://purl.obolibrary.org/obo/UBERON_0005734) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tunica adventitia vasorum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Tunica_externa_(vessels)" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [tunica adventitia of blood vessel](http://purl.obolibrary.org/obo/UBERON_0005734) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tunica externa vasorum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Tunica_externa_(vessels)" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001138" -- [tunica adventitia of blood vessel](http://purl.obolibrary.org/obo/UBERON_0005734) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tunica adventitia vasorum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Tunica_externa_(vessels)" +- [vagina](http://purl.obolibrary.org/obo/UBERON_0000996) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Organ with organ cavity which connects the cervical canal of uterus to the vestibule of vagina.[FMA]" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "FMA" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-11-29" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "FMA:19949" -### tunica media `http://purl.obolibrary.org/obo/UBERON_0002522` -#### Removed -- [tunica media](http://purl.obolibrary.org/obo/UBERON_0002522) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tunica media vasorum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Tunica_media" +- [vagina](http://purl.obolibrary.org/obo/UBERON_0000996) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0002011" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [tunica media](http://purl.obolibrary.org/obo/UBERON_0002522) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tunica media vasorum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001138" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Tunica_media" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.688" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0002011" +- [vagina](http://purl.obolibrary.org/obo/UBERON_0000996) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "'The distal end of the oviducts differentiates as a vagina in Metatheria and Eutheria.' Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective, Third Edition (2001) Orlando Fla.: Harcourt College Publishers, p.688" -### tympanic cavity `http://purl.obolibrary.org/obo/UBERON_0004114` -#### Removed -- [tympanic cavity](http://purl.obolibrary.org/obo/UBERON_0004114) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cavitas tympani" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Tympanic_cavity" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### vagina orifice `http://purl.obolibrary.org/obo/UBERON_0012317` #### Added -- [tympanic cavity](http://purl.obolibrary.org/obo/UBERON_0004114) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cavitas tympani" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [vagina orifice](http://purl.obolibrary.org/obo/UBERON_0012317) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Tympanic_cavity" +### vagina sebaceous gland `http://purl.obolibrary.org/obo/UBERON_0003485` -### tympanic membrane `http://purl.obolibrary.org/obo/UBERON_0002364` -#### Removed -- [tympanic membrane](http://purl.obolibrary.org/obo/UBERON_0002364) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "paries membranaceus cavi tympani" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9595" +#### Added +- [vagina sebaceous gland](http://purl.obolibrary.org/obo/UBERON_0003485) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### vagina smooth muscle `http://purl.obolibrary.org/obo/UBERON_0004223` +#### Removed +- [vagina smooth muscle](http://purl.obolibrary.org/obo/UBERON_0004223) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:30997" -#### Added -- [tympanic membrane](http://purl.obolibrary.org/obo/UBERON_0002364) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "paries membranaceus cavi tympani" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9595" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### vaginal fluid `http://purl.obolibrary.org/obo/UBERON_0036243` +#### Removed +- [vaginal fluid](http://purl.obolibrary.org/obo/UBERON_0036243) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0003084" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -### type B pancreatic cell `http://purl.obolibrary.org/obo/CL_0000169` + - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) -#### Added -- [type B pancreatic cell](http://purl.obolibrary.org/obo/CL_0000169) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### type D enteroendocrine cell `http://purl.obolibrary.org/obo/CL_0000502` +### vaginal sphincter `http://purl.obolibrary.org/obo/UBERON_0012487` #### Added -- [type D enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000502) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [vaginal sphincter](http://purl.obolibrary.org/obo/UBERON_0012487) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### type EC enteroendocrine cell `http://purl.obolibrary.org/obo/CL_0000577` +### vagus nerve `http://purl.obolibrary.org/obo/UBERON_0001759` +#### Removed +- [vagus nerve](http://purl.obolibrary.org/obo/UBERON_0001759) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Nerve consisting of branchiomotor and visceral efferent fibers which branch and innervate the smooth muscles and glands of the heart, lungs, esophagus, and stomach as well as some throat muscles. Sensory fibers supply mucosa of the mouth and pharynx.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -#### Added -- [type EC enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000577) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010475" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### type G enteroendocrine cell `http://purl.obolibrary.org/obo/CL_0000508` +- [vagus nerve](http://purl.obolibrary.org/obo/UBERON_0001759) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [type G enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000508) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625" -### type I NK T cell `http://purl.obolibrary.org/obo/CL_0000921` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [type I NK T cell](http://purl.obolibrary.org/obo/CL_0000921) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000737" +- [vagus nerve](http://purl.obolibrary.org/obo/UBERON_0001759) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [basal plate metencephalon](http://purl.obolibrary.org/obo/UBERON_0005239) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "motor" -### type I enteroendocrine cell `http://purl.obolibrary.org/obo/CL_0002277` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia" #### Added -- [type I enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0002277) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) - +- [vagus nerve](http://purl.obolibrary.org/obo/UBERON_0001759) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [basal plate metencephalon](http://purl.obolibrary.org/obo/UBERON_0005239) -### type I pneumocyte `http://purl.obolibrary.org/obo/CL_0002062` -#### Added -- [type I pneumocyte](http://purl.obolibrary.org/obo/CL_0002062) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### valve `http://purl.obolibrary.org/obo/UBERON_0003978` +#### Removed +- [valve](http://purl.obolibrary.org/obo/UBERON_0003978) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "valvular" -### type II NK T cell `http://purl.obolibrary.org/obo/CL_0000922` -#### Added -- [type II NK T cell](http://purl.obolibrary.org/obo/CL_0000922) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### vas deferens `http://purl.obolibrary.org/obo/UBERON_0001000` +#### Removed +- [vas deferens](http://purl.obolibrary.org/obo/UBERON_0001000) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Most vertebrates have some form of duct to transfer the sperm from the testes to the urethra. In cartilaginous fish and amphibians, sperm is carried through the archinephric duct, which also partially helps to transport urine from the kidneys. In teleosts, there is a distinct sperm duct, separate from the ureters, and often called the vas deferens, although probably not truly homologous with that in humans. In cartilaginous fishes, the part of the archinephric duct closest to the testis is coiled up to form an epididymis. Below this are a number of small glands secreting components of the seminal fluid. The final portion of the duct also receives ducts from the kidneys in most species. In amniotes, however, the archinephric duct has become a true vas deferens, and is used only for conducting sperm, never urine. As in cartilaginous fish, the upper part of the duct forms the epididymis. In many species, the vas deferens ends in a small sac for storing sperm. The only vertebrates to lack any structure resembling a vas deferens are the primitive jawless fishes, which release sperm directly into the body cavity, and then into the surrounding water through a simple opening in the body wall." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" +- [vas deferens](http://purl.obolibrary.org/obo/UBERON_0001000) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The continuation of the archinephric duct, now called the deferent duct, extends caudally to the cloaca or to the part of the mammalian urethra that is derived from the cloaca.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.670" -### type II pneumocyte `http://purl.obolibrary.org/obo/CL_0002063` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [type II pneumocyte](http://purl.obolibrary.org/obo/CL_0002063) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### type L enteroendocrine cell `http://purl.obolibrary.org/obo/CL_0002279` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001135" -#### Added -- [type L enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0002279) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### type N enteroendocrine cell `http://purl.obolibrary.org/obo/CL_0002280` +### vasa recta ascending limb `http://purl.obolibrary.org/obo/UBERON_0009091` +#### Removed +- [vasa recta ascending limb](http://purl.obolibrary.org/obo/UBERON_0009091) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta parallel to the ascending limb" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "CL" #### Added -- [type N enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0002280) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) - +- [vasa recta ascending limb](http://purl.obolibrary.org/obo/UBERON_0009091) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### umbilical artery `http://purl.obolibrary.org/obo/UBERON_0001310` -#### Removed -- [umbilical artery](http://purl.obolibrary.org/obo/UBERON_0001310) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "a. umbilicalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Umbilical_artery" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### vasa recta cell `http://purl.obolibrary.org/obo/CL_1001036` #### Added -- [umbilical artery](http://purl.obolibrary.org/obo/UBERON_0001310) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "a. umbilicalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [vasa recta cell](http://purl.obolibrary.org/obo/CL_1001036) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cell that is part of a vasa recta." + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:12529271" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Umbilical_artery" + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:24381184" -### umbilical cord `http://purl.obolibrary.org/obo/UBERON_0002331` +### vasa recta descending limb `http://purl.obolibrary.org/obo/UBERON_0009202` #### Removed -- [umbilical cord](http://purl.obolibrary.org/obo/UBERON_0002331) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "funiculus umbilicalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MP:0012134" +- [vasa recta descending limb](http://purl.obolibrary.org/obo/UBERON_0009202) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "This class was created in order to align KUPO with CL. The original class was undefined, and the intended meaning is not clear, may be obsoleted in future. The vasa recta is parallel to the loop of Henles, this may refer to the portion of the vasa recta parallel to the descending limb" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "CL" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +#### Added +- [vasa recta descending limb](http://purl.obolibrary.org/obo/UBERON_0009202) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -- [umbilical cord](http://purl.obolibrary.org/obo/UBERON_0002331) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "chorda umbilicalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MP:0012134" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### vascular endothelial growth factor receptor 2 `http://purl.obolibrary.org/obo/PR_000002112` +#### Removed +- [vascular endothelial growth factor receptor 2](http://purl.obolibrary.org/obo/PR_000002112) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [vascular endothelial growth factor receptor 2 (human)](http://purl.obolibrary.org/obo/PR_P35968) -- [umbilical cord](http://purl.obolibrary.org/obo/UBERON_0002331) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "funiculus umbilicalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Umbilical_cord" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [umbilical cord](http://purl.obolibrary.org/obo/UBERON_0002331) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "chorda umbilicalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MP:0012134" +### vascular plexus `http://purl.obolibrary.org/obo/UBERON_0005629` +#### Removed +- [vascular plexus](http://purl.obolibrary.org/obo/UBERON_0005629) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "In a vascular plexus, the contents of the vessels mix. A plexus allows blood to flow via multiple routes. If one branch of the plexus is obstructed, the blood may flow via the open branches[Wikipedia:Plexus#Circulatory_system]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Plexus#Circulatory_system" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -- [umbilical cord](http://purl.obolibrary.org/obo/UBERON_0002331) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "funiculus umbilicalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Umbilical_cord" +### vascular system `http://purl.obolibrary.org/obo/UBERON_0007798` +#### Removed +- [vascular system](http://purl.obolibrary.org/obo/UBERON_0007798) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ncithesaurus:Vascular_System" -- [umbilical cord](http://purl.obolibrary.org/obo/UBERON_0002331) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "funiculus umbilicalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MP:0012134" +- [vascular system](http://purl.obolibrary.org/obo/UBERON_0007798) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "MA" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### umbilical vein `http://purl.obolibrary.org/obo/UBERON_0002066` +### vasculature `http://purl.obolibrary.org/obo/UBERON_0002049` #### Removed -- [umbilical vein](http://purl.obolibrary.org/obo/UBERON_0002066) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena umbilicalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Umbilical_vein" +- [vasculature](http://purl.obolibrary.org/obo/UBERON_0002049) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "vascular" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [umbilical vein](http://purl.obolibrary.org/obo/UBERON_0002066) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena umbilicalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Umbilical_vein" +### vasculature of eye `http://purl.obolibrary.org/obo/UBERON_0002203` +#### Removed +- [vasculature of eye](http://purl.obolibrary.org/obo/UBERON_0002203) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "not part of the eye in ZFA. Note this changed to a blood vessel in ZFA" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "ZFA" -### undifferentiated genital tubercle `http://purl.obolibrary.org/obo/UBERON_0005876` + +### vasculature of liver `http://purl.obolibrary.org/obo/UBERON_0006877` #### Removed -- [undifferentiated genital tubercle](http://purl.obolibrary.org/obo/UBERON_0005876) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tuberculum phallicum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Genital_tubercle" +- [vasculature of liver](http://purl.obolibrary.org/obo/UBERON_0006877) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "the EHDAA2 term and the FMA term may not be exact equivalents - check" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EHDAA2" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [undifferentiated genital tubercle](http://purl.obolibrary.org/obo/UBERON_0005876) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tuberculum genitale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Genital_tubercle" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### vasculature of respiratory integument `http://purl.obolibrary.org/obo/UBERON_3010200` +#### Removed +- [vasculature of respiratory integument](http://purl.obolibrary.org/obo/UBERON_3010200) [UBPROP_0000004](http://purl.obolibrary.org/obo/UBPROP_0000004) "This class was sourced from an external ontology (amphibian_anatomy). Its definitions, naming conventions and relationships may need to be checked for compatibility with uberon" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://purl.obolibrary.org/obo/aao.owl" -#### Added -- [undifferentiated genital tubercle](http://purl.obolibrary.org/obo/UBERON_0005876) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tuberculum phallicum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Genital_tubercle" -- [undifferentiated genital tubercle](http://purl.obolibrary.org/obo/UBERON_0005876) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tuberculum genitale" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### vasculature of retina `http://purl.obolibrary.org/obo/UBERON_0004864` +#### Removed +- [vasculature of retina](http://purl.obolibrary.org/obo/UBERON_0004864) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "XAO:0004153" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Genital_tubercle" +- [vasculature of retina](http://purl.obolibrary.org/obo/UBERON_0004864) [never_in_taxon](http://purl.obolibrary.org/obo/RO_0002161) [Aves](http://purl.obolibrary.org/obo/NCBITaxon_8782) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:21622558" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:2772405" -### unswitched memory B cell `http://purl.obolibrary.org/obo/CL_0000970` + - [submitter](http://www.geneontology.org/formats/oboInOwl#submitter) "michaelerice" -#### Added -- [unswitched memory B cell](http://purl.obolibrary.org/obo/CL_0000970) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### upper lip `http://purl.obolibrary.org/obo/UBERON_0001834` +### vein `http://purl.obolibrary.org/obo/UBERON_0001638` #### Removed -- [upper lip](http://purl.obolibrary.org/obo/UBERON_0001834) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "labium superius oris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [vein](http://purl.obolibrary.org/obo/UBERON_0001638) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001743" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Upper_lip" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [upper lip](http://purl.obolibrary.org/obo/UBERON_0001834) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "labium superius oris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Upper_lip" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)" -### ureteric bud `http://purl.obolibrary.org/obo/UBERON_0000084` -#### Removed -- [ureteric bud](http://purl.obolibrary.org/obo/UBERON_0000084) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "gemma ureterica" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ureteric_bud" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [vein](http://purl.obolibrary.org/obo/UBERON_0001638) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Part of the circulatory system composed of blood vessels which carry blood from other organs, tissues, and cells to the heart.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -- [ureteric bud](http://purl.obolibrary.org/obo/UBERON_0000084) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "diverticulum metanephricum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ureteric_bud" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010212" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -#### Added -- [ureteric bud](http://purl.obolibrary.org/obo/UBERON_0000084) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "gemma ureterica" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:BJB" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ureteric_bud" +- [vein](http://purl.obolibrary.org/obo/UBERON_0001638) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "venous" -- [ureteric bud](http://purl.obolibrary.org/obo/UBERON_0000084) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "diverticulum metanephricum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [vein](http://purl.obolibrary.org/obo/UBERON_0001638) [UBPROP_0000202](http://purl.obolibrary.org/obo/UBPROP_0000202) [FMA_63814](http://purl.obolibrary.org/obo/FMA_63814) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ureteric_bud" -### urethra smooth muscle layer `http://purl.obolibrary.org/obo/UBERON_0004219` +### vein of abdomen `http://purl.obolibrary.org/obo/UBERON_0013126` #### Removed -- [urethra smooth muscle layer](http://purl.obolibrary.org/obo/UBERON_0004219) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica muscularis urethrae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [vein of abdomen](http://purl.obolibrary.org/obo/UBERON_0013126) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "this class groups all veins that are in the abdomen. The term 'abdominal vein' may have specific meanings in different contexts. The lateral abdominal veins are present in fishes but usually merged or absent in tetrapods; in amphibians, the L&R abdominal veins merge into the ventral abdominal vein" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" - -#### Added -- [urethra smooth muscle layer](http://purl.obolibrary.org/obo/UBERON_0004219) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "tunica muscularis urethrae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### venous blood `http://purl.obolibrary.org/obo/UBERON_0013756` +#### Removed +- [venous blood](http://purl.obolibrary.org/obo/UBERON_0013756) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006187" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -### urethra urothelial cell `http://purl.obolibrary.org/obo/CL_1001430` + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -#### Added -- [urethra urothelial cell](http://purl.obolibrary.org/obo/CL_1001430) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) -### urethral artery `http://purl.obolibrary.org/obo/UBERON_0039355` -#### Removed -- [urethral artery](http://purl.obolibrary.org/obo/UBERON_0039355) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arteria urethralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "A12.2.15.042" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### venous dural sinus `http://purl.obolibrary.org/obo/UBERON_0005486` #### Added -- [urethral artery](http://purl.obolibrary.org/obo/UBERON_0039355) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arteria urethralis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "A12.2.15.042" +- [venous dural sinus](http://purl.obolibrary.org/obo/UBERON_0005486) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### urethral meatus `http://purl.obolibrary.org/obo/UBERON_0012240` +### venous system `http://purl.obolibrary.org/obo/UBERON_0004582` #### Removed -- [urethral meatus](http://purl.obolibrary.org/obo/UBERON_0012240) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "orificium urethrae externum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [venous system](http://purl.obolibrary.org/obo/UBERON_0004582) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [urethral meatus](http://purl.obolibrary.org/obo/UBERON_0012240) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "orificium urethræ externum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [urethral meatus](http://purl.obolibrary.org/obo/UBERON_0012240) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "meatus urinarius" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -#### Added -- [urethral meatus](http://purl.obolibrary.org/obo/UBERON_0012240) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "orificium urethræ externum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000277" -- [urethral meatus](http://purl.obolibrary.org/obo/UBERON_0012240) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "meatus urinarius" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005)" -- [urethral meatus](http://purl.obolibrary.org/obo/UBERON_0012240) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "orificium urethrae externum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### urinary bladder `http://purl.obolibrary.org/obo/UBERON_0001255` +### venous valve `http://purl.obolibrary.org/obo/UBERON_0006675` #### Removed -- [urinary bladder](http://purl.obolibrary.org/obo/UBERON_0001255) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vesica urinaria" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Urinary_bladder" +- [venous valve](http://purl.obolibrary.org/obo/UBERON_0006675) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D055422" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" #### Added -- [urinary bladder](http://purl.obolibrary.org/obo/UBERON_0001255) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vesica urinaria" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Urinary_bladder" +- [venous valve](http://purl.obolibrary.org/obo/UBERON_0006675) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### ventral horn of spinal cord `http://purl.obolibrary.org/obo/UBERON_0002257` +#### Removed +- [ventral horn of spinal cord](http://purl.obolibrary.org/obo/UBERON_0002257) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The anterior horn of the spinal cord (or anterior cornu, or anterior column, or ventral horn) is the ventral (front) grey matter section of the spinal cord. The anterior horn contains motor neurons that affect the axial muscles while the posterior horn receives information regarding touch and sensation. The anterior horn is where the cell bodies of alpha motorneurons are located[Wikipedia:Anterior_horn_of_spinal_cord]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Anterior_horn_of_spinal_cord" -### urorectal septum `http://purl.obolibrary.org/obo/UBERON_0005760` + + +### ventral mesentery `http://purl.obolibrary.org/obo/UBERON_0009668` #### Removed -- [urorectal septum](http://purl.obolibrary.org/obo/UBERON_0005760) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "septum urorectale" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [ventral mesentery](http://purl.obolibrary.org/obo/UBERON_0009668) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "degenerates during development except foregut portion" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Urorectal_septum" -#### Added -- [urorectal septum](http://purl.obolibrary.org/obo/UBERON_0005760) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "septum urorectale" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Urorectal_septum" +### ventral mesogastrium `http://purl.obolibrary.org/obo/UBERON_0005626` +#### Removed +- [ventral mesogastrium](http://purl.obolibrary.org/obo/UBERON_0005626) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The mesentery that originates from the ventral side of the peritoneal cavity.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005133" -### urothelial cell `http://purl.obolibrary.org/obo/CL_0000731` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -#### Added -- [urothelial cell](http://purl.obolibrary.org/obo/CL_0000731) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" +- [ventral mesogastrium](http://purl.obolibrary.org/obo/UBERON_0005626) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The ventral sheet of the primitive mesentery that encloses the stomach. The lesser omentum develops from the ventral mesogastrium. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### uterine cervix `http://purl.obolibrary.org/obo/UBERON_0000002` -#### Removed -- [uterine cervix](http://purl.obolibrary.org/obo/UBERON_0000002) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cervix uteri" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:29927" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [uterine cervix](http://purl.obolibrary.org/obo/UBERON_0000002) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "canalis cervicis uteri" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:17740" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/mesogastrium" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000351" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [uterine cervix](http://purl.obolibrary.org/obo/UBERON_0000002) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "canalis cervicis uteri" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:17740" +### ventral pancreas `http://purl.obolibrary.org/obo/UBERON_0009709` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +#### Added +- [ventral pancreas](http://purl.obolibrary.org/obo/UBERON_0009709) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) -- [uterine cervix](http://purl.obolibrary.org/obo/UBERON_0000002) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cervix uteri" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:29927" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### ventral pancreatic bud `http://purl.obolibrary.org/obo/UBERON_0003924` +#### Removed +- [ventral pancreatic bud](http://purl.obolibrary.org/obo/UBERON_0003924) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "The ventral pancreatic bud becomes the head and uncinate process, and comes from the hepatic diverticulum[WP]" +- [ventral pancreatic bud](http://purl.obolibrary.org/obo/UBERON_0003924) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "the ventral pancreas and liver are derived from a common precursor cell population[PMID:16417468]. TODO - add this relationship." -### uterine resident macrophage `http://purl.obolibrary.org/obo/CL_4033064` +- [ventral pancreatic bud](http://purl.obolibrary.org/obo/UBERON_0003924) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In chick, Xenopus laevis, and the teleost fish Medaka, the pancreas develops from three buds that emerge from the gut tube, two from its ventral aspect, and one from its dorsal aspect. In mouse, although there are initially three buds that arise from the gut tube at the point of contact between the endoderm and the vasculature, the pancreas develops from only two of these buds, one dorsal and one ventral. (...) In this study, we use a transgenic zebrafish line (...). We provide evidence for the existence of two distinct pancreatic anlagen - a ventral anterior bud and a dorsal posterior bud - that join to form the definitive pancreas (reference 1); The pancreas develops from the fusion of distinct endoderm-derived dorsal and ventral diverticula. In humans, by day 35 of development, the ventral pancreatic bud begins to migrate backwards and comes into contact and eventually fuses with the dorsal pancreatic bud during the sixth week of development (reference 2).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [uterine resident macrophage](http://purl.obolibrary.org/obo/CL_4033064) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Uterine macrophages are reported to be evenly distributed throughout the endometrial stroma but with aggregations observed close to the lumen of superficial secretory glands." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36113384" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [uterine resident macrophage](http://purl.obolibrary.org/obo/CL_4033064) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "uterine macrophage" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36113384" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [uterine resident macrophage](http://purl.obolibrary.org/obo/CL_4033064) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A tissue-resident macrophage that is part of the uterus." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36113384" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001429" -- [uterine resident macrophage](http://purl.obolibrary.org/obo/CL_4033064) [label](http://www.w3.org/2000/01/rdf-schema#label) "uterine resident macrophage" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1016/S0012-1606(03)00308-7 Field HA, Dong PD, Beis D, Stainier DY, Formation of the digestive system in zebrafish. II. Pancreas morphogenesis. Developmental Biology (2003), DOI:10.2337/diabetes.49.2.225 Polak M, Bouchareb-Banaei L, Scharfmann R, Czernichow P, Early pattern of differentiation in the human pancreas. Diabetes (2000)" -- [uterine resident macrophage](http://purl.obolibrary.org/obo/CL_4033064) [date](http://purl.org/dc/terms/date) "2024-01-08T16:05:09Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -- [uterine resident macrophage](http://purl.obolibrary.org/obo/CL_4033064) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) -- Class: [uterine resident macrophage](http://purl.obolibrary.org/obo/CL_4033064) +### ventral pancreatic duct `http://purl.obolibrary.org/obo/UBERON_0001064` +#### Removed +- [ventral pancreatic duct](http://purl.obolibrary.org/obo/UBERON_0001064) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "These data show that ducts within the zebrafish pancreas originally arise in situ from isolated progenitor cells rather than arising from reiterative branching of the pancreatic epithelium. This process of pancreatic duct formation in zebrafish may be analogous to the mechanism of duct formation in the mammalian mammary and salivary glands. (...) A related mechanism of duct formation has also been proposed to occur within the mammalian pancreatic epithelium.[uncertain][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -- [uterine resident macrophage](http://purl.obolibrary.org/obo/CL_4033064) EquivalentTo [tissue-resident macrophage](http://purl.obolibrary.org/obo/CL_0000864) and ([part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [uterus](http://purl.obolibrary.org/obo/UBERON_0000995)) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [uterine resident macrophage](http://purl.obolibrary.org/obo/CL_4033064) SubClassOf [part_of](http://purl.obolibrary.org/obo/BFO_0000050) some [uterus](http://purl.obolibrary.org/obo/UBERON_0000995) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [uterine resident macrophage](http://purl.obolibrary.org/obo/CL_4033064) SubClassOf [tissue-resident macrophage](http://purl.obolibrary.org/obo/CL_0000864) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000256" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1016/j.ydbio.2005.04.035 Yee NS, Lorent K, Pack M, Exocrine pancreas development in zebrafish. Developmental Biology (2005)" -### uterine smooth muscle cell `http://purl.obolibrary.org/obo/CL_0002601` +- [ventral pancreatic duct](http://purl.obolibrary.org/obo/UBERON_0001064) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "Upon reaching its final destination, the ventral pancreatic bud fuses with the much larger dorsal pancreatic bud. At this point of fusion, the main ducts of the ventral and dorsal pancreatic buds fuse, forming the duct of Wirsung, the main pancreatic duct." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "WP" -#### Added -- [uterine smooth muscle cell](http://purl.obolibrary.org/obo/CL_0002601) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### uterine tube infundibulum `http://purl.obolibrary.org/obo/UBERON_0003984` +### ventral part of pharyngeal pouch 3 `http://purl.obolibrary.org/obo/UBERON_0010026` #### Removed -- [uterine tube infundibulum](http://purl.obolibrary.org/obo/UBERON_0003984) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "infundibulum tubae uterinae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Infundibulum_of_uterine_tube" +- [ventral part of pharyngeal pouch 3](http://purl.obolibrary.org/obo/UBERON_0010026) [UBPROP_0000011](http://purl.obolibrary.org/obo/UBPROP_0000011) "The ventral wings fuse to form the cytoreticular cells of the thymus[WP] the caudal ventral part of the pouch gives rise to the thymus epithelium" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "MP" + +- [ventral part of pharyngeal pouch 3](http://purl.obolibrary.org/obo/UBERON_0010026) SubClassOf [foregut epithelium](http://purl.obolibrary.org/obo/UBERON_0015833) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [ventral part of pharyngeal pouch 3](http://purl.obolibrary.org/obo/UBERON_0010026) SubClassOf [unilaminar epithelium](http://purl.obolibrary.org/obo/UBERON_0000490) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "EHDAA2" #### Added -- [uterine tube infundibulum](http://purl.obolibrary.org/obo/UBERON_0003984) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "infundibulum tubae uterinae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Infundibulum_of_uterine_tube" +- [ventral part of pharyngeal pouch 3](http://purl.obolibrary.org/obo/UBERON_0010026) SubClassOf [endoderm of foregut](http://purl.obolibrary.org/obo/UBERON_0003258) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### ventral part of pharyngeal pouch 4 `http://purl.obolibrary.org/obo/UBERON_0010028` +#### Removed +- [ventral part of pharyngeal pouch 4](http://purl.obolibrary.org/obo/UBERON_0010028) SubClassOf [foregut epithelium](http://purl.obolibrary.org/obo/UBERON_0015833) -### uterus or analog `http://purl.obolibrary.org/obo/UBERON_0006834` +- [ventral part of pharyngeal pouch 4](http://purl.obolibrary.org/obo/UBERON_0010028) SubClassOf [unilaminar epithelium](http://purl.obolibrary.org/obo/UBERON_0000490) #### Added -- [uterus or analog](http://purl.obolibrary.org/obo/UBERON_0006834) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004924" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [ventral part of pharyngeal pouch 4](http://purl.obolibrary.org/obo/UBERON_0010028) SubClassOf [endoderm of foregut](http://purl.obolibrary.org/obo/UBERON_0003258) -### uvea `http://purl.obolibrary.org/obo/UBERON_0001768` +### ventral part of telencephalon `http://purl.obolibrary.org/obo/UBERON_0000204` #### Removed -- [uvea](http://purl.obolibrary.org/obo/UBERON_0001768) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tunica vasculosa bulbi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Uvea" +- [ventral part of telencephalon](http://purl.obolibrary.org/obo/UBERON_0000204) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "BTO term refers specifically to the avian structure" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "BTO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [ventral part of telencephalon](http://purl.obolibrary.org/obo/UBERON_0000204) SubClassOf [dorsal to](http://purl.obolibrary.org/obo/BSPO_0000098) some [pallium](http://purl.obolibrary.org/obo/UBERON_0000203) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "separated by cell-free region" #### Added -- [uvea](http://purl.obolibrary.org/obo/UBERON_0001768) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "tunica vasculosa bulbi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [ventral part of telencephalon](http://purl.obolibrary.org/obo/UBERON_0000204) SubClassOf [dorsal to](http://purl.obolibrary.org/obo/BSPO_0000098) some [pallium](http://purl.obolibrary.org/obo/UBERON_0000203) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Uvea" - -### vaginal fluid `http://purl.obolibrary.org/obo/UBERON_0036243` +### ventral striatum `http://purl.obolibrary.org/obo/UBERON_0005403` #### Removed -- [vaginal fluid](http://purl.obolibrary.org/obo/UBERON_0036243) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0003084" - - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0003-4423-4370" - -#### Added -- [vaginal fluid](http://purl.obolibrary.org/obo/UBERON_0036243) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0003084" +- [ventral striatum](http://purl.obolibrary.org/obo/UBERON_0005403) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D066328" - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" - - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) +- [ventral striatum](http://purl.obolibrary.org/obo/UBERON_0005403) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The term ventral striatum refers to a composite structure of the endbrain that is defined in the striatopallidal system by connectivity and neurochemical staining. It includes the nucleus accumbens, the most ventral portions of the caudate nucleus and the putamen, the rostrolateral portion of the olfactory tubercle, the islands of Calleja and a rostral subcommissural portion of substantia innominata. The boundary between the ventral striatum and dorsal striatum is indistinct in sections stained for Nissl substance ( Heimer-1995 )." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "neuronames:2341" -### vaginal venous plexus `http://purl.obolibrary.org/obo/UBERON_0001472` -#### Removed -- [vaginal venous plexus](http://purl.obolibrary.org/obo/UBERON_0001472) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "plexus venosus vaginalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Vaginal_venous_plexus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### ventral to `http://purl.obolibrary.org/obo/BSPO_0000102` +#### Removed +- [ventral to](http://purl.obolibrary.org/obo/BSPO_0000102) [has_obo_namespace](http://www.geneontology.org/formats/oboInOwl#hasOBONamespace) "uberon" -#### Added -- [vaginal venous plexus](http://purl.obolibrary.org/obo/UBERON_0001472) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "plexus venosus vaginalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [ventral to](http://purl.obolibrary.org/obo/BSPO_0000102) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BSPO:0000102" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Vaginal_venous_plexus" +- [ventral to](http://purl.obolibrary.org/obo/BSPO_0000102) [label](http://www.w3.org/2000/01/rdf-schema#label) "ventral to" +- [ventral to](http://purl.obolibrary.org/obo/BSPO_0000102) [shorthand](http://www.geneontology.org/formats/oboInOwl#shorthand) "ventral_to" -### vagus nerve `http://purl.obolibrary.org/obo/UBERON_0001759` -#### Removed -- [vagus nerve](http://purl.obolibrary.org/obo/UBERON_0001759) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus vagus [x]" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:5731" +- [ventral to](http://purl.obolibrary.org/obo/BSPO_0000102) [id](http://www.geneontology.org/formats/oboInOwl#id) "ventral_to" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [vagus nerve](http://purl.obolibrary.org/obo/UBERON_0001759) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nervus vagus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Vagus_nerve" +### ventricular system of brain `http://purl.obolibrary.org/obo/UBERON_0005282` +#### Removed +- [ventricular system of brain](http://purl.obolibrary.org/obo/UBERON_0005282) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000005" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0003472" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [vagus nerve](http://purl.obolibrary.org/obo/UBERON_0001759) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus vagus [x]" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:5731" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +#### Added +- [ventricular system of brain](http://purl.obolibrary.org/obo/UBERON_0005282) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -- [vagus nerve](http://purl.obolibrary.org/obo/UBERON_0001759) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nervus vagus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Vagus_nerve" +### ventricular system of central nervous system `http://purl.obolibrary.org/obo/UBERON_0005281` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0003472" +#### Added +- [ventricular system of central nervous system](http://purl.obolibrary.org/obo/UBERON_0005281) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### vasa recta `http://purl.obolibrary.org/obo/UBERON_0004726` +### venule `http://purl.obolibrary.org/obo/UBERON_0001979` #### Removed -- [vasa recta](http://purl.obolibrary.org/obo/UBERON_0004726) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vasa recta renis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:72006" +- [venule](http://purl.obolibrary.org/obo/UBERON_0001979) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Multi-tissue structure part of the blood vasculature formed by the anastomosis of capillaries. Venules carry blood toward the heart.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -- [vasa recta](http://purl.obolibrary.org/obo/UBERON_0004726) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arteriolae rectae renis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:72006" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0005315" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [vasa recta](http://purl.obolibrary.org/obo/UBERON_0004726) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteriolae rectae renis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Vasa_recta" +### vermiform appendix `http://purl.obolibrary.org/obo/UBERON_0001154` +#### Removed +- [vermiform appendix](http://purl.obolibrary.org/obo/UBERON_0001154) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Organ with organ cavity which is continuous proximally with the cecum and distally terminates in the tip of the appendix. Examples: There is only one appendix[FMA:14542]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:14542" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [vermiform appendix](http://purl.obolibrary.org/obo/UBERON_0001154) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "A comparative anatomical approach reveals three apparent morphotypes of the cecal appendix, as well as appendix-like structures in some species that lack a true cecal appendix. Cladistic analyses indicate that the appendix has evolved independently at least twice (at least once in diprotodont marsupials and at least once in Euarchontoglires), shows a highly significant (P < 0.0001) phylogenetic signal in its distribution, and has been maintained in mammalian evolution for 80 million years or longer.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [vasa recta](http://purl.obolibrary.org/obo/UBERON_0004726) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arteriolae rectae renis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:72006" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1111/j.1420-9101.2009.01809.x Smith HF, Fisher RE, Everett ML, Thomas AD, Randal Bollinger R, Parker W, Comparative anatomy and phylogenetic distribution of the mammalian cecal appendix. Journal of Evolutionary Biology (2009)" -- [vasa recta](http://purl.obolibrary.org/obo/UBERON_0004726) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vasa recta renis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001306" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:72006" +- [vermiform appendix](http://purl.obolibrary.org/obo/UBERON_0001154) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "appendiceal" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -- [vasa recta](http://purl.obolibrary.org/obo/UBERON_0004726) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "arteriolae rectae renis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Vasa_recta" +### version `http://www.geneontology.org/formats/oboInOwl#version` +#### Removed +- AnnotationProperty: [version](http://www.geneontology.org/formats/oboInOwl#version) -### vasa recta ascending limb cell `http://purl.obolibrary.org/obo/CL_1001131` -#### Added -- [vasa recta ascending limb cell](http://purl.obolibrary.org/obo/CL_1001131) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### vertebra `http://purl.obolibrary.org/obo/UBERON_0002412` +#### Removed +- [vertebra](http://purl.obolibrary.org/obo/UBERON_0002412) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Endochondral bone that forms around the notochord and is part of the vertebral column.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001189" -### vasa recta descending limb cell `http://purl.obolibrary.org/obo/CL_1001285` + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" -#### Added -- [vasa recta descending limb cell](http://purl.obolibrary.org/obo/CL_1001285) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + +- [vertebra](http://purl.obolibrary.org/obo/UBERON_0002412) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006196" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -### vascular associated smooth muscle cell `http://purl.obolibrary.org/obo/CL_0000359` + - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) -#### Added -- [vascular associated smooth muscle cell](http://purl.obolibrary.org/obo/CL_0000359) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [vertebra](http://purl.obolibrary.org/obo/UBERON_0002412) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Main component of the vertebral column. It consists of two essential parts, a dorsal neural arch and a ventral centrum.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:Pugener_and_Maglia_2008" -### vascular leptomeningeal cell `http://purl.obolibrary.org/obo/CL_4023051` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000691" -#### Added -- [vascular leptomeningeal cell](http://purl.obolibrary.org/obo/CL_4023051) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### vascular leptomeningeal cell (Mmus) `http://purl.obolibrary.org/obo/CL_4023056` -#### Added -- [vascular leptomeningeal cell (Mmus)](http://purl.obolibrary.org/obo/CL_4023056) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +### vertebra cartilage element `http://purl.obolibrary.org/obo/UBERON_0011094` +#### Removed +- [vertebra cartilage element](http://purl.obolibrary.org/obo/UBERON_0011094) [present_in_taxon](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_7764](http://purl.obolibrary.org/obo/NCBITaxon_7764) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "vertebra-like cartilage in hagfish are homologous to gnathostome vertebrae. mesenchymal cells express Pax1/9 and Twist" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMC3157150" -### vascular lymphangioblast `http://purl.obolibrary.org/obo/CL_0005022` +- [vertebra cartilage element](http://purl.obolibrary.org/obo/UBERON_0011094) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "This class is a superclass of individual vertebral cartilage condensations. Note that EHDAA2 represents these as condensation groups" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EHDAA2" -#### Added -- [vascular lymphangioblast](http://purl.obolibrary.org/obo/CL_0005022) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### vascular plexus `http://purl.obolibrary.org/obo/UBERON_0005629` +### vertebral bone 1 `http://purl.obolibrary.org/obo/UBERON_0001092` #### Removed -- [vascular plexus](http://purl.obolibrary.org/obo/UBERON_0005629) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "plexus vasculosus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [vertebral bone 1](http://purl.obolibrary.org/obo/UBERON_0001092) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "First postcranial vertebra, which is modified anteriorly to articulate with the skull.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000709" -#### Added -- [vascular plexus](http://purl.obolibrary.org/obo/UBERON_0005629) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "plexus vasculosus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### vasculature of retina `http://purl.obolibrary.org/obo/UBERON_0004864` -#### Removed -- [vasculature of retina](http://purl.obolibrary.org/obo/UBERON_0004864) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vasa sanguinea retinae" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:76552" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:Duellman_and_Trueb_1994" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [vertebral bone 1](http://purl.obolibrary.org/obo/UBERON_0001092) [UBPROP_0000107](http://purl.obolibrary.org/obo/UBPROP_0000107) "1"^^[nonNegativeInteger](http://www.w3.org/2001/XMLSchema#nonNegativeInteger) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [vertebral bone 1](http://purl.obolibrary.org/obo/UBERON_0001092) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Vertebra that is posteriorly adjacent to the neurocranium.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001167" -#### Added -- [vasculature of retina](http://purl.obolibrary.org/obo/UBERON_0004864) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vasa sanguinea retinae" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:76552" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TAO:wd" -### vein `http://purl.obolibrary.org/obo/UBERON_0001638` + +### vertebral bone 2 `http://purl.obolibrary.org/obo/UBERON_0001093` #### Removed -- [vein](http://purl.obolibrary.org/obo/UBERON_0001638) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Vein" +- [vertebral bone 2](http://purl.obolibrary.org/obo/UBERON_0001093) [UBPROP_0000107](http://purl.obolibrary.org/obo/UBPROP_0000107) "2"^^[nonNegativeInteger](http://www.w3.org/2001/XMLSchema#nonNegativeInteger) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [vertebral bone 2](http://purl.obolibrary.org/obo/UBERON_0001093) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "not the same as ZFA term 'axis'" -#### Added -- [vein](http://purl.obolibrary.org/obo/UBERON_0001638) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vena" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Vein" +- [vertebral bone 2](http://purl.obolibrary.org/obo/UBERON_0001093) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Vertebra that is posteriorly adjacent to vertebra 1.[TAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001168" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -### vein endothelial cell `http://purl.obolibrary.org/obo/CL_0002543` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TAO:wd" -#### Added -- [vein endothelial cell](http://purl.obolibrary.org/obo/CL_0002543) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### vein of lip `http://purl.obolibrary.org/obo/UBERON_0013136` +### vertebral canal `http://purl.obolibrary.org/obo/UBERON_0006692` #### Removed -- [vein of lip](http://purl.obolibrary.org/obo/UBERON_0013136) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vena labialis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - -#### Added -- [vein of lip](http://purl.obolibrary.org/obo/UBERON_0013136) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vena labialis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [vertebral canal](http://purl.obolibrary.org/obo/UBERON_0006692) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Canal formed by the vertebral centra ventrally, the pedicels laterally, and the neural arches dorsally that encloses and protects the spinal cord.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -### vein of lower lip `http://purl.obolibrary.org/obo/UBERON_0003478` -#### Removed -- [vein of lower lip](http://purl.obolibrary.org/obo/UBERON_0003478) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "venae labiales inferiores" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Inferior_labial_vein" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000693" -- [vein of lower lip](http://purl.obolibrary.org/obo/UBERON_0003478) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vena labialis inferior" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -#### Added -- [vein of lower lip](http://purl.obolibrary.org/obo/UBERON_0003478) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vena labialis inferior" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [vertebral canal](http://purl.obolibrary.org/obo/UBERON_0006692) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D013115" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) -- [vein of lower lip](http://purl.obolibrary.org/obo/UBERON_0003478) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "venae labiales inferiores" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Inferior_labial_vein" -### vein of upper lip `http://purl.obolibrary.org/obo/UBERON_0003477` +### vertebral centrum element `http://purl.obolibrary.org/obo/UBERON_0016491` #### Removed -- [vein of upper lip](http://purl.obolibrary.org/obo/UBERON_0003477) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vena labialis superior" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [vertebral centrum element](http://purl.obolibrary.org/obo/UBERON_0016491) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "the main cylindrical portion of the vertebra ventral to the vertebral canal" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "MP:0000141,ISBN:0-683-40008-8,PMID:10572046" -#### Added -- [vein of upper lip](http://purl.obolibrary.org/obo/UBERON_0003477) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vena labialis superior" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [vertebral centrum element](http://purl.obolibrary.org/obo/UBERON_0016491) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Skeletal element that surrounds the notochord.[VSAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000183" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -### venous blood `http://purl.obolibrary.org/obo/UBERON_0013756` -#### Removed -- [venous blood](http://purl.obolibrary.org/obo/UBERON_0013756) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006187" - - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0003-4423-4370" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "VSAO:curator" -#### Added -- [venous blood](http://purl.obolibrary.org/obo/UBERON_0013756) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006187" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +- [vertebral centrum element](http://purl.obolibrary.org/obo/UBERON_0016491) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "The vertebral centrum may be cartilaginous, develop as cartilage but be replaced by bone or mineralized, or form directly through intramembranous ossification." - - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) -### venous dural sinus `http://purl.obolibrary.org/obo/UBERON_0005486` +### vertebral column `http://purl.obolibrary.org/obo/UBERON_0001130` #### Removed -- [venous dural sinus](http://purl.obolibrary.org/obo/UBERON_0005486) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "s. durae matris" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Dural_venous_sinuses" +- [vertebral column](http://purl.obolibrary.org/obo/UBERON_0001130) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Vertebrata is characterized by three synapomorphies. First, vertebrates have a backbone composed of vertebrae (...).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [venous dural sinus](http://purl.obolibrary.org/obo/UBERON_0005486) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "s. durae matris" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Dural_venous_sinuses" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.53" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001142" -### venous plexus `http://purl.obolibrary.org/obo/UBERON_0001593` -#### Removed -- [venous plexus](http://purl.obolibrary.org/obo/UBERON_0001593) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "plexus venosus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [vertebral column](http://purl.obolibrary.org/obo/UBERON_0001130) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Anatomical cluster that consists of all the vertebra in the body.[VSAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Venous_plexus" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "VSAO:curator" -- [venous plexus](http://purl.obolibrary.org/obo/UBERON_0001593) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "rete venosum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VSAO:0000185" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Venous_plexus" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VSAO" -#### Added -- [venous plexus](http://purl.obolibrary.org/obo/UBERON_0001593) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "plexus venosus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [vertebral column](http://purl.obolibrary.org/obo/UBERON_0001130) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The vertebral column consists of a series of vertebrae connected by ligaments. It provides a supporting axis for the body and protects the spinal cord. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Venous_plexus" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [venous plexus](http://purl.obolibrary.org/obo/UBERON_0001593) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "rete venosum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Venous_plexus" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/vertebral+column" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001142" -### venous valve `http://purl.obolibrary.org/obo/UBERON_0006675` + + +### vertebral element `http://purl.obolibrary.org/obo/UBERON_0010913` #### Removed -- [venous valve](http://purl.obolibrary.org/obo/UBERON_0006675) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D055422" +- [vertebral element](http://purl.obolibrary.org/obo/UBERON_0010913) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "vertebral" -#### Added -- [venous valve](http://purl.obolibrary.org/obo/UBERON_0006675) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D055422" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [vertebral element](http://purl.obolibrary.org/obo/UBERON_0010913) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In contrast to lampreys and jawed vertebrates, hagfishes were thought to lack vertebrae. Now, long overlooked vertebral rudiments have been analysed in hagfish, suggesting that vertebrae existed in the last common ancestor of all vertebrates.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001143" -### ventral cochlear nucleus `http://purl.obolibrary.org/obo/UBERON_0002828` -#### Removed -- [ventral cochlear nucleus](http://purl.obolibrary.org/obo/UBERON_0002828) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus acustici accessorici" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:722" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1016/j.cub.2011.07.014 Janvier P, Comparative anatomy: all vertebrates do have vertebrae. Current Biology (2011)" + +- [vertebral element](http://purl.obolibrary.org/obo/UBERON_0010913) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "we include a distinct subclass for bony vertebra" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [vertebral element](http://purl.obolibrary.org/obo/UBERON_0010913) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Typically an endochondral element, in salamanders there is an argument that vertebral development is perichondral and not preformed in cartilage" -- [ventral cochlear nucleus](http://purl.obolibrary.org/obo/UBERON_0002828) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus cochlearis anterior" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:722" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [ventral cochlear nucleus](http://purl.obolibrary.org/obo/UBERON_0002828) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus cochlearis ventralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:722" +### vertebral foramen `http://purl.obolibrary.org/obo/UBERON_0001131` +#### Removed +- [vertebral foramen](http://purl.obolibrary.org/obo/UBERON_0001131) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Opening on the vertebra for a spinal nerve as it emerges from the spinal canal.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000729" -#### Added -- [ventral cochlear nucleus](http://purl.obolibrary.org/obo/UBERON_0002828) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus cochlearis anterior" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:722" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -- [ventral cochlear nucleus](http://purl.obolibrary.org/obo/UBERON_0002828) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus cochlearis ventralis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:722" -- [ventral cochlear nucleus](http://purl.obolibrary.org/obo/UBERON_0002828) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus acustici accessorici" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### vesical vein `http://purl.obolibrary.org/obo/UBERON_0002460` +#### Removed +- [vesical vein](http://purl.obolibrary.org/obo/UBERON_0002460) [UBPROP_0000202](http://purl.obolibrary.org/obo/UBPROP_0000202) [FMA_70911](http://purl.obolibrary.org/obo/FMA_70911) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:722" -### ventral funiculus of spinal cord `http://purl.obolibrary.org/obo/UBERON_0002180` +### vestibular labyrinth `http://purl.obolibrary.org/obo/UBERON_0001862` #### Removed -- [ventral funiculus of spinal cord](http://purl.obolibrary.org/obo/UBERON_0002180) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "funiculus anterior medullae spinalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:74003" +- [vestibular labyrinth](http://purl.obolibrary.org/obo/UBERON_0001862) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "SCTID:181188003" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [vestibular labyrinth](http://purl.obolibrary.org/obo/UBERON_0001862) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:17815" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [vestibular labyrinth](http://purl.obolibrary.org/obo/UBERON_0001862) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D014722" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) -#### Added -- [ventral funiculus of spinal cord](http://purl.obolibrary.org/obo/UBERON_0002180) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "funiculus anterior medullae spinalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:74003" + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +#### Added +- [vestibular labyrinth](http://purl.obolibrary.org/obo/UBERON_0001862) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### ventral horn of spinal cord `http://purl.obolibrary.org/obo/UBERON_0002257` +### vestibular system `http://purl.obolibrary.org/obo/UBERON_0004681` #### Removed -- [ventral horn of spinal cord](http://purl.obolibrary.org/obo/UBERON_0002257) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cornu anterius medullae spinalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Anterior_horn_of_spinal_cord" +- [vestibular system](http://purl.obolibrary.org/obo/UBERON_0004681) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA and NIF have no part information for this class. This is a GAT in FMA" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [vestibular system](http://purl.obolibrary.org/obo/UBERON_0004681) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The vestibular system, which contributes to our balance and our sense of spatial orientation, is the sensory system that provides the dominant input about movement and equilibrioception. Together with the cochlea, a part of the auditory system, it constitutes the labyrinth of the inner ear, situated in the vestibulum in the inner ear. As our movements consist of rotations and translations, the vestibular system comprises two components: the semicircular canal system, which indicate rotational movements; and the otoliths, which indicate linear accelerations. The vestibular system sends signals primarily to the neural structures that control our eye movements, and to the muscles that keep us upright. The projections to the former provide the anatomical basis of the vestibulo-ocular reflex, which is required for clear vision; and the projections to the muscles that control our posture are necessary to keep us upright[Wikipedia:Vestibular_system]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Vestibular_system" -- [ventral horn of spinal cord](http://purl.obolibrary.org/obo/UBERON_0002257) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "columna grisea anterior medullae spinalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:256541" +### vestibulo-auditory system `http://purl.obolibrary.org/obo/UBERON_0002105` +#### Removed +- [vestibulo-auditory system](http://purl.obolibrary.org/obo/UBERON_0002105) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:36002" -#### Added -- [ventral horn of spinal cord](http://purl.obolibrary.org/obo/UBERON_0002257) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cornu anterius medullae spinalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [vestibulo-auditory system](http://purl.obolibrary.org/obo/UBERON_0002105) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The sensory system used for balance and hearing.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Anterior_horn_of_spinal_cord" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" -- [ventral horn of spinal cord](http://purl.obolibrary.org/obo/UBERON_0002257) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "columna grisea anterior medullae spinalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000631" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:256541" -### ventral striatum `http://purl.obolibrary.org/obo/UBERON_0005403` +### vestibulocochlear ganglion `http://purl.obolibrary.org/obo/UBERON_0002827` #### Removed -- [ventral striatum](http://purl.obolibrary.org/obo/UBERON_0005403) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D066328" - -#### Added -- [ventral striatum](http://purl.obolibrary.org/obo/UBERON_0005403) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D066328" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [vestibulocochlear ganglion](http://purl.obolibrary.org/obo/UBERON_0002827) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The sensory ganglion of the ear. (See Anatomical Atlas entry for statoacoustic ganglion by T. Whitfield.)[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000588" -### ventricular cardiac muscle cell `http://purl.obolibrary.org/obo/CL_2000046` +- [vestibulocochlear ganglion](http://purl.obolibrary.org/obo/UBERON_0002827) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "The cell bodies of the cochlear nerve lie within the central aspect of the cochlea and are collectively known as the spiral ganglion. This name reflects the fact that the cell bodies, considered as a unit, have a spiral (or perhaps more accurately, a helical) shape, reflecting the shape of the cochlea. The terms 'cochlear nerve fiber' and 'spiral ganglion cell' are used, to some degree, interchangeably, although the former may be used to more specifically refer to the central axons of the cochlear nerve. These central axons exit the cochlea at its base, where it forms a nerve trunk. In humans, this aspect of the nerve is roughly one inch in length. It projects centrally to the brainstem, where its fibers synapse with the cell bodies of the cochlear nucleus" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Cochlear_nerve" -#### Added -- [ventricular cardiac muscle cell](http://purl.obolibrary.org/obo/CL_2000046) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) +- [vestibulocochlear ganglion](http://purl.obolibrary.org/obo/UBERON_0002827) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(During the development of the inner ear in a vertebrate embryo) As the otic placode invaginates into a cup neuroblasts delaminate from the anterior ventral aspect of the otic epithelium to give rise to neurons of the vestibulocochlear (statoacoustic) ganglion of cranial nerve VIII.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### ventricular system of central nervous system `http://purl.obolibrary.org/obo/UBERON_0005281` -#### Removed -- [ventricular system of central nervous system](http://purl.obolibrary.org/obo/UBERON_0005281) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ventriculi cerebri" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ventricular_system" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "PMID:21452441 Park BY, Saint-Jeannet JP, Induction and Segregation of the Vertebrate Cranial Placodes. Developmental Biology (2010)" -#### Added -- [ventricular system of central nervous system](http://purl.obolibrary.org/obo/UBERON_0005281) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ventriculi cerebri" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Ventricular_system" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000696" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### venule `http://purl.obolibrary.org/obo/UBERON_0001979` +### vestibulocochlear nerve `http://purl.obolibrary.org/obo/UBERON_0001648` #### Removed -- [venule](http://purl.obolibrary.org/obo/UBERON_0001979) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "venula" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Venule" +- [vestibulocochlear nerve](http://purl.obolibrary.org/obo/UBERON_0001648) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "We conclude this section by listing some of the many synapomorphies of craniates, including (...) (5) cranial nerves (...) (reference 1); Phylogenetically, the cranial nerves are thought to have evolved from dorsal and ventral nerves of a few anterior spinal nerves that became incorporated into the braincase. Dorsal and ventral nerves fuse in the trunk but not in the head, and they produce two series: dorsal cranial nerves (V, VII, IX, and X) and ventral cranial nerves (III, IV, VI, and XIII) (reference 2).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [venule](http://purl.obolibrary.org/obo/UBERON_0001979) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "venula" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.625" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Venule" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000695" -### vermiform appendix `http://purl.obolibrary.org/obo/UBERON_0001154` -#### Removed -- [vermiform appendix](http://purl.obolibrary.org/obo/UBERON_0001154) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "appendix vermiformis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Vermiform_appendix" +- [vestibulocochlear nerve](http://purl.obolibrary.org/obo/UBERON_0001648) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Nerve primarily composed of special somatic afferent fibers innervating the inner ear, and is involved in balance, position, and hearing.[AAO]" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:DSM" -- [vermiform appendix](http://purl.obolibrary.org/obo/UBERON_0001154) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "appendix vermiformis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:14542" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010473" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [vermiform appendix](http://purl.obolibrary.org/obo/UBERON_0001154) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "appendix vermiformis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Vermiform_appendix" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### vimentin `http://purl.obolibrary.org/obo/PR_000017298` +#### Removed +- [vimentin](http://purl.obolibrary.org/obo/PR_000017298) [crossSpeciesExactMatch](https://w3id.org/semapv/vocab/crossSpeciesExactMatch) [vimentin (human)](http://purl.obolibrary.org/obo/PR_P08670) -- [vermiform appendix](http://purl.obolibrary.org/obo/UBERON_0001154) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "appendix vermiformis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:14542" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### visceral abdominal adipose tissue `http://purl.obolibrary.org/obo/UBERON_0014454` +#### Removed +- [visceral abdominal adipose tissue](http://purl.obolibrary.org/obo/UBERON_0014454) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Adipose tissue located inside the peritoneal cavity, packed in between internal organs and torso. An excess of visceral fat is known as central obesity, or belly fat, the pot belly or beer belly effect, in which the abdomen protrudes excessively[BTO:0004041]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "BTO:0004041" -### vertebra `http://purl.obolibrary.org/obo/UBERON_0002412` + +### visceral endoderm `http://purl.obolibrary.org/obo/UBERON_0004877` #### Removed -- [vertebra](http://purl.obolibrary.org/obo/UBERON_0002412) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006196" - - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0003-4423-4370" +- [visceral endoderm](http://purl.obolibrary.org/obo/UBERON_0004877) [UBPROP_0000013](http://purl.obolibrary.org/obo/UBPROP_0000013) "Gilbert uses visceral endoderm as a synonym for primitive endoderm/hypoblast" -#### Added -- [vertebra](http://purl.obolibrary.org/obo/UBERON_0002412) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0006196" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" - - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) +### visceral pleura `http://purl.obolibrary.org/obo/UBERON_0002401` +#### Removed +- [visceral pleura](http://purl.obolibrary.org/obo/UBERON_0002401) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Each lung is invested by an exceedingly delicate serous membrane, the pleura, which is arranged in the form of a closed invaginated sac. A portion of the serous membrane covers the surface of the lung and dips into the fissures between its lobes; it is called the pulmonary pleura (or visceral pleura). The visceral pleura is attached directly to the lungs[Wikipedia:Visceral_pleura]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Visceral_pleura" +- [visceral pleura](http://purl.obolibrary.org/obo/UBERON_0002401) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "FMA treats this as part of the lungs" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" -### vertebral bone 1 `http://purl.obolibrary.org/obo/UBERON_0001092` -#### Removed -- [vertebral bone 1](http://purl.obolibrary.org/obo/UBERON_0001092) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "atlas [C I]" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:12519" +#### Added +- [visceral pleura](http://purl.obolibrary.org/obo/UBERON_0002401) SubClassOf [mixed endoderm/mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0000077) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### visceral serous membrane `http://purl.obolibrary.org/obo/UBERON_0022350` #### Added -- [vertebral bone 1](http://purl.obolibrary.org/obo/UBERON_0001092) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "atlas [C I]" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [visceral serous membrane](http://purl.obolibrary.org/obo/UBERON_0022350) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:12519" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### visceral serous pericardium `http://purl.obolibrary.org/obo/UBERON_0002425` +#### Removed +- [visceral serous pericardium](http://purl.obolibrary.org/obo/UBERON_0002425) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:16589" -### vertebral bone 2 `http://purl.obolibrary.org/obo/UBERON_0001093` + +### viscus `http://purl.obolibrary.org/obo/UBERON_0002075` #### Removed -- [vertebral bone 2](http://purl.obolibrary.org/obo/UBERON_0001093) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "axis [C II]" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:12520" +- [viscus](http://purl.obolibrary.org/obo/UBERON_0002075) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0010386" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -#### Added -- [vertebral bone 2](http://purl.obolibrary.org/obo/UBERON_0001093) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "axis [C II]" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "BTO:0001491" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:12520" +- [viscus](http://purl.obolibrary.org/obo/UBERON_0002075) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs." + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -### vertebral canal `http://purl.obolibrary.org/obo/UBERON_0006692` +### visual system `http://purl.obolibrary.org/obo/UBERON_0002104` #### Removed -- [vertebral canal](http://purl.obolibrary.org/obo/UBERON_0006692) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "c. vertebralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Spinal_canal" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [visual system](http://purl.obolibrary.org/obo/UBERON_0002104) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "The sensory system used for sight.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:EJS" -#### Added -- [vertebral canal](http://purl.obolibrary.org/obo/UBERON_0006692) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D013115" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000632" -- [vertebral canal](http://purl.obolibrary.org/obo/UBERON_0006692) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "c. vertebralis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Spinal_canal" -### vertebral foramen `http://purl.obolibrary.org/obo/UBERON_0001131` +### vitelline artery `http://purl.obolibrary.org/obo/UBERON_0006002` #### Removed -- [vertebral foramen](http://purl.obolibrary.org/obo/UBERON_0001131) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "foramen vertebrale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Vertebral_foramen" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [vitelline artery](http://purl.obolibrary.org/obo/UBERON_0006002) SubClassOf [connecting branch of](http://purl.obolibrary.org/obo/RO_0002252) some [dorsal aorta](http://purl.obolibrary.org/obo/UBERON_0005805) + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "ventral branch" #### Added -- [vertebral foramen](http://purl.obolibrary.org/obo/UBERON_0001131) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "foramen vertebrale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Vertebral_foramen" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [vitelline artery](http://purl.obolibrary.org/obo/UBERON_0006002) SubClassOf [connecting branch of](http://purl.obolibrary.org/obo/RO_0002252) some [dorsal aorta](http://purl.obolibrary.org/obo/UBERON_0005805) -### vertebral foramen of atlas `http://purl.obolibrary.org/obo/UBERON_0000219` +### vitelline vein `http://purl.obolibrary.org/obo/UBERON_0005487` #### Removed -- [vertebral foramen of atlas](http://purl.obolibrary.org/obo/UBERON_0000219) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "." - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Atlas_(anatomy)#Vertebral_foramen" +- [vitelline vein](http://purl.obolibrary.org/obo/UBERON_0005487) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "One of two veins that run upward at first in front, and subsequently on either side of the intestinal canal. They unite on the ventral aspect of the canal, and beyond this are connected to one another by two anastomotic branches, one on the dorsal, and the other on the ventral aspect of the duodenal portion of the intestine, which is thus encircled by two venous rings; into the middle or dorsal anastomosis the superior mesenteric vein opens. The portions of the veins above the upper ring become interrupted by the developing liver and broken up by it into a plexus of small capillary-like vessels termed sinusoids.[XAO]" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "XAO" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "XAO:0004147" +- [vitelline vein](http://purl.obolibrary.org/obo/UBERON_0005487) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Within each vertebrate group, the veins compose a few main functional systems that arise embryologically from what seems to be a common developmental pattern. (...) Early in development, three major sets of paired veins are present: the vitelline veins from the yolk sac, the cardinal veins from the body of the embryo itself, and the lateral abdominal veins from the pelvic region. The paired vitelline veins are among the first vessels to appear in the embryo. They arise over the yolk and follow the yolk stalk into the body. They then turn anteriorly, continue along the gut, and enter the sinus venosus.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -### vesical artery `http://purl.obolibrary.org/obo/UBERON_0009027` -#### Removed -- [vesical artery](http://purl.obolibrary.org/obo/UBERON_0009027) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arteria vesicali" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -#### Added -- [vesical artery](http://purl.obolibrary.org/obo/UBERON_0009027) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "arteria vesicali" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000401" -### vesical vein `http://purl.obolibrary.org/obo/UBERON_0002460` -#### Removed -- [vesical vein](http://purl.obolibrary.org/obo/UBERON_0002460) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "venae vesicales" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:70911" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.460" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [vitelline vein](http://purl.obolibrary.org/obo/UBERON_0005487) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "check zfa (no text def). Check vitelline/omphalomesenteric distinction in XAO" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "XAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" -#### Added -- [vesical vein](http://purl.obolibrary.org/obo/UBERON_0002460) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "venae vesicales" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:70911" +### vitreous body `http://purl.obolibrary.org/obo/UBERON_0001798` +#### Removed +- [vitreous body](http://purl.obolibrary.org/obo/UBERON_0001798) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [neurectoderm](http://purl.obolibrary.org/obo/UBERON_0002346) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0781772214" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [notes](http://www.geneontology.org/formats/oboInOwl#notes) "neural ectoderm of optic cup" +#### Added +- [vitreous body](http://purl.obolibrary.org/obo/UBERON_0001798) SubClassOf [has developmental contribution from](http://purl.obolibrary.org/obo/RO_0002254) some [neurectoderm](http://purl.obolibrary.org/obo/UBERON_0002346) -### vestibular labyrinth `http://purl.obolibrary.org/obo/UBERON_0001862` +- [vitreous body](http://purl.obolibrary.org/obo/UBERON_0001798) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### vitreous humor `http://purl.obolibrary.org/obo/UBERON_0001797` #### Removed -- [vestibular labyrinth](http://purl.obolibrary.org/obo/UBERON_0001862) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D014722" +- [vitreous humor](http://purl.obolibrary.org/obo/UBERON_0001797) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D014822" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) -#### Added -- [vestibular labyrinth](http://purl.obolibrary.org/obo/UBERON_0001862) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D014722" + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + + + +### vomer `http://purl.obolibrary.org/obo/UBERON_0002396` +#### Removed +- [vomer](http://purl.obolibrary.org/obo/UBERON_0002396) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D055172" - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +- [vomer](http://purl.obolibrary.org/obo/UBERON_0002396) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "In bony fish, the vomers are flattened, paired, bones forming the anterior part of the roof of the mouth, just behind the premaxillary bones. In many species, they have teeth, supplementing those in the jaw proper; in some extinct species the teeth on the vomers were actually larger than the primary set. In amphibians and reptiles, the vomers become narrower, due to the presence of the enlarged choanae (the inner part of the nostrils) on either side, and they may extend further back in the jaw. They are typically small in birds, where they form the upper hind part of the beak, again being located between the choanae. In mammals, the vomers have become narrower still, and are fused into a single, vertically oriented bone. The development of the hard palate beneath the vomer means that the bone is now located in a nasal chamber, separate from the mouth[WP]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Wikipedia:Vomer#In_other_animals" -### vestibulocochlear ganglion `http://purl.obolibrary.org/obo/UBERON_0002827` -#### Removed -- [vestibulocochlear ganglion](http://purl.obolibrary.org/obo/UBERON_0002827) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus nervi oculomotorii, pars ventralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:496" - - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [vomer](http://purl.obolibrary.org/obo/UBERON_0002396) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Dermal bone that underlies the mesethmoid and inserts in a fossa on the anteroventral surface of the parasphenoid.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" -- [vestibulocochlear ganglion](http://purl.obolibrary.org/obo/UBERON_0002827) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus nervi oculomotorii ventrolateralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:496" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -#### Added -- [vestibulocochlear ganglion](http://purl.obolibrary.org/obo/UBERON_0002827) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus nervi oculomotorii, pars ventralis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000308" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:496" +- [vomer](http://purl.obolibrary.org/obo/UBERON_0002396) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Paired, palatal bones of intramembranous origin that lie ventral to the olfactory region and help to floor the nasal capsules.[AAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "AAO:LAP" -- [vestibulocochlear ganglion](http://purl.obolibrary.org/obo/UBERON_0002827) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nucleus nervi oculomotorii ventrolateralis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-06-20" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:496" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "AAO:0000633" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "AAO" -### vestibulocochlear nerve `http://purl.obolibrary.org/obo/UBERON_0001648` -#### Removed -- [vestibulocochlear nerve](http://purl.obolibrary.org/obo/UBERON_0001648) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus vestibulocochlearis [viii]" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [vomer](http://purl.obolibrary.org/obo/UBERON_0002396) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: overlaps mesethmoid-vomer joint (TAO:0001680)[TAO]" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:50869" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000308" -- [vestibulocochlear nerve](http://purl.obolibrary.org/obo/UBERON_0001648) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nervus octavus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:553" +- [vomer](http://purl.obolibrary.org/obo/UBERON_0002396) [UBPROP_0000005](http://purl.obolibrary.org/obo/UBPROP_0000005) "The vomer is paired in some taxa (e.g., Amia) while unpaired in others (e.g., teleosts).[TAO]" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-06" -- [vestibulocochlear nerve](http://purl.obolibrary.org/obo/UBERON_0001648) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nervus statoacusticus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:553" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "Curator" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000308" -#### Added -- [vestibulocochlear nerve](http://purl.obolibrary.org/obo/UBERON_0001648) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "nervus vestibulocochlearis [viii]" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [vomer](http://purl.obolibrary.org/obo/UBERON_0002396) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship loss: overlaps autopalatine-vomer joint (TAO:0001784)[TAO]" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:50869" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0000308" -- [vestibulocochlear nerve](http://purl.obolibrary.org/obo/UBERON_0001648) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nervus octavus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:553" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -- [vestibulocochlear nerve](http://purl.obolibrary.org/obo/UBERON_0001648) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nervus statoacusticus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:553" +### vomerine dentition `http://purl.obolibrary.org/obo/UBERON_0017615` +#### Removed +- [vomerine dentition](http://purl.obolibrary.org/obo/UBERON_0017615) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "AAO:0000635" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) -### vestibulocochlear nerve root `http://purl.obolibrary.org/obo/UBERON_0002731` +### vomerine tooth `http://purl.obolibrary.org/obo/UBERON_0004767` #### Removed -- [vestibulocochlear nerve root](http://purl.obolibrary.org/obo/UBERON_0002731) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "fibrae nervi statoacustici" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:72499" +- [vomerine tooth](http://purl.obolibrary.org/obo/UBERON_0004767) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "AAO:0000635" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [vomerine tooth](http://purl.obolibrary.org/obo/UBERON_0004767) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Tooth that is attached to the vomer.[TAO]" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001631" -#### Added -- [vestibulocochlear nerve root](http://purl.obolibrary.org/obo/UBERON_0002731) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "fibrae nervi statoacustici" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:72499" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "TAO:wd" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [vomerine tooth](http://purl.obolibrary.org/obo/UBERON_0004767) [UBPROP_0000002](http://purl.obolibrary.org/obo/UBPROP_0000002) "relationship type change: OBO_REL:part_of vomer (TAO:0000308) CHANGED TO: attaches_to vomer (UBERON:0002396)[TAO]" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0001631" -### vip GABAergic cortical interneuron `http://purl.obolibrary.org/obo/CL_4023016` + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -#### Added -- [vip GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023016) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) -### visceral pleura `http://purl.obolibrary.org/obo/UBERON_0002401` +### vomeronasal organ `http://purl.obolibrary.org/obo/UBERON_0002255` #### Removed -- [visceral pleura](http://purl.obolibrary.org/obo/UBERON_0002401) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pleura pulmonalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9734" +- [vomeronasal organ](http://purl.obolibrary.org/obo/UBERON_0002255) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "Generally formed only in tetrapods; lungfish have rudimentary VN organs; true VN organs are not normally found in recent fishes, birds, aquatic reptiles, aquatic mammals (Bertmar 1980). Humans: Its presence in many animals has been widely studied and the importance of the vomeronasal system to the role of reproduction and social behavior (through influence on anterior hypothalamus) has been shown in many studies. Its presence and functionality in humans was controversial, though most studies agree the organ regresses during fetal development. Many genes essential for VNO function in animals (such as TRPC2) are non-functional in humans (Liman ER. Use it or lose it: molecular evolution of sensory signaling in primates. Pflugers Arch. 2006;453(2):125-31.)" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [vomeronasal organ](http://purl.obolibrary.org/obo/UBERON_0002255) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "An organ thought to supplement the olfactory system in receiving pheromonic communication. The sensory part of the organ is in two long, thin sacs, situated on either side of the nasal septum at its base. [TFD][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [visceral pleura](http://purl.obolibrary.org/obo/UBERON_0002401) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pleura visceralis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Visceral_pleura" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000665" -#### Added -- [visceral pleura](http://purl.obolibrary.org/obo/UBERON_0002401) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pleura pulmonalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/vomeronasal+organ" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:9734" +- [vomeronasal organ](http://purl.obolibrary.org/obo/UBERON_0002255) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) the vomeronasal organ is known only in some tetrapods. It is absent in most turtles, crocodiles, birds, some bats, and aquatic mammals. In amphibians, it is in a recessed area off the main nasal cavity. (...) In mammals possesing this organ, it is an isolated area of olfactory membrane within the nasal cavity that is usually connected to the mouth via the nasopalatine duct (reference 1); The opinions concerning the presence and functioning of the vomeronasal organ in humans are controversial. The vomeronasal cavities appear early in human foetuses. (...) Historical examination of the nasal septum revealed the presence of vomeronasal cavities in approximately 70% of adults. In contrast to the situation in other mammals, the organ is not supported by a rigid tube of bone or cartilage (reference 2); (...) the best evidence for the homology of the human VNO to that of other primates (and of mammals in general) is ontogenetic in nature, based on a common embryonic origin from a thickening (vomeronasal primordium) on the medial aspect of each olfactory pit (reference 3); (...) suggesting that lungfish possess a region homologous to the accessory olfactory bulb of tetrapods. Based on these results, it seems appropriate to refer to the recess epithelium as a primordium of the vomeronasal organ (reference 4). [debated][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [visceral pleura](http://purl.obolibrary.org/obo/UBERON_0002401) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pleura visceralis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Visceral_pleura" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000665" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.669 (ref.1), http://www.ncbi.nlm.nih.gov/pubmed/9866877 Doving KB, Trotier D, Review: Structure and function of the vomeronasal organ. The Journal of Experimental Biology (1998) (ref.2), DOI:10.1046/j.1469-7580.2001.19810077.x Smith TD, Siegel MI, Bonar CJ, Bhatnagar KP, Mooney MP, Burrows AM, Smith MA, Maico LM, The existence of the vomeronasal organ in postnatal chimpanzees and evidence for its homology with that of humans. J Anat (2001) (ref.3) , DOI:10.1002/ar.22415 Nakamuta S, Nakamuta N, Taniguchi K, Taniguchi K, Histological and ultrastructural characteristics of the primordial vomeronasal organ in lungfish. Anat Rec (Hoboken) (2012) (ref.4)" -### visceral serous pericardium `http://purl.obolibrary.org/obo/UBERON_0002425` -#### Removed -- [visceral serous pericardium](http://purl.obolibrary.org/obo/UBERON_0002425) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lamina visceralis pericardii serosi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Epicardium" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [visceral serous pericardium](http://purl.obolibrary.org/obo/UBERON_0002425) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "lamina visceralis pericardii serosi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### wall of anal canal `http://purl.obolibrary.org/obo/UBERON_0036362` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Epicardium" +#### Added +- [wall of anal canal](http://purl.obolibrary.org/obo/UBERON_0036362) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### visceromotor neuron `http://purl.obolibrary.org/obo/CL_0005025` +### wall of blood vessel `http://purl.obolibrary.org/obo/UBERON_0035965` #### Added -- [visceromotor neuron](http://purl.obolibrary.org/obo/CL_0005025) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [cellxgene_subset](http://purl.obolibrary.org/obo/cl#cellxgene_subset) - +- [wall of blood vessel](http://purl.obolibrary.org/obo/UBERON_0035965) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### vitelline vein `http://purl.obolibrary.org/obo/UBERON_0005487` -#### Removed -- [vitelline vein](http://purl.obolibrary.org/obo/UBERON_0005487) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vena vitellina" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Vitelline_veins" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### wall of central canal of spinal cord `http://purl.obolibrary.org/obo/UBERON_0036658` #### Added -- [vitelline vein](http://purl.obolibrary.org/obo/UBERON_0005487) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "vena vitellina" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Vitelline_veins" +- [wall of central canal of spinal cord](http://purl.obolibrary.org/obo/UBERON_0036658) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### wall of eyeball `http://purl.obolibrary.org/obo/UBERON_0036925` -### vitreous chamber of eyeball `http://purl.obolibrary.org/obo/UBERON_0001799` -#### Removed -- [vitreous chamber of eyeball](http://purl.obolibrary.org/obo/UBERON_0001799) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "camera postrema bulbi oculi" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58848" +#### Added +- [wall of eyeball](http://purl.obolibrary.org/obo/UBERON_0036925) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### wall of gallbladder `http://purl.obolibrary.org/obo/UBERON_0036343` #### Added -- [vitreous chamber of eyeball](http://purl.obolibrary.org/obo/UBERON_0001799) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "camera postrema bulbi oculi" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58848" +- [wall of gallbladder](http://purl.obolibrary.org/obo/UBERON_0036343) SubClassOf [endoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004119) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### wall of heart `http://purl.obolibrary.org/obo/UBERON_0037144` -### vitreous humor `http://purl.obolibrary.org/obo/UBERON_0001797` -#### Removed -- [vitreous humor](http://purl.obolibrary.org/obo/UBERON_0001797) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "humor vitreus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +#### Added +- [wall of heart](http://purl.obolibrary.org/obo/UBERON_0037144) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58822" +### wall of lacrimal duct `http://purl.obolibrary.org/obo/UBERON_0037237` #### Added -- [vitreous humor](http://purl.obolibrary.org/obo/UBERON_0001797) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "humor vitreus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [wall of lacrimal duct](http://purl.obolibrary.org/obo/UBERON_0037237) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:58822" -- [vitreous humor](http://purl.obolibrary.org/obo/UBERON_0001797) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D014822" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [LexicalMatching](https://w3id.org/semapv/vocab/LexicalMatching) +### wall of membranous labyrinth `http://purl.obolibrary.org/obo/UBERON_0037191` - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +#### Added +- [wall of membranous labyrinth](http://purl.obolibrary.org/obo/UBERON_0037191) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) -### vomer `http://purl.obolibrary.org/obo/UBERON_0002396` -#### Removed -- [vomer](http://purl.obolibrary.org/obo/UBERON_0002396) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D055172" +### wall of orbit `http://purl.obolibrary.org/obo/UBERON_0037089` #### Added -- [vomer](http://purl.obolibrary.org/obo/UBERON_0002396) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D055172" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) +- [wall of orbit](http://purl.obolibrary.org/obo/UBERON_0037089) SubClassOf [neural crest-derived structure](http://purl.obolibrary.org/obo/UBERON_0010313) - - [author_id](https://w3id.org/sssom/author_id) [0000-0001-9439-5346](https://orcid.org/0000-0001-9439-5346) - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" +### wall of ureter `http://purl.obolibrary.org/obo/UBERON_0009916` + +#### Added +- [wall of ureter](http://purl.obolibrary.org/obo/UBERON_0009916) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### vomeronasal organ `http://purl.obolibrary.org/obo/UBERON_0002255` -#### Removed -- [vomeronasal organ](http://purl.obolibrary.org/obo/UBERON_0002255) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "organum vomeronasale" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Vomeronasal_organ" +### wall of urethra `http://purl.obolibrary.org/obo/UBERON_0036521` + +#### Added +- [wall of urethra](http://purl.obolibrary.org/obo/UBERON_0036521) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [vomeronasal organ](http://purl.obolibrary.org/obo/UBERON_0002255) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "organon vomeronasale" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### wall of urinary bladder `http://purl.obolibrary.org/obo/UBERON_0001256` #### Added -- [vomeronasal organ](http://purl.obolibrary.org/obo/UBERON_0002255) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "organon vomeronasale" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [wall of urinary bladder](http://purl.obolibrary.org/obo/UBERON_0001256) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -- [vomeronasal organ](http://purl.obolibrary.org/obo/UBERON_0002255) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "organum vomeronasale" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Vomeronasal_organ" +### wall of uterine tube `http://purl.obolibrary.org/obo/UBERON_0036441` + +#### Added +- [wall of uterine tube](http://purl.obolibrary.org/obo/UBERON_0036441) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### white adipose tissue `http://purl.obolibrary.org/obo/UBERON_0001347` -#### Removed -- [white adipose tissue](http://purl.obolibrary.org/obo/UBERON_0001347) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D052436" +### wall of vagina `http://purl.obolibrary.org/obo/UBERON_0036523` + +#### Added +- [wall of vagina](http://purl.obolibrary.org/obo/UBERON_0036523) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -- [white adipose tissue](http://purl.obolibrary.org/obo/UBERON_0001347) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "textus adiposus albus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:White_adipose_tissue" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### wall of ventricular system of brain `http://purl.obolibrary.org/obo/UBERON_0036661` #### Added +- [wall of ventricular system of brain](http://purl.obolibrary.org/obo/UBERON_0036661) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) + + +### white adipose tissue `http://purl.obolibrary.org/obo/UBERON_0001347` +#### Removed - [white adipose tissue](http://purl.obolibrary.org/obo/UBERON_0001347) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D052436" - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) @@ -27397,22 +38874,22 @@ - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -- [white adipose tissue](http://purl.obolibrary.org/obo/UBERON_0001347) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "textus adiposus albus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [white adipose tissue](http://purl.obolibrary.org/obo/UBERON_0001347) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Adipose tissue, cells of which contain a single large lipid droplet." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:White_adipose_tissue" ### white matter `http://purl.obolibrary.org/obo/UBERON_0002316` #### Removed -- [white matter](http://purl.obolibrary.org/obo/UBERON_0002316) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "substantia alba" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:White_matter" +- [white matter](http://purl.obolibrary.org/obo/UBERON_0002316) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Multi-tissue structure comprised largely of myelinated axons.[TAO]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFIN:curator" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "TAO:0002142" -- [white matter](http://purl.obolibrary.org/obo/UBERON_0002316) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D066127" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "TAO" + + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-08-14" -#### Added - [white matter](http://purl.obolibrary.org/obo/UBERON_0002316) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D066127" - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) @@ -27420,183 +38897,173 @@ - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -- [white matter](http://purl.obolibrary.org/obo/UBERON_0002316) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "substantia alba" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:White_matter" +- [white matter](http://purl.obolibrary.org/obo/UBERON_0002316) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "nlx_anat_101177 seems to have been lost in the transition from NIFGA to Neurolex" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "NIF" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [see also](http://www.w3.org/2000/01/rdf-schema#seeAlso) "https://github.com/SciCrunch/NIF-Ontology/issues/83" +- [white matter](http://purl.obolibrary.org/obo/UBERON_0002316) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "Cell part cluster consisting predominantly of neurites in the brain and the spinal cord[FMA:83929]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "FMA:83929" -### white matter lamina of cerebellum `http://purl.obolibrary.org/obo/UBERON_0014540` -#### Removed -- [white matter lamina of cerebellum](http://purl.obolibrary.org/obo/UBERON_0014540) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "isthmus cinguli" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:163" +- [white matter](http://purl.obolibrary.org/obo/UBERON_0002316) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "The myelination of axons by glial cells was the last major step in the evolution of cells in the vertebrate nervous system, and white-matter tracts are key to the architecture of the mammalian brain.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [white matter lamina of cerebellum](http://purl.obolibrary.org/obo/UBERON_0014540) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "isthmus gyri cinguli" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:163" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1038/nature09614 Nave KA, Myelination and support of axonal integrity by glia. Nature (2010)" -- [white matter lamina of cerebellum](http://purl.obolibrary.org/obo/UBERON_0014540) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "isthmus gyri cingulatus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:163" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0001764" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -- [white matter lamina of cerebellum](http://purl.obolibrary.org/obo/UBERON_0014540) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "isthmus of gyrus fornicatus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:163" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +### white matter of telencephalon `http://purl.obolibrary.org/obo/UBERON_0011299` +#### Removed +- [white matter of telencephalon](http://purl.obolibrary.org/obo/UBERON_0011299) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "CNS white matter that is part of the telencephalon[ZFA:0000597]." + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ZFA:0000597" -- [white matter lamina of cerebellum](http://purl.obolibrary.org/obo/UBERON_0014540) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "isthmus-2" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:163" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) -#### Added -- [white matter lamina of cerebellum](http://purl.obolibrary.org/obo/UBERON_0014540) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "isthmus gyri cinguli" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### white pulp of spleen `http://purl.obolibrary.org/obo/UBERON_0001959` +#### Removed +- [white pulp of spleen](http://purl.obolibrary.org/obo/UBERON_0001959) [UBPROP_0000009](http://purl.obolibrary.org/obo/UBPROP_0000009) "The white pulp contains T cells, B cells and accessory cells. The function of the white pulp is to mount an immunological response to antigens within the blood. The white pulp is present in the form of a periarteriolar lymphoid sheath. This sheath contains B cell follicles and T cells. At the edge of the T zone is a region known as the marginal zone where larger lymphocytes and antigen presenting dendritic cells are located. [Wikipedia:White_pulp]" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:163" -- [white matter lamina of cerebellum](http://purl.obolibrary.org/obo/UBERON_0014540) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "isthmus-2" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:163" +### wrist joint `http://purl.obolibrary.org/obo/UBERON_0001491` +#### Removed +- [wrist joint](http://purl.obolibrary.org/obo/UBERON_0001491) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in FMA this includes radio-carpal and radio-ulnar *ligaments*" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "FMA" -- [white matter lamina of cerebellum](http://purl.obolibrary.org/obo/UBERON_0014540) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "isthmus gyri cingulatus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [wrist joint](http://purl.obolibrary.org/obo/UBERON_0001491) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:19205" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:163" -- [white matter lamina of cerebellum](http://purl.obolibrary.org/obo/UBERON_0014540) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "isthmus of gyrus fornicatus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:163" +### yolk sac `http://purl.obolibrary.org/obo/UBERON_0001040` +#### Removed +- [yolk sac](http://purl.obolibrary.org/obo/UBERON_0001040) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Structures homologous to the four extraembryonic membranes of reptiles and birds appear in mammals: amnion, chorion, yolk sac, and allantois.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000830" -- [white matter lamina of cerebellum](http://purl.obolibrary.org/obo/UBERON_0014540) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "isthmus cinguli" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.187" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NeuroNames:163" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -### white matter of spinal cord `http://purl.obolibrary.org/obo/UBERON_0002318` -#### Removed -- [white matter of spinal cord](http://purl.obolibrary.org/obo/UBERON_0002318) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "substantia alba medullae spinalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:83945" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [yolk sac](http://purl.obolibrary.org/obo/UBERON_0001040) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In therians, a structure homologous to the yolk sac is is present, but contains no yolk platelets. Instead it is filled with fluid [ISBN:0073040584 (Vertebrates, Kardong)]" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [yolk sac](http://purl.obolibrary.org/obo/UBERON_0001040) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "the extraembryonic tissue membrane, formed from the visceral endoderm and the extraembryonic mesoderm, which is located ventral to the embryonic disc and is connected to the presumptive midgut of the embryo; the yolk that it contains is the site of embryonic hematopoiesis and vitelline circulation is involved in early embryonic circulation; it is the origin of the primordial germ cells" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "MP:0001718" -#### Added -- [white matter of spinal cord](http://purl.obolibrary.org/obo/UBERON_0002318) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "substantia alba medullae spinalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +- [yolk sac](http://purl.obolibrary.org/obo/UBERON_0001040) [UBPROP_0000001](http://purl.obolibrary.org/obo/UBPROP_0000001) "One of the extraembryonic fetal membranes that balloons out from the fetal midgut. [TFD][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000830" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:83945" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -### white pulp of spleen `http://purl.obolibrary.org/obo/UBERON_0001959` + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://medical-dictionary.thefreedictionary.com/yolk+sac" + + + +### yolk sac cavity `http://purl.obolibrary.org/obo/UBERON_0005251` #### Removed -- [white pulp of spleen](http://purl.obolibrary.org/obo/UBERON_0001959) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "noduli lymphoidei splenici" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [yolk sac cavity](http://purl.obolibrary.org/obo/UBERON_0005251) [UBPROP_0000008](http://purl.obolibrary.org/obo/UBPROP_0000008) "In mammals, the yolk sac cavity contains fluid rather than platelets" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:0073040584" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:White_pulp" +- [yolk sac cavity](http://purl.obolibrary.org/obo/UBERON_0005251) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "in EHDAA2, there are separate primary and secondary yolk sac cavities" + - [external_ontology](http://www.geneontology.org/formats/oboInOwl#external_ontology) "EHDAA2" -- [white pulp of spleen](http://purl.obolibrary.org/obo/UBERON_0001959) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pulpa alba" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:62805" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +### zeugopod `http://purl.obolibrary.org/obo/UBERON_0002471` +#### Removed +- [zeugopod](http://purl.obolibrary.org/obo/UBERON_0002471) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "zeugopodial" -#### Added -- [white pulp of spleen](http://purl.obolibrary.org/obo/UBERON_0001959) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "noduli lymphoidei splenici" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:White_pulp" -- [white pulp of spleen](http://purl.obolibrary.org/obo/UBERON_0001959) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pulpa alba" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) +### zeugopodial skeleton `http://purl.obolibrary.org/obo/UBERON_0011584` +#### Removed +- [zeugopodial skeleton](http://purl.obolibrary.org/obo/UBERON_0011584) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "zeugopodial" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:62805" +- [zeugopodial skeleton](http://purl.obolibrary.org/obo/UBERON_0011584) [UBPROP_0000007](http://purl.obolibrary.org/obo/UBPROP_0000007) "zygopodial" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +#### Added +- [zeugopodial skeleton](http://purl.obolibrary.org/obo/UBERON_0011584) SubClassOf [mesoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004120) -### yellow bone marrow `http://purl.obolibrary.org/obo/UBERON_0000332` +### zona pellucida `http://purl.obolibrary.org/obo/UBERON_0000086` #### Removed -- [yellow bone marrow](http://purl.obolibrary.org/obo/UBERON_0000332) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "medulla ossium flava" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0000635" +- [zona pellucida](http://purl.obolibrary.org/obo/UBERON_0000086) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "VHOG:0000720" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [zona pellucida](http://purl.obolibrary.org/obo/UBERON_0000086) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "Outside the plasma membrane, three envelopes surround the ovum. The first, the primary egg envelope, lies between the plasma membrane and the surrounding cells of the ovary. The most consistent component of this primary layer is the vitelline membrane, a transparent jacket of fibrous protein. In mammals, the homologous structure is called the zona pellucida.[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [yellow bone marrow](http://purl.obolibrary.org/obo/UBERON_0000332) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "medulla ossium flava" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "BTO:0000635" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.159" -### yolk sac `http://purl.obolibrary.org/obo/UBERON_0001040` + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000720" + + + +### zone of skin `http://purl.obolibrary.org/obo/UBERON_0000014` #### Removed -- [yolk sac](http://purl.obolibrary.org/obo/UBERON_0001040) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "saccus vitellinus" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Yolk_sac" +- [zone of skin](http://purl.obolibrary.org/obo/UBERON_0000014) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EHDAA2:0001844" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [zone of skin](http://purl.obolibrary.org/obo/UBERON_0000014) [IAO_0000232](http://purl.obolibrary.org/obo/IAO_0000232) "Note the distinction between the entire skin of the body, of which there is only 1 in an organism, and zones of skin, of which there can be many. Examples: skin of knee" -- [yolk sac](http://purl.obolibrary.org/obo/UBERON_0001040) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vesicula umbilicalis" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Yolk_sac" +- [zone of skin](http://purl.obolibrary.org/obo/UBERON_0000014) [UBPROP_0000012](http://purl.obolibrary.org/obo/UBPROP_0000012) "we assume that mouse, HOG and GAID all mean zone of skin when they say skin. We also choose skin as an exact synonym, as it is more intuitive" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [zone of skin](http://purl.obolibrary.org/obo/UBERON_0000014) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "(...) it is well-established that neural crest cells contribute to both the dermal skeleton (craniofacial bone, teeth, and the caudal fin rays of teleosts) and the integument, including craniofacial dermis and all pigment cells outside the retina (...).[well established][VHOG]" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" -#### Added -- [yolk sac](http://purl.obolibrary.org/obo/UBERON_0001040) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vesicula umbilicalis" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Yolk_sac" + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" -- [yolk sac](http://purl.obolibrary.org/obo/UBERON_0001040) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "saccus vitellinus" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000860" + + - [source](http://www.geneontology.org/formats/oboInOwl#source) "DOI:10.1111/j.1469-7580.2008.01043.x Vickaryous MK, Sire JY, The integumentary skeleton of tetrapods: origin, evolution, and development. J Anat (2009)" + +- [zone of skin](http://purl.obolibrary.org/obo/UBERON_0000014) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EMAPA:17525" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Yolk_sac" +#### Added +- [zone of skin](http://purl.obolibrary.org/obo/UBERON_0000014) SubClassOf [ectoderm-derived structure](http://purl.obolibrary.org/obo/UBERON_0004121) ### zygomaticotemporal nerve `http://purl.obolibrary.org/obo/UBERON_0036264` #### Removed -- [zygomaticotemporal nerve](http://purl.obolibrary.org/obo/UBERON_0036264) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ramus zygomaticotemporalis nervus zygomatici" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [zygomaticotemporal nerve](http://purl.obolibrary.org/obo/UBERON_0036264) SubClassOf [nerve](http://purl.obolibrary.org/obo/UBERON_0001021) #### Added -- [zygomaticotemporal nerve](http://purl.obolibrary.org/obo/UBERON_0036264) [has exact synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ramus zygomaticotemporalis nervus zygomatici" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FMA:TA" +- [zygomaticotemporal nerve](http://purl.obolibrary.org/obo/UBERON_0036264) SubClassOf [nerve of head region](http://purl.obolibrary.org/obo/UBERON_0011779) ### zygote stage `http://purl.obolibrary.org/obo/UBERON_0000106` #### Removed - [zygote stage](http://purl.obolibrary.org/obo/UBERON_0000106) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "IDOMAL:0000302" - - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0003-4423-4370" + - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + + - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" -- [zygote stage](http://purl.obolibrary.org/obo/UBERON_0000106) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "zygotum" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Zygote" + - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [LATIN](http://purl.obolibrary.org/obo/uberon/core#LATIN) +- [zygote stage](http://purl.obolibrary.org/obo/UBERON_0000106) [UBPROP_0000003](http://purl.obolibrary.org/obo/UBPROP_0000003) "As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]" + - [external_class](http://www.geneontology.org/formats/oboInOwl#external_class) "VHOG:0000745" -#### Added -- [zygote stage](http://purl.obolibrary.org/obo/UBERON_0000106) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "zygotum" - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003011](http://purl.obolibrary.org/obo/OMO_0003011) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "http://bgee.unil.ch/" - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Zygote" + - [ontology](http://www.geneontology.org/formats/oboInOwl#ontology) "VHOG" -- [zygote stage](http://purl.obolibrary.org/obo/UBERON_0000106) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "IDOMAL:0000302" - - [mapping_justification](https://w3id.org/sssom/mapping_justification) [ManualMappingCuration](https://w3id.org/semapv/vocab/ManualMappingCuration) + - [date_retrieved](http://www.geneontology.org/formats/oboInOwl#date_retrieved) "2012-09-17" - - [mapping_provider](https://w3id.org/sssom/mapping_provider) "https://github.com/biopragmatics/biomappings" + - [source](http://www.geneontology.org/formats/oboInOwl#source) "ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107" - - [author_id](https://w3id.org/sssom/author_id) [0000-0003-4423-4370](https://orcid.org/0000-0003-4423-4370) diff --git a/src/ontology/reports/basic-report.tsv b/src/ontology/reports/basic-report.tsv index adc3f2543..d296a82c3 100644 --- a/src/ontology/reports/basic-report.tsv +++ b/src/ontology/reports/basic-report.tsv @@ -1,2590 +1,16149 @@ ?cls ?def ?xrefs - "A mesenchymal stem cell of the amnion membrane." - "Regular cardiac myocyte of a cardiac atrium." "FMA:83108" - "An acidophilic cell of the anterior pituitary that produces growth hormone, somatotropin." "FMA:83095" - "A Vgamma1.1-positive, Vdelta6.3-negative thymocyte that is CD24-negative." - "An undifferentiated cell produced by early cleavages of the fertilized egg (zygote)." "FMA:72551 BTO:0001473" - "OBSOLETE (was not defined before being made obsolete)." - "A pigment cell derived from the neural crest. Contains cartenoid pigments in structures called pterinosomes or xanthosomes. This gives an appearance ranging from a golden yellow to orange and red." - "A CD8-positive, alpha-beta T cell with the phenotype CCR7-negative, CD45RA-positive." - "OBSOLETE: A classification of cells by their microscopic appearance." - "Any goblet cell that is part of the tracheobronchial epithelium." - "An insect renal cell that filters hemolymph and is found with other pericardial nephrocytes in two rows flanking the dorsal vessel." "FBbt:00005058" - - - - "A CD8-positive, alpha-beta T cell that has differentiated into a memory T cell." - "A cell whose primary function is to protect the organism." - - "An epithelial fate stem cell found in flatworms." "BTO:0003039" - "Immature CD1a-positive Langerhans cell is a CD1a-positive Langerhans cell that is CD80-low, CD86-low, and MHCII-low." - "Obsolete. Use PO:0000373 from Plant Ontology instead. Cell containing mucilages or gums or similar carbohydrate material characterized by the property of swelling in water." - "A brush cell found in the epithelium of lobular bronchiole." "FMA:263220" + "Any process that stops, prevents, or reduces the frequency, rate, or extent of plasmacytoid dendritic cell cytokine production." + "Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes." "BILA:0000082 MIAA:0000018 MAT:0000018 AAO:0000129 Wikipedia:Digestive_system galen:DigestiveSystem MESH:D004064 SCTID:278859004 ncithesaurus:Digestive_System MA:0002431 EFO:0000793 TAO:0000339 XAO:0000125 GAID:278 CALOHA:TS-1293 FMA:7152 TADS:0000170 ZFA:0000339 WBbt:0005748 BTO:0000058" + "A developmental process, independent of morphogenetic (shape) change, that is required for the vestibulocochlear nerve to attain its fully functional state. This sensory nerve innervates the membranous labyrinth of the inner ear. The vestibular branch innervates the vestibular apparatus that senses head position changes relative to gravity. The auditory branch innervates the cochlear duct, which is connected to the three bony ossicles which transduce sound waves into fluid movement in the cochlea." + "Any process that stops, prevents, or reduces the frequency, rate or extent of a response to an external stimulus." + "An eomesodermin that is encoded in the genome of mouse." "UniProtKB:O54839" + "Any process that mediates the transfer of information from an AV node cardiac muscle cell to a bundle of His cardiomyocyte." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of dopamine." + "A protein complex composed of two identical immunoglobulin heavy chains of the IgE isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." + "The regulated release of any glucocorticoid hormone into the circulatory system. Glucocorticoids are a class of steroid hormones that regulate a variety of physiological processes, in particular control of the concentration of glucose in blood." + "Any process that modulates the frequency, rate or extent of iron ions import across plasma membrane." + + "A tyrosine-protein kinase receptor UFO that is encoded in the genome of mouse." "UniProtKB:Q00993" "An extracellular matrix secreting cell that secretes collagen." - "Granule cell that is part of the olfactory bulb." - "A GABAergic cortical interneuron that develops from the medial ganglionic eminence and has migrated to the cerebral cortex." - "A fibroblast that is part of the connective tissue of glandular part of prostate." "FMA:261283" - "Obsolete. Use PO:0000274 from Plant Ontology instead. A fiber of the xylem tissue, Two types are recognized in the secondary xylem: fiber tracheids and libriform fibers." - "Obsolete. Use PO:0004010 from Plant Ontology instead. A cell synthesizing protoplasm and producing new cells by division and with only a primary cell wall." - "A cell from the thermogenic form of adipose tissue found in many species, particularly in newborns and hibernating mammals, but also in lesser amounts in adults of other mammals including humans. Brown fat is capable of rapid liberation of energy and seems to be important in the maintenance of body temperature immediately after birth and upon waking from hibernation." "FMA:83435 CALOHA:TS-0099" - "An endocrine cell that is located in the epithelium of the gastrointestinal tract or in the pancreas." "FMA:62930 BTO:0003865" - "A hematopoietic progenitor that has restricted self-renewal capability. Cell is Kit-positive, Ly6-positive, CD150-negative and Flt3-negative." - "Mature dermal dendritic cell is a dermal dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive." - "Obsolete. Use PO:0000078 from Plant Ontology instead. Parenchyma cell with the wall ingrowth (or invaginations) that increase the surface of the plasmalemma. Appears to be specialized for short-distance transfer of solutes." + "Any process that modulates the frequency, rate or extent of cell proliferation in midbrain." + "A mucosa that is part of a ejaculatory duct [Automatically generated definition]." "FMA:19373" + "A lactosylceramide 4-alpha-galactosyltransferase that is encoded in the genome of human." "UniProtKB:Q9NPC4" + "Any process that stops, prevents or reduces the frequency, rate or extent of cardiac neural crest cell migration involved in outflow tract morphogenesis." + "Capsule surrounding lymph node composed of connective tissue with some plain muscle fibers." "UMLS:C0229699 FMA:74604 EMAPA:35524 SCTID:327532004 NCIT:C33028 MA:0000739 Wikipedia:Lymph_node_capsule" + "Spinal cord structure that is part of the ventricular system and is filled with cerebral-spinal fluid and runs the length of the spinal cord." "HBA:9422 Wikipedia:Central_canal_of_spinal_cord EHDAA2:0004361 BAMS:CC NCIT:C12891 TAO:0000938 MA:0001117 BIRNLEX:1409 DMBA:126652042 DHBA:146035108 neuronames:1733 MBA:164 ZFA:0000938 FMA:78497 SCTID:279447004 EMAPA:35789 BAMS:C UMLS:C0459414" - "One of the two haploid cells into which a primary spermatocyte divides, and which in turn gives origin to spermatids." "BTO:0000709 FMA:72293 CALOHA:TS-2195 FBbt:00004941" - "OBSOLETE (was not defined before being made obsolete)." - "An oncocyte located in the parathyroid gland." "FMA:69084" - "An erythroid progenitor cell is Kit-positive, Ly6A-negative, CD41-negative, CD127-negative, and CD123-negative. This cell type is also described as being lin-negative, Kit-positive, CD150-negative, CD41-negative, CD105-positive, and FcgR-negative." "A smooth muscle cell that is part of the tracheobronchial tree." - "A circulating gamma-delta T cell that expresses RORgamma(t), is CD27-negative and is capable of IL-17 secretion." + "The reproductive developmental process whose specific outcome is the progression of the baculum over time, from its formation to the mature structure." + "A homeostatic process involved in the maintenance of a steady state level of monoatomic cations within a cell. Monatomic cations (also called simple cations) are cations consisting of exactly one atom." "Cranial motor neuron which innervates muscles derived from the branchial (pharyngeal) arches." "PMID:14699587" - "A mesothelial cell that is part of the peritoneum." "FMA:86736" - - - "A neuronal receptor that respond to mechanical pressure or distortion in the skin." - "An epithelial cell of the tracheobronchial tree." "FMA:66816" + + "A capillary that is part of a lung." "FMA:14121" + "A hemoglobin subunit zeta that is encoded in the genome of human." "UniProtKB:P02008" + "Any process that modulates the frequency, rate or extent of cell proliferation involved in kidney development." + "The series of events required for an organism to receive a sensory temperature stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process." + "Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation." "A type II pneumocyte is a pneumocyte that modulates the fluid surrounding the alveolar epithelium by secreting and recycling surfactants. This cell type also contributes to tissue repair and can differentiate after injury into a type I pneumocyte. Thicker than squamous alveolar cells, have a rounded apical surface that projects above the level of surrounding epithelium. The free surface is covered by short microvilli." "BTO:0000538 FMA:62501" + "A pelvic girdle region that is in the right side of a multicellular organism." "FMA:16582" "Any dopaminergic neuron that is part of a midbrain." + "An integrin beta-7 that is encoded in the genome of mouse." "UniProtKB:P26011" + "The change in form that occurs when an epithelial cell progresses from its initial formation to its mature state." "A peptide hormone secreting cell that secretes oxytocin stimulating hormone" - "A fibroblast that is part of the subepithelial connective tissue of prostatic gland." "FMA:261275" - "Neuron with one neurite that extends from the cell body." "FMA:67278" - "A CD38-positive IgG memory B cell is a class switched memory B cell that expresses IgG on the cell surface with the phenotype CD38-positive and IgG-positive." + "The part of synaptic transmission occurring in the post-synapse: a signal transduction pathway consisting of neurotransmitter receptor activation and its effects on postsynaptic membrane potential and the ionic composition of the postsynaptic cytosol." + "Opaque fibrous outer layer of the eyeball[ZFA,Kardong,WP]." "XAO:0000183 MESH:D012590 EMAPA:19027 AAO:0010354 NCIT:C12784 ZFA:0005563 UMLS:C0036410 GAID:911 VHOG:0001274 EV:0100342 FMA:58269 SCTID:181163006 Wikipedia:Sclera MA:0000280 BTO:0001606" + "The process whose specific outcome is the progression of a pancreatic PP cell over time, from its formation to the mature structure. A pancreatic polypeptide-producing cell is a cell in the pancreas that produces pancreatic polypeptide." - "A thick walled spore that stores and protects one or more nuclei following sexual reproduction in an Ascomycete." "FAO:0000020 BTO:0000097" - "An epithelial cell of the mucosa associated with facial skeleton." "FMA:70581" - "A small, polyhedral, cell found in rounded groups or curved columns with deeply staining nuclei, scanty basophilic cytoplasm and a few lipid droplets. This cell in the zona glomerulosa produces mineralocorticoids." "FMA:69273" - "Any neuron that is part of a lateral line ganglion." + "Future brain vesicle that gives rise to telencephalic ventricle/lateral ventricles and 3rd ventricle." "EMAPA:16521 SCTID:361480006 TAO:0001259 ZFA:0001259 EHDAA:1356 VHOG:0000644 EHDAA2:0001571 DHBA:10595" + "Any process that increases the extent to which blood vessels can be pervaded by fluid." "An excitatory glutamatergic neuron transcriptomically related to the CT subclass, with a soma preferentially located in the bottom of L6 of the primary motor cortex." - "A GABAergic cortical interneuron that is strongly labelled for α7 nAChRs. These cells have soma found in L1 and have multipolar dendrites with vertically descending axonal collaterals that project deep into the column, usually branching and terminating in L5A." + "GC_ID:1" + "The fibrous connective tissue that surrounds the root of a tooth, separating it from and attaching it to the alveolar bone. It extends from the base of the gingival mucosa to the fundus of the bony socket, and its main function is to hold the tooth in its socket[BTO]." "BTO:0001020 Wikipedia:Periodontal_fiber CALOHA:TS-0763 EMAPA:35679 SCTID:245775004 FMA:56665 GAID:1259 MA:0002467" - "A basal cell found in the bronchus epithelium." "FMA:263120" - "A NK1.1-positive T cell that is CD94-positive." - "An immature microglial cell with a ramified morphology." - "A L2/3 Pvalb-like Sst GABAergic cortical interneuron (Mus musculus) that has Martinotti morphology." - "A pre-BCR-positive precursor B cell that is CD24-high, CD25-positive, CD43-positive, CD45R-positive and BP-positive." - "A conventional dendritic cell that is CD103-positive. This cell type is usually found in non-lymphoid tissue." - "An epithelial cell with a well defined Golgi apparatus that makes up the continuous layer of cells bordering the thymic tissue beneath the capsule." "FMA:72209" + "Any process that modulates the rate, frequency or extent of the differentiation of a neuroendocrine cell in the stomach." + "A developmental process, independent of morphogenetic (shape) change, that is required for the olfactory nerve to attain its fully functional state. The olfactory nerve is a collection of sensory nerve rootlets that extend down from the olfactory bulb to the olfactory mucosa of the upper parts of the nasal cavity. This nerve conducts odor information to the brainstem." - "A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells." - "KUPO:0001074" - "A near-projecting glutamatergic neuron with a soma found in layer 5/6 of the primary motor cortex." "ILX:0770161" - "A short lived plasma cell that secretes IgM." - "A hematopoietic progenitor cell that is committed to the granulocyte and monocyte lineages. These cells are CD123-positive, and do not express Gata1 or Gata2 but do express C/EBPa, and Pu.1." - "A class switched memory B cell that expresses IgA." - "A lymphocyte that can spontaneously kill a variety of target cells without prior antigenic activation via germline encoded activation receptors and also regulate immune responses via cytokine release and direct contact with other cells." "FMA:63147 BTO:0004716 VHOG:0001697 BTO:0000914 CALOHA:TS-0664 FMA:83601" - "A myeloblast committed to the eosinophil lineage." - "A cell specialized to detect chemical substances and relay that information centrally in the nervous system. Chemoreceptors may monitor external stimuli, as in taste and olfaction, or internal stimuli, such as the concentrations of oxygen and carbon dioxide in the blood." - "Any pyramidal cell that is part of a regional part of cerebral cortex." - - "FBbt:00005144" - "A MHC-II-negative classical monocyte located in lymphoid tissue that is F4/80-positive, CD11c-negative, and CD11b-high." - "A promyelocyte committed to the neutrophil lineage. This cell type is GATA-1-positive, C/EBPa-positive, AML-1-positive, MPO-positive, has low expression of PU.1 transcription factor and lacks lactotransferrin expression." "FMA:84196" - "A steroid hormone secreting cell that secretes androgen." - "An immature myeloid leukocyte of heterogeneous phenotype found particularly in cancer and sepsis patients that is capable of suppressing activity of T cells in ex vivo assays. This cell type is CD45-positive, CD11b-positive." - "A cell in the area of mesoderm in the neurulating embryo that flanks and forms simultaneously with the neural tube. The cells of this region give rise to somites." - "A Betz cell that synapses with lower motor neurons directly." - "A zygote in a plant or an animal." + "Any process that controls lipoprotein transport." + "The progression of the seminal vesicle epithelium over time, from its formation to the mature structure." + "Any process that stops, prevents, or reduces the frequency, rate or extent of neurogenesis, the generation of cells within the nervous system." + "A border associated macrophage that is adjacent to a small blood vessel of a brain. A perivascular macrophage expresses the markers CD14, CD16 and CD163. In homeostatic conditions, this central nervous system macrophage has a non-motile cell body with extending and retracting projections through the blood vessel wall." + "Any process that modulates the frequency, rate or extent of mesoderm formation." + "Any process that stops, prevents or reduces the frequency, rate or extent of inner ear receptor cell differentiation." + "Passages external to the liver for the conveyance of bile. These include the common bile duct and the common hepatic duct." "NCIT:C32573 MESH:D017734 SCTID:276158002 MA:0002659 UMLS:C0206187 GAID:281 FMA:14678" + "Appendage girdle complex that when present, encompasses the pelvic appendicular skeleton and the pelvic girdle." "VSAO:0000215 FMA:7184 EMAPA:37863 SCTID:416631005" + "Any process that activates, maintains or increases the frequency, rate or extent of glutamatergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter glutamate." + "A lung lobe is one of the rounded projections that compose the lung[GO]." "NCIT:C34021 galen:LobeOfLung UMLS:C0225752 EMAPA:36281 MA:0003098 FMA:7311 SCTID:245524004" + "A hepatic artery that is part of a right lobe of liver." "EMAPA:37376 FMA:14778 MA:0003097" "A specialized hair cell that has an elongated kinocilium upon which an otolith accretes. The tether cell then anchors the otolith in place." - "A lymphocyte of B lineage that is capable of B cell mediated immunity." "VHOG:0001480 CALOHA:TS-0068 BTO:0000776 FMA:62869" - - "A CD38-negative IgG-negative memory B cell is a IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype CD38-negative and IgG-negative." - "A small pre-B cell that is CD22-positive and CD38-low." - "A round or oval neuroepithelial cell that contacts other type I cells or capillaries. They occur in clusters that are surrounded by sheath cells (type-II cells) in the carotid body. This cell type is capable of secreting a number of neurotransmitters." "FMA:84186" - "A cell that, by division or terminal differentiation, can give rise to other cell types." - "A mesenchymal stem cell of the vertebrae." - "A double negative thymocyte that has a T cell receptor consisting of a gamma chain containing a Vgamma2 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-positive and is found in the fetal thymus." - "An epithelial cell of stratum spinosum of esophageal epithelium." "FMA:70732" - "A stomal cell of the ovary" "FMA:72299" - - "An oncocyte located in the thyroid." "FMA:87169" - "An astrocyte of the spinal cord." - "Any neuromast hair cell that is part of a anterior lateral line." - "FBbt:00005062" - "Any hepatocyte that is part of the liver lobule midzonal region. These cells have mixed functionality in comparison with those in the other two regions of the liver lobule." - - "An epithelial fate stem cell derived form the amnion membrane." + "The controlled breakdown of the basement membrane in the context of a normal process such as imaginal disc eversion." + "The process in which a relatively unspecialized cell acquires specialized features of a trophoblast giant cell of the placenta. Trophoblast giant cells are the cell of the placenta that line the maternal decidua." + "EMAPA:16893 EHDAA:3217 EHDAA2:0000179" + "A large hematopoietic cell (50 to 100 micron) with a lobated nucleus. Once mature, this cell undergoes multiple rounds of endomitosis and cytoplasmic restructuring to allow platelet formation and release." "CALOHA:TS-0611 FMA:83555 BTO:0000843" + "The process whose specific outcome is the progression of the pronephric distal tubule over time, from its formation to the mature structure. A pronephric nephron tubule is an epithelial tube that is part of the pronephros." + "A leukocyte immunoglobulin-like receptor subfamily A member 4 that is encoded in the genome of human." "UniProtKB:P59901" + "Any process that stops, prevents or reduces the frequency, rate or extent of excitatory synapse pruning." + "An adipocyte that is part of subcutaneous adipose tissue." + "GC_ID:1" + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus." + "The middle layer of an artery or vein. [WP,unvetted]." "SCTID:61695000 BTO:0002011 MA:0002855 MESH:D017540 NCIT:C33821 GAID:170 UMLS:C0162867 EMAPA:36298 Wikipedia:Tunica_media FMA:55590" + "An epithelium that is part of a median lingual swelling." "EHDAA2:0001085 EMAPA:17188" + "Any process that modulates the frequency, rate or extent of RNA biosynthetic process." + "The any of the paired peripheral nerves formed by the union of the dorsal and ventral spinal roots from each spinal cord segment[MP,modified]." "SCTID:361099009 GAID:841 MESH:D013127 VHOG:0000824 MA:0000233 BTO:0000870 FMA:5858 Wikipedia:Spinal_nerve NCIT:C12792 neuronames:1228 EMAPA:16989 AAO:0011101 BAMS:spin EHDAA2:0001898 UMLS:C0037941 XAO:0003101" + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a serotonin stimulus." + "The developmental process by which a dorsal root ganglion is generated and organized." + "FMA:56732" "A basal cell that is part of the epithelium of bronchiole." "FMA:263126" - "A long-lived, antigen-experienced T cell that has acquired a memory phenotype including distinct surface markers and the ability to differentiate into an effector T cell upon antigen reexposure." "BTO:0003435" - "A cell with a flagellum surrounded by a collar of microvilli. The motion of the flagellum draws water past the microvilli, serving either a feeding or sensory function. Collar cells are found in multiple animals, including sponges, echinoderms, and cnidarians. They are also found outside animals in the choanoflagellates. Although collar cells are superficially similar, their cytoskeletal structure and functional biology are different in different groups of organisms." - "A plasmacytoid dendritic cell developing in the thymus with phenotype CD11c-negative or low, CD45RA-positive, CD11b-negative, and CD123-positive." - "A CD11c-low plasmacytoid dendritic cell that is CD8alpha-positive and CD4-positive." + "A bistratified ganglion cell with larger, asymetric dendritic fields that terminate in S2 and S4." + "Any process that modulates the frequency, rate, or extent of B cell deletion." + "Any process that modulates the frequency, rate or extent of dopaminergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter dopamine." + "The orderly movement of a lymphoid lineage cell from one site to another. A lymphoid lineage cell, also called a lymphoid lineage restricted progenitor cell, is a progenitor cell restricted to the lymphoid lineage." + "A lymphoid follicle that contains a germinal center." "GAID:946 FMA:55224" + "The portion of the plasma membrane surrounding a plasma membrane bounded cell surface projection." "A hematopoietic stem cell that exists during embryogenesis." - "The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated." "BTO:0000575 CALOHA:TS-0454 FMA:14515" - "An epithelial cell that is part of the sweat gland." "FMA:70952" - - "A T cell which resides in the Peyer's patch of the small intestine." - "Skeletogenic cell that has the potential to develop into a cementoblast." - "A double negative post-natal thymocyte that has a T cell receptor consisting of a gamma chain containing a Vgamma2 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-positive." - "A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped." "BTO:0000452 VHOG:0001482 FMA:63877 CALOHA:TS-0362" - "A stromal cell found in the lamina propria of the vermiform appendix." - - "An epithelial cell of the musculomembranous digestive tube extending from the mouth to the anus." - "A serous secreting cell that is part of the epithelium of bronchiole." "FMA:263084" - "An astrocyte of the forebrain." - "A fat cell that is part of the epicardial fat of right ventricle." "FMA:261297" - "A myoepithelial cell that is part of the acinus of lactiferous gland." "FMA:74469" - "A muscle cell that can develop high tension rapidly. It is usually innervated by a single alpha neuron ." - "A T cell that is located in the intestinal epithelium and is capable of a mucosal immune response." - "A bipolar neuron found in the retina and having connections with photoreceptors cells and neurons in the outer half of the inner plexiform layer. These cells depolatize in response to light to dark transition." + "A blood vessel that is part of a cornea [Automatically generated definition]." "MA:0001241 EMAPA:36611" + "An arachnoid mater that is part of a forebrain [Automatically generated definition]." "EMAPA:37544 MA:0000884" + "Mesenchyme that is part of a developing forelimb stylopod [Automatically generated definition]." "VHOG:0000505 EHDAA2:0002114 EMAPA:17426" + "UMLS:C0447038 NCIT:C32552 SCTID:244216003 FMA:70505" + "EMAPA:35982" + "Any process that mediates the transfer of information between a mesenchymal cell and an endodermal cell." + "A vein that carries deoxygenated blood from the lower half of the body into the right atrium of the heart." "EMAPA:18416 XAO:0000388 FMA:10951 galen:InferiorVenaCava MESH:D014682 GAID:548 VHOG:0001194 SCTID:181369003 EHDAA2:0000611 UMLS:C0042458 Wikipedia:Inferior_vena_cava BTO:0002682 NCIT:C12815 AAO:0011083 MA:0000480" + "Any process that decreases the frequency, rate or extent of muscle contraction of the hindgut, the posterior part of the alimentary canal, including the rectum, and the large intestine." + "The part of the lacrimal duct that connects the lacrimal punctum to the lacrimal sac." "NCIT:C32907 SCTID:263348000 UMLS:C0459631 EMAPA:37624 FMA:58245 Wikipedia:Lacrimal_canaliculi MA:0001294" "A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen." "FMA:81100 CALOHA:TS-0290 BTO:0000424" - "A luminal cell of terminal ducts, i.e.e the terminal branch of a lactiferous duct which alveolar cells drain into." "FMA:87168" - "A megakaroycotye progenitor cell that is CD34-positive, CD41-positive and CD42-positive on the cell surface." - "A cell whose function is determined by the generation or the reception of an electric signal." - "A smooth muscle cell that synthesizes, stores, and secretes the enzyme renin. This cell type are located in the wall of the afferent arteriole at the entrance to the glomerulus. While having a different origin than other kidney smooth muscle cells, this cell type expresses smooth muscle actin upon maturation." "FMA:84138" - "KUPO:0001077" - "An immature cell of the conventional dendritic cell lineage, characterized by high levels of antigen uptake via endocytosis, macropinocytosis, and phagocytosis, and typically found resident in the tissues. Markers for this cell are CD80-low, CD86-low, and MHC-II-low." - "Pioneer neurons establish a pathway in the developing central nervous system and then undergo programmed cell death once the adult axons, which follow them, have made connections with the target site. Thus, they are a transient cell type involved in axon guidance." "FBbt:00005128" - "A mature NK cell that is NK1.1-positive." - "Undifferentiated; mitotic stem cell for other epithelial cell types; rounded or elliptical with little cytoplasm and few organelles; contain cytokeratin intermediate filament." "FMA:62516 BTO:0000939" - "A late basophilic metamyelocyte in which the nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature basophil." - "A glutamatergic neuron with a soma found in cortical layer 6b. They are transcriptomically related to corticothalamic-projecting neurons but have differential projections to the thalamus or anterior cingulate." "ILX:0770163" + "Structures that develop from sex cords in the female. After further development they become the ovarian follicles." "NCIT:C34134 VHOG:0001339 EMAPA:31058 UMLS:C1511527 EHDAA2:0001363 EHDAA:8130 Wikipedia:Cortical_cords" + "Tip of renal pyramid projecting into a minor calyx." "BTO:0003925 SCTID:362214007 Wikipedia:Renal_papilla galen:RenalPapilla FMA:15622 EMAPA:35727 UMLS:C0022666 MESH:D007679 NCIT:C33460 MA:0002730" + "The foremost region of the future forebrain that develops into the diencephalon." "EHDAA:844 EHDAA2:0000600 RETIRED_EHDAA2:0000386 ZFA:0000574 EFO:0003442 EMAPA:16514 TAO:0000574" + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a secretory granule in a T cell. A secretory granule is a small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion." + "A developmental process, independent of morphogenetic (shape) change, that is required for an animal organ to attain its fully functional state. An organ is a tissue or set of tissues that work together to perform a specific function or functions." "An ecto-epithelial cell of the buccal region of the viscerocranial mucosa." "FMA:70577" - "A small medullary thymic epithelial cell with a spindle shape, often arranged in groups and connected to each other by large desmosomes and interdigitations. The cytoplasm is sparse, with scanty organelles and thick bundles of cytokeratin." - "An enteroendorcine cell found in the fundus and pylorus, this cell type has dense round secretory granules that contain ghrelin." "FMA:63209" - "Any cell that is part of a pituitary gland." - "A common lymphoid progenitor that is Kit-low, FLT3-positive, IL7ralpha-positive, and SCA1-low." + "The regulated exocytosis of secretory granules containing preformed mediators such as proteases, lipases, and inflammatory mediators by a neutrophil." + "The orderly movement of an intestinal epithelial cell from one site to another, often during the development of a multicellular organism." - "Any fibroblast that is part of a optic choroid." - "An urothelial cell that is part of the trigone of urinary bladder." "FMA:70598" - "Hematopoietic cells resident in the bone marrow. Include: hematopoietic stem cells (lymphoid stem cells and myeloid stem cells) and the precursor cells for thrombocytes, erythrocytes, basophils, neutrophils, eosinophils, monocytes and lymphocytes." "CALOHA:TS-2109" - "Obsolete. Use PO:0000075 from Plant Ontology instead. An elongated living cell with unevenly thickened nonlignified primary walls." - - "A lymphocyte that resides in the lamina propria of the large intestine." + "EMAPA:35979" + "The part of a synapse that is part of the post-synaptic cell." + "Any process that modulates the frequency, rate or extent of signal transduction." + "A protein complex which is capable of calcitonin family receptor activity. Calcitonin family receptors may form dimers, trimers or tetramers; adrenomedullin and amylin receptors have only been observed as dimers so far." + "A proximal epiphysis that is part of a fibula." "galen:HeadOfFibula UMLS:C0223908 NCIT:C32719 SCTID:182080006 Wikipedia:Head_of_fibula EMAPA:37890 FMA:33729" "A gamma motor neuron that innervates dynamic nuclear bag fibers (bag1 fibers) and enhances the sensitivities of Ia sensory neurons. They alter muscle spindle sensitivity and increases its discharge in response to velocity of muscle length (rather than just magnitude)." - "A neuron that has dendritic processes radiating from the cell body forming a star-like shape." "BTO:0002316" - "Transit-amplifying cells (TACs) are an undifferentiated population in transition between stem cells and differentiated cells." - "A mature CD1a-positive dermal dendritic cell is CD80-high, CD83-positive, CD86-high, and MHCII-high." - "A glandular cell found in the epithelium of the small intestine. Example: Enterocytes, Goblet cells, enteroendocrine cells; Paneth cells; M cells; Somatostatin-secreting Cells (D-cells) ." "CALOHA:TS-1286 FMA:86928" - "FBbt:00005063" - "A Sst GABAergic cortical interneuron with a soma found in L5 and possesses 'T-shaped' martinotti morphologies with local axonal plexus in L5a and translaminar axons restricted to the uppermost part of L1. They show low-threshold spiking patterns with strong rebound firing, and inhibit the L1 apical tuft of nearby pyramidal cells." - "An immature CD1a-positive dermal dendritic cell is CD80-low, CD86-low, and MHCII-low." - "KUPO:0001020" + "A pancreatic lobule that is in_the_left_side_of a exocrine pancreas." "MA:0000722 EMAPA:37711" + "Any process that activates or increases the rate or extent of lymphocyte proliferation." + "The parenchymatous tissue network of the spleen that consists of loose plates or cords (sinuses) infiltrated with red blood cells where most of the blood filtration occurs and degenerate erythrocytes are removed from the circulation." "NCIT:C12992 CALOHA:TS-1263 MA:0000756 Wikipedia:Red_pulp SCTID:27579002 FMA:15844 UMLS:C0229687 EMAPA:35806" + "A germinal center B cell found in a lymph node germinal center dark zone." + "The process in which a myeloid precursor cell acquires the specialized features of a granulocyte. Granulocytes are a class of leukocytes characterized by the presence of granules in their cytoplasm. These cells are active in allergic immune reactions such as arthritic inflammation and rashes. This class includes basophils, eosinophils and neutrophils." + "A smooth muscle of the eye, running radially in the iris that functions as a dilator. [WP,unvetted]." "BTO:0001371 EMAPA:35286 Wikipedia:Iris_dilator_muscle UMLS:C0229190 NCIT:C32463 FMA:49158 MA:0001288 SCTID:280890008" "An epithelial cell found in C. elegans that firmly hold the outer body wall and the lips to the inner cylinder of the pharynx in a manner that keeps these organs from breaking apart, while still giving each organ freedom of movement during feeding." "WBbt:0005793" - "A thymocyte that lacks expression of CD4 and CD8." - "An alpha-beta intraepithelial T cell with the phenotype CD8-alpha-alpha-positive located in the columnar epithelium of the gastrointestinal tract. These cells have a memory phenotype of CD2-negative and CD5-negative." - "A beta motor neuron that innervates nuclear chain fibers." - "A smooth muscle cell of the trachea." - "Obsolete. Use PO:0004011 from Plant Ontology instead. A cell constituting an active locus of meristematic activity in a tissue composed of somewhat older, differentiating cells." - "OBSOLETE: A classification of cells by the number of haploid genome equivalents of their nucleus or nuclei." - "Any muscle cell in which the fibers are not organised into sarcomeres." + "Replacement bone that forms within cartilage." "XAO:0004018 FMA:24321 AAO:0010776 AEO:0000083 EHDAA2:0003083 BTO:0002157 TAO:0001591 VSAO:0000145 ZFA:0001591" + "The adjustable membrane, composed of the stroma and pigmented epithelium, located just in front of the crystalline lens within the eye." "MA:0000273 Wikipedia:Iris_(anatomy) BTO:0000653 NCIT:C12737 EFO:0004245 VHOG:0000101 TAO:0001238 GAID:917 MESH:D007498 XAO:0000185 AAO:0010347 EMAPA:19154 FMA:58235 ZFA:0001238 SCTID:181164000 EV:0100345 CALOHA:TS-0491 UMLS:C0022077" + "The change in morphology and behavior of a mature or immature natural killer T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific." "Mesodermal cell that is axially located and gives rise to the cells of the notochord." - "Any melanocyte of skin that is part of a skin of prepuce of penis." - "A melanocyte that produces pigment within the hair follicle." - "A langerin-positive lymph node dendritic cell that is CD103-negative and CD11b-high." - "An ecto-epithelial cell of the nasal region of the viscerocranial mucosa." "FMA:70554" - "A columnar cell of the cervix uteri." "FMA:86486" - "A natural killer cell that is developmentally immature, has the phenotype CD34-negative, CD56-positive, CD117-positive, CD122-positive,and CD161-positive." - "An epithelial cell that is part of the gallbladder." "FMA:67780" - "A chief cell of parathyroid glands that does not stain with hematoxylin or eosin. This cell is larger, has a larger nucleus and fewer secretory granules than dark chief cells." "FMA:69081" - "Glandular cell of parathyroid epithelium. Example: Parathyroid chief cell and parathyroid oxyphil cells." "CALOHA:TS-1279" - "BTO:0000783" + "Any process that modulates the frequency, rate or extent of metanephric glomerular visceral epithelial cell development." + "The process in which a relatively unspecialized cell acquires the specialized features of a glutamatergic neuron." + "Apparatus located between the lungs and the buccal cavity. This apparatus is composed of a pair of arytenoid cartilages that are supported by the cricoid ring." "AAO:0000267 EHDAA2:0000904" + "A portion of smooth muscle tissue that is part of a venous system [Automatically generated definition]." "MA:0000715 EMAPA:36613" + + "EHDAA2:0001845" "Any hematopoietic stem cell that is part of a umbilical cord blood." - "Any of the immature or mature forms of a granular leukocyte with a nucleus that usually has two lobes connected by one or more slender threads of chromatin, and cytoplasm containing coarse, round granules that are uniform in size and which can be stained by the dye eosin. Eosinophils are CD9-positive, CD191-positive, and CD193-positive." "CALOHA:TS-0279 FMA:62861 BTO:0000399" - "A cellular receptor which mediates the sense of temperature. Thermoreceptor cells in vertebrates are mostly located under the skin. In mammals there are separate types of thermoreceptors for cold and for warmth and pain receptor cells which detect cold or heat extreme enough to cause pain." - "A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages." "BTO:0004730" - - "BTO:0003393" - "A fully differentiated eosinophil, a granular leukocyte with a nucleus that usually has two lobes connected by one or more slender threads, and cytoplasm containing coarse, round granules that are uniform in size and which can be stained by the dye eosin. Cells are also differentiated from other granulocytes by a small nuclear-to-cytoplasm ratio (1:3). This cell type is CD49d-positive." - - "A tissue-resident macrophage located in the bone marrow. This cell type is B220-negative, CD3e-negative, Ly-6C-negative, CD115-positive, F4/80-positive." "BTO:0004732" - "A conventional B cell subject to antigenic stimulation and dependent on T cell help and with a distinct surface marker expression pattern from B-1 B cells. These cells are CD43-negative." - "An OFF-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the outer half of the inner plexiform layer. The dendritic tree is not well filled and the dendrites are more delicate than in type 1 cells. The axon terminal is bushier and exhibits a dense plexus of varicosities in the inner part of sublamina 1 (Ghosh et al., 2004). It can be differentiated from other retinal bipolar neurons by its expression of marker genes: Neto1, Lhx3 and Irx-6 (Shekhar, 2016)." + "The process in which a relatively unspecialized cell acquires specialized features of a lung ciliated cell. A lung ciliated cell is a specialized lung epithelial cell that contains cilia for moving substances released from lung secretory cells." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of organic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "Any process that stops, prevents, or reduces the frequency, rate or extent of muscle cell differentiation." "A peptide hormone secreting cell that produces growth hormone, somatotropin." - "A supporting cell projecting inward from the basement membrane of seminiferous tubules. They surround and nourish the developing male germ cells and secrete androgen binding protein. Their tight junctions with the spermatogonia and spermatocytes provide a blood-testis barrier." "BTO:0001238 FMA:72298 CALOHA:TS-0922 VHOG:0001348" - "A thymic epithelial cell type with low nuclear and cytoplasmic electrondensity; has a round, euchromatic nucleus and occurs in small groups at the corticomedullary junction or scattered singly in the medulla." "FMA:72213" - - "Any of the immature forms of a neutrophil in which neutrophilic specific granules are present but other phenotypic features of the mature form may be lacking." - "A transient hepatic stem cell observed after liver injury with a high nuclear to cytoplasm ratio that can differentiate into mature hepatocytes and bile duct cells. Arises from more than one tissue." "FMA:86576 BTO:0004270" - "A uninucleate spore formed on specialized cells or projections, sterigma, of a conidiophore head." "FAO:0000033" - "A transitional stage B cell that has the phenotype surface IgM-positive, surface IgD-postive, CD21-positive, CD23-positive, CD62L-negative, CD93-positive and is located in the splenic B follicles. This cell type has also been described as IgM-high, CD19-positive, B220-positive, AA4-positive, and CD23-positive." + "A bone that is part of a the pedal digitopodium skeleton - i.e. the toes or the metatarsal skeleton." + "A cell cycle process by which the cell nucleus divides as part of a meiotic cell cycle in the female germline." + "A response to protect an organism from a directly detected or perceived external threat from a nematode or nematodes, which results in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack." + "Any process that modulates the frequency, rate or extent of cardiac muscle cell proliferation." + "Formation of a complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator)." + "The directed movement of histamine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Histamine is a physiologically active amine, found in plant and animal tissue and released from mast cells as part of an allergic reaction in humans." "Cell that has the potential to form a skeletal cell type (e.g. cells in periosteum, cells in marrow) and produce extracellular matrix (often mineralized) and skeletal tissue (often mineralized)." - "A subtype of enteroendocrine cells found in the gastrointestinal mucosa, particularly in the glands of pyloric antrum; duodenum; and ileum. These cell type secretes serotonin and some neurotransmitters including enkephalins and substance P. Their secretory granules stain readily with silver (argentaffin stain)." "FMA:62934 FMA:83132" - "Squamous cell of tonsil epithelium." "CALOHA:TS-1253" - "CD8-positive, alpha-beta memory T cell with the phenotype CCR7-positive, CD127-positive, CD45RA-negative, CD45RO-positive, and CD25-negative." + "The muscles associated with the larynx." "UMLS:C0023054 NCIT:C32934 BTO:0001626 Wikipedia:Muscles_of_larynx GAID:144 MA:0001768 MESH:D007821 EMAPA:35473 FMA:46562 SCTID:181744001" "Cell that is part of the migratory cranial neural crest population. Migratory cranial neural crest cells develop from premigratory cranial neural crest cells and have undergone epithelial to mesenchymal transition and delamination." - "An endothelial cell that lines the vasculature." - "FBbt:00000092" - "KUPO:0001092" + "The ossified region of endochondral and membranous bone located in the clitoris of most mammals except humans; it is homologous to the penile bone (aka as baculum, penis bone or os penis) in male mammals." "MA:0000387 EMAPA:30823" + "The unpaired embryonic prominence that is formed by the tissues surrounding the forebrain vesicle and develops into the forehead and bridge of the nose/snout." "Wikipedia:Frontonasal_prominence EHDAA:4778 EMAPA:16681 VHOG:0001319 SCTID:361486000 EHDAA2:0000578 NCIT:C34182 UMLS:C1517321 FMA:293101" + "EHDAA:4406 FMA:67611 EHDAA2:0004046 galen:Valve EHDAA:1892" + "The directed movement of substances to the plasma membrane in transport vesicles that fuse with the plasma membrane by exocytosis." + "Any process that activates or increases the frequency, rate or extent of the regulated release of saliva." + "EMAPA:35702" - "KUPO:0001112" - "A chromaffin cell that is part of the right ovary." "FMA:74320" - "A CD38-positive naive B cell is a mature B cell that has the phenotype CD38-positive, surface IgD-positive, surface IgM-positive, and CD27-negative, and that has not yet been activated by antigen in the periphery." - "An epithelial cell of the cornea." "FMA:70551 BTO:0004298 CALOHA:TS-0173" - + "Morphogenesis, during the embryonic phase, of a tissue or tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." + "The series of events required for an organism to receive a temperature stimulus, convert it to a molecular signal, and recognize and characterize the signal. Thermoception in larger animals is mainly done in the skin; mammals have at least two types of sensor, for detecting heat (temperatures above body temperature) and cold (temperatures below body temperature)." "Wikipedia:Thermoception" + "The process in which the anatomical structures of an ectodermal placode are generated and organized. An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm." + "The process whose specific outcome is the progression of a parietal peritoneum over time, from its formation to the mature structure." + "Any process that modulates the frequency, rate or extent of calcium ion import across plasma membrane." + "The metanephric distal tubule is a metanephric nephron tubule that begins at the metanephric macula densa and extends to the metanephric connecting tubule[GO]." + "The process aimed at the progression of a nucleate erythrocyte over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell." "A dendritic cell that is located in a vermiform appendix." - "Any osteoblast that is part of a skull." - "A fully differentiated basophil, a granular leukocyte with an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation." "CALOHA:TS-0688 BTO:0001026" - "A hematopoietic stem cell with long term self renewal capability. This cell is Kit-positive, Sca1-positive, CD150-positive, CD90-low, CD34-negative and Flt3-negative." - "A mesothelial fibroblast found in the leptomeninx." - "KUPO:0001047" - "Notochordal cell that is inner portion of the notochord and becomes vacuolated as development proceeds." - "A secondary lymphoid organ macrophage found in the spleen." "FMA:83026" + "A white matter of cerebral lobe that is part of a frontal lobe." "SCTID:362331002 FMA:256178" + "An amacrine cell with a small dendritic field with post-synaptic terminals in S3 and S4." + "Any of the cranial nerves, or their central nervous system analogs (the optic tract, the epiphyseal tract). These analogs are not true nerves, and are instead evaginated sensory afferents emanating from the brain." + "The periodic casting off and regeneration of an outer covering of cuticle, feathers, hair, horns, skin, etc." "An epithelial cell that is part of the outer root sheath." - "An enterocyte that is part of the epithelium of small intestine." "FMA:263086" - "A slow muscle cell that has large amounts of myoglobin, stores energy as triglycerides, generates ATP by the oxidative method and is resistant to fatigue." "MESH:A02.633.565.700 FMA:84413 BTO:0001812 CALOHA:TS-0940" - "KUPO:0001041" - "A columnar/cuboidal epithelial cell that secretes cerebrospinal fluid." + "A vertebral arch that is part of the first cervical vertebra." "SCTID:272708001 Wikipedia:Arch_of_the_atlas FMA:23975" + "Any process that modulates the frequency, rate or extent of establishment of T cell polarity." "KUPO:0001064" - "A smooth muscle cell derived from the neural crest." + + "The expansion of a cardiac muscle cell population by cell division." "A pre-BCR positive B cell that is CD38-high." - "A macrophage located in the vermiform appendix." - - "An epithelial cell found in the lining of the stomach." "FMA:62948" - "A skeletal muscle cell that has become mitotically active - typically following muscle damage." - "A thymocyte found in the fetal thymus." - "A fully differentiated plasma cell that secretes IgM." - - "An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The axon terminal is narrowly stratified and are found just below a calretinin-expressing band in sublamina 4 of the inner plexiform layer." - "A Purkinje myocyte that is part of the atrioventricular bundle." "FMA:83393" - "An intratelencephalic-projecting glutamatergic neuron with a soma found in layer 5 of the human primary motor cortex." "ILX:0770157" - "A pluripotent stem cell has the ability to form cells from all three germ layers (ectoderm, mesoderm, and endoderm). However, unlike totipotent stem cells, they cell can not generate all the cells of the whole organism such as placenta." "FMA:70570" - "Glandular cell of salivary gland. Example: Serous cells, mucous cells, cuboidal epithelial cells of the intercalated ducts, simple cuboidal epithelium of the striated ducts, epithelial cells of excretory ducts." "CALOHA:TS-1282" - - "Any serous secreting cell that is part of the tracheobronchial epithelium." - "A thick walled spore containing one or more haploid nuclei produced by sexual reproduction in an Basidiomycete; formed externally on extrusions of the basidium." "FAO:0000021 BTO:0002166" + + "The initial thyroid precursor, the thyroid primordium, starts as a simple midline thickening and develops to form the thyroid diverticulum. This structure is initially hollow, although it later solidifies and becomes bilobed. The 2 lobes are located on either side of the midline and are connected via an isthmus." "UMLS:C1519512 EHDAA2:0002033 AAO:0011106 NCIT:C34312 XAO:0000444 EMAPA:16361 EHDAA:952 TAO:0001081 ZFA:0001081 BTO:0004709" + "Any process that activates or increases the frequency, rate or extent of stem cell population maintenance." + "The process in which a relatively unspecialized monocyte acquires the specialized features of a multinuclear osteoclast. An osteoclast is a specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue." + "Any process that contributes to cytokine production by a T-helper 2 cell." + "The veins that drain blood from the ileum into the superior mesenteric vein." "UMLS:C1301431 EMAPA:37149 NCIT:C53046 MA:0002140 FMA:15405 Wikipedia:Ileal_veins" + "The upper dilated end of the nasolacrimal duct that is lodged in a deep groove formed by the lacrimal bone and frontal process of the maxilla; it connects the lacrimal canaliculi, which drain tears from the eye's surface, and the nasolacrimal duct, which conveys this fluid into the nasal cavity; like the nasolacrimal duct, the sac is lined by stratified columnar epithelium with mucus-secreting goblet cells, and is surrounded by connective tissue." "FMA:20289 SCTID:362534009 UMLS:C0229289 NCIT:C32909 MA:0001298 Wikipedia:Lacrimal_sac" + "The elevation of thickened mesothelium and underlying mesenchyme found on the ventromedial border of the embryonic mesonephros in which the primordial germ cells become embedded, establishing it as the primordium of the testis or ovary." "EHDAA2:0004044 NCIT:C34321 FMA:321917 Wikipedia:Gonadal_ridge EFO:0001414 SCTID:361399001 NCIT:C34184 AAO:0011047 EMAPA:35899 UMLS:C1512243 UMLS:C0231047 SCTID:308801004 XAO:0000018 BTO:0001402" + + "A lymphatic vessel smooth muscle that is part of a respiratory system [Automatically generated definition]." "MA:0001826 EMAPA:37582" + "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells of the nephron tubule as it progresses from its formation to the mature state." + "The outermost layer of the stomach wall, consisting of layers of connective tissue continuous with the peritoneum." "FMA:14914 EMAPA:35822 MA:0001626 SCTID:1353004 UMLS:C1517453 NCIT:C32662" + "An epithelium that is part of a camera-type eye." "EMAPA:35957 MA:0003162" + "A rhodopsin-like G-protein coupled receptor that is a translation product of the human PTGDR, PTGDR2, PTGER1 to PTGER4, PTGFR, PTGIR, or TBXA2R genes, 1:1 orthologs thereof, or a semi-ortholog thereof. The active form binds prostanoids (prostaglandins and thromboxanes)." "PIRSF:PIRSF001962 IUPHARfam:58" + "The reproductive developmental process whose specific outcome is the progression of the uterus over time, from its formation to the mature structure." + "The process in which the anatomical structures of the Malpighian tubule are generated and organized. This process takes place entirely during the embryonic phase. A Malpighian tubule is a fine, thin-walled excretory tubule in insects which leads into the posterior part of the gut." + "The uterus in pregnancy." "NCIT:C12406 SCTID:362253003 ncithesaurus:Gravid_Uterus UMLS:C1514389" + "The process in which a relatively unspecialized cell acquires specialized features of an noradrenergic neuron that is part of the brainstem." + "A transparent structure that is part of a visual sense organ, the function of which is to direct or focus light onto a photoreceptor array." + "Any process that decreases the rate, frequency or extent of the synthesis or release of any leukotriene following a stimulus as part of an inflammatory response." + "Any process that activates or increases the frequency, rate, extent or direction of cell growth." - "An arterial endothelial cell that is part of the aorta endothelium." "CALOHA:TS-0047 BTO:0003245" - "KUPO:0001038" - "CD8_alpha-positive CD11b-negative dendritic cell is a conventional dendritic cell that is CD11b-negative, CD4-negative and is CD205-positive and CD8_alpha-positive." - "A polychromatiic erythroblast that is Gly-A-positive and CD71-low." - "CD4-positive, alpha-beta memory T cell with the phenotype CCR7-negative, CD127-positive, CD45RA-negative, CD45RO-positive, and CD25-negative." + "A two-lobed endocrine gland found in all vertebrates, located in front of and on either side of the trachea in humans, and producing various hormones, such as triiodothyronine and calcitonin[BTO]." "galen:ThyroidGland MESH:D013961 UMLS:C0040132 EHDAA:2148 AAO:0010544 MA:0000129 CALOHA:TS-1047 MIAA:0000081 EFO:0000861 EV:0100133 NCIT:C12400 VHOG:0000418 FMA:9603 SCTID:181117000 MAT:0000081 XAO:0000162 BTO:0001379 Wikipedia:Thyroid GAID:465 EHDAA2:0002028 EHDAA:2975 EMAPA:17068" + "Enables the transfer of acetylcholine from one side of a membrane to the other. Acetylcholine is an acetic acid ester of the organic base choline and functions as a neurotransmitter, released at the synapses of parasympathetic nerves and at neuromuscular junctions." "Reactome:R-HSA-264615" + "The part of the cortex that is responsible for processing visual information." "An astrocyte of the cerebral cortex." + "CD4-positive, alpha-beta memory T cell with the phenotype CCR7-negative, CD127-positive, CD45RA-negative, CD45RO-positive, and CD25-negative." + "An alveolar duct that is part of a left lung [Automatically generated definition]." "NCIT:C49250 EMAPA:19183 MA:0001776 UMLS:C1708672" "An epithelial cell of the intrahepatic portion of the bile duct. These cells are flattened or cuboidal in shape, and have a small nuclear-to-cytoplasmic ratio relative to large/extrahepatic cholangiocytes." - "KUPO:0001090" - "A type of intrafusal muscle fiber that lies in the center of a muscle spindle. Nuclei are clustered centrally and give the equatorial region a swollen appearance. They are associated with associated with dynamic gamma motor neurons, and the stretching of the equatorial region of the nuclear bag fibers results in an increase in the firing rate of type Ia sensory fibers." - "A group 1 innate lymphoid cell that is non-cytotoxic." - "A pyramidal neuron which has an apical tree which is oriented towards the white matter." - "A cell that takes up and metabolizes substances." - "A CD8-positive, alpha beta memory T cell with the phenotype CD45RA-positive, CD45RO-negative, and CCR7-negative." - "An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue." "BTO:0000751 FMA:62852 CALOHA:TS-0549" - "An endothelial cell found in the glomerulus of the kidney. This cell is flattened, highly fenestrated, and plays a vital role in the formation of glomerular ultrafiltrate." "FMA:70970 BTO:0004632" - "Type of radial astrocyte in the cerebellar cortex that have their cell bodies in the Purkinje cell layer and processes that extend into the molecular layer, terminating with bulbous endfeet at the pial surface. Bergmann glia express high densities of glutamate transporters that limit diffusion of the neurotransmitter glutamate during its release from synaptic terminals. Besides their role in early development of the cerebellum, Bergmann glia are also required for the pruning or addition of synapses." "FMA:54559" - "An immature T cell located in the thymus." "CALOHA:TS-1042 BTO:0001372 XAO:0003159 FMA:72202" - "A slow muscle cell that contains high levels of myoglobin and oxygen storing proteins giving the cell a red appearance." "FMA:84448" - "An enterocyte that is located in the anorectum." - "An epidermal cell which synthesizes keratin and undergoes a characteristic change as it moves upward from the basal layers of the epidermis to the cornified (horny) layer of the skin. Successive stages of differentiation of the keratinocytes forming the epidermal layers are basal cell, spinous or prickle cell, and the granular cell." "CALOHA:TS-0500 BTO:0000667 FMA:62879" - - - "A cell of an exocrine gland; i.e. a gland that discharges its secretion via a duct." "FMA:16014" - "A thermoreceptor cell that detects reduced temperatures." + "Mesenchyme that is part of a developing upper jaw [Automatically generated definition]." "VHOG:0001099 EMAPA:17929 EHDAA2:0002124 EHDAA:8031" + "Any process that activates or increases the frequency, rate or extent of glomerular filtration. Glomerular filtration is the processs whereby blood is filtered by the glomerulus into the renal tubule." + "A protein that is a translation product of the KLRB1 gene or its closely related paralogs (KLRB1A-F). There are lineage-specific expansions in mouse and rat." "PIRSF:PIRSF038804" + "Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types." "BILA:0000055 VHOG:0001762 TGMA:0001847 AAO:0010048 ZFA:0001488 HAO:0000055 TAO:0001488 CARO:0000055 AEO:0000055 XAO:0003037 EHDAA2:0003055" + "A mucosa that is part of a neck of urinary bladder [Automatically generated definition]." "FMA:17846" + "Vein that carries blood away from the liver[ZFA]." "FMA:14337 galen:HepaticVein TAO:0000670 UMLS:C0019155 MA:0003015 Wikipedia:Hepatic_vein ZFA:0000670 EMAPA:19221 AAO:0010216 GAID:534 XAO:0000387 NCIT:C32736 MESH:D006503 SCTID:278191001" + "The regulated production of heat in response to short term environmental changes, such as stress, diet or reduced temperature." + "Large intrinsic neuron located in the granule layer of the cerebellar cortex that extends its dendrites into the molecular layer where they receive contact from parallel fibers. The axon of the Golgi cell ramifies densely in the granule layer and enters into a complex arrangement with mossy fiber terminals and granule cell dendrites to form the cerebellar glomerulus. Llinas, Walton and Lang. In The Synaptic Organization of the Brain. 5th ed. 2004." "MESH:D000080906" + "A vascular endothelial growth factor receptor 2 that is encoded in the genome of human." "DTO:03100560 UniProtKB:P35968" + "MA:0002264 FMA:18890 EMAPA:37158" + "The elimination of ammonium ions from an excretory cell." + "An epithelium that is part of a crypt of Lieberkuhn." "NCIT:C83191 UMLS:C2826787" - "KUPO:0001091" - "KUPO:0001111" - "A CD38-positive IgG-negative memory B cell is an IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype CD38-positive and IgG-negative." - "A macroconidium that has more than one nucleus." "FAO:0000035" - "A NK1.1-positive T cell that is CD94-positive and Ly49Cl-positive." - "A mucus-secreting cell, with numerous apical secretory vesicles containing mucins; nucleus are basally displaced; numerous at the neck of mucus secreting glands" - "A trophoblast cell that arises in the junctional zone (basal plate) of the placenta." - - "An enteroendocrine cell that stores and secretes Ghrelin." "FMA:63418 FMA:63207" + "A funnel shaped proximal portion of the ureter that is formed by convergence of the major calices [MP]." "UMLS:C0227666 EMAPA:17948 GAID:426 MESH:D007682 NCIT:C12887 Wikipedia:Renal_pelvis galen:RenalPelvis SCTID:362221007 CALOHA:TS-2230 FMA:15575 MA:0000374" + "The triangular region on the periphery of the liver lobules that contain a bile duct and a terminal branch of the hepatic artery and portal vein, and may also include a lymphatic vessel." "NCIT:C33341 MA:0002498 FMA:14653 UMLS:C0682620" + "Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity." "EHDAA2:0001929 Wikipedia:Stomodeum FMA:295846 EMAPA:16263 UMLS:C1514977 TGMA:0000135 TAO:0001290 BTO:0004224 NCIT:C34306 ZFA:0001290 XAO:0000269" + "The process in which the anatomical structures of branches in an epithelial tube are generated and organized. A tube is a long hollow cylinder." + "VHOG:0001351 EHDAA2:0000171 EMAPA_RETIRED:16565 EMAPA:16561" "Obsolete. Use PO:0025017 from Plant Ontology instead. A plant cell that arises through meiosis and develops into a gametophyte." - "Wikipedia:Kidney_collecting_duct_cell KUPO:0001012" "Skeletogenic cell that produces cementum (a bony substance that covers the root of a tooth), is part of the odontogenic papilla, and develops from a precementoblast cell." "CALOHA:TS-1164 FMA:63002" - "A fibroblast that is part of upper back skin." - "A striated muscle cell of an arthropod heart that participates in heart contraction." - "A photoreceptor cell that is sensitive to red light." - "A photoreceptor cell that is sensitive to green light." - "A plasmablast that secretes IgM." - "An epithelial cell of the extrahepatic bile ducts, including the left and right hepatic duct, common hepatic duct, and common bile duct. They are columnar in shape, and have a large nuclear-to-cytoplasmic ratio relative to small/intrahepatic cholangiocytes." - "A class switched memory B cell that expresses IgE on the cell surface." - "A CNS neuron of the cerebral cortex." "BTO:0004102 FMA:84104" - "An epithelial cell that is part of the nasolacrimal duct." "FMA:70561" + "A monostratified retinal ganglion cell that has post synaptic terminals in sublaminar layer S2 and is depolarized by decreased illumination of their receptive field center" + "The process whose specific outcome is the progression of the cerebellar molecular layer nerve over time, from its formation to the mature structure. The molecular layer is the outermost layer of the cerebellar cortex. It contains the parallel fibers of the granule cells, interneurons such as stellate and basket cells, and the dendrites of the underlying Purkinje cells." + "An epithelium that is part of a embryonic cloaca." "EHDAA2:0004585" + "Any process that modulates the frequency, rate or extent of placenta blood vessel development." + "Any process that stops, prevents, or reduces the frequency, rate or extent of macrophage apoptotic process." + "Any process that decreases the rate, frequency or extent of epithelial cell proliferation that contributes to the progression of the prostate gland over time." + "Any process that modulates the rate, frequency or extent of kidney development. Kidney development is the process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and excretes the end products of body metabolism in the form of urine." + "A serous membrane that is part of a esophagus [Automatically generated definition]." "EMAPA:35322 FMA:63057 MA:0001571" "A neural crest cell that gives rise to cells of the enteric nervous system." - "A double-positive, alpha-beta thymocyte that is small and not proliferating." - "A fibroblast that is part of villous mesenchyme." - "A brush border epithelial cell located in the proximal tubule of the kidney that detects fluid flow." - "A smooth muscle cell of the bachiocephalic vasculature." - "A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure." - "Lymphatic progenitor cells." - "A cuboidal epithelial cell of the kidney which regulates sodium and potassium balance. The activity of sodium and potassium channels on the cells apical membrane is regulated by aldosterone and vasopressin. In mammals these cells are located in the renal collecting ducts." - "A D cell located in the colon." "FMA:268744" - - "Obsolete. Use PO:0000191 from Plant Ontology instead. A cell in the micropylar end of the embryo sac associated with the egg in the egg apparatus of angiosperms. Plays a vital role in fertilization." - - "A CNS interneuron located in the dorsal horn of the spinal cord." - "A lymphocyte of B lineage with the commitment to express an immunoglobulin complex." - "A skeletal muscle myoblast that is part of a skeletal mucle. These cells are formed following acivation and division of skeletal muscle satellite cells. They form a transient population that is lost when they fuse to form skeletal muscle fibers." - "A transitional myocyte that is part of the interventricular septum." "FMA:263154" - "A specialized epithelial cell that is capable of synthesizing and secreting certain biomolecules." "CALOHA:TS-2085 FMA:86494" - "The set of neurons that receives neural inputs via bipolar, horizontal and amacrine cells. The axons of these cells make up the optic nerve." "BTO:0001800 FMA:67765" - "A metanephric glomerular visceral epithelial cell is a specialized epithelial cell that contains \"feet\" that interdigitate with the \"feet\" of other glomerular epithelial cells in the metanephros." - "A glandular epithelial cell that is part of the stomach." "FMA:86554 CALOHA:TS-1284" - "KUPO:0001081" - "KUPO:0001037" - "KUPO:0001089" - "An intestinal crypt stem cell that is located in the vermiform appendix. These stem cells reside at the bottom of crypts in the appendix and are highly proliferative. They either differentiate into transit amplifying cells or self-renew to form new stem cells." - "A germinal center B cell that is rapidly dividing and has the phenotype IgD-negative, CD38-positive, and CD77-positive. Somatic hypermutation of the immunoglobulin V gene region can occur during proliferation of this cell type." + "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells of the pronephric nephron tubule as it progresses from its formation to the mature state." + "The regulated release of any mineralocorticoid into the circulatory system. Mineralocorticoids are a class of steroid hormones that regulate water and electrolyte metabolism." + "Anteriosuperior, smooth-walled portion of the cavity of the right ventricle, beginning at the supraventricular crest and terminating in the pulmonary trunk." "UMLS:C1881209 SCTID:244379003 NCIT:C61368 FMA:7216 EMAPA:37926" + "The epidermis is the entire outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species[GO]." "BSA:0000073 HAO:0000298 BTO:0000313 WBbt:0005733 TADS:0000109 Wikipedia:Epidermis_(zoology)" + "The process in which a precursor cell type acquires the specialized features of a myeloid progenitor cell. Myeloid progenitor cells include progenitor cells for any of the myeloid lineages." + "The sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the orbit and its contents, the nasal cavity and the skin of the nose and forehead." "AAO:0010648 Wikipedia:Ophthalmic_nerve MA:0001104 VHOG:0001349 NCIT:C33215 EMAPA:17800 BTO:0000926 EHDAA2:0002088 UMLS:C0029082 EHDAA:3744 GAID:837 SCTID:280210000 MESH:D009882 FMA:52621" + "A mucosa that is part of a seminal vesicle [Automatically generated definition]." "SCTID:252260007 FMA:19405" + "A serous sac which is the aggregate of the conjunctiva plus the conjunctival space." "FMA:20291 EMAPA:18233 SCTID:362531001" + "Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to cell cortex." + "The major preaxial endochondral element in the posterior zeugopod[Phenoscape]." + "A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of T cell anergy." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a progesterone stimulus." + "The process in which the anatomical structures of left cardiac ventricle muscle are generated and organized." + "A specialized epithelial cell that is capable of synthesizing and secreting certain biomolecules." "FMA:86494 CALOHA:TS-2085" + "GC_ID:1" + "The aspect of the prostate facing the pubic symphysis." "FMA:19591 SCTID:279696001 NCIT:C13089 UMLS:C0227960" + "Binding to a ribosome." + "FMA:24218 SCTID:123852005 XAO:0000040" + "Any process that stops, prevents or reduces the frequency, rate or extent of trophectodermal cell proliferation." "An enteroendocrine cell that is located in the small intestine." - "A serous secreting cell that is part of the epithelium of trachea." "FMA:263078" - "A cell of the embryo." "WBbt:0007028 FMA:82840 FMA:82841 CALOHA:TS-0263" - "The subcutaneous mechanoreceptors that innervate tylotrich hair follicles." - "A muscle cell that develops tension more slowly than a fast-twitch fiber." "FMA:84448" - "A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex." "CALOHA:TS-1001 VHOG:0001479 BTO:0000782 FMA:62870" - "A pigment cell located in the epithelium of the iris." - "A type II vestibular sensory cell that is part of the epithelium of macula of saccule of membranous labyrinth." "FMA:263198" + "The multiplication or reproduction of epithelial cells, resulting in the expansion of a cell population that contributes to the progression of the prostate gland over time." + "Combining with a signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: ATP + a protein-L-tyrosine = ADP + a protein-L-tyrosine phosphate." "Reactome:R-HSA-169905 Reactome:R-HSA-8987202 Reactome:R-HSA-74742 Reactome:R-HSA-8987070 Reactome:R-HSA-8986995 Reactome:R-HSA-8983300 EC:2.7.10.1 Reactome:R-HSA-8987150 Reactome:R-HSA-167019 Reactome:R-HSA-8950537 Reactome:R-HSA-8950364 Reactome:R-HSA-8983424 Reactome:R-HSA-8950354 Reactome:R-HSA-8987040 Reactome:R-HSA-8950269 MetaCyc:2.7.10.1-RXN Reactome:R-HSA-8982163 Reactome:R-HSA-8853792 Reactome:R-HSA-8950757 Reactome:R-HSA-6784324 Reactome:R-HSA-8950485 Reactome:R-HSA-74711 Reactome:R-HSA-8852552 Reactome:R-HSA-8950453 Reactome:R-HSA-8987042 Reactome:R-HSA-198295 Reactome:R-HSA-8987255 Reactome:R-HSA-167683 Reactome:R-HSA-8950405 Reactome:R-HSA-8950423 Reactome:R-HSA-8986985 Reactome:R-HSA-8987012 Reactome:R-HSA-166544 Reactome:R-HSA-8986994 Reactome:R-HSA-8983371 Reactome:R-HSA-8987084 Reactome:R-HSA-8987141 Reactome:R-HSA-8987179 Reactome:R-HSA-8987129 Reactome:R-HSA-8987096 Reactome:R-HSA-8983309 Reactome:R-HSA-177933 Reactome:R-HSA-8950340 Reactome:R-HSA-8950591" + "An epithelium that is part of a iris [Automatically generated definition]." "MA:0002826 EMAPA:35447 FMA:58517" + "The process in which an antigen-presenting cell expresses peptide antigen in association with an MHC protein complex on its cell surface, including proteolysis and transport steps for the peptide antigen both prior to and following assembly with the MHC protein complex. The peptide antigen is typically, but not always, processed from an endogenous or exogenous protein." + "An NKG2-A/NKG2-B type II integral membrane protein that is encoded in the genome of human." "UniProtKB:P26715 Reactome:R-HSA-3006545" + "An epicardial layer that lines a cardiac ventricle." "ZFA:0005058 TAO:0005058 FMA:12150" + "Epithelium bearing vibratile cilia on the free surface." + "The directed movement of a border cell through the nurse cells to reach the oocyte. An example of this is found in Drosophila melanogaster." + "The regulation of body fluids process in which parasympathetic nerves stimulate the bladder wall muscle to contract and expel urine from the body." "Wikipedia:Urination" + "EMAPA:30478" - - "An erythroblast that is GlyA-positive and CD71-negative." - "A modified epidermal cell located in the stratum basale. They are found mostly in areas where sensory perception is acute. Merkel cells are closely associated with an expanded terminal bulb of an afferent myelinated nerve fiber." "FMA:70548" + "The middle layer of the heart, comprised mainly of striated cardiac muscle fibers." "MESH:D009206 VHOG:0000083 SCTID:362012001 XAO:0000065 NCIT:C12371 galen:Myocardium AAO:0010410 EFO:0000819 RETIRED_EHDAA2:0001220 TAO:0001319 FMA:9462 BTO:0000901 MA:0000164 EHDAA2:0004150 EV:0100022 Wikipedia:Myocardium UMLS:C0027061 CALOHA:TS-0440 ZFA:0001319 BSA:0000089 GAID:173 MAT:0000453" + "Any process that activates or increases the frequency, rate or extent of plasmatocyte differentiation." + "Any process that an organism uses to control its balance, the orientation of the organism (or the head of the organism) in relation to the source of gravity. In humans and animals, balance is perceived through visual cues, the labyrinth system of the inner ears and information from skin pressure receptors and muscle and joint receptors." "A leukocyte with a single non-segmented nucleus in the mature form." "CALOHA:TS-0768 BTO:0000878 FMA:86713" "Cells forming a framework supporting the organ of Corti. Specific cells are those of Claudius, Deiters and Hensen." "A cell within an epithelial cell sheet whose main function is to act as an internal or external covering for a tissue or an organism." - "KUPO:0001078" - "A cell that is capable of detection of a stimulus involved in sensory perception." - "A pre-B-I cell is a precursor B cell that expresses CD34 and surrogate immunoglobulin light chain (VpreB , Lambda 5 (mouse)/14.1 (human)) on the cell surface, and TdT, Rag1,and Rag2 intracellularly. Cell type carries a D-JH DNA rearrangement, and lacks expression of immunglobulin heavy chain protein." - "A mononuclear cell that is part_of a bone marrow." "The outer phalangeal cells of the organ of Corti. This cell holds the base of the hair cell in a cup-shaped depression." "FMA:75725" - "KUPO:0001086" - "A cell that initiates an electrical signal and passes that signal to another cell." - "A smooth muscle cell that is part of the descending colon." "FMA:17520" - "A cell found in fat bodies whose primary function is intermediary metabolism." - "A type of enteocrine cell found in the periphery of the islets of Langerhans that secretes glucagon." "FMA:70585 BTO:0000990" - "A neuron that uses GABA as a vesicular neurotransmitter" "WBbt:0005190 FMA:84788" - "A cranial motor neuron whose soma is located in the midbrain andor hindbrain and which innervates the skeletal muscles of the eye or tongue." - "An OFF-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the outer half of the inner plexiform layer. The dendritic tree is delicate and the dendritic tips appear small when compared with type 1 cells. The axon terminal is stratified and restricted to sublamina 2 of the inner plexiform layer." + "Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA]." "MA:0000322 FMA:7501 CALOHA:TS-2138 SCTID:113234001 Wikipedia:Synovial_joint NCIT:C32461 galen:SynovialJoint ZFA:0005153 TAO:0005153 AEO:0000183 EHDAA2:0003183" + "Any process that modulates the frequency, rate or extent of skeletal muscle growth." + "Any process that stops, prevents, or reduces the frequency, rate or extent of a defense response." + "GC_ID:1" + "The process in which B cells acquire the specialized features of B-1a B cells. B-1a B cells are B-1 cells that express CD5 and arise from fetal liver precursors." + "Any muscle tissue of the distalmost portion of the digestive tract." + "EMAPA:29220" + "Any vein within the general circulation that transports blood back to the right atrium of the heart." "NCIT:C33719 FMA:66644 UMLS:C0447117 SCTID:244389004" + "A lymphocyte antigen 6A-2/6E-1 that is encoded in the genome of mouse." "UniProtKB:P05533" + "Any process in which a receptor is transported to, and/or maintained at the synapse, the junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell." - "A specialized epithelial secretory cell that moves chloride ions and water across the tubule epithelium." "FBbt:00005797" + "The region of the organism associated with the visceral organs." "FMA:231424 BTO:0001489 AEO:0000103" "A basophil mast progenitor cell that is Beta-7 integrin-high, Kit-positive FcRgammaII/III-positive and Sca1-negative." - "An euploid male germ cell of an early stage of spermatogenesis." "FMA:72291 FBbt:00004935 BTO:0000958 EMAPA:31482 CALOHA:TS-2193" - "Any retinal ganglion cell that is part of a retina." - "A myoblast that differentiates into skeletal muscle fibers." "FMA:84799" - "A cell of the adrenal cortex. Cell types include those that synthesize and secrete chemical derivatives (steroids) of cholesterol." "FMA:69545" - "KUPO:0001087" + "The body of stomach is the part of the stomach that lies between the fundus above and the pyloric antrum below; its boundaries are poorly defined[GO]." "EMAPA:35810 BTO:0000505 Wikipedia:Body_of_stomach MA:0002559 SCTID:362140009 galen:GastricCorpus NCIT:C12258 FMA:14560 UMLS:C0227230" + "The process whose specific outcome is the progression of the embryo over time, from zygote formation through a stage including a notochord and neural tube until birth or egg hatching." + "FMA:14621" + "A muscle layer that is part of a fallopian tube." "EMAPA:29046 SCTID:259488000 FMA:18318" + "A B-cell lymphoma 6 protein that is encoded in the genome of mouse." "UniProtKB:P41183" "A precursor cell destined to differentiate into smooth muscle myocytes." "FMA:84798" - "CD8_alpha-negative CD11b-negative dendritic cell is a conventional dendritic cell that is CD11b-negative, CD4-negative CD8_alpha-negative and is CD205-positive. This cell is able to cross- present antigen to CD8-alpha-positive T cells." - "A D cell located in the pancreas. Peripherally placed within the islets like type A cells; contains somatostatin." "FMA:70587 BTO:0000803" - "An innate lymphoid cell in the human with the phenotype CD34-negative, CD56-positive, CD117-positive.Thie cell type may include precusors to NK cells and ILC3 cells." - - "Bottle-shaped with narrow neck; broad, rounded basal portion where nucleus is located; stereocilia and a single kinocilium is present apically; receive nerve bouton at their base from an afferent cup-shaped (chalice or calyx) nerve ending." "FMA:62352" + "The lipid bilayer surrounding a cytoplasmic vesicle." + "The group of motor neurons residing in the pons that innervate the muscles of facial expression." "BAMS:7 VHOG:0001412 BM:Pons-VII BAMS:7N DHBA:12420 BAMS:VII NCIT:C12898 EHDAA2:0004638 FMA:54572 MESH:D065828 EV:0100267 UMLS:C0228740 MA:0001014 EMAPA:35338 SCTID:280166009" + "An endoglin that is encoded in the genome of human." "UniProtKB:P17813" + "A digital artery that is part of a hindlimb [Automatically generated definition]." "MA:0001964 FMA:69713 EMAPA:37214" + "Any process that modulates the frequency, rate or extent of natural killer cell proliferation." "A basophil precursor in the granulocytic series, being a cell intermediate in development between a promyelocyte and a metamyelocyte; in this stage, production of primary granules is complete and basophil-specific granules has started. No nucleolus is present. Markers are being integrin alpha-M-positive, fucosyltransferase FUT4-positive, CD33-positive, CD24-positive, aminopeptidase N-positive." "FMA:83543 BTO:0003456" - "A CD8-positive, CD4-negative thymocyte that is CD24-positive and expresses high levels of the alpha-beta T cell receptor." - "A gamma-delta intraepithelial T cell that has the phenotype CD8-alpha alpha-positive." - "A cell found in the bone marrow. This can include fibroblasts, macrophages, adipocytes, osteoblasts, osteoclasts, endothelial cells and hematopoietic cells." "FMA:83621 BTO:0004850" - "A subset of motor neurons that innervates intrafusal muscle fibers and has small diameter axons." - - + "Epithelial cell of the descending thin limb of the short loop (cortical) nephron limited to the outer medulla (mainly inner strip). It is known in some mammalian species that the short descending limb of the loop of Henle selectively expresses the serine protease Corin, the homeobox TF Uncx, and the urea channel Slc14a2." + "A crystal cell that derives from the larval lymph gland." + "Any process that activates or increases the frequency, rate or extent of nephron tubule epithelial cell differentiation." + "A protein that is a translation product of the human NCR1 gene or a 1:1 ortholog thereof." + "A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses." "TAO:0005251 MESH:D055806 ZFA:0005251" + "The morphogenetic process in which the foregut region specified to become the pancreas forms a bud." + "The directed movement of a protein to a specific location in a postsynaptic membrane." + "A component of a cell contained within (but not including) the plasma membrane. In eukaryotes it includes the nucleus and cytoplasm." "Wikipedia:Intracellular" "A cell of the middle germ layer of the embryo." "FMA:72554" - "OBSOLETE (was not defined before being made obsolete)." - "A thymocyte that has a T cell receptor consisting of a gamma chain that does not contain the Vgamma2 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-negative." - "NK cell that has the phenotype CD56-bright, CD16-negative, and CD84-positive with the function to secrete interferon-gamma but is not cytotoxic." - "An epithelial cell that has a cilia." "FMA:70605" - "OBSOLETED. Commonly used for a cell in root epidermis that gives rise to a root hair. The daughter cell produced by the asymmetric division of a root epidermal cell that gives rise to a root hair." - "A cell of the early embryo at the developmental stage in which the blastomeres, resulting from repeated mitotic divisions of the fertilized ovum (zygote), form a compact cell mass." - "Specialized elongated ventricular ependymal cell that has processes that extend to the outer, or pial, surface of the CNS. Resemble spongioblasts seen in developing brain. Found in the adult brain in the third ventricle, cerebral aqueduct, spinal canal and floor of the fourth ventricle." "FMA:54560 BTO:0001953" - "A specialized mononuclear osteoclast associated with the absorption and removal of cementum." - "A cuboidal epithelial cell of the kidney that regulates acid/base balance." "FMA:86560" - "A chromaffin cell that is part of the adrenal cortex." "FMA:69795" - "A fibroblast of pulmonary artery." - - "A hematopoietic progenitor that has some limited self-renewal capability. Cells are lin-negative, Kit-positive, CD34-positive, and Slamf1-positive." - "A smooth muscle cell that is part of the transverse colon." "FMA:17519" - "An epithelial cell of the pancreas." "BTO:0000028" - + "An orbitosphenoid endochondral element that is composed primarily of a pre-cartilage condensation." "EHDAA2:0003449" + + "The change in morphology and behavior of a eosinophil resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor." + "The chemical reactions and pathways resulting in the breakdown of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another." + "The multiplication or reproduction of blood vessel endothelial cells, resulting in the expansion of a cell population." + "EV:0300051 XAO:1000010 XtroDO:0000083 BILS:0000112 ZFS:0000051 MmusDv:0000043 EFO:0001300 BTO:0002168 OGES:000009" + "The process whose specific outcome is the progression of a serous membrane over time, from its formation to the mature structure." + "Any process that increases the rate, frequency or extent of the transition where a mesenchymal cell establishes apical/basolateral polarity, forms intercellular adhesive junctions, synthesizes basement membrane components and becomes an epithelial cell that will contribute to the shaping of the metanephros." + "Any process that stops, prevents, or reduces the frequency, rate or extent of dendrite morphogenesis." "Immature CD11c-low plasmacytoid dendritic cell is a CD11c-low plasmacytoid dendritic cell that is CD80-low and CD86-low." - "A cell that lines the trabecular meshwork, which is an area of tissue in the eye located around the base of the cornea, near the ciliary body, and is responsible for draining the aqueous humor from the eye via the anterior chamber (the chamber on the front of the eye covered by the cornea). This cell may play a role in regulating intraocular pressure." - "A neuron that releases dopamine as a neurotransmitter." "WBbt:0006746 FMA:84787 BTO:0004032" "A large, progesterone secreting cell in the corpus luteum that develops from the granulosa cells." "FMA:18689" - "KUPO:0001060" - "Any hepatocyte that is part of the liver lobule centrilobular region. These cells are the primary location for the biotransformation of drugs." - "A pigment cell derived from the neural crest. Contains uric acid or other purine crystals deposited in stacks called leucosomes. The crystals reflect light and this gives a white appearance under white light." - "Any of the immature or mature forms of a granular leukocyte that in its mature form has an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse, bluish-black granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation. A basophil is CD123-positive, CD193-positive, CD203c-positive, and FceRIa-positive." "FMA:62862 CALOHA:TS-0073 BTO:0000129" - "A cell that lacks a nucleus." "FMA:68647" - "Neuromast mantle cell is a non-sensory cell. Neuromast mantle cells surround the neuromast support cells and neuromast hair cells, separating the neuromast from the epidermis, and secrete cupula in which the ciliary bundles of all the hair cells are embedded." + "A fallopian tube that is part of a left side of organism [Automatically generated definition]." "UMLS:C0227902 MA:0001716 NCIT:C32959 SCTID:280107002 FMA:18484 EMAPA:37368" "A type II NK T cell that has been recently activated, secretes interferon-gamma, and has the phenotype CD69-positive and downregulated NK markers." - "OBSOLETE (was not defined before being made obsolete)." - "Any endothelial cell of artery that is part of a coronary artery." - - "A chromaffin cell that is part of the paraaortic body." "FMA:69328" - "Odontoblast that non-terminally differentiated, located in the odontogenic papilla and dentine tissue, and transforms from a odontoblast cell." - "A double-positive thymocyte that is undergoing positive selection, has high expression of the alpha-beta T cell receptor, is CD69-positive, and is in the process of down regulating the CD8 co-receptor." + "The directed movement of a pole cell (germline progenitors in insects) from its site of production at the posterior pole of the embryo through to the site where the gonads will form." + "Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in a cardiac muscle cell contributing to the regulation of its contraction." + "Blood vessel formation in the heart when new vessels emerge from the proliferation of pre-existing blood vessels." + "Immune response taking place in the Peyer's patch, nodular lymphoid structures on the serosal surface of the small intestine." "Sympathetic noradrenergic neuron." - - "The peripheral receptor for pain. Includes receptors which are sensitive to painful mechanical stimuli, extreme heat or cold, and chemical stimuli. All mammalian nociceptors are free nerve endings." - - "A gamma motor neuron that innervates static nuclear bag fibers (bag2 fibers) and increases their firing, in response to an increase in the magnitude of change in length, and controls the static sensitivity of the stretch reflex." - "A fetal and neonatal heart cell that undergoes proliferation and is not yet terminally differentiated into a binucleate or a multinucleate cardiac myocyte." - "A CD8-positive, alpha-beta T cell with the phenotype CD69-positive, CD62L-negative, CD127-negative, and CD25-positive, that secretes cytokines." - "Neuron with two neurites that are fused grossly when they protrude from the soma and bifurcate a short distance from the soma." "FMA:67305" - "An acinar cell of salivary gland." + "The developmental process in which an ectodermal placode forms. An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm." + "A thin fold of ectoderm and endoderm that separates the pharyngeal pouches from the pharyngeal clefts in a developing embryo." "EMAPA:32749 FMA:295758 NCIT:C34251 UMLS:C1519040" + "The gradual disintegration of the sperm plasma membrane following insemination. This process is seen in Drosophila after entry of the entire sperm, surrounded by its plasma membrane, into the egg." + "Any process that activates or increase the rate of skeletal muscle regeneration." + "The process whose specific outcome is the progression of the dorsal region of the spinal cord over time, from its formation to the mature structure. The dorsal region of the mature spinal cord contains neurons that process and relay sensory input." + "The multiplication or reproduction of cells, resulting in the expansion of the population in the embryonic placenta." "Any melanocyte of skin that is part of a skin of face." - "A muscle cell that is part of the anterior internodal tract." "FMA:223276" - "A basally situated, mitotically active, columnar-shaped keratinocyte attached to the basement membrane." "FMA:70571" - "A fibroblast that is part of the outer membrane of prostatic capsule." "FMA:261273" - "A lymph node macrophage found in the cortex of lymph nodes, in particular in and around the germinal centers, and that participates in phagocytosis of apoptotic B cells from the germinal centers." - "An enucleate erythrocyte that is Lyg-76-high." - "An undifferentiated columnar cell of the bronchus epithelium" - "An epithelial cell of the hypodermis of Caenorhabditis." "WBbt:0007846" - "An epithelial cell of the parathyroid gland." "FMA:70547" - "Glandular cell of colon epithelium. Example: Goblet cells; enterocytes or absorptive cells; enteroendocrine and M cells." "CALOHA:TS-1274" - "Nucleus with two or more lobes connected by a thin filament that contains no internal chromatin." + "Any process that modulates the frequency, rate or extent of basidiospore formation, a process in which a sexually produced fungal spore is formed on a basidium in the fungi Basidiomycetes." + "Any process that activates or increases the frequency, rate or extent of neutrophil activation." + "The process in which a naive B cell acquires the specialized features of a mature or memory B cell during an immune response." + "The self-renewing division of a stem cell. A stem cell is an undifferentiated cell, in the embryo or adult, that can undergo unlimited division and give rise to one or several different cell types." + "Any process that modulates the frequency, rate or extent of acinar cell proliferation." + "Growth of glial cells, non-neuronal cells that provide support and nutrition, maintain homeostasis, form myelin, and participate in signal transmission in the nervous system." + "Any process that activates or increases the frequency, rate or extent of bone remodeling." + "A disc-shaped structure that is part of the placenta. A placental disc supports fetal development through the exchange of nutrients between maternal and fetal bloodstreams. The placental disc is structured to keep the blood streams separate, while maximizing surface area for the transport of nutrients between them, to maintain an immunological barrier." + "A proenkephalin-B that has been processed by proteolytic cleavage." "Fibroblast from muscle organ." "CALOHA:TS-0643" + "Any process that modulates the physical form of a presynapse." + "A bone that is connected via a shoulder joint (i.e. glenohumeral or acromioclavicular joints). The shoulder bones are the clavicle, scapula and humerus - but note that these are only considered to be shoulder bones when a true shoulder is present, as in most tetrapods." "MA:0000631" "A primordial cell from which an oocyte (ovum) ultimately is developed." "FMA:84772 ISBN:0721662544 EMAPA:17965 VHOG:0000661 EHDAA2:0000505" - - "Hair cell is a mechanoreceptor cell that is sensitive to movement of the hair-like projections (stereocilia and kinocilia) which relay the information centrally in the nervous system." "BTO:0004744" - "A myocardial endocrine cell that is part of the atrium." "FMA:83389" - "An enteroendocrine cell that produces glucagon." "FMA:62939" - - "A M cell that is part of the epithelium proper of small intestine." "FMA:263132" - "A resident monocyte that is Gr-1 low, CD43-positive, and CX3CR1-positive." - "A alpha-beta intraepithelial T cell found in the columnar epithelium of the gastrointestinal tract. Intraepithelial T cells often have distinct developmental pathways and activation requirements." - "An external limiting cell found in the vestibular epithelium." "FMA:75808" - "Type of neuron that is a primary mechanosensory cell, with peripheral neurites innervating the skin with free nerve endings." "AAO:0010316 VHOG:0001484 EFO:0003711" + "A prolongation or process extending from a nerve cell, e.g. an axon or dendrite." "NIF_Subcellular:sao867568886" + "An endothelial transcription factor GATA-2 that is encoded in the genome of mouse." "UniProtKB:O09100" + "Any process that activates, maintains or increases the frequency, rate or extent of frequency, rate or extent of basidiospore formation, a process in which a sexually produced fungal spore is formed on a basidium in the fungi basidiomycetes." + "OBSOLETE. A myoepithelial cell that is part of the mammary gland." + "An array of photoreceptors and any supporting cells found in an eye." + "A gland that is located in or around the ocular region, nearer the outer canthi." + "Formation of myofibrils, the repeating units of striated muscle." "An ecto-epithelial cell of the gingival region of the viscerocranial mucosa." "FMA:70579" - "A S. pombe cell type determined by mat1-Pc and mat1-Pi on the mat1 locus." - "A CD24-high, CD4-low, CD8-low, CD44-negative, NK1.1-negative NK T cell." - "An osteocytelike cell with numerous processes, trapped in a lacuna in the cement of the tooth." "FMA:63003" + "The controlled release of glutamate by a cell, in which the glutamate acts as a neurotransmitter." "An intestinal stem cell that is located in the small intestine crypt of Liberkuhn. These stem cells reside at the bottom of crypts in the small intestine and are highly proliferative. They either differentiate into transit amplifying cells or self-renew to form new stem cells." - "A cell within the primary follicle of the ovary." "FMA:70590" - "The final stage of the nucleated, immature erythrocyte, before nuclear loss. Typically the cytoplasm is described as acidophilic, but it still shows a faint polychromatic tint. The nucleus is small and initially may still have coarse, clumped chromatin, as in its precursor, the polychromatophilic erythroblast, but ultimately it becomes pyknotic, and appears as a deeply staining, blue-black, homogeneous structureless mass. The nucleus is often eccentric and sometimes lobulated." "FMA:84646" - "KUPO:0001030" - - "An acidophil cell of the anterior pitiuatry gland that produces both prolactin and growth hormone." "FMA:83097" - "A progenitor cell committed to the erythroid lineage." "BTO:0004911" - "A large secretory cell found in clusters underlying the epidermis of the abdominal segments of larval abdominal segments." "FBbt:00004995" - "A cell involved in transporting nutrients, minerals, water, gases and other chemicals between cells for a variety of purposes including conveying nutrition to other tissues, removing waste products from the tissues, conveying gases for respiration, distributing heat and repelling invasion of foreign substances." - "A langerin-positive lymph node dendritic cell that is CD103-positive and CD11b-low." + "The process whose specific outcome is the progression of an organismal system whose objective is to provide calibrated responses by an organism to a potential internal or invasive threat, over time, from its formation to the mature structure. A system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a given biological process." + "Any process that stops, prevents or reduces the frequency, rate or extent of calcium ion import across plasma membrane." + "Any member of the network of tubes that return blood from the renal tissues to the systemic circulation." "EMAPA:31450 MA:0002591" + "A lysosome-associated membrane glycoprotein 5 that is encoded in the genome of human." "UniProtKB:Q9UJQ1" + "The process whose specific outcome is the progression of the juxtaglomerular apparatus in the mesonephros over time, from its formation to the mature structure. The juxtaglomerular apparatus is an anatomical structure which consists of juxtaglomerular cells, extraglomerular mesangial cells and the macula densa. The juxtaglomerular apparatus lies adjacent to the glomerulus and regulates kidney function by maintaining the blood flow to the kidney and the filtration rate." - "A chromaffin cell that is part of the ovary." "FMA:74319" - - - "A trophoblast cell that is not part of a placental villous." + "An action potential that occurs in a neuron." + "Any process that modulates the frequency, rate or extent of mesenchymal stem cell differentiation." + "The subclavian artery that supplies the left pectoral appendage." "EMAPA:37100 MA:0002046 FMA:4694 SCTID:244245001 UMLS:C0226262 Wikipedia:Subclavian_artery NCIT:C32972" + "Any process that stops, prevents or reduces the frequency, rate or extent of calcitonin secretion." + "Any process that modulates the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." + "The orderly movement of a cell from one site to another that will contribute to the differentiation of an endothelial cell that will form the blood vessels of the heart." + "A roughly circular bulge in a surface." "AEO:0000205 EHDAA2:0003250 FMA:82506" + "A subdivision of skeleton that supports pharyngeal arch 2." "XAO:0003177 TAO:0001276 AAO:0000665 ZFA:0001276 AAO:0010370" "An innate lymphoid cell precursor in the human with the phenotype CD34-positive, CD56-positive, CD117-positive.Thie cell type may include precusors to NK cells and ILC3 cells." - "A endothelial cell of a lymphatic vessel. The border of the oak leaf-shaped endothelial cell of initial lymphatics are joined by specialized buttons. The discontinuous feature of buttons distinguishes them from zippers in collecting lymphatics, but both types of junctions are composed of proteins typical of adherens junctions and tight junctions found in the endothelium of blood vessels. Buttons seal the sides of flaps of the oak leaf-shaped endothelial cell, leaving open the tips of flaps as routes for fluid entry without disassembly and reformation of intercellular junctions." "FMA:68458 BTO:0004167" - "A B220-positive CD38-positive naive B cell is a CD38-positive naive B cell that has the phenotype B220-positive, CD38-positive, surface IgD-positive, surface IgM-positive, and CD27-negative, and that has not yet been activated by antigen in the periphery." - "A fibroblast in the bone marrow." "FMA:84377" - - "Any fibroblast of lung that is part of a bronchus." - "An endothelial cell found in capillaries." "CALOHA:TS-0112 BTO:0004956 FMA:67756" - "KUPO:0001031" - "A cell that constitutes the basal layer of epithelium in the prostatic duct." "FMA:74226" + "Any process that modulates the frequency, rate or extent of erythrocyte differentiation." + "An umbilical vein that is in the left side of a multicellular organism." "EMAPA:16377 EMAPA:16358 SCTID:308833008 FMA:70320 EHDAA2:0000967" + "Any process that stops, prevents or reduces the frequency, rate or extent of cardiac ventricle development." + "Any process that increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus." + "A lactotransferrin that has been processed by proteolytic cleavage." "A sperm bearing an X chromosome. Chromosomal and genetic sex is established at fertilization in mammals and depends upon whether an X-bearing sperm or a Y-bearing sperm fertilizes the X-bearing ovum." "FMA:84057" - "A cell of a layer of transitional epithelium in the wall of the bladder, ureter, and renal pelvis, external to the lamina propria." "FMA:84127" - "A mesenchymal stem cell that is part of the bone marrow." - "The most primitive precursor in the granulocytic series, having fine, evenly distributed chromatin, several nucleoli, a high nuclear-to-cytoplasmic ration (5:1-7:1), and a nongranular basophilic cytoplasm. They reside in the bone marrow." "FMA:83524 BTO:0000187" - "Stromal cell that forms the internal covering of the vertebrate brain and produces ECM for this and the choroid plexus." - "A cell lining the outside of the blastocyst. After binding to the endometrium, trophoblast cells develop into two distinct layers, an inner layer of mononuclear cytotrophoblast cells and an outer layer of continuous multinuclear cytoplasm, the syncytiotrophoblast cells, which form the early fetal-maternal interface." "FMA:83028" - - "A large pre-B-II cell is a pre-B-II cell that is proliferating and is Rag1-negative and Rag2-negative." - - "BTO:0004185 FMA:67860 Wikipedia:Olfactory_receptor_neuron" - "A progenitor cell of the thrombocyte, a nucleated blood cell involved in coagulation typically seen in birds and other non-mammalian vertebrates." - "Epidermal cells that do not contain keratin. Cell type is usually associated with moist epidermal tissues." "FMA:62880" - "OBSOLETE: A classification of cells by the number of their nuclei." - "A crenated erythrocyte with 30+ crenations, bumps or spurs that are the result of damage due to age or disease." "FMA:81099" - "A L2/3 Pvalb-like Sst GABAergic cortical interneuron (Mus musculus) that has basket morphology." - "An endothelial stalk cell is a specialized endothelial cell that follows behind the tip cell of an angiogenic sprout." - "A fungal cell with two genetically distinct haploid nuclei." - - - "KUPO:0001082" - "A myoepithelial cell that is part of the mammary gland alveolus." "FMA:67802" - - "An interrenal chromaffin cell found in teleosts that contain heterogeneous vesicles with electron-dense granules located asymmetrically within the vesicular membrane." - "A stratified squamous epithelial cell that is part of the anal canal." - "A preadipocyte that is part of the breast." - "An epithelial cell that is part of the collecting duct of renal tubule." "FMA:70982 KUPO:0001059" - "A cell derived from the mesoderm that is found at the periphery of the embryo." - "Obsolete. Use PO:0020019 from Plant Ontology instead. A haploid (1n) spore developing into a female gametophyte in heterosporous plants." + "Any process that modulates the frequency, rate or extent of retina development in camera-type eye." + "A simple columnar epithelium that is part of a fundus of stomach." "VHOG:0000878 EMAPA:17888 EHDAA2:0001921 FMA:17277" + "Any process that stops, prevents, or reduces the frequency, rate or extent of progesterone biosynthetic process." + "The process of regulating the proliferation and elimination of eosinophils such that the total number of eosinophils within a whole or part of an organism is stable over time in the absence of an outside stimulus." + "A semisolid gelatinous mass of coagulated blood that consists of red blood cells, white blood cells, and platelets entrapped in a fibrin network." "BTO:0000102 Wikipedia:Thrombus galen:BloodClot" + "Any process that modulates the frequency, rate or extent of motile cilium assembly." + "An anatomical surface that is part of a bone." + "Any process that modulates the frequency, rate or extent of neutrophil migration." + "Any process that stops, prevents, or reduces the frequency, rate or extent of epidermal cell differentiation." + "An epithelial somatic cell associated with a maturing oocyte." + "Any process that modulates the frequency, rate, or extent of T cell tolerance induction." + "An artery that supplies the pituitary gland." + "Any process that stops, prevents or reduces the frequency, rate or extent of endothelial tube morphogenesis." + "Any process that activates or increases the frequency, rate or extent of cytotoxic T cell degranulation." + "Wall of ventricle which is continuous with the wall of aorta." "FMA:9556" + "Any process that modulates the frequency, rate or extent of protein localization to ciliary membrane." + "The chemical reactions and pathways resulting in the formation of ketones, a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups." + "Any process that modulates the frequency, rate or extent of glial cell migration." + "A fallopian tube that is part of a right side of organism [Automatically generated definition]." "NCIT:C33475 FMA:18483 SCTID:280106006 MA:0001717 EMAPA:37369 UMLS:C0227900" - + "Any process that modulates the frequency, rate or extent of macrophage migration." + "Enables the directed movement of lipids into, out of or within a cell, or between cells." "Reactome:R-HSA-5683714 Reactome:R-HSA-6801250 Reactome:R-HSA-5682311 Reactome:R-HSA-5688397 Reactome:R-HSA-1369028 Reactome:R-HSA-5683672 Reactome:R-HSA-8866329 Reactome:R-HSA-1369052 Reactome:R-HSA-8848053 Reactome:R-HSA-174786 Reactome:R-HSA-5682285" "A smooth muscle cell that is part of the cecum." "FMA:15681" - "An endothelial cell found in the mucosa associated with the facial skeleton." "FMA:70627" - "A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities." - "BTO:0001141" - "A gamma-delta T cell that has an immature phenotype." - "Any basket cell that is part of a cerebellum." - "A cell that originates from the neural crest and differentiates into a pigment cell." "BTO:0003217 FMA:83377" + "Any process that activates or increases the frequency, rate or extent of L-glutamate import into a cell." + "The posterior section of the developing metencephalon recognized transiently within the vertebrate embryo; the rhombic lip extends posteriorly from the roof of the fourth ventricle to dorsal neuroepithelial cell and can be divided into eight structural units based on rhombomeres 1-8 (r1-r8), recognized at early stages of hindbrain development; producing granule cells and five brainstem nuclei, the rhombic lip plays an important role in developing a complex cerebellar neural system." "EMAPA:17074 TAO:0001440 DHBA:10664 Wikipedia:Rhombic_lips XAO:0004135 ZFA:0001440 EHDAA2:0000231" "A smooth muscle cell of the uterus." - "A lymphocyte of B lineage that is devoted to secreting large amounts of immunoglobulin." - "KUPO:0001083" - "This is a cell found in the gastrointestinal tract of mammals and serves as a pacemaker that triggers gut contraction. ICCs mediate inputs from the enteric nervous system to smooth muscle cells and are thought to be the cells from which gastrointestinal stromal tumors (GISTs) arise." "BTO:0003914 FMA:86573" - "A fungal cell with two or more genetically distinct nuclei." - "A giioblast cell that develops from a migratory neural crest cell. The SCP is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has no basal lamina. In rodents SCPs are the only cells in the Schwann cell linage that expresses Cdh19." - "Immature interstitial dendritic cell is a interstitial dendritic cell that is CD80-low, CD86-low, and MHCII-low." - "A cell whose nucleus contains a single haploid genome." - "KUPO:0001029" - "Smooth muscle cell of the carotid artery." - "A type EC enteroendocrine cell type that is numerous in the fundus of the stomach; stores 5-hydroxytryptamine and histamine." "FMA:63208" - "A vascular endothelial cell found in colon blood vessels." "CALOHA:TS-2397" - "Multi fate stem cell that gives rise to both hepatocytes and cholangiocytes as descendants." + "An ectodermal placode that gives rise to any of the cutaneous appendages that protrude from the skin epidermis (heair, feathers, epidermal scales)." + "A uteroglobin that is encoded in the genome of mouse." "UniProtKB:Q06318" + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glucocorticoids." + "An embryonic or larval epithelium that is committed to form part of the nervous system." "FMA:64807 EHDAA2_RETIRED:0004654 BTO:0000314 AEO:0001008" "A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses." - "A B220-positive CD38-positive IgG-negative memory B cell is a CD38-positive IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype B220-positive, CD38-positive, and IgG-negative." - "An endothelial cell that is part of the arteriole." "KUPO:0001097 FMA:67760" - "A sperm cell that is not cabaple of motion (motility)." - "An epithelial cell of the small intestine." "FMA:256159" - "FBbt:00005145" - "FBbt:00005130" - "Skeletogenic cell that secretes dentine matrix, is derived from the odontogenic papilla, and develops from a preodontoblast cell." "FMA:62999 BTO:0001769 CALOHA:TS-0696" - "A circulating gamma-delta T cell that is CD27-positive and capable of producing IFN-gamma." + "A cholinergic axonal fiber projecting from the CNS to a sympathetic ganglion." "SCTID:323517007" + "A CD24-positive, CD-133-positive, vimentin-positive cell found scattered throughout a renal proximal tubule and that may participate in tubular regeneration. Compared to other proximal tubular cell types, this cell contains less cytoplasm, fewer mitochondria and no brush border." + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vacuole." + "A retractable double-layered fold of skin and mucous membrane that covers the glans penis or clitoris. Glands may also be present." "NCIT:C12323" + "An epithelium that is part of a shoulder [Automatically generated definition]." "EMAPA:17422 EHDAA:4182 VHOG:0000761 EHDAA:6230 EHDAA2:0001835" + "The process whose specific outcome is the progression of the optic nerve over time, from its formation to the mature structure. The sensory optic nerve originates from the bipolar cells of the retina and conducts visual information to the brainstem. The optic nerve exits the back of the eye in the orbit, enters the optic canal, and enters the central nervous system at the optic chiasm (crossing) where the nerve fibers become the optic tract just prior to entering the hindbrain." - "An arthroconidium that has only one nucleus." "FAO:0000031" - "A cell with a single nucleus." "A CD8-positive, alpha-beta T cell that has the phenotype CXCR3-negative, CCR6-positive, CCR5-high, CD45RA-negative, and capable of producing IL-17 and some IFNg." - "A cell of the seminiferous tubule epithelium." - "A cell that is specialised to accumulate a particular substance(s)." - - "Immature CD8_alpha-positive CD11b-negative dendritic cell is a CD8_alpha-positive CD11b-negative dendritic cell that is CD80-low, CD86-low, and MHCII-low." - "Glandular cell of uterine cervix epithelium." "CALOHA:TS-1273" - - - "Any hepatocyte that is part of the liver lobule periportal region. These cells are primarily involved in oxidative energy metabolism." - "A secondary lens fiber cell that lacks a nucleus." "FMA:67561" - "An epithelial cell that is part of the glomerular parietal epithelium." "FMA:70968 KUPO:0001035" - "A plasmablast that is CD86-positive." - "KUPO:0001018" - "Any fibroblast that is part of a female gonad." + "A lumican that is encoded in the genome of mouse." "UniProtKB:P51885" + "The lipid bilayer surrounding any of the compartments of the Golgi apparatus." + "A lysosome-associated membrane glycoprotein 5 that is encoded in the genome of mouse." "UniProtKB:Q9D387" + "The process in which relatively unspecialized cells acquire specialized structural and/or functional features of a type B pancreatic cell. A type B pancreatic cell is a cell located towards center of the islets of Langerhans that secretes insulin." + "Organ component of neuraxis that has as its parts the medullary reticular formation, inferior olivary complex and cochlear nuclear complex, among other structures[FMA]. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate[GO]." "TAO:0000545 EV:0100275 BM:Me DMBA:17352 BAMS:Md GAID:590 Wikipedia:Bone_marrow_of_ovary_oblongata neuronames:698 EHDAA:7588 MAT:0000367 MIAA:0000111 SCTID:279104005 EMAPA:17550 UMLS:C1269575 AAO:0010486 NCIT:C12442 EFO:0000924 VHOG:0000181 ZFA:0000545 BTO:0000041 CALOHA:TS-0607 XAO:0003100 UMLS:C0025148 MAT:0000111 MESH:D008526 MA:0000206 FMA:62004 BIRNLEX:957 MBA:354 EHDAA2:0001088 BAMS:MY" + "Any process that modulates the frequency, rate or extent of forebrain neuron differentiation." + "Any process that modulates the frequency, rate or extent of the formation of cellular spores derived from the products of meiosis." + "The developmental process in which the sweat gland placode forms. An sweat gland placode is a thickening of the ectoderm that will give rise to the sweat gland bud." + "The portion of the cytoskeleton contained within the presynapse." + "The fluid-filled space separating the membranous from the osseous labyrinth." "ZFA:0005459 BTO:0002083 FMA:77745 Wikipedia:Perilymphatic_space SCTID:362576001" + "The change in morphology and behavior of a memory T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific." + "A nerve root that is part of a accessory XI nerve." "BIRNLEX:1580 DHBA:12883 neuronames:703 DMBA:17749 Wikipedia:Cranial_root_of_accessory_nerves BAMS:c11n SCTID:280187004" + "Catalysis of a biochemical reaction at physiological temperatures in which one of the substrates is a glycoprotein." "Cell of the nasopharyngeal epithelium." "CALOHA:TS-2398" - "A cell type found in the gastrointestinal and respiratory tracts that is characterized by the presence of a tuft of blunt, squat microvilli (120-140 per cell). Function of this cell type is not known." "FMA:67978" - "An enterocyte that is a part of a vermiform appendix." + "Part of the hippocampal formation that is bounded by the entorhinal cortex and area CA1. It is characterized on the CA1 border by an abrupt widening of the pyramidal cell layer. A molecular layer is present that is continuous with that of CA1, although the stratum radiatum is no longer present. The stratum oriens is also not present. adapted from Paxinos, G. The rat central nervous system, 2nd ed, Academic Press, San Diego, 1995, pg. 468)." "Wikipedia:Subiculum FMA:74414 UMLS:C0152316 SCTID:369097009 neuronames:188 NCIT:C33648 PBA:128012354 BAMS:SUB BAMS:S BM:Tel-Cx-SB MBA:502 MA:0000960 PBA:10054 BIRNLEX:1305 BTO:0003087 DHBA:10302 DMBA:16163 HBA:12896 DHBA:10301 EMAPA:35832" + "The process in which a relatively unspecialized cell acquires specialized features of a neuromast support cell. Support cells are non-sensory cells of the neuromast that extend between the sensory hair cells from the basement membrane to the apical surface; they are surrounded by mantle cells." "A thymocyte that has a T cell receptor consisting of a gamma chain containing Vgamma2 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-negative." - "OBSOLETE: A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite growth/propagation in vitro as part of a immortal cell line." - "A M cell that is part of the epithelium of small intestine." "FMA:263128" - "A pro-B cell that is CD22-positive, CD34-positive, CD38-positive and TdT-positive (has TdT activity). Pre-BCR is expressed on the cell surface. Cell is CD19-negative, CD20-negative, complement receptor type 2-negative and CD10-low. D-to-J recombination of the heavy chain occurs at this stage." - "A peptide hormone secreting cell that secretes secretin stimulating hormone" - "An epithelial cell found in the trachea." "FMA:74793" - "A phagocyte formed by the fusion of mononuclear phagocytes." - "A myeloid dendritic cell found in the blood that is CD16-positive." - "A NK1.1-positive T cell that is Ly49D-positive." - "A large, oval stomach epithelial cell with a central nucleus; source of gastric acid. Secretes HCl." "BTO:0001780 FMA:62901" - "A terminally differentiated, post-mitotic, antibody secreting cell of the B cell lineage with the phenotype CD138-positive, surface immunonoglobulin-negative, and MHC Class II-negative. Plasma cells are oval or round with extensive rough endoplasmic reticulum, a well-developed Golgi apparatus, and a round nucleus having a characteristic cartwheel heterochromatin pattern and are devoted to producing large amounts of immunoglobulin." "FMA:70574 BTO:0000392" + "Cranial nerve that transmits sound and equilibrium (balance) information from the inner ear to the brain." "TAO:0000247 BAMS:8n MBA:933 XAO:0003095 UMLS:C1278835 ZFA:0000247 VHOG:0000695 HBA:9331 BAMS:VIIIn neuronames:553 GAID:839 BAMS:nVIII EMAPA:17801 EHDAA2:0002194 FMA:50869 SCTID:180945001 MESH:D000159 UMLS:C0001162 AAO:0010473 MA:0001109 Wikipedia:Vestibulocochlear_nerve BIRNLEX:890 BTO:0003490 NCIT:C12996" + "Cell-cell signaling in which the ligand is carried between cells by an exosome." + "Any process that stops, prevents, or reduces the frequency, rate or extent of basophil differentiation." + "Any process that stops, prevents or reduces the frequency, rate or extent of T cell costimulation." + "A protein that is a translation product of the mouse Cd209b gene or a 1:1 ortholog thereof." + "A bone marrow proteoglycan isoform 1 that is encoded in the genome of human." "UniProtKB:P13727-1" + "The behavior of an organism in response to an odor." + "A pia mater that is part of a hindbrain [Automatically generated definition]." "EMAPA:17786 EHDAA2:0000772 VHOG:0000466 MA:0000990" + "The segment of the rib that connects to a vertebra[MP]. a small part of the rib composed of the head, neck, tuberculum and a short proximal part of the body[PMID]." "MA:0001400 EMAPA:37495" + "Any process that modulates the frequency, rate or extent of aldosterone secretion." + "A pvalb GABAergic cortical interneuron that is recognizable by the straight terminal axonal 'cartridges' of vertically oriented strings of synaptic boutons. Chandelier PV cells' boutons target exclusively the axon initial segment (AIS) of pyramidal cells, with a single cell innervating hundreds of pyramidal cells in a clustered manner." "ILX:0107356" + "A protein that is a translation product of the human ENG gene or a 1:1 ortholog thereof." "PIRSF:PIRSF038746 IUPHARobj:2895" + "The increase in size or mass of a skeletal muscle. This may be due to a change in the fiber number or size." "A Betz cell that syanpses with spinal interneurons." - "A mature B cell that produces cytokines that can influence CD4 T cell differentiation." - "An eosinophil with a ring-shaped nucleus that is resident in the lung parenchyma. In mouse, lung parenchyma resident eosinophils are IL-5-independent Siglec-F(intermediate) CD62L+ CD101(low). In human, they are Siglec-8+ CD62L+ IL-3R(low)." - - "An OFF-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the outer half of the inner plexiform layer. The cell has a diffuse axon terminal with varicosities in sublaminae 1 and 2 of the inner plexiform layer." - + "A CX3C chemokine receptor 1 that is encoded in the genome of human." "DTO:02100074 UniProtKB:P49238 Reactome:R-HSA-2980688" + "The process whose specific outcome is the progression of the male gonad over time, from its formation to the mature structure." + "A chromaffin paraganglion located at the bifurcation of the aorta or at the origin of the inferior mesenteric artery." "SCTID:276159005 Wikipedia:Organ_of_Zuckerkandl FMA:15647 GAID:444 EMAPA:18223 MESH:D010220 NCIT:C25316 UMLS:C0442134 MA:0001137" + "Mesenteric artery that supplies the whole length of the small intestine except the superior part of the duodenum. It also supplies the cecum and the ascending part of the colon and about half the transverse part of the colon. It arises from the anterior surface of the aorta below the celiac artery at the level of the first lumbar vertebra." "EHDAA2:0001949 Wikipedia:Superior_mesenteric_artery GAID:502 EMAPA:18619 SCTID:362048004 BTO:0002303 UMLS:C0162861 VHOG:0000754 NCIT:C33685 EHDAA:5313 MA:0002005 MESH:D017538 FMA:14749 galen:SuperiorMesentericArtery EHDAA:3358" + "The skull can be divided into two: the neurocranium and the facial skeleton." "FMA:54964" + "A metanephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the metanephros[GO]." + "Orifice at the opposite end of an animal's digestive tract from the mouth. Its function is to expel feces, unwanted semi-solid matter produced during digestion, which, depending on the type of animal, may be one or more of: matter which the animal cannot digest, such as bones; food material after all the nutrients have been extracted, for example cellulose or lignin; ingested matter which would be toxic if it remained in the digestive tract; and dead or excess gut bacteria and other endosymbionts." "TADS:0000066 TGMA:0001279 FMA:15711 BTO:0001680 EV:0100082 WBbt:0005364 SCTID:181262009 UMLS:C0003461 galen:Anus GAID:312 Wikipedia:Anus MA:0000331 CALOHA:TS-2005 NCIT:C43362" + "Any process that modulates the frequency, rate or extent of the formation and development of a tooth or teeth." + "A knoblike tooth primordium that develops into the mature tooth and consists of enamel organ, dental papilla, and dental sac enclosing them." "MESH:D014083 FMA:306006 BTO:0001838 SCTID:53301001 NCIT:C34313 UMLS:C0040442" + "Any process that activates or increases the frequency, rate or extent of pigment cell differentiation." + "The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]." "ZFA:0000255 Wikipedia:Paraxial_mesoderm NCIT:C34244 SCTID:361475002 VHOG:0000114 TAO:0000255 AAO:0010568 XAO:0000259 FMA:293145 EMAPA:16183 EFO:0003515 UMLS:C1284009 EMAPA:16751" "A macrophage that is located in the colon." - "A precursor B cell that is CD45RA-positive, CD43-positive, CD24-positive and BP-1-negative." - "KUPO:0001014" - "A basal cell in the respiratory tract." - "KUPO:0001137" - "A cell of the choroid of the eye." - "Any migratory neural crest cell that is part of a cardiac neural crest." - "A phagocyte in vertebrates that is able to phagocytosis." - "A cell type that varies from squamous to columnar, depending on their activity with microvillus directed luminally. This cell produces and secretes thyroid hormones." "FMA:68782 BTO:0003736 CALOHA:TS-1285" - - "A synovial cell type that resembles fibroblasts, has abundant granular endoplasmic reticulum but contains fewer vacuoles and vesicles. This cell type secretes glycoproteins and hyaluronic acid." "FMA:66788" - "A pyramidal neuron which lacks a clear tuft formation but extends to large radial distances." - "OBSOLETE: The reproductive structure of bacteria, fungi and cryptograms." + "Any process that increases the rate, frequency or extent of keratinocyte proliferation. Keratinocyte proliferation is the multiplication or reproduction of keratinocytes, resulting in the expansion of a cell population." + "A parenchyma that is part of a lung." "FMA:27360 EMAPA:35522 SCTID:201712001 MA:0003168" + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a synapse, the junction between a neuron and a target (neuron, muscle, or secretory cell)." + "A T-cell surface glycoprotein CD1 that is a translation product of the human CD1C gene or a 1:1 ortholog thereof." + "A hypothalamus kisspeptin neuron that coexpresses kisspeptin, neurokinin B and dynorphin." + "Any process that activates or increases the frequency, rate or extent of vascular smooth muscle cell proliferation." + "A renal tubule is a tube that filters, re-absorbs and secretes substances to rid an organism of waste and to play a role in fluid homeostasis." "A megakaryocyte erythroid progenitor cell that is Kit-positive and is Sca1-negative, CD34-negative, CD90-negative, IL7r-alpha-negative and Fcgr II/III-low." - "Cumulus cell is a specialized granulosa cell that surrounds and nourishes the oocyte. This cell-type surrounds the fully-grown oocyte to form a cumulus-oocyte complex (abbr. COC). The terms cumulus oophorus cells, cumulus granulosa cells, cumulus oophorous granulosa cells, granulosa-cumulus cells are used to make a distinction between this cell and the other functionally different subpopulation of granulosa cells at the wall of the Graafian follicle." "BTO:0002236" - "A Purkinje myocyte that is part of the atrioventricular node." "FMA:83386" - "A Be cell that facilitates development of T-helper 1 (Th1) phenotype in CD4-positive T cells, and secretes high levels of interleukin-2, tumor necrosis factor-alpha and interferon-gamma." - "FBbt:00005219" - "A type of interneuron that has two clusters of dendritic branches that originate directly from the soma and extend in opposite directions and axons that form a plexus which spreads widely. Compared to bipolar neurons, bitufted neurons have branching that occur close to the soma." "ILX:0777212" - - "A non-terminally differentiated cell that originates from the neural crest and differentiates into a leucophore." - "Specialized ependymal cell that produces the cerebrospinal fluid from the blood and secretes it into the lumen of the brain and spinal chord." "FMA:70549" + "Any process that modulates the frequency, rate or extent of the regulated release of catecholamines." + "The stroma of the ovary is a peculiar soft tissue, abundantly supplied with blood vessels, consisting for the most part of spindle-shaped cells with a small amount of ordinary connective tissue. These cells have been regarded by some anatomists as unstriped muscle cells, which, indeed, they most resemble; by others as connective-tissue cells. On the surface of the organ this tissue is much condensed, and forms a layer composed of short connective-tissue fibers, with fusiform cells between them. The stroma of the ovary may contain interstitial cells resembling those of the testis." "UMLS:C0737271 CALOHA:TS-1246 EMAPA:28880 Wikipedia:Stroma_of_ovary NCIT:C33638 MA:0002991 FMA:18626 SCTID:259306002" "An asexual 1-celled spore (primarily for perennation, not dissemination). Originates endogenously and singly within part of a pre-existing cell by the contraction of the protoplast. Possesses an inner secondary and often thickened hyaline or brown wall, usually impregnated with hydrophobic material." - "A mesothelial cell capable of circulating in the blood by first losing its squamous character. This cell can incorporate into the regenerating mesothelium." "FMA:86712" - "KUPO:0001017" - "A goblet cell that is located in the colon." - "A non-terminally differentiated cell that originates from the neural crest and differentiates into a cyanophore." - "A corticothalamic-projecting glutamatergic neuron that is located in L6 and lower L5 of the primary motor cortex, with a pyramidal morphology and mostly untufted apical dendrites terminating in midcortical layers. CT VAL/VM (ventroanterior-ventrolateral complex/ventromedial nucleus) cells have a near tonic firing pattern and are distinguished from L6 IT neurons by a lower inter-spike interval adaptation index." - "A visceromotor motor neuron whose soma is located in the hindbrain, and which synapses to parasympathetic neurons that innervate tear glands, sweat glands, and the smooth muscles of the head." - "A reticulocyte that retains the nucleus and other organelles. Found in birds, fish, amphibians and reptiles." - "A secretory cell that is grouped together with other cells of the same type to form grape shaped clusters known as acini (singular acinus)." "FMA:83625" - "An epithelial cell of the retinal pigmented epithelium." "FMA:75802 BTO:0004910" - "Peripheral sensory neuron." - - "Any mesenchymal stem cell of the bone marrow that is part of a femur." - "A goblet cell that is part of the epithelium of gastric cardiac gland." "FMA:263038" - "A thymic macrophage found in the thymic cortex." - "Columnar cell which populate the epithelium of large intestine and absorb water. This cell is the most numerous of the epithelial cell types in the large intestine; bear apical microvilli, contain secretory granules in their apical cytoplasm; secretion appears to be largely mucins, but is also rich in antibodies of the IgA type." "FMA:63638 FMA:66771 BTO:0002484" + "Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres." "CALOHA:TS-1018 AAO:0010479 FMA:62000 MESH:D013687 DHBA:10158 SCTID:263353005 HBA:4007 MBA:567 EMAPA:16910 BAMS:IV MAT:0000421 UMLS:C0039452 PBA:128011350 BIRNLEX:1115 BM:Tel MA:0000183 EV:0100165 ZFA:0000079 BAMS:CB Wikipedia:Telencephalon GAID:621 EHDAA2:0001982 TAO:0000079 BTO:0000239 BAMS:Tel MIAA:0000421 neuronames:31 BAMS:CH VHOG:0000283 EFO:0000912 XAO:0000012" + "The sensory system for the sense of balance." "BTO:0003381 Wikipedia:Vestibular_system FMA:7193 NLXANAT:090819 EMAPA:37986 SCTID:361533001" + "A structural quality inhering in a bearer by virtue of the bearer's having a three dimensional cavity with a narrow or no opening, and often containing an anatomical substance." "OBSOLETE: A goblet cell that is part of the epithelium proper of small intestine." "FMA:263052" - "A supporting cell of the organ of Corti." - "A neuroglial cell of the peripheral nervous system which forms the insulating myelin sheaths of peripheral axons." "FMA:62121 CALOHA:TS-0898" - "A neutrophil precursor in the granulocytic series, being a cell intermediate in development between a promyelocyte and a metamyelocyte; in this stage, production of primary granules is complete and neutrophil-specific granules has started. No nucleolus is present. This cell type is CD13-positive, CD16-negative, integrin alpha-M-positive, CD15-positive, CD33-positive, CD24-positive, C/EBP-a-positive, C/EBPe-positive, PU.1-positive, lactotransferrin-positive, myeloperoxidase-positive and NGAL-positive." "BTO:0003455 FMA:83540" - "Any skin fibroblast that is part of a skin of abdomen." - "A primordial germ cell that is destined to become a male germ cell." "EMAPA:18686 VHOG:0000662 EHDAA2:0001053 FMA:84771" - "A peptide hormone secreting cell that secretes bombesin stimulating hormone." + "Any of the interlobular excretory ducts of a salivary gland which are found in the connective tissue septa and formed by the union of several intralobular striated (secretory) ducts[MP,generalized]." "FMA:60052" + "The process in which a relatively unspecialized cell acquires specialized features of a mesenchymal cell. A mesenchymal cell is a loosely associated cell that is part of the connective tissue in an organism. Mesenchymal cells give rise to more mature connective tissue cell types." "An animal cell that has characteristics of both a fibroblast cell and a smooth muscle cell." - "A transversely striated, synctial cell of skeletal muscle. It is formed when proliferating myoblasts exit the cell cycle, differentiate and fuse." - "A transitional myocyte that is part of the sinoatrial node." "FMA:83384" - "A rod-shpaed cell that forms a single row adjacent to and supporting the inner hair cells." "FMA:75726 FMA:75722" - "A myeloid progenitor cell committed to the monocyte lineage. This cell is CD11b-positive, has basophilic cytoplasm, euchromatin, and the presence of a nucleolus." "CALOHA:TS-1195 FMA:83553" - "A keratinized cell located in the hard palate or gingiva." - "The output neuron of the cerebellar cortex." "BTO:0001011 CALOHA:TS-0845 FMA:67969" - "A pyramidal neuron of the hippocampus." "NIFSTD:sao131261273 SAO:sao131261273" - "Brush cell found in the epithelial layer of the colon." "FMA:263222" - "A cell that secretes ghrelin, the peptide hormone that stimulates hunger." - "KUPO:0001063" - "An endorphine cell that secretes enkephalin." - "A basal cell that is part of the epithelium of trachea." "FMA:263118" - "A promyelocyte committed to the eosinophil lineage." "FMA:84199" - "A B-1 B cell that has the phenotype CD5-positive." - "A goblet cell that is part of the epithelium proper of appendix." "FMA:263069" + "A chemokine receptor CCR1/3/1L that is a translation product of the human CCR1 gene or a 1:1 ortholog thereof." "IUPHARobj:58" + "A gustatory epithelium that is part of a roof of mouth." + "Any process that activates or increases the frequency, rate or extent of branching morphogenesis of a nerve." + "A lactocyte that highly expresses genes associated with lipid production and milk component biosynthesis." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of acetylcholine." + "The granule cell layer contains multiple small round neurons that lack axons. Long dendritic processes of the neurons reach the more superficial layers and inhibit mitral cells and tufted cells. Small distal processes make contacts with the exiting mitral cell axons." "neuronames:2714 BAMS:MOBgr MA:0000971 BTO:0001327 NLXANAT:20090404 MBA:220 DMBA:15909 EMAPA:35609" + "Any collection of muscles that is part of a trunk [Automatically generated definition]." "AAO:0011572 EFO:0003531 FMA:50187" + "Any process that stops, prevents, or reduces the frequency, rate or extent of phagocytosis." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an acetylcholine stimulus." + "Any process that modulates the frequency, rate or extent of hemocyte differentiation." + "A secretory cell of ectodermal origin. This cell may have important functions in fatty acid and hydrocarbon metabolism and is metabolically linked to the fat body and tracheae. This cell is exclusive of arthropods." "FBbt:00004995" + "The lobar bronchus is the major airway within the respiratory tree that starts by division of the principal bronchi on both sides and ends at the point of its own subdivision into tertiary or segmental bronchi[GO]." "SCTID:245509008 Wikipedia:Secondary_bronchus MA:0000437 EHDAA:8213 NCIT:C32998 EHDAA:8187 EMAPA:32696 UMLS:C0225653 EHDAA:8203 EHDAA:4993 FMA:7406 EHDAA:4977 EHDAA:4985 EHDAA:4955 EHDAA:4963 EHDAA:8175 EHDAA:8225" + "A protein that is encoded in the genome of Mus musculus." + "Any process that activates or increases the frequency, rate or extent of CD8-positive, alpha-beta T cell differentiation." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-2 production." "A cell that is found in a zone occupying the bottom region of the crypt; provide the source of most of the cell types of the intestinal epithelium; proliferate by mitotic division; differentiates into columnar or goblet cells." "FMA:63379" - "A macrophage constitutively resident in a particular tissue under non-inflammatory conditions, and capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells." "FMA:84644 FMA:84642" - "A natural killer cell that is developmentally immature and expresses natural killer cell receptors (NKR)." - "A CD24-low, CD44-negative, NK1.1-negative NK T cell." - - - "A fat cell that is part of the epicardial fat of left ventricle." "FMA:261300" + "Any process that modulates the frequency, rate or extent of cardiac muscle fiber development." + "Ossicle that develops within bands of dense, regular connective tissue (e.g., tendons and ligaments). Sesamoids are generally located proximate to a bony prominence, over which the dense regular connective tissue wraps, and/or a joint or articulation." "VSAO:0000137" + "Any apoptotic process in a natural killer cell, a lymphocyte that can spontaneously kill a variety of target cells without prior antigenic activation." + "Any process that stops, prevents, or reduces the frequency, rate or extent of pancreatic A cell differentiation." + "The process in which the anatomical structures of the face are generated and organized. The face is the ventral division of the head." "A myoepithelial cell that is part of the terminal lactiferous duct." "FMA:67804" - "KUPO:0001136" - - "A type D cell found in the stomach." "FMA:83410" + "A retinal ganglion cell C inner that has medium dendritic diversity." "BAMS:1050" + "The bidirectional movement of large protein complexes along microtubules within a cilium that contributes to cilium assembly." "Reactome:R-HSA-5620924.2" + "The part of the biliary tree formed by the union of the cystic duct and the common hepatic duct." "galen:CommonBileDuct Wikipedia:Common_bile_duct UMLS:C0009437 EMAPA:17201 MESH:D003135 NCIT:C12698 TAO:0005165 ZFA:0005165 SCTID:362199009 GAID:282 EHDAA2:0000303 MA:0001631 VHOG:0000214 FMA:14667 EHDAA:3981" "A T cell with a receptor of limited diversity that is capable of immediate effector functions upon stimulation." - "KUPO:0001058" - "A thymocyte that has a T cell receptor consisting of a gamma chain that has as part a Vgamma3 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-negative. This cell-type is found in the fetal thymus with highest numbers occurring at E17-E18." - "Mature CD11c-negative plasmacytoid dendritic cell is a CD11c-negative plasmacytoid dendritic cell is CD80-high, CD86-high, MHCII-high and is CD83-positive." - "A stem cell that can give rise to multiple cell types (i.e. smooth muscle, endothelial) in the developing heart." - "An asexual, nonmotile spore formed by higher fungi; conidia are usually made from the side or tip of specialized sporogenous cells and do not form by progressive cleavage of the cytoplasm." "FAO:0000024 BTO:0000283" - "A goblet cell that is part of the epithelium of intestinal villus." "FMA:263046" - "An epithelial cell that is part of the urethra." "FMA:256165" - "A cell whose primary function is to cause growth by stimulating cell division in its immediate cellular environment." - - "Skeletogenic cell that is terminally differentiated, secretes an avascular, GAG-rich matrix, is embedded in cartilage tissue matrix, retains the ability to divide, and develops from a chondroblast cell." "BTO:0000249 FMA:66782 CALOHA:TS-0138" - "A group 2 innate lymphoid cell in the mouse capable of secreting IL-13 in response to a helminth infection. This cell is lineage-negative, ICOS-positive, IL1RL1-positive, IL7Ralpha-positive, and IL17Br-positive." - "An auditory hair cell located in the macula that is sensitive to auditory stimuli." - "A brush cell found in the epithelium of bronchus." "FMA:263226" - "A specialized, enlarged, connective tissue cell of the decidua with enlarged nucleus, dense membrane‐bound secretory granules and cytoplasmic accumulation of glycogen and lipid droplets. These cells develop by the transformation of endometrial stromal cells during decidualization." "BTO:0002770 BTO:0005756 NCIT:C32429" - "CD8_alpha-negative CD11b-positive dendritic cell is a conventional dendritic cell that is CD11b-positive, CD4-positive and is CD205-negative and CD8_alpha-negative." - "A mucosa-associated lymphoid tissue macrophage found in the mucosa-associated lymphoid tissues of the gut." - "A thymocyte that has a T cell receptor consisting of a gamma chain containing Vgamma2 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-negative. This cell-type is found in the fetal thymus." - "A secondary lymphoid organ macrophage found in a lymph node. This cell is CD169-high." - "Columnar glandular cell with irregular nucleus, copious granular endoplasmic reticulum and supranuclear granules. Secretes a watery fluid containing proteins known as serous fluid." "FMA:62511 BTO:0003687" - "Any lung endothelial cell that is part of a microvascular endothelium." - "A dendritic cell type of distinct morphology, localization, and surface marker expression (CD123-positive) from other dendritic cell types and associated with early stage immune responses, particularly the release of physiologically abundant amounts of type I interferons in response to infection." "BTO:0004625" - "OBSOLETE: Subpopulation of CD4+ cells which induce CD8+ suppressor T cells to suppress antibody production by B cells. They also stimulate other cellular immune responses." - "A CD8-positive alpha beta-positive T cell with the phenotype FoxP3-positive and having suppressor function." - "KUPO:0001057" - "CALOHA:TS-1249" - "KUPO:0001061" - "A regulatory T cell that has not encountered antigen." - "A progenitor cell of the neutrophil lineage." - "A langerin-negative lymph node dendritic cell that is CD103-negative and CD11b-high." - "A neuron which conveys sensory information centrally from the periphery." "FMA:87653" - "An endocrine cell found in the pyloric gland mucosa (antral mucosa) of the stomach of mammals and responsible for the secretion of gastrin and enkephalin. Most abundant in pyloric antrum, pyramidal in form with a narrow apex bearing long microvilli." "FMA:67609 BTO:0004108" + + "Any process that activates or increases the frequency, rate or extent of the controlled release of glutamate." + "The directed movement of substances into, out of or within a lysosome." + "A C-X-C chemokine receptor type 2 that is encoded in the genome of human." "Reactome:R-HSA-373796 Reactome:R-HSA-6804771 DTO:02100076 UniProtKB:P25025" + "Any process that modulates the consistent predetermined time point at which an integrated living unit or organism progresses from an initial condition to a later condition and the rate at which this time point is reached." + "Any synovial joint that connects auditory ossicles." "FMA:60063" + "A specialized epithelial cell that contains \"feet\" that interdigitate with the \"feet\" of other glomerular epithelial cells in the mesonephros." + "The membrane that covers the embryonic cloaca, formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm; the urorectal septum joins the cloacal membrane and divides it into an anal membrane and a urogenital membrane; the point where the urorectal septum intersects the cloacal membrane is the future site of the perineal body; proliferation of mesoderm and ectoderm around the cloacal membrane produces primordial tissues of the external genitalia in both sexes: the genital tubercle, genital folds, and genital swellings." "SCTID:308826008 VHOG:0001198 EHDAA2:0000257 EHDAA:2933 Wikipedia:Cloacal_membrane NCIT:C34128 UMLS:C0231056 EMAPA:16832 EHDAA:214 FMA:295525" + "Any process that modulates the frequency, rate or extent of colon smooth muscle contraction." + "The series of molecular signals initiated by glutamate binding to a glutamate receptor on the surface of the target cell, followed by the movement of ions through a channel in the receptor complex, and ending with the regulation of a downstream cellular process, e.g. transcription." + "Mucus produced in the nasal cavity, by the respiratory segment of the nasal mucosa." "FMA:83688 EMAPA:36552 NCIT:C52551 UMLS:C0225392 Wikipedia:Nasal_mucus#Respiratory_system BTO:0003603 CALOHA:TS-0658 MA:0002535" + "The asymmetric division of cells to produce two daughter cells with different developmental potentials. It is of fundamental significance for the generation of cell diversity." "Wikipedia:Asymmetric_cell_division" + "The many-lobed berry cluster of cells that is the terminous of a gland where the secretion is produced is acinar in form." "FMA:55588 Wikipedia:Acinus" + "The biological process whose specific outcome is the progression of a metanephric mesenchyme from an initial condition to its mature state. This process begins with the formation of metanephric mesenchyme and ends with the mature structure. Metanephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the metanephros." + "The process whose specific outcome is the progression of an atrial cardiac muscle cell over time, from its formation to the mature state. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. The atrium is the part of the heart that receives blood into the organ." + "Any process that activates or increases the frequency, rate or extent of translational elongation." + "Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in development." + "Any process that activates or increases the rate or extent of hemocyte proliferation. Hemocytes are blood cells associated with a hemocoel (the cavity containing most of the major organs of the arthropod body) that are involved in defense and clotting of hemolymph, but not involved in transport of oxygen. An example of this process is found in Drosophila melanogaster." + "The process in which a relatively unspecialized cell acquires the specialized features of an erythrophore cell. Erythrophores are pigment cells derived from the neural crest. They contain pteridine and/or carotenoid pigments in structures called pterinosomes or erythrosomes. This gives them an orange to red appearance." "A CD27-low, CD11b-high natural killer cell that has a higher threshold of activation due to higher expression of inhibitory receptors." - "OBSOLETE (was not defined before being made obsolete)." - "A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells." - "BTO:0002771" - "KUPO:0001013" - - "Neuron found in the spiral ganglion." - "A cell capable of producting norepiniphrine. Norepiniphrine is a catecholamine with multiple roles including as a hormone and a neurotransmitter. In addition, epiniphrine is synthesized from norepiniphrine by the actions of the phenylethanolamine N-methyltransferase enzyme." - "A Langerhans cell that is in the epidermis and is CD45-positive, MHCII-positive, and CD11b-positive." - "A CD8-positive, alpha-beta T cell with the phenotype CD69-positive, CD62L-negative, CD127-negative, CD25-positive, and CCR7-negative." - "KUPO:0001062" - "A multi-fate stem cell that is the source of cells for growth of the mammary gland during puberty and gestation. This cell type gives rise to both the luminal and myoepithelial cell types of the gland, and have been shown to have the ability to regenerate the entire organ in mice. This cell type also plays an important role in carcinogenesis of the breast. This cell type is Lin-, CD24-positive, CD29-hi." + "Any process that activates or increases the frequency, rate or extent of cell migration." + "Any process that modulates the frequency, rate, or extent of tissue remodeling." + "The metacarpophalangeal joints (MCP) are of the condyloid kind, formed by the reception of the rounded heads of the metacarpal bones into shallow cavities on the proximal ends of the first phalanges, with the exception of that of the thumb, which presents more of the characters of a ginglymoid joint. Arthritis of the MCP is a distinguishing feature of Rheumatoid Arthritis, as opposed to the distal interphalangeal joint in osteoarthritis. [WP,unvetted]." "SCTID:280995004 EMAPA:19302 FMA:35246 MESH:D008662 GAID:255 galen:MetacarpoPhalangealJoint Wikipedia:Metacarpophalangeal_joint NCIT:C33106 UMLS:C0025525 SCTID:370651001 MA:0000453" "A specialized mononuclear osteoclast associated with the absorption and removal of bone, precursor of multinuclear osteoclasts." - "A columnar cell of the colon that is part of the colonic epithelium." "FMA:263114" - "An elongated fibrocyte that is part of a tendon. The cytoplasm is stretched between the collagen fibres of the tendon. They have a central cell nucleus with a prominent nucleolus. Tendon cells have a well-developed rough endoplasmic reticulum and they are responsible for synthesis and turnover of tendon fibres and ground substance." - "A gamma-delta intraepithelial T cell that has the phenotype CD4-negative and CD8-negative." - "A neuron of the hippocampus." - "A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers." - "A smooth muscle cell that is part of the small intestine." "FMA:15050" + "The part of the circulatory system that lies within the subcutaneous tissue layers close to the surface of the skin." "FMA:225275" + "The superficial gray matter of the cerebellum. It consists of three main layers, the molecular layer, the Purkinje cell layer and the granule cell layer." "DHBA:10657 UMLS:C1284087 MA:0000199 CALOHA:TS-2000 BAMS:CBX BM:CB-Cbx BIRNLEX:1566 BAMS:CbCx DMBA:16939 VHOG:0001597 Wikipedia:Cerebellar_cortex EMAPA:35211 SCTID:361593004 MESH:D002525 FMA:72248 GAID:596 BAMS:CB neuronames:647 EV:0100294 HBA:4697 NCIT:C49216 MBA:528 BTO:0000043 UMLS:C0007759" + "A sphenoid bone or its cartilage or pre-cartilage precursor." + "The orderly movement of an endothelial cell into the extracellular matrix in order to form new blood vessels during angiogenesis." + "PMID:29367151 GC_ID:1" + "Any process that activates or increases the rate or extent of endothelial cell proliferation." "A transitional myocyte that is part of the middle internodal tract." "FMA:263162" - "An epithelial cell with high nuclear and cytoplasmic electron-density. This cell type is found in the deeper portions of the cortex but is more abundant in the medulla of the thymus." "FMA:72212" - - - - "A type of foam cell derived from a smooth muscle cell containing lipids in small vacuoles and typically seen in atherolosclerotic lesions, as well as other conditions." - "A central nervous system macrophage found at the interface between the blood and the cerebrospinal fluid in the brain. This cell expresses scavenger receptors." - "A microfold cell (M cell) that is part of the anorectum." + "The progression of a cardiac chamber over time, from its formation to the mature structure. A cardiac chamber is an enclosed cavity within the heart." + "FMA:54908 SCTID:361937006 UMLS:C0225486 NCIT:C12244" + "Any process that decreases the rate, frequency, or extent of the regulated release of a peptide hormone from secretory granules." "A precursor in the monocytic series, being a cell intermediate in development between the monoblast and monocyte. This cell is CD11b-positive and has fine azurophil granules." "FMA:83551 BTO:0004657" - "An epidermal cell with apical microvilli or a single apical projection have synaptic associations with nerve fibres in the epidermis." - + "A transitional population of migrating mesenchymal cells that derive from somites and that will become muscle cells." "EHDAA2_RETIRED:0003431 BTO:0000742 EMAPA:32841 EHDAA:1721 ZFA:0001056 TAO:0001056 EHDAA:1739 UMLS:C1513802 EHDAA:1733 FMA:295658 EHDAA:1727 AEO:0001018 NCIT:C34214 XAO:0000315 Wikipedia:Myotome AAO:0011067 VHOG:0001244 SCTID:344535001" "A polarized cell that is juxtaposed to fibrocytes in the underlying spiral ligament. This cell type secretes potassium ions derived from fibrocytes through gap junctions." - "An epidermal cell that is part of a cell cluster organ of the insect integument (such as a sensillum) and that secretes a cuticular specialization that forms a socket around the base of a cuticular specialization produced by a trichogen cell." "FBbt:00005171" - "A cell that is maintained or propagated in a controlled artificial environment for use in an investigation." - "KUPO:0001088" - "An adipose dendritic cell that is SIRPa-positive." - "Immature CD8_alpha-low Langerhans cell is a CD8_alpha-low Langerhans cell that is CD80-low, CD86-low, and MHCII-low." - "A smooth muscle cell that is part of the ileum." "FMA:15066" - "A visceral muscle that is transversely striated. Examples include the visceral muscle cells of arthropods." - "A cell located between the pinealocytes." "FMA:86575" - "One of the two photoreceptor cell types of the vertebrate retina. In rods the photopigment is in stacks of membranous disks separate from the outer cell membrane. Rods are more sensitive to light than cones, but rod mediated vision has less spatial and temporal resolution than cone vision." "FMA:67747 CALOHA:TS-0870 BTO:0001024" - "A hematopoeitic stem cell found in the blood. Normally found in very limited numbers in the peripheral circulation (less than 0.1% of all nucleated cells)." "BTO:0002669 FMA:86711" - "A motor neuron that is capable of directly inducing muscle contraction." - "A cell found throughout the gastrointestinal tract and in the pancreas. They secrete somatostatin in both an endocrine and paracrine manner. Somatostatin inhibits gastrin, cholecystokinin, insulin, glucagon, pancreatic enzymes, and gastric hydrochloric acid. A variety of substances which inhibit gastric acid secretion (vasoactive intestinal peptide, calcitonin gene-related peptide, cholecystokinin, beta-adrenergic agonists, and gastric inhibitory peptide) are thought to act by releasing somatostatin." "FMA:62935" - "OBSOLETE, use term from Plant Ontology. A cell formed after asymmetric division of root epidermal cell that does not give rise to a root hair." - - - "A cell type that encapsulates the capillaries and venules in the kidney. This cell secretes mesangial matrix that provides the structural support for the capillaries." "BTO:0000853 FMA:70972 CALOHA:TS-0617" - "A basophil precursor in the granulocytic series, being a cell intermediate in development between a basophilic myelocyte and a band form basophil. The nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare. Markers are CD11b-positive, CD15-positive, CD16-positive, CD24-positive, CD33-positive, and CD13-positive." "FMA:84198" - "An epithelial cell that has its apical plasma membrane folded into microvilli to provide ample surface for the absorption of nutrients from the intestinal lumen." "FMA:62122 BTO:0000398" - "Pyramidal neurons have a pyramid-shaped soma with a single axon, a large apical dendrite and multiple basal dendrites. The apex and an apical dendrite typically point toward the pial surface and other dendrites and an axon emerging from the base. The axons may have local collaterals but also project outside their region. Pyramidal neurons are found in the cerebral cortex, the hippocampus, and the amygdala." "FMA:86775 NIFSTD:sao862606388 BTO:0003102 FMA:67310" + "The dorsal region of the optic cup that gives rise to the dorsal part of the retina." + "Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs." "FMA:74562 EMAPA:18765 EHDAA2:0004615 CALOHA:TS-2018 MA:0000013" + "Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity." + "An epithelial cell that has its apical plasma membrane folded into microvilli to provide ample surface for the absorption of nutrients from the intestinal lumen." "BTO:0000398 MESH:D020895 FMA:62122" + "An integrin alpha-IIb that is encoded in the genome of human." "UniProtKB:P08514" + "The directed movement of iron ions from outside of a cell into the cytoplasmic compartment. This may occur via transport across the plasma membrane or via endocytosis." + "Any process that stops, prevents or reduces the frequency, rate or extent of pronephric nephron tubule development." "A mature natural killer cell that has the phenotype CD56-low, CD16-positive and which is capable of cytotoxicity and cytokine production." - "Skeletogenic cell that has the potential to transform into an osteoblast, and develops from neural crest or mesodermal cells." "A transitional myocyte that is part of the atrial branch of anterior internodal tract." "FMA:263156" - "A stem cell located in the bulge of the hair follicle that can give rise to regenerate the new follicle with each hair cycle and to reepithelialize the epidermis during wound repair." - "A MHC-II-negative classical monocyte located in lymphoid tissue that is F4/80-positive, CD11c-intermediate, and CD11b-high." - "Gr1-low non-classical monocyte that has low to intermediate expression of the MHC-II complex." - "Interneuromast cell is a neuroectodermal cell deposited by the migrating lateral line primordium between the neuromasts. Interneuromast cells proliferate and migrate to form additional neuromasts." + "KUPO:0001009" "Cell that is part of the migratory trunk neural crest population. Migratory trunk neural crest cells develop from premigratory trunk neural crest cells and have undergone epithelial to mesenchymal transition and delamination." - "An epithelial cell that is part of the amnion." - "An epithelial cell of stratum corneum of esophageal epithelium." "FMA:70733" - "A smooth muscle cell that is located in the anorectum." - "Skeletogenic cell that has the potential to develop into an ameloblast. Located in the inner enamel epithelium, these cells elongate, their nuclei shift distally (away from the dental papilla), and their cytoplasm becomes filled with organelles needed for synthesis and secretion of enamel proteins." - - - "The dead keratin-filled squamous cell of the stratum corneum. This cell type lacks a nucleus." "BTO:0001943 FMA:68650" - "A Feyrter cell that is part of the epithelium of trachea." "FMA:263184" - "A CD8-positive, alpha-beta positive T cell that has the phenotype T-bet-positive, eomesodermin-positive, CXCR3-positive, CCR6-negative, and is capable of producing interferon-gamma." "BTO:0004793 FMA:84793 BTO:0004888" - - "A cell of an endocrine gland, ductless glands that secrete substances which are released directly into the circulation and which influence metabolism and other body functions." "FMA:83809" - "The subcutaneous mechanoreceptors that innervate vellus hairs." - "A pro-T cell that has the phenotype CD4-negative, CD8-negative, CD44-positive, and CD25-negative." - "Any fibroblast that is deriived from the neural crest." - "An endothelial cell of the umbilical vein." "BTO:0004296" - "A type I pneumocyte is a flattened, branched pneumocyte that covers more than 98% of the alveolar surface. This large cell has thin (50-100 nm) cytoplasmic extensions to form the air-blood barrier essential for normal gas exchange." "FMA:62500 BTO:0000780" - - "A resting mature B cell within the Peyer's patch that is CD19-positive, B220-positive, IgM-positive, AA4-negative, CD23-positive, CD43-negative, and CD5-negative." - - "Any endothelial cell of lymphatic vessel that is part of a dermis." - "ncithesaurus:Blastemal_Cell" - "An epithelial cell that is part of the external acoustic meatus." "FMA:70555" - "Derived from the Greek word pyren (the pit of a stone fruit), this is a transient nucleated cell type that results from exclusion of the nucleus from the primitive erythrocyte." - "A type EC enteredocrine cell in the intestines that stores and secretes substance P and 5-hydroxytryptamine." "FMA:62940" - "Obsolete. Use PO:0000115 from Plant Ontology instead. A cell that surrounds a trichome and provides support for the trichome." - "An epithelial cell of the thymus. Epithelial reticular cells are pleomorphic, stellate, non-phagocytic cells which seem to be supportive in function and are held together by desmosomes. They replace the fibroblastoid reticular cells found in other lymphoid organs. Other epithelial cells in the medulla have the ultrastructure of secretory cells. Although different epithelial cells throughout the thymus appear alike by light microscopy their ultrastructure and function varies." "CALOHA:TS-1040 FMA:72208" - "An epidermal cell that is part of a cell cluster organ of the insect integument (such as a sensillum) and that secretes a cuticular specialization, often in the form of a hair, bristle, peg or scale. The base of this specialization is often surrounded by a socket produced by a closely associated tormogen cell." "FBbt:00005169 BTO:0004744" - "A cell found in an organism or derived from an organism exhibiting a phenotype that deviates from the expected phenotype of any native cell type of that organism. Abnormal cells are typically found in disease states or disease models." "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12913" + "Any process that stops, prevents, or reduces the frequency, rate or extent of natural killer cell proliferation." + "Mesenchyme that develops_from a neural crest and is part of a 2nd arch mesenchyme." "EHDAA2:0000068 EMAPA:16281" + "Any process that activates or increases the frequency, rate or extent of mitotic nuclear envelope disassembly." + "The regulated release of serotonin by a platelet or group of platelets." + "Any process involved in the maintenance of an internal steady state of calcium ions in the vacuole or between a vacuole and its surroundings." + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucose stimulus." + "Any process that activates or increases the frequency, rate or extent of defecation." + + "The vasculature consisting of brachiocephalic arteries and veins." + "Acellular anatomical structure whose predominant constituent is keratin." "AEO:0000099 EHDAA2:0003099" + "Any process that modulates the frequency, rate or extent of muscle cell differentiation." + "Any process that activates or increases the frequency, rate or extent of DNA recombination." + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glycine stimulus." + "Arteries which arise from the abdominal aorta and distribute to most of the intestines." "Wikipedia:Mesenteric_artery NCIT:C52975 UMLS:C0025465 EHDAA2:0001123 SCTID:281084003 EHDAA:4343 MA:0002003 XAO:0000370 VHOG:0001117 BTO:0000779 EMAPA:17312 MESH:D008638" + "KUPO:0001006" + "The process in which a relatively unspecialized cell acquires specialized structural and/or functional features of a prolactin secreting cell. A prolactin secreting cell is an acidophilic cell of the anterior pituitary that produces prolactin." + "A telencephalic ventricle that is in_the_right_side_of a telencephalon." "FMA:78449 SCTID:368571000" + "The process that gives rise to the mesoderm. This process pertains to the initial formation of the structure from unspecified parts." + "Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat." + + "Any process that stops, prevents, or reduces the frequency, rate, or extent of monocyte antigen processing and presentation." + "The labyrinth is a system of fluid passages in the inner ear, including both the cochlea, which is part of the auditory system, and the vestibular system, which provides the sense of balance. It is named by analogy with the mythical maze that imprisoned the Minotaur, because of its appearance. The bony labyrinth, or osseous labyrinth, is the network of passages with bony walls lined with periosteum. The bony labyrinth is lined with the membranous labyrinth. There is a layer of perilymph between them. The three parts of the bony labyrinth are the vestibule of the ear, the semicircular canals, and the cochlea. The vestibular system is the region of the inner ear where the semicircular canals converge, close to the cochlea (the hearing organ). The vestibular system works with the visual system to keep objects in focus when the head is moving. Joint and muscle receptors also are important in maintaining balance. The brain receives, interprets, and processes the information from these systems that control our balance. [WP,unvetted]." "BTO:0004686 NCIT:C32336 EMAPA:36569 Wikipedia:Cochlear_labyrinth FMA:61259 MA:0002809 UMLS:C0931689" + "Any process that stops, prevents, or reduces the frequency, rate or extent of pancreatic B cell development." + "A prolactin that is encoded in the genome of human." "UniProtKB:P01236" + "A DRD1-expressing medium spiny neuron that is part of dense, RXFP1-positive cell islands throughout the nucleus accumbens, putamen, and near the adjacent septal nuclei." + "The process whose specific outcome is the progression of the otic vesicle over time, from its formation to the mature structure. The otic vesicle is a transient embryonic structure formed during development of the vertebrate inner ear." + "KUPO:0001007" + "Mesenchyme that develops_from a rhombencephalon neural crest." "EHDAA2:0004423" + "The process whose specific outcome is the progression of a blood vessel over time, from its formation to the mature structure. The blood vessel is the vasculature carrying blood." "A kidney cortical cell that is part of the nephrogenic zone." - "A myoepithelial cell that is part of the primary lactiferous duct." "FMA:74500" - "A megakaryocyte progenitor cell that is CD34-negative, CD41-positive and CD42-positive." "A polarized columnar cell that covesr the lateral surface of the cochlear duct, secretes potassium ions and forms a continuous sheet in contact with the endolymph; marginal cells form extensive interdigitations with the basal and intermediate cells in the normal adult stria." - "An antigen inexperienced CD4-positive, alpha-beta T cell with the phenotype CCR7-positive, CD127-positive and CD62L-positive. This cell type develops in the thymus. This cell type is also described as being CD25-negative, CD62L-high, and CD44-low." - "A skeletal muscle fiber that is part of a muscle spindle. These are specialized muscle fibers that serve as proprioceptors, detecting the amount and rate of change in length of a muscle. They are innervated by both sensory neurons and motor neurons (gamma and beta motorneurons, collectively referred to as fusimotor neurons)." "H3.03.00.0.00012" - - "A macrophage resident in the peritoneum under non-inflammatory conditions. Markers include F4/80-high, CD11b-high, CD68-positive, SIGNR1-positive, CD115-high, MHC-II-negative, and Dectin-1-positive." "FMA:83025 BTO:0001034" - "An epithelial cell that is part of the appendix." "FMA:63602" - "The principal cell type of the dentate gyrus." - - + "A regional part of brain consisting of multiple brain regions that are not related through a simple volummetric part of hierarchy, e.g., basal ganglia[NIF]." "NLXANAT:20090509" + "Any process in which a macromolecule is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell." + "An OFF diffuse bipolar cell that predominantly connects to ON parasol cells and lateral amacrine cells. This cell contains a large number of synaptic ribbons and a small axon arbor area." + "The mucous membrane that lines the inner surface of the eyelids and the front of the eyeball." "EV:0100340 UMLS:C0009758 MESH:D003228 SCTID:181161008 EFO:0000374 MA:0000265 XAO:0000182 AAO:0010343 BTO:0003415 Wikipedia:Conjunctiva CALOHA:TS-2232 FMA:59011 NCIT:C12341 GAID:898" + "An animal opsin that is a translation product of the human OPN4 gene or a 1:1 ortholog thereof." "IUPHARobj:2758" + "A glial fibrillary acidic protein that is encoded in the genome of human." "Reactome:R-HSA-9625195 UniProtKB:P14136 Reactome:R-HSA-1253311" + "The orderly movement of a smooth muscle cell from one site to another, often during the development of a multicellular organism." "A rounded cell that is usually situated next to sinusoids; secretes follicular stimulating hormone (FSH) and luteinizing hormone (LH)." "BTO:0002482 FMA:83100" - "A follicular B cell that is IgD-positive, CD23-negative, and CD38-negative. This naive cell type is activated in the extrafollicular areas through interaction with interdigitating dendritic cells and antigen-specific CD4-positive T cells." - "The stem cell from which glial precursor cell arises from." "FMA:87171" - "A nerve cell where transmission is mediated by nitric oxide." "FMA:84792" - "A PP cell found in intestine." - "KUPO:0001015" - "A smooth muscle cell of the umbilical artery." - "An adult angioblastic cell released from the bone marrow, capable of blood circulation and participation in angiogenesis by differentiating into blood vessel endothelial cells. Their existence is controversial." - "A transitional myocyte that is part of the right branch of atrioventricular bundle." "FMA:263172" - - "Any neuromast mantle cell that is part of a posterior lateral line." - "An epithelial cell of the uterus." "FMA:256161" - "A fibroblast that is part of the dense regular elastic tissue." "FMA:261287" - - "A preadipocyte that is part of subcutaneous tissue." - "A cell in the zona fasciculata that produce glucocorticoids, e.g cortisol." "FMA:69547" - "A giant pyramidal neuron with a soma in layer Vb of the primary motor cortex that sends its axons down the spinal cord via the corticospinal tract, either synapsing directly with alpha motor neurons, or targeting interneurons in the spinal cord. In humans, Betz cells are the largest known in the central nervous system." - - "A group 2 innate lymphoid cell in the human with the phenotype CD25-positive, CD127-positive, CD161-positive, and GATA-3-positive." - "A renal filtration cell is a specialized cell of the renal system that filter fluids by charge, size or both." - "Any fibroblast that is part of skeletal muscle tissue." - "An intratelencephalic-projecting glutamatergic neuron with a soma found in layer 2/3 of the human primary motor cortex." - "FBbt:00001687" - - "A flattened stroma cell forming a sheath or theca outside the basal lamina lining the mature ovarian follicle. Thecal interstitial or stromal cells are steroidogenic, and produce primarily androgens which serve as precusors of estrogens in the granulosa cells." "FMA:18690 BTO:0002850" - "A Paneth cell that is part of the epithelium proper of small intestine." "FMA:263106" - "Endothelial cells forming the walls of the capillaries within the cerebral cortex." "CALOHA:TS-2372" - "A muscle cell that is part of the middle internodal tract." "FMA:223279" - "A pyramidal neuron which lacks a tuft formation but extends small radial distances forming a star-like shape." - "A cultured cell that is freshly isolated from a organismal source, or derives in culture from such a cell prior to the culture being passaged." "BTO:0002290" - "Any native cell that is part of a hypothalamus." - "An innate lymphoid cell that is capable of producing T-helper 2-cell associated cytokines upon stimulation." - "KUPO:0001085" + "The process in which the anatomical structure of the vestibulocochlear nerve is generated and organized. This sensory nerve innervates the membranous labyrinth of the inner ear. The vestibular branch innervates the vestibular apparatus that senses head position changes relative to gravity. The auditory branch innervates the cochlear duct, which is connected to the three bony ossicles which transduce sound waves into fluid movement in the cochlea." + "Any process that activates or increases the frequency, rate, or extent of interleukin-13 production." + "Any process that activates or increases the frequency, rate or extent of the controlled release of bile acid from a cell or a tissue." + "Any process that stops, prevents or reduces the frequency, rate or extent of Schwann cell chemotaxis." + "Cytoarchitectural layer of the retina that is made up of a dense reticulum of fibrils formed by interlaced dendrites of retinal ganglion cells and cells of the inner nuclear layer (adapted from Wikipedia)." "SCTID:280682006 BAMS:Ripl EMAPA:35741 FMA:58704 ZFA:0001329 XAO:0003225 NLXANAT:1005032 NCIT:C32809 TAO:0001329 UMLS:C0229221 NLX:20558 Wikipedia:Inner_plexiform_layer MA:0001312 VHOG:0001168 BTO:0003175" + "An anatomical space that is part of a bone of upper jaw." "AAO:0000621" + "The layers of the laminar structure of the hippocampus." "BIRNLEX:1192 FMA:83679 Wikipedia:Hippocampus_anatomy#Hippocampal_Cells_and_Layers EMAPA:35407 FMA:277842 MA:0002427" + "A shape quality inhering in a bearer by virtue of the degree to which there are subdivisions or offshoots in a bearer entity." + "Any process that activates or increases the frequency, rate or extent of flagellated sperm motility." + "A neural nucleus that is part of a midbrain tectum." "FMA:258766" + "Tolerance induction taking place in the mucosal-associated lymphoid tissue (MALT) mediated by T cells." + "The process in which a relatively unspecialized hemopoietic cell acquires specialized features of a gamma-delta T cell. A gamma-delta T cell is a T cell that expresses a gamma-delta T cell receptor complex." + "A testis that is in the left side of the genitalia [Automatically generated definition]." "MA:0001746 SCTID:367720001 FMA:7212 UMLS:C0227998 EMAPA:37370 NCIT:C49323" + "Enables the transfer of a single solute from one side of a membrane to the other by a mechanism involving conformational change, either by facilitated diffusion or in a membrane potential dependent process if the solute is charged." "Reactome:R-HSA-429767 Wikipedia:Facilitated_diffusion" + "Any process that modulates the frequency, rate or extent of excitatory postsynaptic potential (EPSP). EPSP is a process that leads to a temporary increase in postsynaptic potential due to the flow of positively charged ions into the postsynaptic cell. The flow of ions that causes an EPSP is an excitatory postsynaptic current (EPSC) and makes it easier for the neuron to fire an action potential." + "The stage of development at which the animal is fully formed, including immaturity and maturity. Includes both sexually immature stage, and adult stage." "WBls:0000041 XtroDO:0000084 EFO:0001272 BTO:0001043 BilaDO:0000004 FBdv:00005369" + "A portion of smooth muscle tissue that is part of a digestive system [Automatically generated definition]." "EMAPA:35117 MA:0001523" + "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])"@en + + "GC_ID:1" "A lymphoid progenitor cell of the T cell lineage, with some lineage specific marker expression, but not yet fully committed to the T cell lineage." + "Epithelial layer that is part of the external part of the nose." "FMA:63143" "A smooth muscle cell that is part of any lymphatic vessel." - "A transitional myocyte that is part of the anterior division of left branch of atrioventricular bundle." "FMA:263166" - "A vertebrate phagocyte with a single nucleus." "BTO:0001433" "Obsolete. Use PO:0000071 from Plant Ontology instead. A specialized parenchyma cell associated with a sieve-tube member in angiosperm phloem and arising from the same mother cell as the sieve-tube member." - "A Vgamma1.1-positive, Vdelta6.3-positive thymocyte that is CD24-negative." - "A cell whose primary function is to prevent the transport of stuff across compartments." - "A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment)." "CARO:0000013" - "A monocyte that expresses CD14 and is negative for the lineage markers CD3, CD19, and CD20." - "An IgM memory B cell is an unswitched memory B cell with the phenotype IgM-positive and IgD-negative." - "A smooth muscle cell of the aorta." "BTO:0004577" - "An epithelial cell that lines the peripheral gas exchange region of the lungs of air-breathing vertebrates." "FMA:62499 CALOHA:TS-2168 BTO:0000395" - "A stromal cell of the ovarian medulla." "FMA:256171" - "Squamous cell of oral epithelium." "CALOHA:TS-1252" - "Obsolete. Use PO:0000077 from Plant Ontology instead. Cell variable in form and size, being more or less thick, often lignified, secondary walls. Belongs to the category of subcells and may or may not be devoid of protoplast at maturity." - "A neuron which sends impulses peripherally to activate muscles or secretory cells." - "Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells." "FMA:62864 BTO:0000876 CALOHA:TS-0638" - "A common lymphoid progenitor that is CD10-positive, CD45RA-positive, CD34-positive and CD38-positive." - "Astrocyte-like radial glial cell that extends vertically throughout the retina, with the nucleus are usually in the middle of the inner nuclear layer." - "An enucleate erythrocyte that is GlyA-positive." - "An immature astrocyte." - "A vetebrate lens cell that is any of the elongated, tightly packed cells that make up the bulk of the mature lens in a camera-type eye." - "A splenic macrophage found in the white pulp of the spleen. Markers include F4/80-negative, CD68-positive, and macrosialin-positive." - "Any fibroblast that is part of a reticular layer of dermis." - "A alpha-beta T cell that has a mature phenotype." - - "A CD11b-positive dendritic cell that is CD11b-high, CD45-positive, MHC-II-positive and CD103-negative." - "Glandular cell of oviduct epithelium. Example: peg cells, ciliated cells." "CALOHA:TS-1277" - "A plasmablast that secretes IgA." - "A mechanoreceptor in the organ of Corti. In mammals the outer hair cells are arranged in three rows which are further from the modiolus than the single row of inner hair cells. The motile properties of the outer hair cells may contribute actively to tuning the sensitivity and frequency selectivity of the cochlea." "FMA:62366 BTO:0003666" - "A mammary epithelial cell that occurs in the lumen of the ductal and alveoli structure in the breast." "FMA:73280" - "An extracellular matrix secreting cell that secretes eggshell." - "An intratelencephalic-projecting glutamatergic neuron with a soma found in layer 6 of the human primary motor cortex." "ILX:0770158" - - "A double negative thymocyte that is CD3-positive, CD4-negative, CD8-negative, that that are present in the periphery in very low numbers and predominantly produce INF-gamma, TNF-alpha, and a low amount of TGF-beta, but not IL-2, IL-4, IL-10 or IL-13 upon activation." - "FBbt:00001691" - - "A visceral muscle cell that is striated. Examples include the visceral muscle cells of arhtropods." - "A cell within the follicle of an ovary." "FMA:70589 EMAPA:31247" - "An undifferentiated fibroblast that can be stimulated to form a fat cell." "BTO:0001107" - "A fibroblast of skin." "CALOHA:TS-0935 BTO:0001255" - "A muscle cell that is part of the sinoatrial node." "FMA:67102" - "An epithelial cell that is part of the conjunctiva." "FMA:70552" - "An innate lymphoid cell in the human with the phenotype NKp46-positive that is a precusor for NK cells and ILC3 cells." - "Epithelial cell that is part of the colon epithelium." - - "CD8-positive, alpha-beta positive regulatory T cell with the phenotype CD28-negative and FoxP3-positive." - "Gr1-high monocyte that lacks MHC-II receptor complex." - "Epithelial cells derived from neural plate and neural crest." "FMA:70557 BTO:0004301" + "A rhodopsin-like G-protein coupled receptor that in active form binds to one or more chemokines." "PIRSF:PIRSF038545 IUPHARfam:14" + "The chemical reactions and pathways resulting in the breakdown of histamine, a physiologically active amine, found in plant and animal tissue and released from mast cells as part of an allergic reaction in humans." + "A V(D)J recombination-activating protein 2 that is encoded in the genome of mouse." "UniProtKB:P21784" + "A circumventricular organ that is capable of secreting substances into the cerebrospinal fluid." "neuronames:2857 EMAPA:35759 MA:0002943" + "Any process that modulates the frequency, rate or extent of T-helper 1 cell cytokine production." + "The process whose specific outcome is the progression of the compound eye over time, from its formation to the mature structure. The compound eye is an organ of sight that contains multiple repeating units, often arranged hexagonally. Each unit has its own lens and photoreceptor cell(s) and can generate either a single pixelated image or multiple images, per eye." + "The process in which the anatomical structures of a neuron projection are generated and organized. A neuron projection is any process extending from a neural cell, such as axons or dendrites." + "Any process that modulates the frequency, rate or extent of testosterone biosynthetic process." + "The external genitalia are the outer sex organs, such as the penis or vulva in mammals." "FMA:45643 SCTID:362207005" + "Any process that modulates the frequency, rate or extent of gluconeogenesis, the formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol." + "An organic amino compound that consists of amino acid residues (unmodified amino-acid residues and/or modified amino-acid residues) linked by peptide bonds or derivatives of such bonds." + "Any process that modulates the frequency, rate, or extent of erythrocyte clearance." + "Any process that stops or decreases the rate or extent of oligodendrocyte progenitor proliferation." + "In the human body, the femoral vein is a blood vessel that accompanies the femoral artery in the femoral sheath. It begins at the adductor canal (also known as Hunter's canal) and is a continuation of the popliteal vein. It ends at the inferior margin of the inguinal ligament, where it becomes the external iliac vein. [WP,unvetted]." "Wikipedia:Femoral_vein FMA:21185 SCTID:362071002 UMLS:C0015809 NCIT:C12716 galen:FemoralVein EMAPA:17876 AAO:0010237 MA:0002118 MESH:D005268 GAID:533" + "Any process that stops, prevents or reduces the frequency, rate or extent of renal water transport." + "A serous membrane that is part of a cloaca [Automatically generated definition]." + "Any process in which a polysaccharide is transported to, or maintained in, a specific location." + "The regulation of blood pressure mediated by detection of stimuli and a neurological response." + "A membrane alanyl aminopeptidase-like metallopeptidase that is a translation product of the human ENPEP gene or a 1:1 ortholog thereof." "IUPHARobj:1568" + "The part of the secondary follicle that surrounds the germinal center." "UMLS:C1512987 NCIT:C33053 Wikipedia:Mantle_zone" + "An adipocyte that is part of the epicardial fat of right ventricle." "FMA:261297" + "The directed orientation of natural killer cell signaling molecules and associated membrane rafts towards a chemokine gradient or a contact point with a cell displaying natural killer cell activating ligands." + "A C-type lectin with multiple lectin domains that is a translation product of the human MRC1 gene or a 1:1 ortholog thereof." + "Anatomical system that has as its parts the heart and blood vessels." "BILA:0000016 XAO:0000100 MESH:D002319 NCIT:C12686 SCTID:278198007 MA:0000010 AAO:0011001 GAID:467 EV:0100017 CALOHA:TS-1297 MIAA:0000016 FMA:7161 EHDAA:394 TAO:0000010 EMAPA:16104 BTO:0000088 EFO:0000791 MAT:0000016 WikipediaCategory:Cardiovascular_system XAO:0001010 ZFA:0000010 VHOG:0000302 UMLS:C0007226" + "Cranial neural crest which gives rise to the trigeminal ganglion." "EFO:0003484 VHOG:0000269 EMAPA:16170 ZFA:0000080 EHDAA:667 TAO:0000080 EHDAA2:0002083" + "The process in which a relatively unspecialized cell acquires specialized features of a microglial cell. Microglia are glial cells that act as the immune cells of the central nervous system. They form part of the supporting structure of this system." + "GC_ID:1" + "An epithelial tube that is open at one end only." "AEO:0000115 EHDAA2:0003115" + "In the blood supply of the kidney, the vasa recta renis (or straight arteries of kidney, or straight arterioles of kidney) form a series of straight capillaries in the medulla. They lie parallel to the loop of Henle. These vessels branch off the efferent arterioles of juxtamedullary nephrons (those nephrons closest to the medulla), enter the medulla, and surround the loop of Henle." "EMAPA:30043 MA:0002595 FMA:72006 Wikipedia:Vasa_recta galen:ArteriaeRectae" + "The directed movement of substances from the Golgi to the plasma membrane in transport vesicles that move from the trans-Golgi network to the plasma membrane, where they fuse and release their contents by exocytosis." + "Any process that activates or increases the frequency, rate or extent of epithelial cell apoptotic process." + "The membrane the surrounds the prostate gland." "UMLS:C0227963 NCIT:C13086 SCTID:279682007 FMA:19583" + "A natural cytotoxicity triggering receptor 2 that is encoded in the genome of human." "UniProtKB:O95944" + "Any process that modulates the frequency, rate or extent of gonad development." + "An epithelium that is part of a lower arm [Automatically generated definition]." "EHDAA:6220 VHOG:0001096 EMAPA:17418 EHDAA2:0000554 EHDAA:4174" + "The renal vesicle is the primordial structure of the mesonephric nephron epithelium, and is formed by the condensation of mesenchymal cells[GO]." "ZFA:0005586 SCTID:361407006" + "An interleukin-7 receptor subunit alpha that is encoded in the genome of human." "UniProtKB:P16871" + "The directed movement of substances, into, out of or within a cell, either in a vascular tissue or in the vascular membrane." + "A compact bone tissue that is part of a bone tissue of long bone." "FMA:32674" + "Any process that stops, prevents or reduces the frequency, rate or extent of smooth muscle hypertrophy." "A rounded, mitotically active stem cell which is the source of new cells of the taste bud; located basally." "FMA:62380" - - "A rod-shaped cell found in 3 or 4 rows that lie adjacent to and support the outer hair cells." "FMA:75727" - "A Sst GABAergic cortical interneuron that is both an interneuron and a projecting neuron. They are found in all layers from upper L2/3 down to the bottom of L6. They have long-range projections, some with axons fading into white matter. These cells have low rebound potential, low hyperpolarization sag, and high variability in membrane time constant." - "A somatic epithelial cell of the ovarian follicle/egg chamber." "FBbt:00004904" - "A CD14-positive monocyte that is also CD16-positive and CCR2-negative." - "FBbt:00004905" - "A diploid cell that has derived from a spermatogonium and can subsequently begin meiosis and divide into two haploid secondary spermatocytes." "FMA:72292 CALOHA:TS-2194 BTO:0001115" - "A neurectoderm derived cell that lines the neural lumen." "FMA:70550 BTO:0001724" - "A cell capable of producing epinephrine. Epiniphrine is synthesized from norepiniphrine by the actions of the phenylethanolamine N-methyltransferase enzyme, which is expressed in the adrenal glands, androgenic neurons, and in other cell types." - "A mesodermal cell that is part of the splanchnic layer of lateral plate mesoderm." - "A cell whose primary function is to support other cell types." "BTO:0002315" - "A bipolar neuron found in the retina and having connections with photoreceptors cells and neurons in the inner plexiform layer." - "A smooth muscle cell of the myometrium that enlarges and stretches during pregnancy, and contracts in response to oxytocin." "BTO:0004519" - "A cell of the epithelial lining that produce and secrete mucins." "http://en.wikipedia.org/wiki/Goblet_cell FMA:13148 BTO:0001540" - "A fibroblast that is part of the breast." - "KUPO:0001049" - "An epithelial cell of the placenta." - "Cell that provides some or all mechanical, nutritional and phagocytic support to their neighbors." "BTO:0002315" + "Any process that modulates the frequency, rate or extent of mesenchymal cell apoptotic process involved in metanephros development." + "The directed killing of a target cell by a neutrophil." + "Any process that activates or increases the frequency, rate or extent of hemostasis." + "The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages." "Wikipedia:Inflammation" + "The primitive streak is a structure that forms during the early stages of avian, reptilian and mammalian embryonic development[WP]. the midline ridge of the embryonic epiblast that later develops into mesoderm and endoderm[MP]." "Wikipedia:Primitive_streak EMAPA:16072 UMLS:C0033153 VHOG:0001202 EHDAA2:0001525 FMA:293110 NCIT:C28402 EHDAA:185 SCTID:361438007" + "The epithelial lining of the trachea which contains numerous ciliated cells." "VHOG:0001045 CALOHA:TS-1061 MA:0001862 EHDAA2:0002069 UMLS:C1179002 EMAPA:18409 BTO:0001389 EMAPA:16855 EHDAA:5007 FMA:62015 NCIT:C33797" + "A cartilaginous condensation that has the potential to develop into a hindlimb bone." "EMAPA:32632" + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving any hormone." + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a protein." + "Any process that stops, prevents or reduces the frequency, rate or extent of keratinocyte apoptotic process." + "Any process involved in the carrying out of an immune response by a mast cell." "KUPO:0001106" - "Any glutamatergic neuron that is part of a cerebellum." - - - "Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. In mammals, the contractile fiber resembles those of skeletal muscle but are only one third as large in diameter, are richer in sarcoplasm, and contain centrally located instead of peripheral nuclei." "BTO:0001539 CALOHA:TS-0115 FMA:14067" - "An undifferentiated cell of the prostate epithelium that lacks secretory activity." + "A retinal ganglion A2 cell with dendrites terminating in S4." "BAMS:1061" + "The process whose specific outcome is the progression of the metanephric cortical collecting duct over time, from its formation to the mature structure. The metanephric cortical collecting duct is the portion of the metanephric collecting duct that resides in the renal cortex." + "The pulmonary artery that supplies the left lung." "NCIT:C32971 MA:0002032 FMA:50873 galen:LeftPulmonaryArtery SCTID:244234004 Wikipedia:Left_pulmonary_artery EMAPA:37097 UMLS:C0923925" + "Any process that modulates the frequency, rate or extent of osteoclast development." "A trophoblast that leaves the placenta and invades the endometrium and myometrium. This cell type is crucial in increasing blood flow to the fetus." "FMA:86564 BTO:0002366" - - "A mesenchymal cell of the endocardial cushion. These cells develop via an epithelial to mesenchymal transition when endocardial cells break cell-to-cell contacts and migrate into the cardiac jelly. Cells from this population form the heart septa and valves." - "A recently activated CD4-positive, alpha-beta T cell with the phenotype HLA-DRA-positive, CD38-positive, CD69-positive, CD62L-negative, CD127-negative, and CD25-positive." - "A CD8-positive alpha-beta-positive T cell with the phenotype CXCR3-positive and having suppressor function. They are capable of producing IL-10, suppressing proliferation, and suppressing IFN-gamma production." + "A pronephric nephron is the functional unit of the pronephros[GO]." "AAO:0011091 XAO:0000285" + "A diaphysis that is part of a fibula[Automatically generated definition]." "FMA:33738 SCTID:302528006 Wikipedia:Body_of_fibula EMAPA:37892" + "The region of the hepatic acinus in between zones 1 and 3. Blood in this region has an intermediate oxygen concentration relative to the other two zones of the hepatic acinus. Zone 2 is located in the midzonal region of the liver lobule. Hepatocytes in this region have mixed functionality in comparison with those in zones 1 and 3." + "Any process that activates or increases the frequency, rate or extent of CD4-positive, alpha-beta T cell differentiation." + "The outer layers of solid, hard bone that covers spongy bone; consists of parallel osteons containing mineral deposits and interstitial lamellae." "galen:CorticalBone NCIT:C52714 FMA:24018 Wikipedia:Compact_bone UMLS:C0222661 MA:0001461 SCTID:361728003 EMAPA:35250" + "The process in which neuroepithelial cells of the neural tube give rise to radial glial cells, specialized bipotential progenitors cells of the forebrain. Differentiation includes the processes involved in commitment of a cell to a specific fate." + "Mesenchyme that develops_from a trunk neural crest." "ZFA:0000999 EMAPA:16182 TAO:0000999 EHDAA2:0002093" + "The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications). Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification)." + "One of the two jaw ridges either on the roof of the mouth between the upper teeth and the hard palate or on the bottom of the mouth behind the lower teeth[WP]. The alveolar ridges contain the sockets (alveoli) of the teeth[HP]." "SCTID:245790000 Wikipedia:Alveolar_ridge GAID:215 UMLS:C0447411 BTO:0001383 MA:0003119 EMAPA:35118 MESH:D000539 FMA:313923 NCIT:C89749" "A transitional myocyte that is part of the posterior internodal tract." "FMA:263164" - "CD8-positive, alpha-beta memory T cell with the phenotype CCR7-negative, CD127-positive, CD45RA-negative, CD45RO-positive, and CD25-negative." - "A type II muscle cell that contains a low content of myoglobin, relatively few mitochondria, relatively few blood capillaries and large amounts of glycogen. Type II B fibres are white, geared to generate ATP by anaerobic metabolic processes, not able to supply skeletal muscle fibres continuously with sufficient ATP, fatigue easily, split ATP at a fast rate and have a fast contraction velocity." "FMA:84416" - "Any pericyte cell that is part of a placenta." - - "A trophoblast found at the junction of the placenta. This cell type makes a unique fibronectin-trophouteronectin junction that helps mediate attachment of the placenta to the uterus. This cell type is also found junction of the chorion layer of the external membranes and the decidua." - "A neuroepithelial cells that occurs singly or in small groups, close to the outer follicular borders but within the follicular basement membrane of the thyroid. Expresses a form of the neural cell adhesion molecule (N-CAM) on their surface. Secretes calcitonin, 5-hydroxytryptamine and dopamine." "SCTID:176770005 FMA:68653" - "A M cell that is part of the epithelium proper of duodenum." "FMA:263134" - "FMA:83619" - "A mesothelial cell that is part of the parietal peritoneum." "FMA:72142" - "KUPO:0001102" - - "A peptide hormone secreting cell that secretes gastrin stimulating hormone." + "A maturity quality inhering in a bearer by virtue of the bearer's indirect development, undergoing metamorphosis." + "A vein that is part of a clitoris [Automatically generated definition]." "MA:0002252 SCTID:360819004 EMAPA:37201" + "A lymph node that is located close to the surface." "NCIT:C102716 FMA:12767" + "Any process that modulates the frequency, rate or extent of chromatin binding. Chromatin binding is the selective interaction with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase." + "Any process that activates or increases the frequency, rate or extent of differentiation of regulatory T cells." "Mature CD1a-positive Langerhans cell is a CD1a-positive Langerhans cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive." - "Characteristic early embryonic cell with a bottle or flask shape that is first to migrate inwards at the blastopore during gastrulation in amphibians." "A myoepithelial cell that is part of the main lactiferous duct." "FMA:74499" - "An endothelial cell that is part of the thoracic endothelium." - "a L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex that has inverted pyramidal morphology." - "Fibroblast from foreskin." "CALOHA:TS-0384" - "Mesenchymal derived lymphatic progenitor cells that give rise to the superficial lymphatics." - "The various hormone- or neurotransmitter-secreting cells present throughout the mucosa of the stomach." - "CD133-positive hematopoietic stem cell is a hematopoietic stem cell that is CD34-positive, CD90-positive, and CD133-positive." "FMA:86475 CALOHA:TS-0448" + "Any process that modulates the frequency, rate or extent of photosynthesis." + "The chemical reactions and pathways involving imidazoles, five-membered organic heterocycle containing two nitrogen atoms at positions 1 and 3, or any of its derivatives; compounds containing an imidazole skeleton." + "A rhombomere lateral wall that is part of a rhombomere 1." "TAO:0000781 EMAPA:16482 EHDAA2:0001641 ZFA:0000781" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of juvenile hormone." + "The synthesis or release of nitric oxide following a stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels." + "The process in which an immature myeloid dendritic cell acquires the specialized features of a mature myeloid dendritic cell as part of an immune response." + "Mesenchyme that is part of a developing mammary gland." "EHDAA:6528 VHOG:0001087 EMAPA:17761 EHDAA2:0001058" + "CD133-positive hematopoietic stem cell is a hematopoietic stem cell that is CD34-positive, CD90-positive, and CD133-positive." "CALOHA:TS-0448" "Any epithelial cell of viscerocranial mucosa that is part of a nasal cavity respiratory epithelium." "A dermal dendritic cell that is langerin-positive and CD103-positive." - "A central nervous system macrophage found in the parenchyma of the central nervous system. Marker include CD11b-positive, F4/80-positive, and CD68-positive." "BTO:0000962 BTO:0000078 FMA:54540 FMA:54539" + "An intestinal crypt that is located in the ileum." "FMA:269061 EMAPA:37839" + "A central nervous system macrophage found in the parenchyma of the central nervous system. Marker include CD11b-positive, F4/80-positive, and CD68-positive." "BTO:0000962 BTO:0000078 FMA:54539" "An immature B cell of an intermediate stage between the pre-B cell stage and the mature naive stage with the phenotype surface IgM-positive and CD19-positive, and are subject to the process of B cell selection. A transitional B cell migrates from the bone marrow into the peripheral circulation, and then to the spleen." + "An amicrine that has a wide dendritic field." + "The series of events in which a pheromone stimulus is received by a cell and converted into a molecular signal." "KUPO:0001103" - - "A rod-like cell in the inner ear, having their heads joined and their bases on the basilar membrane widely separated so as to form a spiral tunnel known as the tunnel of Corti." "FMA:75722" - "A mesenchymal stem cell that is part of Wharton's jelly." - "A preadipocyte found in mesenteric tissue." - "A myocardial endocrine cell that is part of the interventricular septum." "FMA:83390" - "A peptide hormone secreting cell that secretes vasopressin stimulating hormone" - - "A glutamatergic neuron, with a soma found in the deeper portion of L5, that has long-range axonal projections including deep subcortical targets outside of the telencephalon and, in some cases, the spinal cord. While the L5 ET neuron projections are not limited to ET targets, they are clearly differentiated from the neuron subclasses whose projections are constrained to intratelencephalic (IT) targets. L5 ET neurons are generally the largest excitatory cortical neurons, typically having a thick apical dendrite with a prominent dendritic tuft in layer 1 and displaying burst-firing physiological characteristics." + "Enables the transfer of water (H2O) from one side of a membrane to the other." "A CD11b-positive dendritic cell located in the serosal portion of the small intestine epithelium. This cell type is CD45-positive, MHC-II-positive, CD11c-low, CD103-negative." - "A sperm cell that is cabaple of motion (motility)." - "An epithelial cell of the cervix." - "A pro-B cell that CD45R/B220-positive, CD43-positive, HSA-low, BP-1-negative and Ly6c-negative. This cell type is also described as being lin-negative, AA4-positive, Kit-positive, IL7Ra-positive and CD45R-positive." - "A progenitor cell that can give rise to plasmacytoid and myeloid dendritic cells, and to monocytes and macrophages. Marker for this cell is Kit-high, CD115-positive, CD135-positive, Cx3cr1-positive, and is Il7ra-negative." - "A respiratory stem cell found at the junction of the terminal (conductive) bronchiole and the respiratory bronchiole. This cell types gives rise to alveolar cell types and club cells in response to lung injury. This cell type expresses markers Scgb1a1 and Sftpc." - "An epithelial cell within one of the pits in the embryonic gastric mucosa from which the gastric glands develop ." "FMA:86552" + "The anteror lateral line ganglia develops from cranial ectodermal placodes and contain sensory neurons that innervate the anterior lateral line system." "EFO:0003683 ZFA:0001391 TAO:0001391" - "An alpha-beta T cell that is found in the lamina propria of mucosal tissues and is restricted by the MR-1 molecule." + "The developmental process pertaining to the initial formation of the semicircular canal from the otic vesicle. This process begins with the regionalization of the vesicle that specifies the area where the vesicles will form and continues through the process of fusion which forms the initial tubes." + "Predominantly gray matter midbrain structure lying dorsal to the crus cerebri and ventral to the midbrain tegmentum. It is divided into a dorsal, cellularly compact region known as the pars compacta and a more ventrally located, containing more loosely packed cells, the pars reticulata. The most lateral region of the reticulata is identified as the pars lateralis (MM)." "EV:0100247 HBA:9072 UMLS:C0038590 BAMS:SN BTO:0000143 VHOG:0001573 MESH:D013378 MAT:0000504 BIRNLEX:789 EFO:0000922 DHBA:12251 Wikipedia:Substantia_nigra neuronames:536 MA:0000210 FMA:67947 NCIT:C12453 EHDAA2:0004711 SCTID:279286002 CALOHA:TS-0990 GAID:581 EMAPA:35835 UMLS:C1269578" + "OBSOLETE An intratelencephalic-projecting glutamatergic neuron with a soma found in layer 2/3 of the human primary motor cortex." + "A V(D)J recombination-activating protein 2 that is encoded in the genome of human." "UniProtKB:P55895 Reactome:R-HSA-5692675" + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the basement membrane." "An CD38-negative unswitched memory B cell is an unswitched memory B cell that has the phenotype CD38-negative, IgD-positive, CD138-negative, and IgG-negative." - "A mesenchymal stem cell of the chorionic membrane." - "A cell capable of processing and presenting lipid and protein antigens to T cells in order to initiate an immune response." + "A zone of skin that is part of a lower lip." "SCTID:281630002 FMA:24767" "An immature natural killer cell that is NK1.1-positive and DX-5 negative." + "A microvillus layer that is striated and found in the intestine." "FMA:70978 NCIT:C33634" "A non-terminally differentiated cell that originates from the neural crest and differentiates into an erythrophore." - "A type of enteroendocrine cell found in the stomach that secretes glucagon." "FMA:83411" - - "An epithelial cell of the anal canal that is keratinized. This cell type is found towards the lower, rectal end of the anal canal." - "A thymocyte that has the phenotype CD4-negative, CD8-negative, CD44-positive, and CD25-positive." - "Any capillary endothelial cell that is part of a placenta." - - "An lower motor neuron whose soma is located in one of the ventral horns of the spinal cord and innervates skeletal muscles of the trunk or head." "NCIT:C12645" - "Any neuromast hair cell that is part of a posterior lateral line." - - "A progenitor cell restricted to the lymphoid lineage." "CALOHA:TS-2025 FMA:70338 BTO:0004731" - "Any fibroblast that is part of a spleen." - "Any pericyte cell that is part of a brain." - "Kolmer-Agduhr neurons are ciliated GABAergic neurons that contact the central canal of the spinal cord and have ipsilateral ascending axons." - "Notochordal cell that is part of the outer epithelium of the notochord and surrounds the vacuolated notochord cells." - "Chondrocyte that is terminally differentiated, produces type X collagen, is large in size, and often associated with the replacement of cartilage by bone (endochondral ossification)." - "KUPO:0001048" + "Any developmental process that results in the creation of defined areas or spaces within the mesonephros to which cells respond and eventually are instructed to differentiate." + "A C-C chemokine receptor type 1 that is encoded in the genome of human." "Reactome:R-HSA-373107 DTO:02100053 UniProtKB:P32246" + "An axon tract that is part of a spinal cord." "UMLS:C1519456 NCIT:C12995 FMA:75683" + "Any process that stops, prevents, or reduces the frequency, rate, or extent of smooth muscle cell chemotaxis." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptide hormone stimulus. A peptide hormone is any of a class of peptides that are secreted into the blood stream and have endocrine functions in living animals." + "A protein complex composed of two identical immunoglobulin heavy chains of the IgE isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgE immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." + "A lamina propria that is part of a prostatic urethra." "FMA:19693 EMAPA:32303" + "Any process that stops, prevents, or reduces the frequency, rate or extent of ossification, the formation of bone or of a bony substance or the conversion of fibrous tissue or of cartilage into bone or a bony substance." + "EMAPA:32657" + "Any process that activates or increases the frequency, rate, or extent of interleukin-10 production." + "Tolerance induction taking place in the Peyer's patches." + "The process whose specific outcome is the progression of a renal interstitial fibroblast over time, from its formation to the mature structure." + "KUPO:0001004" + "The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent." "Wikipedia:Lipid_catabolism" + "Any process that increases the frequency, rate or extent of insulin receptor signaling." + "A bone that is part of a thorax [Automatically generated definition]." "MA:0000559 SCTID:426649006 EMAPA:37247" + "A retinal ganglion cell that has dendrites stratified in two layers of the inner-plexiform layer." - "A smooth muscle cell that is part of the ciliary body." "FMA:70610" - "The secretory neurons of the paraventricular nucleus that synthesize and secrete vasopressin, corticotropin-releasing factor (CRF) and thyrotropin-releasing hormone (TRH) into blood vessels in the hypothalamo-pituitary portal system." - "A sensory neuron of the dorsal root ganglia that senses body position and sends information about how much the muscle is stretched to the spinal cord." - "A melanocyte that produces pigment in the dermis." - - "Keratinocyte from foreskin." "CALOHA:TS-0385" + "EFO:0003439 TAO:0000568 AAO:0000468 ZFA:0000568" + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electrical stimulus." + "A developmental process, independent of morphogenetic (shape) change, that is required for a hair follicle to attain its fully functional state." + "The glandular, anterior lobe of the pituitary gland. The anterior pituitary regulates several physiological processes including stress, growth, and reproduction[WP]. The anterior lobe of the hypophysis (pituitary gland). This lobe contains cells that produce prolactin, growth hormone, thyroid-stimulating hormone, follicle-stimulating hormone and proopiomelanocortin[ZFA]." "UMLS:C1280369 AAO:0010540 TAO:0001282 BM:AHy CALOHA:TS-0794 VHOG:0000141 MESH:D010903 MA:0000177 SCTID:245532007 EHDAA2:0000109 NCIT:C12772 BIRNLEX:1581 FMA:74627 UMLS:C0032008 EMAPA:17514 BTO:0000040 neuronames:407 BAMS:AHY BAMS:AL EFO:0000230 Wikipedia:Adenohypophysis BAMS:APit ZFA:0001282" + "A spheroid quality inhering in a bearer by virtue of the bearer's being oval with two axes of symmetry, as produced by a conical section." "A smooth muscle cell that is part of the colon." "FMA:15663" - - "An interneuron of the hippocampus." "FMA:84777" + "Any process that modulates the frequency, rate or extent of B cell activation." "KUPO:0001101" - - "FBbt:00004903" - "An epithelial cell of the distal convoluted tubule of the kidney that helps regulate systemic levels of potassium, sodium, calcium, and pH." "FMA:70981 KUPO:0001055 FMA:62125" + "The cellular processes that contribute to exocytosis." + "EMAPA:32631" + "Any process that activates or increases the frequency, rate or extent of cholangiocyte apoptotic process." + "An epithelial cell of the distal convoluted tubule of the kidney that helps regulate systemic levels of potassium, sodium, calcium, and pH." "FMA:70981 KUPO:0001055" "A CD38-negative IgG memory B cell is a IgG-positive class switched memory B cell that has class switched and expresses IgG on the cell surface with the phenotype CD38-negative, IgD-negative, and IgG-positive." + "Small bodies containing chromaffin cells occurring outside of the adrenal medulla, most commonly near the sympathetic ganglia and in organs such as the kidney, liver, heart and gonads." "NCIT:C94826 CALOHA:TS-2358 MESH:D010233 UMLS:C0030419" + "Any process that activates or increases the frequency, rate or extent of T-helper 1 cell activation." + + "A trophoblast giant cell derived from the mural trophectoderm." "EMAPA:16066" - "A post-natal thymocyte expressing components of the gamma-delta T cell receptor. This cell type is always double-negative (i.e. CD4-negative, CD8-negative)." - "A CD25-positive, CD27-positive immature gamma-delta T cell found in the thymus that has an immature phenotype (i.e. CD24-high, CD25-high, CD62L-high, CD44-high, CD2-low, CD5-low)." - "A parathyroid chief cell that is not actively secreting hormone. Contains small Golgi complexes with only a few grouped vesicles and membrane-bound secretory granules; glycogen and many lipofuscin granules abound but sacs of granular endoplasmic reticulum are rare and dispersed. In normal humans, inactive chief cells out number active chief cells in a ratio of 3-5:1." - "An epithelial cell of the esophageal gland proper." "FMA:256141" - + "Collections of neurons in the central nervous system that have been demonstrated by histochemical fluorescence to contain the neurotransmitter norepinephrine (noradrenalin)." + "Binding to a sequence-specific DNA binding RNA polymerase II transcription factor, any of the factors that interact selectively and non-covalently with a specific DNA sequence in order to modulate transcription." + "MESH:D032386" + "Any process that modulates the frequency, rate or extent of mesenchymal cell proliferation that contributes to the progression of the prostate gland over time. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets." "A group 3 innate lymphoid cell that express ROR gamma t and IL-7R alpha in the absence of lineage markers (e.g. CD3, CD19, B220, CD11c, Gr-1), with the functional ability to interact with mesenchymal cells through lymphotoxin and tumor necrosis factor. Lymphoid tissue-inducer cells are key to the development of lymph nodes and Peyer’s patches." - "A NK1.1-positive T cell that is Ly49Cl-negative." - "A female germ cell that has entered meiosis." "WBbt:0006797 FMA:18644 FBbt:00004886 BTO:0000964 CALOHA:TS-0711" - "KUPO:0001123" - "Sympathetic neurons are part of the sympathetic nervous system and are primarily adrenergic producing the neurotransmitter noradrenalin along with other neuropeptides." - "An OFF-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the outer half of the inner plexiform layer. The cell body of these cells is in the middle of the inner plexiform layer. The dendritic tree is stout and the axon terminates in sublamina 1. The axonal terminal is wide and has only a few varicosities." - - "An intestinal tuft cell that is a part of a vermiform appendix." - "A B cell of distinct lineage and surface marker expression. B-1 B cells are thought to be the primary source of natural IgM immunoglobulin, that is, IgM produced in large quantities without prior antigenic stimulation and generally reactive against various microorganisms, as well as the source of T-independent IgA immunoglobulin in the mucosal areas. These cells are CD43-positive." - "A supporting cell for the developing female gamete in the ovary of mammals. They develop from the coelomic epithelial cells of the gonadal ridge. Granulosa cells form a single layer around the mammalian oocyte in the primordial ovarian follicle and advance to form a multilayered cumulus oophorus surrounding the ovum in the Graafian follicle. The major functions of granulosa cells include the production of steroids and LH receptors." "FMA:18718 CALOHA:TS-0729 BTO:0000542" - "A myoblast that detemines the properties (size, shape and attachment to the epidermis) of a `somatic muscle myotube` (CL:0008003) . It develops into a somatic muscle myotube via fusion with `fusion component myoblasts` (CL:0000621)." + "A female germ cell that has entered meiosis." "FBbt:00004886 WBbt:0006797 MESH:D009865 FMA:18644 BTO:0000964 CALOHA:TS-0711" + "KUPO:0001005" + "Any process that activates or increases the frequency, rate or extent of corticosteroid hormone secretion." + "OBSOLETE. A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell)." "FMA:72300 BTO:0001268 WBbt:0008378" + "Any process that modulates the frequency, rate or extent of protein localization to membrane." + "A glycophorin-A that is encoded in the genome of human." "UniProtKB:P02724" "A small pre-B-II cell is a pre-B-II cell that is Rag1-positive, Rag2-positive, pre-BCR-negative, and BCR-negative, is not proliferating, and carries a DNA rearrangement of one or more immunoglobulin light chain genes." - + "An elastic tissue that is part of a circulatory system [Automatically generated definition]." "MA:0002857" + "The process in which relatively unspecialized cells acquires specialized structural and functions of a neuroendocrine cell of the prostate gland acinus." - "A cell with long processes running parallel to adjacent axons in the proximal infundibulum of the neurohypophysis. These processes form a three-dimensional network among the axons of the hypothalamic neurosecretory cells and are connected by gap junctions which provide for their metabolic coupling. This cell type constitutes most of the nonexcitable tissue in the neurohypophsis; function may include possibly acting as an intermediate in the modulation of oxytocin and vasopressin release. This cell type is highly variable in size and shape and commonly contain lipid droplets and deposits of lipochrome pigment." "FMA:83503 BTO:0003793" - "Neurons part of the hypothalamic supraoptic and paraventricular nuclei that secrete the hormones, oxytocin and vasopressin into the systemic circulation from the posterior pituitary gland." - "A B220-positive CD38-negative unswitched memory B cell is a CD38-negative unswitched memory B cell that has the phenotype B220-positive, CD38-negative, IgD-positive, CD138-negative, and IgG-negative." - - "A skeletal muscle satellite cell that undergoes symmetric division to produce two adult skeleltal muscle myoblasts." - "An epithelial cell of the parathyroid gland that is arranged in wide, irregular interconnecting columns; responsible for the synthesis and secretion of parathyroid hormone." "BTO:0004712 FMA:69078 CALOHA:TS-2140" - "A cell that transports hormones from neurosecretory cells. This nerve cell is characterized by bipolar shape and endfeet that contact a basal lamina around blood vessels, and/or the pia mater or vitreous body of the eye and additionally contact the ventricular surface or sub-retinal space." + "Any process that mediates the transfer of information from one cell to another and contributes to the progression of the kidney over time, from its formation to the mature organ." + "Any process that modulates the frequency, rate or extent of glycoprotein metabolic process." "A F4/80-negative dendritic cell located in adipose tissue." "Secretory cell that produces a chemical mixture that triggers antipredator behavior. The substance is released only upon disruption of the epidermis. [Behavior of teleost fishes, second edition, edited by Pitcher, 1992]" + "Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein." "Any motor neuron that is part of a brainstem." - "A late neutrophilic metamyelocyte in which the nucleus is indented to more than half the distance to the farthest nuclear margin but in no area being condensed to a single filament. The nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature neutrophil. These cells are fMLP receptor-positive, CD11b-positive, CD35-negative, and CD49d-negative." - "Mature CD8_alpha-positive CD11b-negative dendritic cell is a CD8_alpha-positive CD11b-negative dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive." - "A CD11c-low plasmacytoid dendritic cell that is CD8alpha-negative and CD4-positive." - "Scattered in duodenojejunal mucosa, this enteroendocrine cell secretes secretin and serotonin." "FMA:62936" - "A CD8-positive, alpha-beta T cell with memory phenotype indicated by being CD45RO and CD127-positive. This cell type is also described as being CD25-negative, CD44-high, and CD122-high." - - "A mechanoreceptor cell located in the inner ear that is sensitive to auditory stimuli. The accessory sensory structures are arranged so that appropriate stimuli cause movement of the hair-like projections (stereocilia and kinocilia) which relay the information centrally in the nervous system." "FMA:62364" - "A DN2 thymocyte that is Kit-hi." - "Any cell in the midgut (middle subdivision of a digestive tract) of a larva." "http://en.wikipedia.org/wiki/Insect#Midgut GOC:pr" - "A stem cell that can differentiate into a cardiac myocyte." "FMA:75620" - "An epithelial cell of prostatic duct." "FMA:74224" - "A type of interneuron in the retinal inner nuclear layer which\ncarries information from the inner plexiform layer and the outer\nplexiform layer using GABA." - "A ciliated epithelial cell of the esophagus." - "An epithelial cell of the prostatic acinus." "FMA:74223" + "The process whose specific outcome is the progression of the outer medullary collecting duct over time, from its formation to the mature structure. The outer medullary collecting duct is the portion of the collecting duct that lies in the renal outer medulla." + "A tooth that is on the vomer." "TAO:0001631" + "The process in which the anatomical structure of the accessory nerve is generated and organized. The spinal branch of this motor nerve innervates the trapezius and the sternocleidomastoid muscles. The cranial branch joins the vagus nerve and innervates the same targets as the vagus nerve." + "The process that gives rise to the pons. This process pertains to the initial formation of a structure from unspecified parts. The pons lies above the medulla and next to the cerebellum. The pons conveys information about movement from the cerebral hemisphere to the cerebellum." + "The process in which a relatively unspecialized cell acquires specialized structural and/or functional features that characterize the neurons of the salivary gland." + "The regulated release of dopamine by a cell in which the dopamine acts as a neurotransmitter." + "A depression or hollow in a bone[WP]." "AAO:0010439 VSAO:0005069 FMA:45791 ZFA:0005388 UMLS:C0836913 TAO:0001743 Wikipedia:Fossa#Anatomy" + "Any process that stops, prevents, or reduces the frequency, rate or extent of eosinophil differentiation." + "The process whose specific outcome is the progression of the midgut over time, from its formation to the mature structure. The midgut is the middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine." - - "Any vein endothelial cell that is part of a hindlimb stylopod." + "A subdivision of the head that has as parts the layers deep to the surface of the anterior surface, including the mouth, eyes, and nose (when present). In vertebrates, this includes the facial skeleton and structures superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, etc)." "MESH:D005145 UMLS:C0015450 EMAPA:32763 SCTID:302549007 NCIT:C13071 MA:0002473 HAO:0000316 CALOHA:TS-2216 Wikipedia:Face GAID:64 galen:Face BTO:0003369 FMA:24728" + "A T cell receptor complex in which the TCR heterodimer comprises alpha and beta chains, associated with the CD3 complex; recognizes a complex consisting of an antigen-derived peptide bound to a class I or class II MHC protein." + - "An endothelial cell that is part of the venule." "FMA:67762" - "An interneuron that selectively innervates the axon initial segment of pyramidal cells. Their local axonal clusters are formed by high-frequency branching at shallow angles, often ramifying around, above or below their somata with a high bouton density. The characteristic terminal portions of the axon form short vertical rows of boutons, resembling a chandelier. Chandelier cells can be multipolar or bitufted." "ILX:0777213" - "A bipolar neuron found in the retina that is synapsed by rod photoreceptor cells. These neurons have axons that arborize and synapse to targets in inner plexiform layers 4 and 5 and depolarize in response to light." - "A cell type that is the first of the maturation stages of the granulocytic leukocytes normally found in the bone marrow. Granules are seen in the cytoplasm. The nuclear material of the myelocyte is denser than that of the myeloblast but lacks a definable membrane. The cell is flat and contains increasing numbers of granules as maturation progresses." "BTO:0000734 FMA:83525" - - "An endothelial cell that lines the oral cavitiy including the mucosa of the gums, the palate, the lip, and the cheek." - "A chief cell that is smaller than light chief cells and has a smaller and darker nucleus and a finely granular cytoplasm with many granules." "FMA:69080" - "KUPO:0001043" - "KUPO:0001120" - "A keratocyte is a specialized fibroblast residing in the cornea stroma that has a flattened, dendritic cell located between the lamellae with a large flattened nucleus and lengthy processes which communicate with neighboring cells. This corneal layer, representing about 85-90% of corneal thickness, is built up from highly regular collagenous lamellae and extracellular matrix components. Keratocytes play the major role in keeping it transparent, healing its wounds, and synthesizing its components. This cell type secretes collagen I, V, VI, and keratin sulfate." - "An epithelial cell that is part of the lacrimal sac." "FMA:70560" - "Glial cell of lateral ventricle." "CALOHA:TS-1258" - "A glial cell that develops from a Schwann cell precursor. The immature Schwann cell is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has a basal lamina. Cells can survive without an axon present. Immature Schwann cell can be found communally ensheathing large groups of axons." "ZFA:0001725" + "GC_ID:1 PMID:30257078 PMID:16248873" + "A portion of skeletal muscle tissue that is part of a respiratory system [Automatically generated definition]." "EMAPA:37583 MA:0001829" + "Any process that activates or increases the frequency, rate or extent of nuclease activity, the hydrolysis of ester linkages within nucleic acids." + "A mucosa that is part of a fundus of stomach [Automatically generated definition]." "EMAPA:27151 FMA:17053" + "Any of the ducts that are part of a male reproductive system." + "Any process that stops, prevents or reduces the frequency, rate or extent of osteoclast development." + "A receptor-type tyrosine-protein kinase FLT3 that is encoded in the genome of mouse." "UniProtKB:Q00342" + "Any process that modulates the frequency, rate or extent of epithelial cell migration." + "Anatomical system that consists of the muscular and skeletal systems." "VSAO:0000031 UMLS:C0026860 EMAPA:32714 EV:0100139 SCTID:278858007 CALOHA:TS-1311 VHOG:0001275 MA:0002418 Wikipedia:Musculoskeletal_system XAO:0000168 GAID:98 NCIT:C12754 MESH:D009141 FMA:7482 AAO:0010546" + "GC_ID:1" + "Any process that modulates the frequency, rate or extent of skeletal muscle fiber development. Muscle fibers are formed by the maturation of myotubes. They can be classed as slow, intermediate/fast or fast." + "Any process that activates or increases the frequency, rate or extent of the release into the cytosolic compartment of calcium ions sequestered in the endoplasmic reticulum or mitochondria." + "HBA:4385 UMLS:C0175218 BIRNLEX:2702 BM:Tel-NLOT EMAPA:35599 MBA:619 neuronames:242 FMA:61865 BAMS:LOT DHBA:10309 BAMS:NLOT DMBA:15951" - "An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels." "FMA:67755 CALOHA:TS-1106 BTO:0001854" - "A Lamp5 GABAergic cortical interneuron that has extended axons in the surface of L1. Canopy Lamp5 cells resemble neurogliaform cells in having elongated horizontal axonal arbors largely confined to L1; but the dendritic arbors are wider and have fewer branches, while the axon is less tortuous and extends further from the soma" - "A M cell that is part of the epithelium of intestinal villus." "FMA:263130" - "An epithelial cell that resides in the inner root sheath of the hair follicle." - "A lineage-negative, Kit-positive, CD45-positive mast cell progenitor that is Fc-epsilon RIalpha-low." - "A CNS interneuron located in the spinal cord." + "Any process that modulates the frequency, rate or extent of extracellular vesicular exosome assembly." + "The chemical reactions and pathways resulting in the formation of glycosaminoglycans, any of a group of polysaccharides that contain amino sugars." + "Any process that modulates the frequency, rate or extent of compound eye photoreceptor cell differentiation." + "A muscle cell that can develop high tension rapidly. It is usually innervated by a single alpha neuron." + "Skeletal subdivision that undergoes direct development and includes elements that either develop in association with the basement membrane of the ectoderm or are homologous with such elements; includes dermatocranium, components of the appendicular skeleton, teeth and tooth-like elements of the oropharynx, and integumentary elements." "XAO:0004025 VSAO:0000035" + "ZFA:0001053 TAO:0001053 EFO:0003612" + "A long, thin cell projection that contains F-actin and tubulin, with microtubules centrally located and F-actin peripherally located." "Wikipedia:Membrane_nanotube" + "The dorsal roots contain afferent sensory axons. The dorsal roots of each side continue outwards, along the way forming a dorsal root ganglion (also called a spinal ganglion)." "Wikipedia:Posterior_root_of_spinal_nerve NLXANAT:20090208 NCIT:C32477 TAO:0000652 SCTID:362436008 UMLS:C0205955 FMA:5980 ZFA:0000652 neuronames:1661 BTO:0000360 BAMS:drt" + "The invaginated serous membrane that surrounds the lungs (the visceral portion) and lines the walls of the pleural cavity (parietal portion)." "CALOHA:TS-2081 MESH:D010994 SCTID:181609007 FMA:9583 Wikipedia:Pleura UMLS:C0032225 VHOG:0000394 GAID:360 EFO:0001980 MA:0000433 NCIT:C12469 EV:0100044 BTO:0001791" + "The process whose specific outcome is the progression of an inner ear receptor cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate." "A type II vestibular sensory cell that is part of the epithelium of crista of ampulla of semicircular duct of membranous labyrinth." "FMA:263200" "A promyelocyte with a nucleus that is indented and contains more marginated heterochromatin compared to its precursor cell (myeloblast); cytoplasm is deeply basophilic and contains numerous mitochondria and meandering cysternae of endoplasmic reticulum; largest of the granulocyte lineages." "FMA:83533" - "A stem cell that can give rise to the cells of the liver." "FMA:86577" - "A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative)." "FMA:83036 BTO:0002042 CALOHA:TS-0194" - "A round chondrocyte that first differentiates in the late embryonic growth plate of bone." - "A recently activated CD4-positive, alpha-beta T cell with the phenotype CD69-positive, CD62L-negative, CD127-negative, and CD25-positive." - "A cell that stains readily in the anterior pituitary gland." "FMA:83089" - "Cell that is part of the notochord." - - "KUPO:0001023" - "A preadipocyte that is part of visceral tissue." + "Any process in which a cell is transported to, and/or maintained in, a specific location." + "Any process that activates or increases the frequency, rate or extent of cellular component biogenesis, a process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component." + "Any process that modulates the frequency, rate or extent of cation transmembrane transport." + "An erythroid transcription factor that is encoded in the genome of human." "Reactome:R-HSA-996772 UniProtKB:P15976" + "Any process that modulates the frequency, rate or extent of the directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." - "A germinal center B cell that has the phenotype CD77-negative, IgD-negative, and CD38-positive. These cells have undergone somatic mutation of the B cell receptor." - "An endothelial cell found in the centrilobular region hepatic sinusoid, near the central vein. The fenestrae of these cells are smaller but more numerous compared with those of endothelial cells near the periportal region of the hepatic sinusoid." - "Any mesenchymal stem cell of adipose that is part of a abdomen." - "A Vgamma1.1-positive, Vdelta6.3-positive thymocyte that is CD24-positive." - "A fully differentiated plasma cell that secretes IgG." - "OBSOLETE: A lymphocyte that lacks T or B cell surface markers." "FMA:83601" - "A pericyte of the central nervous system." - "Any neuron that is part of a peripheral nervous system." - "A highly specialized cell type exclusive to and forming neuroepithelium of the Saccus vasculosus, covering the caudal diverticulum of the infundibular recess." - "A stem cell from which all cells of the lymphoid and myeloid lineages develop, including blood cells and cells of the immune system. Hematopoietic stem cells lack cell markers of effector cells (lin-negative). Lin-negative is defined by lacking one or more of the following cell surface markers: CD2, CD3 epsilon, CD4, CD5 ,CD8 alpha chain, CD11b, CD14, CD19, CD20, CD56, ly6G, ter119." "CALOHA:TS-0448 VHOG:0001485 BTO:0000725 FMA:86475 FMA:70337" - "A hematopoietic stem found in the yolk sac. In mice, this cell type is Sca-1-negative, CD45-negative, MHC-negative, HSA-positive, AA4.1-positive, CD44-positive." - "Any mesenchymal stem cell that is part of a placenta." - "An auditory epithelial support cell located in the vestibular epithelium that has many hallmarks of glial cells. This cell type express glial markers such as vimentin, S100, glutamate-aspartate transporter, low affinity neurotrophin receptor p75, glial fibrillary acidic protein, and proteolipid protein." "FMA:75809" - "A fibroblast that is part of the papillary layer of dermis." "FMA:261277" - "A promyelocyte committed to the basophil lineage." "FMA:84208" + "A type 5 cone bipolar cell with diffuse axonal branches." + "Dense connective tissue is mainly composed of collagen type I. Crowded between the collagen fibers are rows of fibroblasts, fiber-forming cells, that manufacture the fibers. Dense connective tissue forms strong, rope-like structures such as tendons and ligaments. Tendons attach skeletal muscles to bones; ligaments connect bones to bones at joints. Ligaments are more stretchy and contain more elastic fibers than tendons. Dense connective tissue also make up the lower layers of the skin (dermis), where it is arranged in sheets." "UMLS:C1511770 AAO:0000121 Wikipedia:Dense_connective_tissue NCIT:C32450" + "Any process that activates or increases the frequency, rate or extent of the regulated release of a catecholamine." + "A protein that is a translation product of the human RNASE2 gene or a 1:1 ortholog thereof." + "The mesectodermal cell layer arising from the trophectoderm that erodes the uterine mucosa and contributes to the formation of the placenta." "UMLS:C0041178 CALOHA:TS-1070 Wikipedia:Trophoblast GAID:1152 MESH:D014327 SCTID:362839005 FMA:83029 NCIT:C93292 BTO:0001079 EV:0100120" + "Any process that modulates the rate, frequency or extent of macrophage chemotaxis. Macrophage chemotaxis is the movement of a macrophage in response to an external stimulus." + "Movement of cilia mediated by motor proteins that contributes to the movement of a cell." + "A bone that is part of an appendage [Automatically generated definition]." + "A cellularity quality inhering in a bearer by virtue of the bearer's consisting of more than one cell." + "Any process that activates or increases the frequency, rate or extent of T cell differentiation." + + "Any process that activates or increases the frequency, rate or extent of glycine import." "A CD8-positive, alpha-beta T cell that regulates overall immune responses as well as the responses of other T cell subsets through direct cell-cell contact and cytokine release." - - "A paneth cell of the appendix." - "A specialized pore forming cell of the follicle, located adjacent to the animal pole of the oocyte. The micropylar cell makes the single micropyle (pore) through the chorion through which the sperm fertilizes the egg." - "A common myeloid progenitor that is CD34-positive, CD38-positive, IL3ra-low, CD10-negative, CD7-negative, CD45RA-negative, and IL-5Ralpha-negative." - "Connective tissue cells of the endometrium, these cells are fibroblastic in appearance. During decidualization they tranform into decidual (stromal) cells, swellling up and adopt an epithelial cell-like appearance due to the accumulation of glycogen and lipid droplets." "FMA:86490 CALOHA:TS-1266" - "A mature alpha-beta T cell of a distinct lineage that bears natural killer markers and a T cell receptor specific for a limited set of ligands. NK T cells have activation and regulatory roles particularly early in an immune response." - "An endocrine cell that has the specialized function to produce and secrete hormones in response to neuronal signals." "FMA:83810 BTO:0002691" - "A basket cell with axonal arbors composed of frequent, short, curvy axonal branches that tend to be near their somata and within the same layer." + "A zone of skin that is part of a shoulder region." "MA:0000635 EMAPA:18059 FMA:34830 SCTID:244131002" + "The process in which the anatomical structures of the digestive tract are generated and organized. The digestive tract is the anatomical structure through which food passes and is processed." + "Dorsolateral placode that gives rise to the anterior lateral line." "ZFA:0001316 TAO:0001316 EFO:0003461 XAO:0004221" "A mesenchymal stem cell of adipose tissue." - "An epithelial cell that is part of the epithelium of a tracheal tube in an open tracheal system, such as that found in insects." - "Any fibroblast that is part of a embryo." - "An endothelial cell that is part of the small intestine Peyer's patch." "FMA:67757" - "A cell type that secretes histamine." - "A mesothelial cell that is part of the epicardium." - "KUPO:0001104" - "A Vgamma1.1-positive, Vdelta6.3-negative thymocyte that is CD24-positive." - "A stem cell that self-renews as well as give rise to a single mature cell type." "FMA:70569" - "A type I vestibular sensory cell that is part of the stato-acoustic epithelium." "FMA:263186" - "A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers." "FMA:83505" - "A CD8alpha alpha positive gamma-delta intraepithelial T cell that expresses a TCR encoded in part by the Vgamma5 gene segment." - "A memory B cell that lacks expression of surface IgD." - "A transitional myocyte that is part of the internodal tract." "FMA:83387" - "A CD24-low, CD44-positive, DX5-high, NK1.1-negative NK T cell." - "A transitional stage B cell that migrates from the bone marrow into the peripheral circulation, and finally to the spleen. This cell type has the phenotype surface IgM-positive, surface IgD-negative, CD21-negative, CD23-negative, and CD62L-negative, and CD93-positive. This cell type has also been described as IgM-high, CD19-positive, B220-positive, AA4-positive, and CD23-negative." - "A mesothelial cell that is part of the dura mater." "FMA:256516" - "Specialized cardiac myocyte that is subendocardially interspersed with the regular cardiac muscle cell. They are uninucleate cylindrical cells, associated end-to-end in long rows, continue from the node to the atrioventricular bundle; relatively short compared to ordinary myocytes but are nearly twice their diameter." "FMA:14146 BTO:0001032" - "A small cell formed by the second meiotic division of oocytes. In mammals, the second polar body may fail to form unless the ovum has been penetrated by a sperm cell." "FMA:18651 EMAPA:16045 EHDAA2:0001820 EMAPA:16034" - "Obsolete. Use PO:0000245 from Plant Ontology instead. In monosporic and bisporic megasporogenesis: the megaspore(s) that do not participate in megagametogenesis." - "A precursor B cell is CD45R-positive, CD43-positive, CD24-positive, and BP-positive. Intracellularly expression of surrogate light chain, Rag1 and Rag2, TdT, occurs while there is no expression of mu heavy chain." - "A glandular epithelial cell of the large intestine." "FMA:87194" - "An interneuron that has spider-like appearance with a small round soma, a large number (7-10) of short, smooth, or slightly beaded primary dendrites that give rise to only a few secondary branches, and a branched axon that establishes a dense axonal mesh with thin shafts." - "An ionocyte that is part of the lung epithelium. The cells from this type are major sources of the CFTR protein in human and mice." - "A mesenchymal stem cell of liver." - "An epithelial cell of the exocrine pancreas." "FMA:70986" + "Any anatomical conduit which is part of the upper respiratory tract." "FMA:265132" + "FMA:14179" + "A cell cycle process comprising the steps by which a cell progresses through male meiosis II, the second meiotic division in the male germline." + "Any process that activates, maintains or increases the rate of skeletal muscle tissue development." + "A muscle layer that is part of an intestine." "FMA:15697" + "A zone of skin that is part of a knee [Automatically generated definition]." "UMLS:C0222275 SCTID:181552001 NCIT:C64859 FMA:37800 EMAPA:18151 MA:0000668" + "A limb joint that is part of a forelimb [Automatically generated definition]." "EMAPA:19204 MA:0000614" + "The intrinsic tongue muscles are an integral part of the tongue and completely contained within the tongue that are innervated by Cranial Nerve XII." "FMA:46701 SCTID:244788005 VHOG:0000748 EHDAA2:0002064 MA:0002327 EHDAA:9152 EMAPA:18280" + "The appearance of immunoglobulin due to biosynthesis or secretion following a cellular stimulus during an immune response, resulting in an increase in its intracellular or extracellular levels." + "A renal cortex interstitium that is part of a left kidney." + "The series of molecular signals initiated by the binding of the peptide hormone prolactin to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." + + "Ovarian vein, each instance of which is a tributary of some left renal vein that drains the left pampiniform plexus of some broad ligament." "FMA:14347" + "An endothelium that is part of a heart [Automatically generated definition]." "BTO:0004293" + "Traditional gross anatomy divided the liver into four lobes based on surface features. The falciform ligament is visible on the front (anterior side) of the liver. This divides the liver into a left anatomical lobe, and a right anatomical lobe." "EMAPA:18306 FMA:13361 NCIT:C49579 UMLS:C0447541 Wikipedia:Liver#Lobes SCTID:245378000 MA:0000360" + "Binding to glycogen." + "A collection of hairs that grows on the external ear." + "An arachnoid mater that surrounds a brain." "VHOG:0000230 NCIT:C49331 MA:0000814 FMA:83981 UMLS:C1707346 EMAPA:32661" + "Any process that modulates the frequency, rate or extent of collagen fibril organization." + "Any process that activates or increases the frequency, rate, or extent of peripheral T cell tolerance induction." + "Any process that activates or increases the frequency, rate or extent of sporulation." + "A blood cell of the circulatory system of arthropods." "FBbt:00005063" + "A mesothelium that is part of a peritoneal cavity." "EHDAA2:0001447 SCTID:34073007 EMAPA:16139 BTO:0003156 FMA:18147" + "Any process that modulates the frequency, rate or extent of cardiac muscle cell differentiation." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-1 production." + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroid hormones,compounds with a 1, 2, cyclopentanoperhydrophenanthrene nucleus that act as hormones." + "Binding to norepinephrine, (3,4-dihydroxyphenyl-2-aminoethanol), a hormone secreted by the adrenal medulla and a neurotransmitter in the sympathetic peripheral nervous system and in some tracts of the CNS. It is also the biosynthetic precursor of epinephrine." + "A complement receptor type 2 that is encoded in the genome of mouse." "UniProtKB:P19070" + "The process in which neuroblasts acquire specialized structural and/or functional features that characterize the mature cerebellar stellate cell. Differentiation includes the processes involved in commitment of a neuroblast to a cerebellar stellate cell fate. A cerebellar stellate cell is an inhibitory GABAergic interneuron found in the cerebellar cortex." "A CD4-positive, CD25-positive, alpha-beta regulatory T cell with the additional phenotype CCR4-positive." - "A cell that secretes glucagon." "FMA:84045" - "A cell with more than one nucleus." "AEO:0000203 WBbt:0008074" - "A common myeloid progenitor that is Kit-positive and CD34-positive, Il7ra-negative, and is SCA1-low and Fcgr2-low and Fcgr3-low." - "A neuron that is part_of a cerebral cortex." - "A lymphoid progenitor cell that is found in bone marrow, gives rise to B cells, T cells, natural killer cells and dendritic cells, and has the phenotype Lin-negative, Kit-positive, Sca-1-positive, FLT3-positive, CD34-positive, CD150 negative, and GlyA-negative." - "A goblet cell that is part of the epithelium proper of ileum." "FMA:263067" + "A urothelial cell that is part of the regenerative layer(s) of cells directly superficial to basal cells in urothelium. The layer of intermediate cells in the urothelium ranges from one to several layers thick depending on the species with intermediate cells attached to adjacent cell layers and one another via desmosomes." "FMA:84155" + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a L-glutamate(1-) stimulus." + "Any process that activates or increases the frequency, rate, or extent of B cell tolerance induction." + "Any process that modulates the rate, frequency, or extent of the production of a cytokine that contributes to the immune response." + "A skin of body that is part of an abdominal segment of trunk [Automatically generated definition]." "FMA:264898 MA:0000530 EMAPA:37063" + "Any process that stops, prevents or reduces the frequency, rate or extent of CD4-positive, alpha-beta T cell activation." + "A LIM/homeobox protein Lhx3 that is encoded in the genome of human." "UniProtKB:Q9UBR4 Reactome:R-HSA-9010582" "OBSOLETE, use term from Plant Ontology. A cell localized in the vascular cambium or phellogen. Its periclinal division can contribute cells either to the outside or to the inside of the axis; in vascular cambium, classified into fusiform initials (source of axial cells of xylem and phloem) and ray initials (source of the ray cells)." - "An immature alpha-beta T cell that is located in the thymus and is CD4-positive and CD8-negative." + "Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in a cardiac muscle cell. This typically occurs via modulation of the activity or expression of voltage-gated ion channels." + "Any microtubule in the nucleus of a cell." + "A protein with core architecture consisting of a Lysosome-associated membrane glycoprotein (Pfam:PF01299) domain. It is a single-pass type I membrane protein that shuttles between lysosomes, endosomes, and the plasma membrane." "PIRSF:PIRSF002462" "A neuron that release noradrenaline (noriphinephrine) as a neurotransmitter." - "A T cell that expresses a T cell receptor complex and has completed T cell selection." - "Common dendritic precursor is a hematopoietic progenitor cell that is CD117-low, CD135-positive, CD115-positive and lacks plasma membrane parts for hematopoietic lineage markers." - "A dermal dendritic cell that is CD1a-negative and CD14-positive." - "A muscle cell in which the fibers are organised into sarcomeres but in which adjacent myofibrils are offset from each other, producing an oblique banding pattern." - "A mesothelial cell that is part of the parietal pleura." "FMA:86738" - "A skeletal muscle satellite cell that divides by stem cell division. A proportion of this population undergoes symmetric stem cell division, producing two skeletal muscle satellite stem cells. The rest undergo asymmetric stem cell division - retaining their identity while budding off a daughter cell that differentiates into an adult skeletal muscle myoblast." - "A skeletal muscle cell that is part of the tongue." - "A type I NK T cell that has the phenotype CD4-negative and CD8-negative." - "CD4-positive alpha-beta T cell with the phenotype FoxP3-positive, CD25-positive, CD62L-positive, and CTLA-4 positive with regulatory function." - "A fully differentiated plasma cell that lives for years, as opposed to months, secretes immunoglobulin, and has the phenotype weakly CD19-positive, CD20-negative, CD38-negative, strongly CD138-positive, MHC Class II-negative, surface immunoglobulin-negative, IgD-negative, and strongly CXCR4-positive. The majority of these cells of this type reside in the bone marrow." - "An adipose macrophage that does not express MHC-II but is F4/80-positive." - "A Paneth cell that is part of the epithelium of crypt of lieberkuhn of small intestine." "FMA:263108" - "The milk-producing cell of the alveolar unit that emerges during pregnancy." "FMA:79866 FMA:74506" - "A cell of the luminal layer of the epithelium in the prostatic acinus." "FMA:74266" - "Epithelial cells derived from general body ectoderm and ectoderm placodes." "FMA:70556" - "A type of glomus or chief cell, is sensitive to hypoxia and produce catecholamines." + "Single layer of a laminar structure, identified by different density, arrangement or size of cells and processes arranged in flattened layers or lamina[CUMBO]." "NLX:149357" + "A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages." + "A furrow or an incomplete tube." "EHDAA2_RETIRED:0003161 AEO:0000161" + + "The epithelial cell layer containing the sensory hair cells and their associated sensory nerve terminals." "EMAPA:32883 MA:0001189" + "A bone that is part of a facial skeleton [Automatically generated definition]." "SCTID:181799005 MA:0001482 EMAPA:19019 EMAPA:35924 UMLS:C0015455 NCIT:C63706 MA:0003159" + "An adventitia that is part of a ureter." "SCTID:47879001 FMA:15892 MA:0002652 EMAPA:28114 SCTID:392273001" + "A bistratified retinal ganglion cell D cell that has medium dendritic arbor and a large dendritic field that terminates in S2 and S4." + "Any process that increases the frequency, rate, or extent of B cell tolerance induction." + "Any process that modulates the frequency, rate or extent of microtubule depolymerization." + "An anatomical junction between two parts of the digestive tract." + "A layer of smooth muscle cells that forms the outer layer of the high endothelial venule of lymph node and pumps to allow flow of lymph fluid carrying lymphocytes." "Any cell in a salivary gland." "http://en.wikipedia.org/wiki/Salivary_gland GOC:pr" - "A goblet cell that is located in the anorectum." - - "A type I NK T cell that has been recently activated, secretes interferon-gamma and interleukin-4, and has phenotype CD4-negative, CD8-negative, CD69-positive, and downregulated NK markers." - "An epithelial cell that is part of the bile duct. Cholangiocytes contribute to bile secretion via net release of bicarbonate and water. They are cuboidal epithelium in the small interlobular bile ducts, but become columnar and mucus secreting in larger bile ducts approaching the porta hepatis and the extrahepatic ducts." "FMA:86481" + "The integrated unit (of the eye) that consists of the conjunctiva, the corneal surface, and the ocular mucosal adnexa including the lid margins and the meibomian gland openings, the lacrimal glands and the lacrimal drainage system, all which are critical to maintain ocular surface integrity and provide protection from external antigens and pathogenic microorganisms." "EMAPA:35336 MA:0002486" + "Each of the canals that links the peritoneal cavity and the caudal part of a pleural cavity." "EHDAA:4128 EMAPA:17707 VHOG:0001505 EHDAA2:0001481 SCTID:361413002" + "Any process that modulates the frequency, rate, or extent of B cell mediated immunity." + "FMA:45733" "An intermediate monocyte that is Gr1-positive, CD43-positive." - "A smooth muscle cell of the bladder." "KUPO:0001122" - "An elongated, contractile cell found wrapped about precapillary arterioles outside the basement membrane. Pericytes are present in capillaries where proper adventitia and muscle layer are missing (thus distingushing this cell type from adventitial cells). They are relatively undifferentiated and may become fibroblasts, macrophages, or smooth muscle cells." "FMA:63174 BTO:0002441" - "A M cell that is part of the epithelium proper of ileum." "FMA:263138" - "A CD4-positive, CD25-positive alpha-beta regulatory T cell that has encountered antigen." - "Neuron with an axon and two or more dendrites." "FMA:67287" - "The cell type from which oligodendrocytes develop. This cell originates from multiple structures within the developing brain including the medial ganglion eminence and the lateral ganglionic eminence. These cells migrate throughout the central nervous system and persist into adulthood where they play an important role in remyelination of injured neurons." - "A photoreceptor cell that detects visible light." - "An absorptive cell of the gut epithelium that endocytoses microorganisms and intact macromolecules from the gut lumen and transports them to the subepithelial space where they are presented to antigen-presenting cells and lymphocytes." "BTO:0003600 FMA:62929" + "A protein that contains one copy of the T-box domain (Pfam:PF00907) and it is involved in the anterior neural specification." + "A C-C chemokine receptor type 4 that is encoded in the genome of mouse." "UniProtKB:P51680" + "The chemical reactions and pathways resulting in the breakdown of serotonin (5-hydroxytryptamine), a monoamine neurotransmitter occurring in the peripheral and central nervous systems, also having hormonal properties." + "The process in which the anatomical structures of the dorsal aorta are generated and organized. The dorsal aorta is a blood vessel in a single-pass circulatory system that carries oxygenated blood from the gills to the rest of the body. In a single-pass circulatory system blood passes once through the heart to supply the body once." + "The process whose specific outcome is the progression of the pancreas over time, from its formation to the mature structure. The pancreas is an endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating hormones." "Wikipedia:Pancreas" + "Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO]." "NCIT:C12666 GAID:446 CALOHA:TS-0016 AAO:0010551 XAO:0000164 MESH:D000311 UMLS:C0001625 MAT:0000071 Wikipedia:Adrenal_gland EV:0100135 BTO:0000047 FMA:9604 galen:AdrenalGland SCTID:181127006 EFO:0000238 MIAA:0000071 EMAPA:18426 MA:0000116" + "The opening of the cloacal chamber to the outside of the organism. Birds maintain a single cloacal opening throughout their lives." + "An anatomical junction between two parts of the intestine." "A cell of the transparent layer of simple cuboidal epithelium over the anterior surface of the lens; transform into lens fiber(s)." "FMA:63181" - "An abnormal cell exhibiting dysregulation of cell proliferation or programmed cell death and capable of forming a neoplasm, an aggregate of cells in the form of a tumor mass or an excess number of abnormal cells (liquid tumor) within an organism." "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12922" - "A mature CD4-positive, CD8-negative alpha-beta T cell found in the thymus that is CD24-low and has high expression of the T cell receptor." - "The inhibitory projection neurons located in the striatum that integrate glutamatergic signals arising from the cerebral cortex and thalamus." "BTO:0004778" + "The process whose specific outcome is the progression of the visual system over time, from its formation to the mature structure, including the eye, parts of the central nervous system (CNS) involved in processing of visual inputs, and connecting nerve pathways." + "Any process that stops or reduces the rate of nuclease activity, the hydrolysis of ester linkages within nucleic acids." "A fibroblast that is part of the conjuctiva of the eye." - "A central nervous system macrophage found in the meninges (the three membranes that surround the brain). This macrophage types is highly phagocytic and expresses scavenger receptors." - "A lymphoid progenitor cell that is committed to the natural killer cell lineage, expressing CD122 (IL-15) receptor, but lacking many of the phenotypic characteristics of later stages of natural killer cell development such as expression of NK activating and inhibitory molecules. In human this cell has the phenotype CD34-positive, CD45RA-positive, CD10-positive, CD117-negative, and CD161 negative." - "A ciliated epithelial cell of the retina, this cell type uptakes sodium chloride and passes it to non-pigmented ciliary epithelial cells." "FMA:70606" - "A leukocyte that lacks granules." "FMA:62855" - "Glandular cell of duodenal epithelium. Example: Enterocytes, Goblet cells, enteroendocrine cells; Paneth cells; M cells; Brunner's gland cell." "CALOHA:TS-1275" - "A non-nucleated disk-shaped cell formed by extrusion from megakaryocytes, found in the blood of all mammals, and mainly involved in blood coagulation." "CALOHA:TS-0803 FMA:62851 BTO:0000132" - "A circulating endothelial cell of the phenotype CD146-positive, CD105-positive, CD45-negative. This cell type is indicative of recent vascular damage." - "FBbt:00004193" - "A cell containing at least one nucleus." "FMA:67513" - "A neuroglial cell of ectodermal origin, i.e., the astrocytes and oligodendrocytes considered together." "CALOHA:TS-2027 BTO:0000771 FMA:54538" + "A change in the morphology or behavior of a hepatic stellate cell resulting from exposure to a cytokine, chemokine, hormone, cellular ligand or soluble factor." + "Binding to a CCR chemokine receptor." + "A bone that is part of a the manual digitopodium skeleton - i.e. the fingers or the metacarpal skeleton." "SCTID:265809008" + "A layer of membrane around a tendon. It has 2 layers: synovial sheath + fibrous tendon sheath." "NCIT:C96299 Wikipedia:Tendon_sheath FMA:45087 UMLS:C0224856 BTO:0000051 SCTID:361885006 FMA:76715" + "A capillary that is part of a small intestine." + "A membranous sac in animals that serves as the receptacle of a liquid or contains gas." "BTO:0000123" + "Embryonic structure that develops into pancreatic bud." "FMA:79792 ZFA:0000254 EFO:0003434 EHDAA2:0001382 EHDAA:2163 EFO:0002579 TAO:0000254 EMAPA:17066 XAO:0001101" + "Cranial neural crest that migrates into the hyoid arch." "XAO:0000025 TAO:0007065 ZFA:0007065" + "Any process that stops, prevents, or reduces the frequency, rate or extent of striated muscle contraction." + "A tube in the kidney that collect and transport urine." "TAO:0005289 ZFA:0005289" + "A blood that is part of a capillary." "NCIT:C32212 FMA:263901" + + "Regional part of fornix consisting of a thin layer of white matter on the surface of the hippocampal formation, bordering the wall of the lateral ventricle and composed of white, myelinated fibers. The alveus arises from cell bodies in the subiculum and hippocampus, and eventually merges with the fimbria of the hippocampus. The fimbria goes on to become the fornix (MM: 2006-10-26)." "neuronames:186 BAMS:Alv FMA:83867 BAMS:alv DHBA:10570 BIRNLEX:1510 HBA:9234 UMLS:C0228247 NCIT:C32058 SCTID:369094002 MBA:466" + "Structure derived from foregut that becomes a lung[GO]." "BTO:0001643 NCIT:C34282 EHDAA2:0004089 UMLS:C1514420 SCTID:361427007 NCIT:C34260 UMLS:C1514897 Wikipedia:Respiratory_bud" + "A cardiac atrium that is in the left side of the heart. It receives oxygenated blood from the pulmonary veins, In mammals this is pumped into the left ventricle, via the Mitral valve." "VHOG:0000369 MA:0000074 XAO:0003191 Wikipedia:Left_atrium EMAPA:17315 EHDAA2:0000275 UMLS:C0225860 AAO:0010247 FMA:7097 BTO:0001702 galen:LeftAtrium NCIT:C12869 SCTID:244387002" + "Any process that stops, prevents, or reduces the frequency, rate or extent of developmental growth." "An intestinal stem cell that is located in the large intestine crypt of Liberkuhn. These stem cells reside at the bottom of crypts in the large intestine and are highly proliferative. They either differentiate into transit amplifying cells or self-renew to form new stem cells." - "A tissue-resident macrophage found in the central nervous system." - "OBSOLETE: A PP cell located in the pancreatic acinus. Obsoleted due to a lack of published evidence that this cell type is actually found in the pancreatic acinus." "FMA:85400" - "A cell of a secondary follicile within the ovary." "FMA:70591" - "A cell that stores and secretes pancreatic polypeptide hormone." "FMA:83409 FMA:62938" - "A plasmacytoid dendritic cell with the phenotype HLA-DRA-positive, CD123-positive, and CD11c-negative." - "A trophoblast cell that has a large volume of cytoplasm, is polyploid and is usually mononuclear but is also occasionally multi-nucleate. This cell type is important in establishing maternal physiology and remodeling of the vasculature of the placenta." - "The various hormone- or neurotransmitter-secreting cells present throughout the mucosa of the intestinal tract." - "A hair follicle matrix region cell which synthesizes keratin and undergoes a characteristic change as it moves upward from the hair bulb to become the hair medulla cortex and hair root sheath." - "KUPO:0001084" + "The connective tissue bundles in the extracellular matrix of tendon tissue that are composed of collagen, and play a role in tissue strength and elasticity." + "An anatomical boundary that adjacent_to a forebrain and adjacent_to a midbrain." "ZFA:0001367 EMAPA:36449 TAO:0001367" + "A mesentery that is part of a rectum [Automatically generated definition]." "EMAPA:18664" + "Any process that stops, prevents or reduces the frequency, rate or extent of prolactin secretion." + "A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]." "UMLS:C0027789 Wikipedia:Neural_crest MAT:0000066 FMA:86666 AAO:0010578 GAID:1310 MESH:D009432 MIAA:0000066 BTO:0001764 ZFA:0000045 SCTID:361462002 CALOHA:TS-0676 neuronames:1366 VHOG:0000057 NCIT:C34222 XAO:0000048 EMAPA:32737 EHDAA2:0004419" + "Any process that modulates the frequency, rate or extent of cell proliferation involved in outflow tract morphogenesis." + "Any muscle that is part of the cervical (neck) region." "UMLS:C0027532 GAID:149 MA:0000587 MESH:D009334 NCIT:C33163 FMA:9617" + "Smooth muscle tissue in all or part of a hepatic duct." "MA:0001640 EMAPA:37598" + "A blood vessel endothelial cell that is part of an arterial endothelium." "KUPO:0001095 BTO:0004758 FMA:67761" - "A neuron of the raphe nuclei." - "A neuron that releases serotonin as a neurotransmitter." "WBbt:0006837 FBbt:00005133" - "A cell from the inner layer of the trophoblast of the early mammalian embryo that gives rise to the outer surface and villi of the chorion. Mononuclear crytoblasts fuse to give rise to a multinuclear cytotrophoblast." "FMA:83042" - - "A CD4-positive, alpha-beta T cell that has differentiated into a memory T cell." - "Forms the terminal part of the cuticle-lined excretory duct of C. elegans." - "A follicular B cell that is IgD-positive and CD23-positive and CD38-positive. This naive cell type is activated in the extrafollicular areas via interaction with dendritic cells and antigen specific T cells." - "Large intrinsic neuron located in the granule layer of the cerebellar cortex that extends its dendrites into the molecular layer where they receive contact from parallel fibers. The axon of the Golgi cell enters ramifies densely in the granule layer and enters into a complex arrangement with mossy fiber terminals and granule cell dendrites to form the cerebellar glomerulus. Llinas, Walton and Lang. In The Synaptic Organization of the Brain. 5th ed. 2004." - "FMA:63847" - "Immature CD8_alpha-negative CD11b-positive dendritic cell is a CD8_alpha-negative CD11b-positive dendritic cell that is CD80-low, CD86-low, and MHCII-low." - - - "A cell with extensive dendritic processes found in the B cell areas (primary follicles and germinal centers) of lymphoid tissue. They are unrelated to the dendritic cell associated with T cells. Follicular dendritic cells have Fc receptors and C3b receptors, but unlike other dendritic cells, they do not process or present antigen in a way that allows recognition by T cells. Instead, they hold antigen in the form of immune complexes on their surfaces for long periods and can present antigen to B cells during an immune response." "FMA:83037 BTO:0004267" - + "A neuron that releases serotonin as a neurotransmitter." "FBbt:00005133 WBbt:0006837 MESH:D059326" + "The process whose specific outcome is the progression of an open tracheal system over time, from its formation to the mature structure. An open tracheal system is a respiratory system, a branched network of epithelial tubes that supplies oxygen to target tissues via spiracles. An example of this is found in Drosophila melanogaster." + "A phalanx located between proximal and distal phalanges." "Wikipedia:Intermediate_phalanges EMAPA:35572 MA:0002915 AAO:0010677 SCTID:299710007" + "Ghrelin secreting cells found in the endocrine pancreas." + "A white matter that is part of a medulla oblongata." "BAMS:mw BIRNLEX:1024 FMA:83944 BIRNLEX:1414 neuronames:778" + "The process that gives rise to the locus ceruleus. This process pertains to the initial formation of a structure from unspecified parts. In mice, the locus ceruleus is a dense cluster of neurons within the dorsorostral pons. This nucleus is the major location of neurons that release norepinephrine throughout the brain, and is responsible for physiological responses to stress and panic." + "Any process that modulates the frequency, rate or extent of plasma membrane organization." + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances." "A precursor B cell that is AA4-positive, IgM-negative, CD19-positive, CD43-positive and HSA-positive." - "Obsolete. Use PO:0030007 from Plant Ontology instead. The apical cell is the upper cell formed after the first division of a plant zygote." - "An immature natural killer cell that is NK1.1-positive, DX5-positive, Ly49-positive, CD27-low and CD11b-low. This cell type is found in high numbers in the liver." - - "A neuron residing in the olfactory bulb that serve to process and refine signals arising from olfactory sensory neurons" - "A cell whose function is determined by its response to an electric signal." + "The progression of the urethra over time from its initial formation to the mature structure. The urethra is a renal system organ that carries urine from the bladder to outside the body." + "Any process that activates or increases the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule." + "An amacrine cell with a small dendritic field that has post-synaptic terminals in S1, S2, S3, and S4." + "An adipocyte that is beige in color, thermogenic, and which differentiates in white fat tissue from a Myf5-negative progenitor." "MESH:D000069797" + "The process in which a precursor cell type acquires the specialized features of a lymphoid progenitor cell. Lymphoid progenitor cells include progenitor cells for any of the lymphoid lineages." + "Any process that stops, prevents or reduces the rate or extent of lymphocyte proliferation." + "Any process that modulates a measurable attribute of any biological process, quality or function." "Any endothelial cell of artery that is part of a umbilical cord." - "A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons." "FMA:54536 BTO:0002606 CALOHA:TS-0415" - "A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin." "VHOG:0001535 CALOHA:TS-0583 FMA:62863 BTO:0000775" - "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 2/3." - "Cytoplasm that exhibits a characteristic staining and color, pale-pink, with Wright-Giemsa stain." - "Glial cell of cerebral cortex." "CALOHA:TS-1256" - "A gut-associated lymphoid tissue macrophage found in lamina propria of the gut." - "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane." "CALOHA:TS-2035 XAO:0003012 VHOG:0001533 GO:0005623 FMA:68646 WBbt:0004017 KUPO:0000002" - "An epithelial cell of the esophagus." "FMA:63071" - "FBbt:00001689" - "A late eosinophilic metamyelocyte in which the nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature eosinophil." - "A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body." "FMA:86667" - - "A male germ cell that develops from the haploid secondary spermatocytes. Without further division, spermatids undergo structural changes and give rise to spermatozoa." "BTO:0001274 EMAPA:31486 FMA:72294 FBbt:00004942 WBbt:0006800 CALOHA:TS-0950" - "KUPO:0001115" - - "A supportive cell that has characteristics of glial cell. Processes of this cell envelope the junctions between glomus cells and nerve endings." "FMA:84188" - "A B220-low CD38-positive naive B cell is a CD38-positive naive B cell that has the phenotype B220-low, CD38-positive, surface IgD-positive, surface IgM-positive, and CD27-negative, that has not yet been activated by antigen in the periphery." - "A hematopoietic stem cell that has plasma membrane part Kit-positive, SCA-1-positive, CD150-positive and CD34-negative." - "Any neuromast support cell that is part of a anterior lateral line." + "An epithelium that is part of a ileum." "MA:0003217 FMA:17233 EMAPA:35423 SCTID:47046000" + "The multiplication or reproduction of osteoclasts, resulting in the expansion of an osteoclast cell population. An osteoclast is a specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue, which typically differentiates from monocytes." + "The aggregation, arrangement and bonding together of a set of components to form a motile cilium." + "Any process that modulates the rate, frequency, or extent of primitive erythrocyte differentiation. Primitive erythrocyte differentiation occurs as part of the process of primitive hemopoiesis." + "Any process that stops, prevents or reduces the frequency, rate or extent of oligodendrocyte apoptotic process." + "Events resulting in the formation of a multilayered cellular sheath surrounding an invader and thus preventing its development. This defense mechanism is often seen in insects in response to nematodes or parasitoids, which are too large to be phagocytosed by individual hemocytes. In some organisms the capsule is blackened due to melanization." + "Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA)." + "An arrangement of closely apposed microtubules running parallel to each other." "NIF_Subcellular:sao1872343973" + "Any process in which a protein is transported to, or maintained at, a specific location on a chromosome." + "The directed movement of an ovarian follicle cell that takes place during oogenesis. During egg chamber formation, follicle cells migrate to envelop the germ-line cysts and move in between cysts. At stage 10B, follicle cells migrate centripetally between the nurse cells and the oocyte, enclosing the anterior of the egg. An example of this is found in Drosophila melanogaster." + "Aqueous substance secreted by the lacrimal gland." "galen:Tears NCIT:C33739 MA:0002508 galen:Tear MESH:D013666 Wikipedia:Tear FMA:59756 ENVO:02000034 UMLS:C0039409 EMAPA:36537 GAID:1173 CALOHA:TS-1016 BTO:0001499" + "Any process that stops, prevents or reduces the frequency, rate or extent of mesenchymal stem cell migration." + "PMID:15371245 GC_ID:1" + "The morphogenetic process in which a bud forms from the embryonic hindgut tube to form the Malpighian tubule. A bud is a protrusion that forms from the tube by localized changes in cell shape and position." "A stromal cell found in the lamina propria of the anorectum." "A thymocyte that has the phenotype CD4-negative, CD8-negative, CD44-negative, CD25-negative, and pre-TCR-positive." - "Obsolete. Use PO:0000431 from Plant Ontology instead. A diploid (2n) cell that undergoes meiosis and produces four haploid (1n) megaspores; also called megaspore mother cell." - "A type of interneuron in the retinal inner nuclear layer which\ncarries information from the inner plexiform layer and the outer\nplexiform layer." - "FBbt:00001685" - - "Any germinal center B cell that is part of a tonsil." - "A hematopoietic multipotent progenitor cell is multipotent, but not capable of long-term self-renewal. These cells are characterized as lacking lineage cell surface markers and being CD34-positive in both mice and humans." "BTO:0000725 CALOHA:TS-0448" - "A specialized mesenchymal cell that resides in the dermal papilla located at the bottom of hair follicles. This cell plays a pivotal roles in hair formation, growth, and cycling." - "A peptide hormone secreting cell that secretes cholecystokin stimulating hormone." + "The formation of an apical junction, a functional unit located near the cell apex at the points of contact between epithelial cells composed of the tight junction, the zonula adherens junction and the desmosomes, by the aggregation, arrangement and bonding together of its constituents." + "An epithelium that is part of a upper respiratory tract [Automatically generated definition]." "EMAPA:35894 MA:0001912" "A fibroblast that is part of the choroid plexus." - - "The flattened smooth myoepithelial cells of mesodermal origin that lie just outside the basal lamina of the seminiferous tubule." - "Granule cell that is part of the hippocampus." - "KUPO:0001116" - "Sympathetic cholinergic neuron." + "KUPO:0001003" + "The progression of the hypothalamus region of the forebrain, from its initial formation to its mature state." + "The layered structure that makes up the stomach, typiclly consists of a serous coat, a muscular coat, a mucous membrane, and other tissue layers in between." "FMA:14582 galen:WallOfStomach MA:0002692 SCTID:279995000 EMAPA:35826" + "The process in which the nipple is generated and organized." + "A stroma that is part of a sclera." "FMA:58365 SCTID:368851004 UMLS:C1704397 NCIT:C33652" "A neuron of the striatum." - "A cell that is a specialized type of pericyte providing structural support for the capillary loops of kidney. A flat, elongated cell with extensive fine cytoplasmic processes found outside the kidney glomerulus near the macula densa and bound laterally by afferent and efferent arterioles. Being phagocytic, this cell participates in the continuous turnover of the basal lamina by removing its outer portion containing residues of filtration, while the lamina is renewed on its inner surface by the endothelial cells." "FMA:84143 KUPO:0001033" - "A cell type that forms the boundary with the surrounding epithelium." "FMA:67941" - "A lineage marker-negative, CD34-positive, IL5r-alpha-positive, and Sca1-negative eosinophil progenitor cell." - "KUPO:0001042" - "An endothelial cell that is part of the venous sinus of spleen. This endothelial cell has an elongated, spindle-shaped, flattened morphology that is parallel to long axis of sinus. This cell type rests on a basement membrane interrupted by numerous narrow slits." "FMA:72140" - "FBbt:00004861" - "A germinal center B cell that founds a germinal center, and has the phenotype IgD-positive, CD38-positive, and CD23-negative." - "A class of large neuroglial (macroglial) cells in the central nervous system - the largest and most numerous neuroglial cells in the brain and spinal cord. Astrocytes (from 'star' cells) are irregularly shaped with many long processes, including those with 'end feet' which form the glial (limiting) membrane and directly and indirectly contribute to the blood-brain barrier. They regulate the extracellular ionic and chemical environment, and 'reactive astrocytes' (along with microglia) respond to injury." "CALOHA:TS-0060 FMA:54537 BTO:0000099" - "Any cell capable of ingesting particulate matter via phagocytosis." "BTO:0001044 FMA:83806" - "Specialized cardiac myocyte which is in the internodal tract and atrioventricular node. The cell is more slender than ordinary atrial myocytes and has more myofibrils than nodal myocytes." "FMA:67142" - "Gr1-low non-classical monocyte that lacks expression of a MHC-II complex." + "The directed movement of a protein to a specific location on a chromosome." + "A urethra that is part of a male reproductive system." "NCIT:C33050 BTO:0004089 UMLS:C0458452 FMA:19668 EMAPA:18692 SCTID:264085007 MA:0002640 Wikipedia:Male_urethra" + "A striated muscle tissue that is associated with soft internal organs (viscera)." + "Any process that activates or increases the frequency, rate or extent of CD4-positive, alpha-beta T cell proliferation." + "The regulated release of parathyroid hormone into the circulatory system." + "An organism containing a developing embryo, fetus, or unborn offspring within the body." "BTO:0004733" + "Any process that increases the rate, frequency or extent of extracellular matrix disassembly. Extracellular matrix disassembly is a process that results in the breakdown of the extracellular matrix." + "The process in which anatomical structures of the oviduct are generated and organized. An oviduct is a tube through which an ova passes from the ovary to the uterus, or from the ovary to the outside of the organism." + "The regulated release of pancreatic polypeptide (PP) from a cell. Pancreatic polypeptide is a 36 amino acid polypeptide secreted by islets of Langerhans cells in the pancreas." + "The process whose specific outcome is the progression of the metanephric glomerular epithelium over time, from its formation to the mature structure. The metanephric glomerular epithelium is an epithelial tissue that covers the outer surfaces of the glomerulus in the metanephros. The metanephric glomerular epithelium consists of both parietal and visceral epithelium. Metanephric glomerular parietal epithelial cells are specialized epithelial cells that form tight junctions as a barrier to protein transport. A metanephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the metanephros." + "The part of the stomach attached to the esophagus. The cardia begins immediately distal to the z-line of the gastroeosphageal junction, where the squamous epithelium of the esophagus gives way to the columnar epithelium of the gastrointestinal tract[WP]." "MESH:D002299 FMA:14561 SCTID:362138004 GAID:319 NCIT:C12256 EMAPA:35811 BTO:0000198 Wikipedia:Cardia UMLS:C0007144 MA:0001609" "An epithelial cell of stratum corneum of esophageal epithelium that lacks keratin." "FMA:263148" "A double negative post-natal thymocyte that has a T cell receptor consisting of a gamma chain that does not contain a Vgamma2 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-positive." - "An endothelial cell that is part of the venous sinus of red pulp of spleen." "FMA:62817" - "KUPO:0001039" - "A respiratory stem cell found at the junction of the terminal (conductive) bronchiole and the respiratory bronchiole, which gives rise to alveolar cell types and club cells in response to lung injury." - "A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a promyelocyte and a metamyelocyte;in this stage, production of primary granules is complete and eosinophil-specific granules has started. No nucleolus is present. These cells are integrin alpha-M-positive, CD13-positive, CD15-positive, CD16-negative, CD24-positive, and CD33-positive." "FMA:83542 BTO:0003454" - "A mouse GABAergic cell located in the cerebral cortex that expresses meis2." - "A motile sperm cell that contain no F-actin, and their motility is powered by a dynamic filament system." - "Infrequent type of columnar epithelial cell. This cell is characterized by the presence of a tuft of blunt, squat microvilli (approximately 120-140/cell) on the cell surface. The microvilli contain filaments that stretch into the underlying cytoplasm. They have a distinctive pear shape with a wide base and a narrow microvillous apex. Function not known." + "Morphogenesis of a sensory organ. A sensory organ is defined as a tissue or set of tissues that work together to receive and transmit signals from external or internal stimuli. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." + "Binding to a steroid, any of a large group of substances that have in common a ring system based on 1,2-cyclopentanoperhydrophenanthrene." + "Any process that activates or increases the frequency, rate or extent of blood vessel remodeling." + "Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints." "FMA:302077" "A progenitor cell committed to the basophil lineage. This cell lacks hematopoietic lineage markers (lin-negative) and is CD34-positive, T1/ST2-low, CD117-negative, and FceRIa-high. This cell also expresses Gata-1, Gata-2 and C/EBPa." - "A leukocyte with a single non-segmented nucleus in the mature form found in the circulatory pool of blood." - "Any cardiac muscle cell that is part of a cardiac ventricle." - "A transitional myocyte that is part of the interatrial septum." "FMA:263152" - "An epithelial cell derived from endoderm." "FMA:69075" - "A stromal cell of the ovarian cortex." "FMA:256169" - "Epithelial cell found on the external side of the tympanic membrane" "FMA:70558" - - "A dermal dendritic cell isolated from skin draining lymph nodes that is langerin-negative, MHC-II-positive, and CD4-negative and CD8a-negative." - "A basophilic erythroblast that is GlyA-positive." - "A CD4-positive, alpha-beta T cell that has the phenotype CXCR3-negative, CCR6-negative." - "A long lived plasma cell that secretes IgE." - "KUPO:0001040" - "A hematopoietic stem cell that resides in the fetal liver. In mice, this cell type is first observed at E10.5. This cell type is MHC-positive, HSA-positive, AA4.1-positive, CD45-positive, Sca-1 positive, CD150-positive, CD48-negative and CD244-negative." - "Any native cell that is part of a inner cell mass." - "A melanocyte that is part of the skin of body." "FMA:72144 CALOHA:TS-2374" - "OBSOLETE: A goblet cell that is part of the epithelium proper of large intestine." "FMA:263071" - "A CD11b-positive dendritic cell that is CD11b-low, CD45-positive, MHC-II-high and CD103-positive that is located in the liver." - "A Lamp5 GABAergic cortical interneuron with layer-adapting morphology. NGC Lamp5 cells have a small round soma, short dendrites, and a wide dense axonal arbor that tends to establish a dense axonal mesh with high connection probability both to themselves and L2 pyramidal cells. NGC Lamp5 cells have unique synaptic properties that distinguish them from other GABAergic interneurons, including the release of GABA to the extracellular space via volume transmission, and the ability to produce GABA-B responses in connected postsynaptic targets." - "A mature alpha-beta T cell of the columnar epithelium of the gastrointestinal tract. Intraepithelial T cells often have distinct developmental pathways and activation requirements." - - "A motor neuron that innervates both intrafusal and extrafusal muscle fibers. Low abundancy. They control both muscle contraction and responsiveness of the sensory feedback from muscle spindles." + "A progenitor cell of the central nervous system that can differentiate into oligodendrocytes or type-2 astrocytes. This cell originates from multiple structures within the developing brain including the medial ganglion eminence and the lateral ganglionic eminence. These cells migrate throughout the central nervous system and persist into adulthood where they play an important role in remyelination of injured neurons." "MESH:D000073637" + "Binding to dopamine, a catecholamine neurotransmitter formed by aromatic-L-amino-acid decarboxylase from 3,4-dihydroxy-L-phenylalanine." + "Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment." "Wikipedia:Cell_signaling" + "Outer serosa layer of the uterus." "UMLS:C0227824 EMAPA:37792 MA:0001729 NCIT:C33298 FMA:17744 Wikipedia:Perimetrium SCTID:253705006" + "A nucleus of brain that is part of a preoptic area." "EV:0100226 CALOHA:TS-0822" + "An eomesodermin that is encoded in the genome of human." "UniProtKB:O95936" + + "A vein that is part of a vas deferens [Automatically generated definition]." "MA:0002100 EMAPA:37514" + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving carbohydrate." + "The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form." "Wikipedia:Morphogenesis" "A cell of the sclera of the eye." - "One of a transient population of pioneering neurons in the cerebral cortex. These cells are slender bipolar cells of the developing marginal zone. One feature of these cells in mammals is that they express the Reelin gene." + "The cell cycle process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets during the meiotic cell cycle in a female." + "The process whose specific outcome is the progression of the parasympathetic nervous system over time, from its formation to the mature structure. The parasympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system. Parasympathetic nerves emerge cranially as pre ganglionic fibers from oculomotor, facial, glossopharyngeal and vagus and from the sacral region of the spinal cord. Most neurons are cholinergic and responses are mediated by muscarinic receptors. The parasympathetic system innervates, for example: salivary glands, thoracic and abdominal viscera, bladder and genitalia." "A proerythoblast that is CD34-negative and GlyA-negative." - "A CD38-positive unswitched memory B cell is an unswitched memory B cell that has the phenotype CD38-positive, IgD-positive, CD138-negative, and IgG-negative." - "A thymic epithelial cell with moderate nuclear and cytoplasmic electron-density. Scattered in the cortex, this cell type is predominant in the mid and deep cortex." "FMA:72211" - "Any microvascular endothelial cell that is part of a brain." - "A CD4-positive, alpha beta memory T cell with the phenotype CD45RA-positive, CD45RO-negative, and CCR7-negative." - "A chromaffin cell that is part of the left ovary." "FMA:74321" - "An extratelencephalic-projecting glutamatergic neuron located in layer 5b of the primary motor cortex that projects to the medulla. MY ET cells are large, big-tufted cells with the apical dendrite often bifurcating close to the soma, suggesting they are corticospinal cells. MY ET cells have bigger hyperpolarization sag, lower input resistance, and smaller AP width, compared to L5 IT neurons." - "FBbt:00004873" - "A dendritic cell of the myeloid lineage." "BTO:0004721" - "An intratelencephalic-projecting glutamatergic neuron with a soma found in L5 of the primary motor cortex." "ILX:0770157" - "A cardiac myocyte that is an excitable cells in the myocardium, specifically in the conducting system of heart." "FMA:67968" - - "A cell located in the outermost proliferative zone of the external germinal layer that can differentiate into astroglial cells and granule cells. This cell type is glial fibrillary acidic protein-positive and NK1-positive." + "Synovial joint that articulates bones of upper and lower jaw." + "Reactions triggered in response to the presence of another organism that act to protect the cell or organism from damage caused by that organism." + "The process in which a precursor cell type acquires the specialized features of a pro-T cell. Pro-T cells are the earliest stage of the T cell lineage but are not fully committed." + "Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope." + "An action potential that occurs in a Purkinje myocyte." + "Any process that stops, prevents or reduces the rate or extent of cell proliferation." "Any fibroblast that is part of a cardiac atrium." - "A cell of a filament of a fungal mycelium." - "An undifferentiated germ cell that proliferates rapidly and gives rise to oocytes." "FMA:83673" - "OBSOLETE (was not defined before being made obsolete)." + "Lateral neurogenic placodes positioned dorsal of the epibranchial placodes." "VHOG:0000103 ZFA:0001310 XAO:0000187 TAO:0001310" + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light." + "The process that gives rise to the superior olivary nucleus. This process pertains to the initial formation of a structure from unspecified parts. In mice, the superior olivary nucleus is a small cylindrical mass on the dorsal surface of the lateral part of the trapezoid body of the pons, and it is situated immediately above the inferior olivary nucleus. It receives projections from the cochlear nucleus and thus is involved in the perception of sound." "An enteroendocrine cell of the small intestine that secretes motilin." "FMA:63420" - "A basal cell that is part of the epithelium of terminal bronchiole." "FMA:263122" - "A hematopoietic stem cell from the aorta-gonad-mesonephros region of the developing embryo. First seen at E10.5 in mouse embryos. May give rise to fetal liver HSC." - "A mature CD14-positive dermal dendritic cell is CD80-high, CD86-high, MHCII-high and is CD83-positive." "A macrophage which is resident in the lamina propria of the large intestine." - "An acidophilic cell of the anterior pituitary that produces prolactin." "FMA:83096" - "A flat keratinocyte immediately below the cornified layer." "FMA:86925" - "A cell specialized to detect and transduce light." "CALOHA:TS-0868 FBbt:00004211 FMA:86740 BTO:0001060" - "An immature CD16-positive myeloid dendritic cell is CD80-low, CD86-low, and MHCII-low." - - "A pre-B-II cell is a precursor B cell that expresses immunoglobulin mu heavy chain (IgHmu+), and lack expression of CD34, TdT, immunoglobulin kappa light chain and immunoglobulin lambda light chain." "CALOHA:TS-0819 BTO:0001133" - "OBSOLETE: A cell line cell that is expected to be capable of replicating a limited number of times in culture before undergoing senescence. Mortal cell line cells cannot be propagated indefinitely (as immortal cell line cells can)." - "A cell of the intermediate pituitary that produces melanocyte stimulating hormone." "BTO:0002277" - "An olfactory receptor cell in which the apical ending of the dendrite is a pronounced ciliated olfactory knob." - "A smooth muscle cell of the esophagus." - "FBbt:00004929" - "A mature alpha-beta T cell that expresses an alpha-beta T cell receptor and the CD4 coreceptor." - "A P/D1 enteroendocrine cell that is argyrophilic and stores vasoactive intestinal polypeptide." "FMA:63207" - - "This cell resembles a glia cell, express the glial marker S100 and act as a supporting cell to type I cell. This cell is located in a small cluster of type I and type II cells near the fork of the carotid artery." "FMA:84187" + "Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints." "FMA:23879 VSAO:0000042 SCTID:129140006" + "A thymic epithelial cell located at the corticomedullary junction." + "A tube or collection of tubes in an animal from the ovaries to the outside of the body." "UMLS:C0029954 EFO:0000974 MESH:D010057 XAO:0003052 EMAPA:18984 BTO:0000980 ZFA:0000560 TAO:0000560 VHOG:0001136 Wikipedia:Oviduct MAT:0000126 MIAA:0000126 AAO:0010533 BSA:0000083 NCIT:C77957 GAID:366" + "Cell motility due to the motion of one or more eukaryotic cilia. A eukaryotic cilium is a specialized organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole." + "An amacrine cell with a wide dendritic field, dendrites in S1, and post-synaptic terminals in S1." + "Gonochoristic organism that can produce male gametes." "FMA:67811 CARO:0000027 TGMA:0001838 ZFA:0000242 HAO:0000027 BILA:0000027 XAO:0003006 TAO:0000242 AAO:0010033 SCTID:362609003 WBbt:0007850" + "Combining with a pathogen-associated molecular pattern (PAMP), a structure conserved among microbial species to initiate an innate immune response." "Wikipedia:Pattern_recognition_receptor" "An asexual spore formed by Oomycetes; formed upon fertilization of an oosphere." "FAO:0000039" - "A fully differentiated neutrophil, a granular leukocyte having a nucleus with three to five lobes connected by slender threads, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes. They are produced in bone marrow at a rate of 5e10-10e10/day and have a half-life of 6-8 hours. Neutrophils are CD15-positive, CD16-positive, CD32-positive, CD43-positive, CD181-positive, and CD182-positive." "BTO:0003473" - "Cytoplasm that exhibits molecular interaction for basic dyes under specific pH conditions." - "Any mononuclear cell that is part of a umbilical cord." + "Any endocardium that is part of the right ventricle of the heart." "NCIT:C102343 EHDAA2:0002188 SCTID:8911002 VHOG:0001235 FMA:9536 EMAPA:17341" "A chromaffin cell of the adrenal medulla that produces epinephrine." "FMA:69322" - "OBSOLETE (was not defined before being made obsolete)." - "An epithelial cell of the proximal tubule of the kidney." "FMA:70973 KUPO:0001044 FMA:62125" - "A mature natural killer cell that is CD11b-positive and CD27-positive." - "A NK1.1-positive T cell that is Ly49H-negative." - "A T cell expressing an alpha-beta T cell receptor and the CD8 coreceptor." - "A smooth muscle cell that is part of the prostate gland." "FMA:84583" - "A NK1.1-positive T cell that is CD94-negative and Ly49Cl-negative." + "Any process that modulates the frequency, rate or extent of tight junction assembly." "An interrenal chromaffin cell found in teleosts that contain small, homogeneous electron-lucent granules that are separated from the vesicular membrane by a visible halo." - "A type of interneuron that has two neurites, usually an axon and a dendrite, extending from opposite poles of an ovoid cell body." "FMA:67282" - "Any macroglial cell that is part of a brain." + "Any process that decreases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle." "A goblet cell that is part of the epithelium of pancreatic duct." "FMA:263058" - "A cell derived from the mesoderm that is located between the paraxial mesoderm and the lateral plate." - - "An elicited macrophage that is recruited into the tissues in response to injury and infection as part of an inflammatory response, expresses high levels of pro-inflammatory cytokines, ROS and NO, and shows potent microbicidal activity." - "An enterocyte that is part of the epithelium proper of duodenum." "FMA:263098" + "The developmental process pertaining to the initial formation of the labyrinthine layer of the placenta." + "A corticothalamic-projecting neuron with a soma found in cortical layer 6." - "A lymphocyte of B lineage that is CD19-positive." - "Any striated muscle cell that is part of a skeletal muscle tissue of pectoralis major." - "A rapidly cycling mature B cell that has distinct phenotypic characteristics and is involved in T-dependent immune responses and located typically in the germinal centers of lymph nodes. This cell type expresses Ly77 after activation." - - - "A motor neuron that is located in the cervical region of the spinal cord and selectively innervates the sternocleidmastoid or trapezius muscle. Unlike other motor neurons, they extend axons dorsally along lateral margins of the spinal cord." - "A paracrine cell is a secretory cell that secretes an agonist into intercellular spaces in which it diffuses to a target cell other than that which produced it." - "An epithelial cell that is part of the lacrimal duct." "FMA:70559" - - - - "A type II vestibular sensory cell that is part of the epithelium of macula of utricle of membranous labyrinth." "FMA:263196" - "A goblet cell that is part of the epithelium of stomach." "FMA:263035" - "An arthroconidium that has more than one nucleus." "FAO:0000037" - "An otic fibrocyte that underlies the stria vascularis and is part of a mesenchymal gap junction network that regulates ionic homeostasis of the endolymph." - "An epithelial cell that is part of the nephron." "FMA:70965" - "KUPO:0001119" - "A pigment cell derived from the neural crest. Contains pteridine and/or carotenoid pigments in structures called pterinosomes or erythrosomes. This gives an orange to red appearance." - "Neural stem cell is characterized as an undifferentiated cell that originates from the neuroectoderm and has the capacity both to perpetually self-renew without differentiating and to generate multiple types of lineage-restricted progenitors." "CALOHA:TS-2360 BTO:0002881 FMA:86684" - "A sebum secreting cell of the skin that secretes sebum into the hair follicles." "BTO:0004613 FMA:70953" - "Mature interstitial dendritic cell is a interstitial dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive." - - - "Any oligodendrocyte that is part of a spinal cord." - - "A cell that is usually basal in position, cuboidal with round nucleus, short microvilli, secretes pepsinogen." "FMA:62902" - "A taste receptor cell that is characterized by morphologically identifiable synaptic contacts with the gustatory nerve fibers and expression of the synaptic membrane protein-25 (SNAP-25) and NCAM." "FMA:67940" - "A cell involved in the formation of a granulocyte." "FMA:83519" - + "A horizontal cell with a large cell body, thick dendrites, and a large dendritic arbor." + "A CSF-1/PDGF receptor-type tyrosine-protein kinase that is a translation product of the human PDGFRA gene or a 1:1 ortholog thereof." "PIRSF:PIRSF500950 IUPHARobj:1803" + "Any process that activates or increases the frequency, rate or extent of gamma-delta T cell activation involved in immune response." + "Organism substance that is composed of sperm cells suspended in seminal fluid." "Wikipedia:Semen UMLS:C2756969 EMAPA:31488 MESH:D012661 NCIT:C13277 MA:0002522 GAID:1169 CALOHA:TS-0917 UMLS:C1518159 NCIT:C13713 BTO:0001230 FMA:62966" + "A circle of arteries that supply blood to the brain. The Circle of Willis comprises the following arteries: Anterior cerebral artery (left and right); Anterior communicating artery; Internal carotid artery (left and right); Posterior cerebral artery (left and right); Posterior communicating artery (left and right).The basilar artery and middle cerebral arteries, supplying the brain, are also considered part of the circle." "EHDAA2:0000252 FMA:50454 GAID:486 Wikipedia:Circle_of_Willis EHDAA:9758 EMAPA:37829 MESH:D002941 SCTID:362047009 neuronames:1468" + "Any process that increases the frequency, rate, or extent of neutrophil chemotaxis. Neutrophil chemotaxis is the directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding." + "A shape quality inhering in a bearer by virtue of the bearer's being curled or wound (especially in concentric rings or spirals)." + "A taste bud that is located on the skin of the trunk." + "Any process that activates or increases the frequency, rate or extent of production of oxytocin." + "An epiphysis that is part of a proximal phalanx of pes." "SCTID:280047006" + "EHDAA:9540 EMAPA:18017 EHDAA2:0000577 FMA:312589" + "A presumptive structure that has the potential to develop into a ganglion." + "Collection of nerve cells in the medial forebrain lying generally in front of the anterior commissure (Maryann Martone)." "MESH:D012686 DHBA:10350 EHDAA2:0004709 neuronames:259 FMA:61845 EMAPA:35763 Wikipedia:Septal_nuclei BIRNLEX:1313 UMLS:C0036687 GAID:637 BAMS:SptN HBA:13002 MA:0002978" + "A lymph node that is part of a hindlimb." "FMA:44310 SCTID:361109000" + "A submucosa that is part of a duodenum [Automatically generated definition]." "EMAPA:27027 EMAPA:27097 MA:0003213 EMAPA:27239 SCTID:76519004 FMA:14943" + "Any process that activates or increases the frequency, rate or extent of chromosome condensation." + "Any intracellular signal transduction in which the signal is passed on within the cell via calcium ions." "Wikipedia:Calcium_signaling" + "A protein that is a translation product of the human IL1RL1 gene or a 1:1 ortholog thereof." "IUPHARobj:1735" - "A Purkinje myocyte that is part of the interventricular septum." "FMA:263182" - "A meso-epithelial cell that lies between the cartilaginous fibers in the synovial membrane of a joint and produces hyaluronic acid." "FMA:66786 BTO:0003652 CALOHA:TS-0995" + "Any process that stops, prevents, or reduces the frequency, rate or extent of lymphocyte death by apoptotic process." + "Any process that modulates the frequency, rate or extent of the directed movement of calcium ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "A nerve that is part of a lower arm [Automatically generated definition]." "EMAPA:37338 MA:0000601" + "The renal system in an anatomical system that maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products." "AAO:0010257 BTO:0001244 NCIT:C12413 VHOG:0000723 MA:0000325 EHDAA:5901 EFO:0000803 UMLS:C1508753 BTO:0003092 GAID:391 MAT:0000027 Wikipedia:Excretory_system FMA:7159 ZFA:0000163 EV:0100095 BILA:0000015 EHDAA2:0001601 EMAPA:17366 MIAA:0000027 TADS:0000162 MESH:D014551 CALOHA:TS-1323 XAO:0000143 WBbt:0005736 TAO:0000163 galen:UrinaryTract SCTID:362204003" "A gut-associated lymphoid tissue macrophage found in tonsils." - - "Mast cell subtype that contains only the serine protease trypase in its granules. These cells are primarily found in mucosal tissue, such as intestinal mucosa and alveoli. They depend upon T-cells for development of phenotype." - "KUPO:0001045" - "A goblet cell that is part of the epithelium of trachea." "FMA:263075" - "A monocyte that responds rapidly to microbial stimuli by secreting cytokines and antimicrobial factors and which is characterized by high expression of CCR2 in both rodents and humans, negative for the lineage markers CD3, CD19, and CD20, and of larger size than non-classical monocytes." - "An early neural cell developing from the early ependymal cell of the neural tube." "FMA:70564" - "A thick walled, sexual, resting spore formed by Zygomycetes; sometimes refers to the spore and the multi-layered cell wall that encloses the spore, the zygosporangium." "FAO:0000040" - "Goblet cells reside throughout the length of the small and large intestine and are responsible for the production and maintenance of the protective mucus blanket by synthesizing and secreting high-molecular-weight glycoproteins known as mucins. Human intestinal goblet cells secrete the MUC2 mucin, as well as a number of typical mucus components: CLCA1, FCGBP, AGR2, ZG16, and TFF3." - "A B cell that is CD19-positive." - "A basket cell that is large, and typically ascends to give rise to many long horizontally and vertically projecting axon collaterals that traverse neighboring columns and can extend through all cortical layers." - "A transitional myocyte that is part of the septal division of left branch of atrioventricular bundle." "FMA:263168" + "The reproductive developmental process whose specific outcome is the progression of the vagina over time, from its formation to the mature structure." + "A quality inhering in a bearer by virtue of the bearer's having a horizontal surface without a slope, tilt, or curvature." + "The differentiation of endothelial cells from progenitor cells during blood vessel development, and the de novo formation of blood vessels and tubes in the central nervous system. The capillary endothelial cells in the brain are specialized to form the blood-brain barrier." + "Any process that increases the frequency, rate or extent of the chemical reactions and pathways resulting in the metabolism of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals." + "A sonic hedgehog protein that is encoded in the genome of mouse." "UniProtKB:Q62226" + "Missing definition for term UBERON:0006183. Please replace it using linked reference." + "A quality inhering in a bearer by virtue of the bearer's surface becoming more extended in a plane." + "The chemical reactions and pathways involving a hexose, any monosaccharide with a chain of six carbon atoms in the molecule." + "A paired box protein PAX-5 that is encoded in the genome of mouse." "UniProtKB:Q02650" + "A loop of Henle that is part of a inner medulla of kidney [Automatically generated definition]." "MA:0002623 EMAPA:28352" + "Nonparenchymatous organ that primarily consists of dense connective tissue organized into a sheet which interconnects two or more organs, separates two or more body spaces from one another, or surrounds an organ or body part. Examples: interosseous membrane of forearm, obturator membrane, tympanic membrane, fibrous pericardium, fascia lata, dura mater. [FMA]." "FMA:7145" + "A distinct elevation of a transient proliferating cell mass of the fetal subventricular zone; this mass contributes most of its cells to the neocortex; however, hippocampal neurons, thalamus, septum and olfactory bulb neurons are also partly derived from the MGE." "PBA:128012834 DHBA:10550 EMAPA:37471" + "A retinal ganglion cell C with medium cell bodies and large dendritic field." "A stromal cell of the pancreas." - "A myeloid dendritic cell with the phenotype HLA-DRA-positive." - "A cell of a platelike structure, especially a thickened plate of ectoderm in the early embryo, from which a sense organ develops." - "A type of intrafusal muscle fiber that has nuclei arranged in a linear row. Unlike nuclear bag fibers, the equatorial region of these fibers (in the centre of the spindle) is not expanded. These fibers are responsible for the detection of changes in muscle length. They are innervated by static gamma motor neurons and are principally associated with type II sensory fibers." "A reticulocyte that is GlyA-positive." - "A mesothelial cell that is part of the pleura." "FMA:86737" - "KUPO:0001117" - "A neuron that uses acetylcholine as a vesicular neurotransmitter." "WBbt:0006840 FMA:84796 BTO:0004902" - "A transit amplifying cell that is part of a crypt of Lieberkuhn of large intestine." - "A natural killer cell that is developmentally immature, has the phenotype CD34-negative, CD56-negative, CD117-positive, CD122-positive,and CD161-positive." - "KUPO:0001046" + "Nerve that carries information from the olfactory epithelium to the olfactory bulb[Butler and Hodos]." "NCIT:C12759 BIRNLEX:1319 UMLS:C1268984 MESH:D009832 HBA:9300 EHDAA2:0001293 EMAPA:17797 AAO:0010088 BTO:0003648 Wikipedia:Olfactory_nerve BAMS:ln TAO:0000249 neuronames:32 UMLS:C0028938 MA:0001096 FMA:46787 EHDAA:6672 MBA:840 GAID:830 SCTID:180937006 VHOG:0000703 BAMS:1n ZFA:0000249 XAO:0000426" + "A forelimb that is on the right side of a pectoral complex." "FMA:7185" "A cell with delicate radiating processes known as desmosomes that form intercellular bridges between other cells of this type. This cell type forms the stratum spinosum (prickle cell layer). A function of this cell is to generate keratin." "FMA:69059" - "A motor neuron that is capable of directly inhibiting muscle contraction." - "A ciliated columnar cell found in the trachea and bronchus. Vary from low to tall columnar; possesses up to 300 cilia at its surface, interspersed with long irregular microvilli with the cilia varying in length from about 6um in the trachea to about 4um in the terminal bronchioles; driving force of the ciliary current in the bronchial tree." "FMA:70542" - "A stromal cell found in the lamina propria of the small intestine." - "A neck cell that secretes mucus within the stomach. Its products are distinct histochemically from those of the surface mucous cells of stomach." "FMA:62954" - "An alpha-beta T cell expressing NK call markers that is CD1d restricted and expresses a diverse TCR repertoire. Type II NKT cells do not become activated by alpha-galactosylceramide when presented by CD1d." + "A transit amplifying cell that is part of a crypt of Lieberkuhn of large intestine." + "A tissue-resident macrophage that is part of the placenta. A Hofbauer cell expresses high levels of growth factors and metalloproteinases that support vasculogenesis, angiogenesis, branching morphogenesis and tissue remodeling. A Hofbauer cell has a fetal origin and is present throughout pregnancy." + "The directed movement of neurotransmitter receptors." + "The expansion of a mast cell population by cell division." + "A portion of connective tissue that is part of a pelvis [Automatically generated definition]." "MA:0000533 EMAPA:37257" + "A lamina propria that is part of a colonic mucosa." "EMAPA:27395 FMA:15657 MA:0003196 SCTID:113284008" + "The transport of organelles or other particles from one location in the cell to another along actin filaments." "Obsolete. Use PO:0000081 from Plant Ontology instead. OBSOLETE, use term from the Plant Ontology. A secondary vascular cell that develops from the fusiform cambial initials and oriented with their longest diameter parallel with the main axis of stem or root. These cells make up the axial system, also known as vertical or longitudinal system." - "A fibroblast that is part of skin of back." - "A cell secreting tears, the fluid secreted by the lacrimal glands. This fluid moistens the conjunctiva and cornea." - "A dendritic cell with the phenotype HLA-DRA-positive." - - "A CD4-positive, alpha-beta T cell that has the phenotype GATA-3-positive, CXCR3-negative, CCR6-negative, and is capable of producing interleukin-4." "FMA:84385 BTO:0001679" - "A progenitor cell of the mast cell lineage. Markers for this cell are FceRIa-low, CD117-positive, CD9-positive, T1/ST2-positive, SCA1-negative, and lineage-negative." - "Glandular cell of gall bladder epithelium." "CALOHA:TS-1278" - "A bulbous cell that is medially placed in one row in the organ of Corti. In contrast to the outer hair cells, the inner hair cells are fewer in number, have fewer sensory hairs, and are less differentiated." "FMA:62365 BTO:0003667" - "A type I NK T cell that has been recently activated, secretes interferon-gamma and IL-4, and has the phenotype CD4-positive, CD69-positive, and downregulated NK markers." - "KUPO:0001028" - "A M cell that is part of the epithelium proper of jejunum." "FMA:263136" - "An endothelial cell found in the periportal region hepatic sinusoid, near the portal triad. The fenestrae of these cells are larger but fewer in number compared with those of endothelial cells near the centrilobular region of the hepatic sinusoid." - "KUPO:0001114" - "A mesenchymal stem cell of the umbilical cord." - "A skeletal muscle myoblast that differentiates into slow muscle fibers." - "A myoepithelial cell that surrounds milk-secreting luminal epithelial cells. This cell type contracts under the stimulation of oxytocin and is attached to the basement membrane by hemidesmosomes and to the adjacent luminal cells by desmosomes. This cell type expresses high level of keratin-14 and is estrogen receptor alpha negative." - "KUPO:0001100" - "KUPO:0001072" - "A cuboidal cell which along with Boettcher's cells form the floor of the external spiral sulcus, external to the organ of Corti." "FMA:79802" - "A fibroblast of the lymphatic system." - "A cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. Progenitors leave bone marrow and mature in connective and mucosal tissue. Mature mast cells are found in all tissues, except the bloodstream. Their phenotype is CD117-high, CD123-negative, CD193-positive, CD200R3-positive, and FceRI-high. Stem-cell factor (KIT-ligand; SCF) is the main controlling signal of their survival and development." "BTO:0000830 FMA:66784 CALOHA:TS-0603" - "A nonkeratinized cell epithleial cell of the inferior part of the anal canal." "FMA:263144" - "A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages. These cells are CD34-positive, and express Gata1, Gata2, C/EBPa, and Pu.1." - "A myoepithelial cell that is part of the lactiferous duct." "FMA:67803" + "Any process that modulates the frequency, rate or extent of lymphocyte activation." + "UMLS:C1179415 FMA:62815 MA:0000761 NCIT:C33605 EMAPA:37751" + "The chemical reactions and pathways resulting in the breakdown of zeaxanthin." + "The aggregation, arrangement and bonding together of the extracellular matrix." + "Any process that modulates the frequency, rate or extent of calcitonin secretion." + "Subserosal tissue of liver. A zone of areolar connective tissue lying beneath the serous coat of the liver and distinguished with difficulty from the fibrous capsule of Glisson." + "Any process that modulates the frequency, rate or extent of eosinophil chemotaxis." + "OBSOLETE: Neurons part of the hypothalamic supraoptic and paraventricular nuclei that secrete the hormones, oxytocin and vasopressin into the systemic circulation from the posterior pituitary gland." + "The cartilaginous form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column." "VHOG:0000584 EMAPA:32669" + "A protein that is a translation product of the human RNASE3 gene or a 1:1 ortholog thereof." + "Any process that activates or increases the frequency, rate or extent of natural killer T cell activation." + "Any process that modulates the frequency, rate, or extent of plasmacytoid dendritic cell cytokine production." + "An EM radiation quality that is independent of the EM wavelength range." + "A capsule that is part of a tonsil [Automatically generated definition]." "FMA:294647 MA:0000776" + "Any process that stops, prevents, or reduces the frequency, rate, or extent of proteolysis associated with antigen processing and presentation." + "The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part." "Wikipedia:Hemostasis" + "An endothelial cell that is part of some peritubular capillary." "KUPO:0001065" + "Any process that modulates the frequency, rate, or extent of the production of molecular mediator of immune response." "A B220-positive CD38-positive unswitched memory B cell is a CD38-positive unswitched memory B cell that has the phenotype B220-positive, CD38-positive, IgD-positive, CD138-negative, and IgG-negative." - "A neurosecretory neuron residing mainly in the hypothalamic supraoptic and paraventricular nuclei and in a number of smaller accessory cell groups between these two nuclei, that secretes the hormones oxytocin and vasopressin." - "A smooth muscle cell of the umbilical vein." - "A smooth muscle cell that is part of any blood vessel." - "A cell found predominately in the blood." "FMA:62844" - "Skeletogenic cell that is typically non-terminally differentiated, secretes an avascular, GAG rich matrix; is not buried in cartilage tissue matrix, retains the ability to divide, located adjacent to cartilage tissue (including within the perichondrium), and develops from prechondroblast (and thus prechondrogenic) cell." "BTO:0003607 FMA:66783" - - - "A cell type found in the basal epithelial layer on the external side of the tympanic membrane. Cell type is flattened with intracellular spaces of variable dimensions." - "Fat cells with light coloration and few mitochondria. They contain a scant ring of cytoplasm surrounding a single large lipid droplet or vacuole." "CALOHA:TS-1119 FMA:83434" - - "An orthochromatophilic erythroblast that is ter119-high, CD71-low, and Kit-negative." - "KUPO:0001073" - "A Lamp 5 GABAergic cortical interneuron with neurogliaform morphology with a soma found in L5,6. L5,6 NGC Lamp5 have deep afterhyperpolarization (AHP) but narrow action potentials (APs). Unlike other deep neurogliaform cells (which are caudal ganglionic eminence (CGE) derived), L5,6 NGC Lamp5 cells are medial ganglionic eminence (MGE)-derived" - "KUPO:0001053" - "A cell pyramidal in shape, with their broad ends facing and forming the greater extent of the lining of the main lumen. Secretes glycoproteins associated with mucus." "FMA:70659" - "A cell, usually of bacteria or yeast, which has partially lost its cell wall." - "A NK1.1-positive T cell that is NKGA2-positive." - "A fibroblast that is part of the tunica adventitia of artery." "FMA:261285" - "CD7-positive lymphoid progenitor cell is a lymphoid progenitor cell that is CD34-positive, CD7-positive and is CD45RA-negative." - "A mature sexual reproductive cell having a single set of unpaired chromosomes." "CALOHA:TS-0395 FBbt:00005412 FMA:18649" - "A progenitor cell committed to the erythroid lineage. This cell is ter119-positive but lacks expression of other hematopoietic lineage markers (lin-negative)." "BTO:0004911" - "A spore formed following meiosis. Sometimes following meiosis, prospores may undergo one or more rounds of mitosis before they are fully mature." "FAO:0000017" - "Any goblet cell that is part of a conjunctiva." - - "Immature CD8_alpha-negative CD11b-negative dendritic cell is a CD8_alpha-negative CD11b-negative dendritic cell that is CD80-low, CD86-low, and MHCII-low." - "An epidermal cell that is part of the germinal matrix." - "An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. This cell has the widest dendritic field and the widest axon terminal of all retinal bipolar cells. The axon terminal is delicate and stratified through sublaminae 4 and 5 of the inner plexiform layer." - "A neurecto-epithelial cell found in the arachnoid villi of dura mater. This cell type facilitates flow of cerebrospinal fluid into the blood." "FMA:86588" - "A basket cell which has simpler dendritic arbors (compared to small or large basket cells), and an axonal plexus of intermediate density, composed of a few long, smooth axonal branches." - "A large nucleated basophilic erythrocyte found in mammalian embryos. This cell type arises from the blood islands of yolk sacs and expresses different types of hemoglobins (beta-H1, gamma-1 and zeta) than adult erythrocytes. Considered a type of erythroblast as this cell type can enucleate in circulation." - "A non-terminally differentiated cell that is capable of developing into a muscle cell." - "KUPO:0001025" - "Any of the immature forms of a basophil, in which basophilic specific granules are present but other phenotypic features of the mature form may be lacking." - "A fibroblasts found in interstitial spaces in the pulmonary tract. Greater numbers of these cells are found in idiopathic pulmonary fibrosis." "FMA:84467" - "The motor neurons of vertebrates that directly innervate skeletal muscles. They receive input from upper motor neurons." "FMA:84632" - "Basket cells are inhibitory GABAergic interneurons of the brain. In general, dendrites of basket cells are free branching and contain smooth spines. Axons are highly branched. The branched axonal arborizations give rise to basket-like structures that surround the soma of the target cell. Basket cells form axo-somatic synapses, meaning their synapses target somas of other cells." - "An endocrine cell that secretes vasoactive intestinal peptide." - "A pyramidal neuron which has a distinctive tuft formation, distal from the soma." - "KUPO:0001098" - "A cell of the outer of the three germ layers of the embryo." "FMA:72549" - "A T cell that is located in a vermiform appendix." - "Any of the immature forms of an eosinophil, in which eosinophilic specific granules are present but other phenotypic features of the mature form may be lacking." - "A somatic stem cell that is part of the epidermis." "FMA:70541" - "A macrophage which is resident in the lamina propria of the small intestine." - "A mature osteoblast that has become embedded in the bone matrix. They occupy a small cavity, called lacuna, in the matrix and are connected to adjacent osteocytes via protoplasmic projections called canaliculi." "CALOHA:TS-1167 BTO:0002038 FMA:66779 VSAO:0000124" - "KUPO:0001113" - "A pericyte of the decidual vasculature." - "Skeletogenic cell that secretes dentine matrix, is derived from odontogenic papilla. Embedded in dentine tissue, and is the transformation of a non-terminally differentiated odontoblast cell." - "KUPO:0001026" - "A granulocyte monocyte progenitor that is Kit-positive, CD34-positive, Fc-gamma receptor II/II-positive, and is Sca-1-negative, Il7ra-negative, Cxc3r1-negative, and CD90-negative." - "A type II vestibular sensory cell that is part of the stato-acoustic epithelium." "FMA:263194" - "A multi-ciliated cell of the retina that lacks visual pigment and contributes to aqueous humor by secreting chloride ions. This cell type maintains gap junctions with pigmented epithelial cells." "FMA:70607" - "Any neuron having a sensory function; an afferent neuron conveying sensory impulses." "FMA:84649 FBbt:00005124 BTO:0001037 WBbt:0005759" - "Cell committed to natural killer cell lineage that has the phenotype CD122-positive, CD34-positive, and CD117-positive. This cell type lacks expression of natural killer receptor proteins." - "A Be cell that facilitates development of T-helper 2 (Th2) phenotype T cells, and secretes high levels of interleukin-2, interleukin-10, interleukin-4, and interleukin-6." - "A short lived plasma cell that secretes IgA. These cells may be found in the bone marrow as well as in the mucosal immune system." - - "A cell specialized to transduce mechanical stimuli and relay that information centrally in the nervous system." - "KUPO:0001071" - "The myoendocrine cellis a specialized myocyte localized mainly in the right and left atrial appendages, and also scattered within other areas of the atria and along the conductive system in the ventricular septum. The most conspicuous feature distinguishing myoendocrine cells from other atrial myoctyes is the presence of membane-bounded secretory granules (these granules contain precursor of cardiodilatins or atrial natriuretic polypeptides)." "FMA:67111" - "An immature B cell that is CD38-negative, CD10-low, CD21-low, and CD22-high." - "A secretory cell found in pancreatic acini that secretes digestive enzymes and mucins. This cell is a typical zymogenic cell, have a basal nucleus and basophilic cytoplasm consisting of regular arrays of granular endoplasmic reticulum with mitochondria and dense secretory granules." "CALOHA:TS-0737 BTO:0000028 FMA:63032" - "Any skin fibroblast that is part of a upper leg skin." - "Obsolete. Use PO:0000290 from Plant Ontology instead. A water conducting cell, tracheid or vessel member." - "A receptor in the vascular system, particularly the aorta and carotid sinus, which is sensitive to stretch of the vessel walls." - "A mature sexual reproductive cell of the female germline." - - - "A plasmatocyte derived from head mesoderm." - "An epithelial cell of the vestibular sensory organ that is characterized by intense enzymatic activities and numerous basal membrane infoldings." - "An epithelial cell located on the basal lamina of the olfactory epithelium." "FMA:62303" - "BTO:0001033" + "Set of all muscles in abdomen." "TAO:0001327 FMA:86917 FMA:71294 ZFA:0001327" + "A protein that is a translation product of the human IRX6 gene or a 1:1 ortholog thereof." + "Missing definition for term UBERON:0005095. Please replace it using linked reference." + "Stratified columnar epithelia is a rare type of epithelial tissue composed of column shaped cells arranged in multiple layers. Stratified columnar epithelia are found in the ocular conjunctiva of the eye, in parts of the pharynx and anus, the female's uterus, the male urethra and vas deferens. Also found in intralobular ducts in salivary glands.[WP]." "UMLS:C0836132 FMA:45564 NCIT:C33620 Wikipedia:Stratified_columnar_epithelia" + "A T-cell surface glycoprotein CD1 that is a translation product of the human CD1D gene or a 1:1 ortholog thereof." + "Any process that stops, prevents or reduces the frequency, rate or extent of protein catabolic process in the vacuole." + "A gland that is typically found in or near the orbital region, in or around either the medial or lateral canthi, and is typically associated with secretions onto the eyeball or associated ducts. Includes the Harderian, nictitans and lacrimal glands." + "A gland that is part of a integumental system [Automatically generated definition]." "EMAPA:17758 VHOG:0000654 EHDAA2:0000837 MA:0000144" + "Any process that activates or increases the frequency, rate or extent of mast cell degranulation." + "The portion of the small intestine that extends from the duodenum to the ileum." "UMLS:C0022378 MA:0000340 VHOG:0000053 GAID:318 FMA:7207 galen:Jejunum CALOHA:TS-0496 MESH:D007583 EMAPA:18666 MIAA:0000045 EV:0100074 MAT:0000045 NCIT:C12388 EFO:0001333 BTO:0000657 SCTID:181248002 Wikipedia:Jejunum" + "The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells." + "The sensory organs in muscle that are involved in the stretch reflex." "MESH:D009470 FMA:83607 NCIT:C13824 UMLS:C0027871 SCTID:12945004 GAID:819" + "A vasculature that is part of a conjunctiva." "FMA:70887" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of a gonadotropin." + "A brain region defined by functional criteria, e.g. auditory cortex, rather than by structural or histological criteria." "NLX:155513" + "MA:0003176 BIRNLEX:2553 EMAPA:35801 SCTID:279779009 UMLS:C0458767 UMLS:C0009198 FMA:75371" + "An enteroendocrine cell found in the ileum and jejunum that produces neurotensin." "FMA:62943" + "In medicine, gonadal vein refers to the blood vessel that carrying blood away from the gonad (testis, ovary) toward the heart. Females : ovarian vein Males : testicular vein [WP,unvetted]." "EHDAA:8703 VHOG:0001340 EHDAA2:0000719 Wikipedia:Gonadal_vein SCTID:278192008" + "A C-C chemokine receptor type 2 that is encoded in the genome of mouse." "UniProtKB:P51683" + "Any process that modulates the frequency, rate or extent of R8 differentiation." + "A mucosa that is part of a nasopharynx [Automatically generated definition]." "SCTID:361938001 FMA:54971" + "The process aimed at the progression of a mesenchymal cell over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell." + + "The expansion of a dendritic cell population by cell division. A dendritic cell is a cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation." + "A sialic acid-binding Ig-like lectin 6 that is encoded in the genome of mouse." "UniProtKB:Q920G3" + "A mechanoreceptor cell of the auditory or vestibular system that is sensitive to auditory stimuli. The accessory sensory structures are arranged so that appropriate stimuli cause movement of the hair-like projections (stereocilia and kinocilia) which relay the information centrally in the nervous system." + "A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm." + "The chemical reactions and pathways involving primary amino compound." + "Lower lateral part of the cerebral hemisphere. (MSH)." "BIRNLEX:1160 UMLS:C1268978 GAID:635 neuronames:125 BAMS:Temporal_lobe EV:0100169 MAT:0000508 HBA:4132 Wikipedia:Temporal_lobe BTO:0001355 EMAPA:18797 MESH:D013702 CALOHA:TS-1020 UMLS:C0039485 SCTID:180921000 FMA:61825 BAMS:TL DHBA:12139 EFO:0000917 NCIT:C12353" + "Signal transduction in which the initial step occurs in a postsynapse." + "A cell morphology that inheres in multipolar neurons with densely branched terminal axonal arborizations that form basket-like structures surrounding and synapsing to the somas of target cells." "ILX:0101123 ilxtr:BasketPhenotype nifext:3" + "The developmental growth process in which an oocyte irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present." + "A bistratified amacrine cell with a small dendritic field that has dendrite stratification in S2, and in S3 and S4." "One of three types of epithelial cells that populate the parathyroid gland; cytological characteristics intermediate between those of the chief cell and of the oxyphil cell. Because only one hormone is produced, the three cell forms are widely believed to be different phases in the life cycle of a single cell type, with the chief cell being its physiologically active stage." "FMA:69324" - "A mesothelial cell that is part of the visceral peritoneum." "FMA:72143" - "A secondary fiber cell that contains a nucleus." "FMA:70949" - - "A chief cell that is bigger than dark chief cells and has a larger and lighter nucleus and a cytoplasm with few granules." "FMA:69079" - "A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation." - "A mature microglial cell that has changed shape to an amoeboid morphology and is capable of cytokine production and antigen presentation." - "An undifferentiated cell that originates from a neural stem cell and has the capacity to generate multiple types of lineage-restricted progenitors but not to self-renew." - "An endothelial progenitor cell that participates in angiogenesis during development." - "A mature cell of the conventional dendritic cell lineage, characterized by a high capacity for antigen presentation and typically found in a lymph node." "FMA:83038" - "One of two small cells formed by the first and second meiotic division of oocytes." "WBbt:0008429 EHDAA2:0004716 XAO:0000262 FMA:85543" - "Obsolete. Use PO:0020099 from Plant Ontology instead. Cell type formed after the first mitotic division of the microgametophye, The nucleus of this cell migrates to the tip of the pollen tube after germination and disintegrates when the pollen tube penetrates the nucellus." - "An IgD-negative CD38-positive IgG memory B cell is a CD38-positive IgG-positive that has class switched and lacks expression of IgD on the cell surface with the phenotype IgD-negative, CD38-positive, and IgG-positive." + "Any process that activates or increases the frequency, rate or extent of melanosome transport." + "Formation of a microvillus, a thin cylindrical membrane-covered projection on the surface of a cell." + "EHDAA2:0004588" + "A ploidy quality inhering in a bearer by virtue of the bearer's containing more than two homologous sets of chromosomes." + "Any process that activates or increases the frequency, rate or extent of small intestine smooth muscle contraction." + "An MHC class II histocompatibility antigen alpha chain DRA that is encoded in the genome of mouse." + "Any process that activates or increases the frequency, rate or extent of myeloid cell differentiation." "A nucleated blood cell involved in coagulation, typically seen in birds and other non-mammalian vertebrates." - "An immature CD14-positive dermal dendritic cell is CD80-low, CD86-low, and MHCII-low." - "A nuclear bag fiber that is sensitive mainly to the rate of change in muscle length." - "A neuroglial cell of the peripheral nervous system inside the basal lamina of the neuromuscular junction providing chemical and physical support to the synapse." - + "An endothelial cell located in a lymph node lymphatic vessel." - "A stromal cell of the prostate." "BTO:0003972" - "Obsolete. Use PO:0000400 from Plant Ontology instead. A cambial cell on the phloem side of the cambial zone that is the source of one or more cells arising by periclinal divisions and differentiating into phloem elements with or without additional divisions in various planes." - "Any blood vessel endothelial cell that is part of a microvascular endothelium." - "An erythrocyte lacking a nucleus." - "A gamma-delta receptor that expresses Vgamma1.1 but does not express Vdelta6.3 chains in the T-cell receptor." - - "A goblet cell that is part of the epithelium of pyloric gland." "FMA:263061" - "A cell of the embryo in the early stage following the blastula, characterized by morphogenetic cell movements, cell differentiation, and the formation of the three germ layers." - "An ILC1 cell in the human with the phenotype CD56-negative, IL-7Ralpha-positive, T-bet-positive." - "A fibroblast that is part of the connective tissue of nonglandular part of prostate." "FMA:261281" - "A NK1.1-positive T cell that is Ly49H-positive." - "Epithelial cell derived from mesoderm or mesenchyme." "FMA:69076" - - "A neuron that is part of nerve found outside the central nervous system." "FMA:84664" - "A large, granular, liver specific natural killer cell that adheres to the endothelial cells of the hepatic sinusoid." + "Any process that decreases the frequency, rate or extent of the developmental process that results in the deposition of coloring matter in an organism." + "Any process, involved in skeletal muscle contraction, that modulates the establishment or extent of the excitatory postsynaptic potential (EPSP). Excitatory postsynaptic potential (EPSP) is a temporay increase in postsynaptic potential due to the flow of positively charged ions into the postsynaptic cell. The flow of ions that causes an EPSP is an excitatory postsynaptic current (EPSC) and makes it easier for the neuron to fire an action potential." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mineralocorticoid stimulus. Mineralocorticoids are hormonal C21 corticosteroids synthesized from cholesterol and characterized by their similarity to aldosterone. Mineralocorticoids act primarily on water and electrolyte balance." + "A bone that is part of a the digitopodium skeleton - i.e. the acropodial skeleton or the metapodial skeleton." + "The junction between the axon of a motor neuron and a muscle fiber. In response to the arrival of action potentials, the presynaptic button releases molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane of the muscle fiber, leading to a change in post-synaptic potential." "Wikipedia:Neuromuscular_junction NIF_Subcellular:sao1124888485" + "A T-cell surface glycoprotein CD8 beta chain isoform 1 that is encoded in the genome of human." "UniProtKB:P10966-1" + "The sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the palate, upper teeth and gingiva, the skin between the palpebral fissure and the mouth, and from the nasal cavity and maxillary sinuses." "EHDAA2:0002087 BTO:0001378 MA:0001103 MESH:D008442 EMAPA:17799 SCTID:280211001 VHOG:0001346 AAO:0010670 Wikipedia:Maxillary_nerve GAID:836 FMA:52724" + "An apical ectodermal ridge that is part of a footplate." "EMAPA:17251 EHDAA2:0000547" + "Any physiological process involved in changing the position of a multicellular organism or an anatomical part of a multicellular organism." "FBbt:00004230" - "Any blood vessel endothelial cell that is part of a microvascular endothelium." - "A neuron whose cell body is within an autonomic ganglion." "FMA:80121" + "Any process that stops or decreases the rate or extent of fat cell proliferation." + "Any process that stops, prevents or reduces the frequency, rate or extent of chromosome organization." + "A bud-like thickening in the epidermis consisting of elongated keratinocytes, which at the distal end are in touch with numerous aggregated specialized dermal fibroblasts, the dermal condensate." "EMAPA:36479" + "A protein that is a translation product of the human CR2 gene or a 1:1 ortholog thereof." "PIRSF:PIRSF002484" + "An integrin alpha-4 that is encoded in the genome of human." "UniProtKB:P13612" "CD8_alpha-low Langerhans cell is a Langerhans cell that is CD205-high and is CD8_alpha-low." - - "A cell that is resistant to stains." "FMA:83626" + "The regionalization process that gives rise to the midbrain-hindbrain boundary. The midbrain-hindbrain domain of the embryonic brain is comprised of the mesencephalic vesicle and the first rhombencephalic vesicle at early somitogenesis stages. An organizing center at the boundary patterns the midbrain and hindbrain primordia of the neural plate." + "A glutamyl aminopeptidase that is encoded in the genome of mouse." "UniProtKB:P16406" + "An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity." "BFO:0000003" + "Any process that modulates the frequency, rate or extent of blastocyst development." + "The chemical reactions and pathways resulting in the breakdown of progesterone, a steroid hormone produced in the ovary which prepares and maintains the uterus for pregnancy. Also found in plants." - "Male germ cell is a germ cell that supports male gamete production." "ncithesaurus:Spermatogenic_Cell MA:0002765 VHOG:0001531 FMA:72290" - - "Any epithelial cell that is part of a female gonad." - "A pigment cell derived from the neural crest. Contains blue pigment of unknown chemical composition in fibrous organelles termed cyanosomes. This gives a blue appearance." - "A skeletal muscle myoblast that differentiates into fast muscle fibers." - "A skeletal muscle fiber that is innervated by alpha motor neuron and generates tension by contracting, thereby allowing for skeletal movement. These fibers make up the large mass of skeletal muscle tissue and are attached to bones by tendons." "TH:H3.03.00.0.00007" - - "An insect excretory cell that regulates haemolymph composition by filtration and filtrate endocytosis." "FMA:83807 BTO:0004597" - "Regular cardiac myocyte of a cardiac ventricle." "FMA:83109" - "A female gamete where meiosis has progressed to metaphase II and is able to participate in fertilization." "BTO:0003801 FBbt:00057012 CALOHA:TS-2191 FMA:67343 MA:0000388 BTO:0000369" - "A smooth muscle cell assocatiated with the vasculature." - "An endocrine cell that secretes juvenile hormone." - - "The neurons that utilize glycine as a neurotransmitter." - "A sperm bearing a Y chromosome. Chromosomal and genetic sex is established at fertilization in mammals and depends upon whether an X-bearing sperm or a Y-bearing sperm fertilizes the X-bearing ovum." "FMA:84058" - "Neuron that is part of the enteric nervous system." + "FMA:18303" + "PMID:11062127 PMID:29367151 PMID:9342353 GC_ID:1" + "The change in morphology and behavior of a T helper 2 cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific." + "Any process that stops, prevents or reduces the frequency, rate or extent of lipoprotein transport." + "Mesenchyme that is part of a developing jaw [Automatically generated definition]." "EMAPA:35454 EMAPA:32907" + "Any of the muscles that are responsible for moving the scapula. In humans these are the levator scapulae, the infraspinatus muscle, the teres major, the teres minor, and the supraspinatus muscle." + "A portion of the large intestine before it becomes the rectum. In mammals, the colon is the most part of the large intestine, excluding the vermiform appendix, the rectum and the anal canal." "XAO:0000243 MA:0000335 VHOG:0000648 AAO:0010400 BTO:0000269 CALOHA:TS-0158 FMA:14543 MAT:0000526 EFO:0000361 TAO:0000706 NCIT:C12382 MESH:D003106 MAP:0000001 EMAPA:18939 UMLS:C0009368 ZFA:0000706 GAID:309 galen:Colon EV:0100079 SCTID:302508007 Wikipedia:Colon_(anatomy)" + "A forelimb bone or its cartilage or pre-cartilage precursor." + "Layer of neocortex lying deep to the internal granule cell layer (layer 4) defined cytoarchitecturally by the predominance of large pyramidal cell bodies." "EMAPA:35259 NLXANAT:090811 PBA:294021878 FMA:77812 neuronames:2450 NCIT:C32653 UMLS:C1517447 MA:0000901 ABA:CTX5" + "A cardiac atrium that is in the right side of the heart. It receives deoxygenated blood. In mammals, this comes from the superior and inferior vena cava and the coronary sinus, and pumps it into the right ventricle through the tricuspid valve." "UMLS:C0225844 FMA:7096 Wikipedia:Right_atrium EHDAA2:0000290 VHOG:0000328 NCIT:C12868 SCTID:244383003 EMAPA:17321 galen:RightAtrium XAO:0003192 MA:0000075 AAO:0010248 BTO:0001703" + "The change in morphology and behavior of a monocyte resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor." + "Any process that decreases the frequency, rate or extent of cell morphogenesis contributing to cell differentiation. Cell morphogenesis involved in differentiation is the change in form (cell shape and size) that occurs when relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history." + "A series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug." + "A male organ involved in reproduction." "WBbt:0008423 MA:0000545" + "Any process that stops, prevents or reduces the rate or extent of progression through the cell cycle." - "Any basket cell that is part of a neocortex." - "A dermal dendritic cell that is langerin-negative, CD103-negative, and CD11b-positive." - "A enteroendocrine cell part of the glands of the gastric mucosa. They produce histamine and peptides such as chromogranins. This cell type respond to gastrin by releasing histamine which acts as a paracrine stimulator of the release of hydrochloric acid from the gastric parietal cells." "BTO:0002692" - "Granule cell that is part of the cerebellum." "BTO:0004278" - "A goblet cell that is part of the epithelium of crypt of lieberkuhn of large intestine." "FMA:263056" + "An organ that is capable of transducing sensory stimulus to the nervous system." "AEO:0000094 UMLS:C0935626 BSA:0000121 EHDAA:500 VHOG:0001407 BTO:0000202 NCIT:C33224 EMAPA:35955 CALOHA:TS-2043 MESH:D012679 GAID:63 EHDAA2:0001824 WBbt:0006929 HAO:0000930 SCTID:244485009 MA:0000017" + "Any process that modulates the frequency, rate or extent of cell migration." + "Any process that modulates the frequency, rate or extent of endothelial cell apoptotic process." + "EHDAA2:0001457 ZFA:0001104 EFO:0003626 EHDAA:962 TAO:0001104" "Glandular cell of seminal vesicle epithelium." "CALOHA:TS-1283" "Obsolete. Use PO:0000084 from Plant Ontology instead. Male gamete, part of male germ unit." - "A venule endothelial cell that is cubodial, expresses leukocyte-specific receptors, and allows for passage of lymphocytes into bloodstream." "FMA:67759" - "A cell that originates in the neural crest, that has certain cytochemical and ultrastructural characteristics and is found scattered throughout the body; types include melanocytes, the cells of the chromaffin system, and cells in the hypothalamus, hypophysis, thyroid, parathyroids, lungs, gastrointestinal tract, and pancreas. This cell type concentrates the amino acid precursors of certain amines and decarboxylate them, forming amines that function as regulators and neurotransmitters. This cell type produces substances such as epinephrine, norepinephrine, dopamine, serotonin, enkephalin, somatostatin, neurotensin, and substance P, the actions of which may affect contiguous cells, nearby groups of cells, or distant cells, thus functioning as local or systemic hormones. The name is an acronym for amine precursor uptake and decarboxylation cell." "FMA:83114 BTO:0003866" - "A Sst GABAergic cortical interneuron with a soma found in lower L5 with mostly local axonal arborization but with some sparse ascending axons. L5 non-Martinotti Sst cells show somatic localization and local axon plexus in L5b and L5b/6 and substantial innervation of L3 and L4, and receive thalamic input from the ventral posteromedial nucleus and specifically target L4 neurons, avoiding L5 pyramidal cells. L5 non-Martinotti Sst cells tend to show a higher input resistance and seem to be less stuttering." - "A motor neuron that is generated only on limb levels and send axons into the limb mesenchyme." - "An enterocyte that is part of the epithelium of intestinal villus." "FMA:263088" - "A circular smooth muscle cell of the iris, innervated by the ciliary nerves (parasympathetic), and acting to contract the pupil. This muscle cell derives from neuroectoderm. This smooth muscle cell results from transformation of epithelial cells to smooth muscle cells." "FMA:70611" - + "The directed movement of a B cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis)." + "Any process that activates or increases the frequency, rate or extent of glia cell differentiation." + "A material entity that minimally consists of a protein." + "The stage in oogenesis when the antral spaces fuse to form a single antral space. The oocyte is suspended in the cumulus oophorous and the first polar body in the perivitelline space." + "Enables the transmembrane transfer of a solute by a channel that opens in response to a specific ion stimulus." - "A follicular dendritic cell located in the Peyer's patch. These cells from a meshwork in which Peyer's patch B cells reside." - "A central nervous system macrophage found in small blood vessels in the brain. Markers include CD14+CD16+CD163+." - "A macrophage located in adipose tissue that is CD45-positive, CD11c-positive, and SIRPa-positive." - "A supporting cell of the vestibular epithelium." "FMA:75607" - "A spore formed from bacteria in the order Actinomycetales." - "A GABAergic cortical interneuron that expresses CCK. L5/6 CCK cells have soma found mainly in L5 and L6 and have large axonal arborization." - "An epithelial cell that is part_of a alveolus of lung." - "A cell found within the dental pulp." "CALOHA:TS-0195 FMA:87170 BTO:0000339" - "A Pvalb GABAergic cortical interneuron that is recognizable by the straight terminal axonal 'cartridges' of vertically oriented strings of synaptic boutons. Chandelier PV cells have soma found in in upper L2/3, with some in deep L5. Chandelier PV cells exhibit fast-spiking but lower firing rate compared to basket cells, and have practically absent hyperpolarization sag. Chandelier PV cells' boutons target exclusively the axon initial segment (AIS) of pyramidal cells, with a single cell innervating hundreds of pyramidal cells in a clustered manner." "ILX:0107356" - "A CD4-positive, alpha-beta T cell that is found in the columnar epithelium of the gastrointestinal tract." - "Any photoreceptor cell that is part of a compound eye." - "A cell present in the developing CNS. Functions as both a precursor cell and as a scaffold to support neuronal migration." - "A goblet cell that is part of the epithelium proper of duodenum." "FMA:263063" - "Any brush cell that is part of the intestinal epithelium." - "The smaller of two types of asexual spores formed by some fungi. An ovoid to pear-shaped asexual spore that contains very little cytoplasm and organelles, is uninucleate, and forms in vegetative hypae within a mycelium. Micronidia are extruded from the hyphal cell wall." "FAO:0000028" - "A glutamatergic neuron located in the cerebral cortex that projects to structures of telencephalic origins." "ILX:0770100" - "Mature CD8_alpha-negative CD11b-positive dendritic cell is a CD8_alpha-negative CD11b-positive dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive." - "FBbt:00004906" - - - "Any dendritic cell that is part of a liver." - "A male germ cell that develops from spermatogonia. The euploid primary spermatocytes undergo meiosis and give rise to the haploid secondary spermatocytes which in turn give rise to spermatids." "CALOHA:TS-0951 BTO:0001275 EMAPA:31484 WBbt:0006799 FMA:84049 FBbt:00004936" + "Behavior that is dependent upon the sensation of chemicals." + "Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to nucleolus." + "A nerve that is part of a toe [Automatically generated definition]." "EMAPA:37348 SCTID:300056004 MA:0000649" + "A monostratified retinal ganglion cell that has a medium soma and a small dendrite field." + "The process whose specific outcome is the progression of the metanephric proximal convoluted tubule over time, from its formation to the mature structure. The metanephric proximal convoluted tubule is the most proximal portion of the metanephric proximal tubule and extends from the metanephric glomerular capsule to the metanephric proximal straight tubule." + "A ciliated cell of the endometrial luminal epithelium." + "An endothelial cell that is part of a central vein of liver." + "Layer of lateral plate mesoderm that forms the future body wall - underlies the ectoderm[WP]." "XAO:0000271 BILA:0000047 Wikipedia:Lateral_plate_mesoderm#Division_into_layers AAO:0011100 FMA:295570" + "Any process that modulates the frequency, rate or extent of neuroblast proliferation." + "Any suture between cranial and/or facial bones." + "Any process that activates or increases the frequency, rate or extent of acinar cell proliferation." + + "Any process that modulates the frequency, rate or extent of the assembly of pseudopodia." + "The process in which an undifferentiated cell acquires the features of a myofibroblast cell." + "A change in the morphology or behavior of a chondrocyte resulting from exposure to an activating factor such as a cellular or soluble ligand. A chondrocyte is a polymorphic cell that forms cartilage." + "An epithelium that is part of a salivary gland [Automatically generated definition]." "CALOHA:TS-2067 EMAPA:32816 BTO:0004421 MA:0001587" + "A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts." "Hormone secreting cell located in the cortex of adrenal gland. Glandular cells in the adrenal cortex secrete mineralocorticoids, glucocorticoids and androgens." "CALOHA:TS-2177" - "A GABAergic neuron located in the cerebral cortex that expresses somatostatin (sst)" "ILX:0770152" - - "A luminal epithelial cell of mammary gland located in acinus of structure." "FMA:74505" - "A chromaffin cell interspersed among the interrenal epithelial layer of the anterior kidney of teloest fish." + "Fibrous joint in which the articulating bones or cartilages of the skull are connected by sutural ligaments (scant amount of collagenous dense connective tissue). Examples: sagittal suture, frontal suture." "EMAPA:35263 Wikipedia:Suture_(joint) FMA:7493 SCTID:244509003 GAID:211 MESH:D003393 MA:0001475" + "The process in which the anatomical structures of cardiac ventricle muscle is generated and organized." + "An immune response which is associated with resistance to intracellular bacteria with a key role in inflammation and tissue injury. This immune response is associated with pathological autoimmune conditions such as multiple sclerosis, arthritis and psoriasis which is typically orchestrated by the production of particular cytokines by T-helper 17 cells, most notably interleukin-17, IL-21 and IL-22." + "Extraembryonic cells of trophoblastic shell surrounding embryo, outside the cytotrophoblast layer, involved with implantation of the blastocyst by eroding extracellular matrix surrounding maternal endometrial cells at site of implantation, also contribute to villi. (dark staining, multinucleated)." "Wikipedia:Syncytiotrophoblast FMA:83040 NCIT:C33918 SCTID:256965005 BTO:0001335 EHDAA:129 UMLS:C1135936 EMAPA:16068 EHDAA:91" + "RETIRED_EHDAA2:0000496 EHDAA:1477 EMAPA:16660" + "A transitional myocyte that is part of the atrial part of atrioventricular bundle." "FMA:263174" + "A vestibular afferent neuron that makes bouton synapses to type II hair cells." "A cell that secretes glycosaminoglycans." - "CD11c-negative plasmacytoid dendritic cell is a leukocyte is CD11c-negative, CD45RA-positive, CD85g-positive(ILT7), CD123-positive, CD303-positive." - "A fibroblast that is part of the mammary gland." + "The specification and formation of the apicobasal polarity of a neuroblast cell, a progenitor of the central nervous system." + "Any collection of muscles that is part of a pelvic appendage." "TAO:0000258 ZFA:0000258" + "Binding to a fMet-Leu-Phe receptor." "An enteroendocrine cell that is located in the anorectum." - "A multi-fate stem cell that is able to differentiate into the pancreas alpha, beta and delta endocrine cells. This cell type expresses neurogenin-3 and Isl-1." - "An ecto-epithelial cell of the palatal region of the viscerocranial mucosa." "FMA:70580" - "A cell that specializes in secretion of surfactant in the alveoli of the lung." - "An epithelial cell that is part of the wall of inferior part of anal canal." "FMA:70562" - "A mature gamma-delta T cell that is found in the columnar epithelium of the gastrointestinal tract. These cells participate in mucosal immune responses." - "An enterocyte that is part of the epithelium of duodenal gland." "FMA:263092" + "An integrin alpha with A domain that is a translation product of the human ITGAE gene or a 1:1 ortholog thereof." "IUPHARobj:2450" + "The movement of an immune cell in response to an external stimulus contributing to an inflammatory response." + "A group of axons linking two or more neuropils and having a common origin, termination[FBbt]." "NLX:147822 FMA:83847 EV:0100304 BIRNLEX:1649" - "A near-projecting glutamatergic neuron with a soma found in layer 5/6 of the human primary motor cortex." "ILX:0770161" - "FBbt:00004910" - "A type II NK T cell that has been recently activated, secretes interleukin-4, and has the phenotype CD69-positive and downregulated NK markers." - - "Cell that is part of the vagal neural crest population. The vagal neural crest arises from the axial level of somites 1-7 and has been described as a hybrid between the head and the trunk populations." - "A cell that is specialized to store a particular substance(s), which is(are) later released from the store for a particular purpose." - "A Martinotti neuron that has axons that form a fan-like plexus." - "A cell that makes up the loose connective tissue of the ovary." "FMA:18709" - "A myoepithelial cell that is part of the tertiary lactiferous duct." "FMA:74502" - "A fast muscle fiber cell that stores energy in the form of glycogen and creatine phosphate." "FMA:84414 BTO:0001813" - "A reticular cell that is part of the splenic cord." "FMA:86497" - "Any neuromast support cell that is part of a posterior lateral line." - "KUPO:0001054" - "A proerythoblast that is Kit-low, Lyg76-positive, and CD71-positive." - "OBSOLETE: The cell characteristic of an organ, as distinguished from associated connective or supporting tissues." "FMA:84638 BTO:0002174" - "A photoreceptor cell that detects ultraviolet light." - "Any fibroblast that is part of a periodontal ligament." + "Any process that modulates the frequency, rate, or extent of T cell mediated immunity." + "A portion of connective tissue that is part of a thorax [Automatically generated definition]." "MA:0000560 EMAPA:37253" + "The region of the hepatic acinus that is closest to the arterial blood supply and has the highest oxygen concentration. Zone 1 is located in the periportal region of the liver lobule, closest to the portal triad. Hepatocytes in this region are primarily involved in oxidative energy metabolism." + "Mesenchyme that is part of a developing knee [Automatically generated definition]." "EMAPA:17495 EHDAA:5163 EHDAA2:0000898 EHDAA:6188 VHOG:0001070" + "Organ part that has the form of a hollow cavity[WP]." "EFO:0002513 UMLS:C0034051 FMA:82493 NCIT:C12986 Wikipedia:Alveolus" + "The chemical reactions and pathways resulting in the formation of nucleobases, nucleosides, nucleotides and nucleic acids." "Any endodermal cell that is part of a anterior visceral endoderm." + "Any process that modulates the frequency, rate or extent of granulosa cell apoptotic process." + "A cellular quality inhering in a bearer by virtue of the bearer's having thin, tail-like projections extending outwards from the cell body." + "The process in which a relatively unspecialized cell acquires the specialized features of a hepatocyte. A hepatocyte is specialized epithelial cell that is organized into interconnected plates called lobules, and is the main structural component of the liver." "A type of interneuron in the retinal inner nuclear layer which\ncarries information from the inner plexiform layer and the outer\nplexiform layer, using dopamine." - - - "Any basal cell of epidermis that is part of a limb." - "A cardiac myocyte that is connected to other cardiac myocytes by transverse intercalated discs (GO:0014704) at a regular interval." "FMA:67967" - "A connective tissue cell of an organ found in the loose connective tissue. These are most often associated with the uterine mucosa and the ovary as well as the hematopoietic system and elsewhere." "FMA:83624 BTO:0002064" - "Glial cell of hippocampus." "CALOHA:TS-1257" - "Neuron that secretes histamine." - "A melanin-containing macrophage that obtains the pigment by phagocytosis of melanosomes." - "A melanocyte located between the epithelial marginal cell layer and the mesodermal basal cell layer within the intrastrial space; the predominant cellular component of the electrogenic machinery that generates an endocochlear potential (80-100 mV) ." + "Any process that activates or increases the frequency, rate or extent of tongue muscle cell differentiation." + "The process whose specific outcome is the progression of a type B pancreatic cell over time, from its formation to the mature structure. A type B pancreatic cell is a cell located towards center of the islets of Langerhans that secretes insulin." + + "Epithelial cell of the descending thin limb of the long loop (juxtamedullary) nephron that spans the outer medulla (inner stripe). It is known in some mammalian species that the long descending limb of the loop of Henle in the outer medulla selectively expresses the secreted activin-antagonist protein follistatin (Fst), the GPI-linked adhesion protein Cdh13, and the protein kinase Stk32a." + "Any process that modulates the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon." + "Any process that activates or increases the frequency, rate or extent of optic nerve formation." + "GC_ID:1" + "A protein that is a translation product of the human EPX gene or a 1:1 ortholog thereof." + "The corpus striatum (striated body) is a compound structure consisting of the caudate nucleus and the lentiform nucleus, which consists of the putamen and the globus pallidus[WP]." "MESH:D003342 SCTID:279318005 UMLS:C0010097 BTO:0001311 EHDAA2:0000596 Wikipedia:Corpus_striatum EV:0100184 BAMS:CSTR EMAPA:17549 neuronames:2339 GAID:667 VHOG:0001175 FMA:77616 EFO:0000381 CALOHA:TS-0183 NCIT:C12448" + "The supporting bundles of muscular fibers lining the walls of the atrial myocardium." "EMAPA:37432 ZFA:0005810" + "Any process that activates, maintains or increases the frequency, rate or extent of the directed movement of amino acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "A CX3C chemokine receptor 1 that is encoded in the genome of mouse." "UniProtKB:Q9Z0D9" + "The process in which a precursor cell type acquires the specialized features of a natural killer cell progenitor." "An otic fibrocyte that is lateral to the basilar membrane and anchoris it to the lateral wall." - "A transitional myocyte that is part of the atrial septal branch of anterior internodal tract." "FMA:263160" - "A progenitor cell that is capable of forming colonies of primitive erythrocytes in the blood island of the yolk sac. First arrive at E7.5 in mouse and expresses CD41." - "A vascular associated smooth muscle cell of the brain vasculature." - "A neuron that releases hypocretin as a neurotransmitter." - "A hemocyte derived from head mesoderm, which enters the hemolymph as acirculating cell." - "Any stellate cell that is part of a dentate gyrus of hippocampal formation." - "A cell of the cuboidal epithelium that covers the lens. The cells of the lens epithelium regulate most of the homeostatic functions of the lens. As ions, nutrients, and liquid enter the lens from the aqueous humor, Na+/K+ ATPase pumps in the lens epithelial cells pump ions out of the lens to maintain appropriate lens osmolarity and volume, with equatorially positioned lens epithelium cells contributing most to this current. The activity of the Na+/K+ ATPases keeps water and current flowing through the lens from the poles and exiting through the equatorial regions. The cells of the lens epithelium also serve as the progenitors for new lens fibers. It constantly lays down fibers in the embryo, fetus, infant, and adult, and continues to lay down fibers for lifelong growth." "FMA:67559" - "A short lived plasma cell that secretes IgG." - "Any native cell that is part of a cardiac septum." - "A transitional myocyte that is part of the atrioventricular bundle." "FMA:83885 FMA:83388" - "A precursor cell destined to differentiate into cardiac muscle cell." "FMA:84797" - "A pro-T cell that is lin-negative, CD25-negative, CD127-negative, CD44-positive and kit-positive." - "A connective tissue cell that normally gives rise to other cells that are organized as three-dimensional masses. In humans, this cell type is CD73-positive, CD90-positive, CD105-positive, CD45-negative, CD34-negative, and MHCII-negative. They may further differentiate into osteoblasts, adipocytes, myocytes, neurons, or chondroblasts in vitro. Originally described as residing in the bone marrow, this cell type is now known to reside in many, if not all, adult organs." "FMA:70546 BTO:0003298 BTO:0002625" - "A glial cell that ensheathes axons of neuron in the peripheral nervous system and are necessary for their maintainance and function." "CALOHA:TS-0898 BTO:0001220" - "A motor neuron that synapses to parasympathetic neurons that innervate tear glands, sweat glands, and the smooth muscles and glands of the pulmonary, cardiovascular, and gastrointestinal systems." + "The appearance of interleukin-5 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." + + "A fibroblast that is part of an interstitial compartment of a kidney." "KUPO:0001102" + "An ion channel protein that has ligand-gated ion channel activity. The ligand-gated ion channel opens when a specific ligand has been bound by the channel complex or one of its constituent parts." "IUPHARfam:697" + "The process in which a myeloid precursor cell acquires the specialized features of a neutrophil." + "The directed movement of gamma-aminobutyric acid (GABA, 4-aminobutyrate) into a cell or organelle." + "Any process that modulates the frequency, rate or extent of excitatory synapse assembly." + "The process whose specific outcome is the progression of the cochlear nucleus over time, from its formation to the mature structure." + "A metastasis-suppressor KiSS-1 that has been processed by proteolytic cleavage." + "A tunica intima that is part of a vein." "EV:0100032 EMAPA:36308 SCTID:2436009 FMA:14353" + "A chondrolectin that is encoded in the genome of human." "UniProtKB:Q9H9P2" + "A chondrolectin that is encoded in the genome of mouse." "UniProtKB:Q9CXM0" + "Any process that stops, prevents or reduces the frequency, rate or extent of pulmonary blood vessel remodeling." "A cell of the adventitial layer of ductal structures such as the uterer, defent duct, biliary duct, etc" "FMA:84639 BTO:0002441" - "Obsolete. Use PO:0020048 from Plant Ontology instead. A haploid (1n) spore developing into a male gametophyte in heterosporous plants; the uninucleate pollen grain in seed plants." - + "Any process that increases the frequency, rate or extent of astrocyte activation." "A GABAergic neuron located in the cerebral cortex that expresses Gamma-synuclein" "ILX:0770150" - "A mast cell that is CD25+." - "A splenic macrophage found in the red-pulp of the spleen, and involved in immune responses to blood-borne pathogens and in the clearance of senescent erythrocytes. Markers include F4/80-positive, CD68-positive, MR-positive, Dectin2-positive, macrosialin-positive, and sialoadhesin-low." + "A dorsal horn of spinal cord that is part of a thoracic spinal cord." "BIRNLEX:1404 SCTID:362442007 UMLS:C0228628" + "Any process that modulates the frequency, rate or extent of lysosomal protein catabolic process." + "Binding to a CX3C chemokine receptor." + "Construction of a stage-1 egg chamber in the anterior part of the germarium, from the progeny of germ-line and somatic stem cells. An example of this is found in Drosophila melanogaster." "An endo-epithelial cell of the respiratory tract." "BTO:0004533" - "Any microvascular endothelial cell that is part of a prostate gland." - "An immature B cell that is IgM-positive, CD45R-positive, CD43-low, CD25-negative, and CD127-negative. This cell type has also been described as being AA4-positive, IgM-positive, CD19-positive, CD43-low/negative, and HSA-positive." - "A transitional myocyte that is part of the ventricular part of atrioventricular bundle." "FMA:263176" - "Any microvascular endothelial cell that is part of a breast." - "An intratelencephalic-projecting glutamatergic neuron with a soma found in layer 2/3 of the marmoset primary motor cortex." - "A chromaffin cell that is part of the adrenal gland." "FMA:69794" - "Neuromast support cell is a non-sensory cell of the neuromast that extend between the sensory hair cells from the basement membrane to the apical surface; neuromast support cells are surrounded by neuromast mantle cells." - "FBbt:00005148" - "A myeloblast committed to the basophil lineage." - "A smooth muscle cell that is part of the jejunum." "FMA:15062" - "An epithelial cell of the mammary gland." "BTO:0004300" - "Epithelial cell found in the ducts of the pancreas. This cell type contributes to the high luminal pH." "FMA:63099" + "The biosynthetic process resulting in the formation of DNA." + "A G protein-coupled receptor signaling pathway initiated by somatostatin binding to the somatostatin receptor (SSTR) on the surface of a target cell, and ending with the regulation of a downstream cellular process." + "An action potential that occurs in an atrioventricular node cardiac muscle cell." + "Any process that modulates the frequency, rate or extent of T-helper 1 cell activation." + "Binding to ammonium ions (NH4+)." + "The process whose specific outcome is the progression of the paramesonephric duct over time, from its formation to the mature structure. Mullerian ducts (or paramesonephric ducts) are paired ducts of the embryo that run down the lateral sides of the urogenital ridge and terminate at the mullerian eminence in the primitive urogenital sinus. In the female, they will develop to form the fallopian tubes, uterus, cervix, and the upper portion of the vagina; in the male, they are lost. These ducts are made of tissue of mesodermal origin." + "The multi-layer basement membrane between the dermis and epidermis that serves to adhere the dermis and epidermis, provide mechanical support for the epidermis, and forms a barrier to cells and large molecules across the junction." "FMA:70963 NCIT:C62356 EMAPA:37866 SCTID:51025007" "An olfactory receptor cell in which the apical ending of the dendrite is a knob that bears numerous microvilli." - "An epidermal progenitor cell that arises from neuroectoderm and in turn gives rise to the epidermal sheath of ventral and cephalic regions." "FBbt:00004994" - "A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage." "CALOHA:TS-0647 BTO:0001441" - "Chemosensitive cells that innervate the vomernasal organ epithelium and are responsible for receiving and transmitting pheromone signals." - "A fetal liver derived enucleated erythrocyte. This erythrocyte resembles adult erythrocytes in that they are small (3- to 6- times smaller than primitive erythrocytes) and produce adult hemaglobins." - "A spore formed following mitosis or mitoses." "FAO:0000023" - "An endothelial cell that lines any of the venous cavities through which blood passes in various glands and organs such as the spleen and liver." "FMA:63134" - "A non-terminally differentiated cell that originates from the neural crest and differentiates into an iridophore." - "A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors." - "A thymocyte expressing the alpha-beta T cell receptor complex as well as both the CD4 and CD8 coreceptors." - "A T cell that is located in the anorectum." - "An efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes or inhibits movement." "WBbt:0005409 FMA:83617 BTO:0000312" - "CALOHA:TS-0949 BTO:0001277" - "A cell type found in the spherical or ovoid clusters of receptor cells found mainly in the epithelium of the tongue and constituting the end organs of the sense of taste." "FMA:67910" - "CD7-negative lymphoid progenitor cell is a lymphoid progenitor cell that is CD34-positive, CD7-negative and CD45RA-negative." - "An epithelial cell that is part of a duct." - "A secondary oocyte is an oocyte that has not completed meiosis II." "FMA:18646 BTO:0003094" - "A fat cell of perirenal fat tissue." - "A macrophage which develops from an inflammatory monocyte and is recruited into the tissues in response to injury and infection as part of an inflammatory response. Markers include CD11b-positive, CD68-positive, and F4/80-positive." "FMA:84643 FMA:84645" - "A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells." "FMA:63368 CALOHA:TS-2086" - "A group 3 innate lymphoid cell in the human with the phenotype IL-7Ralpha-positive, and NKp44-negative." - "A gamma-delta T cell that has a mature phenotype. These cells can be found in tissues and circulation where they express unique TCR repertoire depending on their location." - "OBSOLETE: A classification of cells by their primary end goal or behavior." - "A cell involved in the formation of a monocyte (monopoiesis)." "FMA:83552" - - "Any neuron that is part of a spinal cord medial motor column." + "A transparent, semigelatinous substance that fills the cavity behind the crystalline lens of the eye and in front of the retina." "ENVO:02000032 MA:0001286 ZFA:0005561 FMA:58822 NCIT:C13323 EV:0100344 VHOG:0000795 BTO:0001451 EMAPA:17837 UMLS:C0229096 Wikipedia:Vitreous_humour CALOHA:TS-0308" + "Deepest layer of olfactory cortex." "NLX:152611" + "Any process that contributes to cytokine production by a myeloid dendritic cell." + "Subserosa that is part of the uterine tube. It contains loose connective tissue, blood vessels and lymphatic tissue." + "The reproductive developmental process whose specific outcome is the progression of the cervix over time, from its formation to the mature structure." + "A vasculature that is part of a iris [Automatically generated definition]." "ZFA:0005568" + "Fin or limb undergoing the process of regeneration." "TAO:0001269 EFO:0003657 ZFA:0001269" + "Any process that stops, prevents or reduces the frequency, rate or extent of glycine import into a cell." + "The process in which a relatively unspecialized precursor cell acquires specialized features of a lymphocyte. A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin." + "A lymphatic vessel located in the colon." + "Any apoptotic process that contributes to the shaping of a heart valve." + "Any process that modulates the frequency, rate or extent of activated CD8-positive, alpha-beta T cell apoptotic process." + "Any process in which a protein is transported to, or maintained at, a part of a chromosome that is organized into heterochromatin." + "The process whose specific outcome is the progression of a chondrocyte over time, from its commitment to its mature state. Chondrocyte development does not include the steps involved in committing a chondroblast to a chondrocyte fate." + "A paired organ of the urinary tract that produces urine and maintains bodily fluid homeostasis, blood pressure, pH levels, red blood cell production and skeleton mineralization." "BTO:0000671 UMLS:C0022646 MIAA:0000119 galen:Kidney XAO:0003267 MESH:D007668 CALOHA:TS-0510 Wikipedia:Kidney GAID:423 MAT:0000119 AAO:0000250" + "A cellular structure that forms the internal framework of eukaryotic and prokaryotic cells. The cytoskeleton includes intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles." "Wikipedia:Cytoskeleton" + "The group of neuron cell bodies associated with the ninth cranial nerve." "VHOG:0000702 ZFA:0001301 EHDAA:2838 EHDAA2:0000710 MA:0001077 SCTID:244451008 EMAPA:16795 FMA:53471 TAO:0001301" + "The initial segment of a cranial nerve, leaving the central nervous system." "FMA:52609 TAO:0002190 SCTID:280161004 ZFA:0001663" + "An anatomical cavity that surrounded_by a colon." "SCTID:362156004 EMAPA:18945 FMA:18374" "A cell that is found in the perisinusoidal space of the liver that is capable of multiple roles including storage of retinol, presentation of antigen to T cells (including CD1d-restricted NKT cells), and upon activation, production of extracellular matrix components that can contribute to liver fibrosis. This activated state has a myofibroblast-like phenotype, though it's not clear in the literature if this is terminally differentiated. This cell type comprises approximately 8-15% of total cells in the liver." "CALOHA:TS-0452 FMA:67763 BTO:0002741" - "A dendritic cell arising in thymus that has the phenotype CD11c-positive, CD11b-negative, and CD45RA-negative." - "The exocrine cell of the prostate, this epithelial cell secretes prostatic acid phosphotase and PSA, and is dependent on androgen hormones for survival." - "Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions." "WBbt:0005113 FMA:67313 FBbt:00005125 BTO:0003811" - "FBbt:00005221" - "An adipose dendritic cell that is SIRPa-negative." - "An epithelial cell of the bronchus." "BTO:0002922" - - "A concave nuclear shape where the nucleus is indented to more than half the distance to the farthest nuclear margin, but in no area is the chromatin condensed to a single filament." - "An intermediate muscle cell that has characteristics of both fast and slow muscle cells." "FMA:84450" - "A beta motor neuron that innervates the nuclear bag fibers of muscle spindles." - "Any skin fibroblast that is part of a pedal digit skin." - "A prostate epithelial cell that is CD133-positive, CD44-positive, integrin A2beta3-high. This cell is a stem cell for the prostate epithelium." - "The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system." "BTO:0000938 WBbt:0003679 VHOG:0001483 FBbt:00005106 CALOHA:TS-0683 FMA:54527" + "The distinguishing cell types of the lung alveolar tissue, including pulmonary epithelial cells (pneumocytes), alveolar capillary endothelial cells, interstitial cells (fibroblasts) and alveolar macrophages." "EMAPA:37942" + "Any process that modulates the frequency, rate or extent of vasculogenesis." + "Enables the transfer of bicarbonate from one side of a membrane to the other. Bicarbonate is the hydrogencarbonate ion, HCO3-." "RHEA:28695 Reactome:R-HSA-2752067" + "Any process that stops, prevents, or reduces the frequency, rate or extent of iridophore differentiation." + "Serous membrane layer that lines to a body cavity." "MA:0002448 FMA:15859" + "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together in the nucleus." + "A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN]." "EFO:0003498 ZFA:0000133 TAO:0000133" + "The chemical reactions and pathways resulting in the breakdown of organonitrogen compound." + "The section of the lymph node cortex that faces the subcapsular sinus. In human, it's characterized by specific protein markers." + "Any process that stops, prevents or reduces the frequency, rate or extent of cation transmembrane transport." + "The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system." "FBbt:00005106 BTO:0000938 WBbt:0003679 VHOG:0001483 CALOHA:TS-0683 FMA:54527" + "The directed movement of a lipid from outside of a cell into a cell. This may occur via transport across the plasma membrane or via endocytosis." "A trophoblast giant cell that is derived from ectoplacental cone and, later in gestation, the spongiotrophoblast." - "Obsolete. Consult Plant Ontology instead. A type of sieve element that has relatively undifferentiated sieve areas (with narrow pores), rather uniform in structure on all walls; that is, there are no sieve plates. Typical of gymnosperms and lower vascular plants." - "A basophillic chromophil cell that of the anterior pituitary gland." "FMA:83094" - "A myeloid suppressor cell that is Gr1-high and CD11c-negative." - "An epithelial cell present in the trachea and bronchi; columnar in shape; generally lack cilia; immature forms of ciliated or secretory cells which have been formed from stem cells." "FMA:69060" - "KUPO:0001052" - - "A melanocyte that produces pigment in the epithelium." - "Any leukocyte that is part of a spleen." - "Any pyramidal cell that is part of a primary motor cortex." - - "A motor neuron that innervates a skeletal muscle. These motor neurons are all excitatory and cholinergic." - "KUPO:0001109" - "A effector T cell that provides help in the form of secreted cytokines to other immune cells." "BTO:0002417" - "A CD4-positive, CD8-negative thymocyte that is CD24-positive and expresses high levels of the alpha-beta T cell receptor." - "A large epithelial cell with an extremely acidophilic and granular cytoplasm, containing vast numbers of mitochondria; such cells may undergo neoplastic transformation. From the Greek word onkos meaning swelling, this cell type is found in parathyroid, salivary and thyroid glands." "FMA:67606" - "A densely staining taste receptor cell that contains many dense vacuoles in their apical regions which project into the apical space and bear microvilli. This cell type serves as a supporting cell by surrounding and isolating the other cell types from each other; secrete a dense amorphous material that surrounds the microvilli in the taste pore. This cell type expresses a glial glutumate transporter, GLAST." "FMA:62356" - "A type of cell containing lipids in small vacuoles and typically seen in atherolosclerotic lesions, as well as other conditions." "FMA:83586 BTO:0003872" - - "A macrophage that is located in the anorectum." - "A Sst GABAergic cortical interneuron with a soma found in lower L2/3 and upper 5, L4 Sst cells have martinotti morphology with ascending axons but denser local axons and sparser ‘fanning-out’ projections to L1. L4 Sst cells have smaller membrane time constant to calb2 (L2/3/5 Fan Martinotti Cell) and non-zero afterdepolarization (ADP)." - "Any fibroblast that is part of a gallbladder." - "A T-helper cell that is characterized by secreting interleukin 9 and responding to helminth infections. This cell-type can derives from Th2 cells in the presence of TGF-beta and IL-4. Th2 cytokine production is surpressed." - "An epithelial cell that is part_of a umbilical artery." + "Fibrous joint in which the articulating bones or cartilages of the vertebral column and the limbs as well as articulating ossicles, are connected by skeletal ligaments or membranes. Examples: Intervertebral syndesmosis, inferior tibiofibular joint.[FMA]." "Wikipedia:Syndesmosis MA:0001500 EMAPA:37465 FMA:7494 SCTID:89358004" + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving catecholamine." + "The chemical reactions and pathways resulting in the breakdown of lutein." + "Any process that modulates the frequency, rate or extent of a protein or other molecule binding to a receptor." + "A macula densa that is part of a distal convoluted tubule [Automatically generated definition]." "MA:0001668" + "A large epithelial cell with an extremely acidophilic and granular cytoplasm, containing vast numbers of mitochondria; such cells may undergo neoplastic transformation. From the Greek word onkos meaning swelling, this cell type is found in parathyroid, salivary and thyroid glands." "MESH:D024862 FMA:67606" + "The process whose specific outcome is the progression of the lateral line ganglion over time, from its formation to the mature structure. The lateral line ganglion develops from cranial ectodermal placodes situated between the eye and ear and behind the ear." + "A mucosa that is part of a dorsum of tongue." "FMA:74871 SCTID:245835003" + "PMID:11557979 PMID:10874751 GC_ID:1" + + "A process in which a protein is transported to, or maintained in, a location within a microvillus." + "The enlargement or overgrowth of all or part of the heart muscle due to an increase in size of cardiac muscle cells without cell division." + "Any process involved in the carrying out of an immune response by a myeloid leukocyte." + "Any process that activates or increases the frequency, rate or extent of heart contraction." + "Binding to a carbohydrate derivative." + "A protein that is a translation product of the human TMED1 gene or a 1:1 ortholog thereof." + "The major postaxial endochondral bone in the posterior zeugopod[Phenoscape]." "AAO:0000891 SCTID:302529003 EFO:0003052 BTO:0002346 NCIT:C12718 CALOHA:TS-2203 galen:Fibula UMLS:C0016068 MESH:D005360 GAID:202 Wikipedia:Fibula MA:0001360 EMAPA:19141 FMA:24479" "A fully differentiated plasma cell that lives for months." - "An innate lymphoid cell that is capable of producing the type 1 cytokine IFN-gamma, but not Th2 or Th17 cell-associated cytokines." - - "A cell that can perform photosynthesis, in which carbohydrates are synthesized from carbon dioxide and water, using light as the energy source." - "A pigment cell derived from the neural crest. Contains melanin-filled pigment granules, which gives a brown to black appearance." "VHOG:0001679 CALOHA:TS-0613 BTO:0000847 FMA:70545" - "A fat cell derived from a neural crest cell." + "A portion of organism substance that is secreted by a reproductive gland." + "Maternally driven process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin." + "A cortex that is part of a hair [Automatically generated definition]." "SCTID:318832008 MA:0000156 EMAPA:35387 FMA:70934" "A steroid hormone secreting cell that secretes estradiol." - "An epithelial cell that is part of the glomerular capsule." "KUPO:0001034 FMA:70966" - "A cell comprising the transparent, biconvex body separating the posterior chamber and vitreous body, and constituting part of the refracting mechanism of the mammalian eye." "FMA:70950" - "A motor neuron that passes from the spinal cord toward or to a muscle and conducts an impulse that causes movement." - "A mature male germ cell that develops from a spermatid." "CALOHA:TS-0949 BTO:0002046 BTO:0001277 FBbt:00004954 FMA:67338 WBbt:0006798" - "FBbt:00001686" - - "A segmented neutrophilic cell of the bone marrow reserve pool that expresses CD11b (integrin alpha-M) and high levels of CD16 (low affinity immunoglobulin gamma Fc region receptor III) on its cell surface." - "An CD24-positive CD38-negative IgG-negative memory B cell is a CD38-negative IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype CD24-positive, CD38-negative, and IgG-negative." - "A paneth cell that is located in the anorectum." - "A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers." "FMA:83504 CALOHA:TS-0289 BTO:0001571" - "A progenitor cell with hepatic and biliary lineage potential, identified in mouse and human, and anatomically restricted to the ductal plate of fetal liver." - "A stem cell that can give rise to cell types of the body other than those of the germ-line." "FMA:63368 CALOHA:TS-2086" - "A neuron of the ventral spinal cord." - "An epithelial cell of the integument (the outer layer of an organism)." "FMA:62411 CALOHA:TS-0283 BTO:0001470" - "A scaffolding cell type found in C. elegans, this cell plays a supportive role to the muscle arms. May also have an endocrine role." - "KUPO:0001110" - "Odontoblast that is terminally differentiated and derived from an odontogenic papilla and associated with dentine." - "A paneth cell that is located in the epithelium of the colon." - "A specialized endothelial cell that senses extracellular signals and guides the directed growth of blood vessels." + "A protein that is a translation product of the human NTNG1 gene or a 1:1 ortholog thereof." + "An interneuron with a soma found in the hippocampus." "FMA:84777" + "A nucleated precursor of an erythrocyte that lacks hematopoietic lineage markers." "FMA:83504 CALOHA:TS-0289 MESH:D004900 BTO:0001571" + "Any process that stops, prevents, or reduces the rate of natural killer cell degranulation." + "The process in which the structure of a heart valve is generated and organized." + "The layer located below the cerebral cortex that includes the forebrain, midbrain and hindbrain." "BTO:0002858 NCIT:C98712 UMLS:C0815008 FMA:242188" + "An acellular strand that runs from subcommissural organ caudally through the ventricular system and central canal to the ampulla caudalis. Develops from glycoproteins secreted into CSF." "NLX:151878 Wikipedia:Reissner's_fiber" + "The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate." "NCIT:C93172 XAO:0000016 EMAPA:32857 DMBA:16810 VHOG:0000649 TAO:0000042 EHDAA:5789 EHDAA2:0004395 AAO:0011064 ZFA:0000042 neuronames:2076" "A progenitor cell that can give rise to plasmacytoid and myeloid dendritic cells, and to monocytes and macrophages." - "A large, multipolar lower motor neuron of the brainstem and spinal cord that innervates the extrafusal muscle fibers of skeletal muscle and are directly responsible for initiating their contraction. While their cell bodies are in the CNS (in the anterior gray horn of the spinal cord), they are part of the somatic nervous system - a branch of the PNS." - "A simple columnar cell that populates the entire luminal surface including the gastric pits. This cell types secrete mucus to form a thick protective, lubricant layer over the gastric wall." "FMA:62949" - "CD4-positive, alpha-beta long-lived T cell with the phenotype CD45RO-positive and CD127-positive. This cell type is also described as being CD25-negative, CD44-high, and CD122-high." - "A specialised myocyte that lies between the sinoatrial node and the atrioventricular node and is involved in the conduction of electrical signals." "FMA:223275" - "A cell of a hematopoietic lineage." "FMA:70366 FMA:83598 BTO:0000574 CALOHA:TS-2017" - "A melanocyte that appears darker due to content or amount of melanin granules." + "Any process that activates or increases the frequency, rate or extent of myofibroblast differentiation." + "Any process that stops, prevents, or reduces the frequency, rate or extent of exocytosis." + "Any process that stops, prevents or reduces the rate or extent of mast cell proliferation." "A nucleated, immature erythrocyte in which the nucleus occupies a relatively smaller part of the cell than in its precursor, the basophilic erythroblast. The cytoplasm is beginning to acquire hemoglobin and thus is no longer a purely basophilic, but takes on acidophilic aspects, which becomes progressively more marked as the cell matures. The chromatin of the nucleus is arranged in coarse, deeply staining clumps. This cell is CD71-positive and lacks hematopoeitic lineage markers." "FMA:83506" - "Any neuromast mantle cell that is part of a anterior lateral line." - "KUPO:0001050" - "A precursor in the granulocytic series, being a cell intermediate in development between a myeloblast and myelocyte, that has distinct nucleoli, a nuclear-to-cytoplasmic ratio of 5:1 to 3:1, and containing a few primary cytoplasmic granules. Markers for this cell are fucosyltransferase FUT4-positive, CD33-positive, integrin alpha-M-negative, low affinity immunoglobulin gamma Fc region receptor III-negative, and CD24-negative." "FMA:83530 CALOHA:TS-0825" - "A cell that will develop into a neuron often after a migration phase." "BTO:0000930 FMA:70563" - "KUPO:0001107" - "A myoepithelial cell that is part of the sweat gland." "FMA:67801" + "The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis in the cytoplasm." + "The blood vessels that convey blood from the glomerulocapillary network to the capillary bed of the proximal convoluted tubule." "EMAPA:28275 ZFA:0005308 FMA:77043 SCTID:29926005 MA:0002585 Wikipedia:Efferent_arteriole EMAPA:28233 TAO:0002140" + "A runt-related transcription factor 1 that is encoded in the genome of mouse." "UniProtKB:Q03347" + "An interneuron that is derived from the caudal ganglionic eminence." + "A lamp 5 GABAergic cortical interneuron with neurogliaform morphology with a soma found in L5,6. L5,6 NGC lamp5 have deep afterhyperpolarization (AHP) but narrow action potentials (APs). Unlike other deep neurogliaform cells (which are caudal ganglionic eminence (CGE) derived), L5,6 NGC lamp5 cells are medial ganglionic eminence (MGE)-derived" "BTO:0003689" + "Synovial sac which surrounds parts of one or more tendons. Examples: synovial tendon sheath of manual digit 2, radial bursa." "Wikipedia:Synovial_sheath FMA:40878 BTO:0001823" "An olfactory receptor cell with short cilia growing in an invagination bordered by microvilli." - "Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic cell is a conventional dendritic cell that is CD11b-positive, CD4-negative, CD8_alpha-negative and is CD205-positive." - "A border cell is a slender columnar cell on the medial portion of the basilar membrane." "FMA:79798" - "Neuron of the cerebellum." "FMA:84665 CALOHA:TS-2359" - "A neutrophil precursor in the granulocytic series, being a cell intermediate in development between a myelocyte and the band form neutrophil. The protein synthesis seen in earlier stages decreases or stops; the nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare; and the cytoplasm becomes amphophilic like that of a mature granulocyte. This cell type is integrin alpha-M-positive, CD13-negative, CD15-positive, CD16-positive, CD33-positive, CD24-positive, fMLP receptor-negative and has expression of C/EBP-a, C/EBP-e, PU.1 transcription factor, lactotransferrin, myeloperoxidase and neutrophil gelatinase associated lipocalin." "FMA:84197" + "A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]." "http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg TADS:0000147" + "Tube that connects the pharynx to the stomach. In mammals, the oesophagus connects the buccal cavity with the stomach. The stratified squamous non-keratinised epithelium lining the buccal cavity is continued through the pharynx down into the oesophagus. The lowest part of the oesophagus (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main body of the oesophagus is lined with small, simple mucous glands. Each gland opens into the lumen by a long duct which pierces the muscularis mucosae (Wilson and Washington, 1989). A sphincter is situated at the point where the oesophagus enters the stomach to prevent gastro-oesophageal reflux, i.e. to prevent acidic gastric contents from reaching stratified epithelia of the oesophagus, where they can cause inflammation and irritation (Wilson and Washington, 1989; Brown et al., 1993)." "TAO:0000204 galen:Esophagus MIAA:0000048 AAO:0000145 MESH:D004947 ANISEED:1235301 Wikipedia:Esophagus EHDAA2:0001285 EV:0100069 EFO:0000835 MA:0000352 FMA:7131 ZFA:0000204 BTO:0000959 CALOHA:TS-0700 GAID:291 UMLS:C0014876 VHOG:0000450 NCIT:C12389 EMAPA:16833 EHDAA:2937 SCTID:181245004 XAO:0000127 MAT:0000048" + "Any process that activates or increases the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon." "A cell occurring in the peripheral part of the vitreous body of the eye that may be responsible for production of hyaluronic acid and collagen." "FMA:70620 BTO:0004271" - "KUPO:0001051" - "A plasma cell that is located in a vermiform appendix." - "A progenitor cell of the B cell lineage, with some lineage specific activity such as early stages of recombination of B cell receptor genes, but not yet fully committed to the B cell lineage until the expression of PAX5 occurs." "BTO:0003104" - "A smooth muscle cell that is part of the sigmoid colon." "FMA:17521" - "A transitional myocyte that is part of the posterior division of left branch of atrioventricular bundle." "FMA:263178" + "A pharyngeal pouch that between pharyngeal arches 3 and 4." "NCIT:C34311 Wikipedia:Pharyngeal_pouch_(embryology)#Third_pouch FMA:295682 SCTID:345450001 TAO:0001131 UMLS:C0231070 AAO:0011116 XAO:0000251 RETIRED_EHDAA2:0000076 EMAPA:16586 ZFA:0001131 VHOG:0000966 EHDAA2:0000077 VHOG:0001030 EFO:0003634" + "The process whose specific outcome is the progression of the pharyngeal system over time, from its formation to the mature structure. The pharyngeal system is a transient embryonic complex that is specific to vertebrates. It comprises the pharyngeal arches, bulges of tissues of mesoderm and neural crest derivation through which pass nerves and pharyngeal arch arteries. The arches are separated internally by pharyngeal pouches, evaginations of foregut endoderm, and externally by pharyngeal clefts, invaginations of surface ectoderm. The development of the system ends when the stucture it contributes to are forming: the thymus, thyroid, parathyroids, maxilla, mandible, aortic arch, cardiac outflow tract, external and middle ear." + "Any process that stops, prevents or reduces the frequency, rate or extent of ATP metabolic process." + "A central nervous system neuron that stratifies at one and only one location." + "Any process that activates or increases the frequency, rate or extent of glycine secretion, neurotransmission." + "A long bone that is part of a hindlimb [Automatically generated definition]." "EMAPA:35403 MA:0000300" "A mesenchymal stem cell capable of developing into blood vessel endothelium." - "KUPO:0001108" - "A mucous cell in the epithelium of the stomach." "FMA:63464" - "A fibrocyte that is part of the adventitia of ureter." "FMA:261289" - "Large, stellate fibroblast found along the network of collagen fibers of the reticulum of the spleen; synthesize the matrix components of the reticulum." "FMA:62877" - "Heterochromatin that is arranged in a carthwheel pattern." - "A peptide hormone secreting cell that produces adrenocorticotropin, or corticotropin." - "An alpha-beta T cell that has an immature phenotype and has not completed T cell selection." - "FMA:83620" - "A cell with both myofibrils and secretory granules." - "A memory B cell with the phenotype IgD-negative and CD27-negative." - "A motile sperm cell that contains a slender threadlike microscopic appendage that enables motion." - "A B cell that is located in a vermiform appendix." - "A bipolar neuron found in the retina that is synapsed by rod photoreceptor cells but not by cone photoreceptor cells. These neurons depolarize in response to light." "FMA:67750" - - "A peptide hormone secreting cell pituitary that produces luteinizing hormone." - - "An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The cell has a loose, delicate axon terminal that opens in sublamina 3 of the inner plexiform layer and descends into sublamina 4." - "An epidermal cell that secretes chitinous cuticle from its apical side." - "An interneuron that uses GABA as a vesicular neurotransmitter. These interneurons are inhibitory" + "An interneuron that has double bouquet morphology." + "A specialized extracellular matrix that surrounds the plasma membrane of the ovum of animals. The egg coat provides structural support and can play an essential role in oogenesis, fertilization and early development." + "A muscle organ that consists of skeletal muscle tissue ensheathed in epimysium, that develops from myotome and that is innervated by some somatic motor neuron. Skeletal muscles are typically attached (via a tendon) to a bone but there are exceptions (e.g. intrinsic tongue muscles)." "EHDAA:5978 EHDAA:5035 EHDAA:5043 TAO:0005277 EV:0100377 VHOG:0000319 EFO:0000888 MESH:D018482 GAID:141 AAO:0011099 MIAA:0000302 EMAPA:35988 CALOHA:TS-0933 XAO:0000174 BTO:0001103 ZFA:0005277 MA:0003148 EHDAA:5984 MAT:0000302" + "A change in the morphology or behavior of a plasmacytoid dendritic cell resulting from exposure to an activating factor such as a cellular or soluble ligand, leading to the initiation or perpetuation of an immune response." + "PMID:9727836 PMID:11557979 GC_ID:1" + "Any process that stops, prevents or reduces the frequency, rate or extent of smooth muscle contraction involved in micturition." + "Any process that modulates the frequency, rate or extent of cell proliferation involved in mesonephros development." + "The directed movement of a keratinocyte, epidermal cells which synthesize keratin, from one site to another." + "A portion of connective tissue that is part of a dermis [Automatically generated definition]." "MA:0000799 EMAPA:36509" + "A CSF-1/PDGF receptor-type tyrosine-protein kinase that is a translation product of the human FLT3 gene or a 1:1 ortholog thereof." "IUPHARobj:1807 PIRSF:PIRSF500949" + "The tertiary bronchi (also known as the segmental bronchi) arise from the secondary bronchi. The respiratory epithelium lining their lumen is surrounded by a layer of smooth muscle. This layer is composed of two ribbons of smooth muscle that spiral in opposite directions. The smooth muscle layer is surrounded by irregular plates of hyaline cartilage which help maintain the patency of the airway. Each of the tertiary bronchi serves a specific bronchopulmonary segment. There are 10 tertiary bronchi in the right lung, and eight in the left. The tertiary bronchi get smaller and divide into primary bronchioles. [WP,unvetted]." "NCIT:C33526 MA:0000439 EMAPA:37739 Wikipedia:Segmental_bronchus VHOG:0001446 UMLS:C0444439 FMA:7407 EHDAA:7064 EHDAA:7043 EHDAA:7058 SCTID:245513001 EHDAA:7049 EHDAA:7070" + "The paired veins that carry blood from the yolk sac back to the embryo." "UMLS:C0231091 RETIRED_EHDAA2:0002209 SCTID:2730004 SCTID:308832003 XAO:0000376 XAO:0004147 VHOG:0000401 NCIT:C34329 EMAPA:36021 Wikipedia:Vitelline_veins FMA:70305" + "Any process that stops, prevents, or reduces the frequency, rate or extent of differentiation of CD4-positive, CD25-positive, alpha-beta regulatory T cells." + + "A CD209 molecule that is encoded in the genome of human." "Reactome:R-HSA-2079928 UniProtKB:Q9NNX6" + "The process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and/or excretes the end products of body metabolism in the form of urine." "Wikipedia:Kidney_development" + "A trabecula carnea that is part of a heart left ventricle." "SCTID:190344008 FMA:7271" + "The body or shaft of the humerus is almost cylindrical in the upper half of its extent, prismatic and flattened below, and has three borders and three surfaces." "SCTID:181927007 EMAPA:25051 FMA:13305 Wikipedia:Body_of_humerus MA:0002807 NCIT:C120671" + "The process whose specific outcome is the progression of the outer stripe over time, from its formation to the mature structure. The outer stripe is the region of the kidney outer medulla that lies just below the cortex. The proximal straight tubules (S3) characterize this region." + "An anatomical space that is part of a jejunum." "FMA:14590 EMAPA:18729" + "Any process that stops, prevents or reduces the frequency, rate or extent of gonad development." + "The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances." + "Any collection of muscles that is part of a neck [Automatically generated definition]." "FMA:71290 AAO:0000091 MESH:D009334 EMAPA:36050" "Ciliated cell of the embryonic epidermis and functions in embryonic movements." - "A rounded, inactive form that certain bacteria assume under conditions of extreme temperature, dryness, or lack of food. The bacterium develops a waterproof cell wall that protects it from being dried out or damaged." "BTO:0002779" "Any cell in the retina, the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates." "PMID:10702418" - "A macroconidium that has only one nucleus." "FAO:0000029" - - "A glutamatergic neuron located in the cerebral cortex that projects to structures not derived from telencephalon." "ILX:0770101" - "KUPO:0001096" - "An endothelial cell that is part of the hepatic sinusoid. These cells possess flattened areas containing perforations about 0.1 micrometers in diameter, known as fenestrae. The fenestrae are arranged in groups known as sieve plates." "BTO:000125 FMA:62911" - "Langerhans cell is a conventional dendritic cell that has plasma membrane part CD207. A Langerhans cell is a stellate dendritic cell of myeloid origin, that appears clear on light microscopy and has a dark-staining, indented nucleus and characteristic inclusions (Birbeck granules) in the cytoplasm; Langerhans cells are found principally in the stratum spinosum of the epidermis, but they also occur in other stratified epithelia and have been identified in the lung, lymph nodes, spleen, and thymus." "CALOHA:TS-2375 BTO:0000705 FMA:63072" - "A basophilic erythroblast that is Lyg 76-high and is Kit-negative." - "A cell type that makes up the highly vascular membrane lining the marrow cavity of long bones." "FMA:86495" - "A nonstratified squamous cell located in the ectocervix." "FMA:86483" - "A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a myelocyte and a band form cell. The nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare." "FMA:83541" - "Oval eosinophilic histiocytes with granules and vacuoles found in placenta, which are of mesenchymal origin, in mesoderm of the chorionic villus, particularly numerous in early pregnancy." - "A muscle cell that is part of some visceral muscle" - "A type I vestibular sensory cell that is part of the epithelium of macula of saccule of membranous labyrinth." "FMA:263190" - - "A plasmablast that secretes IgE." - "A tissue-resident macrophage of the renal glomerular mesangium involved in the disposal and degradation of filtration residues, presentation of antigen to T cells and in tissue remodeling." - - "A thymocyte that has the phenotype CD4-negative, CD8-negative, CD44-negative, and CD25-positive and expressing the T cell receptor beta-chain in complex with the pre-T cell receptor alpha chain." - "A basal cell that is part of the urothelium." "FMA:84150" + "Any process that activates or increases the rate of neuroblast proliferation." + "A submucosa that is part of a body of stomach [Automatically generated definition]." "FMA:17059" + "The disaggregation of a protein-DNA complex into its constituent components." + "A loop of Henle that is part of a kidney outer medulla inner stripe." "MA:0002627 EMAPA:29679" + "Portion of embryonic tissue determined by fate mapping to become a structure." "ZFA:0001116 AAO:0000479 TAO:0001116" + "Any process that activates or increases the frequency, rate or extent of T-helper 2 cell cytokine production." + "Any process that modulates the frequency, rate or extent of response to wounding." + "Any process that stops, prevents, or reduces the frequency, rate or extent of crystal cell differentiation." + "Any process that stops, prevents or reduces the frequency, rate or extent of calcium ion binding." + "The process in which the metanephric S-shaped body is generated and organized. The metanephric S-shaped body is the successor of the metanephric comma-shaped body that contributes to the morphogenesis of a nephron in the metanephros." + "A mucosa that is part of a left ureter [Automatically generated definition]." "FMA:17807" + "The small, erectile body located at the anterior end of the vulva." "Wikipedia:Clitoris MESH:D002987 FMA:9909 EMAPA:30819 galen:Clitoris MA:0000382 SCTID:181442003 GAID:385 VHOG:0000700 UMLS:C0008984 EHDAA:9360 NCIT:C12308 EHDAA2:0000255 BTO:0002020" "A cell from the outer syncytial layer of the trophoblast of an early mammalian embryo, directly associated with the maternal blood supply. It secretes hCG in order to maintain progesterone secretion and sustain a pregnancy." "FMA:83043" - "A lymph node macrophage found in the subcapsular sinus of lymph nodes that participates in sensing, clearance, and antigen presentation of lymph-borne particulate antigens. This macrophage is capable of activating invaraint NKT cells and is CD169-positive." - "Any microvascular endothelial cell that is part of a endometrial blood vessel." - "A glandular epithelial cell of the endometrium." "FMA:86489" - "Cylindrical spore formed by development and compartmentation of hyphae; the hyphae are often supporting blastoconidiophores." "FAO:0000041" "A rapidly proliferating population of cells that differentiate from stem cells of the intestinal crypt of the colon. Stem cells located in the crypts of Lieberkühn give rise to proliferating progenitor or transit amplifying cells that differentiate into the four major epithelial cell types. These include columnar absorptive cells or enterocytes, mucous secreting goblet cells, enteroendocrine cells and paneth cells." - "A sweat producing cell of eccrine sweat glands. Pyramidal in shape, with its base resting on the basal lamina or myoepitheliocytes, and its microvillus-covered apical plasma membrane line up the intercellular canaliculi. Cell is not stained by hematoxylin or eosin." "FMA:70658" + "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the juxtaglomerulus cells of the kidney as it progresses from its formation to the mature state." "A cell whose primary function is to shorten." - "A type I vestibular sensory cell that is part of the epithelium of crista of ampulla of semicircular duct of membranous labyrinth." "FMA:263192" - "A specialized cardiac myocyte in the sinoatrial and atrioventricular nodes. The cell is slender and fusiform confined to the nodal center, circumferentially arranged around the nodal artery." "BTO:0004190 FMA:67101" - "A cell that is part of the nervous system." "CALOHA:TS-2040 FMA:70333" - "KUPO:0001024" - - "Any basket cell that is part of a dentate gyrus of hippocampal formation." - "A type of mesothelial fibroblast that is derived from the neural crest, is localized on blood vessels, and is a key component of the pia and arachnoid membranes surrounding the brain." "ILX:0770143" - "A smooth muscle cell that is part of the ascending colon." "FMA:17518" - "A mesenchymal cell that is part of a small mass of condensed mesenchyme in the enamel organ; it differentiates into the dentin and dental pulp." - "A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells." "BTO:0000801 FMA:63261 FMA:83585 CALOHA:TS-0587" - "A M cell that is part of the epithelium proper of appendix." "FMA:263140" - "An IgG-negative double negative memory B cell is a double negative memory B cell with the phenotype IgG-negative, IgD-negative, and CD27-negative." - "A conventional thymic dendritic cell that is CD8alpha-negative." - - "A tissue-resident macrophage resident found in the thymus, involved in the clearance of apoptotic thymocytes." - "OBSOLETE: Adipocytes found in the subcutaneous adipose tissue of breast. The breast consists of three main components, the skin, the subcutaneous adipose tissue and the functional glandular tissue that comprises both parenchyma and stroma." - - "A dermal dendritic cell that is CD1a-positive and CD14-negative." - "A differentiated form of a fungus produced during or as a result of an asexual or sexual reproductive process; usually a cell with a thick cell wall that stores and protects one or more nuclei. Spores may be produced in response to, and are characteristically resistant to, adverse environmental conditions." - "A basophil cell of the anterior pituitary that produces thyroid stimulating hormone, thyrotrophin. This cell type is elongated, polygonal and lie in clusters towards the adenohypophyseal center." "FMA:83099" - "A monocyte that has characteristics of both patrolling and inflammatory monocytes." - "Obsolete. Use PO:0000352 from Plant Ontology instead. Cell containing glucosinolates ('mustard oil glucosides') and myrosinases, enzymes hydrolyzing the glucosinolates. Occurs in eleven dicotyledon families, the two largest of which are the Brassicaceae and Euphorbiaceae." - "KUPO:0001021" - "A germinal center B cell that develops from a Bm3 B cell. This cell has the phenotype IgM-negative, IgD-positive, and CD38-positive." - "A simple columnar epithelial cell that secretes mucin. Rough endoplasmic reticulum, mitochondria, the nucleus, and other organelles are concentrated in the basal portion. The apical plasma membrane projects microvilli to increase surface area for secretion." - "An animal cell that is part of a hair follicle." - "A mature T cell that differentiated and acquired cytotoxic function with the phenotype perforin-positive and granzyme-B positive." "CALOHA:TS-0190 BTO:0000289 FMA:70573" - + "Structural framework that provides support to the nasal sacs and ducts." "SCTID:281486007 FMA:60116 AAO:0000320" + "The human equivalent of a DN3 thymocyte; these thymocytes finish the process of beta selection." + "The process in which a branch forms along the side of a mammary duct." + "The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO]." "FMA:61993 MAT:0000106 BM:MB DHBA:10648 CALOHA:TS-0630 ZFA:0000128 Wikipedia:Midbrain EHDAA2:0001162 BTO:0000138 DMBA:16649 neuronames:462 MIAA:0000106 SCTID:279099009 UMLS:C0025462 MBA:313 AAO:0010149 BIRNLEX:1667 EMAPA:16974 BAMS:MES HBA:9001 MA:0000207 RETIRED_EHDAA2:0001104 EHDAA:3694 XAO:0000014 EFO:0000919 EV:0100242 MESH:D008636 VHOG:0000069 NCIT:C12510 TAO:0000128" + "Granule cell layer is also called the DG principal cell layer. This one of the three layers of dentate gyrus that lies deep to the molecular layer and is made of densely packed layer that is four to eight granule cells thick." "EMAPA:35276 BIRNLEX:4129 MA:0000946 BAMS:DG-sg MBA:632 neuronames:2122 FMA:83146 BAMS:GrDG DMBA:16122 BAMS:sg" + "The collection of all skeletal elements in a free forelimb region. Excludes the pectoral girdle." "XAO:0003061 EMAPA:32623 VSAO:0000151 AAO:0000202 EHDAA2:0002222 FMA:24142 VHOG:0001256" + "Any process that stops, prevents or reduces the frequency, rate or extent of artery morphogenesis." + "A differentiated form of a fungus produced during or as a result of an asexual or sexual reproductive process; usually a cell with a thick cell wall that stores and protects one or more nuclei. Spores may be produced in response to, and are characteristically resistant to, adverse environmental conditions." "MESH:D013172" + "The chemical reactions and pathways involving hyaluronan, the naturally occurring anionic form of hyaluronic acid, any member of a group of glycosaminoglycans, the repeat units of which consist of beta-1,4 linked D-glucuronyl-beta-(1,3)-N-acetyl-D-glucosamine." + "An appendage that is part of an appendage girdle complex." "VSAO:0000067" + "Any process that activates or increases the frequency, rate or extent of the directed movement of organic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "A fibroblastic reticular cell found in the lymph node T cell domain." + "A part of the secondary follicle in which naive B cells reside along with some helper T cells, macrophages and follicular dendritic cells; these are displaced by the expanding germinal centre and form a 'mantle' around it." "MA:0002990 EMAPA:37661" "A gamma-delta receptor that expresses Vgamma1.1-Vdelta6.3 chains in the T-cell receptor." - "A specialized multinuclear osteoclast associated with the absorption and removal of bone." - - - "A cell of the basal layer of the epithelium in the prostatic acinus." "FMA:74265" - "Obsolete. Use PO:0000284 from Plant Ontology instead. An epidermal cell associated with a stoma and at least morphologically distinguishable from the epidermal cells composing the groundmass of the tissue." - "A thymic epithelial cell that has an eccentric, round, or irregularly shaped hetero or euchromatic nucleus. The hallmark of this cell type is the presence of vacuoles, which are clustered in one area of the cytoplasm in the vicinity of the nucleus. The vacuoles are small and acquire a grape-like form, occasionally showing delicate internal microvillous projections." "FMA:72214" - "A smooth muscle cell that is part of a sphincter. A sphincter is a typically circular muscle that normally maintains constriction of a natural body passage or orifice and which relaxes as required by normal physiological functioning." - "A pigment cell is a cell that contains pigment granules." "VHOG:0001678" - "CD11c-low plasmacytoid dendritic cell is a leukocyte that is CD11c-low, CD45R-positive, GR1-positive and CD11b-negative." - "Chondrocyte forming the hyaline cartilage found in joints." "CALOHA:TS-0056" - "Obsolete. Use PO:0000244 from Plant Ontology instead. In monosporic and bisporic megasporogenesis: the megaspore(s) that will undergo megagametogenesis." - "KUPO:0001036" - - "A immature or mature cell in the lineage leading to and including erythrocytes." "CALOHA:TS-0290 FMA:62845 FMA:83516" - + "A G11 retinal ganglion cell that has post synaptic terminals in sublaminar layer S4 and is depolarized by illumination of its receptive field center." "https://orcid.org/0000-0002-5260-9315 https://orcid.org/0000-0001-7258-9596" + "Any process that stops, prevents, or reduces the frequency, rate, or extent of myeloid dendritic cell antigen processing and presentation." + "Binding to a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically." + "A SLAM family member 1 that is encoded in the genome of mouse." "UniProtKB:Q9QUM4" + "The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule." "Wikipedia:Binding_(molecular)" + "A process involved in the sexual cycle seen in females, often with physiologic changes in the endometrium that recur at regular intervals during the reproductive years." + "The process whose specific outcome is the progression of a salivary nucleus over time, from its formation to the mature structure." "A transit amplifying cell that is located in the anorectum." - "An intratelencephalic-projecting glutamatergic neuron with a soma found in layer 6 of the marmoset primary motor cortex." "ILX:0770158" - "A Purkinje myocyte that is part of the internodal tract." "FMA:83392" - "A melanocyte that appears lighter in color." - "Any fibroblast that is part of a pericardium." - "An extratelencephalic-projecting glutamatergic neuron located in layer 5b of the primary motor cortex that does not project to the medulla. Non-MY ET cells are large, big-tufted cells with the apical dendrite often bifurcating close to the soma, suggesting they are corticospinal cells. Non-MY ET cells have bigger hyperpolarization sag, lower input resistance, and smaller AP width, compared to L5 IT neurons." + "A nipple that is in_the_right_side_of a body proper." "FMA:223693" "Contractile cells resembling smooth muscle cells that are present in glands, notably the mammary gland, and aid in secretion. This cell has long weaving dendritic processes containing myofilament." "BTO:0002309 FMA:67799 CALOHA:TS-2379" - "A specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue, which typically differentiates from monocytes. This cell has the following markers: tartrate-resistant acid phosphatase type 5-positive, PU.1-positive, c-fos-positive, nuclear factor NF-kappa-B p100 subunit-positive, tumor necrosis factor receptor superfamily member 11A-positive and macrophage colony-stimulating factor 1 receptor-positive." "FMA:66781 BTO:0000968 CALOHA:TS-0721" - "A stem cell of embryonic origin." "CALOHA:TS-0263 BTO:0001086 FMA:82841" - "A cell of an organism that does not pass on its genetic material to the organism's offspring (i.e. a non-germ line cell)." "FMA:72300 BTO:0001268 WBbt:0008378" + "An extracellular matrix consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that provides not only essential physical scaffolding for the cellular constituents but can also initiate crucial biochemical and biomechanical cues required for tissue morphogenesis, differentiation and homeostasis. The components are secreted by cells in the vicinity and form a sheet underlying or overlying cells such as endothelial and epithelial cells." + "Any process that increases the rate, frequency or extent of peptide hormone processing. Peptide hormone processing is the generation of a mature peptide hormone by posttranslational processing of a prohormone." + "Any process that increases the rate, frequency or extent of branching involved in ureteric bud morphogenesis, the process in which the branching structure of the ureteric bud is generated and organized. The ureteric bud is an epithelial tube that grows out from the metanephric duct. The bud elongates and branches to give rise to the ureter and kidney collecting tubules." + "The regrowth of the endometrium and blood vessels in the uterus following menstruation, resulting from a rise in progesterone levels." + "A runt-related transcription factor 1 that is encoded in the genome of human." "UniProtKB:Q01196 Reactome:R-HSA-5667138 Reactome:R-HSA-8865295" "A goblet cell that is part of the epithelium of principal gastric gland." "FMA:263040" - "Obsolete. Use PO:0000282 from Plant Ontology instead. An outgrowth from the epidermis. Trichomes vary in size and complexity and include hairs, scales, and other structures and may be glandular. In Arabidopsis, patterning of trichome development is not random but does not appear to be lineage-based like stomata." - - "A class switched memory B cell that lacks IgG on the cell surface." - - "Obsolete. Use PO:0000349 from Plant Ontology instead. A relatively unspecialized cell that will give rise to specialized cell types of the epidermis." - "An epithelial cell that is part of the intermediate tubule." "FMA:70980" - "A goblet cell that is part of the epithelium of bronchus." "FMA:263032" - "A lymphocyte that resides in the lamina propria of the small intestine. Lamina propria leukocytes and intraepithelial lymphocytes are the effector compartments of the gut mucosal immune system. Lymphocytes circulate through gut associated lymphoid tissues until recruitment by intestinal antigens. They are involved in the gut immune response." - "An epithelial cell of the anal column." - "A cell type found on the superficial layer of the external side of the tympanic membrane. This cell-type lacks a nucleus." - "Specialized epithelial cells involved in the maintenance of osmotic homeostasis. They are characterized by abundant mitochondria and ion transporters. In amniotes, they are present in the renal system. In freshwater fish, ionocytes in the skin and gills help maintain osmotic homeostasis by absorbing salt from the external environment." - "A cell in vitro that is or has been maintained or propagated as part of a cell culture." - "A specialized cell involved in sensory perception of smell." "FMA:67870" - "A fibroblast-like cell that provides support at neuromuscular junctions in vertebrates and are localized outside the synaptic basal lamina." - "A oligopotent progenitor cell committed to the lymphoid lineage." + "The developmental process pertaining to the initial formation of a lung lobe from unspecified parts. This process begins with the specific processes that contribute to the appearance of the lobe and ends when the structural rudiment is recognizable. A lung lobe is a projection that extends from the lung." + "The process in which an organism retains a population of mesenchymal stem cells that contributes to the shaping of a nephron in the metanephros. A mesenchymal stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized mesenchymal cells." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of mature B cell apoptotic process." + "The 6th pharyngeal arch. contributes to the development of the sternocleidomastoid and trapezius muscles." "EHDAA2:0004075 AAO:0010368 EMAPA:32766 XAO:0000453 ZFA:0001609 FMA:293047 TAO:0001601 VHOG:0001205 SCTID:308772004" + "Any process that modulates the frequency, rate, or extent of peptide secretion." + "A submucosa that is part of an ascending colon [Automatically generated definition]." "FMA:15006" + "A mucosa that is part of a gastroduodenal junction." "BTO:0005415" + "The outer cell layer of the mammary gland epithelium bilayer which is located basal to the luminal (secretory) cells and adjacent to the basement membrane." "EMAPA:37903 FMA:67798 BTO:0002310" + "The outer part of a thymus lobule that surrounds the medulla and is composed of closely packed lymphocytes." "FMA:72205 UMLS:C0229948 EMAPA:35863 NCIT:C33774 MA:0000767 BTO:0002934 Wikipedia:Thymus#Cortex SCTID:188262003" + "Nephrogenic mesenchyme is the tissue made up of loosely connected mesenchymal cells in the nephron." + "A protein that is a translation product of the human NCR2 gene or a 1:1 ortholog thereof." "PIRSF:PIRSF037963" + "Any process that modulates the frequency, rate or extent of eosinophil migration." "A macrophage found in the medullary sinus of the lymph node." - "An interrenal epithelial kidney cell is an epithelial cell found in the anterior kidney of teleosts fish. This cell type is arranged in layers around the posterior cardinal vein and contains many mitochondria with tubulovesicular cristae. Interrenal chromaffin cells are interspersed among the tissue layer created by this cell type." - - "FBbt:00005219" - "Epithelial progenitor cell of the lung. Club cells are dome-shaped with short microvilli but no cilia. They function to protect the bronchiolar epithelium. Club cells also multiply and differentiate into ciliated cells to regenerate the bronchiolar epithelium." "BTO:0004811 FMA:14119" + "A protein with core architecture consisting of a Peptidase family M1 domain (Pfam:PF01433)." "PIRSF:PIRSF005502" + "Any process that activates or increases the frequency, rate or extent of detection of mechanical stimulus involved in sensory perception of touch." + "The process whose specific outcome is the progression of the gonadal mesoderm over time, from its formation to the mature structure. The gonadal mesoderm is the middle layer of the three primary germ layers of the embryo which will go on to form the gonads of the organism." + "The regulated release of norepinephrine by a cell, in which the norepinephrine acts as a neurotransmitter." + "A protein that is a translation product of the human LAMP5 gene or a 1:1 ortholog thereof." "An elongated, spindle-shaped, cell that is located between the basal lamina and the plasmalemma of a muscle fiber. These cells are mostly quiescent, but upon activation they divide to produce cells that generate new muscle fibers." - "An epithelial cell of the large intestine." "BTO:0004297 FMA:256157" - "A basal cell that is part of the epithelium of esophagus." "FMA:70731" - "A cell that secretes motilin, a gastric hormone that at low pH inhibits gastric motor activity, whereas at high pH has a stimulating effect." - "A CD8alpha alpha positive gamma-delta intraepithelial T cell that does not express a TCR partially encoded by the Vgamma5 gene segment." - "A CD4-positive, CD8-negative thymocyte that expresses high levels of the alpha-beta T cell receptor and is CD69-positive." - "The reproductive cell in multicellular organisms." "WBbt:0006796 VHOG:0001534 BTO:0000535" - "An alpha-beta T cell expressing NK cell markers that is CD1d restricted and expresses specific V-alpha chains. NK T cells of this type recognize the glycolipid alpha-galactosylceramide in the context of CD1d." - "A differentiated T cell with ability to traffic to peripheral tissues and is capable of mounting a specific immune response." - "Neuron that secretes the neurotransmitter galanin." - "An intestinal crypt stem cell that is located in the anorectum." - "Any cell in the compound eye, a light sensing organ composed of ommatidia." "PMID:12021768 GOC:pr" - "A short lived plasma cell that secretes IgE." - - "Obsolete. Use PO:0020090 from Plant Ontology instead. OBSOLETED, use term from Plant Ontology. A cell containing the two polar nuclei which, after double fertilization, will develop into the endosperm." - "MERGED DEFINITION: TARGET DEFINITION: A columnar cell of the colon that is part of the epithelium proper of large intestine. SOURCE DEFINITION: An enterocyte that is part of the epithelium proper of large intestine." "FMA:263112 FMA:263090" - "A cell type that secretes 5-Hydroxytryptamine (serotonin)." - "A muscle cell that is part of the posterior internodal tract." "FMA:223280" - - "CD115-positive monocyte is a monocyte that is CD115-positive and CD11b-positive." - - "A progenitor cell committed to the megakaryocyte and erythroid lineages." - "A CD4-positive, alpha-beta T cell with the phenotype CCR7-negative, CD45RA-positive." - "Female germ cell is a germ cell that supports female gamete production." "ncithesaurus:Egg VHOG:0001530 MA:0000388" + "Any process that activates or increases the frequency, rate or extent of protein catabolic process in the vacuole." + "Any process that activates or increases the frequency, rate or extent of isotype switching." + "The pattern specification process that results in the subdivision of an axis or axes of the neural plate in space to define an area or volume in which specific patterns of cell differentiation will take place or in which cells interpret a specific environment." + "The chemical reactions and pathways resulting in the breakdown of catechol-containing compounds. Catechol is a compound containing a pyrocatechol nucleus or substituent." + "Any process that modulates the frequency, rate, or extent of an antimicrobial humoral response." + "The multiplication or reproduction of Schwann cells, resulting in the expansion of their population. Schwann cells are a type of glial cell in the peripheral nervous system." + "White matter that lies deep to the granular cell layer of the cerebellar cortex. It contains afferents to the cerebellar cortex and axons that run between the cerebellar cortex and the deep cerebellar nuclei." "NLXANAT:20081249" + "The transport of a protein driven by polymerization of a microtubule to which it is attached." + "A gland that is part of a stomodeum." "VHOG:0000658" + "Any process that modulates the frequency, rate, or extent of interleukin-10 production." + "The regulated release of cerebrospinal fluid (CSF) from the choroid plexus of the lateral, third and fourth ventricles. The cerebrospinal fluid is a clear liquid that located within the ventricles, spinal canal, and subarachnoid spaces." + "Anatomical region that surrounds the otic vesicle." "EMAPA:16670 EHDAA2:0001343 XAO:0004474" + "A portion of lymphoid tissue that is part of a thymus [Automatically generated definition]." "MA:0002673 NCIT:C38515 UMLS:C1515429 EMAPA:37766 MESH:D013950" + "Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hexose stimulus." "A connective tissue cell of the nucleus pulposus cell of intervertebral disc." - "A hematopoietic multipotent progenitor cell that is CD34-positive, CD38-negative, CD45RA-negative, and CD90-negative." + "The process that gives rise to the cerebellar Purkinje cell layer. This process pertains to the initial formation of a structure from unspecified parts. The Purkinje cell layer lies just underneath the molecular layer of the cerebellar cortex. It contains the neuronal cell bodies of the Purkinje cells that are arranged side by side in a single layer. Candelabrum interneurons are vertically oriented between the Purkinje cells. Purkinje neurons are inhibitory and provide the output of the cerebellar cortex through axons that project into the white matter. Extensive dendritic trees from the Purkinje cells extend upward in a single plane into the molecular layer where they synapse with parallel fibers of granule cells." + "The process in which a relatively unspecialized cell acquires specialized features of a glomerular parietal epithelial cell. Glomerular parietal epithelial cells are specialized epithelial cells that form tight junctions as a barrier to protein transport." + "A cell cycle process by which the cell nucleus divides as part of a meiotic cell cycle in the male germline." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of aldosterone." "Gr1-low non-classical monocyte that has high surface expression of a MHC-II complex." - "A type of monocyte characterized by low expression of CCR2, low responsiveness to monocyte chemoattractant CCL2/MCP1, low phagocytic activity, and decrease size relative to classical monocytes, but increased co-stimulatory activity. May also play a role in tissue repair." - "A P/D1 enteroendocrine cell that is Grimelius positive and stores bombesin-like polypeptide." - "A myeloblast committed to the neutrophil lineage. This cell type is GATA-1 positive, C/EBPa-positive, AML-1-positive, c-myb-positive and has low expression of PU.1 transcription factor." - "A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Form the myelin insulation of nervous pathways, guide neuronal migration during development, and exchange metabolites with neurons. Neuroglia have high-affinity transmitter uptake systems, voltage-dependent and transmitter-gated ion channels, and can release transmitters, but their role in signaling (as in many other functions) is unclear." - "An epithelial cell of the intestine." + "Any process that stops, prevents or reduces the frequency, rate or extent of myeloid dendritic cell chemotaxis." + "The process in which a relatively unspecialized cell acquires specialized features of a glial cell in a lateral line nerve." + "Anatomical cluster that forms the floor and sidewalls of the middle part of the cranium." "XAO:0003174 AAO:0010207 TAO:0000290 ZFA:0000290" + "Any process that stops, prevents or reduces the frequency, rate or extent of lymphoid progenitor cell differentiation." + "The process whose specific outcome is the progression of the salivary gland over time, from its formation to the mature structure. Salivary glands include any of the saliva-secreting exocrine glands of the oral cavity." "A S. pombe mating type determined by the mat1-Mc and mat1-Mi on the mat1 locus." - "A neuron that laterally connects other neurons in the inner nuclear layer of the retina." "BTO:0004120" - "An ecto-epithelial cell of the prostate gland that secretes hormones." "FMA:74390 FMA:86774 CALOHA:TS-1280" - "An epithelial cell of the esophageal cardiac gland that occurs both in the proximal and distal esophagus, within the lamina propia." "FMA:256143" - "Mature CD8_alpha-low Langerhans cell is a CD8_alpha-low Langerhans cell that that is CD80-high, CD86-high, MHCII-high and is CD83-positive." - "A type I vestibular sensory cell that is part of the epithelium of macula of utricle of membranous labyrinth." "FMA:263188" + "An anatomical cavity that surrounded_by a blood vessel." "SCTID:91747007 FMA:312610" + "The directed movement of substances (e.g. macromolecules, small molecules, ions) through the blood-brain barrier." + "The series of events required for an organism to receive a gustatory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Gustation involves the direct detection of chemical composition, usually through contact with chemoreceptor cells. This is a neurological process." "Wikipedia:Taste" + "The process whose specific outcome is the progression of the pronephric nephron over time, from its formation to the mature structure. A pronephric nephron is the functional unit of the pronephros." + "Any process that decreases the rate, frequency, or extent of cartilage development, the process whose specific outcome is the progression of the cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate." "An otic fibrocyte that underlies the spiral prominence and is part of a mesenchymal gap junction network that regulates ionic homeostasis of the endolymph." + "Any process that activates or increases the frequency, rate or extent of the regulated release of epinephrine." "An IgG memory B cell is a class switched memory B cell that is class switched and expresses IgG on the cell surface." - "A class switched memory B cell is a memory B cell that has undergone Ig class switching and therefore is IgM-negative on the cell surface. These cells are CD27-positive and have either IgG, IgE, or IgA on the cell surface." - - "A natural killer cell that is developmentally mature and expresses a variety of inhibitory and activating receptors that recognize MHC class I and other stress related molecules." - - "A peptide hormone secreting cell that secretes androgen binding protein." - "FBbt:00003219" - - "A conidium that has only one nucleus." "FAO:0000025" - "Any basket cell that is part of a Ammon's horn." - - "KUPO:0001094" - "A rapidly proliferating population of cells that differentiate from stem cells of the intestinal crypt of the small intestine. Stem cells located in the crypts of Lieberkühn give rise to proliferating progenitor or transit amplifying cells that differentiate into the four major epithelial cell types. These include columnar absorptive cells or enterocytes, mucous secreting goblet cells, enteroendocrine cells and paneth cells." - "KUPO:0001135" - "An epithelial cell of the lung." "BTO:0004299" - "KUPO:0001068" - "A NK1.1-positive T cell that is Ly49D-negative." + "One of three main pairs of arteries and their branches, which irrigate the cerebrum of the brain." "NCIT:C12691 SCTID:181308008 UMLS:C0007770 MA:0002562 EMAPA:18613 AAO:0010493 CALOHA:TS-0126 XAO:0000367 EHDAA:5294 GAID:484 BTO:0005205 EHDAA2:0000233 Wikipedia:Cerebral_artery MESH:D002536" + "The smooth stratified squamous epithelium that covers the outer surface of the cornea." "EFO:0001917 FMA:58263 ZFA:0001683 TAO:0002187 UMLS:C0459875 MESH:D019573 GAID:895 SCTID:368825001 EMAPA:17162 Wikipedia:Corneal_epithelium BTO:0000287 NCIT:C12928 MA:0001243 CALOHA:TS-0173 EHDAA2:0000319" + "The process in which the anatomical structures of the embryonic heart tube are generated and organized. The embryonic heart tube is an epithelial tube that will give rise to the mature heart." + "Any process that activates or increases the frequency, rate or extent of cardiac conduction." + "A vascular endothelial growth factor receptor 2 that is encoded in the genome of mouse." "UniProtKB:P35918" + "Any process that modulates the frequency, rate or extent of thyroid hormone generation." + "The process controlling the activation and/or rate at which relatively unspecialized cells acquire specialized features. Any process that modulates the rate, frequency or extent of the XXX at a consistent predetermined time point during its development." + "Any protein degradation process, occurring at a presynapse, that regulates synaptic transmission." + "Any process that modulates the frequency, rate, or extent of interleukin-2 production." "An epithelial cell scattered in the cortex, predominant in the outer cortex with a large pale nucleus and a prominent nucleolus." "FMA:72210" - "A hair cell of the ear that contains the organs of balance and hearing." - "A cell whose nucleus, or nuclei, each contain more than two haploid genomes." - - "Interstitial dendritic cell is a conventional dendritic cell that is CD11b-positive, CD1a-positive, CD206-positive, CD209-positive, and CD36-positive." - "Cell of the intestinal epithelium with a brush border made up of many parallel packed microvilli; associated with absorption, particularly of macromolecules." - - "A cell in the hilum of the ovary that produces androgens." "FMA:18710" - "A group 3 innate lymphoid cell in the human with the phenotype IL-7Ralpha-positive." - "A muscle cell that is part of the atrioventricular node." "FMA:67106" - "A smooth muscle cell of the coronary artery." - "An intratelencephalic-projecting glutamatergic with a soma located in upper L5 of the primary motor cortex. These cells have thin untufted apical dendrites." "ILX:0770174" - "A specialized epithelial cell involved in sensory perception. Restricted to special sense organs of the olfactory, gustatory, and vestibulocochlear receptor systems; contain sensory cells surrounded by supportive, non-receptive cells." "BTO:0004301" + "Complex labyrinthine structure that comprises sensory endorgans specialized for vestibular, auditory, and acoustico-vestibular sensation." "Wikipedia:Internal_ear MA:0000237 AAO:0000238 BTO:0000630 MAT:0000145 EHDAA:504 GAID:871 SCTID:181189006 XAO:0000192 ZFA:0000217 NCIT:C12499 CALOHA:TS-0478 EFO:0001363 FMA:60909 EHDAA2:0000831 EMAPA:16194 galen:InnerEar MESH:D007758 TAO:0000217 BIRNLEX:1196 VHOG:0000284 EV:0100361 SCTID:304982002 UMLS:C1268973 MIAA:0000145 UMLS:C0022889" + "The process in which the anatomical structures of a lung lobe are generated and organized. A lung lobe is a projection that extends from the lung." + "Any process involved with the carrying out of an immune response by a B cell, through, for instance, the production of antibodies or cytokines, or antigen presentation to T cells." + + "The process of fusing together the edges of a craniofacial suture." + "A somite that is part of a tail." "EMAPA:16860 XAO:0003143 AAO:0010383" + "Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding." + "Any process that activates or increases the frequency, rate or extent of neutrophil degranulation." + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ammonium stimulus." + "EHDAA:8483 EHDAA2:0000431 EMAPA:17710" + "A disposition inhering in a tumour by virtue of the bearer's disposition to progress, invade surrounding tissues or metastasize." + "Any process that stops, prevents or reduces the frequency, rate or extent of acetylcholine-gated cation channel activity." "A pre-B cell that is pre-BCR-negative, and the kappa- and lambda- light immunoglobulin light chain-negative, CD43-low, and is BP-1-positive, CD45R-positive and CD25-positive. This cell type is also described as being AA4-positive, IgM-negative, CD19-positive, CD43-low/negative, and HSA-positive." - "A CD8-positive, CD4-negative thymocyte that expresses high levels of the alpha-beta T cell receptor and is CD69-positive." - "An IgD-positive CD38-positive IgG memory B cell is a CD38-positive IgG-positive class switched memory B cell that has class switched and expresses IgD on the cell surface with the phenotype IgD-positive, CD38-positive, and IgG-positive." - "A myocardial endocrine cell that is part of the septal division of left branch of atrioventricular bundle." "FMA:263180" - - "A cell that constitutes the luminal layer of epithelium of prostatic duct." "FMA:74225" - "A mesothelial cell that is part of the anterior chamber of eyeball." "FMA:70615" - - "CD4-positive, alpha-beta T cell that produces IL-22." - "An endocranial viscerocranial mucosa cell that is part of viscerocranial mucosa." "FMA:70629" - - - "A secretory cell that discharges its product without loss of cytoplasm." - "A flattened epithelial cell of mesenchymal origin that lines the serous cavity." "FMA:66773" - "A chromaffin cell of the adrenal medulla that produces norepinephrine." "FMA:69321" - "An epithelial supporting cell located in the cochlea." "FMA:79796" - - "Skeletogenic cell that has the potential to develop into a chondroblast; and arises from neural crest, meseosdermal and notochordal and connective tissue cells." - "A tissue-resident macrophage of the reticuloendothelial system found on the luminal surface of the hepatic sinusoids involved in erythrocyte clearance. Markers include F4/80+, CD11b-low, CD68-positive, sialoadhesin-positive, CD163/SRCR-positive. Irregular, with long processes including lamellipodia extending into the sinusoid lumen, have flattened nucleus with cytoplasm containing characteristic invaginations of the plasma membrane (vermiform bodies); lie within the sinusoid lumen attached to the endothelial surface; derived from the bone marrow, form a major part of the body's mononuclear phagocyte system." "BTO:0000685 FMA:14656" - "KUPO:0001133" - "Obsolete. Consult Plant Ontology instead. OBSOLETED, not defined prior to obsoletion." - "A promyelocyte that is considerably smaller, with more condensed chromatin, and nucleoli are no longer conspicuous." "FMA:83534" - "A renal intercalated cell that secretes base and reabsorbs acid in the coritcal collecting duct to mantain acid/base balance." - "A non-terminally differentiated cell that differentiates into a xanthophore." - "A intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layers L2/3-6" - "Skeletogenic cell that has the potential to form an odontoblast, deposits predentine, and arises from a cranial neural crest cell." - "An epithelial cell found in the basal part of the intestinal glands (crypts of Lieberkuhn) including the appendix. Paneth cells synthesize and secrete lysozyme and cryptdins. Numerous in the deeper parts of the intestinal crypts, particularly in the duodenum, rich in zinc, contain large acidophilic granules, with irregular apical microvilli and prominent membrane-bound vacuoles containing matrix." "FMA:62897 BTO:0000993" - "A bipolar neuron found in the retina and having connections with photoreceptors cells and neurons in the inner half of the inner plexiform layer. These cells depolarize in response to light stimulation of their corresponding photoreceptors." - "A columnar chondrocyte that differentiates in the late embryonic growth plate of bone. Columnar chondrocytes vigorously proliferate and form columns in the growth plate." - "A naive B cell is a mature B cell that has the phenotype surface IgD-positive, surface IgM-positive, CD20-positive, CD27-negative and that has not yet been activated by antigen in the periphery." - "An interneuron that has Martinotti morphology. These interneurons are scattered throughout various layers of the cerebral cortex, sending their axons up to the cortical layer I where they form axonal arborization." "nifext_55 ILX:0107375" + "A bistratified amacrine cell with a small dendritic field. Flat bistratified amacrine cells have post-synaptic terminals both on the border of S1 and S2, and on the border of S3 and S4. This cell type releases the neurotransmitter glycine." + "Subdivision of skeletal system that surrounds and protects the brain. Includes the skull base, sensory capsules and the central part of the skull roof." "ZFA:0001580 Wikipedia:Neuroranium FMA:53672 XAO:0003170 TAO:0001580 MA:0000317 SCTID:361731002" + "A preadipocyte that is part of a perirenal fat tissue." + "The chemical reactions and pathways involving amino acids of the serine family, comprising cysteine, glycine, homoserine, selenocysteine and serine." + "Any process that contributes to cytokine production by a mast cell." + "A basement membrane that is part of a nephron tubule." "SCTID:245251000 NCIT:C49273 EMAPA:37490 UMLS:C1709901 MA:0001680" + "An immune response mediated by immunoglobulins, whether cell-bound or in solution." + "A tunica media that is part of a vein." "EV:0100033 SCTID:42049001 EMAPA:36309 FMA:14354" + "An epithelium that consists of columnar epithelial cells. Columnar epithelia are epithelial cells whose heights are at least four times their width. Columnar epithelia are divided into simple (or unilayered), and the rarer stratified (or multi-layered).[WP, modified]." "Wikipedia:Columnar_epithelium" + "Any process that contributes to cytokine production by a CD4-positive, alpha-beta T cell." + "The process that gives rise to the adrenal cortex. This process pertains to the initial formation of a structure from unspecified parts. The adrenogonadal primordium from which the adrenal cortex is formed derives from a condensation of coelomic epithelial cells (the urogenital ridge; the same structure from which gonads and kidney also originate)." + "A hemoglobin subunit beta-1 that is encoded in the genome of mouse." "UniProtKB:P02088" + "The minute canals that pass the prostatic secretions to the urethra." "SCTID:362276000 MA:0002785 Wikipedia:Prostatic_ducts UMLS:C0227965 NCIT:C13102 FMA:19580 EMAPA:36568" + "NLXANAT:20090405" + "The process in which a relatively unspecialized endothelial cell acquires specialized features of an arterial endothelial cell, a thin flattened cell that lines the inside surfaces of arteries." "A T cell that expresses an alpha-beta T cell receptor complex." - - "Obsolete. Use PO:0000353 from Plant Ontology instead. Cell in exodermis or endodermis that remains thin walled when the associated cells develop thick secondary walls. Has casparian strip in endodermis." - "A long, spindle-shaped supporting cells arranged in parallel rows that secretes components of the tectorial membrane and potassium ions into the endolymph." "FMA:79797" - "An ecto-epithelial cell of the paranasal region of the viscerocranial mucosa." "FMA:70578" - "A fully differentiated plasma cell that secretes IgA." - - "A resting mature B cell that has the phenotype IgM-positive, IgD-positive, CD23-positive and CD21-positive, and found in the B cell follicles of the white pulp of the spleen or the corticol areas of the peripheral lymph nodes. This cell type is also described as being CD19-positive, B220-positive, AA4-negative, CD43-negative, and CD5-negative." - "A GABAergic neuron located in the cerebral cortex that expresses Lamp5" "ILX:0770149" + "Primordial follicles are indiscernible to the naked eye and develop to primary, secondary, and finally mature vesicular follicles." "NCIT:C33400 EMAPA:30755 MA:0001710 UMLS:C1514441" "A cell that has a filiform extrusion of the cell surface." "XAO:0000031 VHOG:0001532" - "A specialized cardiomyocyte that transmit signals from the AV node to the cardiac Purkinje fibers." - "An enterocyte that is part of the epithelium of crypt of lieberkuhn of small intestine." "FMA:263094" - "KUPO:0001093" "A GABAergic interneuron located in the cerebral cortex that expresses Parvalbumin." "ILX:0770154" - "CD4-positive, alpha-beta memory T cell with the phenotype CCR7-positive, CD127-positive, CD45RA-negative, CD45RO-positive, and CD25-negative." - "A lymphocyte that is part of a Peyer's patch. These cells have a major role in driving the immune response to antigens sampled from the intestinal lumen, and in regulating the formation of follicle-associated epithelium and M cells in Peyer's patches by converting intestitial enterocytes into M cells." - "A glutamatergic motor neuron with a soma in the brainstem or cerebral cortex. They do not synapse directly to muscles but rather to lower motor neurons, which do. They are the main controllers of voluntary movement." - "KUPO:0001134" + "A somatostatin that is encoded in the genome of mouse." "UniProtKB:P60041" + "The process in which a monoatomic cation is transported across a membrane. Monatomic cations (also called simple cations) are positively charged ions consisting of exactly one atom." + "EMAPA:18646 MA:0002227" + "A pericyte cell located in the kidney interstitium." "KUPO:0001104" + "Any process that modulates the frequency, rate or extent of retrograde dense core granule transport." "A germline cell that contributes to the development of the oocyte by transferring cytoplasm directly to oocyte." "FBbt:00004878 BTO:0000953" "Osteoblast that is non-terminally differentiated and located in cellular bone tissue or under the periosteum in acellular bone." "VSAO:0000117" - "Any hair follicle dermal papilla cell that is part of a scalp." - "A serous secreting cell that is part of the epithelium of bronchus." "FMA:263080" - "A langerin-negative lymph node dendritic cell that is CD103-negative and CD11b-low." - "A CD4-positive, CXCR5-positive, CCR7-negative alpha-beta T cell located in follicles of secondary lymph nodes that expresses is BCL6-high, ICOS-high and PD1-high, and stimulates follicular B cells to undergo class-switching and antibody production." + "The process in which the anatomical structures of the right cardiac ventricle muscle are generated and organized." + "A tooth row that is part of a skeleton of lower jaw." "EHDAA2:0001029 FMA:55635" + "Any process that modulates the frequency, rate or extent of isotype switching." + "The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph]." "Wikipedia:Vertebrate_trachea NCIT:C12428 MA:0000441 BTO:0001388 EHDAA2:0002066 XAO:0000118 EMAPA:16853 EHDAA:3078 MIAA:0000137 MAT:0000137 AAO:0010140 CALOHA:TS-1060 EV:0100040 MESH:D014132 SCTID:181213009 GAID:361 UMLS:C0040578 VHOG:0000371 FMA:7394 EFO:0000935" + "A thymus lobe that is in the left side of a thymus." "FMA:71195 RETIRED_EHDAA2:0000964 SCTID:188079002" "Any animal cell containing pigment granules." - - "A splenic macrophage found in the marginal zone of the spleen, involved in recognition and clearance of particulate material from the splenic circulation. Markers include F4/80-negative, MARCO-positive, SR-A-positive, SIGN-R1-positive, and Dectin2-positive." - "A mature B cell that has the phenotype CD1d-positive and expresses interleukin-10. This cell type has been associated with suppression of chronic inflammatory responses and T cell responses." - "A double-positive thymocyte that is large (i.e. has a high forward scatter signal in flow cytometry) and is actively proliferating." - "Immature dermal dendritic cell is a dermal dendritic cell that is CD80-low, CD86-low, and MHCII-low." - "An innate lymphoid cell in the human with the phenotype CD34-negative, CD117-positive, and a precusor to NK cells, ILC2 cells, and ILC3 cells." - "A cell found in the embryo before the formation of all the gem layers is complete." - "BTO:0004402" - "A progesterone secreting cell in the corpus luteum that develops from theca cells." "FMA:18690 BTO:0002850" - "FBbt:00001789" - "A non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. They develop from specialized myoblasts (smooth muscle myoblast)." "BTO:0004576 FMA:14072 CALOHA:TS-2159" - "An epithelial cell of the cortical portion of the thymus. Epithelial cells in this region are required for positive selection of CD8-positive T cells." "BTO:0004562" - - "A CD24-negative CD38-negative IgG-negative memory B cell is a CD38-negative IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype CD24-negative, CD38-negative, and IgG-negative." - "A disseminated nephrocyte is a nephrocyte that filters hemolymph and is found at scattered locations in the fat body or other tissues." - "KUPO:0001131" + "Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies." "MESH:D007107 UMLS:C0020962 NCIT:C12735 FMA:9825 SCTID:362590003 AAO:0011003 VHOG:0001247 Wikipedia:Immune_system MA:0002711 BILA:0000104 ZFA:0001159 XAO:0003152 GAID:328 BTO:0005810 TAO:0001159" + "Any process that activates or increases the frequency, rate or extent of endothelial cell chemotaxis." + "Translation that occurs at the presynapse, and that modulates chemical synaptic transmission." + "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the mesenchymal cells of the renal system as it progresses from its formation to the mature state." + "An anatomical wall that is part of an aorta, enclosing the luminal space." "MA:0002901 FMA:14156 EMAPA:35139" + "An amacrine cell with a wide dendritic field, dendrites in S3, and post-synaptic terminals in S3. Dendrites of this cell type are straight and minimally branched." + "Any process that activates or increases the frequency, rate or extent of lymphocyte activation." + "An epithelial sheet is a flat surface consisting of closely packed epithelial cells." + "An anatomical wall that is part of a small intestine [Automatically generated definition]." "MA:0002696 EMAPA:35785 NCIT:C33573 FMA:14615 UMLS:C1519375" + "Subcutaneous adipose tissue that is located in the abdominal region." "CALOHA:TS-2406" + "Any process that activates or increases the frequency, rate or extent of B cell activation." + "GC_ID:1" + "The chemical reactions and pathways resulting in the breakdown of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus." "An elicited macrophage characterized by low production of pro-inflammatory and Th1 polarizing cytokines and high expression of arginase-1, and associated with tissue remodelling." + "The endothelial lining of the endocardium." "FMA:83596" "Any Golgi cell that is part of a cerebellum." - "A macrophage that suppresses immune responses." - "Olfactory epithelial support cell is a columnar cell that extends from the epithelial free margin to the basement membrane of the olfactory epithelium. This cell type has a large, vertically, elongate, euchromatic nucleus, along with other nuclei, forms a layer superficial to the cell body of the receptor cell; sends long somewhat irregular microvilli into the mucus layer; at the base, with expanded end-feet containing numerous lamellated dense bodies resembling lipofuscin of neurons." "FMA:62302" - "Any chondrocyte that is part of the tracheobronchial tree." - - "Glandular cell of mammary epithelium. Example: glandular cells of large and intermediate ducts, glandular cells in terminal ducts." "CALOHA:TS-1272" - "A CD4-positive, alpha-beta T cell that has the phenotype T-bet-positive, CXCR3-positive, CCR6-negative, and is capable of producing interferon-gamma." "FMA:84382 BTO:0001678" - "A neuroblast derived from a neural crest cell." - "A smooth muscle cell of the intestine." - - "A parathyroid chief cell that is actively secreting hormone. Have large Golgi complexes with numerous vesicles and small membrane-bound granules; secretory granules are rare, cytoplasmic glycogen sparse, much of the cytoplasm being occupied by flat sacs of granular endoplasmic reticulum in parallel arrays; in normal humans, inactive chief cells outnumber active chief cells in a ratio of 3-5:1" "FMA:69082" - - "An intermediate monocyte that is CD14-positive and with low amounts of CD16." - - - "An unswitched memory B cell is a memory B cell that has the phenotype IgM-positive, IgD-positive, CD27-positive, CD138-negative, IgG-negative, IgE-negative, and IgA-negative." - "A myoepithelial cell that is part of the quarternary lactiferous duct." "FMA:74503" - "An oblong or round asexual spore formed from conidial chains." "FAO:0000042 BTO:0000127" - "OBSOLETE (was not defined before being made obsolete)." - "A glial cell that ensheaths multiple small diameter axons in the peripheral nervous system. The non-myelinating Schwann cell is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has a basal lamina. Cells can survive without an axon present. These cells can de-differentiate into immature Schwann cells." - "KUPO:0001132" - "KUPO:0001056" + "The single layer of epithelial cells that lines the early neural tube and develops into the nervous system and into the neural crest cells." + "Any process that activates or increases the frequency, rate or extent of myeloid dendritic cell chemotaxis." + "An open tracheal system is a respiratory system, a branched network of epithelial tubes that supplies oxygen to target tissues via spiracles. An example of this is found in Drosophila melanogaster." "TADS:0000043 SPD:0000427 BTO:0003870" + "Dermal, epidermal, glandular and pigment structures of the body integument." + "The change in morphology and behavior of a myeloid dendritic cell resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor, leading to the initiation or perpetuation of an immune response." + "The process in which anatomical structures of the mammary gland cord are generated and organized. Mammary gland cords form when the mammary gland bud invades the mammary fat." + "The process in which neuroblasts acquire specialized structural and/or functional features that characterize the mature Lugaro cell. Differentiation includes the processes involved in commitment of a neuroblast to a Lugaro cell fate. A Lugaro cell is an inhibitory GABAergic interneuron found in the cerebellar cortex." + "The series of molecular signals initiated by a ligand the binding to its receptor on the surface of a cell, which contributes to the progression of the heart over time." + "A protein that is a translation product of the human CD59 gene, a 1:1 ortholog thereof, or pro-orthologs thereof." "PIRSF:PIRSF038782" + "Subdivision of the skeletal system which consists of the axial skeleton plus associated joints." "FMA:7483" + "A physical quality inhering in a bearer by virtue of the bearer's parts having the arrangement which exhibits characteristics of solids." + "Any process that stops, prevents, or reduces the frequency, rate or extent of megakaryocyte differentiation." + "The process in which a relatively unspecialized precursor cell acquires the specialized features of a follicular dendritic cell." + "A transparent homogeneous acellular layer, 6 to 9 um thick, lying between the basal lamina of the outer layer of stratified epithelium and the substantia propria of the cornea; it is considered to be a basement membrane." "UMLS:C0229127 TAO:0002155 NCIT:C32226 MA:0001240 Wikipedia:Bowman%27s_membrane ZFA:0001684 FMA:58273 SCTID:281075003" + "The multiplication or reproduction of cells, resulting in the expansion of a cell population." "A tissue-resident macrophage found in a secondary lymphoid organ." - "A sensory neuron of the spinal nerve that senses body position and sends information about how much the muscle is stretched to the spinal cord." - "A keratinocyte of the epidermis that is characterized by containing granules of keratohyalin and lamellar granules." "FMA:70543" - "A myeloid dendritic cell found in the blood that is CD1c-positive." - "Obsolete. Use PO:0000273 from Plant Ontology instead. A cell composing the xylem." - "KUPO:0001065" - "A type D cell of the small intestine." "FMA:268736" - "A goblet cell that is part of the small intestine." "FMA:86929" - - "An enterocyte that is part of the epithelium proper of small intestine." "FMA:263096" - "Any interneuron that is part of a spinal cord ventral column." - - "A specialized cell involved in auditory sensory perception." + "The process leading to shortening and/or development of tension in the urinary bladder smooth muscle tissue involved in the expulsion urine from the body." + + "A cytotoxic T-lymphocyte protein 4 that is encoded in the genome of mouse." "UniProtKB:P09793" - "A phagocytic cell formed by the fusion of macrophages, occurs in chronic inflammatory responses to persistent microorganism such as M.tuberculosis, component of granulomas. Sometimes used to refer to megakaryocytes." "FMA:83035 BTO:0003107" - "A NK1.1-positive T cell that is CD94-negative." - "Cells of the uterine chorion that acquire specialized structural and/or functional features that characterize chorionic trophoblasts. These cells will migrate towards the spongiotrophoblast layer and give rise to syncytiotrophoblasts of the labyrinthine layer." - - "A smooth muscle of the internal thoracic artery." - "BTO:0002051" - "An enteroendocrine cell commonest in the duodenum and jejunum, rare in ileum, that secretes cholecystokinin. This cell type is involved in the regulation of digestive enzymes and bile." "FMA:62937" - "A myoepithelial cell that is part of the dilatator pupillae." "FMA:70619" - "KUPO:0001118" - "A large binucleate cell that forms a 'garland' around the anterior end of the proventriculus (cardia) at its junction with the esophagus in both adults and larvae flies. Each cell is surrounded by a basement membrane and there are numerous micro-invaginations (lacunae) extending from the surface into the cytoplasm. At the mouth of each lacuna is a doubled filament forming a specialised filtration system (diaphragm). The filtrate is endocytosed from the lacunae." "FBbt:00005059 BTO:0004596" - "An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds." "CALOHA:TS-0864 BTO:0001173" - "A conventional thymic dendritic cell that is CD8alpha-positive." - "A CD4-positive, CD25-positive, alpha-beta T cell that regulates overall immune responses as well as the responses of other T cell subsets through direct cell-cell contact and cytokine release." - "A B cell that is mature, having left the bone marrow. Initially, these cells are IgM-positive and IgD-positive, and they can be activated by antigen." - - "An epithelial cell of the kidney cortex." "KUPO:0001016" - "A mouse GABAergic cell located in the marmoset cerebral cortex that expresses meis2." - "An epithelial cell of the medullary thymus. This cell type expresses a diverse range of tissue-specific antigens. This promiscuous gene expression is a cell-autonomous property of medullary epithelial cells and is maintained during the entire period of thymic T cell output." "BTO:0004563" - - "Any keratinocyte that is part of a hair follicle." + "A depression or fissure in the surface of an organ." "Wikipedia:Sulcus_(anatomy)" + "A synapse in which an action potential in the presynaptic cell increases the probability of an action potential occurring in the postsynaptic cell." "Wikipedia:Excitatory_synapse" + "The paired arteries that carry blood to the yolk sac from the dorsal aorta." "EHDAA2:0002208 Wikipedia:Vitelline_arteries EMAPA:16207" + "Any developmental process that results in the creation of defined areas or spaces within the kidney to which cells respond and eventually are instructed to differentiate." + "Epithelium that derives from the mesoderm. [Automatically generated definition]." "FMA:86452" + "A structure found in the red pulp of the spleen between the sinusoids, consisting of fibrils and connective tissue cells with a large population of monocytes and macrophages. These cords contain half of the human body's monocytes as a reserve so that after tissue injury these monocytes can move in and aid locally sourced monocytes in wound healing. Erythrocytes pass through the cords of Billroth before entering the sinusoids. The passage into the sinusoids may be seen as a bottleneck, where erythrocytes need to be flexible in order to pass through. In disorders of erythrocyte shape and/or flexibility, such as hereditary spherocytosis, erythrocytes fail to pass through and get phagocytosed, causing extravascular hemolysis." "UMLS:C0735011 Wikipedia:Cords_of_Billroth NCIT:C33599 FMA:16031 MA:0002671 EMAPA:37752" + "Any process that modulates the frequency, rate or extent of megakaryocyte differentiation." + "A cartilage element of chondrocranium. Example: neurocranial trabecula." "TAO:0001461 ZFA:0001461 EFO:0003690" + "A pyramidal neuron with a soma found in the hippocampus." "SAO:sao131261273 NIFSTD:sao131261273" + "The directed movement of a motile cell or organism in response to an external stimulus." "Wikipedia:Taxis" + "EHDAA:8363 EHDAA2:0000456 FMA:312597 EMAPA:18023" + "The biological process whose specific outcome is the progression of the lung epithelium from an initial condition to its mature state. This process begins with the formation of lung epithelium and ends with the mature structure. The lung epithelium is the specialized epithelium that lines the inside of the lung." + "The chemical reactions and pathways involving epinephrine, a hormone produced by the medulla of the adrenal glands that increases heart activity, improves the power and prolongs the action of muscles, and increases the rate and depth of breathing. It is synthesized by the methylation of norepinephrine." + "An amacrine cell that uses GABA as a neurotransmitter." + "The process in which a relatively unspecialized cell acquires specialized features of a lung goblet cell. A goblet cell is a cell of the epithelial lining that produces and secretes mucins." "A dermal dendritic cell isolated from skin draining lymph nodes that is langerin-positive, MHC-II-positive, and CD4-negative and CD8a-negative." - "A reticulocyte that is Ly76-high and is Kit-negative." - - "A mature CD8-positive, CD4-negative alpha-beta T cell found in the thymus that is CD24-low and has high expression of the T cell receptor." - "OBSOLETE: A classification of cells by the organisms within which they are contained." + "Mesenchyme that is part of a pharyngeal arch 6." "FMA:318209 EMAPA:32765 EHDAA2:0004076" + "The specialized, terminal region of a neuron projection such as an axon or a dendrite." + "A process in which a protein is transported to, or maintained in, a location within a postsynaptic membrane." "A primordial germ cell is a diploid germ cell precursors that transiently exist in the embryo before they enter into close association with the somatic cells of the gonad and become irreversibly committed as germ cells." "FMA:70567" - "KUPO:0001130" - "A cell which moves among different tissues of the body, via blood, lymph, or other medium." - "OBSOLETE: A cell of the lymphoid series that can react with antigen to produce specific cell products called antibodies. Various cell subpopulations, often B cells, can be defined, based on the different classes of immunoglobulins that they synthesize." - "A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns." "BTO:0000902 WBbt:0003675 BTO:0000888 CALOHA:TS-2032 FBbt:00005074 FMA:67328" - "Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes." "CALOHA:TS-0688 BTO:0000130 FMA:62860" - "Immature CD11c-negative plasmacytoid dendritic cell is a CD11c-negative plasmacytoid dendritic cell is CD80-negative, CD86-low and MHCII-low." - "A lower motor neuron that innervates only intrafusal muscle fibers. Unlike the alpha motor neurons, gamma motor neurons do not directly adjust the lengthening or shortening of muscles but function in adjusting the sensitivity of muscle spindles and in keeping muscle spindles taut, thereby allowing the continued firing of alpha neurons." "SAO:143800623 MESH:D009047 FMA:83660" - "A pyramidal neuron which has an apical tree which is oriented parallel to the pia. This is unlike typical pyramidal neurons which have its apical dendrite aligned vertically." + "The morphogenetic process in which a bud forms from an epithelial sheet. A bud is a protrusion that forms form the sheet by localized folding." + "Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body." "MAT:0000032 EMAPA:17213 EHDAA:5047 MESH:D012863 XAO:0004053 MIAA:0000032 SCTID:361378004 VSAO:0000026 GAID:177 MA:0003006 galen:Skeleton AEO:0000168 FMA:23875 EHDAA2:0001843 Wikipedia:Skeleton" + "The process in which a relatively unspecialized T cell acquires the specialized features of a T-helper 1 (Th1) cell. A Th1 cell is a CD4-positive, alpha-beta T cell that has the phenotype T-bet-positive and produces interferon-gamma." + "Any process that stops, prevents or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteoglycans, any glycoprotein in which the carbohydrate units are glycosaminoglycans." + "A G4 retinal ganglion cell that has post sympatic terminals in sublaminar layers S3 and S4 and is depolarized by illumination of its receptive field center." + "A quality inhering in a bearer by virtue of the whether the bearer differs from normal or average." + "Any process that stops, prevents, or reduces the rate or extent of endothelial cell proliferation." + "GC_ID:1" + "GC_ID:1" + "Anatomical cluster which give rise to mature mesonephric nephrons. Zebrafish continously generate new mesonephric nephrons." "ZFA:0005584" + "The chemical reactions and pathways resulting in the breakdown of ADP, adenosine 5'-diphosphate." + "Any cellular process that results in the specification, formation or maintenance of polarized microtubule-based cytoskeletal structures." + "Any process that modulates the frequency, rate or extent of bone development." + "Wall of organ which has as its parts the endocardium, myocardium , epicardium, and the cardiac septum, surrounded by the pericardial sac proper and is continuous with the walls of the systemic and pulmonary arterial and venous trees." "FMA:7274" - - "A cell that moves by its own activities." - "A CD8-positive, alpha-beta T cell that has the phenotype CXCR3-negative, CCR6-negative." - "A preadipocyte that is capable of differentiating into a brown adipocyte. This cell type expresses uncoupling protein-1, PPAR-gamma, PR-domain-containing 16; and PGC-1alpha (peroxisome proliferator-activated receptor-gamma (PPARgamma) coactivator-1alpha)." - "A supporting cell of the anterior pituitary gland involved in trophic and catabolic processes; expresses a broad spectrum of cytokeratins indicative of their epithelial nature." "FMA:83102" - "An enteroendocrine cell which produces a gastrin- and cholecystokinin-like peptide. The apical microvilli-rich plasma membrane is in open contact with the small intestine mucosa. This cell type is devoid of gastrin-17 but contains other fragments of the gastrin polypeptide." "FMA:63421" + "A shape quality inhering in a bearer by virtue of the bearer's being such that every part of the surface or the circumference is equidistant from the center." + "Any process that modulates the frequency, rate or extent of hemopoiesis." + "An epithelium that is part of a bronchus [Automatically generated definition]." "NCIT:C32231 UMLS:C0599333 MA:0001839 EMAPA:32691 FMA:67782 CALOHA:TS-1240 BTO:0001845 EFO:0000307" "A megakaryocyte progenitor cell that is Kit-positive, CD41-positive, CD9-positive, Sca-1-negative, IL7ralpha-negative, CD150-negative, and Fcgamma receptor II/III-low." - "A hematopoietic stem cell of the placenta. This cell type is first observed E10.5 This cell type may give rise to fetal liver hematopoietic stem cells." + "The process aimed at the progression of a cardiac glial cell over time, from its formation to the fully functional mature cell." "A glandular epithelial cell of the esophagus." "FMA:86548" - "A tissue-resident macrophage found in the alveoli of the lungs. Ingests small inhaled particles resulting in degradation and presentation of the antigen to immunocompetent cells. Markers include F4/80-positive, CD11b-/low, CD11c-positive, CD68-positive, sialoadhesin-positive, dectin-1-positive, MR-positive, CX3CR1-negative." "BTO:0000802 CALOHA:TS-0030 FMA:83023" - "Obsolete. Use PO:0020094 from Plant Ontology instead. The female gamete of plants." - "An epithelial cell of the kidney." "KUPO:0001019" - "A T cell which regulates overall immune responses as well as the responses of other T cell subsets through direct cell-cell contact and cytokine release." "FMA:84070 BTO:0004520" - "A DN2 thymocyte that is Kit-low." - "KUPO:0001080" + "Any process that modulates the frequency, rate or extent of smooth muscle contraction." + "The process in which the egg becomes metabolically active, initiates protein and DNA synthesis and undergoes structural changes to its cortex and/or cytoplasm." "Wikipedia:Egg_activation" + + "The increase in heart capillaries that accompanies physiological hypertrophy of cardiac muscle." "A CD4-positive, alpha-beta T cell that has cytotoxic function." + "Any process that stops, prevents or reduces the frequency, rate or extent of T-helper 1 cell cytokine production." + "The part of the retina that contains neurons and photoreceptor cells[GO]." "EMAPA:17171 EHDAA:4763 EHDAA2:0001253 AAO:0011095 MA:0000277 TAO:0000046 VHOG:0000535 FMA:58628 CALOHA:TS-0685 XAO:0003216 NCIT:C33166 EMAPA:18590 BTO:0000929 ZFA:0000046 UMLS:C1518263" + "A cell at the front of a migrating epithelial sheet." + "Replacement ossification wherein bone tissue replaces cartilage." "Wikipedia:Endochondral_ossification" + "A lymphoid follicle containing naive B cells." "FMA:55223" + "The directed movement of proteins along microtubules in neuron projections." + "The process in which a relatively unspecialized cell acquires specialized features of a smooth muscle cell of the prostate glandular acinus." + "A protein that is a translation product of the human SELL gene or a 1:1 ortholog thereof. It is a leukocyte adhesion receptor that play an important role in regulating the inflammatory response by mediating leukocyte tethering and rolling on adherent leukocytes." "PIRSF:PIRSF002421" + "Serous membrane layer that is adjacent to and lines an organ." "FMA:15860" + "Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding." + "Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." "Reactome:R-HSA-265682" + "The process that modulates the force with which blood travels through the systemic arterial circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure." + "Any process that stops, prevents or reduces the frequency, rate or extent of outer hair cell apoptotic process." + + "A strand of hair that is part of a pinna." + "A portion of organism substance that is secreted by a male reproductive gland." "MA:0002521 EMAPA:36541" + "A fibroblast that is part of the connective tissue of prostate." "FMA:261271" + + "A neuroendocrine cell found in the epithelium of the lungs and respiratory tract. This cell type is rounded or elliptical in shape, situated mainly in the basal part of the epithelium; regulates bronchial secretion, smooth muscle contraction, lobular growth, ciliary activity and chemoreception. Cell has an electron-lucent cytoplasm, contains numerous dense-cored vesicles with a clear halo between the core and the limiting membrane." "FMA:14118" + "Any process that stops, prevents, or reduces the frequency, rate or extent of cholinergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter acetylcholine." + "A cellular layer of the dentate gyrus enclosed by the granule cell layer. A number of cell types are located in the polymorphic layer but the most prominent is the mossy cell." "MBA:10704 BIRNLEX:4128 EMAPA:35280 neuronames:2123 BAMS:PoDG MA:0002864 BAMS:po NLX:42439" + "Any process that modulates the frequency, rate or extent of multiplication or reproduction of fibroblast cells." + "A change in the morphology or behavior of a myeloid cell resulting from exposure to an activating factor such as a cellular or soluble ligand, leading to the initiation or perpetuation of an immune response." + + "Any process that modulates the frequency, rate or extent of neural crest cell differentiation." + "A mucous membrane that lines the mouth." "FMA:59660 EMAPA:26937 BTO:0002860 NCIT:C77637 UMLS:C0026639 Wikipedia:Oral_mucosa MESH:D009061 MA:0002794 GAID:951 CALOHA:TS-0716" + "A cathepsin K that is encoded in the genome of mouse." "UniProtKB:P55097" + "One of sublaminar layers S1, S2, S3, or S4." "CP:0001046" + "Combining with a neurotransmitter and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex." + "Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine." "ZFA:0001338 WBbt:0005772 EV:0100071 MA:0000328 CALOHA:TS-0490 BTO:0000648 ANISEED:1235303 AAO:0000246 MESH:D007422 EMAPA:32874 VHOG:0000056 SCTID:256876008 Wikipedia:Intestine TAO:0001338 NCIT:C12736 BSA:0000093 FMA:7199 MIAA:0000043 galen:Intestine XAO:0000129 MA:0001524 UMLS:C0021853 EFO:0000834 GAID:295" + "The gonad of a female organism which contains germ cells." "AAO:0000371 SCTID:181464007 EV:0100111 MESH:D010053 BSA:0000080 Wikipedia:Ovary ZFA:0000403 BTO:0000975 MA:0000384 GAID:367 VHOG:0000251 EFO:0000973 CALOHA:TS-0730 EHDAA2:0001360 MIAA:0000125 FMA:7209 NCIT:C12404 EMAPA:17962 TAO:0000403 XAO:0000258 BILA:0000125 EHDAA:8124 UMLS:C0029939" + "Any process that activates or increases the frequency, rate or extent of mesenchymal cell apoptotic process." + "A specialized type of CD4 positive T cell, the follicular helper T cell (TFH cell), that upregulates CXCR5 expression to enable its follicular localization. These specialised T cells reside in the germinal center of the lymph node." + "Any process that activates or increases the frequency, rate or extent of histamine secretion by mast cell." + "A tooth that is on the roof of the mouth." + "An MHC class II histocompatibility antigen alpha chain that is a translation product of the human HLA-DRA gene or a 1:1 ortholog thereof." + "The cavity within a myotome." "EMAPA:31134 VHOG:0001283" + "The deepest layer of the epidermis, which is composed of dividing stem cells and anchoring cells." "TAO:0001180 ZFA:0001180 Wikipedia:Stratum_germinativum MA:0000803 FMA:67540 SCTID:419481005 AAO:0010598 XAO:0000041 NCIT:C33623 NCIT:C33466 EMAPA:32779 BTO:0000438 UMLS:C0221925" + "Any process that decreases the frequency, rate, or extent of monocyte chemotaxis." + "Glandular cell of exocrine pancreas epithelium. Example: pancreatic acinar cell, glandular cells in pancreatic canaliculi, glandular cells in pancreatic ducts." "CALOHA:TS-1242 BTO:0000028" + "A bone that is part of a forelimb region. Examples: humerus, any of the phalanges. Counter-example: scapula (a bone of the pectoral girdle). Note that we consider the forelimb to end at the shoulder." "MESH:D001133 NCIT:C12983 UMLS:C0003793 SCTID:368532003 GAID:178" + "A horizontal cell with a small cell body, thin dendrites, and small dendritic arbor." + "A cellular quality inhering in a bearer by virtue of the bearer's number of homologous sets of chromosomes in the nucleus or primary chromosome-containing compartment of the cell, each set essentially coding for all the biological traits of the organism." + "The process in which the anatomical structure of the vagus nerve is generated and organized. This nerve is primarily sensory but also has visceromotor components. It originates in the brain stem and controls many autonomic functions of the heart, lungs, stomach, pharynx, larynx, trachea, esophagus and other gastrointestinal tract components. It controls some motor functions such as speech. The sensory branches mediate sensation from the pharynx, larynx, thorax and abdomen; it also innervates taste buds in the epiglottis." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a gravitational stimulus." + "The part of the hindlimb between pelvis and the knee, corresponding to the femur." "EHDAA:6200 MA:0000052 EMAPA:17499 EFO:0001943 FMA:24967 CALOHA:TS-2039 EHDAA:5171 MESH:D013848 VHOG:0000349 UMLS:C0039866 NCIT:C33763 galen:Thigh EHDAA2:0002130 Wikipedia:Thigh BTO:0001376 SCTID:302544002 GAID:50" + "Any process that modulates the rate, frequency or extent of mast cell differentiation, the process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a mast cell. A mast cell is a cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation." + "The connective tissue bundles in the extracellular matrix of aorta tissue that are composed of collagen, and play a role in tissue strength and elasticity." + "A smooth muscle cell that is part of the large intestine." "FMA:15653" + "Any process that activates or increases the frequency, rate or extent of microglial cell activation." + "A mucosa that is part of a biliary tree [Automatically generated definition]." "FMA:14695" + "A pluripotent cell in the yolk sac that can give rise to mesenchymal cells including erythrocytes and endothelial cells." "MESH:D055018" + + "The chemical reactions and pathways resulting in the breakdown of organic and inorganic nitrogenous compounds." + "A protein that is a translation product of the human CD27 gene or a 1:1 ortholog thereof." "IUPHARobj:1876 PIRSF:PIRSF001966" + "A mesentery that surrounds the heart." "VHOG:0000353 EHDAA:432 RETIRED_EHDAA2:0000739 EMAPA:16212" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the depolymerization of the specialized microtubules of the axoneme." + "The small saphenous vein (also lesser saphenous vein), is a relatively large vein of the superficial posterior leg. [WP,unvetted]." "galen:LesserSaphenousVein FMA:44333 SCTID:181404009 NCIT:C33546 Wikipedia:Small_saphenous_vein BTO:0003272 EMAPA:37187 UMLS:C0226827 MA:0002217" + "A lymph node that is part of a forelimb." "SCTID:276155004 FMA:44311" + "Any process that increases the rate, frequency, extent of the regulated release of somatostatin from secretory granules in the D cells of the pancreas." + + "An anatomical structure that has some part that develops from the neural crest." + "A taste receptor cell that is part of a taste bud of a tongue." + "The brain ventricles or their associated choroid plexuses." + "A B220-low CD38-negative unswitched memory B cell is a CD38-negative unswitched memory B cell that has the phenotype B220-low, CD38-negative, IgD-positive, CD138-negative, and IgG-negative." + "The head of a long bone that articulates with a neighboring skeletal element and is separated from the shaft by the epiphyseal plate until bone growth stops. At that time, the plate disappears and the head and shaft are united[MESH,modified]." "MESH:D004838 UMLS:C1708734 FMA:24012 SCTID:244701002 NCIT:C52722 EMAPA:35508 BTO:0000413 MA:0001362 NCIT:C32529 AAO:0000742 Wikipedia:Epiphysis" + "Any process that stops, prevents or reduces the frequency, rate or extent of synaptic vesicle exocytosis." + "The widest and most dilatable part of the male urethra canal which runs almost vertically through the prostate from its base to its apex, lying nearer its anterior than its posterior surface; this portion of the urethral canal is spindle-shaped, being wider in the middle than at either extremity, and narrowest below, where it joins the membranous portion; it is lined by transitional epithelium and contains in its posterior wall, or floor, the orifices of the prostatic utricle, ejaculatory ducts, and prostatic ducts, collectively known as the seminal colliculus (aka verumontanum)." "NCIT:C13101 MA:0002646 FMA:19673 SCTID:279434009 BTO:0003163 UMLS:C0458450 EMAPA:30942 Wikipedia:Prostatic_urethra" + "FMA:17692" + "A region of the forebrain consisting of the caudate nucleus, putamen and fundus striati.[GO]." "BM:N ncithesaurus:Striatum neuronames:225 BAMS:Str NCIT:C111122 PBA:10080 DMBA:15851 EFO:0000109 BTO:0000418 BAMS:STR MESH:D017072 BAMS:Striatum HBA:4277 FMA:83683 MA:0000891 EMAPA:17549 MBA:477 Wikipedia:Striatum DHBA:10333 BIRNLEX:1672 FMA:77618 UMLS:C0162512" + "Any process that stops, prevents or reduces the frequency, rate or extent of dendritic cell differentiation." + "An auditory epithelial support cell that surrounds the nerve fibers and synapses of the auditory inner hair cells." "FMA:79801" + "A pia mater that is part of a telencephalon [Automatically generated definition]." "MA:0000982 EHDAA2:0001992 EMAPA:17777 VHOG:0000476" + + "The process in which a precursor cell type acquires the specialized features of a CD8-positive, alpha-beta regulatory T cell." + "Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP]." "MAT:0000452 VHOG:0001367 MA:0000212 ZFA:0000160 EMAPA:18215 HBA:9002 BTO:0003388 BIRNLEX:1200 neuronames:491 TAO:0000160 SCTID:362392007 BAMS:MTg DHBA:12195 EFO:0000921 Wikipedia:Midbrain_tegmentum UMLS:C0039441 EHDAA2:0004475 FMA:62393 XAO:0004271" + "The series of events involved in the perception of pain in which a chemical stimulus is received and converted into a molecular signal." + "CALOHA:TS-1295 EMAPA:37447 VHOG:0000005 FMA:242787" + + "Any muscle organ that is part of a thorax [Automatically generated definition]." "MA:0000561" + "Any process that activates or increases the frequency, rate or extent of mesenchymal cell proliferation involved in ureter development." + "A protein that is a translation product of the human PDCD1 gene or a 1:1 ortholog thereof." "PIRSF:PIRSF018380 IUPHARobj:2760" + "Any process that modulates the frequency, rate or extent of cell killing, the process in which a cell brings about the death of another cell, either in the same or a different organism." + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving glucocorticoids." + "A scapula endochondral element that is composed primarily of cartilage tissue." "EMAPA:18343 EHDAA2:0001777 EHDAA:8368 VHOG:0001125" + "Any process that stops, prevents, or reduces the rate of mast cell degranulation." + "A cell that is part of an interstitial compartment of an inner renal medulla." "KUPO:0001093" + + "Mesenchyme that develops_from a neural crest and is part of a 1st arch mandibular mesenchyme." "EHDAA2:0000037" + "Presumptive structure of the blastula that will develop into mesoderm." "EFO:0003467 AAO:0000476 TAO:0001377 ZFA:0001377" + "An endothelial cell that is part of a placenta." "EFO:0010708" + "FMA:70506 SCTID:360629008 UMLS:C1182571 NCIT:C32837" + "A cone whose sensitivity measurements have an average spectral peak of 358.2 nm. These cones are described in rat." "BAMS:1029" + "Any process that activates or increases the frequency, rate or extent of the transport of proteins from the Golgi to the plasma membrane." + "Portion of tissue that gives rise to the lens." "ZFA:0001679 VHOG:0001163 EMAPA:17163 TAO:0002205 EHDAA2:0000983 EHDAA:4737 SCTID:361510002" + "The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant." "Wikipedia:Embryogenesis" + "The series of events required for an organism to receive a sensory light stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process." + "A specialized fibroblast found in the medulla of lymph node." + "A retinal neural layer that is immediately adjacent to the inner nuclear layer and comprises 20 percent of the inner plexiform layer of retina." "CP:0000113" + "A metaphysis that is part of a fibula." "FMA:33745" + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond." + "Any process that modulates the frequency, rate or extent of T cell differentiation in the thymus." + "The process whose specific outcome is the progression of the embryo over time, from zygote formation through syncytial blastoderm to the hatching of the first instar larva. An example of this process is found in Drosophila melanogaster." + "The regulated release of juvenile hormones, the three sesquiterpenoid derivatives that function to maintain the larval state of insects at molting and that may be required for other processes, e.g. oogenesis." + "A bistratifed retinal ganglion cell that has small, symmetric dendritic fields that terminate in S1 and S4-S5." + "FMA:259905" + "A GABAergic inhibitory neuron that is derived from the midbrain." + "Any process that stops, prevents or reduces the frequency, rate or extent of glutamate receptor signaling pathway." + "A platelet glycoprotein Ib alpha chain that has been processed by proteolytic cleavage." + "The process in which the anatomical structures of a limb joint are generated and organized. A limb joint is a flexible region that separates the rigid sections of a limb to allow movement in a controlled manner." + "The human equivalent of a DN4 thymocyte." + "A CSF-1/PDGF receptor-type tyrosine-protein kinase that is a translation product of the human KIT gene or a 1:1 ortholog thereof." "IUPHARobj:1805 PIRSF:PIRSF500951" + "Any process that stops, prevents, or reduces the rate of production of oxytocin." + "A developmental process, independent of morphogenetic (shape) change, that is required for the trigeminal nerve to attain its fully functional state. The trigeminal nerve is composed of three large branches. They are the ophthalmic (V1, sensory), maxillary (V2, sensory) and mandibular (V3, motor and sensory) branches. The sensory ophthalmic branch travels through the superior orbital fissure and passes through the orbit to reach the skin of the forehead and top of the head. The maxillary nerve contains sensory branches that reach the pterygopalatine fossa via the inferior orbital fissure (face, cheek and upper teeth) and pterygopalatine canal (soft and hard palate, nasal cavity and pharynx). The motor part of the mandibular branch is distributed to the muscles of mastication, the mylohyoid muscle and the anterior belly of the digastric. The mandibular nerve also innervates the tensor veli palatini and tensor tympani muscles. The sensory part of the mandibular nerve is composed of branches that carry general sensory information from the mucous membranes of the mouth and cheek, anterior two-thirds of the tongue, lower teeth, skin of the lower jaw, side of the head and scalp and meninges of the anterior and middle cranial fossae." + "The process whose specific outcome is the progression of the mammary gland epithelium over time, from its formation to the mature structure. The mammary gland is a large compound sebaceous gland that in female mammals is modified to secrete milk." + "A trans-acting T-cell-specific transcription factor GATA-3 that is encoded in the genome of mouse." "UniProtKB:P23772" + "Any process that activates or increases the frequency, rate or extent of lymphocyte migration." + "The process in which a relatively unspecialized cell acquires specialized features of a bipolar cell, the last neuron to be generated in the retina." + "Movement of organelles or other particles along actin filaments, or sliding of actin filaments past each other, mediated by motor proteins." + "Any process that modulates the frequency, rate or extent of sporulation, the process whose specific outcome is the progression of a spore over time, from its initiation to the mature structure." + "A process in which a protein is transported to, or maintained in, the cell periphery." + "Any cellular process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids." + "Any process resulting in the physical partitioning and separation of an epidermal cell, any of the cells making up the epidermis, into daughter cells." + "The assembly of actin filament bundles; actin filaments are on the same axis but may be oriented with the same or opposite polarities and may be packed with different levels of tightness." + "A mesenchymal cell found in the developing heart and that develops into some part of the heart. These cells derive from intra- and extra-cardiac sources, including the endocardium, epicardium, neural crest, and second heart field." + "The middle colic vein drains the transverse colon. It is a tributary of the superior mesenteric vein, and follows the path of its corresponding artery, the middle colic artery. [WP,unvetted]." "SCTID:9018004 MA:0002181 EMAPA:37174 Wikipedia:Middle_colic_vein FMA:15406" + "FAO:0000032 BTO:0002307" + + "Muscle (organ) which is a part of the abdomen. Examples: external oblique, rectus abdominis." "UMLS:C0000739 GAID:89 Wikipedia:Abdominal_muscle FMA:9620 MA:0000520 SCTID:361352008 EMAPA:35103 NCIT:C32040 MESH:D000009 BTO:0001261" + "Any process that decreases the frequency, rate or extent of astrocyte activation." + "GC_ID:1" + "The neurons that innervate the esophagus, stomach, small and large bowel." "EMAPA:37479 MA:0001145" + "Astrocyte-like radial glial cell that extends vertically throughout the retina, with the nucleus are usually in the middle of the inner nuclear layer." "BTO:0003064" + "A megakaryocyte cell with is CD9-positive and CD41-positive." + "A cylindrical shape quality inhering in a bearer by virtue of the bearer's being imperfectly cylindrical or approximately cylindrical." + "FMA:225251 SCTID:297287005" + "A double negative thymocyte that has a T cell receptor consisting of a gamma chain that has as part a Vgamma3 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-positive. This cell-type is found in the fetal thymus with highest numbers occurring at E17-E18." + "A smooth muscle cell that is part of a bronchiole." + "A monostratified retinal ganglion cell with small to medium soma and small to medium dendritic field." + "An L-selectin that is encoded in the genome of human." "UniProtKB:P14151" + "The developmental process pertaining to the initial formation of the metanephros." + "The process in which the anatomical structures of the soma are generated and organized." + "A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact." + "A developing anatomical structure that has the potential to develop into a myelencephalon." "EHDAA2:0000640" + "A Boettcher cell is a polyhedral cells on the basilar membrane of the cochlea, and is located beneath Claudius cells. A Boettcher cell is considered a supporting cell for the organ of Corti, and is present only in the lower turn of the cochlea. These cells interweave with each other, and project microvilli into the intercellular space. Because of their structural specialization, a Boettcher cell is believed to play a significant role in the function of the cochlea. They demonstrate high levels of calmodulin, and may be involved in mediating Ca(2+) regulation and ion transport." + "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the mesangial cells of the kidney as it progresses from its formation to the mature state." + "Anatomical cavity bounded by the orbital region of the cranium and forming the location of some or all of the eye." "SCTID:280541000 FMA:84961 AAO:0000343 Wikipedia:Orbit_(anatomy) ZFA:0005558" + + "Any process that stops, prevents, or reduces the frequency, rate, or extent of glial cell apoptotic process." + "Any process that modulates the frequency, rate or extent of a response to stress. Response to stress is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." + "An alveolar duct that is part of a right lung [Automatically generated definition]." "MA:0001785 EMAPA:35819 UMLS:C1709958 NCIT:C49277" + "A synovial cell that is macrophage-like, characterized by surface ruffles or lamellipodia, plasma membrane invaginations and associated micropinocytotic vesicles, Golgi apparatus and little granular endoplasmic reticulum." "FMA:66787" + "A ring of smooth muscle cells whose contraction closes the opening of the ring." "EHDAA2:0003143 AEO:0000143 SCTID:362915001" + "The fluid surrounding the ovum and granulosa cells in the ovarian follicle." "UMLS:C1709369 FMA:18665 NCIT:C52556 GAID:372 Wikipedia:Follicular_fluid CALOHA:TS-0728 BTO:0004383 MESH:D015571 MA:0002511" + "A zone of skin that is part of a penis [Automatically generated definition]." "FMA:19638 SCTID:35900000 EMAPA:35675 MA:0002727" + + "Any process that stops, prevents, or reduces the frequency, rate or extent of the binding or confining calcium ions such that they are separated from other components of a biological system." + "A T-box transcription factor TBX21 that is encoded in the genome of human." "UniProtKB:Q9UL17" + "Any process that activates or increases the frequency, rate or extent of microvillus assembly." + "Any joint that connects a rib to another structure (or another rib). Examples: costochondral, costovertebral, interchondral, sternocostal joints." "FMA_RETIRED:64994 MA:0001508 NCIT:C49575 UMLS:C1261194 SCTID:263314001" + "Any process that activates or increases the frequency, rate or extent of cell proliferation involved in outflow tract morphogenesis." + "The process in which the thymus epithelium is generated and organized." + "Any process that increases the rate, frequency, or extent of the directed movement of calcium ions into a cell or organelle." + "A CD2 molecule that is encoded in the genome of human." "UniProtKB:P06729" + "Any process that modulates the frequency, rate or extent of male gonad development." + "Any process that modulates the occurrence or rate of cell death by apoptotic process in neurons." + "The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell, any of the cells making up an epithelium." + "Any melanocyte that is part of a prepuce of penis." + "An epithelial cell that is part of the lacrimal canaliculus." "FMA:70553" + "OBSOLETE: A sporangiospore that is motile, having flagella." "FAO:0000039" + "The multiplication or reproduction of endothelial cells, resulting in the expansion of a cell population. Endothelial cells are thin flattened cells which line the inside surfaces of body cavities, blood vessels, and lymph vessels, making up the endothelium." + "Any process that modulates the frequency, rate or extent of trophoblast cell migration." + "A lamina propria that is part of a duodenum." "FMA:15972 MA:0003209 EMAPA:27255" + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines." + "Any process that stops, prevents or reduces the frequency, rate or extent of cardiac myofibril assembly." + "Any process that modulates the frequency, rate or extent of tendon cell differentiation." + "A Martinotti cell morphology that inheres in neurons which have axons that form a fan-like plexus." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of smooth muscle cell apoptotic process." + "Any process that activates or increases the frequency, rate or extent of muscle tissue development." + "Any process that activates or increases the frequency, rate or extent of epidermal cell differentiation." + "A cell that is part of a kidney." "KUPO:0001010" + "Any process that stops, prevents, or reduces the frequency, rate, or extent of leukocyte activation." + "The assembly and organization of the sperm flagellar axoneme, the bundle of microtubules and associated proteins that forms the core of the eukaryotic sperm flagellum, and is responsible for movement." + "The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup[GO]. Portion of tissue that is comprised of neuroepitheium which has pinched off from the anterior neural keel and will form the optic cup[ZFA]." "SCTID:362864008 NCIT:C34236 FMA:293357 TAO:0000050 UMLS:C0231106 EMAPA:16540 XAO:0000228 Wikipedia:Optic_vesicles ZFA:0000050 AAO:0011039 VHOG:0000165 EHDAA2:0001320" + "Muscles of the upper chest. The term may refer to one of two muscles, the pectoralis major and pectoralis minor. The former is a thick muscle in the anterior portion of the chest. Its action involves flexion, medial rotation, and adduction of the humerus. The latter is a thin muscle located beneath the pectoralis major. Its action involves lowering the scapula and raising the ribs." "NCIT:C33286 MA:0002423 SCTID:181621006 AAO:0010727 MESH:D010369 UMLS:C0030747 GAID:153 CALOHA:TS-0751 FMA:37349 BTO:0000023 EMAPA:35670" + "Rostral segment of the hindbrain that has as its parts the pons (where present) and the cerebellum[WP,modified]." "BIRNLEX:965 DHBA:10655 Wikipedia:Metencephalon MESH:D020540 neuronames:543 EHDAA2:0001149 UMLS:C0376353 NCIT:C32741 GAID:594 EMAPA:17071 CALOHA:TS-2029 MA:0000197 EHDAA:5498 BTO:0000673 FMA:62003 VHOG:0000741 HBA:4833 UMLS:C1516904 BAMS:Met" + "The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development." + "A vertebra that is located in the cervical region of the vertebral column." "MA:0000311 SCTID:181820005 XAO:0003076 MESH:D002574 galen:CervicalVertebra NCIT:C12693 Wikipedia:Cervical_vertebrae FMA:9915 EMAPA:17674 GAID:235" + "The process whose specific outcome is the progression of a preganglionic parasympathetic fiber over time, from its formation to the mature structure. A preganglionic parasympathetic fiber is a cholinergic axonal fiber projecting from the CNS to a parasympathetic ganglion." + "Any process that activates or increases the frequency, rate or extent of gamma-delta T cell differentiation." + "Any process that activates or increases the frequency, rate, or extent of B cell cytokine production." + "Subdivision of head that consists of the upper jaw skeletal elements plus associated soft tissue (skin, lips, muscle)[cjm]." "SCTID:362636001 VHOG:0000454 EMAPA:17924 EHDAA2:0002118 ncithesaurus:Upper_Jaw Wikipedia:Upper_jaw EHDAA:8025 AAO:0000620 FMA:59399 EHDAA2:0004607" + "The series of events contributing to equilibrioception by which an organism senses the position, location, orientation, and movement of the body and its parts. Proprioception plays an important role in the ability of an organism to perceive its orientation with respect to gravity." + "Any process that stops, prevents or reduces the frequency, rate or extent of vesicle fustion with Golgi apparatus." + "Any process that increases the rate or frequency of platelet activation. Platelet activation is a series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue." + "Any process that modulates the frequency, rate or extent of neutrophil activation." + "Any process that modulates the frequency, rate or extent of astrocyte differentiation." + "A killer cell lectin-like receptor 3 that is encoded in the genome of mouse." "UniProtKB:Q64329" + "Any process that activates or increases the frequency, rate or extent of actin filament-based movement." + "Any process that modulates the frequency, rate or extent of myotome development." + "Any process that activates or increases the frequency, rate or extent of dendritic cell differentiation." + "Any process that activates or increases the frequency, rate or extent of protein localization to cilium." + "A (free) limb that is connected to a pelvic girdle region. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the pelvic girdle and its parts." "EHDAA:6094 NCIT:C77625 GAID:1221 GAID:38 EMAPA:17458 VHOG:0000337 EFO:0000883 AAO:0000219 FMA:24879 MIAA:0000395 XAO:0003031 MAT:0000395 galen:LowerExtremity CALOHA:TS-2215 NCIT:C12742 SCTID:182281004 MESH:D006614 EV:0100015 BTO:0002345 EHDAA2:0001033 MA:0000026 UMLS:C0023216 UMLS:C1522391 VSAO:0000150 Wikipedia:Hindlimb" + "Mature CD8_alpha-negative CD11b-negative dendritic cell is a CD8_alpha-negative CD11b-negative dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive." + "Any process that stops, prevents or reduces the frequency, rate or extent of synapse pruning." + "The orderly movement of a mesenchymal cell from one site to another that will contribute to the formation of a limb bud." + "A multicellular anatomical structure that is associated with an embryo and derived from the zygote from which it develops, but which does not contribute to the embryo proper or to structures that are part of the same organism after embryogenesis." "HAO:0000042 BILA:0000042 AAO:0010020 TAO:0000020 ZFA:0000020 CARO:0000042 SCTID:314908006 CALOHA:TS-2119 NCIT:C34055 UMLS:C1282438 XAO:0004005 VHOG:0000292 FMA:85537 EHDAA:46 EHDAA2:0003042 TGMA:0001843 AEO:0000042" + "A transitional stage B cell that expresses surface IgM and IgD, and CD62L. This cell type appears to be an anergic B cell that does not proliferate upon BCR signaling, is found in the spleen and lymph nodes, and has the phenotype surface IgM-positive, surface IgD-positive, CD21-positive, CD23-positive, CD62L-positive, and CD93-positive. This cell type has also been described as IgM-low, CD19-positive, B220-positive, AA4-positive, and CD23-positive (i.e. this cell-type is distinguished from T2 cells by surface expression of IgM)." + "A B-1 B cell that has the phenotype CD5-negative, but having other phenotypic attributes of a B-1 B cell." + "Combining with prolactin and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity." + "ZFA:0001073" + + "An anatomical cavity that surrounded_by a hindgut." "FMA:54367 EMAPA:18396" + + "The deposition or aggregation of coloring matter in a cell." + "Organism at the cleavage stage." "BILA:0000058" + "Any process that modulates the frequency, rate or extent of morphogenesis of an epithelium." + "A transitional population of migrating mesenchymal cells that derive from somites and that will become dermal cells." "AEO:0001017 EHDAA:1719 UMLS:C0180383 AAO:0011028 EHDAA:1731 EHDAA:1737 EHDAA:1725 NCIT:C61572 XAO:0000220 EMAPA:32838 FMA:295656 Wikipedia:Dermatome_(embryology) EHDAA2_RETIRED:0003428" + "Any process that modulates the frequency, rate, or extent of cytotoxic T cell degranulation." + "The section of the pharynx that lies above the soft palate." "Wikipedia:Nasopharynx NCIT:C12423 EMAPA:17670 MAT:0000447 MA:0000443 EHDAA:7086 EV:0100066 VHOG:0000375 EHDAA2:0001239 CALOHA:TS-0663 BTO:0000662 GAID:339 SCTID:181200003 UMLS:C0027442 MESH:D009305 FMA:54878" + "A muscle organ that has_muscle_insertion a occipital bone and has_muscle_origin a sternum." "UMLS:C1710196 MA:0002385 EMAPA:37702 NCIT:C53069" + "Any process that modulates the frequency, rate or extent of pancreatic A cell differentiation." + "A collagen alpha-1(I) chain that is encoded in the genome of mouse." "UniProtKB:P11087" + "The process in which the anatomical structures of venous blood vessels are generated and organized. Veins are blood vessels that transport blood from the body and its organs to the heart." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of T cell antigen processing and presentation." + "Any process that stops, prevents or reduces the frequency, rate or extent of microvillus assembly." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of mast cell cytokine production." + "The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds." "Wikipedia:Photosynthesis" + + "An extracellular matrix secreting cell that secretes glycocalyx." + "The cellular homeostatic process that preserves a muscle cell in a stable functional or structural state." + "Obsolete. Use PO:0000079 from Plant Ontology instead. An elongated cell with approximately wedge-shaped ends, found in the vascular cambium, which gives rise to the elements of the axial system in the secondary vascular tissues." + "The process of the coordinated growth and sprouting of lymph vessels giving rise to the organized lymphatic system." + "A vein that is part of a thoracic cavity [Automatically generated definition]." "EMAPA:37242 MA:0001903" + "Any process that activates or increases the frequency, rate or extent of calcium ion transmembrane transport." + "The process in which the cardiac atrium is generated and organized. A cardiac atrium receives blood from a vein and pumps it to a cardiac ventricle." + "A portion of the gut that is derived from ectoderm." + "A process in which a protein is transported to or maintained in a location within the somatodendritic compartment." + "A type EC enteroendocrine cell in the duodenum and jejunum that stores and secretes motilin and 5-hydroxytryptamine." "FMA:62941" + "The regulated release of catecholamine by a cell in which the catecholamine acts as a neurotransmitter." + "The progression of the sclerotome over time, from its initial formation to the mature structure. The sclerotome is the portion of the somite that will give rise to a vertebra." + "The small neuron in the glomerular layer of the olfactory bulb whose dendrites arborize within a glomerulus, where it receives synaptic input from olfactory receptor cell axon terminals, and also engages in dendrodendritic interactions with mitral and tufted cell dendrites; uses both GABA and dopamine as a neurotransmitter." "NIFEXT:122 BTO:0003796" + "A dorsal mesentery that is part of a midgut." "EMAPA:17040 RETIRED_EHDAA2:0001187 EMAPA:18671 EMAPA:16722 SCTID:361434009" + "The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine." "RESID:AA0039" + "Any process that stops, prevents or reduces the frequency, rate or extent of midbrain dopaminergic neuron differentiation." + "A blood vessel that is part of a tail [Automatically generated definition]." "EMAPA:35848 MA:0000695" + "A groove that is situated between the 2nd and 3rd pharyngeal arch." "EHDAA2:0000057 VHOG:0000972 VHOG:0000568 EHDAA:613 EMAPA:16396" + "A CD8-positive, alpha-beta positive T cell expressing GATA-3 and secreting IL-4." "FMA:84794 BTO:0004794" + "A respiratory bronchiole that is part of a right lung [Automatically generated definition]." "EMAPA:36637 MA:0001788 NCIT:C49285 UMLS:C1709960" + "Any fibroblast that is part of a cardiac ventricle." + "The exocytic fusion of neurotransmitter receptor containing vesicles with the postsynaptic membrane resulting in the integration of NT receptors, enabling them to participate in neurotransmitter reception. This process includes tethering and docking steps that prepare vesicles for fusion." + "The multiplication or reproduction of oligodendrocyte progenitor cells by cell division, resulting in the expansion of their population. Oligodendrocyte progenitors give rise to oligodendrocytes, which form the insulating myelin sheath of axons in the central nervous system." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of acetylcholine into a cell." + "Any process that modulates the rate, frequency, or extent of hair follicle placode formation, the developmental process in which a hair placode forms. An hair follicle placode is a thickening of the ectoderm that will give rise to the hair follicle bud." + "Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." + "The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands [GO]. An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin [ZFIN]." "ZFA:0000118 EHDAA2:0001471 Wikipedia:Pituitary_gland EV:0100132 XAO:0000017 GAID:457 EHDAA:2183 NCIT:C12399 AAO:0010536 EFO:0000857 BAMS:PIT UMLS:C0032005 TAO:0000118 MAT:0000077 MESH:D010902 VHOG:0000143 BTO:0001073 BAMS:Pit BIRNLEX:1353 CALOHA:TS-0798 MIAA:0000077 FMA:13889 EMAPA:35998 MA:0000176 BM:Die-Hy-HY neuronames:399 EHDAA:4477 DHBA:10505 SCTID:181125003 HBA:4634" + "Any process that modulates the frequency, rate or extent of the physical partitioning and separation of a cell into daughter cells." + "Any process that activates or increases the frequency, rate, or extent of a response to biotic stimulus." + "The process in which the structure of a glial cell in a lateral line nerve is generated and organized. This process occurs while the initially relatively unspecialized cell is acquiring the specialized features of a glial cell in a lateral line nerve." + "A mesenchymal stem cell that is part of the apical papilla tooth root." + "Any process that activates, maintains or increases the frequency, rate or extent of myotube differentiation. Myotube differentiation is the process in which a relatively unspecialized cell acquires specialized features of a myotube cell. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse." + "Any process that activates or increases the frequency, rate or extent of dendritic cell apoptotic process." + "The process in which the anatomical structures of a metanephric proximal tubule are generated and organized. The metanephric proximal tubule is a metanephric nephron tubule that connects Bowman's capsule to the descending thin limb of the loop of Henle in the metanephros. It has a brush border epithelial morphology." + "The part of a tooth that is implanted in the gum; the root is normally located below the neck of the tooth, covered by cementum rather than enamel, and attached by the periodontal ligament to the alveolar bone." "GAID:1280 FMA:55624 SCTID:245728004 MESH:D014092 EMAPA:37975" + "A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. This process occurs in the urinary bladder. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. The urinary bladder is a musculomembranous sac along the urinary tract." + "A portion of smooth muscle tissue that is part of a iris [Automatically generated definition]." "MA:0001270 BTO:0000655 EMAPA:35448 FMA:312338" + "A multi-fate stem cell that can give rise to different retinal cell types including rod and cone cells." + + "A kidney interstitium that is part of a right kidney." "FMA:74270" + "Long nephrons are associated with juxtamedullary glomeruli and extend to the inner medulla." "UMLS:C1517630 FMA:272054 NCIT:C32892" + "Any muscle organ that is part of a toe [Automatically generated definition]." "MA:0000648 EMAPA:37333" + "The process in which differentiating motor neurons in the neural tube acquire the specialized structural and/or functional features of lateral motor column neurons. Lateral motor column neurons are generated only on limb levels and send axons into the limb mesenchyme. Differentiation includes the processes involved in commitment of a cell to a specific fate." + "A ridge on the cerebral cortex. It is generally surrounded by one or more sulci ." "BTO:0002495 FMA:83874 neuronames:1211 Wikipedia:Gyrus NCIT:C32290 SCTID:279165009 UMLS:C0458308" + "Any process that stops, prevents or reduces the frequency, rate or extent of corticosteroid hormone secretion." + "A pigment cell that is capable of detecting light stimulus that is involved in visual perception." "FMA:63846" + "Any process that increases the rate, frequency, or extent of the controlled release of molecules that form the extracellular matrix, including carbohydrates and glycoproteins by a cell or a group of cells." + "Cytoplasm that exhibits affinity for both basic and acid stains under specific pH conditions." + "Squamous cell of vaginal epithelium." "CALOHA:TS-1254" + "An activated mature (naive or memory) B cell that is secreting immunoglobulin, typified by being CD27-positive, CD38-positive, CD138-negative." "FMA:84371" + "Any process that stops, prevents, or reduces the frequency, rate or extent of erythrocyte differentiation." + "Anatomical cavity that is the lumen of the skull and contains the brain." "MA:0003061 Wikipedia:Cranial_cavity SCTID:264452006 neuronames:2806 UMLS:C0230041 NCIT:C77638 FMA:9644 EMAPA:37497" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein." + "The production of blood cells from the larval lymph gland. The lymph gland consists of three to six bilaterally paired lobes that are attached to the cardioblasts during larval stages, and it degenerates during pupal stages." + "Fibrous connective tissue that surrounds cartilage." "Wikipedia:Perichondrium SCTID:11881003 TAO:0001643 EMAPA:35676 ZFA:0001634 BTO:0005089 XAO:0004049 MA:0003008 VSAO:0000036 AAO:0010445 FMA:75446" + "A branch of the vagus nerve that supplies motor function and sensation to the larynx (voice box). It travels within the endoneurium. It is the nerve of the 6th Branchial Arch." "MESH:D012009 FMA:6246 Wikipedia:Recurrent_laryngeal_nerve SCTID:24227007 GAID:804 AAO:0010754 VHOG:0001347" + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a superoxide stimulus. Superoxide is the anion, oxygen-, formed by addition of one electron to dioxygen (O2) or any compound containing the superoxide anion." + "A protein that is a translation product of the human ESR1 gene or a 1:1 ortholog thereof." "IUPHARobj:620" + "A hepatic vein that is part of a left lobe of liver." "MA:0003032 EMAPA:37164 SCTID:55188000 FMA:14339" + "A monostratified retinal ganglion cell with large soma and large dendritic field, with medium dendritic arbor, and has dendrites in layers 2 and 5." + "Epithelial cell that is part of segment 3 (S3) of the proximal tubule epithelium." + "A mucous secretion that is produced by glands in the epidermis." + "A glial cell that myelinates or ensheathes axons in the peripheral nervous system." "BTO:0001220 CALOHA:TS-0898 MESH:D012583" + "Any process that stops, prevents, or reduces the frequency, rate or extent of cell motility." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "A protein that is a translation product of the human CD209 gene or a 1:1 ortholog thereof." "IUPHARobj:2930" + "The movement of a mononuclear cell within or between different tissues and organs of the body." + "A chemokine receptor whose active form binds interleukin-8 with high affinity." "PIRSF:PIRSF501022" + "Binding to a vascular endothelial growth factor receptor 2." + "Any process that modulates the frequency, rate or extent of granulosa cell proliferation." + + "A caudal vertebra endochondral element that is composed primarily of a pre-cartilage condensation." "EMAPA:18045" + "A cell that specializes in controlled release of one or more substances." "FMA:86916 BTO:0003659" + "The biological process in which new individuals are produced by one or two multicellular organisms. The new individuals inherit some proportion of their genetic material from the parent or parents." + "EMAPA:17749 EHDAA2:0000340 EHDAA:6002" + "Any process that modulates the frequency, rate or extent of lactation." + "A gland that is part of a skin of body [Automatically generated definition]." "SCTID:110485007 EMAPA:35774 MA:0000146 FMA:71878" + "The developmental process by which a midbrain is generated and organized." + "Any process that activates or increases the frequency, rate or extent of natural killer cell death by apoptotic process." + "The chemical reactions and pathways resulting in the formation of gamma-aminobutyric acid (GABA, 4-aminobutyrate), an amino acid which acts as a neurotransmitter in some organisms." + "The process whose specific outcome is the progression of a collecting duct in the metanephros over time, from its formation to the mature structure. The collecting duct responds to vasopressin and aldosterone to regulate water, electrolyte and acid-base balance. The collecting duct is the final common path through which urine flows before entering the ureter and then emptying into the bladder." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the process of creating protein polymers." + "Any process that modulates the frequency, rate or extent of a respiratory system process, an organ system process carried out by any of the organs or tissues of the respiratory system." + "Muscular duct that propels urine from the kidneys to the urinary bladder, or related organs." "EV:0100097 SCTID:302511008 MIAA:0000120 AAO:0010254 MAT:0000120 FMA:9704 galen:Ureter EFO:0000930 EHDAA2:0002139 MESH:D014513 UMLS:C0041951 XAO:0000144 EMAPA:17950 Wikipedia:Ureter CALOHA:TS-1084 MA:0000378 VHOG:0000605 EHDAA:9341 BTO:0001409 NCIT:C12416 GAID:438" + "It ascends beneath the anterior margin of the trapezius, distributing branches to it, and to the neighboring muscles and lymph glands in the neck, and anastomosing with the superficial branch of the descending branch of the occipital artery." "FMA:10665 UMLS:C0226271 SCTID:161746006 Wikipedia:Superficial_part_of_transverse_cervical_artery MA:0002052 EMAPA:37117 NCIT:C53005" + "A resident monocyte that is Gr-1 high, CD43-negative, CX3CR1-negative, CD115-positive, and B220-negative." + "The process whose specific outcome is the progression of a nephric duct over time, from its initial formation to a mature structure. A nephric duct is a tube that drains a primitive kidney." + "A layer in the central nervous system that lines system of communicating cavities in the brain and spinal cord." "FMA:242770 EMAPA:35209" + + "Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of a protein from a cell." + "A sst GABAergic cortical interneuron that is both an interneuron and a projecting neuron. They are found in all layers from upper L2/3 down to the bottom of L6. They have long-range projections, some with axons fading into white matter. These cells have low rebound potential, low hyperpolarization sag, and high variability in membrane time constant." + "A classical monocyte that is CD14-positive, CD16-negative, CD64-positive, CD163-positive." + "RETIRED_EHDAA2:0000268 EMAPA:16342 EHDAA:1267" + "A cell type that can give rise to basophil and mast cells. This cell is CD34-positive, CD117-positive, CD125-positive, FceRIa-negative, and T1/ST2-negative, and expresses Gata-1, Gata-2, C/EBPa" + "One of the 5 distinct and partially overlapping functional domains of the premigratory neural crest. The vagal and sacral neural crest cells develop into the ganglia of the enteric nervous system, also known as the parasympathetic ganglia." "XAO:0004192" + "Any process that activates or increases the frequency, rate or extent of Schwann cell migration." + "Any sense organ (UBERON:6005155) that is part of some larval head (UBERON:6001730)." + "Any process that activates or increases the frequency, rate or extent of progesterone secretion." + "A protein that is a translation product of the human VPREB1 gene or a 1:1 ortholog thereof. The gene is recently and independently duplicated in mouse and rabbit, giving rise to very closely related VPREB2 genes in those species. The protein associates with the Ig-mu chain to form a molecular complex that is expressed only on the surface of pre-B-cells." "PIRSF:PIRSF038787" + "Any process that stops, prevents or reduces the frequency, rate or extent of establishment of protein localization." + "Any process that activates or increases the frequency, rate or extent of extracellular matrix organization." + "Any process that activates, maintains or increases the frequency, rate or extent of dopaminergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter dopamine." + "A forkhead box protein N1 that is encoded in the genome of mouse." "UniProtKB:Q61575" + "Any process that stops, prevents or reduces the frequency, rate or extent of morphogenesis of an epithelium." + "A C-C chemokine receptor type 6 that is encoded in the genome of mouse." "UniProtKB:O54689" + "The self-renewing division of a germline stem cell, to produce a daughter stem cell and a daughter germ cell which will divide to form one or more gametes." + "Combining with ADP and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex." + "The process whose specific outcome is the progression of the anterior lateral line ganglion over time, from its formation to the mature structure. The anterior lateral line ganglion develops from cranial ectodermal placodes situated between the eye and ear." + "The process in which a glial cell membrane closes around an axon in the central nervous system. This can be a myelinating or a non-myelinating neuron-glial interaction." + + "Binding to a lipid." + "The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space)." "Wikipedia:Nuclear_envelope" + "Trunk ganglion which is part of a bilaterally paired set of sympathetic ganglia located anterior and lateral to the spinal cord." "TAO:0001556 EHDAA:5635 EHDAA2:0001403 ZFA:0001556 Wikipedia:Paravertebral_ganglion SCTID:324478000 MA:0003100 FMA:5891" + "Any process that activates or increases the frequency, rate or extent of lysosome organization." + "A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring." + "A programmed cell death protein 1 that is encoded in the genome of human." "UniProtKB:Q15116" + "Any process that activates or increases the frequency, rate or extent of cell proliferation in midbrain." + "OBSOLETE: A cultured cell that has been passaged at least one time in culture." + "Any process that increases the rate, frequency or extent of mast cell chemotaxis. Mast cell chemotaxis is the movement of a mast cell in response to an external stimulus." + "A macromolecular complex containing separate protein and lipid molecules. Separate in this context means not covalently bound to each other." + "A cell whose primary function is to provide structural support, to provide strength and physical integrity to the organism." + "The aggregation, arrangement and bonding together of a set of components to form a junction between cells." + "A T cell that expresses a gamma-delta T cell receptor complex." + "The process whose specific outcome is the progression of the mesonephric connecting tubule over time, from its formation to the mature structure. The mesonephric connecting tubule is a tubular segment of the mesonephric nephron; it connects the distal tubule to the collecting duct in the mesonephros." + "A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component." + "OBSOLETE. Nucleus with two or more lobes connected by a thin filament that contains no internal chromatin. Examples include the nuclei of mature basophils, eosinophils and neutrophils in mice and humans." + "The developmental process by which a fibrous ring of heart is generated and organized." + "Any process that activates or increases the rate or extent of lipoprotein transport." + "Excretion that is the output of a kidney." "EMAPA:36554 CALOHA:TS-1092 BTO:0001419 MA:0002545 MESH:D014556 MIAA:0000058 FMA:12274 galen:Urine UMLS:C0042036 GAID:1189 NCIT:C13283 EFO:0001939 MAT:0000058 Wikipedia:Urine ENVO:00002047" + "A spiral ganglion neuron that innervates inner hair cells. Type 1 spiral ganglion neurons are myelinated and bipolar." + "The directed movement of a pigment granule to a specific location." + "The process in which a relatively unspecialized cell acquires the specialized features of an eye photoreceptor cell." + "The directed movement of RNA, deoxyribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + + "Any segmental subdivision of a nervous system. Includes metameric developmental segments, such as vertebrates neuromeres." + "Any process that activates or increases the frequency, rate or extent of animal organ morphogenesis." + "The expansion of a gamma-delta T cell population by cell division." + "A cell of the inner of the three germ layers of the embryo." "FMA:72555" + "Any process that stops, prevents or reduces the frequency, rate or extent of mitotic chromosome condensation." + "A process that is part of the meiotic cell cycle." + "A protein that is a translation product of the human RORC gene or a 1:1 ortholog thereof." "IUPHARobj:600" + "Any process that activates, maintains or increases the frequency, rate or extent of cardiac muscle tissue development." + "Subdivision of thorax which includes all structures from the skin to the costal pleura. Examples: There is only one chest wall." "NCIT:C62484 SCTID:181608004 FMA:50060 EMAPA:37233" + + "Binding to a macromolecular complex." + "The multiplication or reproduction of keratinocytes, resulting in the expansion of a cell population. Keratinocytes are epidermal cells which synthesize keratin and undergo a characteristic change as they move upward from the basal layers of the epidermis to the cornified (horny) layer of the skin." + "The part of the conceptus that may be lost before birth or will be discarded at birth, or when the embryo becomes an independent organism." "AEO:0000195 EHDAA2:0000003 EMAPA:16042" + "The enteric nervous system is composed of two ganglionated neural plexuses in the gut wall which form one of the three major divisions of the autonomic nervous system. The enteric nervous system innervates the gastrointestinal tract, the pancreas, and the gall bladder. It contains sensory neurons, interneurons, and motor neurons. Thus the circuitry can autonomously sense the tension and the chemical environment in the gut and regulate blood vessel tone, motility, secretions, and fluid transport. The system is itself governed by the central nervous system and receives both parasympathetic and sympathetic innervation[GO]." "MESH:D017615 CALOHA:TS-2093 EHDAA2:0004202 Wikipedia:Enteric_nervous_system FMA:66070 MIAA:0000102 BIRNLEX:1166 MAT:0000102 BAMS:ENS MA:0000222 TAO:0001155 EFO:0000895 GAID:799 ZFA:0001155 EMAPA:26922 BTO:0002506 UMLS:C0206111" + "The process resulting in the physical partitioning and separation of a neuroblast into daughter cells. A neuroblast is any cell that will divide and give rise to a neuron." + "Division of a stem cell during which it retains its identity and buds off a daughter cell with a new identity." + "Any process that modulates the frequency, rate, or extent of neutrophil apoptotic process." + "Any process that modulates the frequency, rate or extent of glucocorticoid secretion." + "An acidophilic cell of the anterior pituitary that produces growth hormone, somatotropin." "MESH:D052683 FMA:83095" + "EMAPA:35406 MA:0000954" + "Network of tubes that carries blood through the distensible musculomembranous organ that serves to collect and store urine excreted by the kidneys[MP]." "EMAPA:28679" + "The process in which a relatively unspecialized cell acquires specialized features of a club cell. A club cell is an unciliated epithelial cell found in the respiratory and terminal bronchioles." + + "The directed movement of the nucleus along microfilaments within the cell, mediated by motor proteins." + "The process whose specific outcome is the progression of an anterior lateral line neuromast hair cell over time, from its formation to the mature structure. A neuromast hair cell is a hair cell that acts as a sensory receptor of the neuromast; it is morphologically polarized as a result of the relative position of the single kinocilium and the clusters of stereocilia on its apical surface. Cell development does not include the steps involved in committing a cell to a specific fate." + "Any process in which a vesicle is maintained in a specific location within a cell and prevented from moving elsewhere." + "The process in which a relatively unspecialized cell acquires specialized structural and/or functional features of a corticotropic hormone secreting cell. An corticotropic hormone secreting cell is a basophil cell of the anterior pituitary that produces corticotropin." + "A nerve plexus that is part of an autonomic nervous system [Automatically generated definition]." "EMAPA:18224 MA:0000221 SCTID:362482000 FMA:5910" + "A protein complex that spans a membrane and forms a water-filled channel across the phospholipid bilayer allowing selective monoatomic ion transport down its electrochemical gradient." + "A hematopoietic progenitor that has restricted self-renewal capability. Cell is Kit-positive, Ly6-positive, CD150-negative and Flt3-negative." + "A cranial placode which, once specified, invaginates to form an otic cup, which eventually separates from the surface ectoderm to form the otic vesicle or otocyst, a rounded structure without appar- ent polarity. As the otic placode invaginates into a cup neuroblasts delaminate from the anterior ventral aspect of the otic epithelium to give rise to neurons of the vestibulocochlear (statoacoustic) ganglion of cranial nerve VIII[NBK]." "EHDAA2:0001339 TAO:0000138 AAO:0011079 ZFA:0000138 Wikipedia:Otic_placode FMA:293973 EMAPA:16195 NCIT:C34239 VHOG:0000235 XAO:0000223 EHDAA:506 EFO:0003429 UMLS:C1518677" + "A circulating gamma-delta T cell that expresses RORgamma(t), is CD27-negative and is capable of IL-17 secretion." + "Any process that modulates the frequency, rate or extent of skeletal muscle satellite cell proliferation." + "A protein that is a translation product of the human SNCG gene or a 1:1 ortholog thereof." + "The directed movement of histamine into a cell, typically presynaptic neurons or glial cells. Histamine is a physiologically active amine, found in plant and animal tissue and released from mast cells as part of an allergic reaction in humans." + "Any process that modulates the frequency, rate or extent of type B pancreatic cell apoptotic process." + "The chemical reactions and pathways involving ADP, adenosine 5'-diphosphate." + "Any process that stops, prevents or reduces the rate or extent of progression through the meiotic cell cycle." + "Enables the transfer of a protein from one side of a membrane to the other." "Reactome:R-HSA-184269 Reactome:R-HSA-9698930 Reactome:R-HSA-1299475 Reactome:R-HSA-5244404 Reactome:R-HSA-9636375 Reactome:R-HSA-5244428 Reactome:R-HSA-5336420 Reactome:R-HSA-5250616 Reactome:R-HSA-5246514 Reactome:R-HSA-5205661 Reactome:R-HSA-5250884 Reactome:R-HSA-5210943 Reactome:R-HSA-5250972 Reactome:R-HSA-5210947 Reactome:R-HSA-5229111 Reactome:R-HSA-3149434 Reactome:R-HSA-5228406 Reactome:R-HSA-5244506 Reactome:R-HSA-9698933 Reactome:R-HSA-1268022" + "The process in which a relatively unspecialized cell acquires specialized features of a metanephric glomerular epithelial cell. Metanephric glomerular epithelial cells are specialized epithelial cells that form part of the metanephric glomerulus; there are two types, metanephric glomerular parietal epithelial cells and metanephric glomerular visceral epithelial cells." + "An immature microglial cell with a ramified morphology." + "An intracellular signaling module that is part of larger signaling pathways that can be initiated either intracellularly or by cell surface receptors. Intracellular signaling cassettes are discrete signaling units that are often shared by multiple signaling pathways." + "An epithelium that is part of a regenerating fin/limb." "ZFA:0001389 TAO:0001389 EFO:0003682" + "The portion of the primitive mesentery that encloses the stomach; from its dorsal sheet, the greater omentum develops, and from its ventral sheet, the lesser omentum." "SCTID:261623000 VHOG:0000358 EMAPA:17024 EHDAA2:0001922 EHDAA:2999 MA:0001617" + "Primordium that develops into the nervous system." "AAO:0000477" + "The act of sexual union between male and female, involving the transfer of sperm." + "Any joint that is part of a (free) limb." "FMA:321558 SCTID:312683002 EMAPA:36501 MA:0000691 galen:LimbJoint" + "Any process that modulates the rate, frequency or extent of collagen catabolism. Collagen catabolism is the proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix." + "Any process that modulates the frequency, rate or extent of testosterone secretion." + "Any process that modulates the frequency, rate or extent of antral ovarian follicle growth." + "Any process that modulates the frequency, rate or extent of a signaling process." + "The inferior labial vein is the vein receiving blood from the lower lip." "SCTID:422955002 MA:0002253 EMAPA:37202 FMA:52541 Wikipedia:Inferior_labial_vein" + "The process in which the mammary gland cord forms by elongation of the mammary bud. The cord is formed once the elongating bud breaks through the mesenchyme and reaches the fat pad." + "A somite that is part of a trunk." "AAO:0010385 EMAPA:16184 XAO:0000314 EHDAA2:0003438" + "Epithelium pertaining to the trachea and bronchi." "BTO:0002925 CALOHA:TS-1063" + "PMID:30257078 GC_ID:1 PMID:23020233" + "A protein that is a translation product of the human KLRG1 gene or a 1:1 ortholog thereof." + "The cells lining the proximal tubule are cuboidal epithelial cells with deep basal membrane invaginations that provide a large basal surface area. The long microvilli (the brush border) lining the tubule lumen, maximize luminal surface area and make these cells ideally suited for both reabsorptive and secretory functions." "BTO:0003576 FMA:64808" + "A somatic epithelial cell of the insect egg chamber." "FBbt:00004904" + "A syndecan-1 that is encoded in the genome of mouse." "UniProtKB:P18828" + "Any process that modulates the frequency, rate or extent of protein localization to cell leading edge." + "A round or oval neuroepithelial cell that contacts other type I cells or capillaries. They occur in clusters that are surrounded by sheath cells (type-II cells) in the carotid body. This cell type is capable of secreting a number of neurotransmitters." "FMA:84186" + "An epithelial cell of stratum spinosum of esophageal epithelium." "FMA:70732" + "The process resulting in the physical partitioning and separation of a neuroblast into two daughter cells with different developmental potentials." + "The process in which a relatively unspecialized cell acquires specialized features of a stem cell. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells." "Wikipedia:Stem_cell_differentiation" + + "A mitotic cell cycle process which results in the assembly, arrangement, or disassembly of the nuclear inner or outer membrane during mitosis." + "A bilaterally paired branched artery that originates from the aortic arches and divides into and includes as parts the internal and external carotid arteries[cjm]." "VHOG:0000272 FMA:3939 MESH:D017536 Wikipedia:Common_carotid_artery GAID:479 MA:0001926 SCTID:362041005 NCIT:C32352 EHDAA2:0000217 UMLS:C0162859 EHDAA:7331 EMAPA:17855 CALOHA:TS-0116" + "An interneuron whose axon stays entirely within the gray matter region where the cell body resides." "BAMS:1002" + "The process in which calcium ions sequestered in the endoplasmic reticulum, Golgi apparatus or mitochondria are released into the postsynaptic cytosol." + "Any process that activates or increases the frequency, rate or extent of mesenchymal to epithelial transition involved in mesonephros morphogenesis." + "The splanchnic mesoderm in the cardiogenic region where the heart develops; it gives rise to endocardial heart tubes that fuse to form the primordial cardiac tube, the heart primordium[web]. Two migratory heart primordia that move ventrally during the course of neurulation, and then fuse[XAO]." "VHOG:0001641 SCTID:360387000 XAO:0000235 EHDAA2:0000214 EFO:0000315 BILA:0000051 FMA:293143 EHDAA:385 AAO:0011021" + "Any process that activates or increases the frequency, rate or extent of apoptotic process involved in morphogenesis." + "Any process that modulates the frequency, rate, or extent of neutrophil degranulation." + "An endochondral element that is part of a autopod region." + "Any process that increases the rate, frequency or extent of epithelial cell proliferation that contributes to the progression of the prostate gland over time." + "The actin filament-based process in which cytoplasmic actin filaments slide past one another resulting in contraction of all or part of the cell body." + "A membrane-bound cytoplasmic organelle of the endomembrane system that further processes the core oligosaccharides (e.g. N-glycans) added to proteins in the endoplasmic reticulum and packages them into membrane-bound vesicles. The Golgi apparatus operates at the intersection of the secretory, lysosomal, and endocytic pathways." "NIF_Subcellular:sao451912436 Wikipedia:Golgi_apparatus" + "Any process that modulates the frequency, rate or extent of protein localization to plasma membrane." + "Skeletal tissue that is mineralized." "VSAO:0000013 XAO:0004039" + "A change in the morphology or behavior of a plasmacytoid dendritic cell resulting from exposure to an activating factor such as a cellular or soluble ligand." + "A double negative post-natal thymocyte that has a T cell receptor consisting of a gamma chain containing a Vgamma2 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-positive." + "EHDAA:257 ZFA:0001178 RETIRED_EHDAA2:0001273 XAO:0004091 EMAPA:16074 VHOG:0001372 TAO:0001178 EFO:0003643" + "An action potential that occurs in an atrial cardiac muscle cell." + "A cell of an ommatidium that secretes lens materials." "FBbt:00004193" + "An astrocyte of the forebrain." + "The expansion of a natural killer cell population by cell division as part of an immune response." + "The process whose specific outcome is the progression of the prostate gland over time, from its formation to the mature structure. The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid." + "Any process that modulates the frequency, rate or extent of metanephric nephron tubule epithelial cell differentiation." + "GC_ID:1" + "EHDAA2:0004021" + "A luminal cell of terminal ducts, i.e.e the terminal branch of a lactiferous duct which alveolar cells drain into." "FMA:87168" + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glycoprotein stimulus." + "The disaggregation of a cell junction into its constituent components." + "An immature cell of the conventional dendritic cell lineage, characterized by high levels of antigen uptake via endocytosis, macropinocytosis, and phagocytosis, and typically found resident in the tissues. Markers for this cell are CD80-low, CD86-low, and MHC-II-low." + "The change in morphology and behavior of a mature or immature B cell during an immune response, resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific." + "The developmental process pertaining to the initial formation of a kidney rudiment from unspecified parts. A kidney is an organ that filters the blood and excretes the end products of body metabolism in the form of urine." + "The directed movement of organelles or molecules along microtubules in dendrites." + "Any process that activates or increases the frequency, rate or extent of T-helper 17 cell differentiation." + "Obsolete. Use PO:0000075 from Plant Ontology instead. An elongated living cell with unevenly thickened nonlignified primary walls." + "Any process that modulates the frequency, rate, or extent of a humoral immune response." + "The red vascular substance consisting of connective tissue and blood vessels, containing primitive blood cells, macrophages, megakaryocytes, and fat cells. Red marrow is found in the cavities of many bones. It manufactures and releases leukocytes and erythrocytes into the bloodstream." "SCTID:75330005 FMA:74595 SCTID:328538003 BTO:0001160" + "An immature CD1a-positive dermal dendritic cell is CD80-low, CD86-low, and MHCII-low." + "Respiration organ that develops as an outpocketing of the esophagus." "BTO:0000763 UMLS:C0024109 MA:0000415 MESH:D008168 CALOHA:TS-0568 NCIT:C12468 MIAA:0000135 XAO:0000119 EHDAA2:0001042 SCTID:181216001 AAO:0000275 EHDAA:2205 AAO:0010567 GAID:345 FMA:7195 MAT:0000135 EV:0100042 EHDAA:1554 EFO:0000934 EMAPA:16728 galen:Lung Wikipedia:Lung" + "A cone cell that detects long wavelength light. Exact peak of spectra detected differs between species. In humans, spectra peaks at 564-580 nm." + "A vasculature that is part of a musculoskeletal system [Automatically generated definition]." "FMA:239607" + "Any process that stops, prevents or reduces the rate or extent of smooth muscle cell proliferation." + "The mesonephric connecting tubule is a tubular segment of the mesonephric nephron; it connects the distal tubule to the collecting duct in the mesonephros." + "A platelet glycoprotein Ib alpha chain that is encoded in the genome of human." "UniProtKB:P07359" + "Any process leading to the attainment of the full functional capacity of a protein." + "Wikipedia:Sclera#Histology" + "A portion of connective tissue that is part of a trunk [Automatically generated definition]." "MA:0000513 EMAPA:37252" + "Epithelium that derives from the endoderm. Examples: urothelium, transitional epithelium of ureter, epithelium of prostatic gland.[FMA]." "FMA:69065" + "A segment of the eyeball that is filled with refractive media." "NCIT:C32301 SCTID:280540004 EMAPA:37529 BTO:0002085 FMA:58071 MA:0002459 UMLS:C0459556" + "A fibrous membrane, which, in the neck, represents the supraspinal ligaments of the upper vertebrae." "Wikipedia:Nuchal_ligament FMA:13427 EMAPA:19207 BTO:0000952 SCTID:166962007" + "The process in which a relatively unspecialized cell acquires specialized features of an anterior lateral line neuromast support cell. Support cells are non-sensory cells of the neuromast that extend between the sensory hair cells from the basement membrane to the apical surface; they are surrounded by mantle cells." + "A process involving any mechanism for tolerance induction in B cells." + "Opening/conduit between the nasal cavity and the nasopharynx[AAO] The choanae are separated by the vomer[WP]." "MA:0001323 VHOG:0000545 EMAPA:17849 EHDAA2:0000242 EHDAA:7842 AAO:0000093 SCTID:244507001 Wikipedia:Posterior_nasal_apertures FMA:53143 XAO:0000277" + + "The interstitial compartment of the kidney, comprising the extravascular intertubular spaces of the renal parenchyma, with their attendant cellular elements and extracellular substances, bounded on all sides by epithelial and vascular basement membranes." "FMA:70983 MA:0002616 SCTID:362210003 NCIT:C33459 EMAPA:28518" + "A progenitor cell found in the larval epidermis of insects and that gives rise to the adult abdominal epidermis." "FBbt:00001789" + "The elbow is the region surrounding the elbow-joint-the ginglymus or hinge joint in the middle of the arm. Three bones form the elbow joint: the humerus of the upper arm, and the paired radius and ulna of the forearm. The bony prominence at the very tip of the elbow is the olecranon process of the ulna, and the inner aspect of the elbow is called the antecubital fossa. [WP,unvetted,human-specific]." "galen:Elbow SCTID:76248009 EHDAA2:0000429 EHDAA:6212 CALOHA:TS-2222 MESH:D004550 Wikipedia:Elbow VHOG:0000340 GAID:54 EFO:0003069 MA:0000036 EHDAA:4166 FMA:24901 EMAPA:17414" + "A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages." "BTO:0004730" + "A transcription factor SOX-2 that is encoded in the genome of human." "Reactome:R-HSA-452271 UniProtKB:P48431" + "The process whose specific outcome is the progression of the bundle of His over time, from its formation to the mature structure. The bundle of His is part of the His-Purkinje system that transmits signals from the AV node to the cardiac Purkinje fibers." + "Any process that activates or increases the frequency, rate or extent of glutamate secretion, where glutamate acts as a neurotransmitter." + "A portion of mesenchymal tissue associated with an individual pharyngeal arch." "FMA:295694 EMAPA:32755" + "The growth of a growth plate cartilage chondrocyte, where growth contributes to the progression of the chondrocyte over time from one condition to another." + "A thymic epithelial cell type with low nuclear and cytoplasmic electrondensity; has a round, euchromatic nucleus and occurs in small groups at the corticomedullary junction or scattered singly in the medulla." "FMA:72213" + "Outermost layer of an organ[WP]." "FMA:61109 galen:Cortex Wikipedia:Cortex_(anatomy) EFO:0000383 EHDAA:9344" + "Epithelium composed of cells that develops from the ectoderm[FMA,modified]." "FMA:69064" + "Any process that modulates the frequency, rate or extent of microglia differentiation, the process in which a relatively unspecialized cell acquires specialized features of a microglial cell." + "Any gland that is part of the digestive system." "BTO:0000345 AAO:0000130" + "Gray matter structure located on the midline of the forebrain consisting of the septum pellucidum (in some species) and the septal nuclei (Heimer, 1996)." "BAMS:SEP neuronames:255 BIRNLEX:963 BAMS:Spt MA:0000924 UMLS:C0752060 FMA:61842 BTO:0002705 BAMS:Sep EMAPA:32837 BAMS:SA BM:Tel-Spt" + "A renal pelvis that is part of a left ureter." "FMA:15579 SCTID:243436005" + "Any process that modulates the occurrence or rate of mesenchymal stem cell death by apoptotic process that contributes to the shaping of the nephron in the metanephros." + + "A quality inhering in a bearer by virtue of the bearer's having an empty space or cavity within." + "A portion of a prostate that forms a lobe." "NCIT:C52726 MA:0001738 UMLS:C0227970 EMAPA:35712 FMA:19570 SCTID:279692004 BTO:0000548" + "Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of carbohydrates." + "Any process that modulates the frequency, rate or extent of protein localization to chromatin." + + "A mucosa that is part of a cecum [Automatically generated definition]." "BTO:0000213 FMA:14998" + "The process that gives rise to the axial mesoderm. This process pertains to the initial formation of the structure from unspecified parts." + "Any process that modulates the frequency, rate or extent of DNA biosynthetic process." + "A hematopoietic stem cell with long term self renewal capability. This cell is Kit-positive, Sca1-positive, CD150-positive, CD90-low, CD34-negative and Flt3-negative." + "The process in which the anatomical structure of the hypoglossal nerve is generated and organized. This motor nerve innervates all the intrinsic and all but one of the extrinsic muscles of the tongue." + "A neural nucleus that is part of a medulla oblongata." "SCTID:304943004 FMA:258772" + "A columnar/cuboidal epithelial cell that secretes cerebrospinal fluid." + "An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the mouse Fcgr3 gene or a 1:1 ortholog thereof." + "The process whose specific outcome is the progression of the metanephros over time, from its formation to the mature structure. In mammals, the metanephros is the excretory organ of the fetus, which develops into the mature kidney and is formed from the rear portion of the nephrogenic cord. The metanephros is an endocrine and metabolic organ that filters the blood and excretes the end products of body metabolism in the form of urine." + "The directed movement of nitrogen-containing compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "Binding to glutamate, the anion of 2-aminopentanedioic acid." + "A SLAM family member 5 that is encoded in the genome of mouse." "UniProtKB:Q18PI6" + "Any process that modulates the frequency, rate or extent of calcium ion export across the plasma membrane." + "Any neural crest cell differentiation that is involved in thymus development." + "The mucous membrane lining the respiratory tract." "BTO:0000973 MESH:D020545 MA:0001827 FMA:302092 EMAPA:37577 GAID:304" + "Any process that stops, prevents or reduces the frequency, rate or extent of tumor necrosis factor superfamily cytokine production." + "Any process that modulates the frequency, rate or extent of the regulated release of saliva from a cell or a tissue." + "A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. This process occurs in the gastro-intestinal system. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. The gastro-intestinal system generally refers to the digestive structures stretching from the mouth to anus, but does not include the accessory glandular organs (liver, pancreas and biliary tract)." + "Vein of heart that drains the myocardium." "UMLS:C0226654 Wikipedia:Coronary_circulation NCIT:C12882 EHDAA2:0004507 EMAPA:37137 UMLS:C0226737 ZFA:0005814 NCIT:C12878 SCTID:277726009 FMA:12846 galen:CoronaryVein" + "Any process that stops, prevents or reduces the frequency, rate or extent of cell maturation." + "FMA:231590" + "A glial precursor cell that generates oligodendrocytes and type-1 and type-2 astrocytes. It has been shown in some mammals that this cell type may express A2B5, nestin, FGFR-1, FGFR-2, FGFR-3, PLP, and DM-20 antigens. Unlike oligodendrocyte precursor cell, it does not initially express PDGFR-alpha and can differentiate into both type-1 and type-2 astrocytes." + "The developmental process pertaining to the initial formation of a cardiac atrium from unspecified parts. A cardiac atrium receives blood from a vein and pumps it to a cardiac ventricle." + "An M7 retinal ganglion cells with synaptic terminals in S4 and is depolarized by illumination of its receptive field center." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of norepinephrine into a cell." + "The enclosed volume within a sealed membrane or between two sealed membranes. Encompasses the volume enclosed by the membranes of a particular organelle, e.g. endoplasmic reticulum lumen, or the space between the two lipid bilayers of a double membrane surrounding an organelle, e.g. nuclear envelope lumen." + "Any process that modulates the frequency, rate or extent of the binding or confining calcium ions such that they are separated from other components of a biological system." + "A multi-tissue structure that has the potential to develop into a meninx of hindbrain." "EHDAA2:0000610" + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of a ketone, carried out by individual cells." + "The process whose specific outcome is the progression of smooth muscle in the mesonephros over time, from its formation to the mature structure." + + "The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule." + "Any process that decreases the rate, frequency, or extent of the multiplication or reproduction of osteoclasts, resulting in the expansion of an osteoclast cell population." + "A macrophage that is part of the lung connective tissue (pulmonary interstitium). This cell performs tissue remodeling and contributes to barrier immunity through antigen presentation." + "The mass of tissue composed of mesenchymal cells in the lobar bronchus.." "EMAPA:32698" + "Any serous secreting cell that is part of the tracheobronchial epithelium." + "The middle germ layer of the embryo, between the endoderm and ectoderm." "GAID:522 BTO:0000839 EHDAA:124 FMA:69072 SCTID:362854004 AAO:0000304 EV:0100006 EHDAA:183 Wikipedia:Mesoderm MAT:0000174 EMAPA:16083 NCIT:C12750 ZFA:0000041 EFO:0001981 EHDAA2:0001128 XAO:0000050 VHOG:0000152 MIAA:0000174 EHDAA:160 CALOHA:TS-0623 TAO:0000041 MESH:D008648 UMLS:C0025485 BILA:0000037" + "A morphological quality pertaining to the degree to which an object contains an opening, aperture, orifice or vent." + "The movement of a dendritic cell within or between different tissues and organs of the body." + "The appearance of interleukin-2 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." + "A muscle of a pectoral girdle, pectoral fin or anterior limb." "AAO:0010687 FMA:9621 MA:0000615 EMAPA:32624" + "A thick walled spore containing one or more haploid nuclei produced by sexual reproduction in an Basidiomycete; formed externally on extrusions of the basidium." "FAO:0000021 BTO:0002166" + "A nerve that is part of a pelvis [Automatically generated definition]." "EMAPA:37269 MA:0000542" + "The change in morphology and behavior of a neutrophil resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor." + "GC_ID:1" + "The chemical reactions and pathways resulting in the breakdown of hexose, any monosaccharide with a chain of six carbon atoms in the molecule." + "GC_ID:1" + "The process in which a Peyer's patch is generated and organized. Peyer's patches are typically found as nodules associated with gut epithelium with distinct internal structures including B- and T-zones for the activation of lymphocytes." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the proliferation of neuroblasts." + "An enterocyte that is located in the anorectum." + "An epidermal cell which synthesizes keratin and undergoes a characteristic change as it moves upward from the basal layers of the epidermis to the cornified (horny) layer of the skin. Successive stages of differentiation of the keratinocytes forming the epidermal layers are basal cell, spinous or prickle cell, and the granular cell." "CALOHA:TS-0500 BTO:0000667 FMA:62879" + "A jaw muscle that arises from cranial mesenchyme and is innervated by cranial nerves." "Wikipedia:Branchiomeric_musculature XAO:0004325" + "The directed movement of a Schwann cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis)." + "The lamellated connective tissue of the cornea between the Bowman and Descemet membranes." "MESH:D003319 ZFA:0001685 GAID:893 TAO:0002189 NCIT:C12699 CALOHA:TS-1138 SCTID:362511000 MA:0001245 EFO:0002514 UMLS:C0010040 FMA:58306 Wikipedia:Corneal_stroma EMAPA:17602" + + "The mantle layer of the neural tube that lies dorsal to the sulcus limitans and contains primarily sensory neurons and interneurons involved in communication of sensory impulses." "Wikipedia:Alar_plate neuronames:1370" + "KUPO:0001111" + "Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule." "Reactome:R-HSA-6788855 Reactome:R-HSA-6788867" + "The developmental process pertaining to the initial formation of the optic vesicle from the lateral wall of the forebrain. This process begins with the specific processes that contribute to the appearance of the vesicle and ends when the vesicle has evaginated. The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup." + + "GC_ID:1" + + "The process in which the anatomical structures of the glomerulus are generated and organized. The glomerulus is a capillary tuft surrounded by Bowman's capsule in nephrons of the vertebrate kidney." + "The aggregation, arrangement and bonding together of a set of components to form an excitatory synapse." + "Blood vessel that is connected to the yolk sac." "EMAPA:36494" + "A muscular coat that is part of a ureter." "SCTID:3563003 MA:0002654 FMA:15893" + "Partitioning of the blastoderm embryo into trunk segmental units. In Drosophila, the trunk segments include thoracic segments and abdominal segments A1 to A8." + "The process whose specific outcome is the progression of a cerebellar neuron over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell." + "A nerve that is part of a shoulder [Automatically generated definition]." "MA:0000634 EMAPA:37335" + "Any process that stops, prevents or reduces the frequency, rate or extent of secretion by cell." + "Subdivision of skeleton consisting of all skeletal elements in an hindlimb zeugopod region. Typically consists of the tibia and the fibula." "VSAO:0005014 AAO:0000216" + "An epithelium that is part of a intestinal villus." "FMA:63587" + "An epithelial cell that is part of the nasolacrimal duct." "FMA:70561" + "Anatomical space that is an opening in a bone, usually for passage of blood vessels or nerves." "ZFA:0005386 AAO:0010438 VHOG:0001760 TAO:0001736" + "Any process that activates or increases the frequency, rate, or extent of erythrocyte clearance." + "The chemical reactions and pathways involving glycine, aminoethanoic acid." + "Any process that decreases the rate, frequency, or extent of the orderly movement of an endothelial cell into the extracellular matrix to form an endothelium." + "Any process that stops, prevents or reduces the frequency, rate or extent of transport across blood-brain barrier." + "An endothelium that is part of a outflow tract [Automatically generated definition]." "VHOG:0001524 MA:0000490" + "An excitatory granule cell with a soma located in the granular layer of cerebellar cortex. A mature cerebellar granule cell has short dendrites with a characteristic claw-like appearance and a long axon that ascends to the molecular layer where it bifurcates (except in non-teleost fish, where it does not bifurcate) and extends mediolaterally to form parallel fibers." "BTO:0004278" + "A renal pelvis that is part of a metanephros." "VHOG:0000945" + "Lymphatic progenitor cells." + "An anatomical cavity that is part of a bronchus." "FMA:62646 SCTID:199401001" + "A D cell located in the colon." "FMA:268744" + + + "A white matter that is part of the forebrain." "FMA:268634 DHBA:10557" + "The process in which a precursor cell type acquires the specialized features of a pre-B cell. Pre-B cells follow the pro-B cell stage of immature B cell differentiation and undergo rearrangement of heavy chain V, D, and J gene segments." + "A transition where a mesenchymal cell establishes apical/basolateral polarity, forms intercellular adhesive junctions, synthesizes basement membrane components and becomes an epithelial cell." + "A skeletal muscle myoblast that is part of a skeletal mucle. These cells are formed following acivation and division of skeletal muscle satellite cells. They form a transient population that is lost when they fuse to form skeletal muscle fibers." + "A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome." "Wikipedia:Nucleolus NIF_Subcellular:sao1820400233" + "A cardiac septum that divides the left and right atria of the heart." "VHOG:0000385 EHDAA2:0000838 EHDAA:1896 UMLS:C0225836 EMAPA:17011 NCIT:C32818 FMA:7108 SCTID:362016003 galen:InteratrialSeptum MA:0000084 Wikipedia:Interatrial_septum" + "Any process that decreases the rate frequency or extent of gastric secretion. Gastric secretion is the regulated release of gastric acid (hydrochloric acid) by parietal or oxyntic cells during digestion." + "Any process that modulates the frequency, rate or extent of oxygen metabolic process." + "Any process that activates or increases the frequency, rate or extent of cerebral blood circulation." + "A germinal center B cell that is rapidly dividing and has the phenotype IgD-negative, CD38-positive, and CD77-positive. Somatic hypermutation of the immunoglobulin V gene region can occur during proliferation of this cell type." + "The formation of the bundles of intermediate filaments. Intermediate filament-associated proteins (IFAPs) cross-link intermediate filaments with one another, forming a bundle or a network, and with other cell structures, including the plasma membrane. The organization of intermediate filaments and their supportive function in various cells types depends in large part on their linkage to other cell structures via IFAPs." + "Direct ossification that occurs within mesenchyme or an accumulation of relatively unspecialized cells." "Wikipedia:Intramembranous_ossification" + "The process in which the anatomical structure of the cranial nerves are generated and organized. The cerebellar cortex is a thin mantle of gray matter that covers the surface of each cerebral hemisphere. It has a characteristic morphology with convolutions (gyri) and crevices (sulci) that have specific functions. Six layers of nerve cells and the nerve pathways that connect them comprise the cerebellar cortex. Together, these regions are responsible for the processes of conscious thought, perception, emotion and memory as well as advanced motor function." + "A presumptive structure that has the potential to develop into a forebrain-midbrain boundary." "EFO:0003463 ZFA:0001368 TAO:0001368" + "The neck of the rib is the flattened portion which extends lateralward from the head; it is about 2.5 cm. long, and is placed in front of the transverse process of the lower of the two vertebrC& with which the head articulates. Its anterior surface is flat and smooth, its posterior rough for the attachment of the ligament of the neck, and perforated by numerous foramina. Of its two borders the superior presents a rough crest (crista colli costE) for the attachment of the anterior costotransverse ligament; its inferior border is rounded. On the posterior surface at the junction of the neck and body, and nearer the lower than the upper border, is an eminencebthe tubercle; it consists of an articular and a non-articular portion. The articular portion, the lower and more medial of the two, presents a small, oval surface for articulation with the end of the transverse process of the lower of the two vertebrC& to which the head is connected. The non-articular portion is a rough elevation, and affords attachment to the ligament of the tubercle. The tubercle is much more prominent in the upper than in the lower ribs." "SCTID:263359009 Wikipedia:Neck_of_rib FMA:7576 EMAPA:37826" + "The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a cardiac fibroblast. A cardiac fibroblast is a connective tissue cell in the heart which secretes an extracellular matrix rich in collagen and other macromolecules." + "The subcutaneous mechanoreceptors that innervate tylotrich hair follicles." + "The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells." "Wikipedia:Cell_division" + "A specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft). Neurotransmitters cross the synaptic cleft and transmit the signal to the postsynaptic membrane." + "A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex." "CALOHA:TS-1001 VHOG:0001479 BTO:0000782 FMA:62870 MESH:D013601" + "The process of introducing a phosphate group on to a protein." + "A C-type lectin with multiple lectin domains that is a translation product of the mouse LY75 gene or a 1:1 ortholog thereof. It consists of 12 extracellular domains (an N-terminal cysteine-rich domain, a fibronectin type II domain and 10 C-type carbohydrate recognition domains), a transmembrane region and a small cytoplasmic C terminus containing a single Tyr residue, but no obvious kinase domain." + "A part of the brain consisting of a three layered cortex located in the forebrain bordering the medial surface of the lateral ventricle. The term hippocampus is often used synonymously with hippocampal formation which consists of the hippocampus proper or Cornu Ammonis, the dentate gyrus and the subiculum." "BTO:0003705 MIAA:0000114 DMBA:16124 EV:0100180 UMLS:C0019564 neuronames:3157 SCTID:361561007 MESH:D006624 GAID:623 NCIT:C12444 EMAPA:32845 Wikipedia:Hippocampus DHBA:10296 BAMS:CA EFO:0000530 BM:Tel-CAM NCIT:C32374 BIRNLEX:721 MAT:0000114 VHOG:0001177 CALOHA:TS-0460 PBA:128012244 MA:0000191 http://scalablebrainatlas.incf.org/services/thumbnail.php?template=ABA07&size=L&dim=2d3d&format=png®ion=CA FMA:62493 MBA:375 EHDAA2:0004443" + "The process whose specific outcome is the progression of the vasculature over time, from its formation to the mature structure. The vasculature is an interconnected tubular multi-tissue structure that contains fluid that is actively transported around the organism." + "The directed movement of substances that are gaseous in normal living conditions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "A hindlimb that is on the right side of a pelvic complex." "FMA:7187" + "GC_ID:1" + "The process in which a relatively unspecialized cell acquires the specialized features of a Rohon-Beard neuron." + "Any process that modulates the frequency, rate or extent of protein catabolic process in the vacuole." + "A smooth muscle cell that is part of the descending colon." "FMA:17520" + "A portion of smooth muscle tissue that is part of a saphenous vein." + "Any process that activates or increases the frequency, rate or extent of neuron migration." + "Any process that modulates the frequency, rate or extent of dendritic cell differentiation." + "The foramen rotundum is a circular hole in the sphenoid bone that connects the middle cranial fossa and the pterygopalatine fossa." "AAO:0000194 SCTID:369439002 EHDAA:10629 FMA:53154 VHOG:0001543 EHDAA2:0000552 Wikipedia:Foramen_rotundum EMAPA:18712" + "A cranial motor neuron whose soma is located in the midbrain andor hindbrain and which innervates the skeletal muscles of the eye or tongue." + "An OFF-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the outer half of the inner plexiform layer. The dendritic tree is delicate and the dendritic tips appear small when compared with type 1 cells. The axon terminal is stratified and restricted to sublamina 2 of the inner plexiform layer." + "A white matter that is part of the midbrain." "DHBA:10650 FMA:83936 HBA:265505382" + + "An euploid male germ cell of an early stage of spermatogenesis." "FBbt:00004935 FBbt:00004934 FMA:72291 EMAPA:31482 CALOHA:TS-2193 BTO:0000958" + "Combining with a signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: a protein + ATP = a phosphoprotein + ADP." "Reactome:R-HSA-8983063 Reactome:R-HSA-8983059" + "The lipid bilayer surrounding a chitosome." + "Any muscle organ that is part of a pelvic girdle [Automatically generated definition]." "MA:0000537 FMA:37367 EMAPA:18185 EHDAA:8326 RETIRED_EHDAA2:0001430" + "FMA:18211" + "A quality inhering in an anotomical structure by virtue of its capacity to be stained by specific histological dyes." + "A cell of the adrenal cortex. Cell types include those that synthesize and secrete chemical derivatives (steroids) of cholesterol." "FMA:69545" + "The process whose specific outcome is the progression of a tendon over time, from its formation to the mature structure. A tendon is a fibrous, strong, connective tissue that connects muscle to bone or integument and is capable of withstanding tension. Tendons and muscles work together to exert a pulling force." + "A neural cell adhesion molecule 1 that is encoded in the genome of human." "UniProtKB:P13591" + "CD8_alpha-negative CD11b-negative dendritic cell is a conventional dendritic cell that is CD11b-negative, CD4-negative CD8_alpha-negative and is CD205-positive. This cell is able to cross- present antigen to CD8-alpha-positive T cells." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of ecdysteroid." + "Bottle-shaped with narrow neck; broad, rounded basal portion where nucleus is located; stereocilia and a single kinocilium is present apically; receive nerve bouton at their base from an afferent cup-shaped (chalice or calyx) nerve ending." "FMA:62352" + "Any process that activates or increases the frequency, rate or extent of defense response to bacterium." + "A vein that returns blood from the intestines." "EHDAA:4442 NCIT:C53055 BTO:0002781 UMLS:C0025473 RETIRED_EHDAA2:0001125 MA:0002177 EMAPA:17348 MESH:D008642 Wikipedia:Mesenteric_vein SCTID:304045008" + "Binding to a steroid hormone." + "The process in which an antigenically naive CD8-positive, alpha-beta T cell acquires the specialized features of an effector, regulatory, or memory T cell as part of an immune response. Effector T cells include cells which provide T cell help or exhibit cytotoxicity towards other cells." + "A brain that develops_from a neural tube." + "The process in which a relatively unspecialized cell acquires specialized features of a vascular smooth muscle cell." + "The lymphatic system in vertebrates is a network of conduits that carry a clear fluid called lymph. It also includes the lymphoid tissue through which the lymph travels. Lymphoid tissue is found in many organs, particularly the lymph nodes, and in the lymphoid follicles associated with the digestive system such as the tonsils. The system also includes all the structures dedicated to the circulation and production of lymphocytes, which includes the spleen, thymus, bone marrow and the lymphoid tissue associated with the digestive system[WP]." "ZFA:0000385 NCIT:C12746 EMAPA:37664 GAID:931 TAO:0000385 VHOG:0000842 MIAA:0000197 SCTID:362589007 MA:0002435 EHDAA2:0001043 MAT:0000197 UMLS:C0024235 XAO:0003199 Wikipedia:Lymphoid_system FMA:74594 EHDAA:8677" + "The appearance of interleukin-9 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." + "Any process that modulates the frequency, rate or extent of the directed movement of a solute from one side of a membrane to the other." + "The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis)." "Wikipedia:Chemotaxis" + "Any process that modulates the frequency, rate or extent of hair follicle maturation." + "Any process that stops, prevents or reduces the frequency, rate or extent of skeletal muscle fiber differentiation." + "A fibroblast of pulmonary artery." + "FMA:40877" + "Any process that modulates the frequency, rate or extent of glutamatergic neuron differentiation." + "Cell-cell signaling that mediates the transfer of information from an astrocyte to a dopaminergic neuron." + "Any process that activates or increases the frequency, rate or extent of cardiac muscle cell proliferation." + "Any process that stops, prevents or reduces the frequency, rate or extent of iron ions import across plasma membrane." + "A cell that lacks a nucleus." "FMA:68647" + "The process in which a hemopoietic stem cell acquires the specialized features of a B-1 B cell. B-1 B cells are a distinct subset of B cells characterized as being CD5 positive, found predominantly in the peritoneum, pleural cavities, and spleen, and enriched for self-reactivity." + "The tiny blood vessels that receive blood from the efferent arterioles of the glomerulus, and interact with superficial cortical nephrons allowing reabsorption and secretion between blood and the inner lumen of the nephron; peritubular capillaries are situated around the tubule and are at low pressure." "Wikipedia:Peritubular_capillaries MA:0002588 EMAPA:36558" + "Skeletal tissue that is part of the exoskeleton and derived from an odontogenic papilla." "ZFA:0005623 EMAPA:35872 UMLS:C1519551 VSAO:0000063 XAO:0004046 MA:0002540 NCIT:C33794 FMA:63001" + "Any process of regulating the production and elimination of erythrocytes within an organism." + "The portion of the cytoskeleton contained within the postsynapse." + "A blood vessel that is part of an abdomen [Automatically generated definition]." "MA:0000518" + + "The regulation of blood pressure mediated by the signaling molecule vasopressin. Vasopressin is produced in the hypothalamus, and affects vasoconstriction, and renal water transport." + "A portion of smooth muscle tissue that is part of a fallopian tube [Automatically generated definition]." "MA:0001721" + "Neuron with two neurites that are fused grossly when they protrude from the soma and bifurcate a short distance from the soma." "FMA:67305" + "Any of the lymph nodes that are part of a face." "FMA:61222 Wikipedia:Facial_lymph_nodes SCTID:279139005" + "The process whose specific outcome is the progression of the cerebellar granule layer over time, from its formation to the mature structure. The granular layer is the innermost layer of the cerebellar cortex. This layer contains densely packed small neurons, mostly granule cells. Some Golgi cells are found at the outer border. Granule neurons send parallel fibers to the upper molecular layer, where they synapse with Purkinje cell dendrites. Mossy fibers from the pontine nuclei in the white matter synapse with granule cell axons, Golgi cell axons and unipolar brush interneuron axons at cerebellar glomeruli in the granule cell layer." + "An undifferentiated columnar cell of the bronchus epithelium" + "The functional tissue of the central nervous system consisting of neurons and glial cells." + "The fundus glands (or fundic glands, or gastric glands) are found in the body and fundus of the stomach. They are simple tubes, two or more of which open into a single duct." "EMAPA:27161 UMLS:C0017130 NCIT:C32643 Wikipedia:Fundic_glands SCTID:268338004" + "FMA:23254 SCTID:181915009" + "Any process in which a melanosome is transported to, and/or maintained in, a specific location within the cell." + "The hyaline cartilaginous structures that support the bronchi, present as irregular rings in the larger bronchi (and not as regular as in the trachea), and as small plates and islands in the smaller bronchi; as the branching continues through the bronchial tree, the amount of hyaline cartilage in the walls decreases until it is absent in the smallest bronchioles[MP]." "UMLS:C0225604 FMA:62649 EMAPA:35192 NCIT:C49209 SCTID:278980009 MA:0001835" + "Any process that activates or increases the frequency, rate, or extent of natural killer cell cytokine production." + "Any process in which a macromolecule is transported to, or maintained in, a specific location." + "Any process that stops, prevents, or reduces the frequency, rate or extent of spermatid nuclear differentiation." + + "Binding to oxygen (O2)." + "Type of neuron that is a primary mechanosensory cell, with peripheral neurites innervating the skin with free nerve endings." "AAO:0010316 VHOG:0001484 ZFA:0009150 EFO:0003711" + "Cytoplasm that exhibits molecular interaction for basic dyes under specific pH conditions." + "The outermost layer (or layers, depending on the species) of embryonic skin, essential for the development of the epidermis and establishment of the barrier functions. The periderm derives from the outer layer of the ectoderm." "VHOG:0001680 FMA:295662 EHDAA2:0001846 XAO:0000029 UMLS:C1518973 TAO:0001185 ZFA:0001185 NCIT:C34247 EHDAA:6538" + "Any process that modulates the frequency or rate of multiplication or reproduction of Schwann cells, resulting in the expansion of their population. Schwann cells are a type of glial cell in the peripheral nervous system." + "Any process that modulates the frequency, rate or extent of blood coagulation." + "A primary neuron (sensu Teleostei) that is neither a sensory neuron or a motor neuron." + "A portion of smooth muscle tissue that is part of a bronchus [Automatically generated definition]." "EMAPA:35195 MA:0001840 UMLS:C1707055 NCIT:C49213 BTO:0004401" + "Middle subdivision of a digestive tract[CJM]. In vertebrates: The middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine[GO]." "EMAPA:16255 EHDAA2:0001185 NCIT:C34210 SCTID:361410004 TGMA:0001036 EHDAA:983 Wikipedia:Midgut XAO:0000103 MA:0001564 BILA:0000086 UMLS:C0231052 BTO:0000863 VHOG:0000290 EFO:0001950 FMA:45617" + "The developmental process in which the heart is generated and organized. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood." + "A nail that is part of a pedal digit." "NCIT:C33790 UMLS:C0222007 SCTID:244198006 FMA:54328 XAO:0003103 EMAPA:36457" + "The orderly movement of epithelial cells within a renal tubule that contributes to proximal tubule morphogenesis." + "A chromaffin cell that is part of the ovary." "FMA:74319" + "The thick outer layer of the adrenal gland that is in the left side of the abdomen." "FMA:69089" + + "The disaggregation of an tight junction into its constituent components." + "Any apoptotic process in a retinal rod cell, one of the two photoreceptor cell types of the vertebrate retina." + "A trophoblast cell that is not part of a placental villous." + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving polysaccharides." + "The series of events required for an organism to receive an orientational stimulus, convert it to a molecular signal, and recognize and characterize the signal. Equilibrioception refers to a combination of processes by which an organism can perceive its orientation with respect to gravity. In animals, stimuli come from labyrinth system of the inner ears, monitoring the direction of motion; visual stimuli, with information on orientation and motion; pressure receptors, which tell the organism which body surfaces are in contact with the ground; and proprioceptive cues, which report which parts of the body are in motion." "Wikipedia:Equilibrioception" + "Any process that activates or increases the frequency, rate, or extent of plasmacytoid dendritic cell cytokine production." + "EMAPA:17646 EHDAA2:0001147" + "Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information." "MIAA:0000031 FMA:75259 BILA:0000099 AAO:0000555 EMAPA:16192 TAO:0000282 MAT:0000031 ZFA:0000282 EFO:0000805 VHOG:0001674 XAO:0003194 EHDAA2:0003094 Wikipedia:Sensory_system NLXANAT:090816 BAMS:SEN MA:0002442" + "Elastic tissue that is part of a lung [Automatically generated definition]." "MA:0002860" + "The series of molecular signals mediated by the detection of a glucocorticoid hormone." + "Any process that activates or increases the frequency, rate or extent of cell proliferation involved in heart morphogenesis." + "A valve that is part of a ureter." "MA:0002658 EMAPA:37781" + "A cell that constitutes the basal layer of epithelium in the prostatic duct." "FMA:74226" + "Trunk part of spinal nerve, where dorsal and ventral roots meet to form the spinal nerve, before branching off to dorsal and ventral rami." "EHDAA2:0001900 FMA:5929" + "An endoderm that is part of a foregut [Automatically generated definition]." "EHDAA2:0004568 EHDAA:524" + "The most primitive precursor in the granulocytic series, having fine, evenly distributed chromatin, several nucleoli, a high nuclear-to-cytoplasmic ration (5:1-7:1), and a nongranular basophilic cytoplasm. They reside in the bone marrow." "FMA:83524 BTO:0000187" + "A monostratified retinal ganglion cell that has a small dendrite field with a dense dendrite arbor with post synaptic terminals in sublaminer layer S4." + "BTO:0004185 FMA:67860 MESH:D018034 Wikipedia:Olfactory_receptor_neuron" + "Any apoptotic process in a hepatoblast." + "Portion of connective tissue composed of adipocytes enmeshed in areolar tissue." "FMA:20110 MAT:0000015 XAO:0003049 EHDAA2:0003120 MIAA:0000015 VHOG:0001284 TAO:0002134 AAO:0000001 NCIT:C12472 MA:0000009 ZFA:0005345 EV:0100381 GAID:920 SCTID:55603005 AEO:000020 EMAPA:35112 MESH:D000273 UMLS:C0001527 EFO:0000790 Wikipedia:Adipose_tissue CALOHA:TS-0013 BTO:0001487 galen:FattyTissue" + "The organs and associated structures associated with bearing offspring in a female animal." "EV:0100110 FMA:45663 GAID:364 HAO:0000324 BTO:0000083 EHDAA:8116 EFO:0000969 WikipediaCategory:Female_reproductive_system NCIT:C12402 SCTID:361386004 EMAPA:17959 VHOG:0000726 TGMA:0000635 CALOHA:TS-1303 Wikipedia:Female_genitalia UMLS:C0700038 MA:0000381 MIAA:0000028 EHDAA2:0000506 MESH:D005836 XAO:0000156" + "A progenitor cell of the thrombocyte, a nucleated blood cell involved in coagulation typically seen in birds and other non-mammalian vertebrates." + "Any muscle organ that is part of a pelvic appendage (hindlimb or pelvic fin)." + "The assembly of a pseudopodium by rearrangement of the actin cytoskeleton and overlying membrane." + "The orderly movement of a cell from one site to another that will contribute to the formation of an endocardial cushion. The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves." + "A pro-B cell that is CD45R/B220-positive, CD43-positive, HSA-low, BP-1-negative and Ly6c-negative. This cell type is also described as being lin-negative, AA4-positive, Kit-positive, IL7Ra-positive and CD45R-positive." + "The area of white matter of the spinal cord located on either side of the ventral (anterior) medial fissure." "VHOG:0001622 MA:0002751 EV:0100326 neuronames:269" + "An interrenal chromaffin cell found in teleosts that contain heterogeneous vesicles with electron-dense granules located asymmetrically within the vesicular membrane." + "The directed movement of calcium cations into the vacuole across the vacuolar membrane." + "Any process that modulates the frequency, rate or extent of the controlled release of glutamate." + "Is the sensory system for the sense of hearing." "NCIT:C12889 neuronames:2888 FMA:7192 MA:0002443 EMAPA:36002 Wikipedia:Auditory_system UMLS:C0587901 NLXANAT:090817" + "A change in morphology and behavior of a macrophage resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor." + "Organ component of the mammary gland which consists of an aggregate of mammary alveoli that communicate with a lobular lactiferous duct.[FMA]." "FMA:62090 EMAPA:36634 MA:0000793" + "The process whose specific outcome is the progression of vasculature of the renal system over time, from its formation to the mature structure." + "A T-brain transcription factor that is a translation product of the human EOMES gene or a 1:1 ortholog thereof." + "The directed movement of amino acids out of the vacuole, across the vacuolar membrane." + "A cell that is part of a vasa recta." "KUPO:0001068" + "A midget ganglion cell that depolarizes in response to increased light intensity in the center of its receptive field. The majority of input that this cell receives comes from invaginating midget bipolar cells." + "The directed movement of dicarboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "Any process that activates or increases the frequency, rate or extent of translational termination." + "A subdivision of the skeleton that corresponds to the lower part of the mouth. The lower jaw skeleton includes the following elements, when present: lower jaw teeth, the mandible and other lower jaw bones, and Meckel's cartilage." "ZFA:0001273 MA:0001906 XAO:0003084 FMA:54398 EMAPA:17910 AAO:0000274 TAO:0001273 EHDAA:8005 EHDAA2:0004606 VHOG:0000428" + "A CD14 molecule that is encoded in the genome of human." "UniProtKB:P08571" + "An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure[GO]." + "A type EC enteroendocrine cell type that is numerous in the fundus of the stomach; stores 5-hydroxytryptamine and histamine." "FMA:63208" + "A vascular endothelial cell found in colon blood vessels." "CALOHA:TS-2397" + "The subcommissural organ is a circumventricular organ consisting of ependymal and hypendymal cells which secrete SCO-spondin[WP,partially vetted]." "BTO:0001820 neuronames:483 HBA:9489 EMAPA:35828 DMBA:16514 CALOHA:TS-0986 MESH:D013351 GAID:794 Wikipedia:Subcommissural_organ UMLS:C0038533 ZFA:0000683 BAMS:SCO SCTID:369193006 MA:0002941 FMA:72414 DHBA:12101 TAO:0000683 BIRNLEX:1028" + "An anatomical space with at least one opening to another space or the exterior." "EHDAA2:0004616 AEO:0000221" + "An arthroconidium that has only one nucleus." "FAO:0000031" + "The distal elements of the developing limb of vertebrates that will give rise to the autopod (e.g. manus, pes, paw)." + "Morphogenesis of the pancreas. Morphogenesis is the process in which anatomical structures are generated and organized." + "The umbilical artery is a paired artery (with one for each half of the body) that is found in the abdominal and pelvic regions. In the fetus, it extends into the umbilical cord. [WP,unvetted]." "UMLS:C0041632 BTO:0000841 NCIT:C33827 EMAPA:16331 FMA:18820 Wikipedia:Umbilical_artery SCTID:261404000 EMAPA:16372 GAID:516 EHDAA:1026 EHDAA:410 MESH:D014469 CALOHA:TS-1077 MA:0002072 RETIRED_EHDAA2:0002106" + "A cell of the seminiferous tubule epithelium." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus." + "A lymph node that is part of a thorax. Includes lymph nodes of the lungs and mediastinal lymph nodes." "Wikipedia:Lymph_node#Lymph_nodes_of_the_thorax UMLS:C0229745 SCTID:196374005 NCIT:C33769 FMA:12772" + "Any process that activates or increases the frequency, rate or extent of mesodermal cell differentiation." + "All of the contents of a plasma membrane bounded neuron projection, excluding the plasma membrane surrounding the projection." + "Any process that modulates the frequency, rate or extent of the directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "Any process that decreases the frequency, rate or extent of mesenchymal cell proliferation that contributes to the progression of the ureter gland over time. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets." + "An epithelial cell that is part of the glomerular parietal epithelium." "KUPO:0001035 FMA:70968" + "An immunoglobulin lambda-like polypeptide 1 that is encoded in the genome of human." "UniProtKB:P15814" + "The duct that drains bile from the left half of the liver and joins the right hepatic duct to form the common hepatic duct." "NCIT:C32960 MA:0001638 EHDAA2:0000941 EMAPA:32795 UMLS:C0227560 EHDAA:3990 SCTID:245400009 VHOG:0000218 FMA:14670" + "The process of creating a trabecula in the liver. A trabecula is a tissue element in the form of a small beam, strut or rod." + "Any apoptotic process in a smooth muscle cell. Smooth muscle consists of non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels." + "The proximal straight tubule is the part of the descending limb that extends from the proximal convoluted tubule to the descending thin tubule." "ZFA:0005291 MA:0002614 Wikipedia:Proximal_straight_tubule FMA:17716 EMAPA:29661 BTO:0000055 TAO:0005291 EMAPA:29669" + "A bone that is part of a craniocervical region." "EMAPA:37245 MA:0000569" + "The biological process whose specific outcome is the progression of a kidney mesenchyme from an initial condition to its mature state. This process begins with the formation of kidney mesenchyme and ends with the mature structure. Kidney mesenchyme is the tissue made up of loosely connected mesenchymal cells in the kidney." + "A taste bud that is located in the esophagus." + "An arachnoid mater that is part of a spinal cord [Automatically generated definition]." "VHOG:0000234 MA:0001131 EMAPA:17805" + "Any process that activates, maintains or increases the frequency, rate or extent of myotube cell migration." + "Any process that modulates the frequency, rate or extent of a process in which a cell, a substance, or a cellular entity is transported to, or maintained in a specific location within or in the membrane of a cell." + "The process whose specific outcome is the progression of an erythrocyte over time, from its formation to the mature structure." + "A capillary that is part of the coronary system." "ZFA:0005813" + "The chemical reactions and pathways resulting in the breakdown of ketones, a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups." + "Any process that activates or increases the frequency, rate or extent of T-helper 1 cell cytokine production." + "A cone cell that detects short wavelength light. Exact peak of spectra detected differs between species. In humans, spectra peaks at 420-440 nm." + "A terminally differentiated, post-mitotic, antibody secreting cell of the B cell lineage with the phenotype CD138-positive, surface immunonoglobulin-negative, and MHC Class II-negative. Plasma cells are oval or round with extensive rough endoplasmic reticulum, a well-developed Golgi apparatus, and a round nucleus having a characteristic cartwheel heterochromatin pattern and are devoted to producing large amounts of immunoglobulin." "MESH:D010950 FMA:70574 BTO:0000392" + "The cellular avascular layer of the renal tubule luminar surfaces." "EMAPA:36524 BTO:0005239 UMLS:C1709902 NCIT:C49276 MA:0001681" + "Dermal, epidermal, glandular and pigment structures of the external head integument." + "The progression of the proepicardium from its formation to the mature structure. The proepicardium is an outpouching of the septum transversum." + "The inner (visceral) layer of the renal glomerular capsule, overlying the capillaries, composed of podocytes, and separated from the outer (parietal) layer by the capsular (Bowman's) space[BTO]. This epithelial layer is superficially adjacent to the thickened glomerular basement membrane and is made of podocytes. Beneath the visceral layer lie the glomerular capillaries[WP]. This inner epithelial layer of the glomerular capsule surrounds the capillary endothelial cells and is composed of highly specialized epithelial cells (podocytes) that are separated by filtration slits; the inner visceral layer is separated from the outer parietal layer by the urinary space (also known as the Bowman's or capsular space)[MP]." "UMLS:C0227644 SCTID:244093000 NCIT:C33879 MA:0002607 FMA:74273 EMAPA:28254" + "Any process that activates or increases the frequency, rate or extent of mononuclear cell proliferation." + "Any process that modulates the frequency, rate or extent of oocyte maturation." + "A relaxin receptor 1 that is encoded in the genome of human." "UniProtKB:Q9HBX9 DTO:02100761 Reactome:R-HSA-444834" + "Any process that modulates the frequency, rate, extent or direction of cell growth." + "Mesenchyme that is part of a limb/fin bud." + "A phagocyte in vertebrates that is able to phagocytosis." + "Paired appendage that consists of the anterior appendicular skeleton and associated soft and hard tissues, but excludes the pectoral girdle and its associated soft and hard tissues." "VSAO:0000125 VHOG:0001753" + "Any process that activates or increases the frequency, rate or extent of acetylcholine biosynthetic process." + "The specification and formation of anisotropic intracellular organization that contributes to the self-propelled directed movement of an ameboid cell taking part in gastrulation." + "An system process carried out by any of the organs or tissues of the hepaticobiliary system. The hepaticobiliary system is responsible for metabolic and catabolic processing of small molecules absorbed from the blood or gut, hormones and serum proteins, detoxification, storage of glycogen, triglycerides, metals and lipid soluble vitamins and excretion of bile. Included are the synthesis of albumin, blood coagulation factors, complement, and specific binding proteins." + "A T-cell surface glycoprotein CD8 alpha chain that is a translation product of some mRNA whose exon structure and start site selection renders it capable of giving rise to a protein with the amino acid sequence represented by UniProtKB:P01732-1 or a 1:1 ortholog thereof. Having a single-pass transmembrane domain, this form is membrane bound." + "The transport of substances that occurs outside cells." + "The establishment, maintenance and elaboration of an axis in the oocyte. An example of this is found in Drosophila melanogaster." + "An amacrine cell with a wild dendritic field, dendrites in S3, and post-synaptic terminals in S3. Dendrites have spikes, cross over each other, and cover a larger volume than dendrties of W3-1 retinal amacrine cells." + "A Be cell that facilitates development of T-helper 1 (Th1) phenotype in CD4-positive T cells, and secretes high levels of interleukin-2, tumor necrosis factor-alpha and interferon-gamma." + "An oval area in the retina, usually located temporal to the posterior pole of the eye and slightly below the level of the optic disk. It is characterized by the presence of a yellow pigment diffusely permeating the inner layers, contains the fovea centralis in its center, and provides the best phototopic visual acuity. It is devoid of retinal blood vessels, except in its periphery, and receives nourishment from the choriocapillaris of the choroid. (From Cline et al., Dictionary of Visual Science, 4th ed)." "NCIT:C26464 EMAPA:36516 BTO:0003015 EV:0100349 MA:0001306 MESH:D008266 GAID:909 UMLS:C1284755 NCIT:C33044 FMA:58637 Wikipedia:Macula_of_retina SCTID:362517001 UMLS:C0450295 BIRNLEX:2540" + "A mucosa that is part of a transverse colon [Automatically generated definition]." "FMA:15012" + "Any cellular process that results in the specification, formation or maintenance of polarized cytoskeletal structures." + "Any process that stops, prevents or reduces the frequency, rate or extent of aldosterone secretion." + "The arachnoid trabeculae are delicate strands of connective tissue that loosely connect the two innermost layers of the meninges -- the arachnoid mater and the pia mater. They are found within the subarachnoid space where cerebrospinal fluid is also found. Embryologically, the trabeculae are the remnants of the common precursor that forms both the arachnoid and pial layers of the meninges." "BTO:0002500 FMA:83979 Wikipedia:Arachnoid_trabeculae" + "The process in which a relatively unspecialized larval lymph gland-derived hemocyte precursor cell acquires the specialized features of a crystal cell. Crystal cells are a class of cells that contain crystalline inclusions and are involved in the melanization of pathogenic material in the hemolymph." + "The flow of blood through the body of an animal, enabling the transport of nutrients to the tissues and the removal of waste products." + "Any process that activates or increases the frequency, rate or extent of the directed movement of lipids within cells." + "Secretion produced by a sweat gland." "MA:0002539 GAID:1172 ENVO:02000025 NCIT:C13280 UMLS:C0038984 BTO:0001254 FMA:12275 Wikipedia:Sweat MESH:D013542" + "An anatomical space that is part of a duodenum." "FMA:14589 EMAPA:19080" + "Any process that stops, prevents or reduces the frequency, rate or extent of satellite cell proliferation." + "Peripheral sensory neuron." + "Any mesenchymal stem cell of the bone marrow that is part of a femur." + "A ganglion of the sympathetic nervous system. Examples: paravertebral and the prevertebral ganglia, which include the sympathetic chain ganglia, the superior, middle, and inferior cervical ganglia, and the aorticorenal, celiac, and stellate ganglia." "UMLS:C0017071 FMA:5890 SCTID:362485003 EMAPA:17157 CALOHA:TS-0994 AAO:0010773 EHDAA2:0001969 MA:0000226 Wikipedia:Sympathetic_ganglion NCIT:C12467 BTO:0001333" + "The sympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system (the other being the parasympathetic nervous system). The sympathetic preganglionic neurons have their cell bodies in the thoracic and lumbar regions of the spinal cord and connect to the paravertebral chain of sympathetic ganglia. Innervate heart and blood vessels, sweat glands, viscera and the adrenal medulla. Most sympathetic neurons, but not all, use noradrenaline as a post-ganglionic neurotransmitter [GO]." "NCIT:C12795 EFO:0000893 MA:0000225 ZFA:0001576 UMLS:C0039044 EHDAA:3769 MIAA:0000100 UMLS:C1269646 FMA:9906 GAID:710 AAO:0010487 EHDAA2:0001971 SCTID:362484004 BIRNLEX:2516 CALOHA:TS-2050 BTO:0001832 TAO:0001576 MESH:D013564 EMAPA:16985 VHOG:0000384 Wikipedia:Sympathetic_nervous_system" + "Any process that activates or increases the frequency, rate or extent of mitosis." + "The process in which a relatively unspecialized cell acquires the specialized features of a retinal rod cell." + "Any process that activates or increases the frequency, rate or extent of crystal cell differentiation." + "A GABAergic interneuron in human cortical layer 1 that has large rosehip-shaped axonal boutons and compact arborization." + "An anatomical structure that develops from the ectoderm, mesoderm and endoderm." + "A portion of smooth muscle tissue that is part of an iliac artery." + "A transitional myocyte that is part of the sinoatrial node." "FMA:83384" + "A rod-shpaed cell that forms a single row adjacent to and supporting the inner hair cells." "FMA:75726" + "The process in which the structures of a chondrocyte in the growth plate cartilage are generated and organized." + "The process in which a bronchiole is generated and organized. A bronchiole is the first airway branch that no longer contains cartilage; it is a branch of the bronchi." + "A keratinized cell located in the hard palate or gingiva." + "The cortical collecting duct is the portion of the collecting duct that resides in the renal cortex." "MA:0002600 BTO:0002643 EMAPA:28130" + "A cell that secretes ghrelin, the peptide hormone that stimulates hunger." + "Any process that activates or increases the frequency, rate, or extent of T cell cytokine production." + "Any process that activates or increases the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets." + "The process in which germinal centers form. A germinal center is a specialized microenvironment formed when activated B cells enter lymphoid follicles. Germinal centers are the foci for B cell proliferation and somatic hypermutation." + "A macrophage constitutively resident in a particular tissue under non-inflammatory conditions, and capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells." "FMA:84644 FMA:84642" + "The process in which a cellular entity is generated and organized. A cellular entity has granularity above the level of a protein complex but below that of an anatomical system." + "FMA:53671" + "Any process that stops, prevents or reduces the frequency, rate or extent of ovarian follicle development." + "A receptor-type tyrosine-protein phosphatase C that is a translation product of some mRNA whose exon structure and start site selection renders it capable of giving rise to a protein with the amino acid sequence represented by UniProtKB:P08575-4 or a 1:1 ortholog thereof." + "In mammals, the pronephric duct is the predecessor of the Wolffian duct[WP]." "SCTID:361406002 TAO:0000150 NCIT:C34279 UMLS:C1283945 XAO:0000063 AAO:0011088 Wikipedia:Pronephric_duct ZFA:0000150" + "Any tagma (UBERON:6000002) that is part of some adult (UBERON:6003004)." + "A cell that is part of a cardiac valve." + "The chemical reactions and pathways involving glycosphingolipids, any compound with residues of sphingoid and at least one monosaccharide." + "A neuron projection quality that is a characteristic of neurons with both soma and projections entirely within the telencephalon." "ILX:0770100" + "The regulated release of serotonin by a cell as part of an inflammatory response." + "The process in which a monocyte expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex." + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving steroids." + "Developing anatomical structure that develops into the eyeball and associated structures." "TAO:0002201 ZFA:0001678" + "Any process that modulates the frequency, rate or extent of the directed movement of a neurotransmitter into a neuron or glial cell." + "A zone of skin that is part of a digit [Automatically generated definition]." "EMAPA:32615 MA:0003011" + "A rhodopsin-like G-protein coupled receptor that is a translation product of the human AVPR1A, AVPR1B, AVPR2, or OXTR genes, 1:1 orthologs thereof, or a semi-ortholog thereof. These receptors bind vasopressin or oxytocin or related nonapeptides." "PIRSF:PIRSF001841 IUPHARfam:66" + "The multiplication or reproduction of telencephalon oligodendrocyte cells, resulting in the expansion of a cell population." + "The process in which the anatomical structures derived from the histoblast disc are generated and organized. This includes the transformation of histoblast cells into adult structures during pupal metamorphosis. Histoblast cells are cells founded in the embryo that are the progenitors to the adult abdomen." + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a lysosome. A lysosome is a cytoplasmic, membrane-bounded organelle that is found in most animal cells and that contains a variety of hydrolases." + "An integrin alpha lacking A domain that is a translation product of the human ITGA4 gene or a 1:1 ortholog thereof." "IUPHARobj:2443" + "A langerin-negative lymph node dendritic cell that is CD103-negative and CD11b-high." + "A sulcus limitans of neural tube that is part of a future medulla oblongata." "EHDAA2:0001100 EMAPA:17561" + "Multi-tissue structure that arises from the heart rudiment and will become the heart tube." "EHDAA2:0001512 FMA:321916 ZFA:0000149 EHDAA:424 Wikipedia:Primitive_heart_tube EMAPA:16215 TAO:0000149 SCTID:361522004 EHDAA:436" + "An adventitia that is part of a seminal vesicle." "SCTID:252406002 FMA:19403 EMAPA:29775" + "BTO:0002771" + "A T-cell surface glycoprotein CD8 alpha chain isoform 1 that has had the signal peptide removed to yield the mature form." + "Neuron found in the spiral ganglion." + "Any process that activates or increases the frequency, rate or extent of blood coagulation." + "Any process that decreases the rate, frequency or extent of keratinocyte proliferation. Keratinocyte proliferation is the multiplication or reproduction of keratinocytes, resulting in the expansion of a cell population." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipoprotein particle stimulus." + "A CD2 molecule that is encoded in the genome of mouse." "UniProtKB:P08920" + "The regulated release of ghrelin from a cell. Ghrelin is a 28 amino acid hunger-stimulating peptide hormone." + "The anterior lateral line consists of small sensory patches (neuromasts) located superficially on the skin or just under the skin in fluid-filled canals on the head of all fishes and most amphibians. The anterior lateral line develops from cranial ectodermal placodes situated between the eye and ear." "TAO:0001470 ZFA:0001470" + "The directed movement of water (H2O) from one side of an epithelium to the other." + "A CD27 molecule that is encoded in the genome of human." "UniProtKB:P26842" + "The process whose specific outcome is the progression of the hair follicle over time, from its formation to the mature structure. A hair follicle is a tube-like opening in the epidermis where the hair shaft develops and into which the sebaceous glands open." + "Transudate contained in the osseous labyrinth outside the membranous labyrinth.[FMA]." "GAID:1185 FMA:60908 NCIT:C33297 ZFA:0005413 Wikipedia:Perilymph UMLS:C0031059 EMAPA:36549 MA:0002529 MESH:D010498 TAO:0005413" + "A cartilage element that is part of a pedal digit mesenchyme." "EMAPA:32948" + "A skeletal ligament that connects a tibia and connects a tarsal skeleton." "SCTID:41159004 FMA:44055" + "Any process that increases the rate or extent of striated muscle cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a striated muscle cell and result in its death." + + "The process in which the anatomical structures of the pulmonary artery are generated and organized. The pulmonary artery is the artery that carries blood from the heart to the lungs." + "A microfold cell (M cell) that is part of the anorectum." + "A sesamoid element that is part of a tarsal skeleton." + "A long bone that is part of a forelimb [Automatically generated definition]." "EMAPA:35350 MA:0000299" + "A protein that is a translation product of the human CD163 gene or a 1:1 ortholog thereof." + "Any process that stops, prevents or reduces the frequency, rate or extent of mesenchymal cell proliferation involved in lung development." + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucagon stimulus." + "A visceral muscle that is transversely striated. Examples include the visceral muscle cells of arthropods." + "Any triple helical collagen trimer that forms fibrils." + "A carcinoembryonic antigen-related cell adhesion molecule 8 that is encoded in the genome of human." "UniProtKB:P31997" + "A biological process in which an animal physically develops after birth or hatching, involving a conspicuous and relatively abrupt change in the animal's form or structure. Examples include the change from tadpole to frog, and the change from larva to adult. An example of this is found in Drosophila melanogaster." "Wikipedia:Metamorphosis" + "The functional unit of the liver, consisting of a mass of hepatocytes from adjacent liver lobules aligned around the hepatic arterioles and portal venules just as they anastomose into sinusoids." "FMA:14654 EMAPA:35497 NCIT:C32992 SCTID:272214009 MA:0002496 UMLS:C0227519" + "The process in which a myeloid precursor cell acquires specializes features of a megakaryocyte." + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus." + "A zone of skin that is part of a external ear [Automatically generated definition]." "FMA:24775 MA:0001233 SCTID:244073008 NCIT:C49481 EMAPA:35301 UMLS:C0222110" + "Skeletogenic cell that has the potential to transform into an osteoblast, and develops from neural crest or mesodermal cells." + "A region of the retina corresponding to a portion of two adjacent substratum layers." + "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])"@en + "Any process that stops, prevents or reduces the frequency, rate or extent of protein depolymerization." + "A lymphatic vessel that is part of a pectoral appendage." "ZFA:0005302 TAO:0005302" + "The disaggregation of a protein-containing macromolecular complex into its constituent components." + "A gingiva that is part of a lower jaw region." "EMAPA:18967 UMLS:C0227123 NCIT:C54204 FMA:59764 SCTID:304704007" + "A mesonephric nephron tubule is an epithelial tube that is part of the mesonephric nephron, the functional part of the mesonephros[GO]." + "A tube extending from the mouth to the anus." "FMA:45615 BILA:0000083 VHOG:0000309 BTO:0000545 EMAPA:16247 ZFA:0000112 NCIT:C34082 UMLS:C0017189 AAO:0010023 BTO:0000511 TAO:0000112 EHDAA:518 galen:AlimentaryTract WBbt:0005743 EHDAA2:0000726 TGMA:0001819 MA:0000917" + "A biological tissue mass, most commonly a mass of nerve cell bodies." "MIAA:0000343 ZFA:0000190 FMA:5884 EHDAA:5621 AEO:0000135 EFO:0000899 EHDAA:918 EHDAA:2897 TGMA:0001016 MESH:D005724 MAT:0000207 WBbt:0005189 Wikipedia:Ganglion VHOG:0000156 EHDAA2:0003135 NCIT:C12719 EMAPA:32846 BTO:0000497 MIAA:0000207 UMLS:C0017067 NLXANAT:100302 XAO:0000209 BAMS:G EHDAA:4662 CALOHA:TS-0397 TAO:0000190 MA:0002406 AAO:0010426 MAT:0000343 EV:0100372" + "Any process that modulates the frequency, rate or extent of glucose transport across a membrane. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "A smooth muscle cell that is located in the anorectum." + "Any head that is part of some larva." + "The mitral cell layer is composed of pyramidal neurons whose cell bodies are located between the granule cell layer and the plexiform layer." "NLXANAT:100201 MA:0000973 BTO:0001108 DHBA:11329 DMBA:15912 EMAPA:35611 BAMS:Mi" + "Mesenchyme with little extracellular matrix." "EHDAA2:0003146 AEO:0000146" + "Transport systems of this type enable facilitated diffusion of water (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism." "Reactome:R-HSA-507870 Reactome:R-HSA-432010 Reactome:R-HSA-432054 Reactome:R-HSA-507868 Reactome:R-HSA-445714 Reactome:R-HSA-432065 Reactome:R-HSA-432067 RHEA:29667" + "Simple columnar epithelium made up of cells specialized to serve as sensory cells for the reception of external stimuli, as the sensory cells of the cochlea, vestibule, nasal mucosa, and tongue." "FMA:62410 SCTID:309045006 CALOHA:TS-0682" + "An anatomical group whose component structures share a common function." "AEO:0000093" + "The process in which the anatomical structures of the skin are generated and organized. The skin is the external membranous integument of an animal. In vertebrates the skin generally consists of two layers, an outer nonsensitive and nonvascular epidermis (cuticle or skarfskin) composed of cells which are constantly growing and multiplying in the deeper, and being thrown off in the superficial layers, as well as an inner, sensitive and vascular dermis (cutis, corium or true skin) composed mostly of connective tissue." + "The process in which the anatomical structures of the cardiogenic plate are generated and organized. The cardiogenic plate is the first recognizable structure derived from the heart field." + "A thymic medullary epithelial cell that expresses muscle-specific biomarkers." + "A resting mature B cell within the Peyer's patch that is CD19-positive, B220-positive, IgM-positive, AA4-negative, CD23-positive, CD43-negative, and CD5-negative." + "A secretion that is part of a exocrine pancreas [Automatically generated definition]." "NCIT:C33256 MA:0002518 UMLS:C1518867" + "ncithesaurus:Blastemal_Cell" + "The process in which plasma is filtered through the glomerular membrane which consists of capillary endothelial cells, the basement membrane, and epithelial cells. The glomerular filtrate is the same as plasma except it has no significant amount of protein." + "Nerve fibers which project from the central nervous system to autonomic ganglia. In the sympathetic division most preganglionic fibers originate with neurons in the intermediolateral column of the spinal cord, exit via ventral roots from upper thoracic through lower lumbar segments, and project to the paravertebral ganglia; there they either terminate in synapses or continue through the splanchnic nerves to the prevertebral ganglia. In the parasympathetic division the fibers originate in neurons of the brain stem and sacral spinal cord. In both divisions the principal transmitter is acetylcholine but peptide cotransmitters may also be released." "Wikipedia:Preganglionic_nerve_fibers NCIT:C12624 FMA:5923 MESH:D001339" + "A type EC enteredocrine cell in the intestines that stores and secretes substance P and 5-hydroxytryptamine." "FMA:62940" + "Any process that stops, prevents or reduces the frequency, rate or extent of synapse organization." + "The migration of GABAergic interneuron precursors from the subpallium to the cerebral cortex." + "A mitotic cell cycle in which chromosomes are replicated and sister chromatids separate, but spindle formation, nuclear membrane breakdown and nuclear division do not occur, resulting in an increased number of chromosomes in the cell." "Wikipedia:Mitosis#Endomitosis" + "Any of the parasympathetic ganglia of the cardiac plexus between the arch of the aorta and the bifurcation of the pulmonary artery." "EMAPA:36644 SCTID:57098005 FMA:77582" + "The process in which a B cell in the spleen acquires the specialized features of a germinal center B cell. Germinal center B cells are rapidly cycling B cells which have downregulated IgD expression and exhibit high levels of binding by peanut agglutinin (PNA)." + "Any process that activates or increases the frequency, rate or extent of keratinocyte migration." + "Any process that modulates the frequency, rate or extent of dense core granule transport." + "Any process that modulates the frequency, rate or extent of muscle contraction." + "The evagination of the Golgi membrane, resulting in formation of a vesicle." + "A developmental process, independent of morphogenetic (shape) change, that is required for a neuron to attain its fully functional state." + "An axial muscle that originates in the cervical vertebraae inserts on the scapula." "Wikipedia:Levator_scapulae_muscle FMA:32519 AAO:0010689 EHDAA2:0000992 EHDAA:8309 SCTID:279236008" + "Any process that modulates the physical form of a synapse, the junction between a neuron and a target (neuron, muscle, or secretory cell)." + "A developmental process, independent of morphogenetic (shape) change, that is required for the cerebellar cortex to attain its fully functional state. The cerebellar cortex is a thin mantle of gray matter that covers the surface of each cerebral hemisphere. It has a characteristic morphology with convolutions (gyri) and crevices (sulci) that have specific functions. Six layers of nerve cells and the nerve pathways that connect them comprise the cerebellar cortex. Together, these regions are responsible for the processes of conscious thought, perception, emotion and memory as well as advanced motor function." + "A tachykinin-3 that is encoded in the genome of mouse." "UniProtKB:P55099" + "The functional tissue of the kidney, consisting of the nephrons." "BTO:0003604 SCTID:29704000 FMA:15574" + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an aldosterone stimulus." + "The capsule surrounding the inner ear mechanism." "SCTID:361515007 AAO:0010143 VHOG:0000854 EMAPA:17596" + "Any process that activates or increases the frequency, rate or extent of microglial cell mediated cytotoxicity." + "A transitional myocyte that is part of the right branch of atrioventricular bundle." "FMA:263172" + "A cell in the zona fasciculata that produce glucocorticoids, e.g cortisol." "FMA:69547" + "A renal filtration cell is a specialized cell of the renal system that filter fluids by charge, size or both." + "A segment of a digit containing the distal phalanx, and overlapping the distal interphalangeal joint[CJM]. The digit tip is derived from multiple and distinct embryonic origins, and includes the distal bone with associated marrow cavity and haematopoietic cells, ventral (flexor) and dorsal (extensor) tendons, sweat glands with myoepithelial and luminal secreting cells and associated neurons for innervation, dermis with resident melanocytes and dendritic cells, mesenchyme with resident fibroblasts, skin epidermis with hair follicles, a nail organ composed of six specific parts (the root, nail bed, nail plate, eponychium (cuticle), perionychium and hyponychium)." + "The chemical reactions and pathways involving histamine, a physiologically active amine, found in plant and animal tissue and released from mast cells as part of an allergic reaction in humans." + "The progression of a trachea gland over time, from its formation to the mature structure. Trachea glands are found under the mucus of the trachea and secrete mucus, and agents that help protect the lung from injury and infection." + "NCIT:C32895 UMLS:C0227610 FMA:15590 SCTID:279376000" + "The sinus venosus is a large cardiac chamber at the inflow tract that receives venous blood from systemic circulation. precedes the atrium on the venous side of the chordate heart." "UMLS:C0231084 FMA:70303 AAO:0010505 EHDAA2:0001839 EHDAA:480 VHOG:0000177 Wikipedia:Sinus_venosus NCIT:C34299 EMAPA:16237 TAO:0000154 NCIT:C34300 UMLS:C0225857 ZFA:0000154" + "The developmental process pertaining to the initial formation of a mesonephric nephron tubule from unspecified parts. A mesonephric nephron tubule is an epithelial tube that is part of a nephron in the mesonephros." + "The increase in size or mass of an organ. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that function together as to perform a specific function." + "Any process that stops, prevents, or reduces the frequency, rate or extent of myoblast differentiation. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers." + "A vesicle-mediated transport process in which the postsynapse take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle." + "The movement of substances between cells." + "A muscle cell that is part of the middle internodal tract." "FMA:223279" + "A zone of skin that is part of a upper lip." "SCTID:281629007 FMA:24765" + "The process aimed at the progression of an enucleate erythrocyte over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell." + "A transitional myocyte that is part of the anterior division of left branch of atrioventricular bundle." "FMA:263166" + "A vertebrate phagocyte with a single nucleus." "BTO:0001433" + "Any process that modulates the frequency, rate or extent of translation of mRNAs that contribute to the specification of the anterior/posterior axis." + "A submucosa that is part of a lobar bronchus [Automatically generated definition]." "FMA:62669" + "A medium-wave-sensitive opsin that is encoded in the genome of human." + "A cell whose primary function is to prevent the transport of stuff across compartments." + "A cell that is part of kidney interstitium." "KUPO:0001013" + "A proximal metaphysis that is part of a femur." "FMA:32878" + "Any process that modulates the frequency, rate or extent of addition of phosphate groups into an amino acid in a protein." + "Any process that stops, prevents, or reduces the frequency, rate or extent of natural killer cell differentiation as part of an immune response." + "A process that leads to a temporary increase in postsynaptic potential due to the flow of positively charged ions into the postsynaptic cell. The flow of ions that causes an EPSP is an excitatory postsynaptic current (EPSC) and makes it easier for the neuron to fire an action potential." + "The outermost layer of the aorta wall, containing connective tissue and collagen and elastic fibers." "FMA:14283 SCTID:24996002 EMAPA:35136 MA:0002902" + + "Any process that stops, prevents, or reduces the frequency, rate or extent of striated muscle development." + "The process in which a relatively unspecialized cell acquires specialized structural and/or functional features of a Sertoli cell. A Sertoli cell is a supporting cell projecting inward from the basement membrane of seminiferous tubules." + "A submucosa that is part of a bronchiole [Automatically generated definition]." "FMA:62775" + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus." + "Any process that activates or increases the frequency, rate, or extent of interleukin-4 production." + "Any process that stops, prevents or reduces the frequency, rate or extent of microglial cell mediated cytotoxicity." + + "A CD11b-positive dendritic cell that is CD11b-high, CD45-positive, MHC-II-positive and CD103-negative." + "Glandular cell of oviduct epithelium. Example: peg cells, ciliated cells." "CALOHA:TS-1277" + "A region of the serous membrane that forms the innermost layer of the pericardium and the outer surface of the heart." "TAO:0005057 ZFA:0005057 EHDAA2:0002202 UMLS:C0225968 NCIT:C13164 Wikipedia:Epicardium FMA:9461 VHOG:0000119 galen:Epicardium AAO:0010409 XAO:0000316" + "The regulated release of an antimicrobial peptide from a cell or a tissue. Such peptides may have protective properties against bacteria, fungi, viruses, or protozoa." + "A double negative thymocyte that is CD3-positive, CD4-negative, CD8-negative, that that are present in the periphery in very low numbers and predominantly produce INF-gamma, TNF-alpha, and a low amount of TGF-beta, but not IL-2, IL-4, IL-10 or IL-13 upon activation." + "A mammary gland that is part of a cervical region." "MA:0000789" + "A visceral muscle cell that is striated. Examples include the visceral muscle cells of arhtropods." + "An epithelial cell that is part of the lacrimal drainage system." "FMA:70559" + "Portion of tissue that is part of the heart tube and will become the sinus venosus." "TAO:0002234 ZFA:0001722" + "The process in which the anatomical structures of a pronephric nephron tubule are generated and organized from an epithelium. A pronephric nephron tubule is an epithelial tube that is part of the pronephric nephron." + "The process whose specific outcome is the progression of a nephron in the metanephros over time, from its formation to the mature structure. A nephron is the functional unit of the kidney." + "The expulsion of seminal fluid, thick white fluid containing spermatozoa, from the male genital tract." + "The developmental process by which an epicardium is generated and organized." + "The process in which a relatively unspecialized cell acquires specialized features of a blood vessel endothelial cell, a thin flattened cell that lines the inside surfaces of blood vessels." + "Dermal, epidermal, glandular and pigment structures of the tail integument." + "Mesenchyme that is part of a medial nasal prominence." "EHDAA2:0001077 FMA:312659 EMAPA:16810" + "Part of the ear external to the tympanum (eardrum). It typically consists of a tube (the external auditory meatus) that directs sound waves on to the tympanum, and may also include the external pinna, which extends beyond the skull[GO]." "BTO:0002100 NCIT:C12292 VHOG:0000311 EHDAA2:0000462 MAT:0000147 UMLS:C0013453 XAO:0000190 MIAA:0000147 BIRNLEX:1705 MESH:D004431 EV:0100354 GAID:104 Wikipedia:External_ear EHDAA:3786 UMLS:C1269548 SCTID:420893000 EFO:0004221 MA:0000258 AAO:0011037 FMA:52781 EMAPA:16991" + "A urothelial cell that is terminally differentiated and part of the urothelial apical surface that forms the high-resistance barrier of urothelium. Umbrella cells have been described as the largest of urothelial cell types, highly polarized, and, in some species, multinucleated. In the relaxed state, these cells form a dome-shaped structure at the apical pole and can also cover multiple underlying intermediate cells, leading to the name umbrella cells. In contrast, these cells flatten when the bladder is filled." "FMA:84149" + "The chemical reactions and pathways resulting in the formation of any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone." + "The series of events required for an organism to receive a sensory stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process." "Wikipedia:Perception" + + "Cervical lymph nodes are lymph nodes found in the neck. [WP,unvetted]." "NCIT:C32298 FMA:61213 Wikipedia:Cervical_lymph_nodes UMLS:C0588054 MA:0000736 SCTID:181757009" + "Signal transduction in which the initial step occurs in a presynapse." + "The process whose specific outcome is the progression of the anterior lateral line system over time, from its formation to the mature structure. The anterior lateral line system develops from cranial ectodermal placodes, situated between the eye and the ear, that give rise to both the neuromasts and the anterior lateral line sensory nerves that innervate the neuromasts. The anterior lateral line system consists of small sensory patches (neuromasts) located superficially on the skin or just under the skin in fluid-filled canals on the head of all fishes and most amphibians and are innervated by several lateral line nerves, which project to the hindbrain. The anterior lateral line system is stimulated by local water displacements and vibrations, and detects propulsion of the fish through the water, as well as facilitating shoaling, prey capture, and predator and obstacle avoidance." + "Cell-cell signaling that mediates the transfer of information from a glial cell to a neuron. This signaling has been shown to be mediated by various molecules, depending on which glial cells release them, and in which tissues the signaling occurs, e.g. microglial cell-derived nerve growth factor (NGF) in the retina, or microglial cell-derived superoxide ions in the cerebellum." + "A natural cytotoxicity triggering receptor 1 that is encoded in the genome of mouse." "UniProtKB:Q8C567" + "Any process that activates or increases the frequency, rate or extent of neurogenesis, the generation of cells within the nervous system." + "The progression of the glomerulus of the pronephric kidney over time from its initial formation until its mature state. The pronephric glomerulus is part of the pronephric nephron and is restricted to one body segment." + "An anatomical space which is the lumen of some anatomical conduit and connects two or more spaces together[FMA,modified]." "FMA:9338" + "A bipolar neuron found in the retina and having connections with photoreceptors cells and neurons in the inner plexiform layer." + "An absorptive epithelial cell of the human intestine expressing bestrophin-4 (BEST4) calcium-activated ion channels." + "Any process that activates or increases the frequency, rate or extent of bone mineralization involved in bone maturation." + "The process in which the population of cells that make up a tissue undergo directed movement." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism." + "The process in which a relatively unspecialized cell derived from the embryonic head mesoderm acquires the specialized features of a mature hemocyte. Hemocytes are blood cells associated with a hemocoel (the cavity containing most of the major organs of the arthropod body) which are involved in defense and clotting of hemolymph, but not involved in transport of oxygen." + "The directed movement of organelles or molecules along microtubules in neuron projections." "Wikipedia:Axoplasmic_transport" + "A protein that is composed of a long N-terminal extracellular domain, a transmembrane domain and a short cytoplasmic C-terminal domain. The N-terminal domain contains beta-propeller repeats (interrupted by an A domain in a subset of integrins alpha), while the C-terminal domain contains a GFFxR motif." + "The external masculine genital organs, including the penis and scrotum." "BTO:0003097 galen:MaleExternalGenitalia EMAPA:30977 FMA:45642 SCTID:362264000" + "A chemokine receptor that is a translation product of the human CCR5 gene or a 1:1 ortholog thereof. The preferred ligands include CCL3, CCL4, CCL5, CCL8, CCL14." "IUPHARobj:62" + "The series of events in which an (non-living) abiotic stimulus is received by a cell and converted into a molecular signal." + "A transmembrane emp24 domain-containing protein 1 that is encoded in the genome of mouse." "UniProtKB:Q3V009" + "A squamous epithelium that is part of a esophagus." "BTO:0003635 NCIT:C49222 MA:0001567 EMAPA:35324 CALOHA:TS-1250 UMLS:C1707950" + "The process whose specific outcome is the progression of a striated muscle cell over time, from its formation to the mature structure. Striated muscle cells contain fibers that are divided by transverse bands into striations, and cardiac and skeletal muscle are types of striated muscle." + + "A mesenchymal cell of the endocardial cushion. These cells develop via an epithelial to mesenchymal transition when endocardial cells break cell-to-cell contacts and migrate into the cardiac jelly. Cells from this population form the heart septa and valves." + "A neprilysin that is encoded in the genome of mouse." "UniProtKB:Q61391" + "An intestinal villus in the jejunum." "FMA:63301" + "The increase in size or mass of an entire organism, a part of an organism or a cell." + "A CD8-positive alpha-beta-positive T cell with the phenotype CXCR3-positive and having suppressor function. They are capable of producing IL-10, suppressing proliferation, and suppressing IFN-gamma production." + "CD8-positive, alpha-beta memory T cell with the phenotype CCR7-negative, CD127-positive, CD45RA-negative, CD45RO-positive, and CD25-negative." + "A neuron that has its soma located in CA4 of the hippocampus." + "The increase in size or mass of the prostate gland where the increase in size or mass has the specific outcome of the progression of the gland, from its formation to its mature state." + + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an oxygen-containing compound stimulus." + "Any process that activates or increases the frequency, rate or extent of leukocyte proliferation." + "A mesothelial cell that is part of the parietal peritoneum." "FMA:72142" + "The layer of the myocardium composed of projections of contractile myocytes. The trabecular layer is bounded internally by the endocardium. In zebrafish, unlike the trabeculations of higher vertebrates, both atrial and ventricular trabeculae have more strut-like character, and are more uniform without apparent regional differences[ZFA]." "MA:0002866 TAO:0005059 ZFA:0005059 EFO:0003706" + "Parenchymal tissue that consists of the alveoli, grape-like clusters where milk is stored, and branching ducts, which are tubular canals carrying gladular secretions." + "Any apoptotic process in a leukocyte, an achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue." + "Any process that modulates the frequency, rate or extent of cytoplasmic translational termination." + "Mesenchyme that is part of a forelimb bud." + "Binding to a major histocompatibility complex class Ib molecules." + "Binding to a juvenile hormone, a sesquiterpenoid derivative that function to maintain the larval state of insects at molting and that may be required for other processes, e.g. oogenesis." + "Any process that stops, prevents, or reduces the frequency, rate or extent of microtubule polymerization or depolymerization." + "Any process that decreases the rate, frequency, or extent of epithelial to mesenchymal transition. Epithelial to mesenchymal transition where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell." + "A thick watery refractive medium that fills the space between the lens and the cornea[WP]." "EMAPA:18232 ENVO:02000024 NCIT:C13190 SCTID:280587006 MA:0001236 VHOG:0000548 ZFA:0005564 MESH:D001082 Wikipedia:Aqueous_humor FMA:58819 UMLS:C0003662 EHDAA:10196 GAID:890 EHDAA2:0000139" + "The process whose specific outcome is the progression of an appendage over time, from its formation to the mature structure. An appendage is an organ or part that is attached to the trunk of an organism, such as a limb or a branch." + "Bone tissue that forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP]." "MA:0002837 Wikipedia:Intramembranous_ossification" + "Any process that modulates the frequency, rate, or extent of a chronic inflammatory response." + "The simple columnar epithelial lining of the gall bladder." "NCIT:C49227 UMLS:C1180206 MA:0001632 EMAPA:35370 BTO:0001449 CALOHA:TS-1304 FMA:67711" + "Any apoptotic process that is involved in anatomical structure development." + + "A protein that is a translation product of the human THY1 gene or a 1:1 ortholog thereof." "PIRSF:PIRSF038777" + "Any tube, opening or passage that connects two distinct anatomical spaces." "FMA:242873 EHDAA2:0003080 Wikipedia:Foramen AEO:0000080 SCTID:346902003" + "A tyrosine-protein kinase Mer that is encoded in the genome of mouse." "UniProtKB:Q60805" + "Any process that activates or increases the frequency, rate or extent of ureter smooth muscle cell differentiation." + "A low affinity immunoglobulin gamma Fc region receptor II-b that is encoded in the genome of human." "UniProtKB:P31994" + "Any process that stops, prevents or reduces the frequency, rate or extent of myeloid progenitor cell differentiation." + "The progression of a glandular acinus of the prostate gland over time, from its initial formation to the mature structure. The glandular acini are the saclike structures of the gland." + "Any capillary endothelial cell that is part of a placenta." + "Any process that activates or increases the frequency, rate or extent of protein depolymerization." + "Any process that stops, prevents, or reduces the frequency, rate or extent of natural killer cell differentiation." + "A process that directly activates any of the steps required for tolerance, a physiologic state in which the immune system does not react destructively against the components of an organism that harbors it or against antigens that are introduced to it." + + "The initial segment of an olfactory nerve, leaving the central nervous system." "BIRNLEX:1632" + "A progenitor cell restricted to the lymphoid lineage." "CALOHA:TS-2025 FMA:70338 BTO:0004731" + + "A fibroblastic reticular cell found in the lymph node subcapsular sinus." + "The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]." "ZFA:0000008 GAID:571 BIRNLEX:796 MBA:8 EHDAA:2641 BAMS:Br EHDAA:6485 XAO:0000010 galen:Brain MIAA:0000098 EMAPA:16894 neuronames:21 FMA:50801 ABA:Brain UMLS:C1269537 BILA:0000135 EHDAA2:0000183 EFO:0000302 MAT:0000098 DHBA:10155 UMLS:C0006104 BAMS:Brain TAO:0000008 AAO:0010478 HBA:4005 EV:0100164 NCIT:C12439 MA:0000168 MESH:D001921 SCTID:258335003 Wikipedia:Brain BTO:0000142 PBA:3999 VHOG:0000157 MBA:997 CALOHA:TS-0095" + "The sensory system for the sense of touch and pain." "NLXANAT:090818 EMAPA:37954 neuronames:2887 Wikipedia:Somatosensory_system" + "A valve that is part of a vein." "FMA:68095" + "An unilaminar epithelium that surrounds a pelvic appendage bud." "VHOG:0001048 EMAPA:16780 EHDAA2:0001034" + "A melanocyte that produces pigment in the dermis." + "A distal phalanx that is part of a pedal digit [Automatically generated definition]." "UMLS:C0224026 MA:0001380 EMAPA:37310 SCTID:361797001 FMA:75830 NCIT:C52783" + "The process in which a relatively unspecialized cell acquires specialized features of a mammary gland mesenchymal cell. Mammary gland mesenchymal cells form a loosely connected network of cells that surround the mammary ducts." + "Any process involved in the maintenance of an internal steady state of calcium ions within the Golgi apparatus of a cell or between the Golgi and its surroundings." + "An anatomical space that is enclosed by a conjunctiva." "SCTID:280957009 FMA:59083" + "Any process that activates or increases the frequency, rate or extent of cardiac ventricle formation." + "The chemical reactions and pathways resulting in the breakdown of chondroitin sulfate, any member of a group of 10-60 kDa glycosaminoglycans, widely distributed in cartilage and other mammalian connective tissues, the repeat units of which consist of beta-(1,4)-linked D-glucuronyl beta-(1,3)-N-acetyl-D-galactosamine sulfate." + "Tolerance induction in the peripheral lymphoid tissues: blood, lymph nodes, spleen, and mucosal-associated lymphoid tissues." + "Focal thickenings of the embryonic ectoderm that form immediately dorsal and caudal of the clefts between the pharyngeal arches and that produce the neuroblasts that migrate and condense to form the distal cranial ganglia." "FMA:293968 ZFA:0001294 XAO:0000284 TAO:0001294 EFO:0003455 VHOG:0000117 AAO:0011036" + + "The vascular cord is the primordial vasculature that will develop into blood vessels by the process of tubulogenesis[GO]. The vascular cord is composed of angioblast or vascular endothelial cells in a solid linear mass called a cord. The cord then undergoes tubulogenesis to form the lumen of the vessels[ZFA]." "EFO:0003709 ZFA:0005077 TAO:0005077" + + "Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus." + "A D(1A) dopamine receptor that is encoded in the genome of human." "DTO:02100081 UniProtKB:P21728 Reactome:R-HSA-390853" + "Any process that modulates the frequency, rate or extent of sister chromatid segregation during mitosis." + "Any process that stops, prevents, or reduces the frequency, rate or extent of cell adhesion." + "A macrophage receptor MARCO that is encoded in the genome of human." "UniProtKB:Q9UEW3" + "A caudal vertebra endochondral element that is composed primarily of cartilage tissue." "EMAPA:18044 EHDAA2:0000260" + "VHOG:0001384 XAO:0000307 TAO:0007038 ZFA:0007038 AAO:0011012" + "A galectin-1 that is encoded in the genome of human." "UniProtKB:P09382" + "One of two compartments identified in the neostriatum, particularly the caudate nucleus, on the basis of differential staining for several biochemical markers such as acetylcholinesterase and calbindin. In individual sections, the striosomes appear as small patches of differentially high or low staining activity. In three dimensions, they form a 3D labyrinth extending throughout the caudate nucleus and in the putamen." "NLXANAT:20090506" + "The docking of a cytosolic centriole/basal body to the plasma membrane via the ciliary transition fibers. In some species this may happen via an intermediate step, by first docking to the ciliary vesicle via the ciliary transition fibers. The basal body-ciliary vesicle then relocates to the plasma membrane, followed by the ciliary vesicle fusing with the plasma membrane, effectively attaching the basal body to the plasma membrane." "Reactome:R-HSA-5620912.1" + "Any gene expression that is involved in extracellular matrix organization. Gene expression includes both transcription to produce an RNA transcript, and the translation of that mRNA into protein. Protein maturation is included in gene expression when required to form an active form of a product from an inactive precursor form." + "Any process that stops, prevents or reduces the frequency, rate or extent of membrane invagination." + "A bone that is part of a hindlimb digit. Typically phalanges but may include sesamoids." "EMAPA:37309 MA:0000646" + "Binding to a major histocompatibility complex." + + "A localization process that acts on a protein complex; the complex is transported to, or maintained in, a specific location." + "The process pertaining to the initial formation of the mammary gland from unspecified parts. The process begins with formation of the mammary line and ends when the solid mammary bud invades the primary mammary mesenchyme." + "A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." + "Any process carried out at the cellular level that reduces or removes the toxicity of a toxic substance. These may include transport of the toxic substance away from sensitive areas and to compartments or complexes whose purpose is sequestration of the toxic substance." + "An endocardium that is part of a interventricular septum [Automatically generated definition]." "EHDAA2:0000887 VHOG:0000615 EHDAA2:0000886 FMA:83584" + "Any apoptotic process in a fibroblast, a connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules." + "The biological process whose specific outcome is the progression of a nephrogenic mesenchyme from an initial condition to its mature state. This process begins with the formation of nephrogenic mesenchyme and ends with the mature structure. Nephrogenic mesenchyme is the tissue made up of loosely connected mesenchymal cells in the nephron." + "The nonstriated, involuntary muscle tissue located in the wall of the aorta." "NCIT:C49191 UMLS:C1706825 BTO:0001685 EFO:0002775 MA:0000702 EMAPA:35135 CALOHA:TS-0048" + "The process in which the anatomical structures of the tongue are generated and organized. The tongue is the movable, muscular organ on the floor of the mouth of most vertebrates, in man other mammals is the principal organ of taste, aids in the prehension of food, in swallowing, and in modifying the voice as in speech." + "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." "Wikipedia:Enzyme" + "A type of interneuron in the retinal inner nuclear layer which\ncarries information from the inner plexiform layer and the outer\nplexiform layer using GABA." + "The mesonephric glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the mesonephric glomerulus[GO]." + "The process in which the anatomical structures of a dendrite are generated and organized." + "Any process that modulates the frequency, rate or extent of B cell differentiation." + "Any process that modulates the frequency, rate or extent of secretion by cell." + "Any process that modulates the rate frequency or extent of gastric secretion. Gastric secretion is the regulated release of gastric acid (hydrochloric acid) by parietal or oxyntic cells during digestion." + "The process in which a fluid solution, or part of it, changes into a solid or semisolid mass." + "The smooth triangular region of the wall of the urinary bladder formed by the two ureteral orifices and the internal urethral orifice; it is an area in which the muscle fibers are closely adherent to the mucosa." "MA:0002492 NCIT:C12331 EMAPA:35174 UMLS:C0447586 SCTID:272663002 galen:TrigoneOfUrinaryBladder Wikipedia:Trigone_of_urinary_bladder FMA:15910" + "The process whose specific outcome is the progression of mucosal-associated lymphoid tissue over time, from its formation to the mature structure. Mucosal-associated lymphoid tissue is typically found as nodules associated with mucosal epithelia with distinct internal structures including B- and T-zones for the activation of lymphocytes." + "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring within the cell. Includes ribosomes, the cytoskeleton and chromosomes." + "A pre-cartilage condensation that has the potential to develop into a carpal bone." "EHDAA2:0000222 VHOG:0000955 EMAPA:17724 EHDAA:6324" + "A protein that is a translation product of the human GP1BA gene or a 1:1 ortholog thereof." "PIRSF:PIRSF002493" + "The process whose specific outcome is the progression of the stem cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to its specific fate." + "A bipolar neuron found in the retina that is synapsed by rod photoreceptor cells. These neurons have axons that arborize and synapse to targets in inner plexiform layers 4 and 5 and depolarize in response to light." + + "Any process that stops, prevents, or reduces the frequency, rate or extent of meiosis." + "The directed movement of neutral amino acids into the vacuole across the vacuolar membrane." + "FMA:322073" + "A blood vessel that is part of a foot [Automatically generated definition]." "EMAPA:37301 MA:0000642" + "A blood vessel that is part of a toe [Automatically generated definition]." "EMAPA:37302 MA:0000645" + "Bone tissue that is an unmineralized bone matrix deposited by osteoblasts prior to the mineralization of bone tissue." "galen:Osteoid UMLS:C0682561 Wikipedia:Osteoid EMAPA:37923 SCTID:39365008 VSAO:0000046 NCIT:C33228 XAO:0004035 FMA:66830" + "A mucosa that is part of a urethra." "EMAPA:37912 FMA:76904 SCTID:362229009" + "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane and occurring outside the cell." + "A glial cell that develops from a Schwann cell precursor. The immature Schwann cell is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has a basal lamina. Cells can survive without an axon present. Immature Schwann cell can be found communally ensheathing large groups of axons." "ZFA:0001725" + "The third segment of the limb, including either the wrist segment (carpus) or the ankle segment (tarsus)." "Wikipedia:Carpus_and_tarsus_of_land_vertebrates" + "An endothelial cell of the vascular tree, which includes blood vessels and lymphatic vessels." "FMA:67755 CALOHA:TS-1106 BTO:0001854" + "A Lamp5 GABAergic cortical interneuron that has extended axons in the surface of L1. Canopy Lamp5 cells resemble neurogliaform cells in having elongated horizontal axonal arbors largely confined to L1; but the dendritic arbors are wider and have fewer branches, while the axon is less tortuous and extends further from the soma" + "A cuboidal epithelial cell of the kidney which regulates sodium and potassium balance. The activity of sodium and potassium channels on the apical membrane of the cell is regulated by aldosterone and vasopressin. In mammals this cell type is located in the renal collecting duct system." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of ecdysteroids." + "A nerve that is part of a foot [Automatically generated definition]." "MA:0000653 EMAPA:37347" + "A mesenchyme-derived anatomical entity undergoing a transtion to become another structure." "AEO:0001016" + "The process whose specific outcome is the progression of the metanephric long descending thin limb over time, from its formation to the mature structure. The metanephric long descending thin limb is the descending thin limb of a long nephron in the metanephros that has a squamous epithelial morphology. The long descending limb starts in the inner stripe of the outer medulla and extends into the inner medulla." + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a dense core granule. A dense core granule is a secretory organelle found in endocrine cells." + "A B7-related protein that is a translation product of the human CD86 gene or a 1:1 ortholog thereof." "IUPHARobj:2745" + "An epithelium that is part of a hip [Automatically generated definition]." "EMAPA:17491 EHDAA:6180 EHDAA:5155 VHOG:0000779 EHDAA2:0000784" + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus." + "The process in which the anatomical structures of the mesonephric nephron are generated and organized. A mesonephric nephron is the functional unit of the mesonephros." + "A mesodermal signaling center of the hair follicle consisting of closely packed specialized mesenchymal fibroblasts. Framed by the enlarged bulb matrix in anagen." "NCIT:C83189 NCIT:C32710 CALOHA:TS-0431 Wikipedia:Dermal_papillae SCTID:320101005 EMAPA:36484 FMA:70737 BTO:0001858 UMLS:C0221931" + "A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative)." "FMA:83036 BTO:0002042 MESH:D003713 CALOHA:TS-0194" + "Any process that activates or increases the frequency, rate or extent of growth of an organism to reach its usual body size." + "An interleukin-1 receptor-like 1 that is encoded in the genome of mouse." "UniProtKB:P14719" + "The process in which a relatively unspecialized cell acquires specialized features of a satellite cell." + "A cell that stains readily in the anterior pituitary gland." "FMA:83089" + "The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex." + "Any process that modulates the rate or frequency of muscle cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a muscle cell and result in its death." + "A myocardium that is part of a left ventricle of a heart." "SCTID:362021000 FMA:9558 MA:0002983" + "A developmental process, independent of morphogenetic (shape) change, that is required for a blood vessel to attain its fully functional state." + "Cell that is part of the notochord." + "The process in which the anatomical structures of cardiac left ventricular trabecular myocardium are generated and organized." + "Any process that modulates the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury." + "The process in which an antigen-presenting cell expresses a peptide antigen on its cell surface in association with an MHC class II protein complex. The peptide antigen is typically, but not always, processed from a whole protein." + "Any process that modulates the rate, frequency, or extent of the progression of the sclerotome over time, from its initial formation to the mature structure. The sclerotome is the portion of the somite that will give rise to a vertebra." + "Any process that activates, maintains or increases the frequency, rate or extent of the directed movement of amines into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "Either the internal or external pudendal vein, running from the genital-vulvar area and abdomen and down the leg." "EMAPA:37184 MA:0002202 SCTID:395225000" + "OBSOLETE: A lymphocyte that lacks T or B cell surface markers." "FMA:83601" + "Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO)." "CALOHA:TS-0953 UMLS:C0037925 AAO:0010151 Wikipedia:Spinal_cord MAT:0000183 FMA:7647 DHBA:12890 BM:SpC MIAA:0000183 MESH:D013116 EHDAA:2863 BTO:0001279 EV:0100316 EMAPA:17577 TAO:0000075 EFO:0000110 NCIT:C12464 neuronames:22 GAID:695 BIRNLEX:1709 MA:0000216 BAMS:Spinal SCTID:180959008 VHOG:0000601 ZFA:0000075 DMBA:17651 EHDAA2:0001255 XAO:0000020 BAMS:SP" + "A pericyte of the central nervous system." + "Development of a photoreceptor, a sensory cell in the eye that reacts to the presence of light. They usually contain a pigment that undergoes a chemical change when light is absorbed, thus stimulating a nerve." + "Mesenchyme of the carpal region that contributes to the tarsal skeleton." "EMAPA:18502" + "Mesenchyme that is part of a developing hindgut." "EMAPA:16716 EHDAA2:0000780" + "Combining with an extracellular or intracellular peptide to initiate a change in cell activity." + "A gray matter of spinal cord that is part of a thoracic spinal cord." "UMLS:C0228627 SCTID:362441000 BIRNLEX:980" + "The regionalization process that specifies animal organ primordium boundaries resulting in a restriction of organogenesis to a limited spatial domain and keeping the organ separate from surrounding tissues." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells." + "The process whose specific outcome is the progression of an epithelium in the metanephros over time, from its formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure." + "The process whose specific outcome is the progression of a mesangial cell in the kidney over time, from its formation to the mature structure." + "Any process that activates or increases the frequency, rate or extent of male germ-line stem cell asymmetric division." + "A long bone that is part of a limb [Automatically generated definition]." "EMAPA:35495 MA:0000298" + "A paneth cell of the appendix." + "A mature alpha-beta T cell of a distinct lineage that bears natural killer markers and a T cell receptor specific for a limited set of ligands. NK T cells have activation and regulatory roles particularly early in an immune response." + "A cell that is part of the brain vasculature." + "A quality inhering in a bearer by virtue of its constitution." + "A capsule that surrounds a female gonad." "FMA:18662 MA:0001706 SCTID:258491008 UMLS:C0227877 NCIT:C49265 EMAPA:35626" + "FMA:322074" + "The process in which the anatomical structures of branches in the open tracheal system are generated and organized." + "A type I vestibular sensory cell that is part of the stato-acoustic epithelium." "FMA:263186" + "A mucosa that is part of a jejunum [Automatically generated definition]." "MA:0003214 EMAPA:27109 FMA:14949 BTO:0001742 CALOHA:TS-0495 SCTID:362151009" + "A nucleated immature erythrocyte, having cytoplasm generally similar to that of the earlier proerythroblast but sometimes even more basophilic, and usually regular in outline. The nucleus is still relatively large, but the chromatin strands are thicker and more deeply staining, giving a coarser appearance; the nucleoli have disappeared. This cell is CD71-positive and lacks hematopoeitic lineage markers." "FMA:83505" + "A physical quality of a fluid inhering in a bearer by virtue of the bearer's disposition to internal resistance to flow." + "A digital artery that is part of a forelimb [Automatically generated definition]." "EMAPA:37210 SCTID:265791006 MA:0001953" + "SCTID:280667001 MA:0001318" + "A bone that is shaped as a broad flat plate and composed of two thin layers of compact tissue enclosing between them a variable quantity of cancellous tissue, which is the location of red bone marrow." "Wikipedia:Flat_bone NCIT:C32616 galen:FlatBone FMA:7476 UMLS:C0222649 SCTID:332907008" + "A fibroblast located in the portal triad. Hepatic portal fibroblast are a non-parenchymal cell population located adjacent to bile duct epithelia in liver and are distinct from stellate cells. They differentiate into fibrogenic myofibroblasts during chronic injury states producing high levels of collagen." + "A transitional myocyte that is part of the internodal tract." "FMA:83387" + "The process in which a relatively unspecialized cell acquires specialized features of an amacrine cell, an interneuron generated in the inner nuclear layer (INL) of the vertebrate retina. Amacrine cells integrate, modulate, and interpose a temporal domain in the visual message presented to the retinal ganglion cells, with which they synapse in the inner plexiform layer. Amacrine cells lack large axons." + "An interleukin-3 receptor class 2 alpha chain that is encoded in the genome of human." "UniProtKB:P26951" + "A vein arising from the splenic trabecular vein in the hilum of the spleen that drains into the portal vein." "Wikipedia:Splenic_vein EMAPA:37226 MA:0002164 SCTID:278029005 GAID:541 FMA:14331 UMLS:C0038001 galen:SplenicVein NCIT:C33608 MESH:D013162" + "The protruding lymphoid tissue located on the mucosa of the intestine that is composed of densely packed B cell follicles." "GAID:950 MA:0000137 EFO:0001381 EMAPA:19028 UMLS:C0031272 Wikipedia:Peyer's_patch BTO:0001784 NCIT:C12771 CALOHA:TS-0780 MESH:D010581" + "An anatomical wall that is part of a esophagus [Automatically generated definition]." "FMA:12611 EMAPA:35326 MA:0002691" + "OBSOLETE An intratelencephalic-projecting glutamatergic neuron with a soma found in layer 5 of the marmoset primary motor cortex." "ILX:0770157" + "The pharyngeal aponeurosis (or pharyngobasilar fascia, or fibrous coat), is situated between the mucous and muscular layers. It is thick above where the muscular fibers are wanting, and is firmly connected to the basilar portion of the occipital and the petrous portions of the temporal bones. As it descends it diminishes in thickness, and is gradually lost. It is strengthened posteriorly by a strong fibrous band, which is attached above to the pharyngeal spine on the under surface of the basilar portion of the occipital bone, and passes downward, forming a median raphe, which gives attachment to the Constrictores pharyngis." "FMA:55074 Wikipedia:Pharyngobasilar_fascia SCTID:16675008" + "A protein that is a translation product of the human SDC1 gene or a 1:1 ortholog thereof." "PIRSF:PIRSF015854" + "Any process that activates or increases the frequency, rate or extent of basophil degranulation." + "The multiplication or reproduction of male germ cells, resulting in the expansion of a cell population." + "Specialized cardiac myocyte that is subendocardially interspersed with the regular cardiac muscle cell. They are uninucleate cylindrical cells, associated end-to-end in long rows, continue from the node to the atrioventricular bundle; relatively short compared to ordinary myocytes but are nearly twice their diameter." "FMA:14146 BTO:0001032" + "Appendage girdle complex that when present, encompasses the pectoral appendicular skeleton and the pectoral girdle." "EMAPA:37860 SCTID:110716002 FMA:7183 VSAO:0000213" + "An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light." + "The process that gives rise to the medulla oblongata. This process pertains to the initial formation of a structure from unspecified parts. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate." + "The orderly movement of a cell from one site to another that will contribute to the differentiation of an endothelial cell that will form de novo blood vessels and tubes." + "A glandular epithelial cell of the large intestine." "FMA:87194" + "A tissue whose predominant feature is extracellular matrix which may or may not be highly hydrated or calcified." "EHDAA2:0003081 AEO:0000081" + "Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to plasma membrane." + "Binding to a proteoglycan, any glycoprotein in which the carbohydrate units are glycosaminoglycans." + "The fibrous connective tissue surrounding the thymus." "NCIT:C33770 MA:0000766 FMA:72204 UMLS:C0229945 SCTID:188181003 EMAPA:19306" + "A developmental process, independent of morphogenetic (shape) change, that is required for a cranial ganglion to attain its fully functional state." + "A skeletal element that is part of a limb and composed of pre-cartilage tissue." + "The process in which the anatomical structure of the midbrain-hindbrain boundary is generated and organized. The midbrain-hindbrain domain of the embryonic brain is comprised of the mesencephalic vesicle and the first rhombencephalic vesicle at early somitogenesis stages. An organizing center at the boundary patterns the midbrain and hindbrain primordia of the neural plate." + "A nucleus of brain that is part of a dorsal thalamus." + "A goblet cell that is part of the epithelium proper of ileum." "FMA:263067" + "A pouch in the digestive tract that connects the ileum with the ascending colon of the large intestine. It is separated from the ileum by the ileocecal valve, and is the beginning of the large intestine. It is also separated from the colon by the cecocolic junction." "VHOG:0001559 CALOHA:TS-0122 EFO:0000850 SCTID:181256004 GAID:307 galen:Cecum EHDAA2:0000206 MIAA:0000288 FMA:14541 Wikipedia:Cecum UMLS:C0007531 BTO:0000166 NCIT:C12381 EV:0100397 EMAPA:35197 MA:0000334 EHDAA:3913 MESH:D002432" + "Any process that stops, prevents, or reduces the frequency, rate, or extent of a response to biotic stimulus." + "Common dendritic precursor is a hematopoietic progenitor cell that is CD117-low, CD135-positive, CD115-positive and lacks plasma membrane parts for hematopoietic lineage markers." + "EMAPA:37891 FMA:35508" + "A phagocytic hemocyte, responsible for the engulfment of small particles, microbes, and apoptotic tissue debris. It may also secretes antimicrobial peptides and contribute to the production and secretion of proteins of the hemolymph." "FBbt:00001685" + "The process whose specific outcome is the progression of the metanephric distal convoluted tubule over time, from its formation to the mature structure. The metanephric distal convoluted tubule is the first segment of the metanephric nephron lying just downstream from the loop of Henle, immediately after the macula densa. Among other functions, in humans it is responsible for the reabsorption of about 5% of filtered sodium via the thiazide-sensitive Na-Cl symporter." + "Binding to chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase." + "OBSOLETE. A near-projecting glutamatergic neuron with a soma found in layer 5/6 of the marmoset primary motor cortex." "ILX:0770161" + "Any process that activates, maintains or increases the rate of skeletal muscle growth." + "The directed movement of an endothelial cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis)." + "A skeletal muscle cell that is part of the tongue." + + "Mesenchymal cells that are migrating." "EHDAA2:0003152 AEO:0000152" + "A kidney that is part of a right side of organism [Automatically generated definition]." "NCIT:C34005 EMAPA:36590 SCTID:362208000 FMA:7204 UMLS:C0227613 MA:0001683" + "Opening of uterine cervix into the vagina." "UMLS:C1512165 FMA:76836 Wikipedia:External_orifice_of_the_uterus NCIT:C32491 SCTID:362255005" + "A fully differentiated plasma cell that lives for years, as opposed to months, secretes immunoglobulin, and has the phenotype weakly CD19-positive, CD20-negative, CD38-negative, strongly CD138-positive, MHC Class II-negative, surface immunoglobulin-negative, IgD-negative, and strongly CXCR4-positive. The majority of these cells of this type reside in the bone marrow." + "Epithelial cells derived from general body ectoderm and ectoderm placodes." "FMA:70556" + "The chemical reactions and pathways resulting in the formation of chondroitin sulfate proteoglycan, any glycoprotein whose glycosaminoglycan units are chondroitin sulfate. Chondroitin sulfates are a group of 10-60 kDa glycosaminoglycans, widely distributed in cartilage and other mammalian connective tissues; the repeat units consist of beta-(1,4)-linked D-glucuronyl beta-(1,3)-N-acetyl-D-galactosamine sulfate." + "FMA:63243" + "Any process that stops, prevents, or reduces the frequency, rate or extent of multiplication or reproduction of fibroblast cells." + "The chemical reactions and pathways resulting in the breakdown of ecdysteroids, a group of polyhydroxylated ketosteroids which initiate post-embryonic development." + "An epithelium that is part of a forelimb stylopod [Automatically generated definition]." "EMAPA:17425 EHDAA2:0002113 VHOG:0000990" + "The chemical reactions and pathways involving dopamine, a catecholamine neurotransmitter and a metabolic precursor of noradrenaline and adrenaline." + "Any process that activates or increases the frequency, rate or extent of satellite cell differentiation." + "A M cell that is part of the epithelium proper of ileum." "FMA:263138" + "Combining with melatonin, N-acetyl-5-methoxytryptamine, to initiate a change in cell activity. Melatonin is a neuroendocrine substance that stimulates the aggregation of melanosomes in melanophores, thus lightening the skin." + "Mesenchyme that develops_from a neural crest and is part of a entire pharyngeal arch associated mesenchyme." + "FMA:63628" + "Any process that modulates the frequency, rate or extent of the directed movement of the neurotransmitter norepinephrine into a cell." + "A lymphoid progenitor cell that is committed to the natural killer cell lineage, expressing CD122 (IL-15) receptor, but lacking many of the phenotypic characteristics of later stages of natural killer cell development such as expression of NK activating and inhibitory molecules. In human this cell has the phenotype CD34-positive, CD45RA-positive, CD10-positive, CD117-negative, and CD161 negative." + "A ribosome contained within a subcellular membrane-bounded organelle." + "Mesenchyme that is part of a foregut-midgut junction." "EHDAA2:0000570 EMAPA:16364" + "A biological process is the execution of a genetically-encoded biological module or program. It consists of all the steps required to achieve the specific biological objective of the module. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." "Wikipedia:Biological_process" + "The part of the coelemic cavity lumen that is enclosed by the walls of the thorax." "EMAPA:36497 UMLS:C0230139 Wikipedia:Thoracic_cavity MA:0000032 NCIT:C12905 SCTID:243949006 MESH:D035423 FMA:7565 GAID:93" + "Any process that decreases the rate, frequency or extent of glomerulus development, the progression of the glomerulus over time from its initial formation until its mature state. The glomerulus is a capillary tuft surrounded by Bowman's capsule in nephrons of the vertebrate kidney." + "Any process that stops, prevents or reduces the frequency, rate or extent of granulosa cell apoptotic process." + "The edge of the cornea where it joins the sclera; the limbus is a common site for the occurrence of corneal epithelial neoplasm." "Wikipedia:Corneal_limbus FMA:58342 SCTID:63716004 GAID:896 MESH:D016850 EFO:0001403 ZFA:0005570 EMAPA:37835" + "The disaggregation of a cell-cell junction into its constituent components." + "Mesenteric artery that supplies the large intestine from the left colic (or splenic) flexure to the upper part of the rectum, which includes the descending colon, the sigmoid colon, and part of the rectum. Proximally, its territory of distribution overlaps (forms a watershed) with the middle colic artery, and therefore the superior mesenteric artery. The SMA and IMA anastomose via the marginal artery (artery of Drummond). The territory of distribution of the IMA is more or less equivalent to the embryonic hindgut. [WP,unvetted]." "VHOG:0001116 NCIT:C32780 MESH:D017537 EHDAA:4345 EMAPA:18618 BTO:0002302 MA:0002004 UMLS:C0162860 EHDAA2:0000817 GAID:501 Wikipedia:Inferior_mesenteric_artery galen:InferiorMesentericArtery FMA:14750 SCTID:181341006" + "A neuroglial cell of ectodermal origin, i.e., the astrocytes and oligodendrocytes considered together." "CALOHA:TS-2027 BTO:0000771 FMA:54538" + "A strand of hair that is part of a autopod region." + "The process whose specific outcome is the progression of the metanephric nephron epithelium over time, from its formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure. The metanephric nephron epithelium is a tissue that covers the surface of a nephron in the metanephros." + "The central cone shaped core of spongy bone about which turns the spiral canal." "NCIT:C33135 BTO:0001693 MA:0001182 FMA:61278 SCTID:361314007 UMLS:C0229503 EMAPA:35575 Wikipedia:Modiolus_(cochlea)" + "A zone of skin that is part of a hindlimb [Automatically generated definition]." "FMA:23102 EMAPA:32620 UMLS:C0222268 MA:0000665 NCIT:C12297 SCTID:181528008" + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an environmental stimulus." + "A protein that is a translation product of the human TH gene or a 1:1 ortholog thereof." "IUPHARobj:1243" + "Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone." "ZFA:0000028 UMLS:C1514450 BTO:0001887 XAO:0000336 TAO:0000028 NCIT:C34276 AAO:0011044" + "Any process that stops, prevents, or reduces the frequency, rate or extent of mononuclear cell proliferation." + "An anatomical cavity that has the potential to develop into a coelemic cavity lumen." + "A C-C chemokine receptor type 7 that is encoded in the genome of mouse." "UniProtKB:P47774" + "A trophoblast cell that has a large volume of cytoplasm, is polyploid and is usually mononuclear but is also occasionally multi-nucleate. This cell type is important in establishing maternal physiology and remodeling of the vasculature of the placenta." + "Any process that activates or increases the frequency, rate, or extent of a type 2 immune response." + "Lung which consists of the left upper lobe and left lower lobe.[FMA]." "EHDAA:4947 Wikipedia:Left_lung NCIT:C32967 UMLS:C0225730 SCTID:361982005 VHOG:0000618 FMA:7310 EHDAA2:0000943 EMAPA:17653 MA:0000425" + "The process in which a relatively unspecialized cell acquires specialized features of a glial cell in the anterior lateral line nerve." + "The darker-colored muscle tissue of some mammals, composed of slow twitch muscle fibers." "CALOHA:TS-0940 BTO:0002317 UMLS:C0242874 NCIT:C12614" + "A magnocellular neurosecretory cell that is capable of producing and secreting oxytocin." + "An individual member of a collection of basal ganglia. Basal ganglia are subcortical masses of gray matter in the forebrain and midbrain that are richly interconnected and so viewed as a functional system. The nuclei usually included are the caudate nucleus (caudoputamen in rodents), putamen, globus pallidus, substantia nigra (pars compacta and pars reticulata) and the subthalamic nucleus. Some also include the nucleus accumbens and ventral pallidum[NIF,modified]." "SCTID:244434001 DHBA:10332 FMA:62514 CALOHA:TS-1149 BTO:0000235 EFO:0000904" + "A mucosa that is part of a common hepatic duct [Automatically generated definition]." "FMA:14691" + "A ciliated duct part of a tracheal submucosal gland." + "A DRD1-expressing medium spiny neuron that is part of a striosome of dorsal striatum." + "The process whose specific outcome is the progression of a metanephric glomerular visceral epithelial cell over time, from its formation to the mature structure. A metanephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the metanephros." + "A submucosa that is part of a sigmoid colon [Automatically generated definition]." "FMA:15027" + "Any process that activates or increases the frequency, rate or extent of compound eye photoreceptor cell differentiation." + "Portion of ventral mesentery closest to the stomach." "MA:0001621 UMLS:C1519967 TAO:0005133 EHDAA2:0002176 EMAPA:17026 VHOG:0000351 ZFA:0005133 EHDAA:3005 NCIT:C34327" + "The lipid bilayer surrounding a transport vesicle." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a bacterium." + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a tight junction. A tight junction seals cells together in an epithelium in a way that prevents even small molecules from leaking from one side of the sheet to the other." + "An immature natural killer cell that is NK1.1-positive, DX5-positive, Ly49-positive, CD27-low and CD11b-low. This cell type is found in high numbers in the liver." + "The directional movement of tangentially migrating interneurons that are not guided by attaching to extracellular substrates." + "The chemical reactions and pathways involving norepinephrine, a hormone secreted by the adrenal medulla, and a neurotransmitter in the sympathetic peripheral nervous system and in some tracts in the central nervous system. It is also the demethylated biosynthetic precursor of epinephrine." + "The thin innermost layer of the extraembryonic membranes that contains the amniotic fluid; the membrane forms a closed sac in which the embryo and later, the fetus, is suspended and protected." "EHDAA2:0000116 EMAPA:16109 BTO:0000065 MESH:D000650 EV:0100122 Wikipedia:Amnion SCTID:181457005 VHOG:0000721 CALOHA:TS-0033 EHDAA:136 GAID:1298 NCIT:C12365 UMLS:C0002630 FMA:80223" + "Of or pertaining to the period of time immediately following birth, or to the newborn." "NIF_Organism:birnlex_695 MmusDv:0000096 Wikipedia:Infant BTO:0001762 EV:0300037 HsapDv:0000082 OGES:000025 http://neurolex.org/wiki/Category:Newborn_organism http://neurolex.org/wiki/Category:Infant_organism" + "A nerve root that extends_fibers_into a hypoglossal nerve." "UMLS:C0175555 BAMS:12nf neuronames:798 FMA:72632 DMBA:17750 DHBA:12886 BIRNLEX:1288 BAMS:12n BIRNLEX:1588" + "A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin." "MESH:D008214 VHOG:0001535 CALOHA:TS-0583 FMA:62863 BTO:0000775" + "A dorsal mesentery that is part of a caecum." "RETIRED_EHDAA2:0000208" + "A G protein-coupled receptor signaling pathway initiated by a ligand binding to an acetylcholine receptor on the surface of a target cell, and ends with regulation of a downstream cellular process, e.g. transcription." + "Any process that activates or increases the frequency, rate, or extent of interleukin-1 production." + "Any process that modulates the frequency, rate or extent of an endocrine process, a process involving the secretion of or response to endocrine hormones. An endocrine hormone is a hormone released into the circulatory system." + "A high affinity immunoglobulin epsilon receptor subunit alpha that is encoded in the genome of mouse." "UniProtKB:P20489" + "The migration of cells in the developing cerebral cortex in which cells move from the ventricular and/or subventricular zone toward the surface of the brain." + "Any process that activates or increases the frequency, rate or extent of hyaluronan biosynthetic process." + "A cell derived from the specialized ectoderm flanking each side of the embryonic neural plate, which after the closure of the neural tube, forms masses of cells that migrate out from the dorsal aspect of the neural tube to spread throughout the body." "FMA:86667" + "Any process that activates or increases the frequency, rate or extent of eosinophil chemotaxis." + "Epithelium lining the exocrine pancreas." "CALOHA:TS-2108" + "An artery that supplies an ovary." "Wikipedia:Ovarian_artery UMLS:C0226411 SCTID:244280002 EMAPA:18620 NCIT:C33242 FMA:14761 MA:0002012" + "Any process that decreases the frequency, rate, or extent of lipid transporter activity." + "Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." + "A supportive cell that has characteristics of glial cell. Processes of this cell envelope the junctions between glomus cells and nerve endings." "FMA:84188" + "The Sphenofrontal suture is the cranial suture between the sphenoid bone and the frontal bone." "FMA:52938 SCTID:136349005 Wikipedia:Sphenofrontal_suture" + "Any apoptotic process in a vascular associated smooth muscle cell." + "Branch or outpocketing of the digestive tract." + "A type of interneuron in the retinal inner nuclear layer which\ncarries information from the inner plexiform layer and the outer\nplexiform layer." + "A double membrane structure enclosing an organelle, including two lipid bilayers and the region between them. In some cases, an organelle envelope may have more than two membranes." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of B cell apoptotic process." + "A mesonephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the mesonephros[GO]." + "A portion of connective tissue that is part of an arm [Automatically generated definition]." "MA:0000593 EMAPA:37316" + "The pectinate line (anocutaneous line, dentate line, anorectal junction) is a line which divides the upper 2/3rds and lower 1/3rd of the anal canal. Developmentally, this line represents the hindgut-proctodeum junction. It is an important anatomical landmark, and several distinctions can be made based upon the location of a structure relative to this line:." "FMA:75383 SCTID:245445008 EMAPA:19159 Wikipedia:Pectinate_line UMLS:C0821671 NCIT:C34245" + "The process in which the anatomical structures of a tube are generated and organized from the pulmonary artery endothelium. An pulmonary artery endothelium is an epithelium that lines the pulmonary artery." + "The disaggregation of a protein-lipid complex into its constituent components." + "Any apoptotic process in a lens fiber cell. Lens fiber cells are elongated, tightly packed cells that make up the bulk of the mature lens in a camera-type eye." + "Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to cell periphery." + "The layer within the retina where the photoreceptor cell bodies reside." "UMLS:C0229210 SCTID:280678009 BTO:0005600 TAO:0001464 XAO:0003219 MA:0001315 BAMS:Ronl NCIT:C33236 FMA:58684 VHOG:0001170 EMAPA:19157 ZFA:0001464 Wikipedia:Outer_nuclear_layer" + "An endothelial cell that is part of the venous sinus of spleen. This endothelial cell has an elongated, spindle-shaped, flattened morphology that is parallel to long axis of sinus. This cell type rests on a basement membrane interrupted by numerous narrow slits." "FMA:72140" + "Binding to heterocyclic compound." + "Fusion of the membrane of a transport vesicle with its target membrane." + "Any process that modulates the frequency, rate, or extent of tolerance induction to nonself antigen." + "An epithelium that is part of a left lung [Automatically generated definition]." "MA:0003131 EMAPA:17655" + "Any process that activates or increases the frequency, rate or extent of respiratory gaseous exchange." + "An sweat gland placode is a thickening of the ectoderm that will give rise to the sweat gland bud[GO]." + "Any process that modulates synaptic transmission by regulating a catabolic process occurring at a presynapse." + "The movement of a granulocyte in response to an external stimulus." + "Any process that activates, maintains or increases the rate of skeletal muscle fiber development. Muscle fibers are formed by the maturation of myotubes. They can be classed as slow, intermediate/fast or fast." + "The assembly and secretion a set of components to form an extracellular vesicule, a membrane-bounded vesicle that is released into the extracellular region. Extracellular vesicles include exosomes, microvesicles and apoptotic bodies, based on the mechanism by which they are released from cells and differentiated based on their size and content." + "An intestinal villus in the ileum." "FMA:63302" + "UMLS:C1514898 NCIT:C34283 EHDAA2:0004069" + "Any cardiac muscle cell that is part of a cardiac ventricle." + "EMAPA:16389 EHDAA2:0000039" + "A transitional myocyte that is part of the interatrial septum." "FMA:263152" + "A stromal cell of the ovarian cortex." "FMA:256169" + "The process whose specific outcome is the progression of the sympathetic nervous system over time, from its formation to the mature structure. The sympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system (the other being the parasympathetic nervous system). The sympathetic preganglionic neurons have their cell bodies in the thoracic and lumbar regions of the spinal cord and connect to the paravertebral chain of sympathetic ganglia. Innervate heart and blood vessels, sweat glands, viscera and the adrenal medulla. Most sympathetic neurons, but not all, use noradrenaline as a post-ganglionic neurotransmitter." + "The middle ear is the air-filled cavity within the skull of vertebrates that lies between the outer ear and the inner ear. It is linked to the pharynx (and therefore to outside air) via the Eustachian tube and in mammals contains the three ear ossicles, which transmit auditory vibrations from the outer ear (via the tympanum) to the inner ear (via the oval window)[GO]." "SCTID:181185000 EV:0100357 VHOG:0000312 EHDAA2:0001181 EHDAA:5693 BTO:0002099 CALOHA:TS-2233 NCIT:C12274 AAO:0011065 Wikipedia:Middle_ear MIAA:0000146 MAT:0000146 XAO:0000191 UMLS:C1268972 FMA:56513 MESH:D004432 UMLS:C0013455 EMAPA:17000 MA:0000253 GAID:165 BIRNLEX:1695" + "In anatomy, the superior mesenteric vein (SMV) is a blood vessel that drains blood from the small intestine. At its termination behind the neck of the pancreas, the SMV combines with the splenic vein to form the hepatic portal vein. The SMV lies to the right of the similarly named artery, the superior mesenteric artery, which originates from the abdominal aorta. [WP,unvetted]." "FMA:14332 EMAPA:18643 BTO:0002783 Wikipedia:Superior_mesenteric_vein NCIT:C33687 EHDAA:5414 EHDAA2:0001951 SCTID:278031001 MA:0002179 UMLS:C0226742 VHOG:0000552" + "Binding to ice, water reduced to the solid state by cold temperature. It is a white or transparent colorless substance, crystalline, brittle, and viscoidal." + "The process whose specific outcome is the progression of the adrenal cortex over time, from its formation to the mature structure. The adrenal cortex is located at the periphery of the adrenal gland and controls glucose and electrolyte metabolism, response to stress and sexual development through the production of different classes of steroid hormones (glucocorticoids, mineralocorticoids and androgens)." + "Ganglion that has dendrites that form a junction between autonomic nerves originating from the central nervous system and autonomic nerves innervating their target organs in the periphery. There are two subtypes, sympathetic ganglion and parasympathetic ganglion." "UMLS:C0017068 FMA:5889 AEO:0001001 EMAPA:18221 CALOHA:TS-2340 MESH:D005725 NCIT:C12720 MA:0000220 Wikipedia:Autonomic_ganglion" + "An artery that supplies the spleen." "NCIT:C33597 FMA:14773 SCTID:244266009 UMLS:C0037996 GAID:510 MA:0003177 EMAPA:19216 MESH:D013157 MA:0001991 galen:SplenicArtery Wikipedia:Splenic_artery" + "The part in the center of a tooth made up of living soft tissue and cells called odontoblasts[WP]." "MESH:D003782 SCTID:362110007 VHOG:0001469 NCIT:C32451 GAID:1270 ZFA:0005141 Wikipedia:Dental_pulp MA:0001599 BTO:0000339 CALOHA:TS-0195 EMAPA:35274 UMLS:C0011399 FMA:55631 TAO:0005141" + "A motor neuron that innervates both intrafusal and extrafusal muscle fibers. Low abundancy. They control both muscle contraction and responsiveness of the sensory feedback from muscle spindles." + "The superior surface of the tongue divided by the sulcus terminalis into an anterior two-thirds, the presulcal part (pars presulcalis). and a posterior one-third, the postsulcal part (pars postsulcalis)." "UMLS:C0226952 NCIT:C32482 SCTID:66938003 FMA:54651" + "The mitotic divisions of the primary spermatogonial cell (a primordial male germ cell) to form secondary spermatogonia (primary spermatocytes)." + "The multiplication or reproduction of satellite cells, resulting in the expansion of the cell population. Satellite cells are quiescent cells that are located between the basal lamina and the plasmalemma of the muscle fiber, which are the main contributors to postnatal muscle growth. In adult muscle, satellite cells become activated to divide and differentiate in response to muscle damage." + "FMA:58315" + "The specification and formation of anisotropic intracellular organization or cell growth patterns." + "Any process by which the number of skeletal muscle satellite stem cells in a skeletal muscle is maintained during skeletal muscle regeneration. There are at least two mechanisms by which this is achieved. Skeletal muscle satellite stem cell asymmetric division ensures satellite stem cell numbers are kept constant. Symmetric division of these cells amplifies the number of skeletal muscle satellite stem cells." + "A transition where a mesenchymal cell establishes apical/basolateral polarity,forms intercellular adhesive junctions, synthesizes basement membrane components and becomes an epithelial cell that will contribute to the shaping of the metanephros." + "A change in the morphology or behavior of a myeloid leukocyte resulting from exposure to an activating factor such as a cellular or soluble ligand." + "Any process that modulates the frequency, rate or extent of vascular associated smooth muscle cell migration." + "An epithelium that is part of a uterus." "BTO:0003082" + "The process whose specific outcome is the progression of a His-Purkinje cell over time, from its formation to the mature state. These cells form the fibers that regulate cardiac muscle contraction in the ventricles." + "Any process that activates or increases the frequency, rate or extent of euchromatin binding." + "A hematopoietic stem cell from the aorta-gonad-mesonephros region of the developing embryo. First seen at E10.5 in mouse embryos. May give rise to fetal liver HSC." + "Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle cell contraction." + "The cell cycle process in which replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the mitotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner. One homolog of each morphologic type goes into each of the resulting chromosome sets." + "Any process that stops, prevents or reduces the frequency, rate or extent of neuromuscular junction development." + "A pre-B-II cell is a precursor B cell that expresses immunoglobulin mu heavy chain (IgHmu+), and lack expression of CD34, TdT, immunoglobulin kappa light chain and immunoglobulin lambda light chain." "CALOHA:TS-0819 BTO:0001133" + "An epithelium that is part of a distal tubule." "BTO:0003948" + "The anteriormost subdivision of the body that includes the head, jaws, pharyngeal region and the neck (if present). In vertebrates this is the subdivision that includes the cervical vertebrae." "UMLS:C0460004 SCTID:361355005 FMA:280881 NCIT:C12418 CALOHA:TS-2356 EV:0100009 WikipediaCategory:Head_and_neck galen:HeadAndNeck MA:0000006" + "A vein that drains blood from the thymus." "EMAPA:36325 SCTID:303432009 MA:0002246 UMLS:C0226698 Wikipedia:Thymic_veins FMA:4747 NCIT:C53143" + "A smooth muscle cell of the esophagus." + "The chemical reactions and pathways involving organic cyclic compound." + "This cell resembles a glia cell, express the glial marker S100 and act as a supporting cell to type I cell. This cell is located in a small cluster of type I and type II cells near the fork of the carotid artery." "FMA:84187" + "Vascular network that is connected to the yolk sac." "Wikipedia:Vitelline_circulation" + "A dorsal skin of digit that is part of a manual digit." "FMA:38320 FMA:60346" + "The increase in size or mass of a lung. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax." + "Regional part of fornix consisting of a prominent white matter structure adjacent to the hippocampus on the ventricular side continuous with the alveus. Near the splenium the fimbria separates from the hippocampus as the crus of the fornix. [adapted from Wikipedia] (MM: 2006-10-26)." "SCTID:369096000 HBA:9253 BM:Tel-FI MBA:603 NCIT:C32606 DHBA:10575 BAMS:fi neuronames:187 EMAPA:35345 DMBA:17766 Wikipedia:Fimbria_of_hippocampus UMLS:C0152315 BIRNLEX:1502 FMA:83866 MA:0000949 BAMS:FI" + "A cardiac ventricle that is in the right side of the heart." "VHOG:0000717 galen:RightVentricle CALOHA:TS-0443 SCTID:244384009 EMAPA:17340 MA:0000093 UMLS:C0225883 EHDAA2:0000196 FMA:7098 Wikipedia:Right_ventricle NCIT:C12870 BTO:0001630" + "An epithelial tissue layer that lines much of the urinary tract, including the renal pelvis, the ureters, the bladder, and parts of the urethra." "CALOHA:TS-1096 SCTID:57789003 UMLS:C0227598 MESH:D019459 SCTID:30117005 Wikipedia:Urothelium BTO:0003906 EMAPA:37978 FMA:63914 Wikipedia:Transitional_epithelium GAID:935 NCIT:C12884 UMLS:C0225339 FMA:67695" + "A chemokine receptor that is a translation product of the human CXCR4 gene or a 1:1 ortholog thereof. The preferred ligand is CXCL12." "PIRSF:PIRSF501021 IUPHARobj:71" + "The outer medullary collecting duct is the portion of the collecting duct that lies in the renal outer medulla." "EMAPA:28346 MA:0002599" + "Combining with acetylcholine and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex." + "Any process that activates or increases the frequency, rate, or extent of myeloid dendritic cell cytokine production." + "The process whose specific outcome is the progression of a dorsal root ganglion over time, from its formation to the mature structure." + "Any process that modulates the rate, frequency or extent of mast cell chemotaxis. Mast cell chemotaxis is the movement of a mast cell in response to an external stimulus." + "Any process that stops, prevents, or reduces the frequency, rate or extent of natural killer cell activation." + "The process in which the anatomical structures of the paraxial mesoderm are generated and organized." + "Any process that modulates the frequency, rate, or extent of an immunoglobulin mediated immune response." + "Skeletal element that functionally replaces the notochord[VSAP,modified]." "VSAO:0000183" + "A C-C chemokine receptor type 7 that is encoded in the genome of human." "DTO:02100059 UniProtKB:P32248" + "An epithelial cell located in the late distal convoluted tubule." + "A prostaglandin D2 receptor DP2 that is encoded in the genome of human." "UniProtKB:Q9Y5Y4 DTO:02100741 Reactome:R-HSA-416895" + "A motor neuron that is located in the cervical region of the spinal cord and selectively innervates the sternocleidmastoid or trapezius muscle. Unlike other motor neurons, they extend axons dorsally along lateral margins of the spinal cord." + "A tyrosine 3-monooxygenase that is encoded in the genome of human." "UniProtKB:P07101" + "A mucosa that is part of a right ureter [Automatically generated definition]." "FMA:17806" + "A rough elevation at the middle of the lateral side of the shaft of the humerus to which the deltoid muscle attaches." "FMA:23418 Wikipedia:Deltoid_tuberosity MA:0002808 EMAPA:25052 AAO:0000736" + "Any process that activates or increases the frequency, rate or extent of a protein localization." + "The process whose specific outcome is the progression of the sebaceous gland over time, from its formation to the mature structure." + "The process whose specific outcome is the progression of the notochord over time, from its formation to the mature structure. The notochord is a mesoderm-derived structure located ventral of the developing nerve cord. In vertebrates, the notochord serves as a core around which other mesodermal cells form the vertebrae. In the most primitive chordates, which lack vertebrae, the notochord persists as a substitute for a vertebral column." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides." + "A protein with core architecture consisting of a signal sequence, an extracellular region with Class I Histocompatibility antigen, domains alpha 1 and alpha two (Pfam:PF00129) and an Immunoglobulin C1-set domain (Pfam:PF07654), a single-pass transmembrane region, and a very short cytoplasmic region. Forms a heterodimer with beta-2 microglobulin." "PIRSF:PIRSF038798" + "Any process that stops or decreases the rate or extent of brown fat cell proliferation." + "A goblet cell that is part of the epithelium of stomach." "FMA:263035" + "Any process that decreases the rate, frequency or extent of branching involved in ureteric bud morphogenesis, the process in which the branching structure of the ureteric bud is generated and organized. The ureteric bud is an epithelial tube that grows out from the metanephric duct. The bud elongates and branches to give rise to the ureter and kidney collecting tubules." + "A mucosa that is part of a renal pelvis [Automatically generated definition]." "SCTID:243482002 FMA:17931" + "Any process that contributes to cytokine production by a natural killer cell." + "A luminal epithelial cell of the mammary gland that transduces endocrine cues to orchestrate proliferation, architectural remodeling, and differentiation of other cells in the mammary gland via paracrine signaling. This cell expresses high levels of estrogen receptors. In humans, a luminal hormone-sensing cell can be identified by high levels of EpCAM and low levels of CD49f, and in mice it can be identified by low levels of CD29 and high levels of Foxa1, CD133, and Sca1 (Ly6a)." + "Any process that activates or increases the frequency, rate or extent of protein localization to cell leading edge." + "Any mesenchymal cell apoptotic process that is involved in mesonephric nephron morphogenesis." + "The progression of the brainstem from its formation to the mature structure. The brainstem is the part of the brain that connects the brain with the spinal cord." + "An integrin alpha-4 that is encoded in the genome of mouse." "UniProtKB:Q00651" + "An action potential that occurs in a cardiac muscle cell." + "The developmental process pertaining to the initial formation of a nephron tubule from unspecified parts. A nephron tubule is an epithelial tube that is part of the nephron, the functional part of the kidney." + + "A neural crest that has_potential_to_developmentally_contribute_to a diencephalon." "ZFA:0000811 TAO:0000811 EFO:0003573 VHOG:0000798 EMAPA:16518 EHDAA2:0000603" + "Parietal lobe of the right hemisphere of the brain." "BIRNLEX:1729 UMLS:C1281959 FMA:72973 SCTID:314146000" + "A wavelike sequence of involuntary muscular contraction and relaxation that passes along a tubelike structure, such as the intestine, impelling the contents onwards." "Wikipedia:Peristalsis" + "An epithelium that is part of a foregut." "EMAPA:32922 MA:0003204" + "The controlled release of glycine by a cell, in which glycine acts as a neurotransmitter." + "The formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system." "Wikipedia:Neurulation" + "Any process that activates or increases the frequency, rate or extent of natural killer cell differentiation." + "Any endothelium that has the quality of being cylindrical [Automatically generated definition]." + "The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells." + "Mast cell subtype that contains only the serine protease trypase in its granules. These cells are primarily found in mucosal tissue, such as intestinal mucosa and alveoli. They depend upon T-cells for development of phenotype." + "A thin layer of loose connective tissue which lies beneath the epithelium and together with the epithelium constitutes the mucosa[WP]. The lamina propria contains capillaries and a central lacteal (lymph vessel) in the small intestine, as well as lymphoid tissue. Lamina propria also contains glands with the ducts opening on to the mucosal epithelium, that secrete mucus and serous secretions." "Wikipedia:Lamina_propria SCTID:298225002 UMLS:C1179187 FMA:62517 BTO:0002330 NCIT:C32918" + "A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts."@en + "A sphincter muscle surrounding the urethra." "SCTID:277857004 SCTID:277855007 MA:0002650 Wikipedia:Urethral_sphincter EMAPA:37789" + "A portion of smooth muscle tissue that is part of a bronchiole [Automatically generated definition]." "FMA:261045" + "Goblet cells reside throughout the length of the small and large intestine and are responsible for the production and maintenance of the protective mucus blanket by synthesizing and secreting high-molecular-weight glycoproteins known as mucins. Human intestinal goblet cells secrete the MUC2 mucin, as well as a number of typical mucus components: CLCA1, FCGBP, AGR2, ZG16, and TFF3." + "The expansion of a T cell population by cell division. Follows T cell activation." + "A paired appendage that is evolved from a paired fin. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the girdle and its parts." "VHOG:0000336 VSAO:0000121 AAO:0010336 FMA:24875 AEO:0000172 CALOHA:TS-0552 EFO:0000876 GAID:36 Wikipedia:Limb MAT:0000090 SCTID:243996003 galen:Extremity EHDAA:1697 NCIT:C12429 UMLS:C0015385 XAO:0003027 EHDAA:8273 EHDAA2:0003172 EMAPA:16405 MA:0000007 MIAA:0000090" + "A portion of organism substance that secreted_by a zone of skin." "MA:0002537" + + "A cranial nerve fiber tract that innervates the pineal body." "FMA:77600" + "A sst GABAergic cortical interneuron that has \"fanning-out' Martinotti morphology that is found in layer 2/3/5 of the cerebral cortex. They have local axon arbor and long ascending axons that spreads horizontally and arborizes significantly in L1." + "The layer within the retina where the photoreceptor cell receptor segments reside." "FMA:58680 EMAPA:35686 TAO:0000143 XAO:0003215 VHOG:0001165 MA:0001308 Wikipedia:Layer_of_rods_and_cones ZFA:0000143 NCIT:C32954 UMLS:C0229206" + "Any process that modulates the frequency, rate or extent of cardiac muscle myoblast proliferation." + "The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates." "Wikipedia:Haematopoiesis" + "Any process that stops, prevents or reduces the frequency, rate or extent of cardiocyte differentiation." + "The branched tubular glands found in the mucosa of the fundus and body of the stomach which contain parietal cells that secrete hydrochloric acid and zymogenic cells that produce pepsin." "FMA:14919 EMAPA:27181 BTO:0000503" + "Any process that activates or increases the frequency, rate, or extent of lymphocyte mediated immunity." + "An alpha-beta T cell expressing NK call markers that is CD1d restricted and expresses a diverse TCR repertoire. Type II NKT cells do not become activated by alpha-galactosylceramide when presented by CD1d." + "Any process that modulates the frequency, rate or extent of somatic stem cell division." + "The process in which a relatively unspecialized cell acquires the specialized features of a glial cell." + "The process whose specific outcome is the progression of the metanephric thick ascending limb over time, from its formation to the mature structure. The metanephric thick ascending limb is the last part of the metanephric loop of Henle. Its thick, mitochondria-rich epithelium characterizes the outer medulla, and is responsible for very avid active salt transport. At the macula densa, the thick ascending limb connects to the distal convoluted tubule." + "A cell secreting tears, the fluid secreted by the lacrimal glands. This fluid moistens the conjunctiva and cornea." + "The directed movement of substances out of the nucleus." + "The membranous portion of the wall between the two lower chambers of the heart." "FMA:7135 EHDAA2:0004596 MA:0002939 VHOG:0000927 SCTID:278228007 EMAPA:18246" + "Any process that increases the rate, frequency or extent of metanephric glomerulus development, the progression of the metanephric glomerulus over time from its initial formation until its mature state. The metanephric glomerulus is a capillary tuft surrounded by Bowman's capsule in nephrons of the vertebrate kidney, or metanephros." + "Any process that stops, prevents, or reduces the frequency, rate or extent of sporulation." + "Any process that modulates the frequency, rate or extent of chondrocyte differentiation." + "A bulbous cell that is medially placed in one row in the organ of Corti. In contrast to the outer hair cells, the inner hair cells are fewer in number, have fewer sensory hairs, and are less differentiated." "FMA:62365 BTO:0003667" + "The process in which an organism retains a population of mesenchymal stem cells that contributes to the shaping of a nephron in the mesonephros. A mesenchymal stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized mesenchymal cells." + "Any process that activates or increases the frequency, rate or extent of thyroid hormone generation." + "Layer of the glomerular basement membrane adjacent to the glomerular capillary." "FMA:74277 NCIT:C32920 ZFA:0005287 TAO:0005287 UMLS:C1517719" + "Hippocampus (proper) plus dentate gyrus and subiculum[definition derived from NIF comments and ontology alignment]." "FMA:74038 MBA:1089 neuronames:177 MA:0000189 BIRNLEX:715 SCTID:422867004 BAMS:Hi UMLS:C0175202 BTO:0000601 Wikipedia:Hippocampal_formation BM:Tel-HF BAMS:HiF BAMS:HPF PBA:4003 HBA:4249 EMAPA:35405 DHBA:10294" + "Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm." "ZFA:0000155 GAID:1306 EHDAA2:0003436 Wikipedia:Somite EMAPA:31169 NCIT:C34302 XAO:0000058 MIAA:0000068 EHDAA:366 BTO:0001558 TAO:0000155 FMA:85522 AEO:0001015 EHDAA:699 MESH:D019170 AAO:0010569 VHOG:0000191 MAT:0000068 UMLS:C0376449" + "Proximal element of a free limb skeleton consisting of the femur and humerus in the forelimb stylopodium and hindlimb stylopodium respectively[VSAO, modified]." "VSAO:0005007" + "Mesenchyme of the carpal region that contributes to the carpal skeleton." "EHDAA2:0000220 EHDAA:5200" + "The circular lymphoid tissue formed by the lingual, pharyngeal, and faucial tonsils." "FMA:55070 NCIT:C73468 MA:0000752 Wikipedia:Waldeyer's_ring UMLS:C0459892 SCTID:56411004" + "Any process that modulates the frequency, rate or extent of behavior, the internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli." + "EHDAA:1122 EHDAA2:0001315" + "Tela chorioidea that lines the telencephalic ventricle." "neuronames:219 FMA:83712 ZFA:0005160 SCTID:362319004 BAMS:tclv TAO:0005160" + "A smooth muscle cell that is part of any blood vessel." + "A cell found predominately in the blood." "MESH:D001773 FMA:62844" + "Skeletogenic cell that is typically non-terminally differentiated, secretes an avascular, GAG rich matrix; is not buried in cartilage tissue matrix, retains the ability to divide, located adjacent to cartilage tissue (including within the perichondrium), and develops from prechondroblast (and thus prechondrogenic) cell." "BTO:0003607 FMA:66783" + "A cell type found in the basal epithelial layer on the external side of the tympanic membrane. Cell type is flattened with intracellular spaces of variable dimensions." + "The transparent anterior portion of the fibrous coat of the eye that serves as the chief refractory structure." "BTO:0000286 EHDAA:10199 MA:0000266 Wikipedia:Cornea AAO:0010344 CALOHA:TS-0171 VHOG:0000164 EFO:0000377 UMLS:C0010031 XAO:0000180 GAID:892 TAO:0000640 EV:0100341 ZFA:0000640 SCTID:181162001 EHDAA2:0000316 NCIT:C12342 MESH:D003315 EMAPA:17161 FMA:58238" + "The process in which ammonium is transported across a membrane. Ammonium is the cation NH4+." + "Any process that activates or increases the frequency, rate or extent of cardiac chamber morphogenesis." + "An orthochromatophilic erythroblast that is ter119-high, CD71-low, and Kit-negative." + "Any muscle organ that is part of a back [Automatically generated definition]." "EMAPA:35161 MA:0000496 FMA:85216" + "The process in which a relatively unspecialized cell acquires the specialized features of a pigmented cell, such as a melanocyte." + "The cord-like structure in males comprising the vas deferens and associated tissue that runs from the abdomen down to each testis[MP]." "FMA:19937 SCTID:181433005 MESH:D013085 Wikipedia:Spermatic_cord NCIT:C12329 GAID:395 UMLS:C0037855" + "Any process that activates or increases the frequency, rate or extent of photosynthesis." + "The process that mediates interactions between a bundle of His cell and its surroundings that contributes to the process of the bundle of His cell communicating with a Purkinje myocyte in cardiac conduction. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment." + "Any process that activates or increases the frequency, rate or extent of cardiac muscle cell myoblast differentiation." + "Any process that stops, prevents, or reduces the frequency, rate or extent of cardioblast differentiation, the process in which a relatively unspecialized mesodermal cell acquires the specialized structural and/or functional features of a cardioblast. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating." + "A mature sexual reproductive cell having a single set of unpaired chromosomes." "FBbt:00005412 FMA:18649 CALOHA:TS-0395" + "CD7-positive lymphoid progenitor cell is a lymphoid progenitor cell that is CD34-positive, CD7-positive and is CD45RA-negative." + "Any process that modulates the rate frequency or extent of cilium movement involved in ciliary motility." + "The process in which a relatively unspecialized cell acquires the specialized features of a mesoderm cell." + "A protein that is a translation product of the human PDYN gene or a 1:1 ortholog thereof." + "The process in which the anatomical structures of a metanephric nephron tubule are generated and organized. A metanephric nephron tubule is an epithelial tube that is part of the metanephric nephron, the functional part of the metanephros." + "Any process that activates or increases the frequency, rate or extent of basophil differentiation." + "The regulated release of corticotropin by a cell. Corticotropin hormone is a polypeptide hormone synthesized and secreted from corticotropes in the anterior lobe of the pituitary gland in response to corticotropin-releasing hormone (CRH) released by the hypothalamus." + "Any process that modulates the frequency, rate or extent of cerebral blood circulation." + "The initial formation of a blastocyst from a solid ball of cells known as a morula." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ammonium stimulus." + "A substance formed by type II alveolar cells composed of surface-active lipoprotein complex (phospholipoprotein)." "UMLS:C0034085 EMAPA:36551 Wikipedia:Pulmonary_surfactant NCIT:C13273 FMA:62780 MA:0002534" + "A change in the morphology or behavior of a follicular dendritic cell resulting from exposure to an activating factor such as a cellular or soluble ligand, leading to the initiation or perpetuation of an immune response." + "An epithelial cell that is part of the fallopian tube epithelium that secretes mucous fluid and oviduct-specific products through the stimulation of estrogen and luteinizing hormone. The fallopian tube secretory cell has approximately the same height as the ciliated cell and is usually a more narrow columnar cell. The nucleus is ovoid and perpendicular to the long axis of the cell. The chromatin is more dense and the nucleolus smaller than that seen in the ciliated cell." + "The process in which a relatively unspecialized cell acquires specialized features of a white adipocyte, an animal connective tissue cell involved in energy storage. White adipocytes have cytoplasmic lipids arranged in a unique vacuole." + "Any process that increases the rate or extent of heart growth. Heart growth is the increase in size or mass of the heart." + "The series of molecular signals generated as a consequence of an acetylcholine receptor binding to one of its physiological ligands." + "The metanephric short descending thin limb is the descending thin limb of a short nephron in the metanephros that has a squamous epithelial morphology[GO]." + "A supramolecular assembly of fibrillar collagen complexes in the form of a long fiber (fibril) with transverse striations (bands)." + "A granulocyte monocyte progenitor that is Kit-positive, CD34-positive, Fc-gamma receptor II/II-positive, and is Sca-1-negative, Il7ra-negative, Cxc3r1-negative, and CD90-negative." + "Any process that stops, prevents or reduces the frequency, rate or extent of glucocorticoid mediated signaling pathway." + "The series of molecular signals generated as a consequence of a G protein-coupled serotonin receptor binding to one of its physiological ligands." + "The chemical reactions and pathways resulting in the formation of ecdysteroids, a group of polyhydroxylated ketosteroids which initiate post-embryonic development." + "The series of molecular signals mediated by a steroid hormone binding to a receptor." + "A mesenchyme that is part of a urethra." "MA:0002648 EMAPA:37786" + "Any process that determines the size and arrangement of collagen fibrils within an extracellular matrix." + "Any process that activates or increases the frequency, rate or extent of dendrite development." + + "Any process that modulates the frequency, rate or extent of aorta morphogenesis." + "Binding to a modified amino acid." + "A vein that drains the cerebellum." "Wikipedia:Cerebellar_veins SCTID:40693009 FMA:51227 EMAPA:37139 MA:0002093 NCIT:C53032 UMLS:C0226601" + "FMA:242841" + "Any process that activates or increases the frequency, rate or extent of hepatic stellate cell proliferation." + "FMA:234865 ZFA:0005107 TAO:0005107" + "Any process that modulates the frequency, rate or extent of neuron differentiation." + "One of the cartilage structures in the nose that provide form and support[WP]." "Wikipedia:Nasal_cartilage FMA:59502 SCTID:278941001 EMAPA:37681 MA:0001883 CALOHA:TS-0655 UMLS:C0225415 NCIT:C49593" + "An IgD-negative CD38-positive IgG memory B cell is a CD38-positive IgG-positive that has class switched and lacks expression of IgD on the cell surface with the phenotype IgD-negative, CD38-positive, and IgG-positive." + "A dilation of the duodenal papilla that is the opening of the juncture of the common bile duct and the main pancreatic duct." "MESH:D014670 FMA:15076 CALOHA:TS-2348 GAID:283 SCTID:362200007 galen:AmpullaOfVater NCIT:C13011 Wikipedia:Ampulla_of_Vater TAO:0005167 ZFA:0005167 UMLS:C0042425" + "A skeletal joint that connects two carpal bones." "Wikipedia:Intercarpal_articulations UMLS:C1262468 FMA:35292 NCIT:C32264 SCTID:182176003" + "A projection or outgrowth of tissue from a larger body or organ." "Wikipedia:Process_(anatomy) NCIT:C61549 galen:Ridge HAO:0000822 FMA:67601 VSAO:0000180 TAO:0001834 AAO:0010278 XAO:0004020" + "A stromal cell of the prostate." "BTO:0003972" + "A tubuloacinar seromucous gland that is located principally in the submucosa of the trachea. Excretory ducts from this gland pass through the lamina propria to the tracheal lumen." "SCTID:197423006 EMAPA:36574 FMA:7473 MA:0002937" + "Any process that modulates the frequency, rate or extent of satellite cell activation. The satellite cell activation is the process that initiates satellite cell division by causing it to move from quiescence to the G1 stage of the cell cycle. The cell swells and there are a number of other small changes. The cells then start to divide. Following cell division the cells will differentiate." + "Any process that modulates the rate, frequency, or extent of cell projection assembly." + + "Any process that modulates the frequency, rate or extent of Schwann cell migration." + "Lymph is the fluid that is formed when interstitial fluid enters the conduits of the lymphatic system through lymph capillaries[WP]." "VHOG:0001590 CALOHA:TS-0580 galen:Lymph NCIT:C13252 MAT:0000055 BTO:0000855 FMA:9671 EFO:0000871 MA:0002520 GAID:1186 ZFA:0005658 MIAA:0000055 ENVO:02000041 MESH:D008196 EV:0100049 UMLS:C0024202 Wikipedia:Lymph" + "Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to ciliary membrane." + "Any process that decreases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate." + "A joint that connects the hindlimb autopod and zeugopod skeletons." "MA:0000463 UMLS:C0003087 SCTID:182212002 EMAPA:35126 galen:AnkleJoint NCIT:C32078 FMA:35195 Wikipedia:Ankle MESH:D000843 GAID:257 BTO:0004706" + "A smooth muscle tissue that is part of a lobular bronchiole." + "A respiratory airway that is part of an open tracheal system." "SPD:0000434 TADS:0000315 Wikipedia:Invertebrate_trachea" + "The chemical reactions and pathways involving chondroitin sulfate proteoglycan, any glycoprotein whose glycosaminoglycan units are chondroitin sulfate. Chondroitin sulfates are a group of 10-60 kDa glycosaminoglycans, widely distributed in cartilage and other mammalian connective tissues; the repeat units consist of beta-(1,4)-linked D-glucuronyl beta-(1,3)-N-acetyl-D-galactosamine sulfate." + "The process that mediates interactions between an SA node cardiomyocyte and its surroundings that contributes to the process of the SA node cardiomyocyte communicating with an atrial cardiomyocyte in cardiac conduction. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment." + "An organ that aids digestion and stores bile produced by the liver[WP]." "UMLS:C0016976 XAO:0000135 MIAA:0000072 EHDAA2:0000699 EMAPA:17202 AAO:0010114 MAT:0000072 ZFA:0000208 TAO:0000208 galen:Gallbladder EV:0100090 MA:0000356 BTO:0000493 SCTID:181269000 Wikipedia:Gallbladder CALOHA:TS-0394 EHDAA:8062 FMA:7202 EFO:0000853 NCIT:C12377 VHOG:0000221 MESH:D005704" + "Any process that activates or increases the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "MESH:D059331" + "Missing definition for term UBERON:0006376. Please replace it using linked reference." "EMAPA:29671 MA:0002628" + "Any process that modulates the frequency, rate or extent of epidermis development." + "The process in which the vasculature of the cerebellum is generated and organized." + "The process in which the anatomical structures of a mesonephric tubule are generated and organized. A mesonephric tubule is an epithelial tube that is part of the mesonephros." + "A bistratifed retinal amacrine cell with a small dendritic field, dendrite stratification in S1-S2, and a second dendrite stratification in S5. This cell type releases the neurotransmitter glycine." + "Mesenchyme that is part of a developing trachea." "EMAPA:16854 EHDAA2:0002067" + "An ischial bone or its cartilage or pre-cartilage precursor." + "Any process in which an organelle is transported to, and/or maintained in, a specific location." + "A skeletal element that has the potential to participate in endochondral ossification, and may participate in intramembranous ossification." "VSAO:0000139 XAO:0004017 ZFA:0005620" + "Any process that activates or increases the frequency, rate or extent of dendritic cell chemotaxis." + "Any cell-cell adhesion process that modulates the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins." + "A retinal ganglion cell C inner that has dense dendritic diversity." "BAMS:1067" + + "A serous membrane that is part of a urinary bladder [Automatically generated definition]." "EMAPA:28661 MA:0001696 SCTID:5868002 FMA:15932" + "The appearance of interleukin-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." + "Neuron that is part of the enteric nervous system." + "A major subdivision of an organism that is the entire part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. In vertebrares this includes the vertebral column.." "UMLS:C0004600 GAID:30 galen:Back NCIT:C13062 MESH:D001415 EFO:0001405 CALOHA:TS-2223 Wikipedia:Dorsum_(anatomy) SCTID:123961009 FMA:14181 BTO:0001713" + "A portion of skeletal muscle tissue that is part of a lip [Automatically generated definition]." "MA:0001578 EMAPA:37642" + "A portion of connective tissue that is part of a back [Automatically generated definition]." "EMAPA:37256 MA:0000495" + "GC_ID:1" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving phosphates." + "The lipid bilayer surrounding a vesicle associated with the Golgi apparatus." + + + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving glycogen." + "A follicle cell that is part of the stalk connecting adjacent egg chambers." "FBbt:00004910" + "A cell found within the dental pulp." "FMA:87170 CALOHA:TS-0195" + "The portion of the plasma membrane surrounding a muscle cell projection." + "The non-specific expansion of B cell populations within a whole or part of an organism to reach to a total number of B cells which will then remain stable over time in the absence of an external stimulus." + "A goblet cell that is part of the epithelium proper of duodenum." "FMA:263063" + "A killer cell lectin-like receptor subfamily D member 1 that is encoded in the genome of human." "UniProtKB:Q13241 Reactome:R-HSA-2326854" + "The smaller of two types of asexual spores formed by some fungi. An ovoid to pear-shaped asexual spore that contains very little cytoplasm and organelles, is uninucleate, and forms in vegetative hypae within a mycelium. Micronidia are extruded from the hyphal cell wall." "FAO:0000028" + "The multiplication or reproduction of acinar cells, resulting in the expansion of a cell population. An acinar cell is a secretory cell that is grouped together with other cells of the same type to form grape-shaped clusters known as acini (singular acinus)." + "A branch of the external carotid artery that supplies structures of the face. [WP,unvetted]." "UMLS:C0226109 MA:0001950 NCIT:C32578 FMA:49549 EMAPA:19213 SCTID:181328007 Wikipedia:Facial_artery" + "The cell cycle process in which the second meiotic division occurs in the female germline." + "The progression of the pituitary gland over time from its initial formation until its mature state. The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands." + + + "Any muscle tissue that is part of the urethra." "EMAPA:37787 MA:0002649" + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting the presence, absence, or concentration of water." + "A male germ cell that develops from spermatogonia. The euploid primary spermatocytes undergo meiosis and give rise to the haploid secondary spermatocytes which in turn give rise to spermatids." "FBbt:00004936 CALOHA:TS-0951 BTO:0001275 EMAPA:31484 WBbt:0006799 FMA:84049" + "Any process that modulates synaptic transmission by regulating translation occurring at the synapse." + "A low affinity immunoglobulin epsilon Fc receptor that has been processed by proteolytic cleavage." + "A carpal bone that proximally_connected_to a forelimb zeugopod skeleton." "SCTID:306715004 MA:0002557 EMAPA:36164 FMA:33302" + "Any process that increases the rate, frequency or extent of myofibril assembly by organization of muscle actomyosin into sarcomeres. The sarcomere is the repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs." + "An adult angioblastic cell released from the bone marrow, or from the kidney in some teleost species, capable of blood circulation and participation in angiogenesis by differentiating into blood vessel endothelial cells." + "A mesentery of duodenum that is part of a foregut." "EHDAA2:0000564" + "A submucosal gland located in a bronchus." + "EHDAA2:0001762 EMAPA:17328 EMAPA:17010 MA:0001872" + "A mesopodium that is part of a manus. Includes as parts the carpal skeleton and associated tissues[cjm]. The anatomical region surrounding the carpus including the distal parts of the bones of the forearm and the proximal parts of the metacarpus or five metacarpal bones and the series of joints between these bones, thus referred to as wrist joints. This region also includes the carpal tunnel, the anatomical snuff box, the flexor retinaculum, and the extensor retinaculum[WP,unvetted]." "EHDAA:5196 MA:0000039 GAID:59 Wikipedia:Wrist EMAPA:19122 FMA:24922 SCTID:361289009 EHDAA2:0000218 galen:Wrist MESH:D014953 EMAPA:32784 NCIT:C111033" + "The process that gives rise to the cerebellar granule layer. This process pertains to the initial formation of a structure from unspecified parts. The granular layer is the innermost layer of the cerebellar cortex. This layer contains densely packed small neurons, mostly granule cells. Some Golgi cells are found at the outer border. Granule neurons send parallel fibers to the upper molecular layer, where they synapse with Purkinje cell dendrites. Mossy fibers from the pontine nuclei in the white matter synapse with granule cell axons, Golgi cell axons and unipolar brush interneuron axons at cerebellar glomeruli in the granule cell layer." + "System pertaining to a bronchus and alveoli." "MA:0000416 BTO:0000136 EMAPA:32692 CALOHA:TS-1296" + "A thrombomodulin-like receptor that is a translation product of the human THBD gene or a 1:1 ortholog thereof." + "A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died." "Wikipedia:Apoptosis" + "An ecto-epithelial cell of the palatal region of the viscerocranial mucosa." "FMA:70580" + "A bone that is part of an abdominal segment of trunk [Automatically generated definition]." "MA:0000525 EMAPA:37058" + "The simple cuboidal epithelium lining the lumen of kidney collecting ducts." "EMAPA:37885" + "The hierarchical steps resulting in the progressive subdivision of the anterior/posterior axis of the embryo." + "An epithelial cell that is part of the wall of inferior part of anal canal." "FMA:70562" + "The growth of a cardiac muscle cell, where growth contributes to the progression of the cell over time from its initial formation to its mature state." + "The developmental process, independent of morphogenetic (shape) change, that is required for a columna/cuboidal epithelial cell of the intestine to attain its fully functional state. A columnar/cuboidal epithelial cell of the intestine mature as they migrate from the intestinal crypt to the villus." + "Any process that modulates the frequency, rate or extent of lung alveolus development." + "An anatomical space that surrounded_by a trachea." "SCTID:197486000 FMA:7469" + "A process in which a protein is transported to, or maintained in, the location of an actin cytoskeleton." + "The process in which the anatomical structures of the renal capsule are generated and organized. The renal capsule is the tough fibrous layer surrounding the kidney, covered in a thick layer of perinephric adipose tissue. It provides some protection from trauma and damage. During development, it comprises a single layer of flattened cells that lie just above the cortical stroma and the condensed mesenchyme of the nephrogenic zone. It is in this region that the early stages of nephron induction and formation of new generations ureteric bud branches occur, as the kidney expands." + + "A capsule that divides the parenchyma of the pancreas into lobes and lobules." + "Any process that stops, prevents or reduces the frequency, rate or extent of glucocorticoid receptor signaling pathway." + "A reticular cell that is part of the splenic cord." "FMA:86497" + "Cartilaginous joint in which the articulating bones or cartilages are connected by hyaline cartilage. Examples: spheno-occipital synchondrosis, first sternocostal joint.[FMA]." "FMA:7497 SCTID:42903008 MA:0001501 Wikipedia:Synchondrosis EMAPA:35846" + "An outflow tract that is part of a cardiac atrium." "FMA:14141" + "Any process that modulates the frequency, rate or extent of cytoplasmic translational elongation." + "A photoreceptor cell that detects ultraviolet light." + "Any process that modulates the frequency, rate or extent of eosinophil differentiation." + "Cell-cell signaling in either direction across the synaptic cleft." + + "Any basal cell of epidermis that is part of a limb." + "The progression of the respiratory system over time from its formation to its mature structure. The respiratory system carries out respiratory gaseous exchange." + "Foramen that allows the passge of the glossopharyngeal nerve (cranial nerve IX)." + "Neuron that secretes histamine." "FBbt:00007367" + "A portal vein that transports nutrients from the digestive tract to the liver[Kardong]." "MA:0002132 VHOG:0000642 FMA:50735 Wikipedia:Hepatic_portal_vein TAO:0005090 AAO:0010214 ZFA:0005090" + "A life cycle stage that starts with fertilization and ends with the fully formed embryo." "HsapDv:0000002 WBls:0000092 OGES:000022 OGES:000000 WBls:0000102 WBls:0000003 SCTID:296280003 FBdv:00005289 XAO:1000012 EV:0300001 FMA:72652 BilaDO:0000002 MmusDv:0000002" + "Skeletal subdivision that is a segment of the limb skeleton." "VSAO:0005018" + "The larger of two chemoarchitectural compartments identified in the neostriatum through differential staining for various biochemical markers. It usually is identified through differentially high staining for acetylcholinesterase and calbinin D28K." "NLXANAT:20090503" + "A tachykinin-3 that is encoded in the genome of human." "UniProtKB:Q9UHF0" + "Any process that stops, prevents or reduces the frequency or rate of cell fate commitment. Cell fate commitment is the commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells. Positional information is established through protein signals that emanate from a localized source within a cell (the initial one-cell zygote) or within a developmental field." + "A homeostatic process involved in the maintenance of a steady state level of iron ions within a cell." + "The process in which the anatomical structures of the inner ear are generated and organized. The inner ear is the structure in vertebrates that contains the organs of balance and hearing. It consists of soft hollow sensory structures (the membranous labyrinth) containing fluid (endolymph) surrounded by fluid (perilymph) and encased in a bony cavity (the bony labyrinth). It consists of two chambers, the sacculus and utriculus, from which arise the cochlea and semicircular canals respectively." + "Parietal lobe of the left hemisphere of the brain." "FMA:72974 BIRNLEX:1728 SCTID:314147009 UMLS:C1281960" + "A precursor cell destined to differentiate into cardiac muscle cell." "FMA:84797" + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds." + "A strand of hair that is part of a head." "FMA:54241" + "Any process that stops, prevents or reduces the frequency, rate or extent of endothelial cell activation." + "The collection of all skeletal elements in an autopodium region." "VSAO:0005019" + "The pathway leading to secretion of a neurotransmitter from the presynapse as part of synaptic transmission." + "EHDAA2:0004610" + "Any microvascular endothelial cell that is part of a prostate gland." + "An arteriole located in the vermiform appendix." + "An eye with one concave chamber. Note that 'simple' does not imply a reduced level of complexity or acuity." "TGMA:0000729 Wikipedia:Eye#Simple_eyes" + "The regions of the brain that are largely or entirely composed of myelinated nerve cell axons and contain few or no neural cell bodies or dendrites." "NCIT:C49334 MA:0000820 EMAPA:35187 UMLS:C1706995" + "The regulated release of a hormone into the circulatory system." + "The part of the membranous labyrinth that includes the utricle and saccule lodged within the vestibule and the semicircular ducts lodged eccentrically in the corresponding canals." "XAO:0004145 UMLS:C0042606 CALOHA:TS-0479 EHDAA2:0000832 EHDAA:4706 MA:0000245 EMAPA:17286 Wikipedia:Inner_ear FMA:61255 NCIT:C33871 BTO:0001856" + "Development, taking place during the embryonic phase, of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." + "The activities involved in the mental information processing system that receives (registers), modifies, stores, and retrieves informational stimuli. The main stages involved in the formation and retrieval of memory are encoding (processing of received information by acquisition), storage (building a permanent record of received information as a result of consolidation) and retrieval (calling back the stored information and use it in a suitable way to execute a given task)." "Wikipedia:Memory" + "Any process that modulates a qualitative or quantitative trait of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc." + "The epithelial lining of the surface of the coelom." "Wikipedia:Coelomic_epithelium XAO:0000329" + "Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to lysosome." + "A blood that is part of a artery." "FMA:83066" + "A thymocyte expressing the alpha-beta T cell receptor complex as well as both the CD4 and CD8 coreceptors." + "The maternal uterine-derived portion of the placenta." "MAT:0000290 MESH:D003656 SCTID:362842004 UMLS:C0011106 NCIT:C32425 FMA:85538 Wikipedia:Decidua BTO:0001360 EMAPA:35269 CALOHA:TS-0193 GAID:378 MA:0001722 MIAA:0000290" + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of a nitric oxide synthase enzyme." + "Any cell in the midgut (middle subdivision of a digestive tract) of an insect larva." "http://en.wikipedia.org/wiki/Insect#Midgut GOC:pr" + "An undifferentiated neural cell that originates from the neuroectoderm and has the capacity both to perpetually self-renew without differentiating and to generate multiple central nervous system neuronal and glial cell types." "CALOHA:TS-2360 BTO:0002881 FMA:86684" + "A cell that is part of a renal medulla." "KUPO:0001017" + "The directed movement of modified amino acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle tissue development." + "An inter-phalangeal joint that connects a distal phalanx to either a medial or proximal phalanx." "FMA:65024 NCIT:C101529" + "Any process that stops, prevents or reduces the frequency, rate or extent of lung alveolus development." + "The regulated release of epinephrine by a cell in which the epinephrine acts as a neurotransmitter." + "A cell involved in the formation of a monocyte (monopoiesis)." "FMA:83552" + "OBSOLETE: Astrocyte-like radial glial cell that extends vertically throughout the retina, with the nucleus are usually in the middle of the inner nuclear layer." + "The exocrine cell of the prostate, this epithelial cell secretes prostatic acid phosphotase and PSA, and is dependent on androgen hormones for survival." + "The functional units of the liver including the lobules." "SCTID:363535004 XAO:0000454 VHOG:0000539 FMA:17540 AAO:0010405 EMAPA:17203 NCIT:C32735 EHDAA:2201 EHDAA2:0001004 MA:0000366 UMLS:C0736268" + "Middle layer of olfactory cortex lying deep to layer 1 and superficial to layer 3, characterized by a compact layer of cell bodies. It can be divided into a superficial part and a deep part." "NLX:152610" + "Any process that activates or increases the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "Any process that activates or increases the frequency, rate or extent of the regulated release of ecdysteroid." + "Most generally any neuron which is not motor or sensory. Interneurons may also refer to neurons whose axons remain within a particular brain region as contrasted with projection neurons which have axons projecting to other brain regions." "FBbt:00005125 WBbt:0005113 FMA:67313 BTO:0003811" + "Any process that activates or increases the frequency, rate or extent of vascular associated smooth muscle cell migration." + "Any capillary endothelial cell that is part of a lung." + "Cytoplasm that exhibits a characteristic staining and color, red or pink, with Eosin stain." + "Any process that modulates the frequency, rate or extent of T cell costimulation." + "The process whose specific outcome is the progression of the metanephric connecting tubule over time, from its formation to the mature structure. The metanephric connecting tubule is a tubular segment of the metanephric nephron; it connects the distal convoluted tubule to the collecting duct in the metanephros." + "The developmental growth of cardiac muscle tissue that contributes to the shaping of the heart." + "Any process that modulates the frequency, rate, or extent of tolerance induction dependent upon immune response." + "An MHC class II histocompatibility antigen alpha chain DRA that is encoded in the genome of human." "MRO:0000693 UniProtKB:P01903" + "Any leukocyte that is part of a spleen." + "Any process that stops, prevents or reduces the frequency, rate or extent of embryonic camera-type eye development." + "A motor neuron that innervates a skeletal muscle. These motor neurons are all excitatory and cholinergic." + "A ciliated cell of the respiratory system. Ciliated cells are present in airway epithelium." + "The corticospinal fibers that arise from the pyramidal cells within the cerebral cortex layer V of the precentral motor area, the premotor area and the postcentral gyrus, then descend into and through the medulla to form the lateral corticospinal tract and the anterior corticospinal tract." "SCTID:362325000 BIRNLEX:1464 FMA:72634 GAID:702 UMLS:C0034229 MESH:D011712 neuronames:1320 EMAPA:36600 neuronames:800 Wikipedia:Corticospinal_tract BM:CST DHBA:12776 DMBA:17756 MBA:190 BAMS:P MBA:784 BM:Me-PyT HBA:265505574" + "An organelle lumen that is part of an intracellular organelle." + "The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "Any process that activates or increases the frequency, rate or extent of dendritic cell dendrite assembly." + "A ciliated epithelial cell with many cilia." + "A pigment cell derived from the neural crest. Contains melanin-filled pigment granules, which gives a brown to black appearance." "MESH:D008544 VHOG:0001679 CALOHA:TS-0613 BTO:0000847 FMA:70545" + "A cell that can perform photosynthesis, in which carbohydrates are synthesized from carbon dioxide and water, using light as the energy source." + "Any process that modulates the frequency, rate or extent of postsynaptic membrane organization." + "The process in which a relatively unspecialized cell of neural crest origin acquires the specialized features of an odontoblast, a cell on the outer surface of the dental pulp whose biological function is the creation of dentin." + "An epithelial cell of the integument (the outer layer of an organism)." "FMA:62411 MESH:D000078404 CALOHA:TS-0283 BTO:0001470" + "A scaffolding cell type found in C. elegans, this cell plays a supportive role to the muscle arms. May also have an endocrine role." + "A tubular passage that extends from the primitive pit into the head process during the early stages of embryonic development in mammals. It perforates the splanchnopleure layer so that the yolk sac and the amnion are connected temporarily." "NCIT:C34230 UMLS:C1518428 FMA:293127" + "Odontoblast that is terminally differentiated and derived from an odontogenic papilla and associated with dentine." + "Any process that stops, prevents or reduces the frequency, rate or extent of fat cell apoptotic process." + "A specialized endothelial cell that senses extracellular signals and guides the directed growth of blood vessels." + "A submucosa that is part of a large intestine [Automatically generated definition]." "EMAPA:37560 MA:0002690 BTO:0002111 NCIT:C32930 UMLS:C0734204 FMA:14970" + "The right lobe is much larger than the left; the proportion between them being as six to one. It occupies the right hypochondrium, and is separated from the left lobe on its upper surface by the falciform ligament; on its under and posterior surfaces by the left sagittal fossa; and in front by the umbilical notch. It is of a somewhat quadrilateral form, its under and posterior surfaces being marked by three fossæ: the porta and the fossæ for the gall-bladder and inferior vena cava, which separate its left part into two smaller lobes; the quadrate and caudate lobes. [WP,unvetted]." "FMA:13362 Wikipedia:Right_lobe_of_liver EHDAA2:0001008 VHOG:0001424 MA:0000363 SCTID:362182008 UMLS:C0227481 TAO:0005173 EHDAA:4001 ZFA:0005173 NCIT:C33481 EMAPA:18311" + "Combining with any modified low-density lipoprotein (LDL) or other polyanionic ligand and delivering the ligand into the cell via endocytosis. Ligands include acetylated and oxidized LDL, Gram-positive and Gram-negative bacteria, apoptotic cells, amyloid-beta fibrils, and advanced glycation end products (AGEs)." + + "Any process that stops, prevents or reduces the frequency, rate or extent of retrograde axon cargo transport." + "SCTID:282511007 NCIT:C33596" + "KUPO:0001107" + "The growth of a chondrocyte, where growth contributes to the progression of the chondrocyte over time." + "Any process that modulates the frequency, rate or extent of epithelial cell proliferation involved in lung morphogenesis." + "The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." "Wikipedia:Cytoplasm" + "A neutrophil precursor in the granulocytic series, being a cell intermediate in development between a myelocyte and the band form neutrophil. The protein synthesis seen in earlier stages decreases or stops; the nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare; and the cytoplasm becomes amphophilic like that of a mature granulocyte. This cell type is integrin alpha-M-positive, CD13-negative, CD15-positive, CD16-positive, CD33-positive, CD24-positive, fMLP receptor-negative and has expression of C/EBP-a, C/EBP-e, PU.1 transcription factor, lactotransferrin, myeloperoxidase and neutrophil gelatinase associated lipocalin." "FMA:84197" + "A duct joining the pancreas to the common bile duct to supply pancreatic juices which aid in digestion provided by the exocrine pancreas. The pancreatic duct joins the common bile duct just prior to the ampulla of Vater, after which both ducts perforate the medial side of the second portion of the duodenum at the major duodenal papilla." "MA:0000126 EMAPA:17510 EHDAA2:0001396 FMA:16003 SCTID:245385001 UMLS:C0030288 VHOG:0000256 MESH:D010183 NCIT:C12272 EHDAA:6905 Wikipedia:Pancreatic_duct GAID:337 RETIRED_EHDAA2:0002177 BTO:0002362" + "The pattern specification process that results in the subdivision of the otic epithelium in space to define an area or volume in which cells will differentiate to give rise to the semicircular canals." + "A macrophage mannose receptor 1 that is encoded in the genome of mouse." "UniProtKB:Q61830" + "A C-C motif chemokine 3 that is encoded in the genome of human." "UniProtKB:P10147" + "A life span which is relatively low." + "The process whose specific outcome is the progression of a spore over time, from its initiation to the mature structure. A spore is a structure that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction." "Wikipedia:Spore" + "Any of several arteries that arise from the aorta and supply blood to the esophagus." "UMLS:C0226294 NCIT:C32535 FMA:4149 SCTID:56548006" + "Any process that activates or increases the frequency, rate or extent of the directed movement of nucleobases, nucleosides, nucleotides and nucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "An epithelium that is part of a hindlimb stylopod [Automatically generated definition]." "VHOG:0001041 EHDAA2:0002131 EMAPA:17500" + "Cranial nerve fiber tract which is comprised of retinal ganglion cell axons running posterior medially towards the optic chiasm, at which some of the axons cross the midline and after which the structure is termed the optic tract. Transmits visual information from the retina to the brain[ZFA]." "TAO:0000435 EMAPA:17575 NCIT:C12761 FMA:50863 BAMS:2n CALOHA:TS-0713 BIRNLEX:1640 EFO:0004258 MBA:848 XAO:0000188 EHDAA2:0001313 ZFA:0000435 AAO:0010345 EHDAA:6788 DHBA:15544 neuronames:289 BAMS:IIn HBA:9307 GAID:831 Wikipedia:Optic_nerve MA:0001097 VHOG:0000543 SCTID:180938001 UMLS:C0029130 MESH:D009900 BAMS:nII" + "The chemical reactions and pathways involving zeaxanthin." + "The process in which the wraps of cell membrane that constitute myelin are laid down around an axon by an oligodendrocyte in the central nervous system." + "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])"@en + "Cranial ganglion which develops from an epibranchial placode." "TAO:0001555 ZFA:0001555" + "A nerve that is part of a manus [Automatically generated definition]." "EMAPA:37340 MA:0000629" + "A presumptive structure that has the potential to develop into a rhombomere 1." "ZFA:0001207 TAO:0001207" + "KUPO:0001108" + "A membrane alanyl aminopeptidase-like metallopeptidase that is a translation product of the human ANPEP gene or a 1:1 ortholog thereof." "IUPHARobj:1560" + + "The directed movement of glycine from outside of a cell, across the plasma membrane and into the cytosol." + "A fibrocyte that is part of the adventitia of ureter." "FMA:261289" + "Any process that activates or increases the frequency, rate or extent of male germ cell proliferation." + "The chemical reactions and pathways resulting in the formation of dicarboxylic acids, any organic acid containing two carboxyl (-COOH) groups." + "Any process that modulates the frequency, rate, or extent of natural killer cell tolerance induction." + "The portion of the hypothalamus located generally internal to the region of the infundibulum." "UMLS:C0020669 TAO:0006000 BAMS:IHR FMA:62028 neuronames:392 BIRNLEX:1015 MESH:D007033" + "A process in which a protein or protein complex is maintained in a specific location in the cell cortex." + "The cardiac Purkinje fiber is part of the cardiac conduction system that receives signals from the bundle of His and innervates the ventricular cardiac muscle." "MESH:D011690 BTO:0001735 NCIT:C33430 EMAPA:35718 MA:0000096 UMLS:C0034144 FMA:9492 GAID:560 Wikipedia:Purkinje_fiber" + "A myeloperoxidase that has been processed by proteolytic cleavage." + + "Any process that increases the frequency, rate or extent of the regulated release of norepinephrine." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the assembly of pseudopodia." + "An epidermal cell that secretes chitinous cuticle from its apical side." "FBbt:00007325" + "Any biological process involved in the maintenance of the steady-state number of epidermal stem cells within a population of cells." + "Any process that modulates the frequency, rate or extent of erythrophore differentiation." + "A developmental process, independent of morphogenetic (shape) change, that is required for an erythrocyte to attain its fully functional state." + "NCIT:C12990 FMA:45737 UMLS:C0921005" + "Any process that stops, prevents, or reduces the frequency, rate or extent of ovarian cumulus cell differentiation." + "A uteroglobin that is encoded in the genome of human." "UniProtKB:P11684" + "An animal opsin that is a translation product of the human OPN1LW gene or a 1:1 ortholog thereof." "IUPHARobj:2961" + "A glutamatergic neuron located in the cerebral cortex that projects to structures not derived from telencephalon." "ILX:0770101" + "The chemical reactions and pathways involving ecdysteroids, a group of polyhydroxylated ketosteroids ubiquitous in insects and other arthropods, in which they initiate post-embryonic development, including the metamorphosis of immature forms and the development of the reproductive system and the maturation of oocytes in adult females." + "The process resulting in the physical partitioning and separation of a glioblast into daughter cells." + "Any process that activates or increases the frequency, rate or extent of trophoblast cell migration." + "The chemical reactions and pathways resulting in the breakdown of organic hydroxy compound." + "A protein that is a translation product of the human DNTT gene or a 1:1 ortholog thereof." + "RETIRED_EHDAA2:0001422 EMAPA:17748 EHDAA2:0001421" + "Any process that activates, maintains or increases the frequency, rate or extent of cholinergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter acetylcholine." + "A tissue-resident macrophage of the renal glomerular mesangium involved in the disposal and degradation of filtration residues, presentation of antigen to T cells and in tissue remodeling." + "A circular muscle layer of muscular coat that is part of a esophagus." "FMA:67605 MA:0001574 EMAPA:37523" + "The series of events by which an electrical stimulus is received and converted into a molecular signal." + "Any process that modulates the chemical reactions and pathways involving any of a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups." + "Mesenchyme that develops_from the neural crest[Automatically generated definition]." "FMA:293883 EMAPA:32735" + "Any basket cell that is part of a dentate gyrus of hippocampal formation." + "The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites." "NIF_Subcellular:sao1044911821 Wikipedia:Soma_(biology)" + "A lamina propria that is part of a esophagus [Automatically generated definition]." "MA:0001568 FMA:63050 EMAPA:26987 NCIT:C49223 UMLS:C1707949" + "The layer within the retina where the bipolar cells synapse with the photoreceptor cells[ZFA]. Between the inner and outer nuclear layers, the outer plexiform layer (OPL) contains connections between the photoreceptors and bipolar and horizontal cells[GO]." "EMAPA:35744 BTO:0003174 Wikipedia:Outer_plexiform_layer SCTID:280684007 MA:0001316 FMA:58685 UMLS:C0229217 XAO:0003218 NCIT:C33237 TAO:0001330 BAMS:Ropl VHOG:0001171 ZFA:0001330" + "Any process that modulates the frequency, rate or extent of any cellular process that depends upon or alters the actin cytoskeleton." + "A M cell that is part of the epithelium proper of appendix." "FMA:263140" + "The renal vesicle is the primordial structure of the nephron epithelium, and is formed by the condensation of mesenchymal cells." + "A protein that is a translation product of the human LCN2 gene or a 1:1 ortholog thereof." + "The process in which the structures of a photoreceptor cell are generated and organized. This process occurs while the initially relatively unspecialized cell is acquiring the specialized features of a photoreceptor cell, a sensory cell that reacts to the presence of light. An example of this is found in Drosophila melanogaster." + "Cell migration that is accomplished by extension and retraction of a pseudopodium." + "Gland of the lamina epithelialis mucosae which perforate the lamina muscularis, with their adenomeres located in the submucosal connective tissue." "Wikipedia:Submucosal_glands EMAPA:37970 BTO:0003751" + "The regrowth of lost or destroyed tissues." + "The process whose specific outcome is the progression of the vasculature of the retina over time, from its formation to the mature structure." + "Any process that stops, prevents, or reduces the frequency, rate or extent of myeloid cell differentiation." + "A monocyte that has characteristics of both patrolling and inflammatory monocytes." + "Any process that modulates the rate, frequency or extent of glomerulus development, the progression of the glomerulus over time from its initial formation until its mature state. The glomerulus is a capillary tuft surrounded by Bowman's capsule in nephrons of the vertebrate kidney." + "A simple columnar epithelial cell that secretes mucin. Rough endoplasmic reticulum, mitochondria, the nucleus, and other organelles are concentrated in the basal portion. The apical plasma membrane projects microvilli to increase surface area for secretion." + "A bone that is part of a limb [Automatically generated definition]." "EFO:0000945 MAT:0000151 UMLS:C0582791 NCIT:C32223 SCTID:304149004 MIAA:0000151" + "Any process that modulates the frequency, rate, or extent of mast cell cytokine production." + "The process in which a relatively unspecialized cell acquires specialized structural and/or functional features of a renal filtration cell. Renal filtration cells are specialized cells of the renal system that filter fluids by charge, size or both. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state." + "Any process that stops, prevents, or reduces the frequency, rate or extent of mesonephric glomerulus development." + "A specialized multinuclear osteoclast associated with the absorption and removal of bone." + "A broadly stratifying amacrine cell with a small dendritic field and a complex dendritic arbor. Recurving diffuse amacrine cells have post-synaptic terminals in S2, S3, and S4." + "Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal bouton is a specialized region of it." "NIF_Subcellular:sao187426937" + "The progression of the vascular cord over time from its initial formation until its mature state. The vascular cord is the primordial vasculature that will develop into blood vessels by the process of tubulogenesis." + "A gland that is part of an anal canal [Automatically generated definition]." "EMAPA:27543 EMAPA:27221 FMA:15720 FMA:15724 EMAPA:27233 SCTID:245448005 NCIT:C32068 Wikipedia:Anal_gland UMLS:C0162322" + "Any process that modulates the frequency, rate, or extent of leukocyte mediated cytotoxicity." + "The connective tissue located between the respiratory (airway and alveolar) epithelium, the capillary endothelium and pleural mesothelium; it contains basement membrane composed of collagen, elastin, proteoglycans, and fibronectin." "EMAPA:35521 SCTID:201609008 FMA:27533 MA:0001782" + "An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the mouse Fcgr2 gene or a 1:1 ortholog thereof." + "Any process that increases the rate, frequency, or extent of protein tyrosine kinase activity." + "Any process that stops, prevents or reduces the frequency, rate or extent of DNA catabolic process." + "Any process that modulates the frequency, rate, or extent of myeloid cell apoptotic process." + "The the continuous basement membrane found within the membranous labyrinth of the cochlea, known to extend from the limbus, down to the inner sulcus, across the basilar membrane, up to the external sulcus to the spiral prominence and radiating into the spiral ligament ensheathing the root cell processes." "EMAPA:37830" + "Any process that activates or increases the frequency, rate or extent of vesicle fusion with Golgi apparatus." + "A protein complex composed of two identical immunoglobulin heavy chains of the IgA isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and sometimes complexed with J chain or J chain and secretory component. An IgA immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." + "A specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue, which typically differentiates from monocytes. This cell has the following markers: tartrate-resistant acid phosphatase type 5-positive, PU.1-positive, c-fos-positive, nuclear factor NF-kappa-B p100 subunit-positive, tumor necrosis factor receptor superfamily member 11A-positive and macrophage colony-stimulating factor 1 receptor-positive." "FMA:66781 BTO:0000968 MESH:D010010 CALOHA:TS-0721" + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising intermediate filaments and their associated proteins." + "One of the main divisions of the whole organism of arthropods formed from groups of segments." + "Any process that stops, prevents or reduces the frequency, rate or extent of hematopoietic progenitor cell differentiation." + "One of a set of deep furrows which divide the lobules of the cerebellum. Examples: postcentral, primary and secondary furrows." "SCTID:314163001 EMAPA:37818 DHBA:12828 FMA:321547 BAMS:CBf HBA:9406 neuronames:1213" + "A lobar bronchus that is part of a left lung [Automatically generated definition]." "MA:0003133 EMAPA:17388 EMAPA:17656 SCTID:245510003" + "Any process that activates or increases the frequency, rate or extent of immature T cell proliferation." + "A lamina propria that is part of a gallbladder [Automatically generated definition]." "NCIT:C49228 EMAPA:35371 UMLS:C1708175 MA:0001633 FMA:278594" + "A duct made up of simple tubular epithelium that is part of an eccrine sweat gland. The main function of the duct of the eccrine sweat gland is the reabsorption of Na and Cl ions as sweat flows through the duct. It has two cell layers: basal and luminal. It is continuous with the secretory coil and goes towards the skin surface. The distal segment of the duct is relatively straight and connects with the acrosyringium in the epidermis. Most of the ion reabsorption occurs in the proximal part of the duct." "FMA:70617" + "A midventral endochondral skeletal element which represents the origin site of the pectoral muscles[PHENOSCAPE:ad]." "MA:0001331 EMAPA:18344 NCIT:C12793 CALOHA:TS-0972 EHDAA2:0001914 AAO:0000765 EHDAA:9561 Wikipedia:Sternum SCTID:302522007 FMA:7485 VHOG:0000856 UMLS:C0038293 BTO:0001302 MESH:D013249 galen:Sternum GAID:246" + "A quality inhering in a bearer by virtue of the bearer's being a remnant structure from earlier development or evolution." + "Neuromast that is part of the posterior lateral line. Kimmel et al, 1995. (Also see Anatomical Atlas entry for lateral line by T. Whitfield.)." "ZFA:0000940" + "Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions." "Wikipedia:Meiosis" + "A protein that is a translation product of the human CEBPA gene or a 1:1 ortholog thereof." + "Obsolete. Use PO:0000349 from Plant Ontology instead. A relatively unspecialized cell that will give rise to specialized cell types of the epidermis." + "A process in which a ribosome is transported to, and/or maintained in, a specific location." + "A protein that is a translation product of the human TNFRSF11A gene or a 1:1 ortholog thereof." "IUPHARobj:1881 PIRSF:PIRSF038806" + "A developmental process, independent of morphogenetic (shape) change, that is required for the hypoglossal nerve to attain its fully functional state. This motor nerve innervates all the intrinsic and all but one of the extrinsic muscles of the tongue." + "Any process that activates or increases the frequency, rate or extent of secretory granule organization." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving aldosterone." + "The process in which the anatomical structures of a pharyngeal arch artery is generated and organized. The pharyngeal arch arteries are a series of six paired embryological vascular structures, the development of which give rise to several major arteries, such as the stapedial artery, the middle meningeal artery, the internal carotid artery and the pulmonary artery." + "The process in which the anatomical structure of an endothelium is generated and organized. Endothelium refers to the layer of cells lining blood vessels, lymphatics, the heart, and serous cavities, and is derived from bone marrow or mesoderm. Corneal endothelium is a special case, derived from neural crest cells." + "Any process that modulates the rate, frequency or extent of cell proliferation that contributes to the shaping of a heart valve." + "The process whose specific outcome is the progression of a trigeminal ganglion over time, from its formation to the mature structure." + "Any process that modulates the frequency, rate or extent of axonogenesis, the generation of an axon, the long process of a neuron." + "The area of the (spleen) secondary B follicle that surrounds the germinal center and harbors the small recirculating B lymphocytes." "EMAPA:37962" + + "An alveolar macrophage that expresses CCL3." + "A D(1A) dopamine receptor that is encoded in the genome of mouse." "UniProtKB:Q61616" + "Pancreatic juice is slightly alkaline and contains numerous enzymes and inactive enzyme precursors including alpha-amylase, chymotrypsinogen, lipase, procarboxypeptidase, proelastase, prophospholipase A2, ribonuclease, and trypsinogen. Its high concentration of bicarbonate ions helps to neutralize the acid from the stomach." "MESH:D010189 BTO:0000504 GAID:1166 FMA:62973 CALOHA:TS-2235" + "A melanopsin that is encoded in the genome of mouse." "UniProtKB:Q9QXZ9" + "Any process that activates or increases the frequency, rate or extent of gonad development." + "The developmental process pertaining to the initial formation of an anatomical structure from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome." + "A lobe of tissue that is part of a thyroid gland." "UMLS:C0447647 VHOG:0000732 Wikipedia:Lobes_of_thyroid_gland FMA:13367 NCIT:C33784 EHDAA2:0002032 EMAPA:18196 MA:0000131 SCTID:245537001" + "The process whose specific outcome is the progression of a Purkinje myocyte over time, from its formation to the mature structure. The Purkinje myocyte (also known as cardiac Purkinje fiber) is part of the cardiac conduction system that receives signals from the bundle of His and innervates the ventricular cardiac muscle." + "Any regulation of signal transduction that takes place in the extracellular region." + "A tumor necrosis factor ligand superfamily member 5 that is encoded in the genome of human." "Reactome:R-HSA-198113 UniProtKB:P29965" + "An epithelium that is part of a segmental bronchus [Automatically generated definition]." "FMA:86626 MA:0001850 EMAPA:37740" + "An epithelium that is part of a lobar bronchus of left lung." "MA:0003135 EMAPA:17658" + "Terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters. The axon terminus is considered to be the whole region of thickening and the terminal button is a specialized region of it." "NIF_Subcellular:nlx_subcell_20090512" + "A circulatory process that occurs at the level of the vasculature." + "Any process that stops, prevents or reduces the frequency, rate or extent of formation of translation initiation ternary complex." + "The progression of the oviduct epithelium over time from its initial formation to the mature structure. An oviduct is a tube through which an ova passes from the ovary to the uterus, or from the ovary to the outside of the organism. The oviduct epithelium is the specialized epithelium that lines the oviduct." + "The part of the renal cortex nearest to the medulla." "EMAPA:37623 FMA:74288 KUPO:0001008 MA:0001648" + "The directed movement of substances or organelles within the cytosol." + "An epithelium that is undergoing proliferation to provide large numbers of neuronal cells." "AEO:0001009" + "Any process that activates or increases the frequency, rate or extent of the controlled release of a protein from a cell." + "Any process that decreases the rate, frequency or extent of myofibril assembly by organization of muscle actomyosin into sarcomeres. The sarcomere is the repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs." + "The collection of muscles that form attachments to the hip skeleton." "FMA:50227" + "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs." + "The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the B- or T cell receptor to augment B- or T cell activation." + "Any process that activates or increases the frequency, rate, or extent of an acute inflammatory response." + "Epimysium is a layer of connective tissue which ensheaths the entire muscle. It is composed of dense irregular connective tissue. It is continuous with fascia and other connective tissue wrappings of muscle including the endomysium, and perimysium. It is also continuous with tendons where it becomes thicker and collagenous." "NCIT:C32527 UMLS:C0504096 Wikipedia:Epimysium FMA:9726" + "Any process that stops, prevents, or reduces the frequency, rate or extent of chemical reactions and pathways involving a protein." + "A contractility which is relatively low." + "Any process that activates or increases the frequency, rate or extent of synoviocyte proliferation." + "A protein that is a translation product of the human CLEC6A gene or a 1:1 ortholog thereof." "IUPHARobj:2928" + "The chemical reactions and pathways resulting in the formation of melatonin (N-acetyl-5-methoxytryptamine)." + "The process in which a relatively unspecialized cell acquires the specialized features of a mononuclear cell." + "Any muscle organ that is part of a hindlimb zeugopod (lower leg) [Automatically generated definition]." "SCTID:265806001 EMAPA:19318 FMA:22471 MA:0000678" + "The process in which neuroblasts acquire specialized structural and/or functional features that characterize the mature cerebellar granule cell. Differentiation includes the processes involved in commitment of a neuroblast to a granule cell fate. A granule cell is a glutamatergic interneuron found in the cerebellar cortex." + "Any process that stops, prevents or reduces the frequency, rate or extent of lysosomal protein catabolic process." + "A collagen trimer that forms networks." + "A layer of microvilli, Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments[GO,modified]." "FMA:67296 UMLS:C0026049 MESH:D008871 Wikipedia:Microvillus NCIT:C33112" + "A nerve that is part of a wrist [Automatically generated definition]." "MA:0000637 EMAPA:37339" + + "A life span which is relatively normal or average." + "Any process that activates or increases the frequency, rate, or extent of tolerance induction." + "An epithelial cell of the esophageal cardiac gland that occurs both in the proximal and distal esophagus, within the lamina propia." "FMA:256143" + "Any process that activates or increases the frequency, rate or extent of protein localization to membrane." + "A pedal digit metatarsal bone or its cartilage or pre-cartilage precursor." + "Any process that stops, prevents, or reduces the frequency, rate or extent of bone mineralization." + "A lymphocyte located in blood." + "Any region of epithelium that is part of a skin region." "BTO:0004382" + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an aldehyde stimulus." + "A class switched memory B cell is a memory B cell that has undergone Ig class switching and therefore is IgM-negative on the cell surface. These cells are CD27-positive and have either IgG, IgE, or IgA on the cell surface." + "EHDAA2:0001140" + "Any process that modulates the frequency, rate or extent of mesonephric glomerulus development." + + "A scapula bone or its cartilage or pre-cartilage precursor." + "The process in which the anatomical structure of the optic nerve is generated and organized. The sensory optic nerve originates from the bipolar cells of the retina and conducts visual information to the brainstem. The optic nerve exits the back of the eye in the orbit, enters the optic canal, and enters the central nervous system at the optic chiasm (crossing) where the nerve fibers become the optic tract just prior to entering the hindbrain." + + "Any process that stops, prevents, or reduces the frequency, rate, or extent of mast cell apoptotic process." + "A primordium that develops into a clavicle bone." "EHDAA2:0000254" + "The outermost extraembryonic membrane of amniotes." "FMA:80224 EHDAA:150 Wikipedia:Chorion UMLS:C1516505 UMLS:C0008503 GAID:1299 BTO:0000252 EMAPA:16112 MESH:D002823 EHDAA2:0000245 NCIT:C34122 EV:0100121 EFO:0002780 VHOG:0000200 NCIT:C34124 CALOHA:TS-0144" + "Any process that activates or increases the frequency, rate, or extent of a humoral immune response." + "A trigeminal neuron that is responsible for sensation in the face." + "A T-cell surface glycoprotein CD1 that is a translation product of the human CD1A gene or a 1:1 ortholog thereof." + "One of the parts of a holometabolous insect larva that will become a portion of the outside of the adult insect during the pupal transformation." "BTO:0004658 MAT:0000064 MIAA:0000064 Wikipedia:Imaginal_disc" + "An intersegmental rod-shaped bone that forms in the peritoneal membrane and attach to the vertebral parapophyses." "AAO:0000545 UMLS:C0035561 galen:Rib NCIT:C12782 MA:0000315 MESH:D012272 SCTID:302523002 TAO:0000538 GAID:245 EFO:0003066 VHOG:0001154 FMA:7574 CALOHA:TS-2209 ZFA:0000538 EMAPA:18010 Wikipedia:Rib" + "Any process that modulates the frequency, rate or extent of exosomal secretion." + "VHOG:0000767 EMAPA:16054 EHDAA2:0000472" + "A change in the morphology or behavior of a neuroblast resulting from exposure to an activating factor such as a cellular or soluble ligand." + "The tissues that surround the organs that are present within the abdominal cavity. The abdominal wall tissue is composed of layers of fat, parietal peritoneum, fascia, and muscles." "GAID:26 FMA:10429 Wikipedia:Abdominal_wall SCTID:181613000 MESH:D034861 UMLS:C0836916 FMA:259054 EMAPA:37064 NCIT:C77608" + "A protein complex that contains G protein-coupled receptors." + "A neuron with its soma located in the dentate gyrus of the hippocampus." + "The switching of activated B cells from IgM biosynthesis to biosynthesis of other isotypes of immunoglobulin, accomplished through a recombination process involving an intrachromosomal deletion involving switch regions that reside 5' of each constant region gene segment in the immunoglobulin heavy chain locus." "Wikipedia:Immunoglobulin_class_switching" + "A basophilic chromophil cell that of the anterior pituitary gland." "FMA:83094" + + "An amacrine cell with a medium dendritic field and post-synaptic terminals that stratify at S2, with a second stratification that occurs in S3 and S4. This cell type releases the neurotransmitter glycine." + "Any process that modulates the extent of cell adhesion contributing to the shaping of the heart." + "A group 3 innate lymphoid cell in the human with the phenotype IL-7Ralpha-positive." + "Mesenchyme that develops_from a neural crest and is part of a 6th arch mesenchyme." "EHDAA2:0004077" + "The regulated release of acetylcholine by a cell. The acetylcholine acts as a neurotransmitter that acts in both the peripheral nervous system (PNS) and central nervous system (CNS)." + "Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction." + "Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a microvillus." + "The process of creating a trabecula in the spleen. A trabecula is a tissue element in the form of a small beam, strut or rod." + "The process in which a relatively unspecialized cell acquires specialized features of a mesenchymal stem cell that contributes to the shaping of a nephron. A mesenchymal stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized mesenchymal cells." + "An alpha-(1,3)-fucosyltransferase 4 that is encoded in the genome of mouse." "UniProtKB:Q11127" + "A precursor of mature crystal cells." "FBbt:00001689" + "Any process that stops, prevents, or reduces the frequency, rate or extent of sister chromatid segregation." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response to wounding." + "Any process that stops, prevents or reduces the frequency, rate or extent of odontoblast differentiation." + "Any gland, other than the gonad, associated with the genital tract, such as the ampulla of the ductus deferens and the bulbourethral, prostate and vesicular glands of the male." "BTO:0004798" + + + "One of the veins draining a meninix." "SCTID:84842006 FMA:50839" + "A temporal lobe that is part of a left cerebral hemisphere." "UMLS:C1281971 FMA:72972 BIRNLEX:1784 SCTID:314158000" + "A T-cell surface glycoprotein CD8 beta chain that has had the signal peptide removed." + "A lymphocyte antigen 6C2 that is encoded in the genome of mouse." "UniProtKB:P0CW03" + "Any process that modulates the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." + "The nail plate is the hard and translucent portion of the nail, composed of keratin." "Wikipedia:Nail_plate MA:0002708 EMAPA:35583 SCTID:372177002 NCIT:C34216" + "A shape quality inhering in a bearer by virtue of the bearer's being marked by narrow lines or grooves, usually parallel." + "Any process that activates or increases the frequency, rate or extent of natural killer cell activation." + "A promyelocyte that is considerably smaller, with more condensed chromatin, and nucleoli are no longer conspicuous." "FMA:83534" + "A non-terminally differentiated cell that differentiates into a xanthophore." + "The progression of an axon over time. Covers axonogenesis (de novo generation of an axon) and axon regeneration (regrowth), as well as processes pertaining to the progression of the axon over time (fasciculation and defasciculation)." + "A region of muscle in many organs in the vertebrate body, adjacent to the submucosa membrane. It is responsible for gut movement such as peristalsis." "SCTID:86915006 UMLS:C0225358 BTO:0004838 Wikipedia:Muscular_layer" + "The regulated release of dopamine from the somatodendritic compartment (cell body or dendrites) of a neuron." + "The chemical reactions and pathways resulting in the formation of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues." "MetaCyc:GLYCOGENSYNTH-PWY" + "The process whose specific outcome is the progression of a tissue over time, from its formation to the mature structure." "Wikipedia:Histogenesis" + "Skeletogenic cell that has the potential to form an odontoblast, deposits predentine, and arises from a cranial neural crest cell." + "An epithelial cell found in the basal part of the intestinal glands (crypts of Lieberkuhn) including the appendix. Paneth cells synthesize and secrete lysozyme and cryptdins. Numerous in the deeper parts of the intestinal crypts, particularly in the duodenum, rich in zinc, contain large acidophilic granules, with irregular apical microvilli and prominent membrane-bound vacuoles containing matrix." "FMA:62897 BTO:0000993" + "Any biological process involved in the maintenance of the steady-state number of cells within a population of cells in a tissue." + "The physiological response of the kidneys to a decrease in blood flow." + "A sst GABAergic cortical interneuron found in L6 that expresses tyrosine hydroxylase. L6 Th+ SST cells have mostly local axonal arborization within L6." + "The process whose specific outcome is the progression of the ectodermal digestive tract over time, from its formation to the mature structure. The ectodermal digestive tract includes those portions that are derived from ectoderm." + "A bipolar neuron found in the retina and having connections with photoreceptors cells and neurons in the inner half of the inner plexiform layer. These cells depolarize in response to light stimulation of their corresponding photoreceptors." + "The process whose specific outcome is the progression of a neuromast hair cell over time, from its formation to the mature structure. A neuromast hair cell is a hair cell that acts as a sensory receptor of the neuromast; it is morphologically polarized as a result of the relative position of the single kinocilium and the clusters of stereocilia on its apical surface. Cell development does not include the steps involved in committing a cell to a specific fate." + "A columnar chondrocyte that differentiates in the late embryonic growth plate of bone. Columnar chondrocytes vigorously proliferate and form columns in the growth plate." + + "An ecto-epithelial cell of the paranasal region of the viscerocranial mucosa." "FMA:70578" + "A fully differentiated plasma cell that secretes IgA." + "A vertebral endochondral element in the thoracic region of the vertebral column." + + "Any process that stops, prevents or reduces the frequency, rate or extent of distal tip cell migration." + "The directed movement of a protein to a specific location within the extracellular region." + "Any apoptotic process in an activated CD8-positive, alpha-beta T cell." + "EHDAA2:0004512" + "Any process that activates or increases the frequency, rate or extent of cell adhesion." + "Any process that activates or increases the frequency, rate or extent of motile cilium assembly." + "A fold of skin that covers and protects part of the eyeball. Examples: upper eyelid, lower eyelid, nictitating membrane." "VHOG:0000016 EHDAA2:0000487 Wikipedia:Eyelid EMAPA:17829 BTO:0002241 GAID:72 NCIT:C12713 MESH:D005143 FMA:54437 MA:0000268 EHDAA:9037 UMLS:C0015426 EV:0100338 SCTID:265782007" + "The process whose specific outcome is the progression of the vasculature of the cerebellum over time, from its formation to the mature structure." + "Any process that increases the rate, frequency or extent of a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events." + "A ventral horn of spinal cord that is part of a cervical spinal cord." "BIRNLEX:1680 SCTID:174363005 UMLS:C1278740 UMLS:C0228615" + "Any process that modulates the frequency, rate or extent of cardiac muscle tissue development." + "Any process that modulates the frequency, rate or extent of outer hair cell apoptotic process." + "The process in which the anatomical structures of arterial blood vessels are generated and organized. Arteries are blood vessels that transport blood from the heart to the body and its organs." + "An elastic tissue that is part of a bronchus [Automatically generated definition]." "NCIT:C49211 MA:0001838 UMLS:C1707053" + + "A portion of smooth muscle tissue that is part of a mammary gland [Automatically generated definition]." "MA:0000795 EMAPA:37669" + "A mature B cell that has the phenotype CD1d-positive and expresses interleukin-10. This cell type has been associated with suppression of chronic inflammatory responses and T cell responses." + "Any process that modulates the frequency, rate or extent of lymphocyte proliferation." + "Any process that stops, prevents, or reduces the frequency, rate or extent of chondrocyte differentiation." + "A homeostatic process involved in the maintenance of a steady state level of monoatomic ions within a cell. Monatomic ions (also called simple ions) are ions consisting of exactly one atom." + "Any process that activates or increases the frequency, rate, or extent of antigen processing and presentation of peptide antigen." + "A nerve that is part of a finger [Automatically generated definition]." "SCTID:181015006 EMAPA:37341 MA:0000625" + "A CD24-negative CD38-negative IgG-negative memory B cell is a CD38-negative IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype CD24-negative, CD38-negative, and IgG-negative." + "A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a consistently-sized round cross section." + "A sialoadhesin that is encoded in the genome of mouse." "UniProtKB:Q62230" + "The stroma of the bone marrow is all tissue not directly involved in the primary function of hematopoiesis. The yellow bone marrow belongs here, and makes the majority of the bone marrow stroma, in addition to stromal cells located in the red bone marrow. Yellow bone marrow is found in the Medullary cavity. Still, the stroma is indirectly involved in hematopoiesis, since it provides the hematopoietic microenvironment that facilitates hematopoiesis by the parenchymal cells. For instance, they generate colony stimulating factors, affecting hematopoiesis." "Wikipedia:Bone_marrow#Stroma FMA:21426 CALOHA:TS-0085" + "A capillary that is part of the brain." + "Any process that activates or increases the frequency, rate, or extent of an immune effector process." + "An integrin alpha with A domain that is a translation product of the human ITGAX gene or a 1:1 ortholog thereof. Integrin alpha-X complexed with beta-2 is a receptor for fibrinogen. It recognizes the sequence GPR in fibrinogen. It mediates cell-cell interaction during inflammatory responses. It is especially important in monocyte adhesion and chemotaxis." "IUPHARobj:2454" + "An insect excretory cell that regulates hemolymph composition by filtration and filtrate endocytosis." "BTO:0004597" + "A CD33 molecule that is encoded in the genome of mouse." "UniProtKB:Q63994" + "Glandular cell of mammary epithelium. Example: glandular cells of large and intermediate ducts, glandular cells in terminal ducts." "CALOHA:TS-1272" + "GC_ID:1" + "The directed movement of L-glutamate, the L-enantiomer of the anion of 2-aminopentanedioic acid, into a cell or organelle." + "Binding to a peptide with hormonal activity in animals." + "The expansion of a lymphocyte population by cell division." + "Any process that activates or increases the activity of an enzyme." + "A homeobox protein Meis2 that is encoded in the genome of mouse." "UniProtKB:P97367" + "Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to presynapse." + "A shape quality in a bearer by virtue of the bearer's curving inward." + "A tunica adventitia that is part of a vein." "FMA:14355 EMAPA:36310 SCTID:13202006 EV:0100034" + "The formation of the specialized region of ectoderm between the neural ectoderm (neural plate) and non-neural ectoderm. The neural crest gives rise to the neural crest cells that migrate away from this region as neural tube formation procedes." + "Any process that modulates the frequency, rate or extent of neurotransmitter receptor activity. Modulation may be via an effect on ligand affinity, or effector funtion such as ion selectivity or pore opening/closing in ionotropic receptors." + "A submucosa that is part of a ileum [Automatically generated definition]." "SCTID:65374006 FMA:14957" + "Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle." + "Any process that decreases the frequency, rate or extent of the chemical reactions and pathways resulting in the metabolism of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals." + "Any process that increases the rate, frequency or extent of T cell chemotaxis. T cell chemotaxis is the directed movement of a T cell in response to an external stimulus." + "The movement of an organism or part of an organism using mechanoreceptors, the nervous system, striated muscle and/or the skeletal system." + "Any process that stops, prevents, or reduces the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information." + "A blood vessel that is part of a choroid [Automatically generated definition]." "MA:0001237 FMA:76550 EMAPA:17828" + "An anatomical structure that develops (entirely or partially) from the ectoderm." + "GC_ID:1" + "Any process that stops, prevents or reduces the frequency, rate or extent of vascular smooth muscle cell proliferation." + "The fetal urogenital sinus (from which the prostate derives) is a simple cylinder of stratified basal epithelium, surrounded by mesenchyme and positioned between the embryonic bladder and pelvic urethra." "EHDAA2:0004061 EMAPA:31509" + "Cells of the uterine chorion that acquire specialized structural and/or functional features that characterize chorionic trophoblasts. These cells will migrate towards the spongiotrophoblast layer and give rise to syncytiotrophoblasts of the labyrinthine layer." + "Any process that results in the transfer of information from an epithelial cell to a mesenchymal cell where it is interpreted." + "The outer, i.e. cytoplasm-facing in a cellular organelle, lipid bilayer of an organelle envelope." + "Any process that modulates the frequency, rate or extent of amacrine cell differentiation." + "BTO:0002051" + "The part of the forelimb between pectoral region and the elbow, corresponding to the humerus." "EHDAA:6234 galen:Arm EMAPA:17424 MESH:D001132 VHOG:0000343 UMLS:C0446516 NCIT:C32141 MA:0000035 EHDAA2:0002112 FMA:24890 SCTID:302538001 VSAO:0005057 EHDAA:4186 AAO:0000199" + "An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds." "MESH:D012156 CALOHA:TS-0864 BTO:0001173" + "FMA:24293 SCTID:281228008 Wikipedia:Atlas_(anatomy)#Vertebral_foramen" + "Any process that activates or increases the frequency, rate or extent of cell proliferation involved in compound eye morphogenesis." + "A conventional thymic dendritic cell that is CD8alpha-positive." + "Any cellular process that results in the specification, formation or maintenance of anisotropic intracellular organization or cell growth patterns." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving juvenile hormone." + "Cranial nerves that carry afferent and efferent fibers for the lateral line system." "TAO:0001479 AAO:0010077 ZFA:0001479" + "A blood vessel that is part of a pelvis [Automatically generated definition]." "EMAPA:37244 MA:0000531" + "A optical quality inhering in a bearer by virtue of the bearer's not being clear; not transmitting or reflecting light or radiant energy." + "A limbic lobe that is part of a right cerebral hemisphere." "BIRNLEX:1781 FMA:72980" + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells." + "Any process that modulates the frequency, rate, or extent of eosinophil degranulation." + "Any process that stops, prevents or reduces the frequency, rate or extent of oocyte maturation." + + "A ciliated cell of the endometrial epithelium. The cilia of this cell type help move mucus from glandular tissue of the endometrium." + "Skeletal subdivision consisting of the anterior appendicular limb skeleton, excluding the pectoral girdle." "VSAO:0005000" + "The core of the crystalline lens, surrounded by the cortex." "MESH:D007907 BTO:0001633 FMA:58971 SCTID:280628007" + "The process in which a relatively unspecialized cell acquires the specialized features of a luteal cell. Large luteal cells develop from granulosa cells. Small luteal cells develop from theca cells." + "Luminal space of the left ventricle of the heart." "EMAPA:26038 FMA:9466" + "A cholinergic axonal fibers projecting from the CNS to a parasympathetic ganglion." "Wikipedia:Preganglionic_fibers" + "A submucosa that is part of a segmental bronchus [Automatically generated definition]." "FMA:62670" + "An anatomical space that surrounded_by a primitive urogenital sinus." "EHDAA2:0002142" + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an oxygen-containing compound stimulus." + "The thick circular layer of smooth gastric musculature encircling the gastroesophageal junction that functions to reduce backflow into the esophagus from the stomach." "SCTID:267809009 FMA:14915 UMLS:C0227192 EMAPA:18267 galen:LowerEsophagealSphincter MA:0002951 NCIT:C33009" + "One of the two nuclear divisions that occur as part of the meiotic cell cycle." + "The series of events during equilibrioception required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual input plays an important role in the ability of an organism to perceive its orientation with respect to gravity." + "A supporting cell of the anterior pituitary gland involved in trophic and catabolic processes; expresses a broad spectrum of cytokeratins indicative of their epithelial nature." "FMA:83102" + "The reproductive developmental process whose specific outcome is the progression of the seminiferous tubule over time, from its formation to the mature structure. Seminiferous tubules are ducts located in the testicles, and are the specific location of meiosis, and the subsequent creation of gametes, namely spermatozoa." + "Any process that modulates the frequency, rate or extent of xanthophore differentiation." + "A protein that is a translation product of the human SPI1 gene or a 1:1 ortholog thereof." + "Each seminal vesicle consists of a single tube, coiled upon itself, and giving off several irregular cecal diverticula; the separate coils, as well as the diverticula, are connected together by fibrous tissue. When uncoiled, the tube is about the diameter of a quill, and varies in length from 10 to 15 cm.; it ends posteriorly in a cul-de-sac; its anterior extremity becomes constricted into a narrow straight duct called the excretory duct of seminal gland (or duct of the seminal vesicle), which joins with the corresponding ductus deferens to form the ejaculatory duct[WP]." "Wikipedia:Excretory_duct_of_seminal_gland SCTID:279675008 FMA:19473 EMAPA:29282" + "EHDAA2:0004116" + "A nephron that is part of a mesonephros." "AAO:0010387 XAO:0000292 ZFA:0005592" + "A cell that stores epinephrine secretory vesicles. During times of stress, the nervous system signals the vesicles to secrete their hormonal content. Their name derives from their ability to stain a brownish color with chromic salts. Characteristically, they are located in the adrenal medulla and paraganglia of the sympathetic nervous system." "FMA:69263 BTO:0000259" + "The commitment of cells to specific cell fates of the endoderm, ectoderm, or mesoderm as a part of gastrulation." + "An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli." "MA:0000557 EMAPA:37273" + "An artery that supplies oxygenated blood to the cystic duct." "FMA:14835" + "A blood vessel that is part of a hindlimb stylopod [Automatically generated definition]." "EMAPA:37299 MA:0000681" + "The process in which the anatomical structures of veins of the heart are generated and organized." + "The directed movement of an astrocyte guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis)." + "A fibroblast that is part of the heart." + "A specialized receptor organ that is a collection of cells spanning the gustatory epithelium." "SCTID:362099006 Wikipedia:Taste_bud BTO:0000989 ZFA:0001074 MA:0001591 XAO:0000445 TAO:0001074 UMLS:C0039337 MESH:D013650 FMA:54825 EMAPA:35850 GAID:815 VHOG:0000130 NCIT:C96518 CALOHA:TS-1015 BIRNLEX:4101 http://uri.neuinfo.org/nif/nifstd/nifext_14 AAO:0010573" + "A group 3 innate lymphoid cell in the human with the phenotype IL-7Ralpha-positive, and NKp44-positive." + + "An epithelial cell that secretes cuticle." + "Any process that modulates the frequency, rate or extent of T-helper 2 cell cytokine production." + "A protein that is a translation product of the human ENPP3 gene or a 1:1 ortholog thereof." + "Any process that activates or increases the frequency, rate or extent of neural crest cell differentiation." + "Any process in which a cell, substance or cellular entity, such as a protein complex or organelle, is maintained in a location and prevented from moving elsewhere." + "Any process that modulates the frequency, rate, or extent of a type 2 immune response." + "Enables the transmembrane transfer of an ion by a channel that opens when a specific neurotransmitter has been bound by the channel complex or one of its constituent parts." + "A magnocellular neurosecretory cell that is capable of producing and secreting vasopressin." + "The multiplication or reproduction of stem cells, resulting in the expansion of a stem cell population. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells." + "Movement of a vesicle along an actin filament, mediated by motor proteins." + "The intracellular signaling pathway that results in the cessation of cell movement involved in lamination of the cerebral cortex." + "A peptide hormone secreting cell that secretes endorphin." + "An epithelium that is composed primarily of secretory cells." "NCIT:C43370 UMLS:C0682578 UMLS:C1708242 BTO:0002991 NCIT:C45715" + "An arginase-1 that is encoded in the genome of mouse." "UniProtKB:Q61176" + "The directed movement of a protein along a microtubule, mediated by motor proteins." + "A venule located in the vermiform appendix." + "A lymphocyte found in adipose tissue that lacks lineage markers of other lymphocytes but is capable of mediating TH2 cytokine responses. This cell type is found in fat associated lymphoid clusters, proliferates in response to IL2 and produce large amounts of TH2 cytokines such as IL5, IL6 and IL13" + "A patrolling monocyte that is CD14-low and CD16-positive." + "A monostratified retinal ganglion cell with large soma and large dendritic field." "BAMS:1009" + "Portion of tissue that is part of the anterior neural keel and will form the optic vesicle[ZFA]. A paired ectodermal placode that becomes invaginated to form the embryonic lens vesicles." "EHDAA2:0004431 AAO:0011038 XAO:0004090 ZFA:0000570 TAO:0000570 XAO:0000227 EFO:0003541" + "An epithelium that is part of a naris [Automatically generated definition]." "EMAPA:35959 MA:0003172" + "A C-shaped bundle of fibres (axons) in the brain, and carries signals from the hippocampus to the mammillary bodies and septal nuclei. It is typically divided into the columns (crus), body, commissure and the pre-commissural and post-commissural fornix (MM)." "UMLS:C0152334 DHBA:10576 BAMS:f Wikipedia:fornix_of_brain NCIT:C32289 EMAPA:35352 HBA:9249 UMLS:C0458370 DMBA:17767 BIRNLEX:705 MA:0002747 neuronames:268 SCTID:279302004 FMA:83865" + "EHDAA2:0004114" + "The process that gives rise to the cerebellar molecular layer. This process pertains to the initial formation of a structure from unspecified parts. The molecular layer is the outermost layer of the cerebellar cortex. It contains the parallel fibers of the granule cells, interneurons such as stellate and basket cells, and the dendrites of the underlying Purkinje cells." + "The process in which a precursor cell type acquires the specialized features of an immature B cell." + "A vein that is part of a conjunctiva." "SCTID:149885003" + "The chemical reactions and pathways involving monocarboxylic acids, any organic acid containing one carboxyl (COOH) group or anion (COO-)." + "Any process that activates or increases the frequency, rate or extent of natural killer cell degranulation." + "Any process that stops, prevents or reduces the rate or extent of growth, the increase in size or mass of all or part of an organism." + "The directed movement of acetylcholine into a cell, typically presynaptic neurons or glial cells. Acetylcholine is a major neurotransmitter and neuromodulator both in the central and peripheral nervous systems. It also acts as a paracrine signal in various non-neural tissues." + "The process whose specific outcome is the progression of a metanephric long nephron over time, from its formation to the mature structure. Long nephrons are associated with juxtamedullary glomeruli and extend into the inner medulla in the metanephros." + "The characteristic movement of an immature neuron from germinal zones to specific positions where they will reside as they mature." "Wikipedia:Neural_development#Neuron_migration Wikipedia:Neuron_migration" + + "An artery that is part of the placenta." + "An animal opsin that is a translation product of the human OPN1MW, OPN1MW2, or OPN1MW3 genes, 1:1 orthologs thereof, or a semi-ortholog thereof." "IUPHARobj:2962" + "Any process that stops, prevents or reduces the frequency, rate or extent of vascular associated smooth muscle cell migration." + "The aggregation, arrangement and bonding together of a set of components to form a synapse. This process ends when the synapse is mature (functional)." "Wikipedia:Synaptogenesis" + "One of sublaminar layers S3, S4, or S5." "CP:0001045" + "Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]." "galen:Muscle VHOG:0001245 SCTID:71616004 EMAPA:37474 ZFA:0005145 GAID:131 MA:0000015 EV:0100146 XAO:0000172 FMA:5022 TAO:0005145" + "Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in a ventricular cardiac muscle cell contributing to the regulation of its contraction. This typically occurs via modulation of the activity or expression of voltage-gated ion channels." + "A neural nucleus that is part of the spinal cord." "FMA:77011" + "The process that gives rise to the hindbrain. This process pertains to the initial formation of a structure from unspecified parts. The hindbrain is the region consisting of the medulla, pons and cerebellum. Areas of the hindbrain control motor and autonomic functions." + "Any process that modulates the frequency, rate or extent of cardiac chamber morphogenesis." + "Any process that stops, prevents, or reduces the frequency, rate or extent of coagulation." + "Any process that activates or increases the frequency, rate or extent of ATP metabolic process." + "Any process that modulates the frequency, rate or extent of neuron migration." + "The structures associated with drainage of the aqueous humor from the eye, that include the trabecular meshwork, Schlemm's canal, the uveoscleral network, and the aqueous veins." "EMAPA:37427" + "Any exocrine gland whose secretion consists of its own disintegrated secretory cells along with its secretory product; holocrine secretions are produced in the cytoplasm of the cell and released by the rupture of the plasma membrane, which destroys the cell and results in the secretion of the product into the lumen." "Wikipedia:Holocrine BTO:0002325 MA:0003042" + "OBSOLETE: A cell responsible for spontaneous cytotoxicity of a variety of tumor cells without prior immunization. These natural killer cells are found in non-immune humans and experimental animals and are thought by some to be the same as killer cells (killing by antibody-dependent cell cytotoxicity), but they can also kill in the absence of antibody." + "Any process that stops, prevents, or reduces the frequency, rate or extent of xanthophore differentiation." + "Any process that activates or increases the frequency, rate or extent of epithelial cell differentiation involved in kidney development." + "A Peyer's patch that is part of a large intestine." "MA:0001550 EMAPA:35468 FMA:15658" + "Any process that modulates the rate, frequency, or extent of the directed movement of calcium ions into a cell or organelle." + "A neuron that has its soma in the heart." + "Increase in size of antral follicles due to cell proliferation and/or growth of the antral cavity." + "A T-box transcription factor TBX21 that is encoded in the genome of mouse." "UniProtKB:Q9JKD8" + "A cell morphology that inheres in neurons with dendrites that stratify at one and only one location." + "The efferent ducts (or efferent ductules or ductuli efferentes) connect the rete testis with the initial section of the epididymis. The ductuli are unilaminar and composed of columnar ciliated and non-ciliated (absorptive) cells. The ciliated cells serve to stir the luminal fluids, possibly to help ensure homogeneous absorption of water from the fluid produced by the testis, which results in an increase in the concentration of luminal sperm. The epithelium is surrounded by a band of smooth muscle that helps to propel the sperm toward the epididymis." "Wikipedia:Efferent_ducts NCIT:C32492 MA:0000398 EMAPA:18993 UMLS:C0228013 FMA:19081 AAO:0010532" + "The appearance of interleukin-1 beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." + "Enables the transfer of amino acids from one side of a membrane to the other. Amino acids are organic molecules that contain an amino group and a carboxyl group." "Reactome:R-HSA-379426 Reactome:R-HSA-352182 Reactome:R-HSA-375790 Reactome:R-HSA-5653850 Reactome:R-HSA-212642 Reactome:R-HSA-352107 Reactome:R-HSA-375487 Reactome:R-HSA-378513 Reactome:R-HSA-352119 Reactome:R-HSA-379415 Reactome:R-HSA-352191 Reactome:R-HSA-375770 Reactome:R-HSA-352158 Reactome:R-HSA-375473 Reactome:R-HSA-352379 Reactome:R-HSA-888592 Reactome:R-HSA-352364 Reactome:R-HSA-5660890 Reactome:R-HSA-351963 Reactome:R-HSA-352103 Reactome:R-HSA-375405 Reactome:R-HSA-376200 Reactome:R-HSA-352108 Reactome:R-HSA-352385 Reactome:R-HSA-5655702 Reactome:R-HSA-352052 Reactome:R-HSA-375776 Reactome:R-HSA-375417 Reactome:R-HSA-352029 Reactome:R-HSA-351987 Reactome:R-HSA-5659734 Reactome:R-HSA-352174 Reactome:R-HSA-5659674 Reactome:R-HSA-352136 Reactome:R-HSA-352371 Reactome:R-HSA-210439 Reactome:R-HSA-5659755 Reactome:R-HSA-5660694 Reactome:R-HSA-352232 Reactome:R-HSA-8952726 Reactome:R-HSA-352347 Reactome:R-HSA-375768 Reactome:R-HSA-379432 Reactome:R-HSA-5660910 Reactome:R-HSA-352354 Reactome:R-HSA-352059" + "A sst GABAergic cortical interneuron with a soma found in lower L5 with mostly local axonal arborization but with some sparse ascending axons. L5 non-Martinotti sst cells show somatic localization and local axon plexus in L5b and L5b/6 and substantial innervation of L3 and L4, and receive thalamic input from the ventral posteromedial nucleus and specifically target L4 neurons, avoiding L5 pyramidal cells. L5 non-Martinotti sst cells tend to show a higher input resistance and seem to be less stuttering." + "Subdivision of skeleton that includes all dermal bones in the cranial skeleton[ZFA,modified]." "Wikipedia:Skull_roof XAO:0003169 ZFA:0000863 TAO:0000863 AAO:0010154 VHOG:0001665" + "A recently activated CD8-positive, alpha-beta T cell with the phenotype HLA-DRA-positive, CD38-positive, CD69-positive, CD62L-negative, CD127-negative, CCR7-negative, and CD25-positive." + "A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a part of the plasma membrane to form a new membrane-bounded vesicle." "Wikipedia:Endocytosis" + "A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube." + "A cellular quality inhering in a bearer by virtue of bearer's number of nuclei." + "A protein that is a translation product of the human CD34 gene or a 1:1 ortholog thereof. It is a leukocyte membrane protein expressed specifically by lymphohematopoietic progenitor cells. It contains a single-pass transmembrane domain and that show distinct expression on early hematopoietic precursors and vascular-associated tissue. Acts as a scaffold that presents selectin carbohydrate ligands in a clustered, tissue specific manner to allow for higher avidity interactions between leukocytes and endothelial cells during the inflammatory process. In common with related sialomucins (endoglycan and podocalyxin), the extracellular region is dominated by an N-terminal mucin-like domain, which is densely substituted with sialylated O-linked carbohydrates. The mucin-like region is followed by a cysteine-containing and presumably globular domain. This domain may fold into an immunoglobulin-like structure as the positions of 2 of the cysteines are conserved in the C2 set of the immunoglobulin superfamily. The cytoplasmic domain is around 73-76 residues long and highly conserved." "PIRSF:PIRSF028749" + "Any process in which a protein complex is maintained in a specific location within the cytoplasm and is prevented from moving elsewhere." + "SCTID:283392005 UMLS:C0226362 FMA:14765 NCIT:C33474" + "The directed movement of a smooth muscle cell in response to an external stimulus." + "A proximal convoluted tubule that is part of a pronephros." "TAO:0002238 ZFA:0001620" + "FMA:72552" + "A zone of skin that is part of a tail [Automatically generated definition]." "SCTID:67214004 MA:0000700 EMAPA:36502" + "A fibroblast located in the thymic capsule." + "A compact and highly condensed form of chromatin that is refractory to transcription." "Wikipedia:Heterochromatin NIF_Subcellular:sao581845896" + "FMA:242772" + "A myoblast that is committed to a myotube-specific program of differentiation but not yet fused. It undergoes very limited additional proliferation. After fusion, it will take on a muscle identity specified by a `muscle founder cell` (CL:0008006)." + "The earliest cytologically identifiable precursor in the thrombocytic series. This cell is capable of endomitosis and lacks expression of hematopoieitic lineage markers (lin-negative)." "BTO:0001164 CALOHA:TS-0610 MESH:D055016 FMA:84235" + "FMA:19779" + "A mesothelium that is part of a diaphragm [Automatically generated definition]." "EMAPA:18429" + "The progression of the metanephric glomerulus over time from its initial formation until its mature state. The metanephric glomerulus is a capillary tuft which forms a close network with the visceral epithelium (podocytes) and the mesangium to form the filtration barrier and is surrounded by Bowman's capsule in nephrons of the mature vertebrate kidney, or metanephros." + "The nucleus of a male germ cell, a reproductive cell in males." + "Any process that modulates the rate, frequency or extent of macrophage cytokine production. Macrophage cytokine production is the appearance of a chemokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." + "A serous membrane that is part of a large intestine [Automatically generated definition]." "MA:0001546 NCIT:C32929 FMA:14975 EMAPA:37557 UMLS:C1517727" + "Any cell proliferation that is involved in heart valve development." + "Any process that modulates the frequency, rate or extent of cell proliferation involved in compound eye morphogenesis." + "The orderly movement of a microglial cell from one site to another." + "The process whose specific outcome is the progression of a metanephric ascending thin limb over time, from its formation to the mature structure. The metanephric ascending thin limb is a segment of a nephron tubule in the metanephros lying in the inner medulla that is permeable to ions but not to water and has a simple epithelium; active transepithelial solute transport is absent." + "The hemorrhoidal plexus (or rectal venous plexus) surrounds the rectum, and communicates in front with the vesical venous plexus in the male, and the uterovaginal plexus in the female. A free communication between the portal and systemic venous systems is established through the hemorrhoidal plexus." "Wikipedia:Rectal_venous_plexus SCTID:303051005 UMLS:C0226766 NCIT:C32728 FMA:18933" + "Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA)." "Wikipedia:Regulation_of_gene_expression" + "An aminopeptidase N that is encoded in the genome of human." "UniProtKB:P15144" + "The lipid bilayer surrounding a neuronal dense core vesicle." + "Any process that decreases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." + "One of the minute vascular projections of the fetal chorion that combines with maternal uterine tissue to form the placenta." "EHDAA2:0004717 SCTID:360403003 MESH:D002824 NCIT:C34125 UMLS:C0008508 BTO:0001161 Wikipedia:Chorionic_villi" + "Any process that modulates the frequency, rate or extent of actin filament-based movement." + "A developmental process, independent of morphogenetic (shape) change, that is required for the pons to attain its fully functional state. The pons lies above the medulla and next to the cerebellum. The pons conveys information about movement from the cerebral hemisphere to the cerebellum." + "A C-C chemokine receptor type 3 that is encoded in the genome of human." "UniProtKB:P51677 DTO:02100055 Reactome:R-HSA-373106" + + "Any process that activates, maintains or increases the frequency, rate or extent of a signaling process." + "The appearance of interferon-gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon-gamma is also known as type II interferon." + "The process in which a precursor cell type acquires the specialized features of a CD4-positive, alpha-beta intraepithelial T cell. Intraepithelial T cells are found among epithelial cells in mucosal areas and have distinct phenotypes and developmental pathways." + "The process in which the branching structure of the ureteric bud is generated and organized. The ureteric bud is an epithelial tube that grows out from the metanephric duct. The bud elongates and branches to give rise to the ureter and kidney collecting tubules." + "A progenitor cell restricted to the myeloid lineage." "CALOHA:TS-2099 FMA:70339 BTO:0004730" + "The process whose specific outcome is the progression of a osteoclast from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate. An osteoclast is a specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue." + "Any process that stops, prevents or reduces the frequency, rate or extent of erythrocyte apoptotic process." + "The progression of the striatum over time from its initial formation until its mature state. The striatum is a region of the forebrain consisting of the caudate nucleus, putamen and fundus striati." + "A chemokine receptor CCR1/3/1L that is a translation product of the human CCR3 gene or a 1:1 ortholog thereof." "IUPHARobj:60" + "Any portion of smooth muscle tissue that is part of the rectum." + "Any process that increases the rate, frequency, or extent of the growth of a cardiac muscle cell, where growth contributes to the progression of the cell over time from its initial formation to its mature state." + "Any process that stops, prevents, or reduces the frequency, rate or extent of nervous system development, the origin and formation of nervous tissue." + "Any process that modulates the frequency, rate or extent of oligodendrocyte progenitor proliferation." + "The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, as well as translation and maturation for protein-coding genes." "Wikipedia:Gene_expression" + "A blood vessel that is part of a thoracic cavity [Automatically generated definition]." "MA:0000554 EMAPA:37240" + + "An epithelium that is part of a middle ear." "MA:0003169 EMAPA:35673" + "The formation of nodular inflammatory lesions, usually small or granular, firm, persistent, well-structured, and containing compactly grouped T lymphocytes and modified phagocytes such as epithelioid cells, giant cells, and other macrophages. Granuloma formation represents a chronic inflammatory response initiated by various infectious and noninfectious agents. The center of a granuloma consists of fused macrophages, which can become necrotic." + "A process which results in the assembly, arrangement of constituent parts, or disassembly of a postsynaptic membrane, the specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft)." + "A layer of the ovarian follicle that consists of theca cells." "SCTID:361385000 Wikipedia:Theca_of_follicle MA:0001712 EMAPA:35636 EFO:0003629 ZFA:0001113 TAO:0001113 BTO:0002853 FMA:18656" + "The tissue comprised of mesangial cells that fill the triangular space between the macula densa and the afferent and efferent arterioles of the juxtaglomerular apparatus." "EMAPA:28278 MA:0002602 FMA:84141" + "The process in which a venous blood vessel endothelial cell acquires specialized features of a lymphatic vessel endothelial cell, a thin flattened cell that lines the inside surfaces of lymph vessels." + "Binding to a nuclear receptor protein. Nuclear receptor proteins are DNA-binding transcription factors which are regulated by binding to a ligand." + "A response to protect an organism from a directly detected or perceived external threat from an insect or insects to that organism." + "The paired bundles of nerve fibers entering and leaving the spinal cord at each segment. The dorsal and ventral nerve roots join to form the mixed segmental spinal nerves. The dorsal roots are generally afferent, formed by the central projections of the spinal (dorsal root) ganglia sensory cells, and the ventral roots efferent, comprising the axons of spinal motor and autonomic preganglionic neurons. There are, however, some exceptions to this afferent/efferent rule." "ZFA:0005578 GAID:717 UMLS:C0037940 NCIT:C12791 BTO:0000883 MESH:D013126 DHBA:146035120 FMA:14060" + "A neutrophil gelatinase-associated lipocalin that is encoded in the genome of human." "UniProtKB:P80188" + "A frontal cortex that is part of a right cerebral hemisphere." "UMLS:C1281954 SCTID:314141005 FMA:72969 BIRNLEX:1786" + "FMA:242778" + "The irregular bones are bones which, from their peculiar form, cannot be grouped as long bone, short bone, flat bone or sesamoid bone. Irregular bones serve various purposes in the body, such as protection of nervous tissue, affording multiple anchor points for skeletal muscle attachment (as with the sacrum), and maintaining pharynx and trachea support, and tongue attachment (such as the hyoid bone). They consist of cancellous tissue enclosed within a thin layer of compact bone. The irregular bones are: the vertebrC&, sacrum, coccyx, temporal, sphenoid, ethmoid, zygomatic, maxilla, mandible, palatine, inferior nasal concha, and hyoid." "UMLS:C0502414 Wikipedia:Irregular_bone SCTID:421560006 NCIT:C32881 FMA:7477" + "A protein that is a translation product of the human CD4 gene or a 1:1 ortholog thereof. CD4 is an accessory protein for MHC class-II antigen/T-cell receptor interaction. It is the primary receptor for HIV-1. CD4 has four immunoglobulin-like domains in its extracellular region that share the same structure, but can differ in sequence." "PIRSF:PIRSF001977" + + "Prominent lobed neuropils found in annelids and all arthropods except crustaceans. They are thought to be involved in olfactory associative learning and memory[MESH] Mushroom body neuropils are divided into calyces, pedunculus, and its subsequent lobes. In Drosophila these are the alpha, beta, and gamma lobes." "GAID:1231 MESH:D024521 MIAA:0000336 MAT:0000336 Wikipedia:Mushroom_body BTO:0002675 EFO:0000925" + "Any process that stops, prevents or reduces the frequency, rate or extent of meiotic cell cycle process involved in oocyte maturation." + "A nerve root that extends_fibers_into a nerve connecting eye with brain." "BIRNLEX:1328 FMA:84573" + "A channel protein that has water channel activity. A water channel enables facilitated diffusion of water (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism." "IUPHARfam:119" + "The movement of an eosinophil within or between different tissues and organs of the body." + "A lamina propria that is part of a ureter [Automatically generated definition]." "MA:0002653 SCTID:2771005 EMAPA:28841 FMA:15896" + "Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph." "EV:0100050 EFO:0000872 EMAPA:35523 VHOG:0001273 FMA:5034 NCIT:C33027 Wikipedia:Lymph_node MESH:D008198 SCTID:181756000 GAID:947 NCIT:C12745 UMLS:C0024204 TAO_RETIRED:0005318 MAT:0000442 CALOHA:TS-0579 MA:0000139 ZFA_RETIRED:0005318 BTO:0000784 galen:Lymphnode" + "Enables the transmembrane transfer of an ion by a channel that opens when a specific extracellular ligand has been bound by the channel complex or one of its constituent parts." + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cell junction. A cell junction is a specialized region of connection between two cells or between a cell and the extracellular matrix." + "A T cell located in the lymph node paracortex, where macrophages and dendritic cells present antigenic peptides to these naïve T cells, stimulating them to become activated helper T cells or cytotoxic T lymphocytes." + "Any muscle organ that is part of a skin of body [Automatically generated definition]." "EMAPA:18187 MA:0002710 EMAPA:35776 MA:0003139" + "Any sensillum (UBERON:6007152) that is part of some larval head (UBERON:6001730)." + "A blood vessel that is part of a pectoral appendage." "TAO:0005301 ZFA:0005301" + "A vein that is part of a craniocervical region." "EHDAA2:0004542 SCTID:32945007" + "FMA:242780" + "A renin that is encoded in the genome of human." "UniProtKB:P00797" + "Muscle cell which has as its direct parts myofilaments organized into sarcomeres." "FMA:86936 CALOHA:TS-2157 BTO:0002916" + "A double-positive thymocyte that is CD69-positive and has begun positive selection." + "Any process that stops, prevents or reduces the frequency, rate or extent of fibril organization." + "A blood vessel that is part of a lower arm [Automatically generated definition]." "EMAPA:37295 MA:0000597" + "Any process that activates or increases the frequency, rate, or extent of antigen processing and presentation of peptide antigen via MHC class I." + "The middle limb segment of the pelvic free limb, between the autopod and stylopod segments. Includes as parts the hindlimb zeugopodial skeleton, which includes as parts the tibia and fibula, or their cartilage precursors, or evolutionary variants." "galen:Leg EMAPA:17496 VHOG:0000348 MA:0000051 FMA:24979 EHDAA:6190 EHDAA:5165 Wikipedia:Forearm MESH:D007866 SCTID:244015008 UMLS:C1140621 VSAO:0005060 EHDAA2:0001030 NCIT:C32974 EFO:0003051" + "An innate lymphoid cell in the human with the phenotype KLRG1-positive that is a precusor for ILC2 cells." + "Tolerance induction taking place in the gut-associated lymphoid tissue (GALT)." + "Any process that modulates the frequency, rate or extent of alpha-beta T cell proliferation." + "Any process that modulates the frequency, rate or extent of lipid transport across blood-brain barrier." + "A cell of the monocyte, granulocyte, or mast cell lineage." + "The developmental process that results in the creation of defined areas or spaces within the pronephros along the anterior/posterior axis to which cells respond and eventually are instructed to differentiate." + "An eye that is part of a left side of organism [Automatically generated definition]." "FMA:12515 SCTID:362503005 EMAPA:37362 MA:0002949 NCIT:C119334" + + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amines." + "Obsolete. Use PO:0000076 from Plant Ontology instead. OBSOLETE, use term from Plant Ontology. Parenchyma cells containing chloroplasts; a component of leaf mesophyll and other green parenchyma tissue." + "The mucous secreting gland associated with the mucuous membrane lining the uterus." "Wikipedia:Uterine_glands BTO:0003433 SCTID:361377009 BTO:0004518 NCIT:C33842 EMAPA:29919 UMLS:C1183035 MA:0001726" + "Any process that stops, prevents, or reduces the frequency, rate or extent of endocytosis." + "Somite located in the head region, caudal to the otic vesicle." "EMAPA:16172 XAO:0000313 EHDAA2:0003437" + "The process whose specific outcome is the progression of the blood vessels of the heart over time, from its formation to the mature structure." + "Any process that modulates the rate, frequency or extent of a small molecule metabolic process." + "The preoptic periventricular nucleus is located along the midline and is medial to the medial preoptic nucleus.[WP,unvetted]." "neuronames:379 HBA:4549 BIRNLEX:1201 SCTID:369127000 MBA:133 UMLS:C0175314 BAMS:PVpo UMLS:C1289554 Wikipedia:Preoptic_area#Preoptic_periventricular_nucleus FMA:62324 BAMS:POP" + "The process in which the anatomical structures of appendages are generated and organized. An appendage is an organ or part that is attached to the trunk of an organism, such as a limb or a branch." + "A progesterone secreting cell in the corpus luteum. The large luteal cells develop from the granulosa cells. The small luteal cells develop from the theca cells." "FMA:18688 BTO:0003939" + "Any process that activates or increases the frequency, rate or extent of leukocyte cell-cell adhesion." + "A hillock cell that is part of the prostatic urethra." + "The short narrow part of the stomach extending from the pyloric antrum to the pyloric sphincter." "EMAPA:37944 Wikipedia:Pyloric_canal FMA:14580 SCTID:245417002" + "A protein complex that is capable of serotonin receptor activity." + "A plasma cell that is located in the medullary sinus of the lymph node." + "The process aimed at the progression of a microglial cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell." + "The chemical reactions and pathways resulting in the formation of amino acids of the serine family, comprising cysteine, glycine, homoserine, selenocysteine and serine." + + "A T-cell surface glycoprotein CD5 that is encoded in the genome of mouse." "UniProtKB:P13379" + "The series of molecular signals initiated by the binding of a cytokine to a receptor on the surface of a cell, and ending with the regulation of a downstream cellular process, e.g. transcription." + "FMA:19971" + "An interleukin-17 receptor B that is encoded in the genome of human." "UniProtKB:Q9NRM6" + "A mesothelium that is part of a serous pericardium." "SCTID:67300002 EMAPA:16133 FMA:18149 BTO:0003157" + "Any process that modulates the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites)." + "A life span which is relatively high." + "Multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer." "GAID:19 NCIT:C13169 ZFA:0005425 FMA:9581 MESH:D012704 Wikipedia:Serous_membrane UMLS:C0036760 SCTID:362878009 TAO:0005425" + "The self-renewing division of a somatic stem cell, a stem cell that can give rise to cell types of the body other than those of the germ-line." + "Any process involved in the carrying out of an immune response by a leukocyte." + "A melanopsin that is encoded in the genome of human." "DTO:02100466 Reactome:R-HSA-391825 UniProtKB:Q9UHM6" + "Obsolete. Use PO:0020097 from Plant Ontology instead. The cell that will give rise to the generative nuclei which will participate in fertilization." + "Any process that stops, prevents, or reduces the frequency, rate or extent of alpha-beta T cell proliferation." + "Cell layer consisting of lining cells that separates the central nervous system and the bloodstream. The BBB may consist of endothelial cells or glial cells. An endothelial barrier may have arisen independently several times during evolution. In bichir and lungfish the barrier is formed by brain endothelial cells, while in sturgeon it is formed by a complex perivascular glial sheath, but with no detectable tight junctions." "NCIT:C13194 UMLS:C0005854 Wikipedia:Blood-brain_barrier http://uri.neuinfo.org/nif/nifstd/nlx_subcell_100205" + "An arch-shaped structure of the vertebra that extends dorsally (neural arch) or ventrally (hemal arch) from the vertebral centrum." "EMAPA:36614" + "An anatomical wall that is part of a intestine [Automatically generated definition]." "BTO:0000647 FMA:15949 MA:0002693 EMAPA:35444 MA:0001525 NCIT:C49478 UMLS:C1708548" + "Any process that decreases the frequency, rate or extent of the directed killing of a target cell by a neutrophil." + "Synaptic transmission that results in an excitatory postsynaptic potential." + "A change in morphology and behavior of a leukocyte resulting from exposure to a specific antigen, mitogen, cytokine, cellular ligand, or soluble factor." "Wikipedia:Immunologic_activation" + "Any process that activates or increases the frequency, rate or extent of distal tip cell migration." + "Any process that modulates the frequency, rate or extent of cellular response to testosterone stimulus." + "Any process that activates or increases the frequency, rate, or extent of natural killer cell mediated immunity." + "Any process involved in maintaining the steady state of a cell's volume. The cell's volume refers to the three-dimensional space occupied by a cell." + "The process in which a branch forms along the side of the lung epithelial tube." + "Mesenchyme that is part of a developing camera-type eye." "EHDAA2:0000485 VHOG:0001084 EMAPA:16673 EHDAA:2910" + "A gonad prior to differentiating into a definitive testis or ovary." "UMLS:C1512703 EHDAA2:0000716 NCIT:C34192" + "Any process that results in the transfer of information from an epithelial cell to a mesenchymal cell where it is interpreted and contributes to the progression of the prostate gland over time." + "Any process that activates or increases the frequency, rate or extent of astrocyte differentiation." + "A future glans that is part of a female genital tubercle." "EMAPA:19170" + "The chemical reactions and pathways resulting in the formation of heparin, any member of a group of glycosaminoglycans of average Mr (6000-20000), consisting predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues." + "A collection of protruberances derived from pharyngeal arch 2 that develop into the concha, antihelix and antitragus." + "A mesothelial cell that is part of the colon." + "Any process that activates or increases the frequency, rate or extent of an organismal process, any of the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs." + "A megakaryocyte progenitor cell that is CD34-positive, CD41-positive, and CD42-negative." + "An epithelial cell type that lacks the columnar shape typical for other respiratory epithelial cells. This cell type is able to differentiate into other respiratory epithelial cells in response to injury." + "An epithelium that is part of a lobar bronchus of right lung." "MA:0003136 EMAPA:17666" + "A lens fiber cell that develops from primary lens fiber; located towards the center of lens; cell organelles are normally degraded or in the process of being degraded." + "Muscle precursor cell that is adjacent to the notochord and part of the presomitic mesoderm." + + "The chemical reactions and pathways resulting in the breakdown of glycine, aminoethanoic acid." + "The directed movement of substances in neuronal dense core vesicles along axonal microtubules towards the presynapse." + + "The part of the ventral body cavity that is within the abdominal segment of the trunk, which encompasses the abdomen proper plus pelvic cavity." "FMA:12267 Wikipedia:Abdominopelvic_cavity" + "Binding to a keratin filament, an intermediate filament composed of acidic and basic keratins (types I and II), typically expressed in epithelial cells." + "Any apoptotic process in a retinal cell." + "A class of large neuroglial (macroglial) cells in the central nervous system. Form the insulating myelin sheath of axons in the central nervous system." "BTO:0000962 CALOHA:TS-0709 FMA:54540" + "The process in which a relatively unspecialized cell acquires specialized structural and/or functional features of an enteroendocrine cell. Enteroendocrine cells are hormonally active epithelial cells in the gut that constitute the diffuse neuroendocrine system." + "The chemical reactions and pathways resulting in the formation of any conjugated, water-soluble protein in which the covalently attached nonprotein group consists of a lipid or lipids." + "Any cell participating in the inflammatory response to a foreign substance, e.g. neutrophil, macrophage." "http://en.wikipedia.org/wiki/Inflammatory_response GOC:pr" + "Any process that stops, prevents, or reduces the frequency, rate or extent of testosterone biosynthetic process." + "Any process that activates or increases the frequency, rate or extent of chromosome organization." + "The portion of a renal lobe consisting of nephrons grouped around a single medullary ray and draining into a single collecting duct; human kidneys have multilobular, multipapillary architecture while mice and rats have unilobular, unipapillary kidneys." "Wikipedia:Cortical_lobule SCTID:361330004 FMA:17670" + "Any process that modulates the frequency, rate or extent of developmental growth." + "A surface shape quality inhering in a bearer by virtue of the bearer's exhibiting a degree of bending." + "Any process that activates or increases the frequency, rate or extent of blood circulation." + "Any process that activates or increases the frequency, rate or extent of the directed movement of acetylcholine into a cell." + "A change in morphology and behavior of a basophil resulting from exposure to a cytokine, chemokine, soluble factor, or to (at least in mammals) an antigen which the basophil has specifically bound via IgE bound to Fc-epsilonRI receptors, leading to the initiation or perpetuation of an immune response." + "The developmental process pertaining to the initial formation of the primitive streak from unspecified parts. The primitive streak is a ridge of cells running along the midline of the embryo where the mesoderm ingresses. It defines the anterior-posterior axis." + "Any process that stops, prevents or reduces the frequency, rate or extent of collagen fibril organization." + "Any process that activates or increases the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult)." + "Any process that activates or increases the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other." + "A channel protein that has ion channel activity. An ion channel enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism." "IUPHARfam:689" + "A neural plate that develops_from a presumptive hindbrain." "TAO:0007022 ZFA:0007022" + "Any process that activates or increases the frequency, rate or extent of cytoplasmic translational elongation." + "Any process that modulates the rate, frequency, or extent of the process in which a highly ordered sequence of patterning events generates the branched structures of the lung, consisting of reiterated combinations of bud outgrowth, elongation, and dichotomous subdivision of terminal units." + "Any process that activates or increases the frequency, rate or extent of the binding or confining calcium ions such that they are separated from other components of a biological system." + "The narrow, proximal portion of the optic vesicle which connects the embryonic eye and forebrain." "VHOG:0000223 NCIT:C34235 UMLS:C0231107 EHDAA:3816 TAO:0000137 Wikipedia:Optic_stalk EMAPA:16678 ZFA:0000137 EHDAA2:0001318 AAO:0011077 SCTID:308788004 XAO:0000475" + "An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm[GO]." "AEO:0000218" + "Any process that modulates the frequency, rate or extent of cell morphogenesis. Cell morphogenesis is the developmental process in which the shape of a cell is generated and organized." + "A melanocyte that is part of the eyelid." "FMA:59175" + "The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound." "Wikipedia:Hearing_(sense)" + "Any process that modulates the frequency, rate or extent of erythrocyte apoptotic process." + "Mesenchyme that is part of a developing lower jaw [Automatically generated definition]." "EHDAA:8003 VHOG:0001069 EHDAA2:0001024 EMAPA:17916" + "A transverse process that is part of a caudal vertebra." + "The process whereby a membrane-bounded vesicle is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane." + "The orderly movement of a cell from one site to another at least one of which is located in the telencephalon." + "A protein that is a translation product of the human GATA3 gene or a 1:1 ortholog thereof." + "A C-X-C chemokine receptor type 3 that is encoded in the genome of mouse." "UniProtKB:O88410" + "Any microvascular endothelial cell that is part of a adipose tissue." + "Any apoptotic process in a compound eye retinal cell." + "The process in which the limits of an anatomical structure are generated. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome." + "A T-cell surface glycoprotein CD8 beta chain that is a translation product of some mRNA whose exon structure and start site selection renders it capable of giving rise to a protein with the amino acid sequence represented by UniProtKB:P10966-1 or a 1:1 ortholog thereof." + "A reelin that is encoded in the genome of human." "UniProtKB:P78509" + "An IgG-positive double negative memory B cell is a double negative memory B cell with the phenotype IgG-positive, IgD-negative, and CD27-negative." + "Any process that modulates the rate, frequency, or extent of neural crest formation. Neural crest formation is the formation of the specialized region of ectoderm between the neural ectoderm (neural plate) and non-neural ectoderm. The neural crest gives rise to the neural crest cells that migrate away from this region as neural tube formation proceeds." + "Any process in which the protease granzyme B is transported to, or maintained in, a location within a secretory granule in a T cell." + "Region of the embryo into the area in which the kidney rudiment will develop." + "a L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex that has stellate pyramidal morphology." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus." + "The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other." + "A process which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix of the endocardium. The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers." + "The lymph node paracortex is the middle layer of the lymph node and is mostly populated by T cells and dendritic cells. The paracortex also contains specialised blood vessels called high endothelial venules which allow lymphocytes to enter the node." + "Any process that activates or increases the frequency, rate, or extent of antigen processing and presentation." + "The connective tissue that supports the lobules and follicles of the thyroid gland." "SCTID:157862000 FMA:86304" + "Any process that stops, prevents or reduces the frequency, rate or extent of T-helper 17 type immune response." + "Intraepithelial T cells with a memory phenotype of CD2-positive, CD5-positive, and CD44-positive." + "The process in which the anatomical structures of epithelia are generated and organized. An epithelium consists of closely packed cells arranged in one or more layers, that covers the outer surfaces of the body or lines any internal cavity or tube." + "Any process that activates or increases the frequency, rate or extent of hydrolase activity, the catalysis of the hydrolysis of various bonds." + "The chemical reactions and pathways involving a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically." + "The process whose specific outcome is the progression of the gonad over time, from its formation to the mature structure. The gonad is an animal organ that produces gametes; in some species it also produces hormones." + "Any process that stops, prevents, or reduces the frequency, rate or extent of female gonad development." + "Obsolete. Use PO:0000066 from Plant Ontology instead. A cell that constitutes the mesophyll of a hydathode and is located between the xylem endings and the epidermis. Proposed to be involved in the retrieval of solutes from the xylem sap." + "Any apoptotic process in a T cell, a type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex." + "Any process that activates or increases the rate or extent of epithelial cell proliferation, contributing to the restoration of integrity to a damaged tissue following an injury." + "RETIRED_EHDAA2:0002089 EHDAA:924 EMAPA:16663" + "Any process that stops, prevents, or reduces the frequency, rate or extent of immature T cell proliferation." + "Inward fold on the surface of the embryonic ectoderm that develops into an ectodermal terminal part of the digestive tract." "NCIT:C34278 EMAPA:25038 VHOG:0000139 TAO:0000066 AAO:0011087 EHDAA2:0000121 XAO:0001019 Wikipedia:Proctodeum ZFA:0000066 UMLS:C0231054" + "Any tagma (UBERON:6000002) that is part of some embryo (UBERON:6000052)." + "Any process that modulates the frequency, rate or extent of formation of translation initiation ternary complex." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances." + "A nonkeratinized epithelial cell of the anal canal." "FMA:263146" + "An adipose macrophage that does not express F4/80but is MHC-II-positive. This cell type exhibits autofluorescence under typical flow cyometry conditions." + "Combining with insulin receptor ligand and transmitting the signal across the plasma membrane to initiate a change in cell activity." "Reactome:R-HSA-74715" + "The submucous layer of the wall of the urinary bladder." "EMAPA:32275 FMA:15929 BTO:0002117 SCTID:88384001" + "The formation of the notochord from the chordamesoderm. The notochord is composed of large cells packed within a firm connective tissue sheath and is found in all chordates at the ventral surface of the neural tube. In vertebrates, the notochord contributes to the vertebral column." + "Any process that stops, prevents, or reduces the frequency, rate or extent of mesenchymal to epithelial transition involved in mesonephros morphogenesis." + "The biological process whose specific outcome is the progression of a glomerulus vasculature from an initial condition to its mature state. This process begins with the formation of the glomerulus vasculature and ends with the mature structure. The glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the glomerulus." + "Initial section of the oviduct through which the ova pass from the ovary to the uterus." "UMLS:C0015560 FMA:18245 SCTID:181463001 MA:0000385 EHDAA2:0000504 EMAPA:35660 MESH:D005187 CALOHA:TS-0732 Wikipedia:Fallopian_tube GAID:365 galen:FallopianTube NCIT:C12403 EV:0100112" + "A flag amacrine cell with post-synaptic terminals in S3, S4, and S5. This cell type releases the neurotransmitter glycine." + "A form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases, whose actions dismantle a striated muscle cell and result in its death. Striated muscle cells make up striated muscle fibers which are divided by transverse bands into striations." + "A portion of gray matter that is part of a telencephalon." "FMA:83911 BIRNLEX:1067" + "A zone of skin that is part of a clitoris [Automatically generated definition]." "SCTID:361374002 FMA:20168" + "A mature astrocyte that is capable of producing cytokines." + "A structural quality inhering in the bearer by virtue of the bearer consisting of multiple structures lacking any physical connection to each other." + "A lymph node that is part of a head." "SCTID:155136006 FMA:61212" + "The process whose specific outcome is the progression of the nose over time, from its formation to the mature structure. The nose is the specialized structure of the face that serves as the organ of the sense of smell and as part of the respiratory system. Includes the nasi externus (external nose) and cavitas nasi (nasal cavity)." + "Any native cell that is part of a sebaceous gland." + "A lactiferous gland that is located in the thoracic region/breast." "MA:0000797 FMA:62088 EHDAA:6524 Wikipedia:Mammary_gland#Other_mammals EMAPA:36633 EHDAA2:0001056 SCTID:31448001" + "A reticulocyte lacking a nucleus and showing a basophilic reticulum under vital staining due to the presence of ribosomes." "FMA:66785 CALOHA:TS-0864" + "The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood." "Wikipedia:Heart_development" + "A functional unit located near the cell apex at the points of contact between epithelial cells, which in vertebrates is composed of the tight junction, the zonula adherens, and desmosomes and in some invertebrates, such as Drosophila, is composed of the subapical complex (SAC), the zonula adherens and the septate junction. Functions in the regulation of cell polarity, tissue integrity and intercellular adhesion and permeability." + "Any process that decreases the rate, frequency or extent of cell proliferation that contributes to the shaping of a heart valve." + "Any process that stops, prevents or reduces the frequency, rate or extent of neuroinflammatory response." + "A collagen alpha chain that is a translation product of the human COL1A1 or COL1A2 genes, 1:1 orthologs thereof, or a semi-ortholog thereof." + "A bone that is part of a mesopodial skeleton." "MA:0000295 Wikipedia:Carpus_and_tarsus_of_land_vertebrates EMAPA:36579" + "The process, occurring during instar larval or pupal development, by which anatomical structures are generated and organized." + "The change in morphology and behavior of a CD8-positive, alpha-beta T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific." + "Any process that activates or increases the frequency, rate or extent of hematopoietic stem cell migration." + "The regulated release of a peptide hormone from a cell." + "The directed movement of catecholamines, a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine." + "The lipid bilayer surrounding a dense core granule." + "The cell cycle process in which the controlled breakdown of the nuclear membranes during meiotic cell division occurs." + "The region of the liver lobule that is between the periportal and centrilobular regions. The functionally-defined hepatic acinus zone 2 is generally found in this region." + "VHOG:0000320 EMAPA:17078 EHDAA2:0001154" + "Any process that modulates the frequency, rate or extent of thymocyte migration." + "The process in which a relatively unspecialized inner cell acquires specialized features of an auditory hair cell." + "Cartilage tissue that is flexible and contains abundant elastic fibers." "NCIT:C32494 XAO:0004197 VSAO:0000091 Wikipedia:Elastic_cartilage UMLS:C0682559 FMA:64785 MA:0000107 MA:0000485" + "Any skin fibroblast that is part of a arm." + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances." + "Any process that modulates the frequency, rate or extent of the regulated release of a hormone from a cell." + "The apoptotic death of B cells which is part of B cell tolerance induction." + "Any process involved in the maintenance of an internal steady state at the level of the multicellular organism." + "The chemical reactions and pathways involving any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone." + "A killer cell lectin-like receptor subfamily D member 1 that is encoded in the genome of mouse." "UniProtKB:O54707" + "Replacement bone tissue that forms within cartilage[VSAO, modified]." "Wikipedia:Endochondral_ossification MA:0002836 EMAPA:35304" + "EHDAA2:0004589" + "The progression of the ascending aorta over time, from its initial formation to the mature structure. The ascending aorta is the portion of the aorta in a two-pass circulatory system that lies between the heart and the arch of aorta. In a two-pass circulatory system blood passes twice through the heart to supply the body once." + "The aggregation, arrangement and bonding together of a set of components to form a membrane." + "The process in which a relatively unspecialized cell acquires specialized features of a smooth muscle cell surrounding the aorta." + "An otic fibrocyte that resides above the stria vasularis and is part of a mesenchymal gap junction network that regulates ionic homeostasis of the endolymph." + "The male gonad containing two functional parts: the SEMINIFEROUS TUBULES for the production and transport of male germ cells (SPERMATOGENESIS) and the interstitial compartment containing LEYDIG CELLS that produce ANDROGENS.." "SCTID:362280005 MA:0002713 EMAPA:18687" + "Any process that modulates the frequency, rate or extent of the innate immune response, the organism's first line of defense against infection." + + "Any process that modulates the frequency, rate, or extent of myeloid leukocyte differentiation." + + "Electron-dense organelle with a granular internal matrix; contains proteins destined to be secreted." "NIF_Subcellular:sao772007592" + "Any process that decreases the rate, frequency or extent of macrophage chemotaxis. Macrophage chemotaxis is the movement of a macrophage in response to an external stimulus." + "Frontal lobe is the anterior-most of five lobes of the cerebral hemisphere. It is bounded by the central sulcus on its posterior border and by the longitudinal cerebral fissure on its medial border." "neuronames:56 BAMS:Frontal_lobe UMLS:C0016733 FMA:61824 EV:0100167 MESH:D005625 DHBA:12113 SCTID:180920004 NCIT:C12352 EFO:0000913 MAT:0000505 BIRNLEX:928 HBA:4009 BM:Tel-Cx-FR CALOHA:TS-0389 UMLS:C1268977" + "Any muscle organ that is part of a chest [Automatically generated definition]." "BTO:0000508 FMA:9619 EMAPA:17747 CALOHA:TS-1037 MA:0000548" + "An endothelium that is part of a venule [Automatically generated definition]." "FMA:62117 MA:0000716 UMLS:C1179026 EMAPA:36290 NCIT:C49319" + "A enteroendocrine cell type that is numerous in ileum, present in jejunum and large intestine, few in duodenum. This cell type produces glucagon-like immunoreactants (glicentin, glucagon-37, glucagon-29, GLP-1 and -2) and PYY." "FMA:62944" + "A submucosa that is part of a fundus of stomach [Automatically generated definition]." "EMAPA:27153 FMA:17058" + "BTO:0001642" + "Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-5 production." + "The thoracodorsal artery is a branch of the subscapular artery. It travels inferiorly with the thoracodorsal nerve and supplies the latissimus dorsi. [WP,unvetted]." "Wikipedia:Thoracodorsal_artery NCIT:C53018 FMA:66320 EMAPA:37129 MA:0002065 UMLS:C0933449" + "A synapse that uses acetylcholine as a neurotransmitter." + "The process in which the anatomical structures of a seminal vesicle are generated and organized." + "Enables the transfer of ADP, adenosine diphosphate, from one side of a membrane to the other." + "A serous sac that is the aggregate of the peritoneum and the peritoneal cavity, located in the abdominal cavity." "EMAPA:16137 FMA:9908" + "Glandular cell of appendix epithelium. Example: Goblet cells; enterocytes or absorptive cells; enteroendocrine and M cells." "CALOHA:TS-1271" + "Any process that activates or increases the frequency, rate or extent of the regulated release of acetylcholine." + "Enables the transmembrane transfer of an ion by a channel that opens when a specific extracellular ligand has been bound by the channel complex or one of its constituent parts, where channel opening contributes to an increase in membrane potential." "Reactome:R-HSA-432164 Reactome:R-HSA-438037 Reactome:R-HSA-399711 Reactome:R-HSA-420980 Reactome:R-HSA-399712" + "A cluster of cells, largely surrounded by a morphological boundary." "CARO:0020002 FMA:62807" + "A presumptive structure that has the potential to develop into a neural plate." "EFO:0003424 ZFA:0000063 TAO:0000063" + "The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite." "Wikipedia:Extracellular" + "An artery that is part of a thoracic cavity[cjm]." "EMAPA:37241 MESH:D013895 MA:0001902" + "A mature NK T cell that secretes interferon-gamma and enhances type 1 immune responses." + "A renal, cortical lobule, consisting of the ascending or descending limbs of the loop of Henle or of the collecting tubules; medullary rays are regions where parallel arrays of straight tubules travel perpendicular to the capsule and extend from the cortex to the medulla." "FMA:74299 Wikipedia:Bone_marrow_of_ovaryry_ray_(anatomy) BTO:0001155 EMAPA:37906" + "Portion of tissue that is contiguous with the embryo and is comprised of portions of tissue or cells that will not contribute to the embryo." "MIAA:0000061 BTO:0003360 CALOHA:TS-2119 EFO:0001406 MAT:0000061" + "The series of molecular signals initiated by a steroid binding to an intracellular steroid hormone receptor." + "A skeletal joint that is part of a pes [Automatically generated definition]." "FMA:35194 EMAPA:32949 GAID:256 MA:0000464 SCTID:244555001 Wikipedia:Joints_of_foot MESH:D033023" + "A chemokine receptor that is a translation product of the human CXCR5 gene or a 1:1 ortholog thereof. The preferred ligand is CXCL13." "IUPHARobj:72" + + "Any microvascular endothelial cell that is part of a urinary bladder." + + "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of amines into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "A spherical particle containing non-covalently associated proteins and lipids. Examples are plasma lipoprotein particles which transport lipids in the blood or lymph." + "Any process that modulates the frequency, rate or extent of cerebellar neuron development." + "Any process that stops, prevents, or reduces the frequency, rate or extent of skeletal muscle growth." + "Any of the parts of the eye that lie in back of, or dorsal to, the lens (but not inclusive)." "ZFA:0005567 Wikipedia:Posterior_segment_of_eyeball EMAPA:36595 UMLS:C0278450 SCTID:280659009 MA:0002485 FMA:58868 NCIT:C12906" + "An auditory hair cell found in the cochlea." "FMA:62364" + "The muscular portion of the tongue." "BTO:0001386 MA:0001596 NCIT:C52707 Wikipedia:Muscles_of_tongue SCTID:244781004 NCIT:C49301 UMLS:C0448325 EHDAA:9146 FMA:46689 UMLS:C1710437 EMAPA:17883 VHOG:0001390 EHDAA2:0002065" + "Paired endochondral bone that is the dorsal-most of the pelvic bones, offering attachment areas for gluteal muscles on its main surface [PHENOSCAPE:ad]." "GAID:207 MESH:D007085 galen:Ilium FMA:16589 AAO:0000772 UMLS:C0020889 CALOHA:TS-2200 SCTID:182029005 Wikipedia:Ilium_(bone) EMAPA:18726 EFO:0003049 NCIT:C32765 MA:0001336" + "A CD8-positive, alpha-beta T cell with the phenotype CCR7-negative, CD45RA-positive." + "A protein that is a translation product of the mouse Klra8 gene or a 1:1 ortholog thereof." + "Any process that activates or increases the frequency, rate or extent of leukocyte apoptotic process." + "Immature CD1a-positive Langerhans cell is a CD1a-positive Langerhans cell that is CD80-low, CD86-low, and MHCII-low." + "Adipose tissue which is located throughout skeletal muscle and is responsible for the marbling seen in certain cuts of beef. In humans, excess accumulation of intramuscular fat is associated with insulin resistance and type 2 diabetes." "BTO:0004043" + "Any process that stops, prevents or reduces the frequency, rate or extent of thyroid-stimulating hormone secretion." + "Interstitial fluid is a bodily fluid consisting of a solution which bathes and surrounds the cells of multicellular animals. It is the main component of the extracellular fluid, which also includes plasma and transcellular fluid." "ENVO:02000042 NCIT:C120839 Wikipedia:Interstitial_fluid FMA:9673" + "Any process that activates or increases the frequency, rate or extent of exosomal secretion." + "Any process that activates or increases the frequency, rate or extent of thymocyte death by apoptotic process." + "Bilateral mesenchymal mesoderm parallel and immediately adjacent to the neural tube/notochord; it generates a subset of extra-ocular, and other head, muscles." "EMAPA:16171 EHDAA2:0000736 EHDAA:364" + "An eye consisting of multiple light-sensing organs." + "A GABAergic cortical interneuron that develops from the medial ganglionic eminence and has migrated to the cerebral cortex." + "A lamina propria that is part of a mucosa of oral region." "EMAPA:26947" + "The process whose specific outcome is the progression of the vestibulocochlear nerve over time, from its formation to the mature structure. This sensory nerve innervates the membranous labyrinth of the inner ear. The vestibular branch innervates the vestibular apparatus that senses head position changes relative to gravity. The auditory branch innervates the cochlear duct, which is connected to the three bony ossicles which transduce sound waves into fluid movement in the cochlea." + "Anatomical cluster that is located in the posterior region of the cranium and forms the margin of the foramen magnum and occipital condyles." "BTO:0004675 FMA:49187 XAO:0003173 SCTID:362618001 ZFA:0001414 neuronames:2431 TAO:0001414 AAO:0010199" + "The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance, that does not require the replacement of preexisting tissues." + "A receptor-type tyrosine-protein kinase FLT3 that is encoded in the genome of human." "UniProtKB:P36888 DTO:03100154" + "One of the two haploid cells into which a primary spermatocyte divides, and which in turn gives origin to spermatids." "FBbt:00004941 FMA:72293 CALOHA:TS-2195 BTO:0000709" + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a testosterone stimulus." + "The thin bilaminar membrane derived from the prechordal plate that is devoid of mesoderm and formed by the apposition of the stomodeal ectoderm with the foregut endoderm; after the embryonic head fold has evolved it lies at the caudal limit of the stomodeum, forming a septum between the primitive mouth and pharynx; the membrane eventually disappears, and thus a communication is established between the mouth and the future pharynx." "SCTID:361412007 EHDAA2:0000189 FMA:313607 Wikipedia:Buccopharyngeal_membrane EHDAA:536 EMAPA:16259 VHOG:0000380" + "In mammals, the metanephros is the excretory organ of the fetus, which develops into the mature kidney and is formed from the rear portion of the nephrogenic cord. The metanephros is an endocrine and metabolic organ that filters the blood and excretes the end products of body metabolism in the form of urine[GO]." "BTO:0001543 UMLS:C0231049 EMAPA_RETIRED:17207 EHDAA:3089 EHDAA:5911 NCIT:C34209 EHDAA2:0001137 SCTID:308797000 Wikipedia:Metanephros#Metanephros EMAPA:17373 FMA:72172 VHOG:0000039" + "Any signal release from a synapse." + "A neuronal receptor that respond to mechanical pressure or distortion in the skin." + "Any process that stops, prevents, or reduces the frequency, rate or extent of branching morphogenesis of a nerve." + "Dense regular connective tissue connecting two or more adjacent skeletal elements or supporting an organ." "EMAPA:35493 FMA:30319 VHOG:0001272 Wikipedia:Ligament EFO:0001966 MESH:D008022 FMA:21496 galen:Ligament CALOHA:TS-2145 XAO:0004031 TAO:0001682 NCIT:C13046 MA:0000113 SCTID:182358004 UMLS:C0023685 ZFA:0001675" + "A zone of skin that is part of a elbow [Automatically generated definition]." "NCIT:C52755 UMLS:C0222213 SCTID:181534001 EMAPA:18051 FMA:38250 MA:0000610" + "The process whose specific outcome is the progression of the spleen over time, from its formation to the mature structure. The spleen is a large vascular lymphatic organ composed of white and red pulp, involved both in hemopoietic and immune system functions." + "A location, relative to cellular compartments and structures, occupied by a macromolecular machine. There are three types of cellular components described in the gene ontology: (1) the cellular anatomical entity where a gene product carries out a molecular function (e.g., plasma membrane, cytoskeleton) or membrane-enclosed compartments (e.g., mitochondrion); (2) virion components, where viral proteins act, and (3) the stable macromolecular complexes of which gene product are parts (e.g., the clathrin complex)." "NIF_Subcellular:sao1337158144" + "A CD38-positive IgG memory B cell is a class switched memory B cell that expresses IgG on the cell surface with the phenotype CD38-positive and IgG-positive." + "A smooth muscle tissue that is part of a clitoris." "BTO:0005000" + "The process in which a relatively unspecialized cell acquires specialized features of a Malpighian tubule stellate cell. A Malpighian tubule stellate cell is a specialized epithelial secretory cell that moves chloride ions and water across the tubule epithelium." + "A double layer covering the ciliary body that produces aqueous humor." "SCTID:280870004 UMLS:C0459736 EMAPA:35239 CALOHA:TS-0695 NCIT:C32314 Wikipedia:Ciliary_body#Ciliary_epithelium BTO:0001770 MA:0001238 FMA:58464" + "The chemical reactions and pathways involving mucopolysaccharide." + "Any process that activates or increases the frequency, rate or extent of somatic stem cell population maintenance." + "The directed movement of substances into, out of or within a vacuole." + "Any process that increases the rate, frequency or extent of mesonephros development. Mesonephros development is the process whose specific outcome is the progression of the mesonephros over time, from its formation to the mature structure. The mesonephros is an organ that filters the blood and excretes the end products of body metabolism in the form of urine." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of mast cell activation as part of an immune response." + "A conventional dendritic cell that is CD103-positive. This cell type is usually found in non-lymphoid tissue." + "An apical ectodermal ridge that is part of a handplate." "EMAPA:17247 EHDAA2:0000729" + "Smooth muscle found within, and composing the majority of the wall of blood vessels." "ZFA:0005321 Wikipedia:Vascular_smooth_muscle BTO:0001431 MA:0000710 TAO:0005321 UMLS:C1519956 EMAPA:35177 CALOHA:TS-1107 NCIT:C33853 MESH:D009131" + "Any process that modulates the frequency, rate or extent of lamellocyte differentiation. Lamellocytes differentiate massively in the lymph glands after parasitization and are large flat cells devoted to encapsulation of invaders too large to be phagocytosed by plasmatocytes." + "A chemical homeostatic process involved in the maintenance of a steady state level of iron within extracellular body fluids, such as blood, xylem or phloem, of a multicellular organism. This is distinct from maintenance of cellular homeostasis, which occurs within a cell." + "A hematopoietic progenitor cell that is committed to the granulocyte and monocyte lineages. These cells are CD123-positive, and do not express Gata1 or Gata2 but do express C/EBPa, and Pu.1." + "The directed movement of an organelle along a microtubule, mediated by motor proteins. This process begins with the attachment of an organelle to a microtubule, and ends when the organelle reaches its final destination." + "The cleavage of DNA during apoptosis, which usually occurs in two stages: cleavage into fragments of about 50 kbp followed by cleavage between nucleosomes to yield 200 bp fragments." + "A portion of connective tissue that is part of a digit." "MA:0003123 EMAPA:37290" + "Any process that activates or increases the frequency, rate or extent of nitrogen cycle metabolic process." + "The process whose specific outcome is the progression of a myeloid cell over time, from its formation to the mature structure." + "Any pyramidal cell that is part of a regional part of cerebral cortex." + "A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a complex containing RNA and proteins. Includes the biosynthesis of the constituent RNA and protein molecules, and those macromolecular modifications that are involved in synthesis or assembly of the ribonucleoprotein complex." + "The progression of the mesonephric glomerulus over time from its initial formation until its mature state. The mesonephric glomerulus is a capillary tuft which forms a close network with the visceral epithelium (podocytes) and the mesangium to form the filtration barrier and is surrounded by Bowman's capsule in nephrons of the mature vertebrate kidney, or mesonephros." + "A lymph vasculature that is part of a head." "FMA:224562 ZFA:0005298 TAO:0005298" + "A promyelocyte committed to the neutrophil lineage. This cell type is GATA-1-positive, C/EBPa-positive, AML-1-positive, MPO-positive, has low expression of PU.1 transcription factor and lacks lactotransferrin expression." "FMA:84196" + "A nerve that is part of an abdominal segment of trunk [Automatically generated definition]." "EMAPA:37061 MA:0000528" + "The formation of the acrosome from the spermatid Golgi." + "Any process that mediates the transfer of information from an SA node cardiomyocyte to an atrial cardiomyocyte." + "The controlled breakdown of any cell membrane in the context of a normal process such as autophagy." + "A lymphocyte of B lineage that is capable of B cell mediated immunity." "MESH:D001402 VHOG:0001480 CALOHA:TS-0068 BTO:0000776 FMA:62869" + "Any process that stops, prevents or reduces the frequency, rate or extent of glucocorticoid secretion." + "Any process that modulates the frequency, rate or extent of lymphocyte chemotaxis." + "The process whose specific outcome is the progression of the primary male sexual characteristics over time, from their formation to the mature structures. The primary male sexual characteristics are the testes, and they develop in response to sex hormone secretion." + "The process whose specific outcome is the progression of a cardiac neuron over time, from its formation to the mature state." + "A nerve that is part of a hindlimb [Automatically generated definition]." "EMAPA:37342 MA:0000664" + "The formation of the flat, thickened layer of ectodermal cells known as the neural plate. The underlying dorsal mesoderm signals the ectodermal cells above it to elongate into columnar neural plate cells. The neural plate subsequently develops into the neural tube, which gives rise to the central nervous system." + "The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of an angioblast cell. Angioblasts are one of the two products formed from hemangioblast cells (the other being pluripotent hemopoietic stem cells)." + "A quality inhering in a bearer by virtue of the bearer's processing the form of a thin plate sheet or layer." + "The developmental process pertaining to the initial formation of a mesonephric tubule from unspecified parts. A mesonephric tubule is an epithelial tube that is part of the mesonephros." + "A developmental process, independent of morphogenetic (shape) change, that is required for the midbrain-hindbrain boundary to attain its fully functional state. The midbrain-hindbrain domain of the embryonic brain is comprised of the mesencephalic vesicle and the first rhombencephalic vesicle at early somitogenesis stages. An organizing center at the boundary patterns the midbrain and hindbrain primordia of the neural plate." + "Any neuromast hair cell that is part of a anterior lateral line." + "A portal vein that drains the ascending colon. It is a tributary of the superior mesenteric vein, and travels with its corresponding artery, the right colic artery." "FMA:15407" + "A neurecto-epithelial cell that is part of the basal layer of the subcommissural organ and specializes in the secretion of proteins into the subarachnoid space. Hypendymal cells have similar characteristics to ependymal cells and express SCO-spondin." + "The actin cytoskeleton that is part of a postsynapse." + "An epithelial fate stem cell derived form the amnion membrane." + "An enteroendocrine cell found in the fundus and pylorus; this cell type has dense round secretory granules that contain ghrelin." "FMA:63209" + "A blood vessel that is part of the chorionic plate." + "With numerous vascular spaces that may become engorged with blood." "Wikipedia:Erectile_tissue" + "An ependyma that is part of a fourth ventricle [Automatically generated definition]." "MA:0000986 EMAPA:35355 SCTID:369277005 FMA:242835 NCIT:C49232 UMLS:C0228171" + "Any process that modulates the frequency, rate or extent of karyogamy, the creation of a single nucleus from multiple nuclei as a result of membrane fusion." + "GC_ID:1" + "Connective tissue, which consists of a population of connective tissue cells, the intercellular matrix of which contains an irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, mucoid tissue, connective tissue of peritoneum, connective tissue of fibrous pericardium." "FMA:20107" + "Any vesicle associated with the Golgi complex and involved in mediating transport within the Golgi or between the Golgi and other parts of the cell." "NIF_Subcellular:sao819927218" + "An anatomical cavity that is part of a ear vesicle." "EMAPA:25363 EHDAA2:0004121" + "Any process that activates or increases the frequency, rate, or extent of interleukin-2 production." + "EMAPA:37718 FMA:6198 EHDAA2:0001463 MA:0001177" + "The descending aorta is the portion of the aorta in a two-pass circulatory system from the arch of aorta to the point where it divides into the common iliac arteries[GO]. The descending aorta is part of the aorta, the largest artery in the body. The descending aorta is the part of the aorta beginning at the aortic arch that runs down through the chest and abdomen. The descending aorta is divided into two portions, the thoracic and abdominal, in correspondence with the two great cavities of the trunk in which it is situated. Within the abdomen, the descending aorta branches into the two common iliac arteries which serve the legs. [WP,unvetted]." "NCIT:C32455 SCTID:261399002 Wikipedia:Descending_aorta MA:0002571 EMAPA:18606 UMLS:C0011666 FMA:3784" + "A T cell which resides in the Peyer's patch of the small intestine." + "A muscle organ that is part of an arm [Automatically generated definition]." "MA:0000594 EHDAA:8277 EMAPA:36053 RETIRED_EHDAA2:0000142" + "A muscle layer that is part of the rectum." "FMA:15035" + "A myoepithelial cell that is part of the acinus of lactiferous gland." "FMA:74469" + "A trans-acting T-cell-specific transcription factor GATA-3 that is encoded in the genome of human." "Reactome:R-HSA-996768 UniProtKB:P23771" + "FMA:19976 EMAPA:30997 SCTID:253069005" + "Any process that modulates the frequency, rate or extent of sperm capacitation." + "A cholecystokinin that has been processed by proteolytic cleavage." + "A glutamatergic neuron with a soma found in cortical layer 6b. They are transcriptomically related to corticothalamic-projecting neurons but have differential projections to the thalamus or anterior cingulate." "ILX:0770163" + "The multiplication or reproduction of white fat cells by cell division, resulting in the expansion of their population." + "A venule that is part of a lymph node." + "A common lymphoid progenitor that is Kit-low, FLT3-positive, IL7ralpha-positive, and SCA1-low." + "Any fibroblast that is part of a optic choroid." + "Hematopoietic cells resident in the bone marrow. Include: hematopoietic stem cells (lymphoid stem cells and myeloid stem cells) and the precursor cells for thrombocytes, erythrocytes, basophils, neutrophils, eosinophils, monocytes and lymphocytes." "CALOHA:TS-2109" + "GC_ID:1" + "A developmental process, independent of morphogenetic (shape) change, that is required for the optic nerve to attain its fully functional state. The sensory optic nerve originates from the bipolar cells of the retina and conducts visual information to the brainstem. The optic nerve exits the back of the eye in the orbit, enters the optic canal, and enters the central nervous system at the optic chiasm (crossing) where the nerve fibers become the optic tract just prior to entering the hindbrain." + "A respiratory bronchiole that is part of a left lung [Automatically generated definition]." "UMLS:C1708674 NCIT:C49254 MA:0001779 EMAPA:36635" + "A stroma that is part of a chorionic villus (placental villus). A placental villous stroma supports the fetal capillaries and villous trophoblast." + "A zone of skin that is part of a palmar/plantar part of autopod." + "A horse-specific, highly invasive trophoblast cell that invades the endometrium where it forms endometrial cups." + "The directed movement of organelles or molecules along microtubules in a dendrite from the postsynapse towards the cell body." + "A thymocyte that lacks expression of CD4 and CD8." + "GC_ID:1" + "Barrier in the choroid plexus located in the lateral, third, and fourth brain ventricles that controls the entrance of substances into the cerebrospinal fluid from the blood[MP]." + "The process in which immune receptor genes are diversified through recombination of the germline genetic elements within a single genetic locus." + "Any process that activates or increases the rate or extent of smooth muscle cell proliferation." + "The directed movement of carbohydrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbohydrates are a group of organic compounds based of the general formula Cx(H2O)y." + "The series of events that contribute to the perception of pain in which an electrical stimulus is received and converted into a molecular signal." + "The process in which the anatomical structures of the lens are generated and organized. The lens is a transparent structure in the eye through which light is focused onto the retina. An example of this process is found in Mus musculus." + "Glandular cell of parathyroid epithelium. Example: Parathyroid chief cell and parathyroid oxyphil cells." "CALOHA:TS-1279" + "A cellular receptor which mediates the sense of temperature. Thermoreceptor cells in vertebrates are mostly located under the skin. In mammals there are separate types of thermoreceptors for cold and for warmth and pain receptor cells which detect cold or heat extreme enough to cause pain." + "Binding to a growth factor receptor." + "Principal cell that is part of some outer medullary collecting duct. It is known in some mammalian species that this cell may express the epithelial sodium channel (ENaC)." "KUPO:0001132" + "A fully differentiated eosinophil, a granular leukocyte with a nucleus that usually has two lobes connected by one or more slender threads, and cytoplasm containing coarse, round granules that are uniform in size and which can be stained by the dye eosin. Cells are also differentiated from other granulocytes by a small nuclear-to-cytoplasm ratio (1:3). This cell type is CD49d-positive." + "The parasympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system. Parasympathetic nerves emerge cranially as pre ganglionic fibers from oculomotor, facial, glossopharyngeal and vagus and from the sacral region of the spinal cord. Most neurons are cholinergic and responses are mediated by muscarinic receptors. The parasympathetic system innervates, for example: salivary glands, thoracic and abdominal viscera, bladder and genitalia[GO]." "MAT:0000101 BIRNLEX:2517 TAO:0001575 EHDAA:4655 MESH:D010275 UMLS:C1305770 AAO:0010488 ZFA:0001575 BTO:0001833 EMAPA:17270 SCTID:362496006 CALOHA:TS-2094 GAID:708 Wikipedia:Parasympathetic_nervous_system MA:0000223 EFO:0000894 FMA:9907 NCIT:C12764 MIAA:0000101 EHDAA2:0001402 VHOG:0000755 UMLS:C0030510 EHDA:10096" + "A spherical aggregation of cells in the ovary that contains a single oocyte[WP,modified]." "SCTID:361111009 MESH:D006080 NCIT:C33244 MAT:0000449 TAO:0001110 MA:0001707 VHOG:0001536 BTO:0000475 CALOHA:TS-0726 ZFA:0001110 GAID:371 EMAPA:35627 UMLS:C0018120 FMA:18640 Wikipedia:Ovarian_follicle" + "The process that gives rise to the facial nerve. This process pertains to the initial formation of a structure from unspecified parts. This sensory and motor nerve supplies the muscles of facial expression and the expression and taste at the anterior two-thirds of the tongue. The principal branches are the superficial opthalmic, buccal, palatine and hyomandibular. The main trunk synapses within pterygopalatine ganglion in the parotid gland and this ganglion then gives of nerve branches which supply the lacrimal gland and the mucous secreting glands of the nasal and oral cavities." + "An embryonic structure that will either develop into a post-anal tail or recede into a vestigial remnant of the tail." "FMA:85540 EMAPA:16748" + "A nerve plexus that is part of a sympathetic nervous system." "EMAPA:37617 MA:0001160" + "Any of the immature forms of a neutrophil in which neutrophilic specific granules are present but other phenotypic features of the mature form may be lacking." + "Any process that stops, prevents or reduces the frequency, rate or extent of hematopoietic stem cell migration." + "Squamous cell of tonsil epithelium." "CALOHA:TS-1253" + "Combining with glucagon and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex." + "An epithelial cell of the cornea." "FMA:70551 CALOHA:TS-0173 BTO:0004298" + "A bone that is hollow or contains many air cells, such as the mastoid process of the temporal bone[TMD]." "galen:PneumaticBone SCTID:333008005 FMA:7478 Wikipedia:Skeletal_pneumaticity" + "A retractable double-layered fold of skin and mucous membrane that covers the clitoral glans." "UMLS:C0227771 SCTID:362242009 NCIT:C32590 EMAPA:30699 FMA:20169 Wikipedia:Clitoral_hood" + "A squamous epithelium that is part of a stomach." "EMAPA:35824 MA:0001611" + "The process in which a chondroblast acquires specialized structural and/or functional features of a chondrocyte that will contribute to the growth of a bone. A chondrocyte is a polymorphic cell that forms cartilage." + "A neuromere that is part of the presumptive spinal cord." "ZFA:0001332 TAO:0001332" + "Any process that modulates the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine." + "Any process that stops, prevents, or reduces the frequency, rate or extent of skeletal muscle cell proliferation." + "Catalysis of the hydrolysis of any ester bond." "Reactome:R-HSA-9023619 EC:3.1.-.- Reactome:R-HSA-162729 Reactome:R-HSA-9023617 Reactome:R-HSA-9749609" + "Any process that modulates the frequency, rate or extent of meiotic nuclear division, the process in which the nucleus of a diploid cell divides twice forming four haploid cells, one or more of which usually function as gametes." + "The synthesis or release of histamine following a stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels." + "The progression of the seminal vesicle over time, from its formation to the mature structure. The seminal vesicle is a gland that contributes to the production of semen." + "A slow muscle cell that has large amounts of myoglobin, stores energy as triglycerides, generates ATP by the oxidative method and is resistant to fatigue." "FMA:84413 BTO:0001812 CALOHA:TS-0940" + "Any process that modulates the frequency, rate or extent of cardiac chamber formation." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a fungus." + "The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell." + "Any process that modulates the frequency, rate, or extent of CD4-positive, alpha-beta T cell differentiation." + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endomembrane system." + "A nerve that is part of a limb [Automatically generated definition]." "MA:0000693 SCTID:359923002 EMAPA:37291" + "The process whose specific outcome is the progression of the epidermis of the limb over time, from its formation to the mature structure. The limb epidermis is the outer epithelial layer of the limb, it is a complex stratified squamous epithelium." + "A quality of a substance on which or through which electromagnetic radiation impinges or traverses with respect to radiation. This substance quality changes the quality of the incident radiation with respect to any of: intensity, direction, scatter and wavelength." + "A limb segment that is part of a hindlimb." "FMA:24877" + "GC_ID:1" + "GC_ID:1" + "The change in morphology and behavior of a gamma-delta T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific." + "Any process in which the Golgi is transported to, and/or maintained in, a specific location within the cell." + "Enables the transfer of nucleobases, nucleosides, nucleotides and nucleic acids from one side of a membrane to the other." + "Any process that activates or increases the frequency, rate or extent of protein localization to lysosome." + "An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins." "Wikipedia:Ribosome NIF_Subcellular:sao1429207766" + "A joint connecting the forelimb zeugopod skeleton with the carpal skeleton." "GAID:274 SCTID:182178002 FMA:321842 NCIT:C33894 MESH:D014955 galen:WristJoint MA:0000460 UMLS:C1322271 Wikipedia:Wrist" + "A Purkinje myocyte that is part of the atrioventricular bundle." "FMA:83393" + "A gland that is part of a foregut [Automatically generated definition]." "VHOG:0000650 EHDAA2:0000567 EMAPA:16557 EHDAA:950" + "A ligand-gated ion channel protein that is a translation product of the human CHRNA1-7, CHRNA9-10, CHRNB1-4, CHRNG, CHRND, or CHRNE genes, 1:1 orthologs thereof, or a semi-ortholog thereof." "IUPHARfam:76" + "A retinal ganglion cell C that has post-synaptic terminals in S2." + "Any (proper) part of the cytosol of a single cell of sufficient size to still be considered cytosol." + "Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant." "BSA:0000039 CALOHA:TS-0229 FMA:69068 GAID:963 BILA:0000056 EHDAA2_RETIRED:0003236 OGEM:000001 AAO:0011035 VHOG:0001766 ZFA:0000103 MIAA:0000019 MESH:D004622 EMAPA:16039 UMLS:C0013935 BTO:0000379 Wikipedia:Embryo EHDAA2:0000002 AEO:0000169 NCIT:C28147 MAT:0000226 EHDAA:38 XAO:0000113 http://neurolex.org/wiki/Category:Embryonic_organism EFO:0001367 SCTID:57991002" + "A mesentery that is part of a colon [Automatically generated definition]." "SCTID:245457004 FMA:14645 EMAPA:18942" + "The directed movement of the nucleus along microtubules within the cell, mediated by motor proteins." + "The creation of a single nucleus from multiple nuclei as a result of fusing the lipid bilayers that surround each nuclei." "Wikipedia:Karyogamy" + "A temporal lobe that is part of a right cerebral hemisphere." "UMLS:C1281970 BIRNLEX:1785 SCTID:314157005 FMA:72971" + "The chemical reactions and pathways resulting in the formation of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y." + "A submucosa that is part of a respiratory system [Automatically generated definition]." "MA:0001822 EMAPA:37578" + "A vein that drains the pelvis and lower limbs into the inferior vena cava." "galen:CommonIliacVein EMAPA:17874 FMA:14333 MA:0002143 NCIT:C32359 SCTID:181398004 UMLS:C0226758 Wikipedia:Common_iliac_vein" + "CD8_alpha-positive CD11b-negative dendritic cell is a conventional dendritic cell that is CD11b-negative, CD4-negative and is CD205-positive and CD8_alpha-positive." + "A type of intrafusal muscle fiber that lies in the center of a muscle spindle. Nuclei are clustered centrally and give the equatorial region a swollen appearance. They are associated with associated with dynamic gamma motor neurons, and the stretching of the equatorial region of the nuclear bag fibers results in an increase in the firing rate of type Ia sensory fibers." + "An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue." "BTO:0000751 FMA:62852 MESH:D007962 NCIT:C12529 CALOHA:TS-0549" + "The division of the spiral canal of the cochlea that contains the organ of Corti (the neuroepithelial receptor organ for hearing)." "EMAPA:35751 FMA:79789 Wikipedia:Scala_media MA:0002458" + "An endothelial cell found in the glomerulus of the kidney. This cell is flattened, highly fenestrated, and plays a vital role in the formation of glomerular ultrafiltrate." "FMA:70970 BTO:0004632" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the movement of RNA from the cytoplasm into the nucleus." + "A portion of smooth muscle tissue that is part of a urethra [Automatically generated definition]." "FMA:76909 MA:0001691 EMAPA:36630" + + "The compaction of chromatin during apoptosis." "Wikipedia:Pyknosis" + "Cartilaginous joint in which the articulating bones or cartilages are connected by fibrocartilage. Examples: pubic symphysis, intervertebral symphysis, manubriosternal joint.[FMA]." "EMAPA:37758 MA:0001504 Wikipedia:Symphysis FMA:7498 SCTID:1584001" + "Any process that increases the rate, frequency, or extent of the progression of the sclerotome over time, from its initial formation to the mature structure. The sclerotome is the portion of the somite that will give rise to a vertebra." + "Multi-tissue structure that is comprised of neural and non-neural epithelial layers which will form the retina and retinal pigmented epithelium of the mature eye[ZFA]. double walled structured formed by expansion and invagination of the distal end of the optic vesicle that develops into the pigmented and sensory layers of the retina while the mouth of the optic cup eventually forms the pupil of the eye[MP]." "VHOG:0000167 EMAPA:16674 BTO:0005351 EHDAA:2912 TAO:0001202 UMLS:C0231109 EHDAA2:0001303 SCTID:308789007 ZFA:0001202 NCIT:C34233" + "A mucus-secreting cell, with numerous apical secretory vesicles containing mucins; nucleus are basally displaced; numerous at the neck of mucus secreting glands" + "An enteroendocrine cell that stores and secretes Ghrelin." "FMA:63418" + "The disaggregation of a ribosome into its constituent components; includes the dissociation of ribosomal subunits." + "Enables the transmembrane transfer of a solute by a channel that opens when a specific neurotransmitter has been bound by the channel complex or one of its constituent parts." + "An anatomical chamber that is part of the olfactory apparatus, consisting of cavity walls (nasal epithelium and mucosal layers) and the space bounded anteriorly by the nares and posteriorly by the choanae, when these structures are present." "FMA:265136" + "Any process that mediates the transfer of information from mesodermal cells to endodermal cells." + "The core globe-shaped component of the camera-type eye." "VHOG:0001616 Wikipedia:Globe_(human_eye) MIAA:0000283 SCTID:244486005 FMA:12513" + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of juvenile hormone." + "The process aimed at the progression of an astrocyte that resides in the forebrain, from initial commitment of the cell to its fate, to the fully functional differentiated cell. An astrocyte is the most abundant type of glial cell. Astrocytes provide support for neurons and regulate the environment in which they function." + "Any process that stops, prevents or reduces the frequency, rate or extent of skeletal muscle hypertrophy." + "A vein that drains the left pampiniform plexus and empties into the left renal vein." "BTO:0002679 SCTID:53500001 MA:0002220 EMAPA:37383 FMA:14341 NCIT:C52697" + "Any of the smallest contractile units of a myofibril (striated muscle fiber)." + "Any process that modulates the frequency, rate or extent of cyanophore differentiation." + "Extracellular matrix that is mineralized." + "Nucleus located within the hindbrain." "TAO:0002177 ZFA:0001658" + "The characteristic movement of a cell from the dorsal ridge of the neural tube towards the heart and that contributes to heart formation." + "A stage at which the organism is a single cell produced by means of sexual reproduction." "VHOG:0000745 ZFS:0000001 XAO:1000001 FBdv:00005288 EHDAA:27 PdumDv:0000100 NCIT:C12601 BILS:0000106 Wikipedia:Zygote BilaDO:0000005 EFO:0001322" + "The prostate gland stroma is made up of the mesenchymal or fibroblast cells of the prostate gland." "UMLS:C1521760 FMA:45719 EMAPA:35714 MA:0002912 NCIT:C13104" + "A blood vessel of the placenta." "SCTID:280716005" + "Any process that activates or increases the frequency, rate or extent of the innate immune response, the organism's first line of defense against infection." + "A double-positive, alpha-beta thymocyte that is small and not proliferating." + "The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol." "Wikipedia:Gluconeogenesis MetaCyc:GLUCONEO-PWY" + "An adhesion G-protein coupled receptor that is a translation product of the human ADGRE1 gene or a 1:1 ortholog thereof." "IUPHARobj:182 PIRSF:PIRSF038685" + "Any process that stops, prevents or reduces the frequency, rate or extent of dendritic cell dendrite assembly." + "The process whose specific outcome is the progression of the exocrine pancreas over time, from its formation to the mature structure. The exocrine pancreas produces and store zymogens of digestive enzymes, such as chymotrypsinogen and trypsinogen in the acinar cells." + "Any process that modulates the frequency, rate or extent of phagocytosis, the process in which phagocytes engulf external particulate material." + "The metanephric early distal convoluted tubule contains metanephric DCT cells and is vasopressin-insensitive[GO]." + "The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen." + "A cellular transport process in which transported substances are moved in extracellular vesicles between cells; transported substances are enclosed in the vesicle lumen or located in the extracellular vesicle membrane." + "A mesonephric tubule is an epithelial tube that is part of the mesonephros[GO]. Genital ridge that is next to the mesonephros[WP]." "Wikipedia:Mesonephric_tubules VHOG:0000500 EHDAA2:0001134 XAO:0000148 AAO:0010389 EMAPA:16747" + "GC_ID:1" + "A femur endochondral element that is composed primarily of cartilage tissue." "EMAPA:17742" + "The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of an endocardial cell. An endocardial cell is a specialized endothelial cell that makes up the endocardium portion of the heart. The endocardium is the innermost layer of tissue of the heart, and lines the heart chambers." + "The conversion at fertilization of the inactive sperm nucleus into a male pronucleus with its chromosomes processed for the first zygotic division." + "Choroid plexus of the fourth ventricle." "NCIT:C32308 VHOG:0001375 MA:0000983 ZFA:0001446 HBA:9710 BAMS:cp4v BAMS:chp4 EMAPA:32742 UMLS:C0152293 SCTID:42214001 FMA:78492 neuronames:638 DHBA:12808 TAO:0001446 NLX:27388" + "An internal carotid artery that branching_part_of a right common carotid artery plus branches." "FMA:3949 EMAPA:16330 SCTID:161251001" + "One of a a paired bundle of nerve fibers plus ganglia that run from the base of the skull to the coccyx." "CALOHA:TS-2049 FMA:6258 AAO:0010791 XAO:0000211 EV:0100374 Wikipedia:Sympathetic_trunk BAMS:S SCTID:181099004 BTO:0001834" + "The process of regulating the proliferation and elimination of cells of the immune system such that the total number of cells of a particular cell type within a whole or part of an organism is stable over time in the absence of an outside stimulus." + "A non-material anatomical entity of two dimensions. Anatomical boundaries are contiguous structures." "FMA:50705 AEO:0000192 CARO:0000010" + "Any process that activates or increases the frequency, rate or extent of thymocyte migration." + "The process whose specific outcome is the progression of the male genitalia over time, from its formation to the mature structure." + "A portion of trabecula carnea cardiac muscle tissue that is part of a left ventricle [Automatically generated definition]." "FMA:84430" + "Any process that activates or increases the frequency, rate or extent of vesicle fusion." + "A tube in the respiratory system. Examples: bronchus, bronchiole, trachea." "EMAPA:37946 FMA:12224" + "The region of the digestive tract extending from the beginning of the intestines to the anus[GO - gut definition]." "FMA:49179 galen:LowerGastrointestinalTract UMLS:C0226875 Wikipedia:Alimentary_canal#Upper_gastrointestinal_tract SCTID:279973004 NCIT:C33010" + "Any substance in the body or expelled from the body that is in a gaseous state." "FMA:84580" + "Loose connective tissue located at the outer and inner layers of organs. Examples: submucosal connective tissue, tunica adventitia of artery, papillary dermis, superficial fascia of dorsum of hand." "AAO:0000027 SCTID:68477002 FMA:63897" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells." + "Blood-forming tissue, consisting of reticular fibers and cells." "FMA:14073 UMLS:C0229619 CALOHA:TS-2142 NCIT:C13051" + "A set of midline structures surrounding the brainstem of the mammalian brain, originally described anatomically, e.g., hippocampal formation, amygdala, hypothalamus, cingulate cortex. Although the original designation was anatomical, the limbic system has come to be associated with the system in the brain subserving emotional functions. As such, it is very poorly defined and doesn't correspond closely to the anatomical meaning any longer. [BirnLex]." "Wikipedia:Limbic_system SCTID:361342009 BTO:0000928 NCIT:C94541 neuronames:2055 MESH:D008032 UMLS:C0023715 GAID:615 CALOHA:TS-1307 FMA:242000" + "A pulmonary interstitial fibroblast that is part of the alveolus and contains lipid droplets." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external stimulus." + "The process in which a mesenchymal cell, acquires specialized structural and/or functional features of a chondroblast. Differentiation includes the processes involved in commitment of a cell to a chondroblast fate. A chondroblast is a precursor cell to chondrocytes." + "A cell that initiates an electrical signal and passes that signal to another cell." + "Any process that modulates the frequency, rate, or extent of interleukin-8 production." + "A sheet of somatopleure that grows upward over the embryo and eventually meets in the midline enclosing the embryo, eventually giving rise to the amnion and chorion[Kardong]." "EMAPA:16076" + "Any process that activates or increases the frequency, rate or extent of RNA binding." + "A component of the cytoskeleton consisting of a homo or heteropolymeric fiber constructed from an indeterminate number of protein subunits." + "A tyrosine-protein phosphatase non-receptor type substrate 1 that is encoded in the genome of human." "UniProtKB:P78324" + "The chemical reactions and pathways resulting in the formation of glutamate, the anion of 2-aminopentanedioic acid." + "Any process that activates or increases the frequency, rate or extent of natural killer T cell proliferation." + "Any process that modulates the frequency, rate or extent of microglial cell mediated cytotoxicity." + "Any process that stops, prevents or reduces the frequency, rate or extent of epithelial cell differentiation involved in kidney development." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of B cell tolerance induction." + "A myoblast that differentiates into skeletal muscle fibers." "FMA:84799" + "Mesenchyme that is part of a developing ovary [Automatically generated definition]." "VHOG:0001441 EHDAA:8128 EHDAA2:0001362" + "Any process that modulates the frequency, rate or extent of alpha-beta T cell activation." + "Any process that stops, prevents, or reduces the frequency, rate or extent of cell differentiation." + "An innate lymphoid cell in the human with the phenotype CD34-negative, CD56-positive, CD117-positive.Thie cell type may include precusors to NK cells and ILC3 cells." + "A natural cytotoxicity triggering receptor 1 that is encoded in the genome of human." "UniProtKB:O76036" + "An endoderm that is part of a midgut [Automatically generated definition]." "RETIRED_EHDAA2:0001194 EMAPA:16257 VHOG:0001080 EHDAA:987" + "The process in which a relatively unspecialized cell acquires specialized features of a neuron whose cell body resides in the peripheral nervous system." + "An arrangement of nerve fibers, running from the spine where it proceeds through the neck then the axilla and into the arm where it innervates skin and muscle. [WP,modified]." "UMLS:C0006090 EHDAA:3782 FMA:5906 VHOG:0000372 NCIT:C12682 MA:0001180 GAID:842 EMAPA:16988 EHDAA2:0000180 MESH:D001917 SCTID:181002002 Wikipedia:Brachial_plexus" + "Any process that stops, prevents or reduces the frequency, rate or extent of gamma-delta T cell activation involved in immune response." + "A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta." "EMAPA:35144 MA:0000061" + "A part of the His-Purkinje system that transmits signals from the AV node to the cardiac Purkinje fibers[GO]." "MA:0002576 galen:BundleOfHis UMLS:C0006382 MESH:D002036 SCTID:362022007 Wikipedia:Bundle_of_His FMA:9484 NCIT:C32160 GAID:559 EMAPA:35152" + "A V(D)J recombination-activating protein 1 that is encoded in the genome of human." "UniProtKB:P15918 Reactome:R-HSA-5692681" + "The epithelial layer of the vagina." "BTO:0000422 UMLS:C0920840 MA:0001730 EMAPA:30991 CALOHA:TS-1325 NCIT:C49313 FMA:19978" + "Any process that decreases the rate, frequency or extent of collagen catabolism. Collagen catabolism is the proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix." + "Any process that activates or increases the frequency, rate or extent of organelle assembly." + "A pre-cartilage condensation that has the potential to develop into a tibia." "EHDAA2:0002036" + "The outer layer of peritoneum that is attached to the abdominal and pelvic walls." "EMAPA:16591 SCTID:362700006 TAO:0005131 ZFA:0005131 VHOG:0001527 Wikipedia:Parietal_peritoneum AAO:0010816 FMA:21451" + "The lateral area of the two branches of a horseshoe-shaped mesenchymal swelling in the future nasal region of the embryo; it separates the olfactory pit from the developing eye and the ala of the nose/snout develops from it." "EHDAA2:0000916 FMA:295864 Wikipedia:Lateral_nasal_prominence SCTID:308880000 EMAPA:16805 EHDAA:4786" + "The formation of the ectoderm, mesoderm and endoderm during gastrulation." + "A T-cell surface glycoprotein CD1c that is encoded in the genome of human." "MRO:0000890 UniProtKB:P29017" + "A cell of the early embryo at the developmental stage in which the blastomeres, resulting from repeated mitotic divisions of the fertilized ovum (zygote), form a compact cell mass." + "The process whose specific outcome is the progression of a visceral peritoneum over time, from its formation to the mature structure." + "Vascular endothelium found in colon blood vessels." "CALOHA:TS-0162" + "The cellular developmental process in which a relatively unspecialized cell, e.g. embryonic or regenerative cell, acquires specialized structural and/or functional features that characterize a specific cell. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state." "Wikipedia:Cellular_differentiation" + + "A rib endochondral element that is composed primarily of cartilage tissue." "VHOG:0001122 EHDAA:8347 EHDAA2:0001716 EMAPA:17678" + "Any process that modulates the frequency, rate or extent of CD4-positive, alpha-beta T cell activation." + "The series of events in which a light stimulus is received by a cell and converted into a molecular signal as part of the sensory perception of light." + "The paired ventral prominences formed by bifurcation of the first pharyngeal arches in the embryo; the two prominences unite ventrally and fuse to form the mandible and lower lip." "EHDAA:5871 Wikipedia:Mandibular_prominence EHDAA2:0001061 FMA:293051 UMLS:C1512982 NCIT:C34204 EMAPA:17355" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pheromone stimulus." + "An organ that is part of a vestibular system." "UMLS:C0682674 BIRNLEX:2519" + "The type of sexual cycle seen in females, often with physiologic changes in the endometrium that recur at regular intervals during the reproductive years." + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a pseudopodium, a temporary protrusion or retractile process of a cell, associated with cellular movement." + "The chemical reactions and pathways resulting in the formation of catechol-containing compounds. Catechol is a compound containing a pyrocatechol nucleus or substituent." + "Any process in which a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a membrane." + "Binding to a CCR7 chemokine receptor." + "Any process that stops, prevents, or reduces the frequency, rate or extent of natural killer cell proliferation as part of an immune response." + "A protein complex composed of two identical immunoglobulin heavy chains of the IgD isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." + "Any process that modulates the frequency, rate, extent or accuracy of translational elongation." + "RETIRED_EHDAA2:0001454 EMAPA:16549" + "Any nerve that innervates the larynx." "MESH:D007823 SCTID:307013006" + "The paler-colored muscle tissue of some mammals, composed of fast twitch muscle fibers." "NCIT:C12613 UMLS:C0242873 BTO:0002318" + "Binding to a protein component of a cytoskeleton (actin, microtubule, or intermediate filament cytoskeleton)." + "Any process that activates or increases the frequency, rate or extent of collagen catabolism. Collagen catabolism is the proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix." + "A basement membrane of epithelium that is part of a respiratory system." "MA:0001815 EMAPA:37570" + "An organ subunit in the skin that gives rise to cutaneous appendage." + "Any process that stops, prevents or reduces the rate or extent of urothelial cell proliferation." + "A cell that is part of pigmented ciliary epithelium. This cell type uptakes sodium and chloride ions from stromal interstitium and passes the ions to non-pigmented ciliary epithelial cells via gap junctions." "FMA:70606" + "A protein that is a translation product of the human NETO1 gene or a 1:1 ortholog thereof." + "The non-specific expansion of T cell populations within a whole or part of an organism to reach to a total number of T cells which will then remain stable over time in the absence of an external stimulus." + "GC_ID:1" + "A non-secretory ribonuclease that is encoded in the genome of human." "UniProtKB:P10153" + "Any process that modulates the frequency, rate or extent of immature T cell proliferation in the thymus." + "An N-formyl peptide receptor that is a translation product of the human FPR1 gene or a 1:1 ortholog thereof. The preferred ligand is the peptide fMet-Leu-Phe, a bacterial peptide that acts as a chemoattractant in various pathophysiological conditions." "IUPHARobj:222" + "Vein that drains the axilla." "galen:AxillaryVein MA:0002084 EMAPA:18758 GAID:527 Wikipedia:Axillary_vein FMA:13329 NCIT:C32171 MESH:D001367 UMLS:C0004456 SCTID:181389002" + "A thoracic vertebra endochondral element that is composed primarily of a pre-cartilage condensation." + "A C-C motif chemokine 3 that is encoded in the genome of mouse." "UniProtKB:P10855" + "A structure quality inhering in a bearer by virtue of the bearer's being capable of swelling or stretching." + "OBSOLETE. A subset of motor neurons that innervates intrafusal muscle fibers and has small diameter axons." + "The directed movement of monocarboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "An epithelial cell of the parathyroid gland." "FMA:70547" + "A follicle that has reached the most mature stage of folliculogenesis, characterized by the presence of the antrum." "FMA:18641 EMAPA:30763 NCIT:C32692 MA:0002909 SCTID:362261008 UMLS:C0600225" + "A composition quality inhering in a bearer by virtue of the bearer's consisting of keratin." + "The progression of the common bile duct over time, from its formation to the mature structure. The common bile duct is formed from the joining of the common hepatic duct running from the liver, and the cystic duct running from the gallbladder. The common bile duct transports bile from the liver and gallbladder to the intestine." + "The orderly movement of a motor neuron from one site to another. A motor neuron is an efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes movement." + "Any process that activates or increases the frequency, rate or extent of directed movement of RNA from the nucleus into the cytoplasm." + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins." + "A cortical cell layer of the cerebellum. Examples: the granular (inner+outer) layer, molecular layer, Purkinje cell layer, and the ventricular layer of the embryo." "MA:0000201 SCTID:360478008 UMLS:C1707522 BIRNLEX:880 EMAPA:35212 NCIT:C49137 FMA:83141" + "Any process that modulates the frequency, rate or extent of cardiac muscle growth." + + "The chemical reactions and pathways occurring at the level of individual cells resulting in the formation of any of a group of naturally occurring, biologically active amines, such as norepinephrine, histamine, and serotonin, many of which act as neurotransmitters." + "A M cell that is part of the epithelium proper of small intestine." "FMA:263132" + "A resident monocyte that is Gr-1 low, CD43-positive, and CX3CR1-positive." + "A alpha-beta intraepithelial T cell found in the columnar epithelium of the gastrointestinal tract. Intraepithelial T cells often have distinct developmental pathways and activation requirements." + "Cardiac septum which separates the right ventricle from the left ventricle.[FMA]." "Wikipedia:Interventricular_septum FMA:7133 galen:InterventricularSeptum UMLS:C0225870 VHOG:0000386 NCIT:C32874 EHDAA:2603 SCTID:362019005 EMAPA:17333 EFO:0001956 MA:0000085 BTO:0002483" + "Any process that activates or increases the frequency, rate, or extent of tissue remodeling." + "Any process that stops, prevents, or reduces the rate of T cell mediated cytotoxicity." + "A CD24-high, CD4-low, CD8-low, CD44-negative, NK1.1-negative NK T cell." + "Section of colon which is distal to the cecum and proximal to the transversecolon.[FMA,modified]." "FMA:14545 galen:AscendingColon CALOHA:TS-0057 EMAPA:35151 MA:0001541 EFO:0000843 MAT:0000311 MIAA:0000311 SCTID:362162009 Wikipedia:Ascending_colon BTO:0000270 NCIT:C12265 UMLS:C0227375" + "A proenkephalin-B that is encoded in the genome of mouse." "UniProtKB:O35417" + "Any process that stops, prevents or reduces the frequency, rate or extent of mesoderm development." + "A platelet glycoprotein 4 that is encoded in the genome of human." "UniProtKB:P16671" + + "Ossified form of a vertebral centrum, a skeletal element that functionally replaces the notochord[VSAP,modified]." "TAO:0000126 SCTID:362867001 EMAPA:36588 ZFA:0000126 SCTID:361745008 FMA:11945 Wikipedia:Body_of_vertebra UMLS:C0223084 NCIT:C12852 AAO:0000697 MA:0001457" + "Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to nucleus." + "A keratinocyte of the epidermis suprabasal layer. This cell may express the differentiation markers keratin 10 and keratin 1." + "A protein that is a translation product of the human VIM gene or a 1:1 ortholog thereof." + "A protein that is a translation product of the human GAD1 gene or a 1:1 ortholog thereof." "IUPHARobj:1272" + "The formation of either of the compounds secreted by the thyroid gland, mainly thyroxine and triiodothyronine. This is achieved by the iodination and joining of tyrosine molecules to form the precursor thyroglobin, proteolysis of this precursor gives rise to the thyroid hormones." + "The process whose specific outcome is the progression of the respiratory tube over time, from its formation to the mature structure. The respiratory tube is assumed to mean any tube in the respiratory tract." + "Arteriole of villus of small intestine." + "A somatostatin that has been processed by proteolytic cleavage." + "Any process that modulates the frequency, rate or extent of pulmonary blood vessel remodeling." + "Any process that modulates the rate, frequency or extent of T cell chemotaxis. T cell chemotaxis is the directed movement of a T cell in response to an external stimulus." + "A vasculature that is part of a limb/fin." "ZFA:0005095 TAO:0005095" + "Any process that mediates the transfer of information from a bundle of His cardiomyocyte to a Purkinje myocyte." + "Innermost layer of the hair shaft." "BTO:0004671 EMAPA:35389 Wikipedia:Bone_marrow_of_ovary_(hair) SCTID:318929009 MA:0000158" + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism." + "A submucosa that is part of a descending colon [Automatically generated definition]." "FMA:15020" + "The controlled release of a substance by a tissue." + "A taste bud that is located on the roof of the mouth." + "A multicellular organismal process carried out by any of the organs or tissues in an organ system. An organ system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a biological objective." + "A neural crest that has_potential_to_developmentally_contribute_to a telencephalon." "TAO:0000812 EFO:0003574 RETIRED_EHDAA2:0001991 ZFA:0000812 VHOG:0000799" + "Binding to a collagen fibril." + "An endothelial cell found in capillaries." "CALOHA:TS-0112 BTO:0004956 FMA:67756" + "GC_ID:1" + "A retinal ganglion with cell medium cell bodies and medium to large dendritic fields." + "The process in which the controlled movement of a flagellated sperm cell is initiated as part of the process required for flagellated sperm to reach fertilization competence." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus by the chemical structure of the anion portion of a dissociated acid (rather than the acid acting as a proton donor). The acid chemical may be in gaseous, liquid or solid form." + "A metapodium region that is part of a pes." "FMA:24997 MA:0000049 SCTID:280711000 SCTID:370639003 CALOHA:TS-2221" + "An outflow tract of atrium that is part of a left atrium." "FMA:9551" + "Stromal cell that forms the internal covering of the vertebrate brain and produces ECM for this and the choroid plexus." + "A vasculature that is part of a pectoral appendage." "ZFA:0005096 TAO:0005096" + "Any process that activates or increases the frequency, rate or extent of intracellular signal transduction." + + "Any process that reduces the occurrence or rate of mesenchymal stem cell death by apoptotic process that contributes to the shaping of the nephron in the mesonephros." + "Any lymph vessel that is located in the dura mater of the brain." + "An alveolar capillary endothelial cell that is located proximally to alveolar capillary type 1 endothelial cells and in close apposition to alveolar type 1 epithelial cells (also known as type I pneumocytes)." + "Epidermal cells that do not contain keratin. Cell type is usually associated with moist epidermal tissues." "FMA:62880" + "Any process that stops, prevents or reduces the frequency, rate or extent of colon smooth muscle contraction." + "The process in which a protein is transported across a membrane." + "The union of male and female gametes to form a zygote." + "The metanephric nephron epithelium is a tissue that covers the surface of a nephron in the metanephros[GO]." + "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 2/3." + "The autonomic nervous system is composed of neurons that are not under conscious control, and is comprised of two antagonistic components, the sympathetic and parasympathetic nervous systems. The autonomic nervous system regulates key functions including the activity of the cardiac (heart) muscle, smooth muscles (e.g. of the gut), and glands[GO]." "EHDAA:3767 BTO:0002507 UMLS:C0004388 neuronames:2054 MESH:D001341 TAO:0001574 ZFA:0001574 FMA:65553 MA:0000219 CALOHA:TS-2001 VHOG:0000396 GAID:706 UMLS:C1305381 AAO:0000033 Wikipedia:Autonomic_nervous_system BIRNLEX:1123 NCIT:C12673 EHDA:10095 EHDAA2:0000158 SCTID:362481007 EMAPA:16984" + "Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule." + "Anatomical structure that performs a specific function or group of functions [WP]." "WBbt:0003760 SCTID:272625005 MA:0003001 CARO:0020004 EFO:0000634 ENVO:01000162 EMAPA:35949 BIRNLEX:4 NCIT:C13018 Wikipedia:Organ_(anatomy) FMA:67498 UMLS:C0178784" + "Any process that activates or increases the frequency, rate or extent of granulosa cell proliferation." + + "Any process that modulates the frequency, rate or extent of synoviocyte proliferation." + "A basket cell morphology that inheres in neurons that are large, and typically ascend to give rise to many long horizontally and vertically projecting axon collaterals that traverse neighboring columns and can extend through all cortical layers." "ilxtr:LargeBasketPhenotype" + "Any vesicle-mediated transport that occurs in a synapse." + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteoglycans, any glycoprotein in which the carbohydrate units are glycosaminoglycans." + "Any process that activates or increases the frequency, rate or extent of leukocyte mediated cytotoxicity." + "Mesonephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the mesonephros[GO]." "AAO:0011062 EHDAA2:0001132 EMAPA:16745 XAO:0000291" + "The metanephric loop of Henle is a metanephric nephron tubule that connects the proximal convoluted tubule to the distal convoluted tubule in the metanephros[GO]." + + + "An endothelial cell found in the mucosa associated with the facial skeleton." "FMA:70627" + "A dorsal root of spinal cord that overlaps a cervical spinal cord." "BIRNLEX:964 SCTID:175023008 UMLS:C1278751" + "Any process that modulates the frequency, rate or extent of response to calcium ion." + "The directed movement of a melanosome to a specific location." + "BTO:0001141" + "Any process that stops, prevents or reduces the frequency, rate or extent of neuronal action potential." + "The specification of the anterior/posterior axis of the embryo by the products of genes expressed maternally and genes expressed in the zygote." + "Smooth muscle cell of the carotid artery." + "Any process that modulates the frequency, rate or extent of protein depolymerization." + "The process in which a relatively unspecialized cell acquires specialized features of a brown adipocyte, an animal connective tissue cell involved in adaptive thermogenesis. Brown adipocytes contain multiple small droplets of triglycerides and a high number of mitochondria." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of dendritic cell antigen processing and presentation." + "The regulated release of histamine by a cell as part of an inflammatory response." + "A B220-positive CD38-positive IgG-negative memory B cell is a CD38-positive IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype B220-positive, CD38-positive, and IgG-negative." + "The developmental process by which an acoustico-facial VII-VIII ganglion complex is generated and organized." + "The process whose specific outcome is the progression of a short nephron in the metanephros over time, from its formation to the mature structure. Short nephrons are associated with mid-cortical and superficial glomeruli, are situated entirely in the outer medulla, and have no thin ascending limb." + "The process whose specific outcome is the progression of the renal system over time, from its formation to the mature structure. The renal system maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels." + "Any process that stops, prevents or reduces the frequency, rate or extent of hemostasis." + "The process in which the anatomical structures of the diencephalon are generated and organized. The diencephalon is the paired caudal parts of the prosencephalon from which the thalamus, hypothalamus, epithalamus and subthalamus are derived; these regions regulate autonomic, visceral and endocrine function, and process information directed to the cerebral cortex." + "Any process that activates or increases the frequency, rate or extent of terminal button organization." + "A portion of connective tissue that is part of a respiratory system [Automatically generated definition]." "EMAPA:35968 EMAPA:35977 MA:0001814" + "The multiplication or reproduction of smooth muscle cells, resulting in the expansion of a cell population." + "Any process that modulates the frequency, rate, or extent of dendritic cell cytokine production." + "Binding to melatonin." + "A multicellular organismal process involved in the cyclical phases of growth (anagen), regression (catagen), quiescence (telogen), and shedding (exogen) in the life of a hair; one of the collection or mass of filaments growing from the skin of an animal, and forming a covering for a part of the head or for any part or the whole of the body." + "The aggregation, arrangement and bonding together of proteins and DNA molecules to form a protein-DNA complex." + "An organism subdivision that includes both an appendage and its associated girdle region. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc)." "FMA:7182 VSAO:0000214 EMAPA:37858" + "An eosinophil peroxidase that is encoded in the genome of human." "UniProtKB:P11678" + "The transient outer neural tube region that contains the first generated post-mitotic neurons that receive synaptic input from thalamic axons and in turn project axons to the developing cortical plate." "EMAPA:32703 PBA:294021932 https://upload.wikimedia.org/wikipedia/commons/thumb/a/ac/Corticogenesis_in_a_wild-type_mouse_with_captions_in_english_copy.png/360px-Corticogenesis_in_a_wild-type_mouse_with_captions_in_english_copy.png Wikipedia:Subplate neuronames:3233 DHBA:10522" + "The smooth muscle tissue surrounding the urothelium of the kidney pelvis." "MA:0002631 FMA:262022 EMAPA:28120" + "Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a mandibular process mesenchyme." "EHDAA2:0004604" + "The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton)." + "A developmental process, independent of morphogenetic (shape) change, that is required for the superior olivary nucleus to attain its fully functional state. The superior olivary nucleus is a small cylindrical mass on the dorsal surface of the lateral part of the trapezoid body of the pons, and it is situated immediately above the inferior olivary nucleus. It receives projections from the cochlear nucleus and thus is involved in the perception of sound." + "The chemical reactions and pathways resulting in the breakdown of glycosaminoglycans, any one of a group of polysaccharides that contain amino sugars." + "The regulated release of renin into the blood stream by juxtoglomerular cells." + "An organ or element that part of the dorsum of the organism. Examples: spinal cord, vertebrae, muscles of back." "MA:0001901 EMAPA:37274" + "An epithelium that is part of a small intestine [Automatically generated definition]." "FMA:62017 SCTID:45480009 EMAPA:35778 MA:0001553 BTO:0001258 CALOHA:TS-2104 TAO:0005127 ZFA:0005127" + "OBSOLETE: A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite growth/propagation in vitro as part of a immortal cell line." + "A M cell that is part of the epithelium of small intestine." "FMA:263128" + "An epithelium that is part of a elbow [Automatically generated definition]." "EHDAA:4168 VHOG:0001044 EHDAA:6214 EMAPA:17415 EHDAA2:0000430" + "The process in which a relatively unspecialized cell acquires the specialized features of a pericyte cell." + "An assembly of actin filaments that are on the same axis but may be oriented with the same or opposite polarities and may be packed with different levels of tightness." + "A sex cord that is part of a indifferent gonad." "EHDAA2:0004051" + "The progression of the diaphragm over time from its initial formation to the mature structure. The diaphragm is a skeletal muscle that is responsible for contraction and expansion of the lungs." + "The process in which the anatomical structures of the mesonephric glomerulus are generated and organized. The mesonephric glomerulus is a capillary tuft surrounded by Bowman's capsule in nephrons of the vertebrate mesonephros." + "A tubular structure that transports secreted or excreted substances." "NCIT:C12948 ZFA:0005171 XAO:0004000 AAO:0011123 galen:Duct Wikipedia:Duct_(anatomy) TAO:0005171 UMLS:C0687028 SCTID:91726008 FMA:30320" + "Any process that stops, prevents or reduces the frequency, rate or extent of retrograde trans-synaptic signaling by neuropeptide." + "A microtubule in the axoneme of a eukaryotic cilium or flagellum; an axoneme contains nine modified doublet microtubules, which may or may not surround a pair of single microtubules." + "A portion of connective tissue that is part of an abdominal segment of trunk [Automatically generated definition]." "MA:0000526 EMAPA:37059" + "A T-cell surface glycoprotein CD1a that is encoded in the genome of human." "UniProtKB:P06126 MRO:0000888" + "The process in which the spongiotrophoblast layer of the placenta progresses from its formation to its mature state." + "The process in which a relatively unspecialized cell acquires the specialized features of a photoreceptor cell in a camera-type eye." + "A blood vessel that is part of a head [Automatically generated definition]." "SCTID:127865000 EMAPA:36610 MA:0000575" + "A protein that is a translation product of the human CD40LG gene or a 1:1 ortholog thereof." "PIRSF:PIRSF016527" + "Any process that activates or increases the frequency, rate or extent of auditory hair cell differentiation." + "A precursor B cell that is CD45RA-positive, CD43-positive, CD24-positive and BP-1-negative." + "Any process that decreases the frequency, rate, or extent of neutrophil chemotaxis. Neutrophil chemotaxis is the directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding." + "OBSOLETE: The reproductive structure of bacteria, fungi and cryptograms." + "The process in which the anatomical structures of a kidney mesenchymal tissue are generated and organized. Kidney mesenchyme is the tissue made up of loosely connected mesenchymal cells in the kidney." + "An ectoderm that is part of a optic eminence [Automatically generated definition]." "RETIRED_EHDAA2:0001309 EMAPA:16539 VHOG:0001105 EHDAA:940" + "A cilium which may have a variable arrangement of axonemal microtubules and also contains molecular motors. It may beat with a whip-like pattern that promotes cell motility or transport of fluids and other cells across a cell surface, such as on epithelial cells that line the lumenal ducts of various tissues; or they may display a distinct twirling motion that directs fluid flow asymmetrically across the cellular surface to affect asymmetric body plan organization. Motile cilia can be found in single as well as multiple copies per cell." + "A terminal branch of the left or right common carotid artery which supplies oxygenated blood to to the throat, neck glands, tongue, face, mouth, ear, scalp and dura mater of the meninges[MP]." "SCTID:362044002 NCIT:C32551 EFO:0001953 MA:0001929 VHOG:0000265 Wikipedia:External_carotid_artery XAO:0000345 AAO:0010416 UMLS:C0007275 GAID:480 MESH:D002342 FMA:10635 AAO:0010218 BTO:0004696 EMAPA:18611 EHDAA2:0000461" + "The process whose specific outcome is the progression of bone over time, from its formation to the mature structure. Bone is the hard skeletal connective tissue consisting of both mineral and cellular components." + "The mesonephric proximal tubule extends from the capsule to the distal tubule." + "A CD48 molecule that is encoded in the genome of human." "UniProtKB:P09326" + "Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted]." "TAO:0000094 TE:E5.11.2.0.0.0.4 VHOG:0000085 AAO:0011006 Wikipedia:Blood_island_of_umbilical_vesicle EFO:0003489 XAO:0000067 EHDAA:207 NCIT:C34113 ZFA:0000094 UMLS:C1511224" + "A groove that is situated between the 3rd and 4th pharyngeal arch." "VHOG:0000973 VHOG:0000572 EMAPA:16581 EHDAA:1082 EHDAA2:0000074" + "A collection of hairs that is part of a craniocervical region." + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals." + "A muscular coat that is part of a cloaca." + "A near-projecting glutamatergic neuron with a soma found in cortical layer 5/6." + "A non-terminally differentiated cell that originates from the neural crest and differentiates into a cyanophore." + "Combining with a lipoprotein particle and delivering the lipoprotein particle into the cell via endocytosis. A lipoprotein particle, also known as a lipoprotein, is a clathrate complex consisting of a lipid enwrapped in a protein host without covalent binding in such a way that the complex has a hydrophilic outer surface consisting of all the protein and the polar ends of any phospholipids." + "The process whose specific outcome is the progression of an uterine gland over time, from its formation to the mature structure." + "A polymer consisting of an indefinite number of protein or protein complex subunits that have polymerised to form a fiber-shaped structure." + "A sphenoid endochondral element that is composed primarily of a pre-cartilage condensation." "EMAPA:18015 EHDAA2:0003446" + "A primordial germ cell that is destined to become a male germ cell." "EMAPA:18686 VHOG:0000662 EHDAA2:0001053 FMA:84771" + "A chemokine receptor that is a translation product of the human CCR2 gene or a 1:1 ortholog thereof. The preferred ligands include CCL2, CCL7, CCL8, CCL13." "IUPHARobj:59" + "One of the two embryological structures that give rise to the kidney (the other is the ureteric bud). The metanephric blastema mostly develops into nephrons, but can also form parts of the collecting duct system.[WP]. Metanephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the metanephros[GO]." "EHDAA:5021 EHDAA:5915 SCTID:361529008 VHOG:0000540 Wikipedia:Metanephric_blastema EHDAA2:0004062 EHDAA:4041 EMAPA:17375" + "The orderly movement of epithelial cells within a renal tubule that contributes to nephron tubule morphogenesis." + "Any process that modulates the frequency, rate or extent of bone mineralization involved in bone maturation." + + "The process in which the anatomical structures of the notochord are generated and organized. The notochord is a mesoderm-derived structure located ventral of the developing nerve cord. In vertebrates, the notochord serves as a core around which other mesodermal cells form the vertebrae. In the most primitive chordates, which lack vertebrae, the notochord persists as a substitute for a vertebral column." + "A gray matter that is part of a cerebral hemisphere." "FMA:61821 EMAPA:37477 CALOHA:TS-2361 MA:0000944 BTO:0000823" + "Any process that modulates the frequency, rate or extent of dopamine biosynthetic process." + "Any process that stops, prevents or reduces the frequency, rate or extent of oxygen metabolic process." + "A mucosa that is part of a lacrimal canaliculus [Automatically generated definition]." "FMA:85366" + "A female organ involved in reproduction." "MA:0000544 EMAPA:28540" + "The intercostal nerves are the anterior divisions (rami anteriores; ventral divisions) of the thoracic spinal nerves from T1 to T11. Each nerve is connected with the adjoining ganglion of the sympathetic trunk by a gray and a white ramus communicans. The intercostal nerves are distributed chiefly to the thoracic pleura and abdominal peritoneum and differ from the anterior divisions of the other spinal nerves in that each pursues an independent course without plexus formation. The first two nerves supply fibers to the upper limb in addition to their thoracic branches; the next four are limited in their distribution to the parietes of the thorax; the lower five supply the parietes of the thorax and abdomen. The 7th intercostal nerve terminates at the xyphoid process, at the lower end of the sternum. The 10th intercostal nerve terminates at the umbilicus. The twelfth thoracic is distributed to the abdominal wall and groin. [WP,unvetted]." "SCTID:279568001 MESH:D007367 GAID:858 UMLS:C1285089 Wikipedia:Intercostal_nerves FMA:6028 EMAPA:18227 NCIT:C32825" + "Any process that stops, prevents, or reduces the frequency, rate or extent of sister chromatid segregation during mitosis." + "Any process that activates or increases the frequency, rate or extent of skeletal muscle cell proliferation." + "Any process that modulates the activity of an enzyme." + "Cranial nerve which enters the brain between cranial nerves VIII and IX; contains afferents and sensory efferents to the posterior lateral line ganglion and middle ganglion. Fibers from the posterior lateral line ganglion innervate the occipital dorsal lateral line and trunk lateral lines." "ZFA:0000175" + "Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of a protein." + "The region of the mantle layer of the neural tube that lies ventral to the sulcus limitans and contains primarily motor neurons and interneurons." "NCIT:C34111 UMLS:C1511061 AAO:0010561 Wikipedia:Basal_plate_(neural_tube) neuronames:1372 EFO:0001904" + + "Any process that modulates the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information." + "A synovial joint that is part of a pelvic girdle region." "NCIT:C32890 UMLS:C0827002 FMA:35173" + "The process that gives rise to the paraxial mesoderm. This process pertains to the initial formation of the structure from unspecified parts." + "Any process that modulates the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." + "High affinity ammonium transporter complex that enables the transfer of ammonium from one side of a membrane to the other." + "The establishment, maintenance and elaboration of a pattern along a line or a point in an embryo." + "Mesenchyme that has the potential to develop into a dermis." "EHDAA2:0000598" + "A group 2 innate lymphoid cell in the mouse capable of secreting IL-13 in response to a helminth infection. This cell is lineage-negative, ICOS-positive, IL1RL1-positive, IL7Ralpha-positive, and IL17Br-positive." + "A brush cell found in the epithelium of bronchus." "FMA:263226" + "The space within an epithelial sphere." "AEO:0000079" + "A specialized, enlarged, connective tissue cell of the decidua with enlarged nucleus, dense membrane‐bound secretory granules and cytoplasmic accumulation of glycogen and lipid droplets. These cells develop by the transformation of endometrial stromal cells during decidualization." "BTO:0002770 BTO:0005756 NCIT:C32429" + "A secondary lymphoid organ macrophage found in a lymph node. This cell is CD169-high." + "The regulated release of aldosterone into the circulatory system. Aldosterone is a pregnane-based steroid hormone produced by the outer-section (zona glomerulosa) of the adrenal cortex in the adrenal gland, and acts on the distal tubules and collecting ducts of the kidney to cause the conservation of sodium, secretion of potassium, increased water retention, and increased blood pressure. The overall effect of aldosterone is to increase reabsorption of ions and water in the kidney." + "A nucleus of brain that is part of a telencephalon." "TAO:0002178 ZFA:0001660" + "The process in which the anatomical structure of a renal artery is generated and organized. Renal arteries supply the kidneys with blood." + "A gonad with both testicular and ovarian aspects[WP]." "WBbt:0005178 Wikipedia:Ovotestis BTO:0000981 MIAA:0000165 EFO:0000971 MAT:0000165" + "A progenitor cell of the neutrophil lineage." + + "An endothelium that is part of a capillary [Automatically generated definition]." "FMA:62114 EMAPA:36292 BTO:0004954 CALOHA:TS-0112 UMLS:C0006904 MA:0000711 NCIT:C49215" + "The process in which the anatomical structures of the lateral mesoderm are generated and organized." + "Any process that activates or increases the frequency, rate or extent of mesoderm formation." + "Any process that modulates the frequency, rate or extent of tongue muscle cell differentiation." + "OBSOLETE (was not defined before being made obsolete)." + "The process whose specific outcome is the progression of a juxtaglomerulus cell over time, from its formation to the mature structure." + "The volume enclosed within the vacuolar membrane." + "A multi-fate stem cell that is the source of cells for growth of the mammary gland during puberty and gestation. This cell type gives rise to both the luminal and myoepithelial cell types of the gland, and have been shown to have the ability to regenerate the entire organ in mice. This cell type also plays an important role in carcinogenesis of the breast. This cell type is Lin-, CD24-positive, CD29-hi." + "Protein processing that takes place in the vacuole. Most protein processing in the vacuole represents proteolytic cleavage of precursors to form active enzymes." + "Any process that modulates the frequency, rate or extent of gamma-aminobutyric acid catabolic process." + "Any process that activates or increases the frequency, rate or extent of lung alveolus development." + "A thickened portion of ectoderm which serves as the precursor to the lens. SOX2 and Pou2f1 are involved in its development[WP]." "EFO:0003494 Wikipedia:Lens_placode UMLS:C1517770 EMAPA:16672 NCIT:C34202 XAO:0000240 FMA:296767 EHDAA:2908 AAO:0011055 EHDAA2:0000982 ZFA:0000122 VHOG:0000166 TAO:0000122" + "Any immunological memory process that can contribute to the formation of immunological memory." + "A gamma-delta intraepithelial T cell that has the phenotype CD4-negative and CD8-negative." + "One of the fine terminal elements of the bile duct system, leaving the portal canal, and pursuing a course at the periphery of a lobule of the liver[BTO]. the excretory ducts of the liver that connect the interlobular ductules to the right or left hepatic duct[MP]." "EMAPA:37440 ZFA:0005164 BTO:0002840 TAO:0005164" + "Any process that activates or increases the frequency, rate or extent of CD8-positive, alpha-beta T cell proliferation." + "A zone of skin that is part of a hindlimb stylopod [Automatically generated definition]." "MA:0000686 EMAPA:18159 SCTID:181547006 FMA:37790" + "A zone of skin that is part of a forelimb [Automatically generated definition]." "MA:0000617 FMA:23101 NCIT:C12296 SCTID:244130001 UMLS:C0222212 EMAPA:32612" + "The series of events in which a chemical stimulus is received and converted into a molecular signal as part of sensory perception." + "The chemical reactions and pathways involving bile acids, a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine." + "The process whose specific outcome is the progression of a dentin-containing tooth over time, from its formation to the mature structure. A dentin-containing tooth is a hard, bony organ borne on the jaw or other bone of a vertebrate, and is composed mainly of dentin, a dense calcified substance, covered by a layer of enamel." + "Any process that activates or increases the frequency, rate or extent of microtubule depolymerization." + "The main part of the hair which is composed of trichocytes and is divided into the cortex and medulla." "SCTID:361359004 MA:0000159 NCIT:C33543 BTO:0004672 UMLS:C0221961 EMAPA:36498 FMA:70728" + "Any process that modulates the frequency, rate or extent of cardiocyte differentiation." + "Any process that activates or increases the frequency, rate or extent of oocyte maturation." + "A limb bud that develops into a forelimb or pectoral fin." "VHOG:0001754 TAO:0000141 EFO:0003430 ZFA:0000141 VHOG_RETIRED:0001259" + "Any process that increases the occurrence or rate of mesenchymal stem cell death by apoptotic process that contributes to the shaping of the nephron in the mesonephros." + "Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mesenchyme." "EMAPA:16130" + "An endoderm that is part of a anal region." "EHDAA2:0004020 EMAPA:17177" + "The alteration of an amino acid residue in a peptide." + "The process whose specific outcome is the progression of an olfactory bulb tufted cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell." + "Mesenchyme that is part of a developing hindlimb [Automatically generated definition]." "EMAPA:32637 VHOG:0001074" + "A thrombomodulin that is encoded in the genome of mouse." "UniProtKB:P15306" + "Any process that activates, maintains or increases the frequency, rate or extent of ascospore formation, a process in which a sexual spore, named ascospore, from Ascomycete fungi was produced inside an ascus." + "Any process that regulates translation occurring at the postsynapse." + "A skeleton of pelvic girdle that is part of a left pelvic girdle region." "FMA:87594" + "The paired dorsal prominences formed by bifurcation of the first pharyngeal arches in the embryo that unite with the ipsilateral medial nasal process to form the upper jaw." "SCTID:346355001 Wikipedia:Maxillary_prominence EMAPA:17359 EHDAA:5877 EHDAA2:0001070 UMLS:C1513037 NCIT:C34206 FMA:293049" + "A protein that is a translation product of the human LTF gene or a 1:1 ortholog thereof." + "A lymphatic endothelial cell located in the subcapsular sinus ceiling of a lymph node. In human, it's characterized by a unique marker expression (NT5e+ and Caveolin-1+)." + "Any process that stops, prevents, or reduces the frequency, rate or extent of cyanophore differentiation." + "Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species." "MA:0000001 TAO:0100000 AAO:0010841 HAO:0000000 ZFA:0100000 FMA:62955 WBbt:0000100 UMLS:C1515976 TGMA:0001822 BFO:0000004 BILA:0000000 AEO:0000000 NCIT:C12219 XAO:0000000 EHDAA2:0002229 CARO:0000000 BIRNLEX:6" + "The progression of the cardiac skeleton over time, from its formation to the mature structure. The cardiac skeleton is a specialized extracellular matrix that separates the atria from the ventricles and provides physical support for the heart." + "The developmental process pertaining to the initial formation of a pronephric nephron tubule from unspecified parts. A pronephric nephron tubule is an epithelial tube that is part of a nephron in the pronephros." + "Any of the veins that parallel the arcuate arteries, receive blood from the interlobular veins and straight venules, and terminate in the interlobar veins." "FMA:321527 FMA:272193 Wikipedia:Arcuate_vein EMAPA:28221 MA:0002593" + "The progression of the trachea submucosa over time from its formation to the mature structure. The trachea submucosa is made up of the glands and elastic tissue that lie under the mucosa in the trachea." + "A region of the fetal urogenital sinus epithelium destined to become the prostate[GO]." "EMAPA:36141" + "Enables the transmembrane transfer of a solute by a channel that opens in response to a specific stimulus." + "An organ subunit that is part of a hindbrain [Automatically generated definition]." "FMA:61998" + "The directed movement of catecholamine into a cell." + "The process in which the anatomical structures of the axial mesoderm are generated and organized." + "Any process that decreases the rate, frequency, or extent the controlled release of molecules that form the extracellular matrix, including carbohydrates and glycoproteins by a cell or a group of cells." + "The glandular epithelium that lines the endocervix." "NCIT:C96180 SCTID:362256006" + "Any process that stops, prevents, or reduces the frequency, rate or extent of bone resorption." + "Any process that activates or increases the rate or extent of resting T cell proliferation." + "The part of the pancreas that is part of the exocrine system and which produces and store zymogens of digestive enzymes, such as chymotrypsinogen and trypsinogen in the acinar cells [GO]." "TAO:0001249 MA:0002415 Wikipedia:Exocrine_component_of_pancreas UMLS:C0553695 FMA:16017 BTO:0000434 SCTID:248202004 EMAPA:35328 CALOHA:TS-1241 NCIT:C32546 AAO:0010407 ZFA:0001249 XAO:0000137 VHOG:0000048 EV:0100093" + "The process in which a relatively unspecialized cell acquires specialized features of a neuron." + "An adipocyte with light coloration and few mitochondria. It contains a scant ring of cytoplasm surrounding a single large lipid droplet or vacuole." "CALOHA:TS-1119 FMA:83434" + "A pro-T cell that has the phenotype CD4-negative, CD8-negative, CD44-positive, and CD25-negative." + "A forkhead box protein P3 that is encoded in the genome of mouse." "UniProtKB:Q99JB6" + "A thoracic vertebra endochondral element that is composed primarily of a bone tissue." "NCIT:C12798 FMA:9139 SCTID:181821009 MESH:D013904 Wikipedia:Thoracic_vertebrae MA:0000314 GAID:244 EMAPA:18011 UMLS:C0039987" + "An endothelial cell of the umbilical vein." "BTO:0004296" + "The portion of a kidney consisting of a renal medullary pyramid and the renal cortex above it[MP]. It is composed of many renal lobules[WP]." "NCIT:C32894 Wikipedia:Renal_lobe FMA:17881 UMLS:C0736382" + + "Any process that stops, prevents, or reduces the frequency, rate or extent of axonogenesis." + "Any cellular protein catabolic process that takes place in a lysosome." + "A B7-related protein that is a translation product of the human CD80 gene or a 1:1 ortholog thereof." "IUPHARobj:2744" + "Any endothelial cell of lymphatic vessel that is part of a dermis." + "An epithelial cell that is part of the external acoustic meatus." "FMA:70555" + "A macrophage scavenger receptor types I and II that is encoded in the genome of mouse." "UniProtKB:P30204" + "A stage defined by complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm." "FBdv:00005317 BilaDO:0000008 XAO:1000005 EFO:0001296 HsapDv:0000010 BILS:0000109 WBls:0000010 OGES:000019 MmusDv:0000013 ZFS:0000047 OGES:000004" + "The axillary nerve is a nerve of the human body, that comes off the posterior cord of the brachial plexus at the level of the axilla (armpit) and carries nerve fibers from C5 and C6. The axillary nerve travels through the quadrangular space with the posterior circumflex humeral artery and vein. [WP,unvetted]." "EMAPA:18802 MA:0001166 SCTID:181009006 FMA:37072 UMLS:C0228885 NCIT:C52817 Wikipedia:Axillary_nerve" + "Any process that decreases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites)." + "A radiation reflective quality inhering in a bearer by virtue of the ratio of the energy of a wave reflected from its surface to the energy possessed by the wave striking the bearer's surface." + "Any process involved in the carrying out of an immune response by an eosinophil." + "The regulated exocytosis of secretory granules containing preformed mediators such as major basic protein, eosinophil peroxidase, and eosinophil cationic protein by an eosinophil." + "The metanephric comma-shaped body is the precursor structure to the metanephric S-shaped body that contributes to the morphogenesis of a nephron in the metanephros[GO]." + "An iroquois-class homeodomain protein IRX-6 that is encoded in the genome of human." "UniProtKB:P78412" + "A cell found in an organism or derived from an organism exhibiting a phenotype that deviates from the expected phenotype of any native cell type of that organism. Abnormal cells are typically found in disease states or disease models." "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12913" + "The regulated release of vasopressin from secretory granules into the blood." + "A bone that is part of a neck [Automatically generated definition]." "EMAPA:37246 MA:0000584" + "An endothelium that is part of a venous system [Automatically generated definition]." "UMLS:C1710626 NCIT:C49320 MA:0000714 EMAPA:35907" + "Any process that modulates the frequency, rate or extent of lymphoid progenitor cell differentiation." + "A megakaryocyte progenitor cell that is CD34-negative, CD41-positive and CD42-positive." + "A dispersed and relatively uncompacted form of chromatin that is in a transcription-competent conformation." "Wikipedia:Euchromatin NIF_Subcellular:sao445485807" + "Any process that modulates the frequency, rate or extent of hematopoietic stem cell differentiation." + "A macrophage resident in the peritoneum under non-inflammatory conditions. Markers include F4/80-high, CD11b-high, CD68-positive, SIGNR1-positive, CD115-high, MHC-II-negative, and Dectin-1-positive." "FMA:83025 BTO:0001034" + "The chemical reactions and pathways involving organonitrogen compound." + "The process in which neuroepithelial cells of the neural tube give rise to radial glial cells, specialized bipotential progenitors cells of the brain. Differentiation includes the processes involved in commitment of a cell to a specific fate." + "Any process that stops, prevents, or reduces the frequency, rate or extent of blood vessel endothelial cell differentiation." + "A nerve cell where transmission is mediated by nitric oxide." "FMA:84792" + "Binding to a carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates." + "The process whose specific outcome is the progression of the female genitalia over time, from formation to the mature structure." + "An acinus that is part of a sebaceous gland." "FMA:59657" + "Any process that increases the rate or frequency of epithelial cell proliferation that results in the lung attaining its shape." + "A B cell found in the perisinusoidal area of a lymph node. In humans, monocytoid B cells are a morphologically distinct B cell population\n(oval nuclei, abundant cytoplasm, monocyte-like appearance), share many similarities with marginal zone B cells including marker expression, and are increased in disease settings." + "A protein with core architecture consisting of asignal sequence, 5 Ig-like domains, followed by a transmembrane sequence, followed by a Protein tyrosine kinase domain (Pfam:PF07714). However, only 1-3 of the Ig domains are detected by the Pfam HMMs in most of the sequences. Pfam:PF00047 is most common, but other members of the Ig domain clan, Pfam:PF07679 and Pfam:PF07686 can be identified instead. The fourth Ig domain lacks the disulfide-bonded cysteines." "PIRSF:PIRSF000615" + "An interleukin-2 receptor subunit alpha that is encoded in the genome of mouse." "UniProtKB:P01590" + "Any process that modulates the frequency, rate or extent of smooth muscle cell migration." + "A flattened stroma cell forming a sheath or theca outside the basal lamina lining the mature ovarian follicle. Thecal interstitial or stromal cells are steroidogenic, and produce primarily androgens which serve as precusors of estrogens in the granulosa cells." "BTO:0002850" + "An ectoderm that is part of a medial nasal prominence [Automatically generated definition]." "EHDAA2:0001078 FMA:312675 EMAPA:16809 VHOG:0000803" + "A Paneth cell that is part of the epithelium proper of small intestine." "FMA:263106" + "Any process that activates or increases the frequency, rate or extent of apoptotic signaling pathway." + "An anatomical cavity that is part of a esophagus." "EMAPA:18380 SCTID:322648002 FMA:9398" + "The process in which the thalamus changes over time, from its initial formation to its mature state." + "The process in which the population of cells that make up an epithelium undergo directed movement." + "A plexus of nerves situated at the base of the heart that innervate the heart." "FMA:6628 SCTID:280511002 NCIT:C52833 EMAPA:37460 MA:0001138 Wikipedia:Cardiac_plexus UMLS:C0459528" + "FMA:260712" + "A cell that is part of an interstitial compartment of a renal cortex." "KUPO:0001091" + "A hemoglobin subunit that is a translation product of the human HBZ gene or a 1:1 ortholog thereof." + "GC_ID:1" + "The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes." + + "The movement of a cell within a rhombomere. This process is known to occur as an early step in the generation of anatomical structure from a rhombomere." + "An immature astrocyte." + "An immune response which is associated with resistance to extracellular organisms such as helminths and pathological conditions such as allergy, which is orchestrated by the production of particular cytokines, most notably IL-4, IL-5, IL-10, and IL-13, by any of a variety of cell types including T-helper 2 cells, eosinophils, basophils, mast cells, and nuocytes, resulting in enhanced production of certain antibody isotypes and other effects." + "An OFF bipolar cell that is fovea-specific and expresses FEZF1, NXPH1 and NXPH2." + "A splenic macrophage found in the white pulp of the spleen. Markers include F4/80-negative, CD68-positive, and macrosialin-positive." + "The process whose specific outcome is the progression of a neuron whose cell body is located in the central nervous system, from initial commitment of the cell to a neuronal fate, to the fully functional differentiated neuron." + "EMAPA:37767 NCIT:C33781 UMLS:C0229575 FMA:55513 SCTID:176859009 MA:0002675" + "Binding to a CCR2 chemokine receptor." + "A mechanoreceptor in the organ of Corti. In mammals the outer hair cells are arranged in three rows which are further from the modiolus than the single row of inner hair cells. The motile properties of the outer hair cells may contribute actively to tuning the sensitivity and frequency selectivity of the cochlea." "FMA:62366 BTO:0003666" + "The chemical reactions and pathways resulting in the breakdown of a protein at a synapse." + "Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system." "BILS:0000110 XAO:1000006 HsapDv:0000012 MmusDv:0000017 BilaDO:0000009" + "A milk-producing glandular epithelial cell that is part of a mammary gland alveolus and differentiates from a luminal adaptive secretory precursor cell during secretory differentiation (also termed lactogenesis I). Following secretory activation (also termed lactogenesis II), a lactocyte is involved in the synthesis and/or transport of milk constituents including proteins, oligosaccharides, lactose, micronutrients, fat, hormones, immunoglobulins, and cytokines into the lumen of the lactating mammary gland." "FMA:79866 FMA:74506" + "A fibroblast of skin." "CALOHA:TS-0935 BTO:0001255" + "Any process that activates or increases the frequency, rate or extent of male gonad development." + "A lymphatic vessel that is part of a face [Automatically generated definition]." "TAO:0005108 ZFA:0005108 FMA:233946" + "An epithelial cell that is part of the conjunctiva." "FMA:70552" + "An epithelium that is part of a penis [Automatically generated definition]." "EHDAA2:0004039 EMAPA:35674 MA:0001742" + "A lamina propria that is part of a respiratory airway." "EMAPA:35877 MA:0001858 NCIT:C49305 FMA:265157 UMLS:C1710457" + "A protein that is a translation product of the human IGLL1 gene or a 1:1 ortholog thereof." + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures." + "The migration of individual cells within the blastocyst to help establish the multi-layered body plan of the organism (gastrulation). For example, the migration of cells from the surface to the interior of the embryo (ingression)." + "The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult)." + "Any process that modulates the frequency, rate or extent of androgen secretion." + "A neurectoderm derived cell that lines the neural lumen." "FMA:70550 BTO:0001724" + "Endocardium that is part of the right atrium." "EHDAA2:0000274 NCIT:C102339 VHOG:0001228 SCTID:3194006 FMA:7281" + "Any process that activates or increases the frequency, rate or extent of gluconeogenesis." + "A mesodermal cell that is part of the splanchnic layer of lateral plate mesoderm." + "That part of the spine comprising the thoracic vertebrae." "EHDAA:5063 SCTID:243931006 EMAPA:17396 MA:0003155 NCIT:C69315 UMLS:C0581269 BTO:0004150 FMA:9140" + "Any process that stops, prevents or reduces the frequency, rate or extent of tongue muscle cell differentiation." + "The directed movement of organelles or molecules along microtubules from the cell periphery toward the cell body in nerve cell axons." + "Any process that activates or increases the frequency, rate or extent of oxygen metabolic process." + "An endothelium that is part of an arteriole [Automatically generated definition]." "UMLS:C1179024 EMAPA:36286 MA:0000705 FMA:62115 NCIT:C49192" + "A ploidy quality inhering in a bearer by virtue of the bearer's containing an integral multiple of the monoploid number, possibly excluding the sex-determining chromosomes." + "The expansion of a B cell population by cell division following B cell activation during an immune response." + "The urethra is a renal system organ that carries urine from the bladder to outside the body. The epithelium is the tubular, planar layer of cells through which the urine passes.." "UMLS:C1710584 EMAPA:31518 MA:0001686 FMA:85275 NCIT:C49309" + "The pectoralis major is a thick, fan-shaped muscle, situated at the upper front of the chest wall. It makes up the bulk of the chest muscles in the male and lies under the breast in the female. Underneath the pectoralis major is the pectoralis minor, a thin, triangular muscle. [WP,unvetted]." "NCIT:C33284 EMAPA:18179 SCTID:181624003 UMLS:C0585574 VHOG:0000895 EHDAA:8311 MA:0002354 EHDAA2:0001424 FMA:9627 Wikipedia:Pectoralis_major_muscle" + "Any muscle organ that is part of an nose." "SCTID:244730009 FMA:73758 UMLS:C0224219 NCIT:C33158" + "A humerus bone or its cartilage or pre-cartilage precursor." + "Any process that stops, prevents, or reduces the frequency, rate or extent of hair follicle development." + "Any process that modulates the frequency, rate or extent of ossification, the formation of bone or of a bony substance or the conversion of fibrous tissue or of cartilage into bone or a bony substance." + "A subdivision of the autopod consisting of manual digit plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis." + "Any muscle organ that is part of a forelimb stylopod (upper arm)[Automatically generated definition]." "EMAPA:19107 FMA:37370 MA:0000606 SCTID:244979005" + "A process that is part of the mitotic cell cycle." + "A prolactin that is encoded in the genome of mouse." "UniProtKB:P06879" + "A holocrine gland that secretes sebum into the hair follicles, or in hairless areas into ducts.[MP]." "EV:0100161 NCIT:C33519 Wikipedia:Sebaceous_gland BTO:0001980 CALOHA:TS-2384 VHOG:0001468 UMLS:C0036505 MESH:D012627 MA:0002565 GAID:900 FMA:59160 EMAPA:35754 SCTID:361697005" + "Binding to an intermediate filament, a distinct elongated structure, characteristically 10 nm in diameter, that occurs in the cytoplasm of higher eukaryotic cells. Intermediate filaments form a fibrous system, composed of chemically heterogeneous subunits and involved in mechanically integrating the various components of the cytoplasmic space." + "A hillock cell that is located in respiratory epithelium. In some mammalian species, this cell type has been noted to express KRT13 and KRT4 and is postulated to play a role in squamous barrier function and immunomodulation." + + "A sphincter muscle that is part of the gastrointestinal system." "NCIT:C32669 UMLS:C1517464" + "A neuroepithelial cells that occurs singly or in small groups, close to the outer follicular borders but within the follicular basement membrane of the thyroid. Expresses a form of the neural cell adhesion molecule (N-CAM) on their surface. Secretes calcitonin, 5-hydroxytryptamine and dopamine." "SCTID:176770005 FMA:68653" + "Any process that modulates the frequency, rate or extent of the directed movement of substances within cells." + "The chemical reactions and pathways resulting in the formation of organic hydroxy compound." + "Gonochoristic organism that can produce female gametes." "TAO:0000303 CARO:0000028 AAO:0010030 BILA:0000028 XAO:0003005 TGMA:0001839 HAO:0000028 SCTID:362608006 FMA:67812 ZFA:0000303" + "Simple columnar epithelium that constitutes the secretory part of a gland. Examples: epithelium of stomach, luminal epithelium of lactiferous duct.[FMA]." "NCIT:C13182 UMLS:C0225337 FMA:64800" + "Any process that modulates the frequency, rate or extent of leukocyte differentiation." + + "An adult endothelial progenitor cell that is resident of adult vasculature and capable of differentiating to regenerate endothelial cell populations. Endothelial colony forming cells are characterised in vivo by clonal proliferative status, de novo vessel formation, homing to ischemic sites and paracrine support of angiogenesis. These cells are phenotypically similar to endothelial cells." + "A neuron that is responsible for sensation in the face or motor functions such as biting and chewing. Trigeminal neurons extend a single axon shaft along the lateral white matter of the hindbrain and spinal cord. The highly branched axons innervate the integument of the head." + "A monolayer of specialized, flattened, mitochondria-rich cells that lines the posterior surface of the cornea and faces the anterior chamber of the eye[WP]." "UMLS:C0014259 NCIT:C12707 SCTID:368827009 ZFA:0001687 FMA:63882 MA:0001242 EMAPA:35935 GAID:891 TAO:0002186 Wikipedia:Corneal_endothelium MESH:D004728 CALOHA:TS-0172" + "Any process that modulates the frequency, rate or extent of ATP biosynthetic process." + "The chemical reactions and pathways resulting in the breakdown of any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom." + + "Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of substances." + "Muscle contraction of cardiac muscle tissue." + "The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds." "UMLS:C0814992 SCTID:361463007 Wikipedia:Neural_groove neuronames:1363 AAO:0011071 FMA:295624 EMAPA:35594 NCIT:C34224 XAO:0000248" + "Blood vessels of the layer of the placenta where embryonic and maternal blood vessels interdigitate." + "A rod-like cell in the inner ear, having their heads joined and their bases on the basilar membrane widely separated so as to form a spiral tunnel known as the tunnel of Corti." "FMA:75722" + "A glutamatergic neuron, with a soma found in the deeper portion of L5, that has long-range axonal projections including deep subcortical targets outside of the telencephalon and, in some cases, the spinal cord. While the L5 ET neuron projections are not limited to ET targets, they are clearly differentiated from the neuron subclasses whose projections are constrained to intratelencephalic (IT) targets. L5 ET neurons are generally the largest excitatory cortical neurons, typically having a thick apical dendrite with a prominent dendritic tuft in layer 1 and displaying burst-firing physiological characteristics." + "A receptor-type tyrosine-protein phosphatase C isoform CD45RABC that is encoded in the genome of human." "UniProtKB:P08575-3" + "The elimination of substances from peritubular capillaries (or surrounding hemolymph in invertebrates) into the renal tubules to be incorporated subsequently into the urine. Substances that are secreted include organic anions, ammonia, potassium and drugs." + "Any process that stops, prevents or reduces the frequency, rate or extent of male germ cell proliferation." + "Any hollow cylindrical anatomical structure containing a lumen through which substances are transported." "galen:Tube" + "The bone at the lower, posterior part of the skull." "MESH:D009777 EMAPA:25112 SCTID:181796003 GAID:227 Wikipedia:Occipital_bone MA:0001468 UMLS:C0028784 NCIT:C12757 FMA:52735" + "The process in which a relatively unspecialized cell acquires specialized features of a hippocampal interneuron." + "A respiratory stem cell found at the junction of the terminal (conductive) bronchiole and the respiratory bronchiole. This cell types gives rise to alveolar cell types and club cells in response to lung injury. This cell type expresses markers Scgb1a1 and Sftpc." + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein at the synapse." + "A protein that is a translation product of the human AXL gene or a 1:1 ortholog thereof." "IUPHARobj:1835" + + "The progression of the myotome over time, from its formation to the mature structure. The myotome is the portion of the somite that will give rise to muscle." + "A structure that lies outside the plasma membrane and surrounds the entire cell or cells. This does not include the periplasmic space." + "Intercalated cell that is part of some outer medullary collecting duct. It is known in some mammalian species that this cell may contribute in the maintenance of acid/base homeostasis." "KUPO:0001133" + "The directed movement of a lipid from a cell, into the extracellular region." + "Any process that activates, maintains or increases the frequency, rate or extent of the formation of cellular spores derived from the products of meiosis." + "A CD4 molecule that is encoded in the genome of mouse." "UniProtKB:P06332" + "An supramolecular fiber that consists of an insoluble core of polymerized tropoelastin monomers and a surrounding mantle of microfibrils. Elastic fibers provide elasticity and recoiling to tissues and organs, and maintain structural integrity against mechanical strain." + "The orderly movement of epithelial cells within a renal tubule that contributes to metanephric distal tubule morphogenesis." + "Any process that stops, prevents or reduces the frequency, rate or extent of ectoderm development." + "EHDAA2:0002120" + "A mono-stratified retinal ganglion cell that has a medium dendritic field and a sparse dendritic arbor with post sympatic terminals in sublaminar layer S4 and S5." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of muscle hypertrophy." + "The chemical reactions and pathways resulting in the breakdown of juvenile hormones, the three sesquiterpenoid derivatives that function to maintain the larval state of insects at molting and that may be required for other processes, e.g. oogenesis." + + "The pronucleus originating from the spermatozoa that was involved in fertilization." + + "Vasculature that is part of the eye region." "SCTID:123846009 FMA:74743 TAO:0007057 ZFA:0007057" + "A CCAAT/enhancer-binding protein alpha that is encoded in the genome of human." "UniProtKB:P49715 Reactome:R-HSA-381289" + "Any process that stops, prevents, or reduces the frequency, rate or extent of photoreceptor cell differentiation. An example of this process is found in Drosophila melanogaster." + "Any process that modulates the frequency, rate, or extent of myeloid dendritic cell antigen processing and presentation." + "The chemical reactions and pathways resulting in the formation of glucocorticoids, hormonal C21 corticosteroids synthesized from cholesterol." + "The process whose specific outcome is the progression of the cranial nerves over time, from its formation to the mature structure. The cranial nerves are composed of twelve pairs of nerves that emanate from the nervous tissue of the hindbrain. These nerves are sensory, motor, or mixed in nature, and provide the motor and general sensory innervation of the head, neck and viscera. They mediate vision, hearing, olfaction and taste and carry the parasympathetic innervation of the autonomic ganglia that control visceral functions." + "A protein that is a translation product of the human BST2 gene or a 1:1 ortholog thereof." "PIRSF:PIRSF023920" + "A tumor necrosis factor receptor superfamily member 11A that is encoded in the genome of human." "UniProtKB:Q9Y6Q6" + "A precursor of the central nervous system that gives rise to both neurons and glial cells." "FBbt:00005147" + + "Any apoptotic process in a cholangiocyte." + "An artery that supplies blood to the upper urinary bladder." "EMAPA:37123 FMA:18839 NCIT:C52686 MA:0002080 SCTID:113268007 Wikipedia:Superior_vesical_artery UMLS:C0226376" + "An anatomical structure that develops from the neural crest." + "A C-C chemokine receptor type 5 that is encoded in the genome of human." "UniProtKB:P51681 DTO:02100057 Reactome:R-HSA-171279" + "Odontogenic tissue that is avascular non-mineralized matrix that is deposited by preameloblast and ameloblasts that are excluded from the matrix." "VSAO:0000066 XAO:0004202" + "Any of the nuclei of the cochlear nuclear complex." "SCTID:362463009 MA:0001012 Wikipedia:Cochlear_nucleus FMA:54603 EMAPA:35248 ZFA:0001638 GAID:601 TAO:0002243 MESH:D017626 NCIT:C12837" + "KUPO:0001123" + "Any neuromast mantle cell that is part of an anterior lateral line." + "An OFF-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the outer half of the inner plexiform layer. The cell body of these cells is in the middle of the inner plexiform layer. The dendritic tree is stout and the axon terminates in sublamina 1. The axonal terminal is wide and has only a few varicosities." + "Any process that activates or increases the frequency, rate or extent of muscle hypertrophy." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of B cell anergy." + "The process in which the anatomical structure of cardiac atrium muscle is generated and organized." + "A protein that is a translation product of the human IL3RA gene or a 1:1 ortholog thereof." "IUPHARobj:1705" + "Enables the transfer of basic amino acids from one side of a membrane to the other. Basic amino acids have side chains with a positive charge at pH 7.3." "Reactome:R-HSA-8932851 Reactome:R-HSA-8959781" + "Subcortical brain region consisting of paired gray matter bodies in the dorsal diencephalon and forming part of the lateral wall of the third ventricle of the brain. The thalamus represents the major portion of the diencephalon and is commonly divided into cellular aggregates known as nuclear groups.(MeSH). The dorsal topographic division of the interbrain. The macrodissected adult human thalamus was clearly illustrated by Vesalius in 1543 and the term as defined here was introduced by His in 1893. It includes the traditional epithalamus, dorsal thalamus, and ventral thalamus of Herrick (1910, pp. 494, 498). Also see Kuhlenbeck (1927, Ch. 9) and Jones (1985, p. 87)." "DHBA:10390 PBA:128013014 DMBA:16376 CALOHA:TS-1031 VHOG:0000657 BAMS:TH Wikipedia:Thalamus ZFA:0001215 galen:Thalamus MA:0000179 BAMS:Th AAO:0010483 EV:0100195 EFO:0000910 NCIT:C12459 TAO:0001215 BTO:0001365 MIAA:0000109 UMLS:C0039729 HBA:4392 GAID:656 MBA:549 BIRNLEX:954 MAT:0000109 SCTID:244433007 EMAPA:17540 neuronames:300" + "Any process that activates or increases the frequency, rate or extent of mineralocorticoid secretion." + "Any process that modulates the frequency, rate, or extent of an immune effector process." + "The developmental process in which a sebaceous gland placode forms. A sebaceous gland placode is a thickening of the ectoderm that will give rise to the sebaceous gland bud." + "A pre-cartilage condensation that has the potential to develop into a clavicle." "EMAPA:18026" + "Any process that activates or increases the frequency, rate or extent of apical ectodermal ridge formation." + "A G4 retinal ganglion cell that has post sympatic terminals in sublaminar layers S2 and S3 and is depolarized by decreased illumination of their receptive field center" + "Any process that decreases the rate, frequency or extent of a phase of elevated metabolic activity, during which oxygen consumption increases made as a defense response ; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals." + "The biological process in which new individuals are produced by one or two single-celled organisms. The new individuals inherit some proportion of their genetic material from the parent or parents." + "A protein that is a translation product of the human BCL6 gene or a 1:1 ortholog thereof." "IUPHARobj:2957" + "Mature CD8_alpha-positive CD11b-negative dendritic cell is a CD8_alpha-positive CD11b-negative dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive." + "Scattered in duodenojejunal mucosa, this enteroendocrine cell secretes secretin and serotonin." "FMA:62936" + "The process in which a relatively unspecialized cell acquires the specialized features of a cyanophore cell. Cyanophores are pigment cells derived from the neural crest. They contain a blue pigment of unknown chemical composition. The pigment is stored in fibrous organelles termed cyanosomes." + "A protein that is a translation product of the human SCGB1A1 gene or a 1:1 ortholog thereof." + "The cavity that is enclosed by the central nervous system. In vertebrates this is the cavity that includes as parts ventricular cavities and the central canal of the spinal cord that develops from the lumen of the neura tube." "BIRNLEX:1029 FMA:75007" + "The placental layers where embryonic blood vessels are surrounded by trophoblast cells and maternal blood." + "Any process that modulates the frequency, rate or extent of pro-T cell differentiation." + "The process in which the branching structure of the salivary gland is generated and organized." + "Any process that activates or increases the frequency, rate or extent of signal transduction." + "The progression of a mesonephric nephron tubule over time, from its initial formation to the mature structure. A mesonephric nephron tubule is an epithelial tube that is part of the mesonephric nephron, the functional part of the mesonephros." + "Any process that activates or increases the frequency, rate, or extent of dendritic cell antigen processing and presentation." + "Any process that modulates the frequency, rate or extent of protein kinase activity." + "A pre-cartilage condensation that has the potential to develop into a fibula." "EHDAA:6196 EHDAA2:0000509" + "The upper portion of the spiral ligament contains numerous capillary loops and small blood vessels, and is termed the stria vascularis. It produces endolymph for the scala media, one of the three fluid-filled compartments of the cochlea. [WP,unvetted]." "EFO:0001644 UMLS:C0229477 CALOHA:TS-0982 GAID:875 EMAPA:35827 BTO:0001819 Wikipedia:Stria_vascularis FMA:77832 BIRNLEX:2525 SCTID:279842002 MESH:D013316 MA:0001198" + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear outer membrane." + + "Binding to a chemokine receptor." + "Any process that modulates the frequency, rate or extent of stem cell differentiation." + "The directed movement of protein-DNA complexes into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "The progression of the mammary gland fat over time, from its formation to the mature structure. The mammary fat is an adipose structure in the gland that is invaded by the mammary ducts." + "The Purkinje cell layer lies just underneath the molecular layer of the cerebellar cortex. It contains the neuronal cell bodies of the Purkinje cells that are arranged side by side in a single layer. Candelabrum interneurons are vertically oriented between the Purkinje cells. Purkinje neurons are inhibitory and provide the output of the cerebellar cortex through axons that project into the white matter. Extensive dendritic trees from the Purkinje cells extend upward in a single plane into the molecular layer where they synapse with parallel fibers of granule cells." "MBA:1145 UMLS:C0228469 neuronames:365 UMLS:C1289475 BTO:0004909 NCIT:C49140 EMAPA:35223 UMLS:C1709776 SCTID:369046001 BIRNLEX:818 MA:0000997 FMA:83896" + "Any process that activates or increases the frequency, rate or extent of atrial cardiac muscle cell action potential." + "Any apoptotic process in a B cell that is mature, having left the bone marrow." + "Any process that activates or increases the frequency, rate or extent of glomerular visceral epithelial cell apoptotic process." + "The process in which a relatively unspecialized cell acquires the specialized features of a glial cell of the heart." + "KUPO:0001120" + "An eyelid connective tissue that is part of a hypodermis." "MA:0001252 EMAPA:37533 FMA:63975 UMLS:C1707991 NCIT:C49226" + "The posterior lateral line system develops from cranial ectodermal placodes, situated behind the ear, that give rise to both the neuromasts and the posterior lateral line sensory nerves that innervate the neuromasts. The posterior lateral line system consists of small sensory patches (neuromasts) located superficially on the skin or just under the skin in fluid-filled canals on the head of all fishes and most amphibians. The neuromasts are innervated by several lateral line nerves, which project primarily to the hindbrain. The posterior mechanosensory lateral line system is stimulated by local water displacements and vibrations, and detects propulsion of the fish through the water, as well as facilitating shoaling, prey capture, and predator and obstacle avoidance." "ZFA:0001471" + "An epithelium that is part of a footplate." "EMAPA:32655 EHDAA:5145 EHDAA:6144 EHDAA2:0000548" + "Subdivision of telencephalon which is one of a number of subdivisions of each hemisphere separated by both real landmarks (sulci and fissures) and arbitrary boundaries[FMA,modified]." "SCTID:272632001 neuronames:1210 BIRNLEX:922 FMA:61823 BTO:0000445" + "Any process that modulates the frequency, rate or extent of T cell proliferation." + "EHDAA2:0001020" + "An adhesion G protein-coupled receptor E1 that is encoded in the genome of mouse." "UniProtKB:Q61549" + "The process whose specific outcome is the progression of the metanephric capsule over time, from its formation to the mature structure. The metanephric capsule is the tough fibrous layer surrounding the metanephros, covered in a thick layer of perinephric adipose tissue. It provides some protection from trauma and damage." + "Any process that modulates the frequency, rate, or extent of antigen processing and presentation of peptide antigen via MHC class II." + "At the macula densa, the thick ascending limb connects to the distal convoluted tubule[GO]." + "A M cell that is part of the epithelium of intestinal villus." "FMA:263130" + "A potential space between the visceral and parietal layers of the pericardium." "FMA:11350 BSA:0000091 Wikipedia:Pericardial_cavity MA:0000053 EMAPA:16132 EHDAA2:0001434 SCTID:362027001 UMLS:C0225972 NCIT:C38662 EMAPA:16131 TAO:0002220 VHOG:0000556 ZFA:0001655 galen:PericardialSpace" + "A mucosa that is part of a female urethra [Automatically generated definition]." "FMA:239940" + "The process in which a highly ordered sequence of patterning events generates the branched epithelial tubes of the lung, consisting of reiterated combinations of bud outgrowth, elongation, and dichotomous subdivision of terminal units." + "A lineage-negative, Kit-positive, CD45-positive mast cell progenitor that is Fc-epsilon RIalpha-low." + "A T-cell surface glycoprotein CD8 beta chain isoform 1, signal peptide removed form that includes at least one glycosylated residue." + "A minute orifice on the summit of the papillae lacrimales, which is the commencement point of the lacrimal canaliculi." "SCTID:263344003 FMA:59365 Wikipedia:Lacrimal_punctum" + "Any process that stops, prevents or reduces the frequency, rate or extent of compound eye retinal cell apoptotic process." + "Any process that modulates the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure." + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of glucocorticoids." + "Any process that activates or increases the frequency, rate or extent of endothelial cell development." + "The inner cell layer of the mammary epithelium bilayer that lines the luminal surface of mammary gland ducts and alveoli; luminal cells have only limited contact with the underlying basement membrane and surrounding connective tissue; they are secretory epithelial cells characterized by the expression of the receptors for systemic hormones, i.e. estrogens, progesterone and prolactin." "EMAPA:37902 FMA:74458" + "A continuation of the pharynx that is involved in breathing, sound production, and protecting the trachea against food aspiration." "MAT:0000187 BTO:0001208 NCIT:C12420 FMA:55097 MESH:D007830 Wikipedia:Larynx SCTID:181212004 MA:0000414 CALOHA:TS-0532 UMLS:C0023078 EHDAA2:0004063 galen:Larynx AAO:0000268 XAO:0003081 EV:0100039 EMAPA:18333 VHOG:0001279 GAID:108 EFO:0000838 MIAA:0000187" + "Any process that modulates the frequency, rate or extent of progesterone secretion." + "The directed movement of L-glutamate from outside of a cell, across the plasma membrane and into the cytosol." + + "A preadipocyte that is part of visceral tissue." + + "GC_ID:1" + "Subdivision of skull that consists of the facial bones." "EHDAA2:0002206 Wikipedia:Facial_skeleton FMA:53673 EHDAA:8361 EMAPA:18022 MA:0000318" + "An endothelial cell found in the centrilobular region hepatic sinusoid, near the central vein. The fenestrae of these cells are smaller but more numerous compared with those of endothelial cells near the periportal region of the hepatic sinusoid." "EFO:0010706" + "Any process that mediates the transfer of information from one cell to another and contributes to the progression of the metanephros over time, from its formation to the mature organ." + "An epithelium that is part of an eyelid [Automatically generated definition]." "EMAPA:32758 MA:0003163" + "A myoepithelial cell that is part of a submucosal gland of the trachea." + "Any transmitter-gated ion channel activity that is involved in regulation of postsynaptic membrane potential." + "A vein that is part of a vertebral column." "FMA:76735 SCTID:181376008 EMAPA:18255 MA:0002108 Wikipedia:Spinal_veins" + "Any process that modulates the frequency, rate or extent of lipid binding." + "A stem cell from which all cells of the lymphoid and myeloid lineages develop, including blood cells and cells of the immune system. Hematopoietic stem cells lack cell markers of effector cells (lin-negative). Lin-negative is defined by lacking one or more of the following cell surface markers: CD2, CD3 epsilon, CD4, CD5 ,CD8 alpha chain, CD11b, CD14, CD19, CD20, CD56, ly6G, ter119." "CALOHA:TS-0448 VHOG:0001485 BTO:0000725 MESH:D006412 FMA:86475" + "An amacrine cell with a wide dendritic field and post-synaptic terminals in S5. This cell type releases the neurotransmitters gamma-aminobutyric acid (GABA) and serotonin." + "An opening in the skull through which cranial nerve II passes.[MP]." "Wikipedia:Optic_canal EHDAA2:0001312 ZFA:0005428 AAO:0000342 EHDAA:10646 SCTID:361732009 TAO:0002025 FMA:54774 EMAPA:18716 VHOG:0001408" + "A CD7 molecule that is encoded in the genome of human." "UniProtKB:P09564" + "EMAPA:17884" + "Any process that activates or increases the frequency, rate or extent of skeletal muscle cell differentiation." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the formation of a myelin sheath around nerve axons." + "Any process that activates or increases the frequency, rate or extent of myoblast differentiation. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers." + "A specialized pore forming cell of the follicle, located adjacent to the animal pole of the oocyte. The micropylar cell makes the single micropyle (pore) through the chorion through which the sperm fertilizes the egg." + "Any process that increases the frequency, rate or extent of the regulated release of growth hormone from a cell." + "A bistratified amacrine cell with a medium dendritic field and post-synaptic terminals in S1-S2, and S4." + "A protein that is a translation product of the human A4GALT gene or a 1:1 ortholog thereof." + "The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell. Examples of this process are found in Mus musculus and Drosophila melanogaster." "Wikipedia:Oogenesis" + "FMA:76992 PBA:128013091" + "Any cellular process that depends upon or alters the intermediate filament cytoskeleton, that part of the cytoskeleton comprising intermediate filaments and their associated proteins." + "FMA:70471" + "A Vgamma1.1-positive, Vdelta6.3-negative thymocyte that is CD24-positive." + "A G protein-coupled acetylcholine receptor signaling pathway, which contributes to a circulatory system process carried out by the heart." + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances." + "The process in which the iris is generated and organized. The iris is an anatomical structure in the eye whose opening forms the pupil. The iris is responsible for controlling the diameter and size of the pupil and the amount of light reaching the retina." + "A D(1)-like dopamine receptor that is a translation product of the human DRD1 gene or a 1:1 ortholog thereof." "IUPHARobj:214" + "The vaginal plexuses are placed at the sides of the vagina; they communicate with the uterine, vesical, and hemorrhoidal plexuses, and are drained by the vaginal veins, one on either side, into the hypogastric veins. [WP,unvetted]." "FMA:29713 EMAPA:37801 MA:0002257 Wikipedia:Vaginal_venous_plexus SCTID:294653003" + "A memory B cell that lacks expression of surface IgD." + "The knee joint joins the thigh with the leg and consists of two articulations: one between the femur and tibia, and one between the femur and patella. It is the largest and most complicated joint in the human body. The knee is a mobile trocho-ginglymus (i.e. a pivotal hinge joint), which permits flexion and extension as well as a slight medial and lateral rotation[WP,unvetted]." "NCIT:C32898 galen:KneeJoint Wikipedia:Knee EMAPA:19137 MESH:D007719 VHOG:0001003 MA:0000471 UMLS:C0022745 GAID:114 SCTID:182204005 FMA:35175 EFO:0001957" + "PBA:128013078 DHBA:10431 FMA:76989" + "Any process that modulates the frequency, rate or extent of epidermal cell differentiation." + "A dorsal thalamus that is in_the_right_side_of a diencephalon." "FMA:258714" + "An epithelium that is part of a large intestine [Automatically generated definition]." "CALOHA:TS-2105 EMAPA:35466 MA:0001545 FMA:17301" + "The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell." "Wikipedia:Signal_transduction" + "An alpha-beta memory T cell with the phenotype CD45RA-positive." + "Abdominal part of aorta: the distal part of the descending aorta, which is the continuation of the thoracic part and gives rise to the inferior phrenic, lumbar, median sacral, superior and inferior mesenteric, middle suprarenal, renal, and testicular or ovarian arteries, and celiac trunk[BTO]. The abdominal aorta is the largest artery in the abdominal cavity. As part of the aorta, it is a direct continuation of descending aorta(of the thorax). [WP,unvetted]." "SCTID:244231007 FMA:3789 EMAPA:17856 EFO:0002524 GAID:470 MESH:D001012 galen:AbdominalAorta MA:0000474 UMLS:C0003484 NCIT:C32038 Wikipedia:Abdominal_aorta BTO:0002976" + "The process whose specific outcome is the progression of the olfactory nerve over time, from its formation to the mature structure. The olfactory nerve is a collection of sensory nerve rootlets that extend down from the olfactory bulb to the olfactory mucosa of the upper parts of the nasal cavity. This nerve conducts odor information to the brainstem." + "The process whose specific outcome is the progression of sensory organs over time, from its formation to the mature structure." + "Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic DNA fragmentation." + + "A common myeloid progenitor that is Kit-positive and CD34-positive, Il7ra-negative, and is SCA1-low and Fcgr2-low and Fcgr3-low." + "The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation." + "Vasculature that is composed of the tubule structures that carry blood or lymph in the lungs." + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform amines." + "A lymphoid progenitor cell that is found in bone marrow, gives rise to B cells, T cells, natural killer cells and dendritic cells, and has the phenotype Lin-negative, Kit-positive, Sca-1-positive, FLT3-positive, CD34-positive, CD150 negative, and GlyA-negative." + "The regulated release of histamine by a platelet or group of platelets." + "Combining with gamma-aminobutyric acid (GABA), and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity. (GABA, 4-aminobutyrate) is an amino acid which acts as a neurotransmitter in some organisms." + "An optical quality which obtains by virtue of the ability of the bearer to absorb visible light." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of B cell mediated immunity." + "Any process involved in the maintenance of an internal steady state of glucose within an organism or cell." + "A bodily secretion that is produced by the prostate gland." "UMLS:C1709733 EMAPA:36545 Wikipedia:Prostate#Secretions FMA:66884 MA:0002525 NCIT:C52553" + "Binding to histamine, a physiologically active amine, found in plant and animal tissue and released from mast cells as part of an allergic reaction in humans." + "A spermatid in an early stage of maturation that has a round morphology and is transcriptionally active." + "A mesothelial cell that is part of the parietal pleura." "FMA:86738" + "An artery that supplies deep structures of the face. It comes just out behind the neck of the mandible. [WP,unvetted]." "Wikipedia:Maxillary_artery MESH:D008438 EMAPA:17311 UMLS:C0024949 GAID:498 NCIT:C34205 FMA:49675 MA:0001919 EHDAA2:0001069 EHDAA:7357 SCTID:181326006" + "A type I NK T cell that has the phenotype CD4-negative and CD8-negative." + "Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle contraction." + + "Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces." "ncithesaurus:Transudate MESH:D005122 FMA:12276 GAID:1195" + "Any process that stops, prevents, or reduces the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels." + "Acute angle occurring between the iris and the cornea at the periphery of the anterior chamber of the eye[MP]." "SCTID:244498000 FMA:58577" + "The developmental process pertaining to the initial formation of a metanephric tubule." + "Any process that modulates the frequency, rate or extent of stem cell population maintenance." + "The process whose specific outcome is the progression of the medulla oblongata over time, from its formation to the mature structure. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate." + "The morphogenesis of trophectoderm cells." + + "A portion of connective tissue that is part of a bronchus [Automatically generated definition]." "UMLS:C1707052 NCIT:C49210 EMAPA:32690 MA:0001831 EMAPA:35193" + "An epithelium that is part of a lateral lingual swelling." "FMA:313717 EMAPA:17190 EHDAA2:0000913" + "Embryonic ectoderm that gives rise to nervous tissue." "ZFA:0001120 FMA:87657 BILA:0000039 EHDAA:1498 NCIT:C34228 CALOHA:TS-1212 EHDAA:255 EMAPA:16073 TAO:0001120 XAO:0000042 AAO:0011074 UMLS:C1518271 MAT:0000176 MIAA:0000176 VHOG:0000150 EV:0100004 Wikipedia:Neuroectoderm EHDAA2:0001248" + "Any apoptotic process in a hepatocyte, the main structural component of the liver." + "A cell that is part of some vasa recta descending limb." "KUPO:0001071" + "A mesentery that is part of a caecum." "RETIRED_EHDAA2:0000210" + "Binding to a transcription factor, a protein required to initiate or regulate transcription." + "Any process that stops, prevents, or reduces the frequency, rate or extent of endothelial cell differentiation." + "A photoreceptor cell that detects visible light." + "Any process that activates or increases the frequency, rate or extent of dopamine biosynthetic process." + "The process in which the anatomical structures of a distal tubule are generated and organized. The distal tubule is a nephron tubule that begins at the macula densa and extends to the connecting tubule." + "A cell-cell junction that seals cells together in an epithelium in a way that prevents even small molecules from leaking from one side of the sheet to the other." "Wikipedia:Tight_junction" + "A portion of smooth muscle tissue that is part of an artery [Automatically generated definition]." "MA:0000708 NCIT:C49195 CALOHA:TS-1198 FMA:72024 UMLS:C1706851 EMAPA:36285 BTO:0000087" + "The chemical reactions and pathways involving ATP, adenosine triphosphate, a universally important coenzyme and enzyme regulator." + "A parenchyma that is part of a parathyroid gland [Automatically generated definition]." "FMA:55569 EMAPA:35664 MA:0002677" + "Any muscle organ that is part of a hindlimb stylopod (upper leg)[Automatically generated definition]." "BTO:0001367 SCTID:245013005 EMAPA:19144 MA:0000684 FMA:22470" + "A reelin that is encoded in the genome of mouse." "UniProtKB:Q60841" + "Axons of neurons encased in a lipoproteinaceous material called myelin. (MeSH)." "NCIT:C12627 MESH:D009413 GAID:745 FMA:5915 UMLS:C0027750 SCTID:362296008" + "The process in which a relatively unspecialized cell acquires the specialized features of a trophectoderm cell." + "Any process that modulates synaptic transmission by regulating a catabolic process occurring at a postsynapse." + "A hair follicle matrix region cell which synthesizes keratin and undergoes a characteristic change as it moves upward from the hair bulb to become the hair medulla cortex and hair root sheath." + "Mesenchyme that is part of a developing forelimb [Automatically generated definition]." "VHOG:0001109 EMAPA:32628" + "GC_ID:1" + "A neuron of the raphe nuclei." + "Any process that modulates the frequency, rate or extent of gene expression after the production of an RNA transcript." + "Any process that modulates the frequency, rate or extent of protein localization to cell-cell junction." + "Non neural ectoderm that surrounds the presumptive neural plate and gives rise to neurogenic placodes." "ZFA:0007013" + "A(n) smooth muscle cell that is part of a(n) taenia coli." + "An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen." "SCTID:118760003 BTO:0001491 XAO:0003034 FMA:7085 EHDAA:512 NCIT:C28287 UMLS:C0042779 MA:0000019 Wikipedia:Viscus EMAPA:16245 AAO:0010386 MESH:D014781 RETIRED_EHDAA2:0002201" + "The process whose specific outcome is the progression of an ascending thin limb over time, from its formation to the mature structure. The ascending thin limb is a segment of a nephron tubule lying in the inner medulla that is permeable to ions but not to water and has a simple epithelium; active transepithelial solute transport is absent." + "One of two arteries (anterior and posterior choroidal artery) that supply blood to the choroid plexus, optic tract, hippocampus, globus pallidus, and other various brain regions." "NCIT:C32310 SCTID:244210009 UMLS:C0226164" + "A bone that is part of a chest [Automatically generated definition]." "MA:0000547 EMAPA:18025" + "A homeostatic process involved in the maintenance of a steady state level of a chemical within extracellular body fluids, such as blood, xylem or phloem, of a multicellular organism. This is distinct from maintenance of cellular homeostasis, which occurs within a cell." + "Obsolete. Use PO:0030007 from Plant Ontology instead. The apical cell is the upper cell formed after the first division of a plant zygote." + "Subdivision of skeleton which includes upper and lower jaw skeletons." "galen:Jaw UMLS:C0022359 Wikipedia:Jaw BTO:0001749 NCIT:C48821 AAO:0000988 GAID:214 MESH:D007568 FMA:54396 EMAPA:35455 MA:0001905 TAO:0001227 SCTID:181811001 ZFA:0001227" + "An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region." "EMAPA:37062 MA:0000529" + "A neuron residing in the olfactory bulb that serve to process and refine signals arising from olfactory sensory neurons" + + "Any process that modulates the frequency, rate, or extent of interleukin-1 beta production." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of natural killer cell mediated immunity." + "The directed movement of a hemocyte within the embryo. Hemocytes are blood cells associated with a hemocoel (the cavity containing most of the major organs of the arthropod body) which are involved in defense and clotting of hemolymph, but not involved in transport of oxygen. In Drosophila, embryonic hemocytes originate from the head mesoderm as a cluster of cells. The cluster splits into two and one group of cells crosses the amnioserosa. Both populations then spread toward the middle of the embryo and then disperse evenly throughout the embryo." + "The process in which a relatively unspecialized cell acquires the specialized features of an astrocyte residing in the forebrain. An astrocyte is the most abundant type of glial cell. Astrocytes provide support for neurons and regulate the environment in which they function." + "The chemical reactions and pathways resulting in the breakdown of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." + "The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity." "Wikipedia:Behavior" + "A cell whose function is determined by its response to an electric signal." + "Binding to a microtubule, a filament composed of tubulin monomers." "Reactome:R-HSA-9614343" + "Any process that modulates the frequency, rate or extent of organelle transport along microtubule." + "Any process that activates or increases the frequency, rate or extent of endodermal cell differentiation." + "The multiplication or reproduction of cells that contributes to the shaping of a heart valve." + "An epithelial cell of the esophagus." "FMA:63071" + "Reproductive organ that produces and releases eggs (ovary) or sperm (testis)." "GAID:368 BTO:0000534 ZFA:0000413 VHOG:0000397 XAO:0003146 BSA:0000079 HAO:0000379 MA:0002420 Wikipedia:Gonad BILA:0000123 TAO:0000413 FMA:18250 EMAPA:17383 NCIT:C12725 MESH:D006066 AAO:0000213 SCTID:304623008 UMLS:C0018067 WBbt:0005175" + "The process that gives rise to the vagus nerve. This process pertains to the initial formation of a structure from unspecified parts. This nerve is primarily sensory but also has visceromotor components. It originates in the brain stem and controls many autonomic functions of the heart, lungs, stomach, pharynx, larynx, trachea, esophagus and other gastrointestinal tract components. It controls some motor functions such as speech. The sensory branches mediate sensation from the pharynx, larynx, thorax and abdomen; it also innervates taste buds in the epiglottis." + "A layer of epithelial cells on the surface of the mucosa." "BTO:0003752" + "The process in which the anatomical structures of a tube are generated and organized. Epithelial and endothelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system." + "Any process that modulates the frequency, rate or extent of T-helper 2 cell differentiation." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of epinephrine." + "A B220-low CD38-positive naive B cell is a CD38-positive naive B cell that has the phenotype B220-low, CD38-positive, surface IgD-positive, surface IgM-positive, and CD27-negative, that has not yet been activated by antigen in the periphery." + "Luminal space of the right ventricle of the heart." "FMA:9291 EMAPA:26047" + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins in the postsynaptic actin cytoskeleton." + "The process in which an endocardial cushion cell becomes a cell of a cardiac septum." + "Any process that activates or increases the frequency, rate, or extent of interleukin-8 production." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of gamma-aminobutyric acid." + "An organ system subdivision that is the part of the lymphoid system that excludes the lymphatic vessels.." "FMA:74623" + "The process that mediates interactions between an AV node cell and its surroundings that contributes to the process of the AV node cell communicating with a bundle of His cell in cardiac conduction. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment." + "An endoderm that is part of a pharyngeal arch 2." "RETIRED_EHDAA2:0000065 EMAPA:16278 EHDAA2:0000061 EMAPA:16274 VHOG:0001108 EMAPA:16276" + "Sympathetic cholinergic neuron." + "The early distal convoluted tubule contains DCT cells and is vasopressin-insensitive[GO]." + "One of the branches of the splenic artery[MP]." "UMLS:C1710159 NCIT:C49775 MA:0000759 Wikipedia:Trabecular_arteries" + "A longitudinal groove in the neural tube wall that divides the neural tube into dorsal (alar) and ventral (basal) halves (dorsal receives input from sensory neurons, ventral effects motor functions); stretches from the mesencephalon caudad[TMD]." "BAMS:slim neuronames:629 BAMS:slm" + "Any process that stops, prevents or reduces the frequency, rate or extent of histamine secretion by mast cell." + "A homeostatic process involved in the maintenance of a steady state level of calcium ions within a cell." + "Any cell capable of ingesting particulate matter via phagocytosis." "BTO:0001044 MESH:D010586 FMA:83806" + "The orderly movement of a skeletal muscle satellite cell from one site to another. Migration of these cells is a key step in the process of growth and repair of skeletal muscle cells." + "Any process that increases the rate or extent of the developmental process pertaining to the initial formation of the ureteric bud from the Wolffian duct." + "Any process that activates or increases the frequency, rate or extent of monocyte differentiation." + "An epithelium that is part of a anal canal." "EMAPA:18835 FMA:17511" + "Anatomical entity that has no mass." "EHDAA2:0003007 CARO:0000007 AEO:0000007 HAO:0000007 BILA:0000007 FMA:67112 VHOG:0001727 AAO:0010265 TAO:0001835 TGMA:0001827" + "Any collection of muscles that is part of a hindlimb zeugopod." "FMA:50211" + "The metanephros develops from the most caudal part of the nephrogenic cord that is itself derived from the intermediate plate mesoderm." + "Any process that activates, maintains or increases the rate of a response to an external stimulus." + "The change in morphology and behavior of a mature or immature B cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific." + "A synapse that uses glycine as a neurotransmitter." + "A dermal dendritic cell isolated from skin draining lymph nodes that is langerin-negative, MHC-II-positive, and CD4-negative and CD8a-negative." + "A process in which a protein is transported to, or maintained in, a location within a ciliary membrane." + "One of the primary blood vessel sprouts that originate from the dorsal aorta and posterior cardinal vein and align dorsoventrally at the myotomal boundaries between somites." "XAO:0004075 TAO:0001285 EFO:0003664 ZFA:0001285 EMAPA:37389" + "A horseshoe-shaped thickening of the endoderm at the cranial (rostral) end of the primitive streak formed by the involution of Spemann's organizer cells which, together with the notochord, induces the formation of the neural plate from the overlying ectodermal cells and contributes mesodermal type cells to the surrounding tissue." "VHOG:0000086 EHDAA:181 EHDAA2:0001493 FMA:295532 AAO:0011085 XAO:0000079 ZFA:0000060 TAO:0000060 Wikipedia:Prechordal_plate" + "A presumptive structure that has the potential to develop into a midbrain." "BAMS:MES TAO:0000148 EFO:0003432 EHDAA2:0000615 EMAPA:16140 Wikipedia:Mesencephalon ZFA:0000148" + "The controlled release of proteins from a cell." + "The supporting bundles of muscular fibers lining the walls of the ventricles of the heart." "SCTID:118755002 FMA:7269 EMAPA:18626 Wikipedia:Trabeculae_carneae MA:0002831" + "A long lived plasma cell that secretes IgE." + "A stroma that is part of a pancreas." "FMA:63121" + "The formation of spores derived from the products of meiosis. A cellular spore is a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction." + "Any process that stops, prevents, or reduces the frequency, rate or extent of alpha-beta T cell differentiation." + "Any native cell that is part of a inner cell mass." + "The process in which the anatomical structures of a plasma membrane bounded cell projection are generated and organized." + "The promotion of an immune response by natural killer cells through direct recognition of target cells or through the release of cytokines." + "Enables the transfer of carbohydrate from one side of a membrane to the other." + "A mature alpha-beta T cell of the columnar epithelium of the gastrointestinal tract. Intraepithelial T cells often have distinct developmental pathways and activation requirements." + "A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities" + "A change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand, leading to the initiation or perpetuation of an immune response." + "FMA:24219 SCTID:123958008" + "Any process that modulates the frequency, rate or extent of neuroblast migration." + "The differentiation of endothelial cells from progenitor cells that contributes to blood vessel development in the heart, and the de novo formation of blood vessels and tubes." + "A thymic epithelial cell with moderate nuclear and cytoplasmic electron-density. Scattered in the cortex, this cell type is predominant in the mid and deep cortex." "FMA:72211" + "A time quality inhering in a bearer by virtue of the bearer's expected maximum age." + "Any process that modulates the frequency, rate or extent of acetylcholine biosynthetic process." + "Nucleus with two or more lobes connected by a thin filament that contains no internal chromatin." + "Upper central part of the cerebral hemisphere. (MSH)." "MAT:0000506 HBA:4084 EV:0100168 DHBA:12131 MESH:D010296 UMLS:C0030560 BTO:0001001 FMA:61826 EFO:0000914 CALOHA:TS-0747 neuronames:95 Wikipedia:Parietal_lobe NCIT:C12354 BAMS:Parietal_lobe BIRNLEX:1148 SCTID:180922007 GAID:680" + "A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube." "ZFA:0000115 TAO:0000115" + "The chemical reactions and pathways involving dicarboxylic acids, any organic acid containing two carboxyl (COOH) groups or anions (COO-)." + "The descending thin limb is a part of the loop of Henle situated just after the proximal straight tubule (S3). It extends to the tip of the loop of Henle[GO]." "EMAPA:35514 FMA:17719 MA:0002625 Wikipedia:Descending_limb_of_loop_of_Henle" + + "The process whose specific outcome is the progression of the metanephric late distal convoluted tubule over time, from its formation to the mature structure. The metanephric late distal convoluted tubule contains metanephric DCT cells and intercalated (IC) alpha and beta cells and is vasopressin-sensitive." + "A mucosa that is part of a rectum [Automatically generated definition]." "FMA:15033 CALOHA:TS-2107 EMAPA:27081 MA:0003218 SCTID:362167003" + "A nuclear receptor ROR-gamma that is a translation product of some mRNA whose exon structure and start site selection renders it capable of giving rise to a protein with the amino acid sequence represented by UniProtKB:P51450-2 or a 1:1 ortholog thereof." + "A layer of epithelial cells that is part of the eye." "MA:0001301 EMAPA:32871 XAO:0004094 SCTID:362523006 TAO:0001326 Wikipedia:Lens_(anatomy)#Lens_Epithelium BTO:0001873 FMA:58871 CALOHA:TS-0543 ZFA:0001326" + "Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA)." + "A limb/fin field that has the potential to develop into a pelvic appendage bud mesenchyme." "TAO:0001454 ZFA:0001454" + "The process in which a myeloid precursor cell acquires specializes features of an erythrocyte." "Wikipedia:Erythropoiesis" + "OBSOLETE. A near-projecting glutamatergic neuron with a soma found in layer 5/6 of the human primary motor cortex." "ILX:0770161" + "Any process that modulates the frequency, rate, or extent of the self-propelled movement of a cell or organism from one location to another in a behavioral context; the aspect of locomotory behavior having to do with movement." + "A process in which force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis." "Wikipedia:Muscle_contraction" + "A lymphatic vessel located in the vermiform appendix." + "Organ system subdivision that consists primarily of chromaffin cells and their supporting structures." "FMA:79645 MESH:D002838" + "Any process that activates or increases the frequency, rate or extent of cell proliferation involved in kidney development." + "A blood vessel that is part of a iris [Automatically generated definition]." "MA:0001290 EMAPA:37387" + "The controlled release of orexin from a cell in which orexin acts as a neurotransmitter." + "A zone of bone organ that is part of a hyoid bone." "FMA:59494 SCTID:119534005" + "Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch mandibular mesenchyme." "EHDAA2:0000036" + "The expansion of a natural killer cell population by cell division." + "A cell that is part of a renal pelvis." "KUPO:0001018" + "The process in which the anatomical structure of rhombomere 1 is generated and organized. Rhombomeres are transverse segments of the developing rhombencephalon. Rhombomeres are lineage restricted, express different genes from one another, and adopt different developmental fates. Rhombomeres are numbered in an anterior to posterior order." + "Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process." + "Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Interchromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction." + + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the Golgi apparatus." + "A blood vessel that is part of a lung [Automatically generated definition]." "MA:0002457 EMAPA:32867" + "A lobule that is part of a thymus. Divided into an outer cortex and inner medulla and separated from each other by connective tissue septa, but with the medullary tissue continuous from lobule to lobule.[ncit,modified]." "NCIT:C33772 MA:0000770 SCTID:187882006 UMLS:C1522462 FMA:72215" + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving ecdysteroids, a group of polyhydroxylated ketosteroids which initiate post-embryonic development, including the metamorphosis of immature forms and the development of the reproductive system and the maturation of oocytes in adult females." + "Generation of a long process from a neuron whose cell body resides in the central nervous system. The process carries efferent (outgoing) action potentials from the cell body towards target cells." + "GC_ID:1" + "A conical pouch formed from the upper and left angle of the right ventricle in the chordate heart, from which the pulmonary artery arises[WP]. the anteriosuperior, smooth-walled portion of the cavity of the right ventricle, beginning at the supraventricular crest and terminates in the pulmonary trunk[MP]." "Wikipedia:Conus_arteriosus AAO:0010250" + "A transmembrane emp24 domain-containing protein 1 that is encoded in the genome of human." "UniProtKB:Q13445" + "A dopamine receptor that is a product of the DRD2, DRD3, or DRD4 gene. The active form binds dopamine and its activity is mediated by G proteins that cause inhibition of adenylate cyclase." "PIRSF:PIRSF038553" + "The region of the developing mammalian cortex that extends between the ventricular zone and the cortical plate (CP); normally, the IZ is a region of tangential migration of cells, and at midgestation, the lower part of the IZ develops into the subventricular zone." "EMAPA:17545 EMAPA:32712" + "The secretory units of the exocrine pancreas, where fluid containing digestive enzymes is produced; consists of a group of secretory cells surrounding a luminal space that connects to the pancreatic duct." "NCIT:C49268 MA:0002417 EMAPA:35651 SCTID:247604006 UMLS:C0227578 FMA:16011" + "Any process that modulates the occurrence or rate of mesenchymal stem cell death by apoptotic process that contributes to the shaping of the nephron in the mesonephros." + "A myoepithelial cell that is part of a mammary gland and is located in the basal layer. During lactation, a basal-myoepithelial cell of mammary gland contracts under the stimulation of oxytocin. In humans, a basal-myoepithelial cell of mammary gland can be identified by high levels of CD49f and low levels of EpCAM." "FMA:67800 CALOHA:TS-2378" + "The process in which a trachea is generated and organized. The trachea is the portion of the airway that attaches to the bronchi as it branches." + "An epiphysis that is part of a humerus [Automatically generated definition]." "FMA:32825 SCTID:313054009" + "The membrane organization process that joins two lipid bilayers to form a single membrane." "Wikipedia:Lipid_bilayer_fusion" + "Any process that mediates the transfer of information from one cell to another and contributes to the progression of the pronephros over time, from its formation to the mature organ." + "A layer of the ovarian follicle that consists of granulosa cells." "EFO:0003628 Wikipedia:Membrana_granulosa SCTID:258971005 FMA:18660 ZFA:0001112 EMAPA:35633 TAO:0001112 MA:0001460" + "A pia mater that is part of a midbrain [Automatically generated definition]." "RETIRED_EHDAA2:0001110 EHDAA2:0001175 VHOG:0000467 MA:0001061 EMAPA:17794" + "Any process that modulates the frequency, rate or extent of Golgi organization." + "Any process that stops, prevents, or reduces the frequency, rate or extent of imaginal disc growth." + "The directed movement of a carbohydrate from outside of a cell, across the plasma membrane and into the cytosol." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of an adaptive immune response." + "The directed movement of L-histidine across a membrane." + "A protein with core architecture consisting of an as yet unnamed domain in the amino-terminal half and a carboxyl-terminal Lectin C-type domain (Pfam:PF00059)." "PIRSF:PIRSF005558" + "Any process that stops, prevents, or reduces the frequency, rate or extent of erythrophore differentiation." + "An epiphysis that is part of a distal phalanx of manus." "FMA:321561 SCTID:280046002" + + "An adipocyte that is part of the epicardial fat." "FMA:261293" + "A limb joint that is part of a hindlimb [Automatically generated definition]." "SCTID:304573000 MA:0000662 EMAPA:32635" + "A wavelike sequence of involuntary muscular contraction and relaxation that passes along the ureter, impelling the contents onwards. The ureter is one of a pair of thick-walled tubes that transports urine from the kidney pelvis to the urinary bladder." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of an antimicrobial humoral response." + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving lipids." + "A submucosa that is part of an anal canal [Automatically generated definition]." "EMAPA:27227 EMAPA:27217 EMAPA:27535 FMA:85399 SCTID:7892006" + "Any process in which a protease is transported to, or maintained in, a location within a secretory granule in a T cell." + "Any process that stops, prevents or reduces the frequency, rate or extent of cell proliferation involved in kidney development." + "Binding to a cytokine, any of a group of proteins that function to control the survival, growth and differentiation of tissues and cells, and which have autocrine and paracrine activity." + "A zone of skin that is part of a lower arm [Automatically generated definition]." "FMA:38265 MA:0000602 SCTID:181537008 EMAPA:18056" + "The formation of the neural tube from an epithelial cell sheet (the neuroepithelium or neural plate). In primary neurulation, the cells surrounding the neural plate direct the neural plate cells to proliferate, invaginate, and pinch off from the surface to form a hollow epithelial tube. Primary neurulation is the typical mechanism of formation of the anterior neural tube." + "An artery that supplies blood to the lower urinary bladder." "MA:0002079 NCIT:C52685 FMA:18823 UMLS:C0226377 EMAPA:37089 SCTID:43210002 Wikipedia:Inferior_vesical_artery" + "The developmental process pertaining to the initial formation of a heart valve from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable." + + "A blood vessel that is part of a forelimb [Automatically generated definition]." "MA:0000611 EMAPA:37292" + "Luminal space of the right atrium of the heart." "FMA:11359 EMAPA:26020" + "The binding activity of a molecule that brings together two or more molecules through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way." + "The process in which the anatomical structure of the superior olivary nucleus is generated and organized. In mice, the superior olivary nucleus is a small cylindrical mass on the dorsal surface of the lateral part of the trapezoid body of the pons, and it is situated immediately above the inferior olivary nucleus. It receives projections from the cochlear nucleus and thus is involved in the perception of sound." + "A set of teeth in which each tooth that attaches to a vomer." + "The process in which a female gonad is generated and organized." + "Any process that modulates the frequency, rate or extent of the directed movement of organic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "The thick outer layer of the adrenal gland that produces and secretes steroid hormones such as corticosterone, estrone and aldosterone." "EFO:0000237 AAO:0011009 MAT:0000494 MESH:D000302 EV:0100136 XAO:0000165 NCIT:C12396 SCTID:362584002 EMAPA:18427 VHOG:0001481 CALOHA:TS-0015 Wikipedia:Adrenal_cortex BTO:0000045 MA:0000118 UMLS:C0001613 FMA:15632 GAID:447" + "Any process that activates or increases the rate or extent of growth, the increase in size or mass of all or part of an organism." + "A stromal cell found in the lamina propria of the small intestine." + "Combining with a peptide and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex." + "Any process that modulates the frequency, rate or extent of epithelial tube formation." + "A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA]." "MESH:D004727 UMLS:C0014257 EFO:0002548 FMA:63916 galen:Endothelium BTO:0000393 SCTID:27168002 GAID:520 NCIT:C12481 CALOHA:TS-0278" + "Any process that mediates the transfer of information from one cell to another and contributes to the heart process that regulates cardiac muscle contraction; beginning with the generation of an action potential in the sinoatrial node and ending with regulation of contraction of the myocardium." + "Cartilage of the pinna and much of the external ear canal." "SCTID:279627003 MA:0001227 EMAPA:35158 FMA:61013" + "An epithelium that is part of a duct of salivary gland." "FMA:67682" + "Endocardium that is part of the atrium." "ZFA:0001614 MA:0000077 EMAPA:32745 SCTID:192001005 FMA:7284 VHOG:0000606 TAO:0002169" + "The dilated structure that is lined by endothelial cells and located at the arterial pole of the heart just above (distal to) the truncus arteriosus in mammalian embryos; it is the primordial vascular channel from which the aortic arches (and eventually the dorsal aortae) arise; the aortic sac is homologous to the ventral aorta of gill-bearing vertebrates." "EHDAA:9826 SCTID:361527005 FMA:71008 EHDAA2:0004145 RETIRED_EHDAA2:0000133 EMAPA:36461" + "A fibroblast growth factor 8 that is encoded in the genome of human." "UniProtKB:P55075" + "A type I NK T cell that has been recently activated, secretes interferon-gamma and IL-4, and has the phenotype CD4-positive, CD69-positive, and downregulated NK markers." + "The inferior petrosal sinus, within the human head, is an area beneath the brain, which allows blood veins to span the area, from the center of the head downward. It drains from the cavernous sinus (beneath the brain) to the sigmoid sinuses above the internal jugular vein." "FMA:50770 Wikipedia:Inferior_petrosal_sinus EMAPA:19234 SCTID:279263009" + "Any process that increases the rate, frequency, or extent of the multiplication or reproduction of osteoclasts, resulting in the expansion of an osteoclast cell population." + "The chemical reactions and pathways involving C21-steroid hormones, steroid compounds containing 21 carbons which function as hormones." + "Any process that activates or increases the frequency, rate, or extent of glial cell apoptotic process." + "A nonkeratinized cell epithleial cell of the inferior part of the anal canal." "FMA:263144" + "Any process that modulates the frequency, rate or extent of trans-synaptic signaling." + "The chemical reactions and pathways resulting in the formation of amino acids of the glutamine family, comprising arginine, glutamate, glutamine and proline." + "A myoepithelial cell that is part of the lactiferous duct." "FMA:67803" + "The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth." "Wikipedia:Gestation" + "TAO:0007037 AAO:0011082 XAO:0000250 ZFA:0007037 VHOG:0001383" + "A protein that is encoded in the genome of Homo sapiens." + "Muscle tissue composed of cardiac muscle cells, forming the muscles of the heart[ZFA,modified]." "EHDAA2:0003142 EMAPA:32688 ZFA:0005280 FMA:14068 Wikipedia:Cardiac_muscle galen:CardiacMuscle CALOHA:TS-0440 TAO:0005280 BILA:0000134 ncithesaurus:Heart_Muscle BTO:0000199 galen:CardiacMuscleTissue AEO:0000142 AAO:0010245" + + "An epithelial cell that is part of the prostatic urethra." + "The regulation of blood pressure mediated by biochemical signaling: hormonal, autocrine or paracrine." + "The paired channels leading from the lacrimal sacs to the inferior meatus of the nose, through which tears are conducted through the nasal cavity." "MA:0001299 AAO:0000643 VHOG:0000664 Wikipedia:Nasolacrimal_duct EHDAA:9094 EMAPA:17853 UMLS:C0027437 GAID:902 MESH:D009301 SCTID:280643009 NCIT:C33161 EHDAA2:0001237 FMA:9703 EHDAA:7849" + "The femoral artery is a large artery in the muscles of the thigh. It is a continuation of external iliac artery where it enters the femoral triangle at the mid inguinal point behind the inguinal ligament. It leaves femoral triangle through apex beneath the sartorius muscle. It enters the popliteal fossa by passing through the 5th osseo-aponeurotic(adductor hiatus) opening of adductor magnus where it becomes the Popliteal Artery. [WP,unvetted]." "Wikipedia:Femoral_artery AAO:0010222 SCTID:244332003 NCIT:C12715 galen:FemoralArtery CALOHA:TS-0321 FMA:70248 MA:0001951 UMLS:C0015801 BTO:0001624 EMAPA:35342 MESH:D005263 GAID:494" + "A protein that has a core domain structure of signal sequence, propeptide, five Cadherin domains (Pfam:PF00028), a transmembrane region, and a Cadherin cytoplasmic region (Pfam:PF01049). Cadherins function as adhesion molecules that mediate Ca2+-dependent cell-cell adhesion in solid tissues." "PIRSF:PIRSF002504" + "An endothelium of capillary that is part of a respiratory system [Automatically generated definition]." "MA:0001808 EMAPA:37575" + "Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA]." "ZFA:0001498 TAO:0001498 AAO:0010066 HAO:0000070 EHDAA2:0003070 AEO:0000070 UMLS:C0836133 Wikipedia:Simple_squamous_epithelium CARO:0000070 BTO:0002073 BILA:0000070 FMA:45565 NCIT:C13178 XAO:0004010" + "A progenitor cell committed to the erythroid lineage. This cell is ter119-positive but lacks expression of other hematopoietic lineage markers (lin-negative)." "BTO:0004911" + "A spore formed following meiosis. Sometimes following meiosis, prospores may undergo one or more rounds of mitosis before they are fully mature." "FAO:0000017" + "The specialized epithelium of the Peyer's patch." "EMAPA:36506 MA:0000731" + "Any goblet cell that is part of a conjunctiva." + "The process in which a relatively unspecialized cell acquires specialized features of a mesonephric glomerular epithelial cell. Mesonephric glomerular epithelial cells are specialized epithelial cells that form part of the mesonephric glomerulus; there are two types, mesonephric glomerular parietal epithelial cells and mesonephric glomerular visceral epithelial cells." + "A neurecto-epithelial cell found in the arachnoid villi of dura mater. This cell type facilitates flow of cerebrospinal fluid into the blood." "FMA:86588" + "A large nucleated basophilic erythrocyte found in mammalian embryos. This cell type arises from the blood islands of yolk sacs and expresses different types of hemoglobins (beta-H1, gamma-1 and zeta) than adult erythrocytes. Considered a type of erythroblast as this cell type can enucleate in circulation." + "The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon." + "Mesenchyme that develops_from a somatopleure." "EHDAA2:0001120" + "Basket cells are inhibitory GABAergic interneurons of the brain. In general, dendrites of basket cells are free branching and contain smooth spines. Axons are highly branched. The branched axonal arborizations give rise to basket-like structures that surround the soma of the target cell. Basket cells form axo-somatic synapses, meaning their synapses target somas of other cells." + "The motor neurons of vertebrates that directly innervate skeletal muscles. They receive input from upper motor neurons." "FMA:84632" + "The process whose specific outcome is the progression of the mesonephric glomerular mesangium over time, from its formation to the mature structure. The mesonephric glomerular mesangium is the thin membrane connective tissue composed of mesangial cells in the mesonephros, which helps to support the capillary loops in a renal glomerulus." + "A homeostatic process involved in the maintenance of a steady state level of a chemical within a cell." + "Part of choroid plexus contained in the lateral ventricle." "VHOG:0001376 EHDAA2:0004449 FMA:83711 UMLS:C0152289 MA:0000961 neuronames:218 SCTID:70064002 ZFA:0001447 DHBA:10601 HBA:9708 EMAPA:17769 TAO:0001447 NCIT:C32309 NLX:32548 BAMS:cplv" + "The process whose specific outcome is the progression of the connecting tubule over time, from its formation to the mature structure. The connecting tubule is a tubular segment of the nephron; it connects the distal convoluted tubule to the collecting duct." + + "The directed movement of carboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carboxylic acids are organic acids containing one or more carboxyl (COOH) groups or anions (COO-)." + "A small, subcellular membrane-bounded vesicle containing pigment and/or pigment precursor molecules. Pigment granule biogenesis is poorly understood, as pigment granules are derived from multiple sources including the endoplasmic reticulum, coated vesicles, lysosomes, and endosomes." + "Any process that modulates the frequency, rate or extent of endothelial cell differentiation." + "An artery of the systemic circulation, which is the part of the cardiovascular system which carries oxygenated blood away from the heart, to the body, and returns deoxygenated blood back to the heart." "Wikipedia:Artery#Systemic_arteries FMA:66464 EMAPA:37126" + "A collagen heterotrimer containing type IV alpha chains; [alpha1(IV)]2alpha2(IV) trimers are commonly observed, although more type IV alpha chains exist and may be present in type IV trimers; type IV collagen triple helices associate to form 3 dimensional nets within basement membranes." "Wikipedia:Collagen_type_IV" + "A developmental process, independent of morphogenetic (shape) change, that is required for a nerve to attain its fully functional state." + "A protein that is a translation product of the mouse Klra3 gene or a 1:1 ortholog thereof." + "Any process that stops, prevents, or reduces the frequency, rate or extent of behavior, the internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli." + "Any process that activates or increases the frequency, rate or extent of natural killer cell mediated cytotoxicity." + "Cell committed to natural killer cell lineage that has the phenotype CD122-positive, CD34-positive, and CD117-positive. This cell type lacks expression of natural killer receptor proteins." + "GC_ID:1" + "An enterocyte that is part of the epithelium proper of large intestine." "FMA:263112 FMA:263090" + "Any process that stops, prevents or reduces the frequency, rate or extent of hemopoiesis." + "A continuation of the neuron projection bundle component of a nerve inside, crossing or immediately outside the central nervous system." "NLX:144250 NCIT:C54024 UMLS:C0228084 FMA:82524 SCTID:362295007 FMA:5981 Wikipedia:Nerve_root" + "A secretory cell found in pancreatic acini that secretes digestive enzymes and mucins. This cell is a typical zymogenic cell, have a basal nucleus and basophilic cytoplasm consisting of regular arrays of granular endoplasmic reticulum with mitochondria and dense secretory granules." "CALOHA:TS-0737 BTO:0000028 FMA:63032" + "The switching of activated B cells from IgM biosynthesis to IgE biosynthesis, accomplished through a recombination process involving an intrachromosomal deletion between switch regions that reside 5' of the IgM and IgE constant region gene segments in the immunoglobulin heavy chain locus." + + "Cell-cell signaling from post to pre-synapse, across the synaptic cleft, mediated by a lipid." + "The chemical reactions and pathways resulting in the formation of primary amino compound." + "Any process that modulates the frequency, rate or extent of locomotion of a cell or organism." + "An epithelial cell of the vestibular sensory organ that is characterized by intense enzymatic activities and numerous basal membrane infoldings." + "The process in which the anatomical structures of the umbilical cord are generated and organized. The umbilical cord is an organ or embryonic origin consisting of the 2 umbilical arteries and the one umbilical vein. The umbilical cord connects the cardiovascular system of the fetus to the mother via the placenta." + "The formation or growth of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone, involved in response to injury or other physical, physiological or environmental stress stimuli." + "The process that involves the secretion of or response to endocrine hormones. An endocrine hormone is a hormone released into the circulatory system." + "The process in which a relatively unspecialized cell acquires the specialized features of a xanthophore cell. Xanthophores are pigment cells derived from the neural crest. They contain pteridine and/or carotenoid pigments in structures called pterinosomes or xanthosomes. This makes them yellow to orange in appearance." + "A chief cell that is bigger than dark chief cells and has a larger and lighter nucleus and a cytoplasm with few granules." "FMA:69079" + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds." + "A mature microglial cell that has changed shape to an amoeboid morphology and is capable of cytokine production and antigen presentation." + "A CD86 molecule that is encoded in the genome of human." "UniProtKB:P42081" + "A zone of skin that is part of the breast." + "A mature cell of the conventional dendritic cell lineage, characterized by a high capacity for antigen presentation and typically found in a lymph node." "FMA:83038" + "A cluster in the epithalamus that consists of the pineal body and any associated structures, such as the parapineal gland or the parietal organ. The complex is poorly developed in mammals." "ZFA:0001359 TAO:0001359" + "The process that gives rise to the trigeminal ganglion. This process pertains to the initial formation of a structure from unspecified parts." + "A regional part of brain that is part of a cerebellar cortex [Automatically generated definition]." "BIRNLEX:1571 FMA:76924" + "The process in which the anatomical structures of cartilage are generated and organized." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of lipids." + "Enables the energy-independent facilitated diffusion, mediated by passage of a solute through a transmembrane aqueous pore or channel. Stereospecificity is not exhibited but this transport may be specific for a particular molecular species or class of molecules." "Reactome:R-HSA-3779381 Reactome:R-HSA-8953430 TC:1" + "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the mature cells of the hindbrain. Differentiation includes the processes involved in commitment of a cell to a specific fate." + "A gamma-delta receptor that expresses Vgamma1.1 but does not express Vdelta6.3 chains in the T-cell receptor." + "The directed movement of substances into, out of, or within the nucleus." "Wikipedia:Nuclear_transport" + "The segment of the pes that is distal to the metatarsal region and consists of the pedal digits (toes)." "FMA:70664 SCTID:362835004" + "A cell of the embryo in the early stage following the blastula, characterized by morphogenetic cell movements, cell differentiation, and the formation of the three germ layers." + "A physical quality inhering in a bearer by virtue of the bearer's ability of being turned, bowed, or twisted without breaking." + "The negative regulation of fertilization process that takes place as part of egg activation, ensuring that only a single sperm fertilizes the egg." + "The process in which a myoblast migrates along an entire fiber to the site of injury. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers." + "A cellular process that results in the aggregation, arrangement and bonding together of a set of components to form a tight junction. A tight junction seals cells together in an epithelium in a way that prevents even small molecules from leaking from one side of the sheet to the other." + "GC_ID:1" + "Combining with lactoferrin and delivering lactoferrin into the cell via endocytosis. Lactoferrin is an iron-binding glycoprotein which binds ferric iron most efficiently at low pH." + "The upper extremity of the humerus (proximal humerus) consists of a large rounded head joined to the body by a constricted portion called the neck, and two eminences, the greater and lesser tubercles." "FMA:23362 Wikipedia:Upper_extremity_of_humerus SCTID:280028008" + "EMAPA:16545 EHDAA2:0001760 FMA:18821 VHOG:0000523" + "Any process that activates or increases the frequency, rate or extent of hepatic stellate cell activation." + "An endothelium that is part of a trachea." "EHDAA:3082 RETIRED_EHDAA2:0002068" + "SCTID:64626006 UMLS:C0229654 BTO:0002684 FMA:55222 NCIT:C33040" + "The cellular homeostatic process that preserves a neuron in a stable, differentiated functional and structural state." + "The process whose specific outcome is the progression of the adrenal gland over time, from its formation to the mature structure. This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells." + "The process in which a relatively unspecialized cell of the ectoplacental cone acquires specialized features of a spongiotrophoblast of the placenta. A spongiotrophoblast cell is a basophilic cell." + "The process whose specific outcome is the progression of cardiac muscle of the atrium over time, from its formation to the mature structure." + "A gastrulation process in which the initial invagination becomes the mouth and the anus forms second." + "The developmental process pertaining to the initial formation of an epithelial tube." + "A pigment cell derived from the neural crest. Contains blue pigment of unknown chemical composition in fibrous organelles termed cyanosomes. This gives a blue appearance." + "The twelve spinal nerves on each side of the thorax. They include eleven INTERCOSTAL NERVES and one subcostal nerve. Both sensory and motor, they supply the muscles and skin of the thoracic and abdominal walls." "neuronames:1725 MESH:D013900 SCTID:360498003 GAID:857 Wikipedia:Thoracic_nerves FMA:5860" + + "Any process that modulates the frequency, rate or extent of microglial cell activation." + "The process of regulating the proliferation and elimination of macrophage cells such that the total number of myeloid cells within a whole or part of an organism is stable over time in the absence of an outside stimulus." + "The progression of the putamen over time from its initial formation until its mature state. The putamen is the lens-shaped basal ganglion involved with control of voluntary movement in the brain." + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ATP (adenosine 5'-triphosphate) stimulus." + "A female gamete where meiosis has progressed to metaphase II and is able to participate in fertilization." "FBbt:00057012 BTO:0003801 CALOHA:TS-2191 FMA:67343 BTO:0000369 MESH:D010063" + "The process in which the anatomical structures of branches are generated and organized. A branch is a division or offshoot from a main stem. Examples in animals would include blood vessels, nerves, lymphatics and other endothelial or epithelial tubes." + "The process whose specific outcome is the progression of the posterior lateral line neuromast over time, from its formation to the mature structure. The neuromast is the sensory receptor of the anterior lateral line system and is composed of a population of sensory hair cells, and nonsensory supporting cells and mantle cells. Neuromast are located superficially on the epithelium or in lateral line canals." + "A macrophage mannose receptor 1 that is encoded in the genome of human." "UniProtKB:P22897" + "Any process that modulates the frequency, rate or extent of the regulated release of gamma-aminobutyric acid." + "The neurons that utilize glycine as a neurotransmitter." "FBbt:00048032" + "The subdivision of the skeleton of either the pectoral or pelvic girdle." "AAO:0010686 VSAO:0000302" + "A retinal neural layer that is immediately adjacent to the S1 and S3 layers and comprises 20 percent of the inner plexiform layer of retina." "CP:0000114" + "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism." + "One of two openings in the uterine cervix." "FMA:20422" + "Any process that stops, prevents, or reduces the frequency, rate, or extent of natural killer cell tolerance induction." + "Any process that activates or increases the frequency, rate or extent of glutamate receptor signaling pathway." + "Generation of a long process of a CNS neuron, that carries efferent (outgoing) action potentials from the cell body towards target cells in a different central nervous system region." + "Any process that stops, prevents, or reduces the frequency, rate or extent of muscle contraction." + "The flow of blood through the gastric mucosa of an animal, enabling the transport of nutrients and the removal of waste products." + "The dentary is a dermal bone that forms the antero-lateral part of the lower jaw in fishes and amphibians, extending to the whole lower jaw in mammals[VHOG,modified]." "TAO:0000191 ZFA:0000191 EFO:0003508 http://palaeos.com/vertebrates/bones/dermal/images/Dentary1.gif AAO:0000124 VHOG:0001022" + "A thoracic vertebra endochondral element that is composed primarily of cartilage tissue." "EHDAA2:0002014" + "A dermal dendritic cell that is langerin-negative, CD103-negative, and CD11b-positive." + "The process that gives rise to the embryonic heart tube by the cells of the heart field along a linear axis." + "Mesenchyme that develops_from a neural crest and is part of a 1st arch maxillary mesenchyme." "EHDAA2:0000044" + "Any process that modulates the frequency, rate or extent of DNA recombination, a DNA metabolic process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents." + "A venule endothelial cell that is cubodial, expresses leukocyte-specific receptors, and allows for passage of lymphocytes into bloodstream." "FMA:67759" + "A portion of skeletal muscle tissue that is part of a pectoralis major [Automatically generated definition]." "FMA:261968" + "A submucosa that is part of a esophagus [Automatically generated definition]." "SCTID:362128009 FMA:62997 EMAPA:35325 MA:0002724 BTO:0002109" + "Any process that modulates the frequency, rate, or extent of T cell anergy." + "A follicular dendritic cell located in the Peyer's patch. These cells from a meshwork in which Peyer's patch B cells reside." + "A spore formed from bacteria in the order Actinomycetales." + "An epithelial cell that is part_of a alveolus of lung." "MESH:D056809" + "Any process that modulates the frequency, rate or extent of glycinergic synaptic transmission. Glycinergic synaptic transmission is the process of communication from a neuron to another neuron across a synapse using the neurotransmitter glycine." + "The chemical reactions and pathways resulting in the formation of organonitrogen compound." + "A CD4-positive, alpha-beta T cell that is found in the columnar epithelium of the gastrointestinal tract." + "A cell present in the developing CNS. Functions as both a precursor cell and as a scaffold to support neuronal migration." + "The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes." + "Any apoptotic process in an epithelial cell." + "A blood vessel that is part of a brain [Automatically generated definition]." "EMAPA:35182 MA:0002769" + "Mature CD8_alpha-negative CD11b-positive dendritic cell is a CD8_alpha-negative CD11b-positive dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive." + "An estrogen receptor that is encoded in the genome of human." "UniProtKB:P03372 Reactome:R-HSA-446168 Reactome:R-HSA-9020968 DTO:00117511" + "Any process that stops, prevents or reduces the frequency, rate or extent of testosterone secretion." + "The process in which relatively unspecialized cells acquire specialized structural and functional features of a pancreatic polypeptide-producing cell. A pancreatic polypeptide-producing cell is a cell in the pancreas that produces pancreatic polypeptide." + + "A chromaffin cell interspersed among the interrenal epithelial layer of the anterior kidney of teloest fish." + "The movement of an eosinophil in response to an external stimulus." + "The process in which a relatively unspecialized cell derived from the larval lymph gland acquires the specialized features of a mature hemocyte. The lymph gland consists of three to six bilaterally paired lobes that are attached to the cardioblasts during larval stages, and it degenerates during pupal stages. Hemocytes are blood cells associated with a hemocoel (the cavity containing most of the major organs of the arthropod body) which are involved in defense and clotting of hemolymph, but not involved in transport of oxygen. An example of this process is found in Drosophila melanogaster." + "Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 2nd arch mesenchyme." "EHDAA2:0000067 EMAPA:16280" + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving lipoproteins, any conjugated, water-soluble protein in which the nonprotein group consists of a lipid or lipids." + "A sweat gland that is part of a axilla." + + "Dorsal portion of the pons, containing cranial nervee nuclei, ascending and descending tracts and reticular nuclei. It is continuous with the reticular formation of the medulla (Carpenter, A Core Text of Neuroanatomy, 3rd ed, 1985, pg 133)." "FMA:71108 BAMS:PTg DHBA:12416 neuronames:557 BIRNLEX:923 Wikipedia:Pontine_tegmentum HBA:9135 SCTID:362401009 UMLS:C0228426" + "Any process that stops, prevents, or reduces the frequency, rate or extent of immature T cell proliferation in the thymus." + "A mature gamma-delta T cell that is found in the columnar epithelium of the gastrointestinal tract. These cells participate in mucosal immune responses." + "Any process that activates or increases the frequency, rate or extent of protein complex assembly." + "A dorsal root ganglion that is part of a thorax [Automatically generated definition]." "UMLS:C0457467 BIRNLEX:2600 SCTID:278326009 FMA:6006" + "Any process that activates or increases the frequency, rate, or extent of mast cell activation as part of an immune response." + "Any process that stops, prevents, or reduces the rate of eosinophil degranulation." + "The process in which a relatively unspecialized cell acquires specialized features of a cardiac myoblast. A cardiac myoblast is a precursor cell that has been committed to a cardiac muscle cell fate but retains the ability to divide and proliferate throughout life." + "The directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding." + "Any duct branching of of the main epididymis duct." "EMAPA:36525 NCIT:C32484 FMA:18297 UMLS:C0458632 MA:0001735 SCTID:279623004" + "The process whose specific outcome is the progression of the glomerular epithelium over time, from its formation to the mature structure. The glomerular epithelium is an epithelial tissue that covers the outer surfaces of the glomerulus. The glomerular epithelium consists of both parietal and visceral epithelium. Metanephric glomerular parietal epithelial cells are specialized epithelial cells that form tight junctions as a barrier to protein transport. A metanephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the metanephros." + "A phase of elevated metabolic activity, during which oxygen consumption increases following a stimulus as part of an inflammatory response; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals, resulting in an increase in their intracellular or extracellular levels." + "Any process that activates or increases the frequency, rate or extent of bleb assembly." + "The process in which an antigenically naive CD4-positive, alpha-beta T cell acquires the specialized features of an effector, regulatory, or memory T cell as part of an immune response. Effector T cells include cells which provide T cell help or exhibit cytotoxicity towards other cells." + "A proerythoblast that is Kit-low, Lyg76-positive, and CD71-positive." + "Anatomical structure that is an aggregation of similar cells from which cartilages and bones form, and from which chondrogenesis and osteogenesis are initiated during repair and/or regeneration. (Hall and Miyake 1995)." "XAO:0004021 VSAO:0000006" + "The process in which transitional stage B cells acquire the specialized features of mature B cells in the spleen." + "Any process that activates or increases the frequency, rate, or extent of leukocyte mediated immunity." + "A pyramidal cell morphology that inheres in neurons which lack a clear tuft formation but extend to large radial distances." "ilxtr:UntuftedPyramidalPhenotype" + "The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions." + "A cardiac myocyte that is connected to other cardiac myocytes by transverse intercalated discs (GO:0014704) at a regular interval." "FMA:67967" + "The aggregation, arrangement and bonding together of a set of components to form an organelle. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." + "Any process that modulates the frequency, rate or extent of gamma-delta T cell activation involved in immune response." + "A parenchyma that is part of a right lobe of liver [Automatically generated definition]." "EHDAA2:0001010 VHOG:0000840 EMAPA:18317 FMA:71657" + "The process in which a precursor cell type acquires the specialized features of a CD4-positive, gamma-delta intraepithelial T cell. Intraepithelial T cells are found among epithelial cells in mucosal areas and have distinct phenotypes and developmental pathways." + "Any process that modulates the frequency, rate or extent of hepatic stellate cell proliferation." + "Any process that modulates the frequency, rate or extent of amino acid transmembrane transport." + "A sac containing the developing tooth and its odontogenic organ. The dental follicle (DF) differentiates into the periodontal ligament. In addition, it may be the precursor of other cells of the periodontium, including osteoblasts, cementoblasts and fibroblasts. They develop into the alveolar bone, the cementum with Sharpey's fibers and the periodontal ligament fibers respectively." "BTO:0000337 SCTID:110975002 EMAPA:35275 MA:0003121 NCIT:C34138 Wikipedia:Dental_follicle" + "The chemical reactions and pathways resulting in the formation of norepinephrine, a hormone secreted by the adrenal medulla, and a neurotransmitter in the sympathetic peripheral nervous system and in some tracts in the central nervous system. It is also the demethylated biosynthetic precursor of epinephrine." + "The process whose specific outcome is the progression of the cardiac myofibril over time, from its formation to the mature structure. A cardiac myofibril is a myofibril specific to cardiac muscle cells." + "A progenitor cell that is capable of forming colonies of primitive erythrocytes in the blood island of the yolk sac. First arrive at E7.5 in mouse and expresses CD41." + "The chemical reactions and pathways resulting in the breakdown of glutamate, the anion of 2-aminopentanedioic acid." + "Any process that activates or increases the frequency, rate or extent of cell killing." + "A depression or fissure in the surface of the brain. It surrounds the gyri, creating the characteristic appearance of the brain in humans and other large mammals." "DHBA:10610 SCTID:279337001 NCIT:C32292 Wikipedia:Sulcus_(neuroanatomy) neuronames:1208 HBA:9352" + "Any process that activates or increases the frequency, rate or extent of border follicle cell migration." + "An endothelial cell that is part of a uterus." "EFO:0010711" + "Any process that decreases the rate, frequency or extent of macrophage derived foam cell differentiation. Macrophage derived foam cell differentiation is the process in which a macrophage acquires the specialized features of a foam cell. A foam cell is a type of cell containing lipids in small vacuoles and typically seen in atherosclerotic lesions, as well as other conditions." + "Any process that modulates the rate, frequency, or extent of the process whose specific outcome is the progression of a chondrocyte over time, from its commitment to its mature state. Chondrocyte development does not include the steps involved in committing a chondroblast to a chondrocyte fate." + "The orderly movement of epithelial cells within a renal tubule that contributes to distal tubule morphogenesis." + "The process that regulates the coordinated growth and differentiation that establishes the non-random anterior-posterior spatial arrangement of the neural plate." + "Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA]." "HAO:0000073 XAO:0004007 ZFA:0001495 CARO:0000073 NCIT:C33554 TAO:0001495 BILA:0000073 EHDAA2:0003073 FMA:45561 SCTID:309043004 AAO:0010062 BTO:0002073 UMLS:C0682574 AEO:0000073" + "The chemical reactions and pathways resulting in the formation of aldosterone, a corticosteroid hormone that is produced by the zona glomerulosa of the adrenal cortex and regulates salt (sodium and potassium) and water balance." + "Enables the transfer of RNA, ribonucleic acid, from one side of a membrane to the other." "Reactome:R-HSA-203906" + "A developmental process, independent of morphogenetic (shape) change, that is required for the glossopharyngeal nerve to attain its fully functional state. Various sensory and motor branches of the glossopharyngeal nerve supply nerve connections to the pharynx and back of the tongue. The branchial motor component contains motor fibers that innervate muscles that elevate the pharynx and larynx, and the tympanic branch supplies parasympathetic fibers to the otic ganglion." + "A protein-containing complex that is a membrane-bound heterodimeric co-receptor for MHC class-I antigen/T-cell receptor interaction." + "Any process that activates or increases the frequency, rate or extent of dense core granule transport." + "A nail that is part of a manual digit." "UMLS:C0222001 FMA:54327 SCTID:244197001 NCIT:C32609 EMAPA:35349" + "A process in which a protein is transported to, or maintained in, a location within the cytoskeleton." + "Any process that activates or increases the frequency, rate or extent of movement of proteins from the cytoplasm into the nucleus." + "An ion channel complex through which calcium ions pass." + "A submucosa that is part of a cloaca [Automatically generated definition]." + "Any process involved in the maintenance of an internal steady state at the level of the cell." + "Any process that decreases the rate, frequency or extent of extracellular matrix disassembly. Extracellular matrix disassembly is a process that results in the breakdown of the extracellular matrix." + "The intermediate mesoderm is located between the lateral mesoderm and the paraxial mesoderm. It develops into the kidney and gonads." "Wikipedia:Intermediate_mesoderm ZFA:0001206 UMLS:C1284010 AAO:0010575 XAO:0000085 SCTID:361476001 EMAPA:16178 TAO:0001206 VHOG:0000087 FMA:293147 NCIT:C34193 EMAPA:16056" + "The wall of the heart that separates the right atrium and left ventricle; and is located just above the septal cusp of the tricuspid valve." "SCTID:280151006 FMA:7136 Wikipedia:Atrioventricular_septum EMAPA:37431" + "A process involving any mechanism for tolerance induction in macrophages." + "Either of the two lateral lobes that constitute the thymus." "FMA:71193 RETIRED_EHDAA2:0002021" + "The expansion of a T cell population by cell division as part of an immune response." + "An epithelium that is part of a anterior chamber of eyeball." "EHDAA2:0000130" + "An epithelial cell of the mammary gland." "BTO:0004300" + + + "A portion of connective tissue that is part of an ankle [Automatically generated definition]." "EMAPA:37328 MA:0000639" + "Hindbrain segment or neuromere 1." "EHDAA2:0001637 ZFA:0001031 DMBA:16915 EFO:0003608 FMA:295790 DHBA:12667 EMAPA:16290 TAO:0001031" + "A germinal center that is part of the spleen. The spleen germinal center is located in a secondary B follicle in the white pulp of the spleen." "MA:0000764 EMAPA:35803 NCIT:C49760 UMLS:C1710156" + "An embryo that is at the late embryonic stage; this stage covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching." "SCTID:83418008 NCIT:C13235 FMA:63919 CALOHA:TS-0360 UMLS:C0015965 BTO:0000449 MESH:D005333 GAID:552 EFO:0001323" + "Any process that activates or increases the frequency, rate or extent of cardiocyte differentiation." + "The Peyer's patch area normally occupied by T lymphocytes." "EMAPA:37939" + "A vascular network consisting of blood vessels." "TAO:0001079 ZFA:0001079" + "Organism at the gastrula stage." "NCIT:C34057 FMA:293108 Wikipedia:Trilaminar_blastocyst UMLS:C0017199 MIAA:0000179 UMLS:C1284022 MESH:D005775 NCIT:C34058 BILA:0000060 GAID:1302 BTO:0001403 Wikipedia:Gastrula" + "An epiphysis that is part of a phalanx [Automatically generated definition]." "SCTID:280033007" + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds." + "The process whose specific outcome is the progression of the mesoderm over time, from its formation to the mature structure. The mesoderm is the middle germ layer that develops into muscle, bone, cartilage, blood and connective tissue." + "Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP." "Reactome:R-HSA-9673284 Reactome:R-HSA-975139 Reactome:R-HSA-937034 Reactome:R-HSA-9604606 Reactome:R-HSA-156832" + "Any process that activates or increases the frequency, rate or extent of the assembly of pseudopodia." + "The chemical reactions and pathways involving a protein. Includes protein modification." "Wikipedia:Protein_metabolism" + "Combining with an MHC class Ib protein complex and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity. Class Ib here refers to non-classical class I molecules, such as those of the CD1 or HLA-E gene families." + "The process in which the structures of a neuron are generated and organized. This process occurs while the initially relatively unspecialized cell is acquiring the specialized features of a neuron." + "A bone marrow proteoglycan isoform 1, signal peptide removed form that has had the acidic propeptide removed." + "An interleukin-7 receptor subunit alpha that is encoded in the genome of mouse." "UniProtKB:P16872" + "The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles." "Wikipedia:Chromosome_segregation" + "The process in which the anatomical structures of the forelimb are generated and organized. The forelimbs are the front limbs of an animal, e.g. the arms of a human." + "A renal alpha-intercalated cell that is part of the collecting duct of the renal tubule." + "FMA:67521" + "Any process that stops, prevents, or reduces the frequency, rate, or extent of neutrophil apoptotic process." + "A region of the brain consisting of ventral and rostral subcortical regions of the telencephalon, including among others, the basal ganglia, septal nuclei, amygdala, ventral pallidum, substantia innominata, and basal nucleus of Meynert." "Wikipedia:Basal_forebrain BTO:0002444 EMAPA:35164 BM:Tel-BF BIRNLEX:1560 DHBA:10349 PBA:128012976 BAMS:Basal_forebrain HBA:4300 FMA:77700 neuronames:1997" + "A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands." "MAT:0000338 FMA:9903 GAID:715 CALOHA:TS-0808 MA:0000218 BTO:0001028 BAMS:PNS SCTID:362292005 ZFA:0000142 EMAPA:16665 neuronames:3232 Wikipedia:Peripheral_nervous_system VHOG:0000399 EHDAA:2893 MIAA:0000338 MESH:D017933 XAO:0000178 BIRNLEX:1111 UMLS:C0206417 UMLS:C1305921 TAO:0000142 EHDAA2:0001445 EV:0100335 EFO:0000891 BILA:0000081 AAO:0000429 NCIT:C12465" + "Epithelium composed of a single layer of cells, appearing as layered because the column-shaped cells vary in height so the nuclei are at different levels. The basal portions of all the cells are in contact with the basement membrane. It lines the respiratory system and the male reproductive tract. The cilia in the respiratory tract are motile, while the stereocilia in the male reproductive tract are immobile." "NCIT:C13181 FMA:13146 UMLS:C0506992" + + "A sulcus of brain that is part of a frontal cortex." "UMLS:C0459388 NCIT:C32639 HBA:9354" + "Portion of tissue that gives rise to the immature gonad." "ZFA:0001262 EMAPA:17204 EFO:0003651 TAO:0001262 EHDAA:5927 WBbt:0008366 RETIRED_EHDAA2:0002148" + "A prostate epithelial cell that is CD133-positive, CD44-positive, integrin A2beta3-high. This cell is a stem cell for the prostate epithelium." + "The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections." "FMA:67301 FBbt:00005107 Wikipedia:Cell_body" + "The developmental process pertaining to the progression of the optic chiasm from its initial formation to the mature structure. The process begins when the pathfinding of the axons of the developing optic nerve cause some axons to cross at the midline of the brain and ends when the axons are mature." + "Any process that modulates the frequency, rate or extent of cytoplasmic translation." + "The process in which the anatomical structures of a proximal tubule are generated and organized. The proximal tubule is a nephron tubule that connects Bowman's capsule to the descending thin limb of the loop of Henle. It has a brush border epithelial morphology." + "A lymphatic vessel that is part of a pelvic appendage." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a solute from one side of a membrane to the other." + "The expansion of a gamma-delta T cell population by cell division as part of an immune response." + "Any process that activates or increases the frequency, rate or extent of lymphangiogenesis." + "A myofibroblast that is part of an alveoli during alveolarization. The contractile force of this cell elongates the secondary crest, while producing a framework of elastin and tenascin. During the maturation of the septa, secondary crest myofibroblasts, together with matrix fibroblasts, secrete metalloproteinases and other ECM‐remodeling proteins to thin the septal tip ECM. The secondary crest myofibroblast continues producing elastin, eventually undergoing apoptosis during adulthood." + "A effector T cell that provides help in the form of secreted cytokines to other immune cells." "BTO:0002417 MESH:D006377" + "The directed movement of L-histidine from outside of a cell, across the plasma membrane and into the cytosol." + "An organismal quality inhering in a bearer by virtue of the bearer's consisting cells." + "The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome." "NIF_Subcellular:sao1615953555" + "Mesenchyme that is part of a developing toe [Automatically generated definition]." "EMAPA:32947 VHOG:0000463" + "Any process that modulates the frequency, rate or extent of anatomical structure morphogenesis." + "The process in which a relatively unspecialized cell acquires specialized features of a neuron whose cell body resides in the retrotrapezoid nucleus." + "A neuron with a small cell body that is located in a koniocellular layer of the lateral geniculate nucleus (LGN)." "NIFEXT:44" + "Any collection of muscles that is part of a hindlimb stylopod (upper leg / thigh)[Automatically generated definition]." "FMA:50208" + "The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC protein complex. The peptide is typically a fragment of a larger exogenous protein which has been degraded within the cell." + "A dura mater that is part of a diencephalon [Automatically generated definition]." "EMAPA:17766 VHOG:0000258 MA:0000828" + "A pad of fibrocartilage between the articular surfaces of two successive vertebral centra which has nucleus pulposus at its core." "BTO:0003625 SCTID:244570000 NCIT:C49571 MESH:D007403 MA:0000110 Wikipedia:Intervertebral_disk UMLS:C0021815 FMA:10446 EFO:0001370 EMAPA:32739 GAID:105" + + "The directed movement of lipids within cells." + "Any process that decreases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus." + "A medium-wave-sensitive opsin (human) that is a translation product of the OPN1MW3 gene in human." "UniProtKB:P0DN78" + "An astrocyte that is part of the hippocampus." + "One of three half-circular, interconnected tubes located inside each ear[WP]." "MESH:D012665 ZFA:0000431 Wikipedia:Semicircular_canal MA:0000249 EMAPA:32832 GAID:776 EV:0100365 TAO:0000431 NCIT:C33527 UMLS:C0036622 VHOG:0001144 CALOHA:TS-2164 FMA:60186 AAO:0011098 SCTID:279757004 XAO:0000198 BTO:0003383" + "The central part of the thoracic cavity enclosed by the left and right pleurae." "MESH:D008482 CALOHA:TS-2338 UMLS:C0025066 EMAPA:36001 SCTID:181217005 Wikipedia:Mediastinum NCIT:C12748 MA:0003075 FMA:9826 EFO:0003057 GAID:94" + "A segmented neutrophilic cell of the bone marrow reserve pool that expresses CD11b (integrin alpha-M) and high levels of CD16 (low affinity immunoglobulin gamma Fc region receptor III) on its cell surface." + "A protein that is a translation product of the human LGALS1 gene or a 1:1 ortholog thereof." + "A stem cell that can give rise to cell types of the body other than those of the germ-line." "MESH:D053687 CALOHA:TS-2086" + "A strand of hair that is part of a dorsum." "FMA:54320" + "Any process that reduces or removes the toxicity of iron ion. These include transport of iron away from sensitive areas and to compartments or complexes whose purpose is sequestration of iron ion." + "A protein that is produced as the result of proteolytic processing of a longer protein." + "A paneth cell that is located in the epithelium of the colon." + "The process in which a relatively unspecialized cell acquires specialized features of a neuroendocrine cell of the lung epithelium." + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus." + "An elastic tissue that is part of a respiratory system [Automatically generated definition]." "MA:0001820 EMAPA:37579" + "A large, multipolar lower motor neuron of the brainstem and spinal cord that innervates the extrafusal muscle fibers of skeletal muscle and are directly responsible for initiating their contraction. While their cell bodies are in the CNS (in the anterior gray horn of the spinal cord), they are part of the somatic nervous system - a branch of the PNS." + "An epithelium that develops_from a ectoderm and is part of a oral epithelium." "EHDAA2:0004137" + "The series of events involved in the perception of pain in which a stimulus is received and converted into a molecular signal." + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving ecdysteroids." + "UMLS:C0226505 SCTID:6216007 NCIT:C33345 FMA:63191" + "Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-13 production." + "A process in which a protein is transported to, or maintained, in a location within a cell-cell junction." + "Any process that modulates the rate, frequency or extent of peptide hormone processing. Peptide hormone processing is the generation of a mature peptide hormone by posttranslational processing of a prohormone." + "A myoepithelial cell that is part of the sweat gland." "FMA:67801" + "Any process that modulates the frequency, rate or extent of T-helper 1 cell differentiation." + "FMA:76988" + "The process in which a B cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex." + "A monadic quality of continuant that exists at the cellular level of organisation." + "Cd4-negative, CD8_alpha-negative, CD11b-positive dendritic cell is a conventional dendritic cell that is CD11b-positive, CD4-negative, CD8_alpha-negative and is CD205-positive." + "Any of the smallest blood vessels where blood circulates within organ tissues. Microvessels include terminal arterioles, metarterioles, capillaries, and venules (but exclude lymphatic capillaries). Arterioles carry oxygenated blood to the capillaries, and blood flows out of the capillaries through venules into veins." + "Any mesenchymal cell apoptotic process that is involved in metanephric nephron morphogenesis." + "The series of events in which an ultraviolet radiation (UV light) stimulus is received and converted into a molecular signal. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers." + "One of the two fleshy folds which surround the opening of the mouth." "MA:0000343 CALOHA:TS-0558 SCTID:181221003 Wikipedia:Lip VHOG:0000677 MESH:D008046 GAID:76 UMLS:C0023759 TAO:0007006 galen:Lip ZFA:0007006 NCIT:C12220 FMA:59816 BTO:0001647 EMAPA:32839" + "A skeletal muscle organ that is part of the trunk region." "AAO:0000611 XAO:0003230 ZFA:0000473 MA:0000514 FMA:58274 TAO:0000473 EMAPA:35888" + + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a lytic vacuole." + "Any process that modulates the frequency, rate or extent of isotype switching to IgE isotypes." + "EMAPA:37567 MA:0001802" + "Any process that modulates the frequency, rate or extent of a muscle system process, a multicellular organismal process carried out by any of the organs or tissues in a muscle system." + "A myocardium trabecular layer that is part of a cardiac ventricle." "FMA:83511 ZFA:0005060 TAO:0005060" + "A plasma cell that is located in a vermiform appendix." + "A developmental process, independent of morphogenetic (shape) change, that is required for a myoblast to attain its fully functional state. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers." + "A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules." + "MA:0000102 EHDAA:4401 VHOG:0001395 EHDAA2:0001359 EMAPA:17330" + "The progression of the retrotrapezoid nucleus (RTN) over time from it's initial formation to its mature state. The retrotrapezoid nucleus is a group of neurons in the rostral medulla, which are responsible regulating respiration." + "A venule that is located in the anorectum." + "Any process that activates or increases the frequency, rate or extent of serotonin biosynthetic process." + "The multiplication or reproduction of epithelial cells of the submandibular salivary gland, resulting in the expansion of a cell population and the shaping of the gland." + "A macroconidium that has only one nucleus." "FAO:0000029" + "Langerhans cell is a conventional dendritic cell that has plasma membrane part CD207. A Langerhans cell is a stellate dendritic cell of myeloid origin, that appears clear on light microscopy and has a dark-staining, indented nucleus and characteristic inclusions (Birbeck granules) in the cytoplasm; Langerhans cells are found principally in the stratum spinosum of the epidermis, but they also occur in other stratified epithelia and have been identified in the lung, lymph nodes, spleen, and thymus." "CALOHA:TS-2375 BTO:0000705 FMA:63072 MESH:D007801" + "The process of regulating the proliferation and elimination of dendritic cells such that the total number of dendritic cells within a whole or part of an organism is stable over time in the absence of an outside stimulus." + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a serotonin stimulus." + "Catalytic activity that acts to modify a protein." + "Endocardium that is part of the left atrium." "FMA:7286 VHOG:0001226 SCTID:190064008" + "Inflammation of prolonged duration (weeks or months) in which active inflammation, tissue destruction, and attempts at repair are proceeding simultaneously. Although it may follow acute inflammation, chronic inflammation frequently begins insidiously, as a low-grade, smoldering, often asymptomatic response." + "A cell type that makes up the highly vascular membrane lining the marrow cavity of long bones." "FMA:86495" + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures and their associated proteins in the presynaptic cytoskeleton." + "An amacrine cell that uses glycine as a neurotransmitter." + "Any process that decreases the rate or extent of cardiac cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a cardiac muscle cell and result in its death." + "A type I vestibular sensory cell that is part of the epithelium of macula of saccule of membranous labyrinth." "FMA:263190" + "Any process that activates, maintains or increases the frequency, rate or extent of GABAergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter gamma-aminobutyric acid (GABA)." + "A thymocyte that has the phenotype CD4-negative, CD8-negative, CD44-negative, and CD25-positive and expressing the T cell receptor beta-chain in complex with the pre-T cell receptor alpha chain." + "A tube-like opening in the epidermis where the hair shaft develops and into which the sebaceous glands open[GO]." "FMA:70660 UMLS:C0221971 EFO:0002464 EMAPA:29741 VHOG:0001268 CALOHA:TS-0432 Wikipedia:Hair_follicle NCIT:C13317 GAID:934 EMAPA:18771 SCTID:280830006 BTO:0000554 MA:0000154 EV:0100156 MESH:D018859" + "The progression of the cerebral cortex over time from its initial formation until its mature state. The cerebral cortex is the outer layered region of the telencephalon." + "Any process that modulates the frequency, rate or extent of transmission of a nerve impulse, the sequential electrochemical polarization and depolarization that travels across the membrane of a neuron in response to stimulation." + "A lymph node macrophage found in the subcapsular sinus of lymph nodes that participates in sensing, clearance, and antigen presentation of lymph-borne particulate antigens. This macrophage is capable of activating invaraint NKT cells and is CD169-positive." + "Any process that stops, prevents or reduces the frequency, rate or extent of excitatory synapse assembly." + "Cylindrical spore formed by development and compartmentation of hyphae; the hyphae are often supporting blastoconidiophores." "FAO:0000041" + "Any process that modulates the frequency, rate, or extent of lipid transporter activity." + "The progression of the sinus venosus over time, from its formation to the mature structure. The sinus venosus is a heart chamber attached to the atrium on the venous side of the embryonic heart." + "The process in which relatively unspecialized cells of the ectoplacental cone acquire specialized structural and/or functional features that characterize chorionic trophoblasts. These cells will migrate towards the spongiotrophoblast layer and give rise to syncytiotrophoblasts of the labyrinthine layer." + "An anatomical cavity that surrounded_by a lymphatic vessel." "FMA:59681" + + "The chemical reactions and pathways resulting in the breakdown of monocarboxylic acids, any organic acid containing one carboxyl (-COOH) group." + "A smooth muscle cell that is part of the ascending colon." "FMA:17518" + "A dura mater that is part of a forebrain." "EMAPA:37545 MA:0000885" + "A portion of cardiac muscle tissue that is part of a left atrium [Automatically generated definition]." "EMAPA:17320 EHDAA2:0004154 FMA:7285 SCTID:189936008 VHOG:0001225" + "Any process that modulates the rate, frequency or extent of glucose metabolism. Glucose metabolic processes are the chemical reactions and pathways involving glucose, the aldohexose gluco-hexose." + "The directed movement of a T-helper 17 cell in response to an external stimulus." + "A head mesenchyme that develops_from a mesoderm." "AAO:0011051 VHOG:0000185 EHDAA2:0001118 EFO:0003337 EMAPA_RETIRED:16270 TAO:0000998 FMA:293859 XAO:0000053 EFO:0003603 ZFA:0000998 EHDAA:655 EMAPA:16099" + "The reorganization or renovation of existing blood vessels." + "A vesicle found in the cytoplasm of a cell." "NIF_Subcellular:sao180601769" + "A protein complex which is capable of serotonin-activated cation-selective channel activity. Mainly found in pre- and postsynaptic membranes of the brain and gastrointestinal tract. Depending on its location it transports Ca2+, Mg2+, Na+ or K+. It is always a pentamer, containing at least the 5HT3A subunit forming 5HT3A homopentamers or 5HT3A/B heteropentamers. In human, 5HT3A/C, A/D and A/E heteropentamers also exist." + "One of two jugular veins that collect the blood from the brain, the superficial parts of the face, and the neck. [WP,unvetted]." "FMA:4724 RETIRED_EHDAA2:0000878 XAO:0000382 SCTID:181372005 EMAPA:17620 EHDAA2:0000877 NCIT:C32849 Wikipedia:Internal_jugular_vein MA:0002157 galen:InternalJugularVein UMLS:C0226550 AAO:0010236 EHDAA:5407" + "The portion of the renal tubule that constitutes the proximal part of the loop of Henle, has low permeability to ions and urea, and is highly permeable to water; it consists of an initial short thick segment lined by low simple cuboidal epithelium and a long thin segment lined by simple squamous epithelium; however, this distinction is not as important physiologically as in the ascending limb, so often the two are treated as one structure." "UMLS:C0227657 Wikipedia:Descending_limb_of_loop_of_henle SCTID:245350001 MA:0001679 EMAPA:35511 FMA:17705 NCIT:C32456" + "The limb epidermis is the outer epithelial layer of the limb, it is a complex stratified squamous epithelium." "EMAPA:32728" + "Any process that stops, prevents, or reduces the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets." + "The process in which a relatively unspecialized cell acquires the characteristics of a mature hemangioblast. Hemangioblasts are the proposed common precursor of blood and endothelial lineages." + "The process in which the anatomical structures of genitalia are generated and organized. The genitalia are the organs of reproduction or generation, external and internal." + "A cell of the basal layer of the epithelium in the prostatic acinus." "FMA:74265" + "The process whose specific outcome is the progression of an epididymis over time, from its formation to the mature structure." + "Any process that modulates the frequency, rate or extent of Golgi calcium ion export." + "The progression of the olfactory bulb over time from its initial formation until its mature state. The olfactory bulb coordinates neuronal signaling involved in the perception of smell. It receives input from the sensory neurons and outputs to the olfactory cortex." + "CD11c-low plasmacytoid dendritic cell is a leukocyte that is CD11c-low, CD45R-positive, GR1-positive and CD11b-negative." + "Any process that stops, prevents or reduces the frequency, rate or extent of fibroblast apoptotic process." + "Obsolete. Use PO:0000244 from Plant Ontology instead. In monosporic and bisporic megasporogenesis: the megaspore(s) that will undergo megagametogenesis." + "The process in which relatively unspecialized cells acquire specialized structural and/or functional features of an ectodermal cell. Differentiation includes the processes involved in commitment of a cell to a specific fate." + "A Purkinje myocyte that is part of the internodal tract." "FMA:83392" + "A CD19 molecule that is encoded in the genome of mouse." "UniProtKB:P25918" + "A choroid plexus stroma that is part of a fourth ventricle." "MA:0000985" + "The directed movement of RNA from the nucleus to the cytoplasm." + "An extratelencephalic-projecting glutamatergic neuron located in layer 5b of the primary motor cortex that does not project to the medulla. Non-MY ET cells are large, big-tufted cells with the apical dendrite often bifurcating close to the soma, suggesting they are corticospinal cells. Non-MY ET cells have bigger hyperpolarization sag, lower input resistance, and smaller AP width, compared to L5 IT neurons." + "The process that occurs during oogenesis involving the ovarian follicle cells, somatic cells which surround the germ cells of an ovary. An example of this is found in Drosophila melanogaster." + "Any process that modulates the frequency, rate or extent of microtubule binding." + "Irregular connective tissue, the intercellular matrix of which contains a sparse irregular network of collagen and elastic fiber bundles. Examples: areolar tissue, neuroglial tissue, mucoid tissue." "NCIT:C33007 FMA:19783 Wikipedia:Loose_connective_tissue UMLS:C1253917" + "The developmental sequence of events leading to the formation of adult skeletal muscle tissue. The main events are: the fusion of myoblasts to form myotubes that increase in size by further fusion to them of myoblasts, the formation of myofibrils within their cytoplasm and the establishment of functional neuromuscular junctions with motor neurons. At this stage they can be regarded as mature muscle fibers." + "A retinal ganglion cell that originate in the ganglion cell layer of the retina, and project to the parvocellular layers of the lateral geniculate nucleus (LGN). These cells are known as midget retinal ganglion cells due to the small sizes of their dendritic trees and cell bodies." + "An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for acidic dyes under specific pH conditions." + "An amacrine cell with a medium dendritic field and post-synaptic terminals in S2, and in S3-S4." + "The cavernous sinus (or lateral sellar compartment), within the human head, is a large collection of thin-walled veins creating a cavity bordered by the temporal bone of the skull and the sphenoid bone, lateral to the sella turcica." "SCTID:244402005 Wikipedia:Cavernous_sinus UMLS:C0007473 EMAPA:19059 NCIT:C12690 MESH:D002426 FMA:50772 GAID:532" + "The process whose specific outcome is the progression of the skeletal muscle fiber over time, from its formation to the mature structure. Muscle fibers are formed by the maturation of myotubes. They can be classed as slow, intermediate/fast or fast." + "An epithelial tube that is part of the nephron, the functional part of the kidney." "NCIT:C49274 CALOHA:TS-1262 FMA:15627 EMAPA:27782 TAO:0001287 UMLS:C0022674 EV:0100387 MA:0000377 MESH:D007684 GAID:433 ZFA:0001287 BTO:0000343 Wikipedia:Renal_tubule SCTID:361332007 EFO:0003666" + "Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in metanephric nephron tubule development." + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving lipoproteins, any conjugated, water-soluble protein in which the nonprotein group consists of a lipid or lipids." + "An epithelial cell of the anal column." + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism involving those compounds formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism." + "Any process that decreases the rate, frequency or extent of the transition where a mesenchymal cell establishes apical/basolateral polarity,forms intercellular adhesive junctions, synthesizes basement membrane components and becomes an epithelial cell that will contribute to the shaping of the metanephros." + "A specialized cell involved in sensory perception of smell." "FMA:67870" + "Odontoid tissue that is deposited by cementoblasts onto dentine tissue and functions to attach teeth, odontodes and other odontogenic derivatives to bone tissue and the integument." "MA:0002541 Wikipedia:Cementum BTO:0002525 NCIT:C32276 UMLS:C0011343 EMAPA:35203 SCTID:362114003 XAO:0004196 VSAO:0000062 CALOHA:TS-2163 FMA:55630 MESH:D003739" + "Any process that modulates the frequency, rate or extent of B cell chemotaxis." + "Great vessels is a term used to refer collectively to the large vessels that bring blood to and from the heart." "EMAPA:36460 SCTID:304066000 Wikipedia:Great_vessels" + "a KNDy neuron that is located in the arcuate nucleus of the hypothalamus." + "An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition]." "VHOG:0001251 GAID:468 UMLS:C0003842 EMAPA:35147 ZFA:0000005 galen:Artery MESH:D001158 EHDAA2:0003253 FMA:50720 CALOHA:TS-0054 XAO:0000114 NCIT:C12372 TAO:0000005 EFO:0000814 MIAA:0000034 AAO:0010211 Wikipedia:Artery MA:0000064 AEO:0000208 EV:0100026 SCTID:362877004 BTO:0000573 MAT:0000034" + "A protein with core architecture consisting of one Prominin (Pfam:PF05478) domain. The prominins are an emerging family of proteins that, among the multispan membrane proteins, display a novel topology. Mouse and human prominin and prominin-like 1 are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain." "PIRSF:PIRSF017831 PANTHER:PTHR22730" + "Any process that activates or increases the frequency, rate, or extent of germinal center formation." + "The developmental process pertaining to the initial formation of a camera-type eye from unspecified neurectoderm. This process begins with the differentiation of cells that form the optic field and ends when the optic cup has attained its shape." + "Any process that activates or increases the frequency, rate or extent of chondrocyte hypertrophy." + "The crista ampullaris is the sensory organ of rotation located in the semicircular canal of the inner ear. The function of the crista ampullaris is to sense angular acceleration and deceleration." "NCIT:C32063 FMA:77714 MA:0002771 UMLS:C0229465 Wikipedia:Crista_ampullaris EMAPA:32791 SCTID:368953000" + "A thickened round patch of lymphoid tissue located at the ileocecal junction adjacent to the sacculus rotundus." "SCTID:14239003" + "Any process that activates or increases the frequency, rate or extent of osteoblast differentiation." + "Any cell that is located within the interstitium between the cells most prominent in defining a given tissue. \"Interstitial cell\" is a morphological term and refers to a variety of cells with differing origins and phenotypes." + "Any process that modulates the frequency, rate, or extent of B cell tolerance induction." + "Lamina propria that is part_of the small intestine." "SCTID:63588008 FMA:15651 NCIT:C49297 MA:0001554 EMAPA:35779 UMLS:C1711325" + "Any process that increases the rate, frequency, or extent of epithelial to mesenchymal transition. Epithelial to mesenchymal transition is where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell." + "An adhesion G protein-coupled receptor E1 that is encoded in the genome of human." "UniProtKB:Q14246 DTO:02100089" + "Any process that modulates the frequency, rate, or extent of leukocyte activation." + "A developmental process, independent of morphogenetic (shape) change, that is required for the facial nerve to attain its fully functional state. This sensory and motor nerve supplies the muscles of facial expression and the expression and taste at the anterior two-thirds of the tongue. The principal branches are the superficial opthalmic, buccal, palatine and hyomandibular. The main trunk synapses within pterygopalatine ganglion in the parotid gland and this ganglion then gives of nerve branches which supply the lacrimal gland and the mucous secreting glands of the nasal and oral cavities." + "A protein that is a translation product of the human ACP5 gene or a 1:1 ortholog thereof." "PIRSF:PIRSF000898" + "Any process that modulates the frequency, rate, or extent of natural killer cell mediated cytotoxicity." + "Any process that activates or increases the frequency, rate or extent of apoptotic process involved in outflow tract morphogenesis." + "A cell type that secretes 5-Hydroxytryptamine (serotonin)." + "Any process that activates or increases the frequency, rate, or extent of T cell anergy." + "A myocardium that is part of a right ventricle of a heart." "FMA:9535 MA:0002984 SCTID:362020004" + "Any process that activates or increases the frequency, rate or extent of the regulated release of glucagon." + "Portion of tissue on the side of the lumen of the neural tube." "EMAPA:16166 TAO:0001435 EHDAA:2873 ZFA:0001435 EHDAA2:0001257 EHDAA:912 VHOG:0000513" + "The deposition of hydroxyapatite, a form of calcium phosphate with the formula Ca10(PO4)6(OH)2, in bone tissue." + "Any process that activates or increases the frequency, rate or extent of granulosa cell apoptotic process." + "FMA:19979 MA:0002737 EMAPA:35902" + "A complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm." "Wikipedia:Gastrulation" + "Any process that modulates the frequency, rate or extent of the specification, formation or maintenance of anisotropic intracellular organization or cell growth patterns." + "A killer cell lectin-like receptor subfamily B member 1C that is encoded in the genome of mouse." "UniProtKB:P27814" + "The process whose specific outcome is the progression of the corneocyte over time, from its formation to the mature structure. A corneocyte is the last stage of development of a keratinocyte where the keratinocyte flattens, loses its nucleus and eventually delaminates from the epidermis." + "A zone of skin that is above the iliac crest in the pelvic girdle bone/zone." + "A myeloblast committed to the neutrophil lineage. This cell type is GATA-1 positive, C/EBPa-positive, AML-1-positive, c-myb-positive and has low expression of PU.1 transcription factor." + "Any process that stops or reduces the activity of a transporter." + "A transcription factor PU.1 that is encoded in the genome of human." "UniProtKB:P17947 Reactome:R-HSA-8865503" + "The mucous membrane lining the urinary bladder." "NCIT:C32205 EMAPA:35897 FMA:15928 UMLS:C0227691 EFO:0000293 SCTID:362224004 galen:MucousMembraneOfUrinaryBladder MA:0001692" + "Any process that modulates the frequency, rate or extent of pro-B cell differentiation." + "Epithelial tube that transports milk[GO]." "CALOHA:TS-2385 UMLS:C0222613 SCTID:361719004 MA:0000791 NCIT:C32910 EMAPA:35538 BTO:0002845 Wikipedia:Lactiferous_duct FMA:58006" + "A precursor of the cells that form the dorsal vessel of arthropods." "FBbt:00001666" + "An ecto-epithelial cell of the prostate gland that secretes hormones." "FMA:74390 FMA:86774 CALOHA:TS-1280" + "Mature CD8_alpha-low Langerhans cell is a CD8_alpha-low Langerhans cell that that is CD80-high, CD86-high, MHCII-high and is CD83-positive." + "Any process that modulates the frequency, rate or extent of reproductive process." + "The progression of the cystic duct over time, from its formation to the mature structure. The cystic duct runs from the gallbladder to the common bile duct." + "An adrenal gland that is in the right side of the abdomen." "UMLS:C0229559 NCIT:C49325 SCTID:281625001 FMA:15629 MA:0000719 EMAPA:37357" + "A(n) brush cell that is part of a(n) epithelium of lobar bronchus." + "A segment of autopod that is part of a pes." "SCTID:362887000 FMA:24993" + "The nephron epithelium is a tissue that covers the surface of a nephron." + "Any basket cell that is part of a Ammon's horn." + "Any process that modulates the frequency, rate or extent of calcium ion transmembrane transporter activity." + + "A rapidly proliferating population of cells that differentiate from stem cells of the intestinal crypt of the small intestine. Stem cells located in the crypts of Lieberkühn give rise to proliferating progenitor or transit amplifying cells that differentiate into the four major epithelial cell types. These include columnar absorptive cells or enterocytes, mucous secreting goblet cells, enteroendocrine cells and paneth cells." + "A bronchiole that is part of a right lung [Automatically generated definition]." "EMAPA:35425 UMLS:C0225670 NCIT:C49279 MA:0001787 SCTID:200089000" + "The orderly movement of an astrocyte cell through the telencephalon." + "The process in which neuronal axons and dendrites become coated with a segmented lipid-rich sheath (myelin) to enable faster and more energetically efficient conduction of electrical impulses. The sheath is formed by the cell membranes of oligodendrocytes in the central nervous system. Adjacent myelin segments are separated by a non-myelinated stretch of axon called a node of Ranvier." + "The process in which the anatomical structures of embryonic epithelia are generated and organized." + "A NK1.1-positive T cell that is Ly49D-negative." + "An oxytocin receptor that is encoded in the genome of human." "UniProtKB:P30559 DTO:02100725 Reactome:R-HSA-388428" + "Any process that modulates the rate, frequency or extent of keratinocyte proliferation. Keratinocyte proliferation is the multiplication or reproduction of keratinocytes, resulting in the expansion of a cell population." + "The chemical reactions and pathways involving proteoglycans, any glycoprotein in which the carbohydrate units are glycosaminoglycans." + "Any process that modulates the frequency, rate or extent of hyaluronan biosynthetic process." + "Any process that decreases the rate, frequency or extent of the chemical reactions and pathways involving acetylcholine, the acetic acid ester of the organic base choline. Acetylcholine is a major neurotransmitter and neuromodulator both in the central and peripheral nervous systems. It also acts as a paracrine signal in various non-neural tissues." + "Distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP]." "EV:0100098 GAID:0000004 CALOHA:TS-1090 EHDAA2:0000174 MA:0000380 SCTID:302512001 EHDAA:9328 UMLS:C0005682 FMA:15900 Wikipedia:Urinary_bladder EMAPA:18321 NCIT:C12414 VHOG:0000740 galen:UrinaryBladder XAO:0000154 MIAA:0000122 EFO:0000290 MAT:0000122 MESH:D001743 AAO:0000623 BTO:0001418" + "An interleukin-5 receptor subunit alpha that is encoded in the genome of mouse." "UniProtKB:P21183" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of epinephrine into a cell." + "A specialized epithelial cell involved in sensory perception. Restricted to special sense organs of the olfactory, gustatory, and vestibulocochlear receptor systems; contain sensory cells surrounded by supportive, non-receptive cells." "BTO:0004301" + "Any process that stops, prevents, or reduces the frequency, rate or extent of protein complex assembly." + "Any process that stops, prevents, or reduces the frequency, rate or extent of osteoclast differentiation." + "The vesicular release of gamma-aminobutyric acid (GABA). from a presynapse, across a chemical synapse, the subsequent activation of GABA receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse." + "Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins." + "The process in which the anatomical structures of cartilage in the trachea are generated and organized." + "The process whose specific outcome is the progression of the metanephric distal tubule over time, from its formation to the mature structure. The metanephric distal tubule is a metanephric nephron tubule that begins at the metanephric macula densa and extends to the metanephric connecting tubule." + "Any process that modulates the frequency, rate, or extent of peripheral tolerance induction." + "A CD8-positive, CD4-negative thymocyte that expresses high levels of the alpha-beta T cell receptor and is CD69-positive." + "The series of molecular signals mediated by the detection of a hormone." + "Development of a rod cell, one of the sensory cells in the eye that reacts to the presence of light. Rod cells contain the photopigment rhodopsin or porphyropsin and are responsible for vision in dim light." + "Any tagma (UBERON:6000002) that is part of some larva (UBERON:6001727)." + "The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks)." "TADS:0000040 GAID:75 galen:Mouth BTO:0001090 TGMA:0000131 MA:0000341 MAT:0000038 TAO:0000590 SCTID:21082005 ZFA:0000590 MA:0002474 FMA:49184 BTO:0004698 AAO:0010355 VHOG:0000280 MIAA:0000038 EMAPA:16262 MESH:D009055 TAO:0000547 EFO:0000825 http://purl.obolibrary.org/obo/uberon/images/lamprey_sucker_rosava_3238889218.jpg CALOHA:TS-1315 EHDAA:542 VHOG:0000812 XAO:0003029 ZFA:0000547 Wikipedia:Mouth EHDAA2:0001326" + "The regions of the spinal cord that are largely or entirely composed of myelinated nerve cell axons and contain few or no neural cell bodies or dendrites." "BAMS:SCwhite EMAPA:35795 FMA:83945 MA:0000910 SCTID:279436006 DHBA:146035088 NCIT:C33893 UMLS:C0458457" + "The process whose specific outcome is the progression of a megakaryocyte cell over time, from its formation to the mature structure. Megakaryocyte development does not include the steps involved in committing a cell to a megakaryocyte fate. A megakaryocyte is a giant cell 50 to 100 micron in diameter, with a greatly lobulated nucleus, found in the bone marrow." + "The process in which the metanephric comma-shaped body is generated and organized. The metanephric comma-shaped body is the precursor structure to the metanephric S-shaped body that contributes to the morphogenesis of a nephron in the metanephros." + "A neuron that is part of the somatic sensory system. Somatosensory neurons innervate the skin or integument to detect different types of thermal, chemical, and mechanical touch stimuli." + "Any process that activates or increases the frequency, rate or extent of neuronal action potential." + "The fibrous supportive tissue of the mammary gland." "EMAPA:35537 FMA:74483 MA:0002897 FMA:74479" + "The chemical reactions and pathways resulting in the formation of C21-steroid hormones, steroid compounds containing 21 carbons which function as hormones." + "Any process that activates or increases the frequency, rate or extent of T cell differentiation in the thymus." + "Mesenchyme that is part of a pharyngeal arch 4." "FMA:295702 EMAPA:16770 EHDAA:1677 EHDAA2:0000096 VHOG:0001052" + "Any process that modulates the frequency, rate or extent of plasmatocyte differentiation." + "A process in which force is generated within skeletal muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. In the skeletal muscle, the muscle contraction takes advantage of an ordered sarcomeric structure and in most cases it is under voluntary control." + "Binding to hydroxyapatite, the calcium phosphate mineral of formula Ca10(PO4)6(OH)2 found both in rocks of nonorganic origin and as a component of bone and dentin." + "The process that gives rise to the embryonic heart tube. This process pertains to the initial formation of a structure from unspecified parts. The embryonic heart tube is an epithelial tube that will give rise to the mature heart." + "Either of the two roots that come of the vestibulocochlear nerve." "BIRNLEX:1636 FMA:72499 DMBA:17746 neuronames:605 BAMS:8nf BIRNLEX:1519 DHBA:12868" + "An epithelium that is part of an external naris [Automatically generated definition]." "MA:0001321 EMAPA:18596" + "Obsolete. Use PO:0000353 from Plant Ontology instead. Cell in exodermis or endodermis that remains thin walled when the associated cells develop thick secondary walls. Has casparian strip in endodermis." + "The part of the ventral body cavity that is within the pelvis." "MA:0003089 FMA:9738 Wikipedia:Pelvic_cavity EMAPA:37235 SCTID:281903009" + "A region of the brain consisting of a collection of neurons located in the forebrain ventral to the caudate and putamen. (caudoputamen in rodent) and continuous with these structures. There is no distinct boundary between the nucleus accumbens and the caudate/putamen, but in rodents, it can be identified by its lack of traversing fiber bundles in comparison to the dorsal striatum. Its principle neuron is the medium spiny neuron. Together with the neostriatum (caudate nucleus and putamen), the nucleus accumbens forms the striatum." "MBA:56 DHBA:10339 SCTID:427667007 FMA:61889 EMAPA:32789 EFO:0000906 UMLS:C0028633 BAMS:Acb GAID:672 BAMS:ACC BTO:0001862 neuronames:277 EHDAA2:0004707 NCIT:C52733 MESH:D009714 Wikipedia:Nucleus_accumbens BIRNLEX:727 PBA:10092 BAMS:ACB BM:Ac MA:0000892 HBA:4290 MAT:0000512" + "The first part of the small intestine. At the junction of the stomach and the duodenum the alimentary canal is inflected. The duodenum first goes anteriorly for a short distance, turns dorsally, and eventually caudally, thus it is a U-shaped structure with two horizontal sections (a ventral and a dorsal one)." "galen:Duodenum BTO:0000365 CALOHA:TS-0214 NCIT:C12263 EFO:0000851 GAID:284 EMAPA:18852 VHOG:0000052 SCTID:181247007 FMA:7206 MIAA:0000044 MAT:0000044 EV:0100073 AAO:0010402 Wikipedia:Duodenum MESH:D004386 XAO:0000236 UMLS:C0013303 MA:0000338" + "The smooth muscle tissue surrounding the epithelium of the ureter." "EMAPA:28811" + "The process whose specific outcome is the progression of any organ involved in hematopoiesis (also known as hemopoiesis) or lymphoid cell activation over time, from its formation to the mature structure. Such development includes differentiation of resident cell types (stromal cells) and of migratory cell types dependent on the unique microenvironment afforded by the organ for their proper differentiation." + "A sub-portion of the loop of Henle in the nephron of the kidney that is permeable to ions but not to water." "Wikipedia:Thin_ascending_limb_of_loop_of_Henle MA:0001678 EMAPA:28328 FMA:17720 EMAPA:28361" + "Any process that modulates the frequency, rate or extent of the controlled release of a protein from a cell." + "Subcortical brain region lying anterior to the hippocampal formation in the temporal lobe and anterior to the temporal horn of the lateral ventricle in some species. It is usually subdivided into several groups. Functionally, it is not considered a unitary structure (MM)." "VHOG:0001277 BAMS:AMY EMAPA:36051 Wikipedia:Amygdala MA:0000887 BAMS:Amg BTO:0001042 UMLS:C0002708 BIRNLEX:1241 BAMS:Amy EMAPA:32672 SCTID:279404004 BM:Tel-Am HBA:4327 EV:0100190 MIAA:0000289 neuronames:237 FMA:61841 CALOHA:TS-0037 EFO:0000252 BAMS:Amygdala EV:0100189 NCIT:C12440 MESH:D000679 DHBA:10361 BAMS:Amygdaloid_complex MAT:0000289 GAID:616 PBA:4002" + "Any apoptotic process that occurs in a hippocampal neuron." + "A lymphocyte antigen 75 that is encoded in the genome of human." + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a plasma membrane bounded prolongation or process extending from a cell, e.g. a cilium or axon." + "Any process that modulates the frequency, rate or extent of fat cell proliferation." + "An innate lymphoid cell in the human with the phenotype CD34-negative, CD117-positive, and a precusor to NK cells, ILC2 cells, and ILC3 cells." + "A progesterone secreting cell in the corpus luteum that develops from theca cells." "FMA:18690 BTO:0002850" + "A funiculus of neuraxis that is part of a spinal cord." "neuronames:2760 FMA:77460" + "BIRNLEX:2599 UMLS:C0457466 SCTID:278325008 FMA:6005" + "The process in which a relatively unspecialized cell acquires specialized features of a myoblast. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into striated muscle fibers." + "The directed movement of interneurons from the subpallium to the cortex during forebrain development." + "The process in which a myeloid precursor cell acquires specialized features of an erythrocyte without a nucleus. An example of this process is found in Mus musculus." + "SCTID:308881001 EHDAA:4776 EMAPA:16680 EHDAA2:0000581" + "The collection of all skeletal elements in an individual limb or fin." "VSAO:0000301" + "The series of molecular signals generated as a consequence of a serotonin receptor binding to one of its physiological ligands." + "A CD4-positive, alpha-beta T cell that has the phenotype T-bet-positive, CXCR3-positive, CCR6-negative, and is capable of producing interferon-gamma." "FMA:84382 BTO:0001678" + "The process in which a relatively unspecialized cell acquires specialized features of a sinoatrial (SA) node cell. SA node cells are pacemaker cells that are found in the sinoatrial node." + "A neuroblast derived from a neural crest cell." + "Any layer of the epidermis that is superior to the stratum basale." "EMAPA:35315 MA:0000808" + "The series of events involved in the perception of smell in which an olfactory chemical stimulus is received and converted into a molecular signal." + "The process in which the anatomical structures of a prostate gland are generated and organized." + "Any process that activates or increases the frequency, rate or extent of gliogenesis, the formation of mature glia." + + "A portion of smooth muscle tissue that is part of a lower respiratory tract [Automatically generated definition]." "EMAPA:35520 MA:0002410" + "The process of shaping a trabecula in an organ. A trabecula is a small, often microscopic, tissue element in the form of a small beam, strut or rod, which generally has a mechanical function. Trabecula are usually but not necessarily, composed of dense collagenous tissue." + "A natural killer cell receptor 2B4 that is encoded in the genome of mouse." "UniProtKB:Q07763" + "The rapidly proliferating mass of cells at the caudal extremity of the embryo; remnant of the primitive node." "MAT:0000070 XAO:0000107 EHDAA2:0001976 AAO:0011104 ZFA:0000077 EFO:0002748 EMAPA:16580 BTO:0001445 MIAA:0000070 VHOG:0000201 TAO:0000077 EHDAA:1595" + "A post-anal tail that attaches outside the tail." + "Any process that modulates the frequency, rate or extent of eosinophil activation." + "Any process that activates or increases the frequency, rate or extent of eosinophil degranulation." + "A myeloid dendritic cell found in the blood that is CD1c-positive." + "The progression of the descending aorta over time, from its initial formation to the mature structure. The descending aorta is the portion of the aorta in a two-pass circulatory system from the arch of aorta to the point where it divides into the common iliac arteries. In a two-pass circulatory system blood passes twice through the heart to supply the body once." + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving lipids." + "Any process that modulates the frequency, rate or extent of male germ cell proliferation." + "The chemical reactions and pathways resulting in the formation of compounds derived from amino acids, organic acids containing one or more amino substituents." + "Any process that decreases the rate, frequency or extent of mononuclear cell migration. Mononuclear cell migration is the movement of a mononuclear cell within or between different tissues and organs of the body." + "NLXANAT:20090502" + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells." + "A phagocytic cell formed by the fusion of macrophages, occurs in chronic inflammatory responses to persistent microorganism such as M.tuberculosis, component of granulomas. Sometimes used to refer to megakaryocytes." "FMA:83035 MESH:D015726 BTO:0003107" + "The second pharyngeal arch will form the hyoid apparatus. The cranial neural crest cells that populate the second pharyngeal arch emerge primarily from rhombomere 4 and will form skeletal elements." "FMA:293017 TAO:0001596 EHDAA2:0000050 ZFA:0001611 NCIT:C34288 SCTID:308768003 EHDAA:611 EMAPA:16272 AAO:0010363 VHOG:0000297 XAO:0000098 Wikipedia:Second_pharyngeal_arch" + "A lymphatic endothelial cell located in the subcapsular sinus floor of a lymph node. In human, it's characterized by a unique marker expression (TNFRSF9+)." + "A B cell that is mature, having left the bone marrow. Initially, these cells are IgM-positive and IgD-positive, and they can be activated by antigen." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of a nitric-oxide synthase enzyme." + "Any process that activates or increases the frequency, rate or extent of cytotoxic T cell differentiation." + "The directed movement of norepinephrine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Norepinephrine (3,4-dihydroxyphenyl-2-aminoethanol) is a hormone secreted by the adrenal medulla and a neurotransmitter in the sympathetic peripheral nervous system and in some tracts of the CNS. It is also the biosynthetic precursor of epinephrine." + "A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities." + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amino acids." + "The molecular layer of the dentate gyrus that is bounded by the pial surface superficially and the dentate gyrus granule cell layer deep. It is divided into 2 or more sublayers." "BIRNLEX:4127 MBA:10703 BAMS:Mol FMA:83677 neuronames:2121 EMAPA:35279 MA:0003122 BAMS:mo" + "A luminal layer of epithelium that is part of a prostate gland." "FMA:74262" + "The deep auricular artery often arises in common with the anterior tympanic artery. It ascends in the substance of the parotid gland, behind the temporomandibular articulation, pierces the cartilaginous or bony wall of the external acoustic meatus, and supplies its cuticular lining and the outer surface of the tympanic membrane. It gives a branch to the temporomandibular joint." "FMA:49689 Wikipedia:Deep_auricular_artery SCTID:147157007" + "A mature CD8-positive, CD4-negative alpha-beta T cell found in the thymus that is CD24-low and has high expression of the T cell receptor." + "Any process that decreases the rate, frequency or extent of mast cell chemotaxis. Mast cell chemotaxis is the movement of a mast cell in response to an external stimulus." + + "The directed movement of epinephrine into a cell, typically presynaptic neurons or glial cells. Epinephrine is a hormone produced by the medulla of the adrenal glands that increases heart activity, improves the power and prolongs the action of muscles, and increases the rate and depth of breathing. It is synthesized by the methylation of norepinephrine." + "A renal beta-intercalated cell that is part of the cortical collecting duct. The medullary collecting duct does not contain the renal beta-intercalated cell type." + "A thymic medullary epithelial cell that expresses typical tuft cell markers instead of classical mTEC or cTEC markers. This population has a bulbous-like structure." + "The hydrolysis of a peptide bond or bonds within a protein by lysosomal resident proteases contributing to antigen processing and presentation." + "A neuromuscular junction in which the target muscle cell is a somatic muscle myotube, such as an arthropod somatic muscle cell." + "Immature CD11c-negative plasmacytoid dendritic cell is a CD11c-negative plasmacytoid dendritic cell is CD80-negative, CD86-low and MHCII-low." + "The vessels formed within the third pair of branchial arches in embryogenesis." "TAO:0005007 Wikipedia:Aortic_arches#Arch_3 SCTID:308776001 VHOG:0000147 EMAPA:16687 ZFA:0005007 XAO:0000344 AAO:0010419 EHDAA2:0000070" + "The canals that carry bile in the liver between the intralobular ducts and the biliary ductules; interlobular bile ducts are part of the interlobular portal triad." "FMA:15767 MA:0002668 SCTID:83488001 Wikipedia:Interlobular_bile_ducts UMLS:C0227515 NCIT:C32827" + + "Any process that increases the rate, frequency or extent of macrophage chemotaxis. Macrophage chemotaxis is the movement of a macrophage in response to an external stimulus." + "Any process that increases the rate, frequency or extent of macrophage cytokine production. Macrophage cytokine production is the appearance of a chemokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." + "A cell that moves by its own activities." + "Any process that activates or increases the frequency, rate or extent of cation transmembrane transport." + "The change in morphology and behavior of a microglial cell resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor." + "The process whose specific outcome is the progression of the pharyngeal muscle over time, from its formation to the mature structure. A pharyngeal muscle is any muscle that forms part of the pharynx." + "Any process that activates or increases the frequency, rate or extent of calcitonin secretion." + "Any process that stops, prevents, or reduces the frequency, rate or extent of tooth mineralization, the deposition of calcium salts in tooth structures." + "Any process that modulates the frequency, rate, or extent of mast cell apoptotic process." + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." + "http://en.wikipedia.org/wiki/Collecting_duct_system#Intercalated_cells KUPO:0001129" + "Anatomical cavity at the start of the digestive tract that that is enclosed by the mouth. The boundaries and contents vary depending on the species. In vertebrates, the boundaries are the oral opening, the cheeks, the palate and (if present) the palatoglossal arch - if this is not present then the mouth and pharynx form the oropharyngeal cavity. The buccal cavity contains the teeth, tongue and palate (when present)." "TGMA:0000102 FMA:20292 BSA:0000107 WBbt:0005255 HAO:0000669 VHOG:0000188 TAO:0001027 SCTID:181220002 ZFA:0001027 AAO:0000960 EFO:0001975 XAO:0000126 NCIT:C12421 AAO:0000053 EV:0100057 EMAPA:18399 EHDAA:6970 EHDAA2:0001324 CALOHA:TS-1315 EMAPA:17411 UMLS:C0226896" + "A CD38-negative naive B cell is a mature B cell that has the phenotype CD38-negative, surface IgD-positive, surface IgM-positive, and CD27-negative, that has not yet been activated by antigen in the periphery." + "A neural progenitor cell that is the daughter of a neuroblast (sensu arthopoda). The progeny of ganglion mother cells develop into neurons, glia and (occasionally) epithelial cells." "FBbt:00005149" + "The process whose specific outcome is the progression of the myoblast over time, from its formation to the mature structure. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers." + "Any process that stops, prevents or reduces the frequency, rate or extent of extracellular matrix organization." + "Diploid cell produced by the fusion of sperm cell nucleus and egg cell." "BTO:0000854 EHDAA2:0004546 FMA:72395" + "Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified]." "EHDAA2:0003098 FMA:9602 NCIT:C12704 UMLS:C0014133 GAID:335 Wikipedia:Endocrine_gland MESH:D004702 CALOHA:TS-1300 BTO:0001488 AEO:0000098 SCTID:40818001 MA:0002563 EMAPA:35999" + "FMA:83450" + "A leukocyte immunoglobulin-like receptor subfamily member that is a translation product of the human LILRA4 gene or a 1:1 ortholog thereof. This gene is a member of a lineage-specific gene expansion in primates." "IUPHARobj:2896" + "A thymic epithelial cell located within the subcapsular region of the thymus." + "The larger of two types of asexual spores formed by some fungi; usually round or oblong." "FAO:0000038" + "A protein that includes at least one glycosylated residue." + "A flexible rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In some chordates, it persists throughout life as the main axial support of the body, while in most vertebrates it becomes the nucleus pulposus of the intervertebral disc. The notochord is found ventral to the neural tube." "FMA:85521 http://evolution.berkeley.edu/evolibrary/images/history/notochords.jpg Wikipedia:Notochord EHDAA2:0001277 EHDAA:6021 MAT:0000281 NCIT:C12463 EV:0100002 GAID:1311 AAO:0000327 UMLS:C0028439 XAO:0000055 CALOHA:TS-0690 VSAO:0000032 MESH:D009672 SCTID:308820002 VHOG:0000199 EHDAA:1241 BTO:0001768 TAO:0000135 EMAPA:16191 ZFA:0000135" + "The loose collection of neurons that reside in the rostral medulla close to the medullary surface, ventral and immediately caudal of nVII, that are crucial for CO2 sensing in the brain." "MA:0003022 DHBA:12531 DMBA:17327" + "The multiplication or reproduction of epithelial cells, resulting in the expansion of a cell population. Epithelial cells make up the epithelium, the covering of internal and external surfaces of the body, including the lining of vessels and other small cavities. It consists of cells joined by small amounts of cementing substances." + "The small terminal dilation of the alveolar ducts around which the alveoli form pocket-like clusters." "FMA:7317 UMLS:C0225691 NCIT:C32057 EMAPA:35119 BTO:0000061 Wikipedia:Alveolar_sac SCTID:361964007 MA:0000418" + "An endothelial cell that lines a surface of a cardiac valve leaflet. Along with valve interstitial cells, a valve endothelial cell maintains tissue homeostasis for the function of cardiac valves through secreting biochemical signals, matrix proteins and matrix remodeling enzymes." + "A mitotic cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell." + "An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. In mammals, endothelial cell has vimentin filaments and is derived from the mesoderm." "FMA:66772 CALOHA:TS-0278 BTO:0001176" + "The process whose specific outcome is the progression of an epithelial cell over time, from its formation to the mature structure. An epithelial cell is a cell usually found in a two-dimensional sheet with a free surface." + "A subdivision of the autopod that has as part a series of phalanges together with associated vasculature, musculature, integument and nerves. It is continuous with the metapodial subdivision of the autopod, but does not include the metapodials. In species such as humans, fully formed digits are distinct, whereas in other species the digits may be connected by interdigital webbing, or may be completely unseparated (for example, in cetaceans)." "UMLS:C0582802 XAO:0003032 AAO:0011126 MA:0000690 MIAA:0000285 NCIT:C40186 SCTID:361367007 VHOG:0000944 MAT:0000285 EFO:0000881 EMAPA:32725 Wikipedia:Digit_(anatomy) galen:Digit" + "A lymphatic vessel that is part of an endometrium." + "The process in which a relatively unspecialized cell acquires specialized features of a blood vessel endothelial cell of the heart. Blood vessel endothelial cells are thin flattened cells that line the inside surfaces of blood vessels." + "The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation." "EV:0100027 FMA:3734 galen:Aorta Wikipedia:Aorta SCTID:181298001 XAO:0003010 MA:0000062 UMLS:C0003483 EMAPA:18601 MIAA:0000035 NCIT:C12669 AAO:0010213 BTO:0000135 CALOHA:TS-0046 MESH:D001011 GAID:469 MAT:0000035 VHOG:0001523 EFO:0000265" + "BAMS:PVCo UMLS:C0926558 HBA:9533 DHBA:12441 BIRNLEX:2573 neuronames:724 FMA:72572" + "An endoderm that is part of a buccopharyngeal membrane." "EHDAA2:0000191 EMAPA:16261" + "Any process that stops, prevents, or reduces the frequency, rate or extent of monocyte differentiation." + "Any process that activates or increases the frequency, rate or extent of cyanophore differentiation." + "Any process of the immune system that can contribute to the formation of immunological memory or an immune response based upon activation of immunological memory." + "Any process that modulates the frequency, rate, or extent of excretion, the elimination by an organism of the waste products that arise as a result of metabolic activity." + "The process in which a relatively unspecialized hemopoietic precursor cell acquires the specialized features of a leukocyte. A leukocyte is an achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue." + "A cell secreting sweat, the fluid excreted by the sweat glands of mammals. It consists of water containing sodium chloride, phosphate, urea, ammonia, and other waste products." + "A bone marrow proteoglycan isoform 1 that is encoded in the genome of mouse." "UniProtKB:Q61878-1" + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a bile acid stimulus." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of antimicrobial peptide secretion." + "A mesenchyme that is part of a pharyngeal arch 5." + "KUPO:0001124" + "The chemical reactions and pathways resulting in the formation of keratan sulfate, a glycosaminoglycan with repeat units consisting of beta-1,4-linked D-galactopyranosyl-beta-(1,4)-N-acetyl-D-glucosamine 6-sulfate and with variable amounts of fucose, sialic acid and mannose units; keratan sulfate chains are covalently linked by a glycosidic attachment through the trisaccharide galactosyl-galactosyl-xylose to peptidyl-threonine or serine residues." "RESID:AA0247" + "A CD48 molecule that has been processed by proteolytic cleavage." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of peripheral tolerance induction." + "The assembly of a bleb, a cell extension caused by localized decoupling of the cytoskeleton from the plasma membrane and characterized by rapid formation, rounded shape, and scarcity of organelles within the protrusion. Plasma membrane blebbing occurs during apoptosis and other cellular processes, including cell locomotion, cell division, and as a result of physical or chemical stresses." + "UMLS:C0926557 FMA:72571 BIRNLEX:2572 neuronames:723 BAMS:AVCo HBA:9532 DHBA:12440" + "The process whose specific outcome is the progression of the lacrimal gland over time, from its formation to the mature structure. The lacrimal gland produces secretions that lubricate and protect the cornea of the eye." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of antigen processing and presentation of peptide antigen." + "Any process that modulates the frequency, rate or extent of adipocyte differentiation." + "A cartilaginous condensation that has the potential to develop into a clavicle." "EMAPA:18342" + "A high affinity immunoglobulin gamma Fc receptor I that is encoded in the genome of human." "UniProtKB:P12314" + "In human, ductal plate is a double-layered cylindrical structure of bile duct epithelium that surrounds the portal ramifications by the eighth gestational week. After approximately the 12th gestational week, remodelling of ductal plate begins, and maturity is attained by the end of gestation or early postnatal period." + "An embryo at the neurula stage." "NCIT:C34229 BILA:0000061 UMLS:C1518306 BTO:0001766" + "A lin-negative, MHC-II-negative, CD11c-positive, FLT3-positive cell with intermediate expression of SIRP-alpha." + "KUPO:0001128" + "GC_ID:1" + "A myotube that is part of some somatic muscle. Examples include arthropod somatic muscle cells." + "An epithelium that is part of a breast." "BTO:0001428" + "A process, occurring at the cellular level, that is involved in the reproductive function of a single-celled organism." + "Any process that modulates the frequency, rate or extent of vesicle fusion with Golgi apparatus." + "The fluid-filled cavity that lies between the visceral and parietal pleurae." "SCTID:361999006 VHOG:0000581 EMAPA:16773 MA:0000055 EMAPA:16774 BTO:0004422 EHDAA2:0001475 GAID:95 MESH:D035422 Wikipedia:Pleural_cavity UMLS:C0178802 FMA:9740 NCIT:C12840" + "The progression of the glomerulus over time from its initial formation until its mature state. The glomerulus is a capillary tuft which forms a close network with the visceral epithelium (podocytes) and the mesangium to form the filtration barrier and is surrounded by Bowman's capsule in nephrons of the vertebrate kidney. The glomerulus is part of the nephron and is restricted to one body segment." + "The chemical reactions and pathways resulting in the formation of organic cyclic compound." + "Any collection of muscles that is part of a pelvic complex. The pelvic complex comprises the pelvic girdle and the associated limb or fin." "EMAPA:37864 FMA:71297" + "Any process that stops, prevents, or reduces the frequency, rate, or extent of production of any member of the interleukin-17 family of cytokines." + "Enables the facilitated diffusion of a bicarbonate (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism." + "Stromal matrix surrounding blood vessels within the choroid plexus." "EMAPA:36609 MA:0000825" + "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc." "Reactome:R-HSA-2029475 Reactome:R-HSA-8938314 Reactome:R-HSA-5694583 Reactome:R-HSA-1236938 EC:3.-.-.- Reactome:R-HSA-6786190 Reactome:R-HSA-8952137 Reactome:R-HSA-5695964 Reactome:R-HSA-6788295" + "A zone of skin that is part of a back [Automatically generated definition]." "MA:0000498 FMA:22985 SCTID:181492002 FMA:10462 EMAPA:36392" + "A B220-low CD38-positive IgG-negative memory B cell is a CD38-positive IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype B220-low, CD38-positive, and IgG-positive." + "A fibroblast that is part of lung." "CALOHA:TS-0575 BTO:0000764" + "The increase in size or mass of an entire organism, a part of an organism or a cell, where the increase in size or mass has the specific outcome of the progression of the organism over time from one condition to another." + "A natural killer cell that is CD27-high and CD11b-low." + "A mesothelial cell that is part of the visceral pleura." "FMA:86739" + "Any process that modulates the rate, frequency or extent of neutrophil mediated killing of a target cell, the directed killing of a target cell by a neutrophil." + + "A vein of the lower limb that carries blood from the anterior compartment of the leg to the popliteal vein which is forms when it joins with the posterior tibial vein. Like most deep veins, the anterior tibial vein is accompanied by an artery of the same name, the anterior tibial artery, along its course. [WP,unvetted]." "SCTID:281066000 NCIT:C32115 galen:AnteriorTibialVein FMA:44331 Wikipedia:Anterior_tibial_vein MA:0002244 EMAPA:37135 UMLS:C0226833" + "A myoblast that is commited to developing into a somatic muscle." + "An anatomical junction that connects a stomach and connects a duodenum." "SCTID:264014000 FMA:17046" + "The regulated release of acetylcholine by a cell." + "The process in which the anatomical structures of the glomerulus vasculature are generated and organized. The glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the glomerulus." + "Catalysis of the transmembrane transfer of an ion by a channel that opens when glutamate has been bound by the channel complex or one of its constituent parts." + "Any process that decreases the frequency, rate or extent of metanephric nephron tubule epithelial cell differentiation." + "The ciliary processes are formed by the inward folding of the various layers of the choroid, i.e. , the choroid proper and the lamina basalis, and are received between corresponding foldings of the suspensory ligament of the lens." "FMA:76551 SCTID:280860001 Wikipedia:Ciliary_processes" + "The progression of the ventricular septum over time from its formation to the mature structure." + "The thin epithelium-like membrane composed of ependymal cells that lines the ventricular system of the brain and the spinal cord." "SCTID:12766003 NCIT:C13078 GAID:608 neuronames:1856 UMLS:C0014472 MESH:D004805 EMAPA:37865 BTO:0000401 Wikipedia:Ependyma FMA:242791" + "The developmental process, independent of morphogenetic (shape) change, that is required for a glandular epithelial cell to attain its fully functional state. A glandular epithelial cell is a columnar/cuboidal epithelial cell is a cell found in a two dimensional sheet with a free surface exposed to the lumen of a gland." + "A metaphysis that is part of a metaphysis." "FMA:32830" + "A ciliated columnar epithelium that is part of a oviduct." "MA:0001719 FMA:62016" + "The process whose specific outcome is the progression of a cardiac muscle cell over time, from its formation to the mature state." + "GC_ID:1" + "A mucosa that is part of a tongue [Automatically generated definition]." "SCTID:362092002 EFO:0002553 FMA:54807" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient." + "A proximal mesopodial endochondral element that is part of a hindlimb." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving dopamine." + "The directed movement of nucleic acids, single or double-stranded polynucleotides involved in the storage, transmission and transfer of genetic information, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "Pair of nostrils." "FMA:72005 Wikipedia:Nares" + "An intestinal enteroendocrine cell that is located in a vermiform appendix." + "The chemical reactions and pathways resulting in the formation of any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom." + "A pair of lateral diverticula just over the liver rudiment representing the primordia of the lungs, formed by the floor of the foregut just anterior to the liver diverticulum." "EFO:0002578 XAO:0001002 EMAPA:36007 AAO:0011059" + "GC_ID:1" + "One of sublaminar layers S2 or S3." "CP:0000119" + "The process whose specific outcome is the progression of a cranial ganglion over time, from its formation to the mature structure." + "The process in which epiblast cells acquire specialized features of neuroepithelial cells." + "An artery that originates from the abdominal aorta." "SCTID:281470000" + "A mature NK T cell that predominantly secretes type 2 cytokines such as interleukin-4 and interleukin-13 and enhances type 2 immune responses." + "The process in which the anatomical structures of growth plate cartilage are generated and organized." + "An extravillous trophoblast that is polynuclear." "EFO:0010712" + "The collection of all skeletal elements in an forelimb zeugopod region." "FMA:71199 AAO:0000200 VSAO:0005011" + "An elasticity which is relatively normal or average." + "Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism." + "Intertarsal articulations are the joints of the tarsus. The specific intertarsal articulations are: Talocalcaneal articulation Talocalcaneonavicular articulation Calcaneocuboid articulation Cuneonavicular articulation Cuboideonavicular articulation Intercuneiform articulation Cuneocuboid articulation." "GAID:259 NCIT:C33735 SCTID:361283005 SCTID:182221001 EMAPA:37762 MESH:D013640 UMLS:C1527245 FMA:44281 Wikipedia:Intertarsal_articulations MA:0003112" + "A preadipocyte that is part of an omentum." + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amino acid." + "A differentiated cell that functions as a site of nitrogen fixation under aerobic conditions." "BTO:0000600" + "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes." "NIF_Subcellular:sao1456184038" + "Any process that stops, prevents or reduces the frequency, rate or extent of calcium ion export across the plasma membrane." + "Any process that modulates the frequency, rate or extent of glutamatergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter glutamate." + "A distinct juvenile stage many animals undergo before metamorphosis into adults. Animals with indirect development such as insects, amphibians, or cnidarians typically have a larval phase of their life cycle." "ZFS:0000048 EFO:0001303 MIAA:0000400 OGES:000008 Wikipedia:Larva BTO:0000954 BTO:0000915" + "A submucosa that is part of a bronchus [Automatically generated definition]." "MA:0001837 UMLS:C0225601 NCIT:C49214 BTO:0002108 FMA:62653 SCTID:85546005 EMAPA:37449" + "Hat part of the duodenal wall traversed by the ductus choledochus, ductus pancreaticus, and ampulla." "MA:0003108 EMAPA:37478" + "A lining of mostly endodermal origin, covered in epithelium, which is involved in absorption and secretion. They line various body cavities that are exposed to the external environment and internal organs. It is at several places continuous with skin: at the nostrils, the lips, the ears, the genital area, and the anus. The sticky, thick fluid secreted by the mucous membranes and gland is termed mucus. The term mucous membrane refers to where they are found in the body and not every mucous membrane secretes mucus[WP]." "galen:Mucosa FMA:85355 NCIT:C13166 EV:0100382 MESH:D009092 GAID:297 AEO:0000199 Wikipedia:Mucous_membrane UMLS:C0026724 BTO:0000886 CALOHA:TS-2031 FMA:85358 EHDAA2_RETIRED:0003234 SCTID:361693009" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine." + "A low affinity immunoglobulin gamma Fc region receptor III that is encoded in the genome of mouse." "UniProtKB:P08508" + "An epithelial tube that is fated to become a nephron." + "In mammals, the proximal tubule is a nephron tubule that connects Bowman's capsule to the loop of Henle. It has a brush border epithelial morphology[GO]." "CALOHA:TS-0509 EMAPA:28281 MA:0002611 MESH:D007687 BTO:0001498" + "A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol." "Wikipedia:Vacuole" + "An axon tract that is part of a brain." "FMA:83848" + "Gland of the epithelium lining the oral cavity. The most common are the salivary glands." "VHOG:0000652 EHDAA:2181 EHDAA2:0001327 EMAPA:16723 EMAPA:16572" + "A protein that is a translation product of the human MPO gene or a 1:1 ortholog thereof." "IUPHARobj:2789" + "An organ system subdivision that is a network of vessels capable of removing accumulating protein and fluid from the interstitial space and returning it to the vascular space. In some species, this network is connected to the immune system via lymph nodes and lymphocyte-producing organs, with the whole being the lymphoid system." "MA:0002961 CALOHA:TS-2024 AAO:0010522 Wikipedia:Lymphatic_system EMAPA:18248 SCTID:362597000 EFO:0000870 FMA:7162 VHOG:0001761 MESH:D008208" + + "A retinal ganglion B cell that has post synaptic terminals in S2." + "The vessels formed within the first pair of branchial arches in embryogenesis." "ZFA:0005005 EMAPA:16202 EHDAA2:0000007 TAO:0005005 AAO:0010415 SCTID:308774003 VHOG:0000149 XAO:0000342 EMAPA:16685" + "Any apoptotic process in an erythrocyte." + "A Z-shaped canal running through the temporal bone from the internal acoustic meatus to the stylomastoid foramen. It is located within the middle ear region, according to its shape it is divided into three main segments: the labyrinthine, the tympanic, and the mastoidal segment ." "Wikipedia:Facial_canal FMA:54952" + "EMAPA:18808 FMA:49150 AAO:0010038" + "A stromal cell of the endometrium that is fibroblastic in appearance. During decidualization this cell may differentiate into a decidual stromal cell." "FMA:86490 CALOHA:TS-1266" + "A precursor cell with a limited number of potential fates." "FMA:84782 BTO:0000125" + "Nucleus forming a longitudinal cell column in the medulla, close beneath the floor of the 4th ventricle, containing motor neurons that innervate the muscles of the tongue (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 453)." "neuronames:757 DHBA:12545 MBA:773 BAMS:12 EHDAA2:0004635 BM:XII EV:0100286 NCIT:C12899 MA:0001039 EMAPA:35416 BIRNLEX:2644 UMLS:C0228802 VHOG:0001358 ncithesaurus:Nucleus_of_the_Hypoglossal_Nerve Wikipedia:Hypoglossal_nucleus BAMS:12N HBA:9557 SCTID:47361005 BAMS:XII FMA:54505" + "Any protein complex that is capable of carrying out some part of the process of cell adhesion to the cell matrix or to another cell." + "An erythroid progenitor cell that is CD34-positive and is GlyA-negative." "FMA:83517" + "A process that modulates the formation of a microvillus." + "The process in which a relatively unspecialized cell acquires specialized features of a glial cell in the posterior lateral line nerve." + "A developmental process, independent of morphogenetic (shape) change, that is required for an anatomical structure, cell or cellular component to attain its fully functional state." + "The region of the opening of the uterine cervix into the uterine cavity." "FMA:86485 SCTID:264460007 BTO:0003002 UMLS:C0227837 NCIT:C12309" + "An anatomical cavity that surrounded_by a midgut." "FMA:54366 EMAPA:18377" + "Any process that activates or increases the frequency, rate or extent of mesonephric glomerulus development." + + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus arising within the organism." + "The process in which the anatomical structures of the metanephric glomerulus are generated and organized. The metanephric glomerulus is a capillary tuft surrounded by Bowman's capsule in nephrons of the vertebrate kidney, or metanephros." + "Any process that activates or increases the frequency, rate or extent of the regulated release of serotonin." + "Binding to calcitonin, a peptide hormone responsible for reducing serum calcium levels by inhibiting osteoclastic bone reabsorption and promoting renal calcium excretion. It is synthesized and released by the C cells of the thyroid." + "An extremely flattened cell type found on the inner side of the tympanic membrane. The surface of this cell type carries sparse pleomorphic microvilli that are more common near the junctional zones." "FMA:70626" + "A protein that is a translation product of the human CCK gene or a 1:1 ortholog thereof." + "An inhibitory GABAergic interneuron found in the cerebellar cortex." + "Any process that stops, prevents or reduces the frequency, rate or extent of epithelial cell proliferation involved in lung morphogenesis." + "A killer cell lectin-like receptor subfamily G member 1 that is encoded in the genome of mouse." "UniProtKB:O88713" + "Mesenchyme that is part of a 1st arch maxillary component." "EMAPA:16391 EHDAA2:0000041" + "A CD3 epsilon that is encoded in the genome of mouse." "UniProtKB:P22646" + "The appearance of interleukin-13 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." + "The directed movement of amino acids into the vacuole across the vacuolar membrane." + "OBSOLETE (was not defined before being made obsolete)." + "The biological process whose specific outcome is the progression of a mesonephric glomerulus vasculature from an initial condition to its mature state. This process begins with the formation of the mesonephric glomerulus vasculature and ends with the mature structure. The mesonephric glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the mesonephric glomerulus." + "EMAPA:16758 EHDAA2:0000409" + "A G protein-coupled neurotransmitter receptor activity, occurring in the postsynaptic membrane, involved in regulation of postsynaptic membrane potential." + "Binding to an hormone, a naturally occurring substance secreted by specialized cells that affect the metabolism or behavior of cells possessing functional receptors for the hormone. Hormones may be produced by the same, or different, cell as express the receptor." + "The part of the circulatory system that lies deep beneath the subcutaneous tissue layers away from the surface of the skin." + "An intestinal crypt that is located in the colon. The colonic crypts of Lieberkühn are straight and unbranched and lined largely with goblet cells." "SCTID:19447003" + "Vagal neural crest is adjacent to the first seven somites gives rise to both ganglionic and ectomesenchymal derivatives[ZFA]." "EHDAA2:0002156 VHOG:0001208 XAO:0004191 ZFA:0000818 EHDAA:669 TAO:0000818" + "A large vein that connects the femoral vein to the common iliac vein. Their origin is at the inferior margin of the inguinal ligaments and they terminate when they join the internal iliac veins (to form the common iliac veins). Both external iliac veins are accompanied along their course by external iliac arteries. [WP,modified]." "NCIT:C32560 EHDAA2:0000464 Wikipedia:External_iliac_vein FMA:18883 galen:ExternalIliacVein UMLS:C0226761 SCTID:181400000 MA:0002144 EMAPA:37144" + "A cell whose nucleus has two haploid genomes." "FMA:72300" + "Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule." + "Any process that modulates the frequency, rate, or extent of an acute inflammatory response." + "The process whose specific outcome is the progression of an auditory receptor cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate." + "External part of the nose containing the external nares." "EMAPA:37831 FMA:59515 NCIT:C32566 UMLS:C0458561 SCTID:265785009" + "An eosinophil peroxidase that has been processed by proteolytic cleavage." + "An endolymph filled cavity inside the cochlea, located in between the scala tympani and the scala vestibuli, separated by the basilar membrane and Reissner's membrane (the vestibular membrane) respectively. Houses the organ of Corti[WP]." "UMLS:C1323110 CALOHA:TS-0152 Wikipedia:Cochlear_duct SCTID:279849006 BIRNLEX:2562 MESH:D003053 GAID:874 BTO:0001692 UMLS:C1281166 EHDAA2:0000262 VHOG:0000507 NCIT:C32335 FMA:61119 MA:0000243 EMAPA:17598 EHDAA:4718" + "Conventional dendritic cell is a dendritic cell that is CD11c-high." "FMA:84191" + "EHDAA2:0002173 EMAPA:16759" + "The chemical reactions and pathways involving peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another." + + "Any process that stops, prevents, or reduces the rate of cytotoxic T cell degranulation." + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines." + "A mesothelial cell that is part of the small intestine." + "A thermoreceptor cell that detects increased temperatures." + "Any process that decreases the frequency, rate or extent of the regulated release of insulin that contributes to the response of a cell to glucose." + "A skin gland that is part of a camera-type eye [Automatically generated definition]." "EMAPA:37530 MA:0002451" + "The progression of the sweat gland over time, from its formation to the mature structure. Sweat glands secrete an aqueous solution that is used in thermoregulation." + "Any process that stops, prevents or reduces the frequency, rate or extent of cardiac muscle cell differentiation." + "The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code)." + "An inactive fibroblast; cytoplasm is sparse, endoplasmic reticulum is scanty with flattened nucleus. Term used by some histologists; when fibroblasts become relatively inactive in fiber formation. However, this cell has the potential for fibrogenesis in quiescent connective tissue of the adult, as well as during development, other histologists prefer to use the term fibroblast in all circumstances. These cells represent ~0.5% of peripheral blood leukocytes." "FMA:63879" + "A lumican that is encoded in the genome of human." "UniProtKB:P51884" + "The directed movement of a protein from the cytoplasm to the nucleus." + "The chemical reactions and pathways resulting in the formation of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent." + "The process whose specific outcome is the progression of a nail over time, from its formation to the mature structure. A nail is a horn-like envelope covering the outer end of a finger or toe, and consists of the nail plate, the nail matrix and the nail bed below it, and the grooves surrounding it." + "The layer of connective tissue comprised of the endometrial lining of the uterus which fluctuates in thickness throughout the menstrual cycle." "UMLS:C0227849 MA:0002734 EMAPA:35310 CALOHA:TS-1266 FMA:86487 NCIT:C32516 SCTID:254115004" + + "A peptide hormone secreting cell that secretes gastrin." + "A muscle cell with low content of myoglobin and other oxygen storing proteins. This muscle cell has a white appearance." "FMA:84449" + "The connecting tubule is a tubular segment of the nephron; it connects the distal convoluted tubule to the collecting duct[GO]." "Wikipedia:Connecting_tubule EMAPA:27790 BTO:0004539 MA:0002610 EMAPA:28011 EMAPA:27758" + "Any process that modulates the frequency, rate or extent of Schwann cell differentiation." + "The process whose specific outcome is the development of the umbilical cord, from its formation to the mature structure. The umbilical cord is an organ or embryonic origin consisting of the 2 umbilical arteries and the one umbilical vein. The umbilical cord connects the cardiovascular system of the fetus to the mother via the placenta." + "Any region of a nephron tubule that is straight. Examples: distal convoluted tubule, proximal convoluted tuble." "SCTID:245151008 EMAPA:37489 Wikipedia:Tubuli_seminiferi_recti MA:0002634" + "The process in which a relatively unspecialized cell acquires specialized features of a neuron residing in the cerebral cortex." + "Any process that stops, prevents, or reduces the frequency, rate or extent of dendrite development." + "Enables the transfer of organic hydroxy compound from one side of a membrane to the other." + "An interneuron that is derived from the medial ganglionic eminence." + "Any process that modulates the frequency, rate or extent of protein localization to lysosome." + "A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot." "EHDAA2:0001279 VHOG:0001213 UMLS:C1518430 EHDAA:224 NCIT:C34232 EMAPA:16102 FMA:293135" + "A endothelial cell of the venule that is squamous shaped. This is in contrast to the cubodial shape of high endothelial venule cells." + "A stromal cell found in the lamina propria of the colon." + "OBSOLETE (was not defined before being made obsolete)." + "A thymic medullary epithelial cell considered to be a post-AIRE cell. This group of AIRE-mTECs is heterogeneous and also includes mTECs within Hassall's Corpuscles." + "Any process that activates or increases the frequency, rate or extent of cardiac muscle cell contraction." + "The vesicular release of acetylcholine from a presynapse, across a chemical synapse, the subsequent activation of dopamine receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse." + "The caudalmost subdivision of a digestive tract." "FMA:45618 XAO:0000104 MA:0001527 VHOG:0000459 BILA:0000087 TGMA:0001020 EHDAA:975 BTO:0000510 UMLS:C0231053 AAO:0011052 Wikipedia:Hindgut SCTID:362856002 NCIT:C34188 EMAPA:16715 EHDAA2:0000779" + "A bone element that is part of a jaw region." "EMAPA:35453 SCTID:369003004 MA:0003130" + "Any process that activates or increases the frequency, rate or extent of multiplication or reproduction of fibroblast cells." + "Any process that activates or increases the frequency, rate or extent of pro-T cell differentiation." + "The chemical reactions and pathways resulting in the formation of CD4, a CD marker that occurs on T-helper cells and is involved in MHC class II restricted interactions." + "The movement of a thymocyte through distinct intrathymic niches (e.g. medulla, cortex), where it receives a unique set of developmental cues required for T-cell development." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a carbohydrate stimulus." + "The process in which the anatomical structures of the heart rudiment are generated and organized." + "Any process that stops, prevents or reduces the frequency, rate or extent of bleb assembly." + "The process whose specific outcome is the progression of the metanephric short descending thin limb over time, from its formation to the mature structure. The metanephric short descending thin limb is the descending thin limb of a short nephron in the metanephros that has a squamous epithelial morphology." + "Any process that modulates the frequency, rate or extent of apoptotic process involved in development." + "Any process that modulates the frequency, rate or extent of apical ectodermal ridge formation." + "An outgrowth on the lateral trunk of the embryo that develops into a limb or paired fin. The limb/fin bud is divided into ectoderm and mesenchyme[cjm, modified from MP]." "VHOG:0001258" + "A myoepithelial cell that is part of the secondary lactiferous duct." "FMA:74501" + "The progression of a growth plate cartilage chondrocyte over time from after its fate commitment to the mature cell." + "The process in which a Schwann cell membrane closes around an axon in the peripheral nervous system. This can be a myelinating or a non-myelinating neuron-glial interaction." + "Combining with vasopressin to initiate a change in cell activity." + "Any process that starts or increases the frequency, rate or extent of sister chromatid segregation during mitosis." + "Groove between maxillary prominence and lateral nasal process." "FMA:300055 EHDAA:4770 EMAPA:16679 EHDAA2:0001238 Wikipedia:Lacrimal_groove NCIT:C34218 UMLS:C1513875 VHOG:0001307" + "Cranial nerve that branches into the lateral (to body sense organs) and the intestino-accessorial (to the skin, muscles of shoulder, hyoid, larynx, gut, lungs, and heart)." "VHOG:0000737 BIRNLEX:801 FMA:5731 ZFA:0000453 EFO:0002549 HBA:9337 GAID:721 SCTID:362466001 BAMS:Xn BTO:0003472 EMAPA:37797 BAMS:10n MESH:D014630 MBA:917 Wikipedia:Vagus_nerve neuronames:702 UMLS:C0042276 UMLS:C1305910 AAO:0010475 MA:0001106 galen:VagusNerve XAO:0003097 TAO:0000453 NCIT:C12812" + "A mucosa that is part of a right hepatic duct [Automatically generated definition]." "FMA:14692" + "A nodal myocyte that is part of the sinoatrial node." "FMA:83383" + "SCTID:77852007" + "The progression of the hippocampus over time from its initial formation until its mature state." + "Any process that activates or increases the frequency, rate or extent of response to water deprivation." + "FMA:51797 SCTID:149683007" + "The group of sensory neuron cell bodies associated with the facial nerve (seventh cranial nerve)." "EHDAA:5567 Wikipedia:Geniculate_ganglion EHDAA:6644 NCIT:C12721 EHDAA2:0004623 FMA:53414 GAID:718 EFO:0003669 MA:0001076 SCTID:279076005 BAMS:GgVII ZFA:0001291 EHDAA2:0000491 MESH:D005830 TAO:0001291 EMAPA:17569 VHOG:0000707 neuronames:1535 UMLS:C0017406" + "The most anterior region of the braincase. Provides structural support for peripheral olfactory organ." "AAO:0000986" + "A sex gland that is part of a male reproductive system." "EMAPA:19285 MA:0000399 BTO:0000080" + "Any process that decreases the frequency, rate or extent of myotube differentiation. Myotube differentiation is the process in which a relatively unspecialized cell acquires specialized features of a myotube cell. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse." + "A unit of lung supplied by three to five terminal bronchioles and contained by fibrous septa." "FMA:7414" + "An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section." "EFO:0003497 TAO:0000131 ZFA:0000131" + "The somatic process that results in the generation of sequence diversity of immunoglobulins after induction, and contributes to an immune response." + "The process in which the anatomical structures of a nephrogenic mesenchymal tissue are generated and organized. Nephrogenic mesenchyme is the tissue made up of loosely connected mesenchymal cells in the nephron." + "A protein that is a translation product of the human FOS gene or a 1:1 ortholog thereof." + "Developing superficial cortical layer located just under the pia matter, develops from the marginal layer of the neural tube and becomes cortical layer I." "EMAPA:32713 EMAPA:17546 PBA:294021774" + "A lineage marker-negative, CD34-positive, CD38-positive, IL3r-alpha-positive, IL5r-alpha-positive, and CD45RA-negative eosinophil progenitor cell." + "Any process that activates or increases the frequency, rate or extent of adipocyte differentiation." + "Cartilage which is part of the axial skeleton." "ZFA:0001457" + "A gland that is part of a foregut-midgut junction." "EMAPA:17065 EHDAA2:0000574" + "The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium." "EMAPA_RETIRED:16783 MA:0003193 EMAPA:35362 EMAPA:17152" + "Any process that modulates the frequency, rate, or extent of smooth muscle cell apoptotic process." + "Mural cells are pericytes and the vascular smooth muscle cells (vSMCs) of the microcirculation." + "The developmental process pertaining to the initial formation of a metanephric nephron tubule from unspecified parts. A metanephric nephron tubule is an epithelial tube that is part of a nephron in the metanephros." + "A primitive erythrocyte that has undergone enucleation. This cell type is 3-6 fold bigger than the fetal derived erythrocytes that they co-circulate with during fetal development. Expresses epsilon-gamma hemoglobin chains." + "The orderly movement of a lateral motor column neuron from one site to another. A lateral motor column neuron is a motor neuron that is generated only on limb levels and send axons into the limb mesenchyme." + "The process in which the anatomical structures of the liver are generated and organized." + "A neural crest that has_potential_to_developmentally_contribute_to a spinal cord." "VHOG:0001006 EMAPA:16881 EHDAA:696 EMAPA:16163" + "A nerve that transmits from sensory receptors on the surface of the body to the central nervous system." "Wikipedia:Sensory_nerve EHDAA2:0003200 FMA:5868 AEO:0000201" + "A cell located in the synovial joint." "CALOHA:TS-0995" + "A fused bone consisting of the ilium, ischium and pubis. Together with the sacrum and coccyx, it comprises the pelvis. [WP,modified]." "GAID:205 SCTID:361776002 Wikipedia:Hip_bone FMA:16585" + "The support cell that makes the thecogen dendritic cap - a cuticle-like matrix around the tip of the eo-dendrite and which encloses the soma of the eo-neuron." "FBbt:00005173" + "A B cell that is located in the anorectum." + "A proximal epiphysis that is part of a tibia." "Wikipedia:Upper_extremity_of_tibia FMA:33113 UMLS:C0932431 NCIT:C32722 SCTID:302526005" + "Mature CD11c-low plasmacytoid dendritic cell is a CD11c-low plasmacytoid dendritic cell that is CD83-high and is CD80-positive, CD86-positive, and MHCII-positive." + "The chemical reactions and pathways resulting in the breakdown of aldosterone, a corticosteroid hormone that is produced by the zona glomerulosa of the adrenal cortex and regulates salt (sodium and potassium) and water balance." + "A Leydig cell is a testosterone-secreting cell in the interstitial area, between the seminiferous tubules, in the testis." "EMAPA:29655 CALOHA:TS-1150 BTO:0000755 FMA:72297 MESH:D007985" + "Any process that activates or increases the frequency, rate or extent of somatic stem cell division." + "Any process that activates or increases the frequency, rate or extent of renin secretion into blood stream." + "A nucleus of brain that is part of a brainstem." "EMAPA:32790 MA:0000821" + "Any process that increases the occurrence or rate of mesenchymal stem cell death by apoptotic process that contributes to the shaping of the nephron in the metanephros." + "A mechanoreceptor located in the acoustic maculae and the semicircular canals that mediates the sense of balance, movement, and head position. The vestibular hair cells are connected to accessory structures in such a way that movements of the head displace their stereocilia. This influences the membrane potential of the cells which relay information about movements via the vestibular part of the vestibulocochlear nerve to the brain stem." "FMA:62351" + "An immune response against microbes mediated by anti-microbial peptides in body fluid." + "A CD4-negative, CD8-negative, alpha-beta intraepithelial T cell that is found in the columnar epithelium of the gastrointestinal tract." + "A testicular artery that supplies a left testicle." "UMLS:C0734077 FMA:14760 NCIT:C52739 MA:0002041 EMAPA:37099" + "Any process that modulates the frequency, rate or extent of thyroid-stimulating hormone secretion." + "The directed movement of the outgrowing Malpighian tubule guided by specific chemical cues/signals. Movement may be towards a guidance cue (positive chemotaxis) or away from it (negative chemotaxis). Guidance contributes to the final positioning of the tubule." + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a neuromuscular junction that targets a skeletal muscle fiber." + "OBSOLETE. An intratelencephalic-projecting glutamatergic neuron with a soma found in layer 2/3 of the marmoset primary motor cortex." + "Any process that stops, prevents or reduces the frequency, rate or extent of RNA catabolic process." + "The part of the central nervous system that is involved with movement." "NLXANAT:090805" + "The process in which a relatively unspecialized cell acquires specialized features of an anterior lateral line neuromast mantle cell. Mantle cells are non-sensory cells that surround the sensory strip, separating the neuromast from the epidermis. Mantle cells secrete the cupula in which the ciliary bundles of all of the hair cells are embedded." + "A bistratified amacrine cell with a small dendritic field that has post-synaptic terminals in S1 and the border of S1-S2, and termination of a second arbor within the border of S2-S3 and S3." + "Any process that stops, prevents, or reduces the frequency, rate or extent of blood coagulation." + "Any process that modulates the frequency, rate or extent of pancreatic stellate cell proliferation." + "The series of molecular signals initiated by corticosteroid binding to its receptor, and ending with the regulation of a downstream cellular process, e.g. transcription." + "The metanephric connecting tubule is a tubular segment of the metanephric nephron; it connects the distal convoluted tubule to the collecting duct in the metanephros[GO]." + "Any process that modulates the frequency, rate or extent of any cellular process that depends upon or alters the microtubule cytoskeleton." + "A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities." "Wikipedia:Physical_property" + "An artery that supplies blood to the cerebellum." "Wikipedia:Cerebellar_artery SCTID:278102002 EMAPA:37074 EHDAA:5290 EHDAA2:0000228 NCIT:C52845 MA:0001933 UMLS:C0226246" + "The aggregation, arrangement and bonding together of a set of components to form an MHC class II protein complex." + "Subcortical masses of gray matter in the forebrain and midbrain that are richly interconnected and so viewed as a functional system. The nuclei usually included are the caudate nucleus (caudoputamen in rodents), putamen, globus pallidus, substantia nigra (pars compacta and pars reticulata) and the subthalamic nucleus. Some also include the nucleus accumbens and ventral pallidum." "GAID:617 neuronames:2677 UMLS:C0004781 MESH:D001479 MA:0000184 VHOG:0001696 FMA:84013 EMAPA:32673 Wikipedia:Basal_ganglia MBA:623 HBA:4276 BM:Tel-BG BAMS:BG BIRNLEX:826 PBA:4001 NCIT:C12447" + "Data about an ontology part is a data item about a part of an ontology, for example a term"@en + "Any process that stops, prevents or reduces the frequency, rate or extent of hematopoietic stem cell differentiation." + "The process whose specific outcome is the progression of a mesonephric glomerular visceral epithelial cell over time, from its formation to the mature structure. A mesonephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the mesonephros." + "The process in which the membranous septum is generated and organized. The membranous septum is the upper part of ventricular septum." + "A muscle cell that is part of some somatic muscle." "FBbt:00005073" + "A response that results in a state of tolerance to ketone." + "An ectonucleotide pyrophosphatase/phosphodiesterase family member 3 that is encoded in the genome of mouse." "UniProtKB:Q6DYE8" + "The collection of all skeletal elements in a pelvic appendage region." + "Any fluid produced by a serous gland." "Wikipedia:Serous_fluid" + "A bone that is part of a hindlimb region. Examples: any pes phalanx, femur. Counter-examples: ischium, pubis (they are part of the pelvic girdle)." "GAID:198 NCIT:C12982 SCTID:361370006 UMLS:C0448188 EFO:0003842" + "Binding to ADP, adenosine 5'-diphosphate." + "Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 4th arch mesenchyme." "EHDAA2:0000097 EMAPA:16771" + "A maturity quality inhering in a bearer by virtue the bearer's being not fully grown or developed." + "An artery that supplies a cervical thymus." + "The renal vesicle is the primordial structure of the metanephric nephron epithelium, and is formed by the condensation of mesenchymal cells[GO]." "EMAPA:27678 EHDAA2:0001245 EHDAA:9346" + "An amniotic stem cell is a mesenchymalstem cell extracted from amniotic fluid. Amniotic stem cells are able to differentiate into various tissue type such as skin, cartilage, cardiac tissue, nerves, muscle, and bone" + "A human dendritic cell that expresses the AXL and SIGLEC6 genes." + "A ciliated epithelial cell with a single cilium." + "An acidophilic chromophil cell that of the anterior pituitary gland." "FMA:83093" + "A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part." "AAO:0011000 CARO:0001000 FMA:83115" + "An interleukin-5 receptor subunit alpha that is encoded in the genome of human." "UniProtKB:Q01344" + "Catalytic activity that acts to modify DNA." + "Any process that activates or increases the frequency, rate or extent of protein complex disassembly, the disaggregation of a protein complex into its constituent components." + "A cell that is found in the periacinar space of the exocrine pancreas and in perivascular and periductal regions of the pancreas, and has long cytoplasmic processes that encircle the base of the acinus. Expresses several intermediate filament proteins including vimentin and nestin. Shares many of the characteristics of hepatatic stellate cells, but not stellate cells of the central nervous system. Upon activation, this cell type undergoes morphological and gene expression changes that make the cell suggestive of being a type of myofibroblast." "MESH:D058954" + + "A bridge of mesoderm connecting the caudal end of the young embryo with the trophoblastic tissues; the precursor of the umbilical cord." "UMLS:C1516792 NCIT:C34132 BTO:0004705" + "Any process that activates or increases the frequency, rate or extent of natural killer cell proliferation as part of an immune response." + "The removal of tubulin heterodimers from one or both ends of a microtubule." + "The ridge-shaped grey matter of the spinal cord that extends longitudunally through the center of each half of the spinal cord, and are largely or entirely composed of nerve cell bodies and their dendrites and some supportive tissue." "NCIT:C32696 BAMS:Scgrey UMLS:C0475853 MA:0000002 NLXANAT:100204 EMAPA:35792 SCTID:279441003 FMA:256580 neuronames:2619 DHBA:146035048" + "A glycoprotein membrane surrounding the plasma membrane of an oocyte. It is a vital constitutive part of the latter, external but not extraneous to it. The zona pellucida first appears in multilaminar primary oocytes." "EMAPA:16035 ZFA:0001111 UMLS:C0043519 FMA:18674 TAO:0001111 EHDAA:62 MESH:D015044 BTO:0003135 EHDAA:31 MA:0001715 NCIT:C33896 GAID:410 EHDAA2:0002220 Wikipedia:Zona_pellucida" + "The process in which a relatively unspecialized cell acquires specialized structural and/or functional features that characterize the cells of the salivary gland." + "Any process that increases the occurrence or rate of mesenchymal stem cell death by apoptotic process that contributes to the shaping of the nephron." + "A zone of skin that is part of a autopod region." "EMAPA:32723 MA:0003120" + "Any process that modulates the rate, frequency, or extent of superoxide metabolism, the chemical reactions and pathways involving superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species." + + "Gelatinous mucoid tissue that is composed of vitreous humor and fills the cavity behind the crystalline lens of the eye and in front of the retina[MP,modified]." "CALOHA:TS-0308 MA:0002462 SCTID:181170006 UMLS:C0042905 MESH:D014822 GAID:919 FMA:58827 NCIT:C33884" + "The primordial mass of tissue formed by the merging of the medial nasal prominences of the embryo; it contributes to the intermaxillary portion of the upper jaw, the prolabial portion of the upper lip, and the primary palate." "EHDAA2:0000868 EHDAA:7856 FMA:295872 Wikipedia:Intermaxillary_segment" + "The directed movement of a protein to a specific location on or in an organelle. Encompasses establishment of localization in the membrane or lumen of a membrane-bounded organelle." + "A smooth muscle of the pulmonary artery." "BTO:0003336" + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of glycogen." + "A periosteum that is part of a epiphysis [Automatically generated definition]." "FMA:32687" + "Any process that activates or increases the frequency, rate or extent of a neurophysiological process." + "The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone, involved in the progression of the skeleton from its formation to its mature state." + "Either of the two small almond-shaped masses of lymph tissue found on either side of the oropharynx." "FMA:9609 UMLS:C0836921 MA:0000143 GAID:341 UMLS:C1519548 neuronames:671 UMLS:C1519547 EFO:0001401 EMAPA:35871 VHOG:0001139 NCIT:C12802 CALOHA:TS-1053 EV:0100052 MESH:D014066 Wikipedia:Tonsil BTO:0001387" + "Any process that activates or increases the frequency, rate or extent of establishment of protein localization." + "Any process that stops, prevents or reduces the frequency, rate or extent of neutrophil migration." + "OBSOLETE A L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus) that has basket morphology." + "The process in which a carbohydrate is transported across a membrane." + "Cell-cell signaling between presynapse and postsynapse, across the synaptic cleft, that modulates the synaptic transmission properties of the synapse." + + "The inferior labial artery (inferior labial branch of facial artery) arises near the angle of the mouth; it passes upward and forward beneath the Triangularis and, penetrating the Orbicularis oris, runs in a tortuous course along the edge of the lower lip between this muscle and the mucous membrane. It supplies the labial glands, the mucous membrane, and the muscles of the lower lip; and anastomoses with the artery of the opposite side, and with the mental branch of the inferior alveolar artery." "FMA:49567 EMAPA:37429 Wikipedia:Inferior_labial_artery SCTID:145036002 MA:0001916" + "The progression of the nipple over time, from its formation to the mature structure. The nipple is a part of the mammary gland that protrudes from the surface ectoderm." + "A proximal phalanx that is part of a finger [Automatically generated definition]." "UMLS:C0730117 SCTID:361325003 FMA:75816 EMAPA:37307 NCIT:C52786 MA:0001395 SCTID:181986000" + "VHOG:0000522 EHDAA2:0000966 FMA:18822 EMAPA:16544" + "The directed movement of a protein from one location to another within a lipid bilayer." + "Any process that stops, prevents, or reduces the frequency, rate or extent of epidermis development." + "Any process that activates or increases the frequency, rate or extent of chondrocyte differentiation." + "Any process that modulates the frequency, rate or extent of hemocyte proliferation. Hemocytes are blood cells associated with a hemocoel (the cavity containing most of the major organs of the arthropod body) which are involved in defense and clotting of hemolymph, but not involved in transport of oxygen. An example of this is found in Drosophila melanogaster." + "EMAPA:35717 MA:0001784" + "A muscular coat that is part of a prostatic urethra." "FMA:19699 EMAPA:30956" + "Mesenchyme that is part of a mandibular prominence." "EHDAA2:0001062 EMAPA:17357 EHDAA:5861 EHDAA:5873" + "Epithelial layer of the retina, ciliary body, or iris composed of cells containing pigment granules." "GAID:907 MESH:D010857" + "Any process that modulates the frequency, rate or extent of sensory perception, the series of events required for an organism to receive a sensory stimulus, convert it to a molecular signal, and recognize and characterize the signal." + "The increase in size or mass of an entire multicellular organism, as opposed to cell growth." + "A skeletal muscle fiber found in an embryo. In mammalian embryos, skeletal muscle expresses myosin heavy chain-embryonic (MyHC-emb, encoded by the MYH3 gene), which regulates skeletal muscle development." + "A PP cell located in the islets of the pancreas." "MESH:D050418 BTO:0000805 FMA:70588" + "Any cell proliferation that is involved in endocardial cushion morphogenesis." + "Any process that stops, prevents, or reduces the rate of B-1 B cell differentiation." + "Binding to a nuclear estrogen receptor." + "Any process that activates or increases the frequency, rate or extent of pancreatic stellate cell proliferation." + "A memory B cell arising in the germinal center that is IgD-negative and has undergone somatic mutation of the variable region of the immunoglobulin heavy and light chain genes." + "A migrating group of cells originating from the posterior lateral line placode. The primordium deposits seven to nine neuromasts and interneuromasts between them during its posterior migration to the tail. Gompel et al, 2001." "ZFA:0001157" + "A myeloid suppressor cell that is Gr1-low and CD11c-positive." + "Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex." "Reactome:R-HSA-114558 Wikipedia:GPCR Reactome:R-HSA-167408 Reactome:R-HSA-114552" + "The series of events that restore integrity to damaged tissue that contribute to an inflammatory response." + "A stomach epithelial cell that is olumnar in form with a few short apical microvilli; relatively undifferentiated mitotic cell from which other types of gland are derived; few in number, situated in the isthmus region of the gland and base of the gastric pit." "FMA:62953" + "A branched quality inhering in a bearer by virtue of the bearer's having smaller branches arising from larger branches. Resembling a tree in branching structure." + "EMAPA:19001 MA:0001775" + "A neuron that has its soma located in CA1-3 of the hippocampus." + "Any apoptotic process in an activated CD4-positive, alpha-beta T cell." + "Any process that stops, prevents, or reduces the frequency, rate or extent of growth of an organ of an organism." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ATP (adenosine 5'-triphosphate) stimulus." + "Any process that activates or increases the frequency, rate or extent of the regulated release of dopamine." + "A tube that is part of a excretory system." + "The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids." "Wikipedia:Lipid_metabolism" + "The chemical reactions and pathways resulting in the breakdown of heparin, any member of a group of glycosaminoglycans of average Mr (6000-20000), consisting predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of an immune effector process." + "A collection of teeth arranged in some pattern in the mouth or other part of the body. The arrangement may be a simple row, a collection of rows, or a more elaborate structure, such as a toooth whorl." "AAO:0000126 GAID:1249 UMLS:C0011443 NCIT:C13072 FMA:75150 SCTID:245543004 MESH:D003817" + "Any melanocyte that is part of a epidermis." + "A Vgamma1.1-positive, Vdelta6.3-negative thymocyte that is CD24-negative." + "Any process that modulates the rate, frequency or extent of metanephric glomerulus development, the progression of the metanephric glomerulus over time from its initial formation until its mature state. The metanephric glomerulus is a capillary tuft surrounded by Bowman's capsule in nephrons of the vertebrate kidney, or metanephros." + "OBSOLETE (was not defined before being made obsolete)." + "Any goblet cell that is part of the tracheobronchial epithelium." + "Any process that increases the frequency, rate or extent of the regulated release of insulin that contributes to the response of a cell to glucose." + "FMA:15395" + "A CD8-positive, alpha-beta T cell that has differentiated into a memory T cell." + "The epithelial layer of the luminal surfaces of the mammary gland." "VHOG:0001088 CALOHA:TS-0593 NCIT:C12937 UMLS:C0596882 EHDAA2:0001057 BTO:0001430 EHDAA:6526 EMAPA:17760 FMA:74445 MA:0000792" + "A multi-tissue structure consisting of bone and soft tissue that forms a part of the roof of the oral cavity. In mammals this is the combination of the primary palate (premaxilla) and the secondary palate. In early tetrapods it consists of the vomer, pterygoid, parasphenoid, palatine and ectopterygoid bones." "CALOHA:TS-2212 Wikipedia:Palate" + "A brush cell found in the epithelium of lobular bronchiole." "FMA:263220" + "A blood vessel carrying deoxygenated blood far beneath the skin usually accompanying an artery." "UMLS:C0226514 Wikipedia:Deep_vein SCTID:341484008 NCIT:C32444 FMA:76718" + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a corticosteroid hormone stimulus. A corticosteroid is a steroid hormone that is produced in the adrenal cortex. Corticosteroids are involved in a wide range of physiologic systems such as stress response, immune response and regulation of inflammation, carbohydrate metabolism, protein catabolism, blood electrolyte levels, and behavior. They include glucocorticoids and mineralocorticoids." + "A Thy-1 membrane glycoprotein that is encoded in the genome of human." "UniProtKB:P04216" + "Creation of the central hole of a tube in an anatomical structure through which gases and/or liquids flow." + "Obsolete. Use PO:0004010 from Plant Ontology instead. A cell synthesizing protoplasm and producing new cells by division and with only a primary cell wall." + "An endocrine cell that is located in the epithelium of the gastrointestinal tract or in the pancreas." "MESH:D019858 FMA:62930 BTO:0003865" + "A limb segment that is part of a forelimb." "FMA:24876" + "A portion of connective tissue that is part of a nasopharynx [Automatically generated definition]." "EMAPA:37682 MA:0001864" + "EMAPA:32925 SCTID:371401008 FMA:63120 MA:0000724 VHOG:0001430" + "NLX:153848" + "Any process that activates or increases the frequency, rate or extent of ovarian follicle development." + "OBSOLETE (was not defined before being made obsolete)." + "Any process that modulates the frequency, rate or extent of the cytokine mediated signaling pathway." + "Any process that modulates the frequency, rate or extent of the synaptic vesicle cycle." + "Any process that modulates the frequency, rate or extent of dopaminergic neuron differentiation." + "An extraembryonic structure that develops_from a syncytiotrophoblast and is part of a chorion." "EHDAA:156 EHDAA2:0001973" + "A muscular coat that is part of a seminal vesicle [Automatically generated definition]." "MA:0002913 FMA:19404 EMAPA:29773" + "A portion of smooth muscle tissue that is part of a respiratory bronchiole [Automatically generated definition]." "FMA:261055" + "An integrin alpha-M that is encoded in the genome of human." "UniProtKB:P11215" + "Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle fiber development." + "Any process that modulates the frequency, rate or extent of odontoblast differentiation." + "An endothelium that is part of a umbilical artery." "BTO:0000857" + "Neuron with one neurite that extends from the cell body." "FMA:67278" + "A fibroblast that is part of the subepithelial connective tissue of prostatic gland." "FMA:261275" + "The part of the forelimb extending from the shoulder to the autopod[cjm]." "Wikipedia:Arm EFO:0001410 MESH:D001132 EMAPA:17413 CALOHA:TS-2204 MA:0000033 EHDAA:8275 BTO:0001435 VHOG:0000339 GAID:52 EHDAA:6210 EHDAA2:0000140 EHDAA:4164" + "Anterior-most region of dorsal hindbrain within rhombomere 1, adjacent the midbrain-hindbrain boundary." "EHDAA2:0000229 ZFA:0001442 DHBA:10665 TAO:0001442" + "The chemical reactions and pathways involving juvenile hormones, the three sesquiterpenoid derivatives that function to maintain the larval state of insects at molting and that may be required for other processes, e.g. oogenesis." + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a secretory granule in a mast cell. A secretory granule is a small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion." + "A thick walled spore that stores and protects one or more nuclei following sexual reproduction in an Ascomycete." "FAO:0000020 BTO:0000097" + "An epithelial cell of the mucosa associated with facial skeleton." "FMA:70581" + "Mesenchyme surrounding the developing optic cup which develops into the sclera." + "The multiplication or reproduction of fibroblasts, resulting in the expansion of a fibroblast population that contributes to the shaping of the heart." + "Signaling at long or short range between cells that results in the commitment of a cell to a certain fate." + "Any collection of muscles that is part of a limb [Automatically generated definition]." "EMAPA:32700 FMA:50188 EHDAA2:0000995" + "Vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium." "CALOHA:TS-1172 FMA:62971 BTO:0000121 ZFA:0005857 MA:0002513 MESH:D001646 UMLS:C0005388 NCIT:C13192 GAID:1157 ENVO:02000023 Wikipedia:Bile galen:Bile" + "Any process that modulates the frequency, rate or extent of excitatory synapse pruning." + "Any muscle organ that is part of a finger [Automatically generated definition]." "MA:0000624 EMAPA:37331" + "A bone that is part of a forelimb digit. Typically phalanges but may include sesamoids." "MA:0000622 EMAPA:37305" + "Mesenchyme that is part of a developing lower leg [Automatically generated definition]." "VHOG:0000752 EMAPA:17498 EHDAA2:0001032" + "The chemical reactions and pathways resulting in the breakdown of bile acids, any of a group of steroid carboxylic acids occurring in bile." + "The multiplication or reproduction of vascular smooth muscle cells, resulting in the expansion of a cell population. A vascular smooth muscle cell is a non-striated, elongated, spindle-shaped cell found lining the blood vessels." + "The series of molecular signals in which a cell uses calcium ions imported from an extracellular source to convert a signal into a response." + "Any process that activates or increases the frequency, rate or extent of motor neuron migration." + "An elasticity which is relatively high." + "An adipocyte of perirenal fat tissue." + "Any process that modulates the frequency, rate or extent of T-helper 17 cell differentiation." + "Any process that stops or decreases the frequency, rate or extent of glycinergic synaptic transmission. Glycinergic synaptic transmission is the process of communication from a neuron to another neuron across a synapse using the neurotransmitter glycine." + "Any process that modulates the frequency, rate or extent of cell junction assembly." + "A homeostatic process involved in the maintenance of a steady state level of ammonium within a cell." + "The morphogenetic process in which an epithelial sheet bends along a linear axis, contributing to embryonic heart tube formation." + "The process in which a relatively unspecialized cell acquires the specialized features of an oligodendrocyte. An oligodendrocyte is a type of glial cell involved in myelinating the axons of neurons in the central nervous system." + "Any process that stops, prevents or reduces the frequency, rate or extent of cerebral blood circulation." + "An immature myeloid leukocyte of heterogeneous phenotype found particularly in cancer and sepsis patients that is capable of suppressing activity of T cells in ex vivo assays. This cell type is CD45-positive, CD11b-positive." + "The luminal epithelium of the tube that conducts the urine from the renal pelvis to the bladder[MP]." "EMAPA:28089 FMA:15897 MA:0002655" + "Any gaseous product of an excretory process." + "The process whose specific outcome is the progression of a blood vessel of the labyrinthine layer of the placenta over time, from its formation to the mature structure. The embryonic vessels grow through the layer to come in close contact with the maternal blood supply." + "Any process that modulates the frequency, rate or extent of otic vesicle morphogenesis." + "A macrosialin that is encoded in the genome of mouse." "UniProtKB:P31996" + "Any process that stops, prevents or reduces the frequency, rate or extent of lipid localization." + "The joining of 2 or more lipid bilayer membranes that surround the nucleus during the creation of a single nucleus from multiple nuclei." + "Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system." "UMLS:C0037253 FMA:23881 EMAPA:35773 TAO:0000434 CALOHA:TS-1320 XAO:0003060 EHDAA2:0003168 VHOG:0001254 BTO:0001486 AAO:0000566 EFO:0000806 VSAO:0000027 MA:0000018 ZFA:0000434 NCIT:C12788" + "Any process that stops, prevents or reduces the frequency, rate or extent of cytoplasmic translational elongation." + "The pontine raphe nucleus is one of the raphe nuclei. It is located in the pontine tegmentum. [WP,unvetted]." "UMLS:C0175423 FMA:68875 BAMS:RPn DHBA:12475 Wikipedia:Pontine_raphe_nucleus BIRNLEX:1110 MA:0001022 neuronames:589 BAMS:RA-PONS DHBA:12471 HBA:9159 MBA:238 BAMS:PnR" + "An oncocyte located in the thyroid." "FMA:87169" + "Any of the three veins including the common, external and internal iliac veins." "UMLS:C0020888 NCIT:C12734 EMAPA:37151 SCTID:281481002 EHDAA2:0000811 MESH:D007084 MA:0002142" + "A synapse that uses GABA as a neurotransmitter. These synapses are typically inhibitory." + "A long-lived, antigen-experienced T cell that has acquired a memory phenotype including distinct surface markers and the ability to differentiate into an effector T cell upon antigen reexposure." "BTO:0003435" + "The lateral border (or axillary border, or margin) is the thickest of the three borders of the scapula. It begins above at the lower margin of the glenoid cavity, and inclines obliquely downward and backward to the inferior angle. Immediately below the glenoid cavity is a rough impression, the infraglenoid tuberosity, about 2.5 cm. in length, which gives origin to the long head of the Triceps brachii; in front of this is a longitudinal groove, which extends as far as the lower third of this border, and affords origin to part of the Subscapularis. The inferior third is thin and sharp, and serves for the attachment of a few fibers of the Teres major behind, and of the Subscapularis in front." "FMA:23239 EMAPA:25126 Wikipedia:Lateral_border_of_the_scapula" + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a histamine stimulus. Histamine, the biogenic amine 2-(1H-imidazol-4-yl)ethanamine, is involved in local immune responses as well as regulating physiological function in the gut and acting as a neurotransmitter." + "A proximal epiphysis that is part of a metacarpal bone [Automatically generated definition]." "SCTID:272695001 FMA:33795" + "The directed movement of glycine, aminoethanoic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "A blood island that is part of a mesoderm." "EHDAA:170 EHDAA2:0003241" + "A small lytic vacuole that has cell cycle-independent morphology found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions." "NIF_Subcellular:sao585356902 Wikipedia:Lysosome" + "OBSOLETE. A cell that is part of the choroid plexus." + "The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated." "BTO:0000575 CALOHA:TS-0454 FMA:14515" + "The process in which a branch forms along the side of an epithelium." + "Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." + "The cell cycle process in which sister chromatids are organized and then physically separated and apportioned to two or more sets." + "Skeletogenic cell that has the potential to develop into a cementoblast." + "Any process that activates or increases the frequency, rate or extent of antral ovarian follicle growth." + "A stromal cell found in the lamina propria of the vermiform appendix." + "A CD2 molecule that has been processed by proteolytic cleavage." + "The developmental process that results in the creation of defined areas or spaces within the ureteric bud along the anterior/posterior axis to which cells respond and eventually are instructed to differentiate." + "The process in which the anatomical structures of the mesoderm are generated and organized." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amine stimulus. An amine is a compound formally derived from ammonia by replacing one, two or three hydrogen atoms by hydrocarbyl groups." + "A two dimensional anatomical structure that is the boundary between an anatomical structure and an anatomical substance, an anatomical space or the organism's environment. Examples include the surface of your skin, the surface of the lining of your gut; the surface of the endothelium of you aorta that is in contact with blood.n." "UMLS:C1515977 EHDAA2_RETIRED:0003192 NCIT:C34022 CARO:0001002 BILA:0000010 FMA:24137" + "A SLAM family member 1 that is encoded in the genome of human." "UniProtKB:Q13291" + "A mucosa that is part of a trigone of urinary bladder [Automatically generated definition]." "FMA:17847" + "Any process that activates or increases the frequency, rate or extent of chondrocyte development." + "Pioneer neurons establish a pathway in the developing central nervous system and then undergo programmed cell death once the adult axons, which follow them, have made connections with the target site. Thus, they are a transient cell type involved in axon guidance." "FBbt:00005128" + "A ligament that is part of a knee joint." "SCTID:182440009 FMA:44580" + "A thin layer of connective tissue that lines the surface of the bony tissue that forms the medullary cavity of long bones." "Wikipedia:Endosteum FMA:32692 SCTID:57487002 NCIT:C13183 UMLS:C0222658" + "Transit-amplifying cells (TACs) are an undifferentiated population in transition between stem cells and differentiated cells." + "A mature CD1a-positive dermal dendritic cell is CD80-high, CD83-positive, CD86-high, and MHCII-high." + "An Ly-6-like protein that is a translation product of the mouse Ly6g gene or a 1:1 ortholog thereof." + "Binding to a monocarboxylic acid, any organic acid containing one carboxyl (COOH) group or anion (COO-)." + "An anatomical space that is enclosed by a urinary bladder." "EHDAA2:0004058 galen:UrinaryBladderCavity FMA:15924 SCTID:279405003" + "Binding to a G protein-coupled receptor." "Reactome:R-HSA-500717" + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus arising within the organism." + "An alpha-beta intraepithelial T cell with the phenotype CD8-alpha-alpha-positive located in the columnar epithelium of the gastrointestinal tract. These cells have a memory phenotype of CD2-negative and CD5-negative." + "Any process that activates or increases the frequency, rate or extent of macrophage apoptotic process." + "Transfer of an organized electrical impulse across the heart to coordinate the contraction of cardiac muscles. The process begins with generation of an action potential (in the sinoatrial node (SA) in humans) and ends with a change in the rate, frequency, or extent of the contraction of the heart muscles." + "The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord." "TAO:0000012 BIRNLEX:1099 EMAPA:16754 BAMS:CNS ZFA:0000012 Wikipedia:Central_nervous_system NCIT:C12438 EHDAA:828 GAID:570 XAO:0000215 BILA:0000080 EV:0100163 FMA:55675 MA:0000167 MESH:D002490 EFO:0000908 EHDAA2:0000225 UMLS:C0927232 SCTID:278199004 AAO:0000090 neuronames:854 EMAPA:16470 CALOHA:TS-0150 MAT:0000457 BTO:0000227 VHOG:0000293" + "An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the human FCER1A gene or a 1:1 ortholog thereof." "IUPHARobj:2933" + "The chemical reactions and pathways resulting in the breakdown of any conjugated, water-soluble protein in which the covalently attached nonprotein group consists of a lipid or lipids." + "A portion of skeletal muscle tissue that is part of an anal region [Automatically generated definition]." "EMAPA:37393 MA:0001530" + "A melanocyte that produces pigment within the hair follicle." + "Any process that increases the rate, frequency or extent of glucose metabolism. Glucose metabolic processes are the chemical reactions and pathways involving glucose, the aldohexose gluco-hexose." + "The regulated release of luteinizing hormone, a gonadotropic glycoprotein hormone secreted by the anterior pituitary." + "Any process that modulates the frequency, rate or extent of cell communication that contributes to the shaping of the growth plate cartilage." + "A protein with core architecture consisting of a Small cytokines (intecrine/chemokine), interleukin-8 like (Pfam:PF00048) domain." "PIRSF:PIRSF001950" + "Any process that activates or increases the frequency, rate or extent of mesenchymal stem cell differentiation." + "Histologically, the marginal zone pattern of the lymph node is characterized by lymphoid follicles with three distinct layers. The inner layer is composed of follicular center zones, the middle layer of darkly stained mantle zones, and the outer layer of marginal zones. However, the marginal zone pattern is rarely seen in reactive lymph nodes except for mesenteric lymph nodes. Lymph node marginal zones are populated by marginal zone B cells which express CD19 and CD20 and have the phenotypic features of memory B cells." + "Any process that stops, prevents or reduces the frequency, rate or extent of calcium ion transmembrane transporter activity." + "An OFF-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the outer half of the inner plexiform layer. The dendritic tree is not well filled and the dendrites are more delicate than in type 1 cells. The axon terminal is bushier and exhibits a dense plexus of varicosities in the inner part of sublamina 1 (Ghosh et al., 2004). It can be differentiated from other retinal bipolar neurons by its expression of marker genes: Neto1, Lhx3 and Irx-6 (Shekhar, 2016)." + "An G protein-coupled receptor signaling pathway which contributes to a circulatory system process carried out by the heart." + "A paired dermal or endochondral bone that is part of the pectoral girdle. The clavicle may be in contact with the interclavicle or coracoid and forms an attachment site for pectoral musculature. [PHENOSCAPE:ad]." "SCTID:181910004 MESH:D002968 GAID:182 VHOG:0000849 FMA:13321 EMAPA:18721 AAO:0000761 MA:0001329 VSAO:0005031 galen:Clavicle MFMO:0000047 Wikipedia:Clavicle UMLS:C0008913 NCIT:C12695" + "Any process that stops, prevents or reduces the rate of addition of phosphate groups to amino acids within a protein." + "Any process that modulates the frequency, rate or extent of sebum secreting cell proliferation." + "A transient hepatic stem cell observed after liver injury with a high nuclear to cytoplasm ratio that can differentiate into mature hepatocytes and bile duct cells. Arises from more than one tissue." "FMA:86576 BTO:0004270" + "A subtype of enteroendocrine cells found in the gastrointestinal mucosa, particularly in the glands of pyloric antrum; duodenum; and ileum. These cell type secretes serotonin and some neurotransmitters including enkephalins and substance P. Their secretory granules stain readily with silver (argentaffin stain)." "FMA:62934 FMA:83132 MESH:D004759" + "Mesopodial segment of the pes, including the tarsal skeleton and associated tissues." "MA:0000043 EFO:0001409 galen:Ankle GAID:41 CALOHA:TS-2219 SCTID:361292008 Wikipedia:Ankle EMAPA:32783 MESH:D000842 FMA:9665" + "The chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." + "CD8-positive, alpha-beta memory T cell with the phenotype CCR7-positive, CD127-positive, CD45RA-negative, CD45RO-positive, and CD25-negative." + "Any process that activates or increases the frequency, rate or extent of lipid transport across blood-brain barrier." + "The developmental process in which the tooth placode forms. A tooth placode is a thickening of the ectoderm that will give rise to the tooth bud." + "BTO:0004661" + "Any process that decreases the rate, frequency, or extent of protein tyrosine kinase activity." + "Any osteoblast that is part of a skull." + "Any process that increases the rate or extent of cardiac cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a cardiac muscle cell and result in its death." + "Any process that stops, prevents, or reduces the frequency, rate or extent of pancreatic stellate cell proliferation." + "One of: the 4th ventricle median or lateral apertures." "FMA:242766 MA:0002945" + "Any process that stops, prevents or reduces the frequency, rate or extent of astrocyte chemotaxis." + "A chemical homeostatic process involved in the maintenance of a steady state level of water within extracellular body fluids, such as blood, xylem or phloem, of a multicellular organism. This is distinct from maintenance of cellular homeostasis, which occurs within a cell." + "The process whose specific outcome is the progression of the mammary gland over time, from its formation to the mature structure. The mammary gland is a large compound sebaceous gland that in female mammals is modified to secrete milk. Its development starts with the formation of the mammary line and ends as the mature gland cycles between nursing and weaning stages." + "A glial cell of astrocytic lineage with long processes running parallel to adjacent axons in the proximal infundibulum of the neurohypophysis. These processes form a three-dimensional network among the axons of the hypothalamic neurosecretory cells and are connected by gap junctions which provide for their metabolic coupling. This cell type constitutes most of the nonexcitable tissue in the neurohypophsis; function may include possibly acting as an intermediate in the modulation of oxytocin and vasopressin release. This cell type is highly variable in size and shape and commonly contain lipid droplets and deposits of lipochrome pigment." "FMA:83503 BTO:0003793" + "Any process that modulates the frequency, rate, or extent of interleukin-6 production." + "Assembly of the extracellular matrix fibers that enables the matrix to recoil after transient stretching." + "The progression of the endocardial endothelium over time, from its initial formation to the mature structure. The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers." + "Any process that activates or increases the frequency, rate or extent of sebum secreting cell proliferation." + "An ON bipolar cell with a small dendritic tree that forms most of the central (invaginating) elements opposite the synaptic ribbon at the cone triad." + "A protein that is a translation product of the human IL2RB gene or a 1:1 ortholog thereof." "IUPHARobj:1696" + "A thymocyte found in the fetal thymus." + "An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The axon terminal is narrowly stratified and are found just below a calretinin-expressing band in sublamina 4 of the inner plexiform layer." + "Any process that modulates the frequency, rate or extent of the directed movement of proteins from the nucleus to the cytoplasm." + "Subdivision of skeleton that corresponds to metapodium region, between acropodial skeleton and mesopdoial skeleton." "VSAO:0005025" + + "The process, occurring above the cellular level, that is pertinent to the reproductive function of a multicellular organism. This includes the integrated processes at the level of tissues and organs." + "A sympathetic nerve trunk that is part of a thorax [Automatically generated definition]." "NCIT:C52827 MA:0001165 EMAPA:37657 UMLS:C1710393 FMA:6262" + "A protein that is a translation product of the human CD28 gene or a 1:1 ortholog thereof." "IUPHARobj:2863" + "Any process that activates or increases the frequency, rate or extent of the directed movement of a solute from one side of a membrane to the other." + "The process in which the anatomical structures of the nephron epithelium are generated and organized. The nephron epithelium is a tissue that covers the surface of a nephron." + "The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing pancreas." "EMAPA:26220 EFO:0002557" + "Any process that stops, prevents or reduces the frequency, rate or extent of regulated secretory pathway." + "The spiral septum that separates the truncus arteriosus into a ventral pulmonary trunk and the dorsal aorta[MP]. The aorticopulmonary septum is developmentally formed from neural crest, specifically the cardiac neural crest, and actively separates the aorta and pulmonary arteries and fuses with the interventricular septum within the heart during development. The actual mechanism of septation of the outflow tract is poorly understood, but is recognized as a dynamic process with contributions from contractile, hemodynamic, and extracellular matrix interactions." "EHDAA2:0000136 EMAPA:16827 Wikipedia:Aorticopulmonary_septum CALOHA:TS-2409 VHOG:0000502 EHDAA:2592" + "Any process that modulates the frequency, rate or extent of cardiac neural crest cell migration involved in outflow tract morphogenesis." + "The process aimed at the progression of a neuroblast over time, from initial commitment of the cell to a specific state, to the mature neuroblast. It does not include processes where the neuroblast turns into a glial cell or a neuron." + "Venule of villus of small intestine." + "Catalytic activity that acts to modify a nucleic acid." + "KUPO:0001090" + "A group 1 innate lymphoid cell that is non-cytotoxic." + "Any process that stops, prevents, or reduces the frequency, rate or extent of metanephric comma-shaped body morphogenesis." + "A threadlike extension of a nerve cell and consists of an axon and myelin sheath (if it is myelinated) in the nervous system. There are nerve fibers in the central nervous system and peripheral nervous system. A nerve fiber may be myelinated and/or unmyelinated. In the central nervous system (CNS), myelin by oligodendroglia cells is formed. Schwann cells form myelin in the peripheral nervous system (PNS). Schwann cells also make a thin covering in an axon without myelin (in the PNS). A peripheral nerve fiber contains an axon, myelin sheath, schwann cells and its endoneurium. There are no endoneurium and schwann cells in the central nervous system." "SCTID:88545005 FMA:5914 MESH:D009412 Wikipedia:Nervous_system_fiber BAMS:nfi" + "A vasculature that is part of a cerebellum." "FMA:268519" + "Type of radial astrocyte in the cerebellar cortex that have their cell bodies in the Purkinje cell layer and processes that extend into the molecular layer, terminating with bulbous endfeet at the pial surface. Bergmann glia express high densities of glutamate transporters that limit diffusion of the neurotransmitter glutamate during its release from synaptic terminals. Besides their role in early development of the cerebellum, Bergmann glia are also required for the pruning or addition of synapses." "FMA:54559" + "The dense and irregular connective tissue capsule surrounding a parathyroid gland." "UMLS:C0927176 NCIT:C33265 EMAPA:35663 FMA:55566 MA:0002676" + "Mesenchyme that is part of a developing vomeronasal organ [Automatically generated definition]." "EMAPA:18445 EHDAA2:0004103" + "The region of the mantle layer of the neural tube that lies dorsal to the sulcus limitans and contains primarily sensory neurons and interneurons involved in communication of sensory impulses; the alar plate develops into the dorsal horn in the grey matter of the spinal cord." "VHOG:0000899 EMAPA:17149 EMAPA:17581" + "The chemical reactions and pathways involving glycosaminoglycans, any of a group of polysaccharides that contain amino sugars." + "MESH:D011387" + "The process whose specific outcome is the progression of the Malpighian tubule over time, from its formation to the mature structure. A Malpighian tubule is a fine, thin-walled excretory tubule in insects which leads into the posterior part of the gut." + "An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted]." "FMA:34836 EMAPA:37621 SCTID:182238002 galen:JointCapsule MESH:D017746 UMLS:C0206207 Wikipedia:Articular_capsule NCIT:C84388 NCIT:C32259 MA:0001519 GAID:263" + "A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length." + "Thickening of the proximal end of the hair follicle. Contains rapidly proliferating, rather undifferentiated matrix cells (transient amplifying cells), melanocytes and outer root sheath cells." "SCTID:361360009 UMLS:C0221962 MA:0000161 EMAPA:18770 FMA:70666 NCIT:C32706" + "FMA:52568" + "The expansion of a B-1 B cell by cell division. Follows B cell activation." + "Any process that modulates the frequency, rate or extent of cytokine production involved in inflammatory response." + "The process whose specific outcome is the progression of the metanephric cortex over time, from its formation to the mature structure. The metanephric cortex is the outer region of the metanephros." + "A monostratified retinal ganglion cell with large soma and large dendritic field, with medium dendritic arbor, and has dendrites in layers 1 and 5." + "The renal outer medulla is the region of the kidney that lies between the renal cortex and the renal inner medulla[GO]." "BTO:0001746 CALOHA:TS-0508 FMA:17733 MA:0001653 EMAPA:28310" + "The specification and formation of anisotropic intracellular organization of an epithelial cell." + "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells of the mesonephric nephron tubule as it progresses from its formation to the mature state." + "Any process that modulates the frequency, rate or extent of cilium assembly." + "GC_ID:1" + "galen:GastricJuice UMLS:C0017133 MESH:D005750 MA:0002519 Wikipedia:Gastric_juice FMA:62972 NCIT:C32661 BTO:0000501 GAID:1160" + "Any process that stops, prevents or reduces the frequency, rate or extent of CD8-positive, alpha-beta T cell activation." + "Development of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." "Wikipedia:Organogenesis" + "Any process that stops, prevents or reduces the rate of translation initiation as a result of a stimulus indicating the organism is under stress." + "Any of the arteries that arise from a bifurcation of the aorta supplying the pelvic or abdomen. Examples: Common iliac artery, External iliac artery, Internal iliac artery." "Wikipedia:Iliac_artery XAO:0000361 galen:IliacArtery EMAPA:17309 MA:0001971 UMLS:C0020887 BTO:0004665 MESH:D007083 EHDAA:2551 SCTID:244330006 NCIT:C12733 RETIRED_EHDAA2:0000807" + "The process whose specific outcome is the progression of a somatic sensory system over time from its formation to the mature structure. Somatic sensory system is the sensory system for the sense of touch and pain." + "A brush border epithelial cell located in the proximal tubule of the kidney that detects fluid flow." + "A CD80 molecule that is encoded in the genome of human." "UniProtKB:P33681" + "A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure." + "Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction." "VHOG:0000286 UMLS:C0042066 GAID:362 MESH:D014566 BTO:0003091 EFO:0003864 galen:GenitoUrinarySystem XAO:0000140 SCTID:278861008 EHDAA:1013 NCIT:C12810 FMA:280610 BILA:0000122 AAO:0000624 EMAPA:16367 EV:0100094" + "Muscle innervated by the trigeminal nerve (Cranial Nerve V)." "MFMO:0000072" + "The chemical reactions and pathways resulting in the formation of glycosphingolipid, a compound with residues of sphingoid and at least one monosaccharide." + "Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus." + "A limb bone or its cartilage or pre-cartilage precursor." + "An extrahepatic bile duct that has the potential to develop into a common hepatic duct." "EHDAA2:0000595" + "Any process that activates or increases the frequency, rate or extent of cytoplasmic translational initiation." + "Any process that modulates the frequency, rate or extent of the regulated release of luteinizing hormone." + "A hemocyte found in immuno-stimulated larvae." "FBbt:00001687" + "An alveolus that is part of a left lung [Automatically generated definition]." "MA:0001777 UMLS:C1708673 EMAPA:19182 NCIT:C49251" + "Any process that increases the rate, frequency or extent of cell proliferation that contributes to the shaping of a heart valve." + "The process whose specific outcome is the progression of a pancreatic E cell over time, from its formation to the mature structure." + "GC_ID:1" + "Any process that modulates the frequency, rate or extent of vesicle fusion." + "A glutamate decarboxylase 1 that is encoded in the genome of human." "UniProtKB:Q99259" + "KUPO:0001089" + "A vip GABAergic cortical interneuron with bipolar morphology, with a soma found in L2/3. L2/3 bipolar vip cells have extending axons across all layers (with preferences for layers II/III and Va) and a dendritic tree that is vertically more restricted than deeper layer vip cells and extend fewer dendrites into the layers outside their home layer (location of soma). L2/3 bipolar vip cells have great variability in firing patterns, though most are continuous adapting. L2/3 bipolar vip cells are more depolarized in their resting state, had less fast rectification, and had smaller after hyperpolarization than deeper vip cells." + "The dermis, epidermis and hypodermis." "AAO:0000239 galen:Integument FMA:74657 ZFA:0000368 VSAO:0000029 EMAPA:37504 BTO:0000634 Wikipedia:Integument TAO:0000368" + "Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to membrane." + "A subdivision of the central canal of the spinal cord along its anterior-posterior axis. This is typically subdivided into cervical, thoracic, lumbar and sacral segments." "BIRNLEX:717" + "A stem cell that can give rise to the cells of the liver. The term usually refers to the self-renewing pool of hepatocyte precursors in the adult liver (differently from 'hepatoblast', often used for fetal precursors of hepatocytes)." "FMA:86577" + "A vasopressin/oxytocin receptor that is a translation product of the human OXTR gene or a 1:1 ortholog thereof. The preferred ligand is oxytocin." "IUPHARobj:369" + "Any process that stops or reduces the activity of an enzyme." + "The process whose specific outcome is the progression of the ventral region of the spinal cord over time, from its formation to the mature structure. The neurons of the ventral region of the mature spinal cord participate in motor output." + "Any muscle organ that is part of a pectoral girdle region." "FMA:37347" + "A mesothelium that is part of a pericardium [Automatically generated definition]." "RETIRED_EHDAA2:0001436" + + "A VIP peptides that has been processed by proteolytic cleavage." + "A modified epidermal cell located in the stratum basale. They are found mostly in areas where sensory perception is acute. Merkel cells are closely associated with an expanded terminal bulb of an afferent myelinated nerve fiber." "FMA:70548" + "The process whose specific outcome is the progression of an endothelium over time, from its formation to the mature structure. Endothelium refers to the layer of cells lining blood vessels, lymphatics, the heart, and serous cavities, and is derived from bone marrow or mesoderm. Corneal endothelium is a special case, derived from neural crest cells." + "The reproductive developmental process whose specific outcome is the progression of an oviduct over time, from its formation to the mature structure. An oviduct is a tube through which an ova passes from the ovary to the uterus, or from the ovary to the outside of the organism." + "The process in which anatomical structures of the left lung are generated and organized." + "KUPO:0001086" + "The biological process whose specific outcome is the progression of a face from an initial condition to its mature state. The face is the ventral division of the head." + "The chemical reactions and pathways involving lipids, as carried out by individual cells." + "The process in which the anatomical structures of the taste bud are generated and organized. The taste bud is a specialized area of the tongue that contains taste receptors." + "A process in which a protein is transported to, or maintained at, a location in a vacuole." + "One or a subset of adjacent layers of the neocortex." + "The junction between an axon of one neuron and a dendrite of another neuron, a muscle fiber or a glial cell. As the axon approaches the synapse it enlarges into a specialized structure, the presynaptic terminal bouton, which contains mitochondria and synaptic vesicles. At the tip of the terminal bouton is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic terminal bouton secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane." "NIF_Subcellular:sao914572699 Wikipedia:Chemical_synapse" + "Any process that stops, prevents or reduces the frequency, rate or extent of lateral motor column neuron migration." + "The series of events involved in the perception of touch in which a mechanical stimulus is received and converted into a molecular signal." + "The process in which an antigen-presenting cell expresses antigen (peptide or lipid) of exogenous origin on its cell surface in association with an MHC protein complex." + "KUPO:0001087" + "Any process that stops, prevents or reduces the frequency, rate or extent of hepatocyte apoptotic process." + "GC_ID:1" + "An epithelium that is part of a pancreatic duct." "EFO:0002556 FMA:67681" + "A protein that is a translation product of the human SST gene or a 1:1 ortholog thereof." + "A prolongation or process extending from a cell, e.g. a flagellum or axon." + "The process in which the anatomical structures of a pronephric nephron proximal tubule are generated and organized. A pronephric nephron tubule is an epithelial tube that is part of the pronephros." + "Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space." "NIF_Subcellular:sao1687101204" + "Any process that reduces the occurrence or rate of mesenchymal stem cell death by apoptotic process that contributes to the shaping of the nephron in the metanephros." + "The process whose specific outcome is the progression of the loop of Henle over time, from its formation to the mature structure. The loop of Henle is a nephron tubule that connects the proximal convoluted tubule to the distal convoluted tubule." + "A protein that is a translation product of the human IL2RA gene or a 1:1 ortholog thereof." "IUPHARobj:1695 PIRSF:PIRSF001954" + "A glial cell that is part of the hippocampus." "CALOHA:TS-1257" + "Any process that modulates the frequency, rate or extent of ectoderm development." + "A blood vessel that is part of a retina [Automatically generated definition]." "XAO:0004153 EMAPA:36520 GAID:509 MA:0001317 MESH:D012171 SCTID:280692003" + "The reformation of the Golgi following its breakdown and partitioning contributing to Golgi inheritance." + "A point along the course of the gastrointestinal tract where the small intestine (ileum) ends as it opens into the cecal portion of the large intestine; occurs usually within the iliac fossa, demarcated internally as the ileocecal orifice." "SCTID:264021000 FMA:11338 MA:0000332 EMAPA:37601" + "A parasol ganglion cell that depolarizes in response to decreased light intensity in the center of its receptive field. The majority of input that this cell receives comes from DB3a bipolar cells." + "The subdivision of the skeleton that consists of all the skeletal elements at the distalmost end of the autopodium - i.e. the bones of the digits or their cartilaginous precursors[VSAO,modified]." "VSAO:0005028 FMA:231315" + "A chromaffin cell that is part of the adrenal cortex." "FMA:69795" + "Any process that modulates the frequency, rate or extent of keratinocyte migration." + "The process whose specific outcome is the progression of the cerebellum over time, from its formation to the mature structure. The cerebellum is the portion of the brain in the back of the head between the cerebrum and the pons. In mice, the cerebellum controls balance for walking and standing, modulates the force and range of movement and is involved in the learning of motor skills." + "GC_ID:1" + "The process in which the anatomical structures of the right ventricular myocardium are generated and organized." + "The process whose specific outcome is the progression of the lens over time, from its formation to the mature structure. The lens is a transparent structure in the eye through which light is focused onto the retina. An example of this process is found in Mus musculus." + "Any process that modulates the establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane." + "Any apoptotic process that is involved in metanephric collecting duct development." + "An multicellular anatomical structure that has subparts of multiple organs as a part." "CARO:0020001" + "Any process that stops, prevents or reduces the frequency, rate or extent of sebum secreting cell proliferation." + "Any process that activates or increases the frequency, rate or extent of dopaminergic neuron differentiation." + "Any process that prevents the activation of neuroepithelial cell differentiation. Neuroepithelial cell differentiation is the process in which epiblast cells acquire specialized features of neuroepithelial cells." + "The ring-shaped cartilaginous structures that support the trachea." "SCTID:278979006 MA:0001857 NCIT:C49304 Wikipedia:Tracheal_rings UMLS:C1710456 EMAPA:35875 EMAPA:18699 FMA:7434" + "Odontoblast that non-terminally differentiated, located in the odontogenic papilla and dentine tissue, and transforms from a odontoblast cell." + "A protein that is a translation product of the human CD33 gene or a 1:1 ortholog thereof." "IUPHARobj:2601" + "A portion of smooth muscle tissue that is part of a respiratory system [Automatically generated definition]." "MA:0001830 BTO:0001660 EMAPA:35734" + "A vein that drains the adrenal gland." "EHDAA2:0001966 Wikipedia:Suprarenal_vein SCTID:278194009 MA:0002081 MA:0002229 EHDAA:8731 UMLS:C0226717 FMA:14348 NCIT:C53129" + "Any process that increases the rate frequency or extent of a phase of elevated metabolic activity, during which oxygen consumption increases; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals." + "Any process that modulates the frequency, rate, or extent of granuloma formation." + "Any organ component layer that consists of smooth muscle tissue." + "A narrow chalice-shaped cavity between the glomerular and capsular epithelium of the glomerular capsule of the kidney[TFD]. Between the visceral and parietal layers, into which the filtrate enters after passing through the podocytes' filtration slits[WP]. luminal region between the glomerular capsule visceral and parietal layers, into which filtrate enters after passing through the filtration barrier from the glomerular capillaries[MP]." "NCIT:C33840 TAO:0005312 FMA:17676 UMLS:C0227643 EMAPA:27985 Wikipedia:Bowman's_space TAO:0005283 ZFA:0005312 ZFA:0005283 MA:0001664 SCTID:244284006 EMAPA:28263" + "Any process carried out at the cellular level that reduces or removes the toxicity of an aldehyde. These may include transport of aldehydes away from sensitive areas and to compartments or complexes whose purpose is sequestration of the toxic substance." + "A layer of tissue between the muscularis and serosa." "SCTID:2255006 Wikipedia:Subserosa UMLS:C0225334 FMA:45636 NCIT:C94494" + "Binding to insulin, a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms." + "Any process that activates or increases the frequency, rate or extent of vesicle transport along microtubule." + "Any process that stops, prevents, or reduces the frequency, rate or extent of neuroblast migration." + "Any process that stops, prevents or reduces the frequency, rate or extent of steroid hormone secretion." + "A fibroblast that is part of the outer membrane of prostatic capsule." "FMA:261273" + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of external structures that lie outside the plasma membrane and surround the entire cell." + "A lymph node macrophage found in the cortex of lymph nodes, in particular in and around the germinal centers, and that participates in phagocytosis of apoptotic B cells from the germinal centers." + "A CSF-1/PDGF receptor-type tyrosine-protein kinase that is a translation product of the human CSF1R gene or a 1:1 ortholog thereof." "PIRSF:PIRSF500947 IUPHARobj:1806" + "FMA:66284" + "The growth of a growth plate cartilage chondrocyte, where growth contributes to the shaping of the chondrocyte over time." + "The anatomical junction between the descending colon and the sigmoid colon." + "A portion of smooth muscle tissue that is part of a urinary bladder [Automatically generated definition]." "CALOHA:TS-1087 BTO:0001849 MA:0001697 EMAPA:37791" + "Any process that modulates the rate, frequency, or extent of cilium movement, the directed, self-propelled movement of a cilium." + "The process in which a B cell acquires the specialized features of a plasma cell. A plasma cell is a lymphocyte which develops from a B cell and produces high amounts of antibody." + "Hair cell is a mechanoreceptor cell that is sensitive to movement of the hair-like projections (stereocilia and kinocilia) which relay the information centrally in the nervous system." "BTO:0004744" + "A nicotinic acetylcholine receptor protein that is a translation product of the human CHRNA7 gene or a 1:1 ortholog thereof." "IUPHARobj:468" + "The process in which a relatively unspecialized cell acquires the specialized features of a multi-ciliated epithelial cell." + "The initial developmental process that will lead to the formation of an eye." + "An hexagonal, flattened, mitochondria-rich endothelial cell that forms a monolayer on the posterior surface of the cornea (the corneal endothelium). Corneal endothelial cells are derived from the neural crest and are responsible for keeping the cornea transparent by maintaining the tissue in a semi-dry state through the action of their ionic pumps and tight junction barrier." "FMA:70614 CALOHA:TS-0172" + "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities." "RETIRED_EHDAA2:0003186 FMA:85006 UMLS:C0333343 SCTID:361348008 BTO:0001707 AEO:0000186 TAO:0001438 galen:BodyCavity ZFA:0001438 NCIT:C25444 EHDAA2:0000267" + "A zone of skin that is part of a scalp." "FMA:24757" + "The formation of ectoderm during gastrulation." + "A lamina propria that is part of a urethra [Automatically generated definition]." "FMA:85276 MA:0001689 EMAPA:37785" + "A blood vessel cell that is part of a kidney." "KUPO:0001014" + "A germinal center B cell found in a lymph node germinal center light zone." + "The expansion of a mononuclear cell population by cell division. A mononuclear cell is a leukocyte with a single non-segmented nucleus in the mature form." + "Any process in which skeletal muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors. These adaptive events occur in both muscle fibers and associated structures (motoneurons and capillaries), and they involve alterations in regulatory mechanisms, contractile properties and metabolic capacities." + "The directed movement of a L-histidine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "Any process that decreases the rate, frequency or extent of macrophage cytokine production. Macrophage cytokine production is the appearance of a chemokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." + "The process whose specific outcome is the progression of a glomerular parietal epithelial cell over time, from its formation to the mature structure. Glomerular parietal epithelial cells are specialized epithelial cells that form tight junctions as a barrier to protein transport." + "The process whose specific outcome is the progression of the pronephric duct over time, from its formation to the mature structure. The pronephric duct collects the filtrate from the pronephric tubules and opens to the exterior of the pronephric kidney." + "Precursor of type II pneumocyte. These cells do not have lamellar bodies, which are a marker of type II pneumocyte maturity." + "A basal cell that is part of a duct of an airway submucosal gland." + "Any process that stops, prevents, or reduces the frequency, rate or extent of macrophage activation." + "The process in which a relatively unspecialized T cell acquires specialized features of a T-helper 2 (Th2) cell. A Th2 cell is a CD4-positive, alpha-beta T cell that has the phenotype GATA-3-positive and produces interleukin-4." + "FMA:68861 http://neurolex.org/wiki/Category:Rexed_spinal_cord_parcellation_scheme_region Wikipedia:Rexed_laminae" + "A developmental process, independent of morphogenetic (shape) change, that is required for the central nervous system to attain its fully functional state. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord." + "Any process that stops, prevents, or reduces the frequency, rate or extent of mechanoreceptor differentiation." + "Any process that modulates the frequency, rate or extent of the migration of the endothelial cells of blood vessels." + "A progenitor cell committed to the erythroid lineage." "BTO:0004911" + + "The process whose specific outcome is the progression of the midbrain-hindbrain boundary over time, from its formation to the mature structure. The midbrain-hindbrain domain of the embryonic brain is comprised of the mesencephalic vesicle and the first rhombencephalic vesicle at early somitogenesis stages." + "Any process that activates or increases the frequency, rate or extent of natural killer T cell differentiation." + "Any process that stops, prevents, or reduces the frequency, rate or extent of ureter smooth muscle cell differentiation." + "A keratinized stratified squamous epithelium that is part of a tongue." "MA:0002787 FMA:74865" + "The portion of the ureteric bud tube that contributes to the morphogenesis of the metanephros[GO]." + "A endothelial cell of a lymphatic vessel. The border of the oak leaf-shaped endothelial cell of initial lymphatics are joined by specialized buttons. The discontinuous feature of buttons distinguishes them from zippers in collecting lymphatics, but both types of junctions are composed of proteins typical of adherens junctions and tight junctions found in the endothelium of blood vessels. Buttons seal the sides of flaps of the oak leaf-shaped endothelial cell, leaving open the tips of flaps as routes for fluid entry without disassembly and reformation of intercellular junctions." "FMA:68458 BTO:0004167" + "A fibroblast in the bone marrow." "FMA:84377" + "The reproductive developmental process whose specific outcome is the progression of somatic structures that will be used in the process of creating new individuals from one or more parents, from their formation to the mature structures." + "A lobe of thyroid gland that is in the left side of a thyroid gland." "FMA:13369 VHOG:0000734 UMLS:C0229582 SCTID:170784008 MA:0000728 NCIT:C32973 EHDAA2:0000965 EMAPA:18197" + "The area of axial mesoderm that develops into the prechordal plate." + "The process in which a relatively unspecialized cell acquires specialized features of a smooth muscle cell; smooth muscle lacks transverse striations in its constituent fibers and are almost always involuntary." + "Thick, fibrous meningeal covering surrounding the brain and spinal cord. It is the outermost of the three meningeal coverings. It consists of two layers: the periosteal dura linking the inner surface of the skull and the meningeal dura that lies above the arachnoid dural membrane. The meningeal layer draws away from the periosteal layer and certain locations to form the dural reflections." "EMAPA:32664 NLXANAT:090206 GAID:691 BTO:0001637 UMLS:C0013313 NCIT:C32488 SCTID:362301008 Wikipedia:Dura_mater MESH:D004388 FMA:9592 neuronames:1462 CALOHA:TS-2008 MA:0001115" + "Any process that activates or increases the frequency, rate or extent of vasculature development." + "Any fibroblast of lung that is part of a bronchus." + "A ganglion that is part of a abdominal segment of trunk." "SCTID:280508003" + "The process aimed at the progression of a lateral line glial cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell." + + "A cadherin-1 that is encoded in the genome of mouse." "UniProtKB:P09803" + "The process in which a relatively unspecialized cell acquires specialized features of a glandular epithelial cell. A glandular epithelial cell is a columnar/cuboidal epithelial cell found in a two dimensional sheet with a free surface exposed to the lumen of a gland." + "Any process that activates or increases the frequency, rate, or extent of a T-helper 1 type immune response." + "Any process that stops, prevents or reduces the frequency, rate or extent of embryonic pattern specification." + "A quality which inheres in a continuant." "snap:Quality" + "The process in which the anatomical structure of the cerebellar granular layer is generated and organized. The granular layer is the innermost layer of the cerebellar cortex. This layer contains densely packed small neurons, mostly granule cells. Some Golgi cells are found at the outer border. Granule neurons send parallel fibers to the upper molecular layer, where they synapse with Purkinje cell dendrites. Mossy fibers from the pontine nuclei in the white matter synapse with granule cell axons, Golgi cell axons and unipolar brush interneuron axons at cerebellar glomeruli in the granule cell layer." + "GC_ID:1" + "Any process that modulates the frequency, rate or extent of the inflammatory response, the immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents." + "Any process that modulates the rate or extent of gastrulation. Gastrulation is the complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals." + "An endothelial stalk cell is a specialized endothelial cell that follows behind the tip cell of an angiogenic sprout." + "A fungal cell with two genetically distinct haploid nuclei." + "A hepatic artery that is part of a left lobe of liver." "EMAPA:37096 FMA:14779 MA:0003096" + "A developmental process, independent of morphogenetic (shape) change, that is required for an enucleate erythrocyte to attain its fully functional state. An enucleate erythrocyte is an erythrocyte without a nucleus." + "Any process that modulates the rate, frequency, or extent of branching morphogenesis, the process in which the anatomical structures of branches are generated and organized." + "KUPO:0001082" + "A macrophage receptor MARCO that is encoded in the genome of mouse." "UniProtKB:Q60754" + "A stratified squamous epithelial cell that is part of the anal canal." + "A preadipocyte that is part of the breast." + "A portion of connective tissue that is part of a toe [Automatically generated definition]." "EMAPA:37330 MA:0000647" + "A single layer of simple squamous epithelium in the glomerular capsule. Does not function in filtration[UBERON]. outer layer of the glomerular capsule composed of a single layer of simple squamous epithelium[MP]." "TAO:0005253 ZFA:0005253 FMA:74272 MA:0002605 NCIT:C33271 EMAPA:28260 EMAPA:35969 BTO:0002296 UMLS:C0227645 EMAPA:27979 SCTID:362218005" + "Any process that stops, prevents or reduces the frequency, rate or extent of saliva secretion." + + "An external caudal extension of the body. In chordates, the tail is post-anal, in other animals the anus ends in the tail." "MIAA:0000094 BILA:0000117 GAID:1245 Wikipedia:Tail AEO:0000109 EFO:0000963 WBbt:0005741 EHDAA:9198 BTO:0001348 MESH:D013623 MAT:0000094" + "A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities." + "The appearance of tumor necrosis factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Tumor necrosis factor is an inflammatory cytokine produced by macrophages/monocytes during acute inflammation and which is responsible for a diverse range of signaling events within cells, leading to necrosis or apoptosis." + "The chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." + "FMA:54907 NCIT:C12243 SCTID:361936002 UMLS:C0225484" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amides." + "Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to microtubule." + "A gamma-delta T cell that has an immature phenotype." + "KUPO:0001083" + "A giioblast cell that develops from a migratory neural crest cell. The SCP is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has no basal lamina. In rodents SCPs are the only cells in the Schwann cell linage that expresses Cdh19." + "Any process that activates or increases the frequency, rate or extent of trophectodermal cell proliferation." + "Any process that modulates the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "The process in which the right cardiac atrium is generated and organized." + "A cellular potency that is the capacity to produce only one differentiated cell type." + "The directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Neurotransmitters are any chemical substance that is capable of transmitting (or inhibiting the transmission of) a nerve impulse from a neuron to another cell." + "The proximal-distal subdivision of colon that runs transversely across the upper part of the abdomen, from the right to the left colic flexure. Continuous with the descending colon[BTO,modified]." "FMA:14546 EMAPA:35880 EFO:0000844 BTO:0000272 galen:TransverseColon MAT:0000312 NCIT:C12385 UMLS:C0227386 Wikipedia:Transverse_colon SCTID:362163004 MIAA:0000312 MA:0001543 CALOHA:TS-2052" + "The process whose specific outcome is the progression of the mesonephric glomerular epithelium over time, from its formation to the mature structure. The mesonephric glomerular epithelium is an epithelial tissue that covers the outer surfaces of the glomerulus in the mesonephros. The mesonephric glomerular epithelium consists of both parietal and visceral epithelium. Mesonephric glomerular parietal epithelial cells are specialized epithelial cells that form tight junctions as a barrier to protein transport. A mesonephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the mesonephros." + "Any process that modulates the frequency, rate or extent of histamine secretion by mast cell." + "A wall that contains the alveoli." "NCIT:C13085 FMA:14117 SCTID:361965008 MA:0002568 UMLS:C0225695 BTO:0002543 EMAPA:35120" + "Any process that stops, prevents or reduces the frequency, rate or extent of cardiac chamber morphogenesis." + "PMID:17051209 PMID:16151185 PMID:15689432 PMID:17572334 GC_ID:1 PMID:17010206" + "The developmental process pertaining to the initial formation of a left cardiac ventricle from unspecified parts." + "An epithelial cell of the small intestine." "FMA:256159" + "The initial developmental process that will lead to the formation of the vertebrate inner ear. The otic placode forms as a thickening of the head ectoderm adjacent to the developing hindbrain." + "Anatomical organ component composed of a double layer of serous membrane that suspends a viscus from the body wall or connects adjacent viscera and in doing so conveys blood vessels, lymphatics and nerves to and from the viscera. Examples: greater omentum, broad ligament of uterus, sigmoid mesocolon." "AAO:0011061 FMA:7144 SCTID:362707009 UMLS:C0025474 NCIT:C33103 BTO:0001380 EV:0100083 Wikipedia:Mesentery#Mesentery_.28general.29 MESH:D008643 GAID:21 galen:Mesentery" + "The process in which the anatomical structures of a branched epithelium are generated and organized." + "The directed movement of substances from the Golgi to the vacuole." + "A retinal neural layer that is immediately adjacent to the S3 and S5 layer and comprises 20 percent of the inner plexiform layer of retina." "CP:0000116" + "A cadherin-5 that is encoded in the genome of human." "UniProtKB:P33151" + "A CD209 molecule-like protein B that is encoded in the genome of mouse." "UniProtKB:Q8CJ91" + "Any process in which a protein is transported to, or maintained in, a specific location." + "Immature CD8_alpha-positive CD11b-negative dendritic cell is a CD8_alpha-positive CD11b-negative dendritic cell that is CD80-low, CD86-low, and MHCII-low." + "The contractile element of skeletal and cardiac muscle; a long, highly organized bundle of actin, myosin, and other proteins that contracts by a sliding filament mechanism." "Wikipedia:Myofibril" + "Glandular cell of uterine cervix epithelium." "CALOHA:TS-1273" + "A CD19 molecule that is encoded in the genome of human." "UniProtKB:P15391" + "FMA:33061" + + "A basket cell morphology that inheres in neurons which have simpler dendritic arbors (compared to small or large basket cell morphology), and an axonal plexus of intermediate density, composed of a few long, smooth axonal branches." "ilxtr:NestBasketPhenotype" + "A plasmablast that is CD86-positive." + "Any process that stops, prevents or reduces the frequency, rate or extent of microtubule nucleation." + "Short bones are designated as those bones that are as wide as they are long. Their primary function is to provide support and stability with little to no movement. They are one of five types of bones: long, short, flat, irregular and sesamoid. Examples of these bones include the tarsals in the foot and the carpals in the hand." "NCIT:C33545 Wikipedia:Short_bone SCTID:332807009 FMA:7475" + "Any fibroblast that is part of a female gonad." + "The vesicular release of dopamine. from a presynapse, across a chemical synapse, the subsequent activation of dopamine receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse." + "The chemical reactions and pathways involving collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%)." + "EHDAA2:0000314" + "A protein that contains the ADP-ribosyl cyclase domain (Pfam:PF02267)." "PIRSF:PIRSF005736" + "An epithelial cell found in the trachea." "FMA:74793" + "The process whose specific outcome is the progression of cordate pharynx over time, from its formation to the mature structure." + "Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms." "TGMA:0001247 SCTID:272626006 SPD:0000428" + "In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted]." "EMAPA:16164 DHBA:10154 Wikipedia:Neural_tube NCIT:C34226 EHDAA:908 ZFA:0001135 SCTID:362852000 XAO:0003204 FMA:293882 CALOHA:TS-2371 TAO:0001135 VHOG:0000307 EHDAA:2869 MAT:0000069 neuronames:1365 AAO:0010617 MIAA:0000069 BTO:0001057 UMLS:C0231024 EMAPA:16757 EHDAA2:0001254" + "The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm." + "Any cellular process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids." + "Any process that activates or increases the frequency, rate or extent of endothelial cell apoptotic process." + "The directed movement of some substance from outside of a cell, across the plasma membrane and into the cytosol." + "Any process that activates or increases the frequency, rate or extent of gastrulation." + "Any process that activates or increases the frequency, rate or extent of cation channel activity." + "A basal cell in the respiratory tract." + "Any process that stops, prevents, or reduces the frequency, rate or extent of sporulation, the process whose specific outcome is the progression of a spore over time, from its initiation to the mature structure." + "Any process that stops, prevents, or reduces the frequency, rate or extent of B cell activation." + "A cell type that varies from squamous to columnar, depending on their activity with microvillus directed luminally. This cell produces and secretes thyroid hormones." "FMA:68782 BTO:0003736 CALOHA:TS-1285" + "The process in which the branching structure of the prostate gland is generated and organized. A branch is a division or offshoot from a main stem." + "A process in which a lipoprotein is transported to, or maintained in, a specific location in an outer membrane." + "Any migratory neural crest cell that is part of a cardiac neural crest." + "Any process that activates or increases the frequency, rate, or extent of antimicrobial peptide secretion." + "Any process that stops, prevents or reduces the frequency, rate or extent of RNA biosynthetic process." + "The smaller of the two otolith organs in the vestibule." "FMA:61116 BTO:0001805 SCTID:279827000 EHDAA:4712 MA:0000246 UMLS:C0036029 NCIT:C33503 EV:0100369 TAO:0000428 ZFA:0000428 AAO:0000550 XAO:0000196 EMAPA:17290 EHDAA2:0001769 Wikipedia:Saccule VHOG:0000374" + "The regulated release of a melanocyte-stimulating hormone, any of a group of peptide hormones that are produced by cells in the intermediate lobe of the pituitary gland, and stimulate the production of melanin to increase pigmentation." + "Cumulus cell is a specialized granulosa cell that surrounds and nourishes the oocyte. This cell-type surrounds the fully-grown oocyte to form a cumulus-oocyte complex (abbr. COC). The terms cumulus oophorus cells, cumulus granulosa cells, cumulus oophorous granulosa cells, granulosa-cumulus cells are used to make a distinction between this cell and the other functionally different subpopulation of granulosa cells at the wall of the Graafian follicle." "MESH:D054885 BTO:0002236" + "The progression of a heart valve over time, from its formation to the mature structure. A heart valve is a structure that restricts the flow of blood to different regions of the heart and forms from an endocardial cushion." + "A shape quality inhering in a bearer by virtue of the bearer's being marked by narrow lines or grooves, usually parallel, that are oriented transversely relative to the long axis of the bearer." + "The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a cell of the atrioventricular bundle. These cells are specialized cardiomyocytes that transmit signals from the AV node to the cardiac Purkinje fibers." + "Any process that activates or increases the frequency, rate, or extent of an immune system process." + "A non-terminally differentiated cell that originates from the neural crest and differentiates into a leucophore." + "The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules that contributes to the shaping of the heart." + "The process aimed at the progression of a Schwann cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. Schwann cells are found in the peripheral nervous system, where they insulate neurons and axons, and regulate the environment in which neurons function." + "The process that mediates interactions between an atrial cardiomyocyte and its surroundings that contributes to the process of the atrial cardiomyocyte communicating with an AV node cell in cardiac conduction. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment." + "A filamentous structure formed of a two-stranded helical polymer of the protein actin and associated proteins. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. The filaments, comprising polymerized globular actin molecules, appear as flexible structures with a diameter of 5-9 nm. They are organized into a variety of linear bundles, two-dimensional networks, and three dimensional gels. In the cytoskeleton they are most highly concentrated in the cortex of the cell just beneath the plasma membrane." "NIF_Subcellular:sao1588493326 Wikipedia:Actin FMA:63850" + "The part of the aorta that extends from the origin at the heart to the diaphragm, and from which arises numerous branches that supply oxygenated blood to the chest cage and the organs within the chest." "SCTID:302510009 MESH:D001013 NCIT:C33766 BTO:0000157 Wikipedia:Thoracic_aorta GAID:471 galen:ThoracicAorta FMA:3786 UMLS:C1522460 EMAPA:18603 EFO:0002525 MA:0002569" + "A CD4-positive, CXCR5-positive, CCR7-negative alpha-beta T cell located in follicles of secondary lymph nodes that is BCL6-high, ICOS-high and PD1-high, and stimulates follicular B cells to undergo class-switching and antibody production." + "A secretory cell that is grouped together with other cells of the same type to form grape shaped clusters known as acini (singular acinus)." "MESH:D061354 FMA:83625" + "The narrow subcapsular outer zone of the adrenal cortex where aldosterone is produced." "SCTID:21476003 Wikipedia:Zona_glomerulosa MA:0001891 FMA:69225 CALOHA:TS-0017 GAID:449 BTO:0000048 MESH:D015384 EMAPA:35115" + "GC_ID:1" + "A thymic macrophage found in the thymic cortex." + "Any process in which skeletal muscles change their phenotypic profiles in response to altered functional demands and a variety of signals." + "Layer of simple cuboidal cells covering surface of ovary[WP]." "NCIT:C61518 EMAPA:17963 MA:0001711 FMA:18629 EHDAA:8126 SCTID:258308007 UMLS:C0227875 BTO:0004483 Wikipedia:Germinal_epithelium_(female) VHOG:0000630 RETIRED_EHDAA2:0001361" + "SCTID:255782009 FMA:72173" + "Mesenchyme that is part of a developing shoulder [Automatically generated definition]." "EMAPA:17423 VHOG:0001035 EHDAA2:0001837 EHDAA:4184 EHDAA:6232" + "Organ system subdivision that consists of the organs and ducts that are involved in the production and transportation of bile. In most species this is the gallbladder and the bile ducts (biliary tree)." "Wikipedia:Biliary_system SCTID:361354009 NCIT:C12678 GAID:279 FMA:79646 MESH:D001659 MA:0001273" + "A mesentery that is part of a uterus [Automatically generated definition]." "FMA:19816 EMAPA:35562 Wikipedia:Mesometrium MA:0002931 SCTID:250172001" + "A mammary gland duct that is part of a male organism. This structure typically regresses." + "A hillock cell that is part of the urethra." + "Any process that stops, prevents, or reduces the frequency, rate or extent of compound eye photoreceptor development." + "The process in which a relatively unspecialized cell acquires the specialized features of a compound eye cone cell, a cone-shaped cell, that focuses light in a compound eye." + "The jugular foramen is a large aperture in the base of the skull. It is located behind the carotid canal and is formed in front by the petrous portion of the temporal, and behind by the occipital; it is generally larger on the right than on the left side." "NCIT:C12496 Wikipedia:Jugular_foramen AAO:0000249 FMA:56432 EHDAA:10631 VHOG:0001113 SCTID:361735006 EHDAA2:0000893 EMAPA:18713 UMLS:C0222712" + "A surface feature shape quality inhering in a bearer by virtue of the bearer's not having undulating edges forming lobes." + "The small branching sprouts of the dorsal aorta that grow across the medial surface of the somite, turn right angles to grow over that surface and then fuse with other sprouts and form the vertebral arteries adjacent to the neural tube; the intersomitic arteries supply the body wall and persist in the adult as the posterior intercostal, subcostal and the lumbar arteries." "EHDAA:4340 EMAPA:17616 MA:0001985 EHDAA2:0000882 ZFA:0001061 SCTID:360401001 XAO:0004165 TAO:0001061 VHOG:0000225" + "Part of central canal contained within the cervical spinal cord. It is continuous caudally with the thoracic spinal cord central canal and rostrally with the fourth ventricle of the brain via the obex." "FMA:321590 SCTID:280403009 BIRNLEX:1511 UMLS:C0228620" + "The change of a skeletal muscle satellite cell from a mitotically quiescent to a mitotically active state following exposure to some activating factor such as a cellular or soluble ligand. In adult muscle, satellite cells become activated to divide and differentiate in response to muscle damage." + "The multicellular organismal process in which the heart decreases in volume in a characteristic way to propel blood through the body." + "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 3." + "Any process that activates or increases the frequency, rate or extent of plasma membrane bounded cell projection assembly." + "A zone of skin that is part of a pes [Automatically generated definition]." "SCTID:181529000 UMLS:C0222289 MA:0000654 EMAPA:18504 FMA:37834 NCIT:C52750" + "A nerve that is part of an ankle [Automatically generated definition]." "EMAPA:37346 MA:0000640" + "An epithelium that is part of a saccule of membranous labyrinth [Automatically generated definition]." "FMA:75605 MA:0001202 EMAPA:17292 EHDAA:4724 VHOG:0000633 RETIRED_EHDAA2:0001771" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "A CD80 molecule that is encoded in the genome of mouse." "UniProtKB:Q00609" + "A squamous epithelium that is part of a tongue." "MA:0002786" + "TAO:0001334 AAO:0000472 ZFA:0001334 EFO:0003462" + "The directed movement of L-histidine into the vacuole across the vacuolar membrane." + "The convex portion of the aorta between the ascending and descending parts of the aorta; branches from it include the brachiocephalic trunk, the left common carotid artery, and the left subclavian artery; the brachiocephalic trunk further splits to form the right subclavian artery and the right common carotid artery." "GAID:471 EHDAA2:0000132 MA:0000475 Wikipedia:Arch_of_aorta EFO:0002526 SCTID:181300001 FMA:3768 EMAPA:17613 BTO:0000157 VHOG:0001196" + "The tubular structure that conducts gall bladder contents from the gall bladder to the common bile duct." "EMAPA:16841 SCTID:245398005 UMLS:C0010672 MA:0000355 EHDAA2:0000333 TAO:0005166 NCIT:C32421 EHDAA:3045 Wikipedia:Cystic_duct MESH:D003549 GAID:290 VHOG:0000213 galen:CysticDuct ZFA:0005166 FMA:14539" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving RNA." + "A collection of hairs that is part of a face." "FMA:70741" + "An epithelial tube open at both ends that allows fluid flow." "RETIRED_EHDAA2:0003116 AEO_RETIRED:0000116" + "The distal part of adenohypophysis: the part that makes up the main body of the gland." "EMAPA:17515 BAMS:DHP VHOG:0000244 ZFA:0001195 MA:0000854 FMA:74630 BIRNLEX:1022 UMLS:C0175322 EHDAA:7532 AAO:0010542 BTO:0001787 TAO:0001195 EHDAA2:0001416 neuronames:410 Wikipedia:Pars_distalis" + "The outer covering of the calvaria. It is composed of several layers: SKIN; subcutaneous connective tissue; the occipitofrontal muscle which includes the tendonous galea aponeurotica; Loose connective tissue; and the pericranium (the PERIOSTEUM of the SKULL)." "EMAPA:37949 BTO:0001809 MESH:D012535 SCTID:181480002 FMA:46494 CALOHA:TS-0896 GAID:80 NCIT:C89807 galen:Scalp UMLS:C0036270 Wikipedia:Scalp" + "An auditory hair cell located in the macula that is sensitive to auditory stimuli." + "A CNS neuron of the cerebral cortex." "BTO:0004102 FMA:84104" + "A thymocyte that has a T cell receptor consisting of a gamma chain containing Vgamma2 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-negative. This cell-type is found in the fetal thymus." + "The process in which the anatomical structures of the eye are generated and organized. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field." + "The layer of polyhedral cells in the epidermis found between the stratum granulosum and stratum basale; shrinkage and adhesion of these cells gives a spiny or prickly appearance." "MA:0000807 Wikipedia:Stratum_spinosum UMLS:C0221924 EMAPA:32785 SCTID:420086000 BTO:0000435 FMA:67542 NCIT:C12850" + "The progression of the olfactory cortex over time from its initial formation until its mature state. The olfactory cortex is involved in the perception of smell. It receives input from the olfactory bulb and is responsible for the identification of odors." + "Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." + "The self-renewing division of a germline stem cell to produce a daughter stem cell and a daughter germ cell, which will divide to form the gametes." + "A portion of smooth muscle tissue that is part of a spleen [Automatically generated definition]." "MA:0000757 EMAPA:35807" + "Any process that activates or increases the frequency, rate or extent of programmed cell death that occurs in the compound eye retina." + "An endoderm that is part of a thyroid primordium." "VHOG:0001089 EHDAA:956 EMAPA:25357 RETIRED_EHDAA2:0002035" + "The process in which the anatomical structures of an aorta are generated and organized. An aorta is an artery that carries blood from the heart to other parts of the body." + "Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts." + "A mucosa that is part of a large intestine [Automatically generated definition]." "CALOHA:TS-2106 FMA:14969 UMLS:C0734203 NCIT:C32926 MA:0002688 EMAPA:35467" + "An epithelium that is part of a crista ampullaris." "MA:0002870 FMA:75636" + "Any mesenchymal stem cell of adipose tissue that is part of an abdomen." + "An anatomical cavity that is part of a lens vesicle." "EMAPA:17164 EHDAA2:0000986 VHOG:0000531" + "A sonic hedgehog protein that is encoded in the genome of human." "UniProtKB:Q15465" + "A cellular protein localization process in which a protein is transported to, or maintained at, a location within the microtubule cytoskeleton." + "The process in which the anatomical structure of the cranial nerves are generated and organized. The cranial nerves are composed of twelve pairs of nerves that emanate from the nervous tissue of the hindbrain. These nerves are sensory, motor, or mixed in nature, and provide the motor and general sensory innervation of the head, neck and viscera. They mediate vision, hearing, olfaction and taste and carry the parasympathetic innervation of the autonomic ganglia that control visceral functions." + "The process whose specific outcome is the progression of an interneuron residing in the olfactory bulb, from its initial commitment, to the fully functional differentiated cell." + "A denotator type indicates how a term should be interpreted from an ontological perspective."@en + "Anatomical surface, which is the external surface of the whole body. Examples: There is only one body surface." "NCIT:C29667 UMLS:C0489451 SCTID:261060002 FMA:61695" + "An elongated fibrocyte that is part of a tendon. The cytoplasm is stretched between the collagen fibres of the tendon. They have a central cell nucleus with a prominent nucleolus. Tendon cells have a well-developed rough endoplasmic reticulum and they are responsible for synthesis and turnover of tendon fibres and ground substance." + "A organ system process carried out at the level of a muscle. Muscle tissue is composed of contractile cells or fibers." + "The process pertaining to the initial formation of a trachea from unspecified parts. The process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the trachea is recognizable. The trachea is the portion of the airway that attaches to the bronchi as it branches." + "Any process that activates or increases the frequency, rate or extent of chorionic trophoblast cell proliferation." + "A dentine-like hypermineralized substance that covers the tooth tip. Enamel's primary mineral is hydroxylapatite, which is a crystalline calcium phosphate. Unlike dentin and bone, enamel does not contain collagen. Instead, it has two unique classes of proteins called amelogenins and enamelins[WP]." "CALOHA:TS-1057 SCTID:362113009 EMAPA:35303 UMLS:C0011350 MA:0002543 VSAO:0000065 Wikipedia:Enamel_organ XAO:0004198 MESH:D003743 BTO:0001844 FMA:55629 NCIT:C32505" + "Any process that stops, prevents, or reduces the frequency, rate, or extent of antigen processing and presentation." + "An epithelial cell with high nuclear and cytoplasmic electron-density. This cell type is found in the deeper portions of the cortex but is more abundant in the medulla of the thymus." "FMA:72212" + "A perforin-1 that is encoded in the genome of human." "UniProtKB:P14222" + "Any process that modulates the frequency, rate, or extent of mast cell activation as part of an immune response." + "Any process that mediates the transfer of information from a mesenchymal cell to an epithelial cell where it is received and interpreted." + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a melanosome. A melanosome is a tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored." + "Any process that activates or increases the frequency, rate or extent of the regulated release of gamma-aminobutyric acid." + "Any process that modulates the frequency, rate or extent of skeletal muscle." + "A mucosa that is part of a respiratory airway." "FMA:7471 BTO:0001390 SCTID:660006" + "A cell that is maintained or propagated in a controlled artificial environment for use in an investigation." + "A carcinoembryonic antigen-related cell adhesion molecule 8 that has been processed by proteolytic cleavage." + "The organ that functions to filter blood and to store red corpuscles and platelets." "EV:0100055 VHOG:0000120 galen:Spleen SCTID:181279003 CALOHA:TS-0956 MIAA:0000085 AAO:0010395 XAO:0000328 MAT:0000085 Wikipedia:Spleen ZFA:0000436 EFO:0000869 MESH:D013154 NCIT:C12432 FMA:7196 GAID:1289 TAO:0000436 MA:0000141 BTO:0001281 UMLS:C0037993 EMAPA:18767" + "A portion of skeletal muscle tissue that is part of a urethra [Automatically generated definition]." "MA:0001690 EMAPA:37788" + "The capillary loops of the kidney that normally function as a filtration unit[MP]." "Wikipedia:Glomerulus EMAPA:28239" + "An epithelium characterised by its most superficial layer consisting of squamous epithelial cells." "SCTID:40118003 BTO:0002072 Wikipedia:Squamous_epithelium UMLS:C0221909 NCIT:C12848" + "A cell found throughout the gastrointestinal tract and in the pancreas. They secrete somatostatin in both an endocrine and paracrine manner. Somatostatin inhibits gastrin, cholecystokinin, insulin, glucagon, pancreatic enzymes, and gastric hydrochloric acid. A variety of substances which inhibit gastric acid secretion (vasoactive intestinal peptide, calcitonin gene-related peptide, cholecystokinin, beta-adrenergic agonists, and gastric inhibitory peptide) are thought to act by releasing somatostatin." "FMA:62935" + "Any process that reduces or removes the toxicity of a toxic substance. These may include transport of the toxic substance away from sensitive areas and to compartments or complexes whose purpose is sequestration of the toxic substance." + "The process in which the anatomical structures of the neural plate are generated and organized. The neural plate is a specialized region of columnar epithelial cells in the dorsal ectoderm that will give rise to nervous system tissue." + "A basophil precursor in the granulocytic series, being a cell intermediate in development between a basophilic myelocyte and a band form basophil. The nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare. Markers are CD11b-positive, CD15-positive, CD16-positive, CD24-positive, CD33-positive, and CD13-positive." "FMA:84198" + "The series of molecular signals initiated by a ligand binding to a receptor located within a cell." + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of ecdysteroids." + "Any process that modulates the frequency, rate or extent of oligodendrocyte apoptotic process." + "Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature." "MESH:D009417 GAID:609 AEO:0000123 NCIT:C13052 EHDAA2:0003123 FMA:9642 SCTID:91728009 AAO:0000325 UMLS:C0027757" + "A root of cranial nerve that is part of a vagus nerve." "ZFA:0007011 DHBA:12888 BIRNLEX:1456 DMBA:17748 FMA:6213" + "The process in which a relatively unspecialized epithelial cell becomes a more specialized epithelial cell of the mammary gland alveolus." + "A bone that is part of the pes skeleton." "UMLS:C0016505 MESH:D005529 MA:0000643 EMAPA:35354 GAID:192 SCTID:361371005 NCIT:C13068" + "A MHC-II-negative classical monocyte located in lymphoid tissue that is F4/80-positive, CD11c-intermediate, and CD11b-high." + "The interphalangeal articulations of hand are hinge-joints of the phalanges of the hand. There are two sets (except in the thumb): 'proximal interphalangeal joints' (PIP), those between the first (also called proximal) and second (intermediate) phalanges 'distal interphalangeal joints' (DIP), those between the second and third (distal) phalanges A similar group of articulations also function in the toes." "FMA:35285 SCTID:303280009 Wikipedia:Interphalangeal_articulations_of_the_hand EMAPA:36336 NCIT:C32868 UMLS:C0016125" + "Any process that stops, prevents, or reduces the rate of natural killer mediated cytotoxicity." + "Any process that stops, prevents or reduces the frequency, rate or extent of otic vesicle morphogenesis." + "A periosteum that is part of a long bone." "FMA:32677" + "Any process that reduces or removes the toxicity of nitrogenous compounds which are dangerous or toxic. This includes the aerobic conversion of toxic compounds to harmless substances." + "A hemocyte derived from the embryonic head mesoderm, which enters the hemolymph as a circulating cell." + "Mesenchyme that develops_from a neural crest and is part of a 3rd arch mesenchyme." "EHDAA2:0000083 EMAPA:16404 VHOG:0000571" + "The directed movement of lipid molecules passing through the blood-brain barrier." + "Skeletogenic cell that has the potential to develop into an ameloblast. Located in the inner enamel epithelium, these cells elongate, their nuclei shift distally (away from the dental papilla), and their cytoplasm becomes filled with organelles needed for synthesis and secretion of enamel proteins." + "The process in which a relatively unspecialized cell acquires specialized features of a neuron of the heart." + "Transudate contained in the pleural cavity." "BTO:0003080 Wikipedia:Pleural_fluid MA:0002532 FMA:12273 MAT:0000500 ncithesaurus:Pleural_Fluid" + "The chemical reactions and pathways involving glycoproteins, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide." + "A CD8-positive, alpha-beta positive T cell that has the phenotype T-bet-positive, eomesodermin-positive, CXCR3-positive, CCR6-negative, and is capable of producing interferon-gamma." "BTO:0004793 FMA:84793 BTO:0004888" + "An OFF calbindin-negative bipolar cell that has a large dendritic field and stratifies narrowly close to the middle of the inner plexiform layer. Its axon terminal is characterized by regularly branching and varicose processes resembling beads on a string. Most of DB3b contacts with cones are non-triad-associated." + "A circumscribed mass of ectodermal cells which bud off from the dental lamina; it becomes cup-shaped and develops on its internal face the ameloblast layer of cells that produces the enamel cap of a developing tooth." "SCTID:362863002 MA:0001604 Wikipedia:Enamel_organ BTO:0001722 TAO:0005138 EMAPA:32888 MESH:D004658 FMA:312389 CALOHA:TS-0271 ZFA:0005138" + "The process in which nerve cells are generated in the forebrain. This includes the production of neuroblasts from and their differentiation into neurons." + "Outer portion of the renal cortex. Site of formation of medullary and cortical elements." "MA:0002996 EMAPA:27721 http://www.gudmap.org/Images/Organ_Summaries/Metanephros/NZ.png" + "A part of an organism or organ that is continuous with its surroundings and distinguished from its surroundings based on morphology." + "Any process that activates or increases the frequency, rate or extent of activated CD4-positive, alpha-beta T cell apoptotic process." + "Unilaminar epithelium that consists of a single layer of cuboidal cells." "CARO:0000067 ZFA:0001497 NCIT:C33553 FMA:45566 EHDAA2:0003067 Wikipedia:Simple_cuboidal_epithelium AAO:0010064 XAO:0004009 TAO:0001497 BILA:0000067 UMLS:C0836134 HAO:0000067 AEO:0000067" + "A type I pneumocyte is a flattened, branched pneumocyte that covers more than 98% of the alveolar surface. This large cell has thin (50-100 nm) cytoplasmic extensions to form the air-blood barrier essential for normal gas exchange." "FMA:62500 BTO:0000780" + "The anus and surrounding regions. Encompasses both internal and external regions, where present." "MIAA:0000042 SCTID:362680001 NCIT:C32069 MA:0000329 VHOG:0000395 UMLS:C0230120 EFO:0000847 EHDAA2:0000122 EMAPA:16831 MAT:0000042 EHDAA:2931 WBbt:0006919" + "Any process in which a protein is maintained in the nucleus and prevented from moving elsewhere. These include sequestration within the nucleus, protein stabilization to prevent transport elsewhere and the active retrieval of proteins that escape the nucleus." + + "A subdivision of the skeleton of the autopod consisting of the phalanges of a single digit plus the associated metapodial element." + "Any process that modulates the frequency, rate or extent of bile acid metabolic process." + "The precursor of the urethra." "Wikipedia:Urethral_groove SCTID:361531004" + "Obsolete. Use PO:0000115 from Plant Ontology instead. A cell that surrounds a trichome and provides support for the trichome." + "The process in which the anatomical structures of the forebrain are generated and organized. The forebrain is the anterior of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes especially the cerebral hemispheres, the thalamus, and the hypothalamus and especially in higher vertebrates is the main control center for sensory and associative information processing, visceral functions, and voluntary motor functions)." + "An antigen inexperienced CD4-positive, alpha-beta T cell with the phenotype CCR7-positive, CD127-positive and CD62L-positive. This cell type develops in the thymus. This cell type is also described as being CD25-negative, CD62L-high, and CD44-low." + + "The directed movement of proteins along microtubules from the cell periphery toward the cell body in nerve cell axons." + "The process in which the kidney vasculature is generated and organized. Morphogenesis pertains to the creation of form." + "Any process that modulates the frequency, rate or extent of a digestive system process, a physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism." + "Any thin layer or plate." "Wikipedia:Lamina_of_the_vertebral_arch" + "Any process that modulates the rate or extent of progression through the cell cycle." + "Regional part of an anatomical region that is revealed by the use of a stain that reveals chemoarchitecture." "NLXANAT:20090501" + "Any process that activates or increases the frequency, rate or extent of tumor necrosis factor production." + "Any process that activates or increases the frequency, rate, or extent of mast cell activation." + "Any process that activates or increases the frequency, rate or extent of endocytosis." + "A smooth muscle cell of the umbilical artery." + "Any process that activates or increases the frequency, rate or extent of cell division." + "A skeletal muscle fiber found at the fetal and neonatal stages. In mammalian fetuses and neonates, skeletal muscle expresses myosin heavy chain-neonatal (MyHC-neo, encoded by the MYH8 gene). This expression disappears shortly after birth and is replaced by expression of adult heavy chain myosins." + "The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid." "galen:ProstateGland UMLS:C0033572 CALOHA:TS-0828 SCTID:181422007 MIAA:0000078 BTO:0001129 MA:0000404 FMA:9600 Wikipedia:Prostate NCIT:C12410 EFO:0000858 MESH:D011467 GAID:392 VHOG:0001261 MAT:0000078 EV:0100104 EMAPA:19287" + "Any process that stops, prevents or reduces the rate or extent of T cell proliferation." + "A quality of an object that has a value that is normal or average." + "A bone that is part of the dorsal region of an animal." "EMAPA:37248 MA:0000494" + "Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA]." "EHDAA2:0001730 EMAPA:17661 NCIT:C33483 UMLS:C0225706 FMA:7309 Wikipedia:Right_lung EHDAA:4969 SCTID:361967000 VHOG:0000301 MA:0000426" + "The assembly and secretion of an extracellular exosome, a membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane." + "Any fibroblast that is part of skeletal muscle tissue." + + "Enables the transfer of bile acid from one side of a membrane to the other. Bile acids are any of a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine." "Reactome:R-HSA-194130 Reactome:R-HSA-194083 Reactome:R-HSA-5661198 Reactome:R-HSA-5661184 Reactome:R-HSA-9733964 Reactome:R-HSA-194079" + "Any apoptotic process in a B cell, a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity." + "Generation of a long process of a pyramidal cell, that carries efferent (outgoing) action potentials from the cell body in cerebral cortex layer V towards target cells in the gray matter of the spinal cord. This axonal process is a member of those that make up the corticospinal tract." + "This process pertains to the initial formation of a structure from unspecified parts[GO]." + "A myocardium that is part of a bulbus cordis [Automatically generated definition]." "VHOG:0000609 EMAPA:36488" + "A mucosa that is part of a cardia of stomach [Automatically generated definition]." "FMA:17456" + "An artery that supplies the renal cortex." "MA:0002582 EMAPA:28147" + "A migrating group of cells originating from an anterior lateral line placode. The primordium deposits neuromasts and interneuromasts between them during its migration." "ZFA:0005117" + "The intermediate tubule is a nephron tubule that lies between the proximal and distal tubules." "FMA:17718" + "An innate lymphoid cell that is capable of producing T-helper 2-cell associated cytokines upon stimulation." + "Any process that activates or increases the frequency, rate or extent of retrograde dense core granule transport." + "Transudate located within the osseus labyrinth. Otolymph can be further classified with respect to whether it is within the membranous labyrinth (endolymph) or outside the mebranous labyrinth (perilymph)." "MA:0002527 GAID:1183 UMLS:C1518679 NCIT:C33231 MESH:D007761 EMAPA:36547" + "The chemical reactions and pathways resulting in the breakdown of small molecules, any low molecular weight, monomeric, non-encoded molecule." + "The orderly movement of epithelial cells within a renal tubule that contributes to metanephric proximal tubule morphogenesis." + + "Any process that stimulates, induces or increases the rate of myeloid dendritic cell activation." + "A lymphocyte antigen 6G that is encoded in the genome of mouse." "UniProtKB:P35461" + "An IgM memory B cell is an unswitched memory B cell with the phenotype IgM-positive and IgD-negative." + "A portion of connective tissue that is part of a leg [Automatically generated definition]." "MA:0000671 EMAPA:37324" + "Squamous cell of oral epithelium." "CALOHA:TS-1252" + "Any process that activates or increases the frequency, rate or extent of intestinal epithelial cell development." + "White matter that is part of a brainstem [Automatically generated definition]." "SCTID:360442003 MA:0002741 FMA:282112 EMAPA:35189" + "A common lymphoid progenitor that is CD10-positive, CD45RA-positive, CD34-positive and CD38-positive." + "A mucosa that is part of a bronchiole [Automatically generated definition]." "SCTID:10887006 FMA:62774" + "Any process that modulates the frequency, rate or extent of endothelial cell activation." + "A myeloperoxidase that is encoded in the genome of mouse." "UniProtKB:P11247" + "The outer epithelial layer of the skin that is superficial to the dermis." "ZFA:0000105 EFO:0000954 GAID:932 NCIT:C12708 VHOG:0000077 XAO:0000028 CALOHA:TS-0283 MIAA:0000154 MAT:0000154 FMA:70596 BTO:0000404 MESH:D004817 UMLS:C0014520 SCTID:361694003 AAO:0000143 EMAPA:17528 TAO:0000105 Wikipedia:Epidermis_(skin) MA:0000153 EV:0100153" + "An acinus that is part of a salivary gland." "FMA:59870" + "A mature thymus that is entirely part of the cervical region." + "The bilaminar epithelium formed from the myotome and dermatome." "FMA:295654 ZFA:0001513 TAO:0001513 AAO:0010572 NCIT:C34140 EHDAA2:0003259 AEO:0000214 EMAPA:31109 VHOG:0000676 UMLS:C1511786" + "The outer or sperficial part of a bone of the manus." + "A alpha-beta T cell that has a mature phenotype." + + "Any process that stops, prevents, or reduces the frequency, rate or extent of metanephric S-shaped body morphogenesis." + "Cardiac chamber in which blood enters the heart." "EHDAA2:0000154 GAID:555 MA:0000073 CALOHA:TS-0437 ZFA:0000471 UMLS:C0018792 Wikipedia:Heart_atrium TAO:0000471 AAO:0010246 EMAPA:16688 SCTID:261405004 BTO:0000903 galen:Atrium MAT:0000496 NCIT:C12728 EHDAA:1265 VHOG:0000175 FMA:7099 EV:0100019 EFO:0000277 MESH:D006325" + "A mammary epithelial cell that occurs in the lumen of the ductal and alveoli structure in the breast." "FMA:73280" + "Bone tissue forms directly within mesenchyme, and does not replace other tissues[TAO]. Intramembranous ossification is the formation of bone in which osteoblasts secrete a collagen-proteoglycan matrix that binds calcium salts and becomes calcified[GO]. Intramembranous ossification is the way flat bones and the shell of a turtle are formed[GO]. Unlike endochondral ossification, cartilage is not present during intramembranous ossification[WP]." "TAO:0001644 Wikipedia:Intramembranous_ossification EMAPA:36615 ZFA:0001635" + "GC_ID:1" + "Any process that activates or increases the frequency, rate or extent of the formation of a myelin sheath around nerve axons." + "The area of a motile cell closest to the direction of movement." + "The segment of the respiratory tract that starts proximally with the nose and ends distally with the cricoid cartilage, before continuing to the trachea." "FMA:45661 EHDAA2:0002136 Wikipedia:Upper_respiratory_tract SCTID:361381009 MA:0000442 EMAPA:17669 VHOG:0000406" + "The process in which the structures of a glial cell in the anterior lateral line nerve are generated and organized. This process occurs while the initially relatively unspecialized cell is acquiring the specialized features of a glial cell in the anterior lateral line nerve." + "A submucosa that is part of a right hepatic duct [Automatically generated definition]." "FMA:18015" + "The multiplication or reproduction of hepatic stellate cells, resulting in the expansion of a hepatic stellate cell population. Hepatic stellate cells are found in the perisinusoidal space of the liver, and are capable of multiple roles including storage of retinol, presentation of antigen to T cells (including CD1d-restricted NKT cells), and upon activation, production of extracellular matrix components. This cell type comprises approximately 8-15% of total cells in the liver." + "Any process in which a pigment granule is transported to, and/or maintained in, a specific location within the cell." + "A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord." "EFO:0000329 UMLS:C0007806 EV:0100311 VHOG:0001278 ZFA:0001626 MA:0002503 EHDAA2:0004441 GAID:1181 MAT:0000499 CALOHA:TS-0130 TAO:0002184 ENVO:02000029 NCIT:C12692 FMA:20935 MESH:D002555 Wikipedia:Cerebrospinal_fluid BIRNLEX:1798 BTO:0000237" + "A pharyngeal membrane that separates the first pharyngeal cleft from the first pharyngeal pouch." "EMAPA:17281 EHDAA:3788 VHOG:0001427 EMAPA:16121 EMAPA:16992" + "A ridge of epidermal cells that will form the mammary placodes." "Wikipedia:Milk_line EMAPA:18541" + "Artery that supplies blood to the adrenal glands." "ncithesaurus:Adrenal_Artery EMAPA:37124 EHDAA2:0001965 MA:0001914 EHDAA:8596 SCTID:181342004 Wikipedia:Adrenal_artery NCIT:C33708" + "The portion of the collecting duct that resides in the renal medulla." "EMAPA:35459 EMAPA:28061 MA:0002935 BTO:0004536" + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hexose stimulus." + "A white matter that is part of the myelencephalon." "HBA:9298" + "Epithelial cells derived from neural plate and neural crest." "FMA:70557 BTO:0004301" + "A phase of elevated metabolic activity, during which oxygen consumption increases; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals." "Wikipedia:Respiratory_burst" + + "Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-22 production." + "The chemical reactions and pathways involving diatomic oxygen (O2)." + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a pigment granule." + "A skeletal joint that connects a laryngeal cartilage." "FMA:55100" + "Progression of the exocrine system over time, from its formation to a mature structure. The exocrine system is a system of hormones and glands, where the glands secrete straight to a target site via ducts or tubes. The human exocrine system includes the salivary glands, sweat glands and many glands of the digestive system." + "A digit that is part of a manus (hand)." "NCIT:C32608 XAO:0003036 AAO:0000857 galen:Finger NLXANAT:20090602 EMAPA:32642 GAID:57 Wikipedia:Finger UMLS:C0016129 SCTID:283992002 BTO:0004669 MA:0000041 MESH:D005385 FMA:9666 EHDAA2:0000404" + "A homeostatic process in which an organism modulates its internal body temperature." "Wikipedia:Thermoregulation" + "A granule cell that has soma location in the dentate gyrus cell layer of the hippocampal formation and has an elliptical cell body and characteristic cone-shaped tree of spiny apical dendrites. The branches extend throughout the molecular layer and the distal tips of the dendritic tree end just at the hippocampal fissure or at the ventricular surface. The dentate gyrus granule cell is the principal cell type of the dentate gyrus." + "Any process that increases the frequency, rate or extent of glucose transport across a membrane. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "Any process that stops, prevents or reduces the frequency, rate or extent of vascular smooth muscle cell differentiation." + "An epiphysis that is part of a femur [Automatically generated definition]." "MA:0003056 EMAPA:37539 SCTID:314625005 FMA:32838" + + "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value."@en + "The process in which cells that are products of meiosis acquire the specialized features of ascospores. Ascospores are generally found in clusters of four or eight spores within a single mother cell, the ascus, and are characteristic of the ascomycete fungi (phylum Ascomycota)." + "The controlled release of a substance by a cell or a tissue." + "A multi cell part structure that is part of a central nervous system." "FMA:83143" + "Any process that activates or increases the frequency, rate or extent of gamma-delta T cell proliferation." + "Any G protein-coupled acetylcholine receptor signaling pathway that is involved in positive regulation of acetylcholine secretion, neurotransmission." + "A muscular coat that is part of a jejunum." "FMA:14951" + "Any pericyte cell that is part of a placenta." + "A trophoblast found at the junction of the placenta. This cell type makes a unique fibronectin-trophouteronectin junction that helps mediate attachment of the placenta to the uterus. This cell type is also found junction of the chorion layer of the external membranes and the decidua." + "A M cell that is part of the epithelium proper of duodenum." "FMA:263134" + + "Organism at the blastula stage - an early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence." "MESH:D036703 OGEM:000006 BILA:0000059 GAID:1294 Wikipedia:Blastula BTO:0000128" + "Any process that stops, prevents or reduces the frequency, rate or extent of cardiac ventricle formation." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of serotonin." + "Any process that stops, prevents, or reduces the rate of production of a cytokine." + "Any process that modulates the frequency, rate or extent of lens fiber cell differentiation." + "A nerve that is part of a neck [Automatically generated definition]." "MA:0000588 EMAPA:37263" + "A temporary protrusion or retractile process of a cell, associated with flowing movements of the protoplasm, and serving for locomotion and feeding." "Wikipedia:Pseudopod" + "The process in which neuroblasts acquire specialized structural and/or functional features that characterize the mature cerebellar Purkinje cell. Differentiation includes the processes involved in commitment of a neuroblast to a Purkinje cell fate. A Purkinje cell is an inhibitory GABAergic neuron found in the cerebellar cortex that projects to the deep cerebellar nuclei and brain stem." + + "Any process that modulates the rate, frequency, or extent of prostatic bud formation, the morphogenetic process in which a region of the fetal urogenital sinus epithelium is specified to become the prostate, resulting in prostate bud outgrowth." + "An out-pocket of thickened ventral foregut epithelium adjacent to the developing heart. Constitutes the first morphological sign of the embryonic liver. The anterior portion of the hepatic diverticulum gives rise to the liver and intrahepatic biliary tree, while the posterior portion forms the gall bladder and extrahepatic bile ducts." "Wikipedia:Hepatic_diverticulum XAO:0000101 EHDAA:1530 EHDAA2:0000740 UMLS:C1512407 AAO:0011057 NCIT:C34187" + "Any process that activates or increases the frequency, rate or extent of presynapse assembly." + + "A terminal branch of the left or right common carotid artery which supplies oxygenated blood to the brain and eyes[MP]." "UMLS:C0007276 Wikipedia:Internal_carotid_artery XAO:0000366 EHDAA:408 TAO:0005081 VHOG:0000267 MA:0001930 FMA:3947 AAO:0010219 EFO:0001952 NCIT:C32836 AAO:0011054 MESH:D002343 BTO:0004697 EHDAA2:0000873 GAID:481 EMAPA:16328 ZFA:0005081 EHDAA:6389 SCTID:362045001" + "A condensation of odontoblasts that forms the part of a tooth germ that gives rise to dentin and pulp in the mature tooth. It lies below a cellular aggregation known as the enamel organ." "Wikipedia:Dental_papilla GAID:1277 VSAO:0000025 TAO:0005140 EMAPA:32892 VHOG:0001465 XAO:0004045 MA:0001598 MESH:D003771 ZFA:0005140 BTO:0001839 FMA:57662" + "A distal phalanx that is part of a finger [Automatically generated definition]." "MA:0001388 SCTID:182001007 NCIT:C52784 SCTID:361782004 FMA:75818 UMLS:C1269782 EMAPA:35393" + "An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland." "SCTID:272631008 MA:0000522" + "Any process that stops, prevents or reduces the frequency, rate or extent of detection of mechanical stimulus involved in sensory perception of touch." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a calcium ion stimulus." + "Any apoptotic process that contributes to the shaping of an endocardial cushion. The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves." + "The anatomical space that is enclosed by a stomach." "EMAPA:18395 FMA:14585" + "A mesenchymal stem cell of the chorionic membrane." + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of juvenile hormone." + "The cerebrospinal nerves consist of numerous nerve fibers collected together and enclosed in membranous sheaths. A small bundle of fibers, enclosed in a tubular sheath, is called a funiculus; if the nerve is of small size, it may consist only of a single funiculus; but if large, the funiculi are collected together into larger bundles or fasciculi, which are bound together in a common membranous investment. Examples include: Anterior funiculus of the spinal cord Lateral funiculus of the spinal cord Posterior funiculus of the spinal cord Funiculus solitarius of the medulla Funiculus separans." "FMA:76738 Wikipedia:Funiculus_(neurology)" + "Endochondral longbone connecting the pelvic girdle with posterior zeugopodium skeleton.[VSAO, modified]." "XAO:0003214 CALOHA:TS-0322 AAO:0000887 GAID:199 EFO:0001396 EMAPA:19143 VHOG:0001159 SCTID:182046008 FMA:9611 NCIT:C12717 galen:Femur BTO:0001284 Wikipedia:Femur AAO:0000889 MA:0001359 VSAO:0000186 UMLS:C0015811 MESH:D005269" + + "An immunoglobulin iota chain that is encoded in the genome of human." "UniProtKB:P12018" + "The subclasses of motor neurons which project their axons to axial muscles that lie close to the vertebral column; motor neurons in the lateral subdivision of the MMC project their axons to body wall muscles." + "Any neuromast hair cell that is part of a posterior lateral line." + "Any process that modulates the frequency, rate or extent of the formation and development of teeth, the hard, bony appendages which are borne on the jaws, or on other bones in the walls of the mouth or pharynx of most vertebrates." + "Any process that modulates the frequency, rate or extent of basophil differentiation." + "Any process that stops, prevents or reduces the frequency, rate or extent of smooth muscle tissue development." + "The multiplication or reproduction of cells, resulting in the expansion of the population in the metanephros." + "Kolmer-Agduhr neurons are ciliated GABAergic neurons that contact the central canal of the spinal cord and have ipsilateral ascending axons." + "Any process that stops, prevents, or reduces the frequency, rate or extent of a signaling process." + "Keratinocyte from foreskin." "CALOHA:TS-0385" + "The orderly movement of a mesenchymal cell from one site to another, often during the development of a multicellular organism." + "The developmental process in which the size or shape of a cell is generated and organized." + "Any process by which the number of skeletal muscle satellite cells in a skeletal muscle is maintained during muscle regeneration. There are at least three mechanisms by which this is achieved. Skeletal muscle satellite stem cell asymmetric division ensures satellite stem cell numbers are kept constant. Symmetric division of these cells amplifies the number of skeletal muscle satellite stem cells. Some adult skeletal muscle myoblasts (descendants of activated satellite cells) can develop back into quiescent satellite cells, replenishing the overall pool of satellite cells." + "Any process that modulates the frequency, rate or extent of mesodermal cell differentiation." + "Part of spinal cord central canal contained in the thoracic spinal cord. It is continuous rostrally with the cervical spinal cord central canal and caudally with the lumbar spinal cord central canal." "SCTID:71118002 BIRNLEX:1395 FMA:321588 UMLS:C0228637" + "A post-natal thymocyte expressing components of the gamma-delta T cell receptor. This cell type is always double-negative (i.e. CD4-negative, CD8-negative)." + "A think avascular meningeal layer, between the pia mater and the dural mater. It is separated from the pia mater by the subarachnoid space." "Wikipedia:Arachnoid_mater neuronames:1464 EMAPA:32659 NLXANAT:090208 MESH:D001099 NCIT:C32136 BTO:0001636 SCTID:362304000 FMA:9591 GAID:688 EV:0100314 CALOHA:TS-0052 UMLS:C1510935 MA:0001114" + "The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex." + "A cell that is part of a scolopidium and surrounds the dendrite of a scolopidial neuron." "FBbt:00005219" + "Any process that activates or increases the frequency, rate, or extent of B cell antigen processing and presentation." + "A bistratified retinal ganglion cell that has a small dendrite fields with a sparse dendrite arbor terminating in S2 and S3." + "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells of the pronephros as it progresses from its formation to the mature state." + + "Any process that modulates the frequency, rate or extent of hepatocyte apoptotic process." + "Any process that stops, prevents or reduces the frequency, rate or extent of T-helper 2 cell cytokine production." + "Mesenchyme that is part of a developing gonad [Automatically generated definition]." "EMAPA:17385 EMAPA:16858 EHDAA:5012 VHOG:0001090" + "The expansion of a B cell population by cell division. Follows B cell activation." + "The femur neck or neck of the femur is a flattened pyramidal process of bone, connecting the femoral head with the femoral shaft, and forming with the latter a wide angle opening medialward." "UMLS:C0015815 MESH:D005272 GAID:201 Wikipedia:Femur_neck NCIT:C61563 galen:NeckOfFemur FMA:42385 SCTID:361792007" + "The directed movement of L-histidine out of the vacuole, across the vacuolar membrane." + "The innermost layer of a blood vessel which is a lining of endothelial cells facing the lumen[Kardong]." "NCIT:C33820 MESH:D017539 EMAPA:36297 SCTID:8361002 UMLS:C0162864 Wikipedia:Tunica_intima BTO:0002012 FMA:55589 SCTID:87483006 MA:0002861 GAID:523" + "A mucosa that is part of a male urethra [Automatically generated definition]." "FMA:239937" + "A late neutrophilic metamyelocyte in which the nucleus is indented to more than half the distance to the farthest nuclear margin but in no area being condensed to a single filament. The nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature neutrophil. These cells are fMLP receptor-positive, CD11b-positive, CD35-negative, and CD49d-negative." + "A viscosity which is relatively normal or average" + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of bile acids." + "A testicular artery that supplies a right testicle." "MA:0002042 UMLS:C0734076 EMAPA:37382 NCIT:C52738 FMA:14759" + "An epithelial cell of prostatic duct." "FMA:74224" + "Binding to an oxytocin receptor." + "Any process that modulates the rate, frequency, or extent of the process in which a chondroblast acquires specialized structural and/or functional features of a chondrocyte that will contribute to the growth of a bone. A chondrocyte is a polymorphic cell that forms cartilage." + "An epithelial cell of the prostatic acinus." "FMA:74223" + "A prominin-1 that is encoded in the genome of mouse." "UniProtKB:O54990" + + "A rhodopsin-like G-protein coupled receptor that is a translation product of the human FPR1, FPR2, or FPR3 genes, 1:1 orthologs thereof, or a semi-ortholog thereof. The active form binds N-formyl methionyl peptides." "IUPHARfam:23 PIRSF:PIRSF038561" + "The process in which the ciliary body generated and organized. The ciliary body is the circumferential tissue inside the eye composed of the ciliary muscle and ciliary processes." + "Any process that modulates the frequency, rate or extent of the directed movement of lipids within cells." + "A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. This process occurs in the hindgut. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. The hindgut is the posterior part of the alimentary canal, including the rectum, and the large intestine." + "An ectoderm that is part of a lateral nasal prominence." "EMAPA:16806 EHDAA2:0000918" + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a superoxide stimulus. Superoxide is the anion, oxygen-, formed by addition of one electron to dioxygen (O2) or any compound containing the superoxide anion." + "An anatomical structure that is located along the line dividing two regions of an anatomical structure." + "Any process that stops, prevents or reduces the frequency, rate or extent of a protein or other molecule binding to a receptor." + "The cell migration process in which a follicle cell migrates as part of an epithelial sheet between the nurse cells and the oocyte. At the end of migration, they cover the anterior of the oocyte." + "A renal medulla interstitium that is part of a left kidney." + "The process in which the anatomical structures of an epithelial sheet are generated and organized. An epithelial sheet is a flat surface consisting of closely packed epithelial cells." + "KUPO:0001043" + "The chemical reactions and pathways resulting in the breakdown of dicarboxylic acids, any organic acid containing two carboxyl (-COOH) groups." + "The series of events involved in equilibrioception in which a mechanical stimulus is received and converted into a molecular signal. During equilibrioception, mechanical stimuli may be in the form of input from pressure receptors or from the labyrinth system of the inner ears." + "An arrangement of closely apposed microtubules running parallel to each other in the axon hillock and initial segment." "NIF_Subcellular:sao707332678" + "The progression of the pronephric proximal tubule over time, from its formation to the mature structure. A pronephric nephron tubule is an epithelial tube that is part of the pronephros." + "An epithelial cell that is part of the lacrimal sac." "FMA:70560" + "The biological process whose specific outcome is the progression of the roof of the mouth from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure. The roof of the mouth is the partition that separates the nasal and oral cavities." + "Ganglion that develops from a cranial ectodermal placode and contains sensory neurons that innervate a lateral line." "XAO:0004457 ZFA:0000120 TAO:0000120 EFO:0003493" + "An epiphysis that is part of a distal phalanx of pes." "SCTID:280049009" + "The process that gives rise to the cerebellum. This process pertains to the initial formation of a structure from unspecified parts. The cerebellum is the portion of the brain in the back of the head between the cerebrum and the pons. The cerebellum controls balance for walking and standing, modulates the force and range of movement and is involved in the learning of motor skills." + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a secretory granule. A secretory granule is a small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion." + "A glutamate decarboxylase 1 that is encoded in the genome of mouse." "UniProtKB:P48318" + "Any muscle organ that is part of a pes [Automatically generated definition]." "FMA:37369 SCTID:67240005 MA:0000652 BTO:0000477 EMAPA:36160" + "Any process that stops, prevents or reduces the frequency, rate or extent of hematopoietic stem cell proliferation." + "System pertaining to blood vessels in the brain." "FMA:61935 BTO:0003840 SCTID:362029003 EFO:0003491 EMAPA:35186 FMA:242007 ZFA:0000099 TAO:0000099" + "The process whose specific outcome is the progression of a pacemaker cell over time, from its formation to the mature state. Pacemaker cells are specialized cardiomyocytes that are responsible for regulating the timing of heart contractions." + "A bone that is part of a lower leg [Automatically generated definition]." "MA:0000676 EMAPA:35519" + "A lamina propria that is part of a bronchus [Automatically generated definition]." "UMLS:C1707054 FMA:86619 EMAPA:35194 MA:0001836 NCIT:C49212" + "Bone marrow in which the fat cells predominate in the meshes of the reticular network." "SCTID:328639002 FMA:74596 SCTID:5023006 BTO:0000635" + + "Region of liver parenchyma immediately below the capsule. This region is frequently specified in pathology diagnoses." + "One of a pair of right-sided and left-sided blood vessels in the circle of Willis. It connects the three cerebral arteries of the same side. Anteriorly, it is one portion of the terminal trifurcation of the internal carotid artery. The anterior cerebral artery and the middle cerebral artery are the other two branches of the trifurcation. Posteriorly, it communicates with the posterior cerebral artery." "UMLS:C0149559 NCIT:C33357 Wikipedia:Posterior_communicating_artery FMA:50084 MA:0002023 SCTID:181314001 EHDAA2:0004518 TAO:0005001 ZFA:0005001 EHDAA:3352 RETIRED_EHDAA2:0001487 EMAPA:18600" + "The portion of the plasma membrane surrounding a dendrite." + "A vertebra in the trunk region. For tetrapods, includes lumbar and thoracic vertebrae. Excludes caudal/coccygeal vertebra, which are located posteriorly. In tetrapods this includes thoracic, lumbar and sacral vertebrae, and excludes the cervical vertebrae, which are located anteriorly." + "Any gland that is part of an eyelid. This includes sebaceous glands (Zeis gland, tarsal gland) and sweat glands (Moll's gland)." "SCTID:280574000" + "The lipid bilayer surrounding a melanosome." + "Connective, non-functional supportive framework of a biological cell, tissue, or organ. Contrast with parenchyma." "UMLS:C0927195 NCIT:C67387 FMA:81494" + "The appearance of interleukin-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." + "The process whose specific outcome is the progression of the female gonad over time, from its formation to the mature structure." + "A cell projection supported by an assembly of actin filaments, and which lacks microtubules." + "A strand of hair that is part of a tail." "EMAPA:37971" + "A process in which a protein is transported to, or maintained in, a location within a secretory granule." + "A transient embryonic complex that comprises the pharyngeal arches, bulges of tissues of mesoderm and neural crest derivation through which pass nerves and pharyngeal arch arteries. The arches are separated internally by pharyngeal pouches, evaginations of foregut endoderm, and externally by pharyngeal clefts, invaginations of surface ectoderm. The development of the system ends when the stucture it contributes to are forming, which may include (depending on species) the thymus, thyroid, parathyroids, maxilla, mandible, aortic arch, cardiac outflow tract, external and middle ear[GO,modified]." "NCIT:C34248 UMLS:C1519038 FMA:293041 EHDAA2:0000187" + "Saliva-secreting exocrine glands of the oral cavity[GO]." "EFO:0000859 CALOHA:TS-0892 NCIT:C12426 FMA:9597 EHDAA:7987 VHOG:0000376 Wikipedia:Salivary_gland SCTID:181236000 MAT:0000079 EHDAA2:0001775 galen:SalivaryGland BTO:0001203 EV:0100059 MIAA:0000079 EMAPA:17751 UMLS:C0036098 MESH:D012469 MA:0000346 GAID:937" + "A promyelocyte committed to the basophil lineage." "FMA:84208" + + "Any process that activates or increases the frequency, rate or extent of coagulation." + "A luminal layer of epithelium that is part of a endometrium epithelium." "EMAPA:35309 MA:0002733" + "GC_ID:1" + "A glutamyl aminopeptidase that is encoded in the genome of human." "Reactome:R-HSA-2022341 UniProtKB:Q07075" + "Any process that modulates the frequency, rate or extent of the regulated release of glucagon." + "The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules." "Wikipedia:Cell_adhesion" + "Wikipedia:Glans" + "Any process that modulates the frequency, rate or extent of protein maturation." + "Any process in which a lipid is transported to, or maintained in, a specific location." + "A stem cell that self-renews as well as give rise to a single mature cell type." "FMA:70569" + "A neuron with a soma found in the hippocampus." + "Any process that activates or increases the frequency, rate or extent of hemopoiesis." + "Head of the adult organism." + "The process in which a hemocyte precursor cell acquires the characteristics of the phagocytic blood-cell type, the plasmatocyte. Plasmatocytes are a class of arthropod hemocytes important in the cellular defense response." + "The regulated release of dopamine from an axon." + "A nucleate quality inhering in a bearer by virtue of the bearer's having no nucleus." + "The process whose specific outcome is the progression of a cerebral cortex GABAergic interneuron over time, from initial commitment to its fate, to the fully functional differentiated cell." + "A CD24-low, CD44-positive, DX5-high, NK1.1-negative NK T cell." + "An eosinophil cationic protein that is encoded in the genome of human." "UniProtKB:P12724" + "The process of regulating the proliferation and elimination of T cells such that the total number of T cells within a whole or part of an organism is stable over time in the absence of an outside stimulus." + "Obsolete. Use PO:0000245 from Plant Ontology instead. In monosporic and bisporic megasporogenesis: the megaspore(s) that do not participate in megagametogenesis." + "The appearance of interleukin-6 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." + "An arachnoid mater that is part of a hindbrain [Automatically generated definition]." "VHOG:0000236 EMAPA:17784 MA:0000988" + "The outgrowth of neuroectoderm located on the floor of the embryonic hypothalamus that gives rise to the neurohypophysis (posterior lobe) of the pituitary gland." "EHDAA2:0004434 EMAPA:16647" + "The change in form that occurs when an epithelial cell progresses from it initial formation to its mature state, contributing to the process of gastrulation." + "An interneuron that has spider-like appearance with a small round soma, a large number (7-10) of short, smooth, or slightly beaded primary dendrites that give rise to only a few secondary branches, and a branched axon that establishes a dense axonal mesh with thin shafts." + "The space that surrounds an organism." + "A medium-wave-sensitive opsin (human) that is a translation product of the OPN1MW gene in human." "Reactome:R-HSA-391835 UniProtKB:P04001 DTO:02100474" + "The connective tissue bundles in the extracellular matrix of pulmonary tissue that are composed of collagen, and play a role in tissue strength and elasticity." + "An epithelial cell of the exocrine pancreas." "FMA:70986" + "A leukosialin that is encoded in the genome of human." "UniProtKB:P16150" + "Any cellular process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids." + "EHDAA2:0004085" + "Any process that activates or increases the frequency, rate or extent of T cell mediated cytotoxicity." + "A composition quality inhering in a bearer by virtue of the bearer's being composed of or possessing inorganic material." + "Any process that stops, prevents, or reduces the frequency, rate or extent of granulocyte differentiation." + "An external pocketing of pharyngeal ectoderm that contacts a region of endoderm (a pharyngeal pouch) and interdigitates in the anterior and posterior directions by the pharyngeal arches." "Wikipedia:Pharyngeal_groove NCIT:C34250 EMAPA:32750 FMA:295672 UMLS:C1280559 AAO:0010623" + "The progression of the amygdala over time from its initial formation until its mature state. The amygdala is an almond-shaped set of neurons in the medial temporal lobe of the brain that play a key role in processing emotions such as fear and pleasure." + "The outer layer of the epidermis, consisting of several layers of flat keratinized non-nucleated cells." "Wikipedia:Stratum_corneum NCIT:C33625 UMLS:C0221921 MA:0000804 FMA:67545 CALOHA:TS-0981 EMAPA:32787 SCTID:361695002 BTO:0000344 AAO:0010597" + "Any process that decreases the rate, frequency, or extent of the chemical reactions and pathways resulting in the formation of a glycoprotein, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide." + "An immature alpha-beta T cell that is located in the thymus and is CD4-positive and CD8-negative." + "Any process that activates or increases the frequency, rate or extent of leukocyte differentiation." + "Any process that modulates the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid)." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a temperature stimulus." + "A zone of skin that is part of a chest [Automatically generated definition]." "MA:0000553 FMA:61416 EMAPA:37279 SCTID:181496004" + "Posterior part of a vertebra that consists of a pair of pedicles and a pair of laminae, and supports seven processes: four articular processes, two transverse processes one spinous process[WP]. ZFA: A neural arch encloses the neural canal and typically meets its partner to form a neural spine." "MA:0001453 FMA:11946 NCIT:C32138 EFO:0003618 SCTID:317373001 Wikipedia:Vertebral_arch ZFA:0001066 AAO:0000725 TAO:0001066 UMLS:C0223076 VHOG:0001670" + "Any process that activates or increases the frequency, rate or extent of the directed movement of calcium ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "A C-type lectin domain family 7 member A that is encoded in the genome of human." "UniProtKB:Q9BXN2 Reactome:R-HSA-2130683" + "A decussation of the diencephalon where the fibers of the optic nerve cross." "BIRNLEX:1416 HBA:9310 BAMS:och VHOG:0000190 XAO:0004071 DMBA:17783 BAMS:DC SCTID:244453006 AAO:0010622 neuronames:459 FMA:62045 ZFA:0000556 BAMS:ox UMLS:C0029126 NCIT:C90609 EHDAA:10227 MESH:D009897 MA:0001098 GAID:832 BM:Tel-OCX EMAPA:17603 Wikipedia:Optic_chiasm TAO:0000556 MBA:117 BAMS:OC DHBA:10644 EHDAA2:0001302" + "A process that coontributes to the second meiotic division. The second meiotic division separates chromatids resulting in a haploid number of chromosomes." + "The growth of a cell, where growth contributes to the progression of the cell over time from one condition to another." + "Any process that modulates the frequency, rate or extent of cytotoxic T cell differentiation." + "A bronchiole that is part of a secondary pulmonary lobule and the last conducting structure of a non-respiratory bronchiole; after this point, the airways have alveoli in their walls." "Wikipedia:Terminal_bronchiole SCTID:278981008 FMA:7411 UMLS:C0225666 MA:0000424 EMAPA:36282 BTO:0003223 NCIT:C33754" + "The osseous spiral lamina consists of two plates of bone, and between these are the canals for the transmission of the filaments of the acoustic nerve. On the upper plate of that part of the lamina which is outside the vestibular membrane, the periosteum is thickened to form the limbus spiralis (or limbus laminæ spiralis), this ends externally in a concavity, the sulcus spiralis internus, which represents, on section, the form of the letter C. [WP,unvetted]." "FMA:77721 Wikipedia:Limbus_laminae_spiralis EMAPA:35496 MA:0001191" + "A neural arch that is part of a thoracic vertebra." "FMA:9151 SCTID:312764002" + "Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a microvillus on a follicle cell." + "A type of glomus or chief cell, is sensitive to hypoxia and produce catecholamines." + "A signal transducer CD24 that is encoded in the genome of human." "UniProtKB:P25063" + "Paired endochondral long bone that extends between the pectoral girdle and the skeletal parts of the forelimb. [PHENOSCAPE:mah]." "galen:Humerus SCTID:181923006 GAID:183 UMLS:C0020164 EFO:0001398 NCIT:C12731 FMA:13303 VHOG:0001158 Wikipedia:Humerus MA:0001356 MESH:D006811 AAO:0000679 CALOHA:TS-2202 EMAPA:19106 XAO:0003210" + "Any process that modulates the frequency, rate or extent of muscle tissue development." + "A change in morphology and behavior of a lymphocyte resulting from exposure to a specific antigen, mitogen, cytokine, chemokine, cellular ligand, or soluble factor, leading to the initiation or perpetuation of an immune response." + "Any process that increases the frequency, rate or extent of chromatin binding. Chromatin binding is the selective interaction with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase." + "A type I NK T cell that has been recently activated, secretes interferon-gamma and interleukin-4, and has phenotype CD4-negative, CD8-negative, CD69-positive, and downregulated NK markers." + "The thoracic nerves are the spinal nerves emerging from the thoracic vertebrae. [WP,unvetted]." "FMA:71167 SCTID:278750009 Wikipedia:Thoracic_spinal_cord UMLS:C0581620 neuronames:1718 MA:0003082 BIRNLEX:966 NCIT:C12894" + "Any process that modulates the rate, extent or frequency of the process in which cardiac muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors." + "An articular capsule that is part of the glenohumeral joint." "FMA:34944 SCTID:361836001 Wikipedia:Articular_capsule_of_the_humerus" + "An epithelium that is part of a jejunum." "SCTID:57300004 BTO:0001743 MA:0003215 EMAPA:18668 FMA:17232 CALOHA:TS-0494" + "The developmental process pertaining to the initial formation of a nephric duct. A nephric duct is a tube that drains a primitive kidney." + "The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte, megakaryocyte, thrombocyte, or erythrocyte lineages." + "The second stage of the kidney. It serves as the main excretory organ of aquatic vertebrates and as a temporary embryonic kidney in higher vertebrates. It is composed of the mesonephric duct (also called the Wolffian duct), mesonephric tubules, and associated capillary tufts. A single tubule and its associated capillary tuft is called a mesonephric excretory unit; these units are similar in structure and function to nephrons of the adult kidney. The mesonephros is derived from intermediate mesoderm in the vertebrate embryo." "EHDAA:5903 AAO:0010384 ZFA:0000529 UMLS:C0025492 EHDAA:1581 TAO:0000529 EHDAA2:0001130 EFO:0000928 GAID:1308 BTO:0001542 MESH:D001755 FMA:72171 EMAPA:16744 VHOG:0000038 CALOHA:TS-0624 XAO:0000141 NCIT:C26467 SCTID:308799002 Wikipedia:Mesonephros" + "Any process that activates or increases the frequency, rate or extent of endothelial cell differentiation." + "The part of the eye that consists of both the retina and the optic choroid." "SCTID:110701000" + "An anatomical space that surrounded_by a embryonic cloaca." "EHDAA2:0004586" + "A brain ventricle that is part of a telencephalon. In mammals and species with an evaginated telencephalon, this is one of a pair of lateral structures, one in each hemisphere." "GAID:611 VHOG:0000643 HBA:9419 BIRNLEX:1263 SCTID:180930008 EHDAA:3502 DHBA:10596 Wikipedia:Lateral_ventricle CALOHA:TS-1230 BTO:0000879 EFO:0001961 BAMS:LV FMA:78448 NCIT:C12834 EHDAA2:0001984 ZFA:0000696 BM:Tel-LV BAMS:Tel-V MBA:81 UMLS:C0152279 DMBA:126651562 EHDAA:6576 EV:0100307 MA:0000192 TAO:0000696 MESH:D020547 neuronames:209" + "Any process that modulates the frequency, rate or extent of somatic stem cell population maintenance." + "The controlled release of molecules that form the extracellular matrix, including carbohydrates and glycoproteins by a cell." + "Any process that activates or increases the frequency, rate or extent of type B pancreatic cell proliferation." + "The appearance of interleukin-22 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." + "Glandular cell of duodenal epithelium. Example: Enterocytes, Goblet cells, enteroendocrine cells; Paneth cells; M cells; Brunner's gland cell." "CALOHA:TS-1275" + "A pyramidal cell morphology that inheres in neurons which have a distinct tuft formation, distal from the soma." "ilxtr:TuftedPyramidalPhenotype" + "A cell containing at least one nucleus." "FMA:67513" + "Any process that modulates the frequency or rate of myeloid dendritic cell activation." + "The lung vasculature is composed of the tubule structures that carry blood or lymph in the lungs[GO]." "FMA:73750" + "Nodular lymphoid structures on the serosal surface of the small intestine." "EMAPA:35782 SCTID:38986009 FMA:15054 MA:0001557" + "The directed movement of ADP, adenosine diphosphate, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole." + "A retinal ganglion cell C outer that has a medium dendritic field and a dense dendritic arbor." + "An anatomical structure that develops (entirely or partially) from the mesoderm." + "An alpha-(1,3)-fucosyltransferase 4 that is encoded in the genome of human." "Reactome:R-HSA-9034106 UniProtKB:P22083" + "A plasmacytoid dendritic cell with the phenotype HLA-DRA-positive, CD123-positive, and CD11c-negative." + "A submucosa that is part of a jejunum [Automatically generated definition]." "EMAPA:27111 FMA:14950 SCTID:70192009" + "An epithelium that is part of a lacrimal gland [Automatically generated definition]." "EMAPA:36515 MA:0001297" + "A protein that has a core domain composition consisting of an extracellular N-terminal domain that adopts an immunoglobulin fold, a transmembrane domain, and an intracellular C-terminal domain with a single copy of the Immunoreceptor tyrosine-based activation motif (Pfam:PF02189) (ITAM). It constitutes the invariant subunit of the T cell antigen receptor (TCR). TCR is a surface receptor on T cells responsible for recognizing MHC-restricted antigens and initiating the cellular immune response." "PIRSF:PIRSF001993" + "Any process that activates or increases the frequency, rate, or extent of mast cell cytokine production." + "The lipid bilayer surrounding a tertiary granule." + "The progression of a metanephric nephron tubule over time, from its initial formation to the mature structure. A metanephric nephron tubule is an epithelial tube that is part of the metanephric nephron, the functional part of the metanephros." + "A kisspeptin neuron that is located in the hypothalamus. These neurons project to and activate gonadotrophin-releasing hormone neurons (acting via the kisspeptin receptor) in the hypothalamus and stimulate the secretion of gonadotrophin-releasing hormone." + "A pre-cartilage condensation that is part of a manual digit mesenchyme." "VHOG:0000954 EMAPA:32639" + "A trabecula that is part of a spleen." "SCTID:61987002 Wikipedia:Trabeculae_of_spleen NCIT:C33607 EMAPA:35808 FMA:16027 UMLS:C0229688 MA:0000758" + "A serous membrane that is part of a rectum [Automatically generated definition]." "EMAPA:27087 FMA:15039" + "A CD4-positive, alpha-beta T cell that has differentiated into a memory T cell." + "The gastric glands in the pyloric region of the stomach; the pyloric glands secrete mucin, which coats the stomach and protects it, and hormones such as gastrin and enkephalin[MP]." "SCTID:70710007 NCIT:C33431 Wikipedia:Pyloric_gland UMLS:C0227239 EMAPA:27211 FMA:14922" + "The chemical reactions and pathways resulting in the formation of serotonin (5-hydroxytryptamine), a monoamine neurotransmitter occurring in the peripheral and central nervous systems, also having hormonal properties." "Wikipedia:Serotonin" + "Sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals." "BIRNLEX:1062 MAT:0000138 EV:0100353 galen:Ear MA:0000236 UMLS:C0013443 EMAPA:16193 EHDAA:502 MIAA:0000138 UMLS:C0521421 EFO:0000826 BTO:0000368 XAO:0000189 CALOHA:TS-1165 SCTID:1910005 Wikipedia:Ear VHOG:0000330 NCIT:C12394 MESH:D004423 EHDAA2:0000423 FMA:52780 GAID:62 AAO:0011014" + "Any process that modulates the frequency, rate or extent of nervous system development, the origin and formation of nervous tissue." + "A group of bones comprised of hyoid body and two pairs of cornua (i.e. greater cornua and lesser cornua), and lies just below the tongue, above the thyroid cartilage." "MA:0003037 AAO:0000225 http://palaeos.com/vertebrates/bones/gill_arches/images/ReptileHyoids.gif EMAPA:37600 SCTID:410035009 AAO:0000682" + "The developmental process pertaining to the initial formation of a metanephric capsule from unspecified parts. The metanephric capsule is the tough fibrous layer surrounding the metanephros, covered in a thick layer of perinephric adipose tissue. It provides some protection from trauma and damage." + "Any process that decreases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroid hormones,compounds with a 1, 2, cyclopentanoperhydrophenanthrene nucleus that act as hormones." + "Immature CD8_alpha-negative CD11b-positive dendritic cell is a CD8_alpha-negative CD11b-positive dendritic cell that is CD80-low, CD86-low, and MHCII-low." + "A cell with extensive dendritic processes found in the B cell areas (primary follicles and germinal centers) of lymphoid tissue. They are unrelated to the dendritic cell associated with T cells. Follicular dendritic cells have Fc receptors and C3b receptors, but unlike other dendritic cells, they do not process or present antigen in a way that allows recognition by T cells. Instead, they hold antigen in the form of immune complexes on their surfaces for long periods and can present antigen to B cells during an immune response." "MESH:D020566 FMA:83037 BTO:0004267" + "A leukocyte granule-associated proteinase that is a translation product of the human GZMB gene or a 1:1 ortholog thereof." "IUPHARobj:2369" + "Any process that modulates the frequency, rate or extent of oogenesis." + "The groups of nerve cell bodies associated with the twelve cranial nerves." "MAT:0000200 TAO:0000013 EFO:0000902 VHOG:0000076 MA:0000213 MIAA:0000200 EMAPA:16659 SCTID:244448001 BIRNLEX:2597 BTO:0000106 ZFA:0000013 MA:0000214 Wikipedia:Cranial_nerve_ganglion XAO:0000027 FMA:54502" + "An epithelial sac that is part of a Rathke's pouch." "EMAPA:25036 EHDAA2:0001473" + "A transcription factor SOX-2 that is encoded in the genome of mouse." "UniProtKB:P48432" + "Any process that activates or increases the frequency, rate or extent of glial cell migration." + "The ascending aorta is the portion of the aorta in a two-pass circulatory system that lies between the heart and the arch of aorta[GO]. A portion of the aorta commencing at the upper part of the base of the left ventricle, on a level with the lower border of the third costal cartilage behind the left half of the sternum; it passes obliquely upward, forward, and to the right, in the direction of the heart's axis, as high as the upper border of the second right costal cartilage, describing a slight curve in its course, and being situated, about 6 cm behind the posterior surface of the sternum. The total length is about 5 cm in length [Wikipedia]." "FMA:3736 EMAPA:17014 NCIT:C32150 Wikipedia:Ascending_aorta EHDAA2:0000147 UMLS:C0003956 SCTID:181299009 EHDAA:9828 MA:0002570" + "An M9 retinal ganglion cells with synaptic terminals in S2 and is depolarized by illumination of its receptive field center." + "Any process that modulates the frequency, rate or extent of leukocyte apoptotic process." + "The epithelial cell differentiation process in which a relatively unspecialized cell acquires specialized features of an acinar cell, a secretory cell that is grouped together with other cells of the same type to form grape-shaped clusters known as acini." + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids." + "UMLS:C0226363 NCIT:C32957 SCTID:283493001 FMA:14766" + "FMA:20903" + "Any process that modulates the frequency, rate or extent of glial cell proliferation." + "FMA:63144" + "Any process that modulates the frequency, rate or extent of axo-dendritic protein transport." + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving aldosterone." + "A part of the body present only in females." "AEO:0000176" + "The process in which the anatomical structures of a metanephric distal tubule are generated and organized. The metanephric distal tubule is a metanephric nephron tubule that begins at the macula densa and extends to the metanephric connecting tubule." + "An anatomical space that is part of a bone of lower jaw." "AAO:0000273" + "Any process that decreases the rate, frequency, or extent of cilium movement, the directed, self-propelled movement of a cilium." + "Any vesicle that is part of the extracellular region." + "A portion of connective tissue that is part of a chest [Automatically generated definition]." "MA:0000550 EMAPA:37254" + "An roughly circular indentation in a surface." "AEO:0000204" + "A manual digit phalanx bone or its cartilage or pre-cartilage precursor." + "A protein that is a translation product of the human HBA1, HBA2, HBB, HBD, HBE1, HBG1, HBG2, HBM, HBQ1, or HBZ genes, 1:1 orthologs thereof, or semi-orthologs thereof." + "Any process that stops, prevents, or reduces the frequency, rate or extent of gamma-delta T cell differentiation." + "The morphogenetic process in which the foregut region specified to become the lung forms the initial left and right buds." + "A chemokine receptor that is a translation product of the human CX3CR1 gene or a 1:1 ortholog thereof. The preferred ligand is CX3CL1." "IUPHARobj:74 PIRSF:PIRSF501025" + "The process in which the left cardiac ventricle is generated and organized." + "A portion of connective tissue that is part of a larynx [Automatically generated definition]." "UMLS:C1708651 EMAPA:35471 MA:0001754 NCIT:C49245" + "Obsolete. Use PO:0000431 from Plant Ontology instead. A diploid (2n) cell that undergoes meiosis and produces four haploid (1n) megaspores; also called megaspore mother cell." + "Reactions triggered in response to the presence of a fungus that act to protect the cell or organism." + "Mesenchyme that is part of a developing right lung." "EHDAA2:0001739 EMAPA:17662" + "The constricted portion of the urinary bladder, formed by the meeting of its inferolateral surfaces proximal to the opening of the urethra[MP]." "EMAPA:36078 NCIT:C12336 Wikipedia:Neck_of_urinary_bladder UMLS:C0227716 galen:UrinaryBladderNeck SCTID:362227006 FMA:15912 MA:0002491" + "A process in which a protein is transported to, or maintained in, a location within a presynapse." + "Any process that modulates the frequency, rate or extent of mitosis." + "A tunica adventitia that is part of a artery." "EV:0100030 EMAPA:36295 FMA:14274 SCTID:113261001" + "The process whose specific outcome is the progression of the dorsal cochlear nucleus over time, from its formation to the mature structure." + "The innermost layer of the aorta, containing the endothelium and an inner elastic membrane." "MA:0002904 FMA:74419 BTO:0005553 SCTID:362031007 EMAPA:35137" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA." + "The multiplication or reproduction of urothelial cells, resulting in the expansion of a cell population. Urothelial cells make up a layer of transitional epithelium in the wall of the bladder, ureter, and renal pelvis, external to the lamina propria." + "The epithelial layer of the lung." "EMAPA:32860 MA:0001783 BTO:0001653" + "A crypt of Lieberkühn that is part of a large intestine [Automatically generated definition]." "UMLS:C1179777 MA:0001544 NCIT:C32924 FMA:63622 EMAPA:35465" + "A spatially aggregated collection of nerve cell bodies in the CNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections, and including nearby cells that share the same cell type, chemical phenotype, and connections. (CUMBO)." "NCIT:C13197 FMA:83686 AEO:0000136 NLX:28443 Wikipedia:Nucleus_(neuroanatomy)" + "A medium spiny neuron that expresses dopamine type 2 receptors and projects to the external globus pallidus." + "Any process that modulates the rate, frequency or extent of the transition where a mesenchymal cell establishes apical/basolateral polarity,forms intercellular adhesive junctions, synthesizes basement membrane components and becomes an epithelial cell that will contribute to the shaping of the metanephros." + "Any process that stops, prevents, or reduces the frequency, rate or extent of leukocyte proliferation." + "A class of large neuroglial (macroglial) cells in the central nervous system - the largest and most numerous neuroglial cells in the brain and spinal cord. Astrocytes (from 'star' cells) are irregularly shaped with many long processes, including those with 'end feet' which form the glial (limiting) membrane and directly and indirectly contribute to the blood-brain barrier. They regulate the extracellular ionic and chemical environment, and 'reactive astrocytes' (along with microglia) respond to injury." "FMA:54537 CALOHA:TS-0060 BTO:0000099" + "A saclike structure of the prostate gland, comprised of at least three cell layers: an innermost layer of secretory columnar luminal epithelium, a middle layer of squamous basal epithelium that also contains neuroendocrine cells, transit amplifying cells, and stem cells, and an outer layer of smooth muscle intermixed with other stromal cells." "FMA:66808" + "A muscle cell that is involved in the mechanism of insect flight. This encompasses both, cells that power flight and cells that control flight." "FBbt:00003360" + "The process in which the anatomical structures of the pronephric duct are generated and organized. The pronephric duct collects the filtrate from the pronephric tubules and opens to the exterior of the kidney." + "The process in which a plasmacytoid dendritic cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex." + "Any process that modulates the frequency, rate or extent of cilium-dependent cell motility." + "A transferrin receptor protein 1 that is encoded in the genome of mouse." "UniProtKB:Q62351" + "The process in which a relatively unspecialized epithelial cell becomes a more specialized epithelial cell of the mammary gland." + "An endothelial cell that is part of the venous sinus of red pulp of spleen." "FMA:62817" + "A portion of connective tissue that is part of a shoulder [Automatically generated definition]." "EMAPA:37315 MA:0000632" + "Any process that modulates the frequency, rate or extent of protein localization to cell periphery." + "Any process in which proteins and protein complexes involved in translation are transported to, or maintained in, a specific location." + "Short nephrons are associated with mid-cortical and superficial glomeruli, are situated entirely in the outer medulla, and have no thin ascending limb[GO]." + "A motile sperm cell that contain no F-actin, and their motility is powered by a dynamic filament system." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms." + "The orderly movement of a podocyte from one site to another, often during the development of a multicellular organism or multicellular structure. A podocyte is a specialized kidney epithelial cell." + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving dopamine." + "Any process that activates or increases the frequency, rate or extent of R7 cell differentiation." + "An epithelial cell derived from endoderm." "FMA:69075" + "Subdivision of endoskeleton derived from pharyngeal arches." "AAO:0010157 VSAO:0000149 ZFA:0001216 XAO:0003176 VHOG:0000315 Wikipedia:Facial_skeleton TAO:0001216" + "Connective tissue between the cellular elements of a structure." "FMA:86301 SCTID:85293002" + "An epithelium that is part of the mouth and lines the oral cavity, typically stratified squamous, and may be para-, ortho- or non- keratinized. Primary barrier between oral environment and deeper tissues." "ZFA:0000816 AAO:0010357 EMAPA:16839 UMLS:C1709332 TAO:0000816 CALOHA:TS-0715 NCIT:C49595 EHDAA:2187 FMA:265152 XAO:0003201 MA:0000344 EMAPA:26942 VHOG:0000187 BTO:0001775 EHDAA2:0001325" + "EMAPA:16110 EHDAA2:0000117 EHDAA:138 VHOG:0000621 BTO:0000897" + "GC_ID:1" + "Any process involved in the maintenance of an internal steady state of monoatomic cations within an organism or cell. Monatomic cations (also called simple cations) are cations consisting of exactly one atom." + "The chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells." + "A hematopoietic stem cell that resides in the fetal liver. In mice, this cell type is first observed at E10.5. This cell type is MHC-positive, HSA-positive, AA4.1-positive, CD45-positive, Sca-1 positive, CD150-positive, CD48-negative and CD244-negative." + "A groove that is situated between the 1st and 2nd pharyngeal arch." "EMAPA:16119 EHDAA:575 VHOG:0000554 VHOG:0000969 EHDAA2:0000009" + "Any process that decreases the rate, frequency or extent of protein maturation by peptide bond cleavage." + "An endoderm that is part of a hindgut [Automatically generated definition]." "EHDAA:979 RETIRED_EHDAA2:0000781" + "MA:0002615 EMAPA:28402" + "A trophoblast cell that invades the uterine wall to anchor the placenta to the uterus. An interstitial extravillous trophoblast cell differentiates from an extravillous trophoblast cell, becoming hyperchromatic and changing its morphology to a fibroblast-like spindle-shaped cell. In humans, this cell can be distinguished by the expression of placental-specific protein 8, which stimulates migration." + "Missing definition for term UBERON:0005064. Please replace it using linked reference." + + "The metanephric proximal straight tubule is the part of the metanephric descending limb that extends from the metanephric proximal convoluted tubule to the metanephric descending thin tubule[GO]." + "A cerebrospinal fluid-filled space that runs longitudinally through the length of the entire spinal cord. The central canal is contiguous with the ventricular system of the brain. The central canal represents the adult remainder of the neural tube." "Wikipedia:Central_canal FMA:242845 EMAPA:25042" + "A cell morphology that inheres in neurons which are large and non-spiny, with dendrites radiating in a multipolar or bitufted pattern, often favouring the descending side, and axons that ascend directly from the superficial side of the soma, and travel upward without branching." "ilxtr:MartinottiPhenotype" + "A stem cell that is the precursor of male gametes." "FBbt:00004929" + "An intracellular membrane-bounded particle found in fungi and containing chitin synthase; it synthesizes chitin microfibrils. Chitin synthase activity exists in chitosomes and they are proposed to act as a reservoir for regulated transport of chitin synthase enzymes to the division septum." + "The chemical reactions and pathways resulting in the formation of an alpha-amino acid." + "A transition where a mesenchymal cell establishes apical/basolateral polarity,forms intercellular adhesive junctions, synthesizes basement membrane components and becomes an epithelial cell that will contribute to the shaping of the metanephric renal vesicle." + "Any process that stops, prevents or reduces the frequency, rate or extent of lysosome organization." + "Any process that modulates the frequency, rate or extent of multicellular organismal development." + "The junction between the axon of a motor neuron and a muscle fiber. In response to the arrival of action potentials, the presynaptic button releases molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane of the muscle fiber, leading to a post-synaptic potential responsible for muscle contraction." + "Any microvascular endothelial cell that is part of a brain." + "Any process that decreases the rate, frequency, or extent of a response to cytokine stimulus." + "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 2." + "A blood vessel that is part of a hindlimb [Automatically generated definition]." "MA:0000659 EMAPA:37298" + "The process in which platelets bud from long processes extended by megakaryocytes." + "A proteolytic cleavage product that is derived from any of the casein milk proteins." + "A chromaffin cell that is part of the left ovary." "FMA:74321" + "An extratelencephalic-projecting glutamatergic neuron located in layer 5b of the primary motor cortex that projects to the medulla. MY ET cells are large, big-tufted cells with the apical dendrite often bifurcating close to the soma, suggesting they are corticospinal cells. MY ET cells have bigger hyperpolarization sag, lower input resistance, and smaller AP width, compared to L5 IT neurons." + "GC_ID:1" + "Any process that modulates the frequency, rate or extent of meiotic cell cycle process involved in oocyte maturation." + "Muscular valve that controls the flow of digestive juices (bile and pancreatic juice) through the ampulla of Vater into the second part of the duodenum. Relaxed by the hormone Cholecystokinin (CCK) via vasoactive intestinal polypeptide (VIP).[WP]." "Wikipedia:Sphincter_of_ampulla SCTID:181271000 UMLS:C0028872 MESH:D009803 EMAPA:18663 GAID:285 FMA:15077 NCIT:C13065" + "A ring of cells capable of forming a limb." + "A broadly stratifying amacrine cell with a small dendritic field, straight dendrites and post-synaptic terminals in S1, S2, and S3." + "The process pertaining to the initial formation of an animal organ from unspecified parts. The process begins with the specific processes that contribute to the appearance of the discrete structure, such as inductive events, and ends when the structural rudiment of the organ is recognizable, such as a condensation of mesenchymal cells into the organ rudiment. Organs are a natural part or structure in an animal or a plant, capable of performing some special action (termed its function), which is essential to the life or well-being of the whole. The heart and lungs are organs of animals, and the petal and leaf are organs of plants. In animals the organs are generally made up of several tissues, one of which usually predominates, and determines the principal function of the organ." + "A portal system that begins in capillaries in the wall of the digestive tract and and runs as the hepatic portal vein to the liver." "AAO:0010225" + "An undifferentiated germ cell that proliferates rapidly and gives rise to oocytes." "FMA:83673" + "The process whose specific outcome is the progression of the superior salivary nucleus over time, from its formation to the mature structure." + "The process in which immunoglobulin genes are formed through recombination of the germline genetic elements, as known as immunoglobulin gene segments, within a single locus." + "OBSOLETE (was not defined before being made obsolete)." + "The dorsal aorta is a blood vessel in a single-pass circulatory system that carries oxygenated blood from the gills to the rest of the body. In a single-pass circulatory system blood passes once through the heart to supply the body once." "ZFA:0000014 Wikipedia:Dorsal_aorta EHDAA:402 XAO:0000051 EMAPA:18606 VHOG:0000264 TAO:0000014 BTO:0004673 SCTID:338637006 AAO:0011029" + "The intermediate filament cytoskeleton that is part of a postsynapse." + "Any process that modulates the frequency, rate or extent of angiogenesis." + "The process dependent upon B cell antigen receptor signaling in response to self or foreign antigen through which B cells are selected for survival." + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitrogen compound stimulus." + "Dermis-derived entity that is made of skeletal tissue." + "The intersection of sublaminar layers S2 and S3." + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a progesterone stimulus." + "Any process that stops, prevents or reduces the frequency, rate or extent of euchromatin binding." + "A mature alpha-beta T cell that expresses an alpha-beta T cell receptor and the CD4 coreceptor." + "Any process that modulates the frequency, rate or extent of memory T cell activation." + "The process in which neuroblasts acquire specialized structural and/or functional features that characterize the mature eurydendroid cell. Differentiation includes the processes involved in commitment of a neuroblast to a eurydendroid cell fate. A eurydendroid cell is an efferent neuron found in the cerebellar cortex of teleosts." + "A fully differentiated neutrophil, a granular leukocyte having a nucleus with three to five lobes connected by slender threads, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes. They are produced in bone marrow at a rate of 5e10-10e10/day and have a half-life of 6-8 hours. Neutrophils are CD15-positive, CD16-positive, CD32-positive, CD43-positive, CD181-positive, and CD182-positive." "BTO:0003473" + "OBSOLETE (was not defined before being made obsolete)." + "Lymph node germinal centers contain two microenvironments: the light zone and the dark zone. The dark zone is densely populated with B cell blasts and reticular cells." + "One of the two epithelia which make up the tympanic membrane (along with the fibrous layer)." "MA:0001224 NCIT:C49308 UMLS:C1711401 SCTID:70839004 EMAPA:19064" + "Any chamber of the left side of the heart." "SCTID:362008007 FMA:7166" + "A vasculature that is part of a connecting stalk." "EHDAA2:0000313" + "The external iliac artery is a large artery in the pelvic region that carries blood to the lower limb. The external iliac artery is a paired artery, meaning there is one on each side of the body: a right external iliac artery and left external iliac artery. The external iliac artery is accompanied by the external iliac vein, which is located posterior to the artery. [WP,unvetted]." "EMAPA:17614 galen:ExternalIliacArtery SCTID:181352000 EHDAA2:0000463 EHDAA:4337 NCIT:C32558 MA:0001973 Wikipedia:External_iliac_artery UMLS:C0226398 FMA:18805 BTO:0004666" + "A cellular process that results in the breakdown of a Golgi apparatus that contributes to Golgi inheritance." + "The directed movement of calcium ions from outside of a cell, across the plasma membrane and into the cytosol." + + "The part of the blastula that has the potential to develop into a paraxial mesoderm." "XAO:0004134 EFO:0003443 ZFA:0000591 TAO:0000591" + "An enterocyte that is part of the epithelium proper of duodenum." "FMA:263098" + "The vessels formed within the fifth pair of pharyngeal arches in embryogenesis." "Wikipedia:Aortic_arches#Arch_5 AAO:0010421 VHOG:0000145 SCTID:308778000 TAO:0005009 XAO:0000352 ZFA:0005009" + "A lobe of lung that is part of a right lung." "SCTID:272654004 UMLS:C1285106 NCIT:C48944 MA:0001791 EMAPA:35155" + "The process in which T cells that express T cell receptors that are restricted by self MHC protein complexes and tolerant to self antigens are selected for further maturation." "Wikipedia:Thymocyte" + "Any process that activates or increases the frequency, rate or extent of a cellular process, any of those that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." + "The process whose specific outcome is the progression of a sympathetic ganglion over time, from its formation to the mature structure." + "Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism." "UMLS:C1519343 FMA:85544 NCIT:C34076 galen:ComplexSkeletalStructure SCTID:118966000" + "Pancreatic bud that gives rise to the accessory pancreatic duct." "VHOG:0001428 EFO:0003465 EHDAA2:0001385 Wikipedia:Pancreatic_bud AAO:0011031 TAO:0001370 EMAPA:17067 ZFA:0001370 XAO:0000467 SCTID:361435005" + "Enables the transfer of a hexose sugar, a monosaccharide with 6 carbon atoms, from one side of a membrane to the other." "Reactome:R-HSA-5638222 Reactome:R-HSA-189242" + "The multiplication or reproduction of germ cells, reproductive cells in multicellular organisms, resulting in the expansion of a cell population." + "A clavicle that is in the left side of a entire appendicular skeleton." "FMA:13323" + "Any process that activates or increases the frequency, rate or extent of dendrite morphogenesis." + + "The developmental process that results in the creation of defined areas or spaces within the kidney along the anterior/posterior axis to which cells respond and eventually are instructed to differentiate." + "The movement of a myeloid dendritic cell in response to an external stimulus." + "A pedal digit phalanx bone or its cartilage or pre-cartilage precursor." + "Stalk-like part of the brain that includes amongst its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,MP,generalized]." "SCTID:180925009 BAMS:BS VHOG:0001457 NCIT:C12441 CALOHA:TS-0093 neuronames:236 BTO:0000146 EFO:0001962 Wikipedia:Brainstem EV:0100241 MBA:343 MA:0000169 MESH:D001933 BIRNLEX:1565 UMLS:C0006121 TAO:0002156 FMA:79876 ZFA:0001707 EMAPA:32678" + "A type II vestibular sensory cell that is part of the epithelium of macula of utricle of membranous labyrinth." "FMA:263196" + "The process in which a relatively unspecialized T cell acquires specialized features of a mature CD8-positive, alpha-beta T cell." + "A bistratified ganglion cell with small, dense dendritic fields that terminate in S1 and S3." + "A subdivision of a limb or fin skeleton consisting of bones which connects the upper limb or fin to the axial skeleton on each side. It consists of the clavicle and scapula in humans and, in those species with three bones in the pectoral girdle, the coracoid. Some mammalian species (e.g. the dog and the horse) have only the scapula. In humans, the only joints between the shoulder girdle and axial skeleton are the sternoclavicular joints on each side. No joint exists between each scapula and the rib cage; instead the muscular connection between the two permits relatively great mobility of the shoulder girdle in relation to the pelvic girdle. In those species having only the scapula, no joint exists between the forelimb and the thorax, the only attachment being muscular[WP]. Examples: There are only two instances, right and left pectoral girdle skeletons." "TAO:0000407 VSAO:0000156 EHDAA2:0001420 VHOG:0001156 UMLS:C0427245 AAO:0000422 AAO:0000754 FMA:24141 XAO:0003063 MIAA:0000181 MAT:0000181 EFO:0000946 ZFA:0000407 Wikipedia:Pectoral_girdle NCIT:C33547" + "Any process that activates or increases the frequency, rate or extent of photoreceptor cell differentiation. An example of this process is found in Drosophila melanogaster." + "The chemical reactions and pathways resulting in the formation of testosterone, an androgen having 17beta-hydroxy and 3-oxo groups, together with unsaturation at C-4 C-5." + "The movement of a myeloid leukocyte within or between different tissues and organs of the body." + "Any process that activates or increases the frequency, rate or extent of lens fiber cell differentiation." + "An arthroconidium that has more than one nucleus." "FAO:0000037" + "An otic fibrocyte that underlies the stria vascularis and is part of a mesenchymal gap junction network that regulates ionic homeostasis of the endolymph." + "A neuroepithelium some of whose cells are undergoing terminal differentiation to become neuronal cells." "AEO:0001010" + "The process whose specific outcome is the progression of the stomach over time, from its formation to the mature structure. The stomach is an expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ." + "Binding specifically to a substance (cargo) to deliver it to a transport vesicle. Cargo receptors span a membrane (either the plasma membrane or a vesicle membrane), binding simultaneously to cargo molecules and coat adaptors, to efficiently recruit soluble proteins to nascent vesicles." "Reactome:R-HSA-9759202 Reactome:R-HSA-3000122 Reactome:R-HSA-3000137 Reactome:R-HSA-3000112 Reactome:R-HSA-9759209 Reactome:R-HSA-3000103 Reactome:R-HSA-350168" + "The process in which a relatively unspecialized cell acquires specialized features of a glomerular visceral epithelial cell. A glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells." + "Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts." "EHDAA:2219 VHOG:0000393 EHDAA:1568 EMAPA:16737 FMA:265130 SCTID:361110005 EHDAA2:0001606" + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA." + "The intermediate filament cytoskeleton that is part of a presynapse." + "Wikipedia:Iris_muscle MA:0001287 SCTID:280888007 FMA:49154" + "A protein complex composed of two identical immunoglobulin heavy chains of an IgA isotype and two identical immunoglobulin light chains, held together by disulfide bonds, sometimes complexed with J chain or J chain and secretory component, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." + "Any process that activates or increases the frequency, rate, or extent of type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families." + + "Mature interstitial dendritic cell is a interstitial dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive." + "Vein that is central to a lobule in the liver." "ZFA:0005168 FMA:17544 NCIT:C32281 SCTID:272023004 Wikipedia:Central_veins_of_liver TAO:0005168" + "Any process that activates or increases the frequency, rate or extent of imaginal disc growth." + "A C-C motif chemokine 3 that has been processed by proteolytic cleavage." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of macrophage antigen processing and presentation." + "The process in which the anatomical structure of the pulmonary venous blood vessels are generated and organized. Pulmonary veins are blood vessels that transport blood from the lungs to the heart." + "A cell involved in the formation of a granulocyte." "FMA:83519" + "A nerve that arises from the caudal cervical nerves and is primarily the motor nerve of the diaphragm but also sends sensory fibers to the pericardium." "MESH:D010791 VHOG:0000728 EHDAA:4677 GAID:848 FMA:6191 SCTID:280344009 BTO:0001063 EMAPA:17813 Wikipedia:Phrenic_nerve BAMS:phn UMLS:C0031774 NCIT:C52813 MA:0001170" + "The process in which an antigenically naive T cell acquires the specialized features of an effector, regulatory, or memory T cell as part of an immune response. Effector T cells include cells which provide T cell help or exhibit cytotoxicity towards other cells." + "Any portion of gas located in a part of the respiratory system." + "An epithelium that is part of a intrahepatic bile duct [Automatically generated definition]." "NCIT:C43617 EHDAA2:0000743 MA:0002662 UMLS:C1708552 EHDAA:3053" + "Binding to a chemokine receptor in the CXCR family." + "Any process that activates or increases the frequency, rate or extent of cardiac ventricle development." + "A neuron with soma location in the reticular formation with axons that extend into the spinal cord such. Reticulospinal neuron activity can lead to a variety of motor behaviors." + "One of the veins that feed the splenic vein." "NCIT:C49779 Wikipedia:Trabecular_veins MA:0000760 UMLS:C1710160" + "Portion of tissue, that consists of single layer of cells connected to each other by cell junctions. Examples: layer of glial cells; epithelium." "NCIT:C66831" + + "The disaggregation of an excitatory synapse into its constituent components." + "Any process that modulates the frequency, rate or extent of basophil degranulation." + "Any process that activates or increases the frequency, rate or extent of protein localization to plasma membrane." + "A cell morphology that inheres in neurons with dendrites that are bidirectional, emerging from opposite ends of the soma, with the two arbors extending in radial or tangential directions." + "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 6." + "Any process that modulates synaptic transmission by regulating protein degradation at the synapse." + "Any process that modulates the frequency, rate or extent of bone tissue loss (resorption)." + "A basket cell that is large, and typically ascends to give rise to many long horizontally and vertically projecting axon collaterals that traverse neighboring columns and can extend through all cortical layers." + "Enables the transfer of an inorganic molecular entity from the outside of a cell to the inside of the cell across a membrane. An inorganic molecular entity is a molecular entity that contains no carbon." + "A dental pulp cell that possesses stem-cell-like qualities, including self-renewal capability and multi-lineage differentiation." + "The first of the series of pharyngeal arches that develop into jaw bones or their homologs, and their associated nerves and arteries." "XAO:0000097 CALOHA:TS-2089 TAO:0001595 EHDAA2:0000006 NCIT:C34175 VHOG:0000296 MFMO:0000095 ZFA:0001612 FMA:293019 UMLS:C1517197 SCTID:308767008 EHDAA:573 Wikipedia:First_pharyngeal_arch AAO:0010364 EMAPA:16118" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of a hormone from a cell." + "Parenchymal tissue that forms the pineal gland." "NCIT:C41834 UMLS:C1519088" + "Any fat deposit surrounding a visceral organ." + "The proximal free limb segment. Includes as parts the stylopod skeleton." "MIAA:0000093 EFO:0000879 FMA:83014 MAT:0000093 MA:0002717" + "A transverse process that is part of a cervical vertebra." "FMA:9913 FMA:23894 SCTID:280730000" + "A ciliated columnar cell found in the trachea and bronchus. Vary from low to tall columnar; possesses up to 300 cilia at its surface, interspersed with long irregular microvilli with the cilia varying in length from about 6um in the trachea to about 4um in the terminal bronchioles; driving force of the ciliary current in the bronchial tree." "FMA:70542" + "Any process that modulates the frequency, rate or extent of T cell activation." + "A protein that is a translation product of the human PAX5 gene or a 1:1 ortholog thereof." + + "Any process that stops, prevents, or reduces the frequency, rate or extent of the transport of proteins from the Golgi to the plasma membrane." + "An organ cavity that is part of a vagina." "FMA:19982" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of proteins from the nucleus into the cytoplasm." + "The process whose specific outcome is the progression of the metencephalon over time, from its formation to the mature structure." + "A CD4-positive, alpha-beta T cell that has the phenotype GATA-3-positive, CXCR3-negative, CCR6-negative, and is capable of producing interleukin-4." "MESH:D018418 FMA:84385 BTO:0001679" + "GC_ID:1" + "The multiplication or reproduction of epithelial cells, resulting in the expansion of a cell population that contributes to the shaping of the liver." + "Any process that stops, prevents, or reduces the frequency, rate or extent of lymphocyte activation." + "An endothelial cell found in the periportal region hepatic sinusoid, near the portal triad. The fenestrae of these cells are larger but fewer in number compared with those of endothelial cells near the centrilobular region of the hepatic sinusoid." "EFO:0010705" + "Any process that modulates the frequency, rate or extent of cardiac ventricle development." + "A respiratory epithelial cell with topographic nuclear position in between the basal and luminal cell of the airway epithelium. This non-basal, intermediate cell has limited proliferative capacity, ultrastructural features of basal cells and no defined features of the typically differentiated cellular phenotypes." + "Any process that modulates the frequency, rate, or extent of myeloid dendritic cell cytokine production." + "The chemical reactions and pathways resulting in the formation of zeaxanthin." + "The row of jucntional complexes between the plasma membranes of rod segments and the Muller glia cells; this barrier separates the layer of inner and outer segments of the rods and cones from the outer nuclear layer and forms a blood-retina barrier[MP]." "XAO:0003224 MA:0001309 ZFA:0001331 NCIT:C33235 Wikipedia:External_limiting_membrane FMA:58683 SCTID:280676008 TAO:0001331 UMLS:C1518685 EMAPA:36518" + "Any process that decreases the rate, frequency or extent of the enlargement or overgrowth of all or part of the heart due to an increase in size (not length) of individual cardiac muscle fibers, without cell division." + "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid." "Reactome:R-HSA-211247 Reactome:R-HSA-6785986 Reactome:R-HSA-5685994" + "A dura mater that is part of a hindbrain [Automatically generated definition]." "VHOG:0000409 EMAPA:17785 MA:0000989" + "An internal carotid artery that branching_part_of a left common carotid artery plus branches." "SCTID:161452006 EMAPA:16329 FMA:4062" + "The olfactory organ of vertebrates, consisting of nares, olfactory epithelia and the structures and skeletal framework of the nasal cavity." "EV:0100037 UMLS:C0028429 MIAA:0000139 Wikipedia:Nose EHDAA:1502 FMA:46472 ZFA:0000047 CALOHA:TS-2037 TAO:0000047 BTO:0000840 EHDAA2:0001274 EV:0100370 MESH:D009666 SCTID:181195007 MA:0000281 NCIT:C12756 galen:Nose GAID:77 EMAPA:16542 MAT:0000139" + "A C-type lectin domain family 6 member A that is encoded in the genome of human." "Reactome:R-HSA-1472857 UniProtKB:Q6EIG7" + "The directed movement of RNA, ribonucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "Any process that activates or increases the rate or extent of epithelial cell proliferation." + "The chemical reactions and pathways involving any of the compounds secreted by the thyroid gland, largely thyroxine and triiodothyronine." + "Binding to catecholamine." + "The regionalization process that regulates the coordinated growth that establishes the non-random spatial arrangement of the neural tube." + "One of a series of paired bulges that develop along the lateral walls of the foregut. The pharyngeal arches have developmental contributions from endoderm, mesoderm, and neural crest cells and are separated by anterior lateral endoderm out-pockets known as pharyngeal pouches." "EHDAA:571 UMLS:C0080322 FMA:293015 ZFA:0001306 SCTID:308766004 TAO:0001306 NCIT:C34249 MAT:0000242 BTO:0001785 EFO:0000959 GAID:1292 XAO:0000096 EMAPA:16117 Wikipedia:Pharyngeal_arch MESH:D001934 VHOG:0000155 MIAA:0000242 AAO:0010359" + "The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the frontonasal region of the head." "FMA:295821 EHDAA2:0004109 EMAPA:16683" + "Any exocrine gland whose cells bud their secretions off through the plasma membrane producing membrane-bound vesicles in the lumen; the apical portion of the secretory cell of the gland pinches off and enters the lumen; it loses part of its cytoplasm in their secretions; apocrine secretion is functional during hormonal stress or puberty; an example of true apocrine glands are mammary glands, responsible for secreting breast milk." "BTO:0001162 EMAPA:35141 Wikipedia:Apocrine SCTID:361698000 MA:0003040" + "Any process that activates or increases the frequency, rate or extent of estradiol secretion." + "The directed movement of pigment granules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "Any process that activates or increases the rate or extent of progression through the mitotic cell cycle." + "A remnant structure from earlier development or evolution." "Wikipedia:Vestigiality" + "A basket cell which has simpler dendritic arbors (compared to small or large basket cells), and an axonal plexus of intermediate density, composed of a few long, smooth axonal branches." + "The region of the cytosol consisting of all cytosol that is part of the presynapse." + "Any of the immature forms of a basophil, in which basophilic specific granules are present but other phenotypic features of the mature form may be lacking." + "A protein that is a translation product of the human FOXN1 gene or a 1:1 ortholog thereof." "IUPHARobj:2958" + "A cell of the outer of the three germ layers of the embryo." "FMA:72549" + "Any process that activates or increases the frequency, rate or extent of female gonad development." + "The directed movement of ATP, adenosine triphosphate, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + + "A T cell that is located in a vermiform appendix." + "A serous membrane that lines the peritoneal cavity[VHOG,modified]." "AAO:0010814 XAO:0000139 NCIT:C12770 MA:0000449 ZFA:0005120 UMLS:C0031153 galen:Peritoneum GAID:18 EV:0100087 TAO:0005120 BTO:0001472 VHOG:0001257 FMA:9584 CALOHA:TS-2072 Wikipedia:Peritoneum MESH:D010537" + "Any of the immature forms of an eosinophil, in which eosinophilic specific granules are present but other phenotypic features of the mature form may be lacking." + "An Ly-6-like protein that is a translation product of the mouse Ly6a gene or a 1:1 ortholog thereof." + "A somatic stem cell that is part of the epidermis." "FMA:70541" + "A nuclear complex which in mammals consists of four parts, the hypothalamus, epithalamus, ventral thalamus, and dorsal thalamus[WP,modified]." "FMA:258745 EHDAA2:0004469" + "A pericyte of the decidual vasculature." + "An epithelial cell that is part of an endometrial gland." "EFO:0010710" + "Skeletogenic cell that secretes dentine matrix, is derived from odontogenic papilla. Embedded in dentine tissue, and is the transformation of a non-terminally differentiated odontoblast cell." + "The process in which a relatively unspecialized cell acquires the specialized features of the R8 photoreceptor." + "One of sublaminar layers S4 or S5." "CP:0000120" + "Any fibroblast that is derived from the neural crest." + + "A disulfide-bonded, heterotetrameric receptor complex. The alpha chains are entirely extracellular, while each beta chain has one transmembrane domain. The ligand binds to the alpha subunit extracellular domain and the kinase is associated with the beta subunit intracellular domain." + "A mature sexual reproductive cell of the female germline." + + "The directed movement of a vesicle along a microtubule, mediated by motor proteins. This process begins with the attachment of a vesicle to a microtubule, and ends when the vesicle reaches its final destination." + "A pericardium that is part of a outflow tract [Automatically generated definition]." "EMAPA:37707 MA:0000491" + "BTO:0001033" + "The orifice that connects the mouth to the exterior of the body." "FMA:59806" + "The process in which the anatomical structures of a mesonephric proximal tubule are generated and organized. The mesonephric proximal tubule extends from the capsule to the distal tubule." + "A cell of the outer layer of a blastula that gives rise to the ectoderm after gastrulation." + "The process in which a precursor cell type acquires the specialized features of a pro-B cell. Pro-B cells are the earliest stage of the B cell lineage and undergo heavy chain D and J gene rearrangements, although they are not fully committed." + "Any process that modulates the frequency, rate or extent of the inflammatory response to wounding." + "Any process that modulates the rate, frequency or extent of the chemical reactions and pathways involving acetylcholine, the acetic acid ester of the organic base choline. Acetylcholine is a major neurotransmitter and neuromodulator both in the central and peripheral nervous systems. It also acts as a paracrine signal in various non-neural tissues." + "Cell-cell signaling between presynapse and postsynapse, via the release and reception of lipid molecules, that modulates the synaptic transmission properties of the synapse." + "The directed movement of nucleobases, nucleosides, nucleotides and nucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "The process in which the anatomical structures of coronary arteries are generated and organized. Coronary arteries are blood vessels that transport blood to the heart muscle." + "A metastasis-suppressor KiSS-1 that is encoded in the genome of mouse." "UniProtKB:Q6Y4S4" + "A gland that is part of a nasopharynx." "SCTID:178973008 FMA:55076" + "Any process that activates or increases the frequency, rate or extent of exocytosis." + "The sternoclavicular articulation is a double arthrodial joint composed of two portions separated by an articular disc. The parts entering into its formation are the sternal end of the clavicle, the upper and lateral part of the manubrium sterni, and the cartilage of the first rib, visible from the outside as the suprasternal notch. The articular surface of the clavicle is much larger than that of the sternum, and is invested with a layer of cartilage, which is considerably thicker than that on the latter bone. The ligaments of this joint are: Articular capsule Anterior sternoclavicular ligament Posterior sternoclavicular ligament Interclavicular ligament Costoclavicular ligament Articular disk [WP,unvetted]." "GAID:270 EMAPA:19203 FMA:25883 SCTID:182165002 NCIT:C33615 MA:0001507 UMLS:C0038291 Wikipedia:Sternoclavicular_articulation MESH:D013247" + "Any process that activates or increases the frequency, rate or extent of execution phase of apoptosis." + "Any process that activates or increases the frequency, rate or extent of pancreatic A cell differentiation." + "Any blood vessel endothelial cell that is part of a microvascular endothelium." + "Any process that decreases the rate frequency or extent of a phase of elevated metabolic activity, during which oxygen consumption increases; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals." + "A neural crest that has_potential_to_developmentally_contribute_to a midbrain." "EHDAA:360 ZFA:0000935 EHDAA2:0001101 EFO:0003591 TAO:0000935 VHOG:0000796" + "The synthesis or release of serotonin following a stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels." + "The innermost layer of the mesenchymal capsule that surrounds the developing brain, primarily of neural crest origin. The endomeninx forms the leptomeninx." + "A goblet cell that is part of the epithelium of pyloric gland." "FMA:263061" + "Any process that activates or increases the frequency, rate or extent of compound eye retinal cell apoptotic process." + "The process whose specific outcome is the progression of the mushroom body over time, from its formation to the mature structure. The mushroom body is composed of the prominent neuropil structures of the insect central brain, thought to be crucial for olfactory associated learning. These consist mainly of a bulbous calyx and tightly packaged arrays of thin parallel fibers of the Kenyon cells." + "A protein that is a translation product of the human PVALB gene or a 1:1 ortholog thereof." + "A supramolecular complex that consists of collagen triple helices associated to form a network." + "Any process that activates or increases the frequency, rate or extent of natural killer cell differentiation as part of an immune response." + "A portion of connective tissue that is part of a knee [Automatically generated definition]." "EMAPA:37326 MA:0000667" + "An entire span of an organism's life. In metazoans, commences with the zygote stage and ends with the death of the organism." "ncithesaurus:Life MmusDv:0000001 HsapDv:0000001 OGES:000011 FBdv:00000000" + "Mucus-secreting glands in the mucosa of the uterine cervix." "UMLS:C2724437 SCTID:280836000 NCIT:C32296" + "A large, granular, liver specific natural killer cell that adheres to the endothelial cells of the hepatic sinusoid." + "Any process that modulates the frequency, rate or extent of the regulated release of dopamine." + "Subdivision of skeletal system that consists of all ribs in an organism connected to the sternum and the vertebrae. Some vertebrates have abdominal ribs (gastrialia), not connected to the vertebrate - these are not considered part of the rib case." "galen:RibCage Wikipedia:Human_rib_cage SCTID:361741004 Wikipedia:Rib_cage FMA:7480" + "Any blood vessel endothelial cell that is part of a microvascular endothelium." + "Any process that modulates the frequency, rate or extent of midbrain dopaminergic neuron differentiation." + "A neuron whose cell body is within an autonomic ganglion." "FMA:80121" + + "FMA:83105" + "A skeletal muscle myoblast that differentiates into fast muscle fibers." + "Any process that activates or increases the frequency, rate or extent of apoptotic cell clearance." + "The subdivision of the laminated olfactory cortex with only three main layers that receive monosynaptic input from the olfactory bulb via the lateral olfactory tract; it is located bilaterally in the ventrolateral forebrain and is commonly divided into anterior and posterior regions." "EMAPA:32767 BAMS:Pir UMLS:C0228280 Wikipedia:Piriform_cortex MA:0000978 MESH:D066195 EV:0100178 SCTID:369098004 neuronames:165 HBA:10142 DHBA:10311 BIRNLEX:1097 BAMS:PIR BTO:0002651" + "The series of events required for an organism to receive a touch stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process. The perception of touch in animals is mediated by mechanoreceptors in the skin and mucous membranes and is the sense by which contact with objects gives evidence as to certain of their qualities. Different types of touch can be perceived (for example, light, coarse, pressure and tickling) and the stimulus may be external or internal (e.g. the feeling of a full stomach)." "Wikipedia:Touch" + "Fibers, composed of actin, myosin, and associated proteins, found in cells of smooth or striated muscle." + "Any process that activates or increases the frequency, rate or extent of glucocorticoid receptor signaling pathway." + "A tunica intima that is part of a artery." "FMA:14272 EMAPA:36293 EV:0100028 SCTID:40022005 galen:IntimaOfArtery" + "Membrane organ which is attached to the pericardial sac proper and the central tendon of diaphragm and is continuous with the pretracheal fascia.[FMA]." "SCTID:243953008 Wikipedia:Fibrous_pericardium MA:0002738 EMAPA:19029 FMA:9586" + + "A sperm bearing a Y chromosome. Chromosomal and genetic sex is established at fertilization in mammals and depends upon whether an X-bearing sperm or a Y-bearing sperm fertilizes the X-bearing ovum." "FMA:84058" + "A branch of the superior mesenteric artery that supplies the jejunum." "SCTID:265391008 FMA:14808 Wikipedia:Jejunal_arteries" + "Any basket cell that is part of a neocortex." + "Any process that modulates the frequency, rate or extent of mesenchymal stem cell migration." + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of juvenile hormone." + "The portion of the ureteric bud that contributes to the morphogenesis of the ureter. The ureter ureteric bud is the initial structure that forms the ureter[GO]." + "Cordlike masses of epithelial tissue that invaginate from germinal epithelium of the gonad and give rise to seminiferous tubules and rete testes in the male, and primary ovarian follicles and rete ovarii in the female." "NCIT:C34183 SCTID:343823004 UMLS:C1512242 Wikipedia:Sex_cords RETIRED_EHDAA2:0001523" + "Binding to collagen, a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%)." + "The short first aortic arch branch and divides into the right subclavian artery and the right common carotid artery." "GAID:476 galen:BrachioCephalicArtery SCTID:244244002 NCIT:C32814 FMA:3932 EHDAA2:0000835 Wikipedia:Brachiocephalic_artery MA:0001922 UMLS:C0006094 MESH:D016122 EMAPA:17615 EFO:0002550" + "A cell that originates in the neural crest, that has certain cytochemical and ultrastructural characteristics and is found scattered throughout the body; types include melanocytes, the cells of the chromaffin system, and cells in the hypothalamus, hypophysis, thyroid, parathyroids, lungs, gastrointestinal tract, and pancreas. This cell type concentrates the amino acid precursors of certain amines and decarboxylate them, forming amines that function as regulators and neurotransmitters. This cell type produces substances such as epinephrine, norepinephrine, dopamine, serotonin, enkephalin, somatostatin, neurotensin, and substance P, the actions of which may affect contiguous cells, nearby groups of cells, or distant cells, thus functioning as local or systemic hormones. The name is an acronym for amine precursor uptake and decarboxylation cell." "MESH:D001078 FMA:83114 BTO:0003866" + "A portion of smooth muscle tissue that is part of a prostate gland [Automatically generated definition]." "EMAPA:35713 MA:0001741 BTO:0003159 FMA:74245" + "A protein that is a translation product of the human CEBPE gene or a 1:1 ortholog thereof." + + "A monostratified retinal ganglion cell that has a large soma, a medium dendritic field with post synaptic terminals in sublaminar layer S3." + "Any process that modulates the frequency, rate or extent of keratinocyte differentiation." + "The generation of a mature peptide hormone by posttranslational processing of a prohormone." + "An arterial blood vessel that is part of a respiratory system [Automatically generated definition]." "MA:0001800 EMAPA:37565" + "The multiplication or reproduction of fibroblast cells, resulting in the expansion of the fibroblast population." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of luteinizing hormone." + "Tunica media of artery which is continuous with the myocardium of right ventricle.[FMA]." "FMA:85030" + "Any brush cell that is part of the intestinal epithelium." + "Translation that occurs at the synapse." + "Combining with glutamate and transmitting a signal from one side of the membrane to the other by activating an associated G-protein, initiating a change in cell activity." + "A renal vein that drains the left kidney." "MA:0002211 FMA:14336 UMLS:C0508001 SCTID:116356005 NCIT:C52693 EMAPA:37166" + "Any process that activates or increases the frequency, rate or extent of isotype switching to IgE isotypes." + "The process whose specific outcome is the progression of an atrioventricular (AV) node cell over time, from its formation to the mature state." + "The process in which a relatively unspecialized cell acquires specialized features of a posterior lateral line neuromast mantle cell. (N.B. This may be development of neuromast mantle cell type or a set of cells of neuromast mantle cell type. This will involve the change of a cell or set of cells from one cell identity to another). Mantle cells are non-sensory cells that surround the sensory strip, separating the neuromast from the epidermis. Mantle cells secrete the cupula in which the ciliary bundles of all of the hair cells are embedded." + + "A luminal epithelial cell of mammary gland located in acinus of structure." "FMA:74505" + "Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to cell leading edge." + "Muscle tissue that consists primarily of skeletal muscle fibers." "NCIT:C13050 Wikipedia:Skeletal_striated_muscle MA:0002439 EMAPA:32716 SCTID:426215008 FMA:14069 UMLS:C0242692" + "A cellular process that results in the breakdown of a cellular component." + "A lymphatic vessel that is part of a limb/fin." "TAO:0005300 ZFA:0005300" + "An integrin alpha-X that is encoded in the genome of human." "UniProtKB:P20702" + "The synthesis or release of any prostaglandin following a stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels." + "Binding to D- or L-enantiomers of glucose." + "The selective elimination of erythrocytes from the body by autoregulatory mechanisms." + "Any process in which a protein is maintained in a specific location within, or in the membrane of, a cell, and is prevented from moving elsewhere." + "The progression of the mesonephric capsule over time, from its formation to the mature structure. The mesonephric capsule is the tough fibrous layer surrounding the mesonephros, covered in a thick layer of perinephric adipose tissue." + "Granule cell with a soma found in the hippocampus." + "The process in which a relatively unspecialized cell acquires specialized features of a smooth muscle cell of the intestine." + "Any process that activates or increases the frequency, rate or extent of receptor localization to synapse." + "Any process that stops, prevents, or reduces the frequency, rate or extent of thymocyte death by apoptotic process." + "The process in which an antigen-presenting cell expresses a peptide antigen on its cell surface in association with an MHC class I protein complex. Class I here refers to classical class I molecules." + "Any process that activates or increases the frequency, rate or extent of axo-dendritic protein transport." + "Soft tissue that lines the non-cartilaginous surfaces within joints with cavities (synovial joints)." "MESH:D013583 GAID:264 BTO:0001823 VHOG:0001282 FMA:9865 MA:0000114 EV:0100143 EMAPA:37476 EHDAA2_RETIRED:0003181 galen:SynovialMembrane SCTID:361828005 AEO:0000181 EFO:0001393 NCIT:C12473 UMLS:C0039099 Wikipedia:Synovial_membrane" + "The process in which a neuroblast acquires the specialized structural and functional features of a GABAergic neuron." + "Skeletal subdivision of the head including skull (cranium plus mandible), pharyngeal and/or hyoid apparatus." "TAO:0000737 AAO:0010185 AAO:0000971 AAO:0000109 VSAO:0000049 ZFA:0000737 XAO:0003075" + "Any process that modulates the frequency, rate or extent of mitotic chromosome condensation." + "A dorsal thalamus that is in_the_left_side_of a diencephalon." "FMA:258716" + "The biological process whose specific outcome is the progression of a head from an initial condition to its mature state. The head is the anterior-most division of the body." + "The first recognizable structure derived from the heart field." "EMAPA:16106 EHDAA2:0000215 VHOG:0000975" + "Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." + + "A mucosa that is part of a bronchus [Automatically generated definition]." "BTO:0001846 FMA:62652 SCTID:30802009" + "The process whose specific outcome is the progression of the metanephric early distal convoluted tubule over time, from its formation to the mature structure. The metanephric early distal convoluted tubule contains metanephric DCT cells and is vasopressin-insensitive." + "Mesenchyme that is part of a developing hip [Automatically generated definition]." "VHOG:0001029 EMAPA:17492 EHDAA:5157 EHDAA2:0000786 EHDAA:6182" + "Any collection of muscles that is part of a face." "FMA:71288" + "The short descending thin limb is the descending thin limb of a short nephron that has a squamous epithelial morphology[GO]." + "A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component." + "Any apoptotic process in a mast cell, a cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation." + "The migration of a pyramidal neuron precursor from the ventricular zone to the correct layer of the cerebral cortex." + "A vascular associated smooth muscle cell of the brain vasculature." + "An outflow tract that is part of a aorta." "EHDAA2:0001353 EMAPA:17329 MA:0000101 VHOG:0001394" + "VHOG:0001157" + "An iliac endochondral element that is composed primarily of cartilage tissue." "VHOG:0001126 EHDAA2:0000808 EMAPA:18347" + "The process whose specific outcome is the progression of the pronephros over time, from its formation to the mature structure. In mammals, the pronephros is the first of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the pronephros is the fully functional embryonic kidney and is indispensable for larval life." + "A transitional myocyte that is part of the atrioventricular bundle." "FMA:83388" + "Any process that modulates the frequency, rate or extent of cytoplasmic microtubule depolymerization." + "An anatomical space that is enclosed by a cloaca." "ZFA:0000330 TAO:0000330" + + "A process in which a lipoprotein is transported to, or maintained in, a specific location in a membrane." + "A taste bud that is located on the skin of the head." + "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex." + "The division of neuroblasts in the subpallium area of the forebrain. The interneuron precursors that these cells give rise to include GABAergic interneurons and will migrate tangentially." + "The process whose specific outcome is the progression of the superior olivary nucleus over time, from its formation to the mature structure. In mice, the superior olivary nucleus is a small cylindrical mass on the dorsal surface of the lateral part of the trapezoid body of the pons, and it is situated immediately above the inferior olivary nucleus. It receives projections from the cochlear nucleus and thus is involved in the perception of sound." + "The process pertaining to the initial formation of a limb bud from unspecified parts. This process begins with the formation of a local condensation of mesenchyme cells within the prospective limb field, and ends when a limb bud is recognizable." + "ZFA:0005227" + "The process of gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms." + "An immature B cell that is IgM-positive, CD45R-positive, CD43-low, CD25-negative, and CD127-negative. This cell type has also been described as being AA4-positive, IgM-positive, CD19-positive, CD43-low/negative, and HSA-positive." + "Any process that stops, prevents or reduces the frequency, rate or extent of protein maturation." + "The embryonically driven process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin." + "Any process that modulates the frequency, rate or extent of exocytic fusion of neurotransmitter receptor containing vesicles into the postsynaptic membrane." + "A muscle layer that is part of a uterine tube infundibulum." "EMAPA:31264 FMA:18336" + "The process in which a relatively unspecialized cell acquires the specialized features of a retinal cone cell." + + "A fetal liver derived enucleated erythrocyte. This erythrocyte resembles adult erythrocytes in that they are small (3- to 6- times smaller than primitive erythrocytes) and produce adult hemaglobins." + "A non-terminally differentiated cell that originates from the neural crest and differentiates into an iridophore." + "Any process that modulates the levels of hormone within an organism or a tissue. A hormone is any substance formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells in the same organism, upon which it has a specific regulatory action." + "The operation of the mind by which an organism becomes aware of objects of thought or perception; it includes the mental activities associated with thinking, learning, and memory." "Wikipedia:Cognition" + "Any process that activates or increases the frequency, rate or extent of a protein or other molecule binding to a receptor." + "The progression of the reproductive system over time from its formation to the mature structure. The reproductive system consists of the organs that function in reproduction." + "The process in which the anatomical structures of the hypophysis are generated and organized. The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving steroids." + "The part of the digestive system that excludes the hepatobiliary system." "MA:0000323 EMAPA:16246 VHOG:0000412 galen:GastrointestinalTract SCTID:373871007 EHDAA2:0000110 CALOHA:TS-0407 MESH:D041981 FMA:71132 UMLS:C0012240 GAID:294 NCIT:C12378 EHDAA:514 BTO:0000058" + "The biological process whose specific outcome is the progression of a right lung from an initial condition to its mature state. This process begins with the formation of the right lung and ends with the mature structure. The right lung is the lung which is on the right side of the anterior posterior axis looking from a dorsal to ventral aspect." + "The lumen of the epididymis." "SCTID:367722009 FMA:18274" + "The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy)." "Wikipedia:Fertilisation" + "The process in which the branching structure of the mammary gland duct is generated and organized. The mammary gland is a large compound sebaceous gland that in female mammals is modified to secrete milk." + "CALOHA:TS-0949 BTO:0001277" + "The multiplication or reproduction of cells, resulting in the expansion of the dorsal spinal cord cell population." + "A secondary oocyte is an oocyte that has not completed meiosis II." "FMA:18646 BTO:0003094" + "Any process that stops, prevents, or reduces the rate of differentiation of regulatory T cells." + "The process whose specific outcome is the progression of the R7 photoreceptor over time, from its formation to the mature structure. The R7 photoreceptor is the last photoreceptor to develop in the ommatidium." + "Any process that stops, prevents or reduces the frequency, rate or extent of mesoderm formation." + "EHDAA2:0000937" + "The process that gives rise to the lateral mesoderm. This process pertains to the initial formation of the structure from unspecified parts." + "The neuroepithelial sensory receptor in the inferolateral wall of the utricle; hair cells of the neuroepithelium support the statoconial membrane and have terminal arborizations of vestibular nerve fibers around their bodies; normally sensitive to linear acceleration in the longitudinal axis of the body and to gravitational influences." "NCIT:C33046 FMA:74960 EMAPA:35535 EFO:0003474 Wikipedia:Macula_of_utricle SCTID:362568003 UMLS:C0229451 TAO:0000030 MA:0001203 ZFA:0000030" + "Mesenchyme that is part of a footplate." "EMAPA:17488 EHDAA:5149 EHDAA:6172 VHOG_RETIRED:0001055 EMAPA:17252 EHDAA2:0000549" + "The chemical reactions and pathways resulting in the breakdown of C21-steroid hormones, steroid compounds containing 21 carbons which function as hormones." + "The tissues that invest or help to invest and support the teeth, including the periodontal ligament, gingivae, cementum, and alveolar and supporting bone[BTO]." "Wikipedia:Periodontium MESH:D010519 UMLS:C0031093 NCIT:C33304 BTO:0001021 GAID:216 CALOHA:TS-2380" + "A zone of skin that is part of a toe [Automatically generated definition]." "FMA:37852 NCIT:C52719 EMAPA:32942 UMLS:C1708089 MA:0000650 SCTID:181530005" + "A sphincter that is part of an esophagus." "SCTID:277765007" + "The regulated release of an androgen into the circulatory system. Androgens are steroid hormones that stimulate or control the development and maintenance of masculine characteristics in vertebrates." + "The process in which precursor cell type acquires the specialized features of a hematopoietic progenitor cell, a class of cell types including myeloid progenitor cells and lymphoid progenitor cells." + "A submucosa that is part of a pyloric antrum [Automatically generated definition]." "FMA:17060" + "EHDAA2:0001721" + "A Martinotti cell morphology that inheres in neurons which have axons that form a horizontal ramification, making it T-shaped." + "The assembly or remodeling of chromatin composed of DNA complexed with histones, other associated proteins, and sometimes RNA." + "A myeloid suppressor cell that is Gr1-high and CD11c-negative." + "An epithelial cell present in the trachea and bronchi; columnar in shape; generally lack cilia; immature forms of ciliated or secretory cells which have been formed from stem cells." "FMA:69060" + "A CD4-positive, CD8-negative thymocyte that is CD24-positive and expresses high levels of the alpha-beta T cell receptor." + "An antigen-presenting glycoprotein CD1d that is encoded in the genome of human." "UniProtKB:P15813 MRO:0000891" + "The membrane that surrounds the acrosomal lumen. The acrosome is a special type of lysosome in the head of a spermatozoon that contains acid hydrolases and is concerned with the breakdown of the outer membrane of the ovum during fertilization." + "An endoderm that is part of a pharyngeal arch 3." "RETIRED_EHDAA2:0000080 VHOG:0001081 EMAPA:16585 EMAPA:16401 EMAPA:16587 EHDAA2:0000075" + "A zone of skin that is part of a axilla." "FMA:37322 MA:0003087 NCIT:C116164 EMAPA:37349" + "Any process that modulates the frequency, rate or extent of attachment of a cell to another cell." + "An anatomical cavity that is part of the olfactory apparatus. This includes the space bounded anteriorly by the nares and posteriorly by the choanae, when these structures are present." "BTO:0002096 VHOG:0000271 MESH:D009296 ZFA:0000130 Wikipedia:Nasal_cavity EMAPA:17604 GAID:350 FMA:54378 EHDAA2:0001226 NCIT:C12424 MA:0000284 AAO:0000314 SCTID:263481003 EHDAA:6801 TAO:0000130 UMLS:C0027423" + "An epithelium that is part of a duodenum." "SCTID:66036002 CALOHA:TS-2087 EMAPA:19078 FMA:17231 MA:0003208" + "The process in which the cardiac ventricle is generated and organized. A cardiac ventricle receives blood from a cardiac atrium and pumps it out of the heart." + "The process whose specific outcome is the progression of an epithelium over time, from its formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure." + "An integrin alpha-E that is encoded in the genome of mouse." "UniProtKB:Q60677" + "Any process that activates or increases the frequency, rate, or extent of leukocyte migration." + "A motor neuron that passes from the spinal cord toward or to a muscle and conducts an impulse that causes movement." + + "An oxytocin receptor that is encoded in the genome of mouse." "UniProtKB:P97926" + "FMA:54364 SCTID:432899004" + "A(n) neuroendocrine cell that is part of a(n) epithelium of crypt of Lieberkuhn." + "An CD24-positive CD38-negative IgG-negative memory B cell is a CD38-negative IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype CD24-positive, CD38-negative, and IgG-negative." + "A neuron of the ventral spinal cord." + "The process whose specific outcome is the progression of the metanephric macula densa over time, from its formation to the mature structure. The metanephric macula densa is an area of specialized cells in the distal tubule of the metanephros that makes contact with the vascular pole of the glomerulus." + "Any process that stops, prevents or reduces the frequency, rate or extent of mesenchymal cell apoptotic process involved in metanephros development." + "Renal process involved in the maintenance of an internal steady state of water in the body." + "Any process that activates or increases the frequency, rate or extent of myeloid progenitor cell differentiation." + "An ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 that is encoded in the genome of mouse." "UniProtKB:P56528" + "Any process that modulates the frequency, rate, or extent of T cell antigen processing and presentation." + "The process in which bones are generated and organized as a result of the conversion of initial cartilaginous anlage into bone." + "The process in which a relatively unspecialized cell acquires specialized features of a mesenchymal cell of the lung. A mesenchymal cell is a loosely associated cell that is part of the connective tissue in an organism. Mesenchymal cells give rise to more mature connective tissue cell types." + "Any process that activates or increases the rate or extent of cell proliferation." + "Any process that stops, prevents or reduces the frequency, rate or extent of lipid transport across blood-brain barrier." + "The pigmented middle of the three concentric layers that make up an eye, consisting of the iris, ciliary body and choroid[WP,edited]." "UMLS:C0042160 MESH:D014602 SCTID:280648000 EMAPA:35901 NCIT:C12811 FMA:58103 CALOHA:TS-2228 Wikipedia:Uvea MA:0002480 GAID:912" + "A cartilaginous condensation that has the potential to develop into a tarsal bone." "EHDAA2:0001977" + "Any process that stops, prevents, or reduces the frequency, rate, or extent of an adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains. An example of this process is found in the Gnathostomata." + "The appearance of type I interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families." + "The embryonic precursor of the brain." "EHDAA:830 BTO:0004726 BAMS:Enc FMA:312967 RETIRED_EHDAA2:0000591 EMAPA:16089 EHDAA:300 ZFA:0000146 EFO:0003431 TAO:0000146" + "The change in morphology and behavior of a gamma-delta T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific, leading to the initiation or perpetuation of an immune response." + "An anatomical cavity that surrounded_by a stomodeum." + "A transitional myocyte that is part of the posterior division of left branch of atrioventricular bundle." "FMA:263178" + "The tough fibrous layer surrounding the kidney which is covered in a thick layer of perirenal adipose tissue that functions to provide some protection from trauma and damage." "galen:CapsuleOfKidney SCTID:243657006 UMLS:C0227637 NCIT:C12885 FMA:66610 MA:0000370 EMAPA:18679 Wikipedia:Kidney_capsule" + "The process in which a relatively unspecialized T cell acquires specialized features of a mature T follicular helper cell." + "A T-cell surface glycoprotein CD8 beta chain that is encoded in the genome of mouse." "UniProtKB:P10300" + "The process in which any suture between facial bones is generated and organized." + "The mucous lining of the larynx, which is composed of squamous epithelium in the upper larynx and ciliated columnar epithelium in the lower larynx." "UMLS:C0023053 GAID:301 FMA:59662 MESH:D007820 MA:0001766 EMAPA:18334 SCTID:361940006 NCIT:C49246" + "A peptide hormone secreting cell that produces adrenocorticotropin, or corticotropin." + "A tube running from the outer ear to the middle ear. The human ear canal extends from the pinna to the eardrum and is about 26 mm in length and 7 mm in diameter." "galen:ExternalAuditoryMeatus VHOG:0000977 MA:0000260 EV:0100356 Wikipedia:External_acoustic_meatus SCTID:181178004 GAID:864 FMA:61734 EMAPA:17588 EHDAA:8975 MESH:D004424 NCIT:C12498 UMLS:C0013444 EHDAA2:0000460" + + "Skeletal element that forms around the notochord and is part of the vertebral column." "VSAO:0000184 VHOG:0001143" + "An organ cavity that is part of a uterus." "Wikipedia:Uterine_cavity EMAPA:36273 FMA:17745" + "A multilayered tube composed of terminally differentiated hair follicle keratinocytes that is surrounded by the outer root sheath; the layers of the inner root sheath include the companion layer, Henle's layer, Huxley's layer and the inner root sheath cuticle[MP]." "EMAPA:32792 MA:0000779 FMA:70935 BTO:0003971" + "Any process that modulates the frequency, rate or extent of calcium ion transmembrane transport." + "A portion of connective tissue that is part of an abdomen [Automatically generated definition]." "MA:0000519" + "The process in which a neuroblast acquires specialized structural and/or functional features of a Cajal-Retzius cell, one of a transient population of pioneering neurons in the cerebral cortex. These cells are slender bipolar cells of the developing marginal zone. One feature of these cells in mammals is that they express the Reelin gene." + "Any process that decreases the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury." + "Any process that modulates the frequency, rate or extent of photoreceptor cell differentiation. An example of this process is found in Drosophila melanogaster." + "The process in which a relatively unspecialized cell acquires the specialized features of a compound eye pigment cell, a cell of the retina containing screening pigments that functions to screen photoreceptors from light leaking from adjacent ommatidia." + "Dorsal part of the midbrain, consisting of the superior and inferior colliculi and the pretectal nuclei (MM)." "DHBA:12291 BIRNLEX:1032 FMA:83902 BAMS:MTec UMLS:C0039433 TAO:0001353 Wikipedia:Midbrain_tectum SCTID:362394008 MA:0000211 MAT:0000451 neuronames:465 EMAPA:19051 VHOG:0001388 NCIT:C12460 BAMS:Tec EHDAA2:0004474 BM:MB-Tec EFO:0000920 HBA:9101 BTO:0001793" + "Enables the transfer of a substance, usually a specific substance or a group of related substances, from one side of a membrane to the other." "Reactome:R-HSA-5671707 Reactome:R-HSA-5638209 Reactome:R-HSA-6784436 Reactome:R-HSA-429036 Reactome:R-HSA-1236947 Reactome:R-HSA-6784434" + "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition." + "A sex gland that is part of a female reproductive system." "BTO:0000254 MA:0000383" + "Any process that activates or increases the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures." + "A protein that is a translation product of the mouse Klra4 gene or a 1:1 ortholog thereof." + "The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis." + "A specialized cell involved in gustatory sensory perception." "FMA:67910" + "A proximal epiphysis that is part of a phalanx of manus [Automatically generated definition]." "FMA:226482 SCTID:272704004" + "The region extending out from the boundary between sublaminar layers S3 and S4." "CP:0001039" + "An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating hormones[GO]." "SCTID:181277001 EHDAA2:0001367 EFO:0000855 MAT:0000075 ZFA:0000140 XAO:0000136 GAID:334 EMAPA:17503 VHOG:0000050 EHDAA:6893 MESH:D010179 BTO:0000988 CALOHA:TS-0736 FMA:7198 TAO:0000140 Wikipedia:Pancreas NCIT:C12393 EV:0100092 MA:0000120 AAO:0010112 MIAA:0000075 galen:Pancreas UMLS:C0030274" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving lipids." + "A muscle layer that is part of a wall of esophagus." "FMA:62998" + "An epithelium that is part of a extraembryonic structure." + "A portion of the external acoustic meatus epithelium which makes up the outer (cuticular) layer of the tympanic membrane." "SCTID:39725007 FMA:56819" + "A horn-like keratin structure covering the dorsal aspect of the terminal phalanges of fingers and toes[WP]." "MIAA:0000158 MESH:D009262 EV:0100159 FMA:54326 EMAPA:35580 MA:0002703 galen:Nail VHOG:0001361 UMLS:C0027342 MAT:0000158 EFO:0000956 GAID:1320 CALOHA:TS-2034 Wikipedia:Nail_(anatomy) SCTID:72651009 BTO:0001719 NCIT:C33156" + "A fibroblast growth factor 8 that is encoded in the genome of mouse." "UniProtKB:P37237" + "GC_ID:1" + "GC_ID:1" + "The process in which immunoglobulin heavy chain V, D, and J gene segments are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS)." + "A metaphysis that is part of a femur." "FMA:32875 MA:0003052 EMAPA:37540" + "The process in which the anatomical structures of blood vessels are generated and organized. The blood vessel is the vasculature carrying blood." + "Any process that activates or increases the frequency, rate or extent of gamma-aminobutyric acid catabolic process." + "A circular muscle layer of muscular coat that is part of a vermiform appendix smooth muscle." + "A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. This process occurs in the ureter. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. The ureter is one of a pair of thick-walled tubes that transports urine from the kidney pelvis to the urinary bladder." + "A conventional thymic dendritic cell that is CD8alpha-negative." + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of CD4." + "A tissue-resident macrophage resident found in the thymus, involved in the clearance of apoptotic thymocytes." + "A CD44 molecule that is encoded in the genome of mouse." "UniProtKB:P15379" + "The process in which anatomical structures of the right lung are generated and organized." + "Any process that modulates the frequency, rate or extent of the regulated release of epinephrine." + "OBSOLETE: Adipocytes found in the subcutaneous adipose tissue of breast. The breast consists of three main components, the skin, the subcutaneous adipose tissue and the functional glandular tissue that comprises both parenchyma and stroma." + "Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in an atrial cardiac muscle cell contributing to the regulation of its contraction. This typically occurs via modulation of the activity or expression of voltage-gated ion channels." + "The developmental process pertaining to the initial formation of the conus arteriosus from unspecified parts. The conus arteriosus is a valved chamber with thick muscular walls stemming from the ventricle and connecting to the pulmonary trunk." + "Any process that stops, prevents, or reduces the frequency, rate or extent of glutamatergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter glutamate." + "An apical ectodermal ridge that is part of a pelvic appendage bud." "VHOG:0001066 ZFA:0001385 EMAPA:16892 EHDAA2:0003194 EFO:0003681 TAO:0001385" + "A lactotransferrin that is encoded in the genome of mouse." "UniProtKB:P08071" + "Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment." + "Any process that stops, prevents, or reduces the frequency, rate or extent of protein complex disassembly, the disaggregation of a protein complex into its constituent components." + "A maturing ovarian follicle that has two more more layers of granulosa cells, up to the onset of antrum formation." "EMAPA:35632 MA:0002908 FMA:18637" + "A renal intercalated cell that is part of the renal connecting tubule." + "The cervical ganglia are paravertebral ganglia of the sympathetic nervous system. These emerging postganglionic nerves synapse with preganglionic nerves from the thoracic spinal cord. They consist of three paravertebral ganglia: superior cervical ganglion middle cervical ganglion inferior cervical ganglion. The inferior ganglion may be fused with the first thoracic ganglion to form a single structure, the stellate ganglion. Nerves emerging from cervical sympathetic ganglia contribute to the cardiac plexus, among other things." "Wikipedia:Cervical_ganglia SCTID:280533000 FMA:6261" + "A stroma that is part of a liver." "FMA:17553" + "A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains." "Wikipedia:T_cell_receptor" + "An anatomical cavity that surrounded_by a Rathke's pouch." "EMAPA:25037 EHDAA2:0004138" + "The regulated release of proteins by a platelet or group of platelets." + "Tolerance induction taking place in the nasopharyngeal-associated lymphoid tissue (NALT)." + "A pre-cartilage condensation that has the potential to develop into a hindlimb bone." "EMAPA:32638" + "A pigment cell is a cell that contains pigment granules." "VHOG:0001678" + "The process whose specific outcome is the progression of the R8 photoreceptor over time, from its formation to the mature structure. The R8 photoreceptor is the founding receptor of each ommatidium." + "The conic expansion of the corpus spongiosum that forms the head of the penis." "GAID:0000012 EMAPA:18988 SCTID:263378009 EV:0100108 UMLS:C0227948 Wikipedia:Glans_penis FMA:18247 BTO:0003118 NCIT:C12324 MA:0002726 VHOG:0001475" + "The process in which a relatively unspecialized endothelial cell acquires specialized features of a venous endothelial cell, a thin flattened cell that lines the inside surfaces of veins." + "The specification of the anterior/posterior axis of the embryo by products of genes expressed in the zygote; exemplified in insects by the gap genes, pair rule genes and segment polarity gene cascade." + "The process whose specific outcome is the progression of the skin over time, from its formation to the mature structure. The skin is the external membranous integument of an animal. In vertebrates the skin generally consists of two layers, an outer nonsensitive and nonvascular epidermis (cuticle or skarfskin) composed of cells which are constantly growing and multiplying in the deeper, and being thrown off in the superficial layers, as well as an inner vascular dermis (cutis, corium or true skin) composed mostly of connective tissue." + "Glial cell that provides support to the enteric nervous system. It is involved in enteric neurotransmission, in maintaining the integrity of the mucosal barrier of the gut and serves as a link between the nervous and immune systems of the gut. In enteric nerve strands, glial processes ensheath multiaxonal bundles which distinguishes enteric glia from all other peripheral glia. Ultrastructurally, the most conspicuous trait of an enteroglial cell is the presence of 10 nm filaments, which criss-cross the cell body, form axial bundles in the processes and appear to firmly anchor the cells to the ganglionic surfaces. Similar to astrocytes, their main constituent is glial fibrillary acidic protein (GFAP)." + "The chemical reactions and pathways resulting in the breakdown of proteoglycans, any glycoprotein in which the carbohydrate units are glycosaminoglycans." + "The process in which the anatomical structure of the olfactory nerve is generated and organized. The olfactory nerve is a collection of sensory nerve rootlets that extend down from the olfactory bulb to the olfactory mucosa of the upper parts of the nasal cavity. This nerve conducts odor information to the brainstem." + "The process in which a relatively unspecialized cell acquires the specialized features of an endoderm cell, a cell of the inner of the three germ layers of the embryo." + "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the mesenchymal cells of the kidney as it progresses from its formation to the mature state." + "Any process involved in the carrying out of an immune response by a T cell." + "The process whose specific outcome is the progression of the eye over time, from its formation to the mature structure. The eye is the organ of sight." "Wikipedia:Eye_development" + "A protein that is a translation product of the human TAL1 gene or a 1:1 ortholog thereof." + "The process in which a branch forms along the side of a ureteric bud." + "The developmental process pertaining to the initial formation of the ureteric bud from the Wolffian duct. This process begins when the bud protrudes from the duct and ends when it is a recognizable bud." + "The process whose specific outcome is the progression of the fourth ventricle over time, from its formation to the mature structure. The fourth ventricle is an irregularly shaped cavity in the rhombencephalon, between the medulla oblongata, the pons, and the isthmus in front, and the cerebellum behind. It is continuous with the central canal of the cord below and with the cerebral aqueduct above, and through its lateral and median apertures it communicates with the subarachnoid space." + "The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA]." "EHDAA:3514 XAO:0000015 VHOG:0000070 BTO:0000672 MESH:D012249 BIRNLEX:942 FMA:67687 ZFA:0000029 UMLS:C1522180 CALOHA:TS-0457 Wikipedia:Rhombencephalon MBA:1065 MA:0000195 UMLS:C0035507 MIAA:0000107 EHDAA:6487 TAO:0000029 SCTID:303456008 EMAPA:16916 EFO:0000923 DMBA:16808 AAO:0010150 BAMS:HB NCIT:C40336 MAT:0000107 EHDAA2:0000746 neuronames:540 DHBA:10653" + "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 5." + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a ketone, carried out by individual cells." + "Any process that activates or increases the frequency, rate or extent of the process involved in the formation, arrangement of constituent parts, or disassembly of cell projections." + "An M7 retinal ganglion cells with synaptic terminals in S2 and is depolarized by decreased illumination of their receptive field center" + "An epithelial cell that is part of the intermediate tubule." "FMA:70980" + "A goblet cell that is part of the epithelium of bronchus." "FMA:263032" + "Any process that modulates the force with which blood travels through the circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure." "Wikipedia:Blood_pressure#Regulation" + "The progression of muscle tissue over time, from its initial formation to its mature state. Muscle tissue is a contractile tissue made up of actin and myosin fibers." + "A lymphocyte that resides in the lamina propria of the small intestine. Lamina propria leukocytes and intraepithelial lymphocytes are the effector compartments of the gut mucosal immune system. Lymphocytes circulate through gut associated lymphoid tissues until recruitment by intestinal antigens. They are involved in the gut immune response." + "Mesentery that is located in the peritoneum." "TAO:0005129 XAO:0000138 FMA:20570 ZFA:0005129" + "The process in which the anatomical structures of muscle tissue are generated and organized. Muscle tissue consists of a set of cells that are part of an organ and carry out a contractive function." + "A developmental process, independent of morphogenetic (shape) change, that is required for a trigeminal ganglion to attain its fully functional state." + "A protein that is a translation product of the human SLAMF1 gene or a 1:1 ortholog thereof." + "A cell type found on the superficial layer of the external side of the tympanic membrane. This cell-type lacks a nucleus." + "A portion of smooth muscle tissue that is part of a large intestine [Automatically generated definition]." "EMAPA:35469 MA:0001547" + "A fibroblast that is located in the renal cortical interstitium." + "A protein that has channel activity. Channel proteins enable energy-independent facilitated diffusion, mediated by passage of a solute through a transmembrane aqueous pore or channel." + "Anatomical cluster that is located in the anterior region of the cranium and provides structural support for the olfactory organ." "NCIT:C98765 TAO:0000351 ZFA:0000351 XAO:0003172 AAO:0010206 EFO:0003525" + + "Any process that activates or increases the frequency, rate or extent of mechanoreceptor differentiation." + "The Ileocolic Artery is the lowest branch arising from the concavity of the superior mesenteric artery. It passes downward and to the right behind the peritoneum toward the right iliac fossa, where it divides into a superior and an inferior branch; the inferior anastomoses with the end of the superior mesenteric artery, the superior with the right colic artery. Supplies the cecum, ileum, and appendix. [WP,unvetted]." "FMA:14815 MA:0001970 SCTID:244279000 galen:IleocolicArtery Wikipedia:Ileocolic_artery NCIT:C32760 UMLS:C0226323 EMAPA:37083" + "Subdivision of skeletal system that consists of all ribs and rib joints in an organism. In many vertebrates this consists of the combination of the rib cage and all rib joints, but some vertebrates have ribs outside the thoracic rib cage." "TAO:0002100 FMA:265719" + "Any process that activates or increases the rate or extent of glial cell proliferation." + "A cell that secretes motilin, a gastric hormone that at low pH inhibits gastric motor activity, whereas at high pH has a stimulating effect." + "A CD8alpha alpha positive gamma-delta intraepithelial T cell that does not express a TCR partially encoded by the Vgamma5 gene segment." + "Any process that stops, prevents, or reduces the frequency, rate or extent of animal organ morphogenesis." + "Any process that stops, prevents, or reduces the frequency, rate or extent of collagen binding." + "Any process that stops, prevents, or reduces the frequency, rate or extent of R7cell differentiation." + "The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes." "Wikipedia:Cytosol NIF_Subcellular:sao101633890" + "The pattern specification process that results in the subdivision of an axis or axes in space to define an area or volume in which specific patterns of cell differentiation will take place or in which cells interpret a specific environment." + "The directed movement of substances from the cytosol into the Golgi apparatus of a cell." + "An intestinal crypt stem cell that is located in the anorectum." + "Any process that activates or increases the frequency, rate or extent of Schwann cell chemotaxis." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of corticotropic hormone from a cell." + "Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types." "CARO:0000024 XAO:0003041 AEO:0000024 ZFA:0000496 VHOG:0001723 TAO:0000496 TADS:0000598 EHDAA2:0003024 AAO:0010015 BILA:0000024 TGMA:0001837 HAO:0000024" + "A mucosa that is part of a pylorus [Automatically generated definition]." "EMAPA:27199 FMA:17461 BTO:0004110" + "The layer of the developing cerebral cortex that is formed from the first cohort of neurons to migrate out of the cortical ventricular zone; split by the second wave into marginal zone and subplate." "EMAPA:35261" + "Any process that stops, prevents, or reduces the frequency, rate, or extent of peptide secretion." + "Any process that activates or increases the frequency, rate or extent of glutamatergic neuron differentiation." + "External genital organs of the female mammal[WP]." "EV:0100118 VHOG:0001458 EFO:0000978 GAID:383 Wikipedia:Vulva EMAPA:36631 SCTID:265796001 MAT:0000169 CALOHA:TS-1168 galen:Vulva FMA:20462 MIAA:0000169 BTO:0003101 MESH:D014844 MA:0000395 NCIT:C12408 UMLS:C0042993" + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cytokine stimulus." + "Any process that modulates the frequency, rate or extent of the regulated release of growth hormone from a cell." + "Deepest of 3 cytoarchitecturally defined layers of the piriform cortex characterized by a moderately high density of pyramidal cells and large numbers of basal dendrites descending from pyramidal cells in layer 2." "NLXANAT:091009" + "Mesenchyme that is part of a pelvic appendage bud." "EMAPA:16781 TAO:0001386 ZFA:0001386 EHDAA2:0001035" + "Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in morphogenesis." + "Any process that stops, prevents or reduces the frequency, rate or extent of glycoprotein metabolic process." + "The directed movement of melanosomes into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "The left lobe is smaller and more flattened than the right. It is situated in the epigastric and left hypochondriac regions. Its upper surface is slightly convex and is moulded on to the diaphragm; its under surface presents the gastric impression and omental tuberosity. [WP,unvetted]." "FMA:13363 UMLS:C0227486 VHOG:0001423 SCTID:362183003 ZFA:0005172 NCIT:C32965 Wikipedia:Left_lobe_of_liver EHDAA2:0001000 EMAPA:18307 TAO:0005172 EHDAA:3995 MA:0000361" + "MIAA:0000019 CALOHA:TS-2122 FMA:292313 EHDAA2:0003125 AEO:0000125" + "Anatomical structure embedded in or located in the integument that is part of the integumental system. Examples: hair, follicles, skin glands, claws, nails, feathers." "EMAPA:37883 Wikipedia:Skin_appendage" + "The chemical reactions and pathways involving a phenol, any compound containing one or more hydroxyl groups directly attached to an aromatic carbon ring." "UM-BBD_pathwayID:phe" + "The tiny hair-like projections that protrude from the inside of the small intestine that contain blood vessels that capture digested nutrients that are absorbed through the intestinal wall; the villi increase the absorptive surface area of the small intestine by approximately 30-fold." "TAO:0005125 Wikipedia:Intestinal_villus MA:0001563 BTO:0003121 UMLS:C1519988 NCIT:C33874 ZFA:0005125 SCTID:23230007 EMAPA:35784 FMA:15072" + "Any process that modulates the frequency, rate, or extent of natural killer cell degranulation." + "A P/D1 enteroendocrine cell that is Grimelius positive and stores bombesin-like polypeptide." + "Any process that modulates the levels of body fluids." + "A secretion that is part of a pancreas [Automatically generated definition]." "NCIT:C13270 MA:0002516 UMLS:C0030296" + "Triangular calcified papillae (often five) placed radially around the anus of some Holothuriidae." + "Any process that modulates the frequency, rate or extent of DNA catabolic process." + "The process whose specific outcome is the progression of a neuron that resides in the forebrain, from its initial commitment to its fate, to the fully functional differentiated cell." + "Any collection of muscles that is part of an appendage." "TAO:0000207 ZFA:0000207" + "An immunoglobulin gamma Fc receptor I that is a translation product of the human FCGR1A gene or a 1:1 ortholog thereof." + "An ovarian follicle that has one layer of granulosa cells." "EMAPA:35631 BTO:0000410 MA:0002907 SCTID:258665002 FMA:18634" + "A serous membrane that is part of a wall of intestine [Automatically generated definition]." "EMAPA:37619 MA:0001538 FMA:15701" + "The process in which genetic material, in the form of nuclear chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. Nuclear chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles." + "A sonic hedgehog protein that has been processed by proteolytic cleavage." + "A C-C chemokine receptor type 3 that is encoded in the genome of mouse." "UniProtKB:P51678" + "The right lung lobar bronchus mesenchyme is a type of tissue made up of loosely-packed mesenchymal cells in the right lung lobar bronchus." "EMAPA:17665" + "A natural killer cell that is developmentally mature and expresses a variety of inhibitory and activating receptors that recognize MHC class I and other stress related molecules." + + + "A mucus secreting cell of a submucosal gland of the tracheobronchial tree." + "A white matter of spinal cord that is part of a thoracic spinal cord." "SCTID:367881009 BIRNLEX:999 UMLS:C1288557 UMLS:C0228633" + "A process carried out by the organs or tissues of the respiratory system. The respiratory system is an organ system responsible for respiratory gaseous exchange." + "A transverse process of vertebra that is part of a vertebral bone 1." "Wikipedia:Transverse_processes SCTID:181895009 FMA:23981" + "An intestinal crypt that is located in the jejunum." "EMAPA:37840 FMA:269065" + "Any process that activates or increases the rate or extent of cell adhesion to another cell." + "Any collection of muscles that is part of a lower leg or upper leg [Automatically generated definition]." "EHDAA2:0000973" + "A nonskeletal ligament that is part of a liver." "FMA:15820 NCIT:C32997 UMLS:C0230238 SCTID:48536008" + "A unilaminar epithelium that develops_from a ectoderm and is part of a anal region." "EMAPA:25040 EHDAA2:0004019" + "The binding by a cell-adhesion protein on the cell surface to an extracellular matrix component, to mediate adhesion of the cell to another cell." + "A protein that is a translation product of the human PLAUR gene or a 1:1 ortholog thereof." "PIRSF:PIRSF002022" + "A subdivision of a the reproductive tract in a female organism that is the site of embryo development." "WBbt:0006760 TADS:0000421" + "A physical quality inhering in a bearer by virtue of the bearer's disposition to recover its size and shape after deformation in any way." + "The chamber in the eyeball enclosing the vitreous humor, bounded anteriorly by the lens and ciliary body and posteriorly by the posterior wall of the eyeball[BTO,modified]." "FMA:58848 Wikipedia:Vitreous_chamber MA:0002461 BTO:0002087 NCIT:C33885 UMLS:C0229095 EMAPA:37805" + "A protein that is a translation product of the human TBX21 gene or a 1:1 ortholog thereof." + "Any process that modulates the frequency, rate, or extent of interleukin-13 production." + "Any process that activates, maintains or increases the frequency, rate or extent of sporulation, the process whose specific outcome is the progression of a spore over time, from its initiation to the mature structure." + "A keratocyte is a specialized fibroblast residing in the cornea stroma that has a flattened, dendritic morphology; located between the lamellae with a large flattened nucleus, and lengthy processes which communicate with neighboring cells. This corneal layer, representing about 85-90% of corneal thickness, is built up from highly regular collagenous lamellae and extracellular matrix components. Keratocytes play the major role in keeping it transparent, healing its wounds, and synthesizing its components. This cell type secretes collagen I, V, VI, and keratan sulfate." + "A composite substructure of the brainstem that consists of the midbrain reticular formation, the pontine reticular formation and the medullary reticular formation ( Carpenter-1983 )." "EMAPA:35188 neuronames:1223 FMA:77719 Wikipedia:Reticular_formation MESH:D012154 SCTID:361552007 MA:0003185 BAMS:RET NLX:143558" + "Any process that stops, prevents or reduces the frequency, rate or extent of atrial cardiac muscle cell action potential." + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amine stimulus. An amine is a compound formally derived from ammonia by replacing one, two or three hydrogen atoms by hydrocarbyl groups." + + "Anatomical system that consists of all blood and lymph vessels." "NCIT:C33854 UMLS:C0489903 BTO:0001085 MA:0002718 CALOHA:TS-2053 EHDAA2:0004520 EMAPA:35905" + "The process whose specific outcome is the progression of the hindgut over time, from its formation to the mature structure. The hindgut is part of the alimentary canal that lies posterior to the midgut." + "The orderly movement of a Schwann cell from one site to another. A Schwann cell is a glial cell that ensheathes axons of neuron in the peripheral nervous system and is necessary for their maintainance and function." + "CD4-positive, alpha-beta T cell that produces IL-22." + "A blood vessel that is part of a heart [Automatically generated definition]." "EMAPA:35397 MA:0002483" + "Skeletogenic cell that has the potential to develop into a chondroblast; and arises from neural crest, meseosdermal and notochordal and connective tissue cells." + "The collection of muscles that form attachments to the shoulder skeleton." "FMA:50220" + "Obsolete. Consult Plant Ontology instead. OBSOLETED, not defined prior to obsoletion." + "An anatomical wall that is part of a large intestine [Automatically generated definition]." "EMAPA:35470 MA:0002695 FMA:14619" + "The internal feminine genital organs, including the ovaries, uterine tubes, uterus, uterine cervix, and vagina." "SCTID:303518005 FMA:45654 BTO:0003099" + "Any process that activates or increases the frequency, rate or extent of T-helper 2 cell differentiation." + "MA:0001593 NCIT:C33258 EMAPA:32777 UMLS:C0226964 BIRNLEX:4102 UMLS:C1289183 FMA:54819 SCTID:368728006" + "An interneuron that has Martinotti morphology. These interneurons are scattered throughout various layers of the cerebral cortex, sending their axons up to the cortical layer I where they form axonal arborization." "NIFEXT:55 ILX:0107375" + "A portion of trabecula carnea cardiac muscle tissue that is part of a right ventricle [Automatically generated definition]." "FMA:84429" + "An anatomical space that surrounded_by a neural tube." "AAO:0011073 EHDAA:914 EMAPA:16167 EHDAA:2889 VHOG:0001119 XAO:0000252 EHDAA2:0001269" + "The process whose specific outcome is the progression of the inner medullary collecting duct over time, from its formation to the mature structure. The inner medullary collecting duct is the portion of the collecting duct that lies in the renal inner medulla." + "CD4-positive, alpha-beta memory T cell with the phenotype CCR7-positive, CD127-positive, CD45RA-negative, CD45RO-positive, and CD25-negative." + "Any collection of muscles that is part of a pectoral complex. The pectoral complex comprises the pectoral girdle and the associated limb or fin." "EMAPA:37861 FMA:71296" + "An immune response against microbes mediated through a body fluid. Examples of this process are seen in the antimicrobial humoral response of Drosophila melanogaster and Mus musculus." + "Anatomical structure that is an individual member of a species and consists of more than one cell." "EHDAA:1 BIRNLEX:18 EHDAA2:0003103 NCIT:C13041 CARO:0000012 TGMA:0001832 BILA:0000012 FMA:256135 EV:0100016 EFO:0002906 SCTID:243928005 WBbt:0007833 Wikipedia:Multi-cellular_organism EMAPA:25765 ZFA:0001094 BTO:0000042 VHOG:0000671 AAO:0010026 ncithesaurus:Whole_Organism TAO:0001094 galen:Organism BSA:0000038 XAO:0003004 TADS:0000001 HAO:0000012 EHDAA2:0003191 AEO:0000191" + "Zone of long bone that is between the epiphysis and diaphysis. Subdivision of diaphysis which forms the proximal or distal end of diaphysis next to the epiphysis; together with diaphysis proper, it constitutes the diaphysis. Examples: proximal metaphysis of humerus, distal metaphysis of femur.[FMA]." "UMLS:C0222671 NCIT:C52723 MA:0001363 EMAPA:35509 Wikipedia:Metaphysis FMA:24014 SCTID:304581004" + "An epithelium that is part of a lens vesicle." "VHOG:0000532 EMAPA:17165 EHDAA2:0000987" + "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances."@en + "A bushy cell that receives a large number of medium-sized synapses, called modified endbulbs. Globular bushy cells extend to the superior olive on both sides of the brainstem where they give input to the bipolar neurons." + "Immature dermal dendritic cell is a dermal dendritic cell that is CD80-low, CD86-low, and MHCII-low." + "A CD48 molecule that is encoded in the genome of mouse." "UniProtKB:P18181" + "A non-striated, elongated, spindle-shaped cell found lining the digestive tract, uterus, and blood vessels. They develop from specialized myoblasts (smooth muscle myoblast)." "BTO:0004576 FMA:14072 CALOHA:TS-2159" + "Any process that activates or increases the frequency, rate or extent of microtubule polymerization or depolymerization." + "A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas." "CALOHA:TS-2012 Wikipedia:Exocrine_gland MA:0002564 EMAPA:35327 NCIT:C12712 FMA:9596 MESH:D005088 UMLS:C0015282 EHDAA2:0003097 BTO:0000765 GAID:34 SCTID:115976003 AEO:0000097" + "The portion of the yolk sac that is derived from mesoderm and consists of mesenchyme." "EMAPA:16087 EMAPA:16267 EHDAA:168 EHDAA:205 VHOG:0000617 VHOG:0000503 EHDAA2:0002216" + "A macrophage that suppresses immune responses." + "Any process that activates or increases the frequency, rate or extent of memory T cell differentiation." + "The process in which a relatively unspecialized monocyte acquires the specialized features of a macrophage." + "An endothelium that is part of a vena cava [Automatically generated definition]." "MA:0000713 EMAPA:37800 UMLS:C1710623 NCIT:C49318" + "Formation of the amnioserosa, an epithelium that occupies a hole in the embryonic dorsal epidermis. This occurs by the transformation of a narrow strip of cells at the dorsal midline of the blastoderm from columnar to squamous cells, accompanied by a lateral shift." + "A sebaceous gland that is part of a vagina [Automatically generated definition]." "MA:0001732 EMAPA:37793" + "Generation of cells within the nervous system." "Wikipedia:Neurogenesis" + "Any process that stops, prevents or reduces the frequency, rate or extent of a signaling receptor activity." + "The outflow tract septum is a partition in the outflow tract." "XAO:0004141" + + "Organ with organ cavity, which has as parts a serous membrane and a serous cavity . Examples: pleural sac, pericardial sac, tendon sheath, bursa.[FMA]." "SCTID:362890006 FMA:9689" + "The process in which the anatomical structures of the mesonephric renal vesicle are generated and organized. The renal vesicle is the primordial structure of the mesonephric nephron epithelium, and is formed by the condensation of mesenchymal cells." + "The vertical crest of the interior wall of the right atrium that lies to the right of the sinus of the vena cava and separates this from the remainder of the right atrium." "FMA:9236 Wikipedia:Crista_terminalis EMAPA:37837 SCTID:277693004" + "The chemical reactions and pathways resulting in the breakdown of compounds that contain an indole (2,3-benzopyrrole) skeleton." + "A ciliated cell that is part of a ciliated duct of an airway submucosal gland." + "The process in which a relatively unspecialized cell acquires specialized features of an inner cell mass cell." + "Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a vacuole." + "An organ of the digestive tract that is capable of retaining and storing food." "TADS:0000172 BSA:0000123 TGMA:0001041" + "The inner stripe is a deep, centrally located portion of the renal outer medulla and is traversed by thick and thin portions of nephron tubules." "EMAPA:29675 FMA:76663 MA:0002626" + "A specialized, fibroblastic reticular cell of mesenchymal origin found in lymph nodes. In human, it expresses several markers common to myofibroblasts (desmin, vimentin, CD73, CD90, α-smooth muscle actin (αSMA)), and can be differentiated from endothelial cells by its lack of CD31 expression. These cells are critical for the overall organization and function of the lymph node. Lymph node fibroblastic reticular cells (FRCs) can be further classified based on their location, function, and unique marker expression." + "Any process that stops, prevents, or reduces the frequency, rate or extent of cell activation." + "A protein that is a stand alone version of the Glycosyltransferase family 10 (fucosyltransferase) (Pfam:PF00852) domain. Proteins in this class may catalyze alpha-1,3 glycosidic linkages." "PIRSF:PIRSF005726" + "A goblet cell that is part of the small intestine." "FMA:86929" + "FMA:14652" + + "Any process that stops, prevents or reduces the frequency, rate or extent of pro-B cell differentiation." + + "A nuclear receptor ROR-gamma isoform 2 that is encoded in the genome of mouse." "UniProtKB:P51450-2" + "Any process that modulates the frequency, rate or extent of epithelial cell differentiation involved in kidney development." + "A NK1.1-positive T cell that is CD94-negative." + "The process in which the mesonephric comma-shaped body is generated and organized. The mesonephric comma-shaped body is the precursor structure to the mesonephric S-shaped body that contributes to the morphogenesis of a nephron in the mesonephros." + "The regulated release of somatostatin from secretory granules in the D cells of the pancreas." + "A systemic artery that supplies the lung with with oxygenated blood." "Wikipedia:Bronchial_artery SCTID:244247009 GAID:477 EMAPA:18608 FMA:68109 NCIT:C32230 MA:0001923 MESH:D001981 UMLS:C0006257" + "A submucosa that is part of a neck of urinary bladder [Automatically generated definition]." "FMA:17851 EMAPA:32276" + "A smooth muscle of the internal thoracic artery." + "A DRD2-expressing medium spiny neuron that is part of a nucleus accumbens shell or olfactory tubercle." + "A skeletal joint that is part of a manus (hand) [Automatically generated definition]." "SCTID:244546004 EMAPA:32641 Wikipedia:Joints_of_hand MA:0000452" + "The process in which the anatomical structures of the eye are generated and organized during embryonic development." + "An epithelium that is part of a larynx [Automatically generated definition]." "MA:0001765 NCIT:C49247 EMAPA:35472 EHDAA2:0004065 UMLS:C0751258" + "Any process that activates or increases the frequency, rate or extent of renal water transport." + "A lactosylceramide 4-alpha-galactosyltransferase that is encoded in the genome of mouse." "UniProtKB:Q67BJ4" + "Any process that stops, prevents or reduces the frequency, rate or extent of macrophage migration." + "Any process that modulates the rate, frequency, or extent of branching morphogenesis in the salivary gland epithelium." + + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucocorticoid stimulus. Glucocorticoids are hormonal C21 corticosteroids synthesized from cholesterol with the ability to bind with the cortisol receptor and trigger similar effects. Glucocorticoids act primarily on carbohydrate and protein metabolism, and have anti-inflammatory effects." + "Any keratinocyte that is part of a hair follicle." + "A serous sac that has the pleura and the pleural cavity as parts." "SCTID:361996004 FMA:9690 EHDAA2:0004737" + "A T-cell-specific surface glycoprotein CD28 that is encoded in the genome of mouse." "UniProtKB:P31041" + "Any process that modulates the frequency, rate, or extent of myeloid leukocyte mediated immunity." + "The multiplication or reproduction of mesenchymal cells, resulting in the expansion of a cell population that contributes to the progression of the prostate gland over time." + "A reticulocyte that is Ly76-high and is Kit-negative." + "Any process that stops, prevents, or reduces the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell projections." + "The chemical reactions and pathways involving glutamate, the anion of 2-aminopentanedioic acid." "Wikipedia:Glutamic_acid" + "OBSOLETE: A classification of cells by the organisms within which they are contained." + "A collagen trimer containing alpha(I) chains. The most common form of type I collagen is a heterotrimer containing two alpha1(I) chains and one alpha2(I) chain; homotrimers containing three alpha1(I) chains are also found. Type I collagen triple helices associate to form banded fibrils." "Wikipedia:Collagen_type_I" + "A DRD1-expressing medium spiny neuron that is part of a matrix compartment of dorsal striatum." + "Any process that modulates the rate, frequency, or extent of protein tyrosine kinase activity." + "A segment of the pedal digit containing the distal phalanx. Note this class represents a digit segment and thus includes tissues in addition to bone." + "Skeletal element that consists of the scapula and the coracoid[VSAO, modified]." "Wikipedia:Scapulocoracoid TAO:0001455 AAO:0000781 VSAO:0005002 ZFA:0001455" + "Any process that activates or increases the frequency, rate or extent of stem cell differentiation." + "A flexibility which is relatively low." + "Various sensory and motor branches of the glossopharyngeal nerve supply nerve connections to the pharynx and back of the tongue. The branchial motor component contains motor fibers that innervate muscles that elevate the pharynx and larynx, and the tympanic branch supplies parasympathetic fibers to the otic ganglion." + "Any process that modulates the frequency, rate or extent of collagen binding." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen." + "The directed movement of dense core granules along cytoskeletal fibers, such as microtubules or actin filaments." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of iron ions from one side of a membrane to the other by means of some agent such as a transporter or pore." + "A vein that carries deoxygenated blood from the upper half of the body into the right atrium of the heart." "Wikipedia:Superior_vena_cava MESH:D014683 BTO:0002683 SCTID:181368006 EHDAA:8726 FMA:4720 VHOG:0001195 MA:0000481 EMAPA:18417 GAID:549 NCIT:C12816 EHDAA2:0001962 UMLS:C0042459 galen:SuperiorVenaCava" + "OBSOLETE. A mouse GABAergic cell located in the marmoset cerebral cortex that expresses meis2." + "An artery that is part of a vermiform appendix." + + "A testis that is in the right side of the genitalia [Automatically generated definition]." "NCIT:C49326 UMLS:C0227997 FMA:7211 EMAPA:37371 SCTID:367719007 MA:0001747" + "A CD8-positive, alpha-beta T cell that has the phenotype CXCR3-negative, CCR6-negative." + "Any process that modulates the frequency, rate or extent of hepatocyte differentiation." + "KUPO:0001080" + "A receptor-type tyrosine-protein phosphatase C that is a translation product of a transcript that minimally includes the region encoded by the variable exon 4(A)." + "A concave quality inhering in a bearer by virtue of the bearer's curving inward on both sides or surfaces." + + "The process whose specific outcome is the progression of the urinary bladder over time, from its formation to the mature structure. The urinary bladder is an elastic, muscular sac situated in the anterior part of the pelvic cavity in which urine collects before excretion." + "Any process that activates or increases the frequency, rate or extent of bile acid metabolic process." + "The process in which the labyrinthine layer of the placenta is generated and organized." + "The process whose specific outcome is the progression of smooth muscle in the metanephros over time, from its formation to the mature structure." + "The process whose specific outcome is the progression of the bone marrow over time, from its formation to the mature structure." + "The process whose specific outcome is the progression of the cloaca over time, from it's formation to the mature structure. The cloaca is the common chamber into which intestinal, genital and urinary canals open in vertebrates." + "The juxtaglomerular apparatus lies adjacent to the glomerulus and regulates kidney function by maintaining the blood flow to the kidney and the filtration rate[GO]." + + "Any apoptotic process in a myofibroblast cell." + "A tissue-resident macrophage found in the mucosa associated lymphoid tissue." + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amines." + "The fibrous investing tissue, covered by keratinized epithelium, that immediately surrounds a tooth and is contiguous with its periodontal ligament and with the mucosal tissues of the mouth[Glossary of Periodontal Terms 2001]." "MA:0000342 SCTID:181224006 FMA:59762 galen:Gingiva EFO:0001925 EV:0100064 Wikipedia:Gingiva EMAPA:35945 VHOG:0001269 NCIT:C32677 MESH:D005881 UMLS:C0017562 GAID:1257 CALOHA:TS-2074 BTO:0000519" + "The actin cytoskeleton that is part of a presynapse." + "A splenic white pulp macrophage found in and around the germinal centers of the white pulp of the spleen that participates in phagocytosis of apoptotic B cells from the germinal centers. A marker for a cell of this type is Mertk-positive." + "A (free) limb that is connected to a pectoral girdle. The extent of this structure includes autopod, stylopod and zeugopod regions when present, but excludes the pectoral girdle and its parts." "MA:0000025 galen:UpperExtremity EHDAA:6208 MIAA:0000394 Wikipedia:Forelimb CALOHA:TS-2214 BTO:0001729 EMAPA:17412 SCTID:182245002 EV:0100014 EHDAA2:0002133 UMLS:C1140618 GAID:51 MAT:0000394 VSAO:0000148 GAID:1215 VHOG:0000338 XAO:0003030 NCIT:C12671 AAO:0000205 FMA:24878 EFO:0000882 MESH:D005552" + "Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]." "MA:0002437 AAO:0000306 NCIT:C12435 UMLS:C2328219 SCTID:91727004 EHDAA2:0003122 AEO:0000122 FMA:9641 Wikipedia:Muscle_tissue EMAPA:32715 galen:MuscleTissue CALOHA:TS-0642 MESH:D009132" + "OBSOLETE. A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment)." "CARO:0000013" + "A pia mater that is part of a spinal cord [Automatically generated definition]." "NCIT:C49800 EHDAA2:0001896 UMLS:C1710148 EMAPA:17807 VHOG:0000468 MA:0001133" + "The locus ceruleus is a dense cluster of neurons within the dorsorostral pons. This nucleus is the major location of neurons that release norepinephrine throughout the brain, and is responsible for physiological responses to stress and panic[GO]. Bluish region in the superior angle of the fourth ventricle floor, corresponding to melanin-like pigmented nerve cells which lie lateral to the ponto-mesencephalic central gray (griseum centrale). It is also known as nucleus pigmentosus pontis[GAID]." "BTO:0001408 FMA:72478 BAMS:LC BIRNLEX:905 ZFA:0000539 MBA:147 UMLS:C0023951 MESH:D008125 NCIT:C97333 DMBA:16972 BM:Pons-LC EFO:0001963 EMAPA:35502 HBA:9148 GAID:577 DHBA:12819 MA:0001017 TAO:0000539 BAMS:CAE neuronames:583 Wikipedia:Locus_ceruleus SCTID:369016004" + "An epithelium that is part of a pinna." "EHDAA:8983 VHOG:0000632 EHDAA2:0001470 EMAPA:17592" + "The orderly movement of an endothelial cell into the extracellular matrix to form an endothelium." + "A T cell found in the lymph node medullary sinus." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds." + "A GABAergic cortical interneuron that develops from the caudal ganglionic eminence and has migrated to the cerebral cortex." + "The process in which the wraps of cell membrane that constitute myelin are laid down around an axon in the central or peripheral nervous system." + "A specialized osteoclast associated with the absorption and removal of cementum." "FMA:83027 BTO:0002516" + "A amacrine cell with a small dendritic field and post-synaptic terminals in S1, S2, S3, and S4. AB diffuse-1 amacrine cells have a tent-shaped dendritic arbor and undulate dendrites." + "A memory B cell is a mature B cell that is long-lived, readily activated upon re-encounter of its antigenic determinant, and has been selected for expression of higher affinity immunoglobulin. This cell type has the phenotype CD19-positive, CD20-positive, MHC Class II-positive, and CD138-negative." + "A neural arch that is part of a cervical vertebra." "FMA:23893 SCTID:165269004" + "The His-Purkinje system receives signals from the AV node and is composed of the fibers that regulate cardiac muscle contraction in the ventricles." + "The basic functional unit of the kidney. its chief function is to regulate the concentration of water and soluble substances like sodium salts by filtering the blood, reabsorbing what is needed and excreting the rest as urine. A nephron eliminates wastes from the body, regulates blood volume and blood pressure, controls levels of electrolytes and metabolites, and regulates blood pH. Its functions are vital to life and are regulated by the endocrine system by hormones such as antidiuretic hormone, aldosterone, and parathyroid hormone.[WP]." "NCIT:C13048 MA:0000375 CALOHA:TS-1312 FMA:17640 EV:0100384 BTO:0000924 EMAPA:35592 Wikipedia:Nephron MESH:D009399 EMAPA:28491 SCTID:361337001 ZFA:0005282 UMLS:C0027713 GAID:428 TAO:0002153" + + "The chemical reactions and pathways involving any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom." + "The expansion of a neuroblast population by cell division. A neuroblast is any cell that will divide and give rise to a neuron." + "Any process that activates or increases the frequency, rate or extent of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse." + "A chemokine receptor that is a translation product of the human CCR4 gene or a 1:1 ortholog thereof. The preferred ligands include CCL17 and CCL22." "IUPHARobj:61" + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of hormones." + "A cell in the zona reticularis that produce sex hormones." "FMA:69564" + "The process whose specific outcome is the progression of an epithelium in the mesonephros over time, from its formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure." + "KUPO:0001079" + "The process in which the anatomical structures of a tissue are generated and organized." + "The process in which a relatively unspecialized cell acquires specialized features of a columnar/cuboidal epithelial cell of the intestine." + "The process in which spores form outside a specialized end cell known as a basidium. Basidia are characteristic of the basidiomycete fungi (phylum Basidiomycota), and give rise to spores that each contain a haploid nucleus that is the product of meiosis. The spores are usually attached to the basidium by short spikes called sterigmata (singular: sterigma). In most basidiomycetes there are four sterigmata (and four spores) to a basidium." + "The chemical reactions and pathways resulting in the breakdown of any hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone." + "Subdivision of an organism along anterior-posterior axis that is the posteriormost region, extending past the anus (or cloaca, if present), consisting of a tail in some fully formed chordates (or a tail bud in embryos). In animals that have a sacral region, this is the region immediately posterior to this." "XAO:0000087" + "A vein that is part of a tail [Automatically generated definition]." "Wikipedia:Tail_vein MA:0002233 XAO:0000393 EMAPA:37761 AAO:0011105" + "Any biological process involved in the maintenance of an internal steady state of ammonium." + + "Any process that modulates the frequency, rate or extent of supramolecular fiber organization." + + "The process in which the anatomical structures of the adenohypophysis are generated and organized. The adenohypophysis is the anterior part of the pituitary. It secretes a variety of hormones and its function is regulated by the hypothalamus." + "Lower, narrow portion of the uterus where it joins with the top end of the vagina." "BTO:0002249 MESH:D002584 SCTID:181453009 MAT:0000292 galen:CervixUteri EFO:0000979 BTO:0001421 FMA:17740 EMAPA:29927 Wikipedia:Cervix EV:0100114 VHOG:0001359 GAID:376 CALOHA:TS-0134 MA:0000392 UMLS:C0007874 NCIT:C12311" + "The zygomaticotemporal nerve or zygomaticotemporal branch (temporal branch) is derived from the maxillary branch of the trigeminal nerve (Cranial nerve V). It runs along the lateral wall of the orbit in a groove in the zygomatic bone, receives a branch of communication from the lacrimal, and passes through zygomaticotemporal foramen in the zygomatic bone to enter the temporal fossa. It ascends between the bone, and substance of the Temporalis muscle, pierces the temporal fascia about 2.5 cm. above the zygomatic arch, and is distributed to the skin of the side of the forehead, and communicates with the facial nerve and with the auriculotemporal branch of the mandibular nerve. As it pierces the temporal fascia, it gives off a slender twig, which runs between the two layers of the fascia to the lateral angle of the orbit." "FMA:52972 Wikipedia:Zygomaticotemporal_nerve SCTID:280243001" + "The aggregation, arrangement and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex." + "The directed killing of a target cell by a natural killer cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors." + "A mesothelial fibroblast of the arachnoid barrier layer. Arachnoid barrier cells make up the tight-junctioned layer in the leptomeninx that functions as the physiologic barrier between the cerebrospinal fluid in the subarachnoid space and the fenestrated capillaries in the dura." + "A blastoconidium that has only one nucleus." "FAO:0000030" + "KUPO:0001076" + "The portion of the yolk sac that is derived from endoderm and lines the yolk sac." "VHOG:0000626 EMAPA:16086 EHDAA2:0002215 EHDAA:166" + "An organ cavity that is part of a urethra." "SCTID:279432008 FMA:19709" + "A portion of cardiac muscle tissue that is part of a cardiac septum [Automatically generated definition]." "FMA:226279" + "A phagocyte from organisms in the Nematoda or Protostomia clades." + "One of a pair of arteries that is a branch of the abdominal aorta that supplies blood to a male gonad." "Wikipedia:Testicular_artery SCTID:244281003 MA:0002063 EMAPA:18621 FMA:14758" + "Skeletogenic cell that produces enamel, overlies the odontogenic papilla, and arises from the differentiation of a preameloblast cell." "FMA:70576 BTO:0001663" + "A medium-wave-sensitive opsin (human) that is a translation product of the OPN1MW2 gene in human." "UniProtKB:P0DN77" + "A long-wave-sensitive opsin 1 that is encoded in the genome of human." "UniProtKB:P04000 Reactome:R-HSA-419769 DTO:02100475" + "The process in which carboxylic acid is transported across a membrane." + "The glomerular epithelium is an epithelial tissue that covers the outer surfaces of the glomerulus. The glomerular epithelium consists of both parietal and visceral epithelium. Metanephric glomerular parietal epithelial cells are specialized epithelial cells that form tight junctions as a barrier to protein transport. A metanephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the metanephros." "MA:0002847 EMAPA:35458 BTO:0001515" + "Any process that modulates the frequency, rate or extent of natural killer T cell proliferation." + "The process in which the muscular septum is generated and organized. The muscular septum is the lower part of the ventricular septum." + "A functional anatomical construct containing the key estrogen-regulated inputs to gonadotropin-releasing hormone expressing (GnRH) neurons necessary for estrogen positive feedback. The rostral periventricular region of the third ventricle contains a population of neurons, scattered through the nuclei of the anteroventral periventricular (AVPV), periventricular preoptic (PVpo), and median preoptic (MEPO), that project directly to GnRH neurons and express ER-alpha." + "Endoderm-lined chamber that develops as pouch-like dilation of the caudal end of the hindgut and receives the allantois ventrally and two mesonephric ducts laterally; caudally it ends blindly at the cloacal membrane formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm[MP]." "EHDAA2:0000256 EMAPA:27573 Wikipedia:Cloaca_(embryology) EHDAA:4895" + "A zone of skin that is part of a pelvis [Automatically generated definition]." "MA:0000546 EMAPA:37282 FMA:22984 SCTID:181517009" + "A peptide hormone secreting cell that secretes substance P." + "A myoepithelial cell that is part of the intralobular part of terminal lactiferous duct." "FMA:62158" + "A tall supporting cell that is arranged in rows adjacent to the last row of outer phalangeal cells. This cell type constitutes the outer border of the organ of Corti." "FMA:79799" + "A subarachnoid space that is part of a diencephalon [Automatically generated definition]." "VHOG:0001302 EMAPA:19053" + "A lactocyte that highly expresses genes associated with transcription, immune cell function, and cellular stress. A lactocyte type 1 also expresses genes involved in milk component biosynthesis (e.g., LALBA and CSNs), albeit at lower levels than a lactocyte type 2." + "An elongating cell that rapidly obliterates the lumen of the lens vesicle. Subsequently, differentiation of this cell type at the lens equator leads to the formation of secondary fiber cells that come to overlie the primary fibers." "FMA:70613" + "A developmental process, independent of morphogenetic (shape) change, that is required for the cerebellar Purkinje cell layer to attain its fully functional state. The Purkinje cell layer lies just underneath the molecular layer of the cerebellar cortex. It contains the neuronal cell bodies of the Purkinje cells that are arranged side by side in a single layer. Candelabrum interneurons are vertically oriented between the Purkinje cells. Purkinje neurons are inhibitory and provide the output of the cerebellar cortex through axons that project into the white matter. Extensive dendritic trees from the Purkinje cells extend upward in a single plane into the molecular layer where they synapse with parallel fibers of granule cells." + "Any process that modulates the frequency, rate or extent of hematopoietic progenitor cell differentiation." + "A perforin-1 that is encoded in the genome of mouse." "UniProtKB:P10820" + "Binding to a class II major histocompatibility complex." + "The process in which a relatively unspecialized mesodermal cell acquires the specialized structural and/or functional features of a cardioblast. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating." + "A mucosa that is part of an anal canal [Automatically generated definition]." "EMAPA:27531 SCTID:362170004 NCIT:C60784 FMA:74654 UMLS:C0227414" + "An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]." "GAID:288 ZFA:0000123 EFO:0000887 MAT:0000097 AAO:0010111 VHOG:0000257 MESH:D008099 EMAPA:16846 BTO:0000759 MIAA:0000097 UMLS:C0023884 XAO:0000133 EHDAA:2197 galen:Liver SCTID:181268008 EHDAA2:0000997 Wikipedia:Liver TAO:0000123 CALOHA:TS-0564 EV:0100089 FMA:7197 NCIT:C12392 MA:0000358" + "Obsolete. Use PO:0000332 from Plant Ontology instead. An epidermal cell with a characteristic convoluted anticlinal cell wall that gives a jigsaw like appearance to the lamina." + "A cubodial epithelial cell that is continuous with the lining of intercalated ducts that drain the acinus. This cell type secretes a high pH solution to aid in activation of zymogens, and can differentiate into endocrine and exocrine pancreatic cell types." "FMA:62455" + "Any process that stops, prevents or reduces the rate or extent of epithelial cell proliferation." + "The change in morphology and behavior of a natural killer cell in response to a cytokine, chemokine, cellular ligand, or soluble factor." + + "A zone of skin that is part of the external genitalia." + "Any process that modulates the occurrence or rate of thymocyte death by apoptotic process." + + "A serous membrane that is part of a duodenum [Automatically generated definition]." "EMAPA:27247 MA:0003212 FMA:14948 SCTID:1236009" + "Lymphoid tissue located in the appendix." "CALOHA:TS-1268" + "The chemical reactions and pathways resulting in the formation of carboxylic acids, any organic acid containing one or more carboxyl (-COOH) groups." + "Any process that increases the rate, frequency or extent of granulocyte chemotaxis. Granulocyte chemotaxis is the movement of a granulocyte in response to an external stimulus." + "A nucleus of brain that is part of a trigeminal nuclear complex." "GAID:604 MESH:D014278 NCIT:C12807 BM:V BTO:0001074 UMLS:C0040999 CALOHA:TS-2077 EMAPA:35883 http://uri.neuinfo.org/nif/nifstd/nifext_11 MA:0001028 EV:0100271 VHOG:0001353 SCTID:280164007 FMA:71247" + "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])"@en + "GC_ID:1" + "Any negative regulation of signal transduction that takes place in extracellular region." + "A bistratfied retinal ganglion cell with a small dendritic field that has dendrites in the ON and OFF sublamina of the retinal inner plexiform layer and carries blue-ON/yellow-OFF signals. This cell receives bipolar and amacrine input to both the OFF and ON dendritic tree." + "A monostratified retinal ganglion cell with medium soma, sparse dendritic tree, and medium dendritic field." "BAMS:1049" + "A nerve that is part of a back [Automatically generated definition]." "MA:0000497 EMAPA:37268" + "An endothelial cell of viscerocranial mucosa that is part of the tympanic region of the viscerocranial mucosa." "FMA:70628" + "An anatomical space that is enclosed by a fundus of stomach." "EMAPA:18382 FMA:17077" + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a microvillus on a follicle cell. A microvillus is a thin cylindrical membrane-covered projection on the surface of an animal cell containing a core bundle of actin filaments." + "Any process that modulates the frequency, rate or extent of attachment of a cell to another cell or to the extracellular matrix and contributes to the shaping of the growth plate cartilage of an endochondral bone." + "Any process that stops, prevents, or reduces the frequency, rate or extent of differentiation of CD4-positive, CD25-positive, alpha-beta regulatory T cells as part of an immune response." + "A fibroblast of the periodontium." + "An epiphysis that is part of a middle phalanx of pes." "SCTID:280048001" + "Dermal dendritic cell is a conventional dendritic cell that is CD11b-positive, CD205-positive and CD8 alpha-negative." "BTO:0004812" + "The process whose specific outcome is the progression of the late distal convoluted tubule over time, from its formation to the mature structure. The late distal convoluted tubule contains DCT cells and intercalated (IC) alpha and beta cells and is vasopressin-sensitive." + "One of 3 small bones contained within the middle ear space and serve to transmit sounds from the air to the fluid-filled labyrinth. The absence of the auditory ossicles would constitute a moderate-to-severe hearing loss. The term 'ossicles' literally means 'tiny bones' and commonly refers to the auditory ossicles, though the term may refer to any small bone throughout the body. [WP,unvetted]." "AAO:0011015 UMLS:C0013450 EHDAA2:0001183 FMA:52750 MA:0000254 XAO:0000214 EHDAA:5697 SCTID:181184001 VHOG:0000461 EV:0100360 NCIT:C32164 Wikipedia:Auditory_ossicle EMAPA:17824" + "Any process that activates or increases the frequency, rate or extent of protein binding." + "Glandular cell of epididymal epithelium." "CALOHA:TS-1276" + + "EHDAA2:0004181 FMA:9464" + "Any process that stops, prevents or reduces the frequency, rate or extent of vascular endothelial cell proliferation." + "Binding to an amine, a weakly basic organic compound that contains an amino or a substituted amino group." + "An endoderm that is part of a pharyngeal arch 4." "EHDAA2:0004033 RETIRED_EHDAA2:0000095 VHOG:0001092 EMAPA:16765 EMAPA:16767 EMAPA:16769" + "A blood vessel that is part of a limb/fin." "TAO:0005299 ZFA:0005299" + "Any process that modulates the rate, frequency, or extent of the regulated release of a peptide hormone from secretory granules." + "The portion of the nasal mucosa that is part of the respiratory system." "FMA:77198" + "A transversely striated, synctial muscle cell, formed by the fusion of myoblasts." "FBbt:00005812" + "Any process that modulates the rate, frequency or extent of the enlargement or overgrowth of all or part of the heart due to an increase in size (not length) of individual cardiac muscle fibers, without cell division." + "Matrix compartment located in the caudate nucleus." "NLXANAT:20090504" + "Blood vessels supplying the stria vascularis in the cochlea of the inner ear." + "The large glutaminergic nerve cells whose dendrites synapse with axons of the olfactory receptor neurons in the glomerular layer of the olfactory bulb, and whose axons pass centrally in the olfactory tract to the olfactory cortex." + "FMA:79793 EHDAA2:0001384" + + "A fibroblast that is part of the skin of scalp." + "An ectodermal placode that will develop into the components of the lateral line system." "AAO:0010718 XAO:0000440" + "A T-cell surface glycoprotein YE1/48 that is encoded in the genome of mouse." "UniProtKB:P20937" + "The process in which a relatively unspecialized cell acquires specialized features of a mesenchymal stem cell. A mesenchymal stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized mesenchymal cells." + "The series of molecular signals initiated by an extracellular ligand binding to a receptor on the surface of the target cell, where the receptor possesses catalytic activity or is closely associated with an enzyme such as a protein kinase, and ending with the regulation of a downstream cellular process, e.g. transcription." + "The internal volume enclosed by the membranes of a particular organelle; includes the volume enclosed by a single organelle membrane, e.g. endoplasmic reticulum lumen, or the volume enclosed by the innermost of the two lipid bilayers of an organelle envelope, e.g. nuclear lumen." + "A smooth muscle cell that is part of the rectum." "FMA:17522" + "The process in which relatively unspecialized cells acquire specialized structural and functional features of a pancreatic epsilon cell. A pancreatic epsilon cell is a cell in the pancreas that secretes ghrelin." + "An inhibitory, GABAergic projection neuron in the striatum that integrates glutamatergic signals arising from the cerebral cortex and thalamus." "BTO:0004778" + "Any process that modulates the frequency, rate or extent of defecation." + "A crystal cell that derives from the embryonic head mesoderm." "FBbt:00001690" + "A G protein-coupled receptor activity occurring in the postsynaptic membrane that is part of a GPCR signaling pathway that positively regulates ion channel activity in the postsynaptic membrane." + "FMA:79794 EHDAA2:0001387" + "Hard bony, calcareous, or chitinous organ found in the mouth or pharynx of an animal and used in procuring or masticating food." "HAO:0001019" + "The establishment of the sex of a female organism by physical differentiation." + "A serous membrane that is part of a gallbladder [Automatically generated definition]." "SCTID:362197006 EMAPA:35372 FMA:14659 MA:0001634" + "Any process that activates or increases the frequency, rate or extent of the directed movement of histamine into a cell." + "Any process that stops, prevents, or reduces the frequency, rate or extent of basidiospore formation, a process in which a sexually produced fungal spore is formed on a basidium in the fungi basidiomycetes." + "Nephric tubules (nephrons) form embryonically along the nephric ridge. The ridge comprises three regions; anterior, middle and posterior. The functional kidney uses nephrons from only one or two regions of the ridge. A pronephric kidney uses only the nephrons from the anterior region of the ridge. A mesonephric kidney uses only the middle region, a metanephric kidney uses only the posterior region and an opisthonephric kidney uses the middle and posterior regions." "VHOG:0001240 EMAPA:16368 EHDAA2:0001242 EHDAA:1015" + "The process whose specific outcome is the progression of the cerebellar cortex over time, from its formation to the mature structure. The cerebellar cortex is a thin mantle of gray matter that covers the surface of each cerebral hemisphere. It has a characteristic morphology with convolutions (gyri) and crevices (sulci) that have specific functions. Six layers of nerve cells and the nerve pathways that connect them comprise the cerebellar cortex. Together, these regions are responsible for the processes of conscious thought, perception, emotion and memory as well as advanced motor function." + "A muscle of back that is part of a dorsal thoracic segment of trunk." "EMAPA:37261 MA:0000508 SCTID:305071003" + "KUPO:0001075" + "The process whose specific outcome is the progression of a pancreatic delta cell over time, from its formation to the mature structure. A delta cell is a cell of the pancreas that produces somatostatin." + "One of the two small elevations on the mucosa of the duodenum, the major at the entrance of the conjoined pancreatic and common bile ducts and the minor at the entrance of the accessory pancreatic duct." "EMAPA:18662 MA:0003107 FMA:15953 NCIT:C119578 SCTID:245389007" + "The whole of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism." "Wikipedia:Digestion" + "The process in which a relatively unspecialized cell acquires the specialized features of a leucophore cell. Leucophores are pigment cells derived from the neural crest. They contain uric acid or other purine crystals, deposited in stacks called leucosomes. This gives them a white appearance." + "Catalytic activity that acts to modify RNA, driven by ATP hydrolysis." + "A CD4-positive, CD25-positive, CCR4-positive, alpha-beta T regulatory cell with the phenotype HLA-DRA-positive, indicating recent activation." + "Obsolete. Use PO:0000351 from Plant Ontology instead. An epidermal cell that divides to produce the guard cells." + "The regulated release of bile acid, composed of any of a group of steroid carboxylic acids occurring in bile, by a cell or a tissue." + "Cartilage tissue primarily composed of type II collagen (thin fibrils) and a glassy appearance." "MA:0000109 VSAO:0000094 FMA:64783 UMLS:C0225362 NCIT:C32746 Wikipedia:Hyaline_cartilage XAO:0004029 SCTID:39298000 EMAPA:35414" + "Binding to a glycan (polysaccharide) containing a substantial proportion of aminomonosaccharide residues." + "An epithelium surrounding an ovary." "BTO:0003661" + "Osteoblast that is terminally differentiated, located adjacent to acellular or cellular bone tissue within periosteum, and is capable of mineralizing the matrix." "VSAO:0000116" + "The chemical reactions and pathways resulting in the formation of aromatic compounds, any substance containing an aromatic carbon ring." + "The liquid component of blood, in which erythrocytes are suspended." "GAID:1178 MIAA:0000052 Wikipedia:Blood_plasma MESH:D010949 EMAPA:35690 CALOHA:TS-0800 FMA:62970 MAT:0000052 NCIT:C13356 UMLS:C0032105 EFO:0001905 BTO:0000131 MA:0002501" + "FMA:79837" + "Any process that stops, prevents or reduces the frequency, rate or extent of glutamate secretion, neurotransmission." + "Any process that modulates the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein." + "A cardiac myocyte of the interatrial region of the heart." "FMA:228790" + "FMA:223208 UMLS:C1512970 NCIT:C12930" + "Any process that activates or increases the frequency, rate, or extent of smooth muscle cell apoptotic process." + "The chemical reactions and pathways resulting in the formation of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another. This may include the translation of a precursor protein and its subsequent processing into a functional peptide." + "The group of sensory neuron cell bodies associated with the vagus nerve." "SCTID:244452001 VHOG:0000684 Wikipedia:Vagus_ganglion ZFA:0007067 FMA:53472 MA:0001081 TAO:0007067 EMAPA:16798" + "A white matter of spinal cord that is part of a cervical spinal cord." "BIRNLEX:1531 UMLS:C0228616 SCTID:174829001" + "The proliferation of cells in the inner cell mass." + "A blood vessel endothelial cell that is part of the retina." + "Region in the ventral telencephalon, prominent in rodents, but present in all mammals, consisting of a laminated cortical part and the cap/hilus region. It is traditionally viewed as part of the olfactory cortex but recognized by some as having a striatal character. According to many authors, the structure of the OT transitions from cortical like to striatal like along the lateral medial axis. (Maryann Martone)." "BAMS:OT VHOG:0001625 EV:0100177 HBA:10145 MESH:D066208 BAMS:DLT BAMS:OLT MBA:754 EHDAA2:0004701 BM:Tel-OLT Wikipedia:Olfactory_tubercle BTO:0001869 NLXANAT:1005037 BAMS:Tu DHBA:10310 PBA:10096 MA:0000976 EMAPA:35616" + "The crystalline particles composed of calcium carbonate and a protein which adhere to the gelatinous membrane of the maculae of the utricle and saccule (otolithic membrane)." "VHOG:0001676 MESH:D012444 GAID:883 TAO:0000559 ZFA:0000559 MA:0002841 EFO:0003539 Wikipedia:Otolith_organ" + "The transverse cervical artery (transverse artery of neck, transversa colli artery) is a branch of the thyrocervical trunk, running at a higher level than the suprascapular artery." "MA:0001936 FMA:10664 SCTID:244224008 Wikipedia:Transverse_cervical_artery" + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a vasopressin stimulus." + "The series of events involved in visual perception in which a light stimulus is received and converted into a molecular signal." + "The regulated release of norepinephrine by a cell. Norepinephrine is a catecholamine and it acts as a hormone and as a neurotransmitter of most of the sympathetic nervous system." + "An epithelial cell of thyroid gland." "FMA:256167 MESH:D000072637" + "The process whose specific outcome is the progression of a glomerular mesangial cell in the kidney over time, from its formation to the mature structure." + "A blood vessel that is part of a cerebellum." + "Any process that stops, prevents, or reduces the frequency, rate or extent of pro-T cell differentiation." + "The epithelial cells lining the capsule and trabeculae of the thymus." "MA:0000769" + "A fascicle that is part of a spinal cord." "FMA:75799" + "The mammary placode is a transient lens shaped structure that will give rise to the mammary bud proper[GO]." "EMAPA:35541" + "The expansion of a NK T cell population by cell division." + "The ejaculatory duct epithelium is composed of cuboidal to columnar cells between or through which project the terminal parts of the ducts of the unicellular prostate glands." "BTO:0002618 EMAPA:29786" + "The process in which the anatomical structures of the nephron are generated and organized. A nephron is the functional unit of the kidney." + "Vascular endothelium found in blood vessels of the blood-brain-barrier." "BTO:0003248 BTO:0001852 CALOHA:TS-0092" + "A nerve that is part of the trunk region of the body (not to be confused with a nerve trunk)." "EMAPA:37264 MA:0000515" + "The middle free limb segment, between the autopod and stylopod segments. Includes as parts the zeugopodial skeleton. Examples: There are two types of zeugopod: forelimb zeugopod (aka forearm), hindlimb zeugopod (aka crus)." "MA:0002716 EFO:0000878 MAT:0000092 FMA:83016 MIAA:0000092" + "Any blood vessel endothelial cell that is part of a dermis." + "Pertaining to the individual parts making up an aggregate fruit like a many-lobed \"berry,\" such as a raspberry." + "A glutamatergic neuron located in the cerebral cortex that projects axons locally rather than distantly." "ILX:0770103" + "The portion of the plasma membrane surrounding a neuron projection." + "A transport vesicle that mediates transport from an intracellular compartment to the plasma membrane, and fuses with the plasma membrane to release various cargo molecules, such as proteins or hormones, by exocytosis." + "A peptide hormone secreting cell that secretes growth hormone releasing hormone." + "A protein that is a translation product of the human MERTK gene or a 1:1 ortholog thereof." "IUPHARobj:1837" + "The process whose specific outcome is the progression of the accessory nerve over time, from its formation to the mature structure. In mice, the spinal branch of this motor nerve innervates the trapezius and the sternocleidomastoid muscles. The cranial branch joins the vagus nerve and innervates the same targets as the vagus nerve." + "A bud is a protrusion that forms from an epithelial sheet by localized folding." "BTO:0001639" + "The chemical reactions and pathways involving aldehydes, any organic compound with the formula R-CH=O, as carried out by individual cells." + "A vasculature that is part of a liver." "EHDAA2:0003454 FMA:73748 EMAPA:35501" + "An increase in size of a blastocyst due to expansion of the blastocoelic cavity cell shape changes and cell proliferation." + "Any process that modulates the frequency, rate, or extent of macrophage tolerance induction." + "A cartilage that is part of a lower respiratory tract [Automatically generated definition]." "MA:0001819 EMAPA:37547 UMLS:C1708759 NCIT:C49256" + "Any process that modulates the rate, frequency, or extent of the chemical reactions and pathways resulting in the formation of a glycoprotein, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide." + "The sensory trigeminal nerve nuclei are the largest of the cranial nerve nuclei, and extend through the whole of the midbrain, pons and medulla. There is also a distinct trigeminal motor nucleus that is medial to the chief sensory nucleus[WP]." "BIRNLEX:4096 DHBA:266441713 neuronames:2021 Wikipedia:Trigeminal_nerve_nuclei HBA:9203 BM:V UMLS:C0040999 FMA:71248 CALOHA:TS-2077" + "The process in which a precursor cell type acquires the specialized features of an alpha-beta intraepithelial T cell. Intraepithelial T cells are found among epithelial cells in mucosal areas and have distinct phenotypes and developmental pathways." + + "The process in which a relatively unspecialized cell acquires specialized features of an noradrenergic neuron, a neuron that secretes noradrenaline." + "The specification and formation of anisotropic intracellular organization that contributes to the self-propelled directed movement of an ameboid cell." + "During the third week there appears, immediately behind the ventral ends of the two halves of the mandibular arch, a rounded swelling named the tuberculum impar, which was described by His as undergoing enlargement to form the buccal part of the tongue. More recent researches, however, show that this part of the tongue is mainly, if not entirely, developed from a pair of lateral swellings (or distal tongue bud) which rise from the inner surface of the mandibular arch and meet in the middle line." "FMA:313628 Wikipedia:Lateral_lingual_swelling EHDAA2:0000911 VHOG:0000731 EMAPA:17189" + "The process in which the branches of the pancreas are generated and organized." + "The posterior segment of the lamellated connective tissue layer of the cornea." "EMAPA:37415" + "A venous system that is part of a hindbrain." "VHOG:0001322 EMAPA:18632 EHDAA2:0000776" + "FMA:5968" + "Any neuron that is part of a central nervous system." + "Mesenchyme that is part of a developing tongue [Automatically generated definition]." "EHDAA2:0004614 EMAPA:17882" + "A high affinity immunoglobulin epsilon receptor subunit alpha that is encoded in the genome of human." "UniProtKB:P12319" + "Any process that modulates the frequency, rate or extent of white fat cell proliferation." + "A synovial joint that is part of a pectoral girdle region." "FMA:35243 SCTID:303080001" + "Any process that modulates the frequency, rate or extent of estradiol secretion." + "A mature NK T cell that secretes interferon-gamma and enhances Th1 immune responses." + "The lipid bilayer surrounding any membrane-bounded vesicle in the cell." "NIF_Subcellular:sao1153182838" + "Binding to a small molecule, any low molecular weight, monomeric, non-encoded molecule." + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic substance stimulus." + "Thickened areas of the saccule or utricle where the termination of the vestibular nerve occurs[MESH,modified]." "ZFA:0000386 GAID:777 MESH:D008267 TAO:0000386" + "An intestinal crypt stem cell that is located in the colon." + "A thymocyte that has the phenotype CD4-negative, CD8-positive, CD44-negative, CD25-negative, and pre-TCR-positive." + "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells." + "A cuboidal epithelial cell of the kidney which secretes acid and reabsorbs base to regulate acid/base balance." + "A tyrosine-protein phosphatase non-receptor type substrate 1 that is encoded in the genome of mouse." "UniProtKB:P97797" + "Any process that increases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites)." + "The chemical reactions and pathways involving mineralocorticoids, hormonal C21 corticosteroids synthesized from cholesterol. Mineralocorticoids act primarily on water and electrolyte balance." + "Kidney pyramids are the conical arrangements of tubules that constitute the renal medulla in a multi-lobed mammalian kidney; they contain the loops of Henle and the medullary collecting ducts." "UMLS:C0227629 NCIT:C12886 MA:0001654 BTO:0003926 FMA:258870 SCTID:361328001 Wikipedia:Renal_pyramids NCIT:C33436 UMLS:C1514613" + "An organ part that is part of a long bone [Automatically generated definition]." "FMA:24008" + "An alveolar macrophage that expresses metallothionein." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-10 production." + "Squamous cell of uterine cervix epithelium." "CALOHA:TS-1251" + + + "A GABAergic interneuron whose soma is located in the cerebral cortex." + "A light sensing organ composed of ommatidia." "HAO:0000217 TGMA:0000024 BTO:0001921 Wikipedia:Compound_eye" + + "Any process that activates or increases the frequency, rate or extent of lymphocyte death by apoptotic process." + "A muscle tissue that is part of a prostate gland." "SCTID:251498008 UMLS:C1183911 NCIT:C13100" + "An intestinal crypt that is located in the appendix." "SCTID:21512007" + "Any process that modulates the frequency, rate or extent of smooth muscle cell differentiation." + "A brush cell of the epithelium in the terminal bronchiole." "FMA:263228" + "The lipid bilayer surrounding the vacuole and separating its contents from the cytoplasm of the cell." + "Any process that activates or increases the frequency, rate or extent of cholangiocyte proliferation." + "A bone element or fused bone that is part of pelvic girdle." "UMLS:C0030786 SCTID:426214007 MA:0000293 NCIT:C33287" + "Any process that modulates the rate, frequency, or extent of a response to cytokine stimulus." + "The directed movement of calcium (Ca) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "A peptide hormone cell that secretes prolactin." + "A quality of a single cell inhering in the bearer by virtue of the bearer's size or shape or structure." + "Medullary portion of thymus. The reticulum is coarser than in the cortex, the lymphoid cells are relatively fewer in number, and there are found peculiar nest-like bodies, the concentric corpuscles of Hassall. These concentric corpuscles are composed of a central mass, consisting of one or more granular cells, and of a capsule formed of epithelioid cells. They are the remains of the epithelial tubes, which grow out from the third branchial pouches of the embryo to form the thymus. Each follicle is surrounded by a vascular plexus, from which vessels pass into the interior, and radiate from the periphery toward the center, forming a second zone just within the margin of the medullary portion. In the center of the medullary portion there are very few vessels, and they are of minute size." "UMLS:C0229949 EFO:0001969 EMAPA:19305 FMA:72206 SCTID:188344009 NCIT:C33775 BTO:0004560 MA:0000771 Wikipedia:Thymus#Medulla" + "The process in which the anatomical structures of the lung are generated and organized." + "Any process that contributes to cytokine production by a plasmacytoid dendritic cell." + "A goblet cell that is part of the epithelium of crypt of lieberkuhn of small intestine." "FMA:263050" + "The process in which the anatomical structures of a tube are generated and organized from an epithelium. Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system." + "Any process that activates or increases the frequency, rate or extent of glutamate metabolic process." + "The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid." + "A monolayer of pigmented epithelium covering the neural retina; develops from the outer of the two layers of the optic cup[ZFA]. the pigmented cell layer just outside the neurosensory retina that nourishes retinal visual cells, and is firmly attached to the underlying choroid and overlying retinal visual cells[WP]." "VHOG:0000536 SCTID:280662007 MA:0003173 FMA:58627 EMAPA:17172 UMLS:C0035322 XAO:0003217 EMAPA:35738 TAO:0000144 ZFA:0000144 AAO:0011096 Wikipedia:Retinal_pigment_epithelium BTO:0001177 EHDAA2:0001465 MA:0000279 NCIT:C33470 CALOHA:TS-0869 EHDAA:4765" + "Any process that stops, prevents, or reduces the frequency, rate, or extent of T cell tolerance induction." + + "The regulated release of epinephrine by a cell. Epinephrine is a catecholamine hormone secreted by the adrenal medulla and a neurotransmitter, released by certain neurons and active in the central nervous system." + "The process whose specific outcome is the progression of the proximal tubule over time, from its formation to the mature structure. In mammals, the proximal tubule is a nephron tubule that connects Bowman's capsule to the descending thin limb of the loop of Henle. It has a brush border epithelial morphology." + "A meninx that is part of a midbrain [Automatically generated definition]." "MA:0001058 EHDAA2:0001174 RETIRED_EHDAA2:0001109 VHOG:0000012 EMAPA:17791 EHDAA:3708" + "Any process that stops, prevents, or reduces the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope." + "A bone that is part of a lower arm [Automatically generated definition]." "EMAPA:35347 MA:0000598" + "A nerve in the head that carries signals from the cochlea of the inner ear to the brain. It is part of the vestibulocochlear nerve, the 8th cranial nerve which is found in higher vertebrates; the other portion of the 8th cranial nerve is the vestibular nerve which carries spatial orientation information from the semicircular canals. The cochlear nerve is a sensory nerve, one which conducts to the brain information about the environment, in this case acoustic energy impinging on the tympanic membrane. The cochlear nerve arises from within the cochlea and extends to the brainstem, where its fibers make contact with the cochlear nucleus, the next stage of neural processing in the auditory system[WP]." "NCIT:C12697 neuronames:1406 BAMS:cVIIIn BM:VIIIN MA:0001110 UMLS:C0009201 EMAPA:17802 EHDAA2:0002195 Wikipedia:Cochlear_nerve VHOG:0001182 MESH:D003056 BTO:0003490 FMA:53431 MBA:948 SCTID:280286001 GAID:723" + "A blood vessel that is part of a limb [Automatically generated definition]." "EMAPA:36598 MA:0000687" + "Any process that activates or increases the frequency, rate or extent of the regulated release of luteinizing hormone." + "An artery that supplies a thyroid gland." "EHDAA2:0002029 NCIT:C53020 AAO:0010490 EHDAA:7372 MA:0002066 UMLS:C1711424 EMAPA:18622 VHOG:0001366" + "A thin membrane that separates the external ear from the middle ear, consisting of two epithelia (one part of the the external accoustic meatus epithelium, the other part of the tympanic cavity epithelium) with a fibrous layer between them. Its function is to transmit sound from the air to the ossicles inside the middle ear. The malleus bone bridges the gap between the eardrum and the other ossicles. Rupture or perforation of the eardrum can lead to conductive hearing loss. [WP,unvetted]." "Wikipedia:Tympanic_membrane EMAPA:19062 SCTID:181180005 MA:0000257 GAID:870 NCIT:C12502 MESH:D014432 UMLS:C0041445 FMA:9595 XAO:0000212 VHOG:0001146" + "Any of the arteries or veins that supply blood to the heart or return blood from the heart muscles to the circulation." "MESH:D003331 Wikipedia:Coronary_circulation" + "Any process that activates or increases the frequency, rate or extent of epithelial cell differentiation." + "The movement of a Langerhans cell in response to an external stimulus." + "An epithelial cell of a skin gland." "FMA:70657" + "A strong ring of smooth muscle at the end of the pyloric canal which lets food pass from the stomach to the duodenum. It receives sympathetic innervation from the celiac ganglion[WP]." "AAO:0011093 FMA:14916 SCTID:268073008 XAO:0000457 MA:0002952 EMAPA:19251 VHOG:0001466 UMLS:C0227238 NCIT:C33433" + "Any process that increases the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate." + "PMID:11062127 PMID:12684019 GC_ID:1" + "A V(D)J recombination-activating protein 1 that is encoded in the genome of mouse." "UniProtKB:P15919" + "The intermediate fibrous layer of the tympanic membrane." "FMA:56830 MA:0001223 SCTID:44692008 EMAPA:19063" + "The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides." + "Tissue that surrounds the lens nucleus." "MESH:D007904 FMA:58970 SCTID:280626006 BTO:0001632 CALOHA:TS-0542" + "A megakaryocyte erythroid progenitor cell is CD34-positive, CD38-positive and is IL3-receptor alpha-negative and CD45RA-negative." + "A zone of skin that is part of a head [Automatically generated definition]." "MA:0000582 FMA:12166 SCTID:181484006 FMA:24756 NCIT:C52757 UMLS:C0205029" + "The directed movement of substances into, out of or within the Golgi apparatus, mediated by vesicles." + "A contractility which is relatively high." + "Racemose mucous glands beneath the mucous membrane of the pharynx." "FMA:55075 EHDAA2:0001461 BTO:0004849 EHDAA:2967" + "The transient proliferative population of neurons that expands exponentially during late prenatal development; it is a continuous germinal zone distinct from the ventricular zone that surrounds the brain ventricles[MP]." "EMAPA:32665 PBA:128012818 Wikipedia:Ganglionic_eminence DHBA:10549" + "An intratelencephalic-projecting glutamatergic with a soma located in cortical layer 4/5." + "Any process that modulates the rate, frequency or extent of Golgi inheritance. Golgi inheritance is the partitioning of Golgi apparatus between daughter cells at cell division." + "A mucosa that is part of a oral opening [Automatically generated definition]." "SCTID:362083000" + "The process in which a cardiac muscle precursor cell acquires specialized features of a cardiac muscle cell. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction." + "Any process that modulates the frequency, rate or extent of amniotic stem cell differentiation." + "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 4." + "Any muscle organ that is part of a forelimb zeugopod (lower arm)[Automatically generated definition]." "EMAPA:32622 FMA:37371 MA:0000600 SCTID:181631004" + "The adrenal gland medulla that is in the left side of the abdomen." "FMA:69092" + "The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a monocyte." + "Any process that alters the size or shape of a vestibular receptor cell." + "A stem cell that can give rise to multiple lineages of cells." "FMA:84789" + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting the presence, absence, or concentration of oxygen." + "Neuromast hair cell is a hair cell that acts as a sensory receptor of the neuromast; it is morphologically polarized as a result of the relative position of the single kinocilium and the clusters of stereocilia on its apical surface." + "A CD9 molecule that is encoded in the genome of human." "UniProtKB:P21926" + "The glenohumeral joint, commonly known as the shoulder joint, is a multiaxial synovial ball and socket joint and involves articulation between the glenoid fossa of the scapula (shoulder blade) and the head of the humerus (upper arm bone). [WP,unvetted]." "MESH:D012785 NCIT:C33548 Wikipedia:Glenohumeral_joint FMA:25912 EMAPA:19105 SCTID:182168000 UMLS:C0037009 galen:ShoulderJoint GAID:269 VHOG:0001002 MA:0000459" + "Any process that reduces the extent to which blood vessels can be pervaded by fluid." + "GC_ID:1" + "A cell morphology that inheres in neurons which have spiny basal dendrites and resemble pyramidal cells but lose their apical dendrites as they mature. Their axons nearly always emerge from the descending side of the soma, but often recurve and ascend with arc-like collaterals." "ilxtr:SpinyStellatePhenotype" + "A protein that is a translation product of the human CD244 gene or a 1:1 ortholog thereof." + "A glial fibrillary acidic protein that is encoded in the genome of mouse." "UniProtKB:P03995" + "An adventitia that is part of a epididymis." "FMA:19136 EMAPA:30443" + "Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA]." "EHDAA2:0003069 SCTID:309044005 FMA:45562 Wikipedia:Stratified_epithelium BTO:0002074 BILA:0000069 HAO:0000069 AEO:0000069 ZFA:0001494 NCIT:C33622 XAO:0004006 TAO:0001494 UMLS:C0682575 CARO:0000069 AAO:0010059" + "Any process that activates or increases the frequency, rate or extent of the directed movement of epinephrine into a cell." + "The process in which the anatomical structure of the central nervous system is generated and organized. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord." + "An immature alpha-beta T cell that is located in the thymus and is CD8-positive and CD4-negative." + "A CD83 molecule that is encoded in the genome of human." "UniProtKB:Q01151" + "A granule cell that has a soma located in an olfactory bulb granule cell layer. An olfactory granule cell is an interneuron that lacks an axon, makes reciprocal dendro-dendritic synapses with mitral cells and tufted cells and is involved in the fine spatio-temporal tuning of the responses of these principal olfactory bulb neurons to odors." + "The directed movement of a T cell in response to an external stimulus. A T cell is a type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex." + "Any process that activates or increases the frequency, rate, or extent of an adaptive immune response." + "The cell adhesion process in which mammary mesenchyme cells adhere to one another in the initial stages of the formation of mammary fat development." + "The organism subdivision that includes the pelvic girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pelvic girdle regions." "EMAPA:37862 NCIT:C33291 VSAO:0000304 UMLS:C0684083 FMA:16581 SCTID:360010001" + "A somatic muscle cell that is oblquely striated. Examples include the somatic muscles of nematodes." + "Any process that modulates the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other." + "GC_ID:1" + "Any process that modulates the frequency, rate or extent of vacuolar transport." + "A white matter that is part of the hindbrain." "DHBA:10668 FMA:268636" + "A bone marrow stromal antigen 2 that is encoded in the genome of human." "UniProtKB:Q10589" + "Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a maxillary process mesenchyme." "EHDAA2:0004602" + "A material entity consisting of multiple components that are causally integrated." + "The orderly movement of a hepatic stellate cell from one site to another." + "An endothelial cell that is part of a respiratory system lymphatic vessel." "EFO:0010667" + "A size quality which is relatively high." + "Any process that activates or increases the frequency, rate or extent of myofibroblast cell apoptotic process." + "The deep cervical artery (Profunda cervicalis) is an artery of the neck." "Wikipedia:Deep_cervical_artery SCTID:244223002 FMA:10659" + "Any process that modulates the rate, frequency or extent of fibroblast cell migration. Fibroblast cell migration is accomplished by extension and retraction of a pseudopodium." + "An epiphysis that is part of a phalanx of a pes [Automatically generated definition]." "SCTID:314621001" + "Any process that activates or increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope." + "Enables the transmembrane transfer of a cation by a channel that opens when serotonin has been bound by the channel complex or one of its constituent parts." "Reactome:R-HSA-975311 Reactome:R-HSA-9648983" + "An integrin alpha-IIb that is encoded in the genome of mouse." "UniProtKB:Q9QUM0" + "A mesenchymal stem cell of the amnion membrane." + "One of eight distinct lateral lines in the 4-day larva. A sensory system on the surface of the fish, consisting of small sensory patches (neuromasts) distributed in discrete lines over the body surface. The lateral line system is stimulated by local water displacements and vibrations, and detects propulsion of the fish through the water, as well as facilitating shoaling, prey capture, and predator and obstacle avoidance." "AAO:0011024 XAO:0000465 ZFA:0000944 EFO:0003595 TAO:0000944" + "The formation of the prechordal plate. The prechordal plate is a thickening of the endoderm at the cranial end of the primitive streak formed by the involution of Spemann's organizer cells. The prechordal plate and the notochord induce the formation of the neural plate from the overlying ectodermal cells." + "Section of the forelimb skeleton located between the stylopodium and the autopodium." "VSAO:0005010" + "Dense regular connective tissue connecting two or more adjacent skeletal elements[VSAO,modified]." "GAID:118 MA:0003005 FMA:25624 Wikipedia:Ligament#Articular_ligaments AAO:0010444 EHDAA2:0003232 VSAO:0000072 EV:0100144 SCTID:410744003 CALOHA:TS-2146 AEO:0000090" + "A monostratified retinal ganglion cell that has a small soma, a small dendrite field with a dense dendrite arbor, and post synaptic terminals in sublaminer layer S2 and S3." + "The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a cell of the His-Purkinje system. These cells form the fibers regulate cardiac muscle contraction in the ventricles." + "Any process that activates or increases the frequency, rate or extent of calcium ion binding." + "A bone that is part of a pectoral girdle region." "EMAPA:35669 MA:0000292" + "Epibranchial placode between geniculate and nodose. Associated with 2nd branchial cleft." "XAO:0004212 ZFA:0001296 TAO:0001296 EHDAA2:0004207" + "Any process that stops, prevents, or reduces the frequency, rate or extent of gamma-delta T cell activation." + "Any process that stops, prevents or reduces the frequency, rate or extent of prolactin signaling pathway." + "The chemical reactions and pathways resulting in the formation of epinephrine, a hormone produced by the medulla of the adrenal glands that increases heart activity, improves the power and prolongs the action of muscles, and increases the rate and depth of breathing. It is synthesized by the methylation of norepinephrine." + "Vasculature that is part of a head [Automatically generated definition]." "EFO:0003656 TAO:0001267 XAO:0004152 ZFA:0001267 FMA:74710" + "The flattened aspect of the prostate with a slight furrow facing the rectum and anus." "NCIT:C13095 UMLS:C0227961 FMA:19592 SCTID:279697005" + "The phase of elevated metabolic activity, during which oxygen consumption increases, that occurs at fertilization. An enhanced uptake of oxygen leads to the production of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals. Capacitation, a necessary prerequisite event to successful fertilization, can be induced by reactive oxygen species in vitro; hydrogen peroxide is used as an extracellular oxidant to cross-link the protective surface envelopes." + "A skeletal element that is part of a orbital region." + "An oncocyte located in the parathyroid gland." "FMA:69084" + "The proliferation of cells in the trophectoderm." + "The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter." "Wikipedia:Axon NIF_Subcellular:sao1770195789" + "A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP]." "galen:Vagina MAT:0000128 MESH:D014621 FMA:19949 CALOHA:TS-1103 GAID:381 MA:0000394 EFO:0000976 VHOG:0001138 EMAPA:18986 EV:0100117 MIAA:0000128 NCIT:C12407 SCTID:181441005 UMLS:C0042232 Wikipedia:Vagina BTO:0000243" + "The chemical reactions and pathways resulting in the breakdown of any of a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine." + "The regulated release of any corticosteroid hormone into the circulatory system." + "A portion of smooth muscle tissue that is part of a gallbladder [Automatically generated definition]." "NCIT:C49483 MA:0001635 EMAPA:35373 UMLS:C1708179" + "The part of the hypothalamus posterior to the middle region consisting of several nuclei including the medial mamillary nucleus, lateral mamillary nucleus, and posterior hypothalamic nucleus (posterior hypothalamic area). The posterior hypothalamic area is concerned with control of sympathetic responses and is sensitive to conditions of decreasing temperature and controls the mechanisms for the conservation and increased production of heat." "BAMS:PHR GAID:651 HBA:4665 neuronames:411 Wikipedia:Mammillary_process BIRNLEX:1651 UMLS:C0020670 MESH:D007034 FMA:62029 BAMS:PH" + "Any process that activates or increases the frequency, rate or extent of apoptotic process involved in metanephric nephron tubule development." + "A gland that is part of a cloaca." + "Any process that activates or increases the frequency, rate or extent of chromatin organization." + "Binding to a protein." + "The process whose specific outcome is the progression of a collecting duct over time, from its formation to the mature structure. The collecting duct responds to vasopressin and aldosterone to regulate water, electrolyte and acid-base balance. It is the final common path through which urine flows before entering the ureter and then emptying into the bladder." + "The process in which a relatively unspecialized larval lymph gland-derived hemocyte precursor cell acquires the specialized features of the phagocytic blood-cell type, the plasmatocyte." + "Distal portion of the hind limb, including tarsal region, metatarsal region and digits." "MA:0000044 EMAPA:17459 CALOHA:TS-0377 BTO:0000476 EFO:0003065 GAID:40 MESH:D005528 galen:Foot VHOG:0000350 EHDAA2:0000546 SCTID:302545001 NCIT:C32622 Wikipedia:Pes_(anatomy) UMLS:C0016504 FMA:9664" + "A submucosal gland found in a respiratory tract." "EFO:0010666" + "Any process that activates or increases the frequency, rate, or extent of leukocyte chemotaxis." + "A NK1.1-positive T cell that is CD94-positive." + "Any process that modulates the frequency, rate or extent of apoptotic process involved in metanephric collecting duct development." + + "The sum total of mesenchymal tissue in the pharyngeal arch region. Pharyngeal mesenchyme is undifferentiated, loose connective tissue derived mostly from mesoderm, and also contains ectodermally derived neural crest cells." "EHDAA2:0001459 EMAPA:16550 XAO:0004524" + "The series of events by which an organism senses the position, location, orientation, and movement of the body and its parts. Proprioception is mediated by proprioceptors, sensory nerve terminals found in muscles, tendons, and joint capsules, which give information concerning movements and position of the body. The receptors in the labyrinth are sometimes also considered proprioceptors." "Wikipedia:Proprioception" + "Any process that activates or increases the frequency, rate or extent of epithelial cell migration." + "A T cell receptor complex in which the TCR heterodimer comprises gamma and delta chains, associated with the CD3 complex; recognizes antigen directly, without a requirement for processing and presentation by an MHC protein." + "The series of molecular signals initiated by an extracellular ligand binding to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with the regulation of a downstream cellular process, e.g. transcription." + "The series of molecular signals initiated by activation of a ligand-gated ion channel on the surface of a cell. The pathway begins with binding of an extracellular ligand to a ligand-gated ion channel and ends with a molecular function that directly regulates a downstream cellular process, e.g. transcription." + "An epithelial tube that develops from a Mullerian duct in a male. Later degenerates." "EMAPA:29161 EHDAA2:0001052 EMAPA:35661" + "Any vertebral bone that is part of the caudal region of the vertebral column (tail or coccyx)." "UMLS:C0223616 Wikipedia:Caudal_vertebra galen:CoccygealVertebra MA:0001420 TAO:0000326 EMAPA:18374 SCTID:361774004 XAO:0003079 FMA:12527 ZFA:0000326 NCIT:C32334 MA:0000310" + "The mesonephric capsule is the tough fibrous layer surrounding the mesonephros, covered in a thick layer of perinephric adipose tissue." + "An arterial trunk which is continuous with the heart and branches into the pulmonary arteries." "FMA:8612 EMAPA:17015 galen:PulmonaryTrunk NCIT:C116918 EHDAA2:0001576 MA:0002033 EHDAA:9831 VHOG:0001134" + "Any process that increases the rate, frequency, or extent of cilium movement, the directed, self-propelled movement of a cilium." + "In mammals, the pronephros is the first of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the pronephros is the fully functional embryonic kidney and is indispensible for larval life[GO]." "EMAPA:16579 EHDAA2:0001570 UMLS:C0231048 Wikipedia:Pronephros TAO:0000151 FMA:72170 MIAA:0000117 EHDAA:1017 SCTID:308804007 MAT:0000117 VHOG:0000037 BTO:0001541 AAO:0011089 ZFA:0000151 EFO:0000927 NCIT:C34280 XAO:0002000" + "Any process in which striated muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors. These adaptive events occur in both muscle fibers and associated structures (motoneurons and capillaries), and they involve alterations in regulatory mechanisms, contractile properties and metabolic capacities." + "The process in which neuroepithelial cells in the neural tube acquire specialized structural and/or functional features of somatic motor neurons. Somatic motor neurons innervate skeletal muscle targets and are responsible for transmission of motor impulses from the brain to the periphery. Differentiation includes the processes involved in commitment of a cell to a specific fate." + "The process in which the anatomical structures of the external genitalia are generated and organized. The external genitalia are the outer sex organs, such as the penis or vulva in mammals." + "The dense rope-like structures of lymphatic tissue located between the medullary sinuses in the medulla of a lymph node." "EMAPA:37897" + + "A process projection from a part of the vertebra such as centrum or arches. Examples: transverse process, diapophyses, parapophyses, and zygapophyses (both the cranial zygapophyses and the caudal zygapophyses)." "AAO:0000739 Wikipedia:Vertebral_column#Structure_of_individual_vertebrae FMA:24530" + "Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as apoptotic bodies). The cell corpse (or its fragments) may be engulfed by an adjacent cell in vivo, but engulfment of whole cells should not be considered a strict criteria to define cell death as, under some circumstances, live engulfed cells can be released from phagosomes (see PMID:18045538)." + "A nerve fiber that is part of a trigeminal nerve." "UMLS:C0175452 BIRNLEX:974 neuronames:607 FMA:72501 BAMS:5nf" + "Any process that modulates the rate or extent of heart growth. Heart growth is the increase in size or mass of the heart." + "A system of fluid passages in the inner ear, including both the cochlea, which is part of the auditory system, and the vestibular system, which provides the sense of balance. The bony labyrinth, or osseous labyrinth, is the network of passages with bony walls lined with periosteum. The bony labyrinth is lined with the membranous labyrinth. There is a layer of perilymph between them. The three parts of the bony labyrinth are the vestibule of the ear, the semicircular canals, and the cochlea. The vestibular system is the region of the inner ear where the semicircular canals converge, close to the cochlea (the hearing organ). The vestibular system works with the visual system to keep objects in focus when the head is moving. Joint and muscle receptors also are important in maintaining balance. The brain receives, interprets, and processes the information from these systems that control our balance. [WP,unvetted]." "CALOHA:TS-2080 BTO:0004685 AAO:0011078 SCTID:279727008 VHOG:0001219 XAO:0000193 Wikipedia:Bony_labyrinth NCIT:C33227 EMAPA:36580 MA:0000238 EV:0100362 UMLS:C0458699 FMA:60179" + + "The regulated release of histamine by a basophil or group of basophils." + "The pulmonary artery that supplies the right lung." "galen:RightPulmonaryArtery Wikipedia:Right_pulmonary_artery UMLS:C0923924 SCTID:244235003 NCIT:C33489 MA:0002500 EMAPA:37378 FMA:50872" + "A subdivision of the head that corresponds to the jaw skeleton, containing both soft tissue, skeleton and teeth (when present). The jaw region is divided into upper and lower regions." "NCIT:C114916 EMAPA:32905" + "Joint in which the articulating bones or cartilages are connected by ligaments or fibrocartilage without an intervening synovial cavity. Examples: sagittal suture, inferior tibiofibular syndesmosis, costochondral joint, pubic symphysis." "FMA:7491" + "Any process that stops, prevents or reduces the frequency, rate or extent of lymphangiogenesis." + "An astrocyte of the spinal cord." + "A muscle layer that is part of the sigmoid colon." "FMA:15028" + "The row of fused Muller cell processes and astrocytes that separates the retinal nerve fiber layer from the vitreous[MP]." "FMA:58689 NCIT:C32807 TAO:0001029 EMAPA:36519 Wikipedia:Inner_limiting_membrane UMLS:C1512783 XAO:0003222 ZFA:0001029 SCTID:280677004 MA:0001313" + "Any process that stops or reduces the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule." + "A vein that drains blood from the left adrenal gland into the left renal artery." "UMLS:C0226709 Wikipedia:Suprarenal_veins SCTID:85087001 FMA:14349 NCIT:C53138" + "A quality inhering in a bearer by virtue of the bearer's deviation from normal or average." + "A cytoplasmic, membrane bound vesicle that is capable of fusing to the plasma membrane to release its contents into the extracellular space." + "Any process that stops, prevents, or reduces the frequency, rate or extent of calcium-mediated signaling." + "GC_ID:1" + "A CD11c-low plasmacytoid dendritic cell that is CD8alpha-positive and CD4-positive." + "An adventitia that is part of a vas deferens." "SCTID:299803005 FMA:19238 EMAPA:29767" + "The process in which a mesodermal, bone marrow or neural crest cell acquires specialized features of an endothelial cell, a thin flattened cell. A layer of such cells lines the inside surfaces of body cavities, blood vessels, and lymph vessels, making up the endothelium." + "FMA:256176" + "A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped." "BTO:0000452 VHOG:0001482 FMA:63877 CALOHA:TS-0362 NCIT:C12482" + "Any portion of tissue that surrounds a urethra." "SCTID:256880003 BTO:0005081" + "Any process that stops, prevents or reduces the frequency, rate or extent of myoblast proliferation." + "The process whose specific outcome is the progression of the thymus over time, from its formation to the mature structure. The thymus is a symmetric bi-lobed organ involved primarily in the differentiation of immature to mature T cells, with unique vascular, nervous, epithelial, and lymphoid cell components." + "The recognition and removal of an apoptotic cell by a neighboring cell or by a phagocyte." + "Any process that stops, prevents, or reduces the frequency, rate or extent of adipocyte differentiation." + "A sensory epithelium that is part of a gustatory system." "http://uri.neuinfo.org/nif/nifstd/nifext_12 FMA:62412" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving glycogen." + "A serous secreting cell that is part of the epithelium of bronchiole." "FMA:263084" + "The process whose specific outcome is the progression of a granulosa cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a granulosa cell fate." + "Formation of the endocardium of the heart. The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers." + "A cell whose function is determined by the generation or the reception of an electric signal." + "A nitrogen compound metabolic process that contributes to the nitrogen cycle. The nitrogen cycle is a series of metabolic pathways by which nitrogen is converted between various forms and redox states; it encompasses pathways in which nitrogen is acted upon directly, such as nitrification, denitrification, nitrogen fixation, and mineralization." "Wikipedia:Nitrogen_cycle" + "GC_ID:1" + "A late basophilic metamyelocyte in which the nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature basophil." + "Any process that modulates the frequency, rate or extent of retrograde axon cargo transport." + "A change in the morphology or behavior of a keratinocyte resulting from exposure to an activating factor such as a cellular or soluble ligand. Upon activation, keratinocytes become migratory and hyperproliferative, and produce growth factors and cytokines." + "The directed movement of gamma-aminobutyric acid (GABA, 4-aminobutyrate), an amino acid which acts as a neurotransmitter in some organisms, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "The process whose specific outcome is the progression of the renal vesicle over time, from its formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure. The renal vesicle is the primordial structure of the nephron epithelium, and is formed by the condensation of mesenchymal cells." + "An urothelial cell that is part of the trigone of urinary bladder." "FMA:70598" + "Pancreatic bud that gives rise to the major pancreatic duct." "TAO:0001369 EFO:0003464 EHDAA2:0001389 XAO:0001103 SCTID:361437002 AAO:0011111 EMAPA:17256 Wikipedia:Pancreatic_bud ZFA:0001369 VHOG:0001429" + "A neuron that has dendritic processes radiating from the cell body forming a star-like shape." "BTO:0002316" + "The directed movement of proteins in a cell, from one side of a membrane to another by means of some agent such as a transporter or pore." + "A neuron of the dorsal cochlear nucleus with spiny dendrites that receive input from the axons of granule cells and with axons that release GABA and glycine onto cartwheel, pyramidal and giant cell targets." "ILX:0102311" + "Any process that modulates the frequency, rate or extent of glucocorticoid mediated signaling pathway." + "The directed movement of water (H2O) by the renal system." + "A galectin-1 that is encoded in the genome of mouse." "UniProtKB:P16045" + "The progression of a connective tissue over time, from its formation to the mature structure." + "Any vesicle that is part of the intracellular region." + "A SIRP/SHPS-1 family protein that is a translation product of the human SIRPA gene or a 1:1 ortholog thereof." "IUPHARobj:2942" + "Mesenchyme that develops_from a splanchnopleure." "EHDAA2:0001122" + "An individual reproductive unit containing a single oocyte and one or several layers of support cells (Armstrong et al., 2020)." + "A beta motor neuron that innervates nuclear chain fibers." + "Region of wall of right ventricle which is continuous with the lateral and septal walls of right ventricle." "FMA:9553" + "The chemical reactions and pathways resulting in the breakdown of lipids, as carried out by individual cells." + "A membrane-bounded, cytoplasmic secretory granule found in enzyme-secreting cells and visible by light microscopy. Contain zymogen, an inactive enzyme precursor, often of a digestive enzyme." + "A multicellular organismal process involved in the periodic casting off and regeneration of an outer covering of cuticle, feathers, hair, horns, skin." + "A cell that is part of a cortex of kidney." + "An ecto-epithelial cell of the nasal region of the viscerocranial mucosa." "FMA:70554" + "A columnar cell of the cervix uteri." "FMA:86486" + "A venous channel found between layers of dura mater in the brain. Receives blood from internal and external veins of the brain, receive cerebrospinal fluid (CSF) from the subarachnoid space, and ultimately empty into the internal jugular vein." "MA:0002113 EHDAA2:0002169 NCIT:C102627 FMA:50762 EMAPA:18634 SCTID:54944003 Wikipedia:Dural_venous_sinuses VHOG:0001004 EHDAA:6491" + "GC_ID:1" + "The process in which calcium ions sequestered in the endoplasmic reticulum, Golgi apparatus or mitochondria are released into the presynaptic cytosol." + "The process in which the anatomical structure of the medulla oblongata is generated and organized. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate." + "The series of molecular signals initiated by glucocorticoid binding to its receptor." + "A tissue-resident macrophage located in the bone marrow. This cell type is B220-negative, CD3e-negative, Ly-6C-negative, CD115-positive, F4/80-positive." "BTO:0004732" + "The process in which a relatively unspecialized T cell acquires specialized features of a cytotoxic T cell." + "An anatomical junctions that overlaps the foregut and midgut." "VHOG:0000291 EMAPA:16363 EHDAA2:0000569 EHDAA:526" + "A supporting cell projecting inward from the basement membrane of seminiferous tubules. They surround and nourish the developing male germ cells and secrete androgen binding protein. Their tight junctions with the spermatogonia and spermatocytes provide a blood-testis barrier." "BTO:0001238 FMA:72298 CALOHA:TS-0922 VHOG:0001348" + "Cartilage tissue intermediate between hyaline cartilage and dense connective tissue; contains of abundant collagen fibers; chondrocytes often arranged in columns." "Wikipedia:Fibrocartilage UMLS:C0684077 NCIT:C32599 galen:Fibrocartilage XAO:0004028 VSAO:0000103 FMA:64784 MA:0000108 SCTID:91685003" + "The orderly movement of a cardiac progenitor cell to form the heart field. Cardiac progenitor cells are non-terminally differentiated, mesoderm-derived cells that are committed to differentiate into cells of the heart. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating." + "The joining of the lipid bilayer membrane around a vesicle with the lipid bilayer membrane around the vacuole." + "GC_ID:1" + "A prolongation or process extending from a glial cell." + "The process whose specific outcome is the progression of a prolactin secreting cell over time, from its formation to the mature structure. A prolactin secreting cell is an acidophilic cell of the anterior pituitary that produces prolactin." + "An epithelium consisting of myopethelial cells, which are contractile cells resembling smooth muscle cells that are present in glands, notably the mammary gland, and aid in secretion. This cell has long weaving dendritic processes containing myofilament[CL]." "BTO:0002308 Wikipedia:Myoepithelial_cell FMA:67805" + "A transitional stage B cell that has the phenotype surface IgM-positive, surface IgD-postive, CD21-positive, CD23-positive, CD62L-negative, CD93-positive and is located in the splenic B follicles. This cell type has also been described as IgM-high, CD19-positive, B220-positive, AA4-positive, and CD23-positive." + "The regrowth of a lost or destroyed body part, such as an organ or tissue. This process may occur via renewal, repair, and/or growth alone (i.e. increase in size or mass)." "Wikipedia:Regeneration_(biology)" + "The progression of the trabecular meshwork over time, from its formation to the mature structure. The trabecular meshwork is a fenestrated endothelial-like tissue situated at the intersection of the cornea and the iris. The trabecular meshwork provides drainage for the aqueous humor." + "An endothelial cell that lines the vasculature." + "Tolerance induction taking place in the mucosal tissues." + "A layer of of the central nervous system that is part of gray matter." "FMA:83142" + "Any process that stops, prevents, or reduces the frequency, rate or extent of neutrophil differentiation." + "The process whose specific outcome is the progression of the forebrain over time, from its formation to the mature structure. The forebrain is the anterior of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes especially the cerebral hemispheres, the thalamus, and the hypothalamus and especially in higher vertebrates is the main control center for sensory and associative information processing, visceral functions, and voluntary motor functions)." + "The process in which the anatomical structures of lymph vessels are generated and organized. The lymph vessel is the vasculature carrying lymph." + "A portion of smooth muscle tissue that is part of a small intestine [Automatically generated definition]." "EMAPA:35783 MA:0001559" + "A mesothelial fibroblast found in the leptomeninx." + "KUPO:0001047" + "A portion of connective tissue that is part of a limb [Automatically generated definition]." "MA:0000689 EMAPA:37313" + "Notochordal cell that is inner portion of the notochord and becomes vacuolated as development proceeds." + "The progression of the mammillary body over time from its initial formation until its mature state. The mammillary body is a protrusion at the posterior end of the hypothalamus that contains hypothalamic nuclei." + "An enterocyte that is part of the epithelium of small intestine." "FMA:263086" + "GC_ID:1" + "A tetraspanin that is a translation product of the human CD9 gene or a 1:1 ortholog thereof." + "The process whose specific outcome is the progression of the locus ceruleus over time, from its formation to the mature structure. The locus ceruleus is a dense cluster of neurons within the dorsorostral pons. This nucleus is the major location of neurons that release norepinephrine throughout the brain, and is responsible for physiological responses to stress and panic." + "KUPO:0001041" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of juvenile hormone." + "Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to cell-cell junction." + "A macrophage located in the vermiform appendix." + "The pharynx is the part of the digestive system immediately posterior to the mouth[GO]." "MIAA:0000049 MAT:0000049 MESH:D010614" + "Any process that decreases the rate, frequency or extent of kidney development. Kidney development is the process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and excretes the end products of body metabolism in the form of urine." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of a neurotransmitter." + "The chemical reactions and pathways involving any of a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms, as carried out by individual cells. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups." + "The orderly movement of a cell from one site to another that will contribute to the progression of the kidney over time, from its formation to the mature organ." + "An epithelial cell found in the lining of the stomach." "FMA:62948" + "Any process that modulates the rate, frequency or extent of animal organ formation. Organ formation is the process pertaining to the initial formation of an organ from unspecified parts. The process begins with the specific processes that contribute to the appearance of the discrete structure, such as inductive events, and ends when the structural rudiment of the organ is recognizable, such as a condensation of mesenchymal cells into the organ rudiment." + "A C-X-C chemokine receptor type 3 that is encoded in the genome of human." "DTO:02100077 UniProtKB:P49682 Reactome:R-HSA-2980699" + "Binding to an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group." + "A ventricular outflow tract is a portion of either the left ventricle or right ventricle of the heart through which blood passes in order to enter the great arteries. The right ventricular outflow tract (RVOT) is an infundibular extension of the ventricular cavity which connects to the pulmonary artery. The left ventricular outflow tract (LVOT), which connects to the aorta, is nearly indistinguishable from the rest of the ventricle[WP]." "FMA:13225 XAO:0004140 Wikipedia:Ventricular_outflow_tract" + "A fully differentiated plasma cell that secretes IgM." + "The part of the ventral body cavity that is within the abdomen proper (excluding the pelvic cavity)." "NCIT:C12664 MESH:D034841 GAID:17 EFO:0000213 UMLS:C0230168 Wikipedia:Abdominal_cavity FMA:12266 SCTID:361294009 MA:0003057 galen:AbdominalCavity EMAPA:36505" + "Any process that modulates the frequency, rate or extent of the physical partitioning and separation of an epidermal cell into daughter cells. An epidermal cell is any of the cells that make up the epidermis." + "The process whose specific outcome is the progression of the facial nerve over time, from its formation to the mature structure. This sensory and motor nerve supplies the muscles of facial expression and the expression and taste at the anterior two-thirds of the tongue. The principal branches are the superficial opthalmic, buccal, palatine and hyomandibular. The main trunk synapses within pterygopalatine ganglion in the parotid gland and this ganglion then gives off nerve branches which supply the lacrimal gland and the mucous secreting glands of the nasal and oral cavities." + "The portion of the tongue in front of the terminal sulcus. At the apex, thin and narrow, it is directed forward against the lingual surfaces of the lower incisor teeth. It is derived primarily from the first pharyngeal arch." "FMA:229084 EMAPA:37437 NCIT:C32130 UMLS:C0226946 Wikipedia:Anterior_tongue" + "Layer that is part of the CA fields of the hippocampus consisting of a narrow relatively cell free layer located deep to the pyramidal cell layer extending through areas CA1, CA2 and CA3. (adapted from Paxinos The rat central nervous system, 2nd ed, Academic Press, San Diego, 1995)." "BIRNLEX:4113 neuronames:157 MA:0000958 FMA:83893 BAMS:Or EMAPA:35412" + "An arterial endothelial cell that is part of the aorta endothelium." "CALOHA:TS-0047 BTO:0003245" + "The metanephric late distal convoluted tubule contains metanephric DCT cells and intercalated (IC) alpha and beta cells and is vasopressin-sensitive[GO]." + "The region of the liver lobule that is closest to the portal triad. The functionally-defined hepatic acinus zone 1 is generally found in this region." + "KUPO:0001038" + "Any process that modulates the frequency, rate or extent of detection of mechanical stimulus involved in sensory perception of touch." + "Bone element that arises as a result of intramembranous ossification." "TAO:0001645 AEO:0000085 EHDAA2:0003085 ZFA:0001636 XAO:0004014 VSAO:0000023" + "The process whose specific outcome is the progression of the hindbrain over time, from its formation to the mature structure. The hindbrain is the posterior of the three primary divisions of the developing chordate brain, or the corresponding part of the adult brain (in vertebrates, includes the cerebellum, pons, and medulla oblongata and controls the autonomic functions and equilibrium)." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of immunoglobulin production." + "A pyramidal neuron which has an apical tree which is oriented towards the white matter." + "Any process that modulates the frequency, rate or extent of cell proliferation resulting in the maintenance of a steady-state number of cells within a tissue." + "The controlled release of a substance by a cell." "Wikipedia:Secretion" + "Any process that modulates the frequency, rate or extent of endodermal cell differentiation." + "The biological process whose specific outcome is the progression of a metanephric glomerulus vasculature from an initial condition to its mature state. This process begins with the formation of the metanephric glomerulus vasculature and ends with the mature structure. The metanephric glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the metanephric glomerulus." + "Any process that increases the rate, frequency, or extent of neural crest formation. Neural crest formation is the formation of the specialized region of ectoderm between the neural ectoderm (neural plate) and non-neural ectoderm. The neural crest gives rise to the neural crest cells that migrate away from this region as neural tube formation procedes." + "A flexibility which is relatively high." + "A mast/stem cell growth factor receptor that is encoded in the genome of mouse." "UniProtKB:P05532" + "Area of the forebrain between the anterior commissure and optic chiasm." "Wikipedia:Preoptic_area EFO:0002523 UMLS:C1284641 DMBA:15577 BTO:0001796 BM:Die-Hy-POA SCTID:362382004 BAMS:POA EMAPA:36655 MESH:D011301 TAO:0000470 ZFA:0000470 FMA:62313 GAID:644 HBA:4541 CALOHA:TS-0822 UMLS:C0033063 BIRNLEX:1706 neuronames:377" + "Any process that modulates the frequency, rate or extent of glomerular visceral epithelial cell apoptotic process." + "An epithelium that is part of a lower respiratory tract [Automatically generated definition]." "MA:0001481 EMAPA:37549" + "One the veins that drains the vaginal venous plexus, into the hypogastric veins. [WP,modified]." "SCTID:424336009 EMAPA:37796 MA:0002251 FMA:18899" + "A lamina propria that is part of a large intestine." "NCIT:C49298 UMLS:C1708644 FMA:15654" + "Any process that modulates the frequency, rate or extent of metanephric comma-shaped body morphogenesis." + "A DNA nucleotidylexotransferase that is encoded in the genome of human." "UniProtKB:P04053" + "A bistratified retinal ganglion cell that has a dendrite field that terminates in sublaminar layer S2 and a second dendrite field that terminates in sublaminar layer S4." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glucocorticoids." + "The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus contributing to an immune response, resulting in an increase in its intracellular or extracellular levels." + "Subdivision of skeletal system that consists of all the vertebra and associated skeletal elements and joints in the body[modified from VSAO]." "galen:SpinalColumn NCIT:C33588 EHDA:10119 TAO:0001559 XAO:0003074 EFO:0001369 UMLS:C1519455 AAO:0000734 BTO:0000818 MESH:D013131 VHOG:0001142 EMAPA:35919 ZFA:0001559 VSAO:0000185 SCTID:44300000 AAO:0000699 NIF_Subcellular:sao1145756102 UMLS:C0037949 MA:0002416 GAID:106 NCIT:C12998 FMA:13478 Wikipedia:Vertebral_column" + "The process in which a relatively unspecialized cell acquire specialized structural and/or functional features of an epithelial cell of the salivary gland." + "A photoreceptor cell that is sensitive to green light." + "The process whose specific outcome is the progression of an oocyte over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell." + "A morphological quality inhering in a bearer by virtue of the bearer's affording unobstructed passage or view." + "The process in which anatomical structures of the mammary ducts are generated and organized. Mammary ducts are epithelial tubes that transport milk." + "The process in which the anatomical structures of the hindgut are generated and organized, during the embryonic phase." + "Any process that modulates the frequency, rate or extent of mesoderm development." + "A mucosa that is part of a middle ear [Automatically generated definition]." "CALOHA:TS-0631 FMA:59663" + "A neuron projection quality that is a characteristic of neurons with soma in the cerebral cortex and projections to the thalamus." "ILX:0770102" + "The series of events that contribute to electroception in which an electrical stimulus is received and converted into a molecular signal." + "An epithelium that is part of a vomeronasal organ [Automatically generated definition]." "EMAPA:18444 EHDAA2:0004102 FMA:301283 MA:0001328" + "An anatomical junction that divides and overlaps with and atrium and a ventricle in the heart." "EHDAA2:0004149 FMA:85125" + "A fibroblast that is part of villous mesenchyme." + "A cell morphology that inheres in neurons which have two clusters of primary dendrites that originate directly and extend from opposite ends of the soma, and axons that form a plexus which spreads widely. Compared to the narrow vertical axonal projection of bipolar morphology, and the 'horse-tail' axonal cluster of double boquet cells, bitufted morphology has wide horizontal axonal spans, and branching that occur close to the soma. Their vertical projection is also less extensive and crosses mostly to neighboring layers." "ilxtr:BituftedPhenotype" + "Any process that modulates the rate, frequency or extent of a phase of elevated metabolic activity, during which oxygen consumption increases made as a defense response ; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals." + "The process in which a relatively unspecialized cell acquires specialized features of a mesenchymal stem cell that contributes to the shaping of a nephronin the metanephros. A mesenchymal stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized mesenchymal cells." + "Any process that modulates the frequency, rate or extent of protein localization to nucleus." + "Any process that modulates the frequency, rate, or extent of B cell anergy." + "Any process that modulates the frequency, rate or extent of nephron tubule epithelial cell differentiation." + "A blood lymphocyte located in the flowing, circulating blood of the body." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptide stimulus." + "Any process that stops, prevents or reduces the frequency, rate or extent of axo-dendritic protein transport." + "The set of neurons that receives neural inputs via bipolar, horizontal and amacrine cells. The axons of these cells make up the optic nerve." "BTO:0001800 FMA:67765 MESH:D012165" + "A thrombomodulin that is encoded in the genome of human." "UniProtKB:P07204" + "The pseudostratified ciliated epithelium that lines much of the conducting portion of the airway, including part of the nasal cavity and larynx, the trachea, and bronchi." "EMAPA:32827 BTO:0000419 SCTID:321764001 CALOHA:TS-0023 MA:0001480" + "A process in which a calcium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore." + "Cell-cell signaling between presynapse and postsynapse mediated by a peptide ligand crossing the synaptic cleft." + "The nasal vestibule is the most anterior part of the nasal cavity. It's enclosed by the cartilages of nose and lined by the same epithelium of the skin. The other part of the nasal cavity, which is lined by the respiratory epithelium, is called nasal cavity proper. [WP,unvetted]." "CALOHA:TS-0660 Wikipedia:Nasal_vestibule BTO:0001761 SCTID:278940000 FMA:59644" + "KUPO:0001037" + "KUPO:0001081" + "An urethral gland that is part of a female urethra." "FMA:21444 SCTID:279476001 EMAPA:29653" + "Any process that activates or increases the frequency, rate or extent of glucocorticoid secretion." + "The creation of a single organelle from two or more organelles." + "Any process that stops, prevents or reduces the frequency, rate or extent of response to calcium ion." + "A neuromere that is part of the presumptive midbrain." "FMA:61997 EHDAA2:0004352" + "Any process that activates or increases the frequency, rate or extent of thyroid-stimulating hormone secretion." + "A protein that is a translation product of the human MME gene or a 1:1 ortholog thereof." "PIRSF:PIRSF501074 IUPHARobj:1611" + "The process in which a neuroblast acquires specialized features of an interneuron residing in the olfactory bulb." + "A pigment cell located in the epithelium of the iris." + "A type II vestibular sensory cell that is part of the epithelium of macula of saccule of membranous labyrinth." "FMA:263198" + "An erythroblast that is GlyA-positive and CD71-negative." + "The interlobar veins are veins of the renal circulation which drain the renal lobes." "Wikipedia:Interlobar_veins FMA:71631" + "Any process that increases the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid)." + "KUPO:0001078" + "Increase in size of follicles surrounded by two or more layers of granulosa cells up to the onset of antrum formation." + "The directed movement of a protein to a specific location in a vacuole." + "The process in which the anatomical structure of the cerebellar Purkinje cell layer is generated and organized. The Purkinje cell layer lies just underneath the molecular layer of the cerebellar cortex. It contains the neuronal cell bodies of the Purkinje cells that are arranged side by side in a single layer. Candelabrum interneurons are vertically oriented between the Purkinje cells. Purkinje neurons are inhibitory and provide the output of the cerebellar cortex through axons that project into the white matter. Extensive dendritic trees from the Purkinje cells extend upward in a single plane into the molecular layer where they synapse with parallel fibers of granule cells." + "A diaphysis that is part of a femur[Automatically generated definition]." "SCTID:182048009 FMA:32847 Wikipedia:Body_of_femur NCIT:C96209 MA:0003055 EMAPA:37538" + "Any process that stops, prevents or reduces the frequency, rate or extent of estradiol secretion." + "The metanephric S-shaped body is the successor of the metanephric comma-shaped body that contributes to the morphogenesis of a nephron in the metanephros[GO]." + "A(n) myoepithelial cell that is part of a(n) bronchus submucosal gland." + "A large vein or channel for the circulation of venous blood." "UMLS:C0226504 ZFA:0007072 NCIT:C12877 SCTID:341586007 MA:0000070" + "An inter-phalangeal joint that connects a proximal phalanx to either a medial or distal phalanx." "FMA:65022 NCIT:C101528" + "Any process that modulates synaptic transmission by regulating translation occurring at the postsynapse." + "A specialized epithelial secretory cell that moves chloride ions and water across the tubule epithelium." "FBbt:00005797" + "Any process that decreases the rate or frequency of muscle cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a muscle cell and result in its death." + "A neural cell adhesion molecule NCAM that is a translation product of the human NCAM1 gene or a 1:1 ortholog thereof." "IUPHARobj:2769" + "Any retinal ganglion cell that is part of a retina." + "Any process that decreases the rate, frequency, or extent of the process in which a highly ordered sequence of patterning events generates the branched structures of the lung, consisting of reiterated combinations of bud outgrowth, elongation, and dichotomous subdivision of terminal units." + "The process in which a dendritic cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex." + "The region extending out from the boundary between layers S1 and S2." "CP:0001038" + "Any process that stops, prevents or reduces the frequency, rate or extent of myofibroblast cell apoptotic process." + "An extratelencephalic-projecting glutamatergic cortical neuron that is morphologically-defined with a large, spindle-shaped cell body, thick bipolar dendrites with limited branching and a moderate density of spines, and often an axon initial segment that emanates from the side of the cell body. This cell type is associated with markers POU3F, BMP3 and ITGA4." + "A bone that is part of the carpal skeleton. Examples: scaphoid, lunate, capitate[cjm]." "SCTID:83936004 EMAPA:25056 galen:CarpalBone MA:0000296 UMLS:C0007285 GAID:179 Wikipedia:Carpus NCIT:C12688 FMA:23889 MESH:D002348" + "GC_ID:1" + "VHOG:0000911 EMAPA:17580" + + "Any muscle organ that is part of a cloaca." + "Any process that modulates the frequency, rate or extent of small intestine smooth muscle contraction." + "A portion of connective tissue that is part of a prostate gland." "FMA:74165" + "Any process that stops, prevents, or reduces the frequency, rate or extent of GABAergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter gamma-aminobutyric acid (GABA)." + "A compound organ that has the potential to develop into a tongue." "EHDAA2:0000696 EHDAA:2951" + "A glomerular basement membrane that is part of a pronephros." "ZFA:0005313 TAO:0005313" + "The layer of secretory cells which lines the epididymis." "MA:0002825 BTO:0005768 FMA:19153 CALOHA:TS-2063 EMAPA:30445" + "A submucosa that is part of a cystic duct [Automatically generated definition]." "FMA:18013" + "A cell found in the bone marrow. This can include fibroblasts, macrophages, adipocytes, osteoblasts, osteoclasts, endothelial cells and hematopoietic cells." "MESH:D001854 FMA:83621 BTO:0004850" + "A multi-tissue structure that is part of a spinal cord." "BIRNLEX:1496 SCTID:244437008 NCIT:C33969 UMLS:C1268166" + "A cartilaginous joint that connects left and right mandibles/dentary bones. Mandibular symphysis is unpaired[TAO,modified]." "ZFA:0005488 AAO:0000277 TAO:0001851 FMA:75779 Wikipedia:Symphysis_menti MA:0001490" + "A cell morphology that inheres in neurons which have a small round soma, a large number of short, smooth, or slightly beaded primary dendrites that give rise to only a few secondary branches, and a branched axon that establishes a dense axonal mesh with thin shafts." "ilxtr:NeurogliaformPhenotype" + "An integrin alpha-M that is encoded in the genome of mouse." "UniProtKB:P05555" + "OBSOLETE (was not defined before being made obsolete)." + "Any process that contributes to cytokine production by a T-helper 1 cell." + "Any process that stops, prevents or reduces the frequency, rate or extent of defense response to insect." + "High endothelial venules are specialized blood vessels adapted for lymphocyte trafficking. They form a spatially organized network, which controls both the type of lymphocyte and the site of entry into lymphoid tissues. Uniquely, high endothelial venules express vascular addressins that regulate lymphocyte entry into lymphoid organs. They perform this function in all lymphoid organs except the spleen." "NCIT:C32739 BTO:0004528" + "Any process that stops, prevents or reduces the frequency, rate or extent of amacrine cell differentiation." + "GC_ID:1" + "Membranous process coming from capsule of lymph node[WP]." "MA:0000746 Wikipedia:Lymph_node_trabeculae FMA:74605 NCIT:C33035 UMLS:C1184179" + "A muscle tissue that is associated with soft internal organs (viscera)." + "The process in which a relatively unspecialized cell acquires specialized features of a hair cell." + "Any process that modulates the frequency, rate or extent of nitrogen cycle metabolic process." + "A neuron that releases dopamine as a neurotransmitter." "FBbt:00005131 WBbt:0006746 MESH:D059290 FMA:84787 BTO:0004032" + "A neuronal acetylcholine receptor subunit alpha-7 that is encoded in the genome of human." "UniProtKB:P36544 DTO:01100012" + "An otic capsule endochondral element that is composed primarily of a pre-cartilage condensation." "EHDAA2:0000833" + "A blood vessel that is part of a back [Automatically generated definition]." "MA:0000493 EMAPA:37243" + "Epithelial cell that is part of segment 2 (S2) of the proximal tubule epithelium." + "Neuromast mantle cell is a non-sensory cell. Neuromast mantle cells surround the neuromast support cells and neuromast hair cells, separating the neuromast from the epidermis, and secrete cupula in which the ciliary bundles of all the hair cells are embedded." + "The organ of Corti (or spiral organ) is the organ in the inner ear of mammals that contains auditory sensory cells, or 'hair cells.' [WP,unvetted]." "BIRNLEX:2526 ncithesaurus:Spiral_Organ_of_Corti EMAPA:19061 EV:0100364 CALOHA:TS-0717 SCTID:279841009 MA:0001193 GAID:772 BTO:0001691 Wikipedia:Organ_of_Corti FMA:75715 UMLS:C0029207 EFO:0001364 NCIT:C33223" + "The part of the digestive system that contains the liver and the biliary system." "AAO:0011056 NCIT:C43612 CALOHA:TS-1308 VHOG:0000294 Wikipedia:Hepatobiliary_system MAT:0000024 XAO:0000132 UMLS:C1711359 EMAPA:16840 TAO:0000036 EHDAA:2189 EFO:0000800 ZFA:0000036 MIAA:0000024 EHDAA2:0000998 MA:0000324 EV:0100088" + "OBSOLETE (was not defined before being made obsolete)." + "A muscular coat that is part of a urinary bladder." "FMA:15930 UMLS:C1288327 NCIT:C32206" + "The series of molecular signals initiated by serotonin binding to a seratonin receptor on the surface of the target cell, followed by the movement of ions through a channel in the receptor complex. Ends with regulation of a downstream cellular process, e.g. transcription." + "Wide thin-walled blood vessels in the liver. In mammals they have neither veinous or arterial markers." "FMA:17543 MA:0000367 EMAPA:17365 ZFA:0005091 TAO:0005091 VHOG:0000708 SCTID:67435004 Wikipedia:Hepatic_sinusoid EHDAA2:0000999 UMLS:C0227523 NCIT:C32733" + "Visceral serous membrane which is continuous with the parietal serous pericardium and is attached to the myocardium[FMA]." "EMAPA:19032 Wikipedia:Visceral_pericardium VHOG:0000538 FMA:84882 SCTID:243955001 MA:0000484" + "The lymphocytic cell population present in the mucosa of the nasopharyngeal duct of some animals." "UMLS:C2698431 FMA:79771 MA:0003030 NCIT:C77659" + + "Subdivision of vertebral column that corresponds to the trunk of the body, containing the trunk/presacral vertebrae. In organisms that have a thoracic and lumbar distinction, this corresponds to the sum of both of these regions." "NCIT:C92597 FMA:72066 SCTID:281699004" + "GC_ID:1" + "Binding to an immunoglobulin." + "The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage." + "Any process that modulates the frequency, rate, or extent of a response to biotic stimulus." + "An arachnoid mater that is part of a diencephalon [Automatically generated definition]." "MA:0000827 VHOG:0000231 EMAPA:17765" + "Any process that modulates the frequency, rate or extent of endothelial cell development." + "A gland that is part of a larynx submucosa [Automatically generated definition]." "EMAPA:35475 MA:0002729" + "Any process that modulates the frequency, rate, or extent of production of a cytokine." + "A CD8-positive, alpha-beta T cell with the phenotype CD69-positive, CD62L-negative, CD127-negative, and CD25-positive, that secretes cytokines." + "The process whose specific outcome is the progression of an acoustico-facial VII-VIII ganglion complex over time, from its formation to the mature structure." + "A discrete anatomical unit of the lung that is composed of a segmental bronchus and the lung tissue supplied by that bronchus. A bronchopulmonary segment exhibits a pyramidal shape, with its apex pointing towards the center of the lung and its base toward the pleural surface." + "Any process that stops, prevents or reduces the frequency, rate or extent of lipid binding." + "GC_ID:1" + "A muscle cell that is part of the anterior internodal tract." "FMA:223276" + "An epiphysis that is part of a middle phalanx of manus." "SCTID:280045003" + "EHDAA2:0001172 VHOG:0000910 EMAPA:16977" + "Ossicle that is part of the appendicular skeleton." "VSAO:0000131 XAO:0004194" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving any hormone." + "The progression of the conus arteriosus over time, from its formation to the mature structure. The conus arteriosus is a valved chamber with thick muscular walls stemming from the ventricle and connecting to the pulmonary trunk." + "A muscular coat that is part of a vas deferens [Automatically generated definition]." "EMAPA:29270 FMA:19239 MA:0001750 SCTID:299705008" + "A physical quality inhering in a bearer by virtue of the bearer's disposition to being turned, bowed, or twisted without breaking." + "The regulated release of mucus by the mucosa. Mucus is a viscous slimy secretion consisting of mucins and various inorganic salts dissolved in water, with suspended epithelial cells and leukocytes. The mucosa, or mucous membrane, is the membrane covered with epithelium that lines the tubular organs of the body. Mucins are carbohydrate-rich glycoproteins that have a lubricating and protective function." + "Any process that activates or increases angiogenesis." + "The collection of all skeletal elements in a mesopodium. Examples: the tarsal skeleton, the carpal skeleton." "VSAO:0005022" + "Self-propelled movement of a cell or organism from one location to another." + "Any process that modulates the frequency, rate or extent of protein complex disassembly, the disaggregation of a protein complex into its constituent components." + "An epiphysis that is part of a metacarpal bone [Automatically generated definition]." "SCTID:314907001 FMA:33792" + "The outer stripe is the region of the kidney that lies distal to the line of termination of the straight renal tubules." "EMAPA:29663 FMA:76662 MA:0002629" + "The process in which the population of cells that make up a mesenchyme undergo directed movement." + "An epithelial cell that is part of some loop of Henle thin ascending limb." "KUPO:0001050" + "An endoglin that is encoded in the genome of mouse." "UniProtKB:Q63961" + "The morphogenetic process in which the anatomical structures of the compound eye are generated and organized. The adult compound eye is a precise assembly of 700-800 ommatidia. Each ommatidium is composed of 20 cells, identified by cell type and position. An example of compound eye morphogenesis is found in Drosophila melanogaster." + "A C-C chemokine receptor type 5 that is encoded in the genome of mouse." "UniProtKB:P51682" + "GC_ID:1" + "A compartment of the renal cortex situated between basement membranes of epithelia and vessels that contains two contiguous cellular networks in mutual contact, one formed by interstitial fibroblasts, the other by dendritic cells." "Wikipedia:Medullary_interstitium EMAPA:28136 SCTID:243707006 MA:0002608" + "A mono-stratified retinal ganglion cell that has a large dendritic field, a medium dendritic arbor, and a medium length secondary dendrite shaft." "https://orcid.org/0000-0001-7258-9596 https://orcid.org/0000-0002-5260-9315" + "A prolongation or process extending from the soma of an astrocyte and wrapping around neurons." "NIF_Subcellular:sao1630537580" + "Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult)." + "A proximal mesopodial endochondral element that is composed primarily of cartilage tissue." + "EMAPA:16206 VHOG:0000485 EHDAA:406 MA:0000479 EHDAA2:0001720 SCTID:361404004" + "A signal transducer CD24 that is encoded in the genome of mouse." "UniProtKB:P24807" + "The progression of the olfactory placode over time from its initial formation until its mature state. The olfactory placode is a thickening of the neural ectoderm in the head region of the vertebrate embryo which develops into the olfactory region of the nasal cavity." + "Anatomical cavity for the proximal articular surface of the proximal limb or fin element with the scapulocoracoid or equivalent structure." "AAO:0000749 UMLS:C1261046 NCIT:C32682 Wikipedia:Glenoid_cavity FMA:23275 EMAPA:25122 SCTID:181914008" + "The formation of a thickening of the neural ectoderm in the head region of the vertebrate embryo which develops into the olfactory region of the nasal cavity." + "Any process that decreases the rate, frequency or extent of fertilization. Fertilization is the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy)." + "Binding to acetylcholine, an acetic acid ester of the organic base choline that functions as a neurotransmitter, released at the synapses of parasympathetic nerves and at neuromuscular junctions." + "The expansion of an alpha-beta T cell population by cell division as part of an immune response." + "Any process that modulates the amount of urine excreted from the body over a unit of time." + "The process in which the vertebrate retina is organized into three laminae: the outer nuclear layer (ONL), which contains photoreceptor nuclei; the inner nuclear layer (INL), which contains amacrine, bipolar and horizontal cells; and the retinal ganglion cell (RGC) layer. Between the inner and outer nuclear layers, the outer plexiform layer (OPL) contains connections between the photoreceptors and bipolar and horizontal cells. The inner plexiform layer (IPL) is positioned between the INL and the ganglion cell layer and contains the dendrites of RGCs and processes of bipolar and amacrine cells. Spanning all layers of the retina are the radially oriented Mueller glia." + "A neuron projection quality that is a characteristic of neurons that project to the medulla oblongata from other brain regions." + "The fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening." "XAO:0000153 SCTID:302513006 MESH:D014521 CALOHA:TS-1132 MIAA:0000121 EFO:0000931 Wikipedia:Urethra GAID:390 EMAPA:30901 UMLS:C0041967 NCIT:C12417 BTO:0001426 MA:0000379 VHOG:0001264 FMA:19667 MAT:0000121 EV:0100099 galen:Urethra" + "A nerve that is part of a forelimb stylopod [Automatically generated definition]." "EMAPA:37337 MA:0000607" + "Any process that modulates the frequency, rate or extent of calcium ion binding." + "The process in which the anatomical structures of the renal vesicle are generated and organized. The renal vesicle is the primordial structure of the nephron epithelium, and is formed by the condensation of mesenchymal cells." + "A retinal ganglion cell C inner that has sparse dendritic density, and large dendritic field." + "A bone that is part of the tarsal skeleton. Examples: calcaneus, talus, centralia." "SCTID:108372004 GAID:194 FMA:24491 UMLS:C0039316 galen:TarsalBone MESH:D013639 EMAPA:25072 BTO:0002343 MA:0000297 NCIT:C12796" + "An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof." + "The series of events required for an organism to receive a sensory electrical stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process." + "The chemical reactions and pathways resulting in the formation of ADP, adenosine 5'-diphosphate." + "Any process that modulates the frequency, rate, or extent of antigen processing and presentation of peptide antigen." + + "The process that gives rise to the cranial nerves. This process pertains to the initial formation of a structure from unspecified parts. The cranial nerves are composed of twelve pairs of nerves that emanate from the nervous tissue of the hindbrain. These nerves are sensory, motor, or mixed in nature, and provide the motor and general sensory innervation of the head, neck and viscera. They mediate vision, hearing, olfaction and taste and carry the parasympathetic innervation of the autonomic ganglia that control visceral functions." + "A crenated erythrocyte with 30+ crenations, bumps or spurs that are the result of damage due to age or disease." "FMA:81099" + "An exocrine gland whose secretions are excreted via exocytosis from secretory cells into an epithelial-walled duct or ducts and thence onto a bodily surface or into the lumen; the gland releases its product and no part of the gland is lost or damaged." "BTO:0002324 MA:0003041 Wikipedia:Merocrine" + "GC_ID:1 PMID:17572334" + "A flag amacrine cell with post-synaptic terminals in S2 and S3. This cell type releases the neurotransmitter glycine." + "An anatomical structure present only in hermaphrodites." "AEO:0000177 WBbt:0005758 EHDAA2:0003177" + "The subdivision of the skeleton that consists of all the skeletal elements at the distalmost end of the manual autopodium - i.e. the bones of the hands or their cartilaginous precursors[VSAO,modified]." "VSAO:0005029 FMA:71337 Wikipedia:Phalanges_of_the_hand" + "A portion of organism substance that is secreted by a female reproductive gland." "MA:0002510" + "A lamina propria that is part of a mucosa of fundus of stomach." "EMAPA:27163 FMA:17500" + "Organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP]." "VHOG:0001248 AAO:0000959 Wikipedia:Circulatory_system CALOHA:TS-2103" + "Any process that modulates the frequency, rate or extent of skeletal muscle tissue development." + "A small endodermal thickening in the foregut adjacent to the transverse septum. Invaginates forming the hepatic diverticulum." "ZFA:0000124 TAO:0000124 NCIT:C34277 EMAPA:16847 EHDAA2:0000744 AAO:0011058 BTO:0003391 XAO:0003266 EFO:0002577 UMLS:C1514451 EHDAA:973 UMLS:C0734013 EFO:0003428" + + "An anatomical cavity that is part of a segmental bronchus." "FMA:62593" + "Obsolete. Use PO:0020019 from Plant Ontology instead. A haploid (1n) spore developing into a female gametophyte in heterosporous plants." + "That portion of the spine comprising the cervical vertebrae. The neck area of the spine." "EHDAA2:0000238 EMAPA:17215 BTO:0004148 MA:0003154 EHDAA:5051 NCIT:C69313 AAO:0000092 SCTID:260488005 UMLS:C0728985 FMA:24138" + "Any process in which a dense core granule is transported to, and/or maintained in, a specific location within the cell." + "The import of RNA from the cytoplasm to the nucleus." + "The chemical reactions and pathways resulting in the formation of glucans, polysaccharides consisting only of glucose residues." + "The layer located immediately above the pyramidal cell layer in CA2 and CA1 and superficial to the stratum lucidum in CA3. Suprapyramidal region in which CA3 to CA3 associational connections and CA3 to CA1 Schaffer collateral connections are located." "BIRNLEX:1298 neuronames:158 MA:0000959 FMA:83894 EMAPA:35413 BAMS:Rad" + "GC_ID:1" + "Outflow part of atrium which consists of wall and cavity of the outflow part of right atrium and the tricuspid valve.[FMA]." "FMA:9550" + "A submucosa that is part of a trigone of urinary bladder [Automatically generated definition]." "FMA:17852 EMAPA:32304" + "The terminal portion of the intestinal tube, terminating with the anus." "MESH:D012007 EV:0100081 EHDAA2:0001592 CALOHA:TS-1180 SCTID:181261002 MAT:0000050 Wikipedia:Rectum EHDAA:5836 EMAPA:17896 EFO:0000848 galen:Rectum VHOG:0001751 BTO:0001158 AAO:0010401 MA:0000336 GAID:311 UMLS:C0034896 FMA:14544 XAO:0000238 MIAA:0000050 NCIT:C12390" + "A quality of continuant that exist at the anatomical level of organisation and anything under it. This includes, but is not limited to, cells , tissues, and components." + "Any process that activates or increases the frequency, rate or extent of a cytokine mediated signaling pathway." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances." + "Any process that modulates the frequency, rate or extent of transport across the blood-brain barrier." + "Any muscle organ that is part of a manus [Automatically generated definition]." "FMA:37372 EMAPA:32644 MA:0000628 SCTID:110540008" + "Any process that activates or increases the frequency, rate or extent of the formation of a cilium." + "The process in which anatomical structures of the uterus are generated and organized." + "The most superficial layer of the neocortex characterized by a paucity of cell bodies." "neuronames:2444 EMAPA:35255 PBA:294021786 NLXANAT:090807 BTO:0004906 MA:0000897 UMLS:C1709063 NCIT:C33137 FMA:83900 ABA:CTX1" + "An embryonic structure positioned halfway between the prospective eye and ear, adjacent to the future midbrain-hindbrain boundary. The profundal and the trigeminal ganglia are separate distally but fused at their proximal end as they condense around NF stage 24." "XAO:0004093" + "A viscus that is part of a abdomen." "FMA:32413 FMA:67355" + "A process in which a protein is transported to, or maintained in, a location within a lysosome." + "Any process that increases the rate, frequency, or extent of neural retina development, the progression of the neural retina over time from its initial formation to the mature structure. The neural retina is the part of the retina that contains neurons and photoreceptor cells." + "The process whose specific outcome is the progression of the metanephric glomerular mesangium over time, from its formation to the mature structure. The metanephric glomerular mesangium is the thin membrane connective tissue composed of mesangial cells in the metanephros, which helps to support the capillary loops in a renal glomerulus." + "Any process that activates or increases the frequency, rate or extent of hematopoietic progenitor cell differentiation." + "Lining of the head of the uterus (cervix); contains large branched glands; does not undergo sloughing." "BTO:0000411" + "The progression of the dermatome over time, from its initial formation to the mature structure. The dermatome is the portion of a somite that will form skin." + "The controlled breakdown of the nuclear membranes during the second division of meiosis." + "Skeletogenic cell that secretes dentine matrix, is derived from the odontogenic papilla, and develops from a preodontoblast cell." "FMA:62999 MESH:D009804 BTO:0001769 CALOHA:TS-0696" + "Any process that modulates the frequency, rate or extent of melanocyte differentiation." + "Any nerve that innervates the penis." "EMAPA:35057" + "A mucosa that is part of a small intestine [Automatically generated definition]." "MA:0002686 UMLS:C0227261 CALOHA:TS-0941 SCTID:362144000 NCIT:C33568 BTO:0001259 FMA:14933 EMAPA:35780" + + "The process in which a chondroblast acquires specialized structural and/or functional features of a chondrocyte. A chondrocyte is a polymorphic cell that forms cartilage." + "A G11 retinal ganglion cell that has post synaptic terminals in sublaminar layer S2 and is depolarized by decreased illumination of their receptive field center" "https://orcid.org/0000-0001-7258-9596 https://orcid.org/0000-0002-5260-9315" + "A synapse that uses dopamine as a neurotransmitter." + "A longitudinal muscle layer of muscular coat that is part of a large intestine smooth muscle." "EMAPA:37559 MA:0001549 FMA:63637" + "EMAPA:32951" + "The perichondrium consists of two separate layers: an outer fibrous layer and inner chondrogenic layer. The chondrogenic layer remains undifferentiated and can form chondroblasts or chondrocytes." "BTO:0005090 Wikipedia:The_Free_Encyclopedia" + "The commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells within a field of cells that will exhibit a certain pattern of differentiation. Positional information is established through protein signals that emanate from a localized source within a developmental field resulting in specification of a cell type. Those signals are then interpreted in a cell-autonomous manner resulting in the determination of the cell type." + "The developmental process pertaining to the initial formation of the sinus venosus from unspecified parts. The sinus venosus is a heart chamber attached to the atrium on the venous side of the embryonic heart." + "Any process that activates or increases the frequency, rate or extent of immature T cell proliferation in the thymus." + "Any excreted gas that is produced by the digestive tract." "FMA:78440" + "An epithelium that is part of a midgut." "EHDAA2:0001195 MA:0003205 EMAPA:16569 BTO:0005053" + "A protein complex which is capable of protein kinase activity." + "An endothelium that is part of an artery [Automatically generated definition]." "EMAPA:35148 VHOG:0001215 BTO:0004757 NCIT:C49194 AAO:0011013 UMLS:C1179025 XAO:0000357 MA:0000707 FMA:62116" + "Layer of hippocampus area CA3 lying superficial to the pyramidal cell layer that contains mossy fiber axons projecting from the dentate gyrus. A slight thickening in this layer marks the border in some species between areas CA2 and CA3. dapted from Paxinos, G. The rat central nervous system, 2nd ed, Academic Press, San Diego, 1995, pg. 460)." "EMAPA:35411 OldNeuroNames:-975815906 Wikipedia:Stratum_lucidum_of_hippocampus neuronames:1777 UMLS:C0221922 BIRNLEX:4108 BAMS:SLu" + "A bone that is part of the metacarpal skeleton." "EFO:0003886 Wikipedia:Metacarpal_bone UMLS:C0025526 MA:0000302 FMA:9612 galen:Metacarpal NCIT:C12751 SCTID:181977005 SCTID:425761003 EMAPA:36158" + "The process whose specific outcome is the progression of a sinoatrial (SA) node cell over time, from its formation to the mature state. SA node cells are pacemaker cells that are found in the sinoatrial node." + "EMAPA:32849" + "Any biological process involved in the maintenance of the steady-state number of hepatocytes within a population of cells. Hepatocytes are specialized epithelial cells of the liver that are organized into interconnected plates called lobules." + "The chemical reactions and pathways resulting in the breakdown of acetylcholine, the acetic acid ester of the organic base choline." + "EMAPA:32850 VHOG:0000953" + "Predominantly extrahepatic bile duct which is formed by the junction of the right and left hepatic ducts, which are predominantly intrahepatic, and, in turn, joins the cystic duct to form the common bile duct[GAID]. The common hepatic duct is the duct formed by the convergence of the right hepatic duct (which drains bile from the right functional lobe of the liver) and the left hepatic duct (which drains bile from the left functional lobe of the liver). The common hepatic duct then joins the cystic duct coming from the gallbladder to form the common bile duct[WP]." "FMA:14668 Wikipedia:Common_hepatic_duct GAID:286 MESH:D006500 MA:0002660 VHOG:0000220 NCIT:C32356 UMLS:C0019149 SCTID:245403006 EMAPA:19101" + "The covalent alteration of one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological macromolecule, resulting in a change in its properties." + "A mono-stratified retinal ganglion cell that has a large dendritic field and a medium dendritic arbor with post synaptic terminals in sublaminar layer S1 and S2." + "A slender neuron projection bundle[FBbt]; A bundle of anatomical fibers, as of muscle or nerve (American Heritage Dictionary 4th ed)." "UMLS:C1185741 BIRNLEX:872 NCIT:C32586 Wikipedia:Nervous_system_fascicle BTO:0002191 FMA:12235 EMAPA:36605 TGMA:0000088" + "The directed movement of an ammonium ion from outside of a cell, across the plasma membrane and into the cytosol." + + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus." + + "The progression of the intrahepatic bile ducts over time, from their formation to the mature structure. Intrahepatic bile ducts (bile ducts within the liver) collect bile from bile canaliculi in the liver, and connect to the extrahepatic bile ducts (bile ducts outside the liver)." + "A concave nucleus shape where the indentation is smaller than half of the distance to the farthest nuclear margin." + "Any process that stops, prevents or reduces the frequency, rate or extent of skeletal muscle cell differentiation." + "Any process that stops, prevents, or reduces the frequency, rate or extent of growth of an organism to reach its usual body size." + "The metacarpus is the intermediate part of the manus skeleton that is located between the phalanges (bones of the fingers) distally and the carpus which forms the connection to the forearm. The metacarpus consists of metacarpal bones. The metacarpals form a transverse arch to which the rigid row of distal carpal bones are fixed. The peripheral metacarpals (those of the thumb and little finger) form the sides of the cup of the palmar gutter and as they are brought together they deepen this concavity. The index metacarpal is the most firmly fixed, while the thumb metacarpal articulates with the trapezium and acts independently from the others. The middle metacarpals are tightly united to the carpus by intrinsic interlocking bone elements at their bases. The ring metacarpal forms a transitional element of the semi-independent last metacarpal. [WP,unvetted]." "Wikipedia:Metacarpus MESH:D050279 FMA:71336 VSAO:0005026 XAO:0003208 AAO:0000946" + "The process whose specific outcome is the progression of the ureteric bud over time, from its formation to the mature structure." + "The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a mast cell. A mast cell is a cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation." + "The process whose specific outcome is the progression of a caecum over time, from its formation to the mature structure." + "A lymphatic vessel that supplies the small intestine." + "An epithelium that lines the nasal cavity." "FMA:63140 CALOHA:TS-0656 VHOG:0000501 EMAPA:17605 MA:0001324 NCIT:C49261 EHDAA:6803 UMLS:C1709151 EHDAA2:0001227" + "Any process that modulates the frequency, rate or extent of the sensory perception of pain, the series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal." + "The part of the central nervous system lying between the medulla oblongata and the midbrain, ventral to the cerebellum." "DHBA:10661 MIAA:0000115 MESH:D011149 neuronames:547 HBA:9131 EV:0100253 VHOG:0001176 BM:Pons GAID:578 FMA:67943 MBA:771 BTO:0001101 EFO:0001394 Wikipedia:Pons NCIT:C12511 UMLS:C0032639 CALOHA:TS-0813 EHDAA2:0004394 MAT:0000115 BIRNLEX:733 BAMS:PONS UMLS:C1280999 EMAPA:17563 SCTID:279103004 MA:0000204 BAMS:Pons" + "An immunoglobulin gamma Fc receptor II/III/IV that is a translation product of the human FCGR2B gene or a 1:1 ortholog thereof." + "A specialized accessory gland of the skin of mammals that secretes milk. The gland is typically only developed in females, and regresses in males." "MIAA:0000073 SCTID:361720005 EMAPA:17759 MESH:D008321 Wikipedia:Mammary_gland MAT:0000073 EFO:0000854 MA:0000145 VHOG:0000398 EV:0100125 FMA:286452 BTO:0000817 NCIT:C12367 UMLS:C0929301 CALOHA:TS-0595" + "A protein that is a type I transmembrane receptor with an N-terminal cysteine-rich domain, a single Fibronectin type II (FNII) domain (Pfam:PF00040) and eight to ten copies of the Lectin C-type domain (Pfam:PF00059) (CTLDs). The presence of multiple copies of the CTLD domain is a hallmark of this class." "PIRSF:PIRSF002427" + + "A mesothelial cell capable of circulating in the blood by first losing its squamous character. This cell can incorporate into the regenerating mesothelium." "FMA:86712" + "A goblet cell that is located in the colon." + "Any process that stops, prevents or reduces the frequency, rate or extent of muscle tissue development." + "The dorsal portion of the first pharyngeal arch, comprising the upper jaw[ZFIN,VHOG]." "ZFA:0001272 EFO:0003659 TAO:0001272" + "The process in which a subpopulation of granulosa cells surrounding the oocyte acquires the specialized features of an ovarian cumulus cell." + "Any process that activates or increases the frequency, rate or extent of smooth muscle cell differentiation." + "A portion of skeletal muscle tissue that is part of a pharynx [Automatically generated definition]." "EMAPA:18963" + "The lipid bilayer surrounding an azurophil granule, a primary lysosomal granule found in neutrophil granulocytes that contains a wide range of hydrolytic enzymes and is released into the extracellular fluid." + "A transmembrane protein complex composed of an MHC class II alpha and MHC class II beta chain, and with or without a bound peptide or polysaccharide antigen." + "Any process that stops, prevents or reduces the frequency, rate or extent of DNA biosynthetic process." + "Columnar cell which populate the epithelium of large intestine and absorb water. This cell is the most numerous of the epithelial cell types in the large intestine; bear apical microvilli, contain secretory granules in their apical cytoplasm; secretion appears to be largely mucins, but is also rich in antibodies of the IgA type." "FMA:63638 FMA:66771 BTO:0002484" + "The process in which a relatively unspecialized cell acquires specialized features of a skeletal muscle cell, a somatic cell located in skeletal muscle." + "The thick capsule of dense irregular connective tissue that surrounds each adrenal gland and contains scattered elastic fibers; the capsule contains a rich plexus of blood vessels (mainly small arteries) and numerous nerve fibers; some blood vessels and nerves enter the substance of the gland in the trabeculae that extend inward from the capsule and then leave the trabeculae to enter the cortex." "NCIT:C32050 MA:0000117 UMLS:C1181304 FMA:69087" + "SCTID:280300006 FMA:14469 EMAPA:25350 MA:0001107" + "Any process that mediates the transfer of information from one cell to another and contributes to the progression of the lung, from its initial state to the mature structure." + "A neutrophil precursor in the granulocytic series, being a cell intermediate in development between a promyelocyte and a metamyelocyte; in this stage, production of primary granules is complete and neutrophil-specific granules has started. No nucleolus is present. This cell type is CD13-positive, CD16-negative, integrin alpha-M-positive, CD15-positive, CD33-positive, CD24-positive, C/EBP-a-positive, C/EBPe-positive, PU.1-positive, lactotransferrin-positive, myeloperoxidase-positive and NGAL-positive." "BTO:0003455 FMA:83540" + "Any skin fibroblast that is part of a skin of abdomen." + "The process in which the anatomical structures of the mesonephric duct are generated and organized. A mesonephric duct is a tube drains the mesonephros." + "A portion of tissue that will develop into vasculature." "TAO:0005076 ZFA:0005076 EFO:0003708" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways leading to the breakdown of amines." + "The region of the liver lobule that is closest to the central vein. The functionally-defined hepatic acinus zone 3 is generally found in this region." + "Lip that covers the upper portion of the mouth.[TAO]." "VHOG:0001750 Wikipedia:Upper_lip ZFA:0005226 TAO:0001970 MA:0000919 FMA:59817 EMAPA:17925 SCTID:245776003" + "GC_ID:1" + "Cell-cell signaling to, from or within a synapse." + "The process in which nerve cells are generated. This includes the production of neuroblasts and their differentiation into neurons." + "Brush cell found in the epithelial layer of the colon." "FMA:263222" + "A portion of connective tissue that is part of a hand [Automatically generated definition]." "EMAPA:35392 MA:0000620" + "Any process that stops, prevents, or reduces the frequency, rate or extent of biomineral tissue development, the formation of hard tissues that consist mainly of inorganic compounds." + "A muscle of shoulder which attaches to the scapula, clavicle and humerus.[FMA,generalized]." "VHOG:0000846 EFO:0001412 AAO:0010716 MA:0002286 UMLS:C0224234 EHDAA2:0000339 SCTID:181620007 NCIT:C32446 Wikipedia:Deltoid_muscle FMA:32521 EMAPA:18177" + "Part of the hippocampal formation forming a 'V' or 'U' shaped structure with the opening bounded by hippocampal area CA3. It consists of 3 layers from superficial to deep: molecular, granule cell and polymorphic or hilar layer." "HBA:12891 BM:Tel-DG SCTID:279211002 DMBA:16115 EMAPA:19037 Wikipedia:Dentate_gyrus BTO:0002615 CALOHA:TS-2388 GAID:624 UMLS:C0152314 BTO:0002496 MA:0000190 MBA:726 DHBA:10295 BAMS:DG neuronames:179 NCIT:C32452 MESH:D018891 BIRNLEX:1178 FMA:61922 EFO:0001366" + "The process in which an activated T cell acquires specialized features of an exhausted T cell." + "FMA:14468 MA:0001108 SCTID:280299003 EMAPA:17275" + "Generation of the male gamete; specialised haploid cells produced by meiosis and along with a female gamete takes part in sexual reproduction." + "A natural killer cell that is developmentally immature and expresses natural killer cell receptors (NKR)." + "A CD24-low, CD44-negative, NK1.1-negative NK T cell." + + "The increase in size or mass of the heart." + "An anatomical junction that is between the sigmoid colon and rectum." "NCIT:C54188 SCTID:245429006" + "The process in which a relatively unspecialized cell acquires specialized features of a neuron of the posterior lateral line ganglion." + "The process in which a nuclear membrane is synthesized, aggregates, and bonds together." + "An iliac bone or its cartilage or pre-cartilage precursor." + "The process whose specific outcome is the progression of the His-Purkinje system over time, from its formation to the mature structure. The His-Purkinje system receives signals from the AV node and is composed of the fibers that regulate cardiac muscle contraction in the ventricles." + "The regulated release of dopamine by a cell. Dopamine is a catecholamine and a precursor of adrenaline and noradrenaline. It acts as a neurotransmitter in the central nervous system but it is also produced peripherally and acts as a hormone." + "A mesangial cell located among the glomerular capillaries in a renal corpuscle." "KUPO:0001032" + "A portion of the urogenital ridge which is the source of much of the urinary system[WP]." "NCIT:C34219 Wikipedia:Nephrogenic_cord SCTID:361405003 FMA:72168 UMLS:C1283944" + "Any meiotic cell cycle process that is involved in oocyte maturation." + "A portion of cardiac muscle tissue that is part of a trabecula carnea [Automatically generated definition]." "MA:0002833 FMA:84428 EMAPA:36573" + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a vesicle." + "EMAPA:16906 VHOG:0000912 EHDAA2:0000397" + "An epithelial cell that is part of the urethra." "FMA:256165" + "An acinus that is part of a mammary gland." "FMA:74438" + "An asexual, nonmotile spore formed by higher fungi; conidia are usually made from the side or tip of specialized sporogenous cells and do not form by progressive cleavage of the cytoplasm." "FAO:0000024 BTO:0000283" + "A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form." + "A cell whose primary function is to cause growth by stimulating cell division in its immediate cellular environment." + "Skeletogenic cell that is terminally differentiated, secretes an avascular, GAG-rich matrix, is embedded in cartilage tissue matrix, retains the ability to divide, and develops from a chondroblast cell." "BTO:0000249 FMA:66782 CALOHA:TS-0138" + "The progression of the olfactory lobe over time from its initial formation until its mature state. The olfactory lobe is the area of the brain that process the neural inputs for the sense of smell." + "Columnar glandular cell with irregular nucleus, copious granular endoplasmic reticulum and supranuclear granules. Secretes a watery fluid containing proteins known as serous fluid." "FMA:62511 BTO:0003687" + "OBSOLETE: Subpopulation of CD4+ cells which induce CD8+ suppressor T cells to suppress antibody production by B cells. They also stimulate other cellular immune responses." + "A CD8-positive alpha beta-positive T cell with the phenotype FoxP3-positive and having suppressor function." + "CALOHA:TS-1249" + "The process whose specific outcome is the progression of Peyer's patches over time, from their formation to the mature structure. Peyer's patches are typically found as nodules associated with gut epithelium with distinct internal structures including B- and T-zones for the activation of lymphocytes." + "Cranial nerve that innervates the muscles of the tongue." "UMLS:C0020614 MA:0001094 NCIT:C12732 BTO:0003386 AAO:0010477 MESH:D007002 BIRNLEX:820 FMA:50871 Wikipedia:Hypoglossal_nerve BAMS:12n BAMS:XIIn EMAPA:17269 VHOG:0000693 EHDAA2:0000798 GAID:828 neuronames:704 SCTID:362471008 MBA:813 HBA:9343 XAO:0004215 BAMS:nXII EHDAA:2859" + "Programmed cell death of an errant germ line cell that is outside the normal migratory path or ectopic to the gonad. This is an important mechanism of regulating germ cell survival within the embryo." + "A regulatory T cell that has not encountered antigen." + "The process in which an amino acid is transported from one side of the vacuolar membrane to the other." + "An organ that is part of a chest [Automatically generated definition]." "MA:0000552 EMAPA:37272" + "The inferior labial vein is the vein receiving blood from the upper lip." "SCTID:422755007 MA:0002255 FMA:52538 EMAPA:37204 Wikipedia:Superior_labial_vein" + "Enables the transfer of neutral L-amino acids from one side of a membrane to the other. Neutral amino acids have side chains with no charge at pH 7.3." + "Any process that stops, prevents or reduces the frequency, rate or extent of dopamine biosynthetic process." + "Any process that activates or increases the frequency, rate or extent of postsynaptic membrane organization." + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an aldosterone stimulus." + "An OFF diffuse bipolar cell that makes synaptic contact with both L/M and S-cone photoreceptors and only minimal contact with rod photoreceptors." + "The directed orientation of lymphocyte signaling molecules and associated membrane rafts towards a chemokine gradient or a contact point with an appropriate activating cell." + "A sweat gland that is part of the skin of the palmar part of the manus or plantar part of the pes." + "Any process that stops, prevents or reduces the frequency, rate or extent of tight junction disassembly." + "A CD9 molecule that is encoded in the genome of mouse." "UniProtKB:P40240" + "The process whose specific outcome is the progression of rhombomere 1 over time, from its formation to the mature structure. Rhombomeres are transverse segments of the developing rhombencephalon. Rhombomeres are lineage restricted, express different genes from one another, and adopt different developmental fates. Rhombomeres are numbered in anterior to posterior order." + "The median preoptic nucleus is located along the midline in a position significantly dorsal to the other 3 preoptic nuclei, at least in the macaca fascicularis brain. It wraps around the top (dorsal), front, and bottom (ventral) surfaces of the anterior commissure. The median preoptic nucleus generates thirst. Drinking decreases noradrenaline release in the median preoptic nucleus." "neuronames:378 HBA:4548 BM:MPO Wikipedia:Preoptic_area#Median_preoptic_nucleus BIRNLEX:1208 BAMS:MEPO FMA:62323 BAMS:MnPO DHBA:13063 UMLS:C0259793 MBA:452" + "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the mesenchymal cells of bone as it progresses from its formation to the mature state." + "Any process that activates or increases the frequency, rate or extent of artery morphogenesis." + "Subcortical nucleus of telecephalic origin consisting of an elongated gray mass lying lateral to and bordering the lateral ventricle. It is divided into a head, body and tail in some species." "UMLS:C0007461 Wikipedia:Caudate_nucleus SCTID:279297002 BTO:0000211 MAT:0000513 BIRNLEX:1373 EHDAA2:0004461 EV:0100185 HBA:4278 DHBA:10334 GAID:670 BAMS:CA CALOHA:TS-0121 EFO:0000907 BM:Tel-CA neuronames:226 MA:0000894 PBA:10082 FMA:61833 DMBA:15855 BAMS:Cd EMAPA:18207 NCIT:C12451 MESH:D002421" + "Any process that modulates the frequency, rate or extent of apoptotic process involved in outflow tract morphogenesis." + "A smooth muscle cell that is part of the small intestine." "FMA:15050" + "The process in which a precursor cell type acquires the specialized features of a dendritic cell. A dendritic cell is a leukocyte of dendritic lineage specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation." + "Portion of tissue that is the outer layer of the optic cup and will become the retinal pigmented epithelium." "EHDAA2:0001306 VHOG:0000492 TAO:0000064 ZFA:0000064 EMAPA:16677" + "A blood vessel endothelium that is part of a lung [Automatically generated definition]." "BTO:0004128 CALOHA:TS-0573" + "The mesonephric glomerular mesangium is the thin membrane connective tissue composed of mesangial cells in the mesonephros, which helps to support the capillary loops in a renal glomerulus." + "Any process that activates or increases the frequency, rate or extent of synaptic vesicle exocytosis." + "A relaxin receptor 1 that is encoded in the genome of mouse." "UniProtKB:Q6R6I7" + "The process in which neuroepithelial cells in the neural tube acquire specialized structural and/or functional features of basal progenitor cells, neuroblasts that lose their contacts with the ventricular surface. Differentiation includes the processes involved in commitment of a cell to a specific fate." + "The process whose specific outcome is the progression of a columnar/cuboidal epithelial cell of the intestine over time, from its formation to the mature structure." + "Either of a pair of glandular pouches that lie one on either side of the male reproductive tract posterolateral to the urinary bladder and in the human male secrete a sugar- and protein-containing fluid into the ejaculatory duct." "AAO:0010788 EFO:0000986 VHOG:0001379 MAT:0000171 EMAPA:19180 UMLS:C0036628 SCTID:181434004 CALOHA:TS-0919 MA:0000410 GAID:394 MIAA:0000171 EV:0100106 FMA:19386 NCIT:C12787 Wikipedia:Seminal_vesicle MESH:D012669 BTO:0001234" + "The space between the arachnoid and pia mater." "EMAPA:32666 GAID:689 BTO:0000230 Wikipedia:Subarachnoid_space MESH:D013346 FMA:83716 SCTID:362311001" + "A resident stromal cell located in the synovial membrane and responsible for the production of immune-related cytokines and chemokines. This cell type secretes glycoproteins and hyaluronic acid, has abundant granular endoplasmic reticulum, but contains fewer vacuoles and vesicles." "BTO:0003652 FMA:66788" + "An epidermal cell that is part of a cell cluster organ of the insect integument (such as a sensillum) and that secretes a cuticular specialization that forms a socket around the base of a cuticular specialization produced by a trichogen cell." "FBbt:00005171" + "KUPO:0001088" + "An adipose dendritic cell that is SIRPa-positive." + "A smooth muscle cell that is part of the ileum." "FMA:15066" + "A cell located between the pinealocytes." "FMA:86575" + "The cellular developmental process, independent of morphogenetic (shape) change, that is required for a specific cell to attain its fully functional state." + "An anatomical cluster that composed_primarily_of a strand of hair." "FMA:70752" + "Any process that modulates the rate or extent of striated muscle cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a striated muscle cell and result in its death." + "Any process that stops, prevents or reduces the frequency, rate or extent of leukocyte cell-cell adhesion." + "Pyramidal neurons have a pyramid-shaped soma with a single axon, a large apical dendrite and multiple basal dendrites. The apex and an apical dendrite typically point toward the pial surface and other dendrites and an axon emerging from the base. The axons may have local collaterals but also project outside their region. Pyramidal neurons are found in the cerebral cortex, the hippocampus, and the amygdala." "FMA:86775 NIFSTD:sao862606388 BTO:0003102 FMA:67310" + "A protein with core architecture consisting of a signal sequence, followed by 7 Ig-like domains (Pfam:PF00047, Pfam:PF07679, or Pfam:PF07686), a transmembrane region, and a cytoplasmic Protein tyrosine kinase domain." "PIRSF:PIRSF038502" + "A ribosome located in the cytosol." + "The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent." + "A chemokine receptor that is a translation product of the human CXCR3 gene or a 1:1 ortholog thereof. The preferred ligands include CXCL9, CXCL10, CXCL11." "IUPHARobj:70 PIRSF:PIRSF501023" + "The directed movement of proteins along microtubules from the cell body toward the cell periphery in nerve cell axons." + "The process whose specific outcome is the progression of an immature germ cell over time, from its formation to the mature structure (gamete). A germ cell is any reproductive cell in a multicellular organism." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of a myeloid cell apoptotic process." + "Any developmental process that results in the creation of defined areas or spaces within the metanephros to which cells respond and eventually are instructed to differentiate." + "A vein that is part of a respiratory system [Automatically generated definition]." "MA:0001809 EMAPA:37584 MA:0001810" + "The process in which the anatomical structures of the neurohypophysis are generated and organized. The neurohypophysis is the part of the pituitary gland that secretes hormones involved in blood pressure regulation." + "Gr1-low non-classical monocyte that has low to intermediate expression of the MHC-II complex." + "The costocervical trunk arises from the upper and back part of the subclavian artery, behind the scalenus anterior on the right side, and medial to that muscle on the left side. Passing backward, it splits into the deep cervical artery and the supreme intercostal artery (or the Highest intercostal artery), which descends behind the pleura in front of the necks of the first and second ribs, and anastomoses with the first aortic intercostal (3rd posterior intercostal artery). As it crosses the neck of the first rib it lies medial to the anterior division of the first thoracic nerve, and lateral to the first thoracic ganglion of the sympathetic trunk. In the first intercostal space, it gives off a branch which is distributed in a manner similar to the distribution of the aortic intercostals. The branch for the second intercostal space usually joins with one from the highest aortic intercostal artery. This branch is not constant, but is more commonly found on the right side; when absent, its place is supplied by an intercostal branch from the aorta. Each intercostal gives off a posterior branch which goes to the posterior vertebral muscles, and sends a small spinal branch through the corresponding intervertebral foramen to the medulla spinalis and its membranes. [WP,unvetted]." "FMA:10636 Wikipedia:Costocervical_trunk EMAPA:37496 SCTID:244225009 MA:0001939" + "A process required for sperm to reach fertilization competence. Sperm undergo an incompletely understood series of morphological and molecular maturational processes, termed capacitation, involving, among other processes, protein tyrosine phosphorylation and increased intracellular calcium." + "The series of events in which a mechanical stimulus is received and converted into a molecular signal as part of sensory perception." + "A protein that is a translation product of the human FOXP3 gene or a 1:1 ortholog thereof." + "The process in which the anatomical structures of the metanephric glomerulus vasculature are generated and organized. The metanephric glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the metanephric glomerulus." + "An epithelial cell that is part of the amnion." + "An epithelial cell of stratum corneum of esophageal epithelium." "FMA:70733" + "Any process that activates or increases the frequency, rate or extent of endothelial tube morphogenesis." + "The regulated release of gamma-aminobutyric acid by a cell or a tissue. The gamma-aminobutyric acid is the principal inhibitory neurotransmitter in the brain but is also found in several extraneural tissues." + "Any process that increases the rate, frequency or extent of ribosome biogenesis. Ribosome biogenesis is the cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits." + "A change in morphology and behavior of a lymphocyte resulting from exposure to a specific antigen, mitogen, cytokine, chemokine, cellular ligand, or soluble factor." + "Any process that modulates the frequency, rate or extent of the growth of all or part of an organism so that it occurs at its proper speed, either globally or in a specific part of the organism's development." + "Any process that activates or increases the frequency, rate or extent of smooth muscle contraction." + "The process in which the branching structure of the seminal vesicle is generated and organized. A branch is a division or offshoot from a main stem." + "A cell that is part of a nephron tubule." "KUPO:0001020" + "Any process that mediates the transfer of information from endodermal cells to mesodermal cells." + "Any process that activates or increases the frequency, rate or extent of oogenesis." + "A blood vessel that is part of a eyelid [Automatically generated definition]." "MA:0001250 EMAPA:37388" + "The epithelial lining of the luminal space of the kidney pelvis." "MA:0002632 NCIT:C54556 FMA:263264 EMAPA:28077 UMLS:C1709899" + "The regulated release of calcitonin, a peptide hormone that participates in calcium and phosphorus metabolism, from a cell." + "That portion of the chorionic wall in the region of its uterine attachment, which gives rise to chorionic villi; it consists of the mesoderm that lines the chorionic vesicle and, on the maternal side, of the trophoblast that lines the intervillous spaces; in the last half of gestation, the mesodermal connective tissue is largely replaced by fibrinoid material, and the amnionic membrane is adherent to the fetal side of the plate." "SCTID:256391000 UMLS:C0230972 NCIT:C34123 EMAPA:31872 BTO:0002879" + "A shape quality in which a portion of the outermost boundary of an entity folds in space such that a portion that was originally convex is now concave." + "Any bone that is part of the upper jaw skeleton. This includes (when present): the maxilla, the quadrate (in some species)." + "The multiplication or reproduction of cells, resulting in the expansion of a cell population in the midbrain." + "The distal elements of the developing limb of vertebrates that will give rise to the manus (hand)." "EHDAA:4194 FMA:296794 EHDAA:6242 NCIT:C34185 EMAPA:17245 UMLS:C1512334" + "An unpaired bone situated at the base of the skull in front of the temporal bone and basilar part of the occipital bone. The sphenoid bone is one of the seven bones that articulate to form the orbit. Its shape somewhat resembles that of a butterfly or bat with its wings extended." "FMA:52736 MA:0001472 MESH:D013100 UMLS:C0037884 NCIT:C12790 Wikipedia:Sphenoid_bone EMAPA:18340 GAID:230 CALOHA:TS-2343 SCTID:272676008" + "The clusters of neurons in the somatic peripheral nervous system which contain the cell bodies of sensory nerve axons, interneurons and non-neuronal supporting cells." "AEO:0001000 UMLS:C0206429 EMAPA:36596 MESH:D017950 FMA:5885 NCIT:C13060 BTO:0005630 MA:0002566" + "A protein complex that is capable of G protein-coupled serotonin receptor activity." + "A mesopodial endochondral element that is in the most proximal part of the mesopodial skeleton, connected to the zeugopodial skeleton." + "A process in which a calcium ion is transported from one side of a membrane to the other into the cytosol by means of some agent such as a transporter or pore." + "The cellular component assembly that is part of the initial shaping of the component during its developmental progression." + "Any process that modulates the rate or extent of progression through the meiotic cell cycle." + "The first few specialized divisions of an activated animal egg." + "The portion of neural plate anterior to the mid-hindbrain junction." "AAO:0011084 TAO:0007016 ZFA:0007016 VHOG:0001200 XAO:0000045" + "Any process that modulates the frequency, rate or extent of fat cell apoptotic process." + "An epithelial cell of the thymus. Epithelial reticular cells are pleomorphic, stellate, non-phagocytic cells which seem to be supportive in function and are held together by desmosomes. They replace the fibroblastoid reticular cells found in other lymphoid organs. Other epithelial cells in the medulla have the ultrastructure of secretory cells. Although different epithelial cells throughout the thymus appear alike by light microscopy their ultrastructure and function varies." "CALOHA:TS-1040 FMA:72208" + "The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers." "Wikipedia:Coagulation" + "A change in morphology and behavior of a leukocyte resulting from exposure to a specific antigen, mitogen, cytokine, cellular ligand, or soluble factor, leading to the initiation or perpetuation of an immune response." + "The layer of extracellular matrix that lies between the endothelium of the glomerular capillaries and the podocytes of the inner or visceral layer of the Bowman capsule; it is a fusion of the endothelial cell and podocyte basal laminas and acts as a physical barrier and an ion-selective filter." "TAO:0005285 UMLS:C0599297 ZFA:0005285 Wikipedia:Glomerular_basement_membrane EMAPA:28251 NCIT:C32683 SCTID:243897006 FMA:74274 MA:0001659 EMAPA:30965" + "A skeletal muscle fiber that is part of a muscle spindle. These are specialized muscle fibers that serve as proprioceptors, detecting the amount and rate of change in length of a muscle. They are innervated by both sensory neurons and motor neurons (gamma and beta motorneurons, collectively referred to as fusimotor neurons)." "TH:H3.03.00.0.00012" + "A process in which a protein is transported to, or maintained in, a location within a nucleolus." + "The regulated release of ecdysteroids, a group of polyhydroxylated ketosteroids which initiate post-embryonic development." + "Anatomical cluster consisting of adjacent teeth constituting a row." "ZFA:0001642 TAO:0001667 FMA:59415" + "An epithelial cell that is part of the appendix." "FMA:63602" + "The assembly and organization of the sperm flagellum, the microtubule-based axoneme and associated structures that are part of a sperm flagellum (or cilium)." + "A PP cell found in intestine." + "Any process that increases the rate, frequency, or extent of the progression of the dermatome over time, from its initial formation to the mature structure. The dermatome is the portion of a somite that will form skin." + "Joint cavity shared by all the joints of the elbow. The elbow joint is a compound joint that actually comprises three separate joints: the joints connecting the upper and lower arm: 1) Articulatio humero-ulnaris and 2) Articulatio humero-radialis as well as the proximal joint connecting the forarm bones: 3) Articulatio radio-ulnaris proximalis. All three share a joint cavity which is highly sinuated/scalloped/coved. Joint spaces of the elbow summarizes the joint cavity shared by all three adjoining joints of the elbow joint." "FMA:38911" + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a neuron, e.g. an axon, or a dendrite." + "Any process that stops, prevents, or reduces the frequency, rate or extent of cytotoxic T cell differentiation." + "Any process that stops, prevents or reduces the frequency, rate or extent of acinar cell proliferation." + "Any process that increases the rate, frequency or extent of mononuclear cell migration. Mononuclear cell migration is the movement of a mononuclear cell within or between different tissues and organs of the body." + "An epithelial cell of the uterus." "FMA:256161" + "The chemical reactions and pathways resulting in the breakdown of a phenol, any compound containing one or more hydroxyl groups directly attached to an aromatic carbon ring." "MetaCyc:PHENOLDEG-PWY" + "The directed movement of neutral amino acids, amino acids with no net charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "A preadipocyte that is part of subcutaneous tissue." + "A giant pyramidal neuron with a soma in layer Vb of the primary motor cortex that sends its axons down the spinal cord via the corticospinal tract, either synapsing directly with alpha motor neurons, or targeting interneurons in the spinal cord. In humans, Betz cells are the largest known in the central nervous system." + "Any process that activates or increases the frequency, rate or extent of muscle contraction." + "Any process that modulates the frequency, rate or extent of skeletal muscle contraction by depolarization of muscle membrane and ionic fluxes." + "The process whose specific outcome is the progression of a metanephric glomerular epithelial cell over time, from its formation to the mature structure. Metanephric glomerular epithelial cells are specialized epithelial cells that form part of the metanephric glomerulus; there are two types, metanephric glomerular parietal epithelial cells and metanephric glomerular visceral epithelial cells." + "A neuron projection quality that is a characteristic of neurons with projections that terminate locally rather than distantly." "ILX:0770103" + "Mesenchyme that surrounds primitive urogenital sinus." "EMAPA:31500" + "Any process that stops, prevents, or reduces the frequency, rate or extent of auditory hair cell differentiation." + "A portion of smooth muscle tissue that is part of the thoracic aorta." + "An artery that supplies the anterior chest wall and the breasts. It is a paired artery, with one running along each side of the sternum, to continue after its bifurcation as the superior epigastric and musculophrenic arteries. [WP,unvetted]." "EMAPA:18617 NCIT:C52941 MA:0001984 FMA:3960 UMLS:C0226276 SCTID:244239009 EHDAA2:0000880 Wikipedia:Internal_thoracic_artery MA:0001982 EHDAA:8585" + "A mono-stratified retinal ganglion cell that has a medium dendritic field and a medium dendritic arbor with post sympatic terminals in sublaminar layer S2." + "The generation and maintenance of gametes in a multicellular organism. A gamete is a haploid reproductive cell." + "Any process that modulates the frequency, rate or extent of trophectodermal cell proliferation." + "An anatomical space that surrounded_by a digestive tract." "FMA:45677 BTO:0000349 EMAPA:32908" + "KUPO:0001085" + "The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a pericardial nephrocyte. A pericardial nephrocyte is an insect renal cell that filters hemolymph and is found with other pericardial nephrocytes in two rows flanking the dorsal vessel. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state." + "A urethral meatus that is part of a female urethra[Automatically generated definition]." "Wikipedia:External_urethral_orifice_(female) FMA:85266 SCTID:279479008 EMAPA:36453 MA:0002639" + "The directed movement of epinephrine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "Anatomical space which contains portions of one or more body substances and is bounded by the internal surface of one maximally connected anatomical structure. Examples: cranial cavity, pharyngeal recess space, nasal cavity, tooth socket, cavity of serous sac, lumen of stomach, lumen of artery, fornix of vagina." "galen:Cavity MA:0002447 EMAPA:37442 FMA:67552 NCIT:C34007 BIRNLEX:1011" + "A Vgamma1.1-positive, Vdelta6.3-positive thymocyte that is CD24-negative." + "An adipocyte derived from a neural crest cell." + "The series of molecular signals generated as a consequence of the insulin receptor binding to insulin." + "A monocyte that expresses CD14 and is negative for the lineage markers CD3, CD19, and CD20." + "The process whose specific outcome is the progression of a noradrenergic neuron over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell." + "An epithelium that is part of a respiratory bronchiole [Automatically generated definition]." "FMA:62498 UMLS:C1179179 EMAPA:35730 MA:0001773 NCIT:C48943" + "A sac-like cavity ventral to the liver, lying in the sub-mesodermal space and closed by a thin sheet of ectodermal cells, from which the future gall bladder develops." "XAO:0004205 EMAPA:16713 EHDAA:3047 EHDAA2:0000700" + "Any muscle organ that is part of a hip [Automatically generated definition]." "MA:0000657" + "Any process that modulates the frequency, rate or extent of vascular smooth muscle cell proliferation." + "A midget ganglion cell that depolarizes in response to decreased light intensity in the center of its receptive field. The majority of input that this cell receives comes from flat midget bipolar cells." + "A proximal tarsal endochondral element that is composed primarily of a pre-cartilage condensation." + "A change in the morphology or behavior of a fibroblast resulting from exposure to an activating factor such as a cellular or soluble ligand." + "A vacuole that is maintained at an acidic pH and which contains degradative enzymes, including a wide variety of acid hydrolases." + "The adipose capsule of kidney (or perinephric fat or perirenal fat) is a structure between the renal fascia and renal capsule, and may be regarded as a part of the latter. A different structure, the pararenal fat, is the adipose tissue superficial to the renal fascia." "MA:0002975 SCTID:246901006 FMA:15876 Wikipedia:Adipose_capsule_of_kidney EMAPA:36495 FMA:20502" + "A composition quality inhering in an bearer by virtue of the bearer's consisting of collagen." + "A neurosecretory neuron residing mainly in the hypothalamic supraoptic and paraventricular nuclei and in a number of smaller accessory cell groups between these two nuclei, that is capable of secreting the hormones oxytocin or vasopressin, and sometimes both, into the systemic circulation." "ILX:0107463" + "A vetebrate lens cell that is any of the elongated, tightly packed cells that make up the bulk of the mature lens in a camera-type eye." + "The process whose specific outcome is the progression of the cardiac conduction system over time, from its formation to the mature structure. The cardiac conduction system consists of specialized cardiomyocytes that regulate the frequency of heart beat." + "An enucleate erythrocyte that is GlyA-positive." + "The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells." + "A plasmablast that secretes IgA." + "Enables the transfer of iron (Fe) ions from one side of a membrane to the other." "Reactome:R-HSA-5655733 Reactome:R-HSA-5623558 Reactome:R-HSA-904830 Reactome:R-HSA-917936 Reactome:R-HSA-435349" + "A G protein-coupled receptor signaling pathway initiated by glutamate binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process." + + "The process in which the anatomical structures of epithelia of the prostate gland are generated and organized. An epithelium consists of closely packed cells arranged in one or more layers, that covers the outer surfaces of the body or lines any internal cavity or tube." + "An extracellular matrix secreting cell that secretes eggshell." + "One of sublaminar layers S1, S2, or S3." "CP:0001042" + "The process whose specific outcome is the progression of the atrioventricular (AV) node over time, from its formation to the mature structure. The AV node is part of the cardiac conduction system that controls the timing of ventricle contraction by receiving electrical signals from the sinoatrial (SA) node and relaying them to the His-Purkinje system." + "The sensory system for the sense of taste." "MA:0002446 XAO:0003197 ZFA:0001101 MIAA:0000275 TAO:0001101 Wikipedia:Gustatory_system MAT:0000275 AAO:0010577 NLXANAT:090803 BILA:0000143 EFO:0000830 SCTID:423940004 neuronames:2889 FMA:7194" + "Any process that stops, prevents, or reduces the frequency, rate or extent of cell proliferation involved in heart morphogenesis." + "An undifferentiated fibroblast that can be stimulated to form a fat cell." "BTO:0001107" + "A zone of skin that is part of an abdomen [Automatically generated definition]." "FMA:22988 FMA:23000 UMLS:C0222166 SCTID:361707007 MA:0000523 EFO:0000214 NCIT:C52758" + "Any process that modulates the frequency, rate or extent of the directed movement of amines into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "Any process that stops, prevents or reduces the frequency, rate or extent of extracellular matrix assembly." + "A muscle cell that is part of the sinoatrial node." "FMA:67102" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures." + "Any process that activates or increases the frequency, rate or extent of myotome development." + "Portion of tissue that is the inner layer of the optic cup and will become the neural retina." "EMAPA:16675 ZFA:0001071 EHDAA2:0001304 TAO:0001071 VHOG:0000490" + "The process in which anatomical structures of the mammary gland buds are generated and organized. Mammary gland buds form by an outpocketing of the mammary placodes and grow to invade the mammary fat, when they form the mammary cord." + "A developmental process, independent of morphogenetic (shape) change, that is required for the ureter to attain its fully functional state. The ureter is a muscular tube that transports urine from the kidney to the urinary bladder or from the Malpighian tubule to the hindgut." + "A collection of Purkinje fibers that receives signals from the right and left bundle branches and innervates the ventricular cardiac muscle. The Purkinje fiber network creates synchronized contractions of the heart ventricles." + "A cervical vertebra endochondral element that is composed primarily of cartilage tissue." "EHDAA2:0000240" + "The process whose specific outcome is the progression of a somatotropin secreting cell over time, from its formation to the mature structure. A somatotropin secreting cell is an acidophilic cell of the anterior pituitary that produces growth hormone, somatotropin." + "BIRNLEX:1069 HBA:265505486 FMA:83942" + "A gastric gland in the cardiac region of the stomach; cardiac glands are fewer in number than in the fundus and body, and secrete mucin which coats the stomach and protects it[MP]." "SCTID:8894005 Wikipedia:Cardiac_glands EMAPA:37459 FMA:14920" + "A CD14-positive monocyte that is also CD16-positive and CCR2-negative." + "A diploid cell that has derived from a spermatogonium and can subsequently begin meiosis and divide into two haploid secondary spermatocytes." "FMA:72292 CALOHA:TS-2194 BTO:0001115" + "A urokinase plasminogen activator surface receptor that is encoded in the genome of mouse." "UniProtKB:P35456" + "The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon." + "The metanephric ascending thin limb is a segment of a nephron tubule in the metanephros lying in the inner medulla that is permeable to ions but not to water and has a simple epithelium; active transepithelial solute transport is absent[GO]." + "A cell capable of producing epinephrine. Epiniphrine is synthesized from norepiniphrine by the actions of the phenylethanolamine N-methyltransferase enzyme, which is expressed in the adrenal glands, androgenic neurons, and in other cell types." + "An embryonic anatomical entity that will turn into one or more other anatomical entities, perhaps with other anatomical entities, later in development." "AEO:0000132" + "A smooth muscle cell of the myometrium that enlarges and stretches during pregnancy, and contracts in response to oxytocin." "BTO:0004519" + "Intermediate segment of the autopod, between the mesopodial region and and acropodial region. Examples: metacarpal region, metatarsal region." "SCTID:370640001" + "A cell of the epithelial lining that produce and secrete mucins." "http://en.wikipedia.org/wiki/Goblet_cell FMA:13148 BTO:0001540" + "The process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin." + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mineralocorticoid stimulus. Mineralocorticoids are hormonal C21 corticosteroids synthesized from cholesterol and characterized by their similarity to aldosterone. Mineralocorticoids act primarily on water and electrolyte balance." + "The vesicular release of glutamate from a presynapse, across a chemical synapse, the subsequent activation of glutamate receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse." + "The cartilaginous joints of the skull; these include sphenoethmoidal synchondrosis, sphenooccipital synchondrosis, sphenopetrosal synchondrosis, petrooccipital synchondrosis, anterior intraoccipital synchondrosis and posterior intraoccipital synchondrosis." "EMAPA:35264 MA:0001502 FMA:54816 SCTID:314228003" + "Hyperpolarization (vertebrates) or depolarization (invertebrates) of the photoreceptor cell membrane via closing/opening of cation specific channels as a result of signals generated by rhodopsin activation by a photon." + "The creation of greater cell numbers in the forebrain due to cell division of progenitor cells." + "An artery with its origin in the lateral terminal branch of the internal thoracic artery, with distribution to the diaphragm and the intercostal muscles, and with anastomoses to the branches of the pericardiacophrenic and inferior phrenic." "FMA:10645 SCTID:244242003 Wikipedia:Musculophrenic_artery EMAPA:19215" + "A change in morphology and behavior of a macrophage resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor, leading to the initiation or perpetuation of an immune response." + "A dendritic cell that develops from a monocyte." + "A resident-dendritic cell that is part of a kidney." "KUPO:0001110" + "Any process that stops, prevents, or reduces the rate of leukocyte degranulation." + "A mesentery that is part of a foregut-midgut junction." "EHDAA2:0000575 EMAPA:16365 VHOG:0000430" + "A stage that follows the blastula, gastrula and neurula stages. At the pharyngula stage, all vertebrate embryos show remarkable similarities." "ZFS:0000050 OGES:000006 DrerDO:0000052 EFO:0001310 Wikipedia:Pharyngula" + "The part of the aorta that extends from the arch of the aorta to the diaphragm, and from which arises numerous branches that supply oxygenated blood to the chest cage and the organs within the chest." "EFO:0002527 FMA:87217 SCTID:181301002 EMAPA:18605 MA:0002572" + "The process in which the anatomical structure of the cerebellum is generated and organized. The cerebellum is the portion of the brain in the back of the head between the cerebrum and the pons. The cerebellum controls balance for walking and standing, modulates the force and range of movement and is involved in the learning of motor skills." + "The cerebral veins are divisible into external and internal groups according to the outer surfaces or the inner parts of the hemispheres they drain into. The external veins are the superior cerebral veins, inferior cerebral veins, and middle cerebral vein. [WP,unvetted]." "FMA:50981 MESH:D002550 EMAPA:37140 Wikipedia:Cerebral_veins GAID:530 UMLS:C0007797 NCIT:C53037 MA:0002096 XAO:0004160 SCTID:244392000" + "Any process that stops, prevents, or reduces the frequency, rate or extent of microtubule depolymerization; prevention of depolymerization of a microtubule can result from binding by 'capping' at the plus end (e.g. by interaction with another cellular protein of structure) or by exposing microtubules to a stabilizing drug such as taxol." + "A set of neural structures that subserve a specific function, e.g., visual system." "NLXANAT:090802" + "The appearance of a macrophage cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." + "A protein that is a translation product of the human IL17RB gene or a 1:1 ortholog thereof." "IUPHARobj:1739" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving ecdysteroids." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of glycogen." + "Mesenchymal derived lymphatic progenitor cells that give rise to the superficial lymphatics." + "A developmental process, independent of morphogenetic (shape) change, that is required for an anatomical structure to attain its fully functional state." + "An section of a respiratory tract." "FMA:45660 MA:0000434" + "Any process that stops, prevents or reduces the frequency, rate or extent of cerebellar neuron development." + "Any process that modulates the frequency, rate or extent of dendrite development." + "A cartilage tissue that is part of a pelvic appendage." "TAO:0001459 ZFA:0001459" + "The major preaxial endochondral bone in the posterior zeugopod[Phenoscape]." "MA:0001361 AAO:0000890 CALOHA:TS-1048 galen:Tibia SCTID:182061009 EFO:0003054 UMLS:C0040184 NCIT:C12800 EMAPA:19142 Wikipedia:Tibia FMA:24476 BTO:0001252 GAID:204 MESH:D013977" + "An epithelial cell that is part of a ureteric bud. A ureteric bud cell has the potential to induce metanephric mesenchymal cells to proliferate and convert to epithelia that form renal tubules via: (1) the secretion of multiple diffusible growth factors that rescue renal progenitors from apoptosis and stimulate them to proliferate and (2) contact-dependent mechanisms that induce mesenchymal-epithelial conversion." + "One of the gastric glands that secretes the hydrochloric acid of the gastric juice[Stedman's]." "FMA:14923 FMA:14921" + "A mesenchymal stem cell that is part of Wharton's jelly." + "A preadipocyte found in mesenteric tissue." + "A peptide hormone secreting cell that secretes vasopressin stimulating hormone" + "A cell extension caused by localized decoupling of the cytoskeleton from the plasma membrane and characterized by rapid formation, rounded shape, and scarcity of organelles within the protrusion. Blebs are formed during apoptosis and other cellular processes, including cell locomotion, cell division, and as a result of physical or chemical stresses." "Wikipedia:Bleb_(cell_biology)" + "A nerve that is part of a parasympathetic nervous system [Automatically generated definition]." "VHOG:0000641 SCTID:276146002 EHDAA2:0001401 EMAPA:17271 MA:0000224" + "An epithelial cell of the cervix." + "An arachnoid mater that is part of a midbrain [Automatically generated definition]." "MA:0001059 EMAPA:17792 VHOG:0000233" + "An epithelium that is part of a external ear." "EMAPA:35956 MA:0003170" + "Any process that modulates the frequency, rate or extent of L-glutamate import into a cell." + "Any process that modulates the frequency, rate or extent of cell fate commitment. Cell fate commitment is the commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells. Positional information is established through protein signals that emanate from a localized source within a cell (the initial one-cell zygote) or within a developmental field." + "Any process that modulates the frequency, rate or extent of granulocyte differentiation." + "Tolerance induction taking place in the mucosal-associated lymphoid tissue (MALT)." + "A zone of skin that is part of a limb [Automatically generated definition]." "EMAPA:32726 FMA:23100 UMLS:C1282135 MA:0000694 NCIT:C53276 SCTID:314403009" + "Upper portion of the skull that excludes the mandible (when present in the organism)." "MAT:0000340 EFO:0000831 BTO:0001328 MA:0000316 MIAA:0000340 FMA:71325 EHDAA:6029 Wikipedia:Cranium_(anatomy) VHOG:0000334 SCTID:181889008" + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glucocorticoids." + "A T-cell surface glycoprotein CD8 beta chain that is encoded in the genome of human." "UniProtKB:P10966" + "A cartilaginous condensation that has the potential to develop into a forelimb bone." "EMAPA:32626" + "A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude." + "The mesonephric glomerulus is a capillary tuft which forms a close network with the visceral epithelium (podocytes) and the mesangium to form the filtration barrier and is surrounded by Bowman's capsule in nephrons of the mature vertebrate kidney, or mesonephros[GO]." "EMAPA:30568 XAO:0000146 AAO:0010388 VHOG:0001238" + "Development of a photoreceptor, a cell that responds to incident electromagnetic radiation, particularly visible light." + "Any fibroblast that is part of a spleen." + "Any pericyte cell that is part of a brain." + "Generation and organization of a platelet, a non-nucleated disk-shaped cell formed by extrusion from megakaryocytes, found in the blood of all mammals, and mainly involved in blood coagulation." + "Any process that modulates the frequency, rate or extent of hepatic stellate cell migration." + "A bone that is part of a pectoral complex. Examples: scapula, manus phalanx, any carpal bone, any bone of the pectoral fin." "MA:0000612 EMAPA:35933" + "KUPO:0001048" + "The secretory neurons of the paraventricular nucleus that synthesize and secrete vasopressin, corticotropin-releasing factor (CRF) and thyrotropin-releasing hormone (TRH) into blood vessels in the hypothalamo-pituitary portal system." + "The accumulation of pigment in an organism, tissue or cell, either by increased deposition or by increased number of cells." + "A cartilage tissue that is part of a paired limb or fin." "ZFA:0001543 TAO:0001543" + "The process that gives rise to the apical ectodermal ridge. This process pertains to the initial formation of a structure from unspecified parts." + "The thick fibrous membrane that closely invests the entire surface of a bone except the articular cartilage at synovial joints." "UMLS:C0031110 EMAPA:35681 FMA:24041 MA:0002838 MESH:D010521 BTO:0001022 galen:PeriOsteum Wikipedia:Periosteum SCTID:33840008 NCIT:C13184 GAID:925" + "The process in which the anatomical structures of the hypophysis are generated and organized. The hypophysis is an endocrine gland that secretes hormones that regulate many other glands." + "The cytoplasm of a muscle cell; includes the sarcoplasmic reticulum." "Wikipedia:Sarcoplasm" + "A subarachnoid space that is part of a midbrain [Automatically generated definition]." "VHOG:0001304 EMAPA:19055" + "A presumptive structure that has the potential to develop into a endocardium." "TAO:0002233 ZFA:0001724" + "A population of lymphatic endothelial cell precursors that will form the lymph vessels." "UMLS:C1514424 NCIT:C34262" + "Any process that modulates the frequency, rate or extent of vasculature development." + "A neural tube lateral wall that is part of a rhombomere." "EMAPA:32819 EMAPA:35364" + "The chemical reactions and pathways resulting in the breakdown of carbohydrate derivative." + "An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component." "Wikipedia:Antibody" + "Any process that increases the rate frequency or extent of gastric secretion. Gastric secretion is the regulated release of gastric acid (hydrochloric acid) by parietal or oxyntic cells during digestion." + "A CD25-positive, CD27-positive immature gamma-delta T cell found in the thymus that has an immature phenotype (i.e. CD24-high, CD25-high, CD62L-high, CD44-high, CD2-low, CD5-low)." + "A parathyroid chief cell that is not actively secreting hormone. Contains small Golgi complexes with only a few grouped vesicles and membrane-bound secretory granules; glycogen and many lipofuscin granules abound but sacs of granular endoplasmic reticulum are rare and dispersed. In normal humans, inactive chief cells out number active chief cells in a ratio of 3-5:1." + "Adipose tissue that is located in the abdominal region. This includes any subcutaneous fat, visceral fat or encapsulated adipose tissue depots." "EFO:0003771 CALOHA:TS-0002" + "The umbilical vein is a blood vessel present during fetal development that carries oxygenated blood from the placenta to the growing fetus. [WP,unvetted]." "MESH:D014471 CALOHA:TS-1082 EHDAA:1034 EHDAA:488 FMA:70317 SCTID:367567000 Wikipedia:Umbilical_vein EFO:0001940 UMLS:C0041637 RETIRED_EHDAA2:0002107 EV:0100392 EMAPA:16375 EMAPA:16243 MA:0002249 NCIT:C33830 GAID:542 BTO:0001509" + "A NK1.1-positive T cell that is Ly49Cl-negative." + "The regulated release of glucagon from secretory granules in the A (alpha) cells of the pancreas (islets of Langerhans)." + "A developmental process, independent of morphogenetic (shape) change, that is required for the cerebellum to attain its fully functional state. The cerebellum is the portion of the brain in the back of the head between the cerebrum and the pons. The cerebellum controls balance for walking and standing, modulates the force and range of movement and is involved in the learning of motor skills." + "The multiplication or reproduction of cardiac muscle myoblasts, resulting in the expansion of a cardiac muscle myoblast cell population. A cardiac myoblast is a precursor cell that has been committed to a cardiac muscle cell fate but retains the ability to divide and proliferate throughout life." + "Any process in which a protein is transported to, and/or maintained at the postsynapse, the part of a synapse that is part of the post-synaptic cell." + "The chemical reactions and pathways involving compounds that contain an indole (2,3-benzopyrrole) skeleton." + "Any process that modulates the frequency, rate or extent of RNA binding." + "Mesenchyme that is part of a developing trunk." "EFO:0003485 ZFA:0000081 VHOG:0000281 EHDAA2:0002092 EMAPA:16177 TAO:0000081 EHDAA:377" + "Endodermal bud derived from the endodermal epithelium of the embryonic pharyngeal floor[MP]. The thyroid diverticulum is the embryological structure from which thyroid follicular cells derive. It grows from the floor of the pharnyx[WP]." "Wikipedia:Thyroid_diverticulum" + "The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet." + "Binding to an organic acid, any acidic compound containing carbon in covalent linkage." + "A basket cell morphology that inheres in neurons with axonal arbors composed of frequent, short, curvy axonal branches that tend to be near their somata and within the same layer." "ilxtr:SmallBasketPhenotype" + "The spiral-shaped bony canal in the inner ear containing the hair cells that transduce sound. Its core component is the Organ of Corti, the sensory organ of hearing, which is distributed along the partition separating fluid chambers in the coiled tapered tube of the cochlea. [WP,modified]." "TAO:0000374 XAO:0000197 NIFSTD_RETIRED:birnlex_883 Wikipedia:Cochlea MESH:D003051 UMLS:C1278895 FMA:60201 NCIT:C12395 BTO:0000267 AAO:0000253 MIAA:0000144 EMAPA:17597 ZFA:0000374 SCTID:181187008 MAT:0000144 BIRNLEX:1190 GAID:724 EV:0100363 CALOHA:TS-0151 EFO:0000357 MA:0000240 VHOG:0000691 UMLS:C0009195" + "HBA:9287 FMA:83939" + "A B220-positive CD38-negative unswitched memory B cell is a CD38-negative unswitched memory B cell that has the phenotype B220-positive, CD38-negative, IgD-positive, CD138-negative, and IgG-negative." + "A skeletal muscle satellite cell that undergoes symmetric division to produce two adult skeleltal muscle myoblasts." + "An automatic response to a stimulus beginning with a nerve impulse from a receptor and ending with the action of an effector such as a gland or a muscle. Signaling never reaches a level of consciousness." "Wikipedia:Reflex" + "Any process that stops, prevents, or reduces the frequency, rate or extent of natural killer T cell differentiation." + "A shape quality inhering in a bearer by virtue of the bearer's being cylindrical, in which the height is less than the diameter." + "The process in which a relatively unspecialized immature germ cell acquires the specialized features of a mature female gamete." + "An enterocyte that possesses a large supranuclear vacuolar system that preferentially internalizes dietary protein via receptor-mediated and fluid-phase endocytosis for intracellular digestion and trans-cellular transport. In zebrafish these cells are located in the posterior region of the mid intestine throughout life. In mammals they are found in the ileum pre-weaning and later are replaced by mature enterocytes." + "The mesonephric S-shaped body is the successor of the mesonephric comma-shaped body that contributes to the morphogenesis of a nephron in the mesonephros[GO]." + "The chemical reactions and pathways involving glucans, polysaccharides consisting only of glucose residues." + "Any process that modulates the frequency, rate, or extent of natural killer cell mediated immunity." + "An area of conducting tissue between the atria and the ventricles of the heart that conducts the normal electrical impulse from the atria to the ventricles." "Wikipedia:Atrioventricular_node BTO:0005689 MESH:D001283 TAO:0005070 NCIT:C32161 UMLS:C0004247 GAID:558 EMAPA:35153 SCTID:277688002 ZFA:0005070 VHOG:0001474 FMA:9478 EFO:0000276 MA:0000095 MAT:0000498 EHDAA2:0004183" + "Any process that stops, prevents or reduces the frequency, rate or extent of dendritic cell apoptotic process." + "A stem cell that can differentiate into a cardiac myocyte." "FMA:75620" + "Any process that activates or increases the frequency, rate or extent of T cell migration." + "Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle cell proliferation." + "GC_ID:1" + "A protein that is a translation product of the human SIGLEC5 gene or a 1:1 ortholog thereof." + "Any process that modulates the occurrence or rate of mesenchymal stem cell death by apoptotic process that contributes to the shaping of the nephron." + "A mucosa that is part of a lobar bronchus [Automatically generated definition]." "FMA:62668" + "FMA:83940" + "Any process evolved to enable an interaction with an organism of a different species." + "The orderly movement of a hematopoietic stem cell from one site to another. A hematopoietic stem cell is a cell from which all cells of the lymphoid and myeloid lineages develop, including blood cells and cells of the immune system." + "A cell type that is the first of the maturation stages of the granulocytic leukocytes normally found in the bone marrow. Granules are seen in the cytoplasm. The nuclear material of the myelocyte is denser than that of the myeloblast but lacks a definable membrane. The cell is flat and contains increasing numbers of granules as maturation progresses." "FMA:83525 BTO:0000734" + "The series of events involved in sensory perception in which a sensory stimulus is received and converted into a molecular signal." "Wikipedia:Transduction_(physiology)" + "Any process that activates or increases the frequency, rate or extent of neuroepithelial cell differentiation." + "A cranial suture that is part of a cartilaginous joint [Automatically generated definition]." "EMAPA:37463 MA:0001498" + "Any process that stops, prevents or reduces the frequency, rate or extent of vesicle transport along microtubule." + "Any process that modulates the frequency, rate or extent of the regulated release of ecdysteroid from a cell." + "An epithelium that is part of a uterine cervix [Automatically generated definition]." "CALOHA:TS-0137 UMLS:C1711358 MA:0001724 EMAPA:29929 NCIT:C49218 BTO:0000241 EFO:0001913" + "A section dividing a colon along a proximal-distal axis." "FMA:222905" + "The directed movement of a helper T cell in response to an external stimulus." + "Any process that decreases or stops the frequency, rate or extent of the regulated release of growth hormone from a cell." + "Tela chorioidea that lines the fourth ventricle[ZFA]. The tela chorioidea of the fourth ventricle is the name applied to the triangular fold of pia mater which is carried upward between the cerebellum and the medulla oblongata. It consists of two layers, which are continuous with each other in front, and are more or less adherent throughout: The posterior layer covers the antero-inferior surface of the cerebellum. The anterior layer is applied to the structures which form the lower part of the roof of the ventricle, and is continuous inferiorly with the pia mater on the inferior peduncles and closed part of the medulla[WP]." "FMA:78493 BAMS:tc4v TAO:0005158 SCTID:362321009 Wikipedia:Tela_chorioidea_of_fourth_ventricle neuronames:639 ZFA:0005158" + "A protein that is a translation product of some metazoan gene that encodes a signal peptide followed by a single Cathepsin propeptide inhibitor domain (Pfam:PF08246) followed by a single Papain family cysteine protease (Pfam:PF00112) domain at the C terminus." + "A vestibular afferent neuron which posseses a unique postsynaptic terminal, the calyx, which completely covers the basolateral walls of type I hair cells and receives input from multiple ribbon synapses." + "The appearance of any member of the TNF superfamily due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the formation and development of teeth, the hard, bony appendages which are borne on the jaws, or on other bones in the walls of the mouth or pharynx." + "A blood vessel that is part of a chest [Automatically generated definition]." "EMAPA:37239 MA:0000549" + "Any process that modulates the frequency, rate or extent of retrograde trans-synaptic signaling by neuropeptide." + "An artery that supplies the diaphragm." "EMAPA:37108 FMA:69330 MA:0002019 UMLS:C1181536 NCIT:C33320" + "An epithelial cell that resides in the inner root sheath of the hair follicle." + "The directed movement of glucose from outside of a cell, across the plasma membrane and into the cytosol." + "A process in which a monoatomic ion is transported across a membrane. Monatomic ions (also called simple ions) are ions consisting of exactly one atom." + "The process in which cardiac muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors." + "Any process that modulates the frequency, rate or extent of heart morphogenesis." + "Any process that modulates the frequency, rate or extent of myotube cell migration." + "An epithelial cell located in the early distal convoluted tubule." + "The outer or sperficial part of the humerus." "FMA:31542" + "Having both hydrophilic and hydrophobic (or lipophilic) groups." + "The process whose specific outcome is the progression of the neural tube over time, from its formation to the mature structure. The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium." + "The process in which the anatomical structures of the otic vesicle are generated and organized. The otic vesicle is a transient embryonic structure formed during development of the vertebrate inner ear." + "Any process that modulates the frequency, rate, or extent of antigen processing and presentation of peptide antigen via MHC class I." + "The left and right brachiocephalic veins in the upper chest are formed by the union of each corresponding internal jugular vein and subclavian vein. This is at the level of the sternoclavicular joint. These great vessels merge to form the superior vena cava. The brachiocephalic veins are the major veins returning blood to the superior vena cava." "SCTID:181371003 UMLS:C0006095 EHDAA2:0000182 galen:BrachiocephalicVein GAID:529 EHDAA:9868 MESH:D016121 Wikipedia:Brachiocephalic_vein NCIT:C32816 FMA:4723" + "Any of the rounds of incomplete mitosis undergone by a cystoblast to form a cyst of interconnected cells." + "Progression of the endocrine system over time, from its formation to a mature structure. The endocrine system is a system of hormones and ductless glands, where the glands release hormones directly into the blood, lymph or other intercellular fluid, and the hormones circulate within the body to affect distant organs. The major glands that make up the human endocrine system are the hypothalamus, pituitary, thyroid, parathryoids, adrenals, pineal body, and the reproductive glands which include the ovaries and testes." + "Any process that activates or increases the frequency, rate or extent of keratinocyte apoptotic process." + "A bistratifed retinal ganglion cell that has small, symmetric dendritic fields that terminate in S2 and S4." + "The movement of a lymphocyte within or between different tissues and organs of the body." + "Cranial nerve which enters the brain between cranial nerves VI and VII; contains afferents and sensory efferents to the anterior lateral line ganglia." "ZFA:0000425" + "The directed movement of glutamate into the vacuole across the vacuolar membrane." + "The upper conducting airways of the lung; these airways arise from the terminus of the trachea." "MESH:D001980 XAO:0000121 MA:0000436 MAT:0000133 EMAPA:32689 MIAA:0000133 Wikipedia:Bronchus EFO:0000932 FMA:7409 VHOG:0000262 CALOHA:TS-1229 GAID:346 SCTID:181215002 UMLS:C0006255 NCIT:C12683 BTO:0001340 EV:0100041" + "A mucosa that is part of a cystic duct [Automatically generated definition]." "FMA:14690" + "The progression of the male urethra over time from its initial formation to the mature structure. The male urethra is a renal system organ that carries urine from the bladder through the penis to outside the body." + "The multiplication or reproduction of cells, resulting in the expansion of a cell population that contributes to compound eye morphogenesis." + "Any process that activates or increases the frequency, rate or extent of nuclear division, the partitioning of the nucleus and its genetic information." + "The tubules located between the bile canaliculi and interlobular bile ducts near the outer edge of a classic liver lobule." "Wikipedia:Canals_of_Hering SCTID:269922006 SCTID:227002 UMLS:C0227517 FMA:17545 MA:0002669 NCIT:C32255" + "The stomach tissue region surrounding and controlling the distal outlet of the stomach, which opens into the duodenum." "MA:0002560 EMAPA:17631 BTO:0001146 EHDAA:4860 UMLS:C0034196 VHOG:0000420 NCIT:C12260 MESH:D011708 SCTID:362143006 Wikipedia:Pylorus galen:Pylorus EHDAA2:0001580 FMA:14581 GAID:333" + "Enables the transmembrane transfer of an inorganic cation by a channel that opens when a specific ligand has been bound by the channel complex or one of its constituent parts." + "The chemical reactions and pathways by which individual cells transform chemical substances." + "Any process that activates or increases the frequency, rate or extent of the directed movement of proteins within cells." + "A transition where a mesenchymal cell establishes apical/basolateral polarity,forms intercellular adhesive junctions, synthesizes basement membrane components and becomes an epithelial cell that will contribute to the shaping of the renal vesicle." + "A common myeloid progenitor that is CD34-positive, CD38-positive, IL3ra-low, CD10-negative, CD7-negative, CD45RA-negative, and IL-5Ralpha-negative." + "Any process that activates or increases the frequency, rate or extent of skeletal muscle hypertrophy." + "Any process that modulates the frequency, rate or extent of myeloid cell differentiation." + "The part of the cardiovascular system consisting of all arteries." "SCTID:362030008 VHOG:0000273 EHDAA:396 EMAPA:16371 EHDAA2:0000143 MA:0002719 BTO:0004690 EMAPA:16201" + "Any process that modulates the frequency, rate, or extent of tolerance induction." + "A bone that is part of a head [Automatically generated definition]." "SCTID:118646007 MA:0000576 EMAPA:35996" + "An interleukin-2 receptor subunit beta that is encoded in the genome of mouse." "UniProtKB:P16297" + "A blood vessel that is part of a lower leg [Automatically generated definition]." "EMAPA:37300 MA:0000675" + "A zone of skin that is part of a finger [Automatically generated definition]." "SCTID:361711001 UMLS:C1708318 EMAPA:32648 MA:0000626 FMA:38304 NCIT:C52720" + "A cell type that secretes histamine." + "A mesothelial cell that is part of the epicardium." + "A nerve that is located in a thoracic cavity [Automatically generated definition]." "MA:0000556 EMAPA:37267" + "Any process that modulates the frequency, rate or extent of vascular endothelial cell proliferation." + "A CD8alpha alpha positive gamma-delta intraepithelial T cell that expresses a TCR encoded in part by the Vgamma5 gene segment." + "Any process that modulates the frequency, rate or extent of endothelial tube morphogenesis." + "A tissue-resident macrophage that is part of the uterus." + "Epithelium lining the distalmost portion of the digestive tract." "BTO:0005445 WBbt:0005800" + "Any process that modulates the rate, frequency or extent of metanephros development. Metanephros development is the process whose specific outcome is the progression of the metanephros over time, from its formation to the mature structure. The metanephros is an endocrine and metabolic organ that filters the blood and excretes the end products of body metabolism in the form of urine." + "Nucleus that receives projections from or contains neurons that send projections through one of the cranial nerves." "FMA:54501 SCTID:280160003 NLX:28532 EMAPA:37066 Wikipedia:Cranial_nerve_nucleus" + "Any process that activates or increases the frequency, rate or extent of response to wounding." + "Any of the layers that make up the retina[MP]." "SCTID:280657006 EMAPA:35742 XAO:0000266 NCIT:C49328 MA:0001319 FMA:58617 UMLS:C0459649 AAO:0010353" + "Any muscle organ that is part of a forelimb." "FMA:37348 EMAPA:36049 AAO:0000204 BTO:0000479" + "Any process by which an organism or tissue maintains a population of germ-line stem cells." + "Any process that activates or increases the frequency, rate or extent of myoblast proliferation." + "The thick outer layer of the adrenal gland that is in the right side of the abdomen." "FMA:69088" + "The duct of a salivary gland." "Wikipedia:Salivary_duct EMAPA:35750 NCIT:C32486 MA:0001586 GAID:939 BTO:0005115 SCTID:181238004 FMA:59908 MESH:D018987" + "A cell with more than one nucleus." "WBbt:0008074 AEO:0000203" + "Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle myoblast proliferation." + "Any process that activates or increases the frequency, rate or extent of B-1 B cell differentiation." + "Any process that decreases the rate, frequency or extent of metanephric glomerulus development, the progression of the metanephric glomerulus over time from its initial formation until its mature state. The metanephric glomerulus is a capillary tuft surrounded by Bowman's capsule in nephrons of the vertebrate kidney, or metanephros." + "Any process, occuring in a cell, that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation." + "The directed movement of an organic hydroxy compound (organic alcohol) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. An organic hydroxy compound is an organic compound having at least one hydroxy group attached to a carbon atom." + "The process that gives rise to a cranial ganglion. This process pertains to the initial formation of a structure from unspecified parts." + "The synthesis or release of any leukotriene following a stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels." + "The joining of two lipid bilayers to form a single organelle membrane." + "Any process that modulates the frequency, rate or extent of nuclear migration along microtubule." + "The process in which a signal is secreted or discharged into the extracellular medium from a cellular source." + "The expulsion of feces from the rectum." "Wikipedia:Defecation" + "The prostate gland lobe that is located on the lateral side of the organ." "FMA:19577 MA:0003125 NCIT:C13092 EMAPA:29822" + "The process in which a relatively unspecialized cell acquires the specialized features of a cone retinal bipolar cell." + "The hepatic artery proper (also proper hepatic artery), arises from the common hepatic artery and runs alongside the portal vein and the common bile duct to form the portal triad. The hepatic artery proper gives off a small supraduodenal artery to the duodenal bulb. Then the right gastric artery comes off and runs to the left along the lesser curvature of the stomach to meet the left gastric artery, which is a branch of the celiac trunk. It subsequently gives off the cystic artery, which feeds the gallbladder, before bifurcating into the right and left hepatic arteries. Of note, the right and left hepatic arteries may demonstrate variant anatomy. A replaced right hepatic artery may arise from the superior mesenteric artery (SMA) and a replaced left hepatic artery may arise from the left gastric artery." "Wikipedia:Hepatic_artery_proper EMAPA:37217 SCTID:244262006 FMA:14772 MA:0003095" + "A dermal dendritic cell that is CD1a-negative and CD14-positive." + "An epithelium that is part of a hindgut [Automatically generated definition]." "EMAPA:16717 EHDAA2:0000782 MA:0003206" + "Any process that modulates the frequency, rate or extent of hemostasis." + "The first major branch of the abdominal aorta." "GAID:483 Wikipedia:Celiac_artery MESH:D002445 UMLS:C0007569 EMAPA:35202 MA:0001931 EHDAA2:0004519 NCIT:C52846 SCTID:181340007 FMA:50737" + "A T-cell surface glycoprotein CD8 alpha chain that has had the signal peptide removed." + "Enables the transfer of glycine from one side of a membrane to the other. Glycine is aminoethanoic acid." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of lymphocyte anergy." + "Combining with a steroid hormone and transmitting the signal within the cell to initiate a change in cell activity or function." + "A muscle that attaches to an eyelid." "NCIT:C52803 UMLS:C1707990 MA:0000269" + "CD4-positive alpha-beta T cell with the phenotype FoxP3-positive, CD25-positive, CD62L-positive, and CTLA-4 positive with regulatory function." + "Any apoptotic process that contributes to the shaping of the outflow tract. The outflow tract is the portion of the heart through which blood flows into the arteries." + "A cathepsin K that has been processed by proteolytic cleavage." + "An endothelium that is part of a lymphatic vessel [Automatically generated definition]." "MA:0000750 BTO:0004303 UMLS:C1180786 NCIT:C49258 MESH:D004729 TAO:0005258 EMAPA:35533 FMA:68444 ZFA:0005258 CALOHA:TS-2156" + "A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]." "XAO:0004038 SCTID:309311006 VSAO:0000015 ZFA:0005619 MA:0003047 EMAPA:37744" + "An epithelial cell that is part of a renal medulla collecting duct." "KUPO:0001060" + "Any process that activates or increases the frequency, rate, or extent of interleukin-1 beta production." + "Any process that regulates the the local concentration of neurotransmitter receptor at the postsynaptic membrane." + "A structure found in the walls of the ventricles of the brain, consisting of part of the meninges (pia mater in mammals) plus ependyma[cjm]." "neuronames:1378 TAO:0000447 Wikipedia:Tela_chorioidea FMA:242849 ZFA:0000447" + "The directed movement of fluid across epithelia." + "Any process that stops, prevents or reduces the frequency, rate or extent of proteolysis involved in protein catabolic process." + "A sebaceous gland placode is a thickening of the ectoderm that will give rise to the sebaceous gland bud[GO]." + "Binding to glycine, aminoethanoic acid." + "Any process that modulates the frequency, rate or extent of transmembrane transporter activity." + "EHDAA:404 SCTID:361403005 EHDAA2:0000936 EMAPA:16205 MA:0000478 VHOG:0000484" + "The partitioning of Golgi apparatus between daughter cells at cell division." + "A duct that collects and carries secretions of the exocrine pancreas to the intestine." "TAO:0001372 ZFA:0001372 FMA:10419 EHDAA:9194 Wikipedia:Pancreatic_duct SCTID:181278006 VHOG:0000254 EMAPA:32952 MA:0000124" + "A vein that supplies blood to the thymus." "Wikipedia:Thymic_branches_of_internal_thoracic_artery FMA:10647 SCTID:76543001" + "A portion of organism substance that is produced by exocrine glands." "EMAPA:36535 BTO:0002977 BTO:0002979 FMA:9675 galen:Secretion AEO:0001005 UMLS:C1516992 MA:0002504 MESH:D012634 NCIT:C34062" + "The peritoneum responsible for connecting the jejunum and ileum (parts of the small intestine) to the back wall of the abdomen. Between the two sheets of peritoneum are blood vessels, lymph vessels, and nerves. This allows these parts of the small intestine to move relatively freely within the abdominopelvic cavity. The brain, however, cannot map sensation accurately, so sensation is usually referred to the midline, an example of referred pain[WP]." "MA:0001555 EMAPA:37745 SCTID:245456008 FMA:14643 Wikipedia:Mesentery#Mesentery_.28proper.29" + "Any process that stops, prevents or reduces the frequency, rate or extent of activated CD8-positive, alpha-beta T cell apoptotic process." + "Texture quality inhering in a bearer by virtue of the bearer's being marked with one or more channels." + "A protein that is a translation product of the human VIP gene or a 1:1 ortholog thereof." + "The progression of the nucleus accumbens over time from its initial formation until its mature state. The nucleus accumbens is a collection of pleomorphic cells in the caudal part of the anterior horn of the lateral ventricle, in the region of the olfactory tubercle, lying between the head of the caudate nucleus and the anterior perforated substance. It is part of the ventral striatum, a composite structure considered part of the basal ganglia." + "The cardiac conduction system consists of specialized cardiomyocytes that regulate the frequency of heart beat[GO]." "EMAPA:35428 EFO:0003909 MA:0000094 FMA:9476 EV:0100025 EHDAA2:0004185 VHOG:0001271 TAO:0005063 ZFA:0005063 SCTID:281489000 MESH:D006329" + "The expansion of a NK T cell population by cell division as part of an immune response." + "A tissue-resident macrophage found in the central nervous system." + "A thin layer of cartilage, usually hyaline, on the articular surface of bones in synovial joints." "SCTID:305026006 GAID:101 FMA:12264 MESH:D002358 EFO:0001902 AEO:0000179 UMLS:C0007303 CALOHA:TS-0055 NCIT:C32144 MA:0000487 galen:ArticularCartilage EMAPA:35149 BTO:0001572" + "A process in which RNA is transported to and maintained in a part of a chromosome that is organized into chromatin." + "The change in morphology and behavior of a mast cell resulting from exposure to a cytokine, chemokine, soluble factor, or to (at least in mammals) an antigen which the mast cell has specifically bound via IgE bound to Fc-epsilonRI receptors." + "Any of the ducts that form the biliary tree, carrying bile from the liver to the small intestine." "MA:0000354 NCIT:C12376 MESH:D001652 GAID:280 XAO:0000134 Wikipedia:Bile_duct SCTID:276157007 BTO:0000122 ZFA:0001100 EMAPA:35171 CALOHA:TS-0075 AAO:0011019 VHOG:0000212 EV:0100091 TAO:0001100 UMLS:C0005400 FMA:9706" + "Subdivision of head that consists of the lower jaw skeletal elements plus associated soft tissue (skin, lips, muscle)[cjm]." "SCTID:362637005 EHDAA:7995 FMA:59398 MESH:D008334 Wikipedia:Lower_jaw EFO:0003660 VHOG:0000453 EMAPA:17906 EHDAA2:0001018 ncithesaurus:Lower_Jaw AAO:0000272" + "The synthesis, deposition, and organization of the materials in a cell of an ovary; where the cell can then undergo meiosis and form an ovum. An example of this is found in Drosophila melanogaster." + "The cellular DNA metabolic process resulting in the breakdown of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one." + "The various hormone- or neurotransmitter-secreting cells present throughout the mucosa of the intestinal tract." + "A mucosa that is part of a common bile duct [Automatically generated definition]." "FMA:14688" + "The process in which the cochlea is generated and organized." + "An integrin alpha-E that has been processed by proteolytic cleavage." + "A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it." "Wikipedia:Transmembrane_protein Wikipedia:Biological_membrane" + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an abiotic (non-living) stimulus." + "Forms the terminal part of the cuticle-lined excretory duct of C. elegans." + "A protein that is a translation product of the human SIGLEC6 gene or a 1:1 ortholog thereof." + "A skeleton of pelvic girdle that is part of a right pelvic girdle region." "FMA:87593" + "A follicular B cell that is IgD-positive and CD23-positive and CD38-positive. This naive cell type is activated in the extrafollicular areas via interaction with dendritic cells and antigen specific T cells." + "Any process that stops, prevents or reduces the frequency, rate or extent of endothelial cell chemotaxis." + "Any process that increases the rate, frequency or extent of macrophage derived foam cell differentiation. Macrophage derived foam cell differentiation is the process in which a macrophage acquires the specialized features of a foam cell. A foam cell is a type of cell containing lipids in small vacuoles and typically seen in atherosclerotic lesions, as well as other conditions." + "A specific region of the foregut into the area in which the lung will develop." "SCTID:34922002" + "Any mesenchymal cell apoptotic process that is involved in nephron morphogenesis." + + "A nerve that is part of a tympanic cavity [Automatically generated definition]." "MA:0001222 EMAPA:37777" + + "A stage at which the ectoderm, endoderm, and mesoderm develop into the internal organs of the organism." "BilaDO:0000010 Wikipedia:Organogenesis OGES:000032 BILS:0000111 OGES:000005 MmusDv:0000018 HsapDv:0000015" + "Any process that modulates the frequency, rate or extent of renal water transport." + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cell-cell junction. A cell-cell junction is a specialized region of connection between two cells." + "Any process that stops, prevents, or reduces the frequency, rate or extent of lamellocyte differentiation. Lamellocytes differentiate massively in the lymph glands after parasitization and are large flat cells devoted to encapsulation of invaders too large to be phagocytosed by plasmatocytes." + "A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry in the intestine between the stomach and the large intestine." + "A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons." "FBbt:00005144 FMA:54536 BTO:0002606 CALOHA:TS-0415" + "The chemical reactions and pathways resulting in the formation of organic acids, any acidic compound containing carbon in covalent linkage." + "The joining of 2 or more lipid bilayer membranes that surround the nucleus." + "Glial cell of cerebral cortex." "CALOHA:TS-1256" + "Combining with oxytocin to initiate a change in cell activity." + "GC_ID:1" + "The regulated release of any steroid that acts as a hormone into the circulatory system." + "Compound organ that contains one or more macroscopic anatomical spaces." "VHOG:0001730 FMA:55671 AAO:0010016 TAO:0001490 BILA:0000072 TGMA:0001857 HAO:0000072 AEO:0000072 XAO:0003165 CARO:0000072 EHDAA2:0003072 ZFA:0001490" + "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 2/3 of the primary motor cortex." + "A parenchyma that is part of a spleen." "FMA:16029" + "The process whose specific outcome is the progression of adipose tissue over time, from its formation to the mature structure. Adipose tissue is specialized tissue that is used to store fat." + "GC_ID:1" + "The process in which a relatively unspecialized cell acquires specialized features of a lung secretory cell. A lung secretory cell is a specialized epithelial cell of the lung that contains large secretory granules in its apical part." + "Any of the organized aggregations of cells that function as secretory or excretory organs and are associated with reproduction." "MA:0001751" + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from another living organism." + "GC_ID:1" + "Vein that drains right lung and returns blood to the heart." "UMLS:C0226669 SCTID:304056008 MA:0002208 EMAPA:37379 NCIT:C48947" + "A peptide hormone secreting cell that secretes cholecystokin stimulating hormone." + "The chemical reactions and pathways resulting in the breakdown of a protein in the vacuole, usually by the action of vacuolar proteases." + "A proximal epiphysis that is part of a femur [Automatically generated definition]." "SCTID:244702009 FMA:32841" + "Any process that activates or increases the frequency, rate, or extent of plasmacytoid dendritic cell antigen processing and presentation." + "Contributes to development of the cartilage of the larynx, laryngeal, pharyngeal, and soft palate muscles, superior parathyroid gland, and C-cells of the thymus." "TAO:0001599 SCTID:308770007 AAO:0010366 EHDAA2:0000086 EMAPA:16760 VHOG:0000299 XAO:0000449 FMA:293035 ZFA:0001607 EHDAA:1663" + "A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt" + "Any process that decreases the frequency, rate or extent of the regulated release of norepinephrine." + "Any process that decreases the frequency, rate or extent of the formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. This occurs as part of the regulation of muscle adaptation." + "The directed movement of a monoatomic ion into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Monatomic ions (also called simple ions) are ions consisting of exactly one atom." + "The lipid bilayer surrounding a secretory granule." + "A skeletal joint that connects two adjacent metacarpals[FMA,modified]." "Wikipedia:Intermetacarpal_articulations FMA:35288 SCTID:303065007" + "Any process that activates or increases the frequency, rate, or extent of B cell apoptotic process." + "A putamen that is part of a left cerebral hemisphere." "FMA:72829 HBA:4288" + + "The process whose specific outcome is the progression of a keratinocyte over time, from its formation to the mature structure." + "A duct that is located between lobes, within conspicuous, thick connective tissue septa that separate lobes. All interlobar ducts are excretory." + "The developmental process, independent of morphogenetic (shape) change, that is required for a columna/cuboidal epithelial cell to attain its fully functional state. A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube." + "GC_ID:1" + "Presumptive structure of the blastula that will develop into endoderm." "AAO:0000471 ZFA:0000416 EFO:0003437 TAO:0000416" + "The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers[GO]." "FMA:7280 AAO:0010408 TAO:0001320 EMAPA:17868 CALOHA:TS-2075 XAO:0000066 SCTID:362013006 galen:Endocardium Wikipedia:Endocardium EHDAA2:0004153 EFO:0000821 EV:0100021 MESH:D004699 MA:0000076 MAT:0000455 BTO:0000387 NCIT:C13004 ZFA:0001320 EMAPA:32686 UMLS:C0014124 VHOG:0000084 GAID:550" + "Any process that stops, prevents or reduces the frequency, rate or extent of satellite cell differentiation." + "An anatomical structure that has more than one cell as a part." "CARO:0010000" + "The process whose specific outcome is the progression of the instar larva or pupa over time, from its formation to the mature structure. An example of this process is found in Drosophila melanogaster." + "Any process that modulates the frequency, rate or extent of chorionic trophoblast cell proliferation." + "The regionalization process that divides an organism or part of an organism into a series of semi-repetitive parts, or segments, often arranged along a longitudinal axis." "Wikipedia:Segmentation_(biology)" + "The process whose specific outcome is the progression of a cloacal gland over time, from its formation to the mature structure." + "A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a promyelocyte and a metamyelocyte;in this stage, production of primary granules is complete and eosinophil-specific granules has started. No nucleolus is present. These cells are integrin alpha-M-positive, CD13-positive, CD15-positive, CD16-negative, CD24-positive, and CD33-positive." "FMA:83542 BTO:0003454" + "Infrequent type of columnar epithelial cell. This cell is characterized by the presence of a tuft of blunt, squat microvilli (approximately 120-140/cell) on the cell surface. The microvilli contain filaments that stretch into the underlying cytoplasm. They have a distinctive pear shape with a wide base and a narrow microvillous apex. Function not known." + "FMA:23800 EMAPA:25125" + "Any process in which smooth muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors. These adaptive events occur in both muscle fibers and associated structures (motoneurons and capillaries), and they involve alterations in regulatory mechanisms, contractile properties and metabolic capacities." + "Epithelial cell found on the external side of the tympanic membrane" "FMA:70558" + "The specialization of organization of a photoreceptor, a cell that responds to incident electromagnetic radiation, particularly visible light. An example of this process is found in Drosophila melanogaster." + + "Any mesenchymal stem cell of adipose tissue that is part of an orbital region." + "The initial renal anlage that develops from the most rostral part of the nephrogenic cord is termed the pronephros." + "An occluding cell-cell junction that is composed of a branching network of sealing strands that completely encircles the apical end of each cell in an epithelial sheet; the outer leaflets of the two interacting plasma membranes are seen to be tightly apposed where sealing strands are present. Each sealing strand is composed of a long row of transmembrane adhesion proteins embedded in each of the two interacting plasma membranes." "Wikipedia:Tight_junction NIF_Subcellular:sao1939999134" + "The process whose specific outcome is the progression of the vagus nerve over time, from its formation to the mature structure. This nerve is primarily sensory but also has visceromotor components. It originates in the brain stem and controls many autonomic functions of the heart, lungs, stomach, pharynx, larynx, trachea, esophagus and other gastrointestinal tract components. It controls some motor functions such as speech. The sensory branches mediate sensation from the pharynx, larynx, thorax and abdomen; it also innervates taste buds in the epiglottis." + "A diaphysis that is part of a metatarsal bone." "FMA:33826" + "The pampiniform plexus is a network of many small veins found in the male spermatic cord. It is formed by the union of multiple spermatic veins from the back of the testis and tributaries from the epididymis. The veins of the plexus ascend along the cord in front of the ductus deferens. Below the subcutaneous inguinal ring they unite to form three or four veins, which pass along the inguinal canal, and, entering the abdomen through the abdominal inguinal ring, coalesce to form two veins. These again unite to form a single vein, the testicular vein, which opens on the right side into the inferior vena cava, at an acute angle, and on the left side into the left renal vein, at a right angle. The pampinoform plexus forms the chief mass of the cord. In addition to its function in venous return from the testes, the pampiniform plexus also plays a role in the temperature regulation of the testes. It acts as a heat exchanger, cooling blood in adjacent arteries. An abnormal enlargement of the pampiniform plexus is a medical condition called varicocele. [WP,unvetted]." "EMAPA:37385 FMA:19607 SCTID:279661001 Wikipedia:Pampiniform_venous_plexus MA:0001866" + + "Any epithelium that lines one of the bile ducts." "BTO:0000417 NCIT:C43616 MA:0001629 UMLS:C1711208" + "A melanocyte that is part of the skin of body." "FMA:72144 CALOHA:TS-2374" + "Any process that activates or increases the frequency, rate, or extent of myeloid leukocyte differentiation." + "The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings)." + "The process whose specific outcome is the progression of the mesonephric distal tubule over time, from its formation to the mature structure. The mesonephric distal tubule is a mesonephric nephron tubule that begins at the terminal segment of the proximal tubule and ends at the mesonephric connecting tubule." + "The directed movement of iron ions from inside of a cell, across the plasma membrane and into the extracellular region." + "OBSOLETE: A goblet cell that is part of the epithelium proper of large intestine." "FMA:263071" + "The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific." + "A change in the morphology or behavior of an endothelial cell resulting from exposure to an activating factor such as a cellular or soluble ligand, leading to the initiation or perpetuation of an immune response." + "Any process that modulates the frequency, rate or extent of chondrocyte hypertrophy." + "Any process that modulates the frequency, rate or extent of skeletal muscle contraction." + "EMAPA:25124 FMA:23797" + "A(n) endothelial cell that is part of a(n) venule of lymph node." + "A spatially aggregated collection of nerve cell bodies in the PNS, consisting of one or more subpopulations that share cell type, chemical phenotype, and connections. (CUMBO)." "EMAPA:32814 BIRNLEX:2548 MA:0001161 BTO:0001123" + "The process whose specific outcome is the progression of the anterior lateral line over time, from its formation to the mature structure. The anterior lateral line consists of small sensory patches (neuromasts) located superficially on the skin or just under the skin in fluid-filled canals on the head of all fishes and most amphibians. The anterior lateral line develops from cranial ectodermal placodes situated between the eye and ear." + "A smooth muscle cell associated with the vasculature." + "A cell morphology that inheres in neurons with bitufted dendritic morphology but with the special feature of a tight fascicular axonal cylinder that resembles a 'horse tail'." + "A CD4-positive, alpha beta memory T cell with the phenotype CD45RA-positive, CD45RO-negative, and CCR7-negative." + + "The hypoglossal canal is a bony canal in the occipital bone of the skull." "EMAPA:19012 Wikipedia:Hypoglossal_canal SCTID:139380001 FMA:75370" + "Any process that stops, prevents or reduces the frequency, rate or extent of AV node cell action potential." + "AAO:0000247 ZFA:0000236 EFO:0003511 TAO:0000236 XAO:0003269" + "Binding to a member of the calcitonin family (e.g. adrenomedullin, adrenomedullin 2 (intermedin), amylin, calcitonin and calcitonin gene-related peptides (CGRPs))." + "Mesenchyme that is part of a limb bud." + "Any process that stops, prevents, or reduces the frequency, rate or extent of lymphocyte differentiation." + "Any process that modulates the frequency, rate or extent of lung ciliated cell differentiation." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of granuloma formation." + + "An immature CD16-positive myeloid dendritic cell is CD80-low, CD86-low, and MHCII-low." + "A spinal cord segment that adjacent_to a caudal region." "FMA:256635 neuronames:1656 MA:0003084 SCTID:278753006" + "The Atlanto-axial joint is of a complicated nature, comprising no fewer than four distinct joints. There is a pivot articulation between the odontoid process of the axis and the ring formed by the anterior arch and the transverse ligament of the atlas." "Wikipedia:Atlanto-axial_joint NCIT:C32157 MESH:D001268 FMA:25524 UMLS:C0004168 GAID:250 SCTID:361832004" + "A cell of the intermediate pituitary that produces melanocyte stimulating hormone." "BTO:0002277" + "Binding to monomeric or multimeric forms of tubulin, including microtubules." + "Nonsynovial joint in which the articulating bones or cartilages are connected by cartilage. Examples: Spheno-occipital synchondrosis, first sternocostal joint, pubic symphysis.[FMA]." "EMAPA:36581 Wikipedia:Cartilaginous_joint FMA:7496 TAO:0005155 SCTID:58442004 ZFA:0005155 MA:0000320" + "Any positive regulation of calcium-mediated signaling that is involved in cellular response to calcium ion." + + "Any process that activates or increases the rate or extent of T cell proliferation." + "A P/D1 enteroendocrine cell that is argyrophilic and stores vasoactive intestinal polypeptide." "FMA:63207" + "A rib endochondral element that is composed primarily of a pre-cartilage condensation." "VHOG:0000681 EHDAA2:0001717 EHDAA:6026 EMAPA:17397" + "Any process that stops, prevents or reduces the frequency, rate or extent of ventricular cardiac muscle cell action potential." + "The process whose specific outcome is the progression of the posterior lateral line nerve over time, from its formation to the mature structure. The posterior lateral line nerve innervates hair cells of the PLL and projects to an octavolateralis column in the hindbrain that consists of the medial octavolateralis nucleus (MON), the caudal octavolateralis nucleus, and the magnocellular nucleus." + "A mature natural killer cell that is CD11b-positive and CD27-positive." + "A T cell expressing an alpha-beta T cell receptor and the CD8 coreceptor." + "Any process that modulates the frequency, rate or extent of keratinocyte apoptotic process." + "Middle part of an organ, surrounded by the cortex." "galen:Medulla FMA:61108" + "A NK1.1-positive T cell that is CD94-negative and Ly49Cl-negative." + "A phalanx bone or its cartilage or pre-cartilage precursor." + "Any process that activates or increases the frequency, rate or extent of calcium ion import across plasma membrane." + "Enables the transfer of a macromolecule from one side of a membrane to the other." + "The process in which the bronchus is generated and organized. The bronchus is the portion of the airway that connects to the lungs." + "The multiplication or reproduction of Sertoli cells, resulting in the expansion of the Sertoli cell population. A Sertoli cell is a supporting cell projecting inward from the basement membrane of seminiferous tubules." + "An anatomical structure which consists of juxtaglomerular cells, extraglomerular mesangial cells and the macula densa. The juxtaglomerular apparatus lies adjacent to the glomerulus and regulates kidney function by maintaining the blood flow to the kidney and the filtration rate[GO]. a microscopic structure in the kidney, which regulates the function of each nephron. The juxtaglomerular apparatus is named for its proximity to the glomerulus: it is found between the vascular pole of the renal corpuscle and the returning distal convoluted tubule of the same nephron. This location is critical to its function in regulating renal blood flow and glomerular filtration rate. The three cellular components of the apparatus are the macula densa, extraglomerular mesangial cells, and juxtaglomerular cells (also known as granular cells)[WP]." "BTO:0005157 EMAPA:30449 UMLS:C0022445 MESH:D007606 Wikipedia:Juxtaglomerular_apparatus GAID:432 FMA:83599 SCTID:362219002 NCIT:C32891 MA:0002546" + "Any striated muscle cell that is part of a skeletal muscle tissue of pectoralis major." + "The directed movement of substances into the nucleus." + "The latissimus dorsi is the larger, flat, dorso-lateral muscle on the trunk, posterior to the arm, and partly covered by the trapezius on its median dorsal region. [WP,unvetted]." "UMLS:C0224362 VHOG:0000930 EFO:0003067 SCTID:181747008 FMA:13357 NCIT:C33150 EHDAA:8307 EHDAA2:0000932 EMAPA:18178 Wikipedia:Latissimus_dorsi_muscle MA:0002331" + "A paracrine cell is a secretory cell that secretes an agonist into intercellular spaces in which it diffuses to a target cell other than that which produced it." + "Innermost layer of neocortex lying deep to the internal pyramidal cell layer defined cytoarchitecturally by cells of varying size." "neuronames:2451 NLXANAT:090812 PBA:294021896 MA:0000902 ABA:CTX6 FMA:77805 EMAPA:35260" + "A presumptive structure that has the potential to develop into a presomitic mesoderm." "EFO:0003421 ZFA:0000053 TAO:0000053" + "Enables the transfer of ATP, adenosine triphosphate, from one side of a membrane to the other." "Reactome:R-HSA-9717392" + "A blood brain barrier that is composed of endothelial cells." "NIF_Subcellular:nlx_subcell_100205" + "An artery that supplies blood to an eyelid." "SCTID:148571007" + "The aggregate of the coelemic cavity lumen plus the membranes that line the lumen." "EHDAA2:0004731 Wikipedia:Coelom" + "Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells." "Reactome:R-HSA-168313 Reactome:R-HSA-178215" + "A lymph node that is part of a hypodermis." "MA:0003028" + "A pigment cell derived from the neural crest. Contains pteridine and/or carotenoid pigments in structures called pterinosomes or erythrosomes. This gives an orange to red appearance." + "A humerus endochondral element that is composed primarily of cartilage tissue." "VHOG:0001120 EMAPA:17713 EHDAA2:0000787 EHDAA:6240" + "A sebum secreting cell of the skin that secretes sebum into the hair follicles." "BTO:0004613 FMA:70953" + "A cell that is usually basal in position, cuboidal with round nucleus, short microvilli, secretes pepsinogen." "FMA:62902" + "A dense syncitial-like mesenchymal thickening in the dorsal mesogastrium[ISBN]. the embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing spleen[MP]." "XAO:0000326 EHDAA:3003 EHDAA2:0001904 EMAPA:18535" + "The orderly movement of epithelial cells within a renal tubule that contributes to mesonephric distal tubule morphogenesis." + "The single bud-like invagination of the conjunctival fornix epithelium at the temporal aspect of the eye that signals lacrimal gland formation (Int Rev Cytol. 1996;168:1-80. Cell biology of the harderian gland)." "EMAPA:35464" + + "The process of regulating the proliferation and elimination of neutrophils such that the total number of neutrophils within a whole or part of an organism is stable over time in the absence of an outside stimulus." + "Combining with glutamate and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity." + "The wall of the digestive tract. This encompasses all parts of the digestive tract with the exception of the lumen (cavity)." "FMA:45653 BTO:0000547" + "The orderly movement of a sensory neuron from one site to another." + "A Purkinje myocyte that is part of the interventricular septum." "FMA:263182" + "An immune response taking place in the nasopharyngeal-associated lymphoid tissue (NALT). NALT includes the tonsils and adenoids." + "An amicrine that stratifies dendrites at two and only two locations." + "An immune response mediated through a body fluid." "Wikipedia:Humoral_immunity" + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising cytoskeletal filaments and their associated proteins in the postsynaptic cytoskeleton." + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a norepinephrine stimulus. Norepinephrine is a catecholamine that has the formula C8H11NO3; it acts as a hormone, and as a neurotransmitter in most of the sympathetic nervous system." + "Any of the smallest blood vessels connecting arterioles with venules." "CALOHA:TS-2006 EV:0100035 EMAPA:35198 UMLS:C0935624 MA:0000065 BTO:0002045 FMA:63194 NCIT:C12685 MESH:D002196 AAO:0010252 XAO:0000116 EFO:0001906 Wikipedia:Capillary VHOG:0001253 NLXANAT:090902 TAO:0005250 ZFA:0005250" + "A monocyte that responds rapidly to microbial stimuli by secreting cytokines and antimicrobial factors and which is characterized by high expression of CCR2 in both rodents and humans, negative for the lineage markers CD3, CD19, and CD20, and of larger size than non-classical monocytes." + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting the presence, absence, or concentration of water." + "An epithelial cell of the urethra that has an expression profile similar to lung club cells. Club-like cells of the urethra epithelium are similar to lung club cells in their expression of SCGB1A1 and in their enrichment of immunomodulatory programs." + "The smallest division of the artery located between the muscular arteries and the capillaries[GO]." "FMA:63182 MESH:D001160 MA:0000063 ZFA:0005255 VHOG:0001763 TAO:0002138 UMLS:C0003847 Wikipedia:Arteriole NCIT:C12672 EMAPA:35146 SCTID:337724002 BTO:0001997 AAO:0010253" + "A B cell that is CD19-positive." + "Any process that stops, prevents or reduces the frequency, rate or extent of eosinophil chemotaxis." + "The chemical reactions and pathways involving chondroitin sulfate, any member of a group of 10-60 kDa glycosaminoglycans, widely distributed in cartilage and other mammalian connective tissues, the repeat units of which consist of beta-(1,4)-linked D-glucuronyl beta-(1,3)-N-acetyl-D-galactosamine sulfate. They usually occur linked to a protein to form proteoglycans. Two subgroups exist, one in which the sulfate is on the 4-position (chondroitin sulfate A) and the second in which it is in the 6-position (chondroitin sulfate C). They often are polydisperse and often differ in the degree of sulfation from tissue to tissue. The chains of repeating disaccharide are covalently linked to the side chains of serine residues in the polypeptide backbone of a protein by a glycosidic attachment through the trisaccharide unit galactosyl-galactosyl-xylosyl. Chondroitin sulfate B is more usually known as dermatan sulfate." + "The metanephric macula densa is an area of specialized cells in the distal tubule of the metanephros that makes contact with the vascular pole of the glomerulus[GO]." + "Missing definition for term UBERON:0004001. Please replace it using linked reference." "EMAPA:37917 NLXANAT:20090402" + "A transitional myocyte that is part of the septal division of left branch of atrioventricular bundle." "FMA:263168" + "The solid cord of epithelial cells that emerges from the mammary bud and grows down from the primary mammary mesenchyme and into a second stromal compartment, the fat pad precursor, beneath the dermis." + "The metanephric capsule is the tough fibrous layer surrounding the metanephros, covered in a thick layer of perinephric adipose tissue. It provides some protection from trauma and damage[GO]." + "A myeloid dendritic cell with the phenotype HLA-DRA-positive." + "The process whose specific outcome is the progression of the urothelium of the ureter over time, from its formation to the mature structure. The urothelium is an epithelium that makes up the epithelial tube of the ureter." + "A parenchyma that is part of a thyroid follicle [Automatically generated definition]." "BTO:0004579 SCTID:371402001 FMA:55515 EMAPA:37769 MA:0000730" + "Any process that stops, prevents or reduces the frequency, rate or extent of vacuolar transport." + "The process in which a relatively unspecialized cell acquires specialized features of a neuromast mantle cell. Mantle cells are non-sensory cells that surround the sensory strip, separating the neuromast from the epidermis. Mantle cells secrete the cupula in which the ciliary bundles of all of the hair cells are embedded." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-6 production." + "The region of the digestive tract extending from the mouth cavity through pharynx esophagus stomach and duodenum." "FMA:49177 Wikipedia:Alimentary_canal#Upper_gastrointestinal_tract UMLS:C0226874 galen:UpperGastrointestinalTract NCIT:C33837 SCTID:181244000" + "An ischial endochondral element that is composed primarily of a pre-cartilage condensation." "EMAPA:18348 EHDAA2:0000891 EHDAA:7153 VHOG:0000962" + "An epiphysis that is on the proximal side of the bone." "FMA:32821 SCTID:279998003" + "A secretory granule that contains cathepsin and gelatinase and is readily exocytosed upon cell activation; found primarily in mature neutrophil cells." + "A neck cell that secretes mucus within the stomach. Its products are distinct histochemically from those of the surface mucous cells of stomach." "FMA:62954" + "Any process that activates or increases the frequency, rate or extent of gastro-intestinal system smooth muscle contraction." + "Any process that activates or increases the frequency, rate or extent of CD8-positive, alpha-beta T cell activation." + "A cartilage that is part of a external ear [Automatically generated definition]." "NCIT:C49225 MA:0001886 GAID:103 UMLS:C0013445 MESH:D004425 EMAPA:37706 FMA:61339" + "A dendritic cell with the phenotype HLA-DRA-positive." + "A myb proto-oncogene protein that is encoded in the genome of human." "Reactome:R-HSA-992697 UniProtKB:P10242" + "An interleukin-1 receptor-like 1 that is encoded in the genome of human." "UniProtKB:Q01638" + "The multiplication or reproduction of cells, resulting in the expansion of a mesenchymal cell population of the ureter, that contributes to ureter development." + "Any process that modulates the frequency, rate or extent of defense response to fungus." + "An artery that carries deoxygenated blood from heart to the lungs. They are the only arteries (other than umbilical arteries in the fetus) that carry deoxygenated blood.." "SCTID:181380003 XAO:0004162 EMAPA:17008 EHDAA2:0001575 FMA:66326 UMLS:C0034052 MA:0002031 VHOG:0000982 GAID:505 AAO:0010221 EFO:0001399 MESH:D011651 EHDAA:4351 NCIT:C12774 BTO:0000778 Wikipedia:Pulmonary_artery galen:PulmonaryArtery CALOHA:TS-0839" + "Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid)." + "Rostralmost epibranchial placode. Associated with 1st branchial cleft." "XAO:0004211 EHDAA2:0004206 TAO:0001295 ZFA:0001295" + "Any process that activates or increases the frequency, rate or extent of bone resorption." + "A DRD2-expressing medium spiny neuron that is part of a striosome of dorsal striatum." + "Any process that modulates the frequency, rate or extent of cardioblast differentiation, the process in which a relatively unspecialized mesodermal cell acquires the specialized structural and/or functional features of a cardioblast. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating." + "The morphogenetic process in which a region of the fetal urogenital sinus epithelium is specified to become the prostate, resulting in prostate bud outgrowth." + "A cuboidal cell which along with Boettcher's cells form the floor of the external spiral sulcus, external to the organ of Corti." "FMA:79802" + "A neuron of teleosts that develops later than a primary neuron, typically during the larval stages." + "A progenitor cell committed to myeloid lineage, including the megakaryocyte and erythroid lineages. These cells are CD34-positive, and express Gata1, Gata2, C/EBPa, and Pu.1." + "A CD69 molecule that is encoded in the genome of human." "UniProtKB:Q07108" + "Any process that activates or increases the frequency, rate or extent of epidermis development." + "The process whose specific outcome is the progression of the pons over time, from its formation to the mature structure. The pons lies above the medulla and next to the cerebellum. The pons conveys information about movement from the cerebral hemisphere to the cerebellum." + "A solid cord of prostate epithelium." + "Subdivision of the embryo along the anterior/posterior axis into anterior, posterior and terminal regions." + "Any bone that is part of a palate." "UMLS:C1518857 NCIT:C33248 EMAPA:37930" + "The arcuate nucleus (or infundibular nucleus) is an aggregation of neurons in the mediobasal hypothalamus, adjacent to the third ventricle and the median eminence. The arcuate nucleus includes several important populations of neurons, including: Neuroendocrine neurons, Centrally-projecting neurons and Others. [WP,unvetted]." "EMAPA:35142 BM:HAr BAMS:ARH EV:0100230 MESH:D001111 UMLS:C0003741 FMA:62329 BTO:0002473 BTO:0005534 MA:0000847 HBA:12913 BAMS:ArcH BAMS:Arc neuronames:395 MBA:223 BIRNLEX:1638 NCIT:C52711 Wikipedia:Arcuate_nucleus DHBA:10492 GAID:647" + "The directed movement of proteins in a cell, including the movement of proteins between specific compartments or structures within a cell, such as organelles of a eukaryotic cell." + "Any process that stops, prevents, or reduces the frequency, rate or extent of protein localization to chromatin." + "The process whose specific outcome is the progression of lung cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate." + "A segment of the hindlimb that corresponds to the joint connecting a hindlimb stylopod and zeugopod." "GAID:48 SCTID:361291001 MESH:D007717 galen:Knee VHOG:0000347 EHDAA:5159 EHDAA:6184 FMA:24974 BTO:0003595 EHDAA2:0000895 MA:0000046 CALOHA:TS-2220 EMAPA:17493" + "The usually crescent-shaped opening of the urinary bladder into the urethra, placed at the anteroinferior angle (apex) of the urinary bladder trigone." "Wikipedia:Internal_urethral_orifice SCTID:362228001 FMA:85263" + "The inner layer of the glomerulus, within the basement membrane surrounding the glomerular capillaries." "NCIT:C33101 UMLS:C0017655 BTO:0002494 EMAPA:36561 Wikipedia:Mesangium FMA:84139 MA:0002617" + "A cell, usually of bacteria or yeast, which has partially lost its cell wall." + "A NK1.1-positive T cell that is NKGA2-positive." + "A pancreatic lobule that is in_the_right_side_of a exocrine pancreas." "EMAPA:37712 MA:0000723" + "The trabecular sinus is the lymph-filled space outside the trabeculae between lobules of the lymph node. This is a continuation of the subcapsular sinus which receives the afferent vessels and is present beneath the capsule. This space is traversed by both reticular fibers and cells in the lymph." + "The first vertebral bone in the vertebral column." "Wikipedia:Atlas_(anatomy) AAO:0000709 UMLS:C0004170 MA:0001421 FMA:12519 ZFA:0001167 EMAPA:19431 EHDAA:10606 TAO:0001167 SCTID:181818007 NCIT:C32239 MESH:D001270 GAID:236" + "A cell surface glycoprotein CD200 receptor 3 that is encoded in the genome of mouse." "UniProtKB:Q5UKY4" + "A vascular plexus that is part of a right lung." "EHDAA2:0001757 EMAPA:17668" + "An organelle found in cnidoblast (nematoblast) cells. When matured, these stinging organelles store toxins and can deliver them when the cnidocil (a short extension of the cnidocyst) is stimulated by a prey or another stimulus." "Wikipedia:Cnidocyte" + "Any (proper) part of the cytoplasm of a single cell of sufficient size to still be considered cytoplasm." + "A pyramidal neuron which has a distinctive tuft formation, distal from the soma." + "The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms." "Wikipedia:Reproduction" + "The chemical reactions and pathways resulting in the breakdown of compounds derived from amino acids, organic acids containing one or more amino substituents." + "The movement of a glial cell along the axons in a lateral line nerve." + "An epithelium that is part of a vermiform appendix." "CALOHA:TS-2062 FMA:63581 EHDAA2:0004561" + "The parietal pleura that lines the mediastinum." "Wikipedia:Mediastinal_pleura UMLS:C0225789 SCTID:362002008 FMA:9736 NCIT:C94820" + "The process in which a myeloid precursor cell acquires specializes features of an erythrocyte with a nucleus, as found in non-mammalian vertebrates such as birds." + "A macrophage which is resident in the lamina propria of the small intestine." + "A sst GABAergic cortical interneuron with a soma found in L5 and possesses 'T-shaped' Martinotti morphologies with local axonal plexus in L5a and translaminar axons restricted to the uppermost part of L1. They show low-threshold spiking patterns with strong rebound firing, and inhibit the L1 apical tuft of nearby pyramidal cells." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of leukocyte chemotaxis." + "A vascular endothelial growth factor receptor that is a translation product of the human KDR gene or a 1:1 ortholog thereof." "IUPHARobj:1813" + "A vein that is part of a abdomen." "SCTID:281473003" + "Any skeletal muscle organ in the hypodermis / superficial fascia." "MA:0003140 EMAPA:18188" + "A portion of smooth muscle tissue that is part of a terminal bronchiole [Automatically generated definition]." "FMA:261051" + "A protein with a domain composition consisting of a large extracellular domain, including five Ig-like C2-type domains followed by two copies of the Fibronectin type-III domain (Pfam:PF00041), a single-pass transmembrane domain and a short cytoplasmic C-terminal domain." "PIRSF:PIRSF002507" + "The connection between the embryo proper and extraembryonic tissues." + "Any process in an organism that results in the killing of its own cells or those of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions." + "Any process that modulates the rate, frequency or extent of mononuclear cell migration. Mononuclear cell migration is the movement of a mononuclear cell within or between different tissues and organs of the body." + "FMA:24023" + "A tendon that has the potential to develop into a central tendon." "EMAPA:25035 EHDAA:4118 EHDAA2:0000593" + "The change in morphology and behavior of a dendritic cell resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor." + "A secondary fiber cell that contains a nucleus." "FMA:70949" + "Muscle (organ) which is a part of the pelvis. Examples: levator ani,." "FMA:19086 EMAPA:37481 MA:0000534" + "Any process that stops, prevents, or reduces the frequency, rate, or extent of a T-helper 1 type immune response." + "A medulla that is part of a thyroid [Automatically generated definition]." "EMAPA:37768 MA:0000132" + "Any process that activates or increases the frequency, rate or extent of the process of creating protein polymers." + "Any suture between facial bones." + "A lymphatic endothelial cell located in a lymph node trabecula." + "The outermost layer of the mesenchymal capsule that surrounds the developing brain, of mixed paraxial mesoderm and neural crest origin. The ectomeninx forms the dura mater (both inner layer and outer chondrogenic layer)." "EHDAA2:0004317" + "Any process that stops, prevents or reduces the frequency, rate or extent of basophil degranulation." + "A neuroglial cell of the peripheral nervous system inside the basal lamina of the neuromuscular junction providing chemical and physical support to the synapse." + "The multiplication or reproduction of osteoblasts, resulting in the expansion of an osteoblast cell population. An osteoblast is a bone-forming cell which secretes an extracellular matrix. Hydroxyapatite crystals are then deposited into the matrix to form bone." + "Any process that contributes to cytokine production by a B cell." + "A compound molecular function in which an effector function is controlled by one or more regulatory components." + "A developmental process, independent of morphogenetic (shape) change, that is required for an osteoclast cell to attain its fully functional state. An osteoclast is a specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue, and which typically differentiates from monocytes." + "The area of the spleen in which T cells surround the central arteriole." "EMAPA:37750 FMA:62810 MA:0000765" + "The inner serous membrane of the pulmonary pleural. The visceral pleura lines the lungs." "EMAPA:16777 EHDAA2:0002205 NCIT:C33881 UMLS:C0225776 VHOG:0001496 SCTID:361997008 FMA:9734 MA:0002489" + "The process whose specific outcome is the progression of the brain ventricular system over time, from its formation to the mature structure. The brain ventricular system consists of four communicating cavities within the brain that are continuous with the central canal of the spinal cord. These cavities include two lateral ventricles, the third ventricle and the fourth ventricle. Cerebrospinal fluid fills the ventricles and is produced by the choroid plexus." + "Any process that activates or increases the frequency, rate or extent of lipid binding." + "The controlled release of a peptide from a cell or a tissue." + "The process that gives rise to the olfactory nerve. This process pertains to the initial formation of a structure from unspecified parts. The olfactory nerve is a collection of sensory nerve rootlets that extend down from the olfactory bulb to the olfactory mucosa of the upper parts of the nasal cavity. This nerve conducts odor information to the brainstem." + "One of: the common carotid artery, or its branches, the external and internal carotid arteries." "FMA:70504 ZFA:0000097 SCTID:362040006 CALOHA:TS-0116 MAT:0000501 VHOG:0000266 EMAPA:18609 TAO:0000097 UMLS:C0007272 NCIT:C12687 AAO:0010217 BTO:0000168 EV:0100379 EHDAA:6385 MESH:D002339 EFO:0000818 galen:CarotidArtery MA:0001925 SCTID:69105007 GAID:478 Wikipedia:Carotid_artery" + "Any process that stops, prevents, or reduces the rate of neutrophil degranulation." + + "A protein that is a translation product of the human RUNX1 gene or a 1:1 ortholog thereof." + "A monostratified retinal ganglion cell that has a small soma, an assymetric dendritic field with post synaptic terminals in sublaminar layer S3." + "Any neural crest cell migration that is involved in autonomic nervous system development." + "Any process that modulates the frequency, rate or extent of smooth muscle tissue development." + "A smooth muscle tissue that is part of a ejaculatory duct." "EMAPA:32289 FMA:19372" + "The multiplication or reproduction of cells, resulting in the expansion of the population in the pronephros." + "Any process that decreases the rate, frequency, or extent of neural retina development, the progression of the neural retina over time from its initial formation to the mature structure. The neural retina is the part of the retina that contains neurons and photoreceptor cells." + "The process in which a relatively unspecialized cell acquires specialized features of an epidermal cell, any of the cells making up the epidermis." + "Any process that activates or increases the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus." + "A renal system process in which water, ions, glucose and proteins are taken up from the collecting ducts, glomerulus and proximal and distal loops of the nephron. In non-mammalian species, absorption may occur in related structures (e.g. protein absorption is observed in nephrocytes in Drosophila, see PMID:23264686)." + "The part of the cervix uteri that protrudes into the vagina and is lined with stratified squamous epithelium." "SCTID:264459002 NCIT:C12310 FMA:86484 FMA:77056 BTO:0001850 CALOHA:TS-1098 UMLS:C0227829 Wikipedia:Vaginal_portion_of_cervix" + "An intermingling of fiber fascicles from adjacent spinal nerves to form a network." "NCIT:C49601 MA:0000235 VHOG:0000925 EHDAA2:0001899 FMA:5903 SCTID:42280003 EMAPA:16987 UMLS:C0228603" + + "The process in which the anatomical structure of the facial nerve is generated and organized. This sensory and motor nerve supplies the muscles of facial expression and the expression and taste at the anterior two-thirds of the tongue. The principal branches are the superficial opthalmic, buccal, palatine and hyomandibular. The main trunk synapses within pterygopalatine ganglion in the parotid gland and this ganglion then gives of nerve branches which supply the lacrimal gland and the mucous secreting glands of the nasal and oral cavities." + "Any apoptotic process that is involved in blood vessel morphogenesis." + "Gray matter of the temporal region of the neocortex, located in the temporal lobe in gyrencephalic animals." "FMA:242201 MA:0000941 SCTID:362343001 DHBA:10235 DMBA:16044 NLX:94939 BM:Tel-Cx-Te" + "A quality of an object that has a value that is increased compared to normal or average." + "A skeletal muscle fiber that is innervated by alpha motor neuron and generates tension by contracting, thereby allowing for skeletal movement. These fibers make up the large mass of skeletal muscle tissue and are attached to bones by tendons." "TH:H3.03.00.0.00007" + "Any process that stops, prevents or reduces the frequency, rate or extent of dopaminergic neuron differentiation." + "An outermost connective tissue covering of an organ, vessel, or other structure[WP]." "BTO:0002010 Wikipedia:Adventitia SCTID:30180000 FMA:45635" + "Any process that stops, prevents or reduces the frequency, rate or extent of chondrocyte hypertrophy." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of dendritic cell cytokine production." + "The process whose specific outcome is the progression of the retina over time, from its formation to the mature structure. The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates." + "Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures." "Wikipedia:Cloaca SCTID:362857006 MESH:D002988 ZFA:0005781 XAO:0000244 GAID:1206 VHOG:0001186 SCTID:370631000 UMLS:C0008987 AAO:0000095 NCIT:C34127" + "A vein that is part of a vermiform appendix." + "A stem cell found in the interstitial compartment of the neonatal testis; it is capable of self-renewal as well as differentiation into steroidogenic cells (adult Leydig cells). Intermediate stages of development include progenitor Leydig cells and immature Leydig cells." + "A diaphysis that is part of a metacarpal bone." "FMA:33804" + "A cerebral hemisphere that is in the left side of a brain." "FMA:61819 UMLS:C0228176 SCTID:362323007 NCIT:C32955 BIRNLEX:1795" + "The directed movement of a glycoprotein, a protein that contains covalently bound glycose (i.e. monosaccharide) residues, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements." "SCTID:272627002 EMAPA:37843" + "BTO:0002439" + "Any process that stops, prevents or reduces the frequency, rate or extent of lactation." + "A prominin-1 that is encoded in the genome of human." "UniProtKB:O43490" + "An anatomical cavity that surrounded_by a anal canal." "EMAPA:18836 FMA:17357" + "The slightly constricted part of a tooth, between the crown and the root." "NCIT:C32346 SCTID:28638008 FMA:55627" + "Enables the transfer of an ion from one side of a membrane to the other." + "The process whose specific outcome is the progression of a tendon sheath over time, from its formation to the mature structure. A tendon sheath is a layer of membrane around a tendon. It permits the tendon to move." + "A transferase complex capable of catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor)." + "Any process that stops, prevents or reduces the frequency, rate or extent of small intestine smooth muscle contraction." + "A homeostatic process involved in the maintenance of a steady state level of oxygen within a cell." + "Any process in which a chromosome is transported to, or maintained in, a specific location." + "The process in which a relatively unspecialized cell acquires specialized features of a myotube cell. Myotube differentiation starts with myoblast fusion and the appearance of specific cell markers (this is the cell development step). Then individual myotubes can fuse to form bigger myotubes and start to contract. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse." + "The process in which the structure of the smooth muscle tissue surrounding the aorta is generated and organized. An aorta is an artery that carries blood from the heart to other parts of the body." + "Any apoptotic process in a melanocyte, the main structural component of the epidermis." + "FMA:242234" + "A supporting cell of the vestibular epithelium." "FMA:75607" + "A neural decussation that is part of a diencephalon." "FMA:62446" + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a microvillus, a thin cylindrical membrane-covered projection on the surface of a cell." + "The chemical reactions and pathways by which a cell derives energy from stored compounds such as fats or glycogen." + "Any process that modulates the frequency, rate, or extent of interleukin-9 production." + "Any process that activates or increases the frequency, rate or extent of melanocyte differentiation." + "A protein that is a translation product of the human CD7 gene or a 1:1 ortholog thereof." "PIRSF:PIRSF038791" + "The multiplication or reproduction of cholangiocytes, resulting in the expansion of the cholangiocyte population. A cholangiocyte is an epithelial cell that is part of the bile duct. Cholangiocytes contribute to bile secretion via net release of bicarbonate and water." + "Any process that modulates the frequency, rate or extent of B cell proliferation." + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a calcium ion stimulus." + "A glutamatergic neuron located in the cerebral cortex that projects to structures of telencephalic origins." "ILX:0770100" + "The process whose specific outcome is the progression of the cerebellar Purkinje cell layer over time, from its formation to the mature structure. The Purkinje cell layer lies just underneath the molecular layer of the cerebellar cortex. It contains the neuronal cell bodies of the Purkinje cells that are arranged side by side in a single layer. Candelabrum interneurons are vertically oriented between the Purkinje cells. Purkinje neurons are inhibitory and provide the output of the cerebellar cortex through axons that project into the white matter. Extensive dendritic trees from the Purkinje cells extend upward in a single plane into the molecular layer where they synapse with parallel fibers of granule cells." + "Fluid contained within the notochordal canal." + "Wall of ventricle which is continuous with the wall of pulmonary trunk." "FMA:9533" + "A middle phalanx that is part of a finger [Automatically generated definition]." "UMLS:C0223828 FMA:75817 MA:0001394 NCIT:C12863 SCTID:371230003 SCTID:113223004 EMAPA:37306" + "A vascular network formed by frequent anastomoses between the blood vessels (arteries or veins) of a part." "XAO:0004143 EHDAA2:0004112 AEO:0000219 FMA:5900 EMAPA:35904" + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides." + "The progression of the substantia nigra over time from its initial formation until its mature state. The substantia nigra is the layer of gray substance that separates the posterior parts of the cerebral peduncles (tegmentum mesencephali) from the anterior parts; it normally includes a posterior compact part with many pigmented cells (pars compacta) and an anterior reticular part whose cells contain little pigment (pars reticularis)." + "Any process that modulates the rate, frequency, or extent of chromosome condensation, the progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells." + "Any process that modulates the frequency, rate, or extent of smooth muscle cell chemotaxis." + "The dense connective tissue which contains predominantly elastic fibers and is found in the tunica media of the aorta wall." "MA:0002859" + "An elasticity which is relatively low." + "Any process that modulates the frequency, rate, or extent of antimicrobial peptide production." + "A protein that is a translation product of the human MEIS2 gene or a 1:1 ortholog thereof." + "Any process that stops, prevents or reduces the frequency, rate or extent of thyroid hormone generation." + "The process whose specific outcome is the progression of the thick ascending limb over time, from its formation to the mature structure. The thick ascending limb is the last part of the loop of Henle. Its thick, mitochondria-rich epithelium characterizes the outer medulla, and is responsible for very avid active salt transport. At the macula densa, the thick ascending limb connects to the distal convoluted tubule." + "The process in which a B cell acquires the specialized features of a memory B cell. Memory B cells are cells that can respond rapidly to antigen re-exposure by production of high-affinity antibody." + "A multicellular organism that existence_ends_with a post-juvenile adult stage and existence_starts_with a post-juvenile adult stage." "galen:Adult HAO:0000087 BILA:0000078 UMLS:C0001675 NCIT:C17600 TAO:0002046 http://neurolex.org/wiki/Category:Adult_organism" + "The process in which protein polymers, compounds composed of a large number of component monomers, are broken down. Depolymerization occurs by the successive removal of monomers from an existing poly- or oligomeric protein." + "Any process that modulates the frequency, rate or extent of natural killer cell activation." + "The Pectoralis minor is a thin, triangular muscle, situated at the upper part of the chest, beneath the Pectoralis major. [WP,unvetted]." "EHDAA2:0001425 MA:0002355 UMLS:C0224347 FMA:13109 Wikipedia:Pectoralis_minor_muscle EMAPA:18180 VHOG:0000902 SCTID:181625002 EHDAA:8313 NCIT:C33285" + "A vessel through which blood circulates in the body." "SCTID:361097006 MESH:D001808 NCIT:C12679 MA:0000060 EMAPA:35993 FMA:50722 AEO:0000207 EFO:0000817 NLXANAT:090901 UMLS:C0005847 EHDAA2:0003252 GAID:169 VHOG:0001250 XAO:0001011 Wikipedia:Blood_vessel AAO:0011004 ZFA:0005314 EMAPA:32743 TAO:0002137 CALOHA:TS-0080 MAT:0000393 FMA:63183 EHDAA:240 BTO:0001102" + "Any process that modulates the frequency, rate or extent of ATP metabolic process." + "Any process that modulates the frequency, rate or extent of hepatic stellate cell activation." + "The part of the ear that projects from the head, connecting to the external acoustic meatus." "galen:Auricle EHDAA2:0001467 EV:0100355 VHOG:0000460 MA:0000259 SCTID:421159007 EMAPA:17589 UMLS:C0928075 Wikipedia:Pinna_(anatomy) NCIT:C32165 FMA:56580" + "Any process that stimulates, induces or increases the rate of macrophage activation." + "A cell that is specialized to store a particular substance(s), which is(are) later released from the store for a particular purpose." + "A muscle layer that is part of a large intestine." "NCIT:C32927 UMLS:C0734205 FMA:14971" + "A protein with core architecture consisting of a signal sequence, a Class II histocompatibility antigen, alpha domain (Pfam:PF00993) and an Immunoglobulin C1-set domain (Pfam:PF07654); these form the extracellular domain and are followed by a single-pass transmembrane region and a small cytoplasmic region." + "Any neuromast support cell that is part of a posterior lateral line." + "An epithelium that is part of a lower jaw [Automatically generated definition]." "EHDAA2:0001019 VHOG:0000802 EHDAA:7999 EMAPA:35516" + "A protein that is a translation product of the human ICOS gene or a 1:1 ortholog thereof." "IUPHARobj:2939" + "The median slit located inferior and posterior to the external urethral orifice in the female; the exit for menstrual flow and birth and the entrance for the penis during sexual intercourse; the size and appearance of the vaginal orifice varies inversely with that of the hymen (G. membrane), a thin fold of mucous membrane that surrounds the vaginal orifice." "EMAPA:37983 FMA:19984 Wikipedia:Vaginal_orifice" + "A coiling which is relatively low." + "A low affinity immunoglobulin epsilon Fc receptor that is encoded in the genome of mouse." "UniProtKB:P20693" + "The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte lineage." + "Any fibroblast that is part of a periodontal ligament." + "A mucosa that is part of a pyloric antrum [Automatically generated definition]." "FMA:17055 BTO:0004107" + "Any process that stops, prevents or reduces the frequency, rate or extent of satellite cell activation involved in skeletal muscle regeneration." + "Apocrine sweat glands are sweat glands composed of a coiled secretory portion located at the junction of the dermis and subcutaneous fat, from which a straight portion inserts and secretes into the infundibular portion of the hair follicle. The ducts of apocrine glands open into the canals of hair follicles. The stimulus for the secretion of apocrine sweat glands is adrenaline, which is a hormone carried in the blood[WP]." "FMA:59155 MESH:D001050 EMAPA:37426 SCTID:399916008 Wikipedia:Apocrine_sweat_gland BTO:0001458 UMLS:C0930083 NCIT:C32132" + "Any process that activates or increases the frequency, rate or extent of hair follicle maturation." + "A protein with a core domain architecture consisting of an extracellular domain containing two or three copies of the Immunoglobulin domain (Pfam:PF00047), followed by a single-pass transmembrane region and a small intracellular domain." "PIRSF:PIRSF001981" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of RNA from the nucleus into the cytoplasm." + "A DRD1-expressing medium spiny neuron that is part of a nucleus accumbens shell or olfactory tubercle." + "Any process that activates or increases the frequency, rate or extent of vacuolar transport." + "The progression of the taste bud over time, from its formation to the mature state. The taste bud is a specialized area of the tongue that contains taste receptors." + "A segment of the autopod consisting of both acropodial region and metapodial region, but excluding the mesopodial/basopodial region." + "The directed movement of bile acid and bile salts into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "A prolongation or process extending from a cell and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon." + "A transitional myocyte that is part of the atrial septal branch of anterior internodal tract." "FMA:263160" + "The first step in ossification of the cartilage is that the cartilage cells, at the point where ossification is commencing and which is termed a ossification center, enlarge and arrange themselves in rows. The matrix in which they are imbedded increases in quantity, so that the cells become further separated from each other. A deposit of calcareous material now takes place in this matrix, between the rows of cells, so that they become separated from each other by longitudinal columns of calcified matrix, presenting a granular and opaque appearance. Here and there the matrix between two cells of the same row also becomes calcified, and transverse bars of calcified substance stretch across from one calcareous column to another. Thus there are longitudinal groups of the cartilage cells enclosed in oblong cavities, the walls of which are formed of calcified matrix which cuts off all nutrition from the cells; the cells, in consequence, atrophy, leaving spaces called the primary areolC&." "FMA:75436 Wikipedia:Ossification_center" + "The stage in oogenesis when many layers of follicle cells surround the oocyte. There is a yolk nucleus (Balbiani's Body) near the germinal vesicle." + "Erectile tissue at the end of the clitoris, which is continuous with the intermediate part of the vestibulovaginal bulbs[BTO]. The clitoral glans (glans clitoridis) is an external portion of the clitoris[WP]." "Wikipedia:Clitoral_glans SCTID:362241002 FMA:19999 EMAPA:30829 UMLS:C0227769 BTO:0003117 NCIT:C32681" + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the cytoplasm. The cytoplasm is all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures." + "Lymphatic vessel that exits the lymph node. The efferent lymphatic vessel commences from the lymph sinuses of the medullary portion of the lymph nodes and leave the lymph nodes either to veins or greater nodes. Efferent lymphatic vessels are also found in the thymus and spleen. This is in contrast to afferent lymphatic vessels, which are found only in lymph nodes." "Wikipedia:Efferent_lymph_vessel MA:0000749" + + "A pro-T cell that is lin-negative, CD25-negative, CD127-negative, CD44-positive and kit-positive." + "A connective tissue cell that normally gives rise to other cells that are organized as three-dimensional masses. In humans, this cell type is CD73-positive, CD90-positive, CD105-positive, CD45-negative, CD34-negative, and MHCII-negative. They may further differentiate into osteoblasts, adipocytes, myocytes, neurons, or chondroblasts in vitro. Originally described as residing in the bone marrow, this cell type is now known to reside in many, if not all, adult organs." "FMA:70546 BTO:0003298 BTO:0002625" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the release into the cytosolic compartment of calcium ions sequestered in the endoplasmic reticulum or mitochondria." + "The upper tract of the renal system. The renal pelvis is the large cavity in the middle of each kidney. Urine drains from each kidney through a long tube called the ureter, into the bladder, where it is stored until it is passed from the body through the urethra." "NCIT:C54419" + "A taste bud that is located on the tongue, situated on a gustatory papilla." + "A mast cell that is CD25+." + "The process that initiates skeletal muscle satellite cell division by causing it to move from quiescence to the G1 stage of the cell cycle. The cell swells and there are a number of other small changes. The cells then start to divide. Following cell division the cells will differentiate. In adult muscle, satellite cells become activated to divide and differentiate in response to muscle damage." + "A meninx that is part of a telencephalon [Automatically generated definition]." "MA:0000979 VHOG:0000010 EHDAA:5476 EMAPA:17774 EHDAA2:0001990" + "A process in which a protein is transported to, or maintained in, a specific location in a membrane." + "The chemical reactions and pathways resulting in the breakdown of lipid droplets and hydrolysis of stored triglycerides occurring through the orchestrated activation of cytosolic lipases." + "The enlargement or overgrowth of all or part of a muscle organ or tissue due to an increase in the size of its muscle cells. Physiological hypertrophy is a normal process during development." + "A protein with a core domain architecture consisting of an extracellular domain containing two copies of the Immunoglobulin domain (Pfam:PF00047), followed by a single-pass transmembrane region and a small intracellular domain. The active protein is a low affinity receptor for immunoglobulin gamma chain Fc region. Human II-a, II-b, and II-c represent a recent gene expansion and are equally related to mouse II, III, and IV. Human III-A and III-B are closely related and closer to mouse IV than to mouse III." "PIRSF:PIRSF001980" + "A protein that is a translation product of the human SHH gene or a 1:1 ortholog thereof." + "Any membrane that is part of a pigment granule." + "An ON diffuse bipolar cell that has a large dendritic field and large axon terminals, which show little or no overlap. This cell predominantly connects to narrow thorny ganglion cells." + "Any process that modulates the frequency, rate or extent of the regulated release of insulin." + "ZFA:0000238" + "A protein that is a translation product of the human KLRD1 gene or a 1:1 ortholog thereof." + "The process in which any suture between cranial and/or facial bones is generated and organized." + "The chemical reactions and pathways resulting in the breakdown of mineralocorticoids, hormonal C21 corticosteroids synthesized from cholesterol." + "An endothelial cell that lines any of the venous cavities through which blood passes in various glands and organs such as the spleen and liver." "FMA:63134" + "A papilla that contain taste buds, including the fungiform, foliate, and circumvallate papillae." + "Any collection of muscles that is part of a pelvic girdle [Automatically generated definition]." "AAO:0000427 FMA:50248 EHDAA2:0001429 EMAPA:18184 FMA:50205" + "PMID:25450099 GC_ID:1 PMID:22839753" + "A portion of cardiac muscle tissue that is part of a right atrium [Automatically generated definition]." "VHOG:0001227 SCTID:362018002 FMA:7282 EHDAA2:0004155 EMAPA:17326" + "A relatively undifferentiated cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells." "FMA:63368 CALOHA:TS-2086" + "The outflow tract is the portion of the heart through which blood flows into the arteries." "XAO:0004139 VHOG:0000670 EHDAA2:0001351 EHDAA:464 EMAPA:16346 MA:0000100 EHDAA:798" + "A gamma-delta T cell that has a mature phenotype. These cells can be found in tissues and circulation where they express unique TCR repertoire depending on their location." + + "Any process that activates or increases the frequency, rate or extent of cardiac muscle cell differentiation." + "A muscle organ that is part of an abdominal segment of trunk [Automatically generated definition]." "EMAPA:37060 MA:0000527" + "The process in which the anatomical structures derived from an imaginal disc are generated and organized. The imaginal discs are epithelial infoldings in the larvae of holometabolous insects that develop into adult appendages (legs, antennae, wings, etc.) during metamorphosis from larval to adult form." + "The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins." "NIF_Subcellular:sao1663586795 Wikipedia:Cell_membrane" + "Any process that modulates the frequency, rate or extent of cholinergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter acetylcholine." + "An adipose dendritic cell that is SIRPa-negative." + "An intermediate muscle cell that has characteristics of both fast and slow muscle cells." "FMA:84450" + "Any process that activates or increases the frequency, rate or extent of skeletal muscle fiber differentiation." + "A ligament that is part of a larynx and connexts the cartilages of the larynx." "UMLS:C0458519 SCTID:279508004 EMAPA:37626 MA:0001755 NCIT:C32933 FMA:55131" + "Any skin fibroblast that is part of a pedal digit skin." + "Any process that modulates the frequency, rate or extent of T-helper 17 type immune response." + "Any process that stops, prevents, or reduces the frequency, rate or extent of leukocyte apoptotic process." + "The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus." + + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitrogen compound stimulus." + "A closed epithelium with a lumen." "EHDAA2:0003119 AEO:0000119" + "Any process that activates or increases the frequency, rate or extent of neural precursor cell proliferation." + "Enables the transfer of L-glutamate from one side of a membrane to the other. L-glutamate is the anion of 2-aminopentanedioic acid." "Reactome:R-HSA-5624256 Reactome:R-HSA-428052 RHEA:66336 Reactome:R-HSA-210444" + "A gray matter of spinal cord that is part of a cervical spinal cord." "SCTID:362438009 UMLS:C0228610 BIRNLEX:1521" + "A glial cell that is part of the perineurium. This cell type has thin long bipolar cytoplasmic processes, pinocytotic vesicles, fragments of external lamina and/or external lamina-like material, attachment plaques, and desmosome-like junctions. Perineurial cells historically have been referred to as fibroblasts because of shape; however, unlike fibroblasts, a perineurial cell: does not have a compact nucleus and large endoplasmic reticulum; does have a double basement membrane opposed to a single basal lamina; is carefully joined to other perineurial cells by tight junctions into a single sheet as opposed to arranged in a large mass; and finally, can surround a small axon bundle at a nerve terminal whereas a fibroblast cannot." + "Any apoptotic process in a Sertoli cell." + "A zone of skin that is part of a forelimb stylopod [Automatically generated definition]." "SCTID:181531009 FMA:37721 EMAPA:18062 MA:0000608" + "A columnar epithelial cell that is part of an insect imaginal disc." "FBbt:00007108" + "PMID:15371245 PMID:15019624 GC_ID:1" + "Any process that activates or increases the frequency, rate or extent of sensory perception of pain." + "The area where the jejunum ends and the ileum part of the intestine begins. Although there is no clear distinct section, the ileum is narrower and has smaller villi than the jejunum." + "A spherical embryonic mass of blastomeres formed before the blastula and resulting from cleavage of the fertilized ovum." "GAID:1295 MESH:D009028 EHDAA2:0000005 SCTID:361474003 FMA:292334 UMLS:C0026573 NCIT:C34212 BTO:0001508 Wikipedia:Morula" + "A tissue-resident macrophage that is part of some kidney." "KUPO:0001109" + "A paneth cell that is located in the anorectum." + "The aggregation, arrangement and bonding together of a set of components to form a tight junction, an occluding cell-cell junction that is composed of a branching network of sealing strands that completely encircles the apical end of each cell in an epithelial sheet." + "A protein that is a translation product of the human RELN gene or a 1:1 ortholog thereof." + "Any process that modulates the frequency, rate or extent of cardiac muscle cell myoblast differentiation." + "Mesenchyme that is part of a developing left lung." "EMAPA:16730 EMAPA:17654 EHDAA2:0000944" + "A stem cell that is the precursor of female gametes." "FBbt:00004873" + "The acquisition and processing of information and/or the storage and retrieval of this information over time." + "The separation of a multi-nucleate cell or syncytium into individual cells. An example of this is found in Drosophila melanogaster embryo development." + "A shape that inheres in a 2 dimensional entity, such as a cross section or projection of a 3 dimensional entity." + "The directed movement of some substance from a cell, into the extracellular region. This may occur via transport across the plasma membrane or via exocytosis." + "A melanocyte that appears darker due to content or amount of melanin granules." + "Any process that activates or increases the frequency, rate or extent of retrograde axon cargo transport." + "Any process that stops, prevents or reduces the frequency, rate or extent of melanosome transport." + "Compaction of chromatin structure prior to meiosis in eukaryotic cells." + "Any process that modulates the frequency, rate or extent of cardiac ventricle formation." + "A process in which a protein is transported to, or maintained in, a location within a ciliary transition zone." + "The process in which the anatomical structures of the intermediate mesoderm are generated and organized." + "The self-renewing division of a germline stem cell in the female gonad, to produce a daughter stem cell and a daughter germ cell, which will divide to form the female gametes." + "Any process that stops, prevents or reduces the frequency, rate or extent of CD8-positive, alpha-beta T cell proliferation." + "Surface shape that refers to the inward or outward curvature of the surface." + "Neuron of the cerebellum." "FMA:84665 CALOHA:TS-2359" + "The process in which a relatively unspecialized satellite cell acquires specialized features of a myoblast. This occurs as part of skeletal muscle regeneration. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers." + "The orderly movement of a lymphatic endothelial cell from one site to another in the wall of a lymphatic vessel." + "The directed movement of proteins from the Golgi to a secretory granule. The secretory granule is a membrane-bounded particle, usually protein, formed in the granular endoplasmic reticulum and the Golgi complex." + "Any process that activates or increases the frequency, rate or extent of neutrophil migration." + "Formation of a prolongation or process extending and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon." + "A metanephric nephron is the functional unit of the metanephros[GO]." "VHOG:0000719" + "A bistratified retinal ganglion cell that has a small dendritic field with sparse density that terminates at the intersection of the S4-S5 sublaminar level, and a second dendrite field that is medium in size and degree of arborization that terminates in sublaminar layer S2." + "Multi-tissue structure that is part of a compound organ." "TGMA:0001835 HAO:0000019 XAO:0003039 AEO:0000019 CARO:0000019 ZFA:0001489 TAO:0001489 BILA:0000019 EHDAA2:0003019 AAO:0010017" + "A smooth muscle cell that is part of the sigmoid colon." "FMA:17521" + "Any process that activates or increases the frequency, rate or extent of megakaryocyte differentiation." + "The right branch of the atrioventricular bundle that separates just below the bundle of His, descends the septal wall of the right ventricle and connects to the terminal Purkinje fibers[MP]." "FMA:9486 SCTID:277689005 galen:RightBundleBranch EMAPA:37359" + "The thymic connective tissue which extends into the parenchyma." "MA:0002674 NCIT:C33773 UMLS:C1515431" + "Any process that activates or increases the frequency, rate or extent of extracellular matrix assembly." + "A gingiva that is part of a upper jaw region." "EMAPA:18970 UMLS:C0227121 SCTID:304703001 NCIT:C54205 FMA:59763" + "Any process that modulates the frequency, rate or extent of protein localization to cilium." + "Combining with any member of the calcitonin family (e.g. adrenomedullin, adrenomedullin 2 (intermedin), amylin, calcitonin and calcitonin gene-related peptides (CGRPs)) to initiate a change in cell activity." + "Any process that modulates the frequency, rate or extent of protein localization to microtubule." + "The appearance of immunoglobulin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." + "An alpha-beta T cell that has an immature phenotype and has not completed T cell selection." + "A valve that is part of a right atrium [Automatically generated definition]." "MA:0001871 EMAPA:17327 EHDAA2:0000302" + "A cell with both myofibrils and secretory granules." + "A memory B cell with the phenotype IgD-negative and CD27-negative." + "A B cell that is located in a vermiform appendix." + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen." + "An region of the mesoderm that includes anterior lateral mesoderm of the first heart field plus contiguous pharyngeal mesoderm that gives rise to second-heart-field-derived regions of the heart and branchiomeric muscles." + "Formation of hard tissues that consist mainly of inorganic compounds, and also contain a small amounts of organic matrices that are believed to play important roles in their formation." "Wikipedia:Biomineralization" + "A choroid plexus epithelium that is part of a lateral ventricle [Automatically generated definition]." "EHDAA2:0004450 FMA:242815 MA:0000962 UMLS:C1711323 NCIT:C49248" + "The process whose specific outcome is the progression of the glomerular endothelium over time, from its formation to the mature structure. The glomerular endothelium is an epithelial tissue that covers the internal surfaces of the glomerulus." + "Any process that activates or increases the frequency, rate or extent of collagen fibril organization." + "An interneuron that uses GABA as a vesicular neurotransmitter. These interneurons are inhibitory" + "A rounded, inactive form that certain bacteria assume under conditions of extreme temperature, dryness, or lack of food. The bacterium develops a waterproof cell wall that protects it from being dried out or damaged." "BTO:0002779" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of iron ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "A nucleus of brain that is part of a thalamus." "BTO:0002452 SCTID:279115000 FMA:256693 MA:0002992 Wikipedia:List_of_thalamic_nuclei EMAPA:35859" + "Cartilaginous form of a vertebral centrum, a skeletal element that functionally replaces the notochord[VSAP,modified]." "SCTID:317278007" + "A paneth cell that is part of the epithelium of crypt of Lieberkuhn of small intestine." "FMA:263108" + "An endothelial cell that is part of the hepatic sinusoid. These cells possess flattened areas containing perforations about 0.1 micrometers in diameter, known as fenestrae. The fenestrae are arranged in groups known as sieve plates." "FMA:62911 BTO:000125" + "Arteries that supply the spinal cord." "NCIT:C33587 MA:0002043 UMLS:C0447043 ZFA:0000682 SCTID:244228006 EHDAA2:0001890 Wikipedia:Spinal_artery EMAPA:18241 TAO:0000682 EHDAA:4355" + "The process whose specific outcome is the progression of a glomerular visceral epithelial cell over time, from its formation to the mature structure. A glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells." + "Any process that mediates the transfer of information from one cell to another." + "Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut." "XAO:0000090 EMAPA:16062 UMLS:C0014144 CALOHA:TS-0273 GAID:1305 EHDAA2:0000436 Wikipedia:Endoderm MESH:D004707 EV:0100005 MAT:0000175 VHOG:0000154 BILA:0000038 ZFA:0000017 BTO:0000800 MIAA:0000175 TAO:0000017 FMA:69071 SCTID:362855003 AAO:0000139 EFO:0002545 NCIT:C12706" + "A basophilic erythroblast that is Lyg 76-high and is Kit-negative." + "A nonstratified squamous cell located in the ectocervix." "FMA:86483" + "A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a myelocyte and a band form cell. The nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare." "FMA:83541" + "A CCAAT/enhancer-binding protein epsilon that is encoded in the genome of human." "UniProtKB:Q15744 Reactome:R-HSA-3234072" + "Any neural crest cell differentiation that is involved in parathyroid gland development." + "A glandular epithelial cell of the endometrium." "FMA:86489" + "The neurological system process in which a signal is transmitted through the nervous system by a combination of action potential propagation and synaptic transmission." + + "A germinal center that is located in a lymph node." "EMAPA:35528 MA:0002989 SCTID:327147000 CALOHA:TS-1269 BTO:0003671 NCIT:C49757" + "The multiplication or reproduction of granulosa cells, resulting in the expansion of the granulosa cells population. A granulosa cell is a supporting cell for the developing female gamete in the ovary of mammals. They develop from the coelomic epithelial cells of the gonadal ridge." + "A specialized cardiac myocyte in the sinoatrial and atrioventricular nodes. The cell is slender and fusiform confined to the nodal center, circumferentially arranged around the nodal artery." "BTO:0004190 FMA:67101" + "An exocrine gland that is part of a integumental system." + "A CD86 molecule that is encoded in the genome of mouse." "UniProtKB:P42082" + "A C-C motif chemokine 3/4 that is a translation product of the human CCL3 gene or a 1:1 ortholog thereof." + "The controlled release of glycine by a cell." + "Any process that modulates the frequency, rate or extent of progesterone biosynthetic process." + "The process whose specific outcome is the progression of the endocrine pancreas over time, from its formation to the mature structure. The endocrine pancreas is made up of islet cells that produce insulin, glucagon and somatostatin." + "The biological process whose specific outcome is the progression of a chorion from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure. The chorion is an extraembryonic membrane." + "Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity." "MA:0000012 GAID:439 EFO:0002969 TAO:0001158 FMA:9668 Wikipedia:Endocrine_system UMLS:C0014136 NCIT:C12705 AAO:0010279 VHOG:0000098 XAO:0000158 MESH:D004703 EMAPA:35306 SCTID:278876000 ZFA:0001158 CALOHA:TS-1301 EHDAA2:0002224 EV:0100128" + "A shape quality inhering in a bearer by virtue of the bearer's having parallel chains in undulate fashion on the border." + "AAO:0010367 XAO:0000451 ZFA:0001608 SCTID:308771006 VHOG:0001204 TAO:0001600 FMA:293045" + + "Any process that stops, prevents or reduces the frequency, rate or extent of lymphocyte migration." + "The process whose specific outcome is the progression of the neural plate over time, from its formation to the mature structure. The neural plate is a flat, thickened layer of ectodermal cells. The underlying dorsal mesoderm signals the ectodermal cells above it to elongate into columnar neural plate cells. The neural plate subsequently develops into the neural tube, which gives rise to the central nervous system." + "Any developmental process that results in the creation of defined areas or spaces within an organism to which cells respond and eventually are instructed to differentiate into the anatomical structures of the renal system." + "A homeostatic process involved in the maintenance of an internal steady state within a defined tissue of an organism, including control of cellular proliferation and death and control of metabolic function." + "The chemical reactions and pathways resulting in the formation of an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group." + "GC_ID:1" + "The upper layer of the dermis beneath the epidermis, composed of dense irregular connective tissue[ncit,modified]." "UMLS:C0221930 Wikipedia:Papillary_dermis NCIT:C33630 UMLS:C0682598 NCIT:C94819 MA:0000800 EMAPA:35282 MA:0000802 FMA:64776" + + "The connecting cord from the developing embryo to the placenta." "MESH:D014470 EHDAA:158 Wikipedia:Umbilical_cord FMA:85541 UMLS:C0041633 BTO:0001415 EFO:0001415 SCTID:280644003 NCIT:C34320 EMAPA:26115 MAT:0000280 EV:0100127 EHDAA2:0000312 MIAA:0000280 GAID:517 CALOHA:TS-1078" + "Irregular connective tissue is an irregular connective tissue, the intercellular matrix of which contains a dense irregular network of collagen and elastic fiber bundles. Examples: connective tissue of peritoneum, connective tissue of fibrous pericardium." "Wikipedia:Dense_irregular_connective_tissue NCIT:C32882 FMA:20109 UMLS:C0738366" + "A portion of skeletal muscle tissue that is part of a diaphragm [Automatically generated definition]." "FMA:261898" + "A vitelline vein that is in the right side of a multicellular organism." "EHDAA2:0001766 SCTID:361445007 EMAPA:16699 FMA:70306 EMAPA:16381" + "Any process that activates or increases the frequency, rate or extent of fat cell apoptotic process." + "Any process that activates or increases the frequency, rate or extent of mesenchymal stem cell migration." + "Portion of connective tissue with various types of white blood cells enmeshed in it, most numerous being the lymphocytes[WP]." "NCIT:C13049 galen:LymphoidTissue Wikipedia:Lymphoid_tissue MESH:D008221 UMLS:C0024296 BTO:0000753 SCTID:181768009 CALOHA:TS-0584 MA:0002436 FMA:55220 GAID:342" + "Any process that increases the rate, frequency or extent of metanephros development. Metanephros development is the process whose specific outcome is the progression of the metanephros over time, from its formation to the mature structure. The metanephros is an organ that filters the blood and excretes the end products of body metabolism in the form of urine." + + "A cell that makes up the loose connective tissue of the thymus." + "An airway through which respiratory air passes in organisms." "Wikipedia:Trachea SCTID:361380005" + "The process in which zygospores are formed. Zygospores are characteristic of the zygomycete fungi (phylum Zygomycota) thick-walled and darkly colored, and usually heavily ornamented as well, with many spines or ridges. It is formed between two specialized organs called suspensors, which are themselves usually heavily ornamented, one from each mating partner. The zygospore forms between them and then breaks away." + "Any process that modulates the frequency, rate or extent of CD8-positive, alpha-beta T cell proliferation." + "A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]." "DHBA:10153 XAO:0000249 VHOG:0000068 EHDAA:346 RETIRED_EHDAA2:0001252 UMLS:C0920623 Wikipedia:Neural_plate EHDAA:902 AAO:0011072 NCIT:C34225 BTO:0001765 TAO:0000132 neuronames:1362 DMBA:15565 ZFA:0000132 FMA:293879 EMAPA:35593" + "Skeletal element that is often isolated, small, and variable in composition." "Wikipedia:Ossicles VSAO:0000132" + "Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor)." "Reactome:R-HSA-2161193 EC:2.7.1.-" + "The deposition of hydroxyapatite, involved in the progression of the skeleton from its formation to its mature state." + "Any process that activates or increases the activity of an ion transporter." + "A quality that has a value that is increased compared to normal or average." + "Cell-cell signaling to or from a synapse, mediated by a peptide." + "A vip GABAergic cortical interneuron that expresses cck. L5/6 cck cells have soma found mainly in L5 and L6 and have large axonal arborization." + "An epithelium that is part of a toe [Automatically generated definition]." "VHOG:0001031 EMAPA:32946" + "The process in which neuronal axons and dendrites become coated with a segmented lipid-rich sheath (myelin) to enable faster and more energetically efficient conduction of electrical impulses. The sheath is formed by the cell membranes of Schwann cells in the peripheral nervous system. Adjacent myelin segments are separated by a non-myelinated stretch of axon called a node of Ranvier." + "AAO:0010208 ZFA:0000189 XAO:0003175 TAO:0000189" + "Any process that modulates the rate, frequency, or extent of plasma membrane bounded cell projection assembly." + + "White matter tract that contains projections from the olfactory bulb to other parts of the brain." "UMLS:C0162435 DHBA:12074 EMAPA:35615 BTO:0003647 BIRNLEX:1663 neuronames:283 MA:0000975 DHBA:12073 HBA:9302 BAMS:olf NCIT:C33207 SCTID:362356008 Wikipedia:Olfactory_tract FMA:77626" + "Any process that modulates the frequency, rate or extent of crystal cell differentiation." + "A cell located in the outermost proliferative zone of the external germinal layer that can differentiate into astroglial cells and granule cells. This cell type is glial fibrillary acidic protein-positive and HNK1-positive." + "A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures." "Wikipedia:Collagen" + "The regulated release of gamma-aminobutyric acid by a cell, in which the gamma-aminobutyric acid acts as a neurotransmitter." + "Any process that stops, prevents or reduces the frequency, rate or extent of apical ectodermal ridge formation." + "The chemical reactions and pathways resulting in the formation of proteoglycans, any glycoprotein in which the carbohydrate units are glycosaminoglycans." + "The migration of individual cells into the embryo involved in deuterostomic gastrulation." + "The change in morphology and behavior of a granulocyte resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor." + "A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions." "ENVO:02000036 Wikipedia:Saliva GAID:1167 MESH:D012463 galen:Saliva CALOHA:TS-0891 MAT:0000444 BTO:0001202 FMA:59862 UMLS:C0036087 NCIT:C13275 EMAPA:36536 MA:0002507" + "A pre-cartilage condensation that has the potential to develop into a patella." "EMAPA:18510" + + "Binding to a bile acid, a steroid carboxylic acids occurring in bile." + "A oligopotent progenitor cell committed to the lymphoid lineage." + "Any collection of muscles that is part of a thorax [Automatically generated definition]." "BTO:0000508 EMAPA:37260 FMA:71293" + "Binding to a peptide, an organic compound comprising two or more amino acids linked by peptide bonds." + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of aldosterone." + "The controlled breakdown of the nuclear membranes, for example during cellular division." + "An interrenal epithelial kidney cell is an epithelial cell found in the anterior kidney of teleosts fish. This cell type is arranged in layers around the posterior cardinal vein and contains many mitochondria with tubulovesicular cristae. Interrenal chromaffin cells are interspersed among the tissue layer created by this cell type." + "The process in which the anatomical structures of the skeleton are generated and organized." + "GC_ID:1" + "The small branching blood vessels in the kidney glomerulus that receives blood from the kidney afferent arterioles; these capillaries are under high pressure for filtering within the glomerulus." "UMLS:C0226356 FMA:274259 EMAPA:28245 TAO:0005284 MA:0002587 SCTID:362049007 NCIT:C32684 ZFA:0005284" + "FMA:61298" + "A nervous system structure composed primarily of nerve cell bodies (somas). May also include dendrites and the initial unmyelinated portion of axons." "VHOG:0001768 EHDAA2_RETIRED:0004658 TAO:0002197 ZFA:0001681 HBA:4006 neuronames:2869 EHDAA2:0003136 NCIT:C32695 UMLS:C0018220 Wikipedia:Gray_matter EMAPA:37596 AEO:0001012 MA:0001112 FMA:67242" + "Any process that modulates the frequency, rate or extent of an iron transmembrane transporter activity." + "A transcription factor NF-kappa-B subunit that is a translation product of the human NFKB2 gene or a 1:1 ortholog thereof." + "The biological process whose specific outcome is the progression of a larynx from an initial condition to its mature state. This process begins with the formation of the larynx and ends with the mature structure. A larynx is a continuation of the pharynx that is involved in breathing, sound production, and protecting the trachea against food aspiration." + "Portion of semisolid bodily waste discharged through the anus[MW,modified]." "BTO:0000440 MAT:0000053 MA:0002509 galen:Feces UMLS:C0015733 FMA:64183 NCIT:C13234 ENVO:00002003 MIAA:0000053 MESH:D005243 CALOHA:TS-2345 Wikipedia:Feces GAID:1199" + "Any process that stops, prevents or reduces the frequency, rate or extent of brown fat cell differentiation." + "Neuron that secretes the neurotransmitter galanin." + "OBSOLETE A neuron that is part of nerve found outside the central nervous system." "FMA:84664" + "The directed movement of proteins into an intracellular organelle, across a membrane." + "Any sense organ that functions in (some) detection of chemical stimulus involved in sensory perception of taste (GO:0050912)." "FMA:77853" + "The process in which a precursor cell type acquires the specialized features of a Langerhans cell." + "A muscle cell that is part of the posterior internodal tract." "FMA:223280" + "GC_ID:1 PMID:8581300 PMID:8603894 PMID:17600185" + "The process of sparing immature T cells which react with self-MHC protein complexes with low affinity levels from apoptotic death." + "The progression of a metanephric tubule over time, from its initial formation to the mature structure. A metanephric tubule is an epithelial tube that is part of the metanephros." + "The movement of a monocyte in response to an external stimulus." + "Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]." "EMAPA:31159 ZFA:0001080 AEO:0000212 AAO:0010571 VHOG:0000680 Wikipedia:Sclerotome EHDAA2:0003439 UMLS:C0183176 TAO:0001080 NCIT:C34287 XAO:0000397 FMA:295652" + "Any process that stops, prevents or reduces the frequency, rate or extent of lung ciliated cell differentiation." + + "CD115-positive monocyte is a monocyte that is CD115-positive and CD11b-positive." + "The process in which a relatively unspecialized cell acquires specialized features of a medium spiny neuron residing in the striatum." + "Any process that increases the frequency, rate or extent of a digestive system process, a physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism." + "A cartilage tissue that is part of a pectoral appendage." "ZFA:0000257 TAO:0000257" + "A muscle layer that is part of a epididymis." "EMAPA:30747 FMA:19149" + "A blood vessel that is part of a neck [Automatically generated definition]." "MA:0000583 EMAPA:37236" + "A specialized area of membrane on either the presynaptic or the postsynaptic side of a synapse, the junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell." + "The expansion of a hematopoietic stem cell population by cell division. A hematopoietic stem cell is a stem cell from which all cells of the lymphoid and myeloid lineages develop." + "The biological process whose specific outcome is the progression of a lung-associated mesenchyme from an initial condition to its mature state. This process begins with the formation of lung-associated mesenchyme and ends with the mature structure. Lung-associated mesenchyme is the tissue made up of loosely connected mesenchymal cells in the lung." + "An excitatory glutamatergic interneuron found in the granular layer of the cerebellar cortex and also in the granule cell domain of the cochlear nucleus. Unipolar brush cells have a round or oval cell body with usually a single short dendrite that ends in a brush-like tuft of short dendrites unique to them known as dendrioles." + "Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO]." "FMA:30316" + "Any process that modulates the frequency, rate, or extent of production of any member of the interleukin-17 family of cytokines." + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amides." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus." + "An epithelial cell part of respiratory tract epithelium that is a precursor of a multi-ciliated cell. This cell actively amplifies centrioles, a required step for multiciliogenesis." + "Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. Wikipedia: The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri)." "EHDAA:2331 EHDAA:2349 MA:0000565 AEO:0000111 CALOHA:TS-1183 EMAPA:32856 EHDAA:646 SCTID:361918002 EHDAA:640 FMA:14074 EHDAA:295 NCIT:C33105 UMLS:C0086610 Wikipedia:Mesothelium EHDAA:6073 EHDAA2_RETIRED:0003111 BTO:0002422" + "Any process that modulates the frequency, rate or extent of bone remodeling, the processes of bone formation and resorption that combine to maintain skeletal integrity." + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a testosterone stimulus." + "Anatomical projection that is composed of bone tissue." "FMA:75433 ZFA:0001637" + "A CD14 molecule that is encoded in the genome of mouse." "UniProtKB:P10810" + "A(n) endothelial cell that is part of a(n) efferent lymphatic vessel." + "The chemical reactions and pathways resulting in the breakdown into fatty acids and monoglycerides of lipids in the small intestine. Lipids are broken down by lipases released by the pancreas." + "The portion of the hindlimb that contains both the stylopod and zeugopod." "EHDAA2:0000972 CALOHA:TS-2206 EHDAA:6176 GAID:49 MA:0000047 EHDAA:8289 EFO:0001411 Wikipedia:Leg#Limb EMAPA:17489 BTO:0000721 EHDAA:5151 MESH:D035002 VHOG:0000345" + "A germinal center that is part of a tonsil." "CALOHA:TS-1288" + "The mass of tissue made up of mesenchymal cells in the lung." "EMAPA:32866" + + "Any process that modulates the frequency, rate or extent of presynapse assembly." + "A mucosa that is part of a lip region [Automatically generated definition]." "NCIT:C12226" + "The process in which glial cells envelop neuronal cell bodies and/or axons to form an insulating layer. This can take the form of myelinating or non-myelinating ensheathment." + "A layer of cuboidal epithelial cells bounded anteriorly by the capsule of the lens and posteriorly by the lens cortex." "EHDAA:9059 NCIT:C33641 RETIRED_EHDAA2:0000976 MA:0001302 EMAPA:17304 EHDAA2:0000984 SCTID:362521008 FMA:70612 VHOG:0001425 UMLS:C1182652 EMAPA:17839" + "Any process involved in the carrying out of an immune response by a lymphocyte." + "The process in which a post-anal tail is generated and organized. A post-anal tail is a muscular region of the body that extends posterior to the anus. The post-anal tail may aid locomotion and balance." + "Any process that activates or increases the frequency, rate or extent of meiosis." + "An epithelial cell of the lung." "BTO:0004299" + "Any process that prevents the establishment or decreases the extent of the excitatory postsynaptic potential (EPSP) which is a temporary increase in postsynaptic potential due to the flow of positively charged ions into the postsynaptic cell. The flow of ions that causes an EPSP is an excitatory postsynaptic current (EPSC) and makes it easier for the neuron to fire an action potential." + "Any process that stops, prevents or reduces the frequency, rate or extent of cell proliferation in midbrain." + + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a supramolecular fiber, a polymer consisting of an indefinite number of protein or protein complex subunits that have polymerised to form a fiber-shaped structure." + "A sac-like expansion of the ventral wall of the intestine, narrowed into a yolk stalk near the body[Hyman's]. Membranous sac attached to an embryo, providing early nourishment in the form of yolk in bony fishes, sharks, reptiles, birds, and primitive mammals. It functions as the developmental circulatory system of the human embryo, before internal circulation begins. In the mouse, the yolk sac is the first site of blood formation, generating primitive macrophages and erythrocytes[WP]." "EHDAA2:0002212 Wikipedia:Yolk_sac NCIT:C14128 EMAPA:16085 GAID:1301 VHOG:0000830 SCTID:362845002 UMLS:C0043425 CALOHA:TS-1130 EHDAA:164 FMA:87180 EFO:0003078 MESH:D015017 BTO:0001471" + "A hair cell of the ear that contains the organs of balance and hearing." + "Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult)." + "Any process that modulates the frequency, rate or extent of pancreatic B cell development." + "The chemical reactions and pathways involving amino acids of the glutamine family, comprising arginine, glutamate, glutamine and proline." + "The glomus forms from the splanchnic intermediate mesoderm and is the vascularized filtration unit, filtering the blood before it enters the tubules. The glomus is external to the nephron and extends over more than one body segment." "AAO:0011049 TAO:0001557 XAO:0000318 ZFA:0001557 SCTID:360548001 VHOG:0001237" + "The multiplication or reproduction of pancreatic stellate cells, resulting in the expansion of a pancreatic stellate cell population. Pancreatic stellate cells are found in the periacinar space of the exocrine pancreas and in perivascular and periductal regions of the pancreas, and have long cytoplasmic processes that encircle the base of the acinus." + "A process in which a protein is transported to, or maintained in, a location within a cell junction." + "A longitudinal muscle layer of muscular coat that is part of a vermiform appendix smooth muscle." + "Any process that stops, prevents or reduces the frequency, rate or extent of endothelial cell apoptotic process." + "A neuron that is part of a peripheral nervous system." "FMA:84664" + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a chemical stimulus." + "The process by which an organism or tissue maintains a population of stem cells of a single type. This can be achieved by a number of mechanisms: stem cell asymmetric division maintains stem cell numbers; stem cell symmetric division increases them; maintenance of a stem cell niche maintains the conditions for commitment to the stem cell fate for some types of stem cell; stem cells may arise de novo from other cell types." + "The regulated release of serotonin by a cell, in which released serotonin acts as a neurotransmitter." + "The elastic, clear, membrane-like structure, that is outer most layer of the lens." "EMAPA:18237 Wikipedia:Lens_(anatomy)#Lens_capsule FMA:58881 VHOG:0000550 EHDAA2:0000977 SCTID:244500004 ZFA:0005574 NCIT:C32975 MA:0001300 UMLS:C0229232" + + "The dorsal metatarsal veins are veins which drain the metatarsus of the foot. [WP,unvetted]." "NCIT:C52689 MA:0002105 FMA:44377 EMAPA:37143 Wikipedia:Dorsal_metatarsal_veins UMLS:C0835053" + "The process in which the right cardiac ventricle is generated and organized." + "A myocardial endocrine cell that is part of the septal division of left branch of atrioventricular bundle." "FMA:263180" + "Layer of the retina formed by expansion of the fibers of the optic nerve." "TAO:0002212 VHOG:0001169 Wikipedia:Nervous_system_fiber_layer ZFA:0001619 SCTID:280671003 FMA:58688 MA:0001314 XAO:0003220 EMAPA:18591 DMBA:15652" + "Any process that stops, prevents or reduces the frequency, rate or extent of serotonin biosynthetic process." + "The process whose specific outcome is the progression of the tongue over time, from its formation to the mature structure. The tongue is the movable, muscular organ on the floor of the mouth of most vertebrates, in many other mammals is the principal organ of taste, aids in the prehension of food, in swallowing, and in modifying the voice as in speech." + "A blood vessel endothelium that is part of a respiratory system [Automatically generated definition]." "MA:0001805 EMAPA:35732" + "A horseshoe shaped bone situated in the anterior midline of the neck between the chin and the thyroid cartilage. The hyoid bone provides attachment to the muscles of the floor of the mouth and the tongue above, the larynx below, and the epiglottis and pharynx behind. [WP,modified]." "GAID:197 EMAPA:18650 Wikipedia:Hyoid_bone AAO:0000684 NCIT:C32752 SCTID:263352000 MESH:D006928 MA:0001484 UMLS:C0020417 FMA:52749 VHOG:0001325" + "Any mesenchymal cell apoptotic process that is involved in metanephros development." + "A scavenger receptor cysteine-rich type 1 protein M130 that has been processed by proteolytic cleavage." + "Cytoarchitectural layer of retina that contains somata of retinal ganglion cells, bounded by the stratum opticum and the inner plexiform layer." "VHOG:0001166 ZFA:0000024 XAO:0003223 SCTID:280670002 NLX:36500 NLXANAT:1005030 TAO:0000024 FMA:58687 EMAPA:35739 NCIT:C32652 BAMS:Rgcl MA:0001310 CALOHA:TS-0867 Wikipedia:Ganglion_cell_layer BTO:0003398" + "Any process that modulates the frequency, rate or extent of hair follicle development." + "An acinus that is part of a lacrimal gland." "FMA:85250" + "A mucosa that is part of a pharynx [Automatically generated definition]." "BTO:0001047 FMA:55031 EMAPA:26957 SCTID:362121003 MA:0003143" + "Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-9 production." + "A large superficial muscle that extends longitudinally from the occipital bone to the lower thoracic vertebrae and laterally to the spine of the scapula (shoulder blade). Its functions are to move the scapulae and support the arm. The trapezius has three functional regions: the superior region (descending part), which supports the weight of the arm; the intermediate region (transverse part), which retracts the scapulae; and the inferior region (ascending part), which medially rotates and depresses the scapulae. [WP,unvetted]." "Wikipedia:Trapezius_muscle FMA:9626 UMLS:C0224361 EMAPA:18183 VHOG:0000834 NCIT:C33809 SCTID:181740005 MA:0002398" + + "ZFA:0001431" + "The part of a synapse that is part of the presynaptic cell." + "Part of peripheral nervous system that includes the somatic parts of the cranial and spinal nerves and their ganglia and the peripheral sensory receptors." "MAT:0000099 EFO:0000892 Wikipedia:Somatic_nervous_system FMA:9904 NLXANAT:100301 MA:0002850 MIAA:0000099" + "A fluid that is composed of blood plasma and erythrocytes." "galen:Blood BTO:0000089 MESH:D001769 Wikipedia:Blood XAO:0000124 EFO:0000296 AAO:0000046 EHDAA2:0000176 VHOG:0000224 EMAPA:16332 GAID:965 MA:0000059 UMLS:C0005767 EV:0100047 EHDAA:418 MIAA:0000315 CALOHA:TS-0079 ZFA:0000007 FMA:9670 NCIT:C12434 ENVO:02000027 TAO:0000007" + "Any process that modulates the frequency, rate or extent of embryonic camera-type eye development." + "Any apoptotic process in a retinal cone cell, one of the two photoreceptor cell types of the vertebrate retina." + "A tachykinin-3 that has been processed by proteolytic cleavage." + "The process that gives rise to a rhombomere boundary. This process pertains to the initial formation of a boundary delimiting a rhombomere. Rhombomeres are transverse segments of the developing rhombencephalon that are lineage restricted, express different genes from one another, and adopt different developmental fates. Rhombomeres are numbered in anterior to posterior order." + "A lymphocyte that is part of a Peyer's patch. These cells have a major role in driving the immune response to antigens sampled from the intestinal lumen, and in regulating the formation of follicle-associated epithelium and M cells in Peyer's patches by converting intestitial enterocytes into M cells." + "A pre-cartilage condensation that has the potential to develop into a forelimb bone." "EMAPA:32625" + "Any process that stops, prevents, or reduces the frequency, rate or extent of hair follicle maturation." + "The process in which a relatively unspecialized cell acquires specialized features of a neuron whose cell body resides in the central nervous system." + "The directed movement of substances along cytoskeletal fibers such as microfilaments or microtubules within a cell." + "Any hair follicle dermal papilla cell that is part of a scalp." + "A protein that is a translation product of the human CLEC4C gene or a 1:1 ortholog thereof." + "Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic signaling pathway." + "A type of type 3 cone bipolar cell with distinctive curly dendrites." + "Any part or collection of parts of the central or peripheral nervous system. Parts may span both CNS and PNS." "UMLS:C1518256 NCIT:C13040 SCTID:25087005 BIRNLEX:1157" + "The process in which the anatomical structures of the ear are generated and organized. The ear is the sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of cytokine production contributing to an immune response." + "Any process that modulates the frequency, rate or extent of muscle adaptation." + "Any process that modulates the frequency, rate or extent of euchromatin binding." + "A splenic macrophage found in the marginal zone of the spleen, involved in recognition and clearance of particulate material from the splenic circulation. Markers include F4/80-negative, MARCO-positive, SR-A-positive, SIGN-R1-positive, and Dectin2-positive." + "Any process that modulates synaptic transmission by regulating translation occurring at the presynapse." + "The chemical reactions and pathways involving keratan sulfate, a glycosaminoglycan with repeat units consisting of beta-1,4-linked D-galactopyranosyl-beta-(1,4)-N-acetyl-D-glucosamine 6-sulfate and with variable amounts of fucose, sialic acid and mannose units; keratan sulfate chains are covalently linked by a glycosidic attachment through the trisaccharide galactosyl-galactosyl-xylose to peptidyl-threonine or serine residues." + "A cell found in the embryo before the formation of all the gem layers is complete." + "An epithelial cell of the cortical portion of the thymus. Epithelial cells in this region are required for positive selection of CD8-positive T cells." "BTO:0004562" + + "Any apoptotic process in an outer hair cell." + "Functional part of an organ in the body. This is in contrast to the stroma, which refers to the structural tissue of organs, being exactly, connective tissues." "EHDAA:9196 NCIT:C74601 Wikipedia:Parenchyma EHDAA:9202 EHDAA:3905 EHDAA:4005 EHDAA:9182 EHDAA:8086 EHDAA:6899 EHDAA:9190 UMLS:C0933845 EHDAA:3999 FMA:45732 EHDAA:3015 EHDAA:6994 EHDAA:6903" + "The zone between the red and white pulp of the spleen containing numerous macrophages and lymphocytes, and a rich plexus of sinusoids supplied by white pulp arterioles carrying blood-borne antigens." "EMAPA:36650 MA:0000755 UMLS:C1711368 Wikipedia:Marginal_zone CALOHA:TS-2395 NCIT:C49767 FMA:15852" + "Any process that modulates the frequency, rate or extent of brown fat cell proliferation." + "Binding to fibrinogen, a highly soluble hexameric glycoprotein complex that is found in blood plasma and is converted to fibrin by thrombin in the coagulation cascade." + "The chemical reactions and pathways resulting in the breakdown of a glycoprotein, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide." + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an epinephrine stimulus. Epinephrine is a catecholamine that has the formula C9H13NO3; it is secreted by the adrenal medulla to act as a hormone, and released by certain neurons to act as a neurotransmitter active in the central nervous system." + "A disseminated nephrocyte is a nephrocyte that filters hemolymph and is found at scattered locations in the fat body or other tissues." + "An indentation of the olfactory placode which ends when the pits hollows out to form the nasopharynx[GO]." "XAO:0004073 EHDAA2:0001295 FMA:295840 EMAPA:16800 EHDAA:4772 AAO:0011068 SCTID:361485001 Wikipedia:Nasal_pit XAO:0000275 EFO:0003496" + "A duct that is part of a sebaceous gland." "FMA:70947 NCIT:C33520" + "A collection of all skeletal elements in some subdivision of the vertebral column." "FMA:16201" + "A coiling which is relatively high." + "The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a cell that will form part of the cardiac organ of an individual." + "Cranial neural crest that gives rise to the facio-acoustic ganglion." "ZFA:0000762 EMAPA:16312 EHDAA:658 VHOG:0000268 EHDAA2:0000492 TAO:0000762" + "A spinal cord segment that adjacent_to a cervical region." "MA:0003081 SCTID:180960003 FMA:71166 neuronames:1654 BIRNLEX:1499 UMLS:C1278837 UMLS:C0581619 NCIT:C12892" + "The orderly movement of epithelial cells within a renal tubule that contributes to metanephric nephron tubule morphogenesis." + "Formation of dendrites, branched cellular projections (or cytoplasmic extension) that are extended from the surface of a dendritic immune cell, and which enable the cell to sample luminal pathogens and increase the surface area for antigen presentation to T cells." + "The process in which the anatomical structure of a trigeminal ganglion is generated and organized." + "An intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layer 6 that expresses Car3." + "A developmental process, independent of morphogenetic (shape) change, that is required for bone to attain its fully functional state." + "An intermediate monocyte that is CD14-positive and with low amounts of CD16." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level." + "An unswitched memory B cell is a memory B cell that has the phenotype IgM-positive, IgD-positive, CD27-positive, CD138-negative, IgG-negative, IgE-negative, and IgA-negative." + "Any process that modulates the frequency, rate or extent of the release into the cytosolic compartment of calcium ions sequestered in the endoplasmic reticulum or mitochondria." + "Any process that modulates the frequency, rate, or extent of monocyte antigen processing and presentation." + "BTO:0004626" + "The chemical reactions and pathways involving a compound containing a pyrocatechol (1,2-benzenediol) nucleus or substituent." + "Material anatomical entity that forms the outermost boundary of an anatomical structure." "ZFA:0005594 AAO:0010270" + "A myofibril of a skeletal muscle fiber." + "The morphogenetic process in which a bud forms from the mammary placode. A mammary bud is bulb of epithelial cells that is distinct from the surrounding epidermis." + "Any process that modulates the frequency, rate or extent of macrophage differentiation." + "The process by which an organelle membrane interacts with another membrane via molecular tethers that physically bridge the two membranes and attach them to each other." + "An anatomical wall that is part of a cardiac ventricle [Automatically generated definition]." "MA:0002791 NCIT:C119295 FMA:13884" + + "An enterocyte that is part of the epithelium proper of small intestine." "FMA:263096" + "The change in morphology and behavior of a basophil resulting from exposure to a cytokine, chemokine, soluble factor, or to (at least in mammals) an antigen which the basophil has specifically bound via IgE bound to Fc-epsilonRI receptors." "Wikipedia:Basophil_activation" + "The process in which anatomical structures of the mammary gland are generated and organized. Morphogenesis refers to the creation of shape. The mammary gland is a large compound sebaceous gland that in female mammals is modified to secrete milk." + "The process in which a relatively unspecialized cell acquires specialized features of a striated muscle cell; striated muscle fibers are divided by transverse bands into striations, and cardiac and voluntary muscle are types of striated muscle." + "A protein complex composed of an Fc-gamma RIII alpha chain and an Fc-epsilon RI gamma chain dimer with or without an Fc-epsilon RI beta chain and additional signaling components. The complex functions primarily as an activating receptor for IgG." + "A lymphoid follicle that is part of a lymph node." "EMAPA:35527 MA:0000742" + "A developmental process in which a progressive change in the state of some part of an organism, germline or somatic, specifically contributes to its ability to form offspring." + "The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction." "Wikipedia:Sporogenesis" + + "Any process that stops, prevents, or reduces the frequency, rate or extent of transmission of a nerve impulse, the sequential electrochemical polarization and depolarization that travels across the membrane of a neuron in response to stimulation." + "A myoepithelial cell that is part of the dilatator pupillae." "FMA:70619" + "A large binucleate cell that forms a 'garland' around the anterior end of the proventriculus (cardia) at its junction with the esophagus in both adults and larvae flies. Each cell is surrounded by a basement membrane and there are numerous micro-invaginations (lacunae) extending from the surface into the cytoplasm. At the mouth of each lacuna is a doubled filament forming a specialised filtration system (diaphragm). The filtrate is endocytosed from the lacunae." "FBbt:00005059 BTO:0004596" + "Any synovial joint that is part of a (free) limb." "FMA:258776" + "Any cellular process that results in the specification, formation or maintenance of the apicobasal polarity of a neuroblast cell, a progenitor of the central nervous system." + "Any process that modulates the frequency, rate or extent of T-helper 2 cell activation." + "An epithelium that is part of a seminal vesicle [Automatically generated definition]." "CALOHA:TS-2069 MA:0001745 UMLS:C1710049 NCIT:C49295 EMAPA:29771" + "An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc)." "VSAO:0000303 EMAPA:37854 FMA:24874" + "Any process that stops, prevents, or reduces the frequency, rate or extent of embryonic development." + "An epithelial cell of the kidney cortex." "KUPO:0001016" + "A C-X-C chemokine receptor type 5 that is encoded in the genome of mouse." "UniProtKB:Q04683" + "The first few specialized divisions of an activated animal egg; Stage consisting of division of cells in the early embryo. The zygotes of many species undergo rapid cell cycles with no significant growth, producing a cluster of cells the same size as the original zygote. The different cells derived from cleavage are called blastomeres and form a compact mass called the morula. Cleavage ends with the formation of the blastula." "Wikipedia:Cleavage_(embryo) ZFS:0000046 BilaDO:0000006 OGES:000020 MESH:D002970 BILS:0000107 XAO:1000004 OGES:000015 PdumDv:0000200 MmusDv:0000004 EFO:0001290 FBdv:00000054" + + "A single extraembryonic epithelium, which closes the germband dorsally." "BTO:0004800 EFO:0000250" + "Any process that activates or increases the frequency, rate or extent of iron ions import across plasma membrane." + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of carbohydrates." + "Any process that decreases the frequency, rate or extent of mesenchymal cell proliferation. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets." + "Any process that stops, prevents or reduces the frequency, rate or extent of L-glutamate import into a cell." + "A preadipocyte that is capable of differentiating into a brown adipocyte. This cell type expresses uncoupling protein-1, PPAR-gamma, PR-domain-containing 16; and PGC-1alpha (peroxisome proliferator-activated receptor-gamma (PPARgamma) coactivator-1alpha)." + "An organ that detects light." "MIAA:0000140 GAID:69 EFO:0000827 CALOHA:TS-0309 Wikipedia:Eye BILA:0000017 BTO:0000439 MESH:D005123 EV:0100336 MAT:0000140" + "An enteroendocrine cell which produces a gastrin- and cholecystokinin-like peptide. The apical microvilli-rich plasma membrane is in open contact with the small intestine mucosa. This cell type is devoid of gastrin-17 but contains other fragments of the gastrin polypeptide." "FMA:63421" + "Any process that stops, prevents, or reduces the frequency, rate or extent of T-helper 1 cell differentiation." + "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together." + "Enables the transfer of polysaccharides from one side of a membrane to the other. A polysaccharide is a polymer of many (typically more than 10) monosaccharide residues linked glycosidically." + "A tissue-resident macrophage found in the alveoli of the lungs. Ingests small inhaled particles resulting in degradation and presentation of the antigen to immunocompetent cells. Markers include F4/80-positive, CD11b-/low, CD11c-positive, CD68-positive, sialoadhesin-positive, dectin-1-positive, MR-positive, CX3CR1-negative." "BTO:0000802 CALOHA:TS-0030 FMA:83023" + "Obsolete. Use PO:0020094 from Plant Ontology instead. The female gamete of plants." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the movement of proteins from the cytoplasm into the nucleus." + "One of the two photoreceptor cell types in the vertebrate retina. In cones the photopigment is in invaginations of the cell membrane of the outer segment. Cones are less sensitive to light than rods, but they provide vision with higher spatial and temporal acuity, and the combination of signals from cones with different pigments allows color vision." "FMA:67748 CALOHA:TS-0866 BTO:0001036" + "A thick plate of cells derived from the neural ectoderm in the head region of the embryo that develops into the olfactory region of the nasal cavity." "EMAPA:16543 ZFA:0000048 Wikipedia:Nasal_placode AAO:0011076 EFO:0003420 XAO:0000005 EHDAA2:0001232 FMA:293971 TAO:0000048 VHOG:0000186 EHDAA:1504" + "Any process that modulates the frequency, rate or extent of the directed movement of nucleobases, nucleosides, nucleotides and nucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "The spinal accessory nucleus lies within the cervical spinal cord (C1-C5) in the ventral horn. The nucleus ambiguus is classically said to provide the 'cranial component' of the accessory nerve. However, the very existence of this cranial component has been recently questioned and seen as contributing exclusively to the vagus nerve. The terminology continues to be used in describing both human anatomy, and that of other animals." "Wikipedia:Spinal_accessory_nucleus EMAPA:37067 MA:0001033 neuronames:2003 FMA:83965" + "A macromolecular complex containing both protein and DNA molecules." + "The structure containing the glomerular capsule and the glomerulus that serves as the initial blood-filtering component of a nephron." "VHOG:0001262 BTO:0000333 Wikipedia:Renal_corpuscle EMAPA:28236 TAO:0005281 EV:0100385 SCTID:361329009 FMA:15625 MA:0000376 ZFA:0005281 NCIT:C33456 UMLS:C0227635 EMAPA:35726 CALOHA:TS-1317" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the formation and development of a tooth or teeth." + "A precursor B cell is a B cell with the phenotype CD10-positive." "CALOHA:TS-0819 BTO:0001133" + "Any process that modulates the frequency, rate or extent of a response to an external stimulus." + "Any process that activates or increases the rate or extent of osteoblast proliferation." + "Any process that activates or increases the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule." + "The process in which a relatively unspecialized cell acquires the specialized features of a rod bipolar cell." + "Stage succeeding embryo, including mature structure." "OGES:000010 OGES:000024 WBls:0000103 WBls:0000022 WBls:0000093 OGES:000014 BilaDO:0000003" + "The process whose specific outcome is the progression of the intermediate mesoderm over time, from its formation to the mature structure. The intermediate mesoderm is located between the lateral mesoderm and the paraxial mesoderm. It develops into the kidney and gonads." + "Any process that stops, prevents, or reduces the rate of leukocyte mediated cytotoxicity." + "A programmed cell death protein 1 that is encoded in the genome of mouse." "UniProtKB:Q02242" + "KUPO:0001002" + "Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding." + "A mature natural killer cell that is CD27-high and CD11b-high. This cell type is capable of interferon-gamma secretion." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of histamine into a cell." + "The chemical reactions and pathways resulting in the formation of progesterone, a steroid hormone produced in the ovary which prepares and maintains the uterus for pregnancy. Also found in plants." + "A B220-low CD38-positive unswitched memory B cell is a CD38-positive unswitched memory B cell that has the phenotype B220-low, CD38-positive, IgD-positive, CD138-negative, and IgG-negative." + "Gr1-high monocyte that has a MHC-II receptor complex." + "Any process that activates or increases the frequency, rate or extent of forebrain neuron differentiation." + "A specialized epithelial cell that contains \"feet\" that interdigitate with the \"feet\" of other glomerular epithelial cells in the metanephros." + "A hindlimb bone or its cartilage or pre-cartilage precursor." + "A T-cell surface glycoprotein CD5 that is encoded in the genome of human." "UniProtKB:P06127" + "KUPO:0001070" + "The initial attachment of a membrane or protein to a target membrane. Docking requires only that the proteins come close enough to interact and adhere." + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of juvenile hormone." + "Any process that modulates the frequency, rate or extent of skeletal muscle contraction by changing the calcium ion signals that trigger contraction." + "The directed movement of RNA to a specific location." + "A blastoconidium that has more than one nucleus." "FAO:0000036" + "The chemical reactions and pathways resulting in the formation of hexose, any monosaccharide with a chain of six carbon atoms in the molecule." + + "A conducting pathway in the conducting tissue of heart through which electrical activity spreads from the SA node to the AV node." "FMA:9479" + "A connective tissue cell found in bone." + "A mucosa that is part of a left hepatic duct [Automatically generated definition]." "FMA:14693" + "The chemical reactions and pathways resulting in the formation of dopamine, a catecholamine neurotransmitter and a metabolic precursor of noradrenaline and adrenaline." + "An organ system subdivision that is the part of the lymphoid system that includes the pulmonary lymphatic vessels." "FMA:67999" + "Glomerulus of the mature vertebrate kidney, or metanephros." "VHOG:0001242" + "The bone that is situated in the orbit on either side of the presphenoid; it generally forms a part of the sphenoid in the adult, and may be independent in the young." "AAO:0000345 Wikipedia:Lesser_wing_of_sphenoid_bone SCTID:361737003 ZFA:0000253 EMAPA:18719 VHOG:0001153 TAO:0000253 MA:0002773 FMA:52869" + "Any of the eight ligaments pertaining to the uterus including the anterior, posterior, lateral, sacro-uterine and round ligaments." "SCTID:272668006 NCIT:C61360" + "NLX:144263" + "The movement of a leukocyte in response to an external stimulus." + "A free floating cell, including amebocytes and eleocytes, in the coelom of certain animals, especially annelids." "WBbt:0005751 BTO:0002856" + + "A subpopulation of amacrine cell that migrate further than other amacrine cells, and come to lie basal to the inner plexiform layer (IPL) in the ganglion cell layer. Displaced amacrine cells still have their neurites extending apically into the IPL, and therefore exhibit an inverted polarity with respect to the other amacrine cells." + "Closed space within the ectoplacental cone, formed by the fusion of the parts of the amniotic fold that separate it from the amniotic cavity[MP]. a developmental cavity that exists in some mammals and is derived by division of the proamniotic space; it is further removed from the embryo than the amniotic cavity in some mammals." "EMAPA:16080" + "A presumptive structure that has the potential to develop into a pronephric mesoderm." "TAO:0001070 EFO:0003619 ZFA:0001070" + "A protein that has G protein-coupled receptor (GPCR) activity. Each GPCR consists of a single polypeptide with an extracellular N-terminus, an intracellular C-terminus and seven hydrophobic transmembrane domains (TM1-TM7) linked by three extracellular loops (ECL1-ECL3) and three intracellular loops (ICL1-ICL3). GPCRs function as part of a heterotrimeric complex to transmit an extracellular signal across the membrane by activating an associated G-protein via the exchange of GDP for GTP on the alpha subunit." "IUPHARfam:694" + "Binding to chondroitin sulfate, a glycosaminoglycan made up of two alternating monosaccharides: D-glucuronic acid (GlcA) and N-acetyl-D-galactosamine (GalNAc)." + "Combining with cholecystokinin and transmitting the signal across the membrane by activating an associated G-protein to initiate a change in cell activity. Cholecystokinin can act as a neuropeptide or as a gastrointestinal hormone." + "A bulbous anterior projection of the olfactory lobe that is the place of termination of the olfactory nerves and is especially well developed in lower vertebrates (as fishes)[BTO]." "MA:0000194 neuronames:279 Wikipedia:Olfactory_bulb EV:0100173 BAMS:Olf EHDAA2:0004705 DHBA:10307 SCTID:279394006 VHOG:0000033 AAO:0010165 BM:Tel-OB UMLS:C0028936 MESH:D009830 BIRNLEX:1137 BAMS:DLB HBA:9303 FMA:77624 NCIT:C28401 CALOHA:TS-0702 XAO:0004180 GAID:633 BAMS:OB TAO:0000402 BTO:0000961 EMAPA:32809 ZFA:0000402" + "Any process that modulates the rate, frequency or extent of fertilization. Fertilization is the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy)." + "Any process that activates or increases the frequency, rate or extent of blood vessel branching." + "A monostratified retinal ganglion cell with large soma and medium dendritic field, with dense dendritic arbor." + "Any process that activates or increases the frequency, rate or extent of protein localization to synapse." + "A compact bone tissue that is part of a diaphysis." "FMA:32678" + "A nuclear bag fiber that is sensitive only changes in muscle length but not the rate of that change." + "The chemical reactions and pathways involving glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues in alpha-(1->4) glycosidic linkage, joined together by alpha-(1->6) glycosidic linkages." + "Ganglion containing neurons that receive innervation from parasympathetic neurons in the central nervous system and subserves parasympathetic functions through innervation of smooth muscle, cardiac muscle and glands." "FMA:5894 UMLS:C0017069 EHDAA2:0001400 NCIT:C52557 EMAPA:32813 Wikipedia:Parasympathetic_ganglion NLXANAT:100303 BTO:0001256 SCTID:279284004 MA:0002469" + "The chemical reactions and pathways resulting in the breakdown of an organic substance, any molecular entity containing carbon." + "An anastomosing network of delicate tubules located in the hilum of the testicle (mediastinum testis) that carries sperm from the seminiferous tubules to the vasa efferentia[WP]." "FMA:19834 MESH:D012152 Wikipedia:Rete_testis UMLS:C0035278 MA:0003013 GAID:399 EMAPA:18332 NCIT:C33467 SCTID:279617009" + "KUPO:0001069" + "The metatarsus or metatarsal bones are a group of five long bones in the pes located between the tarsal bones of the hind- and mid-pes and the phalanges of the toes. Lacking individual names, the metatarsal bones are numbered from the medial side (side of big toe): the first, second, third, fourth, and fifth metatarsal. The metatarsals are analogous to the metacarpal bones of the manus. [WP,unvetted]." "UMLS:C0025584 BTO:0002347 MESH:D008682 Wikipedia:Metatarsal_bone EMAPA:36159 NCIT:C12752 FMA:24492 EMAPA:32940 SCTID:302532000 galen:Metatarsal MA:0000303 GAID:193" + "The metathalamus is a composite structure of the thalamus, consisting of the medial geniculate nucleus and the lateral geniculate nucleus. [WP,unvetted]." "SCTID:361550004 EV:0100217 EMAPA:35376 Wikipedia:Metathalamus MBA:1008 BAMS:Metathalamus neuronames:351 BAMS:MetThal MA:0000868 FMA:62023 BAMS:MTh BIRNLEX:1461 BAMS:GENd" + "A primary neuron (sensu Teleostei) that has a sensory function." + "The process whose specific outcome is the progression of the cartilage that will provide a scaffold for mineralization of endochondral bones as they elongate or grow." + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds." + "Any process that activates or increases the frequency, rate, or extent of T cell mediated immunity." + "Body substance in a liquid or semi-solid state in the eyeball which serves to refract light." "MA:0001911" + "The increase in size or mass of an intramembranous bone that contributes to the shaping of the bone." + "A ligament that is part of a diaphragm." "EMAPA:19236 FMA:58280" + "Any process that modulates the frequency, rate or extent of cardiac muscle contraction." + "A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition." + "Any process that activates or increases the frequency, rate or extent of vasculogenesis." + "A ring of ribrous tissue that surrounds the atrioventricular and arterial orifices." "EMAPA:37422 FMA:9497 BTO:0003628 Wikipedia:Fibrous_rings_of_heart" + "A myeloid dendritic cell found in the blood, lymph nodes, tonsil, bone marrow, and spleen that is CD141-positive (BDCA-3), XCR1-positive, and Clec9A-positive. This cell-type can cross-present antigen to CD8-positive T cells and can produce inteferon-beta." + "The pair of anatomical structures comprised of a left lung and right lung." "FMA:68877" + "The combination of pericardial sac (a double-walled sac containing the heart and the roots of the great vessels) plus fibrous pericardium." "VHOG:0001280 FMA:9869 BSA:0000090 EHDAA:5376 UMLS:C0031050 GAID:569 NCIT:C13005 AAO:0010817 ZFA:0000054 CALOHA:TS-0761 MA:0000099 EV:0100023 SCTID:181295003 XAO:0004182 MAT:0000454 EFO:0000820 galen:Pericardium Wikipedia:Pericardium MESH:D010496 RETIRED_EHDAA2:0001443 BTO:0000717" + "KUPO:0001066" + "An epithelium of the lobular bronchiole." + "Tissue that is part of some adrenal gland." "NCIT:C32051" + "The process in which the anatomical structures of the pronephros are generated and organized. In mammals, the pronephros is the first of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the pronephros is the fully functional embryonic kidney and is indispensable for larval life." + "The progression of the retinal pigment epithelium over time, from its initial formation to the mature structure. The retinal pigment epithelium is the melanin-containing layer of cells between the retina and the choroid that absorbs scattered and reflected light and removes waste products produced by the photoreceptor cells." + "A specialized multinuclear osteoclast associated with the absorption and removal of cementum." + "Any process that stops, prevents, or reduces the frequency, rate or extent of dopaminergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter dopamine." + "The directed movement of a vesicle along a cytoskeletal fiber such as a microtubule or and actin filament, mediated by motor proteins." + "Any dermis lymphatic vessel endothelial cell that is part of a microvascular endothelium." + "The directed movement of the nucleus to a specific location within a cell." + "The cell protoplasm after removal of the cell wall." "MESH:D011523" + "The slender connective tissue fiber in the extracellular matrix of skin tissue that is composed of microfibrils and amorphous elastin and is characterized by great elasticity." "EMAPA:37841" + "The process whose specific outcome is the progression of the digestive system over time, from its formation to the mature structure. The digestive system is the entire structure in which digestion takes place. Digestion is all of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism." + "An epithelium that is part of a utricle of membranous labyrinth [Automatically generated definition]." "RETIRED_EHDAA2:0002155 FMA:75604 VHOG:0000634 MA:0001204 EMAPA:17295 EHDAA:4730" + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane." + "The sole is the bottom of the foot." "CALOHA:TS-0379 BTO:0005078 SCTID:57999000 UMLS:C0230463 NCIT:C33326 Wikipedia:Sole_(foot) galen:SoleOfFoot FMA:25000" + "The chemical reactions and pathways resulting in the formation of bile acids, any of a group of steroid carboxylic acids occurring in bile." + "Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack." + "Any process that stops, prevents, or reduces the frequency, rate or extent of zygospore formation, a process in which a thick-walled spore of some algae and fungi is formed by union of two similar sexual cells, usually serves as a resting spore, and produces the sporophytic phase." + "Any process that activates or increases the frequency, rate or extent of cell motility." + "A polychromatophilic erythroblast that is Lyg 76-high and is Kit-negative." + "KUPO:0001067" + "A proximal phalanx that is part of a pedal digit [Automatically generated definition]." "SCTID:85533000 NCIT:C52785 FMA:75828 MA:0001387 UMLS:C0224020 EMAPA:37312" + "Any process that activates or increases the frequency, rate or extent of plasma cell differentiation." + "The external part of the developing pharynx that is made of ectoderm. During vertebrate development, pockets form in pharyngeal ectoderm between the pharyngeal arches." "ZFA:0001379 TAO:0001379" + "Any process that activates or increases the frequency, rate or extent of sperm capacitation." + "The directed movement of serotonin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Serotonin (5-hydroxytryptamine) is a monoamine neurotransmitter occurring in the peripheral and central nervous systems." + "The biological process whose specific outcome is the progression of a pharynx from an initial condition to its mature state. The pharynx is the part of the digestive system immediately posterior to the mouth." + "A C-type lectin domain family 7 member A that is encoded in the genome of mouse." "UniProtKB:Q6QLQ4" + "FMA:23356 NCIT:C33164" + "The enzymatic generation of superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species, by a cell in response to environmental stress, thereby mediating the activation of various stress-inducible signaling pathways." + "A specialized epithelial cell that contains \"feet\" that interdigitate with the \"feet\" of other glomerular epithelial cells in the pronephros." + "A presumptive structure that has the potential to develop into a forebrain." "TAO:0000062 EFO:0003423 BAMS:Pros EHDAA2:0000661 ZFA:0000062 EMAPA:16640 Wikipedia:Prosencephalon EHDAA:2643" + "The process whose specific outcome is the progression of an extraembryonic membrane over time, from its formation to the mature structure." + "A goblet cell located in the nasal epithelium." "MP:0002262" + "A chromatophore that is part of the dermis." + "Any process that modulates the frequency, rate or extent of striated muscle development." + "A gut-associated lymphoid tissue macrophage found in the Peyer's patches." + "The process whose specific outcome is the progression of the lateral line over time, from its formation to the mature structure. The lateral line consists of small sensory patches (neuromasts) located superficially on the skin or just under the skin in fluid-filled canals on the head and body of all fishes and most amphibians. The lateral line develops from cranial ectodermal placodes situated behind the ear and between the eye and ear." + "Any process that activates or increases the frequency, rate or extent of response to calcium ion." + "Any process that modulates the frequency, rate or extent of extracellular matrix assembly." + "The process in which the anatomical structures of the olfactory placode are generated and organized. The olfactory placode is a thickening of the neural ectoderm in the head region of the vertebrate embryo which develops into the olfactory region of the nasal cavity." + "The process in which a relatively unspecialized hemocyte precursor cell acquires the specialized features of a lamellocyte. Lamellocytes are a hemocyte lineage that exists only in larvae, but are seldom observed in healthy animals. Lamellocytes differentiate massively in the lymph glands after parasitization and are large flat cells devoted to encapsulation of invaders too large to be phagocytosed by plasmatocytes." + "A memory regulatory T cell with phenotype CD4-positive, CD25-positive, CD127lo, CCR4-positive, and CD45RO-positive." + "Any process that modulates the frequency, rate or extent of smooth muscle contraction involved in micturition." + "Any process that activates or increases the frequency, rate or extent of vascular smooth muscle cell differentiation." + "A zone of skin that is part of a thorax [Automatically generated definition]." "FMA:23029 MA:0000564 SCTID:281723000 EMAPA:37765 FMA:23028" + "Pia mater or arachnoid mater." "neuronames:2347 Wikipedia:Leptomeninges SCTID:362303006 UMLS:C0228126 CALOHA:TS-0546 FMA:231515 NCIT:C32979 NLXANAT:090207 BTO:0001634" + "A CD34 molecule that is encoded in the genome of mouse." "UniProtKB:Q64314" + "The process whose specific outcome is the progression of the branchiomeric skeletal muscle over time, from its formation to the mature structure. The branchiomeric muscle is derived from cranial mesoderm and controls facial expression, pharyngeal and laryngeal function, operating the jaw. The muscle begins its development with the differentiation of the muscle cells and ends with the mature muscle. Branchiomeric muscles of mammals correspond to the gill musculature of fish." + "A fibroblast that is part of the areolar connective tissue." "FMA:261279" + "A photoreceptor cell that is sensitive to blue light." + "A ribonucleoprotein complex that contains aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator)." + "A transparent homogeneous acellular layer found between the substantia propria and the endothelial layer of the cornea[MP]." "TAO:0002157 FMA:58309 MA:0001246 SCTID:281076002 EMAPA:18804 ZFA:0001686 Wikipedia:Descemet%27s_membrane NCIT:C32454 MESH:D003886 GAID:894 UMLS:C0011665" + "A neurogenic placode that arises at the level of the midbrain-hindbrain boundary and develops into a trigeminal ganglion." "EHDAA2:0004209 VHOG:0000109 TAO:0000162 XAO:0000225 ZFA:0000162 EFO:0003433" + "An epithelium that is part of a lower leg [Automatically generated definition]." "VHOG:0001050 EHDAA2:0001031 EMAPA:17497" + "The process whose specific outcome is the progression of a lens fiber cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a lens fiber cell fate. A lens fiber cell is any of the elongated, tightly packed cells that make up the bulk of the mature lens in a camera-type eye." + "The directed movement of organelles or molecules along microtubules from the cell body toward the cell periphery in nerve cell axons." + "BTO:0004638 FMA:13119 SCTID:88410004" + "The chemical reactions and pathways involving any oxoacid; an oxoacid is a compound which contains oxygen, at least one other element, and at least one hydrogen bound to oxygen, and which produces a conjugate base by loss of positive hydrogen ion(s) (hydrons)." + "Mast cell subtype whose granules contain both the serine proteases tryptase and chymase. These cells are primarily found in connective tissue, such as the peritoneal cavity, skin, and intestinal submucosa. Their development is T-cell independent." + "A clavicle that is in the right side of a entire appendicular skeleton." "FMA:13322" + "Enables the transfer of gamma-aminobutyric acid from one side of a membrane to the other. Gamma-aminobutyric acid is 4-aminobutyrate (GABA)." + "Any bone that is part of the lower jaw skeleton. This includes (when present): the dentary/mandible, the articular, the splenial, the suprangular." + "A ciliated cell of the bronchus." + "A non-mucous, epithelial secretory cell that is part of the tracheobronchial tree. A club cell has short microvilli but no cilia. A club cell is able to multiply and differentiate into ciliated cells to regenerate the bronchiolar epithelium and it also protects the tracheobronchial epithelium." "BTO:0004811 FMA:14119" + "Multi fate stem cell that gives rise to both hepatocytes and cholangiocytes as descendants. The term often refers to fetal precursors of hepatocytes (differently from 'hepatic stem cell', usually applied to the self-renewing pool of hepatocyte precursors in the adult liver). Hepatoblasts may also be endogenous, as some stem cells found in the liver come from the bone marrow via blood circulation." + "A portion of skeletal muscle tissue that is part of a deltoid [Automatically generated definition]." "FMA:261732" + "The chemical reactions and pathways involving organic acids, any acidic compound containing carbon in covalent linkage." + "The process in which a relatively unspecialized myeloid precursor cell acquires specialized features of a basophil cell." + "An anatomical boundary that corresponds to some physical discontinuity." "CARO:0001004" + "An epithelial cell that is part of the viscerocranial mucosa." "FMA:70583" + "A blood vessel that is part of a kidney [Automatically generated definition]." "TAO:0005306 ZFA:0005306 MA:0001682" + "OBSOLETE: A walled spore produced in a sporangium." + "Obsolete. Consult Plant Ontology instead. The cell in the phloem tissue concerned with mainly longitudinal conduction of food materials. Classified into sieve cell and sieve tube member." + "A process in which a protein is transported to, or maintained in, a location within a motile cilium." + "ZFA:0000228" + "Medullary venules are a continuation of high endothelial venules which condense repeatedly in the interfollicular cortex and peripheral deep cortical unit and then transition to medullary venules at the corticomedullary junction. The medullary venules condense and return centripetally to the hilar vein." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the cyclical phases of growth (anagen), regression (catagen), quiescence (telogen), and shedding (exogen) in the life of a hair." + "A homeostatic process involved in the maintenance of a steady state level of water within a cell." + "The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell of the prostate gland." + "The larger of the two otolith organs in the vestibule." "VHOG:0000289 AAO:0000625 MA:0000247 FMA:61113 TAO:0000700 NCIT:C33844 EHDAA2:0002153 EV:0100368 EMAPA:17293 BTO:0001807 EHDAA:4726 AAO:0011109 SCTID:279817006 XAO:0000195 Wikipedia:Utricle_(ear) ZFA:0000700 UMLS:C0042158" + "Any process that activates or increases the frequency, rate or extent of hematopoietic stem cell proliferation." + "The developmental process that results in the deposition of coloring matter in an organism, tissue or cell." + "The expansion of an activated CD4-positive, alpha-beta T cell population by cell division." + "Formation and maintenance of a polarized microtubule array originating from a microtubule-organizing center (MTOC) in the oocyte. An example of this is found in Drosophila melanogaster." + "A bistratified amacrine cell with a medium dendritic field, a flat and sparse dendritic arbor, and post-synaptic terminals at the intersections of S1 and S2, and S3 and S4." + "Any process that stops, prevents or reduces the frequency, rate or extent of protein localization to cilium." + "This cell type produces and secretes melatonin and forms the pineal parenchyma. Extending from each cell body, which has a spherical, oval or lobulated mucleus, are one or more tortuous basophilic processes, containing parallel microtubules known as synaptic ribbons. These processes end in expanded terminal buds near capillaries or less, frequently, ependymal cells of the pineal recess. The terminal buds contain granular endoplasmic reticulum, mitochondria and electron-dense cored vesicles, which store monoamines and polypeptide hormones, release of which appears to require sympathetic innervation." "FMA:83417 BTO:0001068" + "Obsolete. Use PO:0000289 from Plant Ontology instead. One of the series of cellular components of a sieve tube. It shows a more or less pronounced differentiation between sieve plates (wide pores) and lateral sieve areas (narrow pores). Also sieve tube element and the obsolete sieve tube segment." + "A muscular coat that is part of a duodenum." "SCTID:362147007 FMA:14944" + "Any process that modulates the frequency, rate or extent of gastric mucosal blood circulation." + "Any process that modulates the rate, frequency, extent of the regulated release of somatostatin from secretory granules in the D cells of the pancreas." + "A vip GABAergic cortical interneuron with a soma found in L5. L5 vip cells have mostly local morphology with some deep-projecting axons. They show only moderate resistance, comparable to that of sst subclass and unlike typical Vip subclass cells that tend to show high input resistance. L5 vip cells show particularly low resting membrane potential." + "GC_ID:1" + "Ossicle that is part of the axial skeleton." "VSAO:0000133" + "Any process that activates or increases the frequency, rate or extent of microglial cell migration." + "A taste receptor cell that has a short microvilli, a projecting apical region, a large rounded nucleus, and expresses taste chemoreceptors thus making them the transducing cell for taste qualities." "FMA:62381" + "EMAPA:35312 FMA:5896 UMLS:C0501399 MA:0001144 NCIT:C52709 Wikipedia:Enteric_ganglia" + "Any process that activates or increases the frequency, rate or extent of pancreatic B cell development." + "A terminal bronchiole that is part of a left lung [Automatically generated definition]." "UMLS:C1708675 MA:0001780 NCIT:C49255 EMAPA:36636" + "A diffuse collection of lymphpoid cells that participate in airway immune responses." "FMA:62821 UMLS:C1179418 MA:0000135 NCIT:C32234" + "Any process that modulates the frequency, rate or extent of protein binding." + "The formation of a solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts." + "Any process that stops, prevents, or reduces the frequency, rate or extent of branchiomeric skeletal muscle development. Branchiomeric skeletal muscle development is the process whose specific outcome is the progression of the branchiomeric skeletal muscle over time, from its formation to the mature structure." + "A ciliated tubular structure in a submucosal gland connecting the submucosal gland collecting duct with the surface epithelium." + "A nail, hoof or claw." "MESH:D006724" + "The chemical reactions and pathways involving an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group, as carried out by individual cells." + "Any process that stops, prevents or reduces the frequency, rate or extent of lung goblet cell differentiation." + "Any process that modulates the frequency, rate, or extent of memory T cell differentiation." + "Any process that modulates the frequency, rate or extent of the regulated release of insulin that contributes to the response of a cell to glucose." + "A muscle that acts on the pharynx[WP, vetted]." "GAID:154 TAO:0000172 FMA:46619 Wikipedia:Pharyngeal_muscles BTO:0001048 EFO:0003504 NCIT:C13075 ZFA:0000172 UMLS:C0031346 SCTID:244798004 MESH:D010609 MA:0001797" + "The progression of the hepaticobiliary system over time, from its formation to the mature structure. The hepaticobiliary system is responsible for metabolic and catabolic processing of small molecules absorbed from the blood or gut, hormones and serum proteins, detoxification, storage of glycogen, triglycerides, metals and lipid soluble vitamins and excretion of bile. Included are the synthesis of albumin, blood coagulation factors, complement, and specific binding proteins." + "One of the pair of mesenchymal swellings (folds) located on either side of the cloacal membrane during the indifferent stage of embryonic development; cranial to the cloacal membrane the folds unite to form the genital tubercle; caudally the folds are subdivided into urogenital folds anteriorly and anal folds posteriorly." "EHDAA2:0004009" + "A tissue macrophage that is in the pleural space." "FMA:83024" + "A portal vein that drains the descending colon. It is a tributary of the inferior mesenteric vein, and follows the path of its corresponding artery, the left colic artery." "FMA:15394" + "The lacrimal glands are paired almond-shaped glands, located in or near the orbital region, that secrete the aqueous layer of the tear film.[WP]." "Wikipedia:Lacrimal_gland CALOHA:TS-0512 EMAPA:35463 SCTID:181147003 MA:0001296 BTO:0000044 Wikipedia:Preorbital_gland EFO:0001389 UMLS:C0022907 EV:0100339 FMA:59101 VHOG:0001476 NCIT:C12346" + "The directed movement of dopamine into a cell." + "Any process that modulates the frequency or amplitude of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse. Amplitude, in this case, refers to the change in postsynaptic membrane potential due to a single instance of synaptic transmission." + "The directed movement of a neurotransmitter receptor complex along microtubules in nerve cell dendrites towards the postsynapse." + "An otic fibrocyte that lines the otic capsule." + "The radial migration of a pyramidal neuron along radial glial cells." + "Any process that stops, prevents or reduces the rate or extent of hemocyte proliferation. Hemocytes are blood cells associated with a hemocoel (the cavity containing most of the major organs of the arthropod body) which are involved in defense and clotting of hemolymph, but not involved in transport of oxygen. An example of this is found in Drosophila melanogaster." + "Any process that activates or increases the frequency, rate or extent of outer hair cell apoptotic process." + "A somatic cell located in skeletal muscle." "FMA:9727 CALOHA:TS-2158 BTO:0004392" + "Any process that activates or increases the frequency, rate or extent of macrophage differentiation." + "The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage." + "The movement of organelles or other particles from one location in the cell to another along microtubules, driven by motor activity." + "Any process that activates or increases the frequency, rate or extent of smooth muscle hypertrophy." + "Any gland that is part of the diencephalon. Examples: pineal gland, neurohypophysis." "EHDAA2:0000395 VHOG:0000653 EMAPA:16897" + "Mesenchyme that develops_from a neural crest and is part of a 4th arch mesenchyme." "VHOG:0000580 EHDAA2:0000098 EMAPA:16772" + "Dorsal part (roof region) of the telencephalon[GO]." "DMBA:15903 TAO:0007007 neuronames:3240 Wikipedia:Avian_pallium Wikipedia:Pallium_(neuroanatomy) TAO:0000505 BTO:0003399 SCTID:369224000 ZFA:0000505 EFO:0003534" + "White matter that is part of a diencephalon [Automatically generated definition]." "ZFA:0000338 FMA:83931 TAO:0000338 BIRNLEX:1678" + "A cell whose primary function is intermediary metabolism." + "A cellular component that forms a specialized region of connection between two or more cells, or between a cell and the extracellular matrix, or between two membrane-bound components of a cell, such as flagella." "Wikipedia:Cell_junction" + "The process in which a relatively unspecialized cell acquires the specialized features of a DN4 thymocyte. A DN4 thymocyte is a CD4-,CD8- thymocyte that is also CD44-,CD25-." + "A bipolar neuron found in the retina and having connections with photoreceptors cells and neurons in the outer half of the inner plexiform layer. These cells depolarize in response to light to dark transition." + "Any process that activates or increases the frequency, rate, or extent of myeloid dendritic cell antigen processing and presentation." + "One of of the pair of folds derived from the cloacal folds which give rise to a portion of the external genitalia; in male embryos they close over the urethral plate and fuse to form the spongy (penile) urethra and ventral aspect of the penis, not including the glans; failure of fusion of the urethral folds leads to hypospadias; in female embryos they fuse only anterior to the anus and form the labia minora[MP]." "Wikipedia:Urogenital_folds EMAPA:30888 FMA:321919 EHDAA2:0004022" + "A portion of connective tissue that is part of a wrist [Automatically generated definition]." "EMAPA:37320 MA:0000636" + "A non-polarised cell precursor cell that is part of some mesenchyme, is associated with the cell matrix but is not connected to other cells and is capable of migration." + "An epithelial cell that remains from the disintegration of the epithelial root sheath involved in the development of teeth." "FMA:62987" + "The aggregation, arrangement and bonding together of a set of components to form an extracellular vesicular exosome, a membrane-bounded vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Exosomes are defined by their size, which generally ranges from 30 nm to 100 nm." + "Any process that modulates the frequency, rate or extent of hydrolase activity, the catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." + "An oligodendrocyte precursor cell that is committed to differentiate." + "A small cell formed by the first meiotic division of oocytes." "VHOG:0000464 EMAPA:16032 EHDAA2:0000541 FMA:18650" + "A C-X-C chemokine receptor type 1 that is encoded in the genome of human." "Reactome:R-HSA-373805 Reactome:R-HSA-6804780 UniProtKB:P25024 DTO:02100075" + "Any process that stops, prevents or reduces the frequency, rate or extent of dendritic cell chemotaxis." + "Any process that modulates the frequency, rate or extent of movement of proteins from the cytoplasm to the nucleus." + "One of the laterally paired arteries that supply the gonads." "Wikipedia:Gonadal_artery" + "The chemical reactions and pathways involving acetylcholine, the acetic acid ester of the organic base choline. Acetylcholine is a major neurotransmitter and neuromodulator both in the central and peripheral nervous systems. It also acts as a paracrine signal in various non-neural tissues." + "The process in which bones are generated and organized as a result of the conversion of another structural tissue into bone." + "Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats." "Wikipedia:Immune_system" + "Any process that activates or increases the frequency, rate or extent of differentiation of CD4-positive, CD25-positive, alpha-beta regulatory T cells." + "The process that gives rise to neurohypophysis. This process pertains to the initial formation of a structure from unspecified parts. The neurohypophysis is the part of the pituitary gland that secretes hormones involved in blood pressure regulation." + "A pre-BCR-negative large pre-B-II cell is a large pre-B-II cell that is pre-B cell receptor-negative, composed of surrogate light chain protein (SL), which is composed of VpreB and Lambda 5/14.1, in complex with immunoglobulin mu heavy chain (IgHmu), on the cell surface, and lack a DNA rearrangement of immunoglobulin light chain genes." + "An alpha-type platelet-derived growth factor receptor that is encoded in the genome of human." "UniProtKB:P16234 DTO:03100403" + + "Combining with somatostatin to initiate a change in cell activity. Somatostatin is a peptide hormone that regulates the endocrine system by signaling via G protein-coupled somatostatin receptors. Somatostatin has two active forms produced by proteolytic cleavage: a 14 amino acid peptide (SST-14) and a 28 amino acid peptide (SST-28)." + "A cell that secretes insulin and is located towards the center of the islets of Langerhans." "EV:0200009 ncithesaurus:Beta_Cell MA:0002419 BTO:0000783 FMA:70586" + "The popliteal vein course runs alongside the popliteal artery but carries the blood from the knee joint and muscles in the thigh and calf back to the heart. Its origin is defined by the junction of the posterior tibial vein and anterior tibial vein. It drains the peroneal vein before reaching the knee joint and turns into the femoral vein when leaving the adductor canal (also known as Hunter's canal). The popliteal artery extends from the femoral artery behind the popliteal fossa which is the space behind the knee. [WP,unvetted]." "FMA:44327 MA:0002197 galen:PoplitealVein EMAPA:37181 Wikipedia:Popliteal_vein GAID:537 MESH:D011152 UMLS:C0032652 NCIT:C33339 SCTID:281065001" + "A ligament that is part of a middle ear." + "A secondary follicle that is located in a lymph node." "EMAPA:35531 MA:0000744 FMA:312352" + "A gland that is part of a epidermis." "FMA:59153" + "The large, irregular bone located at the base and side of the skull; consists of three parts at birth: squamous, tympanic, and petrous." "FMA:52737 EHDAA:6035 NCIT:C12797 VHOG:0000800 SCTID:181795004 Wikipedia:Temporal_bone EMAPA:17682 MA:0001476 MESH:D013701 GAID:232 UMLS:C0039484" + "The process in which the anatomical structures of a metanephric mesenchymal tissue are generated and organized. Metanephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the metanephros." + "Dorsal components of the striatum comprising the caudate nucleus and the putamen, in species that have distinct nuclei; the caudoputamen in species which don't." "EMAPA:36575 NLXANAT:1010001 MA:0002971 FMA:77620 BTO:0004701 BAMS:Dorsal_striatum BAMS:STRd Wikipedia:Dorsal_striatum PBA:10081 MBA:485 neuronames:2340 BAMS:StrD" + "A tumor necrosis factor ligand superfamily member 5 that is encoded in the genome of mouse." "UniProtKB:P27548" + "The developmental process pertaining to the initial formation of the heart from unspecified parts. This process begins with the specific processes that contribute to the appearance of the heart field and the arrival of cardiac neural crest to the heart region. The process ends when the structural rudiment is recognizable." + "An epithelial cell that is part of some loop of Henle thick ascending limb segment located in the renal cortex." "KUPO:0001052" + "A sac-like structure that is found in the mature gland[GO]." "MA:0002760 FMA:73285 EMAPA:36566" + "Tubular connection between the epidermal surface and the most distal part of the inner root sheath. Contains the hair shaft." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of hormones." + "GC_ID:1" + "A protein that is a translation product of the human CD69 gene or a 1:1 ortholog thereof. A type II transmembrane protein with a C-type lectin binding domain in the extracellular portion of the molecule. Involved in lymphocyte proliferation and functions as a signal transmitting receptor in lymphocytes, natural killer (NK) cells, and platelets." + "A thin membrane which helps to support the capillary loops in a renal glomerulus. It is connective tissue composed of mesangial cells - myofibroblasts phenotypically related to vascular smooth muscle cells (muscle, smooth, vascular), phagocytes and the mesangial extracellular matrix." "GAID:430 MA:0002606 Wikipedia:Glomerular_mesangium EMAPA:27961 MESH:D005920 SCTID:244574009 FMA:84140" + "Any process that activates or increases the frequency, rate or extent of T-helper cell differentiation." + "A reflex process in which a response to an angular or linear acceleration stimulus begins with an afferent nerve impulse from a receptor in the inner ear and ends with the compensatory action of eye muscles. Signaling never reaches a level of consciousness." + "Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration." + "A collecting duct of renal tubule that is part of a metanephros [Automatically generated definition]." "VHOG:0000983" + "A multi-organ-part structure that consists of three vessels of the portal lobule including the bile duct, a terminal branch of the hepatic artery and portal vein, and may also include a lymphatic vessel." "Wikipedia:Portal_triad MA:0002499 NCIT:C33342 FMA:17523 SCTID:362192000 UMLS:C0227514" + "The stage of being a sexually mature adult animal." "OGES:000027 XAO:1000093 BILS:0000113 ZFS:0000044 OGES:000026 EV:0300064 MmusDv:0000110 EV:0300070 MIAA:0000403" + "A DRD2-expressing medium spiny neuron that is part of a matrix compartment of dorsal striatum." + "Mesenchyme that is part of a handplate." "EMAPA:17457 EMAPA:17248 EHDAA2:0000731" + "Any process that stops, prevents or reduces the frequency, rate or extent of receptor localization to synapse." + "The establishment of the sex of an organism by physical differentiation." "Wikipedia:Sexual_differentiation" + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a protein." + "An inducible T-cell costimulator that is encoded in the genome of mouse." "UniProtKB:Q9WVS0" + "An endothelial cell that lines the intracavitary lumen of the heart, separating the circulating blood from the underlying myocardium. This cell type releases a number of vasoactive substances including prostacyclin, nitrous oxide and endothelin." "FMA:75621" + "Mesenchyme that is part of a developing pinna [Automatically generated definition]." "EHDAA2:0001469 EHDAA:8981 VHOG:0000747 EMAPA:17591" + "Proximal-most phalanx within a digit." "AAO:0010680 EMAPA:35716 SCTID:299708005 MA:0002916 Wikipedia:Proximal_phalanges" + "A vascular plexus that is part of a left lung." "EMAPA:17660 EHDAA2:0000963" + "An adipocyte that is part of the epicardial fat of left ventricle." "FMA:261300" + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving juvenile hormone." + "A portion of connective tissue that is part of a hindlimb [Automatically generated definition]." "MA:0000661 EMAPA:37322" + "The portion of the plasma membrane surrounding the leading edge of a motile cell." + "A macrophage scavenger receptor types I and II that is encoded in the genome of human." "UniProtKB:P21757" + "The reflex process in which a mechanical stimulus applied to the eye elicits a response of the eyelid closing." + "An enteroendocrine cell that is located in the colon." + "Any process that modulates the physical form of a postsynapse." + "A prostanoid receptor that is a translation product of the human PTGDR2 gene or a 1:1 ortholog thereof. The preferred ligand is 11-dehydro-thromboxane B2. This receptor is not closely related to the prostaglandin D2 receptor encoded by PGD2." "PIRSF:PIRSF038608 IUPHARobj:339" + "Short nephrons are associated with mid-cortical glomeruli, and have no short ascending limb, so the limb is situated in the outer medulla." "FMA:272051" + "A developmental process, independent of morphogenetic (shape) change, that is required for a nucleate erythrocyte to attain its fully functional state. A nucleate erythrocyte is an erythrocyte with a nucleus." + "The process in which a relatively unspecialized cell acquires specialized features of the embryonic placenta." + "Any process that stops, prevents or reduces the frequency, rate or extent of sperm capacitation." + "A pharyngeal puch that is between the pharyngeal arches 2 and 3." "EHDAA2:0000058 VHOG:0000967 RETIRED_EHDAA2:0000060 UMLS:C0231069 SCTID:345349000 EMAPA:16275 AAO:0011115 XAO:0000247 ZFA:0001130 TAO:0001130 EFO:0003633 FMA:295676 Wikipedia:Pharyngeal_pouch_(embryology)#Second_pouch NCIT:C34289 VHOG:0000561" + "Any process that activates or increases the frequency, rate or extent of striated muscle cell differentiation." + "An ureter that is part of a left side of organism [Automatically generated definition]." "UMLS:C0227683 FMA:15572 MA:0001684 EMAPA:37372 NCIT:C49324 SCTID:276340002" + "FMA:58098" + "Any process that activates or increases the frequency, rate or extent of tooth mineralization, the deposition of calcium salts in tooth structures." + "Any process that stops, prevents or reduces the frequency, rate or extent of gastrulation." + "A portion of cardiac muscle tissue that is part of a right ventricle [Automatically generated definition]." "FMA:83452 VHOG:0001236 EMAPA:17342" + "Any process that modulates the frequency, rate or extent of T-helper cell differentiation." + "A proenkephalin-B that is encoded in the genome of human." "UniProtKB:P01213" + "Any process that modulates the frequency, rate or extent of serotonin biosynthetic process." + "An anatomical collection that is arranged in a line." + "A lamina propria that is part of a urinary bladder [Automatically generated definition]." "MA:0001695 FMA:15935 EMAPA:30088 UMLS:C1706967 NCIT:C48940" + "A T-cell acute lymphocytic leukemia protein 1 that is encoded in the genome of human." "Reactome:R-HSA-8956511 UniProtKB:P17542" + "An immature or mature cell of the first erythroid lineage to arise during embryonic development." + "Any process that activates or increases the frequency, rate or extent of lymphocyte differentiation." + "Any process that activates or increases the frequency, rate or extent of reproductive process." + "The directed movement of substances from the Golgi to other parts of the cell, including organelles and the plasma membrane, mediated by small transport vesicles." + "A gland that secretes a seminal fluid." "WBbt:0006870" + "The orderly movement of a glial cell, non-neuronal cells that provide support and nutrition, maintain homeostasis, form myelin, and participate in signal transmission in the nervous system." + "The movement of a macrophage in response to an external stimulus." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the innate immune response." + "A cardiac myofibril is a myofibril specific to cardiac muscle cells." + "Any collection of muscles that is part of a hindlimb [Automatically generated definition]." "FMA:50399" + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving steroids." + "A dorsal skin of digit that is part of a pedal digit." "FMA:37868 FMA:60523" + "Any process that modulates the frequency, rate, or extent of B cell apoptotic process." + "Obsolete. Use PO:0000293 from Plant Ontology instead. One of a pair of cells flanking the stomatal pore and causing the opening and closing of the pore by changes in turgor." + "A renal medulla interstitium that is part of a right kidney." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of an immune system process." + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving phosphates." + "The movement of a granulocyte within or between different tissues and organs of the body." + "The controlled release of a peptide from a cell in which the peptide acts as a neurotransmitter." + "The developmental process pertaining to the initial formation of a cardiac ventricle from unspecified parts. A cardiac ventricle receives blood from a cardiac atrium and pumps it out of the heart." + "A bodily secretion that is produced by a gland of anal sac." + "A renal system process in which water is taken up from the collecting ducts and proximal and distal loops of the nephron. In non-mammalian species, absorption may occur in related structures." + "The lingual septum consists of a vertical layer of fibrous tissue, extending throughout the entire length of the median plane of the tongue, though not quite reaching the dorsum. It is thicker behind than in front, and occasionally contains a small fibrocartilage, about 6 mm. in length. It is well displayed by making a vertical section across the organ." "FMA:54813 Wikipedia:Lingual_septum SCTID:368727001 EMAPA:18274" + "An enterocyte that is part of the epithelium proper of ileum." "FMA:263102" + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cholecystokinin stimulus." + "Any process in which a vesicle or vesicles are transported to, and/or maintained in, a specific location." + "A neuron of the substantia nigra." + "A part of the lymph node cortex in which B lymphocytes home to primary follicles to survey follicular dendritic cells (FDCs); antigen stimulated B cells proliferate and differentiate within the follicles forming distinctive germinal centers." "MA:0002851" + + "An epithelial cell that is part of a cortical collecting duct." "KUPO:0001063" + "A taste bud that is located external to the digestive tube, on the head or body, as found in species such as goldfish." + "The process in which the branches of the fetal placental villi are generated and organized. The villous part of the placenta is called the labyrinth layer." + "Any process that activates or increases the frequency, rate, or extent of a chronic inflammatory response." + "A mature B cell that is located in the marginal zone of the spleen with the phenotype CD23-negative and CD21-positive and expressing a B cell receptor usually reactive to bacterial cell wall components or senescent self components such as oxidized-LDL. This cell type is also described as being CD19-positive, B220-positive, IgM-high, AA4-negative, CD35-high." + "The subclavian vein is a paired large vein, one on either side of the body. Their diameter is approximately that of the smallest finger." "FMA:4725 EHDAA:4455 UMLS:C0038532 AAO:0010510 MA:0002221 EHDAA2:0001934 GAID:546 EMAPA:17621 NCIT:C12794 Wikipedia:Subclavian_vein galen:SubclavianVein SCTID:181388005 MESH:D013350" + "Any process that activates or increases the frequency, rate or extent of ventricular cardiac muscle cell action potential." + "A basal cell that is part of the epithelium of respiratory bronchiole." "FMA:263124" + "A T cell that has not completed T cell selection." "CALOHA:TS-1042 BTO:0001372" + "A cell morphology that inheres in neurons which have two principal dendrites that emerge from the soma and begin to branch some distance from it, have few spines, and branch in narrow fields. This is in contrast to bitufted morphology where branching occurs close to the soma." "nifext:2 ILX:0101312 ilxtr:BipolarPhenotype" + "A neuromuscular junction that functions in the excitation of somatic muscle myotubes, such as an arthropod somatic muscle cells." + "A urethral meatus that is part of a male urethra[Automatically generated definition]." "EMAPA:36434 FMA:85265 Wikipedia:External_urethral_orifice_(male) SCTID:279478000 MA:0002642" + "Any process that modulates the frequency, rate or extent of lysosome organization." + "A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an inorganic substance stimulus." + "The progression of the hepatic duct over time, from its formation to the mature structure. The hepatic duct is the duct that leads from the liver to the common bile duct." + "The process in which the anatomical structures of the epidermis are generated and organized. The epidermis is the outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species." + "A specialized kidney epithelial cell, contained within a glomerulus, that contains \"feet\" that interdigitate with the \"feet\" of other podocytes." "FMA:70967 BTO:0002295" + "GC_ID:1" + "An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers." "FMA:83518" + "Any process that stops, prevents or reduces the frequency, rate or extent of calcium ion transmembrane transport." + "Any process that activates or increases the frequency, rate or extent of lymphoid progenitor cell differentiation." + "Any process that modulates the frequency, rate or extent of asymmetric cell division." + "An endothelium that is part of a right lung." "EHDAA2:0001755" + "The process whose specific outcome is the progression of a lymph vessel over time, from its formation to the mature structure." + "A pigment cell derived from the neural crest. Contains cartenoid pigments in structures called pterinosomes or xanthosomes. This gives an appearance ranging from a golden yellow to orange and red." + "Any apoptotic process in a nurse cell. During late oogenesis, following the transfer of substances from the nurse cells to the oocyte, nurse cell remnants are cleared from the egg chamber by apoptotic process." + "A natural killer cell receptor NKG2 that is a translation product of the human KLRC1 gene or a 1:1 ortholog thereof." "IUPHARobj:2849" + "The series of events in which a chemical stimulus is received by a cell and converted into a molecular signal." + "A transcription factor PU.1 that is encoded in the genome of mouse." "UniProtKB:P17433" + "A major subdivision of a mature or developing limb, including both skeletal elements (or the mesenchyme that gives rise to the skeletal elements) and associated tissues, such as muscle, connective tissue, integument. Examples: autopod region, zeugopod region, stylopod region, metapodial region, arm region. Excludes the limb girdles." "UMLS:C1268195 MA:0002889 NCIT:C38630 FMA:241863" + "The process in which a neuroblast or one of its progeny commits to a pyramidal neuron fate, migrates from the ventricular zone to the appropriate layer in the cortex and develops into a mature neuron." + "Any process that modulates the frequency, rate or extent of glycine import into a cell." + "A fibroblast that is part of the connective tissue of glandular part of prostate." "FMA:261283" + "A cell from the thermogenic form of adipose tissue found in many species, particularly in newborns and hibernating mammals, but also in lesser amounts in adults of other mammals including humans. Brown fat is capable of rapid liberation of energy and seems to be important in the maintenance of body temperature immediately after birth and upon waking from hibernation." "FMA:83435 CALOHA:TS-0099" + "One of the arteries supplying a meninix[Automatically generated definition]." "EMAPA:37104 MA:0002001 MESH:D008576 Wikipedia:Meningeal_arteries GAID:499" + "Obsolete. Use PO:0000274 from Plant Ontology instead. A fiber of the xylem tissue, Two types are recognized in the secondary xylem: fiber tracheids and libriform fibers." + "The process in which the anatomical structures of the foregut are generated and organized." + "A transferrin receptor protein 1 that is encoded in the genome of human." "UniProtKB:P02786 Reactome:R-HSA-434330 Reactome:R-HSA-434196 Reactome:R-HSA-8869124 Reactome:R-HSA-917983 Reactome:R-HSA-8961829" + "A bone marrow stromal antigen 2 that is encoded in the genome of mouse." "UniProtKB:Q8R2Q8" + "A platelet glycoprotein 4 that is encoded in the genome of mouse." "UniProtKB:Q08857" + "Any process that activates or increases the frequency, rate, or extent of an immunoglobulin mediated immune response." + "Obsolete. Use PO:0000078 from Plant Ontology instead. Parenchyma cell with the wall ingrowth (or invaginations) that increase the surface of the plasmalemma. Appears to be specialized for short-distance transfer of solutes." + "The collection of all meningeal layers that line a central nervous system." "EHDAA2:0004661 NCIT:C12349 Wikipedia:Meninges SCTID:362879001 UMLS:C0228116 neuronames:1465 FMA:231572" + "An erythroid progenitor cell is Kit-positive, Ly6A-negative, CD41-negative, CD127-negative, and CD123-negative. This cell type is also described as being lin-negative, Kit-positive, CD150-negative, CD41-negative, CD105-positive, and FcgR-negative." + "The change in morphology and behavior of a eosinophil resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor, leading to the initiation or perpetuation of an immune response." + "The three-lobed cloverleaf-shaped aponeurosis situated at the center of the diaphragm; the central tendon is fused with the fibrous pericardium that provides attachment for the muscle fibers." "FMA:58279 VHOG:0001399 EMAPA:17702 UMLS:C0230162 NCIT:C34119 Wikipedia:Central_tendon_of_diaphragm SCTID:244943002" + "A C-X-C chemokine receptor type 5 that is encoded in the genome of human." "Reactome:R-HSA-444505 UniProtKB:P32302 DTO:02100079" + "An epithelial cell of the tracheobronchial tree." "FMA:66816" + "The directed movement of basic amino acids, amino acids with a pH above 7, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "Mesenchyme that is part of a pharyngeal arch 3." "VHOG:0001083 FMA:295700 EMAPA:16402 EHDAA:1094 EHDAA2:0000081" + "The dorsal venous arch of the foot is a superficial vein that connects the small saphenous vein and the great saphenous vein. Anatomically, it is defined by where the dorsal veins of the first and fifth digit, respectively, meet the great saphenous vein and small saphenous vein." "SCTID:231189006 Wikipedia:Dorsal_venous_arch_of_the_foot MA:0002110 FMA:44356 EMAPA:37521" + "The developmental process pertaining to the initial formation of a right cardiac ventricle from unspecified parts." + "The chemical reactions and pathways resulting in the breakdown of nucleobases, nucleosides, nucleotides and nucleic acids." + "Any process that modulates the extent to which blood vessels can be pervaded by fluid." + "Any apoptotic process in a motor neuron, an efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes movement." + "A process in which an iron ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore." + "A small, polyhedral, cell found in rounded groups or curved columns with deeply staining nuclei, scanty basophilic cytoplasm and a few lipid droplets. This cell in the zona glomerulosa produces mineralocorticoids." "FMA:69273" + "Any neuron that is part of a lateral line ganglion." + "Binding to a CXCR4 chemokine receptor." + "Any process that activates or increases the frequency, rate or extent of hemocyte differentiation." + "Cytoarchitectural layer of retina containing closely packed cell bodies, the majority of which are bipolar cells (adapted from Wikipedia)." "NLX:93816 SCTID:362520009 TAO:0000119 BTO:0003176 Wikipedia:Inner_nuclear_layer EMAPA:19155 NLXANAT:1005031 NCIT:C32808 MA:0001311 VHOG:0001167 FMA:58686 UMLS:C0229211 ZFA:0000119 XAO:0003221 BAMS:Rinl" + "A meninx that is part of a brain [Automatically generated definition]." "VHOG:0000013 CALOHA:TS-2147 EMAPA:32662 SCTID:180949007 MA:0000813" + "A meninx that is part of a forebrain [Automatically generated definition]." "MA:0000883 EMAPA:37543" + "A pre-BCR-positive precursor B cell that is CD24-high, CD25-positive, CD43-positive, CD45R-positive and BP-positive." + "An explosive cell containing one giant secretory organelle called a cnidocyst (also known as a cnida (plural cnidae) or nematocyst) that contains a toxin responsible for the stings delivered by a cnidarian to other organisms. Cnidae are used to capture prey and as a defense against predators. The presence of cnidocytes defines the phylum Cnidaria (corals, sea anemones, hydrae, jellyfish, etc.)." + "Any process, acting in the postsynapse that results in modulation of chemical synaptic transmission." + "Any of the metabolic zones found in the liver. Liver tissue is heterogenous at the level of morphometry and histochemistry. This heterogeneity is linked to the position of a cell within the functional unit of the tissue, which, in turn, is related to the blood supply: cells located in the upstream zone differ from those in the downstream zone with respect to subcellular structures, key enzymes, translocators, and receptors and, therefore, have different metabolic capacities. This is the basis for 'metabolic zonation', a concept first proposed in mammals for carbohydrate metabolism and later expanded to include amino acid and ammonia metabolism, xenobiotic metabolism, protective metabolism, and formation of plasma proteins." + "A near-projecting glutamatergic neuron with a soma found in layer 5/6 of the primary motor cortex." "ILX:0770161" + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipid stimulus." + "Any process that activates or increases the frequency, rate or extent of the directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "A lymphocyte that can spontaneously kill a variety of target cells without prior antigenic activation via germline encoded activation receptors and also regulate immune responses via cytokine release and direct contact with other cells." "MESH:D007694 FMA:63147 BTO:0004716 VHOG:0001697 BTO:0000914 CALOHA:TS-0664 FMA:83601" + "A zone of skin that is part of a hip region." "EMAPA:18148 MA:0000658 SCTID:181518004 FMA:45282" + "A mucosa that is part of a terminal bronchiole [Automatically generated definition]." "FMA:263232" + "A tube lumen that is part of a mesonephric duct." "EHDAA2:0001244" + "The transverse or costal processes of a vertebra, two in number, project one at either side from the point where the lamina joins the pedicle, between the superior and inferior articular processes. They serve for the attachment of muscles and ligaments. [WP,unvetted]." "XAO:0003102 AAO:0000698 MA:0001456 SCTID:264238006 Wikipedia:Transverse_process FMA:11949" + "The process whose specific outcome is the progression of smooth muscle over time, from its formation to the mature structure." + "The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." + "A dura mater that is part of a spinal cord [Automatically generated definition]." "UMLS:C0228124 SCTID:362302001 EMAPA:17806 NCIT:C49799 FMA:71237 VHOG:0000411 MA:0001132" + "Any process that stops, prevents or reduces the frequency, rate or extent of presynapse assembly." + "A cell that, by division or terminal differentiation, can give rise to other cell types." + "Any process that modulates the rate, frequency, or extent of microtubule-based movement, the movement of organelles, other microtubules and other particles along microtubules, mediated by motor proteins." + "A cadherin-1 that has been processed by proteolytic cleavage." + "The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-)." + "GC_ID:1" + "Any process that modulates the frequency, rate, or extent of lymphocyte mediated immunity." + "Any hepatocyte that is part of the liver lobule midzonal region. These cells have mixed functionality in comparison with those in the other two regions of the liver lobule." + "The process in which a relatively unspecialized cell acquires specialized features of a neuromast hair cell. Hair cells are the sensory receptors of the neuromast and are located in a portion of the neuromast called the sensory strip. Each hair cell of the neuromast is morphologically polarized as a result of the relative position of the single kinocilium and the clusters of stereocilia on its apical surface. There are approximately seven hair cells within each neuromast, with each hair cell innervated by afferent and efferent neurons." + "The process in which a relatively unspecialized cell acquires specialized features of an atrioventricular (AV) node cell. AV node cells are pacemaker cells that are found in the atrioventricular node." + "A gyrus that is part of a frontal cortex." "NCIT:C32636 UMLS:C0228195" + "The process in which the anatomical structure of a cardiac septum is generated and organized. A cardiac septum is a partition that separates parts of the heart." + "Any process in which the nucleus is maintained in a specific location within a cell and prevented from moving elsewhere." + "The attachment of a leukocyte to another cell via adhesion molecules." + "The process whose specific outcome is the progression of the anterior lateral line nerve over time, form its formation to the mature structure. The anterior lateral line nerve contains efferent axons that innervate hair cells of the ALL and afferent axons that project to an octavolateralis column in the hindbrain. The octavolateralis column consists of the medial octavolateralis nucleus (MON), the caudal octavolateralis nucleus, and the magnocellular nucleus." + "An epiphysis that is part of a phalanx of a manus [Automatically generated definition]." "SCTID:314620000 FMA:240707" + "Any cellular process that depends upon or alters the actin cytoskeleton, that part of the cytoskeleton comprising actin filaments and their associated proteins." + "An arterial blood vessel that is part of a kidney [Automatically generated definition]." "EMAPA:31436 MA:0002578" + "A plasmacytoid dendritic cell developing in the thymus with phenotype CD11c-negative or low, CD45RA-positive, CD11b-negative, and CD123-positive." + "The chemical reactions and pathways resulting in the formation of carbohydrate derivative." + "A transmembrane protein complex which enables the transfer of a substance from one side of a membrane to the other." + "The establishment of the sex of a male organism by physical differentiation." + "A vein that is part of the placenta." + "An anatomical structure that develops from the endoderm and the mesoderm." + "The process whose specific outcome is the progression of a pancreatic A cell over time, from its formation to the mature structure. A pancreatic A cell is a cell in the pancreas that secretes glucagon." + "In a saddle joint (sellar joint, articulation by reciprocal reception) the opposing surfaces are reciprocally concave-convex." "Wikipedia:Saddle_joint SCTID:23059003 FMA:75298" + "The process in which relatively unspecialized cells acquire specialized structural and/or functional features of an epithelial cell that characterize the cells of the kidney as it progresses from its formation to the mature state." + "A T cell that is located in the intestinal epithelium and is capable of a mucosal immune response." "MESH:D000075942" + "A blood vessel that drains blood from the large intestine that usually terminates when reaching the splenic vein, which goes on to form the portal vein with the superior mesenteric vein (SMV). Anatomical variations include the IMV draining into the confluence of the SMV and splenic vein and the IMV draining in the SMV. The IMV lies to the right of the similarly name artery, the inferior mesenteric artery, which originates from the abdominal aorta. [WP,unvetted]." "BTO:0002782 VHOG:0001118 Wikipedia:Inferior_mesenteric_vein SCTID:281055007 MA:0002178 UMLS:C0226754 EHDAA:8712 EHDAA2:0000819 NCIT:C32782 EMAPA:18642 FMA:15391" + "KUPO:0001077" + "A mature NK cell that is NK1.1-positive." + "Front (ventral) portion of the vascular, pigmentary, or middle coat of the eye, including the ciliary body and the iris." "SCTID:280656002 EMAPA:37417" + "A small medullary thymic epithelial cell with a spindle shape, often arranged in groups and connected to each other by large desmosomes and interdigitations. The cytoplasm is sparse, with scanty organelles and thick bundles of cytokeratin." + "EHDAA2:0000101 SCTID:361482003" + + "The multiplication or reproduction of cells, resulting in the expansion of a cell population that contributes to the shaping of the heart." + "Any process that stops, prevents, or reduces the frequency, rate or extent of striated muscle cell differentiation." + "Renal artery that supplies the left kidney." "SCTID:19215005 UMLS:C0226333 EMAPA:37098 NCIT:C52741 FMA:14753 MA:0002036" + "Any process that stops, prevents, or reduces the frequency, rate or extent of blood vessel morphogenesis." + "The sensory system subserving the sense of vision." "http://uri.neuinfo.org/nif/nifstd/FMAID_7191 BILA:0000140 UMLS:C0587900 TAO:0001127 NCIT:C12888 MA:0002444 SCTID:281831001 FMA:7191 ZFA:0001127 AAO:0000632 XAO:0003198 Wikipedia:Visual_system EMAPA:36003" + "Any process that stops, prevents or reduces the frequency, rate or extent of androgen secretion." + "Any process that modulates the frequency, rate or extent of differentiation of CD4-positive, CD25-positive, alpha-beta regulatory T cells." + "An artery that connects two larger arteries." "NCIT:C52851 EMAPA:18598 UMLS:C1707451 MA:0001938" + "Any process that decreases the rate, frequency, or extent of hair follicle placode formation, the developmental process in which a hair placode forms. An hair follicle placode is a thickening of the ectoderm that will give rise to the hair follicle bud." + "A langerin-positive lymph node dendritic cell that is CD103-negative and CD11b-high." + "The ileocolic vein is a vein which drains the ileum, colon, and cecum. [WP,unvetted]." "UMLS:C0226744 SCTID:36208008 Wikipedia:Ileocolic_vein NCIT:C53047 MA:0002141 EMAPA:37150 FMA:15408" + "A proximal-distal subdivision of the digestive tract." "FMA:71131" + "A protein that is a translation product of the human CD22 gene or a 1:1 ortholog thereof." "IUPHARobj:2786" + "A chief cell of parathyroid glands that does not stain with hematoxylin or eosin. This cell is larger, has a larger nucleus and fewer secretory granules than dark chief cells." "FMA:69081" + "Any process that stops or decreases the rate or extent of hepatocyte differentiation." + "Any process that modulates the frequency, rate, or extent of monocyte chemotaxis." + "The expansion of an alpha-beta T cell population by cell division." + "Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles." "XAO:0004012 galen:SkeletalStructure AAO:0011129 ZFA:0005494 TAO:0001890 VSAO:0000128" + "A submucosa that is part of a cardia of stomach [Automatically generated definition]." "FMA:17457" + "A cellular potency that is the capacity to form multiple differentiated cell types." + "The process whose specific outcome is the progression of the endoderm over time, from its formation to the mature structure. The endoderm is the innermost germ layer that develops into the gastrointestinal tract, the lungs and associated tissues." + "Any process that modulates the rate, frequency, or extent of brown fat cell differentiation. Brown fat cell differentiation is the process in which a relatively unspecialized cell acquires specialized features of a brown adipocyte, an animal connective tissue cell involved in adaptive thermogenesis. Brown adipocytes contain multiple small droplets of triglycerides and a high number of mitochondria." + "The tibial tuberosity is on the anterior side of a tibia and is where a patella ligament attaches." + "Any process that modulates the frequency, rate or extent of vascular associated smooth muscle cell apoptotic process." + "EFO:0003562 EHDAA:2671 EHDAA2:0001981 EHDAA:1993 EMAPA:16914" + "Any process that activates or increases the frequency, rate or extent of leucophore differentiation." + "A(n) smooth muscle cell that is part of a(n) large intestine smooth muscle circular layer." + "A chromaffin cell that is part of the right ovary." "FMA:74320" + "A CD38-positive naive B cell is a mature B cell that has the phenotype CD38-positive, surface IgD-positive, surface IgM-positive, and CD27-negative, and that has not yet been activated by antigen in the periphery." + "Layer of neocortex lying deep to the external pyramidal cell layer defined cytoarchitecturally by the presence of numerous small cells." "neuronames:2449 NCIT:C32844 FMA:77811 PBA:294021852 MA:0000900 UMLS:C1512872 ABA:CTX4 EMAPA:35258 NLXANAT:090810" + "Portion of tissue composed of mesenchymal cells (motile cells that develop from epthelia via an epithelial to mesenchymal transition) and surrounding extracellular material. Mesenchyme has different embryological origins in different metazoan taxa - in many invertebrates it derives in whole or part from ectoderm. In vertebrates it derives largely from mesoderm, and sometimes the terms are used interchangeably, e.g. lateral plate mesoderm/mesenchyme." "NCIT:C13301 CALOHA:TS-0620 UMLS:C0162415 VHOG:0000170 EHDAA2:0003145 EV:0100007 ZFA:0000393 AAO:0010427 AEO:0000145 BTO:0001393 XAO:0003046 TAO:0000393 Wikipedia:Mesenchyme" + + "The chemical reactions and pathways resulting in the formation of chondroitin sulfate, any member of a group of 10-60 kDa glycosaminoglycans, widely distributed in cartilage and other mammalian connective tissues, the repeat units of which consist of beta-(1,4)-linked D-glucuronyl beta-(1,3)-N-acetyl-D-galactosamine sulfate." + "A fully differentiated basophil, a granular leukocyte with an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation." "CALOHA:TS-0688 BTO:0001026" + "Any process that stops, prevents, or reduces the frequency, rate, or extent of muscle adaptation." + "The regulated release of gastric acid (hydrochloric acid) by parietal or oxyntic cells during digestion." + "A bone in the skull that separates the nasal cavity from the brain. As such, it is located at the roof of the nose, between the two orbits. The cubical bone is lightweight due to a spongy construction. The ethmoid bone is one of the bones that makes up the orbit of the eye[WP]." "UMLS:C0015027 NCIT:C12711 Wikipedia:Ethmoid_bone VHOG:0001317 MESH:D005004 FMA:52740 EMAPA:19018 SCTID:272674006 BTO:0004140 MA:0001483 GAID:212" + "Any process that activates or increases the frequency, rate, or extent of the production of molecular mediator of immune response." + "A fibroblast that synthesizes collagen and uses it to produce reticular fibers, thus providing structural support. Reticular cells are found in many organs, including the spleen, lymph nodes and kidneys. Subtypes of reticular cells include epithelial, mesenchymal, and fibroblastic reticular cells. Fibroblastic reticular cells are involved in directing B cells and T cells to specific regions within a tissue, whereas epithelial and mesenchymal reticular cells are associated with certain areas of the brain." "FMA:62877" + "EMAPA:37597 MA:0002449" + "A slow mechanism of blood pressure regulation that responds to changes in pressure resulting from fluid and salt intake by modulating the quantity of blood in the circulatory system." + + "An integrin alpha that lacks an A domain. This type of integrin is often cleaved into heavy and light chains." "PIRSF:PIRSF005666" + "A pyramidal neuron with soma located in the amygdala." + "A pluripotent stem cell has the ability to form cells from all three germ layers (ectoderm, mesoderm, and endoderm). However, unlike totipotent stem cells, they cell can not generate all the cells of the whole organism such as placenta." "MESH:D039904 FMA:70570" + "A zone of skin that is part of a dorsal thoracic segment of trunk." "EMAPA:37280 MA:0000510 SCTID:304890003" + "A circulatory system process carried out by the heart. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood." + "Any of the parts of the eye that lie in front of, or ventral to, the lens (inclusive)." "NCIT:C12668 FMA:58865 Wikipedia:Anterior_segment_of_eyeball ZFA:0005566 SCTID:280658001 EMAPA:36594 MA:0002484 UMLS:C0003153 MESH:D000869" + "It extends to the tip of the metanephric loop of Henle[GO]." + "Any process that modulates the rate or frequency of platelet activation. Platelet activation is a series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue." + "The superior ophthalmic vein begins at the inner angle of the orbit in a vein named the nasofrontal which communicates anteriorly with the angular vein; it pursues the same course as the ophthalmic artery, and receives tributaries corresponding to the branches of that vessel. Forming a short single trunk, it passes between the two heads of the Rectus lateralis and through the medial part of the superior orbital fissure, and ends in the cavernous sinus. The ethmoidal veins drain into the superior ophthalmic vein. Vorticose veins also drain into the superior ophthalmic vein." "Wikipedia:Superior_ophthalmic_vein FMA:51246 SCTID:149481004" + "Any process that activates or increases the frequency, rate or extent of the regulated release of a hormone from a cell." + "A(n) goblet cell that is part of a(n) epithelium of lobar bronchus." + "The process of regulating the proliferation and elimination of B cells such that the total number of B cells within a whole or part of an organism is stable over time in the absence of an outside stimulus." + "Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in a Purkinje myocyte. This typically occurs via modulation of the activity or expression of voltage-gated ion channels." + "Any process that modulates the frequency, rate or extent of CD8-positive, alpha-beta T cell activation." + "A process of exocytosis in which soluble proteins and other substances are initially stored in secretory vesicles for later release. It is found mainly in cells that are specialized for secreting products such as hormones, neurotransmitters, or digestive enzymes rapidly on demand." + "Tolerance induction of natural killer cells." + + "A mucosa that is part of an appendix [Automatically generated definition]." "CALOHA:TS-2022 SCTID:362155000 FMA:14991" + "A muscle of the tympanic cavity that attaches to an auditory ossicle." "Wikipedia:Muscles_of_auditory_ossicles UMLS:C1513769 MA:0000256 SCTID:244778009 FMA:49026 NCIT:C33148 EMAPA:37776" + "The nodules of small undifferentiated B lymphocytes and follicular dendritic cells located in the spleen white pulp." "EMAPA:37960 FMA:15843" + "An artery of the neck." "UMLS:C1707349 NCIT:C52850 EMAPA:37075" + "The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA]." "VSAO:0000093 ZFA:0000317 MIAA:0000148 XAO:0003073 MA:0002986 EMAPA:37721 EFO:0000942 TAO:0000317 MAT:0000148 VHOG:0000317 EHDAA:5049 FMA:71221 EHDAA2:0000161 AAO:0000034" + "An immature T cell located in the thymus." "MESH:D060168 CALOHA:TS-1042 BTO:0001372 XAO:0003159 FMA:72202" + "Any process that modulates the frequency, rate or extent of muscle hypertrophy." + "The process in which a relatively unspecialized epithelial cell becomes a more specialized epithelial cell of the mammary gland cord. Epithelial cells of the mammary cord give it its funnel-like shape and some are cornified." + "Any process that stops, prevents or reduces the frequency, rate or extent of motor neuron migration." + "The tarsometatarsal articulations are arthrodial joints in the pes." "FMA:35216 Wikipedia:Tarsometatarsal_articulations SCTID:182222008" + "Enables the transfer of a peptide from one side of a membrane to the other." "Reactome:R-HSA-1500817" + "A cell of an exocrine gland; i.e. a gland that discharges its secretion via a duct." "FMA:16014" + "A thermoreceptor cell that detects reduced temperatures." + "A platelet glycoprotein Ib alpha chain that is encoded in the genome of mouse." "UniProtKB:O35930" + "The biological process whose specific outcome is the progression of a lobar bronchus mesenchyme from an initial condition to its mature state. This process begins with the formation of the lobar bronchus mesenchyme and ends with the mature structure. The lobar bronchus mesenchyme is the mass of tissue composed of mesenchymal cells in the lobar bronchus." + "A monostratified retinal ganglion cell with large soma and large dendritic field, with dense dendritic arbor." + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving carbohydrates." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of amino acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "Embryonic structure that gives rise to the telencephalon." "EHDAA2:0004424 EMAPA:36024 ZFA:0000571 TAO:0000571" + "A macroconidium that has more than one nucleus." "FAO:0000035" + "The process in which an antigen-presenting cell expresses antigen (peptide or polysaccharide) on its cell surface in association with an MHC class II protein complex." + "The directed movement of substances that are in liquid form in normal living conditions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "A trophoblast cell that arises in the junctional zone (basal plate) of the placenta." + "A lobe of lung that is part of a left lung." "SCTID:272655003 EHDAA:2981 UMLS:C1285107 NCIT:C48945" + "Any process that modulates the frequency, rate, or extent of germinal center formation." + "The mesonephric distal tubule is a mesonephric nephron tubule that begins at the macula densa and extends to the mesonephric connecting tubule." + "The process in which a newly activated T cell acquires specialized features of a memory T cell." + "Any process in which an organism voluntarily modulates its posture, the alignment of its anatomical parts." + "A membrane-spanning 4-domains subfamily A member 1 that is encoded in the genome of mouse." "UniProtKB:P19437" + "Any process that activates or increases the frequency, rate or extent of lateral motor column neuron migration." + "A lower motor neuron whose soma is located in the anterior horn. Anterior horn motor neurons project from the anterior portion of the grey matter in the spinal cord to some skeletal muscles." "NCIT:C12645" + "Any of the sebaceous glands that are in the eyelid. Examples: gland of Zeis (services eyelashes), gland of Meibom (tarsal gland - unconnected to eyelids)." + "The process that mediates interactions between a Purkinje myocyte and its surroundings that contributes to the process of the Purkinje myocyte communicating with a ventricular cardiac muscle cell in cardiac conduction. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment." + "Connective tissue, which consists of fibroblasts, the intercellular matrix of which contains a regular network of collagen and elastic fiber bundles. Examples: bone (tissue), cartilage (tissue), dense regular connective tissue." "FMA:20103" + "A muscle organ that attaches to a tail vertebra [Automatically generated definition]." "BTO:0001905 SCTID:113230005 AAO:0000081 EMAPA:37759 MA:0000699" + "An integrin alpha-IIb that has been processed by proteolytic cleavage." + "An epithelial cell of the extrahepatic bile ducts, including the left and right hepatic duct, common hepatic duct, and common bile duct. They are columnar in shape, and have a large nuclear-to-cytoplasmic ratio relative to small/intrahepatic cholangiocytes." + "Any process that stops, prevents, or reduces the frequency, rate or extent of an organismal process, the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs." + "A morphologic quality inhering in a bearer by virtue of the bearer's relative size, organization and distribution of its surface elements or the representation or invention of the appearance of its surface; visual and tactile surface characteristics." + "A retinal ganglion A cell with dense arbor near soma." + "A(n) vein endothelial cell that is part of a(n) respiratory system." + "Any process that activates or increases the frequency, rate or extent of the directed movement of substances between the nucleus and the cytoplasm." + "The progression of the neural retina over time from its initial formation to the mature structure. The neural retina is the part of the retina that contains neurons and photoreceptor cells." + "Any process that modulates the frequency, rate or extent of epithelial cell differentiation." + "The process in which a relatively unspecialized cell acquires specialized features of a neural crest cell." + "The distalmost portion of the digestive tract, derived from the hindgut, and terminating with the anus." "WBbt:0005773" + "A CNS interneuron located in the dorsal horn of the spinal cord." + "The lipid bilayer surrounding a zymogen granule." + "A lymphocyte of B lineage with the commitment to express an immunoglobulin complex." + "The galea aponeurotica (epicranial aponeurosis, aponeurosis epicranialis) is a tough layer of dense fibrous tissue which covers the upper part of the cranium; behind, it is attached, in the interval between its union with the Occipitales, to the external occipital protuberance and highest nuchal lines of the occipital bone; in front, it forms a short and narrow prolongation between its union with the Frontales. On either side it gives origin to the Auriculares anterior and superior; in this situation it loses its aponeurotic character, and is continued over the temporal fascia to the zygomatic arch as a layer of laminated areolar tissue. It is closely connected to the integument by the firm, dense, fibro-fatty layer which forms the superficial fascia of the scalp: it is attached to the pericranium by loose cellular tissue, which allows the aponeurosis, carrying with it the integument to move through a considerable distance." "EMAPA:19210 FMA:46768 Wikipedia:Galea_aponeurotica SCTID:368677009" + "Any collection of muscles that is part of a foot [Automatically generated definition]." "FMA:50214" + "BIRNLEX:749" + "A hepatic sinusoid that is part of a left lobe of liver." "EMAPA:18309 EHDAA2:0001001 VHOG:0000709" + "Any process that stops, prevents, or reduces the frequency, rate, or extent of leukocyte mediated immunity." + "Morphogenesis of a kidney. A kidney is an organ that filters the blood and excretes the end products of body metabolism in the form of urine." + "A portion of cardiac muscle tissue that is part of a myocardium [Automatically generated definition]." "MA:0002441 FMA:261726" + "A serous secreting cell that is part of the epithelium of trachea." "FMA:263078" + "Mesenchyme that is part of a developing testis [Automatically generated definition]." "EMAPA:35858 VHOG:0001442 EHDAA:8150 EHDAA2:0002010" + "Any process that stops, prevents or reduces the frequency, rate or extent of cholangiocyte apoptotic process." + "A blood vessel that is part of an arm [Automatically generated definition]." "MA:0000591 EMAPA:37293" + "An ON bipolar cell type with dendrites selectively contacting S-cones." + "A rib bone or its cartilage or pre-cartilage precursor." + "Any process that activates or increases the frequency, rate or extent of muscle adaptation." + "A muscle cell that develops tension more slowly than a fast-twitch fiber." + "Any sensillum (UBERON:6007152) that is part of some larva (UBERON:6001727)." + "The somatic process allowing for the production of immune receptors whose specificity is not encoded in the germline genomic sequences." + "The process in which a relatively unspecialized cell acquires specialized structural and/or functional features of an adrenal chromaffin cell. An adrenal chromaffin cell is a neuroendocrine cell that stores epinephrine secretory vesicles." + "Binding to a lipoprotein particle. A lipoprotein particle, also known as a lipoprotein, is a clathrate complex consisting of a lipid enwrapped in a protein host without covalent binding in such a way that the complex has a hydrophilic outer surface consisting of all the protein and the polar ends of any phospholipids." + "Any process that modulates the frequency, rate or extent of the assembly of actin filament bundles." + "The progression of the mammary gland lobule over time, from its formation to the mature structure. A mammary gland lobule is a small rounded projection of the mammary gland." + "Any process that stops, prevents, or reduces the frequency, rate or extent of reproductive process." + "A layer of dense irregular connective tissue that lines organs and supports the mucosa, as well as joins the mucosa to the bulk of underlying smooth muscle. [WP,unvetted]." "Wikipedia:Submucosa FMA:85392 NCIT:C13167 UMLS:C0225344 FMA:85391 BTO:0002107 SCTID:68439008" + "A stem cell that gives rise to the follicle cells that surround the oocyte in female arthropods." "FBbt:00004903" + "A pre-B-I cell is a precursor B cell that expresses CD34 and surrogate immunoglobulin light chain (VpreB , Lambda 5 (mouse)/14.1 (human)) on the cell surface, and TdT, Rag1,and Rag2 intracellularly. Cell type carries a D-JH DNA rearrangement, and lacks expression of immunglobulin heavy chain protein." + "A cytotoxic T-lymphocyte protein 4 that is encoded in the genome of human." "UniProtKB:P16410" + "An OFF calbindin-positive bipolar cell that has a large dendritic field and stratifies narrowly close to the middle of the inner plexiform layer. Its axon terminal is characterized by regularly branching and varicose processes resembling beads on a string. Most of DB3a contacts with cones are triad-associated." + "The ciliary muscle is a ring of smooth muscle in the middle layer of the eye that controls the eye's accommodation for viewing objects at varying distances and regulates the flow of aqueous humour through Schlemm's canal. [WP,unvetted]." "EMAPA:35240 BTO:0000654 SCTID:280862009 MA:0001269 UMLS:C0559230 Wikipedia:Ciliary_muscle FMA:49151 NCIT:C32315" + "A type of enteocrine cell found in the periphery of the islets of Langerhans that secretes glucagon." "FMA:70585 BTO:0000990 MESH:D050416" + "A neuron that uses GABA as a vesicular neurotransmitter" "FBbt:00007228 WBbt:0005190 MESH:D059330 FMA:84788" + "GC_ID:1" + "The veins that run parallel to the phrenic arteries which include the two superior and two inferior phrenic veins." "EMAPA:37180 UMLS:C1709532 NCIT:C53062 MA:0002194" + "The process whose specific outcome is the progression of the epidermis over time, from its formation to the mature structure. The epidermis is the outer epithelial layer of an animal, it may be a single layer that produces an extracellular material (e.g. the cuticle of arthropods) or a complex stratified squamous epithelium, as in the case of many vertebrate species." + "The reorganization or renovation of existing tissues. This process can either change the characteristics of a tissue such as in blood vessel remodeling, or result in the dynamic equilibrium of a tissue such as in bone remodeling." + "Mesenchyme that is part of a hindlimb bud." + "Any process that activates or increases the frequency, rate or extent of inner ear receptor cell differentiation." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving lipoproteins, any conjugated, water-soluble protein in which the nonprotein group consists of a lipid or lipids." + "The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "Any process that activates or increases the frequency, rate or extent of striated muscle development." + "BIRNLEX:2665 FMA:62420 SCTID:278748001 MA:0003080" + "A gamma-delta intraepithelial T cell that has the phenotype CD8-alpha alpha-positive." + "The cellular developmental process by which a cell becomes a heterocyst, a cell that carries out nitrogen fixation. This process involves changes to the cell wall, expression of nitrogenase and other proteins involved in nitrogen fixation, and degradation of photosystem II, which produces oxygen. This process is known to occur in some cyanobacteria." + "Binding to cadherin, a type I membrane protein involved in cell adhesion." + "An interneuron located in the cerebral cortex that expresses the oxytocin receptor. These interneurons also express somatostatin." + "Region of the scapula where the latter meets with the clavicle: attachment point of the clavicle to the scapula in some taxa." "EMAPA:25119 GAID:187 UMLS:C0001209 FMA:23260 NCIT:C32048 Wikipedia:Acromion MESH:D000174 AAO:0000826 SCTID:181911000 VSAO:0005067 MA:0002805" + "A mono-stratified retinal ganglion cell that has a small dendritic field and dense dendritic arbor." + "The process whose specific outcome is the progression of the lateral line system over time, from its formation to the mature structure. The lateral line system is a network of sensory organs (neuromasts) and lateral line nerves located superficially on the skin or just under the skin in fluid-filled canals on the head and body of all fishes and most amphibians. The lateral line system develops from cranial ectodermal placodes situated between the eye and ear." + "A thymocyte that has a T cell receptor consisting of a gamma chain that does not contain the Vgamma2 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-negative." + "The synthesis or release of any molecular mediator of the immune response, resulting in an increase in its intracellular or extracellular levels." + "An epithelial cell that has a cilia." "FMA:70605" + "OBSOLETED. Commonly used for a cell in root epidermis that gives rise to a root hair. The daughter cell produced by the asymmetric division of a root epidermal cell that gives rise to a root hair." + "Specialized elongated ventricular ependymal cell that has processes that extend to the outer, or pial, surface of the CNS. Resemble spongioblasts seen in developing brain. Found in the adult brain in the third ventricle, cerebral aqueduct, spinal canal and floor of the fourth ventricle." "FMA:54560 BTO:0001953" + "Any process that activates or increases the frequency, rate or extent of export of iron ions from inside of a cell, across the plasma membrane and into the extracellular region." + "SCTID:360409004 neuronames:2499 NCIT:C34259" + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins." + "A GABAergic interneuron located in the cerebral cortex that expresses reelin (rln)." + "Any process that stops, prevents or reduces the frequency, rate or extent of cation channel activity." + "A gray matter that has the potential to develop into a facial nucleus." "EHDAA2:0004639" + "A hematopoietic progenitor that has some limited self-renewal capability. Cells are lin-negative, Kit-positive, CD34-positive, and Slamf1-positive." + "A segment of autopod that is part of a manus." "FMA:24945 SCTID:127950000" + + "Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent." "Wikipedia:Mitosis" + "The process in which the anatomical structure of the trigeminal nerve is generated and organized. The trigeminal nerve is composed of three large branches. They are the ophthalmic (V1, sensory), maxillary (V2, sensory) and mandibular (V3, motor and sensory) branches. The sensory ophthalmic branch travels through the superior orbital fissure and passes through the orbit to reach the skin of the forehead and top of the head. The maxillary nerve contains sensory branches that reach the pterygopalatine fossa via the inferior orbital fissure (face, cheek and upper teeth) and pterygopalatine canal (soft and hard palate, nasal cavity and pharynx). The motor part of the mandibular branch is distributed to the muscles of mastication, the mylohyoid muscle and the anterior belly of the digastric. The mandibular nerve also innervates the tensor veli palatini and tensor tympani muscles. The sensory part of the mandibular nerve is composed of branches that carry general sensory information from the mucous membranes of the mouth and cheek, anterior two-thirds of the tongue, lower teeth, skin of the lower jaw, side of the head and scalp and meninges of the anterior and middle cranial fossae." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a histamine stimulus. Histamine, the biogenic amine 2-(1H-imidazol-4-yl)ethanamine, is involved in local immune responses as well as regulating physiological function in the gut and acting as a neurotransmitter." + "The process whose specific outcome is the progression of the metanephric pyramids over time, from their formation to the mature structures. Metanephric pyramids are the conical masses that constitute the renal medulla in a metanephros; they contain the loops of Henle and the medullary collecting ducts." + "A subdivision of the muscular system corresponding to a subdisivision of an organism." "MA:0000165 NCIT:C13056 EFO:0001949 ZFA:0000548 TAO:0000548 BTO:0000887 EMAPA:35577 WBbt:0005737 VSAO:0005038 FMA:32558 Wikipedia:Muscular_system UMLS:C0026845" + "Any process that activates or increases the frequency, rate or extent of neuroblast migration." + "Any process that activates or increases the frequency, rate or extent of ovarian cumulus cell differentiation." + "A chromaffin cell that is part of the paraaortic body." "FMA:69328" + "A double-positive thymocyte that is undergoing positive selection, has high expression of the alpha-beta T cell receptor, is CD69-positive, and is in the process of down regulating the CD8 co-receptor." + "A complement component C1q receptor that is encoded in the genome of mouse." "UniProtKB:O89103" + "A neuromuscular junction in which the target muscle cell is a somatic muscle cell, such as those found in nematodes and arthropods." + "Epithelium that is part of a developing tooth or dental organ." "UMLS:C1709309 NCIT:C54296 AAO:0011027 EMAPA:32903 XAO:0003203 ZFA:0005134 BTO:0001723 MA:0003151 TAO:0005134 VHOG:0001443" + "A CD44 molecule that is encoded in the genome of human." "UniProtKB:P16070" + "Any process that stops, prevents or reduces the frequency, rate or extent of retina development in camera-type eye." + "A nerve that is part of a chest [Automatically generated definition]." "MA:0000551 EMAPA:37266" + "Any process that stops, prevents or reduces the frequency, rate or extent of aorta morphogenesis." + "Transynaptic signaling in which the ligand is carried across the synapse by an exosome." + "The chemical reactions and pathways resulting in the breakdown of amino acids of the glutamine family, comprising arginine, glutamate, glutamine and proline." + "A muscle layer that is part of a small intestine." "NCIT:C33569 UMLS:C0227269 SCTID:362145004 FMA:14932" + "An enucleate erythrocyte that is Lyg-76-high." + "Any process that stops or reduces the rate of deoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid." + "A diaphysis that is part of a tibia." "MA:0003049 EMAPA:37770 SCTID:302525009 Wikipedia:Body_of_tibia FMA:33125" + "The adenohypophyseal placode forms the anterior lobe of the pituitary gland and gives rise to the endocrine secretory cells of the pituitary." "TAO:0001198 ZFA:0001198 XAO:0004208 EFO:0000229" + "Glands of Moll, also known as ciliary glands, are modified apocrine sweat glands that are found on the margin of the eyelid. They are next to the base of the eyelashes, and anterior to the Meibomian glands within the distal eyelid margin. These glands are relatively large and tubular-shaped. The glands of Moll are named after Dutch oculist Jacob Anton Moll (1832-1914). Glands of Moll empty into the adjacent lashes. Glands of Moll and Zeis secrete lipid that adds to the superficial layer of the tear film, retarding evaporation. The glands of Moll are prone to infection and blockage of its duct with sebum and cell debris. Blockage of the gland's duct causes swelling which can manifest itself as a stye." "SCTID:280586002 Wikipedia:Gland_of_Moll FMA:59159 NCIT:C32679" + "A vertebra in the trunk or cervical region. Includes all cervical, thoracic and lumbar vertebrae, but excludes caudal vertebra." "XAO:0003077 EMAPA:37722 MA:0002869" + "The polygonal structure of the liver that consists of hepatocytes radiating outward from a hepatic vein." "UMLS:C0227518 Wikipedia:Lobules_of_liver NCIT:C32732 SCTID:362194004 MA:0002494 EMAPA:35499 FMA:14471" + "The developmental process pertaining to the initial formation of a renal capsule from unspecified parts. The renal capsule is the tough fibrous layer surrounding the kidney, covered in a thick layer of perinephric adipose tissue. It provides some protection from trauma and damage. During development, it comprises a single layer of flattened cells that lie just above the cortical stroma and the condensed mesenchyme of the nephrogenic zone. It is in this region that the early stages of nephron induction and formation of new generations ureteric bud branches occur, as the kidney expands." + "A stromal cell that is part of the thymus." + "A developmental process, independent of morphogenetic (shape) change, that is required for the cerebellar molecular layer to attain its fully functional state. The molecular layer is the outermost layer of the cerebellar cortex. It contains the parallel fibers of the granule cells, interneurons such as stellate and basket cells, and the dendrites of the underlying Purkinje cells." + "Any process that stops, prevents, or reduces the frequency, rate or extent of keratinocyte differentiation." + "The process in which the anatomical structure of the endocardium is generated and organized. The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers." + "The process whose specific outcome is the progression of the inner stripe over time, from its formation to the mature structure. The inner stripe is a deep, centrally located portion of the renal outer medulla and is traversed by thin descending and thick ascending portions of the loops of Henle." + "A proximal epiphysis that is part of a metatarsal bone [Automatically generated definition]." "SCTID:119545008 FMA:33817" + "Any process that modulates the frequency, rate, or extent of leukocyte chemotaxis." + "Any process that activates or increases the frequency, rate or extent of excitatory synapse assembly." + "The process in which the structures of a chondrocyte that will contribute to bone development are generated and organized." + "Any process that stops, prevents or reduces the frequency, rate or extent of RNA binding." + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a carbohydrate stimulus." + "A S. pombe cell type determined by mat1-Pc and mat1-Pi on the mat1 locus." + "Any collection of muscles that is part of a pectoral appendage." "ZFA:0000563 EFO:0003540 TAO:0000563" + "A border associated macrophage which is part of a dura matter. This macrophage phagocytoses intruding pathogens and foreign molecules detected in the bloodstream or in the cerebrospinal fluid. This cell has an amoeboid body with dynamic protrusions in homeostasis." + "Any process that modulates the frequency, rate or extent of secretory granule organization." + "The series of events required for an organism to receive a sensory chemical stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process." + "Any process that stops, prevents or reduces the frequency, rate or extent of epithelial cell apoptotic process." + "A proximal epiphysis that is part of a phalanx [Automatically generated definition]." + "The infolding of a membrane." + "A change in the morphology or behavior of a leukocyte resulting from exposure to an activating factor such as a cellular or soluble ligand, leading to the initiation or perpetuation of an inflammatory response." + "The epithelial layer that lines the luminal space of the esophagus." "MA:0001565 EMAPA:16835 UMLS:C1179544 TAO:0001499 NCIT:C49221 BTO:0001578 EFO:0003041 ZFA:0001499 EHDAA2:0001287 FMA:63063 CALOHA:TS-0698" + "The directed movement of lactoferrin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "A type of type 3 cone bipolar cell with distinctive crescent-shaped dendrites." + "The cellular avascular layer of the kidney luminar surfaces." "CALOHA:TS-0505 MA:0002846 EMAPA:35457 BTO:0000059" + "A rhodopsin-like G-protein coupled receptor that is a translation product of the human OPN1LW, OPN1MW, OPN1SW, RHO, OPN3, OPN4, or OPN5 genes, 1:1 orthologs thereof, or a semi-ortholog thereof in Metazoa. The active form binds a vitamin A-based retinaldehyde chromophore through a Schiff base linkage to a Lys residue in the seventh transmembrane alpha helix." "IUPHARfam:975 PIRSF:PIRSF038544" + "Bone element that is adjacent to the notochord." "TAO:0001639 VSAO:0000307 AAO:0010777 ZFA:0001629" + "The establishment, maintenance and elaboration of the anterior/posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism." + "A cell involved in transporting nutrients, minerals, water, gases and other chemicals between cells for a variety of purposes including conveying nutrition to other tissues, removing waste products from the tissues, conveying gases for respiration, distributing heat and repelling invasion of foreign substances." + "A langerin-positive lymph node dendritic cell that is CD103-positive and CD11b-low." + "Any process that activates or increases the frequency, rate or extent of oligodendrocyte differentiation." + "Any process that modulates the frequency, rate or extent of compound eye photoreceptor development." + "The cartilage or bony capsule surrounding the inner ear mechanism." "MA:0000252 EMAPA:37466" + "Any process that activates or increases the rate or extent of fat cell proliferation." + "The tubules in the testes where spermatogenesis occurs." "NCIT:C34293 FMA:19825 Wikipedia:Seminiferous_tubule CALOHA:TS-1239 GAID:400 MAT:0000503 EMAPA:18685 EFO:0001404 SCTID:279614002 BTO:0001235 EMAPA:31476 UMLS:C1519236 EV:0100380 MESH:D012671 NCIT:C13047 UMLS:C0036630 MA:0000412 XAO:0003088 VHOG:0001363 AAO:0010399" + "A follicle cell that migrates from the anterior pole of the insect egg chamber to the anterior of the oocyte where they participate in the formation of the micropyle." "FBbt:00004905" + "OBSOLETE. A CNS neuron of the cerebral cortex." "BTO:0004102 FMA:84104" + "Any process that activates or increases the frequency, rate or extent of protein localization to cell-cell junction." + "The process whose specific outcome is the progression of a neuron whose cell body is located in the peripheral nervous system, from initial commitment of the cell to a neuronal fate, to the fully functional differentiated neuron." + "Any process that increases the rate or extent of the process whose specific outcome is the progression of an oocyte over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell." + "A blood that is part of a vein." "FMA:83067" + "A fold of tissue which extends into the peritoneal cavity of the developing embryo and participates in the separation of the pleural and peritoneal cavities." "EMAPA:17709 SCTID:361429005 EHDAA2:0001483 NCIT:C34256 UMLS:C1283968 Wikipedia:Pleuroperitoneal VHOG:0000757" + "The process in which a relatively unspecialized cell acquires the characteristics of a mature hemocyte. Hemocytes are blood cells associated with a hemocoel (the cavity containing most of the major organs of the arthropod body) which are involved in defense and clotting of hemolymph, but not involved in transport of oxygen." + "A SLAM family member 5 that is encoded in the genome of human." "UniProtKB:Q9UIB8" + "A bone that is part of a forelimb stylopod [Automatically generated definition]." "MA:0000604 EMAPA:35892" + "A cell junction that forms a connection between two or more cells of an organism; excludes direct cytoplasmic intercellular bridges, such as ring canals in insects." "NIF_Subcellular:sao1922892319" + "The process aimed at the progression of a cardiac neural crest cell over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell that contributes to the development of the heart." + "A portion of an organ, such as the liver, lung, breast, or brain." "FMA:45728 UMLS:C0796494 NCIT:C13393" + "EHDAA2:0004070" + "Any process that activates or increases the frequency, rate or extent of a small molecule metabolic process." + "A portion of connective tissue that is part of a forelimb stylopod [Automatically generated definition]." "MA:0000605 EMAPA:37317" + "A duct that is located within a lobule, with no more connective tissue intervening between ducts and secretory units (i.e., acini or tubules) than between adjacent secretory units. Intercalated and striated ducts are intralobular." "SCTID:205214009" + "A protein that is a translation product of the human CEACAM8 gene or a 1:1 ortholog thereof." + "The smooth muscle layer of the stomach wall that functions to churn and mix food and gastric secretions as well as to move food along the digestive tract to the intestines." "SCTID:362132003 FMA:14909" + "Any process that modulates the frequency, rate or extent of growth of the body of an organism so that it reaches its usual body size." + "An intervertebral disk that connects a vertebral bone 1 and connects a vertebral bone 2." "EMAPA:19416" + "The chemical reactions and pathways involving organic hydroxy compound." + "External opening or orifice of the urethra through which urine and seminal fluid (in males only) leave the body; in males the meatus presents as a vertical slit normally positioned at the tip of glans penis; in females the meatus is located between the clitoris and the vagina in the vulvular vestibule of the female genitalia[MP]." "EMAPA:37977 SCTID:181424008 Wikipedia:Urinary_meatus FMA:19650" + "Binding to a carboxylic acid, an organic acid containing one or more carboxyl (COOH) groups or anions (COO-)." + "The orderly movement of epithelial cells within the mammary line that contributes to the formation of the mammary placode." + "Any process that mediates the transfer of information from an atrial cardiomyocyte to an AV node cell." + "A mesentery of duodenum that is part of a midgut." "EHDAA2:0001193" + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism." + "Any process that activates or increases the frequency, rate, or extent of cytokine production that contributes to an immune response." + "One of the three major regions of the conjunctiva." "SCTID:29445007 FMA:59023 Wikipedia:Conjunctiva#Gross_anatomy" + "The directed movement of iron (Fe) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "Sweat that is produced by the glands on the palmar and plantar surfaces." "FMA:63084" + "Any process that modulates the frequency, rate or extent of apoptotic process involved in morphogenesis." + "Any of the numerous small mucous-secreting glands located in the wall of the penile urethra." "SCTID:303562001 UMLS:C1314737 EMAPA:29645 Wikipedia:Urethral_gland NCIT:C49311 FMA:21443" + "The process whose specific outcome is the progression of a neuron over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell." + "Any process that modulates the frequency, rate, or extent of interferon type I production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families." + "Any process that activates or increases the frequency, rate or extent of mitotic chromosome condensation." + "A killer cell lectin-like receptor 4 that is encoded in the genome of mouse." "UniProtKB:Q60651" + "Any process that modulates the frequency, rate or extent of the directed movement of a neurotransmitter into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "The process whose specific outcome is the progression of the renal cortex over time, from its formation to the mature structure. The renal cortex is the outer region of the kidney." + "A fungal cell with two or more genetically distinct nuclei." + "The outermost part of the spinal canal. It is the space within the canal (formed by the surrounding vertebrae) lying outside the dura mater." "GAID:243 MESH:D004824 SCTID:281866004 FMA:71228 Wikipedia:Epidural_space" + "The process whose specific outcome is the progression of the circulatory system over time, from its formation to the mature structure. The circulatory system is the organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis." + "The process whose specific outcome is the progression of the short descending thin limb over time, from its formation to the mature structure. The short descending thin limb is the descending thin limb of a short nephron that has a squamous epithelial morphology." + "The multiplication or reproduction of chorionic trophoblast cells, resulting in the expansion of their population." + "A bodily secretion that is produced by a seminal vesicle." "FMA:62969 BTO:0002053 NCIT:C33529 MA:0002526 UMLS:C0227987 UMLS:C0036614 NCIT:C52552" + "A vasa recta that is part of a inner medulla of kidney [Automatically generated definition]." "EMAPA:36559 MA:0002596" + "Any process that activates or increases the frequency, rate or extent of G protein-coupled receptor signaling pathway activity." + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of non-sensory hairs. These hairs are polarized cellular extensions that cover much of the insect epidermis." + "Any process that modulates the rate, frequency, or extent of the multiplication or reproduction of osteoclasts, resulting in the expansion of an osteoclast cell population." + "Any process that modulates the frequency, rate or extent of synapse assembly, the aggregation, arrangement and bonding together of a set of components to form a synapse." + "The growth of an epithelial cell dependent on cycles of endoreplication, where growth contributes to the shaping of the Malpighian tubule." + "Any process that modulates the frequency, rate or extent of the regulated release of a gonadotropin." + "The chemical reactions and pathways resulting in the formation of ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator." + "The complete extent of cell cortex that underlies some some region of the plasma membrane." + "The developmental process pertaining to the initial formation of a cardiac right atrium from unspecified parts." + "The process whose specific outcome is the progression of the larva over time, from its formation to the mature structure. The larva is the early, immature form of an that at birth or hatching is fundamentally unlike its parent and must metamorphose before assuming the adult characters." + "The movement of a T cell within or between different tissues and organs of the body." + "The late distal convoluted tubule contains DCT cells and intercalated (IC) alpha and beta cells and is vasopressin-sensitive[GO]." + "A gland that is part of a hemolymphoid system [Automatically generated definition]." "EMAPA:18766 MA:0002962" + "An organism subdivision that extends from the head to the pectoral girdle, encompassing the cervical vertebral column." "FMA:7155 BTO:0000420 Wikipedia:Neck UMLS:C0027530 AEO:0000108 galen:Neck NCIT:C13063 EHDAA2:0003108 SCTID:302550007 EFO:0000967 CALOHA:TS-2045 EMAPA:35587 MAT:0000297 MESH:D009333 MIAA:0000297 GAID:86 MA:0000024" + "Any process that increases the rate, frequency, or extent of the regulated release of a peptide hormone from secretory granules." + "A protein complex which is capable of catalytic activity." + "Any collection of muscles that is part of a forelimb [Automatically generated definition]." "FMA:50396" + "An organ that functions as a secretory or excretory organ." "EHDAA:2161 MA:0003038 WikipediaCategory:Glands Wikipedia:Gland galen:Gland SCTID:134358001 FMA:7146 MAT:0000021 MIAA:0000021 EFO:0000797 AAO:0000212 NCIT:C13319 EHDAA2:0003096 FMA:86294 AEO:0000096 BTO:0000522 EMAPA:18425 HAO:0000375 UMLS:C1285092" + "One of two hemispherical bulges on the base of the posterior hypothalamus (Butler and Hodos, Comparative Vertebrate Neuroanatomy, 2nd ed., 2005, pg 455)." "UMLS:C0024670 EMAPA:35542 BAMS:MBO ZFA:0000334 FMA:74877 DHBA:15546 MESH:D008326 BAMS:mmb BAMS:MB HBA:12909 neuronames:412 TAO:0000334 MA:0000174 UMLS:C1305759 Wikipedia:Mammillary_body NCIT:C33052 BIRNLEX:865 GAID:652 SCTID:279306001 DMBA:15723 MBA:331" + "Muscle that is part of the respiratory system." + "A cell type found in the gastrointestinal and respiratory tracts that is characterized by the presence of a tuft of blunt, squat microvilli (120-140 per cell). Function of this cell type is not known." "FMA:67978" + "Primordia are populations of contiguous cells that are morphologically distinct and already correspond in extent to a later organ/tissue[FBbt, Hartenstein, V. (2004)]." "NCIT:C34275 BTO:0001886 FMA:86589 EHDAA2:0003171 EFO:0001652 Wikipedia:Primordium MAT:0000482 AEO:0000171 UMLS:C0678727 XAO:0003043" + "A change in the morphology or behavior of a follicular dendritic cell resulting from exposure to an activating factor such as a cellular or soluble ligand." + "Any process that modulates the frequency, rate or extent of coagulation, the process in which a fluid solution, or part of it, changes into a solid or semisolid mass." + "The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites." + "Anatomical cavity bounded by visceral and parietal peritoneum." "SCTID:181616008 MA:0000054 GAID:24 NCIT:C12769 BTO:0001782 EMAPA:16138 VHOG:0000852 FMA:14704 Wikipedia:Peritoneal_cavity EHDAA2:0001446 UMLS:C1704247 MESH:D010529" + "Any process that activates or increases the frequency, rate or extent of production of a cytokine." + "Enables the transfer of modified amino acids from one side of a membrane to the other." + "A myeloid dendritic cell found in the blood that is CD16-positive." + "A NK1.1-positive T cell that is Ly49D-positive." + "A large, oval stomach epithelial cell with a central nucleus; source of gastric acid. Secretes HCl." "BTO:0001780 FMA:62901" + "An organ that houses olfactory neurons and is responsible for the sense of smell. Examples include the vertebrate nose and the Drosophila dorsal organ." "FMA:77659 BTO:0001772 VHOG:0000287 XAO:0000273 AAO:0010180" + "The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord." "Wikipedia:Neural_development" + "Any process that modulates the frequency, rate or extent of defense response to insect." + "A transferrin receptor protein 1 that has been processed by proteolytic cleavage." + "The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or a transporter complex, a pore or a motor protein." + "A mature B cell that produces cytokines that can influence CD4 T cell differentiation." + "Any process that modulates the frequency, rate or extent of striated muscle contraction." + "Cytoarchitectural part of the olfactory bulb, lying superior to the mitral cell layer and inferior to the glomerular layer. The EPL is mostly neuropil composed almost entirely of mitral and tulfted cell dendrites and granule cell dendrites and their synaptic inputs." "DMBA:15913 MA:0000969 EMAPA:35607 BAMS:EPl BTO:0001319 NLXANAT:20090403" + "A submucosa that is part of a biliary tree [Automatically generated definition]." "FMA:18009" + "Any process that increases the frequency, rate or extent of the formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells." + "Any process that increases the rate, frequency or extent of protein maturation by peptide bond cleavage." + "Any vertebra endochondral element that is part of the caudal region of the vertebral column (tail or coccyx)." + "A mucosa that is part of a esophagus [Automatically generated definition]." "EMAPA:26981 BTO:0002859 NCIT:C32538 UMLS:C0227176 MA:0002680 FMA:62996 SCTID:362127004" + "Any process that modulates the frequency, rate or extent of immature T cell proliferation." + "The anterior lateral line system develops from cranial ectodermal placodes, situated between the eye and the ear, that give rise to both the neuromasts and the anterior lateral line sensory nerves that innervate the neuromasts. The anterior lateral line system consists of small sensory patches (neuromasts) located superficially on the skin or just under the skin in fluid-filled canals on the head of all fishes and most amphibians and are innervated by several lateral line nerves, which project to the hindbrain. The anterior lateral line system is stimulated by local water displacements and vibrations, and detects propulsion of the fish through the water, as well as facilitating shoaling, prey capture, and predator and obstacle avoidance." "ZFA:0001468 TAO:0001468 EFO:0003691" + "A portion of smooth muscle tissue that is part of a trigone of urinary bladder [Automatically generated definition]." "EMAPA:28649 MA:0001700" + "EHDAA2:0004071" + "Any process that activates or increases the frequency, rate or extent of eye photoreceptor development." + "An interstitial cell that is part of a cardiac valve leaflet. Along with valve endothelial cells, a valve interstitial cell maintains tissue homeostasis for the function of cardiac valves through secreting biochemical signals, matrix proteins and matrix remodeling enzymes." + "Any process that activates or increases the frequency, rate or extent of bone mineralization." + "A cartilage element that is part of a splanchnocranium." "TAO:0001460 EFO:0003689 ZFA:0001460" + "An alpha-type platelet-derived growth factor receptor that is encoded in the genome of mouse." "UniProtKB:P26618" + "A mucosa that is part of a vagina [Automatically generated definition]." "BTO:0005676 FMA:19975 SCTID:362245006" + "A Purkinje myocyte that is part of the atrioventricular node." "FMA:83386" + "Any process that stops, prevents, or reduces the frequency, rate or extent of osteoblast differentiation." + "A cranial nerve fiber tract that innervates the parietal eye." + "Any process that activates or increases the frequency, rate or extent of programmed cell death that occurs in the retina." + "A cranial nerve that originates from neurons in the medulla and in the cervical spinal cord." "FMA:6720 NCIT:C32041 AAO:0010476 GAID:825 XAO:0004214 VHOG:0000699 EHDAA:2855 FMA:80284 EHDAA2:0000106 UMLS:C0000905 BAMS:11n EMAPA:17265 MESH:D000055 Wikipedia:Spinal_accessory_nerve neuronames:2085 BAMS:XIn SCTID:362469008 BIRNLEX:812 HBA:9340 UMLS:C1305777 MA:0001088 MBA:717" + "Selectively enables the transmembrane transfer of a cation by a channel that opens upon binding acetylcholine." + "An aminopeptidase N that is encoded in the genome of mouse." "UniProtKB:P97449" + "Any process that modulates the frequency, rate or extent of glia cell differentiation." + "The process whose specific outcome is the progression of the metanephric descending thin limb over time, from its formation to the mature structure. The metanephric descending thin limb is a part of the metanephric loop of Henle situated just after the proximal straight tubule (S3). It extends to the tip of the metanephric loop of Henle." + "The process whose specific outcome is the progression of the macula densa over time, from its formation to the mature structure. The macula densa is an area of specialized cells in the distal tubule that makes contact with the vascular pole of the glomerulus." + "A corticothalamic-projecting glutamatergic neuron that is located in L6 and lower L5 of the primary motor cortex, with a pyramidal morphology and mostly untufted apical dendrites terminating in midcortical layers. CT VAL/VM (ventroanterior-ventrolateral complex/ventromedial nucleus) cells have a near tonic firing pattern and are distinguished from L6 IT neurons by a lower inter-spike interval adaptation index." + "A reticulocyte that retains the nucleus and other organelles. Found in birds, fish, amphibians and reptiles." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of juvenile hormone." + "A protein that is a translation product of the human CD83 gene or a 1:1 ortholog thereof." + "A goblet cell that is part of the epithelium of gastric cardiac gland." "FMA:263038" + "A supporting cell of the organ of Corti." + "An endothelium that is part of an arterial system [Automatically generated definition]." "NCIT:C49329 EMAPA:35145 UMLS:C1706849 MA:0000703" + "The change in morphology and behavior of a microglial cell resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor, leading to the initiation or perpetuation of an immune response." + "A pouch of ectoderm that grows out from the upper surface of the embryonic stomodeum and gives rise to the anterior and intermediate lobes of the pituitary gland[MP]. In embryogenesis, Rathke's pouch is a depression in the roof of the developing mouth in front of the buccopharyngeal membrane. It gives rise to the anterior pituitary (adenohypophysis), a part of the endocrine system[WP]." "FMA:302929 Wikipedia:Rathke's_pouch neuronames:1516 EMAPA:16725 NCIT:C34281 UMLS:C0229548 VHOG:0000674 SCTID:362583008 EHDAA2:0001588 NCIT:C54098 XAO:0000430 AAO:0011094 SCTID:61127000 UMLS:C1709841" + "A viscosity quality inhering in a bearer by virtue of the bearer's having viscosity." + "A mesentery that is part of a urinary system [Automatically generated definition]." "MA:0003233 EMAPA:17367" + "The progression of the mammary gland alveolus over time, from its formation to its mature state. The mammary gland alveolus is a sac-like structure that is found in the mature gland." + "Any process that activates or increases the frequency, rate or extent of activation." + "A high endothelial venule that is located in the vermiform appendix." + "Any process that modulates the frequency, rate or extent of intestinal epithelial cell development." + "A joint that connects two adjacent metatarsals." "Wikipedia:Intermetatarsal_articulations SCTID:361868009 FMA:35219" + "An endorphine cell that secretes enkephalin." + "A promyelocyte committed to the eosinophil lineage." "FMA:84199" + "The directed movement of a protein to a part of a chromosome that is organized into chromatin." + "A goblet cell that is part of the epithelium proper of appendix." "FMA:263069" + "A retinal ganglion cell B that has a very small but very dense dendritic field, and has post synaptic terminals in S2." "BAMS:1048" + "Any process that stops, prevents, or reduces the frequency, rate or extent of natural killer T cell proliferation." + "Any process in which an organelle is maintained in a specific location within a cell and prevented from moving elsewhere." + "A mucosa that is part of a prostatic urethra [Automatically generated definition]." "FMA:77079" + "Any process that modulates the frequency, rate, or extent of interleukin-22 production." + "Mucus produced in the respiratory tract." "NCIT:C93171 UMLS:C0225378" + "Any sense organ that is part of some larva." + "The epithelial layer of the alveoli[MP]. The layer of cells covering the lining of the tiny air sacs at the end of the bronchioles[BTO]." "FMA:63915 NCIT:C12867 BTO:0003511 MA:0001771 EMAPA:35121" + "The inner layer of peritoneum that is wrapped around organs located inside the intraperitoneal space." "Wikipedia:Visceral_peritoneum SCTID:362702003 TAO:0005132 ZFA:0005132 FMA:14703 VHOG:0001528 EMAPA:16592" + "A type D cell found in the stomach." "FMA:83410" + "Any apoptotic process in an inflammatory cell, any cell participating in the inflammatory response to a foreign substance e.g. neutrophil, macrophage." + "A retinal ganglion cell that is depolarized by decreased illumination of their receptive field center." + "Anatomical structure that is part of the head consisting entirely of cranium and mandible[WP]." "WikipediaCategory:Skull CALOHA:TS-2344 MESH:D012886 SCTID:110530005 EHDAA2:0000325 NCIT:C12789 GAID:82 Wikipedia:Skull FMA:46565 UMLS:C0037303 BTO:0001295 EMAPA:17680 galen:Skull" + "A stem cell that can give rise to multiple cell types (i.e. smooth muscle, endothelial) in the developing heart." + "An M9 retinal ganglion cell with synaptic terminals in S4 that is depolarized by decreased illumination of their receptive field center" + "A Thy-1 membrane glycoprotein that is encoded in the genome of mouse." "UniProtKB:P01831" + "A subdivision of an anatomical system." "SCTID:91690000 FMA:67509" + "The progression of the lateral geniculate nucleus over time from its initial formation until its mature state. The lateral geniculate nucleus is the primary processor of visual information received from the retina." + "The gingival sulcus is an area of potential space between a tooth and the surrounding gingival tissue and is lined by sulcular epithelium. The depth of the sulcus (Latin for groove) is bounded by two entities: apically by the gingival fibers of the connective tissue attachment and coronally by the free gingival margin." "Wikipedia:Gingival_sulcus NCIT:C114645 FMA:74580 SCTID:245753001" + "Capillary that has pores in the endothelial cells (60-80 nm in diameter) that are spanned by a diaphragm of radially oriented fibrils and allow small molecules and limited amounts of protein to diffuse." "FMA:63196 NCIT:C32595 TAO:0005260 UMLS:C1179615 ZFA:0005260 Wikipedia:Capillary#Types" + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an epinephrine stimulus. Epinephrine is a catecholamine that has the formula C9H13NO3; it is secreted by the adrenal medulla to act as a hormone, and released by certain neurons to act as a neurotransmitter active in the central nervous system." + "CD8_alpha-negative CD11b-positive dendritic cell is a conventional dendritic cell that is CD11b-positive, CD4-positive and is CD205-negative and CD8_alpha-negative." + "Any process that increases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment." + "An epithelium that is part of a knee [Automatically generated definition]." "EHDAA:6186 EMAPA:17494 VHOG:0000810 EHDAA2:0000896 EHDAA:5161" + "Any process that modulates the frequency, rate or extent of establishment of cell polarity." + "A cadherin-1 that is encoded in the genome of human." "UniProtKB:P12830" + "The process in which an endocardial cushion cell give rise to a cell that is part of a heart valve." + "The chemical reactions and pathways resulting in the formation of acetylcholine, the acetic acid ester of the organic base choline." + "An erythroid transcription factor that is encoded in the genome of mouse." "UniProtKB:P17679" + "A nucleus of brain that is part of a diencephalon." "TAO:0002191 ZFA:0001659" + "Any process that modulates the frequency, rate or extent of the regulated release of corticotropic hormone from a cell." + "Any process that activates or increases the frequency, rate or extent of the controlled release of a substance from a cell or a tissue." + "The process whose specific outcome is the progression of the mechanosensory lateral line system over time, from its formation to the mature structure. The mechanosensory lateral line system consists of small sensory patches (neuromasts) located superficially on the skin or just under the skin in fluid-filled canals on the head and body of all fishes and most amphibians. The neuromasts are innervated by several lateral line nerves, which project primarily to the hindbrain. The mechanosensory lateral line system is stimulated by local water displacements and vibrations, and detects propulsion of the fish through the water, as well as facilitating shoaling, prey capture, and predator and obstacle avoidance." + "GC_ID:1" + "Any apoptotic process in a fat cell." + "A gamete-nursing cell that derives from the somatic tissues of the gonad (del Pino, 2021)." + "A microtubule-based process that results in the transport of proteins." + "A pre-cartilage condensation that is part of a pedal digit mesenchyme." "EMAPA:32950 VHOG:0000952" + "A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells." + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a neuromuscular junction." + "Any membrane-enclosed lumen that is part of a tertiary granule." + "The mediastinum testis is a network of fibrous connective tissue that extends from the upper to near the lower extremity of the testis, and is wider above than below. From its front and sides numerous imperfect septa (trabeculæ) are given off, which radiate toward the surface of the organ, and are attached to the tunica albuginea. They divide the interior of the organ into a number of incomplete spaces, called lobules. These are somewhat cone-shaped, being broad at their bases at the surface of the gland, and becoming narrower as they converge to the mediastinum. The mediastinum supports the rete testis and blood vessels of the testis in their passage to and from the substance of the gland[WP]." "FMA:19812 SCTID:362279007 MA:0003240 Wikipedia:Mediastinum_testis EMAPA:18331" + "The process in which the anatomical structure of the rhombomere is generated and organized. Rhombomeres are transverse segments of the developing rhombencephalon. Rhombomeres are lineage restricted, express different genes from one another, and adopt different developmental fates." + "Any process that activates or increases the frequency, rate or extent of natural killer cell proliferation." + "The embryonic anlage of the external genitalia, which emerges as paired swellings ventral to the cloacal membrane, is proposed to be derived from all three germ layers, and gives rise to the penis, clitoris, scrotum, labia, and foreskin." "EHDAA:5925 EHDAA2:0000705 Wikipedia:Genital_tubercle FMA:302888 VHOG:0000583 SCTID:308798005 EMAPA:17382" + "A process in which a protein is transported to, or maintained in, a location within a cilium." + "The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y." "Wikipedia:Carbohydrate_metabolism" + "A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities. Cell lacks hematopoeitic lineage markers." + "A protein that is a standalone version of the Hormone_1 domain (Pfam:PF00103). In the immature form, the domain is preceded by a signal peptide." + "Any process that modulates the frequency, rate or extent of the process of gaseous exchange between an organism and its environment." + "Any process that modulates the frequency, rate, or extent of antigen processing and presentation." + "The process in which a relatively unspecialized epidermal cell acquires the specialized features of a sebaceous gland cell." + "A portion of smooth muscle tissue that is part of an arteriole [Automatically generated definition]." "MA:0000706 FMA:312251 EMAPA:36287" + "The synthesis or release of any molecular mediator of the inflammatory response following an inflammatory stimulus, resulting in an increase in its intracellular or extracellular levels." + "The process whose specific outcome is the progression of the ovarian follicle over time, from its formation to the mature structure." + "A limb bud that develops into a forelimb." "EMAPA:16406 FMA:296782 SCTID:346062002 AAO:0010381 XAO:0003065 EHDAA:1699 BTO:0001645 RETIRED_EHDAA2:0003198 MIAA:0000065" + "Ectodermal placode that does not develop into a component of the nervous system." + "Stomach mucosa that is lined with glandular epithelium and part of a stomach glandular region." "EMAPA:27167 MA:0001614" + "The macula densa is an area of specialized cells in the distal tubule that makes contact with the vascular pole of the glomerulus[GO]." "NCIT:C33043 MA:0002603 BTO:0003940 EMAPA:28399 FMA:86333 UMLS:C0227662 Wikipedia:Macula_densa SCTID:244657003" + "The series of events that restore integrity to a damaged tissue, following an injury." "Wikipedia:Wound_healing" + "A hematopoeitic stem cell found in the blood. Normally found in very limited numbers in the peripheral circulation (less than 0.1% of all nucleated cells)." "MESH:D000072916 BTO:0002669 FMA:86711" + "A motor neuron that is capable of directly inducing muscle contraction." + "A portion of connective tissue that is part of a lower leg [Automatically generated definition]." "MA:0000677 EMAPA:37327" + "The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.)." + "Learning by associating a stimulus (the cause) with a particular outcome (the effect)." "Wikipedia:Learning#Associative_learning" + "A form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases, whose actions dismantle a muscle cell and result in its death. A muscle cell is a mature contractile cell, commonly known as a myocyte, that forms one of three kinds of muscle." + "The process in which a relatively unspecialized cell acquires the specialized features of a granulosa cell, a supporting cell for the developing female gamete in the ovary of mammals." + "The aggregation, arrangement and bonding together of the mature ribosome and of its subunits." + "The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell." + "GC_ID:1" + "OBSOLETE. A respiratory stem cell found at the junction of the terminal (conductive) bronchiole and the respiratory bronchiole, which gives rise to alveolar cell types and club cells in response to lung injury." + "The chemical reactions and pathways resulting in the breakdown of an alpha-amino acid." + "A stem cell located in the bulge of the hair follicle that can give rise to regenerate the new follicle with each hair cycle and to reepithelialize the epidermis during wound repair." + "The process in which glucose is transported across a membrane." + "Any process that increases the rate, frequency, or extent of the orderly movement of an endothelial cell into the extracellular matrix to form an endothelium." + "A form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases, whose actions dismantle a cardiac muscle cell and result in its death. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction." + "An immune response which is associated with resistance to intracellular bacteria, fungi, and protozoa, and pathological conditions such as arthritis, and which is typically orchestrated by the production of particular cytokines by T-helper 1 cells, most notably interferon-gamma, IL-2, and lymphotoxin." + "Any process that modulates the frequency, rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule." + "Hepatic serous coat; peritoneal covering of the liver, enclosing almost all except for a triangular area on its posterior surface (the 'bare area of the liver') and a smaller area where the liver and gallbladder are in direct contact." + "Any process that modulates the frequency, rate or extent of translational termination." + "Any process that increases the rate, frequency or extent of mast cell differentiation, the process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a mast cell. A mast cell is a cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation." + "Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location." + "Any process that stops, prevents or reduces the frequency, rate or extent of platelet formation." + "The morphogenetic process in which an epithelial sheet bends along a linear axis." + "A sesamoid element that is composed primarily of cartilage tissue." "FMA:55379" + "A cell of an endocrine gland, ductless glands that secrete substances which are released directly into the circulation and which influence metabolism and other body functions." "FMA:83809" + "An amacrine cell with a medium dendritic field and post-synaptic terminals in S2 and S3. This cell type releases the neurotransmitter gamma-aminobutyric acid (GABA)." + "BTO:0003122" + "Any process that activates or increases the frequency, rate or extent of alpha-beta T cell proliferation." + "The process in which a relatively unspecialized cell acquires the specialized features of a natural killer cell." + "The process that gives rise to the intermediate mesoderm. This process pertains to the initial formation of the structure from unspecified parts." + "Any process that modulates the frequency, rate or extent of a multicellular organismal process, the processes pertinent to the function of a multicellular organism above the cellular level; includes the integrated processes of tissues and organs." + "Any process that stops, prevents, or reduces the frequency, rate or extent of gliogenesis, the formation of mature glia." + "Any process that decreases the rate, frequency or extent of fibroblast cell migration. Fibroblast cell migration is accomplished by extension and retraction of a pseudopodium." + "The mesonephric macula densa is an area of specialized cells in the distal tubule of the mesonephros that makes contact with the vascular pole of the glomerulus[GO]." + "Any process that modulates the frequency, rate or extent of lymphangiogenesis." + "Any process that modulates the frequency, rate or extent of eye photoreceptor development." + "A cathepsin-like protease that is a translation product of the human CTSK gene or a 1:1 ortholog thereof." "IUPHARobj:2350" + "FMA:24028" + "The process in which the anatomical structures of the brain are generated and organized. The brain is one of the two components of the central nervous system and is the center of thought and emotion. It is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.)." + "Any muscle organ that is part of a hindlimb [Automatically generated definition]." "AAO:0000222 EFO:0001928 FMA:37368" + "A sensory system that is capable of olfaction (the sensory perception of smell)." "SCTID:362290002 ZFA:0001149 BILA:0000144 EFO:0001973 NLXANAT:090806 TAO:0001149 Wikipedia:Olfactory_system XAO:0003196 FMA:7190 AAO:0000334 UMLS:C0228065 MA:0002445 EMAPA:36004 AAO:0000978 NCIT:C94501" + "An epidermal cell that is part of a cell cluster organ of the insect integument (such as a sensillum) and that secretes a cuticular specialization, often in the form of a hair, bristle, peg or scale. The base of this specialization is often surrounded by a socket produced by a closely associated tormogen cell." "FBbt:00005169 BTO:0004744" + "A subdivision of the autopod that corresponds to one or more bones arranged in series branching from the main limb axis." + "A telencephalic ventricle that is in_the_left_side_of a telencephalon." "FMA:78450 SCTID:368593005" + "OBSOLETE. An intratelencephalic-projecting glutamatergic neuron with a soma found in layer 6 of the human primary motor cortex." "ILX:0770158" + "A myoepithelial cell that is part of the primary lactiferous duct." "FMA:74500" + "The interphalangeal articulations of the foot (articulations of the phalanges) are ginglymoid joints, and each has a plantar and two collateral ligaments. The arrangement of these ligaments is similar to that in the metatarsophalangeal articulations: the Extensor tendons supply the places of dorsal ligaments." "SCTID:182225005 Wikipedia:Interphalangeal_articulations_of_the_foot FMA:35225 UMLS:C0040356 MESH:D014033 EMAPA:36337 NCIT:C33789 NCIT:C32867" + "Any process that decreases the frequency, rate or extent of a digestive system process, a physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism." + "The process in which B cells produce antibodies with increased antigen affinity. This is accomplished by somatic hypermutation and selection for B cells which produce higher affinity antibodies to antigen." + "A process that results in a parallel arrangement of microtubules." + "The lymph nodes located in the mesentery, of which there are 3 classes: ileocolic, juxtaintestinal mesenteric, and central superior group." "NCIT:C77641 EMAPA:35561 UMLS:C0229792 MA:0002829 FMA:12795 BTO:0000767 Wikipedia:Mesenteric_lymph_nodes" + "Any process that activates, maintains or increases the rate of developmental growth." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of a catecholamine." + "The movement of a cellular component as a result of microtubule polymerization." + "Alterations undergone by nuclei at the molecular and morphological level as part of the execution phase of apoptosis." + "A serous membrane that is part of a fundus of stomach." "FMA:17073 EMAPA:27157" + "The stem cell from which glial precursor cell arises from." "FMA:87171" + "Enables the facilitated diffusion of a calcium ion (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism." "Reactome:R-HSA-8949145 Reactome:R-HSA-9663785 Reactome:R-HSA-210420 Reactome:R-HSA-3295579 Reactome:R-HSA-8949178 Reactome:R-HSA-139855 Reactome:R-HSA-139854" + "One of two laterally paired arteries that supplies the pectoral appendages, usually branching from the dorsal aorta." "MA:0002045 AAO:0010232 XAO:0000365 NCIT:C33643 UMLS:C0038530 MESH:D013348 SCTID:265790007 FMA:3951 TAO:0005086 EMAPA:17617 Wikipedia:Subclavian_artery ZFA:0005086 GAID:511 EHDAA:4357 EHDAA2:0001933" + "The expansion of an immature T cell population by cell division." + "Any collection of muscles that is part of a back [Automatically generated definition]." "FMA:71291" + "Enables the transfer of acidic amino acids from one side of a membrane to the other. Acidic amino acids have side chains with a negative charge at pH 7.3." "Reactome:R-HSA-372448" + "A protein that is a translation product of the human CD84 gene or a 1:1 ortholog thereof." + "Any process that stops, prevents, or reduces the rate of the chemical reactions and pathways resulting in the formation of substances." + "Any neuromast mantle cell that is part of a posterior lateral line." + + "A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses." "NLX:147821 CARO:0001001" + "Fluid that lines the vaginal walls that consists of multiple secretions that collect in the vagina from different glands." + "A fibroblast that is part of the dense regular elastic tissue." "FMA:261287" + "The parenchymatous tissue of the spleen that surrounds splenic blood vessels, consists of compact masses of lymphatic cells and is where foreign material removed from the blood is used to initiate an immune reaction that results in the production of antibodies." "EMAPA:35809 NCIT:C12993 CALOHA:TS-1264 UMLS:C0229686 FMA:62805 Wikipedia:White_pulp MA:0000762" + "The asymmetric division of a skeletal muscle satellite stem cell to produce two daughter cells, one of which is destined to differentiate and the other to be a quiescent cell that restocks the satellite cell pool." + "The comma-shaped body is the precursor structure to the S-shaped body that contributes to the morphogenesis of the nephron." "ZFA:0005588 EMAPA:27681" + "Smooth and glossy outer protective cell layer of hair shaft." "FMA:70933 MA:0000157 EMAPA:35388" + "The raphe nuclei are thin plates of cells in and immediately adjacent to the sagittal plane." "Wikipedia:Raphe_nuclei FMA:84017 ZFA:0001429 BAMS:RA NLXANAT:20090205 UMLS:C0034671 NCIT:C97335 neuronames:2495 TAO:0001429 MESH:D011903 MA:0003147 EMAPA:35721" + "Endoskeletal elements that encase the brain, nose, inner ear[cjm]. that part of the neurocranium formed by endochondral ossification and comprising the bones of the base of the skull[TFD]." "VHOG:0000288 TAO:0001424 EMAPA:17681 Wikipedia:Chondrocranium EHDAA2:0000243 ZFA:0001424 AAO:0010169" + "The process in which antigen-activated dendritic cells acquire the specialized features of a mature conventional dendritic cell. Mature conventional dendritic cells upregulate the surface expression of MHC molecules, chemokine receptors and adhesion molecules, and increase the number of dendrites (cytoplasmic protrusions) in preparation for migration to lymphoid organs where they present antigen to T cells." + "A midline, cone like structure located in the dorso-caudal roof of the 3rd ventricle, attached by peduncles to the habenular and posterior commissures. The stalk contains nerve fibers, blood vessels, connective tissue and parenchymal cells (Paxinos, The Rat Central Nervous System, 2nd ed, pg 399)." "NCIT:C12398 TAO:0000019 XAO:0000160 BTO:0001067 MESH:D010870 EHDAA:7523 EV:0100221 MBA:953 galen:PinealGland VHOG:0000051 BAMS:Pi neuronames:297 ZFA:0000019 EFO:0000865 EMAPA:18778 UMLS:C0031939 BM:P BIRNLEX:1184 AAO:0010549 Wikipedia:Pineal_gland SCTID:181126002 EV:0100131 EHDAA2:0001466 GAID:453 NLXANAT:1010009 FMA:62033 MA:0000175 HBA:4532 CALOHA:TS-0789 BAMS:PIN DHBA:10460 MAT:0000448" + "Any process that stops, prevents or reduces the frequency, rate or extent of anterograde dense core granule transport." + "The chemical reactions and pathways resulting in the formation of compounds that contain an indole (2,3-benzopyrrole) skeleton." + "Endothelial cells forming the walls of the capillaries within the cerebral cortex." "CALOHA:TS-2372" + "The process aimed at the progression of an astrocyte over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. An astrocyte is the most abundant type of glial cell. Astrocytes provide support for neurons and regulate the environment in which they function." + "Any process that activates or increases the frequency, rate, or extent of interleukin-6 production." + "Any process that activates, maintains or increases the frequency, rate or extent of smooth muscle cell migration." + "A multilayered structure surrounding all or part of a cell; encompasses one or more lipid bilayers, and may include a cell wall layer; also includes the space between layers." + "Any process that increases the rate, frequency or extent of microtubule nucleation. Microtubule nucleation is the 'de novo' formation of a microtubule, in which tubulin heterodimers form metastable oligomeric aggregates, some of which go on to support formation of a complete microtubule. Microtubule nucleation usually occurs from a specific site within a cell." + "A pyramidal neuron which lacks a tuft formation but extends small radial distances forming a star-like shape." + "A cultured cell that is freshly isolated from a organismal source, or derives in culture from such a cell prior to the culture being passaged." "BTO:0002290" + "Any native cell that is part of a hypothalamus." + "A filament composed of acidic and basic keratins (types I and II), typically expressed in epithelial cells. The keratins are the most diverse classes of IF proteins, with a large number of keratin isoforms being expressed. Each type of epithelium always expresses a characteristic combination of type I and type II keratins." + "The process in which a relatively unspecialized cell acquires specialized features of a posterior lateral line neuromast hair cell. (N.B. This may be development of neuromast hair cell type or a set of cell of neuromast hair cell type. This will involve the change of a cell or set of cells from one cell identity to another). Hair cells are the sensory receptors of the neuromast and are located in a portion of the neuromast called the sensory strip. Each hair cell of the neuromast is morphologically polarized as a result of the relative position of the single kinocilium and the clusters of stereocilia on its apical surface. There are approximately seven hair cells within each neuromast, with each hair cell innervated by afferent and efferent neurons." + "A multicellular organismal process by which exposure to an activating factor such as a cellular or soluble ligand results in a change in the morphology or behavior of a cell." + "A smooth muscle cell of the aorta." "BTO:0004577" + "An epithelial cell that lines the peripheral gas exchange region of the lungs of air-breathing vertebrates." "FMA:62499 CALOHA:TS-2168 BTO:0000395" + "The orderly movement of microglial cells through the telencephalon." + "A organ system process carried out by any of the organs or tissues of the renal system. The renal system maintains fluid balance, and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products. In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels; in other species, the renal system may comprise related structures (e.g., nephrocytes and malpighian tubules in Drosophila)." + "The process in which anatomical structures are generated and organized during the embryonic phase. The embryonic phase begins with zygote formation. The end of the embryonic phase is organism-specific. For example, it would be at birth for mammals, larval hatching for insects and seed dormancy in plants." + "Layer of neocortex lying deep to the external granule cell layer defined cytoarchitecturally by numerous small pyramidal neurons." "NCIT:C32571 PBA:294021824 UMLS:C1517046 MA:0000899 neuronames:2448 FMA:77810 ABA:CTX3 EMAPA:35257 NLXANAT:090809" + "Barrier between the perineurium of peripheral nerves and the vascular endothelium of endoneurial capillaries. The perineurium acts as a diffusion barrier, but ion permeability at the blood-nerve barrier is still higher than at the blood-brain barrier[GO]." "Wikipedia:Blood-nerve_barrier" + "A collection of anatomical structures that are alike in terms of their morphology or developmental origin." + "A vasculature that is part of a muscle organ [Automatically generated definition]." "FMA:87123" + "A plasmatocyte derived from the embryonic head mesoderm." + "A protein that is a translation product of the human LHX3 gene or a 1:1 ortholog thereof." + "The metanephric glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the metanephric glomerulus[GO]." + "A taste bud that is located in the pharynx." + "Any process that stops, prevents or reduces the frequency, rate or extent of gamma-aminobutyric acid catabolic process." + "The progression of the neurohypophysis over time from its initial formation until its mature state. The neurohypophysis is the part of the pituitary gland that secretes hormones involved in blood pressure regulation." + "Any chamber of the right side of the heart." "SCTID:362007002 FMA:7165" + "An organ cavity that surrounded_by a bone." "FMA:24021" + "Neural crest cells (NCCs) originating in the anterior part of the developing embryo and residing between the mid-diencephalon and the forming hindbrain; cranial NCCs migrate dorsolaterally to form the craniofacial mesenchyme that differentiates into various craniofacial cartilages and bones, cranial neurons, glia, and connective tissues of the face; these cells enter the pharyngeal pouches and arches where they give rise to thymic cells, bones of the middle ear and jaw (mandible), and the odontoblasts of the tooth primordia; like their counterparts in the trunk, cranial NCCs also contribute to the developing peripheral nervous system, along with the pigmented cell (i.e. melanocyte) lineage." "AAO:0010580 XAO:0001001 Wikipedia:Cranial_neural_crest TAO:0001194 EHDAA2:0004420 EMAPA:16091 ZFA:0001194 VHOG:0000063 EFO:0003645" + "Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features." + "Subdivision of trunk proper, which is demarcated from the neck by the plane of the superior thoracic aperture and from the abdomen internally by the inferior surface of the diaphragm and externally by the costal margin and associated with the thoracic vertebral column and ribcage and from the back of the thorax by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines; together with the abdomen and the perineum, it constitutes the trunk proper[FMA]." "EMAPA:37232 CALOHA:TS-1039 GAID:91 NCIT:C12799 EV:0100010 NCIT:C25389 galen:Chest Wikipedia:Chest FMA:9576 MIAA:0000295 UMLS:C1527391 MESH:D013909 MAT:0000295 MA:0000031 EFO:0000965 galen:Thorax UMLS:C0817096 BTO:0001368" + "The progression of the caudate nucleus over time from its initial formation until its mature state. The caudate nucleus is the C-shaped structures of the striatum containing input neurons involved with control of voluntary movement in the brain." + "A network of orbital structures of the eye that secrete and drain tears from the surface of the eyeball into the nasal cavity; these parts include the lacrimal glands, lacrimal lake, lacrimal ducts, lacrimal canals, lacrimal sacs, nasolacrimal ducts, and lacrimal puncta." "FMA:55605 GAID:901 Wikipedia:Lacrimal_apparatus NCIT:C32905 MESH:D007765 EMAPA:35462 UMLS:C0022903 MA:0000274" + "Any process of the innate immune response that takes place in the mucosal tissues." + "The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features of a mature cell found in the lung. Differentiation includes the processes involved in commitment of a cell to a specific fate." + "Any process that activates or increases the frequency, rate or extent of pulmonary blood vessel remodeling." + "A ventral horn of spinal cord that is part of a thoracic spinal cord." "UMLS:C0228632 UMLS:C1288552 BIRNLEX:1410 SCTID:367876000" + "The collecting duct is a portion of the nephron through which water flows, moving passively down its concentration gradient." "EV:0100391 CALOHA:TS-0860 ZFA:0005294 GAID:434 TAO:0005294 FMA:15628 BTO:0000761 Wikipedia:Collecting_tubule MESH:D007685 MA:0000371 SCTID:28202009 EMAPA:28407" + "Any process that modulates the frequency, rate, or extent of a T-helper 1 type immune response." + "Epithelial cell that is part of the colon epithelium." + "The process in which a precursor cell type acquires the specialized features of a CD8-positive, gamma-delta intraepithelial T cell. Intraepithelial T cells are found among epithelial cells in mucosal areas and have distinct phenotypes and developmental pathways." + "The cell cortex of the leading edge of a cell." + "MA:0003203 EHDAA2:0004566 EMAPA:32911" + "EMAPA:17533 EHDAA:5435 EHDAA2:0000449 VHOG:0000913" + "Programmed cell death that occurs in the retina to remove excess cells between ommatidia, thus resulting in a hexagonal lattice, precise with respect to cell number and position surrounding each ommatidium." + "A cell morphology that inheres in neurons with dendrites that stratify at two and only two locations." + "The chemical reactions and pathways involving superoxide, the superoxide anion O2- (superoxide free radical), or any compound containing this species." + "Any process that modulates the frequency, rate or extent of somitogenesis." + "The tissue made up of epithelial cells that lines the inside of the lobar bronchus." "MA:0001842 EMAPA:32695 FMA:86624" + "The process resulting in the transition of the otic placode into the otic vesicle, a transient embryonic structure formed during development of the vertebrate inner ear." + "A part of a wall of an organ that forms a layer." "FMA:82485" + "Binding to a CCR6 chemokine receptor." + "A nuclear factor NF-kappa-B p100 subunit that is encoded in the genome of mouse." "UniProtKB:Q9WTK5" + "An epithelial cell that is part of an outer medullary collecting duct." "KUPO:0001062" + "A regulatory system of the body that integrates the nervous system and the endocrine system. This system is formed by specialized neuroendocrine cells located mainly in the nervous system and neuroendocrine glands. However, they can also be found as either single cells or small clusters of cells dispersed throughout the surface epithelium of different tissues. The neuroendocrine system functions through the release of neurotransmitters and neurohormones, enabling communication between the endocrine and nervous systems to govern vitally important processes that include growth, reproduction, metabolism and energy homeostasis, electrolyte and water balance, and responses to stress." + "The molecular layer is the outermost layer of the cerebellar cortex. It contains the parallel fibers of the granule cells, interneurons such as stellate and basket cells, and the dendrites of the underlying Purkinje cells." "FMA:83897 BAMS:thf MA:0000996 CALOHA:TS-1248 UMLS:C1289474 neuronames:366 UMLS:C0228469 NCIT:C49139 MBA:1144 UMLS:C1709064 BIRNLEX:810 EMAPA:35221 SCTID:369045002" + "The specific behavior of an organism that is associated with reproduction." + "A cell whose primary function is to support other cell types." "BTO:0002315" + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of CD4." + "A gamma-synuclein that is encoded in the genome of human." "UniProtKB:O76070" + "One of the curved arteries at the corticomedullary border of the kidney that arise from the interlobar arteries and give rise to the interlobular arteries." "MA:0002583 EMAPA:28215 FMA:70497 Wikipedia:Arcuate_arteries_of_the_kidney" + "Any process that modulates the frequency, rate or extent of astrocyte activation." + "A progenitor cell with the potential to differentiate into luminal epithelial cells of mammary glands. In mouse, CD61 and c-kit were found to be coexpressed by the majority of, but not all, committed luminal progenitor cells." + "A morphological quality inhering in a bearer by virtue of the bearer's ratios of distances between its features (points, edges, surfaces and also holes etc)." + "Any process that stops, prevents or reduces the frequency, rate or extent of microglial cell migration." + "The process in which a macrophage expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex." + "A fibroblast that is part of the breast." + "The joining of two lipid bilayers that surround the Golgi apparatus to form a single Golgi membrane." + "An epithelium that is part of a frontonasal prominence." "EHDAA2:0004108 EMAPA:32918" + "A gamete-nursing cell that derives from a germline cell (del Pino, 2021)." + "The largest lung subunit in which all airways participate in gas exchange, and it is composed of the parenchyma of the respiratory bronchioles, alveolar ducts, and alveoli." "NCIT:C33426 Wikipedia:Acinus#The_Lungs SCTID:361365004 EMAPA:37941 UMLS:C0225696 FMA:7313" + "Any process that activates or increases the frequency, rate or extent of cellular response to insulin stimulus." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electrical stimulus. This process occurs as part of the regulation of muscle adaptation." + "Any glutamatergic neuron that is part of a cerebellum." + "A cardiovascular system that is part of a conceptus." "NCIT:C34148 FMA:305965 EHDAA2:0000216" + "The process in which a precursor cell type acquires the specialized features of a T cell via a differentiation pathway dependent upon transit through the thymus." + "A protein that is a translation product of the Ly76 gene in mouse." + "The organ of hearing located on the left side of the head[ncit,modified]." "NCIT:C81259 FMA:53642 SCTID:368592000 UMLS:C0229299" + "Cell migration that is accomplished by extension and retraction of a fibroblast pseudopodium. A fibroblast is a connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules." + "The chemical reactions and pathways resulting in the formation of aldehydes, any organic compound with the formula R-CH=O." + "The increase in size or mass of a bone that contributes to the shaping of that bone." + "The collecting duct is the final common path through which urine flows before entering the ureter and then emptying into the bladder[GO]." "XAO:0000151 AAO:0010390" + "A protein that is a translation product of the human CD5 gene or a 1:1 ortholog thereof." + "A scapula endochondral element that is composed primarily of a pre-cartilage condensation." "EHDAA:6041 EHDAA2:0001778 VHOG:0000960 EMAPA:18027" + "A biological process in which synaptic vesicles are loaded with neurotransmitters, move to the active zone, exocytose and are then recycled via endocytosis, ultimately leading to reloading with neurotransmitters." + "Enables the transmembrane transfer of a calcium ions by a channel that opens when a specific ligand has been bound by the channel complex or one of its constituent parts." + "Any process that modulates the frequency, rate or extent of pigmented cell differentiation." + "A mesentery that is part of a duodenum [Automatically generated definition]." "EMAPA:19081" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of a substance from a cell or a tissue." + "The series of events by which a mechanical stimulus is received and converted into a molecular signal." + "Any process that modulates the frequency, rate or extent of the directed movement of iron ions (Fe) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "A portion of cardiac muscle tissue that is part of an atrium [Automatically generated definition]." "FMA:7283" + "An endothelial cell that is part of the thoracic endothelium." + "A mucosa that is part of a ileum [Automatically generated definition]." "BTO:0000619 FMA:14956 CALOHA:TS-0470 EMAPA:35424 MA:0003216 SCTID:85458007" + "a L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex that has inverted pyramidal morphology." + "The regrowth of a lost or destroyed animal organ." + "A blood vessel that is part of a tympanic cavity [Automatically generated definition]." "MA:0001219 EMAPA:37775" + "Any process that stops, prevents or reduces the frequency, rate or extent of export of iron ions from inside of a cell, across the plasma membrane and into the extracellular region." + "Any process that modulates the frequency, rate or extent of defense response to bacterium." + "A loop of Henle that is part of a kidney outer medulla outer stripe." "MA:0002630 EMAPA:29665" + "An ovary that is part of a left side of organism [Automatically generated definition]." "EMAPA:37366 UMLS:C0227874 NCIT:C32969 FMA:7214 SCTID:280124008 MA:0001704" + "The various hormone- or neurotransmitter-secreting cells present throughout the mucosa of the stomach." + "A neuron that is capable of some neurotansmission by glutamate secretion." "FBbt:00100291 WBbt:0006829" + "Any process that stops, prevents, or reduces the frequency, rate, or extent of antigen processing and presentation of peptide antigen via MHC class I." + "Any process that modulates the frequency, rate or extent of neuromuscular junction development." + "A myocardial endocrine cell that is part of the interventricular septum." "FMA:83390" + "The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP]." "MESH:D020405 EV:0100154 ZFA:0001119 TAO:0001119 UMLS:C0011646 SCTID:361696001 MA:0000152 BTO:0000294 EFO:0000953 GAID:1321 AAO:0000128 MIAA:0000153 FMA:70323 CALOHA:TS-2076 NCIT:C12701 Wikipedia:Dermis VHOG:0000108 EMAPA:17527 MAT:0000153 XAO:0000217" + "EHDAA2:0000033 EMAPA:16384" + "The formation of a thickened region of the neurectoderm that is roughly triangular in cross section. The neural keel develops from the neural plate and develops into the neural rod. Neural keel formation occurs during primary neurulation in teleosts." + "Any process that modulates the frequency, rate or extent of membrane invagination." + "Any process that modulates the frequency, rate, or extent of mast cell degranulation." + "An epithelial cell within one of the pits in the embryonic gastric mucosa from which the gastric glands develop ." "FMA:86552" + "GC_ID:1" + "A cover or envelope partly or wholly surrounding a structure. Examples: egg shell, articular capsules, renal capsules[WP]." "galen:Capsule EHDAA:4739 FMA:85272 EHDAA:9061 Wikipedia:Capsule_(anatomy)" + "The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity." + "The female muscular organ of gestation in which the developing embryo or fetus is nourished until birth." "EMAPA:29915 galen:Uterus FMA:17558 Wikipedia:Uterus EFO:0000975 MAT:0000127 MIAA:0000127 NCIT:C12405 BTO:0001424 EV:0100113 UMLS:C0042149 MA:0000389 VHOG:0001137 MESH:D014599 SCTID:181452004 GAID:172 CALOHA:TS-1102" + "Any process that activates or increases the frequency, rate or extent of spermatid nuclear differentiation." + "A cell capable of processing and presenting lipid and protein antigens to T cells in order to initiate an immune response." + "Any process that stops, prevents or reduces the frequency, rate or extent of cardiac conduction." + "An epithelial cell of the anal canal that is keratinized. This cell type is found towards the lower, rectal end of the anal canal." + "An amacrine cell with a wide dendritic field, dendrites in S2, and post-synaptic terminals in S1." + "The directed movement of hexose from outside of a cell, across the plasma membrane and into the cytosol." + "Any process that modulates the frequency, rate or extent of neuron maturation, the process leading to the attainment of the full functional capacity of a neuron. This process is independent of morphogenetic change." + + "Any process that stops, prevents, or reduces the frequency, rate or extent of cell killing." + "The process whose specific outcome is the progression of a tube over time, from its initial formation to a mature structure. Epithelial and endothelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues including lung and trachea, kidney, the mammary gland, the vascular system and the gastrointestinal and urinary-genital tracts." + "An external ear that is in the left side of a multicellular organism." "EMAPA:37360 FMA:53644 SCTID:368589004" + "The process in which a precursor cell type acquires the specialized features of a gamma-delta intraepithelial T cell. Intraepithelial T cells are found among epithelial cells in mucosal areas and have distinct phenotypes and developmental pathways." + "A portion of connective tissue that is part of a lower respiratory tract [Automatically generated definition]." "MA:0002409 EMAPA:37548" + "The directed orientation of T cell signaling molecules and associated membrane rafts towards a chemokine gradient or a contact point with antigen presenting cell." + "A sensory neuron of the dorsal root ganglia that senses body position and sends information about how much the muscle is stretched to the spinal cord." + "Any process that modulates the frequency, rate or extent of execution phase of apoptosis." + "A mammalian developmental stage that covers the period from birth until weaning." + "A protein that is a translation product of the mouse Klra1 gene or a 1:1 ortholog thereof." + "The controlled release of glutamate by a cell. The glutamate is the most abundant excitatory neurotransmitter in the nervous system." + "An intrinsic neuron of the mushroom body of arthropods and annelids. They have tightly packed, cytoplasm-poor cell bodies." "FBbt:00003686" + "Dense connective tissue that separates the atria from the ventricles and provides physical support for the heart." "Wikipedia:Cardiac_skeleton EMAPA:36645 FMA:9496" + "The process in which nitrogen is taken from its relatively inert molecular form (N2) in the atmosphere and converted into nitrogen compounds useful for other chemical processes, such as ammonia, nitrate and nitrogen dioxide." "Wikipedia:Nitrogen_fixation MetaCyc:N2FIX-PWY" + "The process whose specific outcome is the progression of the blastocyst over time, from its formation to the mature structure. The mammalian blastocyst is a hollow ball of cells containing two cell types, the inner cell mass and the trophectoderm." + "The movement of a neutrophil within or between different tissues and organs of the body." + "A cartilage that is part of a neck [Automatically generated definition]." "EMAPA:37251 MA:0000586" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving carbohydrate." + "An epithelial cell of the esophageal gland proper." "FMA:256141" + "Functional system which consists of structures involved in respiration." "MA:0000327 EHDAA:2203 BTO:0000203 EHDAA2:0001604 XAO:0000117 MAT:0000030 CALOHA:TS-1319 ZFA:0000272 UMLS:C0035237 TAO:0000272 MIAA:0000030 SCTID:278197002 EFO:0000804 NCIT:C12779 AAO:0000541 MESH:D012137 EV:0100036 EMAPA:16727 VHOG:0000202 GAID:78 Wikipedia:Respiratory_system FMA:7158" + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipoprotein particle stimulus." + "A nerve that is part of a forelimb [Automatically generated definition]." "EMAPA:37334 MA:0000616" + "Any process that modulates the frequency, rate or extent of microtubule polymerization or depolymerization by the addition or removal of tubulin heterodimers from a microtubule." + "Sympathetic neurons are part of the sympathetic nervous system and are primarily adrenergic producing the neurotransmitter noradrenalin along with other neuropeptides." + "A blood vessel that is part of a trachea." "MA:0001852 EMAPA:35874" + "Any process that modulates the frequency, rate or extent of intracellular signal transduction." + "A sebaceous gland that is part of a camera-type eye. Example: a tarsal gland." "MA:0002452 EMAPA:37531" + "An immune response taking place in mucosal tissues, including those of the intestinal tract, nasal and upper respiratory tract, and genital tract." + "The elimination by an organism of the waste products that arise as a result of metabolic activity. These products include water, carbon dioxide (CO2), and nitrogenous compounds." "Wikipedia:Excretion" + "Any process that activates or increases the frequency, rate, or extent of an adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains. An example of this process is found in the Gnathostomata." + "A process in which a protein is transported to, or maintained in, a location within a cell leading edge." + "The process whose specific outcome is the progression of the cortical collecting duct over time, from its formation to the mature structure. The cortical collecting duct is the portion of the collecting duct that resides in the renal cortex." + "The series of molecular signals initiated by the binding of glutamate to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." + "A vitelline vein that is in the left side of a multicellular organism." "EHDAA2:0000971 EMAPA:16380 SCTID:361446008 EMAPA:16698 FMA:70307" + "Any process that modulates the frequency, rate or extent of glycine secretion, neurotransmission." + "A trabecula that is part of a liver." + "A neural plate that develops_from a future forebrain." "ZFA:0007018 TAO:0007018" + "Any process that activates or increases the frequency, rate or extent of cytokine production involved in inflammatory response." + "An ectoderm that is part of a buccopharyngeal membrane." "EMAPA:16260 EHDAA2:0000190" + "Any process that stops, prevents or reduces the frequency, rate or extent of establishment of T cell polarity." + "Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell projections." + "Subdivision of thorax, which in humans is the posterior part of the thorax and is demarcated from the chest by the external surface of the posterolateral part of the rib cage and the anterior surface of the thoracic vertebral column; together with the chest, it constitutes the thorax." "EMAPA:37234 SCTID:362666008 MA:0000028 FMA:24217" + "FMA:42854 SCTID:304907005 EMAPA:37308 MA:0000655" + "A portion of semen in a coagulated state." + "A receptor-type tyrosine-protein phosphatase C isoform CD45R that is a translation product of some mRNA whose exon structure and start site selection renders it capable of giving rise to a protein with the amino acid sequence represented by UniProtKB:P08575-8 or a 1:1 ortholog thereof." + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprised of intermediate filament and their associated proteins in the postsynaptic cytoskeleton." + "The series of events in which a gravitational stimulus is received and converted into a molecular signal." + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving glycogen." + "The chemical reactions and pathways resulting in the formation of lutein." + "Pulmonary veins are blood vessels that transport blood from the lungs to the heart[GO]." "BTO:0001799 VHOG:0001133 Wikipedia:Pulmonary_vein EHDAA:2629 NCIT:C12776 GAID:543 EMAPA:18645 CALOHA:TS-0840 AAO:0010521 SCTID:430160002 EHDAA2:0001579 MESH:D011667 XAO:0000394 galen:PulmonaryVein UMLS:C0034090 FMA:66643 MA:0002206" + "A ciliated epithelial cell of the esophagus." + "A sphincter muscle that is part of a vagina." + "An arrangement of nerve fibers, running from the spine that travels to the pelvic appendage where it innervates skin and muscle." "FMA:5907 SCTID:181049003 GAID:849 UMLS:C0024093 NCIT:C52805 EMAPA:17587 Wikipedia:Lumbosacral_plexus MESH:D008160 MA:0001181 EHDAA2:0001040 BAMS:lsp EHDAA:4673 VHOG:0000926" + "The multiplication or reproduction of epithelial cells, resulting in the expansion of a cell population that contributes to the shaping of the lung." + "A high endothelial venule that is part of a of lymph node." + "A cell that supports the development of a gamete by providing it cytoplasmic material (including entire organelles) by direct cross-membrane channels (del Pino, 2021)." "BTO:0000953" + "Any process that activates or increases the frequency, rate or extent of lamellocyte differentiation. Lamellocytes differentiate massively in the lymph glands after parasitization and are large flat cells devoted to encapsulation of invaders too large to be phagocytosed by plasmatocytes." + "Multi-tissue structure that is part of the heart tube and will become the cardiac atrium." "TAO:0002228 FMA:71005 ZFA:0001718" + "A metapodium region that is part of a manus." "CALOHA:TS-2218 EMAPA:32654 SCTID:370638006 MA:0000042 FMA:24925" + "A tyrosine-protein kinase receptor UFO that is encoded in the genome of human." "UniProtKB:P30530 DTO:03100553" + "A CCAAT/enhancer-binding protein alpha that is encoded in the genome of mouse." "UniProtKB:P53566" + "The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord." "VHOG:0000107 AAO:0011017 EFO:0003647 Wikipedia:Chordamesoderm TAO:0001204 XAO:0000205 ZFA:0001204" + "One of sublaminar layers S1 or S2." "CP:0000118" + "Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]." "BILA:0000066 FMA:9639 EMAPA:32738 BTO:0000416 UMLS:C0014609 HAO:0000066 XAO:0003045 CALOHA:TS-0288 Wikipedia:Epithelium SCTID:31610004 TAO:0001486 VHOG:0000387 MESH:D004848 CARO:0000066 NCIT:C12710 GAID:402 AEO:0000066 AAO:0000144 EHDAA2:0003066 ZFA:0001486 AAO:0010055 MA:0003060" + "The cytoplasm of an ovum." + "A chief cell that is smaller than light chief cells and has a smaller and darker nucleus and a finely granular cytoplasm with many granules." "FMA:69080" + "A duct that is part of a digestive system [Automatically generated definition]." "ZFA:0005162 TAO:0005162" + "The directed movement of a substance from one side of an epithelium to the other." + "The directed movement of neuronal dense core vesicles along axonal microtubules towards the cell body." + "Any process that activates or increases the frequency, rate or extent of protein localization to ciliary membrane." + "The cyclical phases of growth (anagen), regression (catagen), quiescence (telogen), and shedding (exogen) in the life of a hair; one of the collection or mass of filaments growing from the skin of an animal, and forming a covering for a part of the head or for any part or the whole of the body." + "A thymic medullary epithelial cell considered to be a pre-AIRE mTEC population." + "A subdivision of the manus skeleton consisting of both manual acropodial skeleton and metacarpal skeleton, but excluding the carpal skeleton." + "Cranial ectodermal placode with potential to develop into a component of the nervous system, such as nerves or ganglia." "TAO:0001309 Wikipedia:Neurogenic_placodes ZFA:0001309 XAO:0004620 EFO:0003460" + "Any process that modulates the rate, frequency, or extent of branching involved in mammary gland duct morphogenesis." + "Any process that activates, maintains or increases the frequency, rate or extent of cardiac muscle fiber development." + "Any process that decreases the rate, frequency, or extent of the process whose specific outcome is the progression of a chondrocyte over time, from its commitment to its mature state. Chondrocyte development does not include the steps involved in committing a chondroblast to a chondrocyte fate." + "Any process that stops, prevents or reduces the rate or extent of B cell proliferation." + "The part of the cardiovascular system consisting of all pulmonary arteries and all pulmonary veins." "Wikipedia:Pulmonary_circulation FMA:45621" + "A process in which a protein is transported to, or maintained in, a location within an euchromatin." + "A kidney that is part of a left side of organism [Automatically generated definition]." "UMLS:C0227614 MA:0001655 SCTID:362209008 FMA:7205 NCIT:C34006 EMAPA:36589" + "Any process that activates or increases the frequency, rate, or extent of granuloma formation." + "A round chondrocyte that first differentiates in the late embryonic growth plate of bone." + "Musculature system of the pharyngeal and head regions." "MA:0000571 ZFA:0000328 TAO:0000328 EMAPA:37259" + "The series of events required for an organism to receive a sensory mechanical stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process." + "A Vgamma1.1-positive, Vdelta6.3-positive thymocyte that is CD24-positive." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of tissue remodeling." + "A morphological quality inhering in a bearer by virtue of the bearer's affording blocked passage or view." + "A protein that is a component of collagen. Collagens are trimeric molecules in which each chain comprises a repeating Gly-X-Y triplet, in which X and Y can be any residue but are usually proline and hydroxyproline, respectively. This results in a left-handed helix that combines with other two to form a triple-helical structure." + "Any process that modulates the frequency, rate or extent of myofibroblast differentiation." + "An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions." "EMAPA:37271 MA:0000563" + "The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present." + "A hematopoietic stem found in the yolk sac. In mice, this cell type is Sca-1-negative, CD45-negative, MHC-negative, HSA-positive, AA4.1-positive, CD44-positive." + "The orderly movement of a myotube cell from one site to another, often during the development of a multicellular organism. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate, and fuse." + "The process in which the anatomical structures of the metanephros are generated and organized." + "An auditory epithelial support cell located in the vestibular epithelium that has many hallmarks of glial cells. This cell type express glial markers such as vimentin, S100, glutamate-aspartate transporter, low affinity neurotrophin receptor p75, glial fibrillary acidic protein, and proteolipid protein." "FMA:75809" + "A fibroblast that is part of the papillary layer of dermis." "FMA:261277" + "A T-cell surface glycoprotein CD8 alpha chain that is encoded in the genome of human." "UniProtKB:P01732" + "The internal iliac artery (formerly known as the hypogastric artery) is the main artery of the pelvis. [WP,unvetted]." "NCIT:C32845 FMA:18808 galen:InternalIliacArtery EMAPA:17860 SCTID:181346001 UMLS:C0226364 BTO:0004667 Wikipedia:Internal_iliac_artery MA:0001974" + "The directed movement of any conjugated, water-soluble protein in which the nonprotein group consists of a lipid or lipids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "A mature thymus that is entirely part of thoracic region." + "An endothelium that is part of a left lung." "EHDAA2:0000961" + "Neurotransmitter receptor activity occuring in the postsynaptic membrane during synaptic transmission." + "An epithelial cell that is part of the epithelium of a tracheal tube in an open tracheal system, such as that found in insects." "FBbt:00005038" + "An endothelial cell that is part of the small intestine Peyer's patch." "FMA:67757" + "A region of the cilium between the basal body and proximal segment that is characterized by Y-shaped assemblages that connect axonemal microtubules to the ciliary membrane. The ciliary transition zone appears to function as a gate that controls ciliary membrane composition and separates the cytosol from the ciliary plasm." + "Any process that activates or increases the frequency, rate or extent of the directed movement of a neurotransmitter into a neuron or glial cell." + "A stem cell that is the precursor of gametes." "FBbt:00004861" + "EHDAA2:0000450 EMAPA:17535 VHOG:0000884 EHDAA:5437" + "Any process that modulates the frequency, rate or extent of motor neuron migration." + "The biological process whose specific outcome is the progression of a lung lobe from an initial condition to its mature state. This process begins with the formation of a lung lobe by branching morphogenesis and ends with the mature structure. A lung lobe is one of the rounded projections that compose the lung." + "Any process that modulates the frequency, rate or extent of dendritic cell apoptotic process." + "Any process that modulates the frequency, rate or extent of acetylcholine-gated cation channel activity." + "Any process that activates or increases the frequency, rate or extent of aorta morphogenesis." + "Any process that activates or increases the rate or extent of mast cell proliferation." + "The multiplication or reproduction of type B synoviocytes by cell division, resulting in the expansion of their population. A type B synoviocyte is a fibroblast-like cell found in synovial tissues." + "A transitional stage B cell that migrates from the bone marrow into the peripheral circulation, and finally to the spleen. This cell type has the phenotype surface IgM-positive, surface IgD-negative, CD21-negative, CD23-negative, and CD62L-negative, and CD93-positive. This cell type has also been described as IgM-high, CD19-positive, B220-positive, AA4-positive, and CD23-negative." + "Any structure that is placed on one side of the left-right axis of a bilaterian." + "A mesothelial cell that is part of the dura mater." "FMA:256516" + "A large epithelial cell found in the thymus. This cell type may internalize thymocytes through extensions of plasma membrane. The cell surface and cytoplasmic vacuoles of a thymic nurse cell express MHC Class I and MHC Class II antigens. The interaction of these antigens with a developing thymocyte determines whether the thymocyte undergoes positive or negative selection." + "Structures of the dermis, epidermis, glands and pigment cells recognizable on the external surfaces of the integument." + "A stage of the apoptotic process that starts with the controlled breakdown of the cell through the action of effector caspases or other effector molecules (e.g. cathepsins, calpains etc.). Key steps of the execution phase are rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died." + "A small cell formed by the second meiotic division of oocytes. In mammals, the second polar body may fail to form unless the ovum has been penetrated by a sperm cell." "FMA:18651 EMAPA:16045 EHDAA2:0001820 EMAPA:16034" + "The process in which the anatomical structures of the mesonephric capsule are generated and organized. The mesonephric capsule is the tough fibrous layer surrounding the mesonephros, covered in a thick layer of perinephric adipose tissue. It provides some protection from trauma and damage." + "A forkhead box protein N1 that is encoded in the genome of human." "UniProtKB:O15353" + "The region of the cytosol consisting of all cytosol that is part of the postsynapse." + "A portion of interstitial tissue that is part of a inner medulla of kidney [Automatically generated definition]." "EMAPA:28364 MA:0002620" + "An bone foramen in the ethmoid bone." "Wikipedia:Ethmoidal_foramina" + "Tolerance induction of mature B cells in the peripheral lymphoid tissues: the blood, lymph nodes, spleen, and mucosal-associated lymphoid tissue." + "The process in which the cytoplasm of the outermost cells of the vertebrate epidermis is replaced by keratin. Keratinization occurs in the stratum corneum, feathers, hair, claws, nails, hooves, and horns." + "Any process that stops, prevents or reduces the frequency, rate or extent of forebrain neuron differentiation." + "The process whose specific outcome is the progression of the urogenital system over time, from its formation to the mature structure." + "A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a nucleolus, a small, dense body one or more of which are present in the nucleus of eukaryotic cells." + "The process whose specific outcome is the progression of cardiac muscle over time, from its formation to the mature structure." + "The process whose specific outcome is the progression of the anterior lateral line neuromast over time, from its formation to the mature structure. The neuromast is the sensory receptor of the anterior lateral line system and is composed of a population of sensory hair cells, and nonsensory supporting cells and mantle cells. Neuromast are located superficially on the epithelium or in lateral line canals." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of plasmacytoid dendritic cell antigen processing and presentation." + "The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically." + "Any portion of cardiac muscle tissue that is part of the conducting system of heart or the Purkinje fibers." "FMA:83378 EHDAA2:0004528" + "The multiplication or reproduction of sebocytes by cell division, resulting in the expansion of their population. A sebocyte is an epithelial cell that makes up the sebaceous glands, and secrete sebum." + "A venule that is part of a respiratory system [Automatically generated definition]." "MA:0001813 EMAPA:37587" + "A portions of the gut that is derived from endoderm." "EMAPA:32930" + "A netrin-G1 that is encoded in the genome of mouse." "UniProtKB:Q8R4G0" + "Any process that modulates the frequency, rate or extent of mechanoreceptor differentiation." + "The assembly and organization of an axoneme, the bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements." + "A cartilaginous condensation that has the potential to develop into a patella." "EMAPA:19140" + "All of the contents of a plasma membrane bounded cell projection, excluding the plasma membrane surrounding the projection." + "Any process that activates or increases the frequency, rate or extent of anterograde dense core granule transport." + "A naris that provides one of the small external openings of the head that give passage to air for breathing." "AAO:0000024 MA:0001320 UMLS:C0595944 NCIT:C33178 XAO:0003033 TAO:0000550 ZFA:0000550 VHOG:0000544 EMAPA:17848 Wikipedia:Nostril EHDAA:9085 FMA:59645 AAO:0000983 SCTID:276165005 EHDAA2:0001275 AAO:0010358" + "The hydrolysis of a peptide bond or bonds within a protein contributing to antigen processing and presentation." + "A part of the body present only in males." "WBbt:0005757 AEO:0000175" + "The process occurring in the embryo by which the anatomical structures of the post-embryonic eye are generated and organized." + "Any process that decreases the rate, frequency, or extent of the directed movement of calcium ions into a cell or organelle." + "Any process that modulates the frequency, rate or extent of leucophore differentiation." + "Any process that activates or increases the frequency, rate or extent of metanephric glomerular visceral epithelial cell development." + "Any process that activates or increases the frequency, rate, or extent of B cell mediated immunity." + "Skeletal element that is composed of bone tissue." "XAO:0000169 FMA:5018 MA:0001459 SCTID:90780006 MIAA:0000299 AAO:0000047 BTO:0000140 ENVO:00002039 EFO:0000298 MAT:0000299 ZFA:0001514 NCIT:C12366 VSAO:0000057 TAO:0001514 AEO:0000082 FMA:30317 UMLS:C0262950 VHOG:0001190 GAID:92 EHDAA2:0003082 CALOHA:TS-0088 galen:Bone EMAPA:32782 EV:0100140 Wikipedia:Bone" + "The process in which the anatomical structures of the hair follicle are generated and organized." + "Thickened trophoblast of the blastocyst in rodents that becomes the fetal portion of the placenta." "BTO:0001715 EMAPA:16059" + "A differentiated flat keratinocyte that is part of a nail plate. An onychocyte is firmly adherent and does not desquamate." + "The orderly movement of epithelial cells within a renal tubule that contributes to mesonephric nephron tubule morphogenesis." + "A smooth muscle cell of the bladder." "KUPO:0001122" + "Any process that contributes to cytokine production by a dendritic cell." + "A CD4-positive, CD25-positive alpha-beta regulatory T cell that has encountered antigen." + "PMID:10490293 PMID:10939677 PMID:11411719 PMID:8123559 GC_ID:11 PMID:11321083 PMID:8590690 PMID:10425795 PMID:10843050 PMID:9336922 PMID:11211268 PMID:11321113 PMID:10939673 PMID:11760965 PMID:25527841 PMID:11542149 PMID:10425797 PMID:270744 PMID:32628106 PMID:2112744 PMID:11541975 PMID:11542064 PMID:11540071 PMID:10939651 PMID:36748408 PMID:9103655 PMID:10425796 PMID:12054223" + "Cranial nerves are nerves that emerge directly from the brain, in contrast to spinal nerves, which emerge from segments of the spinal cord." "TAO:0000641 SCTID:244447006 UMLS:C0010268 EMAPA:17264 MBA:967 XAO:0003089 BTO:0001104 EHDAA2:0000323 XAO:0000429 BIRNLEX:1623 GAID:802 FMA:5865 neuronames:1227 UMLS:C1269897 ZFA:0000641 MA:0000215 AAO:0000108 VHOG:0000279 HBA:9299 NCIT:C12700 MESH:D003391 Wikipedia:Cranial_nerve BAMS:cran" + "Cardiac chamber through which blood leaves the heart." "UMLS:C0018827 AAO:0010249 EMAPA:17331 SCTID:277699000 MESH:D006352 CALOHA:TS-0444 GAID:568 galen:Ventricle Wikipedia:Ventricle_(heart) EHDAA2:0004164 VHOG:0000435 MAT:0000497 EFO:0000317 BTO:0000862 ZFA:0000009 MA:0000091 NCIT:C12730 TAO:0000009 EV:0100020 EHDAA:1912 FMA:7100 XAO:0003193" + "A metaphysis that is in the proximal side of a diaphysis." "FMA:32823" + "An epiphysis that is part of a proximal phalanx of manus." "SCTID:280044004" + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of bile acids." + "The aggregation, arrangement and bonding together of a set of components to form a postsynapse." + "An abnormal cell exhibiting dysregulation of cell proliferation or programmed cell death and capable of forming a neoplasm, an aggregate of cells in the form of a tumor mass or an excess number of abnormal cells (liquid tumor) within an organism." "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12922" + "The occipital artery arises opposite the facial artery, its path is below the posterior belly of digastric to the occipital region. This artery supplies blood to the back of the scalp and sterno-mastoid muscles. Other muscles it supplies are deep muscles in the back and neck. [WP,unvetted]." "EMAPA:37672 NCIT:C33194 MA:0002009 Wikipedia:Occipital_artery UMLS:C0226117 SCTID:244219005 FMA:49586" + "A vertebrate nasal chemosensory system that is responsible for detecting intraspecific pheromonal cues as well as environmental odorants." + "An umbilical vein that is in the right side of a multicellular organism." "SCTID:361447004 FMA:70319 EMAPA:16359 EMAPA:16378 EHDAA2:0001761" + "A neuron in the posterior ventral cochlear nucleus that is distinguished by their long, thick and tentacle-shaped dendrites that typically emanate from one side of the cell body." + "The white substance of the spinal cord lying on either side between the ventral median fissure and the ventral roots of the spinal nerves." "TAO:0000605 FMA:74003 ZFA:0000605 SCTID:362429007 NLX:379 Wikipedia:Ventral_funiculus neuronames:1304" + "The process in which renin-angiotensin modulates the force with which blood passes through the circulatory system." + "A portion of cardiac muscle tissue that is part of a left ventricle [Automatically generated definition]." "VHOG:0001234 EMAPA:17339 FMA:83453" + "A blind-ended tube connected to the cecum, from which it develops embryologically[WP]." "BTO:0000084 Wikipedia:Vermiform_appendix MESH:D001065 VHOG:0001306 MIAA:0000287 NCIT:C12380 galen:AppendixVermiformis EV:0100080 EV:0100076 EHDAA2:0000588 SCTID:181255000 MAT:0000287 FMA:14542 UMLS:C0003617 GAID:308 EMAPA:35140 MA:0001540 CALOHA:TS-1267 EFO:0000849" + "An ON bipolar cell that has large dendritic and axonal fields." + "A complex and coordinated series of cellular movements, including germ band extension, that occurs at the end of cleavage during embryonic development. An example of this process is found in Drosophila melanogaster." + "The triangular flat bone of the nasal septum." "AAO:0000633 FMA:9710 TAO:0000308 ZFA:0000308 Wikipedia:Vomer MA:0001496 SCTID:272678009 UMLS:C0242403 NCIT:C33888" + "OBSOLETE: A PP cell located in the pancreatic acinus. Obsoleted due to a lack of published evidence that this cell type is actually found in the pancreatic acinus." "FMA:85400" + "A large nerve that supplies nearly the whole of the skin of the leg, the muscles of the back of the thigh, and those of the leg and foot. It begins in the lower back and runs through the buttock and down the lower limb." "EFO:0001417 EMAPA:18577 EHDAA2:0001779 NCIT:C52810 FMA:19034 MA:0001172 VHOG:0000894 CALOHA:TS-0899 GAID:852 EHDAA:5659 BIRNLEX:1133 UMLS:C0036394 BTO:0001221 MESH:D012584 Wikipedia:Sciatic_nerve SCTID:181050003" + "EMAPA:37987 BTO:0004378 FMA:67473" + "A cell that stores and secretes pancreatic polypeptide hormone." "FMA:83409 FMA:62938" + "Any process that activates, maintains or increases the frequency, rate or extent of nervous system development, the origin and formation of nervous tissue." + "A protein complex facilitating transport of molecules (proteins, small molecules, nucleic acids) into, out of or within a cell, or between cells." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism." + "Extension of the dorsal aorta in the tail." "TAO:0000011 VHOG:0000123 AAO:0011023 EFO:0003472 ZFA:0000011 XAO:0000364 Wikipedia:Caudal_artery" + "A zone of skin that is part of a neck [Automatically generated definition]." "UMLS:C0205030 FMA:23022 FMA:23021 SCTID:361705004 EMAPA:37277 MA:0000590 NCIT:C52756" + "A hole in the diaphragm through which the esophagus passes." "FMA:58289" + "Any process that modulates the frequency, rate or extent of oligodendrocyte differentiation." + "KUPO:0001084" + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an iron ion stimulus." + "A cell from the inner layer of the trophoblast of the early mammalian embryo that gives rise to the outer surface and villi of the chorion. Mononuclear crytoblasts fuse to give rise to a multinuclear cytotrophoblast." "FMA:83042" + + "Any epithelial cell proliferation that is involved in renal tubule morphogenesis." + "Any process that stops, prevents or reduces the frequency, rate or extent of thymocyte migration." + "One of the three layers of the dentate gyrus of the hippocampal formation." "MA:0002429 FMA:83678 EMAPA:35278" + "Any process that stops, prevents or reduces the frequency, rate or extent of mesodermal cell differentiation." + "A stratified squamous epithelium consisting of a basal layer; it is keratinized or parakeratinized[BTO]." "BTO:0004998 FMA:62423 NCIT:C49239 MA:0001576 UMLS:C1179154" + "A smooth muscle tissue that is part of a respiratory system venous blood vessel." "MA:0001812 EMAPA:37586" + "Visceral intrapericardial fat contiguous with the myocardial surface." "FMA:9871" + "FMA:63212 MESH:D024022 NCIT:C32339 NIF_Subcellular:sao7547390221" + "A multicellular organism that is at the juvenile stage." "http://neurolex.org/wiki/Category:Juvenile_organism TAO:0002047 BILA:0000076" + "Any process that activates or increases the frequency, rate or extent of striated muscle contraction." + "Any process in which a chromosome is maintained in a specific location within a cell and prevented from moving elsewhere." + + "A substance formed from the secretion of one or more glands of the male genital tract in which sperm cells are suspended." "FMA:62967 MIAA:0000057 MAT:0000057 MA:0002523 EMAPA:36543 BTO:0001232 CALOHA:TS-0918" + "Any process that activates or increases the frequency, rate or extent of germ cell proliferation." + "The lingual nerve is a branch of the mandibular nerve (CN V3), itself a branch of the trigeminal nerve, which supplies sensory innervation to the tongue. It also carries fibers from the facial nerve, which return taste information from the anterior two thirds of the tongue." "Wikipedia:Lingual_nerve EMAPA:19168 BAMS:5lg FMA:53218 MA:0001102 SCTID:280260006 MESH:D008036 GAID:835" + "An enterocyte that is part of the epithelium of crypt of Lieberkuhn of small intestine." "FMA:263094" + "A boundary delimiting a rhombomere." + "The regulated release of neurotransmitter from the presynapse into the synaptic cleft via calcium-regulated exocytosis during synaptic transmission." + "The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a thrombocyte, a nucleated cell found in all vertebrates but mammals involved in hemostasis." + "A gut-associated lymphoid tissue macrophage found in lamina propria of the gut." + "A SCO-spondin that is encoded in the genome of mouse." "UniProtKB:Q8CG65" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of any intracellular steroid hormone receptor signaling pathway." + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms." + + "The process whose specific outcome is the progression of a tooth or teeth over time, from formation to the mature structure(s). A tooth is any hard bony, calcareous, or chitinous organ found in the mouth or pharynx of an animal and used in procuring or masticating food." "Wikipedia:Odontogenesis" + "The developmental process pertaining to the initial formation of a mesonephric capsule from unspecified parts. The mesonephric capsule is the tough fibrous layer surrounding the mesonephros, covered in a thick layer of perinephric adipose tissue. It provides some protection from trauma and damage." + "Any process that modulates the frequency, rate or extent of export of iron ions from inside of a cell, across the plasma membrane and into the extracellular region." + "Any neuromast support cell that is part of a anterior lateral line." + "The process in which a relatively unspecialized cell acquires specialized structural and/or functional features of a neuroendocrine cell. A neuroendocrine cell is a cell that receives input form a neuron which controls the secretion of an endocrine substance." + "Limb segment that consists of the long bones of the pes. The metatarsals are analogous to the metacarpal bones of the manus." "XAO:0003212 Wikipedia:Metatarsus FMA:71340 VSAO:0005027 AAO:0000221 MESH:D008684" + "GC_ID:1" + "A specialized mesenchymal cell that resides in the dermal papilla located at the bottom of hair follicles. This cell plays a pivotal roles in hair formation, growth, and cycling." + "Any process involved in the maintenance of an internal steady state of lipid within an organism or cell." + "A circular muscle layer of muscular coat that is part of a small intestine smooth muscle." "SCTID:54658003 FMA:14935 MA:0001560 EMAPA:37562" + "EMAPA:17953 MA:0002998 EHDAA:7007 EHDAA2:0001143 VHOG:0001241 EHDAA:8105" + "A CD3 epsilon that is encoded in the genome of human." "UniProtKB:P07766" + "The controlled release of orexin from a cell or a tissue." + "A germinal center B cell that founds a germinal center, and has the phenotype IgD-positive, CD38-positive, and CD23-negative." + "Any process that activates or increases the frequency, rate or extent of nuclear migration along microtubule." + "A specific region of the lateral mesoderm that will form the majority of the mesodermal component of the right ventricle, arterial pole (outflow tract) and venous pole (inflow tract)." "XAO:0004186" + "A cell junction that mechanically attaches a cell (and its cytoskeleton) to neighboring cells or to the extracellular matrix." + "Any process that modulates the frequency, rate or extent of bleb assembly." + "Mesenchyme that is part of a developing finger [Automatically generated definition]." "EMAPA:32645 EHDAA2:0000407 VHOG:0001416" + "A cord of epithelial cells without a lumen and usually several cells thick." "EHDAA2:0004052 AEO:0000216" + "That part of an axon close to and including the growth cone or the axon terminus." + "A hepatic sinusoid that is part of a right lobe of liver." "EHDAA2:0001009 EMAPA:18316 VHOG:0000710" + "Any process that modulates the frequency, rate or extent of adipose tissue development." + "Any process that modulates the frequency, rate or extent of muscle development." + "Mesenchyme that is part of a pharyngeal arch 2." "VHOG:0001102 FMA:295698 EHDAA:625 EHDAA2:0000066 EMAPA:16279" + "Any process that modulates the frequency, rate or extent of osteoblast differentiation." + "Any process that modulates the frequency, rate, or extent of peripheral T cell tolerance induction." + "A leukocyte with a single non-segmented nucleus in the mature form found in the circulatory pool of blood." + "The progression of the urethra epithelium over time from its initial formation to the mature structure. The urethra is a renal system organ that carries urine from the bladder to outside the body. The epithelium is the tubular, planar layer of cells through which the urine passes." + + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cholecystokinin stimulus." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glycogen." + "The oval neuroepithelial sensory receptor in the anterior wall of the saccule; hair cells of the neuroepithelium support the statoconial membrane and have terminal arborizations of vestibular nerve fibers around their bodies." "NCIT:C33045 XAO:0004136 ZFA:0007000 Wikipedia:Macula_of_saccule TAO:0007000 UMLS:C0229468 FMA:74944 SCTID:362572004 EMAPA:35534 MA:0001201" + "The truncus arteriosus and bulbus cordis are divided by the aorticopulmonary septum. The truncus arteriosus gives rise to the ascending aorta and the pulmonary trunk. The bulbus cordis gives rise to the smooth parts (outflow tract) of the left and right ventricles." "EMAPA:35887 GAID:554 EHDAA2:0004143 NCIT:C34317 UMLS:C1519589 MA:0000103 SCTID:308828009 FMA:70301 Wikipedia:Truncus_arteriosus_(embryology) MESH:D014338" + "Interacting selectively and non-covalently and stoichiometrically with neuropeptides, peptides with direct synaptic effects (peptide neurotransmitters) or indirect modulatory effects on the nervous system (peptide neuromodulators)." + "An acinus that is part of a exocrine gland." + "One of the two elevated edges of the neural groove[GO,MP]." "neuronames:1364 EHDAA2:0001249 FMA:295618 XAO:0004087 NCIT:C34223 SCTID:361461009 Wikipedia:Neural_fold UMLS:C0814993" + "Mesenchyme that is part of a extraembryonic membrane." + "Any process that activates or increases the frequency, rate or extent of T-helper 1 cell differentiation." + "Any process that modulates the rate, frequency, or extent of vesicle-mediated transport, the directed movement of substances, either within a vesicle or in the vesicle membrane, into, out of or within a cell." + "Primary lysosomal granule found in neutrophil granulocytes. Contains a wide range of hydrolytic enzymes and is released into the extracellular fluid." + "The perichondrium consists of two separate layers: an outer fibrous layer and inner chondrogenic layer. The fibrous layer contains fibroblasts, which produce collagenous fibers." "Wikipedia:The_Free_Encyclopedia BTO:0005091" + "The process of binding or confining calcium ions such that they are separated from other components of a biological system." + "An otic capsule endochondral element that is composed primarily of cartilage tissue." "TAO:0001500 ZFA:0001500 EMAPA:18803 EHDAA2:0001333 EMAPA:37467 EHDAA:4704" + "Any process that activates or increases the frequency, rate or extent of motor neuron apoptotic process." + "A segment of the manual digit containing the distal phalanx." "SCTID:312543003" + "A CD38-positive unswitched memory B cell is an unswitched memory B cell that has the phenotype CD38-positive, IgD-positive, CD138-negative, and IgG-negative." + "The squamous epithelium of the cervical portio is similar to that of the vagina, except that it is generally smooth and lacks rete pegs. Colposcopically, it appears featureless except for a fine network of vessels which is sometimes visible. The relative opacity and pale pink coloration of the squamous epithelium derives from its multi-layered histology and the location of its supporting vessels below the basement membrane." "NCIT:C49219 UMLS:C1707351 MA:0001725" + "Odontogenic tissue that is collagen-rich and characteristic of vertebrate teeth and tooth-like structures (e.g., odontodes) deposited by preodontoblasts and odontoblasts that are typically excluded from the matrix." "XAO:0004052 EMAPA:36439 VSAO:0000071" + "A continuation of the Dorsal venous arch of the foot and is the origin of the long saphenous vein." "FMA:44420 Wikipedia:Medial_marginal_vein EMAPA:37170 MA:0002171" + "Any process that activates, maintains or increases the frequency, rate or extent of frequency, rate or extent of zygospore formation, a process in which a thick-walled spore of some algae and fungi is formed by union of two similar sexual cells, usually serves as a resting spore, and produces the sporophytic phase." + "An exocrine cell characterized by loss of part of the cytoplasm during the process of secretion. The secreted substance is accumulated at the apical end and is either budded off through the plasma membrane producing secreted vesicles or dissolved in the cytoplasm that is lost during secretion." + "Mesenchyme that is part of a developing middle ear." "EHDAA2:0001182 EMAPA:17001" + "The series of events required for an organism to receive an olfactory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Olfaction involves the detection of chemical composition of an organism's ambient medium by chemoreceptors. This is a neurological process." "Wikipedia:Olfaction" + "The process in which relatively unspecialized cells acquire specialized structural and functional features that characterize a pancreatic delta cell. A delta cell is a cell of the pancreas that produces somatostatin." + "Any process that stops, prevents, or reduces the frequency, rate or extent of smooth muscle cell migration." + "Any process that decreases the rate, frequency, or extent of neural crest formation. Neural crest formation is the formation of the specialized region of ectoderm between the neural ectoderm (neural plate) and non-neural ectoderm. The neural crest gives rise to the neural crest cells that migrate away from this region as neural tube formation procedes." + "A blood vessel that is part of a manus [Automatically generated definition]." "MA:0000618 EMAPA:37296" + "A mature CD14-positive dermal dendritic cell is CD80-high, CD86-high, MHCII-high and is CD83-positive." + "A nerve that is part of a head." + "Any collection of muscles that is part of the forelimb stylopod region [Automatically generated definition]." "FMA:50202" + "Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome." "CARO:0000003 MA:0003000 AEO:0000003 FMA:67135 http://dbpedia.org/ontology/AnatomicalStructure TAO:0000037 AAO:0010825 HAO:0000003 FMA:305751 ZFA:0000037 SCTID:362889002 EHDAA2:0003003 TGMA:0001823 XAO:0003000 BILA:0000003 VHOG:0001759 MESH:D000825 GAID:781 EMAPA:0" + "The layer of flattened cells containing basophilic granules of keratohyalin and lying just above the stratum spinosum (spiny layer) of the epidermis." "SCTID:418563001 MA:0000805 NCIT:C33627 FMA:70344 BTO:0000361 EMAPA:32786 Wikipedia:Stratum_granulosum UMLS:C0221923" + "The embryonic vessels grow through the layer to come in close contact with the maternal blood supply." + "Any process that modulates the frequency, rate or extent of the activity of any intracellular steroid hormone receptor signaling pathway." + "NCIT:C41168 FMA:79770" + "A mesentery that is part of a digestive system [Automatically generated definition]." "EMAPA:37068 MA:0001900" + "OBSOLETE: A cell line cell that is expected to be capable of replicating a limited number of times in culture before undergoing senescence. Mortal cell line cells cannot be propagated indefinitely (as immortal cell line cells can)." + + "An olfactory receptor cell in which the apical ending of the dendrite is a pronounced ciliated olfactory knob." + + "The directed movement of bicarbonate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "Mucosal layer that lines the intestine." "FMA:15695 NCIT:C49241 EMAPA:35440 GAID:296 BTO:0000642 MA:0001537 MESH:D007413 UMLS:C0021839 SCTID:362080002" + "The medial border of the scapula (vertebral border, medial margin) is the longest of the three borders, and extends from the medial to the inferior angle. It is arched, intermediate in thickness between the superior and the axillary borders, and the portion of it above the spine forms an obtuse angle with the part below. This border presents an anterior and a posterior lip, and an intermediate narrow area. The anterior lip affords attachment to the Serratus anterior; the posterior lip, to the Supraspinatus above the spine, the Infraspinatus below; the area between the two lips, to the Levator scapulC& above the triangular surface at the commencement of the spine, to the Rhomboideus minor on the edge of that surface, and to the Rhomboideus major below it; this last is attached by means of a fibrous arch, connected above to the lower part of the triangular surface at the base of the spine, and below to the lower part of the border." "Wikipedia:Medial_border_of_scapula SCTID:368187009 EMAPA:25127 FMA:23242" + "Inflammation which comprises a rapid, short-lived, relatively uniform response to acute injury or antigenic challenge and is characterized by accumulations of fluid, plasma proteins, and granulocytic leukocytes. An acute inflammatory response occurs within a matter of minutes or hours, and either resolves within a few days or becomes a chronic inflammatory response." + "A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis." + "A digitopodium region that is part of a pes[Obol]. This includes the toes and metatarsal region, but excludes the tarsals region." + "Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 3rd arch mesenchyme." "EHDAA2:0000082 EMAPA:16403" + "Any process that increases the rate, extent or frequency of the process in which cardiac muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors." + "The regulated release of histamine by a mast cell or group of mast cells." + "The meiotic divisions undergone by the primary and secondary spermatocytes to produce haploid spermatids." + "Any process that stops, prevents, or reduces the frequency, rate or extent of mesonephric nephron tubule epithelial cell differentiation." + "Binding to an organic cyclic compound, any molecular entity that contains carbon arranged in a cyclic molecular structure." + "Any process that increases the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury." + "A rhodopsin-like G-protein coupled receptor that is a translation product of the human DRD1 to DRD5 genes, 1:1 orthologs thereof, or pro-orthologs thereof." "IUPHARfam:20" + "A pelvic girdle region that is in the left side of a multicellular organism." "FMA:16583" + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of a nitric-oxide synthase enzyme." + "Any process that activates or increases the frequency, rate or extent of amacrine cell differentiation." + "A multicellular organism that existence_starts_with a post-embryonic stage." "MA:0002405" + "The formation of mature glucagon by proteolysis of the precursor proglucagon." + "A subdivision of the musculature of the body in the pectoral girdle region. Includes pectoral and shoulder muscles." "AAO:0000423 EMAPA:37857 FMA:33519" + "A lymphocyte of B lineage that is CD19-positive." + "Control of the spatial distribution of intermediate filaments; includes organizing filaments into meshworks, bundles, or other structures, as by cross-linking." + "A(n) neuroendocrine cell that is part of a(n) epithelium of lobar bronchus." + "The introduction of semen or sperm into the genital tract of a female." "Wikipedia:Insemination" + "MA:0000846 EMAPA:35421 neuronames:2292 BAMS:PVZ VHOG:0000623 MBA:157 FMA:77682" + "The multiplication or reproduction of cells, resulting in the expansion of a mesenchymal cell population. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets." + "A netrin-G1 that is encoded in the genome of human." "UniProtKB:Q9Y2I2" + "An adrenal gland that is in the left side of the abdomen." "FMA:15630 UMLS:C0229560 SCTID:281626000 MA:0000718 EMAPA:37356 NCIT:C49322" + "The subdivision of the face that includes the eye (eyeball plus adnexa such as eyelids) and the orbit of the skull and associated parts of the face such as the eyebrows, if present." "FMA:260119" + + "The secretory unit of a mucous gland. The acinar portion is composed of mucous secreting cells." "FMA:86278" + "A T-cell acute lymphocytic leukemia protein 1 that is encoded in the genome of mouse." "UniProtKB:P22091" + "The process in which the anatomical structures of the middle ear are generated and organized. The middle ear is the air-filled cavity within the skull of vertebrates that lies between the outer ear and the inner ear. It is linked to the pharynx (and therefore to outside air) via the Eustachian tube and in mammals contains the three ear ossicles, which transmit auditory vibrations from the outer ear (via the tympanum) to the inner ear (via the oval window)." + "The proximal convoluted tubule is the most proximal portion of the proximal tubule and extends from the glomerular capsule to the proximal straight tubule." "UMLS:C1514580 ZFA:0005290 EMAPA:28287 TAO:0005290 Wikipedia:Proximal_convoluted_tubule EV:0100388 CALOHA:TS-2198 SCTID:362220008 MA:0001669 NCIT:C33417 FMA:17693" + "A future glans that is part of a male genital tubercle." "EMAPA:29252" + "The minute opening of a taste bud on the surface of the oral mucosa through which the gustatory hairs of the specialised neuroepithelial gustatory cells project." "NCIT:C33738 UMLS:C0226971 SCTID:368724008 FMA:63589" + "Any process that activates or increases the frequency, rate or extent of DNA biosynthetic process." + "A homeobox protein Meis2 that is encoded in the genome of human." "UniProtKB:O14770" + "PMID:30257078 PMID:23020233 GC_ID:1" + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a terminal button. A terminal button is the terminal inflated portion of the axon, containing the specialized apparatus necessary to release neurotransmitters." + "Any oligodendrocyte that is part of a spinal cord." + "Any process that stops, prevents, or reduces the frequency, rate or extent of epithelial cell migration." + "Any process that decreases the rate, frequency or extent of a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events." + "A taste receptor cell that is characterized by morphologically identifiable synaptic contacts with the gustatory nerve fibers and expression of the synaptic membrane protein-25 (SNAP-25) and NCAM." "FMA:67940" + "The orderly movement of a mesenchymal stem cell from one site to another." + "Any process that modulates the frequency, rate or extent of nucleus organization." + "The aggregation, arrangement and bonding together of a cellular component." + "A limb joint that is part of an autopod [Automatically generated definition]." "EMAPA:35160 MA:0002715" + "DHBA:10649 FMA:83913" + "Any process that decreases the rate, frequency or extent of mesonephros development. Mesonephros development is the process whose specific outcome is the progression of the mesonephros over time, from its formation to the mature structure. The mesonephros is an organ that filters the blood and excretes the end products of body metabolism in the form of urine." + "The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells." + "The submucous layer of the wall of the uterine tube." "BTO:0002116 SCTID:245489008" + "Paired organ that connects the primitive kidney Wolffian body (or mesonephros) to the cloaca and serves as the anlage for certain male reproductive organs. the Wolffian duct is what remains of the pronephric duct after the atrophy of the pronephros[WP]. In Zebrafish: Duct of the adult kidney (mesonephros), present bilaterally ventral to the somites and leading to the cloacal chamber[ZFA]." "AAO:0000637 ZFA:0000546 GAID:1315 MESH:D014928 EHDAA2:0001243 NCIT:C26469 XAO:0000242 Wikipedia:Mesonephric_duct UMLS:C0043204 EHDAA:1590 TAO:0000546 SCTID:308800003" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving catecholamine." + "A shape quality inhering in a bearer by virtue of the bearer's being partly divided into a determinate number of regions." + "Any process that activates or increases the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient." + "Any process that activates or increases the activity of a transporter." + "Any process that modulates the frequency, rate or extent of receptor localization to synapse." + "The inner portion of the adrenal gland that consists mainly of chromaffin cells which produce, store and secrete neurotransmitters such as epinephrine and norepinephrine." "FMA:15633 EMAPA:18428 SCTID:362585001 Wikipedia:Adrenal_medulla XAO:0000166 MESH:D019439 MAT:0000495 EFO:0000852 GAID:451 EV:0100137 UMLS:C0001629 AAO:0011010 CALOHA:TS-0018 MA:0000119 BTO:0000049 VHOG:0001378 NCIT:C12397" + "The process that results in the generation of glial cells. This includes the production of glial progenitors and their differentiation into mature glia." + "A portion of connective tissue that is part of a neck [Automatically generated definition]." "MA:0000585 EMAPA:37250" + "The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column." "BTO:0000020 SCTID:302553009 EV:0100011 MAT:0000298 EMAPA:35102 CALOHA:TS-0001 Wikipedia:Abdomen galen:Abdomen MIAA:0000298 EFO:0000968 MESH:D000005 FMA:9577 MA:0000029 GAID:16" + "A membrane-bounded organelle, specialized for the storage and secretion of various substances (surfactant phospholipids, glycoproteins and acid phosphates) which are arranged in the form of tightly packed, concentric, membrane sheets or lamellae. Has some similar properties to, but is distinct from, a lysosome." "NIF_Subcellular:sao1379604862" + "A neuron that uses acetylcholine as a vesicular neurotransmitter." "FBbt:00007173 WBbt:0006840 MESH:D059329 FMA:84796 BTO:0004902" + "Any process that activates or increases the frequency, rate or extent of the directed movement of iron ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "BAMS:MEZ FMA:77683 neuronames:2291 EMAPA:35419 MBA:467 MA:0000837 BAMS:MZ" + "A neuropilin and tolloid-like protein 1 that is encoded in the genome of mouse." "UniProtKB:Q8R4I7" + "The pronephric nephron tubule is an epithelial tube that is part of the pronephric nephron and connects the filtration unit (glomerulus or glomus) of the pronephros to the pronephric duct[GO]." "XAO:0004105 TAO:0001558 ZFA:0001558" + "A size quality which is relatively low." + "An epithelial swelling on the Wolffian duct that elongates to invade the adjacent metanephric mesenchyme[MP]." "BTO:0001646 EMAPA:17209 VHOG:0000541 SCTID:361528000 EHDAA:3091 NCIT:C34207 UMLS:C1284058 EHDAA2:0002140 EHDAA:5917 Wikipedia:Ureteric_bud" + "The movement of a leukocyte within or between different tissues and organs of the body contributing to an inflammatory response." + "Any process that modulates the rate, frequency, or extent of the progression of the dermatome over time, from its initial formation to the mature structure. The dermatome is the portion of a somite that will form skin." + "Any process that activates or increases the frequency, rate, or extent of mature B cell apoptotic process." + "Any process that increases the rate, frequency or extent of a phase of elevated metabolic activity, during which oxygen consumption increases made as a defense response ; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals." + "Any process that stops, prevents or reduces the frequency, rate or extent of secretory granule organization." + "Any process that modulates the frequency, rate or extent of auditory hair cell differentiation." + "The continuous network of membranes encompassing the nuclear outer membrane and the endoplasmic reticulum membrane." + "A M cell that is part of the epithelium proper of jejunum." "FMA:263136" + "Any process that modulates the frequency, rate or extent of R7 differentiation." + "A skeletal muscle myoblast that differentiates into slow muscle fibers." + "An autopod endochondral element that is composed primarily of cartilage tissue." + "KUPO:0001072" + "A fibroblast of the lymphatic system." + "An anatomical surface that is part of a tongue." "FMA:54647 SCTID:314870004" + "The sensory system for the sense of proprioception." "NLXANAT:090814" + "An organ that is part of a immune system [Automatically generated definition]." + "A smooth muscle cell of the umbilical vein." + "Any process that activates or increases the frequency, rate, or extent of antimicrobial peptide production." + "A hole in a tube[GO]." "AEO:0000078 EHDAA2:0004618 RETIRED_EHDAA2:0003078" + "Any process that activates or increases the frequency, rate or extent of tumor necrosis factor superfamily cytokine production." + "Any process that stops, prevents, or reduces the frequency, rate or extent of T-helper 2 cell differentiation." + "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." "Reactome:R-HSA-8868783 EC:2.-.-.- Reactome:R-HSA-5668414 Reactome:R-HSA-1483186 Reactome:R-HSA-1483089" + "Any process that modulates the frequency, rate or extent of protein localization to presynapse." + "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a ribonucleoprotein complex." + "A developmental process, independent of morphogenetic (shape) change, that is required for the vagus nerve to attain its fully functional state. This nerve is primarily sensory but also has visceromotor components. It originates in the brain stem and controls many autonomic functions of the heart, lungs, stomach, pharynx, larynx, trachea, esophagus and other gastrointestinal tract components. It controls some motor functions such as speech. The sensory branches mediate sensation from the pharynx, larynx, thorax and abdomen; it also innervates taste buds in the epiglottis." + "KUPO:0001073" + "KUPO:0001053" + "The chemical reactions and pathways resulting in the breakdown of primary amino compound." + "The process in which a relatively unspecialized cell acquires specialized structural and/or functional features that characterize an acinar cell of the salivary gland. Acinar cells are protein-secreting cells in the gland." + "The formation of mesodermal clusters that are arranged segmentally along the anterior posterior axis of an embryo." "Wikipedia:Somitogenesis" + "An intervertebral disk that is part of a tail [Automatically generated definition]." "MA:0000698 EMAPA:19592" + "Any process that stops, prevents or reduces the frequency, rate or extent of optic nerve formation." + "Immature CD8_alpha-negative CD11b-negative dendritic cell is a CD8_alpha-negative CD11b-negative dendritic cell that is CD80-low, CD86-low, and MHCII-low." + "A submucosa that is part of a common bile duct [Automatically generated definition]." "FMA:18011" + "FMA:268630 DHBA:10654" + "The process whose specific outcome is the creation of the forebrain-midbrain boundary." + "A non-terminally differentiated cell that is capable of developing into a muscle cell." + "Mesenchyme that is part of a developing lower arm [Automatically generated definition]." "EHDAA:6222 EHDAA2:0000555 VHOG:0000504 EMAPA:17419 EHDAA:4176" + "A fibroblasts found in interstitial spaces in the pulmonary tract. Greater numbers of these cells are found in idiopathic pulmonary fibrosis." "FMA:84467" + + "The chemical reactions and pathways resulting in the breakdown of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y." + "The posterior region of the neck, including the suboccipital region." "BTO:0000957 FMA:24189 SCTID:304036007 SCTID:182326009" + "Any process that activates or increases the frequency, rate or extent of prolactin signaling pathway." + "Any process that activates or increases the frequency, rate or extent of regulated secretory pathway." + "The collection of all skeletal elements in a pectoral complex - i.e. the combination of free limb or fin plus pectoral girdle." "FMA:24139" + "A cervical vertebra endochondral element that is composed primarily of a pre-cartilage condensation." + "The vessels formed within the fourth pair of branchial arches in embryogenesis." "ZFA:0005008 EHDAA2:0000087 XAO:0000355 Wikipedia:Aortic_arches#Arch_4 TAO:0005008 SCTID:308777005 EMAPA:17004 AAO:0010420" + "The fibrous membrane forming the innermost of the three coverings that surrounds the brain within the cranial cavity that is firmly attached to the glial capsule." "NCIT:C49335 VHOG:0000470 UMLS:C1706994 MA:0000816 EMAPA:32667" + "Anatomical system that has as its parts the organs concerned with reproduction." "WBbt:0005747 GAID:363 UMLS:C1261210 MA:0000326 EV:0100100 EFO:0000809 Wikipedia:Reproductive_system CALOHA:TS-1318 FMA:7160 EHDAA2:0001603 HAO:0000374 MIAA:0000305 HAO:0000895 XAO:0000142 SCTID:278875001 BILA:0000103 ZFA:0000632 TAO:0000632 BTO:0000081 NCIT:C12841 EHDAA:5923 AAO:0010258 EMAPA:17381 VHOG:0000182" + "A mucosa that is part of a fallopian tube [Automatically generated definition]." "FMA:18319" + "A muscular coat that is part of a ileum." "FMA:14958 BTO:0005574" + "A mature osteoblast that has become embedded in the bone matrix. They occupy a small cavity, called lacuna, in the matrix and are connected to adjacent osteocytes via protoplasmic projections called canaliculi." "CALOHA:TS-1167 BTO:0002038 FMA:66779 VSAO:0000124" + "DHBA:10157 FMA:268608" + "The process of regulating the proliferation and elimination of B cells of the B-1 subset such that the total number of B-1 B cells within a whole or part of an organism is stable over time in the absence of an outside stimulus. B-1 B cells are a distinct subset of B cells characterized as being CD5 positive, found predominantly in the peritoneum, pleural cavities, and spleen, and enriched for self-reactivity." + "Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts." "SCTID:309312004 TAO:0001501 MA:0000104 XAO:0000170 EV:0100141 ZFA:0005622 MIAA:0000189 NCIT:C12373 MESH:D002356 BTO:0000206 UMLS:C0007301 FMA:37377 EMAPA:32730 EFO:0000949 VHOG:0001207 NCIT:C32268 MAT:0000189 EHDAA2:0003087 Wikipedia:Cartilage AAO:0000060 VSAO:0000040 galen:Cartilage AEO:0000087 GAID:99" + "Any neuron having a sensory function; an afferent neuron conveying sensory impulses." "FBbt:00005124 WBbt:0005759 MESH:D011984 FMA:84649 BTO:0001037" + "A C-C chemokine receptor type 1 that is encoded in the genome of mouse." "UniProtKB:P51675" + "A Be cell that facilitates development of T-helper 2 (Th2) phenotype T cells, and secretes high levels of interleukin-2, interleukin-10, interleukin-4, and interleukin-6." + "A cell specialized to transduce mechanical stimuli and relay that information centrally in the nervous system." + "An inducible T-cell costimulator that is encoded in the genome of human." "UniProtKB:Q9Y6W8" + "Any process that modulates the frequency, rate, or extent of interleukin-5 production." + "Thin cylindrical membrane-covered projections on the surface of an animal cell containing a core bundle of actin filaments. Present in especially large numbers on the absorptive surface of intestinal cells." "Wikipedia:Microvillus NIF_Subcellular:sao671419673" + "The directed movement of organelles or molecules along microtubules in axons." "Wikipedia:Axoplasmic_transport" + "A mucous gland that is part of the skin." "EMAPA:35775 MA:0000148" + "Any process that stops, prevents or reduces the frequency, rate or extent of microglial cell activation." + "Any process that activates or increases the frequency, rate or extent of cell junction assembly." + "A mesothelial cell that is part of the visceral peritoneum." "FMA:72143" + "Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of plasma membrane bounded cell projections." + "Epithelium located in the intersomitic region." "XAO:0004077" + "Any process that modulates the frequency, rate or extent of optic nerve formation." + "An undifferentiated cell that originates from a neural stem cell and has the capacity to generate multiple types of lineage-restricted progenitors but not to self-renew." + "A cytoarchitectural term denoting the layer of the hippocampus in which pyramidal cells are predominant. Its location is superficial to the Stratum oriens; it is deep to the Stratum radiatum in area CA1 and area CA2 and deep to the Stratum lucidum in area CA3 (Stephan-75) (NeuroNames)." "EMAPA:35409 BTO:0001066 FMA:83895 BAMS:Py BIRNLEX:1444 MA:0000956 neuronames:156" + "A progenitor cell that is a tissue-resident mesenchymal cell, important for skeletal muscle regeneration, and able to differentiate into both adipocytes or fibroblasts." + "Any process that modulates the rate, frequency, or extent of the growth of a cardiac muscle cell, where growth contributes to the progression of the cell over time from its initial formation to its mature state." + "Anatomical structure that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO]." "MAT:0000188 AEO:0000182 EFO:0000948 XAO:0000171 RETIRED_EHDAA2:0003182 UMLS:C0022417 MESH:D007596 FMA:7490 MA:0000319 VSAO:0000101 SCTID:302536002 VHOG:0001276 NCIT:C13044 GAID:102 galen:Joint ZFA:0001596 TAO:0000367 CALOHA:TS-2023 BTO:0001686 Wikipedia:Joint EMAPA:35456 MIAA:0000188" + "Obsolete. Use PO:0020099 from Plant Ontology instead. Cell type formed after the first mitotic division of the microgametophye, The nucleus of this cell migrates to the tip of the pollen tube after germination and disintegrates when the pollen tube penetrates the nucellus." + "The regulated release of testosterone into the circulatory system. Testosterone is an androgen having 17beta-hydroxy and 3-oxo groups, together with unsaturation at C-4-C-5." + "A pre-cartilage condensation that is part of a trachea." "EHDAA2:0002070 EHDAA:7082" + "The multiplication or reproduction of striated muscle cells, resulting in the expansion of a cell population. Striated muscles contain fibers that are divided by transverse bands into striations, and cardiac and skeletal muscle are types of striated muscle." + "The process in which a relatively unspecialized cell acquires the specialized features of an astrocyte. An astrocyte is the most abundant type of glial cell. Astrocytes provide support for neurons and regulate the environment in which they function." + "Any process that modulates the frequency, rate or extent of neural precursor cell proliferation." + "Any portion of gas located in a part of the respiratory system that is composed primarily of air." "FMA:84581" + "An ectoderm that is part of a footplate." "EMAPA:17250" + "The orderly movement of a colonic epithelial cell from one site to another, often during the development of a multicellular organism." + "The thin membranous structure between the two heart atria or the thick muscular structure between the two heart ventricles." "GAID:562 MESH:D006346 SCTID:362014000 EMAPA:35400 MA:0000083 UMLS:C0018819 NCIT:C49485 FMA:7180" + "Binding to a torso (tor) protein, a receptor tyrosine kinase." + "An alveolar capillary endothelial cell that is located distally to alveolar capillary type 2 endothelial cells." + "A NK1.1-positive T cell that is Ly49H-positive." + "Any of any of the secretory or sensory organs located in the brain region around or in relation to the ventricular system that are characterized by extensive vasculature and a lack of a normal blood brain barrier (BBB) and allow for the linkage between the central nervous system and peripheral blood flow." "neuronames:1242 MA:0002942 NLXANAT:20090312 FMA:84081 Wikipedia:Circumventricular_organs EMAPA:35243" + "Any process that modulates the frequency, rate or extent of distal tip cell migration." + "BILA:0000142" + "The process whose specific outcome is the progression of a cartilage element over time, from its formation to the mature structure. Cartilage elements are skeletal elements that consist of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate." "Wikipedia:Chondrogenesis" + "The process whose specific outcome is the progression of the metanephric proximal straight tubule over time, from its formation to the mature structure. The metanephric proximal straight tubule is the part of the metanephric descending limb that extends from the metanephric proximal convoluted tubule to the metanephric descending thin tubule." + "Coarse, bluish-black staining cytoplasmic granules, bounded by a plasma membrane and found in mast cells and basophils. Contents include histamine, heparin, chondroitin sulfates, chymase and tryptase." + "A tributary of the superior mesenteric vein that drains the jejunum." "EMAPA:37160 FMA:15402 MA:0002153 Wikipedia:Jejunal_veins" + + "Any process that activates or increases the frequency, rate or extent of adipose tissue development." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a yeast species." + "Any process that stops, prevents or reduces the frequency, rate or extent of Schwann cell migration." + "An epithelium that is part of a finger [Automatically generated definition]." "VHOG:0001032 EHDAA2:0000406 EMAPA:32647" + "Any process that modulates the potential difference across a post-synaptic membrane." + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments. Includes processes that control the spatial distribution of actin filaments, such as organizing filaments into meshworks, bundles, or other structures, as by cross-linking." + "A tartrate-resistant acid phosphatase type 5 that is encoded in the genome of human." "UniProtKB:P13686" + "Any process that stops, prevents or reduces the frequency, rate or extent of type B pancreatic cell apoptotic process." + "The transmission of vibrations via ossicles to the inner ear." + "Any process that stops, prevents or reduces the frequency, rate or extent of hepatic stellate cell proliferation." + "Blood located in the placenta." + "Any process that stops, prevents, or reduces the frequency, rate or extent of locomotion of a cell or organism." + "A cylindrical shape that is hollow." + "A portion of striated muscle tissue that is part of a prostate gland [Automatically generated definition]." "FMA:45716" + "A type of reproduction that combines the genetic material of two gametes (such as a sperm or egg cell or fungal spores). The gametes have an haploid genome (with a single set of chromosomes, the product of a meiotic division) and combines with one another to produce a zygote (diploid)." "Wikipedia:Sexual_reproduction" + "An integrin alpha-2 that is encoded in the genome of mouse." "UniProtKB:Q62469" + "Area of the Peyer's patch where B cells proliferate and differentiate into plasma cells." "NCIT:C49600 MA:0000734 UMLS:C1711398 EMAPA:35684" + "A mesentery that is part of a hindgut [Automatically generated definition]." "EMAPA:16718" + "The sum of epicardial and paracardial fat deposits." "ZFA:0005765 SCTID:42267001" + "A trabecula carnea that is part of a heart right ventricle." "SCTID:192373001 FMA:7270" + "A motor neuron that is generated only on limb levels and send axons into the limb mesenchyme." + "A primary nodular lymphoid tissue that is part of a tonsil." "FMA:86018" + "An embryo stage that covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching." "FBdv:00005333 OGES:000023 EV:0300011 MIAA:0000399 SCTID:367619004 FMA:63631 EVM:2990031 MmusDv:0000031" + "A protein complex capable of catalyzing the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor)." + "Any biological process involved in the maintenance of the steady-state number of cells within a population of cells." + "A neural precursor of the central nervous system." "FBbt:00005146" + "A type 5 cone bipolar cell with narrowly stratified post synaptic terminals." + "Any process that activates or increases the frequency, rate or extent of prolactin secretion." + "A meninx that is part of a spinal cord [Automatically generated definition]." "CALOHA:TS-2148 VHOG:0000443 EHDAA:2865 SCTID:181097002 MA:0001130 EMAPA:17804 UMLS:C0037938 EHDAA2:0001895 NCIT:C12350" + "The movement of a dendritic cell in response to an external stimulus." + "The stratified epithelial lining of the seminiferous tubules, consisting of the developing spermatozoa and the supporting Sertoli cells, which are tall, columnar type cells that line the tubule." "Wikipedia:Germinal_epithelium_(male) UMLS:C0036629 EHDAA:8148 RETIRED_EHDAA2:0002009 MA:0001748 EMAPA:35761 MESH:D012670 BTO:0001811 NCIT:C49296 GAID:401 CALOHA:TS-0920 VHOG:0000631 FMA:19885" + "Translation that occurs at the postsynapse." + "A renal intercalated cell that secretes base and reabsorbs acid in the distal segments of the kidney tubule to maintain acid/base balance." + "Any process that increases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." + "CD11c-negative plasmacytoid dendritic cell is a leukocyte is CD11c-negative, CD45RA-positive, CD85g-positive(ILT7), CD123-positive, CD303-positive." + "A cell that specializes in secretion of surfactant in the alveoli of the lung." + "The portion of neural plate posterior to the mid-hindbrain junction." "TAO:0007017 VHOG:0001201 XAO:0000046 ZFA:0007017" + "An unilaminar epithelium that surrounds a pectoral appendage bud." "EHDAA2:0002134 EMAPA:16407 VHOG:0001047" + "The directed movement of a monoatomic cation, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Monatomic cations (also called simple cations) are positively charged ions consisting of exactly one atom." + "The process whose specific outcome is the progression of the deltoid tuberosity over time, from its formation to the mature structure. The deltoid tuberosity is the region on the shaft of the humerus to which the deltoid muscle attaches. The deltoid tuberosity develops through endochondral ossification in a two-phase process; an initiating tendon-dependent phase, and a muscle-dependent growth phase." + "A thermogenic form of adipose tissue that is composed of brown adipocytes[MP,modified]." "CALOHA:TS-0099 MAT:0000198 BTO:0000156 MESH:D002001 FMA:20118 MA:0000057 UMLS:C0006298 EMAPA:19209 MIAA:0000198 GAID:921 SCTID:15965003 NCIT:C32235 Wikipedia:Brown_adipose_tissue EFO:0000812" + "The process in which relatively unspecialized cells acquire specialized structural and/or functional features of leading edge cells, cells at the front of a migrating epithelial sheet." + "SCTID:22943007 FMA:25054" + "The orderly movement of a slow muscle cell from one site to another." + "Any process that activates or increases the frequency, rate or extent of protein localization to cell cortex." + "An amicrine that has a narrow dendritic field." + "A relaxin family peptide receptor protein that is a translation product of the human RXFP1 gene or a 1:1 ortholog thereof. This receptor is expressed in the brain, kidney, testis, placenta, uterus, ovary, adrenal, prostate, skin and heart." "IUPHARobj:351" + "Any process involved in the maintenance of a steady-state level of a surface-active agent that maintains the surface tension of a liquid." + "A cell that makes up the loose connective tissue of the ovary." "FMA:18709" + "A myoepithelial cell that is part of the tertiary lactiferous duct." "FMA:74502" + "An arginase-1 that is encoded in the genome of human." "UniProtKB:P05089 Reactome:R-HSA-70561 Reactome:R-HSA-6801011 Reactome:R-HSA-6806221 Reactome:R-HSA-6798764" + "Any process that activates or increases the frequency, rate or extent of the regulated release of juvenile hormone." + "Any process that modulates the rate, frequency or extent of the synthesis or release of any leukotriene following a stimulus as part of an inflammatory response." + "Any process that increases the frequency, rate or extent of cardiac muscle contraction." + "Functional unit of the kidney that forms urine, consisting of two parts, the nephron and the collecting tubule." "FMA:17691" + "The appearance of any member of the interleukin-17 family of cytokines due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." + "The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds." "Wikipedia:Protein_catabolism" + "Any process that modulates the frequency, rate or extent of the regulated release of norepinephrine." + "A connective tissue cell of an organ found in the loose connective tissue. These are most often associated with the uterine mucosa and the ovary as well as the hematopoietic system and elsewhere." "FMA:83624 BTO:0002064" + "A cone cell that detects ultraviolet (UV) wavelength light." + "Any process that modulates the frequency, rate or extent of spermatid nuclear differentiation." + "A phalanx that is part of a forelimb autopod[Automatically generated definition]." "Wikipedia:Phalanges_of_the_hand UMLS:C0223792 MA:0000306 EMAPA:32650 http://mbe.oxfordjournals.org/content/26/3/613/F1.large.jpg AAO:0000947 NCIT:C52771 SCTID:181976001 SCTID:361100001 FMA:23914" + "A retinal neural layer that is immediately adjacent to the retinal ganglion cell layer and comprises 20 percent of the ganglion plexiform layer of retina." "CP:0000117" + "Any process that activates or increases the rate or extent of urothelial cell proliferation." + "A melanocyte located between the epithelial marginal cell layer and the mesodermal basal cell layer within the intrastrial space; the predominant cellular component of the electrogenic machinery that generates an endocochlear potential (80-100 mV) ." + "Any process that activates or increases the frequency, rate or extent of calcium ion transmembrane transporter activity." + "GC_ID:1" + "A neuron that releases hypocretin as a neurotransmitter." + "Anterior subdivision of a digestive tract." "EHDAA:520 AAO:0011042 UMLS:C0231051 FMA:45616 EHDAA2:0000557 NCIT:C34180 XAO:0000232 MA:0001526 BILA:0000085 SCTID:361409009 TGMA:0001014 BTO:0000507 VHOG:0000285 Wikipedia:Foregut EMAPA:16548" + "Any process that modulates the frequency, rate or extent of movement of RNA from the cytoplasm to the nucleus." + "Any stellate cell that is part of a dentate gyrus of hippocampal formation." + "Any native cell that is part of a cardiac septum." + "A short lived plasma cell that secretes IgG." + "Any apoptotic process that contributes to the shaping of an anatomical structure." + "A nerve that is part of a lower leg [Automatically generated definition]." "MA:0000679 EMAPA:37345" + "The chemical reactions and pathways involving any conjugated, water-soluble protein in which the covalently attached nonprotein group consists of a lipid or lipids." + "An arteriole that arises from the hilar artery of a lymph node and radiates centrifugally, branching in the medulla." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of peripheral T cell tolerance induction." + "A motor neuron that synapses to parasympathetic neurons that innervate tear glands, sweat glands, and the smooth muscles and glands of the pulmonary, cardiovascular, and gastrointestinal systems." + "Any apoptotic process in a lymphocyte, a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin." + "A bone marrow proteoglycan that has had the signal peptide removed." + "Obsolete. Use PO:0020048 from Plant Ontology instead. A haploid (1n) spore developing into a male gametophyte in heterosporous plants; the uninucleate pollen grain in seed plants." + "An epithelial cell that is part of a collecting duct of an airway submucosal gland." + "The section of the lymph node capsule that faces the subcapsular sinus. In human, it's characterized by specific protein markers." + "The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a garland nephrocyte. A garland nephrocyte is an insect renal cell that filters hemolymph and forms a ring with other garland nephrocytes around the esophagus. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state." + "A ganglion that is part of a central nervous system [Automatically generated definition]." "FMA:83843 EMAPA:16658 EHDAA2:0000227" + "Any process that modulates the rate, frequency or extent of cell differentiation that contributes to the progression of the placenta over time, from its initial condition to its mature state." + "An epiphysis that is part of a tibia [Automatically generated definition]." "FMA:33112 MA:0003113 SCTID:314626006 EMAPA:37771" + "The process whose specific outcome is the progression of a trachea over time, from its formation to the mature structure. The trachea is the portion of the airway that attaches to the bronchi as it branches." + "A parvalbumin alpha that is encoded in the genome of human." "UniProtKB:P20472" + "A neuron of the human embryonic marginal zone which display, as a salient feature, radial ascending processes that contact the pial surface, and a horizontal axon plexus located in the deep marginal zone. One feature of these cells in mammals is that they express the Reelin gene." + "A lobar bronchus that is part of a right lung [Automatically generated definition]." "SCTID:245511004 MA:0003134 EMAPA:17664" + "A transitional myocyte that is part of the ventricular part of atrioventricular bundle." "FMA:263176" + "Any process that activates or increases the frequency, rate or extent of lymphocyte chemotaxis." + "Any microvascular endothelial cell that is part of a breast." + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of polysaccharides." + "The directed movement of substances (e.g. macromolecules, small molecules, ions) through the blood-cerebrospinal fluid barrier." + "The process whose specific outcome is the progression of the vasculature of the kidney over time, from its formation to the mature structure." + "Binding to a prostanoid receptor." + "Any process that stops, prevents or reduces the frequency, rate or extent of cell proliferation involved in mesonephros development." + "A CD7 molecule that is encoded in the genome of mouse." "UniProtKB:P50283" + "A myeloblast committed to the basophil lineage." + "A smooth muscle cell that is part of the jejunum." "FMA:15062" + "A bone tissue that is part of a long bone." "FMA:83117 SCTID:425475006" + "Any process that activates or increases the frequency, rate or extent of CD4-positive, alpha-beta T cell activation." + "Epithelial cell found in the ducts of the pancreas. This cell type contributes to the high luminal pH." "FMA:63099" + "Any process that stops, prevents or reduces the frequency, rate or extent of border follicle cell migration." + "EMAPA:16844 VHOG:0000215 MA:0001636" + "A glandular epithelium that is part of a uterine cervix." "UMLS:C1707350 NCIT:C54414" + "The orderly movement of a vascular associated smooth muscle cell from one site to another." + "The bronchial veins are small vessels that return blood from the larger bronchi and structures at the roots of the lungs. The right side drains into the azygos vein, while the left side drains into the left superior intercostal vein or the accessory hemiazygos vein. The bronchial veins are counterparts to the bronchial arteries. The veins, however, do not return all of the blood supplied by the arteries; much of the blood that is carried in the bronchial arteries is returned to the heart via the pulmonary veins. [WP,unvetted]." "UMLS:C0226650 EMAPA:36284 MA:0002088 Wikipedia:Bronchial_veins NCIT:C53031 FMA:4749 SCTID:198293000" + "The profunda femoris artery (also known as the deep femoral artery, or the deep artery of the thigh) is a branch of the femoral artery that, as its name suggests, travels more deeply (posteriorly) than the rest of the femoral artery. [WP,unvetted]." "SCTID:181348000 Wikipedia:Deep_femoral_artery FMA:20741 MA:0002027 NCIT:C32436 EMAPA:37216 UMLS:C0226455" + "The cell cycle process in which chromatin structure is compacted prior to and during mitosis in eukaryotic cells." + "Any process that stops, prevents or reduces the frequency, rate or extent of neural crest cell differentiation." + "A process in which a calcium ion is transported from one side of a Golgi membrane to the other by means of some agent such as a transporter or pore." + "The process whose specific outcome is the progression of the paraxial mesoderm over time, from its formation to the mature structure. The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube." + "The detachment of cells from radial glial fibers at the appropriate time when they cease to migrate and form distinct layer in the cerebral cortex." + "The process by which an organism or tissue maintains a population of female germ-line stem cells." + "CD7-negative lymphoid progenitor cell is a lymphoid progenitor cell that is CD34-positive, CD7-negative and CD45RA-negative." + "FMA:66809" + "The chemical reactions and pathways resulting in the breakdown of dopamine, a catecholamine neurotransmitter and a metabolic precursor of noradrenaline and adrenaline." + "The process in which a relatively unspecialized thymocyte acquires specialized features of a T-helper cell." + "The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value."@en + "Any process that modulates the frequency, rate or extent of anterograde dense core granule transport." + "The developmental process pertaining to the initial formation of the pronephros. In mammals, the pronephros is the first of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the pronephros is the fully functional embryonic kidney and is indispensable for larval life." + "OBSOLETE: A classification of cells by their primary end goal or behavior." + "The epithelial lining of the luminal space of the urinary bladder." "FMA:15936 MA:0001693 EMAPA:28601 SCTID:25631003 UMLS:C0225339 CALOHA:TS-1088 BTO:0001694" + "The process aimed at the progression of an oligodendrocyte over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. An oligodendrocyte is a type of glial cell involved in myelinating the axons in the central nervous system." + "A macrophage colony-stimulating factor 1 receptor that is encoded in the genome of mouse." "UniProtKB:P09581" + "Situated just caudal to the acetabulum, the foramen is bound dorsally by the illium and ventrally by the ischium. The foramen transmitts the ischiadic nerves and vessels (Baumel et al. 1993)." + "A dendritic cell arising in thymus that has the phenotype CD11c-positive, CD11b-negative, and CD45RA-negative." + "The bundle of microtubules and associated proteins that forms the core of cilia (also called flagella) in eukaryotic cells and is responsible for their movements." "Wikipedia:Axoneme" + "A process in which a protein is transported to, or maintained in, a location within a vacuolar membrane." + "The process whose specific outcome is the progression of the long descending thin limb over time, from its formation to the mature structure. The long descending thin limb is the descending thin limb of a long nephron that has a squamous epithelial morphology. The long descending limb starts in the inner stripe of the outer medulla and extends into the inner medulla." + "Any process that modulates the frequency, rate or extent of the assembly, disassembly or arrangement of constituent parts of the basement membrane." + + "EHDAA2:0000789 FMA:312291 VHOG:0001477 EHDAA:4733 MA:0000272 EMAPA:17302" + "Receiving a signal and transmitting it in a cell to initiate an immune response." + "The regulated release of hormones, substances with a specific regulatory effect on a particular organ or group of cells." + "The region of a neuron that includes the cell body (cell soma) and dendrite(s), but excludes the axon." + "A macrosialin that is encoded in the genome of human." "UniProtKB:P34810" + "An amacrine cell with a small, asymteric dendritic field." + "Any pyramidal cell that is part of a primary motor cortex." + "A renal system process in which fluid circulating through the body is filtered through a barrier system." + "Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle." "EHDAA2_RETIRED:0003154 EFO:0000807 SCTID:361692004 BILA:0000118 AEO:0000154 CARO:0002001 EHDAA2:0000836 TADS:0000108 UMLS:C0037267 NCIT:C12907 MAT:0000033 EV:0100151 MA:0000014 Wikipedia:Integumentary_system EHDAA:6520 HAO:0000421 EMAPA:17524 FMA:72979 VHOG:0000403 galen:Surface CALOHA:TS-1299 XAO:0000176 MESH:D034582 MIAA:0000033" + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleolus." + "Any process that stops, prevents, or reduces the frequency, rate or extent of keratinocyte migration." + "The outer serous membrane of the pulmonary pleural." "FMA:9733 Wikipedia:Parietal_pleura UMLS:C0225777 MA:0002488 EMAPA:16776 NCIT:C33273 VHOG:0001495 SCTID:361998003" + "The process that results in the patterns of cell differentiation that will arise in an embryo." + "Any process that activates or increases the frequency, rate or extent of axonogenesis." + "AEO:0000149 EHDAA2_RETIRED:0003149" + "Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids." + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon." + "An innate lymphoid cell that is capable of producing the type 1 cytokine IFN-gamma, but not Th2 or Th17 cell-associated cytokines." + "A CCAAT/enhancer-binding protein epsilon that is encoded in the genome of mouse." "UniProtKB:Q6PZD9" + "An epithelial cell that is part of the glomerular capsule." "KUPO:0001034 FMA:70966" + "The chemical reactions and pathways resulting in the formation of a phenol, any compound containing one or more hydroxyl groups directly attached to an aromatic carbon ring." + "A progenitor cell with hepatic and biliary lineage potential, identified in mouse and human, and anatomically restricted to the ductal plate of fetal liver." + "FMA:65507 MA:0001178" + + "Any process that activates or increases the frequency, rate or extent of the directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "Any process that modulates the frequency, rate, or extent of immunoglobulin production." + "Any process that stops, prevents or reduces the frequency, rate or extent of trophoblast cell migration." + "Any process that modulates the frequency, rate or extent of ureter smooth muscle cell differentiation." + "A cell of a hematopoietic lineage." "FMA:70366 FMA:83598 BTO:0000574 CALOHA:TS-2017" + "Binding to an RNA molecule or a portion thereof." "Reactome:R-HSA-203922" + "Any process that stops, prevents or reduces the frequency, rate or extent of cardiac muscle cell myoblast differentiation." + "GC_ID:1" + "Any muscle organ that is part of a pectoral appendage (forelimb or pectoral fin)." + "Any process that modulates the rate, frequency or extent of myofibril assembly by organization of muscle actomyosin into sarcomeres. The sarcomere is the repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs." + "Any process that activates, maintains or increases the frequency, rate or extent of branchiomeric skeletal muscle development. Branchiomeric skeletal muscle development is the process whose specific outcome is the progression of the branchiomeric skeletal muscle over time, from its formation to the mature structure." + "The immediate defensive reaction by vertebrate tissue to injury caused by chemical or physical agents." + "The enlargement or overgrowth of all or part of an organ due to an increase in size (not length) of individual muscle fibers without cell division. In the case of skeletal muscle cells this happens due to the additional synthesis of sarcomeric proteins and assembly of myofibrils." + "Any process in which the axon of a neuron is insulated, and that insulation maintained, thereby preventing dispersion of the electrical signal." + "The process whose specific outcome is the progression of the renal outer medulla over time, from its formation to the mature structure. The renal outer medulla is the region of the kidney that lies between the renal cortex and the renal inner medulla." + "A serous membrane that is part of a vermiform appendix." "FMA:14997 SCTID:22488003" + "Any process that stops, prevents, or reduces the frequency, rate, or extent of leukocyte migration." + "Any B cell selection process that occurs in the periphery." + "An endothelium that lines the blood vasculature. Other endothelia may line lymph vessels, the heart." "UMLS:C1706972 NCIT:C53395 TAO:0005257 ZFA:0005257 BTO:0000766 MA:0000709 EMAPA:35176 CALOHA:TS-2155" + "OBSOLETE. An intratelencephalic-projecting glutamatergic neuron with a soma found in layer 6 of the marmoset primary motor cortex." "ILX:0770158" + "The directed movement of acidic amino acids, amino acids with a pH below 7, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "An epithelium that is part of a digestive system [Automatically generated definition]." "MA:0001520 EMAPA:32683" + "A mucous cell in the epithelium of the stomach." "FMA:63464" + "A nerve root that extends_fibers_into a trigeminal nerve." "TAO:0000192 ZFA:0000192 BIRNLEX:1346 DMBA:17739 DHBA:12865 SCTID:280185007 FMA:52610" + "A bipolar neuron found in the retina that is synapsed by rod photoreceptor cells but not by cone photoreceptor cells. These neurons depolarize in response to light." "FMA:67750" + "A peptide hormone secreting cell pituitary that produces luteinizing hormone." + "A somatostatin that is encoded in the genome of human." "UniProtKB:P61278" + "The formation of spores derived from the products of meiosis." + "Any process that activates or increases the frequency, rate or extent of progesterone biosynthetic process." + "An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The cell has a loose, delicate axon terminal that opens in sublamina 3 of the inner plexiform layer and descends into sublamina 4." + "The biological process whose specific outcome is the progression of a neural nucleus from its initial condition to its mature state. A neural nucleus is an anatomical structure consisting of a discrete aggregate of neuronal soma." + "The process in which a relatively unspecialized cell acquires specialized features of an anterior lateral line neuromast hair cell. Neuromast hair cells are the sensory receptors of the neuromast and are located in a portion of the neuromast called the sensory strip. Each hair cell of the neuromast is morphologically polarized as a result of the relative position of the single kinocilium and the clusters of stereocilia on its apical surface. There are approximately seven hair cells within each neuromast, with each hair cell innervated by afferent and efferent neurons." + "Any process that modulates the frequency, rate or extent of cholangiocyte proliferation." + "Any process in which a protein complex is maintained in a location and prevented from moving elsewhere. These include sequestration, stabilization to prevent transport elsewhere and the active retrieval of protein complexes that move away." + "A notochord that has persisted beyond the embryonic stage." + "The process whose specific outcome is the progression of the renal capsule over time, from its formation to the mature structure. The renal capsule is the tough fibrous layer surrounding the kidney, covered in a thick layer of perinephric adipose tissue. It provides some protection from trauma and damage. During development, it comprises a single layer of flattened cells that lie just above the cortical stroma and the condensed mesenchyme of the nephrogenic zone. It is in this region that the early stages of nephron induction and formation of new generations ureteric bud branches occur, as the kidney expands." + "A lymphoid follicle that is part of a Peyer's patch." "MA:0000732" + "The process whose specific outcome is the progression of the lateral mesoderm over time, from its formation to the mature structure." + "The anatomical junction between the duodenum and the jejunum." "FMA:15957 WikipediaVersioned:Duodenojejunal_flexure&oldid=937307798 TA2:2952 https://orcid.org/0000-0003-4183-8865" + "An integrin alpha-E that is encoded in the genome of human." "UniProtKB:P38570" + "Nonsynovial joint in which the articulating bones or cartilages are connected by ligaments. Examples: sagittal suture, inferior tibiofibular syndesmosis, gomphosis.[FMA]." "Wikipedia:Fibrous_joint ZFA:0005156 AEO:0000178 EHDAA2:0003178 EMAPA:35344 MA:0000321 SCTID:37772004 TAO:0005156 FMA:7492" + "A plasmablast that secretes IgE." + + "The process whose specific outcome is the progression of the rhombomere over time, from its formation to the mature structure. Rhombomeres are transverse segments of the developing rhombencephalon. Rhombomeres are lineage restricted, express different genes from one another, and adopt different developmental fates." + "A vasa recta that is part of a outer medulla of kidney [Automatically generated definition]." "MA:0002597 EMAPA:36560" + "Any process that stops, prevents, or reduces the frequency, rate, or extent of myeloid leukocyte differentiation." + "The region of the hepatic acinus immediately surrounding the central veins. This region has the lowest oxygen concentration in the acinus. Zone 3 is located in the centrilobular region of the liver lobule, closest to the central vein. Hepatocytes in this region are the primary location for the biotransformation of drugs." + "The increase in size or mass of the spongiotrophoblast layer of the placenta where the increase in size or mass contributes to the progression of that layer over time from its formation to its mature state." + "Any process that modulates the frequency, rate or extent of G protein-coupled receptor signaling pathway." + "A submucosa that is part of a larynx [Automatically generated definition]." "EMAPA:35474 SCTID:361941005 FMA:321584 MA:0002728" + "A granzyme B that is encoded in the genome of human." "UniProtKB:P10144" + "A GABAergic interneuron that selectively innervates the axon initial segment of pyramidal cells. Their local axonal clusters are formed by high-frequency branching at shallow angles, often ramifying around, above or below their somata with a high bouton density. The characteristic terminal portions of the axon form short vertical rows of boutons, resembling the candlesticks and candles of a chandelier. Chandelier cells can be multipolar or bitufted." "ILX:0777213" + "A cell that is part of the nervous system." "FMA:70333 CALOHA:TS-2040" + + "A transition where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell." + "The series of events involved in the perception of gravity in which a sensory mechanical stimulus is received and converted into a molecular signal." + "Any process that modulates the frequency, rate or extent of myotube differentiation. Myotube differentiation is the process in which a relatively unspecialized cell acquires specialized features of a myotube cell. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse." + "Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a entire pharyngeal arch associated mesenchyme." + "A protein that is a translation product of the human CD14 gene or a 1:1 ortholog thereof." "PIRSF:PIRSF002017" + "A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells." "BTO:0000801 FMA:63261 FMA:83585 MESH:D008264 CALOHA:TS-0587" + "A meninx that is part of a diencephalon [Automatically generated definition]." "MA:0000826 EHDAA2:0000399 VHOG:0000009 EHDAA:5458 EMAPA:17764" + "Any small, fluid-filled, spherical organelle enclosed by membrane." "Wikipedia:Vesicle_(biology) NIF_Subcellular:sao221389602" + "An IgG-negative double negative memory B cell is a double negative memory B cell with the phenotype IgG-negative, IgD-negative, and CD27-negative." + "The lower segment of the trunk, inferioposterior to the abdomen proper, in the transition area between the trunk and the lower limbs." "EMAPA:35931 GAID:87 CALOHA:TS-2227 galen:Pelvis Wikipedia:Pelvis UMLS:C0030797 NCIT:C12767 EFO:0002805 EV:0100012 FMA:9578 MESH:D010388 SCTID:229765004 BTO:0001006 MA:0000030" + "Any process in an organism in which a relatively long-lasting adaptive behavioral change occurs in response to (repeated) exposure to an olfactory cue." + "A neuromere that is part of the presumptive forebrain." "FMA:61996" + "A bone marrow proteoglycan that is encoded in the genome of human." "UniProtKB:P13727" + + "A cellular process in which two or more cells combine together, their plasma membrane fusing, producing a single cell. In some cases, nuclei fuse, producing a polyploid cell, while in other cases, nuclei remain separate, producing a syncytium." + "Any process that activates or increases the frequency, rate or extent of an iron transmembrane transporter activity." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of bile acids." + "The chemical reactions and pathways resulting in the formation of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically." + "Any process that modulates the frequency, rate or extent of GABAergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter gamma-aminobutyric acid (GABA)." + "An anatomical space that is enclosed by a terminal part of digestive tract." + "An artery that supplies blood to the urinary bladder." "SCTID:244307000 MA:0002078 EMAPA:37131" + "An insulin family protein that is a translation product of the human INS gene or a 1:1 ortholog thereof." + "Obsolete. Use PO:0000352 from Plant Ontology instead. Cell containing glucosinolates ('mustard oil glucosides') and myrosinases, enzymes hydrolyzing the glucosinolates. Occurs in eleven dicotyledon families, the two largest of which are the Brassicaceae and Euphorbiaceae." + "A spiral ganglion neuron that innervates outer hair cells. Type 1 spiral ganglion neurons are unmyelinated and unipolar." + "Any process that activates or increases the frequency, rate or extent of T cell death by apoptotic process." + "A protein that is a translation product of the human IL7R gene or a 1:1 ortholog thereof." "PIRSF:PIRSF001960 IUPHARobj:1698" + "An animal cell that is part of a hair follicle." + + "A vertebral endochondral element in the cervical region of the vertebral column." + "A reproductive process that is a step in the formation and maturation of an ovum or female gamete from a primordial female germ cell." + "The section of the renal tubule in the kidney medulla with a hairpin bend; consists of a descending limb and an ascending limb, and is situated between the proximal convoluted tubule to the distal convoluted tubule; it functions to reabsorb water and ions from the urine." "MESH:D008138 MA:0001675 EV:0100390 VHOG:0001270 SCTID:361335009 UMLS:C0023986 EMAPA:19280 BTO:0004608 NCIT:C33006 FMA:17698 GAID:437 Wikipedia:Loop_of_Henle" + "Any process that modulates the rate, frequency, or extent of the process in which a chondroblast acquires specialized structural and/or functional features of a chondrocyte that will contribute to the development of a bone. A chondrocyte is a polymorphic cell that forms cartilage." + + "A thymic epithelial cell that has an eccentric, round, or irregularly shaped hetero or euchromatic nucleus. The hallmark of this cell type is the presence of vacuoles, which are clustered in one area of the cytoplasm in the vicinity of the nucleus. The vacuoles are small and acquire a grape-like form, occasionally showing delicate internal microvillous projections." "FMA:72214" + "Combining with calcitonin and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex." + "A ligament that does not connect two skeletal elements." "MA:0003004 FMA:25625 SCTID:410746001" + "The developmental process by which male germ line stem cells self renew or give rise to successive cell types resulting in the development of a spermatozoa." "Wikipedia:Spermatogenesis" + "Any process that activates or increases the frequency, rate or extent of skeletal muscle satellite cell proliferation." + "Presumptive structure of the blastula that will develop into ectoderm." "EFO:0003466 AAO:0000470 TAO:0001376 ZFA:0001376 XAO:0004132" + "The process in which the anatomical structures of a cell projection are generated and organized." + "A portion of organism substance that secreted_by a respiratory system." "NCIT:C13722 EMAPA:36550 MA:0002533 UMLS:C1514899" + "A first transient wave of blood cell production that, in vertebrates, gives rise to erythrocytes (red blood cells) and myeloid cells." + "The multiplication or reproduction of glial cells by cell division, resulting in the expansion of their population. Glial cells exist throughout the nervous system, and include Schwann cells, astrocytes, and oligodendrocytes among others." + "Mesenchyme that develops_from a neural crest and is part of a maxillary process mesenchyme." "EHDAA2:0004601" + "The type of heart connective tissue found in the endocardial layer that consists mainly of elastic fibers." "MA:0002858" + "An orbitosphenoid endochondral element that is composed primarily of cartilage tissue." "EHDAA2:0001329 EHDAA:9554" + "The removal of tubulin heterodimers from one or both ends of a cytoplasmic microtubule." + "The subclavian artery that supplies the right pectoral appendage." "SCTID:244246000 NCIT:C33490 MA:0002047 EHDAA2:0004514 Wikipedia:Subclavian_artery EMAPA:37384 FMA:3953 UMLS:C0226261" + "A T-cell surface glycoprotein CD1 that is encoded in the genome of human." "MRO:0000634" + "Any process that modulates the frequency, rate or extent of blood circulation." + "A stem cell of embryonic origin." "MESH:D053595 CALOHA:TS-0263 BTO:0001086 FMA:82841" + "A sialic acid-binding Ig-like lectin 5 that is encoded in the genome of human." "UniProtKB:O15389" + "A class switched memory B cell that lacks IgG on the cell surface." + + "A submucosa that is part of an appendix [Automatically generated definition]." "FMA:14992 SCTID:86833001" + "A thick plate of mesodermal tissue that occupies the space between the thoracic cavity and yolk stalk in the early embryo, forming a transverse partition partially separating the coelomic cavity into thoracic and abdominal portions. It gives rise to the central tendon of the diaphragm[VHOG]." "Wikipedia:Septum_transversum FMA:295593 SCTID:308819008 VHOG:0000019 UMLS:C0231004 NCIT:C34296 EMAPA:16318 EHDAA:736 EHDAA2:0001829" + "Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule." + "FMA:83912" + "An interleukin-17 receptor B that is encoded in the genome of mouse." "UniProtKB:Q9JIP3" + "The series of events involved in the perception of pain in which a mechanical stimulus is received and converted into a molecular signal." + "The subscapular artery, the largest branch of the axillary artery, arises at the lower border of the Subscapularis, which it follows to the inferior angle of the scapula, where it anastomoses with the lateral thoracic and intercostal arteries and with the descending branch of the transverse cervical, and ends in the neighboring muscles. About 4 cm. from its origin it gives off two branches, first the scapular circumflex artery and then the thoracodorsal artery. [WP,unvetted]." "MA:0002050 Wikipedia:Subscapular_artery FMA:22677 SCTID:244311006 EMAPA:37116 UMLS:C0226422 NCIT:C33650" + "The middle layer of the aorta wall, containing the smooth muscle layer and elastic fibers." "SCTID:48467007 FMA:74433 MA:0002903 EMAPA:35138" + "Small finger-like extension of a Schwann cell that contacts the nodal membrane." "NIF_Subcellular:sao1890444066" + "A cranial nerve nucleus that is associated with a vagus nerve." "FMA:54573 SCTID:362467005" + "The chemical reactions and pathways resulting in the formation of glycine, aminoethanoic acid." "MetaCyc:GLYCINE-SYN2-PWY" + "The regulated release of proinsulin from secretory granules accompanied by cleavage of proinsulin to form mature insulin. In vertebrates, insulin is secreted from B granules in the B cells of the vertebrate pancreas and from insulin-producing cells in insects." + + "Any process that activates or increases the frequency, rate or extent of alpha-beta T cell activation." + "Any process that activates or increases the frequency, rate or extent of enzymatic generation of superoxide by a cell." + + "Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers." "FMA:82482 galen:Wall" + "Vascular layer containing connective tissue, of the eye lying between the retina and the sclera. The choroid provides oxygen and nourishment to the outer layers of the retina. Along with the ciliary body and iris, the choroid forms the uveal tract[WP]." "EMAPA:19077 MESH:D002829 VHOG:0001568 UMLS:C0008520 GAID:913 CALOHA:TS-2054 EV:0100347 ZFA:0005229 MA:0000263 NCIT:C12344 TAO:0005229 FMA:58298 SCTID:181172003 BTO:0001829 Wikipedia:Choroid" + "Region of ovarian follicle filled with follicular fluid." "EMAPA:37867 Wikipedia:Follicular_antrum FMA:18675" + "Any of the mucous, serous, or mixed glands that empty their secretions onto the surface of the tongue." "EMAPA:25097" + "Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in an atrioventricular node myocyte. This typically occurs via modulation of the activity or expression of voltage-gated ion channels." + "A low affinity immunoglobulin epsilon Fc receptor that is encoded in the genome of human." "UniProtKB:P06734 Reactome:R-HSA-2127280" + "The progression of a muscle structure over time, from its formation to its mature state. Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms." + "The chemical reactions and pathways resulting in the breakdown of melatonin (N-acetyl-5-methoxytryptamine)." + "The process in which a relatively unspecialized cell acquires specialized features of an interstitial cell of Cajal. An interstitial cell of Cajal is an intestinal neuroepithelial cell that serves as a pacemaker to trigger gut contraction." + "The synthesis or release of a cytokine following a inflammatory stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels." + "An enclosed, cable-like bundle of axons in the peripheral nervous system originating in a nerve root in the central nervous system (or a condensed nervous structure) connecting with peripheral structures." "EV:0100371 SCTID:244457007 NCIT:C12466 MA:0000217 EMAPA:32808 TAO:0007009 EHDAA:3776 EHDAA:4657 MESH:D010525 BIRNLEX:1615 NCIT:C12768 NLX:147826 FMA:65132 XAO:0003047 FMA:65239 SCTID:256864008 BSA:0000098 GAID:747 MA:0000228 BTO:0001027 BAMS:n EMAPA:32815 XAO:0000204 EHDAA:2851 GAID:758 EHDAA2:0003137 AEO:0000137 Wikipedia:Nervous_system UMLS:C0031119 galen:Nerve VHOG:0000901 BTO:0000925 UMLS:C0027740 ZFA:0007009 CALOHA:TS-0772 AAO:0011070" + "The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates." "EFO:0000832 MESH:D012160 BAMS:R EMAPA:17168 BTO:0001175 FMA:58301 AAO:0010352 MBA:304325711 TAO:0000152 GAID:755 UMLS:C0035298 EV:0100348 NCIT:C12343 XAO:0000009 NIFSTD_RETIRED:birnlex_1156 MIAA:0000142 EHDAA2:0001627 ZFA:0000152 CALOHA:TS-0865 UMLS:C1278894 neuronames:1862 SCTID:181171005 EHDAA:4757 Wikipedia:Retina MA:0000276 MAT:0000142 BIRNLEX:1153 VHOG:0000229" + "The formation of bone or of a bony substance, or the conversion of fibrous tissue or of cartilage into bone or a bony substance." "Wikipedia:Ossification" + "A protein that is a translation product of the human TFRC gene or a 1:1 ortholog thereof." + "Any process that stops, prevents or reduces the frequency, rate or extent of bone development." + "Any cell in the compound eye, a light sensing organ composed of ommatidia." "PMID:12021768 GOC:pr" + "The process aimed at the progression of a neural crest cell over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell." + "FMA:83520" + "Any process that activates or increases the frequency, rate or extent of the directed movement of substances within cells." + "A short lived plasma cell that secretes IgE." + "Any process that activates or increases the frequency, rate or extent of fertilization." + "Any process that stops, prevents or reduces the frequency, rate or extent of cytokine production involved in inflammatory response." + "A cerebral hemisphere that is in the right side of a brain." "SCTID:362322002 BIRNLEX:1797 UMLS:C0228175 NCIT:C33472 FMA:67292" + "Any of the veins that carries deoxygenated blood from a part of the body into the right atrium of the heart." "AAO:0010215 UMLS:C0042460 FMA:321896 MA:0000068 BTO:0001438 NCIT:C12817 SCTID:244405007 EMAPA:18415 Wikipedia:Venae_cavae GAID:547 MESH:D014684" + "An anatomical space that surrounded_by a open tracheal system trachea." + "An anatomical system that eliminates waste products that arise as a result of metabolic activity." + "The process whose specific outcome is the progression of the distal convoluted tubule over time, from its formation to the mature structure. The distal convoluted tubule is the first segment of the nephron lying just downstream from the loop of Henle, immediately after the macula densa. Among other functions, in humans it is responsible for the reabsorption of about 5% of filtered sodium via the thiazide-sensitive Na-Cl symporter." + "Missing definition for term UBERON:0008921. Please replace it using linked reference." + "A type of monocyte characterized by low expression of CCR2, low responsiveness to monocyte chemoattractant CCL2/MCP1, low phagocytic activity, and decrease size relative to classical monocytes, but increased co-stimulatory activity. May also play a role in tissue repair." + "Any process that stops, prevents, or reduces the frequency, rate or extent of oligodendrocyte differentiation." + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and the processes involved in the liberation of energy from these substances." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of tolerance induction." + "A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Form the myelin insulation of nervous pathways, guide neuronal migration during development, and exchange metabolites with neurons. Neuroglia have high-affinity transmitter uptake systems, voltage-dependent and transmitter-gated ion channels, and can release transmitters, but their role in signaling (as in many other functions) is unclear." + + "A neuron that laterally connects other neurons in the inner nuclear layer of the retina." "BTO:0004120" + "A cell that anchors the cell body of a scolopidial neuron to the integument." "FBbt:00005221" + "The attachment of one cell to another cell via adhesion molecules." + "Any process that stops, prevents or reduces the frequency, rate or extent of monocyte activation." + "A type I vestibular sensory cell that is part of the epithelium of macula of utricle of membranous labyrinth." "FMA:263188" + "The metanephric glomerular mesangium is the thin membrane connective tissue composed of mesangial cells in the metanephros, which helps to support the capillary loops in a renal glomerulus[GO]." + "Any process that modulates the frequency, rate or extent of melanosome transport." + "A limbic lobe that is part of a left cerebral hemisphere." "FMA:72981 BIRNLEX:1780" + "The process in which a relatively unspecialized cell acquires specialized features of a tongue muscle cell." + "Nucleus containing parasympathetic neurons giving rise to the parasympathetic division of the facial nerve, innervating the salivary glands (Brodal, Neurological Anatomy, 3rd ed., 1981, pg 703)." "BAMS:SuS SCTID:369028007 MBA:462 EHDAA2:0004646 BIRNLEX:1131 UMLS:C0175447 BAMS:SSN neuronames:590 HBA:9194 DHBA:12435 MA:0001027 FMA:72482 EMAPA:37756 Wikipedia:Superior_salivatory_nucleus" + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells." + + "Any process that modulates the frequency, rate or extent of mesenchymal cell proliferation involved in lung development." + "The process whose specific outcome is the progression of the ureter over time, from its formation to the mature structure. The ureter is a muscular tube that transports urine from the kidney to the urinary bladder or from the Malpighian tubule to the hindgut." + "Any process that stops, prevents or reduces the frequency, rate or extent of respiratory gaseous exchange." + "A neural nucleus that is part of the brain." "SCTID:426465002 NCIT:C49346 EMAPA:35185 FMA:83840 UMLS:C1706993 MA:0000811 ZFA:0005575" + "MIAA:0000204 MAT:0000204" + "The process whose specific outcome is the progression of the mesonephric nephron epithelium over time, from its formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure. The mesonephric nephron epithelium is a tissue that covers the surface of a nephron in the mesonephros." + "Serous membrane which is divided into parietal and visceral serous pericardium." "Wikipedia:Serous_pericardium EMAPA:19030 SCTID:243954002 MA:0002739 FMA:9582" + "A mono-stratified retinal ganglion cell that has a large dendritic field and a sparse dendritic arbor with post synaptic terminals in sublaminar layer S4." + "An unstimulated network of follicular dendritic cells and small resting B cells in the lymph node cortex." "EMAPA:35530 MA:0000743 FMA:312350" + "Any process that modulates the frequency, rate or extent of natural killer cell differentiation as part of an immune response." + "Any process that modulates the frequency, rate or extent of the directed movement of RNA from the nucleus to the cytoplasm." + "A structural cell that is part of optic choroid." + "An epithelium that is part of a nasopharynx [Automatically generated definition]." "VHOG:0001038 CALOHA:TS-0662 EMAPA:17672 BTO:0004480 MA:0001865 NCIT:C49263 EHDAA2:0001241 UMLS:C1179157 FMA:62452 EHDAA:7090" + "An anatomical wall that is part of a uterus [Automatically generated definition]." "BTO:0003083 FMA:17560 SCTID:245485002" + "Any process that modulates the frequency, rate or extent of germ cell proliferation." + + "The area of the white pulp where the affinity maturation of B cells and the generation of memory B cells and plasma cells occur." "NCIT:C33602 EMAPA:35804 SCTID:35845000 MA:0002672 UMLS:C1519475" + "The process in which a solute is transported from one side of the vacuolar membrane to the other." + "Cell of the intestinal epithelium with a brush border made up of many parallel packed microvilli; associated with absorption, particularly of macromolecules." + "Any process that increases the rate, frequency, or extent of the process in which a highly ordered sequence of patterning events generates the branched structures of the lung, consisting of reiterated combinations of bud outgrowth, elongation, and dichotomous subdivision of terminal units." + "A cell in the hilum of the ovary that produces androgens." "FMA:18710" + "A vein that is part of a thorax [Automatically generated definition]." "EMAPA:37197 MA:0002235 UMLS:C0226629 NCIT:C53142 SCTID:281472008" + "The process whose specific outcome is the progression of the parathyroid gland over time, from its formation to the mature structure. The parathyroid gland is an organ specialised for secretion of parathyroid hormone." + "A muscle cell that is part of the atrioventricular node." "FMA:67106" + "A smooth muscle cell of the coronary artery." + "Any process that modulates the frequency, rate or extent of mast cell proliferation." + "A lung resident memory CD8-positive, alpha-beta T cell that is CD103-positive." + "Any process that modulates the frequency, rate or extent of extracellular matrix organization." + "A blood vessel that drains from from an eyelid." "SCTID:152208004 FMA:51997" + "Any process that modulates the frequency, rate or extent of zygospore formation, a process in which a thick-walled spore of some algae and fungi is formed by union of two similar sexual cells, usually serves as a resting spore, and produces the sporophytic phase." + "Any process that modulates the rate, frequency or extent of granulocyte chemotaxis. Granulocyte chemotaxis is the movement of a granulocyte in response to an external stimulus." + "Anlagen are populations of contiguous cells, typically arranged in one plane, that are morphologically indistinct, but that already correspond in extent to a later organ/tissue." "EHDAA2:0003170 AEO:0000170 EFO:0001649 Wikipedia:Anlage_(biology)" + "An amacrine cell with a wide dendritic field, dendrites in S4, and post-synaptic terminals in S4." + "A secondary neuron (sensu Teleostei) that has a motor function." + "The multiplication or reproduction of cells, resulting in the expansion of a cell population in the hindbrain." + "The process whose specific outcome is the progression of an osteoblast over time, from its formation to the mature structure. Osteoblast development does not include the steps involved in committing a cranial neural crest cell or an osteoprogenitor cell to an osteoblast fate. An osteoblast is a cell that gives rise to bone." + "The directed movement of calcium ion into a cytosol." + "The breakdown of the nucleus into small membrane-bounded compartments, or blebs, each of which contain compacted DNA." + "A flattened epithelial cell of mesenchymal origin that lines the serous cavity." "FMA:66773" + "Any process that stops, prevents or reduces the frequency, rate or extent of gastric mucosal blood circulation." + "One of the cartilaginous structures surrounding the embryonic spinal cord, formed by the dorsal growth of the dorsolateral arcualia; it is the primordium of the vertebral arch." "BTO:0001763" + + "A tissue-resident macrophage of the reticuloendothelial system found on the luminal surface of the hepatic sinusoids involved in erythrocyte clearance. Markers include F4/80+, CD11b-low, CD68-positive, sialoadhesin-positive, CD163/SRCR-positive. Irregular, with long processes including lamellipodia extending into the sinusoid lumen, have flattened nucleus with cytoplasm containing characteristic invaginations of the plasma membrane (vermiform bodies); lie within the sinusoid lumen attached to the endothelial surface; derived from the bone marrow, form a major part of the body's mononuclear phagocyte system." "BTO:0000685 FMA:14656" + "The directed movement of a protein to a specific location in an euchromatin." + "Any process that modulates the frequency, rate or extent of macrophage apoptotic process." + "Any process that activates or increases the frequency, rate or extent of apoptotic DNA fragmentation." + "Polarization of the oocyte along its anterior-posterior axis. An example of this is found in Drosophila melanogaster." + "GC_ID:1" + "Any process that modulates the frequency, rate or extent of epithelial cell proliferation." + "The process in which immunoglobulin genes are formed through recombination of the germline genetic elements, also known as immunoglobulin gene segments, within a single locus following the induction of and contributing to an immune response." + "A naive B cell is a mature B cell that has the phenotype surface IgD-positive, surface IgM-positive, CD20-positive, CD27-negative and that has not yet been activated by antigen in the periphery." + "A optical quality inhering in a bearer by virtue of the bearer's lacking opacity." + "A structure embedded in the superior olivary complex that is driven by input pathways from the octopus cells in the cochlear nucleus and the neurons of the medial nucleus of the trapezoid body." + "Any process that stops, prevents or reduces the frequency, rate or extent of eosinophil activation." + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of lipids." + "A long, spindle-shaped supporting cells arranged in parallel rows that secretes components of the tectorial membrane and potassium ions into the endolymph." "FMA:79797" + "A mono-stratified retinal ganglion cell that has a large dendritic field, a medium dendritic arbor, and a long secondary dendrite shaft with post synaptic terminals in sublaminar layer S4." "https://orcid.org/0000-0001-7258-9596 https://orcid.org/0000-0002-5260-9315" + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell." + "Any process that modulates the frequency, rate or extent of the growth of the imaginal disc." + "A skeletal element that is part of a limb and composed of cartilage tissue." + "A gland that is part of a eye. The eye is a compound unit which depending on the species may consist of an eyeballs plus associated ducts and integumentary structures. Eye glands therefore include the various types of lacrimal gland, the various types of apocrine and sebaceous glands associated with the eyelid." "MA:0000267 EMAPA:35334" + "Any process that stops, prevents, or reduces the frequency, rate or extent of angiogenesis." + "A glutamatergic motor neuron with a soma in the brainstem or cerebral cortex. They do not synapse directly to muscles but rather to lower motor neurons, which do. They are the main controllers of voluntary movement." + "A serous secreting cell that is part of the epithelium of bronchus." "FMA:263080" + "Any process that modulates the frequency, rate or extent of cell proliferation involved in heart morphogenesis." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an abiotic (not derived from living organisms) stimulus." + "A langerin-negative lymph node dendritic cell that is CD103-negative and CD11b-low." + "A monostratified retinal ganglion cell that has post synaptic terminals in sublaminar layer S4 and is depolarized by illumination of its receptive field center." + "The assembly of a cilium, a specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface. Each cilium is bounded by an extrusion of the cytoplasmic membrane, and contains a regular longitudinal array of microtubules, anchored basally in a centriole." "Reactome:R-HSA-5617833.2" + "A double-positive thymocyte that is large (i.e. has a high forward scatter signal in flow cytometry) and is actively proliferating." + "FMA:85375" + "Any process that increases the rate, frequency, or extent of a response to cytokine stimulus." + "Any process that modulates the frequency, rate or extent of monocyte differentiation." + "Any process in which a protein is maintained in a location and prevented from moving elsewhere. These include sequestration, stabilization to prevent transport elsewhere and the active retrieval of proteins that do move away." + "SCTID:304404008 FMA:12241" + "The process in which immune receptor V, D, and J, or V and J gene segments, depending on the specific receptor, are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS)." "Wikipedia:V(D)J_recombination" + "The process whose specific outcome is the progression of the glomerular mesangium over time, from its formation to the mature structure. The glomerular mesangium is the thin membrane connective tissue composed of mesangial cells, which helps to support the capillary loops in a renal glomerulus." + "Any apoptotic process in a glial cell, a non-neuronal cell of the nervous system." + "Any process, acting in the presynapse that results in modulation of chemical synaptic transmission." + "A collagen alpha-1(I) chain that has been processed by proteolytic cleavage." + "Olfactory epithelial support cell is a columnar cell that extends from the epithelial free margin to the basement membrane of the olfactory epithelium. This cell type has a large, vertically, elongate, euchromatic nucleus, along with other nuclei, forms a layer superficial to the cell body of the receptor cell; sends long somewhat irregular microvilli into the mucus layer; at the base, with expanded end-feet containing numerous lamellated dense bodies resembling lipofuscin of neurons." "FMA:62302" + "An pulmonary artery endothelium is an epithelium that lines the pulmonary artery[GO]." "BTO:0000137" + "A smooth muscle cell of the intestine." + + "The developmental process in which a ventricular septum is generated and organized. A ventricular septum is an anatomical structure that separates the lower chambers (ventricles) of the heart from one another." + "Luminal space of the left atrium of the heart." "FMA:9465 EMAPA:26011" + "An early growth response protein 2 that is encoded in the genome of human." "Reactome:R-HSA-977385 UniProtKB:P11161" + "The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide." "Wikipedia:Phosphorylation" + "A keratinocyte of the epidermis that is characterized by containing granules of keratohyalin and lamellar granules." "FMA:70543" + "A vein that drains a lip." "SCTID:367664002" + "The part of the future brain that is derived from the mantle layer of the neural tube." "EMAPA:32680 MA:0000812 DHBA:10508" + "Obsolete. Use PO:0000273 from Plant Ontology instead. A cell composing the xylem." + "The cervical nerves are the spinal nerves from the cervical vertebrae. Although there are seven cervical vertebrae (C1-C7), there are eight cervical nerves (C1-C8). All nerves except C8 emerge above their corresponding vertebrae, while the C8 nerve emerges below the C7 vertebra. (In the other portions of the spine, the nerve emerges below the vertebra with the same name. Dorsal (posterior) distribution includes the greater occipital (C2) and third occipital (C3). Ventral (anterior) distribution includes the cervical plexus (C1-C4) and brachial plexus (C5-C8) [WP,unvetted]." "FMA:5859 UMLS:C0228815 SCTID:360497008 NCIT:C32299 Wikipedia:Cervical_nerves NLXANAT:20090207 BAMS:cern neuronames:2351" + "Any process that modulates the frequency, rate or extent of lymphocyte differentiation." + "An immunoglobulin-like complex that is present in at least the plasma membrane of pre-B cells, and that is composed of two identical immunoglobulin heavy chains and two surrogate light chains, each composed of the lambda-5 and VpreB proteins, and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins." + "The cell cycle process in which sister chromatids are organized and then physically separated and randomly apportioned to two sets during the second division of the meiotic cell cycle." + "The chemical reactions and pathways resulting in the formation of glycoproteins, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide." + "Catalysis of the hydrolysis of ester linkages within nucleic acids." + "Any of the striated muscles that move the eye and include: superior rectus, inferior rectus, medial rectus, lateral rectus, superior oblique, inferior oblique, retractor bulbi." "MA:0001268 EMAPA:18807" + "The progression of a nephron tubule over time, from its initial formation to the mature structure. A nephron tubule is an epithelial tube that is part of the nephron, the functional part of the kidney." + "An enteroendocrine cell commonest in the duodenum and jejunum, rare in ileum, that secretes cholecystokinin. This cell type is involved in the regulation of digestive enzymes and bile." "FMA:62937" + "Any process that modulates the frequency, rate or extent of pronephric nephron tubule development." + "Any process that modulates the frequency, rate or extent of cardiac muscle contraction by changing the calcium ion signals that trigger contraction." + "A CD4-positive, CD25-positive, alpha-beta T cell that regulates overall immune responses as well as the responses of other T cell subsets through direct cell-cell contact and cytokine release." + "An epithelial tube that will give rise to the mature heart." "ZFA:0000360 AAO:0010411 TAO:0000360 NCIT:C34161 EMAPA:32685 XAO:0000337 EFO:0003526" + "Any process that modulates the frequency, rate or extent of blood vessel endothelial cell differentiation." + "The directed movement of a T-helper 1 cell in response to an external stimulus." + "The anterior segment of the lamellated connective tissue layer of the cornea." "EMAPA:37414" + "An alpha-beta CD8 T cell that resides in the lung." + "The primordial mouth region of the developing head." "FMA:293105" + "Any process that modulates the frequency, rate or extent of mesenchymal cell proliferation that contributes to the progression of the ureter gland over time. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets." + "The chemical reactions and pathways resulting in the breakdown of an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group." + "A quality inhering in a bearer by virtue of the bearer's lacking complete growth, differentiation, or development." + "Any process that activates or increases the frequency, rate, or extent of antigen processing and presentation of peptide antigen via MHC class II." + "A cartilage element that is part of a respiratory system [Automatically generated definition]." "EMAPA:18694 MA:0001818" + "A fold of peritoneum originating at the stomach and supporting the viscera." "UMLS:C0028977 EV:0100084 CALOHA:TS-2004 FMA:14650 SCTID:362710002 MESH:D009852 NCIT:C33209 galen:Omentum GAID:23" + "Periosteum that is part of a skull." "FMA:76623" + "Any process that stops, prevents or reduces the frequency, rate or extent of glycine secretion, neurotransmission." + "A sulcus limitans of neural tube that is part of a future spinal cord." "VHOG:0001548 EHDAA2:0001265 EMAPA:17584" + "A reflex that occurs in response to suckling, beginning with a nerve impulse from a receptor in the mammary gland and ending with the ejection of milk from the gland. Signaling never reaches a level of consciousness." + + "OBSOLETE: A cell of the lymphoid series that can react with antigen to produce specific cell products called antibodies. Various cell subpopulations, often B cells, can be defined, based on the different classes of immunoglobulins that they synthesize." + "A mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns." "FBbt:00005074 BTO:0000902 WBbt:0003675 BTO:0000888 CALOHA:TS-2032 FMA:67328" + "A retinal cell that is immature or undifferentiated." + "The process in which a relatively unspecialized cell acquires specialized structural and/or functional features of an ionocyte. Ionocytes are specialized epithelial cells that contribute to osmotic homeostasis." + "A delimited region of dense mesenchyme within looser mesenchyme." "EHDAA:8979 EHDAA2_RETIRED:0003148 AEO:0000148" + "One of the skeletal muscles of the head and neck, spine, and ribs." "MA:0003153 RETIRED_EHDAA2:0000160 EMAPA:18167 TAO:0001954 EHDAA:5982" + "Any process that modulates the frequency, rate, or extent of antimicrobial peptide secretion." + "A lower motor neuron that innervates only intrafusal muscle fibers. Unlike the alpha motor neurons, gamma motor neurons do not directly adjust the lengthening or shortening of muscles but function in adjusting the sensitivity of muscle spindles and in keeping muscle spindles taut, thereby allowing the continued firing of alpha neurons." "SAO:143800623 MESH:D009047 FMA:83660" + "The inner layer of the muscular coat." "FMA:62899 BTO:0005213" + "A pyramidal neuron which has an apical tree which is oriented parallel to the pia. This is unlike typical pyramidal neurons which have its apical dendrite aligned vertically." + "A serous membrane that is part of a small intestine [Automatically generated definition]." "MA:0001558 FMA:14938 SCTID:8266009 EMAPA:37561" + "One of sublaminar layers S1, S3, or S4." "CP:0001044" + "The bone forming the forehead and roof of the eye orbit." "FMA:52734 Wikipedia:Frontal_bone EMAPA:19016 MA:0001466 UMLS:C0016732 SCTID:181793006 VSAO:0000208 MESH:D005624 AAO:0000206 GAID:226 NCIT:C32635" + "A hematopoietic stem cell of the placenta. This cell type is first observed E10.5 This cell type may give rise to fetal liver hematopoietic stem cells." + "Any process that modulates the frequency, rate, or extent of neutrophil chemotaxis. Neutrophil chemotaxis is the directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding." + "An epithelial cell of the kidney." "KUPO:0001019" + "A portion of smooth muscle tissue that is part of an iliac vein." + "A part of the epithalamus present in some animal species. The eye may be photoreceptive and is usually associated with the pineal gland, regulating circadian rhythmicity and hormone production for thermoregulation. The parietal eye is a part of the epithalamus, which can be divided into two major parts; the epiphysis (the pineal organ, or pineal gland if mostly endocrine) and the parietal organ (often called the parietal eye, or third eye if it is photoreceptive). It arises as an anterior evagination of the pineal organ or as a separate outgrowth of the roof of the diencephalon. In some species, it protrudes through the skull.[4] The parietal eye uses a different biochemical method of detecting light than rod cells or cone cells in a normal vertebrate eye[WP]." "Wikipedia:Parietal_eye" + "The cochlear nuclei consist of: (a) the dorsal cochlear nucleus, corresponding to the tuberculum acusticum on the dorso-lateral surface of the inferior peduncle; and (b) the ventral or accessory cochlear nucleus, placed between the two divisions of the nerve, on the ventral aspect of the inferior peduncle. [WP,unvetted]." "neuronames:720 BM:Me-Co Wikipedia:Cochlear_nuclei UMLS:C0152411 EV:0100260 FMA:72240 BIRNLEX:1151 DHBA:12437 MBA:607 HBA:9528 BAMS:CN" + + "SCTID:360394002 NCIT:C34268 UMLS:C1514442 BILA:0000084" + "A squamous cell that has keratin in the esophagus." "FMA:86549" + "Any muscle organ that is part of either the head or the neck." "NCIT:C32716 UMLS:C0448281" + "GC_ID:1" + "A smooth muscle cell of the subclavian artery." + "All of the contents of a dendrite, excluding the surrounding plasma membrane." + "A kisspeptin neuron that is located in the dentate gyrus of the hippocampus." + "An epithelium that is part of a rectum [Automatically generated definition]." "FMA:17510 VHOG:0001037 MA:0003219 EHDAA2:0001594 EMAPA:17898 CALOHA:TS-2066" + "The process in which the anatomical structures of cardiac muscle tissue are generated and organized." + "The regulated exocytosis of secretory granules containing preformed mediators such as histamine, serotonin, and neutral proteases by a basophil." + "One of the seven small groups of granule cells in the polymorph layer of the olfactory tubercle and one large group, the insula magna, which lies along the border between septum, nucleus accumbens and nucleus of the diagonal band." "BIRNLEX:1113 HBA:265504792 DHBA:10358 BAMS:ICj BAMS:IClj PBA:10095 Wikipedia:Islands_of_Calleja GAID:632 FMA:61888 neuronames:276 EMAPA:35452 MA:0000977 BAMS:isl BM:Tel-ISC MBA:481 BAMS:ISC UMLS:C0262264 MESH:D020670" + "An preBRC-positive large pre-B-II cell is a large pre-B-II cell that is pre-B cell receptor-positive, composed of surrogate light chain protein (SL), which is composed of VpreB , Lambda 5/14.1, in complex with immunoglobulin mu heavy chain (IgHmu) on the cell surface." + "Any process that modulates the frequency, rate or extent of metanephric S-shaped body morphogenesis." + "A lymphocyte that lacks characteristic T cell, B cell, myeloid cell, and dendritic cell markers, that functions as part of the innate immune response to produce cytokines and other effector responses." + "A goblet cell that is part of the epithelium of large intestine." "FMA:263054" + "Any process that modulates a cellular process that is involved in the progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events." + "Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue." "AEO:0000040 AAO:0010268 EHDAA2:0003040 CARO:0000040 TAO:0000382 FMA:63863 HAO:0000040 XAO:0003162 ZFA:0000382 TGMA:0001841 BILA:0000040" + "Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function." + "An enterocyte that is part of the epithelium proper of jejunum." "FMA:263100" + "The multiplication or reproduction of hemocytes, resulting in the expansion of the cell population. Hemocytes are blood cells associated with a hemocoel (the cavity containing most of the major organs of the arthropod body) which are involved in defense and clotting of hemolymph, but not involved in transport of oxygen." + "An ovary that is part of a right side of organism [Automatically generated definition]." "FMA:7213 MA:0001705 NCIT:C33487 SCTID:280123002 UMLS:C0227873 EMAPA:37367" + "A developmental process involving two tissues in which one tissue (the inducer) produces a signal that directs cell fate commitment of cells in the second tissue (the responder)." + "A bushy cell that receives only few large excitatory endbulb synapses from auditory nerves. Spherical bush cells give excitatory input to the lateral and medial parts of the superior olive." + "A non-neuronal cell that surrounds the neuronal cell bodies of the ganglia." "FMA:54550" + "Skeletal element that forms as a replacement or substitution of another element or tissue." "ZFA:0005624 XAO:0004016 VSAO:0000135" + "A B-cell lymphoma 6 protein that is encoded in the genome of human." "UniProtKB:P41182 Reactome:R-HSA-5223066" + "Outermost layer of cells surrounding the embryo." "EFO:0003425 ZFA:0000086 TAO:0000086" + "Vein that drains left lung and returns blood to the heart." "SCTID:304057004 UMLS:C0226670 MA:0002207 EMAPA:37165 NCIT:C48946" + "Any process that activates or increases the frequency, rate or extent of xanthophore differentiation." + "Innermost region of the mammalian kidney." "CALOHA:TS-0506 FMA:17734 BTO:0001745 MA:0001652 EMAPA:28349" + "A retinal ganglion cell that has a small dendritic field and a medium dendritic arbor with post sympatic terminals in sublaminar layer S3." + "Parietal serous membrane which is part of the pericardium and forms the outer layer of the pericardial sac." "EHDAA:3422 FMA:9870 MA:0000483 EMAPA:19031 VHOG:0000537 Wikipedia:Parietal_pericardium UMLS:C0225969 EHDAA:5378 SCTID:243956000 NCIT:C94500" + "Blood vessels in respiratory skin." + "The autonomic nerve is a small nerve which carries postganglionic sympathetic and parasympathetic neurons from the zygomaticotemporal nerve; a branch of the maxillary nerve, to the lacrimal nerve; a branch of the ophthalmic nerve. These neurons derive from the superior cervical ganglion and the pterygopalatine ganglion respectively. They will travel to the lacrimal gland via the lacrimal nerve. Parasympathetic will induce lacrimation and vice versa." "Wikipedia:Autonomic_nerve SCTID:276145003 EMAPA:37957 MESH:D017776 FMA:5866" + "A protein that is a translation product of the human FCER2 gene or a 1:1 ortholog thereof." "IUPHARobj:2935 PIRSF:PIRSF002426" + "The sclera and cornea form the fibrous tunic of the bulb of the eye; the sclera is opaque, and constitutes the posterior five-sixths of the tunic; the cornea is transparent, and forms the anterior sixth." "SCTID:361318005 Wikipedia:Fibrous_tunic_of_eyeball FMA:58102" + "The process whose specific outcome is the progression of the subpallium over time, from its formation to the mature structure. The subpallium is the base region of the telencephalon." + "A pre-B cell precursor is CD19-low, CD22-positive , CD34-positive, CD38-positive." + "A region of the lens consisting of packed elongated enucleate cells packed with crystallin." "FMA:76827 EHDAA:4745 RETIRED_EHDAA2:0000979 EHDAA:9065 UMLS:C0229224 Wikipedia:Lens_(anatomy)#Lens_fibers VHOG:0000444 NCIT:C32976 XAO:0004096 EMAPA:17841 CALOHA:TS-0544 BTO:0000724 MA:0001304" + "A CNS neuron of the dorsal spinal cord." + "Anatomical system that consists of the glands and parts of glands that produce exocrine secretions and help to integrate and control bodily metabolic activity. Exocrine glands are glands that secrete their products (hormones) into ducts (duct glands). They are the counterparts to endocrine glands, which secrete their products (hormones) directly into the bloodstream (ductless glands) or release hormones (paracrines) that affect only target cells nearby the release site. [Wikipedia]." "CALOHA:TS-2057 MA:0002411 NCIT:C12957 Wikipedia:Exocrine_gland FMA:85539 UMLS:C1516995 WikipediaCategory:Exocrine_system EHDAA2:0002225 EMAPA:35329" + "The behavioral interactions between organisms for the purpose of mating, or sexual reproduction resulting in the formation of zygotes." "Wikipedia:Mating_behaviour" + "A SCO-spondin that is encoded in the genome of human." "UniProtKB:A2VEC9" + "The tibial nerve is a branch of the sciatic nerve. The tibial nerve passes through the popliteal fossa to pass below the arch of soleus. In the popliteal fossa the nerve gives off branches to gastrocnemius, popliteus, soleus and plantaris muscles, an articular branch to the knee joint, and a cutaneous branch that will become the sural nerve. The sural nerve is joined by fibres from the common peroneal nerve and runs down the calf to supply the lateral side of the foot. Below the soleus muscle the nerve lies close to the tibia and supplies the tibialis posterior, the flexor digitorum longus and the flexor hallucis longus. The nerve passes into the foot running posterior to the medial malleolus. Here it is bound down by the flexor retinaculum in company with the posterior tibial artery. [WP,unvetted]." "MA:0001173 MESH:D013979 GAID:854 SCTID:181078002 Wikipedia:Tibial_nerve NCIT:C52809 EMAPA:36512 FMA:19035 UMLS:C0040186" + "The process whose specific outcome is the progression of the digestive tract over time, from its formation to the mature structure. The digestive tract is the anatomical structure through which food passes and is processed." + "A synapse that uses glutamate as a neurotransmitter." + "OBSOLETE: A cell in a tissue that markedly differs in form, size, or contents from other cells in the same tissue." + "Skeletal muscle satellite cell asymmetric division that occurs during a process in which damaged muscle tissue is being rebuilt." + "A zone of skin that is part of a lower leg [Automatically generated definition]." "SCTID:244180007 EMAPA:18156 MA:0000680" + "A process in which a protein is transported to, or maintained in, a location within a Golgi membrane." + "The directed movement of ammonium ions from one side of an epithelium to the other." + "Kidney mesenchyme is the tissue made up of loosely connected mesenchymal cells in the kidney[GO]." + "The group of neurons that serve as the primary processor of visual information received from the retina via the optic tract and send processed information to the visual cortex of the occipital lobe." "MA:0000869 NCIT:C32556 DHBA:10429 EMAPA:35478 neuronames:352 PBA:128013070 SCTID:362377006 UMLS:C0086526 BIRNLEX:1662 EFO:0001988 EV:0100219 Wikipedia:Lateral_geniculate_body BAMS:C.gl. BTO:0004366 BTO:0004367 BAMS:LG FMA:62209" + "A physical, chemical, or biochemical process carried out by living organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism." + "Any process that activates or increases the frequency, rate or extent of R8 cell differentiation." + "An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina." "NCIT:C13191 UMLS:C0004799 AAO:0010596 Wikipedia:Basement_membrane FMA:63872 GAID:915 SCTID:68989006" + "The upper ventral region of the torso of an organism." "SCTID:181131000 MESH:D001940 BTO:0000149 NCIT:C12971 FMA:9601 galen:Breast CALOHA:TS-2083 Wikipedia:Breast EV:0100124 GAID:33 UMLS:C0006141" + "A rounded or elliptical epithelial cell, with pale-staining open face nucleus and pale cytoplasm rich in free ribosomes and clusters of centrioles; form a distinct basal zone spaced slightly from the basal surface of the epithelium." "FMA:67874" + "EMAPA:31862 FMA:296719 EHDAA2:0000474 EMAPA:31863 VHOG:0000616" + "Projection of skin containing the outlets for 15-20 lactiferous ducts arranged cylindrically around the tip." "MESH:D009558 NCIT:C12299 SCTID:265780004 MA:0000796 galen:Nipple EMAPA:36508 Wikipedia:Nipple GAID:35 FMA:67771 CALOHA:TS-2234 UMLS:C0028109 BTO:0000821" + "A lamp5 GABAergic cortical interneuron with layer-adapting morphology. NGC lamp5 cells have a small round soma, short dendrites, and a wide dense axonal arbor that tends to establish a dense axonal mesh with high connection probability both to themselves and L2 pyramidal cells. NGC lamp5 cells have unique synaptic properties that distinguish them from other GABAergic interneurons, including the release of GABA to the extracellular space via volume transmission, and the ability to produce GABA-B responses in connected postsynaptic targets." + "A luminal epithelial cell of the lactiferous duct. This cuboidal epithelial cell expresses keratin-18 and is estrogen-receptor alpha positive." "FMA:74504" + "The process in which the anatomical structure of a cranial ganglion is generated and organized." + "A tuft cell that is a part of the colon." + "Any process that modulates the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient." + "The series of events involved in the perception of pain in which a temperature stimulus is received and converted into a molecular signal." + "Cell condensation that is an aggregation of mesenchymal cells that are committed to differentiate into chondroblasts and chondrocytes." "XAO:0004022 EHDAA2_RETIRED:0003147 VSAO:0000092 AEO:0000147 EMAPA:32731" + "A cardiac chamber surrounds an enclosed cavity within the heart." "SCTID:276456008 FMA:7095" + "A strand of hair that is part of a face." "SCTID:368910000 FMA:54360" + "The terminal part of the large intestine, continuous proximally with the rectum and distally terminates with the anus." "EMAPA:18256 BTO:0001978 NCIT:C12375 UMLS:C0227411 SCTID:245438008 FMA:15703 galen:AnalCanal MA:0000330 CALOHA:TS-2160 Wikipedia:Anal_canal" + "A collection of protruberances derived from pharyngeal arch 1 that develop into the tragus, crus of the helix, and helix." + "Any process that activates or increases the frequency, rate or extent of gastric mucosal blood circulation." + "Mesenchyme that develops_from a neural crest and is part of a mandibular process mesenchyme." "EHDAA2:0004603" + "A lysosome-associated membrane protein that is a translation product of the human CD68 gene or a 1:1 ortholog thereof." + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein at the presynapse." + "Cartilage pertaining to the tibia." "FMA:33923 BTO:0000207" + "A lamina propria that is part of a respiratory system [Automatically generated definition]." "EMAPA:37576 MA:0001821" + "An endothelial cell that is part of the vein." "KUPO:0001099 FMA:62104" + "A ploidy quality inhering in a bearer by virtue of the bearer's containing a single set of homologous chromosomes." + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving RNA." + "An epithelial sac of invaginated ectoderm formed from the otic placode that gives rise to the structures of the inner ear[MP]." "ZFA:0000051 XAO:0000006 BTO:0002661 TAO:0000051 AAO:0011080 UMLS:C1518678 VHOG:0001148 Wikipedia:Otic_vesicle EMAPA:16669 EHDAA2:0001342 NCIT:C34240 FMA:302920 SCTID:308792006" + "Any process that modulates the frequency, rate or extent of postsynapse assembly, the aggregation, arrangement and bonding together of a set of components to form a postsynapse." + "A mucous gland that is part of a larynx [Automatically generated definition]." "EMAPA:37631 MA:0001767" + "Any process that activates or increases the frequency, rate or extent of erythrophore differentiation." + "Any process that activates or increases the frequency, rate or extent of microtubule polymerization." + "A cell secreting sebun, an oily substance secreted by sebaceous glands, composed of keratin, fat, and cellular debris." + "OBSOLETE: A class of lymphocytes characterized by the lack of surface markers specific for either T or B cells." + "The process whose specific outcome is the progression of the facial nucleus over time, from its formation to the mature structure." + "A pore-like structure surrounding the entire circumference of the anterior chamber of the eye through which aqueous humor circulates[MP]." "NCIT:C12803 GAID:897 FMA:77660 Wikipedia:Trabecular_meshwork SCTID:280694002 EFO:0003077 BTO:0001605 MESH:D014129 UMLS:C0040573 CALOHA:TS-1058 EV:0100352 MA:0003086" + "Neuromast that is part of the anterior lateral line. Kimmel et al, 1995. (Also see Anatomical Atlas entry for lateral line by T. Whitfield.)." "ZFA:0001472" + "A differentiated genital tubercle that is part of a female reproductive system." "RETIRED_EHDAA2:0000500 EHDAA:8118 EMAPA:18680 VHOG:0000666" + "Neuron of lateral ventricle." "CALOHA:TS-1261" + "A protein that is a translation product of the human CTLA4 gene or a 1:1 ortholog thereof." "IUPHARobj:2743" + "Any process that stops, prevents or reduces the rate or extent of osteoblast proliferation." + "Part of cerebral hemisphere located on the medial surface, forming a ring around the brain stem." "HBA:4219 UMLS:C0458337 DHBA:12155 BIRNLEX:1128 SCTID:279215006 BAMS:Limbic_lobe FMA:72719 Wikipedia:Limbic_lobe BAMS:LL neuronames:834 CALOHA:TS-2061" + "A natural killer cell receptor 2B4 that is encoded in the genome of human." "UniProtKB:Q9BZW8" + "An endocrine cell that is part of the pancreas." + "GC_ID:1" + "Any process that stops, prevents or reduces the frequency, rate or extent of cellular response to insulin stimulus." + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving glucocorticoids." + "Any process that modulates the frequency, rate or extent of renin secretion into blood stream." + "A kidney cell that is part of an interstitial compartment of an outer renal medulla." "KUPO:0001094" + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the metabolism of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals." + "Any process that mediates the transfer of information from one cell to another and contributes to the progression of the mesonephros over time, from its formation to the mature organ." + "Any process in which a protein is transported to, or maintained at, a part of a chromosome that is organized into chromatin." + "The process in which a relatively unspecialized cell acquires the specialized features of a tendon cell. Tendon cell are elongated fibrocytes in which the cytoplasm is stretched between the collagen fibres of the tendon. Tendon cells have a central cell nucleus with a prominent nucleolus, a well-developed rough endoplasmic reticulum, and are responsible for synthesis and turnover of tendon fibres and ground substance." + "Any process that activates or increases the frequency, rate, or extent of dendritic cell cytokine production." + "An epithelium that is part of a oviduct [Automatically generated definition]." "BTO:0002402 EMAPA:29043 CALOHA:TS-1316 MA:0001718" + "Any process that stops, prevents, or reduces the frequency, rate, or extent of B cell antigen processing and presentation." + "Binding to a T cell receptor, the antigen-recognizing receptor on the surface of T cells." + "A composite structure of the telencephalon that is defined in the striatopallidal system by connectivity and neurochemical staining. It includes the nucleus accumbens, the most ventral portions of the caudate nucleus and the putamen, the rostrolateral portion of the anterior perforated substance, the islands of Calleja and a rostral subcommissural portion of substantia innominata. The boundary between the ventral striatum and dorsal striatum is indistinct in sections stained for Nissl substance (Heimer-1995; adapted from Brain Info)." "MBA:493 DMBA:15858 EMAPA:36576 NLX:57107 BAMS:STRv EFO:0001936 Wikipedia:Ventral_striatum PBA:10091 FMA:77614 BAMS:StrV neuronames:2341 MA:0002972 BAMS:Ventral_striatum BTO:0004702" + "Any process that activates or increases the frequency, rate or extent of phagocytosis." + "A meninx that is part of a hindbrain [Automatically generated definition]." "EHDAA:3688 EHDAA2:0000770 MA:0000987 VHOG:0000011 EMAPA:17783" + + "Any organ component layer that consists of muscle tissue." "NCIT:C75444 FMA:45634 UMLS:C0225358" + "The mucous membrane that lines the nasal cavity[MP]." "EMAPA:36026 GAID:302 FMA:59684 Wikipedia:Mucous_membrane_of_nose CALOHA:TS-0657 SCTID:310211009 BTO:0000912" + "Any process that modulates the frequency, rate or extent of astrocyte chemotaxis." + "Any process that modulates the frequency, rate or extent of cardiac muscle cell contraction." + "Steps required to transform a dense core granule generated at the trans-Golgi network into a fully formed and transmissible dense core granule. Dense core granule maturation proceeds through clathrin-mediated membrane remodeling events and is essential for efficient processing of cargo within dense core granules as well as for removing factors that might otherwise interfere with dense core granule trafficking and exocytosis." + "Any process involved in the maintenance of an internal steady state of monoatomic ions within an organism or cell. Monatomic ions (also called simple ions) are ions consisting of exactly one atom." + "The orderly movement of cells from one site to another in the cerebral cortex." + "Volcano-shaped lateral line sensory organ located in characteristic positions within the skin epithelium and containing hair cells and their support elements." "AAO:0001004 TAO:0000243 EFO:0003513 ZFA:0000243" + "The cellular process that ensures successive accurate and complete genome replication and chromosome segregation." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of calcium ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "The chemical reactions and pathways resulting in the breakdown of glucans, polysaccharides consisting only of glucose residues." + "A myb proto-oncogene protein that is encoded in the genome of mouse." "UniProtKB:P06876" + "A protein c-Fos that is encoded in the genome of human." "Reactome:R-HSA-450216 UniProtKB:P01100" + "A cardiac ventricle that is in the left side of the heart." "BTO:0001629 EMAPA:17337 Wikipedia:Left_ventricle EHDAA2:0002178 galen:LeftVentricle NCIT:C12871 SCTID:244385005 MA:0000092 UMLS:C0225897 CALOHA:TS-0439 VHOG:0000718 FMA:7101" + "Any osteoblast that is part of a femur." + "A delimited region of dense mesenchyme within looser mesenchyme whose cells are committed to become chondroblasts." "EMAPA:32736 AEO:0000150 EHDAA2:0003150" + "Any process that modulates the frequency, rate or extent of border follicle cell migration." + "A physical quality inhering in a bearer by virtue of the bearer's parts having the arrangement which exhibits characteristics of liquids." + "Any process that stops, prevents, or reduces the frequency, rate or extent of melanocyte differentiation." + "Binding to euchromatin, a dispersed and relatively uncompacted form of chromatin." + + "The unique bone located in the glans penis of most mammals except humans; it is used for copulation and varies in size and shape by species." "Wikipedia:Baculum EMAPA:29769 MA:0000406 SCTID:27962002" + "Any process that modulates the frequency, rate or extent of terminal button organization." + "The breakdown of structures such as organelles, proteins, or other macromolecular structures during apoptosis." + "A C-X-C chemokine receptor type 4 that is encoded in the genome of mouse." "UniProtKB:P70658" + "A nephric duct is a tube that drains a primitive kidney[GO]." "Wikipedia:Wolffian_duct EMAPA:16577" + "A submucosa that is part of a colon [Automatically generated definition]." "SCTID:61647009 MA:0003200 FMA:14985 EMAPA:27379" + "A process in which force is generated within striated muscle tissue, resulting in the shortening of the muscle. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. Striated muscle is a type of muscle in which the repeating units (sarcomeres) of the contractile myofibrils are arranged in registry throughout the cell, resulting in transverse or oblique striations observable at the level of the light microscope." + "Any process that modulates the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "A protein that is a translation product of the human LUM gene or a 1:1 ortholog thereof." + "A neoplastic cell that is capable of entering a surrounding tissue" "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12917" + "A cadherin that is a translation product of the human CDH1 gene or a 1:1 ortholog thereof." + "Circulating macrophages and tissue macrophages (alveolar macrophages) of lung." "CALOHA:TS-0576" + "Cranial nerve that branches into the ramus communicans (to the skin), the pretrematic (to the walls of the pharynx and mouth, viscero-sensory fibers), and the larval post-trematic branch (lost in the adult)." "EMAPA:17268 NCIT:C12723 SCTID:362465002 GAID:827 FMA:50870 VHOG:0000701 MA:0001093 ZFA:0000668 EHDAA2:0000709 TAO:0000668 HBA:9334 UMLS:C0017679 neuronames:701 EHDAA:3733 BTO:0004979 MESH:D005930 BAMS:IXn AAO:0010474 MBA:808 BIRNLEX:899 XAO:0003096 UMLS:C1305752 Wikipedia:Glossopharyngeal_nerve BAMS:9n" + "Any process that modulates the frequency, rate or extent of vesicle transport along microtubule." + "Any apoptotic process in a neutrophil, any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes." + "The addition of tubulin heterodimers to one or both ends of a microtubule." + "Any process that modulates the frequency, rate or extent of glutamate secretion, neurotransmission." + "A dorsal horn of spinal cord that is part of a cervical spinal cord." "UMLS:C0228611 BIRNLEX:1673 SCTID:362439001" + "Any process that activates or increases the frequency, rate or extent of embryonic development." + "BILA:0000139" + "Any process that stops, prevents, or reduces the frequency, rate or extent of programmed cell death that occurs in the compound eye retina." + "A subdivision of the digestive tract in humans that includes the rectum, the anal canal and the anus." + "An integrin alpha-X that is encoded in the genome of mouse." "UniProtKB:Q9QXH4" + "The adrenal gland medulla that is in the right side of the abdomen." "FMA:69091" + "Any process that stops, prevents or reduces the frequency, rate or extent of tendon cell differentiation." + "An immune response mediated by cells expressing specific receptors for antigens produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory)." "Wikipedia:Adaptive_immune_system" + "A protein that is a translation product of the human MS4A1 gene or a 1:1 ortholog thereof." "IUPHARobj:2628 PIRSF:PIRSF001995" + "An anatomical wall that lines the insider of a urinary bladder." "EMAPA:35175 MA:0002493 FMA:15902 NCIT:C48941 SCTID:362225003 UMLS:C0458421 BTO:0001462" + "Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures." "CARO:0000005 NCIT:C94478 TGMA:0001825 HAO:0000005 VHOG:0001728 FMA:5897 AEO:0000005 EHDAA2:0003005 TAO:0001668 BILA:0000005 XAO:0003190 AAO:0010110 UMLS:C0524461 ZFA:0001643" + "Any process that activates or increases the frequency, rate or extent of pro-B cell differentiation." + "An artery that supplies the liver." "MA:0001963 GAID:496 BTO:0004307 ZFA:0005161 FMA:14769 SCTID:76015000 NCIT:C32729 TAO:0005161 MESH:D006499 EMAPA:17859 galen:HepaticArtery UMLS:C0019145" + "A protein that is a translation product of the human CD48 gene or a 1:1 ortholog thereof." "PIRSF:PIRSF001973" + + "The controlled release of a fluid by a cell or tissue in an animal." + "Obsolete. Use PO:0000355 from Plant Ontology instead. A fiber like tracheid in the secondary xylem; commonly thick walled, with pointed ends and bordered pits that have lenticular to slit like apertures." + "Any microvascular endothelial cell that is part of a female urethra." + "A concave 3-D shape quality inhering in a bearer by virtue of the bearer's having the shape of a kidney." + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond." + "The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a disseminated nephrocyte. A disseminated nephrocyte is an insect renal cell that filters hemolymph and is found at scattered locations in the fat body or other tissues. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state." + "A major subdivision of an organism that divides an organism along an axis perpedicular to the main body anterior-posterior axis. In vertebrates, this is typically a fin or limb segment. In insects, this includes segments of appendages such as antennae, as well as segments of the insect leg." + "A lymphocyte antigen 75 that is encoded in the genome of mouse." "UniProtKB:Q60767" + "An endoderm that is part of a thymus primordium." + "Any of three grooves in the temporal lobe including the inferior, middle, and superior temporal sulci." "HBA:9377 UMLS:C0459389 NCIT:C33744" + "Any apoptotic process in a myeloid cell, a cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage." + "Mostly cylindrical, resemble Type 1 in their contents and the presence of a kinocilium and stereocilium apically; much greater variation in size, some almost span the entire thickness of the sensory epithelium, while others are smaller than Type 1; receive multiple efferent nerve boutons around their bases as well as afferent endings, which are small expansions rather than chalices." "FMA:67909" + "Mesenchyme that is part of a lateral nasal prominence." "EHDAA2:0000917 FMA:312665 EMAPA:16807" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the covalent alteration of one or more amino acid residues within a protein." + "The part of the arterial system which carries oxygenated blood away from the heart to the body, and returns deoxygenated blood back to the heart." "Wikipedia:Systemic_circulation#Arteries FMA:45623" + "Any process that modulates the frequency, rate or extent of osteoblast proliferation." + "A granulocyte monocyte progenitor is CD34-positive, CD38-positive, IL-3receptor-alpha-positive and is CD45RA-negative." + "Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine." + "Combining with the biogenic amine serotonin and transmitting the signal across the membrane by activating an associated G-protein. Serotonin (5-hydroxytryptamine) is a neurotransmitter and hormone found in vertebrates and invertebrates." "Wikipedia:5-HT_receptor" + "An appendage segment that is part of a limb/fin." + "The biological process whose specific outcome is the progression of lung connective tissue from an initial condition to its mature state. This process begins with the formation of lung connective tissue and ends with the mature structure. The lung connective tissue is a material made up of fibers forming a framework and support structure for the lungs." + "An innate lyphoid cell with an immature phenotype." + "A developmental process, independent of morphogenetic (shape) change, that is required for the medulla oblongata to attain its fully functional state. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate." + "Any process that stops, prevents, or reduces the frequency, rate or extent of neuron maturation." + "A mucus secreting cell of a submucosal gland of the bronchus." + + "Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 6th arch mesenchyme." "EHDAA2:0004078" + "A collection of brainstem nuclei that functions in multiple aspects of hearing and is an important component of the ascending and descending auditory pathways of the auditory system." "HBA:9177 Wikipedia:Superior_olivary_complex VHOG:0001381 UMLS:C0175427 neuronames:569 EV:0100263 MBA:398 MA:0001026 DHBA:12462 BAMS:SOC EMAPA:35840 FMA:72247 BIRNLEX:1307" + "The superior labial artery (superior labial branch of facial artery) is larger and more tortuous than the inferior labial artery. It follows a similar course along the edge of the upper lip, lying between the mucous membrane and the Orbicularis oris, and anastomoses with the artery of the opposite side. It supplies the upper lip, and gives off in its course two or three vessels which ascend to the nose; a septal branch ramifies on the nasal septum as far as the point of the nose, and an alar branch supplies the ala of the nose." "EMAPA:37430 Wikipedia:Superior_labial_artery MA:0001917 SCTID:145137009 FMA:49570" + "Any cytoplasm that is part of a axon." + "Any process that stops, prevents, or reduces the frequency, rate or extent of cardiac muscle growth." + "A subdivision of the autopod consisting of pedal digit plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers." + "The process of synaptic transmission from a neuron to a muscle, across a synapse." + "The developmental process pertaining to the initial formation of the taste bud from unspecified parts. The taste bud is a specialized area of the tongue that contains taste receptors." + "A nerve fiber that is located in the serosa of vermiform appendix." + "Any process that stops, prevents or reduces the frequency, rate or extent of neuron migration." + "An estrogen receptor that is encoded in the genome of mouse." "UniProtKB:P19785" + "Any cellular process that depends upon or alters the microtubule cytoskeleton, that part of the cytoskeleton comprising microtubules and their associated proteins." + "A strand of hair that is part of a manus." + "GC_ID:1" + "Motor neuron that innervate muscles that control eye, jaw, and facial movements of the vertebrate head and parasympathetic neurons that innervate certain glands and organs." "PMID:14699587" + "GC_ID:1" + "An acellular anatomical structure that is the bounding layer of a anatomical structure." "FMA:63871" + "Mucosa-associated lymphoid tissue in digestive tract. includes Peyer's patches, appendix, and solitary lymph nodules[GO]." "NCIT:C12936 MA:0000136 Wikipedia:Gut-associated_lymphoid_tissue UMLS:C0596638 FMA:62820" + "De novo generation of a long process of a neuron, including the terminal branched region. Refers to the morphogenesis or creation of shape or form of the developing axon, which carries efferent (outgoing) action potentials from the cell body towards target cells." + "A distinct juvenile form many animals undergo before metamorphosis into adults. Animals with indirect development such as insects, amphibians, or cnidarians typically have a larval phase of their life cycle." "Wikipedia:Larva HAO:0000459 AEO:0000126 BTO:0000707 TAO:0002048" + "A type II muscle cell that contains large amounts of myoglobin, has many mitochondria and very many blood capillaries. Type II A cells are red, have a very high capacity for generating ATP by oxidative metabolic processes, split ATP at a very rapid rate, have a fast contraction velocity and are resistant to fatigue." "FMA:84415 BTO:0001813" + "A supporting cell that is attached to the basement membrane and forms rows that support the hair cells." "FMA:79800" + "A tubular structure that contains, conveys body fluid, such as blood or lymph." + "A venous system that overlaps a umbilical cord and is part of a entire extraembryonic component." "VHOG:0000282 EHDAA2:0000479 EMAPA:16374" + "A trophoblast cell that invades the maternal spiral arteries and replace the endothelial lining, remodeling the vessels and allowing for adequate blood transport into the placenta. An endovascular extravillous trophoblast cell differentiates from an extravillous trophoblast cell. In humans, this cell can be distinguished by the expression of CD56." + "Any process that stops, prevents, or reduces the frequency, rate or extent of T cell activation." + "A digit that is part of a pes (foot)." "AAO:0000888 MA:0000048 NCIT:C33788 XAO:0003035 EMAPA:32649 SCTID:116667001 UMLS:C0040357 GAID:44 Wikipedia:Toe galen:Toe FMA:25046 BTO:0002348" + "Any process that activates or increases the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor." + + "The cranial ganglion that is associated with and extends fibers into the trigeminal nerve." "MA:0001080 Wikipedia:Trigeminal_ganglion VHOG:0000694 ZFA:0000295 AAO:0011107 EFO:0000903 BAMS:5Gn FMA:52618 MESH:D012668 BAMS:GV XAO:0000427 BTO:0001231 EHDAA:2113 EMAPA:16797 NCIT:C62642 GAID:725 neuronames:1402 TAO:0000295 EHDAA2:0002085 UMLS:C0040995 SCTID:244449009 XAO:0000428 MAT:0000511" + "A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a membrane." + "A bone that is part of the region of the hindlimb that includes the zeugopod and stylopod. Examples: patella, femur, tibia. Counter-examples: any pes phalanx." "MESH:D007867 EMAPA:37304 MA:0000670" + "A nuclear receptor ROR-gamma that is encoded in the genome of mouse." "UniProtKB:P51450" + "The cleavage of a peptide bond in a precursor form of a signaling receptor ligand, resulting in the mature (active) form of the ligand." + "A subdivision of the skeleton of the autopod consisting of the phalanges of manual digit plus the associated metapodial element." + "Any process that decreases the rate or frequency of platelet activation. Platelet activation is a series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue." + "An endothelium that is part of a glomerular capillary." "SCTID:243993006 MA:0001658 NCIT:C32522 UMLS:C0227647" + "The process in which neuroepithelial cells in the ventral neural tube acquire specialized structural and/or functional features of radial glial cells. Radial cell precursors differentiate into both neuronal cell types and mature radial glial cells. Mature radial glial cells regulate the axon growth and pathfinding processes that occur during white matter patterning of the developing spinal cord. Differentiation includes the processes involved in commitment of a cell to a specific fate." + "Any endothelial cell that is part of a spleen." + "CD4-positive, alpha-beta T cell with the phenotype RORgamma-t-positive, CXCR3-negative, CCR6-positive, and capable of producing IL-17." "MESH:D058504" + "Any process that modulates the frequency, rate or extent of a neurophysiological process, an organ system process carried out by any of the organs or tissues of the nervous system." + "Dense regular connective tissue that connects muscle to bone[VSAO]." "Wikipedia:Tendon EHDAA2:0003091 GAID:276 UMLS:C0039508 MESH:D013710 SCTID:256667004 BTO:0001356 CALOHA:TS-1021 AEO:0000091 NCIT:C13045 MA:0000115 FMA:9721 EV:0100149 EMAPA:35854 ZFA:0005647 XAO:0000173 galen:Tendon VHOG:0001286 VSAO:0000073" + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of glucocorticoids." + "Formation of a small group of cells (pole cells) at the posterior pole of the insect blastula. They are the first cells to cellularize after the arrival of nuclei at the end of the syncytial blastula stage and are the precursors to the insect germ cells." + "A simple columnar epithelium that looks stratified but is not, because its cells are arranged with their nuclei at different levels." "Wikipedia:Pseudostratified_columnar_epithelium NCIT:C33419 UMLS:C1514590 FMA:45572 NCIT:C49316 UMLS:C0836138" + "A protein that has a core domain composition consisting of a Rel homology domain (RHD) (Pfam:PF00554), an IPT/TIG domain (Pfam:PF01833), six copies of the Ankyrin repeat (Pfam:PF00023), a Death domain (Pfam:PF00531) and a C-terminal PEST region." "PIRSF:PIRSF036310" + "An anatomical structure that is undergoing regeneration." "XAO:0004059 TAO:0005147 EHDAA2:0003233 AEO:0000200 ZFA:0005147" + "Any process that activates or increases the frequency, rate or extent of melanosome organization." + "A smooth muscle cell that is part of the duodenum." "FMA:15058" + "A subarachnoid space that is part of a hindbrain [Automatically generated definition]." "VHOG:0001303 EMAPA:18211" + "Any process that increases the rate, frequency or extent of the synthesis or release of any leukotriene following a stimulus as part of an inflammatory response." + + "Any process that modulates the frequency, rate or extent of the developmental process that results in the deposition of coloring matter in an organism." + + "A thymic macrophage found in the thymic medulla." + "Obsolete. Use PO:0004531 from Plant Ontology instead. A cell characterized by conspicuous and rather stable accumulation of starch." + + "An anatomical space that is enclosed by a pleuroperitoneal canal." "EMAPA:25034 EHDAA2:0004736" + "Any process that modulates the rate, frequency or extent of extracellular matrix disassembly. Extracellular matrix disassembly is a process that results in the breakdown of the extracellular matrix." + "The directed movement of a protein to a specific location in a plasma membrane." + "Any process that stops, prevents or reduces the frequency, rate or extent of stem cell population maintenance." + "A differentiated genital tubercle that is part of a male reproductive system." "RETIRED_EHDAA2:0001048 VHOG:0000667 EMAPA:17969 EHDAA:8138" + "A protein complex composed of two identical immunoglobulin heavy chains of the IgD isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgD immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." + "A membrane-spanning 4-domains subfamily A member 1 that is encoded in the genome of human." "UniProtKB:P11836" + "A developing mesenchymal capsule that covers the developing brain and spinal cord and is the precursor of the meningeal cluster. In mammals this gives rise to the arachnoid mater, pia mater and dura mater. In cyclostomes and fishes, the future meninx gives rise to a single meningeal layer, the primitive meninx." "EHDAA2:0004453" + "CD4-positive alpha-beta T cell with regulatory function that produces IL-10." + "A cell found within the adrenal medulla that secrete biogenic amine hormones upon stimulation." "FMA:69262" + "Companion vein of the thoracodorsal artery, draining the apical part of the latissimus dorsi and merging with the circumflex scapular vein to form a subscapular vein." "FMA:71213 EMAPA:37198 MA:0002238" + "Any process that modulates the frequency, rate or extent of sister chromatid segregation." + "Most dorsal part of the thalamus, comprising the pineal gland and habenular nuclei in most vertebrates. In a few vertebrates, it also includes the parietal eye. (Butler and Hodos, Comparative Vertebrate Neuroanatomy, 2nd ed, 2005, pg. 345-346." "BAMS:Epi EV:0100220 MAT:0000422 EMAPA:17532 HBA:4520 EFO:0000918 EHDAA:5433 BIRNLEX:1710 BAMS:ETh MIAA:0000422 NCIT:C12457 UMLS:C0152361 neuronames:292 GAID:455 CALOHA:TS-2060 VHOG:0000178 FMA:62009 BM:Die-Epi SCTID:281487003 Wikipedia:Epithalamus AAO:0010482 MBA:958 BAMS:EPI DHBA:10451 MESH:D019261 ZFA:0000509 MA:0000172 EHDAA2:0000448 PBA:128013147 TAO:0000509 BAMS:EpT BTO:0000175" + "The progression of the atrial septum over time, from its initial formation to the mature structure." + "The process in which a relatively unspecialized cell acquires specialized structural and/or functional features of a Leydig cell. A Leydig cell is a testosterone-secreting cell in the interstitial area, between the seminiferous tubules, in the testis." + "The process in which a precursor cell type acquires the specialized features of a CD8-positive, alpha-beta intraepithelial T cell. Intraepithelial T cells are found among epithelial cells in mucosal areas and have distinct phenotypes and developmental pathways." + "An epithelial cell of the prostate." "FMA:66817 FMA:256163" + "The expansion of an activated CD8-positive, alpha-beta T cell population by cell division." + "EHDAA2:0001472 EMAPA:32796" + "The process in which the anatomical structures of the semicircular canals are generated and organized." + + "The process of regulating the proliferation and elimination of mast cells such that the total number of mast cells within a whole or part of an organism is stable over time in the absence of an outside stimulus." + "A trigeminal neuron that is responsible for motor functions such as biting and chewing." + "An epithelium that is part of a female urethra." "EMAPA:30470 FMA:19774" + "Epithelioid macrophage is an activated macrophage that resembles an epithelial cell with finely granular, pale eosinophilic cytoplasm and central, ovoid nucleus (oval or elongate). This cell type is able to merge into one another to form aggregates. The presence of such aggregates may characterize some pathologic conditions, mainly granulomatous inflammation." "FMA:83514" + "An interneuron that has its soma located in the cerebral cortex." + "The corticobulbar and corticospinal tracts combined." "Wikipedia:Pyramidal_tracts" + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a biotic stimulus, a stimulus caused or produced by a living organism." + "The process in which the anatomical structures of a mesenchymal tissue are generated and organized. A mesenchymal tissue is made up of loosely packed stellate cells." + "The process in which bone which forms superficially in the organism are generated and organized." + "The change in morphology and behavior of a natural killer cell resulting from exposure a cytokine, chemokine, cellular ligand, or soluble factor, leading to the initiation or perpetuation of an immune response." + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA." + "The process in which a relatively unspecialized cell acquires specialized features of a type I pneumocyte. A type I pneumocyte is a flattened cell with greatly attenuated cytoplasm and a paucity of organelles." + "A neural plate that develops_from a future spinal cord." "VHOG:0000439 ZFA:0007021 FMA:312957 TAO:0007021" + "A skeletal muscle satellite cell that is mitotically quiescent. These cells are wedge shaped and have a large nuclear to cytoplasmic ratio with few organelles, a small nucleus and condensed interphase chromatin. Satellite cells typically remain in this state until activated following muscle damage." + "Any process that stops, prevents or reduces the frequency, rate or extent of T-helper 17 cell differentiation." + "The process in which the anatomical structures of the metanephric renal vesicle are generated and organized. The renal vesicle is the primordial structure of the metanephric nephron epithelium, and is formed by the condensation of mesenchymal cells." + "Any process that activates or increases the frequency, rate or extent of morphogenesis of an epithelium." + "Any process that stops, prevents or reduces the frequency, rate or extent of somatic stem cell population maintenance." + "EMAPA:32956 EMAPA:35568 VHOG:0000948" + "An extension of a neural arches dorsal to the neural canal[TAO,modified]." "FMA:11948 Wikipedia:Spinous_process ZFA:0001336 AAO:0000705 MA:0001455 NCIT:C116112 TAO:0001336 SCTID:264259004 EMAPA:25107" + "The process by which an organism or tissue maintains a population of male germ-line stem cells." + "A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a eosinophilic myelocyte and a band form eosinophil. The nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare. Markers are integrin alpha-M-positive, fucosyltransferase FUT4-positive, low affinity immunoglobulin gamma Fc region receptor III-positive, CD33-positive, CD24-positive and aminopeptidase N-negative." + "The lingual artery arises from the external carotid between the superior thyroid and facial artery[WP]." "UMLS:C0226104 SCTID:181327002 Wikipedia:Lingual_artery MA:0001992 EMAPA:36324 FMA:49526 AAO:0010492 NCIT:C52961" + "A nipple that is in_the_left_side_of a body proper." "FMA:223695" + "The caudally located, distinct elevation of a transient proliferating cell mass of the fetal subventricular zone, located adjacent to the lateral ventricle." "EFO:0001911 PBA:128012846 DHBA:10552 EMAPA:37469" + "The process in which a relatively unspecialized cell acquires specialized features of an ameloblast, a cylindrical epithelial cell in the innermost layer of the enamel organ." + "The process in which the anatomical structures of a tube are generated and organized from an endothelium. Endothelium refers to the layer of cells lining blood vessels, lymphatics, the heart, and serous cavities, and is derived from bone marrow or mesoderm. Corneal endothelium is a special case, derived from neural crest cells." + + "Cartilage that will provide a scaffold for mineralization of endochondral bones as they elongate or grow." + "The regrowth of skeletal muscle tissue to repair injured or damaged muscle fibers in the postnatal stage." + "A leukocyte with abundant granules in the cytoplasm." "BTO:0000539 CALOHA:TS-0422 FMA:62854 BTO:0001026" + "Any process that stops, prevents, or reduces the frequency, rate or extent of plasmatocyte differentiation." + "Cell-cell signaling from post to pre-synapse, across the synaptic cleft." + "Any process that modulates the rate, frequency, or extent of neural retina development, the progression of the neural retina over time from its initial formation to the mature structure. The neural retina is the part of the retina that contains neurons and photoreceptor cells." + "A bone that is part of a appendage girdle region." "MA:0000291 EMAPA:35379" + "Any process that modulates the frequency, rate or extent of ovarian follicle development." + "The vesicular release of glycine from a presynapse, across a chemical synapse, the subsequent activation of glycine receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse." + "Any process that modulates the frequency, rate or extent of skeletal muscle contraction by variation of the pattern of stimulation by nervous system." + "Any collection of muscles that is part of a lower arm [Automatically generated definition]." "FMA:39089" + "The process in which a relatively unspecialized cell acquires specialized features of a hematopoietic stem cell. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells." + "Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding." + "Any process that activates or increases the frequency, rate or extent of platelet formation." + "A reproductive process occurring in the mother that allows an embryo or fetus to develop within it." + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus." + "Any process that activates or increases the frequency, rate or extent of macrophage migration." + "Any process that modulates the frequency, rate or extent of smooth muscle hypertrophy." + "A stem cell from which all cells of the body can form." "MESH:D039901 FMA:84790" + "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other." "CARO:0020000" + "A vein that conducts blood from the digestive organs, spleen, pancreas, and gallbladder to the liver[BTO]." "galen:PortalVein UMLS:C0032718 MESH:D011169 NCIT:C33343 EHDAA2:0001485 EMAPA:17349 GAID:540 CALOHA:TS-0814 BTO:0001792 MA:0002198 SCTID:362064007 FMA:66645 XAO:0000392 VHOG:0000656 EHDAA:6510" + "The progression of the pineal gland over time from its initial formation until its mature state. The pineal gland is an endocrine gland that secretes melatonin and is involved in circadian rhythms." + "A homeostatic process involved in the maintenance of an internal steady state of a carbohydrate within an organism or cell." + "Any process that modulates the rate, frequency or extent of macrophage derived foam cell differentiation. Macrophage derived foam cell differentiation is the process in which a macrophage acquires the specialized features of a foam cell. A foam cell is a type of cell containing lipids in small vacuoles and typically seen in atherosclerotic lesions, as well as other conditions." + "A serous secreting cell that is part of the epithelium of terminal bronchiole." "FMA:263082" + + "Any process that modulates the rate, frequency or extent of epithelial cell proliferation that contributes to the progression of the prostate gland over time." + "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells of the metanephric nephron tubule as it progresses from its formation to the mature state." + "An adipose tissue that is part of a dermis [Automatically generated definition]." "MA:0000798" + "An intestinal tuft cell that is located in the anorectum." + "Any process that modulates the frequency, rate or extent of natural killer cell proliferation as part of an immune response." + "Any process that stops, prevents, or reduces the frequency, rate or extent of natural killer cell death by apoptotic process." + "The evagination of a membrane, resulting in formation of a vesicle." + "Any process that activates or increases the frequency, rate or extent of endothelial cell activation." + "A hematopoietic stem cell capable of rapid replenishment of myeloerythroid progenitors and limited self renewal capability. This cell is Kit-positive, Sca1-positive, CD34-positive, CD150-positive, and is Flt3-negative." + "Any muscle organ that is part of a respiratory system [Automatically generated definition]." "MA:0001828 EMAPA:35733" + "An endoderm that is part of a foregut-midgut junction." "EHDAA2:0000572 EMAPA:18403" + "Any process that decreases the rate or extent of heart growth. Heart growth is the increase in size or mass of the heart." + "A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent." "NIF_Subcellular:sao1702920020 Wikipedia:Cell_nucleus" + "Any apoptotic process that is involved in metanephric nephron tubule development." + "Any process that modulates the frequency, rate or extent of platelet formation." + "A mast/stem cell growth factor receptor that is encoded in the genome of human." "UniProtKB:P10721 DTO:03100231" + "Any process that stops, prevents, or reduces the frequency, rate or extent of hemocyte differentiation." + "Any process that activates or increases the frequency, rate or extent of cardioblast differentiation, the process in which a relatively unspecialized mesodermal cell acquires the specialized structural and/or functional features of a cardioblast. A cardioblast is a cardiac precursor cell. It is a cell that has been committed to a cardiac fate, but will undergo more cell division rather than terminally differentiating." + "Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels." "Wikipedia:Angiogenesis" + "The structure of the outer structural layer of the rodent placenta[MP]." "EMAPA:31876 BTO:0005402" + "The secretory unit of a serous gland. The acinar portion is composed of serous secreting cells." "FMA:86279" + "A CD33 molecule that is encoded in the genome of human." "UniProtKB:P20138" + "Any process that decreases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment." + "Mesenchyme that is part of a 1st arch mandibular component." "EMAPA:16385 EHDAA2:0000034" + "Any process that modulates the frequency, rate or extent of embryonic development." + "Any cellular process that results in the specification, formation or maintenance of polarized cytoskeletal structures that contribute to the cell polarity of a migrating ameboid cell." + + "OBSOLETE: A goblet cell that is part of the epithelium of small intestine." "FMA:263042" + "A neuropilin and tolloid-like protein 1 that is encoded in the genome of human." "UniProtKB:Q8TDF5" + "A CD34 molecule that is encoded in the genome of human." "UniProtKB:P28906" + "Any process that stops, prevents or reduces the frequency, rate or extent of glomerular visceral epithelial cell apoptotic process." + "A LIM/homeobox protein Lhx3 that is encoded in the genome of mouse." "UniProtKB:P50481" + "Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form." "ZFA:0000279 TAO:0000279 VHOG:0000559 XAO:0000057 AAO:0011086 EMAPA:16752 EMAPA:16189 EFO:0001982" + "Any process that activates or increases the frequency, rate or extent of signaling receptor activity." + "The process whose specific outcome is the progression of the midbrain over time, from its formation to the mature structure. The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)." + "A lamina propria that is part of an ileum." + + "A natural killer cell subset that is found in the decidual of the uterus and is CD56-high, Galectin-1-positive and CD16-negative. This cell type represents the most abundant immune cell type in the decidual during the first trimester of pregnancy." + "Any microvascular endothelial cell that is part of the dermis." + "GC_ID:1" + "NCIT:C34274 UMLS:C1514448 Wikipedia:Primordial_phallus" + "A vestibular reflex by which a response to a linear acceleration stimulus begins with an afferent nerve impulse from a receptor in the otolith and ends with the compensatory action of eye muscles. Signaling never reaches a level of consciousness." + "The process whose specific outcome is the progression of the spinal cord over time, from its formation to the mature structure. The spinal cord primarily conducts sensory and motor nerve impulses between the brain and the peripheral nervous tissues." + "Any process that activates or increases the frequency, rate or extent of activated CD8-positive, alpha-beta T cell apoptotic process." + "A chromaffin cell that is part of the paraganglion." "FMA:69335" + "Any process that modulates the rate, frequency, or extent of cell proliferation involved in embryonic placenta development." + "Granule cell that is part of the cerebral cortex." + "A trophoblast of placental villi. These cells fuse to form synctial trophoplast - the placental side of the interface between the placenta and maternal blood sinusoids in the decidua." "BTO:0006119 BTO:0006208" + "Any process that activates or increases the frequency, rate or extent of lung ciliated cell differentiation." + + "Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures." + + "Layer of the glomerular basement membrane adjacent to the podocytes and capsular space." "NCIT:C32919 TAO:0005288 FMA:74275 UMLS:C1517718 ZFA:0005288" + "A double-walled sac containing the heart and the roots of the great vessels." "SCTID:361326002 FMA:9868 RETIRED_EHDAA2:0001443" + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of aldosterone." + "An epithelium that is part of a bronchiole [Automatically generated definition]." "FMA:69077 NCIT:C48942 EMAPA:32693 UMLS:C1181296 CALOHA:TS-0570 BTO:0001866 MA:0001772" + "OBSOLETE: A classification of cells by their microscopic appearance." + + + "The tissue underlying the tunica mucosa of the pharynx." "FMA:75144 SCTID:19594009 BTO:0002113" + "A proximal carpal endochondral element that is composed primarily of a pre-cartilage condensation." + + "Any process that stops, prevents or reduces the frequency, rate or extent of male germ-line stem cell asymmetric division." + "The outermost layer of the neural tube that consists of axons from the developing mantle layer and will form the white matter." "EMAPA:17151 neuronames:1368" + "Any process that stops, prevents or reduces the frequency, rate or extent of postsynaptic membrane organization." + "A bone that is part of a cranium." "SCTID:181792001" + "An artery in males that provides blood to the vas deferens. The artery usually arises from the anterior trunk of the superior vesical artery. It accompanies the vas deferens into the testis, where it anastomoses with the testicular artery. In this way it also supplies blood to the testis and epididymis. A small branch supplies the ureter[WP]." "FMA:18930 MA:0001940 Wikipedia:Artery_to_the_ductus_deferens EMAPA:37513 SCTID:279659005" + "A mucosa that is part of a duodenum [Automatically generated definition]." "MA:0003207 SCTID:362146003 EMAPA:27235 BTO:0000367 FMA:14942 CALOHA:TS-0213" + "The orderly movement of an interneuron from one site to another." + "Any process that modulates the frequency, rate, or destination of vesicle-mediated transport to, from or within the Golgi apparatus." + "The enlargement or overgrowth of all or part of the heart muscle due to an increase in size of cardiac muscle cells without cell division. This process contributes to the developmental growth of the heart." + "The pair of depressions of thickened otic placode epithelium, that further develops into the otic vesicles." "EHDAA2:0001336 EMAPA:16536 NCIT:C34238 EHDAA:929 Wikipedia:Otic_pit VHOG:0001147 FMA:302911" + "Any process that activates or increases the frequency, rate or extent of epithelial tube formation." + "The epithelial component of the choroid plexus. Consists of cuboidal epithelial cells surrounding a core of capillaries and loose connective tissue." "UMLS:C1516506 NCIT:C42079 MA:0000824 EMAPA:36608 FMA:242811" + "A muscle that is part of the eye region." "MA:0000271 EMAPA:35335 AAO:0000156" + "A mesothelial cell that is part of the peritoneum." "FMA:86736" + "MESH:D005057" + "A rib that is ventrally connected to the sternum." "FMA:7592 Wikipedia:True_ribs EMAPA:37774 SCTID:368044009 MA:0001419" + "The distal elements of the developing limb of vertebrates that will give rise to the pes (foot)." "EHDAA:5143 UMLS:C1517291 NCIT:C34177 FMA:296800 EMAPA:17249 EHDAA:6096" + "The process in which the anatomical structures of the metanephric capsule are generated and organized. The metanephric capsule is the tough fibrous layer surrounding the metanephros, covered in a thick layer of perinephric adipose tissue. It provides some protection from trauma and damage." + "The directed movement of organic acids, any acidic compound containing carbon in covalent linkage, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "The posterior lateral line ganglion develops from a cranial ectodermal placode and contains sensory neurons that innervate the posterior lateral line system." "ZFA:0001314" + "The developmental process pertaining to the initial formation of a mesonephric duct. A mesonephric duct is a tube that drains the mesonephros." + "Any process that stops, prevents or reduces the frequency, rate or extent of hepatic stellate cell activation." + "GC_ID:1" + "The funnel-like expansion of the abdominal extremity of the uterine tube[MP]." "SCTID:362262001 Wikipedia:Infundibulum_of_uterine_tube FMA:18307 EMAPA:29897" + "Any of the layers of the myocardium. Example: compact layer, trabecular layer." "EMAPA:37475 MA:0000080" + "The progression of the venous blood vessel over time from its initial formation to the mature structure. Venous blood vessels carry blood back to the heart after the capillary bed." + "A vein that drains blood from the right adrenal gland into the inferior vena cava." "UMLS:C0226721 NCIT:C53131 SCTID:69354005 FMA:14343" + "A bronchiole that is the first segment of the respiratory zone." "SCTID:128517006 UMLS:C1261270 BTO:0003222 FMA:7412 NCIT:C33465 Wikipedia:Respiratory_bronchiole EMAPA:35729 MA:0000423" + "The directed movement of a T-helper 2 cell in response to an external stimulus." + "The metatarsophalangeal articulations are the joints between the metatarsal bones of the foot and the proximal bones of the toes . They are condyloid joints meaning an elliptical or rounded surface (of the metatarsal bones) come close to the shallow cavities (of the proximal phalanges). The ligaments are the plantar and two collateral." "SCTID:302535003 SCTID:239747005 GAID:258 galen:MetatarsoPhalangealJoint Wikipedia:Metatarsophalangeal_articulations MESH:D008683 SCTID:370752004 NCIT:C33108 UMLS:C0025589 FMA:35222" + "A process in which a protein is transported to, or maintained in, a location within a bicellular tight junction." + "The dorsal cochlear nucleus (DCN, also known as the 'tuberculum acousticum'), is a cortex-like structure on the dorso-lateral surface of the brainstem. Along with the ventral cochlear nucleus, it forms the cochlear nucleus, where all auditory nerve fibers from the cochlea form their first synapses. [WP,unvetted]." "NCIT:C32471 SCTID:280179000 Wikipedia:Dorsal_cochlear_nucleus BIRNLEX:2569 HBA:9530 MBA:96 DHBA:12438 UMLS:C1281210 BAMS:DCo BM:Me-CD FMA:54624 BAMS:DCO UMLS:C0175499 BAMS:DC EMAPA:35289 neuronames:721" + "A basal cell found in the bronchus epithelium." "FMA:263120" + + "The thin layer of flat cells that line the aorta and form a barrier between circulating blood in the lumen and the rest of the vessel wall." "EFO:0002597 BTO:0000394 MA:0000701 NCIT:C49190 CALOHA:TS-0047 UMLS:C1706824 EMAPA:35134" + "Any process that stops, prevents or reduces the frequency, rate or extent of B cell chemotaxis." + "Combining with an extracellular amine and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex." + "Any process that stops, prevents or reduces the frequency, rate or extent of lymphocyte chemotaxis." + "An organ of sight that includes the camera-type eyeball and supporting structures such as the lacrimal apparatus, the conjunctiva, the eyelid." "NCIT:C12401 UMLS:C1280202 EHDAA2:0000484 BIRNLEX:1169 TAO:0000107 UMLS:C0015392 BTO:0004688 AAO:0010340 EMAPA:16198 MA:0000261 EHDAA:936 SCTID:181143004 VHOG:0000275 FMA:54448 ZFA:0000107 XAO:0000179" + "An epithelial cell with a well defined Golgi apparatus that makes up the continuous layer of cells bordering the thymic tissue beneath the capsule." "FMA:72209" + "A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells." + "Any process that activates or increases the frequency, rate or extent of eosinophil differentiation." + "A ring of striated muscle cells whose contraction closes the opening of the ring." "AEO:0000144 EHDAA2:0003144" + "A class switched memory B cell that expresses IgA." + "A myeloblast committed to the eosinophil lineage." + "The orderly movement of epithelial cells within a renal tubule that contributes to mesonephric proximal tubule morphogenesis." + "EHDAA:595 EHDAA2:0000038 EMAPA:16388" + + + "A MHC-II-negative classical monocyte located in lymphoid tissue that is F4/80-positive, CD11c-negative, and CD11b-high." + "A steroid hormone secreting cell that secretes androgen." + "A pericyte cell that is part of a lung." "EFO:0010669" + "The chemical reactions and pathways involving melatonin (N-acetyl-5-methoxytryptamine)." + "Any process that stops, prevents or reduces the frequency, rate or extent of synoviocyte proliferation." + "FMA:9560" + "Any process that modulates the frequency, rate or extent of cardiac myofibril assembly." + "An adipocyte that is part of the breast." "CALOHA:TS-2377" + "The chemical reactions and pathways resulting in the breakdown of hyaluronan, the naturally occurring anionic form of hyaluronic acid, any member of a group of glycosaminoglycans, the repeat units of which consist of beta-1,4 linked D-glucuronyl-beta-(1,3)-N-acetyl-D-glucosamine." + "A vein that begins near the upper part of the greater sciatic foramen, passes upward behind and slightly medial to the hypogastric artery and, at the brim of the pelvis, joins with the external iliac to form the common iliac vein. [WP,unvetted]." "EHDAA2:0000874 galen:InternalIliacVein MA:0002145 NCIT:C32847 FMA:18884 Wikipedia:Internal_iliac_vein MA:0002139 VHOG:0000749 UMLS:C0226764 SCTID:181399007 EMAPA:37148" + "A small pre-B cell that is CD22-positive and CD38-low." + "A white matter of cerebral lobe that is part of a temporal lobe." "FMA:256186 SCTID:362344007" + "Lymph vessel formation when new vessels emerge from the proliferation of pre-existing vessels." "Wikipedia:Lymphangiogenesis" + "A nerve trunk that is part of a sympathetic nervous system [Automatically generated definition]." "EHDAA2:0001970 EMAPA:35845 MA:0000227" + "An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for basic dyes under specific pH conditions." + "Any process that modulates the frequency, rate or extent of CD4-positive, alpha-beta T cell proliferation." + "A sinusoidal space that is part of a hepatic sinusoid." "FMA:262090" + "Any process that decreases the frequency or extent of the multiplication or reproduction of Schwann cells, resulting in the expansion of their population. Schwann cells are a type of glial cell in the peripheral nervous system." + "The directed movement of basic amino acids out of the vacuole, across the vacuolar membrane." + "A collagenous capsule covering the external surface of the liver." "SCTID:362185005 FMA:15813 Wikipedia:Fibrous_capsule_of_Glisson" + "Any process that activates or increases the frequency, rate or extent of protein localization to presynapse." + "A bone that is part of a autopod region. Note that this incudes the carpal and tarsal bones." + "Any process that activates or increases the frequency, rate or extent of tight junction disassembly." + "Any process that stops, prevents, or reduces the frequency, rate or extent of natural killer T cell activation." + "Any smooth muscle tissue that is part of a metanephros." + "Any process that modulates the frequency, rate or extent of synaptic vesicle exocytosis." + + "Epithelial cell of the descending thin limb of the long loop (juxtamedullary) nephron that spans the inner medulla. It is known in some mammalian species that the long descending limb of the loop of Henle in the inner medulla selectively expresses the nuclear receptor Nr2e3, the Ig kappa chain Igkc, and the secreted protein dermokine (Dmkn). SLC14A2, which expresses a urea transporter, is also expressed in the inner medulla." + "A cell with a flagellum surrounded by a collar of microvilli. The motion of the flagellum draws water past the microvilli, serving either a feeding or sensory function. Collar cells are found in multiple animals, including sponges, echinoderms, and cnidarians. They are also found outside animals in the choanoflagellates. Although collar cells are superficially similar, their cytoskeletal structure and functional biology are different in different groups of organisms." + "The testis cords are precursors to the rete testis. They play several different roles in the development of the male genitals[WP]." "VHOG:0001321 Wikipedia:Testis_cords EHDAA:8152 EHDAA2:0002011 EMAPA:29098" + "Any process that modulates the frequency, rate or extent of apoptotic process involved in metanephric nephron tubule development." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of tolerance induction to nonself antigen." + "The vascularized and branched structures arising from the rodent trophoblast-derived epithelium that allow an increase its surface area for the efficient exchange of nutrients and wastes between the maternal and fetal circulation." + + "The thickened portion of the vascular tunic, which lies between the choroid and the iris, composed of ciliary muscle and ciliary processes." "BTO:0000260 GAID:916 Wikipedia:Ciliary_body EV:0100346 AAO:0010341 XAO:0000186 UMLS:C0008779 SCTID:263340007 NCIT:C12345 MA:0000264 FMA:58295 MESH:D002924 VHOG:0000102 CALOHA:TS-0694 neuronames:1571 EMAPA:19065" + "The chemical reactions and pathways resulting in the formation of monocarboxylic acids, any organic acid containing one carboxyl (-COOH) group." + "The process in which neuroblasts acquire specialized structural and/or functional features that characterize the mature cerebellar Golgi cell. Differentiation includes the processes involved in commitment of a neuroblast to a Golgi cell fate. A cerebellar Golgi cell is an inhibitory GABAergic interneuron found in the cerebellar cortex." + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." + + "A laminar subdivision of the neocortex that is comprised of a part of layer V and a part of layer VI." + "The lacrimal nerve is the smallest of the three branches of the ophthalmic division of the trigeminal nerve." "FMA:52628 SCTID:280218007 NCIT:C32908 Wikipedia:Lacrimal_nerve" + "Any process that activates or increases the frequency, rate or extent of colon smooth muscle contraction." + "A subdivision of the skeleton of the autopod consisting of the phalanges of pedal digit plus the associated metapodial element." + "A megakaroycotye progenitor cell that is CD34-positive, CD41-positive and CD42-positive on the cell surface." + "A smooth muscle cell that synthesizes, stores, and secretes the enzyme renin. This cell type are located in the wall of the afferent arteriole at the entrance to the glomerulus. While having a different origin than other kidney smooth muscle cells, this cell type expresses smooth muscle actin upon maturation." "FMA:84138" + "A sphincter muscle that is part of a anal region." "EMAPA:36052" + "Undifferentiated; mitotic stem cell for other epithelial cell types; rounded or elliptical with little cytoplasm and few organelles; contain cytokeratin intermediate filament." "FMA:62516 BTO:0000939" + "An iliac endochondral element that is composed primarily of a pre-cartilage condensation." "EHDAA2:0000809 EHDAA:9568 VHOG:0000964 EMAPA:18029" + "Any process that modulates the frequency, rate or extent of the directed movement of amino acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "A lymph node that is located deeper within the organism, further from the surface." "FMA:12768" + + "An axon tract that is part of a diencephalon." "FMA:62447" + "A lymphocyte that resides in the lamina propria of the large intestine." + "The mucosal layer that lines the stomach." "EMAPA:35817 GAID:321 Wikipedia:Gastric_mucosa FMA:14907 UMLS:C0017136 BTO:0001308 NCIT:C32656 SCTID:362131005 MA:0002683 galen:GastricMucosa MESH:D005753 CALOHA:TS-0404" + "A glandular cell found in the epithelium of the small intestine. Example: Enterocytes, Goblet cells, enteroendocrine cells; Paneth cells; M cells; Somatostatin-secreting Cells (D-cells) ." "CALOHA:TS-1286 FMA:86928" + + "The smallest morphological and functional unit of the compound eye that consists of a usually limited and often constant number of rhabdomeric photoreceptor cells, cornea-secreting epithelial cells, and interommatidial pigment cells, and may additionally contain crystalline cone cells." "MIAA:0000143 HAO:0000666 Wikipedia:Ommatidium BTO:0001922 MAT:0000143" + "A smooth muscle cell of the trachea." + "Obsolete. Use PO:0004011 from Plant Ontology instead. A cell constituting an active locus of meristematic activity in a tissue composed of somewhat older, differentiating cells." + "OBSOLETE: A classification of cells by the number of haploid genome equivalents of their nucleus or nuclei." + "Any muscle cell in which the fibers are not organised into sarcomeres." + "A natural killer cell that is developmentally immature, has the phenotype CD34-negative, CD56-positive, CD117-positive, CD122-positive,and CD161-positive." + "The cellular developmental process in which a specific cell progresses from an immature to a mature state. Cell development start once cell commitment has taken place." + "A rhodopsin-like G-protein coupled receptor that is a translation product of the human RXFP1 to RXFP4 genes, 1:1 orthologs thereof, or a semi-ortholog thereof. The active form binds relaxins." "PIRSF:PIRSF038662 IUPHARfam:60" + + "EMAPA:37958 SCTID:181098007" + "The distal sub-portion of the ascending loop of Henle which is lined by simple cuboidal epithelium and enters the renal cortex to empty a hypotonic filtrate into the distal convoluted tubule." "SCTID:244953001 EMAPA:29671 FMA:17722 EMAPA:28396 EMAPA:35512 MA:0001677 Wikipedia:Thick_ascending_limb_of_loop_of_Henle" + + "A conventional B cell subject to antigenic stimulation and dependent on T cell help and with a distinct surface marker expression pattern from B-1 B cells. These cells are CD43-negative." + "Any process that modulates the frequency, rate or extent of hematopoietic stem cell proliferation." + + "The formation of the endoderm during gastrulation." + "The process in which a cardiac chamber is generated and organized. A cardiac chamber is an enclosed cavity within the heart." + "A nerve that is part of a leg [Automatically generated definition]." "MA:0000673 EMAPA:37343" + + "Any process that stops, prevents, or reduces the frequency, rate, or extent of tolerance induction dependent upon immune response." + "Any process that stops, prevents or reduces the frequency, rate or extent of gastro-intestinal system smooth muscle contraction." + "Any process that modulates the frequency, rate or extent of ascospore formation. An example of this process is found in Saccharomyces cerevisiae." + "HBA:9370 SCTID:314145001" + "Combining with a polysaccharide and transmitting the signal to initiate an innate immune response. A polysaccharide is a polymer of many (typically more than 10) monosaccharide residues linked glycosidically." + "Any process that activates or increases the frequency, rate or extent of compound eye photoreceptor development." + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein at the postsynapse." + "A protein that is a member of a family that includes translation products of genes CD86, CD276, ICOSLG, and others. These are membrane-anchored proteins with a small intracellular domain and an extracellular domain with signal sequence, an Immunoglobulin V-set domain (Pfam:PF07686), and a CD80-like C2-set immunoglobulin domain (Pfam:PF08205)." + "A uninucleate spore formed on specialized cells or projections, sterigma, of a conidiophore head." "FAO:0000033" + "The morphogenesis of an embryonic epithelium into a tube-shaped structure." + "A quality of an object that has a value that is decreased compared to normal or average." + "Submucosal tissue in the small intestines." "MA:0001562 SCTID:691000 FMA:14934 EMAPA:37564 Wikipedia:Small_intestinal_submucosa BTO:0002112 NCIT:C33572 UMLS:C0227268" + "EMAPA:17570 EHDAA2:0004313" + "Portion of tissue that consists of the precursors of the pronephric glomus or glomerulus; derived from the medial portion of the pronephric intermediate mesoderm." "XAO:0000110" + "A hindlimb that is on the left side of a pelvic complex." "FMA:7188" + "Any collection of muscles that is part of a body wall [Automatically generated definition]." "WBbt:0005813 FMA:86931 EMAPA:37853 BTO:0001863 BSA:0000058" + "An epithelium that is part of an endometrium [Automatically generated definition]." "MA:0002731 SCTID:253526009 EMAPA:35307" + "An epithelial cell that is part of some inner medullary collecting duct." "KUPO:0001061" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of T cell mediated immunity." + "A fascicle that is part of a brain." "FMA:83844" + "A primitive nephron that is part of a metanephros." "EHDAA2:0001516" + "The process in which a relatively unspecialized cell acquires the specialized features of an acinar cell of sebaceous gland." + "An epithelium that is part of a upper jaw [Automatically generated definition]." "EHDAA:8027 EMAPA:18971 EHDAA2:0002119" + "The orderly movement of a cell from one site to another that contribute to the formation of the heart. The initial heart structure is made up of mesoderm-derived heart progenitor cells and neural crest-derived cells." + "A secondary lymphoid organ macrophage found in the spleen." "FMA:83026" + "Any complex of actin, myosin, and accessory proteins." + "A precursor B cell that is CD45R-positive, CD43-positive, CD24-positive, and BP-positive. Intracellularly expression of surrogate light chain, Rag1 and Rag2, TdT, occurs while there is no expression of mu heavy chain." + "Any process that modulates the frequency, rate or extent of mitotic nuclear envelope disassembly." + "The orderly movement of a cell from one site to another that will contribute to the progression of the metanephric kidney over time, from its formation to the mature organ." + "The process in which the anatomical structures of the trabecular cardiac ventricle muscle are generated and organized." + "The process whose specific outcome is the progression of the tracheal cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate." + "A cup-like sac at the expanded beginning of a tubular component of a nephron that contains the glomerulus." "SCTID:361331000 MA:0001660 FMA:15626 KUPO:0001001 AAO:0010526 NCIT:C32225 ZFA:0005254 EMAPA:27973 TAO:0005310 UMLS:C0524448 EMAPA:28257 TAO:0005254 ZFA:0005310 Wikipedia:Bowman%27s_capsule BTO:0002297" + "Any process that modulates the frequency, rate or extent of neuromuscular synaptic transmission." + "The change in morphology and behavior of an alpha-beta T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific." + "Subdivision of digestive tract that connects the stomach to the large intestine and is where much of the digestion and absorption of food takes place (with the exception of ruminants). The mammalian small intestine is long and coiled and can be differentiated histologically into: duodenum, jejunem, ileum[WP,cjm,Kardong]." "EV:0100072 EFO:0000841 VHOG:0000055 NCIT:C12386 MIAA:0000047 UMLS:C0021852 ZFA:0001323 galen:SmallIntestine MESH:D007421 BTO:0000651 GAID:313 EMAPA:32834 AAO:0010397 MAT:0000047 MA:0000337 Wikipedia:Small_intestine SCTID:181250005 TAO:0001323 CALOHA:TS-0942 FMA:7200 XAO:0000130" + "Limb extensor that runs from ilium to femur." + "A process in which muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors. These adaptive events occur in both muscle fibers and associated structures (motoneurons and capillaries), and they involve alterations in regulatory mechanisms, contractile properties and metabolic capacities." + "An extraembryonic structure that develops_from a ectoderm and is part of a chorion." "BTO:0005145 EMAPA:16113" + "An integrin alpha that contains an A domain. A hallmark of this class is the presence of a von Willebrand factor type A domain (Pfam:PF00092) (I-domain) of approximately 200 amino acid residues at the N terminus, which confers divalent cation binding properties. Unlike other integrin alpha proteins, they do not undergo proteolytic cleavage." "PIRSF:PIRSF002497" + "The process whose specific outcome is the progression of the posterior lateral line system over time, from its formation to the mature structure. The posterior lateral line system develops from cranial ectodermal placodes, situated behind the ear, that give rise to both the neuromasts and the posterior lateral line sensory nerves that innervate the neuromasts. The posterior lateral line system consists of small sensory patches (neuromasts) located superficially on the skin or just under the skin in fluid-filled canals on the head of all fishes and most amphibians. The neuromasts are innervated by several lateral line nerves, which project primarily to the hindbrain. The posterior mechanosensory lateral line system is stimulated by local water displacements and vibrations, and detects propulsion of the fish through the water, as well as facilitating shoaling, prey capture, and predator and obstacle avoidance." + "Glandular cell of salivary gland. Example: Serous cells, mucous cells, cuboidal epithelial cells of the intercalated ducts, simple cuboidal epithelium of the striated ducts, epithelial cells of excretory ducts." "CALOHA:TS-1282" + "A retinal ganglion cell B that has medium body size, medium dendritic field and dense dendritic arbor, and has post synaptic terminals in S2." "BAMS:1047" + "A tributary of the iliac vein that drains the urinary bladder." "SCTID:12683000 EMAPA:37205 Wikipedia:Vesical_veins MA:0002263" + "A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong]." "EFO:0000840 EV:0100077 BTO:0000706 galen:LargeIntestine NCIT:C12379 EMAPA:19252 VHOG:0000054 SCTID:181254001 AAO:0010396 GAID:306 FMA:7201 MA:0000333 XAO:0000131 CALOHA:TS-1306 UMLS:C0021851 Wikipedia:Large_intestine_(anatomy) MESH:D007420 MIAA:0000046" + "A polychromatiic erythroblast that is Gly-A-positive and CD71-low." + "A neuron that uses neuropeptides as transmitters." "FBbt:00004101" + "Any process that stops or reduces the activity of an ion transporter." + "A cell that takes up and metabolizes substances." + "A CD8-positive, alpha beta memory T cell with the phenotype CD45RA-positive, CD45RO-negative, and CCR7-negative." + "The process in which the anatomical structure of the cerebellar molecular layer is generated and organized. The molecular layer is the outermost layer of the cerebellar cortex. It contains the parallel fibers of the granule cells, interneurons such as stellate and basket cells, and the dendrites of the underlying Purkinje cells." + "The axilla is the area directly under the joint where the forelimb connects to the shoulder." "CALOHA:TS-2208 SCTID:362732006 galen:Axilla NCIT:C12674 EFO:0001395 UMLS:C0004454 FMA:24864 MESH:D001365 Wikipedia:Axilla" + "The part of the cerebral cortex that receives projections from the motor thalamus and which projects to motor neurons in the brainstem and spinal cord. The motor cortex corresponds to Brodmann's area 4 (MM). The primary motor cortex, or M1, is located on the precentral gyrus and on the anterior paracentral lobule on the medial surface of the brain. Of the three motor cortex areas, stimulation of the primary motor cortex requires the least amount of electrical current to elicit a movement. http://neuroscience.uth.tmc.edu/s3/chapter03.html." "BM:Tel-Cx-M1 MA:0000907 MESH:D009044 FMA:224854 Wikipedia:Primary_motor_cortex SCTID:11931008 EFO:0002472 UMLS:C0026607 BTO:0004348 neuronames:1910 MBA:985 NCIT:C97339 EMAPA:35704 NLX:143555 BAMS:M1 DHBA:10162 BAMS:MO BAMS:MOp" + "Any process that modulates the frequency, rate, or extent of interleukin-4 production." + "A quality inhering in a bearer by virtue of the bearer's exhibiting no deviation from normal or average." + "Programmed cell death that occurs in the developing retina." + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glycogen." + "A process in which protein is transported from one region of the plasma membrane to another." + "Any process that stops, prevents, or reduces the frequency, rate or extent of skeletal muscle tissue development." + "A NK1.1-positive T cell that is CD94-positive and Ly49Cl-positive." + "An ion channel complex through which cations pass." + "The process in which a hemocyte precursor cell acquires the characteristics of a crystal cell, a class of cells that contain crystalline inclusions and are involved in the melanization of pathogenic material in the hemolymph." + "A cone whose sensitivity measurements have an average spectral peak of 510 nm. These cones are described in rat." "BAMS:1028" + "A GABAergic cell located in the cerebral cortex that expresses meis2." + "The ureteral branches of renal artery are small branches which supply the ureter." "FMA:70491 SCTID:65376008 EMAPA:37676 MA:0002074 Wikipedia:Ureteral_branches_of_renal_artery" + "A cadherin-5 that is encoded in the genome of mouse." "UniProtKB:P55284" + "A fibroblast that is part of upper back skin." + "A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile." + "Combining with a cytokine and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity." + "Any process that stops, prevents or reduces the frequency, rate or extent of cellular response to testosterone stimulus." + "A striated muscle cell of an arthropod heart that participates in heart contraction." + "NCIT:C12893 BIRNLEX:955 SCTID:180966009 FMA:16422 UMLS:C0581631" + "EMAPA:18772 FMA:294628 MA:0000162" + "A small cluster of cells of various types which form a discrete structure, largely delimited by a morphological boundary and whose components work together to make the whole structure capable of a specific function." "CARO:0010001" + "EHDAA2:0000031 EHDAA:583 EMAPA:16382 VHOG:0000510" + "A class switched memory B cell that expresses IgE on the cell surface." + "Any process that stops, prevents or reduces the rate or extent of mitosis. Mitosis is the division of the eukaryotic cell nucleus to produce two daughter nuclei that, usually, contain the identical chromosome complement to their mother." + "An endothelium that is part of a sclera." + "A laminar subdivision of the neocortex that is comprised of a part of layer II and a part of layer III." + "Chordotonal organs are arthropod sensory structures consisting of special sensilla called the scolopidia, which are mechano-transducers and respond mainly to stretch or flexion. In insects, they consist of bundles of internal sensilla, each of which has a cap cell, an enveloping cell and one or more sense cells. The distal end of the organ is usually attached to the cuticle of the body wall, marked by a pit, a thickened disc or a nodule of chitin, and the base of the organ is connected with the hypodermis, often by a special ligament." "EFO:0000940 MAT:0000209 Wikipedia:Chordotonal_organ MIAA:0000209" + "Any collagen timer that is part of a basement membrane." + "A dense accumulation of exocrine glands in the pancreas often surrounding islets of Langerhans." "MA:0000721 EMAPA:37710 FMA:16012" + "PMID:29367151 GC_ID:1" + "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells of the kidney as it progresses from its formation to the mature state." + "Any process that activates or increases the frequency, rate or extent of cardiac neural crest cell migration involved in outflow tract morphogenesis." + "An ectoderm that is part of a pharyngeal arch 2." "VHOG:0001062 EHDAA2:0000055 EMAPA:16397 RETIRED_EHDAA2:0000064 EMAPA:16398 EMAPA:16277" + "The process of communication from a neuron to a smooth muscle in the bladder that contributes to the expulsion of urine from the body." + "The process in which the anatomical structure of superior vena cava generated and organized. The superior vena cava is a blood vessel that transports blood from the upper body to the heart." + "A serous membrane that is part of a jejunum [Automatically generated definition]." "EMAPA:27115 FMA:14955" + + "A protein that is a translation product of the human MSR1 gene or a 1:1 ortholog thereof." + "The directed movement of a neurotransmitter receptor complex along microtubules from the cell body toward the cell periphery in nerve cell axons." + "The directed movement of proteins from the Golgi to the plasma membrane in transport vesicles that move from the trans-Golgi network to the plasma membrane." + "Subdivision of skeleton that is an anterolateral part of the cranium and structurally supports the eye. Includes bones formed and located in sclerotic layer of eyeball." "TAO:0001410 BTO:0004687 ZFA:0001410 FMA:53074 galen:Orbit Wikipedia:Orbit_(anatomy) MESH:D009915 NCIT:C12347 GAID:223 UMLS:C0029180 MA:0002482 XAO:0003171" + "Any process that decreases the rate, frequency or extent of granulocyte chemotaxis. Granulocyte chemotaxis is the movement of a granulocyte in response to an external stimulus." + "A transitional myocyte that is part of the interventricular septum." "FMA:263154" + "The process in which a relatively unspecialized cell acquires specialized features of a cardiac neural crest cell that will migrate to the heart and contribute to its development. Cardiac neural crest cells are specialized cells that migrate toward the heart from the third, fourth and sixth pharyngeal arches." + "One of a number of vertical folds, produced by an infolding of the mucous membrane and some of the muscular tissue in the upper half of the lumen of the anal canal[WP]." "NCIT:C32067 Wikipedia:Anal_columns FMA:15713 SCTID:245444007 UMLS:C0227428" + "Any process that modulates the frequency, rate or extent of the regulated release of acetylcholine." + "Any process in which the nucleus is transported to, and/or maintained in, a specific location within the cell." + "The process in which a relatively unspecialized cell acquires the specialized features of a Schwann cell. Schwann cells are found in the peripheral nervous system, where they insulate neurons and axons, and regulate the environment in which neurons function." + "A nerve root that extends_fibers_into a facial nerve." "FMA:53418 BAMS:7n BAMS:7nf DMBA:17742 SCTID:280186008 BIRNLEX:1513 DHBA:12862 neuronames:579" + "The regulated release of progesterone, a steroid hormone, by the corpus luteum of the ovary and by the placenta." + "The series of events required for an organism to receive a gravitational stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process." + "A B lymphocyte that resides in the mantle zone of the lymph node germinal center. These are generally IgM and IgD positive activated B cells that form a 'corona' around the germinal center and are part of the establishment of a secondary lymphatic follicule." + "The process whose specific outcome is the progression of a spermatid over time, from its formation to the mature structure." "Wikipedia:Spermiogenesis" + "A cell of the embryo." "WBbt:0007028 FMA:82840 CALOHA:TS-0263" + "The process in which an amino acid is transported across a membrane." + + "End of the life of an organism." "XAO:0000437 XtroDO:0000085" + "A fibroblastic reticular cell found in the lymph node germinal center dark zone (B cell zone)." + "The process whose specific outcome is the progression of the primary female sexual characteristics over time, from their formation to the mature structure. The primary female sexual characteristics are the ovaries, and they develop in response to sex hormone secretion." + + "A membrane that is one of the two lipid bilayers of an organelle envelope or the outermost membrane of single membrane bound organelle." "NIF_Subcellular:sao830981606" + "The process in which immunoglobulin light chain V and J gene segments are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS)." + "A mononuclear cell that is part_of a bone marrow." + "The contractile fiber of smooth muscle cells." + "The medial circumflex femoral artery (internal circumflex artery, medial femoral circumflex artery) is an artery in the upper thigh that helps supply blood to the neck of the femur. [WP,unvetted]." "Wikipedia:Medial_circumflex_femoral_artery EMAPA:37670 MA:0001996 FMA:20799 SCTID:244326008" + "A collection of channels that connects the conjunctival sac with the nasal cavity, encompassing the lacrimal ducts, the lacrimal sac and the naso-lacrimal duct." "MA:0001295 FMA:61063 EMAPA:19245 SCTID:280426002" + "The chemical reactions and pathways resulting in the breakdown of glycosphingolipid, a compound with residues of sphingoid and at least one monosaccharide." + "The process of regulating the proliferation and elimination of basophils such that the total number of basophils within a whole or part of an organism is stable over time in the absence of an outside stimulus." + "The broad region around and including the plasma membrane of a cell, encompassing the cell cortex (inside the cell), the plasma membrane, and any external encapsulating structures." + "A spiral thickening of the fibrous lining of the cochlear wall. Spiral ligament secures the membranous cochlear duct to the bony spiral canal of the cochlea. Its spiral ligament fibrocytes function in conjunction with the stria vascularis to mediate cochlear ion homeostasis." "MA:0001192 FMA:77834 UMLS:C0229477 SCTID:279840005 MESH:D055493 Wikipedia:Spiral_ligament BIRNLEX:2524 EMAPA:35798" + "Any process that activates or increases the frequency, rate or extent of microtubule binding." + "Part of the metencephalon that lies in the posterior cranial fossa behind the brain stem. It is concerned with the coordination of movement[MESH]. A large dorsally projecting part of the brain concerned especially with the coordination of muscles and the maintenance of bodily equilibrium, situated between the brain stem and the back of the cerebrum , and formed in humans of two lateral lobes and a median lobe[BTO]. Brain structure derived from the anterior hindbrain, and perhaps including posterior midbrain. The cerebellum plays a role in somatic motor function, the control of muscle tone, and balance[ZFA]." "neuronames:643 EHDAA2:0000232 BIRNLEX:1489 EV:0100293 VHOG:0000024 CALOHA:TS-0125 MA:0000198 EMAPA:17787 UMLS:C0007765 ZFA:0000100 MIAA:0000110 MESH:D002531 BAMS:CB MAT:0000110 NCIT:C12445 BAMS:Cb XAO:0003098 GAID:595 Wikipedia:Cerebellum HBA:4696 MBA:512 SCTID:180924008 EFO:0000327 UMLS:C1268981 BM:CB FMA:67944 AAO:0010485 BTO:0000232 DHBA:10656 TAO:0000100" + "Any process that modulates the frequency, rate or extent of leukocyte cell-cell adhesion." + "A complex of collagen trimers such as a fibril or collagen network." + "A CD3 subunit with immunoglobulin domain that is a translation product of the human CD3E gene or a 1:1 ortholog thereof." "IUPHARobj:2742" + "Any process that modulates the rate or extent of cardiac cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a cardiac muscle cell and result in its death." + "A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome." + "A lymph node that is part of a pancreas [Automatically generated definition]." "UMLS:C0229783 MA:0002881 NCIT:C77642 SCTID:276170003 FMA:16626" + "A D cell located in the pancreas. Peripherally placed within the islets like type A cells; contains somatostatin." "FMA:70587 BTO:0000803" + "Any process that decreases the rate or extent of the process whose specific outcome is the progression of an oocyte over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell." + "Any process that stops, prevents or reduces the frequency, rate or extent of execution phase of apoptosis." + "The parts of the orbital region that are outside of the the eyeball, including the lacrimal apparatus, the extraocular muscles and the eyelids, eyelashes, eyebrows and the conjunctiva." "SCTID:120612006 NCIT:C32574 UMLS:C0229243 Wikipedia:Accessory_visual_structures FMA:76554" + "A muscular coat that is part of a digestive tract." + "A G-protein coupled receptor that contains the 7 transmembrane receptor (rhodopsin family) domain (Pfam:PF00001), which includes 7 transmembrane helices (TMI-TM7) with 3 intracellular loops (IL1-IL3) and 3 extracellular loops (EL1-EL3) between the helices. The amino-terminal region is extracellular and the carboxyl-terminal region is intracellular. Rhodopsin-like G-protein coupled receptors (GPCRs) are unique among the several classes of GPCRs in that most have a very short amino-terminal segment and several characteristic sequence motifs, particularly NSxxNPxxY in TM7 and D/E-R-Y/F between TM3 and loop IL2. Most bind their ligands within a cavity between the TM regions." "IUPHAR:GPCRListForward?class=A PIRSF:PIRSF800006" + "In anatomy, in the occipital bone, the foramen magnum is one of the several oval or circular apertures in the base of the skull, through which the medulla oblongata (an extension of the spinal cord) enters and exits the skull vault. Apart from the transmission of the medulla oblongata and its membranes, the foramen magnum transmits the Spinal Accessory nerve, vertebral arteries, the anterior and posterior spinal arteries, the membrana tectoria and alar ligaments. [WP,unvetted]." "TAO:0002045 EMAPA:37868 FMA:75306 ZFA:0005387 AAO:0010826 SCTID:244679008 NCIT:C12495 Wikipedia:Foramen_magnum MESH:D005539 UMLS:C0016519 GAID:228" + "The lobe at the anterior part of each cerebral hemisphere, responsible for olfactory functions." "NCIT:C33204 MIAA:0000116 BTO:0001362 EMAPA:17778 neuronames:2078 UMLS:C0178780 EHDAA:5480 EHDAA2_RETIRED:0001294 MA:0002413 EFO:0000108 VHOG:0000833" + "A portion of connective tissue that is part of a elbow [Automatically generated definition]." "MA:0000609 EMAPA:37318" + "A portion of connective tissue that is part of a head [Automatically generated definition]." "MA:0000577" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of insulin." + + "Any process that activates or increases the frequency, rate or extent of aortic smooth muscle cell differentiation." + "EHDAA2:0001836 EHDAA:8493 EMAPA:17712" + "Any process that modulates the physical form or the activity of a synapse, the junction between a neuron and a target (neuron, muscle, or secretory cell)." + "A specialized mononuclear osteoclast associated with the absorption and removal of cementum." + "A cuboidal epithelial cell of the kidney that regulates acid/base balance." "FMA:86560" + "The tubules that carry lymph throughout the body that are in the interior of the body or limbs." "SCTID:14033005 FMA:52012 UMLS:C1282746 NCIT:C32439" + "Subdivision of long bone which forms the part of the bone between the two epiphyses, excluding the metaphyses[FMA,modified]." "FMA:24013 GAID:189 SCTID:361729006 Wikipedia:Diaphysis EMAPA:35504 MESH:D018483" + "Any process that modulates the rate, frequency, or extent of the controlled release of molecules that form the extracellular matrix, including carbohydrates and glycoproteins by a cell or a group of cells." + "A protein that is a translation product of the human SOX2 gene or a 1:1 ortholog thereof." + "A smooth muscle cell that is part of the transverse colon." "FMA:17519" + "An epithelial cell of the pancreas." "BTO:0000028" + "A cell that lines the trabecular meshwork, which is an area of tissue in the eye located around the base of the cornea, near the ciliary body, and is responsible for draining the aqueous humor from the eye via the anterior chamber (the chamber on the front of the eye covered by the cornea). This cell may play a role in regulating intraocular pressure." + "Any hepatocyte that is part of the liver lobule centrilobular region. These cells are the primary location for the biotransformation of drugs." + "Any of the immature or mature forms of a granular leukocyte that in its mature form has an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse, bluish-black granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation. A basophil is CD123-positive, CD193-positive, CD203c-positive, and FceRIa-positive." "FMA:62862 CALOHA:TS-0073 BTO:0000129" + "A pigment cell derived from the neural crest. Contains uric acid or other purine crystals deposited in stacks called leucosomes. The crystals reflect light and this gives a white appearance under white light." + "The jelly-like substance in the middle of the spinal disc which is a remnant of the notochord." "SCTID:316586000 MA:0000112 EMAPA:18008 FMA:76703 FMA:13550 Wikipedia:Nucleus_pulposus BTO:0003626" + "A process in which a protein is transported to, or maintained in, a specific location in the plasma membrane." + "The process whose specific outcome is the progression of the cartilage that will provide a scaffold for mineralization of endochondral bones." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of a type 2 immune response." + "Any process that activates or increases the frequency, rate or extent of translational initiation." + "A zone of skin that is part of a lip [Automatically generated definition]." "EMAPA:37643 NCIT:C12291 SCTID:244092005 MA:0001579 UMLS:C0222101 FMA:24764" + "Any process that modulates the rate, frequency, or extent of olfactory learning. Olfactory learning is any process in an organism in which a relatively long-lasting adaptive behavioral change occurs in response to (repeated) exposure to an olfactory cue." + "Any process that modulates the frequency, rate or extent of dendritic cell chemotaxis." + "The set of processes resulting in differentiation of theca and granulosa cells into luteal cells and in the formation of a corpus luteum after ovulation." "Wikipedia:Luteal_phase Wikipedia:Luteinization" + "Embryonic structure that gives rise to the midbrain hindbrain boundary." "EFO:0003446 XAO:0004086 TAO:0001187 ZFA:0001187" + "Any process that stops, prevents or reduces the frequency, rate or extent of microtubule binding." + "A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. This process occurs in the urinary tract. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. The urinary tract consists of organs of the body that produce and discharge urine. These include the kidneys, ureters, bladder, and urethra." + "A GABAergic interneuron that has its soma located in the striatum and that has an enriched expression of the gene TAC3." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances between the cytoplasm and the nucleus." + "Any process that modulates the frequency, rate or extent of protein complex assembly." + "A basally situated, mitotically active, columnar-shaped keratinocyte attached to the basement membrane." "FMA:70571" + "Any process in which a protein is maintained in a specific location a specific location on or in an organelle, and is prevented from moving elsewhere. Encompasses establishment of localization in the membrane or lumen of a membrane-bounded organelle." + "A muscular organ in the floor of the mouth." "CALOHA:TS-1050 NCIT:C12422 Wikipedia:Tongue MAT:0000040 EMAPA:17185 AAO:0010360 MESH:D014059 MA:0000347 EFO:0000833 EHDAA:9144 BTO:0001385 TAO:0005333 MIAA:0000040 XAO:0000446 SCTID:181226008 ZFA:0005333 VHOG:0000419 UMLS:C0040408 GAID:816 FMA:54640 EV:0100058 EHDAA2:0002062" + "The process whose specific outcome is the progression of a posterior lateral line neuromast hair cell over time, from its formation to the mature structure. A neuromast hair cell is a hair cell that acts as a sensory receptor of the neuromast; it is morphologically polarized as a result of the relative position of the single kinocilium and the clusters of stereocilia on its apical surface. Cell development does not include the steps involved in committing a cell to a specific fate." + "Glandular cell of gallbladder epithelium." "CALOHA:TS-1278" + "Glandular cell of colon epithelium. Example: Goblet cells; enterocytes or absorptive cells; enteroendocrine and M cells." "CALOHA:TS-1274" + "An intestinal crypt that is located in the duodenum." "EMAPA:37838 FMA:269063" + "A muscle that is attached to a vertebra of the vertebral column." "FMA:22594" + "The process that gives rise to a tendon. This process pertains to the initial formation of a tendon from unspecified parts." + "The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, a mesodermal or neural crest cell that gives rise to bone." + "A metastasis-suppressor KiSS-1 that is encoded in the genome of human." "UniProtKB:Q15726" + "An enteroendocrine cell that produces glucagon." "FMA:62939" + "The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds." "Wikipedia:Proteolysis" + "Any process that stops, prevents or reduces the frequency, rate or extent of eosinophil migration." + "Skeletal element within the mouth (or in some species, upper part of the digestive tract) that is composed of dentine and is used in procuring or masticating food." "MESH:D014070 NCIT:C12506 GAID:1260 TAO:0001625 SCTID:302214001 MAT:0000041 MIAA:0000041 CALOHA:TS-1055 Wikipedia:Tooth UMLS:C0040426 XAO:0000431 EFO:0000839 EV:0100063 AEO:0000220 VHOG:0001733 EMAPA:32906 MA:0000348 FMA:12516 BTO:0000397 EHDAA2:0004605" + "A process in which a protein is transported to, or maintained in, the location of an actin filament bundle." + "Any process that stops, prevents, or reduces the frequency, rate or extent of synapse assembly, the aggregation, arrangement and bonding together of a set of components to form a synapse." + "A cell within the primary follicle of the ovary." "FMA:70590" + "The disaggregation of a nucleus into its constituent components." + "Layer of nonkeratinized squamous epithelium lining the conjunctiva, overlying scleral tissue." "BTO:0005131 NCIT:C32365 FMA:62131 EFO:0001916 UMLS:C1179037" + "The final stage of the nucleated, immature erythrocyte, before nuclear loss. Typically the cytoplasm is described as acidophilic, but it still shows a faint polychromatic tint. The nucleus is small and initially may still have coarse, clumped chromatin, as in its precursor, the polychromatophilic erythroblast, but ultimately it becomes pyknotic, and appears as a deeply staining, blue-black, homogeneous structureless mass. The nucleus is often eccentric and sometimes lobulated." "FMA:84646" + "Any process that stops, prevents or reduces the frequency, rate or extent of acetylcholine biosynthetic process." + "The major nerves supplying sympathetic innervation to the abdomen, including the greater, lesser, and lowest (or smallest) splanchnic nerves that are formed by preganglionic fibers from the spinal cord which pass through the paravertebral ganglia and then to the celiac ganglia and plexuses and the lumbar splanchnic nerves carry fibers which pass through the lumbar paravertebral ganglia to the mesenteric and hypogastric ganglia." "SCTID:264198001 GAID:800 FMA:5883 Wikipedia:Splanchnic_nerves BAMS:spn EMAPA:37959 MESH:D013153" + "The progression of a pyramidal neuron from its initial formation to its mature state." + "Any process that activates or increases the frequency, rate or extent of lactation." + "An alpha-(1,3)-fucosyltransferase that is a translation product of the human FUT4 gene or a 1:1 ortholog thereof." + "Any process that modulates the frequency, rate or extent of branchiomeric skeletal muscle development. Branchiomeric skeletal muscle development is the process whose specific outcome is the progression of the branchiomeric skeletal muscle over time, from its formation to the mature structure." + "Any process that stops, prevents, or reduces the rate of CD8-positive, alpha-beta T cell differentiation." + "GC_ID:1" + "EHDAA2:0001841 EMAPA:16239 VHOG:0000489 FMA:70318 EHDAA:484" + "The process whose specific outcome is the progression of the oenocyte over time, from its formation to the mature structure. The oenocytes are large secretory cells found in clusters underlying the epidermis of larval abdominal segments." + "An epithelium that is part of a male urethra." "EMAPA:30467 FMA:19684" + "Binding to a protein or protein complex in the presence of calcium." + "A neuron that releases catecholamine as a neurotransmitter." + "The muscle system process that results in enlargement or overgrowth of all or part of a muscle organ due to an increase in the size of its muscle cells. Physiological hypertrophy is a normal process during development (it stops in cardiac muscle after adolescence) and can also be brought on in response to demand. In athletes cardiac and skeletal muscles undergo hypertrophy stimulated by increasing muscle activity on exercise. Smooth muscle cells in the uterus undergo hypertrophy during pregnancy." "Wikipedia:Muscle_hypertrophy" + "The directed movement of amino acids, organic acids containing one or more amino substituents, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "A B220-positive CD38-positive naive B cell is a CD38-positive naive B cell that has the phenotype B220-positive, CD38-positive, surface IgD-positive, surface IgM-positive, and CD27-negative, and that has not yet been activated by antigen in the periphery." + "A bronchiole that is part of a left lung [Automatically generated definition]." "SCTID:200484003 UMLS:C0225674 NCIT:C49252 EMAPA:19000 MA:0001778" + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." + "Any process that activates or increases the frequency, rate or extent of neuron maturation." + "Any process that activates or increases the frequency, rate or extent of keratinocyte differentiation." + "FMA:87177" + "FMA:14383 SCTID:281248001 MA:0000229 EMAPA:16986 BTO:0000927 MA:0002408 EHDAA:4675 FMA:5913" + "A protein that is a translation product of the human CD8A gene or a 1:1 ortholog thereof. CD8 is a transmembrane that is a co-receptor for MHC class-I antigen/T-cell receptor interaction. The most common form of CD8 is composed of a CD8 alpha and a CD8 beta chain." + "A mesenchymal stem cell that is part of the bone marrow." + "Any process that decreases the frequency, rate, or extent of the self-propelled movement of a cell or organism from one location to another in a behavioral context; the aspect of locomotory behavior having to do with movement." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of an acute inflammatory response." + "Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens." "Wikipedia:Innate_immune_system" + "GC_ID:1" + "The upper (superior) side of the tongue." "FMA:54646" + "EMAPA:35869 MA:0003178" + "A C-C chemokine receptor type 6 that is encoded in the genome of human." "UniProtKB:P51684 Reactome:R-HSA-373089 DTO:02100058" + "Enables the transmembrane transfer of a calcium ion by a channel that opens when glutamate has been bound by the channel complex or one of its constituent parts." + "A mucosa that is part of a gastrointestinal system." "EMAPA:36591 BTO:0005568 BTO:0000546 MA:0001521 SCTID:410433007" + "Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion. It allows the fetus to move freely without the walls of the uterus being too tight against its body. Buoyancy is also provided. The composition of the fluid changes over the course of gestation. Initially, amniotic fluid is similar to maternal plasma, mainly water with electrolytes. As the fetus develops, proteins, carbohydrates, lipids, phospholipids originating from the lungs, fetal cells, and urea are deposited in the fluid." "NCIT:C13188 EMAPA:36771 CALOHA:TS-0034 MESH:D000653 VHOG:0001267 EV:0100123 UMLS:C0002638 GAID:1155 FMA:305905 BTO:0000068 MA:0002893 ENVO:02000021" + "OBSOLETE: A classification of cells by the number of their nuclei." + "Any apoptotic process in a type B pancreatic cell, a cell located towards center of the islets of Langerhans that secretes insulin." + "A glial cell that myelinates axonal processes." + "The Ejaculatory ducts (ductus ejaculatorii) are paired structures in male anatomy, about 2 cm in length. Each ejaculatory duct is formed by the union of the vas deferens with the duct of the seminal vesicle. They pass through the prostate, and empty into the urethra at the Colliculus seminalis. During ejaculation, semen passes through the ducts and exits the body via the penis[WP,unvetted]." "MA:0003247 NCIT:C32493 UMLS:C0013747 EMAPA:19088 SCTID:279665005 MIAA:0000170 Wikipedia:Ejaculatory_duct FMA:19325 GAID:388 MAT:0000170 BTO:0001580 MESH:D004543 CALOHA:TS-0211 EFO:0000985" + "Any process that modulates the rate frequency or extent of a phase of elevated metabolic activity, during which oxygen consumption increases; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals." + "A myoepithelial cell that is part of the mammary gland alveolus." "FMA:67802" + "Any process that activates or increases the frequency, rate or extent of bone development." + "A cell morphology that inheres in neurons which possess three or more neurites, usually a single axon and many dendrites and dendritic branches." "NLX:378 ILX:0107196" + "Any process that activates, maintains or increases the frequency, rate or extent of synapse assembly, the aggregation, arrangement and bonding together of a set of components to form a synapse." + "A hemocyte that synthesizes and secretes melanins as part of the antimicrobial immune response. It is characterized morphologically by crystal inclusions of phenoloxidases in its cytoplasm, hence its name." + "Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue." "NCIT:C12703 EHDAA2:0000428 GAID:1304 MIAA:0000173 XAO:0000001 EV:0100003 VHOG:0000153 SCTID:362851007 MAT:0000173 EFO:0000414 CALOHA:TS-0216 FMA:69070 Wikipedia:Ectoderm TAO:0000016 MESH:D004475 ZFA:0000016 MAT:0000155 BILA:0000036 AAO:0000137 BTO:0000315 EMAPA:16069 UMLS:C0013574" + "Paired appendage that consists of the posterior appendicular skeleton and associated soft and hard tissues, but excludes the pelvic girdle and its associated soft and hard tissues." "VSAO:0000126" + "The directed movement of an amide, any compound containing one, two, or three acyl groups attached to a nitrogen atom, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "The process in which the anatomical structures of the ascending aorta are generated and organized. The ascending aorta is the portion of the aorta in a two-pass circulatory system that lies between the heart and the arch of aorta. In a two-pass circulatory system blood passes twice through the heart to supply the body once." + "The process in which the anatomical structures of a metanephric tubule are generated and organized from an epithelium. A metanephric tubule is an epithelial tube that is part of the metanephros." + "The process in which the anatomical structures of ganglion are generated and organized." + "GC_ID:1" + "An epithelial cell that is part of the collecting duct of renal tubule." "FMA:70982 KUPO:0001059" + "A broad fold of peritoneum that extends from the side of the uterus to the wall of the pelvis." "SCTID:362723009 MESH:D001956 FMA:16516 NCIT:C12318 UMLS:C0006205 Wikipedia:Broad_ligament_of_the_uterus" + "A sesamoid bone that is part of a pes." "SCTID:244675002 FMA:45096" + "White matter tract that contains projections from the olfactory bulb to the olfactory cortex (Maryann Martone)." "UMLS:C0152330 HBA:265505514 neuronames:284 FMA:61971 EV:0100175 BM:Tel-LOT BAMS:LOTR MBA:665 DMBA:17773 BIRNLEX:1559 BAMS:LDTR SCTID:369107001 BAMS:lot DHBA:12075 BAMS:lo Wikipedia:Lateral_olfactory_stria" + "The parathyroid gland is an endocrine gland for secretion of parathyroid hormone, usually found as a pair, embedded in the connective tissue capsule on the posterior surface of the thyroid gland. Parathyroid regulates calcium and phosphorous metabolism." "UMLS:C0030518 XAO:0000167 Wikipedia:Parathyroid_gland VHOG:0001188 SCTID:181121007 MESH:D010280 BTO:0000997 EFO:0000862 GAID:452 AAO:0010545 MA:0000128 MIAA:0000082 NCIT:C12765 EV:0100134 FMA:13890 EMAPA:32812 CALOHA:TS-0745 MAT:0000082" + "The process in which the comma-shaped body is generated and organized. The comma-shaped body is the precursor structure to the S-shaped body that contributes to the morphogenesis of the nephron." + "Immature interstitial dendritic cell is a interstitial dendritic cell that is CD80-low, CD86-low, and MHCII-low." + "A cell whose nucleus contains a single haploid genome." + "A coiling which is normal or average." + "Any process that activates or increases the frequency, rate or extent of cell maturation." + "Any process that activates or increases the frequency, rate, or extent of proteolysis associated with antigen processing and presentation." + "Any process that modulates the frequency, rate, or extent of CD8-positive, alpha-beta T cell differentiation." + "An endothelial cell that is part of the arteriole." "KUPO:0001097 FMA:67760" + + "A structure that will develop into a diaphragm." "EHDAA2:0000599" + "A specific region of the urogenital sinus epithelium into the area in which the prostate gland will develop." + "A homeostatic process involved in the maintenance of a steady state level of amino acids within a cell." + "A cell that is specialised to accumulate a particular substance(s)." + "A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane." + "The expansion of a CD8-positive, alpha-beta T cell population by cell division." + "A size quality which is relatively normal or average" + "The process in which immature B cells from the bone marrow become mature B cells in the spleen. Transitional stage B cells are subdivided into transitional one (T1) and transitional two (T2) stages and are short-lived and functionally incompetent." + "Any process that stops, prevents or reduces the frequency, rate or extent of chromatin organization." + "Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic." "MIAA:0000369 EFO:0001650 AAO:0010466 MAT:0000369 XAO:0000305" + "EMAPA:35460" + "An integrin alpha lacking A domain that is a translation product of the human ITGA2B gene or a 1:1 ortholog thereof." "IUPHARobj:2441" + "The respiratory conducting tubes distal to the respiratory bronchiole that lead to the alveolar sacs and the alveoli." "NCIT:C32056 UMLS:C0391892 Wikipedia:Alveolar_duct MA:0000417 EMAPA:32694 FMA:7341" + "Any process that modulates the frequency, rate or extent of the directed movement of iron ions (Fe) from one side of a membrane to the other by means of some agent such as a transporter or pore." + "A zone of skin that is part of a prepuce of clitoris." "FMA:27886 SCTID:367670008" + "Any process that activates or increases the frequency, rate or extent of cilium-dependent cell motility." + "A spermatid in a late stage of maturation that has an elongated morphology and is transcriptionally inert when the acrosome is fully developed." + "Multilaminar epithelium which consists of more than one layer of squamous cells only one layer of which is in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, epithelium of wall of esophagus.[FMA]." "NCIT:C13180 Wikipedia:Stratified_squamous_epithelium FMA:45563 UMLS:C0836131" + "A thymus lobe that is in the right side of a thymus." "RETIRED_EHDAA2:0001758 SCTID:187981000 FMA:71194" + "Any process that modulates the frequency, rate or extent of calcium-mediated signaling, the process in which a cell uses calcium ions to convert an extracellular signal into a response." + "EMAPA:28322" + "Any process that modulates the frequency, rate or extent of corticosteroid hormone secretion." + "TAO:0000229 ZFA:0000229" + "Any process that modulates the frequency, rate, or extent of T cell mediated cytotoxicity." + "The movement of a leukocyte within or between different tissues and organs of the body." + "The process in which a relatively unspecialized cell acquires the specialized features of an oenocyte. Oenocytes are large secretory cells found in clusters underlying the epidermis of larval abdominal segments." + "A complete three dimensional shape in which for every line connecting pair of points on the object is within the object. Or: a shape lacking cavities. Contrast: concave." "Image:http://upload.wikimedia.org/wikipedia/commons/0/06/Convex_polygon_illustration1.png" + "The directed, self-propelled movement of a cilium (aka flagellum) that contributes to the movement of a flagellated sperm." "Wikipedia:Sperm_motility" + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a vasopressin stimulus." + + "An L-selectin that has been processed by proteolytic cleavage." + "The portion of the small intestine that extends from the jejunum to the colon." "BTO:0000620 galen:Ileum AAO:0010403 MIAA:0000282 CALOHA:TS-0472 FMA:7208 XAO:0000237 MESH:D007082 GAID:315 NCIT:C12387 EV:0100075 EFO:0001334 MAT:0000282 EMAPA:32764 SCTID:181249005 MA:0000339 VHOG:0000647 Wikipedia:Ileum UMLS:C0020885" + "Any process that stops, prevents or reduces the frequency, rate or extent of granulosa cell proliferation." + "FMA:260877" + "KUPO:0001137" + "The rightmost of the two common carotid arteries, originating from in the neck from the brachiocephalic trunk." "EMAPA:35749 UMLS:C0226086 FMA:3941 NCIT:C33473 MA:0001928 Wikipedia:Right_common_carotid_artery SCTID:362042003" + "Any process that activates or increases the frequency, rate, or extent of leukocyte activation." + "An integrin alpha with A domain that is a translation product of the human ITGA2 gene or a 1:1 ortholog thereof." "IUPHARobj:2440" + "The process whose specific outcome is the progression of the hypoglossal nerve over time, from its formation to the mature structure. This motor nerve innervates all the intrinsic and all but one of the extrinsic muscles of the tongue." + "The process in which the neural tube is divided into specific regions along the rostrocaudal axis." + "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform lutein." + "A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity." "FMA:86140" + "Subdivision of skeletal system that consists of all skeletal elements in the thoracic region of the trunk. In most vertebrates this is the rib cage and sternum." "FMA:77169 Wikipedia:Thoracic_skeleton EHDAA2:0002013" + "The process in which the anatomical structures of a mesonephric nephron tubule are generated and organized. A mesonephric nephron tubule is an epithelial tube that is part of the mesonephric nephron, the functional part of the mesonephros." + "GC_ID:1" + "Any process that modulates the frequency, rate or extent of dendrite morphogenesis." + "Specialized ependymal cell that produces the cerebrospinal fluid from the blood and secretes it into the lumen of the brain and spinal chord." "FMA:70549" + "An OFF bipolar cell with a small dendritic tree that provides most of the triad-associated basal (flat) contacts at cone pedicles." + "The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a nephrocyte. A nephrocyte is an insect renal cell that filters hemolymph. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state." + "A visceromotor motor neuron whose soma is located in the hindbrain, and which synapses to parasympathetic neurons that innervate tear glands, sweat glands, and the smooth muscles of the head." + "An epithelial cell of the retinal pigmented epithelium." "FMA:75802 BTO:0004910" + "DHBA:12682 EMAPA:32917" + "The chemical reactions and pathways resulting in the breakdown of norepinephrine, a hormone secreted by the adrenal medulla, and a neurotransmitter in the sympathetic peripheral nervous system and in some tracts in the central nervous system. It is also the demethylated biosynthetic precursor of epinephrine." "Wikipedia:Norepinephrine#Degradation" + "Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function." "UMLS:C0460002 AAO:0000007 EMAPA:16103 CARO:0000011 SCTID:278195005 BILA:0000011 TAO:0001439 AEO:0000011 NCIT:C12919 MA:0000003 WBbt:0005746 ZFA:0001439 galen:AnatomicalSystem BSA:0000049 HAO:0000011 VHOG:0001725 WBbt:0005763 BIRNLEX:14 XAO:0003002 EHDAA:392 TGMA:0001831 EV:0100000 CALOHA:TS-2088 Wikipedia:Organ_system FMA:7149 EHDAA2:0003011" + "A joint that connects the tibia and the fibula." "Wikipedia:Tibiofibular_joint FMA:35181 SCTID:244554002" + "The progression of the adenohypophysis over time from its initial formation until its mature state. The adenohypophysis is the anterior part of the pituitary. It secretes a variety of hormones and its function is regulated by the hypothalamus." + "The process in which the mesonephric S-shaped body is generated and organized. The mesonephric S-shaped body is the successor of the mesonephric comma-shaped body that contributes to the morphogenesis of a nephron in the mesonephros." + "A proximal mesopodial endochondral element that is composed primarily of a bone tissue." + "The process in which a chondroblast acquires specialized structural and/or functional features of a chondrocyte that will contribute to the development of a bone. A chondrocyte is a polymorphic cell that forms cartilage." + "A border associated macrophage found at the interface between the blood and the cerebrospinal fluid in the brain. This central nervous system macrophage has a star-like shaped body and expresses scavenger receptors." + "A transversely striated, synctial cell of skeletal muscle. It is formed when proliferating myoblasts exit the cell cycle, differentiate and fuse." "MESH:D018485" + "An immune response mediated by lymphocytes expressing specific receptors for antigen produced through a somatic diversification process that includes somatic recombination of germline gene segments encoding immunoglobulin superfamily domains. Recombined receptors for antigen encoded by immunoglobulin superfamily domains include T cell receptors and immunoglobulins (antibodies) produced by B cells. The first encounter with antigen elicits a primary immune response that is slow and not of great magnitude. T and B cells selected by antigen become activated and undergo clonal expansion. A fraction of antigen-reactive T and B cells become memory cells, whereas others differentiate into effector cells. The memory cells generated during the primary response enable a much faster and stronger secondary immune response upon subsequent exposures to the same antigen (immunological memory). An example of this is the adaptive immune response found in Mus musculus." + "The directed movement of a carbohydrate derivative into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "The process whose specific outcome is the progression of the posterior lateral line ganglion over time, from its formation to the mature structure. The posterior lateral line ganglion develops from cranial ectodermal placodes situated behind the ear." + "A sulcus limitans of neural tube that is part of a future myelencephalon." "EHDAA2:0001945" + "A myeloid progenitor cell committed to the monocyte lineage. This cell is CD11b-positive, has basophilic cytoplasm, euchromatin, and the presence of a nucleolus." "CALOHA:TS-1195 FMA:83553" + "A process in which a protein is transported to, or maintained in, a location within an organelle." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a neurotransmitter into a neuron or glial cell." + "Binding to a protein-lipid complex, any macromolecular complex that contains both protein and lipid molecules." + "White matter that is part of a cerebral hemisphere." "CALOHA:TS-2362 FMA:241998 UMLS:C1284115 EMAPA:35237 BIRNLEX:711 neuronames:189 BAMS:cw FMA:61822 SCTID:361691006 FMA:256174 UMLS:C0152295 BTO:0000236 NCIT:C49347 MA:0000945" + "A B-1 B cell that has the phenotype CD5-positive." + "A basal cell that is part of the epithelium of trachea." "FMA:263118" + "Any cellular metabolic process involving nucleic acids." + "A lobe of thyroid gland that is in the right side of a thyroid gland." "MA:0000729 VHOG:0000733 FMA:13368 NCIT:C33491 UMLS:C0229581 SCTID:170482008 EHDAA2:0001759 EMAPA:18198" + "The process in which vesicles are directed to specific destination membranes. Targeting involves coordinated interactions among cytoskeletal elements (microtubules or actin filaments), motor proteins, molecules at the vesicle membrane and target membrane surfaces, and vesicle cargo." + "A shape that inheres in a 3 dimensional entity." + "GC_ID:1" + "Hermaphroditic organism that produces both male and female gametes at the same time." "AAO:0010046 HAO:0000046 BILA:0000046 CARO:0000046 TADS:0000609" + "Anatomical structure that overlaps the outer epithelial layer and is adjacent to the space surrounding the organism." "TAO:0000292 galen:SurfaceRegion Wikipedia:Surface_structure VSAO:0000001 EHDAA2_RETIRED:0003010 XAO:0003028 ZFA:0000292 AAO:0010337 AEO_RETIRED:0000010" + "An epithelium that is part of a handplate." "EHDAA2:0000730 EMAPA:32630" + "A nucleus of brain that is part of a hypothalamus." "FMA:258762 BTO:0002449 SCTID:279304003 EMAPA:35417 MA:0002426" + "The process in which the anatomical structures of the outflow tract are generated and organized. The outflow tract is the portion of the heart through which blood flows into the arteries." + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ketone stimulus." + "Any process that stops, prevents, or reduces the frequency, rate or extent of isotype switching to IgE isotypes." + "The movement of a leukocyte within or between different tissues and organs of the body as part of an immune response." + "A compound tubular submucosal gland found in that portion of the duodenum which is above the hepatopancreatic sphincter (Sphincter of Oddi). The main function of these glands is to produce a mucus-rich alkaline secretion (containing bicarbonate)[WP]." "BTO:0002376 GAID:314 UMLS:C0006323 MA:0001551 FMA:15060 EMAPA:36522 MESH:D002011 NCIT:C13010 Wikipedia:Brunner's_glands SCTID:41298001" + "An afferent neuron of the vestibular system that innervate the base of the hair cell and increase or decrease their neural firing rate as the receptor cell is excited or inhibited." + "KUPO:0001136" + "The process in which a relatively unspecialized cell acquires specialized features of a neuron that will reside in the forebrain." + "The process in which the anatomical structure of the retina is generated and organized." + "A dura mater that is part of a midbrain [Automatically generated definition]." "MA:0001060 EMAPA:17793 VHOG:0000410" + "Mature CD11c-negative plasmacytoid dendritic cell is a CD11c-negative plasmacytoid dendritic cell is CD80-high, CD86-high, MHCII-high and is CD83-positive." + "The regulated release of a gonadotropin, any hormone that stimulates the gonads, especially follicle-stimulating hormone and luteinizing hormone." + "A CD83 molecule that is encoded in the genome of mouse." "UniProtKB:O88324" + "A cell morphology that inheres in neurons that have dendritic processes radiating from the cell body forming a star-like shape." "SAO:9271919883 ILX:0111036" + "Enables the transfer of cation from one side of a membrane to the other." + "A goblet cell that is part of the epithelium of intestinal villus." "FMA:263046" + "Any process that contributes to cytokine production by a myeloid cell." + "A region of somite adjacent to presomitic mesoderm." "XAO:0004074 ZFA:0001462 TAO:0001462" + "A mucosa-associated lymphoid tissue macrophage found in the mucosa-associated lymphoid tissues of the gut." + "An integrin alpha with A domain that is a translation product of the human ITGAM gene or a 1:1 ortholog thereof. They constitute subunits of the integrin alpha-M/beta-2 receptor. This receptor is implicated in various adhesive interactions of monocytes, macrophages and granulocytes as well as in mediating the uptake of complement-coated particles. It is also a receptor for fibrinogen, factor X and ICAM1." "IUPHARobj:2452" + "The process in which a relatively unspecialized cell acquires specialized features of a hippocampal pyramidal neuron, a pyramidal cell of the hippocampus." + "FMA:83521" + "A dendritic cell type of distinct morphology, localization, and surface marker expression (CD123-positive) from other dendritic cell types and associated with early stage immune responses, particularly the release of physiologically abundant amounts of type I interferons in response to infection." "BTO:0004625" + "KUPO:0001057" + "Any process that enhances the establishment or increases the extent of the excitatory postsynaptic potential (EPSP) which is a temporary increase in postsynaptic potential due to the flow of positively charged ions into the postsynaptic cell. The flow of ions that causes an EPSP is an excitatory postsynaptic current (EPSC) and makes it easier for the neuron to fire an action potential." + "A dendritic cell that captures antigens in a lung and migrates to a lymph node or to the spleen to activate T cells." + "The process in which the vasculature of the retina is generated and organized." + "Any process that modulates the frequency, rate or extent of myeloid progenitor cell differentiation." + "A portion of connective tissue that is part of a foot [Automatically generated definition]." "MA:0000644 EMAPA:37329" + "Any process that stops, prevents, or reduces the frequency, rate or extent of bone remodeling." + "An epithelium that is part of a colon [Automatically generated definition]." "BTO:0001709 CALOHA:TS-0163 MA:0003195 SCTID:42978003 FMA:17302 EMAPA:18941 TAO:0005128 ZFA:0005128" + "A Langerhans cell that is in the epidermis and is CD45-positive, MHCII-positive, and CD11b-positive." + "Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions." + "A CD8-positive, alpha-beta T cell with the phenotype CD69-positive, CD62L-negative, CD127-negative, CD25-positive, and CCR7-negative." + "Any process that activates or increases the frequency, rate or extent of synapse pruning." + "The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome." "Wikipedia:Translation_(genetics)" + "Merging of two or more vacuoles, or of vacuoles and vesicles within a cell to form a single larger vacuole." + "The process preceding formation of the peptide bond between the first two amino acids of a protein in the cytoplasm. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA." + "A round nodule, small eminence, or warty outgrowth on an anatomical surface, such as bones, skin, or within the lungs (in the case of tuberculosis). They are also found on the leading edge of Humpback Whale's flippers, improving fluid flow over the flipper's surface[WP]." "AAO:0010605 FMA:75429 Wikipedia:Tubercle_(anatomy) BTO:0002173" + "The process whose specific outcome is the progression of a peritoneum over time, from its formation to the mature structure." + "The anatomical space within the intestine." "ZFA:0005807 WBbt:0005791 FMA:14586 TADS:0000495" + "The stages of blood cell formation that take place after completion of embryonic development." + "The chemical reactions and pathways resulting in the formation of any of a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine." "Wikipedia:Catecholamines" + "An early growth response protein 2 that is encoded in the genome of mouse." "UniProtKB:P08152" + "The directed movement of substances from the Golgi to lysosomes." + "The process in which a relatively unspecialized cell acquires specialized features of a smooth muscle cell in the ureter." + "A dense core vesicle (granule) that is part of a neuron. These vesicles typically contain neuropeptides. They can be found in all parts of neurons, including the soma, dendrites, axonal swellings (varicosities) and synaptic terminals." + "Peripheral portion of the lymph node, underneath the capsule[WP]." "UMLS:C0933402 FMA:66253 EMAPA:35525 MA:0000740 NCIT:C33029 Wikipedia:Cortex_of_lymph_node" + "The process whose specific outcome is the progression of the skin epidermis over time, from its formation to the mature structure." + "A cellular process that results in the controlled breakdown of synapse. After it starts the process is continuous until the synapse has disappeared." + "The process whose specific outcome is the progression of a mesonephric glomerular epithelial cell over time, from its formation to the mature structure. Mesonephric glomerular epithelial cells are specialized epithelial cells that form part of the mesonephric glomerulus; there are two types, mesonephric glomerular parietal epithelial cells and mesonephric glomerular visceral epithelial cells." + "Either of a pair of lingual muscles with origin in the mandible, with insertion to the lingual fascia below the mucous membrane and epiglottis, with nerve supply from the hypoglossal nerve, and whose action depresses and protrudes the tongue." "FMA:46690 EHDAA2:0000704 Wikipedia:Genioglossus_muscle UMLS:C0224194 NCIT:C52928 MA:0002307 VHOG:0000847 EHDAA:9150 AAO:0010660 SCTID:244784007 EMAPA:18276" + "A type of foam cell derived from a smooth muscle cell containing lipids in small vacuoles and typically seen in atherolosclerotic lesions, as well as other conditions." + "Any apoptotic process in a mesenchymal cell. A mesenchymal cell is a loosely associated cell that is part of the connective tissue in an organism. Mesenchymal cells give rise to more mature connective tissue cell types." + "A portion of connective tissue that is part of a lobar bronchus [Automatically generated definition]." "EMAPA:37647 MA:0001841" + "Any process that stops, prevents or reduces the frequency, rate or extent of retrograde dense core granule transport." + "Any process that activates or increases the frequency, rate or extent of granulocyte differentiation." + "Any process that stops, prevents, or reduces the frequency, rate or extent of isotype switching." + "A lactiferous gland that is part of the abdominal region [Automatically generated definition]." "SCTID:68037003 EMAPA:36507 MA:0000787 SCTID:113191002" + "Any process that stops, prevents, or reduces the rate of memory T cell differentiation." + "A macromolecular localization process in which RNA is transported to and maintained in a location within the nucleus." + "A foramen within a vertebral element through which the spinal cord runs. It is formed by the anterior segment, and the posterior part, the vertebral arch." "SCTID:280734009 AAO:0000729 MA:0001454 EMAPA:37803 FMA:13479 Wikipedia:Vertebral_foramen" + "A zone of skin that is part of a leg [Automatically generated definition]." "FMA:37828 MA:0000674 EMAPA:37352 UMLS:C0222279 NCIT:C52749" + "Any process that activates or increases the frequency, rate or extent of lung goblet cell differentiation." + "An embryonic structure that is derived from the inner cell mass and lies above the hypoblast and gives rise to the three primary germ layers." "EHDAA2:0000444 UMLS:C1516906 EMAPA:16050 EHDAA:75 EHDAA:42 NCIT:C34164" + "One of the two photoreceptor cell types of the vertebrate retina. In rods the photopigment is in stacks of membranous disks separate from the outer cell membrane. Rods are more sensitive to light than cones, but rod mediated vision has less spatial and temporal resolution than cone vision." "FMA:67747 CALOHA:TS-0870 BTO:0001024" + "Any signal transduction that is involved in cellular response to ammonium ion." + "The cellular developmental process by which a cell establishes the intrinsic character of a cell or tissue region irreversibly committing it to a particular fate." + + "A tubule that extends from the posterior part of the digestive tract which absorbs solutes, water, and wastes from the surrounding hemolymph. Each tubule consists of a single layer of cells that is closed off at the distal end with the proximal end joining the alimentary canal at the junction between the midgut and hindgut[WP,modified]." "GAID:1228 SCTID:41055008 TADS:0000163 EFO:0000243 MESH:D008317 MIAA:0000123 BTO:0000810 Wikipedia:Malpighian_tubule TGMA:0001038 MAT:0000123" + "The subdivision of the skeleton that consists of all the skeletal elements at the distalmost end of the pedal autopodium - i.e. the bones of the foot or their cartilaginous precursors[cjm]." "FMA:78512 VSAO:0005030 Wikipedia:Phalanges_of_the_foot" + "Any process that decreases the rate, frequency or extent of mast cell differentiation, the process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of a mast cell. A mast cell is a cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation." + "Any of the coil glands of the skin that secrete sweat." "CALOHA:TS-0993 Wikipedia:Sweat_gland MA:0000150 UMLS:C0038989 EV:0100160 GAID:943 BTO:0001331 FMA:59152 EMAPA:35844 MESH:D013545 VHOG:0001467 NCIT:C33712 SCTID:361700009" + "The process whose specific outcome is the formation of the central canal of the spinal cord from its formation to the mature structure. The central canal is a spinal cord structure that is part of the ventricular system and is filled with cerebral-spinal fluid and runs the length of the spinal cord." + "Interneuromast cell is a neuroectodermal cell deposited by the migrating lateral line primordium between the neuromasts. Interneuromast cells proliferate and migrate to form additional neuromasts." + "Any process that decreases the rate, frequency or extent of blood vessel remodeling, the reorganization or renovation of existing blood vessels." + "Any process that stops or reduces the frequency, rate or extent of chromatin binding. Chromatin binding is the selective interaction with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase." + "The binding by a cell-adhesion protein on a cell surface to an adhesion molecule on another cell surface or an external substrate, to mediate adhesion of the cell to the external substrate or to another cell." + "Any process that modulates the frequency, rate or extent of cellular response to insulin stimulus." + "The process in which a relatively unspecialized cell acquires specialized structural and/or functional features of a somatotropin secreting cell. A somatotropin secreting cell is an acidophilic cell of the anterior pituitary that produces growth hormone, somatotropin." + "A branchiness quality inhering in a bearer by virtue of the bearer's having branches." + "A protein that is a translation product of the human TAC3 gene or a 1:1 ortholog thereof." + "The chemical reactions and pathways involving the ammonium ion." + "A medium spiny neuron that expresses both DRD1 and DRD2 and is part of an extra-striosomal part of dorsal striatum." + "The chemical reactions and pathways resulting in the breakdown of organic cyclic compound." + "A Feyrter cell that is part of the epithelium of trachea." "FMA:263184" + "The subcutaneous mechanoreceptors that innervate vellus hairs." + "The fundus is the portion of the stomach that lies above the cardiac notch, and contains the fundic glands[GO, Kardong]." "EFO:0002554 VHOG:0000421 NCIT:C12257 EMAPA:17886 GAID:320 EHDAA2:0001919 SCTID:362139007 MESH:D005748 Wikipedia:Fundus_(stomach) EHDAA:4844 MA:0001612 BTO:0000502 FMA:14559 galen:GastricFundus UMLS:C0017129" + "The process whose specific outcome is the progression of the ammon gyrus over time, from its formation to the mature structure. The ammon gyrus, often subdivided into the CA1 and CA3 regions, is one of the two interlocking gyri of the hippocampus that is rich in large pyramidal neurons." + "A process in which a protein is transported to, or maintained at, a microtubule." + "A(n) serous secreting cell that is part of a(n) bronchus submucosal gland." + "Any process that activates or increases the frequency, rate or extent of proteolysis involved in protein catabolic process." + "A network of blunt ended vessels lacking direct connection to the blood vascular system. These vessels collect and drain fluids and macromolecules from interstitial spaces throughout the animal. They derive from a subpopulation of endothelial cells and have walls that are much thinner than the blood carrying vessels. Lymphatic vessels are usually classified as either superficial or deep." "FMA:63815 ZFA:0005105" + "The increase in size or mass of an anatomical structure that contributes to the structure attaining its shape." + "Any process that activates or increases the rate or extent of oligodendrocyte progenitor proliferation." + "The process whose specific outcome is the progression of the pallium over time, from its formation to the mature structure. The pallium is the roof region of the telencephalon." + "The process whose specific outcome is the progression of a gland over time, from its formation to the mature structure. A gland is an organ specialised for secretion." + + "Outer cortical portion of the kidney, between the renal capsule and the renal medulla." "BTO:0001166 MA:0000372 FMA:15581 galen:CortexOfKidney CALOHA:TS-0503 Wikipedia:Renal_cortex MESH:D007672 NCIT:C12739 UMLS:C0022655 SCTID:362211004 EMAPA:17952 GAID:424" + "A prolongation or process extending from a muscle cell. A muscle cell is a mature contractile cell, commonly known as a myocyte. This cell has as part of its cytoplasm myofibrils organized in various patterns." + "Any process that modulates the frequency, rate or extent of the transport of proteins from the Golgi to the plasma membrane." + "Any process that stops, prevents or reduces the frequency, rate or extent of progesterone secretion." + "Cell motility due to movement of eukaryotic cilia or bacterial-type flagella or archaeal-type flagella." + "A glandular epithelium that lines the stomach. The stomach's glandular epithelium is characterized by the presence of gastric glands." "MA:0002784 FMA:63458 EMAPA:35814" + "Any process that stops, prevents, or reduces the frequency, rate, or extent of natural killer cell cytokine production." + "Subdivision of trunk that lies between the head and the abdomen." "MA:0000022 SCTID:302551006 FMA:259209 EMAPA:35862 Wikipedia:Thorax" + "A zone of skin that is part of a external nose." "FMA:24763 EMAPA:37684 MA:0003090" + "The progression of the cornea over time, from its formation to the mature structure. The cornea is the transparent structure that covers the anterior of the eye." + + + "The process in which a relatively unspecialized cell acquires specialized features of a Malpighian tubule tip cell. A Malpighian tubule tip cell is a mitogenic signaling cell that controls the proliferation of its neighboring cells." + + "KUPO:0001015" + "The directed movement of a natural killer cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis)." + "A T-cell-specific surface glycoprotein CD28 that is encoded in the genome of human." "UniProtKB:P10747" + "Lymphatic vessel that is part of the mesentery." + + "A hepatic vein that is part of a right lobe of liver." "SCTID:18135006 FMA:14338 MA:0003034 EMAPA:37377" + "A group 2 innate lymphoid cell in the human with the phenotype CD25-positive, CD127-positive, CD161-positive, and GATA-3-positive." + + "A lymphatic endothelial cell located in the ceiling part of a lymph node medulla." + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures containing both actin and myosin or paramyosin. The myosin may be organized into filaments." + + "An epiphysis that is part of a fibula [Automatically generated definition]." "FMA:33726" + "The process aimed at the progression of a myotube cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse." + "A cell morphology that inheres in neurons which are small and round, and make highly specialized synapses with the axon initial segments of pyramidal neurons, wrapping them with candle-shaped synaptic 'cartridges'." "nifext:4 ILX:0102028 ilxtr:ChandelierPhenotype" + "The series of events in which a temperature stimulus (hot or cold) is received and converted into a molecular signal." + "A muscle that is part of the region of the hindlimb between the pelvis and ankle." "BTO:0000722 MA:0000672 RETIRED_EHDAA2:0000974 Wikipedia:Leg_muscle EHDAA:8291" + "The process whose specific outcome is the progression of the trigeminal nerve over time, from its formation to the mature structure. The trigeminal nerve is composed of three large branches. They are the ophthalmic (V1, sensory), maxillary (V2, sensory) and mandibular (V3, motor and sensory) branches. The sensory ophthalmic branch travels through the superior orbital fissure and passes through the orbit to reach the skin of the forehead and top of the head. The maxillary nerve contains sensory branches that reach the pterygopalatine fossa via the inferior orbital fissure (face, cheek and upper teeth) and pterygopalatine canal (soft and hard palate, nasal cavity and pharynx). The motor part of the mandibular branch is distributed to the muscles of mastication, the mylohyoid muscle and the anterior belly of the digastric. The mandibular nerve also innervates the tensor veli palatini and tensor tympani muscles. The sensory part of the mandibular nerve is composed of branches that carry general sensory information from the mucous membranes of the mouth and cheek, anterior two-thirds of the tongue, lower teeth, skin of the lower jaw, side of the head and scalp and meninges of the anterior and middle cranial fossae." + "An epithelium surrounding a gonad." "EHDAA:5931 UMLS:C1517534 NCIT:C32676 EHDAA:4032" + "Any process that modulates the frequency, rate or extent of juvenile hormone secretion." + "Any process that modulates the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hormone stimulus." + "The phase of growth and gene expression that male germ cells undergo as they enter the spermatocyte stage. The cells grow in volume and transcribe most of the gene products needed for the morphological events that follow meiosis." + "Any process that activates or increases the frequency, rate or extent of eosinophil activation." + "A cartilage element that is part of a manual digit mesenchyme." "EMAPA:32658" + "Any process that activates or increases the frequency, rate or extent of oligodendrocyte apoptotic process." + "Obsolete. Use PO:0000077 from Plant Ontology instead. Cell variable in form and size, being more or less thick, often lignified, secondary walls. Belongs to the category of subcells and may or may not be devoid of protoplast at maturity." + "Mutations occurring somatically that result in amino acid changes in the rearranged V regions of immunoglobulins." + "Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells." "FMA:62864 BTO:0000876 CALOHA:TS-0638" + + + "The process in which the anatomical structures of a mesonephric mesenchymal tissue are generated and organized. Mesonephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the mesonephros." + "Any process that stops, prevents, or reduces the frequency, rate or extent of smooth muscle cell differentiation." + "Any process in which a substance or cellular entity, such as a protein complex or organelle, is maintained in a specific location within, or in the membrane of, a cell, and is prevented from moving elsewhere." + "A C/C-C motif small inducible chemokine that is a translation product of the CCL3, CCL3L1/CCL3L3, or CCL4 gene." "PIRSF:PIRSF500569" + "Any fibroblast that is part of a reticular layer of dermis." + "Left part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane." + "Trunk portion of the neural crest. The trunk neural crest lies between the vagal and sacral neural crest and gives rise to two groups of cells. One group migrates dorsolateral and populates the skin, forming pigment cells and the other migrates ventrolateral through the anterior sclerotome to become the epinephrine-producing cells of the adrenal gland and the neurons of the sympathetic nervous system. Some cells remain in the sclerotome to form the dorsal root ganglia [Wikipedia]." "XAO:0000319 TAO:0001024 Wikipedia:Trunk_neural_crest VHOG:0000062 EFO:0003605 EHDAA2:0001901 AAO:0010582 ZFA:0001024" + "A bone marrow proteoglycan that is a translation product of some mRNA whose exon structure and start site selection renders it capable of giving rise to a protein with the amino acid sequence represented by UniProtKB:P13727-1 or a 1:1 ortholog thereof." + "Any process that decreases the rate, frequency or extent of metanephros development. Metanephros development is the process whose specific outcome is the progression of the metanephros over time, from its formation to the mature structure. The metanephros is an organ that filters the blood and excretes the end products of body metabolism in the form of urine." + "A shape quality inhering in a bearer by virtue of the bearer's being wound in a continuous series of loops." + "A membranous fold of the heart that prevents reflux of fluid." "UMLS:C0018826 NCIT:C12729 SCTID:181285005 BTO:0000564 Wikipedia:Cardiac_valve EV:0100024 VHOG:0000818 MESH:D006351 FMA:7110 XAO:0004126 TAO:0005065 ZFA:0005065 EMAPA:17869 GAID:176 galen:HeartValve MA:0000086" + "A blood vasculature that is part of a head." "TAO:0005297 ZFA:0005297" + "Binding to glycosphingolipid, a compound with residues of sphingoid and at least one monosaccharide." + "FBbt:00001691" + + "The process in which bone which forms deep in the organism are generated and organized." + "The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus." "Wikipedia:Steroid_metabolism" + "The appearance of interleukin-4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." + "A carpus bone or its cartilage or pre-cartilage precursor." + "Binding to a DNA-binding transcription factor, a protein that interacts with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a gene to modulate transcription." + "A T-cell surface glycoprotein CD8 beta chain isoform 1 that has had the signal peptide removed to yield the mature form." + "A choroid plexus epithelium that is part of a fourth ventricle [Automatically generated definition]." "UMLS:C1707392 MA:0000984 NCIT:C49230 FMA:242823" + "Muscle tissue which is unstriated, composed primarily of smooth muscle fibers surrounded by a reticulum of collagen and elastic fibers. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length[GO]." "AEO:0000141 galen:SmoothMuscle FMA:14070 CALOHA:TS-0943 VHOG:0001246 EFO:0000889 EHDAA2:0003141 NCIT:C12437 EMAPA:32717 UMLS:C1267092 BTO:0001260 AAO:0010244 XAO:0000175 GAID:167 ZFA:0005274 Wikipedia:Smooth_muscle_tissue MAT:0000303 TAO:0005274 galen:SmoothMuscleTissue MESH:D009130 WBbt:0005781 MA:0000166 EV:0100378 MIAA:0000303" + "The chemical reactions and pathways resulting in the formation of hyaluronan, the naturally occurring anionic form of hyaluronic acid, any member of a group of glycosaminoglycans, the repeat units of which consist of beta-1,4 linked D-glucuronyl-beta-(1,3)-N-acetyl-D-glucosamine." + "The process in which the anatomical structures of the hindlimb are generated and organized." + "The layer of the ovarian stroma lying immediately beneath the tunica albuginea, composed of connective tissue cells and fibers, among which are scattered primary and secondary (antral) follicles in various stages of development; the cortex varies in thickness according to the age of the individual, becoming thinner with advancing years; included in the follicles are the cumulus oophorus, membrana granulosa (and the granulosa cells inside it), corona radiata, zona pellucida, and primary oocyte; the zona pellucida, theca of follicle, antrum and liquor folliculi are also contained in the follicle; also in the cortex is the corpus luteum derived from the follicles." "FMA:18613 UMLS:C0227878 EMAPA:37927 NCIT:C33243" + "An innate lymphoid cell in the human with the phenotype NKp46-positive that is a precusor for NK cells and ILC3 cells." + "The process in which a relatively unspecialized cell acquires the specialized features of a photoreceptor cell, as found in the eye, the primary visual organ of most organisms." + "An organ component layer that is part of a integumental system." "SCTID:314820002" + "The specialization of the spermatid nucleus during the development of a spermatid into a mature male gamete competent for fertilization." + "PMID:10425795 PMID:8590690 PMID:12054223 PMID:9103655 PMID:10939673 PMID:36748408 PMID:11542017 PMID:7520741 PMID:2112744 PMID:10425797 PMID:11321113 PMID:10939677 PMID:32628106 PMID:11542087 PMID:11540071 PMID:11211268 PMID:11760965 PMID:10843050 PMID:11321083 PMID:10425796 PMID:8123559 PMID:10490293 PMID:10939651 PMID:8186100 PMID:9336922 PMID:270744 GC_ID:11 PMID:11411719" + "Clear to pale yellow watery secretions from the glands lining the small intestine walls. Secretion is stimulated by the mechanical pressure of partly digested food in the intestine." "MA:0002515 Wikipedia:Succus_entericus MESH:D007419 UMLS:C0021849 FMA:62974 BTO:0000644 GAID:1162 NCIT:C32875" + "CD8-positive, alpha-beta positive regulatory T cell with the phenotype CD28-negative and FoxP3-positive." + "Any process that modulates the frequency, rate or extent of the controlled release of a substance from a cell or a tissue." + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an iron ion stimulus." + "A mucosa that is part of a lobular bronchiole." + "The directed movement of L-glutamate out of the vacuole, across the vacuolar membrane." + "A duct that is located between lobules, within the thin connective tissue septa that separate lobules. All interlobular ducts are excretory." "NCIT:C32828 UMLS:C1512857 Wikipedia:Interlobular_ducts" + "The epithelial layer covering the biliary system. This includes the epithelium of the gallbladder (when present) as well as the intrahepatic and extrahepatic bile ducts." "BTO:0001513" + "Combining with a neuropeptide to initiate a change in cell activity." + "Any process that activates or increases the frequency, rate or extent of type B pancreatic cell apoptotic process." + "The progression of the cochlea over time from its formation to the mature structure. The cochlea is the snail-shaped portion of the inner ear that is responsible for the detection of sound." + "A neuron found in the anterior part of the ventral cochlear nucleus that has the appearance of bushes, having short dendrites. Bushy cells give outputs to different parts of the superior olivary complex." + "A tunica media that is part of a artery." "FMA:14273 UMLS:C1710627 NCIT:C49321 EMAPA:36294 SCTID:84300001 EV:0100029" + "An epithelial cell of the placenta." + "Cell that provides some or all mechanical, nutritional and phagocytic support to their neighbors." "BTO:0002315" + "The myofibril assembly process that results in the organization of muscle actomyosin into sarcomeres. The sarcomere is the repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs." + "An interleukin-2 receptor subunit alpha that is encoded in the genome of human." "UniProtKB:P01589" + "Intrinsic membrane that arises from embryonic germ layers and grow to surround the developing embryo." "SCTID:362840007 FMA:305915 EHDAA2:0004714" + "An undifferentiated cell of the prostate epithelium that lacks secretory activity." + "A venule located in the colon." + "Outermost layer of cells in the blastodermic vesicle, which will develop into the trophoblast layer and then contact the endometrium and take part in establishing the embryo's means of nutrition." "EMAPA:16046 BTO:0001840 VHOG:0000979 EHDAA2:0002091 EHDAA:56" + "The process of creating a trabecula in an organ. A trabecula is a small, often microscopic, tissue element in the form of a small beam, strut or rod, which generally has a mechanical function. Trabecula are usually but not necessarily, composed of dense collagenous tissue." + "The intersection of sublaminar layers S4 and S5." + "PMID:32761142 PMID:30365038 GC_ID:1" + "The smooth muscle coat of the uterus, which forms the main mass of the organ and surrounds and supports the endometrium." "Wikipedia:Myometrium VHOG:0001281 MA:0000391 SCTID:279879004 UMLS:C0027088 EFO:0001970 MESH:D009215 NCIT:C12314 CALOHA:TS-0652 BTO:0000907 FMA:17743 EMAPA:29923 GAID:171 EV:0100116" + "A C-C chemokine receptor type 2 that is encoded in the genome of human." "Reactome:R-HSA-2976755 UniProtKB:P41597 DTO:02100054" + "The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified]." "Wikipedia:Lower_respiratory_tract FMA:45662 VHOG:0000382 SCTID:281488008 MA:0000435 EMAPA:16738 EHDAA2:0001036" + "Am unpaired external naris that lies in the midline of the head." + "A central nervous system macrophage that is part of a choroid plexus, a meninx and a perivascular space. A border associated macrophage interacts with various components of the CNS vasculature and meninges, it participates in immune surveillance and in the regulation of the blood brain barrier." + "Any process that modulates the frequency, rate, or extent of macrophage antigen processing and presentation." + "A portion of smooth muscle tissue that is part of an arterial system [Automatically generated definition]." "MA:0000704 EMAPA:36503" + + "The chemical reactions and pathways resulting in the formation of a nitric-oxide synthase, an enzyme which catalyzes the reaction L-arginine + n NADPH + n H+ + m O2 = citrulline + nitric oxide + n NADP+." + "The process, occurring after animal embryonic development, by which anatomical structures are generated and organized." + "The process in which the anatomical structure of the glossopharyngeal nerve is generated and organized. Various sensory and motor branches of the glossopharyngeal nerve supply nerve connections to the pharynx and back of the tongue. The branchial motor component contains motor fibers that innervate muscles that elevate the pharynx and larynx, and the tympanic branch supplies parasympathetic fibers to the otic ganglion." + "A protein with core architecture consisting of a large extracellular region containing one Integrin, beta chain domain (Pfam:PF00362), up to four EGF-like domains (Pfam:PF07974), and an Integrin beta tail domain (Pfam:PF07965), followed by a single-pass transmembrane region and a small cytoplasmic region often containing an Integrin beta cytoplasmic domain (Pfam:PF08725)." "PIRSF:PIRSF002512" + "Mesenchyme that is part of a developing hindlimb stylopod [Automatically generated definition]." "EHDAA2:0002132 EMAPA:17501 VHOG:0000506" + "Any process that modulates the frequency or rate of macrophage activation." + "The process whose specific outcome is the formation of dentin, the mineralized tissue that constitutes the major bulk of teeth. Dentin may be one of three types: primary dentin, secondary dentin, and tertiary dentin." + "EFO:0003704 ZFA:0005041 TAO:0005041" + "One of sublaminar layers S2, S3, or S4." "CP:0001043" + "OBSOLETE. An intratelencephalic-projecting glutamatergic neuron with a soma found in layer 5 of the human primary motor cortex." "ILX:0770157" + "The multiplication or reproduction of skeletal muscle cells, resulting in the expansion of a cell population." + "Any process that stops, prevents, or reduces the frequency, rate or extent of translational termination." + "The chemical reactions and pathways resulting in the formation of small molecules, any low molecular weight, monomeric, non-encoded molecule." + "The leftmost of the two common carotid arteries, originating from the aortic arch in the thorax." "UMLS:C0226087 MA:0001927 NCIT:C32956 SCTID:362043008 FMA:4058 EMAPA:35491 Wikipedia:Left_common_carotid_artery" + "An interneuron that has its cell body in a central nervous system." + "An alpha-beta T cell that is found in the lamina propria of mucosal tissues and is restricted by the MR-1 molecule." + "Any process that activates or increases the frequency, rate or extent of mesoderm development." + "GC_ID:1 PMID:25249442" + "Any process that stops, prevents or reduces the frequency, rate or extent of placenta blood vessel development." + "Subdivision of skeleton which which consists of all the skeletal elements in in the pectoral and pelvic appendage complexes[cjm]." "XAO:0003166 Wikipedia:Appendicular_skeleton MIAA:0000278 VSAO:0000076 MAT:0000278 FMA:71222 EFO:0000951 AAO:0000747 NCIT:C49477 UMLS:C0222646 SCTID:322050006 MA:0000290 EMAPA:32729" + "Subcutaneous adipose tissue that is located in the peritoneal cavity." "BTO:0004041 CALOHA:TS-2405" + "Any process that activates or increases the frequency, rate or extent of secretion by cell." + "Any process that activates or increases the frequency, rate or extent of protein localization to cell periphery." + "The supporting bundles of muscular fibers lining the walls of the atria[MP]." + "The process whose specific outcome is the progression of a sensory system over time from its formation to the mature structure." + "An epithelium that is part of a otic placode [Automatically generated definition]." "ZFA:0007068 EHDAA2:0001341 EMAPA:16197 VHOG:0000636 EHDAA:510" + "EMAPA:35113 FMA:69086 SCTID:68594002 MA:0001887" + "A protein that is a translation product of the human ARG1 gene or a 1:1 ortholog thereof." "IUPHARobj:1244" + + "A thrombomodulin-like receptor that is a translation product of the human CD93 gene or a 1:1 ortholog thereof." + "The process in which relatively unspecialized cells, acquire specialized structural and/or functional features of inner ear receptor cells. Inner ear receptor cells are mechanorecptors found in the inner ear responsible for transducing signals involved in balance and sensory perception of sound." + "GC_ID:1" + "The metanephric cortical collecting duct is the portion of the metanephric collecting duct that resides in the renal cortex[GO]." + "An apocrine gland that is part of a skin of body." "MA:0000147" + "EMAPA:16794 SCTID:361514006 EHDAA2:0000494" + "A cellular localization process whereby a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a cell including the localization of substances or cellular entities to the cell membrane." + + "The process whose specific outcome is the progression of the endocardium over time, from its formation to the mature structure. The endocardium is an anatomical structure comprised of an endothelium and an extracellular matrix that forms the innermost layer of tissue of the heart, and lines the heart chambers." + "Any process that modulates the frequency, rate or extent of plasma cell differentiation." + "A branched cellular projection (or cytoplasmic extension) that is extended from the surface of a dendritic immune cell, and which enables the cell to sample luminal pathogens and increase the surface area for antigen presentation to T cells." + "A ploidy quality inhering in a bearer by virtue of the bearer's having two copies (homologs) of each chromosome, usually one from the mother and one from the father." + "Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis." "FMA:86166 SCTID:20795001 MAT:0000284 MA:0000151 Wikipedia:Skin EV:0100152 MESH:D012867 EHDAA:6530 GAID:933 VHOG:0000860 MIAA:0000284" + "Any process that modulates the rate, frequency, or extent of glucan biosynthesis. Glucan biosynthetic processes are the chemical reactions and pathways resulting in the formation of glucans, polysaccharides consisting only of glucose residues." + "A thin musculomebranous barrier that separates the abdominal and thoracic cavities. Often used for breathing control." "Wikipedia:Thoracid_diaphragm MAT:0000502 EMAPA:17701 EV:0100376 BTO:0000341 EHDAA2:0003495 VHOG:0000713 FMA:13295 UMLS:C0011980 MA:0001904 SCTID:181614006 CALOHA:TS-0198 EFO:0000937 GAID:158 MESH:D003964 NCIT:C12702" + "Any process in which a protein is maintained in a specific location in a vacuole, and is prevented from moving elsewhere." + "EMAPA:37720 FMA:85315 MA:0001176" + "Joint fluid is a transudate of plasma that is actively secreted by synovial cells." "ENVO:02000039 Wikipedia:Synovial_fluid UMLS:C0039097 GAID:265 MESH:D013582 NCIT:C33718 galen:SynovialFluid ZFA:0005154 BTO:0001339 FMA:12277 TAO:0005154 CALOHA:TS-0996 MA:0002544" + "The postsynapse of a neuromuscular junction. In vertebrate muscles this includes the motor end-plate, consisting of postjunctional folds of the sarcolemma." + "The tubular intestinal glands found in the mucosal membranes." "EMAPA:35266 NCIT:C32411 UMLS:C1621887 SCTID:118652008 MA:0001535 Wikipedia:Intestinal_crypt FMA:63621" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of nucleobases, nucleosides, nucleotides and nucleic acids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glycoprotein stimulus." + "A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry of the large intestine, exclusive of the rectum. The colon is that part of the large intestine that connects the small intestine to the rectum." + "The medullary portion of the lymph node, which contains large blood vessels, sinuses and medullary cords that contain antibody-secreting plasma cells." "EMAPA:35529 MA:0000745 FMA:66254" + "Cell-cell signaling from postsynapse to presynapse, across the synaptic cleft, mediated by a neuropeptide." + "The process in which a relatively unspecialized myeloid precursor cell acquires the specializes features of an eosinophil." + "Any process by which an organism retains a population of somatic stem cells, undifferentiated cells in the embryo or adult which can undergo unlimited division and give rise to cell types of the body other than those of the germ-line." + "Any process that modulates the frequency, rate or extent of mesenchymal cell apoptotic process." + "A B cell of distinct lineage and surface marker expression. B-1 B cells are thought to be the primary source of natural IgM immunoglobulin, that is, IgM produced in large quantities without prior antigenic stimulation and generally reactive against various microorganisms, as well as the source of T-independent IgA immunoglobulin in the mucosal areas. These cells are CD43-positive." + "An intestinal tuft cell that is a part of a vermiform appendix." + "A supporting cell for the developing female gamete in the ovary of mammals. They develop from the coelomic epithelial cells of the gonadal ridge. Granulosa cells form a single layer around the mammalian oocyte in the primordial ovarian follicle and advance to form a multilayered cumulus oophorus surrounding the ovum in the Graafian follicle. The major functions of granulosa cells include the production of steroids and LH receptors." "FMA:18718 CALOHA:TS-0729 BTO:0000542" + "Mesenchyme that is part of a developing elbow [Automatically generated definition]." "EMAPA:17416 EHDAA:4170 EHDAA:6216 EHDAA2:0000432 VHOG:0001075" + "A myoblast that detemines the properties (size, shape and attachment to the epidermis) of a `somatic muscle myotube` (CL:0008003) . It develops into a somatic muscle myotube via fusion with `fusion component myoblasts` (CL:0000621)." + "A merocrine, unbranched, unbranched, coiled, tubular gland sweat gland. In humans, distributed over almost all of the body surface, and promote cooling by evaporation of their secretion." "MESH:D004439 BTO:0002323 UMLS:C0013492 FMA:59154 NCIT:C32490 GAID:945 MA:0003039 SCTID:361699008 Wikipedia:Eccrine_sweat_gland" + "Renal process that modulates the force with which blood travels through the circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure." + "Any biological process involved in the maintenance of the steady-state number of hematopoietic stem cells within a population of cells." + "A blood vessel that is part of a endometrium." "SCTID:254200009" + "The serratus ventralis is a muscle that originates on the surface of the upper eight or nine ribs at the side of the chest and inserts along the entire anterior length of the medial border of the scapula. [WP,unvetted]." "FMA:13397 VHOG:0000679 EHDAA:9463 MA:0002378 NCIT:C53014 UMLS:C1710059 EMAPA:18525 SCTID:181748003 EHDAA2:0001832 Wikipedia:Serratus_anterior_muscle" + "An epithelial cell of the parathyroid gland that is arranged in wide, irregular interconnecting columns; responsible for the synthesis and secretion of parathyroid hormone." "BTO:0004712 FMA:69078 CALOHA:TS-2140" + "Any process that modulates the frequency, rate, or extent of plasmacytoid dendritic cell antigen processing and presentation." + "The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets during M phase of the meiotic cell cycle." + "Any process that increases the rate, frequency or extent of the chemical reactions and pathways involving acetylcholine, the acetic acid ester of the organic base choline. Acetylcholine is a major neurotransmitter and neuromodulator both in the central and peripheral nervous systems. It also acts as a paracrine signal in various non-neural tissues." + "A CD11c-low plasmacytoid dendritic cell that is CD8alpha-negative and CD4-positive." + "A GABAergic cortical interneuron that expresses cck. L5/6 cck cells have soma found mainly in L5 and L6 and have large axonal arborization." + "Any muscle organ that is part of a esophagus [Automatically generated definition]." "MA:0002682 EMAPA:26983 SCTID:360961009" + "The biological process whose specific outcome is the progression of a lung vasculature from an initial condition to its mature state. This process begins with the formation of the lung vasculature and ends with the mature structure. The lung vasculature is composed of the tubule structures that carry blood or lymph in the lungs." + "A DN2 thymocyte that is Kit-hi." + "Any process that modulates the frequency, rate, or extent of mast cell activation." + "The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells." + "The pronounced, dorsolaterally oriented ridge of grey matter in each lateral half of the spinal cord[MP]. the dorsal (more towards the back) grey matter of the spinal cord. It receives several types of sensory information from the body, including light touch, proprioception, and vibration. This information is sent from receptors of the skin, bones, and joints through sensory neurons whose cell bodies lie in the dorsal root ganglion[WP]. The dorsal region of the mature spinal cord contains neurons that process and relay sensory input[GO]." "MA:0001119 SCTID:180961004 NCIT:C32473 ZFA:0000649 BIRNLEX:2667 UMLS:C0228575 VHOG:0001287 BM:SpC-DH EMAPA:35790 Wikipedia:Posterior_horn_of_spinal_cord FMA:256530 TAO:0000649 neuronames:1686 EMAPA:18574 UMLS:C0228564 BAMS:DH" + "Any process that modulates the frequency, rate or extent of skeletal muscle cell differentiation." + "Any process that stops, prevents, or reduces the frequency, rate or extent of gluconeogenesis." + "Any vein endothelial cell that is part of a hindlimb stylopod." + "A protein with four transmembrane domains, small intracellular amino- and carboxyl-terminal regions, and two extracellular loops, a small one (EC1) and a larger one (EC2) of about 100 residues. The EC2 loop contains at least 4 cysteine residues, including a highly conserved 'CCG' motif." "PIRSF:PIRSF002419" + "The process in which the anatomical structures of muscle are generated and organized." + "Any process that stops, prevents or reduces the frequency, rate or extent of response to wounding." + "Any process that stops, prevents, or reduces the frequency, rate or extent of gamma-delta T cell proliferation." + "A border associated macrophage that is part of a meninx. This macrophage type is elongated and amoeboid spindle-shaped with limited mobility. This macrophage is highly phagocytic, expresses scavenger receptors, has dynamic protrusions and extends its processes during inflammation." + "The process in which the anatomical structure of the locus ceruleus is generated and organized. In mice, the locus ceruleus is a dense cluster of neurons within the dorsorostral pons. This nucleus is the major location of neurons that release norepinephrine throughout the brain, and is responsible for physiological responses to stress and panic." + "Any process that modulates the frequency, rate or extent of cardiac conduction." + "Part of the ventricular system of the brain, forming a single large irregularly shaped cavity located on the midline of the rhombencephalon, between the medulla, pons and the isthmus ventrally and the cerebellum dorsally. It is continuous with the cerebral aqueduct anteriorally and the central canal of the spinal cord posteriorly. It communicates with the subarachnoid space through its lateral and median apertures." "VHOG:0000006 MA:0000196 BTO:0003426 EHDAA2:0000100 MESH:D020546 DHBA:10669 BAMS:V4 HBA:9421 ZFA:0000110 EHDAA:896 NCIT:C12828 BM:Pons-4V neuronames:621 Wikipedia:Fourth_ventricle BIRNLEX:1256 TAO:0000110 CALOHA:TS-2015 EMAPA:16917 DMBA:126651782 GAID:610 XAO:0003099 AAO:0011043 UMLS:C0149556 DHBA:12805 EV:0100310 MBA:145 SCTID:180932000 FMA:78469 BAMS:4V" + "A luminal layer of epithelium that is part of a ureter." "EMAPA:37779 MA:0002656" + "Tolerance induction dependent upon an immune response, typically a response by a mature T or B cell in the periphery resulting tolerance towards an antigen via induction of anergy, cellular deletion, or regulatory T cell activation." + "A serous membrane that is part of a colon [Automatically generated definition]." "SCTID:90132000 FMA:14990 MA:0003199 EMAPA:27387" + "An epithelium that is part of a vas deferens [Automatically generated definition]." "MA:0001749 EMAPA:29274 NCIT:C49315 UMLS:C1710617 FMA:225317" + "A zone of skin that is part of an ankle [Automatically generated definition]." "NCIT:C52751 UMLS:C0222286 FMA:37831 MA:0000641 SCTID:181560000 EMAPA:37353" + "The process whose specific outcome is the progression of the renal inner medulla over time, from its formation to the mature structure. The renal inner medulla is unique to mammalian kidneys and is the innermost region of the mammalian kidney." + "Glial cell of lateral ventricle." "CALOHA:TS-1258" + "Any process that decreases the rate, frequency or extent of ribosome biogenesis. Ribosome biogenesis is the cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits." + "An anatomical surface that is part of a cartilage element." "FMA:76668" + "A protein complex which is capable of GABA receptor activity. Upon binding of gamma-aminobutyric acid (GABA) it transmits the signal from one side of the membrane to the other to initiate a change in cell activity. Major inhibitory receptor in vertebrate brain. Also found in other vertebrate tissues, invertebrates and possibly in plants. Effective benzodiazepine receptor." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a catecholamine stimulus. A catecholamine is any of a group of biogenic amines that includes 4-(2-aminoethyl)pyrocatechol [4-(2-aminoethyl)benzene-1,2-diol] and derivatives formed by substitution." + "Any process that activates or increases the frequency, rate or extent of retrograde trans-synaptic signaling by neuropeptide." + "The portion of mesentery attached to the greater curvature of the stomach is named the dorsal mesentery (or dorsal mesogastrium, when referring to the portion at the stomach), and the part which suspends the colon is termed the mesocolon. The dorsal mesogastrium develops into the greater omentum." "VHOG:0000352 EHDAA2:0000416 EMAPA:17025 Wikipedia:Dorsal_mesentery EHDAA:3001 NCIT:C34142 MA:0001618 UMLS:C1512038" + "A part of a cellular organism that is either an immaterial entity or a material entity with granularity above the level of a protein complex but below that of an anatomical system. Or, a substance produced by a cellular organism with granularity above the level of a protein complex." + "Any process that stops, prevents, or reduces the frequency, rate or extent of translational elongation." + "Any process that activates or increases the frequency, rate or extent of membrane invagination." + "A recently activated CD4-positive, alpha-beta T cell with the phenotype CD69-positive, CD62L-negative, CD127-negative, and CD25-positive." + "Any process that stops, prevents, or reduces the frequency, rate or extent of translational initiation." + "Any process that modulates the frequency, rate or extent of glutamate metabolic process." + "A region of nephron tubule that is part of a cortex of kidney." "EMAPA:18976 MA:0002609" + "Any process that stops, prevents or reduces the frequency, rate or extent of cilium assembly." + "A long bone is a bone that has a shaft and 2 ends and is longer than it is wide. Long bones have a thick outside layer of compact bone and an inner medullary cavity containing bone marrow. The ends of a long bone contain spongy bone and an epiphyseal plate or line depending on the stage of development. The epiphyseal plate is a hyaline cartilage, where new bone growth takes place, lengthening the bone prior to adulthood. Bone lengthening ceases when this cartilage is lost, leaving a remnant referred to as an epiphyseal line." "Wikipedia:Long_bone NCIT:C33003 galen:LongBone SCTID:332709000 BTO:0004256 MA:0002802 UMLS:C0222647 FMA:7474 EMAPA:35503" + "The submucous layer of the wall of the rectum." "BTO:0002114 FMA:15034 EMAPA:27083 SCTID:71683001" + "The junction between the ureter and the renal pelvis of the kidney." "SCTID:264130006 NCIT:C106203 FMA:15898 EMAPA:37782 MA:0003021" + "A submucosa that is part of a left hepatic duct [Automatically generated definition]." "FMA:18017" + "Any process that stops, prevents or reduces the rate or extent of resting T cell proliferation." + "The process in which a relatively unspecialized cell acquires specialized features of a keratinocyte." + "Any process that modulates the frequency, rate or extent of T cell migration." + "A non-keratinized stratified squamous epithelium that is part of a tongue." "FMA:62130" + "The regulated release of histamine by a cell or tissue. It is formed by decarboxylation of histidine and it acts through receptors in smooth muscle and in secretory systems." + "Any process that activates or increases the frequency, rate or extent of erythrocyte differentiation." + "Mesenchyme that develops_from a neural crest and is part of a 1st arch mesenchyme." "EMAPA:16129" + "Any process that activates or increases the frequency, rate or extent of eosinophil migration." + "The delicate vascular connective tissue that lies between the anterior surface of the iris and the pars iridica retinae." "FMA:58526 EMAPA:35451 ZFA:0005569 Wikipedia:Iris_stroma SCTID:280882008 MA:0002777" + "The process in which calcium salts are deposited into calcareous tooth structures such as dental enamel, dentin and cementum." + "The process whose specific outcome is the progression of the imaginal disc over time, from its formation to the metamorphosis to form adult structures. Imaginal discs are epithelial infoldings in the larvae of holometabolous insects that develop into adult structures (legs, antennae, wings, etc.)." + "A basket cell with axonal arbors composed of frequent, short, curvy axonal branches that tend to be near their somata and within the same layer." + "The multiplication or reproduction of cells, resulting in the expansion of a mesenchymal cell population of the ureteric bud, that contributes to ureteric bud development." + "The central region of trunk mesoderm. This tissue forms the notochord." "ZFA:0000091 EFO:0003426 AAO:0000478 TAO:0000091" + "A quality in which events occur in sequence." + "Any process that modulates the frequency, rate or extent of gamma-delta T cell differentiation." + + "The change in morphology and behavior of a mast cell resulting from exposure to a cytokine, chemokine, soluble factor, or to (at least in mammals) an antigen which the mast cell has specifically bound via IgE bound to Fc-epsilonRI receptors, leading to the initiation or perpetuation of an immune response." + "A cellular process that results in the aggregation, arrangement and bonding together of a set of components to form a cell junction." + "Any process that increases the frequency, rate, or extent of the self-propelled movement of a cell or organism from one location to another in a behavioral context; the aspect of locomotory behavior having to do with movement." + "A sulcus limitans of neural tube that is part of a future metencephalon." "EHDAA2:0001161 EMAPA:17567" + "The process whose specific outcome is the progression of the autonomic nervous system over time, from its formation to the mature structure. The autonomic nervous system is composed of neurons that are not under conscious control, and is comprised of two antagonistic components, the sympathetic and parasympathetic nervous systems. The autonomic nervous system regulates key functions including the activity of the cardiac (heart) muscle, smooth muscles (e.g. of the gut), and glands." + "The directed movement of the Golgi to a specific location." + "Any process that stops, prevents, or reduces the frequency, rate or extent of microglia differentiation, the process in which a relatively unspecialized cell acquires specialized features of a microglial cell." + "An ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 that is encoded in the genome of human." "Reactome:R-HSA-8938080 UniProtKB:P28907" + "Any process that activates or increases the frequency, rate or extent of midbrain dopaminergic neuron differentiation." + "A capillary that is part of a respiratory system [Automatically generated definition]." "MA:0001807 EMAPA:37574" + "An ionocyte that is part of the lung epithelium. The cells from this type are major sources of the CFTR protein in human and mice." + "Rearrangements of the microtubule cytoskeleton that contribute to the movement of cells along radial glial cells as a component of the process of cerebral cortex glial-mediated radial migration." + "A cell that secretes glucagon." "FMA:84045" + "A protein that is a translation product of the human CHODL gene or a 1:1 ortholog thereof." + "Binding to an iron (Fe) ion." + "Any nerve that innervates the pinna." "EMAPA:36513 MA:0001232" + "Any collection of muscles that is part of an arm [Automatically generated definition]." "EHDAA2:0000141" + "The directed killing of a target cell by a microglial cell." + "The directed movement of hormones into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "Any process that modulates the frequency, rate or extent of activated CD4-positive, alpha-beta T cell apoptotic process." + "A T cell that expresses a T cell receptor complex and has completed T cell selection." + "A lamina propria that is part of a gastrointestinal system." "NCIT:C49299 UMLS:C1708197 MA:0001899" + "A muscle cell in which the fibers are organised into sarcomeres but in which adjacent myofibrils are offset from each other, producing an oblique banding pattern." + "A mucosa that is part of a nasolacrimal duct [Automatically generated definition]." "FMA:59664" + "A mucosa that is part of a segmental bronchus [Automatically generated definition]." "FMA:62666" + "Any process that modulates the frequency, rate, or extent of B-1 B cell differentiation. B-1 B cells are a distinct subset of B cells characterized as being CD5 positive, found predominantly in the peritoneum, pleural cavities, and spleen, and enriched for self-reactivity." + "A skeletal muscle satellite cell that divides by stem cell division. A proportion of this population undergoes symmetric stem cell division, producing two skeletal muscle satellite stem cells. The rest undergo asymmetric stem cell division - retaining their identity while budding off a daughter cell that differentiates into an adult skeletal muscle myoblast." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glycine stimulus." + "An epithelial cell that is part of some loop of Henle thick ascending limb. It is known in some mammalian species that this cell may express the Na+-K+-2Cl− cotransporter (NKCC2) apically." "KUPO:0001049" + "A bone that is part of a neurocranium [Automatically generated definition]." "EMAPA:35238 MA:0001478 SCTID:120229002" + "Any process that activates or increases the frequency, rate or extent of the formation and development of a tooth or teeth." + "A pia mater that is part of a diencephalon [Automatically generated definition]." "MA:0000829 VHOG:0000475 EHDAA2:0000400 EMAPA:17767" + "Any process that activates or increases the frequency, rate or extent of growth of an organ of an organism." + "The process in which an antigenically naive CD4-positive, alpha-beta T cell acquires the specialized features of a CD4-positive, CD25-positive, alpha-beta regulatory T cell as part of an immune response." + "A tiny smooth muscle that connects the hair follicle with the dermis." "MA:0000778 EMAPA:26775 FMA:67821 BTO:0005132 Wikipedia:Arrector_pili_muscle SCTID:319910005" + "A cell of the luminal layer of the epithelium in the prostatic acinus." "FMA:74266" + "An epithelium that is part of a ear." "EMAPA:32800 MA:0003161" + "Any process that activates or increases the frequency, rate or extent of collagen binding." + "Bone tissue mineralized with hydroxyapatite." + "A sesamoid bone that is part of a manus." "SCTID:368448000 FMA:42353" + "A goblet cell that is located in the anorectum." + "Any process that modulates the frequency, rate or extent of neutrophil differentiation." + "Any process that stops, prevents or reduces the frequency, rate or extent of hepatic stellate cell migration." + "The process whose specific outcome is the progression of the dentate gyrus over time, from its formation to the mature structure. The dentate gyrus is one of two interlocking gyri of the hippocampus. It contains granule cells, which project to the pyramidal cells and interneurons of the CA3 region of the ammon gyrus." + "A CD4 molecule that is encoded in the genome of human." "UniProtKB:P01730" + "Anatomical system that consists of all the joints of the body." "FMA:23878 VSAO:0000181 EMAPA:35150 MA:0003007 SCTID:361827000" + "An absorptive cell of the gut epithelium that endocytoses microorganisms and intact macromolecules from the gut lumen and transports them to the subepithelial space where they are presented to antigen-presenting cells and lymphocytes." "BTO:0003600 FMA:62929" + "The orderly movement of a macrophage from one site to another." + "An arteriole that is part of a lymph node." + "A bone that is part of the manus skeleton. Note that this includes the carpal bones." "SCTID:426741001 MA:0000619 EMAPA:35391" + "Any process that stops, prevents, or reduces the frequency, rate or extent of macrophage differentiation." + "The process resulting in the physical partitioning and separation of a myoblast into daughter cells. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers." + "The process in which the anatomical structures of a mesonephric distal tubule are generated and organized. The mesonephric distal tubule is a mesonephric nephron tubule that begins at the macula densa and extends to the mesonephric connecting tubule." + "A nerve that is part of an abdomen [Automatically generated definition]." "MA:0000521" + "A blood vessel that is part of a leg [Automatically generated definition]." "MA:0000669 EMAPA:36500" + "A leukocyte that lacks granules." "FMA:62855" + "A non-nucleated disk-shaped cell formed by extrusion from megakaryocytes, found in the blood of all mammals, and mainly involved in blood coagulation." "CALOHA:TS-0803 FMA:62851 BTO:0000132" + "An artery that enters the lymph node at the hilum and branches into smaller arterioles." + "A circulating endothelial cell of the phenotype CD146-positive, CD105-positive, CD45-negative. This cell type is indicative of recent vascular damage." + "Any process that stops, prevents or reduces the frequency, rate or extent of mesenchymal cell apoptotic process." + "Any process that stops, prevents or reduces the frequency, rate or extent of CD4-positive, alpha-beta T cell proliferation." + "Any process that stops, prevents or reduces the frequency, rate or extent of bile acid metabolic process." + "Any portion of the aorta including the ascending and descending aorta, and aortic arch or a portion of the aortic orifice of the left ventricle." "FMA:13087 UMLS:C0506947 NCIT:C34027 SCTID:119203005" + "An ependyma that is part of a lateral ventricle [Automatically generated definition]." "NCIT:C49249 MA:0000964 UMLS:C0228162 FMA:242825 SCTID:369275002 EMAPA:35488" + "Any process that stops, prevents, or reduces the frequency, rate or extent of skeletal muscle fiber development. Muscle fibers are formed by the maturation of myotubes. They can be classed as slow, intermediate/fast or fast." + "A cell of a secondary follicile within the ovary." "FMA:70591" + "The process whose specific outcome is the progression of the metanephric proximal tubule over time, from its formation to the mature structure. The metanephric proximal tubule is a metanephric nephron tubule that connects Bowman's capsule to the descending thin limb of the loop of Henle in the metanephros. It has a brush border epithelial morphology." + "The process in which the anatomical structures of the nephric duct are generated and organized. A nephric duct is a tube that drains a primitive kidney." + "A mesothelium that is part of a pleural cavity [Automatically generated definition]." "EMAPA:16775 EHDAA2:0001476 FMA:18148 BTO:0003155" + "A protein that is a translation product of the human CD24 gene or a 1:1 ortholog thereof." + "A basement membrane that is part of a trachea." "MA:0001854 EMAPA:37552 UMLS:C1710455 NCIT:C49302" + "Any neural crest cell migration that is involved in sympathetic nervous system development." + "Any process that modulates the frequency, rate or extent of cation channel activity." + "Any process that stops, prevents, or reduces the frequency, rate or extent of DNA recombination." + "A viscosity which relatively low." + "The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a hepatic stellate cell." + "An amicrine that has a medium dendritic field." + "The directed movement of acetylcholine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Acetylcholine is an acetic acid ester of the organic base choline and functions as a neurotransmitter, released at the synapses of parasympathetic nerves and at neuromuscular junctions." + "An endothelium that is part of a vein [Automatically generated definition]." "VHOG:0001216 UMLS:C1179027 AAO:0011110 EMAPA:36288 NCIT:C49317 BTO:0004756 XAO:0000358 MA:0000712 FMA:62118" + "Any of the organized aggregations of cells that function as secretory or excretory organs and that release hormones in response to neural stimuli." "MA:0000720" + "The process that gives rise to a mesonephric glomerular capillary. This process pertains to the initial formation of a structure from unspecified parts." + "An epithelium that is part of a cloaca." "ZFA:0005783 EMAPA:27577 EMAPA:36070" + "The enlargement or overgrowth of all or part of an organ due to an increase in size of its smooth muscle cells without cell division. Physiological hypertrophy is a normal process during development, and can also occur in mature structures on demand. In the uterus, smooth muscle cells undergo hypertrophy during pregnancy." + "The regulated release of saliva from the salivary glands. In man, the saliva is a turbid and slightly viscous fluid, generally of an alkaline reaction, and is secreted by the parotid, submaxillary, and sublingual glands. In the mouth the saliva is mixed with the secretion from the buccal glands. In man and many animals, saliva is an important digestive fluid on account of the presence of the peculiar enzyme, ptyalin." "Wikipedia:Salivation" + "Any process that activates or increases the frequency, rate or extent of formation of translation initiation ternary complex." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the cytokine mediated signaling pathway." + "The process in which a cell of the mammary placode becomes a cell of the mammary gland bud." + "Any process that activates or increases the frequency, rate or extent of RNA biosynthetic process." + "Any process that activates or increases the frequency, rate or extent of apoptotic process involved in development." + "The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity." "MESH:D012809 NCIT:C33550 EFO:0000846 NCIT:C12384 MIAA:0000314 MAT:0000314 CALOHA:TS-2044 EMAPA:36391 SCTID:362166007 galen:SigmoidColon Wikipedia:Sigmoid_colon BTO:0000645 UMLS:C0682612 UMLS:C0227391 FMA:14548" + "Erythrocyte differentiation which occurs as part of the process of primitive hemopoiesis." + "An arteriole that is located in the anorectum." + "A protein that is a translation product of the human PTPRC gene or a 1:1 ortholog thereof. It is composed of an extracellular domain, a single transmembrane segment and two tandem intracytoplasmic protein-tyrosine phosphatase domains. Contains 1 to 3 copies of the Fibronectin type III domain (Pfam:PF00041) followed by two copies of the Protein-tyrosine phosphatase (Pfam:PF00102) domain. Receptor-type tyrosine-protein phosphatase C (CD45) regulates signal transduction and lymphocyte activation by specific association with receptor molecules on T and B cells. Multiple isoforms of CD45 (180-235 kDa) can be generated asa result of alternative splicing of three variable exons 4(A), 5(B) and 6(C), encoding sequences at the N-terminal extracellular domain of the molecule." "IUPHARobj:1852 PIRSF:PIRSF002004" + "An endothelium that is part of the cardiovascular system." "NCIT:C13053 MA:0000717 XAO:0000356 UMLS:C0014261 VHOG:0001217 MESH:D004730 ZFA:0001639 TAO:0002171 EMAPA:35201 BTO:0001853 GAID:519" + "Any process that modulates the frequency, rate or extent of attachment of a cell to another cell or to the extracellular matrix." + "Any process that modulates the frequency, rate or extent of protein processing, a protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein." + "Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location." + "The developmental process, independent of morphogenetic (shape) change, that is required for an epithelial cell of the salivary gland to attain its fully functional state." + "A C-type lectin domain family 4 member K that is encoded in the genome of mouse." "UniProtKB:Q8VBX4" + "Any process that contributes to cytokine production by a T cell." + "Any process pertaining to the functions of the nervous and muscular systems of an organism." + "A late eosinophilic metamyelocyte in which the nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature eosinophil." + "EHDAA2:0002094" + "Any process that activates or increases the frequency, rate or extent of erythrocyte apoptotic process." + "The chemical reactions and pathways resulting in the formation of mineralocorticoids, hormonal C21 corticosteroids synthesized from cholesterol." + "KUPO:0001115" + "The controlled release of acid by a cell or a tissue." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon." + "Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance." "galen:ConnectiveTissue GAID:100 EFO:0000952 TAO:0001641 XAO:0001017 MIAA:0000301 BTO:0000421 AAO:0000098 NCIT:C12374 CALOHA:TS-2009 UMLS:C0009780 MAT:0000301 VSAO:0000017 ZFA:0001632 FMA:9640 SCTID:361919005 MA:0000011 MESH:D003238 EMAPA:35251" + "A macrophage that expresses the T cell receptor complex at the cell surface." + "Any process that stops, prevents or reduces the frequency, rate or extent of T-helper 1 cell activation." + + "A hematopoietic multipotent progenitor cell is multipotent, but not capable of long-term self-renewal. These cells are characterized as lacking lineage cell surface markers and being CD34-positive in both mice and humans." "BTO:0000725 CALOHA:TS-0448" + "Metanephric pyramids are the conical masses that constitute the renal medulla in a metanephros; they contain the loops of Henle and the medullary collecting ducts[GO]." + "Any process that modulates the rate, frequency, or extent of cartilage development, the process whose specific outcome is the progression of the cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate." + "The primitive cartilagionous skeletal structure of the fetal skull that grows to envelop the rapidly growing embyonic brain. In humans, the chondrocranium begins forming at 28 days from mesenchymal condensations and is fully formed between week 7 and 9 of fetal development. While the majority of the chondrocranium is succeeded by the bony skull in most higher vertebrates, some components do persist into adulthood.[1] In Cartilagious fishes and Agnathans, the chondrocranium persist throughout life.[2] Embryologically, the chondrocranium represent the basal cranial structure, and lay the base for the formation of the endocranium in higher vertebrates[WP]." "FMA:76621 UMLS:C1516496 NCIT:C34121 XAO:0003059 Wikipedia:Chondrocranium SCTID:155540009 AAO:0000094 EHDAA:6031" + "The flattened smooth myoepithelial cells of mesodermal origin that lie just outside the basal lamina of the seminiferous tubule." + "KUPO:0001116" + "GC_ID:1" + "Any process that activates or increases the frequency, rate or extent of calcium ion export across the plasma membrane." + "A cell that is a specialized type of pericyte providing structural support for the capillary loops of kidney. A flat, elongated cell with extensive fine cytoplasmic processes found outside the kidney glomerulus near the macula densa and bound laterally by afferent and efferent arterioles. Being phagocytic, this cell participates in the continuous turnover of the basal lamina by removing its outer portion containing residues of filtration, while the lamina is renewed on its inner surface by the endothelial cells." "FMA:84143 KUPO:0001033" + "The increase in mass of imaginal discs by cell proliferation prior to metamorphosis. Imaginal discs are epithelial infoldings in the larvae of holometabolous insects that develop into adult structures (legs, antennae, wings, etc.) during metamorphosis from larval to adult form." + "The directed movement of nuclei within the syncytial embryo of insects. These precise temporal and spatial patterns of nuclear movement are coordinated with mitotic divisons and are required during blastoderm formation to reposition dividing nuclei from the interior of the syncytial embryo to the cortex." + "A cell type that forms the boundary with the surrounding epithelium." "FMA:67941" + "KUPO:0001042" + "GC_ID:1" + "Specialized cardiac myocyte which is in the internodal tract and atrioventricular node. The cell is more slender than ordinary atrial myocytes and has more myofibrils than nodal myocytes." "FMA:67142" + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving juvenile hormone." + "An ureter that is part of a right side of organism [Automatically generated definition]." "SCTID:276251000 FMA:15571 EMAPA:37373 MA:0001685 NCIT:C49327 UMLS:C0227682" + "A quality that has a value that is decreased compared to normal or average." + "Enables the transmembrane transfer of an ion by a channel that opens when a specific ligand has been bound by the channel complex or one of its constituent parts." "Reactome:R-HSA-451311 Reactome:R-HSA-622325 Reactome:R-HSA-629595 Reactome:R-HSA-622326 Reactome:R-HSA-451310" + "Any process that activates or increases the frequency, rate or extent of osteoclast differentiation." + "Any process that modulates the frequency, rate or extent of prolactin signaling pathway." + "KUPO:0001039" + "The series of molecular signals initiated by a ligand binding to its receptor, in which the activated receptor promotes the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, and ends with regulation of a downstream cellular process. The pathway can start from the plasma membrane, Golgi or nuclear membrane." + "The multiplication or reproduction of Leydig cells, resulting in the expansion of a cell population. Leydig cells are interstitial cells located adjacent to the seminiferous tubules in the testis which produce testosterone." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-4 production." + "Any process that reduces the occurrence or rate of mesenchymal stem cell death by apoptotic process that contributes to the shaping of the nephron." + "A basophilic erythroblast that is GlyA-positive." + "The process in which a relatively unspecialized cell acquires specialized features of an adipocyte, an animal connective tissue cell specialized for the synthesis and storage of fat." + "A CD4-positive, alpha-beta T cell that has the phenotype CXCR3-negative, CCR6-negative." + "A specialized axon terminus which is produced by retinal cone cells. Pedicles are large, conical, flat end-feet (8-10 micrometers diameter) of the retinal cone axon that lie more or less side by side on the same plane at the outer edge of the outer plexiform layer (OPL)." + "The area at the bottom of the stomach on the caudal side of the pyloric canal that contains gastrin-producing G cells, which stimulate acid production, and the luminal pH-sensitive population of somatostatin-producing D cells." "NCIT:C12259 MESH:D011706 FMA:14579 GAID:332 Wikipedia:Pyloric_antrum galen:PyloricAntrum SCTID:362142001 UMLS:C0034193 EFO:0002555 BTO:0001732 MA:0001624 EMAPA:17891" + "A urokinase plasminogen activator surface receptor that is encoded in the genome of human." "UniProtKB:Q03405" + "KUPO:0001040" + "Any process that activates or increases the frequency, rate or extent of iridophore differentiation." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of a chronic inflammatory response." + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix." + "A CD11b-positive dendritic cell that is CD11b-low, CD45-positive, MHC-II-high and CD103-positive that is located in the liver." + + "Any process that stops, prevents or reduces the frequency, rate or extent of blood vessel branching." + "Combining with histamine to initiate a change in cell activity. Histamine is a physiologically active amine, found in plant and animal tissue and released from mast cells as part of an allergic reaction in humans." + "The process whose specific outcome is the progression of a blood vessel of the placenta over time, from its formation to the mature structure." + "Any process that mediates the transfer of information from a mesenchymal cell to an epithelial cell and contributes to the development of the lung." + "An epithelium that is part of a respiratory system [Automatically generated definition]." "EMAPA:32826 CALOHA:TS-0023 MA:0001823" + "A organ system process carried out by any of the organs or tissues of the circulatory system. The circulatory system is an organ system that moves extracellular fluids to and from tissue within a multicellular organism." "Wikipedia:Circulatory_system" + "Region of cervical epithelium where columnar epithelium of endocervic and the stratified non-keratinising squamous epithelium of the ectocervic meet." "SCTID:280451001 NCIT:C97148" + "A neuroendocrine cell that secretes gonadotropin-releasing hormone (GnRH). A GnRH neuron is born in the nasal placode during embryonic development and migrates through the nose and forebrain to the hypothalamus. This cell regulates reproduction by secreting GnRH into the pituitary portal vessels to induce the release of gonadotropins into the general circulation." + "A tyrosine 3-monooxygenase that is encoded in the genome of mouse." "UniProtKB:P24529" + "A portion of cardiac muscle tissue that is part of an interventricular septum [Automatically generated definition]." "EHDAA2:0004158 EMAPA:17335 VHOG:0000999 FMA:84084" + "Any process that modulates the frequency, rate or extent of blood vessel branching." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of mucus from a cell or a tissue." + "The multiplication or reproduction of epithelial cells, resulting in the expansion of a cell population and contributing to the shaping of a Malpighian tubule." + "A dendritic cell of the myeloid lineage." "BTO:0004721" + "Any process in which a lysosome is transported to, and/or maintained in, a specific location." + "An intratelencephalic-projecting glutamatergic neuron with a soma found in L5 of the primary motor cortex." "ILX:0770157" + "Any process that activates or increases the frequency, rate or extent of the cyclical phases of growth (anagen), regression (catagen), quiescence (telogen), and shedding (exogen) in the life of a hair." + "Any process that activates, maintains or increases the frequency, rate or extent of cardiac muscle growth." + "Any process that activates or increases the frequency, rate or extent of smooth muscle contraction involved in micturition." + "Combining with an acetylcholine receptor ligand and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity." + "The orderly movement of a neuroblast from one site to another, often during the development of a multicellular organism or multicellular structure. A neuroblast is any cell that will divide and give rise to a neuron." + "The characteristic movement of trunk neural crest cells from the neural tube to other locations in the vertebrate embryo." + "A neuron with three or more neurites, usually an axon and multiple dendrites." "FMA:67287" + "A sphincter muscle that is part of a cloaca." "NCIT:C34129 UMLS:C1516658" + "A protein that is a translation product of the human GFAP gene or a 1:1 ortholog thereof." + "A basal cell that is part of the epithelium of terminal bronchiole." "FMA:263122" + "Multi-tissue structure that is part of the heart tube and will become the cardiac ventricle." "SCTID:361524003 Wikipedia:Embryonic_ventricle NCIT:C34160 EMAPA:16350 ZFA:0001719 FMA:71006 EHDAA2:0001531 TAO:0002231" + "Any process that activates or increases the frequency, rate or extent of tendon cell differentiation." + "A flat keratinocyte immediately below the cornified layer." "FMA:86925" + "The process in which hormones modulate the force with which blood passes through the circulatory system. A hormone is one of a group of substances formed in very small amounts in one specialized organ or group of cells and carried (sometimes in the bloodstream) to another organ or group of cells, in the same organism, upon which they have a specific regulatory action." + + "Any process that modulates the frequency, rate, or extent of production of oxytocin." + "A primordium that has the potential to develop into a saliva-secreting gland." + "Any process that modulates the frequency, rate or extent of differentiation of CD4-positive, CD25-positive, alpha-beta regulatory T cells as part of an immune response." + "A mass of cells that develop into the body of the embryo and some extraembryonic tissues." "Wikipedia:Inner_cell_mass SCTID:361456007 VHOG:0000742 EHDAA2:0000830 FMA:86557 NCIT:C13740 EFO:0000547 EHDAA:40 UMLS:C1283994 EMAPA:16041" + "Any process that modulates the frequency, rate or extent of flagellated sperm motility." + "Tolerance induction of T cells in the periphery, in this case, any location in the body other than the thymus." + "Any process contributing to lymphocyte anergy, a state of functional inactivation." + "Any mononuclear cell that is part of a umbilical cord." + "A NK1.1-positive T cell that is Ly49H-negative." + "Any macroglial cell that is part of a brain." + "A fibroblast that is located in the renal medulla interstitium." + "The glomerular layer is the most superficial layer, consisting of mitral cell dendritic arborizations (glomeruli), olfactory nerve fibers, and periglomerular cells. Periglomerular cells contact multiple mitral cell dendrites within the glomeruli and provide lateral inhibition of neighboring glomeruli while allowing excitation of a specific mitral cell dendritic tree. Each mitral cell is contacted by at least 1000 olfactory nerve fibers[BTO]. Portion of tissue which is located in between the primary olfactory fiber layer and the external cellular layer of the olfactory bulb[ZFA]." "ZFA:0000357 BTO:0001317 neuronames:2710 BAMS:Gl MBA:212 MA:0000970 NLXANAT:1005007 TAO:0000357 DHBA:11327 EMAPA:35608" + "Any process that modulates the frequency, rate or extent of nuclease activity, the hydrolysis of ester linkages within nucleic acids." + "A cell derived from the mesoderm that is located between the paraxial mesoderm and the lateral plate." + "The chemical reactions and pathways resulting in the breakdown of glucocorticoids, hormonal C21 corticosteroids synthesized from cholesterol." + "The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups." + "Any process that modulates the frequency, rate or extent of branching morphogenesis of a nerve." + + "Any process that modulates the frequency, rate or extent of cytoplasmic translational initiation." + "An elicited macrophage that is recruited into the tissues in response to injury and infection as part of an inflammatory response, expresses high levels of pro-inflammatory cytokines, ROS and NO, and shows potent microbicidal activity." + "The expansion of a CD4-positive, alpha-beta T cell population by cell division." + "A portion of tissue that is part of an embryo." "CALOHA:TS-2100" + "Any process that increases the rate, frequency, or extent of cartilage development, the process whose specific outcome is the progression of the cartilage over time, from its formation to the mature structure. Cartilage is a connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate." + "A process that results in the assembly, arrangement of constituent parts, or disassembly of an actin filament bundle." + "The chemical reactions and pathways resulting in the breakdown of glucose, the aldohexose gluco-hexose." + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a presynapse." + "Subdivision of vertebral column that corresponds to the caudal subdivision of the body, containing the caudal vertebrae." "AAO:0000082 EMAPA:18043 MA:0003158" + "An embryonic group of progenitor cells that forms from an outpouching of the septum transversum near the venous pole of the heart and gives rise to the epicardium." "EMAPA:36025 ZFA:0005808" + "A homeostatic process involved in the maintenance of an internal steady state within a defined anatomical structure of an organism, including control of cellular proliferation and death and control of metabolic function. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome." + "Any process that stops, prevents, or reduces the frequency, rate or extent of T-helper cell differentiation." + "Any process that modulates the frequency, rate or extent of Schwann cell chemotaxis." + + + "A portion of connective tissue that is part of a trachea." "EMAPA:35876 MA:0001853" + "A cytoskeletal structure that forms a distinct elongated structure, characteristically 10 nm in diameter, that occurs in the cytoplasm of eukaryotic cells. Intermediate filaments form a fibrous system, composed of chemically heterogeneous subunits and involved in mechanically integrating the various components of the cytoplasmic space. Intermediate filaments may be divided into five chemically distinct classes: Type I, acidic keratins; Type II, basic keratins; Type III, including desmin, vimentin and others; Type IV, neurofilaments and related filaments; and Type V, lamins." "NIF_Subcellular:sao952483289 FMA:63851 Wikipedia:Intermediate_filament" + "A C-X-C chemokine receptor type 4 that is encoded in the genome of human." "UniProtKB:P61073 Reactome:R-HSA-2980772 DTO:02100078" + "A developmental process, independent of morphogenetic (shape) change, that is required for the cerebellar granular layer to attain its fully functional state. The granular layer is the innermost layer of the cerebellar cortex. This layer contains densely packed small neurons, mostly granule cells. Some Golgi cells are found at the outer border. Granule neurons send parallel fibers to the upper molecular layer, where they synapse with Purkinje cell dendrites. Mossy fibers from the pontine nuclei in the white matter synapse with granule cell axons, Golgi cell axons and unipolar brush interneuron axons at cerebellar glomeruli in the granule cell layer." + + "UMLS:C1512086 NCIT:C25787" + "Any process that stops or reduces the rate of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor." + "The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific, leading to the initiation or perpetuation of an immune response." + "The segment of the manus that is distal to the metacarpal region and consists of the manual digits (fingers)." "FMA:75592" + "A developmental process, independent of morphogenetic (shape) change, that is required for the olfactory placode to attain its fully functional state. The olfactory placode is a thickening of the neural ectoderm in the head region of the vertebrate embryo which develops into the olfactory region of the nasal cavity." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-1 beta production." + "The process whose specific outcome is the progression of the lymph gland over time, from its formation to the mature structure. The lymph gland is one of the sites of hemocyte differentiation. It consists of three to six bilaterally paired lobes that are attached to the cardioblasts during larval stages, and it degenerates during pupal stages." + "KUPO:0001119" + "Any process that activates or increases the frequency, rate or extent of the directed movement of norepinephrine into a cell." + "A portion of skeletal muscle tissue that is part of a esophagus [Automatically generated definition]." "EMAPA:36523 MA:0001572" + "The multiplication or reproduction of cells, resulting in the expansion of a cell population that contributes to the shaping of the outflow tract." + "Any process that activates or increases the frequency, rate or extent of the regulated release of a neurotransmitter." + "The posterior part of the developing vertebrate hindbrain or the corresponding part of the adult brain composed of the medulla oblongata and a portion of the fourth ventricle; as well as the glossopharyngeal nerve (CN IX), vagus nerve (CN X), accessory nerve (CN XI), hypoglossal nerve (CN XII), and a portion of the vestibulocochlear nerve (CN VIII).[BTO,WP]." "EHDAA:5526 CALOHA:TS-0607 Wikipedia:Myelencephalon EHDAA2:0001207 EMAPA:17082 VHOG:0000456 HBA:9512 MA:0000205 CALOHA:TS-2365 DHBA:10662 BTO:0000758" + + "Combining with a neurotransmitter and transmitting the signal to initiate a change in cell activity." + "KUPO:0001045" + "Any process that modulates the frequency, rate, or extent of endothelial cell proliferation." + "The series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal. Pain is medically defined as the physical sensation of discomfort or distress caused by injury or illness, so can hence be described as a harmful stimulus which signals current (or impending) tissue damage. Pain may come from extremes of temperature, mechanical damage, electricity or from noxious chemical substances. This is a neurological process." "Wikipedia:Nociception" + "A thick walled, sexual, resting spore formed by Zygomycetes; sometimes refers to the spore and the multi-layered cell wall that encloses the spore, the zygosporangium." "FAO:0000040" + "Anatomical structure of largely lymphoid tissue that functions in cell-mediated immunity by being the site where T cells develop." "EFO:0000860 GAID:464 NCIT:C12433 AAO:0010548 EV:0100138 MIAA:0000080 BTO:0001374 EMAPA:18768 MESH:D013950 VHOG:0000253 TAO:0001078 Wikipedia:Thymus XAO:0000163 ZFA:0001078 EHDAA2:0002017 CALOHA:TS-1043 UMLS:C0040113 MA:0000142 FMA:9607 EHDAA:9119 MAT:0000080 SCTID:118507000" + "A process that results in the breakdown of the extracellular matrix." + "Any process that modulates the frequency, rate, or extent of antigen processing and presentation of antigen (peptide or polysaccharide) via MHC class II." + "A type of intrafusal muscle fiber that has nuclei arranged in a linear row. Unlike nuclear bag fibers, the equatorial region of these fibers (in the centre of the spindle) is not expanded. These fibers are responsible for the detection of changes in muscle length. They are innervated by static gamma motor neurons and are principally associated with type II sensory fibers." + "A mesothelial cell that is part of the pleura." "FMA:86737" + "Any process that modulates the frequency, rate or extent of vascular smooth muscle cell differentiation." + "The mesonephric comma-shaped body is the precursor structure to the mesonephric S-shaped body that contributes to the morphogenesis of a nephron in the mesonephros[GO]." + "KUPO:0001117" + "KUPO:0001046" + "The process of biting and mashing food with the teeth prior to swallowing." + "A motor neuron that is capable of directly inhibiting muscle contraction." + "Artery that receives blood from the renal cortex[MP, modified]." "MA:0002592 EMAPA:28152" + "A mature B cell located in the marginal zone of the lymph node." + "Any process that stops, prevents or reduces the frequency, rate or extent of glutamatergic neuron differentiation." + "The process in which a B cell in the spleen acquires the specialized features of a marginal zone B cell. Marginal zone B cells are localized in a distinct anatomical region of the spleen that represents the major antigen-filtering and scavenging area (by specialized macrophages resident there). It appears that they are preselected to express a BCR repertoire similar to B-1 B cells, biased toward bacterial cell wall constituents and senescent self-components (such as oxidized LDL)." + "The process in which a precursor cell type acquires the specialized features of a CD8-positive, alpha-beta cytotoxic T cell." + + "EMAPA:17789 EHDAA2:0001152 DHBA:12695" + + "A progenitor cell of the mast cell lineage. Markers for this cell are FceRIa-low, CD117-positive, CD9-positive, T1/ST2-positive, SCA1-negative, and lineage-negative." + "The directed movement of a protein from the nucleus into the cytoplasm." + "The flow of blood through the network of arteries and veins supplying the cerebrum, enabling the transport of nutrients to the tissues and the removal of waste products." + "A CD27 molecule that is encoded in the genome of mouse." "UniProtKB:P41272" + "KUPO:0001114" + "SCTID:363673006 EMAPA:30807" + "KUPO:0001100" + "SCTID:363130003 FMA:75634" + "The migration of mesenchymal tissue that contributes to the formation of a limb bud." + "A submucosa that is part of a cecum [Automatically generated definition]." "FMA:14999" + "A cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. Progenitors leave bone marrow and mature in connective and mucosal tissue. Mature mast cells are found in all tissues, except the bloodstream. Their phenotype is CD117-high, CD123-negative, CD193-positive, CD200R3-positive, and FceRI-high. Stem-cell factor (KIT-ligand; SCF) is the main controlling signal of their survival and development." "BTO:0000830 FMA:66784 CALOHA:TS-0603" + "Any process that modulates the frequency, rate or extent of cell proliferation." + "Any process that activates or increases the frequency, rate, or extent of mast cell apoptotic process." + "A portion of interstitial tissue that is part of a outer medulla of kidney [Automatically generated definition]." "MA:0002621 EMAPA:28337" + "The muscular portion of the wall between the two lower chambers of the heart." "MA:0002940 EMAPA:18247 RETIRED_EHDAA2:0000888 EHDAA:2607 FMA:7134 EHDAA2:0000885" + "MA:0000579 EMAPA:25133" + + "A neuron that stratifies dendrites at two and only two locations." + "The arachnoid barrier layer is a part of the arachnoid meningeal layer. It is formed by tight junctions between the endothelial cells of cerebral capillaries in the arachnoid mater." "FMA:231559 BTO:0002498" + "The dorsal portion of the embryonic first endodermal pharyngeal pouch; it develops into the middle ear cavity." "VHOG:0001297 EMAPA:17002 EHDAA:6772 NCIT:C34318 EHDAA2:0004115 SCTID:361516008 MA:0001218 UMLS:C1284046" + "One of the minute vessels that collect deoxygenated blood from the capillary plexuses returns it to the veins." "TAO:0005315 SCTID:341687009 BTO:0002626 ZFA:0005315 UMLS:C0042520 Wikipedia:Venule MA:0000071 NCIT:C12818 EMAPA:35917 MESH:D014699 FMA:63130 VHOG:0001765" + "Binding to one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function." "Wikipedia:Ligand_(biochemistry)" + "A protein that in active form is a serine protease that cleaves peptide bonds on the carboxyl side of lysine or arginine amino acids within amino acid chains." + "A process, occurring at the cellular level, that is involved in the reproductive function of a multicellular organism." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of T cell cytokine production." + "A cell pyramidal in shape, with their broad ends facing and forming the greater extent of the lining of the main lumen. Secretes glycoproteins associated with mucus." "FMA:70659" + "Any process that activates or increases the frequency, rate or extent of protein localization to nucleus." + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptide stimulus." + "The process in which the anatomical structure of the hindbrain is generated and organized. The hindbrain is the region consisting of the medulla, pons and cerebellum. Areas of the hindbrain control motor and autonomic functions." + "The process in which a relatively unspecialized cell acquires specialized features of a vestibular hair cell." + "An intervertebral disk that is part of a cervical region of vertebral column. A cervical intervertebral disk connects at least one cervical vertebra, either to another cervical vertebra, or at one point on the vertebral colummn, to a thoracic vertebra." "FMA:13895 SCTID:68818006 EMAPA:19415" + + "An epithelium that is part of a ectocervix." "SCTID:361376000" + "Anatomical conduit that connects two adjacent body spaces (or a body space with the space surrounding the organism)[FMA,modified]." "FMA:3724 SCTID:91837002" + "A tarsal bone that connected_to a hindlimb zeugopod skeleton." + "A choroid plexus macrophage that is part of the apical surface of some choroid plexus epithelium. This macrophage has a star-like shaped body." + "Any process that modulates the frequency, rate, or extent of glial cell apoptotic process." + "SCTID:279975006" + "The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell that contributes to the epithelium of the lung." + "An endocrine cell that secretes vasoactive intestinal peptide." + "KUPO:0001098" + "An eye that is part of a right side of organism [Automatically generated definition]." "EMAPA:37363 NCIT:C119333 MA:0002950 SCTID:362502000 FMA:12514" + "Any process that activates or increases the frequency, rate or extent of the inflammatory response to wounding." + "Any process that stops, prevents or reduces the frequency, rate or extent of lens fiber cell differentiation." + "Any process that stops, prevents, or reduces the frequency, rate or extent of skeletal muscle regeneration." + "KUPO:0001113" + "Endochondral bones that are often elongate and arranged in rows of articulating elements, and form the visible part of the digits." "Wikipedia:Phalanx_bones EMAPA:32614 galen:Phalanx NCIT:C33317 FMA:321661 VSAO:0000199 CALOHA:TS-2211 UMLS:C0222682 MA:0000304 SCTID:290029003" + "Any process that stops, prevents, or reduces the frequency, rate or extent of alpha-beta T cell activation." + "The thin layer of gray matter on the surface of the cerebral hemisphere that develops from the telencephalon. It consists of the neocortex (6 layered cortex or isocortex), the hippocampal formation and the olfactory cortex." "VHOG:0000722 BM:Tel-Cx BTO:0000233 GAID:629 DHBA:10159 SCTID:362880003 EHDAA:5464 CALOHA:TS-0091 UMLS:C0007776 MAT:0000108 EV:0100166 EHDAA2:0000234 BAMS:C MA:0000185 neuronames:39 PBA:128011354 FMA:61830 BAMS:Cerebral_cortex BAMS:Cx MBA:688 BIRNLEX:1494 EMAPA:17544 MIAA:0000108 Wikipedia:Cerebral_cortex MESH:D002540 EFO:0000328 BAMS:CTX HBA:4008 NCIT:C12443" + "A mucosa that is part of a descending colon [Automatically generated definition]." "FMA:15019" + "Any process that modulates the occurrence or rate of cell death by apoptotic process." + "Any process that modulates the frequency, rate or extent of striated muscle cell differentiation." + "The aggregation, arrangement and bonding together of a set of components to form a ciliary transition zone." + "SCTID:13152008" + "The myoendocrine cellis a specialized myocyte localized mainly in the right and left atrial appendages, and also scattered within other areas of the atria and along the conductive system in the ventricular septum. The most conspicuous feature distinguishing myoendocrine cells from other atrial myoctyes is the presence of membane-bounded secretory granules (these granules contain precursor of cardiodilatins or atrial natriuretic polypeptides)." "FMA:67111" + "An immature B cell that is CD38-negative, CD10-low, CD21-low, and CD22-high." + "Any process that activates or increases the frequency, rate, or extent of peptide secretion." + "Obsolete. Use PO:0000290 from Plant Ontology instead. A water conducting cell, tracheid or vessel member." + "A macromolecular complex that contains both RNA and protein molecules." "Wikipedia:Ribonucleoprotein" + "Any process that modulates the frequency, rate or extent of leukocyte proliferation." + + "An anatomical space that surrounded_by a rectum." "EMAPA:18388 EHDAA2:0004587 FMA:14598 SCTID:259740004" + "The epithelial layer of the stomach ." "CALOHA:TS-2068 SCTID:64977002 EMAPA:17023 BTO:0000500 MA:0001610 VHOG:0001433 EHDAA2:0001918 FMA:17091" + "The progression of an ectodermal placode over time from its initial formation until its mature state. An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm." + "A nuclear bag fiber that is sensitive mainly to the rate of change in muscle length." + "Any process that stops, prevents or reduces the frequency, rate or extent of exosomal secretion." + "A cartilage element that lies between two successive vertebral centra." "AAO:0000795" + "Any process that modulates the frequency, rate or extent of aortic smooth muscle cell differentiation." + "Obsolete. Use PO:0000400 from Plant Ontology instead. A cambial cell on the phloem side of the cambial zone that is the source of one or more cells arising by periclinal divisions and differentiating into phloem elements with or without additional divisions in various planes." + "A process in which a protein is transported to or maintained in a location within an axon." + "The series of events by which an electrical stimulus is received and converted into a molecular signal. This occurs as part of the regulation of muscle adaptation." + "An external organ of a male organism that is specialized to deliver sperm during copulation. Intromittent organs are found most often in terrestrial species, as most aquatic species fertilize their eggs externally, although there are exceptions[WP]." "HAO:0000091 TAO:0002036 Wikipedia:Intromittent_organ AAO:0010255 TGMA:0000585" + "Any process that activates or increases the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes." + "FMA:32888" + "The process in which the conus arteriosus is generated and organized. The conus arteriosus is a valved chamber with thick muscular walls stemming from the ventricle and connecting to the pulmonary trunk." + "Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation." "ZFA:0001477 WBbt:0005729 NCIT:C12801 TGMA:0001844 BIRNLEX:19 CARO:0000043 BILA:0000043 EHDAA2:0003043 XAO:0003040 EMAPA:35868 MESH:D014024 TAO:0001477 AAO:0010054 AEO:0000043 AAO:0000607 MA:0003002 VHOG:0001757 FMA:9637 UMLS:C0040300 galen:Tissue HAO:0000043 CALOHA:TS-2090" + "A neuron that is capable of some hormone secretion in response to neuronal signals." "FBbt:00005130 FMA:83810 BTO:0002691" + "Any process that modulates the frequency, rate, or extent of proteolysis associated with antigen processing and presentation." + "A portion of smooth muscle tissue that is part of a outflow tract [Automatically generated definition]." "EMAPA:37708 MA:0000492" + "Any epithelial cell that is part of a female gonad." + "The chemical reactions and pathways resulting in the formation of L-glutamate, the L enantiomer anion of 2-aminopentanedioic acid." + "Any nerve that innervates the iris." "MA:0001291 EMAPA:35449" + "Any process that activates or increases the frequency, rate, or extent of interleukin-22 production." + "A parasol ganglion cell that depolarizes in response to increased light intensity in the center of its receptive field. The majority of input that this cell receives comes from DB4 bipolar cells." + "EMAPA:32916 DHBA:12694" + "Any process in which the vacuole is transported to, and/or maintained in, a specific location within the cell." + "The tubules that carry lymph throughout the body that are just beneath the surface of the skin." "NCIT:C33663 UMLS:C1282745 SCTID:20315002 FMA:52011" + "The group of nerve cell bodies that conveys auditory sensation from the organ of Corti to the hindbrain and resides on the cochlear part of the vestibulocochlear nerve (eighth cranial nerve)[MP]. distributed to the hair cells of the spiral organ. The cochlear fibers arise in bipolar cells in the spiral ganglion in the modiolus." "neuronames:1405 BAMS:GcVIII VHOG:0001183 MA:0001085 MESH:D013136 EHDAA2:0002198 SCTID:368955007 FMA:53445 BTO:0001688 Wikipedia:Spiral_ganglion GAID:722 EMAPA:17572" + "Any process that modulates the frequency, rate or extent of protein localization to cell cortex." + "The loose fold of skin that covers the penis." "VHOG:0001342 MA:0001744 FMA:27648 SCTID:39059001" + "Enables the transfer of the hexose monosaccharide glucose from one side of a membrane to the other." "Reactome:R-HSA-5653873 Reactome:R-HSA-499981" + + "A tail that extends from the posterior tip of the organism to the anus, contains muscle and skeleton." "AAO:0010338 ZFA:0001117 UMLS:C0039259 MA:0000008 NCIT:C77663 XAO:0003026 TAO:0001117" + "A enteroendocrine cell part of the glands of the gastric mucosa. They produce histamine and peptides such as chromogranins. This cell type respond to gastrin by releasing histamine which acts as a paracrine stimulator of the release of hydrochloric acid from the gastric parietal cells." "BTO:0002692" + "An epithelium that is part of a cochlear duct of membranous labyrinth [Automatically generated definition]." "EHDAA:4722 RETIRED_EHDAA2:0000264 VHOG:0000640 EMAPA:17600" + "GC_ID:1" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of lipids within cells." + "Any process that modulates the frequency, rate or extent of endothelial cell chemotaxis." + "A retinal amacrine cell with a medium dendritic field and post-synaptic terminals in S1, S2, S3, and S4. This cell type releases the neurotransmitter gamma-aminobutyric acid (GABA)." + "A macrophage located in adipose tissue that is CD45-positive, CD11c-positive, and SIRPa-positive." + "Mesenchyme enclosed by a dental organ that gives rise to an odontogenic papilla." "VHOG_RETIRED:0001444 EMAPA:32891 ZFA:0005139 TAO:0005139 MA:0003152" + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving aldosterone." + "Hair in the nose." "FMA:53670 Wikipedia:Nasal_hair SCTID:368885003" + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a norepinephrine stimulus. Norepinephrine is a catecholamine that has the formula C8H11NO3; it acts as a hormone, and as a neurotransmitter in most of the sympathetic nervous system." + "An early stage of embryonic development in animals. It is produced by cleavage of a fertilized ovum and consists of a spherical layer of around 128 cells surrounding a central fluid-filled cavity called the blastocoel. The blastula follows the morula and precedes the gastrula in the developmental sequence." "BilaDO:0000007 WBls:0000005 OGES:000003 XAO:1000003 MmusDv:0000007 Wikipedia:Blastula OGES:000016 OGES:000021 ZFS:0000045 BILS:0000108 HsapDv:0000006 EFO:0001282" + "The regulated release of serotonin by a basophil or group of basophils." + "Any process that stops, prevents or reduces the frequency, rate or extent of renin secretion into blood stream." + "The embryonic connective tissue made up of loosely aggregated mesenchymal cells, supported by interlaminar jelly, that gives rise to the developing cardiac structures." "EMAPA:36438 EHDAA2:0004162" + "Any process that stops, prevents, or reduces the frequency, rate, or extent of antigen processing and presentation of peptide antigen via MHC class II." + "The mitotic cell cycle process in which the controlled partial or complete breakdown of the nuclear membranes during occurs during mitosis." + "Any process that stops, prevents or reduces the frequency, rate or extent of defecation." + "Any process that activates or increases the frequency, rate or extent of vascular endothelial cell proliferation." + "NCIT:C52947 EMAPA:37092 UMLS:C1708633 MA:0001987" + "An tooth placode is a thickening of the ectoderm that will give rise to the tooth bud[GO]." "ZFA:0001153 BTO:0001511 TAO:0001153" + "Spherical outcropping of the respiratory bronchioles and primary site of gas exchange with the blood. Alveoli are particular to mammalian lungs. Different structures are involved in gas exchange in other vertebrates[WP]." "SCTID:361364000 EMAPA:32682 GAID:349 BTO:0000060 CALOHA:TS-0031 MA:0000420 VHOG:0001445 FMA:7318 Wikipedia:Pulmonary_alveolus MESH:D011650 EFO:0001985" + "The aggregation, arrangement and bonding together of a set of components to form a basement membrane, a part of the extracellular region that consists of a thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue." + "A GABAergic neuron located in the cerebral cortex that expresses somatostatin (sst)" "ILX:0770152" + "A conduit enclosed within the vertebral foramen of the vertebrae through which the spinal cord passes." "SCTID:361746009 Wikipedia:Spinal_canal NCIT:C34221 AAO:0000693 FMA:9680 NCIT:C33869 UMLS:C1522467 GAID:242 UMLS:C0037922" + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of structures formed of microtubules and associated proteins in the cytoplasm of a cell." + "A protein that is a translation product of the human SSPO gene or a 1:1 ortholog thereof." + "A pia mater that is part of a forebrain [Automatically generated definition]." "EMAPA:37546 MA:0000886" + "A portion of bone tissue that is part of a epiphysis [Automatically generated definition]." "FMA:241364" + "A zone of skin that is part of a wrist [Automatically generated definition]." "NCIT:C52752 FMA:38280 MA:0000638 SCTID:181540008 EMAPA:37351 UMLS:C0222223" + "Enables the facilitated diffusion of a monoatomic ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size)." + "A vasculature that is part of a chordate pharynx." "TAO:0005003 ZFA:0005003" + "A cell that is part of a tip of a renal papilla." "KUPO:0001112" + "A fibroblast that is part of the mammary gland." + "A protein that is the translation product of any of the LY6 genes (LY6A-LY6I)." "PIRSF:PIRSF002021" + "A sst GABAergic interneuron does not have Martinotti morphology with a soma found in L5/6 of the cerebral cortex." + "A hemoglobin subunit zeta that is encoded in the genome of mouse." "UniProtKB:P06467" + "Attachment of the blastocyst to the uterine lining." + "Any process that activates or increases the frequency, rate or extent of T-helper 17 type immune response." + + "Any process that activates or increases the frequency, rate or extent of cell death of neurons by apoptotic process." + "The process whose specific outcome is the progression of the lateral ventricles over time, from the formation to the mature structure. The two lateral ventricles are a cavity in each of the cerebral hemispheres derived from the cavity of the embryonic neural tube. They are separated from each other by the septum pellucidum, and each communicates with the third ventricle by the foramen of Monro, through which also the choroid plexuses of the lateral ventricles become continuous with that of the third ventricle." + "The chemical reactions and pathways resulting in the formation of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. Includes polymerization of ribonucleotide monomers. Refers not only to transcription but also to e.g. viral RNA replication." + "Cell that is part of the vagal neural crest population. The vagal neural crest arises from the axial level of somites 1-7 and has been described as a hybrid between the head and the trunk populations." + "A fast muscle fiber cell that stores energy in the form of glycogen and creatine phosphate." "FMA:84414 BTO:0001813" + "The glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the glomerulus." + "The multiplication or reproduction of cells, resulting in the expansion of a mesenchymal cell population that contributes to the progression of the lung over time. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets." + "OBSOLETE: The cell characteristic of an organ, as distinguished from associated connective or supporting tissues." "FMA:84638 BTO:0002174" + "The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image." "Wikipedia:Visual_perception" + "A vasculature that is part of a post-anal tail." "XAO:0004151 ZFA:0005037 TAO:0005037" + "An ON diffuse bipolar cell that predominantly connects to ON parasol cells and lateral amacrine cells." + "An endothelium that is part of a lymph node [Automatically generated definition]." "EMAPA:35526 MA:0000741" + "The series of events involved in the perception of sound vibration in which the vibration is received and converted into a molecular signal." + "Any process that increases the frequency, rate or extent of hepatic stellate cell migration." + "A melanin-containing macrophage that obtains the pigment by phagocytosis of melanosomes." + "A homeostatic process involved in the maintenance of a steady state level of glutamate within a cell." + "A contractility quality inhering in a bearer by virtue of the bearer's ability of contracting or being contracted." + "A lamina propria that is part of a jejunum." + "A gray matter that is part of a brain [Automatically generated definition]." "EMAPA:35184 UMLS:C1707348 NCIT:C49333 MA:0000810" + "The jugular veins are veins that bring deoxygenated blood from the head back to the heart via the superior vena cava." "SCTID:244403000 MA:0002154 EMAPA:18638 CALOHA:TS-0497 MESH:D007601 GAID:536 Wikipedia:Jugular_vein UMLS:C0022427 NCIT:C12738 BTO:0001744" + "An epithelium that is part of a lip." "TAO:0005334 BTO:0004468 ZFA:0005334" + "A longitudinal muscle layer of muscular coat that is part of a colon smooth muscle." + "Any cell that is part of the esophageal non-keratinized stratified squamous epithelium. In humans, the esophagus, which requires flexibility to accommodate swallowing of a bolus, is covered with a non-keratinized epithelium." + "A protein that is a translation product of the human CD207 gene or a 1:1 ortholog thereof." + "A cell of the cuboidal epithelium that covers the lens. The cells of the lens epithelium regulate most of the homeostatic functions of the lens. As ions, nutrients, and liquid enter the lens from the aqueous humor, Na+/K+ ATPase pumps in the lens epithelial cells pump ions out of the lens to maintain appropriate lens osmolarity and volume, with equatorially positioned lens epithelium cells contributing most to this current. The activity of the Na+/K+ ATPases keeps water and current flowing through the lens from the poles and exiting through the equatorial regions. The cells of the lens epithelium also serve as the progenitors for new lens fibers. It constantly lays down fibers in the embryo, fetus, infant, and adult, and continues to lay down fibers for lifelong growth." "FMA:67559" + "The joining of the lipid bilayer membrane around a vesicle to the lipid bilayer membrane around the Golgi." + "Any process that activates, maintains or increases the frequency, rate or extent of activation of satellite cell involved in skeletal muscle regeneration. The activation of satellite cell is the process that initiates satellite cell division by causing it to move from quiescence to the G1 stage of the cell cycle. The cell swells and there are a number of other small changes. The cells then start to divide. Following cell division the cells will differentiate." + "Epithelial layer that lines the intestine." "ZFA:0005124 TAO:0005124 SCTID:266135004 FMA:17229 UMLS:C0226890 Wikipedia:Intestinal_epithelium MA:0001536 BTO:0000781 EMAPA:32873 NCIT:C49240" + "Enables the transfer of nucleic acids from one side of a membrane to the other. Nucleic acids are single or double-stranded polynucleotides involved in the storage, transmission and transfer of genetic information." + "A process of chromosome organization that is involved in a meiotic cell cycle." + "Enables the transfer of ammonium from one side of a membrane to the other. Ammonium is the cation NH4+ which is formed from N2 by root-nodule bacteria in leguminous plants and is an excretory product in ammonotelic animals." "RHEA:28747 Reactome:R-HSA-446277 Reactome:R-HSA-5623051 Reactome:R-HSA-444393 Reactome:R-HSA-446278 Reactome:R-HSA-444419 Reactome:R-HSA-444416" + "The primordial embryonic connective tissue of the developing limbs, autopods and digits, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to limb connective tissue, bone and musculature in conjunction with myotome cells." "EMAPA:32705" + "A splenic macrophage found in the red-pulp of the spleen, and involved in immune responses to blood-borne pathogens and in the clearance of senescent erythrocytes. Markers include F4/80-positive, CD68-positive, MR-positive, Dectin2-positive, macrosialin-positive, and sialoadhesin-low." + "Any process that modulates the frequency, rate or extent of lymphocyte migration." + "Grey matter neocortex region of a lobe of the cerebral hemisphere." "FMA:242197" + "A mucosa that is part of a left uterine tube [Automatically generated definition]." "FMA:18453" + "Any anatomical space that is part of a vertebral column." "AAO:0000700" + "Any process that activates or increases the frequency, rate or extent of cardiac muscle myoblast proliferation." + "One of a series of paired embryological vascular structures formed within a pharyngeal arch; in the adult, some of these vessels give rise to the great vessels[MP]." "ZFA:0005004 EFO:0003695 TAO:0005004 EMAPA:16684 NCIT:C32123 EHDAA:7327 AAO:0010414 UMLS:C0003489 XAO:0000341 VHOG:0000122 Wikipedia:Aortic_arches EHDAA2:0000186 EHDAA:398" + "A joint that connects one phalanx to another along a proximodistal axis." "FMA:42765 EMAPA:37884 NCIT:C101527 galen:InterphalangealJoint" + "A chromaffin cell that is part of the adrenal gland." "FMA:69794" + "A portion of the respiratory and digestive tracts; its distal limit is the superior part of the esophagus and it connects the nasal and oral cavities with the esophagus and larynx; it contains the valleculae and the pyriform recesses; its upper limits are the nasal cavity and cranial base.[FEED]." "galen:Pharynx GAID:155 MESH:D010614 EHDAA:2947 EHDAA2:0001458 ZFA:0000056 MA:0000432 FMA:46688 EMAPA:16706 BTO:0001049 VHOG:0000462 EFO:0000836 XAO:0003227 Wikipedia:Pharynx CALOHA:TS-0785 UMLS:C0031354 AAO:0000967 NCIT:C12425 EV:0100065 SCTID:181211006 TAO:0000056" + "Portion of neural crest that develops from the dorsal neural tube. It overlaps the vagal neural crest and migrates to populate the pharyngeal arches 3, 4 and 6 (producing structures in the head) and to the heart, forming connective tissue that separates the great vessels of the heart. [Wikipedia]." "XAO:0004190 ZFA:0001648 Wikipedia:Cardiac_neural_crest TAO:0002173" + "Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins." + "Neuromast support cell is a non-sensory cell of the neuromast that extend between the sensory hair cells from the basement membrane to the apical surface; neuromast support cells are surrounded by neuromast mantle cells." + "An L-selectin that is encoded in the genome of mouse." "UniProtKB:P18337" + "The first segment of the nephron lying just downstream from the loop of Henle, immediately after the macula densa." "EMAPA:28393 Wikipedia:Distal_convoluted_tubule MA:0001666 FMA:17721 SCTID:361336005 NCIT:C32469 EV:0100389 UMLS:C0022676" + "Any process that modulates the frequency, rate or extent of tight junction disassembly." + "The process in which myelin sheaths are formed and maintained around neurons. Oligodendrocytes in the brain and spinal cord and Schwann cells in the peripheral nervous system wrap axons with compact layers of their plasma membrane. Adjacent myelin segments are separated by a non-myelinated stretch of axon called a node of Ranvier." "Wikipedia:Myelin" + "Removal of the sperm nuclear envelope, allowing entry of maternal factors into the sperm nucleus." + "Either of two main superficial veins of the leg, one larger than the other, that begin at the foot." "MESH:D012501 UMLS:C0036186 CALOHA:TS-0893 MA:0002215 EMAPA:37186 BTO:0001808 NCIT:C33511" + "Any process that modulates the frequency, rate or extent of neuroinflammatory response." + "A spore formed following mitosis or mitoses." "FAO:0000023" + "A region of the stomach that is lined with glandular epithelium." "EMAPA:17623 UMLS:C0227197 NCIT:C77661 MA:0001613 SCTID:27633001" + "Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present." "EFO:0000966 ZFA:0001115 MA:0000004 galen:Trunk BTO:0001493 BILA:0000116 NCIT:C33816 CALOHA:TS-1071 XAO:0000054 SCTID:262225004 AAO:0010339 MIAA:0000296 Wikipedia:Torso XAO:0003025 EMAPA:31857 FMA:7181 TAO:0001115 MAT:0000296 UMLS:C0460005" + "A mesenchymal cell in embryonic development found in a contracting mass and that gives rise to osteoprogenitors." + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving DNA." + "The movement of a cell along the process of a radial glial cell involved in cerebral cortex glial-mediated radial migration." + "Any process that mediates the transfer of information from a mesenchymal cell to an epithelial cell where it is received and interpreted contributing to the progression of the prostate gland over time." + "The metanephric cortex is the outer region of the metanephros[GO]." "VHOG:0000714" + "A submucosa that is part of a common hepatic duct [Automatically generated definition]." "FMA:18014" + "Any process that modulates the frequency, rate, or extent of leukocyte mediated immunity." + "An epithelial cell that is part of a duct." + "A cartilaginous condensation that has the potential to develop into a fibula." "EMAPA:18154" + "A joint that connects the bones of the crus to the proximal tarsal bones." "Wikipedia:Crurotarsal" + "The process whose specific outcome is the progression of the hypoglossal nucleus over time, from its formation to the mature structure." + "Any process in an organism in which a relatively long-lasting adaptive behavioral change occurs as the result of experience." "Wikipedia:Learning" + "A mucosa that is part of a right uterine tube [Automatically generated definition]." "FMA:18452" + "An anatomical boundary that adjacent_to a epithelium." "FMA:70997" + "Any process that activates or increases the frequency, rate or extent of androgen secretion." + "The synthesis or release of products of arachidonic acid metabolism following a stimulus as part of an inflammatory response, resulting in an increase in their intracellular or extracellular levels." + "Any process that stops, prevents, or reduces the frequency, rate or extent of leucophore differentiation." + "Any neuron that is part of a spinal cord medial motor column." + "Any process that stops, prevents, or reduces the frequency, rate or extent of microtubule polymerization." + "Any process that stops, prevents or reduces the frequency, rate or extent of adipose tissue development." + "A muscle cell that is part of some visceral muscle." "FBbt:00005070" + + "The process whose specific outcome is the progression of the diencephalon over time, from its formation to the mature structure. The diencephalon is the paired caudal parts of the prosencephalon from which the thalamus, hypothalamus, epithalamus and subthalamus are derived; these regions regulate autonomic, visceral and endocrine function, and process information directed to the cerebral cortex." + "The chemical reactions and pathways resulting in the breakdown of keratan sulfate, a glycosaminoglycan with repeat units consisting of beta-1,4-linked D-galactopyranosyl-beta-(1,4)-N-acetyl-D-glucosamine 6-sulfate and with variable amounts of fucose, sialic acid and mannose units; keratan sulfate chains are covalently linked by a glycosidic attachment through the trisaccharide galactosyl-galactosyl-xylose to peptidyl-threonine or serine residues." + "A T-cell surface glycoprotein CD8 alpha chain isoform 1 that is encoded in the genome of human." "UniProtKB:P01732-1" + "A precursor of mature hemocytes." "FBbt:00005062" + "Any process that activates or increases the frequency, rate or extent of B cell chemotaxis." + "A cell that is part of non-pigmented ciliary epithelium. This cell type participates in aqueous humor formation by releasing solute, principally sodium and chloride ions received from pigmented epithelial cells via gap junctions, into the aqueous humor of the eye." "FMA:70607" + "A beta motor neuron that innervates the nuclear bag fibers of muscle spindles." + "Any process that modulates the frequency, rate or extent of skeletal muscle cell proliferation." + "The process in which the neural fold is formed. The edges of the neural plate thicken and move up to form a U-shaped structure called the neural groove." + "The multiplication or reproduction of cells, resulting in the expansion of the population in the kidney." + "The process in which a relatively unspecialized T cell acquires specialized features of a mature CD4-positive, alpha-beta T cell." + "Any process that modulates the frequency, rate or extent of nurse cell apoptotic process." + "Obsolete. Consult Plant Ontology instead. A type of sieve element that has relatively undifferentiated sieve areas (with narrow pores), rather uniform in structure on all walls; that is, there are no sieve plates. Typical of gymnosperms and lower vascular plants." + "The establishment, maintenance and elaboration of a pattern along a line or around a point." + "A choroid plexus stroma that is part of a lateral ventricle." "MA:0000963" + "A G protein-coupled receptor signaling pathway initiated by cholecystokinin binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process, e.g. transcription." "Wikipedia:Cholecystokinin" + "Any process that modulates the frequency, rate or extent of heart contraction. Heart contraction is the process in which the heart decreases in volume in a characteristic way to propel blood through the body." + "The directed killing of a target cell by a T cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors." + "The multiplication or reproduction of neural precursor cells, resulting in the expansion of a cell population. A neural precursor cell is either a nervous system stem cell or a nervous system progenitor cell." + "A complex network of conduits that begins with the canals of Hering (intralobar bile duct) and progressively merges into a system of interlobular, septal, and major ducts which then coalesce to form the extrahepatic bile ducts, which finally deliver bile to the intestine, and in some species to the gallbladder." "Wikipedia:Biliary_tract UMLS:C0005423 SCTID:181267003 EMAPA:35172 AAO:0011020 XAO:0000455 FMA:14665" + "A type of cell containing lipids in small vacuoles and typically seen in atherolosclerotic lesions, as well as other conditions." "MESH:D005487 FMA:83586 BTO:0003872" + "Missing definition for term UBERON:0004133. Please replace it using linked reference." + "The process in which the anatomical structures of the head are generated and organized. The head is the anterior-most division of the body." + "The process whose specific outcome is the progression of the thyroid gland over time, from its formation to the mature structure. The thyroid gland is an endoderm-derived gland that produces thyroid hormone." + "Any action potential process that regulates skeletal muscle contraction." + "A macrophage that is located in the anorectum." + "The ridge of mesoderm covered with endoderm that in the early developing embryo partitions the endodermal cloaca into the primary urogenital sinus (ventrally) and the anorectal canal of the hindgut (dorsally); the urorectal septum eventually fuses with the cloacal membrane, dividing it into a dorsal anal membrane and a larger ventral urogenital membrane - this area of fusion is represented in the adult by the perineal body[MP]." "EHDAA:5921 EHDAA2:0002152 EMAPA:17212 Wikipedia:Urorectal_septum UMLS:C1519838 MA:0003235 NCIT:C34323 VHOG:0000018" + "The process in which the structures of a chondrocyte are generated and organized. This process occurs while the initially relatively unspecialized cell is acquiring the specialized features of a chondrocyte." + "Any process that modulates the frequency, rate or extent of a system process, a multicellular organismal process carried out by any of the organs or tissues in an organ system." + "Any process that modulates the frequency, rate or extent of the formation of a myelin sheath around nerve axons." + "Mineralized bone tissue that always includes non-terminally differentiated osteoblasts and osteocytes." + "Fatty lubricant matter secreted by sebaceous glands, and made of made of triglyceride oils, wax, squalene, and metabolytes of fat-producing cells[BTO,WP]." "ENVO:02000037 MESH:D012629 BTO:0001981 MA:0002538 GAID:1168 Wikipedia:Sebaceous_glands#Sebum FMA:61304 NCIT:C13276 UMLS:C0036511" + "An integrin alpha-2 that is encoded in the genome of human." "UniProtKB:P17301" + "Any process that activates or increases the frequency, rate or extent of the regulated release of a gonadotropin." + "A mature male germ cell that develops from a spermatid." "FBbt:00004954 CALOHA:TS-0949 BTO:0002046 BTO:0001277 FMA:67338 WBbt:0006798" + "Any process that stops, prevents, or reduces the frequency, rate, or extent of erythrocyte clearance." + "Any process that stops, prevents, or reduces the frequency, rate or extent of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus." + "The process in which a relatively unspecialized cell acquires specialized features of a cardiac muscle cell in the atrium. Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. The atrium is the part of the heart that receives blood into the organ." + "A nerve that innervates an eyelid." "MA:0001255 EMAPA:37535" + "Any process that modulates the frequency, rate or extent of cell motility." + "A cell of a layer of transitional epithelium in the wall of the proximal urethra, bladder, ureter or renal pelvis, external to the lamina propria." "FMA:84127" + "A ring of cells capable of forming a limb or paired fin[Gilbert,modified]." + "The process in which a relatively unspecialized cell acquires the specialized features of the R7 photoreceptor." + "A T-cell surface glycoprotein CD8 alpha chain that is encoded in the genome of mouse." "UniProtKB:P01731" + "Binding to bicarbonate ions (CHO3-)." + "The expansion of a memory T cell population by cell division." + "A small subcellular vesicle, surrounded by a membrane, that is formed from the Golgi apparatus and contains a highly concentrated protein destined for secretion. Secretory granules move towards the periphery of the cell and upon stimulation, their membranes fuse with the cell membrane, and their protein load is exteriorized. Processing of the contained protein may take place in secretory granules." + "The process aimed at the progression of a glial cell in the posterior lateral line nerve over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell." + "A specialised myocyte that lies between the sinoatrial node and the atrioventricular node and is involved in the conduction of electrical signals." "FMA:223275" + "Any process that activates or increases the frequency, rate or extent of memory T cell activation." + "The process whose specific outcome is the progression of the glomerular basement membrane over time, from its formation to the mature structure. The glomerular basement membrane is the basal laminal portion of the glomerulus which performs the actual filtration." + + "Any process that activates or increases the frequency, rate, or extent of tolerance induction dependent upon immune response." + "Any process that stops, prevents, or reduces the frequency, rate or extent of cell division." + "A cell that will develop into a neuron often after a migration phase." "FMA:70563 BTO:0000930" + "A precursor in the granulocytic series, being a cell intermediate in development between a myeloblast and myelocyte, that has distinct nucleoli, a nuclear-to-cytoplasmic ratio of 5:1 to 3:1, and containing a few primary cytoplasmic granules. Markers for this cell are fucosyltransferase FUT4-positive, CD33-positive, integrin alpha-M-negative, low affinity immunoglobulin gamma Fc region receptor III-negative, and CD24-negative." "FMA:83530 CALOHA:TS-0825" + "The process whose specific outcome is the progression of a columnar/cuboidal epithelial cell over time, from its formation to the mature structure. A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube." + "Any process that modulates the frequency, rate or extent of a signaling receptor activity. Receptor activity is when a molecule combines with an extracellular or intracellular messenger to initiate a change in cell activity." + "Any process that activates or increases the frequency, rate or extent of T-helper 2 cell activation." + "Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP]." "BTO:0001314 TAO:0001136 NCIT:C33645 ZFA:0001136 Wikipedia:Hypodermis UMLS:C0278403 FMA:70544 CALOHA:TS-2366 EMAPA:37505" + "Any process that activates or increases the frequency, rate or extent of glycoprotein metabolic process." + "Mesenchyme whose cells are embedded in obvious amounts of extracellular matrix." "AEO:0000151 EHDAA2:0003151" + "Any process that activates, maintains or increases the rate of a response to a stimulus. Response to stimulus is a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus." + "The orderly movement of mesodermal cells from one site to another." + "Any process that stops, prevents, or reduces the frequency, rate or extent of T cell differentiation in the thymus." + "A muscle that attaches to the hyopid bone and to the tongue and is innervated by cranial nerve XII." "FMA:46691 AAO:0010663 NCIT:C53161 SCTID:244785008 UMLS:C0224196 Wikipedia:Hyoglossus_muscle EMAPA:18277 MA:0002317 MFMO:0000064" + "Any process that stops or reduces the rate of hydrolase activity, the catalysis of the hydrolysis of various bonds." + "Any process that stops, prevents, or reduces the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule." + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving catecholamines." + "The valve-like structure found at the site of entry of the ureter into the urinary bladder, normally displays an oblique angulation through the detrusor to avoid reflux of urine up the ureters and the kidney." "NCIT:C106202 FMA:15899 SCTID:261187001 MA:0003020 EMAPA:37783" + "A metanephric nephron tubule is an epithelial tube that is part of the metanephric nephron, the functional part of the metanephros[GO]." + "The metanephric proximal convoluted tubule is the most proximal portion of the metanephric proximal tubule and extends from the metanephric glomerular capsule to the metanephric proximal straight tubule[GO]." "VHOG:0001570" + "A motile sperm cell that contains a slender threadlike microscopic appendage that enables motion." + "An antigen-presenting glycoprotein CD1d that is encoded in the genome of mouse." "UniProtKB:P11609" + "Any process that stops or decreases the rate or extent of glial cell proliferation." + "The removal of tubulin heterodimers from one or both ends of an axonemal microtubule. An axonemal microtubule is a microtubule in the axoneme of a cilium or flagellum; an axoneme contains nine modified doublet microtubules surrounding a pair of single microtubules." + "Thoracic splanchnic nerves are splanchnic nerves that arise from the sympathetic trunk in the thorax and travel inferiorly to provide sympathetic innervation to the abdomen. The nerves contain preganglionic sympathetic and general visceral afferent fibers." "FMA:6280 Wikipedia:Thoracic_splanchnic_nerves" + "An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system." "FMA:62983 Wikipedia:Myelin NIF_Subcellular:sao593830697" + "KUPO:0001096" + "An orifice that is part of a lower urinary tract." "EMAPA:35965 MA:0002867" + "Any process that modulates the frequency, rate or extent of gamma-delta T cell proliferation." + "An endothelium that is part of an iliac vein." + "Nerve fibers crossing the midline of the neuraxis relative to their point of origin, on a course to from one level of the nervous system to another. (CUMBO, Heimer, L. The Human Brain, 2nd ed., 1995, pg 6)." "NLX:144064 FMA:83858 NCIT:C28351" + "The process in which the epidermis of the nipple sheath is uplifted to form an umbrella-like projection." + "Any process that stops, prevents or reduces the frequency, rate or extent of motor neuron apoptotic process." + "Combining with the biogenic amine serotonin and transmitting a signal across a membrane by activating some effector activity. Serotonin (5-hydroxytryptamine) is a neurotransmitter and hormone found in vertebrates and invertebrates." + "Any apoptotic process in an oligodendrocyte. Oligodendrocytes belong to a class of large neuroglial (macroglial) cells in the central nervous system, where they form the insulating myelin sheath of axons." + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances." + "An epithelium that lines the lumen of the digestive tract." "MA:0003201 EMAPA:32928 EHDAA2:0004567 UMLS:C0836205 BTO:0000956 NCIT:C12963 XAO:0003200 ZFA:0005123 TAO:0005123" + "A vasculature that is part of a trunk [Automatically generated definition]." "ZFA:0005024 TAO:0005024 FMA:74712" + "Any process that activates or increases the rate or extent of white fat cell proliferation." + "A fibroblast located between thymic lobules." + + "The process whose specific outcome is the progression of ventricular cardiac muscle over time, from its formation to the mature structure." + "An epithelium that is part of a pylorus." "EHDAA2:0001582 RETIRED_EHDAA2:0001927 EMAPA:17633" + "Any process that activates or increases the frequency, rate or extent of water channel activity." + "Any process that modulates the frequency, rate or extent of cell maturation." + "Any microvascular endothelial cell that is part of a endometrial blood vessel." + "The process in which a relatively unspecialized T cell acquires specialized features of a regulatory T cell. Regulatory T cells control or suppress immune responses through a variety of mechanisms and subsets include the CD4+CD25+ cell type as well as certain CD8+ cell types." + "Mesenchyme that is part of a optic eminence." "RETIRED_EHDAA2:0001310 EMAPA:16324 VHOG:0001073 EHDAA:942" + "Any biological process involved in the maintenance of an internal steady state of a chemical." + "Binding to a calcium ion (Ca2+)." + "The part of the cardiac conduction system that controls the timing of heart muscle contraction. It relays electrical signals to the AV node[GO]. Subdivision of conducting system of heart at the junction of the right atrium and the superior vena cava, around the sinoatrial nodal branch of right coronary artery and is continuous with the internodal tract[FMA]." "EMAPA:35772 MA:0000097 SCTID:277687007 BTO:0004358 ZFA:0005069 MESH:D012849 TAO:0005069 Wikipedia:Sinoatrial_node GAID:561 NCIT:C33555 UMLS:C0037189 EHDAA2:0004184 FMA:9477" + "A blood brain barrier composed of glial cells." + "A sweat producing cell of eccrine sweat glands. Pyramidal in shape, with its base resting on the basal lamina or myoepitheliocytes, and its microvillus-covered apical plasma membrane line up the intercellular canaliculi. Cell is not stained by hematoxylin or eosin." "FMA:70658" + "Any process that decreases the rate, frequency or extent of the differentiation of a neuroendocrine cell in the stomach." + "Any process that modulates the frequency, rate or extent of melanosome organization." + "A type I vestibular sensory cell that is part of the epithelium of crista of ampulla of semicircular duct of membranous labyrinth." "FMA:263192" + "The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified]." "VSAO:0000033 XAO:0004042 MIAA:0000025 MA:0002888 AAO:0000307 BTO:0001485 MAT:0000025 BTO:0001369 FMA:72954 EFO:0000801 BILA:0000088" + "Enables the transfer of DNA, deoxyribonucleic acid, from one side of a membrane to the other." + "Any process that modulates the frequency, rate or extent of neurogenesis, the generation of cells in the nervous system." + "Any process that modulates the frequency, rate or extent of iridophore differentiation." + "Skeletal subdivision consisting of a set of bones linking the axial series to the hindlimb zeugopodium and offering anchoring areas for hindlimb and caudal musculature." "ZFA:0000565 EHDAA:8324 EHDAA:7149 VSAO:0000155 http://people.eku.edu/ritchisong/pectoralgirdles.gif galen:PelvicGirdle XAO:0003064 EFO:0000947 VHOG:0000305 EMAPA:18028 Wikipedia:Pelvis MAT:0000182 FMA:87592 TAO:0000565 AAO:0000768 EHDAA2:0001426 AAO:0000426 MIAA:0000182" + "A mesenchymal cell that is part of a small mass of condensed mesenchyme in the enamel organ; it differentiates into the dentin and dental pulp." + "A mucosa that is part of a vas deferens [Automatically generated definition]." "SCTID:299626000 FMA:19240" + "Self-propelled movement of a cell or organism from one location to another in a behavioral context; the aspect of locomotory behavior having to do with movement." + "A muscular coat that is part of a colon." "FMA:14986 EMAPA:27383 SCTID:362158003 MA:0003198" + "A thin, loose vascular connective tissue that makes up the membranes surrounding joints and the sheaths protecting tendons (particularly flexor tendons in the hands and feet) where they pass over bony prominences. Synovial tissue contains synovial cells, which secrete a viscous liquid called synovial fluid; this liquid contains protein and hyaluronic acid and serves as a lubricant and nutrient for the joint cartilage surfaces[BTO]. Synovial tissue can be found in tendons (tissues that connect muscle to bone), bursae (fluid-filled, cushioning sacs found in spaces between tendons, ligaments, and bones), and the cavity (hollow enclosed area) that separates the bones of a freely movable joint, such as the knee or elbow[BTO]." "BTO:0001338 CALOHA:TS-0998 FMA:66762" + "The chemical reactions and pathways resulting in the breakdown of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings)." + "Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." + "The regulated exocytosis of secretory granules containing preformed mediators such as histamine, serotonin, and neutral proteases by a mast cell." + + "A basophil cell of the anterior pituitary that produces thyroid stimulating hormone, thyrotrophin. This cell type is elongated, polygonal and lie in clusters towards the adenohypophyseal center." "MESH:D052684 FMA:83099" + "A spatiotemporal region encompassing some part of the life cycle of an organism." "FMA:24120 EFO:0000399 MmusDv:0000000 ZFS:0100000 XAO:1000000 FBdv:00007012 HsapDv:0000000 PdumDv:0000090 BILS:0000105 ZFS:0000000 MESH:D008018 OlatDv:0000010 WBls:0000002 ncithesaurus:Developmental_Stage" + "A germinal center B cell that develops from a Bm3 B cell. This cell has the phenotype IgM-negative, IgD-positive, and CD38-positive." + "Ovarian vein, each instance of which is a tributary of some inferior vena cava that drains the right pampiniform plexus of some broad ligament." "FMA:14342" + "A transmembrane protein complex composed of an MHC alpha chain and, in most cases, either an MHC class II beta chain or an invariant beta2-microglobin chain, and with or without a bound peptide, lipid, or polysaccharide antigen." + "A sst GABAergic cortical interneuron with a soma found in lower L2/3 and upper 5, L4 Sst cells have Martinotti morphology with ascending axons but denser local axons and sparser ‘fanning-out’ projections to L1. L4 sst cells have smaller membrane time constant to calb2 (L2/3/5 fan Martinotti Cell) and non-zero afterdepolarization (ADP)." + + + "OBSOLETE. A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell." + "Any process that activates or increases the frequency, rate or extent of locomotion of a cell or organism." + "Any process that activates or increases the frequency, rate, or extent of monocyte antigen processing and presentation." + "Any process that stops, prevents or reduces the frequency, rate or extent of mitotic nuclear envelope disassembly." + + "Any process that stops, prevents, or reduces the frequency, rate, or extent of myeloid dendritic cell cytokine production." + "A immature or mature cell in the lineage leading to and including erythrocytes." "FMA:83516 FMA:62845 CALOHA:TS-0290" + "The elongated structure connected to the posterior surface of the testis that transports, stores, and matures spermatozoa between testis and vas deferens." "Wikipedia:Epididymis MAT:0000130 FMA:18255 BTO:0000408 galen:Epididymis SCTID:181432000 CALOHA:TS-0285 EFO:0000982 UMLS:C0014533 GAID:397 EMAPA:19290 MA:0000397 MESH:D004822 VHOG:0001265 EV:0100103 NCIT:C12328 MIAA:0000130" + "The activation of endogenous cellular processes that result in the death of a cell as part of its development." + "Any protein complex that is part of the plasma membrane." + "A parenchyma that is part of a left lobe of liver [Automatically generated definition]." "VHOG:0000839 FMA:71658 EHDAA2:0001002 EMAPA:18310" + "The progression of an endothelial cell over time, from its formation to the mature structure." + "A melanocyte that appears lighter in color." + "The cartilaginous structures that support the larynx." "BTO:0003660 MA:0001758 EHDAA:8157 NCIT:C12281 UMLS:C0023050 FMA:55108 VHOG:0001550 EMAPA:18697 GAID:107 SCTID:263482005 MESH:D007817" + "A lysosome before it has fused with a vesicle or vacuole." "NIF_Subcellular:sao1140587416" + "An adipocyte that is part of omentum tissue." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of the production of molecular mediator of immune response." + "The process whose specific outcome is the progression of a vestibular receptor cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate." + "Any process that modulates the frequency, rate or extent of proteolysis involved in cellular catabolic process." + "Obsolete. Use PO:0000282 from Plant Ontology instead. An outgrowth from the epidermis. Trichomes vary in size and complexity and include hairs, scales, and other structures and may be glandular. In Arabidopsis, patterning of trichome development is not random but does not appear to be lineage-based like stomata." + "The chemical reactions and pathways occurring at the level of individual cells involving any of a group of naturally occurring, biologically active amines, such as norepinephrine, histamine, and serotonin, many of which act as neurotransmitters." + "A portion of skeletal muscle tissue that is part of a eye [Automatically generated definition]." "EHDAA2:0000486 EMAPA:17844 EHDAA:2923" + "A gonad of a male animal. A gonad produces and releases sperm." "AAO:0000606 VHOG:0000252 FMA:7210 EHDAA:8146 EFO:0000984 ZFA:0000598 MAT:0000132 galen:Testis EV:0100102 SCTID:181431007 BSA:0000085 MIAA:0000132 MA:0000411 BILA:0000124 BTO:0001363 UMLS:C0039597 WBbt:0006794 EMAPA:17972 MESH:D013737 TAO:0000598 CALOHA:TS-1030 EHDAA2:0002007 Wikipedia:Testis GAID:396 XAO:0000157 NCIT:C12412 HAO:0001007" + "An adult endothelial progenitor cell characterised in vivo by homing to ischemic sites and paracrine support of angiogenesis. These cells do not form colonies." + "Enables the transfer of amines, including polyamines, from one side of a membrane to the other. Amines are organic compounds that are weakly basic in character and contain an amino (-NH2) or substituted amino group." + "Any process that modulates the frequency, rate or extent of gliogenesis, the formation of mature glia." + "Specialized epithelial cells involved in the maintenance of osmotic homeostasis. They are characterized by abundant mitochondria and ion transporters. In amniotes, they are present in the renal system. In freshwater fish, ionocytes in the skin and gills help maintain osmotic homeostasis by absorbing salt from the external environment." + "A cell in vitro that is or has been maintained or propagated as part of a cell culture." "MESH:D002478" + "The morphogenetic process in which an epithelial sheet bends along a linear axis and gives rise to a pouch that will form a semicircular canal." + "Any process that modulates the frequency, rate or extent of synapse pruning." + "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells of the spinal cord. Differentiation includes the processes involved in commitment of a cell to a specific fate." + "The directed movement of oxygen (O2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "Any process that modulates the frequency, rate or extent of motor neuron apoptotic process." + "EHDAA2:0001267 EMAPA:17585" + "An epithelial cell of the large intestine." "BTO:0004297 FMA:256157" + "The process in which the frontal suture is generated and organized." + "A basal cell that is part of the epithelium of esophagus." "FMA:70731" + "Ganglion which is located in the trunk." "MAT:0000344 ZFA:0001573 MIAA:0000344 EFO:0000901 TAO:0001573" + "A gray matter that has the potential to develop into a superior salivatory nucleus." "EHDAA2:0004644" + "A CD4-positive, CD8-negative thymocyte that expresses high levels of the alpha-beta T cell receptor and is CD69-positive." + "The progression of the dorsal aorta over time, from its initial formation to the mature structure. The dorsal aorta is a blood vessel in a single-pass circulatory system that carries oxygenated blood from the gills to the rest of the body. In a single-pass circulatory system blood passes once through the heart to supply the body once." + "A subdivision of the autopod consisting of digit plus the region incorporating a single metapodial element. These segments are typically repeated along the pre-axiom to post-axial axis." + "The orderly movement of a corneal epithelial cell from one site to another, often during the development of a multicellular organism." + "FMA:70643" + "The chemical reactions and pathways involving glucocorticoids, hormonal C21 corticosteroids synthesized from cholesterol. Glucocorticoids act primarily on carbohydrate and protein metabolism, and have anti-inflammatory effects." + "The distribution of vacuoles into daughter cells after mitosis or meiosis, mediated by interactions between vacuoles and the cytoskeleton." + "An alpha-beta T cell expressing NK cell markers that is CD1d restricted and expresses specific V-alpha chains. NK T cells of this type recognize the glycolipid alpha-galactosylceramide in the context of CD1d." + "A filament, mostly protein, that grows from follicles found in the dermis[WP]." "Wikipedia:Hair UMLS:C0018494 SCTID:361702001 GAID:71 EMAPA:18769 NCIT:C32705 BTO:0001501 MIAA:0000160 MA:0000155 MAT:0000160 EFO:0000958 MESH:D006197 VHOG:0001191 CALOHA:TS-0430 EV:0100157 FMA:53667" + "Any process that modulates the frequency, rate, or extent of an immune system process." + "Any process that decreases the rate, frequency, extent of the regulated release of somatostatin from secretory granules in the D cells of the pancreas." + "An urothelium that is part of a urethra [Automatically generated definition]." "EMAPA:35896 NCIT:C49310 UMLS:C1710585 MA:0001687" + "The segment of the autopod that is distal to the metapodial region and consists of the digits." + "A limb/fin field that has the potential to develop into a pectoral appendage bud mesenchyme." "ZFA:0001453 TAO:0001453" + "A pulmonary interstitial fibroblast that is part of the alveolus and localizes to vascular adventitia." + "The directed movement of calcium ions (Ca2+) into, out of or within the Golgi apparatus." + "A portion of connective tissue that is part of a tail [Automatically generated definition]." "EMAPA:16749 MA:0000697" + "Obsolete. Use PO:0020090 from Plant Ontology instead. OBSOLETED, use term from Plant Ontology. A cell containing the two polar nuclei which, after double fertilization, will develop into the endosperm." + "Any process that stops, prevents, or reduces the frequency, rate or extent of male gonad development." + "A portion of skeletal muscle tissue that is part of a trapezius [Automatically generated definition]." "FMA:261938" + "In the circulatory system of animals, a portal venous system occurs when a capillary bed drains into another capillary bed through veins, without first going through the heart. Both capillary beds and the blood vessels that connect them are considered part of the portal venous system. They are relatively uncommon as the majority of capillary beds drain into veins which then drain into the heart, not into another capillary bed. Portal venous systems are considered venous because the blood vessels that join the two capillary beds are either veins or venules. Examples of such systems include the hepatic portal system and the hypophyseal portal system. Unqualified, 'portal venous system' often refers to the hepatic portal system. For this reason, 'portal vein' most commonly refers to the hepatic portal vein[WP]." "FMA:45628 Wikipedia:Portal_venous_system NCIT:C33344 SCTID:362063001 MESH:D011168 UMLS:C0226727" + "The process of coordinated growth and sprouting of blood vessels giving rise to the organized vascular system." + "Female germ cell is a germ cell that supports female gamete production." "ncithesaurus:Egg VHOG:0001530 MA:0000388" + "A hematopoietic multipotent progenitor cell that is CD34-positive, CD38-negative, CD45RA-negative, and CD90-negative." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances within cells." + "A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information." "Wikipedia:Chromosome" + "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein-lipid complex." + "The lipid bilayer that forms the outer-most layer of an organelle." + "The progression of the visceral serous pericardium from its formation to the mature structure. The visceral serous pericardium is the inner layer of the pericardium." + "Any process that modulates the frequency, rate or extent of animal organ morphogenesis." + "A prominin that is a translation product of the human PROM1 gene or a 1:1 ortholog thereof." + "The organ of hearing located on the right side of the head." "NCIT:C81285 FMA:53641 UMLS:C0229298 SCTID:368570004" + "Any process that modulates the frequency, rate or extent of type B pancreatic cell proliferation." + "Cell-cell signaling between presynapse and postsynapse, via the vesicular release and reception of neuropeptide molecules, that modulates the synaptic transmission properties of the synapse." + "Any process that activates or increases the frequency, rate or extent of AV node cell action potential." + "A plexus of autonomic nerve fibers within the wall of the digestive tube, and made up of the submucosal, myenteric, and subserosal plexuses; it contains visceral afferent fibers, sympathetic postganglionic fibers, parasympathetic preganglionic and postganglionic fibers, and parasympathetic postganglionic cell bodies." "FMA:77597 MA:0001147 EMAPA:35446 BTO:0002437" + + "The disaggregation of a protein-RNA complex into its constituent components." + "Any process that modulates the frequency, rate or extent of apoptotic cell clearance." + "A conidium that has only one nucleus." "FAO:0000025" + "Development of a cone cell, one of the sensory cells in the eye that reacts to the presence of light. Cone cells contain the photopigment iodopsin or cyanopsin and are responsible for photopic (daylight) vision." + "The series of events in which an oxygen stimulus is received by a cell and converted into a molecular signal." + "The division of a cell nucleus into two nuclei, with DNA and other nuclear contents distributed between the daughter nuclei." + "The process whose specific outcome is the progression of the pole cell over time, from its formation to the mature structure." + "A neuron projection quality that is a characteristic of neurons whose soma is located in the telencephalon and that project to structures outside the telencephalon" "ILX:0770101" + "FMA:53133" + "The thoracic ganglia are paravertebral ganglia. The thoracic portion of the sympathetic trunk typically has 12 thoracic ganglia. Emerging from the ganglia are thoracic splancic nerves (the cardiopulmonary, the greater, lesser, and least splanchic nerves) that help provide sympathetic innervation to abdominal structures. Also, the ganglia of the thoracic sympathetic trunk have both white and gray rami communicantes. The white rami carry sympathetic fibers arising in the spinal cord into the sympathetic trunk. [WP,unvetted]." "MA:0001159 Wikipedia:Thoracic_ganglion EHDAA:4664 VHOG:0000515 SCTID:181102004 UMLS:C0229010 EMAPA:17158 FMA:6471 NCIT:C52829 RETIRED_EHDAA2:0002012 BTO:0001831" + "A basal cell that is part of the urothelium. Compared to other urothelial cell types, a basal cell of the urothelium is positioned along the basement membrane, is the most undifferentiated and serves a progenitor role." "FMA:84150" + "An endothelium of artery that is part of a respiratory system [Automatically generated definition]." "MA:0001801 EMAPA:37566" + "KUPO:0001135" + "Any process that stops, prevents, or reduces the frequency, rate or extent of establishment or maintenance of neuroblast polarity." + "Any cadherin binding that occurs as part of the process of cell-cell adhesion." + "A cell that contains more than two haploid sets of chromosomes." + "The progression of a skeletal muscle organ over time from its initial formation to its mature state. A skeletal muscle organ includes the skeletal muscle tissue and its associated connective tissue." + "The connective tissue that surrounds the spleen." "UMLS:C0229681 FMA:15849 MA:0000753 SCTID:329635002 EMAPA:35802 NCIT:C33598" + "A retinal ganglion B3 cell with dentrites terminating in S4." "BAMS:1010" + "Any process that modulates the frequency, rate or extent of exocytosis." + "An epithelium that is part of the respiratory segment of the nasal mucosa [Automatically generated definition]." "EMAPA:17607 MA:0001326 EHDAA2:0001230 EHDAA:6807 NCIT:C49262 UMLS:C1709152" + "Any process that modulates the frequency, rate, or extent of T cell cytokine production." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of mast cell activation." + "An IgD-positive CD38-positive IgG memory B cell is a CD38-positive IgG-positive class switched memory B cell that has class switched and expresses IgD on the cell surface with the phenotype IgD-positive, CD38-positive, and IgG-positive." + "The process aimed at the progression of a glial cell in the anterior lateral line nerve over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell." + "Binding to a cell adhesion molecule." + "Any process that activates or increases the frequency, rate or extent of defense response to insect." + "The process in which the anatomical structures of the ureter are generated and organized. The ureter is a muscular tube that transports urine from the kidney to the urinary bladder." + "An endocranial viscerocranial mucosa cell that is part of viscerocranial mucosa." "FMA:70629" + + "The movement of a mast cell in response to an external stimulus." + "Anatomical projection that is composed of cartilage tissue." "FMA:284626" + "Hair that grows on the scalp." + "Any process contributing to anergy in T cells, a state of functional inactivation which is part of T cell tolerance induction." + "Any process that decreases the frequency, rate or extent of the directed movement of proteins within cells." + "A cell that is part of a collecting duct of renal tubule." "Wikipedia:Kidney_collecting_duct_cell KUPO:0001012" + "A intratelencephalic-projecting glutamatergic neuron with a soma found in cortical layers L2/3-6" + "That portion of the nasal mucosa containing the sensory endings for olfaction; the organ of smell[MESH]." "EMAPA:37918 FMA:77199 NCIT:C33205 UMLS:C0028937 Wikipedia:Olfactory_mucosa MESH:D009831 CALOHA:TS-2197 GAID:303" + "Any process that modulates the frequency, rate or extent of T cell differentiation." + "A proximal tarsal endochondral element that is composed primarily of cartilage tissue." + "Any apoptotic process in a keratinocyte. A keratinocyte is an epidermal cell which synthesizes keratin and undergoes a characteristic change as it moves upward from the basal layers of the epidermis to the cornified (horny) layer of the skin." + "FMA:60053" + "A retinal ganglion A cell found in the retina with large somata, often polygonal in shape. The dendritic fields consist of three to seven stout dendrites that are sparce near soma. Dendrites terminate in S4." "BAMS:1045" + "A retinal ganglion cell located in the ganglion cell layer of the retina. This cell projects to magnocellular cells in the lateral geniculate nucleus (LGN). They have large cell bodies and extensive, branching dendritic networks that contribute to their large receptive fields." + "The laminar structure of the heart." + "A suture joining a sphenoid bone with the alae of a vomer to form a schindylesis type of joint." + "Any protein complex that is part of the plasma membrane and which functions as a signaling receptor." + "A nerve that is part of a thorax [Automatically generated definition]." "MESH:D013900 EMAPA:37265 SCTID:359876006 MA:0000562" + "Any process that activates or increases the frequency, rate or extent of B cell differentiation." + "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells of the mesonephros as it progresses from its formation to the mature state." + "A specialized cardiomyocyte that transmit signals from the AV node to the cardiac Purkinje fibers." + "The process in which an antigenically naive gamma-delta T cell acquires the specialized features of an effector, regulatory, or memory T cell and contributes to an immune response. Effector T cells include cells which provide T cell help or exhibit cytotoxicity towards other cells." + "A primary neuron (sensu Teleostei) that has a motor function." + "A pharyngeal pouch between pharyngeal arch 4 and arch 5 or 6 (a fifth arch never establishes in amniotes)." "UMLS:C0231071 EFO:0003637 NCIT:C34181 ZFA:0001134 AAO:0011117 EMAPA:16766 VHOG:0000578 FMA:295688 EHDAA2:0000091 VHOG:0000971 Wikipedia:Pharyngeal_pouch_(embryology)#Fourth_pouch SCTID:362858001 TAO:0001134 XAO:0000254 RETIRED_EHDAA2:0000090" + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a catecholamine stimulus. A catecholamine is any of a group of biogenic amines that includes 4-(2-aminoethyl)pyrocatechol [4-(2-aminoethyl)benzene-1,2-diol] and derivatives formed by substitution." + "A macrophage colony-stimulating factor 1 receptor that is encoded in the genome of human." "DTO:03100090 UniProtKB:P07333" + "KUPO:0001134" + "A spinal nerve root that is part of a thoracic nerve." "BIRNLEX:836 FMA:14064" + "A nerve that innervates the sole of the foot. Planar nerves arise from the posterior branch of the tibial nerve." "SCTID:181074000 UMLS:C0446824 Wikipedia:Plantar_nerve https://upload.wikimedia.org/wikipedia/commons/thumb/1/16/Gray834.svg/180px-Gray834.svg.png NCIT:C77674" + "The process of activating or increasing the rate or extent of mesenchymal cell proliferation. Mesenchymal cells are loosely organized embryonic cells." + "Any process that activates or increases the frequency, rate, or extent of interleukin-9 production." + "The multiplication or reproduction of fat cells by cell division, resulting in the expansion of their population. A fat cell is an animal connective tissue cell specialized for the synthesis and storage of fat." + "Any process that activates, maintains or increases the frequency or rate of cell fate commitment. Cell fate commitment is the commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells. Positional information is established through protein signals that emanate from a localized source within a cell (the initial one-cell zygote) or within a developmental field." + "FMA:19780" + "Any process that modulates the rate, frequency or extent of ribosome biogenesis. Ribosome biogenesis is the cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits." + "KUPO:0001131" + "GC_ID:1" + "A surface feature shape quality inhering in a bearer by virtue of the bearer's one part being layered over another connected part." + "Any process that stops, prevents, or reduces the frequency, rate or extent of programmed cell death that occurs in the retina." + "Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in an SA node cardiac myocyte. This typically occurs via modulation of the activity or expression of voltage-gated ion channels." + "Ventral part (base region) of the telencephalon." "BTO:0003401 TAO:0000304 EFO:0003522 ZFA:0000304 DMBA:15751" + "A nucleate quality inhering in a bearer by virtue of the bearer's having one or more nucleus." + "An excitatory neuron that has its soma located in the thalamic complex." + "A developmental process, independent of morphogenetic (shape) change, that is required for a type B pancreatic cell to attain its fully functional state. A type B pancreatic cell is a cell located towards center of the islets of Langerhans that secretes insulin." + "Any process that activates, maintains or increases the frequency, rate or extent of transmission of a nerve impulse, the sequential electrochemical polarization and depolarization that travels across the membrane of a neuron in response to stimulation." + + "A forelimb that is on the left side of a pectoral complex." "FMA:7186" + + + "Translation that occurs at the presynapse." + "The directed movement of some substance from outside of a cell into a cell. This may occur via transport across the plasma membrane or via endocytosis." + "A glial cell that ensheaths multiple small diameter axons in the peripheral nervous system. The non-myelinating Schwann cell is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has a basal lamina. Cells can survive without an axon present. These cells can de-differentiate into immature Schwann cells." + "KUPO:0001056" + "Any process that activates or increases the frequency, rate or extent of directed movement of proteins from the nucleus into the cytoplasm." + "Anatomical divisons of the brain according to one or more criteria, e.g. cytoarchitectural, gross anatomy. Parts may be contiguous in 3D or not, e.g., basal ganglia." "BIRNLEX:1167 NCIT:C13031 UMLS:C0445620 FMA:55676 SCTID:384763002" + "Binding to a CCR3 chemokine receptor." + "The chemical reactions and pathways involving carbohydrate derivative." + "Any muscle organ that is part of a limb [Automatically generated definition]." "MA:0000692" + "A specialized cell involved in auditory sensory perception." + "A blood vessel that is part of a liver." "EMAPA:35498 MA:0003137" + "Any process that stops, prevents, or reduces the frequency, rate, or extent of myeloid leukocyte mediated immunity." + "A structure in the head of a spermatozoon that contains acid hydrolases, and is concerned with the breakdown of the outer membrane of the ovum during fertilization. It lies just beneath the plasma membrane and is derived from the lysosome." "Wikipedia:Acrosome" + "A portion of connective tissue that is part of a finger [Automatically generated definition]." "MA:0000623 EMAPA:37321" + "The regrowth of neural tissue following its loss or destruction." + + "Any process that modulates the frequency, rate or extent of transepithelial transport." + "The ependymal cell layer that lines the brain ventricles." "MA:0000809 FMA:242837 MESH:D004805 EMAPA:35183" + "KUPO:0001118" + "A collagen alpha-1(I) chain that is encoded in the genome of human." "UniProtKB:P02452" + "A choroid plexus macrophage that is part of a choroid plexus stroma." + "The structure from the trachea, bronchi, and bronchioles that forms the airways that supply air to the lungs. The lining of the tracheobronchial tree consists of ciliated columnar epithelial cells." "FMA:7393 NCIT:C117875 Wikipedia:Tracheobronchial_tree SCTID:361384001" + "The second vertebral bone in the vertebral column." "ZFA:0001168 GAID:237 Wikipedia:Axis_(anatomy) SCTID:181819004 EMAPA:19432 UMLS:C0004457 TAO:0001168 NCIT:C32240 MESH:D001368 MA:0001422 EHDAA:10608 FMA:12520" + "Steps required to transform an immature secretory vesicle into a mature secretory vesicle. Typically proceeds through homotypic membrane fusion and membrane remodeling." + "The immediate defensive reaction by neural vertebrate tissue to infection or injury caused by chemical or physical agents." + "A pyramidal family morphology that inheres in neurons which have an apical tree which is oriented parallel to the pia." "ilxtr:HorizontalPyramidalPhenotype" + "The process whose specific outcome is the progression of a glomerular epithelial cell over time, from its formation to the mature structure. Glomerular epithelial cells are specialized epithelial cells that form part of the glomerulus; there are two types, glomerular parietal epithelial cells and glomerular visceral epithelial cells." + "An epithelial cell of the medullary thymus. This cell type expresses a diverse range of tissue-specific antigens. This promiscuous gene expression is a cell-autonomous property of medullary epithelial cells and is maintained during the entire period of thymic T cell output." "BTO:0004563" + "A skeletal muscle satellite cell that has become mitotically active - typically following muscle damage." + "A macula densa that is part of an ascending limb of loop of Henle [Automatically generated definition]." "MA:0002604" + "Any process that stops, prevents, or reduces the frequency, rate or extent of T cell death by apoptotic process." + "A network formed by blood vessels and the tela choroidea which secretes CSF into the ventricular spaces." "UMLS:C0008524 MA:0000823 CALOHA:TS-0145 BAMS:chp TAO:0001443 neuronames:1377 NCIT:C12694 BTO:0000258 SCTID:264450003 BAMS:GHP FMA:61934 BAMS:CHP Wikipedia:Choroid_plexus BAMS:chpl GAID:607 ZFA:0001443 MESH:D002831 MBA:108 VHOG:0001377 EFO:0001915 EMAPA:32741" + "Any process that activates or increases the frequency, rate or extent of the assembly of actin filament bundles." + + "The process in which the anatomical structure of the pons is generated and organized. The pons lies above the medulla and next to the cerebellum. The pons conveys information about movement from the cerebral hemisphere to the cerebellum." + "The change in form (cell shape and size) that occurs during the differentiation of an endothelial cell." + "An integrin beta-7 that is encoded in the genome of human." "UniProtKB:P26010" + "A nucleus of brain that spans a midbrain tegmentum." "FMA:258768 ZFA:0005577" + "Any process that stops, prevents or reduces the frequency, rate or extent of water channel activity." + "The conducting airway of the lungs found terminal to the bronchi; these structures contain neither cartilage nor mucous-secreting glands; the epithelium of the bronchioles becomes thinner with each branching." "EHDAA:8199 EHDAA:8171 Wikipedia:Bronchiole SCTID:278982001 UMLS:C0006270 FMA:7410 CALOHA:TS-2003 EMAPA:32697 VHOG:0000675 MA:0000422 EHDAA:8183 NCIT:C12684 BTO:0002375 EHDAA:8221" + "A D(2) dopamine receptor that is encoded in the genome of mouse." "UniProtKB:P61168" + "KUPO:0001130" + "A cell which moves among different tissues of the body, via blood, lymph, or other medium." + "The process occurring during the embryonic phase whose specific outcome is the progression of the eye over time, from its formation to the mature structure." + "The progression of the limbic system over time from its initial formation until its mature state. The limbic system is a collection of structures in the brain involved in emotion, motivation and emotional aspects of memory." + "Any process that activates or increases the frequency, rate or extent of cardiac myofibril assembly." + "Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes." "MESH:D009504 CALOHA:TS-0688 BTO:0000130 FMA:62860" + "The regulated exocytosis of secretory granules containing preformed mediators such as perforin and granzymes by a natural killer cell." + "Any process that modulates the frequency, rate or extent of insulin receptor signaling." + "Anterior portion of the neocortex, lying anterior to the central sulcus in humans. It is bounded by the parietal cortex posteriorly and the temporal cortex laterally[NIFSTD,modified]." "FMA:242199 DHBA:10161 DMBA:16002 GAID:674 MA:0000905 BTO:0000484 EMAPA:35357 NLXANAT:20090601 Wikipedia:Frontal_lobe" + "The directed movement of a chromosome to a specific location." + "The deepest layer of the neocortex. While layer 6b is considered part of layer 6, it is distinct morphologically, genetically, and developmentally from the rest of layer 6. Neurons in L6b project to cortical targets and higher-order thalamus and develop from a precursor population that arises from the subplate." + "Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of lipids." + "Fusion of intracellular membrane-bounded vesicles with the pre-synaptic membrane of the neuronal cell resulting in release of neurotransmitter into the synaptic cleft." + "Any process that activates or increases the frequency, rate or extent of translation initiation as a result of a stimulus indicating the organism is under stress." + "The process in which the anatomical structures of male genitalia are generated and organized." + "The orderly movement of a cell from one site to another at least one of which is located in the forebrain." + "FMA:54243" + "Any process that activates or increases the frequency, rate or extent of T cell costimulation." + "Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in hippocampal neurons." + "A D(2) dopamine receptor that is encoded in the genome of human." "UniProtKB:P14416 Reactome:R-HSA-390816 DTO:02100082" + "A T cell which regulates overall immune responses as well as the responses of other T cell subsets through direct cell-cell contact and cytokine release." "FMA:84070 MESH:D050378 BTO:0004520" "A glutamatergic neuron located in the cerebral cortex that projects to the thalamus." - "One of the two photoreceptor cell types in the vertebrate retina. In cones the photopigment is in invaginations of the cell membrane of the outer segment. Cones are less sensitive to light than rods, but they provide vision with higher spatial and temporal acuity, and the combination of signals from cones with different pigments allows color vision." "FMA:67748 CALOHA:TS-0866 BTO:0001036" - "A CD38-negative naive B cell is a mature B cell that has the phenotype CD38-negative, surface IgD-positive, surface IgM-positive, and CD27-negative, that has not yet been activated by antigen in the periphery." - "A cell that stores epinephrine secretory vesicles. During times of stress, the nervous system signals the vesicles to secrete their hormonal content. Their name derives from their ability to stain a brownish color with chromic salts. Characteristically, they are located in the adrenal medulla and paraganglia of the sympathetic nervous system." "FMA:69263 BTO:0000259" - "http://en.wikipedia.org/wiki/Collecting_duct_system#Intercalated_cells KUPO:0001129" + "A neuromuscular junction in which the target muscle cell is a myotube." "Obsolete. Use PO:0020047 from Plant Ontology instead. A diploid (2n) cell that undergoes meiosis and forms four haploid (1n) microspores; also called microspore mother cell and, in seed plants, pollen mother cell." - "A neural progenitor cell that is the daughter of a neuroblast (sensu arthopoda). The progeny of ganglion mother cells develop into neurons, glia and (occasionally) epithelial cells." "FBbt:00005149" - "A cell at the front of a migrating epithelial sheet." + "A protein that is a translation product of the human MARCO gene or a 1:1 ortholog thereof." + "The developmental process by which an intramembranous bone is generated and organized." + "Any process that modulates the frequency, rate or extent of water channel activity." + "A cell located in the heart, including both muscle and non muscle cells." "FMA:83808 BTO:0001539 CALOHA:TS-0115 FMA:84791" + "A subdivision of the pectoral complex consisting of the structures in the region of the shoulder joint (which connects the humerus, scapula and clavicle)." "EHDAA2:0001834 SCTID:361103004 EMAPA:17421 GAID:60 MA:0000038 NCIT:C25203 UMLS:C0037004 CALOHA:TS-2229 galen:Shoulder Wikipedia:Shoulder EHDAA:4180 FMA:25202 VHOG:0000342 MESH:D012782 EFO:0003068 EHDAA:6228" + "Any process that modulates the frequency, rate or extent of tooth mineralization, the deposition of calcium salts in tooth structures." + "A megakaryocyte that is resident in the lung connective tissue." + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a postsynapse." + "A physical quality that is the ability to contract or shrink." + "A mucosa-associated lymphoid tissue macrophage found in the nasal and bronchial mucosa-associated lymphoid tissues." + "FMA:75136" + "Any protein complex that is capable of carrying out some part of the process of cell-cell adhesion." + "A basement membrane that is part of a bronchus." "MA:0001832 EMAPA:37809 UMLS:C1707051 NCIT:C49208" + "A tartrate-resistant acid phosphatase type 5 that is encoded in the genome of mouse." "UniProtKB:Q05117" + "FMA:62811" + "Any process that increases the rate, frequency or extent of fibroblast cell migration. Fibroblast cell migration is accomplished by extension and retraction of a pseudopodium." + "Any process that activates or increases the frequency, rate or extent of progression through the meiotic cell cycle." + "An ectoderm that is part of a pharyngeal arch 3." "RETIRED_EHDAA2:0000079 EHDAA2:0000072 EMAPA:16400 EMAPA:16584 VHOG:0000946 EMAPA:16582" + "OBSOLETE. A native cell that is part of some Metazoa." + "A capillary that is part of the colon." + "A portion of smooth muscle tissue that is part of a intestine [Automatically generated definition]." "BTO:0000643 EMAPA:35441 UMLS:C1708547 MA:0001539 NCIT:C49243 EMAPA:35443" + "Any process that stops, prevents or reduces the frequency, rate or extent of terminal button organization." + "A part of the body present only in a specific gender." "WBbt:0005752 AEO:0000174" + "An ischial endochondral element that is composed primarily of cartilage tissue." "EHDAA:9570 EHDAA2:0000890 EMAPA:26930" + "A highly soluble, elongated protein complex found in blood plasma and involved in clot formation. It is converted into fibrin monomer by the action of thrombin. In the mouse, fibrinogen is a hexamer, 46 nm long and 9 nm maximal diameter, containing two sets of nonidentical chains (alpha, beta, and gamma) linked together by disulfide bonds." + "A vertebra that has a transverse process." + "Any process that modulates the frequency, rate or extent of lateral motor column neuron migration." + "A receptor-type tyrosine-protein phosphatase C that is a translation product of some mRNA whose exon structure and start site selection renders it capable of giving rise to a protein with the amino acid sequence represented by UniProtKB:P08575-3 or a 1:1 ortholog thereof." + "The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered." + "A breast that is part of a male organism." "NCIT:C33048 UMLS:C0222604 FMA:19901" + "Any process that stops, prevents or reduces the frequency, rate or extent of cytoplasmic translation." + "A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column." + "An action potential that occurs in a cardiac muscle cell and is involved in its contraction." + "A lymphatic vessel that is part of a respiratory system [Automatically generated definition]." "EMAPA:37580 MA:0001824" + "The orderly movement of a spinal cord motor neuron from one site to another. A spinal cord motor neuron is a motor neuron that passes from the spinal cord toward or to a muscle and conducts an impulse that causes movement." + "FMA:54242" + "Any process that stops, prevents, or reduces the frequency, rate or extent of enzymatic generation of superoxide by a cell." + "Any process that stops, prevents or reduces the frequency, rate or extent of somatic stem cell division." + "Any process that modulates the frequency, rate or extent of lipid localization." + "The chemical reactions and pathways resulting in the breakdown of carboxylic acids, any organic acid containing one or more carboxyl (-COOH) groups." + "Distal segment of the fore limb, including carpal region, metacarpal region and digits." "NCIT:C32712 EMAPA:17428 galen:Hand NLXANAT:20090603 VHOG:0000344 AAO:0010803 GAID:56 UMLS:C0018563 MA:0000037 CALOHA:TS-2213 Wikipedia:Manus_(anatomy) FMA:9712 MESH:D006225 EHDAA2:0000728 BTO:0004668 SCTID:302539009" + "One of two bilateral, largely symmetrical organ subdivisions within the telencephalon which contain the cerebral cortex and cerebral white matter.[FMA]." "VHOG:0001639 UMLS:C0242202 MBA:403 EMAPA:16653 FMA:61817 DMBA:15739 galen:CerebralHemisphere AAO:0010480 SCTID:278251007 BAMS:HEM EFO:0002521 Wikipedia:Cerebral_hemisphere MA:0000133 BIRNLEX:1042 neuronames:241 NCIT:C12351 CALOHA:TS-2007 BTO:0000231 UMLS:C0228174" + "A fibroblast of the aortic adventitia." + "A neuron that is derived from a precursor cell in the lateral ganglion eminence." + "EFO:0003677 ZFA:0001321 TAO:0001321" + "Binding to an amino acid, organic acids containing one or more amino substituents." + "MA:0001859 EMAPA:35878" + "A cell characteristically found lining hollow organs that are subject to great mechanical change due to contraction and distention; originally thought to represent a transition between stratified squamous and columnar epithelium." "FMA:66778" + "The directed movement of norepinephrine into a cell, typically presynaptic neurons or glial cells. Norepinephrine (3,4-dihydroxyphenyl-2-aminoethanol) is a hormone secreted by the adrenal medulla and a neurotransmitter in the sympathetic peripheral nervous system and in some tracts of the CNS. It is also the biosynthetic precursor of epinephrine." + "Binding to a component of the extracellular matrix." + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an acetylcholine stimulus." + "An immature B cell is a B cell that has the phenotype surface IgM-positive and surface IgD-negative, and have not undergone class immunoglobulin class switching or peripheral encounter with antigen and activation." + "The principal glutaminergic neuron located in the outer third of the external plexiform layer of the olfactory bulb; a single short primary dendrite traverses the outer external plexiform layer and terminates within an olfactory glomerulus in a tuft of branches, where it receives the input from olfactory receptor neuron axon terminals; axons of the tufted cells transfer information to a number of areas in the brain, including the piriform cortex, entorhinal cortex, olfactory tubercle, and amygdala." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amino acid stimulus. An amino acid is a carboxylic acids containing one or more amino groups." + "A muscle cell that is part of the atrial septal branch of anterior internodal tract." "FMA:223278" + "A stromal cell that is part_of a bone marrow." + "The characteristic movement of cells from the dorsal ridge of the neural tube to a variety of locations in a vertebrate embryo." + "The directed movement of a protein to a specific location in a membrane." + "A humerus endochondral element that is composed primarily of a pre-cartilage condensation." "EHDAA:4192 EHDAA2:0000788 EMAPA:17427 VHOG:0000950" + "An astrocyte of the cerebellum." + "Any process that modulates the frequency, rate or extent of resting T cell proliferation." + "A myocardium that is part of a outflow tract [Automatically generated definition]." "EHDAA2:0001358 VHOG:0000603 MA:0000489 EMAPA:35623" + "A vascular system that overlaps a umbilical cord and is part of a entire extraembryonic component." "EHDAA2:0000478 EMAPA:16370 VHOG:0001396" + "Any process that modulates the rate, frequency or extent of blood vessel remodeling, the reorganization or renovation of existing blood vessels." + "The progression of a somite from its initial formation to the mature structure. Somites are mesodermal clusters that are arranged segmentally along the anterior posterior axis of an embryo." + "The somatic process that results in the generation of sequence diversity of immunoglobulins." + "The soft tissue that fills the cavities of bones." "MIAA:0000084 BTO:0000141 EV:0100046 MAT:0000084 galen:BoneMarrow EMAPA:32760 MESH:D001853 VHOG:0001218 CALOHA:TS-0087 MA:0000134 UMLS:C0005953 BTO:0000829 AAO:0011007 XAO:0000123 EFO:0000868 FMA:9608 Wikipedia:Bone_marrow GAID:1287 SCTID:421320006 NCIT:C12431" + "A head that is part of a embryo." "CALOHA:TS-0246 FMA:293011" + "The process in which the anatomical structures of the descending aorta are generated and organized. The descending aorta is the portion of the aorta in a two-pass circulatory system from the arch of aorta to the point where it divides into the common iliac arteries. In a two-pass circulatory system blood passes twice through the heart to supply the body once." + + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of hormones." + "A bone that is part of a trunk [Automatically generated definition]." "MA:0000512 EMAPA:36583 SCTID:427358002" + + "Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon." + "Any process that increases the frequency, rate or extent of cell morphogenesis contributing to cell differentiation. Cell morphogenesis involved in differentiation is the change in form (cell shape and size) that occurs when relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history." + "Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate." "Reactome:R-HSA-8848975 Reactome:R-HSA-399947 Reactome:R-HSA-2395412 Reactome:R-HSA-5654418 Reactome:R-HSA-1225960 Reactome:R-HSA-399946 Reactome:R-HSA-9026890 Reactome:R-HSA-399934 Reactome:R-HSA-2730862 Reactome:R-HSA-8851890 Reactome:R-HSA-912629 Reactome:R-HSA-5654634 Reactome:R-HSA-429441 Reactome:R-HSA-2424487 Reactome:R-HSA-5218806 Reactome:R-HSA-2404199 Reactome:R-HSA-9034875 Reactome:R-HSA-9032601 Reactome:R-HSA-1839110 Reactome:R-HSA-9612085 Reactome:R-HSA-5654655 Reactome:R-HSA-2730886 Reactome:R-HSA-2454208 Reactome:R-HSA-1472121 Reactome:R-HSA-5690702 Reactome:R-HSA-982807 Reactome:R-HSA-9698005 Reactome:R-HSA-8874078 Reactome:R-HSA-5654151 Reactome:R-HSA-9712085 Reactome:R-HSA-373747 Reactome:R-HSA-9634390 Reactome:R-HSA-8848077 Reactome:R-HSA-9037040 Reactome:R-HSA-9670412 Reactome:R-HSA-8874080 Reactome:R-HSA-8942607 Reactome:R-HSA-1963581 Reactome:R-HSA-9606163 Reactome:R-HSA-9672173 Reactome:R-HSA-1433506 Reactome:R-HSA-9700175 Reactome:R-HSA-8876230 Reactome:R-HSA-388833 Reactome:R-HSA-983703 Reactome:R-HSA-452122 Reactome:R-HSA-2033488 Reactome:R-HSA-1248655 Reactome:R-HSA-202168 Reactome:R-HSA-8956659 Reactome:R-HSA-2033490 Reactome:R-HSA-1888198 Reactome:R-HSA-2029453 Reactome:R-HSA-9665709 Reactome:R-HSA-418872 Reactome:R-HSA-9033284 Reactome:R-HSA-873922 Reactome:R-HSA-212710 Reactome:R-HSA-5637795 Reactome:R-HSA-879907 Reactome:R-HSA-1524186 Reactome:R-HSA-2454239 Reactome:R-HSA-8849463 Reactome:R-HSA-9673761 Reactome:R-HSA-418163 Reactome:R-HSA-4420128 Reactome:R-HSA-5654397 Reactome:R-HSA-5654575 Reactome:R-HSA-9700171 Reactome:R-HSA-8849032 Reactome:R-HSA-1295540 Reactome:R-HSA-8848776 Reactome:R-HSA-4420121 Reactome:R-HSA-9701488 Reactome:R-HSA-1839065 Reactome:R-HSA-2029989 Reactome:R-HSA-8857577 Reactome:R-HSA-8849102 Reactome:R-HSA-9669890 Reactome:R-HSA-9665032 Reactome:R-HSA-9674558 Reactome:R-HSA-445091 Reactome:R-HSA-9664275 Reactome:R-HSA-5218640 Reactome:R-HSA-190408 Reactome:R-HSA-2201322 Reactome:R-HSA-2586555 Reactome:R-HSA-909718 Reactome:R-HSA-191636 Reactome:R-HSA-391871 Reactome:R-HSA-983709 Reactome:R-HSA-1250195 Reactome:R-HSA-4420206 Reactome:R-HSA-9680248 Reactome:R-HSA-2012082 Reactome:R-HSA-9706350 Reactome:R-HSA-9664278 Reactome:R-HSA-114600 Reactome:R-HSA-2130194 Reactome:R-HSA-6806974 Reactome:R-HSA-8876246 RHEA:10596 Reactome:R-HSA-2730882 Reactome:R-HSA-2029459 Reactome:R-HSA-2396594 Reactome:R-HSA-210291 Reactome:R-HSA-5654587 Reactome:R-HSA-9726848 Reactome:R-HSA-5218809 Reactome:R-HSA-5607745 Reactome:R-HSA-8964252 Reactome:R-HSA-5654149 Reactome:R-HSA-5655284 Reactome:R-HSA-9665411 Reactome:R-HSA-452100 Reactome:R-HSA-1251922 Reactome:R-HSA-9026502 Reactome:R-HSA-9029155 Reactome:R-HSA-9733314 Reactome:R-HSA-5357429 Reactome:R-HSA-6790087 Reactome:R-HSA-452097 Reactome:R-HSA-5654408 Reactome:R-HSA-8937807 Reactome:R-HSA-2029984 Reactome:R-HSA-202216 Reactome:R-HSA-391866 Reactome:R-HSA-9011241 Reactome:R-HSA-5654545 Reactome:R-HSA-2671829 Reactome:R-HSA-391865 Reactome:R-HSA-1307963 Reactome:R-HSA-5621355 Reactome:R-HSA-9672175 Reactome:R-HSA-202307 Reactome:R-HSA-2671742 Reactome:R-HSA-1247844 Reactome:R-HSA-1839098 Reactome:R-HSA-1295609 Reactome:R-HSA-2395801 Reactome:R-HSA-9665705 Reactome:R-HSA-9012650 Reactome:R-HSA-5218851 Reactome:R-HSA-5654628 Reactome:R-HSA-190427 Reactome:R-HSA-8849068 Reactome:R-HSA-5686587 Reactome:R-HSA-9700186 Reactome:R-HSA-112333 Reactome:R-HSA-2424486 Reactome:R-HSA-5655278 Reactome:R-HSA-9706344 Reactome:R-HSA-873924 Reactome:R-HSA-2012073 Reactome:R-HSA-2029268 Reactome:R-HSA-68954 Reactome:R-HSA-879909 Reactome:R-HSA-8848758 Reactome:R-HSA-5654653 Reactome:R-HSA-5621363 Reactome:R-HSA-9021609 Reactome:R-HSA-9709918 Reactome:R-HSA-9613023 Reactome:R-HSA-8847977 Reactome:R-HSA-9698003 Reactome:R-HSA-508282 Reactome:R-HSA-190385 Reactome:R-HSA-9666425 Reactome:R-HSA-8848873 Reactome:R-HSA-9006323 Reactome:R-HSA-9606162 Reactome:R-HSA-8857555 Reactome:R-HSA-9018572 Reactome:R-HSA-5654607 Reactome:R-HSA-3928610 Reactome:R-HSA-388831 Reactome:R-HSA-9712087 Reactome:R-HSA-2033486 Reactome:R-HSA-9027273 Reactome:R-HSA-5654578 Reactome:R-HSA-354124 EC:2.7.10.2 Reactome:R-HSA-2029449 Reactome:R-HSA-1839067 Reactome:R-HSA-171011 Reactome:R-HSA-873919 Reactome:R-HSA-9664588 Reactome:R-HSA-9703438 Reactome:R-HSA-5218642 Reactome:R-HSA-873918 Reactome:R-HSA-9700181 Reactome:R-HSA-190413 Reactome:R-HSA-9700647 Reactome:R-HSA-2038944 Reactome:R-HSA-202291 Reactome:R-HSA-2730860 Reactome:R-HSA-8848606 Reactome:R-HSA-5655341 Reactome:R-HSA-418859 Reactome:R-HSA-1470009 Reactome:R-HSA-9665389 Reactome:R-HSA-1433418 Reactome:R-HSA-1248694 Reactome:R-HSA-9006332 Reactome:R-HSA-8948143 Reactome:R-HSA-9700168 Reactome:R-HSA-170156 Reactome:R-HSA-202245 Reactome:R-HSA-9034814 Reactome:R-HSA-9733323 Reactome:R-HSA-391156 Reactome:R-HSA-2395439 Reactome:R-HSA-909729 Reactome:R-HSA-9029151 Reactome:R-HSA-170991 Reactome:R-HSA-190388 Reactome:R-HSA-2197698 Reactome:R-HSA-5218828 Reactome:R-HSA-5607750 Reactome:R-HSA-2671850 Reactome:R-HSA-8853309 Reactome:R-HSA-8937728 Reactome:R-HSA-190326 Reactome:R-HSA-445085 Reactome:R-HSA-389762 Reactome:R-HSA-5218830 Reactome:R-HSA-8937844 Reactome:R-HSA-354073 Reactome:R-HSA-5654428 Reactome:R-HSA-2730843 Reactome:R-HSA-202233 Reactome:R-HSA-1963586 Reactome:R-HSA-389083 Reactome:R-HSA-389354 Reactome:R-HSA-9700164 Reactome:R-HSA-909730 Reactome:R-HSA-434836 Reactome:R-HSA-205289 Reactome:R-HSA-1671691 Reactome:R-HSA-3928604 Reactome:R-HSA-190429 Reactome:R-HSA-8855237 Reactome:R-HSA-9603420 Reactome:R-HSA-8848818 Reactome:R-HSA-909726 Reactome:R-HSA-419646 Reactome:R-HSA-9032532 Reactome:R-HSA-2012087 Reactome:R-HSA-9664261 Reactome:R-HSA-389159 Reactome:R-HSA-2038387 Reactome:R-HSA-2730888 Reactome:R-HSA-5655268 Reactome:R-HSA-380780 Reactome:R-HSA-5218812 Reactome:R-HSA-5654147 Reactome:R-HSA-8848436 Reactome:R-HSA-5654407 Reactome:R-HSA-8874082 Reactome:R-HSA-9712086 Reactome:R-HSA-2730851 Reactome:R-HSA-177937 Reactome:R-HSA-202165 Reactome:R-HSA-201521 Reactome:R-HSA-1963582 Reactome:R-HSA-3928583 Reactome:R-HSA-8875817 Reactome:R-HSA-1168394 Reactome:R-HSA-373750 Reactome:R-HSA-8983872 Reactome:R-HSA-8876948 Reactome:R-HSA-8851933 Reactome:R-HSA-5654222 Reactome:R-HSA-443817 Reactome:R-HSA-9027425 Reactome:R-HSA-6784006 Reactome:R-HSA-9665704 Reactome:R-HSA-6784319 Reactome:R-HSA-9670418 Reactome:R-HSA-9625487 Reactome:R-HSA-428888 Reactome:R-HSA-202174 Reactome:R-HSA-5683930 Reactome:R-HSA-9612996 Reactome:R-HSA-5655270 Reactome:R-HSA-8848005 Reactome:R-HSA-5654631 Reactome:R-HSA-5654582 Reactome:R-HSA-9026579 Reactome:R-HSA-9026464 Reactome:R-HSA-1225952 Reactome:R-HSA-2023460 Reactome:R-HSA-9604767 Reactome:R-HSA-1982066 Reactome:R-HSA-1250348 Reactome:R-HSA-5637796 Reactome:R-HSA-8848124 Reactome:R-HSA-183058 Reactome:R-HSA-879925 Reactome:R-HSA-177934 Reactome:R-HSA-9712082 Reactome:R-HSA-1250315 Reactome:R-HSA-202248 Reactome:R-HSA-3928580 Reactome:R-HSA-451942 Reactome:R-HSA-1839112 Reactome:R-HSA-445084 Reactome:R-HSA-2428926 Reactome:R-HSA-429449 Reactome:R-HSA-9034714 Reactome:R-HSA-174164 Reactome:R-HSA-5655301 Reactome:R-HSA-377640 Reactome:R-HSA-2033485 Reactome:R-HSA-9027272 Reactome:R-HSA-8848726 Reactome:R-HSA-2586553 Reactome:R-HSA-9606159 Reactome:R-HSA-69195 Reactome:R-HSA-3928648 Reactome:R-HSA-9026510 Reactome:R-HSA-2424484 Reactome:R-HSA-9700193 Reactome:R-HSA-5655243 Reactome:R-HSA-8853325 Reactome:R-HSA-5218820 Reactome:R-HSA-2023455 Reactome:R-HSA-8853313 Reactome:R-HSA-9762209 Reactome:R-HSA-8857583 Reactome:R-HSA-9703437 Reactome:R-HSA-389086 Reactome:R-HSA-8867041 Reactome:R-HSA-9028728 Reactome:R-HSA-1169421 Reactome:R-HSA-1433542 Reactome:R-HSA-8857925 Reactome:R-HSA-2404193 Reactome:R-HSA-372693 Reactome:R-HSA-9669911 Reactome:R-HSA-909732 Reactome:R-HSA-210872 Reactome:R-HSA-432129 Reactome:R-HSA-9032854 Reactome:R-HSA-186786 Reactome:R-HSA-177930 Reactome:R-HSA-2730884 Reactome:R-HSA-8849042 Reactome:R-HSA-3215391 Reactome:R-HSA-191062 Reactome:R-HSA-2730833 Reactome:R-HSA-3928627 Reactome:R-HSA-4420117 Reactome:R-HSA-1433488 Reactome:R-HSA-182969 Reactome:R-HSA-5624486 Reactome:R-HSA-3928578 Reactome:R-HSA-8964242 Reactome:R-HSA-9674567 Reactome:R-HSA-374701 Reactome:R-HSA-170070 Reactome:R-HSA-9699578 Reactome:R-HSA-9673756 Reactome:R-HSA-9664976 Reactome:R-HSA-9624014 Reactome:R-HSA-9032426 Reactome:R-HSA-9695834 Reactome:R-HSA-8875451 Reactome:R-HSA-445076 Reactome:R-HSA-4093332 Reactome:R-HSA-5654605 Reactome:R-HSA-1433454 Reactome:R-HSA-3928594 Reactome:R-HSA-5621370 Reactome:R-HSA-983707 Reactome:R-HSA-9024726 Reactome:R-HSA-2730858" + + "The expansion of a muscle cell population by cell division." + "Any process that modulates the frequency, rate or extent of natural killer T cell differentiation." + "Obsolete. Consult Plant Ontology. A cell that develops from the ray initial and composes all rays (panels of tissue variable in height and width, formed by the ray initials in the vascular cambium and extending radially in the secondary xylem and secondary phloem) in the secondary vascular tissues." + "The internal genitalia are the internal sex organs such as the uterine tube, the uterus and the vagina in female mammals, and the testis, seminal vesicle, ejaculatory duct and prostate in male mammals." "FMA:45652" + "The process in which a relatively unspecialized cell acquires specialized features of a mesenchymal cell of the salivary gland. A mesenchymal cell is a loosely associated cell that is part of the connective tissue in an organism. Mesenchymal cells give rise to more mature connective tissue cell types." + "A plasmablast that secretes IgD, and which occur in a small proportion of B cells in the adult." + "Binding to hyaluronic acid, a polymer composed of repeating dimeric units of glucuronic acid and N-acetyl glucosamine." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a steroid hormone stimulus." + "The chemical reactions and pathways involving compounds derived from amino acids, organic acids containing one or more amino substituents." + "Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism." + "The process whose specific outcome is the progression of an otic placode over time, from its formation to the mature structure." + "The process in which a relatively unspecialized cell acquires specialized features of a myotube cell. Myotube differentiation starts with myoblast fusion and the appearance of specific cell markers (this is the cell development step). Then individual myotubes can fuse to form bigger myotubes and start to contract. This process occurs as part of the process of skeletal muscle regeneration. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse." + "Any process that modulates the frequency, rate or extent of alpha-beta T cell differentiation." + "The narrowest portion of the gallbladder and distal to the cystic duct." "SCTID:245394007 UMLS:C0227546 NCIT:C32649 Wikipedia:Neck_of_gallbladder FMA:14538" + "The central sulcus is a fold in the cerebral cortex of brains in vertebrates. Also called the central fissure, it was originally called the fissure of Rolando or the Rolandic fissure, after Luigi Rolando. The central sulcus is a prominent landmark of the brain, separating the parietal lobe from the frontal lobe and the primary motor cortex from the primary somatosensory cortex. [WP,unvetted]." "BAMS:cs UMLS:C1281071 Wikipedia:Central_sulcus BM:Tel-Cx-CS BIRNLEX:4035 NCIT:C32280 UMLS:C0228188 SCTID:279340001 HBA:9403 FMA:83752 DHBA:10614 neuronames:48" + "A M cell that is part of the epithelium proper of large intestine." "FMA:263142" + "Any process that modulates the frequency, rate or extent of the regulated release of a neurotransmitter from a cell." + "Enables the transfer of lactoferrin from one side of a membrane to the other." + "An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions." "EMAPA:37270 MA:0000516" + "A type I NK T cell that has the phenotype CD4-positive." + "The regulated exocytosis of secretory granules by a leukocyte." + "Any process that modulates the frequency, rate or extent of the directed movement of a protein to a specific location." + "A retinal ganglion cell C outer that has dense dendritic diversity." + "A substance produced by the cervix and endocervical glands[BTO]. Thick acidic mucus that blocks the cervical os after mestruation[WP]. This 'infertile' mucus blocks spermatozoa from entering the uterus." "BTO:0000242 FMA:83689 Wikipedia:Mucus#Reproductive_system MESH:D002582" + "A multifate stem cell found in skeletal muscle than can differentiate into many different cell types, including muscle. Distinct cell type from satellite cell." "FMA:86767" + "A gamma-synuclein that is encoded in the genome of mouse." "UniProtKB:Q9Z0F7" + "Obsolete. Use PO:0000301 from Plant Ontology instead. A tracheary element of the xylem that has no perforations, as contrasted with a vessel member. May occur in primary and in secondary xylem. May have any kind of secondary wall thickening found in tracheary elements." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an electromagnetic radiation stimulus. Electromagnetic radiation is a propagating wave in space with electric and magnetic components. These components oscillate at right angles to each other and to the direction of propagation." + "The chemical reactions and pathways resulting in the breakdown of glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues." "MetaCyc:GLYCOCAT-PWY" + "The series of events in which a temperature stimulus is received and converted into a molecular signal as part of thermoception." + + "The second nuclear division of meiosis, in which the two chromatids in each chromosome are separated, resulting in four daughter nuclei from the two nuclei produced in meiosis II." "Wikipedia:Meiosis#Meiosis_II" + "Any process that stops, prevents or reduces the frequency, rate or extent of bone mineralization involved in bone maturation." + "A protein that is a translation product of the human SPN gene or a 1:1 ortholog thereof." "PIRSF:PIRSF001994" + "A shape quality inhering in a circular disk by virtue of the bearer's having a segment of another circle removed from its edge, so that what remains is a shape enclosed by two circular arcs of different diameters which intersect at two points (usually in such a manner that the enclosed shape does not include the center of the original circle)." "Image:http://upload.wikimedia.org/wikipedia/commons/7/74/Crescent.svg" + "Glandular cell of rectal epithelium. Example: Goblet cell; enterocytes or absorptive cells; enteroendocrine and M cells." "CALOHA:TS-1281" + "The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism." "Wikipedia:Catabolism" + "Any process that activates or increases the frequency, rate or extent of a defense response." + "Connective tissue composed of elastic fibers." "FMA:20113 MA:0002853 MESH:D004547 Wikipedia:Elastic_fiber SCTID:27197004 NCIT:C32495 GAID:926" + "A vasculature that is part of a retina [Automatically generated definition]." "MESH:D012171 FMA:76552" + "An epithelium that is part of a wrist [Automatically generated definition]." "EHDAA2:0000219 EHDAA:5198" + "An intestinal villus in the duodenum." "FMA:63300" + "Any process that modulates the frequency, rate or extent of osteoclast differentiation." + "The orderly movement of an epithelial cell from one site to another, often during the development of a multicellular organism." + "A Martinotti neuron that has axons that form a horizontal ramification, making it T-shaped." + "The directed movement a dense core granule within a cell." + "A terminal bronchiole that is part of a right lung [Automatically generated definition]." "EMAPA:36638 UMLS:C1709961 MA:0001789 NCIT:C49294" + "Any process that modulates the frequency, rate, or extent of natural killer cell cytokine production." + "Any process that decreases the rate, extent or frequency of the process in which cardiac muscle adapts, with consequent modifications to structural and/or functional phenotypes, in response to a stimulus. Stimuli include contractile activity, loading conditions, substrate supply, and environmental factors." + "Any process that stops, prevents, or reduces the frequency, rate or extent of heart contraction." + "A middle phalanx that is part of a toe [Automatically generated definition]." "MA:0001386 FMA:75829 EMAPA:37311 SCTID:83207005" + "The chemical reactions and pathways resulting in the breakdown of insulin." + "Any process that stops, prevents or reduces the frequency, rate or extent of chromosome condensation." + "One of five swellings formed during the development of the face." "SCTID:89066004 FMA:293103" + "A transition where a mesenchymal cell establishes apical/basolateral polarity,forms intercellular adhesive junctions, synthesizes basement membrane components and becomes an epithelial cell that will contribute to the shaping of the mesonephric renal vesicle." + "A ligament that attaches the liver to the anterior body wall. It is a broad and thin antero-posterior peritoneal fold, falciform in shape, its base being directed downward and backward and its apex upward and backward. It is a remnant of the ventral mesentery of the fetus. It is situated in an antero-posterior plane but lies obliquely, so that one surface faces forward and is in contact with the peritoneum behind the right rectus and the diaphragm, while the other is directed backward and is in contact with the left lobe of the liver. It is attached by its left margin to the under surface of the diaphragm and the posterior surface of the sheath of the right Rectus as low down as the umbilicus; by its right margin it extends from the notch on the anterior margin of the liver, as far back as the posterior surface. It is composed of two layers of peritoneum closely united together. Its base or free edge contains between its layers the round ligament and the paraumbilical veins[WP]." "VHOG:0000355 SCTID:362705001 MA:0001622 EHDAA2:0000499 Wikipedia:Falciform_ligament UMLS:C0230240 NCIT:C32582 EHDAA:4856 EMAPA:18288 FMA:15823" + "The anterior facial vein (facial vein) commences at the side of the root of the nose, and is a direct continuation of the angular vein where it also receives a small nasal branch. It lies behind the facial artery and follows a less tortuous course. It receives blood from the external palatine vein before it either joins the anterior branch of the retromandibular vein to form the common facial vein, or drains directly into the internal jugular vein. [WP,unvetted]." "UMLS:C0226532 SCTID:181374006 NCIT:C32579 FMA:50874 AAO:0010513 EMAPA:19220 Wikipedia:Facial_vein MA:0002115" + "Any process that stops, prevents or reduces the frequency, rate or extent of nitrogen cycle metabolic process." + "A B-cell receptor CD22 that is encoded in the genome of mouse." "UniProtKB:P35329" + "Any process that activates or increases the frequency, rate or extent of asymmetric cell division." + "Any process that increases the frequency, rate or extent of the developmental process that results in the deposition of coloring matter in an organism." + "Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation." + "The directed movement of calcium ions into a cell or organelle." + "The process in which the anatomical structures of blood vessels of the heart are generated and organized. The blood vessel is the vasculature carrying blood." + + "The directed movement of amines, including polyamines, organic compounds containing one or more amino groups, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "A serous membrane that is part of a digestive system [Automatically generated definition]." "EMAPA:37592 MA:0001522" + "A goblet cell that is part of the epithelium proper of jejunum." "FMA:263065" + "A calcareous tooth that is part of the lower jaw region. In mammals, the lower jaw teeth are attached to the mandible (dentary)." "EMAPA:17917 EHDAA:8009 UMLS:C1708757 NCIT:C49582 FMA:321647 MA:0001907 SCTID:422032003" + "Any process that stops, prevents, or reduces the frequency, rate or extent of astrocyte differentiation." + "Any of the tissue layers that comprise a blood vessel. Examples: tunica media, tunica adventitia." "EMAPA:36296 MA:0002854" + "The process in which a relatively unspecialized cell acquires specialized features of a posterior lateral line neuromast support cell. Support cells are non-sensory cells of the neuromast that extend between the sensory hair cells from the basement membrane to the apical surface; they are surrounded by mantle cells." + "The process whose specific outcome is the progression of a nephron in the mesonephros over time, from its formation to the mature structure. A nephron is the functional unit of the kidney." + "A cuboidal epithelium that is part of a oviduct." "MA:0001720" + "A(n) smooth muscle cell that is part of a(n) large intestine smooth muscle longitudinal layer." + + "Any process that modulates the frequency, rate or extent of programmed cell death that occurs in the compound eye retina." + "The chemical reactions and pathways resulting in the breakdown of aldehydes, any organic compound with the formula R-CH=O." + "A portion of smooth muscle tissue that is part of a vagina [Automatically generated definition]." "BTO:0004999 MA:0001733" + "Any process that stops, prevents or reduces the frequency, rate or extent of blood circulation." + "GC_ID:1 PMID:9342353 PMID:11062127" + "A transitional myocyte that is part of the left branch of atrioventricular bundle." "FMA:263170" + "A skeletal joint that connects a mesopodium bone and connects a proximal phalanx." + "Any process that modulates the frequency, rate or extent of gene expression as a consequence of a process in which a signal is released and/or conveyed from one location to another." + "The process in which a relatively unspecialized cell acquires specialized features of a neuroblast. There are at least four stages through which the pluripotent cells of epiblast or blastula become neuroblasts." + "The process of creating a trabecula in the heart. A trabecula is a tissue element in the form of a small beam, strut or rod." + "Any of the vesicles of the constitutive secretory pathway, which carry cargo from the endoplasmic reticulum to the Golgi, between Golgi cisternae, from the Golgi to the ER (retrograde transport) or to destinations within or outside the cell." "NIF_Subcellular:sao885490876" + "The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]." "UMLS:C0027763 SCTID:278196006 EV:0100162 FMA:7157 BIRNLEX:844 WBbt:0005735 neuronames:3236 GAID:466 VHOG:0000402 MA:0000016 AAO:0000324 EFO:0000802 MAT:0000026 EMAPA:16469 XAO:0000177 EHDAA2:0001246 EHDAA:826 ZFA:0000396 BTO:0001484 CALOHA:TS-1313 MIAA:0000026 TAO:0000396 Wikipedia:Nervous_system MESH:D009420 NCIT:C12755 BILA:0000079" + "The developmental process in which the mammary placode forms. The mammary placode is a transient lens shaped structure that will give rise to the mammary bud proper." + "A flat or angular epithelial cell with condensed nuclei and darkly staining cytoplasm containing numerous intermediate filaments inserted into desmosomes contacting surrounding supporting cells; lie in contact with the basal lamina of olfactory epithelium." "FMA:62304" + "Any of the tubular branching vessels that carry blood from the capillaries toward the heart." "TAO:0000082 MIAA:0000037 CALOHA:TS-1108 UMLS:C0042449 Wikipedia:Vein BTO:0000234 EV:0100031 NCIT:C12814 EHDAA2:0003254 GAID:492 ZFA:0000082 galen:Vein MAT:0000037 SCTID:181367001 EMAPA:35906 FMA:50723 EFO:0000816 MESH:D014680 XAO:0000115 MA:0000067 AEO:0000209 VHOG:0001743 AAO:0010212" + "Any process that decreases the frequency, rate or extent of nephron tubule epithelial cell differentiation." + "Any process that stops, prevents or reduces the frequency, rate or extent of ATP biosynthetic process." + "A cartilaginous condensation that has the potential to develop into a carpal bone." "EHDAA2:0000221 VHOG:0001123 EMAPA:18102 EHDAA:8544" + "A submucosa that is part of a transverse colon [Automatically generated definition]." "FMA:15013" + "A goblet cell that is part of the epithelium of crypt of Lieberkuhn of large intestine." "FMA:263056" + "A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component." + "Any process that mediates the transfer of information from one cell to another and contributes to the progression of the mammary gland, from its initial state to the mature structure." + "Obsolete. Use PO:0000082 from Plant Ontology instead. A meristemic ray cell in the vascular cambium that gives rise to ray cells of the secondary xylem and secondary phloem." + "Enables the transfer of carboxylic acids from one side of a membrane to the other. Carboxylic acids are organic acids containing one or more carboxyl (COOH) groups or anions (COO-)." "Reactome:R-HSA-390347" + "Tolerance induction taking place in the mucosal-associated lymphoid tissue (MALT) mediated by B cells." + "Lymph node germinal centers contain two microenvironments: the light zone and the dark zone. The light zone is sparsely populated with B cells and includes additional cell types such as follicular dendritic cells, lymph node tingible macrophages and T follicular helper cells." + "The collection of muscles that acts on the pharynx." "FMA:264609 TAO:0001307 ZFA:0001307" + "An epithelial cell derived from ectoderm." "FMA:69074" + "A pyramidal cell morphology that inheres in neurons which have an apical tree which is oriented towards the white matter." "ilxtr:InvertedPyramidalPhenotype" + "A pyramidal cell morphology that inheres in neurons which lack a tuft formation but extend to small radial distances forming a star-like shape." "ilxtr:StarPyramidalPhenotype" + "A DRD1-expressing, medium spiny neuron-like granule cell that is part of an Island of Calleja." + "A physical quality inhering in an entity exhibiting the physical characteristics of an amorphous (non-crystalline) form of matter between a gas and a solid that has a definite volume, but no definite shape." + "Supports paraganglial type 1 cell." + "Any process that stops, prevents or reduces the frequency, rate or extent of endothelial cell development." + "Any process that activates or increases the frequency, rate or extent of transport across blood-brain barrier." + "Terminal segment of free limb, immediately distal to the zeugopod region. The fully developed autopod consists of the autopod skeleton plus associated structures such as integument, muscle tissue, vasculature etc. The autopod is divided into mesopodial, metapodiual, and acropodial segments. Examples: human hand, mouse paw, human foot." "NCIT:C77660 UMLS:C0687080 EFO:0000877 MAT:0000091 MA:0002714 FMA:83015 MIAA:0000091 BTO:0004359 SCTID:95936004 EMAPA:32722" + "A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone." "MESH:D003239 FMA:63875 CALOHA:TS-2096" + "A flattened, almost circular bilaminar plate of cells formed when the inner cell mass (aka embryoblast) forms two epithelial layers, each of a distinct lineage, separated by an extracellular basement membrane: the external (dorsal) layer is called the epiblast and the internal (ventral) layer is called the hypoblast (aka primitive endoderm); together, they compose the bilaminar embryonic disc." "Wikipedia:Bilaminar_disc NCIT:C34112 UMLS:C1283997 FMA:293863" + "The process in which an embryonic mesoderm-derived hemocyte precursor cell acquires the specialized features of a crystal cell. Crystal cells are a class of cells that contain crystalline inclusions and are involved in the melanization of pathogenic material in the hemolymph." + "GC_ID:1" + "A progenitor cell that is able to differentiate into the pancreas alpha, beta and delta endocrine cells. This cell type expresses neurogenin-3 and Isl-1." + "Any process involved in the carrying out of an immune response by a basophil." + "The process aimed at the progression of a myotube cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. This occurs as part of the process of skeletal muscle regeneration. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse." + "A set of structures containing cerebrospinal fluid in the brain. It is continuous with the central canal of the spinal cord[WP]." "neuronames:2497 FMA:242675 EHDAA2:0004362 EV:0100306 TAO:0001261 MBA:73 Wikipedia:Ventricular_system EFO:0003650 ZFA:0001261" + "Anatomical projection that is composed of bone or cartilage tissue." + "Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process." + "Any process that activates or increases the frequency, rate, or extent of tolerance induction to nonself antigen." + "Any developmental process that results in the creation of defined areas or spaces within the pronephros to which cells respond and eventually are instructed to differentiate." + + "Any process that stops, prevents or reduces the frequency, rate or extent of endodermal cell differentiation." + "Any process that modulates the frequency, rate or extent of microtubule polymerization." + "Nucleus in the anterior part of the hypothalamus. (MSH) * one of the magnocellular hypothalamic nuclei, an elongated plate of large, deeply staining cells located close to the third ventricle in the anterior hypothalamic area; major source of oxytocin and to a lesser extent, of antidiuretic hormone, neurohormones, which are carried to the neurohypophysis along the paraventriculohypophysial tract. (CSP)." "UMLS:C0030532 GAID:643 BAMS:PVH neuronames:387 SCTID:369131006 EFO:0002469 MA:0000848 BM:Die-Hy-PAH BTO:0002476 Wikipedia:Paraventricular_nucleus_of_hypothalamus HBA:12905 MESH:D010286 BAMS:PAH BIRNLEX:1407 EV:0100229 BAMS:Pa MBA:38 EMAPA:35665 DHBA:10476 FMA:62320" + "Any process that modulates the frequency, rate or extent of myoblast differentiation. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers." + "An action potential that occurs in a bundle of His cell." + "Any process that modulates the rate, frequency or extent of microtubule nucleation. Microtubule nucleation is the 'de novo' formation of a microtubule, in which tubulin heterodimers form metastable oligomeric aggregates, some of which go on to support formation of a complete microtubule. Microtubule nucleation usually occurs from a specific site within a cell." + "CD4-positive alpha-beta T cell with the phenotype CD25-positive, CTLA-4-positive, and FoxP3-positive with regulatory function." + "Any of several small branches of the internal carotid artery that supply the trigeminal ganglion and the walls of the cavernous and petrosal sinuses." "BTO:0002996 FMA:70527" + "A CD8-positive, alpha-beta T cell that has not experienced activation via antigen contact and has the phenotype CD45RA-positive, CCR7-positive and CD127-positive. This cell type is also described as being CD25-negative, CD62L-high and CD44-low." + "An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction that stains and colors, pale-pink, with Wright-Giemsa stain." + "The process whose specific outcome is the progression of a muscle cell over time, from its formation to the mature structure. Muscle cell development does not include the steps involved in committing an unspecified cell to the muscle cell fate." + "The chemical reactions and pathways resulting in the breakdown of amino acids of the serine family, comprising cysteine, glycine, homoserine, selenocysteine and serine." + "Any process that activates or increases the frequency, rate or extent of supramolecular fiber organization." + "A GABAergic neuron located in the cerebral cortex that expresses vasoactive intestinal polypeptide" "ILX:0770151" + "A medium spiny neuron that expresses dopamine type 1 receptors and projects to the globus pallidus internus or the substantia nigra pars reticulata." + "The invagination of the optic vesicle to form two-walled indentations, the optic cups, that will go on to form the retina. This process begins with the optic vesicle becoming a two-walled structure and its subsequent shape changes. It does not include the fate commitment of cells to become the pigmented retina and the neural retina. An example of this process is found in Mus musculus." + "The distal end of the tail." "XAO:0004057 EMAPA:37760 MA:0002848" + "Any process that stops, prevents, or reduces the frequency, rate or extent of neuron differentiation." + "A protein that is a translation product of the human PRG2 gene or a 1:1 ortholog thereof." + "The fibrous connective tissue layer beneath the stomach mucosa." "FMA:14908 UMLS:C0227211 NCIT:C32663 SCTID:52459002 BTO:0002110 EMAPA:35825 MA:0002685" + "Any hematopoietic cell that is a precursor of some other hematopoietic cell type." + "Multicellular organism that can produce both male and female gametes." "TADS:0000601 HAO:0000029 BILA:0000029 AAO:0010035 WBbt:0007849 CARO:0000029" + "An ectoderm that is part of a pharyngeal arch 4." "EMAPA:16762 EHDAA2:0004032 EMAPA:16768 VHOG:0001095 EMAPA:16764 RETIRED_EHDAA2:0000094" + "A C-C chemokine receptor type 4 that is encoded in the genome of human." "UniProtKB:P51679 Reactome:R-HSA-373090 DTO:02100056" + "A muscle cell that is part of the atrial branch of anterior internodal tract." "FMA:223277" + "The process whose specific outcome is the progression of a mesenchymal tissue over time, from its formation to the mature structure. A mesenchymal tissue is made up of loosely packed stellate cells." + "The dorsal part of the body wall." + "The process in which neuroepithelial cells of the neural tube give rise to Brgmann glial cells, specialized bipotential progenitors cells of the cerebellum. Differentiation includes the processes involved in commitment of a cell to a specific fate." + + "The process in which a relatively unspecialized cell acquires specialized features of a GABAergic interneuron residing in the cerebral cortex." + "The actin filament-based process in which cytoplasmic actin filaments slide past one another resulting in contraction of a cardiac muscle cell." + "A basophil chromphil cell of the anterior pitiutary gland that produce adrenocorticotropic hormone, melanocyte-stimulating hormone and lipotropin. This cell type is irregular in shape and has short dendritic processes which are inserted among other neighboring cells;" "BTO:0002509 FMA:83098 MESH:D052680" + "Any process in which a protein is transported to, and/or maintained at the synapse, the junction between a nerve fiber of one neuron and another neuron or muscle fiber or glial cell." + "Any process that modulates the frequency, rate, or extent of an adaptive immune response." + "The developmental process pertaining to the formation and shaping of the optic vesicle. This process begins with the specific processes that contribute to the appearance of the vesicle and ends when the vesicle has evaginated. The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup." + "Directed movement of the oocyte, following its specification, from its original central position in the cyst to a posterior position relative to the nurse cells of the egg chamber, and its maintenance in this posterior location. This is the first sign of anterior-posterior asymmetry in the developing egg chamber." + "Anatomical entity that has mass." "HAO:0000006 VHOG:0001721 AAO:0010264 FMA:67165 BILA:0000006 TAO:0001836 AEO:0000006 EHDAA2:0003006 CARO:0000006 TGMA:0001826" + "The most anterior region of the brain including both the telencephalon and diencephalon." "VHOG:0000383 FMA:61992 UMLS:C0085140 MAT:0000105 XAO:0000011 BIRNLEX:1509 Wikipedia:Forebrain ZFA:0000109 BTO:0000478 SCTID:362291003 AAO:0010147 EHDAA2:0000556 BAMS:FB DHBA:10156 neuronames:27 MESH:D016548 BAMS:Forebrain MIAA:0000105 MA:0000170 EHDAA:3470 TAO:0000109 CALOHA:TS-0380 EFO:0000909 NCIT:C40185 DMBA:15566 EMAPA:16895" + "One of the system of communicating cavities in the brain that are continuous with the central canal of the spinal cord, that like it are derived from the medullary canal of the embryo, that are lined with an epithelial ependyma, and that contain a serous fluid." "neuronames:2497 HBA:9418 EFO:0001914 MESH:D002552 SCTID:180929003 MA:0000818 UMLS:C0007799 EMAPA:32674 BIRNLEX:1356 FMA:78447 BTO:0001442 NCIT:C12356" + "A loose connective tissue sheath surrounding each peripheral nerve. Composed mainly of colagen and fibroblasts, it forms a substantial covering over nerve trunks, then thins to an incomplete layer around smaller branches near their terminations. The epineurium is continuous centrally with the dura. Peripherally, it usually ends near the termination of a nerve fiber, but it may continue as the capsule of Meissner corpuscles and a few other encapsulated endings. Nolte, J. The Human Brain 3rd edition." "SCTID:64482002 FMA:12234 UMLS:C0205889 Wikipedia:Epineurium NLXANAT:090203 NCIT:C32528 EMAPA:37848 BTO:0003154" + "Obsolete. Use PO:0020093 from Plant Ontology instead. OBSOLETE, use term from plant ontology. A cell located at the chalazal end of the mature embryo sac in angiosperms." + "The process that gives rise to the central nervous system. This process pertains to the initial formation of a structure from unspecified parts. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain, spinal cord and spinal nerves. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord." + "One of the three blood vessels, usually one large umbilical vein and two small umbilical arteries, buried within Wharton's jelly, that transport blood to and from the placenta, where exchange between the mother and fetus takes place; the umbilical vein carries oxygenated, nutrient-rich blood from the placenta to the fetus, and the umbilical arteries carry deoxygenated, nutrient-depleted blood from the fetus to the placenta." "EMAPA:36493 SCTID:408728001" + "The outermost layer of a blood vessel, composed mainly of fibrous tissue." "EMAPA:36299 NCIT:C33818 UMLS:C0225342 SCTID:61066005 Wikipedia:Tunica_externa_(vessels) BTO:0002010" + "An internal pocketing of pharyngeal endoderm that contacts a region of ectoderm (a pharyngeal cleft) and interdigitates in the anterior and posterior directions with the pharyngeal arches." "EHDAA:1086 EMAPA:32752 EHDAA:617 EHDAA:1669 Wikipedia:Pharyngeal_pouch_(embryology) SCTID:34674002 ZFA:0001106 VHOG:0001203 EFO:0003627 XAO:0000282 NCIT:C34252 TAO:0001106 AAO:0011113 EHDAA:579 UMLS:C0231067 FMA:293063" + "Any process that activates or increases the frequency, rate, or extent of peripheral tolerance induction." + "Any apoptotic process in a regulatory T cell." + "The process in which a relatively unspecialized cell acquires specialized features of a columnar/cuboidal epithelial cell. A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube." + "Any cellular process that results in the specification, formation or maintenance of polarized cytoskeletal structures that contribute to the cell polarity of a migrating ameboid cell taking part in gastrulation." + "Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth." + "A transudate found in the serous sac." "FMA:20932" + "The nucleus of a germ cell, a reproductive cell in multicellular organisms." + "The progression of a cardiac septum over time, from its initial formation to the mature structure." + "Any process that modulates the frequency, rate or extent of the deposition or modulates the distribution of coloring matter in an organism." + + "Any process that modulates the frequency, rate or extent of cell activation, the change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand." + "A layer of of the central nervous system that is composed of white matter." "FMA:83898" + "A the thin septum that separates adjacent pulmonary alveoli, containing connective tissue constituents of the respiratory tissue and the capillary network of the blood supply of the lung." "NCIT:C49473 BTO:0003149 MA:0000421 UMLS:C1706784 Wikipedia:Alveolar_septum EMAPA:35433" + "A frontal cortex that is part of a left cerebral hemisphere." "UMLS:C1281955 BIRNLEX:1787 SCTID:314142003 FMA:72970" + "A plasmablast that secretes IgG." + "Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another and contributes to the physical shaping or formation of the camera-type eye." + "A bone of the metapodial skeleton." "EMAPA:37284 MA:0000301" + "A bone marrow proteoglycan that is encoded in the genome of mouse." "UniProtKB:Q61878" + "A division of the stomach. The stomach can be divided based on mucosal histology (glandular epithelium and gastric glands) and the relative position and type of gastric gland." "EMAPA:35821 MA:0002561 FMA:14558 Wikipedia:Stomach#Sections SCTID:245415005" + "The ventral grey column of the spinal cord[MP]. The neurons of the ventral region of the mature spinal cord participate in motor output[GO]." "UMLS:C0228590 EMAPA:18575 BAMS:VH FMA:256541 BTO:0005151 MA:0001134 UMLS:C0228569 Wikipedia:Anterior_horn_of_spinal_cord EMAPA:35794 NCIT:C33859 TAO:0000702 BIRNLEX:2668 SCTID:279443000 neuronames:1751 VHOG:0001288 ZFA:0000702" + "The lateral line consists of small sensory patches (neuromasts) located superficially on the skin or just under the skin in fluid-filled canals on the head and body of all fishes and most amphibians. The lateral line develops from cranial ectodermal placodes situated behind the ear and between the eye and ear." "AAO:0011128 TAO:0001469 XAO:0004002 Wikipedia:Lateral_line ZFA:0001469" + "Any process that modulates the frequency, rate or extent of myoblast proliferation." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipid stimulus." + "A primary oocyte is an oocyte that has not completed female meosis I." "FMA:18645 BTO:0000512" + "Any process that modulates the rate, frequency, or extent of the orderly movement of an endothelial cell into the extracellular matrix to form an endothelium." + "A thymic medullary epithelial cell that expresses neuroendocrine biomarkers." + "A convex 3-D shape quality inhering in a bearer by virtue of the bearer's exhibiting a by virtue of the bearer's exhibiting a consistently sized and approximately round cross-section along its length, which is many times larger than its diameter." + "The directed movement of a lymphocyte in response to an external stimulus." + "The chemical reactions and pathways involving gamma-aminobutyric acid (GABA, 4-aminobutyrate), an amino acid which acts as a neurotransmitter in some organisms." + "The series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered." + "Any process that modulates the frequency, rate, or extent of leukocyte migration." + "A mucosa that is part of a upper lip [Automatically generated definition]." "NCIT:C12224 FMA:59832 UMLS:C0226933 SCTID:362088009" + "Obsolete. Use PO:0002002 from Plant Ontology instead. The lower cell formed after the first division of a plant zygote." + "A subdivision of the pes skeleton consisting of both pedal acropodial skeleton and metatarsal skeleton, but excluding the tarsal skeleton." + "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." + "The chemical reactions and pathways occurring at the level of individual cells resulting in the breakdown of biogenic amines, any of a group of naturally occurring, biologically active amines, such as norepinephrine, histamine, and serotonin, many of which act as neurotransmitters." + "A skeletal joint that is part of a appendage girdle region." "MA:0001505" + "A zone of skin that is part of a manus [Automatically generated definition]." "SCTID:181527003 EMAPA:18486 NCIT:C52753 MA:0000630 FMA:38295 UMLS:C0222224" + + "Any process that stops, prevents, or reduces the frequency, rate or extent of insulin receptor signaling." + "A protein that is a translation product of the human MYB gene or a 1:1 ortholog thereof." + "A paneth cell that is part of the epithelium of small intestine." "FMA:263104" + "A non-sensory cell that extends from the basement membrane to the apical surface of the auditory epithelium and provides support for auditory hair cells." + "Any process that modulates the frequency, rate or extent of chromatin organization." + "A limb bud that develops into a hindlimb." "SCTID:346164003 XAO:0003066 RETIRED_EHDAA2:0003197 EHDAA:2358 MIAA:0000256 AAO:0010382 EMAPA:16779" + "Sensory system responsible for the perception of spatial orientation and auditory stimuli." "EMAPA:37985 XAO:0003195 TAO:0001138 AAO:0000631 FMA:78500 ZFA:0001138" + "Any apoptotic process in a thymocyte, an immature T cell located in the thymus." + "A tumor necrosis factor receptor superfamily member 11A that is encoded in the genome of mouse." "UniProtKB:O35305" + "A B cell found in the lymph node medullary sinus." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the migration of the endothelial cells of blood vessels." + "The parenchyma of the spleen, consisting of lymphocytes and macrophages. It lies between the splenic trabecula. Red pulp is the part suffused with blood and white pulp consists of areas of lymphatic tissue where there are sleeves of lymphocytes and macrophages." "MA:0002487 NCIT:C33603 FMA:15845 UMLS:C0229691 EMAPA:35805 SCTID:13515001" + "An agranular supporting cell of the anterior pituitary (adenohypophysis) that is characterized by a star-like morphology and ability to form follicles. Folliculostellate cells communicate with each other and with endocrine cells via gap junctions." + "Multilayered ectodermal region at the distal tip of a limb or fin bud necessary for the proper development of the underlying mesenchyme[MP,modified]. Along with the zone of polarizing activity, it is a crucial organizing region during limb development[WP]." "ZFA:0001702 XAO:0004121 EMAPA:32744 NCIT:C34109 Wikipedia:Apical_ectodermal_ridge UMLS:C1516037 AAO:0010760 TAO:0002146" + + "The process whose specific outcome is the progression of the ear over time, from its formation to the mature structure. The ear is the sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals." + "An anatomical structure that connects two structures." "FMA:5898 SCTID:91833003" + "The increase in size or mass of a cardiac muscle, where the increase in size or mass has the specific outcome of the progression of the organism over time from one condition to another." + "Any of the three loop-shaped membranous inner tubular parts of the semicircular canals that are about one-fourth the diameter of the corresponding outer bony canals, that communicate at each end with the utricle, and that have near one end an expanded ampulla containing an area of sensory epithelium." "FMA:61122 NCIT:C33528 SCTID:279833009 MA:0000251 VHOG:0000238 UMLS:C1323109 EMAPA:32830" + + "The movement of a plasmacytoid dendritic cell in response to an external stimulus." + "Any process that activates or increases the frequency, rate or extent of the inflammatory response." + "An angiotensinogenase that is a translation product of the human REN gene or a 1:1 ortholog thereof." "IUPHARobj:2413" + "A C-X-C chemokine receptor type 2 that is encoded in the genome of mouse." "UniProtKB:P35343" + "Gray matter of the central nervous system which is a collection of clustered nuclei." "FMA:256381 FMA:84059" + "A lineage negative, Sca1-negative basophil progenitor cell that is Fc epsilon RIalpha-high." + "The layer of endometrial epithelium adjacent to the uterine cavity." "NCIT:C32189 FMA:86492" + "Gray matter of the parietal region of the neocortex, located in the parietal lobe of gyrencephalic animals. It is continuous anteriorly with the frontal cortex, posteriorly with the occipital cortex and medially with the insular cortex and with the temporal cortex on the posterior/inferior border." "SCTID:369217001 FMA:242203 DHBA:10208 EMAPA:35667 NLX:79282 neuronames:2473 MA:0000916 DMBA:16016" + "The progression of an endocardial cell over time, from its formation to the mature cell. An endocardial cell is a specialized endothelial cell that makes up the endocardium portion of the heart." + "A depression in the inner retinal surface within the macula lutea, the photoreceptor layer of which is entirely cones and which is specialized for maximum visual acuity." "BIRNLEX:2543 VHOG:0001572 MESH:D005584 FMA:58658 Wikipedia:Fovea_centralis_in_macula UMLS:C0016622 EMAPA:37589 UMLS:C0450290 EV:0100350 SCTID:264479005 MA:0001307 GAID:910 CALOHA:TS-2055 NCIT:C26463" + "A dura mater that is part of a telencephalon [Automatically generated definition]." "MA:0000981 EMAPA:17776" + "The outer, i.e. cytoplasm-facing, lipid bilayer of the nuclear envelope; continuous with the endoplasmic reticulum of the cell and sometimes studded with ribosomes." "NIF_Subcellular:sao1617136075" + "A neuron that develops during the early segmentation stages in teleosts, before the neural tube is formed." + "PMID:29367151 GC_ID:1" + "A cluster of neuroendocrine cells derived from neural crest. Paraganglia may be chromaffin or nonchromaffin." "Wikipedia:Paraganglion SCTID:281695005 FMA:15648" + "GC_ID:1" + "Neural tissue consisting of myelinated axons connecting grey matter areas of the central nervous system." "HBA:9218 UMLS:C0682708 neuronames:2870 MA:0001135 AEO:0000139 EMAPA:35927 AEO:0001011 ZFA:0001682 TAO:0002142 PBA:294022044 TAO:0002143 FMA:83929 TAO:0000145 Wikipedia:White_matter NCIT:C33892 NLXANAT:101177 NLX:412 VHOG:0001764" + "The process whose specific outcome is the progression of a corticotropic hormone secreting cell over time, from its formation to the mature structure. An corticotropic hormone secreting cell is a basophil cell of the anterior pituitary that produces corticotropin." + "The process in which vesicles formed at the trans-Golgi network are directed to the plasma membrane surrounding the base of the cilium, including the ciliary pocket, mediated by molecules at the vesicle membrane and target membrane surfaces." + "A retractable double-layered fold of skin and mucous membrane that covers the glans penis and protects the urinary meatus when the penis is not erect." "MA:0000407 BTO:0001113 CALOHA:TS-0383 UMLS:C0227952 Wikipedia:Foreskin EFO:0001664 EMAPA:18989 FMA:19639 SCTID:181426005 NCIT:C33049" + "The regulated release of catecholamines by a cell. The catecholamines are a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine." + "The process aimed at the progression of a glial cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell." + "The chemical reactions and pathways involving serotonin (5-hydroxytryptamine), a monoamine neurotransmitter occurring in the peripheral and central nervous systems, also having hormonal properties." + "Any process that stops, prevents or reduces the frequency, rate or extent of an iron transmembrane transporter activity." + "A developing anatomical structure that has the potential to develop into a metencephalon." "EHDAA2:0000623" + "A T-cell surface glycoprotein CD8 alpha chain isoform 1, signal peptide removed form that includes at least one glycosylated residue." + "Organ that is part of the hematopoietic system." "BTO:0004605 FMA:7143 MA:0000747 SCTID:361338006 EMAPA:37665" + "Any process that modulates the frequency, rate or extent of the regulated release of mucus from a cell or a tissue." + "A vesicle-mediated transport process in which the presynapse take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle." + "Missing definition for term UBERON:0005066. Please replace it using linked reference." + "Any process that stops, prevents, or reduces the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes." + "Any process that activates or increases the frequency, rate or extent of vascular associated smooth muscle cell apoptotic process." + "An Ly-6-like protein that is a translation product of the mouse Ly6c2 gene or a 1:1 ortholog thereof." + "A submucosa that is part of a trachea." "UMLS:C0225586 EMAPA:35879 FMA:7472 MA:0001860 SCTID:4419000 BTO:0002115 NCIT:C49307" + "The change in morphology and behavior of an alpha-beta T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific, leading to the initiation or perpetuation of an immune response." + "Any process that modulates the frequency, rate or extent of cholangiocyte apoptotic process." + "A cartilaginous condensation that has the potential to develop into a tibia." "EMAPA:18155" + "A neural crest that has_potential_to_developmentally_contribute_to a hindbrain." "EMAPA:35747 VHOG:0001210 TAO:0007063 ZFA:0007063 EHDAA:362 EHDAA2:0001628" + "Any process that stops, prevents or reduces the frequency, rate or extent of leukocyte differentiation." + "A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues." "Wikipedia:Extracellular_matrix NIF_Subcellular:nlx_subcell_20090513" + "A type II NK T cell that has been recently activated, secretes interferon-gamma and interleukin-4, and has the phenotype CD69-positive and downregulated NK markers." + "An innate lymphoid cell that constituitively expresses RORgt and is capable of expressing IL17A and/or IL-22." + "Any process that modulates the activity of a transporter." + "Any process that activates or increases the frequency, rate or extent of protein localization to nucleolus." + "A transition where a mesenchymal cell establishes apical/basolateral polarity, forms intercellular adhesive junctions, synthesizes basement membrane components and becomes an epithelial cell that will contribute to the shaping of the mesonephros." + + "Lymphatic progenitor cells, derived from the veins, that give rise to lymphatic endothelial cells." + "The angular vein formed by the junction of the frontal vein and supraorbital vein, runs obliquely downward, on the side of the root of the nose, to the level of the lower margin of the orbit, where it becomes the anterior facial vein. It receives the external nasal veins of the ala nasi, and communicates with the superior ophthalmic vein through the nasofrontal vein, thus establishing an important anastomosis between the anterior facial vein and the cavernous sinus." "SCTID:151804007 Wikipedia:Angular_vein FMA:50893" + "The progression of the right horn of the sinus venosus from its formation to the mature structure." + "A splenic macrophage found in the areas surrounding the white pulp of the spleen, adjacent to the marginal sinus. Markers include F4/80-negative, Dectin2-low, sialoadhesin-positive." + "A bone marrow proteoglycan that has been processed by proteolytic cleavage." + "The process in which a relatively unspecialized cell acquires the specialized features of a foam cell. A foam cell is a type of cell containing lipids in small vacuoles and typically seen in atherosclerotic lesions, as well as other conditions." + "Any process that activates or increases the frequency, rate, or extent of production of any member of the interleukin-17 family of cytokines." + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a steroid hormone stimulus." + "The progression of a cardiac cushion over time, from its initial formation to the mature structure. The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves." + "Any process that decreases the rate or extent of striated muscle cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a striated muscle cell and result in its death." + "A naive regulatory T cell with the phenotype CD4-positive, CD25-positive, CD127lo, CCR4-positive, and CD45RO-negative." + "The process whose specific outcome is the progression of the nephron over time, from its formation to the mature structure. A nephron is the functional unit of the kidney." + "A fat-storing cell found mostly in the abdominal cavity and subcutaneous tissue of mammals. Fat is usually stored in the form of triglycerides." "FMA:63880 CALOHA:TS-0012 BTO:0000443" + "Any process that stops, prevents or reduces the frequency, rate or extent of vasculogenesis." + "A microtubule-based process that results in the transport of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules." + "Regular cardiac myocyte of a cardiac atrium." "FMA:83108" + "Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs." "CARO:0000081" + "A luminal epithelial cell of the mammary gland that can proliferate and has the potential to differentiate into a lactocyte during pregnancy. In humans, a luminal adaptive secretory precursor cell can be identified by high levels of the markers EpCAM and CD49f, and in mice it can be identified by low levels of CD29 and high levels of CD14, Kit, CD61, and Tspan8." + "An endothelium that is part of a peritubular capillary." + "An undifferentiated cell produced by early cleavages of the fertilized egg (zygote)." "FMA:72551 BTO:0001473" + "An insect renal cell that filters hemolymph and is found with other pericardial nephrocytes in two rows flanking the dorsal vessel." "FBbt:00005058" + "The embryonic structure that gives rise to the corneal ectoderm." "VHOG:0001296 EHDAA:938 EMAPA:16322 RETIRED_EHDAA2:0001308" + "Any process that activates or increases the frequency, rate or extent of the migration of the endothelial cells of blood vessels." + "A cell whose primary function is to protect the organism." + "The process in which a relatively unspecialized hemopoietic precursor cell acquires the specialized features of a plasmacytoid dendritic cell." + "An epithelial fate stem cell found in flatworms." "BTO:0003039" + "The ossified form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column." "NCIT:C12933 EMAPA:32740 AAO:0000691 XAO:0004019 CALOHA:TS-2352 TAO:0001189 EFO:0001371 UMLS:C0549207 Wikipedia:Vertebra SCTID:181817002 FMA:9914 galen:Vertebra ZFA:0001189 MA:0000309" + "A bone that is part of a reproductive organ." + "Obsolete. Use PO:0000373 from Plant Ontology instead. Cell containing mucilages or gums or similar carbohydrate material characterized by the property of swelling in water." + "The abdominal segment of the torso." "Wikipedia:Lumbar FMA:259211 EMAPA:35104 MA:0000021 SCTID:362875007" + "Any process that modulates the frequency, rate or extent of biomineral tissue development, the formation of hard tissues that consist mainly of inorganic compounds." + "On the interior surface of the temporal bone, behind the rough surface of the apex, is the large circular aperture of the carotid canal, which ascends at first vertically, and then, making a bend, runs horizontally forward and medialward. It transmits into the cranium, the internal carotid artery, and the carotid plexus of nerves. Sympathetics to the head also pass through the carotid canal. They have several motor functions: raise the eyelid (superior tarsal muscle), dilate pupil, innervate sweat glands of face and scalp and constricts blood vessels in head[WP]." "Wikipedia:Carotid_canal FMA:55805 EMAPA:18707" + "Any process that activates or increases the frequency, rate, or extent of macrophage antigen processing and presentation." + "Mature dermal dendritic cell is a dermal dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive." + "A structure, usually a circular muscle, that normally maintains constriction of a natural body passage or orifice and which relaxes as required by normal physiological functioning." "FMA:75004 UMLS:C1409894 NCIT:C28381 Wikipedia:Sphincter" + "EMAPA:32754 EHDAA2:0004621 FMA:293087" + "Any mucus produced by a mucosae of the respiratory system. This includes the mucus produced in the nasal cavity (nasal mucus) and mucus produced in the respiratory tract (phlegm)." + "A nucleate quality inhering in a bearer by virtue of the bearer's having more than one nucleus." + "A mucosa that is part of a lower lip [Automatically generated definition]." "NCIT:C12225 UMLS:C0226939 SCTID:362089001 FMA:59833" + "Any process that stops, prevents or reduces the frequency, rate or extent of intracellular signal transduction." + "Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells." "TAO:0000113 FMA:76622 EHDAA2:0000732 EMAPA_RETIRED:16269 ZFA:0000113 EHDAA:179 EMAPA:16098 EFO:0003492 VHOG:0000332" + "A zone of skin that is part of an arm [Automatically generated definition]." "EMAPA:37350 MA:0000596 NCIT:C52754 UMLS:C0222204" + "A portion of smooth muscle tissue that is part of a esophagus [Automatically generated definition]." "FMA:72025 EMAPA:35323 MA:0001573" + "The directed movement of organelles or molecules along microtubules from the cell body toward the postsynapse in dendrites." + "The base or posterior surface of the urinary bladder contains the trigone of the bladder and the outlet where urine empties through the internal urethral orifice." "NCIT:C48939 Wikipedia:Fundus_of_the_urinary_bladder#Fundus MA:0001694 EHDAA:9330 UMLS:C0447584 FMA:15908 EMAPA:35173 EMAPA_RETIRED:18322 VHOG:0001184 SCTID:362226002 EHDAA2:0000582" + "Any process that modulates the frequency, rate or extent of mesonephric nephron tubule epithelial cell differentiation." + "FMA:15889" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving DNA." + "A protein that is a translation product of the human CLEC7A gene or a 1:1 ortholog thereof." "IUPHARobj:2927" + "A myeloperoxidase that is encoded in the genome of human." "UniProtKB:P05164" + "GC_ID:1" + "Cell-cell signaling from pre to post-synapse, across the synaptic cleft." + "Alveolar smooth muscle is a type of non-striated muscle, found within the walls of the alveolus." "MA:0002759 EMAPA:35122" + "A bony structure embedded in skin, roughly equivalent to osteoderms." + "The change in morphology and behavior of an endothelial cell resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor." + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving phosphates." + "A GABAergic cortical interneuron that is strongly labelled for α7 nAChRs. These cells have soma found in L1 and have multipolar dendrites with vertically descending axonal collaterals that project deep into the column, usually branching and terminating in L5A." + "FMA:55268" + "A protein that is a translation product of the human FGF8 gene or a 1:1 ortholog thereof." + "The regulated release of prolactin, a peptide hormone that stimulates lactation, from secretory granules in the anterior pituitary." + "Dermal, epidermal, glandular and pigment structures of the limb integument." + "Any process that activates or increases the frequency, rate, or extent of natural killer cell tolerance induction." + "The process whose specific outcome is the progression of the mesonephros over time, from its formation to the mature structure. In mammals, the mesonephros is the second of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the mesonephros will form the mature kidney." + "In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA]." "FMA:296704 BTO:0004593 VHOG:0000243 MIAA:0000067 Wikipedia:Epiblast MAT:0000067" + "Enables the transfer of organic acids from one side of a membrane to the other. Organic acids are acidic compound containing carbon in covalent linkage." + "Sensory ganglia located on the dorsal spinal roots within the vertebral column. The spinal ganglion cells are pseudounipolar. The single primary branch bifurcates sending a peripheral process to carry sensory information from the periphery and a central branch which relays that information to the spinal cord or brain. (MSH) * ganglion found on the posterior root of each spinal nerve, composed of the unipolar nerve cell bodies of the sensory neurons of the nerve. (CSP)." "TAO:0000200 ZFA:0000200 MIAA:0000162 CALOHA:TS-0954 BIRNLEX:2596 AAO:0011032 BTO:0001264 Wikipedia:Dorsal_root_ganglion SCTID:244455004 UMLS:C0017070 EMAPA:16667 VHOG:0000222 EMAPA:16668 BIRNLEX:2598 EHDAA:2899 EHDAA2:0000418 EHDAA2:0001897 MAT:0000162 NCIT:C12462 FMA:5888 MA:0000232 EFO:0000900 MA:0000231 EMAPA:18372 XAO:0000210 EV:0100373" + "The process whose specific outcome is the progression of the genitalia over time, from its formation to the mature structure." + "The process whose specific outcome is the progression of the sinoatrial (SA) node over time, from its formation to the mature structure. The SA node is part of the cardiac conduction system that controls the timing of heart muscle contraction. It relays electrical signals to the AV node." + "A short lived plasma cell that secretes IgM." + "The directed movement of neurotransmitter receptor to the postsynaptic membrane in transport vesicles." + "Any protein complex that is capable of functioning as a neurotransmitter receptor." + "Epithelium that consists of epithelial cells not arranged in one ore more layers." "BILA:0000071 ZFA:0001493 AEO:0000071 CARO:0000071 EHDAA2:0003071 FMA:61741 HAO:0000071 XAO:0004004 TAO:0001493 AAO:0010057" + "Any process that alters the size or shape of an auditory receptor cell." + "Organized structure of distinctive morphology and function, occurring outside the cell. Includes, for example, extracellular membrane vesicles (EMVs) and the cellulosomes of anaerobic bacteria and fungi." + "A lymphocyte that has gotten larger after being stimulated by an antigen." "BTO:0000772 EFO:0000572 FMA:83030" + "The progression of the mesonephric proximal tubule over time, from its formation to the mature structure. The mesonephric proximal tubule extends from the capsule to the distal tubule." + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of ecdysteroids." + "A cell specialized to detect chemical substances and relay that information centrally in the nervous system. Chemoreceptors may monitor external stimuli, as in taste and olfaction, or internal stimuli, such as the concentrations of oxygen and carbon dioxide in the blood." + "Any process in which the Golgi is maintained in a specific location within a cell and prevented from moving elsewhere." + "Any process that stops, prevents or reduces the frequency, rate or extent of type B pancreatic cell proliferation." + "The process in which a relatively unspecialized cell acquires the specialized features of an iridophore. Iridophores are pigment cells derived from the neural crest. They contain guanidine or other purine crystals deposited in stacks called reflecting platets or iridisomes. This gives them a silver, gold, or iridescent appearance." + "The entire complement of dendrites for a neuron, consisting of each primary dendrite and all its branches." "NIF_Subcellular:sao172297168" + "The process in which a monocyte acquires the specialized features of a foam cell. A foam cell is a type of cell containing lipids in small vacuoles and typically seen in atherosclerotic lesions, as well as other conditions." + "The process whose specific outcome is the progression of a substantia propria of cornea over time, from its formation to the mature structure." + "A cell in the area of mesoderm in the neurulating embryo that flanks and forms simultaneously with the neural tube. The cells of this region give rise to somites." + "A Betz cell that synapses with lower motor neurons directly." + "A zygote in a plant or an animal." "MESH:D015053" + "The directed movement of L-glutamate into the vacuole across the vacuolar membrane." + "GC_ID:1" + "A CD38-negative IgG-negative memory B cell is a IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype CD38-negative and IgG-negative." + "A mesenchymal stem cell of the vertebrae." + "A double negative thymocyte that has a T cell receptor consisting of a gamma chain containing a Vgamma2 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-positive and is found in the fetal thymus." + "A stomal cell of the ovary" "FMA:72299" + "Any process that modulates the frequency, rate or extent of cellular component biogenesis, a process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component." + "Any process that activates or increases the frequency, rate, or extent of antigen processing and presentation of antigen (peptide or polysaccharide) via MHC class II." + "A renal pelvis that is part of a right ureter." "FMA:15578 SCTID:243419002" + "A mesentery that is part of a midgut [Automatically generated definition]." "EMAPA:16721 VHOG:0000413 EHDAA2:0001202 EHDAA:3031 EMAPA:17197 EMAPA:17039" + + "Ventral mesentery is the part of the peritoneum closest to the navel." "EHDAA2:0004569 Wikipedia:Ventral_mesentery SCTID:361430000" + "One of the veins of the lower leg; empty into the popliteal vein." "UMLS:C0447138 MA:0002243 EMAPA:37199 NCIT:C33787" + "Modulation of synaptic transmittion by cell-cell signaling across the synaptic cleft from postsynapse to presynapse, mediated by a neuropeptide." + "Any process that stops, prevents, or reduces the frequency, rate or extent of ascospore formation, a process in which a sexual spore, named ascospore, from Ascomycete fungi was produced inside an ascus." + "Enables the transfer of carbohydrate derivative from one side of a membrane to the other." + + "Distal-most phalanx within a digit." "SCTID:299711006 Wikipedia:Distal_phalanges EMAPA:35287 MA:0002914 AAO:0010676" + "Any portion of the ducts that carry bile from the liver to the common bile duct. This may include both intrahapetic components (parts of left and right hepatic ducts) and extrahapetic components (common hepatic duct, plus hilar portion)." "SCTID:245399002 UMLS:C0917710 FMA:71891 EMAPA:16843 galen:HepaticDuct EHDAA2:0000741 VHOG:0000219 MA:0000357 NCIT:C32730 EHDAA:3049" + "A blood vessel that is part of an abdominal segment of trunk [Automatically generated definition]." "EMAPA:37057 MA:0000524" + "An epithelial cell that is part of the sweat gland." "FMA:70952" + "The Atlanto-occipital joint (articulation between the atlas and the occipital bone) consists of a pair of condyloid joints. The atlanto-occipital joint is a synovial joint. The ligaments connecting the bones are: Two Articular capsules; Posterior atlantoöccipital membrane; Anterior atlantoöccipital membrane; Lateral atlantoöccipital." "SCTID:361831006 NCIT:C32158 ncithesaurus:Atlanto-occipital_Joint-Atlanto FMA:24939 UMLS:C0004169 Wikipedia:Atlanto-occipital_joint" + "The change in morphology and behavior of a CD4-positive, alpha-beta T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific." + "Binding to somatostatin, a polypeptide hormone involved in regulating pancreatic alpha and pancreatic beta cells and controlling growth hormone secretion as well as many other functions. Somatostatin is produced by several cell types including pancreatic delta cells. There are several different mature forms of somatostatin." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucose stimulus." + "An epithelial cell of the musculomembranous digestive tube extending from the mouth to the anus." + "A quality inhering in a cell by virtue of the cell having a high nuclear/cytoplasmic ratio." + "Any process that modulates the frequency, rate or extent of ovarian cumulus cell differentiation." + "Endochondral bone that is dorsoventrally compressed and provides attachment site for muscles of the pectoral appendage." "Wikipedia:Scapula TAO:0000583 SCTID:302517007 CALOHA:TS-0897 VSAO:0000157 ZFA:0000583 MA:0001330 EFO:0001400 UMLS:C0036277 VHOG:0001398 AAO:0000751 BTO:0001218 NCIT:C12783 FMA:13394 galen:Scapula MESH:D012540 EMAPA:18722 GAID:186" + "The series of events in which an external stimulus is received by a cell and converted into a molecular signal." + "Any process that modulates the frequency, rate, or extent of interleukin-1 production." + "Any cell that is part of a pituitary gland." + "A portion of smooth muscle tissue that is part of a trachea [Automatically generated definition]." "NCIT:C49306 EMAPA:19192 FMA:262010 MA:0001863 UMLS:C1710458 BTO:0001391" + "A collection of protruberances derived from pharyngeal arches 1 and 2 that develop into the folds of the pinna and gradually shift upwards and backwards to their final position on the head." "VHOG:0001364 EHDAA2:0000155 EHDAA:4685 EMAPA:17280 NCIT:C34110" + + "galen:Diverticulum" + "A receptor-type tyrosine-protein phosphatase C that is encoded in the genome of mouse." "UniProtKB:P06800" + "Any process that modulates the frequency, rate or extent of tumor necrosis factor production." + "EHDAA2:0002079" + "The orderly movement of a cell specialized to produce haploid gametes through the embryo from its site of production to the place where the gonads will form." + "Any process that activates or increases the frequency, rate or extent of glycinergic synaptic transmission. Glycinergic synaptic transmission is the process of communication from a neuron to another neuron across a synapse using the neurotransmitter glycine." + "Any process that stops, prevents or reduces the frequency, rate or extent of mesenchymal stem cell differentiation." + "Any process that modulates the frequency, rate or extent of male germ-line stem cell asymmetric division." + "FMA:15890" + "Any process that stops, prevents or reduces the frequency, rate or extent of cell junction assembly." + "Any process that modulates the frequency, rate or extent of glucocorticoid receptor signaling pathway." + "A surface shape quality inhering in a bearer by virtue of the bearer's shape of features present on its surface or outer shell." + "Any melanocyte of skin that is part of a skin of prepuce of penis." + "The layer of endometrial epithelium adjacent to the myometrium." "FMA:86493 NCIT:C32642" + "The chemical reactions and pathways resulting in the breakdown of a protein at a presynapse." + "Cranial neural crest that migrates into the mandibular arch." "ZFA:0007064 XAO:0000024 TAO:0007064" + "Any process that activates or increases the frequency, rate or extent of the activity of any intracellular steroid hormone receptor signaling pathway." + "An epithelial cell that is part of the gallbladder." "FMA:67780" + "BTO:0000783" + "Any of the immature or mature forms of a granular leukocyte with a nucleus that usually has two lobes connected by one or more slender threads of chromatin, and cytoplasm containing coarse, round granules that are uniform in size and which can be stained by the dye eosin. Eosinophils are CD9-positive, CD191-positive, and CD193-positive." "CALOHA:TS-0279 FMA:62861 BTO:0000399 MESH:D004804" + "Sum of all sensory systems in an organism." "FMA:78499" + "Any process that activates or increases the frequency, rate or extent of the directed movement of iron ions from one side of a membrane to the other by means of some agent such as a transporter or pore." + "Any process that stops, prevents or reduces the frequency, rate or extent of tight junction assembly." + "A serous membrane that is part of a fallopian tube." "FMA:18316 SCTID:259593000" + "Mesenchyme of the digit region." "NCIT:C34141 EMAPA:32719 UMLS:C1511959" + "The series of events involved in the perception of taste in which a gustatory chemical stimulus is received and converted into a molecular signal." + "Any process that stops, prevents or reduces the frequency, rate or extent of myofibroblast differentiation." + "The chemical reactions and pathways resulting in the breakdown of the peptide calcitonin." + "An epithelial, transitional cell type between basal and secretory; located in stratified, non-ciliated structures (called hillocks) with high cell turnover in epithelium. In some mammalian species, this cell type has been noted to express KRT13 and is postulated to play a role in squamous barrier function and immunomodulation." + "A metanephric tubule is an epithelial tube that is part of the metanephros[GO]." "VHOG:0001526" + "Any process that decreases the rate, frequency, or extent of the growth of a cardiac muscle cell, where growth contributes to the progression of the cell over time from its initial formation to its mature state." + "Any process that activates, maintains or increases the frequency, rate or extent of microglia differentiation, the process in which a relatively unspecialized cell acquires specialized features of a microglial cell." + "The process in which a relatively unspecialized cell acquires the specialized features of a Meynert cell." + "The specification of the anterior/posterior axis of the embryo by gradients of maternally-transcribed gene products; exemplified in insects by the morphogens, bicoid and nanos." + "Any process that modulates the frequency, rate or extent of embryonic pattern specification." + "A killer cell lectin-like receptor subfamily B member 1 that is encoded in the genome of human." "UniProtKB:Q12918 Reactome:R-HSA-2132225" + "NLXANAT:20090508" + "FMA:19676" + "Any process that activates or increases the frequency, rate or extent of biomineral tissue development, the formation of hard tissues that consist mainly of inorganic compounds." + "A blood vessel that is part of a thorax [Automatically generated definition]." "MA:0000558 EMAPA:37238" + "The taeniae coli (also teniae coli) are three separate longitudinal ribbons of smooth muscle on the outside of the ascending, transverse, descending and sigmoid colons. They are visible, and can be seen just below the serosa or fibrosa. They are the Mesocolic, Free and Omental Coli. The teniae coli contracts length wise to produce the haustra, the bulges in the colon. The bands converge at the root of the vermiform appendix and the rectum. These bands correspond to the outer layer of the muscularis externa, in other portions of the digestive tract." "Wikipedia:Taenia_coli FMA:15041 SCTID:362160001" + "The process in which the labyrinthine layer of the placenta progresses, from its formation to its mature state." + "The progression of a mesonephric tubule over time, from its initial formation to the mature structure. A mesonephric tubule is an epithelial tube that is part of the mesonephros." + "The prostate epithelium." "NCIT:C13103 MA:0001737 CALOHA:TS-2065 FMA:79643 FMA:66812 EMAPA:35711 BTO:0002397 UMLS:C1179826" + "Any process that activates or increases the frequency, rate or extent of apoptotic process involved in metanephric collecting duct development." + "Blood that remains in the placenta and in the attached umbilical cord after childbirth[WP]." "MESH:D005312 CALOHA:TS-1079 EFO:0001942 Wikipedia:Cord_blood BTO:0004053" + "The process in which the branching structure of the mammary gland cord is generated and organized. The mammary gland cord is a solid epithelial structure that will hollow out, forming the mammary duct." + "The outer layer of the muscular coat." "FMA:62900 BTO:0005214" + "Any process that modulates the frequency, rate or extent of spore formation." + "A mucosa that is part of a cloaca [Automatically generated definition]." + "Any portion of submucosa that lines the digestive tract." + "The extraembryonic tissue that is responsible for the proper orientation of the anterior-posterior axis of the embryo and for appropriate patterning of adjacent embryonic tissue." "BTO:0003361 EMAPA:36068" + "Any process that modulates the occurrence or rate of cell death by apoptotic process in hippocampal neurons." + "The organ covering the body that consists of the dermis and epidermis." "galen:Skin SCTID:181469002 MESH:D012867 EMAPA:17525 FMA:7163 NCIT:C12470 XAO:0000023 BTO:0001253 MFMO:0000099 EFO:0000962 EHDAA2:0001844 CALOHA:TS-0934 Wikipedia:Skin UMLS:C1123023" + "Binding to a nucleic acid." + "NLXANAT:20090507" + "A smooth muscle cell derived from the neural crest." + "A vein that drains a thyroid gland." "EMAPA:18648 SCTID:303420005" + "A developmental process, independent of morphogenetic (shape) change, that is required for an oocyte to attain its fully functional state. Oocyte maturation commences after reinitiation of meiosis commonly starting with germinal vesicle breakdown, and continues up to the second meiotic arrest prior to fertilization." "Wikipedia:Oocyte_maturation" + "Any process that modulates the frequency, rate or extent of steroid hormone secretion." + "The process in which a relatively unspecialized cell acquires specialized features of a metanephric glomerular visceral epithelial cell. A metanephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the metanephros." + "Combining with corticotropin to initiate a change in cell activity." + "The process in which the anatomical structures of a pronephric nephron distal tubule are generated and organized. A pronephric nephron tubule is an epithelial tube that is part of the pronephros." + "A process carried out by the nervous system that is required for the proper control of respiratory gaseous exchange. This process occurs in the respiratory center of the brain in vertebrates." + "Wide vessels in the spleen that drain into trabecular veins[WP]." "FMA:63199 Wikipedia:Red_pulp#Sinusoids SCTID:9081000" + + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells." + "An artery that supplies the myocardium." "CALOHA:TS-0176 Wikipedia:Coronary_circulation#Coronary_anatomy FMA:49893 VHOG:0001557 ZFA:0005812 EV:0100383 EFO:0002551 SCTID:181294004 NCIT:C12843 MA:0002453 galen:CoronaryArtery BTO:0000290 UMLS:C0205042 EMAPA:19160" + "A process in which a protein is transported to, or maintained in, the cell cortex." + "The middle of the face including the nose and its associated bony structures[MW]." "FMA:285406 MA:0001910" + "Visceral endoderm, a population of extraembyonic endoderm, is an extraembryonic tissue that functions in a regulatory capacity but does not contribute directly to the formation of any adult organs[PMID:15905405]. primitive endoderm-derived tissue which remains in contact with and surrounds the extra-embryonic ectoderm and the epiblast and provides signals for the differentiation and patterning of the epiblast; a small number of visceral endoderm cells also contribute to the endoderm of the embryonic gut[MP]." "BTO:0003487 EMAPA:16058" + "The outer neural tube region in which post-mitotic neuroblasts migrate along radial glia to form the adult cortical layers[MP]." "MBA:695 neuronames:2702 BAMS:CTXpl DHBA:10515 EMAPA:32711 PBA:294021914" + "Any apoptotic process in a granulosa cell." + "The orderly movement of melanocytes from one site to another, often during the development of a multicellular organism. A melanocyte is a pigment cell derived from the neural crest. It contains melanin-filled pigment granules, which give a brown to black appearance." + "The collection of all skeletal elements in an individual limb." "EHDAA2:0002221 EMAPA:32702 VSAO:0000300" + "ZFA:0001156" + "A structural quality that inheres in a bearer by virtue of the bearer's containing hollow areas." + "An ADP-ribosyl cyclase that is a translation product of the human CD38 gene or a 1:1 ortholog thereof." "IUPHARobj:2766" + "Regional part of telencephalon in some species, e.g., rodent, equivalent to the dorsal striatum (caudate nucleus and putamen). Unlike the dorsal striatum of primates, for example, the caudoputamen is not split into separate nuclei by the fibers of the internal capsule. Rather, the internal capsule splits into fiber bundles which course through the structure." "BM:Tel-C-Pu BAMS:CPu BAMS:CP EFO:0001912 BTO:0000212 NLXANAT:100312 MA:0000893 EMAPA:19095 MBA:672" + "A slow muscle cell that contains high levels of myoglobin and oxygen storing proteins giving the cell a red appearance." "FMA:84448" + "The orderly movement of a distal tip cell." + "Any process that modulates the frequency or rate of heart contraction." + "The directed movement of L-glutamate across a membrane." + "The process whose specific outcome is the progression of the ventral cochlear nucleus over time, from its formation to the mature structure." + "The portion of the colon between the left colic flexure and the sigmoid colon at the pelvic brim; the portion of the descending colon lying in the left iliac fossa is sometimes called the iliac colon." "EFO:0000845 UMLS:C0227389 MAT:0000313 BTO:0000641 Wikipedia:Descending_colon FMA:14547 galen:DescendingColon CALOHA:TS-2010 SCTID:362165006 MA:0001542 MIAA:0000313 NCIT:C12268 EMAPA:35285" + "NLXANAT:20090505" + "A peritubular capillary that is part of a outer medulla of kidney." "EMAPA:35461 MA:0002589" + "The regulated release of thyroid-stimulating hormone, a peptide hormone that stimulates the activity of the thyroid gland, from secretory granules in the anterior pituitary." + "Any process that stops, prevents, or reduces the frequency, rate or extent of neural precursor cell proliferation." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of lymphocyte mediated immunity." + "Any process that stops, prevents, or reduces the frequency, rate or extent of G protein-coupled receptor signaling pathway." + "A CD38-positive IgG-negative memory B cell is an IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype CD38-positive and IgG-negative." + "An alveolus that is part of a right lung [Automatically generated definition]." "UMLS:C1709959 NCIT:C49278 MA:0001786 EMAPA:35997" + "The main division of the lateral geniculate body; consists of two magnocellular layers [TA] (strata magnocellularia [TA]) and four parvocellular layers [TA] (strata parvocellularia [TA]) and serves as a processing station in the major pathway from the retina to the cerebral cortex, receiving fibers from the optic tract and giving rise to the geniculocalcarine radiation to the visual cortex in the occipital lobe." "MBA:170 UMLS:C0175292 BAMS:LGd MA:0002775 neuronames:353 BM:GLd DHBA:10430 BIRNLEX:1595 PBA:128013074 FMA:62214 HBA:4440 DMBA:16436 BAMS:DLG EMAPA:35290" + "Combining with an extracellular or intracellular signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity or state as part of signal transduction." "Reactome:R-HSA-193672" + "Any process that activates or increases the frequency, rate or extent of astrocyte chemotaxis." + "Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system." "EHDAA2:0003114 AEO:0000114" + "A protein c-Fos that is encoded in the genome of mouse." "UniProtKB:P01101" + "Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts)." "FMA:64781 XAO:0004030 Wikipedia:Dense_regular_connective_tissue VSAO:0000050 UMLS:C0225333 SCTID:22560007 NCIT:C33453" + "The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the B cell receptor to augment B cell activation." + "A photoreceptor cell that is sensitive to red light." + "A pigment cell derived from the neural crest. The cell contains flat light-reflecting platelets, probably of guanine, in stacks called reflecting platelets or iridisomes. The color-generating components produce a silver, gold, or iridescent color." + "SCTID:362606005 FMA:12237 BIRNLEX:1019" + "A plasmablast that secretes IgM." + "The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane. Syncytia are normally derived from single cells that fuse or fail to complete cell division." + "Any process that activates or increases the frequency, rate, or extent of B cell deletion." + "Binding to a complex of RNA and protein." + "An enterocyte found in the small intestine of newborn mammals and characterized by the presence of an apical canalicular system (ACS) leading to production of large vacuoles, important for colostral macromolecule uptake. After birth, the vacuolated fetal-type enterocytes are replaced with enterocytes lacking an ACS." + "Transudate contained in the pericardial cavity.[FMA]." "Wikipedia:Pericardial_fluid BTO:0001016 MA:0002530 FMA:9887" + "Any process that stops, prevents, or reduces the frequency, rate or extent of muscle development." + "A sensory epithelium inside the nasal cavity that is responsible for detecting odors[WP]." "FMA:64803 VHOG:0000985 Wikipedia:Olfactory_epithelium EHDAA2:0001228 EHDAA:4774 EMAPA:17606 CALOHA:TS-0703 EFO:0001972 BTO:0000108 SCTID:37623003 TAO:0000554 neuronames:1900 BIRNLEX:2703 ZFA:0000554 NCIT:C33203 UMLS:C0599332 MA:0001325 MAT:0000445 AAO:0010158" + "The process whose specific outcome is the progression of the enteric nervous system over time, from its formation to the mature structure. The enteric nervous system is composed of two ganglionated neural plexuses in the gut wall which form one of the three major divisions of the autonomic nervous system. The enteric nervous system innervates the gastrointestinal tract, the pancreas, and the gallbladder. It contains sensory neurons, interneurons, and motor neurons. Thus the circuitry can autonomously sense the tension and the chemical environment in the gut and regulate blood vessel tone, motility, secretions, and fluid transport. The system is itself governed by the central nervous system and receives both parasympathetic and sympathetic innervation." + "A smooth muscle cell of the bachiocephalic vasculature." + "Tissue surrounding the loop of Henle in the renal medulla." "EMAPA:18326 Wikipedia:Bone_marrow_of_ovaryry_interstitium MA:0002619 SCTID:245693005" + "Any process that modulates the frequency, rate or extent of artery morphogenesis." + "Organized structure of distinctive morphology and function, bounded by a lipid bilayer membrane and occurring outside the cell." + "An interleukin-2 receptor subunit beta that is encoded in the genome of human." "UniProtKB:P14784" + "A change in the morphology or behavior of an astrocyte resulting from exposure to an activating factor such as a cellular or soluble ligand, leading to the initiation or perpetuation of an immune response." + "A collection of connected epithelial tubes with a single portal." "AEO:0000117 EHDAA2:0003117" + "Obsolete. Use PO:0000191 from Plant Ontology instead. A cell in the micropylar end of the embryo sac associated with the egg in the egg apparatus of angiosperms. Plays a vital role in fertilization." + "The process in which a relatively unspecialized cell acquires specialized features of a melanocyte." + "The chemical reactions and pathways involving heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells. They are similar to heparan sulfates but are of somewhat higher average Mr (6000-20000) and contain fewer N-acetyl groups and more N-sulfate and O-sulfate groups; they may be attached in the same manner to protein, forming proteoglycans. They consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues." + "An elasticity quality inhering in a bearer by virtue of the bearer's ability to recover its size and shape after deformation in any way." + "A protein with core architecture consisting of a signal sequence, a Lectin C-type domain (Pfam:PF00059), 5 or 6 EGF-like domains (Pfam:PF00008, Pfam:PF09064, or Pfam:PF07645), a transmembrane region, and a small cytoplasmic region (36-51 amino acids)." "PIRSF:PIRSF001775" + "A groove that is situated between the 4th and 5th pharyngeal arch." "VHOG:0000968 VHOG:0000577 EMAPA:16761 EHDAA2:0000089 RETIRED_EHDAA2:0000088 EHDAA:1665" + "EHDAA2:0000897 EHDAA:8467 EMAPA:17740" + "Any process that activates or increases the rate or extent of B cell proliferation." + "A glandular epithelial cell that is part of the stomach." "FMA:86554 CALOHA:TS-1284" + "An intestinal crypt stem cell that is located in the vermiform appendix. These stem cells reside at the bottom of crypts in the appendix and are highly proliferative. They either differentiate into transit amplifying cells or self-renew to form new stem cells." + "The directed movement of water (H2O) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "An anatomical structure that develops (entirely or partially) from the endoderm." + "Any process in which a protein is transported from one specific location in the extracellular region to another, or maintained in a specific extracellular location." + "Any process that modulates the frequency, rate or extent of inner ear receptor cell differentiation." + "A laminar subdivision of the neocortex that is comprised of a part of layer IV and a part of layer V." + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear envelope." + "Any microtubule in a dendrite, a neuron projection." "NIF_Subcellular:sao110773650" + "The process whose specific outcome is the progression of the camera-type eye over time, from its formation to the mature structure. The camera-type eye is an organ of sight that receives light through an aperture and focuses it through a lens, projecting it on a photoreceptor field." + "Binding to a vascular endothelial growth factor receptor." + "The process in which an organism retains a population of mesenchymal stem cells that contributes to the shaping of a nephron. A mesenchymal stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized mesenchymal cells." + "A cell that is capable of detection of a stimulus involved in sensory perception." "MESH:D011984" + "Any process that regulates translation occurring at the synapse." + "A cell found in fat bodies whose primary function is intermediary metabolism." + "The process in which the left cardiac atrium is generated and organized." + "A proximal straight tubule that is part of a pronephros." "ZFA:0001621 TAO:0002239" + "The process of regulating the proliferation and elimination of monocytes such that the total number of monocytes within a whole or part of an organism is stable over time in the absence of an outside stimulus." + "The process aimed at the progression of a vascular smooth muscle cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell. A vascular smooth muscle cell is a non-striated, elongated, spindle-shaped cell found lining the blood vessels." + "A receptor-type tyrosine-protein phosphatase C that is encoded in the genome of human." "UniProtKB:P08575" + "An affinity inhering in an anatomical structure by virtue of the bearer exhibiting a molecular interaction for both basic and acid stains under specific pH conditions." + "Binding to NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters." + "Mesenchyme that is part of a maxillary prominence." "FMA:312691 EMAPA:17361 EHDAA2:0001071" + "Any process that stops, prevents or reduces the frequency, rate or extent of a protein localization." + "The process that gives rise to the trigeminal nerve. This process pertains to the initial formation of a structure from unspecified parts. The trigeminal nerve is composed of three large branches. They are the ophthalmic (V1, sensory), maxillary (V2, sensory) and mandibular (V3, motor and sensory) branches. The sensory ophthalmic branch travels through the superior orbital fissure and passes through the orbit to reach the skin of the forehead and top of the head. The maxillary nerve contains sensory branches that reach the pterygopalatine fossa via the inferior orbital fissure (face, cheek and upper teeth) and pterygopalatine canal (soft and hard palate, nasal cavity and pharynx). The motor part of the mandibular branch is distributed to the muscles of mastication, the mylohyoid muscle and the anterior belly of the digastric. The mandibular nerve also innervates the tensor veli palatini and tensor tympani muscles. The sensory part of the mandibular nerve is composed of branches that carry general sensory information from the mucous membranes of the mouth and cheek, anterior two-thirds of the tongue, lower teeth, skin of the lower jaw, side of the head and scalp and meninges of the anterior and middle cranial fossae." + "A neuroendocrine cell that is part of the prostate epithelium." + "The process in which a relatively unspecialized cell acquires specialized features of a hepatoblast. A hepatoblast is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into hepatocytes and cholangiocytes." + "A cone cell that detects medium wavelength light. Exact peak of spectra detected differs between species. In humans, spectra peaks at 534-545 nm." + "A process in which force is generated within phasic smooth muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. In the phasic smooth muscle, the muscle contraction occurs without an ordered sarcomeric structure. Phasic smooth muscle contraction occurs in a series of discrete contractions and relaxations." + "Any process that stops, prevents or reduces the frequency, rate or extent of neutrophil activation." + "A CD8-positive, CD4-negative thymocyte that is CD24-positive and expresses high levels of the alpha-beta T cell receptor." + "The division of the zygote into two daughter cells that will adopt developmentally distinct potentials." + "A white matter of cerebral lobe that is part of a limbic lobe." "FMA:261091" + "Any process that modulates the frequency, rate or extent of stem cell proliferation. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells." + "Any process that activates or increases the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels." + "Recombination occurring within or between DNA molecules in somatic cells." + "A strand of hair that is part of a axilla." "SCTID:280911007 FMA:54253" + "NK cell that has the phenotype CD56-bright, CD16-negative, and CD84-positive with the function to secrete interferon-gamma but is not cytotoxic." + "A protein that is a translation product of the human BEST4 gene or a 1:1 ortholog thereof." + "The pre-cartilaginous form of a vertebral element, a skeletal element that forms around the notochord and is part of the vertebral column." "VHOG:0000582 EMAPA:32671" + "Any process that stops, prevents, or reduces the frequency, rate, or extent of germinal center formation." + "The giant, cup-shaped axon terminal of a vestibular afferent neuron, serving as a post-synaptic contact to a type I hair cell." + "A tooth row that is part of a skeleton of upper jaw." "EHDAA2:0002129 FMA:55634" + "The posterior part of the pituitary gland that secretes hormones involved in blood pressure regulation such as oxytocin and antidiuretic hormon." "BM:NY TAO:0001271 VHOG:0000142 MESH:D010904 EHDAA2:0001271 BIRNLEX:1586 EMAPA:17519 BTO:0000937 UMLS:C1280368 Wikipedia:Neurohypophysis ZFA:0001271 NCIT:C12773 AAO:0010537 BAMS:NHP neuronames:401 DMBA:15691 CALOHA:TS-0815 BAMS:NL FMA:74628 EHDAA:7536 BAMS:NHY UMLS:C0032009 BAMS:PPit MA:0000178 SCTID:245527006" + "An acidophil cell of the anterior pituitary gland that produces both prolactin and growth hormone." "FMA:83097" + "A(n) endothelial cell that is part of a(n) arteriole of lymph node." + "A C-type lectin domain family 4 member C that is encoded in the genome of human." "Reactome:R-HSA-2130705 Reactome:R-HSA-6801022 UniProtKB:Q8WTT0 Reactome:R-HSA-6800186 Reactome:R-HSA-6800915" + + "Any process that stops, prevents, or reduces the frequency, rate, or extent of antigen processing and presentation of antigen (peptide or polysaccharide) via MHC class II." + "Collagen-rich odontogenic tissue characteristic of teeth and tooth-like skeletal elements (e.g., odontodes); mature dentine is mineralized and develops from predentine tissue; often (but not always) tubular and acellular." "SCTID:362112004 XAO:0004051 UMLS:C0011429 BTO:0003453 VSAO:0000069 TAO:0005143 GAID:1272 ZFA:0005143 Wikipedia:Dentin VHOG:0001589 MESH:D003804 MA:0002542 EMAPA:35281 NCIT:C32453 FMA:55628" + "Any process that modulates the frequency, rate, or extent of lymphocyte anergy." + "Any endothelial cell of artery that is part of a coronary artery." + "The distal tubule is a nephron tubule that consists of the distal convoluted tubule and distal straight tubule segments." "CALOHA:TS-0504 MA:0002633 MESH:D007686 EMAPA:28387 BTO:0000482" + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving DNA." + "A protein complex composed of two identical immunoglobulin heavy chains of an IgG isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." + "Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]." "VHOG:0000118 UMLS:C1517749 EHDAA2:0000919 AAO:0010574 ZFA:0000121 SCTID:361477005 FMA:293149 EHDAA:379 XAO:0000311 TAO:0000121 NCIT:C34199 EMAPA:16179 Wikipedia:Lateral_plate_mesoderm" + "A zone of skin that is part of a craniocervical region." "NCIT:C12294 UMLS:C1522650 MA:0000574 EMAPA:37276" + "An artery that supplies oxygenated blood to the ear." "NCIT:C52849 UMLS:C1706858 EMAPA:37072 MA:0001918" + "A femur bone or its cartilage or pre-cartilage precursor." + "Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in a neuron. This typically occurs via modulation of the activity or expression of voltage-gated ion channels." + "The portion of the plasma membrane surrounding a cilium." + "Any process that modulates the frequency, rate or extent of microglial cell migration." + "A portion of the tympanic cavity epithelium which makes up the outer (cuticular) layer of the tympanic membrane." "FMA:56844 SCTID:36411006" + "A taste bud that is located on a lip." + "The process in which the anatomical structures of the salivary gland are generated and organized." + "The peripheral receptor for pain. Includes receptors which are sensitive to painful mechanical stimuli, extreme heat or cold, and chemical stimuli. All mammalian nociceptors are free nerve endings." + "A joint that connects the forelimb zeugopod and stylopod skeletons[Obol]." "EMAPA:19102 MESH:D004551 GAID:253 VHOG:0000997 UMLS:C0013770 galen:ElbowJoint SCTID:182169008 NCIT:C32497 FMA:35289 Wikipedia:Elbow MA:0000451" + "A mucosa that is part of a gallbladder [Automatically generated definition]." "SCTID:362196002 FMA:14662" + "The enlarged, fluid filled nucleus of a primary oocyte, the development of which is suspended in prophase I of the first meiotic division between embryohood and sexual maturity." + "A vein that is part of a ureter [Automatically generated definition]." "EMAPA:37679 MA:0002250" + "A gamma motor neuron that innervates static nuclear bag fibers (bag2 fibers) and increases their firing, in response to an increase in the magnitude of change in length, and controls the static sensitivity of the stretch reflex." + "A fetal and neonatal heart cell that undergoes proliferation and is not yet terminally differentiated into a binucleate or a multinucleate cardiac myocyte." + "Each renal artery gives off some small inferior suprarenal branches to the suprarenal gland, the ureter, and the surrounding cellular tissue and muscles. [WP,unvetted]." "NCIT:C52737 UMLS:C0226334 SCTID:303426004 MA:0002056 FMA:69264 Wikipedia:Inferior_suprarenal_artery EMAPA:37088" + "An epithelium that is part of a pharynx [Automatically generated definition]." "BTO:0005240 MA:0002725 RETIRED_EHDAA2:0001460 ZFA:0001174 XAO:0003202 EMAPA:16708 BSA:0000112 TAO:0001174" + "The process whose specific outcome is the progression of a spermatid over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell." + "An acinar cell of salivary gland." + "A protein complex composed of two identical immunoglobulin heavy chains of the IgM isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and in its circulating form complexed with J chain in polymeric forms. An IgM immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." + "Any process that mediates interactions between a cell and its surroundings that contributes to the process of cardiac conduction. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment." + "A cellular potency that is the capacity to form multiple differentiated cell types of a specific lineage and lack self renewing capacity." + "The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring." + "An unconventional T lymphocyte population within the thymic medulla that is potentially a thymic resident population." + "Any process that stops, prevents or reduces the frequency, rate or extent of cilium-dependent cell motility." + "The biological process whose specific outcome is the progression of a bronchus from an initial condition to its mature state. This process begins with the formation of the bronchus and ends with the mature structure. The bronchus is the portion of the airway that connects to the lungs." + "The process in which the prostate glandular acini are generated and organized. The glandular acini are the saclike structures of the gland." + "The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions." "VHOG:0000277 UMLS:C1267406 EHDAA:486 NCIT:C33858 MA:0002720 EHDAA2:0002171 BTO:0004692 EMAPA:16240 SCTID:362060003" + "Skeletal subdivision that undergoes indirect development and includes elements that develop as a replacement or substitution of other elements or tissues." "Wikipedia:Endoskeleton VSAO:0000037 XAO:0004026" + "The atrial part of middle layer of the heart, comprised of involuntary muscle." "MA:0000081 ZFA:0001374 EMAPA:32746 EFO:0003087 VHOG:0000602 TAO:0001374 FMA:83509 SCTID:191910002" + "An epithelial cell of the hypodermis of Caenorhabditis." "WBbt:0007846" + "A portion of smooth muscle tissue that is part of a neck of urinary bladder [Automatically generated definition]." "MA:0001699 EMAPA:30123 FMA:67990" + "A structure created during embryogenesis when the lateral mesoderm splits into two layers - the outer (or somatic) layer becomes applied to the inner surface of the ectoderm, and with it forms the somatopleure.[WP]." "Wikipedia:Somatopleure VHOG:0000557 UMLS:C1519423 NCIT:C34301 FMA:295566 EHDAA2:0001847 EMAPA:16180 EHDAA:381" + "NCIT:C12749 FMA:82500 MESH:D008566 FMA:30322" + "An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation." "CALOHA:TS-0636 VHOG:0001263 NCIT:C13401 MA:0002552 EMAPA:36540 galen:Milk MAT:0000056 ENVO:02000031 UMLS:C1511310 EV:0100126 Wikipedia:Breast_milk MIAA:0000056 FMA:62100 GAID:1230 MESH:D008892 BTO:0000868" + "Any process that stops, prevents or reduces the frequency, rate or extent of dense core granule transport." + "Any apoptotic process that contributes to the shaping of the heart." + "The process in which the anatomical structures of branches in a nerve are generated and organized. This term refers to an anatomical structure (nerve) not a cell (neuron)." + "The ventral part of the cloaca remaining after septation of the rectum, which further develops into part of the bladder, part of the prostatic part of the male urethra and the urethra and vestibule in females." "EHDAA:5029 EHDAA2:0004060 SCTID:50961009 VHOG:0000414 EHDAA:5919 UMLS:C0231057 Wikipedia:Definitive_urogenital_sinus EMAPA:17379 NCIT:C34322" + "A myocardial endocrine cell that is part of the atrium." "FMA:83389" + "The disaggregation of an organelle into its constituent components." + "Enables the directed movement of a neurotransmitter into, out of or within a cell, or between cells. Neurotransmitters are any chemical substance that is capable of transmitting (or inhibiting the transmission of) a nerve impulse from a neuron to another cell." "Reactome:R-HSA-374896 Reactome:R-HSA-374919" + "Any process that activates or increases the frequency, rate or extent of retina development in camera-type eye." + "Elastic tissue layer that lines a blood vessel layer." "EMAPA:36300 MA:0002856" + "Any process that modulates the frequency, rate or extent of the directed movement of a protein to a specific location on a chromosome." + "An external limiting cell found in the vestibular epithelium." "FMA:75808" + "A mesenchyme that is part of a chorion." "EMAPA:16266 RETIRED_EHDAA2:0000247 EHDAA2:0003245 EMAPA:16114 VHOG:0000620 EHDAA:154" + "BAMS:AHR BIRNLEX:1005 FMA:62027 neuronames:2381 MESH:D007032 DHBA:266441551 HBA:4570 neuronames:376 UMLS:C0020653 HBA:12902" + "A calcareous tooth that is part of the upper jaw region. In mammals, the upper jaw teeth are attached to the maxilla." "NCIT:C49792 SCTID:422279005 EHDAA:8045 UMLS:C1710581 MA:0001909 EMAPA:17938" + "An osteocytelike cell with numerous processes, trapped in a lacuna in the cement of the tooth." "FMA:63003" + "The aggregation, arrangement and bonding together of a set of components to form a melanosome, a tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored." + "Any process that modulates the frequency, rate or extent of actin filament organization." + "Any process that activates or increases the frequency, rate or extent of DNA catabolic process." + "KUPO:0001030" + "The collection of muscles that are part of the larynx." "FMA:264611 FMA:46616 MESH:D007821 Wikipedia:Muscles_of_larynx" + "The process where neuronal precursors migrate tangentially in the telencephalon, primarily guided by interactions that do not require cell-cell contact." + "The process in which a monocyte acquires the specialized features of a dendritic cell, an immunocompetent cell of the lymphoid and hemopoietic systems and skin." "Wikipedia:Dendritic_cell" + "The orderly movement of a pericyte cell from one site to another." + "The ring of fibrocartilage and fibrous tissue forming the circumference of the intervertebral disc; surrounds the nucleus pulposus, which is prone to herniation when the annulus fibrosus is compromised." "MA:0000111 FMA:13551 EMAPA:32670 Wikipedia:Annulus_fibrosus_disci_intervertebralis BTO:0003629" + "Any process that modulates the frequency, rate or extent of hematopoietic stem cell migration." + "The enlargement or overgrowth of all or part of an organ due to an increase in size of muscle cells without cell division. In the case of striated muscle, this happens due to the additional synthesis of sarcomeric proteins and assembly of myofibrils." + "An arteriole that is part of a respiratory system [Automatically generated definition]." "MA:0001803 EMAPA:37568" + "Any process that results in the transfer of information from an epithelial cell to a mesenchymal cell and contributes to the progression of the lung over time from its initial formation to the mature organ." + "Any process that modulates the occurrence or rate of lymphocyte death by apoptotic process." + "The chemical reactions and pathways involving aldosterone, a corticosteroid hormone that is produced by the zona glomerulosa of the adrenal cortex and regulates salt (sodium and potassium) and water balance." + "An organ involved in reproduction." "SCTID:128181006 TGMA:0000591 UMLS:C0017420 MA:0001752 EMAPA:37731 WBbt:0008422 MESH:D005835 NCIT:C25177" + "The S-shaped body is the successor of the comma-shaped body that contributes to the morphogenesis of the nephron." "EMAPA:27756 ZFA:0005589" + "The progression of the female urethra over time from its initial formation to the mature structure. The female urethra is a renal system organ that carries urine from the bladder to outside the body, exiting above the vaginal opening." + "The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a water deprivation stimulus, prolonged deprivation of water." + "The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class I protein complex. The peptide antigen is typically, but not always, processed from a whole protein. Class I here refers to classical class I molecules." + "A pyramidal neuron with soma located in the cerebral cortex." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucagon stimulus." + "KUPO:0001031" + "The rhombencephalon (or hindbrain) is a developmental categorization of portions of the central nervous system in vertebrates. The rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. In the human embryo eight rhombomeres can be distinguished, from caudal to rostral: Rh7-Rh1 and the isthmus (the most rostral rhombomere). A rare disease of the rhombencephalon, 'rhombencephalosynapsis' is characterized by a missing vermis resulting in a fused cerebellum. Patients generally present with cerebellar ataxia. The caudal rhombencephalon has been generally considered as the initiation site for neural tube closure." "ZFA:0000569 FMA:295640 EHDAA2:0001630 EFO:0003440 TAO:0000569 BAMS:HB Wikipedia:Rhombencephalon CALOHA:TS-2118" + "A process in which a protein is transported to, or maintained in, a location within a cytoplasmic microtubule." + "A large pre-B-II cell is a pre-B-II cell that is proliferating and is Rag1-negative and Rag2-negative." + "A cell lining the outside of the blastocyst. After binding to the endometrium, trophoblast cells develop into two distinct layers, an inner layer of mononuclear cytotrophoblast cells and an outer layer of continuous multinuclear cytoplasm, the syncytiotrophoblast cells, which form the early fetal-maternal interface." "FMA:83028" + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amides." + "A mucosa that is part of a uterine tube infundibulum [Automatically generated definition]." "FMA:18357" + "The process whose specific outcome is the progression of a glandular epithelial cell over time, from its formation to the mature structure. A glandular epithelial cell is a columnar/cuboidal epithelial cell is a cell found in a two dimensional sheet with a free surface exposed to the lumen of a gland." + "The directed movement of an organelle to a specific location." + "Any apoptotic process in a neuron, the basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system." + "The tubular intestinal glands found in the mucosal membranes of the small intestine." "UMLS:C0227267 MA:0001552 EMAPA:35777 NCIT:C33565 FMA:15693 SCTID:52688008" + "A paired box protein PAX-5 that is encoded in the genome of human." "Reactome:R-HSA-158583 UniProtKB:Q02548" + "A plasmatocyte that derives from the larval lymph gland." + "Any process that activates or increases the frequency, rate or extent of lipid localization." + "A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm." "UMLS:C1708239 VHOG:0001223 Wikipedia:Germ_layer NCIT:C12950 GAID:1303 BTO:0000556 FMA:69069 UMLS:C0920502 XAO:0003011 MESH:D005855 AAO:0000480 EMAPA:36033 ZFA:0001122 TAO:0001122 NCIT:C54105 BILA:0000035" + "A membrane that is a (regional) part of the plasma membrane." + "The process that modulates the frequency, rate or extent of cell proliferation in the dorsal spinal cord." + + "A lymph node that is part of an abdomen [Automatically generated definition]." "EMAPA:35992 SCTID:245342005 FMA:12787 MA:0002827" + "A neural cell adhesion molecule 1 that is encoded in the genome of mouse." "UniProtKB:P13595" + "A cell derived from the mesoderm that is found at the periphery of the embryo." + "An fMet-Leu-Phe receptor that is encoded in the genome of human." "UniProtKB:P21462 Reactome:R-HSA-6800878 Reactome:R-HSA-6799143 Reactome:R-HSA-375450 Reactome:R-HSA-6800929 DTO:02100098" + "Any process that stops, prevents or reduces the frequency, rate or extent of cytoplasmic translational initiation." + "The aggregation, arrangement and bonding together of a set of components to form a presynapse." + "A protein that is a translation product of the human KISS1 gene or a 1:1 ortholog thereof." + "Any process that modulates the frequency, rate or extent of protein localization to synapse." + "The shape change of an epithelial cell from a columnar to squamous cell morphology that contributes to the shaping of the Malpighian tubule." + "Any basket cell that is part of a cerebellum." + "A cell that originates from the neural crest and differentiates into a pigment cell." "FMA:83377 BTO:0003217" + "Any process that decreases the rate, frequency, or extent of the progression of the dermatome over time, from its initial formation to the mature structure. The dermatome is the portion of a somite that will form skin." + "This is a cell found in the gastrointestinal tract of mammals and serves as a pacemaker that triggers gut contraction. ICCs mediate inputs from the enteric nervous system to smooth muscle cells and are thought to be the cells from which gastrointestinal stromal tumors (GISTs) arise." "BTO:0003914 FMA:86573" + "A lymphocyte of B lineage that is devoted to secreting large amounts of immunoglobulin." + "Nucleus located in the midbrain." "ZFA:0001665 SCTID:279285003 TAO:0002209" + "An ectonucleotide pyrophosphatase/phosphodiesterase family member 3 that is encoded in the genome of human." "UniProtKB:O14638 Reactome:R-HSA-8939012" + "The process whose specific outcome is the progression of the ectoderm over time, from its formation to the mature structure. In animal embryos, the ectoderm is the outer germ layer of the embryo, formed during gastrulation." + "KUPO:0001029" + "A precursor of the central nervous system that gives rise to glial cells only." "FBbt:00005145" + + "The chemical reactions and pathways resulting in the breakdown of a protein at a postsynapse." + "A cadherin that is a translation product of the human CDH5 gene or a 1:1 ortholog thereof." + "A receptor complex found on immature T cells consisting of a T cell receptor beta chain and the pre-TCR-alpha chain, along with additional signaling components including CD3 family members and additional signaling proteins." + "A polymer of five or six IgM core units each composed of two identical immunoglobulin heavy chains of the IgM isotype and two identical immunoglobulin light chains, held together by disulfide bonds; the individual IgM core units are held together via disulfide bonds with a single J chain polypeptide acting as a bridge between two of the polymeric units. Circulating IgM is present in the extracellular space, in mucosal areas or other tissues, or in the blood or lymph." + "The petrous portion of the temporal bone or pyramid is pyramidal and is wedged in at the base of the skull between the sphenoid and occipital bones. Directed medially, forward, and a little upward, it presents for examination a base, an apex, three surfaces, and three angles, and contains, in its interior, the essential parts of the organ of hearing. The petrous portion is among the most basal elements of the skull and forms part of the endocranium.[WP,unvetted]." "MA:0001477 GAID:234 VHOG:0001553 NCIT:C32316 EHDAA2:0001452 SCTID:361733004 Wikipedia:Petrous_part_of_the_temporal_bone MESH:D010579 EMAPA:17683 FMA:52871 UMLS:C1261761" + "An organ or element that is part of the pelvic region. Examples: reproductive organs (in some organisms), urinary bladder, bones of the pelvis." "MA:0000543 EMAPA:37275" + "A duct or series of ducts that transports sperm from the gonad. In mammals this is from the seminiferous tubules through rete testis, vas efferentia, epididymis, vas deferens, ejeculatory duct to the urethra." "TAO:0001268 FMA:55678 ZFA:0001268" + "A sperm cell that is not cabaple of motion (motility)." + + "Any negative regulation of cell differentiation that is involved in stem cell population maintenance." + "A circulating gamma-delta T cell that is CD27-positive and capable of producing IFN-gamma." + "A cell with a single nucleus." + "Any process in which a lipoprotein is transported to, or maintained in, a specific location." + "The process in which a relatively unspecialized cell acquires specialized features of a glomerular epithelial cell. Glomerular epithelial cells are specialized epithelial cells that form part of the glomerulus; there are two types, glomerular parietal epithelial cells and glomerular visceral epithelial cells." + "A cell that is part of an interstitum of a renal medulla." "KUPO:0001092" + "Any process that activates or increases the frequency, rate or extent of neuromuscular synaptic transmission." + "Any process that stops, prevents or reduces the frequency, rate or extent of intestinal epithelial cell development." + + "Any hepatocyte that is part of the liver lobule periportal region. These cells are primarily involved in oxidative energy metabolism." + "A secondary lens fiber cell that lacks a nucleus." "FMA:67561" + "Any process involved in the carrying out of an immune response by a neutrophil." + "Any process that modulates the frequency, rate or extent of differentiation of regulatory T cells." + "The process in which the anatomical structures of a nephron tubule are generated and organized. A nephron tubule is an epithelial tube that is part of the nephron, the functional part of the kidney." + "The process in which B cells acquire the specialized features of B-1b B cells. B-1b B cells are B-1 cells that do not express CD5." + "Binding to a major histocompatibility complex molecule; a set of molecules displayed on cell surfaces that are responsible for lymphocyte recognition and antigen presentation." + "Any process that stops, prevents, or reduces the frequency, rate or extent of pigment cell differentiation." + "A KLRB1-like protein that is a translation product of the human KLRB1 gene or a 1:1 ortholog thereof." + "The part of the pancreas that is part of the endocrine system and is made up of islet cells, which produce insulin, glucagon and somatostatin." "MA:0001582 EV:0100129 ZFA:0001260 EMAPA:35305 Wikipedia:Islets_of_Langerhans EFO:0002542 FMA:16018 CALOHA:TS-1302 TAO:0001260 SCTID:361339003 VHOG:0000049 BTO:0000650 NCIT:C32509" + "The process in which a precursor cell type acquires the specialized features of a NK T cell." + "The group of neuron cell bodies associated with the eighth cranial nerve during embryogenesis; splits in later development to form the cochlear and vestibular ganglia." "EMAPA:16982 BIRNLEX:2564 EFO:0003543 UMLS:C0037959 EHDAA:5569 XAO:0004142 MA:0001084 VHOG:0000696 EMAPA:17571 ZFA:0000588 neuronames:496 EHDAA:6653 TAO:0000588 EHDAA2:0002196" + "A mesoderm that has the potential to develop into a pronephros." "AAO:0011090 ZFA:0000067 TAO:0000067 VHOG:0001239 EFO:0003479 XAO:0000264" + "A protein that is encoded in the genome of some Eukaryota." + "An enterocyte that is a part of a vermiform appendix." + "The chemical reactions and pathways resulting in the formation of a protein in the cytoplasm. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein." + "Fusion of the membrane of a vesicle with the plasma membrane, thereby releasing its contents into the extracellular space." + "A pro-B cell that is CD22-positive, CD34-positive, CD38-positive and TdT-positive (has TdT activity). Pre-BCR is expressed on the cell surface. Cell is CD19-negative, CD20-negative, complement receptor type 2-negative and CD10-low. D-to-J recombination of the heavy chain occurs at this stage." + "Any process that modulates the frequency, rate or extent of cell proliferation that contributes to the shaping of the kidney." + "A Thy-1 membrane glycoprotein that has been processed by proteolytic cleavage." + "A peptide hormone secreting cell that secretes secretin stimulating hormone" + "A phagocyte formed by the fusion of mononuclear phagocytes." + "Any process that modulates the frequency, rate or extent of mononuclear cell proliferation." + "The progression of an epithelium of the uterus over time from its initial formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure." + "The process whose specific outcome is the progression of the primary sexual characteristics over time, from their formation to the mature structures. The primary sexual characteristics are the testes in males and the ovaries in females and they develop in response to sex hormone secretion." + "A cellular component that consists of an indeterminate number of proteins or macromolecular complexes, organized into a regular, higher-order structure such as a polymer, sheet, network or a fiber." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of CD4." + "The process in which angiotensinogen metabolites in the bloodstream modulate the force with which blood passes through the circulatory system. The process begins when renin is released and cleaves angiotensinogen." + "Any process contributing to anergy in B cells, a state of functional inactivation which is part of B cell tolerance induction." + "An eosinophil with a ring-shaped nucleus that is resident in the lung parenchyma. In mouse, lung parenchyma resident eosinophils are IL-5-independent Siglec-F(intermediate) CD62L+ CD101(low). In human, they are Siglec-8+ CD62L+ IL-3R(low)." + "Any process that activates or increases the frequency, rate or extent of the regulated release of mucus from a cell or a tissue." + "An OFF-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the outer half of the inner plexiform layer. The cell has a diffuse axon terminal with varicosities in sublaminae 1 and 2 of the inner plexiform layer." + "The part of the trunk that is in the dorsum[cjm]." "EMAPA:35162 FMA:25056 Wikipedia:Human_back MA:0000020" + "The orderly movement of a neural crest cell from one site to another that will contribute to the morphogenesis of the outflow tract." + "The spherical enlargement at the base of each semicircular canal where they connect with the utricle, containing the crista ampullaris which detects movement of the fluid within the canals." "MA:0002770 Wikipedia:Osseous_ampullae SCTID:279759001 EMAPA:32831" + "Any process that activates or increases the frequency, rate or extent of behavior, the internally coordinated responses (actions or inactions) of whole living organisms (individuals or groups) to internal or external stimuli." + "A chemokine receptor that is a translation product of the human CCR1 or CCR3 genes, the mouse CCR1L1 gene, 1:1 orthologs thereof, or a semi-ortholog thereof." "PIRSF:PIRSF501024" + "A pyramidal neuron which lacks a clear tuft formation but extends to large radial distances." + "The progression of the aorta over time, from its initial formation to the mature structure. An aorta is an artery that carries blood from the heart to other parts of the body." + "Any process that modulates the frequency, rate or extent of urothelial cell proliferation." + "Passages within the liver for the conveyance of bile. Includes right and left hepatic ducts even though these may join outside the liver to form the common hepatic duct." "TAO:0005169 UMLS:C0005401 GAID:287 MESH:D001653 SCTID:362193005 NCIT:C12677 MA:0001630 FMA:15766 ZFA:0005169" + "A type of interneuron that has two clusters of dendritic branches that originate directly from the soma and extend in opposite directions and axons that form a plexus which spreads widely. Compared to bipolar neurons, bitufted neurons have branching that occur close to the soma." "ILX:0777212" + "Any process that activates or increases the frequency, rate or extent of neuron differentiation." + "Any process that decreases the rate, frequency or extent of cell differentiation that contributes to the progression of the placenta over time, from its initial condition to its mature state." + "Any microtubule bundle that is part of a cytoplasm." + "The human equivalent of a DN2 thymocyte; typically contains two phases, in the latter of which these thymocytes begin the process of beta selection." + "Any process that activates or increases the frequency, rate or extent of cerebellar neuron development." + "The lipid bilayer surrounding an exocytic vesicle." + "A neuron that has its soma located in the mammillary body." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the assembly of actin filament bundles." + "A complement receptor type 2 that is encoded in the genome of human." "UniProtKB:P20023" + "A neuroglial cell of the peripheral nervous system which forms the insulating myelin sheaths of peripheral axons." "FMA:62121 CALOHA:TS-0898" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of glutamate." + "A peptide hormone secreting cell that secretes bombesin stimulating hormone." + "The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones." "Wikipedia:Anabolism" + "A proximal carpal endochondral element that is composed primarily of cartilage tissue." + "The chemical reactions and pathways resulting in the breakdown of organic acids, any acidic compound containing carbon in covalent linkage." + "The multiplication or reproduction of myoblasts, resulting in the expansion of a myoblast cell population. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers." + "A developmental process, independent of morphogenetic (shape) change, that is required for the hindbrain to attain its fully functional state. The hindbrain is the region consisting of the medulla, pons and cerebellum. Areas of the hindbrain control motor and autonomic functions." + "The output neuron of the cerebellar cortex." "BTO:0001011 CALOHA:TS-0845 FMA:67969" + "A longitudinal muscle layer of muscular coat that is part of a small intestine smooth muscle." "FMA:14936 EMAPA:37563 SCTID:59150006 MA:0001561" + "A C-type lectin domain family 6 member A that is encoded in the genome of mouse." "UniProtKB:Q9JKF4" + "A small, often microscopic, tissue element in the form of a small beam, strut or rod, generally having a mechanical function, and usually but not necessarily composed of dense collagenous tissue. On histological section, a trabecula can look like a septum, but in three dimensions they are topologically distinct, with trabeculae being roughly rod or pillar-shaped and septa being sheet-like. Trabeculae are usually composed of dense fibrous tissue, i.e. mainly of collagen, and in most cases provide mechanical strengthening or stiffening to a soft solid organ, such as the spleen. They can be composed of other materials, such as bone or muscle[WP]." "BTO:0002501 FMA:85273 Wikipedia:Trabecula" + "Any apoptotic process in a glomerular visceral epithelial cell." + "A supportive cell with a small, oval-shaped body and one to five telopodes. Telopodes are cytoplasmic protrusions from tens to hundreds of micrometers long and mostly below 0.2 microns of caliber." + "Any nerve that innervates the clitoris." "EMAPA:35044" + "Any process that stops, prevents or reduces the frequency, rate or extent of glial cell migration." + "The long descending limb starts in the inner stripe of the outer medulla and extends into the inner medulla[GO]." + "The developmental process pertaining to the initial formation of the mesonephros." + + "Any process that activates or increases the frequency, rate or extent of cell differentiation." + "Any process that modulates the frequency, rate or extent of natural killer T cell activation." + "A sialic acid-binding Ig-like lectin 6 that is encoded in the genome of human." "UniProtKB:O43699" + "A high endothelial venule that is located in a Peyer's patch in the small intestine." + "The process whose specific outcome is the progression of the juxtaglomerular apparatus over time, from its formation to the mature structure. The juxtaglomerular apparatus is an anatomical structure that lies adjacent to the glomerulus and regulates kidney function." + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glycogen." + "A renal vein that drains the right kidney." "NCIT:C52695 UMLS:C0508000 EMAPA:37381 FMA:14335 MA:0002212 SCTID:116357001" + + + "A perichondrial fibroblast that is part of the lung." + "KUPO:0001058" + "Subdivision of skeleton that is the collection of all skeletal elements in a manus, which is the distal section of the anterior forelimb skeleton consisting of the mesopodium, the metapodium and the acropodium (e.g. including the wrist, palm, and fingers)[Phenoscape]." "EHDAA2:0002227 VSAO:0005020 EMAPA:32643 FMA:24159" + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving dopamine." + "Any process that activates or increases the frequency, rate, or extent of neutrophil apoptotic process." + "A thymocyte that has a T cell receptor consisting of a gamma chain that has as part a Vgamma3 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-negative. This cell-type is found in the fetal thymus with highest numbers occurring at E17-E18." + "Any apoptotic process in a dendritic cell, a cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation." + "The series of molecular signals in which a cell uses calcium ions released from an intracellular store to convert a signal into a response." + "Any process that modulates the frequency, rate or extent of organelle assembly." + + "Any process that stops, prevents or reduces the frequency, rate or extent of flagellated sperm motility." + + "A complement component C1q receptor that is encoded in the genome of human." "UniProtKB:Q9NPY3" + "The process in which the anatomical structures of the metanephric nephron are generated and organized. A metanephric nephron is the functional unit of the metanephros." + "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts."@en + "The multiplication or reproduction of brown fat cells by cell division, resulting in the expansion of their population. A brown fat cell is a fat cell found the thermogenic form of adipose tissue found in newborns of many species." + "Any lung endothelial cell that is part of a microvascular endothelium." + "The controlled release of histamine by a cell, in which the histamine acts as a neurotransmitter." + "Any process that activates or increases the frequency, rate or extent of deoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid." + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids." + "The series of events in which a visible light stimulus is received by a cell and converted into a molecular signal. A visible light stimulus is electromagnetic radiation that can be perceived visually by an organism; for organisms lacking a visual system, this can be defined as light with a wavelength within the range 380 to 780 nm." + "Reactions triggered in response to the presence of a symbiont that act to protect or prevent damage to the host." + "A mucosa that is part of a sigmoid colon [Automatically generated definition]." "FMA:15026" + "Either of the pair of major vessels which arise from the renal hilus and return blood from the kidneys, suprarenal gland and the ureter to the inferior vena cava." "EHDAA2:0001602 SCTID:116358006 EMAPA:28376 GAID:544 Wikipedia:Renal_vein EHDAA:8722 MESH:D012082 MA:0002210 NCIT:C33462 UMLS:C0035092 galen:RenalVein BTO:0002681 FMA:14334" + "The process in which the wraps of cell membrane that constitute myelin are laid down around an axon by Schwann cells in the peripheral nervous system." + "A neuron which conveys sensory information centrally from the periphery." "FMA:87653" + "A nucleate quality inhering in a bearer by virtue of the bearer's having one nucleus." + "A chemokine receptor that is a translation product of the human CCR6 gene or a 1:1 ortholog thereof. The preferred ligand is CCL20." "IUPHARobj:63" + "Any process that activates or increases the frequency, rate or extent of placenta blood vessel development." + "A somatotropin hormone family member that is a translation product of the human PRL gene or a 1:1 ortholog thereof." + "An endocrine cell found in the pyloric gland mucosa (antral mucosa) of the stomach of mammals and responsible for the secretion of gastrin and enkephalin. Most abundant in pyloric antrum, pyramidal in form with a narrow apex bearing long microvilli." "FMA:67609 BTO:0004108" + "The mesonephric nephron epithelium is a tissue that covers the surface of a nephron in the mesonephros[GO]." + "A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body." "Wikipedia:Cilium FMA:67181 NIF_Subcellular:sao787716553" + "A submucosa that is part of a intestine." "FMA:15696" + "Cartilage tissue that is not mineralized." "XAO:0004044 VSAO:0000089" + "Any process that modulates the frequency, rate or extent of a defense response." + "A cell capable of producting norepiniphrine. Norepiniphrine is a catecholamine with multiple roles including as a hormone and a neurotransmitter. In addition, epiniphrine is synthesized from norepiniphrine by the actions of the phenylethanolamine N-methyltransferase enzyme." + "Anatomical system that is involved in the production of hematopoietic cells." "MAT:0000022 EMAPA:35402 BTO:0000570 XAO:0000122 VHOG:0001624 NCIT:C12909 Wikipedia:Haematopoiesis MIAA:0000022 CALOHA:TS-0449 MA:0002434 FMA:9667 EFO:0000798 TAO:0005023 GAID:1008 MESH:D006413 ZFA:0005023 SCTID:362587009 UMLS:C0018957 EV:0100045 AAO:0011002" + "A lymphocyte of B lineage that has gotten larger after being stimulated by an antigen." "FMA:83031 EFO:0005293" + "A columnar cell of the colon that is part of the colonic epithelium." "FMA:263114" + "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time."@en + "A proximal mesopodial endochondral element that is part of a forelimb." + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving any hormone." + "FMA:15704" + "Mucus is a bodily fluid consisting of a slippery secretion of the lining of the mucous membranes in the body. It is a viscous colloid containing antiseptic enzymes (such as lysozyme) and immunoglobulins. Mucus is produced by goblet cells in the mucous membranes that cover the surfaces of the membranes. It is made up of mucins and inorganic salts suspended in water." "GAID:1164 galen:Mucus ENVO:02000040 MESH:D009093 UMLS:C0026727 NCIT:C13259 Wikipedia:Mucus CALOHA:TS-2144 FMA:66938" + "A renal beta-intercalated cell that is part of the renal connecting tubule." + "An epidermal cell with apical microvilli or a single apical projection have synaptic associations with nerve fibres in the epidermis." + "An endothelium of vein that is part of a respiratory system [Automatically generated definition]." "MA:0001811 EMAPA:37585" + "The process whose specific outcome is the progression of a pigment cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a pigment cell fate." + "Any process that modulates the frequency, rate, or extent of an adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains. An example of this process is found in the Gnathostomata." + "Any process that stops, prevents, or reduces the frequency, rate or extent of eye photoreceptor development." + "Cranial nerve that branches into the supraorbital (supplying the skin of the eye region and the lateral line organs here), the palatine (to the roof of the buccal cavity), and the hyomandibular (dividing into the jugular and mental branches)." "neuronames:551 HBA:9328 BAMS:Viin UMLS:C0015462 SCTID:362460007 AAO:0010472 MBA:798 BM:Pons-VIIN EHDAA2:0000489 Wikipedia:Facial_nerve EHDAA:3729 GAID:719 VHOG:0000706 XAO:0003094 BAMS:7n MESH:D005154 BIRNLEX:827 MA:0001091 FMA:50868 BAMS:VIIn NCIT:C12714 ZFA:0000664 EMAPA:17796 BAMS:nVII TAO:0000664" + + "Any process that activates or increases the frequency, rate or extent of osteoclast development." + "Immature CD8_alpha-low Langerhans cell is a CD8_alpha-low Langerhans cell that is CD80-low, CD86-low, and MHCII-low." + "The process in which the anatomical structure of the pericardium is generated and organized." + "OBSOLETE, use term from Plant Ontology. A cell formed after asymmetric division of root epidermal cell that does not give rise to a root hair." + "An adult endothelial progenitor cell characterised in vivo by homing to ischemic sites and paracrine support of angiogenesis. They may form discrete colonies." + "A cell type that encapsulates the capillaries and venules in the kidney. This cell secretes mesangial matrix that provides the structural support for the capillaries." "BTO:0000853 FMA:70972 MESH:D050527 CALOHA:TS-0617" + "The change in morphology and behavior of a neutrophil resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor, leading to the initiation or perpetuation of an immune response." + "Any process that modulates the frequency, rate or extent of dendritic cell dendrite assembly." + "The differential increase in size or mass of the prostate gland that contributes to the gland attaining its form." + "Catalysis of the reaction: ATP + [tyrosine-3-monooxygenase] = ADP + phospho-[tyrosine-3-monooxygenase]." "RHEA:17133 MetaCyc:2.7.11.6-RXN EC:2.7.11.6" + "The division of the forebrain that develops from the foremost primary cerebral vesicle." "DHBA:10389 BAMS:Di AAO:0010481 NCIT:C12456 XAO:0000013 EV:0100194 HBA:4391 MBA:1129 MAT:0000420 ZFA:0000101 EFO:0000911 UMLS:C0012144 EHDAA:3472 VHOG:0000318 BAMS:Zh. MESH:D004027 BIRNLEX:1503 GAID:618 BTO:0000342 TAO:0000101 BAMS:DiE BM:Die MIAA:0000420 neuronames:288 EHDAA:1969 BAMS:DI EHDAA:2645 DMBA:16308 EMAPA:16896 BAMS:IB Wikipedia:Diencephalon SCTID:279328001 EHDAA2:0000385 CALOHA:TS-0199 PBA:128013010 MA:0000171 FMA:62001" + "The paracortex and interfollicular cortex of the lymph node in which T lymphocytes home to survey dendritic cells." "SCTID:326870003 MA:0002852 EMAPA:37663" + "Any process that stops, prevents, or reduces the frequency, rate, or extent of B cell deletion." + "An adventitia that is part of a esophagus." "FMA:63006 SCTID:85950006" + "A process involving any mechanism for tolerance induction in T cells." + "The process in which a neuroblast acquires the specialized structural and functional features of a dopaminergic neuron, a neuron that secretes dopamine." + "A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins." + "Any process that modulates the developmental process pertaining to the initial formation of the ureteric bud from the Wolffian duct." + "A leukosialin that is encoded in the genome of mouse." "UniProtKB:P15702" + "The aggregation, arrangement and bonding together of a set of components to form a postsynaptic membrane, a specialized area of membrane facing the presynaptic membrane on the tip of the nerve ending and separated from it by a minute cleft (the synaptic cleft)." + "The process whose specific outcome is the progression of the lateral line nerve over time, form its formation to the mature structure. Lateral line nerves project primarily to an octavolateralis column in the hindbrain that consists of the medial octavolateralis nucleus (MON), the caudal octavolateralis nucleus, and the magnocellular nucleus." + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amino acid stimulus. An amino acid is a carboxylic acids containing one or more amino groups." + "A vasculature that is part of a kidney." "EMAPA:28457 ZFA:0005305 TAO:0005305" + "GC_ID:1" + "Any process that activates or increases the frequency, rate or extent of amniotic stem cell differentiation." + "A vimentin that is encoded in the genome of mouse." "UniProtKB:P20152" + "The process in which the anatomical structures of the hindgut are generated and organized." + "EHDAA2:0003425" + "The embryo and its adnexa (appendages or adjunct parts) or associated membranes (i.e. the products of conception) The conceptus includes all structures that develop from the zygote, both embryonic and extraembryonic. It includes the embryo as well as the embryonic part of the placenta and its associated membranes - amnion, chorion (gestational sac), and yolk sac[WP]." "UMLS:C1516779 EHDAA2:0003235 NCIT:C34131 Wikipedia:Conceptus AEO:0000194 BTO:0003834 EMAPA:36040 EHDAA2:0000001" + "Any process of the immune system that executes a component of an immune response. An effector immune process takes place after its activation." + "Subdivision of urinary system which consists of the kidney and the ureters." "FMA:45658 NCIT:C61107 galen:UpperUrinaryTract SCTID:181413006" + "Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not." "galen:BodyFluid FMA:280556 EMAPA:37441 Wikipedia:Body_fluid MESH:D001826 GAID:266 BIRNLEX:20" + "The dead keratin-filled squamous cell of the stratum corneum. This cell type lacks a nucleus." "BTO:0001943 FMA:68650" + "A high affinity immunoglobulin gamma Fc receptor I that is encoded in the genome of mouse." "UniProtKB:P26151" + "A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells." "Wikipedia:Melanosome" + "An epithelium that is part of a tongue [Automatically generated definition]." "EHDAA2:0004598 BTO:0000992 MA:0001592 UMLS:C1710436 FMA:284658 NCIT:C49300 CALOHA:TS-1051 EMAPA:17881" + "Sum total of mesenchyme in the embryo." "EMAPA:16097 EHDAA:177 EHDAA2:0001113" + "FMA:67951" + "A multicellular structure that is a part of an organ." "EFO:0000635 AAO:0011124 BIRNLEX:16 FMA:82472 SCTID:113343008 SCTID:91717005" + "The ventral cochlear nucleus (or anterior, or accessory), placed between the two divisions of the cochlear nerve, is on the ventral aspect of the inferior peduncle. Composed of several regions of distinct cell types, this nucleus serves primarily as a relay station for ascending auditory information. Bushy cells in the anterior ventral cochlear nucleus (AVCN), which receive end bulbs of held from auditory nerve fibers, project to the superior olivary complex through the trapezoid body and intermediate acoustic stria. Other cell types project to the lateral lemniscus and the inferior colliculus directly. [WP,unvetted]." "DHBA:12439 Wikipedia:Ventral_cochlear_nucleus BAMS:VCO HBA:9531 BM:CV FMA:54621 BIRNLEX:2567 neuronames:722 BAMS:VC MBA:101 SCTID:280178008 UMLS:C0175500" + "Any process that activates or increases the frequency, rate or extent of fibroblast apoptotic process." + "Any process that modulates the frequency, rate or extent of mesenchymal cell proliferation. A mesenchymal cell is a cell that normally gives rise to other cells that are organized as three-dimensional masses, rather than sheets." + "Derived from the Greek word pyren (the pit of a stone fruit), this is a transient nucleated cell type that results from exclusion of the nucleus from the primitive erythrocyte." + "Any process that stops, prevents or reduces the frequency, rate or extent of oogenesis." + "The major postaxial endochondral element in the posterior zeugopod[Phenoscape]." + "The process in which a relatively unspecialized cell acquires the specialized features of a DN2 thymocyte. A DN2 thymocyte is a CD4-,CD8- thymocyte that is also CD44+,CD25-." + "Any process that stops, prevents, or reduces the frequency, rate or extent of myotube cell migration." + "A muscle organ that attaches the tongue to some other structure." "EHDAA:9148 EHDAA2:0002063 EMAPA:18275 SCTID:244782006 VHOG:0000825 FMA:46699 MA:0002296" + "The process in which immunoglobulin gene segments are recombined within a single locus utilizing the conserved heptamer and nonomer recombination signal sequences (RSS). For immunoglobulin heavy chains V, D, and J gene segments are joined, and for immunoglobulin light chains V and J gene segments are joined." + "A cholecystokinin that is encoded in the genome of mouse." "UniProtKB:P09240" + "An endothelial cell that is part of a hepatic portal vein." "EFO:0010704" + "A portion of smooth muscle tissue that is part of a stomach [Automatically generated definition]." "BTO:0001818 MA:0001627 EMAPA:35823" + "A sst GABAergic cortical interneuron that also expresses Chodl. These neurons are rare and correspond to the only known cortical interneurons with long-range projection." + + "The process in which neuroepithelial cells in the neural tube acquire specialized structural and/or functional features of ventral spinal cord interneurons. Ventral spinal cord interneurons are cells located in the ventral portion of the spinal cord that transmit signals between sensory and motor neurons and are required for reflexive responses. Differentiation includes the processes involved in commitment of a cell to a specific fate." + "Any process that modulates the frequency, rate or extent of growth of an organ of an organism." + "A follicular B cell that is IgD-positive, CD23-negative, and CD38-negative. This naive cell type is activated in the extrafollicular areas through interaction with interdigitating dendritic cells and antigen-specific CD4-positive T cells." + "Any of the nuclei that comprise the superior olivary complex (superior olive). This includes both the primary nuclei such as the lateral and medial nuclei, as well as periolivary nuclei." "SCTID:369024009 FMA:72246" + "Any process that stops, prevents or reduces the frequency, rate or extent of hyaluronan biosynthetic process." + "The process in which a relatively unspecialized cell acquires specialized features of a lens fiber cell, any of the elongated, tightly packed cells that make up the bulk of the mature lens in the camera-type eye. The cytoplasm of a lens fiber cell is devoid of most intracellular organelles including the cell nucleus, and contains primarily crystallins, a group of water-soluble proteins expressed in vary large quantities." + "Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts." "ZFA:0005621 EMAPA:35179 MA:0002780 MESH:D001842 UMLS:C0391978 NCIT:C13076 XAO:0004040 Wikipedia:Bone_tissue VSAO:0000047 FMA:224804 galen:BoneTissue CALOHA:TS-2011" + "An epithelium that is part of a vestibular labyrinth." "BTO:0005581 EMAPA:32884 EMAPA:35921 FMA:75606 MA:0002892 RETIRED_EHDAA2:0000834" + "A process in which RNA is transported to, or maintained in, a specific location." + "A smooth muscle tissue that is part of a hypodermis." "FMA:77862" + "Any of the three large depressions in the posterior, middle, and anterior aspects of the floor of the cranial cavity." "FMA:321144" + "The process in which immune receptor genes are diversified through somatic mutation." + "FMA:83856" + "Any gland that is part os the respiratory system." + "Combining with a glucocorticoid and transmitting the signal within the cell trigger a change in cell activity or function." + "The process in which a naive natural killer cell acquires the specialized features of an effector natural killer T cell as part of an immune response." + "Anatomical junction where subdivisions of two or more neural trees interconnect with one another to form a network through which nerve fibers of the constituent nerve trees become regrouped; together with other nerve plexuses, nerves and ganglia, it constitutes the peripheral nervous system. Examples: cervical nerve plexus, brachial nerve plexus, sacral nerve plexus[FMA]." "EMAPA:37683 BTO:0000205 AEO:0000138 FMA:5901 EHDAA2:0003138 Wikipedia:Nervous_system_plexus MA:0002407 SCTID:122455009 NCIT:C12929 UMLS:C0501403 EHDAA:3780" + "Cranial neural crest which gives rise to the glossopharyngeal ganglion." "TAO:0007066 EHDAA:660 EHDAA2:0000714 ZFA:0007066" + "Any process that modulates the frequency, rate or extent of smooth muscle cell proliferation." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of a humoral immune response." + "EMAPA:32720" + "The process in which the anatomical structures of the mesonephros are generated and organized." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucocorticoid stimulus. Glucocorticoids are hormonal C21 corticosteroids synthesized from cholesterol with the ability to bind with the cortisol receptor and trigger similar effects. Glucocorticoids act primarily on carbohydrate and protein metabolism, and have anti-inflammatory effects." + "A organ system process carried out by any of the organs or tissues of neurological system." + "Any endocardium that is part of the left ventricle of the heart." "SCTID:191004004 EHDAA2:0002182 EMAPA:17338 FMA:9559 VHOG:0001233" + "A shape quality inhering in a bearer by virtue of the bearer's being marked by narrow lines or grooves, usually parallel, that are oriented obliquely relative to the long axis of the bearer." + "Diencephalic white matter (tract) which is comprised of retinal ganglion cell axons after which they have passed through the optic chiasm[ZFA]. Predominantly white matter structure found in diencephalon consisting of fibers originating in the retina. The optic tract is considered to extend from the point of the optic chiasm and terminates largely, although not exclusively, in the lateral geniculate complex. Other fibers end in the superior colliculus and other structures in the diencephalon, midbrain and brainstem (MM)[NIF]." "SCTID:280952003 GAID:735 UMLS:C0152405 neuronames:460 DHBA:10589 MESH:D014795 ZFA:0000252 XAO:0004101 MA:0001099 BM:Tel-OT NCIT:C33218 BIRNLEX:1684 Wikipedia:Optic_tract DMBA:17785 TAO:0000252 MBA:125 BAMS:opt EMAPA:35617 HBA:9309 FMA:62046 VHOG:0001164" + "The directed movement of organic substances into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. An organic substance is a molecular entity that contains carbon." + "Any process that modulates the frequency, rate or extent of chromosome segregation, the process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets." + "Any process that activates or increases the frequency, rate or extent of embryonic pattern specification." + "Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." + "The myosin-based contraction and retraction of a pseudopodium." + "FMA:62449" + "a KNDy neuron that is located in the rostral periventricular region of the third ventricle." + "Any process that activates or increases the frequency, rate or extent of the regulated release of corticotropin hormone from a cell." + "Immune response taking place in the gut-associated lymphoid tissue (GALT). GALT includes Peyer's patches, appendix, and solitary lymph nodules." + "Anatomical structure that is part of an embryo." "XAO:0003042 CALOHA:TS-2110 SCTID:667009 NCIT:C13229 BILA:0000034 RETIRED_EHDAA2:0003169 BTO:0000174 UMLS:C0013948 MESH:D004628 TAO:0001105 AAO:0000138 EFO:0000461 GAID:407 FMA:69067 VSAO:0000178 ZFA:0001105" + "A bone that is part of a pelvic complex. Examples: pubis, ischium, fot phalanx, any tarsal bone, any bone of the pelvic fin or girdle." "EMAPA:35934 MA:0000660" + "A collection of two or more connected limb segments. Examples: arm (comprising stylopod and zeugopod regions)." + "A stromal cell of the ovarian medulla." "FMA:256171" + "EMAPA:32721" + "A neuron which sends impulses peripherally to activate muscles or secretory cells." + "The third branchial arch contributes to the development of the hyoid bone, stylopharyngeus muscle, inferior parathyroid gland, and thymus." "VHOG:0000298 EMAPA:16399 EHDAA:1080 XAO:0000447 AAO:0010365 EHDAA2:0000069 FMA:293029 TAO:0001598 SCTID:308769006 ZFA:0001606" + "An epithelium that is part of a thymus, forming a supporting framework[MP,modified]." "ZFA:0005779 EMAPA:35864 UMLS:C1711423 NCIT:C45713 VHOG:0001426 BTO:0001836 EHDAA2:0002019 MA:0000768 CALOHA:TS-1040" + "The progression of the gallbladder over time, from its initial formation to the mature structure. The gallbladder is a cavitated organ that stores bile." + "Any protein complex that is part of a membrane and which functions as a cargo receptor." + "A lymphatic vessel that is part of a lung." "SCTID:321862009 FMA:234006" + "A secretion that is part of a endocrine pancreas [Automatically generated definition]." "MA:0002517 UMLS:C1518866 NCIT:C33255" + "FMA:66178" + "A vein that drains a lacrimal gland." "FMA:51779 SCTID:149582008" + "Mesenchyme that is part of a developing eyelid." "EMAPA:32759" + "A non-connected functional system that is composed primarily of a gland." "EHDAA2:0002223" + "Sweat that is produced by the glands of the axilla." "FMA:63085" + "The process whose specific outcome is the progression of a cardiac atrium over time, from its formation to the mature structure. A cardiac atrium receives blood from a vein and pumps it to a cardiac ventricle." + "The directed extracellular movement of amino acids." + "A tumor necrosis factor ligand superfamily member 5 that has been processed by proteolytic cleavage." + "The orderly movement of a cell from one site to another that will contribute to the formation of new blood vessels in the heart from pre-existing blood vessels." + "The process in which the structures of an oocyte are generated and organized. This process occurs while the initially relatively unspecialized cell is acquiring the specialized features of an oocyte." + "Any process that activates or increases the frequency, rate or extent of nurse cell apoptotic process." + "A cell within the follicle of an ovary." "FMA:70589 EMAPA:31247" + "Any process that activates or increases the frequency, rate or extent of the regulated release of insulin." + "An insulin gene translation product that is encoded in the genome of human." "UniProtKB:P01308" + "An external ear that is in the right side of a multicellular organism." "FMA:53643 EMAPA:37361 SCTID:368567003" + "A mesenchyme that is part of a amnion." "EMAPA:16265 VHOG:0000622 EHDAA2:0000118 EMAPA:16111 EHDAA:140" + "Enables the calcium concentration-regulatable energy-independent passage of cations across a lipid bilayer down a concentration gradient." "Reactome:R-HSA-9717383" + "A sphenoid endochondral element that is composed primarily of cartilage tissue." "EHDAA2:0001888" + "A small outgrowth of the pharyngeal epithelium that is the site of lymphocyte cell production[ZFA]. [PMID]." "EHDAA:2969 TAO:0001077 ZFA:0001077 EMAPA:17523 EFO:0003622 EHDAA2:0002023" + "Neurotransmitter receptor activity occurring in the postsynaptic membrane that is involved in regulating postsynaptic membrane potential, either directly (ionotropic receptors) or indirectly (e.g. via GPCR activation of an ion channel)." + "A quality inhering in a structure by virtue of it consisting of many of repeated, similar or identical subunits, arranged in some orderly array." + "Bone tissue that has a regular parallel alignment of collagen into sheets (lamellae) and is mechanically strong." "Wikipedia:Bone#Woven_or_lamellar galen:LamellarBone MA:0002781 FMA:224806 EMAPA:37625" + "Gr1-high monocyte that lacks MHC-II receptor complex." + "Subdivision of skeleton that consists of endochondral elements distal to the zeugopodial skeletal elements which constitute the proximal region of the posterior autopod skeleton[PHENOSCAPE:ad]." "EMAPA:19133 VHOG:0001160 VSAO:0005024 AAO:0000220 FMA:71339 MA:0000050 XAO:0003211 Wikipedia:Tarsus_(skeleton) SCTID:264228001 GAID:1223 SCTID:361796005" + "A rod-shaped cell found in 3 or 4 rows that lie adjacent to and support the outer hair cells." "FMA:75727" + "Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified]." "SCTID:361725000 UMLS:C0222645 Wikipedia:Axial_skeleton EMAPA:17214 NCIT:C32172 AAO:0000963 XAO:0004011 VSAO:0000056 MA:0000308" + "The process in which tubulin alpha-beta heterodimers begin aggregation to form an oligomeric tubulin structure (a microtubule seed). Microtubule nucleation is the initiating step in the formation of a microtubule in the absence of any existing microtubules ('de novo' microtubule formation)." "Wikipedia:Microtubule_nucleation" + "The nucleus of the female germ cell, a reproductive cell in females." + "A nuclear factor NF-kappa-B p100 subunit that is encoded in the genome of human." "UniProtKB:Q00653 Reactome:R-HSA-2677931" + "The process that gives rise to the cerebellar cortex. This process pertains to the initial formation of a structure from unspecified parts. The cerebellar cortex is a thin mantle of gray matter that covers the surface of each cerebral hemisphere. It has a characteristic morphology with convolutions (gyri) and crevices (sulci) that have specific functions. Six layers of nerve cells and the nerve pathways that connect them comprise the cerebellar cortex. Together, these regions are responsible for the processes of conscious thought, perception, emotion and memory as well as advanced motor function." + "Organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell." "Wikipedia:Placenta NCIT:C13272 MAT:0000279 VHOG:0001266 UMLS:C0032043 EV:0100119 MA:0000386 BTO:0001078 SCTID:181455002 MIAA:0000279 MESH:D010920 FMA:63934 GAID:379 CALOHA:TS-0799 EFO:0001407 EMAPA:35689" + "A syndecan-1 that is encoded in the genome of human." "UniProtKB:P18827" + "EMAPA:16092 ZFA:0000417 TAO:0000417 EFO:0003438 EHDAA2:0000674 EHDAA:898 EMAPA:16755" + "A naris that is located inside the nasal cavity and connects to the pharynx." "NCIT:C32856" + "A retinal neural layer that is immediately adjacent to the S2 and S4 layers and comprises 20 percent of the inner plexiform layer of retina." "CP:0000115" + "The process that gives rise to a glomerular capillary. This process pertains to the initial formation of a structure from unspecified parts." + "Any process that stops, prevents or reduces the frequency, rate or extent of neuromuscular synaptic transmission." + "A portion of connective tissue that is part of a hindlimb stylopod [Automatically generated definition]." "MA:0000683 EMAPA:37325" + "The biological process whose specific outcome is the progression of a bronchiole from an initial condition to its mature state. This process begins with the formation of the bronchiole and ends with the mature structure. A bronchiole is the first airway branch that no longer contains cartilage; it is a branch of the bronchi." + "An interleukin-3 receptor class 2 alpha chain that is encoded in the genome of mouse." "UniProtKB:P26952" + "The process in which a relatively unspecialized cell acquires specialized structural and/or functional features of a thyroid-stimulating hormone-secreting cell. A thyroid-stimulating hormone-secreting cell is a basophil cell of the anterior pituitary that produces thyroid-stimulating hormone, thyrotrophin." + "Any process that stops, prevents, or reduces the frequency, rate or extent of myeloid dendritic cell activation." + "SCTID:277967008" + "Any process that decreases the rate, frequency, or extent of prostatic bud formation, the morphogenetic process in which a region of the fetal urogenital sinus epithelium is specified to become the prostate, resulting in prostate bud outgrowth." + "Cardiac muscle cells are striated muscle cells that are responsible for heart contraction. In mammals, the contractile fiber resembles those of skeletal muscle but are only one third as large in diameter, are richer in sarcoplasm, and contain centrally located instead of peripheral nuclei." "MESH:D032383 BTO:0001539 CALOHA:TS-0115 FMA:14067" + "A blood vessel that carries blood from the capillaries toward the heart." "FMA:86188 EMAPA:35932 MA:0000066" + "The progression of the renal tubule over time from its formation to the mature form. A renal tubule is a tube that filters, re-absorbs and secretes substances to rid an organism of waste and to play a role in fluid homeostasis." + "A recently activated CD4-positive, alpha-beta T cell with the phenotype HLA-DRA-positive, CD38-positive, CD69-positive, CD62L-negative, CD127-negative, and CD25-positive." + "The process in which specialized cells known as osteoclasts degrade the organic and inorganic portions of bone, and endocytose and transport the degradation products." "Wikipedia:Bone_resorption" + "A region or zone on the surface of an organism that encompasses skin and any adnexa, down through muscles and bounded by underlying skeletal support structures." + "A thin sheet of small neurons located in the wall of the third ventricle, a composite structure of the hypothalamus." "TAO:0000260 FMA:84354 Wikipedia:Periventricular_nucleus ZFA:0000260" + "A secretory duct that transports sperm from the testis. In mammals this is a continuation of the epididymis and ends in the prostatic urethra where it terminates to form ejaculatory duct." "UMLS:C0042360 NCIT:C12813 MESH:D014649 EMAPA:18681 VHOG:0001135 galen:VasDeferens EFO:0000981 MIAA:0000129 Wikipedia:Vas_deferens CALOHA:TS-1105 BTO:0001427 MA:0000413 SCTID:245467009 EV:0100105 FMA:19234 GAID:404" + "A type II muscle cell that contains a low content of myoglobin, relatively few mitochondria, relatively few blood capillaries and large amounts of glycogen. Type II B fibres are white, geared to generate ATP by anaerobic metabolic processes, not able to supply skeletal muscle fibres continuously with sufficient ATP, fatigue easily, split ATP at a fast rate and have a fast contraction velocity." "FMA:84416" + "Any process that stops, prevents, or reduces the frequency, rate or extent of smooth muscle contraction." + "Mesenchyme that is part of a pharyngeal arch 1." "EMAPA:16128" + "Any process that activates or increases the frequency, rate or extent of otic vesicle morphogenesis." + "A peptide hormone secreting cell that secretes gastrin stimulating hormone." + "Characteristic early embryonic cell with a bottle or flask shape that is first to migrate inwards at the blastopore during gastrulation in amphibians." + "A mucosa that is part of an ascending colon [Automatically generated definition]." "FMA:15005" + "A space between the capsule and the cortex which allows the free movement of lymphatic fluid and so contains a sparsity of lymphocytes. It is continuous with the similar lymph sinuses that flank the trabeculae." "UMLS:C1518051 NCIT:C33033 FMA:312355 MA:0003027 NCIT:C33642 UMLS:C1518052 EMAPA:37662 Wikipedia:Subcapsular_sinus" + "Fibroblast from foreskin." "CALOHA:TS-0384" + "A killer cell lectin-like receptor 8 that is encoded in the genome of mouse." "UniProtKB:Q60682" + "Any process that modulates the frequency, rate or extent of the cyclical phases of growth (anagen), regression (catagen), quiescence (telogen), and shedding (exogen) in the life of a hair." + "Any process that stops, prevents or reduces the frequency, rate or extent of cholangiocyte proliferation." + "Any process that modulates the frequency, rate or extent of the process of creating protein polymers." + "Any process that stops, prevents or reduces the frequency, rate or extent of sensory perception of pain." + "All of the contents of a cilium, excluding the plasma membrane surrounding the cilium." + "Any process that stops, prevents or reduces the frequency, rate or extent of vascular associated smooth muscle cell apoptotic process." + "A bodily fluid that is located in the coelom." "BTO:0001708" + "A protein that is a translation product of the mouse Ren1 or Ren2 genes, 1:1 orthologs thereof, or a semi-ortholog thereof." + "MA:0003220 EMAPA:32904" + "The directed orientation of B cell signaling molecules and associated membrane rafts towards a chemokine gradient of a contact point with an antigen displaying cell." + "Any of the veins that parallel the interlobular arteries, receiving blood from the peritubular capillary plexus and empty into the arcuate veins." "Wikipedia:Interlobular_veins MA:0002594 FMA:71634 EMAPA:28218" + "A sperm cell that is cabaple of motion (motility)." + "A gland that is part of the intestinal mucosa. Examples include the intestinal crypts, duodenal gland[cjm]." "SCTID:266297002 FMA:15052 BTO:0000640" + "The thicker, deeper layer of the dermis, comprised of criss-crossing collagen fibers that form a strong elastic network and also containing blood and lymph vessels, nerves and nerve endings, and hair follicles." "MA:0000801 UMLS:C1514988 NCIT:C94818 NCIT:C33631 UMLS:C0682599 FMA:64778 Wikipedia:Reticular_dermis EMAPA:35283" + "The developmental process in which atrial septum is generated and organized. The atrial septum separates the upper chambers (the atria) of the heart from one another." + "The channels in the lymph node medulla that separate the medullary cords and are crossed by a reticulum of cells and fibers and bounded by littoral cells; lymph flows through the medullary sinus from the cortical sinuses and into the efferent lymphatic vessels." "FMA:312359 EMAPA:37898" + "A progenitor cell that can give rise to plasmacytoid and myeloid dendritic cells, and to monocytes and macrophages. Marker for this cell is Kit-high, CD115-positive, CD135-positive, Cx3cr1-positive, and is Il7ra-negative." + "A gland in which the principal secretory cells are mucus secreting cells." "FMA:62888 EMAPA:37913 BTO:0001979 Wikipedia:Mucous_gland AAO:0010601" + "Any process that activates or increases the frequency, rate, or extent of myeloid leukocyte mediated immunity." + "A congregation of multiple veins." "EMAPA:36327 SCTID:322151008 MA:0000069 FMA:4767 Wikipedia:Venous_plexus" + "A forkhead box protein P3 that is encoded in the genome of human." "UniProtKB:Q9BZS1 Reactome:R-HSA-8865539" + "Any process that stops, prevents, or reduces the frequency, rate, or extent of tumor necrosis factor production." + "Any process that stops, prevents, or reduces the frequency, rate or extent of glia cell differentiation." + "An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face." "ZFA:0005249 FMA:69050 BTO:0003718 TAO:0005249" + "A type of enteroendocrine cell found in the stomach that secretes glucagon." "FMA:83411" + "A thymocyte that has the phenotype CD4-negative, CD8-negative, CD44-positive, and CD25-positive." + "Any process that activates or increases the frequency, rate or extent of hair follicle development." + "The process in which a relatively unspecialized cell acquires specialized features of a type II pneumocyte. A type II pneumocyte is a surfactant secreting cell that contains abundant cytoplasm containing numerous lipid-rich multilamellar bodies." + "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the glomerular mesangial cells of the kidney as it progresses from its formation to the mature state." + "Any process that increases the rate, frequency or extent of the enlargement or overgrowth of all or part of the heart due to an increase in size (not length) of individual cardiac muscle fibers, without cell division." + "Small blood vessel similar to a capillary but with a fenestrated endothelium. Sinusoids are found in the liver, lymphoid tissue, endocrine organs, and hematopoietic organs such as the bone marrow and the spleen. Sinusoids found within terminal villi of the placenta are not comparable to these; they possess a continuous endothelium and complete basal lamina[WP]." "ZFA:0005261 Wikipedia:Sinusoid_(blood_vessel) FMA:63131 SCTID:340163004 TAO:0005261" + "Notochordal cell that is part of the outer epithelium of the notochord and surrounds the vacuolated notochord cells." + "Chondrocyte that is terminally differentiated, produces type X collagen, is large in size, and often associated with the replacement of cartilage by bone (endochondral ossification)." + "A smooth muscle cell that is part of the ciliary body." "FMA:70610" + "A renal principal cell located in the connecting tubule." + "The movement of an immune cell in response to an external stimulus a part of an immune response." + "Any process that activates or increases the frequency, rate, or extent of T cell tolerance induction." + "A mesenchyme that is part of a chorionic villus." + "Masses of developing blood cells attached to endothelium in the yolk sac." "EHDAA2:0000177 EMAPA:16115" + "A process in which force is generated within smooth muscle tissue, resulting in a change in muscle geometry. This process occurs in the intestine. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis. The intestine is the section of the alimentary canal from the stomach to the anal canal. It includes the large intestine and small intestine." + "Stratified squamous epithelium is a stratified squamous epithelium, the cells of which synthesizes but does not accumulate keratin. Examples: epithelium of vagina, epithelium of wall of esophagus." "Wikipedia:Stratified_squamous_epithelium#Nonkeratinized FMA:45569" + "The chemical reactions and pathways resulting in the breakdown of gamma-aminobutyric acid (GABA, 4-aminobutyrate), an amino acid which acts as a neurotransmitter in some organisms." "MetaCyc:4AMINOBUTMETAB-PWY" + "A G-protein coupled receptor with a 7 transmembrane (secretin family) domain (Pfam:PF00002) preceded by an amino-terminal region containing one or more functional domains with adhesion-like motifs." "IUPHAR:GPCRListForward?class=adhesion IUPHARfam:17" + "The process in which relatively unspecialized cells acquire specialized structural and/or functional features cells that make up the notochord. Differentiation includes the processes involved in commitment of a cell to a notochord cell fate." + "The expansion of a leukocyte population by cell division." + "The aggregation, arrangement and bonding together of a set of components to form a non-membrane-bounded organelle." + "Bone that forms as a replacement of another structural tissue." "ZFA:0001628 TAO:0001637 AAO:0010768" + "The directed movement of substances within a cell." + "The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves[GO]. Swellings of tissue present between the endocardial and myocardial cell layers that will give rise to the interstitial cells of the cardiac valves[ZFA]." "TAO:0001317 EHDAA:2586 FMA:70302 EHDAA2:0000434 XAO:0004189 VHOG:0000932 MA:0000078 EHDAA2:0004028 ZFA:0001317 Wikipedia:Atrioventricular_cushions EMAPA:16696" + "The external portion of an animal body derived from ectoderm and mesoderm layers that encloses the body cavity." "EMAPA:32761 BTO:0000139 FMA:10427 SCTID:281483004 galen:BodyWall" + "Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another." + "Any process that increases the rate, frequency, or extent of the chemical reactions and pathways resulting in the formation of a glycoprotein, a protein that contains covalently bound glycose (i.e. monosaccharide) residues; the glycose occurs most commonly as oligosaccharide or fairly small polysaccharide but occasionally as monosaccharide." + "A sphincter muscle that is part of the iris." "FMA:49157 MA:0001289 SCTID:280889004 Wikipedia:Iris_sphincter_muscle BTO:0000656 EMAPA:35788 UMLS:C0229189 NCIT:C33586" + "Any process that stops, prevents or reduces the frequency, rate or extent of natural killer cell chemotaxis." + "An enlarged chamber in the blood sinus capable of accumulating a large volume of blood." "ZFA:0007073" + "A cell that transports hormones from neurosecretory cells. This nerve cell is characterized by bipolar shape and endfeet that contact a basal lamina around blood vessels, and/or the pia mater or vitreous body of the eye and additionally contact the ventricular surface or sub-retinal space." "MESH:D063928" + "Any process that activates or increases the frequency, rate or extent of protein localization to chromatin." + "Any process that activates or increases the frequency, rate or extent of protein kinase activity." + "A CD8-positive, alpha-beta T cell with memory phenotype indicated by being CD45RO and CD127-positive. This cell type is also described as being CD25-negative, CD44-high, and CD122-high." + "The joint between adjacent vertebral bodies. May be composed of the nucleus pulposus, annular ligament, and the anterior and posterior longitudinal ligaments." "SCTID:244512000 MA:0001514 FMA:25511 EMAPA:37622 UMLS:C1182940 NCIT:C49577" + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amino acids of the glutamine family, comprising arginine, glutamate, glutamine and proline." + "Any process that activates or increases the frequency, rate or extent of cell proliferation in dorsal spinal cord." + "The duct that drains bile from the right half of the liver and joins the left hepatic duct to form the common hepatic duct." "EHDAA2:0001727 UMLS:C0227557 NCIT:C33476 MA:0001639 FMA:14669 VHOG:0000217 EMAPA:32797 SCTID:245401008 EHDAA:3992" + "A flexibility which is relatively normal or average." + "A transient endocrine gland that develops from the postovulatory or atretic follicles and secretes progesterone; it is thought to be related to egg retention[PMID]." "FMA:18619 GAID:369 NCIT:C26465 MA:0002834 EMAPA:29886 UMLS:C0010092 MESH:D003338 BTO:0000292 Wikipedia:Corpus_luteum SCTID:257943001 CALOHA:TS-0181" + "The change in morphology and behavior of a monocyte resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor, leading to the initiation or perpetuation of an immune response." + "The process whose specific outcome is the progression of the early distal convoluted tubule over time, from its formation to the mature structure. The early distal convoluted tubule contains DCT cells and is vasopressin-insensitive." + "The process in which a relatively unspecialized monocyte acquires the specialized features of an osteoclast. An osteoclast is a specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue." + "An epithelium surrounding a testis." "BTO:0001364 EMAPA:17973" + "A mesentery that is part of a jejunum [Automatically generated definition]." "FMA:14651 EMAPA:18670 SCTID:261286003" + "An endothelial cell that is part of the venule." "FMA:67762" + "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the cells of the metanephros as it progresses from its formation to the mature state." + "The developmental process pertaining to the initial formation of the heart rudiment." + "Heterochromatin that is arranged in a carthwheel pattern." + "Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process in hippocampal neurons." + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins in the presynaptic actin cytoskeleton." + "GC_ID:1" + "The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm." "EHDAA:350 EHDAA2:0001968 EHDAA:7860 EHDAA:4790 FMA:87656 EHDAA:1494 Wikipedia:External_ectoderm NCIT:C34309 EHDAA:4796 EHDAA:4784 UMLS:C1515087 EMAPA:16096" + "An organism subdivision that includes the pectoral girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pectoral girdle regions." "galen:ShoulderGirdle FMA:23217 SCTID:229759004 EMAPA:37856 VSAO:0000305" + "A structural quality which is held by a bearer when the latter's disposition the presence of abnormally proliferating masses of cells." + "An endothelial cell that lines the oral cavitiy including the mucosa of the gums, the palate, the lip, and the cheek." + "The vessels formed within the sixth pair of branchial arches in embryogenesis." "AAO:0010422 EHDAA2:0000102 ZFA:0005016 SCTID:308779008 XAO:0000353 Wikipedia:Aortic_arches#Arch_6 TAO:0005016 VHOG:0000144 EMAPA:17005" + "A G protein-coupled receptor signaling pathway initiated by somatostatin binding to a somatostatin receptor (SSTR), and ending with the regulation of a downstream cellular process, e.g. transcription." + "The regulated release of milk from the mammary glands and the period of time that a mother lactates to feed her young." "Wikipedia:Lactation" + "Any process that modulates the frequency, rate, or extent of B cell antigen processing and presentation." + "A developmental process, independent of morphogenetic (shape) change, that is required for the accessory nerve to attain its fully functional state. The spinal branch of this motor nerve innervates the trapezius and the sternocleidomastoid muscles. The cranial branch joins the vagus nerve and innervates the same targets as the vagus nerve." + "A zone of skin part of some gonad." + "The aggregation, arrangement and bonding together of a set of components to form an MHC protein complex." + "The directed movement of neutral amino acids out of the vacuole, across the vacuolar membrane." + "The process whose specific outcome is the progression of the pericardium over time, from its formation to the mature structure. The pericardium is a double-walled sac that contains the heart and the roots of the aorta, vena cava and the pulmonary artery." + "The process in which the anatomical structures of the pronephric glomerulus are generated and organized. The pronephric glomerulus is part of the pronephric nephron and is restricted to one body segment." + "Binding to a stem cell factor receptor (SCFR), a type III transmembrane kinase receptor." + "The process in which a relatively unspecialized cell acquires specialized features of a mesonephric glomerular visceral epithelial cell. A mesonephric glomerular visceral epithelial cell is a specialized epithelial cell that contains 'feet' that interdigitate with the 'feet' of other glomerular epithelial cells in the mesonephros." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "Any process that modulates the frequency, rate or extent of the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures containing both actin and myosin or paramyosin." + "The processes by which anatomical structures that are only present in the male organism are generated and organized." + "The process in which a trophoblast cell acquires specialized features of an epithelial cell of the placental labyrinthine layer." + "Any process that mediates the transfer of information from a Purkinje myocyte to a ventricular cardiac muscle cell." + "A nerve trunk that is part of a vagus nerve." "EHDAA2:0002160 SCTID:280308004 EHDAA:4659 EMAPA:17272 FMA:6221 MA:0001150 VHOG:0000736" + "EMAPA:35958 MA:0003171" + "A CNS interneuron located in the spinal cord." + "The blood vessels that branch from the kidney interlobular artery, convey blood to the glomerular capillaries, and play an important role in the regulation of blood pressure as a part of the tubuloglomerular feedback mechanism." "EMAPA:28230 SCTID:67498004 TAO:0002139 FMA:77042 ZFA:0005307 MA:0002579 EMAPA:28266 Wikipedia:Afferent_arterioles" + "Any developmental process that results in the creation of defined areas or spaces within an organism to which cells respond and eventually are instructed to differentiate." + "A high affinity interleukin-8 receptor that is a translation product of the human CXCR1 gene or a 1:1 ortholog thereof." "IUPHARobj:68" + "The nucleus of either the ovum or the spermatozoon following fertilization. Thus, in the fertilized ovum, there are two pronuclei, one originating from the ovum, the other from the spermatozoon that brought about fertilization; they approach each other, but do not fuse until just before the first cleavage, when each pronucleus loses its membrane to release its contents." "Wikipedia:Pronucleus" + "A mucosa that is part of a ureter [Automatically generated definition]." "FMA:15894 galen:MucousMembraneOfUreter SCTID:40476001" + "A neuronal acetylcholine receptor subunit alpha-7 that is encoded in the genome of mouse." "UniProtKB:P49582" + "The lipid bilayer surrounding a lytic vacuole and separating its contents from the cytoplasm of the cell." + "The connective tissue bundles in the extracellular matrix of bone tissue that are composed of collagen, and play a role in tissue strength and elasticity." + "KUPO:0001023" + "GC_ID:1" + "A follicle cell that migrates from the dorso-anterior part of the oocyte associated follicular epithelium, in between the nurse cells and the oocyte, and participates in the formation of the operculum." "FBbt:00004906" + "A germinal center B cell that has the phenotype CD77-negative, IgD-negative, and CD38-positive. These cells have undergone somatic mutation of the B cell receptor." + "A pharyngeal pouch that is between pharyngeal arches 1 and 2." "FMA:295668 EMAPA:16124 TAO:0001128 AAO:0011114 UMLS:C0231068 VHOG:0000970 SCTID:345248006 VHOG:0000555 NCIT:C34176 EFO:0003631 EHDAA2:0000016 EMAPA:16125 XAO:0000102 Wikipedia:Pharyngeal_pouch_(embryology)#First_pouch ZFA:0001128" + "A fully differentiated plasma cell that secretes IgG." + "A stratified epithelium that surrounds the hair follicle that merges proximally with the basal layer of the interfollicular epidermis and distally with the hair bulb." "BTO:0003969 FMA:70943 MA:0000780 NCIT:C62490 SCTID:319224003 EMAPA:32793 Wikipedia:Outer_root_sheath" + "The process whose specific outcome is the progression of the posterior lateral line over time, from its formation to the mature structure. The posterior lateral line consists of small sensory patches (neuromasts) located superficially on the skin or just under the skin in fluid-filled canals on the body and trunk of all fishes and most amphibians. The posterior lateral line develops from cranial ectodermal placodes situated behind the ear." + "The joint that is formed by the union of the humerus, the scapula (or shoulder blade), and the clavicle (or collarbone). Commonly thought of as a single joint, the shoulder is actually made up of two separate joints - the glenohumeral and acromioclavicular joints." "SCTID:361835002" + "A highly specialized cell type exclusive to and forming neuroepithelium of the Saccus vasculosus, covering the caudal diverticulum of the infundibular recess." + "The chemical reactions and pathways resulting in many of the chemical changes of compounds that are not necessarily required for growth and maintenance of cells, and are often unique to a taxon. In multicellular organisms secondary metabolism is generally carried out in specific cell types, and may be useful for the organism as a whole. In unicellular organisms, secondary metabolism is often used for the production of antibiotics or for the utilization and acquisition of unusual nutrients." "Wikipedia:Secondary_metabolism" + "A gelatinous substance within the umbilical cord, largely made up of mucopolysaccharides (hyaluronic acid and chondroitin sulfate). It also contains some fibroblasts and macrophages. It is derived from Extra Embryonic Mesoderm[WP]." "Wikipedia:Wharton's_jelly EMAPA:26127 EMAPA:35925 SCTID:368069009" + "Any mesenchymal stem cell that is part of a placenta." + "An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins." + "The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome." + "The central area of the two limbs of a horseshoe-shaped mesenchymal swelling that lie medial to the olfactory placode or pit in the future nasal region of the embryo; it joins with the ipsilateral maxillary prominence in the formation of half of the upper jaw, and the nasal tip and philtrum of the upper lip develop from it." "Wikipedia:Medial_nasal_prominence EMAPA:16808 VHOG:0000804 FMA:295858 EHDAA:4792 EHDAA2:0001076 SCTID:308877001" + "The internal masculine genital organs, including the testes, epididymides, deferent ducts, seminal vesicles, prostate, ejaculatory ducts, and bulbourethral glands." "FMA:45655 SCTID:310536002 BTO:0003096" + "Any process that stops, prevents or reduces the frequency, rate or extent of plasma cell differentiation." + "A cellular process that results in the breakdown of a cilium." + "Any process that modulates the frequency, rate or extent of myofibroblast cell apoptotic process." + "Any process that modulates the frequency, rate or extent of the directed movement of substances between the nucleus and the cytoplasm." + "Any fibroblast that is part of a embryo." + "Any process that stops, prevents, or reduces the frequency, rate or extent of epithelial cell differentiation." + "The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins." "Wikipedia:Cell_cortex" + "A vein that carries deoxygenated blood from a single male gonad. It is the male equivalent of the ovarian vein, and is the venous counterpart of the testicular artery. It is a paired vein, with one supplying each testis." "FMA:14344 EMAPA:18647 NCIT:C53050 SCTID:264496006 UMLS:C0226718 BTO:0002678 Wikipedia:Testicular_vein MA:0002218 MA:0002234" + "Subdivision of the skeletal system which consists of the appendicular skeleton plus associated joints." "FMA:7484 VSAO:0000306" + "Mucosa that is part of a colon. The mucosa of the colon is lined by a simple columnar epithelium with a thin brush border and numerous goblet cells." "BTO:0000271 FMA:85388 CALOHA:TS-0164 FMA:14984 MA:0003194 EFO:0003038 EMAPA:27375 SCTID:362157008" + "Any process that modulates the frequency, rate, or extent of cytokine production that contributes to an immune response." + "The inner medullary collecting duct is the portion of the collecting duct that lies in the renal inner medulla." "BTO:0004544 EMAPA:28370 MA:0002598" + "Any process that modulates the frequency, rate or extent of secondary metabolism, the chemical reactions and pathways involving compounds that are not necessarily required for growth and maintenance of cells, and are often unique to a taxon." + "A neutrophil gelatinase-associated lipocalin that is encoded in the genome of mouse." "UniProtKB:P11672" + "The regulated release of neurotransmitter into the synaptic cleft involved in skeletal muscle contraction. A neurotransmitter is any of a group of substances that are released on excitation from the axon terminal of a presynaptic neuron of the central or peripheral nervous system and travel across the synaptic cleft to either excite or inhibit the target cell. Among the many substances that have the properties of a neurotransmitter are acetylcholine, noradrenaline, adrenaline, dopamine, glycine, gamma aminobutyrate, glutamic acid, substance P, enkephalins, endorphins and serotonin." + "A mucus secreting cell that is part of a submucosal gland of the trachea." + "Any process that stops, prevents or reduces the frequency, rate or extent of parathyroid hormone secretion." + "Any process that modulates the frequency, rate or extent of tumor necrosis factor superfamily cytokine production." + "A mesenchymal stem cell of liver." + "A neuron projection that has a short, tapering, morphology. Dendrites receive and integrate signals from other neurons or from sensory stimuli, and conduct nerve impulses towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body." "NIF_Subcellular:sao1211023249 Wikipedia:Dendrite" + "The connective tissue bundles in the extracellular matrix of corneal stroma that are composed of collagen, and play a role in tissue strength and elasticity." + "A portion of skeletal muscle tissue in the trunk." "SCTID:244848007" + "A distinct elevation of a transient proliferating cell mass of the fetal subventricular zone; this mass contributes most of its cells to the striatum; however, neocortex, thalamus, septum and olfactory bulb neurons are also partly derived from the LGE." "DHBA:10551 PBA:128012822 EMAPA:37470" + "During the third week of embryological development there appears, immediately behind the ventral ends of the two halves of the mandibular arch, a rounded swelling named the tuberculum impar, which was described by His as undergoing enlargement to form the buccal part of the tongue. More recent researches, however, show that this part of the tongue is mainly, if not entirely, developed from a pair of lateral swellings which rise from the inner surface of the mandibular arch and meet in the middle line. The site of their meeting remains post-embryonically as the median sulcus of the tongue. The tuberculum impar is said to form the central part of the tongue immediately in front of the foramen cecum, but Hammar insists that it is purely a transitory structure and forms no part of the adult tongue[WP, Gray's]." "FMA:312476 EMAPA:17187 VHOG:0000730 SCTID:308821003 Wikipedia:Tuberculum_impar EHDAA2:0001081" + "Developmental growth that contributes to the shaping of the heart." + "Mesenchyme that is part of a developing face." "FMA:302884 EMAPA:35337" + "A protein that is a translation product of the human EGR2 gene or a 1:1 ortholog thereof." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism." + "A connective tissue that surrounds a skeletal muscle tissue." "EMAPA:37743 MA:0002868" + "Any process that stops, prevents or reduces the frequency, rate or extent of cell proliferation involved in compound eye morphogenesis." + "The chemical reactions and pathways involving insulin." + "Any process that stops, prevents, or reduces the frequency, rate or extent of T cell differentiation." + "Any process that modulates the activity of an ion transporter." + "Any process that modulates the frequency, rate, or extent of B cell cytokine production." + "A nuclear receptor ROR-gamma that is encoded in the genome of human." "DTO:00117492 Reactome:R-HSA-446177 UniProtKB:P51449" + "A glycophorin that is a translation product of the human GYPA gene or a 1:1 ortholog thereof. It is the major sialoglycoprotein of the erythrocyte membrane. Structurally, glycophorin A consists of an N-terminal extracellular domain, heavily glycosylated on Ser and threonine residues, followed by a transmembrane region and a C-terminal cytoplasmic domain." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of antimicrobial peptide production." + "Any process that activates or increases the frequency, rate or extent of calcium-mediated signaling." + "The actin filament-based movement by which cytoplasmic actin filaments slide past one another resulting in a contraction that propels the cell from one place to another." + "The process whose specific outcome is the progression of the telencephalon over time, from its formation to the mature structure. The telencephalon is the paired anteriolateral division of the prosencephalon plus the lamina terminalis from which the olfactory lobes, cerebral cortex, and subcortical nuclei are derived." + "An adipose macrophage that does not express MHC-II but is F4/80-positive." + "Any process that activates or increases the frequency, rate or extent of cell proliferation involved in mesonephros development." + "The subclasses of motor neurons which are organized into longitudinally oriented columns that occupy distinct and, in some cases, discontinuous domains along the rostrocaudal axis of the spinal cord; motor neurons within a single column send their axons to a common peripheral target." + "Any process that modulates the frequency, rate or extent of lung goblet cell differentiation." + "An elastic tissue that is part of a trachea [Automatically generated definition]." "MA:0001861" + "GC_ID:1" + "An epithelial cell that is part of the bile duct. Cholangiocytes contribute to bile secretion via net release of bicarbonate and water. They are cuboidal epithelium in the small interlobular bile ducts, but become columnar and mucus secreting in larger bile ducts approaching the porta hepatis and the extrahepatic ducts." "FMA:86481" + "Any process that increases the rate, frequency, or extent of brown fat cell differentiation. Brown fat cell differentiation is the process in which a relatively unspecialized cell acquires specialized features of a brown adipocyte, an animal connective tissue cell involved in adaptive thermogenesis. Brown adipocytes contain multiple small droplets of triglycerides and a high number of mitochondria." + "An elongated, contractile cell found wrapped about precapillary arterioles outside the basement membrane. Pericytes are present in capillaries where proper adventitia and muscle layer are missing (thus distingushing this cell type from adventitial cells). They are relatively undifferentiated and may become fibroblasts, macrophages, or smooth muscle cells." "FMA:63174 BTO:0002441" + "MA:0003174 EMAPA:35952" + "The clusters of hormone-producing cells that are scattered throughout the pancreas." "GAID:324 XAO:0000159 EFO:0000856 MESH:D007515 NCIT:C12608 MAT:0000076 VHOG:0000646 AAO:0010406 Wikipedia:Islets_of_Langerhans BTO:0000991 FMA:16016 CALOHA:TS-0741 EV:0100130 UMLS:C0022131 EMAPA:32927 MIAA:0000076 MA:0000127" + "The progression of a chondrocyte over time from after its commitment to its mature state where the chondrocyte will contribute to the shaping of an endochondral bone." + "Subcortical nucleus of telencephalic , which together with the caudate nucleus, forms the striatum. The putamen lies lateral to the internal capsule and medial to the external medullary lamina, and is separated from the caudate nucleus by the fibers of the internal capsule for most of its length, except at its anterior portion." "EV:0100187 UMLS:C0034169 Wikipedia:Putamen BM:Tel-Pu PBA:10086 DHBA:10338 CALOHA:TS-2041 NCIT:C12452 MA:0000895 VHOG:0001456 BIRNLEX:809 MESH:D011699 FMA:61834 neuronames:230 HBA:4287 DMBA:15857 BAMS:Pu BAMS:PU EMAPA:35719 GAID:671 SCTID:281512002" + "A mature CD4-positive, CD8-negative alpha-beta T cell found in the thymus that is CD24-low and has high expression of the T cell receptor." + "A process in which a protein is transported to, or maintained in, a location within a secretory granule in a T cell." + "Any process that stops, prevents or reduces the frequency, rate or extent of a small molecule metabolic process." + "The process in which a B cell in the spleen acquires the specialized features of a follicular B cell. Follicular B cells are major population of mature recirculating B cells in the spleen and are located in the B-cell follicle region." + "An immune response taking place in the liver." + "The directed movement of amino acids from inside of a cell, across the plasma membrane and into the extracellular region." + "The process in which the embryonic placenta is generated and organized." + "An action potential that occurs in a sinoatrial node cardiac muscle cell." + "Layer of neocortex lying just deep to molecular layer characterized by numerous small cell bodies." "NLXANAT:090808 neuronames:2446 UMLS:C1517039 EMAPA:35256 ABA:CTX2 NCIT:C32557 PBA:294021800 MA:0000898 FMA:77804" + "Skeletal element that is composed of cartilage tissue and may be permanent or transient." "XAO:0004013 VSAO:0000000 FMA:55107 ZFA:0001501 AAO:0011130 CALOHA:TS-0118" + "The directed movement of basic amino acids from one side of a membrane to the other." + "A renal alpha-intercalated cell that is part of the renal connecting tubule." + "Lip that covers the lower portion of the mouth.[TAO]." "SCTID:245777007 TAO:0002060 MA:0000921 ZFA:0005225 FMA:59818 Wikipedia:Lower_lip EMAPA:17909 UMLS:C0458583 NCIT:C94572" + "The process whose specific outcome is the progression of a ganglion over time, from its formation to the mature structure." + "Any process that stops, prevents or reduces the frequency, rate or extent of nuclear migration along microtubule." + "The process whose specific outcome is the progression of the hemocyte over time, from its formation to the mature structure. Hemocytes are blood cells associated with a hemocoel (the cavity containing most of the major organs of the arthropod body) which are involved in defense and clotting of hemolymph, but not involved in transport of oxygen." + "The process whose specific outcome is the progression of the embryonic heart tube over time, from its formation to the mature structure. The heart tube forms as the heart rudiment from the heart field." + "The creation of two or more organelles by division of one organelle." + "The metanephric glomerular endothelium is an epithelial tissue that covers the internal surfaces of the glomerulus of the metanephros[GO]." + "The appearance of interleukin-8 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals." + + "A collagen-containing extracellular matrix consisting of a thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers." "Wikipedia:Basement_membrane" + "An fMet-Leu-Phe receptor that is encoded in the genome of mouse." "UniProtKB:P33766" + "The chemical reactions and pathways by which a cell derives energy from organic compounds; results in the oxidation of the compounds from which energy is released." + "A transparent and refractive lens located posterior to the iris. The lens of camera-type eye refracts light to be focused on the retina." "VHOG:0000169 SCTID:181169005 MA:0000275 MIAA:0000141 XAO:0000008 AAO:0010348 EMAPA:17838 BTO:0000723 Wikipedia:Lens_(anatomy) MESH:D007908 RETIRED_EHDAA2:0000975 ZFA:0000035 MAT:0000141 TAO:0000035 CALOHA:TS-0545 FMA:58241 NCIT:C12743 EV:0100343 UMLS:C0023317 EHDAA:9057" + "A bone that is part of an appendage girdle complex (i.e. any bone in a limb, fin or girdle)." "MA:0000688 EMAPA:35494" + "A capillary tuft which forms a close network with the visceral epithelium (podocytes) and the mesangium to form the filtration barrier and is surrounded by Bowman's capsule in nephrons of the vertebrate kidney[GO]." "Wikipedia:Glomerulus MESH:D007678 UMLS:C0022663 SCTID:362217000 ZFA:0001288 TAO:0001288 FMA:15624 MA:0001657 EMAPA:28329 EV:0100386 CALOHA:TS-0862 EFO:0003667 NCIT:C13250 BTO:0000530" + "The deep groove which separates the two hemispheres of the vertebrate brain. The falx cerebri, a dural brain covering, lies within the medial longitudinal fissure. [WP,unvetted]." "UMLS:C0228186 neuronames:35 NCIT:C33005 HBA:9401 BIRNLEX:4041 DHBA:10622 SCTID:369225004 Wikipedia:Medial_longitudinal_fissure BAMS:lfh BAMS:lf FMA:83727" + "The ophthalmic artery is a branch of the internal carotid artery which supplies branches to supply the eye and other structures in the orbit. It enters the orbit together with the Optic nerve through the Optic foramen/canal. [WP,modified]." "MESH:D009880 NCIT:C33216 EMAPA:17007 UMLS:C0029078 Wikipedia:Ophthalmic_artery XAO:0000368 EHDAA:7363 EHDAA2:0001300 MA:0002011 SCTID:181310005 AAO:0010497 GAID:503 FMA:49868" + "A muscular coat that is part of a anal canal." "FMA:15708 SCTID:362171000" + "The process whose specific outcome is the progression of a light-responsive receptor in the compound eye over time, from its formation to the mature structure." + "The volume enclosed by the nuclear inner membrane." + "An endothelium that is part of a umbilical vein." "CALOHA:TS-1081 BTO:0001416" + "A zone of skin that is part of a skin of pes." "SCTID:181566006 FMA:37849" + "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane." "FBbt:00007002 CALOHA:TS-2035 MESH:D002477 XAO:0003012 VHOG:0001533 GO:0005623 FMA:68646 WBbt:0004017 KUPO:0000002" + "Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination in a cardiac muscle cell of the bundle of His. This typically occurs via modulation of the activity or expression of voltage-gated ion channels." + "The developmental process in which a hair placode forms. An hair follicle placode is a thickening of the ectoderm that will give rise to the hair follicle bud." + "FMA:64804" + + + "A male germ cell that develops from the haploid secondary spermatocytes. Without further division, spermatids undergo structural changes and give rise to spermatozoa." "FBbt:00004942 BTO:0001274 EMAPA:31486 FMA:72294 WBbt:0006800 CALOHA:TS-0950" + "A neuron that expresses kisspeptin. These neurons are predominantly located in the hypothalamus, but also found in other parts of the brain including the hippocampal dentate gyrus." + "Any process that stops, prevents or reduces the frequency, rate or extent of cardiac chamber formation." + "A hematopoietic stem cell that has plasma membrane part Kit-positive, SCA-1-positive, CD150-positive and CD34-negative." + "The head is the anterior-most division of the body [GO]." "GAID:61 WBbt:0005739 AEO:0000106 UMLS:C0018670 SCTID:302548004 BIRNLEX:1230 MA:0000023 HAO:0000397 XAO:0003024 SPD:0000016 galen:Head Wikipedia:Head EFO:0000964 MIAA:0000294 BILA:0000115 NCIT:C12419 EHDAA2:0003106 MESH:D006257 BTO:0000282 FMA:7154 VHOG:0001644 EMAPA:31858 MAT:0000294 ZFA:0001114 TGMA:0000002 AAO:0010335 TAO:0001114 CALOHA:TS-0436" + "Any process that increases the rate, frequency, or extent of hair follicle placode formation, the developmental process in which a hair placode forms. An hair follicle placode is a thickening of the ectoderm that will give rise to the hair follicle bud." + "The process whose specific outcome is the formation of the hindbrain-spinal cord boundary." + "A protein with core architecture consisting of a signal sequence, one Immunoglobulin V-set domain (Pfam:PF07686), two Immunoglobulin C1-set domains (Pfam:PF07654), a single-pass transmembrane region and a very small cytoplasmic region." "PIRSF:PIRSF038063" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "Any germinal center B cell that is part of a tonsil." + "Any skeletal muscle that is part of the head region." "MA:0000578 BTO:0000021 ZFA:0001652 EFO:0003524 EHDAA2:0000322 AAO:0000107 FMA:9616 EMAPA:18172 SCTID:244718003" + + "A chemokine receptor that is a translation product of the human CCR7 gene or a 1:1 ortholog thereof. The preferred ligands are CCL19 and CCL21." "IUPHARobj:64" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving glucocorticoids." + "The process whose specific outcome is the progression of the peripheral nervous system over time, from its formation to the mature structure. The peripheral nervous system is one of the two major divisions of the nervous system. Nerves in the PNS connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands." + "Any process that modulates the frequency, rate or extent of programmed cell death that occurs in the retina." + "The directed movement of a protein to a specific location." + "The mammalian blastocyst is a hollow ball of cells containing two cell types, the inner cell mass and the trophectoderm[GO]." "EMAPA:36035 EFO:0000295 MESH:D001755 Wikipedia:Blastocyst FMA:83041 CALOHA:TS-0076 NCIT:C13739 GAID:1153 BTO:0001099 UMLS:C1281743 SCTID:308837009 EV:0100394" + "A lineage marker-negative, CD34-positive, IL5r-alpha-positive, and Sca1-negative eosinophil progenitor cell." + "Any process that modulates the rate, frequency or extent of mesonephros development. Mesonephros development is the process whose specific outcome is the progression of the mesonephros over time, from its formation to the mature structure. The mesonephros is an endocrine and metabolic organ that filters the blood and excretes the end products of body metabolism in the form of urine." + "Any process that modulates the frequency, rate or extent of natural killer cell differentiation." + "A ring of fibrous or fibrocartilaginous tissue (as of an intervertebral disk or surrounding an orifice of the heart)." "FMA:76704 BTO:0003627" + "Gr1-low non-classical monocyte that lacks expression of a MHC-II complex." + "Muscles of the pelvic girdle, hindlimb or pelvic fin." "EMAPA:32634 AAO:0000218 FMA:9622 MA:0000663" + "Any process that stops, prevents or reduces the rate or extent of cell adhesion to another cell." + "The directed movement of basic amino acids into the vacuole across the vacuolar membrane." + "A portion of bone tissue that is part of a proximal epiphysis [Automatically generated definition]." "FMA:241372" + "A primordium that has the potential to develop into a stomach." "NCIT:C34305 EFO:0002580 UMLS:C1514976" + "The medullary cavities of the bones where bone marrow is stored." "Wikipedia:Bone_marrow_of_ovaryry_cavity MA:0002783 FMA:75147 FMA:83698" + "The process in which a myeloid dendritic cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex." + "Any process that activates or increases the frequency, rate, or extent of T cell antigen processing and presentation." + "A digitopodium region that is part of a manus[Obol]. This includes the fingers and metacarpal region, but excludes the carpal region." + "The part of the venous system that drains the lungs[Kardong]." "Wikipedia:Pulmonary_venous_system" + + "The movement of a mast cell within or between different tissues and organs of the body." + "Any process that modulates the occurrence or rate of natural killer cell death by apoptotic process." + "The collecting duct system of the kidney consists of a series of tubules and ducts that connect the nephrons to the ureter. It participates in electrolyte and fluid balance through reabsorption and excretion, processes regulated by the hormones aldosterone and antidiuretic hormone." "SCTID:279371005 FMA:265239 Wikipedia:Collecting_duct_system" + "The process in which a relatively unspecialized cell acquires specialized features of a mechanoreceptor, a cell specialized to transduce mechanical stimuli and relay that information centrally in the nervous system." + "The lipid bilayer surrounding a lamellar body. A lamellar body is a membrane-bounded organelle, specialized for the storage and secretion of various substances (surfactant phospholipids, glycoproteins and acid phosphates) which are arranged in the form of tightly packed, concentric, membrane sheets or lamellae. Has some similar properties to, but is distinct from, a lysosome." + "A portion of smooth muscle tissue that is part of a lymphatic vessel [Automatically generated definition]." "EMAPA:36313 NCIT:C49260 UMLS:C1708791 MA:0000751 FMA:262026" + "A plasma membrane that is part of a sperm cell." + "A vertebral foramen that is part of a cervical vertebra." "FMA:13480 SCTID:280833008" + "The series of events in which a stimulus is received by a cell or organism and converted into a molecular signal." + "An amacrine cell with a flat dendritic arbor and a medium dendritic field. Starburst amacrine cells have post-synaptic terminals in S2. This cell type releases the neurotransmitters gamma-aminobutyric acid (GABA) and acetylcholine." + "Any process that modulates the frequency, rate or extent of glutamate receptor signaling pathway." + "The chemical reactions and pathways resulting in the breakdown of imidazoles, five-membered organic heterocycle containing two nitrogen atoms at positions 1 and 3, or any of its derivatives; compounds containing an imidazole skeleton." + "Any process that activates or increases the frequency, rate or extent of ATP biosynthetic process." + "The dense region demarcating the thymus medulla from the surrounding cortex that is characterized by numerous blood vessels (predominantly arterioles) with some perivascular connective tissue, mature and immature T lymphocytes, dendritic cells, variable numbers of perivascular B-lymphocytes and plasma cells; site of entry of bone marrow stem cells and exit of mature, functional T cells." "EMAPA:37974" + "Any process that stops, prevents, or reduces the frequency, rate or extent of synaptic transmission, the process of communication from a neuron to a target (neuron, muscle, or secretory cell) across a synapse." + "Right part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane." + "A protein that is a translation product of a gene that encodes a standalone Insulin (Pfam:PF00049) domain preceded by a signal peptide." + "The process in which a relatively unspecialized cell acquires specialized features of a muscle cell." + "Any process that modulates the frequency, rate or extent of gastro-intestinal system smooth muscle contraction." + "The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state." + "A gland that is part of a digestive tract [Automatically generated definition]." "EMAPA:18815 MA:0003202" + "A zone of skin that is part of a trunk [Automatically generated definition]." "NCIT:C12295 FMA:12167 SCTID:181489001 UMLS:C0205031 EMAPA:37278 FMA:23093 MA:0000517" + "An external genitalia that is part of a female reproductive system [Automatically generated definition]." "galen:FemaleExternalGenitalia FMA:45649 BTO:0003100 SCTID:362234008 EMAPA:30984" + "An artery that supplies a renal lobe." "FMA:71637 Wikipedia:Interlobar_arteries EMAPA:37091 SCTID:62802007" + "A cardiac myocyte that is an excitable cells in the myocardium, specifically in the conducting system of heart." "FMA:67968" + "The granular layer is the innermost layer of the cerebellar cortex. This layer contains densely packed small neurons, mostly granule cells. Some Golgi cells are found at the outer border. Granule neurons send parallel fibers to the upper molecular layer, where they synapse with Purkinje cell dendrites. Mossy fibers from the pontine nuclei in the white matter synapse with granule cell axons, Golgi cell axons and unipolar brush interneuron axons at cerebellar glomeruli in the granule cell layer." "MA:0000993 CALOHA:TS-1247 EMAPA:35217 MBA:1143 UMLS:C1708253 NCIT:C49138 BTO:0004425 FMA:83140 BIRNLEX:779 neuronames:363" + "The process that gives rise to the vestibulocochlear nerve. This process pertains to the initial formation of a structure from unspecified parts. This sensory nerve innervates the membranous labyrinth of the inner ear. The vestibular branch innervates the vestibular apparatus that senses head position changes relative to gravity. The auditory branch innervates the cochlear duct, which is connected to the three bony ossicles which transduce sound waves into fluid movement in the cochlea." + "A cell of a filament of a fungal mycelium." + "An integrin beta that is a translation product of the human ITGB7 gene or a 1:1 ortholog thereof." "IUPHARobj:2461" + + "Connective tissue consisting of fat-storing cells and arranged in lobular groups or along minor blood vessels[MP,modified]." "Wikipedia:White_adipose_tissue CALOHA:TS-1119 EFO:0000813 UMLS:C1704223 MIAA:0000199 BTO:0001456 FMA:20117 MAT:0000199 NCIT:C33889 MA:0000058 EMAPA:35926" + "A protein that is a translation product of the human SIGLEC1 gene or a 1:1 ortholog thereof." + "A partion of white matter that is part of a telencephalon. This can be further subdivided in some species, for example, into hemisphere white matter and the corpus callosum." "FMA:83930 ZFA:0000597 TAO:0000597 BIRNLEX:1075 HBA:9230 HBA:9219" + "A cell specialized to detect and transduce light." "FMA:86740 CALOHA:TS-0868 BTO:0001060" + "Any process that modulates the frequency, rate or extent of mesenchymal to epithelial transition involved in mesonephros morphogenesis." + "The process in which the renal system vasculature is generated and organized. Morphogenesis pertains to the creation of form." + "The biological process whose specific outcome is the progression of a mesonephric mesenchyme from an initial condition to its mature state. This process begins with the formation of mesonephric mesenchyme and ends with the mature structure. Mesonephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the mesonephros." + "EHDAA2:0001371" + "The proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix, usually carried out by proteases secreted by nearby cells." + "Any process that stops, prevents, or reduces the frequency, rate or extent of B cell differentiation." + "EHDAA2:0001393" + "Cell-cell signaling that mediates the transfer of information from a neuron to a glial cell. This signaling has been shown to be mediated by various molecules released by different types of neurons, e.g. glutamate, gamma-amino butyric acid (GABA), noradrenaline, acetylcholine, dopamine and adenosine." + "A lymph node that is located in a kidney [Automatically generated definition]." "UMLS:C2699031 FMA:276799 MA:0002882 NCIT:C77646" + "The process aimed at the progression of a cardiac neural crest cell over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell that contributes to the shaping of the outflow tract." + "An epithelial cell of the proximal tubule of the kidney." "FMA:70973 KUPO:0001044" + "A smooth muscle cell that is part of the prostate gland." "FMA:84583" + "A type of interneuron that has two neurites, usually an axon and a dendrite, extending from opposite poles of an ovoid cell body." "FMA:67282" + "An epidermal invagination that has as parts a hair follicle, a sebaceous gland, and arrector pili muscle." "FMA:70661 Wikipedia:Pilosebaceous_unit EMAPA:36582" + "A bone that is part of a hindlimb stylopod [Automatically generated definition]." "MA:0000682 EMAPA:35893" + "MA:0001151 FMA:18157 EMAPA:37798" + "The bulb region adjacent to the dermal papilla that contains rapidly proliferating matrix cells that give rise to the various cell lineages of the hair shaft and inner root sheath." "EMAPA:37878 FMA:70772" + "Any process that decreases the frequency, rate or extent of glucose transport across a membrane. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "The lacrimal artery arises close to the optic foramen, and is one of the largest branches derived from the ophthalmic artery: not infrequently it is given off before the artery enters the orbit. It accompanies the lacrimal nerve along the upper border of the Lateral Rectus, supplies the lacrimal gland. [WP,unvetted]." "MA:0001988 FMA:49927 SCTID:369324002 Wikipedia:Lacrimal_artery UMLS:C0226171 NCIT:C52948 EMAPA:37094" + "The process whose specific outcome is the progression of the kidney pyramids over time, from its formation to the mature structure. Kidney pyramids are the conical masses that constitute the renal medulla in a multi-lobed mammalian kidney; they contain the loops of Henle and the medullary collecting ducts." + "The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins." + "Any biological process, occurring at the level of a multicellular organism, pertinent to its function." + "The process whose specific outcome is the progression of a cardiac ventricle over time, from its formation to the mature structure. A cardiac ventricle receives blood from a cardiac atrium and pumps it out of the heart." + "A rapidly cycling mature B cell that has distinct phenotypic characteristics and is involved in T-dependent immune responses and located typically in the germinal centers of lymph nodes. This cell type expresses Ly77 after activation." + + "Any process that modulates the frequency, rate or extent of the formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells." + "A pre-cartilage condensation that has the potential to develop into a tarsal bone." "EHDAA2:0001978" + "The developmental process, independent of morphogenetic (shape) change, that is required for an epithelial cell to attain its fully functional state. An epithelial cell is a cell usually found in a two-dimensional sheet with a free surface." + "The white laminae of cerebellum is subdivision of the cerebellar cortex comprised of myelinated axons lying deep to the granule cell layer of the cerebellar cortex." "neuronames:163 UMLS:C0228472 SCTID:362413004 BIRNLEX:1105" + "The glomerular endothelium is an epithelial tissue that covers the internal surfaces of the glomerulus." "BTO:0004631" + "A reproductive process occurring in the embryo or fetus that allows the embryo or fetus to develop within the mother." + "Any process that increases the frequency, rate or extent of the directed killing of a target cell by a neutrophil." + "Tooth that is attached to a dentary/mandible[TAO,modified]." "AAO:0000125 AAO:0000641 SCTID:245547003 TAO:0001628" + "Any process that activates or increases the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure." + "An intervertebral disk that is part of a thoracic region of vertebral column. A thoracic intervertebral disk connects at least one thoracic vertebra, either to another thoracic vertebra, or at one point on the vertebral colummn, to a lumbar vertebra." "EMAPA:19489 FMA:10455" + "A bulb of epithelial cells that forms from the mammary placode that develops into the mammary gland." "EMAPA:35536" + "FMA:15089" + "Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-8 production." + "An epithelial cell that is part of the nephron." "FMA:70965" + "A concave nuclear shape where the nucleus is indented to more than half the distance to the farthest nuclear margin, but in no area is the chromatin condensed to a single filament." + "Subdivision of skeleton that consists of the endochondral elements distal to the anterior limb/fin zeugopodial skeletal elements which constitute the proximal region of the anterior autopod skeleton[PHENOSCAPE:ad]." "http://palaeos.com/vertebrates/glossary/images/382x366xUnciform1.jpg.pagespeed.ic.NirdxtwNVu.jpg XAO:0003207 VHOG:0001161 VSAO:0005023 AAO:0000201 FMA:71335 Wikipedia:Carpus MA:0000040" + "Any process that stops, prevents, or reduces the frequency, rate or extent of glomerular filtration. Glomerular filtration is the processs whereby blood is filtered by the glomerulus into the renal tubule." + "The process whose specific outcome is the progression of the mesonephric macula densa over time, from its formation to the mature structure. The mesonephric macula densa is an area of specialized cells in the distal tubule of the mesonephros that makes contact with the vascular pole of the glomerulus." + "The chemical reactions and pathways resulting in the formation of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%)." + "The process whose specific outcome is the progression of a pronephric nephron tubule over time, from its formation to the mature structure. The pronephric nephron tubule is an epithelial tube that is part of the pronephric nephron and connects the filtration unit (glomerulus or glomus) of the pronephros to the pronephric duct." + "A cathepsin K that is encoded in the genome of human." "UniProtKB:P43235" + "A kidney interstitium that is part of a left kidney." "FMA:74271" + "An anatomical space that is enclosed by a pharynx." "FMA:54935 SCTID:180543003 EMAPA:18381 BTO:0002097 BSA:0000113 XAO:0000105 AAO:0010435" + "A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity." "ENVO:02000022 EHDAA2_RETIRED:0003184 BTO:0000491 galen:Excretion FMA:9674 AEO:0000184" + "A goblet cell that is part of the epithelium of trachea." "FMA:263075" + "The directed movement of dopamine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Dopamine is a catecholamine neurotransmitter and a metabolic precursor of noradrenaline and adrenaline." + "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein-DNA complex." + "Any process that increases the frequency, rate, or extent of monocyte chemotaxis." + "An early neural cell developing from the early ependymal cell of the neural tube." "FMA:70564" + "The chemical reactions and pathways resulting in the formation of juvenile hormones, the three sesquiterpenoid derivatives that function to maintain the larval state of insects at molting and that may be required for other processes, e.g. oogenesis." + "A telopode is a plasma membrane bounded cell projection that is present on a telocyte and is tens to hundreds of microns long. Telopodes form a labyrinthine system communicating through gap junctions." + "Any process that activates or increases the frequency, rate or extent of ossification, the formation of bone or of a bony substance or the conversion of fibrous tissue or of cartilage into bone or a bony substance." + "A cell of a platelike structure, especially a thickened plate of ectoderm in the early embryo, from which a sense organ develops." + "Any process that modulates the frequency, rate or extent of epithelial cell apoptotic process." + "A complete three dimensional shape in which there is a line connecting pair of points on the object that lies outside the object. Or: a shape with cavities. Contrast: concave." "Image:http://en.wikipedia.org/wiki/Image:Convex_polygon_illustration2.png" + "The process whose specific outcome is the progression of the skeletal myofibril over time, from its formation to the mature structure. A skeletal myofibril is a myofibril specific to skeletal muscle cells." + "A natural killer cell that is developmentally immature, has the phenotype CD34-negative, CD56-negative, CD117-positive, CD122-positive,and CD161-positive." + "A change in morphology and behavior of a glial cell resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor." + "An anatomical boundary that adjacent_to a hindbrain and adjacent_to a spinal cord." + "Any process that increases the frequency, rate, or extent of lipid transporter activity." + "Mesenchyme that develops_from a cranial neural crest." "TAO:0000787 EFO:0003572 ZFA:0000787 EMAPA:16169 EMAPA:16271 EMAPA_RETIRED:16271 EHDAA2:0000735" + "Any process that modulates the frequency, rate or extent of stem cell division." + "A fibroblast that is part of skin of back." + "Any process that modulates the frequency, rate or extent of compound eye retinal cell apoptotic process." + "Any process that activates or increases the frequency, rate or extent of meiotic cell cycle process involved in oocyte maturation." + "An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium." "MA:0000353 AAO:0000579 FMA:7148 VHOG:0000408 EV:0100070 UMLS:C0038351 Wikipedia:Stomach XAO:0000128 EFO:0000837 SCTID:181246003 EHDAA2:0001915 TAO:0002121 ANISEED:1235297 MIAA:0000051 BTO:0001307 GAID:293 MESH:D013270 NCIT:C12391 CALOHA:TS-0980 EMAPA:17021 MAT:0000051 EHDAA:2993 galen:Stomach" + "A vimentin that is encoded in the genome of human." "Reactome:R-HSA-9659977 UniProtKB:P08670 Reactome:R-HSA-9657898 Reactome:R-HSA-9646687 Reactome:R-HSA-9660019" + "An epithelial cell that is part of some loop of Henle thin descending limb." "KUPO:0001054" + "Renal artery that supplies the right kidney." "UMLS:C0226332 EMAPA:37380 SCTID:36800007 FMA:14752 MA:0002037 NCIT:C52740" + "The process whose specific outcome is the progression of a striated muscle over time, from its formation to the mature structure. Striated muscle contain fibers that are divided by transverse bands into striations, and cardiac and skeletal muscle are types of striated muscle. Skeletal muscle myoblasts fuse to form myotubes and eventually multinucleated muscle fibers. The fusion of cardiac cells is very rare and can only form binucleate cells." + "KUPO:0001028" + "A mesenchymal stem cell of the umbilical cord." + "One of sublaminar layers S3 or S4." "CP:0001040" + "The distal part of the loop of Henle that is impermeable to water and actively pumps sodium out of the filtrate to generate the hypertonic interstitium that drives countercurrent exchange; it consists of an initial very thin segment lined by simple squamous epithelium followed by a distal thick segment lined by simple cuboidal epithelium[MP]." "EMAPA:35510 NCIT:C32154 UMLS:C0227658 SCTID:245434005 Wikipedia:Ascending_limb_of_loop_of_Henle FMA:17717 MA:0001676" + "A quality that inheres in an entire organism or part of an organism." + "A mucosa that is part of a body of stomach [Automatically generated definition]." "FMA:17054" + "The process whose specific outcome is the progression of a nerve over time, from its formation to the mature structure." + "Any process that activates or increases the frequency, rate or extent of movement of RNA from the cytoplasm into the nucleus." + "An epithelium that is part of a mesonephros [Automatically generated definition]." + "The process whose specific outcome is the progression of the metanephric loop of Henle over time, from its formation to the mature structure. The metanephric loop of Henle is a metanephric nephron tubule that connects the proximal convoluted tubule to the distal convoluted tubule in the metanephros." + "A sesamoid element that is composed of bone tissue." "UMLS:C0036846 MESH:D012716 NCIT:C33541 GAID:210 EMAPA:36620 galen:SessamoidBone AEO:0000086 EHDAA2:0003086 Wikipedia:Sesamoid_bone FMA:32672 MA:0001375 SCTID:362914002" + + "The movement of an epithelial cell with respect to other epithelial cells that contributes to the shaping of the Malpighian tubule." + "A thymic medullary epithelial cell that expresses AIRE or other canonical markers of mature mTECs like Fezf2." + "Any process that modulates the frequency, rate or extent of spore formation from the products of meiosis. An example of this is found in Saccharomyces cerevisiae." + "The process whose specific outcome is the progression of a collecting duct in the mesonephros over time, from its formation to the mature structure. The collecting duct regulates water, electrolyte and acid-base balance. The collecting duct is the final common path through which urine flows before entering the ureter and then emptying into the bladder." + "Keratinized stratified squamous epithelium is a stratified squamous epithelium, the cells of which synthesize and accumulate keratin." "FMA:45568 Wikipedia:Stratified_squamous_epithelium#Keratinized" + "A portion of connective tissue that is part of a eyelid [Automatically generated definition]." "NCIT:C49482 UMLS:C1707989 MA:0001251 EMAPA:37532" + "Any process that activates or increases the frequency, rate or extent of the covalent alteration of one or more amino acid residues within a protein." + "A fibroblast that is part of the tunica adventitia of artery." "FMA:261285" + "Any process that stops, prevents or reduces the frequency, rate or extent of defense response to bacterium." + "An anatomical wall that is part of a ureter." "SCTID:279397004 FMA:15888" + "Any of the numerous small mucous-secreting glands located in the wall of the male or female urethra that help protect the epithelium from the corrosive urine." "EMAPA:37784 MA:0001688 FMA:19683 SCTID:279477005" + "Any process that activates or increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a vacuole." + "A muscle organ that attaches_to a clavicle and attaches_to a occipital bone." "MA:0002276 NCIT:C52895 EMAPA:37688" + "An epidermal cell that is part of the germinal matrix." + "Any process that reduces or removes the toxicity of inorganic compounds. These include transport of such compounds away from sensitive areas and to compartments or complexes whose purpose is sequestration of inorganic compounds." + "The chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo formation and steroid interconversion by modification." "Wikipedia:Steroid_metabolisms#Steroid_biosynthesis" + "An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. This cell has the widest dendritic field and the widest axon terminal of all retinal bipolar cells. The axon terminal is delicate and stratified through sublaminae 4 and 5 of the inner plexiform layer." + "The regulated release of proinsulin from secretory granules (B granules) in the B cells of the pancreas; accompanied by cleavage of proinsulin to form mature insulin, in response to a glucose stimulus." + "Any process that stops, prevents, or reduces the frequency, rate, or extent of type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families." + "FMA:15090" + "An interconnected tubular multi-tissue structure that contains fluid that is actively transported around the heart." "FMA:73747 ZFA:0005811" + "KUPO:0001025" + "The modification of peptidyl-tyrosine." + "A submucosa that is part of a pylorus [Automatically generated definition]." "EMAPA:27201 FMA:17462" + "A vein that carries deoxygenated blood from its corresponding ovary to inferior vena cava or one of its tributaries." "FMA:14346 SCTID:278193003 NCIT:C53058 EMAPA:18644 Wikipedia:Ovarian_vein UMLS:C0226720 MA:0002186" + "Any process that stops or reduces the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid)." + "EMAPA:37799 MA:0001152 FMA:18151" + "ZFA:0007044 TAO:0007044" + "An epithelium that is part of a foregut-midgut junction." "EHDAA2:0000573 EMAPA:16564" + "A retinal ganglion cell C outer that has symmetrical and dense dendritic dendritic tree with a large dendritic field." "BAMS:1066" + "Any process that activates or increases the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "KUPO:0001026" + "A subdivision of the skeleton that corresponds to the upper part of the mouth. The lower jaw skeleton includes the following elements, when present: upper jaw teeth, the maxilla and other lower jaw bones." "VHOG:0000429 EHDAA:8041 XAO:0003087 EHDAA2:0002128 MA:0001908 FMA:54397 AAO:0000622 EMAPA:17927" + "A type II vestibular sensory cell that is part of the stato-acoustic epithelium." "FMA:263194" + "The left branch of the atrioventricular bundle that separates at the bundle of His, descends the septal wall of the left ventricle and connects to the terminal Purkinje fiber[MP]." "galen:LeftBundleBranch EMAPA:37358 FMA:9487 SCTID:277690001" + "A D(2)-like dopamine receptor that is a translation product of the human DRD2 gene or a 1:1 ortholog thereof." "IUPHARobj:215" + "A short lived plasma cell that secretes IgA. These cells may be found in the bone marrow as well as in the mucosal immune system." + "Binding to estradiol." + "A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ." "EHDAA:420 UMLS:C0018787 TAO:0000114 CALOHA:TS-0445 EV:0100018 XAO:0000064 BILA:0000020 MAT:0000036 EMAPA:16105 Wikipedia:Heart GAID:174 ZFA:0000114 EHDAA2:0000738 MESH:D006321 EFO:0000815 AAO:0010210 MA:0000072 SCTID:302509004 VHOG:0000276 MIAA:0000036 FMA:7088 NCIT:C12727 galen:Heart BTO:0000562" + "A VIP peptides that is encoded in the genome of mouse." "UniProtKB:P32648" + "A blood vessel that is part of a finger [Automatically generated definition]." "EMAPA:37297 MA:0000621" + "A zone of skin that is part of a eyelid [Automatically generated definition]." "MA:0001256 FMA:24760 NCIT:C52718 UMLS:C0222088 SCTID:245947005 EMAPA:37536" + "The common iliac arteries are two large arteries, about 4cm long in adults but more than a centimetre in diameter, that originate from the aortic bifurcation. The arteries run inferolaterally, along the medial border of the psoas muscles to the pelvic brim, where they bifurcate into the external iliac artery and internal iliac artery. The common iliac artery, and all of its branches, exist as paired structures (that is to say, there is one on the left side and one on the right). The distribution of the common iliac artery is basically the pelvis and lower limb on the corresponding side. Both common iliac arteries are accompanied along their course by common iliac veins. [WP,unvetted]." "UMLS:C1261084 FMA:14764 Wikipedia:Common_iliac_artery EHDAA2:0000311 NCIT:C32357 SCTID:362050007 EMAPA:17310 MA:0001972 EHDAA:2553" + "A vessel that contains or conveys lymph, that originates as an interfibrillar or intercellular cleft or space in a tissue or organ, and that if small has no distinct walls or walls composed only of endothelial cells and if large resembles a vein in structure[BTO]." "NCIT:C33038 BTO:0000752 MAT:0000443 CALOHA:TS-2102 VHOG:0001249 EFO:0000873 MA:0000138 SCTID:279089004 EMAPA:35532 XAO:0000375 FMA:30315 Wikipedia:Lymphatic_vessel AAO:0011005 UMLS:C0229889" + "Any skin fibroblast that is part of a upper leg skin." + "Missing definition for term UBERON:0005321. Please replace it using linked reference." + "FMA:10483" + "A receptor in the vascular system, particularly the aorta and carotid sinus, which is sensitive to stretch of the vessel walls." + "Diffuse system of small concentrations of lymphoid tissue found in various sites of the body such as the gastrointestinal tract, thyroid, breast, lung, salivary glands, eye, and skin[WP]. Mucosal-associated lymphoid tissue is typically found as nodules associated with mucosal epithelia with distinct internal structures including B- and T-zones for the activation of lymphocytes[GO]." "NCIT:C12910 Wikipedia:Mucosa-associated_lymphoid_tissue FMA:62819 MA:0000140 UMLS:C0599921" + "An epithelial cell located on the basal lamina of the olfactory epithelium." "FMA:62303" + "Any process that activates or increases the frequency, rate or extent of the formation and development of teeth, the hard, bony appendages that are borne on the jaws, or on other bones in the walls of the mouth or pharynx of most vertebrates." + "An anatomical cavity that surrounded_by a synovial joint." "FMA:11356" + "The fibrous membrane forming the outer of the three coverings that surrounds the brain within the cranial cavity; consists of two layers including the periosteal layer and the meningeal layer." "UMLS:C0459393 FMA:71236 MA:0000815 NCIT:C49332 EMAPA:32668 SCTID:309321003 VHOG:0000270" + "Ossification that requires the replacement of a preexisting tissue prior to bone tissue formation." + "Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a chromosome." + "Combining with melanocortin to initiate a change in cell activity." + "A protein that is a translation product of the mouse Cd200r3 gene or a 1:1 ortholog thereof." + "Any process that activates or increases the frequency, rate, or extent of B cell anergy." + "MA:0002732 FMA:86488 EMAPA:35308" + "Any process that activates or increases the frequency, rate, or extent of myeloid cell apoptotic process." + "An endothelial progenitor cell that participates in angiogenesis during development." + "A tyrosine-protein kinase Mer that is encoded in the genome of human." "UniProtKB:Q12866 DTO:03100312" + "One of two small cells formed by the first and second meiotic division of oocytes." "WBbt:0008429 EHDAA2:0004716 XAO:0000262 MESH:D059705 FMA:85543" + "The biological process whose specific outcome is the progression of a left lung from an initial condition to its mature state. This process begins with the formation of the left lung and ends with the mature structure. The left lung is the lung which is on the left side of the anterior posterior axis looking from a dorsal to ventral aspect." + "Either of two openings transmitting nerves and blood vessels to or from the orbit." "SCTID:280546005 EMAPA:18717 EHDAA2:0001328 EHDAA:10648" + "Septum that divides the ovary, the basal portion of a carpel or group of fused carpels, that encloses the ovule(s)[GO]." + "An immature CD14-positive dermal dendritic cell is CD80-low, CD86-low, and MHCII-low." + "A bone marrow proteoglycan isoform 1 that has had the signal peptide removed." + "The process in which the ureteric bud is generated and organized." + "An erythrocyte lacking a nucleus." + "The process whose specific outcome is the progression of smooth muscle in the kidney over time, from its formation to the mature structure." + "The process of regulating the proliferation and elimination of myeloid cells such that the total number of myeloid cells within a whole or part of an organism is stable over time in the absence of an outside stimulus." + "The process in which the anatomical structures of the mesonephric glomerulus vasculature are generated and organized. The mesonephric glomerulus vasculature is composed of the tubule structures that carry blood or lymph in the mesonephric glomerulus." + "An ILC1 cell in the human with the phenotype CD56-negative, IL-7Ralpha-positive, T-bet-positive." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a dopamine stimulus." + "A fibroblast that is part of the connective tissue of nonglandular part of prostate." "FMA:261281" + "A putamen that is part of a right cerebral hemisphere." "HBA:4289 FMA:72828" + "Epithelial cell derived from mesoderm or mesenchyme." "FMA:69076" + "A venule that is part of a lung and drains oxygenated blood from pulmonary capillaries. A pulmonary venule merges into a pulmonary vein branch that runs in the pulmonary interlobular septa." + "A cell that is part of some vasa recta ascending limb." "KUPO:0001074" + "Any process that activates or increases the frequency, rate or extent of steroid hormone secretion." + "The process in which the bronchus cartilage is generated and organized. The bronchus cartilage is the connective tissue of the portion of the airway that connects to the lungs." + "A vein that drains the right pampiniform plexus and empties into the inferior vena cava." "NCIT:C52696 FMA:14345 SCTID:90988008 BTO:0002680 MA:0002219 EMAPA:37167" + "FMA:19623" + "Any process that modulates the frequency, rate or extent of apoptotic signaling pathway." + "Any process that activates or increases the frequency, rate or extent of tight junction assembly." + "The chemical reactions and pathways resulting in the formation of histamine, a physiologically active amine, found in plant and animal tissue and released from mast cells as part of an allergic reaction in humans." + "Any process that modulates the rate or extent of progress through the mitotic cell cycle." + "An arteriole located in the colon." + "A cell that is resistant to stains." "FMA:83626" + "Any process that stops or decreases the rate or extent of white fat cell proliferation." + "A DNA nucleotidylexotransferase that is encoded in the genome of mouse." "UniProtKB:P09838" + "A killer cell lectin-like receptor subfamily G member 1 that is encoded in the genome of human." "UniProtKB:Q96E93 Reactome:R-HSA-198006" + "Fat deposits in the mediastinum outside the parietal pericardium ." + "The metanephric distal convoluted tubule is a portion of the metanephric nephron tubule that connects the metanephric loop of Henle to the collecting duct[GO]." "VHOG:0001569" + "Subdivision of skeleton that is the collection of all skeletal elements in a pes, which is the distal section of the posterior hindlimb skeleton consisting of the mesopodium, the metapodium and the acropodium (e.g. including the ankle, sole, and toes)[Phenoscape]." "EHDAA2:0002228 FMA:24222 VSAO:0005021" + "Regular cardiac myocyte of a cardiac ventricle." "FMA:83109" + "The process in which the anatomical structures of a limb are generated and organized. A limb is a paired appendage of a tetrapod used for locomotion or grasping." + "Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in neurons." + "An endocrine cell that secretes juvenile hormone." "FBbt:00058020" + "Any process that activates or increases the frequency, rate or extent of extracellular vesicular exosome assembly." + + "Any process that modulates the frequency, rate, or extent of mature B cell apoptotic process." + "An epithelium that is part of a parathyroid gland." "CALOHA:TS-2141 NCIT:C48258 UMLS:C1709466" + "An organ that is capable of detecting electrical stimulus." + "A trypsin that is a serine protease of the granules from mast cells, cytotoxic T lymphocytes and/or natural killer cells. Leukocyte granule-associated proteinase is a component of the immune system that protect higher organisms against viral infection and cellular transformation. Members of this class have features that are strongly conserved including: consensus sequences at their N-termini and around the three catalytic residues, activation from zymogenic forms, and conserved disulphide bridges." + "The progression of the semicircular canal from its initial formation to the mature structure." + "The directed movement of proteins from the Golgi to a transport vesicle. Continuously secreted proteins are sorted into transport vesicles that fuse with the plasma membrane, releasing their contents by exocytosis." + "An epithelial cell that is part of some loop of Henle thick ascending limb segment located in the renal medulla." "KUPO:0001051" + "The process that gives rise to the glossopharyngeal nerve. This process pertains to the initial formation of a structure from unspecified parts. Various sensory and motor branches of the glossopharyngeal nerve supply nerve connections to the pharynx and back of the tongue. The branchial motor component contains motor fibers that innervate muscles that elevate the pharynx and larynx, and the tympanic branch supplies parasympathetic fibers to the otic ganglion." + "A gastrulation process in which the initial invagination becomes the anus and the mouth forms second." + "An enterocyte that is part of the epithelium of intestinal villus." "FMA:263088" + "A circular smooth muscle cell of the iris, innervated by the ciliary nerves (parasympathetic), and acting to contract the pupil. This muscle cell derives from neuroectoderm. This smooth muscle cell results from transformation of epithelial cells to smooth muscle cells." "FMA:70611" + "Anterosuperior fibrous portion of the left ventricle that connects to the ascending aorta." "FMA:9473 SCTID:264070001 Wikipedia:Aortic_vestibule EMAPA:37925" + "The chemical reactions and pathways involving any of a group of physiologically important biogenic amines that possess a catechol (3,4-dihydroxyphenyl) nucleus and are derivatives of 3,4-dihydroxyphenylethylamine." + "The collection of all skeletal elements in a pelvic complex - i.e. the combination of free limb or fin plus pelvic girdle." "FMA:24140" + "Any process that modulates the frequency, rate or extent of neurotransmitter receptor activity involved in synaptic transmission. Modulation may be via an effect on ligand affinity, or effector funtion such as ion selectivity or pore opening/closing in ionotropic receptors." + "Any process that stops, prevents or reduces the frequency, rate or extent of protein catabolic process." + "The process in which a relatively unspecialized cell acquires the specialized features of a respiratory basal cell." + "The progression of the septum transversum from its initial formation to the mature structure. The septum transversum is a portion of the trunk mesenchyme." + "Any process that activates or increases the frequency, rate or extent of protein maturation." + "Any photoreceptor cell that is part of a compound eye." "FBbt:00004211" + "A nucleus accumbens shell and olfactory tubercle D1 medium spiny neuron that co-expresses TAC3 and the DRD1 receptor." + "A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell." "Wikipedia:Programmed_cell_death" + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear inner or outer membrane." + "A scavenger receptor cysteine-rich type 1 protein M130 that is encoded in the genome of mouse." "UniProtKB:Q2VLH6" + "Any dendritic cell that is part of a liver." + "A manual digit metacarpus bone or its cartilage or pre-cartilage precursor." + "The process in which a relatively unspecialized cell acquires specialized features of a neuroendocrine cell of the stomach epithelium." + "Any process that increases the frequency or rate of the multiplication or reproduction of Schwann cells, resulting in the expansion of their population. Schwann cells are a type of glial cell in the peripheral nervous system." + "An endothelial transcription factor GATA-2 that is encoded in the genome of human." "UniProtKB:P23769 Reactome:R-HSA-996735" + "The process in which a relatively unspecialized cell acquires specialized features of a lateral line ganglion neuron." + "A germ cell that supports male gamete production. In some species, non-germ cells known as Sertoli cells also play a role in spermatogenesis." "ncithesaurus:Spermatogenic_Cell MA:0002765 VHOG:0001531 FMA:72290" + "The process in which a relatively unspecialized T cell acquires the specialized features of a T-helper 17 (Th17) cell. A Th17 cell is a CD4-positive, alpha-beta T cell with the phenotype RORgamma-t-positive that produces IL-17." + "A parvalbumin alpha that is encoded in the genome of mouse." "UniProtKB:P32848" + "A protein that is a translation product of the human IL5RA gene or a 1:1 ortholog thereof." "IUPHARobj:1706 PIRSF:PIRSF018419" + "An enterocyte that is part of the epithelium of duodenal gland." "FMA:263092" + "The chemical reactions and pathways resulting in the formation of any steroid hormone, naturally occurring substances secreted by specialized cells that affects the metabolism or behavior of other cells possessing functional receptors for the hormone." + "The developmental process pertaining to the initial formation of an endocardial cushion. The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves." + "A protein that is a translation product of the human CD2 gene or a 1:1 ortholog thereof." "PIRSF:PIRSF001984 IUPHARobj:2600" + "An organ thought to supplement the olfactory system in receiving pheromonic communication. The sensory part of the organ is in two long, thin sacs, situated on either side of the nasal septum at its base." "EFO:0001934 XAO:0000272 MA:0000289 EHDAA:7865 neuronames:1566 EMAPA:17612 MESH:D019147 EHDAA2:0002211 Wikipedia:Vomeronasal_organ AAO:0000997 FMA:77280 GAID:354 BTO:0002608 SCTID:361346007 VHOG:0000665" + + "A type II NK T cell that has been recently activated, secretes interleukin-4, and has the phenotype CD69-positive and downregulated NK markers." + "One of the racemose glands in the walls of the esophagus that in humans are small and serve principally to lubricate the food but in some birds secrete a milky fluid on which the young are fed." "FMA:9404 BTO:0003634 NCIT:C32536 UMLS:C0227178 SCTID:322749003 Wikipedia:Esophageal_glands" + "Anatomical projection that is part of the integumentl system." + "A Martinotti neuron that has axons that form a fan-like plexus." + "Surface layer of the olfactory cortex that contains dendrites, fiber systems and a small number of neurons. It has been divided into a superficial part and a deep part." "NLX:152609" + "Any process that increases the rate, frequency or extent of kidney development. Kidney development is the process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and excretes the end products of body metabolism in the form of urine." + "Subdivision of long bone which forms the part of the bone between two metaphyses. Note that the diaphysis includes the metaphyses, but the diaphysis proper excludes these." "MA:0002803 FMA:32688" + "OBSOLETE. A renal beta-intercalated cell that is part of the cortical collecting duct. The medullary collecting duct does not contain the renal beta-intercalated cell type." + "An iroquois-class homeodomain protein IRX-6 that is encoded in the genome of mouse." "UniProtKB:Q9ER75" + "A wall, dividing a cavity or structure into smaller ones[WP]." "AAO:0011127 FMA:86461 Wikipedia:Septum" + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cytokine stimulus." + "The process whose specific outcome is the progression of the descending thin limb over time, from its formation to the mature structure. The descending thin limb is a part of the loop of Henle situated just after the proximal straight tubule (S3). It extends to the tip of the loop of Henle." + "The process in which a smooth muscle cell acquires the specialized features of a foam cell. A foam cell is a type of cell containing lipids in small vacuoles and typically seen in atherosclerotic lesions, as well as other conditions." + "Any process that activates or increases the frequency, rate or extent of leukocyte degranulation." + "Ligament that joins successive centra. Important in controlling the stiffness of the vertebral column when it flexes." "FMA:31892 SCTID:244590009" + "The process whose specific outcome is the progression of a Sertoli cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a Sertoli cell fate." + "An unconventional T lymphocyte population within the thymic medulla that expresses both alpha/beta and gamma/delta T cell signatures." + "The developmental process that results in the creation of defined areas or spaces within the neural plate to which cells respond and eventually are instructed to differentiate." + "Any process that modulates the frequency, rate or extent of cell differentiation that contributes to the maintenance of a steady state of a cell type within a tissue." + "A protein complex composed of two identical immunoglobulin heavy chains of an IgG isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgG immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." + "A developmental process, independent of morphogenetic (shape) change, that is required for ganglion to attain its fully functional state." + "A dopamine receptor that is a product of the DRD1 or DRD5 gene. The active form binds dopamine and its activity is mediated by G proteins that cause activation of adenylate cyclase." "PIRSF:PIRSF038629" + "Any process that activates or increases the frequency, rate or extent of hepatocyte apoptotic process." + "Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels." + "Portion of tissue that is dorsolateral to the floor plate and part of the midbrain." "EHDAA2:0004375 ZFA:0000761 TAO:0000761 DHBA:12322 EFO:0003567" + "Anatomical space that is an opening in a bone of the skull." "Wikipedia:Foramina_of_the_skull SCTID:276742007 FMA:53165" + "The orderly movement of a muscle cell from one site to another, often during the development of a multicellular organism." + "A limb bud that develops into a hindlimb or pelvic fin." "TAO:0001384 VHOG:0001260 EFO:0003469 ZFA:0001384" + "Binding to a cytokine receptor." + "The formation of mature insulin by proteolysis of the precursor preproinsulin. The signal sequence is first cleaved from preproinsulin to form proinsulin; proinsulin is then cleaved to release the C peptide, leaving the A and B chains of mature insulin linked by disulfide bridges." + "The developmental process, independent of morphogenetic (shape) change, that is required for an epithelial cell of the prostate gland to attain its fully functional state. An epithelial cell is a cell usually found in a two-dimensional sheet with a free surface." + "A protein that is a translation product of the human RAG1 gene or a 1:1 ortholog thereof." + "Any process that activates or increases the frequency, rate or extent of stem cell proliferation." + "Any process that stops, prevents or reduces the frequency, rate or extent of plasma membrane bounded cell projection assembly." + "The progression of the eyelid in a camera-type eye from its formation to the mature state. The eyelid is a membranous cover that helps protect and lubricate the eye." + "A segment of the developing hindbrain[ZFA]. In the vertebrate embryo, a rhombomere is a transiently divided segment of the developing neural tube, within the hindbrain region (a neuromere) in the area that will eventually become the rhombencephalon. The rhombomeres appear as a series of slightly constricted swellings in the neural tube, caudal to the cephalic flexure.[WP]." "MAT:0000272 Wikipedia:Rhombomere EMAPA:16148 TAO:0001064 RETIRED_EHDAA2:0000669 XAO:0004079 MIAA:0000272 VHOG:0000672 FMA:295666 ZFA:0001064 DHBA:12664 EFO:0003617" + "The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse." "Wikipedia:Neurotransmission" + "Any process that stops, prevents, or reduces the frequency, rate or extent of nurse cell apoptotic process." + "The process whose specific outcome is the progression of the nephron epithelium over time, from its formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure. The nephron epithelium is a tissue that covers the surface of a nephron." + "A structure created during embryogenesis when the lateral mesoderm splits into two layers - the inner (or splanchnic) layer adheres to the endoderm, and with it forms the splanchnopleure[WP]." "EHDAA:383 EHDAA2:0001903 FMA:295564 Wikipedia:Splanchnopleure VHOG:0000558 NCIT:C34303 UMLS:C1519472 EMAPA:16181" + "The process whose specific outcome is the progression of a blood vessel of the retina over time, from its formation to the mature structure." + "Ophthalmic veins are veins which drain the eye. More specifically, they can refer to: Superior ophthalmic vein Inferior ophthalmic vein." "EHDAA2:0004113 XAO:0004169 EMAPA:19313 Wikipedia:Ophthalmic_veins" + "Anatomical group whose component anatomical structures lie in close proximity to each other." "VHOG:0001737" + "Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane." "Wikipedia:Organelle NIF_Subcellular:sao1539965131" + "The process whose specific outcome is the progression of the dendrite over time, from its formation to the mature structure." + "The process whose specific outcome is the progression of the proximal straight tubule over time, from its formation to the mature structure. The proximal straight tubule is the part of the descending limb that extends from the proximal convoluted tubule to the descending thin tubule." + "An epidermal progenitor cell that arises from neuroectoderm and in turn gives rise to the epidermal sheath of ventral and cephalic regions." "FBbt:00004994" + "A cell of the monocyte, granulocyte, mast cell, megakaryocyte, or erythroid lineage." "MESH:D022423 CALOHA:TS-0647 BTO:0001441" + "Chemosensitive cells that innervate the vomernasal organ epithelium and are responsible for receiving and transmitting pheromone signals." + "Any process that activates or increases the frequency, rate or extent of parathyroid hormone secretion." + "Any biological process involved in the maintenance of an internal steady state." + "Any process that activates or increases the rate or extent of brown fat cell proliferation." + "A T cell that is located in the anorectum." + "An efferent neuron that passes from the central nervous system or a ganglion toward or to a muscle and conducts an impulse that causes or inhibits movement." "FBbt:00005123 WBbt:0005409 FMA:83617 BTO:0000312" + "A polymeric supramolecular structure." + "Any process that modulates the rate, frequency or extent of the progression of the cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate." + "Any process that activates or increases the frequency, rate or extent of T cell activation." + "Epithelial cell that is part of segment 1 (S1) of the proximal tubule epithelium." + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of amides." + "The process whose specific outcome is the progression of a cranial skeletal system over time, from its formation to the mature structure. The cranial skeletal system is the skeletal subdivision of the head, and includes the skull (cranium plus mandible), pharyngeal and/or hyoid apparatus." + "The chemical reactions and pathways resulting in the formation of organic and inorganic nitrogenous compounds." + "A macrophage which develops from an inflammatory monocyte and is recruited into the tissues in response to injury and infection as part of an inflammatory response. Markers include CD11b-positive, CD68-positive, and F4/80-positive." "FMA:84643 FMA:84645" + "A group 3 innate lymphoid cell in the human with the phenotype IL-7Ralpha-positive, and NKp44-negative." + "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." "Wikipedia:Metabolism" + "The process whose specific outcome is the progression of an organismal system over time, from its formation to the mature structure. A system is a regularly interacting or interdependent group of organs or tissues that work together to carry out a given biological process." + "Endocardium that is part of the cardiac ventricle." "MA:0000079 EMAPA:32747 SCTID:192172004 ZFA:0001615 FMA:12148 VHOG:0000607 TAO:0002247" + "GC_ID:1" + "An eosinophil peroxidase that is encoded in the genome of mouse." "UniProtKB:P49290" + "Aggregate brain region defined as those areas of cerebral cortex receiving direct synaptic input from the olfactory bulb (Price, 1973). It usually includes the piriform cortex and sometimes other areas." "MA:0000193 EHDAA:5482 VHOG:0000325 BAMS:OLF UMLS:C0162434 FMA:276600 HBA:265504406 BIRNLEX:2707 neuronames:2275 EHDAA2:0001289 BTO:0001446 MESH:D066194 Wikipedia:Olfactory_cortex EMAPA:17779" + "The directed movement of neurotransmitters into neurons or glial cells. This process leads to inactivation and recycling of neurotransmitters." + "The nasal glands are the seromucous glands in the respiratory region of the nasal mucous membrane. The three major types of nasal glands are anterior serous glands, seromucous glands, and Bowman glands." "NCIT:C22725 UMLS:C1522269 FMA:321518 SCTID:368881007 EMAPA:37871 Wikipedia:Nasal_glands" + "Any process that increases the frequency, rate or extent of muscle contraction of the hindgut, the posterior part of the alimentary canal, including the rectum, and the large intestine." + "Any process that modulates the frequency, rate, or extent of dendritic cell antigen processing and presentation." + "Any process that stops, prevents, or reduces the frequency, rate or extent of vesicle fusion." + "A cell morphology that inheres in neurons which have a pyramidal shaped soma, a single axon, a large apical dendrite and multiple basal dendrites." "SAO:1465673360 ILX:0109553" + "An epithelial cell of the bronchus." "BTO:0002922" + "Mesenchyme that develops_from a head mesenchyme from mesoderm and is part of a 1st arch maxillary mesenchyme." "EHDAA2:0000043" + "The process whose specific outcome is the progression of lymph nodes over time, from their formation to the mature structure. A lymph node is a round, oval, or bean shaped structure localized in clusters along the lymphatic vessels, with a distinct internal structure including specialized vasculature and B- and T-zones for the activation of lymphocytes." + "Assembly or disassembly of microtubules by the addition or removal of tubulin heterodimers from a microtubule." + "Any process that modulates the occurrence or rate of cell death by apoptosis that results in the maintenance of the steady-state number of cells within a tissue." + "Any process that modulates the frequency, rate or extent of membrane disassembly." + "A circumventricular organ that is capable of monitoring the levels of substances to the cerebrospinal fluid." "EMAPA:37741 neuronames:2856 MA:0002944" + "Any process that activates, maintains or increases the rate of muscle development." + "A melanocyte that produces pigment in the epithelium." + "A densely staining taste receptor cell that contains many dense vacuoles in their apical regions which project into the apical space and bear microvilli. This cell type serves as a supporting cell by surrounding and isolating the other cell types from each other; secrete a dense amorphous material that surrounds the microvilli in the taste pore. This cell type expresses a glial glutumate transporter, GLAST." "FMA:62356" + "Trophoblast cell migration that is accomplished by extension and retraction of a pseudopodium. Trophoblast cells line the outside of the blastocyst." + "A lymph node that is part of a bronchus." "UMLS:C1305372 NCIT:C32232 MA:0003078" + "A scavenger receptor cysteine-rich type 1 protein M130 that is encoded in the genome of human." "UniProtKB:Q86VB7" + "Any fibroblast that is part of a gallbladder." + "A T-helper cell that is characterized by secreting interleukin 9 and responding to helminth infections. This cell-type can derives from Th2 cells in the presence of TGF-beta and IL-4. Th2 cytokine production is surpressed." + "Cell-cell signaling from postsynapse to presynapse, across the synaptic cleft, mediated by a lipid ligand." + "Artery that supplies the axilla." "FMA:22654 SCTID:181321001 galen:AxillaryArtery Wikipedia:Axillary_artery MA:0002573 UMLS:C0004455 GAID:473 NCIT:C32169 MESH:D001366 EMAPA:18749" + "An epithelial cell that is part_of a umbilical artery." + "The appearance of oxytocin, a cyclic nonapeptide hormone with amino acid sequence CYIQNCPLG, due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Oxytocin is the principal uterine-contracting and milk-ejecting hormone of the posterior pituitary, and together with the neuropeptide vasopressin, is believed to influence social cognition and behavior. It also acts as a neurotransmitter in the brain." + "A cell comprising the transparent, biconvex body separating the posterior chamber and vitreous body, and constituting part of the refracting mechanism of the mammalian eye." "FMA:70950" + "A portion of connective tissue that is part of a forelimb [Automatically generated definition]." "MA:0000613 EMAPA:37314" + "The branches of the arcuate arteries of the kidney that radiate outward throught the renal columns and supply the glomeruli[MP]. The first set of renal bloodvessels, the interlobular arteries (or cortical radiate arteries, or cortical radial arteries), are given off at right angles from the side of the arcuate arteries looking toward the cortical substance, and pass directly outward between the medullary rays to reach the fibrous tunic, where they end in the capillary network of this part. These vessels do not anastomose with each other, but form what are called end-arteries. In their outward course they give off lateral branches; these are the afferent vessels for the renal corpuscles; they enter the capsule, and end in the glomerulus. From each tuft the corresponding efferent vessel arises, and, having made its egress from the capsule near to the point where the afferent vessel enters, breaks up into a number of branches, which form a dense plexus within Bowman's capsule." "SCTID:76147008 MA:0002584 UMLS:C1512856 NCIT:C32826 EMAPA:28212 Wikipedia:Interlobular_arteries FMA:70498" + "An alpha-beta CD4 T cell that resides in the lung." + "The process in which an immature plasmacytoid dendritic cell acquires the specialized features of a mature plasmacytoid dendritic cell contributing to an immune response." + "Any process that activates or increases the frequency, rate or extent of alpha-beta T cell differentiation." + "The process in which a relatively unspecialized cell acquires the specialized features of a DN3 thymocyte. A DN3 thymocyte is a CD4-,CD8- thymocyte that is also CD44+,CD25+." + "The process whereby a relatively unspecialized cell acquires specialized features of an amniotic stem cell. An amniotic stem cell is a mesenchymal stem cell extracted from amniotic fluid. Amniotic stem cells are able to differentiate into various tissue types such as skin, cartilage, cardiac tissue, nerves, muscle, and bone." + "A simple columnar cell that populates the entire luminal surface including the gastric pits. This cell types secrete mucus to form a thick protective, lubricant layer over the gastric wall." "FMA:62949" + "CD4-positive, alpha-beta long-lived T cell with the phenotype CD45RO-positive and CD127-positive. This cell type is also described as being CD25-negative, CD44-high, and CD122-high." + "Binding to heparin, a member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues." + "An area of cerebral cortex defined on the basis of cytoarchitecture that have six layers. Starting from the cortical surface the layers are: molecular layer (I), external granular layer (II), external pyramidal layer (III), internal granular layer (IV), internal pyramidal layer (V), and multiform layer (VI). Neocortex is most prominent in the frontal lobe, the parietal lobe, the temporal lobe and the occipital lobe, less so in the cingulate gyrus, the parahippocampal gyrus and the insula. It is composed of two subdivisions: true isocortex and proisocortex (Carpenter-83)(NN)." "FMA:62429 MESH:D019579 BAMS:NCX BIRNLEX:2547 MA:0002754 BTO:0000920 GAID:677 EMAPA:32842 MBA:315 BAMS:Iso-cortex UMLS:C0175173 BAMS:ISO Wikipedia:Neocortex PBA:294021746 EMAPA:35589 neuronames:757 EHDAA2:0004662 DHBA:10160" + "The process whose specific outcome is the progression of an esophagus over time, from its formation to the mature structure." + "The orderly movement of an anterior visceral endoderm cell from one site to another." + "A B-cell receptor CD22 that is encoded in the genome of human." "UniProtKB:P20273" + "Any process that activates or increases the rate or extent of hepatocyte differentiation." + "The series of events required for an organism to receive an electrical stimulus, convert it to a molecular signal, and recognize and characterize the signal. Many fish possess an electroception sense; for example, the electric eel uses low voltage pulses of electricity for navigation and prey location." "Wikipedia:Electroreception" + "Any process that modulates the frequency, rate or extent of the directed movement of the neurotransmitter acetylcholine into a cell." + "Cytoskeletal structure made from intermediate filaments, typically organized in the cytosol as an extended system that stretches from the nuclear envelope to the plasma membrane. Some intermediate filaments run parallel to the cell surface, while others traverse the cytosol; together they form an internal framework that helps support the shape and resilience of the cell." + "A border cell is a slender columnar cell on the medial portion of the basilar membrane." "FMA:79798" + "GC_ID:1" + "A developmental process, independent of morphogenetic (shape) change, that is required for a platelet to attain its fully functional state. A platelet is a non-nucleated disk-shaped cell formed by extrusion from megakaryocytes, found in the blood of all mammals, and mainly involved in blood coagulation." + + "The regulated release of serotonin by a mast cell or group of mast cells." + "A progenitor cell of the B cell lineage, with some lineage specific activity such as early stages of recombination of B cell receptor genes, but not yet fully committed to the B cell lineage until the expression of PAX5 occurs." "BTO:0003104" + "A nerve that is part of a hindlimb stylopod [Automatically generated definition]." "EMAPA:37344 MA:0000685" + "The process in which the larynx is generated and organized. The larynx is a continuation of the pharynx that is involved in breathing, sound production, and protecting the trachea against food aspiration." + "FMA:65265 MA:0001175 EMAPA:37719" + "The progression of the heart rudiment over time, from its initial formation to the mature structure. The heart rudiment is a cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube." + "Any process that stops, prevents or reduces the frequency, rate or extent of vasculature development." + "A protein that is a translation product of the human GATA2 gene or a 1:1 ortholog thereof." + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hormone stimulus." + "The cavity formed by the tubotympanic recess epithelium." "EHDAA2:0002095" + "The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division." "Wikipedia:Cell_cycle" + "An epithelium consisting of cuboidal epithelial cells." "Wikipedia:Cuboidal_epithelium NCIT:C32415 UMLS:C0682577" + "The process in which the structures of a glial cell in the posterior lateral line nerve are generated and organized. This process occurs while the initially relatively unspecialized cell is acquiring the specialized features of a glial cell in the posterior lateral line nerve." + "OBSOLETE A L2/3 pvalb-like sst GABAergic cortical interneuron (Mus musculus) that has Martinotti morphology." + "A portion of connective tissue that is part of a hip [Automatically generated definition]." "MA:0000656 EMAPA:37323" + "A neural cell adhesion molecule that is involved in neuronal development, synaptic plasticity, and regeneration." "PIRSF:PIRSF501037" + "Any process that stops, prevents or reduces the frequency, rate or extent of epithelial tube formation." + + "A complement receptor type 1 that is encoded in the genome of human." "UniProtKB:P17927" + "Any process that stops, prevents or reduces the frequency, rate or extent of photosynthesis." + "The great saphenous vein (GSV), also greater saphenous vein, is the large (subcutaneous) superficial vein of the leg and thigh. The terms 'safaina' (Greek) and 'el safin' (Arabic) have both been claimed as the origin for the word 'saphenous'. [WP,unvetted]." "galen:GreatSaphenousVein EMAPA:37147 Wikipedia:Great_saphenous_vein galen:GreaterSaphenousVein FMA:21376 SCTID:181402008 NCIT:C33004 MA:0002216 BTO:0003271 UMLS:C0392907" + "A protein that is a translation product of the human CD44 gene or a 1:1 ortholog thereof." + "PMID:12878460 PMID:11214319 PMID:11214318 GC_ID:1" + "DMBA:17747 BIRNLEX:1533 DHBA:12887" + "Any process that stops, prevents, or reduces the frequency, rate or extent of Schwann cell differentiation." + "The directed, self-propelled movement of a cilium." + "A broadly stratifying amacrine cell that has a small dendritic field and post-synaptic terminals in S2 and S3. This cell type releases the neurotransmitter glycine." + "A skeletal ligament that is part of a sternoclavicular joint." "FMA:63980 SCTID:182386007" + "Any process that increases the rate or frequency of muscle cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a muscle cell and result in its death." + "A blood vessel that is part of a respiratory system [Automatically generated definition]." "EMAPA:35995 MA:0001799 EMAPA:35731" + "Any process that stops, prevents or reduces the frequency, rate or extent of stem cell differentiation." + "The process whose specific outcome is the progression of an embryo over time, from zygote formation until the end of the embryonic life stage. The end of the embryonic life stage is organism-specific and may be somewhat arbitrary; for mammals it is usually considered to be birth, for insects the hatching of the first instar larva from the eggshell." + "Any process that modulates the frequency, rate or extent of natural killer cell chemotaxis." + "The nodules of antigen-activated, differentiating B cells, follicular dendritic cells, antigen-presenting T cells and macrophages in the spleen white pulp." "EMAPA:37961" + "A neuromuscular junction in which the target muscle cell is a skeletal muscle fiber." + "A blood vessel that is part of a forelimb stylopod [Automatically generated definition]." "EMAPA:37294 MA:0000603" + "A muscle innervated by a facial nerve." "NCIT:C13073 MA:0003160 SCTID:25903009 MESH:D005152 Wikipedia:Facial_muscles XAO:0001013 FMA:46751 GAID:143 MFMO:0000005 UMLS:C0015460" + "A collagen homotrimer of alpha1(II) chains; type II collagen triple helices associate to form fibrils." "Wikipedia:Collagen_type_II" + + "Juxtaglomerular apparatus of the mature vertebrate kidney, or metanephros." + "The directed movement of iron ions from outside of a cell, across the plasma membrane and into the cytosol." + "A protein that is a translation product of the human CR1 gene or a 1:1 ortholog thereof." + "The series of events in which a stimulus indicating lowered oxygen tension is received by a cell and converted into a molecular signal. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level." + "The process in which a precursor cell type acquires the specialized features of an alpha-beta T cell. An alpha-beta T cell is a T cell that expresses an alpha-beta T cell receptor complex." + "A tuft cell located in the small intestine." + "Endochondral bone that is paired, forming the posterior part of the pelvis, articulating with the pubis and ilium." "NCIT:C32884 FMA:16592 SCTID:182025004 galen:Ischium Wikipedia:Ischium EMAPA:18727 GAID:208 UMLS:C0022122 MESH:D007512 AAO:0000860 VSAO:0005006 MA:0001337" + "KUPO:0001024" + "Any process that activates or increases the frequency, rate or extent of neuromuscular junction development." + "The multiplication or reproduction of subpallium cells in the forebrain, resulting in the expansion of a cell population." + "A type of mesothelial fibroblast that is derived from the neural crest, is localized on blood vessels, and is a key component of the pia and arachnoid membranes surrounding the brain." "ILX:0770143" + "The movement of a basophil in response to an external stimulus." + "A neuron of the vertebrate central nervous system that is small in size. This general class includes small neurons in the granular layer of the cerebellar cortex, cerebral cortex neurons that are not pyramidal cells and small neurons without axons found in the olfactory bulb." "BTO:0003393" + "An epithelium that is part of a right lung [Automatically generated definition]." "MA:0003132 EMAPA:17663" + "Any process that activates or increases the frequency, rate, or extent of an antimicrobial humoral response." + "A developmental process, independent of morphogenetic (shape) change, that is required for a cranial nerve to attain its fully functional state. The cranial nerves are composed of twelve pairs of nerves that emanate from the nervous tissue of the hindbrain. These nerves are sensory, motor, or mixed in nature, and provide the motor and general sensory innervation of the head, neck and viscera. They mediate vision, hearing, olfaction and taste and carry the parasympathetic innervation of the autonomic ganglia that control visceral functions." + "The series of events in which a temperature stimulus is received and converted into a molecular signal as part of sensory perception." + "Any process that modulates the frequency, rate or extent of gamma-delta T cell activation." + "Any process that stops, prevents or reduces the frequency, rate or extent of stem cell proliferation." + "A prostaglandin D2 receptor DP2 that is encoded in the genome of mouse." "UniProtKB:Q9Z2J6" + "A dermal dendritic cell that is CD1a-positive and CD14-negative." + "The process whose specific outcome is the progression of the juxtaglomerular apparatus in the metanephros over time, from its formation to the mature structure. The juxtaglomerular apparatus is an anatomical structure which consists of juxtaglomerular cells, extraglomerular mesangial cells and the macula densa. The juxtaglomerular apparatus lies adjacent to the glomerulus and regulates kidney function by maintaining the blood flow to the kidney and the filtration rate." + "A quality inhering in a bearer by virtue of the extent to which the bearer is capable of being stretched or swollen." + "Any process that modulates the frequency, rate or extent of the directed movement of the neurotransmitter histamine into a cell." + "A mucosa that is part of a lacrimal sac [Automatically generated definition]." "FMA:72061" + "PMID:15522813 PMID:12082125 GC_ID:1 PMID:11214319" + + "Any process involved in the maintenance of an internal steady state of calcium ions within an organism or cell." + "KUPO:0001021" + "Major subdivision of an organism that protrudes from the body[DOS, CARO]." "EFO:0000799 BTO:0001492 VSAO:0000075 EHDAA2:0003193 EMAPA:37283 UMLS:C0598782 NCIT:C61460 MESH:D005121 XAO:0000218 Wikipedia:Appendage EV:0100155 HAO:0000144 AEO:0000193 MIAA:0000023 BILA:0000018 MAT:0000023 CARO:0010003" + "Any process that activates or increases the frequency, rate or extent of differentiation of CD4-positive, CD25-positive, alpha-beta regulatory T cells as part of an immune response." + "A mature T cell that differentiated and acquired cytotoxic function with the phenotype perforin-positive and granzyme-B positive." "CALOHA:TS-0190 BTO:0000289 FMA:70573" + "Any muscle organ that is part of a shoulder [Automatically generated definition]." "MA:0000633 FMA:33531 EMAPA:36154" + "Mesenchyme that is part of a otic placode." "EMAPA:16196 EHDAA2:0001340" + "Any microtubule cytoskeleton organization that is involved in mitosis." + "Any process that modulates the occurrence or rate of T cell death by apoptotic process." + "The process whose specific outcome is the progression of the axial mesoderm over time, from its formation to the mature structure. The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord." + "Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body." "NCIT:C13236 HAO:0000004 XAO:0004001 AEO:0000004 TAO:0001487 BILA:0000004 ZFA:0001487 AAO:0010839 CALOHA:TS-2101 VHOG:0001726 TGMA:0001824 SPD:0000008 MA:0002450 CARO:0000004 galen:BodySubstance FMA:9669 EHDAA2:0003004 EMAPA:35178" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the formation of cellular spores derived from the products of meiosis." + "Small cavity surrounding the bones of the middle ear." "SCTID:362551002 Wikipedia:Tympanic_cavity EMAPA:37778 EHDAA2:0004119 FMA:56461 BTO:0002098" + "Orifice of the olfactory system. The naris is the route by which odorants enter the olfactory system[MAH]." "MA:0000282 galen:Naris SCTID:272650008 EHDAA2:0001225 EHDAA:9083 VHOG:0000663 EMAPA:17847 AAO:0000311" + "Obsolete. Use PO:0000284 from Plant Ontology instead. An epidermal cell associated with a stoma and at least morphologically distinguishable from the epidermal cells composing the groundmass of the tissue." + "A cholecystokinin that is encoded in the genome of human." "UniProtKB:P06307" + "The process in which the anatomical structure of the endocardial cushion is generated and organized. The endocardial cushion is a specialized region of mesenchymal cells that will give rise to the heart septa and valves." + "A smooth muscle cell that is part of a sphincter. A sphincter is a typically circular muscle that normally maintains constriction of a natural body passage or orifice and which relaxes as required by normal physiological functioning." + "Any process that modulates the frequency, rate or extent of translational initiation." + "Chondrocyte forming the hyaline cartilage found in joints." "CALOHA:TS-0056" + "Any process that stops, prevents, or reduces the frequency, rate, or extent of an immunoglobulin mediated immune response." + "KUPO:0001036" + "The process in which the anatomical structures of the internal genitalia are generated and organized. The internal genitalia are the internal sex organs such as the uterine tube, the uterus and the vagina in female mammals, and the testis, seminal vesicle, ejaculatory duct and prostate in male mammals." + "PMID:11214319 PMID:12082125 PMID:12878460 GC_ID:1 PMID:15522813" + "The aggregation, arrangement and bonding together of proteins and lipids to form a protein-lipid complex." + "The process whose specific outcome is the progression of a bone cell over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell." + "Any fibroblast that is part of a pericardium." + "Any process that stops, prevents or reduces the frequency, rate or extent of germ cell proliferation." + "Any process that activates or increases the frequency, rate or extent of lysosomal protein catabolic process." + "The differentiation of endothelial cells from progenitor cells during blood vessel development, and the de novo formation of blood vessels and tubes." "Wikipedia:Vasculogenesis" + "The layer of glia and differentiating neurons that forms as a second layer around the germinal neuroepithium; as this develops it comes to lie between the ventricular and marginal layers and includes the basal and alar plates. Develops into neurons and glia forming a gray matter layer." "neuronames:1367 EMAPA:17148 EMAPA:35360" + "Any process that activates or increases the frequency, rate or extent of odontoblast differentiation." + "The glandular mucous membrane lining of the uterine cavity that is hormonally responsive during the estrous/menstrual cycle and during pregnancy." "MAT:0000319 EFO:0000980 SCTID:278867007 GAID:377 EV:0100115 MESH:D004717 VHOG:0001285 EMAPA:29917 NCIT:C12313 Wikipedia:Endometrium CALOHA:TS-0276 BTO:0001422 MA:0000390 UMLS:C0014180 FMA:17742 MIAA:0000319" + "A membranous sac that develops from the posterior part of the alimentary canal in the embryos of mammals, birds, and reptiles, and it is important in the formation of the umbilical cord and placenta in mammals[VHOG]." "NCIT:C34101 SCTID:308825007 RETIRED_EHDAA2:0000114 VHOG:0000738 EMAPA:16107 MESH:D000482 UMLS:C0002084 Wikipedia:Allantois BTO:0000474 EHDAA2:0001504 EMAPA_RETIRED:16084" + "A neuron projection bundle that connects the retina or its analog in the eye with the brain. This includes the vertebrate optic nerve (not truly a nerve) as well as analogous structures such as the Bolwig nerve in Drosophila." "EV:0100351 BTO:0000966 TADS:0000232" + "A holocrine gland of the dermis that secretes sebum into hair follicles." "SCTID:115977007 MA:0000149" + "A low affinity immunoglobulin gamma Fc region receptor II that is encoded in the genome of mouse." "UniProtKB:P08101" + "A gland in which the principal secretory cells are serous secreting cells." "EMAPA:37950 BTO:0001837 Wikipedia:Serous_gland FMA:62889" + "The series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription." + "Any process that activates or increases the frequency, rate or extent of testosterone secretion." + "Any process that activates or increases the frequency, rate or extent of natural killer cell chemotaxis." + "The process whose specific outcome is the formation of tooth enamel, occurring in two stages: secretory stage and maturation stage." + "A protein that is a translation product of the human GATA1 gene or a 1:1 ortholog thereof." + "An artery that is part of a respiratory system [Automatically generated definition]." "MA:0001804 EMAPA:37569" + "Any process that modulates the frequency, rate or extent of endocytosis." + "The process whose specific outcome is the progression of the distal tubule over time, from its formation to the mature structure. In mammals, the distal tubule is a nephron tubule that begins at the macula densa and extends to the connecting tubule." + "The process in which the prostate gland stroma is generated and organized. The prostate gland stroma is made up of the mesenchymal or fibroblast cells of the prostate gland." + "Any process that stops, prevents, or reduces the frequency, rate or extent of post-embryonic development. Post-embryonic development is defined as the process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure." + "A urethra that is part of a female reproductive system." "EMAPA:28747 UMLS:C0458485 FMA:19669 BTO:0004088 SCTID:264469008 NCIT:C32591 MA:0002637 Wikipedia:Female_urethra" + "The directed movement of calcium ions (Ca2+) out of the Golgi apparatus into the cytosol." + "The mesentery that originates from the dorsal side of the peritoneal cavity[ZFA]." "EHDAA:3957 EHDAA2:0004560 FMA:79795 EHDAA:3033 EHDAA:3921 ZFA:0005130 Wikipedia:Mesentery#Development EHDAA:3971 TAO:0005130 EHDAA:3934 SCTID:308823000 EHDAA:3019" + "The process in which an antigenically naive alpha-beta T cell acquires the specialized features of an effector, regulatory, or memory T cell during an immune response. Effector T cells include cells which provide T cell help or exhibit cytotoxicity towards other cells." + "A neprilysin that is encoded in the genome of human." "UniProtKB:P08473" + "A renal cortex interstitium that is part of a right kidney." + "That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid." "NIF_Subcellular:sao1425028079" + "A blood vessel smooth muscle that is part of a respiratory system [Automatically generated definition]." "EMAPA:37573 MA:0001806" + "Any material entity that is located in the digestive tract. This includes undigested food and liquid as well as unexcreted waste products. It also includes other entities such as ingested stones used to aid digestion. Any microbial cells or cell populations are also included." + "The process in which the sinus venosus is generated and organized. The sinus venosus is a heart chamber attached to the atrium on the venous side of the embryonic heart." + "The directed killing of a target cell by a leukocyte." + "Enables the energy-independent passage of monoatomic cations across a lipid bilayer down a concentration gradient." "Reactome:R-HSA-426223 Reactome:R-HSA-9754616 Reactome:R-HSA-9706720 Reactome:R-HSA-4420052 Reactome:R-HSA-1296043 Reactome:R-HSA-2089943 Reactome:R-HSA-1168376 Reactome:R-HSA-169683 Reactome:R-HSA-9712190" + "Any anatomical structure that is part of the reproductive system." + "Simple columnar epithelium in which the luminal side of the cells bears cilia. Examples: epithelium of trachea, epithelium of uterine tube.[FMA]." "FMA:64798" + "A fibroblast-like cell that provides support at neuromuscular junctions in vertebrates and are localized outside the synaptic basal lamina." + "An anatomical space with no opening to another space or to the exterior." "AEO:0000222" + "A cellular quality that arises by virtue of whether the bearer's disposition to differentiate into one or more mature cell types." + "Combining with a protein hormone to initiate a change in cell activity." + "The regulated release of serotonin by a cell. Serotonin (5-hydroxytryptamine, or 5-HT) is a monoamine synthesised in serotonergic neurons in the central nervous system, enterochromaffin cells in the gastrointestinal tract and some immune system cells." + "A transverse unitary subdivision of the neural tube that shares a common dorsoventral structure (floor, basal, alar, and roof plates), but each having differential molecular identities and fates; they comprise the secondary prosencephalon, diencephalon (prosomeres), the midbrain (mesomeres), and the hindbrain (rhombomeres)." "NLX:147842 ZFA:0001328 Wikipedia:Neuromere TAO:0001328" + "The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues." "Wikipedia:Cell_migration" + "Any process that stops, prevents or reduces the frequency, rate or extent of amniotic stem cell differentiation." + "An outgrowth on the lateral trunk of the embryo that develops into a limb. The limb bud is divided into ectoderm and mesenchyme[cjm, modified from MP]." "MESH:D018878 EMAPA:35944 Wikipedia:Limb_bud FMA:296780 BTO:0001640 XAO:0003161 GAID:1307 AAO:0010375 NCIT:C34203 UMLS:C0282505" + "A white matter of cerebral lobe that is part of a parietal lobe." "FMA:256184 SCTID:369200008" + "Any process that modulates the frequency, rate or extent of the directed movement of proteins within cells." + "The process in which relatively unspecialized cells acquire specialized structural and/or functional features that characterize the interstitial fibroblast of the kidney as it progresses from its formation to the mature state." + "The process that gives rise to the hypoglossal nerve. This process pertains to the initial formation of a structure from unspecified parts. This motor nerve innervates all the intrinsic and all but one of the extrinsic muscles of the tongue." + "Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." + "A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle." "XAO:0004185" + "Any process that modulates the frequency, rate or extent of regulated secretory pathway." + "The reproductive cell in multicellular organisms." "WBbt:0006796 VHOG:0001534 NCIT:C12597 BTO:0000535" + "The process in which a relatively unspecialized cell acquires specialized features of a skeletal muscle fiber cell. Skeletal muscle fiber differentiation starts with myoblast fusion and the appearance of specific cell markers (this is the cell development step). Then individual skeletal muscle fibers fuse to form bigger myotubes and start to contract." + "Any apoptotic process in a macrophage, a mononuclear phagocyte present in a variety of tissues." + "A ciliated duct part of a bronchial submucosal gland." + "A differentiated T cell with ability to traffic to peripheral tissues and is capable of mounting a specific immune response." + "Long nephrons are associated with juxtamedullary glomeruli and extend into the inner medulla in the metanephros[GO]." + "A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles." "Wikipedia:Endomembrane_system" + "The process in which relatively unspecialized cells acquire specialized structural and functional features of a pancreatic A cell. A pancreatic A cell is a cell in the pancreas that secretes glucagon." + "The reorganization or renovation of existing pulmonary blood vessels." + "EHDAA2:0000933" + "Any process that activates or increases the frequency, rate or extent of neutrophil differentiation." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an external biotic stimulus, an external stimulus caused by, or produced by living things." + "A CD4-positive, alpha-beta T cell with the phenotype CCR7-negative, CD45RA-positive." + "A progenitor cell committed to the megakaryocyte and erythroid lineages." + + "Any process that activates or increases the frequency, rate or extent of muscle cell differentiation." + "The progression of the epithalamus over time from its initial formation until its mature state. The epithalamus is the small dorsomedial area of the thalamus including the habenular nuclei and associated fiber bundles, the pineal body, and the epithelial roof of the third ventricle." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals." + "A femur endochondral element that is composed primarily of a pre-cartilage condensation." "EMAPA:17502 VHOG:0000951 EHDAA2:0000508" + "The embryonic pancreas develops from two separate anlagen in the foregut epithelium, one dorsal and two ventral pancreatic buds[PMID]." "NCIT:C34242 TAO:0001390 ZFA:0001390 SCTID:360398004 EFO:0003470 UMLS:C1283285 Wikipedia:Pancreatic_bud EMAPA:35645" + "An epithelial cell of the intestine." + "The process resulting in the release of a polypeptide chain from the ribosome in the cytoplasm, usually in response to a termination codon." + "EHDAA2:0000993" + "Binding to serotonin (5-hydroxytryptamine), a monoamine neurotransmitter occurring in the peripheral and central nervous systems, also having hormonal properties." + "The progression of the olfactory bulb mitral cell layer over time from its initial formation until its mature state. The mitral cell layer is composed of pyramidal neurons whose cell bodies are located between the granule cell layer and the plexiform layer." + "Cytoplasm that exhibits a characteristic staining and color, pale-pink, with Wright-Giemsa stain." + "The process whose specific outcome is the progression of a cardiac fibroblast over time, from its formation to the mature state. A cardiac fibroblast is a connective tissue cell of the heart which secretes an extracellular matrix rich in collagen and other macromolecules." + "The partitioning of organelles between daughter cells at cell division." + "Any process that activates or increases the frequency, rate, or extent of interleukin-5 production." + "Any process that modulates the frequency, rate or extent of skeletal muscle fiber differentiation." + "A peptide hormone secreting cell that secretes androgen binding protein." + "Any process that stops, prevents or reduces the rate or extent of progression through the mitotic cell cycle." + "GC_ID:1" + "One of sublaminar layers S1, S2, or S5." "CP:0001041" + "EHDAA2:0001423" + "A blood vessel that is part of a trunk [Automatically generated definition]." "EMAPA:37237 MA:0000511" + "Any process that modulates the frequency, rate or extent of fibroblast apoptotic process." + "A reticular cell involved in directing B cells and T cells to specific regions within a tissue." + "Any process that stops, prevents, or reduces the frequency, rate or extent of R8 cell differentiation." + "Any process in which a secretory granule is transported to, and/or maintained in, a specific location within the cell." + "The terminal portions of the medullary collecting ducts are the papillary ducts, which end at the renal papilla and empty into a minor calyx." "BTO:0004540 Wikipedia:Duct_of_Bellini SCTID:110623009 EMAPA:35655 MA:0001646" + "The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord." "EHDAA2:0001278 EHDAA:264 UMLS:C1518429 NCIT:C34231 VHOG:0001212 EMAPA:16101" + "An anatomical junctions that overlaps the mouth and foregut." "EMAPA:16258 EHDAA:534 RETIRED_EHDAA2:0001205 VHOG:0000592" + "An epithelium that is part of a efferent duct." "EMAPA:29747 MA:0001734 FMA:19195" + "Any process that modulates the frequency, rate or extent of the covalent alteration of one or more amino acid residues within a protein." + "The process in which any suture between cranial bones is generated and organized." + "FMA:62798" + "The orderly movement of glial cells through the telencephalon." + "Any process that stops, prevents or reduces the frequency, rate or extent of the controlled release of bile acid from a cell or a tissue." + "A process in which a protein is transported to, or maintained in, a location within the Golgi apparatus." + "EHDAA2:0001833 EHDAA:5992" + "Interstitial dendritic cell is a conventional dendritic cell that is CD11b-positive, CD1a-positive, CD206-positive, CD209-positive, and CD36-positive." + "Any process that increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroid hormones,compounds with a 1, 2, cyclopentanoperhydrophenanthrene nucleus that act as hormones." + "An intratelencephalic-projecting glutamatergic with a soma located in upper L5 of the primary motor cortex. These cells have thin untufted apical dendrites." "ILX:0770174" + "The directed movement of some substance from inside of a cell, across the plasma membrane and into the extracellular region." + "A nuclear factor NF-kappa-B p100 subunit that has been processed by proteolytic cleavage." + "The process in which the anatomical structures of the eye are generated and organized." + "The process in which the anatomical structures of the pronephric nephron are generated and organized. A pronephric nephron is the functional unit of the pronephros." + "A high affinity interleukin-8 receptor that is a translation product of the human CXCR2 gene or a 1:1 ortholog thereof." "IUPHARobj:69" + "A cell that constitutes the luminal layer of epithelium of prostatic duct." "FMA:74225" + "A mesothelial cell that is part of the anterior chamber of eyeball." "FMA:70615" + "Cranial nerve that has three branches - the ophthalmic (supplying the skin of the nose and upper jaw), the maxillary and the mandibular (supplying the lower jaw)." "BAMS:Vn BIRNLEX:869 MFMO:0000093 BM:VN EMAPA:17576 BAMS:5n neuronames:549 FMA:50866 VHOG:0000704 MA:0001100 BAMS:nV Wikipedia:Trigeminal_nerve HBA:9322 ZFA:0000697 EFO:0001402 UMLS:C0040996 MESH:D014276 EHDAA:3738 AAO:0010470 MBA:901 SCTID:362459002 NCIT:C12806 TAO:0000697 BTO:0001072 GAID:726 EHDAA2:0002084 XAO:0003092" + "A multimeric assembly of four or five subunits which form a structure with an extracellular N-terminus and a large loop that together form the ligand binding domain. The C-terminus is intracellular. The ionotropic glutamate receptor complex itself acts as a ligand-gated ion channel; on binding glutamate, charged ions pass through a channel in the center of the receptor complex." + "The process whose specific outcome is the progression of a mesonephric duct over time, from its initial formation to a mature structure. A mesonephric duct is a tube drains the mesonephros." + "The osseous cochlea is the bony foundation that forms the small shell arrangement for the cochlear nerve." "MA:0000239 EMAPA:35620" + "Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle." "NIF_Subcellular:sao1846835077 Wikipedia:Microtubule" + "An arachnoid mater that is part of a telencephalon." "MA:0000980 EMAPA:17775" + "The process whose specific outcome is the progression of a short nephron over time, from its formation to the mature structure. Short nephrons are associated with mid-cortical and superficial glomeruli, are situated entirely in the outer medulla, and have no thin ascending limb." + "The ependymal cell layer that lines the spinal cord." "FMA:242839 SCTID:369278000 EMAPA:35791 MA:0001125" + "Paired ducts of the embryo that run down the lateral sides of the urogenital ridge and terminate at the mullerian eminence in the primitive urogenital sinus. In the female, they will develop to form the fallopian tubes, uterus, and the upper portion of the vagina; in the male, they are lost. These ducts are made of tissue of mesodermal origin[WP]. develops either by lengthwise splitting of the archinephric duct (in chondrichthyans and some amphibians) or by a elongated invagination of the coelomic epithelium (other vertebrates) In males, the oviducts regress. The cranial end of the oviduct maintains an opening into the coelom (which primitively may have been the anteriormost coelomic funnels connecting the nephrocoel with the coelom). This opening is the ostium tubae[USM]." "SCTID:308802006 GAID:1309 XAO:0000330 VHOG:0001199 EMAPA:27665 EHDAA2:0004048 NCIT:C13260 MESH:D009095 Wikipedia:Paramesonephric_duct RETIRED_EHDAA2:0001399 UMLS:C0026732 AAO:0010141" + "A secretory cell that discharges its product without loss of cytoplasm." + "Any process that modulates the frequency, rate or extent of deoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid." + "Any process that activates or increases the frequency, rate or extent of blood vessel endothelial cell differentiation." + "The biological process whose specific outcome is the progression of the olfactory pit from an initial condition to its mature state. This process begins with the formation of the olfactory pit, which is an indentation of the olfactory placode, and ends when the pits hollows out to form the nasopharynx." + "A chromaffin cell of the adrenal medulla that produces norepinephrine." "FMA:69321" + "An epithelial supporting cell located in the cochlea." "FMA:79796" + "Any process that modulates the frequency, rate or extent of parathyroid hormone secretion." + "A channel containing perilymph passing through the temporal bone, connecting the scala tympani of the cochlea to the subarachnoid space." "EMAPA:35677 MA:0000248 Wikipedia:Perilymphatic_duct AAO:0000136 SCTID:368950002 FMA:77822 ZFA:0005461" + "Any collection of muscles that is part of a manus [Automatically generated definition]." "FMA:42368" + "The division of a vacuole within a cell to form two or more separate vacuoles." + "The process that gives rise to the rhombomere. This process pertains to the initial formation of a structure from unspecified parts. Rhombomeres are transverse segments of the developing rhombencephalon. Rhombomeres are lineage restricted, express different genes from one another, and adopt different developmental fates." + "The developmental process pertaining to the initial formation of the renal vesicle from condensed mesenchymal cells. The renal vesicle is the primordial structure of the nephron epithelium, and is formed by the condensation of mesenchymal cells." + "The directed movement of an amino acid from outside of a cell, across the plasma membrane and into the cytosol." + "A developmental process, independent of morphogenetic (shape) change, that is required for the locus ceruleus to attain its fully functional state. The locus ceruleus is a dense cluster of neurons within the dorsorostral pons. This nucleus is the major location of neurons that release norepinephrine throughout the brain, and is responsible for physiological responses to stress and panic." + "A receptor-type tyrosine-protein phosphatase C isoform CD45RO that is encoded in the genome of human." "UniProtKB:P08575-4" + "A GABAergic neuron located in the cerebral cortex that expresses Lamp5" "ILX:0770149" + "An epithelium that is part of a caecum." "EHDAA2:0000209" + "The developmental process pertaining to the initial formation of an endothelial tube." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting a decline in the level of oxygen." + "A small, narrow, peg-shaped epithelial cell with little cytoplasm that is part of oviduct epithelium. This cell is rarer than the ciliated and secretory epithelial cells of the fallopian tube epithelium and is often found intercalated between them. Peg cells are generally distributed basally along the epithelium and have been found in high concentrations at the fimbriated, distal end of the fallopian tube in humans. It may have a regenerative/stem-cell function. In humans, markers include EPCAM, CD44, and ITGA6." + "Any process that stops, prevents, or reduces the frequency, rate or extent of glutamate metabolic process." + "The process whose specific outcome is the progression of a limb over time, from its formation to the mature structure. A limb is an appendage of an animal used for locomotion or grasping. Examples include legs, arms or some types of fin." "Wikipedia:Limb_development" + "A retinal ganglion A2 cell with dendrites terminating in S2." "BAMS:1065" + "The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a Purkinje myocyte (also known as cardiac Purkinje fiber cell). These cells are specialized cardiomyocytes that receive signals from the bundle of His and innervate the ventricular cardiac muscle." + "An epithelial sheet bent on a linear axis." + "Receiving a signal and transmitting it in the cell to initiate a change in cell activity. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response." + "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane." "NIF_Subcellular:sao414196390" + "An axon of a hippocampal granule cell, including dentate gyrus granule cell and CA3 granule cell, characterized by expansions (mossy fiber expansions) giving the fibers a mossy appearance. These unmyelinated axons were first described by Ramon y Cajal." "NIF_Subcellular:nlx_subcell_100312" + "Enables the transmembrane transfer of a solute by a channel that opens when a specific ligand has been bound by the channel complex or one of its constituent parts." + "Any process that modulates the frequency, rate or extent of response to water deprivation." + "BTO:0004402" + "The region demarcating the renal medulla from the surrounding cortex; end-stage renal failure may be associated with loss of the normal corticomedullary boundary." "EMAPA:37886" + "A contractility which is relatively normal or average." + "A monostratified retinal ganglion cell that contains opsin." + "Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." + "Musculature of the head and neck, spine, and ribs." "EHDAA2:0000159 EMAPA:18166" + "EHDAA2:0003242" + "The base of skull is the most inferior area of the skull, composed of the endocranium and lower parts of the skull roof." "MA:0002840 MESH:D019291 FMA:52801 SCTID:181890004 MFMO:0000044 NCIT:C12493 Wikipedia:Base_of_skull UMLS:C0149543" + "Any chondrocyte that is part of the tracheobronchial tree." + "A vertebral foramen that is part of a thoracic vertebra." "SCTID:280834002 FMA:9143" + "An immune response taking place in an organ or tissues such as the liver, brain, mucosa, or nervous system tissues." + "The chemical reactions and pathways resulting in the formation of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings)." + "In anatomy, the common hepatic artery is a short blood vessel that supplies oxygenated blood to the liver, pylorus (a part of the stomach), duodenum (a part of the small intestine) and pancreas. It arises from the celiac artery and has the following branches:." "SCTID:244263001 MA:0003094 galen:CommonHepaticArtery EHDAA2:0000308 EMAPA:37206 EHDAA:8570 FMA:14771 Wikipedia:Common_hepatic_artery" + + "A parathyroid chief cell that is actively secreting hormone. Have large Golgi complexes with numerous vesicles and small membrane-bound granules; secretory granules are rare, cytoplasmic glycogen sparse, much of the cytoplasm being occupied by flat sacs of granular endoplasmic reticulum in parallel arrays; in normal humans, inactive chief cells outnumber active chief cells in a ratio of 3-5:1" "FMA:69082" + "A myoepithelial cell that is part of the quarternary lactiferous duct." "FMA:74503" + "The smallest anatomical unit of the lung, measuring 0.50 to 2.00 cm in diameter. Each lobule is composed of 4-8 terminal bronchioles and their distal alveolar ducts and sacs. The lobules are separated by fibrous interlobular septa." "NCIT:C33428 FMA:75739" + "An oblong or round asexual spore formed from conidial chains." "FAO:0000042 BTO:0000127" + "The process whose specific outcome is the progression of the neuromast over time, from its formation to the mature structure. The neuromast is the sensory organ of the lateral line and is composed of a population of sensory hair cells, and nonsensory supporting cells and mantle cells. Neuromasts are located superficially on the epithelium or in lateral line canals." + "Enables the transfer of an amide, any compound containing one, two, or three acyl groups attached to a nitrogen atom, from one side of a membrane to the other." + "OBSOLETE (was not defined before being made obsolete)." + "A G protein-coupled receptor signaling pathway initiated by a neuropeptide binding to its receptor on the surface of a target cell, and ending with the regulation of a downstream cellular process." + "A rib that is attached to a cervical vertebra." "EMAPA:37825" + "A cell of mesodermal origin that is closely associated with the epithelium of an imaginal disc. It is a precursor of some of the insect's adult muscles." "FBbt:00003219" + "FMA:14657" + "A sensory neuron of the spinal nerve that senses body position and sends information about how much the muscle is stretched to the spinal cord." + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptide hormone stimulus. A peptide hormone is any of a class of peptides that are secreted into the blood stream and have endocrine functions in living animals." + "Any process that modulates the frequency, rate, or extent of leukocyte degranulation." + "A type D cell of the small intestine." "FMA:268736" + "Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in metanephric collecting duct development." + "A protein that is a translation product of the human RAG2 gene or a 1:1 ortholog thereof." + "Any interneuron that is part of a spinal cord ventral column." + "Primordium that develops into the central nervous system." + "The chemical reactions and pathways resulting in the breakdown of epinephrine, a hormone produced by the medulla of the adrenal glands that increases heart activity, improves the power and prolongs the action of muscles, and increases the rate and depth of breathing. It is synthesized by the methylation of norepinephrine." + "A process of secretion by a cell that results in the release of intracellular molecules (e.g. hormones, matrix proteins) contained within a membrane-bounded vesicle. Exocytosis can occur either by full fusion, when the vesicle collapses into the plasma membrane, or by a kiss-and-run mechanism that involves the formation of a transient contact, a pore, between a granule (for exemple of chromaffin cells) and the plasma membrane. The latter process most of the time leads to only partial secretion of the granule content. Exocytosis begins with steps that prepare vesicles for fusion with the membrane (tethering and docking) and ends when molecules are secreted from the cell." "Wikipedia:Exocytosis" + "A serous membrane that is part of a uterine tube infundibulum." "EMAPA:29903 FMA:18324" + "A line of sensory organs and associated structures along the sides of fish and amphibia that detect vibrations and pressure changes." "MIAA:0000249 Wikipedia:Lateral_line_system AAO:0000975 MAT:0000249 VHOG:0001243 XAO:0000095 EFO:0000941 ZFA:0000034 TAO:0000034 AAO:0000269" + "Cluster of cells comprising a portion of tissue which gives rise to new mesonephric nephrons. The cluster contains self-renewing stem cells." "ZFA:0005587" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of lipids." + "Any process involved in the controlled movement of a sperm cell." + "A capillary that is part of the anorectum." + "A peritubular capillary that is part of a cortex of kidney." "EMAPA:37488 MA:0002590" + "The series of events in which a light stimulus (in the form of photons) is received and converted into a molecular signal." + "A protein that is a translation product of the human CD8B gene or a 1:1 ortholog thereof. CD8 is a transmembrane receptor that is a co-receptor for MHC class-I antigen/T-cell receptor interaction. The most common form of CD8 is composed of a CD8 alpha and a CD8 beta chain." "PIRSF:PIRSF002020" + "A circular muscle layer of muscular coat that is part of a colon smooth muscle." + "A circular muscle layer of muscular coat that is part of a large intestine smooth muscle." "MA:0001548 FMA:81160 EMAPA:37558" + "The process whose specific outcome is the progression of a long nephron over time, from its formation to the mature structure. Long nephrons are associated with juxtamedullary glomeruli and extend into the inner medulla." + "Any process that activates or increases the frequency, rate, or extent of lymphocyte anergy." + "A substance that is secreted by a mammary gland. The substance may differ depending on phase, with colostrum produced during pregancy/early lactation, and milk produced afterwards." "EMAPA:36538 MA:0002505" + "The process in which neuroepithelial cells in the ventral neural tube acquire specialized structural and/or functional features of motor neurons. Motor neurons innervate an effector (muscle or glandular) tissue and are responsible for transmission of motor impulses from the brain to the periphery. Differentiation includes the processes involved in commitment of a cell to a specific fate." + "Any process that modulates the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." + "Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument." "TAO:0001308 XAO:0003013 AAO:0010053 BILA:0000032 MIAA:0000293 CARO:0000032 MA:0002433 MESH:D001829 UMLS:C0229962 galen:BodyPart TGMA:0001840 FMA:7153 AEO:0000032 CALOHA:TS-2084 HAO:0000032 VHOG:0001758 ZFA:0001308 EMAPA:36031 NCIT:C32221 MAT:0000293 Wikipedia:Body_part EFO:0000808 EHDAA2:0003032 BIRNLEX:7" + + "A lactotransferrin that is encoded in the genome of human." "UniProtKB:P02788" + "An apical ectodermal ridge that is part of a pectoral appendage bud." "VHOG:0001064 EMAPA:16778 TAO:0000736 EHDAA2:0000138 TAO:0000085 EFO:0003487 ZFA:0000085" + "A tarsus bone or its cartilage or pre-cartilage precursor." + "A sheet of extracellular matrix." "FMA:9722 ZFA:0005652 EHDAA2:0003092 UMLS:C0225205 AEO:0000092 SCTID:331712004 Wikipedia:Aponeurosis NCIT:C32133" + "The bidirectional movement of large protein complexes along microtubules within a cilium, mediated by motor proteins." "Wikipedia:Intraflagellar_transport" + "The mammary fat is an adipose structure in the gland that is invaded by the mammary ducts." "EMAPA:35539 MA:0002911" + "Membrane organ that surrounds the brain and the spinal cord." "UMLS:C0025285 NLXANAT:090204 MA:0001113 BTO:0000144 ZFA:0001355 NCIT:C12348 MAT:0000113 Wikipedia:Meninx TAO:0001355 EMAPA:32660 EFO:0000867 GAID:687 FMA:9589 CALOHA:TS-1177 VHOG:0001295 MESH:D008578" + "A protein that is a translation product of the human CD36 gene or a 1:1 ortholog thereof." + "The orderly movement of an astrocyte, a class of large neuroglial (macroglial) cells in the central nervous system, the largest and most numerous neuroglial cells in the brain and spinal cord." + "The change in morphology and behavior of a mature or immature natural killer T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific, leading to the initiation or perpetuation of an immune response." + "The stages of blood cell formation that take place within the embryo." + "FMA:62007 ZFA:0000653 BM:Die-Th EHDAA2:0000692 HBA:4393 neuronames:1455 DMBA:16396 PBA:128013018 BAMS:DOR TAO:0000653 MA:0000180 DHBA:10391 ncithesaurus:Dorsal_Thalamus EMAPA:35295 BAMS:Dorsal_thalamus" + "Any process that stops, prevents or reduces the frequency, rate or extent of mineralocorticoid secretion." + "A DN2 thymocyte that is Kit-low." + "Any process that activates or increases the frequency, rate or extent of mesenchymal cell proliferation involved in lung development." + "Any protein complex that is part of a membrane." + "Any process that activates or increases the frequency, rate or extent of embryonic camera-type eye development." + "Any process that modulates the frequency, rate or extent of glomerular filtration. Glomerular filtration is the process in which blood is filtered by the glomerulus into the renal tubule." "An erythrocyte having a nucleus." - "Diploid cell produced by the fusion of sperm cell nucleus and egg cell." "BTO:0000854 EHDAA2:0004546 FMA:72395" + "The process in which an organic acid is transported across a membrane." "Brush cell of the epithelium in the trachea." "FMA:263224" - "A cell located in the heart, including both muscle and non muscle cells." "FMA:83808 BTO:0001539 CALOHA:TS-0115 FMA:84791" - "A squamous cell that has keratin in the esophagus." "FMA:86549" - "A fibroblast that is part of the heart." - "A group 3 innate lymphoid cell in the human with the phenotype IL-7Ralpha-positive, and NKp44-positive." - + "The increase in size or mass of an endochondral bone that contributes to the shaping of the bone." + "A change in morphology and behavior of an astrocyte resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor." "An intratelencephalic-projecting glutamatergic neuron with a soma found in L6 of the primary motor cortex. These cells are short untufted pyramidal cells, which could be stellate or inverted." "ILX:0770158" - - "A neuroendocrine cell found in the epithelium of the lungs and respiratory tract. This cell type is rounded or elliptical in shape, situated mainly in the basal part of the epithelium; regulates bronchial secretion, smooth muscle contraction, lobular growth, ciliary activity and chemoreception. Cell has an electron-lucent cytoplasm, contains numerous dense-cored vesicles with a clear halo between the core and the limiting membrane." "FMA:14118" - "The larger of two types of asexual spores formed by some fungi; usually round or oblong." "FAO:0000038" - "A fibroblast that is part of the connective tissue of prostate." "FMA:261271" - "An epithelial cell that secretes cuticle." - "A precursor B cell is a B cell with the phenotype CD10-positive." "CALOHA:TS-0819 BTO:0001133" - "Cell of the single layer of large flattened cells covering the surface of the cornea." "FMA:70614 CALOHA:TS-0172" - "A smooth muscle cell of the subclavian artery." + "A CD69 molecule that is encoded in the genome of mouse." "UniProtKB:P37217" + "A melanocyte located in the vascular uvea and involved in photoprotection, regulation of oxidative damage and immune responses." + "A bone that is part of the region of the forelimb that includes the zeugopod and stylopod. Examples: patella, femur, tibia." "MA:0000592 EMAPA:37303" + "The series of molecular signals generated by the binding of gamma-aminobutyric acid (GABA, 4-aminobutyrate), an amino acid which acts as a neurotransmitter in some organisms, to its receptor on the surface of a target cell." + "A cartilage element that is part of the cranial skeleton." "ZFA:0001458 TAO:0001458" "A transitional myocyte that is part of the anterior internodal tract." "FMA:263158" - "A tissue-resident macrophage found in the mucosa associated lymphoid tissue." - "A mucosa-associated lymphoid tissue macrophage found in the nasal and bronchial mucosa-associated lymphoid tissues." - "A splenic white pulp macrophage found in and around the germinal centers of the white pulp of the spleen that participates in phagocytosis of apoptotic B cells from the germinal centers. A marker for a cell of this type is Mertk-positive." - "An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal. In mammals, endothelial cell has vimentin filaments and is derived from the mesoderm." "FMA:66772 CALOHA:TS-0278 BTO:0001176" + "A vein where lymph node venules condense and which exits at the lymph node hilum. It is also called hilar vein." + "The neck region of a bone organ." + "Mesenchyme that is part of a pectoral appendage bud." "ZFA:0000789 EHDAA2:0002135 EMAPA:16408 EHDAA:1703 TAO:0000789" + "The process in which the anatomical structures of the outflow tract septum are generated and organized. The outflow tract septum is a partition in the outflow tract." + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of structures in the space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane, and also covers the host cell environment outside an intracellular parasite." "A mesothelial cell that is located in a vermiform appendix." - "An preBRC-positive large pre-B-II cell is a large pre-B-II cell that is pre-B cell receptor-positive, composed of surrogate light chain protein (SL), which is composed of VpreB , Lambda 5/14.1, in complex with immunoglobulin mu heavy chain (IgHmu) on the cell surface." - "A peptide hormone secreting cell that secretes endorphin." - - "Glandular cell of exocrine pancreas epithelium. Example: pancreatic acinar cell, glandular cells in pancreatic canaliculi, glandular cells in pancreatic ducts." "CALOHA:TS-1242 BTO:0000028" - "A mature natural killer cell that is CD27-high and CD11b-high. This cell type is capable of interferon-gamma secretion." - "A CNS neuron of the forebrain." - "A lymphocyte that lacks characteristic T cell, B cell, myeloid cell, and dendritic cell markers, that functions as part of the innate immune response to produce cytokines and other effector responses." + "Any process that modulates the frequency, rate or extent of mineralocorticoid secretion." + "The multiplication or reproduction of cells, resulting in the expansion of the population in the mesonephros." + "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances." + "Any process that stops, prevents or reduces the frequency, rate or extent of motile cilium assembly." + "A ciliated cell of the endometrial glandular epithelium." + "An action potential that occurs in a ventricular cardiac muscle cell." + "The part of the venous system that drains the general body tissues[Kardong]." "FMA:45626 Wikipedia:Systemic_venous_system" + "Any process that activates or increases the frequency, rate or extent of mesenchymal cell apoptotic process involved in metanephros development." "A bipolar neuron found in the retina and having connections with cone photoreceptor cells and neurons in the inner plexiform layer." - "A goblet cell that is part of the epithelium of large intestine." "FMA:263054" - "A lymphocyte found in adipose tissue that lacks lineage markers of other lymphocytes but is capable of mediating TH2 cytokine responses. This cell type is found in fat associated lymphoid clusters, proliferates in response to IL2 and produce large amounts of TH2 cytokines such as IL5, IL6 and IL13" - "A T cell found in the lymph node medullary sinus." - "An enterocyte that is part of the epithelium proper of jejunum." "FMA:263100" - "A B220-low CD38-positive unswitched memory B cell is a CD38-positive unswitched memory B cell that has the phenotype B220-low, CD38-positive, IgD-positive, CD138-negative, and IgG-negative." - "A patrolling monocyte that is CD14-low and CD16-positive." - "Gr1-high monocyte that has a MHC-II receptor complex." - "A cell secreting sweat, the fluid excreted by the sweat glands of mammals. It consists of water containing sodium chloride, phosphate, urea, ammonia, and other waste products." - "A non-neuronal cell that surrounds the neuronal cell bodies of the ganglia." "FMA:54550" - "A Vip GABAergic cortical interneuron with bipolar morphology, with a soma found in L2/3. L2/3 bipolar Vip Cells have extending axons across all layers (with preferences for layers II/III and Va) and a dendritic tree that is vertically more restricted than deeper layer VIP cells and extend fewer dendrites into the layers outside their home layer (location of soma). L2/3 Bipolar Vip Cells have great variability in firing patterns, though most are continuous adapting. L2/3 Bipolar Vip Cells are more depolarized in their resting state, had less fast rectification, and had smaller after hyperpolarization than deeper Vip cells." - "A GABAergic cortical interneuron that develops from the caudal ganglionic eminence and has migrated to the cerebral cortex." - "KUPO:0001070" - "A specialized osteoclast associated with the absorption and removal of cementum." "FMA:83027 BTO:0002516" + "A CNS neuron of the forebrain." + "The process in which a relatively unspecialized cell acquires specialized features of a pacemaker cell. Pacemaker cells are specialized cardiomyocytes that are responsible for regulating the timing of heart contractions." + "Any process that activates or increases the frequency, rate, or extent of smooth muscle cell chemotaxis." + "Any process that modulates the frequency, rate or extent of female gonad development." + "The process in which a precursor cell type acquires the specialized features of a CD4-positive, CD25-positive, alpha-beta regulatory T cell." + "A gustatory epithelium that is part of a tongue." "UMLS:C1179150 BIRNLEX:4099" + "A process in which a protein transports or maintains the localization of another protein to the nucleus." + "A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity consisting of particles that have neither a defined volume nor defined shape." "OBSOLETE: Initial population of prestalk cells that activate the ecmA promoter at the mound stage and that presumably further differentiate into pstA and pstO cells." - "KUPO:0001124" - "A smooth muscle cell that is part of the large intestine." "FMA:15653" - "A blastoconidium that has more than one nucleus." "FAO:0000036" + "Any collagen trimer that passes through a lipid bilayer membrane." + "A mesentery that is part of a esophagus [Automatically generated definition]." "EMAPA:16836 EHDAA2:0001288 EHDAA:2943 VHOG:0000415 MA:0001569" "A type of foam cell derived from a macrophage containing lipids in small vacuoles and typically seen in atherolosclerotic lesions, as well as other conditions." - "A memory B cell is a mature B cell that is long-lived, readily activated upon re-encounter of its antigenic determinant, and has been selected for expression of higher affinity immunoglobulin. This cell type has the phenotype CD19-positive, CD20-positive, MHC Class II-positive, and CD138-negative." - "A pluripotent cell in the yolk sac that can give rise to mesenchymal cells including erythrocytes and endothelial cells." - "A connective tissue cell found in bone." - - - - - "A pre-B cell precursor is CD19-low, CD22-positive , CD34-positive, CD38-positive." - "A CNS neuron of the dorsal spinal cord." - "A cell in the zona reticularis that produce sex hormones." "FMA:69564" - "KUPO:0001079" - "A lin-negative, MHC-II-negative, CD11c-positive, FLT3-positive cell with intermediate expression of SIRP-alpha." - "A fibroblast of the aortic adventitia." - "KUPO:0001128" - "A B220-low CD38-negative unswitched memory B cell is a CD38-negative unswitched memory B cell that has the phenotype B220-low, CD38-negative, IgD-positive, CD138-negative, and IgG-negative." - "OBSOLETE: A cell responsible for spontaneous cytotoxicity of a variety of tumor cells without prior immunization. These natural killer cells are found in non-immune humans and experimental animals and are thought by some to be the same as killer cells (killing by antibody-dependent cell cytotoxicity), but they can also kill in the absence of antibody." - "OBSOLETE: A cell in a tissue that markedly differs in form, size, or contents from other cells in the same tissue." - "A cell characteristically found lining hollow organs that are subject to great mechanical change due to contraction and distention; originally thought to represent a transition between stratified squamous and columnar epithelium." "FMA:66778" - "An auditory epithelial support cell that surrounds the nerve fibers and synapses of the auditory inner hair cells." "FMA:79801" - "A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina." "FMA:66768 CALOHA:TS-2026 FBbt:00000124 CARO:0000077 WBbt:0003672 BTO:0000414" - - "A free floating cell, including amebocytes and eleocytes, in the coelom of certain animals, especially annelids." "WBbt:0005751 BTO:0002856" - "A fat cell that is part of subcutaneous adipose tissue." - - "A glomerular visceral epithelial cell is a specialized kidney epithelial cell that contains \"feet\" that interdigitate with the \"feet\" of other glomerular epithelial cells." "FMA:70967 BTO:0002295" - "A myotube that is part of some somatic muscle. Examples include arthropod somatic muscle cells." - "The principal glutaminergic neuron located in the outer third of the external plexiform layer of the olfactory bulb; a single short primary dendrite traverses the outer external plexiform layer and terminates within an olfactory glomerulus in a tuft of branches, where it receives the input from olfactory receptor neuron axon terminals; axons of the tufted cells transfer information to a number of areas in the brain, including the piriform cortex, entorhinal cortex, olfactory tubercle, and amygdala." - - "An immature B cell is a B cell that has the phenotype surface IgM-positive and surface IgD-negative, and have not undergone class immunoglobulin class switching or peripheral encounter with antigen and activation." - - - - "An intratelencephalic-projecting glutamatergic neuron with a soma found in layer 5 of the marmoset primary motor cortex." "ILX:0770157" - "A muscle cell that is part of the atrial septal branch of anterior internodal tract." "FMA:223278" - "A stromal cell that is part_of a bone marrow." - "A rounded or elliptical epithelial cell, with pale-staining open face nucleus and pale cytoplasm rich in free ribosomes and clusters of centrioles; form a distinct basal zone spaced slightly from the basal surface of the epithelium." "FMA:67874" - "A mesothelial fibroblast of the arachnoid barrier layer. Arachnoid barrier cells make up the tight-junctioned layer in the leptomeninx that functions as the physiologic barrier between the cerebrospinal fluid in the subarachnoid space and the fenestrated capillaries in the dura." - "A recently activated CD8-positive, alpha-beta T cell with the phenotype HLA-DRA-positive, CD38-positive, CD69-positive, CD62L-negative, CD127-negative, CCR7-negative, and CD25-positive." - "A blastoconidium that has only one nucleus." "FAO:0000030" - "A luminal epithelial cell of the lactiferous duct. This cuboidal epithelial cell expresses keratin-18 and is estrogen-receptor alpha positive." "FMA:74505 FMA:74504" - "KUPO:0001076" - "A columnar/cuboidal epithelial cell is a cell usually found in a two dimensional sheet with a free surface. Columnar/cuboidal epithelial cells take on the shape of a column or cube." - "A phagocyte from organisms in the Nematoda or Protostomia clades." - "A tuft cell that is a part of the colon." - "An astrocyte of the cerebellum." - "A B220-low CD38-positive IgG-negative memory B cell is a CD38-positive IgG-negative class switched memory B cell that lacks IgG on the cell surface with the phenotype B220-low, CD38-positive, and IgG-positive." - "Skeletogenic cell that produces enamel, overlies the odontogenic papilla, and arises from the differentiation of a preameloblast cell." "FMA:70576 BTO:0001663" - "FBbt:00001666" - "A natural killer cell that is CD27-high and CD11b-low." - "A fibroblast that is part of lung." "CALOHA:TS-0575 BTO:0000764" - "A mesothelial cell that is part of the visceral pleura." "FMA:86739" - "A nuclear bag fiber that is sensitive only changes in muscle length but not the rate of that change." - "FMA:72552" - "KUPO:0001010" + "Any process that increases the rate, frequency or extent of glomerulus development, the progression of the glomerulus over time from its initial formation until its mature state. The glomerulus is a capillary tuft surrounded by Bowman's capsule in nephrons of the vertebrate kidney." + "The directed movement of polysaccharides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A polysaccharide is a polymer of many (typically more than 10) monosaccharide residues linked glycosidically." + "The directed movement of a motile cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis)." + "Accompanying vein of internal pudendal artery." "Wikipedia:Internal_pudendal_veins SCTID:14885008 FMA:18917" + "One of the layers of the neocortex. These layers are defined by distinctive populations of cells based on somata size, shape, or density, that are aligned into sheets." "MA:0000186 EMAPA:35588 FMA:83138 ABA:CTX1-6b" + "A nerve that is part of an arm [Automatically generated definition]." "MA:0000595 EMAPA:37336" + "A medium spiny neuron that exhibits transcriptional divergence from direct and indirect spiny projection neurons, for example, enrichment in Casz1, Otof, Cacng5 and Pcdh8 noted in mice. Whilst in general medium spiny neurons have been found to be differentially distributed across the basal ganglia, the eccentric medium spiny neuron cell type has been found to be more evenly distributed throughout cerebral nuclei." + "An angle of the scapula formed by the union of the vertebral and axillary borders; its dorsal surface affords attachment to the Teres major and frequently to a few fibers of the Latissimus dorsi.[WP,unvetted]." "Wikipedia:Inferior_angle_of_scapula EMAPA:25128 FMA:13315" + "The process in which a preadipocyte acquires specialized features of a white adipocyte of the mammary gland. White adipocytes have cytoplasmic lipids arranged in a unique vacuole." + "Any process that stops, prevents or reduces the frequency, rate or extent of activated CD4-positive, alpha-beta T cell apoptotic process." + "A subdivision of the autopod skeleton consisting of both acropodial skeleon and metapodial skeleton, but excluding the mesopodial/basopodial skeleton." + "The process in which the anatomical structures of the gonads are generated and organized. A gonad is an animal organ producing gametes, e.g. the testes or the ovary in mammals." + "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an L-glutamate stimulus." + "The multiplication or reproduction of pancreatic B cells, resulting in the expansion of an pancreatic B cell population. Pancreatic B cell are cells of the pancreas that secrete insulin." + "Anatomical projection that protrudes from the skin. Examples: hair, nail, feather, claw, hoof, horn, wattle, spur, beak, antler, bristle and some scales." "CALOHA:TS-0051 SCTID:276160000 FMA:71012" + "A capillary that is part of a kidney [Automatically generated definition]." "MA:0002586 EMAPA:31443 SCTID:275409003" + "Any process that modulates the frequency, rate or extent of amino acid import into a cell." + "A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina." "FBbt:00000124 FMA:66768 CALOHA:TS-2026 CARO:0000077 WBbt:0003672 BTO:0000414" + "The process whose specific outcome is the progression of the chorionic trophoblast over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a specific fate." + "The prostatic veins form a well-marked prostatic plexus which lies partly in the fascial sheath of the prostate and partly between the sheath and the prostatic capsule. It communicates with the pudendal and vesical plexuses." "SCTID:303052003 Wikipedia:Prostatic_venous_plexus FMA:29711" + "The process in which a relatively unspecialized cell acquires the specialized structural and/or functional features of a cardiac endothelial cell." + "The middle colic artery is a branch of the superior mesenteric artery that mostly supplies the transverse colon. It arises just below the pancreas, and, passing downward and forward between the layers of the transverse mesocolon, divides into two branches: right and left. The right branch anastomoses with the right colic artery The left branch anastomoses with the left colic artery, a branch of the inferior mesenteric artery. The arches thus formed are placed about two fingers' breadth from the transverse colon, to which they distribute branches. [WP,unvetted]." "Wikipedia:Middle_colic_artery NCIT:C52981 EMAPA:37106 galen:MiddleColicArtery FMA:14810 UMLS:C0226328 SCTID:244276007 MA:0002007" + "The biological process whose specific outcome is the progression of a lobar bronchus epithelium from an initial condition to its mature state. This process begins with the formation of the lobar bronchus epithelium and ends with the mature structure. The lobar bronchus epithelium is the tissue made up of epithelial cells that lines the inside of the lobar bronchus." + "GAID:767 SCTID:46920005 MESH:D036421 NCIT:C33835 FMA:5916 UMLS:C0501409" + "Subdivision of urinary system which consists of the urinary bladder and the urethra." "FMA:45659 MA:0002636 galen:LowerUrinaryTract SCTID:181420004" + "A large sesamoid bone found in the distal femur/proximal tibial region of the hindlimb of tetrapods. The patella is the attachment site for proximal hindlimb tendons.[PHENOSCAPE:ad]." "EMAPA:35668 FMA:24485 SCTID:182083008 MA:0001374 MESH:D010329 UMLS:C0030647 NCIT:C33282 galen:Patella GAID:203 Wikipedia:Patella" + "Any portion of cartilage tissue that is part of the sternum." "FMA:32567" + "Unilaminar epithelium, which consists of a single layer of columnar cells. Examples: ciliated columnar epithelium, gastric epithelium, microvillus columnar epithelium.[FMA]." "TAO:0001496 AAO:0010063 AEO:0000068 Wikipedia:Simple_columnar_epithelium ZFA:0001496 SCTID:32210007 NCIT:C33552 BILA:0000068 XAO:0004008 CARO:0000068 EHDAA2_RETIRED:0003068 FMA:45567 UMLS:C0836135 HAO:0000068" + "Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in outflow tract morphogenesis." + "Any process that modulates the frequency, rate or extent of the directed movement of the neurotransmitter epinephrine into a cell." + "The hip region is located lateral to the gluteal region (i.e. the buttock), inferior to the iliac crest, and overlying the greater trochanter of the thigh bone. In adults, three of the bones of the pelvis have fused into the hip bone which forms part of the hip region. The hip joint, scientifically referred to as the acetabulofemoral joint (art. coxae), is the joint between the femur and acetabulum of the pelvis and its primary function is to support the weight of the body in both static (e.g. standing) and dynamic (e.g. walking or running) postures. [WP,modified]." "NCIT:C64193 UMLS:C0019552 EHDAA2:0000783 BTO:0001457 EHDAA:5153 VHOG:0000346 EMAPA:17490 MA:0000045 galen:Hip EFO:0001929 SCTID:302543008 EHDAA:6178 FMA:24964 MESH:D006615 CALOHA:TS-2226 Wikipedia:Hip GAID:47" + "A hemocyte that derives from the larval lymph gland." "FBbt:00005917" + "The series of events in which an electrical stimulus is received by a cell and converted into a molecular signal as part of sensory perception." + "The biological process whose specific outcome is the progression of a lobar bronchus from an initial condition to its mature state. This process begins with the formation of the lobar bronchus and ends with the mature structure. The lobar bronchus is the major airway within the respiratory tree that starts by division of the principal bronchi on both sides and ends at the point of its own subdivision into tertiary or segmental bronchi." + "The process in which the S-shaped body is generated and organized. The S-shaped body is the successor of the comma-shaped body that contributes to the morphogenesis of the nephron." + "Any process that activates or increases the frequency, rate or extent of neuroinflammatory response." + "A neuroendocrine cell that is part of respiratory epithelium of the lung and is involved in the sensory detection of environmental stimuli, including hypoxia, nicotine and air pressure. Ultrastructurally, this cell type is characterized by the presence of cytoplasmic dense core granules, which are considered the storage sites of amine and peptide hormones. Lung neuroendocrine cells are innervated and appear as solitary cells or as clustered masses, localized at airway bifurcation sites, called neuroepithelial bodies that can release serotonin in response to hypoxia and interact with sensory nerve terminals. Lung neuroendocrine cells also function as reserve stem cells that repair the surrounding epithelium after injury." + "Any process that modulates the rate, frequency, or extent of prostate gland branching, the process in which the branching structure of the prostate gland is generated and organized. A branch is a division or offshoot from a main stem." + "A specialized brain region of the ventral diencephalon arising near the end of the segmentation period; the embryonic hypothalamic region will give rise to the posterior pituitary gland as well as a number of brain nuclei. [ZFA]. One of the most important functions of the hypothalamus is to link the nervous system to the endocrine system via the pituitary gland (hypophysis).[Wikipedia]." "SCTID:264483005 MAT:0000112 DHBA:10467 AAO:0010484 HBA:4540 galen:Hypothalamus MA:0000173 BIRNLEX:734 BM:Die-Hy Wikipedia:Hypothalamus VHOG:0000179 EHDAA:5446 GAID:460 MIAA:0000112 MESH:D007031 NCIT:C12458 ZFA:0000032 XAO:0004070 neuronames:292 EV:0100225 BAMS:HY BTO:0000614 CALOHA:TS-0469 FMA:62008 EMAPA:17536 UMLS:C0020663 BAMS:Hy EFO:0000107 MBA:1097 TAO:0000032 EHDAA2:0000802" "An enteroendocrine cell of duodenum and jejunum that produces gastric inhibitory peptide." "FMA:62942" - "A myoblast that is commited to developing into a somatic muscle." - "A peptide hormone secreting cell that secretes substance P." - "A myoepithelial cell that is part of the intralobular part of terminal lactiferous duct." "FMA:62158" - "A tall supporting cell that is arranged in rows adjacent to the last row of outer phalangeal cells. This cell type constitutes the outer border of the organ of Corti." "FMA:79799" - "A pyramidal neuron with soma located in the cerebral cortex." - "A myoblast that is committed to a myotube-specific program of differentiation but not yet fused. It undergoes very limited additional proliferation. After fusion, it will take on a muscle identity specified by a `muscle founder cell` (CL:0008006)." - "An elongating cell that rapidly obliterates the lumen of the lens vesicle. Subsequently, differentiation of this cell type at the lens equator leads to the formation of secondary fiber cells that come to overlie the primary fibers." "FMA:70613" - - "KUPO:0001069" - "The earliest cytologically identifiable precursor in the thrombocytic series. This cell is capable of endomitosis and lacks expression of hematopoieitic lineage markers (lin-negative)." "BTO:0001164 CALOHA:TS-0610 FMA:84235" + "Any process that decreases the rate, frequency or extent of peptide hormone processing. Peptide hormone processing is the generation of a mature peptide hormone by posttranslational processing of a prohormone." + "A multicellular organism process which involves another multicellular organism of the same or different species." + "An artery that is part of a digit [Automatically generated definition]." "MA:0001941 EMAPA:37076 SCTID:181335004" + "A portion of adipose tissue that is part of the hypodermis, beneath the dermis." "FMA:74315 MA:0000473 EMAPA:35829 BTO:0004042" + "Portion of neural tube that gives rise to the midbrain." "ZFA:0007039 TAO:0007039" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amino acid." + "The epithelium that forms the surface of the tonsil dips into the underlying connective tissue in numerous places, forming crypts kown as tonsillar crypts. Stratified squamous epithelium, that may be heavily infiltrated by lymphocytes. Epithelial cells are present in the germinal as well as in the periphery of the nodule." "CALOHA:TS-2070" + "The regionalization process in which specific areas of cell differentiation are determined along the anterior-posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism." + "A C-type lectin domain family 4 member K that is encoded in the genome of human." "UniProtKB:Q9UJ71 Reactome:R-HSA-1216519 Reactome:R-HSA-1236762 Reactome:R-HSA-1236852" "An interneuron (also called relay neuron, association neuron or local circuit neuron) is a multipolar neuron which connects afferent neurons and efferent neurons in neural pathways. Like motor neurons, interneuron cell bodies are always located in the central nervous system (CNS)." "FMA:84776" "A double-positive thymocyte that is undergoing positive selection, has high expression of the alpha-beta T cell receptor, is CD69-positive, and is in the process of down regulating the CD4 co-receptor." - "Obsolete. Use PO:0000332 from Plant Ontology instead. An epidermal cell with a characteristic convoluted anticlinal cell wall that gives a jigsaw like appearance to the lamina." - "A cubodial epithelial cell that is continuous with the lining of intercalated ducts that drain the acinus. This cell type secretes a high pH solution to aid in activation of zymogens, and can differentiate into endocrine and exocrine pancreatic cell types." "FMA:62455" - + "A vesicle-mediated transport process that results in the engulfment of external particulate material by phagocytes and their delivery to the lysosome. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles." "Wikipedia:Phagocytosis" + "Skeletal element that forms superficially in the organism, usually in association with the ectoderm[VSAO]." "VSAO:0000130 ZFA:0001590 Wikipedia:Dermal_bone TAO:0001590 XAO:0004015 AAO:0010769" + "The process of regulating the proliferation and elimination of lymphocytes such that the total number of lymphocytes within a whole or part of an organism is stable over time in the absence of an outside stimulus." "A mesothelial cell that has undergone mesothelial-to-mesenchymal transition (MMT) to become a fibroblast cell." - "Obsolete. Consult Plant Ontology. A cell that develops from the ray initial and composes all rays (panels of tissue variable in height and width, formed by the ray initials in the vascular cambium and extending radially in the secondary xylem and secondary phloem) in the secondary vascular tissues." - "An endothelial cell that is part of the vein." "KUPO:0001099 FMA:62104" - "A Sst GABAergic cortical interneuron transcriptomically between the Sst and the Pvalb families with a soma found in L2/3. Some L2/3 PV-like SST cells have Martinotti morphology while some have basket cell morphology. L2/3 PV-like SST cells have lower AP width and higher firing rate than typical Sst subclass cells. L2/3 PV-like SST cells have high maximum firing rate variability, with many classified as belonging to the Pvalb subclass on the basis of electrophysiology." - "A plasmablast that secretes IgD, and which occur in a small proportion of B cells in the adult." - "FBbt:00005147" - - - "A cell secreting sebun, an oily substance secreted by sebaceous glands, composed of keratin, fat, and cellular debris." - "OBSOLETE: A class of lymphocytes characterized by the lack of surface markers specific for either T or B cells." - - "A myeloid dendritic cell found in the blood, lymph nodes, tonsil, bone marrow, and spleen that is CD141-positive (BDCA-3), XCR1-positive, and Clec9A-positive. This cell-type can cross-present antigen to CD8-positive T cells and can produce inteferon-beta." - "A M cell that is part of the epithelium proper of large intestine." "FMA:263142" - "An intestinal enteroendocrine cell that is located in a vermiform appendix." - "Neuron of lateral ventricle." "CALOHA:TS-1261" - "KUPO:0001066" - "A type I NK T cell that has the phenotype CD4-positive." - "A specialized multinuclear osteoclast associated with the absorption and removal of cementum." - "A progenitor cell restricted to the myeloid lineage." "CALOHA:TS-2099 FMA:70339 BTO:0004730" - "A multifate stem cell found in skeletal muscle than can differentiate into many different cell types, including muscle. Distinct cell type from satellite cell." "FMA:86767" - "An endothelial cell of viscerocranial mucosa that is part of the tympanic region of the viscerocranial mucosa." "FMA:70628" - "A mesenchymal cell found in the developing heart and that develops into some part of the heart. These cells derive from intra- and extra-cardiac sources, including the endocardium, epicardium, neural crest, and second heart field." - "Obsolete. Use PO:0000301 from Plant Ontology instead. A tracheary element of the xylem that has no perforations, as contrasted with a vessel member. May occur in primary and in secondary xylem. May have any kind of secondary wall thickening found in tracheary elements." - "Any dermis lymphatic vessel endothelial cell that is part of a microvascular endothelium." - "FAO:0000032 BTO:0002307" - "A mature NK T cell that predominantly secretes type 2 cytokines such as interleukin-4 and interleukin-13 and enhances type 2 immune responses." - "The cell protoplasm after removal of the cell wall." - "An endocrine cell that is part of the pancreas." + "Increase in size of primary follicles including oocyte growth and granulosa and/or theca cell proliferation until more than one layer of granulosa cells is present (preantral follicle)." + "An intromittent organ in certain biologically male organisms. In placental mammals, this also serves as the organ of urination." "EMAPA:18682 Wikipedia:Penis BTO:0000405 GAID:389 CALOHA:TS-0758 EV:0100107 EHDAA2:0001433 VHOG:0000727 UMLS:C0030851 MA:0000408 MESH:D010413 EMAPA_RETIRED:18996 EFO:0000987 MIAA:0000186 MAT:0000186 EHDAA:9380 NCIT:C12409 galen:Penis SCTID:265793009 FMA:9707" + "Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of glucagon." + "The process in which hexose is transported across a membrane. Hexoses are aldoses with a chain of six carbon atoms in the molecule." + "A protein that is a translation product of the human PRF1 gene or a 1:1 ortholog thereof." + "A hemoglobin subunit that is a translation product of the human HBB gene, a 1:1 ortholog thereof, or pro-orthologs thereof." + "A receptor-type tyrosine-protein phosphatase C isoform CD45RA that is encoded in the genome of human." "UniProtKB:P08575-8" + "The space in the eye, filled with aqueous humor, and bounded anteriorly by the cornea and a small portion of the sclera and posteriorly by a small portion of the ciliary body, the iris, and part of the crystalline lens." "SCTID:181160009 MA:0000262 VHOG:0001431 EMAPA:18231 EHDAA:9033 BTO:0002084 FMA:58078 MESH:D000867 EHDAA2:0000129 Wikipedia:Anterior_chamber_of_eyeball NCIT:C12667 GAID:889 UMLS:C0003151" + "A portion of smooth muscle tissue that is part of an anal region [Automatically generated definition]." "MA:0001532 EMAPA:37394" + "An anatomical cavity that is part of a lobar bronchus." "FMA:62520" + "The progression of the artery over time, from its initial formation to the mature structure. An artery is a blood vessel that carries blood away from the heart to a capillary bed." + "A protein that contains an extracellular Glycophorin A domain (Pfam:PF01102), followed by a single-pass transmembrane region and a small intracellular domain. A protein that is an integral protein of the red cell membrane. Proteins in this class are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane." "PIRSF:PIRSF002466" + "A nonmembrane-bound oligomeric protein complex that participates in bidirectional transport of molecules (cargo) along axonemal microtubules." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of glucocorticoids." + "An orbitosphenoid bone or its cartilage or pre-cartilage precursor." + "Directly binding to a specific protein and delivering it to a specific cellular location." "Reactome:R-HSA-9662818 Reactome:R-HSA-9662747" + "The organs associated with producing offspring in the gender that produces spermatozoa." "Wikipedia:Male_reproductive_system_(human) UMLS:C1963704 BTO:0000082 MESH:D005837 GAID:386 UMLS:C0017422 TGMA:0000634 MA:0000396 VHOG:0000725 EHDAA2:0001054 EFO:0000970 CALOHA:TS-1310 SCTID:361340001 NCIT:C12722 EHDAA:8136 FMA:45664 HAO:0000505 EV:0100101 XAO:0000155 EMAPA:17968" + "Any process that modulates the frequency, rate or extent of the regulated release of serotonin." "A mature NK T cell that secretes interleukin-4 and enhances Th2 immune responses." - - "A fibroblast of the periodontium." - "A megakaryocyte cell with is CD9-positive and CD41-positive." - "Glandular cell of rectal epithelium. Example: Goblet cell; enterocytes or absorptive cells; enteroendocrine and M cells." "CALOHA:TS-1281" + "The process in which calcium ions sequestered in the endoplasmic reticulum, Golgi apparatus or mitochondria are released into the cytosolic compartment." + "The process in which the renal tubule is generated by specification of cell fate, through the maintenance of cell polarity, regulated cell proliferation and morphogenetic cell rearrangements, shape changes and growth. A renal tubule is a tube that filters, re-absorbs and secretes substances to rid an organism of waste and to play a role in fluid homeostasis." + "A smooth muscle tissue that is part of a umbilical cord." "BTO:0001847" + "An epithelium that is part of a extrahepatic bile duct [Automatically generated definition]." "EHDAA2:0000742 MA:0002661 UMLS:C1711347 NCIT:C43618 EHDAA:3051" "A melanocyte of the retina. This cell type is distinct from pigmented retinal epithelium." - "A polychromatophilic erythroblast that is Lyg 76-high and is Kit-negative." - "KUPO:0001067" "Skeletogenic cell that secretes osteoid, is capable of producing mineralized (hydroxyapatite) matrix, is located adjacent to or within osteoid tissue, and arises from the transformation of a preosteoblast cell." "BTO:0001593 FMA:66780 CALOHA:TS-0720" - "Dermal dendritic cell is a conventional dendritic cell that is CD11b-positive, CD205-positive and CD8 alpha-negative." "BTO:0004812" - "A double negative thymocyte that has a T cell receptor consisting of a gamma chain that has as part a Vgamma3 segment, and a delta chain. This cell type is CD4-negative, CD8-negative and CD24-positive. This cell-type is found in the fetal thymus with highest numbers occurring at E17-E18." - "A differentiated cell that functions as a site of nitrogen fixation under aerobic conditions." "BTO:0000600" - "Glandular cell of epididymal epithelium." "CALOHA:TS-1276" - "KUPO:0001121" - "A Boettcher cell is a polyhedral cells on the basilar membrane of the cochlea, and is located beneath Claudius cells. A Boettcher cell is considered a supporting cell for the organ of Corti, and is present only in the lower turn of the cochlea. These cells interweave with each other, and project microvilli into the intercellular space. Because of their structural specialization, a Boettcher cell is believed to play a significant role in the function of the cochlea. They demonstrate high levels of calmodulin, and may be involved in mediating Ca(2+) regulation and ion transport." - "A Martinotti neuron that has axons that form a horizontal ramification, making it T-shaped." - - "BTO:0003064" + "The process in which vesicles are directed to specific destination membranes during transport to, from or within the Golgi apparatus; mediated by the addition of specific coat proteins, including COPI and COPII proteins and clathrin, to the membrane during vesicle formation." + "Any process that modulates the rate or extent of the process whose specific outcome is the progression of an oocyte over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell." + "The deep nuclei of telencephalic origin found in the basal region of the forebrain." "UMLS:C0004781 EV:0100182 BAMS:BNC BAMS:BG BIRNLEX:1629 neuronames:224" + "The synthesis or release of an antimicrobial peptide during an immune response, resulting in an increase in intracellular or extracellular levels. Such peptides may have protective properties against bacteria, fungi, viruses, or protozoa." + "The process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites)." + "A spherical or tubular structure in a submucosal gland that produces and secretes mucus and other substances into the ducts leading to the surface epithelium." + + "The process in which bones are generated and organized." + "A KLRB1-like protein that is a translation product of the mouse Klrb1c gene or a 1:1 ortholog thereof." + "The process that gives rise to ganglion. This process pertains to the initial formation of a structure from unspecified parts." "Parasympathetic neurons are part of the parasympathetic nervous sysem and the cell bodies lie in the brain and sacral region of the spinal cord. The neurons are mainly cholinergic." "A cell of a fetus which is suspended in the amniotic fluid. Amniocytes are considered to arise from several tissues including fetal skin, the fetal urinary tract, umbilical cord, and the inner amniotic surface." "BTO:0000066" - "A Sst GABAergic cortical interneuron that has \"fanning-out' Martinotti morphology that is found in layer 2/3/5 of the cerebral cortex. They have local axon arbor and long ascending axons that spreads horizontally and arborizes significantly in L1." - "A fat cell that is part of the epicardial fat." "FMA:261293" + "Any process that modulates the extent to which blood vessels can be pervaded by fluid contributing to an acute inflammatory response." + "A conductive airway that branches into terminal bronchioles." + "The process whose specific outcome is the progression of the alveolus over time, from its formation to the mature structure. The alveolus is a sac for holding air in the lungs; formed by the terminal dilation of air passageways." + "The process in which a relatively unspecialized cell acquires the specialized features of a midbrain dopaminergic neuron." "A CD24-low, CD44-positive, DX5-low, NK1.1-negative NK T cell." - "A transversely striated, synctial muscle cell, formed by the fusion of myoblasts." - "A synovial cell that is macrophage-like, characterized by surface ruffles or lamellipodia, plasma membrane invaginations and associated micropinocytotic vesicles, Golgi apparatus and little granular endoplasmic reticulum." "FMA:66787" - "A goblet cell located in the nasal epithelium." "MP:0002262" - "Any osteoblast that is part of a femur." + "The cavity formed by the walls of the cervix." "BTO:0002249 FMA:17746 Wikipedia:Canal_of_the_cervix" + "Any apoptotic process in an endothelial cell. An endothelial cell comprises the outermost layer or lining of anatomical structures and can be squamous or cuboidal." "A CD4-positive, alpha-beta T cell that cooperates with other lymphocytes via direct contact or cytokine release to initiate a variety of immune functions." "CALOHA:TS-1146 FMA:70572" - "The large glutaminergic nerve cells whose dendrites synapse with axons of the olfactory receptor neurons in the glomerular layer of the olfactory bulb, and whose axons pass centrally in the olfactory tract to the olfactory cortex." - - "A nucleus size quality which is relatively high compared to the amount of cytoplasm present in the same cell." - "A gut-associated lymphoid tissue macrophage found in the Peyer's patches." - "Interneuron of the vertebrate retina. They integrate, modulate, and interpose a temporal domain in the visual message presented to the retinal ganglion cells, with which they synapse in the inner plexiform layer. They lack large axons." "FMA:67766 FBbt:00005127 BTO:0004044" - - "A precursor cell with a limited number of potential fates." "BTO:0000125 FMA:84782" - "An erythroid progenitor cell that is CD34-positive and is GlyA-negative." "FMA:83517" - "A memory regulatory T cell with phenotype CD4-positive, CD25-positive, CD127lo, CCR4-positive, and CD45RO-positive." - "Muscle cell which has as its direct parts myofilaments organized into sarcomeres." "BTO:0002916 CALOHA:TS-2157 FMA:86936" - - "A double-positive thymocyte that is CD69-positive and has begun positive selection." - "A fibroblast that is part of the skin of scalp." - "A photoreceptor cell that is sensitive to blue light." - "A goblet cell that is part of the epithelium proper of jejunum." "FMA:263065" - "A fibroblast that is part of the areolar connective tissue." "FMA:261279" - "An innate lymphoid cell in the human with the phenotype KLRG1-positive that is a precusor for ILC2 cells." - "A smooth muscle cell that is part of the rectum." "FMA:17522" - "An extremely flattened cell type found on the inner side of the tympanic membrane. The surface of this cell type carries sparse pleomorphic microvilli that are more common near the junctional zones." "FMA:70626" - "A neoplastic cell that is capable of entering a surrounding tissue" "https://ncit.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&code=C12917" - "Any melanocyte that is part of a prepuce of penis." - "Circulating macrophages and tissue macrophages (alveolar macrophages) of lung." "CALOHA:TS-0576" - "Mast cell subtype whose granules contain both the serine proteases tryptase and chymase. These cells are primarily found in connective tissue, such as the peritoneal cavity, skin, and intestinal submucosa. Their development is T-cell independent." - "An epithelial cell that is part of the lacrimal canaliculus." "FMA:70553" - "An inhibitory GABAergic interneuron found in the cerebellar cortex." - "A cell of the monocyte, granulocyte, or mast cell lineage." - "OBSOLETE: A sporangiospore that is motile, having flagella." "FAO:0000039" - "Obsolete. Use PO:0000076 from Plant Ontology instead. OBSOLETE, use term from Plant Ontology. Parenchyma cells containing chloroplasts; a component of leaf mesophyll and other green parenchyma tissue." - "A ciliated cell of the bronchus." - "OBSOLETE (was not defined before being made obsolete)." - "A transitional myocyte that is part of the left branch of atrioventricular bundle." "FMA:263170" - "KUPO:0001075" - "A progesterone secreting cell in the corpus luteum. The large luteal cells develop from the granulosa cells. The small luteal cells develop from the theca cells." "FMA:18688 BTO:0003939" - "An epithelial cell that is part of the viscerocranial mucosa." "FMA:70583" - "OBSOLETE: A walled spore produced in a sporangium." - "A cell whose nucleus has two haploid genomes." "FMA:72300" - "Obsolete. Consult Plant Ontology instead. The cell in the phloem tissue concerned with mainly longitudinal conduction of food materials. Classified into sieve cell and sieve tube member." - "A CD4-positive, CD25-positive, CCR4-positive, alpha-beta T regulatory cell with the phenotype HLA-DRA-positive, indicating recent activation." - "Obsolete. Use PO:0000351 from Plant Ontology instead. An epidermal cell that divides to produce the guard cells." - "A flat or angular epithelial cell with condensed nuclei and darkly staining cytoplasm containing numerous intermediate filaments inserted into desmosomes contacting surrounding supporting cells; lie in contact with the basal lamina of olfactory epithelium." "FMA:62304" - - "A fat cell that is part of the breast." "CALOHA:TS-2377" + "Any collection of skeletal muscles that is part of a head [Automatically generated definition]." "FMA:71287 EMAPA:18171" + "A smooth muscle cell that is part of a placenta." "EFO:0010709" + "The inner portion of the kidney consisting of the renal pyramids." "BTO:0001167 GAID:425 UMLS:C0022664 NCIT:C12740 CALOHA:TS-1157 MA:0000373 galen:MedullaOfKidney SCTID:30737000 Wikipedia:Renal_medulla MESH:D007679 EMAPA:19279" + "Any process that stops, prevents, or reduces the frequency, rate or extent of asymmetric cell division." + "Interneuron of the vertebrate retina. They integrate, modulate, and interpose a temporal domain in the visual message presented to the retinal ganglion cells, with which they synapse in the inner plexiform layer. They lack large axons." "FMA:67766 BTO:0004044" + "The process whose specific outcome is the progression of the inner ear over time, from its formation to the mature structure." + "An entity that has temporal parts and that happens, unfolds or develops through time."@en + "Any process that modulates the rate, frequency or extent of branching involved in ureteric bud morphogenesis, the process in which the branching structure of the ureteric bud is generated and organized. The ureteric bud is an epithelial tube that grows out from the metanephric duct. The bud elongates and branches to give rise to the ureter and kidney collecting tubules." + "A glomerular capillary that is part of a pronephros." "ZFA:0005309 TAO:0005309" + "A zone of skin that is part of the face." "UMLS:C0222084 SCTID:361703006 EMAPA:36657 FMA:24758 NCIT:C33561" + "The middle limb segment of the pectoral free limb, between the autopod and stylopod segments. Includes as parts the forelimb zeugopodial skeleton, which includes as parts the radius and ulna, or their cartilage precursors, or evolutionary variants." "GAID:55 UMLS:C0016536 EFO:0003053 EMAPA:17417 EHDAA2:0000553 MA:0000034 FMA:9663 VSAO:0005058 EHDAA:4172 EHDAA:6218 SCTID:362741001 NCIT:C32628 galen:Forearm BTO:0001447 Wikipedia:Forearm CALOHA:TS-2205 VHOG:0000341 MESH:D005542" + "A transient fetal dilation of the distal (or cranial) heart tube located where the arterial trunk joins the ventral roots of the aortic arches." "FMA:70300 Wikipedia:Bulbus_cordis SCTID:361525002 EMAPA:16333 EHDAA2:0000197 EHDAA:438 UMLS:C1284055 EHDAA:768 NCIT:C34114" + "The directed movement of calcium ions from inside of a cell, across the plasma membrane and into the extracellular region." + "The carpometacarpal joints (CMC) are joints in the wrist that articulates the distal row of carpal bones and the proximal bases of the metacarpal bones." "UMLS:C0224620 NCIT:C32265 Wikipedia:Carpometacarpal_joint SCTID:361842002 FMA:35287" + "Any process that activates or increases the frequency, rate or extent of cytoplasmic translation." + "Any process that modulates the frequency, rate or extent of myeloid dendritic cell chemotaxis." + "Binding to epinephrine, a hormone produced by the medulla of the adrenal glands that increases heart activity, improves the power and prolongs the action of muscles, and increases the rate and depth of breathing. It is synthesized by the methylation of norepinephrine." + "A scalar EM radiation quality which obtains by the capacity of the bearer to scatter or reflect radiation." + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving RNA." + "Any process that activates or increases the frequency, rate or extent of Schwann cell differentiation." + "A VIP peptides that is encoded in the genome of human." "UniProtKB:P01282" + "The process whose specific outcome is the progression of an epithelium in the kidney over time, from its formation to the mature structure. An epithelium is a tissue that covers the internal or external surfaces of an anatomical structure." + "Red bone marrow located in the sternum." + "A vein that drains the urethra." "FMA:21270" + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a bile acid stimulus." + "The regulated exocytosis of secretory granules containing preformed mediators such as perforin and granzymes by a cytotoxic T cell." + "Any process that activates or increases the frequency, rate or extent of aldosterone secretion." + "A strand of hair that is part of a trunk." "FMA:54250" + "A squamous epithelium that is part of a vagina." "EMAPA:37794 UMLS:C1711259 NCIT:C49314 MA:0001731" + "Any microtubule in the cytoplasm of a cell." + "A urothelial cell that is part of the urothelium of the urinary bladder." "NCIT:C32210 KUPO:0001121" + "An epithelial ciliated cell that is part of the fallopian tube. This cell type is found mainly on the apex of the mucosal folds and contributes, together with peristaltic contractions, to the self-propulsion of spermatozoa, the transport of ovum during ovulation and the transport of the fertilized ovum to the intramural fallopian tube. A fallopian tube ciliated cell has a columnar shape and contains an oval or round nucleus, often located perpendicular or parallel to the long axis of the cell." + "The regulated release of growth hormone from secretory granules into the blood." + "A regulatory T cell present in the B cell follicles and germinal centers of lymphoid tissues. In humans, it is CXCR5+." + "The developmental process pertaining to the initial formation of a left cardiac atrium from unspecified parts." + "The process that gives rise to rhombomere 1. This process pertains to the initial formation of a structure from unspecified parts. Rhombomeres are transverse segments of the developing rhombencephalon. Rhombomeres are lineage restricted, express different genes from one another, and adopt different developmental fates. Rhombomeres are numbered in anterior to posterior order." + "A mono-stratified retinal ganglion cell that has a small dendritic field and a sparse dendritic arbor with post sympatic terminals in sublaminar layer S3." "Epidermal cell rich in mitochondria. In amphibians, appears during metamorphosis." - "Obsolete. Use PO:0000355 from Plant Ontology instead. A fiber like tracheid in the secondary xylem; commonly thick walled, with pointed ends and bordered pits that have lenticular to slit like apertures." - "Any microvascular endothelial cell that is part of a female urethra." - "Osteoblast that is terminally differentiated, located adjacent to acellular or cellular bone tissue within periosteum, and is capable of mineralizing the matrix." "VSAO:0000116" - "Obsolete. Use PO:0000082 from Plant Ontology instead. A meristemic ray cell in the vascular cambium that gives rise to ray cells of the secondary xylem and secondary phloem." - "Conventional dendritic cell is a dendritic cell that is CD11c-high." "FMA:84191" - "Mature CD8_alpha-negative CD11b-negative dendritic cell is a CD8_alpha-negative CD11b-negative dendritic cell that is CD80-high, CD86-high, MHCII-high and is CD83-positive." + "A protein that is a translation product of the human CD19 gene or a 1:1 ortholog thereof. It is composed of an N-terminal extracellular domain containing two Ig-like C2-type (immunoglobulin-like) domains, followed by a single-pass transmembrane segment and a cytoplasmic C-terminal tail. CD19 expression is restricted to members of the B cell lineage. It functions as a co-receptor for B-cell antigen receptor (BCR), regulating signal transduction." "PIRSF:PIRSF016630 IUPHARobj:2764" + "The change in morphology and behavior of a T-helper 1 cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific." + "A physical quality inhering in a neuron by virtue of the relative location of its soma and the regions to which it projects and makes synaptic contacts in." + "Any process that stops, prevents or reduces the frequency, rate or extent of T cell migration." + "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of glycogen." + "A beta-globin that is a translation product of the mouse Hbb-b1 gene or a 1:1 ortholog thereof." "A stromal cell found in the lamina propria of the large intestine." - "A cardiac myocyte of the interatrial region of the heart." "FMA:228790" - "An epithelial cell derived from ectoderm." "FMA:69074" - "A mesothelial cell that is part of the small intestine." - "A transitional stage B cell that expresses surface IgM and IgD, and CD62L. This cell type appears to be an anergic B cell that does not proliferate upon BCR signaling, is found in the spleen and lymph nodes, and has the phenotype surface IgM-positive, surface IgD-positive, CD21-positive, CD23-positive, CD62L-positive, and CD93-positive. This cell type has also been described as IgM-low, CD19-positive, B220-positive, AA4-positive, and CD23-positive (i.e. this cell-type is distinguished from T2 cells by surface expression of IgM)." - "A thermoreceptor cell that detects increased temperatures." - "Intraglomerular mesangial cells are specialized pericytes located among the glomerular capillaries within a renal corpuscle of a kidney." "KUPO:0001032" - "A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair." "CALOHA:TS-0650 FBbt:00005083 FMA:70335 BTO:0000222 VHOG:0001529" - "Mostly cylindrical, resemble Type 1 in their contents and the presence of a kinocilium and stereocilium apically; much greater variation in size, some almost span the entire thickness of the sensory epithelium, while others are smaller than Type 1; receive multiple efferent nerve boutons around their bases as well as afferent endings, which are small expansions rather than chalices." "FMA:67909" - "A blood vessel endothelial cell that is part of the retina." - "Obsolete. Use PO:0020097 from Plant Ontology instead. The cell that will give rise to the generative nuclei which will participate in fertilization." - "A B-1 B cell that has the phenotype CD5-negative, but having other phenotypic attributes of a B-1 B cell." - "A granulocyte monocyte progenitor is CD34-positive, CD38-positive, IL-3receptor-alpha-positive and is CD45RA-negative." - "This cell type produces and secretes melatonin and forms the pineal parenchyma. Extending from each cell body, which has a spherical, oval or lobulated mucleus, are one or more tortuous basophilic processes, containing parallel microtubules known as synaptic ribbons. These processes end in expanded terminal buds near capillaries or less, frequently, ependymal cells of the pineal recess. The terminal buds contain granular endoplasmic reticulum, mitochondria and electron-dense cored vesicles, which store monoamines and polypeptide hormones, release of which appears to require sympathetic innervation." "BTO:0001068 FMA:83417" - "Supports paraganglial type 1 cell." - "An inactive fibroblast; cytoplasm is sparse, endoplasmic reticulum is scanty with flattened nucleus. Term used by some histologists; when fibroblasts become relatively inactive in fiber formation. However, this cell has the potential for fibrogenesis in quiescent connective tissue of the adult, as well as during development, other histologists prefer to use the term fibroblast in all circumstances. These cells represent ~0.5% of peripheral blood leukocytes." "FMA:63879" - "Obsolete. Use PO:0000289 from Plant Ontology instead. One of the series of cellular components of a sieve tube. It shows a more or less pronounced differentiation between sieve plates (wide pores) and lateral sieve areas (narrow pores). Also sieve tube element and the obsolete sieve tube segment." - + "A cell morphology that inheres in neurons with only one process, a neurite, that extends from the cell body. The neurite then branches to form dendritic and axonal processes." + "A nucleate quality inhering in a bearer by virtue of the bearer's having two nuclei." + "A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair." "FBbt:00005083 VHOG:0001529 FMA:70335 CALOHA:TS-0650 BTO:0000222" + "A biological process that directly contributes to the process of producing new individuals, involving another organism." + "Any process that activates or increases the frequency, rate or extent of cardiac chamber formation." + "The process whose specific outcome is the progression of the proximal convoluted tubule over time, from its formation to the mature structure. The proximal convoluted tubule is the most proximal portion of the proximal tubule and extends from the glomerular capsule to the proximal straight tubule." + "Any process that stops, prevents, or reduces the frequency, rate or extent of a neurophysiological process." + "The process in which the anatomical structures of the outer ear are generated and organized. The outer ear is the part of the ear external to the tympanum (eardrum). It consists of a tube (the external auditory meatus) that directs sound waves on to the tympanum, and may also include the external pinna, which extends beyond the skull." + "The process of creating protein polymers, compounds composed of a large number of component monomers; polymeric proteins may be made up of different or identical monomers. Polymerization occurs by the addition of extra monomers to an existing poly- or oligomeric protein." "An epithelial cell that is part of a nephron tubule." "KUPO:0001022 FMA:86785" - "A cell of the supporting or framework tissue of the body, arising chiefly from the embryonic mesoderm and including adipose tissue, cartilage, and bone." "CALOHA:TS-2096 FMA:63875" - "A Vip GABAergic cortical interneuron that expresses CCK. L5/6 CCK cells have soma found mainly in L5 and L6 and have large axonal arborization." - "An epithelial cell of thyroid gland." "FMA:256167" - "Neuroendocrine cells that are born in the nasal placode during embryonic development and migrate through the nose and forebrain to the hypothalamus, where they regulate reproduction." - "An innate lyphoid cell with an immature phenotype." - "A ciliated epithelial cell with many cilium." - "A near-projecting glutamatergic neuron with a soma found in layer 5/6 of the marmoset primary motor cortex." "ILX:0770161" - "A peptide hormone secreting cell that secretes gastrin." - "A muscle cell with low content of myoglobin and other oxygen storing proteins. This muscle cell has a white appearance." "FMA:84449" - "A taste receptor cell that has a short microvilli, a projecting apical region, a large rounded nucleus, and expresses taste chemoreceptors thus making them the transducing cell for taste qualities." "FMA:62381" - - "An enteroendorcine cell found in the ileum and jejunum that produces neurotensin." "FMA:62943" - "WBbt:0006829" - "Any blood vessel endothelial cell that is part of a dermis." - - "A endothelial cell of the venule that is squamous shaped. This is in contrast to the cubodial shape of high endothelial venule cells." - "A stromal cell found in the lamina propria of the colon." - "An extracellular matrix secreting cell that secretes glycocalyx." - "A glutamatergic neuron located in the cerebral cortex that projects axons locally rather than distantly." "ILX:0770103" - "Obsolete. Use PO:0000079 from Plant Ontology instead. An elongated cell with approximately wedge-shaped ends, found in the vascular cambium, which gives rise to the elements of the axial system in the secondary vascular tissues." - "OBSOLETE (was not defined before being made obsolete)." - "A peptide hormone secreting cell that secretes growth hormone releasing hormone." - "A mesothelial cell that is part of the colon." - "CD4-positive alpha-beta T cell with the phenotype CD25-positive, CTLA-4-positive, and FoxP3-positive with regulatory function." + "GC_ID:1" + "The process in which the anatomical structures of the nose are generated and organized. The nose is the specialized structure of the face that serves as the organ of the sense of smell and as part of the respiratory system. Includes the nasi externus (external nose) and cavitas nasi (nasal cavity)." + "The process of shaping a trabecula in the heart. A trabecula is a small, often microscopic, tissue element in the form of a small beam, strut or rod, which generally has a mechanical function. Trabecula are usually but not necessarily, composed of dense collagenous tissue." + "The process whose specific outcome is the progression of a thyroid-stimulating hormone-secreting cell over time, from its formation to the mature structure. A thyroid-stimulating hormone-secreting cell is a basophil cell of the anterior pituitary that produces thyroid stimulating hormone, thyrotrophin." + "Any region of a nephron tubule that is convoluted. Examples: distal convoluted tubule, proximal convoluted tuble." "Wikipedia:Convoluted_tubule SCTID:361333002 NCIT:C49479 UMLS:C1707510 MA:0001665 EMAPA:35725" + "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane." + "EHDAA2:0000996 EMAPA:17186 VHOG:0000449" + "A secretion that is part of a esophagus [Automatically generated definition]." "MA:0002514 UMLS:C0227179 NCIT:C52555 FMA:79662" + "The motor and sensory nerve subdivision of the trigeminal nerve that transmits sensory information from the auricle, the external acoustic meatus, tympanic membrane, temporal region, the cheek, the skin overlying the mandible, the anterior portion of the tongue, the floor of the mouth, lower teeth and gingiva and transmits motor information from the muscles of mastication, the mylohyoid muscle and digastric muscle and the muscles tensor tympani and tensor veli palatini." "AAO:0010688 GAID:834 Wikipedia:Mandibular_nerve FMA:52996 BTO:0001375 MA:0001101 AAO:0010703 EHDAA2:0002086 MESH:D008340 UMLS:C0024695 VHOG:0001345 SCTID:280212008 NCIT:C32779 EMAPA:17798" + "A homeostatic process involved in the maintenance of a steady state level of glucose within a cell." + "The directed movement of a vesicle to a specific location." + "A pharyngeal arch that is posterior to the hyoid arch. i.e. any pharyngeal arch with a number 3 or higher." "ZFA:0001613 AAO:0010362 EFO:0003694 XAO:0000099 BTO:0002152 TAO:0001597" + "Any process that modulates the frequency, rate or extent of enzymatic generation of superoxide by a cell." + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a lysosomal membrane. A lysosomal membrane is the lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm." + "The self-renewing division of a germline stem cell in the male gonad, to produce a daughter stem cell and a daughter germ cell, which will divide to form the male gametes." + "Any process that modulates the rate, frequency, or extent of epithelial to mesenchymal transition. Epithelial to mesenchymal transition where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell." + "Transudate contained in the peritoneal cavity." "FMA:16515 ncithesaurus:Peritoneal_Fluid Wikipedia:Peritoneal_fluid BTO:0001031 EMAPA:35683 MA:0002531" + "Muscle tissue that contains fibers that are divided by transverse bands into striations." "galen:StriatedMuscle UMLS:C1331262 EHDAA2:0003140 CALOHA:TS-2047 AAO:0010762 WBbt:0005779 NCIT:C12436 MA:0002438 Wikipedia:Striated_muscle FMA:67905 AEO:0000140 EMAPA:36390" + "An lymphatic vessel endothelium that is part of a respiratory system [Automatically generated definition]." "MA:0001825 EMAPA:37581" + "Any process that increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle." + "Any process that activates or increases the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein." + "GC_ID:1" + "Enables the transfer of L-histidine from one side of a membrane to the other. L-histidine is 2-amino-3-(1H-imidazol-4-yl)propanoic acid." + "A bestrophin-4 that is encoded in the genome of human." "Reactome:R-HSA-2744358 DTO:01100033 UniProtKB:Q8NFU0" + "Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP]." "Wikipedia:Lateral_plate_mesoderm#Division_into_layers XAO:0000276 BILA:0000044 FMA:295568 AAO:0011102" + "The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex." "Wikipedia:Antigen_presentation" + "The external portion of the prostate including the anterior, inferolateral, lateral and posterior surfaces." "UMLS:C0426735 NCIT:C13091 SCTID:279694003 FMA:19590" + "The process whose specific outcome is the progression of a cardiac cell over time, from its formation to the mature state. A cardiac cell is a cell that will form part of the cardiac organ of an individual." + "Any process that stops, prevents or reduces the frequency, rate or extent of chorionic trophoblast cell proliferation." + "An anatomical wall that is part of an artery [Automatically generated definition]." "FMA:14155 BTO:0002009 galen:ArterialWall" "Ectoderm destined to be nervous tissue." - "A megakaryocyte progenitor cell that is CD34-positive, CD41-positive, and CD42-negative." - "An epithelial cell type that lacks the columnar shape typical for other respiratory epithelial cells. This cell type is able to differentiate into other respiratory epithelial cells in response to injury." - "A CD8-positive, alpha-beta T cell that has not experienced activation via antigen contact and has the phenotype CD45RA-positive, CCR7-positive and CD127-positive. This cell type is also described as being CD25-negative, CD62L-high and CD44-low." - "A mesonephric glomerular visceral epithelial cell is a specialized epithelial cell that contains \"feet\" that interdigitate with the \"feet\" of other glomerular epithelial cells in the mesonephros" - "A tissue macrophage that is in the pleural space." "FMA:83024" - "Motor neuron that innervate muscles that control eye, jaw, and facial movements of the vertebrate head and parasympathetic neurons that innervate certain glands and organs." "PMID:14699587" - "A lens fiber cell that develops from primary lens fiber; located towards the center of lens; cell organelles are normally degraded or in the process of being degraded." - "Muscle precursor cell that is adjacent to the notochord and part of the presomitic mesoderm." + "Any process that activates or increases the frequency, rate or extent of gamma-delta T cell activation." + "A portion of connective tissue that is part of a thoracic cavity [Automatically generated definition]." "MA:0000555 EMAPA:37255" + + "A blood vessel that supplies or drains an ear." "EMAPA:37386 MA:0001226" + "Middle layer of the glomerular basement membrane." "FMA:74276 ZFA:0005286 NCIT:C32916 TAO:0005286 UMLS:C1235665" + "The orderly movement of a myoblast from one site to another, often during the development of a multicellular organism. A myoblast is a cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers." + "The expansion of an immature T cell population by cell division in the thymus." "A regular cardiac myocyte of the interventricular region of the heart." "FMA:228792" - "A type EC enteroendocrine cell in the duodenum and jejunum that stores and secretes motilin and 5-hydroxytryptamine." "FMA:62941" - "A myoepithelial cell that is part of the secondary lactiferous duct." "FMA:74501" - "A type II muscle cell that contains large amounts of myoglobin, has many mitochondria and very many blood capillaries. Type II A cells are red, have a very high capacity for generating ATP by oxidative metabolic processes, split ATP at a very rapid rate, have a fast contraction velocity and are resistant to fatigue." "FMA:84415 BTO:0001813" - "A supporting cell that is attached to the basement membrane and forms rows that support the hair cells." "FMA:79800" - "The small neuron in the glomerular layer of the olfactory bulb whose dendrites arborize within a glomerulus, where it receives synaptic input from olfactory receptor cell axon terminals, and also engages in dendrodendritic interactions with mitral and tufted cell dendrites; uses both GABA and dopamine as a neurotransmitter." "NIFSTD:nifext_122 BTO:0003796" - "A GABAergic neuron located in the cerebral cortex that expresses vasoactive intestinal polypeptide" "ILX:0770151" - "An otic fibrocyte that lines the otic capsule." + "A neural arch that is part of a vertebral bone 2." "FMA:24053" + "One of two laterally paired arteries that supplies the kidneys. These are large arteries that branch from the dorsal aorta in primitive vertebrates." "EFO:0002552 EHDAA:5321 EHDAA2:0004100 EMAPA:28373 TAO:0000420 MA:0002035 SCTID:181339005 EHDAA:8594 MESH:D012077 GAID:507 ZFA:0000420 galen:RenalArtery UMLS:C0035065 FMA:14751 AAO:0010223 Wikipedia:Renal_artery NCIT:C12778 BTO:0001165 RETIRED_EHDAA2:0001600" + "Any process that activates or increases the rate or extent of progression through the cell cycle." + "The orderly movement of a cell from one site to another that will contribute to the progression of the heart over time, from its initial formation, to the mature organ." + "The metanephric proximal tubule is a metanephric nephron tubule that connects Bowman's capsule to the descending thin limb of the loop of Henle in the metanephros. It has a brush border epithelial morphology[GO]." "A mature B cell subset originally defined as having being CD45R-positive, IgM-positive, IgD-positive and CD43-negative. Subsequent research demonstrated being CD21-positive and CD23-negative and CD93 negative." - - "A somatic cell located in skeletal muscle." "FMA:9727 CALOHA:TS-2158 BTO:0004392" - "A class of large neuroglial (macroglial) cells in the central nervous system. Form the insulating myelin sheath of axons in the central nervous system." "BTO:0000962 CALOHA:TS-0709 FMA:54540" - "A nodal myocyte that is part of the sinoatrial node." "FMA:83383" - "Any cell participating in the inflammatory response to a foreign substance, e.g. neutrophil, macrophage." "http://en.wikipedia.org/wiki/Inflammatory_response GOC:pr" - "Any hematopoietic cell that is a precursor of some other hematopoietic cell type." - "A Vip GABAergic cortical interneuron with a soma found in L5. L5 Vip cells have mostly local morphology with some deep-projecting axons. They show only moderate resistance, comparable to that of Sst subclass and unlike typical Vip subclass cells that tend to show high input resistance. L5 Vip cells show particularly low resting membrane potential." - "Any neuron that is part of a central nervous system." + "The process whose specific outcome is the progression of an allantois over time, from its formation to the mature structure." + "Any process that regulates translation occurring at the presynapse." + "Any of the veins carrying deoxygenated blood from the subcutaneous tissue layers." "Wikipedia:Superficial_vein UMLS:C0226513 FMA:76719 SCTID:341382008 NCIT:C33666" + "Any process that stops, prevents, or reduces the frequency, rate, or extent of B cell cytokine production." + "Any process that activates or increases the frequency, rate or extent of smooth muscle tissue development." + "Any process that stops, prevents or reduces the frequency, rate or extent of melanosome organization." + "A fibroblast that is part of the fibrous layer of the perichondrium. This cell is responsible for collagen fiber production." "A conventional dendritic cell that expresses CD11b (ITGAM)." - "A cell whose primary function is intermediary metabolism." - "A muscle cell that is part of the atrial branch of anterior internodal tract." "FMA:223277" - "A pigment cell derived from the neural crest. The cell contains flat light-reflecting platelets, probably of guanine, in stacks called reflecting platets or iridisomes. The color-generating components produce a silver, gold, or iridescent color." - "A CD8-positive, alpha-beta positive T cell expressing GATA-3 and secreting IL-4." "FMA:84794 BTO:0004794" - "Any fibroblast that is part of a cardiac ventricle." - - "A fat cell that is beige in color, thermogenic, and which differentiates in white fat tissue from a Myf5-negative progenitor." + "An anatomical space that is enclosed by a sinusoid." "FMA:63133" + "Any process that stops, prevents or reduces the frequency, rate or extent of aortic smooth muscle cell differentiation." + "A vasculature that is part of a organ." "FMA:74612" + "A star-shaped glial cell that is part of some retina. This cell links neurons to blood vessels and may provide structural and physiological support to optic nerve head axons." "A type of mouse mesothelial fibroblast that is derived from the neural crest, is localized on blood vessels, and is a key component of the pia and arachnoid membranes surrounding the brain." - "A non-polarised cell precursor cell that is part of some mesenchyme, is associated with the cell matrix but is not connected to other cells and is capable of migration." - "Any endothelial cell that is part of a spleen." - "CD4-positive, alpha-beta T cell with the phenotype RORgamma-t-positive, CXCR3-negative, CCR6-positive, and capable of producing IL-17." - "A basophil chromphil cell of the anterior pitiutary gland that produce adrenocorticotropic hormone, melanocyte-stimulating hormone and lipotropin. This cell type is irregular in shape and has short dendritic processes which are inserted among other neighboring cells;" "BTO:0002509 FMA:83098" - "An epithelial cell that remains from the disintegration of the epithelial root sheath involved in the development of teeth." "FMA:62987" - - "A mature NK T cell that secretes interferon-gamma and enhances Th1 immune responses." - "A lineage marker-negative, CD34-positive, CD38-positive, IL3r-alpha-positive, IL5r-alpha-positive, and CD45RA-negative eosinophil progenitor cell." - "An intestinal crypt stem cell that is located in the colon." - "A myofibroblast that lies in the connective tissue of the spinal cord that has a distinctly lamellar arrangement." + "The regulated release of estradiol into the circulatory system." + "Subdivision of skeleton consisting of all skeletal elements in an hindlimb region." "XAO:0003062 AAO:0000217 VHOG:0001255 FMA:24144 EMAPA:32633 VSAO:0000152 EHDAA2:0002226" + "A phalanx that is part of a hindlimb autopod[Automatically generated definition]." "Wikipedia:Phalanges_of_the_foot MA:0000305 SCTID:302533005 ncithesaurus:Phalanx_of_the_Foot UMLS:C0584876 EMAPA:32941 AAO:0000930 FMA:24493 NCIT:C52772" + "The radial migration of neuronal or glial precursor cells along radial glial cells during the development of the cerebral cortex." + "Sense organ embedded in the integument and consisting of one or a cluster of sensory neurons and associated sensory structures, support cells and glial cells forming a single organised unit with a largely bona-fide boundary.[FBbt]." "TGMA:0000540 HAO:0000933 MIAA:0000163 Wikipedia:Sensillum BTO:0001237 MAT:0000163 EFO:0000939" + "A section through the tube or network of tubes that connects the ovaries to the outside of the body." "FMA:18302" + "Any joint connecting the acromonion of the scapula and clavicle." "Wikipedia:Acromioclavicular_joint FMA:25898 MESH:D000173 UMLS:C0001208 SCTID:182166001 NCIT:C32047 GAID:249" + "A metaphysis that is part of a tibia." "EMAPA:37772 MA:0003106 FMA:33135" + "Any process that modulates the frequency, rate or extent of bone mineralization." "Mature T cell not yet exposed to antigen with the phenotype CCR7-positive, CD45RA-positive, and CD127-positive. This cell type is also described as being CD25-negative, CD62L-high and CD44-low." - "A thymocyte that has the phenotype CD4-negative, CD8-positive, CD44-negative, CD25-negative, and pre-TCR-positive." - "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells." - "A cuboidal epithelial cell of the kidney which secretes acid and reabsorbs base to regulate acid/base balance." - "A smooth muscle cell that is part of the duodenum." "FMA:15058" - "Obsolete. Use PO:0020093 from Plant Ontology instead. OBSOLETE, use term from plant ontology. A cell located at the chalazal end of the mature embryo sac in angiosperms." - "Mural cells are pericytes and the vascular smooth muscle cells (vSMCs) of the microcirculation." - "A primitive erythrocyte that has undergone enucleation. This cell type is 3-6 fold bigger than the fetal derived erythrocytes that they co-circulate with during fetal development. Expresses epsilon-gamma hemoglobin chains." - "A CD8-positive, alpha-beta T cell that is capable of killing target cells in an antigen specific manner with the phenotype perforin-positive and granzyme B-positive." "FMA:70573 CALOHA:TS-0190" - - "A melanocyte that is part of the eyelid." "FMA:59175" - "A small cell formed by the first meiotic division of oocytes." "VHOG:0000464 EMAPA:16032 EHDAA2:0000541 FMA:18650" - "A thymic macrophage found in the thymic medulla." - "A multi-fate stem cell that can give rise to different retinal cell types including rod and cone cells." - "Squamous cell of uterine cervix epithelium." "CALOHA:TS-1251" - "Obsolete. Use PO:0004531 from Plant Ontology instead. A cell characterized by conspicuous and rather stable accumulation of starch." - + "The process that gives rise to adenohypophysis. This process pertains to the initial formation of a structure from unspecified parts. The adenohypophysis is the anterior part of the pituitary. It secretes a variety of hormones and its function is regulated by the hypothalamus." + "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a neuronal dense core vesicle." + "A CD8-positive, alpha-beta T cell that is capable of killing target cells in an antigen specific manner with the phenotype perforin-positive and granzyme B-positive." "CALOHA:TS-0190" + "Any process that stops, prevents or reduces the frequency, rate or extent of cell proliferation in dorsal spinal cord." + "Highly vascular stroma found in the center of the ovary that forms from embryonic mesenchyme and contains blood vessels, lymphatic vessels, and nerves; this stroma forms the tissue of the hilum by which the ovarian ligament is attached, and through which the blood vessels enter; it does not contain any ovarian follicles." "NCIT:C33245 Wikipedia:Medulla_of_ovary UMLS:C0227879 EMAPA:37928 FMA:18616" "CD1a-positive Langerhans cell is a Langerhans_cell that is CD1a-positive and CD324-positive." - "A GABAergic interneuron whose soma is located in the cerebral cortex." - "The support cell that makes the thecogen dendritic cap - a cuticle-like matrix around the tip of the eo-dendrite and which encloses the soma of the eo-neuron." - "A B cell that is located in the anorectum." + "The directed movement of molecules between the nucleus and the cytoplasm." + "Any process that modulates the frequency, rate or extent of the controlled release of bile acid from a cell or a tissue." "A cell involved in the elimination of metabolic and foreign toxins, and in maintaining the ionic, acid-base and water balance of biological fluids." "WBbt:0005812" - "Any microvascular endothelial cell that is part of a adipose tissue." - "Mature CD11c-low plasmacytoid dendritic cell is a CD11c-low plasmacytoid dendritic cell that is CD83-high and is CD80-positive, CD86-positive, and MHCII-positive." - "A pre-BCR-negative large pre-B-II cell is a large pre-B-II cell that is pre-B cell receptor-negative, composed of surrogate light chain protein (SL), which is composed of VpreB and Lambda 5/14.1, in complex with immunoglobulin mu heavy chain (IgHmu), on the cell surface, and lack a DNA rearrangement of immunoglobulin light chain genes." - - - "A pigment cell that is capable of detecting light stimulus that is involved in visual perception." "FMA:63846" - "Squamous cell of vaginal epithelium." "CALOHA:TS-1254" - "A Leydig cell is a testosterone-secreting cell in the interstitial area, between the seminiferous tubules, in the testis." "EMAPA:29655 CALOHA:TS-1150 BTO:0000755 FMA:72297" - "CD4-positive alpha-beta T cell with regulatory function that produces IL-10." - "A cell found within the adrenal medulla that secrete biogenic amine hormones upon stimulation." "FMA:69262" - "A brush cell of the epithelium in the terminal bronchiole." "FMA:263228" - "An activated mature (naive or memory) B cell that is secreting immunoglobulin, typified by being CD27-positive, CD38-positive, CD138-negative." "FMA:84371" - "A mechanoreceptor located in the acoustic maculae and the semicircular canals that mediates the sense of balance, movement, and head position. The vestibular hair cells are connected to accessory structures in such a way that movements of the head displace their stereocilia. This influences the membrane potential of the cells which relay information about movements via the vestibular part of the vestibulocochlear nerve to the brain stem." "FMA:62351" - "An IgG-positive double negative memory B cell is a double negative memory B cell with the phenotype IgG-positive, IgD-negative, and CD27-negative." - - "A plasmablast that secretes IgG." - "A CD4-negative, CD8-negative, alpha-beta intraepithelial T cell that is found in the columnar epithelium of the gastrointestinal tract." - "A cell that secretes insulin and is located towards the center of the islets of Langerhans." "EV:0200009 ncithesaurus:Beta_Cell MA:0002419 BTO:0000783 FMA:70586" - "a L6 intratelencephalic projecting glutamatergic neuron of the primary motor cortex that has stellate pyramidal morphology." - "An epithelial cell of the prostate." "FMA:66817 FMA:256163" - "A peptide hormone cell that secretes prolactin." - - "Cytoplasm that exhibits affinity for both basic and acid stains under specific pH conditions." - "Epithelioid macrophage is an activated macrophage that resembles an epithelial cell with finely granular, pale eosinophilic cytoplasm and central, ovoid nucleus (oval or elongate). This cell type is able to merge into one another to form aggregates. The presence of such aggregates may characterize some pathologic conditions, mainly granulomatous inflammation." "FMA:83514" - "A primary oocyte is an oocyte that has not completed female meosis I." "FMA:18645 BTO:0000512" - "Intraepithelial T cells with a memory phenotype of CD2-positive, CD5-positive, and CD44-positive." - - "A goblet cell that is part of the epithelium of crypt of lieberkuhn of small intestine." "FMA:263050" - "Obsolete. Use PO:0000066 from Plant Ontology instead. A cell that constitutes the mesophyll of a hydathode and is located between the xylem endings and the epidermis. Proposed to be involved in the retrieval of solutes from the xylem sap." - "A skeletal muscle satellite cell that is mitotically quiescent. These cells are wedge shaped and have a large nuclear to cytoplasmic ratio with few organelles, a small nucleus and condensed interphase chromatin. Satellite cells typically remain in this state until activated following muscle damage." - "A fat cell that is part of omentum tissue." + "Any process that stops, prevents or reduces the frequency, rate or extent of extracellular vesicular exosome assembly." + "The process that gives rise to the optic nerve. This process pertains to the initial formation of a structure from unspecified parts. The sensory optic nerve originates from the bipolar cells of the retina and conducts visual information to the brainstem. The optic nerve exits the back of the eye in the orbit, enters the optic canal, and enters the central nervous system at the optic chiasm (crossing) where the nerve fibers become the optic tract just prior to entering the hindbrain." + "Combining with ATP and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex." + "BAMS:AVPe UMLS:C0262200 FMA:62314 HBA:4550 BAMS:AVPV BIRNLEX:1401 MBA:272 DHBA:13061 neuronames:382" + "Any process that modulates the frequency, rate or extent of skeletal muscle hypertrophy." + "The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA." + "Organ with organ cavity which consists of the vestibular labyrinth and the cochlear labyrinth. The membranous labyrinth is lodged within the bony labyrinth and has the same general form; it is, however, considerably smaller and is partly separated from the bony walls by a quantity of fluid, the perilymph.[FMA, WP]." "VHOG:0000729 SCTID:263790009 Wikipedia:Membranous_labyrinth UMLS:C0458700 EHDAA:4698 AAO:0011060 FMA:61022 EHDAA2:0000899 XAO:0000194 MA:0000242 EV:0100367 NCIT:C33090" + "Any process that stops, prevents, or reduces the frequency, rate or extent of compound eye photoreceptor cell differentiation." + "A bone that is part of a post-anal tail." "EMAPA:18042 MA:0000696" + "The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom." "UMLS:C1512940 NCIT:C34195 Wikipedia:Intraembryonic_coelom VHOG:0000316 EMAPA:16088 EHDAA:251" + "Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to another (acceptor)." "EC:2.7.-.-" + "Any process that activates or increases the frequency, rate or extent of glucocorticoid mediated signaling pathway." + "The hydrolysis of a peptide bond or bonds within a protein as part of the chemical reactions and pathways resulting in the breakdown of a protein by individual cells." + "A viscosity which relatively high." + "OBSOLETE A sst GABAergic cortical interneuron transcriptomically between the sst and the pvalb families with a soma found in L2/3. Some L2/3 PV-like sst cells have Martinotti morphology while some have basket cell morphology. L2/3 PV-like sst cells have lower AP width and higher firing rate than typical Sst subclass cells. L2/3 PV-like sst cells have high maximum firing rate variability, with many classified as belonging to the pvalb subclass on the basis of electrophysiology." + "Generation of the female gamete; specialised haploid cells produced by meiosis and along with a male gamete takes part in sexual reproduction." + "The chemical reactions and pathways involving progesterone, a steroid hormone produced in the ovary which prepares and maintains the uterus for pregnancy. Also found in plants." + "An anatomical cavity that is part of a yolk sac [Automatically generated definition]." "FMA:63942 VHOG:0000843 EMAPA:16055" + "A sialoadhesin that is encoded in the genome of human." "UniProtKB:Q9BZZ2" + "Any process that modulates the frequency, rate or extent of apoptotic DNA fragmentation." + "This gland can either be a discrete structure located bilaterally above each kidney, or a cluster of cells in the head kidney that perform the functions of the adrenal gland. In either case, this organ consists of two cells types, aminergic chromaffin cells and steroidogenic cortical cells[GO]." + "The process whose specific outcome is the progression of smooth muscle in the ureter over time, from its formation to the mature structure." + "The repeating unit of a myofibril in a muscle cell, composed of an array of overlapping thick and thin filaments between two adjacent Z discs." "Wikipedia:Sarcomere" "A fibrocyte of the cochlea that has specialized structural and molecular adaptions." - "Obsolete. Use PO:0002002 from Plant Ontology instead. The lower cell formed after the first division of a plant zygote." - "A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a eosinophilic myelocyte and a band form eosinophil. The nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare. Markers are integrin alpha-M-positive, fucosyltransferase FUT4-positive, low affinity immunoglobulin gamma Fc region receptor III-positive, CD33-positive, CD24-positive and aminopeptidase N-negative." - "A cell that specializes in controlled release of one or more substances." "FMA:86916 BTO:0003659" - "A muscle cell that is part of some somatic muscle." - "A paneth cell that is part of the epithelium of small intestine." "FMA:263104" - "A nonkeratinized epithelial cell of the anal canal." "FMA:263146" - "A non-sensory cell that extends from the basement membrane to the apical surface of the auditory epithelium and provides support for auditory hair cells." - "An adipose macrophage that does not express F4/80but is MHC-II-positive. This cell type exhibits autofluorescence under typical flow cyometry conditions." - "An endothelial cell that lines the intracavitary lumen of the heart, separating the circulating blood from the underlying myocardium. This cell type releases a number of vasoactive substances including prostacyclin, nitrous oxide and endothelin." "FMA:75621" + + "An epithelium that is part of a prepuce of penis [Automatically generated definition]." "UMLS:C1709639 EMAPA:30655 NCIT:C49270 MA:0001753" + "An amacrine cell with a medium dendritic field and post-synaptic terminals in S2, S3, and S4. This cell type releases the neurotransmitter gamma-aminobutyric acid (GABA)." + "Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea." "ZFA:0001688 TAO:0002188" + "The space between a blood vessel and the pia mater." "Wikipedia:Virchow-Robin_space NCIT:C83196 UMLS:C0225983 SCTID:342298001" + "A portion of smooth muscle tissue that is part of a epididymis [Automatically generated definition]." "MA:0001736" + "A neural plate that develops_from a presumptive midbrain." "TAO:0007019 ZFA:0007019" + "An endothelium that is part of the placental artery." + "A suture that connects the two frontal bones of the skull." "EMAPA:19226 EMAPA:35358 SCTID:136854008 MA:0002796 FMA:52989 Wikipedia:Frontal_suture" + "A layer of thin, concentrically arranged cells with interspersed collagen that lies within the epineurium. The perineurium is a component of the blood–nerve barrier and is essential for protecting axons and their associated Schwann cells from ionic flux, toxins and infection." "EMAPA:37849 NCIT:C33302 Wikipedia:Perineurium FMA:52585 UMLS:C0205890 BTO:0003153 NLXANAT:090205 SCTID:362299001 NCIT:C41407" + "The orderly movement of a cell that will reside in the hindbrain." "A mature gamma-delta T cell located in the epidermis that regulates wound healing." - "A B cell found in the lymph node medullary sinus." "A NK1.1-positive T cell that is Ly49Cl-positive." - "A leukocyte with abundant granules in the cytoplasm." "BTO:0000539 CALOHA:TS-0422 FMA:62854 BTO:0001026" "An immature alpha-beta T-cell that express Egr2. These cells give rise to T cells expressing NK markers." - - "An amniotic stem cell is a mesenchymalstem cell extracted from amniotic fluid. Amniotic stem cells are able to differentiate into various tissue type such as skin, cartilage, cardiac tissue, nerves, muscle, and bone" - "An enteroendocrine cell that is located in the colon." - "A resident monocyte that is Gr-1 high, CD43-negative, CX3CR1-negative, CD115-positive, and B220-negative." - "A ciliated epithelial cell with a single cilium." - "A mature astrocyte that is capable of producing cytokines." - "A classical monocyte that is CD14-positive, CD16-negative, CD64-positive, CD163-positive." - "An acidophilic chromophil cell that of the anterior pituitary gland." "FMA:83093" - "An epithelial cell of a skin gland." "FMA:70657" - "A cell type that can give rise to basophil and mast cells. This cell is CD34-positive, CD117-positive, CD125-positive, FceRIa-negative, and T1/ST2-negative, and expresses Gata-1, Gata-2, C/EBPa" + "The process in which a T cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex." + "Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response." + "The process in which a relatively unspecialized cell acquires the specialized features of an enterocyte." + "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a dopamine stimulus." + "A cell that is adjacent to a vessel. A perivascular cell plays a crucial role in maintaining vascular function and tissue homeostasis. This cell type regulates vessel integrity and flow dynamics." + "A zone of skin that is above the clavicle zone in the pectoral girdle region." + "Any of a number of short transversospinal muscles chiefly developed in cervical, lumbar, and thoracic regions, arising from the transverse process of one vertebra and inserted into the root of the spinous process of the next two or three vertebrae above, with nerve supply from the dorsal branches of the spinal nerve, and whose actions rotate the vertebral column." "SCTID:244872002 FMA:23081" + "The process that gives rise to the accessory nerve. This process pertains to the initial formation of a structure from unspecified parts. The spinal branch of this motor nerve innervates the trapezius and the sternocleidomastoid muscles. The cranial branch joins the vagus nerve and innervates the same targets as the vagus nerve." - "Any native cell that is part of a sebaceous gland." "A conidium that has more than one nucleus." "FAO:0000033" - "A lineage negative, Sca1-negative basophil progenitor cell that is Fc epsilon RIalpha-high." - "A stem cell from which all cells of the body can form." "FMA:84790" - "A cell that is found in the periacinar space of the exocrine pancreas and in perivascular and periductal regions of the pancreas, and has long cytoplasmic processes that encircle the base of the acinus. Expresses several intermediate filament proteins including vimentin and nestin. Shares many of the characteristics of hepatatic stellate cells, but not stellate cells of the central nervous system. Upon activation, this cell type undergoes morphological and gene expression changes that make the cell suggestive of being a type of myofibroblast." - "A reticulocyte lacking a nucleus and showing a basophilic reticulum under vital staining due to the presence of ribosomes." "CALOHA:TS-0864 FMA:66785" - - "A serous secreting cell that is part of the epithelium of terminal bronchiole." "FMA:263082" - - "A giant cell 50 to 100 micron in diameter, with a greatly lobulated nucleus, found in the bone marrow; mature blood platelets are released from its cytoplasm." "CALOHA:TS-0611 FMA:83555 BTO:0000843" - "An intestinal tuft cell that is located in the anorectum." - "A pyramidal neuron with soma located in the amygdala." - "Ghrelin secreting cells found in the exocrine pancreas." - "A megakaryocyte erythroid progenitor cell is CD34-positive, CD38-positive and is IL3-receptor alpha-negative and CD45RA-negative." - + "Any process that modulates the frequency, rate or extent of a system process, a multicellular organismal process carried out by the renal system." + "A pyramidal family morphology that inheres in neurons which have a standard pyramidal shape with its apical dendrite aligned vertically." "ilxtr:PyramidalPhenotype" + "Any process that modulates the frequency, rate or extent of protein localization to nucleolus." + "EMAPA:35578 EHDAA2:0001842" + "Any process that activates or increases the frequency, rate or extent of establishment of T cell polarity." + "Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic cell clearance." + "A mucosa that is part of a respiratory bronchiole [Automatically generated definition]." "FMA:263238" + "A phase of elevated metabolic activity, during which oxygen consumption increases made as part of a defense response ; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals." + "A collection of activated B cells at the center of a secondary follicle, formed after B cells become activated and migrate to the center." "EV:0100051 MESH:D018858 BTO:0003671 Wikipedia:Germinal_center UMLS:C0282491 NCIT:C13337" "An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The axon terminal is restricted to sublamina 3 of the inner plexiform layer. It is narrowly stratified and branched. The dendritic tree has many delicate branches." - "An immature or mature cell of the first erythroid lineage to arise during embryonic development." - "A cell that is within the developmental lineage of gametes and is able to pass along its genetic material to offspring." - "A smooth muscle of the pulmonary artery." "BTO:0003336" - "A hematopoietic stem cell capable of rapid replenishment of myeloerythroid progenitors and limited self renewal capability. This cell is Kit-positive, Sca1-positive, CD34-positive, CD150-positive, and is Flt3-negative." - - "OBSOLETE: A cultured cell that has been passaged at least one time in culture." - "Obsolete. Use PO:0000293 from Plant Ontology instead. One of a pair of cells flanking the stomatal pore and causing the opening and closing of the pore by changes in turgor." - "Any skin fibroblast that is part of a arm." - "A stem cell that can give rise to multiple lineages of cells." "FMA:84789" - "A cell whose primary function is to provide structural support, to provide strength and physical integrity to the organism." - - "Neuromast hair cell is a hair cell that acts as a sensory receptor of the neuromast; it is morphologically polarized as a result of the relative position of the single kinocilium and the clusters of stereocilia on its apical surface." - "A T cell that expresses a gamma-delta T cell receptor complex." - "Cytoplasm that exhibits a characteristic staining and color, red or pink, with Eosin stain." - "An otic fibrocyte that resides above the stria vasularis and is part of a mesenchymal gap junction network that regulates ionic homeostasis of the endolymph." - "OBSOLETE: A goblet cell that is part of the epithelium of small intestine." "FMA:263042" - + "A portion of cardiac muscle tissue that is part of a interatrial septum [Automatically generated definition]." "FMA:84083" + "A developmental process, independent of morphogenetic (shape) change, that is required for the pronephros to attain its fully functional state. In mammals, the pronephros is the first of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the pronephros is the fully functional embryonic kidney and is indispensable for larval life." + "The process that gives rise to a metanephric glomerular capillary. This process pertains to the initial formation of a structure from unspecified parts." + "Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels and contribute to the series of events that restore integrity to a damaged tissue, following an injury." + "The process whose specific outcome is the progression of the muscle over time, from its formation to the mature structure. The muscle is an organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work." + "Any process by which the numbers of cells of a particular type or in a tissue are maintained." + "The process whose specific outcome is the progression of the metanephric glomerular endothelium over time, from its formation to the mature structure. The metanephric glomerular endothelium is an epithelial tissue that covers the internal surfaces of the glomerulus of the metanephros." + "Any process that activates or increases the frequency, rate or extent of ectoderm development." + "The process in which the anatomical structures of a gland are generated and organized." + "Any process that stops, prevents or reduces the frequency, rate or extent of organelle assembly." + "A process in which a protein is transported to, or maintained at, a location within a nuclear envelope." + "Any process that activates or increases the frequency, rate, or extent of immunoglobulin production." + "An epithelium that lines a terminal bronchiole." "FMA:62794 UMLS:C1179400 MA:0001774 EMAPA:36283 NCIT:C33755" + "The directed movement of a ribonucleoprotein complex along microtubules in nerve cell dendrites." "An ON-bipolar neuron found in the retina and having connections with cone photoreceptors cells and neurons in the inner half of the inner plexiform layer. The dendritic tree is wide and the dendritic convergence indicates cone selectivity. The axon terminal is sparsely branched and terminates in sublamina 5 of the inner plexiform layer." - "An enterocyte that is part of the epithelium proper of ileum." "FMA:263102" - "An apocrine cell is a secretory cell characterized loss of part of the cytoplasm during the process of secretion - secretions are budded off through the plasma membrane producing membrane bound vesicles containing the secreted substance." - "A neuron of the substantia nigra." - "A supportive cell of the vertebrate pituitary that provides macromolecular transport and secretes hormones." - "A myoepithelial cell that is part of the mammary gland." "FMA:67800 CALOHA:TS-2378" - "An immature alpha-beta T cell that is located in the thymus and is CD8-positive and CD4-negative." - - "A type II NK T cell that has been recently activated, secretes interferon-gamma and interleukin-4, and has the phenotype CD69-positive and downregulated NK markers." - "A natural killer cell subset that is found in the decidual of the uterus and is CD56-high, Galectin-1-positive and CD16-negative. This cell type represents the most abundant immune cell type in the decidual during the first trimester of pregnancy." - "A enteroendocrine cell type that is numerous in ileum, present in jejunum and large intestine, few in duodenum. This cell type produces glucagon-like immunoreactants (glicentin, glucagon-37, glucagon-29, GLP-1 and -2) and PYY." "FMA:62944" - "An innate lymphoid cell that constituitively expresses RORgt and is capable of expressing IL17A and/or IL-22." - "A PP cell located in the islets of the pancreas." "BTO:0000805 FMA:70588" - "A somatic muscle cell that is oblquely striated. Examples include the somatic muscles of nematodes." - "A mature B cell that is located in the marginal zone of the spleen with the phenotype CD23-negative and CD21-positive and expressing a B cell receptor usually reactive to bacterial cell wall components or senescent self components such as oxidized-LDL. This cell type is also described as being CD19-positive, B220-positive, IgM-high, AA4-negative, CD35-high." - "A concave nucleus shape where the indentation is smaller than half of the distance to the farthest nuclear margin." - - - "Lymphatic progenitor cells, derived from the veins, that give rise to lymphatic endothelial cells." - "A basal cell that is part of the epithelium of respiratory bronchiole." "FMA:263124" - "Glandular cell of appendix epithelium. Example: Goblet cells; enterocytes or absorptive cells; enteroendocrine and M cells." "CALOHA:TS-1271" - "A splenic macrophage found in the areas surrounding the white pulp of the spleen, adjacent to the marginal sinus. Markers include F4/80-negative, Dectin2-low, sialoadhesin-positive." - "A T cell that has not completed T cell selection." "CALOHA:TS-1042 BTO:0001372" - "A chromaffin cell that is part of the paraganglion." "FMA:69335" - "A memory B cell arising in the germinal center that is IgD-negative and has undergone somatic mutation of the variable region of the immunoglobulin heavy and light chain genes." - "A cell of the inner of the three germ layers of the embryo." "FMA:72555" - "Granule cell that is part of the cerebral cortex." - "A myeloid suppressor cell that is Gr1-low and CD11c-positive." - "A trophoblast of placental villi. These cells fuse to form synctial trophoplast - the placental side of the interface between the placenta and maternal blood sinusoids in the decidua." "BTO:0006119 BTO:0006208" - "A mature NK T cell that secretes interferon-gamma and enhances type 1 immune responses." - "An insect immune cell that develops from plasmatocyte." "FBbt:00001688" + "Any process that stops, prevents, or reduces the frequency, rate, or extent of CD4-positive, alpha-beta T cell differentiation." + "The vessels formed within the second pair of branchial arches in embryogenesis." "XAO:0000343 SCTID:308775002 EMAPA:16203 ZFA:0005006 TAO:0005006 AAO:0010418 EMAPA:16686 EHDAA2:0000051 Wikipedia:Aortic_arches#Arches_1_and_2 VHOG:0000148" + "Enables the transfer of calcium (Ca) ions from one side of a membrane to the other." "RHEA:29671 Reactome:R-HSA-2534359" + "An epiphysis that is part of a metatarsal bone [Automatically generated definition]." "SCTID:313057002 FMA:33814" + "The innermost layer of the leptomeninges, consisting of a delicate membrane closely covering the surface of the brain and spinal cord,and lying under the arachnoid membrane. The pia, unlike the arachnoid, extends into the sulci in gyrencephalic animals." "EHDAA:2685 Wikipedia:Pia_mater BTO:0001635 EHDAA:2833 UMLS:C0031869 RETIRED_EHDAA2:0001464 neuronames:1463 EHDAA:3692 SCTID:362305004 EHDAA:6566 MESH:D010841 EHDAA:3710 EHDAA:1367 EHDAA:2867 EHDAA2:0004318 GAID:693 FMA:9590 EHDAA:6583 EHDAA:2099 EHDAA:2001 NLXANAT:090209 EMAPA:32663 NCIT:C33321 EHDAA:1961 MA:0001116" + "A protein complex composed of a subunit or subunits capable of binding the Fc portion of an immunoglobulin with additional signaling components. The complex functions as a receptor for immunoglobulin." + "A strand of hair that is part of a pes." + "Any process that activates or increases the frequency, rate or extent of hematopoietic stem cell differentiation." + "The directed movement of neurotransmitter receptor to the plasma membrane in transport vesicles." + "The developmental process pertaining to the initial formation of a cardiac chamber from unspecified parts. A cardiac chamber is an enclosed cavity within the heart." + "Tolerance induction in response to nonself antigens." + "A collagen type I alpha chain that is a translation product of the human COL1A1 gene or a 1:1 ortholog thereof." + "A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity characterized by particles arranged such that their shape and volume are relatively stable." + "Any process that modulates the frequency, rate or extent of muscle contraction of the hindgut, the posterior part of the alimentary canal, including the rectum, and the large intestine." + "The continuous turnover of bone matrix and mineral that involves first, an increase in resorption (osteoclastic activity) and later, reactive bone formation (osteoblastic activity). The process of bone remodeling takes place in the adult skeleton at discrete foci. The process ensures the mechanical integrity of the skeleton throughout life and plays an important role in calcium homeostasis. An imbalance in the regulation of bone resorption and bone formation results in many of the metabolic bone diseases, such as osteoporosis." "Wikipedia:Bone_remodeling" + "A quality of a single physical entity which is held by a bearer when the latter exhibits a state of growth, differentiation, or development." + "A retinal ganglion cell C outer that has medium dendritic density and field size." + "The change in form (cell shape and size) that occurs when a neuromast hair cell progresses from its initial formation to its mature state. A neuromast hair cell is a hair cell that acts as a sensory receptor of the neuromast; it is morphologically polarized as a result of the relative position of the single kinocilium and the clusters of stereocilia on its apical surface." + "A primordial germ cell of insects. Such cells form at the posterior pole of the early embryo." "FBbt:00000092" "Chondrocyte forming the hyaline cartilage found in the knee joint." - "A stomach epithelial cell that is olumnar in form with a few short apical microvilli; relatively undifferentiated mitotic cell from which other types of gland are derived; few in number, situated in the isthmus region of the gland and base of the gastric pit." "FMA:62953" - "Any microvascular endothelial cell that is part of a urinary bladder." - "An immature, nucleated erythrocyte occupying the stage of erythropoeisis that follows formation of erythroid progenitor cells. This cell is CD71-positive, has both a nucleus and a nucleolus, and lacks hematopoeitic lineage markers." "FMA:83518" - "A naive regulatory T cell with the phenotype CD4-positive, CD25-positive, CD127lo, CCR4-positive, and CD45RO-negative." - + "Muscular layer of the cardiac ventricle composed of a compact myocardial layer surrounding the trabecular layer." "MA:0000082 VHOG:0000604 ZFA:0005061 FMA:12151 SCTID:192084000 TAO:0005061 EMAPA:32748 EFO:0003088" + "The chemical reactions and pathways involving an alpha-amino acid." + "The process in which the anatomical structures of the diaphragm are generated and organized." + "PMID:11791233 PMID:11743200 GC_ID:1" "A mature CD16-positive myeloid dendritic cell is CD80-high, CD83-positive, CD86-high, and MHCII-high." - "A fat-storing cell found mostly in the abdominal cavity and subcutaneous tissue of mammals. Fat is usually stored in the form of triglycerides." "FMA:63880 CALOHA:TS-0012 BTO:0000443" - "Any melanocyte that is part of a epidermis." + "A portion of connective tissue that is part of a lower arm [Automatically generated definition]." "MA:0000599 EMAPA:37319" diff --git a/src/ontology/reports/cl-edit.owl-obo-report.tsv b/src/ontology/reports/cl-edit.owl-obo-report.tsv index 72c59aee6..95e437bf8 100644 --- a/src/ontology/reports/cl-edit.owl-obo-report.tsv +++ b/src/ontology/reports/cl-edit.owl-obo-report.tsv @@ -142,8 +142,6 @@ WARN missing_definition CL:0001030 IAO:0000115 WARN missing_definition CL:0001658 IAO:0000115 WARN missing_definition CL:0002551 IAO:0000115 WARN missing_definition CL:0002552 IAO:0000115 -WARN missing_definition CL:0002579 IAO:0000115 -WARN missing_definition CL:0002581 IAO:0000115 WARN missing_definition CL:0002598 IAO:0000115 WARN missing_definition CL:0002602 IAO:0000115 WARN missing_definition CL:0002621 IAO:0000115 @@ -197,15 +195,11 @@ WARN missing_definition CL:1000615 IAO:0000115 WARN missing_definition CL:1000616 IAO:0000115 WARN missing_definition CL:1000617 IAO:0000115 WARN missing_definition CL:1000618 IAO:0000115 -WARN missing_definition CL:1000681 IAO:0000115 -WARN missing_definition CL:1000682 IAO:0000115 WARN missing_definition CL:1000691 IAO:0000115 -WARN missing_definition CL:1000692 IAO:0000115 WARN missing_definition CL:1000693 IAO:0000115 WARN missing_definition CL:1000695 IAO:0000115 WARN missing_definition CL:1000696 IAO:0000115 WARN missing_definition CL:1000697 IAO:0000115 -WARN missing_definition CL:1000699 IAO:0000115 WARN missing_definition CL:1000702 IAO:0000115 WARN missing_definition CL:1000703 IAO:0000115 WARN missing_definition CL:1000706 IAO:0000115 @@ -218,13 +212,10 @@ WARN missing_definition CL:1000720 IAO:0000115 WARN missing_definition CL:1000721 IAO:0000115 WARN missing_definition CL:1000746 IAO:0000115 WARN missing_definition CL:1000768 IAO:0000115 -WARN missing_definition CL:1000803 IAO:0000115 -WARN missing_definition CL:1000804 IAO:0000115 WARN missing_definition CL:1000838 IAO:0000115 WARN missing_definition CL:1000839 IAO:0000115 WARN missing_definition CL:1000849 IAO:0000115 WARN missing_definition CL:1000850 IAO:0000115 -WARN missing_definition CL:1000854 IAO:0000115 WARN missing_definition CL:1000891 IAO:0000115 WARN missing_definition CL:1000892 IAO:0000115 WARN missing_definition CL:1000893 IAO:0000115 @@ -235,7 +226,6 @@ WARN missing_definition CL:1001006 IAO:0000115 WARN missing_definition CL:1001009 IAO:0000115 WARN missing_definition CL:1001016 IAO:0000115 WARN missing_definition CL:1001021 IAO:0000115 -WARN missing_definition CL:1001036 IAO:0000115 WARN missing_definition CL:1001045 IAO:0000115 WARN missing_definition CL:1001052 IAO:0000115 WARN missing_definition CL:1001064 IAO:0000115 @@ -374,6 +364,7 @@ INFO missing_superclass CL:0000847 rdfs:subClassOf INFO missing_superclass CL:0000857 rdfs:subClassOf INFO missing_superclass CL:0000858 rdfs:subClassOf INFO missing_superclass CL:0000865 rdfs:subClassOf +INFO missing_superclass CL:0000880 rdfs:subClassOf INFO missing_superclass CL:0000909 rdfs:subClassOf INFO missing_superclass CL:0000937 rdfs:subClassOf INFO missing_superclass CL:0000938 rdfs:subClassOf @@ -552,7 +543,6 @@ INFO missing_superclass CL:0010005 rdfs:subClassOf INFO missing_superclass CL:0010006 rdfs:subClassOf INFO missing_superclass CL:0010007 rdfs:subClassOf INFO missing_superclass CL:0010008 rdfs:subClassOf -INFO missing_superclass CL:0010009 rdfs:subClassOf INFO missing_superclass CL:0010010 rdfs:subClassOf INFO missing_superclass CL:0010011 rdfs:subClassOf INFO missing_superclass CL:0010012 rdfs:subClassOf diff --git a/src/ontology/subsets/blood_and_immune_upper_slim.json b/src/ontology/subsets/blood_and_immune_upper_slim.json index f2b3e3a5d..fe2c37d13 100644 --- a/src/ontology/subsets/blood_and_immune_upper_slim.json +++ b/src/ontology/subsets/blood_and_immune_upper_slim.json @@ -4,9 +4,9 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-02-13" + "val" : "2024-04-05" } ], - "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-02-13/subsets/blood_and_immune_upper_slim.owl" + "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-04-05/subsets/blood_and_immune_upper_slim.owl" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/BFO_0000002", @@ -78,18 +78,6 @@ "val" : "BFO:0000050" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "is part of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my brain is part of my body (continuant parthood, two material entities)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this day is part of this year (occurrent parthood)" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." }, { @@ -98,42 +86,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "part_of" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000002" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000003" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000004" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000017" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000019" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000020" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000031" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "part_of" @@ -164,18 +122,6 @@ "val" : "BFO:0000051" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has part" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my body has part my brain (continuant parthood, two material entities)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this year has part this day (occurrent parthood)" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." }, { @@ -184,21 +130,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has_part" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_part" @@ -217,26 +154,11 @@ "val" : "BFO:0000062" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "preceded by" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is preceded by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "preceded_by" - }, { - "pred" : "http://purl.org/dc/terms/source", - "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "preceded_by" @@ -255,14 +177,8 @@ "val" : "BFO:0000063" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "precedes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "precedes" @@ -282,26 +198,11 @@ "val" : "BFO:0000066" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "occurs in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "occurs_in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "unfolds in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "unfolds_in" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "occurs_in" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Occurs_in" @@ -315,412 +216,12 @@ "definition" : { "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" }, - "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ], - "xrefs" : [ { - "val" : "BFO:0000067" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "site of" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "contains_process" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - } ] + "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000141", "lbl" : "immaterial entity", "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000096", - "lbl" : "anterior to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000096" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "anterior_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000097", - "lbl" : "distal to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000097" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "distal_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000098", - "lbl" : "dorsal to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000098" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dorsal_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000099", - "lbl" : "posterior to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000099" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "posterior_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000100", - "lbl" : "proximal to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000100" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "proximal_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000102", - "lbl" : "ventral to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000102" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "ventral_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000107", - "lbl" : "deep to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000107" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "deep_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000108", - "lbl" : "superficial to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000108" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "superficial_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000120", - "lbl" : "in left side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000120" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_left_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000121", - "lbl" : "in right side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000121" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_right_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000122", - "lbl" : "in posterior side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000122" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_posterior_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000123", - "lbl" : "in anterior side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000123" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_anterior_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000124", - "lbl" : "in proximal side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000124" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_proximal_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "lbl" : "in lateral side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000126" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_lateral_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001100", - "lbl" : "in superficial part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001100" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_superficial_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001101", - "lbl" : "in deep part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001101" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_deep_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001106", - "lbl" : "proximalmost part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001106" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "proximalmost_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001107", - "lbl" : "immediately deep to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001107" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "immediately_deep_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001108", - "lbl" : "distalmost part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001108" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "distalmost_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001113", - "lbl" : "preaxialmost part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001113" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "preaxialmost_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001115", - "lbl" : "postaxialmost part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001115" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "postaxialmost_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0005001", - "lbl" : "intersects midsagittal plane of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0005001" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "intersects_midsagittal_plane_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0015014", - "lbl" : "immediately superficial to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0015014" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "immediately_superficial_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0015101", - "lbl" : "in dorsal side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0015101" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_dorsal_side_of" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000000", "lbl" : "cell", @@ -14816,13 +14317,7 @@ }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000002", "lbl" : "example to be eventually removed", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "example to be eventually removed" - } ] - } + "type" : "INDIVIDUAL" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000028", "lbl" : "symbol", @@ -14834,14 +14329,7 @@ "meta" : { "definition" : { "val" : "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "failed exploratory term" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person:Alan Ruttenberg" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000115", @@ -14852,20 +14340,8 @@ "val" : "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "definition" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2012-04-05: \nBarry Smith\n\nThe official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. \n\nOn the specifics of the proposed definition:\n\nWe don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Daniel Schober" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" } ] } }, { @@ -14875,32 +14351,7 @@ "meta" : { "definition" : { "val" : "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology." - }, - "xrefs" : [ { - "val" : "IAO:0000116" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "editor note" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Daniel Schober" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "editor_note" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000120", @@ -14909,11 +14360,7 @@ "meta" : { "definition" : { "val" : "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "metadata complete" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000121", @@ -14922,11 +14369,7 @@ "meta" : { "definition" : { "val" : "Term created to ease viewing/sort terms for development purpose, and will not be included in a release" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "organizational term" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000122", @@ -14935,11 +14378,7 @@ "meta" : { "definition" : { "val" : "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\"" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "ready for release" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000123", @@ -14948,11 +14387,7 @@ "meta" : { "definition" : { "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "metadata incomplete" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000124", @@ -14961,11 +14396,7 @@ "meta" : { "definition" : { "val" : "Nothing done yet beyond assigning a unique class ID and proposing a preferred term." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "uncurated" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000125", @@ -14974,31 +14405,18 @@ "meta" : { "definition" : { "val" : "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "pending final vetting" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000226", "lbl" : "placeholder removed", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "placeholder removed" - } ] - } + "type" : "INDIVIDUAL" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000227", "lbl" : "terms merged", "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "terms merged" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "An editor note should explain what were the merged terms and the reason for the merge." } ] @@ -15009,9 +14427,6 @@ "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "term imported" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use." } ] @@ -15022,9 +14437,6 @@ "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "term split" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created." } ] @@ -15036,17 +14448,7 @@ "meta" : { "definition" : { "val" : "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has obsolescence reason" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Melanie Courtot" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000233", @@ -15061,29 +14463,8 @@ "val" : "IAO:0000233" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "term tracker item" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_class_level", - "val" : "true" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", "val" : "true" @@ -15098,17 +14479,8 @@ "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "universal" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf" } ] } }, { @@ -15120,14 +14492,8 @@ "val" : "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "defined class" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" } ] } }, { @@ -15139,14 +14505,8 @@ "val" : "A named class expression is a logical expression that is given a name. The name can be used in place of the expression." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "named class expression" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" } ] } }, { @@ -15156,17 +14516,7 @@ "meta" : { "definition" : { "val" : "Terms with this status should eventually replaced with a term from another ontology." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "to be replaced with external ontology term" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "group:OBI" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000424", @@ -15175,17 +14525,7 @@ "meta" : { "definition" : { "val" : "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "expand expression to" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "ObjectProperty: RO_0002104\nLabel: has plasma membrane part\nAnnotations: IAO_0000424 \"http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\"\n" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000428", @@ -15194,17 +14534,7 @@ "meta" : { "definition" : { "val" : "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "requires discussion" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "group:OBI" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000700", @@ -15218,20 +14548,8 @@ "val" : "IAO:0000700" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has ontology root term" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Nicolas Matentzoglu" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_class_level", - "val" : "true" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", "val" : "true" @@ -15248,20 +14566,7 @@ "definition" : { "val" : "Use on obsolete terms, relating the term to another term that can be used as a substitute" }, - "comments" : [ "Add as annotation triples in the granting ontology" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "term replaced by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person:Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Person:Alan Ruttenberg" - } ] + "comments" : [ "Add as annotation triples in the granting ontology" ] } }, { "id" : "http://purl.obolibrary.org/obo/NCBITaxon_1", @@ -15296,9 +14601,6 @@ "val" : "PMID:15371245" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_family" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15313,7 +14615,7 @@ "pred" : "hasExactSynonym", "val" : "Mus" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003003", + "synonymType" : "http://purl.obolibrary.org/obo/ncbitaxon#genbank_common_name", "pred" : "hasExactSynonym", "val" : "mice" }, { @@ -15325,9 +14627,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_genus" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15350,9 +14649,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_species" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "NCBITaxon:85055" }, { @@ -15369,9 +14665,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15390,9 +14683,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "NCBITaxon:40673" }, { @@ -15427,9 +14717,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15452,9 +14739,6 @@ "val" : "PMID:11791233" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15477,9 +14761,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_suborder" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15526,9 +14807,6 @@ "val" : "PMID:30257078" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_superkingdom" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15550,9 +14828,6 @@ "val" : "PMID:15522813" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_superorder" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15577,9 +14852,6 @@ "val" : "PMID:15522813" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15598,9 +14870,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15619,9 +14888,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15640,9 +14906,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15665,9 +14928,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15698,9 +14958,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_kingdom" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15714,9 +14971,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15735,9 +14989,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15755,9 +15006,6 @@ "val" : "PMID:15371245" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15771,9 +15019,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_subfamily" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "NCBITaxon:109679" }, { @@ -15799,9 +15044,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_class" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15815,9 +15057,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15840,9 +15079,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_phylum" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15869,9 +15105,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15894,9 +15127,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15910,9 +15140,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_superclass" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15931,9 +15158,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_subgenus" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15952,9 +15176,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_subphylum" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15989,9 +15210,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -16014,9 +15232,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_order" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -16032,15 +15247,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/77" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", - "val" : "https://orcid.org/0000-0001-5208-3432" } ] } }, { @@ -16052,9 +15261,6 @@ "val" : "Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'part disjoint with' 'defined by construct' \"\"\"\n PREFIX owl: \n PREFIX : some (\n and some (\n and some (\n and some ?Y)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { @@ -21281,33 +19963,9 @@ "definition" : { "val" : "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " }, - "xrefs" : [ { - "val" : "RO:0002103" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that part_of some ( that has_part some ( that some Y?)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "synapsed_by" } ] } }, { @@ -21319,29 +19977,8 @@ "val" : "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9990-8331" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-1617-8244" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19243617" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( and some ?Y)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] } }, { @@ -21353,26 +19990,8 @@ "val" : "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. " }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "synapsed in" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (\n http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some (\n http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { @@ -21384,20 +20003,8 @@ "val" : "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "synapses in" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that some ( that some Y?)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { @@ -21410,23 +20017,8 @@ }, "comments" : [ "N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part some (\n ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( \n\t‘synapse ; GO:0045202’ that has_part some (\n\t ‘post-synaptic membrane ; GO:0045211’ that part_of some N2))))" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that part_of some ( that some ( that some Y?)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { @@ -21438,23 +20030,8 @@ "val" : "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has synapse in" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that some Y?)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { @@ -21470,20 +20047,11 @@ "val" : "RO:0002131" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "overlaps" @@ -21496,26 +20064,7 @@ "meta" : { "definition" : { "val" : "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has fasciculating component" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", - "val" : "(forall (?x ?y) \n\t(iff \n\t\t(has_fasciculating_neuron_projection ?x ?y)\n\t\t(exists (?nps ?npbs)\t\t\n\t\t\t(and \n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?x)\n\t\t\t\t(\"neuron projection ; GO0043005\" ?y)\n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n\t\t\t\t(part_of ?nps ?y)\n\t\t\t\t(part_of ?npbs ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))\n\n\n" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002134", @@ -21525,30 +20074,9 @@ "definition" : { "val" : "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." }, - "xrefs" : [ { - "val" : "RO:0002134" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that ( some ( that some Y?)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "innervates" } ] } }, { @@ -21559,31 +20087,7 @@ "definition" : { "val" : "X continuous_with Y if and only if X and Y share a fiat boundary." }, - "xrefs" : [ { - "val" : "RO:0002150" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "connected to" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "continuous_with" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "FMA:85972" } ] @@ -21596,23 +20100,7 @@ "definition" : { "val" : "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." }, - "comments" : [ "VBO calls this homologous_to" ], - "xrefs" : [ { - "val" : "RO:0002158" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Consider obsoleting and merging with child relation, 'in homology relationship with'" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "homologous_to" - } ] + "comments" : [ "VBO calls this homologous_to" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -21622,33 +20110,9 @@ "definition" : { "val" : "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." }, - "xrefs" : [ { - "val" : "RO:0002160" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "lactation SubClassOf 'only in taxon' some 'Mammalia'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "only_in_taxon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" @@ -21656,48 +20120,15 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002161", - "lbl" : "never_in_taxon", + "lbl" : "never in taxon", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL." }, - "xrefs" : [ { - "val" : "RO:0002161" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "tooth SubClassOf 'never in taxon' value 'Aves'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", - "val" : "Class: EquivalentTo: ?X and (RO_0002162 some ?Y)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", - "val" : "Class: ?X DisjointWith: RO_0002162 some ?Y " - }, { "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_class_level", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "never_in_taxon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" @@ -21713,31 +20144,7 @@ }, "comments" : [ "Connects a biological entity to its taxon of origin." ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002162" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9227-417X" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_taxon" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] @@ -21752,26 +20159,11 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" @@ -21785,22 +20177,7 @@ "definition" : { "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" }, - "xrefs" : [ { - "val" : "RO:0002170" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "connected_to" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" }, { @@ -21810,42 +20187,16 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002175", - "lbl" : "present_in_taxon", + "lbl" : "present in taxon", "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S" }, "comments" : [ "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "applicable for taxon" - } ], - "xrefs" : [ { - "val" : "RO:0002175" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_class_level", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "present_in_taxon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" @@ -21859,25 +20210,7 @@ "definition" : { "val" : "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." }, - "xrefs" : [ { - "val" : "RO:0002176" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The M8 connects Glasgow and Edinburgh" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "connects" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" }, { @@ -21892,20 +20225,7 @@ "meta" : { "definition" : { "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." - }, - "xrefs" : [ { - "val" : "RO:0002177" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "attached to part of (anatomical structure to anatomical structure)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "attaches_to_part_of" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002178", @@ -21915,21 +20235,9 @@ "definition" : { "val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." }, - "xrefs" : [ { - "val" : "RO:0002178" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "supplies" } ] } }, { @@ -21940,21 +20248,9 @@ "definition" : { "val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." }, - "xrefs" : [ { - "val" : "RO:0002179" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "drains" } ] } }, { @@ -21970,23 +20266,11 @@ "val" : "RO:0002180" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_component" @@ -22003,32 +20287,7 @@ "definition" : { "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" }, - "comments" : [ "This is the transitive form of the develops from relation" ], - "xrefs" : [ { - "val" : "RO:0002202" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9114-8737" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-1980-3228" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "develops_from" - } ] + "comments" : [ "This is the transitive form of the develops from relation" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002203", @@ -22038,29 +20297,7 @@ "definition" : { "val" : "inverse of develops from" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "xrefs" : [ { - "val" : "RO:0002203" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-1980-3228" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "develops_into" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002206", @@ -22069,17 +20306,7 @@ "meta" : { "definition" : { "val" : "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002207", @@ -22093,31 +20320,6 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "has developmental precursor" - } ], - "xrefs" : [ { - "val" : "RO:0002207" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "FBbt" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002202" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "directly_develops_from" } ] } }, { @@ -22128,14 +20330,7 @@ "definition" : { "val" : "inverse of directly develops from" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "developmental precursor of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002211", @@ -22150,30 +20345,6 @@ "val" : "RO:0002211" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-7476-6306" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-3837-8864" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GO" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Regulation precludes parthood; the regulatory process may not be within the regulated process." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "regulates (processual)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "false" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -22194,15 +20365,6 @@ "val" : "RO:0002212" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "negatively regulates (process to process)" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002211" }, { @@ -22226,18 +20388,6 @@ "val" : "RO:0002213" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "positively regulates (process to process)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002211" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -22258,32 +20408,8 @@ "val" : "RO:0002215" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "osteoclast SubClassOf 'capable of' some 'bone resorption'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has function realized in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20123131" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/21208450" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "capable_of" @@ -22301,17 +20427,8 @@ "val" : "RO:0002216" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has function in" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "capable_of_part_of" @@ -22327,26 +20444,7 @@ "meta" : { "definition" : { "val" : "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" - }, - "xrefs" : [ { - "val" : "RO:0002219" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "surrounded_by" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002220", @@ -22361,35 +20459,11 @@ "val" : "RO:0002220" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The epidermis layer of a vertebrate is adjacent to the dermis." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This relation acts as a join point with BSPO" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "adjacent_to" @@ -22403,26 +20477,7 @@ "definition" : { "val" : "inverse of surrounded by" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "xrefs" : [ { - "val" : "RO:0002221" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "surrounds" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002222", @@ -22430,23 +20485,7 @@ "type" : "PROPERTY", "meta" : { "comments" : [ "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations." ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://en.wikipedia.org/wiki/Allen%27s_interval_algebra" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." - }, { - "pred" : "http://purl.org/dc/terms/source", - "val" : "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002223", @@ -22456,29 +20495,7 @@ "definition" : { "val" : "inverse of starts with" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002223" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Allen" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "starts" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002224", @@ -22493,26 +20510,8 @@ "val" : "RO:0002224" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "started by" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "starts_with" @@ -22525,23 +20524,7 @@ "meta" : { "definition" : { "val" : "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" - }, - "xrefs" : [ { - "val" : "RO:0002225" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "develops_from_part_of" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002226", @@ -22550,29 +20533,7 @@ "meta" : { "definition" : { "val" : "x develops_in y if x is located in y whilst x is developing" - }, - "xrefs" : [ { - "val" : "RO:0002226" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "EHDAA2" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Jonathan Bard, EHDAA2" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "develops_in" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002229", @@ -22582,26 +20543,7 @@ "definition" : { "val" : "inverse of ends with" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002229" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "ends" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002230", @@ -22616,23 +20558,8 @@ "val" : "RO:0002230" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "finished by" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "ends_with" @@ -22651,15 +20578,6 @@ "val" : "RO:0002231" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "starts with process that occurs in" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -22680,15 +20598,6 @@ "val" : "RO:0002232" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "ends with process that occurs in" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -22709,15 +20618,6 @@ "val" : "RO:0002233" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "consumes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -22741,15 +20641,6 @@ "val" : "RO:0002234" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "produces" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -22768,22 +20659,7 @@ "definition" : { "val" : "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." }, - "xrefs" : [ { - "val" : "RO:0002252" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004036", - "val" : "http://purl.obolibrary.org/obo/BFO_0000050" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "connecting_branch_of" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/issues/2212" } ] @@ -22796,11 +20672,7 @@ "definition" : { "val" : "inverse of connecting branch of" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004036", - "val" : "http://purl.obolibrary.org/obo/BFO_0000051" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002254", @@ -22809,26 +20681,7 @@ "meta" : { "definition" : { "val" : "x has developmental contribution from y iff x has some part z such that z develops from y" - }, - "xrefs" : [ { - "val" : "RO:0002254" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_developmental_contribution_from" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002255", @@ -22838,14 +20691,7 @@ "definition" : { "val" : "inverse of has developmental contribution from" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002256", @@ -22854,44 +20700,7 @@ "meta" : { "definition" : { "val" : "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" - }, - "xrefs" : [ { - "val" : "RO:0002256" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9114-8737" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "induced by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GO:0001759" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "developmentally_induced_by" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002257", @@ -22900,14 +20709,7 @@ "meta" : { "definition" : { "val" : "Inverse of developmentally induced by" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002258", @@ -22919,17 +20721,8 @@ }, "comments" : [ "This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "false" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "In general you should not use this relation to make assertions - use one of the more specific relations below this one" } ] } }, { @@ -22942,9 +20735,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of" } ] @@ -22963,9 +20753,6 @@ "val" : "affects" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within" } ] @@ -22978,27 +20765,9 @@ "definition" : { "val" : "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" }, - "xrefs" : [ { - "val" : "RO:0002285" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "replaces" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "developmentally_replaces" } ] } }, { @@ -23008,31 +20777,12 @@ "meta" : { "definition" : { "val" : "Inverse of developmentally preceded by" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002287", "lbl" : "part of developmental precursor of", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002292", "lbl" : "expresses", @@ -23040,14 +20790,7 @@ "meta" : { "definition" : { "val" : "y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002295", @@ -23061,14 +20804,8 @@ "val" : "RO:0002295" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" @@ -23093,18 +20830,6 @@ "val" : "RO:0002296" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "every flower development (GO:0009908) results in development of some flower (PO:0009046)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.geneontology.org/GO.doc.development.shtml" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -23114,7 +20839,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -23122,21 +20847,6 @@ "val" : "RO:0002297" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:mtg_berkeley_2013" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -23157,21 +20867,6 @@ "val" : "RO:0002298" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:mtg_berkeley_2013" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -23192,21 +20887,6 @@ "val" : "RO:0002299" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:mtg_berkeley_2013" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -23228,12 +20908,6 @@ "val" : "RO:0002304" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002411" - }, { - "pred" : "http://purl.org/dc/terms/creator", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -23259,9 +20933,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002411" - }, { - "pred" : "http://purl.org/dc/terms/creator", - "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" @@ -23284,18 +20955,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "inheres in part of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" @@ -23314,15 +20973,6 @@ "val" : "RO:0002315" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:mtg_berkeley_2013" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -23337,14 +20987,7 @@ "meta" : { "definition" : { "val" : "A relationship that holds via some environmental process" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002323", @@ -23353,17 +20996,7 @@ "meta" : { "definition" : { "val" : "A mereological relationship or a topological relationship" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002324", @@ -23372,14 +21005,7 @@ "meta" : { "definition" : { "val" : "A relationship that holds between entities participating in some developmental process (GO:0032502)" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002327", @@ -23391,30 +21017,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a particular instances of akt-2 enables some instance of protein kinase activity" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "catalyzes" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "executes" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is catalyzing" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is executing" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Enables" } ] @@ -23426,23 +21028,7 @@ "meta" : { "definition" : { "val" : "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." - }, - "xrefs" : [ { - "val" : "RO:0002328" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This is a grouping relation that collects relations used for the purpose of connecting structure and function" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "functionally_related_to" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002329", @@ -23451,14 +21037,7 @@ "meta" : { "definition" : { "val" : "this relation holds between c and p when c is part of some c', and c' is capable of p." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "false" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002330", @@ -23467,14 +21046,7 @@ "meta" : { "definition" : { "val" : "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002331", @@ -23485,15 +21057,6 @@ "val" : "c involved_in p if and only if c enables some process p', and p' is part of p" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "actively involved in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "enables part of" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Involved_in" } ] @@ -23510,18 +21073,6 @@ "val" : "RO:0002332" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "regulates levels of (process to entity)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -23539,9 +21090,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Enabled_by" } ] @@ -23559,12 +21107,6 @@ "val" : "RO:0002334" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "regulated by (processual)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -23585,9 +21127,6 @@ "val" : "RO:0002335" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -23608,9 +21147,6 @@ "val" : "RO:0002336" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -23625,14 +21161,7 @@ "meta" : { "definition" : { "val" : "A relationship that holds via some process of localization" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is a grouping relation." - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002338", @@ -23647,9 +21176,6 @@ "val" : "RO:0002338" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -23670,9 +21196,6 @@ "val" : "RO:0002339" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -23692,9 +21215,6 @@ "val" : "RO:0002341" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -23715,9 +21235,6 @@ "val" : "RO:0002342" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -23734,12 +21251,6 @@ "val" : "RO:0002343" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'pollen tube growth' results_in growth_of some 'pollen tube'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -23756,12 +21267,6 @@ "val" : "RO:0002344" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -23776,23 +21281,7 @@ "meta" : { "definition" : { "val" : "is member of is a mereological relation between a item and a collection." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "An organism that is a member of a population of organisms" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is member of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "member part of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "SIO" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002351", @@ -23801,23 +21290,7 @@ "meta" : { "definition" : { "val" : "has member is a mereological relation between a collection and an item." - }, - "xrefs" : [ { - "val" : "RO:0002351" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "SIO" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_member" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002352", @@ -23827,20 +21300,7 @@ "definition" : { "val" : "inverse of has input" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002352" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "input_of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002353", @@ -23855,14 +21315,8 @@ "val" : "RO:0002353" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "output_of" @@ -23871,26 +21325,11 @@ }, { "id" : "http://purl.obolibrary.org/obo/RO_0002354", "lbl" : "formed as result of", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002360", "lbl" : "has dendrite location", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.org/dc/terms/source", - "val" : "http://neurolex.org/wiki/Property:DendriteLocation" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002371", "lbl" : "attached to", @@ -23899,23 +21338,7 @@ "definition" : { "val" : "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002371" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "attached to (anatomical structure to anatomical structure)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "attaches_to" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002372", @@ -23925,22 +21348,7 @@ "definition" : { "val" : "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." }, - "xrefs" : [ { - "val" : "RO:0002372" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Wikipedia:Insertion_(anatomy)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_muscle_origin" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://dbpedia.org/property/origin" } ] @@ -23953,22 +21361,7 @@ "definition" : { "val" : "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." }, - "xrefs" : [ { - "val" : "RO:0002373" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Wikipedia:Insertion_(anatomy)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_muscle_insertion" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://dbpedia.org/property/insertion" } ] @@ -23982,21 +21375,6 @@ "val" : "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004036", - "val" : "http://purl.obolibrary.org/obo/BFO_0000050" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png" }, { @@ -24013,46 +21391,7 @@ "val" : "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002376" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Deschutes River tributary_of Columbia River" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "inferior epigastric vein tributary_of external iliac vein" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "drains into" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "drains to" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "tributary channel of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://en.wikipedia.org/wiki/Tributary" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.medindia.net/glossary/venous_tributary.htm" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "tributary_of" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://dbpedia.org/ontology/drainsTo" }, { @@ -24067,17 +21406,7 @@ "meta" : { "definition" : { "val" : "x spatially_coextensive_with y if and inly if x and y have the same location" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A lump of clay and a statue" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002380", @@ -24088,22 +21417,7 @@ "val" : "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002380" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "branching_part_of" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/issues/2212" }, { @@ -24118,14 +21432,7 @@ "meta" : { "definition" : { "val" : "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002385", @@ -24134,23 +21441,7 @@ "meta" : { "definition" : { "val" : "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" - }, - "xrefs" : [ { - "val" : "RO:0002385" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_potential_to_developmentally_contribute_to" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002386", @@ -24159,14 +21450,7 @@ "meta" : { "definition" : { "val" : "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002387", @@ -24175,23 +21459,7 @@ "meta" : { "definition" : { "val" : "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" - }, - "xrefs" : [ { - "val" : "RO:0002387" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_potential_to_develop_into" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002388", @@ -24200,14 +21468,7 @@ "meta" : { "definition" : { "val" : "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002404", @@ -24221,12 +21482,6 @@ "val" : "RO:0002404" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -24243,12 +21498,6 @@ "val" : "RO:0002405" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -24265,15 +21514,6 @@ "val" : "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "indirectly activates" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002579", - "val" : "http://purl.obolibrary.org/obo/RO_0002213" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Indirectly_positively_regulates" } ] @@ -24287,15 +21527,6 @@ "val" : "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "indirectly inhibits" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002579", - "val" : "http://purl.obolibrary.org/obo/RO_0002212" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Indirectly_negatively_regulates" } ] @@ -24312,12 +21543,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." } ] } }, { @@ -24333,9 +21558,6 @@ "val" : "RO:0002411" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -24355,12 +21577,6 @@ "val" : "RO:0002412" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002411" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -24386,12 +21602,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "influences (processual)" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" @@ -24413,12 +21623,6 @@ "val" : "RO:0002427" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -24433,11 +21637,7 @@ "meta" : { "definition" : { "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002429", @@ -24446,14 +21646,7 @@ "meta" : { "definition" : { "val" : "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002428" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002430", @@ -24464,9 +21657,6 @@ "val" : "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002428" } ] @@ -24482,12 +21672,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "OWL does not allow defining object properties via a Union" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "involved in or reguates" } ] } }, { @@ -24505,15 +21689,6 @@ "val" : "enables activity in" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A protein that enables activity in a cytosol." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "executes activity in" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Is_active_in" } ] @@ -24525,20 +21700,7 @@ "meta" : { "definition" : { "val" : "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." - }, - "xrefs" : [ { - "val" : "RO:0002433" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "contributes_to_morphology_of" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002434", @@ -24559,18 +21721,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Considering relabeling as 'pairwise interacts with'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" - }, { - "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", - "val" : "http://purl.obolibrary.org/obo/MI_0914" } ] } }, { @@ -24582,20 +21735,8 @@ "val" : "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "binds" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "molecularly binds with" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ECO_0000353" - }, { - "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", - "val" : "http://purl.obolibrary.org/obo/MI_0915" } ] } }, { @@ -24606,12 +21747,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Axiomatization to GO to be added later" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." } ] } }, { @@ -24625,13 +21760,6 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "molecularly controls" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" } ] } }, { @@ -24645,16 +21773,6 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "molecularly decreases activity of" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "directly inhibits" } ] } }, { @@ -24668,31 +21786,12 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "molecularly increases activity of" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "directly activates" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002464", "lbl" : "helper property (not for use in curation)", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002473", "lbl" : "composed primarily of", @@ -24701,29 +21800,7 @@ "definition" : { "val" : "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002473" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "composed_primarily_of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002479", @@ -24733,22 +21810,12 @@ "definition" : { "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002481", "lbl" : "is kinase activity", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002485", "lbl" : "receives input from", @@ -24757,9 +21824,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "See notes for inverse relation" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { @@ -24770,24 +21834,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002487", "lbl" : "relation between physical entity and a process or stage", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage." - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002488", "lbl" : "existence starts during", @@ -24795,20 +21847,7 @@ "meta" : { "definition" : { "val" : "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." - }, - "xrefs" : [ { - "val" : "RO:0002488" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_starts_during" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002489", @@ -24817,20 +21856,7 @@ "meta" : { "definition" : { "val" : "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." - }, - "xrefs" : [ { - "val" : "RO:0002489" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_starts_with" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002490", @@ -24840,11 +21866,7 @@ "definition" : { "val" : "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002491", @@ -24858,19 +21880,6 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "exists during" - } ], - "xrefs" : [ { - "val" : "RO:0002491" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_starts_and_ends_during" } ] } }, { @@ -24881,24 +21890,7 @@ "definition" : { "val" : "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "ceases_to_exist_during" - } ], - "xrefs" : [ { - "val" : "RO:0002492" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_ends_during" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002493", @@ -24908,20 +21900,7 @@ "definition" : { "val" : "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "xrefs" : [ { - "val" : "RO:0002493" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_ends_with" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002494", @@ -24930,20 +21909,7 @@ "meta" : { "definition" : { "val" : "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" - }, - "xrefs" : [ { - "val" : "RO:0002494" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "transformation_of" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002495", @@ -24952,23 +21918,7 @@ "meta" : { "definition" : { "val" : "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" - }, - "xrefs" : [ { - "val" : "RO:0002495" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002494" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "immediate_transformation_of" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002496", @@ -24978,20 +21928,7 @@ "definition" : { "val" : "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "xrefs" : [ { - "val" : "RO:0002496" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_starts_during_or_after" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002497", @@ -25001,20 +21938,7 @@ "definition" : { "val" : "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "xrefs" : [ { - "val" : "RO:0002497" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_ends_during_or_before" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002500", @@ -25023,11 +21947,7 @@ "meta" : { "definition" : { "val" : "A relationship between a material entity and a process where the material entity has some causal role that influences the process" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002501", @@ -25036,17 +21956,7 @@ "meta" : { "definition" : { "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002502", @@ -25054,9 +21964,6 @@ "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/BFO_0000169" } ] @@ -25069,15 +21976,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." } ] } }, { @@ -25087,55 +21985,18 @@ "meta" : { "definition" : { "val" : "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." - }, - "xrefs" : [ { - "val" : "RO:0002551" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has supporting framework" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_skeleton" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002559", "lbl" : "causally influenced by", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "causally influenced by (entity-centric)" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002563", "lbl" : "interaction relation helper property", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29" }, { @@ -25146,13 +22007,7 @@ }, { "id" : "http://purl.obolibrary.org/obo/RO_0002564", "lbl" : "molecular interaction relation helper property", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002565", "lbl" : "results in movement of", @@ -25166,11 +22021,6 @@ "val" : "RO:0002565" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -25185,20 +22035,7 @@ "meta" : { "definition" : { "val" : "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "causally influences (entity-centric)" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002567", @@ -25207,14 +22044,7 @@ "meta" : { "definition" : { "val" : "A relation that holds between elements of a musculoskeletal system or its analogs." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002568", @@ -25223,23 +22053,7 @@ "meta" : { "definition" : { "val" : "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." - }, - "xrefs" : [ { - "val" : "RO:0002568" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Wikipedia:Antagonist_(muscle)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_muscle_antagonist" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002569", @@ -25249,20 +22063,7 @@ "definition" : { "val" : "inverse of branching part of" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002569" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_branching_part" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002570", @@ -25272,26 +22073,7 @@ "definition" : { "val" : "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002570" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "UBERON:cjm" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "conduit_for" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002571", @@ -25301,23 +22083,7 @@ "definition" : { "val" : "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002571" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "lumen_of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002572", @@ -25327,20 +22093,7 @@ "definition" : { "val" : "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002572" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "luminal_space_of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002576", @@ -25350,20 +22103,7 @@ "definition" : { "val" : "inverse of has skeleton" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "xrefs" : [ { - "val" : "RO:0002576" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "skeleton_of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002578", @@ -25378,18 +22118,6 @@ "val" : "RO:0002578" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "directly regulates (processual)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002211" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -25397,24 +22125,6 @@ "val" : "directly_regulates" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002581", - "lbl" : "is a defining property chain axiom", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002582", - "lbl" : "is a defining property chain axiom where second argument is reflexive", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R." - } - } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002584", "lbl" : "has part structure that is capable of", @@ -25422,14 +22132,7 @@ "meta" : { "definition" : { "val" : "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002586", @@ -25503,12 +22206,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] } }, { @@ -25518,14 +22215,7 @@ "meta" : { "definition" : { "val" : "Holds between c and p if and only if c is capable of some activity a, and a regulates p." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "pyrethroid -> growth" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002597", @@ -25534,11 +22224,7 @@ "meta" : { "definition" : { "val" : "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002598", @@ -25547,14 +22233,7 @@ "meta" : { "definition" : { "val" : "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "renin -> arteriolar smooth muscle contraction" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002608", @@ -25568,9 +22247,6 @@ "val" : "RO:0002608" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -25591,15 +22267,6 @@ "val" : "RO:0002629" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "directly positively regulates (process to process)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002578" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -25623,12 +22290,6 @@ "val" : "RO:0002630" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "directly negatively regulates (process to process)" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002578" }, { @@ -25656,17 +22317,8 @@ "val" : "RO:0003000" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9114-8737" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "produces" @@ -25685,17 +22337,8 @@ "val" : "RO:0003001" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9114-8737" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "produced_by" @@ -25804,9 +22447,6 @@ "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002264" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { @@ -25847,9 +22487,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002263" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { @@ -25908,9 +22545,6 @@ "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002418" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { @@ -25941,11 +22575,7 @@ "meta" : { "definition" : { "val" : "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0012000", @@ -26207,9 +22837,6 @@ "xrefs" : [ "PMID:19243617" ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" - }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1617-8244" }, { @@ -26227,9 +22854,6 @@ "xrefs" : [ "PMID:19243617" ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" - }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1617-8244" }, { @@ -26250,21 +22874,6 @@ "val" : "utilizes" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A diagnostic testing device utilizes a specimen." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9625-1899" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-2620-0345" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "See github ticket https://github.com/oborel/obo-relations/issues/497" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-11-08T12:00:00Z" } ] @@ -26407,12 +23016,6 @@ "val" : "galen:Tube" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts)" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "tubular" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -26458,16 +23061,11 @@ "xrefs" : [ "FMA:82482" ] } ], "xrefs" : [ { - "val" : "EMAPA:25036" - }, { "val" : "FMA:82482" }, { "val" : "galen:Wall" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in FMA, serosa is a wall" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0009915" }, { @@ -26505,8 +23103,6 @@ "val" : "EHDAA2:0003003" }, { "val" : "EMAPA:0" - }, { - "val" : "FBbt:00007001" }, { "val" : "FMA:305751" }, { @@ -26606,12 +23202,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26650,9 +23240,6 @@ "val" : "SCTID:91717005" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "currently defined in a very broad sense, may be replaced by more specific classes in the future" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { @@ -26783,9 +23370,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "ncit:Death is an outcome" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26863,9 +23447,6 @@ "val" : "WBls:0000103" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -26982,12 +23563,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "the WBls class 'all stages' belongs here as it is the superclass of other WBls stages" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27040,8 +23615,6 @@ "val" : "EHDAA:27" }, { "val" : "FBdv:00005288" - }, { - "val" : "IDOMAL:0000302" }, { "val" : "NCIT:C12601" }, { @@ -27056,9 +23629,6 @@ "val" : "ZFS:0000001" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -27236,12 +23806,6 @@ "val" : "XAO:1000006" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002174", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7955" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In zebrafish, the times of neurulation and segmentation overlap so extensively there is no distinct neurula period of development, such as occurs largely before segmentation in amphibian embryos." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -27374,8 +23938,6 @@ "val" : "EHDAA:542" }, { "val" : "EMAPA:16262" - }, { - "val" : "FBbt:00003126" }, { "val" : "FMA:49184" }, { @@ -27418,21 +23980,6 @@ "val" : "http://purl.obolibrary.org/obo/uberon/images/lamprey_sucker_rosava_3238889218.jpg" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "oral" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -27510,23 +24057,8 @@ "val" : "galen:Blood" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid." - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27659,8 +24191,6 @@ "val" : "BTO:0001485" }, { "val" : "EFO:0000801" - }, { - "val" : "EMAPA:35578" }, { "val" : "FMA:72954" }, { @@ -27683,12 +24213,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system that consists of the muscles of the body.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27739,8 +24263,6 @@ "val" : "EHDAA2:0003004" }, { "val" : "EMAPA:35178" - }, { - "val" : "FBbt:00007019" }, { "val" : "FMA:9669" }, { @@ -27813,8 +24335,6 @@ "val" : "CARO:0000005" }, { "val" : "EHDAA2:0003005" - }, { - "val" : "FBbt:00007017" }, { "val" : "FMA:5897" }, { @@ -27868,8 +24388,6 @@ "val" : "CARO:0000006" }, { "val" : "EHDAA2:0003006" - }, { - "val" : "FBbt:00007016" }, { "val" : "FMA:67165" }, { @@ -27920,8 +24438,6 @@ "val" : "CARO:0000007" }, { "val" : "EHDAA2:0003007" - }, { - "val" : "FBbt:00007015" }, { "val" : "FMA:67112" }, { @@ -28000,14 +24516,10 @@ "val" : "EMAPA:16103" }, { "val" : "EV:0100000" - }, { - "val" : "FBbt:00004856" }, { "val" : "FMA:7149" }, { "val" : "HAO:0000011" - }, { - "val" : "IDOMAL:0002460" }, { "val" : "MA:0000003" }, { @@ -28116,8 +24628,6 @@ "val" : "EMAPA:25765" }, { "val" : "EV:0100016" - }, { - "val" : "FBbt:00000001" }, { "val" : "FMA:256135" }, { @@ -28159,9 +24669,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "organismal" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28211,8 +24718,6 @@ "val" : "EHDAA2:0003032" }, { "val" : "EMAPA:36031" - }, { - "val" : "FBbt:00007009" }, { "val" : "FMA:7153" }, { @@ -28287,8 +24792,6 @@ "val" : "CARO:0000040" }, { "val" : "EHDAA2:0003040" - }, { - "val" : "FBbt:00007013" }, { "val" : "FMA:63863" }, { @@ -28327,8 +24830,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "xrefs" : [ { - "val" : "FBbt:00007277" - }, { "val" : "VHOG:0001737" } ], "basicPropertyValues" : [ { @@ -28385,8 +24886,6 @@ "val" : "EHDAA2:0003043" }, { "val" : "EMAPA:35868" - }, { - "val" : "FBbt:00007003" }, { "val" : "FMA:9637" }, { @@ -28457,8 +24956,6 @@ "val" : "CARO:0000055" }, { "val" : "EHDAA2:0003055" - }, { - "val" : "FBbt:00007010" }, { "val" : "HAO:0000055" }, { @@ -28523,8 +25020,6 @@ "val" : "EHDAA2:0003066" }, { "val" : "EMAPA:32738" - }, { - "val" : "FBbt:00007005" }, { "val" : "FMA:9639" }, { @@ -28553,12 +25048,6 @@ "val" : "ZFA:0001486" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "epithelial" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -28615,9 +25104,6 @@ "val" : "ZFA:0001498" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Unilaminar epithelium that consists of a single layer of squamous cells.[CARO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -28677,9 +25163,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Epithelium that consists of a single layer of epithelial cells.[CARO]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28722,18 +25205,6 @@ "val" : "Wikipedia:Thorax" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000026" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000033" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0002417" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -28782,14 +25253,10 @@ "val" : "EHDAA:38" }, { "val" : "EMAPA:16039" - }, { - "val" : "FBbt:00000052" }, { "val" : "FMA:69068" }, { "val" : "GAID:963" - }, { - "val" : "IDOMAL:0000646" }, { "val" : "MAT:0000226" }, { @@ -28816,12 +25283,6 @@ "val" : "http://neurolex.org/wiki/Category:Embryonic_organism" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "embryonic" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -28870,8 +25331,6 @@ "val" : "BTO:0000556" }, { "val" : "EMAPA:36033" - }, { - "val" : "FBbt:00000110" }, { "val" : "FMA:69069" }, { @@ -28898,9 +25357,6 @@ "val" : "ZFA:0001122" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -28936,8 +25392,6 @@ "val" : "EMAPA:16069" }, { "val" : "EV:0100003" - }, { - "val" : "FBbt:00000111" }, { "val" : "FMA:69070" }, { @@ -28968,15 +25422,6 @@ "val" : "ZFA:0000016" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "ectodermal" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -29016,8 +25461,6 @@ "val" : "EMAPA:16062" }, { "val" : "EV:0100005" - }, { - "val" : "FBbt:00000125" }, { "val" : "FMA:69071" }, { @@ -29046,12 +25489,6 @@ "val" : "ZFA:0000017" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "endodermal" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -29106,8 +25543,6 @@ "val" : "EMAPA:16083" }, { "val" : "EV:0100006" - }, { - "val" : "FBbt:00000126" }, { "val" : "FMA:69072" }, { @@ -29138,18 +25573,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Primary germ layer that is the middle of the embryonic germ layers.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "mesodermal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0003263" @@ -29209,8 +25632,6 @@ "val" : "EHDAA2:0001929" }, { "val" : "EMAPA:16263" - }, { - "val" : "FBbt:00000439" }, { "val" : "FMA:295846" }, { @@ -29231,18 +25652,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "stomodeal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -29336,21 +25745,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "cardiac" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -29439,12 +25833,6 @@ "val" : "galen:Joint" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -29482,10 +25870,6 @@ "val" : "CALOHA:TS-1293" }, { "val" : "EFO:0000793" - }, { - "val" : "EV:0100056" - }, { - "val" : "FBbt:00005055" }, { "val" : "FMA:7152" }, { @@ -29520,15 +25904,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "digestive" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -29554,17 +25929,12 @@ "val" : "AAO:0000959" }, { "val" : "CALOHA:TS-2103" - }, { - "val" : "MESH:D002319" }, { "val" : "VHOG:0001248" }, { "val" : "Wikipedia:Circulatory_system" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "the cardiovascular system and the lymphatic system are parts of the circulatory system" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_147099" }, { @@ -29573,18 +25943,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6157" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002174", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6231" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -29636,13 +25997,9 @@ "val" : "musculature system" } ], "xrefs" : [ { - "val" : "AAO:0011066" - }, { "val" : "BTO:0000887" }, { "val" : "EFO:0001949" - }, { - "val" : "EMAPA:32715" }, { "val" : "EMAPA:35577" }, { @@ -29665,12 +26022,6 @@ "val" : "ZFA:0000548" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0001474" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -29722,8 +26073,6 @@ "val" : "EMAPA:16469" }, { "val" : "EV:0100162" - }, { - "val" : "FBbt:00005093" }, { "val" : "FMA:7157" }, { @@ -29763,21 +26112,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "nervous" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "neural" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -29841,8 +26175,6 @@ "val" : "EMAPA:16754" }, { "val" : "EV:0100163" - }, { - "val" : "FBbt:00005094" }, { "val" : "FMA:55675" }, { @@ -29878,18 +26210,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Part of the nervous system which includes the brain and spinal cord.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The brain and spinal cord. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO)." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -29932,8 +26252,6 @@ "val" : "EFO:0001652" }, { "val" : "EHDAA2:0003171" - }, { - "val" : "FBbt:00005495" }, { "val" : "FMA:86589" }, { @@ -29996,8 +26314,6 @@ "val" : "FMA:293882" }, { "val" : "MAT:0000069" - }, { - "val" : "MESH:D054259" }, { "val" : "MIAA:0000069" }, { @@ -30020,18 +26336,6 @@ "val" : "neuronames:1365" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -30063,8 +26367,6 @@ "val" : "CARO:0000000" }, { "val" : "EHDAA2:0002229" - }, { - "val" : "FBbt:10000000" }, { "val" : "FMA:62955" }, { @@ -30154,27 +26456,6 @@ "val" : "ZFA:0000434" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0001016" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "System that provides physical support to the organism.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "skeletal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -30258,30 +26539,6 @@ "val" : "galen:Bone" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0001015" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0001630" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0002385" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Skeletal element that is composed of bone tissue.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -30334,14 +26591,10 @@ "val" : "EHDAA:518" }, { "val" : "EMAPA:16247" - }, { - "val" : "FBbt:00003125" }, { "val" : "FMA:45615" }, { "val" : "MA:0000917" - }, { - "val" : "MESH:D041981" }, { "val" : "NCIT:C34082" }, { @@ -30368,21 +26621,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The alimentary or digestive tract, and associated organs.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "FMA also has a term 'gastrointestinal tract', but this includes the liver." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000013", - "val" : "we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -30404,10 +26642,6 @@ "xrefs" : [ "ZFA:0005145" ] } ], "xrefs" : [ { - "val" : "AAO:0011066" - }, { - "val" : "EMAPA:32715" - }, { "val" : "EMAPA:37474" }, { "val" : "EV:0100146" @@ -30431,15 +26665,6 @@ "val" : "galen:Muscle" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of tissue composed of contractile fibers.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "muscular" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -30584,21 +26809,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Any of the vessels through which blood circulates in the body.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "annelids have blood vessels, but this class is not applicable to annelids." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -30642,9 +26852,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "endothelial" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -30680,9 +26887,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "vascular" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -30732,8 +26936,6 @@ "val" : "CALOHA:TS-2110" }, { "val" : "EFO:0000461" - }, { - "val" : "FBbt:00004208" }, { "val" : "FMA:69067" }, { @@ -30758,18 +26960,6 @@ "val" : "ZFA:0001105" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in FMA embryo is_a embryonic structure" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -30832,12 +27022,6 @@ "val" : "XAO:0003034" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -30869,8 +27053,6 @@ "val" : "EHDAA2:0000161" }, { "val" : "EHDAA:5049" - }, { - "val" : "EMAPA:17214" }, { "val" : "EMAPA:37721" }, { @@ -30879,8 +27061,6 @@ "val" : "MA:0002986" }, { "val" : "MAT:0000148" - }, { - "val" : "MESH:D013131" }, { "val" : "MIAA:0000148" }, { @@ -30895,18 +27075,6 @@ "val" : "ZFA:0000317" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -30979,18 +27147,6 @@ "val" : "galen:Trunk" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000026" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000033" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -31076,15 +27232,6 @@ "val" : "XAO:0000168" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system that provides locomotion and physical support to the organism.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "musculoskeletal" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -31144,9 +27291,6 @@ "val" : "Wikipedia:Thoracic_cavity" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In many species, the diaphragm separates thoracic and abdominal cavities" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -31213,8 +27357,6 @@ "val" : "BTO:0001707" }, { "val" : "EHDAA2:0000267" - }, { - "val" : "FBbt:00005060" }, { "val" : "FMA:85006" }, { @@ -31233,15 +27375,6 @@ "val" : "galen:BodyCavity" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In mammals it forms the peritoneal, pleural, and pericardial cavities" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0000169" }, { @@ -31319,27 +27452,6 @@ "val" : "http://evolution.berkeley.edu/evolibrary/images/history/notochords.jpg" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "notochordal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -31426,32 +27538,8 @@ "val" : "ZFA:0000155" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "EDITOR_NOTE currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7712" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Post-cranial axial segments which form sclerotome and dermomyotome.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "somitic" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -31510,8 +27598,6 @@ "val" : "NCIT:C34222" }, { "val" : "SCTID:361462002" - }, { - "val" : "TAO:0000045" }, { "val" : "UMLS:C0027789" }, { @@ -31526,24 +27612,6 @@ "val" : "neuronames:1366" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "EDITOR_NOTE consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams)." - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002174", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_117565" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -31602,8 +27670,6 @@ "val" : "EMAPA:16073" }, { "val" : "EV:0100004" - }, { - "val" : "FBbt:00001057" }, { "val" : "FMA:87657" }, { @@ -31626,15 +27692,6 @@ "val" : "ZFA:0001120" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "neurectodermal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000013", - "val" : "we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -31717,12 +27774,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000009", - "val" : "In adults, marrow in large bones produces new blood cells[Wikipedia:Bone_marrow]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -31795,18 +27846,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "MA also has set of connective tissues" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -31863,12 +27902,6 @@ "val" : "galen:MuscleTissue" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0003714" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -31953,18 +27986,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system that consists of the blood and blood forming tissues.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "hematopoietic" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -32014,9 +28035,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -32083,9 +28101,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "see https://github.com/obophenotype/uberon/issues/27" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -32138,9 +28153,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -32234,12 +28246,6 @@ "val" : "ZFA:0000279" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -32301,21 +28307,6 @@ "val" : "ZFA:0000094" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -32351,9 +28342,6 @@ "val" : "ZFA:0001204" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -32396,8 +28384,6 @@ "val" : "EMAPA:35593" }, { "val" : "FMA:293879" - }, { - "val" : "MESH:D054258" }, { "val" : "NCIT:C34225" }, { @@ -32418,12 +28404,6 @@ "val" : "neuronames:1362" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -32483,15 +28463,6 @@ "val" : "ZFA:0000255" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -32559,18 +28530,6 @@ "val" : "ZFA:0000121" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "subclass of mesoderm in ZFA." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0006258" }, { @@ -32617,15 +28576,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "should probably be merged with heart rudiment." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -32656,8 +28606,6 @@ "val" : "AAO:0010571" }, { "val" : "AEO:0000212" - }, { - "val" : "BTO:0006255" }, { "val" : "EHDAA2:0003439" }, { @@ -32680,15 +28628,6 @@ "val" : "ZFA:0001080" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Skeletogenic portion of somites.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "part_of somite in XAO" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -32736,9 +28675,6 @@ "val" : "ZFA:0000496" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -32801,15 +28737,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "mesenchymal" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -32871,9 +28798,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -32896,13 +28820,8 @@ "val" : "AEO:0000114" }, { "val" : "EHDAA2:0003114" - }, { - "val" : "FBbt:00007474" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -32957,9 +28876,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "FMA has both conduit and conduit space. In EHDAA2 this is a surface feature" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -32981,9 +28897,6 @@ "xrefs" : [ "FBbt:00025998" ] } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Grouping term for query purposes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33004,9 +28917,6 @@ "xrefs" : [ "FBbt:00025990" ] } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Grouping term for query purposes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33047,9 +28957,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -33091,9 +28998,6 @@ "val" : "XAO:0004185" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33137,9 +29041,6 @@ "val" : "ZFA:0000360" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33220,17 +29121,8 @@ "val" : "galen:Skeleton" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000383" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "skeletal" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -33263,9 +29155,6 @@ "val" : "ZFA:0000115" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33299,14 +29188,10 @@ "val" : "CALOHA:TS-1297" }, { "val" : "EFO:0000791" - }, { - "val" : "EHDAA2:0000216" }, { "val" : "EHDAA:394" }, { "val" : "EMAPA:16104" - }, { - "val" : "EMAPA:16370" }, { "val" : "EV:0100017" }, { @@ -33341,14 +29226,8 @@ "val" : "ZFA:0000010" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph." - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -33524,8 +29403,6 @@ "val" : "BILA:0000060" }, { "val" : "BTO:0001403" - }, { - "val" : "FBbt:00005317" }, { "val" : "FMA:293108" }, { @@ -33548,9 +29425,6 @@ "val" : "Wikipedia:Trilaminar_blastocyst" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "We explicitly merge the NCITA terms here" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0007012" }, { @@ -33582,9 +29456,6 @@ "val" : "ZFA:0005619" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33613,12 +29484,6 @@ "val" : "galen:SkeletalStructure" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33711,9 +29576,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider merging with 'endothelium'" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -33753,9 +29615,6 @@ "val" : "XAO:0000276" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33796,12 +29655,6 @@ "val" : "ZFA:0000091" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Notochord rudiment[ZFIN:ZDB-PUB-961014-576]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33820,9 +29673,6 @@ "pred" : "hasNarrowSynonym", "val" : "joint" } ], - "xrefs" : [ { - "val" : "FBbt:00005811" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -33858,14 +29708,9 @@ "xrefs" : [ "FMA:71131" ] } ], "xrefs" : [ { - "val" : "FBbt:00100315" - }, { "val" : "FMA:71131" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct." - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { @@ -33920,9 +29765,6 @@ "val" : "neuronames:1363" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33960,9 +29802,6 @@ "val" : "neuronames:1364" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33990,9 +29829,6 @@ "val" : "ZFA:0000133" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34018,14 +29854,9 @@ "val" : "muscle element" } ], "xrefs" : [ { - "val" : "EMAPA:32715" - }, { "val" : "FMA:30316" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34203,8 +30034,6 @@ "val" : "CALOHA:TS-2122" }, { "val" : "EHDAA2:0003125" - }, { - "val" : "FBbt:00007006" }, { "val" : "FMA:292313" }, { @@ -34244,8 +30073,6 @@ "xrefs" : [ "EMAPA:16208" ] } ], "xrefs" : [ { - "val" : "BTO:0006179" - }, { "val" : "EHDAA2:0001512" }, { "val" : "EHDAA:424" @@ -34335,9 +30162,6 @@ "val" : "Wikipedia:Basement_membrane" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell." - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_80999" }, { @@ -34391,8 +30215,6 @@ "val" : "AAO:0000963" }, { "val" : "EMAPA:17214" - }, { - "val" : "EMAPA:18043" }, { "val" : "MA:0000308" }, { @@ -34411,9 +30233,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -34451,9 +30270,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO - check ordering; awaiting confirmation from JB" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -34691,9 +30507,6 @@ "val" : "Wikipedia:Squamous_epithelium" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34864,9 +30677,6 @@ "val" : "UMLS:C1514442" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34896,16 +30706,11 @@ "xrefs" : [ "FBbt:00003154" ] } ], "xrefs" : [ { - "val" : "SPD:0000130" - }, { "val" : "TADS:0000147" }, { "val" : "http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34933,9 +30738,6 @@ "val" : "ZFA:0000131" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34997,9 +30799,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider merging" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Region of the gastrula which gives rise to the neural plate.[TAO]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -35145,8 +30944,6 @@ "val" : "EFO:0001649" }, { "val" : "EHDAA2:0003170" - }, { - "val" : "FBbt:00005426" }, { "val" : "Wikipedia:Anlage_(biology)" } ], @@ -35186,12 +30983,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -35311,8 +31102,6 @@ } ], "xrefs" : [ { "val" : "CARO:0010000" - }, { - "val" : "FBbt:00100313" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", @@ -35397,9 +31186,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Grouping term for query purposes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -35462,9 +31248,6 @@ "val" : "VSAO:0000042" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -35528,8 +31311,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "xrefs" : [ { - "val" : "FBbt:00007330" - }, { "val" : "FMA:67509" }, { "val" : "SCTID:91690000" @@ -35670,9 +31451,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_147099" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "coelomic" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -35742,9 +31520,6 @@ "val" : "UMLS:C0229619" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "Bone marrow in humans, kidney interstitium in Danio, within a stroma of reticuloendothelial tissue" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -35828,15 +31603,10 @@ "val" : "AEO:0000103" }, { "val" : "BTO:0001489" - }, { - "val" : "EMAPA:36031" }, { "val" : "FMA:231424" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -35909,8 +31679,6 @@ }, "xrefs" : [ { "val" : "AEO:0000093" - }, { - "val" : "FBbt:00007278" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -35928,9 +31696,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This class is primarily to implement taxon constraints. It may be removed in the future." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -35961,9 +31726,6 @@ "pred" : "hasRelatedSynonym", "val" : "cardiac structure" } ], - "xrefs" : [ { - "val" : "SPD:0000130" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -36148,8 +31910,6 @@ "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], "xrefs" : [ { "val" : "CARO:0020000" - }, { - "val" : "FBbt:00007276" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", @@ -36560,120 +32320,6 @@ "val" : "uberon" } ] } - }, { - "id" : "http://purl.org/dc/elements/1.1/creator", - "lbl" : "creator", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/elements/1.1/creator" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-creator" - } ] - } - }, { - "id" : "http://purl.org/dc/elements/1.1/description", - "lbl" : "description", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/elements/1.1/description" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-description" - } ] - } - }, { - "id" : "http://purl.org/dc/elements/1.1/title", - "lbl" : "title", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/elements/1.1/title" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-title" - } ] - } - }, { - "id" : "http://purl.org/dc/terms/contributor", - "lbl" : "contributor", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/terms/contributor" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-contributor" - } ] - } - }, { - "id" : "http://purl.org/dc/terms/date", - "lbl" : "date", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/terms/date" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dcterms-date" - } ] - } - }, { - "id" : "http://purl.org/dc/terms/license", - "lbl" : "license", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/terms/license" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dcterms-license" - } ] - } }, { "id" : "http://www.geneontology.org/formats/oboInOwl#SubsetProperty", "lbl" : "subset_property", @@ -36707,9 +32353,6 @@ "val" : "An alternative label for a class or property which has a more general meaning than the preferred name/primary label." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/18" }, { @@ -36730,9 +32373,6 @@ "val" : "An alternative label for a class or property which has the exact same meaning than the preferred name/primary label." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/20" }, { @@ -36749,9 +32389,6 @@ "val" : "An alternative label for a class or property which has a more specific meaning than the preferred name/primary label." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/19" }, { @@ -36772,9 +32409,6 @@ "val" : "An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/21" }, { @@ -36807,35 +32441,10 @@ "val" : "http://www.w3.org/2000/01/rdf-schema#seeAlso" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "seeAlso" } ] } - }, { - "id" : "http://xmlns.com/foaf/0.1/depiction", - "lbl" : "depiction", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://xmlns.com/foaf/0.1/depiction" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "depiction" - } ] - } } ], "edges" : [ { "sub" : "http://purl.obolibrary.org/obo/BFO_0000004", @@ -44294,17 +39903,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0004921", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts" - } ] - } - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0001106", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0001555" + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004921" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -44406,13 +40005,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000463", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000468", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "this relationship may be too strong and may be weakened in future" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000468" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000463", "pred" : "http://purl.obolibrary.org/obo/RO_0000086", @@ -44630,13 +40223,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000926", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000923", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "sometimes not considered primary" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000923" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000926", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -44978,6 +40565,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000055" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -45148,13 +40739,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002204", "pred" : "http://purl.obolibrary.org/obo/RO_0002254", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000926", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "check ctenophore" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000926" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002204", "pred" : "http://purl.obolibrary.org/obo/RO_0002492", @@ -45178,13 +40763,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002323", "pred" : "http://purl.obolibrary.org/obo/RO_0002494", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0003886", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "definitional" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0003886" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002323", "pred" : "http://purl.obolibrary.org/obo/RO_0002572", @@ -45209,6 +40788,10 @@ "val" : "VSAO" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", "pred" : "is_a", @@ -45217,14 +40800,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0011137" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000098", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0001555" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000102", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0001049" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -45301,6 +40876,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010314" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "is_a", @@ -45321,16 +40900,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_89593", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "ISBN:0073040584" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_89593" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -45354,13 +40924,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "http://purl.obolibrary.org/obo/RO_0002473", - "obj" : "http://purl.obolibrary.org/obo/CL_0000333", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/CL_0000333" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "http://purl.obolibrary.org/obo/RO_0002488", @@ -45387,6 +40951,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002371", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000479" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0002371", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002371", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -45473,13 +41041,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002390", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0003061", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "definitional" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0003061" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002405", "pred" : "is_a", @@ -45640,10 +41202,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0003077", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0015212" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0003077", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000922" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003077", "pred" : "http://purl.obolibrary.org/obo/RO_0002488", @@ -45891,6 +41449,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004140", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0002050" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004140", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004140", "pred" : "is_a", @@ -45945,6 +41507,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004151", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000064" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004151", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004151", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -46062,19 +41628,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004755", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/CL_0007001", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#date_retrieved", - "val" : "2012-08-14" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#external_class", - "val" : "VSAO:0000015" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "VSAO" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/CL_0007001" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004765", "pred" : "is_a", @@ -46202,14 +41756,14 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005062", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0015212" + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010371" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005062", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0005061" + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0015212" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005062", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000126", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0005061" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005068", @@ -46568,13 +42122,11 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006984", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0010199", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "via morphological boundary in CARO" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010199" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0007005", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007005", "pred" : "is_a", @@ -46638,13 +42190,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007100", "pred" : "http://purl.obolibrary.org/obo/RO_0002215", - "obj" : "http://purl.obolibrary.org/obo/GO_0008015", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "GO uses blood circulation generically to include the haemolymphatic fluid of arthropods" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/GO_0008015" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007135", "pred" : "is_a", @@ -46660,16 +42206,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007282", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0009618", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#consistent_with", - "val" : "https://github.com/obophenotype/uberon/wiki/The-neural-crest" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "EDHAA2" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0009618" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007282", "pred" : "http://purl.obolibrary.org/obo/RO_0002387", @@ -46835,6 +42372,10 @@ "val" : "EHDAA2" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0009881", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0009881", "pred" : "is_a", @@ -47067,6 +42608,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0012275", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0012429", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0012429", "pred" : "is_a", @@ -47179,10 +42724,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0015212", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0015212", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000465" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0015212", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -48509,10 +44050,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000057" - }, { - "sub" : "http://purl.obolibrary.org/obo/uberon/core#anteriorly_connected_to", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BSPO_0000099" }, { "sub" : "http://purl.obolibrary.org/obo/uberon/core#anteriorly_connected_to", "pred" : "subPropertyOf", @@ -48521,10 +44058,6 @@ "sub" : "http://purl.obolibrary.org/obo/uberon/core#anteriorly_connected_to", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/uberon/core#transitively_anteriorly_connected_to" - }, { - "sub" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BSPO_0000100" }, { "sub" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", "pred" : "subPropertyOf", @@ -48541,18 +44074,10 @@ "sub" : "http://purl.obolibrary.org/obo/uberon/core#layer_part_of", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000050" - }, { - "sub" : "http://purl.obolibrary.org/obo/uberon/core#posteriorly_connected_to", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BSPO_0000096" }, { "sub" : "http://purl.obolibrary.org/obo/uberon/core#posteriorly_connected_to", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002170" - }, { - "sub" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BSPO_0000097" }, { "sub" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to", "pred" : "subPropertyOf", @@ -48769,10 +44294,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012001", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012005" - }, { - "sub" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", - "pred" : "inverseOf", - "obj" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to" } ], "logicalDefinitionAxioms" : [ { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000034", @@ -51724,13 +47245,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002082", "fillerId" : "http://purl.obolibrary.org/obo/GO_0040016" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0000165", - "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0004921" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BSPO_0001106", - "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0001555" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0000179", "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000463" ], @@ -52212,13 +47726,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002387", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0002049" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0015212", - "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0000465" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0016879", "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0006598" ], @@ -52542,8 +48049,8 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002551", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061", "http://purl.obolibrary.org/obo/UBERON_0000475" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465", "http://purl.obolibrary.org/obo/UBERON_0010912" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002566", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], @@ -52601,10 +48108,6 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0019000", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/uberon/core#channel_for", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0004111" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000463" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] @@ -52636,21 +48139,12 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002287", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002210" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002329", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002215" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002496" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002497" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002479", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/BFO_0000066" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/RO_0000057" ] @@ -52669,24 +48163,12 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000066", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000066", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002314", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0000052", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0001025", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0001025", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002005", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002005", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002005", "http://purl.obolibrary.org/obo/RO_0002380" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002100", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002100", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/uberon/core#extends_fibers_into", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002100", "http://purl.obolibrary.org/obo/RO_0013001" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002102", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002102", "http://purl.obolibrary.org/obo/BFO_0000050" ] @@ -52702,24 +48184,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002131", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002131", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002134", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002134", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002150", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002170", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002176", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002178", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002202", "http://purl.obolibrary.org/obo/RO_0002162" ] @@ -52756,9 +48223,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0019002", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002213", "http://purl.obolibrary.org/obo/RO_0019002" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002216", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002215", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002215", "http://purl.obolibrary.org/obo/RO_0002162" ] @@ -52807,9 +48271,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002254", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002256", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002258", "http://purl.obolibrary.org/obo/RO_0002496" ] @@ -52831,9 +48292,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004031", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/BFO_0000051" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002432", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/BFO_0000066" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002327", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002017" ] @@ -52897,15 +48355,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002339", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002339", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002177", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002371", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002371", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002387", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002407", "http://purl.obolibrary.org/obo/RO_0002629" ] @@ -52918,15 +48367,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002488", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002488", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002488", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002492", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002492", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002492", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002496", "http://purl.obolibrary.org/obo/BFO_0000050" ] @@ -52945,9 +48388,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002497", "http://purl.obolibrary.org/obo/RO_0002082" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/uberon/core#indirectly_supplies", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002569", "http://purl.obolibrary.org/obo/RO_0002178" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/uberon/core#indirectly_supplies", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002569", "http://purl.obolibrary.org/obo/uberon/core#indirectly_supplies" ] @@ -52966,12 +48406,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002630", "http://purl.obolibrary.org/obo/RO_0002630" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0003000", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0003001", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0013001", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0013001", "http://purl.obolibrary.org/obo/BFO_0000050" ] diff --git a/src/ontology/subsets/blood_and_immune_upper_slim.obo b/src/ontology/subsets/blood_and_immune_upper_slim.obo index 35057603f..671299a14 100644 --- a/src/ontology/subsets/blood_and_immune_upper_slim.obo +++ b/src/ontology/subsets/blood_and_immune_upper_slim.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: cl/releases/2024-02-13/subsets/blood_and_immune_upper_slim.owl +data-version: cl/releases/2024-04-05/subsets/blood_and_immune_upper_slim.owl subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -88,7 +88,7 @@ synonymtypedef: synonym "" synonymtypedef: SYSTEMATIC "" synonymtypedef: systematic_synonym "" ontology: cl/subsets/blood_and_immune_upper_slim -property_value: owl:versionInfo "2024-02-13" xsd:string +property_value: owl:versionInfo "2024-04-05" xsd:string [Term] id: BFO:0000002 @@ -159,7 +159,7 @@ is_a: UBERON:0000061 ! anatomical structure disjoint_from: GO:0031012 ! extracellular matrix disjoint_from: GO:0032991 ! protein-containing complex disjoint_from: GO:0043226 ! organelle -relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms +relationship: RO:0002160 NCBITaxon:131567 ! only in taxon cellular organisms [Term] id: CL:0000007 @@ -182,8 +182,8 @@ is_a: CL:0011115 ! precursor cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0017145 ! stem cell division relationship: capable_of GO:0017145 ! stem cell division -relationship: in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000037 @@ -233,8 +233,8 @@ relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surfac relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -relationship: develops_from CL:0000566 ! angioblastic mesenchymal cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000566 ! develops from angioblastic mesenchymal cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000038 @@ -251,7 +251,7 @@ synonym: "erythroid stem cell" RELATED [] xref: BTO:0004911 is_a: CL:0000764 ! erythroid lineage cell is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor cell -relationship: develops_from CL:0000050 ! megakaryocyte-erythroid progenitor cell +relationship: RO:0002202 CL:0000050 ! develops from megakaryocyte-erythroid progenitor cell [Term] id: CL:0000040 @@ -273,11 +273,11 @@ intersection_of: has_part CL:0017503 ! basophilic cytoplasm intersection_of: has_part GO:0000791 ! euchromatin intersection_of: has_part GO:0005730 ! nucleolus intersection_of: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M -relationship: develops_from CL:0002009 ! macrophage dendritic cell progenitor relationship: has_part CL:0017503 ! basophilic cytoplasm relationship: has_part GO:0000791 ! euchromatin relationship: has_part GO:0005730 ! nucleolus relationship: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M +relationship: RO:0002202 CL:0002009 ! develops from macrophage dendritic cell progenitor [Term] id: CL:0000048 @@ -314,7 +314,7 @@ is_a: CL:0002032 {is_inferred="true"} ! hematopoietic oligopotent progenitor cel disjoint_from: CL:0000050 ! megakaryocyte-erythroid progenitor cell disjoint_from: CL:0000051 ! common lymphoid progenitor disjoint_from: CL:0000557 ! granulocyte monocyte progenitor cell -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000050 @@ -340,7 +340,7 @@ disjoint_from: CL:0000557 ! granulocyte monocyte progenitor cell disjoint_from: CL:0002009 ! macrophage dendritic cell progenitor relationship: capable_of GO:0030218 ! erythrocyte differentiation relationship: capable_of GO:0030219 ! megakaryocyte differentiation -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000051 @@ -363,7 +363,7 @@ is_a: CL:0011026 ! progenitor cell intersection_of: CL:0002032 ! hematopoietic oligopotent progenitor cell intersection_of: capable_of GO:0030098 ! lymphocyte differentiation relationship: capable_of GO:0030098 ! lymphocyte differentiation -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000052 @@ -410,8 +410,8 @@ xref: FMA:63877 xref: NCIT:C12482 xref: VHOG:0001482 is_a: CL:0002320 ! connective tissue cell -relationship: develops_from CL:0000134 ! mesenchymal stem cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000066 @@ -430,8 +430,8 @@ xref: WBbt:0003672 is_a: CL:0000000 ! cell disjoint_from: CL:0000738 ! leukocyte relationship: part_of UBERON:0000483 ! epithelium -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000071 @@ -444,9 +444,9 @@ is_a: CL:0000076 {is_inferred="true"} ! squamous epithelial cell is_a: CL:0002139 ! endothelial cell of vascular tree intersection_of: CL:0000076 ! squamous epithelial cell intersection_of: part_of UBERON:0004638 ! blood vessel endothelium -relationship: develops_from CL:0002546 ! embryonic blood vessel endothelial progenitor cell relationship: part_of UBERON:0004638 ! blood vessel endothelium -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0002546 ! develops from embryonic blood vessel endothelial progenitor cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000076 @@ -499,8 +499,8 @@ intersection_of: CL:0000542 ! lymphocyte intersection_of: capable_of GO:0002456 ! T cell mediated immunity disjoint_from: CL:0000945 ! lymphocyte of B lineage relationship: capable_of GO:0002456 ! T cell mediated immunity -relationship: develops_from CL:0000827 ! pro-T cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000827 ! develops from pro-T cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000092 @@ -528,7 +528,6 @@ intersection_of: part_of UBERON:0001474 ! bone element intersection_of: RO:0002104 PR:000001954 ! has plasma membrane part tumor necrosis factor receptor superfamily member 11A intersection_of: RO:0002104 PR:000002062 ! has plasma membrane part macrophage colony-stimulating factor 1 receptor relationship: capable_of GO:0045453 ! bone resorption -relationship: develops_from CL:0000576 ! monocyte relationship: has_part PR:000001850 ! cathepsin K relationship: has_part PR:000001937 ! tartrate-resistant acid phosphatase type 5 relationship: has_part PR:000001944 ! transcription factor PU.1 @@ -536,6 +535,7 @@ relationship: has_part PR:000007597 ! protein c-Fos relationship: has_part PR:000011178 ! nuclear factor NF-kappa-B p100 subunit relationship: RO:0002104 PR:000001954 ! has plasma membrane part tumor necrosis factor receptor superfamily member 11A relationship: RO:0002104 PR:000002062 ! has plasma membrane part macrophage colony-stimulating factor 1 receptor +relationship: RO:0002202 CL:0000576 ! develops from monocyte [Term] id: CL:0000094 @@ -568,10 +568,10 @@ relationship: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon relationship: CL:4030046 PR:000001024 ! lacks_plasma_membrane_part neural cell adhesion molecule 1 relationship: CL:4030046 PR:000001084 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD8 alpha chain relationship: has_part GO:0030141 ! secretory granule -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M relationship: RO:0002104 PR:000001332 ! has plasma membrane part carcinoembryonic antigen-related cell adhesion molecule 8 relationship: RO:0002104 PR:000001969 ! has plasma membrane part urokinase plasminogen activator surface receptor +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000097 @@ -611,13 +611,13 @@ relationship: capable_of GO:0002690 ! positive regulation of leukocyte chemotaxi relationship: capable_of GO:0002830 ! positive regulation of type 2 immune response relationship: capable_of GO:0030210 ! heparin biosynthetic process relationship: CL:4030046 PR:000001865 ! lacks_plasma_membrane_part interleukin-3 receptor class 2 alpha chain -relationship: develops_from CL:0000831 ! mast cell progenitor relationship: has_part GO:0030141 ! secretory granule -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002104 PR:000001255 ! has plasma membrane part C-C chemokine receptor type 3 relationship: RO:0002104 PR:000006169 ! has plasma membrane part cell surface glycoprotein CD200 receptor 3 +relationship: RO:0002202 CL:0000831 ! develops from mast cell progenitor relationship: RO:0015015 PR:000002065 ! has high plasma membrane amount mast/stem cell growth factor receptor relationship: RO:0015015 PR:000007431 ! has high plasma membrane amount high affinity immunoglobulin epsilon receptor subunit alpha +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000113 @@ -630,7 +630,7 @@ is_a: CL:0000518 {is_inferred="true"} ! phagocyte (sensu Vertebrata) is_a: CL:0000842 ! mononuclear cell intersection_of: CL:0000518 ! phagocyte (sensu Vertebrata) intersection_of: bearer_of PATO:0001407 ! mononucleate -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000115 @@ -645,7 +645,7 @@ xref: CALOHA:TS-0278 xref: FMA:66772 is_a: CL:0000213 ! lining cell is_a: CL:0002078 ! meso-epithelial cell -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000133 @@ -726,8 +726,8 @@ xref: FMA:67328 xref: WBbt:0003675 is_a: CL:0000183 ! contractile cell is_a: CL:0000393 ! electrically responsive cell -relationship: develops_from CL:0000056 ! myoblast -property_value: depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI +relationship: RO:0002202 CL:0000056 ! develops from myoblast +property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI [Term] id: CL:0000211 @@ -845,8 +845,8 @@ intersection_of: CL:4030046 PR:000001945 ! lacks_plasma_membrane_part transferri relationship: bearer_of PATO:0002039 ! biconcave relationship: CL:4030045 GO:0005840 ! lacks_part ribosome relationship: CL:4030046 PR:000001945 ! lacks_plasma_membrane_part transferrin receptor protein 1 -relationship: develops_from CL:0000558 ! reticulocyte -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000558 ! develops from reticulocyte +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000233 @@ -868,8 +868,8 @@ is_a: CL:0000458 ! serotonin secreting cell is_a: CL:0000763 {is_inferred="true"} ! myeloid cell relationship: bearer_of PATO:0001874 ! discoid relationship: capable_of_part_of GO:0007596 ! blood coagulation -relationship: develops_from CL:0000556 ! megakaryocyte -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000556 ! develops from megakaryocyte +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000234 @@ -909,8 +909,8 @@ intersection_of: capable_of GO:0002504 ! antigen processing and presentation of intersection_of: capable_of GO:0006909 ! phagocytosis intersection_of: capable_of GO:0031268 ! pseudopodium organization relationship: capable_of GO:0031268 ! pseudopodium organization -relationship: develops_from CL:0000576 ! monocyte -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000576 ! develops from monocyte +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000236 @@ -932,7 +932,7 @@ is_a: CL:0000945 {is_inferred="true"} ! lymphocyte of B lineage intersection_of: CL:0000945 ! lymphocyte of B lineage intersection_of: capable_of GO:0019724 ! B cell mediated immunity relationship: capable_of GO:0019724 ! B cell mediated immunity -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000255 @@ -941,8 +941,8 @@ subset: cellxgene_subset xref: MESH:D005057 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell -intersection_of: only_in_taxon NCBITaxon:2759 ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +intersection_of: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota [Term] id: CL:0000325 @@ -967,7 +967,7 @@ xref: FMA:86667 is_a: CL:0000219 ! motile cell is_a: CL:0011012 ! neural crest cell is_a: CL:0011026 ! progenitor cell -relationship: develops_from CL:0007004 ! premigratory neural crest cell +relationship: RO:0002202 CL:0007004 ! develops from premigratory neural crest cell [Term] id: CL:0000335 @@ -993,8 +993,8 @@ is_a: CL:0000007 ! early embryonic cell (metazoa) is_a: CL:0000255 ! eukaryotic cell is_a: CL:0010017 ! zygote intersection_of: CL:0010017 ! zygote -intersection_of: only_in_taxon NCBITaxon:33208 ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +intersection_of: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa [Term] id: CL:0000393 @@ -1045,7 +1045,7 @@ relationship: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon relationship: CL:4030046 PR:000001024 ! lacks_plasma_membrane_part neural cell adhesion molecule 1 relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-spanning 4-domains subfamily A member 1 relationship: has_part GO:0042613 ! MHC class II protein complex -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000457 @@ -1075,7 +1075,7 @@ name: phagocyte (sensu Vertebrata) def: "A phagocyte in vertebrates that is able to phagocytosis." [GOC:tfm] is_a: CL:0000234 ! phagocyte is_a: CL:0000255 ! eukaryotic cell -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata [Term] id: CL:0000540 @@ -1096,8 +1096,8 @@ is_a: CL:0000393 ! electrically responsive cell is_a: CL:0000404 ! electrically signaling cell is_a: CL:0002319 ! neural cell relationship: capable_of GO:0019226 ! transmission of nerve impulse -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://www.swissbiopics.org/api/image/Neuron_cells.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Neuron_cells.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000542 @@ -1120,10 +1120,10 @@ intersection_of: has_part CL:0017500 ! neutrophillic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin disjoint_from: CL:0000766 ! myeloid leukocyte relationship: bearer_of PATO:0040072 ! high nuclear/cytoplasmic ratio -relationship: develops_from CL:0000051 ! common lymphoid progenitor relationship: has_part CL:0017500 ! neutrophillic cytoplasm relationship: has_part GO:0000792 ! heterochromatin -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000051 ! develops from common lymphoid progenitor +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000547 @@ -1166,10 +1166,10 @@ relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-span relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD5 relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G -relationship: develops_from CL:0000038 ! erythroid progenitor cell relationship: has_part CL:0017503 ! basophilic cytoplasm relationship: has_part GO:0005730 ! nucleolus relationship: RO:0002104 PR:000001945 ! has plasma membrane part transferrin receptor protein 1 +relationship: RO:0002202 CL:0000038 ! develops from erythroid progenitor cell [Term] id: CL:0000549 @@ -1207,10 +1207,10 @@ intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017504 ! polychromatophilic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin intersection_of: RO:0002104 PR:000001945 ! has plasma membrane part transferrin receptor protein 1 -relationship: develops_from CL:0000549 ! basophilic erythroblast relationship: has_part CL:0017504 ! polychromatophilic cytoplasm relationship: has_part GO:0000792 ! heterochromatin relationship: RO:0002104 PR:000001945 ! has plasma membrane part transferrin receptor protein 1 +relationship: RO:0002202 CL:0000549 ! develops from basophilic erythroblast [Term] id: CL:0000552 @@ -1226,9 +1226,9 @@ is_a: CL:0000765 {is_inferred="true"} ! erythroblast intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017502 ! acidophilic cytoplasm intersection_of: participates_in GO:0030263 ! apoptotic chromosome condensation -relationship: develops_from CL:0000550 ! polychromatophilic erythroblast relationship: has_part CL:0017502 ! acidophilic cytoplasm relationship: participates_in GO:0030263 ! apoptotic chromosome condensation +relationship: RO:0002202 CL:0000550 ! develops from polychromatophilic erythroblast [Term] id: CL:0000553 @@ -1282,8 +1282,8 @@ relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surfac relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -relationship: develops_from CL:0000050 ! megakaryocyte-erythroid progenitor cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000050 ! develops from megakaryocyte-erythroid progenitor cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000556 @@ -1302,8 +1302,8 @@ xref: FMA:83555 is_a: CL:0000763 {is_inferred="true"} ! myeloid cell disjoint_from: CL:0000764 ! erythroid lineage cell relationship: bearer_of PATO:0001393 ! euploid -relationship: develops_from CL:0000553 ! megakaryocyte progenitor cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000553 ! develops from megakaryocyte progenitor cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000557 @@ -1339,8 +1339,8 @@ relationship: CL:4030045 PR:000007857 ! lacks_part erythroid transcription facto relationship: CL:4030045 PR:000007858 ! lacks_part endothelial transcription factor GATA-2 relationship: has_part PR:000001944 ! transcription factor PU.1 relationship: has_part PR:000005307 ! CCAAT/enhancer-binding protein alpha -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002104 PR:000001865 ! has plasma membrane part interleukin-3 receptor class 2 alpha chain +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000558 @@ -1379,8 +1379,8 @@ relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-span relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD5 relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G -relationship: develops_from CL:0000552 ! orthochromatic erythroblast relationship: RO:0002104 PR:000001945 ! has plasma membrane part transferrin receptor protein 1 +relationship: RO:0002202 CL:0000552 ! develops from orthochromatic erythroblast [Term] id: CL:0000559 @@ -1398,10 +1398,10 @@ intersection_of: CL:0002194 ! monopoietic cell intersection_of: capable_of GO:0030224 ! monocyte differentiation intersection_of: has_part GO:0042582 ! azurophil granule intersection_of: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M -relationship: develops_from CL:0000040 ! monoblast relationship: has_part GO:0042582 ! azurophil granule -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M +relationship: RO:0002202 CL:0000040 ! develops from monoblast +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000566 @@ -1417,10 +1417,10 @@ intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: RO:0002104 PR:000001444 ! has plasma membrane part cadherin-5 intersection_of: RO:0002104 PR:000002112 ! has plasma membrane part vascular endothelial growth factor receptor 2 intersection_of: RO:0002104 PR:000016043 ! has plasma membrane part T-cell acute lymphocytic leukemia protein 1 -relationship: develops_from CL:0000134 ! mesenchymal stem cell relationship: RO:0002104 PR:000001444 ! has plasma membrane part cadherin-5 relationship: RO:0002104 PR:000002112 ! has plasma membrane part vascular endothelial growth factor receptor 2 relationship: RO:0002104 PR:000016043 ! has plasma membrane part T-cell acute lymphocytic leukemia protein 1 +relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell [Term] id: CL:0000576 @@ -1445,8 +1445,8 @@ intersection_of: capable_of GO:0043011 ! myeloid dendritic cell differentiation relationship: capable_of GO:0030225 ! macrophage differentiation relationship: capable_of GO:0030316 ! osteoclast differentiation relationship: capable_of GO:0043011 ! myeloid dendritic cell differentiation -relationship: develops_from CL:0000559 ! promonocyte -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000559 ! develops from promonocyte +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000647 @@ -1468,9 +1468,9 @@ intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: bearer_of PATO:0001908 ! multinucleate intersection_of: participates_in GO:0002432 ! granuloma formation intersection_of: participates_in GO:0002544 ! chronic inflammatory response -relationship: develops_from CL:0000235 ! macrophage relationship: participates_in GO:0002432 ! granuloma formation relationship: participates_in GO:0002544 ! chronic inflammatory response +relationship: RO:0002202 CL:0000235 ! develops from macrophage [Term] id: CL:0000680 @@ -1479,9 +1479,9 @@ def: "A non-terminally differentiated cell that is capable of developing into a subset: cellxgene_subset is_a: CL:0000055 ! non-terminally differentiated cell intersection_of: CL:0011115 ! precursor cell -intersection_of: develops_into CL:0000187 ! muscle cell -relationship: develops_from CL:0000222 ! mesodermal cell -relationship: develops_into CL:0000187 ! muscle cell +intersection_of: RO:0002203 CL:0000187 ! develops into muscle cell +relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell +relationship: RO:0002203 CL:0000187 ! develops into muscle cell [Term] id: CL:0000723 @@ -1516,10 +1516,10 @@ intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0002505 ! nucleated intersection_of: capable_of GO:0001667 ! ameboidal-type cell migration relationship: capable_of GO:0001667 ! ameboidal-type cell migration -relationship: develops_from CL:0000037 ! hematopoietic stem cell -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0002405 ! immune system -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002202 CL:0000037 ! develops from hematopoietic stem cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000762 @@ -1533,7 +1533,7 @@ intersection_of: CL:0000763 ! myeloid cell intersection_of: bearer_of PATO:0001407 ! mononucleate intersection_of: capable_of GO:0007596 ! blood coagulation relationship: capable_of GO:0007596 ! blood coagulation -relationship: develops_from CL:0000828 ! thromboblast +relationship: RO:0002202 CL:0000828 ! develops from thromboblast [Term] id: CL:0000763 @@ -1545,8 +1545,8 @@ xref: CALOHA:TS-0647 xref: MESH:D022423 is_a: CL:0000988 {is_inferred="true"} ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell -intersection_of: develops_from CL:0000049 ! common myeloid progenitor -relationship: develops_from CL:0000049 ! common myeloid progenitor +intersection_of: RO:0002202 CL:0000049 ! develops from common myeloid progenitor +relationship: RO:0002202 CL:0000049 ! develops from common myeloid progenitor [Term] id: CL:0000764 @@ -1560,7 +1560,7 @@ xref: CALOHA:TS-0290 xref: FMA:62845 xref: FMA:83516 is_a: CL:0000763 ! myeloid cell -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000765 @@ -1603,8 +1603,8 @@ relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-span relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD5 relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G -relationship: develops_from CL:0000547 ! proerythroblast relationship: has_part GO:0005634 ! nucleus +relationship: RO:0002202 CL:0000547 ! develops from proerythroblast [Term] id: CL:0000766 @@ -1614,7 +1614,7 @@ subset: cellxgene_subset is_a: CL:0000738 {is_inferred="true"} ! leukocyte is_a: CL:0000763 ! myeloid cell intersection_of: CL:0000738 ! leukocyte -intersection_of: develops_from CL:0000049 ! common myeloid progenitor +intersection_of: RO:0002202 CL:0000049 ! develops from common myeloid progenitor [Term] id: CL:0000767 @@ -1638,12 +1638,12 @@ intersection_of: RO:0002104 PR:000001950 ! has plasma membrane part tumor necros intersection_of: RO:0015015 PR:000001255 ! has high plasma membrane amount C-C chemokine receptor type 3 intersection_of: RO:0015015 PR:000001865 ! has high plasma membrane amount interleukin-3 receptor class 2 alpha chain intersection_of: RO:0015015 PR:000007431 ! has high plasma membrane amount high affinity immunoglobulin epsilon receptor subunit alpha -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002104 PR:000001344 ! has plasma membrane part ectonucleotide pyrophosphatase/phosphodiesterase family member 3 relationship: RO:0002104 PR:000001950 ! has plasma membrane part tumor necrosis factor ligand superfamily member 5 relationship: RO:0015015 PR:000001255 ! has high plasma membrane amount C-C chemokine receptor type 3 relationship: RO:0015015 PR:000001865 ! has high plasma membrane amount interleukin-3 receptor class 2 alpha chain relationship: RO:0015015 PR:000007431 ! has high plasma membrane amount high affinity immunoglobulin epsilon receptor subunit alpha +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000771 @@ -1670,12 +1670,12 @@ intersection_of: RO:0002104 PR:000001255 ! has plasma membrane part C-C chemokin intersection_of: RO:0002104 PR:000001307 ! has plasma membrane part CD44 molecule intersection_of: RO:0002104 PR:000001343 ! has plasma membrane part CD69 molecule intersection_of: RO:0002104 PR:000005178 ! has plasma membrane part CD9 molecule -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002104 PR:000001254 ! has plasma membrane part C-C chemokine receptor type 1 relationship: RO:0002104 PR:000001255 ! has plasma membrane part C-C chemokine receptor type 3 relationship: RO:0002104 PR:000001307 ! has plasma membrane part CD44 molecule relationship: RO:0002104 PR:000001343 ! has plasma membrane part CD69 molecule relationship: RO:0002104 PR:000005178 ! has plasma membrane part CD9 molecule +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000775 @@ -1704,9 +1704,9 @@ is_a: CL:0000094 {is_inferred="true"} ! granulocyte intersection_of: CL:0000094 ! granulocyte intersection_of: RO:0002104 PR:000001479 ! has plasma membrane part low affinity immunoglobulin gamma Fc region receptor II intersection_of: RO:0002104 PR:000001879 ! has plasma membrane part leukosialin -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002104 PR:000001479 ! has plasma membrane part low affinity immunoglobulin gamma Fc region receptor II relationship: RO:0002104 PR:000001879 ! has plasma membrane part leukosialin +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000782 @@ -1723,9 +1723,9 @@ is_a: CL:0000766 ! myeloid leukocyte is_a: CL:0000990 {is_inferred="true"} ! conventional dendritic cell intersection_of: CL:0000990 ! conventional dendritic cell intersection_of: CL:4030046 PR:000001865 ! lacks_plasma_membrane_part interleukin-3 receptor class 2 alpha chain -intersection_of: develops_from CL:0000763 ! myeloid cell +intersection_of: RO:0002202 CL:0000763 ! develops from myeloid cell relationship: CL:4030046 PR:000001865 ! lacks_plasma_membrane_part interleukin-3 receptor class 2 alpha chain -relationship: develops_from CL:0000763 ! myeloid cell +relationship: RO:0002202 CL:0000763 ! develops from myeloid cell [Term] id: CL:0000784 @@ -1748,7 +1748,7 @@ is_a: CL:0000451 {is_inferred="true"} ! dendritic cell intersection_of: CL:0000451 ! dendritic cell intersection_of: capable_of GO:0032606 ! type I interferon production relationship: capable_of GO:0032606 ! type I interferon production -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000785 @@ -1769,8 +1769,8 @@ disjoint_from: CL:0000816 ! immature B cell disjoint_from: CL:0000817 ! precursor B cell disjoint_from: CL:0000818 ! transitional stage B cell relationship: capable_of GO:0042113 ! B cell activation -relationship: develops_from CL:0000818 ! transitional stage B cell relationship: output_of GO:0002335 ! mature B cell differentiation +relationship: RO:0002202 CL:0000818 ! develops from transitional stage B cell [Term] id: CL:0000786 @@ -1800,11 +1800,11 @@ intersection_of: RO:0002104 PR:000001935 ! has plasma membrane part syndecan-1 relationship: CL:4030046 GO:0019814 ! lacks_plasma_membrane_part immunoglobulin complex relationship: CL:4030046 GO:0042613 ! lacks_plasma_membrane_part MHC class II protein complex relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-spanning 4-domains subfamily A member 1 -relationship: develops_from CL:0000980 ! plasmablast relationship: has_part CL:0017508 ! cartwheel heterochromatin relationship: has_part GO:0005794 ! Golgi apparatus -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002104 PR:000001935 ! has plasma membrane part syndecan-1 +relationship: RO:0002202 CL:0000980 ! develops from plasmablast +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000789 @@ -1837,8 +1837,8 @@ synonym: "gd T cell" RELATED OMO:0003000 [] is_a: CL:0000084 {is_inferred="true"} ! T cell intersection_of: CL:0000084 ! T cell intersection_of: RO:0002104 GO:0042106 ! has plasma membrane part gamma-delta T cell receptor complex -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002104 GO:0042106 ! has plasma membrane part gamma-delta T cell receptor complex +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000816 @@ -1860,10 +1860,10 @@ intersection_of: RO:0002104 GO:0071753 ! has plasma membrane part IgM immunoglob intersection_of: RO:0002104 PR:000001289 ! has plasma membrane part membrane-spanning 4-domains subfamily A member 1 relationship: CL:4030044 GO:0045190 ! has_not_completed isotype switching relationship: CL:4030046 GO:0071738 ! lacks_plasma_membrane_part IgD immunoglobulin complex -relationship: develops_from CL:0000954 ! small pre-B-II cell -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002104 GO:0071753 ! has plasma membrane part IgM immunoglobulin complex relationship: RO:0002104 PR:000001289 ! has plasma membrane part membrane-spanning 4-domains subfamily A member 1 +relationship: RO:0002202 CL:0000954 ! develops from small pre-B-II cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000817 @@ -1880,8 +1880,8 @@ intersection_of: CL:4030046 GO:0071753 ! lacks_plasma_membrane_part IgM immunogl intersection_of: RO:0002104 PR:000001898 ! has plasma membrane part neprilysin disjoint_from: CL:0000826 ! pro-B cell relationship: CL:4030046 GO:0071753 ! lacks_plasma_membrane_part IgM immunoglobulin complex -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002104 PR:000001898 ! has plasma membrane part neprilysin +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000818 @@ -1905,12 +1905,12 @@ intersection_of: RO:0002104 PR:000001289 ! has plasma membrane part membrane-spa intersection_of: RO:0015015 PR:000001408 ! has high plasma membrane amount ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 intersection_of: RO:0015015 PR:000001932 ! has high plasma membrane amount signal transducer CD24 relationship: CL:4030044 GO:0002335 ! has_not_completed mature B cell differentiation -relationship: develops_from CL:0000816 ! immature B cell -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002104 GO:0071753 ! has plasma membrane part IgM immunoglobulin complex relationship: RO:0002104 PR:000001289 ! has plasma membrane part membrane-spanning 4-domains subfamily A member 1 +relationship: RO:0002202 CL:0000816 ! develops from immature B cell relationship: RO:0015015 PR:000001408 ! has high plasma membrane amount ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 relationship: RO:0015015 PR:000001932 ! has high plasma membrane amount signal transducer CD24 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000826 @@ -1935,11 +1935,11 @@ intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: has_part PR:000001903 ! paired box protein PAX-5 intersection_of: has_part PR:000006611 ! DNA nucleotidylexotransferase intersection_of: participates_in GO:0033152 ! immunoglobulin V(D)J recombination -relationship: develops_from CL:0000051 ! common lymphoid progenitor relationship: has_part PR:000001903 ! paired box protein PAX-5 relationship: has_part PR:000006611 ! DNA nucleotidylexotransferase relationship: participates_in GO:0033152 ! immunoglobulin V(D)J recombination -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000051 ! develops from common lymphoid progenitor +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000827 @@ -1955,7 +1955,7 @@ is_a: CL:0000838 {is_inferred="true"} ! lymphoid lineage restricted progenitor c intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: capable_of GO:0030217 ! T cell differentiation relationship: capable_of GO:0030217 ! T cell differentiation -relationship: develops_from CL:0000051 ! common lymphoid progenitor +relationship: RO:0002202 CL:0000051 ! develops from common lymphoid progenitor [Term] id: CL:0000828 @@ -1969,7 +1969,7 @@ intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: bearer_of PATO:0001407 ! mononucleate intersection_of: capable_of GO:0002574 ! thrombocyte differentiation relationship: capable_of GO:0002574 ! thrombocyte differentiation -relationship: develops_from CL:0000050 ! megakaryocyte-erythroid progenitor cell +relationship: RO:0002202 CL:0000050 ! develops from megakaryocyte-erythroid progenitor cell [Term] id: CL:0000831 @@ -2025,11 +2025,11 @@ relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte an relationship: CL:4030046 PR:000002979 ! lacks_plasma_membrane_part lymphocyte antigen 6A-2/6E-1 relationship: CL:4030046 PR:000002980 ! lacks_plasma_membrane_part lymphocyte antigen 6C2 relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -relationship: develops_from CL:0002028 ! basophil mast progenitor cell relationship: has_part PR:000007857 ! erythroid transcription factor relationship: has_part PR:000007858 ! endothelial transcription factor GATA-2 relationship: RO:0002104 PR:000005178 ! has plasma membrane part CD9 molecule relationship: RO:0002104 PR:000016401 ! has plasma membrane part transmembrane emp24 domain-containing protein 1 +relationship: RO:0002202 CL:0002028 ! develops from basophil mast progenitor cell relationship: RO:0015015 PR:000009143 ! has high plasma membrane amount integrin beta-7 relationship: RO:0015016 PR:000002065 ! has low plasma membrane amount mast/stem cell growth factor receptor relationship: RO:0015016 PR:000007431 ! has low plasma membrane amount high affinity immunoglobulin epsilon receptor subunit alpha @@ -2079,9 +2079,9 @@ relationship: CL:4030046 PR:000001869 ! lacks_plasma_membrane_part interleukin-7 relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -relationship: develops_from CL:0000037 ! hematopoietic stem cell -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule +relationship: RO:0002202 CL:0000037 ! develops from hematopoietic stem cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000838 @@ -2116,7 +2116,7 @@ is_a: CL:0011026 ! progenitor cell intersection_of: CL:0002031 ! hematopoietic lineage restricted progenitor cell intersection_of: capable_of GO:0030099 ! myeloid cell differentiation relationship: capable_of GO:0030099 ! myeloid cell differentiation -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000842 @@ -2159,8 +2159,8 @@ def: "A lymphocyte of B lineage with the commitment to express an immunoglobulin comment: Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells). Lymphocytes of B cell lineage can be distinguished from those of T cell lineage by their lack of CD3e (as part of the T cell receptor complex). subset: human_reference_atlas is_a: CL:0000542 {is_inferred="true"} ! lymphocyte -relationship: develops_from CL:0000826 ! pro-B cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000826 ! develops from pro-B cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000946 @@ -2229,10 +2229,10 @@ intersection_of: RO:0015015 PR:000001408 ! has high plasma membrane amount ADP-r intersection_of: RO:0015015 PR:000001963 ! has high plasma membrane amount CD27 molecule relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-spanning 4-domains subfamily A member 1 relationship: CL:4030046 PR:000001935 ! lacks_plasma_membrane_part syndecan-1 -relationship: develops_from CL:0000785 ! mature B cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000785 ! develops from mature B cell relationship: RO:0015015 PR:000001408 ! has high plasma membrane amount ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 relationship: RO:0015015 PR:000001963 ! has high plasma membrane amount CD27 molecule +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000988 @@ -2266,8 +2266,8 @@ xref: FMA:84191 is_a: CL:0000451 {is_inferred="true"} ! dendritic cell intersection_of: CL:0000451 ! dendritic cell intersection_of: RO:0015015 PR:000001013 ! has high plasma membrane amount integrin alpha-X -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0015015 PR:000001013 ! has high plasma membrane amount integrin alpha-X +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0001012 @@ -2284,9 +2284,9 @@ subset: human_reference_atlas is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001474 ! bone element -relationship: dc-contributor https://orcid.org/0000-0001-9990-8331 relationship: part_of UBERON:0001474 ! bone element -relationship: present_in_taxon NCBITaxon:9606 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2011-11-16T04:28:16Z [Term] @@ -2320,7 +2320,7 @@ relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surfac relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:27Z [Term] @@ -2340,9 +2340,9 @@ relationship: capable_of GO:0001816 ! cytokine production relationship: capable_of GO:0045087 ! innate immune response relationship: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule relationship: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon -relationship: dc-contributor https://orcid.org/0000-0001-9990-8331 -relationship: present_in_taxon NCBITaxon:9606 -property_value: dcterms-date "2017-01-30T20:20:48Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 +property_value: http://purl.org/dc/terms/date "2017-01-30T20:20:48Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0001200 @@ -2352,12 +2352,12 @@ comment: Types of B lineage lymphocytes include B cells and antibody secreting c is_a: CL:0000945 ! lymphocyte of B lineage intersection_of: CL:0000945 ! lymphocyte of B lineage intersection_of: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon -intersection_of: in_taxon NCBITaxon:40674 ! Mammalia intersection_of: RO:0002104 PR:000001002 ! has plasma membrane part CD19 molecule +intersection_of: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia relationship: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon -relationship: dc-contributor https://orcid.org/0000-0001-9990-8331 -relationship: in_taxon NCBITaxon:40674 ! Mammalia relationship: RO:0002104 PR:000001002 ! has plasma membrane part CD19 molecule +relationship: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 [Term] id: CL:0001201 @@ -2372,9 +2372,9 @@ is_a: CL:0000236 ! B cell is_a: CL:0001200 ! lymphocyte of B lineage, CD19-positive intersection_of: CL:0001200 ! lymphocyte of B lineage, CD19-positive intersection_of: capable_of GO:0019724 ! B cell mediated immunity -intersection_of: in_taxon NCBITaxon:40674 ! Mammalia intersection_of: RO:0002104 PR:000001002 ! has plasma membrane part CD19 molecule -relationship: dc-contributor https://orcid.org/0000-0001-9990-8331 +intersection_of: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 [Term] id: CL:0002009 @@ -2390,8 +2390,8 @@ intersection_of: capable_of GO:0030224 ! monocyte differentiation intersection_of: capable_of GO:0043011 ! myeloid dendritic cell differentiation relationship: capable_of GO:0030224 ! monocyte differentiation relationship: capable_of GO:0043011 ! myeloid dendritic cell differentiation -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000557 ! granulocyte monocyte progenitor cell +relationship: RO:0002202 CL:0000557 ! develops from granulocyte monocyte progenitor cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-19T02:51:58Z [Term] @@ -2417,12 +2417,12 @@ relationship: capable_of GO:0030221 ! basophil differentiation relationship: capable_of GO:0060374 ! mast cell differentiation relationship: CL:4030046 PR:000007431 ! lacks_plasma_membrane_part high affinity immunoglobulin epsilon receptor subunit alpha relationship: CL:4030046 PR:000016401 ! lacks_plasma_membrane_part transmembrane emp24 domain-containing protein 1 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000557 ! granulocyte monocyte progenitor cell relationship: has_part PR:000005307 ! CCAAT/enhancer-binding protein alpha relationship: has_part PR:000007857 ! erythroid transcription factor relationship: has_part PR:000007858 ! endothelial transcription factor GATA-2 relationship: RO:0002104 PR:000001867 ! has plasma membrane part interleukin-5 receptor subunit alpha +relationship: RO:0002202 CL:0000557 ! develops from granulocyte monocyte progenitor cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-27T12:46:33Z [Term] @@ -2435,8 +2435,8 @@ intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001400 ! unipotent disjoint_from: CL:0002032 ! hematopoietic oligopotent progenitor cell relationship: bearer_of PATO:0001400 ! unipotent -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002032 ! hematopoietic oligopotent progenitor cell +relationship: RO:0002202 CL:0002032 ! develops from hematopoietic oligopotent progenitor cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:20Z [Term] @@ -2449,8 +2449,8 @@ is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001401 ! oligopotent relationship: bearer_of PATO:0001401 ! oligopotent -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000837 ! hematopoietic multipotent progenitor cell +relationship: RO:0002202 CL:0000837 ! develops from hematopoietic multipotent progenitor cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:27Z [Term] @@ -2460,9 +2460,9 @@ def: "An epithelial cell derived from ectoderm." [FMA:69074, GOC:tfm] xref: FMA:69074 is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell -intersection_of: develops_from CL:0000221 ! ectodermal cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000221 ! ectodermal cell +intersection_of: RO:0002202 CL:0000221 ! develops from ectodermal cell +relationship: RO:0002202 CL:0000221 ! develops from ectodermal cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T03:38:22Z [Term] @@ -2473,9 +2473,9 @@ synonym: "epithelial mesenchymal cell" EXACT [] xref: FMA:69076 is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell -intersection_of: develops_from CL:0000222 ! mesodermal cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000222 ! mesodermal cell +intersection_of: RO:0002202 CL:0000222 ! develops from mesodermal cell +relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T03:49:14Z [Term] @@ -2489,7 +2489,7 @@ is_a: CL:0000738 {is_inferred="true"} ! leukocyte intersection_of: CL:0000738 ! leukocyte intersection_of: CL:4030045 GO:0030141 ! lacks_part secretory granule relationship: CL:4030045 GO:0030141 ! lacks_part secretory granule -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-07-22T11:30:33Z [Term] @@ -2504,8 +2504,8 @@ xref: MESH:D001854 is_a: CL:0001035 {is_inferred="true"} ! bone cell intersection_of: CL:0001035 ! bone cell intersection_of: part_of UBERON:0002371 ! bone marrow -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002371 ! bone marrow +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-07-22T04:48:15Z [Term] @@ -2520,7 +2520,7 @@ xref: BTO:0001854 xref: CALOHA:TS-1106 xref: FMA:67755 is_a: CL:0000115 ! endothelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T02:06:40Z [Term] @@ -2533,7 +2533,7 @@ is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor ce intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: capable_of GO:0030851 ! granulocyte differentiation relationship: capable_of GO:0030851 ! granulocyte differentiation -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-30T12:54:27Z [Term] @@ -2545,7 +2545,7 @@ is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor ce intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: capable_of GO:0030224 ! monocyte differentiation relationship: capable_of GO:0030224 ! monocyte differentiation -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-30T01:27:48Z [Term] @@ -2557,7 +2557,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0002505 ! nucleated relationship: bearer_of PATO:0002505 ! nucleated -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T03:32:33Z [Term] @@ -2568,7 +2568,7 @@ is_a: CL:0000457 ! biogenic amine secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0001821 ! histamine secretion relationship: capable_of GO:0001821 ! histamine secretion -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T03:04:42Z [Term] @@ -2581,8 +2581,8 @@ xref: FMA:70333 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001016 ! nervous system -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001016 ! nervous system +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T01:34:57Z [Term] @@ -2596,8 +2596,8 @@ xref: MESH:D003239 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0002384 ! connective tissue -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002384 ! connective tissue +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T03:01:54Z [Term] @@ -2608,7 +2608,7 @@ xref: CALOHA:TS-0263 xref: FMA:82840 xref: WBbt:0007028 is_a: CL:0000000 ! cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T03:39:21Z [Term] @@ -2624,7 +2624,7 @@ is_a: CL:0000084 {is_inferred="true"} ! T cell intersection_of: CL:0000084 ! T cell intersection_of: CL:4030044 GO:0045058 ! has_not_completed T cell selection relationship: CL:4030044 GO:0045058 ! has_not_completed T cell selection -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-12T01:56:17Z [Term] @@ -2640,8 +2640,8 @@ xref: FMA:84791 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0007100 ! primary circulatory organ -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0007100 ! primary circulatory organ +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T09:37:22Z [Term] @@ -2650,7 +2650,7 @@ name: embryonic blood vessel endothelial progenitor cell def: "An endothelial progenitor cell that participates in angiogenesis during development." [GOC:tfm] comment: See CL:0002619. is_a: CL:0000222 ! mesodermal cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T04:20:39Z [Term] @@ -2678,9 +2678,9 @@ relationship: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon relationship: CL:4030046 PR:000001084 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD8 alpha chain relationship: CL:4030046 PR:000001874 ! lacks_plasma_membrane_part KLRB1-like protein relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0002104 PR:000002065 ! has plasma membrane part mast/stem cell growth factor receptor relationship: RO:0002104 PR:000002979 ! has plasma membrane part lymphocyte antigen 6A-2/6E-1 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-08-29T10:08:02Z [Term] @@ -2690,7 +2690,7 @@ def: "Cell that has the potential to form a skeletal cell type (e.g. cells in pe comment: Needs logical definition. Should be capable_of skeletal system morphogenesis? or skeletal tissue development? needs to be added to GO. NOTES:a cell type of the early embryo (see also: mesenchymal cells) that will give rise to mineralized connective tissue. Scleroblasts can differentiate into osteoblasts (bone-forming cells), chondroblasts (cartilage-forming cells), odontoblasts (dentin-forming cells), ameloblasts (enamel-forming cells). The mesenchymal cells developing into osteoblasts and chondroblasts are derived from the mesoderm. Those developing into odontoblasts are neural crest cells. Those developing into ameloblasts are derived from the ectoderm. (http://www.copewithcytokines.de/cope.cgi?key=scleroblasts) synonym: "scleroblast" EXACT [GO_REF:0000034] is_a: CL:0000000 ! cell -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-15T02:51:27Z [Term] @@ -2698,9 +2698,9 @@ id: CL:0007004 name: premigratory neural crest cell def: "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells." [UBERONREF:0000002] is_a: CL:0011012 ! neural crest cell -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 -relationship: develops_from CL:0000133 ! neurectodermal cell relationship: part_of UBERON:0002342 ! neural crest +relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-27T08:27:35Z [Term] @@ -2720,7 +2720,7 @@ synonym: "mesenchyme cell" EXACT [] is_a: CL:0000219 ! motile cell relationship: capable_of GO:0016477 ! cell migration relationship: part_of UBERON:0003104 ! mesenchyme -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0010017 @@ -2728,7 +2728,7 @@ name: zygote def: "A zygote in a plant or an animal." [] xref: MESH:D015053 is_a: CL:0000000 ! cell -relationship: seeAlso https://github.com/obophenotype/cell-ontology/issues/786 +property_value: seeAlso https://github.com/obophenotype/cell-ontology/issues/786 [Term] id: CL:0011012 @@ -2745,9 +2745,9 @@ def: "A precursor cell that has a tendency to differentiate into a specific type subset: cellxgene_subset is_a: CL:0011115 ! precursor cell intersection_of: CL:0011115 ! precursor cell -intersection_of: develops_from CL:0000034 ! stem cell -relationship: dc-contributor https://orcid.org/0000-0001-5208-3432 -relationship: develops_from CL:0000034 ! stem cell +intersection_of: RO:0002202 CL:0000034 ! develops from stem cell +relationship: RO:0002202 CL:0000034 ! develops from stem cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011115 @@ -2793,7 +2793,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0070046 ! neutrophillic relationship: bearer_of PATO:0070046 ! neutrophillic -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-05-25T01:36:34Z [Term] @@ -2805,7 +2805,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0002418 ! acidophilic relationship: bearer_of PATO:0002418 ! acidophilic -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-22T04:23:25Z [Term] @@ -2816,7 +2816,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0002094 ! basophilic relationship: bearer_of PATO:0002094 ! basophilic -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-22T04:24:54Z [Term] @@ -2827,7 +2827,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0070047 ! polychromatophilic relationship: bearer_of PATO:0070047 ! polychromatophilic -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-28T04:25:23Z [Term] @@ -2835,7 +2835,7 @@ id: CL:0017508 name: cartwheel heterochromatin def: "Heterochromatin that is arranged in a carthwheel pattern." [GOC:tfm] is_a: GO:0000792 ! heterochromatin -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-28T04:28:35Z [Term] @@ -2860,8 +2860,8 @@ is_a: CL:0000080 ! circulating cell is_a: CL:0000842 ! mononuclear cell intersection_of: CL:0000842 ! mononuclear cell intersection_of: part_of UBERON:0000178 ! blood -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0000178 ! blood +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-02-11T17:29:04Z [Term] @@ -2873,7 +2873,7 @@ is_a: CL:0000542 ! lymphocyte is_a: CL:2000001 ! peripheral blood mononuclear cell intersection_of: CL:0000542 ! lymphocyte intersection_of: part_of UBERON:0000178 ! blood -property_value: dcterms-date "2022-11-04T14:40:00Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2022-11-04T14:40:00Z" xsd:dateTime [Term] id: GO:0000278 @@ -2892,8 +2892,8 @@ is_a: GO:0007049 ! cell cycle intersection_of: GO:0007049 ! cell cycle intersection_of: has_part GO:0140014 ! mitotic nuclear division relationship: has_part GO:0140014 ! mitotic nuclear division -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota [Term] id: GO:0000280 @@ -2966,7 +2966,7 @@ namespace: biological_process def: "A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities." [GOC:dph, GOC:go_curators, GOC:tb, ISBN:978-0-07-139011-8] comment: Action potentials typically propagate across excitable membranes. This class covers both action potentials that propagate and those that fail to do so. is_a: GO:0042391 ! regulation of membrane potential -relationship: never_in_taxon NCBITaxon:4895 +property_value: RO:0002161 NCBITaxon:4895 [Term] id: GO:0001667 @@ -3063,8 +3063,8 @@ def: "A multicellular organismal process by which exposure to an activating fact subset: goslim_pir is_a: GO:0009987 ! cellular process is_a: GO:0032501 ! multicellular organismal process -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24416" xsd:anyURI [Term] @@ -3205,8 +3205,8 @@ synonym: "acquired immune response" EXACT [ISBN:068340007X] synonym: "immune memory response" EXACT [GOC:add] xref: Wikipedia:Adaptive_immune_system is_a: GO:0006955 ! immune response -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0002252 @@ -3325,7 +3325,7 @@ subset: goslim_mouse subset: goslim_pir xref: Wikipedia:Immune_system is_a: GO:0008150 ! biological_process -relationship: never_in_taxon NCBITaxon:4895 +property_value: RO:0002161 NCBITaxon:4895 [Term] id: GO:0002377 @@ -3398,9 +3398,9 @@ synonym: "leukocyte immune effector process" EXACT [] is_a: GO:0002252 ! immune effector process intersection_of: GO:0002376 ! immune system process intersection_of: process_has_causal_agent CL:0000738 ! leukocyte -relationship: in_taxon NCBITaxon:7742 {all_only="true"} ! Vertebrata -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: process_has_causal_agent CL:0000738 ! leukocyte +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 {all_only="true"} ! in taxon Vertebrata [Term] id: GO:0002449 @@ -3795,9 +3795,9 @@ def: "Any process that modulates the frequency, rate, or extent of an adaptive i is_a: GO:0002819 ! regulation of adaptive immune response intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0002460 ! adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains -relationship: in_taxon NCBITaxon:7776 {all_only="true"} ! Gnathostomata -relationship: only_in_taxon NCBITaxon:7776 ! Gnathostomata relationship: regulates GO:0002460 ! adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains +relationship: RO:0002160 NCBITaxon:7776 ! only in taxon Gnathostomata +relationship: RO:0002162 NCBITaxon:7776 {all_only="true"} ! in taxon Gnathostomata [Term] id: GO:0002824 @@ -3995,8 +3995,8 @@ namespace: cellular_component def: "A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures." [GOC:dos, GOC:mah, ISBN:0721639976, PMID:19693541, PMID:21421911] xref: Wikipedia:Collagen is_a: GO:0032991 ! protein-containing complex -relationship: in_taxon NCBITaxon:33208 {all_only="true", source="PMID:12382326"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 {source="PMID:12382326"} ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 {source="PMID:12382326"} ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true", source="PMID:12382326"} ! in taxon Metazoa [Term] id: GO:0005587 @@ -4077,8 +4077,8 @@ xref: NIF_Subcellular:sao1702920020 xref: Wikipedia:Cell_nucleus is_a: GO:0043231 ! intracellular membrane-bounded organelle disjoint_from: GO:0005737 ! cytoplasm -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota [Term] id: GO:0005694 @@ -4147,7 +4147,7 @@ subset: goslim_plant xref: NIF_Subcellular:sao585356902 xref: Wikipedia:Lysosome is_a: GO:0000323 ! lytic vacuole -relationship: never_in_taxon NCBITaxon:4751 +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0005766 @@ -4198,10 +4198,10 @@ synonym: "Golgi ribbon" NARROW [] xref: NIF_Subcellular:sao451912436 xref: Wikipedia:Golgi_apparatus is_a: GO:0043231 ! intracellular membrane-bounded organelle -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota relationship: part_of GO:0005737 ! cytoplasm relationship: part_of GO:0012505 ! endomembrane system +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota [Term] id: GO:0005840 @@ -4489,7 +4489,7 @@ namespace: biological_process def: "A vesicle-mediated transport process that results in the engulfment of external particulate material by phagocytes and their delivery to the lysosome. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles." [ISBN:0198506732] xref: Wikipedia:Phagocytosis is_a: GO:0006897 ! endocytosis -relationship: never_in_taxon NCBITaxon:4751 +property_value: RO:0002161 NCBITaxon:4751 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24907" xsd:anyURI [Term] @@ -4518,11 +4518,11 @@ synonym: "type I programmed cell death" NARROW [] xref: Wikipedia:Apoptosis is_a: GO:0012501 ! programmed cell death relationship: ends_with GO:0097194 ! execution phase of apoptosis -relationship: in_taxon NCBITaxon:33154 {all_only="true"} ! Opisthokonta -relationship: never_in_taxon NCBITaxon:2 -relationship: never_in_taxon NCBITaxon:4896 -relationship: only_in_taxon NCBITaxon:33154 ! Opisthokonta +relationship: RO:0002160 NCBITaxon:33154 ! only in taxon Opisthokonta +relationship: RO:0002162 NCBITaxon:33154 {all_only="true"} ! in taxon Opisthokonta relationship: starts_with GO:0097190 ! apoptotic signaling pathway +property_value: RO:0002161 NCBITaxon:2 +property_value: RO:0002161 NCBITaxon:4896 [Term] id: GO:0006921 @@ -4595,8 +4595,8 @@ subset: goslim_generic synonym: "inflammation" BROAD [] xref: Wikipedia:Inflammation is_a: GO:0006952 ! defense response -relationship: in_taxon NCBITaxon:7742 {all_only="true"} ! Vertebrata -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 {all_only="true"} ! in taxon Vertebrata [Term] id: GO:0006955 @@ -5033,8 +5033,8 @@ namespace: biological_process def: "The process whose specific outcome is the progression of an embryo over time, from zygote formation until the end of the embryonic life stage. The end of the embryonic life stage is organism-specific and may be somewhat arbitrary; for mammals it is usually considered to be birth, for insects the hatching of the first instar larva from the eggshell." [GOC:go_curators, GOC:isa_complete, GOC:mtg_sensu] synonym: "embryogenesis" BROAD [] is_a: GO:0009790 ! embryo development -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0009888 @@ -5047,14 +5047,14 @@ xref: Wikipedia:Histogenesis is_a: GO:0048856 ! anatomical structure development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0000479 ! tissue -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: never_in_taxon NCBITaxon:147554 -relationship: never_in_taxon NCBITaxon:33630 -relationship: never_in_taxon NCBITaxon:33682 -relationship: never_in_taxon NCBITaxon:38254 -relationship: never_in_taxon NCBITaxon:4891 -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota relationship: results_in_development_of UBERON:0000479 ! tissue +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota +property_value: RO:0002161 NCBITaxon:147554 +property_value: RO:0002161 NCBITaxon:33630 +property_value: RO:0002161 NCBITaxon:33682 +property_value: RO:0002161 NCBITaxon:38254 +property_value: RO:0002161 NCBITaxon:4891 [Term] id: GO:0009987 @@ -5301,7 +5301,7 @@ namespace: biological_process def: "The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues." [GOC:cjm, GOC:dph, GOC:ems, GOC:pf, Wikipedia:Cell_migration] xref: Wikipedia:Cell_migration is_a: GO:0048870 ! cell motility -relationship: never_in_taxon NCBITaxon:4890 +property_value: RO:0002161 NCBITaxon:4890 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24787" xsd:anyURI [Term] @@ -5573,7 +5573,7 @@ subset: goslim_drosophila subset: goslim_flybase_ribbon xref: Wikipedia:Cell_junction is_a: GO:0110165 ! cellular anatomical entity -relationship: never_in_taxon NCBITaxon:4751 +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0030097 @@ -5640,8 +5640,8 @@ def: "A small subcellular vesicle, surrounded by a membrane, that is formed from comment: Note that the term 'secretory vesicle' is sometimes used in this sense, but can also mean 'transport vesicle ; GO:0030133'. synonym: "secretory vesicle" BROAD [] is_a: GO:0099503 ! secretory vesicle -relationship: never_in_taxon NCBITaxon:4890 relationship: part_of GO:0012505 ! endomembrane system +property_value: RO:0002161 NCBITaxon:4890 [Term] id: GO:0030154 @@ -5843,8 +5843,8 @@ def: "Any process that modulates the frequency, rate or extent of cell migration is_a: GO:2000145 ! regulation of cell motility intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0016477 ! cell migration -relationship: never_in_taxon NCBITaxon:4890 relationship: regulates GO:0016477 ! cell migration +property_value: RO:0002161 NCBITaxon:4890 [Term] id: GO:0030335 @@ -6069,10 +6069,10 @@ subset: goslim_pir synonym: "organismal physiological process" EXACT [] synonym: "single-multicellular organism process" RELATED [] is_a: GO:0008150 ! biological_process -relationship: never_in_taxon NCBITaxon:2 -relationship: never_in_taxon NCBITaxon:2157 -relationship: never_in_taxon NCBITaxon:4896 -relationship: never_in_taxon NCBITaxon:4932 +property_value: RO:0002161 NCBITaxon:2 +property_value: RO:0002161 NCBITaxon:2157 +property_value: RO:0002161 NCBITaxon:4896 +property_value: RO:0002161 NCBITaxon:4932 created_by: jl creation_date: 2012-09-19T16:07:47Z @@ -6300,8 +6300,8 @@ subset: goslim_plant synonym: "growth pattern" RELATED [] synonym: "non-developmental growth" RELATED [GOC:mah] is_a: GO:0008150 ! biological_process -relationship: in_taxon NCBITaxon:131567 {all_only="true"} ! cellular organisms -relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms +relationship: RO:0002160 NCBITaxon:131567 ! only in taxon cellular organisms +relationship: RO:0002162 NCBITaxon:131567 {all_only="true"} ! in taxon cellular organisms [Term] id: GO:0040011 @@ -6311,7 +6311,7 @@ def: "Self-propelled movement of a cell or organism from one location to another subset: goslim_chembl subset: goslim_pir is_a: GO:0008150 ! biological_process -relationship: never_in_taxon NCBITaxon:451864 +property_value: RO:0002161 NCBITaxon:451864 [Term] id: GO:0040012 @@ -6452,8 +6452,8 @@ is_a: GO:0031099 ! regeneration is_a: GO:0048589 ! developmental growth intersection_of: GO:0031099 ! regeneration intersection_of: results_in_maturation_of UBERON:0000479 ! tissue -relationship: never_in_taxon NCBITaxon:4751 relationship: results_in_maturation_of UBERON:0000479 ! tissue +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0042330 @@ -6553,8 +6553,8 @@ name: chordate embryonic development namespace: biological_process def: "The process whose specific outcome is the progression of the embryo over time, from zygote formation through a stage including a notochord and neural tube until birth or egg hatching." [GOC:mtg_sensu] is_a: GO:0009792 ! embryo development ending in birth or egg hatching -relationship: in_taxon NCBITaxon:7711 {all_only="true"} ! Chordata -relationship: only_in_taxon NCBITaxon:7711 ! Chordata +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {all_only="true"} ! in taxon Chordata [Term] id: GO:0043011 @@ -6796,7 +6796,7 @@ synonym: "interspecies interaction" EXACT [] synonym: "interspecies interaction between organisms" EXACT [] synonym: "interspecies interaction with other organisms" EXACT [] is_a: GO:0008150 ! biological_process -relationship: never_in_taxon NCBITaxon:4895 +property_value: RO:0002161 NCBITaxon:4895 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20191" xsd:anyURI [Term] @@ -6854,8 +6854,8 @@ synonym: "synaptic junction" EXACT [] xref: NIF_Subcellular:sao914572699 xref: Wikipedia:Chemical_synapse is_a: GO:0030054 ! cell junction -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0045321 @@ -6870,8 +6870,8 @@ is_a: GO:0002376 ! immune system process intersection_of: GO:0001775 ! cell activation intersection_of: has_primary_input CL:0000738 ! leukocyte relationship: has_primary_input CL:0000738 ! leukocyte -relationship: in_taxon NCBITaxon:7742 {all_only="true"} ! Vertebrata -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 {all_only="true"} ! in taxon Vertebrata [Term] id: GO:0045453 @@ -7385,8 +7385,8 @@ is_a: GO:0003008 ! system process intersection_of: GO:0003008 ! system process intersection_of: has_participant UBERON:0001016 ! nervous system relationship: has_participant UBERON:0001016 ! nervous system -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13824" xsd:anyURI [Term] @@ -7426,9 +7426,9 @@ is_a: GO:0002376 ! immune system process is_a: GO:0016477 ! cell migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0000738 ! leukocyte -relationship: in_taxon NCBITaxon:7742 {all_only="true"} ! Vertebrata -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: results_in_movement_of CL:0000738 ! leukocyte +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 {all_only="true"} ! in taxon Vertebrata [Term] id: GO:0050920 @@ -7746,8 +7746,8 @@ name: collagen-containing extracellular matrix namespace: cellular_component def: "An extracellular matrix consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that provides not only essential physical scaffolding for the cellular constituents but can also initiate crucial biochemical and biomechanical cues required for tissue morphogenesis, differentiation and homeostasis. The components are secreted by cells in the vicinity and form a sheet underlying or overlying cells such as endothelial and epithelial cells." [GOC:BHF, GOC:rph, PMID:21123617] is_a: GO:0031012 ! extracellular matrix -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa created_by: dph creation_date: 2018-04-13T12:47:21Z @@ -8276,9 +8276,9 @@ subset: goslim_synapse is_a: GO:0007267 ! cell-cell signaling intersection_of: GO:0007267 ! cell-cell signaling intersection_of: occurs_in GO:0045202 ! synapse -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa relationship: occurs_in GO:0045202 ! synapse -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0099537 @@ -8579,18 +8579,16 @@ namespace: ncbi_taxonomy xref: GC_ID:1 xref: PMID:15371245 is_a: NCBITaxon:337687 ! Muroidea -property_value: has_rank NCBITaxon:family [Term] id: NCBITaxon:10088 name: Mus namespace: ncbi_taxonomy -synonym: "mice" EXACT OMO:0003003 [] +synonym: "mice" EXACT genbank_common_name [] synonym: "mouse" EXACT OMO:0003003 [] synonym: "Mus" EXACT scientific_name [] xref: GC_ID:1 is_a: NCBITaxon:39107 ! Murinae -property_value: has_rank NCBITaxon:genus [Term] id: NCBITaxon:10090 @@ -8601,7 +8599,6 @@ synonym: "house mouse" EXACT genbank_common_name [] synonym: "mouse" EXACT OMO:0003003 [] xref: GC_ID:1 is_a: NCBITaxon:862507 ! Mus -property_value: has_rank NCBITaxon:species [Term] id: NCBITaxon:117570 @@ -8609,7 +8606,6 @@ name: Teleostomi namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:7776 ! Gnathostomata -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:117571 @@ -8619,7 +8615,6 @@ alt_id: NCBITaxon:40673 synonym: "bony vertebrates" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:117570 ! Teleostomi -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:131567 @@ -8635,7 +8630,6 @@ name: Dipnotetrapodomorpha namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:8287 ! Sarcopterygii -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:1437010 @@ -8646,7 +8640,6 @@ xref: GC_ID:1 xref: PMID:11743200 xref: PMID:11791233 is_a: NCBITaxon:9347 ! Eutheria -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:1963758 @@ -8656,7 +8649,6 @@ synonym: "mice and others" EXACT genbank_common_name [] synonym: "Sciurognathi" RELATED in_part [] xref: GC_ID:1 is_a: NCBITaxon:9989 ! Rodentia -property_value: has_rank NCBITaxon:suborder [Term] id: NCBITaxon:2759 @@ -8673,7 +8665,6 @@ xref: GC_ID:1 xref: PMID:23020233 xref: PMID:30257078 is_a: NCBITaxon:131567 ! cellular organisms -property_value: has_rank NCBITaxon:superkingdom [Term] id: NCBITaxon:314146 @@ -8685,7 +8676,6 @@ xref: PMID:12082125 xref: PMID:12878460 xref: PMID:15522813 is_a: NCBITaxon:1437010 ! Boreoeutheria -property_value: has_rank NCBITaxon:superorder [Term] id: NCBITaxon:314147 @@ -8697,7 +8687,6 @@ xref: PMID:11214319 xref: PMID:12082125 xref: PMID:15522813 is_a: NCBITaxon:314146 ! Euarchontoglires -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:32523 @@ -8706,7 +8695,6 @@ namespace: ncbi_taxonomy synonym: "tetrapods" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:1338369 ! Dipnotetrapodomorpha -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:32524 @@ -8715,7 +8703,6 @@ namespace: ncbi_taxonomy synonym: "amniotes" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:32523 ! Tetrapoda -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:32525 @@ -8724,7 +8711,6 @@ namespace: ncbi_taxonomy synonym: "Theria" EXACT scientific_name [] xref: GC_ID:1 is_a: NCBITaxon:40674 ! Mammalia -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:33154 @@ -8734,7 +8720,6 @@ synonym: "Fungi/Metazoa group" RELATED synonym [] synonym: "opisthokonts" RELATED synonym [] xref: GC_ID:1 is_a: NCBITaxon:2759 ! Eukaryota -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:33208 @@ -8746,7 +8731,6 @@ synonym: "metazoans" EXACT genbank_common_name [] synonym: "multicellular animals" EXACT OMO:0003003 [] xref: GC_ID:1 is_a: NCBITaxon:33154 ! Opisthokonta -property_value: has_rank NCBITaxon:kingdom [Term] id: NCBITaxon:33213 @@ -8754,7 +8738,6 @@ name: Bilateria namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:6072 ! Eumetazoa -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:33511 @@ -8763,7 +8746,6 @@ namespace: ncbi_taxonomy synonym: "deuterostomes" EXACT OMO:0003003 [] xref: GC_ID:1 is_a: NCBITaxon:33213 ! Bilateria -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:337687 @@ -8773,7 +8755,6 @@ xref: GC_ID:1 xref: PMID:15019624 xref: PMID:15371245 is_a: NCBITaxon:1963758 ! Myomorpha -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:39107 @@ -8782,7 +8763,6 @@ namespace: ncbi_taxonomy alt_id: NCBITaxon:109679 xref: GC_ID:1 is_a: NCBITaxon:10066 ! Muridae -property_value: has_rank NCBITaxon:subfamily [Term] id: NCBITaxon:40674 @@ -8792,7 +8772,6 @@ synonym: "mammals" EXACT genbank_common_name [] synonym: "mammals" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:32524 ! Amniota -property_value: has_rank NCBITaxon:class [Term] id: NCBITaxon:6072 @@ -8800,7 +8779,6 @@ name: Eumetazoa namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:33208 ! Metazoa -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:7711 @@ -8810,7 +8788,6 @@ synonym: "chordates" EXACT genbank_common_name [] synonym: "chordates" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:33511 ! Deuterostomia -property_value: has_rank NCBITaxon:phylum [Term] id: NCBITaxon:7742 @@ -8821,7 +8798,6 @@ synonym: "vertebrates" EXACT genbank_common_name [] synonym: "vertebrates" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:89593 ! Craniata -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:7776 @@ -8831,7 +8807,6 @@ synonym: "Gnathostomata" EXACT scientific_name [] synonym: "jawed vertebrates" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:7742 ! Vertebrata -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:8287 @@ -8839,7 +8814,6 @@ name: Sarcopterygii namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:117571 ! Euteleostomi -property_value: has_rank NCBITaxon:superclass [Term] id: NCBITaxon:862507 @@ -8848,7 +8822,6 @@ namespace: ncbi_taxonomy synonym: "Mus" EXACT scientific_name [] xref: GC_ID:1 is_a: NCBITaxon:10088 ! Mus -property_value: has_rank NCBITaxon:subgenus [Term] id: NCBITaxon:89593 @@ -8857,7 +8830,6 @@ namespace: ncbi_taxonomy synonym: "Craniata" EXACT scientific_name [] xref: GC_ID:1 is_a: NCBITaxon:7711 ! Chordata -property_value: has_rank NCBITaxon:subphylum [Term] id: NCBITaxon:9347 @@ -8870,7 +8842,6 @@ synonym: "placentals" EXACT genbank_common_name [] synonym: "placentals" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:32525 ! Theria -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:9989 @@ -8880,7 +8851,6 @@ synonym: "rodent" EXACT genbank_common_name [] synonym: "rodents" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:314147 ! Glires -property_value: has_rank NCBITaxon:order [Term] id: PATO:0000001 @@ -8939,7 +8909,6 @@ subset: value_slim synonym: "ramified" EXACT [] synonym: "ramiform" EXACT [] is_a: PATO:0002009 ! branchiness -property_value: RO:0002604 PATO:0000414 [Term] id: PATO:0000411 @@ -9099,7 +9068,6 @@ def: "A quality inhering in a bearer by virtue of the bearer's lacking complete subset: value_slim synonym: "underdeveloped" RELATED [] is_a: PATO:0000261 ! maturity -property_value: RO:0002604 PATO:0001701 [Term] id: PATO:0001548 @@ -9129,7 +9097,6 @@ comment: This refers to the disposition of the bearer. subset: disposition_slim subset: value_slim is_a: PATO:0001579 ! contractility -property_value: RO:0002604 PATO:0001691 [Term] id: PATO:0001857 @@ -9139,7 +9106,6 @@ def: "A shape quality in a bearer by virtue of the bearer's curving inward." [Wo subset: cell_quality subset: value_slim is_a: PATO:0002005 ! concavity -property_value: RO:0002604 PATO:0001355 [Term] id: PATO:0001873 @@ -9227,7 +9193,6 @@ subset: attribute_slim xref: Image:http\://upload.wikimedia.org/wikipedia/commons/0/06/Convex_polygon_illustration1.png is_a: PATO:0002266 ! 3-D shape relationship: RO:0015011 PATO:0002006 ! has cross section 2-D shape -property_value: RO:0002604 PATO:0002008 [Term] id: PATO:0002009 @@ -9253,7 +9218,6 @@ namespace: quality def: "A concave quality inhering in a bearer by virtue of the bearer's curving inward on both sides or surfaces." [PATOC:GVG] subset: value_slim is_a: PATO:0001857 ! concave -property_value: RO:0002604 PATO:0002040 [Term] id: PATO:0002045 @@ -9265,7 +9229,7 @@ synonym: "dendriform" EXACT [] synonym: "dendroid" EXACT [] synonym: "dendroidal" EXACT [] is_a: PATO:0000402 ! branched -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-02-15T08:11:41Z [Term] @@ -9275,7 +9239,7 @@ namespace: quality def: "A quality inhering in a bearer by virtue of the bearer's having an empty space or cavity within." [url:http\://www.merriam-webster.com/dictionary/hollow] subset: value_slim is_a: PATO:0002014 ! structure, cavities -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-09-18T02:19:20Z [Term] @@ -9287,7 +9251,7 @@ subset: disposition_slim subset: mpath_slim subset: value_slim is_a: PATO:0070045 ! anatomical histological quality -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-10-05T12:05:23Z [Term] @@ -9297,7 +9261,7 @@ namespace: quality def: "A quality inhering in a bearer by virtue of its constitution." [PATOC:GVG] subset: attribute_slim is_a: PATO:0001018 ! physical quality -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-03-15T04:35:27Z [Term] @@ -9306,7 +9270,7 @@ name: 3-D shape namespace: quality def: "A shape that inheres in a 3 dimensional entity." [PATOC:OREGON] is_a: PATO:0000052 ! shape -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-10-05T12:31:16Z [Term] @@ -9319,7 +9283,7 @@ synonym: "tube-shaped" EXACT [] synonym: "tubulate" EXACT [] is_a: PATO:0001873 ! cylindrical is_a: PATO:0002078 ! hollow -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-06-08T06:33:50Z [Term] @@ -9329,7 +9293,7 @@ namespace: quality def: "A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt" [wiktionary:superellipse] synonym: "Lamé curve" EXACT [] is_a: PATO:0002006 ! 2-D shape -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-10-12T12:45:16Z [Term] @@ -9342,7 +9306,7 @@ subset: mpath_slim subset: value_slim synonym: "eosinophilic" EXACT [] is_a: PATO:0070045 ! anatomical histological quality -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2012-12-17T03:01:19Z [Term] @@ -9353,7 +9317,7 @@ def: "A nucleate quality inhering in a bearer by virtue of the bearer's having o subset: mpath_slim subset: value_slim is_a: PATO:0001404 ! nucleate quality -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2013-10-21T05:44:34Z [Term] @@ -9362,7 +9326,7 @@ name: disconnected namespace: quality def: "A structural quality inhering in the bearer by virtue of the bearer consisting of multiple structures lacking any physical connection to each other." [GOC:dos] is_a: PATO:0000141 ! structure -relationship: dc-contributor https://orcid.org/0000-0002-7073-9172 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2014-12-12T08:43:17Z [Term] @@ -9489,7 +9453,6 @@ synonym: "T200" BROAD [PRO:DNx] xref: IUPHARobj:1852 xref: PIRSF:PIRSF002004 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P08575 [Term] id: PR:000001012 @@ -9508,7 +9471,6 @@ synonym: "leukocyte adhesion receptor MO1" EXACT [] synonym: "neutrophil adherence receptor" EXACT [] xref: IUPHARobj:2452 is_a: PR:000001005 ! integrin alpha with A domain -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P11215 [Term] id: PR:000001013 @@ -9525,7 +9487,6 @@ synonym: "leukocyte adhesion glycoprotein p150,95 alpha chain" EXACT [] synonym: "leukocyte adhesion receptor p150,95" EXACT [] xref: IUPHARobj:2454 is_a: PR:000001005 ! integrin alpha with A domain -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P20702 [Term] id: PR:000001018 @@ -9581,7 +9542,6 @@ synonym: "NCAM-1" EXACT [] synonym: "NCAM1" EXACT PRO-short-label [PRO:DNx] xref: IUPHARobj:2769 is_a: PR:000001023 ! neural cell adhesion molecule NCAM -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P13591 [Term] id: PR:000001083 @@ -9618,7 +9578,6 @@ synonym: "MAL" RELATED Gene-based [] synonym: "T-cell surface glycoprotein Lyt-2" EXACT [] synonym: "T-lymphocyte differentiation antigen T8/Leu-2" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P01732 [Term] id: PR:000001094 @@ -9674,7 +9633,6 @@ synonym: "RANTES-R" EXACT [] synonym: "SCYAR1" RELATED Gene-based [] xref: IUPHARobj:58 is_a: PR:000001197 ! chemokine receptor CCR1/3/1L -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P32246 [Term] id: PR:000001255 @@ -9696,7 +9654,6 @@ synonym: "macrophage inflammatory protein 1-alpha receptor-like 2" EXACT [] synonym: "MIP-1 alpha RL2" EXACT [] xref: IUPHARobj:60 is_a: PR:000001197 ! chemokine receptor CCR1/3/1L -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P51677 [Term] id: PR:000001281 @@ -9779,7 +9736,6 @@ synonym: "CEACAM8" EXACT PRO-short-label [PRO:DNx] synonym: "CGM6" RELATED Gene-based [] synonym: "non-specific cross-reacting antigen NCA-95" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P31997 [Term] id: PR:000001343 @@ -9816,7 +9772,6 @@ synonym: "PDNP3" RELATED Gene-based [] synonym: "phosphodiesterase I beta" EXACT [] synonym: "phosphodiesterase I/nucleotide pyrophosphatase 3" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:O14638 [Term] id: PR:000001355 @@ -9855,7 +9810,6 @@ synonym: "NIM-R5 antigen" EXACT [] synonym: "T10" EXACT [] xref: IUPHARobj:2766 is_a: PR:000001281 ! ADP-ribosyl cyclase -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P28907 [Term] id: PR:000001444 @@ -9869,7 +9823,6 @@ synonym: "CDH5" EXACT PRO-short-label [PRO:DNx] synonym: "vascular endothelial cadherin" EXACT [] synonym: "VE-cadherin" EXACT [] is_a: PR:000001327 ! cadherin -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P33151 [Term] id: PR:000001479 @@ -9921,7 +9874,6 @@ synonym: "lymphocyte antigen 1" EXACT [] synonym: "lymphocyte antigen T1/Leu-1" EXACT [] synonym: "Lyt-1" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P06127 [Term] id: PR:000001850 @@ -9937,7 +9889,6 @@ synonym: "CTSO" RELATED Gene-based [] synonym: "CTSO2" RELATED Gene-based [] xref: IUPHARobj:2350 is_a: PR:000040662 ! cathepsin-like protease -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P43235 [Term] id: PR:000001861 @@ -9983,7 +9934,6 @@ synonym: "IL5RA" EXACT PRO-short-label [PRO:DNx] xref: IUPHARobj:1706 xref: PIRSF:PIRSF018419 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q01344 [Term] id: PR:000001869 @@ -10001,7 +9951,6 @@ synonym: "IL7R" EXACT PRO-short-label [PRO:DNx] xref: IUPHARobj:1698 xref: PIRSF:PIRSF001960 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P16871 [Term] id: PR:000001874 @@ -10029,7 +9978,6 @@ synonym: "sialophorin" EXACT [] synonym: "SPN" EXACT PRO-short-label [PRO:DNx] xref: PIRSF:PIRSF001994 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P16150 [Term] id: PR:000001889 @@ -10064,7 +10012,6 @@ synonym: "skin fibroblast elastase" EXACT [] xref: IUPHARobj:1611 xref: PIRSF:PIRSF501074 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P08473 [Term] id: PR:000001903 @@ -10077,7 +10024,6 @@ synonym: "BSAP" EXACT [] synonym: "Pax-5" RELATED Gene-based [] synonym: "PAX5" EXACT PRO-short-label [PRO:DNx] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q02548 [Term] id: PR:000001932 @@ -10096,7 +10042,6 @@ synonym: "R13-Ag" EXACT [] synonym: "small cell lung carcinoma cluster 4 antigen" EXACT [] synonym: "X62 heat stable antigen" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P25063 [Term] id: PR:000001935 @@ -10111,7 +10056,6 @@ synonym: "Synd-1" RELATED Gene-based [] synonym: "SYND1" EXACT [] xref: PIRSF:PIRSF015854 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P18827 [Term] id: PR:000001937 @@ -10128,7 +10072,6 @@ synonym: "TrATPase" EXACT [] synonym: "type 5 acid phosphatase" EXACT [] xref: PIRSF:PIRSF000898 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P13686 [Term] id: PR:000001944 @@ -10142,7 +10085,6 @@ synonym: "Sfpi-1" RELATED Gene-based [] synonym: "Sfpi1" RELATED Gene-based [] synonym: "SPI1" EXACT PRO-short-label [PRO:DNx] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P17947 [Term] id: PR:000001945 @@ -10159,7 +10101,6 @@ synonym: "TFRC" EXACT PRO-short-label [PRO:DNx] synonym: "TR" RELATED [] synonym: "Trfr" RELATED Gene-based [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P02786 [Term] id: PR:000001950 @@ -10193,7 +10134,6 @@ synonym: "TNFRSF11A" EXACT PRO-short-label [PRO:DNx] xref: IUPHARobj:1881 xref: PIRSF:PIRSF038806 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q9Y6Q6 [Term] id: PR:000001963 @@ -10226,7 +10166,6 @@ synonym: "UPAR" RELATED Gene-based [] synonym: "uPAR" EXACT [] xref: PIRSF:PIRSF002022 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q03405 [Term] id: PR:000001971 @@ -10255,7 +10194,6 @@ synonym: "proto-oncogene c-Fms" EXACT [] xref: IUPHARobj:1806 xref: PIRSF:PIRSF500947 is_a: PR:000001810 ! CSF-1/PDGF receptor-type tyrosine-protein kinase -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P07333 [Term] id: PR:000002065 @@ -10291,7 +10229,6 @@ synonym: "VEGFR-2" EXACT [] synonym: "VEGFR2" RELATED Gene-based [] xref: IUPHARobj:1813 is_a: PR:000001971 ! vascular endothelial growth factor receptor -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P35968 [Term] id: PR:000002976 @@ -10361,7 +10298,6 @@ synonym: "RAG1" EXACT PRO-short-label [PRO:DNx] synonym: "RING finger protein 74" EXACT [] synonym: "RNF74" RELATED Gene-based [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P15918 [Term] id: PR:000003460 @@ -10372,7 +10308,6 @@ comment: Category=gene. Requested by=CL. synonym: "RAG-2" EXACT [] synonym: "RAG2" EXACT PRO-short-label [PRO:DNx] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P55895 [Term] id: PR:000005178 @@ -10405,7 +10340,6 @@ synonym: "C/EBP alpha" EXACT [] synonym: "CEBP" RELATED Gene-based [] synonym: "CEBPA" EXACT PRO-short-label [PRO:DNx] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P49715 [Term] id: PR:000006169 @@ -10433,7 +10367,6 @@ synonym: "terminal addition enzyme" EXACT [] synonym: "terminal deoxynucleotidyltransferase" EXACT [] synonym: "terminal transferase" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P04053 [Term] id: PR:000007431 @@ -10448,7 +10381,6 @@ synonym: "FcERI" RELATED [] synonym: "IgE Fc receptor subunit alpha" EXACT [] xref: IUPHARobj:2933 is_a: PR:000001355 ! immunoglobulin gamma Fc receptor II/III/IV -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P12319 [Term] id: PR:000007597 @@ -10463,7 +10395,6 @@ synonym: "G0S7" RELATED Gene-based [] synonym: "proto-oncogene protein c-fos" EXACT [] synonym: "transcription factor AP-1 subunit c-Fos" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P01100 [Term] id: PR:000007857 @@ -10480,7 +10411,6 @@ synonym: "GF-1" RELATED [] synonym: "GF1" RELATED Gene-based [] synonym: "NF-E1 DNA-binding protein" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P15976 [Term] id: PR:000007858 @@ -10491,7 +10421,6 @@ comment: Category=gene. Requested by=CL. synonym: "GATA-binding protein 2" EXACT [] synonym: "GATA2" EXACT PRO-short-label [PRO:DNx] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P23769 [Term] id: PR:000009143 @@ -10505,7 +10434,6 @@ synonym: "ITGB7" EXACT PRO-short-label [PRO:DNx] synonym: "M290 IEL antigen" EXACT [] xref: IUPHARobj:2461 is_a: PR:000001861 ! integrin beta -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P26010 [Term] id: PR:000011178 @@ -10522,7 +10450,6 @@ synonym: "NFKB2" EXACT PRO-short-label [PRO:DNx] synonym: "nuclear factor of kappa light polypeptide gene enhancer in B-cells 2" EXACT [] synonym: "oncogene Lyt-10" EXACT [] is_a: PR:000001753 ! transcription factor NF-kappa-B subunit -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q00653 [Term] id: PR:000014841 @@ -10536,7 +10463,6 @@ synonym: "SHH" EXACT PRO-short-label [PRO:DNx] synonym: "Shh unprocessed N-terminal signaling and C-terminal autoprocessing domains" EXACT [] synonym: "ShhNC" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q15465 [Term] id: PR:000016043 @@ -10554,7 +10480,6 @@ synonym: "TAL-1" EXACT [] synonym: "TAL1" EXACT PRO-short-label [PRO:DNx] synonym: "TCL5" RELATED Gene-based [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P17542 [Term] id: PR:000016401 @@ -10570,7 +10495,6 @@ synonym: "p24gamma1" EXACT [] synonym: "putative T1/ST2 receptor-binding protein" EXACT [] synonym: "TMED1" EXACT PRO-short-label [PRO:DNx] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q13445 [Term] id: PR:000025796 @@ -10588,8 +10512,8 @@ def: "A protein that is encoded in the genome of Mus musculus." [PRO:DAN] synonym: "mouse protein" EXACT PRO-short-label [PRO:DAN] is_a: PR:000036194 ! eukaryotic protein intersection_of: PR:000000001 ! protein -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus -relationship: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus +relationship: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:000030035 @@ -10614,8 +10538,8 @@ def: "A protein that is encoded in the genome of some Eukaryota." [PRO:DAN] synonym: "Eukaryota protein" EXACT [PRO:DAN] is_a: PR:000000001 ! protein intersection_of: PR:000000001 ! protein -intersection_of: only_in_taxon NCBITaxon:2759 ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +intersection_of: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota [Term] id: PR:000040662 @@ -10626,7 +10550,7 @@ comment: Category=family. synonym: "cathepsin" NARROW [PRO:DAN] synonym: "fam:CTS" EXACT PRO-short-label [PRO:DNx] is_a: PR:000036194 ! eukaryotic protein -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa [Term] id: PR:000050567 @@ -10652,9 +10576,9 @@ subset: common_anatomy subset: upper_level xref: BFO:0000003 disjoint_from: UBERON:0001062 ! anatomical entity -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000025 @@ -10666,11 +10590,9 @@ synonym: "duct" NARROW [] xref: galen:Tube is_a: UBERON:0004111 ! anatomical conduit intersection_of: UBERON:0004111 ! anatomical conduit -intersection_of: has_quality PATO:0002299 ! tubular +intersection_of: RO:0000086 PATO:0002299 ! has quality tubular relationship: has_part UBERON:0013522 ! subdivision of tube -relationship: has_quality PATO:0002299 ! tubular -property_value: IAO:0000232 "not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts)" xsd:string -property_value: UBPROP:0000007 "tubular" xsd:string +relationship: RO:0000086 PATO:0002299 ! has quality tubular [Term] id: UBERON:0000055 @@ -10682,7 +10604,7 @@ subset: human_reference_atlas subset: pheno_slim is_a: UBERON:0004111 ! anatomical conduit relationship: channel_for UBERON:0006314 ! bodily fluid -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000060 @@ -10694,13 +10616,11 @@ subset: upper_level synonym: "organ wall" RELATED [FMA:82482] synonym: "wall" BROAD [] synonym: "wall of organ" EXACT [FMA:82482] -xref: EMAPA:25036 xref: FMA:82482 xref: galen:Wall is_a: UBERON:0000064 ! organ part relationship: adjacent_to UBERON:0002553 ! anatomical cavity relationship: has_part UBERON:0004923 ! organ component layer -property_value: UBPROP:0000012 "in FMA, serosa is a wall" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0000061 @@ -10717,7 +10637,6 @@ xref: BILA:0000003 xref: CARO:0000003 xref: EHDAA2:0003003 xref: EMAPA:0 -xref: FBbt:00007001 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:305751 xref: FMA:67135 xref: GAID:781 @@ -10732,10 +10651,10 @@ xref: VHOG:0001759 xref: XAO:0003000 xref: ZFA:0000037 is_a: UBERON:0000465 ! material anatomical entity -relationship: existence_ends_during_or_before UBERON:0000071 ! death stage -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0002497 UBERON:0000071 ! existence ends during or before death stage +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000062 @@ -10762,14 +10681,12 @@ xref: Wikipedia:Organ_(anatomy) is_a: UBERON:0010000 ! multicellular anatomical structure disjoint_from: UBERON:0034921 ! multi organ part structure relationship: capable_of GO:0008150 ! biological_process -relationship: has_boundary UBERON:0006984 ! anatomical surface -relationship: never_in_taxon NCBITaxon:110815 {source="Wikipedia"} relationship: part_of UBERON:0000467 ! anatomical system -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: UBPROP:0000001 "Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." xsd:string {source="GO:0048513"} -property_value: UBPROP:0000012 "CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4" xsd:string +relationship: RO:0002002 UBERON:0006984 ! has 2D boundary anatomical surface +property_value: RO:0002161 NCBITaxon:110815 {source="Wikipedia"} +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000064 @@ -10790,10 +10707,9 @@ xref: SCTID:113343008 xref: SCTID:91717005 is_a: UBERON:0010000 ! multicellular anatomical structure relationship: part_of UBERON:0000062 ! organ -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: IAO:0000232 "currently defined in a very broad sense, may be replaced by more specific classes in the future" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000066 @@ -10842,7 +10758,7 @@ is_a: UBERON:0000105 ! life cycle stage disjoint_from: UBERON:0000092 ! post-embryonic stage relationship: precedes UBERON:0000066 ! fully formed stage relationship: precedes UBERON:0000092 ! post-embryonic stage -relationship: simultaneous_with GO:0009790 ! embryo development +relationship: RO:0002082 GO:0009790 ! simultaneous with embryo development [Term] id: UBERON:0000071 @@ -10855,11 +10771,10 @@ xref: XAO:0000437 xref: XtroDO:0000085 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage -relationship: ends UBERON:0000104 ! life cycle -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: UBPROP:0000012 "ncit:Death is an outcome" xsd:string {external_ontology="ncit"} +relationship: RO:0002229 UBERON:0000104 ! ends life cycle +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000075 @@ -10876,9 +10791,9 @@ xref: NCIT:C34076 xref: SCTID:118966000 xref: UMLS:C1519343 {source="ncithesaurus:Skeletal_System_Part"} is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision -relationship: composed_primarily_of UBERON:0004765 ! skeletal element -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0001434 ! skeletal system +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002473 UBERON:0004765 ! composed primarily of skeletal element [Term] id: UBERON:0000092 @@ -10898,9 +10813,8 @@ xref: WBls:0000103 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage relationship: preceded_by UBERON:0000068 ! embryo stage -relationship: simultaneous_with GO:0009791 ! post-embryonic development +relationship: RO:0002082 GO:0009791 ! simultaneous with post-embryonic development property_value: seeAlso "https://github.com/obophenotype/uberon/issues/344" xsd:anyURI -property_value: UBPROP:0000008 "In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)" xsd:string [Term] id: UBERON:0000104 @@ -10922,9 +10836,9 @@ is_a: BFO:0000003 ! occurrent is_a: UBERON:0000000 ! processual entity relationship: ends_with UBERON:0000071 ! death stage relationship: has_part UBERON:0000105 ! life cycle stage -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 property_value: seeAlso "https://github.com/obophenotype/uberon/issues/532" xsd:anyURI [Term] @@ -10953,12 +10867,10 @@ xref: ZFS:0000000 xref: ZFS:0100000 is_a: UBERON:0000000 ! processual entity relationship: part_of UBERON:0000104 ! life cycle -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: editor_note "this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here" xsd:string -property_value: UBPROP:0000012 "the WBls class 'all stages' belongs here as it is the superclass of other WBls stages" xsd:string -property_value: UBPROP:0000012 "we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage" xsd:string +property_value: IAO:0000116 "this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000106 @@ -10978,7 +10890,6 @@ xref: BILS:0000106 xref: EFO:0001322 xref: EHDAA:27 xref: FBdv:00005288 -xref: IDOMAL:0000302 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C12601 xref: PdumDv:0000100 xref: VHOG:0000745 @@ -10988,9 +10899,8 @@ xref: ZFS:0000001 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage -relationship: seeAlso EMAPA:16033 -relationship: starts UBERON:0000104 ! life cycle -property_value: UBPROP:0000003 "As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000745", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107", source="http://bgee.unil.ch/"} +relationship: RO:0002223 UBERON:0000104 ! starts life cycle +property_value: seeAlso EMAPA:16033 [Term] id: UBERON:0000107 @@ -11013,10 +10923,10 @@ xref: ZFS:0000046 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage intersection_of: UBERON:0000105 ! life cycle stage -intersection_of: simultaneous_with GO:0040016 ! embryonic cleavage +intersection_of: RO:0002082 GO:0040016 ! simultaneous with embryonic cleavage relationship: immediately_preceded_by UBERON:0000106 ! zygote stage relationship: part_of UBERON:0000068 ! embryo stage -relationship: simultaneous_with GO:0040016 ! embryonic cleavage +relationship: RO:0002082 GO:0040016 ! simultaneous with embryonic cleavage [Term] id: UBERON:0000108 @@ -11040,8 +10950,8 @@ is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000107 ! cleavage stage -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI -property_value: editor_note "consider adding a preceding stage 'morula stage' as part of cleavage" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI +property_value: IAO:0000116 "consider adding a preceding stage 'morula stage' as part of cleavage" xsd:string [Term] id: UBERON:0000109 @@ -11068,10 +10978,10 @@ xref: XAO:1000005 xref: ZFS:0000047 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000108 {source="BILS"} ! blastula stage -relationship: simultaneous_with GO:0007369 ! gastrulation +relationship: RO:0002082 GO:0007369 ! simultaneous with gastrulation +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0000110 @@ -11085,14 +10995,12 @@ xref: MmusDv:0000017 xref: XAO:1000006 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000109 ! gastrula stage -relationship: simultaneous_with GO:0001841 ! neural tube formation -property_value: RO:0002174 NCBITaxon:7955 +relationship: RO:0002082 GO:0001841 ! simultaneous with neural tube formation +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa property_value: seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/343" xsd:anyURI -property_value: UBPROP:0000008 "In zebrafish, the times of neurulation and segmentation overlap so extensively there is no distinct neurula period of development, such as occurs largely before segmentation in amphibian embryos." xsd:string [Term] id: UBERON:0000111 @@ -11109,9 +11017,9 @@ xref: OGES:000032 xref: Wikipedia:Organogenesis is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000068 ! embryo stage -relationship: simultaneous_with GO:0048513 ! animal organ development +relationship: RO:0002082 GO:0048513 ! simultaneous with animal organ development +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa property_value: seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/533" xsd:anyURI @@ -11147,7 +11055,6 @@ xref: EFO:0000825 xref: EHDAA2:0001326 xref: EHDAA:542 xref: EMAPA:16262 -xref: FBbt:00003126 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:49184 xref: GAID:75 xref: galen:Mouth @@ -11168,19 +11075,11 @@ xref: Wikipedia:Mouth xref: XAO:0003029 xref: ZFA:0000547 xref: ZFA:0000590 -is_a: UBERON:0004921 {notes="the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts"} ! subdivision of digestive tract -intersection_of: UBERON:0004921 ! subdivision of digestive tract -intersection_of: proximalmost_part_of UBERON:0001555 ! digestive tract -relationship: develops_from UBERON:0035804 ! future mouth -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: proximalmost_part_of UBERON:0001555 ! digestive tract -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI +is_a: UBERON:0004921 ! subdivision of digestive tract +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002202 UBERON:0035804 ! develops from future mouth +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/661" xsd:anyURI -property_value: UBPROP:0000001 "Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010355", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000812", ontology="VHOG", source="DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "oral" xsd:string -property_value: UBPROP:0000011 "some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives" xsd:string -property_value: UBPROP:0000012 "in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0000178 @@ -11221,15 +11120,10 @@ is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000179 ! haemolymphatic fluid relationship: has_part CL:0000232 {source="CL:tm"} ! erythrocyte relationship: has_part UBERON:0001969 ! blood plasma -relationship: immediate_transformation_of UBERON:0006596 {source="Bgee:AN"} ! presumptive blood -relationship: located_in UBERON:0002049 {source="https://github.com/obophenotype/uberon/issues/1330"} ! vasculature relationship: part_of UBERON:0002390 ! hematopoietic system -relationship: present_in_taxon NCBITaxon:9606 -property_value: IAO:0000232 "This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid." xsd:string -property_value: UBPROP:0000001 "A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000007", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000046", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000002 "relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000046", ontology="AAO"} -property_value: UBPROP:0000003 "Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000224", ontology="VHOG", source="DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006) ", source="http://bgee.unil.ch/"} +relationship: RO:0001025 UBERON:0002049 {source="https://github.com/obophenotype/uberon/issues/1330"} ! located in vasculature +relationship: RO:0002495 UBERON:0006596 {source="Bgee:AN"} ! immediate transformation of presumptive blood +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000179 @@ -11242,9 +11136,9 @@ xref: CARO:0000081 is_a: UBERON:0006314 ! bodily fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: part_of UBERON:0002193 ! hemolymphoid system -relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0002193 ! hemolymphoid system +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 creation_date: 2009-04-08T04:38:19Z [Term] @@ -11264,11 +11158,11 @@ xref: OGEM:000006 xref: Wikipedia:Blastula is_a: UBERON:0000922 ! embryo intersection_of: UBERON:0000468 ! multicellular organism -intersection_of: existence_starts_and_ends_during UBERON:0000108 ! blastula stage -relationship: develops_from UBERON:0007010 ! cleaving embryo -relationship: existence_starts_and_ends_during UBERON:0000108 ! blastula stage -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI -property_value: editor_note "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" xsd:string +intersection_of: RO:0002491 UBERON:0000108 ! existence starts and ends during blastula stage +relationship: RO:0002202 UBERON:0007010 ! develops from cleaving embryo +relationship: RO:0002491 UBERON:0000108 ! existence starts and ends during blastula stage +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI +property_value: IAO:0000116 "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" xsd:string [Term] id: UBERON:0000383 @@ -11291,7 +11185,6 @@ xref: BILA:0000088 xref: BTO:0001369 xref: BTO:0001485 xref: EFO:0000801 -xref: EMAPA:35578 xref: FMA:72954 xref: MA:0002888 xref: MAT:0000025 @@ -11300,15 +11193,13 @@ xref: VSAO:0000033 xref: XAO:0004042 is_a: UBERON:0011216 ! organ system subdivision intersection_of: UBERON:0011216 ! organ system subdivision -intersection_of: composed_primarily_of UBERON:0001015 ! musculature +intersection_of: RO:0002473 UBERON:0001015 ! composed primarily of musculature relationship: capable_of GO:0003012 ! muscle system process -relationship: composed_primarily_of UBERON:0001015 ! musculature -relationship: never_in_taxon NCBITaxon:6040 -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: present_in_taxon NCBITaxon:9606 -property_value: editor_note "consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77" xsd:string -property_value: UBPROP:0000001 "Anatomical system that consists of the muscles of the body.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000033", ontology="VSAO", source="VSAO:curator"} -property_value: UBPROP:0000012 "we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA" xsd:string {external_ontology="MA"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002473 UBERON:0001015 ! composed primarily of musculature +property_value: IAO:0000116 "consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77" xsd:string +property_value: RO:0002161 NCBITaxon:6040 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000463 @@ -11330,7 +11221,6 @@ xref: CALOHA:TS-2101 xref: CARO:0000004 xref: EHDAA2:0003004 xref: EMAPA:35178 -xref: FBbt:00007019 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9669 xref: galen:BodySubstance xref: HAO:0000004 @@ -11343,11 +11233,11 @@ xref: VHOG:0001726 xref: XAO:0004001 xref: ZFA:0001487 is_a: UBERON:0000465 ! material anatomical entity -relationship: has_quality PATO:0002198 ! quality of a substance -relationship: part_of UBERON:0000468 {notes="this relationship may be too strong and may be weakened in future"} ! multicellular organism -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: part_of UBERON:0000468 ! multicellular organism +relationship: RO:0000086 PATO:0002198 ! has quality quality of a substance +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000464 @@ -11365,7 +11255,6 @@ xref: AEO:0000005 xref: BILA:0000005 xref: CARO:0000005 xref: EHDAA2:0003005 -xref: FBbt:00007017 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:5897 xref: HAO:0000005 xref: NCIT:C94478 @@ -11376,10 +11265,10 @@ xref: VHOG:0001728 xref: XAO:0003190 xref: ZFA:0001643 is_a: UBERON:0000466 ! immaterial anatomical entity -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -relationship: surrounded_by UBERON:0000061 ! anatomical structure +relationship: RO:0002219 UBERON:0000061 ! surrounded by anatomical structure +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000465 @@ -11393,7 +11282,6 @@ xref: AEO:0000006 xref: BILA:0000006 xref: CARO:0000006 xref: EHDAA2:0003006 -xref: FBbt:00007016 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67165 xref: HAO:0000006 xref: TAO:0001836 @@ -11402,9 +11290,9 @@ xref: VHOG:0001721 is_a: BFO:0000040 ! material entity is_a: UBERON:0001062 ! anatomical entity disjoint_from: UBERON:0000466 ! immaterial anatomical entity -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000466 @@ -11419,7 +11307,6 @@ xref: AEO:0000007 xref: BILA:0000007 xref: CARO:0000007 xref: EHDAA2:0003007 -xref: FBbt:00007015 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67112 xref: HAO:0000007 xref: TAO:0001835 @@ -11427,9 +11314,9 @@ xref: TGMA:0001827 xref: VHOG:0001727 is_a: BFO:0000141 ! immaterial entity is_a: UBERON:0001062 ! anatomical entity -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000467 @@ -11457,11 +11344,9 @@ xref: EHDAA2:0003011 xref: EHDAA:392 xref: EMAPA:16103 xref: EV:0100000 -xref: FBbt:00004856 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7149 xref: galen:AnatomicalSystem xref: HAO:0000011 -xref: IDOMAL:0002460 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: MA:0000003 xref: NCIT:C12919 xref: SCTID:278195005 @@ -11477,11 +11362,11 @@ xref: ZFA:0001439 is_a: UBERON:0000061 ! anatomical structure relationship: has_part UBERON:0000062 ! organ relationship: part_of UBERON:0000468 ! multicellular organism -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -relationship: present_in_taxon NCBITaxon:9606 -relationship: seeAlso EHDAA2:0001330 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:9606 +property_value: seeAlso EHDAA2:0001330 [Term] id: UBERON:0000468 @@ -11512,7 +11397,6 @@ xref: EHDAA2:0003191 xref: EHDAA:1 xref: EMAPA:25765 xref: EV:0100016 -xref: FBbt:00000001 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:256135 xref: galen:Organism xref: HAO:0000012 @@ -11528,11 +11412,10 @@ xref: Wikipedia:Multi-cellular_organism xref: XAO:0003004 xref: ZFA:0001094 is_a: UBERON:0010000 ! multicellular anatomical structure -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: editor_note "TODO - split body and mc organism? body continues after death stage" xsd:string -property_value: UBPROP:0000007 "organismal" xsd:string +property_value: IAO:0000116 "TODO - split body and mc organism? body continues after death stage" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000475 @@ -11557,7 +11440,6 @@ xref: CARO:0000032 xref: EFO:0000808 xref: EHDAA2:0003032 xref: EMAPA:36031 -xref: FBbt:00007009 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7153 xref: galen:BodyPart xref: HAO:0000032 @@ -11575,10 +11457,10 @@ xref: XAO:0003013 xref: ZFA:0001308 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure relationship: part_of UBERON:0000468 ! multicellular organism -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: editor_note "Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency" xsd:string +property_value: IAO:0000116 "Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000476 @@ -11593,7 +11475,6 @@ xref: AEO:0000040 xref: BILA:0000040 xref: CARO:0000040 xref: EHDAA2:0003040 -xref: FBbt:00007013 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:63863 xref: HAO:0000040 xref: TAO:0000382 @@ -11602,9 +11483,9 @@ xref: XAO:0003162 xref: ZFA:0000382 is_a: UBERON:0000061 ! anatomical structure disjoint_from: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000477 @@ -11613,12 +11494,11 @@ namespace: uberon def: "Anatomical group whose component anatomical structures lie in close proximity to each other." [FBbt:00007277] subset: common_anatomy subset: upper_level -xref: FBbt:00007277 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: VHOG:0001737 is_a: UBERON:0034923 ! disconnected anatomical group -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000479 @@ -11640,7 +11520,6 @@ xref: CALOHA:TS-2090 xref: CARO:0000043 xref: EHDAA2:0003043 xref: EMAPA:35868 -xref: FBbt:00007003 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9637 xref: galen:Tissue xref: HAO:0000043 @@ -11657,10 +11536,10 @@ xref: ZFA:0001477 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure relationship: has_part GO:0031012 ! extracellular matrix relationship: part_of UBERON:0000468 ! multicellular organism -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: editor_note "changed label and definition to reflect CARO2" xsd:string +property_value: IAO:0000116 "changed label and definition to reflect CARO2" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000481 @@ -11675,7 +11554,6 @@ xref: AEO:0000055 xref: BILA:0000055 xref: CARO:0000055 xref: EHDAA2:0003055 -xref: FBbt:00007010 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: HAO:0000055 xref: TAO:0001488 xref: TGMA:0001847 @@ -11684,9 +11562,9 @@ xref: XAO:0003037 xref: ZFA:0001488 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure relationship: has_part UBERON:0000479 ! tissue -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000483 @@ -11708,7 +11586,6 @@ xref: CALOHA:TS-0288 xref: CARO:0000066 xref: EHDAA2:0003066 xref: EMAPA:32738 -xref: FBbt:00007005 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9639 xref: GAID:402 xref: HAO:0000066 @@ -11725,14 +11602,12 @@ xref: ZFA:0001486 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue -intersection_of: composed_primarily_of CL:0000066 ! epithelial cell -relationship: composed_primarily_of CL:0000066 ! epithelial cell +intersection_of: RO:0002473 CL:0000066 ! composed primarily of epithelial cell relationship: has_part GO:0005911 ! cell-cell junction relationship: has_part UBERON:0005769 ! basement membrane of epithelium -relationship: only_in_taxon NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! Metazoa -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI -property_value: UBPROP:0000003 "The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000387", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.59", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "epithelial" xsd:string +relationship: RO:0002160 NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! only in taxon Metazoa +relationship: RO:0002473 CL:0000066 ! composed primarily of epithelial cell +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI [Term] id: UBERON:0000487 @@ -11761,8 +11636,7 @@ is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0006914 ! squamous epithelium intersection_of: UBERON:0000490 ! unilaminar epithelium intersection_of: has_part CL:0000076 ! squamous epithelial cell -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Unilaminar epithelium that consists of a single layer of squamous cells.[CARO]" xsd:string {date_retrieved="2012-06-20", external_class="CARO:0000070", ontology="CARO", source="FMA:45565", source="http://orcid.org/0000-0001-9114-8737"} +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI [Term] id: UBERON:0000490 @@ -11787,8 +11661,7 @@ xref: UMLS:C0682574 {source="ncithesaurus:Simple_Epithelium"} xref: XAO:0004007 xref: ZFA:0001495 is_a: UBERON:0000483 ! epithelium -property_value: editor_note "consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable" xsd:string -property_value: UBPROP:0000001 "Epithelium that consists of a single layer of epithelial cells.[CARO]" xsd:string {date_retrieved="2012-06-20", external_class="CARO:0000073", ontology="CARO", source="FMA:45561", source="http://orcid.org/0000-0001-9114-8737"} +property_value: IAO:0000116 "consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable" xsd:string [Term] id: UBERON:0000915 @@ -11808,12 +11681,8 @@ xref: Wikipedia:Thorax is_a: UBERON:0009569 {source="FMA"} ! subdivision of trunk is_a: UBERON:0011676 ! subdivision of organism along main body axis intersection_of: UBERON:0011676 ! subdivision of organism along main body axis -intersection_of: has_skeleton UBERON:0014477 ! thoracic skeleton -relationship: has_skeleton UBERON:0014477 ! thoracic skeleton -property_value: IAO:0000232 "note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest" xsd:string -property_value: RO:0002171 UBERON:0000026 -property_value: RO:0002171 UBERON:0000033 -property_value: RO:0002171 UBERON:0002417 +intersection_of: RO:0002551 UBERON:0014477 ! has skeleton thoracic skeleton +relationship: RO:0002551 UBERON:0014477 ! has skeleton thoracic skeleton [Term] id: UBERON:0000922 @@ -11838,11 +11707,9 @@ xref: EHDAA2:0000002 xref: EHDAA2_RETIRED:0003236 xref: EHDAA:38 xref: EMAPA:16039 -xref: FBbt:00000052 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69068 xref: GAID:963 xref: http://neurolex.org/wiki/Category\:Embryonic_organism -xref: IDOMAL:0000646 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: MAT:0000226 xref: MESH:D004622 xref: MIAA:0000019 @@ -11856,14 +11723,12 @@ xref: XAO:0000113 xref: ZFA:0000103 is_a: UBERON:0000468 ! multicellular organism intersection_of: UBERON:0000468 ! multicellular organism -intersection_of: existence_ends_with UBERON:0000068 ! embryo stage -intersection_of: existence_starts_with UBERON:0000068 ! embryo stage -relationship: existence_ends_with UBERON:0000068 ! embryo stage -relationship: existence_starts_with UBERON:0000068 ! embryo stage -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" xsd:anyURI +intersection_of: RO:0002489 UBERON:0000068 ! existence starts with embryo stage +intersection_of: RO:0002493 UBERON:0000068 ! existence ends with embryo stage +relationship: RO:0002489 UBERON:0000068 ! existence starts with embryo stage +relationship: RO:0002493 UBERON:0000068 ! existence ends with embryo stage +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/503" xsd:anyURI -property_value: UBPROP:0000007 "embryonic" xsd:string -property_value: UBPROP:0000012 "Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo" xsd:string {external_ontology="ZFA"} [Term] id: UBERON:0000923 @@ -11882,7 +11747,6 @@ xref: AAO:0000480 xref: BILA:0000035 xref: BTO:0000556 xref: EMAPA:36033 -xref: FBbt:00000110 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69069 xref: GAID:1303 xref: MESH:D005855 @@ -11896,8 +11760,7 @@ xref: Wikipedia:Germ_layer xref: XAO:0003011 xref: ZFA:0001122 is_a: UBERON:0010316 ! germ layer / neural crest -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001223", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0000924 @@ -11917,7 +11780,6 @@ xref: EFO:0000414 xref: EHDAA2:0000428 xref: EMAPA:16069 xref: EV:0100003 -xref: FBbt:00000111 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69070 xref: GAID:1304 xref: MAT:0000155 @@ -11934,11 +11796,8 @@ xref: XAO:0000001 xref: ZFA:0000016 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000221 ! ectodermal cell -relationship: immediate_transformation_of UBERON:0006601 {source="Bgee:AN"} ! presumptive ectoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png" xsd:anyURI -property_value: UBPROP:0000001 "Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000137", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000153", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "ectodermal" xsd:string +relationship: RO:0002495 UBERON:0006601 {source="Bgee:AN"} ! immediate transformation of presumptive ectoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png" xsd:anyURI [Term] id: UBERON:0000925 @@ -11958,7 +11817,6 @@ xref: EFO:0002545 xref: EHDAA2:0000436 xref: EMAPA:16062 xref: EV:0100005 -xref: FBbt:00000125 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69071 xref: GAID:1305 xref: MAT:0000175 @@ -11974,11 +11832,9 @@ xref: XAO:0000090 xref: ZFA:0000017 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000223 ! endodermal cell -relationship: immediate_transformation_of UBERON:0006595 {source="Bgee:AN"} ! presumptive endoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png" xsd:anyURI -property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000154", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "endodermal" xsd:string +relationship: RO:0002495 UBERON:0006595 {source="Bgee:AN"} ! immediate transformation of presumptive endoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png" xsd:anyURI [Term] id: UBERON:0000926 @@ -12004,7 +11860,6 @@ xref: EHDAA:160 xref: EHDAA:183 xref: EMAPA:16083 xref: EV:0100006 -xref: FBbt:00000126 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69072 xref: GAID:522 xref: MAT:0000174 @@ -12018,15 +11873,11 @@ xref: VHOG:0000152 xref: Wikipedia:Mesoderm xref: XAO:0000050 xref: ZFA:0000041 -is_a: UBERON:0000923 {notes="sometimes not considered primary"} ! germ layer +is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000222 ! mesodermal cell -relationship: immediate_transformation_of UBERON:0006603 {source="Bgee:AN"} ! presumptive mesoderm -relationship: never_in_taxon NCBITaxon:6040 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" xsd:anyURI -property_value: UBPROP:0000001 "Primary germ layer that is the middle of the embryonic germ layers.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000304", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000152", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "mesodermal" xsd:string -property_value: UBPROP:0000008 "sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates" xsd:string {source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} +relationship: RO:0002495 UBERON:0006603 {source="Bgee:AN"} ! immediate transformation of presumptive mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" xsd:anyURI +property_value: RO:0002161 NCBITaxon:6040 [Term] id: UBERON:0000930 @@ -12048,7 +11899,6 @@ synonym: "stomodeal-hypophyseal primordium" BROAD [XAO:0000269] xref: BTO:0004224 xref: EHDAA2:0001929 xref: EMAPA:16263 -xref: FBbt:00000439 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:295846 xref: NCIT:C34306 xref: TAO:0001290 @@ -12058,15 +11908,11 @@ xref: Wikipedia:Stomodeum xref: XAO:0000269 xref: ZFA:0001290 is_a: UBERON:0013522 ! subdivision of tube -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000924 ! ectoderm relationship: part_of UBERON:0035804 ! future mouth -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI -property_value: editor_note "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" xsd:string -property_value: UBPROP:0000001 "Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001290", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx" xsd:string {source="MP:0012522", taxon="NCBITaxon:40674"} -property_value: UBPROP:0000007 "stomodeal" xsd:string -property_value: UBPROP:0000008 "This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity." xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI +property_value: IAO:0000116 "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" xsd:string [Term] id: UBERON:0000948 @@ -12115,22 +11961,17 @@ is_a: UBERON:0007100 ! primary circulatory organ is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0007100 ! primary circulatory organ intersection_of: has_part UBERON:0004151 ! cardiac chamber -relationship: contributes_to_morphology_of UBERON:0004535 ! cardiovascular system -relationship: develops_from UBERON:0004141 ! heart tube relationship: has_part UBERON:0004151 ! cardiac chamber -relationship: never_in_taxon NCBITaxon:6239 -relationship: never_in_taxon NCBITaxon:7227 -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0015410 {source="MA"} ! heart plus pericardium -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI -property_value: UBPROP:0000001 "Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000114", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010210", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000002 "relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010210", ontology="AAO"} -property_value: UBPROP:0000003 "As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000276", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "cardiac" xsd:string +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002202 UBERON:0004141 ! develops from heart tube +relationship: RO:0002433 UBERON:0004535 ! contributes to morphology of cardiovascular system +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI +property_value: RO:0002161 NCBITaxon:6239 +property_value: RO:0002161 NCBITaxon:7227 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000982 @@ -12170,10 +12011,8 @@ xref: XAO:0000171 xref: ZFA:0001596 is_a: UBERON:0004905 ! articulation disjoint_from: UBERON:0001474 ! bone element -relationship: connects UBERON:0004765 ! skeletal element -relationship: contributes_to_morphology_of UBERON:0001434 ! skeletal system -property_value: UBPROP:0000001 "Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000101", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000367", ontology="TAO", source="TAO:pem"} +relationship: RO:0002176 UBERON:0004765 ! connects skeletal element +relationship: RO:0002433 UBERON:0001434 ! contributes to morphology of skeletal system [Term] id: UBERON:0001007 @@ -12194,8 +12033,6 @@ xref: BILA:0000082 xref: BTO:0000058 xref: CALOHA:TS-1293 xref: EFO:0000793 -xref: EV:0100056 -xref: FBbt:00005055 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7152 xref: GAID:278 xref: galen:DigestiveSystem @@ -12221,11 +12058,8 @@ disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system relationship: capable_of GO:0022600 ! digestive system process -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000129", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000007 "digestive" xsd:string -property_value: UBPROP:0000012 "many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class" xsd:string {external_ontology="MA"} +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001009 @@ -12237,7 +12071,6 @@ subset: uberon_slim synonym: "systema cardiovasculare" RELATED OMO:0003011 [Wikipedia:Circulatory_system] xref: AAO:0000959 xref: CALOHA:TS-2103 -xref: MESH:D002319 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: VHOG:0001248 xref: Wikipedia:Circulatory_system is_a: UBERON:0000467 ! anatomical system @@ -12247,17 +12080,13 @@ disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system relationship: capable_of GO:0003013 ! circulatory system process -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} -relationship: never_in_taxon NCBITaxon:6073 -relationship: never_in_taxon NCBITaxon:6157 -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI -property_value: IAO:0000232 "the cardiovascular system and the lymphatic system are parts of the circulatory system" xsd:string -property_value: RO:0002174 NCBITaxon:6231 {notes="WBbt coelomocyte currently classified as circulating cell"} -property_value: UBPROP:0000001 "Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000959", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001248", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.493", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} +property_value: RO:0002161 NCBITaxon:6073 +property_value: RO:0002161 NCBITaxon:6157 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001015 @@ -12277,10 +12106,8 @@ synonym: "musculature system" RELATED [] synonym: "musculi" EXACT OMO:0003011 [FMA:32558, FMA:TA] synonym: "set of muscles" EXACT [FMA:32558] synonym: "set of skeletal muscles" EXACT [MA:0000165] -xref: AAO:0011066 xref: BTO:0000887 xref: EFO:0001949 -xref: EMAPA:32715 xref: EMAPA:35577 xref: FMA:32558 xref: MA:0000165 @@ -12292,11 +12119,9 @@ xref: WBbt:0005737 xref: Wikipedia:Muscular_system xref: ZFA:0000548 is_a: UBERON:0011216 ! organ system subdivision -relationship: composed_primarily_of UBERON:0001630 ! muscle organ relationship: part_of UBERON:0000383 ! musculature of body -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png" xsd:anyURI -property_value: RO:0002171 UBERON:0001474 -property_value: UBPROP:0000012 "In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here." xsd:string {external_ontology="FMA"} +relationship: RO:0002473 UBERON:0001630 ! composed primarily of muscle organ +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png" xsd:anyURI [Term] id: UBERON:0001016 @@ -12322,7 +12147,6 @@ xref: EHDAA2:0001246 xref: EHDAA:826 xref: EMAPA:16469 xref: EV:0100162 -xref: FBbt:00005093 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7157 xref: GAID:466 xref: MA:0000016 @@ -12345,20 +12169,15 @@ disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system relationship: capable_of GO:0050877 ! nervous system process -relationship: composed_primarily_of CL:0002319 ! neural cell -relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: has_part CL:0000540 ! neuron -relationship: immediate_transformation_of UBERON:0016880 {source="Bgee:AN"} ! future nervous system -relationship: never_in_taxon NCBITaxon:6040 -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI -property_value: UBPROP:0000001 "A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000396", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000324", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000402", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.117", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "nervous" xsd:string -property_value: UBPROP:0000007 "neural" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002473 CL:0002319 ! composed primarily of neural cell +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +relationship: RO:0002495 UBERON:0016880 {source="Bgee:AN"} ! immediate transformation of future nervous system +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI +property_value: RO:0002161 NCBITaxon:6040 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001017 @@ -12387,7 +12206,6 @@ xref: EHDAA:828 xref: EMAPA:16470 xref: EMAPA:16754 xref: EV:0100163 -xref: FBbt:00005094 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:55675 xref: GAID:570 xref: MA:0000167 @@ -12404,15 +12222,11 @@ xref: XAO:0000215 xref: ZFA:0000012 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0011216 {source="FBbt", source="cjm"} ! organ system subdivision -relationship: immediate_transformation_of UBERON:0016879 {source="Bgee:AN"} ! future central nervous system -relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0001016 ! nervous system -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "Part of the nervous system which includes the brain and spinal cord.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000090", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "The brain and spinal cord. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000012", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO)." xsd:string {source="BIRNLEX:1099"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000293", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 (reference 1), ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 (reference 2), DOI:10.1016/j.cell.2007.02.040 Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud'homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007) (reference 3)", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002495 UBERON:0016879 {source="Bgee:AN"} ! immediate transformation of future central nervous system +property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001048 @@ -12431,7 +12245,6 @@ xref: AEO:0000171 xref: BTO:0001886 xref: EFO:0001652 xref: EHDAA2:0003171 -xref: FBbt:00005495 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:86589 xref: MAT:0000482 xref: NCIT:C34275 @@ -12463,7 +12276,6 @@ xref: EMAPA:16164 xref: EMAPA:16757 xref: FMA:293882 xref: MAT:0000069 -xref: MESH:D054259 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: MIAA:0000069 xref: NCIT:C34226 xref: neuronames:1365 @@ -12478,12 +12290,8 @@ is_a: UBERON:0003914 {source="EHDAA2"} ! epithelial tube is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0016879 ! future central nervous system -relationship: develops_from UBERON:0005068 ! neural rod -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010617", ontology="AAO", source="AAO:JOR"} -property_value: UBPROP:0000001 "The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000307", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/neural+tube"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000307", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000011 "The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium" xsd:string {source="GO:0021915"} +relationship: RO:0002202 UBERON:0005068 ! develops from neural rod +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0001062 @@ -12499,7 +12307,6 @@ xref: BILA:0000000 xref: BIRNLEX:6 xref: CARO:0000000 xref: EHDAA2:0002229 -xref: FBbt:10000000 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:62955 xref: HAO:0000000 xref: MA:0000001 @@ -12510,9 +12317,9 @@ xref: UMLS:C1515976 {source="ncithesaurus:Anatomic_Structure_System_or_Substance xref: WBbt:0000100 xref: XAO:0000000 xref: ZFA:0100000 -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0001434 @@ -12549,18 +12356,11 @@ disjoint_from: UBERON:0001474 ! bone element disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system -relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: has_part UBERON:0004288 ! skeleton relationship: has_part UBERON:0004770 ! articular system relationship: part_of UBERON:0002204 ! musculoskeletal system -property_value: RO:0002171 UBERON:0001016 +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/The-skeletal-system" xsd:anyURI -property_value: UBPROP:0000001 "Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000434", ontology="TAO", source="TAO:wd"} -property_value: UBPROP:0000001 "Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000027", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "System that provides physical support to the organism.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000566", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000003 "By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001254", ontology="VHOG", source="DOI:10.1159/000324245 Donoghue PCJ, Sansom IJ, Origin and early evolution of vertebrate skeletonization. Microscopy research and technique (2002)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "skeletal" xsd:string -property_value: UBPROP:0000012 "GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates" xsd:string {external_ontology="GO"} [Term] id: UBERON:0001474 @@ -12603,19 +12403,11 @@ xref: XAO:0000169 xref: ZFA:0001514 is_a: UBERON:0004765 ! skeletal element intersection_of: UBERON:0004765 ! skeletal element -intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue +intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue disjoint_from: UBERON:0001630 ! muscle organ disjoint_from: UBERON:0005090 ! muscle structure -relationship: composed_primarily_of UBERON:0002481 {source="VSAO-modified"} ! bone tissue -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata -property_value: RO:0002171 UBERON:0001015 -property_value: RO:0002171 UBERON:0001630 -property_value: RO:0002171 UBERON:0002385 -property_value: UBPROP:0000001 "Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000047", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000001 "Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001514", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Skeletal element that is composed of bone tissue.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000057", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000002 "relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000047", ontology="AAO"} -property_value: UBPROP:0000003 "The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001190", ontology="VHOG", source="DOI:10.1159/000324245 Murdock DJ, Donoghue PC, Evolutionary Origins of Animal Skeletal Biomineralization. Cells Tissues Organs (2011)", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002473 UBERON:0002481 {source="VSAO-modified"} ! composed primarily of bone tissue [Term] id: UBERON:0001555 @@ -12639,11 +12431,9 @@ xref: BTO:0000545 xref: EHDAA2:0000726 xref: EHDAA:518 xref: EMAPA:16247 -xref: FBbt:00003125 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45615 xref: galen:AlimentaryTract xref: MA:0000917 -xref: MESH:D041981 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: NCIT:C34082 xref: TAO:0000112 xref: TGMA:0001819 @@ -12652,18 +12442,13 @@ xref: VHOG:0000309 xref: WBbt:0005743 xref: ZFA:0000112 is_a: UBERON:0000025 ! tube -relationship: connects UBERON:0000165 ! mouth -relationship: immediate_transformation_of UBERON:0007026 {source="NCBIBook:NBK10107"} ! presumptive gut -relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} -relationship: never_in_taxon NCBITaxon:41324 {source="DOI:10.1371/journal.pone.0016309"} -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0001007 ! digestive system -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "The alimentary or digestive tract, and associated organs.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000112", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000309", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "FMA also has a term 'gastrointestinal tract', but this includes the liver." xsd:string {external_ontology="FMA"} -property_value: UBPROP:0000012 "we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509" xsd:string {external_ontology="MA"} -property_value: UBPROP:0000013 "we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002176 UBERON:0000165 ! connects mouth +relationship: RO:0002495 UBERON:0007026 {source="NCBIBook:NBK10107"} ! immediate transformation of presumptive gut +property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} +property_value: RO:0002161 NCBITaxon:41324 {source="DOI:10.1371/journal.pone.0016309"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001630 @@ -12675,8 +12460,6 @@ subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "muscle" BROAD [ZFA:0005145] -xref: AAO:0011066 -xref: EMAPA:32715 xref: EMAPA:37474 {source="MA:th"} xref: EV:0100146 xref: FMA:5022 @@ -12691,12 +12474,9 @@ xref: ZFA:0005145 is_a: UBERON:0000062 ! organ is_a: UBERON:0005090 ! muscle structure intersection_of: UBERON:0000062 ! organ -intersection_of: composed_primarily_of UBERON:0002385 ! muscle tissue -relationship: composed_primarily_of UBERON:0002385 ! muscle tissue +intersection_of: RO:0002473 UBERON:0002385 ! composed primarily of muscle tissue relationship: part_of UBERON:0001015 ! musculature -property_value: UBPROP:0000001 "Portion of tissue composed of contractile fibers.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005145", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001245", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.75", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "muscular" xsd:string +relationship: RO:0002473 UBERON:0002385 ! composed primarily of muscle tissue [Term] id: UBERON:0001969 @@ -12727,12 +12507,12 @@ is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000179 ! haemolymphatic fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: has_part GO:0005577 ! fibrinogen complex -intersection_of: has_quality PATO:0001548 ! quality of a liquid intersection_of: part_of UBERON:0000178 ! blood -intersection_of: surrounds CL:0000232 ! erythrocyte +intersection_of: RO:0000086 PATO:0001548 ! has quality quality of a liquid +intersection_of: RO:0002221 CL:0000232 ! surrounds erythrocyte relationship: has_part GO:0005577 ! fibrinogen complex relationship: part_of UBERON:0000178 ! blood -relationship: surrounds CL:0000232 ! erythrocyte +relationship: RO:0002221 CL:0000232 ! surrounds erythrocyte [Term] id: UBERON:0001981 @@ -12774,22 +12554,18 @@ xref: XAO:0001011 xref: ZFA:0005314 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000055 ! vessel +is_a: UBERON:0004120 ! mesoderm-derived structure relationship: capable_of_part_of GO:0008015 ! blood circulation relationship: channel_for UBERON:0000178 ! blood -relationship: develops_from UBERON:0004872 ! splanchnic layer of lateral plate mesoderm -relationship: develops_from UBERON:0006965 {source="GO:0072360"} ! vascular cord relationship: has_part CL:0000071 {source="AEO"} ! blood vessel endothelial cell relationship: has_part UBERON:0007500 {source="EHDAA2"} ! epithelial tube open at both ends -relationship: has_quality PATO:0002045 ! dendritic relationship: part_of UBERON:0004537 ! blood vasculature -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI -property_value: editor_note "consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus" xsd:string -property_value: UBPROP:0000001 "Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001250", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000001 "Any of the vessels through which blood circulates in the body.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011004", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001250", ontology="VHOG", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "annelids have blood vessels, but this class is not applicable to annelids." xsd:string -property_value: UBPROP:0000012 "FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX" xsd:string {external_ontology="FMA"} +relationship: RO:0000086 PATO:0002045 ! has quality dendritic +relationship: RO:0002202 UBERON:0004872 ! develops from splanchnic layer of lateral plate mesoderm +relationship: RO:0002202 UBERON:0006965 {source="GO:0072360"} ! develops from vascular cord +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: IAO:0000116 "consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001986 @@ -12813,11 +12589,10 @@ xref: UMLS:C0014257 {source="ncithesaurus:Endothelium"} is_a: UBERON:0000487 {source="FMA-text-def", source="https://github.com/obophenotype/uberon/issues/225"} ! simple squamous epithelium is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0000483 ! epithelium -intersection_of: composed_primarily_of CL:0000115 ! endothelial cell -relationship: composed_primarily_of CL:0000115 ! endothelial cell -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000007 "endothelial" xsd:string +intersection_of: RO:0002473 CL:0000115 ! composed primarily of endothelial cell +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002473 CL:0000115 ! composed primarily of endothelial cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002049 @@ -12834,13 +12609,12 @@ xref: FMA:69050 xref: TAO:0005249 xref: ZFA:0005249 is_a: UBERON:0000477 {source="FMA"} ! anatomical cluster -relationship: composed_primarily_of UBERON:0000055 ! vessel relationship: has_part UBERON:0000179 ! haemolymphatic fluid relationship: part_of UBERON:0007798 ! vascular system -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI -property_value: editor_note "see also: vascular system. Consider merging?" xsd:string -property_value: UBPROP:0000007 "vascular" xsd:string +relationship: RO:0002473 UBERON:0000055 ! composed primarily of vessel +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: IAO:0000116 "see also: vascular system. Consider merging?" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002050 @@ -12860,7 +12634,6 @@ xref: BILA:0000034 xref: BTO:0000174 xref: CALOHA:TS-2110 xref: EFO:0000461 -xref: FBbt:00004208 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69067 xref: GAID:407 xref: MESH:D004628 @@ -12876,10 +12649,6 @@ is_a: UBERON:0005423 ! developing anatomical structure intersection_of: UBERON:0005423 ! developing anatomical structure intersection_of: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0000922 ! embryo -property_value: UBPROP:0000001 "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000138", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001105", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000178", ontology="VSAO", source="ZFIN:curator"} -property_value: UBPROP:0000012 "in FMA embryo is_a embryonic structure" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0002075 @@ -12910,10 +12679,8 @@ xref: Wikipedia:Viscus xref: XAO:0003034 is_a: UBERON:0005177 ! trunk region element intersection_of: UBERON:0000062 ! organ -intersection_of: located_in UBERON:0002323 ! coelemic cavity lumen -relationship: located_in UBERON:0002323 ! coelemic cavity lumen -property_value: UBPROP:0000001 "An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010386", ontology="AAO", source="BTO:0001491"} -property_value: UBPROP:0000012 "general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs." xsd:string {external_ontology="FMA"} +intersection_of: RO:0001025 UBERON:0002323 ! located in coelemic cavity lumen +relationship: RO:0001025 UBERON:0002323 ! located in coelemic cavity lumen [Term] id: UBERON:0002090 @@ -12931,12 +12698,10 @@ xref: AAO:0000034 xref: EFO:0000942 xref: EHDAA2:0000161 xref: EHDAA:5049 -xref: EMAPA:17214 xref: EMAPA:37721 {source="MA:th"} xref: FMA:71221 xref: MA:0002986 xref: MAT:0000148 -xref: MESH:D013131 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: MIAA:0000148 xref: TAO:0000317 xref: VHOG:0000317 @@ -12944,14 +12709,10 @@ xref: VSAO:0000093 xref: XAO:0003073 xref: ZFA:0000317 is_a: UBERON:0010912 ! subdivision of skeleton -relationship: develops_from UBERON:0003089 ! sclerotome relationship: part_of UBERON:0005944 ! axial skeleton plus cranial skeleton relationship: part_of UBERON:0011138 ! postcranial axial skeletal system +relationship: RO:0002202 UBERON:0003089 ! develops from sclerotome property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" xsd:anyURI -property_value: UBPROP:0000001 "Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000093", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000034", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000001 "The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000317", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000317", ontology="VHOG", source="DOI:10.1186/1742-9994-8-4 Schilling N, Evolution of the axial system in craniates: morphology and function of the perivertebral musculature. Frontiers in Zoology (2011)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0002100 @@ -12987,10 +12748,6 @@ xref: XAO:0003025 xref: ZFA:0001115 is_a: UBERON:0011676 ! subdivision of organism along main body axis relationship: part_of UBERON:0013702 ! body proper -property_value: RO:0002171 UBERON:0000026 {exceptions="ZFA", source="https://github.com/obophenotype/uberon/issues/378", status="pending"} -property_value: RO:0002171 UBERON:0000033 -property_value: UBPROP:0000001 "Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010339", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001115", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0002193 @@ -13006,7 +12763,7 @@ xref: EMAPA:18765 xref: FMA:74562 xref: MA:0000013 is_a: UBERON:0000467 {source="MA"} ! anatomical system -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria [Term] id: UBERON:0002204 @@ -13034,13 +12791,10 @@ is_a: UBERON:0000467 ! anatomical system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system relationship: capable_of_part_of GO:0040011 ! locomotion -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: has_developmental_contribution_from UBERON:0000926 {notes="check ctenophore"} ! mesoderm relationship: has_part UBERON:0000383 ! musculature of body relationship: has_part UBERON:0001434 ! skeletal system -property_value: UBPROP:0000001 "Anatomical system that provides locomotion and physical support to the organism.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010546", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001275", ontology="VHOG", source="DOI:10.1002/jez.b.21246 Shearman RM, Burke AC, The lateral somitic frontier in ontogeny and phylogeny. Journal of Experimental Zoology (2009)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "musculoskeletal" xsd:string +relationship: RO:0002254 UBERON:0000926 ! has developmental contribution from mesoderm +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage [Term] id: UBERON:0002224 @@ -13067,13 +12821,12 @@ xref: UMLS:C0230139 {source="ncithesaurus:Thoracic_Cavity"} xref: Wikipedia:Thoracic_cavity is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0000915 ! thoracic segment of trunk intersection_of: part_of UBERON:0002323 ! coelemic cavity lumen -relationship: luminal_space_of UBERON:0000915 ! thoracic segment of trunk +intersection_of: RO:0002572 UBERON:0000915 ! luminal space of thoracic segment of trunk relationship: part_of UBERON:0002323 ! coelemic cavity lumen -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI -property_value: UBPROP:0000008 "In many species, the diaphragm separates thoracic and abdominal cavities" xsd:string +relationship: RO:0002572 UBERON:0000915 ! luminal space of thoracic segment of trunk +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI [Term] id: UBERON:0002323 @@ -13097,7 +12850,6 @@ synonym: "ventral body cavity" NARROW [NCBITaxon:7742] xref: AEO:0000186 xref: BTO:0001707 xref: EHDAA2:0000267 -xref: FBbt:00005060 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:85006 xref: galen:BodyCavity xref: NCIT:C25444 @@ -13107,11 +12859,8 @@ xref: TAO:0001438 xref: UMLS:C0333343 {source="ncithesaurus:Cavity"} xref: ZFA:0001438 is_a: UBERON:0002553 ! anatomical cavity -relationship: luminal_space_of UBERON:0011997 ! coelom -relationship: transformation_of UBERON:0003886 {evidence="definitional"} ! future coelemic cavity lumen -property_value: UBPROP:0000001 "Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]." xsd:string {date_retrieved="2012-09-12", external_class="ZFA:0001438", ontology="ZFA", source="ZFIN:curator"} -property_value: UBPROP:0000001 "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]." xsd:string {date_retrieved="2012-09-12", external_class="BTO:0001707", ontology="BTO", source="BTO"} -property_value: UBPROP:0000008 "In mammals it forms the peritoneal, pleural, and pericardial cavities" xsd:string +relationship: RO:0002494 UBERON:0003886 ! transformation of future coelemic cavity lumen +relationship: RO:0002572 UBERON:0011997 ! luminal space of coelom [Term] id: UBERON:0002328 @@ -13149,23 +12898,15 @@ xref: XAO:0000055 xref: ZFA:0000135 is_a: UBERON:0000062 {source="PMID:15890825"} ! organ is_a: UBERON:0000481 {source="VSAO"} ! multi-tissue structure +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004121 ! ectoderm-derived structure -relationship: develops_from UBERON:0004880 {source="ZFA"} ! chordamesoderm -relationship: develops_from UBERON:0006267 {source="EHDAA2"} ! notochordal plate -relationship: dorsal_to UBERON:0001555 ! digestive tract -relationship: existence_starts_during UBERON:0000068 ! embryo stage -relationship: only_in_taxon NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! Chordata relationship: part_of UBERON:0011137 ! axial skeletal system relationship: produces PR:000014841 ! sonic hedgehog protein -relationship: ventral_to UBERON:0001049 ! neural tube -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000032", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000135", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000327", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000002 "relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000327", ontology="AAO"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000199", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "notochordal" xsd:string -property_value: UBPROP:0000011 "In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord." xsd:string +relationship: RO:0002160 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! only in taxon Chordata +relationship: RO:0002202 UBERON:0004880 {source="ZFA"} ! develops from chordamesoderm +relationship: RO:0002202 UBERON:0006267 {source="EHDAA2"} ! develops from notochordal plate +relationship: RO:0002488 UBERON:0000068 ! existence starts during embryo stage +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0002329 @@ -13204,18 +12945,10 @@ xref: XAO:0000058 xref: ZFA:0000155 is_a: UBERON:0005423 ! developing anatomical structure is_a: UBERON:0007503 {source="EHDAA2"} ! epithelial vesicle -relationship: develops_from UBERON:0003059 {source="ZFA"} ! presomitic mesoderm -relationship: never_in_taxon NCBITaxon:7712 {source="PMID:17237766"} -relationship: only_in_taxon NCBITaxon:7711 {source="GOTAX:0000352"} ! Chordata -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: IAO:0000232 "EDITOR_NOTE currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk" xsd:string -property_value: UBPROP:0000001 "Post-cranial axial segments which form sclerotome and dermomyotome.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010569", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000001 "Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000155", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000002 "relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000155", ontology="TAO"} -property_value: UBPROP:0000002 "relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000155", ontology="TAO"} -property_value: UBPROP:0000002 "relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010569", ontology="AAO"} -property_value: UBPROP:0000003 "(...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000191", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.40, DOI:10.1093/icb/43.1.137 Balavoine G, Adoutte A, The segmented urbilateria: a testable scenario. Integrative and Comparative Biology (2003)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "somitic" xsd:string +relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata +relationship: RO:0002202 UBERON:0003059 {source="ZFA"} ! develops from presomitic mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: RO:0002161 NCBITaxon:7712 {source="PMID:17237766"} [Term] id: UBERON:0002342 @@ -13242,28 +12975,22 @@ xref: MIAA:0000066 xref: NCIT:C34222 xref: neuronames:1366 xref: SCTID:361462002 -xref: TAO:0000045 xref: UMLS:C0027789 {source="ncithesaurus:Neural_Crest"} xref: VHOG:0000057 xref: Wikipedia:Neural_crest xref: XAO:0000048 xref: ZFA:0000045 is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0010316 ! germ layer / neural crest -relationship: composed_primarily_of CL:0000333 {notes="pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! migratory neural crest cell -relationship: develops_from UBERON:0003075 {source="BTO"} ! neural plate -relationship: develops_from UBERON:0005062 {source="PMID:11523831"} ! neural fold -relationship: existence_starts_during UBERON:0000110 {source="PMID:11523831"} ! neurula stage -relationship: only_in_taxon NCBITaxon:89593 {notes="Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells", source="ISBN:0073040584"} ! Craniata relationship: part_of UBERON:0002346 {source="XAO", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! neurectoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI -property_value: IAO:0000232 "EDITOR_NOTE consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams)." xsd:string -property_value: RO:0002174 NCBITaxon:117565 {source="ISBN:0073040584", source="PMID:17377535"} -property_value: UBPROP:0000001 "A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000045", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010578", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831]" xsd:string {source="PMID:11523831"} -property_value: UBPROP:0000003 "We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000057", ontology="VHOG", source="DOI:10.1111/j.1469-7580.2012.01495.x Hall BK, Gillis JA, Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues. J Anat (2012)", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata +relationship: RO:0002202 UBERON:0003075 {source="BTO"} ! develops from neural plate +relationship: RO:0002202 UBERON:0005062 {source="PMID:11523831"} ! develops from neural fold +relationship: RO:0002473 CL:0000333 ! composed primarily of migratory neural crest cell +relationship: RO:0002488 UBERON:0000110 {source="PMID:11523831"} ! existence starts during neurula stage +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI [Term] id: UBERON:0002346 @@ -13286,7 +13013,6 @@ xref: EHDAA:1498 xref: EHDAA:255 xref: EMAPA:16073 xref: EV:0100004 -xref: FBbt:00001057 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:87657 xref: MAT:0000176 xref: MIAA:0000176 @@ -13300,9 +13026,6 @@ xref: ZFA:0001120 is_a: UBERON:0000923 ! germ layer is_a: UBERON:0004121 ! ectoderm-derived structure relationship: has_part CL:0000133 ! neurectodermal cell -property_value: UBPROP:0000003 "(...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000150", ontology="VHOG", source="DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "neurectodermal" xsd:string -property_value: UBPROP:0000013 "we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here" xsd:string [Term] id: UBERON:0002371 @@ -13338,6 +13061,7 @@ xref: VHOG:0001218 xref: Wikipedia:Bone_marrow xref: XAO:0000123 is_a: UBERON:0000479 ! tissue +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000479 ! tissue intersection_of: has_part UBERON:0012429 ! hematopoietic tissue intersection_of: part_of UBERON:0001474 ! bone element @@ -13346,12 +13070,10 @@ relationship: has_part UBERON:0012429 ! hematopoietic tissue relationship: part_of UBERON:0001474 ! bone element relationship: part_of UBERON:0002390 {source="FMA", source="MA"} ! hematopoietic system relationship: part_of UBERON:0002405 ! immune system -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg" xsd:anyURI -property_value: editor_note "consider placement of NCIT:C53466 medullary bone" xsd:string -property_value: editor_note "TODO - create superclass for bone marrow / head kidney. both are portions of tissue in the hematopoetic system. also consider adding as subclass of zone of bone organ for consistency with FMA. See also: Leydig and epigonal organs" xsd:string -property_value: UBPROP:0000003 "The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001218", ontology="VHOG", source="DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood Cells and Blood Cell Development in the Animal Kingdom. Annual Review of Cell and Developmental Biology (2006)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000009 "In adults, marrow in large bones produces new blood cells[Wikipedia:Bone_marrow]" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg" xsd:anyURI +property_value: IAO:0000116 "consider placement of NCIT:C53466 medullary bone" xsd:string +property_value: IAO:0000116 "TODO - create superclass for bone marrow / head kidney. both are portions of tissue in the hematopoetic system. also consider adding as subclass of zone of bone organ for consistency with FMA. See also: Leydig and epigonal organs" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002384 @@ -13385,12 +13107,8 @@ xref: VSAO:0000017 xref: XAO:0001017 xref: ZFA:0001632 is_a: UBERON:0000479 ! tissue -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000098", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000001 "Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001641", ontology="TAO", source="TAO:wd"} -property_value: UBPROP:0000001 "Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000017", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} -property_value: UBPROP:0000012 "MA also has set of connective tissues" xsd:string {external_ontology="MA"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002385 @@ -13418,13 +13136,11 @@ xref: Wikipedia:Muscle_tissue is_a: UBERON:0000479 ! tissue is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000479 ! tissue -intersection_of: composed_primarily_of CL:0000187 ! muscle cell +intersection_of: RO:0002473 CL:0000187 ! composed primarily of muscle cell relationship: capable_of GO:0006936 ! muscle contraction -relationship: composed_primarily_of CL:0000187 ! muscle cell -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0001015 ! musculature -property_value: RO:0002171 UBERON:0003714 -property_value: UBPROP:0000001 "One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000306", ontology="AAO", source="AAO:LAP"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002473 CL:0000187 ! composed primarily of muscle cell [Term] id: UBERON:0002390 @@ -13467,14 +13183,10 @@ xref: ZFA:0005023 is_a: UBERON:0000467 ! anatomical system is_a: UBERON:0004120 ! mesoderm-derived structure disjoint_from: UBERON:0002405 ! immune system -relationship: develops_from UBERON:0003061 {evidence="definitional"} ! blood island -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0002193 {source="FMA"} ! hemolymphoid system -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "Anatomical system that consists of the blood and blood forming tissues.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011002", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001624", ontology="VHOG", source="DOI:10.1016/j.coph.2010.05.004 Ellett F, Lieschke GJ, Zebrafish as a model for vertebrate hematopoiesis. Current Opinion in Pharmacology (2010)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "hematopoietic" xsd:string -property_value: UBPROP:0000008 "In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes" xsd:string {source="WP"} +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002202 UBERON:0003061 ! develops from blood island +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002405 @@ -13502,10 +13214,9 @@ xref: XAO:0003152 xref: ZFA:0001159 is_a: UBERON:0015203 ! non-connected functional system relationship: capable_of GO:0002376 ! immune system process -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: present_in_taxon NCBITaxon:9606 relationship: protects UBERON:0000468 ! multicellular organism -property_value: UBPROP:0000003 "The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001247", ontology="VHOG", source="PMID:21046016 Dzik JM, The ancestry and cumulative evolution of immune reactions. Acta biochimica Polonica (2010)", source="http://bgee.unil.ch/"} +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002481 @@ -13534,10 +13245,9 @@ xref: XAO:0004040 xref: ZFA:0005621 is_a: UBERON:0004755 {source="VSAO"} ! skeletal tissue disjoint_from: UBERON:0005090 ! muscle structure -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0001474 ! bone element -property_value: editor_note "see https://github.com/obophenotype/uberon/issues/27" xsd:string -property_value: UBPROP:0000001 "Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000047", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +property_value: IAO:0000116 "see https://github.com/obophenotype/uberon/issues/27" xsd:string [Term] id: UBERON:0002532 @@ -13561,9 +13271,8 @@ xref: VHOG:0000243 xref: Wikipedia:Epiblast is_a: UBERON:0002050 ! embryonic structure relationship: has_part CL:0000352 ! epiblast cell -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" xsd:anyURI -property_value: editor_note "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" xsd:string -property_value: UBPROP:0000003 "In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000243", ontology="VHOG", source="DOI:10.1146/annurev.cellbio.042308.113344 Zorn AM, Wells JM, Vertebrate endoderm development and organ formation. Annual Review of Cell Developmental Biology (2009)", source="http://bgee.unil.ch/"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" xsd:anyURI +property_value: IAO:0000116 "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" xsd:string [Term] id: UBERON:0002553 @@ -13579,7 +13288,7 @@ xref: galen:Cavity xref: MA:0002447 xref: NCIT:C34007 is_a: UBERON:0000464 ! anatomical space -relationship: location_of UBERON:0000463 ! organism substance +relationship: RO:0001015 UBERON:0000463 ! location of organism substance [Term] id: UBERON:0003059 @@ -13605,13 +13314,11 @@ xref: XAO:0000057 xref: ZFA:0000279 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0005423 ! developing anatomical structure -intersection_of: has_potential_to_develop_into UBERON:0002329 ! somite -intersection_of: immediate_transformation_of UBERON:0007282 ! presumptive segmental plate -relationship: has_potential_to_develop_into UBERON:0002329 ! somite -relationship: immediate_transformation_of UBERON:0007282 {source="Bgee:AN"} ! presumptive segmental plate +intersection_of: RO:0002387 UBERON:0002329 ! has potential to develop into somite +intersection_of: RO:0002495 UBERON:0007282 ! immediate transformation of presumptive segmental plate relationship: part_of UBERON:0003077 ! paraxial mesoderm -property_value: UBPROP:0000001 "Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000279", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000559", ontology="VHOG", source="DOI:10.1006/dbio.2001.0460 Schubert M, Holland LZ, Dale Stokes M and Holland ND, Three Amphoxius Wnt Genes (AmphiWnt3, AmphiWnt5, and AmphiWnt6) Associated with the Tail Bud: the Evolution of Somitogenesis in Chordates. Developmental Biology (2001)", source="http://bgee.unil.ch/"} +relationship: RO:0002387 UBERON:0002329 ! has potential to develop into somite +relationship: RO:0002495 UBERON:0007282 {source="Bgee:AN"} ! immediate transformation of presumptive segmental plate [Term] id: UBERON:0003061 @@ -13641,13 +13348,8 @@ xref: Wikipedia:Blood_island_of_umbilical_vesicle xref: XAO:0000067 xref: ZFA:0000094 is_a: UBERON:0006598 ! presumptive structure -relationship: develops_from UBERON:0003081 ! lateral plate mesoderm -relationship: has_potential_to_develop_into UBERON:0002390 ! hematopoietic system -property_value: UBPROP:0000001 "Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000094", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011006", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000002 "relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000094", ontology="TAO"} -property_value: UBPROP:0000003 "Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000085", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450, DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual Review of Cell and Developmental Biology (2006)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac" xsd:string {external_ontology="EHDAA2"} +relationship: RO:0002202 UBERON:0003081 ! develops from lateral plate mesoderm +relationship: RO:0002387 UBERON:0002390 ! has potential to develop into hematopoietic system [Term] id: UBERON:0003068 @@ -13665,11 +13367,10 @@ xref: Wikipedia:Chordamesoderm xref: XAO:0000205 xref: ZFA:0001204 is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0000926 ! mesoderm -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0000926 ! mesoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000107", ontology="VHOG", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002202 UBERON:0000926 ! develops from mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003075 @@ -13689,7 +13390,6 @@ xref: EHDAA:346 xref: EHDAA:902 xref: EMAPA:35593 xref: FMA:293879 -xref: MESH:D054258 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C34225 xref: neuronames:1362 xref: RETIRED_EHDAA2:0001252 @@ -13702,12 +13402,10 @@ xref: ZFA:0000132 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0016879 ! future central nervous system -relationship: developmentally_induced_by UBERON:0002328 {source="Wikipedia"} ! notochord -relationship: immediate_transformation_of UBERON:0007284 {source="Bgee:AN"} ! presumptive neural plate -relationship: only_in_taxon NCBITaxon:7711 {source="GOTAX:0000352"} ! Chordata -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI -property_value: UBPROP:0000001 "The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000132", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000068", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata +relationship: RO:0002256 UBERON:0002328 {source="Wikipedia"} ! developmentally induced by notochord +relationship: RO:0002495 UBERON:0007284 {source="Bgee:AN"} ! immediate transformation of presumptive neural plate +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI [Term] id: UBERON:0003077 @@ -13736,13 +13434,9 @@ xref: ZFA:0000255 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue is_a: UBERON:0015212 ! lateral structure -relationship: existence_starts_during UBERON:0000109 ! gastrula stage -relationship: immediate_transformation_of UBERON:0007285 {source="Bgee:AN"} ! presumptive paraxial mesoderm -relationship: in_lateral_side_of UBERON:0000922 ! embryo -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010568", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000114", ontology="VHOG", source="DOI:10.1002/dvdy.21177 Kusakabe R and Kuratani S. Evolutionary perspectives from development of mesodermal components in the lamprey. Developmental dynamics (2007)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here)" xsd:string {external_ontology="ZFA"} +relationship: RO:0002488 UBERON:0000109 ! existence starts during gastrula stage +relationship: RO:0002495 UBERON:0007285 {source="Bgee:AN"} ! immediate transformation of presumptive paraxial mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003081 @@ -13774,14 +13468,10 @@ is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0000926 {source="EHDAA2", source="VHOG"} ! mesoderm -relationship: surrounds UBERON:0003887 ! intraembryonic coelom -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010574", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000001 "The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000118", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000118", ontology="VHOG", source="DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "subclass of mesoderm in ZFA." xsd:string {external_ontology="ZFA"} +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002221 UBERON:0003887 ! surrounds intraembryonic coelom +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003084 @@ -13799,14 +13489,11 @@ xref: UMLS:C1514450 {source="ncithesaurus:Primordium_of_the_Heart"} xref: XAO:0000336 xref: ZFA:0000028 is_a: UBERON:0001048 {source="Obol"} ! primordium -relationship: develops_from UBERON:0003081 {source="ZFA"} ! lateral plate mesoderm -relationship: develops_from UBERON:0004140 ! primary heart field -relationship: develops_from UBERON:0007005 {source="XAO"} ! cardiogenic splanchnic mesoderm relationship: part_of UBERON:0004535 {source="ZFA"} ! cardiovascular system -property_value: editor_note "should probably be merged with heart rudiment." xsd:string -property_value: UBPROP:0000001 "Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000028", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011044", ontology="AAO", source="XAO:curator"} -property_value: UBPROP:0000002 "relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000028", ontology="TAO"} +relationship: RO:0002202 UBERON:0003081 {source="ZFA"} ! develops from lateral plate mesoderm +relationship: RO:0002202 UBERON:0004140 ! develops from primary heart field +relationship: RO:0002202 UBERON:0007005 {source="XAO"} ! develops from cardiogenic splanchnic mesoderm +property_value: IAO:0000116 "should probably be merged with heart rudiment." xsd:string [Term] id: UBERON:0003089 @@ -13820,7 +13507,6 @@ synonym: "sclerotomes" EXACT OMO:0003004 [TAO:0001080] synonym: "sclerotomus" RELATED OMO:0003011 [Wikipedia:Sclerotome] xref: AAO:0010571 xref: AEO:0000212 -xref: BTO:0006255 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: EHDAA2:0003439 xref: EMAPA:31159 xref: FMA:295652 @@ -13833,12 +13519,9 @@ xref: XAO:0000397 xref: ZFA:0001080 is_a: UBERON:0005856 {source="EHDAA2"} ! developing mesenchymal condensation is_a: UBERON:0007530 {source="EHDAA2"} ! migrating mesenchyme population -relationship: develops_from UBERON:0002329 {source="ZFA"} ! somite -relationship: only_in_taxon NCBITaxon:7742 {source="VHOG:0000680"} ! Vertebrata -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI -property_value: UBPROP:0000001 "Skeletogenic portion of somites.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010571", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000680", ontology="VHOG", source="DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "part_of somite in XAO" xsd:string {external_ontology="XAO"} +relationship: RO:0002160 NCBITaxon:7742 {source="VHOG:0000680"} ! only in taxon Vertebrata +relationship: RO:0002202 UBERON:0002329 {source="ZFA"} ! develops from somite +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI [Term] id: UBERON:0003103 @@ -13861,7 +13544,6 @@ xref: VHOG:0001723 xref: XAO:0003041 xref: ZFA:0000496 is_a: UBERON:0000062 ! organ -property_value: IAO:0000232 "this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs" xsd:string [Term] id: UBERON:0003104 @@ -13891,15 +13573,12 @@ xref: XAO:0003046 xref: ZFA:0000393 is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue -intersection_of: composed_primarily_of CL:0008019 ! mesenchymal cell -relationship: composed_primarily_of CL:0008019 ! mesenchymal cell -relationship: functionally_related_to GO:0032502 ! developmental process -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI -property_value: editor_note "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" xsd:string -property_value: UBPROP:0000001 "A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000393", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010427", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000007 "mesenchymal" xsd:string +intersection_of: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002328 GO:0032502 ! functionally related to developmental process +relationship: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI +property_value: IAO:0000116 "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" xsd:string [Term] id: UBERON:0003886 @@ -13912,11 +13591,11 @@ synonym: "body cavity precursor" RELATED [] synonym: "future coelomic cavity lumen" EXACT [] is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: has_potential_to_develop_into UBERON:0002323 ! coelemic cavity lumen -relationship: existence_ends_during UBERON:0000111 ! organogenesis stage -relationship: existence_starts_during UBERON:0000109 ! gastrula stage -relationship: has_potential_to_develop_into UBERON:0002323 ! coelemic cavity lumen +intersection_of: RO:0002387 UBERON:0002323 ! has potential to develop into coelemic cavity lumen relationship: part_of UBERON:0000926 ! mesoderm +relationship: RO:0002387 UBERON:0002323 ! has potential to develop into coelemic cavity lumen +relationship: RO:0002488 UBERON:0000109 ! existence starts during gastrula stage +relationship: RO:0002492 UBERON:0000111 ! existence ends during organogenesis stage [Term] id: UBERON:0003887 @@ -13932,10 +13611,9 @@ xref: UMLS:C1512940 {source="ncithesaurus:Intraembryonic_Coelom"} xref: VHOG:0000316 xref: Wikipedia:Intraembryonic_coelom is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0003081 {source="Wikipedia"} ! lateral plate mesoderm relationship: part_of UBERON:0011997 ! coelom -property_value: editor_note "consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults" xsd:string -property_value: UBPROP:0000003 "(...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000316", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.166", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003081 {source="Wikipedia"} ! develops from lateral plate mesoderm +property_value: IAO:0000116 "consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults" xsd:string [Term] id: UBERON:0003914 @@ -13945,12 +13623,10 @@ def: "Epithelial tubes transport gases, liquids and cells from one site to anoth synonym: "epithelial or endothelial tube" EXACT [] xref: AEO:0000114 xref: EHDAA2:0003114 -xref: FBbt:00007474 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000025 ! tube is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium -intersection_of: has_quality PATO:0002299 ! tubular -property_value: IAO:0000232 "contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers" xsd:string +intersection_of: RO:0000086 PATO:0002299 ! has quality tubular [Term] id: UBERON:0004111 @@ -13970,15 +13646,14 @@ xref: SCTID:346902003 xref: Wikipedia:Foramen is_a: UBERON:0010000 ! multicellular anatomical structure intersection_of: UBERON:0010000 ! multicellular anatomical structure -intersection_of: conduit_for UBERON:0000061 ! anatomical structure intersection_of: has_part UBERON:0013686 ! anatomical conduit space -relationship: conduit_for UBERON:0000061 ! anatomical structure -relationship: connects UBERON:0000464 {cardinality="2"} ! anatomical space +intersection_of: RO:0002570 UBERON:0000061 ! conduit for anatomical structure relationship: has_part UBERON:0013686 ! anatomical conduit space -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: UBPROP:0000012 "FMA has both conduit and conduit space. In EHDAA2 this is a surface feature" xsd:string {external_ontology="FMA"} +relationship: RO:0002176 UBERON:0000464 {cardinality="2"} ! connects anatomical space +relationship: RO:0002570 UBERON:0000061 ! conduit for anatomical structure +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0004120 @@ -13989,9 +13664,8 @@ subset: grouping_class synonym: "mesodermal derivative" EXACT [FBbt:00025998] is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: develops_from UBERON:0000926 ! mesoderm -relationship: develops_from UBERON:0000926 ! mesoderm -property_value: IAO:0000232 "Grouping term for query purposes" xsd:string +intersection_of: RO:0002202 UBERON:0000926 ! develops from mesoderm +relationship: RO:0002202 UBERON:0000926 ! develops from mesoderm [Term] id: UBERON:0004121 @@ -14002,9 +13676,8 @@ subset: grouping_class synonym: "ectodermal deriviative" EXACT [FBbt:00025990] is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: develops_from UBERON:0000924 ! ectoderm -relationship: develops_from UBERON:0000924 ! ectoderm -property_value: IAO:0000232 "Grouping term for query purposes" xsd:string +intersection_of: RO:0002202 UBERON:0000924 ! develops from ectoderm +relationship: RO:0002202 UBERON:0000924 ! develops from ectoderm [Term] id: UBERON:0004139 @@ -14020,9 +13693,8 @@ xref: EHDAA2:0000215 xref: EMAPA:16106 xref: VHOG:0000975 is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0003084 ! heart primordium -property_value: editor_note "TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO" xsd:string -property_value: UBPROP:0000003 "(In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000975", ontology="VHOG", source="PMID:15611355 Gittenberger-de Groot AC, Bartelings MM, Deruiter MC, Poelmann RE, Basics of cardiac development for the understanding of congenital heart malformations. Pediatric Research (2005)", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003084 ! develops from heart primordium +property_value: IAO:0000116 "TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO" xsd:string [Term] id: UBERON:0004140 @@ -14036,11 +13708,11 @@ synonym: "PHF" RELATED OMO:0003000 [XAO:0004185] synonym: "primary heart field" EXACT [PMID:17276708, XAO:0004185] xref: XAO:0004185 is_a: UBERON:0002050 ! embryonic structure +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007688 ! anlage relationship: part_of UBERON:0003081 {source="GO:0003128"} ! lateral plate mesoderm relationship: part_of UBERON:0036146 {source="https://orcid.org/0000-0003-3308-6245"} ! cardiopharyngeal field -property_value: UBPROP:0000012 "this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138]" xsd:string {external_ontology="GO"} [Term] id: UBERON:0004141 @@ -14063,8 +13735,7 @@ xref: ZFA:0000360 is_a: UBERON:0003914 ! epithelial tube is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0012275 ! meso-epithelium -relationship: immediate_transformation_of UBERON:0005498 {source="ZFA-modified"} ! primitive heart tube -property_value: UBPROP:0000001 "the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube." xsd:string {source="MP:0012700"} +relationship: RO:0002495 UBERON:0005498 {source="ZFA-modified"} ! immediate transformation of primitive heart tube [Term] id: UBERON:0004151 @@ -14077,6 +13748,7 @@ synonym: "heart chamber" EXACT [] xref: FMA:7095 xref: SCTID:276456008 is_a: UBERON:0000064 ! organ part +is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0000948 ! heart [Term] @@ -14107,13 +13779,10 @@ xref: Wikipedia:Skeleton xref: XAO:0004053 is_a: UBERON:0034925 ! anatomical collection disjoint_from: UBERON:0004770 ! articular system -relationship: has_member UBERON:0004765 ! skeletal element relationship: part_of UBERON:0001434 ! skeletal system -relationship: present_in_taxon NCBITaxon:9606 -property_value: RO:0002171 UBERON:0000383 +relationship: RO:0002351 UBERON:0004765 ! has member skeletal element +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/The-skeletal-system" xsd:anyURI -property_value: UBPROP:0000001 "Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000026", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070"} -property_value: UBPROP:0000007 "skeletal" xsd:string [Term] id: UBERON:0004291 @@ -14125,8 +13794,7 @@ synonym: "rudimentary heart" EXACT [ZFA:0000115] xref: TAO:0000115 xref: ZFA:0000115 is_a: UBERON:0012275 ! meso-epithelium -relationship: develops_from UBERON:0004139 ! cardiogenic plate -property_value: UBPROP:0000001 "The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000115", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002202 UBERON:0004139 ! develops from cardiogenic plate [Term] id: UBERON:0004535 @@ -14145,10 +13813,8 @@ xref: BILA:0000016 xref: BTO:0000088 xref: CALOHA:TS-1297 xref: EFO:0000791 -xref: EHDAA2:0000216 xref: EHDAA:394 xref: EMAPA:16104 -xref: EMAPA:16370 xref: EV:0100017 xref: FMA:7161 xref: GAID:467 @@ -14174,9 +13840,7 @@ intersection_of: part_of UBERON:0001009 ! circulatory system relationship: has_part UBERON:0000948 ! heart relationship: has_part UBERON:0001981 ! blood vessel relationship: part_of UBERON:0001009 ! circulatory system -relationship: present_in_taxon NCBITaxon:9606 -property_value: IAO:0000232 "we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph." xsd:string -property_value: UBPROP:0000003 "The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000302", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.451", source="http://bgee.unil.ch/"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004537 @@ -14194,11 +13858,11 @@ xref: ZFA:0001079 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature -intersection_of: composed_primarily_of UBERON:0001981 ! blood vessel -relationship: composed_primarily_of UBERON:0001981 ! blood vessel -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +intersection_of: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel +relationship: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004638 @@ -14220,7 +13884,7 @@ is_a: UBERON:0004852 ! cardiovascular system endothelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0001981 ! blood vessel relationship: part_of UBERON:0001981 ! blood vessel -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004716 @@ -14237,12 +13901,12 @@ xref: NCIT:C34131 xref: UMLS:C1516779 {source="ncithesaurus:Conceptus"} xref: Wikipedia:Conceptus is_a: UBERON:0000061 ! anatomical structure -relationship: develops_from CL:0000365 ! animal zygote -relationship: existence_ends_with UBERON:0000068 ! embryo stage -relationship: existence_starts_with UBERON:0000068 ! embryo stage relationship: has_part UBERON:0002050 ! embryonic structure relationship: has_part UBERON:0016887 ! entire extraembryonic component -property_value: editor_note "EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus" xsd:string +relationship: RO:0002202 CL:0000365 ! develops from animal zygote +relationship: RO:0002489 UBERON:0000068 ! existence starts with embryo stage +relationship: RO:0002493 UBERON:0000068 ! existence ends with embryo stage +property_value: IAO:0000116 "EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus" xsd:string [Term] id: UBERON:0004734 @@ -14262,7 +13926,6 @@ synonym: "trilaminar disk" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "trilaminar germ" RELATED [https://orcid.org/0000-0002-6601-2165] xref: BILA:0000060 xref: BTO:0001403 -xref: FBbt:00005317 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:293108 xref: GAID:1302 xref: MESH:D005775 @@ -14275,10 +13938,9 @@ xref: Wikipedia:Gastrula xref: Wikipedia:Trilaminar_blastocyst is_a: UBERON:0000922 ! embryo intersection_of: UBERON:0000468 ! multicellular organism -intersection_of: existence_starts_and_ends_during UBERON:0000109 ! gastrula stage -relationship: develops_from UBERON:0000307 ! blastula -relationship: existence_starts_and_ends_during UBERON:0000109 ! gastrula stage -property_value: UBPROP:0000012 "We explicitly merge the NCITA terms here" xsd:string {external_ontology="NCIT"} +intersection_of: RO:0002491 UBERON:0000109 ! existence starts and ends during gastrula stage +relationship: RO:0002202 UBERON:0000307 ! develops from blastula +relationship: RO:0002491 UBERON:0000109 ! existence starts and ends during gastrula stage [Term] id: UBERON:0004755 @@ -14293,9 +13955,8 @@ xref: VSAO:0000015 xref: XAO:0004038 xref: ZFA:0005619 is_a: UBERON:0002384 {source="VSAO"} ! connective tissue -relationship: develops_from CL:0007001 {date_retrieved="2012-08-14", external_class="VSAO:0000015", source="VSAO"} ! skeletogenic cell relationship: part_of UBERON:0004765 ! skeletal element -property_value: UBPROP:0000001 "A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000015", notes="taken from version of VSAO used in TAO and used directly in Uberon", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} +relationship: RO:0002202 CL:0007001 ! develops from skeletogenic cell [Term] id: UBERON:0004765 @@ -14312,8 +13973,6 @@ xref: XAO:0004012 xref: ZFA:0005494 is_a: UBERON:0000062 ! organ relationship: part_of UBERON:0001434 {source="VSAO"} ! skeletal system -property_value: UBPROP:0000001 "Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000128", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001890", ontology="TAO", source="TAO:VSAO_workshop"} [Term] id: UBERON:0004770 @@ -14331,12 +13990,12 @@ xref: SCTID:361827000 xref: VSAO:0000181 is_a: UBERON:0034925 ! anatomical collection intersection_of: UBERON:0034925 ! anatomical collection -intersection_of: has_member UBERON:0000982 ! skeletal joint -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: functionally_related_to GO:0040011 ! locomotion -relationship: has_member UBERON:0000982 ! skeletal joint -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +intersection_of: RO:0002351 UBERON:0000982 ! has member skeletal joint relationship: part_of UBERON:0001434 {source="FMA"} ! skeletal system +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002328 GO:0040011 ! functionally related to locomotion +relationship: RO:0002351 UBERON:0000982 ! has member skeletal joint +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage [Term] id: UBERON:0004852 @@ -14361,8 +14020,7 @@ is_a: UBERON:0001986 ! endothelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0004535 ! cardiovascular system relationship: part_of UBERON:0004535 ! cardiovascular system -property_value: editor_note "consider merging with 'endothelium'" xsd:string -property_value: UBPROP:0000003 "Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001217", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207", source="http://bgee.unil.ch/"} +property_value: IAO:0000116 "consider merging with 'endothelium'" xsd:string [Term] id: UBERON:0004872 @@ -14380,7 +14038,6 @@ xref: Wikipedia:Lateral_plate_mesoderm#Division_into_layers xref: XAO:0000276 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0003081 ! lateral plate mesoderm -property_value: UBPROP:0000012 "We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors" xsd:string {external_ontology="BILA"} [Term] id: UBERON:0004880 @@ -14398,10 +14055,8 @@ xref: EFO:0003426 xref: TAO:0000091 xref: ZFA:0000091 is_a: UBERON:0002050 ! embryonic structure -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0003068 ! axial mesoderm -property_value: UBPROP:0000001 "Notochord rudiment[ZFIN:ZDB-PUB-961014-576]." xsd:string {source="ZFIN:ZDB-PUB-961014-576"} -property_value: UBPROP:0000012 "WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord." xsd:string +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata [Term] id: UBERON:0004905 @@ -14410,7 +14065,6 @@ namespace: uberon def: "Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts." [http://orcid.org/0000-0002-6601-2165] subset: grouping_class synonym: "joint" NARROW [] -xref: FBbt:00005811 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0034921 ! multi organ part structure relationship: part_of UBERON:0004770 ! articular system @@ -14426,15 +14080,13 @@ synonym: "gut section" RELATED [FBbt:00100315] synonym: "intestinal tract" RELATED [] synonym: "segment of intestinal tract" RELATED [] synonym: "subdivision of alimentary system" RELATED [FMA:71131] -xref: FBbt:00100315 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:71131 is_a: UBERON:0013522 ! subdivision of tube intersection_of: UBERON:0013522 ! subdivision of tube intersection_of: subdivision_of UBERON:0001555 ! digestive tract relationship: part_of UBERON:0001555 ! digestive tract -relationship: present_in_taxon NCBITaxon:9606 relationship: subdivision_of UBERON:0001555 ! digestive tract -property_value: IAO:0000232 "intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct." xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004923 @@ -14444,8 +14096,8 @@ def: "A part of a wall of an organ that forms a layer." [http://orcid.org/0000-0 subset: upper_level xref: FMA:82485 is_a: UBERON:0000064 ! organ part -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000060 ! anatomical wall +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0005061 @@ -14463,7 +14115,6 @@ xref: Wikipedia:Neural_groove xref: XAO:0000248 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0003075 ! neural plate -property_value: UBPROP:0000001 "The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]." xsd:string {source="Wikipedia:Neural_groove"} [Term] id: UBERON:0005062 @@ -14483,10 +14134,9 @@ xref: XAO:0004087 is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0005157 ! epithelial fold is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0015212 ! lateral structure -relationship: in_lateral_side_of UBERON:0005061 ! neural groove relationship: part_of UBERON:0005061 ! neural groove -property_value: UBPROP:0000001 "In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]." xsd:string {source="Wikipedia:Neural_fold"} [Term] id: UBERON:0005068 @@ -14499,8 +14149,7 @@ xref: EFO:0003498 xref: TAO:0000133 xref: ZFA:0000133 is_a: UBERON:0016879 ! future central nervous system -relationship: develops_from UBERON:0007135 ! neural keel -property_value: UBPROP:0000001 "An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000133", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002202 UBERON:0007135 ! develops from neural keel [Term] id: UBERON:0005090 @@ -14510,12 +14159,10 @@ def: "Muscle structures are contractile cells, tissues or organs that are found synonym: "muscle" RELATED [] synonym: "muscle element" RELATED [] synonym: "musculus" EXACT [FMA:30316] -xref: EMAPA:32715 xref: FMA:30316 is_a: UBERON:0000061 ! anatomical structure relationship: has_part CL:0000187 ! muscle cell -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: IAO:0000232 "in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0005157 @@ -14552,8 +14199,8 @@ xref: MA:0000557 is_a: UBERON:0002075 ! viscus is_a: UBERON:0005181 ! thoracic segment organ intersection_of: UBERON:0000062 ! organ -intersection_of: located_in UBERON:0002224 ! thoracic cavity -relationship: located_in UBERON:0002224 ! thoracic cavity +intersection_of: RO:0001025 UBERON:0002224 ! located in thoracic cavity +relationship: RO:0001025 UBERON:0002224 ! located in thoracic cavity [Term] id: UBERON:0005181 @@ -14618,14 +14265,13 @@ synonym: "developmental tissue" RELATED [MIAA:0000019] xref: AEO:0000125 xref: CALOHA:TS-2122 xref: EHDAA2:0003125 -xref: FBbt:00007006 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:292313 xref: MIAA:0000019 is_a: UBERON:0000465 ! material anatomical entity relationship: capable_of GO:0032502 ! developmental process -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0005498 @@ -14635,7 +14281,6 @@ def: "Multi-tissue structure that arises from the heart rudiment and will become subset: vertebrate_core synonym: "early primitive heart tube" NARROW [EMAPA:16208] synonym: "primitive heart tube" EXACT [EMAPA:16215] -xref: BTO:0006179 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: EHDAA2:0001512 xref: EHDAA:424 xref: EHDAA:436 @@ -14647,8 +14292,8 @@ xref: Wikipedia:Primitive_heart_tube xref: ZFA:0000149 is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004120 ! mesoderm-derived structure -relationship: develops_from UBERON:0004291 {source="ZFA"} ! heart rudiment relationship: part_of UBERON:0000922 ! embryo +relationship: RO:0002202 UBERON:0004291 {source="ZFA"} ! develops from heart rudiment [Term] id: UBERON:0005764 @@ -14661,9 +14306,9 @@ is_a: UBERON:0000476 ! acellular anatomical structure intersection_of: UBERON:0000476 ! acellular anatomical structure intersection_of: bounding_layer_of UBERON:0000061 ! anatomical structure relationship: bounding_layer_of UBERON:0000061 ! anatomical structure -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0005769 @@ -14683,12 +14328,11 @@ xref: Wikipedia:Basement_membrane is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005764 {source="FMA"} ! acellular membrane relationship: adjacent_to CL:0000066 ! epithelial cell -relationship: composed_primarily_of GO:0005604 ! basement membrane relationship: has_part GO:0005587 ! collagen type IV trimer -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa relationship: part_of UBERON:0000483 ! epithelium -relationship: present_in_taxon NCBITaxon:80999 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} -property_value: IAO:0000232 "this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell." xsd:string +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002473 GO:0005604 ! composed primarily of basement membrane +property_value: RO:0002175 NCBITaxon:80999 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} [Term] id: UBERON:0005856 @@ -14701,7 +14345,7 @@ xref: EHDAA2_RETIRED:0003148 xref: EHDAA:8979 is_a: UBERON:0007524 {source="AEO"} ! dense mesenchyme tissue is_a: UBERON:0011585 {source="cjm"} ! cell condensation -relationship: composed_primarily_of CL:0000335 {source="AEO-modified-relation"} ! mesenchyme condensation cell +relationship: RO:0002473 CL:0000335 {source="AEO-modified-relation"} ! composed primarily of mesenchyme condensation cell [Term] id: UBERON:0005944 @@ -14714,7 +14358,6 @@ subset: uberon_slim synonym: "skeleton axiale" RELATED OMO:0003011 [Wikipedia:Axial_skeleton] xref: AAO:0000963 xref: EMAPA:17214 -xref: EMAPA:18043 xref: MA:0000308 xref: NCIT:C32172 xref: SCTID:361725000 @@ -14723,13 +14366,12 @@ xref: VSAO:0000056 xref: Wikipedia:Axial_skeleton xref: XAO:0004011 is_a: UBERON:0010912 ! subdivision of skeleton -relationship: contributes_to_morphology_of UBERON:0001434 ! skeletal system -relationship: develops_from UBERON:0003089 ! sclerotome relationship: part_of UBERON:0011137 ! axial skeletal system -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg" xsd:anyURI +relationship: RO:0002202 UBERON:0003089 ! develops from sclerotome +relationship: RO:0002433 UBERON:0001434 ! contributes to morphology of skeletal system +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" xsd:anyURI -property_value: UBPROP:0000001 "Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000056", ontology="VSAO", source="PSPUB:0000170"} [Term] id: UBERON:0006267 @@ -14747,9 +14389,8 @@ is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium -relationship: develops_from UBERON:0006268 {source="EHDAA2"} ! notochordal process -property_value: editor_note "TODO - check ordering; awaiting confirmation from JB" xsd:string -property_value: UBPROP:0000001 "The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001212", ontology="VHOG", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0006268 {source="EHDAA2"} ! develops from notochordal process +property_value: IAO:0000116 "TODO - check ordering; awaiting confirmation from JB" xsd:string [Term] id: UBERON:0006268 @@ -14768,8 +14409,8 @@ xref: NCIT:C34232 xref: UMLS:C1518430 {source="ncithesaurus:Notochordal_Process"} xref: VHOG:0001213 is_a: UBERON:0005423 ! developing anatomical structure -relationship: develops_from UBERON:0000924 {source="EHDAA2"} ! ectoderm -relationship: only_in_taxon NCBITaxon:7711 ! Chordata +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002202 UBERON:0000924 {source="EHDAA2"} ! develops from ectoderm [Term] id: UBERON:0006314 @@ -14788,8 +14429,8 @@ xref: MESH:D001826 xref: Wikipedia:Body_fluid is_a: UBERON:0000463 ! organism substance intersection_of: UBERON:0000463 ! organism substance -intersection_of: has_quality PATO:0001548 ! quality of a liquid -relationship: has_quality PATO:0001548 ! quality of a liquid +intersection_of: RO:0000086 PATO:0001548 ! has quality quality of a liquid +relationship: RO:0000086 PATO:0001548 ! has quality quality of a liquid [Term] id: UBERON:0006595 @@ -14803,11 +14444,11 @@ xref: TAO:0000416 xref: ZFA:0000416 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0000925 ! endoderm intersection_of: part_of UBERON:0000307 ! blastula -relationship: has_potential_to_develop_into UBERON:0000925 ! endoderm -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +intersection_of: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm relationship: part_of UBERON:0000307 ! blastula +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm [Term] id: UBERON:0006596 @@ -14821,8 +14462,8 @@ xref: TAO:0000568 xref: ZFA:0000568 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0000178 ! blood -relationship: has_potential_to_develop_into UBERON:0000178 ! blood +intersection_of: RO:0002387 UBERON:0000178 ! has potential to develop into blood +relationship: RO:0002387 UBERON:0000178 ! has potential to develop into blood [Term] id: UBERON:0006598 @@ -14836,10 +14477,10 @@ xref: TAO:0001116 xref: ZFA:0001116 is_a: UBERON:0002050 ! embryonic structure intersection_of: UBERON:0005423 ! developing anatomical structure -intersection_of: has_potential_to_develop_into UBERON:0000061 ! anatomical structure intersection_of: part_of UBERON:0000922 ! embryo -relationship: has_potential_to_develop_into UBERON:0000061 ! anatomical structure -property_value: editor_note "Consider merging with anlage" xsd:string +intersection_of: RO:0002387 UBERON:0000061 ! has potential to develop into anatomical structure +relationship: RO:0002387 UBERON:0000061 ! has potential to develop into anatomical structure +property_value: IAO:0000116 "Consider merging with anlage" xsd:string [Term] id: UBERON:0006601 @@ -14855,11 +14496,11 @@ xref: XAO:0004132 xref: ZFA:0001376 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0000924 ! ectoderm intersection_of: part_of UBERON:0000307 ! blastula -relationship: has_potential_to_develop_into UBERON:0000924 ! ectoderm -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +intersection_of: RO:0002387 UBERON:0000924 ! has potential to develop into ectoderm relationship: part_of UBERON:0000307 ! blastula +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002387 UBERON:0000924 ! has potential to develop into ectoderm [Term] id: UBERON:0006603 @@ -14873,11 +14514,11 @@ xref: TAO:0001377 xref: ZFA:0001377 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0000926 ! mesoderm intersection_of: part_of UBERON:0000307 ! blastula -relationship: has_potential_to_develop_into UBERON:0000926 ! mesoderm -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +intersection_of: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm relationship: part_of UBERON:0000307 ! blastula +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm [Term] id: UBERON:0006914 @@ -14893,7 +14534,6 @@ is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: has_part CL:0000076 ! squamous epithelial cell relationship: has_part CL:0000076 ! squamous epithelial cell -property_value: UBPROP:0000012 "FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium" xsd:string {external_ontology="FBbt"} [Term] id: UBERON:0006965 @@ -14924,7 +14564,7 @@ xref: EHDAA2_RETIRED:0003192 xref: FMA:24137 xref: NCIT:C34022 xref: UMLS:C1515977 {source="ncithesaurus:Anatomic_Surface"} -is_a: UBERON:0010199 {notes="via morphological boundary in CARO"} ! bona-fide anatomical boundary +is_a: UBERON:0010199 ! bona-fide anatomical boundary [Term] id: UBERON:0007005 @@ -14947,13 +14587,14 @@ xref: FMA:293143 xref: SCTID:360387000 xref: VHOG:0001641 xref: XAO:0000235 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue -relationship: developmentally_induced_by UBERON:0009881 ! anterior lateral plate mesoderm -relationship: develops_from UBERON:0004872 ! splanchnic layer of lateral plate mesoderm relationship: part_of UBERON:0004140 ! primary heart field relationship: part_of UBERON:0009881 ! anterior lateral plate mesoderm -property_value: editor_note "consider FBbt:00005541 ! cardiogenic mesoderm" xsd:string -property_value: editor_note "review EHDAA2 placement" xsd:string +relationship: RO:0002202 UBERON:0004872 ! develops from splanchnic layer of lateral plate mesoderm +relationship: RO:0002256 UBERON:0009881 ! developmentally induced by anterior lateral plate mesoderm +property_value: IAO:0000116 "consider FBbt:00005541 ! cardiogenic mesoderm" xsd:string +property_value: IAO:0000116 "review EHDAA2 placement" xsd:string [Term] id: UBERON:0007010 @@ -14963,10 +14604,10 @@ def: "Organism at the cleavage stage." [OBOL:automatic] xref: BILA:0000058 is_a: UBERON:0000922 ! embryo intersection_of: UBERON:0000468 ! multicellular organism -intersection_of: existence_ends_with UBERON:0000107 ! cleavage stage -intersection_of: existence_starts_with UBERON:0000107 ! cleavage stage -relationship: existence_ends_with UBERON:0000107 ! cleavage stage -relationship: existence_starts_with UBERON:0000107 ! cleavage stage +intersection_of: RO:0002489 UBERON:0000107 ! existence starts with cleavage stage +intersection_of: RO:0002493 UBERON:0000107 ! existence ends with cleavage stage +relationship: RO:0002489 UBERON:0000107 ! existence starts with cleavage stage +relationship: RO:0002493 UBERON:0000107 ! existence ends with cleavage stage [Term] id: UBERON:0007026 @@ -14985,12 +14626,11 @@ xref: SCTID:360394002 xref: UMLS:C1514442 {source="ncithesaurus:Primordial_Gut"} is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001555 ! digestive tract -relationship: existence_starts_during UBERON:0000109 ! gastrula stage -relationship: has_developmental_contribution_from UBERON:0000925 ! endoderm -relationship: has_developmental_contribution_from UBERON:0000926 ! mesoderm -relationship: has_potential_to_develop_into UBERON:0001555 ! digestive tract -property_value: UBPROP:0000011 "The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis" xsd:string {source="NCBIBook:NBK10107"} +intersection_of: RO:0002387 UBERON:0001555 ! has potential to develop into digestive tract +relationship: RO:0002254 UBERON:0000925 ! has developmental contribution from endoderm +relationship: RO:0002254 UBERON:0000926 ! has developmental contribution from mesoderm +relationship: RO:0002387 UBERON:0001555 ! has potential to develop into digestive tract +relationship: RO:0002488 UBERON:0000109 ! existence starts during gastrula stage [Term] id: UBERON:0007100 @@ -15003,14 +14643,12 @@ synonym: "adult heart" RELATED [FBbt:00003154] synonym: "dorsal tube" NARROW [Wikipedia:Heart] synonym: "heart" NARROW [GO:0007507] xref: http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg -xref: SPD:0000130 xref: TADS:0000147 is_a: UBERON:0015228 ! circulatory organ intersection_of: UBERON:0015228 ! circulatory organ intersection_of: capable_of GO:0008015 ! blood circulation -relationship: capable_of GO:0008015 {notes="GO uses blood circulation generically to include the haemolymphatic fluid of arthropods"} ! blood circulation +relationship: capable_of GO:0008015 ! blood circulation relationship: has_part CL:0002494 ! cardiocyte -property_value: UBPROP:0000008 "note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis" xsd:string [Term] id: UBERON:0007135 @@ -15023,8 +14661,7 @@ xref: EFO:0003497 xref: TAO:0000131 xref: ZFA:0000131 is_a: UBERON:0016879 ! future central nervous system -relationship: develops_from UBERON:0003075 ! neural plate -property_value: UBPROP:0000001 "An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000131", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002202 UBERON:0003075 ! develops from neural plate [Term] id: UBERON:0007282 @@ -15038,9 +14675,9 @@ xref: TAO:0000053 xref: ZFA:0000053 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0003059 ! presomitic mesoderm -relationship: develops_from UBERON:0009618 {consistent_with="https://github.com/obophenotype/uberon/wiki/The-neural-crest", source="EDHAA2"} ! trunk paraxial mesoderm -relationship: has_potential_to_develop_into UBERON:0003059 ! presomitic mesoderm +intersection_of: RO:0002387 UBERON:0003059 ! has potential to develop into presomitic mesoderm +relationship: RO:0002202 UBERON:0009618 ! develops from trunk paraxial mesoderm +relationship: RO:0002387 UBERON:0003059 ! has potential to develop into presomitic mesoderm [Term] id: UBERON:0007284 @@ -15055,12 +14692,11 @@ xref: TAO:0000063 xref: ZFA:0000063 is_a: UBERON:0016879 ! future central nervous system intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0003075 ! neural plate -relationship: develops_from UBERON:0002346 ! neurectoderm -relationship: has_potential_to_develop_into UBERON:0003075 ! neural plate +intersection_of: RO:0002387 UBERON:0003075 ! has potential to develop into neural plate relationship: part_of UBERON:0004734 ! gastrula -property_value: editor_note "consider merging" xsd:string -property_value: UBPROP:0000001 "Region of the gastrula which gives rise to the neural plate.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000063", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002202 UBERON:0002346 ! develops from neurectoderm +relationship: RO:0002387 UBERON:0003075 ! has potential to develop into neural plate +property_value: IAO:0000116 "consider merging" xsd:string [Term] id: UBERON:0007285 @@ -15076,10 +14712,10 @@ xref: XAO:0004134 xref: ZFA:0000591 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 {source="https://github.com/obophenotype/uberon/issues/1277"} ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0003077 {source="https://github.com/obophenotype/uberon/issues/1277"} ! paraxial mesoderm intersection_of: part_of UBERON:0000307 {source="https://github.com/obophenotype/uberon/issues/1277"} ! blastula -relationship: has_potential_to_develop_into UBERON:0003077 ! paraxial mesoderm +intersection_of: RO:0002387 UBERON:0003077 {source="https://github.com/obophenotype/uberon/issues/1277"} ! has potential to develop into paraxial mesoderm relationship: part_of UBERON:0000307 ! blastula +relationship: RO:0002387 UBERON:0003077 ! has potential to develop into paraxial mesoderm [Term] id: UBERON:0007500 @@ -15120,7 +14756,7 @@ is_a: UBERON:0003104 ! mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: participates_in GO:0016477 ! cell migration relationship: participates_in GO:0016477 ! cell migration -property_value: editor_note "this class will be an important part of the NC reorganization" xsd:string +property_value: IAO:0000116 "this class will be an important part of the NC reorganization" xsd:string [Term] id: UBERON:0007688 @@ -15135,7 +14771,6 @@ synonym: "organ field" RELATED [] xref: AEO:0000170 xref: EFO:0001649 xref: EHDAA2:0003170 -xref: FBbt:00005426 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: Wikipedia:Anlage_(biology) is_a: UBERON:0000479 {source="FBbt"} ! tissue is_a: UBERON:0005423 {source="AEO", source="FBbt"} ! developing anatomical structure @@ -15156,10 +14791,8 @@ xref: NCIT:C33854 xref: UMLS:C0489903 {source="ncithesaurus:Vascular_System"} is_a: UBERON:0000467 ! anatomical system relationship: part_of UBERON:0004535 {source="MA"} ! cardiovascular system -relationship: present_in_taxon NCBITaxon:9606 -property_value: editor_note "consider merging with vasculature" xsd:string -property_value: UBPROP:0000001 "The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]." xsd:string {source="ncithesaurus:Vascular_System"} -property_value: UBPROP:0000012 "in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system" xsd:string {external_ontology="MA"} +property_value: IAO:0000116 "consider merging with vasculature" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0009142 @@ -15171,10 +14804,10 @@ xref: EHDAA2:0001113 xref: EHDAA:177 xref: EMAPA:16097 is_a: UBERON:0000477 ! anatomical cluster -relationship: composed_primarily_of UBERON:0003104 ! mesenchyme -relationship: has_developmental_contribution_from UBERON:0000926 {source="EHDAA2"} ! mesoderm relationship: part_of UBERON:0000922 ! embryo -property_value: editor_note "consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)" xsd:string +relationship: RO:0002254 UBERON:0000926 {source="EHDAA2"} ! has developmental contribution from mesoderm +relationship: RO:0002473 UBERON:0003104 ! composed primarily of mesenchyme +property_value: IAO:0000116 "consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)" xsd:string [Term] id: UBERON:0009569 @@ -15208,6 +14841,7 @@ synonym: "ALPM" EXACT [ZFA:0005041] xref: EFO:0003704 xref: TAO:0005041 xref: ZFA:0005041 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue relationship: part_of UBERON:0003081 {source="ZFA"} ! lateral plate mesoderm @@ -15220,15 +14854,14 @@ subset: common_anatomy subset: upper_level synonym: "multicellular structure" EXACT [FBbt:00100313] xref: CARO:0010000 -xref: FBbt:00100313 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: has_quality PATO:0001993 ! multicellular +intersection_of: RO:0000086 PATO:0001993 ! has quality multicellular relationship: has_part CL:0000000 ! cell -relationship: has_quality PATO:0001993 ! multicellular -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0000086 PATO:0001993 ! has quality multicellular +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0010199 @@ -15257,12 +14890,12 @@ is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000463 ! organism substance intersection_of: UBERON:0000463 ! organism substance intersection_of: output_of GO:0007596 ! blood coagulation -relationship: develops_from UBERON:0000178 {source="BTO"} ! blood relationship: has_part CL:0000232 ! erythrocyte relationship: has_part CL:0000233 ! platelet relationship: has_part CL:0000738 ! leukocyte relationship: has_part GO:0005577 ! fibrinogen complex relationship: output_of GO:0007596 ! blood coagulation +relationship: RO:0002202 UBERON:0000178 {source="BTO"} ! develops from blood [Term] id: UBERON:0010314 @@ -15272,9 +14905,8 @@ def: "An anatomical structure that has some part that develops from the neural c subset: grouping_class is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: has_developmental_contribution_from UBERON:0002342 ! neural crest -relationship: has_developmental_contribution_from UBERON:0002342 ! neural crest -property_value: IAO:0000232 "Grouping term for query purposes" xsd:string +intersection_of: RO:0002254 UBERON:0002342 ! has developmental contribution from neural crest +relationship: RO:0002254 UBERON:0002342 ! has developmental contribution from neural crest [Term] id: UBERON:0010316 @@ -15282,7 +14914,7 @@ name: germ layer / neural crest namespace: uberon is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0005291 ! embryonic tissue -relationship: develops_from UBERON:0002532 ! epiblast (generic) +relationship: RO:0002202 UBERON:0002532 ! develops from epiblast (generic) [Term] id: UBERON:0010371 @@ -15294,8 +14926,8 @@ xref: FMA:69064 is_a: UBERON:0000483 ! epithelium is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000483 ! epithelium -intersection_of: develops_from UBERON:0000924 ! ectoderm -relationship: composed_primarily_of CL:0002077 ! ecto-epithelial cell +intersection_of: RO:0002202 UBERON:0000924 ! develops from ectoderm +relationship: RO:0002473 CL:0002077 ! composed primarily of ecto-epithelial cell [Term] id: UBERON:0010912 @@ -15311,7 +14943,6 @@ xref: VSAO:0000042 is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision relationship: part_of UBERON:0000075 {source="UBERONREF:0000003"} ! subdivision of skeletal system relationship: part_of UBERON:0004288 {source="VSAO"} ! skeleton -property_value: UBPROP:0000001 "Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000042", notes="incorrect", ontology="VSAO", source="VSAO:curator"} [Term] id: UBERON:0011137 @@ -15332,7 +14963,7 @@ synonym: "axial skeletal system" BROAD [https://github.com/obophenotype/uberon/w synonym: "post-cranial axial skeletal system" EXACT [] xref: FMA:302077 is_a: UBERON:0000075 {source="FMA"} ! subdivision of skeletal system -relationship: develops_from UBERON:0003089 {source="cjm"} ! sclerotome +relationship: RO:0002202 UBERON:0003089 {source="cjm"} ! develops from sclerotome property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" xsd:anyURI [Term] @@ -15343,15 +14974,14 @@ def: "A subdivision of an anatomical system." [http://orcid.org/0000-0002-6601-2 subset: common_anatomy subset: human_reference_atlas subset: upper_level -xref: FBbt:00007330 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67509 xref: SCTID:91690000 is_a: UBERON:0010000 {source="FBbt"} ! multicellular anatomical structure relationship: part_of UBERON:0000467 ! anatomical system -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0011585 @@ -15361,7 +14991,7 @@ def: "Anatomical structure that is an aggregation of similar cells from which ca xref: VSAO:0000006 xref: XAO:0004021 is_a: UBERON:0000061 {source="VSAO"} ! anatomical structure -property_value: editor_note "consider obsoleting, coordinate with VSAO" xsd:string +property_value: IAO:0000116 "consider obsoleting, coordinate with VSAO" xsd:string [Term] id: UBERON:0011676 @@ -15374,7 +15004,7 @@ synonym: "body segment" RELATED [] synonym: "main body segment" RELATED [] is_a: UBERON:0000475 ! organism subdivision relationship: part_of UBERON:0013701 ! main body axis -property_value: editor_note "Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem" xsd:string +property_value: IAO:0000116 "Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem" xsd:string [Term] id: UBERON:0011695 @@ -15405,10 +15035,9 @@ synonym: "schizocoelom" NARROW [] xref: EHDAA2:0004731 xref: Wikipedia:Coelom is_a: UBERON:0000481 {source="EHDAA2"} ! multi-tissue structure -relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -property_value: editor_note "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." xsd:string -property_value: UBPROP:0000007 "coelomic" xsd:string +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +property_value: IAO:0000116 "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." xsd:string +property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} [Term] id: UBERON:0012275 @@ -15421,7 +15050,7 @@ xref: FMA:86452 is_a: UBERON:0000483 ! epithelium is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000483 ! epithelium -intersection_of: develops_from UBERON:0000926 ! mesoderm +intersection_of: RO:0002202 UBERON:0000926 ! develops from mesoderm [Term] id: UBERON:0012429 @@ -15437,12 +15066,12 @@ xref: CALOHA:TS-2142 xref: FMA:14073 xref: NCIT:C13051 xref: UMLS:C0229619 {source="ncithesaurus:Hematopoietic_Tissue"} +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0034769 {source="FMA"} ! lymphomyeloid tissue intersection_of: UBERON:0000479 ! tissue intersection_of: site_of GO:0030097 ! hemopoiesis relationship: part_of UBERON:0002390 {source="defitional"} ! hematopoietic system relationship: site_of GO:0030097 ! hemopoiesis -property_value: UBPROP:0000008 "Bone marrow in humans, kidney interstitium in Danio, within a stroma of reticuloendothelial tissue" xsd:string [Term] id: UBERON:0013522 @@ -15463,11 +15092,11 @@ subset: common_anatomy synonym: "foramen space" NARROW [] xref: FMA:9338 is_a: UBERON:0000464 {source="FMA"} ! anatomical space -relationship: connects UBERON:0000464 {cardinality="2"} ! anatomical space -relationship: luminal_space_of UBERON:0004111 ! anatomical conduit -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0002176 UBERON:0000464 {cardinality="2"} ! connects anatomical space +relationship: RO:0002572 UBERON:0004111 ! luminal space of anatomical conduit +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0013701 @@ -15476,7 +15105,7 @@ namespace: uberon def: "A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages." [https://orcid.org/0000-0002-6601-2165] subset: non_informative is_a: UBERON:0000475 ! organism subdivision -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0013702 @@ -15488,11 +15117,9 @@ synonym: "body" RELATED [AEO:0000103] synonym: "whole body" RELATED [BTO:0001489] xref: AEO:0000103 xref: BTO:0001489 -xref: EMAPA:36031 xref: FMA:231424 is_a: UBERON:0000475 {source="AEO"} ! organism subdivision relationship: part_of UBERON:0013701 ! main body axis -property_value: UBPROP:0000001 "Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]." xsd:string {source="FMA:231424"} [Term] id: UBERON:0014477 @@ -15510,7 +15137,7 @@ xref: Wikipedia:Thoracic_skeleton is_a: UBERON:0010912 ! subdivision of skeleton relationship: part_of UBERON:0000915 ! thoracic segment of trunk relationship: part_of UBERON:0002090 ! postcranial axial skeleton -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0014903 @@ -15522,9 +15149,9 @@ xref: TAO:0005076 xref: ZFA:0005076 is_a: UBERON:0001048 ! primordium intersection_of: UBERON:0001048 ! primordium -intersection_of: has_potential_to_develop_into UBERON:0002049 ! vasculature -relationship: has_potential_to_develop_into UBERON:0002049 ! vasculature +intersection_of: RO:0002387 UBERON:0002049 ! has potential to develop into vasculature relationship: part_of UBERON:0011695 ! embryonic cardiovascular system +relationship: RO:0002387 UBERON:0002049 ! has potential to develop into vasculature [Term] id: UBERON:0015203 @@ -15532,7 +15159,6 @@ name: non-connected functional system namespace: uberon def: "An anatomical group whose component structures share a common function." [AEO:0000093, AEO:JB, FBbt:00007278, FBC:DOS] xref: AEO:0000093 -xref: FBbt:00007278 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0034923 ! disconnected anatomical group [Term] @@ -15543,11 +15169,7 @@ def: "Any structure that is placed on one side of the left-right axis of a bilat subset: grouping_class subset: non_informative is_a: UBERON:0000061 ! anatomical structure -intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: in_lateral_side_of UBERON:0000465 ! material anatomical entity -relationship: in_lateral_side_of UBERON:0000465 ! material anatomical entity -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -property_value: IAO:0000232 "This class is primarily to implement taxon constraints. It may be removed in the future." xsd:string +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria [Term] id: UBERON:0015228 @@ -15560,10 +15182,9 @@ synonym: "cardiac structure" RELATED [] synonym: "circulatory vessel" NARROW [] synonym: "heart" BROAD [] synonym: "heart or heart like organ" EXACT [] -xref: SPD:0000130 is_a: UBERON:0003103 ! compound organ -relationship: has_quality PATO:0001690 ! contractile relationship: part_of UBERON:0001009 ! circulatory system +relationship: RO:0000086 PATO:0001690 ! has quality contractile [Term] id: UBERON:0015410 @@ -15575,7 +15196,7 @@ xref: EMAPA:37597 {source="MA:th"} xref: MA:0002449 is_a: UBERON:0005178 {source="MA"} ! thoracic cavity element relationship: part_of UBERON:0004535 ! cardiovascular system -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0015757 @@ -15595,10 +15216,10 @@ synonym: "future CNS" EXACT [] synonym: "presumptive central nervous system" EXACT [] is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001017 ! central nervous system -relationship: develops_from UBERON:0000924 ! ectoderm -relationship: has_potential_to_develop_into UBERON:0001017 ! central nervous system +intersection_of: RO:0002387 UBERON:0001017 ! has potential to develop into central nervous system relationship: part_of UBERON:0016880 ! future nervous system +relationship: RO:0002202 UBERON:0000924 ! develops from ectoderm +relationship: RO:0002387 UBERON:0001017 ! has potential to develop into central nervous system [Term] id: UBERON:0016880 @@ -15610,9 +15231,9 @@ synonym: "presumptive nervous system" EXACT [AAO:0000477] xref: AAO:0000477 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001016 ! nervous system -relationship: existence_starts_during_or_after UBERON:0000111 ! organogenesis stage -relationship: has_potential_to_develop_into UBERON:0001016 ! nervous system +intersection_of: RO:0002387 UBERON:0001016 ! has potential to develop into nervous system +relationship: RO:0002387 UBERON:0001016 ! has potential to develop into nervous system +relationship: RO:0002496 UBERON:0000111 ! existence starts during or after organogenesis stage [Term] id: UBERON:0016887 @@ -15626,8 +15247,8 @@ xref: EHDAA2:0000003 xref: EMAPA:16042 is_a: UBERON:0000481 {source="AEO"} ! multi-tissue structure relationship: adjacent_to UBERON:0002050 ! embryonic structure -relationship: existence_starts_and_ends_during UBERON:0000068 ! embryo stage relationship: part_of UBERON:0004716 {source="AEO"} ! conceptus +relationship: RO:0002491 UBERON:0000068 ! existence starts and ends during embryo stage [Term] id: UBERON:0034769 @@ -15646,10 +15267,10 @@ subset: common_anatomy synonym: "anatomical cluster" RELATED [CARO:0020001] xref: CARO:0020001 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure -relationship: composed_primarily_of UBERON:0000064 ! organ part -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0002473 UBERON:0000064 ! composed primarily of organ part +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0034923 @@ -15658,14 +15279,13 @@ namespace: uberon def: "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other." [CARO:0020000] subset: common_anatomy xref: CARO:0020000 -xref: FBbt:00007276 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000465 {source="CARO"} ! material anatomical entity -relationship: composed_primarily_of UBERON:0000061 ! anatomical structure relationship: has_component UBERON:0000061 {minCardinality="2"} ! anatomical structure -relationship: has_quality PATO:0010001 ! disconnected -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0000086 PATO:0010001 ! has quality disconnected +relationship: RO:0002473 UBERON:0000061 ! composed primarily of anatomical structure +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0034925 @@ -15674,11 +15294,11 @@ namespace: uberon def: "A collection of anatomical structures that are alike in terms of their morphology or developmental origin." [http://orcid.org/0000-0002-6601-2165] subset: common_anatomy is_a: UBERON:0000465 ! material anatomical entity -relationship: has_member UBERON:0000061 ! anatomical structure -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: editor_note "resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected" xsd:string +relationship: RO:0002351 UBERON:0000061 ! has member anatomical structure +property_value: IAO:0000116 "resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0035804 @@ -15703,6 +15323,12 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007688 ! anlage +[Typedef] +id: BFO:0000067 +name: contains process +def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] +comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant + [Typedef] id: CL:4030044 name: has_not_completed @@ -15722,11 +15348,6 @@ id: RO:0000052 name: characteristic of def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." [] comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. -property_value: IAO:0000111 "inheres in" xsd:string -property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string -property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string -property_value: IAO:0000118 "inheres_in" xsd:string -property_value: RO:0001900 RO:0001901 is_functional: true is_a: RO:0002314 ! characteristic of part of inverse_of: bearer_of ! bearer of @@ -15736,10 +15357,7 @@ id: RO:0000079 name: function of def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. -property_value: editor_note "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string -property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string -property_value: IAO:0000118 "function_of" xsd:string -property_value: IAO:0000118 "is function of" xsd:string +property_value: IAO:0000116 "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string is_a: RO:0000052 ! characteristic of inverse_of: RO:0000085 ! has function @@ -15748,22 +15366,16 @@ id: RO:0000080 name: quality of def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. -property_value: editor_note "A quality inheres in its bearer at all times for which the quality exists." xsd:string -property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string -property_value: IAO:0000118 "is quality of" xsd:string -property_value: IAO:0000118 "quality_of" xsd:string +property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string is_a: RO:0000052 ! characteristic of -inverse_of: has_quality ! has quality +inverse_of: RO:0000086 ! has quality [Typedef] id: RO:0000081 name: role of def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. -property_value: editor_note "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string -property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string -property_value: IAO:0000118 "is role of" xsd:string -property_value: IAO:0000118 "role_of" xsd:string +property_value: IAO:0000116 "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string is_a: RO:0000052 ! characteristic of inverse_of: RO:0000087 ! has role @@ -15771,19 +15383,22 @@ inverse_of: RO:0000087 ! has role id: RO:0000085 name: has function def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] -property_value: editor_note "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string -property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string -property_value: IAO:0000118 "has_function" xsd:string +property_value: IAO:0000116 "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string domain: BFO:0000004 ! independent continuant is_a: bearer_of ! bearer of +[Typedef] +id: RO:0000086 +name: has quality +def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] +property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string +is_a: bearer_of ! bearer of + [Typedef] id: RO:0000087 name: has role def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] -property_value: editor_note "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string -property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string -property_value: IAO:0000118 "has_role" xsd:string +property_value: IAO:0000116 "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string domain: BFO:0000004 ! independent continuant is_a: bearer_of ! bearer of @@ -15808,12 +15423,7 @@ id: RO:0001000 name: derives from def: "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" [] subset: ro-eco -property_value: editor_note "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." xsd:string -property_value: IAO:0000112 "this cell derives from this parent cell (cell division)" xsd:string -property_value: IAO:0000112 "this nucleus derives from this parent nucleus (nuclear division)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000118 "derives_from" xsd:string -property_value: IAO:0000232 "This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations." xsd:string +property_value: IAO:0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." xsd:string inverse_of: RO:0001001 ! derives into [Typedef] @@ -15821,33 +15431,57 @@ id: RO:0001001 name: derives into def: "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" [] subset: ro-eco -property_value: editor_note "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." xsd:string -property_value: IAO:0000112 "this parent cell derives into this cell (cell division)" xsd:string -property_value: IAO:0000112 "this parent nucleus derives into this nucleus (nuclear division)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000118 "derives_into" xsd:string +property_value: IAO:0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." xsd:string + +[Typedef] +id: RO:0001015 +name: location of +def: "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" [] +property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +is_transitive: true +inverse_of: RO:0001025 ! located in + +[Typedef] +id: RO:0001025 +name: located in +def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +property_value: IAO:0000116 "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" xsd:string +property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Located_in" xsd:anyURI +domain: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +range: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +is_transitive: true +transitive_over: part_of ! part of [Typedef] id: RO:0002000 name: 2D boundary of def: "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" [] -property_value: editor_note "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string -property_value: editor_note "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string -property_value: IAO:0000112 "the surface of my skin is a 2D boundary of my body" xsd:string -property_value: IAO:0000118 "2D_boundary_of" xsd:string -property_value: IAO:0000118 "boundary of" xsd:string -property_value: IAO:0000118 "is 2D boundary of" xsd:string -property_value: IAO:0000118 "is boundary of" xsd:string -property_value: IAO:0000118 "surface of" xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string +is_a: RO:0002323 ! mereotopologically related to +inverse_of: RO:0002002 ! has 2D boundary + +[Typedef] +id: RO:0002002 +name: has 2D boundary +def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000141 ! immaterial entity is_a: RO:0002323 ! mereotopologically related to -inverse_of: has_boundary ! has 2D boundary + +[Typedef] +id: RO:0002005 +name: innervated_by +domain: UBERON:0000061 ! anatomical structure +inverse_of: RO:0002134 ! innervates [Typedef] id: RO:0002006 name: has synaptic terminal of -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: overlaps ! overlaps inverse_of: RO:0002130 ! has synaptic terminal in @@ -15929,16 +15563,23 @@ id: RO:0002081 name: before or simultaneous with comment: Primitive instance level timing relation between events subset: ro-eco -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000118 "<=" xsd:string is_a: RO:0002222 ! temporally related to +[Typedef] +id: RO:0002082 +name: simultaneous with +def: "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." [] +comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) +subset: ro-eco +is_symmetric: true +is_transitive: true +is_a: RO:0002081 ! before or simultaneous with + [Typedef] id: RO:0002086 name: ends after comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) subset: ro-eco -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string is_transitive: true is_a: RO:0002222 ! temporally related to @@ -15946,25 +15587,16 @@ is_a: RO:0002222 ! temporally related to id: RO:0002100 name: has soma location def: "Relation between a neuron and a material anatomical entity that its soma is part of." [] -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron range: UBERON:0000465 ! material anatomical entity is_a: overlaps ! overlaps -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] [Typedef] id: RO:0002101 name: fasciculates with def: "relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.\n" [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "fasciculates with" xsd:string -property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: overlaps ! overlaps inverse_of: RO:0002132 ! has fasciculating neuron projection @@ -15973,27 +15605,23 @@ inverse_of: RO:0002132 ! has fasciculating neuron projection id: RO:0002102 name: axon synapses in def: "Relation between a neuron and some structure its axon forms (chemical) synapses in." [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: RO:0002113 ! has presynaptic terminal in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "BFO_0000051 some (\n GO_0030424 and BFO_0000051 some (\n GO_0042734 and BFO_0000050 some (\n GO_0045202 and BFO_0000050 some ?Y)))" [] +[Typedef] +id: RO:0002103 +name: synapsed by +def: "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " [] +is_a: RO:0002485 ! receives input from +inverse_of: RO:0002120 ! synapsed to +expand_expression_to: "BFO_0000051 some (GO_0045211 that part_of some (GO_0045202 that has_part some (GO_0042734 that BFO_0000050 some Y?)))" [] + [Typedef] id: RO:0002104 name: has plasma membrane part def: "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part." [] -property_value: IAO:0000112 "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9990-8331 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 -property_value: RO:0001900 RO:0001901 domain: UBERON:0000465 ! material anatomical entity range: UBERON:0000465 ! material anatomical entity is_a: has_part ! has part @@ -16003,29 +15631,19 @@ expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] id: RO:0002110 name: has postsynaptic terminal in def: "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. " [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "synapsed in" xsd:string -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: RO:0002130 ! has synaptic terminal in inverse_of: RO:0002113 ! has presynaptic terminal in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (\n http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some (\n http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))" [] [Typedef] id: RO:0002113 name: has presynaptic terminal in def: "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input." [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000118 "synapses in" xsd:string -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: RO:0002130 ! has synaptic terminal in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000050 some Y?)" [] [Typedef] @@ -16033,11 +15651,6 @@ id: RO:0002120 name: synapsed to def: " Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.\n " [] comment: N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part some (\n ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( \n ‘synapse ; GO:0045202’ that has_part some (\n ‘post-synaptic membrane ; GO:0045211’ that part_of some N2)))) -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 is_a: RO:0002486 ! sends output to expand_expression_to: "BFO_0000051 some (GO_0042734 that part_of some (GO_0045202 that BFO_0000051 some (GO_0045211 that BFO_0000050 some Y?)))" [] @@ -16045,103 +15658,270 @@ expand_expression_to: "BFO_0000051 some (GO_0042734 that part_of some (GO_004520 id: RO:0002130 name: has synaptic terminal in def: "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "has synapse in" xsd:string -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: overlaps ! overlaps -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "RO_0002131 some (GO_0045202 that BFO_0000050 some Y?)" [] [Typedef] id: RO:0002132 name: has fasciculating neuron projection def: "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "has fasciculating component" xsd:string -property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string -property_value: RO:0001900 RO:0001901 is_a: overlaps ! overlaps +[Typedef] +id: RO:0002134 +name: innervates +def: "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." [] +transitive_over: part_of ! part of +expand_expression_to: "RO_0002132 some (GO_0043005 that (RO_0002131 some (GO_0045202 that BFO_0000050 some Y?)))" [] + +[Typedef] +id: RO:0002150 +name: continuous with +def: "X continuous_with Y if and only if X and Y share a fiat boundary." [] +property_value: seeAlso "FMA:85972" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000004 ! independent continuant +is_symmetric: true +is_a: RO:0002323 ! mereotopologically related to + +[Typedef] +id: RO:0002158 +name: shares ancestor with +def: "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." [] +comment: VBO calls this homologous_to +is_symmetric: true +is_transitive: true +is_a: RO:0002320 ! evolutionarily related to + +[Typedef] +id: RO:0002160 +name: only in taxon +def: "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." [] +property_value: IAO:0000116 "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" xsd:string +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints +is_a: RO:0002162 ! in taxon + +[Typedef] +id: RO:0002162 +name: in taxon +def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." [] +comment: Connects a biological entity to its taxon of origin. +subset: ro-eco +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints +holds_over_chain: capable_of RO:0002162 +holds_over_chain: extends_fibers_into RO:0002162 +holds_over_chain: has_part RO:0002162 +holds_over_chain: part_of RO:0002162 +holds_over_chain: results_in_developmental_progression_of RO:0002162 +holds_over_chain: RO:0002202 RO:0002162 +holds_over_chain: RO:0002206 RO:0002162 +holds_over_chain: RO:0002225 RO:0002162 +holds_over_chain: RO:0002254 RO:0002162 +is_a: RO:0002320 ! evolutionarily related to + [Typedef] id: RO:0002163 name: spatially disjoint from def: "A is spatially_disjoint_from B if and only if they have no parts in common" [] subset: ro-eco -property_value: editor_note "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" xsd:anyURI is_a: RO:0002323 ! mereotopologically related to expand_expression_to: "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" [] +[Typedef] +id: RO:0002170 +name: connected to +def: "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" [] +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI +is_a: RO:0002323 ! mereotopologically related to + +[Typedef] +id: RO:0002176 +name: connects +def: "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." [] +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI +domain: BFO:0000004 ! independent continuant +is_a: RO:0002323 ! mereotopologically related to + +[Typedef] +id: RO:0002177 +name: attached to part of +def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000061 ! anatomical structure +is_a: RO:0002323 ! mereotopologically related to +is_a: RO:0002567 ! biomechanically related to + +[Typedef] +id: RO:0002178 +name: supplies +def: "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." [] +property_value: IAO:0000116 "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" xsd:string +is_a: RO:0002170 ! connected to + +[Typedef] +id: RO:0002179 +name: drains +def: "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." [] +property_value: IAO:0000116 "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" xsd:string +is_a: RO:0002170 ! connected to + +[Typedef] +id: RO:0002202 +name: develops from +def: "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" [] +comment: This is the transitive form of the develops from relation +domain: BFO:0000004 ! independent continuant +range: BFO:0000004 ! independent continuant +is_transitive: true +is_a: RO:0002254 ! has developmental contribution from +is_a: RO:0002258 ! developmentally preceded by +inverse_of: RO:0002203 ! develops into + +[Typedef] +id: RO:0002203 +name: develops into +def: "inverse of develops from" [] +subset: RO:0002259 +is_transitive: true +is_a: RO:0002286 ! developmentally succeeded by +is_a: RO:0002387 ! has potential to develop into +is_a: RO:0002388 ! has potential to directly develop into + [Typedef] id: RO:0002206 name: expressed in def: "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" [] -property_value: IAO:0000112 "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000002 ! continuant range: UBERON:0000465 ! material anatomical entity is_a: RO:0002330 ! genomically related to inverse_of: RO:0002292 ! expresses -transitive_over: part_of ! part_of +transitive_over: part_of ! part of + +[Typedef] +id: RO:0002207 +name: directly develops from +def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] +comment: TODO - add child relations from DOS +synonym: "has developmental precursor" EXACT [] +is_a: RO:0002202 ! develops from +inverse_of: RO:0002210 ! directly develops into [Typedef] id: RO:0002210 name: directly develops into def: "inverse of directly develops from" [] subset: RO:0002259 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000118 "developmental precursor of" xsd:string -is_a: develops_into ! develops into +is_a: RO:0002203 ! develops into + +[Typedef] +id: RO:0002219 +name: surrounded by +def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" [] +is_a: adjacent_to ! adjacent to +inverse_of: RO:0002221 ! surrounds + +[Typedef] +id: RO:0002221 +name: surrounds +def: "inverse of surrounded by" [] +subset: RO:0002259 +is_a: adjacent_to ! adjacent to [Typedef] id: RO:0002222 name: temporally related to comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. subset: ro-eco -property_value: http://purl.org/dc/terms/source "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" xsd:anyURI -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent +[Typedef] +id: RO:0002223 +name: starts +def: "inverse of starts with" [] +subset: ro-eco +is_a: part_of ! part of +is_a: RO:0002222 ! temporally related to +inverse_of: starts_with ! starts with + +[Typedef] +id: RO:0002225 +name: develops from part of +def: "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" [] +holds_over_chain: RO:0002207 part_of +is_a: RO:0002202 ! develops from + +[Typedef] +id: RO:0002226 +name: develops in +def: "x develops_in y if x is located in y whilst x is developing" [] +domain: UBERON:0001062 ! anatomical entity +holds_over_chain: RO:0002207 RO:0001025 +is_a: RO:0002258 ! developmentally preceded by + +[Typedef] +id: RO:0002229 +name: ends +def: "inverse of ends with" [] +subset: ro-eco +is_a: part_of ! part of +is_a: RO:0002222 ! temporally related to +inverse_of: ends_with ! ends with + +[Typedef] +id: RO:0002252 +name: connecting branch of +def: "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." [] +property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 +is_a: RO:0002170 ! connected to +is_a: RO:0002375 ! in branching relationship with +inverse_of: RO:0002253 ! has connecting branch + [Typedef] id: RO:0002253 name: has connecting branch def: "inverse of connecting branch of" [] subset: RO:0002259 -property_value: RO:0004036 BFO:0000051 is_a: RO:0002375 ! in branching relationship with +[Typedef] +id: RO:0002254 +name: has developmental contribution from +def: "x has developmental contribution from y iff x has some part z such that z develops from y" [] +domain: UBERON:0001062 ! anatomical entity +range: UBERON:0001062 ! anatomical entity +holds_over_chain: has_part RO:0002202 +is_a: RO:0002258 ! developmentally preceded by +inverse_of: RO:0002255 ! developmentally contributes to + [Typedef] id: RO:0002255 name: developmentally contributes to def: "inverse of has developmental contribution from" [] subset: RO:0002259 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -holds_over_chain: develops_into part_of -is_a: has_potential_to_developmentally_contribute_to ! has potential to developmentally contribute to +holds_over_chain: RO:0002203 part_of is_a: RO:0002286 ! developmentally succeeded by +is_a: RO:0002385 ! has potential to developmentally contribute to + +[Typedef] +id: RO:0002256 +name: developmentally induced by +def: "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" [] +domain: UBERON:0000465 ! material anatomical entity +range: UBERON:0000465 ! material anatomical entity +is_a: RO:0002258 ! developmentally preceded by +inverse_of: RO:0002257 ! developmentally induces [Typedef] id: RO:0002257 name: developmentally induces def: "Inverse of developmentally induced by" [] -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002286 ! developmentally succeeded by is_a: RO:0002386 ! has potential to developmentally induce @@ -16150,10 +15930,7 @@ id: RO:0002258 name: developmentally preceded by def: "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p" [] comment: This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from -property_value: editor_note "false" xsd:boolean -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string +property_value: IAO:0000116 "false" xsd:boolean domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant is_a: RO:0002324 ! developmentally related to @@ -16164,7 +15941,6 @@ id: RO:0002263 name: acts upstream of def: "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: IAO:0000112 "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." xsd:string property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of holds_over_chain: RO:0002327 causally_upstream_of is_a: RO:0002264 ! acts upstream of or within @@ -16175,25 +15951,26 @@ name: acts upstream of or within def: "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term synonym: "affects" RELATED [] -property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within" xsd:anyURI holds_over_chain: RO:0002327 causally_upstream_of_or_within is_a: RO:0002500 ! causal agent in process +[Typedef] +id: RO:0002285 +name: developmentally replaces +def: "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" [] +property_value: IAO:0000116 "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" xsd:string +is_a: RO:0002258 ! developmentally preceded by + [Typedef] id: RO:0002286 name: developmentally succeeded by def: "Inverse of developmentally preceded by" [] -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002384 ! has developmental potential involving [Typedef] id: RO:0002287 name: part of developmental precursor of -property_value: IAO:0000112 "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: part_of RO:0002210 is_a: RO:0002286 ! developmentally succeeded by @@ -16201,80 +15978,58 @@ is_a: RO:0002286 ! developmentally succeeded by id: RO:0002292 name: expresses def: "y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." [] -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002330 ! genomically related to [Typedef] id: RO:0002314 name: characteristic of part of def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." [] -property_value: editor_note "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "inheres in part of" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: RO:0000052 part_of {RO:0002582="true"} is_a: RO:0002502 ! depends on -transitive_over: part_of ! part_of +transitive_over: part_of ! part of [Typedef] id: RO:0002320 name: evolutionarily related to def: "A relationship that holds via some environmental process" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." xsd:string [Typedef] id: RO:0002323 name: mereotopologically related to def: "A mereological relationship or a topological relationship" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string -property_value: RO:0001900 RO:0001901 [Typedef] id: RO:0002324 name: developmentally related to def: "A relationship that holds between entities participating in some developmental process (GO:0032502)" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" xsd:string [Typedef] id: RO:0002327 name: enables def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "catalyzes" xsd:string -property_value: IAO:0000118 "executes" xsd:string -property_value: IAO:0000118 "has" xsd:string -property_value: IAO:0000118 "is catalyzing" xsd:string -property_value: IAO:0000118 "is executing" xsd:string -property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string property_value: seeAlso "https://wiki.geneontology.org/Enables" xsd:anyURI is_a: capable_of ! capable of inverse_of: RO:0002333 ! enabled by transitive_over: has_part ! has part transitive_over: RO:0002017 ! has component activity +[Typedef] +id: RO:0002328 +name: functionally related to +def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] + [Typedef] id: RO:0002329 name: part of structure that is capable of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "false" xsd:boolean -holds_over_chain: part_of capable_of {RO:0002581="true"} -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002330 name: genomically related to def: "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant @@ -16282,31 +16037,25 @@ range: BFO:0000002 ! continuant id: RO:0002331 name: involved in def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "actively involved in" xsd:string -property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Involved_in" xsd:anyURI holds_over_chain: RO:0002327 part_of is_a: participates_in ! participates in is_a: RO:0002431 ! involved in or involved in regulation of -transitive_over: part_of ! part_of +transitive_over: part_of ! part of [Typedef] id: RO:0002333 name: enabled by def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso "https://wiki.geneontology.org/Enabled_by" xsd:anyURI -is_a: functionally_related_to ! functionally related to is_a: has_participant ! has participant +is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002337 name: related via localization to def: "A relationship that holds via some process of localization" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is a grouping relation." xsd:string domain: BFO:0000015 ! process range: BFO:0000002 ! continuant @@ -16314,84 +16063,134 @@ range: BFO:0000002 ! continuant id: RO:0002350 name: member of def: "is member of is a mereological relation between a item and a collection." [] -property_value: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string -property_value: IAO:0000118 "is member of" xsd:string -property_value: IAO:0000118 "member part of" xsd:string -property_value: IAO:0000119 "SIO" xsd:string -property_value: RO:0001900 RO:0001901 -is_a: part_of ! part_of -inverse_of: has_member ! has member +is_a: part_of ! part of +inverse_of: RO:0002351 ! has member + +[Typedef] +id: RO:0002351 +name: has member +def: "has member is a mereological relation between a collection and an item." [] +is_a: has_part ! has part + +[Typedef] +id: RO:0002352 +name: input of +def: "inverse of has input" [] +subset: ro-eco +subset: RO:0002259 +is_a: participates_in ! participates in +is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002354 name: formed as result of -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: output_of ! output of [Typedef] id: RO:0002360 name: has dendrite location -property_value: http://purl.org/dc/terms/source "http://neurolex.org/wiki/Property:DendriteLocation" xsd:anyURI -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps [Typedef] -id: RO:0002375 -name: in branching relationship with -def: "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" xsd:string -property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string -property_value: RO:0004036 BFO:0000050 -property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png -property_value: seeAlso "https://github.com/obophenotype/uberon/issues/170" xsd:anyURI -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: RO:0002323 ! mereotopologically related to +id: RO:0002371 +name: attached to +def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] +subset: ro-eco +is_symmetric: true +is_a: RO:0002170 ! connected to +is_a: RO:0002177 ! attached to part of [Typedef] -id: RO:0002379 -name: spatially coextensive with -def: "x spatially_coextensive_with y if and inly if x and y have the same location" [] -property_value: IAO:0000112 "A lump of clay and a statue" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" xsd:string -is_a: overlaps ! overlaps +id: RO:0002372 +name: has muscle origin +def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] +property_value: seeAlso http://dbpedia.org/property/origin +domain: UBERON:0000061 {comment="We need to import uberon muscle to create a stricter domain constraint"} ! anatomical structure +is_a: RO:0002371 ! attached to +is_a: RO:0002567 ! biomechanically related to + +[Typedef] +id: RO:0002373 +name: has muscle insertion +def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] +property_value: seeAlso http://dbpedia.org/property/insertion +domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} ! anatomical structure +is_a: RO:0002371 ! attached to +is_a: RO:0002567 ! biomechanically related to + +[Typedef] +id: RO:0002375 +name: in branching relationship with +def: "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." [] +property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png +property_value: seeAlso "https://github.com/obophenotype/uberon/issues/170" xsd:anyURI +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002323 ! mereotopologically related to + +[Typedef] +id: RO:0002376 +name: tributary of +def: "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." [] +subset: ro-eco +property_value: seeAlso http://dbpedia.org/ontology/drainsTo +property_value: seeAlso "http://en.wikipedia.org/wiki/Tributary" xsd:anyURI +is_a: RO:0002170 ! connected to +is_a: RO:0002375 ! in branching relationship with + +[Typedef] +id: RO:0002379 +name: spatially coextensive with +def: "x spatially_coextensive_with y if and inly if x and y have the same location" [] +is_a: overlaps ! overlaps + +[Typedef] +id: RO:0002380 +name: branching part of +def: "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" [] +subset: ro-eco +property_value: seeAlso "FMA:85994" xsd:string +property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 +is_a: part_of ! part of +is_a: RO:0002375 ! in branching relationship with +inverse_of: RO:0002569 ! has branching part [Typedef] id: RO:0002384 name: has developmental potential involving def: "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: UBERON:0001062 ! anatomical entity range: UBERON:0001062 ! anatomical entity is_a: RO:0002324 ! developmentally related to +[Typedef] +id: RO:0002385 +name: has potential to developmentally contribute to +def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] +is_a: RO:0002384 ! has developmental potential involving + [Typedef] id: RO:0002386 name: has potential to developmentally induce def: "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002384 ! has developmental potential involving + +[Typedef] +id: RO:0002387 +name: has potential to develop into +def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] is_a: RO:0002384 ! has developmental potential involving [Typedef] id: RO:0002388 name: has potential to directly develop into def: "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: has_potential_to_develop_into ! has potential to develop into +is_a: RO:0002387 ! has potential to develop into [Typedef] id: RO:0002407 name: indirectly positively regulates def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "indirectly activates" xsd:string -property_value: RO:0002579 RO:0002213 property_value: seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates" xsd:anyURI holds_over_chain: directly_positively_regulates directly_positively_regulates holds_over_chain: directly_positively_regulates RO:0002407 @@ -16405,9 +16204,6 @@ transitive_over: directly_positively_regulates ! directly positively regulates id: RO:0002409 name: indirectly negatively regulates def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "indirectly inhibits" xsd:string -property_value: RO:0002579 RO:0002212 property_value: seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates" xsd:anyURI holds_over_chain: directly_negatively_regulates directly_negatively_regulates holds_over_chain: directly_negatively_regulates RO:0002409 @@ -16420,15 +16216,12 @@ transitive_over: directly_negatively_regulates ! directly negatively regulates id: RO:0002410 name: causally related to def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] -property_value: editor_note "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string [Typedef] id: RO:0002428 name: involved in regulation of def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002327 regulates holds_over_chain: RO:0002331 regulates is_a: RO:0002263 ! acts upstream of @@ -16438,8 +16231,6 @@ is_a: RO:0002431 ! involved in or involved in regulation of id: RO:0002429 name: involved in positive regulation of def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0004049 RO:0002428 holds_over_chain: RO:0002327 positively_regulates holds_over_chain: RO:0002331 positively_regulates is_a: RO:0002428 ! involved in regulation of @@ -16448,7 +16239,6 @@ is_a: RO:0002428 ! involved in regulation of id: RO:0002430 name: involved in negative regulation of def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002428 holds_over_chain: RO:0002327 negatively_regulates holds_over_chain: RO:0002331 negatively_regulates @@ -16458,11 +16248,9 @@ is_a: RO:0002428 ! involved in regulation of id: RO:0002431 name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] -property_value: editor_note "OWL does not allow defining object properties via a Union" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "involved in or reguates" xsd:string -is_a: functionally_related_to ! functionally related to +property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string is_a: RO:0002264 ! acts upstream of or within +is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process [Typedef] @@ -16470,12 +16258,14 @@ id: RO:0002432 name: is active in def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [https://orcid.org/0000-0002-6601-2165, https://orcid.org/0000-0002-7073-9172] synonym: "enables activity in" EXACT [] -property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "executes activity in" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Is_active_in" xsd:anyURI -holds_over_chain: RO:0002327 occurs_in {RO:0002581="true"} -is_a: functionally_related_to ! functionally related to +is_a: overlaps ! overlaps +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002433 +name: contributes to morphology of +def: "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." [] is_a: overlaps ! overlaps [Typedef] @@ -16484,11 +16274,8 @@ name: interacts with def: "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." [] subset: ro-eco synonym: "in pairwise interaction with" EXACT [] -property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0914" xsd:anyURI -property_value: editor_note "Considering relabeling as 'pairwise interacts with'" xsd:anyURI -property_value: editor_note "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string +property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI +property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity @@ -16498,10 +16285,6 @@ is_symmetric: true id: RO:0002436 name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] -property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0915" xsd:anyURI -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "binds" xsd:string -property_value: IAO:0000118 "molecularly binds with" xsd:string property_value: seeAlso ECO:0000353 is_symmetric: true is_a: RO:0002434 ! interacts with @@ -16509,9 +16292,7 @@ is_a: RO:0002434 ! interacts with [Typedef] id: RO:0002447 name: phosphorylates -property_value: editor_note "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string +property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string is_a: RO:0002436 ! molecularly interacts with [Typedef] @@ -16519,8 +16300,6 @@ id: RO:0002448 name: directly regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." [] synonym: "molecularly controls" EXACT [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002436 ! molecularly interacts with @@ -16531,9 +16310,6 @@ id: RO:0002449 name: directly negatively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] synonym: "molecularly decreases activity of" EXACT [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 -property_value: IAO:0000118 "directly inhibits" xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002448 ! directly regulates activity of @@ -16543,9 +16319,6 @@ id: RO:0002450 name: directly positively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] synonym: "molecularly increases activity of" EXACT [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 -property_value: IAO:0000118 "directly activates" xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002448 ! directly regulates activity of @@ -16553,61 +16326,136 @@ is_a: RO:0002448 ! directly regulates activity of [Typedef] id: RO:0002464 name: helper property (not for use in curation) -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string + +[Typedef] +id: RO:0002473 +name: composed primarily of +def: "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." [] +subset: ro-eco +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: has_part ! has part [Typedef] id: RO:0002479 name: has part that occurs in def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] subset: ro-eco -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant -holds_over_chain: has_part occurs_in {RO:0002581="true"} [Typedef] id: RO:0002481 name: is kinase activity -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002564 ! molecular interaction relation helper property [Typedef] id: RO:0002485 name: receives input from -property_value: editor_note "See notes for inverse relation" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: connected_to ! connected to +property_value: IAO:0000116 "See notes for inverse relation" xsd:string +is_a: RO:0002170 ! connected to inverse_of: RO:0002486 ! sends output to [Typedef] id: RO:0002486 name: sends output to -property_value: editor_note "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: connected_to ! connected to +property_value: IAO:0000116 "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." xsd:string +is_a: RO:0002170 ! connected to [Typedef] id: RO:0002487 name: relation between physical entity and a process or stage -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage." xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000003 ! occurrent +[Typedef] +id: RO:0002488 +name: existence starts during +def: "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." [] +is_a: RO:0002490 ! existence overlaps +is_a: RO:0002496 ! existence starts during or after +transitive_over: part_of ! part of + +[Typedef] +id: RO:0002489 +name: existence starts with +def: "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." [] +is_a: RO:0002488 ! existence starts during + [Typedef] id: RO:0002490 name: existence overlaps def: "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" [] comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002487 ! relation between physical entity and a process or stage +[Typedef] +id: RO:0002491 +name: existence starts and ends during +def: "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +synonym: "exists during" EXACT [] +is_a: RO:0002488 ! existence starts during +is_a: RO:0002492 ! existence ends during + +[Typedef] +id: RO:0002492 +name: existence ends during +def: "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +is_a: RO:0002490 ! existence overlaps +is_a: RO:0002497 ! existence ends during or before +transitive_over: part_of ! part of + +[Typedef] +id: RO:0002493 +name: existence ends with +def: "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +is_a: RO:0002492 ! existence ends during + +[Typedef] +id: RO:0002494 +name: transformation of +def: "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" [] +is_transitive: true +is_a: RO:0002202 ! develops from + +[Typedef] +id: RO:0002495 +name: immediate transformation of +def: "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" [] +is_a: RO:0002207 ! directly develops from +is_a: RO:0002494 ! transformation of + +[Typedef] +id: RO:0002496 +name: existence starts during or after +def: "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +holds_over_chain: part_of RO:0002496 +holds_over_chain: RO:0002258 RO:0002496 +is_a: RO:0002487 ! relation between physical entity and a process or stage +transitive_over: part_of ! part of +transitive_over: preceded_by ! preceded by +transitive_over: RO:0002082 ! simultaneous with + +[Typedef] +id: RO:0002497 +name: existence ends during or before +def: "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +holds_over_chain: part_of RO:0002497 +holds_over_chain: RO:0002286 RO:0002497 +is_a: RO:0002487 ! relation between physical entity and a process or stage +transitive_over: part_of ! part of +transitive_over: precedes ! precedes +transitive_over: RO:0002082 ! simultaneous with + [Typedef] id: RO:0002500 name: causal agent in process def: "A relationship between a material entity and a process where the material entity has some causal role that influences the process" [] -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_a: RO:0002595 ! causal relation between material entity and a process inverse_of: process_has_causal_agent ! process has causal agent @@ -16615,9 +16463,6 @@ inverse_of: process_has_causal_agent ! process has causal agent id: RO:0002501 name: causal relation between processes def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent is_a: RO:0002410 ! causally related to @@ -16625,33 +16470,35 @@ is_a: RO:0002410 ! causally related to [Typedef] id: RO:0002502 name: depends on -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso BFO:0000169 [Typedef] id: RO:0002506 name: causal relation between entities -property_value: editor_note "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: IAO:0000116 "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant is_a: RO:0002410 ! causally related to +[Typedef] +id: RO:0002551 +name: has skeleton +def: "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." [] +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000465 {IAO:0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} ! material anatomical entity +is_a: has_part ! has part +inverse_of: RO:0002576 ! skeleton of +is_asymmetric: true + [Typedef] id: RO:0002559 name: causally influenced by -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string is_a: RO:0002506 ! causal relation between entities inverse_of: RO:0002566 ! causally influences [Typedef] id: RO:0002563 name: interaction relation helper property -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29 property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI is_a: RO:0002464 ! helper property (not for use in curation) @@ -16659,17 +16506,12 @@ is_a: RO:0002464 ! helper property (not for use in curation) [Typedef] id: RO:0002564 name: molecular interaction relation helper property -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002563 ! interaction relation helper property [Typedef] id: RO:0002566 name: causally influences def: "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant is_a: RO:0002506 ! causal relation between entities @@ -16678,20 +16520,66 @@ is_a: RO:0002506 ! causal relation between entities id: RO:0002567 name: biomechanically related to def: "A relation that holds between elements of a musculoskeletal system or its analogs." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string domain: UBERON:0000061 ! anatomical structure range: UBERON:0000061 ! anatomical structure -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002568 +name: has muscle antagonist +def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] +is_a: RO:0002567 ! biomechanically related to + +[Typedef] +id: RO:0002569 +name: has branching part +def: "inverse of branching part of" [] +subset: ro-eco +subset: RO:0002259 +is_transitive: true +is_a: has_part ! has part +is_a: RO:0002375 ! in branching relationship with + +[Typedef] +id: RO:0002570 +name: conduit for +def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] +subset: ro-eco +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: overlaps ! overlaps + +[Typedef] +id: RO:0002571 +name: lumen of +def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] +subset: ro-eco +range: BFO:0000040 ! material entity +is_a: part_of ! part of + +[Typedef] +id: RO:0002572 +name: luminal space of +def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" [] +subset: ro-eco +domain: BFO:0000141 ! immaterial entity +is_a: RO:0002571 ! lumen of + +[Typedef] +id: RO:0002576 +name: skeleton of +def: "inverse of has skeleton" [] +subset: RO:0002259 +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000061 ! anatomical structure +is_a: part_of ! part of [Typedef] id: RO:0002584 name: has part structure that is capable of def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" [] -property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: has_part capable_of -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to is_a: RO:0002595 ! causal relation between material entity and a process [Typedef] @@ -16704,9 +16592,7 @@ is_a: has_input ! has input id: RO:0002595 name: causal relation between material entity and a process def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." [] -property_value: editor_note "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000040 ! material entity range: BFO:0000015 ! process is_a: RO:0002410 ! causally related to @@ -16715,8 +16601,6 @@ is_a: RO:0002410 ! causally related to id: RO:0002596 name: capable of regulating def: "Holds between c and p if and only if c is capable of some activity a, and a regulates p." [] -property_value: IAO:0000112 "pyrethroid -> growth" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations holds_over_chain: capable_of regulates is_a: RO:0002500 ! causal agent in process @@ -16724,7 +16608,6 @@ is_a: RO:0002500 ! causal agent in process id: RO:0002597 name: capable of negatively regulating def: "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." [] -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations holds_over_chain: capable_of negatively_regulates is_a: RO:0002596 ! capable of regulating @@ -16732,8 +16615,6 @@ is_a: RO:0002596 ! capable of regulating id: RO:0002598 name: capable of positively regulating def: "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." [] -property_value: IAO:0000112 "renin -> arteriolar smooth muscle contraction" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations holds_over_chain: capable_of positively_regulates is_a: RO:0002596 ! capable of regulating @@ -16742,7 +16623,7 @@ id: RO:0004031 name: enables subfunction def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] holds_over_chain: RO:0002327 has_part -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z @@ -16750,7 +16631,6 @@ creation_date: 2018-01-25T23:20:13Z id: RO:0004032 name: acts upstream of or within, positive effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: RO:0004049 RO:0002264 property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0004047 is_a: RO:0002264 ! acts upstream of or within @@ -16773,7 +16653,6 @@ id: RO:0004034 name: acts upstream of, positive effect def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: RO:0004049 RO:0002263 property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 causally_upstream_of,_positive_effect is_a: RO:0002263 ! acts upstream of @@ -16806,7 +16685,6 @@ creation_date: 2018-03-13T23:55:05Z [Typedef] id: RO:0004047 name: causally upstream of or within, positive effect -property_value: RO:0004049 RO:0002418 property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect is_a: causally_upstream_of_or_within ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 @@ -16816,7 +16694,6 @@ creation_date: 2018-03-13T23:55:19Z id: RO:0011002 name: regulates activity of def: "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." [] -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002566 ! causally influences @@ -16871,7 +16748,7 @@ name: has synaptic IO in region def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region." [] synonym: "has synaptic input or output in" EXACT [] is_a: RO:0002130 ! has synaptic terminal in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:26:52Z @@ -16883,7 +16760,7 @@ synonym: "has sensory dendrite location" EXACT [] synonym: "has sensory terminal in" EXACT [] synonym: "has sensory terminal location" EXACT [] is_a: RO:0002360 ! has dendrite location -transitive_over: part_of ! part_of +transitive_over: part_of ! part of created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-20T12:10:09Z @@ -16926,9 +16803,8 @@ comment: Example: a spherical object has the quality of being spherical, and the id: RO:0015015 name: has high plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: dc-contributor https://orcid.org/0000-0003-1617-8244 -property_value: dc-contributor https://orcid.org/0000-0003-1940-6740 -property_value: IAO:0000112 "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part @@ -16936,9 +16812,8 @@ is_a: RO:0002104 ! has plasma membrane part id: RO:0015016 name: has low plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: dc-contributor https://orcid.org/0000-0003-1617-8244 -property_value: dc-contributor https://orcid.org/0000-0003-1940-6740 -property_value: IAO:0000112 "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part @@ -16947,11 +16822,6 @@ id: RO:0017001 name: device utilizes material def: "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." [] synonym: "utilizes" BROAD [] -property_value: IAO:0000112 "A diagnostic testing device utilizes a specimen." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 -property_value: IAO:0000117 https://orcid.org/0000-0003-2620-0345 -property_value: IAO:0000232 "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." xsd:string -property_value: IAO:0000232 "See github ticket https://github.com/oborel/obo-relations/issues/497" xsd:string holds_over_chain: capable_of has_input creation_date: 2021-11-08T12:00:00Z @@ -16972,65 +16842,24 @@ creation_date: 2020-06-08T17:21:33Z id: adjacent_to name: adjacent to namespace: external -namespace: uberon def: "x adjacent to y if and only if x and y share a boundary." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002220 -property_value: editor_note "This relation acts as a join point with BSPO" xsd:string -property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} -property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string -property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string -property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000004 ! independent continuant is_a: RO:0002163 ! spatially disjoint from -[Typedef] -id: anterior_to -name: anterior to -namespace: uberon -xref: BSPO:0000096 - [Typedef] id: anteriorly_connected_to name: anteriorly connected to namespace: uberon def: "x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] -is_a: connected_to ! connected to -is_a: posterior_to ! posterior to +is_a: RO:0002170 ! connected to is_a: transitively_anteriorly_connected_to ! transitively anteriorly connected to -[Typedef] -id: attaches_to -name: attached to -namespace: uberon -def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] -subset: ro-eco -xref: RO:0002371 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000589 "attached to (anatomical structure to anatomical structure)" xsd:string -is_symmetric: true -is_a: attaches_to_part_of ! attached to part of -is_a: connected_to ! connected to - -[Typedef] -id: attaches_to_part_of -name: attached to part of -namespace: uberon -def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] -xref: RO:0002177 -property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string -domain: UBERON:0000061 ! anatomical structure -range: UBERON:0000061 ! anatomical structure -holds_over_chain: attaches_to part_of {RO:0002582="true"} -is_a: RO:0002323 ! mereotopologically related to -is_a: RO:0002567 ! biomechanically related to - [Typedef] id: bearer_of name: bearer of @@ -17038,13 +16867,7 @@ name: has characteristic namespace: external def: "Inverse of characteristic_of" [] xref: RO:0000053 -property_value: editor_note "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string -property_value: IAO:0000111 "bearer of" xsd:string -property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string -property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string -property_value: IAO:0000118 "bearer_of" xsd:string -property_value: IAO:0000118 "is bearer of" xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string range: BFO:0000020 ! specifically dependent continuant is_inverse_functional: true @@ -17052,45 +16875,20 @@ is_inverse_functional: true id: bounding_layer_of name: bounding layer of namespace: external -namespace: uberon def: "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000" [] comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. subset: ro-eco xref: RO:0002007 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 range: BFO:0000040 ! material entity -is_a: part_of ! part_of - -[Typedef] -id: branching_part_of -name: branching part of -namespace: uberon -def: "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" [] -subset: ro-eco -xref: RO:0002380 -property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso "FMA:85994" xsd:string -property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 -is_a: part_of ! part_of -is_a: RO:0002375 ! in branching relationship with -inverse_of: has_branching_part ! has branching part +is_a: part_of ! part of [Typedef] id: capable_of name: capable of namespace: external -namespace: uberon def: "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " [] subset: ro-eco xref: RO:0002215 -property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string -property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "has function realized in" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 -property_value: IAO:0000232 "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000015 ! process is_a: capable_of_part_of ! capable of part of @@ -17099,14 +16897,10 @@ is_a: capable_of_part_of ! capable of part of id: capable_of_part_of name: capable of part of namespace: external -namespace: uberon def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] xref: RO:0002216 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "has function in" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: capable_of part_of {RO:0002582="true"} -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process [Typedef] @@ -17115,8 +16909,6 @@ name: causally downstream of namespace: external def: "inverse of upstream of" [] xref: RO:0002404 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of_or_within ! causally downstream of or within is_a: preceded_by ! preceded by inverse_of: causally_upstream_of ! causally upstream of @@ -17128,8 +16920,6 @@ namespace: external def: "inverse of causally upstream of or within" [] subset: RO:0002259 xref: RO:0002427 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_transitive: true is_a: RO:0002501 ! causal relation between processes @@ -17141,7 +16931,6 @@ def: "p is causally upstream of q iff p is causally related to q, the end of p p subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002411 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within is_a: precedes ! precedes @@ -17154,7 +16943,6 @@ def: "p is causally upstream of, negative effect q iff p is casually upstream of subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 -property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_negative_effect is_a: causally_upstream_of ! causally upstream of @@ -17169,8 +16957,6 @@ comment: holds between x and y if and only if x is causally upstream of y and th subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002304 -property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 -property_value: RO:0004049 RO:0002411 property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_positive_effect is_a: causally_upstream_of ! causally upstream of is_a: RO:0004047 ! causally upstream of or within, positive effect @@ -17182,9 +16968,7 @@ namespace: external def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] synonym: "affects" RELATED [] xref: RO:0002418 -property_value: editor_note "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "influences (processual)" xsd:string +property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string is_transitive: true is_a: RO:0002501 ! causal relation between processes inverse_of: causally_downstream_of_or_within ! causally downstream of or within @@ -17194,510 +16978,81 @@ id: channel_for name: channel for namespace: uberon synonym: "carries" BROAD [] -domain: UBERON:0004111 ! anatomical conduit -range: UBERON:0000463 ! organism substance [Typedef] id: channels_from name: channels_from namespace: uberon -is_transitive: true [Typedef] id: channels_into name: channels_into namespace: uberon -is_transitive: true [Typedef] -id: composed_primarily_of -name: composed primarily of -namespace: uberon -def: "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." [] -subset: ro-eco -xref: RO:0002473 -property_value: IAO:0000112 "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: RO:0001900 RO:0001901 -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: has_part ! has part +id: directly_negatively_regulates +name: directly negatively regulates +namespace: external +def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0002630 +property_value: RO:0004050 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates" xsd:anyURI +is_a: directly_regulates ! directly regulates +is_a: negatively_regulates ! negatively regulates [Typedef] -id: conduit_for -name: conduit for -namespace: uberon -def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] -subset: ro-eco -xref: RO:0002570 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "UBERON:cjm" xsd:string -property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: overlaps ! overlaps +id: directly_positively_regulates +name: directly positively regulates +namespace: external +def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0002629 +property_value: seeAlso "https://wiki.geneontology.org/Directly_positively_regulates" xsd:anyURI +is_a: directly_regulates ! directly regulates +is_a: positively_regulates ! positively regulates [Typedef] -id: connected_to -name: connected to -namespace: uberon -def: "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" [] -xref: RO:0002170 -property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI -property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI -is_a: RO:0002323 ! mereotopologically related to +id: directly_regulates +name: directly regulates +namespace: external +def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0002578 +is_a: immediately_causally_upstream_of ! immediately causally upstream of +is_a: regulates ! regulates [Typedef] -id: connecting_branch_of -name: connecting branch of -namespace: uberon -def: "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." [] -xref: RO:0002252 -property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." xsd:string -property_value: RO:0004036 BFO:0000050 -property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 -is_a: connected_to ! connected to -is_a: RO:0002375 ! in branching relationship with -inverse_of: RO:0002253 ! has connecting branch - -[Typedef] -id: connects -name: connects -namespace: uberon -def: "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." [] -xref: RO:0002176 -property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string -property_value: IAO:0000112 "The M8 connects Glasgow and Edinburgh" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI -property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI -domain: BFO:0000004 ! independent continuant -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: contains_process -name: contains process -namespace: uberon -def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] -comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant -xref: BFO:0000067 -property_value: IAO:0000111 "site of" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - -[Typedef] -id: continuous_with -name: continuous with -namespace: uberon -def: "X continuous_with Y if and only if X and Y share a fiat boundary." [] -xref: RO:0002150 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "connected to" xsd:string -property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string -property_value: RO:0001900 RO:0001901 -property_value: seeAlso "FMA:85972" xsd:string -domain: BFO:0000004 ! independent continuant -range: BFO:0000004 ! independent continuant -is_symmetric: true -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: contributes_to_morphology_of -name: contributes to morphology of -namespace: uberon -def: "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." [] -xref: RO:0002433 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: overlaps ! overlaps - -[Typedef] -id: dc-contributor -name: contributor -namespace: uberon -xref: http://purl.org/dc/terms/contributor -is_metadata_tag: true - -[Typedef] -id: dc-creator -name: creator -namespace: uberon -xref: http://purl.org/dc/elements/1.1/creator -is_metadata_tag: true - -[Typedef] -id: dc-description -name: description -namespace: uberon -xref: http://purl.org/dc/elements/1.1/description -is_metadata_tag: true - -[Typedef] -id: dc-title -name: title -namespace: uberon -xref: http://purl.org/dc/elements/1.1/title -is_metadata_tag: true - -[Typedef] -id: dcterms-date -name: date -namespace: uberon -xref: http://purl.org/dc/terms/date -is_metadata_tag: true - -[Typedef] -id: dcterms-license -name: license -namespace: uberon -xref: http://purl.org/dc/terms/license -is_metadata_tag: true - -[Typedef] -id: deep_to -name: deep to -namespace: uberon -xref: BSPO:0000107 - -[Typedef] -id: depiction -name: depiction -namespace: uberon -xref: http://xmlns.com/foaf/0.1/depiction -is_metadata_tag: true - -[Typedef] -id: developmentally_induced_by -name: developmentally induced by -namespace: uberon -def: "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" [] -xref: RO:0002256 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "induced by" xsd:string -property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string -property_value: IAO:0000119 "GO:0001759" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 -property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string -domain: UBERON:0000465 ! material anatomical entity -range: UBERON:0000465 ! material anatomical entity -is_a: RO:0002258 ! developmentally preceded by -inverse_of: RO:0002257 ! developmentally induces - -[Typedef] -id: developmentally_replaces -name: developmentally replaces -namespace: uberon -def: "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" [] -xref: RO:0002285 -property_value: editor_note "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "replaces" xsd:string -is_a: RO:0002258 ! developmentally preceded by - -[Typedef] -id: develops_from -name: develops from -namespace: uberon -def: "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" [] -comment: This is the transitive form of the develops from relation -xref: RO:0002202 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 -domain: BFO:0000004 ! independent continuant -range: BFO:0000004 ! independent continuant -is_transitive: true -is_a: has_developmental_contribution_from ! has developmental contribution from -is_a: RO:0002258 ! developmentally preceded by -inverse_of: develops_into ! develops into - -[Typedef] -id: develops_from_part_of -name: develops from part of -namespace: uberon -def: "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" [] -xref: RO:0002225 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -holds_over_chain: directly_develops_from part_of -is_a: develops_from ! develops from - -[Typedef] -id: develops_in -name: develops in -namespace: uberon -def: "x develops_in y if x is located in y whilst x is developing" [] -xref: RO:0002226 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "EHDAA2" xsd:string -property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string -domain: UBERON:0001062 ! anatomical entity -holds_over_chain: directly_develops_from located_in -is_a: RO:0002258 ! developmentally preceded by - -[Typedef] -id: develops_into -name: develops into -namespace: uberon -def: "inverse of develops from" [] -subset: RO:0002259 -xref: RO:0002203 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 -is_transitive: true -is_a: has_potential_to_develop_into ! has potential to develop into -is_a: RO:0002286 ! developmentally succeeded by -is_a: RO:0002388 ! has potential to directly develop into - -[Typedef] -id: directly_develops_from -name: directly develops from -namespace: uberon -def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] -comment: TODO - add child relations from DOS -synonym: "has developmental precursor" EXACT [] -xref: RO:0002207 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000119 "FBbt" xsd:string -property_value: RO:0002575 RO:0002202 -is_a: develops_from ! develops from -inverse_of: RO:0002210 ! directly develops into - -[Typedef] -id: directly_negatively_regulates -name: directly negatively regulates -namespace: external -def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -xref: RO:0002630 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string -property_value: RO:0004050 RO:0002578 -property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates" xsd:anyURI -is_a: directly_regulates ! directly regulates -is_a: negatively_regulates ! negatively regulates - -[Typedef] -id: directly_positively_regulates -name: directly positively regulates -namespace: external -def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -xref: RO:0002629 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string -property_value: RO:0004049 RO:0002578 -property_value: seeAlso "https://wiki.geneontology.org/Directly_positively_regulates" xsd:anyURI -is_a: directly_regulates ! directly regulates -is_a: positively_regulates ! positively regulates - -[Typedef] -id: directly_regulates -name: directly regulates -namespace: external -def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -xref: RO:0002578 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly regulates (processual)" xsd:string -property_value: RO:0002575 RO:0002211 -is_a: immediately_causally_upstream_of ! immediately causally upstream of -is_a: regulates ! regulates - -[Typedef] -id: distal_to -name: distal to -namespace: uberon -xref: BSPO:0000097 - -[Typedef] -id: distally_connected_to -name: distally connected to +id: distally_connected_to +name: distally connected to namespace: uberon def: "x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] -is_a: connected_to ! connected to -is_a: proximal_to ! proximal to +is_a: RO:0002170 ! connected to is_a: transitively_distally_connected_to ! transitively distally connected to -inverse_of: proximally_connected_to ! proximally connected to - -[Typedef] -id: distalmost_part_of -name: distalmost part of -namespace: uberon -xref: BSPO:0001108 - -[Typedef] -id: dorsal_to -name: dorsal to -namespace: uberon -xref: BSPO:0000098 - -[Typedef] -id: drains -name: drains -namespace: uberon -def: "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." [] -xref: RO:0002179 -property_value: editor_note "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 -is_a: connected_to ! connected to - -[Typedef] -id: editor_note -name: editor note -namespace: uberon -def: "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology." [] -xref: IAO:0000116 -property_value: IAO:0000111 "editor note" xsd:string -property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000117 "PERSON:Daniel Schober" xsd:string -property_value: IAO:0000119 "GROUP:OBI:" xsd:string -is_metadata_tag: true - -[Typedef] -id: ends -name: ends -namespace: uberon -def: "inverse of ends with" [] -subset: ro-eco -xref: RO:0002229 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: part_of ! part_of -is_a: RO:0002222 ! temporally related to -inverse_of: ends_with ! ends with [Typedef] id: ends_with name: ends with namespace: external -namespace: uberon def: "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002230 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "finished by" xsd:string is_transitive: true is_a: has_part ! has part is_a: RO:0002222 ! temporally related to -[Typedef] -id: existence_ends_during -name: existence ends during -namespace: uberon -def: "Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely." [https://orcid.org/0000-0002-6601-2165] -def: "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -synonym: "ceases_to_exist_during" EXACT [] -xref: RO:0002492 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_ends_during_or_before ! existence ends during or before -is_a: RO:0002490 ! existence overlaps -transitive_over: part_of ! part_of - -[Typedef] -id: existence_ends_during_or_before -name: existence ends during or before -namespace: uberon -def: "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -xref: RO:0002497 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -holds_over_chain: part_of existence_ends_during_or_before -holds_over_chain: RO:0002286 existence_ends_during_or_before -is_a: RO:0002487 ! relation between physical entity and a process or stage -transitive_over: part_of ! part_of -transitive_over: precedes ! precedes -transitive_over: simultaneous_with ! simultaneous with - -[Typedef] -id: existence_ends_with -name: existence ends with -namespace: uberon -def: "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -xref: RO:0002493 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_ends_during ! existence ends during - -[Typedef] -id: existence_starts_and_ends_during -name: existence starts and ends during -namespace: uberon -def: "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -synonym: "exists during" EXACT [] -xref: RO:0002491 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_ends_during ! existence ends during -is_a: existence_starts_during ! existence starts during - -[Typedef] -id: existence_starts_during -name: existence starts during -namespace: uberon -def: "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." [] -xref: RO:0002488 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_starts_during_or_after ! existence starts during or after -is_a: RO:0002490 ! existence overlaps -transitive_over: part_of ! part_of - -[Typedef] -id: existence_starts_during_or_after -name: existence starts during or after -namespace: uberon -def: "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -xref: RO:0002496 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -holds_over_chain: part_of existence_starts_during_or_after -holds_over_chain: RO:0002258 existence_starts_during_or_after -is_a: RO:0002487 ! relation between physical entity and a process or stage -transitive_over: part_of ! part_of -transitive_over: preceded_by ! preceded by -transitive_over: simultaneous_with ! simultaneous with - -[Typedef] -id: existence_starts_with -name: existence starts with -namespace: uberon -def: "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." [] -xref: RO:0002489 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_starts_during ! existence starts during - [Typedef] id: extends_fibers_into name: extends_fibers_into namespace: uberon def: "X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y" [https://orcid.org/0000-0002-7073-9172] -holds_over_chain: RO:0002100 RO:0013001 -is_symmetric: true -is_a: connected_to ! connected to +is_a: RO:0002170 ! connected to [Typedef] id: filtered_through @@ -17706,75 +17061,17 @@ namespace: uberon def: "Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity." [] comment: Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed -[Typedef] -id: functionally_related_to -name: functionally related to -namespace: uberon -def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] -xref: RO:0002328 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string - -[Typedef] -id: has_boundary -name: has 2D boundary -namespace: uberon -def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] -xref: RO:0002002 -property_value: editor_note "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string -property_value: editor_note "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string -property_value: IAO:0000112 "my body has 2D boundary the surface of my skin" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "has boundary" xsd:string -property_value: IAO:0000118 "has_2D_boundary" xsd:string -property_value: RO:0001900 RO:0001901 -domain: BFO:0000040 ! material entity -range: BFO:0000141 ! immaterial entity -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: has_branching_part -name: has branching part -namespace: uberon -def: "inverse of branching part of" [] -subset: ro-eco -subset: RO:0002259 -xref: RO:0002569 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_transitive: true -is_a: has_part ! has part -is_a: RO:0002375 ! in branching relationship with - [Typedef] id: has_component name: has component namespace: external -namespace: uberon def: "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] subset: ro-eco xref: RO:0002180 -property_value: editor_note "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency is_a: has_part ! has part -[Typedef] -id: has_developmental_contribution_from -name: has developmental contribution from -namespace: uberon -def: "x has developmental contribution from y iff x has some part z such that z develops from y" [] -xref: RO:0002254 -property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: UBERON:0001062 ! anatomical entity -range: UBERON:0001062 ! anatomical entity -holds_over_chain: has_part develops_from -is_a: RO:0002258 ! developmentally preceded by -inverse_of: RO:0002255 ! developmentally contributes to - [Typedef] id: has_end_location name: has end location @@ -17782,9 +17079,6 @@ namespace: external def: "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" [] subset: ro-eco xref: RO:0002232 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "ends with process that occurs in" xsd:string domain: BFO:0000015 ! process range: BFO:0000004 ! independent continuant holds_over_chain: ends_with occurs_in @@ -17808,14 +17102,11 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002233 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "consumes" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Has_input" xsd:anyURI domain: BFO:0000015 ! process holds_over_chain: starts_with has_input is_a: has_participant ! has participant -inverse_of: input_of ! input of +inverse_of: RO:0002352 ! input of [Typedef] id: has_low_plasma_membrane_amount @@ -17825,52 +17116,6 @@ property_value: term_tracker_item https://github.com/obophenotype/cell-ontology/ is_obsolete: true replaced_by: RO:0015016 -[Typedef] -id: has_member -name: has member -namespace: uberon -def: "has member is a mereological relation between a collection and an item." [] -xref: RO:0002351 -property_value: IAO:0000119 "SIO" xsd:string -property_value: RO:0001900 RO:0001901 -is_a: has_part ! has part - -[Typedef] -id: has_muscle_antagonist -name: has muscle antagonist -namespace: uberon -def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] -xref: RO:0002568 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "Wikipedia:Antagonist_(muscle)" xsd:string -is_a: RO:0002567 ! biomechanically related to - -[Typedef] -id: has_muscle_insertion -name: has muscle insertion -namespace: uberon -def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] -xref: RO:0002373 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string -property_value: seeAlso http://dbpedia.org/property/insertion -domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} ! anatomical structure -is_a: attaches_to ! attached to -is_a: RO:0002567 ! biomechanically related to - -[Typedef] -id: has_muscle_origin -name: has muscle origin -namespace: uberon -def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] -xref: RO:0002372 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string -property_value: seeAlso http://dbpedia.org/property/origin -domain: UBERON:0000061 {comment="We need to import uberon muscle to create a stricter domain constraint"} ! anatomical structure -is_a: attaches_to ! attached to -is_a: RO:0002567 ! biomechanically related to - [Typedef] id: has_negative_regulatory_component_activity name: has negative regulatory component activity @@ -17888,13 +17133,9 @@ id: has_ontology_root_term name: has ontology root term name: preferred_root namespace: external -namespace: uberon def: "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root." [] xref: IAO:0000700 -property_value: IAO:0000111 "has ontology root term" xsd:string -property_value: IAO:0000117 "Nicolas Matentzoglu" xsd:string is_metadata_tag: true -is_class_level: true [Typedef] id: has_output @@ -17906,9 +17147,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002234 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "produces" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Has_output" xsd:anyURI holds_over_chain: ends_with has_output is_a: has_participant ! has participant @@ -17920,62 +17158,29 @@ name: has part name: has_part namespace: external namespace: quality -namespace: uberon def: "a core relation that holds between a whole and its part" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000051 -property_value: editor_note "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string -property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string -property_value: IAO:0000111 "has part" xsd:string -property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string -property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string -property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string -property_value: IAO:0000118 "has_part" xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string is_transitive: true is_a: overlaps ! overlaps [Typedef] -id: has_participant -name: has participant -namespace: external -def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] -xref: RO:0000057 -property_value: editor_note "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string -property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string -property_value: IAO:0000111 "has participant" xsd:string -property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string -property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string -property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string -property_value: IAO:0000118 "has_participant" xsd:string -domain: BFO:0000003 ! occurrent -range: BFO:0000002 ! continuant -holds_over_chain: has_part has_participant - -[Typedef] -id: has_potential_to_develop_into -name: has potential to develop into -namespace: uberon -def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] -xref: RO:0002387 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: RO:0002384 ! has developmental potential involving - -[Typedef] -id: has_potential_to_developmentally_contribute_to -name: has potential to developmentally contribute to -namespace: uberon -def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] -xref: RO:0002385 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: RO:0002384 ! has developmental potential involving - -[Typedef] +id: has_participant +name: has participant +namespace: external +def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] +xref: RO:0000057 +property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string +domain: BFO:0000003 ! occurrent +range: BFO:0000002 ! continuant +holds_over_chain: has_part has_participant + +[Typedef] id: has_primary_input name: has primary input namespace: external @@ -18010,17 +17215,6 @@ is_a: has_primary_input_or_output ! has primary input or output created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z -[Typedef] -id: has_quality -name: has quality -namespace: uberon -def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] -xref: RO:0000086 -property_value: editor_note "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string -property_value: IAO:0000112 "this apple has quality this red color" xsd:string -property_value: IAO:0000118 "has_quality" xsd:string -is_a: bearer_of ! bearer of - [Typedef] id: has_regulatory_component_activity name: has regulatory component activity @@ -18032,24 +17226,6 @@ is_a: RO:0002017 ! has component activity created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z -[Typedef] -id: has_skeleton -name: has skeleton -namespace: uberon -def: "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." [] -xref: RO:0002551 -property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "has supporting framework" xsd:string -property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string -domain: UBERON:0000061 ! anatomical structure -domain: UBERON:0000475 ! organism subdivision -range: UBERON:0000465 {IAO:0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} ! material anatomical entity -range: UBERON:0010912 ! subdivision of skeleton -is_a: has_part ! has part -inverse_of: skeleton_of ! skeleton of -is_asymmetric: true - [Typedef] id: has_small_molecule_activator name: has small molecule activator @@ -18068,9 +17244,6 @@ namespace: external def: "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y" [] subset: ro-eco xref: RO:0002231 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "starts with process that occurs in" xsd:string domain: BFO:0000015 ! process range: BFO:0000004 ! independent continuant holds_over_chain: starts_with occurs_in @@ -18085,9 +17258,8 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002339 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of [Typedef] id: has_target_start_location @@ -18098,41 +17270,14 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002338 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in -transitive_over: part_of ! part_of - -[Typedef] -id: homologous_to -name: shares ancestor with -namespace: uberon -def: "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." [] -comment: VBO calls this homologous_to -xref: RO:0002158 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000232 "Consider obsoleting and merging with child relation, 'in homology relationship with'" xsd:string -is_symmetric: true -is_transitive: true -is_a: RO:0002320 ! evolutionarily related to - -[Typedef] -id: immediate_transformation_of -name: immediate transformation of -namespace: uberon -def: "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" [] -xref: RO:0002495 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0002575 RO:0002494 -is_a: directly_develops_from ! directly develops from -is_a: transformation_of ! transformation of +transitive_over: part_of ! part of [Typedef] id: immediately_causally_downstream_of name: immediately causally downstream of namespace: external xref: RO:0002405 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of ! causally downstream of is_a: immediately_preceded_by ! immediately preceded by inverse_of: immediately_causally_upstream_of ! immediately causally upstream of @@ -18143,26 +17288,15 @@ name: immediately causally upstream of namespace: external def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] xref: RO:0002412 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: immediately_precedes ! immediately precedes -[Typedef] -id: immediately_deep_to -name: immediately deep to -namespace: uberon -xref: BSPO:0001107 - [Typedef] id: immediately_preceded_by name: immediately preceded by namespace: external -namespace: uberon comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) xref: RO:0002087 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000118 "starts_at_end_of" xsd:string holds_over_chain: starts_with ends_with is_a: preceded_by ! preceded by inverse_of: immediately_precedes ! immediately precedes @@ -18174,228 +17308,22 @@ namespace: external comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) subset: ro-eco xref: RO:0002090 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "ends_at_start_of" xsd:string -property_value: IAO:0000118 "meets" xsd:string -property_value: RO:0002575 BFO:0000063 holds_over_chain: ends_with starts_with is_a: precedes ! precedes -[Typedef] -id: immediately_superficial_to -name: immediately superficial to -namespace: uberon -xref: BSPO:0015014 - -[Typedef] -id: in_anterior_side_of -name: in anterior side of -namespace: uberon -xref: BSPO:0000123 - -[Typedef] -id: in_deep_part_of -name: in deep part of -namespace: uberon -xref: BSPO:0001101 - -[Typedef] -id: in_dorsal_side_of -name: in dorsal side of -namespace: uberon -xref: BSPO:0015101 - -[Typedef] -id: in_lateral_side_of -name: in lateral side of -namespace: uberon -xref: BSPO:0000126 - -[Typedef] -id: in_left_side_of -name: in left side of -namespace: uberon -xref: BSPO:0000120 - -[Typedef] -id: in_posterior_side_of -name: in posterior side of -namespace: uberon -xref: BSPO:0000122 - -[Typedef] -id: in_proximal_side_of -name: in proximal side of -namespace: uberon -xref: BSPO:0000124 - -[Typedef] -id: in_right_side_of -name: in right side of -namespace: uberon -xref: BSPO:0000121 - -[Typedef] -id: in_superficial_part_of -name: in superficial part of -namespace: uberon -xref: BSPO:0001100 - -[Typedef] -id: in_taxon -name: in taxon -namespace: uberon -def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." [] -comment: Connects a biological entity to its taxon of origin. -subset: ro-eco -xref: RO:0002162 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9227-417X -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -holds_over_chain: attaches_to in_taxon -holds_over_chain: capable_of in_taxon -holds_over_chain: connected_to in_taxon -holds_over_chain: connects in_taxon -holds_over_chain: continuous_with in_taxon -holds_over_chain: developmentally_induced_by in_taxon -holds_over_chain: develops_from in_taxon -holds_over_chain: develops_from_part_of in_taxon -holds_over_chain: existence_ends_during in_taxon -holds_over_chain: existence_starts_during in_taxon -holds_over_chain: extends_fibers_into in_taxon -holds_over_chain: has_developmental_contribution_from in_taxon -holds_over_chain: has_part in_taxon -holds_over_chain: has_potential_to_develop_into in_taxon -holds_over_chain: innervated_by in_taxon -holds_over_chain: overlaps in_taxon -holds_over_chain: part_of in_taxon -holds_over_chain: produced_by in_taxon -holds_over_chain: produces in_taxon -holds_over_chain: results_in_developmental_progression_of in_taxon -holds_over_chain: RO:0002206 in_taxon -holds_over_chain: supplies in_taxon -is_a: RO:0002320 ! evolutionarily related to - [Typedef] id: indirectly_supplies name: indirectly_supplies namespace: uberon def: "a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s." [] -property_value: editor_note "add to RO" xsd:string -holds_over_chain: has_branching_part indirectly_supplies -holds_over_chain: has_branching_part supplies -is_transitive: true - -[Typedef] -id: innervated_by -name: innervated_by -namespace: uberon -xref: RO:0002005 -property_value: http://purl.org/spar/cito/citesAsAuthority "http://www.ncbi.nlm.nih.gov/pubmed/22402613" xsd:anyURI -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -domain: UBERON:0000061 ! anatomical structure -inverse_of: innervates ! innervates -transitive_over: branching_part_of ! branching part of - -[Typedef] -id: innervates -name: innervates -namespace: uberon -def: "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." [] -xref: RO:0002134 -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 -transitive_over: part_of ! part_of -expand_expression_to: "RO_0002132 some (GO_0043005 that (RO_0002131 some (GO_0045202 that BFO_0000050 some Y?)))" [] - -[Typedef] -id: input_of -name: input of -namespace: uberon -def: "inverse of has input" [] -subset: ro-eco -subset: RO:0002259 -xref: RO:0002352 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: functionally_related_to ! functionally related to -is_a: participates_in ! participates in - -[Typedef] -id: intersects_midsagittal_plane_of -name: intersects midsagittal plane of -namespace: uberon -xref: BSPO:0005001 +property_value: IAO:0000116 "add to RO" xsd:string +holds_over_chain: RO:0002569 indirectly_supplies [Typedef] id: layer_part_of name: layer part of namespace: uberon -is_a: part_of ! part_of - -[Typedef] -id: located_in -name: located in -namespace: uberon -def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -xref: RO:0001025 -property_value: editor_note "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" xsd:string -property_value: editor_note "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:located_in" xsd:string -property_value: IAO:0000111 "located in" xsd:string -property_value: IAO:0000112 "my brain is located in my head" xsd:string -property_value: IAO:0000112 "this rat is located in this cage" xsd:string -property_value: IAO:0000118 "located_in" xsd:string -property_value: RO:0001900 RO:0001901 -property_value: seeAlso "https://wiki.geneontology.org/Located_in" xsd:anyURI -domain: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant -range: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant -is_transitive: true -transitive_over: part_of ! part_of - -[Typedef] -id: location_of -name: location of -namespace: uberon -def: "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" [] -xref: RO:0001015 -property_value: editor_note "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: IAO:0000111 "is location of" xsd:string -property_value: IAO:0000112 "my head is the location of my brain" xsd:string -property_value: IAO:0000112 "this cage is the location of this rat" xsd:string -property_value: IAO:0000118 "location_of" xsd:string -property_value: RO:0001900 RO:0001901 -is_transitive: true -inverse_of: located_in ! located in - -[Typedef] -id: lumen_of -name: lumen of -namespace: uberon -def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] -subset: ro-eco -xref: RO:0002571 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 https://orcid.org/0000-0002-6601-2165 -range: BFO:0000040 ! material entity -is_a: part_of ! part_of - -[Typedef] -id: luminal_space_of -name: luminal space of -namespace: uberon -def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" [] -subset: ro-eco -xref: RO:0002572 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: BFO:0000141 ! immaterial entity -is_a: lumen_of ! lumen of +is_a: part_of ! part of [Typedef] id: negatively_regulated_by @@ -18404,7 +17332,6 @@ namespace: external def: "inverse of negatively regulates" [] subset: RO:0002259 xref: RO:0002335 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -18416,9 +17343,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002212 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002211 holds_over_chain: ends_with negatively_regulates is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect @@ -18431,30 +17355,11 @@ name: negatively regulates characteristic namespace: gene_ontology def: "A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C." [] xref: RO:0019002 -property_value: dc-contributor https://orcid.org/0000-0002-8688-6599 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 holds_over_chain: negatively_regulates positively_regulates_characteristic holds_over_chain: positively_regulates negatively_regulates_characteristic is_a: regulates_characteristic ! regulates characteristic -[Typedef] -id: never_in_taxon -name: never in taxon -name: never_in_taxon -namespace: uberon -def: "S never_in_taxon T iff: S SubClassOf in_taxon only not T." [PMID:20973947] -def: "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL." [] -xref: RO:0002161 -property_value: IAO:0000112 "tooth SubClassOf 'never in taxon' value 'Aves'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 -property_value: OMO:0002000 "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" xsd:string -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -expand_assertion_to: "Class: EquivalentTo: ?X and (RO_0002162 some ?Y)" [] -expand_assertion_to: "Class: ?X DisjointWith: RO_0002162 some ?Y " [] -is_metadata_tag: true -is_class_level: true - [Typedef] id: occurs_in name: occurs in @@ -18465,64 +17370,38 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000066 -property_value: IAO:0000111 "occurs in" xsd:string -property_value: IAO:0000118 "occurs_in" xsd:string -property_value: IAO:0000118 "unfolds in" xsd:string -property_value: IAO:0000118 "unfolds_in" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl property_value: seeAlso "https://wiki.geneontology.org/Occurs_in" xsd:anyURI domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant holds_over_chain: part_of occurs_in -inverse_of: contains_process ! contains process -transitive_over: part_of ! part_of - -[Typedef] -id: only_in_taxon -name: only in taxon -namespace: uberon -def: "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." [] -xref: RO:0002160 -property_value: editor_note "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" xsd:string -property_value: IAO:0000112 "lactation SubClassOf 'only in taxon' some 'Mammalia'" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -is_a: in_taxon ! in taxon +inverse_of: BFO:0000067 ! contains process +transitive_over: part_of ! part of [Typedef] id: output_of name: output of namespace: external -namespace: uberon def: "inverse of has output" [] subset: ro-eco subset: RO:0002259 xref: RO:0002353 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: functionally_related_to ! functionally related to is_a: participates_in ! participates in +is_a: RO:0002328 ! functionally related to [Typedef] id: overlaps name: overlaps namespace: external -namespace: uberon def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002131 -property_value: IAO:0000114 IAO:0000125 -property_value: RO:0001900 RO:0001901 holds_over_chain: has_part overlaps -holds_over_chain: has_part part_of {RO:0002582="true"} holds_over_chain: part_of part_of is_symmetric: true is_a: RO:0002323 ! mereotopologically related to -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] [Typedef] @@ -18531,29 +17410,15 @@ name: part of name: part_of namespace: external namespace: quality -namespace: uberon def: "a core relation that holds between a part and its whole" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000050 -property_value: editor_note "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string -property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string -property_value: IAO:0000111 "is part of" xsd:string -property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string -property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string -property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string -property_value: IAO:0000118 "part_of" xsd:string -property_value: RO:0001900 RO:0001901 -property_value: RO:0040042 BFO:0000002 -property_value: RO:0040042 BFO:0000003 -property_value: RO:0040042 BFO:0000004 -property_value: RO:0040042 BFO:0000017 -property_value: RO:0040042 BFO:0000019 -property_value: RO:0040042 BFO:0000020 -property_value: RO:0040042 BFO:0000031 +property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string @@ -18566,14 +17431,8 @@ inverse_of: has_part ! has part id: participates_in name: participates in namespace: external -namespace: uberon def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] xref: RO:0000056 -property_value: IAO:0000111 "participates in" xsd:string -property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string -property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string -property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string -property_value: IAO:0000118 "participates_in" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000003 ! occurrent inverse_of: has_participant ! has participant @@ -18585,7 +17444,6 @@ namespace: external def: "inverse of positively regulates" [] subset: RO:0002259 xref: RO:0002336 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -18597,10 +17455,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002213 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "positively regulates (process to process)" xsd:string -property_value: RO:0004049 RO:0002211 holds_over_chain: ends_with positively_regulates holds_over_chain: negatively_regulates negatively_regulates is_transitive: true @@ -18614,49 +17468,25 @@ name: positively regulates characteristic namespace: gene_ontology def: "A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C." [] xref: RO:0019001 -property_value: dc-contributor https://orcid.org/0000-0002-8688-6599 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 holds_over_chain: positively_regulates positively_regulates_characteristic is_a: regulates_characteristic ! regulates characteristic -[Typedef] -id: postaxialmost_part_of -name: postaxialmost part of -namespace: uberon -xref: BSPO:0001115 - -[Typedef] -id: posterior_to -name: posterior to -namespace: uberon -xref: BSPO:0000099 - [Typedef] id: posteriorly_connected_to name: posteriorly connected to namespace: uberon def: "x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] -is_a: anterior_to ! anterior to -is_a: connected_to ! connected to - -[Typedef] -id: preaxialmost_part_of -name: preaxialmost part of -namespace: uberon -xref: BSPO:0001113 +is_a: RO:0002170 ! connected to [Typedef] id: preceded_by name: preceded by namespace: external -namespace: uberon def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000062 -property_value: editor_note "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string -property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string -property_value: IAO:0000111 "preceded by" xsd:string -property_value: IAO:0000118 "is preceded by" xsd:string -property_value: IAO:0000118 "preceded_by" xsd:string +property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent holds_over_chain: part_of preceded_by @@ -18668,53 +17498,30 @@ inverse_of: precedes ! precedes id: precedes name: precedes namespace: external -namespace: uberon def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000063 -property_value: IAO:0000111 "precedes" xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent holds_over_chain: part_of precedes is_transitive: true is_a: RO:0002222 ! temporally related to -[Typedef] -id: present_in_taxon -name: present in taxon -name: present_in_taxon -namespace: uberon -def: "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S" [] -def: "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S." [https://orcid.org/0000-0002-6601-2165] -comment: The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology. -synonym: "applicable for taxon" EXACT [] -xref: RO:0002175 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: OMO:0002000 "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" xsd:string -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -is_metadata_tag: true -is_class_level: true - [Typedef] id: process_has_causal_agent name: process has causal agent namespace: external def: "Inverse of 'causal agent in process'" [] xref: RO:0002608 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_a: RO:0002410 ! causally related to [Typedef] id: produced_by name: produced by namespace: external -namespace: uberon def: "a produced_by b iff some process that occurs_in b has_output a." [] subset: ro-eco xref: RO:0003001 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity @@ -18722,13 +17529,10 @@ range: BFO:0000040 ! material entity id: produces name: produces namespace: external -namespace: uberon def: "a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix." [] comment: Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. subset: ro-eco xref: RO:0003000 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity inverse_of: produced_by ! produced by @@ -18738,27 +17542,14 @@ id: protects name: protects namespace: uberon -[Typedef] -id: proximal_to -name: proximal to -namespace: uberon -xref: BSPO:0000100 - [Typedef] id: proximally_connected_to name: proximally connected to namespace: uberon def: "x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] -is_a: connected_to ! connected to -is_a: distal_to ! distal to +is_a: RO:0002170 ! connected to is_a: transitively_proximally_connected_to ! transitively proximally connected to -[Typedef] -id: proximalmost_part_of -name: proximalmost part of -namespace: uberon -xref: BSPO:0001106 - [Typedef] id: regulated_by name: regulated by @@ -18766,8 +17557,6 @@ namespace: external def: "inverse of regulates" [] subset: RO:0002259 xref: RO:0002334 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000589 "regulated by (processual)" xsd:string domain: BFO:0000015 ! process range: BFO:0000015 ! process is_transitive: true @@ -18782,14 +17571,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 -property_value: IAO:0000117 https://orcid.org/0000-0001-7476-6306 -property_value: IAO:0000117 https://orcid.org/0000-0002-3837-8864 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GO" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string -property_value: IAO:0000589 "regulates (processual)" xsd:string -property_value: IAO:0000600 "false" xsd:boolean domain: BFO:0000015 ! process range: BFO:0000015 ! process holds_over_chain: directly_regulates directly_regulates @@ -18805,7 +17586,7 @@ name: regulates characteristic namespace: gene_ontology def: "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C." [] xref: RO:0019000 -property_value: dc-contributor https://orcid.org/0000-0002-8688-6599 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 domain: BFO:0000015 ! process range: PATO:0000001 ! quality holds_over_chain: regulates regulates_characteristic @@ -18817,13 +17598,9 @@ name: regulates levels of namespace: external def: "p regulates levels of c if p regulates some amount (PATO:0000070) of c" [] xref: RO:0002332 -property_value: IAO:0000112 "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "regulates levels of (process to entity)" xsd:string domain: BFO:0000015 ! process range: BFO:0000040 ! material entity -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to [Typedef] id: results_in_acquisition_of_features_of @@ -18834,9 +17611,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002315 -property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string range: UBERON:0000061 ! anatomical structure is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -18871,10 +17645,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002296 -property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "http://www.geneontology.org/GO.doc.development.shtml" xsd:anyURI is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -18884,9 +17654,7 @@ name: results in developmental progression of namespace: external def: "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." [] xref: RO:0002295 -property_value: editor_note "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000116 "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string property_value: seeAlso Ontology:extensions domain: GO:0008150 ! biological_process range: UBERON:0001062 ! anatomical entity @@ -18918,16 +17686,12 @@ is_a: has_participant ! has participant [Typedef] id: results_in_formation_of name: results in formation of +name: results in formation of anatomical entity namespace: external subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002297 -property_value: IAO:0000112 "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." xsd:string -property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of inverse_of: RO:0002354 ! formed as result of @@ -18949,8 +17713,6 @@ id: results_in_growth_of name: results in growth of namespace: external xref: RO:0002343 -property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -18963,11 +17725,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002299 -property_value: IAO:0000112 " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" xsd:string -property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -18980,11 +17737,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002298 -property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." xsd:string -property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -18997,8 +17749,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002565 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure [Typedef] @@ -19017,7 +17767,6 @@ namespace: external def: "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002342 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in is_a: RO:0002021 ! occurs across @@ -19027,7 +17776,6 @@ name: results in transport along namespace: external def: "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " [] xref: RO:0002341 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002337 ! related via localization to [Typedef] @@ -19035,36 +17783,13 @@ id: results_in_transport_to_from_or_in name: results in transport to from or in namespace: external xref: RO:0002344 -property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002337 ! related via localization to -[Typedef] -id: seeAlso -name: see also -namespace: uberon -xref: http://www.w3.org/2000/01/rdf-schema#seeAlso -is_metadata_tag: true - [Typedef] id: sexually_homologous_to name: sexually_homologous_to namespace: uberon -is_a: homologous_to ! shares ancestor with - -[Typedef] -id: simultaneous_with -name: simultaneous with -namespace: uberon -def: "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." [] -comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) -subset: ro-eco -xref: RO:0002082 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -is_symmetric: true -is_transitive: true -is_a: RO:0002081 ! before or simultaneous with +is_a: RO:0002158 ! shares ancestor with [Typedef] id: site_of @@ -19073,46 +17798,13 @@ namespace: uberon def: "c site_of p if c is the bearer of a disposition that is realized by a process that has p as part." [] synonym: "capable_of_has_part" RELATED [] -[Typedef] -id: skeleton_of -name: skeleton of -namespace: uberon -def: "inverse of has skeleton" [] -subset: RO:0002259 -xref: RO:0002576 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: UBERON:0000061 ! anatomical structure -range: UBERON:0000061 ! anatomical structure -is_a: part_of ! part_of - -[Typedef] -id: starts -name: starts -namespace: uberon -def: "inverse of starts with" [] -subset: ro-eco -xref: RO:0002223 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "Allen" xsd:string -is_a: part_of ! part_of -is_a: RO:0002222 ! temporally related to -inverse_of: starts_with ! starts with - [Typedef] id: starts_with name: starts with namespace: external -namespace: uberon def: "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002224 -property_value: IAO:0000112 "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "started by" xsd:string is_transitive: true is_a: has_part ! has part is_a: RO:0002222 ! temporally related to @@ -19123,139 +17815,36 @@ name: subdivision of namespace: uberon comment: placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B -[Typedef] -id: superficial_to -name: superficial to -namespace: uberon -xref: BSPO:0000108 - -[Typedef] -id: supplies -name: supplies -namespace: uberon -def: "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." [] -xref: RO:0002178 -property_value: editor_note "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 -is_a: connected_to ! connected to - -[Typedef] -id: surrounded_by -name: surrounded by -namespace: uberon -def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" [] -xref: RO:0002219 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0001900 RO:0001901 -is_a: adjacent_to ! adjacent to -inverse_of: surrounds ! surrounds - -[Typedef] -id: surrounds -name: surrounds -namespace: uberon -def: "inverse of surrounded by" [] -subset: RO:0002259 -xref: RO:0002221 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0001900 RO:0001901 -is_a: adjacent_to ! adjacent to - -[Typedef] -id: synapsed_by -name: synapsed by -namespace: uberon -def: "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " [] -xref: RO:0002103 -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 -is_a: RO:0002485 ! receives input from -inverse_of: RO:0002120 ! synapsed to -expand_expression_to: "BFO_0000051 some (GO_0045211 that part_of some (GO_0045202 that has_part some (GO_0042734 that BFO_0000050 some Y?)))" [] - [Typedef] id: term_tracker_item name: term tracker item namespace: external -namespace: uberon def: "An IRI or similar locator for a request or discussion of an ontology term." [] comment: The 'tracker item' can associate a tracker with a specific ontology term. xref: IAO:0000233 -property_value: IAO:0000111 "term tracker item" xsd:string -property_value: IAO:0000112 "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" xsd:string -property_value: IAO:0000119 "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" xsd:string is_metadata_tag: true -is_class_level: true - -[Typedef] -id: transformation_of -name: transformation of -namespace: uberon -def: "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" [] -xref: RO:0002494 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_transitive: true -is_a: develops_from ! develops from [Typedef] id: transitively_anteriorly_connected_to name: transitively anteriorly connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI -is_transitive: true [Typedef] id: transitively_distally_connected_to name: transitively distally connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI -is_transitive: true [Typedef] id: transitively_proximally_connected_to name: transitively proximally connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI -is_transitive: true - -[Typedef] -id: tributary_of -name: tributary of -namespace: uberon -def: "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." [] -subset: ro-eco -xref: RO:0002376 -property_value: IAO:0000112 "Deschutes River tributary_of Columbia River" xsd:string -property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "drains into" xsd:string -property_value: IAO:0000118 "drains to" xsd:string -property_value: IAO:0000118 "tributary channel of" xsd:string -property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Tributary" xsd:string -property_value: IAO:0000119 "http://www.medindia.net/glossary/venous_tributary.htm" xsd:string -property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" xsd:anyURI -property_value: seeAlso http://dbpedia.org/ontology/drainsTo -property_value: seeAlso "http://en.wikipedia.org/wiki/Tributary" xsd:anyURI -is_a: connected_to ! connected to -is_a: RO:0002375 ! in branching relationship with [Typedef] id: trunk_part_of name: trunk_part_of namespace: uberon -is_a: part_of ! part_of - -[Typedef] -id: ventral_to -name: ventral to -namespace: uberon -xref: BSPO:0000102 +is_a: part_of ! part of diff --git a/src/ontology/subsets/blood_and_immune_upper_slim.owl b/src/ontology/subsets/blood_and_immune_upper_slim.owl index d0c2dbd2b..75f5291d1 100644 --- a/src/ontology/subsets/blood_and_immune_upper_slim.owl +++ b/src/ontology/subsets/blood_and_immune_upper_slim.owl @@ -10,28 +10,21 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" - xmlns:cito="http://purl.org/spar/cito/" xmlns:core="http://purl.obolibrary.org/obo/uberon/core#" xmlns:foaf="http://xmlns.com/foaf/0.1/" - xmlns:obo2="http://www.geneontology.org/formats/oboInOwl#http://purl.obolibrary.org/obo/" xmlns:pato="http://purl.obolibrary.org/obo/pato#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" - xmlns:skos="http://www.w3.org/2004/02/skos/core#" xmlns:swrl="http://www.w3.org/2003/11/swrl#" - xmlns:sssom="https://w3id.org/sssom/" - xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#" xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:terms="http://purl.org/dc/terms/" - xmlns:vocab="https://w3id.org/semapv/vocab/" - xmlns:terms1="http://www.geneontology.org/formats/oboInOwl#http://purl.org/dc/terms/" xmlns:uberon="http://purl.obolibrary.org/obo/uberon#" xmlns:ubprop="http://purl.obolibrary.org/obo/ubprop#" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - 2024-02-13 + + 2024-04-05 @@ -55,29 +48,9 @@ - - - - - - - - - - - - - - - - - - - definition - The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith @@ -99,8 +72,6 @@ We don't have definitions of 'meaning' or 'expression' Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition @@ -110,72 +81,28 @@ We also have the outstanding issue of how to aim different definitions to differ - editor note - An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obofoundry.org/obo/obi> - IAO:0000116 - uberon - editor_note - true - editor_note - editor note editor note - - - - - - - - - - - - - - - - - - - has obsolescence reason Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. - PERSON:Alan Ruttenberg - PERSON:Melanie Courtot has obsolescence reason - - - - - - - term tracker item - the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ - An IRI or similar locator for a request or discussion of an ontology term. - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg IAO:0000233 external - uberon term_tracker_item - true true term_tracker_item The 'tracker item' can associate a tracker with a specific ontology term. @@ -185,63 +112,23 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - - expand expression to - ObjectProperty: RO_0002104 -Label: has plasma membrane part -Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" - A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones - Chris Mungall expand expression to expand expression to - - - - - - - - - - - - - - - - - - - - - - - - - has ontology root term Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. - Nicolas Matentzoglu IAO:0000700 external - uberon has_ontology_root_term - true true has_ontology_root_term has ontology root term @@ -251,20 +138,10 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - - - - - - - term replaced by - Use on obsolete terms, relating the term to another term that can be used as a substitute - Person:Alan Ruttenberg - Person:Alan Ruttenberg Add as annotation triples in the granting ontology term replaced by term replaced by @@ -275,24 +152,6 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - 'part disjoint with' 'defined by construct' """ - PREFIX owl: <http://www.w3.org/2002/07/owl#> - PREFIX : <http://example.org/ - CONSTRUCT { - [ - a owl:Restriction ; - owl:onProperty :part_of ; - owl:someValuesFrom ?a ; - owl:disjointWith [ - a owl:Restriction ; - owl:onProperty :part_of ; - owl:someValuesFrom ?b - ] - ] - } - WHERE { - ?a :part_disjoint_with ?b . - } Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. @@ -305,11 +164,9 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation) A synonym type for describing abbreviations or initalisms - 2023-03-03 abbreviation @@ -335,11 +192,9 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form) A synonym type for describing pluralization synonyms - 2023-03-03 plural form @@ -354,23 +209,10 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - - - - - - - tooth SubClassOf 'never in taxon' value 'Aves' - S never_in_taxon T iff: S SubClassOf in_taxon only not T. x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL. - - - - Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: ?X and (RO_0002162 some ?Y) - Class: ?X DisjointWith: RO_0002162 some ?Y PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> @@ -394,34 +236,9 @@ CONSTRUCT { WHERE { ?x never_in_taxon: ?taxon . } - RO:0002161 - uberon - never_in_taxon - true - true - never_in_taxon never in taxon - never_in_taxon - - - - S never_in_taxon T iff: S SubClassOf in_taxon only not T. - PMID:20973947 - - - - - - - - - - - - - @@ -429,9 +246,6 @@ WHERE { S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S - S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S. - - PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> @@ -456,24 +270,10 @@ WHERE { )) as ?witness) BIND(CONCAT(STR(?x), " in taxon ", STR(?taxon)) AS ?label) } - RO:0002175 - applicable for taxon - uberon - present_in_taxon - true - true - present_in_taxon The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology. present in taxon - present_in_taxon - - - - S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S. - https://orcid.org/0000-0002-6601-2165 - @@ -485,60 +285,6 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL - is a defining property chain axiom - - - - - - - - If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. - is a defining property chain axiom where second argument is reflexive - - - - - - - - - - - - - - - - - - - - - - @@ -549,126 +295,6 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -927,12 +553,6 @@ WHERE { - - - - - - @@ -1363,14 +983,7 @@ WHERE { - - http://purl.org/dc/elements/1.1/creator - uberon - dc-creator - true - dc-creator - creator - + @@ -1382,14 +995,7 @@ WHERE { - - http://purl.org/dc/elements/1.1/description - uberon - dc-description - true - dc-description - description - + @@ -1401,71 +1007,25 @@ WHERE { - - http://purl.org/dc/elements/1.1/title - uberon - dc-title - true - dc-title - title - + - - http://purl.org/dc/terms/contributor - uberon - dc-contributor - true - dc-contributor - contributor - - - - - - - - - - - - - + - - http://purl.org/dc/terms/date - uberon - dcterms-date - true - dcterms-date - date - + - - http://purl.org/dc/terms/license - uberon - dcterms-license - true - dcterms-license - license - - - - - - - + @@ -1475,18 +1035,6 @@ WHERE { - - - - - - - - - - - - @@ -1503,18 +1051,6 @@ WHERE { - - - - - - - - - - - - @@ -1523,18 +1059,6 @@ WHERE { - - - - - - - - - - - - @@ -1551,66 +1075,6 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -1623,7 +1087,6 @@ WHERE { An alternative label for a class or property which has a more general meaning than the preferred name/primary label. - https://github.com/information-artifact-ontology/ontology-metadata/issues/18 has broad synonym has_broad_synonym @@ -1644,7 +1107,6 @@ WHERE { An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. - https://github.com/information-artifact-ontology/ontology-metadata/issues/20 has exact synonym has_exact_synonym @@ -1657,7 +1119,6 @@ WHERE { An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. - https://github.com/information-artifact-ontology/ontology-metadata/issues/19 has narrow synonym has_narrow_synonym @@ -1678,7 +1139,6 @@ WHERE { An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. - https://github.com/information-artifact-ontology/ontology-metadata/issues/21 has related synonym has_related_synonym @@ -1687,12 +1147,6 @@ WHERE { - - - - - - @@ -1717,30 +1171,6 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - - - @@ -1753,72 +1183,12 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -1833,60 +1203,6 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -1903,9 +1219,6 @@ WHERE { http://www.w3.org/2000/01/rdf-schema#seeAlso - uberon - seeAlso - true seeAlso see also @@ -1918,63 +1231,9 @@ WHERE { - - - - - - - - http://xmlns.com/foaf/0.1/depiction - uberon - depiction - true - depiction - depiction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + @@ -1995,29 +1254,15 @@ WHERE { - is part of - my brain is part of my body (continuant parthood, two material entities) - my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) - this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. - part_of - - - - - - - - BFO:0000050 external quality - uberon part_of @@ -2040,22 +1285,15 @@ A continuant cannot be part of an occurrent: use 'participates in'. An - has part - my body has part my brain (continuant parthood, two material entities) - my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) - this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. - has_part - BFO:0000051 external quality - uberon has_part @@ -2080,15 +1318,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. - preceded by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. - is preceded by - preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 external - uberon preceded_by preceded_by @@ -2109,11 +1342,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. - precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. BFO:0000063 external - uberon precedes precedes @@ -2137,11 +1368,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - occurs_in - unfolds in - unfolds_in BFO:0000066 external occurs_in @@ -2150,7 +1377,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. occurs_in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant - occurs in occurs in https://wiki.geneontology.org/Occurs_in @@ -2161,308 +1387,13 @@ A continuant cannot have an occurrent as part: use 'participates in'. - site of [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - BFO:0000067 - uberon - contains_process - contains_process Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant - - contains process contains process - - - - BSPO:0000096 - uberon - anterior_to - anterior_to - anterior to - - - - - - - - BSPO:0000097 - uberon - distal_to - distal_to - distal to - - - - - - - - BSPO:0000098 - uberon - dorsal_to - dorsal_to - dorsal to - - - - - - - - BSPO:0000099 - uberon - posterior_to - posterior_to - posterior to - - - - - - - - BSPO:0000100 - uberon - proximal_to - proximal_to - proximal to - - - - - - - - BSPO:0000102 - uberon - ventral_to - ventral_to - ventral to - - - - - - - - BSPO:0000107 - uberon - deep_to - deep_to - deep to - - - - - - - - BSPO:0000108 - uberon - superficial_to - superficial_to - superficial to - - - - - - - - BSPO:0000120 - uberon - in_left_side_of - in_left_side_of - in left side of - - - - - - - - BSPO:0000121 - uberon - in_right_side_of - in_right_side_of - in right side of - - - - - - - - BSPO:0000122 - uberon - in_posterior_side_of - in_posterior_side_of - in posterior side of - - - - - - - - BSPO:0000123 - uberon - in_anterior_side_of - in_anterior_side_of - in anterior side of - - - - - - - - BSPO:0000124 - uberon - in_proximal_side_of - in_proximal_side_of - in proximal side of - - - - - - - - BSPO:0000126 - uberon - in_lateral_side_of - in_lateral_side_of - in lateral side of - - - - - - - - BSPO:0001100 - uberon - in_superficial_part_of - in_superficial_part_of - in superficial part of - - - - - - - - BSPO:0001101 - uberon - in_deep_part_of - in_deep_part_of - in deep part of - - - - - - - - BSPO:0001106 - uberon - proximalmost_part_of - proximalmost_part_of - proximalmost part of - - - - - - - - BSPO:0001107 - uberon - immediately_deep_to - immediately_deep_to - immediately deep to - - - - - - - - BSPO:0001108 - uberon - distalmost_part_of - distalmost_part_of - distalmost part of - - - - - - - - BSPO:0001113 - uberon - preaxialmost_part_of - preaxialmost_part_of - preaxialmost part of - - - - - - - - BSPO:0001115 - uberon - postaxialmost_part_of - postaxialmost_part_of - postaxialmost part of - - - - - - - - BSPO:0005001 - uberon - intersects_midsagittal_plane_of - intersects_midsagittal_plane_of - intersects midsagittal plane of - - - - - - - - BSPO:0015014 - uberon - immediately_superficial_to - immediately_superficial_to - immediately superficial to - - - - - - - - BSPO:0015101 - uberon - in_dorsal_side_of - in_dorsal_side_of - in dorsal side of - - - - @@ -2522,12 +1453,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - inheres in - this fragility is a characteristic of this vase - this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. - inheres_in - Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of @@ -2539,14 +1465,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - bearer of - this apple is bearer of this red color - this vase is bearer of this fragility Inverse of characteristic_of A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. - bearer_of - is bearer of - RO:0000053 external bearer_of @@ -2563,15 +1483,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. - participates in - this blood clot participates in this blood coagulation - this input material (or this output material) participates in this process - this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process - participates_in RO:0000056 external - uberon participates_in participates_in participates in @@ -2589,14 +1503,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - has participant - this blood coagulation has participant this blood clot - this investigation has participant this investigator - this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. - has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 external has_participant @@ -2612,11 +1520,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. - function_of - is function of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. function of @@ -2628,11 +1533,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. - is quality of - quality_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. quality of @@ -2644,11 +1546,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. - is role of - role_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. role of @@ -2660,10 +1559,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. - has_function has function @@ -2673,15 +1570,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. - has_quality - RO:0000086 - uberon - has_quality - has_quality - has quality has quality @@ -2692,10 +1582,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. - has_role has role @@ -2729,13 +1617,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this cell derives from this parent cell (cell division) - this nucleus derives from this parent nucleus (nuclear division) - a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. - derives_from - This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. derives from @@ -2745,12 +1628,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this parent cell derives into this cell (cell division) - this parent nucleus derives into this nucleus (nuclear division) - a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. - derives_into derives into @@ -2762,18 +1641,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - is location of - my head is the location of my brain - this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - location_of - - RO:0001015 - uberon - location_of - location_of - location of location of @@ -2789,21 +1658,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. - located in - my brain is located in my head - this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - located_in - - http://www.obofoundry.org/ro/#OBO_REL:located_in - RO:0001025 - uberon - located_in - located_in - located in located in https://wiki.geneontology.org/Located_in @@ -2827,16 +1685,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. - the surface of my skin is a 2D boundary of my body a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - 2D_boundary_of - boundary of - is 2D boundary of - is boundary of - surface of - 2D boundary of @@ -2848,19 +1699,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. - my body has 2D boundary the surface of my skin a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - - has boundary - has_2D_boundary - - RO:0002002 - uberon - has_boundary - has_boundary - has 2D boundary has 2D boundary @@ -2871,17 +1712,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - http://www.ncbi.nlm.nih.gov/pubmed/22402613 - RO:0002005 - uberon - innervated_by - innervated_by - innervated_by innervated_by @@ -2892,8 +1722,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - has synaptic terminal of @@ -2913,10 +1741,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - RO:0002007 external - uberon bounding_layer_of bounding_layer_of @@ -3095,8 +1921,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland - <= Primitive instance level timing relation between events before or simultaneous with @@ -3111,15 +1935,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time. - - David Osumi-Sutherland - RO:0002082 - uberon - simultaneous_with - simultaneous_with t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) - simultaneous with simultaneous with @@ -3130,7 +1947,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after @@ -3147,11 +1963,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland - starts_at_end_of RO:0002087 external - uberon immediately_preceded_by immediately_preceded_by X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) @@ -3169,11 +1982,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - - David Osumi-Sutherland - ends_at_start_of - meets - RO:0002090 external immediately_precedes @@ -3196,12 +2004,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between a neuron and a material anatomical entity that its soma is part of. - <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) - has soma location @@ -3213,33 +2018,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. - - fasciculates with - (forall (?x ?y) - (iff - (fasciculates_with ?x ?y) - (exists (?nps ?npbs) - (and - ("neuron ; CL_0000540" ?x) - ("neuron projection bundle ; CARO_0001001" ?y) - ("neuron projection segment ; CARO_0001502" ?nps) - ("neuron projection bundle segment ; CARO_0001500' " ?npbs) - (part_of ?npbs ?y) - (part_of ?nps ?x) - (part_of ?nps ?npbs) - (forall (?npbss) - (if - (and - ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) - (part_of ?npbss ?npbs) - ) - (overlaps ?nps ?npbss) - )))))) - - fasciculates with @@ -3254,16 +2034,11 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between a neuron and some structure its axon forms (chemical) synapses in. - - <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y))) - - axon synapses in @@ -3285,18 +2060,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. - - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) - - - RO:0002103 - uberon - synapsed_by - synapsed_by - synapsed by synapsed by @@ -3308,15 +2073,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] - Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. - - - - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) - has plasma membrane part @@ -3332,16 +2090,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. - - - synapsed in http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)) - - has postsynaptic terminal in @@ -3356,12 +2108,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. - synapses in <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) - - has presynaptic terminal in @@ -3382,14 +2130,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. - - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) - - N1 synapsed_to some N2 Expands to: N1 SubclassOf ( @@ -3411,13 +2154,8 @@ N1 SubclassOf ( - A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. - - has synapse in <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) - - has synaptic terminal in @@ -3432,10 +2170,6 @@ N1 SubclassOf ( - - - - @@ -3444,13 +2178,10 @@ N1 SubclassOf ( - x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) - RO:0002131 external - uberon overlaps @@ -3459,15 +2190,6 @@ N1 SubclassOf ( overlaps overlaps - - - - - - - - true - @@ -3486,35 +2208,7 @@ N1 SubclassOf ( - The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. - - has fasciculating component - (forall (?x ?y) - (iff - (has_fasciculating_neuron_projection ?x ?y) - (exists (?nps ?npbs) - (and - ("neuron projection bundle ; CARO_0001001" ?x) - ("neuron projection ; GO0043005" ?y) - ("neuron projection segment ; CARO_0001502" ?nps) - ("neuron projection bundle segment ; CARO_0001500" ?npbs) - (part_of ?nps ?y) - (part_of ?npbs ?x) - (part_of ?nps ?npbs) - (forall (?npbss) - (if - (and - ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) - (part_of ?npbss ?npbs) - ) - (overlaps ?nps ?npbss) - )))))) - - - - - has fasciculating neuron projection @@ -3527,19 +2221,10 @@ N1 SubclassOf ( - Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - <http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) - - - RO:0002134 - uberon - innervates - innervates - innervates innervates @@ -3552,17 +2237,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - X continuous_with Y if and only if X and Y share a fiat boundary. - - connected to - The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) - - RO:0002150 - uberon - continuous_with - continuous_with - continuous with continuous with FMA:85972 @@ -3575,13 +2250,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a. - Consider obsoleting and merging with child relation, 'in homology relationship with' - RO:0002158 - uberon - homologous_to - homologous_to VBO calls this homologous_to shares ancestor with @@ -3592,19 +2261,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - lactation SubClassOf 'only in taxon' some 'Mammalia' - x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria - - - - RO:0002160 - uberon - only_in_taxon - only_in_taxon only in taxon @@ -3623,30 +2283,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - - - - - - - - - - - - - - - - - - - - - @@ -3667,53 +2303,16 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. - - - - - RO:0002162 - uberon - in_taxon - in_taxon Connects a biological entity to its taxon of origin. in taxon @@ -3725,14 +2324,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. - - - Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) - spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern @@ -3750,14 +2344,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b - - RO:0002170 - uberon - connected_to - connected_to - connected to connected to https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern @@ -3770,15 +2357,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - The M8 connects Glasgow and Edinburgh - a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system. - - RO:0002176 - uberon - connects - connects - connects connects https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern @@ -3793,28 +2372,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. - attached to part of (anatomical structure to anatomical structure) - RO:0002177 - uberon - attaches_to_part_of - attaches_to_part_of - attached to part of attached to part of - - - - - - - - true - @@ -3824,12 +2384,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy. Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure - - RO:0002178 - uberon - supplies - supplies - supplies supplies @@ -3841,12 +2395,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure. Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure - - RO:0002179 - uberon - drains - drains - drains drains @@ -3856,14 +2404,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. - For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. - RO:0002180 external - uberon has_component has_component @@ -3883,18 +2427,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y - - - - - RO:0002202 - uberon - develops_from - develops_from This is the transitive form of the develops from relation - develops from develops from @@ -3907,17 +2441,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of develops from - - - - RO:0002203 - uberon - develops_into - develops_into - develops into develops into @@ -3934,10 +2459,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - 'neural crest cell' SubClassOf expresses some 'Wnt1 gene' - x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process - expressed in @@ -3964,19 +2486,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. - - - FBbt - - RO:0002207 has developmental precursor - uberon - directly_develops_from - directly_develops_from TODO - add child relations from DOS - directly develops from directly develops from @@ -3986,9 +2498,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of directly develops from - developmental precursor of directly develops into @@ -4016,14 +2526,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. - - - - - GO - Regulation precludes parthood; the regulatory process may not be within the regulated process. - regulates (processual) - false RO:0002211 external regulates @@ -4048,9 +2550,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. - - - negatively regulates (process to process) RO:0002212 external @@ -4081,10 +2580,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. - - - positively regulates (process to process) - RO:0002213 external positively_regulates @@ -4104,17 +2599,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) - osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. - - has function realized in - - - For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". RO:0002215 external - uberon capable_of capable_of @@ -4129,31 +2616,15 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. - - has function in RO:0002216 external - uberon capable_of_part_of capable_of_part_of capable of part of capable of part of - - - - - - - - true - @@ -4162,15 +2633,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x - - - RO:0002219 - uberon - surrounded_by - surrounded_by - surrounded by surrounded by @@ -4182,18 +2645,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. - The epidermis layer of a vertebrate is adjacent to the dermis. - The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. - The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. - x adjacent to y if and only if x and y share a boundary. This relation acts as a join point with BSPO - - RO:0002220 external - uberon adjacent_to @@ -4202,12 +2657,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.adjacent to adjacent to - - - - A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. - - @@ -4215,16 +2664,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of surrounded by - - - RO:0002221 - uberon - surrounds - surrounds - surrounds surrounds @@ -4235,11 +2676,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. - https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to @@ -4253,17 +2689,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of starts with - - Chris Mungall - Allen - RO:0002223 - uberon - starts - starts - starts starts @@ -4275,15 +2702,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor - x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - - Chris Mungall - started by RO:0002224 external - uberon starts_with starts_with @@ -4301,14 +2722,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x develops from part of y if and only if there exists some z such that x develops from z and z is part of y - - RO:0002225 - uberon - develops_from_part_of - develops_from_part_of - develops from part of develops from part of @@ -4323,16 +2737,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x develops_in y if x is located in y whilst x is developing - - EHDAA2 - Jonathan Bard, EHDAA2 - RO:0002226 - uberon - develops_in - develops_in - develops in develops in @@ -4344,16 +2749,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of ends with - - Chris Mungall - RO:0002229 - uberon - ends - ends - ends ends @@ -4365,14 +2762,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - - Chris Mungall - finished by RO:0002230 external - uberon ends_with ends_with @@ -4392,10 +2784,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y - - starts with process that occurs in RO:0002231 external has_start_location @@ -4417,10 +2806,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y - - ends with process that occurs in RO:0002232 external has_end_location @@ -4442,10 +2828,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. - - consumes RO:0002233 external has_input @@ -4470,10 +2853,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. - - produces RO:0002234 external has_output @@ -4495,13 +2875,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1. b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t. - - RO:0002252 - uberon - connecting_branch_of - connecting_branch_of connecting branch of @@ -4513,7 +2887,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of connecting branch of - has connecting branch @@ -4531,15 +2904,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] - x has developmental contribution from y iff x has some part z such that z develops from y - - RO:0002254 - uberon - has_developmental_contribution_from - has_developmental_contribution_from - has developmental contribution from has developmental contribution from @@ -4554,9 +2919,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of has developmental contribution from - developmentally contributes to @@ -4570,21 +2933,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T - - - - induced by - - Developmental Biology, Gilbert, 8th edition, figure 6.5(F) - GO:0001759 - We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm] - RO:0002256 - uberon - developmentally_induced_by - developmentally_induced_by - developmentally induced by developmentally induced by @@ -4595,9 +2944,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Inverse of developmentally induced by - developmentally induces @@ -4610,11 +2957,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false - - In general you should not use this relation to make assertions - use one of the more specific relations below this one This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from developmentally preceded by @@ -4629,7 +2973,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. acts upstream of @@ -4646,7 +2989,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects @@ -4660,16 +3002,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage - - replaces - RO:0002285 - uberon - developmentally_replaces - developmentally_replaces - developmentally replaces developmentally replaces @@ -4679,9 +3013,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Inverse of developmentally preceded by - developmentally succeeded by @@ -4695,9 +3027,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue - - part of developmental precursor of @@ -4707,9 +3036,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process. - expresses @@ -4721,10 +3048,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. - RO:0002295 external results_in_developmental_progression_of @@ -4741,11 +3066,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - every flower development (GO:0009908) results in development of some flower (PO:0009046) - p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. - - http://www.geneontology.org/GO.doc.development.shtml RO:0002296 external results_in_development_of @@ -4765,11 +3086,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. - every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) - - - GOC:mtg_berkeley_2013 RO:0002297 external results_in_formation_of @@ -4778,7 +3094,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. results_in_formation_of results in formation of - results in formation of + results in formation of anatomical entity @@ -4788,12 +3104,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. - tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) - The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. - - GOC:mtg_berkeley_2013 RO:0002298 external results_in_morphogenesis_of @@ -4812,12 +3123,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process - bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) - The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. - - GOC:mtg_berkeley_2013 RO:0002299 external results_in_maturation_of @@ -4837,8 +3143,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. - - RO:0002304 external causally_upstream_of,_positive_effect @@ -4859,7 +3163,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. - RO:0002305 external causally_upstream_of,_negative_effect @@ -4876,32 +3179,15 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of characteristic of part of - - inheres in part of - - characteristic of part of - - - - - - - - true - @@ -4911,10 +3197,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity - - GOC:mtg_berkeley_2013 RO:0002315 external results_in_acquisition_of_features_of @@ -4932,8 +3215,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A relationship that holds via some environmental process - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. evolutionarily related to @@ -4943,9 +3224,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A mereological relationship or a topological relationship - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships - mereotopologically related to @@ -4955,8 +3233,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A relationship that holds between entities participating in some developmental process (GO:0032502) - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development developmentally related to @@ -4975,15 +3251,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - a particular instances of akt-2 enables some instance of protein kinase activity c enables p iff c is capable of p and c acts to execute p. - - catalyzes - executes - has - is catalyzing - is executing - This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. enables https://wiki.geneontology.org/Enables @@ -4995,13 +3263,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. - - This is a grouping relation that collects relations used for the purpose of connecting structure and function - RO:0002328 - uberon - functionally_related_to - functionally_related_to - functionally related to functionally related to @@ -5011,24 +3272,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - this relation holds between c and p when c is part of some c', and c' is capable of p. - - false part of structure that is capable of - - - - - - - - true - @@ -5038,8 +3284,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts. - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism genomically related to @@ -5059,9 +3303,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. c involved_in p if and only if c enables some process p', and p' is part of p - - actively involved in - enables part of involved in https://wiki.geneontology.org/Involved_in @@ -5074,11 +3315,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid p regulates levels of c if p regulates some amount (PATO:0000070) of c - - - regulates levels of (process to entity) RO:0002332 external regulates_levels_of @@ -5095,7 +3332,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of enables - enabled by https://wiki.geneontology.org/Enabled_by @@ -5111,8 +3347,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of regulates - - regulated by (processual) RO:0002334 external regulated_by @@ -5129,7 +3363,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of negatively regulates - RO:0002335 external negatively_regulated_by @@ -5146,7 +3379,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of positively regulates - RO:0002336 external positively_regulated_by @@ -5164,8 +3396,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A relationship that holds via some process of localization - - Do not use this relation directly. It is a grouping relation. related via localization to @@ -5180,7 +3410,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. - RO:0002338 external has_target_start_location @@ -5203,7 +3432,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. - RO:0002339 external has_target_end_location @@ -5222,7 +3450,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l - RO:0002341 external results_in_transport_along @@ -5239,7 +3466,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. - RO:0002342 external results_in_transport_across @@ -5256,8 +3482,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - 'pollen tube growth' results_in growth_of some 'pollen tube' - RO:0002343 external results_in_growth_of @@ -5272,8 +3496,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) - RO:0002344 external results_in_transport_to_from_or_in @@ -5289,12 +3511,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - An organism that is a member of a population of organisms is member of is a mereological relation between a item and a collection. - is member of - member part of - SIO - member of @@ -5306,13 +3523,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. has member is a mereological relation between a collection and an item. - SIO - - RO:0002351 - uberon - has_member - has_member - has member has member @@ -5324,14 +3534,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of has input - - RO:0002352 - uberon - input_of - input_of - input of input of @@ -5343,10 +3547,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of has output - RO:0002353 external - uberon output_of @@ -5361,7 +3563,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - formed as result of @@ -5371,8 +3572,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - http://neurolex.org/wiki/Property:DendriteLocation has dendrite location @@ -5385,14 +3584,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a - - attached to (anatomical structure to anatomical structure) - RO:0002371 - uberon - attaches_to - attaches_to - attached to attached to @@ -5405,13 +3597,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. - - Wikipedia:Insertion_(anatomy) - RO:0002372 - uberon - has_muscle_origin - has_muscle_origin - has muscle origin has muscle origin @@ -5431,13 +3616,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. - - Wikipedia:Insertion_(anatomy) - RO:0002373 - uberon - has_muscle_insertion - has_muscle_insertion - has muscle insertion has muscle insertion @@ -5456,12 +3634,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships - This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) - in branching relationship with https://github.com/obophenotype/uberon/issues/170 @@ -5474,23 +3647,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Deschutes River tributary_of Columbia River - inferior epigastric vein tributary_of external iliac vein - x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. - - drains into - drains to - tributary channel of - http://en.wikipedia.org/wiki/Tributary - http://www.medindia.net/glossary/venous_tributary.htm - This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries) - RO:0002376 - uberon - tributary_of - tributary_of - tributary of tributary of http://en.wikipedia.org/wiki/Tributary @@ -5508,10 +3666,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location - - This relation is added for formal completeness. It is unlikely to be used in many practical scenarios spatially coextensive with @@ -5529,15 +3684,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y - - RO:0002380 - uberon - branching_part_of - branching_part_of - branching part of branching part of FMA:85994 @@ -5551,9 +3699,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). - has developmental potential involving @@ -5563,14 +3709,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y - - RO:0002385 - uberon - has_potential_to_developmentally_contribute_to - has_potential_to_developmentally_contribute_to - has potential to developmentally contribute to has potential to developmentally contribute to @@ -5580,9 +3719,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y - has potential to developmentally induce @@ -5592,14 +3729,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x has the potential to develop into y iff x develops into y or if x is capable of developing into y - - RO:0002387 - uberon - has_potential_to_develop_into - has_potential_to_develop_into - has potential to develop into has potential to develop into @@ -5609,9 +3739,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y - has potential to directly develop into @@ -5623,9 +3751,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of upstream of - RO:0002404 external causally_downstream_of @@ -5642,8 +3768,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - RO:0002405 external immediately_causally_downstream_of @@ -5677,9 +3801,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. - - indirectly activates - indirectly positively regulates https://wiki.geneontology.org/Indirectly_positively_regulates @@ -5705,9 +3826,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. - - indirectly inhibits - indirectly negatively regulates https://wiki.geneontology.org/Indirectly_negatively_regulates @@ -5733,8 +3851,6 @@ For the second, we consider a relationship to be regulatory if the system in whi For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to @@ -5753,7 +3869,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. - RO:0002411 external causally_upstream_of @@ -5772,8 +3887,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. - - RO:0002412 external immediately_causally_upstream_of @@ -5792,8 +3905,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 - - influences (processual) RO:0002418 external affects @@ -5810,8 +3921,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different inverse of causally upstream of or within - - RO:0002427 external causally_downstream_of_or_within @@ -5836,7 +3945,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' regulates some p - involved in regulation of @@ -5855,8 +3963,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' positively regulates some p - - involved in positive regulation of @@ -5875,7 +3981,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' negatively regulates some p - involved in negative regulation of @@ -5890,8 +3995,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union - - involved in or reguates involved in or involved in regulation of @@ -5902,28 +4005,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - - executes activity in enables activity in is active in https://wiki.geneontology.org/Is_active_in - - - - - - - - true - @@ -5939,11 +4026,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. - - RO:0002433 - uberon - contributes_to_morphology_of - contributes_to_morphology_of contributes to morphology of @@ -5958,13 +4040,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different A relationship that holds between two entities in which the processes executed by the two entities are causally connected. This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. Considering relabeling as 'pairwise interacts with' - - Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. in pairwise interaction with interacts with http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ - http://purl.obolibrary.org/obo/MI_0914 @@ -5975,12 +4054,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. - - binds - molecularly binds with molecularly interacts with - http://purl.obolibrary.org/obo/MI_0915 @@ -5990,8 +4065,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different Axiomatization to GO to be added later - - An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. phosphorylates @@ -6012,8 +4085,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. - - molecularly controls directly regulates activity of @@ -6033,9 +4104,6 @@ A and B can be physically interacting but not necessarily. Immediately upstream The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. - - - directly inhibits molecularly decreases activity of directly negatively regulates activity of @@ -6055,9 +4123,6 @@ For example, A and B may be gene products and binding of B by A negatively regul The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. - - - directly activates molecularly increases activity of directly positively regulates activity of @@ -6067,8 +4132,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. helper property (not for use in curation) @@ -6080,16 +4143,8 @@ For example, A and B may be gene products and binding of B by A positively regul - 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. - - - - RO:0002473 - uberon - composed_primarily_of - composed_primarily_of composed primarily of @@ -6100,24 +4155,10 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. - has part that occurs in - - - - - - - - true - @@ -6125,7 +4166,6 @@ For example, A and B may be gene products and binding of B by A positively regul - is kinase activity @@ -6137,7 +4177,6 @@ For example, A and B may be gene products and binding of B by A positively regul See notes for inverse relation - receives input from @@ -6148,7 +4187,6 @@ For example, A and B may be gene products and binding of B by A positively regul This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. - sends output to @@ -6159,8 +4197,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. relation between physical entity and a process or stage @@ -6176,11 +4212,6 @@ For example, A and B may be gene products and binding of B by A positively regul x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). - - RO:0002488 - uberon - existence_starts_during - existence_starts_during existence starts during @@ -6191,11 +4222,6 @@ For example, A and B may be gene products and binding of B by A positively regul x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). - - RO:0002489 - uberon - existence_starts_with - existence_starts_with existence starts with @@ -6206,7 +4232,6 @@ For example, A and B may be gene products and binding of B by A positively regul x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence overlaps @@ -6219,12 +4244,7 @@ For example, A and B may be gene products and binding of B by A positively regul x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) - - RO:0002491 exists during - uberon - existence_starts_and_ends_during - existence_starts_and_ends_during The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts and ends during @@ -6240,23 +4260,10 @@ For example, A and B may be gene products and binding of B by A positively regul - Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). - - RO:0002492 - ceases_to_exist_during - uberon - existence_ends_during - existence_ends_during The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during - - - - Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. - https://orcid.org/0000-0002-6601-2165 - @@ -6265,11 +4272,6 @@ For example, A and B may be gene products and binding of B by A positively regul x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). - - RO:0002493 - uberon - existence_ends_with - existence_ends_with The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends with @@ -6282,11 +4284,6 @@ For example, A and B may be gene products and binding of B by A positively regul x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships - - RO:0002494 - uberon - transformation_of - transformation_of transformation of @@ -6298,12 +4295,6 @@ For example, A and B may be gene products and binding of B by A positively regul x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t - - - RO:0002495 - uberon - immediate_transformation_of - immediate_transformation_of immediate transformation of @@ -6334,11 +4325,6 @@ For example, A and B may be gene products and binding of B by A positively regul x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). - - RO:0002496 - uberon - existence_starts_during_or_after - existence_starts_during_or_after The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts during or after @@ -6370,11 +4356,6 @@ For example, A and B may be gene products and binding of B by A positively regul x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. - - RO:0002497 - uberon - existence_ends_during_or_before - existence_ends_during_or_before The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during or before @@ -6387,7 +4368,6 @@ For example, A and B may be gene products and binding of B by A positively regul A relationship between a material entity and a process where the material entity has some causal role that influences the process - causal agent in process @@ -6400,9 +4380,6 @@ For example, A and B may be gene products and binding of B by A positively regul p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. - - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes @@ -6411,7 +4388,6 @@ For example, A and B may be gene products and binding of B by A positively regul - depends on @@ -6425,9 +4401,6 @@ For example, A and B may be gene products and binding of B by A positively regul The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch - - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between entities @@ -6441,18 +4414,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - - Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. - - has supporting framework - The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). - RO:0002551 - uberon - has_skeleton - has_skeleton has skeleton @@ -6469,9 +4432,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - causally influenced by (entity-centric) causally influenced by @@ -6481,7 +4441,6 @@ For example, A and B may be gene products and binding of B by A positively regul - interaction relation helper property http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ @@ -6493,7 +4452,6 @@ For example, A and B may be gene products and binding of B by A positively regul - molecular interaction relation helper property @@ -6504,8 +4462,6 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - - RO:0002565 external results_in_movement_of @@ -6535,10 +4491,6 @@ For example, A and B may be gene products and binding of B by A positively regul The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). - - - - causally influences (entity-centric) causally influences @@ -6551,8 +4503,6 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between elements of a musculoskeletal system or its analogs. - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. biomechanically related to @@ -6563,12 +4513,6 @@ For example, A and B may be gene products and binding of B by A positively regul m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. - - Wikipedia:Antagonist_(muscle) - RO:0002568 - uberon - has_muscle_antagonist - has_muscle_antagonist has muscle antagonist @@ -6581,13 +4525,8 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of branching part of - - RO:0002569 - uberon - has_branching_part - has_branching_part has branching part @@ -6600,14 +4539,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. - - UBERON:cjm - This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. - RO:0002570 - uberon - conduit_for - conduit_for conduit for @@ -6619,13 +4551,7 @@ For example, A and B may be gene products and binding of B by A positively regul x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - - - RO:0002571 - uberon - lumen_of - lumen_of lumen of @@ -6637,12 +4563,7 @@ For example, A and B may be gene products and binding of B by A positively regul s is luminal space of x iff s is lumen_of x and s is an immaterial entity - - RO:0002572 - uberon - luminal_space_of - luminal_space_of luminal space of @@ -6655,12 +4576,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has skeleton - - RO:0002576 - uberon - skeleton_of - skeleton_of skeleton of @@ -6672,10 +4588,6 @@ For example, A and B may be gene products and binding of B by A positively regul p directly regulates q iff p is immediately causally upstream of q and p regulates q. - - - directly regulates (processual) - RO:0002578 external directly_regulates @@ -6697,9 +4609,7 @@ For example, A and B may be gene products and binding of B by A positively regul - gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p - has part structure that is capable of @@ -6769,8 +4679,6 @@ For example, A and B may be gene products and binding of B by A positively regul A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - - causal relation between material entity and a process @@ -6784,9 +4692,7 @@ For example, A and B may be gene products and binding of B by A positively regul - pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. - capable of regulating @@ -6801,7 +4707,6 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. - capable of negatively regulating @@ -6815,9 +4720,7 @@ For example, A and B may be gene products and binding of B by A positively regul - renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. - capable of positively regulating @@ -6828,7 +4731,6 @@ For example, A and B may be gene products and binding of B by A positively regul Inverse of 'causal agent in process' - RO:0002608 external process_has_causal_agent @@ -6844,9 +4746,6 @@ For example, A and B may be gene products and binding of B by A positively regul p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. - - directly positively regulates (process to process) - RO:0002629 external directly_positively_regulates @@ -6866,8 +4765,6 @@ For example, A and B may be gene products and binding of B by A positively regul p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. - - directly negatively regulates (process to process) RO:0002630 external @@ -6894,12 +4791,9 @@ For example, A and B may be gene products and binding of B by A positively regul - a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. - RO:0003000 external - uberon produces produces @@ -6915,12 +4809,9 @@ For example, A and B may be gene products and binding of B by A positively regul - a produced_by b iff some process that occurs_in b has_output a. - RO:0003001 external - uberon produced_by produced_by @@ -7027,7 +4918,6 @@ For example, A and B may be gene products and binding of B by A positively regul - 2018-01-26T23:49:30Z @@ -7065,7 +4955,6 @@ For example, A and B may be gene products and binding of B by A positively regul c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive - 2018-01-26T23:53:14Z @@ -7112,7 +5001,6 @@ For example, A and B may be gene products and binding of B by A positively regul - 2018-03-13T23:55:19Z causally upstream of or within, positive effect @@ -7128,7 +5016,6 @@ For example, A and B may be gene products and binding of B by A positively regul The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. - regulates activity of @@ -7375,7 +5262,6 @@ For example, A and B may be gene products and binding of B by A positively regul - 'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)') A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. @@ -7395,7 +5281,6 @@ For example, A and B may be gene products and binding of B by A positively regul - 'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor') A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. @@ -7417,12 +5302,7 @@ For example, A and B may be gene products and binding of B by A positively regul - A diagnostic testing device utilizes a specimen. X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. - - - A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. - See github ticket https://github.com/oborel/obo-relations/issues/497 2021-11-08T12:00:00Z utilizes device utilizes material @@ -7548,7 +5428,6 @@ For example, A and B may be gene products and binding of B by A positively regul - x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y. @@ -7568,8 +5447,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - carries uberon channel_for @@ -7581,7 +5458,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uberon channels_from channels_from @@ -7592,7 +5468,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uberon channels_into channels_into @@ -7603,10 +5478,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y. uberon distally_connected_to @@ -7625,11 +5498,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y uberon extends_fibers_into @@ -7659,11 +5527,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - @@ -7691,7 +5554,6 @@ For example, A and B may be gene products and binding of B by A positively regul - x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y. uberon @@ -7720,7 +5582,6 @@ For example, A and B may be gene products and binding of B by A positively regul - x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y. @@ -7774,7 +5635,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uberon transitively_anteriorly_connected_to transitively anteriorly connected to @@ -7786,7 +5646,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uberon transitively_distally_connected_to transitively distally connected to @@ -7798,7 +5657,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uberon transitively_proximally_connected_to transitively proximally connected to @@ -11949,6 +9807,12 @@ For example, A and B may be gene products and binding of B by A positively regul reticulocyte + + + + + true + @@ -11958,12 +9822,6 @@ For example, A and B may be gene products and binding of B by A positively regul PMID:15946868 PMID:2037622 - - - - - true - @@ -20042,32 +17900,32 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer - + - + - + PMID:12382326 - + PMID:12382326 @@ -32168,7 +30026,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 PMID:15371245 ncbi_taxonomy @@ -32182,7 +30039,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 Mus mice @@ -32201,7 +30057,7 @@ For example, A and B may be gene products and binding of B by A positively regul mice - + @@ -32216,7 +30072,6 @@ For example, A and B may be gene products and binding of B by A positively regul - NCBITaxon:85055 GC_ID:1 house mouse @@ -32244,7 +30099,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 ncbi_taxonomy NCBITaxon:117570 @@ -32257,7 +30111,6 @@ For example, A and B may be gene products and binding of B by A positively regul - NCBITaxon:40673 GC_ID:1 bony vertebrates @@ -32297,7 +30150,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 ncbi_taxonomy NCBITaxon:1338369 @@ -32310,7 +30162,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 PMID:11743200 PMID:11791233 @@ -32332,7 +30183,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 mice and others ncbi_taxonomy @@ -32359,7 +30209,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 PMID:23020233 PMID:30257078 @@ -32423,7 +30272,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 PMID:11214319 PMID:12082125 @@ -32440,7 +30288,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 PMID:11214319 PMID:12082125 @@ -32463,7 +30310,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 tetrapods ncbi_taxonomy @@ -32483,7 +30329,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 amniotes ncbi_taxonomy @@ -32503,7 +30348,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 Theria ncbi_taxonomy @@ -32523,7 +30367,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 ncbi_taxonomy Fungi/Metazoa group @@ -32550,7 +30393,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 metazoans multicellular animals @@ -32591,7 +30433,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 ncbi_taxonomy NCBITaxon:33213 @@ -32604,7 +30445,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 deuterostomes ncbi_taxonomy @@ -32624,7 +30464,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 PMID:15019624 PMID:15371245 @@ -32639,7 +30478,6 @@ For example, A and B may be gene products and binding of B by A positively regul - NCBITaxon:109679 GC_ID:1 ncbi_taxonomy @@ -32653,7 +30491,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 mammals ncbi_taxonomy @@ -32680,7 +30517,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 ncbi_taxonomy NCBITaxon:6072 @@ -32693,7 +30529,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 chordates ncbi_taxonomy @@ -32720,7 +30555,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 Vertebrata vertebrates @@ -32754,7 +30588,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 Gnathostomata jawed vertebrates @@ -32781,7 +30614,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 ncbi_taxonomy NCBITaxon:8287 @@ -32794,7 +30626,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 Mus ncbi_taxonomy @@ -32814,7 +30645,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 Craniata ncbi_taxonomy @@ -32834,7 +30664,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 eutherian mammals placental mammals @@ -32882,7 +30711,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 rodent ncbi_taxonomy @@ -33017,7 +30845,6 @@ For example, A and B may be gene products and binding of B by A positively regul A branchiness quality inhering in a bearer by virtue of the bearer's having branches. - ramified ramiform quality @@ -33345,7 +31172,6 @@ For example, A and B may be gene products and binding of B by A positively regul A quality inhering in a bearer by virtue of the bearer's lacking complete growth, differentiation, or development. - quality underdeveloped PATO:0001501 @@ -33407,7 +31233,6 @@ For example, A and B may be gene products and binding of B by A positively regul A contractility quality inhering in a bearer by virtue of the bearer's ability of contracting or being contracted. - quality PATO:0001690 @@ -33429,7 +31254,6 @@ For example, A and B may be gene products and binding of B by A positively regul A shape quality in a bearer by virtue of the bearer's curving inward. - quality PATO:0001857 @@ -33625,7 +31449,6 @@ For example, A and B may be gene products and binding of B by A positively regul A complete three dimensional shape in which for every line connecting pair of points on the object is within the object. Or: a shape lacking cavities. Contrast: concave. - Image:http://upload.wikimedia.org/wikipedia/commons/0/06/Convex_polygon_illustration1.png quality PATO:0002007 @@ -33686,7 +31509,6 @@ For example, A and B may be gene products and binding of B by A positively regul A concave quality inhering in a bearer by virtue of the bearer's curving inward on both sides or surfaces. - quality PATO:0002039 @@ -34193,7 +32015,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001006 Category=gene. Requested by=CL. receptor-type tyrosine-protein phosphatase C - @@ -34243,7 +32064,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001012 Category=gene. Requested by=CL. integrin alpha-M - @@ -34290,7 +32110,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001013 Category=gene. Requested by=CL. integrin alpha-X - @@ -34428,7 +32247,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001024 Category=gene. Requested by=CL. neural cell adhesion molecule 1 - @@ -34513,7 +32331,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001084 Category=gene. Requested by=CL. T-cell surface glycoprotein CD8 alpha chain - @@ -34664,7 +32481,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001254 Category=gene. Requested by=CL. C-C chemokine receptor type 1 - @@ -34722,7 +32538,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001255 Category=gene. Requested by=CL. C-C chemokine receptor type 3 - @@ -34936,7 +32751,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001332 Category=gene. Requested by=CL. carcinoembryonic antigen-related cell adhesion molecule 8 - @@ -35023,7 +32837,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001344 Category=gene. Requested by=CL. ectonucleotide pyrophosphatase/phosphodiesterase family member 3 - @@ -35109,7 +32922,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001408 Category=gene. Requested by=CL. ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 - @@ -35141,7 +32953,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001444 Category=gene. Requested by=CL. cadherin-5 - @@ -35263,7 +33074,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001839 Category=gene. Requested by=CL. T-cell surface glycoprotein CD5 - @@ -35303,7 +33113,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001850 Category=gene. Requested by=CL. cathepsin K - @@ -35421,7 +33230,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001867 Category=gene. Requested by=CL. interleukin-5 receptor subunit alpha - @@ -35463,7 +33271,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001869 Category=gene. Requested by=CL. interleukin-7 receptor subunit alpha - @@ -35520,7 +33327,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001879 Category=gene. Requested by=CL. leukosialin - @@ -35597,7 +33403,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001898 Category=gene. Requested by=CL. neprilysin - @@ -35634,7 +33439,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001903 Category=gene. Requested by=CL. paired box protein PAX-5 - @@ -35677,7 +33481,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001932 Category=gene. The mouse ortholog is Cd24a. Mouse protein Cd24b likely also orthologous. Currently it is not in UniProt. Requested by=CL. signal transducer CD24 - @@ -35716,7 +33519,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001935 Category=gene. Requested by=CL. syndecan-1 - @@ -35763,7 +33565,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001937 Category=gene. Requested by=CL. tartrate-resistant acid phosphatase type 5 - @@ -35807,7 +33608,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001944 Category=gene. Requested by=CL. transcription factor PU.1 - @@ -35854,7 +33654,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001945 Category=gene. Requested by=CL. transferrin receptor protein 1 - @@ -35955,7 +33754,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001954 Category=gene. Requested by=CL. tumor necrosis factor receptor superfamily member 11A - @@ -36036,7 +33834,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001969 Category=gene. Requested by=CL. urokinase plasminogen activator surface receptor - @@ -36106,7 +33903,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000002062 Category=gene. Requested by=CL. macrophage colony-stimulating factor 1 receptor - @@ -36202,7 +33998,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000002112 Category=gene. Requested by=CL. vascular endothelial growth factor receptor 2 - @@ -36398,7 +34193,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000003457 Category=gene. Requested by=CL. V(D)J recombination-activating protein 1 - @@ -36433,7 +34227,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000003460 Category=gene. Requested by=CL. V(D)J recombination-activating protein 2 - @@ -36526,7 +34319,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000005307 Category=gene. Requested by=CL. CCAAT/enhancer-binding protein alpha - @@ -36596,7 +34388,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000006611 Category=gene. Requested by=CL. DNA nucleotidylexotransferase - @@ -36635,7 +34426,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000007431 Category=gene. Requested by=CL. high affinity immunoglobulin epsilon receptor subunit alpha - @@ -36674,7 +34464,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000007597 Category=gene. Requested by=CL. protein c-Fos - @@ -36715,7 +34504,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000007857 Category=gene. Requested by=CL. erythroid transcription factor - @@ -36756,7 +34544,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000007858 Category=gene. Requested by=CL. endothelial transcription factor GATA-2 - @@ -36788,7 +34575,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000009143 Category=gene. Requested by=CL. integrin beta-7 - @@ -36823,7 +34609,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000011178 Category=gene. Requested by=CL. nuclear factor NF-kappa-B p100 subunit - @@ -36861,7 +34646,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000014841 Category=gene. sonic hedgehog protein - @@ -36903,7 +34687,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000016043 Category=gene. Requested by=CL. T-cell acute lymphocytic leukemia protein 1 - @@ -36955,7 +34738,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000016401 Category=gene. Requested by=CL. transmembrane emp24 domain-containing protein 1 - @@ -37306,8 +35088,6 @@ For example, A and B may be gene products and binding of B by A positively regul Any hollow cylindrical anatomical structure containing a lumen through which substances are transported. - not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts) - tubular galen:Tube anatomical tube duct @@ -37369,10 +35149,8 @@ For example, A and B may be gene products and binding of B by A positively regul Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. - in FMA, serosa is a wall UBERON:0009915 wall - EMAPA:25036 FMA:82482 galen:Wall wall of organ @@ -37388,12 +35166,6 @@ For example, A and B may be gene products and binding of B by A positively regul Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. FMA:82482 - - - - in FMA, serosa is a wall - FMA - @@ -37429,7 +35201,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0000003 EHDAA2:0003003 EMAPA:0 - FBbt:00007001 FMA:305751 FMA:67135 GAID:781 @@ -37457,12 +35228,6 @@ For example, A and B may be gene products and binding of B by A positively regul Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. CARO:0000003 - - - - FBbt:00007001 - - @@ -37500,8 +35265,6 @@ For example, A and B may be gene products and binding of B by A positively regul - Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. - CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4 BIRNLEX:4 CARO:0020004 EFO:0000634 @@ -37535,12 +35298,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia - - - - Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. - GO:0048513 - @@ -37567,7 +35324,6 @@ For example, A and B may be gene products and binding of B by A positively regul A multicellular structure that is a part of an organ. - currently defined in a very broad sense, may be replaced by more specific classes in the future @@ -37724,7 +35480,6 @@ For example, A and B may be gene products and binding of B by A positively regul - ncit:Death is an outcome XAO:0000437 XtroDO:0000085 uberon @@ -37739,12 +35494,6 @@ For example, A and B may be gene products and binding of B by A positively regul End of the life of an organism. XAO:0000437 - - - - ncit:Death is an outcome - ncit - @@ -37830,7 +35579,6 @@ For example, A and B may be gene products and binding of B by A positively regul Stage succeeding embryo, including mature structure. - In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997) BilaDO:0000003 OGES:000010 OGES:000014 @@ -37916,8 +35664,6 @@ For example, A and B may be gene products and binding of B by A positively regul - the WBls class 'all stages' belongs here as it is the superclass of other WBls stages - we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage BILS:0000105 EFO:0000399 FBdv:00007012 @@ -37968,13 +35714,11 @@ For example, A and B may be gene products and binding of B by A positively regul A stage at which the organism is a single cell produced by means of sexual reproduction. - As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG] BILS:0000106 BilaDO:0000005 EFO:0001322 EHDAA:27 FBdv:00005288 - IDOMAL:0000302 NCIT:C12601 PdumDv:0000100 VHOG:0000745 @@ -38000,24 +35744,6 @@ For example, A and B may be gene products and binding of B by A positively regul A stage at which the organism is a single cell produced by means of sexual reproduction. Wikipedia:Zygote - - - - As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG] - 2012-09-17 - VHOG:0000745 - VHOG - ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107 - http://bgee.unil.ch/ - - - - - IDOMAL:0000302 - - - https://github.com/biopragmatics/biomappings - @@ -38165,7 +35891,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -38201,14 +35927,14 @@ For example, A and B may be gene products and binding of B by A positively regul gastrula stage - + - + BILS @@ -38286,8 +36012,6 @@ For example, A and B may be gene products and binding of B by A positively regul Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system. - - In zebrafish, the times of neurulation and segmentation overlap so extensively there is no distinct neurula period of development, such as occurs largely before segmentation in amphibian embryos. BILS:0000110 BilaDO:0000009 HsapDv:0000012 @@ -38358,24 +36082,7 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - @@ -38389,11 +36096,6 @@ For example, A and B may be gene products and binding of B by A positively regul The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks). - Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO] - Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG] - oral - some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives - in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips AAO:0010355 BTO:0001090 BTO:0004698 @@ -38402,7 +36104,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA2:0001326 EHDAA:542 EMAPA:16262 - FBbt:00003126 FMA:49184 GAID:75 MA:0000341 @@ -38448,12 +36149,6 @@ For example, A and B may be gene products and binding of B by A positively regul https://github.com/obophenotype/uberon/issues/661 http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg - - - - - the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts - @@ -38461,37 +36156,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Mouth https://github.com/obophenotype/uberon/wiki/The-digestive-tract - - - - Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO] - 2012-06-20 - AAO:0010355 - AAO - AAO:BJB - - - - - Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG] - 2012-09-17 - VHOG:0000812 - VHOG - DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008) - http://bgee.unil.ch/ - - - - - in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips - FMA - - - - - FBbt:00003126 - - @@ -38582,22 +36246,17 @@ For example, A and B may be gene products and binding of B by A positively regul - + - - + + A fluid that is composed of blood plasma and erythrocytes. - This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid. - A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO] - Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO] - relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] - Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG] AAO:0000046 BTO:0000089 CALOHA:TS-0079 @@ -38632,34 +36291,34 @@ For example, A and B may be gene products and binding of B by A positively regul blood - + - + - + - + CL:tm - + https://github.com/obophenotype/uberon/issues/1330 - + Bgee:AN @@ -38671,42 +36330,6 @@ For example, A and B may be gene products and binding of B by A positively regul http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/9 - - - - A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO] - 2012-08-14 - TAO:0000007 - TAO - ZFIN:curator - - - - - Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO] - 2012-06-20 - AAO:0000046 - AAO - AAO:LAP - - - - - relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] - 2012-06-20 - AAO:0000046 - AAO - - - - - Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG] - 2012-09-17 - VHOG:0000224 - VHOG - DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006) - http://bgee.unil.ch/ - @@ -38870,14 +36493,11 @@ For example, A and B may be gene products and binding of B by A positively regul consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77 - Anatomical system that consists of the muscles of the body.[VSAO] - we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA AAO:0000307 BILA:0000088 BTO:0001369 BTO:0001485 EFO:0000801 - EMAPA:35578 FMA:72954 MA:0002888 MAT:0000025 @@ -38905,21 +36525,6 @@ For example, A and B may be gene products and binding of B by A positively regul The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified]. VSAO:0000033 - - - - Anatomical system that consists of the muscles of the body.[VSAO] - 2012-08-14 - VSAO:0000033 - VSAO - VSAO:curator - - - - - we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA - MA - @@ -38963,7 +36568,12 @@ For example, A and B may be gene products and binding of B by A positively regul - + + + + + + @@ -38981,7 +36591,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0000004 EHDAA2:0003004 EMAPA:35178 - FBbt:00007019 FMA:9669 HAO:0000004 MA:0002450 @@ -39005,28 +36614,12 @@ For example, A and B may be gene products and binding of B by A positively regul organism substance - - - - - - - - - this relationship may be too strong and may be weakened in future - Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007019 - - @@ -39081,7 +36674,6 @@ For example, A and B may be gene products and binding of B by A positively regul BILA:0000005 CARO:0000005 EHDAA2:0003005 - FBbt:00007017 FMA:5897 HAO:0000005 NCIT:C94478 @@ -39105,12 +36697,6 @@ For example, A and B may be gene products and binding of B by A positively regul Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures. http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007017 - - @@ -39142,7 +36728,6 @@ For example, A and B may be gene products and binding of B by A positively regul BILA:0000006 CARO:0000006 EHDAA2:0003006 - FBbt:00007016 FMA:67165 HAO:0000006 TAO:0001836 @@ -39160,12 +36745,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical entity that has mass. http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007016 - - @@ -39183,7 +36762,6 @@ For example, A and B may be gene products and binding of B by A positively regul BILA:0000007 CARO:0000007 EHDAA2:0003007 - FBbt:00007015 FMA:67112 HAO:0000007 TAO:0001835 @@ -39202,12 +36780,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical entity that has no mass. http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007015 - - @@ -39250,10 +36822,8 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA:392 EMAPA:16103 EV:0100000 - FBbt:00004856 FMA:7149 HAO:0000011 - IDOMAL:0002460 MA:0000003 NCIT:C12919 SCTID:278195005 @@ -39293,20 +36863,6 @@ For example, A and B may be gene products and binding of B by A positively regul system GO:0048731 - - - - FBbt:00004856 - - - - - - IDOMAL:0002460 - - - https://github.com/biopragmatics/biomappings - @@ -39344,7 +36900,6 @@ For example, A and B may be gene products and binding of B by A positively regul - organismal organism AAO:0010026 AEO:0000191 @@ -39359,7 +36914,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA:1 EMAPA:25765 EV:0100016 - FBbt:00000001 FMA:256135 HAO:0000012 NCIT:C13041 @@ -39404,12 +36958,6 @@ For example, A and B may be gene products and binding of B by A positively regul VHOG:0000671 WBbt:0007833 - - - - FBbt:00000001 - - @@ -39470,7 +37018,6 @@ For example, A and B may be gene products and binding of B by A positively regul EFO:0000808 EHDAA2:0003032 EMAPA:36031 - FBbt:00007009 FMA:7153 HAO:0000032 MA:0002433 @@ -39513,12 +37060,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:DOS http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007009 - - @@ -39560,7 +37101,6 @@ For example, A and B may be gene products and binding of B by A positively regul BILA:0000040 CARO:0000040 EHDAA2:0003040 - FBbt:00007013 FMA:63863 HAO:0000040 TAO:0000382 @@ -39586,12 +37126,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue. http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007013 - - @@ -39610,7 +37144,6 @@ For example, A and B may be gene products and binding of B by A positively regul - FBbt:00007277 VHOG:0001737 uberon UBERON:0000477 @@ -39624,12 +37157,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical group whose component anatomical structures lie in close proximity to each other. FBbt:00007277 - - - - FBbt:00007277 - - @@ -39663,7 +37190,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0000043 EHDAA2:0003043 EMAPA:35868 - FBbt:00007003 FMA:9637 HAO:0000043 MA:0003002 @@ -39699,12 +37225,6 @@ For example, A and B may be gene products and binding of B by A positively regul Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. CARO:0000043 - - - - FBbt:00007003 - - @@ -39745,7 +37265,6 @@ For example, A and B may be gene products and binding of B by A positively regul BILA:0000055 CARO:0000055 EHDAA2:0003055 - FBbt:00007010 HAO:0000055 TAO:0001488 TGMA:0001847 @@ -39772,12 +37291,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0000055 http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007010 - - @@ -39816,7 +37329,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -39824,8 +37337,6 @@ For example, A and B may be gene products and binding of B by A positively regul Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]. - The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG] - epithelial AAO:0000144 AAO:0010055 AEO:0000066 @@ -39835,7 +37346,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0000066 EHDAA2:0003066 EMAPA:32738 - FBbt:00007005 FMA:9639 GAID:402 HAO:0000066 @@ -39860,14 +37370,14 @@ For example, A and B may be gene products and binding of B by A positively regul epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg - + - + http://palaeos.com/metazoa/porifera/homoscleromorpha.html @@ -39877,22 +37387,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Epithelium http://orcid.org/0000-0001-9114-8737 - - - - The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG] - 2012-09-17 - VHOG:0000387 - VHOG - ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.59 - http://bgee.unil.ch/ - - - - - FBbt:00007005 - - @@ -39925,7 +37419,6 @@ For example, A and B may be gene products and binding of B by A positively regul Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA]. - Unilaminar epithelium that consists of a single layer of squamous cells.[CARO] AAO:0010066 AEO:0000070 BILA:0000070 @@ -39957,16 +37450,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Simple_squamous_epithelium http://orcid.org/0000-0001-9114-8737 - - - - Unilaminar epithelium that consists of a single layer of squamous cells.[CARO] - 2012-06-20 - CARO:0000070 - CARO - FMA:45565 - http://orcid.org/0000-0001-9114-8737 - @@ -39989,7 +37472,6 @@ For example, A and B may be gene products and binding of B by A positively regul Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA]. consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable - Epithelium that consists of a single layer of epithelial cells.[CARO] AAO:0010062 AEO:0000073 BILA:0000073 @@ -40018,16 +37500,6 @@ For example, A and B may be gene products and binding of B by A positively regul FMA:45561 http://orcid.org/0000-0001-9114-8737 - - - - Epithelium that consists of a single layer of epithelial cells.[CARO] - 2012-06-20 - CARO:0000073 - CARO - FMA:45561 - http://orcid.org/0000-0001-9114-8737 - @@ -40073,10 +37545,6 @@ For example, A and B may be gene products and binding of B by A positively regul Subdivision of trunk that lies between the head and the abdomen. - note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest - - - EMAPA:35862 FMA:259209 MA:0000022 @@ -40150,8 +37618,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. - embryonic - Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo AAO:0011035 AEO:0000169 BILA:0000056 @@ -40163,10 +37629,8 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA2_RETIRED:0003236 EHDAA:38 EMAPA:16039 - FBbt:00000052 FMA:69068 GAID:963 - IDOMAL:0000646 MAT:0000226 MESH:D004622 MIAA:0000019 @@ -40202,26 +37666,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0009790 Wikipedia:Embryo - - - - Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo - ZFA - - - - - FBbt:00000052 - - - - - - IDOMAL:0000646 - - - https://github.com/biopragmatics/biomappings - @@ -40254,13 +37698,11 @@ For example, A and B may be gene products and binding of B by A positively regul A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm. - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] embryonic tissue AAO:0000480 BILA:0000035 BTO:0000556 EMAPA:36033 - FBbt:00000110 FMA:69069 GAID:1303 MESH:D005855 @@ -40291,28 +37733,12 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Germ_layer https://github.com/obophenotype/uberon/issues/203 - - - - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - 2012-09-17 - VHOG:0001223 - VHOG - ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 - http://bgee.unil.ch/ - embryonic tissue FMA:69069 - - - - FBbt:00000110 - - @@ -40351,11 +37777,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. - Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO] - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - ectodermal AAO:0000137 BILA:0000036 BTO:0000315 @@ -40364,7 +37787,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA2:0000428 EMAPA:16069 EV:0100003 - FBbt:00000111 FMA:69070 GAID:1304 MAT:0000155 @@ -40389,14 +37811,14 @@ For example, A and B may be gene products and binding of B by A positively regul ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -40405,31 +37827,6 @@ For example, A and B may be gene products and binding of B by A positively regul Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. Wikipedia:Ectoderm - - - - Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO] - 2012-06-20 - AAO:0000137 - AAO - AAO:EJS - - - - - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - 2012-09-17 - VHOG:0000153 - VHOG - ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 - http://bgee.unil.ch/ - - - - - FBbt:00000111 - - @@ -40455,10 +37852,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - endodermal AAO:0000139 BILA:0000038 BTO:0000800 @@ -40467,7 +37862,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA2:0000436 EMAPA:16062 EV:0100005 - FBbt:00000125 FMA:69071 GAID:1305 MAT:0000175 @@ -40492,14 +37886,14 @@ For example, A and B may be gene products and binding of B by A positively regul http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -40508,22 +37902,6 @@ For example, A and B may be gene products and binding of B by A positively regul Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. Wikipedia:Endoderm - - - - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - 2012-09-17 - VHOG:0000154 - VHOG - ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 - http://bgee.unil.ch/ - - - - - FBbt:00000125 - - @@ -40550,13 +37928,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + The middle germ layer of the embryo, between the endoderm and ectoderm. - Primary germ layer that is the middle of the embryonic germ layers.[AAO] - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - mesodermal - sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates UBERON:0003263 AAO:0000304 BILA:0000037 @@ -40569,7 +37943,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA:183 EMAPA:16083 EV:0100006 - FBbt:00000126 FMA:69072 GAID:522 MAT:0000174 @@ -40595,20 +37968,14 @@ For example, A and B may be gene products and binding of B by A positively regul mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + - - sometimes not considered primary - - - - - + Bgee:AN @@ -40617,37 +37984,6 @@ For example, A and B may be gene products and binding of B by A positively regul The middle germ layer of the embryo, between the endoderm and ectoderm. Wikipedia:Mesoderm - - - - Primary germ layer that is the middle of the embryonic germ layers.[AAO] - 2012-06-20 - AAO:0000304 - AAO - AAO:EJS - - - - - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - 2012-09-17 - VHOG:0000152 - VHOG - ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 - http://bgee.unil.ch/ - - - - - sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates - https://github.com/obophenotype/uberon/wiki/The-neural-crest - - - - - FBbt:00000126 - - @@ -40694,15 +38030,10 @@ For example, A and B may be gene products and binding of B by A positively regul Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity. consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence - Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO] - the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx - stomodeal - This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity. stomodeal-hypophyseal primordium BTO:0004224 EHDAA2:0001929 EMAPA:16263 - FBbt:00000439 FMA:295846 NCIT:C34306 TAO:0001290 @@ -40735,34 +38066,12 @@ For example, A and B may be gene products and binding of B by A positively regul http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/326 - - - - Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO] - 2012-08-14 - TAO:0001290 - TAO - ZFIN:curator - - - - - the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx - MP:0012522 - NCBITaxon:40674 - stomodeal-hypophyseal primordium XAO:0000269 - - - - FBbt:00000439 - - @@ -40827,7 +38136,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -40856,11 +38165,6 @@ For example, A and B may be gene products and binding of B by A positively regul - Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO] - Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO] - relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO] - As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG] - cardiac AAO:0010210 BILA:0000020 BTO:0000562 @@ -40904,14 +38208,14 @@ For example, A and B may be gene products and binding of B by A positively regul https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb - + - + MA @@ -40921,42 +38225,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Heart http://orcid.org/0000-0002-6601-2165 - - - - Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO] - 2012-08-14 - TAO:0000114 - TAO - ZFIN:curator - - - - - Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO] - 2012-06-20 - AAO:0010210 - AAO - AAO:BJB - - - - - relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO] - 2012-06-20 - AAO:0010210 - AAO - - - - - As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG] - 2012-09-17 - VHOG:0000276 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481 - http://bgee.unil.ch/ - @@ -41002,8 +38270,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical structure that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO]. - Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO] - Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO] articulation joint AEO:0000182 @@ -41048,24 +38314,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Joint http://dx.plos.org/10.1371/journal.pone.0051070 - - - - Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO] - 2012-08-14 - VSAO:0000101 - VSAO - PSPUB:0000170 - - - - - Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO] - 2012-08-14 - TAO:0000367 - TAO - TAO:pem - @@ -41136,16 +38384,11 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes. - An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO] - digestive - many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class AAO:0000129 BILA:0000082 BTO:0000058 CALOHA:TS-1293 EFO:0000793 - EV:0100056 - FBbt:00005055 FMA:7152 GAID:278 MA:0002431 @@ -41182,27 +38425,6 @@ For example, A and B may be gene products and binding of B by A positively regul NLM:alimentary+system Wikipedia:Digestive_system - - - - An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO] - 2012-06-20 - AAO:0000129 - AAO - AAO:BJB - - - - - many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class - MA - - - - - FBbt:00005055 - - @@ -41234,17 +38456,12 @@ For example, A and B may be gene products and binding of B by A positively regul Organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP]. - the cardiovascular system and the lymphatic system are parts of the circulatory system - - Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO] - We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG] AAO:0000959 CALOHA:TS-2103 - MESH:D002319 VHOG:0001248 Wikipedia:Circulatory_system uberon @@ -41267,38 +38484,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Acoelomorpha - - - - - WBbt coelomocyte currently classified as circulating cell - - - - - Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO] - 2012-06-20 - AAO:0000959 - AAO - AAO:BJB - - - - - We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG] - 2012-09-17 - VHOG:0001248 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.493 - http://bgee.unil.ch/ - - - - - MESH:D002319 - - https://github.com/biopragmatics/biomappings - @@ -41326,12 +38511,8 @@ For example, A and B may be gene products and binding of B by A positively regul A subdivision of the muscular system corresponding to a subdisivision of an organism. - - In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here. - AAO:0011066 BTO:0000887 EFO:0001949 - EMAPA:32715 EMAPA:35577 FMA:32558 MA:0000165 @@ -41367,12 +38548,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Muscular_system https://orcid.org/0000-0002-6601-2165 - - - - In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here. - FMA - @@ -41436,7 +38611,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -41444,11 +38619,6 @@ For example, A and B may be gene products and binding of B by A positively regul The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]. - A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO] - Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO] - Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG] - nervous - neural AAO:0000324 BILA:0000079 BIRNLEX:844 @@ -41459,7 +38629,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA:826 EMAPA:16469 EV:0100162 - FBbt:00005093 FMA:7157 GAID:466 MA:0000016 @@ -41491,14 +38660,14 @@ For example, A and B may be gene products and binding of B by A positively regul http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -41513,40 +38682,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Nervous_system ZFIN:curator - - - - A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO] - 2012-08-14 - TAO:0000396 - TAO - ZFIN:curator - - - - - Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO] - 2012-06-20 - AAO:0000324 - AAO - AAO:BJB - - - - - Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG] - 2012-09-17 - VHOG:0000402 - VHOG - ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.117 - http://bgee.unil.ch/ - - - - - FBbt:00005093 - - @@ -41592,14 +38727,10 @@ For example, A and B may be gene products and binding of B by A positively regul - + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. - Part of the nervous system which includes the brain and spinal cord.[AAO] - The brain and spinal cord. Kimmel et al, 1995.[TAO] - The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO). - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG] AAO:0000090 BAMS:CNS BILA:0000080 @@ -41612,7 +38743,6 @@ For example, A and B may be gene products and binding of B by A positively regul EMAPA:16470 EMAPA:16754 EV:0100163 - FBbt:00005094 FMA:55675 GAID:570 MA:0000167 @@ -41641,7 +38771,7 @@ For example, A and B may be gene products and binding of B by A positively regul central nervous system - + @@ -41655,7 +38785,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + Bgee:AN @@ -41672,46 +38802,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Acoelomorpha - - - - Part of the nervous system which includes the brain and spinal cord.[AAO] - 2012-06-20 - AAO:0000090 - AAO - AAO:BJB - - - - - The brain and spinal cord. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000012 - TAO - ZFIN:curator - - - - - The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO). - BIRNLEX:1099 - - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG] - 2012-09-17 - VHOG:0000293 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 (reference 1), ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 (reference 2), DOI:10.1016/j.cell.2007.02.040 Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud'homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007) (reference 3) - http://bgee.unil.ch/ - - - - - FBbt:00005094 - - @@ -41763,7 +38853,6 @@ For example, A and B may be gene products and binding of B by A positively regul BTO:0001886 EFO:0001652 EHDAA2:0003171 - FBbt:00005495 FMA:86589 MAT:0000482 NCIT:C34275 @@ -41797,12 +38886,6 @@ For example, A and B may be gene products and binding of B by A positively regul FB:FBrf0089570 http://flybase.org/reports/FBrf0178740.html - - - - FBbt:00005495 - - @@ -41839,10 +38922,6 @@ For example, A and B may be gene products and binding of B by A positively regul In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted]. - Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO] - The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG] - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] - The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium AAO:0010617 BTO:0001057 CALOHA:TS-2371 @@ -41854,7 +38933,6 @@ For example, A and B may be gene products and binding of B by A positively regul EMAPA:16757 FMA:293882 MAT:0000069 - MESH:D054259 MIAA:0000069 NCIT:C34226 SCTID:362852000 @@ -41888,49 +38966,6 @@ For example, A and B may be gene products and binding of B by A positively regul In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted]. Wikipedia:Neural_tube - - - - Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO] - 2012-06-20 - AAO:0010617 - AAO - AAO:JOR - - - - - The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG] - 2012-09-17 - VHOG:0000307 - VHOG - http://bgee.unil.ch/ - http://medical-dictionary.thefreedictionary.com/neural+tube - - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] - 2012-09-17 - VHOG:0000307 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 - http://bgee.unil.ch/ - - - - - The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium - GO:0021915 - - - - - MESH:D054259 - - - https://github.com/biopragmatics/biomappings - @@ -41961,7 +38996,6 @@ For example, A and B may be gene products and binding of B by A positively regul BIRNLEX:6 CARO:0000000 EHDAA2:0002229 - FBbt:10000000 FMA:62955 HAO:0000000 MA:0000001 @@ -41985,12 +39019,6 @@ For example, A and B may be gene products and binding of B by A positively regul FMA:62955 http://orcid.org/0000-0001-9114-8737 - - - - FBbt:10000000 - - @@ -42048,13 +39076,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system. - - Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO] - Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO] - System that provides physical support to the organism.[AAO] - By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG] - skeletal - GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates AAO:0000566 BTO:0001486 CALOHA:TS-1320 @@ -42090,50 +39111,6 @@ For example, A and B may be gene products and binding of B by A positively regul VSAO:0000027 http://dx.plos.org/10.1371/journal.pone.0051070 - - - - Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO] - 2012-08-14 - TAO:0000434 - TAO - TAO:wd - - - - - Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO] - 2012-08-14 - VSAO:0000027 - VSAO - GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 - PSPUB:0000170 - - - - - System that provides physical support to the organism.[AAO] - 2012-06-20 - AAO:0000566 - AAO - AAO:LAP - - - - - By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG] - 2012-09-17 - VHOG:0001254 - VHOG - DOI:10.1159/000324245 Donoghue PCJ, Sansom IJ, Origin and early evolution of vertebrate skeletonization. Microscopy research and technique (2002) - http://bgee.unil.ch/ - - - - - GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates - GO - @@ -42176,18 +39153,10 @@ For example, A and B may be gene products and binding of B by A positively regul - + Skeletal element that is composed of bone tissue. - - - - Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO] - Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO] - Skeletal element that is composed of bone tissue.[VSAO] - relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] - The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG] AAO:0000047 AEO:0000082 BTO:0000140 @@ -42226,14 +39195,14 @@ For example, A and B may be gene products and binding of B by A positively regul bone element - + - + VSAO-modified @@ -42246,51 +39215,6 @@ For example, A and B may be gene products and binding of B by A positively regul http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/277 - - - - Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO] - 2012-06-20 - AAO:0000047 - AAO - AAO:LAP - - - - - Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO] - 2012-08-14 - TAO:0001514 - TAO - ZFIN:curator - - - - - Skeletal element that is composed of bone tissue.[VSAO] - 2012-08-14 - VSAO:0000057 - VSAO - PSPUB:0000170 - - - - - relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] - 2012-06-20 - AAO:0000047 - AAO - - - - - The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG] - 2012-09-17 - VHOG:0001190 - VHOG - DOI:10.1159/000324245 Murdock DJ, Donoghue PC, Evolutionary Origins of Animal Skeletal Biomineralization. Cells Tissues Organs (2011) - http://bgee.unil.ch/ - @@ -42344,16 +39268,11 @@ For example, A and B may be gene products and binding of B by A positively regul - + A tube extending from the mouth to the anus. - The alimentary or digestive tract, and associated organs.[TAO] - The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] - FMA also has a term 'gastrointestinal tract', but this includes the liver. - we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509 - we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this gut AAO:0010023 BILA:0000083 @@ -42362,10 +39281,8 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA2:0000726 EHDAA:518 EMAPA:16247 - FBbt:00003125 FMA:45615 MA:0000917 - MESH:D041981 NCIT:C34082 TAO:0000112 TGMA:0001819 @@ -42387,14 +39304,14 @@ For example, A and B may be gene products and binding of B by A positively regul digestive tract - + - + NCBIBook:NBK10107 @@ -42416,50 +39333,6 @@ For example, A and B may be gene products and binding of B by A positively regul DOI:10.1371/journal.pone.0016309 - - - - The alimentary or digestive tract, and associated organs.[TAO] - 2012-08-14 - TAO:0000112 - TAO - ZFIN:curator - - - - - The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0000309 - VHOG - ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 - http://bgee.unil.ch/ - - - - - FMA also has a term 'gastrointestinal tract', but this includes the liver. - FMA - - - - - we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509 - MA - - - - - FBbt:00003125 - - - - - - MESH:D041981 - - https://github.com/biopragmatics/biomappings - @@ -42510,12 +39383,7 @@ For example, A and B may be gene products and binding of B by A positively regul Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]. - Portion of tissue composed of contractile fibers.[TAO] - It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG] - muscular muscle - AAO:0011066 - EMAPA:32715 EMAPA:37474 EV:0100146 FMA:5022 @@ -42541,25 +39409,6 @@ For example, A and B may be gene products and binding of B by A positively regul Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]. GO:0007517 - - - - Portion of tissue composed of contractile fibers.[TAO] - 2012-08-14 - TAO:0005145 - TAO - ZFIN:curator - - - - - It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG] - 2012-09-17 - VHOG:0001245 - VHOG - ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.75 - http://bgee.unil.ch/ - @@ -42678,14 +39527,15 @@ For example, A and B may be gene products and binding of B by A positively regul + - - + + @@ -42698,7 +39548,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -42714,11 +39564,6 @@ For example, A and B may be gene products and binding of B by A positively regul A vessel through which blood circulates in the body. consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus - Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG] - Any of the vessels through which blood circulates in the body.[AAO] - The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] - annelids have blood vessels, but this class is not applicable to annelids. - FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX vascular element AAO:0011004 AEO:0000207 @@ -42757,34 +39602,34 @@ For example, A and B may be gene products and binding of B by A positively regul blood vessel http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg - + - + - + - + AEO - + EHDAA2 - + GO:0072360 @@ -42794,40 +39639,6 @@ For example, A and B may be gene products and binding of B by A positively regul BTO:0001102 Wikipedia:Blood_vessel - - - - Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG] - 2012-09-17 - VHOG:0001250 - VHOG - http://bgee.unil.ch/ - - - - - Any of the vessels through which blood circulates in the body.[AAO] - 2012-06-20 - AAO:0011004 - AAO - AAO:EJS - - - - - The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] - 2012-09-17 - VHOG:0001250 - VHOG - DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006) - http://bgee.unil.ch/ - - - - - FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX - FMA - @@ -42892,7 +39703,6 @@ For example, A and B may be gene products and binding of B by A positively regul A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA]. - endothelial BTO:0000393 CALOHA:TS-0278 EFO:0002548 @@ -42960,7 +39770,6 @@ For example, A and B may be gene products and binding of B by A positively regul An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face. see also: vascular system. Consider merging? - vascular BTO:0003718 FMA:69050 TAO:0005249 @@ -43018,16 +39827,11 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical structure that is part of an embryo. - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO] - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO] - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO] - in FMA embryo is_a embryonic structure AAO:0000138 BILA:0000034 BTO:0000174 CALOHA:TS-2110 EFO:0000461 - FBbt:00004208 FMA:69067 GAID:407 MESH:D004628 @@ -43058,45 +39862,6 @@ For example, A and B may be gene products and binding of B by A positively regul BTO:0000174 ZFIN:curator - - - - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO] - 2012-06-20 - AAO:0000138 - AAO - AAO:BJB - - - - - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO] - 2012-08-14 - TAO:0001105 - TAO - ZFIN:curator - - - - - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO] - 2012-08-14 - VSAO:0000178 - VSAO - ZFIN:curator - - - - - in FMA embryo is_a embryonic structure - FMA - - - - - FBbt:00004208 - - @@ -43153,8 +39918,6 @@ For example, A and B may be gene products and binding of B by A positively regul An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen. - An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO] - general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs. AAO:0010386 BTO:0001491 EHDAA:512 @@ -43189,21 +39952,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Viscus https://github.com/obophenotype/mouse-anatomy-ontology/issues/14 - - - - An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO] - 2012-06-20 - AAO:0010386 - AAO - BTO:0001491 - - - - - general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs. - FMA - @@ -43260,21 +40008,15 @@ For example, A and B may be gene products and binding of B by A positively regul The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA]. - Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO] - The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO] - The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO] - The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG] axial skeleton AAO:0000034 EFO:0000942 EHDAA2:0000161 EHDAA:5049 - EMAPA:17214 EMAPA:37721 FMA:71221 MA:0002986 MAT:0000148 - MESH:D013131 MIAA:0000148 TAO:0000317 VHOG:0000317 @@ -43300,43 +40042,6 @@ For example, A and B may be gene products and binding of B by A positively regul https://sourceforge.net/tracker/?func=detail&aid=2983975&group_id=76834&atid=974957 https://sourceforge.net/tracker/?func=detail&atid=1205376&aid=2983977&group_id=76834 - - - - Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO] - 2012-08-14 - VSAO:0000093 - VSAO - PSPUB:0000170 - - - - - The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO] - 2012-06-20 - AAO:0000034 - AAO - AAO:LAP - - - - - The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO] - 2012-08-14 - TAO:0000317 - TAO - ZFIN:curator - - - - - The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG] - 2012-09-17 - VHOG:0000317 - VHOG - DOI:10.1186/1742-9994-8-4 Schilling N, Evolution of the axial system in craniates: morphology and function of the perivertebral musculature. Frontiers in Zoology (2011) - http://bgee.unil.ch/ - @@ -43350,13 +40055,6 @@ For example, A and B may be gene products and binding of B by A positively regul EMAPA:37721 MA:th - - - - MESH:D013131 - - https://github.com/biopragmatics/biomappings - @@ -43371,10 +40069,6 @@ For example, A and B may be gene products and binding of B by A positively regul Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present. - - - Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO] - Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO] AAO:0010339 BILA:0000116 BTO:0001493 @@ -43414,32 +40108,6 @@ For example, A and B may be gene products and binding of B by A positively regul UBERONREF:0000006 Wikipedia:Torso - - - - - ZFA - https://github.com/obophenotype/uberon/issues/378 - pending - - - - - Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO] - 2012-06-20 - AAO:0010339 - AAO - AAO:BJB - - - - - Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO] - 2012-08-14 - TAO:0001115 - TAO - ZFIN:curator - @@ -43521,7 +40189,12 @@ For example, A and B may be gene products and binding of B by A positively regul - + + + + + + @@ -43531,9 +40204,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that consists of the muscular and skeletal systems. - Anatomical system that provides locomotion and physical support to the organism.[AAO] - There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG] - musculoskeletal AAO:0010546 CALOHA:TS-1311 EMAPA:32714 @@ -43555,16 +40225,6 @@ For example, A and B may be gene products and binding of B by A positively regul musculoskeletal system - - - - - - - - - check ctenophore - @@ -43573,25 +40233,6 @@ For example, A and B may be gene products and binding of B by A positively regul VSAO:curator https://github.com/obophenotype/uberon/issues/77 - - - - Anatomical system that provides locomotion and physical support to the organism.[AAO] - 2012-06-20 - AAO:0010546 - AAO - AAO:EJS - - - - - There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG] - 2012-09-17 - VHOG:0001275 - VHOG - DOI:10.1002/jez.b.21246 Shearman RM, Burke AC, The lateral somitic frontier in ontogeny and phylogeny. Journal of Experimental Zoology (2009) - http://bgee.unil.ch/ - @@ -43633,7 +40274,6 @@ For example, A and B may be gene products and binding of B by A positively regul The part of the coelemic cavity lumen that is enclosed by the walls of the thorax. - In many species, the diaphragm separates thoracic and abdominal cavities EMAPA:36497 FMA:7565 GAID:93 @@ -43691,7 +40331,12 @@ For example, A and B may be gene products and binding of B by A positively regul - + + + + + + @@ -43699,15 +40344,11 @@ For example, A and B may be gene products and binding of B by A positively regul The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities. - Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]. - The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]. - In mammals it forms the peritoneal, pleural, and pericardial cavities UBERON:0000169 body cavity AEO:0000186 BTO:0001707 EHDAA2:0000267 - FBbt:00005060 FMA:85006 NCIT:C25444 RETIRED_EHDAA2:0003186 @@ -43732,52 +40373,18 @@ For example, A and B may be gene products and binding of B by A positively regul EDITOR_NOTE check the FMA placement here; ncit placement of body cavity here probably not correct coelemic cavity lumen - - - - - - - - - definitional - The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities. BTO:0001707 - - - - Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]. - 2012-09-12 - ZFA:0001438 - ZFA - ZFIN:curator - - - - - The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]. - 2012-09-12 - BTO:0001707 - BTO - BTO - body cavity BTO:0001707 - - - - FBbt:00005060 - - @@ -43834,6 +40441,7 @@ For example, A and B may be gene products and binding of B by A positively regul + @@ -43841,21 +40449,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - + + + @@ -43869,13 +40465,6 @@ For example, A and B may be gene products and binding of B by A positively regul A flexible rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In some chordates, it persists throughout life as the main axial support of the body, while in most vertebrates it becomes the nucleus pulposus of the intervertebral disc. The notochord is found ventral to the neural tube. - Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO] - Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO] - Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO] - relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO] - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG] - notochordal - In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord. AAO:0000327 BTO:0001768 CALOHA:TS-0690 @@ -43910,15 +40499,15 @@ For example, A and B may be gene products and binding of B by A positively regul notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + @@ -43937,19 +40526,19 @@ For example, A and B may be gene products and binding of B by A positively regul - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -43962,51 +40551,6 @@ For example, A and B may be gene products and binding of B by A positively regul https://github.com/obophenotype/uberon/issues/25 https://github.com/obophenotype/uberon/issues/271 - - - - Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO] - 2012-08-14 - VSAO:0000032 - VSAO - PSPUB:0000170 - - - - - Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000135 - TAO - ZFIN:curator - - - - - Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO] - 2012-06-20 - AAO:0000327 - AAO - AAO:LAP - - - - - relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO] - 2012-06-20 - AAO:0000327 - AAO - - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG] - 2012-09-17 - VHOG:0000199 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 - http://bgee.unil.ch/ - @@ -44034,18 +40578,10 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. - EDITOR_NOTE currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk - Post-cranial axial segments which form sclerotome and dermomyotome.[AAO] - Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO] - relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO] - relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO] - relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO] - (...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG] - somitic mesodermal cluster AAO:0010569 AEO:0001015 @@ -44081,11 +40617,11 @@ For example, A and B may be gene products and binding of B by A positively regul somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + @@ -44098,13 +40634,13 @@ For example, A and B may be gene products and binding of B by A positively regul - + GOTAX:0000352 - + ZFA @@ -44120,58 +40656,6 @@ For example, A and B may be gene products and binding of B by A positively regul PMID:17237766 - - - - Post-cranial axial segments which form sclerotome and dermomyotome.[AAO] - 2012-06-20 - AAO:0010569 - AAO - AAO:EJS - - - - - Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000155 - TAO - ZFIN:curator - - - - - relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO] - 2012-08-14 - TAO:0000155 - TAO - - - - - relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO] - 2012-08-14 - TAO:0000155 - TAO - - - - - relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO] - 2012-06-20 - AAO:0010569 - AAO - - - - - (...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0000191 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.40, DOI:10.1093/icb/43.1.137 Balavoine G, Adoutte A, The segmented urbilateria: a testable scenario. Integrative and Comparative Biology (2003) - http://bgee.unil.ch/ - @@ -44216,20 +40700,25 @@ For example, A and B may be gene products and binding of B by A positively regul + - - - - - - + + + + + + + + + + + + + + + + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. - EDITOR_NOTE consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams). - - A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO] - Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO] - A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831] - We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG] AAO:0010578 BTO:0001764 CALOHA:TS-0676 @@ -44242,7 +40731,6 @@ For example, A and B may be gene products and binding of B by A positively regul MIAA:0000066 NCIT:C34222 SCTID:361462002 - TAO:0000045 UMLS:C0027789 VHOG:0000057 Wikipedia:Neural_crest @@ -44262,66 +40750,45 @@ For example, A and B may be gene products and binding of B by A positively regul http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - - - - - + - + - - - - - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - - Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells - ISBN:0073040584 - - - - - + BTO - + PMID:11523831 - - pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest - - - - - + PMID:11523831 @@ -44330,47 +40797,6 @@ For example, A and B may be gene products and binding of B by A positively regul A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. MP:0009846 - - - - - ISBN:0073040584 - PMID:17377535 - - - - - A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000045 - TAO - ZFIN:curator - - - - - Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO] - 2012-06-20 - AAO:0010578 - AAO - AAO:EJS - - - - - A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831] - PMID:11523831 - - - - - We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG] - 2012-09-17 - VHOG:0000057 - VHOG - DOI:10.1111/j.1469-7580.2012.01495.x Hall BK, Gillis JA, Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues. J Anat (2012) - http://bgee.unil.ch/ - @@ -44412,9 +40838,6 @@ For example, A and B may be gene products and binding of B by A positively regul Embryonic ectoderm that gives rise to nervous tissue. - (...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG] - neurectodermal - we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here AAO:0011074 BILA:0000039 CALOHA:TS-1212 @@ -44423,7 +40846,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA:255 EMAPA:16073 EV:0100004 - FBbt:00001057 FMA:87657 MAT:0000176 MIAA:0000176 @@ -44452,22 +40874,6 @@ For example, A and B may be gene products and binding of B by A positively regul Embryonic ectoderm that gives rise to nervous tissue. Wikipedia:Neuroectoderm - - - - (...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG] - 2012-09-17 - VHOG:0000150 - VHOG - DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) - http://bgee.unil.ch/ - - - - - FBbt:00001057 - - @@ -44509,13 +40915,14 @@ For example, A and B may be gene products and binding of B by A positively regul + - + @@ -44538,8 +40945,6 @@ For example, A and B may be gene products and binding of B by A positively regul TODO - create superclass for bone marrow / head kidney. both are portions of tissue in the hematopoetic system. also consider adding as subclass of zone of bone organ for consistency with FMA. See also: Leydig and epigonal organs consider placement of NCIT:C53466 medullary bone - The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG] - In adults, marrow in large bones produces new blood cells[Wikipedia:Bone_marrow] AAO:0011007 BTO:0000141 BTO:0000829 @@ -44573,14 +40978,14 @@ For example, A and B may be gene products and binding of B by A positively regul bone marrow http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg - + - + FMA MA @@ -44591,16 +40996,6 @@ For example, A and B may be gene products and binding of B by A positively regul MGI:cwg MP:0002397 - - - - The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG] - 2012-09-17 - VHOG:0001218 - VHOG - DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood Cells and Blood Cell Development in the Animal Kingdom. Annual Review of Cell and Developmental Biology (2006) - http://bgee.unil.ch/ - @@ -44644,10 +41039,6 @@ For example, A and B may be gene products and binding of B by A positively regul Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance. - One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO] - Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO] - Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO] - MA also has set of connective tissues AAO:0000098 BTO:0000421 CALOHA:TS-2009 @@ -44688,40 +41079,6 @@ For example, A and B may be gene products and binding of B by A positively regul http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/23 - - - - One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO] - 2012-06-20 - AAO:0000098 - AAO - AAO:LAP - - - - - Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO] - 2012-08-14 - TAO:0001641 - TAO - TAO:wd - - - - - Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO] - 2012-08-14 - VSAO:0000017 - VSAO - GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 - PSPUB:0000170 - - - - - MA also has set of connective tissues - MA - @@ -44784,8 +41141,6 @@ For example, A and B may be gene products and binding of B by A positively regul Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]. - - One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO] AAO:0000306 AEO:0000122 CALOHA:TS-0642 @@ -44816,15 +41171,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Muscle_tissue https://sourceforge.net/tracker/index.php?func=detail&aid=2801266&group_id=36855&atid=440764 - - - - One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO] - 2012-06-20 - AAO:0000306 - AAO - AAO:LAP - @@ -44851,21 +41197,22 @@ For example, A and B may be gene products and binding of B by A positively regul - + - + + + + + + Anatomical system that is involved in the production of hematopoietic cells. - Anatomical system that consists of the blood and blood forming tissues.[AAO] - Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG] - hematopoietic - In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes AAO:0011002 BTO:0000570 CALOHA:TS-0449 @@ -44903,57 +41250,22 @@ For example, A and B may be gene products and binding of B by A positively regul hematopoietic system - + - - - - - + FMA - - - - - definitional - Anatomical system that is involved in the production of hematopoietic cells. Wikipedia:Haematopoiesis - - - - Anatomical system that consists of the blood and blood forming tissues.[AAO] - 2012-06-20 - AAO:0011002 - AAO - AAO:EJS - - - - - Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG] - 2012-09-17 - VHOG:0001624 - VHOG - DOI:10.1016/j.coph.2010.05.004 Ellett F, Lieschke GJ, Zebrafish as a model for vertebrate hematopoiesis. Current Opinion in Pharmacology (2010) - http://bgee.unil.ch/ - - - - - In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes - WP - @@ -44993,7 +41305,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies. - The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG] AAO:0011003 BILA:0000104 BTO:0005810 @@ -45023,16 +41334,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies. Wikipedia:Immune_system - - - - The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG] - 2012-09-17 - VHOG:0001247 - VHOG - PMID:21046016 Dzik JM, The ancestry and cumulative evolution of immune reactions. Acta biochimica Polonica (2010) - http://bgee.unil.ch/ - @@ -45061,7 +41362,6 @@ For example, A and B may be gene products and binding of B by A positively regul Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts. see https://github.com/obophenotype/uberon/issues/27 - Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO] CALOHA:TS-2011 EMAPA:35179 FMA:224804 @@ -45101,16 +41401,6 @@ For example, A and B may be gene products and binding of B by A positively regul VSAO:0000047 http://dx.plos.org/10.1371/journal.pone.0051070 - - - - Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO] - 2012-08-14 - VSAO:0000047 - VSAO - GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 - PSPUB:0000170 - @@ -45156,7 +41446,6 @@ For example, A and B may be gene products and binding of B by A positively regul In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA]. MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class - In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG] BTO:0004593 FMA:296704 MAT:0000067 @@ -45184,16 +41473,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Epiblast ZFIN:curator - - - - In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG] - 2012-09-17 - VHOG:0000243 - VHOG - DOI:10.1146/annurev.cellbio.042308.113344 Zorn AM, Wells JM, Vertebrate endoderm development and organ formation. Annual Review of Cell Developmental Biology (2009) - http://bgee.unil.ch/ - @@ -45291,10 +41570,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. - Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO] - It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG] AAO:0011086 EFO:0001982 EMAPA:16189 @@ -45316,14 +41593,14 @@ For example, A and B may be gene products and binding of B by A positively regul presomitic mesoderm - + - + Bgee:AN @@ -45332,25 +41609,6 @@ For example, A and B may be gene products and binding of B by A positively regul Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. ZFIN:curator - - - - Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000279 - TAO - ZFIN:curator - - - - - It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG] - 2012-09-17 - VHOG:0000559 - VHOG - DOI:10.1006/dbio.2001.0460 Schubert M, Holland LZ, Dale Stokes M and Holland ND, Three Amphoxius Wnt Genes (AmphiWnt3, AmphiWnt5, and AmphiWnt6) Associated with the Tail Bud: the Evolution of Somitogenesis in Chordates. Developmental Biology (2001) - http://bgee.unil.ch/ - @@ -45389,11 +41647,6 @@ For example, A and B may be gene products and binding of B by A positively regul Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted]. - Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO] - Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO] - relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO] - Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG] - EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac ventral lateral plate mesoderm AAO:0011006 EFO:0003489 @@ -45426,48 +41679,6 @@ For example, A and B may be gene products and binding of B by A positively regul Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted]. Wikipedia:Blood_island_of_umbilical_vesicle - - - - Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000094 - TAO - ZFIN:curator - - - - - Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO] - 2012-06-20 - AAO:0011006 - AAO - AAO:EJS - - - - - relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO] - 2012-08-14 - TAO:0000094 - TAO - - - - - Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0000085 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450, DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual Review of Cell and Developmental Biology (2006) - http://bgee.unil.ch/ - - - - - EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac - EHDAA2 - @@ -45506,7 +41717,6 @@ For example, A and B may be gene products and binding of B by A positively regul The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord. - The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] AAO:0011017 EFO:0003647 TAO:0001204 @@ -45529,15 +41739,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0048318 Wikipedia:Chordamesoderm - - - - The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] - 2012-09-17 - VHOG:0000107 - VHOG - http://bgee.unil.ch/ - @@ -45553,12 +41754,10 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. - The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO] - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] AAO:0011072 BTO:0001765 DHBA:10153 @@ -45567,7 +41766,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA:902 EMAPA:35593 FMA:293879 - MESH:D054258 NCIT:C34225 RETIRED_EHDAA2:0001252 TAO:0000132 @@ -45587,34 +41785,34 @@ For example, A and B may be gene products and binding of B by A positively regul neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -45626,33 +41824,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Neural_plate ZFIN:curator - - - - The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000132 - TAO - ZFIN:curator - - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] - 2012-09-17 - VHOG:0000068 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 - http://bgee.unil.ch/ - - - - - MESH:D054258 - - - https://github.com/biopragmatics/biomappings - @@ -45675,23 +41846,14 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. - Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO] - Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG] - note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here) AAO:0010568 EFO:0003515 EMAPA:16183 @@ -45716,7 +41878,7 @@ For example, A and B may be gene products and binding of B by A positively regul paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -45729,7 +41891,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + Bgee:AN @@ -45739,31 +41901,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0048339 https://github.com/obophenotype/uberon/issues/30 - - - - Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO] - 2012-06-20 - AAO:0010568 - AAO - AAO:EJS - - - - - Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG] - 2012-09-17 - VHOG:0000114 - VHOG - DOI:10.1002/dvdy.21177 Kusakabe R and Kuratani S. Evolutionary perspectives from development of mesodermal components in the lamprey. Developmental dynamics (2007) - http://bgee.unil.ch/ - - - - - note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here) - ZFA - @@ -45801,7 +41938,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -45815,10 +41952,6 @@ For example, A and B may be gene products and binding of B by A positively regul Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]. - Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO] - The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] - A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG] - subclass of mesoderm in ZFA. UBERON:0006258 AAO:0010574 EHDAA2:0000919 @@ -45845,7 +41978,7 @@ For example, A and B may be gene products and binding of B by A positively regul lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -45858,7 +41991,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + EHDAA2 VHOG @@ -45869,40 +42002,6 @@ For example, A and B may be gene products and binding of B by A positively regul MP:0010117 Wikipedia:Lateral_plate_mesoderm - - - - Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO] - 2012-06-20 - AAO:0010574 - AAO - AAO:EJS - - - - - The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] - 2012-09-17 - VHOG:0000118 - VHOG - http://bgee.unil.ch/ - - - - - A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG] - 2012-09-17 - VHOG:0000118 - VHOG - DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) - http://bgee.unil.ch/ - - - - - subclass of mesoderm in ZFA. - ZFA - @@ -45942,20 +42041,17 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + - + Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. should probably be merged with heart rudiment. - Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO] - The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO] - relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO] AAO:0011044 BTO:0001887 NCIT:C34276 @@ -45970,15 +42066,15 @@ For example, A and B may be gene products and binding of B by A positively regul heart primordium - + - + - + @@ -45991,19 +42087,19 @@ For example, A and B may be gene products and binding of B by A positively regul - + ZFA - + ZFA - + XAO @@ -46012,32 +42108,6 @@ For example, A and B may be gene products and binding of B by A positively regul Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. ZFIN:curator - - - - Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO] - 2012-08-14 - TAO:0000028 - TAO - ZFIN:curator - - - - - The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO] - 2012-06-20 - AAO:0011044 - AAO - XAO:curator - - - - - relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO] - 2012-08-14 - TAO:0000028 - TAO - @@ -46058,15 +42128,11 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. - Skeletogenic portion of somites.[AAO] - The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG] - part_of somite in XAO AAO:0010571 AEO:0000212 - BTO:0006255 EHDAA2:0003439 EMAPA:31159 FMA:295652 @@ -46087,11 +42153,11 @@ For example, A and B may be gene products and binding of B by A positively regul sclerotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + - + @@ -46110,13 +42176,13 @@ For example, A and B may be gene products and binding of B by A positively regul - + VHOG:0000680 - + ZFA @@ -46127,39 +42193,6 @@ For example, A and B may be gene products and binding of B by A positively regul XB:curator https://github.com/obophenotype/uberon/issues/316 - - - - Skeletogenic portion of somites.[AAO] - 2012-06-20 - AAO:0010571 - AAO - AAO:EJS - - - - - The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG] - 2012-09-17 - VHOG:0000680 - VHOG - DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) - http://bgee.unil.ch/ - - - - - part_of somite in XAO - XAO - - - - - BTO:0006255 - - - https://github.com/biopragmatics/biomappings - @@ -46188,7 +42221,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types. - this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs AAO:0010015 AEO:0000024 BILA:0000024 @@ -46252,9 +42284,6 @@ For example, A and B may be gene products and binding of B by A positively regul Portion of tissue composed of mesenchymal cells (motile cells that develop from epthelia via an epithelial to mesenchymal transition) and surrounding extracellular material. Mesenchyme has different embryological origins in different metazoan taxa - in many invertebrates it derives in whole or part from ectoderm. In vertebrates it derives largely from mesoderm, and sometimes the terms are used interchangeably, e.g. lateral plate mesoderm/mesenchyme. the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense - A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO] - Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO] - mesenchymal AAO:0010427 AEO:0000145 BTO:0001393 @@ -46289,24 +42318,6 @@ For example, A and B may be gene products and binding of B by A positively regul https://en.wikipedia.org/wiki/Mesenchyme https://github.com/obophenotype/uberon/issues/1641 - - - - A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000393 - TAO - ZFIN:curator - - - - - Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO] - 2012-06-20 - AAO:0010427 - AAO - AAO:EJS - @@ -46390,10 +42401,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults - (...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG] EHDAA:251 EMAPA:16088 NCIT:C34195 @@ -46406,14 +42416,14 @@ For example, A and B may be gene products and binding of B by A positively regul intraembryonic coelom - + - + Wikipedia @@ -46423,16 +42433,6 @@ For example, A and B may be gene products and binding of B by A positively regul MGI:anna MP:0012187 - - - - (...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG] - 2012-09-17 - VHOG:0000316 - VHOG - ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.166 - http://bgee.unil.ch/ - @@ -46465,10 +42465,8 @@ For example, A and B may be gene products and binding of B by A positively regul Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. - contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers AEO:0000114 EHDAA2:0003114 - FBbt:00007474 epithelial or endothelial tube uberon UBERON:0003914 @@ -46481,12 +42479,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0060562 PMID:12526790 - - - - FBbt:00007474 - - @@ -46532,7 +42524,6 @@ For example, A and B may be gene products and binding of B by A positively regul - FMA has both conduit and conduit space. In EHDAA2 this is a surface feature AEO:0000080 EHDAA2:0003080 FMA:242873 @@ -46554,12 +42545,6 @@ For example, A and B may be gene products and binding of B by A positively regul Any tube, opening or passage that connects two distinct anatomical spaces. http://orcid.org/0000-0002-6601-2165 - - - - FMA has both conduit and conduit space. In EHDAA2 this is a surface feature - FMA - @@ -46604,7 +42589,6 @@ For example, A and B may be gene products and binding of B by A positively regul An anatomical structure that develops (entirely or partially) from the mesoderm. - Grouping term for query purposes mesodermal derivative uberon UBERON:0004120 @@ -46648,7 +42632,6 @@ For example, A and B may be gene products and binding of B by A positively regul An anatomical structure that develops (entirely or partially) from the ectoderm. - Grouping term for query purposes ectodermal deriviative uberon UBERON:0004121 @@ -46682,7 +42665,6 @@ For example, A and B may be gene products and binding of B by A positively regul The first recognizable structure derived from the heart field. TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO - (In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG] EHDAA2:0000215 EMAPA:16106 VHOG:0000975 @@ -46701,16 +42683,6 @@ For example, A and B may be gene products and binding of B by A positively regul The first recognizable structure derived from the heart field. GO:0003142 - - - - (In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG] - 2012-09-17 - VHOG:0000975 - VHOG - PMID:15611355 Gittenberger-de Groot AC, Bartelings MM, Deruiter MC, Poelmann RE, Basics of cardiac development for the understanding of congenital heart malformations. Pediatric Research (2005) - http://bgee.unil.ch/ - @@ -46736,12 +42708,12 @@ For example, A and B may be gene products and binding of B by A positively regul + - - + + A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. - this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138] XAO:0004185 first heart field primary heart field @@ -46752,24 +42724,24 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0004140 primary heart field - + - + - + GO:0003128 - + https://orcid.org/0000-0003-3308-6245 @@ -46780,12 +42752,6 @@ For example, A and B may be gene products and binding of B by A positively regul GOC:mtg_heart GOC:rl - - - - this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138] - GO - @@ -46828,9 +42794,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + An epithelial tube that will give rise to the mature heart. - the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube. AAO:0010411 EFO:0003526 EMAPA:32685 @@ -46848,14 +42813,14 @@ For example, A and B may be gene products and binding of B by A positively regul heart tube - + - + ZFA-modified @@ -46865,12 +42830,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0003143 GOC:mtg_heart - - - - the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube. - MP:0012700 - @@ -46896,6 +42855,7 @@ For example, A and B may be gene products and binding of B by A positively regul + @@ -46939,10 +42899,7 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body. - - Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO] - skeletal AEO:0000168 EHDAA2:0001843 EHDAA:5047 @@ -46975,15 +42932,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body. VSAO:0000026 - - - - Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO] - 2012-08-14 - VSAO:0000026 - VSAO - GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 - @@ -46998,7 +42946,6 @@ For example, A and B may be gene products and binding of B by A positively regul A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube. - The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO] TAO:0000115 ZFA:0000115 heart cone @@ -47013,15 +42960,6 @@ For example, A and B may be gene products and binding of B by A positively regul A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube. GO:0003313 - - - - The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO] - 2012-08-14 - TAO:0000115 - TAO - ZFIN:curator - @@ -47080,18 +43018,14 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that has as its parts the heart and blood vessels. - we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph. - The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG] AAO:0011001 BILA:0000016 BTO:0000088 CALOHA:TS-1297 EFO:0000791 - EHDAA2:0000216 EHDAA:394 EMAPA:16104 - EMAPA:16370 EV:0100017 FMA:7161 GAID:467 @@ -47125,16 +43059,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that has as its parts the heart and blood vessels. BTO:0000088 - - - - The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG] - 2012-09-17 - VHOG:0000302 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.451 - http://bgee.unil.ch/ - @@ -47355,11 +43279,9 @@ For example, A and B may be gene products and binding of B by A positively regul Organism at the gastrula stage. - We explicitly merge the NCITA terms here UBERON:0007012 BILA:0000060 BTO:0001403 - FBbt:00005317 FMA:293108 GAID:1302 MESH:D005775 @@ -47391,18 +43313,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Gastrula Wikipedia:Trilaminar_blastocyst - - - - We explicitly merge the NCITA terms here - NCIT - - - - - FBbt:00005317 - - @@ -47482,9 +43392,13 @@ For example, A and B may be gene products and binding of B by A positively regul - + + + + + + A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]. - A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO] EMAPA:37744 MA:0003047 SCTID:309311006 @@ -47496,24 +43410,12 @@ For example, A and B may be gene products and binding of B by A positively regul Four classes of mineralized tissues are found in vertebrates: bone, cartilage, dentine, and enamel. We think of cartilage and bone as skeletal tissues and of enamel and dentine as dental tissues, but enamel and dentine arose evolutionarily together with bone as skeletal tissues in the dermal skeleton (exoskeleton) of early vertebrates. Scales and teeth of sharks are examples of dermal skeletal elements that are still composed of the three ancient components-enamel, dentine, and bone. Cartilage, on the other hand, provided the basis for the second vertebrate skeletal system, the endoskeleton (Smith and Hall, 1990; Hall, 1998a,b). some invertebrate skeletal tissues have surprisingly bone-like features. Examples include chondrocytes interconnected by cell processes in cephalopod cartilages (Cole and Hall, 2004a,b), and the calcium phosphate layer in the shells of brachiopods (Rodland et al., 2003). However, neither bone nor mineralized cartilage have been found in invertebrates. Editors notes: TODO - develops_from skeletal tissue - - - - VSAO - - - - - 2012-08-14 - VSAO:0000015 - VSAO - @@ -47524,17 +43426,6 @@ For example, A and B may be gene products and binding of B by A positively regul http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/134 - - - - A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO] - 2012-08-14 - VSAO:0000015 - taken from version of VSAO used in TAO and used directly in Uberon - VSAO - GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 - PSPUB:0000170 - @@ -47548,10 +43439,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. - Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO] - Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO] AAO:0011129 TAO:0001890 VSAO:0000128 @@ -47564,14 +43453,14 @@ For example, A and B may be gene products and binding of B by A positively regul skeletal element - + - + VSAO @@ -47580,24 +43469,6 @@ For example, A and B may be gene products and binding of B by A positively regul Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. https://orcid.org/0000-0002-6601-2165 - - - - Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO] - 2012-08-14 - VSAO:0000128 - VSAO - PSPUB:0000170 - - - - - Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO] - 2012-08-14 - TAO:0001890 - TAO - TAO:VSAO_workshop - @@ -47616,7 +43487,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -47655,14 +43526,14 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0004770 articular system - + - + FMA @@ -47715,7 +43586,6 @@ For example, A and B may be gene products and binding of B by A positively regul An endothelium that is part of the cardiovascular system. consider merging with 'endothelium' - Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] BTO:0001853 EMAPA:35201 GAID:519 @@ -47740,16 +43610,6 @@ For example, A and B may be gene products and binding of B by A positively regul An endothelium that is part of the cardiovascular system. https://orcid.org/0000-0002-6601-2165 - - - - Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] - 2012-09-17 - VHOG:0001217 - VHOG - ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207 - http://bgee.unil.ch/ - @@ -47784,7 +43644,6 @@ For example, A and B may be gene products and binding of B by A positively regul Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP]. - We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors visceral mesoderm AAO:0011102 BILA:0000044 @@ -47804,12 +43663,6 @@ For example, A and B may be gene products and binding of B by A positively regul Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP]. Wikipedia:Lateral_plate_mesoderm#Division_into_layers - - - - We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors - BILA - @@ -47844,8 +43697,6 @@ For example, A and B may be gene products and binding of B by A positively regul The central region of trunk mesoderm. This tissue forms the notochord. - Notochord rudiment[ZFIN:ZDB-PUB-961014-576]. - WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord. AAO:0000478 EFO:0003426 TAO:0000091 @@ -47866,12 +43717,6 @@ For example, A and B may be gene products and binding of B by A positively regul The central region of trunk mesoderm. This tissue forms the notochord. https://orcid.org/0000-0002-6601-2165 - - - - Notochord rudiment[ZFIN:ZDB-PUB-961014-576]. - ZFIN:ZDB-PUB-961014-576 - @@ -47904,7 +43749,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts. - FBbt:00005811 joint uberon UBERON:0004905 @@ -47917,12 +43761,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts. http://orcid.org/0000-0002-6601-2165 - - - - FBbt:00005811 - - @@ -47954,9 +43792,7 @@ For example, A and B may be gene products and binding of B by A positively regul A proximal-distal subdivision of the digestive tract. - intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct. - FBbt:00100315 FMA:71131 uberon alimentary system subdivision @@ -47975,12 +43811,6 @@ For example, A and B may be gene products and binding of B by A positively regul A proximal-distal subdivision of the digestive tract. http://orcid.org/0000-0002-6601-2165 - - - - FBbt:00100315 - - @@ -48045,7 +43875,6 @@ For example, A and B may be gene products and binding of B by A positively regul The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds. - The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]. AAO:0011071 EMAPA:35594 FMA:295624 @@ -48067,12 +43896,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Neural_groove http://orcid.org/0000-0002-6601-2165 - - - - The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]. - Wikipedia:Neural_groove - @@ -48088,6 +43911,7 @@ For example, A and B may be gene products and binding of B by A positively regul + @@ -48095,14 +43919,7 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - One of the two elevated edges of the neural groove[GO,MP]. - In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]. EHDAA2:0001249 FMA:295618 NCIT:C34223 @@ -48125,12 +43942,6 @@ For example, A and B may be gene products and binding of B by A positively regul MP:0011256 Wikipedia:Neural_fold - - - - In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]. - Wikipedia:Neural_fold - @@ -48157,7 +43968,6 @@ For example, A and B may be gene products and binding of B by A positively regul A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN]. - An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO] EFO:0003498 TAO:0000133 ZFA:0000133 @@ -48174,15 +43984,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0014024 ZFA:0000133 - - - - An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000133 - TAO - ZFIN:curator - @@ -48209,8 +44010,6 @@ For example, A and B may be gene products and binding of B by A positively regul Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO]. - in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila - EMAPA:32715 FMA:30316 musculus uberon @@ -48434,7 +44233,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -48450,14 +44249,14 @@ For example, A and B may be gene products and binding of B by A positively regul trunk mesenchyme - + - + EHDAA2 @@ -48537,7 +44336,6 @@ For example, A and B may be gene products and binding of B by A positively regul AEO:0000125 CALOHA:TS-2122 EHDAA2:0003125 - FBbt:00007006 FMA:292313 MIAA:0000019 uberon @@ -48548,12 +44346,6 @@ For example, A and B may be gene products and binding of B by A positively regul developing anatomical structure - - - - FBbt:00007006 - - @@ -48574,9 +44366,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + Multi-tissue structure that arises from the heart rudiment and will become the heart tube. - BTO:0006179 EHDAA2:0001512 EHDAA:424 EHDAA:436 @@ -48593,14 +44384,14 @@ For example, A and B may be gene products and binding of B by A positively regul primitive heart tube - + - + ZFA @@ -48609,14 +44400,6 @@ For example, A and B may be gene products and binding of B by A positively regul Multi-tissue structure that arises from the heart rudiment and will become the heart tube. ZFA:0000149 - - - - BTO:0006179 - - - https://github.com/biopragmatics/biomappings - @@ -48708,7 +44491,6 @@ For example, A and B may be gene products and binding of B by A positively regul An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina. - this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell. AAO:0010596 FMA:63872 @@ -48776,7 +44558,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 @@ -48786,7 +44568,7 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0005856 developing mesenchymal condensation - + @@ -48805,7 +44587,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + AEO-modified-relation @@ -48847,10 +44629,8 @@ For example, A and B may be gene products and binding of B by A positively regul Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified]. - Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO] AAO:0000963 EMAPA:17214 - EMAPA:18043 MA:0000308 NCIT:C32172 SCTID:361725000 @@ -48878,15 +44658,6 @@ For example, A and B may be gene products and binding of B by A positively regul https://github.com/obophenotype/uberon/issues/44 https://github.com/obophenotype/uberon/wiki/The-axial-skeleton - - - - Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO] - 2012-08-14 - VSAO:0000056 - VSAO - PSPUB:0000170 - @@ -48910,10 +44681,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB - The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG] EHDAA2:0001278 EHDAA:264 EMAPA:16101 @@ -48925,7 +44695,7 @@ For example, A and B may be gene products and binding of B by A positively regul notochordal plate - + @@ -48938,7 +44708,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + EHDAA2 @@ -48947,15 +44717,6 @@ For example, A and B may be gene products and binding of B by A positively regul The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. VHOG:0001212 - - - - The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG] - 2012-09-17 - VHOG:0001212 - VHOG - http://bgee.unil.ch/ - @@ -48975,7 +44736,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -48992,14 +44753,14 @@ For example, A and B may be gene products and binding of B by A positively regul The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -49360,7 +45121,6 @@ For example, A and B may be gene products and binding of B by A positively regul An epithelium characterised by its most superficial layer consisting of squamous epithelial cells. - FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium BTO:0002072 NCIT:C12848 SCTID:40118003 @@ -49376,12 +45136,6 @@ For example, A and B may be gene products and binding of B by A positively regul An epithelium characterised by its most superficial layer consisting of squamous epithelial cells. Wikipedia:Squamous_epithelium - - - - FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium - FBbt - @@ -49456,12 +45210,6 @@ For example, A and B may be gene products and binding of B by A positively regul Old definition: 'Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.' Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism. anatomical surface - - - - - via morphological boundary in CARO - @@ -49480,6 +45228,7 @@ For example, A and B may be gene products and binding of B by A positively regul + @@ -49654,7 +45403,6 @@ For example, A and B may be gene products and binding of B by A positively regul - The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis BILA:0000084 NCIT:C34268 SCTID:360394002 @@ -49670,12 +45418,6 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0007026 presumptive gut - - - - The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis - NCBIBook:NBK10107 - @@ -49706,10 +45448,13 @@ For example, A and B may be gene products and binding of B by A positively regul - + + + + + + A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]. - note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis - SPD:0000130 TADS:0000147 http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg dorsal tube @@ -49721,16 +45466,6 @@ For example, A and B may be gene products and binding of B by A positively regul Gene notes: Bmp, Nkx, Gata primary circulatory organ - - - - - - - - - GO uses blood circulation generically to include the haemolymphatic fluid of arthropods - @@ -49769,7 +45504,6 @@ For example, A and B may be gene products and binding of B by A positively regul An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. - An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO] EFO:0003497 TAO:0000131 ZFA:0000131 @@ -49785,15 +45519,6 @@ For example, A and B may be gene products and binding of B by A positively regul An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. ZFIN:ZDB-PUB-961014-576 - - - - An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000131 - TAO - ZFIN:curator - @@ -49818,7 +45543,12 @@ For example, A and B may be gene products and binding of B by A positively regul - + + + + + + @@ -49835,17 +45565,6 @@ For example, A and B may be gene products and binding of B by A positively regul presumptive segmental plate - - - - - - - - - https://github.com/obophenotype/uberon/wiki/The-neural-crest - EDHAA2 - @@ -49897,7 +45616,6 @@ For example, A and B may be gene products and binding of B by A positively regul A presumptive structure that has the potential to develop into a neural plate. consider merging - Region of the gastrula which gives rise to the neural plate.[TAO] EFO:0003424 TAO:0000063 ZFA:0000063 @@ -49914,15 +45632,6 @@ For example, A and B may be gene products and binding of B by A positively regul A presumptive structure that has the potential to develop into a neural plate. OBOL:automatic - - - - Region of the gastrula which gives rise to the neural plate.[TAO] - 2012-08-14 - TAO:0000063 - TAO - ZFIN:curator - @@ -49941,7 +45650,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -49967,7 +45676,7 @@ For example, A and B may be gene products and binding of B by A positively regul presumptive paraxial mesoderm - + @@ -49983,7 +45692,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + https://github.com/obophenotype/uberon/issues/1277 @@ -50059,7 +45768,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -50067,7 +45776,7 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0007524 dense mesenchyme tissue - + @@ -50080,7 +45789,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + AEO @@ -50140,7 +45849,6 @@ For example, A and B may be gene products and binding of B by A positively regul AEO:0000170 EFO:0001649 EHDAA2:0003170 - FBbt:00005426 Wikipedia:Anlage_(biology) developmental field uberon @@ -50170,12 +45878,6 @@ For example, A and B may be gene products and binding of B by A positively regul FBbt:00005426 http://flybase.org/reports/FBrf0178740.html - - - - FBbt:00005426 - - @@ -50183,12 +45885,10 @@ For example, A and B may be gene products and binding of B by A positively regul - + Anatomical system that consists of all blood and lymph vessels. consider merging with vasculature - The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]. - in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system BTO:0001085 CALOHA:TS-2053 EHDAA2:0004520 @@ -50202,14 +45902,14 @@ For example, A and B may be gene products and binding of B by A positively regul vascular system - + - + MA @@ -50218,18 +45918,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that consists of all blood and lymph vessels. http://orcid.org/0000-0002-6601-2165 - - - - The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]. - ncithesaurus:Vascular_System - - - - - in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system - MA - @@ -50249,7 +45937,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -50266,14 +45954,14 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -50329,7 +46017,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -50337,14 +46025,14 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -50365,8 +46053,9 @@ For example, A and B may be gene products and binding of B by A positively regul + - + EFO:0003704 TAO:0005041 ZFA:0005041 @@ -50376,14 +46065,14 @@ For example, A and B may be gene products and binding of B by A positively regul anterior lateral plate mesoderm - + - + ZFA @@ -50427,7 +46116,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0010000 - FBbt:00100313 multicellular structure uberon UBERON:0010000 @@ -50441,12 +46129,6 @@ For example, A and B may be gene products and binding of B by A positively regul An anatomical structure that has more than one cell as a part. CARO:0010000 - - - - FBbt:00100313 - - @@ -50523,7 +46205,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -50543,14 +46225,14 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0010210 blood clot - + - + BTO @@ -50597,7 +46279,6 @@ For example, A and B may be gene products and binding of B by A positively regul An anatomical structure that has some part that develops from the neural crest. - Grouping term for query purposes uberon UBERON:0010314 @@ -50672,10 +46353,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. - Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO] FMA:23879 SCTID:129140006 VSAO:0000042 @@ -50686,11 +46366,11 @@ For example, A and B may be gene products and binding of B by A positively regul subdivision of skeleton - + - + @@ -50703,13 +46383,13 @@ For example, A and B may be gene products and binding of B by A positively regul - + UBERONREF:0000003 - + VSAO @@ -50719,16 +46399,6 @@ For example, A and B may be gene products and binding of B by A positively regul UBERONREF:0000003 https://orcid.org/0000-0002-6601-2165 - - - - Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO] - 2012-08-14 - VSAO:0000042 - incorrect - VSAO - VSAO:curator - @@ -50780,7 +46450,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system FMA:302077 @@ -50790,7 +46460,7 @@ For example, A and B may be gene products and binding of B by A positively regul postcranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton - + @@ -50803,7 +46473,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + cjm @@ -50837,7 +46507,6 @@ For example, A and B may be gene products and binding of B by A positively regul - FBbt:00007330 FMA:67509 SCTID:91690000 uberon @@ -50859,12 +46528,6 @@ For example, A and B may be gene products and binding of B by A positively regul A subdivision of an anatomical system. http://orcid.org/0000-0002-6601-2165 - - - - FBbt:00007330 - - @@ -50981,7 +46644,6 @@ For example, A and B may be gene products and binding of B by A positively regul The aggregate of the coelemic cavity lumen plus the membranes that line the lumen. EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining. - coelomic EHDAA2:0004731 Wikipedia:Coelom enterocoelom @@ -51075,8 +46737,9 @@ For example, A and B may be gene products and binding of B by A positively regul + - + @@ -51084,7 +46747,6 @@ For example, A and B may be gene products and binding of B by A positively regul Blood-forming tissue, consisting of reticular fibers and cells. - Bone marrow in humans, kidney interstitium in Danio, within a stroma of reticuloendothelial tissue CALOHA:TS-2142 FMA:14073 NCIT:C13051 @@ -51098,7 +46760,7 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0012429 hematopoietic tissue - + @@ -51111,7 +46773,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + defitional @@ -51274,10 +46936,8 @@ For example, A and B may be gene products and binding of B by A positively regul The region of the organism associated with the visceral organs. - Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]. AEO:0000103 BTO:0001489 - EMAPA:36031 FMA:231424 uberon body @@ -51298,12 +46958,6 @@ For example, A and B may be gene products and binding of B by A positively regul The region of the organism associated with the visceral organs. AEO:0000103 - - - - Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]. - FMA:231424 - @@ -51416,7 +47070,6 @@ For example, A and B may be gene products and binding of B by A positively regul An anatomical group whose component structures share a common function. AEO:0000093 - FBbt:00007278 uberon UBERON:0015203 non-connected functional system @@ -51430,36 +47083,13 @@ For example, A and B may be gene products and binding of B by A positively regul FBC:DOS FBbt:00007278 - - - - FBbt:00007278 - - - - - - - - - - - - - - - - - - - @@ -51467,7 +47097,6 @@ For example, A and B may be gene products and binding of B by A positively regul Any structure that is placed on one side of the left-right axis of a bilaterian. - This class is primarily to implement taxon constraints. It may be removed in the future. uberon UBERON:0015212 @@ -51501,7 +47130,6 @@ For example, A and B may be gene products and binding of B by A positively regul A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile. heart - SPD:0000130 cardiac pump heart or heart like organ circulatory vessel @@ -51689,7 +47317,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -51712,7 +47340,7 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0016887 entire extraembryonic component - + @@ -51725,7 +47353,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + AEO @@ -51833,7 +47461,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0020000 - FBbt:00007276 uberon UBERON:0034923 @@ -51851,12 +47478,6 @@ For example, A and B may be gene products and binding of B by A positively regul Material anatomical entity consisting of multiple anatomical structures that are not connected to each other. CARO:0020000 - - - - FBbt:00007276 - - @@ -51970,7 +47591,6 @@ For example, A and B may be gene products and binding of B by A positively regul - example to be eventually removed example to be eventually removed @@ -51979,9 +47599,7 @@ For example, A and B may be gene products and binding of B by A positively regul - failed exploratory term The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job - Person:Alan Ruttenberg failed exploratory term @@ -51990,7 +47608,6 @@ For example, A and B may be gene products and binding of B by A positively regul - metadata complete Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. metadata complete @@ -52000,7 +47617,6 @@ For example, A and B may be gene products and binding of B by A positively regul - organizational term Term created to ease viewing/sort terms for development purpose, and will not be included in a release organizational term @@ -52010,7 +47626,6 @@ For example, A and B may be gene products and binding of B by A positively regul - ready for release Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release @@ -52020,7 +47635,6 @@ For example, A and B may be gene products and binding of B by A positively regul - metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete @@ -52030,7 +47644,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated @@ -52040,7 +47653,6 @@ For example, A and B may be gene products and binding of B by A positively regul - pending final vetting All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting @@ -52050,7 +47662,6 @@ For example, A and B may be gene products and binding of B by A positively regul - placeholder removed placeholder removed @@ -52059,7 +47670,6 @@ For example, A and B may be gene products and binding of B by A positively regul - terms merged An editor note should explain what were the merged terms and the reason for the merge. terms merged @@ -52069,7 +47679,6 @@ For example, A and B may be gene products and binding of B by A positively regul - term imported This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. term imported @@ -52079,7 +47688,6 @@ For example, A and B may be gene products and binding of B by A positively regul - term split This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. term split @@ -52089,10 +47697,7 @@ For example, A and B may be gene products and binding of B by A positively regul - universal Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. - Alan Ruttenberg - A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf universal @@ -52101,10 +47706,8 @@ For example, A and B may be gene products and binding of B by A positively regul - defined class A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. - Alan Ruttenberg defined class @@ -52113,10 +47716,8 @@ For example, A and B may be gene products and binding of B by A positively regul - named class expression A named class expression is a logical expression that is given a name. The name can be used in place of the expression. named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions - Alan Ruttenberg named class expression @@ -52125,10 +47726,7 @@ For example, A and B may be gene products and binding of B by A positively regul - to be replaced with external ontology term Terms with this status should eventually replaced with a term from another ontology. - Alan Ruttenberg - group:OBI to be replaced with external ontology term @@ -52137,10 +47735,7 @@ For example, A and B may be gene products and binding of B by A positively regul - requires discussion A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. - Alan Ruttenberg - group:OBI requires discussion @@ -52151,9 +47746,7 @@ For example, A and B may be gene products and binding of B by A positively regul The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. - https://github.com/information-artifact-ontology/ontology-metadata/issues/77 - https://orcid.org/0000-0001-5208-3432 out of scope @@ -52233,24 +47826,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - @@ -52302,69 +47877,48 @@ For example, A and B may be gene products and binding of B by A positively regul /////////////////////////////////////////////////////////////////////////////////////// --> - - - - - - - - - - - - - + - + - + - + - + - + - + - + - + - + - + - + - + - - - - - - - - - @@ -52377,8 +47931,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -52388,7 +47942,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -52398,7 +47952,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -52415,79 +47969,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - true - MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z - infer input from direct reg - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + @@ -52506,7 +47989,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -52516,8 +47999,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52527,8 +48010,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52545,67 +48028,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - - - - - - - true - GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' - involved in BP - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + @@ -52623,8 +48047,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52634,8 +48058,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52645,8 +48069,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52663,8 +48087,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52681,8 +48105,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52692,8 +48116,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52703,8 +48127,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52721,8 +48145,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52739,8 +48163,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52750,8 +48174,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52761,8 +48185,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52779,8 +48203,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52797,8 +48221,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52808,8 +48232,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52824,8 +48248,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52842,8 +48266,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52853,8 +48277,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52869,8 +48293,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52887,8 +48311,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52898,8 +48322,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52914,8 +48338,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52932,8 +48356,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52943,8 +48367,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52959,8 +48383,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52977,8 +48401,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52988,8 +48412,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -53004,8 +48428,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -53065,8 +48489,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -53076,8 +48500,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -53092,8 +48516,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -53108,9 +48532,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -53120,8 +48544,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -53135,9 +48559,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -53152,9 +48576,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -53164,8 +48588,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -53179,7 +48603,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + diff --git a/src/ontology/subsets/blood_and_immune_upper_slim.tsv b/src/ontology/subsets/blood_and_immune_upper_slim.tsv index ed97b6166..19def9327 100644 --- a/src/ontology/subsets/blood_and_immune_upper_slim.tsv +++ b/src/ontology/subsets/blood_and_immune_upper_slim.tsv @@ -1,392 +1,389 @@ ?x ?label -_:Bfc26b7c9X2D6e5eX2D4e75X2D81bcX2D5596fb9a64a9genid1011 -_:Bfc26b7c9X2D6e5eX2D4e75X2D81bcX2D5596fb9a64a9genid1024 -_:Bfc26b7c9X2D6e5eX2D4e75X2D81bcX2D5596fb9a64a9genid1038 -_:Bfc26b7c9X2D6e5eX2D4e75X2D81bcX2D5596fb9a64a9genid1054 -_:Bfc26b7c9X2D6e5eX2D4e75X2D81bcX2D5596fb9a64a9genid1072 -_:Bfc26b7c9X2D6e5eX2D4e75X2D81bcX2D5596fb9a64a9genid1079 -_:Bfc26b7c9X2D6e5eX2D4e75X2D81bcX2D5596fb9a64a9genid1085 -_:Bfc26b7c9X2D6e5eX2D4e75X2D81bcX2D5596fb9a64a9genid1097 -_:Bfc26b7c9X2D6e5eX2D4e75X2D81bcX2D5596fb9a64a9genid1107 -_:Bfc26b7c9X2D6e5eX2D4e75X2D81bcX2D5596fb9a64a9genid1115 -_:Bfc26b7c9X2D6e5eX2D4e75X2D81bcX2D5596fb9a64a9genid112 -_:Bfc26b7c9X2D6e5eX2D4e75X2D81bcX2D5596fb9a64a9genid115 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+_:Bd3a92e4aX2D59e9X2D479fX2D9102X2D86cde55c1e05genid719 +_:Bd3a92e4aX2D59e9X2D479fX2D9102X2D86cde55c1e05genid76 +_:Bd3a92e4aX2D59e9X2D479fX2D9102X2D86cde55c1e05genid772 +_:Bd3a92e4aX2D59e9X2D479fX2D9102X2D86cde55c1e05genid789 +_:Bd3a92e4aX2D59e9X2D479fX2D9102X2D86cde55c1e05genid79 +_:Bd3a92e4aX2D59e9X2D479fX2D9102X2D86cde55c1e05genid809 +_:Bd3a92e4aX2D59e9X2D479fX2D9102X2D86cde55c1e05genid824 +_:Bd3a92e4aX2D59e9X2D479fX2D9102X2D86cde55c1e05genid879 +_:Bd3a92e4aX2D59e9X2D479fX2D9102X2D86cde55c1e05genid910 +_:Bd3a92e4aX2D59e9X2D479fX2D9102X2D86cde55c1e05genid954 +_:Bd3a92e4aX2D59e9X2D479fX2D9102X2D86cde55c1e05genid967 +_:Bd3a92e4aX2D59e9X2D479fX2D9102X2D86cde55c1e05genid981 +_:Bd3a92e4aX2D59e9X2D479fX2D9102X2D86cde55c1e05genid997 "continuant" "occurrent" "independent continuant" diff --git a/src/ontology/subsets/eye_upper_slim.json b/src/ontology/subsets/eye_upper_slim.json index 8b2e399be..800e7810c 100644 --- a/src/ontology/subsets/eye_upper_slim.json +++ b/src/ontology/subsets/eye_upper_slim.json @@ -4,9 +4,9 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-02-13" + "val" : "2024-04-05" } ], - "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-02-13/subsets/eye_upper_slim.owl" + "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-04-05/subsets/eye_upper_slim.owl" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/BFO_0000002", @@ -78,18 +78,6 @@ "val" : "BFO:0000050" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "is part of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my brain is part of my body (continuant parthood, two material entities)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this day is part of this year (occurrent parthood)" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." }, { @@ -98,42 +86,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "part_of" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000002" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000003" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000004" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000017" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000019" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000020" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000031" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "part_of" @@ -164,18 +122,6 @@ "val" : "BFO:0000051" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has part" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my body has part my brain (continuant parthood, two material entities)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this year has part this day (occurrent parthood)" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." }, { @@ -184,21 +130,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has_part" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_part" @@ -217,26 +154,11 @@ "val" : "BFO:0000062" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "preceded by" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is preceded by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "preceded_by" - }, { - "pred" : "http://purl.org/dc/terms/source", - "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "preceded_by" @@ -255,14 +177,8 @@ "val" : "BFO:0000063" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "precedes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "precedes" @@ -282,26 +198,11 @@ "val" : "BFO:0000066" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "occurs in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "occurs_in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "unfolds in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "unfolds_in" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "occurs_in" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Occurs_in" @@ -315,412 +216,12 @@ "definition" : { "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" }, - "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ], - "xrefs" : [ { - "val" : "BFO:0000067" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "site of" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "contains_process" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - } ] + "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000141", "lbl" : "immaterial entity", "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000096", - "lbl" : "anterior to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000096" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "anterior_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000097", - "lbl" : "distal to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000097" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "distal_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000098", - "lbl" : "dorsal to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000098" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dorsal_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000099", - "lbl" : "posterior to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000099" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "posterior_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000100", - "lbl" : "proximal to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000100" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "proximal_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000102", - "lbl" : "ventral to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000102" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "ventral_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000107", - "lbl" : "deep to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000107" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "deep_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000108", - "lbl" : "superficial to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000108" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "superficial_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000120", - "lbl" : "in left side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000120" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_left_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000121", - "lbl" : "in right side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000121" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_right_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000122", - "lbl" : "in posterior side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000122" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_posterior_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000123", - "lbl" : "in anterior side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000123" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_anterior_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000124", - "lbl" : "in proximal side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000124" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_proximal_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "lbl" : "in lateral side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000126" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_lateral_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001100", - "lbl" : "in superficial part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001100" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_superficial_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001101", - "lbl" : "in deep part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001101" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_deep_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001106", - "lbl" : "proximalmost part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001106" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "proximalmost_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001107", - "lbl" : "immediately deep to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001107" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "immediately_deep_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001108", - "lbl" : "distalmost part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001108" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "distalmost_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001113", - "lbl" : "preaxialmost part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001113" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "preaxialmost_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001115", - "lbl" : "postaxialmost part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001115" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "postaxialmost_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0005001", - "lbl" : "intersects midsagittal plane of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0005001" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "intersects_midsagittal_plane_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0015014", - "lbl" : "immediately superficial to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0015014" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "immediately_superficial_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0015101", - "lbl" : "in dorsal side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0015101" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_dorsal_side_of" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000000", "lbl" : "cell", @@ -754,13 +255,17 @@ } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000005", - "lbl" : "fibroblast neural crest derived", + "lbl" : "neural crest derived fibroblast", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Any fibroblast that is deriived from the neural crest.", + "val" : "Any fibroblast that is derived from the neural crest.", "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] - } + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "fibroblast neural crest derived" + } ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000006", @@ -10345,13 +9850,7 @@ }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000002", "lbl" : "example to be eventually removed", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "example to be eventually removed" - } ] - } + "type" : "INDIVIDUAL" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000028", "lbl" : "symbol", @@ -10363,14 +9862,7 @@ "meta" : { "definition" : { "val" : "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "failed exploratory term" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person:Alan Ruttenberg" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000115", @@ -10381,20 +9873,8 @@ "val" : "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "definition" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2012-04-05: \nBarry Smith\n\nThe official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. \n\nOn the specifics of the proposed definition:\n\nWe don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Daniel Schober" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" } ] } }, { @@ -10404,32 +9884,7 @@ "meta" : { "definition" : { "val" : "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology." - }, - "xrefs" : [ { - "val" : "IAO:0000116" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "editor note" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Daniel Schober" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "editor_note" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000120", @@ -10438,11 +9893,7 @@ "meta" : { "definition" : { "val" : "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "metadata complete" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000121", @@ -10451,11 +9902,7 @@ "meta" : { "definition" : { "val" : "Term created to ease viewing/sort terms for development purpose, and will not be included in a release" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "organizational term" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000122", @@ -10464,11 +9911,7 @@ "meta" : { "definition" : { "val" : "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\"" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "ready for release" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000123", @@ -10477,11 +9920,7 @@ "meta" : { "definition" : { "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "metadata incomplete" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000124", @@ -10490,11 +9929,7 @@ "meta" : { "definition" : { "val" : "Nothing done yet beyond assigning a unique class ID and proposing a preferred term." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "uncurated" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000125", @@ -10503,31 +9938,18 @@ "meta" : { "definition" : { "val" : "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "pending final vetting" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000226", "lbl" : "placeholder removed", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "placeholder removed" - } ] - } + "type" : "INDIVIDUAL" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000227", "lbl" : "terms merged", "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "terms merged" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "An editor note should explain what were the merged terms and the reason for the merge." } ] @@ -10538,9 +9960,6 @@ "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "term imported" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use." } ] @@ -10551,9 +9970,6 @@ "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "term split" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created." } ] @@ -10565,17 +9981,7 @@ "meta" : { "definition" : { "val" : "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has obsolescence reason" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Melanie Courtot" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000233", @@ -10590,29 +9996,8 @@ "val" : "IAO:0000233" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "term tracker item" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_class_level", - "val" : "true" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", "val" : "true" @@ -10627,17 +10012,8 @@ "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "universal" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf" } ] } }, { @@ -10649,14 +10025,8 @@ "val" : "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "defined class" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" } ] } }, { @@ -10668,14 +10038,8 @@ "val" : "A named class expression is a logical expression that is given a name. The name can be used in place of the expression." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "named class expression" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" } ] } }, { @@ -10685,17 +10049,7 @@ "meta" : { "definition" : { "val" : "Terms with this status should eventually replaced with a term from another ontology." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "to be replaced with external ontology term" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "group:OBI" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000424", @@ -10704,17 +10058,7 @@ "meta" : { "definition" : { "val" : "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "expand expression to" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "ObjectProperty: RO_0002104\nLabel: has plasma membrane part\nAnnotations: IAO_0000424 \"http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\"\n" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000428", @@ -10723,17 +10067,7 @@ "meta" : { "definition" : { "val" : "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "requires discussion" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "group:OBI" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000700", @@ -10747,20 +10081,8 @@ "val" : "IAO:0000700" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has ontology root term" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Nicolas Matentzoglu" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_class_level", - "val" : "true" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", "val" : "true" @@ -10777,20 +10099,7 @@ "definition" : { "val" : "Use on obsolete terms, relating the term to another term that can be used as a substitute" }, - "comments" : [ "Add as annotation triples in the granting ontology" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "term replaced by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person:Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Person:Alan Ruttenberg" - } ] + "comments" : [ "Add as annotation triples in the granting ontology" ] } }, { "id" : "http://purl.obolibrary.org/obo/NCBITaxon_1", @@ -10825,9 +10134,6 @@ "val" : "PMID:15371245" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_family" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -10842,7 +10148,7 @@ "pred" : "hasExactSynonym", "val" : "Mus" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003003", + "synonymType" : "http://purl.obolibrary.org/obo/ncbitaxon#genbank_common_name", "pred" : "hasExactSynonym", "val" : "mice" }, { @@ -10854,9 +10160,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_genus" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -10879,9 +10182,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_species" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "NCBITaxon:85055" }, { @@ -10898,9 +10198,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -10919,9 +10216,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "NCBITaxon:40673" }, { @@ -10956,9 +10250,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -10981,9 +10272,6 @@ "val" : "PMID:11791233" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11006,9 +10294,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_suborder" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11055,9 +10340,6 @@ "val" : "PMID:30257078" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_superkingdom" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11079,9 +10361,6 @@ "val" : "PMID:15522813" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_superorder" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11106,9 +10385,6 @@ "val" : "PMID:15522813" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11127,9 +10403,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11148,9 +10421,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11169,9 +10439,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11194,9 +10461,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11227,9 +10491,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_kingdom" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11243,9 +10504,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11264,9 +10522,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11284,9 +10539,6 @@ "val" : "PMID:15371245" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11300,9 +10552,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_subfamily" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "NCBITaxon:109679" }, { @@ -11328,9 +10577,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_class" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11344,9 +10590,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11369,9 +10612,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_phylum" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11398,9 +10638,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11423,9 +10660,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11439,9 +10673,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_superclass" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11460,9 +10691,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_subgenus" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11481,9 +10709,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_subphylum" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11518,9 +10743,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11543,9 +10765,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_order" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11561,15 +10780,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/77" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", - "val" : "https://orcid.org/0000-0001-5208-3432" } ] } }, { @@ -11581,9 +10794,6 @@ "val" : "Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'part disjoint with' 'defined by construct' \"\"\"\n PREFIX owl: \n PREFIX : some (\n and some (\n and some (\n and some ?Y)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { @@ -14807,33 +13577,9 @@ "definition" : { "val" : "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " }, - "xrefs" : [ { - "val" : "RO:0002103" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that part_of some ( that has_part some ( that some Y?)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "synapsed_by" } ] } }, { @@ -14845,29 +13591,8 @@ "val" : "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9990-8331" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-1617-8244" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19243617" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( and some ?Y)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] } }, { @@ -14879,26 +13604,8 @@ "val" : "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. " }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "synapsed in" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (\n http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some (\n http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { @@ -14910,20 +13617,8 @@ "val" : "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "synapses in" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that some ( that some Y?)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { @@ -14936,23 +13631,8 @@ }, "comments" : [ "N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part some (\n ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( \n\t‘synapse ; GO:0045202’ that has_part some (\n\t ‘post-synaptic membrane ; GO:0045211’ that part_of some N2))))" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that part_of some ( that some ( that some Y?)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { @@ -14964,23 +13644,8 @@ "val" : "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has synapse in" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that some Y?)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { @@ -14996,20 +13661,11 @@ "val" : "RO:0002131" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "overlaps" @@ -15022,26 +13678,7 @@ "meta" : { "definition" : { "val" : "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has fasciculating component" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", - "val" : "(forall (?x ?y) \n\t(iff \n\t\t(has_fasciculating_neuron_projection ?x ?y)\n\t\t(exists (?nps ?npbs)\t\t\n\t\t\t(and \n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?x)\n\t\t\t\t(\"neuron projection ; GO0043005\" ?y)\n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n\t\t\t\t(part_of ?nps ?y)\n\t\t\t\t(part_of ?npbs ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))\n\n\n" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002134", @@ -15051,30 +13688,9 @@ "definition" : { "val" : "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." }, - "xrefs" : [ { - "val" : "RO:0002134" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that ( some ( that some Y?)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "innervates" } ] } }, { @@ -15085,31 +13701,7 @@ "definition" : { "val" : "X continuous_with Y if and only if X and Y share a fiat boundary." }, - "xrefs" : [ { - "val" : "RO:0002150" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "connected to" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "continuous_with" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "FMA:85972" } ] @@ -15122,23 +13714,7 @@ "definition" : { "val" : "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." }, - "comments" : [ "VBO calls this homologous_to" ], - "xrefs" : [ { - "val" : "RO:0002158" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Consider obsoleting and merging with child relation, 'in homology relationship with'" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "homologous_to" - } ] + "comments" : [ "VBO calls this homologous_to" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -15148,33 +13724,9 @@ "definition" : { "val" : "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." }, - "xrefs" : [ { - "val" : "RO:0002160" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "lactation SubClassOf 'only in taxon' some 'Mammalia'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "only_in_taxon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" @@ -15182,48 +13734,15 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002161", - "lbl" : "never_in_taxon", + "lbl" : "never in taxon", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL." }, - "xrefs" : [ { - "val" : "RO:0002161" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "tooth SubClassOf 'never in taxon' value 'Aves'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", - "val" : "Class: EquivalentTo: ?X and (RO_0002162 some ?Y)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", - "val" : "Class: ?X DisjointWith: RO_0002162 some ?Y " - }, { "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_class_level", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "never_in_taxon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" @@ -15239,31 +13758,7 @@ }, "comments" : [ "Connects a biological entity to its taxon of origin." ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002162" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9227-417X" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_taxon" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] @@ -15278,26 +13773,11 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" @@ -15311,22 +13791,7 @@ "definition" : { "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" }, - "xrefs" : [ { - "val" : "RO:0002170" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "connected_to" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" }, { @@ -15336,42 +13801,16 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002175", - "lbl" : "present_in_taxon", + "lbl" : "present in taxon", "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S" }, "comments" : [ "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "applicable for taxon" - } ], - "xrefs" : [ { - "val" : "RO:0002175" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_class_level", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "present_in_taxon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" @@ -15385,25 +13824,7 @@ "definition" : { "val" : "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." }, - "xrefs" : [ { - "val" : "RO:0002176" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The M8 connects Glasgow and Edinburgh" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "connects" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" }, { @@ -15418,20 +13839,7 @@ "meta" : { "definition" : { "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." - }, - "xrefs" : [ { - "val" : "RO:0002177" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "attached to part of (anatomical structure to anatomical structure)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "attaches_to_part_of" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002178", @@ -15441,21 +13849,9 @@ "definition" : { "val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." }, - "xrefs" : [ { - "val" : "RO:0002178" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "supplies" } ] } }, { @@ -15466,21 +13862,9 @@ "definition" : { "val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." }, - "xrefs" : [ { - "val" : "RO:0002179" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "drains" } ] } }, { @@ -15496,23 +13880,11 @@ "val" : "RO:0002180" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_component" @@ -15529,32 +13901,7 @@ "definition" : { "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" }, - "comments" : [ "This is the transitive form of the develops from relation" ], - "xrefs" : [ { - "val" : "RO:0002202" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9114-8737" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-1980-3228" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "develops_from" - } ] + "comments" : [ "This is the transitive form of the develops from relation" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002203", @@ -15564,29 +13911,7 @@ "definition" : { "val" : "inverse of develops from" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "xrefs" : [ { - "val" : "RO:0002203" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-1980-3228" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "develops_into" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002206", @@ -15595,17 +13920,7 @@ "meta" : { "definition" : { "val" : "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002207", @@ -15619,31 +13934,6 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "has developmental precursor" - } ], - "xrefs" : [ { - "val" : "RO:0002207" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "FBbt" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002202" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "directly_develops_from" } ] } }, { @@ -15654,14 +13944,7 @@ "definition" : { "val" : "inverse of directly develops from" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "developmental precursor of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002211", @@ -15676,30 +13959,6 @@ "val" : "RO:0002211" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-7476-6306" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-3837-8864" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GO" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Regulation precludes parthood; the regulatory process may not be within the regulated process." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "regulates (processual)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "false" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -15720,15 +13979,6 @@ "val" : "RO:0002212" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "negatively regulates (process to process)" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002211" }, { @@ -15752,18 +14002,6 @@ "val" : "RO:0002213" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "positively regulates (process to process)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002211" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -15784,32 +14022,8 @@ "val" : "RO:0002215" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "osteoclast SubClassOf 'capable of' some 'bone resorption'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has function realized in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20123131" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/21208450" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "capable_of" @@ -15827,17 +14041,8 @@ "val" : "RO:0002216" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has function in" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "capable_of_part_of" @@ -15853,26 +14058,7 @@ "meta" : { "definition" : { "val" : "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" - }, - "xrefs" : [ { - "val" : "RO:0002219" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "surrounded_by" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002220", @@ -15887,35 +14073,11 @@ "val" : "RO:0002220" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The epidermis layer of a vertebrate is adjacent to the dermis." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This relation acts as a join point with BSPO" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "adjacent_to" @@ -15929,26 +14091,7 @@ "definition" : { "val" : "inverse of surrounded by" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "xrefs" : [ { - "val" : "RO:0002221" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "surrounds" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002222", @@ -15956,23 +14099,7 @@ "type" : "PROPERTY", "meta" : { "comments" : [ "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations." ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://en.wikipedia.org/wiki/Allen%27s_interval_algebra" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." - }, { - "pred" : "http://purl.org/dc/terms/source", - "val" : "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002223", @@ -15982,29 +14109,7 @@ "definition" : { "val" : "inverse of starts with" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002223" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Allen" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "starts" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002224", @@ -16019,26 +14124,8 @@ "val" : "RO:0002224" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "started by" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "starts_with" @@ -16051,23 +14138,7 @@ "meta" : { "definition" : { "val" : "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" - }, - "xrefs" : [ { - "val" : "RO:0002225" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "develops_from_part_of" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002226", @@ -16076,29 +14147,7 @@ "meta" : { "definition" : { "val" : "x develops_in y if x is located in y whilst x is developing" - }, - "xrefs" : [ { - "val" : "RO:0002226" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "EHDAA2" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Jonathan Bard, EHDAA2" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "develops_in" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002229", @@ -16108,26 +14157,7 @@ "definition" : { "val" : "inverse of ends with" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002229" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "ends" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002230", @@ -16142,23 +14172,8 @@ "val" : "RO:0002230" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "finished by" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "ends_with" @@ -16177,15 +14192,6 @@ "val" : "RO:0002231" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "starts with process that occurs in" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16206,15 +14212,6 @@ "val" : "RO:0002232" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "ends with process that occurs in" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16235,15 +14232,6 @@ "val" : "RO:0002233" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "consumes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16267,15 +14255,6 @@ "val" : "RO:0002234" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "produces" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16294,22 +14273,7 @@ "definition" : { "val" : "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." }, - "xrefs" : [ { - "val" : "RO:0002252" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004036", - "val" : "http://purl.obolibrary.org/obo/BFO_0000050" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "connecting_branch_of" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/issues/2212" } ] @@ -16322,11 +14286,7 @@ "definition" : { "val" : "inverse of connecting branch of" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004036", - "val" : "http://purl.obolibrary.org/obo/BFO_0000051" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002254", @@ -16335,26 +14295,7 @@ "meta" : { "definition" : { "val" : "x has developmental contribution from y iff x has some part z such that z develops from y" - }, - "xrefs" : [ { - "val" : "RO:0002254" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_developmental_contribution_from" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002255", @@ -16364,14 +14305,7 @@ "definition" : { "val" : "inverse of has developmental contribution from" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002256", @@ -16380,44 +14314,7 @@ "meta" : { "definition" : { "val" : "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" - }, - "xrefs" : [ { - "val" : "RO:0002256" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9114-8737" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "induced by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GO:0001759" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "developmentally_induced_by" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002257", @@ -16426,14 +14323,7 @@ "meta" : { "definition" : { "val" : "Inverse of developmentally induced by" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002258", @@ -16445,17 +14335,8 @@ }, "comments" : [ "This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "false" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "In general you should not use this relation to make assertions - use one of the more specific relations below this one" } ] } }, { @@ -16468,9 +14349,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of" } ] @@ -16489,9 +14367,6 @@ "val" : "affects" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within" } ] @@ -16504,27 +14379,9 @@ "definition" : { "val" : "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" }, - "xrefs" : [ { - "val" : "RO:0002285" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "replaces" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "developmentally_replaces" } ] } }, { @@ -16534,31 +14391,12 @@ "meta" : { "definition" : { "val" : "Inverse of developmentally preceded by" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002287", "lbl" : "part of developmental precursor of", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002292", "lbl" : "expresses", @@ -16566,14 +14404,7 @@ "meta" : { "definition" : { "val" : "y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002295", @@ -16587,14 +14418,8 @@ "val" : "RO:0002295" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" @@ -16619,18 +14444,6 @@ "val" : "RO:0002296" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "every flower development (GO:0009908) results in development of some flower (PO:0009046)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.geneontology.org/GO.doc.development.shtml" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16640,7 +14453,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -16648,21 +14461,6 @@ "val" : "RO:0002297" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:mtg_berkeley_2013" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16683,21 +14481,6 @@ "val" : "RO:0002298" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:mtg_berkeley_2013" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16718,21 +14501,6 @@ "val" : "RO:0002299" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:mtg_berkeley_2013" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16754,12 +14522,6 @@ "val" : "RO:0002304" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002411" - }, { - "pred" : "http://purl.org/dc/terms/creator", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16785,9 +14547,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002411" - }, { - "pred" : "http://purl.org/dc/terms/creator", - "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" @@ -16810,18 +14569,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "inheres in part of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" @@ -16840,15 +14587,6 @@ "val" : "RO:0002315" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:mtg_berkeley_2013" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16863,14 +14601,7 @@ "meta" : { "definition" : { "val" : "A relationship that holds via some environmental process" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002323", @@ -16879,17 +14610,7 @@ "meta" : { "definition" : { "val" : "A mereological relationship or a topological relationship" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002324", @@ -16898,14 +14619,7 @@ "meta" : { "definition" : { "val" : "A relationship that holds between entities participating in some developmental process (GO:0032502)" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002327", @@ -16917,30 +14631,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a particular instances of akt-2 enables some instance of protein kinase activity" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "catalyzes" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "executes" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is catalyzing" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is executing" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Enables" } ] @@ -16952,23 +14642,7 @@ "meta" : { "definition" : { "val" : "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." - }, - "xrefs" : [ { - "val" : "RO:0002328" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This is a grouping relation that collects relations used for the purpose of connecting structure and function" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "functionally_related_to" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002329", @@ -16977,14 +14651,7 @@ "meta" : { "definition" : { "val" : "this relation holds between c and p when c is part of some c', and c' is capable of p." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "false" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002330", @@ -16993,14 +14660,7 @@ "meta" : { "definition" : { "val" : "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002331", @@ -17011,15 +14671,6 @@ "val" : "c involved_in p if and only if c enables some process p', and p' is part of p" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "actively involved in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "enables part of" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Involved_in" } ] @@ -17036,18 +14687,6 @@ "val" : "RO:0002332" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "regulates levels of (process to entity)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17065,9 +14704,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Enabled_by" } ] @@ -17085,12 +14721,6 @@ "val" : "RO:0002334" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "regulated by (processual)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17111,9 +14741,6 @@ "val" : "RO:0002335" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17134,9 +14761,6 @@ "val" : "RO:0002336" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17151,14 +14775,7 @@ "meta" : { "definition" : { "val" : "A relationship that holds via some process of localization" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is a grouping relation." - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002338", @@ -17173,9 +14790,6 @@ "val" : "RO:0002338" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17196,9 +14810,6 @@ "val" : "RO:0002339" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17218,9 +14829,6 @@ "val" : "RO:0002341" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17241,9 +14849,6 @@ "val" : "RO:0002342" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17260,12 +14865,6 @@ "val" : "RO:0002343" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'pollen tube growth' results_in growth_of some 'pollen tube'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17282,12 +14881,6 @@ "val" : "RO:0002344" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17302,23 +14895,7 @@ "meta" : { "definition" : { "val" : "is member of is a mereological relation between a item and a collection." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "An organism that is a member of a population of organisms" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is member of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "member part of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "SIO" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002351", @@ -17327,23 +14904,7 @@ "meta" : { "definition" : { "val" : "has member is a mereological relation between a collection and an item." - }, - "xrefs" : [ { - "val" : "RO:0002351" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "SIO" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_member" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002352", @@ -17353,20 +14914,7 @@ "definition" : { "val" : "inverse of has input" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002352" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "input_of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002353", @@ -17381,14 +14929,8 @@ "val" : "RO:0002353" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "output_of" @@ -17397,26 +14939,11 @@ }, { "id" : "http://purl.obolibrary.org/obo/RO_0002354", "lbl" : "formed as result of", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002360", "lbl" : "has dendrite location", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.org/dc/terms/source", - "val" : "http://neurolex.org/wiki/Property:DendriteLocation" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002371", "lbl" : "attached to", @@ -17425,23 +14952,7 @@ "definition" : { "val" : "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002371" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "attached to (anatomical structure to anatomical structure)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "attaches_to" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002372", @@ -17451,22 +14962,7 @@ "definition" : { "val" : "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." }, - "xrefs" : [ { - "val" : "RO:0002372" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Wikipedia:Insertion_(anatomy)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_muscle_origin" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://dbpedia.org/property/origin" } ] @@ -17479,22 +14975,7 @@ "definition" : { "val" : "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." }, - "xrefs" : [ { - "val" : "RO:0002373" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Wikipedia:Insertion_(anatomy)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_muscle_insertion" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://dbpedia.org/property/insertion" } ] @@ -17507,78 +14988,24 @@ "definition" : { "val" : "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004036", - "val" : "http://purl.obolibrary.org/obo/BFO_0000050" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/issues/170" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002376", - "lbl" : "tributary of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002376" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Deschutes River tributary_of Columbia River" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "inferior epigastric vein tributary_of external iliac vein" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "drains into" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "drains to" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "tributary channel of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://en.wikipedia.org/wiki/Tributary" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.medindia.net/glossary/venous_tributary.htm" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "tributary_of" + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png" }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/170" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002376", + "lbl" : "tributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://dbpedia.org/ontology/drainsTo" }, { @@ -17593,17 +15020,7 @@ "meta" : { "definition" : { "val" : "x spatially_coextensive_with y if and inly if x and y have the same location" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A lump of clay and a statue" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002380", @@ -17614,22 +15031,7 @@ "val" : "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002380" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "branching_part_of" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/issues/2212" }, { @@ -17644,14 +15046,7 @@ "meta" : { "definition" : { "val" : "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002385", @@ -17660,23 +15055,7 @@ "meta" : { "definition" : { "val" : "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" - }, - "xrefs" : [ { - "val" : "RO:0002385" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_potential_to_developmentally_contribute_to" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002386", @@ -17685,14 +15064,7 @@ "meta" : { "definition" : { "val" : "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002387", @@ -17701,23 +15073,7 @@ "meta" : { "definition" : { "val" : "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" - }, - "xrefs" : [ { - "val" : "RO:0002387" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_potential_to_develop_into" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002388", @@ -17726,14 +15082,7 @@ "meta" : { "definition" : { "val" : "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002404", @@ -17747,12 +15096,6 @@ "val" : "RO:0002404" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17769,12 +15112,6 @@ "val" : "RO:0002405" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17791,15 +15128,6 @@ "val" : "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "indirectly activates" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002579", - "val" : "http://purl.obolibrary.org/obo/RO_0002213" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Indirectly_positively_regulates" } ] @@ -17813,15 +15141,6 @@ "val" : "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "indirectly inhibits" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002579", - "val" : "http://purl.obolibrary.org/obo/RO_0002212" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Indirectly_negatively_regulates" } ] @@ -17838,12 +15157,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." } ] } }, { @@ -17859,9 +15172,6 @@ "val" : "RO:0002411" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17881,12 +15191,6 @@ "val" : "RO:0002412" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002411" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17912,12 +15216,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "influences (processual)" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" @@ -17939,12 +15237,6 @@ "val" : "RO:0002427" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17959,11 +15251,7 @@ "meta" : { "definition" : { "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002429", @@ -17972,14 +15260,7 @@ "meta" : { "definition" : { "val" : "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002428" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002430", @@ -17990,9 +15271,6 @@ "val" : "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002428" } ] @@ -18008,12 +15286,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "OWL does not allow defining object properties via a Union" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "involved in or reguates" } ] } }, { @@ -18031,15 +15303,6 @@ "val" : "enables activity in" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A protein that enables activity in a cytosol." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "executes activity in" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Is_active_in" } ] @@ -18051,20 +15314,7 @@ "meta" : { "definition" : { "val" : "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." - }, - "xrefs" : [ { - "val" : "RO:0002433" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "contributes_to_morphology_of" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002434", @@ -18085,18 +15335,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Considering relabeling as 'pairwise interacts with'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" - }, { - "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", - "val" : "http://purl.obolibrary.org/obo/MI_0914" } ] } }, { @@ -18108,20 +15349,8 @@ "val" : "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "binds" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "molecularly binds with" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ECO_0000353" - }, { - "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", - "val" : "http://purl.obolibrary.org/obo/MI_0915" } ] } }, { @@ -18132,12 +15361,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Axiomatization to GO to be added later" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." } ] } }, { @@ -18151,13 +15374,6 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "molecularly controls" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" } ] } }, { @@ -18171,16 +15387,6 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "molecularly decreases activity of" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "directly inhibits" } ] } }, { @@ -18194,31 +15400,12 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "molecularly increases activity of" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "directly activates" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002464", "lbl" : "helper property (not for use in curation)", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002473", "lbl" : "composed primarily of", @@ -18227,29 +15414,7 @@ "definition" : { "val" : "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002473" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "composed_primarily_of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002479", @@ -18259,22 +15424,12 @@ "definition" : { "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002481", "lbl" : "is kinase activity", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002485", "lbl" : "receives input from", @@ -18283,9 +15438,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "See notes for inverse relation" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { @@ -18296,24 +15448,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002487", "lbl" : "relation between physical entity and a process or stage", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage." - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002488", "lbl" : "existence starts during", @@ -18321,20 +15461,7 @@ "meta" : { "definition" : { "val" : "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." - }, - "xrefs" : [ { - "val" : "RO:0002488" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_starts_during" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002489", @@ -18343,20 +15470,7 @@ "meta" : { "definition" : { "val" : "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." - }, - "xrefs" : [ { - "val" : "RO:0002489" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_starts_with" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002490", @@ -18366,11 +15480,7 @@ "definition" : { "val" : "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002491", @@ -18384,19 +15494,6 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "exists during" - } ], - "xrefs" : [ { - "val" : "RO:0002491" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_starts_and_ends_during" } ] } }, { @@ -18407,24 +15504,7 @@ "definition" : { "val" : "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "ceases_to_exist_during" - } ], - "xrefs" : [ { - "val" : "RO:0002492" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_ends_during" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002493", @@ -18434,20 +15514,7 @@ "definition" : { "val" : "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "xrefs" : [ { - "val" : "RO:0002493" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_ends_with" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002494", @@ -18456,20 +15523,7 @@ "meta" : { "definition" : { "val" : "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" - }, - "xrefs" : [ { - "val" : "RO:0002494" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "transformation_of" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002495", @@ -18478,23 +15532,7 @@ "meta" : { "definition" : { "val" : "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" - }, - "xrefs" : [ { - "val" : "RO:0002495" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002494" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "immediate_transformation_of" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002496", @@ -18504,20 +15542,7 @@ "definition" : { "val" : "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "xrefs" : [ { - "val" : "RO:0002496" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_starts_during_or_after" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002497", @@ -18527,20 +15552,7 @@ "definition" : { "val" : "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "xrefs" : [ { - "val" : "RO:0002497" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_ends_during_or_before" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002500", @@ -18549,11 +15561,7 @@ "meta" : { "definition" : { "val" : "A relationship between a material entity and a process where the material entity has some causal role that influences the process" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002501", @@ -18562,17 +15570,7 @@ "meta" : { "definition" : { "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002502", @@ -18580,9 +15578,6 @@ "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/BFO_0000169" } ] @@ -18595,15 +15590,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." } ] } }, { @@ -18613,55 +15599,18 @@ "meta" : { "definition" : { "val" : "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." - }, - "xrefs" : [ { - "val" : "RO:0002551" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has supporting framework" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_skeleton" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002559", "lbl" : "causally influenced by", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "causally influenced by (entity-centric)" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002563", "lbl" : "interaction relation helper property", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29" }, { @@ -18672,13 +15621,7 @@ }, { "id" : "http://purl.obolibrary.org/obo/RO_0002564", "lbl" : "molecular interaction relation helper property", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002565", "lbl" : "results in movement of", @@ -18692,11 +15635,6 @@ "val" : "RO:0002565" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -18711,20 +15649,7 @@ "meta" : { "definition" : { "val" : "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "causally influences (entity-centric)" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002567", @@ -18733,14 +15658,7 @@ "meta" : { "definition" : { "val" : "A relation that holds between elements of a musculoskeletal system or its analogs." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002568", @@ -18749,23 +15667,7 @@ "meta" : { "definition" : { "val" : "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." - }, - "xrefs" : [ { - "val" : "RO:0002568" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Wikipedia:Antagonist_(muscle)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_muscle_antagonist" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002569", @@ -18775,20 +15677,7 @@ "definition" : { "val" : "inverse of branching part of" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002569" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_branching_part" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002570", @@ -18798,26 +15687,7 @@ "definition" : { "val" : "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002570" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "UBERON:cjm" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "conduit_for" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002571", @@ -18827,23 +15697,7 @@ "definition" : { "val" : "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002571" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "lumen_of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002572", @@ -18853,20 +15707,7 @@ "definition" : { "val" : "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002572" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "luminal_space_of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002576", @@ -18876,20 +15717,7 @@ "definition" : { "val" : "inverse of has skeleton" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "xrefs" : [ { - "val" : "RO:0002576" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "skeleton_of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002578", @@ -18904,18 +15732,6 @@ "val" : "RO:0002578" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "directly regulates (processual)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002211" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -18923,24 +15739,6 @@ "val" : "directly_regulates" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002581", - "lbl" : "is a defining property chain axiom", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002582", - "lbl" : "is a defining property chain axiom where second argument is reflexive", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R." - } - } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002584", "lbl" : "has part structure that is capable of", @@ -18948,14 +15746,7 @@ "meta" : { "definition" : { "val" : "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002586", @@ -19029,12 +15820,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] } }, { @@ -19044,14 +15829,7 @@ "meta" : { "definition" : { "val" : "Holds between c and p if and only if c is capable of some activity a, and a regulates p." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "pyrethroid -> growth" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002597", @@ -19060,11 +15838,7 @@ "meta" : { "definition" : { "val" : "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002598", @@ -19073,14 +15847,7 @@ "meta" : { "definition" : { "val" : "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "renin -> arteriolar smooth muscle contraction" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002608", @@ -19094,9 +15861,6 @@ "val" : "RO:0002608" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -19117,15 +15881,6 @@ "val" : "RO:0002629" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "directly positively regulates (process to process)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002578" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -19149,12 +15904,6 @@ "val" : "RO:0002630" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "directly negatively regulates (process to process)" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002578" }, { @@ -19182,17 +15931,8 @@ "val" : "RO:0003000" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9114-8737" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "produces" @@ -19211,17 +15951,8 @@ "val" : "RO:0003001" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9114-8737" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "produced_by" @@ -19330,9 +16061,6 @@ "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002264" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { @@ -19373,9 +16101,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002263" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { @@ -19434,9 +16159,6 @@ "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002418" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { @@ -19467,11 +16189,7 @@ "meta" : { "definition" : { "val" : "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0012000", @@ -19733,9 +16451,6 @@ "xrefs" : [ "PMID:19243617" ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" - }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1617-8244" }, { @@ -19753,9 +16468,6 @@ "xrefs" : [ "PMID:19243617" ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" - }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1617-8244" }, { @@ -19776,21 +16488,6 @@ "val" : "utilizes" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A diagnostic testing device utilizes a specimen." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9625-1899" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-2620-0345" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "See github ticket https://github.com/oborel/obo-relations/issues/497" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-11-08T12:00:00Z" } ] @@ -19986,15 +16683,6 @@ "val" : "ZFA:0000107" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A cavitated compound organ that transduces light waves into neural signals.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "FMA distinguishes Eye (subdivision of face) which has its parts an Eyeball (organ), as well as other structures, and the orbit of skull. MA includes eyelid, conjunctiva and lacrimal apparatus as part of MA:eye - consistent with FMA - so we can infer that MA:eye is more like FMA:eye than FMA:eyeball. For other AOs this distinction is less meaningful - e.g. ZFA has no eyelid; XAO has no eyelid, but it has conjuctiva, which is considered part of the xao:eye. GO considers eyelid development part of eye development. See also notes on optic nerve - XAO, AAO and BTO consider this part of the eye. MA considers the eye muscles part of the eye, whereas FMA has a class 'orbital content' for this" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -20062,8 +16750,6 @@ "val" : "EHDAA:500" }, { "val" : "EMAPA:35955" - }, { - "val" : "FBbt:00005155" }, { "val" : "GAID:63" }, { @@ -20111,12 +16797,6 @@ "val" : "galen:Tube" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts)" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "tubular" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -20201,18 +16881,6 @@ "val" : "galen:Head" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000948" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -20261,15 +16929,6 @@ "val" : "ZFA:0005425" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -20341,16 +17000,11 @@ "xrefs" : [ "FMA:82482" ] } ], "xrefs" : [ { - "val" : "EMAPA:25036" - }, { "val" : "FMA:82482" }, { "val" : "galen:Wall" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in FMA, serosa is a wall" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0009915" }, { @@ -20388,8 +17042,6 @@ "val" : "EHDAA2:0003003" }, { "val" : "EMAPA:0" - }, { - "val" : "FBbt:00007001" }, { "val" : "FMA:305751" }, { @@ -20489,12 +17141,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -20529,12 +17175,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -20573,9 +17213,6 @@ "val" : "SCTID:91717005" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "currently defined in a very broad sense, may be replaced by more specific classes in the future" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { @@ -20706,9 +17343,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "ncit:Death is an outcome" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -20805,8 +17439,6 @@ "xrefs" : [ "MP:0012532" ] } ], "xrefs" : [ { - "val" : "BTO:0006242" - }, { "val" : "EHDAA2:0001968" }, { "val" : "EHDAA:1494" @@ -20834,12 +17466,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0002346" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "(or external ectoderm) forms the following structures: Skin Epithelium of the mouth and nasal cavity saliavary glands, and glands of mouth and nasal cavity Enamel - as a side note dentin and dental pulp are formed from ectomesenchyme which is derived from ectoderm Epithelium of pineal and pituitary glands Lens and cornea of the eye Apical ectodermal ridge inducing development of the limb buds of the embryo. Sensory receptors in epidermis" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -20883,9 +17509,6 @@ "val" : "WBls:0000103" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -21002,12 +17625,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "the WBls class 'all stages' belongs here as it is the superclass of other WBls stages" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -21060,8 +17677,6 @@ "val" : "EHDAA:27" }, { "val" : "FBdv:00005288" - }, { - "val" : "IDOMAL:0000302" }, { "val" : "NCIT:C12601" }, { @@ -21076,9 +17691,6 @@ "val" : "ZFS:0000001" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -21256,12 +17868,6 @@ "val" : "XAO:1000006" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002174", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7955" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In zebrafish, the times of neurulation and segmentation overlap so extensively there is no distinct neurula period of development, such as occurs largely before segmentation in amphibian embryos." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -21333,8 +17939,6 @@ } ], "xrefs" : [ { "val" : "CARO:0001001" - }, { - "val" : "FBbt:00005099" }, { "val" : "NLX:147821" } ], @@ -21449,8 +18053,6 @@ "val" : "EHDAA:542" }, { "val" : "EMAPA:16262" - }, { - "val" : "FBbt:00003126" }, { "val" : "FMA:49184" }, { @@ -21493,21 +18095,6 @@ "val" : "http://purl.obolibrary.org/obo/uberon/images/lamprey_sucker_rosava_3238889218.jpg" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "oral" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -21585,23 +18172,8 @@ "val" : "galen:Blood" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid." - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -21734,8 +18306,6 @@ "val" : "BTO:0001485" }, { "val" : "EFO:0000801" - }, { - "val" : "EMAPA:35578" }, { "val" : "FMA:72954" }, { @@ -21758,12 +18328,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system that consists of the muscles of the body.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -21814,8 +18378,6 @@ "val" : "EHDAA2:0003004" }, { "val" : "EMAPA:35178" - }, { - "val" : "FBbt:00007019" }, { "val" : "FMA:9669" }, { @@ -21888,8 +18450,6 @@ "val" : "CARO:0000005" }, { "val" : "EHDAA2:0003005" - }, { - "val" : "FBbt:00007017" }, { "val" : "FMA:5897" }, { @@ -21943,8 +18503,6 @@ "val" : "CARO:0000006" }, { "val" : "EHDAA2:0003006" - }, { - "val" : "FBbt:00007016" }, { "val" : "FMA:67165" }, { @@ -21995,8 +18553,6 @@ "val" : "CARO:0000007" }, { "val" : "EHDAA2:0003007" - }, { - "val" : "FBbt:00007015" }, { "val" : "FMA:67112" }, { @@ -22075,14 +18631,10 @@ "val" : "EMAPA:16103" }, { "val" : "EV:0100000" - }, { - "val" : "FBbt:00004856" }, { "val" : "FMA:7149" }, { "val" : "HAO:0000011" - }, { - "val" : "IDOMAL:0002460" }, { "val" : "MA:0000003" }, { @@ -22191,8 +18743,6 @@ "val" : "EMAPA:25765" }, { "val" : "EV:0100016" - }, { - "val" : "FBbt:00000001" }, { "val" : "FMA:256135" }, { @@ -22234,9 +18784,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "organismal" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -22286,8 +18833,6 @@ "val" : "EHDAA2:0003032" }, { "val" : "EMAPA:36031" - }, { - "val" : "FBbt:00007009" }, { "val" : "FMA:7153" }, { @@ -22362,8 +18907,6 @@ "val" : "CARO:0000040" }, { "val" : "EHDAA2:0003040" - }, { - "val" : "FBbt:00007013" }, { "val" : "FMA:63863" }, { @@ -22402,8 +18945,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "xrefs" : [ { - "val" : "FBbt:00007277" - }, { "val" : "VHOG:0001737" } ], "basicPropertyValues" : [ { @@ -22460,8 +19001,6 @@ "val" : "EHDAA2:0003043" }, { "val" : "EMAPA:35868" - }, { - "val" : "FBbt:00007003" }, { "val" : "FMA:9637" }, { @@ -22532,8 +19071,6 @@ "val" : "CARO:0000055" }, { "val" : "EHDAA2:0003055" - }, { - "val" : "FBbt:00007010" }, { "val" : "HAO:0000055" }, { @@ -22598,8 +19135,6 @@ "val" : "EHDAA2:0003066" }, { "val" : "EMAPA:32738" - }, { - "val" : "FBbt:00007005" }, { "val" : "FMA:9639" }, { @@ -22628,12 +19163,6 @@ "val" : "ZFA:0001486" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "epithelial" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -22690,9 +19219,6 @@ "val" : "ZFA:0001498" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Unilaminar epithelium that consists of a single layer of squamous cells.[CARO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -22791,9 +19317,6 @@ "val" : "ZFA:0001490" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -22850,9 +19373,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Epithelium that consists of a single layer of epithelial cells.[CARO]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -22895,18 +19415,6 @@ "val" : "Wikipedia:Thorax" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000026" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000033" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0002417" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -22955,14 +19463,10 @@ "val" : "EHDAA:38" }, { "val" : "EMAPA:16039" - }, { - "val" : "FBbt:00000052" }, { "val" : "FMA:69068" }, { "val" : "GAID:963" - }, { - "val" : "IDOMAL:0000646" }, { "val" : "MAT:0000226" }, { @@ -22989,12 +19493,6 @@ "val" : "http://neurolex.org/wiki/Category:Embryonic_organism" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "embryonic" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -23043,8 +19541,6 @@ "val" : "BTO:0000556" }, { "val" : "EMAPA:36033" - }, { - "val" : "FBbt:00000110" }, { "val" : "FMA:69069" }, { @@ -23071,9 +19567,6 @@ "val" : "ZFA:0001122" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -23109,8 +19602,6 @@ "val" : "EMAPA:16069" }, { "val" : "EV:0100003" - }, { - "val" : "FBbt:00000111" }, { "val" : "FMA:69070" }, { @@ -23141,15 +19632,6 @@ "val" : "ZFA:0000016" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "ectodermal" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -23189,8 +19671,6 @@ "val" : "EMAPA:16062" }, { "val" : "EV:0100005" - }, { - "val" : "FBbt:00000125" }, { "val" : "FMA:69071" }, { @@ -23219,12 +19699,6 @@ "val" : "ZFA:0000017" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "endodermal" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -23279,8 +19753,6 @@ "val" : "EMAPA:16083" }, { "val" : "EV:0100006" - }, { - "val" : "FBbt:00000126" }, { "val" : "FMA:69072" }, { @@ -23311,18 +19783,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Primary germ layer that is the middle of the embryonic germ layers.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "mesodermal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0003263" @@ -23382,8 +19842,6 @@ "val" : "EHDAA2:0001929" }, { "val" : "EMAPA:16263" - }, { - "val" : "FBbt:00000439" }, { "val" : "FMA:295846" }, { @@ -23404,18 +19862,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "stomodeal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -23543,18 +19989,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Do not classify under 'cranial nerve', as this is not a true nerve - should be classified as evaginated sensory afferent[ISBN:0471888893]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A collection of nerve cells that project visual information from the eyes to the brain. (Source: BioGlossary, www.Biology-Text.com)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Fibrous, somatic sensory element covered by a fibrous connective-tissue sheath and is continuous with the layer of nerve cells on the inner surface of the eye.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup (reference 1); The (optic) stalk persists as the optic nerve (reference 2).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "(relaion to eye): MA, XAO, AAO and BTO consider this part of the eye. This is in contrast to GO, FMA, EHDAA2 (FMA has a class 'intra-ocular part of optic nerve' which represents the region of overlap). Relation to brain: part of diencephalon in EHDAA2, ZFA. In NIF, has the optic nerve root as part, which is a feature part of the diencphalon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -23645,21 +20079,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "cardiac" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -23734,8 +20153,6 @@ "val" : "EMAPA:16894" }, { "val" : "EV:0100164" - }, { - "val" : "FBbt:00005095" }, { "val" : "FMA:50801" }, { @@ -23785,18 +20202,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO)" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -23828,9 +20233,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO - merge with cell layer?" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "laminar" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -23933,12 +20335,6 @@ "val" : "neuronames:459" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The point at which fibers of the optic nerves cross.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The chiasm has been studied in great detail in some animals, while in others relatively little or nothing is known. Although there are some gross architectural features that are conserved within some animals, such as birds and fish, the general picture is one of diversity. This review will attempt to consider the key features of such diversity of chiasmatic organisation in vertebrates and the mechanisms that sculpt them from the limited literature that is available. However, as so much research has been undertaken on the structure and development of the chiasm in laboratory animals, any review must consider the information that has been gleaned from them and hope that future studies will determine whether the features revealed in these animals, and the underlying mechanisms that generate them, have a common vertebrate plan.[uncertain][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -24013,12 +20409,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "corneal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals. In fish, and aquatic vertebrates in general, the cornea plays no role in focusing light, since it has virtually the same refractive index as water" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -24110,17 +20500,8 @@ "val" : "ZFA:0000035" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0002049" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "This class excludes compound eye corneal lenses." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -24220,15 +20601,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The portion of the eye developing from the optic primordium and including the neural retina and the retinal pigment layer. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "retinal" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -24265,8 +20637,6 @@ "val" : "EFO:0000827" }, { "val" : "EV:0100336" - }, { - "val" : "FBbt:00005162" }, { "val" : "GAID:69" }, { @@ -24279,20 +20649,8 @@ "val" : "Wikipedia:Eye" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This class encompasses a variety of light-detecting structures from different phyla with no implication of homology, from the compound insect eye to the vertebrate camera-type eye (distinct classes are provided for each)" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "ocular" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "optic" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000010", - "val" : "Note that whilst this is classified as an organ, it is in fact more of a unit composed of different structures: in Drosophila, it includes the interommatidial bristle as a part; we consider here the vertebrate eye to include the eyeball/eye proper as a part, with the eye having as parts (when present): eyelids, conjuctiva," }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -24372,12 +20730,6 @@ "val" : "galen:Joint" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -24415,10 +20767,6 @@ "val" : "CALOHA:TS-1293" }, { "val" : "EFO:0000793" - }, { - "val" : "EV:0100056" - }, { - "val" : "FBbt:00005055" }, { "val" : "FMA:7152" }, { @@ -24453,15 +20801,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "digestive" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -24487,17 +20826,12 @@ "val" : "AAO:0000959" }, { "val" : "CALOHA:TS-2103" - }, { - "val" : "MESH:D002319" }, { "val" : "VHOG:0001248" }, { "val" : "Wikipedia:Circulatory_system" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "the cardiovascular system and the lymphatic system are parts of the circulatory system" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_147099" }, { @@ -24506,18 +20840,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6157" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002174", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6231" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -24569,13 +20894,9 @@ "val" : "musculature system" } ], "xrefs" : [ { - "val" : "AAO:0011066" - }, { "val" : "BTO:0000887" }, { "val" : "EFO:0001949" - }, { - "val" : "EMAPA:32715" }, { "val" : "EMAPA:35577" }, { @@ -24598,12 +20919,6 @@ "val" : "ZFA:0000548" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0001474" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -24655,8 +20970,6 @@ "val" : "EMAPA:16469" }, { "val" : "EV:0100162" - }, { - "val" : "FBbt:00005093" }, { "val" : "FMA:7157" }, { @@ -24696,21 +21009,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "nervous" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "neural" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -24774,8 +21072,6 @@ "val" : "EMAPA:16754" }, { "val" : "EV:0100163" - }, { - "val" : "FBbt:00005094" }, { "val" : "FMA:55675" }, { @@ -24811,18 +21107,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Part of the nervous system which includes the brain and spinal cord.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The brain and spinal cord. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO)." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -24865,17 +21149,12 @@ "val" : "BIRNLEX:1649" }, { "val" : "EV:0100304" - }, { - "val" : "FBbt:00005100" }, { "val" : "FMA:83847" }, { "val" : "NLX:147822" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "White matter structure of CNS that contains axons that arise predominantly in one central nervous system part and terminate in another. Tracts are generally named by their region or origin followed by their region of primary termination, e.g., mammillothalamic tract contains axons that arise from neurons in the mammillary bodies and terminate in the thalamus. (CUMBO)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -24997,8 +21276,6 @@ "val" : "EHDAA2:0003094" }, { "val" : "EMAPA:16192" - }, { - "val" : "FBbt:00007692" }, { "val" : "FMA:75259" }, { @@ -25021,12 +21298,6 @@ "val" : "ZFA:0000282" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -25071,8 +21342,6 @@ "val" : "EFO:0001652" }, { "val" : "EHDAA2:0003171" - }, { - "val" : "FBbt:00005495" }, { "val" : "FMA:86589" }, { @@ -25135,8 +21404,6 @@ "val" : "FMA:293882" }, { "val" : "MAT:0000069" - }, { - "val" : "MESH:D054259" }, { "val" : "MIAA:0000069" }, { @@ -25159,18 +21426,6 @@ "val" : "neuronames:1365" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -25202,8 +21457,6 @@ "val" : "CARO:0000000" }, { "val" : "EHDAA2:0002229" - }, { - "val" : "FBbt:10000000" }, { "val" : "FMA:62955" }, { @@ -25327,18 +21580,6 @@ "val" : "galen:SmoothMuscleTissue" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) the first bilateral animals possessed only smooth muscles with the molecular repertoire necessary to build a striated muscle. (...) it is more parsimonious to regard striated muscle cells as a sister cell type to the smooth muscle cells. In this scenario, striated and smooth muscles would have arisen in the stem lineage that led to the Nephrozoa (i.e. all Bilateria exclusive the acoelomorphs) (Hejnol et al., 2009), from an 'acoel-like' smooth muscle, by segregation and divergence of functions and through differential recruitment of additional genes[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000013", - "val" : "GO uses visceral and smooth interchangeably. However visceral can also be used in the sense of the viscera. Many fly annotations to smooth muscle terms. If we want to be inclusive of insects have to have a general definition of tissue that includes cells." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -25445,12 +21686,6 @@ "val" : "galen:Back" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "dorsal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In humans, called the back, a large posterior area of the human body, rising from the top of the buttocks to the back of the neck and the shoulders. It is the surface opposite to the chest, its height being defined by the vertebral column (commonly referred to as the spine or backbone) and its breadth being supported by the ribcage and shoulders. The spinal canal runs through the spine and provides nerves to the rest of the body" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -25512,27 +21747,6 @@ "val" : "ZFA:0000434" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0001016" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "System that provides physical support to the organism.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "skeletal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -25616,18 +21830,6 @@ "val" : "galen:Face" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The area that extends from the median ocellus to the oral foramen[HAO]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "facial" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "The face develops from outward growth of tissue located rostral to the cranium & pharynx. The lower jaw and most of the upper jaw are formed by growth of the first pharyngeal (branchial) arch. The upper incisor region and the nose and forehead (frontal region) are formed from tissue located rostral to the neural tube (frontonasal prominence)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -25683,14 +21885,10 @@ "val" : "EHDAA:518" }, { "val" : "EMAPA:16247" - }, { - "val" : "FBbt:00003125" }, { "val" : "FMA:45615" }, { "val" : "MA:0000917" - }, { - "val" : "MESH:D041981" }, { "val" : "NCIT:C34082" }, { @@ -25717,21 +21915,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The alimentary or digestive tract, and associated organs.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "FMA also has a term 'gastrointestinal tract', but this includes the liver." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000013", - "val" : "we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -25809,10 +21992,6 @@ "xrefs" : [ "ZFA:0005145" ] } ], "xrefs" : [ { - "val" : "AAO:0011066" - }, { - "val" : "EMAPA:32715" - }, { "val" : "EMAPA:37474" }, { "val" : "EV:0100146" @@ -25836,15 +22015,6 @@ "val" : "galen:Muscle" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of tissue composed of contractile fibers.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "muscular" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -25907,24 +22077,6 @@ "val" : "Wikipedia:Eyelid" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "blepharic" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "palpebral" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In humans the upper and lower eyelid consists of the following layers, starting anteriorly: (1) skin, (2) a layer of subcutaneous connective tissue, (3) a layer of striated muscle fibres of the orbicularis muscle, (4) a layer of submuscular connective tissue, (5) a fibrous layer, including the tarsal plates, (6) a layer of smooth muscle, (7) the palpebral conjunctiva." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "Consider adding 'eye surface', like MA" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "FMA divides this into skin, fascia, conjunctiva" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000202", - "val" : "http://purl.obolibrary.org/obo/FMA_75178" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -25997,12 +22149,6 @@ "val" : "Wikipedia:Anterior_chamber_of_eyeball" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The part of the eyeball between the cornea and the iris, filled with aqueous humor. [TFD][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "space in EHDAA2 - consider adding Cavity of anterior chamber of eyeball" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -26077,9 +22223,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7955" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "uveal" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26151,18 +22294,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The opaque muscular contractile diaphragm suspended in the aqueous humour in front of the lens of the eye. The organ is perforated by the pupil and continues peripherally with the ciliary body. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "iridial" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "The avian iris and ciliary body undergoes a transition from smooth-to-striated muscle during embryonic development [DOI:dx.doi.org/10.1006/dbio.1998.9019]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26270,15 +22401,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of tissue comprised of four to six layers of nonkeratinized, stratified squamous cells and represents approximately 60% of the thickness of the cornea.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In Humans: It consists of several layers of cells. The cells of the deepest layer are columnar; then follow two or three layers of polyhedral cells, the majority of which are prickle cells similar to those found in the stratum mucosum of the cuticle. Lastly, there are three or four layers of squamous cells, with flattened nuclei" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In zebrafish: nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26336,27 +22458,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The sclera, also known as the white part of the eye, is the opaque (usually white, though certain animals, such as horses and lizards, can have black sclera), fibrous, protective, outer layer of the eye containing collagen and elastic fiber. It is derived from the neural crest. In children, it is thinner and shows some of the underlying pigment, appearing slightly blue. In the elderly, however, fatty deposits on the sclera can make it appear slightly yellow. The sclera forms the posterior five sixths of the connective tissue coat of the globe. It is continuous with the dura mater and the cornea, and maintains the shape of the globe, offering resistance to internal and external forces, and provides an attachment for the extraocular muscle insertions. The sclera is perforated by plenty of nerves and vessels passing through the posterior scleral foramen, the hole that is formed by the optic nerve. At the optic disk the outer two-thirds of the sclera continues with the dura mater (outer coat of the brain) via the dural sheath of the optic nerve. The inner third joins with some choroidal tissue to form a plate (lamina cribrosa) across the optic nerve with perforations through which the optic fibers (fasciculi). The thickness of the sclera varies from 1mm at the posterior pole to 0.3 mm just behind the rectus muscle insertions. The sclera's blood vessels are mainly on the surface, and together with the conjunctiva (which lies on top) This is a thin layer covering the sclera. Along with the vessels of the conjunctiva, those of the sclera renders the inflamed eye bright red. [WP,unvetted][Wikipedia:Sclera]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The tough, usually white, outer coat of the eyeball, covering all the posterior surface and continuous anteriorly with the cornea. [TFD][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "scleral" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "in fish, reptiles and monotremes the connective tissue of the sclera is skeletal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000010", - "val" : "continuous with the dura mater and the cornea; The sclera forms the posterior five-sixths of the connective tissue coat of the globe." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "Majority derives from NC that surrounds optic cup of neurectoderm; a small temporal portion develops from the mesoderm that contributes to striated extra-ocular muscles and vascular endothelia[Rada&Johnson]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "Seko et al demonstrate chondrogenic potential and identify this as connective tissue[DOI:10.1371/journal.pone.0003709]." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26428,9 +22529,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26520,12 +22618,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "choroidal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "MP treats posterior uvea and optic choroid as distinct" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26588,15 +22680,6 @@ "val" : "ZFA:0001685" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of tissue that is located basal to Bowman's layer and distal to Descemet's membrane and is comprised largely of connective tissue.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship type change: subclass tissue (CARO:0000043) CHANGED TO: develops_from tissue (UBERON:0000479)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship type change: subclass tissue (CARO:0000043) CHANGED TO: has_developmental_contribution_from tissue (UBERON:0000479)[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -26696,9 +22779,6 @@ "val" : "XAO:0000266" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "MA does not treat internal/external limiting memranes as layers - these are classified as laminae. Here we follow other ontologies in grouping with other layers. MA also treats retinal pigment epithelium and neural retina epithelium as distinct from the layers. We follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers - these are also classified as layers, giving us over the usual 10 layers" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -26812,15 +22892,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A monolayer of pigmented epithelium covering the neural retina; develops from the outer of the two layers of the optic cup. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The monolayer of pigmented epithelium covering the neural retina.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26885,12 +22956,6 @@ "val" : "ZFA:0000143" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "we follow MA and ZFA in subdividing this into inner and outer segments" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -27063,9 +23128,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27145,12 +23207,6 @@ "val" : "ZFA:0001330" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The layer within the retina where the bipolar cells synapse with the photoreceptor cells.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -27237,12 +23293,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The layer of the retina composed of the cell bodies of bipolar cells, horizontal cells, and some of the cell bodies of amacrine cells[BTO:0003176]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27333,15 +23383,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "a layer of the retina that consists of retinal ganglion cells[WP]. innermost nuclear layer of the retina, which contains neurons that project axons through the optic nerve to the brain[Wikipedia:Ganglion_cell_layer]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "NIFSTD class appears to be retired in nlx[http://neurolex.org/wiki/Nlx_anat_1005030]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27429,9 +23470,6 @@ "val" : "ZFA:0001619" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0005888" }, { @@ -27509,9 +23547,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO - check frog/fish" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Membrane on the apical surface of the retina. The retinal vasculature becomes adhered to the apical surface of the ILM by 30dpf[ZFIN:ZDB-PUB-071023-7, ZFIN:ZDB-PUB-120529-3]." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27599,18 +23634,6 @@ "val" : "ZFA:0001329" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The inner plexiform layer (IPL) is positioned between the INL and the ganglion cell layer and contains the dendrites of RGCs and processes of bipolar and amacrine cells[GO][GO:0010842]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The layer within the retina where the bipolar cells synapse with the dendrites of the ganglion cells.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "http://neurolex.org/wiki/Nlx_anat_1005032 appears to be retired" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -27671,15 +23694,6 @@ "val" : "ZFA:0005564" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The fluid produced by the ciliary process in the eye and occupying the anterior and posterior chambers. It provides nourishment for the lens and cornea and maintains the ocular pressure, and hence the optical integrity of the eyeball. [TFD][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "FMA says A+P chambers, and MA states A chamber. ZFA states A chamber and tha it is produced primarily by dorsal ciliary epithelial cells.To be investigated across taxa." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -27747,8 +23761,6 @@ "val" : "FMA:58822" }, { "val" : "MA:0001286" - }, { - "val" : "MESH:D014822" }, { "val" : "NCIT:C13323" }, { @@ -27921,9 +23933,6 @@ "val" : "ZFA:0005566" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0001802" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -28029,8 +24038,6 @@ "val" : "CALOHA:TS-2232" }, { "val" : "EFO:0000374" - }, { - "val" : "EMAPA:18233" }, { "val" : "EV:0100340" }, { @@ -28055,9 +24062,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "conjunctival" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28141,21 +24145,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Most anterior of the three regions of the brain consisting of the telencephalon and diencephalon.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The most anterior region the brain including both the telencephalon and diencephalon. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship loss: develops_from forebrain neural tube (TAO:0007041)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "In craniate embryos, neural expression of Distal-less-related genes is exclusively in the forebrain (...). Because the major neural expression domain of amphioxus AmphiDll is in the anterior three-fourths of the cerebral vesicle, we suggest that this region of the neural tube is homologous to parts of the craniate forebrain. This conclusion is strongly supported by three-dimensional, computer-assisted reconstruction of the neural tube of amphioxus based on serial transmission electron microscopy. At the neuroanatomical level, a number of detailed homologies are indicated between the anterior three-fourths of the amphioxus cerebral vesicle and the diencephalic region of the craniate forebrain. If one assumes that the amphioxus condition fairly represents the nervous system of the proximate ancestor of the craniates, one can suggest that they evolved from a creature that had the beginnings of a forebrain.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "prosencephalic" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28249,30 +24238,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "developmental relationships need revised" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0001894" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0002028" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Middle part of the brain composed of the optic tectum and penducular region.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "mesencephalic" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "part of brainstem in ABA - we reject this in favor of ISBN:0471888893 which has an implicit overlaps relationships" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28397,30 +24365,6 @@ "val" : "neuronames:288" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0001891" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0002028" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7762" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The more posterior and ventral of two forebrain neuromeres, the other being the telencephalon; major derivatives are the eye cups, the brain pretectal region, the thalamus, hypothalamus, and epithalamus (including the habenula and epiphysis). Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Unpaired part of the forebrain comprised of three major parts; the epithalamus, thalamus, and hypothalamus.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "diencephalic" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in ABA, this is part of the brain stem" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -28526,15 +24470,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Posterior portion of the hindbrain which controls respiration, heartbeat, digestion, and swallowing as well as some locomotor responses.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The posterior region of the brain that is continuous with the spinal cord. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-17, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Classical anatomical studies subdivided the vertebrate rhombencephalon into pons and medulla oblongata. (...) The medulla oblongata appears therefore as a tagma, that is, a group of segmental units (pseudorhombomeres, in this case) sharing some morphological and molecular characteristics, and in some aspects different from the segmental units present in adjoining brain regions, pons and spinal cord.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28586,8 +24521,6 @@ "val" : "DHBA:10589" }, { "val" : "DMBA:17785" - }, { - "val" : "EMAPA:16678" }, { "val" : "EMAPA:35617" }, { @@ -28701,8 +24634,6 @@ "val" : "MA:0000212" }, { "val" : "MAT:0000452" - }, { - "val" : "MESH:D013681" }, { "val" : "SCTID:362392007" }, { @@ -28723,9 +24654,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28874,21 +24802,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Any of the vessels through which blood circulates in the body.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "annelids have blood vessels, but this class is not applicable to annelids." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28992,9 +24905,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "endothelial" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -29058,8 +24968,6 @@ "val" : "HBA:4006" }, { "val" : "MA:0001112" - }, { - "val" : "MESH:D066128" }, { "val" : "NCIT:C32695" }, { @@ -29076,9 +24984,6 @@ "val" : "neuronames:2869" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Multi-tissue comprised of neurons, dendrites, axon terminals, glial cells, and capillaries.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -29158,35 +25063,11 @@ "val" : "neuronames:540" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0001891" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0001894" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7762" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Posterior part of the brain consisting of the cerebellum and medulla oblongata.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The most posterior of the three principal regions of the brain, forming the rhombencephalon and all or most of the metencephalon. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship loss: develops_from hindbrain neural tube (TAO:0007043)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "rhombencephalic" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in MA, brainstem and hindbrain and part-of siblings under brain, consistent with FMA and NIF. See also notes for cerebellum. We weaken the relation in ABA to overlaps" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -29225,9 +25106,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "vascular" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -29277,8 +25155,6 @@ "val" : "CALOHA:TS-2110" }, { "val" : "EFO:0000461" - }, { - "val" : "FBbt:00004208" }, { "val" : "FMA:69067" }, { @@ -29303,18 +25179,6 @@ "val" : "ZFA:0001105" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in FMA embryo is_a embryonic structure" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -29377,12 +25241,6 @@ "val" : "XAO:0003034" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -29414,8 +25272,6 @@ "val" : "EHDAA2:0000161" }, { "val" : "EHDAA:5049" - }, { - "val" : "EMAPA:17214" }, { "val" : "EMAPA:37721" }, { @@ -29424,8 +25280,6 @@ "val" : "MA:0002986" }, { "val" : "MAT:0000148" - }, { - "val" : "MESH:D013131" }, { "val" : "MIAA:0000148" }, { @@ -29440,18 +25294,6 @@ "val" : "ZFA:0000317" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -29524,18 +25366,6 @@ "val" : "galen:Trunk" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000026" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000033" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -29586,9 +25416,6 @@ "val" : "http://uri.neuinfo.org/nif/nifstd/FMAID_7191" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The sensory system used for sight.[AAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0007036" }, { @@ -29732,9 +25559,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "not part of the eye in ZFA. Note this changed to a blood vessel in ZFA" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -29792,15 +25616,6 @@ "val" : "XAO:0000168" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system that provides locomotion and physical support to the organism.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "musculoskeletal" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -29860,9 +25675,6 @@ "val" : "Wikipedia:Thoracic_cavity" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In many species, the diaphragm separates thoracic and abdominal cavities" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -29981,18 +25793,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO - add superclass to unify with VNC?" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000955" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Part of the central nervous system which descends from the hindbrain within the vertebral column.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -30097,24 +25900,6 @@ "val" : "neuronames:236" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0001890" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0002037" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0002314" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,adopted][ZFA:0001707]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "the stalk-like part of the brain that comprises the midbrain (aka mesencephalon), the pons (aka pons Varolii), and the medulla oblongata, and connects the cerebral hemispheres with the cervical spinal cord[MP]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -30177,8 +25962,6 @@ "val" : "HBA:9218" }, { "val" : "MA:0001135" - }, { - "val" : "MESH:D066127" }, { "val" : "NCIT:C33892" }, { @@ -30205,18 +25988,6 @@ "val" : "neuronames:2870" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Cell part cluster consisting predominantly of neurites in the brain and the spinal cord[FMA:83929]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Multi-tissue structure comprised largely of myelinated axons.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The myelination of axons by glial cells was the last major step in the evolution of cells in the vertebrate nervous system, and white-matter tracts are key to the architecture of the mammalian brain.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "nlx_anat_101177 seems to have been lost in the transition from NIFGA to Neurolex" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -30283,8 +26054,6 @@ "val" : "BTO:0001707" }, { "val" : "EHDAA2:0000267" - }, { - "val" : "FBbt:00005060" }, { "val" : "FMA:85006" }, { @@ -30303,15 +26072,6 @@ "val" : "galen:BodyCavity" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In mammals it forms the peritoneal, pleural, and pericardial cavities" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0000169" }, { @@ -30389,27 +26149,6 @@ "val" : "http://evolution.berkeley.edu/evolibrary/images/history/notochords.jpg" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "notochordal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -30496,32 +26235,8 @@ "val" : "ZFA:0000155" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "EDITOR_NOTE currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7712" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Post-cranial axial segments which form sclerotome and dermomyotome.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "somitic" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -30580,8 +26295,6 @@ "val" : "NCIT:C34222" }, { "val" : "SCTID:361462002" - }, { - "val" : "TAO:0000045" }, { "val" : "UMLS:C0027789" }, { @@ -30596,24 +26309,6 @@ "val" : "neuronames:1366" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "EDITOR_NOTE consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams)." - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002174", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_117565" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -30672,8 +26367,6 @@ "val" : "EMAPA:16073" }, { "val" : "EV:0100004" - }, { - "val" : "FBbt:00001057" }, { "val" : "FMA:87657" }, { @@ -30696,15 +26389,6 @@ "val" : "ZFA:0001120" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "neurectodermal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000013", - "val" : "we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -30773,18 +26457,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "MA also has set of connective tissues" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -30841,12 +26513,6 @@ "val" : "galen:MuscleTissue" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0003714" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -30931,18 +26597,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system that consists of the blood and blood forming tissues.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "hematopoietic" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -31054,9 +26708,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -31098,8 +26749,6 @@ "val" : "AAO:0010466" }, { "val" : "EFO:0001650" - }, { - "val" : "FMA:293966" }, { "val" : "MAT:0000369" }, { @@ -31110,12 +26759,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Do not merge with neurogenic placode" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000013", - "val" : "The term placode or placodes also applies to developing organs such as teeth, mammary glands, hair follicles, feathers and scales. We include a separate parent class for this. to avoid confusion, we include neurogenic placode as a subclass" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -31274,9 +26917,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider adding class for organizer. Consider adding separate class for isthmus as a structure" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -31307,9 +26947,6 @@ "val" : "ZFA:0007016" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -31337,9 +26974,6 @@ "val" : "ZFA:0007017" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -31397,12 +27031,6 @@ "val" : "ZFA:0000279" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -31464,21 +27092,6 @@ "val" : "ZFA:0000094" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -31514,9 +27127,6 @@ "val" : "ZFA:0001204" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -31586,9 +27196,6 @@ "val" : "ZFA:0000570" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "TODO - check that GO's optic placode is the same as ZFA's eye primordium; we may want to have separate term for ocular primordium precursor. XAO has both optic field and eye primordium." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0005060" }, { @@ -31644,9 +27251,6 @@ "val" : "ZFA:0001202" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -31700,15 +27304,6 @@ "val" : "ZFA:0000122" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Ectodermal primordium of the lens of the eye. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "Classical transplantation experiments using amphibian embryos suggested that the optic vesicle is the source of lens-inducing signals sufficient to generate lens tissues in competent ectoderm (reviewed in Grainger et al., 1996). More recent findings suggest a multistep model for lens induction. There is now good evidence that lens specification occurs at the neurula stage, before the optic vesicle contact the surface ectoderm, and that neural crest cell migration in the frontonasal region is required to restrict the position of the lens placode (Bailey et al., 2006)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -31751,8 +27346,6 @@ "val" : "EMAPA:35593" }, { "val" : "FMA:293879" - }, { - "val" : "MESH:D054258" }, { "val" : "NCIT:C34225" }, { @@ -31773,12 +27366,6 @@ "val" : "neuronames:1362" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -31803,9 +27390,6 @@ "val" : "ZFA:0007037" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -31862,15 +27446,6 @@ "val" : "ZFA:0000255" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -31897,9 +27472,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO - add grouping class for the anterior end of the neural tube at all stages" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -31965,18 +27537,6 @@ "val" : "ZFA:0000121" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "subclass of mesoderm in ZFA." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0006258" }, { @@ -32023,15 +27583,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "should probably be merged with heart rudiment." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -32062,8 +27613,6 @@ "val" : "AAO:0010571" }, { "val" : "AEO:0000212" - }, { - "val" : "BTO:0006255" }, { "val" : "EHDAA2:0003439" }, { @@ -32086,15 +27635,6 @@ "val" : "ZFA:0001080" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Skeletogenic portion of somites.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "part_of somite in XAO" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -32149,12 +27689,6 @@ "val" : "ZFA:0000137" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The evagination from the neural tube of the developing embryo which develops the optic cup at its extremity; the stalk persists as the optic nerve. [TFD][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -32219,15 +27753,6 @@ "val" : "ZFA:0001194" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anterior most portion of the neural crest. Migrates in three highly conserved streams: mandibular, hyoid and branchial.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Neural crest that is part of the head.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -32272,9 +27797,6 @@ "val" : "ZFA:0000496" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -32337,15 +27859,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "mesenchymal" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -32446,8 +27959,6 @@ } ], "xrefs" : [ { "val" : "EMAPA:35187" - }, { - "val" : "HBA:9218" }, { "val" : "MA:0000820" }, { @@ -32515,8 +28026,6 @@ "xrefs" : [ "OBOL:automatic" ] } ], "xrefs" : [ { - "val" : "EMAPA:16098" - }, { "val" : "MA:0000577" } ], "basicPropertyValues" : [ { @@ -32566,12 +28075,6 @@ "val" : "UMLS:C0027757" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "FMA definition includes vasculature" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -32628,9 +28131,6 @@ "val" : "XAO:0000252" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0005713" }, { @@ -32671,9 +28171,6 @@ "val" : "ZFA:0000935" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -32719,9 +28216,6 @@ "val" : "ZFA:0000811" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -32763,12 +28257,6 @@ "val" : "ZFA:0007063" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Cranial neural crest that is part of the hindbrain.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -32801,9 +28289,6 @@ "val" : "VHOG:0001006" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -32861,9 +28346,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -32891,9 +28373,6 @@ "val" : "UMLS:C0927195" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "stromal" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -32968,9 +28447,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -32993,13 +28469,8 @@ "val" : "AEO:0000114" }, { "val" : "EHDAA2:0003114" - }, { - "val" : "FBbt:00007474" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33073,9 +28544,6 @@ "xrefs" : [ "NCBIBook:NBK10047" ] } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "As the cells adjacent to the lumen continue to divide, the migrating cells form a second layer around the original neural tube. This layer becomes progressively thicker as more cells are added to it from the germinal neuroepithelium. This new layer is called the mantle (or intermediate) zone, and the germinal epithelium is now called the ventricular zone (and, later, the ependyma)[NCBIBook:NBK10047]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33123,9 +28591,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The layer of undifferentiated, proliferating cells that line the neural tube lumen" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -33233,9 +28698,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "note the FMA class is more narrow though, and is more like eye + muscles + vasculature. The FMA also has FMA:72951 orbital part of eye" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in HP covers eyelid, eyebrow." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -33291,9 +28753,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "FMA has both conduit and conduit space. In EHDAA2 this is a surface feature" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -33315,9 +28774,6 @@ "xrefs" : [ "FBbt:00025998" ] } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Grouping term for query purposes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33338,9 +28794,6 @@ "xrefs" : [ "FBbt:00025990" ] } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Grouping term for query purposes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33399,9 +28852,6 @@ "val" : "ZFA:0000050" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -33445,9 +28895,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -33489,9 +28936,6 @@ "val" : "XAO:0004185" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33535,9 +28979,6 @@ "val" : "ZFA:0000360" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33640,17 +29081,8 @@ "val" : "galen:Skeleton" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000383" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "skeletal" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -33683,9 +29115,6 @@ "val" : "ZFA:0000115" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33778,9 +29207,6 @@ "val" : "ZFA:0001686" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Acellular anatomical structure composed of collagen, Descemet's membrane is secreted as a basement membrane of the corneal endothelium. Located between the stroma and the corneal endothelium, it is approximately 0.15 micrometer thick at 6 months post-fertilization.[ZFIN]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -33859,12 +29285,6 @@ "val" : "ZFA:0001684" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Acellular anatomical structure that is the zone of collagen fibers adjacent the basement membrane of the corneal epithelium.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33888,9 +29308,6 @@ "val" : "FMA:78499" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33924,14 +29341,10 @@ "val" : "CALOHA:TS-1297" }, { "val" : "EFO:0000791" - }, { - "val" : "EHDAA2:0000216" }, { "val" : "EHDAA:394" }, { "val" : "EMAPA:16104" - }, { - "val" : "EMAPA:16370" }, { "val" : "EV:0100017" }, { @@ -33966,14 +29379,8 @@ "val" : "ZFA:0000010" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph." - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -34199,8 +29606,6 @@ "val" : "BILA:0000060" }, { "val" : "BTO:0001403" - }, { - "val" : "FBbt:00005317" }, { "val" : "FMA:293108" }, { @@ -34223,9 +29628,6 @@ "val" : "Wikipedia:Trilaminar_blastocyst" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "We explicitly merge the NCITA terms here" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0007012" }, { @@ -34257,12 +29659,6 @@ "val" : "galen:SkeletalStructure" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34355,9 +29751,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider merging with 'endothelium'" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -34397,9 +29790,6 @@ "val" : "XAO:0000276" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34440,12 +29830,6 @@ "val" : "ZFA:0000091" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Notochord rudiment[ZFIN:ZDB-PUB-961014-576]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34464,9 +29848,6 @@ "pred" : "hasNarrowSynonym", "val" : "joint" } ], - "xrefs" : [ { - "val" : "FBbt:00005811" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -34502,14 +29883,9 @@ "xrefs" : [ "FMA:71131" ] } ], "xrefs" : [ { - "val" : "FBbt:00100315" - }, { "val" : "FMA:71131" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct." - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { @@ -34564,9 +29940,6 @@ "val" : "neuronames:1363" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34604,9 +29977,6 @@ "val" : "neuronames:1364" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34634,9 +30004,6 @@ "val" : "ZFA:0000133" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34661,12 +30028,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consder adding placodal ectoderm as a distinct class? Also place placodal ectoderm as develops_from ectoderm; need to check taxon-appropriateness" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "With the exception of the adenohypophysis, homologues of the nonneurogenic placodes (e.g. placodes giving rise to the teeth, hair follicles and lens), appear to be lacking in invertebrate chordates." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in GO, covers optic, otic, olfactory, mammary, hair, tooth, sebaceous - and also insect structures" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -34693,14 +30054,9 @@ "val" : "muscle element" } ], "xrefs" : [ { - "val" : "EMAPA:32715" - }, { "val" : "FMA:30316" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34746,15 +30102,10 @@ "val" : "AAO:0011000" }, { "val" : "CARO:0001000" - }, { - "val" : "FBbt:00007060" }, { "val" : "FMA:83115" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "we go with the FMA classification rather than the CARO one. FMA def: 'Anatomical cluster which has as direct parts cell parts from two or more cells.'" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34906,9 +30257,6 @@ "val" : "ZFA:0000113" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Mesoderm that will give rise, along with cranial neural crest cells, to connective tissue, bone and musculature in the head. (Source: BioGlossary, www.Biology-Text.com)[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34981,26 +30329,12 @@ "val" : "HBA:9512" }, { "val" : "MA:0000205" - }, { - "val" : "MESH:D054024" }, { "val" : "VHOG:0000456" }, { "val" : "Wikipedia:Myelencephalon" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002174", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7955" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000013", - "val" : "the terms metencephalon and myelencephalon are only meaningful in mammals and birds - Neuroanatomy of the Zebrafish Brain. Note that its not clear if this refers to the developing medulla oblongata - MA (adult) has two distinct classes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -35047,9 +30381,6 @@ "pred" : "hasExactSynonym", "val" : "light-sensitive tissue" } ], - "xrefs" : [ { - "val" : "FBbt:00004200" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -35070,9 +30401,6 @@ "val" : "lens" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000009", - "val" : "directing or focusing light onto light receptors" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -35100,8 +30428,6 @@ "val" : "CALOHA:TS-2122" }, { "val" : "EHDAA2:0003125" - }, { - "val" : "FBbt:00007006" }, { "val" : "FMA:292313" }, { @@ -35179,9 +30505,6 @@ "val" : "ZFA:0000064" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -35243,9 +30566,6 @@ "val" : "ZFA:0001071" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -35298,15 +30618,6 @@ "val" : "ZFA:0001679" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A vesicle formed from the lens pit of the embryo, developing into the crystalline lens. [TFD][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "the lens of zebrafish (and other teleosts) forms from delamination of cells from the lens placode; thus, there is no formation of a hollow lens vesicle, in contrast to the situation in mammals and birds (Glass and Dahm, 2004) [PMID:16496288] The lens of the zebrafish forms by delamination of lens placodal cells and not through invagination. This results in a solid spherical mass as opposed to a hollow lens vesicle. Detachment of the solid lens vesicle of zebrafish at 24b26 hpf is accomplished in part by apoptosis, similar to mammals" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -35350,8 +30661,6 @@ "xrefs" : [ "EMAPA:16208" ] } ], "xrefs" : [ { - "val" : "BTO:0006179" - }, { "val" : "EHDAA2:0001512" }, { "val" : "EHDAA:424" @@ -35394,9 +30703,6 @@ "val" : "VHOG:0001477" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A depression in the front of the vitreous body, lodging the lens. [adapted_from_the_definition_of_the_hyaloid_fossa]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -35467,9 +30773,6 @@ "val" : "Wikipedia:Basement_membrane" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell." - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_80999" }, { @@ -35572,8 +30875,6 @@ "val" : "AAO:0000963" }, { "val" : "EMAPA:17214" - }, { - "val" : "EMAPA:18043" }, { "val" : "MA:0000308" }, { @@ -35592,9 +30893,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -35654,9 +30952,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "neurofibrous" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -35697,9 +30992,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7776" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "http://www1.pbrc.hawaii.edu/~danh/MyelinEvolution/evolution.html, http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=6134604, Wikipedia:Myelin#Invertebrate_myelin" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -35789,9 +31081,6 @@ "val" : "ZFA:0000146" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -35916,9 +31205,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO - check ordering; awaiting confirmation from JB" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -36017,9 +31303,6 @@ "val" : "MA:0001911" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000009", - "val" : "ocular refraction" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -36087,18 +31370,6 @@ "val" : "MIAA:0000049" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "currently this is an extremely generic class, encompassing both protostomes and deuterostomes." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0006012", - "val" : "2023-04-20" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "branchial" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "pharyngeal" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -36286,9 +31557,6 @@ "val" : "Wikipedia:Squamous_epithelium" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -36459,9 +31727,6 @@ "val" : "UMLS:C1514442" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -36491,16 +31756,11 @@ "xrefs" : [ "FBbt:00003154" ] } ], "xrefs" : [ { - "val" : "SPD:0000130" - }, { "val" : "TADS:0000147" }, { "val" : "http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -36528,9 +31788,6 @@ "val" : "ZFA:0000131" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -36623,9 +31880,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO - unify naming conventions" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The embryonic rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. Rhombomeres Rh7-Rh4 form the myelencephalon that will give the medulla oblongata. Rhombomeres Rh3-Rh1 form the metencephalon that will form the pons and the cerebellum[NPX:PDR]." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -36721,9 +31975,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider merging" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Region of the gastrula which gives rise to the neural plate.[TAO]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -36925,9 +32176,6 @@ "val" : "SCTID:280667001" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "MA does treat internal/external limiting membranes as layers - these are classified as laminae. We do not follow this convention. However, we do following MA is grouping these terms together" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -37022,8 +32270,6 @@ "val" : "EFO:0001649" }, { "val" : "EHDAA2:0003170" - }, { - "val" : "FBbt:00005426" }, { "val" : "Wikipedia:Anlage_(biology)" } ], @@ -37092,12 +32338,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -37418,8 +32658,6 @@ } ], "xrefs" : [ { "val" : "CARO:0010000" - }, { - "val" : "FBbt:00100313" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", @@ -37513,12 +32751,6 @@ "val" : "Wikipedia:Globe_(human_eye)" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "See notes for camera-type eye" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000202", - "val" : "http://purl.obolibrary.org/obo/FMA_264089" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -37599,9 +32831,6 @@ "val" : "ZFA:0001678" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Multi-tissue structure that consists of the structures that develop into the retina and lens.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -37617,9 +32846,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Grouping term for query purposes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -37635,9 +32861,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Grouping term for query purposes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -37794,9 +33017,6 @@ "val" : "VSAO:0000042" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -37887,8 +33107,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "xrefs" : [ { - "val" : "FBbt:00007330" - }, { "val" : "FMA:67509" }, { "val" : "SCTID:91690000" @@ -37931,9 +33149,6 @@ "val" : "FMA:49150" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Muscles within the eye (bulbus oculi).[AAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -38195,9 +33410,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_147099" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "coelomic" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -38367,15 +33579,39 @@ "val" : "AEO:0000103" }, { "val" : "BTO:0001489" - }, { - "val" : "EMAPA:36031" }, { "val" : "FMA:231424" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]." + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0014387", + "lbl" : "mesenchyme derived from neural crest", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Mesenchyme that develops_from the neural crest[Automatically generated definition].", + "xrefs" : [ "OBOL:automatic", "https://github.com/obophenotype/uberon/issues/248" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "mesenchyme from neural crest" + }, { + "pred" : "hasExactSynonym", + "val" : "neural crest derived mesenchyme" }, { + "pred" : "hasExactSynonym", + "val" : "neural crest mesenchyme" + } ], + "xrefs" : [ { + "val" : "EMAPA:32735" + }, { + "val" : "FMA:293883" + } ], + "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -38448,8 +33684,6 @@ }, "xrefs" : [ { "val" : "AEO:0000093" - }, { - "val" : "FBbt:00007278" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -38467,9 +33701,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This class is primarily to implement taxon constraints. It may be removed in the future." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -38500,9 +33731,6 @@ "pred" : "hasRelatedSynonym", "val" : "cardiac structure" } ], - "xrefs" : [ { - "val" : "SPD:0000130" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -38895,8 +34123,6 @@ "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], "xrefs" : [ { "val" : "CARO:0020000" - }, { - "val" : "FBbt:00007276" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", @@ -39427,120 +34653,6 @@ "val" : "uberon" } ] } - }, { - "id" : "http://purl.org/dc/elements/1.1/creator", - "lbl" : "creator", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/elements/1.1/creator" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-creator" - } ] - } - }, { - "id" : "http://purl.org/dc/elements/1.1/description", - "lbl" : "description", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/elements/1.1/description" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-description" - } ] - } - }, { - "id" : "http://purl.org/dc/elements/1.1/title", - "lbl" : "title", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/elements/1.1/title" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-title" - } ] - } - }, { - "id" : "http://purl.org/dc/terms/contributor", - "lbl" : "contributor", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/terms/contributor" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-contributor" - } ] - } - }, { - "id" : "http://purl.org/dc/terms/date", - "lbl" : "date", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/terms/date" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dcterms-date" - } ] - } - }, { - "id" : "http://purl.org/dc/terms/license", - "lbl" : "license", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/terms/license" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dcterms-license" - } ] - } }, { "id" : "http://www.geneontology.org/formats/oboInOwl#SubsetProperty", "lbl" : "subset_property", @@ -39574,9 +34686,6 @@ "val" : "An alternative label for a class or property which has a more general meaning than the preferred name/primary label." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/18" }, { @@ -39597,9 +34706,6 @@ "val" : "An alternative label for a class or property which has the exact same meaning than the preferred name/primary label." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/20" }, { @@ -39616,9 +34722,6 @@ "val" : "An alternative label for a class or property which has a more specific meaning than the preferred name/primary label." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/19" }, { @@ -39639,9 +34742,6 @@ "val" : "An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/21" }, { @@ -39674,35 +34774,10 @@ "val" : "http://www.w3.org/2000/01/rdf-schema#seeAlso" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "seeAlso" } ] } - }, { - "id" : "http://xmlns.com/foaf/0.1/depiction", - "lbl" : "depiction", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://xmlns.com/foaf/0.1/depiction" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "depiction" - } ] - } } ], "edges" : [ { "sub" : "http://purl.obolibrary.org/obo/BFO_0000004", @@ -41424,10 +36499,20 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0010009", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000287" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0010009", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0009004" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0010009", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000019" + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000966", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/cell-ontology/issues/2245" + } ] + } }, { "sub" : "http://purl.obolibrary.org/obo/CL_0010017", "pred" : "is_a", @@ -44198,20 +39283,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000019", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000966" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000019", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000033" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000019", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0003072", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "definitional" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0003072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000019", "pred" : "http://purl.obolibrary.org/obo/RO_0002492", @@ -44624,10 +39699,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000153", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000475" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000153", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000096", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000154" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000153", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -44643,17 +39714,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0004921", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts" - } ] - } - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0001106", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0001555" + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004921" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -44755,13 +39816,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000463", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000468", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "this relationship may be too strong and may be weakened in future" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000468" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000463", "pred" : "http://purl.obolibrary.org/obo/RO_0000086", @@ -44991,13 +40046,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000926", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000923", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "sometimes not considered primary" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000923" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000926", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -45028,10 +40077,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000930", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000941", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000941", "pred" : "is_a", @@ -45132,10 +40177,6 @@ "val" : "FMA" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000955", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000123", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000468" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000955", "pred" : "http://purl.obolibrary.org/obo/RO_0002433", @@ -45239,13 +40280,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000964", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0004348", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "definitional" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004348" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000964", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -45258,6 +40293,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000964", "pred" : "http://purl.obolibrary.org/obo/RO_0002433", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001801" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0000965", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000965", "pred" : "is_a", @@ -45721,6 +40760,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001711", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000064" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001711", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001711", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -45761,6 +40804,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001766", "pred" : "http://purl.obolibrary.org/obo/RO_0002433", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001801" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001768", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001768", "pred" : "is_a", @@ -45771,6 +40818,10 @@ "val" : "FMA" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001768", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010314" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001768", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -45817,6 +40868,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001769", "pred" : "http://purl.obolibrary.org/obo/RO_0002433", "obj" : "http://purl.obolibrary.org/obo/UBERON_0011892" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001772", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010313" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001772", "pred" : "is_a", @@ -45843,6 +40898,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001773", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000064" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001773", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010313" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001773", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -45877,22 +40936,6 @@ "val" : "ISBN:0781772214" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0001773", - "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0007213", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#inferred_by", - "val" : "cjm" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "ISBN:0781772214" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "Wikipedia" - } ] - } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001773", "pred" : "http://purl.obolibrary.org/obo/RO_0002433", @@ -45979,6 +41022,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001777", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0003891" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001777", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010313" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001777", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -45986,19 +41033,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001777", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0007213", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#inferred_by", - "val" : "cjm" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "ISBN:0781772214" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "Wikipedia" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0007213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001777", "pred" : "http://purl.obolibrary.org/obo/RO_0002220", @@ -46055,6 +41090,10 @@ "val" : "Wikipedia" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001781", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001781", "pred" : "is_a", @@ -46075,10 +41114,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001782", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001781" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0001782", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0010371" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001782", "pred" : "is_a", @@ -46152,16 +41187,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001789", "pred" : "http://purl.obolibrary.org/obo/RO_0002131", - "obj" : "http://purl.obolibrary.org/obo/CL_0000287", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "soma" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "ZFA" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/CL_0000287" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001789", "pred" : "http://purl.obolibrary.org/obo/RO_0002220", @@ -46286,6 +41312,10 @@ "val" : "MA" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001794", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010314" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001794", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -46345,19 +41375,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001796", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0001766", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "FMA def states A and P" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "located_in in EHDAA2" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "VHOG" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0001766" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001796", "pred" : "http://purl.obolibrary.org/obo/RO_0002433", @@ -46382,6 +41400,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001798", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0003566" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001798", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001798", "pred" : "is_a", @@ -46399,16 +41421,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001798", "pred" : "http://purl.obolibrary.org/obo/RO_0002254", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0002346", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "neural ectoderm of optic cup" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "ISBN:0781772214" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0002346" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001798", "pred" : "http://purl.obolibrary.org/obo/RO_0002473", @@ -46431,22 +41444,16 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000063" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001801", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0010230", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "FMA" - } ] - } + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001801", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000123", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0010230", "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "cjm" + "val" : "FMA" } ] } }, { @@ -46459,22 +41466,16 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000063" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001802", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0010230", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "FMA" - } ] - } + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001802", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000122", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0010230", "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "cjm" + "val" : "FMA" } ] } }, { @@ -46491,6 +41492,10 @@ "val" : "FMA" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001811", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001811", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -46537,10 +41542,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001890", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0002616" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0001890", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001890", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -46552,21 +41553,11 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001890", "pred" : "http://purl.obolibrary.org/obo/RO_0002495", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0006240", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "definitional" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0006240" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001891", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0002616" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0001891", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001891", "pred" : "is_a", @@ -46574,13 +41565,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001891", "pred" : "http://purl.obolibrary.org/obo/RO_0002254", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0003849", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "definitional" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0003849" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001891", "pred" : "http://purl.obolibrary.org/obo/RO_0002433", @@ -46599,10 +41584,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001894", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0002616" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0001894", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001894", "pred" : "is_a", @@ -46614,13 +41595,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001894", "pred" : "http://purl.obolibrary.org/obo/RO_0002254", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0003851", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "definitional" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0003851" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001894", "pred" : "http://purl.obolibrary.org/obo/RO_0002433", @@ -46628,17 +41603,15 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001894", "pred" : "http://purl.obolibrary.org/obo/RO_0002495", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0006222", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "definitional" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0006222" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001896", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000064" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001896", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001896", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -46737,6 +41710,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000055" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -46795,10 +41772,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001985", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0010313" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0001985", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0010371" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001985", "pred" : "is_a", @@ -46852,23 +41825,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002028", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0002616" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0002028", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002028", "pred" : "http://purl.obolibrary.org/obo/RO_0002131", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0002298", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "modified-source-relation" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "ABA" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0002298" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002028", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -47020,13 +41980,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002204", "pred" : "http://purl.obolibrary.org/obo/RO_0002254", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000926", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "check ctenophore" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000926" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002204", "pred" : "http://purl.obolibrary.org/obo/RO_0002492", @@ -47080,23 +42034,11 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002240", "pred" : "http://purl.obolibrary.org/obo/RO_0002254", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0003853", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "definitional" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0003853" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002240", "pred" : "http://purl.obolibrary.org/obo/RO_0002495", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0006241", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "definitional" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0006241" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002298", "pred" : "is_a", @@ -47132,13 +42074,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002323", "pred" : "http://purl.obolibrary.org/obo/RO_0002494", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0003886", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "definitional" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0003886" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002323", "pred" : "http://purl.obolibrary.org/obo/RO_0002572", @@ -47163,6 +42099,10 @@ "val" : "VSAO" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", "pred" : "is_a", @@ -47171,14 +42111,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0011137" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000098", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0001555" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000102", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0001049" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -47255,6 +42187,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010314" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "is_a", @@ -47275,16 +42211,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_89593", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "ISBN:0073040584" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_89593" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -47308,13 +42235,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "http://purl.obolibrary.org/obo/RO_0002473", - "obj" : "http://purl.obolibrary.org/obo/CL_0000333", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/CL_0000333" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "http://purl.obolibrary.org/obo/RO_0002488", @@ -47394,13 +42315,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002390", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0003061", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "definitional" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0003061" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002506", "pred" : "is_a", @@ -47486,6 +42401,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002616", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000073" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0002616", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002616", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -47501,16 +42420,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003052", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0007651", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#inconsistent_with", - "val" : "ZFA" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/106/" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0007651" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003052", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -47539,6 +42449,10 @@ "val" : "ZFA" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0003056", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003056", "pred" : "is_a", @@ -47547,10 +42461,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0003056", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0003075" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0003056", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000096", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0009615" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003057", "pred" : "is_a", @@ -47559,10 +42469,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0003057", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0003075" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0003057", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000099", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0009615" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003059", "pred" : "is_a", @@ -47635,6 +42541,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0003071", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0006598" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0003071", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010371" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003071", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -47696,6 +42606,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0003073", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0006598" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0003073", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010312" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003073", "pred" : "is_a", @@ -47796,10 +42710,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0003077", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0015212" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0003077", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000922" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003077", "pred" : "http://purl.obolibrary.org/obo/RO_0002488", @@ -47975,10 +42885,18 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0003098", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", "obj" : "http://purl.obolibrary.org/obo/UBERON_0003072" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0003099", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003099", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0005291" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0003099", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010314" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003099", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -48007,6 +42925,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0003104", "pred" : "http://purl.obolibrary.org/obo/RO_0002473", "obj" : "http://purl.obolibrary.org/obo/CL_0008019" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0003314", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0007213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003314", "pred" : "is_a", @@ -48029,6 +42951,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0003386", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001135" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0003386", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003386", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -48195,10 +43121,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0003902", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001781" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0003902", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003902", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -48237,6 +43159,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004022", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0005291" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004022", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010371" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004022", "pred" : "is_a", @@ -48299,6 +43225,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004061", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0005291" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004061", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010371" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004061", "pred" : "is_a", @@ -48316,16 +43246,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004061", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0004022", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "by division" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "NCBIBook:NBK10047" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004022" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004061", "pred" : "http://purl.obolibrary.org/obo/RO_0002220", @@ -48334,6 +43255,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004061", "pred" : "http://purl.obolibrary.org/obo/RO_0002220", "obj" : "http://purl.obolibrary.org/obo/UBERON_0004062" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004062", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004062", "pred" : "is_a", @@ -48345,13 +43270,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004062", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0004061", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "forms from axons" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004061" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004062", "pred" : "http://purl.obolibrary.org/obo/RO_0002220", @@ -48446,6 +43365,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004140", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0002050" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004140", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004140", "pred" : "is_a", @@ -48500,6 +43423,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004151", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000064" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004151", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004151", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -48508,6 +43435,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004277", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001630" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004277", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004277", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -48554,6 +43485,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004367", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0005769" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004367", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010313" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004367", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -48584,6 +43519,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004370", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0005769" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004370", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010313" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004370", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -48676,6 +43615,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004732", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001016" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004733", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004733", "pred" : "is_a", @@ -48823,14 +43766,14 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005062", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0015212" + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010371" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005062", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0005061" + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0015212" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005062", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000126", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0005061" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005068", @@ -48956,10 +43899,6 @@ "val" : "EHDAA2" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0005290", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005290", "pred" : "is_a", @@ -48967,13 +43906,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005290", "pred" : "http://purl.obolibrary.org/obo/RO_0002495", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0010096", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "definitional" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010096" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005291", "pred" : "is_a", @@ -49022,6 +43955,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0005424", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0006598" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0005424", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010312" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005424", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -49034,6 +43971,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0005425", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0006598" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0005425", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010312" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005425", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -49046,6 +43987,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0005426", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000479" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0005426", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005426", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -49070,6 +44015,10 @@ "val" : "Obol" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0005427", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010312" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005427", "pred" : "is_a", @@ -49206,6 +44155,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0005906", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/UBERON_0002553" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0005908", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005908", "pred" : "is_a", @@ -49239,13 +44192,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005908", "pred" : "http://purl.obolibrary.org/obo/RO_0002220", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0001801", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#modified_from", - "val" : "MA" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0001801" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005944", "pred" : "is_a", @@ -49408,6 +44355,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0006311", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000063" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0006311", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006311", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -49547,13 +44498,11 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006984", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0010199", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "via morphological boundary in CARO" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010199" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0007005", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007005", "pred" : "is_a", @@ -49617,13 +44566,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007100", "pred" : "http://purl.obolibrary.org/obo/RO_0002215", - "obj" : "http://purl.obolibrary.org/obo/GO_0008015", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "GO uses blood circulation generically to include the haemolymphatic fluid of arthropods" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/GO_0008015" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007135", "pred" : "is_a", @@ -49642,6 +44585,10 @@ "val" : "ZFA" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0007213", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0014387" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007213", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -49703,16 +44650,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007282", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0009618", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#consistent_with", - "val" : "https://github.com/obophenotype/uberon/wiki/The-neural-crest" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "EDHAA2" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0009618" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007282", "pred" : "http://purl.obolibrary.org/obo/RO_0002387", @@ -49993,16 +44931,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0009615", "pred" : "http://purl.obolibrary.org/obo/RO_0002495", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0007281", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "https://github.com/obophenotype/uberon/issues/438" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "Bgee:AN" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0007281" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0009616", "pred" : "is_a", @@ -50053,6 +44982,10 @@ "val" : "EHDAA2" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0009881", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0009881", "pred" : "is_a", @@ -50078,7 +45011,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0009920", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0005253" + "obj" : "http://purl.obolibrary.org/obo/UBERON_0007213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0009920", "pred" : "is_a", @@ -50137,6 +45070,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0010230", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000020" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0010230", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0010230", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -50181,6 +45118,10 @@ "val" : "ZFA" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0010286", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0010286", "pred" : "is_a", @@ -50202,13 +45143,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0010312", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0003071", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "definitional" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0003071" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0010312", "pred" : "http://purl.obolibrary.org/obo/RO_0002254", @@ -50263,16 +45198,20 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000063" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0010409", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000019" + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0010409", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000108", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0022288" + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000019" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0010427", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000481" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0010427", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0010427", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -50341,6 +45280,10 @@ "val" : "cjm" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0011215", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0011215", "pred" : "is_a", @@ -50363,6 +45306,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0011216", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000467" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0011222", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0011222", "pred" : "is_a", @@ -50451,6 +45398,10 @@ "val" : "ZFA" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0011892", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0011892", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -50503,6 +45454,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0012430", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PR_000050567" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0012430", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0012430", "pred" : "is_a", @@ -50593,6 +45548,14 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0013702", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0013701" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0014387", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0003104" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0014387", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010313" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0014477", "pred" : "is_a", @@ -50625,10 +45588,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0015212", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0015212", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000465" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0015212", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -50663,6 +45622,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0015808", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0007625" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0015808", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010371" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0015808", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -50727,6 +45690,14 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0019207", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000481" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0019207", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0019207", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010314" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0019207", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -50815,10 +45786,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0034713", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0015212" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0034713", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000033" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0034713", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -52071,10 +47038,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000057" - }, { - "sub" : "http://purl.obolibrary.org/obo/uberon/core#anteriorly_connected_to", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BSPO_0000099" }, { "sub" : "http://purl.obolibrary.org/obo/uberon/core#anteriorly_connected_to", "pred" : "subPropertyOf", @@ -52083,10 +47046,6 @@ "sub" : "http://purl.obolibrary.org/obo/uberon/core#anteriorly_connected_to", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/uberon/core#transitively_anteriorly_connected_to" - }, { - "sub" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BSPO_0000100" }, { "sub" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", "pred" : "subPropertyOf", @@ -52103,18 +47062,10 @@ "sub" : "http://purl.obolibrary.org/obo/uberon/core#layer_part_of", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000050" - }, { - "sub" : "http://purl.obolibrary.org/obo/uberon/core#posteriorly_connected_to", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BSPO_0000096" }, { "sub" : "http://purl.obolibrary.org/obo/uberon/core#posteriorly_connected_to", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002170" - }, { - "sub" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BSPO_0000097" }, { "sub" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to", "pred" : "subPropertyOf", @@ -52331,10 +47282,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012001", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012005" - }, { - "sub" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", - "pred" : "inverseOf", - "obj" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to" } ], "logicalDefinitionAxioms" : [ { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000005", @@ -53886,13 +48833,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002082", "fillerId" : "http://purl.obolibrary.org/obo/GO_0040016" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0000165", - "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0004921" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BSPO_0001106", - "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0001555" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0000179", "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000463" ], @@ -54806,6 +49746,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0000086", "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000608" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0014387", + "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0003104" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002202", + "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0002342" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0014903", "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001048" ], @@ -54813,13 +49760,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002387", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0002049" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0015212", - "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0000465" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0015808", "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000483" ], @@ -55173,8 +50113,8 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002551", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061", "http://purl.obolibrary.org/obo/UBERON_0000475" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465", "http://purl.obolibrary.org/obo/UBERON_0010912" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002566", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], @@ -55235,10 +50175,6 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0019000", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/uberon/core#channel_for", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0004111" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000463" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] @@ -55270,21 +50206,12 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002287", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002210" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002329", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002215" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002496" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002497" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002479", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/BFO_0000066" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/RO_0000057" ] @@ -55303,24 +50230,12 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000066", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000066", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002314", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0000052", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0001025", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0001025", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002005", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002005", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002005", "http://purl.obolibrary.org/obo/RO_0002380" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002100", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002100", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/uberon/core#extends_fibers_into", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002100", "http://purl.obolibrary.org/obo/RO_0013001" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002102", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002102", "http://purl.obolibrary.org/obo/BFO_0000050" ] @@ -55336,24 +50251,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002131", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002131", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002134", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002134", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002150", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002170", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002176", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002178", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002202", "http://purl.obolibrary.org/obo/RO_0002162" ] @@ -55390,9 +50290,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0019002", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002213", "http://purl.obolibrary.org/obo/RO_0019002" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002216", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002215", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002215", "http://purl.obolibrary.org/obo/RO_0002162" ] @@ -55441,9 +50338,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002254", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002256", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002258", "http://purl.obolibrary.org/obo/RO_0002496" ] @@ -55465,9 +50359,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004031", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/BFO_0000051" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002432", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/BFO_0000066" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002327", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002017" ] @@ -55531,15 +50422,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002339", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002339", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002177", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002371", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002371", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002387", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002407", "http://purl.obolibrary.org/obo/RO_0002629" ] @@ -55552,15 +50434,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002488", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002488", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002488", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002492", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002492", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002492", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002496", "http://purl.obolibrary.org/obo/BFO_0000050" ] @@ -55579,9 +50455,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002497", "http://purl.obolibrary.org/obo/RO_0002082" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/uberon/core#indirectly_supplies", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002569", "http://purl.obolibrary.org/obo/RO_0002178" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/uberon/core#indirectly_supplies", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002569", "http://purl.obolibrary.org/obo/uberon/core#indirectly_supplies" ] @@ -55600,12 +50473,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002630", "http://purl.obolibrary.org/obo/RO_0002630" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0003000", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0003001", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0013001", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0013001", "http://purl.obolibrary.org/obo/BFO_0000050" ] diff --git a/src/ontology/subsets/eye_upper_slim.obo b/src/ontology/subsets/eye_upper_slim.obo index 998c256f5..d5390cbe7 100644 --- a/src/ontology/subsets/eye_upper_slim.obo +++ b/src/ontology/subsets/eye_upper_slim.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: cl/releases/2024-02-13/subsets/eye_upper_slim.owl +data-version: cl/releases/2024-04-05/subsets/eye_upper_slim.owl subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -88,7 +88,7 @@ synonymtypedef: synonym "" synonymtypedef: SYSTEMATIC "" synonymtypedef: systematic_synonym "" ontology: cl/subsets/eye_upper_slim -property_value: owl:versionInfo "2024-02-13" xsd:string +property_value: owl:versionInfo "2024-04-05" xsd:string [Term] id: BFO:0000002 @@ -159,16 +159,17 @@ is_a: UBERON:0000061 ! anatomical structure disjoint_from: GO:0031012 ! extracellular matrix disjoint_from: GO:0032991 ! protein-containing complex disjoint_from: GO:0043226 ! organelle -relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms +relationship: RO:0002160 NCBITaxon:131567 ! only in taxon cellular organisms [Term] id: CL:0000005 -name: fibroblast neural crest derived -def: "Any fibroblast that is deriived from the neural crest." [https://orcid.org/0000-0001-5208-3432] +name: neural crest derived fibroblast +def: "Any fibroblast that is derived from the neural crest." [https://orcid.org/0000-0001-5208-3432] +synonym: "fibroblast neural crest derived" EXACT [] is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast -intersection_of: develops_from CL:0000333 ! migratory neural crest cell -relationship: develops_from CL:0000008 ! migratory cranial neural crest cell +intersection_of: RO:0002202 CL:0000333 ! develops from migratory neural crest cell +relationship: RO:0002202 CL:0000008 ! develops from migratory cranial neural crest cell [Term] id: CL:0000006 @@ -198,7 +199,7 @@ id: CL:0000030 name: glioblast subset: cellxgene_subset is_a: CL:0000055 ! non-terminally differentiated cell -relationship: develops_from CL:0000133 ! neurectodermal cell +relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell [Term] id: CL:0000031 @@ -210,7 +211,7 @@ xref: BTO:0000930 xref: FMA:70563 is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0000255 ! eukaryotic cell -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata [Term] id: CL:0000034 @@ -227,8 +228,8 @@ is_a: CL:0011115 ! precursor cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0017145 ! stem cell division relationship: capable_of GO:0017145 ! stem cell division -relationship: in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000037 @@ -278,8 +279,8 @@ relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surfac relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -relationship: develops_from CL:0000566 ! angioblastic mesenchymal cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000566 ! develops from angioblastic mesenchymal cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000038 @@ -296,7 +297,7 @@ synonym: "erythroid stem cell" RELATED [] xref: BTO:0004911 is_a: CL:0000764 ! erythroid lineage cell is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor cell -relationship: develops_from CL:0000050 ! megakaryocyte-erythroid progenitor cell +relationship: RO:0002202 CL:0000050 ! develops from megakaryocyte-erythroid progenitor cell [Term] id: CL:0000048 @@ -331,7 +332,7 @@ synonym: "pluripotent stem cell (bone marrow)" RELATED [ISBN:0878932437] xref: BTO:0004730 is_a: CL:0002032 {is_inferred="true"} ! hematopoietic oligopotent progenitor cell disjoint_from: CL:0000050 ! megakaryocyte-erythroid progenitor cell -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000050 @@ -355,7 +356,7 @@ intersection_of: capable_of GO:0030218 ! erythrocyte differentiation intersection_of: capable_of GO:0030219 ! megakaryocyte differentiation relationship: capable_of GO:0030218 ! erythrocyte differentiation relationship: capable_of GO:0030219 ! megakaryocyte differentiation -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000052 @@ -402,8 +403,8 @@ xref: FMA:63877 xref: NCIT:C12482 xref: VHOG:0001482 is_a: CL:0002320 ! connective tissue cell -relationship: develops_from CL:0000134 ! mesenchymal stem cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000066 @@ -421,8 +422,8 @@ xref: FMA:66768 xref: WBbt:0003672 is_a: CL:0000000 ! cell relationship: part_of UBERON:0000483 ! epithelium -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000071 @@ -435,9 +436,9 @@ is_a: CL:0000076 {is_inferred="true"} ! squamous epithelial cell is_a: CL:0002139 ! endothelial cell of vascular tree intersection_of: CL:0000076 ! squamous epithelial cell intersection_of: part_of UBERON:0004638 ! blood vessel endothelium -relationship: develops_from CL:0002546 ! embryonic blood vessel endothelial progenitor cell relationship: part_of UBERON:0004638 ! blood vessel endothelium -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0002546 ! develops from embryonic blood vessel endothelial progenitor cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000075 @@ -446,7 +447,7 @@ def: "A columnar/cuboidal epithelial cell is a cell usually found in a two dimen subset: cellxgene_subset subset: human_reference_atlas is_a: CL:0000066 ! epithelial cell -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000076 @@ -466,7 +467,7 @@ xref: FMA:66773 is_a: CL:0000076 ! squamous epithelial cell is_a: CL:0000213 ! lining cell is_a: CL:0002078 ! meso-epithelial cell -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000081 @@ -486,7 +487,7 @@ id: CL:0000095 name: neuron associated cell subset: cellxgene_subset is_a: CL:0002319 ! neural cell -relationship: develops_from CL:0000133 ! neurectodermal cell +relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell [Term] id: CL:0000099 @@ -499,7 +500,7 @@ xref: FBbt:00005125 xref: FMA:67313 xref: WBbt:0005113 is_a: CL:0000540 ! neuron -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000101 @@ -540,14 +541,14 @@ xref: CALOHA:TS-0278 xref: FMA:66772 is_a: CL:0000213 ! lining cell is_a: CL:0002078 ! meso-epithelial cell -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000117 name: CNS neuron (sensu Vertebrata) is_a: CL:0000540 ! neuron -relationship: develops_from CL:0000031 ! neuroblast (sensu Vertebrata) relationship: part_of UBERON:0001017 ! central nervous system +relationship: RO:0002202 CL:0000031 ! develops from neuroblast (sensu Vertebrata) [Term] id: CL:0000123 @@ -555,8 +556,8 @@ name: neuron associated cell (sensu Vertebrata) subset: cellxgene_subset is_a: CL:0000095 ! neuron associated cell is_a: CL:0000255 ! eukaryotic cell -relationship: develops_from CL:0000333 ! migratory neural crest cell -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell [Term] id: CL:0000125 @@ -584,7 +585,7 @@ xref: BTO:0000771 xref: CALOHA:TS-2027 xref: FMA:54538 is_a: CL:0000125 ! glial cell -relationship: develops_from CL:0000339 ! glioblast (sensu Vertebrata) +relationship: RO:0002202 CL:0000339 ! develops from glioblast (sensu Vertebrata) [Term] id: CL:0000127 @@ -598,7 +599,7 @@ xref: BTO:0000099 xref: CALOHA:TS-0060 xref: FMA:54537 is_a: CL:0000126 ! macroglial cell -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000132 @@ -611,9 +612,9 @@ xref: CALOHA:TS-0172 xref: FMA:70614 is_a: CL:0000115 ! endothelial cell is_a: CL:0000710 ! neurecto-epithelial cell -relationship: develops_from CL:0000008 ! migratory cranial neural crest cell relationship: part_of UBERON:0001985 ! corneal endothelium -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000008 ! develops from migratory cranial neural crest cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000133 @@ -671,11 +672,11 @@ xref: MESH:D008544 xref: VHOG:0001679 is_a: CL:0000147 ! pigment cell intersection_of: CL:0000147 ! pigment cell -intersection_of: develops_from CL:0000541 ! melanoblast intersection_of: has_part GO:0042470 ! melanosome -relationship: develops_from CL:0000541 ! melanoblast +intersection_of: RO:0002202 CL:0000541 ! develops from melanoblast relationship: has_part GO:0042470 ! melanosome -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000541 ! develops from melanoblast +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000149 @@ -717,8 +718,8 @@ xref: FMA:67328 xref: WBbt:0003675 is_a: CL:0000183 ! contractile cell is_a: CL:0000393 ! electrically responsive cell -relationship: develops_from CL:0000056 ! myoblast -property_value: depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI +relationship: RO:0002202 CL:0000056 ! develops from myoblast +property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI [Term] id: CL:0000192 @@ -736,8 +737,8 @@ xref: CALOHA:TS-2159 xref: FMA:14072 is_a: CL:0008000 ! non-striated muscle cell is_a: CL:0008007 ! visceral muscle cell -relationship: develops_from CL:0000514 ! smooth muscle myoblast -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000514 ! develops from smooth muscle myoblast +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000197 @@ -764,7 +765,7 @@ is_a: CL:0000006 {is_inferred="true"} ! neuronal receptor cell intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0050962 ! detection of light stimulus involved in sensory perception relationship: capable_of GO:0050962 ! detection of light stimulus involved in sensory perception -property_value: depiction "https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg" xsd:anyURI [Term] id: CL:0000211 @@ -847,8 +848,8 @@ intersection_of: CL:4030046 PR:000001945 ! lacks_plasma_membrane_part transferri relationship: bearer_of PATO:0002039 ! biconcave relationship: CL:4030045 GO:0005840 ! lacks_part ribosome relationship: CL:4030046 PR:000001945 ! lacks_plasma_membrane_part transferrin receptor protein 1 -relationship: develops_from CL:0000558 ! reticulocyte -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000558 ! develops from reticulocyte +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000255 @@ -857,8 +858,8 @@ subset: cellxgene_subset xref: MESH:D005057 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell -intersection_of: only_in_taxon NCBITaxon:2759 ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +intersection_of: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota [Term] id: CL:0000287 @@ -870,7 +871,7 @@ is_a: CL:0000210 ! photoreceptor cell intersection_of: CL:0000210 ! photoreceptor cell intersection_of: part_of UBERON:0000970 ! eye relationship: part_of UBERON:0000970 ! eye -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000293 @@ -908,7 +909,7 @@ xref: FMA:86667 is_a: CL:0000219 ! motile cell is_a: CL:0011012 ! neural crest cell is_a: CL:0011026 ! progenitor cell -relationship: develops_from CL:0007004 ! premigratory neural crest cell +relationship: RO:0002202 CL:0007004 ! develops from premigratory neural crest cell [Term] id: CL:0000335 @@ -932,7 +933,7 @@ name: pigment cell (sensu Vertebrata) def: "Any animal cell containing pigment granules." [GOC:tfm, ISBN:0721662544] is_a: CL:0000147 ! pigment cell is_a: CL:0000255 ! eukaryotic cell -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata [Term] id: CL:0000347 @@ -942,8 +943,8 @@ subset: eye_upper_slim is_a: CL:0000293 ! structural cell intersection_of: CL:0000293 ! structural cell intersection_of: part_of UBERON:0001773 ! sclera -relationship: develops_from CL:0000008 ! migratory cranial neural crest cell relationship: part_of UBERON:0001773 ! sclera +relationship: RO:0002202 CL:0000008 ! develops from migratory cranial neural crest cell [Term] id: CL:0000348 @@ -953,8 +954,8 @@ subset: eye_upper_slim is_a: CL:0000293 ! structural cell intersection_of: CL:0000293 ! structural cell intersection_of: part_of UBERON:0001776 ! optic choroid -relationship: develops_from CL:0000008 ! migratory cranial neural crest cell relationship: part_of UBERON:0001776 ! optic choroid +relationship: RO:0002202 CL:0000008 ! develops from migratory cranial neural crest cell [Term] id: CL:0000352 @@ -974,8 +975,8 @@ is_a: CL:0000007 ! early embryonic cell (metazoa) is_a: CL:0000255 ! eukaryotic cell is_a: CL:0010017 ! zygote intersection_of: CL:0010017 ! zygote -intersection_of: only_in_taxon NCBITaxon:33208 ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +intersection_of: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa [Term] id: CL:0000393 @@ -993,7 +994,7 @@ is_a: CL:0000099 ! interneuron is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000099 ! interneuron intersection_of: RO:0002100 UBERON:0001017 ! has soma location central nervous system -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000404 @@ -1011,8 +1012,8 @@ synonym: "satellite cell" RELATED [] xref: FMA:84798 is_a: CL:0000056 ! myoblast intersection_of: CL:0000056 ! myoblast -intersection_of: develops_into CL:0000192 ! smooth muscle cell -relationship: develops_into CL:0000192 ! smooth muscle cell +intersection_of: RO:0002203 CL:0000192 ! develops into smooth muscle cell +relationship: RO:0002203 CL:0000192 ! develops into smooth muscle cell [Term] id: CL:0000526 @@ -1022,7 +1023,7 @@ subset: human_reference_atlas synonym: "input neuron" EXACT [] xref: FMA:87653 is_a: CL:0000540 ! neuron -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000529 @@ -1049,8 +1050,8 @@ is_a: CL:0000393 ! electrically responsive cell is_a: CL:0000404 ! electrically signaling cell is_a: CL:0002319 ! neural cell relationship: capable_of GO:0019226 ! transmission of nerve impulse -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://www.swissbiopics.org/api/image/Neuron_cells.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Neuron_cells.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000541 @@ -1061,7 +1062,7 @@ xref: BTO:0003217 xref: FMA:83377 is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0011026 ! progenitor cell -relationship: develops_from CL:0000333 ! migratory neural crest cell +relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell [Term] id: CL:0000547 @@ -1104,10 +1105,10 @@ relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-span relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD5 relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G -relationship: develops_from CL:0000038 ! erythroid progenitor cell relationship: has_part CL:0017503 ! basophilic cytoplasm relationship: has_part GO:0005730 ! nucleolus relationship: RO:0002104 PR:000001945 ! has plasma membrane part transferrin receptor protein 1 +relationship: RO:0002202 CL:0000038 ! develops from erythroid progenitor cell [Term] id: CL:0000549 @@ -1145,10 +1146,10 @@ intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017504 ! polychromatophilic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin intersection_of: RO:0002104 PR:000001945 ! has plasma membrane part transferrin receptor protein 1 -relationship: develops_from CL:0000549 ! basophilic erythroblast relationship: has_part CL:0017504 ! polychromatophilic cytoplasm relationship: has_part GO:0000792 ! heterochromatin relationship: RO:0002104 PR:000001945 ! has plasma membrane part transferrin receptor protein 1 +relationship: RO:0002202 CL:0000549 ! develops from basophilic erythroblast [Term] id: CL:0000552 @@ -1164,9 +1165,9 @@ is_a: CL:0000765 {is_inferred="true"} ! erythroblast intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017502 ! acidophilic cytoplasm intersection_of: participates_in GO:0030263 ! apoptotic chromosome condensation -relationship: develops_from CL:0000550 ! polychromatophilic erythroblast relationship: has_part CL:0017502 ! acidophilic cytoplasm relationship: participates_in GO:0030263 ! apoptotic chromosome condensation +relationship: RO:0002202 CL:0000550 ! develops from polychromatophilic erythroblast [Term] id: CL:0000553 @@ -1220,8 +1221,8 @@ relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surfac relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -relationship: develops_from CL:0000050 ! megakaryocyte-erythroid progenitor cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000050 ! develops from megakaryocyte-erythroid progenitor cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000556 @@ -1240,8 +1241,8 @@ xref: FMA:83555 is_a: CL:0000763 {is_inferred="true"} ! myeloid cell disjoint_from: CL:0000764 ! erythroid lineage cell relationship: bearer_of PATO:0001393 ! euploid -relationship: develops_from CL:0000553 ! megakaryocyte progenitor cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000553 ! develops from megakaryocyte progenitor cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000558 @@ -1280,8 +1281,8 @@ relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-span relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD5 relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G -relationship: develops_from CL:0000552 ! orthochromatic erythroblast relationship: RO:0002104 PR:000001945 ! has plasma membrane part transferrin receptor protein 1 +relationship: RO:0002202 CL:0000552 ! develops from orthochromatic erythroblast [Term] id: CL:0000561 @@ -1297,10 +1298,10 @@ xref: BTO:0004044 xref: FMA:67766 is_a: CL:0000099 ! interneuron is_a: CL:0009004 ! retinal cell -relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0000966 ! retina -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002120 CL:0000740 ! synapsed to retinal ganglion cell +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000566 @@ -1316,10 +1317,10 @@ intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: RO:0002104 PR:000001444 ! has plasma membrane part cadherin-5 intersection_of: RO:0002104 PR:000002112 ! has plasma membrane part vascular endothelial growth factor receptor 2 intersection_of: RO:0002104 PR:000016043 ! has plasma membrane part T-cell acute lymphocytic leukemia protein 1 -relationship: develops_from CL:0000134 ! mesenchymal stem cell relationship: RO:0002104 PR:000001444 ! has plasma membrane part cadherin-5 relationship: RO:0002104 PR:000002112 ! has plasma membrane part vascular endothelial growth factor receptor 2 relationship: RO:0002104 PR:000016043 ! has plasma membrane part T-cell acute lymphocytic leukemia protein 1 +relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell [Term] id: CL:0000573 @@ -1332,8 +1333,8 @@ xref: BTO:0001036 xref: CALOHA:TS-0866 xref: FMA:67748 is_a: CL:0010009 ! camera-type eye photoreceptor cell -relationship: develops_from CL:0002672 ! retinal progenitor cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0002672 ! develops from retinal progenitor cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000575 @@ -1351,7 +1352,7 @@ is_a: CL:0002159 ! general ecto-epithelial cell intersection_of: CL:0000076 ! squamous epithelial cell intersection_of: part_of UBERON:0001772 ! corneal epithelium relationship: part_of UBERON:0001772 ! corneal epithelium -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000604 @@ -1364,8 +1365,8 @@ xref: BTO:0001024 xref: CALOHA:TS-0870 xref: FMA:67747 is_a: CL:0010009 ! camera-type eye photoreceptor cell -relationship: develops_from CL:0002672 ! retinal progenitor cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0002672 ! develops from retinal progenitor cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000636 @@ -1381,7 +1382,7 @@ xref: BTO:0003064 is_a: CL:0000681 ! radial glial cell is_a: CL:0009004 ! retinal cell relationship: part_of UBERON:0000966 ! retina -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000679 @@ -1396,7 +1397,7 @@ is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0061535 ! glutamate secretion, neurotransmission relationship: capable_of GO:0061535 ! glutamate secretion, neurotransmission -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000680 @@ -1405,9 +1406,9 @@ def: "A non-terminally differentiated cell that is capable of developing into a subset: cellxgene_subset is_a: CL:0000055 ! non-terminally differentiated cell intersection_of: CL:0011115 ! precursor cell -intersection_of: develops_into CL:0000187 ! muscle cell -relationship: develops_from CL:0000222 ! mesodermal cell -relationship: develops_into CL:0000187 ! muscle cell +intersection_of: RO:0002203 CL:0000187 ! develops into muscle cell +relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell +relationship: RO:0002203 CL:0000187 ! develops into muscle cell [Term] id: CL:0000681 @@ -1417,7 +1418,7 @@ comment: Unlike that of mammals, the brain of adult teleost fish exhibits an int subset: cellxgene_subset synonym: "forebrain radial glial cell" NARROW [] is_a: CL:0000125 ! glial cell -relationship: develops_from CL:0000710 ! neurecto-epithelial cell +relationship: RO:0002202 CL:0000710 ! develops from neurecto-epithelial cell [Term] id: CL:0000710 @@ -1430,8 +1431,8 @@ xref: FMA:70557 is_a: CL:0000075 ! columnar/cuboidal epithelial cell is_a: CL:0002077 ! ecto-epithelial cell intersection_of: CL:0002077 ! ecto-epithelial cell -intersection_of: develops_from CL:0000133 ! neurectodermal cell -relationship: develops_from CL:0000133 ! neurectodermal cell +intersection_of: RO:0002202 CL:0000133 ! develops from neurectodermal cell +relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell [Term] id: CL:0000723 @@ -1459,8 +1460,8 @@ xref: BTO:0001800 xref: FMA:67765 xref: MESH:D012165 is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002100 UBERON:0000966 ! has soma location retina +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000745 @@ -1474,8 +1475,8 @@ synonym: "HCs" RELATED OMO:0003004 [doi:10.1038/s41598-020-66092-9] synonym: "horizontal cell" EXACT [] xref: BTO:0004120 is_a: CL:0000099 ! interneuron -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002100 UBERON:0003902 ! has soma location retinal neural layer +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000748 @@ -1493,8 +1494,8 @@ is_a: CL:0008028 ! visual system neuron is_a: CL:0009004 ! retinal cell intersection_of: CL:0000103 ! bipolar neuron intersection_of: RO:0002100 UBERON:0001791 ! has soma location inner nuclear layer of retina -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002100 UBERON:0001791 ! has soma location inner nuclear layer of retina +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000763 @@ -1506,8 +1507,8 @@ xref: CALOHA:TS-0647 xref: MESH:D022423 is_a: CL:0000988 {is_inferred="true"} ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell -intersection_of: develops_from CL:0000049 ! common myeloid progenitor -relationship: develops_from CL:0000049 ! common myeloid progenitor +intersection_of: RO:0002202 CL:0000049 ! develops from common myeloid progenitor +relationship: RO:0002202 CL:0000049 ! develops from common myeloid progenitor [Term] id: CL:0000764 @@ -1521,7 +1522,7 @@ xref: CALOHA:TS-0290 xref: FMA:62845 xref: FMA:83516 is_a: CL:0000763 ! myeloid cell -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000765 @@ -1564,8 +1565,8 @@ relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-span relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD5 relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G -relationship: develops_from CL:0000547 ! proerythroblast relationship: has_part GO:0005634 ! nucleus +relationship: RO:0002202 CL:0000547 ! develops from proerythroblast [Term] id: CL:0000837 @@ -1612,9 +1613,9 @@ relationship: CL:4030046 PR:000001869 ! lacks_plasma_membrane_part interleukin-7 relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -relationship: develops_from CL:0000037 ! hematopoietic stem cell -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule +relationship: RO:0002202 CL:0000037 ! develops from hematopoietic stem cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000839 @@ -1632,7 +1633,7 @@ is_a: CL:0011026 ! progenitor cell intersection_of: CL:0002031 ! hematopoietic lineage restricted progenitor cell intersection_of: capable_of GO:0030099 ! myeloid cell differentiation relationship: capable_of GO:0030099 ! myeloid cell differentiation -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000988 @@ -1658,8 +1659,8 @@ intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001400 ! unipotent disjoint_from: CL:0002032 ! hematopoietic oligopotent progenitor cell relationship: bearer_of PATO:0001400 ! unipotent -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002032 ! hematopoietic oligopotent progenitor cell +relationship: RO:0002202 CL:0002032 ! develops from hematopoietic oligopotent progenitor cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:20Z [Term] @@ -1672,8 +1673,8 @@ is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001401 ! oligopotent relationship: bearer_of PATO:0001401 ! oligopotent -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000837 ! hematopoietic multipotent progenitor cell +relationship: RO:0002202 CL:0000837 ! develops from hematopoietic multipotent progenitor cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:27Z [Term] @@ -1683,9 +1684,9 @@ def: "An epithelial cell derived from ectoderm." [FMA:69074, GOC:tfm] xref: FMA:69074 is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell -intersection_of: develops_from CL:0000221 ! ectodermal cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000221 ! ectodermal cell +intersection_of: RO:0002202 CL:0000221 ! develops from ectodermal cell +relationship: RO:0002202 CL:0000221 ! develops from ectodermal cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T03:38:22Z [Term] @@ -1696,9 +1697,9 @@ synonym: "epithelial mesenchymal cell" EXACT [] xref: FMA:69076 is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell -intersection_of: develops_from CL:0000222 ! mesodermal cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000222 ! mesodermal cell +intersection_of: RO:0002202 CL:0000222 ! develops from mesodermal cell +relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T03:49:14Z [Term] @@ -1713,7 +1714,7 @@ xref: BTO:0001854 xref: CALOHA:TS-1106 xref: FMA:67755 is_a: CL:0000115 ! endothelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T02:06:40Z [Term] @@ -1722,7 +1723,7 @@ name: general ecto-epithelial cell def: "Epithelial cells derived from general body ectoderm and ectoderm placodes." [GOC:tfm] xref: FMA:70556 is_a: CL:0002077 ! ecto-epithelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-26T08:31:08Z [Term] @@ -1733,8 +1734,8 @@ subset: eye_upper_slim xref: FMA:70950 is_a: CL:0000066 ! epithelial cell is_a: CL:0000306 ! crystallin accumulating cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0000965 ! lens of camera-type eye +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T10:38:03Z [Term] @@ -1746,7 +1747,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0002505 ! nucleated relationship: bearer_of PATO:0002505 ! nucleated -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T03:32:33Z [Term] @@ -1760,9 +1761,9 @@ subset: human_reference_atlas synonym: "PE cell" EXACT [https://doi.org/10.1016/j.exer.2003.09.021] xref: FMA:70606 is_a: CL:0000529 ! pigmented epithelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001778 ! ciliary epithelium -relationship: present_in_taxon NCBITaxon:9606 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-09-13T04:09:27Z [Term] @@ -1777,9 +1778,9 @@ synonym: "nonpigmented ciliary epithelial cell" EXACT [PMID:10913011] synonym: "NPE cell" EXACT [https://doi.org/10.1016/j.exer.2003.09.021] xref: FMA:70607 is_a: CL:0000710 ! neurecto-epithelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001778 ! ciliary epithelium -relationship: present_in_taxon NCBITaxon:9606 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-09-13T04:09:31Z [Term] @@ -1792,8 +1793,8 @@ xref: FMA:70333 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001016 ! nervous system -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001016 ! nervous system +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T01:34:57Z [Term] @@ -1807,8 +1808,8 @@ xref: MESH:D003239 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0002384 ! connective tissue -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002384 ! connective tissue +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T03:01:54Z [Term] @@ -1819,7 +1820,7 @@ xref: CALOHA:TS-0263 xref: FMA:82840 xref: WBbt:0007028 is_a: CL:0000000 ! cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T03:39:21Z [Term] @@ -1831,12 +1832,12 @@ subset: eye_upper_slim subset: human_reference_atlas synonym: "corneal fibroblast" EXACT [] synonym: "corneal keratocyte" EXACT [] -is_a: CL:0000005 ! fibroblast neural crest derived +is_a: CL:0000005 ! neural crest derived fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001777 ! substantia propria of cornea -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001777 ! substantia propria of cornea -relationship: present_in_taxon NCBITaxon:9606 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-09-22T01:57:40Z [Term] @@ -1848,8 +1849,8 @@ is_a: CL:0000148 ! melanocyte is_a: CL:0009004 ! retinal cell intersection_of: CL:0000148 ! melanocyte intersection_of: part_of UBERON:0000966 ! retina -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0000966 ! retina +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-03T03:25:32Z [Term] @@ -1865,8 +1866,8 @@ xref: FMA:84791 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0007100 ! primary circulatory organ -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0007100 ! primary circulatory organ +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T09:37:22Z [Term] @@ -1875,7 +1876,7 @@ name: embryonic blood vessel endothelial progenitor cell def: "An endothelial progenitor cell that participates in angiogenesis during development." [GOC:tfm] comment: See CL:0002619. is_a: CL:0000222 ! mesodermal cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T04:20:39Z [Term] @@ -1888,9 +1889,9 @@ is_a: CL:0000066 ! epithelial cell is_a: CL:0000342 {is_inferred="true"} ! pigment cell (sensu Vertebrata) intersection_of: CL:0000342 ! pigment cell (sensu Vertebrata) intersection_of: part_of UBERON:0002506 ! iris epithelium -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002506 ! iris epithelium -relationship: present_in_taxon NCBITaxon:9606 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2011-03-01T05:28:52Z [Term] @@ -1904,9 +1905,9 @@ is_a: CL:0000071 {is_inferred="true"} ! blood vessel endothelial cell is_a: CL:0009004 ! retinal cell intersection_of: CL:0000071 ! blood vessel endothelial cell intersection_of: part_of UBERON:0000966 ! retina -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0000966 ! retina -relationship: present_in_taxon NCBITaxon:9606 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2011-03-06T03:28:27Z [Term] @@ -1923,10 +1924,10 @@ is_a: CL:0000149 ! visual pigment cell is_a: CL:0009004 ! retinal cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001782 ! pigmented layer of retina -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: has_part GO:0042470 ! melanosome relationship: part_of UBERON:0001782 ! pigmented layer of retina -relationship: present_in_taxon NCBITaxon:9606 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2011-03-06T03:37:09Z [Term] @@ -1934,8 +1935,8 @@ id: CL:0002672 name: retinal progenitor cell def: "A multi-fate stem cell that can give rise to different retinal cell types including rod and cone cells." [GOC:tfm, PMID:20959166, PMID:21148186] is_a: CL:0000048 ! multi fate stem cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000133 ! neurectodermal cell +relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-08-16T02:38:01Z [Term] @@ -1953,9 +1954,9 @@ id: CL:0007004 name: premigratory neural crest cell def: "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells." [UBERONREF:0000002] is_a: CL:0011012 ! neural crest cell -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 -relationship: develops_from CL:0000133 ! neurectodermal cell relationship: part_of UBERON:0002342 ! neural crest +relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-27T08:27:35Z [Term] @@ -1991,7 +1992,7 @@ synonym: "mesenchyme cell" EXACT [] is_a: CL:0000219 ! motile cell relationship: capable_of GO:0016477 ! cell migration relationship: part_of UBERON:0003104 ! mesenchyme -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0008028 @@ -2000,7 +2001,7 @@ is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron intersection_of: capable_of_part_of GO:0007601 ! visual perception relationship: capable_of_part_of GO:0007601 ! visual perception -relationship: dc-contributor https://orcid.org/0000-0002-7073-9172 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-09T19:12:36Z [Term] @@ -2019,9 +2020,10 @@ id: CL:0010009 name: camera-type eye photoreceptor cell synonym: "camera type eye photoreceptor cell" EXACT [] is_a: CL:0000287 ! eye photoreceptor cell +is_a: CL:0009004 ! retinal cell intersection_of: CL:0000210 ! photoreceptor cell intersection_of: part_of UBERON:0000019 ! camera-type eye -relationship: part_of UBERON:0000019 ! camera-type eye +relationship: part_of UBERON:0000966 {seeAlso="https://github.com/obophenotype/cell-ontology/issues/2245"} ! retina [Term] id: CL:0010017 @@ -2029,7 +2031,7 @@ name: zygote def: "A zygote in a plant or an animal." [] xref: MESH:D015053 is_a: CL:0000000 ! cell -relationship: seeAlso https://github.com/obophenotype/cell-ontology/issues/786 +property_value: seeAlso https://github.com/obophenotype/cell-ontology/issues/786 [Term] id: CL:0011012 @@ -2046,9 +2048,9 @@ def: "A precursor cell that has a tendency to differentiate into a specific type subset: cellxgene_subset is_a: CL:0011115 ! precursor cell intersection_of: CL:0011115 ! precursor cell -intersection_of: develops_from CL:0000034 ! stem cell -relationship: dc-contributor https://orcid.org/0000-0001-5208-3432 -relationship: develops_from CL:0000034 ! stem cell +intersection_of: RO:0002202 CL:0000034 ! develops from stem cell +relationship: RO:0002202 CL:0000034 ! develops from stem cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011104 @@ -2080,7 +2082,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0002418 ! acidophilic relationship: bearer_of PATO:0002418 ! acidophilic -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-22T04:23:25Z [Term] @@ -2091,7 +2093,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0002094 ! basophilic relationship: bearer_of PATO:0002094 ! basophilic -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-22T04:24:54Z [Term] @@ -2102,7 +2104,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0070047 ! polychromatophilic relationship: bearer_of PATO:0070047 ! polychromatophilic -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-28T04:25:23Z [Term] @@ -2138,8 +2140,8 @@ def: "Any neuron that is part of a central nervous system." [GOC:TermGenie] is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0001017 ! has soma location central nervous system -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: RO:0002100 UBERON:0001017 ! has soma location central nervous system +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-25T01:17:43Z [Term] @@ -2149,9 +2151,9 @@ def: "A retinal cell that is immature or undifferentiated." [PMID:17565741] subset: eye_upper_slim synonym: "retinal stem cell" EXACT [PMID:17565741] is_a: CL:0009004 ! retinal cell -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 -relationship: dc-contributor https://orcid.org/0000-0002-0819-0473 relationship: part_of UBERON:0000966 ! retina +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 [Term] id: CL:4033015 @@ -2164,9 +2166,9 @@ is_a: CL:0000127 ! astrocyte is_a: CL:0009004 ! retinal cell intersection_of: CL:0000127 ! astrocyte intersection_of: part_of UBERON:0000966 ! retina -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: part_of UBERON:0000966 ! retina -property_value: dcterms-date "2023-03-02T14:38:32Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-03-02T14:38:32Z" xsd:dateTime [Term] id: GO:0000278 @@ -2185,8 +2187,8 @@ is_a: GO:0007049 ! cell cycle intersection_of: GO:0007049 ! cell cycle intersection_of: has_part GO:0140014 ! mitotic nuclear division relationship: has_part GO:0140014 ! mitotic nuclear division -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota [Term] id: GO:0000280 @@ -2238,7 +2240,7 @@ namespace: biological_process def: "A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities." [GOC:dph, GOC:go_curators, GOC:tb, ISBN:978-0-07-139011-8] comment: Action potentials typically propagate across excitable membranes. This class covers both action potentials that propagate and those that fail to do so. is_a: GO:0042391 ! regulation of membrane potential -relationship: never_in_taxon NCBITaxon:4895 +property_value: RO:0002161 NCBITaxon:4895 [Term] id: GO:0001677 @@ -2390,7 +2392,7 @@ subset: goslim_mouse subset: goslim_pir xref: Wikipedia:Immune_system is_a: GO:0008150 ! biological_process -relationship: never_in_taxon NCBITaxon:4895 +property_value: RO:0002161 NCBITaxon:4895 [Term] id: GO:0003008 @@ -2489,8 +2491,8 @@ namespace: cellular_component def: "A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures." [GOC:dos, GOC:mah, ISBN:0721639976, PMID:19693541, PMID:21421911] xref: Wikipedia:Collagen is_a: GO:0032991 ! protein-containing complex -relationship: in_taxon NCBITaxon:33208 {all_only="true", source="PMID:12382326"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 {source="PMID:12382326"} ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 {source="PMID:12382326"} ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true", source="PMID:12382326"} ! in taxon Metazoa [Term] id: GO:0005587 @@ -2571,8 +2573,8 @@ xref: NIF_Subcellular:sao1702920020 xref: Wikipedia:Cell_nucleus is_a: GO:0043231 ! intracellular membrane-bounded organelle disjoint_from: GO:0005737 ! cytoplasm -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota [Term] id: GO:0005694 @@ -2809,8 +2811,8 @@ def: "The directed movement of a neurotransmitter into, out of or within a cell, subset: goslim_pir synonym: "sodium:neurotransmitter transport" NARROW [] is_a: GO:0006810 ! transport -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0006865 @@ -2848,11 +2850,11 @@ synonym: "type I programmed cell death" NARROW [] xref: Wikipedia:Apoptosis is_a: GO:0012501 ! programmed cell death relationship: ends_with GO:0097194 ! execution phase of apoptosis -relationship: in_taxon NCBITaxon:33154 {all_only="true"} ! Opisthokonta -relationship: never_in_taxon NCBITaxon:2 -relationship: never_in_taxon NCBITaxon:4896 -relationship: only_in_taxon NCBITaxon:33154 ! Opisthokonta +relationship: RO:0002160 NCBITaxon:33154 ! only in taxon Opisthokonta +relationship: RO:0002162 NCBITaxon:33154 {all_only="true"} ! in taxon Opisthokonta relationship: starts_with GO:0097190 ! apoptotic signaling pathway +property_value: RO:0002161 NCBITaxon:2 +property_value: RO:0002161 NCBITaxon:4896 [Term] id: GO:0006921 @@ -3372,8 +3374,8 @@ namespace: biological_process def: "The process whose specific outcome is the progression of an embryo over time, from zygote formation until the end of the embryonic life stage. The end of the embryonic life stage is organism-specific and may be somewhat arbitrary; for mammals it is usually considered to be birth, for insects the hatching of the first instar larva from the eggshell." [GOC:go_curators, GOC:isa_complete, GOC:mtg_sensu] synonym: "embryogenesis" BROAD [] is_a: GO:0009790 ! embryo development -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0009888 @@ -3386,14 +3388,14 @@ xref: Wikipedia:Histogenesis is_a: GO:0048856 ! anatomical structure development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0000479 ! tissue -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: never_in_taxon NCBITaxon:147554 -relationship: never_in_taxon NCBITaxon:33630 -relationship: never_in_taxon NCBITaxon:33682 -relationship: never_in_taxon NCBITaxon:38254 -relationship: never_in_taxon NCBITaxon:4891 -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota relationship: results_in_development_of UBERON:0000479 ! tissue +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota +property_value: RO:0002161 NCBITaxon:147554 +property_value: RO:0002161 NCBITaxon:33630 +property_value: RO:0002161 NCBITaxon:33682 +property_value: RO:0002161 NCBITaxon:38254 +property_value: RO:0002161 NCBITaxon:4891 [Term] id: GO:0009987 @@ -3561,7 +3563,7 @@ namespace: biological_process def: "The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues." [GOC:cjm, GOC:dph, GOC:ems, GOC:pf, Wikipedia:Cell_migration] xref: Wikipedia:Cell_migration is_a: GO:0048870 ! cell motility -relationship: never_in_taxon NCBITaxon:4890 +property_value: RO:0002161 NCBITaxon:4890 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24787" xsd:anyURI [Term] @@ -3778,7 +3780,7 @@ subset: goslim_drosophila subset: goslim_flybase_ribbon xref: Wikipedia:Cell_junction is_a: GO:0110165 ! cellular anatomical entity -relationship: never_in_taxon NCBITaxon:4751 +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0030097 @@ -4021,10 +4023,10 @@ subset: goslim_pir synonym: "organismal physiological process" EXACT [] synonym: "single-multicellular organism process" RELATED [] is_a: GO:0008150 ! biological_process -relationship: never_in_taxon NCBITaxon:2 -relationship: never_in_taxon NCBITaxon:2157 -relationship: never_in_taxon NCBITaxon:4896 -relationship: never_in_taxon NCBITaxon:4932 +property_value: RO:0002161 NCBITaxon:2 +property_value: RO:0002161 NCBITaxon:2157 +property_value: RO:0002161 NCBITaxon:4896 +property_value: RO:0002161 NCBITaxon:4932 created_by: jl creation_date: 2012-09-19T16:07:47Z @@ -4190,7 +4192,7 @@ def: "Self-propelled movement of a cell or organism from one location to another subset: goslim_chembl subset: goslim_pir is_a: GO:0008150 ! biological_process -relationship: never_in_taxon NCBITaxon:451864 +property_value: RO:0002161 NCBITaxon:451864 [Term] id: GO:0040016 @@ -4215,11 +4217,11 @@ namespace: cellular_component def: "A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells." [GOC:jl, PMID:11584301] xref: Wikipedia:Melanosome is_a: GO:0048770 ! pigment granule -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: never_in_taxon NCBITaxon:4895 -relationship: never_in_taxon NCBITaxon:6237 {source="GOC:kmv"} -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa relationship: part_of CL:0000148 ! melanocyte +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa +property_value: RO:0002161 NCBITaxon:4895 +property_value: RO:0002161 NCBITaxon:6237 {source="GOC:kmv"} [Term] id: GO:0042592 @@ -4271,8 +4273,8 @@ xref: NIF_Subcellular:sao867568886 is_a: GO:0120025 ! plasma membrane bounded cell projection intersection_of: GO:0120025 ! plasma membrane bounded cell projection intersection_of: part_of CL:0000540 ! neuron -relationship: never_in_taxon NCBITaxon:4751 relationship: part_of CL:0000540 ! neuron +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0043009 @@ -4280,8 +4282,8 @@ name: chordate embryonic development namespace: biological_process def: "The process whose specific outcome is the progression of the embryo over time, from zygote formation through a stage including a notochord and neural tube until birth or egg hatching." [GOC:mtg_sensu] is_a: GO:0009792 ! embryo development ending in birth or egg hatching -relationship: in_taxon NCBITaxon:7711 {all_only="true"} ! Chordata -relationship: only_in_taxon NCBITaxon:7711 ! Chordata +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {all_only="true"} ! in taxon Chordata [Term] id: GO:0043025 @@ -4328,9 +4330,9 @@ xref: FMA:62983 xref: NIF_Subcellular:sao593830697 xref: Wikipedia:Myelin is_a: GO:0110165 ! cellular anatomical entity -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa relationship: part_of CL:0000125 ! glial cell +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0043226 @@ -4551,8 +4553,8 @@ xref: FBbt:00005107 xref: FMA:67301 xref: Wikipedia:Cell_body is_a: GO:0110165 ! cellular anatomical entity -relationship: never_in_taxon NCBITaxon:4890 relationship: part_of CL:0000000 ! cell +property_value: RO:0002161 NCBITaxon:4890 created_by: jl creation_date: 2010-02-05T10:37:16Z @@ -4573,8 +4575,8 @@ synonym: "synaptic junction" EXACT [] xref: NIF_Subcellular:sao914572699 xref: Wikipedia:Chemical_synapse is_a: GO:0030054 ! cell junction -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0046903 @@ -4809,8 +4811,8 @@ is_a: GO:0003008 ! system process intersection_of: GO:0003008 ! system process intersection_of: has_participant UBERON:0001016 ! nervous system relationship: has_participant UBERON:0001016 ! nervous system -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13824" xsd:anyURI [Term] @@ -4990,10 +4992,10 @@ synonym: "positioning within cell" NARROW [] is_a: GO:0051234 ! establishment of localization intersection_of: GO:0051234 ! establishment of localization intersection_of: occurs_in CL:0000000 ! cell -relationship: in_taxon NCBITaxon:131567 {all_only="true"} ! cellular organisms relationship: occurs_in CL:0000000 ! cell -relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms relationship: part_of GO:0051641 ! cellular localization +relationship: RO:0002160 NCBITaxon:131567 ! only in taxon cellular organisms +relationship: RO:0002162 NCBITaxon:131567 {all_only="true"} ! in taxon cellular organisms [Term] id: GO:0051716 @@ -5133,8 +5135,8 @@ name: collagen-containing extracellular matrix namespace: cellular_component def: "An extracellular matrix consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that provides not only essential physical scaffolding for the cellular constituents but can also initiate crucial biochemical and biomechanical cues required for tissue morphogenesis, differentiation and homeostasis. The components are secreted by cells in the vicinity and form a sheet underlying or overlying cells such as endothelial and epithelial cells." [GOC:BHF, GOC:rph, PMID:21123617] is_a: GO:0031012 ! extracellular matrix -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa created_by: dph creation_date: 2018-04-13T12:47:21Z @@ -5531,9 +5533,9 @@ subset: goslim_synapse is_a: GO:0007267 ! cell-cell signaling intersection_of: GO:0007267 ! cell-cell signaling intersection_of: occurs_in GO:0045202 ! synapse -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa relationship: occurs_in GO:0045202 ! synapse -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0099537 @@ -5567,10 +5569,10 @@ subset: goslim_synapse is_a: GO:0023061 ! signal release intersection_of: GO:0023061 ! signal release intersection_of: occurs_in GO:0045202 ! synapse -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa relationship: occurs_in GO:0045202 ! synapse -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa relationship: part_of GO:0099536 ! synaptic signaling +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0110165 @@ -5762,18 +5764,16 @@ namespace: ncbi_taxonomy xref: GC_ID:1 xref: PMID:15371245 is_a: NCBITaxon:337687 ! Muroidea -property_value: has_rank NCBITaxon:family [Term] id: NCBITaxon:10088 name: Mus namespace: ncbi_taxonomy -synonym: "mice" EXACT OMO:0003003 [] +synonym: "mice" EXACT genbank_common_name [] synonym: "mouse" EXACT OMO:0003003 [] synonym: "Mus" EXACT scientific_name [] xref: GC_ID:1 is_a: NCBITaxon:39107 ! Murinae -property_value: has_rank NCBITaxon:genus [Term] id: NCBITaxon:10090 @@ -5784,7 +5784,6 @@ synonym: "house mouse" EXACT genbank_common_name [] synonym: "mouse" EXACT OMO:0003003 [] xref: GC_ID:1 is_a: NCBITaxon:862507 ! Mus -property_value: has_rank NCBITaxon:species [Term] id: NCBITaxon:117570 @@ -5792,7 +5791,6 @@ name: Teleostomi namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:7776 ! Gnathostomata -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:117571 @@ -5802,7 +5800,6 @@ alt_id: NCBITaxon:40673 synonym: "bony vertebrates" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:117570 ! Teleostomi -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:131567 @@ -5818,7 +5815,6 @@ name: Dipnotetrapodomorpha namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:8287 ! Sarcopterygii -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:1437010 @@ -5829,7 +5825,6 @@ xref: GC_ID:1 xref: PMID:11743200 xref: PMID:11791233 is_a: NCBITaxon:9347 ! Eutheria -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:1963758 @@ -5839,7 +5834,6 @@ synonym: "mice and others" EXACT genbank_common_name [] synonym: "Sciurognathi" RELATED in_part [] xref: GC_ID:1 is_a: NCBITaxon:9989 ! Rodentia -property_value: has_rank NCBITaxon:suborder [Term] id: NCBITaxon:2759 @@ -5856,7 +5850,6 @@ xref: GC_ID:1 xref: PMID:23020233 xref: PMID:30257078 is_a: NCBITaxon:131567 ! cellular organisms -property_value: has_rank NCBITaxon:superkingdom [Term] id: NCBITaxon:314146 @@ -5868,7 +5861,6 @@ xref: PMID:12082125 xref: PMID:12878460 xref: PMID:15522813 is_a: NCBITaxon:1437010 ! Boreoeutheria -property_value: has_rank NCBITaxon:superorder [Term] id: NCBITaxon:314147 @@ -5880,7 +5872,6 @@ xref: PMID:11214319 xref: PMID:12082125 xref: PMID:15522813 is_a: NCBITaxon:314146 ! Euarchontoglires -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:32523 @@ -5889,7 +5880,6 @@ namespace: ncbi_taxonomy synonym: "tetrapods" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:1338369 ! Dipnotetrapodomorpha -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:32524 @@ -5898,7 +5888,6 @@ namespace: ncbi_taxonomy synonym: "amniotes" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:32523 ! Tetrapoda -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:32525 @@ -5907,7 +5896,6 @@ namespace: ncbi_taxonomy synonym: "Theria" EXACT scientific_name [] xref: GC_ID:1 is_a: NCBITaxon:40674 ! Mammalia -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:33154 @@ -5917,7 +5905,6 @@ synonym: "Fungi/Metazoa group" RELATED synonym [] synonym: "opisthokonts" RELATED synonym [] xref: GC_ID:1 is_a: NCBITaxon:2759 ! Eukaryota -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:33208 @@ -5929,7 +5916,6 @@ synonym: "metazoans" EXACT genbank_common_name [] synonym: "multicellular animals" EXACT OMO:0003003 [] xref: GC_ID:1 is_a: NCBITaxon:33154 ! Opisthokonta -property_value: has_rank NCBITaxon:kingdom [Term] id: NCBITaxon:33213 @@ -5937,7 +5923,6 @@ name: Bilateria namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:6072 ! Eumetazoa -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:33511 @@ -5946,7 +5931,6 @@ namespace: ncbi_taxonomy synonym: "deuterostomes" EXACT OMO:0003003 [] xref: GC_ID:1 is_a: NCBITaxon:33213 ! Bilateria -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:337687 @@ -5956,7 +5940,6 @@ xref: GC_ID:1 xref: PMID:15019624 xref: PMID:15371245 is_a: NCBITaxon:1963758 ! Myomorpha -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:39107 @@ -5965,7 +5948,6 @@ namespace: ncbi_taxonomy alt_id: NCBITaxon:109679 xref: GC_ID:1 is_a: NCBITaxon:10066 ! Muridae -property_value: has_rank NCBITaxon:subfamily [Term] id: NCBITaxon:40674 @@ -5975,7 +5957,6 @@ synonym: "mammals" EXACT genbank_common_name [] synonym: "mammals" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:32524 ! Amniota -property_value: has_rank NCBITaxon:class [Term] id: NCBITaxon:6072 @@ -5983,7 +5964,6 @@ name: Eumetazoa namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:33208 ! Metazoa -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:7711 @@ -5993,7 +5973,6 @@ synonym: "chordates" EXACT genbank_common_name [] synonym: "chordates" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:33511 ! Deuterostomia -property_value: has_rank NCBITaxon:phylum [Term] id: NCBITaxon:7742 @@ -6004,7 +5983,6 @@ synonym: "vertebrates" EXACT genbank_common_name [] synonym: "vertebrates" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:89593 ! Craniata -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:7776 @@ -6014,7 +5992,6 @@ synonym: "Gnathostomata" EXACT scientific_name [] synonym: "jawed vertebrates" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:7742 ! Vertebrata -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:8287 @@ -6022,7 +5999,6 @@ name: Sarcopterygii namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:117571 ! Euteleostomi -property_value: has_rank NCBITaxon:superclass [Term] id: NCBITaxon:862507 @@ -6031,7 +6007,6 @@ namespace: ncbi_taxonomy synonym: "Mus" EXACT scientific_name [] xref: GC_ID:1 is_a: NCBITaxon:10088 ! Mus -property_value: has_rank NCBITaxon:subgenus [Term] id: NCBITaxon:89593 @@ -6040,7 +6015,6 @@ namespace: ncbi_taxonomy synonym: "Craniata" EXACT scientific_name [] xref: GC_ID:1 is_a: NCBITaxon:7711 ! Chordata -property_value: has_rank NCBITaxon:subphylum [Term] id: NCBITaxon:9347 @@ -6053,7 +6027,6 @@ synonym: "placentals" EXACT genbank_common_name [] synonym: "placentals" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:32525 ! Theria -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:9989 @@ -6063,7 +6036,6 @@ synonym: "rodent" EXACT genbank_common_name [] synonym: "rodents" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:314147 ! Glires -property_value: has_rank NCBITaxon:order [Term] id: PATO:0000001 @@ -6122,7 +6094,6 @@ subset: value_slim synonym: "ramified" EXACT [] synonym: "ramiform" EXACT [] is_a: PATO:0002009 ! branchiness -property_value: RO:0002604 PATO:0000414 [Term] id: PATO:0000411 @@ -6144,7 +6115,6 @@ def: "A morphological quality inhering in a bearer by virtue of the bearer's aff subset: value_slim synonym: "blocked" RELATED [] is_a: PATO:0000136 ! closure -property_value: RO:0002604 PATO:0000610 [Term] id: PATO:0000947 @@ -6180,7 +6150,6 @@ synonym: "clouding" RELATED [] synonym: "cloudy" RELATED [] synonym: "non-transparent" EXACT [] is_a: PATO:0000957 ! opacity -property_value: RO:0002604 PATO:0000964 [Term] id: PATO:0000964 @@ -6192,7 +6161,6 @@ subset: value_slim synonym: "clear" EXACT [] synonym: "hyaline" EXACT [] is_a: PATO:0000957 ! opacity -property_value: RO:0002604 PATO:0000963 [Term] id: PATO:0001018 @@ -6333,7 +6301,6 @@ comment: This refers to the disposition of the bearer. subset: disposition_slim subset: value_slim is_a: PATO:0001579 ! contractility -property_value: RO:0002604 PATO:0001691 [Term] id: PATO:0001857 @@ -6343,7 +6310,6 @@ def: "A shape quality in a bearer by virtue of the bearer's curving inward." [Wo subset: cell_quality subset: value_slim is_a: PATO:0002005 ! concavity -property_value: RO:0002604 PATO:0001355 [Term] id: PATO:0001873 @@ -6411,7 +6377,6 @@ subset: attribute_slim xref: Image:http\://upload.wikimedia.org/wikipedia/commons/0/06/Convex_polygon_illustration1.png is_a: PATO:0002266 ! 3-D shape relationship: RO:0015011 PATO:0002006 ! has cross section 2-D shape -property_value: RO:0002604 PATO:0002008 [Term] id: PATO:0002009 @@ -6437,7 +6402,6 @@ namespace: quality def: "A concave quality inhering in a bearer by virtue of the bearer's curving inward on both sides or surfaces." [PATOC:GVG] subset: value_slim is_a: PATO:0001857 ! concave -property_value: RO:0002604 PATO:0002040 [Term] id: PATO:0002045 @@ -6449,7 +6413,7 @@ synonym: "dendriform" EXACT [] synonym: "dendroid" EXACT [] synonym: "dendroidal" EXACT [] is_a: PATO:0000402 ! branched -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-02-15T08:11:41Z [Term] @@ -6459,7 +6423,7 @@ namespace: quality def: "A quality inhering in a bearer by virtue of the bearer's having an empty space or cavity within." [url:http\://www.merriam-webster.com/dictionary/hollow] subset: value_slim is_a: PATO:0002014 ! structure, cavities -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-09-18T02:19:20Z [Term] @@ -6471,7 +6435,7 @@ subset: disposition_slim subset: mpath_slim subset: value_slim is_a: PATO:0070045 ! anatomical histological quality -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-10-05T12:05:23Z [Term] @@ -6482,7 +6446,7 @@ def: "A quality inhering in a bearer by virtue of the bearer's processing the fo subset: mpath_slim subset: value_slim is_a: PATO:0000141 ! structure -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-10-06T04:37:14Z [Term] @@ -6492,7 +6456,7 @@ namespace: quality def: "A quality inhering in a bearer by virtue of its constitution." [PATOC:GVG] subset: attribute_slim is_a: PATO:0001018 ! physical quality -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-03-15T04:35:27Z [Term] @@ -6502,7 +6466,7 @@ namespace: quality def: "A cylindrical shape quality inhering in a bearer by virtue of the bearer's being imperfectly cylindrical or approximately cylindrical." [url:http\://www.thefreedictionary.com/Subcylindrical] subset: value_slim is_a: PATO:0001873 ! cylindrical -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-07-13T04:22:30Z [Term] @@ -6511,7 +6475,7 @@ name: 3-D shape namespace: quality def: "A shape that inheres in a 3 dimensional entity." [PATOC:OREGON] is_a: PATO:0000052 ! shape -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-10-05T12:31:16Z [Term] @@ -6524,7 +6488,7 @@ synonym: "tube-shaped" EXACT [] synonym: "tubulate" EXACT [] is_a: PATO:0001873 ! cylindrical is_a: PATO:0002078 ! hollow -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-06-08T06:33:50Z [Term] @@ -6535,7 +6499,7 @@ def: "A convex 3-D shape quality inhering in a bearer by virtue of the bearer's comment: Note that a fiber shaped object may take any circuitous or straight path through space (think of a length of string or rope). subset: value_slim is_a: PATO:0002226 ! subcylindrical -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-09-09T04:50:10Z [Term] @@ -6545,7 +6509,7 @@ namespace: quality def: "A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt" [wiktionary:superellipse] synonym: "Lamé curve" EXACT [] is_a: PATO:0002006 ! 2-D shape -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-10-12T12:45:16Z [Term] @@ -6558,7 +6522,7 @@ subset: mpath_slim subset: value_slim synonym: "eosinophilic" EXACT [] is_a: PATO:0070045 ! anatomical histological quality -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2012-12-17T03:01:19Z [Term] @@ -6569,7 +6533,7 @@ def: "A nucleate quality inhering in a bearer by virtue of the bearer's having o subset: mpath_slim subset: value_slim is_a: PATO:0001404 ! nucleate quality -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2013-10-21T05:44:34Z [Term] @@ -6578,7 +6542,7 @@ name: disconnected namespace: quality def: "A structural quality inhering in the bearer by virtue of the bearer consisting of multiple structures lacking any physical connection to each other." [GOC:dos] is_a: PATO:0000141 ! structure -relationship: dc-contributor https://orcid.org/0000-0002-7073-9172 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2014-12-12T08:43:17Z [Term] @@ -6588,7 +6552,7 @@ namespace: quality def: "A quality of a single cell inhering in the bearer by virtue of the bearer's size or shape or structure." [ORCID:0000-0002-7073-9172] comment: Use this term for morphologies that can *only* inhere in a cell, e.g. morphological qualities inhering in a cell by virtue of the presence, location or shape of one or more cell parts. is_a: PATO:0000051 ! morphology -relationship: dc-contributor https://orcid.org/0000-0002-7073-9172 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2021-01-23T11:31:53Z [Term] @@ -6620,7 +6584,7 @@ xref: ILX:0101312 xref: ilxtr:BipolarPhenotype xref: nifext:2 is_a: PATO:0070027 ! bitufted dendrite cell morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070027 @@ -6629,7 +6593,7 @@ namespace: quality def: "A cell morphology that inheres in neurons with dendrites that are bidirectional, emerging from opposite ends of the soma, with the two arbors extending in radial or tangential directions." [PMID:18568015] comment: This morphology type is distinct from bitufted cell morphology in that it refers to bitufted dendrite morphology rather than bitufted cell morphology. is_a: PATO:0010006 ! cell morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070044 @@ -6737,7 +6701,6 @@ synonym: "leukocyte adhesion receptor MO1" EXACT [] synonym: "neutrophil adherence receptor" EXACT [] xref: IUPHARobj:2452 is_a: PR:000001005 ! integrin alpha with A domain -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P11215 [Term] id: PR:000001018 @@ -6793,7 +6756,6 @@ synonym: "NCAM-1" EXACT [] synonym: "NCAM1" EXACT PRO-short-label [PRO:DNx] xref: IUPHARobj:2769 is_a: PR:000001023 ! neural cell adhesion molecule NCAM -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P13591 [Term] id: PR:000001083 @@ -6830,7 +6792,6 @@ synonym: "MAL" RELATED Gene-based [] synonym: "T-cell surface glycoprotein Lyt-2" EXACT [] synonym: "T-lymphocyte differentiation antigen T8/Leu-2" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P01732 [Term] id: PR:000001289 @@ -6874,7 +6835,6 @@ synonym: "CDH5" EXACT PRO-short-label [PRO:DNx] synonym: "vascular endothelial cadherin" EXACT [] synonym: "VE-cadherin" EXACT [] is_a: PR:000001327 ! cadherin -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P33151 [Term] id: PR:000001839 @@ -6889,7 +6849,6 @@ synonym: "lymphocyte antigen 1" EXACT [] synonym: "lymphocyte antigen T1/Leu-1" EXACT [] synonym: "Lyt-1" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P06127 [Term] id: PR:000001869 @@ -6907,7 +6866,6 @@ synonym: "IL7R" EXACT PRO-short-label [PRO:DNx] xref: IUPHARobj:1698 xref: PIRSF:PIRSF001960 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P16871 [Term] id: PR:000001889 @@ -6936,7 +6894,6 @@ synonym: "TFRC" EXACT PRO-short-label [PRO:DNx] synonym: "TR" RELATED [] synonym: "Trfr" RELATED Gene-based [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P02786 [Term] id: PR:000001971 @@ -6965,7 +6922,6 @@ synonym: "VEGFR-2" EXACT [] synonym: "VEGFR2" RELATED Gene-based [] xref: IUPHARobj:1813 is_a: PR:000001971 ! vascular endothelial growth factor receptor -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P35968 [Term] id: PR:000002976 @@ -7010,7 +6966,6 @@ synonym: "SHH" EXACT PRO-short-label [PRO:DNx] synonym: "Shh unprocessed N-terminal signaling and C-terminal autoprocessing domains" EXACT [] synonym: "ShhNC" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q15465 [Term] id: PR:000016043 @@ -7028,7 +6983,6 @@ synonym: "TAL-1" EXACT [] synonym: "TAL1" EXACT PRO-short-label [PRO:DNx] synonym: "TCL5" RELATED Gene-based [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P17542 [Term] id: PR:000025796 @@ -7046,8 +7000,8 @@ def: "A protein that is encoded in the genome of Mus musculus." [PRO:DAN] synonym: "mouse protein" EXACT PRO-short-label [PRO:DAN] is_a: PR:000036194 ! eukaryotic protein intersection_of: PR:000000001 ! protein -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus -relationship: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus +relationship: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:000036194 @@ -7057,8 +7011,8 @@ def: "A protein that is encoded in the genome of some Eukaryota." [PRO:DAN] synonym: "Eukaryota protein" EXACT [PRO:DAN] is_a: PR:000000001 ! protein intersection_of: PR:000000001 ! protein -intersection_of: only_in_taxon NCBITaxon:2759 ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +intersection_of: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota [Term] id: PR:000050567 @@ -7084,9 +7038,9 @@ subset: common_anatomy subset: upper_level xref: BFO:0000003 disjoint_from: UBERON:0001062 ! anatomical entity -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000019 @@ -7123,15 +7077,11 @@ is_a: UBERON:0000047 ! simple eye is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0015212 ! lateral structure -relationship: develops_from UBERON:0003072 {evidence="definitional"} ! optic cup -relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: has_part UBERON:0000965 ! lens of camera-type eye relationship: has_part UBERON:0000966 ! retina -relationship: in_lateral_side_of UBERON:0000033 ! head relationship: part_of UBERON:0004088 ! orbital region -property_value: UBPROP:0000001 "A cavitated compound organ that transduces light waves into neural signals.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000107", ontology="TAO", source="TAO:wd"} -property_value: UBPROP:0000003 "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000275", ontology="VHOG", source="DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "FMA distinguishes Eye (subdivision of face) which has its parts an Eyeball (organ), as well as other structures, and the orbit of skull. MA includes eyelid, conjunctiva and lacrimal apparatus as part of MA:eye - consistent with FMA - so we can infer that MA:eye is more like FMA:eye than FMA:eyeball. For other AOs this distinction is less meaningful - e.g. ZFA has no eyelid; XAO has no eyelid, but it has conjuctiva, which is considered part of the xao:eye. GO considers eyelid development part of eye development. See also notes on optic nerve - XAO, AAO and BTO consider this part of the eye. MA considers the eye muscles part of the eye, whereas FMA has a class 'orbital content' for this" xsd:string {external_ontology="FMA"} +relationship: RO:0002202 UBERON:0003072 ! develops from optic cup +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage [Term] id: UBERON:0000020 @@ -7156,7 +7106,6 @@ xref: CALOHA:TS-2043 xref: EHDAA2:0001824 xref: EHDAA:500 xref: EMAPA:35955 -xref: FBbt:00005155 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: GAID:63 xref: HAO:0000930 xref: MA:0000017 @@ -7171,7 +7120,7 @@ intersection_of: UBERON:0000062 ! organ intersection_of: capable_of GO:0050906 ! detection of stimulus involved in sensory perception relationship: capable_of GO:0050906 ! detection of stimulus involved in sensory perception relationship: part_of UBERON:0001032 ! sensory system -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" xsd:anyURI [Term] id: UBERON:0000025 @@ -7183,11 +7132,9 @@ synonym: "duct" NARROW [] xref: galen:Tube is_a: UBERON:0004111 ! anatomical conduit intersection_of: UBERON:0004111 ! anatomical conduit -intersection_of: has_quality PATO:0002299 ! tubular +intersection_of: RO:0000086 PATO:0002299 ! has quality tubular relationship: has_part UBERON:0013522 ! subdivision of tube -relationship: has_quality PATO:0002299 ! tubular -property_value: IAO:0000232 "not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts)" xsd:string -property_value: UBPROP:0000007 "tubular" xsd:string +relationship: RO:0000086 PATO:0002299 ! has quality tubular [Term] id: UBERON:0000033 @@ -7230,12 +7177,8 @@ xref: Wikipedia:Head xref: XAO:0003024 xref: ZFA:0001114 is_a: UBERON:0011676 ! subdivision of organism along main body axis -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0007811 ! craniocervical region -property_value: RO:0002171 UBERON:0000948 -property_value: UBPROP:0000001 "Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010335", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001114", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001644", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.82", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria [Term] id: UBERON:0000042 @@ -7262,11 +7205,8 @@ is_a: UBERON:0004120 ! mesoderm-derived structure relationship: has_part UBERON:0001136 ! mesothelium relationship: has_part UBERON:0002384 ! connective tissue relationship: part_of UBERON:0000060 ! anatomical wall -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png" xsd:anyURI -property_value: UBPROP:0000001 "A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005425", ontology="TAO", source="Wikipedia:Serous_membrane"} -property_value: UBPROP:0000001 "a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP]" xsd:string {source="Wikipedia:Serous_membrane"} -property_value: UBPROP:0000012 "in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA." xsd:string {external_ontology="FMA"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png" xsd:anyURI [Term] id: UBERON:0000047 @@ -7289,7 +7229,7 @@ subset: human_reference_atlas subset: pheno_slim is_a: UBERON:0004111 ! anatomical conduit relationship: channel_for UBERON:0006314 ! bodily fluid -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000060 @@ -7301,13 +7241,11 @@ subset: upper_level synonym: "organ wall" RELATED [FMA:82482] synonym: "wall" BROAD [] synonym: "wall of organ" EXACT [FMA:82482] -xref: EMAPA:25036 xref: FMA:82482 xref: galen:Wall is_a: UBERON:0000064 ! organ part relationship: adjacent_to UBERON:0002553 ! anatomical cavity relationship: has_part UBERON:0004923 ! organ component layer -property_value: UBPROP:0000012 "in FMA, serosa is a wall" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0000061 @@ -7324,7 +7262,6 @@ xref: BILA:0000003 xref: CARO:0000003 xref: EHDAA2:0003003 xref: EMAPA:0 -xref: FBbt:00007001 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:305751 xref: FMA:67135 xref: GAID:781 @@ -7339,10 +7276,10 @@ xref: VHOG:0001759 xref: XAO:0003000 xref: ZFA:0000037 is_a: UBERON:0000465 ! material anatomical entity -relationship: existence_ends_during_or_before UBERON:0000071 ! death stage -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0002497 UBERON:0000071 ! existence ends during or before death stage +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000062 @@ -7369,14 +7306,12 @@ xref: Wikipedia:Organ_(anatomy) is_a: UBERON:0010000 ! multicellular anatomical structure disjoint_from: UBERON:0034921 ! multi organ part structure relationship: capable_of GO:0008150 ! biological_process -relationship: has_boundary UBERON:0006984 ! anatomical surface -relationship: never_in_taxon NCBITaxon:110815 {source="Wikipedia"} relationship: part_of UBERON:0000467 ! anatomical system -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: UBPROP:0000001 "Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." xsd:string {source="GO:0048513"} -property_value: UBPROP:0000012 "CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4" xsd:string +relationship: RO:0002002 UBERON:0006984 ! has 2D boundary anatomical surface +property_value: RO:0002161 NCBITaxon:110815 {source="Wikipedia"} +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000063 @@ -7389,9 +7324,7 @@ synonym: "organ segment" RELATED [FMA:86140] synonym: "segment of organ" RELATED [FMA:86140] xref: FMA:86140 is_a: UBERON:0000064 ! organ part -property_value: editor_note "FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction" xsd:string -property_value: UBPROP:0000001 "Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball." xsd:string {source="FMA:86140", version="3"} -property_value: UBPROP:0000001 "Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal." xsd:string {source="FMA:86140", version="1"} +property_value: IAO:0000116 "FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction" xsd:string [Term] id: UBERON:0000064 @@ -7412,10 +7345,9 @@ xref: SCTID:113343008 xref: SCTID:91717005 is_a: UBERON:0010000 ! multicellular anatomical structure relationship: part_of UBERON:0000062 ! organ -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: IAO:0000232 "currently defined in a very broad sense, may be replaced by more specific classes in the future" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000066 @@ -7464,7 +7396,7 @@ is_a: UBERON:0000105 ! life cycle stage disjoint_from: UBERON:0000092 ! post-embryonic stage relationship: precedes UBERON:0000066 ! fully formed stage relationship: precedes UBERON:0000092 ! post-embryonic stage -relationship: simultaneous_with GO:0009790 ! embryo development +relationship: RO:0002082 GO:0009790 ! simultaneous with embryo development [Term] id: UBERON:0000071 @@ -7477,11 +7409,10 @@ xref: XAO:0000437 xref: XtroDO:0000085 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage -relationship: ends UBERON:0000104 ! life cycle -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: UBPROP:0000012 "ncit:Death is an outcome" xsd:string {external_ontology="ncit"} +relationship: RO:0002229 UBERON:0000104 ! ends life cycle +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000073 @@ -7498,8 +7429,8 @@ xref: UMLS:C1518256 {source="ncithesaurus:Nervous_System_Part"} is_a: UBERON:0000481 ! multi-tissue structure intersection_of: UBERON:0000481 ! multi-tissue structure intersection_of: part_of UBERON:0001016 ! nervous system -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 relationship: part_of UBERON:0001016 ! nervous system +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2009-06-18T09:00:04Z [Term] @@ -7517,9 +7448,9 @@ xref: NCIT:C34076 xref: SCTID:118966000 xref: UMLS:C1519343 {source="ncithesaurus:Skeletal_System_Part"} is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision -relationship: composed_primarily_of UBERON:0004765 ! skeletal element -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0001434 ! skeletal system +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002473 UBERON:0004765 ! composed primarily of skeletal element [Term] id: UBERON:0000076 @@ -7529,7 +7460,6 @@ def: "The surface (external) layer of ectoderm which begins to proliferate short subset: pheno_slim synonym: "surface (external) ectoderm" EXACT [] synonym: "surface ectoderm" EXACT [MP:0012532] -xref: BTO:0006242 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: EHDAA2:0001968 xref: EHDAA:1494 xref: EHDAA:350 @@ -7545,10 +7475,8 @@ xref: Wikipedia:External_ectoderm is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0005291 ! embryonic tissue relationship: part_of UBERON:0000924 {source="EHDAA2"} ! ectoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1d/Ectoderm.png" xsd:anyURI -property_value: editor_note "merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube)" xsd:string -property_value: RO:0002171 UBERON:0002346 -property_value: UBPROP:0000011 "(or external ectoderm) forms the following structures: Skin Epithelium of the mouth and nasal cavity saliavary glands, and glands of mouth and nasal cavity Enamel - as a side note dentin and dental pulp are formed from ectomesenchyme which is derived from ectoderm Epithelium of pineal and pituitary glands Lens and cornea of the eye Apical ectodermal ridge inducing development of the limb buds of the embryo. Sensory receptors in epidermis" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1d/Ectoderm.png" xsd:anyURI +property_value: IAO:0000116 "merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube)" xsd:string [Term] id: UBERON:0000092 @@ -7568,9 +7496,8 @@ xref: WBls:0000103 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage relationship: preceded_by UBERON:0000068 ! embryo stage -relationship: simultaneous_with GO:0009791 ! post-embryonic development +relationship: RO:0002082 GO:0009791 ! simultaneous with post-embryonic development property_value: seeAlso "https://github.com/obophenotype/uberon/issues/344" xsd:anyURI -property_value: UBPROP:0000008 "In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)" xsd:string [Term] id: UBERON:0000104 @@ -7592,9 +7519,9 @@ is_a: BFO:0000003 ! occurrent is_a: UBERON:0000000 ! processual entity relationship: ends_with UBERON:0000071 ! death stage relationship: has_part UBERON:0000105 ! life cycle stage -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 property_value: seeAlso "https://github.com/obophenotype/uberon/issues/532" xsd:anyURI [Term] @@ -7623,12 +7550,10 @@ xref: ZFS:0000000 xref: ZFS:0100000 is_a: UBERON:0000000 ! processual entity relationship: part_of UBERON:0000104 ! life cycle -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: editor_note "this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here" xsd:string -property_value: UBPROP:0000012 "the WBls class 'all stages' belongs here as it is the superclass of other WBls stages" xsd:string -property_value: UBPROP:0000012 "we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage" xsd:string +property_value: IAO:0000116 "this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000106 @@ -7648,7 +7573,6 @@ xref: BILS:0000106 xref: EFO:0001322 xref: EHDAA:27 xref: FBdv:00005288 -xref: IDOMAL:0000302 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C12601 xref: PdumDv:0000100 xref: VHOG:0000745 @@ -7658,9 +7582,8 @@ xref: ZFS:0000001 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage -relationship: seeAlso EMAPA:16033 -relationship: starts UBERON:0000104 ! life cycle -property_value: UBPROP:0000003 "As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000745", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107", source="http://bgee.unil.ch/"} +relationship: RO:0002223 UBERON:0000104 ! starts life cycle +property_value: seeAlso EMAPA:16033 [Term] id: UBERON:0000107 @@ -7683,10 +7606,10 @@ xref: ZFS:0000046 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage intersection_of: UBERON:0000105 ! life cycle stage -intersection_of: simultaneous_with GO:0040016 ! embryonic cleavage +intersection_of: RO:0002082 GO:0040016 ! simultaneous with embryonic cleavage relationship: immediately_preceded_by UBERON:0000106 ! zygote stage relationship: part_of UBERON:0000068 ! embryo stage -relationship: simultaneous_with GO:0040016 ! embryonic cleavage +relationship: RO:0002082 GO:0040016 ! simultaneous with embryonic cleavage [Term] id: UBERON:0000108 @@ -7710,8 +7633,8 @@ is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000107 ! cleavage stage -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI -property_value: editor_note "consider adding a preceding stage 'morula stage' as part of cleavage" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI +property_value: IAO:0000116 "consider adding a preceding stage 'morula stage' as part of cleavage" xsd:string [Term] id: UBERON:0000109 @@ -7738,10 +7661,10 @@ xref: XAO:1000005 xref: ZFS:0000047 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000108 {source="BILS"} ! blastula stage -relationship: simultaneous_with GO:0007369 ! gastrulation +relationship: RO:0002082 GO:0007369 ! simultaneous with gastrulation +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0000110 @@ -7755,14 +7678,12 @@ xref: MmusDv:0000017 xref: XAO:1000006 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000109 ! gastrula stage -relationship: simultaneous_with GO:0001841 ! neural tube formation -property_value: RO:0002174 NCBITaxon:7955 +relationship: RO:0002082 GO:0001841 ! simultaneous with neural tube formation +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa property_value: seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/343" xsd:anyURI -property_value: UBPROP:0000008 "In zebrafish, the times of neurulation and segmentation overlap so extensively there is no distinct neurula period of development, such as occurs largely before segmentation in amphibian embryos." xsd:string [Term] id: UBERON:0000111 @@ -7779,9 +7700,9 @@ xref: OGES:000032 xref: Wikipedia:Organogenesis is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000068 ! embryo stage -relationship: simultaneous_with GO:0048513 ! animal organ development +relationship: RO:0002082 GO:0048513 ! simultaneous with animal organ development +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa property_value: seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/533" xsd:anyURI @@ -7795,7 +7716,6 @@ synonym: "funiculus" EXACT [] synonym: "nerve fiber bundle" EXACT [FBbt:00005099] synonym: "neural fiber bundle" EXACT [] xref: CARO:0001001 -xref: FBbt:00005099 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: NLX:147821 is_a: UBERON:0005162 ! multi cell part structure relationship: has_part GO:0043005 ! neuron projection @@ -7807,15 +7727,14 @@ name: anterior region of body namespace: uberon is_a: UBERON:0000475 ! organism subdivision disjoint_from: UBERON:0000154 {source="lexical"} ! posterior region of body -relationship: anterior_to UBERON:0000154 ! posterior region of body -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria [Term] id: UBERON:0000154 name: posterior region of body namespace: uberon is_a: UBERON:0000475 ! organism subdivision -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria [Term] id: UBERON:0000165 @@ -7849,7 +7768,6 @@ xref: EFO:0000825 xref: EHDAA2:0001326 xref: EHDAA:542 xref: EMAPA:16262 -xref: FBbt:00003126 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:49184 xref: GAID:75 xref: galen:Mouth @@ -7870,19 +7788,11 @@ xref: Wikipedia:Mouth xref: XAO:0003029 xref: ZFA:0000547 xref: ZFA:0000590 -is_a: UBERON:0004921 {notes="the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts"} ! subdivision of digestive tract -intersection_of: UBERON:0004921 ! subdivision of digestive tract -intersection_of: proximalmost_part_of UBERON:0001555 ! digestive tract -relationship: develops_from UBERON:0035804 ! future mouth -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: proximalmost_part_of UBERON:0001555 ! digestive tract -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI +is_a: UBERON:0004921 ! subdivision of digestive tract +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002202 UBERON:0035804 ! develops from future mouth +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/661" xsd:anyURI -property_value: UBPROP:0000001 "Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010355", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000812", ontology="VHOG", source="DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "oral" xsd:string -property_value: UBPROP:0000011 "some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives" xsd:string -property_value: UBPROP:0000012 "in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0000178 @@ -7923,15 +7833,10 @@ is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000179 ! haemolymphatic fluid relationship: has_part CL:0000232 {source="CL:tm"} ! erythrocyte relationship: has_part UBERON:0001969 ! blood plasma -relationship: immediate_transformation_of UBERON:0006596 {source="Bgee:AN"} ! presumptive blood -relationship: located_in UBERON:0002049 {source="https://github.com/obophenotype/uberon/issues/1330"} ! vasculature relationship: part_of UBERON:0002390 ! hematopoietic system -relationship: present_in_taxon NCBITaxon:9606 -property_value: IAO:0000232 "This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid." xsd:string -property_value: UBPROP:0000001 "A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000007", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000046", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000002 "relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000046", ontology="AAO"} -property_value: UBPROP:0000003 "Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000224", ontology="VHOG", source="DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006) ", source="http://bgee.unil.ch/"} +relationship: RO:0001025 UBERON:0002049 {source="https://github.com/obophenotype/uberon/issues/1330"} ! located in vasculature +relationship: RO:0002495 UBERON:0006596 {source="Bgee:AN"} ! immediate transformation of presumptive blood +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000179 @@ -7944,9 +7849,9 @@ xref: CARO:0000081 is_a: UBERON:0006314 ! bodily fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: part_of UBERON:0002193 ! hemolymphoid system -relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0002193 ! hemolymphoid system +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 creation_date: 2009-04-08T04:38:19Z [Term] @@ -7966,11 +7871,11 @@ xref: OGEM:000006 xref: Wikipedia:Blastula is_a: UBERON:0000922 ! embryo intersection_of: UBERON:0000468 ! multicellular organism -intersection_of: existence_starts_and_ends_during UBERON:0000108 ! blastula stage -relationship: develops_from UBERON:0007010 ! cleaving embryo -relationship: existence_starts_and_ends_during UBERON:0000108 ! blastula stage -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI -property_value: editor_note "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" xsd:string +intersection_of: RO:0002491 UBERON:0000108 ! existence starts and ends during blastula stage +relationship: RO:0002202 UBERON:0007010 ! develops from cleaving embryo +relationship: RO:0002491 UBERON:0000108 ! existence starts and ends during blastula stage +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI +property_value: IAO:0000116 "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" xsd:string [Term] id: UBERON:0000383 @@ -7993,7 +7898,6 @@ xref: BILA:0000088 xref: BTO:0001369 xref: BTO:0001485 xref: EFO:0000801 -xref: EMAPA:35578 xref: FMA:72954 xref: MA:0002888 xref: MAT:0000025 @@ -8002,15 +7906,13 @@ xref: VSAO:0000033 xref: XAO:0004042 is_a: UBERON:0011216 ! organ system subdivision intersection_of: UBERON:0011216 ! organ system subdivision -intersection_of: composed_primarily_of UBERON:0001015 ! musculature +intersection_of: RO:0002473 UBERON:0001015 ! composed primarily of musculature relationship: capable_of GO:0003012 ! muscle system process -relationship: composed_primarily_of UBERON:0001015 ! musculature -relationship: never_in_taxon NCBITaxon:6040 -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: present_in_taxon NCBITaxon:9606 -property_value: editor_note "consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77" xsd:string -property_value: UBPROP:0000001 "Anatomical system that consists of the muscles of the body.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000033", ontology="VSAO", source="VSAO:curator"} -property_value: UBPROP:0000012 "we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA" xsd:string {external_ontology="MA"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002473 UBERON:0001015 ! composed primarily of musculature +property_value: IAO:0000116 "consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77" xsd:string +property_value: RO:0002161 NCBITaxon:6040 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000463 @@ -8032,7 +7934,6 @@ xref: CALOHA:TS-2101 xref: CARO:0000004 xref: EHDAA2:0003004 xref: EMAPA:35178 -xref: FBbt:00007019 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9669 xref: galen:BodySubstance xref: HAO:0000004 @@ -8045,11 +7946,11 @@ xref: VHOG:0001726 xref: XAO:0004001 xref: ZFA:0001487 is_a: UBERON:0000465 ! material anatomical entity -relationship: has_quality PATO:0002198 ! quality of a substance -relationship: part_of UBERON:0000468 {notes="this relationship may be too strong and may be weakened in future"} ! multicellular organism -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: part_of UBERON:0000468 ! multicellular organism +relationship: RO:0000086 PATO:0002198 ! has quality quality of a substance +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000464 @@ -8067,7 +7968,6 @@ xref: AEO:0000005 xref: BILA:0000005 xref: CARO:0000005 xref: EHDAA2:0003005 -xref: FBbt:00007017 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:5897 xref: HAO:0000005 xref: NCIT:C94478 @@ -8078,10 +7978,10 @@ xref: VHOG:0001728 xref: XAO:0003190 xref: ZFA:0001643 is_a: UBERON:0000466 ! immaterial anatomical entity -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -relationship: surrounded_by UBERON:0000061 ! anatomical structure +relationship: RO:0002219 UBERON:0000061 ! surrounded by anatomical structure +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000465 @@ -8095,7 +7995,6 @@ xref: AEO:0000006 xref: BILA:0000006 xref: CARO:0000006 xref: EHDAA2:0003006 -xref: FBbt:00007016 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67165 xref: HAO:0000006 xref: TAO:0001836 @@ -8104,9 +8003,9 @@ xref: VHOG:0001721 is_a: BFO:0000040 ! material entity is_a: UBERON:0001062 ! anatomical entity disjoint_from: UBERON:0000466 ! immaterial anatomical entity -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000466 @@ -8121,7 +8020,6 @@ xref: AEO:0000007 xref: BILA:0000007 xref: CARO:0000007 xref: EHDAA2:0003007 -xref: FBbt:00007015 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67112 xref: HAO:0000007 xref: TAO:0001835 @@ -8129,9 +8027,9 @@ xref: TGMA:0001827 xref: VHOG:0001727 is_a: BFO:0000141 ! immaterial entity is_a: UBERON:0001062 ! anatomical entity -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000467 @@ -8159,11 +8057,9 @@ xref: EHDAA2:0003011 xref: EHDAA:392 xref: EMAPA:16103 xref: EV:0100000 -xref: FBbt:00004856 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7149 xref: galen:AnatomicalSystem xref: HAO:0000011 -xref: IDOMAL:0002460 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: MA:0000003 xref: NCIT:C12919 xref: SCTID:278195005 @@ -8179,11 +8075,11 @@ xref: ZFA:0001439 is_a: UBERON:0000061 ! anatomical structure relationship: has_part UBERON:0000062 ! organ relationship: part_of UBERON:0000468 ! multicellular organism -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -relationship: present_in_taxon NCBITaxon:9606 -relationship: seeAlso EHDAA2:0001330 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:9606 +property_value: seeAlso EHDAA2:0001330 [Term] id: UBERON:0000468 @@ -8214,7 +8110,6 @@ xref: EHDAA2:0003191 xref: EHDAA:1 xref: EMAPA:25765 xref: EV:0100016 -xref: FBbt:00000001 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:256135 xref: galen:Organism xref: HAO:0000012 @@ -8230,11 +8125,10 @@ xref: Wikipedia:Multi-cellular_organism xref: XAO:0003004 xref: ZFA:0001094 is_a: UBERON:0010000 ! multicellular anatomical structure -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: editor_note "TODO - split body and mc organism? body continues after death stage" xsd:string -property_value: UBPROP:0000007 "organismal" xsd:string +property_value: IAO:0000116 "TODO - split body and mc organism? body continues after death stage" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000475 @@ -8259,7 +8153,6 @@ xref: CARO:0000032 xref: EFO:0000808 xref: EHDAA2:0003032 xref: EMAPA:36031 -xref: FBbt:00007009 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7153 xref: galen:BodyPart xref: HAO:0000032 @@ -8277,10 +8170,10 @@ xref: XAO:0003013 xref: ZFA:0001308 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure relationship: part_of UBERON:0000468 ! multicellular organism -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: editor_note "Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency" xsd:string +property_value: IAO:0000116 "Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000476 @@ -8295,7 +8188,6 @@ xref: AEO:0000040 xref: BILA:0000040 xref: CARO:0000040 xref: EHDAA2:0003040 -xref: FBbt:00007013 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:63863 xref: HAO:0000040 xref: TAO:0000382 @@ -8304,9 +8196,9 @@ xref: XAO:0003162 xref: ZFA:0000382 is_a: UBERON:0000061 ! anatomical structure disjoint_from: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000477 @@ -8315,12 +8207,11 @@ namespace: uberon def: "Anatomical group whose component anatomical structures lie in close proximity to each other." [FBbt:00007277] subset: common_anatomy subset: upper_level -xref: FBbt:00007277 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: VHOG:0001737 is_a: UBERON:0034923 ! disconnected anatomical group -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000479 @@ -8342,7 +8233,6 @@ xref: CALOHA:TS-2090 xref: CARO:0000043 xref: EHDAA2:0003043 xref: EMAPA:35868 -xref: FBbt:00007003 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9637 xref: galen:Tissue xref: HAO:0000043 @@ -8359,10 +8249,10 @@ xref: ZFA:0001477 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure relationship: has_part GO:0031012 ! extracellular matrix relationship: part_of UBERON:0000468 ! multicellular organism -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: editor_note "changed label and definition to reflect CARO2" xsd:string +property_value: IAO:0000116 "changed label and definition to reflect CARO2" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000481 @@ -8377,7 +8267,6 @@ xref: AEO:0000055 xref: BILA:0000055 xref: CARO:0000055 xref: EHDAA2:0003055 -xref: FBbt:00007010 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: HAO:0000055 xref: TAO:0001488 xref: TGMA:0001847 @@ -8386,9 +8275,9 @@ xref: XAO:0003037 xref: ZFA:0001488 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure relationship: has_part UBERON:0000479 ! tissue -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000483 @@ -8410,7 +8299,6 @@ xref: CALOHA:TS-0288 xref: CARO:0000066 xref: EHDAA2:0003066 xref: EMAPA:32738 -xref: FBbt:00007005 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9639 xref: GAID:402 xref: HAO:0000066 @@ -8427,14 +8315,12 @@ xref: ZFA:0001486 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue -intersection_of: composed_primarily_of CL:0000066 ! epithelial cell -relationship: composed_primarily_of CL:0000066 ! epithelial cell +intersection_of: RO:0002473 CL:0000066 ! composed primarily of epithelial cell relationship: has_part GO:0005911 ! cell-cell junction relationship: has_part UBERON:0005769 ! basement membrane of epithelium -relationship: only_in_taxon NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! Metazoa -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI -property_value: UBPROP:0000003 "The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000387", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.59", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "epithelial" xsd:string +relationship: RO:0002160 NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! only in taxon Metazoa +relationship: RO:0002473 CL:0000066 ! composed primarily of epithelial cell +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI [Term] id: UBERON:0000487 @@ -8463,8 +8349,7 @@ is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0006914 ! squamous epithelium intersection_of: UBERON:0000490 ! unilaminar epithelium intersection_of: has_part CL:0000076 ! squamous epithelial cell -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Unilaminar epithelium that consists of a single layer of squamous cells.[CARO]" xsd:string {date_retrieved="2012-06-20", external_class="CARO:0000070", ontology="CARO", source="FMA:45565", source="http://orcid.org/0000-0001-9114-8737"} +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI [Term] id: UBERON:0000488 @@ -8511,7 +8396,6 @@ is_a: UBERON:0003103 ! compound organ intersection_of: UBERON:0003103 ! compound organ intersection_of: has_part UBERON:0002553 ! anatomical cavity relationship: has_part UBERON:0002553 ! anatomical cavity -property_value: IAO:0000232 "this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future" xsd:string [Term] id: UBERON:0000490 @@ -8536,8 +8420,7 @@ xref: UMLS:C0682574 {source="ncithesaurus:Simple_Epithelium"} xref: XAO:0004007 xref: ZFA:0001495 is_a: UBERON:0000483 ! epithelium -property_value: editor_note "consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable" xsd:string -property_value: UBPROP:0000001 "Epithelium that consists of a single layer of epithelial cells.[CARO]" xsd:string {date_retrieved="2012-06-20", external_class="CARO:0000073", ontology="CARO", source="FMA:45561", source="http://orcid.org/0000-0001-9114-8737"} +property_value: IAO:0000116 "consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable" xsd:string [Term] id: UBERON:0000915 @@ -8557,12 +8440,8 @@ xref: Wikipedia:Thorax is_a: UBERON:0009569 {source="FMA"} ! subdivision of trunk is_a: UBERON:0011676 ! subdivision of organism along main body axis intersection_of: UBERON:0011676 ! subdivision of organism along main body axis -intersection_of: has_skeleton UBERON:0014477 ! thoracic skeleton -relationship: has_skeleton UBERON:0014477 ! thoracic skeleton -property_value: IAO:0000232 "note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest" xsd:string -property_value: RO:0002171 UBERON:0000026 -property_value: RO:0002171 UBERON:0000033 -property_value: RO:0002171 UBERON:0002417 +intersection_of: RO:0002551 UBERON:0014477 ! has skeleton thoracic skeleton +relationship: RO:0002551 UBERON:0014477 ! has skeleton thoracic skeleton [Term] id: UBERON:0000922 @@ -8587,11 +8466,9 @@ xref: EHDAA2:0000002 xref: EHDAA2_RETIRED:0003236 xref: EHDAA:38 xref: EMAPA:16039 -xref: FBbt:00000052 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69068 xref: GAID:963 xref: http://neurolex.org/wiki/Category\:Embryonic_organism -xref: IDOMAL:0000646 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: MAT:0000226 xref: MESH:D004622 xref: MIAA:0000019 @@ -8605,14 +8482,12 @@ xref: XAO:0000113 xref: ZFA:0000103 is_a: UBERON:0000468 ! multicellular organism intersection_of: UBERON:0000468 ! multicellular organism -intersection_of: existence_ends_with UBERON:0000068 ! embryo stage -intersection_of: existence_starts_with UBERON:0000068 ! embryo stage -relationship: existence_ends_with UBERON:0000068 ! embryo stage -relationship: existence_starts_with UBERON:0000068 ! embryo stage -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" xsd:anyURI +intersection_of: RO:0002489 UBERON:0000068 ! existence starts with embryo stage +intersection_of: RO:0002493 UBERON:0000068 ! existence ends with embryo stage +relationship: RO:0002489 UBERON:0000068 ! existence starts with embryo stage +relationship: RO:0002493 UBERON:0000068 ! existence ends with embryo stage +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/503" xsd:anyURI -property_value: UBPROP:0000007 "embryonic" xsd:string -property_value: UBPROP:0000012 "Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo" xsd:string {external_ontology="ZFA"} [Term] id: UBERON:0000923 @@ -8631,7 +8506,6 @@ xref: AAO:0000480 xref: BILA:0000035 xref: BTO:0000556 xref: EMAPA:36033 -xref: FBbt:00000110 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69069 xref: GAID:1303 xref: MESH:D005855 @@ -8645,8 +8519,7 @@ xref: Wikipedia:Germ_layer xref: XAO:0003011 xref: ZFA:0001122 is_a: UBERON:0010316 ! germ layer / neural crest -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001223", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0000924 @@ -8666,7 +8539,6 @@ xref: EFO:0000414 xref: EHDAA2:0000428 xref: EMAPA:16069 xref: EV:0100003 -xref: FBbt:00000111 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69070 xref: GAID:1304 xref: MAT:0000155 @@ -8683,11 +8555,8 @@ xref: XAO:0000001 xref: ZFA:0000016 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000221 ! ectodermal cell -relationship: immediate_transformation_of UBERON:0006601 {source="Bgee:AN"} ! presumptive ectoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png" xsd:anyURI -property_value: UBPROP:0000001 "Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000137", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000153", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "ectodermal" xsd:string +relationship: RO:0002495 UBERON:0006601 {source="Bgee:AN"} ! immediate transformation of presumptive ectoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png" xsd:anyURI [Term] id: UBERON:0000925 @@ -8707,7 +8576,6 @@ xref: EFO:0002545 xref: EHDAA2:0000436 xref: EMAPA:16062 xref: EV:0100005 -xref: FBbt:00000125 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69071 xref: GAID:1305 xref: MAT:0000175 @@ -8723,11 +8591,9 @@ xref: XAO:0000090 xref: ZFA:0000017 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000223 ! endodermal cell -relationship: immediate_transformation_of UBERON:0006595 {source="Bgee:AN"} ! presumptive endoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png" xsd:anyURI -property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000154", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "endodermal" xsd:string +relationship: RO:0002495 UBERON:0006595 {source="Bgee:AN"} ! immediate transformation of presumptive endoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png" xsd:anyURI [Term] id: UBERON:0000926 @@ -8753,7 +8619,6 @@ xref: EHDAA:160 xref: EHDAA:183 xref: EMAPA:16083 xref: EV:0100006 -xref: FBbt:00000126 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69072 xref: GAID:522 xref: MAT:0000174 @@ -8767,15 +8632,11 @@ xref: VHOG:0000152 xref: Wikipedia:Mesoderm xref: XAO:0000050 xref: ZFA:0000041 -is_a: UBERON:0000923 {notes="sometimes not considered primary"} ! germ layer +is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000222 ! mesodermal cell -relationship: immediate_transformation_of UBERON:0006603 {source="Bgee:AN"} ! presumptive mesoderm -relationship: never_in_taxon NCBITaxon:6040 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" xsd:anyURI -property_value: UBPROP:0000001 "Primary germ layer that is the middle of the embryonic germ layers.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000304", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000152", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "mesodermal" xsd:string -property_value: UBPROP:0000008 "sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates" xsd:string {source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} +relationship: RO:0002495 UBERON:0006603 {source="Bgee:AN"} ! immediate transformation of presumptive mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" xsd:anyURI +property_value: RO:0002161 NCBITaxon:6040 [Term] id: UBERON:0000930 @@ -8797,7 +8658,6 @@ synonym: "stomodeal-hypophyseal primordium" BROAD [XAO:0000269] xref: BTO:0004224 xref: EHDAA2:0001929 xref: EMAPA:16263 -xref: FBbt:00000439 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:295846 xref: NCIT:C34306 xref: TAO:0001290 @@ -8807,15 +8667,11 @@ xref: Wikipedia:Stomodeum xref: XAO:0000269 xref: ZFA:0001290 is_a: UBERON:0013522 ! subdivision of tube -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000924 ! ectoderm relationship: part_of UBERON:0035804 ! future mouth -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI -property_value: editor_note "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" xsd:string -property_value: UBPROP:0000001 "Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001290", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx" xsd:string {source="MP:0012522", taxon="NCBITaxon:40674"} -property_value: UBPROP:0000007 "stomodeal" xsd:string -property_value: UBPROP:0000008 "This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity." xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI +property_value: IAO:0000116 "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" xsd:string [Term] id: UBERON:0000941 @@ -8865,22 +8721,17 @@ xref: VHOG:0000543 xref: Wikipedia:Optic_nerve xref: XAO:0000188 xref: ZFA:0000435 -is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0011215 ! central nervous system cell part cluster is_a: UBERON:0034713 ! cranial neuron projection bundle intersection_of: UBERON:0034713 ! cranial neuron projection bundle intersection_of: extends_fibers_into UBERON:0000959 ! optic chiasma -intersection_of: innervates UBERON:0000966 ! retina -relationship: develops_from UBERON:0003902 {source="EHDAA2"} ! retinal neural layer +intersection_of: RO:0002134 UBERON:0000966 ! innervates retina relationship: extends_fibers_into UBERON:0000959 ! optic chiasma relationship: extends_fibers_into UBERON:0003098 ! optic stalk -relationship: innervates UBERON:0000966 ! retina relationship: part_of UBERON:0002104 ! visual system -property_value: editor_note "Do not classify under 'cranial nerve', as this is not a true nerve - should be classified as evaginated sensory afferent[ISBN:0471888893]" xsd:string -property_value: UBPROP:0000001 "A collection of nerve cells that project visual information from the eyes to the brain. (Source: BioGlossary, www.Biology-Text.com)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000435", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Fibrous, somatic sensory element covered by a fibrous connective-tissue sheath and is continuous with the layer of nerve cells on the inner surface of the eye.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010345", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup (reference 1); The (optic) stalk persists as the optic nerve (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000543", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429, http://medical-dictionary.thefreedictionary.com/optic+stalk", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "(relaion to eye): MA, XAO, AAO and BTO consider this part of the eye. This is in contrast to GO, FMA, EHDAA2 (FMA has a class 'intra-ocular part of optic nerve' which represents the region of overlap). Relation to brain: part of diencephalon in EHDAA2, ZFA. In NIF, has the optic nerve root as part, which is a feature part of the diencphalon" xsd:string {external_ontology="MA"} +relationship: RO:0002134 UBERON:0000966 ! innervates retina +relationship: RO:0002202 UBERON:0003902 {source="EHDAA2"} ! develops from retinal neural layer +property_value: IAO:0000116 "Do not classify under 'cranial nerve', as this is not a true nerve - should be classified as evaginated sensory afferent[ISBN:0471888893]" xsd:string [Term] id: UBERON:0000948 @@ -8929,22 +8780,17 @@ is_a: UBERON:0007100 ! primary circulatory organ is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0007100 ! primary circulatory organ intersection_of: has_part UBERON:0004151 ! cardiac chamber -relationship: contributes_to_morphology_of UBERON:0004535 ! cardiovascular system -relationship: develops_from UBERON:0004141 ! heart tube relationship: has_part UBERON:0004151 ! cardiac chamber -relationship: never_in_taxon NCBITaxon:6239 -relationship: never_in_taxon NCBITaxon:7227 -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0015410 {source="MA"} ! heart plus pericardium -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI -property_value: UBPROP:0000001 "Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000114", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010210", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000002 "relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010210", ontology="AAO"} -property_value: UBPROP:0000003 "As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000276", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "cardiac" xsd:string +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002202 UBERON:0004141 ! develops from heart tube +relationship: RO:0002433 UBERON:0004535 ! contributes to morphology of cardiovascular system +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI +property_value: RO:0002161 NCBITaxon:6239 +property_value: RO:0002161 NCBITaxon:7227 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000955 @@ -8978,7 +8824,6 @@ xref: EHDAA:2641 xref: EHDAA:6485 xref: EMAPA:16894 xref: EV:0100164 -xref: FBbt:00005095 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:50801 xref: GAID:571 xref: galen:Brain @@ -9002,20 +8847,15 @@ xref: XAO:0000010 xref: ZFA:0000008 is_a: UBERON:0000062 {source="GO"} ! organ is_a: UBERON:0004121 ! ectoderm-derived structure -relationship: composed_primarily_of CL:0002319 ! neural cell -relationship: contributes_to_morphology_of UBERON:0001016 ! nervous system -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: immediate_transformation_of UBERON:0006238 {source="Bgee:AN"} ! future brain -relationship: in_anterior_side_of UBERON:0000468 ! multicellular organism relationship: part_of UBERON:0001017 {source="FMA"} ! central nervous system -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI -property_value: editor_note "requires review for applicability to invertebrate structures, e.g. synganglion" xsd:string -property_value: UBPROP:0000001 "Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000008", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010478", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO)" xsd:string {source="http://neurolex.org/wiki/Cumbo_terms"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000157", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165", source="http://bgee.unil.ch/"} +relationship: RO:0002433 UBERON:0001016 ! contributes to morphology of nervous system +relationship: RO:0002473 CL:0002319 ! composed primarily of neural cell +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +relationship: RO:0002495 UBERON:0006238 {source="Bgee:AN"} ! immediate transformation of future brain +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI +property_value: IAO:0000116 "requires review for applicability to invertebrate structures, e.g. synganglion" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000957 @@ -9029,11 +8869,10 @@ synonym: "laminar tissue" EXACT [] xref: Wikipedia:Lamina_of_the_vertebral_arch is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue -intersection_of: has_quality PATO:0002124 ! laminar -relationship: has_quality PATO:0002124 ! laminar -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/80/Laminaarcusvertebrae.png" xsd:anyURI -property_value: editor_note "TODO - merge with cell layer?" xsd:string -property_value: UBPROP:0000007 "laminar" xsd:string +intersection_of: RO:0000086 PATO:0002124 ! has quality laminar +relationship: RO:0000086 PATO:0002124 ! has quality laminar +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/80/Laminaarcusvertebrae.png" xsd:anyURI +property_value: IAO:0000116 "TODO - merge with cell layer?" xsd:string [Term] id: UBERON:0000959 @@ -9083,9 +8922,7 @@ intersection_of: extends_fibers_into UBERON:0001908 ! optic tract intersection_of: part_of UBERON:0001894 ! diencephalon relationship: extends_fibers_into UBERON:0000941 ! cranial nerve II relationship: extends_fibers_into UBERON:0001908 ! optic tract -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b3/1543%2CVisalius%27OpticChiasma.jpg" xsd:anyURI -property_value: UBPROP:0000001 "The point at which fibers of the optic nerves cross.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010622", ontology="AAO", source="AAO:DSM"} -property_value: UBPROP:0000003 "The chiasm has been studied in great detail in some animals, while in others relatively little or nothing is known. Although there are some gross architectural features that are conserved within some animals, such as birds and fish, the general picture is one of diversity. This review will attempt to consider the key features of such diversity of chiasmatic organisation in vertebrates and the mechanisms that sculpt them from the limited literature that is available. However, as so much research has been undertaken on the structure and development of the chiasm in laboratory animals, any review must consider the information that has been gleaned from them and hope that future studies will determine whether the features revealed in these animals, and the underlying mechanisms that generate them, have a common vertebrate plan.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000190", ontology="VHOG", source="DOI:10.1016/j.preteyeres.2005.04.005 Jeffery G, Erskine L, Variations in the architecture and development of the vertebrate optic chiasm. Progress in retinal and eye research (2005)", source="http://bgee.unil.ch/"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b3/1543%2CVisalius%27OpticChiasma.jpg" xsd:anyURI [Term] id: UBERON:0000964 @@ -9123,21 +8960,19 @@ xref: ZFA:0000640 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0010000 ! multicellular anatomical structure is_a: UBERON:0010313 ! neural crest-derived structure -relationship: continuous_with UBERON:0001773 ! sclera -relationship: contributes_to_morphology_of UBERON:0001801 ! anterior segment of eyeball -relationship: developmentally_induced_by UBERON:0005426 ! lens vesicle -relationship: develops_from UBERON:0004348 {evidence="definitional"} ! optic eminence -relationship: develops_from UBERON:0005427 ! corneal primordium relationship: has_part UBERON:0001772 ! corneal epithelium relationship: has_part UBERON:0004370 ! anterior limiting lamina of cornea -relationship: has_quality PATO:0000964 ! transparent relationship: part_of UBERON:0001801 {source="MA"} ! anterior segment of eyeball relationship: part_of UBERON:0010409 {source="MA"} ! ocular surface region relationship: part_of UBERON:0012430 {source="FMA-isa"} ! tunica fibrosa of eyeball -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI -property_value: UBPROP:0000007 "corneal" xsd:string -property_value: UBPROP:0000008 "Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals. In fish, and aquatic vertebrates in general, the cornea plays no role in focusing light, since it has virtually the same refractive index as water" xsd:string +relationship: RO:0000086 PATO:0000964 ! has quality transparent +relationship: RO:0002150 UBERON:0001773 ! continuous with sclera +relationship: RO:0002202 UBERON:0004348 ! develops from optic eminence +relationship: RO:0002202 UBERON:0005427 ! develops from corneal primordium +relationship: RO:0002256 UBERON:0005426 ! developmentally induced by lens vesicle +relationship: RO:0002433 UBERON:0001801 ! contributes to morphology of anterior segment of eyeball +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000965 @@ -9176,15 +9011,13 @@ xref: VHOG:0000169 xref: Wikipedia:Lens_(anatomy) xref: XAO:0000008 xref: ZFA:0000035 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005389 ! transparent eye structure -relationship: contributes_to_morphology_of UBERON:0001801 ! anterior segment of eyeball -relationship: developmentally_induced_by UBERON:0003902 ! retinal neural layer -relationship: develops_from UBERON:0005426 ! lens vesicle relationship: part_of UBERON:0001801 ! anterior segment of eyeball -relationship: present_in_taxon NCBITaxon:9606 -property_value: RO:0002171 UBERON:0002049 -property_value: UBPROP:0000003 "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000169", ontology="VHOG", source="DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "This class excludes compound eye corneal lenses." xsd:string +relationship: RO:0002202 UBERON:0005426 ! develops from lens vesicle +relationship: RO:0002256 UBERON:0003902 ! developmentally induced by retinal neural layer +relationship: RO:0002433 UBERON:0001801 ! contributes to morphology of anterior segment of eyeball +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000966 @@ -9232,18 +9065,15 @@ xref: XAO:0000009 xref: ZFA:0000152 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005388 ! photoreceptor array -relationship: develops_from UBERON:0003072 {source="EHDAA2"} ! optic cup relationship: has_part CL:0000573 {source="FMA"} ! retinal cone cell relationship: has_part CL:0000604 {source="FMA"} ! retinal rod cell relationship: has_part CL:0000740 {source="FMA"} ! retinal ganglion cell -relationship: never_in_taxon NCBITaxon:6656 relationship: part_of UBERON:0001802 ! posterior segment of eyeball relationship: part_of UBERON:0019207 ! chorioretinal region -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png" xsd:anyURI -property_value: UBPROP:0000001 "The portion of the eye developing from the optic primordium and including the neural retina and the retinal pigment layer. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000152", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000229", ontology="VHOG", source="DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "retinal" xsd:string +relationship: RO:0002202 UBERON:0003072 {source="EHDAA2"} ! develops from optic cup +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png" xsd:anyURI +property_value: RO:0002161 NCBITaxon:6656 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000970 @@ -9263,7 +9093,6 @@ xref: BTO:0000439 xref: CALOHA:TS-0309 xref: EFO:0000827 xref: EV:0100336 -xref: FBbt:00005162 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: GAID:69 xref: MAT:0000140 xref: MESH:D005123 @@ -9274,11 +9103,7 @@ relationship: capable_of GO:0009584 ! detection of visible light relationship: has_part CL:0000149 {source="PMID:21062451"} ! visual pigment cell relationship: has_part CL:0000210 {source="PMID:21062451"} ! photoreceptor cell relationship: part_of UBERON:0002104 ! visual system -relationship: present_in_taxon NCBITaxon:9606 -property_value: IAO:0000232 "This class encompasses a variety of light-detecting structures from different phyla with no implication of homology, from the compound insect eye to the vertebrate camera-type eye (distinct classes are provided for each)" xsd:string -property_value: UBPROP:0000007 "ocular" xsd:string -property_value: UBPROP:0000007 "optic" xsd:string -property_value: UBPROP:0000010 "Note that whilst this is classified as an organ, it is in fact more of a unit composed of different structures: in Drosophila, it includes the interommatidial bristle as a part; we consider here the vertebrate eye to include the eyeball/eye proper as a part, with the eye having as parts (when present): eyelids, conjuctiva," xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000982 @@ -9317,10 +9142,8 @@ xref: Wikipedia:Joint xref: XAO:0000171 xref: ZFA:0001596 is_a: UBERON:0004905 ! articulation -relationship: connects UBERON:0004765 ! skeletal element -relationship: contributes_to_morphology_of UBERON:0001434 ! skeletal system -property_value: UBPROP:0000001 "Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000101", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000367", ontology="TAO", source="TAO:pem"} +relationship: RO:0002176 UBERON:0004765 ! connects skeletal element +relationship: RO:0002433 UBERON:0001434 ! contributes to morphology of skeletal system [Term] id: UBERON:0001007 @@ -9341,8 +9164,6 @@ xref: BILA:0000082 xref: BTO:0000058 xref: CALOHA:TS-1293 xref: EFO:0000793 -xref: EV:0100056 -xref: FBbt:00005055 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7152 xref: GAID:278 xref: galen:DigestiveSystem @@ -9368,11 +9189,8 @@ disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0022600 ! digestive system process -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000129", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000007 "digestive" xsd:string -property_value: UBPROP:0000012 "many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class" xsd:string {external_ontology="MA"} +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001009 @@ -9384,7 +9202,6 @@ subset: uberon_slim synonym: "systema cardiovasculare" RELATED OMO:0003011 [Wikipedia:Circulatory_system] xref: AAO:0000959 xref: CALOHA:TS-2103 -xref: MESH:D002319 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: VHOG:0001248 xref: Wikipedia:Circulatory_system is_a: UBERON:0000467 ! anatomical system @@ -9394,17 +9211,13 @@ disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0003013 ! circulatory system process -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} -relationship: never_in_taxon NCBITaxon:6073 -relationship: never_in_taxon NCBITaxon:6157 -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI -property_value: IAO:0000232 "the cardiovascular system and the lymphatic system are parts of the circulatory system" xsd:string -property_value: RO:0002174 NCBITaxon:6231 {notes="WBbt coelomocyte currently classified as circulating cell"} -property_value: UBPROP:0000001 "Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000959", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001248", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.493", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} +property_value: RO:0002161 NCBITaxon:6073 +property_value: RO:0002161 NCBITaxon:6157 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001015 @@ -9424,10 +9237,8 @@ synonym: "musculature system" RELATED [] synonym: "musculi" EXACT OMO:0003011 [FMA:32558, FMA:TA] synonym: "set of muscles" EXACT [FMA:32558] synonym: "set of skeletal muscles" EXACT [MA:0000165] -xref: AAO:0011066 xref: BTO:0000887 xref: EFO:0001949 -xref: EMAPA:32715 xref: EMAPA:35577 xref: FMA:32558 xref: MA:0000165 @@ -9439,11 +9250,9 @@ xref: WBbt:0005737 xref: Wikipedia:Muscular_system xref: ZFA:0000548 is_a: UBERON:0011216 ! organ system subdivision -relationship: composed_primarily_of UBERON:0001630 ! muscle organ relationship: part_of UBERON:0000383 ! musculature of body -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png" xsd:anyURI -property_value: RO:0002171 UBERON:0001474 -property_value: UBPROP:0000012 "In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here." xsd:string {external_ontology="FMA"} +relationship: RO:0002473 UBERON:0001630 ! composed primarily of muscle organ +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png" xsd:anyURI [Term] id: UBERON:0001016 @@ -9469,7 +9278,6 @@ xref: EHDAA2:0001246 xref: EHDAA:826 xref: EMAPA:16469 xref: EV:0100162 -xref: FBbt:00005093 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7157 xref: GAID:466 xref: MA:0000016 @@ -9492,20 +9300,15 @@ disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0050877 ! nervous system process -relationship: composed_primarily_of CL:0002319 ! neural cell -relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: has_part CL:0000540 ! neuron -relationship: immediate_transformation_of UBERON:0016880 {source="Bgee:AN"} ! future nervous system -relationship: never_in_taxon NCBITaxon:6040 -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI -property_value: UBPROP:0000001 "A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000396", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000324", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000402", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.117", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "nervous" xsd:string -property_value: UBPROP:0000007 "neural" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002473 CL:0002319 ! composed primarily of neural cell +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +relationship: RO:0002495 UBERON:0016880 {source="Bgee:AN"} ! immediate transformation of future nervous system +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI +property_value: RO:0002161 NCBITaxon:6040 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001017 @@ -9534,7 +9337,6 @@ xref: EHDAA:828 xref: EMAPA:16470 xref: EMAPA:16754 xref: EV:0100163 -xref: FBbt:00005094 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:55675 xref: GAID:570 xref: MA:0000167 @@ -9551,15 +9353,11 @@ xref: XAO:0000215 xref: ZFA:0000012 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0011216 {source="FBbt", source="cjm"} ! organ system subdivision -relationship: immediate_transformation_of UBERON:0016879 {source="Bgee:AN"} ! future central nervous system -relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0001016 ! nervous system -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "Part of the nervous system which includes the brain and spinal cord.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000090", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "The brain and spinal cord. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000012", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO)." xsd:string {source="BIRNLEX:1099"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000293", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 (reference 1), ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 (reference 2), DOI:10.1016/j.cell.2007.02.040 Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud'homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007) (reference 3)", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002495 UBERON:0016879 {source="Bgee:AN"} ! immediate transformation of future central nervous system +property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001018 @@ -9577,12 +9375,10 @@ synonym: "tract" RELATED [] synonym: "tract of neuraxis" EXACT [FMA:83847] xref: BIRNLEX:1649 xref: EV:0100304 -xref: FBbt:00005100 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:83847 xref: NLX:147822 is_a: UBERON:0000122 ! neuron projection bundle is_a: UBERON:0011215 ! central nervous system cell part cluster -property_value: UBPROP:0000001 "White matter structure of CNS that contains axons that arise predominantly in one central nervous system part and terminate in another. Tracts are generally named by their region or origin followed by their region of primary termination, e.g., mammillothalamic tract contains axons that arise from neurons in the mammillary bodies and terminate in the thalamus. (CUMBO)" xsd:string {source="http://neurolex.org/wiki/Cumbo_terms"} [Term] id: UBERON:0001019 @@ -9630,7 +9426,6 @@ xref: BILA:0000099 xref: EFO:0000805 xref: EHDAA2:0003094 xref: EMAPA:16192 -xref: FBbt:00007692 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:75259 xref: MA:0002442 xref: MAT:0000031 @@ -9645,9 +9440,7 @@ is_a: UBERON:0015203 ! non-connected functional system relationship: capable_of_part_of GO:0007600 ! sensory perception relationship: overlaps UBERON:0001016 ! nervous system relationship: part_of UBERON:0004456 ! entire sense organ system -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" xsd:anyURI -property_value: UBPROP:0000003 "An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001674", ontology="VHOG", source="DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" xsd:anyURI [Term] id: UBERON:0001048 @@ -9666,7 +9459,6 @@ xref: AEO:0000171 xref: BTO:0001886 xref: EFO:0001652 xref: EHDAA2:0003171 -xref: FBbt:00005495 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:86589 xref: MAT:0000482 xref: NCIT:C34275 @@ -9698,7 +9490,6 @@ xref: EMAPA:16164 xref: EMAPA:16757 xref: FMA:293882 xref: MAT:0000069 -xref: MESH:D054259 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: MIAA:0000069 xref: NCIT:C34226 xref: neuronames:1365 @@ -9713,12 +9504,8 @@ is_a: UBERON:0003914 {source="EHDAA2"} ! epithelial tube is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0016879 ! future central nervous system -relationship: develops_from UBERON:0005068 ! neural rod -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010617", ontology="AAO", source="AAO:JOR"} -property_value: UBPROP:0000001 "The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000307", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/neural+tube"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000307", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000011 "The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium" xsd:string {source="GO:0021915"} +relationship: RO:0002202 UBERON:0005068 ! develops from neural rod +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0001062 @@ -9734,7 +9521,6 @@ xref: BILA:0000000 xref: BIRNLEX:6 xref: CARO:0000000 xref: EHDAA2:0002229 -xref: FBbt:10000000 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:62955 xref: HAO:0000000 xref: MA:0000001 @@ -9745,9 +9531,9 @@ xref: UMLS:C1515976 {source="ncithesaurus:Anatomic_Structure_System_or_Substance xref: WBbt:0000100 xref: XAO:0000000 xref: ZFA:0100000 -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0001135 @@ -9792,14 +9578,10 @@ xref: ZFA:0005274 is_a: UBERON:0002385 ! muscle tissue intersection_of: UBERON:0002385 ! muscle tissue intersection_of: has_part CL:0000192 ! smooth muscle cell -relationship: composed_primarily_of CL:0000192 ! smooth muscle cell relationship: has_part CL:0000192 ! smooth muscle cell relationship: has_part GO:0071953 ! elastic fiber -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/3/3b/Glatte_Muskelzellen.jpg" xsd:anyURI -property_value: UBPROP:0000001 "A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005274", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010244", ontology="AAO", source="AAO:CAM"} -property_value: UBPROP:0000003 "(...) the first bilateral animals possessed only smooth muscles with the molecular repertoire necessary to build a striated muscle. (...) it is more parsimonious to regard striated muscle cells as a sister cell type to the smooth muscle cells. In this scenario, striated and smooth muscles would have arisen in the stem lineage that led to the Nephrozoa (i.e. all Bilateria exclusive the acoelomorphs) (Hejnol et al., 2009), from an 'acoel-like' smooth muscle, by segregation and divergence of functions and through differential recruitment of additional genes[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001246", ontology="VHOG", source="DOI:10.1002/jez.b.21416 Chiodin M, Achatz JG, Wanninger A, Martinez P, Molecular architecture of muscles in an acoel and its evolutionary implications. Journal of Experimental Zoology (2011)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000013 "GO uses visceral and smooth interchangeably. However visceral can also be used in the sense of the viscera. Many fly annotations to smooth muscle terms. If we want to be inclusive of insects have to have a general definition of tissue that includes cells." xsd:string +relationship: RO:0002473 CL:0000192 ! composed primarily of smooth muscle cell +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/3/3b/Glatte_Muskelzellen.jpg" xsd:anyURI [Term] id: UBERON:0001136 @@ -9827,11 +9609,11 @@ xref: Wikipedia:Mesothelium is_a: UBERON:0000487 ! simple squamous epithelium is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0000487 ! simple squamous epithelium -intersection_of: develops_from UBERON:0000926 ! mesoderm intersection_of: part_of UBERON:0000042 ! serous membrane -relationship: composed_primarily_of CL:0000077 {source="FMA"} ! mesothelial cell +intersection_of: RO:0002202 UBERON:0000926 ! develops from mesoderm relationship: part_of UBERON:0000042 ! serous membrane -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/25/Mesothelium_peritoneal_wash_high_mag.jpg" xsd:anyURI +relationship: RO:0002473 CL:0000077 {source="FMA"} ! composed primarily of mesothelial cell +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/25/Mesothelium_peritoneal_wash_high_mag.jpg" xsd:anyURI [Term] id: UBERON:0001137 @@ -9855,10 +9637,8 @@ xref: SCTID:123961009 xref: UMLS:C0004600 {source="ncithesaurus:Back"} xref: Wikipedia:Dorsum_(anatomy) is_a: UBERON:0000475 ! organism subdivision -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/432px-Gray-back.PNG" xsd:anyURI -property_value: UBPROP:0000007 "dorsal" xsd:string -property_value: UBPROP:0000008 "In humans, called the back, a large posterior area of the human body, rising from the top of the buttocks to the back of the neck and the shoulders. It is the surface opposite to the chest, its height being defined by the vertebral column (commonly referred to as the spine or backbone) and its breadth being supported by the ribcage and shoulders. The spinal canal runs through the spine and provides nerves to the rest of the body" xsd:string +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/432px-Gray-back.PNG" xsd:anyURI [Term] id: UBERON:0001434 @@ -9894,18 +9674,11 @@ intersection_of: has_part UBERON:0004770 ! articular system disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0004456 ! entire sense organ system -relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: has_part UBERON:0004288 ! skeleton relationship: has_part UBERON:0004770 ! articular system relationship: part_of UBERON:0002204 ! musculoskeletal system -property_value: RO:0002171 UBERON:0001016 +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/The-skeletal-system" xsd:anyURI -property_value: UBPROP:0000001 "Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000434", ontology="TAO", source="TAO:wd"} -property_value: UBPROP:0000001 "Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000027", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "System that provides physical support to the organism.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000566", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000003 "By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001254", ontology="VHOG", source="DOI:10.1159/000324245 Donoghue PCJ, Sansom IJ, Origin and early evolution of vertebrate skeletonization. Microscopy research and technique (2002)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "skeletal" xsd:string -property_value: UBPROP:0000012 "GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates" xsd:string {external_ontology="GO"} [Term] id: UBERON:0001444 @@ -9944,13 +9717,9 @@ xref: SCTID:302549007 xref: UMLS:C0015450 {source="ncithesaurus:Face"} xref: Wikipedia:Face is_a: UBERON:0001444 ! subdivision of head -relationship: contributes_to_morphology_of UBERON:0000033 ! head relationship: has_part UBERON:0000165 ! mouth -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Mona_Lisa_headcrop.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face." xsd:string {source="FMA:24728"} -property_value: UBPROP:0000001 "The area that extends from the median ocellus to the oral foramen[HAO]." xsd:string {source="HAO:0000316", source="http://api.hymao.org/api/ref/67791", taxon="NCBITaxon:7399"} -property_value: UBPROP:0000007 "facial" xsd:string -property_value: UBPROP:0000011 "The face develops from outward growth of tissue located rostral to the cranium & pharynx. The lower jaw and most of the upper jaw are formed by growth of the first pharyngeal (branchial) arch. The upper incisor region and the nose and forehead (frontal region) are formed from tissue located rostral to the neural tube (frontonasal prominence)" xsd:string {source="vanat.cvm.umn.edu/TFFlectPDFs/LectFaceDevelop.pdf"} +relationship: RO:0002433 UBERON:0000033 ! contributes to morphology of head +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Mona_Lisa_headcrop.jpg" xsd:anyURI [Term] id: UBERON:0001555 @@ -9974,11 +9743,9 @@ xref: BTO:0000545 xref: EHDAA2:0000726 xref: EHDAA:518 xref: EMAPA:16247 -xref: FBbt:00003125 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45615 xref: galen:AlimentaryTract xref: MA:0000917 -xref: MESH:D041981 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: NCIT:C34082 xref: TAO:0000112 xref: TGMA:0001819 @@ -9987,18 +9754,13 @@ xref: VHOG:0000309 xref: WBbt:0005743 xref: ZFA:0000112 is_a: UBERON:0000025 ! tube -relationship: connects UBERON:0000165 ! mouth -relationship: immediate_transformation_of UBERON:0007026 {source="NCBIBook:NBK10107"} ! presumptive gut -relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} -relationship: never_in_taxon NCBITaxon:41324 {source="DOI:10.1371/journal.pone.0016309"} -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0001007 ! digestive system -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "The alimentary or digestive tract, and associated organs.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000112", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000309", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "FMA also has a term 'gastrointestinal tract', but this includes the liver." xsd:string {external_ontology="FMA"} -property_value: UBPROP:0000012 "we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509" xsd:string {external_ontology="MA"} -property_value: UBPROP:0000013 "we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002176 UBERON:0000165 ! connects mouth +relationship: RO:0002495 UBERON:0007026 {source="NCBIBook:NBK10107"} ! immediate transformation of presumptive gut +property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} +property_value: RO:0002161 NCBITaxon:41324 {source="DOI:10.1371/journal.pone.0016309"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001605 @@ -10024,8 +9786,8 @@ is_a: UBERON:0003386 {source="MA"} ! smooth muscle of eye is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0011222 {source="FMA"} ! intra-ocular muscle relationship: part_of UBERON:0001775 {source="FMA"} ! ciliary body -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/28/Gray872.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/28/Gray872.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001630 @@ -10037,8 +9799,6 @@ subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "muscle" BROAD [ZFA:0005145] -xref: AAO:0011066 -xref: EMAPA:32715 xref: EMAPA:37474 {source="MA:th"} xref: EV:0100146 xref: FMA:5022 @@ -10053,12 +9813,9 @@ xref: ZFA:0005145 is_a: UBERON:0000062 ! organ is_a: UBERON:0005090 ! muscle structure intersection_of: UBERON:0000062 ! organ -intersection_of: composed_primarily_of UBERON:0002385 ! muscle tissue -relationship: composed_primarily_of UBERON:0002385 ! muscle tissue +intersection_of: RO:0002473 UBERON:0002385 ! composed primarily of muscle tissue relationship: part_of UBERON:0001015 ! musculature -property_value: UBPROP:0000001 "Portion of tissue composed of contractile fibers.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005145", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001245", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.75", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "muscular" xsd:string +relationship: RO:0002473 UBERON:0002385 ! composed primarily of muscle tissue [Term] id: UBERON:0001711 @@ -10087,17 +9844,12 @@ xref: UMLS:C0015426 {source="ncithesaurus:Eyelid"} xref: VHOG:0000016 xref: Wikipedia:Eyelid is_a: UBERON:0000064 ! organ part +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: capable_of GO:0060082 ! eye blink reflex -relationship: contributes_to_morphology_of UBERON:0000019 ! camera-type eye relationship: part_of UBERON:0000019 {source="multiple"} ! camera-type eye relationship: protects UBERON:0010409 ! ocular surface region -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/84/Eye_makeup.jpg" xsd:anyURI -property_value: UBPROP:0000007 "blepharic" xsd:string -property_value: UBPROP:0000007 "palpebral" xsd:string -property_value: UBPROP:0000008 "In humans the upper and lower eyelid consists of the following layers, starting anteriorly: (1) skin, (2) a layer of subcutaneous connective tissue, (3) a layer of striated muscle fibres of the orbicularis muscle, (4) a layer of submuscular connective tissue, (5) a fibrous layer, including the tarsal plates, (6) a layer of smooth muscle, (7) the palpebral conjunctiva." xsd:string -property_value: UBPROP:0000012 "Consider adding 'eye surface', like MA" xsd:string {external_ontology="MA"} -property_value: UBPROP:0000012 "FMA divides this into skin, fascia, conjunctiva" xsd:string {external_ontology="FMA"} -property_value: UBPROP:0000202 FMA:75178 +relationship: RO:0002433 UBERON:0000019 ! contributes to morphology of camera-type eye +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/84/Eye_makeup.jpg" xsd:anyURI [Term] id: UBERON:0001766 @@ -10126,11 +9878,9 @@ xref: UMLS:C0003151 {source="ncithesaurus:Anterior_Chamber_of_the_Eye"} xref: VHOG:0001431 xref: Wikipedia:Anterior_chamber_of_eyeball is_a: UBERON:0006311 {source="FMA"} ! chamber of eyeball -relationship: contributes_to_morphology_of UBERON:0001801 ! anterior segment of eyeball relationship: part_of UBERON:0001801 ! anterior segment of eyeball -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI -property_value: UBPROP:0000001 "The part of the eyeball between the cornea and the iris, filled with aqueous humor. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001431", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/anterior+chamber"} -property_value: UBPROP:0000012 "space in EHDAA2 - consider adding Cavity of anterior chamber of eyeball" xsd:string {external_ontology="EHDAA2"} +relationship: RO:0002433 UBERON:0001801 ! contributes to morphology of anterior segment of eyeball +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI [Term] id: UBERON:0001768 @@ -10156,16 +9906,17 @@ xref: NCIT:C12811 xref: SCTID:280648000 xref: UMLS:C0042160 {source="ncithesaurus:Uvea"} xref: Wikipedia:Uvea +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004923 {source="FMA"} ! organ component layer -relationship: contributes_to_morphology_of UBERON:0000019 ! camera-type eye +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: has_part UBERON:0001769 ! iris relationship: has_part UBERON:0001775 ! ciliary body relationship: has_part UBERON:0001776 ! optic choroid relationship: part_of UBERON:0001801 ! anterior segment of eyeball -relationship: present_in_taxon NCBITaxon:7955 {source="DOI:10.1177/0192623311409597"} -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/eb/Gray869.png" xsd:anyURI -property_value: editor_note "TODO - check child terms, isa vs partof. See also MA:0001284 ! tunica vasculosa plexus" xsd:string -property_value: UBPROP:0000007 "uveal" xsd:string +relationship: RO:0002433 UBERON:0000019 ! contributes to morphology of camera-type eye +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/eb/Gray869.png" xsd:anyURI +property_value: IAO:0000116 "TODO - check child terms, isa vs partof. See also MA:0001284 ! tunica vasculosa plexus" xsd:string +property_value: RO:0002175 NCBITaxon:7955 {source="DOI:10.1177/0192623311409597"} [Term] id: UBERON:0001769 @@ -10200,14 +9951,10 @@ xref: XAO:0000185 xref: ZFA:0001238 is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004121 ! ectoderm-derived structure -relationship: contributes_to_morphology_of UBERON:0011892 ! anterior uvea -relationship: develops_from UBERON:0004128 {source="XAO"} ! optic vesicle relationship: part_of UBERON:0011892 ! anterior uvea -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "The opaque muscular contractile diaphragm suspended in the aqueous humour in front of the lens of the eye. The organ is perforated by the pupil and continues peripherally with the ciliary body. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000101", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000101", ontology="VHOG", source="DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "iridial" xsd:string -property_value: UBPROP:0000008 "The avian iris and ciliary body undergoes a transition from smooth-to-striated muscle during embryonic development [DOI:dx.doi.org/10.1006/dbio.1998.9019]" xsd:string +relationship: RO:0002202 UBERON:0004128 {source="XAO"} ! develops from optic vesicle +relationship: RO:0002433 UBERON:0011892 ! contributes to morphology of anterior uvea +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001772 @@ -10249,17 +9996,15 @@ xref: TAO:0002187 xref: UMLS:C0459875 {source="ncithesaurus:Corneal_Epithelium"} xref: Wikipedia:Corneal_epithelium xref: ZFA:0001683 +is_a: UBERON:0010313 ! neural crest-derived structure is_a: UBERON:0015808 ! eye epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: bounding_layer_of UBERON:0000964 ! cornea relationship: bounding_layer_of UBERON:0000964 ! cornea -relationship: contributes_to_morphology_of UBERON:0000964 ! cornea -relationship: develops_from UBERON:0000076 {source="ISBN:0781772214"} ! external ectoderm -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png" xsd:anyURI -property_value: UBPROP:0000001 "Portion of tissue comprised of four to six layers of nonkeratinized, stratified squamous cells and represents approximately 60% of the thickness of the cornea.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002187", ontology="TAO", source="ZFIN:ZDB-PUB-061010-3"} -property_value: UBPROP:0000008 "In Humans: It consists of several layers of cells. The cells of the deepest layer are columnar; then follow two or three layers of polyhedral cells, the majority of which are prickle cells similar to those found in the stratum mucosum of the cuticle. Lastly, there are three or four layers of squamous cells, with flattened nuclei" xsd:string -property_value: UBPROP:0000008 "In zebrafish: nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals" xsd:string +relationship: RO:0002202 UBERON:0000076 {source="ISBN:0781772214"} ! develops from external ectoderm +relationship: RO:0002433 UBERON:0000964 ! contributes to morphology of cornea +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001773 @@ -10288,21 +10033,14 @@ xref: Wikipedia:Sclera xref: XAO:0000183 xref: ZFA:0005563 is_a: UBERON:0000064 ! organ part -relationship: contributes_to_morphology_of UBERON:0000019 ! camera-type eye -relationship: develops_from UBERON:0003314 {source="ISBN:0781772214"} ! eye mesenchyme -relationship: develops_from UBERON:0007213 {inferred_by="cjm", source="ISBN:0781772214", source="Wikipedia"} ! mesenchyme derived from head neural crest +is_a: UBERON:0010313 ! neural crest-derived structure relationship: has_part CL:0000347 {source="ZFA"} ! scleral cell -relationship: has_quality PATO:0000963 ! opaque relationship: part_of UBERON:0012430 {source="FMA"} ! tunica fibrosa of eyeball -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI -property_value: UBPROP:0000001 "The sclera, also known as the white part of the eye, is the opaque (usually white, though certain animals, such as horses and lizards, can have black sclera), fibrous, protective, outer layer of the eye containing collagen and elastic fiber. It is derived from the neural crest. In children, it is thinner and shows some of the underlying pigment, appearing slightly blue. In the elderly, however, fatty deposits on the sclera can make it appear slightly yellow. The sclera forms the posterior five sixths of the connective tissue coat of the globe. It is continuous with the dura mater and the cornea, and maintains the shape of the globe, offering resistance to internal and external forces, and provides an attachment for the extraocular muscle insertions. The sclera is perforated by plenty of nerves and vessels passing through the posterior scleral foramen, the hole that is formed by the optic nerve. At the optic disk the outer two-thirds of the sclera continues with the dura mater (outer coat of the brain) via the dural sheath of the optic nerve. The inner third joins with some choroidal tissue to form a plate (lamina cribrosa) across the optic nerve with perforations through which the optic fibers (fasciculi). The thickness of the sclera varies from 1mm at the posterior pole to 0.3 mm just behind the rectus muscle insertions. The sclera's blood vessels are mainly on the surface, and together with the conjunctiva (which lies on top) This is a thin layer covering the sclera. Along with the vessels of the conjunctiva, those of the sclera renders the inflamed eye bright red. [WP,unvetted][Wikipedia:Sclera]." xsd:string {source="Wikipedia:Sclera"} -property_value: UBPROP:0000001 "The tough, usually white, outer coat of the eyeball, covering all the posterior surface and continuous anteriorly with the cornea. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001274", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/sclera"} -property_value: UBPROP:0000007 "scleral" xsd:string -property_value: UBPROP:0000008 "in fish, reptiles and monotremes the connective tissue of the sclera is skeletal" xsd:string -property_value: UBPROP:0000010 "continuous with the dura mater and the cornea; The sclera forms the posterior five-sixths of the connective tissue coat of the globe." xsd:string -property_value: UBPROP:0000011 "Majority derives from NC that surrounds optic cup of neurectoderm; a small temporal portion develops from the mesoderm that contributes to striated extra-ocular muscles and vascular endothelia[Rada&Johnson]." xsd:string -property_value: UBPROP:0000011 "Seko et al demonstrate chondrogenic potential and identify this as connective tissue[DOI:10.1371/journal.pone.0003709]." xsd:string +relationship: RO:0000086 PATO:0000963 ! has quality opaque +relationship: RO:0002202 UBERON:0003314 {source="ISBN:0781772214"} ! develops from eye mesenchyme +relationship: RO:0002433 UBERON:0000019 ! contributes to morphology of camera-type eye +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001775 @@ -10335,14 +10073,13 @@ xref: Wikipedia:Ciliary_body xref: XAO:0000186 is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004121 ! ectoderm-derived structure -relationship: contributes_to_morphology_of UBERON:0011892 ! anterior uvea -relationship: develops_from UBERON:0002346 {source="ISBN:0781772214"} ! neurectoderm relationship: has_part UBERON:0001605 ! ciliary muscle relationship: has_part UBERON:0010427 ! ciliary processes relationship: part_of UBERON:0011892 ! anterior uvea -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI -property_value: UBPROP:0000003 "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000102", ontology="VHOG", source="DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0002346 {source="ISBN:0781772214"} ! develops from neurectoderm +relationship: RO:0002433 UBERON:0011892 ! contributes to morphology of anterior uvea +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001776 @@ -10381,15 +10118,13 @@ disjoint_from: UBERON:0011892 {source="lexical"} ! anterior uvea relationship: adjacent_to UBERON:0000966 ! retina relationship: adjacent_to UBERON:0001773 ! sclera relationship: adjacent_to UBERON:0011892 ! anterior uvea -relationship: contributes_to_morphology_of UBERON:0001768 ! uvea relationship: overlaps UBERON:0001802 {source="Wikipedia"} ! posterior segment of eyeball relationship: part_of UBERON:0001768 {source="MA"} ! uvea relationship: part_of UBERON:0019207 ! chorioretinal region -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI -property_value: editor_note "check choroid vs choroid layer; check ZFA/TAO placement - no homology assertion in VHOG. Note this is entirely in the posterior region of eyeball in ZFA" xsd:string -property_value: UBPROP:0000007 "choroidal" xsd:string -property_value: UBPROP:0000012 "MP treats posterior uvea and optic choroid as distinct" xsd:string {external_ontology="MP"} +relationship: RO:0002433 UBERON:0001768 ! contributes to morphology of uvea +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: IAO:0000116 "check choroid vs choroid layer; check ZFA/TAO placement - no homology assertion in VHOG. Note this is entirely in the posterior region of eyeball in ZFA" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001777 @@ -10418,17 +10153,15 @@ xref: UMLS:C0010040 {source="ncithesaurus:Corneal_Stroma"} xref: Wikipedia:Corneal_stroma xref: ZFA:0001685 is_a: UBERON:0003891 ! stroma +is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0003891 ! stroma intersection_of: part_of UBERON:0000964 ! cornea relationship: adjacent_to UBERON:0004367 ! Descemet's membrane relationship: adjacent_to UBERON:0004370 ! anterior limiting lamina of cornea -relationship: contributes_to_morphology_of UBERON:0000964 ! cornea -relationship: develops_from UBERON:0007213 {inferred_by="cjm", source="ISBN:0781772214", source="Wikipedia"} ! mesenchyme derived from head neural crest relationship: part_of UBERON:0000964 ! cornea -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png" xsd:anyURI -property_value: UBPROP:0000001 "Portion of tissue that is located basal to Bowman's layer and distal to Descemet's membrane and is comprised largely of connective tissue.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002189", ontology="TAO", source="ZFIN:ZDB-PUB-061010-3"} -property_value: UBPROP:0000002 "relationship type change: subclass tissue (CARO:0000043) CHANGED TO: develops_from tissue (UBERON:0000479)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002189", ontology="TAO"} -property_value: UBPROP:0000002 "relationship type change: subclass tissue (CARO:0000043) CHANGED TO: has_developmental_contribution_from tissue (UBERON:0000479)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002189", ontology="TAO"} +relationship: RO:0002202 UBERON:0007213 ! develops from mesenchyme derived from head neural crest +relationship: RO:0002433 UBERON:0000964 ! contributes to morphology of cornea +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png" xsd:anyURI [Term] id: UBERON:0001778 @@ -10454,8 +10187,8 @@ intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001775 ! ciliary body relationship: has_part GO:0048770 {source="MP"} ! pigment granule relationship: part_of UBERON:0001775 {source="MA"} ! ciliary body -relationship: present_in_taxon NCBITaxon:9606 relationship: produces UBERON:0001796 {source="Wikipedia"} ! aqueous humor of eyeball +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001781 @@ -10476,10 +10209,10 @@ xref: NCIT:C49328 xref: SCTID:280657006 xref: UMLS:C0459649 {source="ncithesaurus:Retina_Layer"} xref: XAO:0000266 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0022303 ! nervous system cell part layer -relationship: contributes_to_morphology_of UBERON:0000966 ! retina relationship: part_of UBERON:0000966 ! retina -property_value: UBPROP:0000012 "MA does not treat internal/external limiting memranes as layers - these are classified as laminae. Here we follow other ontologies in grouping with other layers. MA also treats retinal pigment epithelium and neural retina epithelium as distinct from the layers. We follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers - these are also classified as layers, giving us over the usual 10 layers" xsd:string {external_ontology="MA"} +relationship: RO:0002433 UBERON:0000966 ! contributes to morphology of retina [Term] id: UBERON:0001782 @@ -10526,19 +10259,15 @@ xref: XAO:0003217 xref: ZFA:0000144 is_a: UBERON:0000957 ! lamina is_a: UBERON:0001781 ! layer of retina -is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0015808 ! eye epithelium intersection_of: UBERON:0001781 ! layer of retina -intersection_of: immediate_transformation_of UBERON:0005424 ! presumptive retinal pigmented epithelium +intersection_of: RO:0002495 UBERON:0005424 ! immediate transformation of presumptive retinal pigmented epithelium relationship: adjacent_to UBERON:0001787 {source="Wikipedia"} ! photoreceptor layer of retina relationship: adjacent_to UBERON:0003902 ! retinal neural layer relationship: has_part GO:0048770 ! pigment granule -relationship: immediate_transformation_of UBERON:0005424 ! presumptive retinal pigmented epithelium -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI -property_value: UBPROP:0000001 "A monolayer of pigmented epithelium covering the neural retina; develops from the outer of the two layers of the optic cup. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000144", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "The monolayer of pigmented epithelium covering the neural retina.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011096", ontology="AAO", source="ZFA:0000144"} -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000536", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} +relationship: RO:0002495 UBERON:0005424 ! immediate transformation of presumptive retinal pigmented epithelium +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001787 @@ -10568,9 +10297,7 @@ is_a: UBERON:0001781 ! layer of retina relationship: adjacent_to UBERON:0001788 ! outer limiting layer of retina relationship: has_part CL:0000287 {source="ZFA"} ! eye photoreceptor cell relationship: part_of UBERON:0003902 ! retinal neural layer -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001165", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "we follow MA and ZFA in subdividing this into inner and outer segments" xsd:string {external_ontology="MA"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI [Term] id: UBERON:0001788 @@ -10638,11 +10365,10 @@ xref: XAO:0003219 xref: ZFA:0001464 is_a: UBERON:0001781 ! layer of retina relationship: adjacent_to UBERON:0001790 ! outer plexiform layer of retina -relationship: contributes_to_morphology_of UBERON:0003902 ! retinal neural layer -relationship: overlaps CL:0000287 {notes="soma", source="ZFA"} ! eye photoreceptor cell +relationship: overlaps CL:0000287 ! eye photoreceptor cell relationship: part_of UBERON:0003902 ! retinal neural layer -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001170", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} +relationship: RO:0002433 UBERON:0003902 ! contributes to morphology of retinal neural layer +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001790 @@ -10675,10 +10401,8 @@ xref: XAO:0003218 xref: ZFA:0001330 is_a: UBERON:0001781 ! layer of retina relationship: adjacent_to UBERON:0001791 ! inner nuclear layer of retina -relationship: contributes_to_morphology_of UBERON:0003902 ! retinal neural layer relationship: part_of UBERON:0003902 ! retinal neural layer -property_value: UBPROP:0000001 "The layer within the retina where the bipolar cells synapse with the photoreceptor cells.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001330", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001171", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} +relationship: RO:0002433 UBERON:0003902 ! contributes to morphology of retinal neural layer [Term] id: UBERON:0001791 @@ -10716,14 +10440,12 @@ xref: XAO:0003221 xref: ZFA:0000119 is_a: UBERON:0001781 ! layer of retina relationship: adjacent_to UBERON:0001795 ! inner plexiform layer of retina -relationship: contributes_to_morphology_of UBERON:0003902 ! retinal neural layer relationship: has_part CL:0000561 ! amacrine cell relationship: has_part CL:0000745 ! retina horizontal cell relationship: has_part CL:0000748 ! retinal bipolar neuron relationship: part_of UBERON:0003902 ! retinal neural layer -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "The layer of the retina composed of the cell bodies of bipolar cells, horizontal cells, and some of the cell bodies of amacrine cells[BTO:0003176]." xsd:string {source="BTO:0003176"} -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001167", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} +relationship: RO:0002433 UBERON:0003902 ! contributes to morphology of retinal neural layer +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001792 @@ -10762,14 +10484,11 @@ xref: XAO:0003223 xref: ZFA:0000024 is_a: UBERON:0001781 {source="FMA"} ! layer of retina relationship: adjacent_to UBERON:0001793 ! nerve fiber layer of retina -relationship: composed_primarily_of CL:0000740 ! retinal ganglion cell -relationship: contributes_to_morphology_of UBERON:0003902 ! retinal neural layer relationship: part_of UBERON:0003902 {source="FMA"} ! retinal neural layer -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI -property_value: UBPROP:0000001 "a layer of the retina that consists of retinal ganglion cells[WP]. innermost nuclear layer of the retina, which contains neurons that project axons through the optic nerve to the brain[Wikipedia:Ganglion_cell_layer]." xsd:string {source="Wikipedia:Ganglion_cell_layer"} -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001166", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "NIFSTD class appears to be retired in nlx[http://neurolex.org/wiki/Nlx_anat_1005030]" xsd:string {external_ontology="NIF"} +relationship: RO:0002433 UBERON:0003902 ! contributes to morphology of retinal neural layer +relationship: RO:0002473 CL:0000740 ! composed primarily of retinal ganglion cell +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001793 @@ -10803,11 +10522,10 @@ xref: XAO:0003220 xref: ZFA:0001619 is_a: UBERON:0001781 ! layer of retina relationship: adjacent_to UBERON:0001794 ! inner limiting layer of retina -relationship: composed_primarily_of GO:0030424 ! axon -relationship: contributes_to_morphology_of UBERON:0003902 ! retinal neural layer relationship: overlaps UBERON:0000941 ! cranial nerve II relationship: part_of UBERON:0003902 {source="FMA"} ! retinal neural layer -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001169", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} +relationship: RO:0002433 UBERON:0003902 ! contributes to morphology of retinal neural layer +relationship: RO:0002473 GO:0030424 ! composed primarily of axon [Term] id: UBERON:0001794 @@ -10836,12 +10554,12 @@ xref: Wikipedia:Inner_limiting_membrane xref: XAO:0003222 xref: ZFA:0001029 is_a: UBERON:0007619 {source="MA"} ! limiting membrane of retina +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: adjacent_to UBERON:0001797 ! vitreous humor relationship: has_part CL:0000127 ! astrocyte relationship: has_part GO:0043005 ! neuron projection relationship: overlaps CL:0000636 ! Mueller cell -property_value: editor_note "TODO - check frog/fish" xsd:string -property_value: UBPROP:0000001 "Membrane on the apical surface of the retina. The retinal vasculature becomes adhered to the apical surface of the ILM by 30dpf[ZFIN:ZDB-PUB-071023-7, ZFIN:ZDB-PUB-120529-3]." xsd:string {source="ZFIN:ZDB-PUB-071023-7, ZFIN:ZDB-PUB-120529-3"} +property_value: IAO:0000116 "TODO - check frog/fish" xsd:string [Term] id: UBERON:0001795 @@ -10881,16 +10599,12 @@ intersection_of: adjacent_to UBERON:0001791 ! inner nuclear layer of retina intersection_of: adjacent_to UBERON:0001792 ! ganglionic layer of retina relationship: adjacent_to UBERON:0001791 ! inner nuclear layer of retina relationship: adjacent_to UBERON:0001792 ! ganglionic layer of retina -relationship: contributes_to_morphology_of UBERON:0003902 ! retinal neural layer relationship: has_part GO:0030425 ! dendrite relationship: overlaps CL:0000740 ! retinal ganglion cell relationship: overlaps CL:0000748 ! retinal bipolar neuron relationship: part_of UBERON:0003902 ! retinal neural layer -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI -property_value: UBPROP:0000001 "The inner plexiform layer (IPL) is positioned between the INL and the ganglion cell layer and contains the dendrites of RGCs and processes of bipolar and amacrine cells[GO][GO:0010842]." xsd:string {source="GO:0010842"} -property_value: UBPROP:0000001 "The layer within the retina where the bipolar cells synapse with the dendrites of the ganglion cells.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001329", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001168", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "http://neurolex.org/wiki/Nlx_anat_1005032 appears to be retired" xsd:string +relationship: RO:0002433 UBERON:0003902 ! contributes to morphology of retinal neural layer +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI [Term] id: UBERON:0001796 @@ -10919,12 +10633,9 @@ xref: Wikipedia:Aqueous_humor xref: ZFA:0005564 is_a: UBERON:0006312 ! ocular refractive media is_a: UBERON:0006314 ! bodily fluid -relationship: contributes_to_morphology_of UBERON:0001766 ! anterior chamber of eyeball -relationship: part_of UBERON:0001766 {notes="FMA def states A and P", notes="located_in in EHDAA2", source="VHOG"} ! anterior chamber of eyeball -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI -property_value: UBPROP:0000001 "The fluid produced by the ciliary process in the eye and occupying the anterior and posterior chambers. It provides nourishment for the lens and cornea and maintains the ocular pressure, and hence the optical integrity of the eyeball. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000548", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/aqueous+humour"} -property_value: UBPROP:0000003 "(...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000548", ontology="VHOG", source="DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424 and p.426 and p.429 and Figure 12-24", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "FMA says A+P chambers, and MA states A chamber. ZFA states A chamber and tha it is produced primarily by dorsal ciliary epithelial cells.To be investigated across taxa." xsd:string {external_ontology="FMA"} +relationship: part_of UBERON:0001766 ! anterior chamber of eyeball +relationship: RO:0002433 UBERON:0001766 ! contributes to morphology of anterior chamber of eyeball +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI [Term] id: UBERON:0001797 @@ -10950,17 +10661,16 @@ xref: ENVO:02000032 xref: EV:0100344 xref: FMA:58822 xref: MA:0001286 -xref: MESH:D014822 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: NCIT:C13323 xref: UMLS:C0229096 {source="ncithesaurus:Vitreous_Humor"} xref: VHOG:0000795 xref: Wikipedia:Vitreous_humour xref: ZFA:0005561 is_a: UBERON:0006312 ! ocular refractive media -relationship: has_quality PATO:0000964 ! transparent -relationship: located_in UBERON:0005606 ! hyaloid cavity relationship: part_of UBERON:0001798 ! vitreous body -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +relationship: RO:0000086 PATO:0000964 ! has quality transparent +relationship: RO:0001025 UBERON:0005606 ! located in hyaloid cavity +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI [Term] id: UBERON:0001798 @@ -10978,12 +10688,13 @@ xref: NCIT:C33884 xref: SCTID:181170006 xref: UMLS:C0042905 {source="ncithesaurus:Vitreous_Body"} is_a: UBERON:0003566 ! head connective tissue +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0011825 {source="FMA"} ! loose connective tissue -relationship: composed_primarily_of UBERON:0001797 ! vitreous humor -relationship: has_developmental_contribution_from UBERON:0002346 {notes="neural ectoderm of optic cup", source="ISBN:0781772214"} ! neurectoderm relationship: part_of UBERON:0001799 ! vitreous chamber of eyeball -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI -property_value: editor_note "distinciton between body and humor requires more work. These may be merged in future. Note that FMA includes the hyaloid canal as part of the vitreous body" xsd:string +relationship: RO:0002254 UBERON:0002346 ! has developmental contribution from neurectoderm +relationship: RO:0002473 UBERON:0001797 ! composed primarily of vitreous humor +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: IAO:0000116 "distinciton between body and humor requires more work. These may be merged in future. Note that FMA includes the hyaloid canal as part of the vitreous body" xsd:string [Term] id: UBERON:0001799 @@ -11007,9 +10718,9 @@ xref: UMLS:C0229095 {source="ncithesaurus:Vitreous_Chamber"} xref: Wikipedia:Vitreous_chamber is_a: UBERON:0006311 ! chamber of eyeball intersection_of: UBERON:0006311 ! chamber of eyeball -intersection_of: location_of UBERON:0001798 ! vitreous body -relationship: location_of UBERON:0001798 ! vitreous body +intersection_of: RO:0001015 UBERON:0001798 ! location of vitreous body relationship: part_of UBERON:0001802 ! posterior segment of eyeball +relationship: RO:0001015 UBERON:0001798 ! location of vitreous body [Term] id: UBERON:0001801 @@ -11035,12 +10746,11 @@ xref: UMLS:C0003153 {source="ncithesaurus:Anterior_Eye_Segment"} xref: Wikipedia:Anterior_segment_of_eyeball xref: ZFA:0005566 is_a: UBERON:0000063 ! organ subunit +is_a: UBERON:0004121 ! ectoderm-derived structure disjoint_from: UBERON:0001802 {source="lexical"} ! posterior segment of eyeball -relationship: contributes_to_morphology_of UBERON:0000019 ! camera-type eye -relationship: in_anterior_side_of UBERON:0010230 {source="cjm"} ! eyeball of camera-type eye relationship: part_of UBERON:0010230 {source="FMA"} ! eyeball of camera-type eye -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Cataract_in_human_eye.png" xsd:anyURI -property_value: RO:0002171 UBERON:0001802 {exceptions="ZFA", source="https://github.com/obophenotype/uberon/issues/378", status="pending"} +relationship: RO:0002433 UBERON:0000019 ! contributes to morphology of camera-type eye +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Cataract_in_human_eye.png" xsd:anyURI [Term] id: UBERON:0001802 @@ -11065,10 +10775,10 @@ xref: UMLS:C0278450 {source="ncithesaurus:Posterior_Eye_Segment"} xref: Wikipedia:Posterior_segment_of_eyeball xref: ZFA:0005567 is_a: UBERON:0000063 ! organ subunit -relationship: contributes_to_morphology_of UBERON:0000019 ! camera-type eye -relationship: in_posterior_side_of UBERON:0010230 {source="cjm"} ! eyeball of camera-type eye +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0010230 {source="FMA"} ! eyeball of camera-type eye -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +relationship: RO:0002433 UBERON:0000019 ! contributes to morphology of camera-type eye +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI [Term] id: UBERON:0001811 @@ -11087,7 +10797,6 @@ xref: AAO:0010343 xref: BTO:0003415 xref: CALOHA:TS-2232 xref: EFO:0000374 -xref: EMAPA:18233 xref: EV:0100340 xref: FMA:59011 xref: GAID:898 @@ -11099,15 +10808,15 @@ xref: UMLS:C0009758 {source="ncithesaurus:Conjunctiva"} xref: Wikipedia:Conjunctiva xref: XAO:0000182 is_a: UBERON:0000060 {source="FMA"} ! anatomical wall +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: adjacent_to UBERON:0001711 ! eyelid relationship: adjacent_to UBERON:0001773 ! sclera -relationship: contributes_to_morphology_of UBERON:0001801 ! anterior segment of eyeball -relationship: develops_from UBERON:0000076 {source="ISBN:0781772214"} ! external ectoderm relationship: part_of UBERON:0005908 {source="cjm"} ! conjunctival sac relationship: part_of UBERON:0010409 {source="MA"} ! ocular surface region -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png" xsd:anyURI -property_value: UBPROP:0000007 "conjunctival" xsd:string +relationship: RO:0002202 UBERON:0000076 {source="ISBN:0781772214"} ! develops from external ectoderm +relationship: RO:0002433 UBERON:0001801 ! contributes to morphology of anterior segment of eyeball +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001890 @@ -11148,18 +10857,12 @@ xref: Wikipedia:Forebrain xref: XAO:0000011 xref: ZFA:0000109 is_a: UBERON:0002616 ! regional part of brain -is_a: UBERON:0004121 ! ectoderm-derived structure disjoint_from: UBERON:0002298 ! brainstem -relationship: contributes_to_morphology_of UBERON:0000955 ! brain -relationship: develops_from UBERON:0003080 ! anterior neural tube -relationship: immediate_transformation_of UBERON:0006240 {evidence="definitional"} ! future forebrain -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI -property_value: UBPROP:0000001 "Most anterior of the three regions of the brain consisting of the telencephalon and diencephalon.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010147", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "The most anterior region the brain including both the telencephalon and diencephalon. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000109", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000002 "relationship loss: develops_from forebrain neural tube (TAO:0007041)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000109", ontology="TAO"} -property_value: UBPROP:0000003 "In craniate embryos, neural expression of Distal-less-related genes is exclusively in the forebrain (...). Because the major neural expression domain of amphioxus AmphiDll is in the anterior three-fourths of the cerebral vesicle, we suggest that this region of the neural tube is homologous to parts of the craniate forebrain. This conclusion is strongly supported by three-dimensional, computer-assisted reconstruction of the neural tube of amphioxus based on serial transmission electron microscopy. At the neuroanatomical level, a number of detailed homologies are indicated between the anterior three-fourths of the amphioxus cerebral vesicle and the diencephalic region of the craniate forebrain. If one assumes that the amphioxus condition fairly represents the nervous system of the proximate ancestor of the craniates, one can suggest that they evolved from a creature that had the beginnings of a forebrain.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000383", ontology="VHOG", source="PMID:8787764 Holland ND, Panganiban G, Henyey EL, Holland LZ, Sequence and developmental expression of AmphiDll, an amphioxus Distal-less gene transcribed in the ectoderm, epidermis and nervous system: insights into evolution of craniate forebrain and neural crest. Development (1996)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "prosencephalic" xsd:string +relationship: RO:0002202 UBERON:0003080 ! develops from anterior neural tube +relationship: RO:0002433 UBERON:0000955 ! contributes to morphology of brain +relationship: RO:0002495 UBERON:0006240 ! immediate transformation of future forebrain +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001891 @@ -11204,21 +10907,13 @@ xref: Wikipedia:Midbrain xref: XAO:0000014 xref: ZFA:0000128 is_a: UBERON:0002616 ! regional part of brain -is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest -relationship: contributes_to_morphology_of UBERON:0000955 ! brain -relationship: has_developmental_contribution_from UBERON:0003849 {evidence="definitional"} ! mesencephalic neural crest -relationship: immediate_transformation_of UBERON:0009616 {source="Bgee:AN"} ! presumptive midbrain -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/f9/Human_brain_inferior_view_description.JPG" xsd:anyURI -property_value: editor_note "developmental relationships need revised" xsd:string -property_value: RO:0002171 UBERON:0001894 {exceptions="ZFA", exceptions_url="https://github.com/obophenotype/uberon/issues/378", source="ABA", status="pending"} -property_value: RO:0002171 UBERON:0002028 {exceptions="ZFA", source="ABA", status="pending"} -property_value: UBPROP:0000001 "Middle part of the brain composed of the optic tectum and penducular region.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010149", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000128", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000069", ontology="VHOG", source="DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "mesencephalic" xsd:string -property_value: UBPROP:0000012 "part of brainstem in ABA - we reject this in favor of ISBN:0471888893 which has an implicit overlaps relationships" xsd:string {external_ontology="ABA"} +relationship: RO:0002254 UBERON:0003849 ! has developmental contribution from mesencephalic neural crest +relationship: RO:0002433 UBERON:0000955 ! contributes to morphology of brain +relationship: RO:0002495 UBERON:0009616 {source="Bgee:AN"} ! immediate transformation of presumptive midbrain +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f9/Human_brain_inferior_view_description.JPG" xsd:anyURI +property_value: IAO:0000116 "developmental relationships need revised" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001894 @@ -11274,21 +10969,12 @@ xref: Wikipedia:Diencephalon xref: XAO:0000013 xref: ZFA:0000101 is_a: UBERON:0002616 ! regional part of brain -is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest -relationship: contributes_to_morphology_of UBERON:0001890 ! forebrain -relationship: has_developmental_contribution_from UBERON:0003851 {evidence="definitional"} ! diencephalon neural crest -relationship: immediate_transformation_of UBERON:0006222 {evidence="definitional"} ! future diencephalon relationship: part_of UBERON:0001890 ! forebrain -relationship: present_in_taxon NCBITaxon:7762 {notes="not well differentiated from the cerebrum. (Ariens, p. 868)", source="PMID:8932866"} -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI -property_value: RO:0002171 UBERON:0001891 {exceptions="ZFA", source="ABA", source="https://github.com/obophenotype/uberon/issues/378", status="pending"} -property_value: RO:0002171 UBERON:0002028 {source="ABA"} -property_value: UBPROP:0000001 "The more posterior and ventral of two forebrain neuromeres, the other being the telencephalon; major derivatives are the eye cups, the brain pretectal region, the thalamus, hypothalamus, and epithalamus (including the habenula and epiphysis). Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000101", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Unpaired part of the forebrain comprised of three major parts; the epithalamus, thalamus, and hypothalamus.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010481", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000318", ontology="VHOG", source="DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "diencephalic" xsd:string -property_value: UBPROP:0000012 "in ABA, this is part of the brain stem" xsd:string {external_ontology="ABA"} +relationship: RO:0002254 UBERON:0003851 ! has developmental contribution from diencephalon neural crest +relationship: RO:0002433 UBERON:0001890 ! contributes to morphology of forebrain +relationship: RO:0002495 UBERON:0006222 ! immediate transformation of future diencephalon +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI [Term] id: UBERON:0001896 @@ -11337,16 +11023,14 @@ xref: Wikipedia:Bone_marrow_of_ovary_oblongata xref: XAO:0003100 xref: ZFA:0000545 is_a: UBERON:0000064 ! organ part +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: capable_of GO:0002027 ! regulation of heart rate relationship: capable_of GO:0043576 ! regulation of respiratory gaseous exchange relationship: capable_of GO:0044058 ! regulation of digestive system process relationship: part_of UBERON:0002298 ! brainstem relationship: part_of UBERON:0005290 ! myelencephalon -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/6b/Illu_pituitary_pineal_glands.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Posterior portion of the hindbrain which controls respiration, heartbeat, digestion, and swallowing as well as some locomotor responses.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010486", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "The posterior region of the brain that is continuous with the spinal cord. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-17, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000181", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "Classical anatomical studies subdivided the vertebrate rhombencephalon into pons and medulla oblongata. (...) The medulla oblongata appears therefore as a tagma, that is, a group of segmental units (pseudorhombomeres, in this case) sharing some morphological and molecular characteristics, and in some aspects different from the segmental units present in adjoining brain regions, pons and spinal cord.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000181", ontology="VHOG", source="DOI:10.1016/j.ydbio.2008.08.017 Marin F, Aroca P, Puelles L, Hox gene colinear expression in the avian medulla oblongata is correlated with pseudorhombomeric domains. Developmental Biology (2008)", source="http://bgee.unil.ch/"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6b/Illu_pituitary_pineal_glands.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001908 @@ -11367,7 +11051,6 @@ xref: BIRNLEX:1684 xref: BM:Tel-OT xref: DHBA:10589 xref: DMBA:17785 -xref: EMAPA:16678 xref: EMAPA:35617 xref: FMA:62046 xref: GAID:735 @@ -11385,17 +11068,17 @@ xref: Wikipedia:Optic_tract xref: XAO:0004101 xref: ZFA:0000252 is_a: UBERON:0011591 ! tract of diencephalon -relationship: contributes_to_morphology_of UBERON:0003544 ! brain white matter relationship: extends_fibers_into UBERON:0000941 ! cranial nerve II relationship: extends_fibers_into UBERON:0000959 ! optic chiasma -relationship: innervates UBERON:0000966 ! retina relationship: part_of UBERON:0002104 ! visual system relationship: part_of UBERON:0003931 ! diencephalic white matter -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray773.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI -property_value: editor_note "relationships need checking by expert. NIF and ZFA both state part of diencepahalon; MA says part of optic nerve II. in uberon, CNS and PNS are spatially disjoint, and axon tracts are part of the CNS so we make the relationship to CNII 'continuous_with'" xsd:string +relationship: RO:0002134 UBERON:0000966 ! innervates retina +relationship: RO:0002433 UBERON:0003544 ! contributes to morphology of brain white matter +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray773.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI +property_value: IAO:0000116 "relationships need checking by expert. NIF and ZFA both state part of diencepahalon; MA says part of optic nerve II. in uberon, CNS and PNS are spatially disjoint, and axon tracts are part of the CNS so we make the relationship to CNII 'continuous_with'" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001943 @@ -11425,7 +11108,6 @@ xref: FMA:62393 xref: HBA:9002 xref: MA:0000212 xref: MAT:0000452 -xref: MESH:D013681 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: neuronames:491 {source="BIRNLEX:1200"} xref: SCTID:362392007 xref: TAO:0000160 @@ -11435,12 +11117,11 @@ xref: Wikipedia:Midbrain_tegmentum xref: XAO:0004271 xref: ZFA:0000160 is_a: UBERON:0002616 ! regional part of brain -relationship: develops_from UBERON:0010285 {source="ZFA"} ! midbrain basal plate relationship: part_of UBERON:0001891 ! midbrain relationship: part_of UBERON:0002298 ! brainstem -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray712.png" xsd:anyURI -property_value: UBPROP:0000003 "Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001367", ontology="VHOG", source="DOI:10.1016/j.brainresbull.2005.05.001 Villar-Cheda B, Abalo XM, Anadon R, Rodicio MC, The tegmental proliferation region in the sea lamprey. Brain Research Bulletin (2005)", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0010285 {source="ZFA"} ! develops from midbrain basal plate +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray712.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001969 @@ -11471,12 +11152,12 @@ is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000179 ! haemolymphatic fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: has_part GO:0005577 ! fibrinogen complex -intersection_of: has_quality PATO:0001548 ! quality of a liquid intersection_of: part_of UBERON:0000178 ! blood -intersection_of: surrounds CL:0000232 ! erythrocyte +intersection_of: RO:0000086 PATO:0001548 ! has quality quality of a liquid +intersection_of: RO:0002221 CL:0000232 ! surrounds erythrocyte relationship: has_part GO:0005577 ! fibrinogen complex relationship: part_of UBERON:0000178 ! blood -relationship: surrounds CL:0000232 ! erythrocyte +relationship: RO:0002221 CL:0000232 ! surrounds erythrocyte [Term] id: UBERON:0001981 @@ -11518,22 +11199,18 @@ xref: XAO:0001011 xref: ZFA:0005314 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000055 ! vessel +is_a: UBERON:0004120 ! mesoderm-derived structure relationship: capable_of_part_of GO:0008015 ! blood circulation relationship: channel_for UBERON:0000178 ! blood -relationship: develops_from UBERON:0004872 ! splanchnic layer of lateral plate mesoderm -relationship: develops_from UBERON:0006965 {source="GO:0072360"} ! vascular cord relationship: has_part CL:0000071 {source="AEO"} ! blood vessel endothelial cell relationship: has_part UBERON:0007500 {source="EHDAA2"} ! epithelial tube open at both ends -relationship: has_quality PATO:0002045 ! dendritic relationship: part_of UBERON:0004537 ! blood vasculature -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI -property_value: editor_note "consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus" xsd:string -property_value: UBPROP:0000001 "Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001250", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000001 "Any of the vessels through which blood circulates in the body.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011004", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001250", ontology="VHOG", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "annelids have blood vessels, but this class is not applicable to annelids." xsd:string -property_value: UBPROP:0000012 "FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX" xsd:string {external_ontology="FMA"} +relationship: RO:0000086 PATO:0002045 ! has quality dendritic +relationship: RO:0002202 UBERON:0004872 ! develops from splanchnic layer of lateral plate mesoderm +relationship: RO:0002202 UBERON:0006965 {source="GO:0072360"} ! develops from vascular cord +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: IAO:0000116 "consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001985 @@ -11561,15 +11238,14 @@ xref: Wikipedia:Corneal_endothelium xref: ZFA:0001687 is_a: UBERON:0001986 ! endothelium is_a: UBERON:0010313 ! neural crest-derived structure -is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0015808 ! eye epithelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0000964 ! cornea relationship: adjacent_to UBERON:0001766 ! anterior chamber of eyeball -relationship: contributes_to_morphology_of UBERON:0000964 ! cornea relationship: part_of UBERON:0000964 ! cornea -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png" xsd:anyURI +relationship: RO:0002433 UBERON:0000964 ! contributes to morphology of cornea +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001986 @@ -11593,11 +11269,10 @@ xref: UMLS:C0014257 {source="ncithesaurus:Endothelium"} is_a: UBERON:0000487 {source="FMA-text-def", source="https://github.com/obophenotype/uberon/issues/225"} ! simple squamous epithelium is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0000483 ! epithelium -intersection_of: composed_primarily_of CL:0000115 ! endothelial cell -relationship: composed_primarily_of CL:0000115 ! endothelial cell -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000007 "endothelial" xsd:string +intersection_of: RO:0002473 CL:0000115 ! composed primarily of endothelial cell +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002473 CL:0000115 ! composed primarily of endothelial cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002020 @@ -11623,7 +11298,6 @@ xref: EMAPA:37596 {source="MA:th"} xref: FMA:67242 xref: HBA:4006 xref: MA:0001112 -xref: MESH:D066128 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C32695 xref: neuronames:2869 xref: TAO:0002197 @@ -11632,9 +11306,8 @@ xref: VHOG:0001768 xref: Wikipedia:Gray_matter xref: ZFA:0001681 is_a: UBERON:0011215 ! central nervous system cell part cluster -relationship: composed_primarily_of GO:0043025 ! neuronal cell body -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg" xsd:anyURI -property_value: UBPROP:0000001 "Multi-tissue comprised of neurons, dendrites, axon terminals, glial cells, and capillaries.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002197", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002473 GO:0043025 ! composed primarily of neuronal cell body +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg" xsd:anyURI [Term] id: UBERON:0002028 @@ -11676,22 +11349,13 @@ xref: Wikipedia:Rhombencephalon xref: XAO:0000015 xref: ZFA:0000029 is_a: UBERON:0002616 ! regional part of brain -is_a: UBERON:0004121 ! ectoderm-derived structure -relationship: contributes_to_morphology_of UBERON:0000955 ! brain -relationship: immediate_transformation_of UBERON:0007277 {source="Bgee:AN"} ! presumptive hindbrain -relationship: only_in_taxon NCBITaxon:89593 ! Craniata -relationship: overlaps UBERON:0002298 {notes="modified-source-relation", source="ABA"} ! brainstem -relationship: present_in_taxon NCBITaxon:7762 {source="PMID:8932866"} -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI -property_value: RO:0002171 UBERON:0001891 {exceptions="ZFA", source="ABA", source="https://github.com/obophenotype/uberon/issues/378", status="pending"} -property_value: RO:0002171 UBERON:0001894 {source="ABA"} -property_value: UBPROP:0000001 "Posterior part of the brain consisting of the cerebellum and medulla oblongata.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010150", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "The most posterior of the three principal regions of the brain, forming the rhombencephalon and all or most of the metencephalon. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000029", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000002 "relationship loss: develops_from hindbrain neural tube (TAO:0007043)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000029", ontology="TAO"} -property_value: UBPROP:0000003 "Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000070", ontology="VHOG", source="DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "rhombencephalic" xsd:string -property_value: UBPROP:0000012 "in MA, brainstem and hindbrain and part-of siblings under brain, consistent with FMA and NIF. See also notes for cerebellum. We weaken the relation in ABA to overlaps" xsd:string {external_ontology="MA"} +relationship: overlaps UBERON:0002298 ! brainstem +relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata +relationship: RO:0002433 UBERON:0000955 ! contributes to morphology of brain +relationship: RO:0002495 UBERON:0007277 {source="Bgee:AN"} ! immediate transformation of presumptive hindbrain +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:7762 {source="PMID:8932866"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002049 @@ -11708,13 +11372,12 @@ xref: FMA:69050 xref: TAO:0005249 xref: ZFA:0005249 is_a: UBERON:0000477 {source="FMA"} ! anatomical cluster -relationship: composed_primarily_of UBERON:0000055 ! vessel relationship: has_part UBERON:0000179 ! haemolymphatic fluid relationship: part_of UBERON:0007798 ! vascular system -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI -property_value: editor_note "see also: vascular system. Consider merging?" xsd:string -property_value: UBPROP:0000007 "vascular" xsd:string +relationship: RO:0002473 UBERON:0000055 ! composed primarily of vessel +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: IAO:0000116 "see also: vascular system. Consider merging?" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002050 @@ -11734,7 +11397,6 @@ xref: BILA:0000034 xref: BTO:0000174 xref: CALOHA:TS-2110 xref: EFO:0000461 -xref: FBbt:00004208 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69067 xref: GAID:407 xref: MESH:D004628 @@ -11750,10 +11412,6 @@ is_a: UBERON:0005423 ! developing anatomical structure intersection_of: UBERON:0005423 ! developing anatomical structure intersection_of: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0000922 ! embryo -property_value: UBPROP:0000001 "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000138", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001105", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000178", ontology="VSAO", source="ZFIN:curator"} -property_value: UBPROP:0000012 "in FMA embryo is_a embryonic structure" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0002075 @@ -11784,10 +11442,8 @@ xref: Wikipedia:Viscus xref: XAO:0003034 is_a: UBERON:0005177 ! trunk region element intersection_of: UBERON:0000062 ! organ -intersection_of: located_in UBERON:0002323 ! coelemic cavity lumen -relationship: located_in UBERON:0002323 ! coelemic cavity lumen -property_value: UBPROP:0000001 "An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010386", ontology="AAO", source="BTO:0001491"} -property_value: UBPROP:0000012 "general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs." xsd:string {external_ontology="FMA"} +intersection_of: RO:0001025 UBERON:0002323 ! located in coelemic cavity lumen +relationship: RO:0001025 UBERON:0002323 ! located in coelemic cavity lumen [Term] id: UBERON:0002090 @@ -11805,12 +11461,10 @@ xref: AAO:0000034 xref: EFO:0000942 xref: EHDAA2:0000161 xref: EHDAA:5049 -xref: EMAPA:17214 xref: EMAPA:37721 {source="MA:th"} xref: FMA:71221 xref: MA:0002986 xref: MAT:0000148 -xref: MESH:D013131 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: MIAA:0000148 xref: TAO:0000317 xref: VHOG:0000317 @@ -11818,14 +11472,10 @@ xref: VSAO:0000093 xref: XAO:0003073 xref: ZFA:0000317 is_a: UBERON:0010912 ! subdivision of skeleton -relationship: develops_from UBERON:0003089 ! sclerotome relationship: part_of UBERON:0005944 ! axial skeleton plus cranial skeleton relationship: part_of UBERON:0011138 ! postcranial axial skeletal system +relationship: RO:0002202 UBERON:0003089 ! develops from sclerotome property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" xsd:anyURI -property_value: UBPROP:0000001 "Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000093", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000034", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000001 "The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000317", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000317", ontology="VHOG", source="DOI:10.1186/1742-9994-8-4 Schilling N, Evolution of the axial system in craniates: morphology and function of the perivertebral musculature. Frontiers in Zoology (2011)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0002100 @@ -11861,10 +11511,6 @@ xref: XAO:0003025 xref: ZFA:0001115 is_a: UBERON:0011676 ! subdivision of organism along main body axis relationship: part_of UBERON:0013702 ! body proper -property_value: RO:0002171 UBERON:0000026 {exceptions="ZFA", source="https://github.com/obophenotype/uberon/issues/378", status="pending"} -property_value: RO:0002171 UBERON:0000033 -property_value: UBPROP:0000001 "Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010339", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001115", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0002104 @@ -11892,7 +11538,6 @@ xref: XAO:0003198 xref: ZFA:0001127 is_a: UBERON:0001032 ! sensory system relationship: capable_of_part_of GO:0007601 ! visual perception -property_value: UBPROP:0000001 "The sensory system used for sight.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000632", ontology="AAO", source="AAO:EJS"} [Term] id: UBERON:0002193 @@ -11908,7 +11553,7 @@ xref: EMAPA:18765 xref: FMA:74562 xref: MA:0000013 is_a: UBERON:0000467 {source="MA"} ! anatomical system -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria [Term] id: UBERON:0002200 @@ -11957,12 +11602,11 @@ is_a: UBERON:0002200 ! vasculature of head is_a: UBERON:0006876 ! vasculature of organ intersection_of: UBERON:0002049 ! vasculature intersection_of: part_of UBERON:0000019 ! camera-type eye -relationship: develops_from UBERON:0003314 {source="ISBN:0781772214"} ! eye mesenchyme relationship: part_of UBERON:0000019 ! camera-type eye -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI -property_value: UBPROP:0000012 "not part of the eye in ZFA. Note this changed to a blood vessel in ZFA" xsd:string {external_ontology="ZFA"} +relationship: RO:0002202 UBERON:0003314 {source="ISBN:0781772214"} ! develops from eye mesenchyme +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002204 @@ -11990,13 +11634,10 @@ is_a: UBERON:0000467 ! anatomical system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of_part_of GO:0040011 ! locomotion -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: has_developmental_contribution_from UBERON:0000926 {notes="check ctenophore"} ! mesoderm relationship: has_part UBERON:0000383 ! musculature of body relationship: has_part UBERON:0001434 ! skeletal system -property_value: UBPROP:0000001 "Anatomical system that provides locomotion and physical support to the organism.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010546", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001275", ontology="VHOG", source="DOI:10.1002/jez.b.21246 Shearman RM, Burke AC, The lateral somitic frontier in ontogeny and phylogeny. Journal of Experimental Zoology (2009)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "musculoskeletal" xsd:string +relationship: RO:0002254 UBERON:0000926 ! has developmental contribution from mesoderm +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage [Term] id: UBERON:0002224 @@ -12023,13 +11664,12 @@ xref: UMLS:C0230139 {source="ncithesaurus:Thoracic_Cavity"} xref: Wikipedia:Thoracic_cavity is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0000915 ! thoracic segment of trunk intersection_of: part_of UBERON:0002323 ! coelemic cavity lumen -relationship: luminal_space_of UBERON:0000915 ! thoracic segment of trunk +intersection_of: RO:0002572 UBERON:0000915 ! luminal space of thoracic segment of trunk relationship: part_of UBERON:0002323 ! coelemic cavity lumen -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI -property_value: UBPROP:0000008 "In many species, the diaphragm separates thoracic and abdominal cavities" xsd:string +relationship: RO:0002572 UBERON:0000915 ! luminal space of thoracic segment of trunk +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI [Term] id: UBERON:0002240 @@ -12085,19 +11725,16 @@ is_a: UBERON:0000489 ! cavitated compound organ is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005174 ! dorsal region element is_a: UBERON:0010314 ! structure with developmental contribution from neural crest -relationship: develops_from UBERON:0003076 ! posterior neural tube -relationship: has_developmental_contribution_from UBERON:0003853 {evidence="definitional"} ! spinal cord neural crest relationship: has_part CL:0005000 {source="ZFA"} ! spinal cord interneuron -relationship: immediate_transformation_of UBERON:0006241 {evidence="definitional"} ! future spinal cord relationship: part_of UBERON:0001017 ! central nervous system -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/58/Spinal_cord_direv.svg" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Spinal_Cord.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Spinal_Cord.glb" xsd:anyURI -property_value: editor_note "TODO - add superclass to unify with VNC?" xsd:string -property_value: RO:0002171 UBERON:0000955 {exceptions="ZFA", source="https://github.com/obophenotype/uberon/issues/378", status="pending"} -property_value: UBPROP:0000001 "Part of the central nervous system which descends from the hindbrain within the vertebral column.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010151", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000601", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003076 ! develops from posterior neural tube +relationship: RO:0002254 UBERON:0003853 ! has developmental contribution from spinal cord neural crest +relationship: RO:0002495 UBERON:0006241 ! immediate transformation of future spinal cord +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/58/Spinal_cord_direv.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Spinal_Cord.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Spinal_Cord.glb" xsd:anyURI +property_value: IAO:0000116 "TODO - add superclass to unify with VNC?" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002298 @@ -12137,17 +11774,11 @@ xref: VHOG:0001457 xref: Wikipedia:Brainstem xref: ZFA:0001707 is_a: UBERON:0002616 ! regional part of brain -relationship: continuous_with UBERON:0002240 ! spinal cord -relationship: contributes_to_morphology_of UBERON:0000955 ! brain relationship: has_part UBERON:0001896 ! medulla oblongata relationship: has_part UBERON:0001943 ! midbrain tegmentum -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b7/Gray719.png" xsd:anyURI -property_value: RO:0002171 UBERON:0001890 {notes="we apply a strict definition"} -property_value: RO:0002171 UBERON:0002037 {exceptions="ZFA", source="ABA", source="https://github.com/obophenotype/uberon/issues/378", status="pending"} -property_value: RO:0002171 UBERON:0002314 {notes="we apply a strict definition"} -property_value: UBPROP:0000001 "Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002156", ontology="TAO", source="ISBN:3764351209"} -property_value: UBPROP:0000001 "Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,adopted][ZFA:0001707]." xsd:string {source="ZFA:0001707"} -property_value: UBPROP:0000001 "the stalk-like part of the brain that comprises the midbrain (aka mesencephalon), the pons (aka pons Varolii), and the medulla oblongata, and connects the cerebral hemispheres with the cervical spinal cord[MP]" xsd:string {source="MP:0005277"} +relationship: RO:0002150 UBERON:0002240 ! continuous with spinal cord +relationship: RO:0002433 UBERON:0000955 ! contributes to morphology of brain +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b7/Gray719.png" xsd:anyURI [Term] id: UBERON:0002316 @@ -12170,7 +11801,6 @@ xref: EMAPA:35927 xref: FMA:83929 xref: HBA:9218 xref: MA:0001135 -xref: MESH:D066127 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C33892 xref: neuronames:2870 xref: NLX:412 @@ -12184,13 +11814,9 @@ xref: VHOG:0001764 xref: Wikipedia:White_matter xref: ZFA:0001682 is_a: UBERON:0011215 ! central nervous system cell part cluster -relationship: composed_primarily_of UBERON:0006135 ! myelinated nerve fiber -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/d7/Grey_matter_and_white_matter_-_very_high_mag.jpg" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg" xsd:anyURI -property_value: UBPROP:0000001 "Cell part cluster consisting predominantly of neurites in the brain and the spinal cord[FMA:83929]." xsd:string {source="FMA:83929"} -property_value: UBPROP:0000001 "Multi-tissue structure comprised largely of myelinated axons.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002142", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "The myelination of axons by glial cells was the last major step in the evolution of cells in the vertebrate nervous system, and white-matter tracts are key to the architecture of the mammalian brain.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001764", ontology="VHOG", source="DOI:10.1038/nature09614 Nave KA, Myelination and support of axonal integrity by glia. Nature (2010)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "nlx_anat_101177 seems to have been lost in the transition from NIFGA to Neurolex" xsd:string {external_ontology="NIF", seeAlso="https://github.com/SciCrunch/NIF-Ontology/issues/83"} +relationship: RO:0002473 UBERON:0006135 ! composed primarily of myelinated nerve fiber +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d7/Grey_matter_and_white_matter_-_very_high_mag.jpg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg" xsd:anyURI [Term] id: UBERON:0002323 @@ -12214,7 +11840,6 @@ synonym: "ventral body cavity" NARROW [NCBITaxon:7742] xref: AEO:0000186 xref: BTO:0001707 xref: EHDAA2:0000267 -xref: FBbt:00005060 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:85006 xref: galen:BodyCavity xref: NCIT:C25444 @@ -12224,11 +11849,8 @@ xref: TAO:0001438 xref: UMLS:C0333343 {source="ncithesaurus:Cavity"} xref: ZFA:0001438 is_a: UBERON:0002553 ! anatomical cavity -relationship: luminal_space_of UBERON:0011997 ! coelom -relationship: transformation_of UBERON:0003886 {evidence="definitional"} ! future coelemic cavity lumen -property_value: UBPROP:0000001 "Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]." xsd:string {date_retrieved="2012-09-12", external_class="ZFA:0001438", ontology="ZFA", source="ZFIN:curator"} -property_value: UBPROP:0000001 "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]." xsd:string {date_retrieved="2012-09-12", external_class="BTO:0001707", ontology="BTO", source="BTO"} -property_value: UBPROP:0000008 "In mammals it forms the peritoneal, pleural, and pericardial cavities" xsd:string +relationship: RO:0002494 UBERON:0003886 ! transformation of future coelemic cavity lumen +relationship: RO:0002572 UBERON:0011997 ! luminal space of coelom [Term] id: UBERON:0002328 @@ -12266,23 +11888,15 @@ xref: XAO:0000055 xref: ZFA:0000135 is_a: UBERON:0000062 {source="PMID:15890825"} ! organ is_a: UBERON:0000481 {source="VSAO"} ! multi-tissue structure +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004121 ! ectoderm-derived structure -relationship: develops_from UBERON:0004880 {source="ZFA"} ! chordamesoderm -relationship: develops_from UBERON:0006267 {source="EHDAA2"} ! notochordal plate -relationship: dorsal_to UBERON:0001555 ! digestive tract -relationship: existence_starts_during UBERON:0000068 ! embryo stage -relationship: only_in_taxon NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! Chordata relationship: part_of UBERON:0011137 ! axial skeletal system relationship: produces PR:000014841 ! sonic hedgehog protein -relationship: ventral_to UBERON:0001049 ! neural tube -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000032", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000135", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000327", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000002 "relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000327", ontology="AAO"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000199", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "notochordal" xsd:string -property_value: UBPROP:0000011 "In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord." xsd:string +relationship: RO:0002160 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! only in taxon Chordata +relationship: RO:0002202 UBERON:0004880 {source="ZFA"} ! develops from chordamesoderm +relationship: RO:0002202 UBERON:0006267 {source="EHDAA2"} ! develops from notochordal plate +relationship: RO:0002488 UBERON:0000068 ! existence starts during embryo stage +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0002329 @@ -12321,18 +11935,10 @@ xref: XAO:0000058 xref: ZFA:0000155 is_a: UBERON:0005423 ! developing anatomical structure is_a: UBERON:0007503 {source="EHDAA2"} ! epithelial vesicle -relationship: develops_from UBERON:0003059 {source="ZFA"} ! presomitic mesoderm -relationship: never_in_taxon NCBITaxon:7712 {source="PMID:17237766"} -relationship: only_in_taxon NCBITaxon:7711 {source="GOTAX:0000352"} ! Chordata -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: IAO:0000232 "EDITOR_NOTE currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk" xsd:string -property_value: UBPROP:0000001 "Post-cranial axial segments which form sclerotome and dermomyotome.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010569", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000001 "Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000155", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000002 "relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000155", ontology="TAO"} -property_value: UBPROP:0000002 "relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000155", ontology="TAO"} -property_value: UBPROP:0000002 "relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010569", ontology="AAO"} -property_value: UBPROP:0000003 "(...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000191", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.40, DOI:10.1093/icb/43.1.137 Balavoine G, Adoutte A, The segmented urbilateria: a testable scenario. Integrative and Comparative Biology (2003)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "somitic" xsd:string +relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata +relationship: RO:0002202 UBERON:0003059 {source="ZFA"} ! develops from presomitic mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: RO:0002161 NCBITaxon:7712 {source="PMID:17237766"} [Term] id: UBERON:0002342 @@ -12359,28 +11965,22 @@ xref: MIAA:0000066 xref: NCIT:C34222 xref: neuronames:1366 xref: SCTID:361462002 -xref: TAO:0000045 xref: UMLS:C0027789 {source="ncithesaurus:Neural_Crest"} xref: VHOG:0000057 xref: Wikipedia:Neural_crest xref: XAO:0000048 xref: ZFA:0000045 is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0010316 ! germ layer / neural crest -relationship: composed_primarily_of CL:0000333 {notes="pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! migratory neural crest cell -relationship: develops_from UBERON:0003075 {source="BTO"} ! neural plate -relationship: develops_from UBERON:0005062 {source="PMID:11523831"} ! neural fold -relationship: existence_starts_during UBERON:0000110 {source="PMID:11523831"} ! neurula stage -relationship: only_in_taxon NCBITaxon:89593 {notes="Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells", source="ISBN:0073040584"} ! Craniata relationship: part_of UBERON:0002346 {source="XAO", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! neurectoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI -property_value: IAO:0000232 "EDITOR_NOTE consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams)." xsd:string -property_value: RO:0002174 NCBITaxon:117565 {source="ISBN:0073040584", source="PMID:17377535"} -property_value: UBPROP:0000001 "A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000045", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010578", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831]" xsd:string {source="PMID:11523831"} -property_value: UBPROP:0000003 "We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000057", ontology="VHOG", source="DOI:10.1111/j.1469-7580.2012.01495.x Hall BK, Gillis JA, Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues. J Anat (2012)", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata +relationship: RO:0002202 UBERON:0003075 {source="BTO"} ! develops from neural plate +relationship: RO:0002202 UBERON:0005062 {source="PMID:11523831"} ! develops from neural fold +relationship: RO:0002473 CL:0000333 ! composed primarily of migratory neural crest cell +relationship: RO:0002488 UBERON:0000110 {source="PMID:11523831"} ! existence starts during neurula stage +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI [Term] id: UBERON:0002346 @@ -12403,7 +12003,6 @@ xref: EHDAA:1498 xref: EHDAA:255 xref: EMAPA:16073 xref: EV:0100004 -xref: FBbt:00001057 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:87657 xref: MAT:0000176 xref: MIAA:0000176 @@ -12417,9 +12016,6 @@ xref: ZFA:0001120 is_a: UBERON:0000923 ! germ layer is_a: UBERON:0004121 ! ectoderm-derived structure relationship: has_part CL:0000133 ! neurectodermal cell -property_value: UBPROP:0000003 "(...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000150", ontology="VHOG", source="DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "neurectodermal" xsd:string -property_value: UBPROP:0000013 "we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here" xsd:string [Term] id: UBERON:0002384 @@ -12453,12 +12049,8 @@ xref: VSAO:0000017 xref: XAO:0001017 xref: ZFA:0001632 is_a: UBERON:0000479 ! tissue -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000098", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000001 "Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001641", ontology="TAO", source="TAO:wd"} -property_value: UBPROP:0000001 "Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000017", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} -property_value: UBPROP:0000012 "MA also has set of connective tissues" xsd:string {external_ontology="MA"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002385 @@ -12486,14 +12078,12 @@ xref: Wikipedia:Muscle_tissue is_a: UBERON:0000479 ! tissue is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000479 ! tissue -intersection_of: composed_primarily_of CL:0000187 ! muscle cell +intersection_of: RO:0002473 CL:0000187 ! composed primarily of muscle cell disjoint_from: UBERON:0003714 ! neural tissue relationship: capable_of GO:0006936 ! muscle contraction -relationship: composed_primarily_of CL:0000187 ! muscle cell -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0001015 ! musculature -property_value: RO:0002171 UBERON:0003714 -property_value: UBPROP:0000001 "One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000306", ontology="AAO", source="AAO:LAP"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002473 CL:0000187 ! composed primarily of muscle cell [Term] id: UBERON:0002390 @@ -12536,14 +12126,10 @@ xref: ZFA:0005023 is_a: UBERON:0000467 ! anatomical system is_a: UBERON:0004120 ! mesoderm-derived structure disjoint_from: UBERON:0004456 ! entire sense organ system -relationship: develops_from UBERON:0003061 {evidence="definitional"} ! blood island -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0002193 {source="FMA"} ! hemolymphoid system -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "Anatomical system that consists of the blood and blood forming tissues.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011002", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001624", ontology="VHOG", source="DOI:10.1016/j.coph.2010.05.004 Ellett F, Lieschke GJ, Zebrafish as a model for vertebrate hematopoiesis. Current Opinion in Pharmacology (2010)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "hematopoietic" xsd:string -property_value: UBPROP:0000008 "In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes" xsd:string {source="WP"} +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002202 UBERON:0003061 ! develops from blood island +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002506 @@ -12567,10 +12153,10 @@ is_a: UBERON:0000488 {source="FMA"} ! atypical epithelium is_a: UBERON:0015808 ! eye epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001769 ! iris -relationship: contributes_to_morphology_of UBERON:0001769 ! iris relationship: has_part GO:0048770 {source="MP"} ! pigment granule relationship: part_of UBERON:0001769 {source="MA"} ! iris -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002433 UBERON:0001769 ! contributes to morphology of iris +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002532 @@ -12594,9 +12180,8 @@ xref: VHOG:0000243 xref: Wikipedia:Epiblast is_a: UBERON:0002050 ! embryonic structure relationship: has_part CL:0000352 ! epiblast cell -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" xsd:anyURI -property_value: editor_note "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" xsd:string -property_value: UBPROP:0000003 "In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000243", ontology="VHOG", source="DOI:10.1146/annurev.cellbio.042308.113344 Zorn AM, Wells JM, Vertebrate endoderm development and organ formation. Annual Review of Cell Developmental Biology (2009)", source="http://bgee.unil.ch/"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" xsd:anyURI +property_value: IAO:0000116 "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" xsd:string [Term] id: UBERON:0002546 @@ -12610,16 +12195,13 @@ synonym: "ectodermal placode" BROAD INCONSISTENT [FMA:293966, PMID:22512454] synonym: "placode" BROAD [Wikipedia:Placode] xref: AAO:0010466 xref: EFO:0001650 -xref: FMA:293966 xref: MAT:0000369 xref: MIAA:0000369 xref: XAO:0000305 is_a: UBERON:0005085 {source="cjm"} ! ectodermal placode -relationship: only_in_taxon NCBITaxon:7711 {source="PMID:11523831", source="PMID:22512454"} ! Chordata relationship: part_of UBERON:0000033 ! head -property_value: editor_note "Do not merge with neurogenic placode" xsd:string -property_value: UBPROP:0000008 "Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons" xsd:string {source="PMID:11523831"} -property_value: UBPROP:0000013 "The term placode or placodes also applies to developing organs such as teeth, mammary glands, hair follicles, feathers and scales. We include a separate parent class for this. to avoid confusion, we include neurogenic placode as a subclass" xsd:string +relationship: RO:0002160 NCBITaxon:7711 {source="PMID:11523831", source="PMID:22512454"} ! only in taxon Chordata +property_value: IAO:0000116 "Do not merge with neurogenic placode" xsd:string [Term] id: UBERON:0002553 @@ -12635,7 +12217,7 @@ xref: galen:Cavity xref: MA:0002447 xref: NCIT:C34007 is_a: UBERON:0000464 ! anatomical space -relationship: location_of UBERON:0000463 ! organism substance +relationship: RO:0001015 UBERON:0000463 ! location of organism substance [Term] id: UBERON:0002616 @@ -12657,10 +12239,11 @@ xref: NCIT:C13031 xref: SCTID:384763002 xref: UMLS:C0445620 {source="ncithesaurus:Brain_Part"} is_a: UBERON:0000073 ! regional part of nervous system +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000481 ! multi-tissue structure intersection_of: part_of UBERON:0000955 ! brain -relationship: composed_primarily_of UBERON:0003714 ! neural tissue relationship: part_of UBERON:0000955 ! brain +relationship: RO:0002473 UBERON:0003714 ! composed primarily of neural tissue [Term] id: UBERON:0003052 @@ -12690,16 +12273,15 @@ xref: VHOG:0000649 xref: XAO:0000016 xref: ZFA:0000042 is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0007651 {inconsistent_with="ZFA", source="https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/106/"} ! anatomical junction +is_a: UBERON:0007651 ! anatomical junction intersection_of: UBERON:0007651 ! anatomical junction intersection_of: overlaps UBERON:0001891 ! midbrain intersection_of: overlaps UBERON:0002028 ! hindbrain -relationship: immediate_transformation_of UBERON:0009615 {source="ZFA"} ! midbrain hindbrain boundary neural plate relationship: overlaps UBERON:0001891 ! midbrain relationship: overlaps UBERON:0002028 ! hindbrain relationship: part_of UBERON:0000955 {source="ZFA"} ! brain -property_value: editor_note "consider adding class for organizer. Consider adding separate class for isthmus as a structure" xsd:string -property_value: UBPROP:0000003 "Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000649", ontology="VHOG", source="DOI:10.1016/j.ydbio.2005.02.008 Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005)", source="http://bgee.unil.ch/"} +relationship: RO:0002495 UBERON:0009615 {source="ZFA"} ! immediate transformation of midbrain hindbrain boundary neural plate +property_value: IAO:0000116 "consider adding class for organizer. Consider adding separate class for isthmus as a structure" xsd:string [Term] id: UBERON:0003056 @@ -12712,10 +12294,9 @@ xref: TAO:0007016 xref: VHOG:0001200 xref: XAO:0000045 xref: ZFA:0007016 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue -relationship: anterior_to UBERON:0009615 ! midbrain hindbrain boundary neural plate relationship: part_of UBERON:0003075 ! neural plate -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001200", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003057 @@ -12729,8 +12310,6 @@ xref: XAO:0000046 xref: ZFA:0007017 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0003075 ! neural plate -relationship: posterior_to UBERON:0009615 ! midbrain hindbrain boundary neural plate -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001201", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003059 @@ -12756,13 +12335,11 @@ xref: XAO:0000057 xref: ZFA:0000279 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0005423 ! developing anatomical structure -intersection_of: has_potential_to_develop_into UBERON:0002329 ! somite -intersection_of: immediate_transformation_of UBERON:0007282 ! presumptive segmental plate -relationship: has_potential_to_develop_into UBERON:0002329 ! somite -relationship: immediate_transformation_of UBERON:0007282 {source="Bgee:AN"} ! presumptive segmental plate +intersection_of: RO:0002387 UBERON:0002329 ! has potential to develop into somite +intersection_of: RO:0002495 UBERON:0007282 ! immediate transformation of presumptive segmental plate relationship: part_of UBERON:0003077 ! paraxial mesoderm -property_value: UBPROP:0000001 "Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000279", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000559", ontology="VHOG", source="DOI:10.1006/dbio.2001.0460 Schubert M, Holland LZ, Dale Stokes M and Holland ND, Three Amphoxius Wnt Genes (AmphiWnt3, AmphiWnt5, and AmphiWnt6) Associated with the Tail Bud: the Evolution of Somitogenesis in Chordates. Developmental Biology (2001)", source="http://bgee.unil.ch/"} +relationship: RO:0002387 UBERON:0002329 ! has potential to develop into somite +relationship: RO:0002495 UBERON:0007282 {source="Bgee:AN"} ! immediate transformation of presumptive segmental plate [Term] id: UBERON:0003061 @@ -12792,13 +12369,8 @@ xref: Wikipedia:Blood_island_of_umbilical_vesicle xref: XAO:0000067 xref: ZFA:0000094 is_a: UBERON:0006598 ! presumptive structure -relationship: develops_from UBERON:0003081 ! lateral plate mesoderm -relationship: has_potential_to_develop_into UBERON:0002390 ! hematopoietic system -property_value: UBPROP:0000001 "Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000094", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011006", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000002 "relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000094", ontology="TAO"} -property_value: UBPROP:0000003 "Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000085", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450, DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual Review of Cell and Developmental Biology (2006)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac" xsd:string {external_ontology="EHDAA2"} +relationship: RO:0002202 UBERON:0003081 ! develops from lateral plate mesoderm +relationship: RO:0002387 UBERON:0002390 ! has potential to develop into hematopoietic system [Term] id: UBERON:0003068 @@ -12816,11 +12388,10 @@ xref: Wikipedia:Chordamesoderm xref: XAO:0000205 xref: ZFA:0001204 is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0000926 ! mesoderm -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0000926 ! mesoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000107", ontology="VHOG", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002202 UBERON:0000926 ! develops from mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003071 @@ -12850,12 +12421,12 @@ is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0001048 ! primordium is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0006598 ! presumptive structure +is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0001048 ! primordium -intersection_of: has_potential_to_develop_into UBERON:0000019 ! camera-type eye -relationship: develops_from UBERON:0003056 ! pre-chordal neural plate -relationship: has_potential_to_develop_into UBERON:0000019 ! camera-type eye +intersection_of: RO:0002387 UBERON:0000019 ! has potential to develop into camera-type eye relationship: part_of UBERON:0003056 {source="PMID:16496288", source="XAO"} ! pre-chordal neural plate -property_value: UBPROP:0000012 "TODO - check that GO's optic placode is the same as ZFA's eye primordium; we may want to have separate term for ocular primordium precursor. XAO has both optic field and eye primordium." xsd:string {external_ontology="GO"} +relationship: RO:0002202 UBERON:0003056 ! develops from pre-chordal neural plate +relationship: RO:0002387 UBERON:0000019 ! has potential to develop into camera-type eye [Term] id: UBERON:0003072 @@ -12880,10 +12451,9 @@ xref: VHOG:0000167 xref: ZFA:0001202 is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004121 ! ectoderm-derived structure -relationship: developmentally_induced_by UBERON:0003073 ! lens placode -relationship: develops_from UBERON:0004128 {source="ZFA"} ! optic vesicle relationship: part_of UBERON:0010312 {source="ZFA"} ! immature eye -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000167", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0004128 {source="ZFA"} ! develops from optic vesicle +relationship: RO:0002256 UBERON:0003073 ! developmentally induced by lens placode [Term] id: UBERON:0003073 @@ -12911,16 +12481,14 @@ xref: XAO:0000240 xref: ZFA:0000122 is_a: UBERON:0002546 ! cranial placode is_a: UBERON:0006598 ! presumptive structure +is_a: UBERON:0010312 ! immature eye is_a: UBERON:0011814 {source="NCBIBook:NBK53175"} ! non-neurogenic ectodermal placode intersection_of: UBERON:0005085 ! ectodermal placode -intersection_of: has_potential_to_develop_into UBERON:0000965 ! lens of camera-type eye -relationship: developmentally_induced_by UBERON:0004128 ! optic vesicle -relationship: has_potential_to_develop_into UBERON:0000965 ! lens of camera-type eye +intersection_of: RO:0002387 UBERON:0000965 ! has potential to develop into lens of camera-type eye relationship: part_of UBERON:0010312 {source="ZFA"} ! immature eye -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png" xsd:anyURI -property_value: UBPROP:0000001 "Ectodermal primordium of the lens of the eye. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000122", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000166", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000011 "Classical transplantation experiments using amphibian embryos suggested that the optic vesicle is the source of lens-inducing signals sufficient to generate lens tissues in competent ectoderm (reviewed in Grainger et al., 1996). More recent findings suggest a multistep model for lens induction. There is now good evidence that lens specification occurs at the neurula stage, before the optic vesicle contact the surface ectoderm, and that neural crest cell migration in the frontonasal region is required to restrict the position of the lens placode (Bailey et al., 2006)" xsd:string {source="NCBIBook:NBK53175"} +relationship: RO:0002256 UBERON:0004128 ! developmentally induced by optic vesicle +relationship: RO:0002387 UBERON:0000965 ! has potential to develop into lens of camera-type eye +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png" xsd:anyURI [Term] id: UBERON:0003075 @@ -12940,7 +12508,6 @@ xref: EHDAA:346 xref: EHDAA:902 xref: EMAPA:35593 xref: FMA:293879 -xref: MESH:D054258 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C34225 xref: neuronames:1362 xref: RETIRED_EHDAA2:0001252 @@ -12953,12 +12520,10 @@ xref: ZFA:0000132 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0016879 ! future central nervous system -relationship: developmentally_induced_by UBERON:0002328 {source="Wikipedia"} ! notochord -relationship: immediate_transformation_of UBERON:0007284 {source="Bgee:AN"} ! presumptive neural plate -relationship: only_in_taxon NCBITaxon:7711 {source="GOTAX:0000352"} ! Chordata -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI -property_value: UBPROP:0000001 "The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000132", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000068", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata +relationship: RO:0002256 UBERON:0002328 {source="Wikipedia"} ! developmentally induced by notochord +relationship: RO:0002495 UBERON:0007284 {source="Bgee:AN"} ! immediate transformation of presumptive neural plate +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI [Term] id: UBERON:0003076 @@ -12971,9 +12536,8 @@ xref: XAO:0000250 xref: ZFA:0007037 is_a: UBERON:0002050 ! embryonic structure disjoint_from: UBERON:0003080 {source="lexical"} ! anterior neural tube -relationship: develops_from UBERON:0003057 ! chordal neural plate relationship: part_of UBERON:0001049 ! neural tube -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001383", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003057 ! develops from chordal neural plate [Term] id: UBERON:0003077 @@ -13002,13 +12566,9 @@ xref: ZFA:0000255 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue is_a: UBERON:0015212 ! lateral structure -relationship: existence_starts_during UBERON:0000109 ! gastrula stage -relationship: immediate_transformation_of UBERON:0007285 {source="Bgee:AN"} ! presumptive paraxial mesoderm -relationship: in_lateral_side_of UBERON:0000922 ! embryo -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010568", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000114", ontology="VHOG", source="DOI:10.1002/dvdy.21177 Kusakabe R and Kuratani S. Evolutionary perspectives from development of mesodermal components in the lamprey. Developmental dynamics (2007)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here)" xsd:string {external_ontology="ZFA"} +relationship: RO:0002488 UBERON:0000109 ! existence starts during gastrula stage +relationship: RO:0002495 UBERON:0007285 {source="Bgee:AN"} ! immediate transformation of presumptive paraxial mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003080 @@ -13020,10 +12580,9 @@ xref: VHOG:0001384 xref: XAO:0000307 xref: ZFA:0007038 is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0003056 ! pre-chordal neural plate relationship: part_of UBERON:0001049 ! neural tube -property_value: editor_note "TODO - add grouping class for the anterior end of the neural tube at all stages" xsd:string -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001384", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003056 ! develops from pre-chordal neural plate +property_value: IAO:0000116 "TODO - add grouping class for the anterior end of the neural tube at all stages" xsd:string [Term] id: UBERON:0003081 @@ -13055,14 +12614,10 @@ is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0000926 {source="EHDAA2", source="VHOG"} ! mesoderm -relationship: surrounds UBERON:0003887 ! intraembryonic coelom -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010574", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000001 "The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000118", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000118", ontology="VHOG", source="DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "subclass of mesoderm in ZFA." xsd:string {external_ontology="ZFA"} +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002221 UBERON:0003887 ! surrounds intraembryonic coelom +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003084 @@ -13080,14 +12635,11 @@ xref: UMLS:C1514450 {source="ncithesaurus:Primordium_of_the_Heart"} xref: XAO:0000336 xref: ZFA:0000028 is_a: UBERON:0001048 {source="Obol"} ! primordium -relationship: develops_from UBERON:0003081 {source="ZFA"} ! lateral plate mesoderm -relationship: develops_from UBERON:0004140 ! primary heart field -relationship: develops_from UBERON:0007005 {source="XAO"} ! cardiogenic splanchnic mesoderm relationship: part_of UBERON:0004535 {source="ZFA"} ! cardiovascular system -property_value: editor_note "should probably be merged with heart rudiment." xsd:string -property_value: UBPROP:0000001 "Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000028", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011044", ontology="AAO", source="XAO:curator"} -property_value: UBPROP:0000002 "relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000028", ontology="TAO"} +relationship: RO:0002202 UBERON:0003081 {source="ZFA"} ! develops from lateral plate mesoderm +relationship: RO:0002202 UBERON:0004140 ! develops from primary heart field +relationship: RO:0002202 UBERON:0007005 {source="XAO"} ! develops from cardiogenic splanchnic mesoderm +property_value: IAO:0000116 "should probably be merged with heart rudiment." xsd:string [Term] id: UBERON:0003089 @@ -13101,7 +12653,6 @@ synonym: "sclerotomes" EXACT OMO:0003004 [TAO:0001080] synonym: "sclerotomus" RELATED OMO:0003011 [Wikipedia:Sclerotome] xref: AAO:0010571 xref: AEO:0000212 -xref: BTO:0006255 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: EHDAA2:0003439 xref: EMAPA:31159 xref: FMA:295652 @@ -13114,12 +12665,9 @@ xref: XAO:0000397 xref: ZFA:0001080 is_a: UBERON:0005856 {source="EHDAA2"} ! developing mesenchymal condensation is_a: UBERON:0007530 {source="EHDAA2"} ! migrating mesenchyme population -relationship: develops_from UBERON:0002329 {source="ZFA"} ! somite -relationship: only_in_taxon NCBITaxon:7742 {source="VHOG:0000680"} ! Vertebrata -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI -property_value: UBPROP:0000001 "Skeletogenic portion of somites.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010571", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000680", ontology="VHOG", source="DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "part_of somite in XAO" xsd:string {external_ontology="XAO"} +relationship: RO:0002160 NCBITaxon:7742 {source="VHOG:0000680"} ! only in taxon Vertebrata +relationship: RO:0002202 UBERON:0002329 {source="ZFA"} ! develops from somite +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI [Term] id: UBERON:0003098 @@ -13145,11 +12693,9 @@ xref: XAO:0000475 xref: ZFA:0000137 is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0034705 {source="EHDAA2"} ! developing neuroepithelium -relationship: develops_from UBERON:0003072 ! optic cup relationship: part_of UBERON:0001894 ! diencephalon -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png" xsd:anyURI -property_value: UBPROP:0000001 "The evagination from the neural tube of the developing embryo which develops the optic cup at its extremity; the stalk persists as the optic nerve. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000223", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/optic+stalk"} -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000223", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003072 ! develops from optic cup +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png" xsd:anyURI [Term] id: UBERON:0003099 @@ -13175,12 +12721,11 @@ xref: VHOG:0000063 xref: Wikipedia:Cranial_neural_crest xref: XAO:0001001 xref: ZFA:0001194 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: has_part CL:0000008 ! migratory cranial neural crest cell relationship: part_of UBERON:0002342 ! neural crest -property_value: UBPROP:0000001 "Anterior most portion of the neural crest. Migrates in three highly conserved streams: mandibular, hyoid and branchial.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010580", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000001 "Neural crest that is part of the head.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001194", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000063", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003103 @@ -13203,7 +12748,6 @@ xref: VHOG:0001723 xref: XAO:0003041 xref: ZFA:0000496 is_a: UBERON:0000062 ! organ -property_value: IAO:0000232 "this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs" xsd:string [Term] id: UBERON:0003104 @@ -13233,15 +12777,12 @@ xref: XAO:0003046 xref: ZFA:0000393 is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue -intersection_of: composed_primarily_of CL:0008019 ! mesenchymal cell -relationship: composed_primarily_of CL:0008019 ! mesenchymal cell -relationship: functionally_related_to GO:0032502 ! developmental process -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI -property_value: editor_note "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" xsd:string -property_value: UBPROP:0000001 "A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000393", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010427", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000007 "mesenchymal" xsd:string +intersection_of: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002328 GO:0032502 ! functionally related to developmental process +relationship: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI +property_value: IAO:0000116 "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" xsd:string [Term] id: UBERON:0003314 @@ -13253,12 +12794,13 @@ xref: EHDAA2:0000485 xref: EHDAA:2910 xref: EMAPA:16673 xref: VHOG:0001084 +is_a: UBERON:0007213 ! mesenchyme derived from head neural crest is_a: UBERON:0009891 ! facial mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0000019 ! camera-type eye -relationship: develops_from UBERON:0009920 {source="EHDAA2"} ! optic neural crest relationship: part_of UBERON:0000019 ! camera-type eye -property_value: editor_note "TODO - change mesenchyme relationships to precursor_of" xsd:string +relationship: RO:0002202 UBERON:0009920 {source="EHDAA2"} ! develops from optic neural crest +property_value: IAO:0000116 "TODO - change mesenchyme relationships to precursor_of" xsd:string [Term] id: UBERON:0003386 @@ -13270,11 +12812,12 @@ synonym: "ocular smooth muscle" EXACT [MA:0001268] xref: EMAPA:18807 xref: MA:0001268 is_a: UBERON:0001135 ! smooth muscle tissue +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0000019 ! camera-type eye -relationship: contributes_to_morphology_of UBERON:0001015 ! musculature relationship: part_of UBERON:0000019 ! camera-type eye -property_value: editor_note "Not clear if we need this and intra-ocular muscle. See issue #331. MA includes ciliary and iris smooth muscle" xsd:string +relationship: RO:0002433 UBERON:0001015 ! contributes to morphology of musculature +property_value: IAO:0000116 "Not clear if we need this and intra-ocular muscle. See issue #331. MA includes ciliary and iris smooth muscle" xsd:string [Term] id: UBERON:0003544 @@ -13288,15 +12831,14 @@ synonym: "white matter of brain" EXACT [OBOL:automatic] synonym: "white matter of neuraxis of brain" EXACT [OBOL:automatic] synonym: "white substance of brain" EXACT [OBOL:automatic] xref: EMAPA:35187 -xref: HBA:9218 xref: MA:0000820 xref: NCIT:C49334 xref: UMLS:C1706995 {source="ncithesaurus:Brain_White_Matter"} is_a: UBERON:0002316 ! white matter intersection_of: UBERON:0002316 ! white matter intersection_of: part_of UBERON:0000955 ! brain -relationship: contributes_to_morphology_of UBERON:0000955 ! brain relationship: part_of UBERON:0000955 ! brain +relationship: RO:0002433 UBERON:0000955 ! contributes to morphology of brain [Term] id: UBERON:0003566 @@ -13314,13 +12856,12 @@ synonym: "portion of connective tissue of adult head" EXACT [OBOL:automatic] synonym: "portion of connective tissue of head" EXACT [OBOL:automatic] synonym: "textus connectivus of adult head" EXACT [OBOL:automatic] synonym: "textus connectivus of head" EXACT [OBOL:automatic] -xref: EMAPA:16098 xref: MA:0000577 is_a: UBERON:0002384 ! connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0000033 ! head relationship: part_of UBERON:0000033 ! head -relationship: transformation_of UBERON:0005253 ! head mesenchyme +relationship: RO:0002494 UBERON:0005253 ! transformation of head mesenchyme [Term] id: UBERON:0003714 @@ -13346,8 +12887,6 @@ intersection_of: has_part CL:0000540 ! neuron relationship: has_part CL:0000125 ! glial cell relationship: has_part CL:0000540 ! neuron relationship: part_of UBERON:0001016 ! nervous system -property_value: UBPROP:0000001 "One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000325", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000012 "FMA definition includes vasculature" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0003842 @@ -13371,10 +12910,9 @@ xref: VHOG:0001119 xref: XAO:0000252 is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0001049 ! neural tube -relationship: luminal_space_of UBERON:0001049 ! neural tube +intersection_of: RO:0002572 UBERON:0001049 ! luminal space of neural tube relationship: part_of UBERON:0001049 ! neural tube -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001119", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} +relationship: RO:0002572 UBERON:0001049 ! luminal space of neural tube [Term] id: UBERON:0003849 @@ -13394,9 +12932,8 @@ xref: ZFA:0000935 is_a: UBERON:0002342 ! neural crest is_a: UBERON:0003099 {source="ZFA"} ! cranial neural crest intersection_of: UBERON:0002342 ! neural crest -intersection_of: has_potential_to_developmentally_contribute_to UBERON:0001891 ! midbrain -relationship: has_potential_to_developmentally_contribute_to UBERON:0001891 ! midbrain -property_value: UBPROP:0000003 "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000796", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43", source="http://bgee.unil.ch/"} +intersection_of: RO:0002385 UBERON:0001891 ! has potential to developmentally contribute to midbrain +relationship: RO:0002385 UBERON:0001891 ! has potential to developmentally contribute to midbrain [Term] id: UBERON:0003851 @@ -13416,9 +12953,8 @@ xref: VHOG:0000798 xref: ZFA:0000811 is_a: UBERON:0002342 ! neural crest intersection_of: UBERON:0002342 ! neural crest -intersection_of: has_potential_to_developmentally_contribute_to UBERON:0001894 ! diencephalon -relationship: has_potential_to_developmentally_contribute_to UBERON:0001894 ! diencephalon -property_value: UBPROP:0000003 "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000798", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43", source="http://bgee.unil.ch/"} +intersection_of: RO:0002385 UBERON:0001894 ! has potential to developmentally contribute to diencephalon +relationship: RO:0002385 UBERON:0001894 ! has potential to developmentally contribute to diencephalon [Term] id: UBERON:0003852 @@ -13438,10 +12974,8 @@ xref: ZFA:0007063 is_a: UBERON:0002342 ! neural crest is_a: UBERON:0003099 {source="ZFA"} ! cranial neural crest intersection_of: UBERON:0002342 ! neural crest -intersection_of: has_potential_to_developmentally_contribute_to UBERON:0002028 ! hindbrain -relationship: has_potential_to_developmentally_contribute_to UBERON:0002028 ! hindbrain -property_value: UBPROP:0000001 "Cranial neural crest that is part of the hindbrain.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0007063", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001210", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43", source="http://bgee.unil.ch/"} +intersection_of: RO:0002385 UBERON:0002028 ! has potential to developmentally contribute to hindbrain +relationship: RO:0002385 UBERON:0002028 ! has potential to developmentally contribute to hindbrain [Term] id: UBERON:0003853 @@ -13456,9 +12990,8 @@ xref: EMAPA:16881 xref: VHOG:0001006 is_a: UBERON:0002342 ! neural crest intersection_of: UBERON:0002342 ! neural crest -intersection_of: has_potential_to_developmentally_contribute_to UBERON:0002240 ! spinal cord -relationship: has_potential_to_developmentally_contribute_to UBERON:0002240 ! spinal cord -property_value: UBPROP:0000003 "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001006", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43", source="http://bgee.unil.ch/"} +intersection_of: RO:0002385 UBERON:0002240 ! has potential to developmentally contribute to spinal cord +relationship: RO:0002385 UBERON:0002240 ! has potential to developmentally contribute to spinal cord [Term] id: UBERON:0003886 @@ -13471,11 +13004,11 @@ synonym: "body cavity precursor" RELATED [] synonym: "future coelomic cavity lumen" EXACT [] is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: has_potential_to_develop_into UBERON:0002323 ! coelemic cavity lumen -relationship: existence_ends_during UBERON:0000111 ! organogenesis stage -relationship: existence_starts_during UBERON:0000109 ! gastrula stage -relationship: has_potential_to_develop_into UBERON:0002323 ! coelemic cavity lumen +intersection_of: RO:0002387 UBERON:0002323 ! has potential to develop into coelemic cavity lumen relationship: part_of UBERON:0000926 ! mesoderm +relationship: RO:0002387 UBERON:0002323 ! has potential to develop into coelemic cavity lumen +relationship: RO:0002488 UBERON:0000109 ! existence starts during gastrula stage +relationship: RO:0002492 UBERON:0000111 ! existence ends during organogenesis stage [Term] id: UBERON:0003887 @@ -13491,10 +13024,9 @@ xref: UMLS:C1512940 {source="ncithesaurus:Intraembryonic_Coelom"} xref: VHOG:0000316 xref: Wikipedia:Intraembryonic_coelom is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0003081 {source="Wikipedia"} ! lateral plate mesoderm relationship: part_of UBERON:0011997 ! coelom -property_value: editor_note "consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults" xsd:string -property_value: UBPROP:0000003 "(...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000316", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.166", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003081 {source="Wikipedia"} ! develops from lateral plate mesoderm +property_value: IAO:0000116 "consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults" xsd:string [Term] id: UBERON:0003891 @@ -13507,9 +13039,8 @@ xref: FMA:81494 xref: NCIT:C67387 xref: UMLS:C0927195 {source="ncithesaurus:Stroma_Connective_Tissue"} is_a: UBERON:0000064 ! organ part -relationship: composed_primarily_of UBERON:0002384 ! connective tissue -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: UBPROP:0000007 "stromal" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002473 UBERON:0002384 ! composed primarily of connective tissue [Term] id: UBERON:0003902 @@ -13541,14 +13072,12 @@ xref: VHOG:0000535 xref: XAO:0003216 xref: ZFA:0000046 is_a: UBERON:0001781 ! layer of retina -is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0001781 ! layer of retina -intersection_of: immediate_transformation_of UBERON:0005425 ! presumptive neural retina -relationship: developmentally_induced_by UBERON:0005426 ! lens vesicle +intersection_of: RO:0002495 UBERON:0005425 ! immediate transformation of presumptive neural retina relationship: has_part CL:0000210 ! photoreceptor cell -relationship: immediate_transformation_of UBERON:0005425 {source="Bgee:AN"} ! presumptive neural retina -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000535", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} +relationship: RO:0002256 UBERON:0005426 ! developmentally induced by lens vesicle +relationship: RO:0002495 UBERON:0005425 {source="Bgee:AN"} ! immediate transformation of presumptive neural retina +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003914 @@ -13558,12 +13087,10 @@ def: "Epithelial tubes transport gases, liquids and cells from one site to anoth synonym: "epithelial or endothelial tube" EXACT [] xref: AEO:0000114 xref: EHDAA2:0003114 -xref: FBbt:00007474 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000025 ! tube is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium -intersection_of: has_quality PATO:0002299 ! tubular -property_value: IAO:0000232 "contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers" xsd:string +intersection_of: RO:0000086 PATO:0002299 ! has quality tubular [Term] id: UBERON:0003931 @@ -13595,11 +13122,11 @@ synonym: "germinal neuroepithelial layer" EXACT [http://orcid.org/0000-0002-6601 synonym: "germinal neuroepithelium" EXACT [NCBIBook:NBK10047] synonym: "original neural tube" EXACT [NCBIBook:NBK10047] is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0034706 {source="NCBIBook:NBK10047"} ! proliferating neuroepithelium relationship: adjacent_to UBERON:0003842 ! neural tube lumen relationship: bounding_layer_of UBERON:0001049 ! neural tube relationship: part_of UBERON:0001049 ! neural tube -property_value: UBPROP:0000011 "As the cells adjacent to the lumen continue to divide, the migrating cells form a second layer around the original neural tube. This layer becomes progressively thicker as more cells are added to it from the germinal neuroepithelium. This new layer is called the mantle (or intermediate) zone, and the germinal epithelium is now called the ventricular zone (and, later, the ependyma)[NCBIBook:NBK10047]" xsd:string [Term] id: UBERON:0004060 @@ -13620,10 +13147,9 @@ is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0034706 {source="NCBIBook:NBK10047"} ! proliferating neuroepithelium relationship: adjacent_to UBERON:0003842 ! neural tube lumen -relationship: immediate_transformation_of UBERON:0004022 {source="NCBIBook:NBK10047"} ! germinal neuroepithelium relationship: part_of UBERON:0001049 ! neural tube -property_value: editor_note "consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure" xsd:string -property_value: UBPROP:0000001 "The layer of undifferentiated, proliferating cells that line the neural tube lumen" xsd:string {source="MP:0009689"} +relationship: RO:0002495 UBERON:0004022 {source="NCBIBook:NBK10047"} ! immediate transformation of germinal neuroepithelium +property_value: IAO:0000116 "consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure" xsd:string [Term] id: UBERON:0004061 @@ -13637,11 +13163,12 @@ xref: EMAPA:17148 xref: EMAPA:35360 xref: neuronames:1367 is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0034707 {source="NCBIBook:NBK10047"} ! differentiating neuroepithelium relationship: adjacent_to UBERON:0004060 ! neural tube ventricular layer relationship: adjacent_to UBERON:0004062 ! neural tube marginal layer -relationship: develops_from UBERON:0004022 {notes="by division", source="NCBIBook:NBK10047"} ! germinal neuroepithelium relationship: part_of UBERON:0001049 ! neural tube +relationship: RO:0002202 UBERON:0004022 ! develops from germinal neuroepithelium [Term] id: UBERON:0004062 @@ -13653,10 +13180,11 @@ synonym: "brain marginal zone" RELATED [] synonym: "neural tube marginal zone" EXACT [MP:0009691] xref: EMAPA:17151 xref: neuronames:1368 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005162 ! multi cell part structure relationship: adjacent_to UBERON:0004061 ! neural tube mantle layer -relationship: develops_from UBERON:0004061 {notes="forms from axons"} ! neural tube mantle layer relationship: part_of UBERON:0001049 ! neural tube +relationship: RO:0002202 UBERON:0004061 ! develops from neural tube mantle layer [Term] id: UBERON:0004088 @@ -13674,8 +13202,7 @@ synonym: "orbital part of face" EXACT [http://orcid.org/0000-0002-6601-2165] xref: FMA:260119 is_a: UBERON:0001444 ! subdivision of head relationship: part_of UBERON:0001456 ! face -property_value: editor_note "note the FMA class is more narrow though, and is more like eye + muscles + vasculature. The FMA also has FMA:72951 orbital part of eye" xsd:string -property_value: UBPROP:0000012 "in HP covers eyelid, eyebrow." xsd:string {external_ontology="HP:0000284"} +property_value: IAO:0000116 "note the FMA class is more narrow though, and is more like eye + muscles + vasculature. The FMA also has FMA:72951 orbital part of eye" xsd:string [Term] id: UBERON:0004111 @@ -13695,15 +13222,14 @@ xref: SCTID:346902003 xref: Wikipedia:Foramen is_a: UBERON:0010000 ! multicellular anatomical structure intersection_of: UBERON:0010000 ! multicellular anatomical structure -intersection_of: conduit_for UBERON:0000061 ! anatomical structure intersection_of: has_part UBERON:0013686 ! anatomical conduit space -relationship: conduit_for UBERON:0000061 ! anatomical structure -relationship: connects UBERON:0000464 {cardinality="2"} ! anatomical space +intersection_of: RO:0002570 UBERON:0000061 ! conduit for anatomical structure relationship: has_part UBERON:0013686 ! anatomical conduit space -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: UBPROP:0000012 "FMA has both conduit and conduit space. In EHDAA2 this is a surface feature" xsd:string {external_ontology="FMA"} +relationship: RO:0002176 UBERON:0000464 {cardinality="2"} ! connects anatomical space +relationship: RO:0002570 UBERON:0000061 ! conduit for anatomical structure +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0004120 @@ -13714,9 +13240,8 @@ subset: grouping_class synonym: "mesodermal derivative" EXACT [FBbt:00025998] is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: develops_from UBERON:0000926 ! mesoderm -relationship: develops_from UBERON:0000926 ! mesoderm -property_value: IAO:0000232 "Grouping term for query purposes" xsd:string +intersection_of: RO:0002202 UBERON:0000926 ! develops from mesoderm +relationship: RO:0002202 UBERON:0000926 ! develops from mesoderm [Term] id: UBERON:0004121 @@ -13727,9 +13252,8 @@ subset: grouping_class synonym: "ectodermal deriviative" EXACT [FBbt:00025990] is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: develops_from UBERON:0000924 ! ectoderm -relationship: develops_from UBERON:0000924 ! ectoderm -property_value: IAO:0000232 "Grouping term for query purposes" xsd:string +intersection_of: RO:0002202 UBERON:0000924 ! develops from ectoderm +relationship: RO:0002202 UBERON:0000924 ! develops from ectoderm [Term] id: UBERON:0004128 @@ -13757,12 +13281,11 @@ xref: XAO:0000228 xref: ZFA:0000050 is_a: UBERON:0000479 ! tissue is_a: UBERON:0004121 ! ectoderm-derived structure -relationship: developmentally_induced_by UBERON:0004880 ! chordamesoderm -relationship: develops_from UBERON:0002346 {source="GO-def"} ! neurectoderm -relationship: develops_from UBERON:0003071 {source="ZFA"} ! eye primordium relationship: part_of UBERON:0010312 {source="ZFA"} ! immature eye -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e0/Gray863.png" xsd:anyURI -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000165", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0002346 {source="GO-def"} ! develops from neurectoderm +relationship: RO:0002202 UBERON:0003071 {source="ZFA"} ! develops from eye primordium +relationship: RO:0002256 UBERON:0004880 ! developmentally induced by chordamesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e0/Gray863.png" xsd:anyURI [Term] id: UBERON:0004139 @@ -13778,9 +13301,8 @@ xref: EHDAA2:0000215 xref: EMAPA:16106 xref: VHOG:0000975 is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0003084 ! heart primordium -property_value: editor_note "TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO" xsd:string -property_value: UBPROP:0000003 "(In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000975", ontology="VHOG", source="PMID:15611355 Gittenberger-de Groot AC, Bartelings MM, Deruiter MC, Poelmann RE, Basics of cardiac development for the understanding of congenital heart malformations. Pediatric Research (2005)", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003084 ! develops from heart primordium +property_value: IAO:0000116 "TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO" xsd:string [Term] id: UBERON:0004140 @@ -13794,11 +13316,11 @@ synonym: "PHF" RELATED OMO:0003000 [XAO:0004185] synonym: "primary heart field" EXACT [PMID:17276708, XAO:0004185] xref: XAO:0004185 is_a: UBERON:0002050 ! embryonic structure +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007688 ! anlage relationship: part_of UBERON:0003081 {source="GO:0003128"} ! lateral plate mesoderm relationship: part_of UBERON:0036146 {source="https://orcid.org/0000-0003-3308-6245"} ! cardiopharyngeal field -property_value: UBPROP:0000012 "this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138]" xsd:string {external_ontology="GO"} [Term] id: UBERON:0004141 @@ -13821,8 +13343,7 @@ xref: ZFA:0000360 is_a: UBERON:0003914 ! epithelial tube is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0012275 ! meso-epithelium -relationship: immediate_transformation_of UBERON:0005498 {source="ZFA-modified"} ! primitive heart tube -property_value: UBPROP:0000001 "the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube." xsd:string {source="MP:0012700"} +relationship: RO:0002495 UBERON:0005498 {source="ZFA-modified"} ! immediate transformation of primitive heart tube [Term] id: UBERON:0004151 @@ -13835,6 +13356,7 @@ synonym: "heart chamber" EXACT [] xref: FMA:7095 xref: SCTID:276456008 is_a: UBERON:0000064 ! organ part +is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0000948 ! heart [Term] @@ -13847,10 +13369,11 @@ xref: AAO:0000156 xref: EMAPA:35335 xref: MA:0000271 is_a: UBERON:0001630 ! muscle organ +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0001630 ! muscle organ intersection_of: part_of UBERON:0000019 ! camera-type eye -relationship: contributes_to_morphology_of UBERON:0000019 ! camera-type eye relationship: part_of UBERON:0000019 {source="MA"} ! camera-type eye +relationship: RO:0002433 UBERON:0000019 ! contributes to morphology of camera-type eye [Term] id: UBERON:0004288 @@ -13880,13 +13403,10 @@ xref: Wikipedia:Skeleton xref: XAO:0004053 is_a: UBERON:0034925 ! anatomical collection disjoint_from: UBERON:0004770 ! articular system -relationship: has_member UBERON:0004765 ! skeletal element relationship: part_of UBERON:0001434 ! skeletal system -relationship: present_in_taxon NCBITaxon:9606 -property_value: RO:0002171 UBERON:0000383 +relationship: RO:0002351 UBERON:0004765 ! has member skeletal element +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/The-skeletal-system" xsd:anyURI -property_value: UBPROP:0000001 "Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000026", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070"} -property_value: UBPROP:0000007 "skeletal" xsd:string [Term] id: UBERON:0004291 @@ -13898,8 +13418,7 @@ synonym: "rudimentary heart" EXACT [ZFA:0000115] xref: TAO:0000115 xref: ZFA:0000115 is_a: UBERON:0012275 ! meso-epithelium -relationship: develops_from UBERON:0004139 ! cardiogenic plate -property_value: UBPROP:0000001 "The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000115", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002202 UBERON:0004139 ! develops from cardiogenic plate [Term] id: UBERON:0004348 @@ -13912,7 +13431,7 @@ xref: EMAPA:16322 xref: RETIRED_EHDAA2:0001308 xref: VHOG:0001296 is_a: UBERON:0006598 ! presumptive structure -relationship: has_potential_to_develop_into UBERON:0000964 ! cornea +relationship: RO:0002387 UBERON:0000964 ! has potential to develop into cornea [Term] id: UBERON:0004367 @@ -13941,6 +13460,7 @@ xref: UMLS:C0011665 {source="ncithesaurus:Descemet_s_Membrane"} xref: Wikipedia:Descemet%27s_membrane xref: ZFA:0001686 is_a: UBERON:0005769 ! basement membrane of epithelium +is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0005769 ! basement membrane of epithelium intersection_of: adjacent_to UBERON:0001777 ! substantia propria of cornea intersection_of: adjacent_to UBERON:0001985 ! corneal endothelium @@ -13948,11 +13468,10 @@ intersection_of: part_of UBERON:0000964 ! cornea disjoint_from: UBERON:0004370 {source="lexical"} ! anterior limiting lamina of cornea relationship: adjacent_to UBERON:0001777 ! substantia propria of cornea relationship: adjacent_to UBERON:0001985 ! corneal endothelium -relationship: has_quality PATO:0000964 ! transparent relationship: part_of UBERON:0000964 ! cornea relationship: produced_by UBERON:0001985 {source="Cline et al"} ! corneal endothelium +relationship: RO:0000086 PATO:0000964 ! has quality transparent property_value: seeAlso "https://github.com/obophenotype/uberon/issues/15" xsd:anyURI -property_value: UBPROP:0000001 "Acellular anatomical structure composed of collagen, Descemet's membrane is secreted as a basement membrane of the corneal endothelium. Located between the stroma and the corneal endothelium, it is approximately 0.15 micrometer thick at 6 months post-fertilization.[ZFIN]" xsd:string {date_retrieved="2016-05-01", external_class="TAO:0002157", ontology="ZFIN", source="ZFIN:ZDB-PUB-061010-3", source="https://orcid.org/0000-0001-9114-8737"} [Term] id: UBERON:0004370 @@ -13980,13 +13499,12 @@ xref: UMLS:C0229127 {source="ncithesaurus:Bowman_s_Membrane"} xref: Wikipedia:Bowman%27s_membrane xref: ZFA:0001684 is_a: UBERON:0005769 ! basement membrane of epithelium +is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0005769 ! basement membrane of epithelium -intersection_of: attaches_to UBERON:0001772 ! corneal epithelium intersection_of: part_of UBERON:0000964 ! cornea -relationship: attaches_to UBERON:0001772 ! corneal epithelium +intersection_of: RO:0002371 UBERON:0001772 ! attached to corneal epithelium relationship: part_of UBERON:0000964 ! cornea -property_value: UBPROP:0000001 "Acellular anatomical structure that is the zone of collagen fibers adjacent the basement membrane of the corneal epithelium.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002155", ontology="TAO", source="ZFIN:ZDB-PUB-061010-3"} -property_value: UBPROP:0000008 "Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals" xsd:string +relationship: RO:0002371 UBERON:0001772 ! attached to corneal epithelium [Term] id: UBERON:0004456 @@ -13997,9 +13515,8 @@ subset: uberon_slim synonym: "sense organ system" EXACT [FMA:78499] xref: FMA:78499 is_a: UBERON:0000467 ! anatomical system -relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: overlaps UBERON:0001016 ! nervous system -property_value: UBPROP:0000012 "note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs" xsd:string +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage [Term] id: UBERON:0004535 @@ -14018,10 +13535,8 @@ xref: BILA:0000016 xref: BTO:0000088 xref: CALOHA:TS-1297 xref: EFO:0000791 -xref: EHDAA2:0000216 xref: EHDAA:394 xref: EMAPA:16104 -xref: EMAPA:16370 xref: EV:0100017 xref: FMA:7161 xref: GAID:467 @@ -14047,9 +13562,7 @@ intersection_of: part_of UBERON:0001009 ! circulatory system relationship: has_part UBERON:0000948 ! heart relationship: has_part UBERON:0001981 ! blood vessel relationship: part_of UBERON:0001009 ! circulatory system -relationship: present_in_taxon NCBITaxon:9606 -property_value: IAO:0000232 "we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph." xsd:string -property_value: UBPROP:0000003 "The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000302", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.451", source="http://bgee.unil.ch/"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004537 @@ -14067,11 +13580,11 @@ xref: ZFA:0001079 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature -intersection_of: composed_primarily_of UBERON:0001981 ! blood vessel -relationship: composed_primarily_of UBERON:0001981 ! blood vessel -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +intersection_of: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel +relationship: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004638 @@ -14093,7 +13606,7 @@ is_a: UBERON:0004852 ! cardiovascular system endothelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0001981 ! blood vessel relationship: part_of UBERON:0001981 ! blood vessel -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004716 @@ -14110,12 +13623,12 @@ xref: NCIT:C34131 xref: UMLS:C1516779 {source="ncithesaurus:Conceptus"} xref: Wikipedia:Conceptus is_a: UBERON:0000061 ! anatomical structure -relationship: develops_from CL:0000365 ! animal zygote -relationship: existence_ends_with UBERON:0000068 ! embryo stage -relationship: existence_starts_with UBERON:0000068 ! embryo stage relationship: has_part UBERON:0002050 ! embryonic structure relationship: has_part UBERON:0016887 ! entire extraembryonic component -property_value: editor_note "EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus" xsd:string +relationship: RO:0002202 CL:0000365 ! develops from animal zygote +relationship: RO:0002489 UBERON:0000068 ! existence starts with embryo stage +relationship: RO:0002493 UBERON:0000068 ! existence ends with embryo stage +property_value: IAO:0000116 "EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus" xsd:string [Term] id: UBERON:0004732 @@ -14128,7 +13641,7 @@ is_a: UBERON:0000063 ! organ subunit intersection_of: UBERON:0000063 ! organ subunit intersection_of: part_of UBERON:0001016 ! nervous system relationship: part_of UBERON:0001016 ! nervous system -property_value: editor_note "revisit this after CARO is revised and/or we have defined metameric segment; note that with the additional of an A/P axis constraint this corresponds to what Richter at al call a neuromere (PMID:21062451)" xsd:string +property_value: IAO:0000116 "revisit this after CARO is revised and/or we have defined metameric segment; note that with the additional of an A/P axis constraint this corresponds to what Richter at al call a neuromere (PMID:21062451)" xsd:string [Term] id: UBERON:0004733 @@ -14139,6 +13652,7 @@ subset: non_informative synonym: "hindbrain segment" EXACT [FMA:61998] synonym: "segment of hindbrain" EXACT [FMA:61998] xref: FMA:61998 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004732 ! segmental subdivision of nervous system intersection_of: UBERON:0000063 ! organ subunit intersection_of: part_of UBERON:0002028 ! hindbrain @@ -14162,7 +13676,6 @@ synonym: "trilaminar disk" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "trilaminar germ" RELATED [https://orcid.org/0000-0002-6601-2165] xref: BILA:0000060 xref: BTO:0001403 -xref: FBbt:00005317 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:293108 xref: GAID:1302 xref: MESH:D005775 @@ -14175,10 +13688,9 @@ xref: Wikipedia:Gastrula xref: Wikipedia:Trilaminar_blastocyst is_a: UBERON:0000922 ! embryo intersection_of: UBERON:0000468 ! multicellular organism -intersection_of: existence_starts_and_ends_during UBERON:0000109 ! gastrula stage -relationship: develops_from UBERON:0000307 ! blastula -relationship: existence_starts_and_ends_during UBERON:0000109 ! gastrula stage -property_value: UBPROP:0000012 "We explicitly merge the NCITA terms here" xsd:string {external_ontology="NCIT"} +intersection_of: RO:0002491 UBERON:0000109 ! existence starts and ends during gastrula stage +relationship: RO:0002202 UBERON:0000307 ! develops from blastula +relationship: RO:0002491 UBERON:0000109 ! existence starts and ends during gastrula stage [Term] id: UBERON:0004765 @@ -14195,8 +13707,6 @@ xref: XAO:0004012 xref: ZFA:0005494 is_a: UBERON:0000062 ! organ relationship: part_of UBERON:0001434 {source="VSAO"} ! skeletal system -property_value: UBPROP:0000001 "Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000128", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001890", ontology="TAO", source="TAO:VSAO_workshop"} [Term] id: UBERON:0004770 @@ -14214,12 +13724,12 @@ xref: SCTID:361827000 xref: VSAO:0000181 is_a: UBERON:0034925 ! anatomical collection intersection_of: UBERON:0034925 ! anatomical collection -intersection_of: has_member UBERON:0000982 ! skeletal joint -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: functionally_related_to GO:0040011 ! locomotion -relationship: has_member UBERON:0000982 ! skeletal joint -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +intersection_of: RO:0002351 UBERON:0000982 ! has member skeletal joint relationship: part_of UBERON:0001434 {source="FMA"} ! skeletal system +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002328 GO:0040011 ! functionally related to locomotion +relationship: RO:0002351 UBERON:0000982 ! has member skeletal joint +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage [Term] id: UBERON:0004852 @@ -14244,8 +13754,7 @@ is_a: UBERON:0001986 ! endothelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0004535 ! cardiovascular system relationship: part_of UBERON:0004535 ! cardiovascular system -property_value: editor_note "consider merging with 'endothelium'" xsd:string -property_value: UBPROP:0000003 "Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001217", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207", source="http://bgee.unil.ch/"} +property_value: IAO:0000116 "consider merging with 'endothelium'" xsd:string [Term] id: UBERON:0004872 @@ -14263,7 +13772,6 @@ xref: Wikipedia:Lateral_plate_mesoderm#Division_into_layers xref: XAO:0000276 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0003081 ! lateral plate mesoderm -property_value: UBPROP:0000012 "We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors" xsd:string {external_ontology="BILA"} [Term] id: UBERON:0004880 @@ -14281,10 +13789,8 @@ xref: EFO:0003426 xref: TAO:0000091 xref: ZFA:0000091 is_a: UBERON:0002050 ! embryonic structure -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0003068 ! axial mesoderm -property_value: UBPROP:0000001 "Notochord rudiment[ZFIN:ZDB-PUB-961014-576]." xsd:string {source="ZFIN:ZDB-PUB-961014-576"} -property_value: UBPROP:0000012 "WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord." xsd:string +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata [Term] id: UBERON:0004905 @@ -14293,7 +13799,6 @@ namespace: uberon def: "Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts." [http://orcid.org/0000-0002-6601-2165] subset: grouping_class synonym: "joint" NARROW [] -xref: FBbt:00005811 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0034921 ! multi organ part structure relationship: part_of UBERON:0004770 ! articular system @@ -14309,15 +13814,13 @@ synonym: "gut section" RELATED [FBbt:00100315] synonym: "intestinal tract" RELATED [] synonym: "segment of intestinal tract" RELATED [] synonym: "subdivision of alimentary system" RELATED [FMA:71131] -xref: FBbt:00100315 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:71131 is_a: UBERON:0013522 ! subdivision of tube intersection_of: UBERON:0013522 ! subdivision of tube intersection_of: subdivision_of UBERON:0001555 ! digestive tract relationship: part_of UBERON:0001555 ! digestive tract -relationship: present_in_taxon NCBITaxon:9606 relationship: subdivision_of UBERON:0001555 ! digestive tract -property_value: IAO:0000232 "intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct." xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004923 @@ -14327,8 +13830,8 @@ def: "A part of a wall of an organ that forms a layer." [http://orcid.org/0000-0 subset: upper_level xref: FMA:82485 is_a: UBERON:0000064 ! organ part -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000060 ! anatomical wall +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0005061 @@ -14346,7 +13849,6 @@ xref: Wikipedia:Neural_groove xref: XAO:0000248 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0003075 ! neural plate -property_value: UBPROP:0000001 "The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]." xsd:string {source="Wikipedia:Neural_groove"} [Term] id: UBERON:0005062 @@ -14366,10 +13868,9 @@ xref: XAO:0004087 is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0005157 ! epithelial fold is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0015212 ! lateral structure -relationship: in_lateral_side_of UBERON:0005061 ! neural groove relationship: part_of UBERON:0005061 ! neural groove -property_value: UBPROP:0000001 "In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]." xsd:string {source="Wikipedia:Neural_fold"} [Term] id: UBERON:0005068 @@ -14382,8 +13883,7 @@ xref: EFO:0003498 xref: TAO:0000133 xref: ZFA:0000133 is_a: UBERON:0016879 ! future central nervous system -relationship: develops_from UBERON:0007135 ! neural keel -property_value: UBPROP:0000001 "An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000133", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002202 UBERON:0007135 ! develops from neural keel [Term] id: UBERON:0005085 @@ -14395,9 +13895,7 @@ xref: AEO:0000218 is_a: UBERON:0001048 ! primordium is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0000924 ! ectoderm -property_value: editor_note "consder adding placodal ectoderm as a distinct class? Also place placodal ectoderm as develops_from ectoderm; need to check taxon-appropriateness" xsd:string -property_value: UBPROP:0000008 "With the exception of the adenohypophysis, homologues of the nonneurogenic placodes (e.g. placodes giving rise to the teeth, hair follicles and lens), appear to be lacking in invertebrate chordates." xsd:string -property_value: UBPROP:0000012 "in GO, covers optic, otic, olfactory, mammary, hair, tooth, sebaceous - and also insect structures" xsd:string {external_ontology="GO", source="https://github.com/geneontology/go-ontology/issues/12223#issuecomment-215692347"} +property_value: IAO:0000116 "consder adding placodal ectoderm as a distinct class? Also place placodal ectoderm as develops_from ectoderm; need to check taxon-appropriateness" xsd:string [Term] id: UBERON:0005090 @@ -14407,12 +13905,10 @@ def: "Muscle structures are contractile cells, tissues or organs that are found synonym: "muscle" RELATED [] synonym: "muscle element" RELATED [] synonym: "musculus" EXACT [FMA:30316] -xref: EMAPA:32715 xref: FMA:30316 is_a: UBERON:0000061 ! anatomical structure relationship: has_part CL:0000187 ! muscle cell -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: IAO:0000232 "in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0005157 @@ -14432,11 +13928,9 @@ synonym: "multi-cell-component structure" EXACT [CARO:0001000] synonym: "multi-cell-part structure" EXACT [CARO:0001000] xref: AAO:0011000 xref: CARO:0001000 -xref: FBbt:00007060 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:83115 is_a: UBERON:0000061 ! anatomical structure -relationship: composed_primarily_of GO:0005575 ! cellular_component -property_value: UBPROP:0000012 "we go with the FMA classification rather than the CARO one. FMA def: 'Anatomical cluster which has as direct parts cell parts from two or more cells.'" xsd:string {external_ontology="CARO", external_ontology="FMA"} +relationship: RO:0002473 GO:0005575 ! composed primarily of cellular_component [Term] id: UBERON:0005174 @@ -14481,8 +13975,8 @@ xref: MA:0000557 is_a: UBERON:0002075 ! viscus is_a: UBERON:0005181 ! thoracic segment organ intersection_of: UBERON:0000062 ! organ -intersection_of: located_in UBERON:0002224 ! thoracic cavity -relationship: located_in UBERON:0002224 ! thoracic cavity +intersection_of: RO:0001025 UBERON:0002224 ! located in thoracic cavity +relationship: RO:0001025 UBERON:0002224 ! located in thoracic cavity [Term] id: UBERON:0005181 @@ -14524,7 +14018,6 @@ intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0000033 ! head relationship: part_of UBERON:0000033 ! head relationship: part_of UBERON:0009142 {source="EHDAA2"} ! entire embryonic mesenchyme -property_value: UBPROP:0000001 "Mesoderm that will give rise, along with cranial neural crest cells, to connective tissue, bone and musculature in the head. (Source: BioGlossary, www.Biology-Text.com)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000113", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0005256 @@ -14565,17 +14058,11 @@ xref: EHDAA:5526 xref: EMAPA:17082 xref: HBA:9512 xref: MA:0000205 -xref: MESH:D054024 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: VHOG:0000456 xref: Wikipedia:Myelencephalon -is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004733 ! segmental subdivision of hindbrain -relationship: immediate_transformation_of UBERON:0010096 {evidence="definitional"} ! future myelencephalon -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI -property_value: RO:0002174 NCBITaxon:7955 -property_value: UBPROP:0000001 "The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000456", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/myelencephalon"} -property_value: UBPROP:0000003 "The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000456", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000013 "the terms metencephalon and myelencephalon are only meaningful in mammals and birds - Neuroanatomy of the Zebrafish Brain. Note that its not clear if this refers to the developing medulla oblongata - MA (adult) has two distinct classes" xsd:string +relationship: RO:0002495 UBERON:0010096 ! immediate transformation of future myelencephalon +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI [Term] id: UBERON:0005291 @@ -14598,14 +14085,13 @@ name: photoreceptor array namespace: uberon def: "An array of photoreceptors and any supporting cells found in an eye." [https://orcid.org/0000-0002-6601-2165] synonym: "light-sensitive tissue" EXACT [] -xref: FBbt:00004200 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0004923 ! organ component layer intersection_of: UBERON:0004923 ! organ component layer -intersection_of: composed_primarily_of CL:0000210 ! photoreceptor cell intersection_of: part_of UBERON:0000970 ! eye -relationship: composed_primarily_of CL:0000210 ! photoreceptor cell +intersection_of: RO:0002473 CL:0000210 ! composed primarily of photoreceptor cell relationship: part_of UBERON:0000970 ! eye relationship: part_of UBERON:0001016 ! nervous system +relationship: RO:0002473 CL:0000210 ! composed primarily of photoreceptor cell [Term] id: UBERON:0005389 @@ -14615,9 +14101,8 @@ def: "A transparent structure that is part of a visual sense organ, the function subset: grouping_class synonym: "lens" NARROW [] is_a: UBERON:0000061 ! anatomical structure -relationship: has_quality PATO:0000964 ! transparent relationship: part_of UBERON:0000970 ! eye -property_value: UBPROP:0000009 "directing or focusing light onto light receptors" xsd:string +relationship: RO:0000086 PATO:0000964 ! has quality transparent [Term] id: UBERON:0005423 @@ -14630,14 +14115,13 @@ synonym: "developmental tissue" RELATED [MIAA:0000019] xref: AEO:0000125 xref: CALOHA:TS-2122 xref: EHDAA2:0003125 -xref: FBbt:00007006 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:292313 xref: MIAA:0000019 is_a: UBERON:0000465 ! material anatomical entity relationship: capable_of GO:0032502 ! developmental process -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0005424 @@ -14660,11 +14144,11 @@ xref: TAO:0000064 xref: VHOG:0000492 xref: ZFA:0000064 is_a: UBERON:0006598 ! presumptive structure +is_a: UBERON:0010312 ! immature eye intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001782 ! pigmented layer of retina -relationship: has_potential_to_develop_into UBERON:0001782 ! pigmented layer of retina +intersection_of: RO:0002387 UBERON:0001782 ! has potential to develop into pigmented layer of retina relationship: part_of UBERON:0003072 ! optic cup -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000492", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} +relationship: RO:0002387 UBERON:0001782 ! has potential to develop into pigmented layer of retina [Term] id: UBERON:0005425 @@ -14687,11 +14171,11 @@ xref: TAO:0001071 xref: VHOG:0000490 xref: ZFA:0001071 is_a: UBERON:0006598 ! presumptive structure +is_a: UBERON:0010312 ! immature eye intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0003902 ! retinal neural layer -relationship: has_potential_to_develop_into UBERON:0003902 ! retinal neural layer +intersection_of: RO:0002387 UBERON:0003902 ! has potential to develop into retinal neural layer relationship: part_of UBERON:0003072 ! optic cup -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000490", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} +relationship: RO:0002387 UBERON:0003902 ! has potential to develop into retinal neural layer [Term] id: UBERON:0005426 @@ -14713,10 +14197,8 @@ xref: TAO:0002205 xref: VHOG:0001163 xref: ZFA:0001679 is_a: UBERON:0000479 ! tissue -relationship: develops_from UBERON:0003073 ! lens placode -property_value: UBPROP:0000001 "A vesicle formed from the lens pit of the embryo, developing into the crystalline lens. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001163", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/lens+vesicle"} -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001163", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000011 "the lens of zebrafish (and other teleosts) forms from delamination of cells from the lens placode; thus, there is no formation of a hollow lens vesicle, in contrast to the situation in mammals and birds (Glass and Dahm, 2004) [PMID:16496288] The lens of the zebrafish forms by delamination of lens placodal cells and not through invagination. This results in a solid spherical mass as opposed to a hollow lens vesicle. Detachment of the solid lens vesicle of zebrafish at 24b26 hpf is accomplished in part by apoptosis, similar to mammals" xsd:string {source="ZFA"} +is_a: UBERON:0004121 ! ectoderm-derived structure +relationship: RO:0002202 UBERON:0003073 ! develops from lens placode [Term] id: UBERON:0005427 @@ -14727,6 +14209,7 @@ xref: TAO:0002188 xref: ZFA:0001688 is_a: UBERON:0000479 {source="ZFA"} ! tissue is_a: UBERON:0001048 {source="Obol"} ! primordium +is_a: UBERON:0010312 ! immature eye is_a: UBERON:0010313 ! neural crest-derived structure relationship: part_of UBERON:0000019 {source="ZFA"} ! camera-type eye @@ -14738,7 +14221,6 @@ def: "Multi-tissue structure that arises from the heart rudiment and will become subset: vertebrate_core synonym: "early primitive heart tube" NARROW [EMAPA:16208] synonym: "primitive heart tube" EXACT [EMAPA:16215] -xref: BTO:0006179 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: EHDAA2:0001512 xref: EHDAA:424 xref: EHDAA:436 @@ -14750,8 +14232,8 @@ xref: Wikipedia:Primitive_heart_tube xref: ZFA:0000149 is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004120 ! mesoderm-derived structure -relationship: develops_from UBERON:0004291 {source="ZFA"} ! heart rudiment relationship: part_of UBERON:0000922 ! embryo +relationship: RO:0002202 UBERON:0004291 {source="ZFA"} ! develops from heart rudiment [Term] id: UBERON:0005606 @@ -14766,7 +14248,6 @@ xref: VHOG:0001477 is_a: UBERON:0002553 ! anatomical cavity is_a: UBERON:0012467 ! enclosed anatomical space relationship: part_of UBERON:0002203 ! vasculature of eye -property_value: UBPROP:0000001 "A depression in the front of the vitreous body, lodging the lens. [adapted_from_the_definition_of_the_hyaloid_fossa]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001477", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/hyaloid+fossa"} [Term] id: UBERON:0005764 @@ -14779,9 +14260,9 @@ is_a: UBERON:0000476 ! acellular anatomical structure intersection_of: UBERON:0000476 ! acellular anatomical structure intersection_of: bounding_layer_of UBERON:0000061 ! anatomical structure relationship: bounding_layer_of UBERON:0000061 ! anatomical structure -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0005769 @@ -14801,12 +14282,11 @@ xref: Wikipedia:Basement_membrane is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005764 {source="FMA"} ! acellular membrane relationship: adjacent_to CL:0000066 ! epithelial cell -relationship: composed_primarily_of GO:0005604 ! basement membrane relationship: has_part GO:0005587 ! collagen type IV trimer -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa relationship: part_of UBERON:0000483 ! epithelium -relationship: present_in_taxon NCBITaxon:80999 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} -property_value: IAO:0000232 "this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell." xsd:string +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002473 GO:0005604 ! composed primarily of basement membrane +property_value: RO:0002175 NCBITaxon:80999 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} [Term] id: UBERON:0005856 @@ -14819,7 +14299,7 @@ xref: EHDAA2_RETIRED:0003148 xref: EHDAA:8979 is_a: UBERON:0007524 {source="AEO"} ! dense mesenchyme tissue is_a: UBERON:0011585 {source="cjm"} ! cell condensation -relationship: composed_primarily_of CL:0000335 {source="AEO-modified-relation"} ! mesenchyme condensation cell +relationship: RO:0002473 CL:0000335 {source="AEO-modified-relation"} ! composed primarily of mesenchyme condensation cell [Term] id: UBERON:0005906 @@ -14844,8 +14324,9 @@ synonym: "subbrillar sac" NARROW [NCBITaxon:8570] xref: EMAPA:18233 xref: FMA:20291 xref: SCTID:362531001 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005906 {source="FMA"} ! serous sac -relationship: adjacent_to UBERON:0001801 {modified_from="MA"} ! anterior segment of eyeball +relationship: adjacent_to UBERON:0001801 ! anterior segment of eyeball relationship: part_of UBERON:0000019 {source="FMA"} ! camera-type eye relationship: part_of UBERON:0035639 {source="HPO:pr"} ! ocular adnexa @@ -14860,7 +14341,6 @@ subset: uberon_slim synonym: "skeleton axiale" RELATED OMO:0003011 [Wikipedia:Axial_skeleton] xref: AAO:0000963 xref: EMAPA:17214 -xref: EMAPA:18043 xref: MA:0000308 xref: NCIT:C32172 xref: SCTID:361725000 @@ -14869,13 +14349,12 @@ xref: VSAO:0000056 xref: Wikipedia:Axial_skeleton xref: XAO:0004011 is_a: UBERON:0010912 ! subdivision of skeleton -relationship: contributes_to_morphology_of UBERON:0001434 ! skeletal system -relationship: develops_from UBERON:0003089 ! sclerotome relationship: part_of UBERON:0011137 ! axial skeletal system -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg" xsd:anyURI +relationship: RO:0002202 UBERON:0003089 ! develops from sclerotome +relationship: RO:0002433 UBERON:0001434 ! contributes to morphology of skeletal system +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" xsd:anyURI -property_value: UBPROP:0000001 "Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000056", ontology="VSAO", source="PSPUB:0000170"} [Term] id: UBERON:0006134 @@ -14897,8 +14376,7 @@ is_a: UBERON:0005162 ! multi cell part structure relationship: extends_fibers_into CL:0000540 ! neuron relationship: has_part GO:0030424 ! axon relationship: part_of UBERON:0001019 ! nerve fasciculus -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000007 "neurofibrous" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0006135 @@ -14916,12 +14394,11 @@ is_a: UBERON:0006134 ! nerve fiber intersection_of: UBERON:0006134 ! nerve fiber intersection_of: has_part GO:0043209 ! myelin sheath relationship: has_part GO:0043209 ! myelin sheath -relationship: never_in_taxon NCBITaxon:117569 -relationship: never_in_taxon NCBITaxon:7762 -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -relationship: present_in_taxon NCBITaxon:7776 ! Gnathostomata -property_value: editor_note "consider adding link to UBERON:0002316 ! white matter of neuraxis" xsd:string -property_value: UBPROP:0000008 "http://www1.pbrc.hawaii.edu/~danh/MyelinEvolution/evolution.html, http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=6134604, Wikipedia:Myelin#Invertebrate_myelin" xsd:string +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +property_value: IAO:0000116 "consider adding link to UBERON:0002316 ! white matter of neuraxis" xsd:string +property_value: RO:0002161 NCBITaxon:117569 +property_value: RO:0002161 NCBITaxon:7762 +property_value: RO:0002175 NCBITaxon:7776 [Term] id: UBERON:0006222 @@ -14941,9 +14418,9 @@ xref: TAO:0000574 xref: ZFA:0000574 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001894 ! diencephalon -relationship: has_potential_to_develop_into UBERON:0001894 ! diencephalon +intersection_of: RO:0002387 UBERON:0001894 ! has potential to develop into diencephalon relationship: part_of UBERON:0006240 {source="EHDAA2"} ! future forebrain +relationship: RO:0002387 UBERON:0001894 ! has potential to develop into diencephalon [Term] id: UBERON:0006238 @@ -14969,9 +14446,8 @@ xref: RETIRED_EHDAA2:0000591 xref: TAO:0000146 xref: ZFA:0000146 is_a: UBERON:0006598 ! presumptive structure -relationship: has_potential_to_develop_into UBERON:0000955 ! brain relationship: part_of UBERON:0002346 ! neurectoderm -property_value: UBPROP:0000001 "The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO)" xsd:string {source="http://neurolex.org/wiki/Cumbo_terms"} +relationship: RO:0002387 UBERON:0000955 ! has potential to develop into brain [Term] id: UBERON:0006240 @@ -14995,10 +14471,10 @@ xref: Wikipedia:Prosencephalon xref: ZFA:0000062 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001890 ! forebrain -relationship: has_potential_to_develop_into UBERON:0001890 ! forebrain +intersection_of: RO:0002387 UBERON:0001890 ! has potential to develop into forebrain relationship: part_of UBERON:0006238 ! future brain -property_value: editor_note "TODO. Add relationships to neural plate (both ZFA and EMAPA time this with the neural plate)" xsd:string +relationship: RO:0002387 UBERON:0001890 ! has potential to develop into forebrain +property_value: IAO:0000116 "TODO. Add relationships to neural plate (both ZFA and EMAPA time this with the neural plate)" xsd:string [Term] id: UBERON:0006241 @@ -15018,9 +14494,9 @@ xref: EMAPA:16755 xref: TAO:0000417 xref: ZFA:0000417 is_a: UBERON:0006598 ! presumptive structure -relationship: has_potential_to_develop_into UBERON:0001049 {source="EHDAA2"} ! neural tube -relationship: has_potential_to_develop_into UBERON:0002240 ! spinal cord relationship: part_of UBERON:0001017 ! central nervous system +relationship: RO:0002387 UBERON:0001049 {source="EHDAA2"} ! has potential to develop into neural tube +relationship: RO:0002387 UBERON:0002240 ! has potential to develop into spinal cord [Term] id: UBERON:0006267 @@ -15038,9 +14514,8 @@ is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium -relationship: develops_from UBERON:0006268 {source="EHDAA2"} ! notochordal process -property_value: editor_note "TODO - check ordering; awaiting confirmation from JB" xsd:string -property_value: UBPROP:0000001 "The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001212", ontology="VHOG", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0006268 {source="EHDAA2"} ! develops from notochordal process +property_value: IAO:0000116 "TODO - check ordering; awaiting confirmation from JB" xsd:string [Term] id: UBERON:0006268 @@ -15059,8 +14534,8 @@ xref: NCIT:C34232 xref: UMLS:C1518430 {source="ncithesaurus:Notochordal_Process"} xref: VHOG:0001213 is_a: UBERON:0005423 ! developing anatomical structure -relationship: develops_from UBERON:0000924 {source="EHDAA2"} ! ectoderm -relationship: only_in_taxon NCBITaxon:7711 ! Chordata +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002202 UBERON:0000924 {source="EHDAA2"} ! develops from ectoderm [Term] id: UBERON:0006311 @@ -15078,11 +14553,12 @@ xref: NCIT:C32301 xref: SCTID:280540004 xref: UMLS:C0459556 {source="ncithesaurus:Chamber_of_the_Eye"} is_a: UBERON:0000063 ! organ subunit +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000063 ! organ subunit -intersection_of: location_of UBERON:0006312 ! ocular refractive media intersection_of: part_of UBERON:0000019 ! camera-type eye -relationship: location_of UBERON:0006312 ! ocular refractive media +intersection_of: RO:0001015 UBERON:0006312 ! location of ocular refractive media relationship: part_of UBERON:0000019 ! camera-type eye +relationship: RO:0001015 UBERON:0006312 ! location of ocular refractive media [Term] id: UBERON:0006312 @@ -15092,7 +14568,6 @@ def: "Body substance in a liquid or semi-solid state in the eyeball which serves xref: MA:0001911 is_a: UBERON:0000463 ! organism substance relationship: part_of UBERON:0000019 ! camera-type eye -property_value: UBPROP:0000009 "ocular refraction" xsd:string [Term] id: UBERON:0006314 @@ -15111,8 +14586,8 @@ xref: MESH:D001826 xref: Wikipedia:Body_fluid is_a: UBERON:0000463 ! organism substance intersection_of: UBERON:0000463 ! organism substance -intersection_of: has_quality PATO:0001548 ! quality of a liquid -relationship: has_quality PATO:0001548 ! quality of a liquid +intersection_of: RO:0000086 PATO:0001548 ! has quality quality of a liquid +relationship: RO:0000086 PATO:0001548 ! has quality quality of a liquid [Term] id: UBERON:0006562 @@ -15127,11 +14602,7 @@ xref: MAT:0000049 xref: MESH:D010614 xref: MIAA:0000049 is_a: UBERON:0004921 ! subdivision of digestive tract -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -property_value: IAO:0000232 "currently this is an extremely generic class, encompassing both protostomes and deuterostomes." xsd:string -property_value: IAO:0006012 "2023-04-20" xsd:string -property_value: UBPROP:0000007 "branchial" xsd:string -property_value: UBPROP:0000007 "pharyngeal" xsd:string +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria [Term] id: UBERON:0006595 @@ -15145,11 +14616,11 @@ xref: TAO:0000416 xref: ZFA:0000416 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0000925 ! endoderm intersection_of: part_of UBERON:0000307 ! blastula -relationship: has_potential_to_develop_into UBERON:0000925 ! endoderm -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +intersection_of: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm relationship: part_of UBERON:0000307 ! blastula +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm [Term] id: UBERON:0006596 @@ -15163,8 +14634,8 @@ xref: TAO:0000568 xref: ZFA:0000568 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0000178 ! blood -relationship: has_potential_to_develop_into UBERON:0000178 ! blood +intersection_of: RO:0002387 UBERON:0000178 ! has potential to develop into blood +relationship: RO:0002387 UBERON:0000178 ! has potential to develop into blood [Term] id: UBERON:0006598 @@ -15178,10 +14649,10 @@ xref: TAO:0001116 xref: ZFA:0001116 is_a: UBERON:0002050 ! embryonic structure intersection_of: UBERON:0005423 ! developing anatomical structure -intersection_of: has_potential_to_develop_into UBERON:0000061 ! anatomical structure intersection_of: part_of UBERON:0000922 ! embryo -relationship: has_potential_to_develop_into UBERON:0000061 ! anatomical structure -property_value: editor_note "Consider merging with anlage" xsd:string +intersection_of: RO:0002387 UBERON:0000061 ! has potential to develop into anatomical structure +relationship: RO:0002387 UBERON:0000061 ! has potential to develop into anatomical structure +property_value: IAO:0000116 "Consider merging with anlage" xsd:string [Term] id: UBERON:0006601 @@ -15197,11 +14668,11 @@ xref: XAO:0004132 xref: ZFA:0001376 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0000924 ! ectoderm intersection_of: part_of UBERON:0000307 ! blastula -relationship: has_potential_to_develop_into UBERON:0000924 ! ectoderm -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +intersection_of: RO:0002387 UBERON:0000924 ! has potential to develop into ectoderm relationship: part_of UBERON:0000307 ! blastula +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002387 UBERON:0000924 ! has potential to develop into ectoderm [Term] id: UBERON:0006603 @@ -15215,11 +14686,11 @@ xref: TAO:0001377 xref: ZFA:0001377 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0000926 ! mesoderm intersection_of: part_of UBERON:0000307 ! blastula -relationship: has_potential_to_develop_into UBERON:0000926 ! mesoderm -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +intersection_of: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm relationship: part_of UBERON:0000307 ! blastula +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm [Term] id: UBERON:0006876 @@ -15249,7 +14720,6 @@ is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: has_part CL:0000076 ! squamous epithelial cell relationship: has_part CL:0000076 ! squamous epithelial cell -property_value: UBPROP:0000012 "FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium" xsd:string {external_ontology="FBbt"} [Term] id: UBERON:0006965 @@ -15280,7 +14750,7 @@ xref: EHDAA2_RETIRED:0003192 xref: FMA:24137 xref: NCIT:C34022 xref: UMLS:C1515977 {source="ncithesaurus:Anatomic_Surface"} -is_a: UBERON:0010199 {notes="via morphological boundary in CARO"} ! bona-fide anatomical boundary +is_a: UBERON:0010199 ! bona-fide anatomical boundary [Term] id: UBERON:0007005 @@ -15303,13 +14773,14 @@ xref: FMA:293143 xref: SCTID:360387000 xref: VHOG:0001641 xref: XAO:0000235 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue -relationship: developmentally_induced_by UBERON:0009881 ! anterior lateral plate mesoderm -relationship: develops_from UBERON:0004872 ! splanchnic layer of lateral plate mesoderm relationship: part_of UBERON:0004140 ! primary heart field relationship: part_of UBERON:0009881 ! anterior lateral plate mesoderm -property_value: editor_note "consider FBbt:00005541 ! cardiogenic mesoderm" xsd:string -property_value: editor_note "review EHDAA2 placement" xsd:string +relationship: RO:0002202 UBERON:0004872 ! develops from splanchnic layer of lateral plate mesoderm +relationship: RO:0002256 UBERON:0009881 ! developmentally induced by anterior lateral plate mesoderm +property_value: IAO:0000116 "consider FBbt:00005541 ! cardiogenic mesoderm" xsd:string +property_value: IAO:0000116 "review EHDAA2 placement" xsd:string [Term] id: UBERON:0007010 @@ -15319,10 +14790,10 @@ def: "Organism at the cleavage stage." [OBOL:automatic] xref: BILA:0000058 is_a: UBERON:0000922 ! embryo intersection_of: UBERON:0000468 ! multicellular organism -intersection_of: existence_ends_with UBERON:0000107 ! cleavage stage -intersection_of: existence_starts_with UBERON:0000107 ! cleavage stage -relationship: existence_ends_with UBERON:0000107 ! cleavage stage -relationship: existence_starts_with UBERON:0000107 ! cleavage stage +intersection_of: RO:0002489 UBERON:0000107 ! existence starts with cleavage stage +intersection_of: RO:0002493 UBERON:0000107 ! existence ends with cleavage stage +relationship: RO:0002489 UBERON:0000107 ! existence starts with cleavage stage +relationship: RO:0002493 UBERON:0000107 ! existence ends with cleavage stage [Term] id: UBERON:0007026 @@ -15341,12 +14812,11 @@ xref: SCTID:360394002 xref: UMLS:C1514442 {source="ncithesaurus:Primordial_Gut"} is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001555 ! digestive tract -relationship: existence_starts_during UBERON:0000109 ! gastrula stage -relationship: has_developmental_contribution_from UBERON:0000925 ! endoderm -relationship: has_developmental_contribution_from UBERON:0000926 ! mesoderm -relationship: has_potential_to_develop_into UBERON:0001555 ! digestive tract -property_value: UBPROP:0000011 "The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis" xsd:string {source="NCBIBook:NBK10107"} +intersection_of: RO:0002387 UBERON:0001555 ! has potential to develop into digestive tract +relationship: RO:0002254 UBERON:0000925 ! has developmental contribution from endoderm +relationship: RO:0002254 UBERON:0000926 ! has developmental contribution from mesoderm +relationship: RO:0002387 UBERON:0001555 ! has potential to develop into digestive tract +relationship: RO:0002488 UBERON:0000109 ! existence starts during gastrula stage [Term] id: UBERON:0007100 @@ -15359,14 +14829,12 @@ synonym: "adult heart" RELATED [FBbt:00003154] synonym: "dorsal tube" NARROW [Wikipedia:Heart] synonym: "heart" NARROW [GO:0007507] xref: http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg -xref: SPD:0000130 xref: TADS:0000147 is_a: UBERON:0015228 ! circulatory organ intersection_of: UBERON:0015228 ! circulatory organ intersection_of: capable_of GO:0008015 ! blood circulation -relationship: capable_of GO:0008015 {notes="GO uses blood circulation generically to include the haemolymphatic fluid of arthropods"} ! blood circulation +relationship: capable_of GO:0008015 ! blood circulation relationship: has_part CL:0002494 ! cardiocyte -property_value: UBPROP:0000008 "note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis" xsd:string [Term] id: UBERON:0007135 @@ -15379,8 +14847,7 @@ xref: EFO:0003497 xref: TAO:0000131 xref: ZFA:0000131 is_a: UBERON:0016879 ! future central nervous system -relationship: develops_from UBERON:0003075 ! neural plate -property_value: UBPROP:0000001 "An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000131", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002202 UBERON:0003075 ! develops from neural plate [Term] id: UBERON:0007213 @@ -15400,9 +14867,10 @@ xref: EMAPA_RETIRED:16271 xref: TAO:0000787 xref: ZFA:0000787 is_a: UBERON:0005253 {source="ZFA"} ! head mesenchyme +is_a: UBERON:0014387 ! mesenchyme derived from neural crest intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: develops_from UBERON:0003099 ! cranial neural crest -relationship: develops_from UBERON:0003099 ! cranial neural crest +intersection_of: RO:0002202 UBERON:0003099 ! develops from cranial neural crest +relationship: RO:0002202 UBERON:0003099 ! develops from cranial neural crest [Term] id: UBERON:0007277 @@ -15424,13 +14892,12 @@ xref: Wikipedia:Rhombencephalon xref: ZFA:0000569 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0002028 ! hindbrain -relationship: develops_from UBERON:0003076 {source="XAO-abduced"} ! posterior neural tube -relationship: has_developmental_contribution_from UBERON:0003852 {source="cjm"} ! rhombencephalon neural crest -relationship: has_potential_to_develop_into UBERON:0002028 ! hindbrain +intersection_of: RO:0002387 UBERON:0002028 ! has potential to develop into hindbrain relationship: part_of UBERON:0006238 ! future brain -property_value: editor_note "TODO - unify naming conventions" xsd:string -property_value: UBPROP:0000001 "The embryonic rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. Rhombomeres Rh7-Rh4 form the myelencephalon that will give the medulla oblongata. Rhombomeres Rh3-Rh1 form the metencephalon that will form the pons and the cerebellum[NPX:PDR]." xsd:string {source="NPX:PDR"} +relationship: RO:0002202 UBERON:0003076 {source="XAO-abduced"} ! develops from posterior neural tube +relationship: RO:0002254 UBERON:0003852 {source="cjm"} ! has developmental contribution from rhombencephalon neural crest +relationship: RO:0002387 UBERON:0002028 ! has potential to develop into hindbrain +property_value: IAO:0000116 "TODO - unify naming conventions" xsd:string [Term] id: UBERON:0007281 @@ -15446,9 +14913,9 @@ xref: XAO:0004086 xref: ZFA:0001187 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0003052 ! midbrain-hindbrain boundary -relationship: has_potential_to_develop_into UBERON:0003052 ! midbrain-hindbrain boundary +intersection_of: RO:0002387 UBERON:0003052 ! has potential to develop into midbrain-hindbrain boundary relationship: part_of UBERON:0006238 {source="ZFA"} ! future brain +relationship: RO:0002387 UBERON:0003052 ! has potential to develop into midbrain-hindbrain boundary [Term] id: UBERON:0007282 @@ -15462,9 +14929,9 @@ xref: TAO:0000053 xref: ZFA:0000053 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0003059 ! presomitic mesoderm -relationship: develops_from UBERON:0009618 {consistent_with="https://github.com/obophenotype/uberon/wiki/The-neural-crest", source="EDHAA2"} ! trunk paraxial mesoderm -relationship: has_potential_to_develop_into UBERON:0003059 ! presomitic mesoderm +intersection_of: RO:0002387 UBERON:0003059 ! has potential to develop into presomitic mesoderm +relationship: RO:0002202 UBERON:0009618 ! develops from trunk paraxial mesoderm +relationship: RO:0002387 UBERON:0003059 ! has potential to develop into presomitic mesoderm [Term] id: UBERON:0007284 @@ -15479,12 +14946,11 @@ xref: TAO:0000063 xref: ZFA:0000063 is_a: UBERON:0016879 ! future central nervous system intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0003075 ! neural plate -relationship: develops_from UBERON:0002346 ! neurectoderm -relationship: has_potential_to_develop_into UBERON:0003075 ! neural plate +intersection_of: RO:0002387 UBERON:0003075 ! has potential to develop into neural plate relationship: part_of UBERON:0004734 ! gastrula -property_value: editor_note "consider merging" xsd:string -property_value: UBPROP:0000001 "Region of the gastrula which gives rise to the neural plate.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000063", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002202 UBERON:0002346 ! develops from neurectoderm +relationship: RO:0002387 UBERON:0003075 ! has potential to develop into neural plate +property_value: IAO:0000116 "consider merging" xsd:string [Term] id: UBERON:0007285 @@ -15500,10 +14966,10 @@ xref: XAO:0004134 xref: ZFA:0000591 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 {source="https://github.com/obophenotype/uberon/issues/1277"} ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0003077 {source="https://github.com/obophenotype/uberon/issues/1277"} ! paraxial mesoderm intersection_of: part_of UBERON:0000307 {source="https://github.com/obophenotype/uberon/issues/1277"} ! blastula -relationship: has_potential_to_develop_into UBERON:0003077 ! paraxial mesoderm +intersection_of: RO:0002387 UBERON:0003077 {source="https://github.com/obophenotype/uberon/issues/1277"} ! has potential to develop into paraxial mesoderm relationship: part_of UBERON:0000307 ! blastula +relationship: RO:0002387 UBERON:0003077 ! has potential to develop into paraxial mesoderm [Term] id: UBERON:0007418 @@ -15576,7 +15042,7 @@ is_a: UBERON:0003104 ! mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: participates_in GO:0016477 ! cell migration relationship: participates_in GO:0016477 ! cell migration -property_value: editor_note "this class will be an important part of the NC reorganization" xsd:string +property_value: IAO:0000116 "this class will be an important part of the NC reorganization" xsd:string [Term] id: UBERON:0007619 @@ -15588,7 +15054,6 @@ xref: MA:0001318 xref: SCTID:280667001 is_a: UBERON:0001781 {source="UBERON"} ! layer of retina relationship: part_of UBERON:0003902 ! retinal neural layer -property_value: UBPROP:0000012 "MA does treat internal/external limiting membranes as layers - these are classified as laminae. We do not follow this convention. However, we do following MA is grouping these terms together" xsd:string {external_ontology="MA"} [Term] id: UBERON:0007625 @@ -15616,10 +15081,10 @@ synonym: "junction" BROAD [] xref: FMA:5898 xref: SCTID:91833003 is_a: UBERON:0000061 {source="FMA"} ! anatomical structure -relationship: connects UBERON:0000061 {minCardinality="2"} ! anatomical structure -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0002176 UBERON:0000061 {minCardinality="2"} ! connects anatomical structure +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0007688 @@ -15634,7 +15099,6 @@ synonym: "organ field" RELATED [] xref: AEO:0000170 xref: EFO:0001649 xref: EHDAA2:0003170 -xref: FBbt:00005426 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: Wikipedia:Anlage_(biology) is_a: UBERON:0000479 {source="FBbt"} ! tissue is_a: UBERON:0005423 {source="AEO", source="FBbt"} ! developing anatomical structure @@ -15652,7 +15116,7 @@ intersection_of: UBERON:0001018 ! axon tract intersection_of: part_of UBERON:0000955 ! brain relationship: part_of UBERON:0000955 ! brain relationship: part_of UBERON:0002316 {source="cjm"} ! white matter -property_value: editor_note "the NIFSTD class 'nerve tract' is classified under 'regional part of brain', so it may seem like it belongs here, but actually includes spinal cord tracts" xsd:string +property_value: IAO:0000116 "the NIFSTD class 'nerve tract' is classified under 'regional part of brain', so it may seem like it belongs here, but actually includes spinal cord tracts" xsd:string [Term] id: UBERON:0007798 @@ -15670,10 +15134,8 @@ xref: NCIT:C33854 xref: UMLS:C0489903 {source="ncithesaurus:Vascular_System"} is_a: UBERON:0000467 ! anatomical system relationship: part_of UBERON:0004535 {source="MA"} ! cardiovascular system -relationship: present_in_taxon NCBITaxon:9606 -property_value: editor_note "consider merging with vasculature" xsd:string -property_value: UBPROP:0000001 "The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]." xsd:string {source="ncithesaurus:Vascular_System"} -property_value: UBPROP:0000012 "in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system" xsd:string {external_ontology="MA"} +property_value: IAO:0000116 "consider merging with vasculature" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0007811 @@ -15711,10 +15173,10 @@ xref: EHDAA2:0001113 xref: EHDAA:177 xref: EMAPA:16097 is_a: UBERON:0000477 ! anatomical cluster -relationship: composed_primarily_of UBERON:0003104 ! mesenchyme -relationship: has_developmental_contribution_from UBERON:0000926 {source="EHDAA2"} ! mesoderm relationship: part_of UBERON:0000922 ! embryo -property_value: editor_note "consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)" xsd:string +relationship: RO:0002254 UBERON:0000926 {source="EHDAA2"} ! has developmental contribution from mesoderm +relationship: RO:0002473 UBERON:0003104 ! composed primarily of mesenchyme +property_value: IAO:0000116 "consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)" xsd:string [Term] id: UBERON:0009569 @@ -15752,9 +15214,9 @@ synonym: "midbrain-hindbrain boundary neural plate" EXACT [ZFA:0007044] xref: TAO:0007044 xref: ZFA:0007044 is_a: UBERON:0006598 ! presumptive structure -relationship: immediate_transformation_of UBERON:0007281 {notes="https://github.com/obophenotype/uberon/issues/438", source="Bgee:AN"} ! presumptive midbrain hindbrain boundary relationship: part_of UBERON:0003075 {source="ZFA"} ! neural plate -property_value: editor_note "TODO - developmental relationships for lines" xsd:string +relationship: RO:0002495 UBERON:0007281 ! immediate transformation of presumptive midbrain hindbrain boundary +property_value: IAO:0000116 "TODO - developmental relationships for lines" xsd:string [Term] id: UBERON:0009616 @@ -15775,12 +15237,12 @@ xref: Wikipedia:Mesencephalon xref: ZFA:0000148 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001891 ! midbrain -relationship: develops_from UBERON:0003080 ! anterior neural tube -relationship: develops_from UBERON:0010286 {source="ZFA"} ! midbrain neural tube -relationship: has_potential_to_develop_into UBERON:0001891 ! midbrain +intersection_of: RO:0002387 UBERON:0001891 ! has potential to develop into midbrain relationship: part_of UBERON:0006238 {source="ZFA"} ! future brain -property_value: editor_note "TODO - unify naming conventions" xsd:string +relationship: RO:0002202 UBERON:0003080 ! develops from anterior neural tube +relationship: RO:0002202 UBERON:0010286 {source="ZFA"} ! develops from midbrain neural tube +relationship: RO:0002387 UBERON:0001891 ! has potential to develop into midbrain +property_value: IAO:0000116 "TODO - unify naming conventions" xsd:string [Term] id: UBERON:0009618 @@ -15802,6 +15264,7 @@ synonym: "ALPM" EXACT [ZFA:0005041] xref: EFO:0003704 xref: TAO:0005041 xref: ZFA:0005041 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue relationship: part_of UBERON:0003081 {source="ZFA"} ! lateral plate mesoderm @@ -15825,7 +15288,7 @@ name: optic neural crest namespace: uberon xref: EHDAA2:0001315 xref: EHDAA:1122 -is_a: UBERON:0005253 ! head mesenchyme +is_a: UBERON:0007213 ! mesenchyme derived from head neural crest is_a: UBERON:0007530 {source="EHDAA2"} ! migrating mesenchyme population relationship: part_of UBERON:0007213 {source="EHDAA2"} ! mesenchyme derived from head neural crest @@ -15838,15 +15301,14 @@ subset: common_anatomy subset: upper_level synonym: "multicellular structure" EXACT [FBbt:00100313] xref: CARO:0010000 -xref: FBbt:00100313 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: has_quality PATO:0001993 ! multicellular +intersection_of: RO:0000086 PATO:0001993 ! has quality multicellular relationship: has_part CL:0000000 ! cell -relationship: has_quality PATO:0001993 ! multicellular -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0000086 PATO:0001993 ! has quality multicellular +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0010096 @@ -15856,9 +15318,9 @@ def: "A developing anatomical structure that has the potential to develop into a xref: EHDAA2:0000640 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0005290 ! myelencephalon -relationship: has_potential_to_develop_into UBERON:0005290 ! myelencephalon +intersection_of: RO:0002387 UBERON:0005290 ! has potential to develop into myelencephalon relationship: part_of UBERON:0002028 ! hindbrain +relationship: RO:0002387 UBERON:0005290 ! has potential to develop into myelencephalon [Term] id: UBERON:0010199 @@ -15887,10 +15349,9 @@ xref: SCTID:244486005 xref: VHOG:0001616 xref: Wikipedia:Globe_(human_eye) is_a: UBERON:0000020 ! sense organ -relationship: contributes_to_morphology_of UBERON:0000019 ! camera-type eye +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0000019 {source="FMA"} ! camera-type eye -property_value: IAO:0000232 "See notes for camera-type eye" xsd:string -property_value: UBPROP:0000202 FMA:264089 +relationship: RO:0002433 UBERON:0000019 ! contributes to morphology of camera-type eye [Term] id: UBERON:0010285 @@ -15916,9 +15377,10 @@ namespace: uberon def: "Portion of neural tube that gives rise to the midbrain." [ZFA:0007039] xref: TAO:0007039 xref: ZFA:0007039 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue relationship: part_of UBERON:0003080 {source="ZFA"} ! anterior neural tube -property_value: editor_note "we follow ZFA in temporally dividing midbrain NT from presumptive midbrain, but in future this may be collapsed" xsd:string +property_value: IAO:0000116 "we follow ZFA in temporally dividing midbrain NT from presumptive midbrain, but in future this may be collapsed" xsd:string [Term] id: UBERON:0010312 @@ -15930,10 +15392,9 @@ xref: TAO:0002201 xref: ZFA:0001678 is_a: UBERON:0005423 ! developing anatomical structure intersection_of: UBERON:0005423 ! developing anatomical structure -intersection_of: has_developmental_contribution_from UBERON:0003071 ! eye primordium -relationship: develops_from UBERON:0003071 {evidence="definitional"} ! eye primordium -relationship: has_developmental_contribution_from UBERON:0003071 ! eye primordium -property_value: UBPROP:0000001 "Multi-tissue structure that consists of the structures that develop into the retina and lens.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002201", ontology="TAO", source="ZFIN:curator"} +intersection_of: RO:0002254 UBERON:0003071 ! has developmental contribution from eye primordium +relationship: RO:0002202 UBERON:0003071 ! develops from eye primordium +relationship: RO:0002254 UBERON:0003071 ! has developmental contribution from eye primordium [Term] id: UBERON:0010313 @@ -15944,9 +15405,8 @@ subset: grouping_class is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: develops_from UBERON:0002342 ! neural crest -relationship: develops_from UBERON:0002342 ! neural crest -property_value: IAO:0000232 "Grouping term for query purposes" xsd:string +intersection_of: RO:0002202 UBERON:0002342 ! develops from neural crest +relationship: RO:0002202 UBERON:0002342 ! develops from neural crest [Term] id: UBERON:0010314 @@ -15956,9 +15416,8 @@ def: "An anatomical structure that has some part that develops from the neural c subset: grouping_class is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: has_developmental_contribution_from UBERON:0002342 ! neural crest -relationship: has_developmental_contribution_from UBERON:0002342 ! neural crest -property_value: IAO:0000232 "Grouping term for query purposes" xsd:string +intersection_of: RO:0002254 UBERON:0002342 ! has developmental contribution from neural crest +relationship: RO:0002254 UBERON:0002342 ! has developmental contribution from neural crest [Term] id: UBERON:0010316 @@ -15966,7 +15425,7 @@ name: germ layer / neural crest namespace: uberon is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0005291 ! embryonic tissue -relationship: develops_from UBERON:0002532 ! epiblast (generic) +relationship: RO:0002202 UBERON:0002532 ! develops from epiblast (generic) [Term] id: UBERON:0010371 @@ -15978,8 +15437,8 @@ xref: FMA:69064 is_a: UBERON:0000483 ! epithelium is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000483 ! epithelium -intersection_of: develops_from UBERON:0000924 ! ectoderm -relationship: composed_primarily_of CL:0002077 ! ecto-epithelial cell +intersection_of: RO:0002202 UBERON:0000924 ! develops from ectoderm +relationship: RO:0002473 CL:0002077 ! composed primarily of ecto-epithelial cell [Term] id: UBERON:0010409 @@ -15993,8 +15452,8 @@ synonym: "ocular surface" EXACT [] xref: EMAPA:35336 xref: MA:0002486 is_a: UBERON:0000063 ! organ subunit +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0000019 ! camera-type eye -relationship: superficial_to UBERON:0022288 ! surface of eyeball [Term] id: UBERON:0010427 @@ -16011,12 +15470,13 @@ xref: FMA:76551 xref: SCTID:280860001 xref: Wikipedia:Ciliary_processes is_a: UBERON:0000481 ! multi-tissue structure +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001775 ! ciliary body -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/Gray875.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-l.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-r.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-l.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-r.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/Gray875.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-l.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-r.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-l.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-r.glb" xsd:anyURI [Term] id: UBERON:0010912 @@ -16032,7 +15492,6 @@ xref: VSAO:0000042 is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision relationship: part_of UBERON:0000075 {source="UBERONREF:0000003"} ! subdivision of skeletal system relationship: part_of UBERON:0004288 {source="VSAO"} ! skeleton -property_value: UBPROP:0000001 "Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000042", notes="incorrect", ontology="VSAO", source="VSAO:curator"} [Term] id: UBERON:0011137 @@ -16053,7 +15512,7 @@ synonym: "axial skeletal system" BROAD [https://github.com/obophenotype/uberon/w synonym: "post-cranial axial skeletal system" EXACT [] xref: FMA:302077 is_a: UBERON:0000075 {source="FMA"} ! subdivision of skeletal system -relationship: develops_from UBERON:0003089 {source="cjm"} ! sclerotome +relationship: RO:0002202 UBERON:0003089 {source="cjm"} ! develops from sclerotome property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" xsd:anyURI [Term] @@ -16065,6 +15524,7 @@ subset: upper_level synonym: "cell part cluster of neuraxis" EXACT [FMA:83143] synonym: "neuraxis layer" EXACT [FMA:83143] xref: FMA:83143 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005162 ! multi cell part structure intersection_of: UBERON:0005162 ! multi cell part structure intersection_of: part_of UBERON:0001017 ! central nervous system @@ -16078,15 +15538,14 @@ def: "A subdivision of an anatomical system." [http://orcid.org/0000-0002-6601-2 subset: common_anatomy subset: human_reference_atlas subset: upper_level -xref: FBbt:00007330 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67509 xref: SCTID:91690000 is_a: UBERON:0010000 {source="FBbt"} ! multicellular anatomical structure relationship: part_of UBERON:0000467 ! anatomical system -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0011222 @@ -16097,9 +15556,9 @@ synonym: "intrinsic ocular muscle" EXACT [EMAPA:18808] xref: AAO:0010038 xref: EMAPA:18808 xref: FMA:49150 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004277 ! eye muscle relationship: part_of UBERON:0003386 {source="EMAPA"} ! smooth muscle of eye -property_value: UBPROP:0000001 "Muscles within the eye (bulbus oculi).[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010038", ontology="AAO", source="AAO:EJS"} [Term] id: UBERON:0011585 @@ -16109,7 +15568,7 @@ def: "Anatomical structure that is an aggregation of similar cells from which ca xref: VSAO:0000006 xref: XAO:0004021 is_a: UBERON:0000061 {source="VSAO"} ! anatomical structure -property_value: editor_note "consider obsoleting, coordinate with VSAO" xsd:string +property_value: IAO:0000116 "consider obsoleting, coordinate with VSAO" xsd:string [Term] id: UBERON:0011591 @@ -16134,7 +15593,7 @@ synonym: "body segment" RELATED [] synonym: "main body segment" RELATED [] is_a: UBERON:0000475 ! organism subdivision relationship: part_of UBERON:0013701 ! main body axis -property_value: editor_note "Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem" xsd:string +property_value: IAO:0000116 "Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem" xsd:string [Term] id: UBERON:0011695 @@ -16198,11 +15657,12 @@ synonym: "ventral uveal tract" EXACT [] xref: EMAPA:37417 {source="MA:th"} xref: SCTID:280656002 is_a: UBERON:0000481 {source="ZFA"} ! multi-tissue structure -relationship: contributes_to_morphology_of UBERON:0001768 ! uvea -relationship: contributes_to_morphology_of UBERON:0001801 ! anterior segment of eyeball +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: has_part UBERON:0001769 ! iris relationship: has_part UBERON:0001775 ! ciliary body relationship: part_of UBERON:0001768 {source="MP"} ! uvea +relationship: RO:0002433 UBERON:0001768 ! contributes to morphology of uvea +relationship: RO:0002433 UBERON:0001801 ! contributes to morphology of anterior segment of eyeball [Term] id: UBERON:0011997 @@ -16217,10 +15677,9 @@ synonym: "schizocoelom" NARROW [] xref: EHDAA2:0004731 xref: Wikipedia:Coelom is_a: UBERON:0000481 {source="EHDAA2"} ! multi-tissue structure -relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -property_value: editor_note "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." xsd:string -property_value: UBPROP:0000007 "coelomic" xsd:string +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +property_value: IAO:0000116 "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." xsd:string +property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} [Term] id: UBERON:0012275 @@ -16233,7 +15692,7 @@ xref: FMA:86452 is_a: UBERON:0000483 ! epithelium is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000483 ! epithelium -intersection_of: develops_from UBERON:0000926 ! mesoderm +intersection_of: RO:0002202 UBERON:0000926 ! develops from mesoderm [Term] id: UBERON:0012430 @@ -16248,12 +15707,13 @@ xref: FMA:58102 xref: SCTID:361318005 xref: Wikipedia:Fibrous_tunic_of_eyeball is_a: PR:000050567 ! protein-containing material entity +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004923 {source="FMA"} ! organ component layer is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: has_part UBERON:0000964 ! cornea relationship: has_part UBERON:0001773 ! sclera relationship: part_of UBERON:0010230 ! eyeball of camera-type eye -relationship: present_in_taxon NCBITaxon:7955 {source="DOI:10.1177/0192623311409597"} +property_value: RO:0002175 NCBITaxon:7955 {source="DOI:10.1177/0192623311409597"} [Term] id: UBERON:0012467 @@ -16264,8 +15724,8 @@ synonym: "closed anatomical space" EXACT [] xref: AEO:0000222 is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: has_quality PATO:0000608 ! closed -relationship: has_quality PATO:0000608 ! closed +intersection_of: RO:0000086 PATO:0000608 ! has quality closed +relationship: RO:0000086 PATO:0000608 ! has quality closed [Term] id: UBERON:0013522 @@ -16286,11 +15746,11 @@ subset: common_anatomy synonym: "foramen space" NARROW [] xref: FMA:9338 is_a: UBERON:0000464 {source="FMA"} ! anatomical space -relationship: connects UBERON:0000464 {cardinality="2"} ! anatomical space -relationship: luminal_space_of UBERON:0004111 ! anatomical conduit -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0002176 UBERON:0000464 {cardinality="2"} ! connects anatomical space +relationship: RO:0002572 UBERON:0004111 ! luminal space of anatomical conduit +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0013701 @@ -16299,7 +15759,7 @@ namespace: uberon def: "A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages." [https://orcid.org/0000-0002-6601-2165] subset: non_informative is_a: UBERON:0000475 ! organism subdivision -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0013702 @@ -16311,11 +15771,24 @@ synonym: "body" RELATED [AEO:0000103] synonym: "whole body" RELATED [BTO:0001489] xref: AEO:0000103 xref: BTO:0001489 -xref: EMAPA:36031 xref: FMA:231424 is_a: UBERON:0000475 {source="AEO"} ! organism subdivision relationship: part_of UBERON:0013701 ! main body axis -property_value: UBPROP:0000001 "Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]." xsd:string {source="FMA:231424"} + +[Term] +id: UBERON:0014387 +name: mesenchyme derived from neural crest +namespace: uberon +def: "Mesenchyme that develops_from the neural crest[Automatically generated definition]." [https://github.com/obophenotype/uberon/issues/248, OBOL:automatic] +synonym: "mesenchyme from neural crest" EXACT [] +synonym: "neural crest derived mesenchyme" EXACT [] +synonym: "neural crest mesenchyme" EXACT [] +xref: EMAPA:32735 +xref: FMA:293883 +is_a: UBERON:0003104 ! mesenchyme +is_a: UBERON:0010313 ! neural crest-derived structure +intersection_of: UBERON:0003104 ! mesenchyme +intersection_of: RO:0002202 UBERON:0002342 ! develops from neural crest [Term] id: UBERON:0014477 @@ -16333,7 +15806,7 @@ xref: Wikipedia:Thoracic_skeleton is_a: UBERON:0010912 ! subdivision of skeleton relationship: part_of UBERON:0000915 ! thoracic segment of trunk relationship: part_of UBERON:0002090 ! postcranial axial skeleton -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0014903 @@ -16345,9 +15818,9 @@ xref: TAO:0005076 xref: ZFA:0005076 is_a: UBERON:0001048 ! primordium intersection_of: UBERON:0001048 ! primordium -intersection_of: has_potential_to_develop_into UBERON:0002049 ! vasculature -relationship: has_potential_to_develop_into UBERON:0002049 ! vasculature +intersection_of: RO:0002387 UBERON:0002049 ! has potential to develop into vasculature relationship: part_of UBERON:0011695 ! embryonic cardiovascular system +relationship: RO:0002387 UBERON:0002049 ! has potential to develop into vasculature [Term] id: UBERON:0015203 @@ -16355,7 +15828,6 @@ name: non-connected functional system namespace: uberon def: "An anatomical group whose component structures share a common function." [AEO:0000093, AEO:JB, FBbt:00007278, FBC:DOS] xref: AEO:0000093 -xref: FBbt:00007278 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0034923 ! disconnected anatomical group [Term] @@ -16366,11 +15838,7 @@ def: "Any structure that is placed on one side of the left-right axis of a bilat subset: grouping_class subset: non_informative is_a: UBERON:0000061 ! anatomical structure -intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: in_lateral_side_of UBERON:0000465 ! material anatomical entity -relationship: in_lateral_side_of UBERON:0000465 ! material anatomical entity -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -property_value: IAO:0000232 "This class is primarily to implement taxon constraints. It may be removed in the future." xsd:string +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria [Term] id: UBERON:0015228 @@ -16383,10 +15851,9 @@ synonym: "cardiac structure" RELATED [] synonym: "circulatory vessel" NARROW [] synonym: "heart" BROAD [] synonym: "heart or heart like organ" EXACT [] -xref: SPD:0000130 is_a: UBERON:0003103 ! compound organ -relationship: has_quality PATO:0001690 ! contractile relationship: part_of UBERON:0001009 ! circulatory system +relationship: RO:0000086 PATO:0001690 ! has quality contractile [Term] id: UBERON:0015410 @@ -16398,7 +15865,7 @@ xref: EMAPA:37597 {source="MA:th"} xref: MA:0002449 is_a: UBERON:0005178 {source="MA"} ! thoracic cavity element relationship: part_of UBERON:0004535 ! cardiovascular system -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0015808 @@ -16408,6 +15875,7 @@ def: "An epithelium that is part of a camera-type eye." [OBOL:automatic] xref: EMAPA:35957 xref: MA:0003162 is_a: UBERON:0007625 ! pigment epithelium of eye +is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000019 ! camera-type eye relationship: part_of UBERON:0000019 ! camera-type eye @@ -16422,10 +15890,10 @@ synonym: "future CNS" EXACT [] synonym: "presumptive central nervous system" EXACT [] is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001017 ! central nervous system -relationship: develops_from UBERON:0000924 ! ectoderm -relationship: has_potential_to_develop_into UBERON:0001017 ! central nervous system +intersection_of: RO:0002387 UBERON:0001017 ! has potential to develop into central nervous system relationship: part_of UBERON:0016880 ! future nervous system +relationship: RO:0002202 UBERON:0000924 ! develops from ectoderm +relationship: RO:0002387 UBERON:0001017 ! has potential to develop into central nervous system [Term] id: UBERON:0016880 @@ -16437,9 +15905,9 @@ synonym: "presumptive nervous system" EXACT [AAO:0000477] xref: AAO:0000477 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001016 ! nervous system -relationship: existence_starts_during_or_after UBERON:0000111 ! organogenesis stage -relationship: has_potential_to_develop_into UBERON:0001016 ! nervous system +intersection_of: RO:0002387 UBERON:0001016 ! has potential to develop into nervous system +relationship: RO:0002387 UBERON:0001016 ! has potential to develop into nervous system +relationship: RO:0002496 UBERON:0000111 ! existence starts during or after organogenesis stage [Term] id: UBERON:0016887 @@ -16453,8 +15921,8 @@ xref: EHDAA2:0000003 xref: EMAPA:16042 is_a: UBERON:0000481 {source="AEO"} ! multi-tissue structure relationship: adjacent_to UBERON:0002050 ! embryonic structure -relationship: existence_starts_and_ends_during UBERON:0000068 ! embryo stage relationship: part_of UBERON:0004716 {source="AEO"} ! conceptus +relationship: RO:0002491 UBERON:0000068 ! existence starts and ends during embryo stage [Term] id: UBERON:0019207 @@ -16468,6 +15936,8 @@ synonym: "retinachoroid" EXACT [] synonym: "retinachoroidal region" EXACT [] xref: SCTID:110701000 is_a: UBERON:0000481 ! multi-tissue structure +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: has_part UBERON:0000966 ! retina relationship: has_part UBERON:0001776 ! optic choroid relationship: part_of UBERON:0010230 ! eyeball of camera-type eye @@ -16484,7 +15954,7 @@ is_a: UBERON:0003544 ! brain white matter intersection_of: UBERON:0002316 ! white matter intersection_of: part_of UBERON:0001890 ! forebrain relationship: part_of UBERON:0001890 ! forebrain -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0019304 @@ -16519,11 +15989,11 @@ synonym: "layer" BROAD [CUMBO:CUMBO] xref: NLX:149357 is_a: UBERON:0005162 ! multi cell part structure intersection_of: UBERON:0005162 ! multi cell part structure -intersection_of: has_quality PATO:0002124 ! laminar intersection_of: part_of UBERON:0001016 ! nervous system -relationship: has_quality PATO:0002124 ! laminar +intersection_of: RO:0000086 PATO:0002124 ! has quality laminar relationship: part_of UBERON:0001016 ! nervous system -property_value: editor_note "this is currently used to group some cellular layers that may not strictly conform to the CARO definition of cell-part layer. Consider genericisizing and introducing subtypes for cellular layer, fibrous layer and cell soma layer" xsd:string +relationship: RO:0000086 PATO:0002124 ! has quality laminar +property_value: IAO:0000116 "this is currently used to group some cellular layers that may not strictly conform to the CARO definition of cell-part layer. Consider genericisizing and introducing subtypes for cellular layer, fibrous layer and cell soma layer" xsd:string [Term] id: UBERON:0034705 @@ -16570,9 +16040,8 @@ synonym: "neuron projection bundle from brain" RELATED [http://orcid.org/0000-00 is_a: UBERON:0000122 ! neuron projection bundle is_a: UBERON:0015212 ! lateral structure relationship: extends_fibers_into UBERON:0000955 ! brain -relationship: in_lateral_side_of UBERON:0000033 ! head -relationship: only_in_taxon NCBITaxon:89593 ! Craniata -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0034921 @@ -16583,10 +16052,10 @@ subset: common_anatomy synonym: "anatomical cluster" RELATED [CARO:0020001] xref: CARO:0020001 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure -relationship: composed_primarily_of UBERON:0000064 ! organ part -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0002473 UBERON:0000064 ! composed primarily of organ part +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0034923 @@ -16595,14 +16064,13 @@ namespace: uberon def: "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other." [CARO:0020000] subset: common_anatomy xref: CARO:0020000 -xref: FBbt:00007276 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000465 {source="CARO"} ! material anatomical entity -relationship: composed_primarily_of UBERON:0000061 ! anatomical structure relationship: has_component UBERON:0000061 {minCardinality="2"} ! anatomical structure -relationship: has_quality PATO:0010001 ! disconnected -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0000086 PATO:0010001 ! has quality disconnected +relationship: RO:0002473 UBERON:0000061 ! composed primarily of anatomical structure +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0034925 @@ -16611,11 +16079,11 @@ namespace: uberon def: "A collection of anatomical structures that are alike in terms of their morphology or developmental origin." [http://orcid.org/0000-0002-6601-2165] subset: common_anatomy is_a: UBERON:0000465 ! material anatomical entity -relationship: has_member UBERON:0000061 ! anatomical structure -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: editor_note "resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected" xsd:string +relationship: RO:0002351 UBERON:0000061 ! has member anatomical structure +property_value: IAO:0000116 "resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0035639 @@ -16673,9 +16141,9 @@ xref: AAO:0010270 xref: ZFA:0005594 is_a: UBERON:0000465 ! material anatomical entity relationship: bounding_layer_of UBERON:0000061 ! anatomical structure -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:8600004 @@ -16685,9 +16153,15 @@ def: "A muscle tissue that is associated with soft internal organs (viscera)." [ comment: It is quite common to refer to visceral muscles as smooth muscles, by analogy with vertebrates; however, most visceral muscles in arthropods are actually striated. {xref="https://en.wikipedia.org/wiki/Smooth_muscle", xref="FBbt:00005070", comment="PMID:8720463"} synonym: "visceral muscle" EXACT [] {comment="BTO:0002780"} is_a: UBERON:0002385 ! muscle tissue -relationship: composed_primarily_of CL:0008007 ! visceral muscle cell -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -property_value: dcterms-date "2023-02-16T10:17:46Z" xsd:dateTime +relationship: RO:0002473 CL:0008007 ! composed primarily of visceral muscle cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-02-16T10:17:46Z" xsd:dateTime + +[Typedef] +id: BFO:0000067 +name: contains process +def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] +comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant [Typedef] id: CL:4030044 @@ -16708,11 +16182,6 @@ id: RO:0000052 name: characteristic of def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." [] comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. -property_value: IAO:0000111 "inheres in" xsd:string -property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string -property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string -property_value: IAO:0000118 "inheres_in" xsd:string -property_value: RO:0001900 RO:0001901 is_functional: true is_a: RO:0002314 ! characteristic of part of inverse_of: bearer_of ! bearer of @@ -16722,10 +16191,7 @@ id: RO:0000079 name: function of def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. -property_value: editor_note "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string -property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string -property_value: IAO:0000118 "function_of" xsd:string -property_value: IAO:0000118 "is function of" xsd:string +property_value: IAO:0000116 "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string is_a: RO:0000052 ! characteristic of inverse_of: RO:0000085 ! has function @@ -16734,22 +16200,16 @@ id: RO:0000080 name: quality of def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. -property_value: editor_note "A quality inheres in its bearer at all times for which the quality exists." xsd:string -property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string -property_value: IAO:0000118 "is quality of" xsd:string -property_value: IAO:0000118 "quality_of" xsd:string +property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string is_a: RO:0000052 ! characteristic of -inverse_of: has_quality ! has quality +inverse_of: RO:0000086 ! has quality [Typedef] id: RO:0000081 name: role of def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. -property_value: editor_note "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string -property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string -property_value: IAO:0000118 "is role of" xsd:string -property_value: IAO:0000118 "role_of" xsd:string +property_value: IAO:0000116 "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string is_a: RO:0000052 ! characteristic of inverse_of: RO:0000087 ! has role @@ -16757,19 +16217,22 @@ inverse_of: RO:0000087 ! has role id: RO:0000085 name: has function def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] -property_value: editor_note "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string -property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string -property_value: IAO:0000118 "has_function" xsd:string +property_value: IAO:0000116 "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string domain: BFO:0000004 ! independent continuant is_a: bearer_of ! bearer of +[Typedef] +id: RO:0000086 +name: has quality +def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] +property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string +is_a: bearer_of ! bearer of + [Typedef] id: RO:0000087 name: has role def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] -property_value: editor_note "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string -property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string -property_value: IAO:0000118 "has_role" xsd:string +property_value: IAO:0000116 "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string domain: BFO:0000004 ! independent continuant is_a: bearer_of ! bearer of @@ -16794,12 +16257,7 @@ id: RO:0001000 name: derives from def: "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" [] subset: ro-eco -property_value: editor_note "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." xsd:string -property_value: IAO:0000112 "this cell derives from this parent cell (cell division)" xsd:string -property_value: IAO:0000112 "this nucleus derives from this parent nucleus (nuclear division)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000118 "derives_from" xsd:string -property_value: IAO:0000232 "This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations." xsd:string +property_value: IAO:0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." xsd:string inverse_of: RO:0001001 ! derives into [Typedef] @@ -16807,33 +16265,58 @@ id: RO:0001001 name: derives into def: "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" [] subset: ro-eco -property_value: editor_note "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." xsd:string -property_value: IAO:0000112 "this parent cell derives into this cell (cell division)" xsd:string -property_value: IAO:0000112 "this parent nucleus derives into this nucleus (nuclear division)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000118 "derives_into" xsd:string +property_value: IAO:0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." xsd:string + +[Typedef] +id: RO:0001015 +name: location of +def: "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" [] +property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +is_transitive: true +inverse_of: RO:0001025 ! located in + +[Typedef] +id: RO:0001025 +name: located in +def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +property_value: IAO:0000116 "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" xsd:string +property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Located_in" xsd:anyURI +domain: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +range: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +is_transitive: true +transitive_over: part_of ! part of [Typedef] id: RO:0002000 name: 2D boundary of def: "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" [] -property_value: editor_note "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string -property_value: editor_note "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string -property_value: IAO:0000112 "the surface of my skin is a 2D boundary of my body" xsd:string -property_value: IAO:0000118 "2D_boundary_of" xsd:string -property_value: IAO:0000118 "boundary of" xsd:string -property_value: IAO:0000118 "is 2D boundary of" xsd:string -property_value: IAO:0000118 "is boundary of" xsd:string -property_value: IAO:0000118 "surface of" xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string +is_a: RO:0002323 ! mereotopologically related to +inverse_of: RO:0002002 ! has 2D boundary + +[Typedef] +id: RO:0002002 +name: has 2D boundary +def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000141 ! immaterial entity is_a: RO:0002323 ! mereotopologically related to -inverse_of: has_boundary ! has 2D boundary + +[Typedef] +id: RO:0002005 +name: innervated_by +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000122 ! neuron projection bundle +inverse_of: RO:0002134 ! innervates [Typedef] id: RO:0002006 name: has synaptic terminal of -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: overlaps ! overlaps inverse_of: RO:0002130 ! has synaptic terminal in @@ -16915,16 +16398,23 @@ id: RO:0002081 name: before or simultaneous with comment: Primitive instance level timing relation between events subset: ro-eco -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000118 "<=" xsd:string is_a: RO:0002222 ! temporally related to +[Typedef] +id: RO:0002082 +name: simultaneous with +def: "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." [] +comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) +subset: ro-eco +is_symmetric: true +is_transitive: true +is_a: RO:0002081 ! before or simultaneous with + [Typedef] id: RO:0002086 name: ends after comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) subset: ro-eco -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string is_transitive: true is_a: RO:0002222 ! temporally related to @@ -16932,25 +16422,16 @@ is_a: RO:0002222 ! temporally related to id: RO:0002100 name: has soma location def: "Relation between a neuron and a material anatomical entity that its soma is part of." [] -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron range: UBERON:0000465 ! material anatomical entity is_a: overlaps ! overlaps -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] [Typedef] id: RO:0002101 name: fasciculates with def: "relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.\n" [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "fasciculates with" xsd:string -property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron range: UBERON:0000122 ! neuron projection bundle is_a: overlaps ! overlaps @@ -16960,27 +16441,23 @@ inverse_of: RO:0002132 ! has fasciculating neuron projection id: RO:0002102 name: axon synapses in def: "Relation between a neuron and some structure its axon forms (chemical) synapses in." [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: RO:0002113 ! has presynaptic terminal in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "BFO_0000051 some (\n GO_0030424 and BFO_0000051 some (\n GO_0042734 and BFO_0000050 some (\n GO_0045202 and BFO_0000050 some ?Y)))" [] +[Typedef] +id: RO:0002103 +name: synapsed by +def: "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " [] +is_a: RO:0002485 ! receives input from +inverse_of: RO:0002120 ! synapsed to +expand_expression_to: "BFO_0000051 some (GO_0045211 that part_of some (GO_0045202 that has_part some (GO_0042734 that BFO_0000050 some Y?)))" [] + [Typedef] id: RO:0002104 name: has plasma membrane part def: "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part." [] -property_value: IAO:0000112 "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9990-8331 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 -property_value: RO:0001900 RO:0001901 domain: UBERON:0000465 ! material anatomical entity range: UBERON:0000465 ! material anatomical entity is_a: has_part ! has part @@ -16990,29 +16467,19 @@ expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] id: RO:0002110 name: has postsynaptic terminal in def: "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. " [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "synapsed in" xsd:string -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: RO:0002130 ! has synaptic terminal in inverse_of: RO:0002113 ! has presynaptic terminal in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (\n http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some (\n http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))" [] [Typedef] id: RO:0002113 name: has presynaptic terminal in def: "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input." [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000118 "synapses in" xsd:string -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: RO:0002130 ! has synaptic terminal in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000050 some Y?)" [] [Typedef] @@ -17020,11 +16487,6 @@ id: RO:0002120 name: synapsed to def: " Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.\n " [] comment: N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part some (\n ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( \n ‘synapse ; GO:0045202’ that has_part some (\n ‘post-synaptic membrane ; GO:0045211’ that part_of some N2)))) -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 is_a: RO:0002486 ! sends output to expand_expression_to: "BFO_0000051 some (GO_0042734 that part_of some (GO_0045202 that BFO_0000051 some (GO_0045211 that BFO_0000050 some Y?)))" [] @@ -17032,104 +16494,272 @@ expand_expression_to: "BFO_0000051 some (GO_0042734 that part_of some (GO_004520 id: RO:0002130 name: has synaptic terminal in def: "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "has synapse in" xsd:string -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: overlaps ! overlaps -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "RO_0002131 some (GO_0045202 that BFO_0000050 some Y?)" [] [Typedef] id: RO:0002132 name: has fasciculating neuron projection def: "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "has fasciculating component" xsd:string -property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string -property_value: RO:0001900 RO:0001901 domain: UBERON:0000122 ! neuron projection bundle is_a: overlaps ! overlaps +[Typedef] +id: RO:0002134 +name: innervates +def: "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." [] +domain: UBERON:0000122 ! neuron projection bundle +transitive_over: part_of ! part of +expand_expression_to: "RO_0002132 some (GO_0043005 that (RO_0002131 some (GO_0045202 that BFO_0000050 some Y?)))" [] + +[Typedef] +id: RO:0002150 +name: continuous with +def: "X continuous_with Y if and only if X and Y share a fiat boundary." [] +property_value: seeAlso "FMA:85972" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000004 ! independent continuant +is_symmetric: true +is_a: RO:0002323 ! mereotopologically related to + +[Typedef] +id: RO:0002158 +name: shares ancestor with +def: "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." [] +comment: VBO calls this homologous_to +is_symmetric: true +is_transitive: true +is_a: RO:0002320 ! evolutionarily related to + +[Typedef] +id: RO:0002160 +name: only in taxon +def: "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." [] +property_value: IAO:0000116 "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" xsd:string +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints +is_a: RO:0002162 ! in taxon + +[Typedef] +id: RO:0002162 +name: in taxon +def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." [] +comment: Connects a biological entity to its taxon of origin. +subset: ro-eco +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints +holds_over_chain: capable_of RO:0002162 +holds_over_chain: extends_fibers_into RO:0002162 +holds_over_chain: has_part RO:0002162 +holds_over_chain: part_of RO:0002162 +holds_over_chain: results_in_developmental_progression_of RO:0002162 +holds_over_chain: RO:0002202 RO:0002162 +holds_over_chain: RO:0002206 RO:0002162 +holds_over_chain: RO:0002225 RO:0002162 +holds_over_chain: RO:0002254 RO:0002162 +is_a: RO:0002320 ! evolutionarily related to + [Typedef] id: RO:0002163 name: spatially disjoint from def: "A is spatially_disjoint_from B if and only if they have no parts in common" [] subset: ro-eco -property_value: editor_note "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" xsd:anyURI is_a: RO:0002323 ! mereotopologically related to expand_expression_to: "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" [] +[Typedef] +id: RO:0002170 +name: connected to +def: "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" [] +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI +is_a: RO:0002323 ! mereotopologically related to + +[Typedef] +id: RO:0002176 +name: connects +def: "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." [] +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI +domain: BFO:0000004 ! independent continuant +is_a: RO:0002323 ! mereotopologically related to + +[Typedef] +id: RO:0002177 +name: attached to part of +def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000061 ! anatomical structure +is_a: RO:0002323 ! mereotopologically related to +is_a: RO:0002567 ! biomechanically related to + +[Typedef] +id: RO:0002178 +name: supplies +def: "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." [] +property_value: IAO:0000116 "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" xsd:string +is_a: RO:0002170 ! connected to + +[Typedef] +id: RO:0002179 +name: drains +def: "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." [] +property_value: IAO:0000116 "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" xsd:string +is_a: RO:0002170 ! connected to + +[Typedef] +id: RO:0002202 +name: develops from +def: "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" [] +comment: This is the transitive form of the develops from relation +domain: BFO:0000004 ! independent continuant +range: BFO:0000004 ! independent continuant +is_transitive: true +is_a: RO:0002254 ! has developmental contribution from +is_a: RO:0002258 ! developmentally preceded by +inverse_of: RO:0002203 ! develops into + +[Typedef] +id: RO:0002203 +name: develops into +def: "inverse of develops from" [] +subset: RO:0002259 +is_transitive: true +is_a: RO:0002286 ! developmentally succeeded by +is_a: RO:0002387 ! has potential to develop into +is_a: RO:0002388 ! has potential to directly develop into + [Typedef] id: RO:0002206 name: expressed in def: "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" [] -property_value: IAO:0000112 "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000002 ! continuant range: UBERON:0000465 ! material anatomical entity is_a: RO:0002330 ! genomically related to inverse_of: RO:0002292 ! expresses -transitive_over: part_of ! part_of +transitive_over: part_of ! part of + +[Typedef] +id: RO:0002207 +name: directly develops from +def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] +comment: TODO - add child relations from DOS +synonym: "has developmental precursor" EXACT [] +is_a: RO:0002202 ! develops from +inverse_of: RO:0002210 ! directly develops into [Typedef] id: RO:0002210 name: directly develops into def: "inverse of directly develops from" [] subset: RO:0002259 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000118 "developmental precursor of" xsd:string -is_a: develops_into ! develops into +is_a: RO:0002203 ! develops into + +[Typedef] +id: RO:0002219 +name: surrounded by +def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" [] +is_a: adjacent_to ! adjacent to +inverse_of: RO:0002221 ! surrounds + +[Typedef] +id: RO:0002221 +name: surrounds +def: "inverse of surrounded by" [] +subset: RO:0002259 +is_a: adjacent_to ! adjacent to [Typedef] id: RO:0002222 name: temporally related to comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. subset: ro-eco -property_value: http://purl.org/dc/terms/source "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" xsd:anyURI -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent [Typedef] -id: RO:0002253 -name: has connecting branch -def: "inverse of connecting branch of" [] -subset: RO:0002259 -property_value: RO:0004036 BFO:0000051 -is_a: RO:0002375 ! in branching relationship with +id: RO:0002223 +name: starts +def: "inverse of starts with" [] +subset: ro-eco +is_a: part_of ! part of +is_a: RO:0002222 ! temporally related to +inverse_of: starts_with ! starts with [Typedef] -id: RO:0002255 -name: developmentally contributes to -def: "inverse of has developmental contribution from" [] -subset: RO:0002259 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -holds_over_chain: develops_into part_of -is_a: has_potential_to_developmentally_contribute_to ! has potential to developmentally contribute to -is_a: RO:0002286 ! developmentally succeeded by +id: RO:0002225 +name: develops from part of +def: "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" [] +holds_over_chain: RO:0002207 part_of +is_a: RO:0002202 ! develops from [Typedef] -id: RO:0002257 -name: developmentally induces -def: "Inverse of developmentally induced by" [] -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +id: RO:0002226 +name: develops in +def: "x develops_in y if x is located in y whilst x is developing" [] +domain: UBERON:0001062 ! anatomical entity +holds_over_chain: RO:0002207 RO:0001025 +is_a: RO:0002258 ! developmentally preceded by + +[Typedef] +id: RO:0002229 +name: ends +def: "inverse of ends with" [] +subset: ro-eco +is_a: part_of ! part of +is_a: RO:0002222 ! temporally related to +inverse_of: ends_with ! ends with + +[Typedef] +id: RO:0002252 +name: connecting branch of +def: "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." [] +property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 +is_a: RO:0002170 ! connected to +is_a: RO:0002375 ! in branching relationship with +inverse_of: RO:0002253 ! has connecting branch + +[Typedef] +id: RO:0002253 +name: has connecting branch +def: "inverse of connecting branch of" [] +subset: RO:0002259 +is_a: RO:0002375 ! in branching relationship with + +[Typedef] +id: RO:0002254 +name: has developmental contribution from +def: "x has developmental contribution from y iff x has some part z such that z develops from y" [] +domain: UBERON:0001062 ! anatomical entity +range: UBERON:0001062 ! anatomical entity +holds_over_chain: has_part RO:0002202 +is_a: RO:0002258 ! developmentally preceded by +inverse_of: RO:0002255 ! developmentally contributes to + +[Typedef] +id: RO:0002255 +name: developmentally contributes to +def: "inverse of has developmental contribution from" [] +subset: RO:0002259 +holds_over_chain: RO:0002203 part_of +is_a: RO:0002286 ! developmentally succeeded by +is_a: RO:0002385 ! has potential to developmentally contribute to + +[Typedef] +id: RO:0002256 +name: developmentally induced by +def: "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" [] +domain: UBERON:0000465 ! material anatomical entity +range: UBERON:0000465 ! material anatomical entity +is_a: RO:0002258 ! developmentally preceded by +inverse_of: RO:0002257 ! developmentally induces + +[Typedef] +id: RO:0002257 +name: developmentally induces +def: "Inverse of developmentally induced by" [] is_a: RO:0002286 ! developmentally succeeded by is_a: RO:0002386 ! has potential to developmentally induce @@ -17138,10 +16768,7 @@ id: RO:0002258 name: developmentally preceded by def: "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p" [] comment: This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from -property_value: editor_note "false" xsd:boolean -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string +property_value: IAO:0000116 "false" xsd:boolean domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant is_a: RO:0002324 ! developmentally related to @@ -17152,7 +16779,6 @@ id: RO:0002263 name: acts upstream of def: "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: IAO:0000112 "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." xsd:string property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of holds_over_chain: RO:0002327 causally_upstream_of is_a: RO:0002264 ! acts upstream of or within @@ -17163,25 +16789,26 @@ name: acts upstream of or within def: "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term synonym: "affects" RELATED [] -property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within" xsd:anyURI holds_over_chain: RO:0002327 causally_upstream_of_or_within is_a: RO:0002500 ! causal agent in process +[Typedef] +id: RO:0002285 +name: developmentally replaces +def: "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" [] +property_value: IAO:0000116 "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" xsd:string +is_a: RO:0002258 ! developmentally preceded by + [Typedef] id: RO:0002286 name: developmentally succeeded by def: "Inverse of developmentally preceded by" [] -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002384 ! has developmental potential involving [Typedef] id: RO:0002287 name: part of developmental precursor of -property_value: IAO:0000112 "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: part_of RO:0002210 is_a: RO:0002286 ! developmentally succeeded by @@ -17189,80 +16816,58 @@ is_a: RO:0002286 ! developmentally succeeded by id: RO:0002292 name: expresses def: "y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." [] -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002330 ! genomically related to [Typedef] id: RO:0002314 name: characteristic of part of def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." [] -property_value: editor_note "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "inheres in part of" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: RO:0000052 part_of {RO:0002582="true"} is_a: RO:0002502 ! depends on -transitive_over: part_of ! part_of +transitive_over: part_of ! part of [Typedef] id: RO:0002320 name: evolutionarily related to def: "A relationship that holds via some environmental process" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." xsd:string [Typedef] id: RO:0002323 name: mereotopologically related to def: "A mereological relationship or a topological relationship" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string -property_value: RO:0001900 RO:0001901 [Typedef] id: RO:0002324 name: developmentally related to def: "A relationship that holds between entities participating in some developmental process (GO:0032502)" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" xsd:string [Typedef] id: RO:0002327 name: enables def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "catalyzes" xsd:string -property_value: IAO:0000118 "executes" xsd:string -property_value: IAO:0000118 "has" xsd:string -property_value: IAO:0000118 "is catalyzing" xsd:string -property_value: IAO:0000118 "is executing" xsd:string -property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string property_value: seeAlso "https://wiki.geneontology.org/Enables" xsd:anyURI is_a: capable_of ! capable of inverse_of: RO:0002333 ! enabled by transitive_over: has_part ! has part transitive_over: RO:0002017 ! has component activity +[Typedef] +id: RO:0002328 +name: functionally related to +def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] + [Typedef] id: RO:0002329 name: part of structure that is capable of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "false" xsd:boolean -holds_over_chain: part_of capable_of {RO:0002581="true"} -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002330 name: genomically related to def: "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant @@ -17270,31 +16875,25 @@ range: BFO:0000002 ! continuant id: RO:0002331 name: involved in def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "actively involved in" xsd:string -property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Involved_in" xsd:anyURI holds_over_chain: RO:0002327 part_of is_a: participates_in ! participates in is_a: RO:0002431 ! involved in or involved in regulation of -transitive_over: part_of ! part_of +transitive_over: part_of ! part of [Typedef] id: RO:0002333 name: enabled by def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso "https://wiki.geneontology.org/Enabled_by" xsd:anyURI -is_a: functionally_related_to ! functionally related to is_a: has_participant ! has participant +is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002337 name: related via localization to def: "A relationship that holds via some process of localization" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is a grouping relation." xsd:string domain: BFO:0000015 ! process range: BFO:0000002 ! continuant @@ -17302,84 +16901,134 @@ range: BFO:0000002 ! continuant id: RO:0002350 name: member of def: "is member of is a mereological relation between a item and a collection." [] -property_value: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string -property_value: IAO:0000118 "is member of" xsd:string -property_value: IAO:0000118 "member part of" xsd:string -property_value: IAO:0000119 "SIO" xsd:string -property_value: RO:0001900 RO:0001901 -is_a: part_of ! part_of -inverse_of: has_member ! has member +is_a: part_of ! part of +inverse_of: RO:0002351 ! has member + +[Typedef] +id: RO:0002351 +name: has member +def: "has member is a mereological relation between a collection and an item." [] +is_a: has_part ! has part + +[Typedef] +id: RO:0002352 +name: input of +def: "inverse of has input" [] +subset: ro-eco +subset: RO:0002259 +is_a: participates_in ! participates in +is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002354 name: formed as result of -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: output_of ! output of [Typedef] id: RO:0002360 name: has dendrite location -property_value: http://purl.org/dc/terms/source "http://neurolex.org/wiki/Property:DendriteLocation" xsd:anyURI -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps +[Typedef] +id: RO:0002371 +name: attached to +def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] +subset: ro-eco +is_symmetric: true +is_a: RO:0002170 ! connected to +is_a: RO:0002177 ! attached to part of + +[Typedef] +id: RO:0002372 +name: has muscle origin +def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] +property_value: seeAlso http://dbpedia.org/property/origin +domain: UBERON:0000061 {comment="We need to import uberon muscle to create a stricter domain constraint"} ! anatomical structure +is_a: RO:0002371 ! attached to +is_a: RO:0002567 ! biomechanically related to + +[Typedef] +id: RO:0002373 +name: has muscle insertion +def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] +property_value: seeAlso http://dbpedia.org/property/insertion +domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} ! anatomical structure +is_a: RO:0002371 ! attached to +is_a: RO:0002567 ! biomechanically related to + [Typedef] id: RO:0002375 name: in branching relationship with def: "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" xsd:string -property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string -property_value: RO:0004036 BFO:0000050 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png property_value: seeAlso "https://github.com/obophenotype/uberon/issues/170" xsd:anyURI domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002323 ! mereotopologically related to +[Typedef] +id: RO:0002376 +name: tributary of +def: "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." [] +subset: ro-eco +property_value: seeAlso http://dbpedia.org/ontology/drainsTo +property_value: seeAlso "http://en.wikipedia.org/wiki/Tributary" xsd:anyURI +is_a: RO:0002170 ! connected to +is_a: RO:0002375 ! in branching relationship with + [Typedef] id: RO:0002379 name: spatially coextensive with def: "x spatially_coextensive_with y if and inly if x and y have the same location" [] -property_value: IAO:0000112 "A lump of clay and a statue" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" xsd:string is_a: overlaps ! overlaps +[Typedef] +id: RO:0002380 +name: branching part of +def: "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" [] +subset: ro-eco +property_value: seeAlso "FMA:85994" xsd:string +property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 +is_a: part_of ! part of +is_a: RO:0002375 ! in branching relationship with +inverse_of: RO:0002569 ! has branching part + [Typedef] id: RO:0002384 name: has developmental potential involving def: "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: UBERON:0001062 ! anatomical entity range: UBERON:0001062 ! anatomical entity is_a: RO:0002324 ! developmentally related to +[Typedef] +id: RO:0002385 +name: has potential to developmentally contribute to +def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] +is_a: RO:0002384 ! has developmental potential involving + [Typedef] id: RO:0002386 name: has potential to developmentally induce def: "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002384 ! has developmental potential involving + +[Typedef] +id: RO:0002387 +name: has potential to develop into +def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] is_a: RO:0002384 ! has developmental potential involving [Typedef] id: RO:0002388 name: has potential to directly develop into def: "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: has_potential_to_develop_into ! has potential to develop into +is_a: RO:0002387 ! has potential to develop into [Typedef] id: RO:0002407 name: indirectly positively regulates def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "indirectly activates" xsd:string -property_value: RO:0002579 RO:0002213 property_value: seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates" xsd:anyURI holds_over_chain: directly_positively_regulates directly_positively_regulates holds_over_chain: directly_positively_regulates RO:0002407 @@ -17393,9 +17042,6 @@ transitive_over: directly_positively_regulates ! directly positively regulates id: RO:0002409 name: indirectly negatively regulates def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "indirectly inhibits" xsd:string -property_value: RO:0002579 RO:0002212 property_value: seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates" xsd:anyURI holds_over_chain: directly_negatively_regulates directly_negatively_regulates holds_over_chain: directly_negatively_regulates RO:0002409 @@ -17408,15 +17054,12 @@ transitive_over: directly_negatively_regulates ! directly negatively regulates id: RO:0002410 name: causally related to def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] -property_value: editor_note "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string [Typedef] id: RO:0002428 name: involved in regulation of def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002327 regulates holds_over_chain: RO:0002331 regulates is_a: RO:0002263 ! acts upstream of @@ -17426,8 +17069,6 @@ is_a: RO:0002431 ! involved in or involved in regulation of id: RO:0002429 name: involved in positive regulation of def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0004049 RO:0002428 holds_over_chain: RO:0002327 positively_regulates holds_over_chain: RO:0002331 positively_regulates is_a: RO:0002428 ! involved in regulation of @@ -17436,7 +17077,6 @@ is_a: RO:0002428 ! involved in regulation of id: RO:0002430 name: involved in negative regulation of def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002428 holds_over_chain: RO:0002327 negatively_regulates holds_over_chain: RO:0002331 negatively_regulates @@ -17446,11 +17086,9 @@ is_a: RO:0002428 ! involved in regulation of id: RO:0002431 name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] -property_value: editor_note "OWL does not allow defining object properties via a Union" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "involved in or reguates" xsd:string -is_a: functionally_related_to ! functionally related to +property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string is_a: RO:0002264 ! acts upstream of or within +is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process [Typedef] @@ -17458,12 +17096,14 @@ id: RO:0002432 name: is active in def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [https://orcid.org/0000-0002-6601-2165, https://orcid.org/0000-0002-7073-9172] synonym: "enables activity in" EXACT [] -property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "executes activity in" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Is_active_in" xsd:anyURI -holds_over_chain: RO:0002327 occurs_in {RO:0002581="true"} -is_a: functionally_related_to ! functionally related to +is_a: overlaps ! overlaps +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002433 +name: contributes to morphology of +def: "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." [] is_a: overlaps ! overlaps [Typedef] @@ -17472,11 +17112,8 @@ name: interacts with def: "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." [] subset: ro-eco synonym: "in pairwise interaction with" EXACT [] -property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0914" xsd:anyURI -property_value: editor_note "Considering relabeling as 'pairwise interacts with'" xsd:anyURI -property_value: editor_note "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string +property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI +property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity @@ -17486,10 +17123,6 @@ is_symmetric: true id: RO:0002436 name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] -property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0915" xsd:anyURI -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "binds" xsd:string -property_value: IAO:0000118 "molecularly binds with" xsd:string property_value: seeAlso ECO:0000353 is_symmetric: true is_a: RO:0002434 ! interacts with @@ -17497,9 +17130,7 @@ is_a: RO:0002434 ! interacts with [Typedef] id: RO:0002447 name: phosphorylates -property_value: editor_note "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string +property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string is_a: RO:0002436 ! molecularly interacts with [Typedef] @@ -17507,8 +17138,6 @@ id: RO:0002448 name: directly regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." [] synonym: "molecularly controls" EXACT [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002436 ! molecularly interacts with @@ -17519,9 +17148,6 @@ id: RO:0002449 name: directly negatively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] synonym: "molecularly decreases activity of" EXACT [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 -property_value: IAO:0000118 "directly inhibits" xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002448 ! directly regulates activity of @@ -17531,9 +17157,6 @@ id: RO:0002450 name: directly positively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] synonym: "molecularly increases activity of" EXACT [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 -property_value: IAO:0000118 "directly activates" xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002448 ! directly regulates activity of @@ -17541,61 +17164,136 @@ is_a: RO:0002448 ! directly regulates activity of [Typedef] id: RO:0002464 name: helper property (not for use in curation) -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string + +[Typedef] +id: RO:0002473 +name: composed primarily of +def: "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." [] +subset: ro-eco +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: has_part ! has part [Typedef] id: RO:0002479 name: has part that occurs in def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] subset: ro-eco -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant -holds_over_chain: has_part occurs_in {RO:0002581="true"} [Typedef] id: RO:0002481 name: is kinase activity -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002564 ! molecular interaction relation helper property [Typedef] id: RO:0002485 name: receives input from -property_value: editor_note "See notes for inverse relation" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: connected_to ! connected to +property_value: IAO:0000116 "See notes for inverse relation" xsd:string +is_a: RO:0002170 ! connected to inverse_of: RO:0002486 ! sends output to [Typedef] id: RO:0002486 name: sends output to -property_value: editor_note "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: connected_to ! connected to +property_value: IAO:0000116 "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." xsd:string +is_a: RO:0002170 ! connected to [Typedef] id: RO:0002487 name: relation between physical entity and a process or stage -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage." xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000003 ! occurrent +[Typedef] +id: RO:0002488 +name: existence starts during +def: "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." [] +is_a: RO:0002490 ! existence overlaps +is_a: RO:0002496 ! existence starts during or after +transitive_over: part_of ! part of + +[Typedef] +id: RO:0002489 +name: existence starts with +def: "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." [] +is_a: RO:0002488 ! existence starts during + [Typedef] id: RO:0002490 name: existence overlaps def: "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" [] comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002487 ! relation between physical entity and a process or stage +[Typedef] +id: RO:0002491 +name: existence starts and ends during +def: "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +synonym: "exists during" EXACT [] +is_a: RO:0002488 ! existence starts during +is_a: RO:0002492 ! existence ends during + +[Typedef] +id: RO:0002492 +name: existence ends during +def: "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +is_a: RO:0002490 ! existence overlaps +is_a: RO:0002497 ! existence ends during or before +transitive_over: part_of ! part of + +[Typedef] +id: RO:0002493 +name: existence ends with +def: "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +is_a: RO:0002492 ! existence ends during + +[Typedef] +id: RO:0002494 +name: transformation of +def: "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" [] +is_transitive: true +is_a: RO:0002202 ! develops from + +[Typedef] +id: RO:0002495 +name: immediate transformation of +def: "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" [] +is_a: RO:0002207 ! directly develops from +is_a: RO:0002494 ! transformation of + +[Typedef] +id: RO:0002496 +name: existence starts during or after +def: "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +holds_over_chain: part_of RO:0002496 +holds_over_chain: RO:0002258 RO:0002496 +is_a: RO:0002487 ! relation between physical entity and a process or stage +transitive_over: part_of ! part of +transitive_over: preceded_by ! preceded by +transitive_over: RO:0002082 ! simultaneous with + +[Typedef] +id: RO:0002497 +name: existence ends during or before +def: "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +holds_over_chain: part_of RO:0002497 +holds_over_chain: RO:0002286 RO:0002497 +is_a: RO:0002487 ! relation between physical entity and a process or stage +transitive_over: part_of ! part of +transitive_over: precedes ! precedes +transitive_over: RO:0002082 ! simultaneous with + [Typedef] id: RO:0002500 name: causal agent in process def: "A relationship between a material entity and a process where the material entity has some causal role that influences the process" [] -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_a: RO:0002595 ! causal relation between material entity and a process inverse_of: process_has_causal_agent ! process has causal agent @@ -17603,9 +17301,6 @@ inverse_of: process_has_causal_agent ! process has causal agent id: RO:0002501 name: causal relation between processes def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent is_a: RO:0002410 ! causally related to @@ -17613,33 +17308,35 @@ is_a: RO:0002410 ! causally related to [Typedef] id: RO:0002502 name: depends on -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso BFO:0000169 [Typedef] id: RO:0002506 name: causal relation between entities -property_value: editor_note "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: IAO:0000116 "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant is_a: RO:0002410 ! causally related to +[Typedef] +id: RO:0002551 +name: has skeleton +def: "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." [] +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000465 {IAO:0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} ! material anatomical entity +is_a: has_part ! has part +inverse_of: RO:0002576 ! skeleton of +is_asymmetric: true + [Typedef] id: RO:0002559 name: causally influenced by -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string is_a: RO:0002506 ! causal relation between entities inverse_of: RO:0002566 ! causally influences [Typedef] id: RO:0002563 name: interaction relation helper property -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29 property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI is_a: RO:0002464 ! helper property (not for use in curation) @@ -17647,17 +17344,12 @@ is_a: RO:0002464 ! helper property (not for use in curation) [Typedef] id: RO:0002564 name: molecular interaction relation helper property -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002563 ! interaction relation helper property [Typedef] id: RO:0002566 name: causally influences def: "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant is_a: RO:0002506 ! causal relation between entities @@ -17666,20 +17358,66 @@ is_a: RO:0002506 ! causal relation between entities id: RO:0002567 name: biomechanically related to def: "A relation that holds between elements of a musculoskeletal system or its analogs." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string domain: UBERON:0000061 ! anatomical structure range: UBERON:0000061 ! anatomical structure -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002568 +name: has muscle antagonist +def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] +is_a: RO:0002567 ! biomechanically related to + +[Typedef] +id: RO:0002569 +name: has branching part +def: "inverse of branching part of" [] +subset: ro-eco +subset: RO:0002259 +is_transitive: true +is_a: has_part ! has part +is_a: RO:0002375 ! in branching relationship with + +[Typedef] +id: RO:0002570 +name: conduit for +def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] +subset: ro-eco +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: overlaps ! overlaps + +[Typedef] +id: RO:0002571 +name: lumen of +def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] +subset: ro-eco +range: BFO:0000040 ! material entity +is_a: part_of ! part of + +[Typedef] +id: RO:0002572 +name: luminal space of +def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" [] +subset: ro-eco +domain: BFO:0000141 ! immaterial entity +is_a: RO:0002571 ! lumen of + +[Typedef] +id: RO:0002576 +name: skeleton of +def: "inverse of has skeleton" [] +subset: RO:0002259 +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000061 ! anatomical structure +is_a: part_of ! part of [Typedef] id: RO:0002584 name: has part structure that is capable of def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" [] -property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: has_part capable_of -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to is_a: RO:0002595 ! causal relation between material entity and a process [Typedef] @@ -17692,9 +17430,7 @@ is_a: has_input ! has input id: RO:0002595 name: causal relation between material entity and a process def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." [] -property_value: editor_note "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000040 ! material entity range: BFO:0000015 ! process is_a: RO:0002410 ! causally related to @@ -17703,8 +17439,6 @@ is_a: RO:0002410 ! causally related to id: RO:0002596 name: capable of regulating def: "Holds between c and p if and only if c is capable of some activity a, and a regulates p." [] -property_value: IAO:0000112 "pyrethroid -> growth" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations holds_over_chain: capable_of regulates is_a: RO:0002500 ! causal agent in process @@ -17712,7 +17446,6 @@ is_a: RO:0002500 ! causal agent in process id: RO:0002597 name: capable of negatively regulating def: "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." [] -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations holds_over_chain: capable_of negatively_regulates is_a: RO:0002596 ! capable of regulating @@ -17720,8 +17453,6 @@ is_a: RO:0002596 ! capable of regulating id: RO:0002598 name: capable of positively regulating def: "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." [] -property_value: IAO:0000112 "renin -> arteriolar smooth muscle contraction" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations holds_over_chain: capable_of positively_regulates is_a: RO:0002596 ! capable of regulating @@ -17730,7 +17461,7 @@ id: RO:0004031 name: enables subfunction def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] holds_over_chain: RO:0002327 has_part -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z @@ -17738,7 +17469,6 @@ creation_date: 2018-01-25T23:20:13Z id: RO:0004032 name: acts upstream of or within, positive effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: RO:0004049 RO:0002264 property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0004047 is_a: RO:0002264 ! acts upstream of or within @@ -17761,7 +17491,6 @@ id: RO:0004034 name: acts upstream of, positive effect def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: RO:0004049 RO:0002263 property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 causally_upstream_of,_positive_effect is_a: RO:0002263 ! acts upstream of @@ -17794,7 +17523,6 @@ creation_date: 2018-03-13T23:55:05Z [Typedef] id: RO:0004047 name: causally upstream of or within, positive effect -property_value: RO:0004049 RO:0002418 property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect is_a: causally_upstream_of_or_within ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 @@ -17804,7 +17532,6 @@ creation_date: 2018-03-13T23:55:19Z id: RO:0011002 name: regulates activity of def: "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." [] -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002566 ! causally influences @@ -17859,7 +17586,7 @@ name: has synaptic IO in region def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region." [] synonym: "has synaptic input or output in" EXACT [] is_a: RO:0002130 ! has synaptic terminal in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:26:52Z @@ -17872,7 +17599,7 @@ synonym: "has sensory terminal in" EXACT [] synonym: "has sensory terminal location" EXACT [] domain: CL:0000101 ! sensory neuron is_a: RO:0002360 ! has dendrite location -transitive_over: part_of ! part_of +transitive_over: part_of ! part of created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-20T12:10:09Z @@ -17915,9 +17642,8 @@ comment: Example: a spherical object has the quality of being spherical, and the id: RO:0015015 name: has high plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: dc-contributor https://orcid.org/0000-0003-1617-8244 -property_value: dc-contributor https://orcid.org/0000-0003-1940-6740 -property_value: IAO:0000112 "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part @@ -17925,9 +17651,8 @@ is_a: RO:0002104 ! has plasma membrane part id: RO:0015016 name: has low plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: dc-contributor https://orcid.org/0000-0003-1617-8244 -property_value: dc-contributor https://orcid.org/0000-0003-1940-6740 -property_value: IAO:0000112 "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part @@ -17936,11 +17661,6 @@ id: RO:0017001 name: device utilizes material def: "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." [] synonym: "utilizes" BROAD [] -property_value: IAO:0000112 "A diagnostic testing device utilizes a specimen." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 -property_value: IAO:0000117 https://orcid.org/0000-0003-2620-0345 -property_value: IAO:0000232 "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." xsd:string -property_value: IAO:0000232 "See github ticket https://github.com/oborel/obo-relations/issues/497" xsd:string holds_over_chain: capable_of has_input creation_date: 2021-11-08T12:00:00Z @@ -17961,65 +17681,24 @@ creation_date: 2020-06-08T17:21:33Z id: adjacent_to name: adjacent to namespace: external -namespace: uberon def: "x adjacent to y if and only if x and y share a boundary." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002220 -property_value: editor_note "This relation acts as a join point with BSPO" xsd:string -property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} -property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string -property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string -property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000004 ! independent continuant is_a: RO:0002163 ! spatially disjoint from -[Typedef] -id: anterior_to -name: anterior to -namespace: uberon -xref: BSPO:0000096 - [Typedef] id: anteriorly_connected_to name: anteriorly connected to namespace: uberon def: "x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] -is_a: connected_to ! connected to -is_a: posterior_to ! posterior to +is_a: RO:0002170 ! connected to is_a: transitively_anteriorly_connected_to ! transitively anteriorly connected to -[Typedef] -id: attaches_to -name: attached to -namespace: uberon -def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] -subset: ro-eco -xref: RO:0002371 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000589 "attached to (anatomical structure to anatomical structure)" xsd:string -is_symmetric: true -is_a: attaches_to_part_of ! attached to part of -is_a: connected_to ! connected to - -[Typedef] -id: attaches_to_part_of -name: attached to part of -namespace: uberon -def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] -xref: RO:0002177 -property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string -domain: UBERON:0000061 ! anatomical structure -range: UBERON:0000061 ! anatomical structure -holds_over_chain: attaches_to part_of {RO:0002582="true"} -is_a: RO:0002323 ! mereotopologically related to -is_a: RO:0002567 ! biomechanically related to - [Typedef] id: bearer_of name: bearer of @@ -18027,13 +17706,7 @@ name: has characteristic namespace: external def: "Inverse of characteristic_of" [] xref: RO:0000053 -property_value: editor_note "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string -property_value: IAO:0000111 "bearer of" xsd:string -property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string -property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string -property_value: IAO:0000118 "bearer_of" xsd:string -property_value: IAO:0000118 "is bearer of" xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string range: BFO:0000020 ! specifically dependent continuant is_inverse_functional: true @@ -18041,45 +17714,20 @@ is_inverse_functional: true id: bounding_layer_of name: bounding layer of namespace: external -namespace: uberon def: "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000" [] comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. subset: ro-eco xref: RO:0002007 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 range: BFO:0000040 ! material entity -is_a: part_of ! part_of - -[Typedef] -id: branching_part_of -name: branching part of -namespace: uberon -def: "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" [] -subset: ro-eco -xref: RO:0002380 -property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso "FMA:85994" xsd:string -property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 -is_a: part_of ! part_of -is_a: RO:0002375 ! in branching relationship with -inverse_of: has_branching_part ! has branching part +is_a: part_of ! part of [Typedef] id: capable_of name: capable of namespace: external -namespace: uberon def: "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " [] subset: ro-eco xref: RO:0002215 -property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string -property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "has function realized in" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 -property_value: IAO:0000232 "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000015 ! process is_a: capable_of_part_of ! capable of part of @@ -18088,14 +17736,10 @@ is_a: capable_of_part_of ! capable of part of id: capable_of_part_of name: capable of part of namespace: external -namespace: uberon def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] xref: RO:0002216 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "has function in" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: capable_of part_of {RO:0002582="true"} -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process [Typedef] @@ -18104,8 +17748,6 @@ name: causally downstream of namespace: external def: "inverse of upstream of" [] xref: RO:0002404 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of_or_within ! causally downstream of or within is_a: preceded_by ! preceded by inverse_of: causally_upstream_of ! causally upstream of @@ -18117,8 +17759,6 @@ namespace: external def: "inverse of causally upstream of or within" [] subset: RO:0002259 xref: RO:0002427 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_transitive: true is_a: RO:0002501 ! causal relation between processes @@ -18130,7 +17770,6 @@ def: "p is causally upstream of q iff p is causally related to q, the end of p p subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002411 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within is_a: precedes ! precedes @@ -18143,7 +17782,6 @@ def: "p is causally upstream of, negative effect q iff p is casually upstream of subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 -property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_negative_effect is_a: causally_upstream_of ! causally upstream of @@ -18158,8 +17796,6 @@ comment: holds between x and y if and only if x is causally upstream of y and th subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002304 -property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 -property_value: RO:0004049 RO:0002411 property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_positive_effect is_a: causally_upstream_of ! causally upstream of is_a: RO:0004047 ! causally upstream of or within, positive effect @@ -18171,9 +17807,7 @@ namespace: external def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] synonym: "affects" RELATED [] xref: RO:0002418 -property_value: editor_note "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "influences (processual)" xsd:string +property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string is_transitive: true is_a: RO:0002501 ! causal relation between processes inverse_of: causally_downstream_of_or_within ! causally downstream of or within @@ -18183,287 +17817,16 @@ id: channel_for name: channel for namespace: uberon synonym: "carries" BROAD [] -domain: UBERON:0004111 ! anatomical conduit -range: UBERON:0000463 ! organism substance [Typedef] id: channels_from name: channels_from namespace: uberon -is_transitive: true [Typedef] id: channels_into name: channels_into namespace: uberon -is_transitive: true - -[Typedef] -id: composed_primarily_of -name: composed primarily of -namespace: uberon -def: "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." [] -subset: ro-eco -xref: RO:0002473 -property_value: IAO:0000112 "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: RO:0001900 RO:0001901 -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: has_part ! has part - -[Typedef] -id: conduit_for -name: conduit for -namespace: uberon -def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] -subset: ro-eco -xref: RO:0002570 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "UBERON:cjm" xsd:string -property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: overlaps ! overlaps - -[Typedef] -id: connected_to -name: connected to -namespace: uberon -def: "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" [] -xref: RO:0002170 -property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI -property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: connecting_branch_of -name: connecting branch of -namespace: uberon -def: "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." [] -xref: RO:0002252 -property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." xsd:string -property_value: RO:0004036 BFO:0000050 -property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 -is_a: connected_to ! connected to -is_a: RO:0002375 ! in branching relationship with -inverse_of: RO:0002253 ! has connecting branch - -[Typedef] -id: connects -name: connects -namespace: uberon -def: "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." [] -xref: RO:0002176 -property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string -property_value: IAO:0000112 "The M8 connects Glasgow and Edinburgh" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI -property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI -domain: BFO:0000004 ! independent continuant -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: contains_process -name: contains process -namespace: uberon -def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] -comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant -xref: BFO:0000067 -property_value: IAO:0000111 "site of" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - -[Typedef] -id: continuous_with -name: continuous with -namespace: uberon -def: "X continuous_with Y if and only if X and Y share a fiat boundary." [] -xref: RO:0002150 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "connected to" xsd:string -property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string -property_value: RO:0001900 RO:0001901 -property_value: seeAlso "FMA:85972" xsd:string -domain: BFO:0000004 ! independent continuant -range: BFO:0000004 ! independent continuant -is_symmetric: true -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: contributes_to_morphology_of -name: contributes to morphology of -namespace: uberon -def: "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." [] -xref: RO:0002433 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: overlaps ! overlaps - -[Typedef] -id: dc-contributor -name: contributor -namespace: uberon -xref: http://purl.org/dc/terms/contributor -is_metadata_tag: true - -[Typedef] -id: dc-creator -name: creator -namespace: uberon -xref: http://purl.org/dc/elements/1.1/creator -is_metadata_tag: true - -[Typedef] -id: dc-description -name: description -namespace: uberon -xref: http://purl.org/dc/elements/1.1/description -is_metadata_tag: true - -[Typedef] -id: dc-title -name: title -namespace: uberon -xref: http://purl.org/dc/elements/1.1/title -is_metadata_tag: true - -[Typedef] -id: dcterms-date -name: date -namespace: uberon -xref: http://purl.org/dc/terms/date -is_metadata_tag: true - -[Typedef] -id: dcterms-license -name: license -namespace: uberon -xref: http://purl.org/dc/terms/license -is_metadata_tag: true - -[Typedef] -id: deep_to -name: deep to -namespace: uberon -xref: BSPO:0000107 - -[Typedef] -id: depiction -name: depiction -namespace: uberon -xref: http://xmlns.com/foaf/0.1/depiction -is_metadata_tag: true - -[Typedef] -id: developmentally_induced_by -name: developmentally induced by -namespace: uberon -def: "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" [] -xref: RO:0002256 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "induced by" xsd:string -property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string -property_value: IAO:0000119 "GO:0001759" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 -property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string -domain: UBERON:0000465 ! material anatomical entity -range: UBERON:0000465 ! material anatomical entity -is_a: RO:0002258 ! developmentally preceded by -inverse_of: RO:0002257 ! developmentally induces - -[Typedef] -id: developmentally_replaces -name: developmentally replaces -namespace: uberon -def: "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" [] -xref: RO:0002285 -property_value: editor_note "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "replaces" xsd:string -is_a: RO:0002258 ! developmentally preceded by - -[Typedef] -id: develops_from -name: develops from -namespace: uberon -def: "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" [] -comment: This is the transitive form of the develops from relation -xref: RO:0002202 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 -domain: BFO:0000004 ! independent continuant -range: BFO:0000004 ! independent continuant -is_transitive: true -is_a: has_developmental_contribution_from ! has developmental contribution from -is_a: RO:0002258 ! developmentally preceded by -inverse_of: develops_into ! develops into - -[Typedef] -id: develops_from_part_of -name: develops from part of -namespace: uberon -def: "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" [] -xref: RO:0002225 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -holds_over_chain: directly_develops_from part_of -is_a: develops_from ! develops from - -[Typedef] -id: develops_in -name: develops in -namespace: uberon -def: "x develops_in y if x is located in y whilst x is developing" [] -xref: RO:0002226 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "EHDAA2" xsd:string -property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string -domain: UBERON:0001062 ! anatomical entity -holds_over_chain: directly_develops_from located_in -is_a: RO:0002258 ! developmentally preceded by - -[Typedef] -id: develops_into -name: develops into -namespace: uberon -def: "inverse of develops from" [] -subset: RO:0002259 -xref: RO:0002203 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 -is_transitive: true -is_a: has_potential_to_develop_into ! has potential to develop into -is_a: RO:0002286 ! developmentally succeeded by -is_a: RO:0002388 ! has potential to directly develop into - -[Typedef] -id: directly_develops_from -name: directly develops from -namespace: uberon -def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] -comment: TODO - add child relations from DOS -synonym: "has developmental precursor" EXACT [] -xref: RO:0002207 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000119 "FBbt" xsd:string -property_value: RO:0002575 RO:0002202 -is_a: develops_from ! develops from -inverse_of: RO:0002210 ! directly develops into [Typedef] id: directly_negatively_regulates @@ -18474,8 +17837,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002630 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002578 property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates" xsd:anyURI is_a: directly_regulates ! directly regulates @@ -18490,9 +17851,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002629 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string -property_value: RO:0004049 RO:0002578 property_value: seeAlso "https://wiki.geneontology.org/Directly_positively_regulates" xsd:anyURI is_a: directly_regulates ! directly regulates is_a: positively_regulates ! positively regulates @@ -18506,187 +17864,34 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002578 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly regulates (processual)" xsd:string -property_value: RO:0002575 RO:0002211 is_a: immediately_causally_upstream_of ! immediately causally upstream of is_a: regulates ! regulates -[Typedef] -id: distal_to -name: distal to -namespace: uberon -xref: BSPO:0000097 - [Typedef] id: distally_connected_to name: distally connected to namespace: uberon def: "x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] -is_a: connected_to ! connected to -is_a: proximal_to ! proximal to +is_a: RO:0002170 ! connected to is_a: transitively_distally_connected_to ! transitively distally connected to -inverse_of: proximally_connected_to ! proximally connected to - -[Typedef] -id: distalmost_part_of -name: distalmost part of -namespace: uberon -xref: BSPO:0001108 - -[Typedef] -id: dorsal_to -name: dorsal to -namespace: uberon -xref: BSPO:0000098 - -[Typedef] -id: drains -name: drains -namespace: uberon -def: "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." [] -xref: RO:0002179 -property_value: editor_note "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 -is_a: connected_to ! connected to - -[Typedef] -id: editor_note -name: editor note -namespace: uberon -def: "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology." [] -xref: IAO:0000116 -property_value: IAO:0000111 "editor note" xsd:string -property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000117 "PERSON:Daniel Schober" xsd:string -property_value: IAO:0000119 "GROUP:OBI:" xsd:string -is_metadata_tag: true - -[Typedef] -id: ends -name: ends -namespace: uberon -def: "inverse of ends with" [] -subset: ro-eco -xref: RO:0002229 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: part_of ! part_of -is_a: RO:0002222 ! temporally related to -inverse_of: ends_with ! ends with [Typedef] id: ends_with name: ends with namespace: external -namespace: uberon def: "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002230 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "finished by" xsd:string is_transitive: true is_a: has_part ! has part is_a: RO:0002222 ! temporally related to -[Typedef] -id: existence_ends_during -name: existence ends during -namespace: uberon -def: "Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely." [https://orcid.org/0000-0002-6601-2165] -def: "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -synonym: "ceases_to_exist_during" EXACT [] -xref: RO:0002492 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_ends_during_or_before ! existence ends during or before -is_a: RO:0002490 ! existence overlaps -transitive_over: part_of ! part_of - -[Typedef] -id: existence_ends_during_or_before -name: existence ends during or before -namespace: uberon -def: "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -xref: RO:0002497 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -holds_over_chain: part_of existence_ends_during_or_before -holds_over_chain: RO:0002286 existence_ends_during_or_before -is_a: RO:0002487 ! relation between physical entity and a process or stage -transitive_over: part_of ! part_of -transitive_over: precedes ! precedes -transitive_over: simultaneous_with ! simultaneous with - -[Typedef] -id: existence_ends_with -name: existence ends with -namespace: uberon -def: "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -xref: RO:0002493 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_ends_during ! existence ends during - -[Typedef] -id: existence_starts_and_ends_during -name: existence starts and ends during -namespace: uberon -def: "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -synonym: "exists during" EXACT [] -xref: RO:0002491 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_ends_during ! existence ends during -is_a: existence_starts_during ! existence starts during - -[Typedef] -id: existence_starts_during -name: existence starts during -namespace: uberon -def: "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." [] -xref: RO:0002488 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_starts_during_or_after ! existence starts during or after -is_a: RO:0002490 ! existence overlaps -transitive_over: part_of ! part_of - -[Typedef] -id: existence_starts_during_or_after -name: existence starts during or after -namespace: uberon -def: "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -xref: RO:0002496 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -holds_over_chain: part_of existence_starts_during_or_after -holds_over_chain: RO:0002258 existence_starts_during_or_after -is_a: RO:0002487 ! relation between physical entity and a process or stage -transitive_over: part_of ! part_of -transitive_over: preceded_by ! preceded by -transitive_over: simultaneous_with ! simultaneous with - -[Typedef] -id: existence_starts_with -name: existence starts with -namespace: uberon -def: "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." [] -xref: RO:0002489 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_starts_during ! existence starts during - [Typedef] id: extends_fibers_into name: extends_fibers_into namespace: uberon def: "X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y" [https://orcid.org/0000-0002-7073-9172] -holds_over_chain: RO:0002100 RO:0013001 -is_symmetric: true -is_a: connected_to ! connected to +is_a: RO:0002170 ! connected to [Typedef] id: filtered_through @@ -18695,75 +17900,17 @@ namespace: uberon def: "Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity." [] comment: Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed -[Typedef] -id: functionally_related_to -name: functionally related to -namespace: uberon -def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] -xref: RO:0002328 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string - -[Typedef] -id: has_boundary -name: has 2D boundary -namespace: uberon -def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] -xref: RO:0002002 -property_value: editor_note "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string -property_value: editor_note "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string -property_value: IAO:0000112 "my body has 2D boundary the surface of my skin" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "has boundary" xsd:string -property_value: IAO:0000118 "has_2D_boundary" xsd:string -property_value: RO:0001900 RO:0001901 -domain: BFO:0000040 ! material entity -range: BFO:0000141 ! immaterial entity -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: has_branching_part -name: has branching part -namespace: uberon -def: "inverse of branching part of" [] -subset: ro-eco -subset: RO:0002259 -xref: RO:0002569 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_transitive: true -is_a: has_part ! has part -is_a: RO:0002375 ! in branching relationship with - [Typedef] id: has_component name: has component namespace: external -namespace: uberon def: "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] subset: ro-eco xref: RO:0002180 -property_value: editor_note "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency is_a: has_part ! has part -[Typedef] -id: has_developmental_contribution_from -name: has developmental contribution from -namespace: uberon -def: "x has developmental contribution from y iff x has some part z such that z develops from y" [] -xref: RO:0002254 -property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: UBERON:0001062 ! anatomical entity -range: UBERON:0001062 ! anatomical entity -holds_over_chain: has_part develops_from -is_a: RO:0002258 ! developmentally preceded by -inverse_of: RO:0002255 ! developmentally contributes to - [Typedef] id: has_end_location name: has end location @@ -18771,9 +17918,6 @@ namespace: external def: "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" [] subset: ro-eco xref: RO:0002232 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "ends with process that occurs in" xsd:string domain: BFO:0000015 ! process range: BFO:0000004 ! independent continuant holds_over_chain: ends_with occurs_in @@ -18797,14 +17941,11 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002233 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "consumes" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Has_input" xsd:anyURI domain: BFO:0000015 ! process holds_over_chain: starts_with has_input is_a: has_participant ! has participant -inverse_of: input_of ! input of +inverse_of: RO:0002352 ! input of [Typedef] id: has_low_plasma_membrane_amount @@ -18814,52 +17955,6 @@ property_value: term_tracker_item https://github.com/obophenotype/cell-ontology/ is_obsolete: true replaced_by: RO:0015016 -[Typedef] -id: has_member -name: has member -namespace: uberon -def: "has member is a mereological relation between a collection and an item." [] -xref: RO:0002351 -property_value: IAO:0000119 "SIO" xsd:string -property_value: RO:0001900 RO:0001901 -is_a: has_part ! has part - -[Typedef] -id: has_muscle_antagonist -name: has muscle antagonist -namespace: uberon -def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] -xref: RO:0002568 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "Wikipedia:Antagonist_(muscle)" xsd:string -is_a: RO:0002567 ! biomechanically related to - -[Typedef] -id: has_muscle_insertion -name: has muscle insertion -namespace: uberon -def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] -xref: RO:0002373 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string -property_value: seeAlso http://dbpedia.org/property/insertion -domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} ! anatomical structure -is_a: attaches_to ! attached to -is_a: RO:0002567 ! biomechanically related to - -[Typedef] -id: has_muscle_origin -name: has muscle origin -namespace: uberon -def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] -xref: RO:0002372 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string -property_value: seeAlso http://dbpedia.org/property/origin -domain: UBERON:0000061 {comment="We need to import uberon muscle to create a stricter domain constraint"} ! anatomical structure -is_a: attaches_to ! attached to -is_a: RO:0002567 ! biomechanically related to - [Typedef] id: has_negative_regulatory_component_activity name: has negative regulatory component activity @@ -18877,13 +17972,9 @@ id: has_ontology_root_term name: has ontology root term name: preferred_root namespace: external -namespace: uberon def: "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root." [] xref: IAO:0000700 -property_value: IAO:0000111 "has ontology root term" xsd:string -property_value: IAO:0000117 "Nicolas Matentzoglu" xsd:string is_metadata_tag: true -is_class_level: true [Typedef] id: has_output @@ -18895,9 +17986,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002234 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "produces" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Has_output" xsd:anyURI holds_over_chain: ends_with has_output is_a: has_participant ! has participant @@ -18909,60 +17997,27 @@ name: has part name: has_part namespace: external namespace: quality -namespace: uberon def: "a core relation that holds between a whole and its part" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000051 -property_value: editor_note "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string -property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string -property_value: IAO:0000111 "has part" xsd:string -property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string -property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string -property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string -property_value: IAO:0000118 "has_part" xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string is_transitive: true is_a: overlaps ! overlaps [Typedef] -id: has_participant -name: has participant -namespace: external -def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] -xref: RO:0000057 -property_value: editor_note "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string -property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string -property_value: IAO:0000111 "has participant" xsd:string -property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string -property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string -property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string -property_value: IAO:0000118 "has_participant" xsd:string -domain: BFO:0000003 ! occurrent -range: BFO:0000002 ! continuant -holds_over_chain: has_part has_participant - -[Typedef] -id: has_potential_to_develop_into -name: has potential to develop into -namespace: uberon -def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] -xref: RO:0002387 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: RO:0002384 ! has developmental potential involving - -[Typedef] -id: has_potential_to_developmentally_contribute_to -name: has potential to developmentally contribute to -namespace: uberon -def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] -xref: RO:0002385 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: RO:0002384 ! has developmental potential involving +id: has_participant +name: has participant +namespace: external +def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] +xref: RO:0000057 +property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string +domain: BFO:0000003 ! occurrent +range: BFO:0000002 ! continuant +holds_over_chain: has_part has_participant [Typedef] id: has_primary_input @@ -18999,17 +18054,6 @@ is_a: has_primary_input_or_output ! has primary input or output created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z -[Typedef] -id: has_quality -name: has quality -namespace: uberon -def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] -xref: RO:0000086 -property_value: editor_note "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string -property_value: IAO:0000112 "this apple has quality this red color" xsd:string -property_value: IAO:0000118 "has_quality" xsd:string -is_a: bearer_of ! bearer of - [Typedef] id: has_regulatory_component_activity name: has regulatory component activity @@ -19021,24 +18065,6 @@ is_a: RO:0002017 ! has component activity created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z -[Typedef] -id: has_skeleton -name: has skeleton -namespace: uberon -def: "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." [] -xref: RO:0002551 -property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "has supporting framework" xsd:string -property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string -domain: UBERON:0000061 ! anatomical structure -domain: UBERON:0000475 ! organism subdivision -range: UBERON:0000465 {IAO:0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} ! material anatomical entity -range: UBERON:0010912 ! subdivision of skeleton -is_a: has_part ! has part -inverse_of: skeleton_of ! skeleton of -is_asymmetric: true - [Typedef] id: has_small_molecule_activator name: has small molecule activator @@ -19057,9 +18083,6 @@ namespace: external def: "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y" [] subset: ro-eco xref: RO:0002231 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "starts with process that occurs in" xsd:string domain: BFO:0000015 ! process range: BFO:0000004 ! independent continuant holds_over_chain: starts_with occurs_in @@ -19074,9 +18097,8 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002339 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of [Typedef] id: has_target_start_location @@ -19087,41 +18109,14 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002338 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in -transitive_over: part_of ! part_of - -[Typedef] -id: homologous_to -name: shares ancestor with -namespace: uberon -def: "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." [] -comment: VBO calls this homologous_to -xref: RO:0002158 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000232 "Consider obsoleting and merging with child relation, 'in homology relationship with'" xsd:string -is_symmetric: true -is_transitive: true -is_a: RO:0002320 ! evolutionarily related to - -[Typedef] -id: immediate_transformation_of -name: immediate transformation of -namespace: uberon -def: "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" [] -xref: RO:0002495 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0002575 RO:0002494 -is_a: directly_develops_from ! directly develops from -is_a: transformation_of ! transformation of +transitive_over: part_of ! part of [Typedef] id: immediately_causally_downstream_of name: immediately causally downstream of namespace: external xref: RO:0002405 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of ! causally downstream of is_a: immediately_preceded_by ! immediately preceded by inverse_of: immediately_causally_upstream_of ! immediately causally upstream of @@ -19132,26 +18127,15 @@ name: immediately causally upstream of namespace: external def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] xref: RO:0002412 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: immediately_precedes ! immediately precedes -[Typedef] -id: immediately_deep_to -name: immediately deep to -namespace: uberon -xref: BSPO:0001107 - [Typedef] id: immediately_preceded_by name: immediately preceded by namespace: external -namespace: uberon comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) xref: RO:0002087 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000118 "starts_at_end_of" xsd:string holds_over_chain: starts_with ends_with is_a: preceded_by ! preceded by inverse_of: immediately_precedes ! immediately precedes @@ -19163,230 +18147,22 @@ namespace: external comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) subset: ro-eco xref: RO:0002090 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "ends_at_start_of" xsd:string -property_value: IAO:0000118 "meets" xsd:string -property_value: RO:0002575 BFO:0000063 holds_over_chain: ends_with starts_with is_a: precedes ! precedes -[Typedef] -id: immediately_superficial_to -name: immediately superficial to -namespace: uberon -xref: BSPO:0015014 - -[Typedef] -id: in_anterior_side_of -name: in anterior side of -namespace: uberon -xref: BSPO:0000123 - -[Typedef] -id: in_deep_part_of -name: in deep part of -namespace: uberon -xref: BSPO:0001101 - -[Typedef] -id: in_dorsal_side_of -name: in dorsal side of -namespace: uberon -xref: BSPO:0015101 - -[Typedef] -id: in_lateral_side_of -name: in lateral side of -namespace: uberon -xref: BSPO:0000126 - -[Typedef] -id: in_left_side_of -name: in left side of -namespace: uberon -xref: BSPO:0000120 - -[Typedef] -id: in_posterior_side_of -name: in posterior side of -namespace: uberon -xref: BSPO:0000122 - -[Typedef] -id: in_proximal_side_of -name: in proximal side of -namespace: uberon -xref: BSPO:0000124 - -[Typedef] -id: in_right_side_of -name: in right side of -namespace: uberon -xref: BSPO:0000121 - -[Typedef] -id: in_superficial_part_of -name: in superficial part of -namespace: uberon -xref: BSPO:0001100 - -[Typedef] -id: in_taxon -name: in taxon -namespace: uberon -def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." [] -comment: Connects a biological entity to its taxon of origin. -subset: ro-eco -xref: RO:0002162 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9227-417X -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -holds_over_chain: attaches_to in_taxon -holds_over_chain: capable_of in_taxon -holds_over_chain: connected_to in_taxon -holds_over_chain: connects in_taxon -holds_over_chain: continuous_with in_taxon -holds_over_chain: developmentally_induced_by in_taxon -holds_over_chain: develops_from in_taxon -holds_over_chain: develops_from_part_of in_taxon -holds_over_chain: existence_ends_during in_taxon -holds_over_chain: existence_starts_during in_taxon -holds_over_chain: extends_fibers_into in_taxon -holds_over_chain: has_developmental_contribution_from in_taxon -holds_over_chain: has_part in_taxon -holds_over_chain: has_potential_to_develop_into in_taxon -holds_over_chain: innervated_by in_taxon -holds_over_chain: overlaps in_taxon -holds_over_chain: part_of in_taxon -holds_over_chain: produced_by in_taxon -holds_over_chain: produces in_taxon -holds_over_chain: results_in_developmental_progression_of in_taxon -holds_over_chain: RO:0002206 in_taxon -holds_over_chain: supplies in_taxon -is_a: RO:0002320 ! evolutionarily related to - [Typedef] id: indirectly_supplies name: indirectly_supplies namespace: uberon def: "a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s." [] -property_value: editor_note "add to RO" xsd:string -holds_over_chain: has_branching_part indirectly_supplies -holds_over_chain: has_branching_part supplies -is_transitive: true - -[Typedef] -id: innervated_by -name: innervated_by -namespace: uberon -xref: RO:0002005 -property_value: http://purl.org/spar/cito/citesAsAuthority "http://www.ncbi.nlm.nih.gov/pubmed/22402613" xsd:anyURI -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -domain: UBERON:0000061 ! anatomical structure -range: UBERON:0000122 ! neuron projection bundle -inverse_of: innervates ! innervates -transitive_over: branching_part_of ! branching part of - -[Typedef] -id: innervates -name: innervates -namespace: uberon -def: "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." [] -xref: RO:0002134 -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 -domain: UBERON:0000122 ! neuron projection bundle -transitive_over: part_of ! part_of -expand_expression_to: "RO_0002132 some (GO_0043005 that (RO_0002131 some (GO_0045202 that BFO_0000050 some Y?)))" [] - -[Typedef] -id: input_of -name: input of -namespace: uberon -def: "inverse of has input" [] -subset: ro-eco -subset: RO:0002259 -xref: RO:0002352 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: functionally_related_to ! functionally related to -is_a: participates_in ! participates in - -[Typedef] -id: intersects_midsagittal_plane_of -name: intersects midsagittal plane of -namespace: uberon -xref: BSPO:0005001 +property_value: IAO:0000116 "add to RO" xsd:string +holds_over_chain: RO:0002569 indirectly_supplies [Typedef] id: layer_part_of name: layer part of namespace: uberon -is_a: part_of ! part_of - -[Typedef] -id: located_in -name: located in -namespace: uberon -def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -xref: RO:0001025 -property_value: editor_note "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" xsd:string -property_value: editor_note "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:located_in" xsd:string -property_value: IAO:0000111 "located in" xsd:string -property_value: IAO:0000112 "my brain is located in my head" xsd:string -property_value: IAO:0000112 "this rat is located in this cage" xsd:string -property_value: IAO:0000118 "located_in" xsd:string -property_value: RO:0001900 RO:0001901 -property_value: seeAlso "https://wiki.geneontology.org/Located_in" xsd:anyURI -domain: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant -range: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant -is_transitive: true -transitive_over: part_of ! part_of - -[Typedef] -id: location_of -name: location of -namespace: uberon -def: "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" [] -xref: RO:0001015 -property_value: editor_note "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: IAO:0000111 "is location of" xsd:string -property_value: IAO:0000112 "my head is the location of my brain" xsd:string -property_value: IAO:0000112 "this cage is the location of this rat" xsd:string -property_value: IAO:0000118 "location_of" xsd:string -property_value: RO:0001900 RO:0001901 -is_transitive: true -inverse_of: located_in ! located in - -[Typedef] -id: lumen_of -name: lumen of -namespace: uberon -def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] -subset: ro-eco -xref: RO:0002571 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 https://orcid.org/0000-0002-6601-2165 -range: BFO:0000040 ! material entity -is_a: part_of ! part_of - -[Typedef] -id: luminal_space_of -name: luminal space of -namespace: uberon -def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" [] -subset: ro-eco -xref: RO:0002572 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: BFO:0000141 ! immaterial entity -is_a: lumen_of ! lumen of +is_a: part_of ! part of [Typedef] id: negatively_regulated_by @@ -19395,7 +18171,6 @@ namespace: external def: "inverse of negatively regulates" [] subset: RO:0002259 xref: RO:0002335 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -19407,9 +18182,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002212 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002211 holds_over_chain: ends_with negatively_regulates is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect @@ -19422,30 +18194,11 @@ name: negatively regulates characteristic namespace: gene_ontology def: "A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C." [] xref: RO:0019002 -property_value: dc-contributor https://orcid.org/0000-0002-8688-6599 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 holds_over_chain: negatively_regulates positively_regulates_characteristic holds_over_chain: positively_regulates negatively_regulates_characteristic is_a: regulates_characteristic ! regulates characteristic -[Typedef] -id: never_in_taxon -name: never in taxon -name: never_in_taxon -namespace: uberon -def: "S never_in_taxon T iff: S SubClassOf in_taxon only not T." [PMID:20973947] -def: "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL." [] -xref: RO:0002161 -property_value: IAO:0000112 "tooth SubClassOf 'never in taxon' value 'Aves'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 -property_value: OMO:0002000 "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" xsd:string -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -expand_assertion_to: "Class: EquivalentTo: ?X and (RO_0002162 some ?Y)" [] -expand_assertion_to: "Class: ?X DisjointWith: RO_0002162 some ?Y " [] -is_metadata_tag: true -is_class_level: true - [Typedef] id: occurs_in name: occurs in @@ -19456,64 +18209,38 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000066 -property_value: IAO:0000111 "occurs in" xsd:string -property_value: IAO:0000118 "occurs_in" xsd:string -property_value: IAO:0000118 "unfolds in" xsd:string -property_value: IAO:0000118 "unfolds_in" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl property_value: seeAlso "https://wiki.geneontology.org/Occurs_in" xsd:anyURI domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant holds_over_chain: part_of occurs_in -inverse_of: contains_process ! contains process -transitive_over: part_of ! part_of - -[Typedef] -id: only_in_taxon -name: only in taxon -namespace: uberon -def: "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." [] -xref: RO:0002160 -property_value: editor_note "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" xsd:string -property_value: IAO:0000112 "lactation SubClassOf 'only in taxon' some 'Mammalia'" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -is_a: in_taxon ! in taxon +inverse_of: BFO:0000067 ! contains process +transitive_over: part_of ! part of [Typedef] id: output_of name: output of namespace: external -namespace: uberon def: "inverse of has output" [] subset: ro-eco subset: RO:0002259 xref: RO:0002353 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: functionally_related_to ! functionally related to is_a: participates_in ! participates in +is_a: RO:0002328 ! functionally related to [Typedef] id: overlaps name: overlaps namespace: external -namespace: uberon def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002131 -property_value: IAO:0000114 IAO:0000125 -property_value: RO:0001900 RO:0001901 holds_over_chain: has_part overlaps -holds_over_chain: has_part part_of {RO:0002582="true"} holds_over_chain: part_of part_of is_symmetric: true is_a: RO:0002323 ! mereotopologically related to -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] [Typedef] @@ -19522,29 +18249,15 @@ name: part of name: part_of namespace: external namespace: quality -namespace: uberon def: "a core relation that holds between a part and its whole" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000050 -property_value: editor_note "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string -property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string -property_value: IAO:0000111 "is part of" xsd:string -property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string -property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string -property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string -property_value: IAO:0000118 "part_of" xsd:string -property_value: RO:0001900 RO:0001901 -property_value: RO:0040042 BFO:0000002 -property_value: RO:0040042 BFO:0000003 -property_value: RO:0040042 BFO:0000004 -property_value: RO:0040042 BFO:0000017 -property_value: RO:0040042 BFO:0000019 -property_value: RO:0040042 BFO:0000020 -property_value: RO:0040042 BFO:0000031 +property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string @@ -19557,14 +18270,8 @@ inverse_of: has_part ! has part id: participates_in name: participates in namespace: external -namespace: uberon def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] xref: RO:0000056 -property_value: IAO:0000111 "participates in" xsd:string -property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string -property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string -property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string -property_value: IAO:0000118 "participates_in" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000003 ! occurrent inverse_of: has_participant ! has participant @@ -19576,7 +18283,6 @@ namespace: external def: "inverse of positively regulates" [] subset: RO:0002259 xref: RO:0002336 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -19588,10 +18294,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002213 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "positively regulates (process to process)" xsd:string -property_value: RO:0004049 RO:0002211 holds_over_chain: ends_with positively_regulates holds_over_chain: negatively_regulates negatively_regulates is_transitive: true @@ -19605,49 +18307,25 @@ name: positively regulates characteristic namespace: gene_ontology def: "A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C." [] xref: RO:0019001 -property_value: dc-contributor https://orcid.org/0000-0002-8688-6599 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 holds_over_chain: positively_regulates positively_regulates_characteristic is_a: regulates_characteristic ! regulates characteristic -[Typedef] -id: postaxialmost_part_of -name: postaxialmost part of -namespace: uberon -xref: BSPO:0001115 - -[Typedef] -id: posterior_to -name: posterior to -namespace: uberon -xref: BSPO:0000099 - [Typedef] id: posteriorly_connected_to name: posteriorly connected to namespace: uberon def: "x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] -is_a: anterior_to ! anterior to -is_a: connected_to ! connected to - -[Typedef] -id: preaxialmost_part_of -name: preaxialmost part of -namespace: uberon -xref: BSPO:0001113 +is_a: RO:0002170 ! connected to [Typedef] id: preceded_by name: preceded by namespace: external -namespace: uberon def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000062 -property_value: editor_note "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string -property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string -property_value: IAO:0000111 "preceded by" xsd:string -property_value: IAO:0000118 "is preceded by" xsd:string -property_value: IAO:0000118 "preceded_by" xsd:string +property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent holds_over_chain: part_of preceded_by @@ -19659,53 +18337,30 @@ inverse_of: precedes ! precedes id: precedes name: precedes namespace: external -namespace: uberon def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000063 -property_value: IAO:0000111 "precedes" xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent holds_over_chain: part_of precedes is_transitive: true is_a: RO:0002222 ! temporally related to -[Typedef] -id: present_in_taxon -name: present in taxon -name: present_in_taxon -namespace: uberon -def: "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S" [] -def: "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S." [https://orcid.org/0000-0002-6601-2165] -comment: The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology. -synonym: "applicable for taxon" EXACT [] -xref: RO:0002175 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: OMO:0002000 "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" xsd:string -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -is_metadata_tag: true -is_class_level: true - [Typedef] id: process_has_causal_agent name: process has causal agent namespace: external def: "Inverse of 'causal agent in process'" [] xref: RO:0002608 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_a: RO:0002410 ! causally related to [Typedef] id: produced_by name: produced by namespace: external -namespace: uberon def: "a produced_by b iff some process that occurs_in b has_output a." [] subset: ro-eco xref: RO:0003001 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity @@ -19713,13 +18368,10 @@ range: BFO:0000040 ! material entity id: produces name: produces namespace: external -namespace: uberon def: "a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix." [] comment: Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. subset: ro-eco xref: RO:0003000 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity inverse_of: produced_by ! produced by @@ -19729,27 +18381,14 @@ id: protects name: protects namespace: uberon -[Typedef] -id: proximal_to -name: proximal to -namespace: uberon -xref: BSPO:0000100 - [Typedef] id: proximally_connected_to name: proximally connected to namespace: uberon def: "x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] -is_a: connected_to ! connected to -is_a: distal_to ! distal to +is_a: RO:0002170 ! connected to is_a: transitively_proximally_connected_to ! transitively proximally connected to -[Typedef] -id: proximalmost_part_of -name: proximalmost part of -namespace: uberon -xref: BSPO:0001106 - [Typedef] id: regulated_by name: regulated by @@ -19757,8 +18396,6 @@ namespace: external def: "inverse of regulates" [] subset: RO:0002259 xref: RO:0002334 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000589 "regulated by (processual)" xsd:string domain: BFO:0000015 ! process range: BFO:0000015 ! process is_transitive: true @@ -19773,14 +18410,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 -property_value: IAO:0000117 https://orcid.org/0000-0001-7476-6306 -property_value: IAO:0000117 https://orcid.org/0000-0002-3837-8864 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GO" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string -property_value: IAO:0000589 "regulates (processual)" xsd:string -property_value: IAO:0000600 "false" xsd:boolean domain: BFO:0000015 ! process range: BFO:0000015 ! process holds_over_chain: directly_regulates directly_regulates @@ -19796,7 +18425,7 @@ name: regulates characteristic namespace: gene_ontology def: "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C." [] xref: RO:0019000 -property_value: dc-contributor https://orcid.org/0000-0002-8688-6599 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 domain: BFO:0000015 ! process range: PATO:0000001 ! quality holds_over_chain: regulates regulates_characteristic @@ -19808,13 +18437,9 @@ name: regulates levels of namespace: external def: "p regulates levels of c if p regulates some amount (PATO:0000070) of c" [] xref: RO:0002332 -property_value: IAO:0000112 "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "regulates levels of (process to entity)" xsd:string domain: BFO:0000015 ! process range: BFO:0000040 ! material entity -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to [Typedef] id: results_in_acquisition_of_features_of @@ -19825,9 +18450,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002315 -property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string range: UBERON:0000061 ! anatomical structure is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -19862,10 +18484,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002296 -property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "http://www.geneontology.org/GO.doc.development.shtml" xsd:anyURI is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -19875,9 +18493,7 @@ name: results in developmental progression of namespace: external def: "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." [] xref: RO:0002295 -property_value: editor_note "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000116 "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string property_value: seeAlso Ontology:extensions domain: GO:0008150 ! biological_process range: UBERON:0001062 ! anatomical entity @@ -19909,16 +18525,12 @@ is_a: has_participant ! has participant [Typedef] id: results_in_formation_of name: results in formation of +name: results in formation of anatomical entity namespace: external subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002297 -property_value: IAO:0000112 "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." xsd:string -property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of inverse_of: RO:0002354 ! formed as result of @@ -19940,8 +18552,6 @@ id: results_in_growth_of name: results in growth of namespace: external xref: RO:0002343 -property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -19954,11 +18564,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002299 -property_value: IAO:0000112 " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" xsd:string -property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -19971,11 +18576,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002298 -property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." xsd:string -property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -19988,8 +18588,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002565 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure [Typedef] @@ -20008,7 +18606,6 @@ namespace: external def: "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002342 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in is_a: RO:0002021 ! occurs across @@ -20018,7 +18615,6 @@ name: results in transport along namespace: external def: "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " [] xref: RO:0002341 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002337 ! related via localization to [Typedef] @@ -20026,36 +18622,13 @@ id: results_in_transport_to_from_or_in name: results in transport to from or in namespace: external xref: RO:0002344 -property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002337 ! related via localization to -[Typedef] -id: seeAlso -name: see also -namespace: uberon -xref: http://www.w3.org/2000/01/rdf-schema#seeAlso -is_metadata_tag: true - [Typedef] id: sexually_homologous_to name: sexually_homologous_to namespace: uberon -is_a: homologous_to ! shares ancestor with - -[Typedef] -id: simultaneous_with -name: simultaneous with -namespace: uberon -def: "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." [] -comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) -subset: ro-eco -xref: RO:0002082 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -is_symmetric: true -is_transitive: true -is_a: RO:0002081 ! before or simultaneous with +is_a: RO:0002158 ! shares ancestor with [Typedef] id: site_of @@ -20064,46 +18637,13 @@ namespace: uberon def: "c site_of p if c is the bearer of a disposition that is realized by a process that has p as part." [] synonym: "capable_of_has_part" RELATED [] -[Typedef] -id: skeleton_of -name: skeleton of -namespace: uberon -def: "inverse of has skeleton" [] -subset: RO:0002259 -xref: RO:0002576 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: UBERON:0000061 ! anatomical structure -range: UBERON:0000061 ! anatomical structure -is_a: part_of ! part_of - -[Typedef] -id: starts -name: starts -namespace: uberon -def: "inverse of starts with" [] -subset: ro-eco -xref: RO:0002223 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "Allen" xsd:string -is_a: part_of ! part_of -is_a: RO:0002222 ! temporally related to -inverse_of: starts_with ! starts with - [Typedef] id: starts_with name: starts with namespace: external -namespace: uberon def: "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002224 -property_value: IAO:0000112 "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "started by" xsd:string is_transitive: true is_a: has_part ! has part is_a: RO:0002222 ! temporally related to @@ -20114,139 +18654,36 @@ name: subdivision of namespace: uberon comment: placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B -[Typedef] -id: superficial_to -name: superficial to -namespace: uberon -xref: BSPO:0000108 - -[Typedef] -id: supplies -name: supplies -namespace: uberon -def: "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." [] -xref: RO:0002178 -property_value: editor_note "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 -is_a: connected_to ! connected to - -[Typedef] -id: surrounded_by -name: surrounded by -namespace: uberon -def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" [] -xref: RO:0002219 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0001900 RO:0001901 -is_a: adjacent_to ! adjacent to -inverse_of: surrounds ! surrounds - -[Typedef] -id: surrounds -name: surrounds -namespace: uberon -def: "inverse of surrounded by" [] -subset: RO:0002259 -xref: RO:0002221 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0001900 RO:0001901 -is_a: adjacent_to ! adjacent to - -[Typedef] -id: synapsed_by -name: synapsed by -namespace: uberon -def: "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " [] -xref: RO:0002103 -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 -is_a: RO:0002485 ! receives input from -inverse_of: RO:0002120 ! synapsed to -expand_expression_to: "BFO_0000051 some (GO_0045211 that part_of some (GO_0045202 that has_part some (GO_0042734 that BFO_0000050 some Y?)))" [] - [Typedef] id: term_tracker_item name: term tracker item namespace: external -namespace: uberon def: "An IRI or similar locator for a request or discussion of an ontology term." [] comment: The 'tracker item' can associate a tracker with a specific ontology term. xref: IAO:0000233 -property_value: IAO:0000111 "term tracker item" xsd:string -property_value: IAO:0000112 "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" xsd:string -property_value: IAO:0000119 "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" xsd:string is_metadata_tag: true -is_class_level: true - -[Typedef] -id: transformation_of -name: transformation of -namespace: uberon -def: "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" [] -xref: RO:0002494 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_transitive: true -is_a: develops_from ! develops from [Typedef] id: transitively_anteriorly_connected_to name: transitively anteriorly connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI -is_transitive: true [Typedef] id: transitively_distally_connected_to name: transitively distally connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI -is_transitive: true [Typedef] id: transitively_proximally_connected_to name: transitively proximally connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI -is_transitive: true - -[Typedef] -id: tributary_of -name: tributary of -namespace: uberon -def: "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." [] -subset: ro-eco -xref: RO:0002376 -property_value: IAO:0000112 "Deschutes River tributary_of Columbia River" xsd:string -property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "drains into" xsd:string -property_value: IAO:0000118 "drains to" xsd:string -property_value: IAO:0000118 "tributary channel of" xsd:string -property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Tributary" xsd:string -property_value: IAO:0000119 "http://www.medindia.net/glossary/venous_tributary.htm" xsd:string -property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" xsd:anyURI -property_value: seeAlso http://dbpedia.org/ontology/drainsTo -property_value: seeAlso "http://en.wikipedia.org/wiki/Tributary" xsd:anyURI -is_a: connected_to ! connected to -is_a: RO:0002375 ! in branching relationship with [Typedef] id: trunk_part_of name: trunk_part_of namespace: uberon -is_a: part_of ! part_of - -[Typedef] -id: ventral_to -name: ventral to -namespace: uberon -xref: BSPO:0000102 +is_a: part_of ! part of diff --git a/src/ontology/subsets/eye_upper_slim.owl b/src/ontology/subsets/eye_upper_slim.owl index 379bb2999..d878a3456 100644 --- a/src/ontology/subsets/eye_upper_slim.owl +++ b/src/ontology/subsets/eye_upper_slim.owl @@ -10,28 +10,21 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" - xmlns:cito="http://purl.org/spar/cito/" xmlns:core="http://purl.obolibrary.org/obo/uberon/core#" xmlns:foaf="http://xmlns.com/foaf/0.1/" - xmlns:obo2="http://www.geneontology.org/formats/oboInOwl#http://purl.obolibrary.org/obo/" xmlns:pato="http://purl.obolibrary.org/obo/pato#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" - xmlns:skos="http://www.w3.org/2004/02/skos/core#" xmlns:swrl="http://www.w3.org/2003/11/swrl#" - xmlns:sssom="https://w3id.org/sssom/" - xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#" xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:terms="http://purl.org/dc/terms/" - xmlns:vocab="https://w3id.org/semapv/vocab/" - xmlns:terms1="http://www.geneontology.org/formats/oboInOwl#http://purl.org/dc/terms/" xmlns:uberon="http://purl.obolibrary.org/obo/uberon#" xmlns:ubprop="http://purl.obolibrary.org/obo/ubprop#" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - 2024-02-13 + + 2024-04-05 @@ -55,29 +48,9 @@ - - - - - - - - - - - - - - - - - - - definition - The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith @@ -99,8 +72,6 @@ We don't have definitions of 'meaning' or 'expression' Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition @@ -110,72 +81,28 @@ We also have the outstanding issue of how to aim different definitions to differ - editor note - An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obofoundry.org/obo/obi> - IAO:0000116 - uberon - editor_note - true - editor_note - editor note editor note - - - - - - - - - - - - - - - - - - - has obsolescence reason Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. - PERSON:Alan Ruttenberg - PERSON:Melanie Courtot has obsolescence reason - - - - - - - term tracker item - the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ - An IRI or similar locator for a request or discussion of an ontology term. - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg IAO:0000233 external - uberon term_tracker_item - true true term_tracker_item The 'tracker item' can associate a tracker with a specific ontology term. @@ -185,63 +112,23 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - - expand expression to - ObjectProperty: RO_0002104 -Label: has plasma membrane part -Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" - A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones - Chris Mungall expand expression to expand expression to - - - - - - - - - - - - - - - - - - - - - - - - - has ontology root term Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. - Nicolas Matentzoglu IAO:0000700 external - uberon has_ontology_root_term - true true has_ontology_root_term has ontology root term @@ -251,20 +138,10 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - - - - - - - term replaced by - Use on obsolete terms, relating the term to another term that can be used as a substitute - Person:Alan Ruttenberg - Person:Alan Ruttenberg Add as annotation triples in the granting ontology term replaced by term replaced by @@ -275,24 +152,6 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - 'part disjoint with' 'defined by construct' """ - PREFIX owl: <http://www.w3.org/2002/07/owl#> - PREFIX : <http://example.org/ - CONSTRUCT { - [ - a owl:Restriction ; - owl:onProperty :part_of ; - owl:someValuesFrom ?a ; - owl:disjointWith [ - a owl:Restriction ; - owl:onProperty :part_of ; - owl:someValuesFrom ?b - ] - ] - } - WHERE { - ?a :part_disjoint_with ?b . - } Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. @@ -305,11 +164,9 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation) A synonym type for describing abbreviations or initalisms - 2023-03-03 abbreviation @@ -335,11 +192,9 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form) A synonym type for describing pluralization synonyms - 2023-03-03 plural form @@ -354,23 +209,10 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - - - - - - - tooth SubClassOf 'never in taxon' value 'Aves' - S never_in_taxon T iff: S SubClassOf in_taxon only not T. x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL. - - - - Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: ?X and (RO_0002162 some ?Y) - Class: ?X DisjointWith: RO_0002162 some ?Y PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> @@ -394,34 +236,9 @@ CONSTRUCT { WHERE { ?x never_in_taxon: ?taxon . } - RO:0002161 - uberon - never_in_taxon - true - true - never_in_taxon never in taxon - never_in_taxon - - - - S never_in_taxon T iff: S SubClassOf in_taxon only not T. - PMID:20973947 - - - - - - - - - - - - - @@ -429,9 +246,6 @@ WHERE { S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S - S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S. - - PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> @@ -456,24 +270,10 @@ WHERE { )) as ?witness) BIND(CONCAT(STR(?x), " in taxon ", STR(?taxon)) AS ?label) } - RO:0002175 - applicable for taxon - uberon - present_in_taxon - true - true - present_in_taxon The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology. present in taxon - present_in_taxon - - - - S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S. - https://orcid.org/0000-0002-6601-2165 - @@ -485,60 +285,6 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL - is a defining property chain axiom - - - - - - - - If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. - is a defining property chain axiom where second argument is reflexive - - - - - - - - - - - - - - - - - - - - - - @@ -549,126 +295,6 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -927,12 +553,6 @@ WHERE { - - - - - - @@ -1363,14 +983,7 @@ WHERE { - - http://purl.org/dc/elements/1.1/creator - uberon - dc-creator - true - dc-creator - creator - + @@ -1382,14 +995,7 @@ WHERE { - - http://purl.org/dc/elements/1.1/description - uberon - dc-description - true - dc-description - description - + @@ -1401,71 +1007,25 @@ WHERE { - - http://purl.org/dc/elements/1.1/title - uberon - dc-title - true - dc-title - title - + - - http://purl.org/dc/terms/contributor - uberon - dc-contributor - true - dc-contributor - contributor - - - - - - - - - - - - - + - - http://purl.org/dc/terms/date - uberon - dcterms-date - true - dcterms-date - date - + - - http://purl.org/dc/terms/license - uberon - dcterms-license - true - dcterms-license - license - - - - - - - + @@ -1475,18 +1035,6 @@ WHERE { - - - - - - - - - - - - @@ -1503,18 +1051,6 @@ WHERE { - - - - - - - - - - - - @@ -1523,18 +1059,6 @@ WHERE { - - - - - - - - - - - - @@ -1551,66 +1075,6 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -1623,7 +1087,6 @@ WHERE { An alternative label for a class or property which has a more general meaning than the preferred name/primary label. - https://github.com/information-artifact-ontology/ontology-metadata/issues/18 has broad synonym has_broad_synonym @@ -1644,7 +1107,6 @@ WHERE { An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. - https://github.com/information-artifact-ontology/ontology-metadata/issues/20 has exact synonym has_exact_synonym @@ -1657,7 +1119,6 @@ WHERE { An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. - https://github.com/information-artifact-ontology/ontology-metadata/issues/19 has narrow synonym has_narrow_synonym @@ -1678,7 +1139,6 @@ WHERE { An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. - https://github.com/information-artifact-ontology/ontology-metadata/issues/21 has related synonym has_related_synonym @@ -1687,12 +1147,6 @@ WHERE { - - - - - - @@ -1717,30 +1171,6 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - - - @@ -1753,72 +1183,12 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -1833,60 +1203,6 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -1903,9 +1219,6 @@ WHERE { http://www.w3.org/2000/01/rdf-schema#seeAlso - uberon - seeAlso - true seeAlso see also @@ -1918,63 +1231,9 @@ WHERE { - - - - - - - - http://xmlns.com/foaf/0.1/depiction - uberon - depiction - true - depiction - depiction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + @@ -1995,29 +1254,15 @@ WHERE { - is part of - my brain is part of my body (continuant parthood, two material entities) - my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) - this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. - part_of - - - - - - - - BFO:0000050 external quality - uberon part_of @@ -2040,22 +1285,15 @@ A continuant cannot be part of an occurrent: use 'participates in'. An - has part - my body has part my brain (continuant parthood, two material entities) - my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) - this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. - has_part - BFO:0000051 external quality - uberon has_part @@ -2080,15 +1318,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. - preceded by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. - is preceded by - preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 external - uberon preceded_by preceded_by @@ -2109,11 +1342,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. - precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. BFO:0000063 external - uberon precedes precedes @@ -2137,11 +1368,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - occurs_in - unfolds in - unfolds_in BFO:0000066 external occurs_in @@ -2150,7 +1377,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. occurs_in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant - occurs in occurs in https://wiki.geneontology.org/Occurs_in @@ -2161,308 +1387,13 @@ A continuant cannot have an occurrent as part: use 'participates in'. - site of [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - BFO:0000067 - uberon - contains_process - contains_process Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant - - contains process contains process - - - - BSPO:0000096 - uberon - anterior_to - anterior_to - anterior to - - - - - - - - BSPO:0000097 - uberon - distal_to - distal_to - distal to - - - - - - - - BSPO:0000098 - uberon - dorsal_to - dorsal_to - dorsal to - - - - - - - - BSPO:0000099 - uberon - posterior_to - posterior_to - posterior to - - - - - - - - BSPO:0000100 - uberon - proximal_to - proximal_to - proximal to - - - - - - - - BSPO:0000102 - uberon - ventral_to - ventral_to - ventral to - - - - - - - - BSPO:0000107 - uberon - deep_to - deep_to - deep to - - - - - - - - BSPO:0000108 - uberon - superficial_to - superficial_to - superficial to - - - - - - - - BSPO:0000120 - uberon - in_left_side_of - in_left_side_of - in left side of - - - - - - - - BSPO:0000121 - uberon - in_right_side_of - in_right_side_of - in right side of - - - - - - - - BSPO:0000122 - uberon - in_posterior_side_of - in_posterior_side_of - in posterior side of - - - - - - - - BSPO:0000123 - uberon - in_anterior_side_of - in_anterior_side_of - in anterior side of - - - - - - - - BSPO:0000124 - uberon - in_proximal_side_of - in_proximal_side_of - in proximal side of - - - - - - - - BSPO:0000126 - uberon - in_lateral_side_of - in_lateral_side_of - in lateral side of - - - - - - - - BSPO:0001100 - uberon - in_superficial_part_of - in_superficial_part_of - in superficial part of - - - - - - - - BSPO:0001101 - uberon - in_deep_part_of - in_deep_part_of - in deep part of - - - - - - - - BSPO:0001106 - uberon - proximalmost_part_of - proximalmost_part_of - proximalmost part of - - - - - - - - BSPO:0001107 - uberon - immediately_deep_to - immediately_deep_to - immediately deep to - - - - - - - - BSPO:0001108 - uberon - distalmost_part_of - distalmost_part_of - distalmost part of - - - - - - - - BSPO:0001113 - uberon - preaxialmost_part_of - preaxialmost_part_of - preaxialmost part of - - - - - - - - BSPO:0001115 - uberon - postaxialmost_part_of - postaxialmost_part_of - postaxialmost part of - - - - - - - - BSPO:0005001 - uberon - intersects_midsagittal_plane_of - intersects_midsagittal_plane_of - intersects midsagittal plane of - - - - - - - - BSPO:0015014 - uberon - immediately_superficial_to - immediately_superficial_to - immediately superficial to - - - - - - - - BSPO:0015101 - uberon - in_dorsal_side_of - in_dorsal_side_of - in dorsal side of - - - - @@ -2522,12 +1453,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - inheres in - this fragility is a characteristic of this vase - this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. - inheres_in - Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of @@ -2539,14 +1465,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - bearer of - this apple is bearer of this red color - this vase is bearer of this fragility Inverse of characteristic_of A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. - bearer_of - is bearer of - RO:0000053 external bearer_of @@ -2563,15 +1483,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. - participates in - this blood clot participates in this blood coagulation - this input material (or this output material) participates in this process - this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process - participates_in RO:0000056 external - uberon participates_in participates_in participates in @@ -2589,14 +1503,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - has participant - this blood coagulation has participant this blood clot - this investigation has participant this investigator - this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. - has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 external has_participant @@ -2612,11 +1520,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. - function_of - is function of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. function of @@ -2628,11 +1533,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. - is quality of - quality_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. quality of @@ -2644,11 +1546,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. - is role of - role_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. role of @@ -2660,10 +1559,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. - has_function has function @@ -2673,15 +1570,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. - has_quality - RO:0000086 - uberon - has_quality - has_quality - has quality has quality @@ -2692,10 +1582,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. - has_role has role @@ -2729,13 +1617,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this cell derives from this parent cell (cell division) - this nucleus derives from this parent nucleus (nuclear division) - a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. - derives_from - This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. derives from @@ -2745,12 +1628,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this parent cell derives into this cell (cell division) - this parent nucleus derives into this nucleus (nuclear division) - a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. - derives_into derives into @@ -2762,18 +1641,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - is location of - my head is the location of my brain - this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - location_of - - RO:0001015 - uberon - location_of - location_of - location of location of @@ -2789,21 +1658,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. - located in - my brain is located in my head - this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - located_in - - http://www.obofoundry.org/ro/#OBO_REL:located_in - RO:0001025 - uberon - located_in - located_in - located in located in https://wiki.geneontology.org/Located_in @@ -2827,16 +1685,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. - the surface of my skin is a 2D boundary of my body a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - 2D_boundary_of - boundary of - is 2D boundary of - is boundary of - surface of - 2D boundary of @@ -2848,19 +1699,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. - my body has 2D boundary the surface of my skin a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - - has boundary - has_2D_boundary - - RO:0002002 - uberon - has_boundary - has_boundary - has 2D boundary has 2D boundary @@ -2872,17 +1713,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - http://www.ncbi.nlm.nih.gov/pubmed/22402613 - RO:0002005 - uberon - innervated_by - innervated_by - innervated_by innervated_by @@ -2893,8 +1723,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - has synaptic terminal of @@ -2925,10 +1753,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - RO:0002007 external - uberon bounding_layer_of bounding_layer_of @@ -3107,8 +1933,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland - <= Primitive instance level timing relation between events before or simultaneous with @@ -3123,15 +1947,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time. - - David Osumi-Sutherland - RO:0002082 - uberon - simultaneous_with - simultaneous_with t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) - simultaneous with simultaneous with @@ -3142,7 +1959,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after @@ -3159,11 +1975,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland - starts_at_end_of RO:0002087 external - uberon immediately_preceded_by immediately_preceded_by X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) @@ -3181,11 +1994,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - - David Osumi-Sutherland - ends_at_start_of - meets - RO:0002090 external immediately_precedes @@ -3208,12 +2016,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between a neuron and a material anatomical entity that its soma is part of. - <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) - has soma location @@ -3226,33 +2031,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. - - fasciculates with - (forall (?x ?y) - (iff - (fasciculates_with ?x ?y) - (exists (?nps ?npbs) - (and - ("neuron ; CL_0000540" ?x) - ("neuron projection bundle ; CARO_0001001" ?y) - ("neuron projection segment ; CARO_0001502" ?nps) - ("neuron projection bundle segment ; CARO_0001500' " ?npbs) - (part_of ?npbs ?y) - (part_of ?nps ?x) - (part_of ?nps ?npbs) - (forall (?npbss) - (if - (and - ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) - (part_of ?npbss ?npbs) - ) - (overlaps ?nps ?npbss) - )))))) - - fasciculates with @@ -3267,16 +2047,11 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between a neuron and some structure its axon forms (chemical) synapses in. - - <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y))) - - axon synapses in @@ -3298,18 +2073,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. - - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) - - - RO:0002103 - uberon - synapsed_by - synapsed_by - synapsed by synapsed by @@ -3321,15 +2086,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] - Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. - - - - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) - has plasma membrane part @@ -3345,16 +2103,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. - - - synapsed in http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)) - - has postsynaptic terminal in @@ -3369,12 +2121,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. - synapses in <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) - - has presynaptic terminal in @@ -3395,14 +2143,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. - - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) - - N1 synapsed_to some N2 Expands to: N1 SubclassOf ( @@ -3424,13 +2167,8 @@ N1 SubclassOf ( - A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. - - has synapse in <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) - - has synaptic terminal in @@ -3445,10 +2183,6 @@ N1 SubclassOf ( - - - - @@ -3457,13 +2191,10 @@ N1 SubclassOf ( - x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) - RO:0002131 external - uberon overlaps @@ -3472,15 +2203,6 @@ N1 SubclassOf ( overlaps overlaps - - - - - - - - true - @@ -3500,35 +2222,7 @@ N1 SubclassOf ( - The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. - - has fasciculating component - (forall (?x ?y) - (iff - (has_fasciculating_neuron_projection ?x ?y) - (exists (?nps ?npbs) - (and - ("neuron projection bundle ; CARO_0001001" ?x) - ("neuron projection ; GO0043005" ?y) - ("neuron projection segment ; CARO_0001502" ?nps) - ("neuron projection bundle segment ; CARO_0001500" ?npbs) - (part_of ?nps ?y) - (part_of ?npbs ?x) - (part_of ?nps ?npbs) - (forall (?npbss) - (if - (and - ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) - (part_of ?npbss ?npbs) - ) - (overlaps ?nps ?npbss) - )))))) - - - - - has fasciculating neuron projection @@ -3542,19 +2236,10 @@ N1 SubclassOf ( - Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - <http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) - - - RO:0002134 - uberon - innervates - innervates - innervates innervates @@ -3567,17 +2252,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - X continuous_with Y if and only if X and Y share a fiat boundary. - - connected to - The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) - - RO:0002150 - uberon - continuous_with - continuous_with - continuous with continuous with FMA:85972 @@ -3590,13 +2265,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a. - Consider obsoleting and merging with child relation, 'in homology relationship with' - RO:0002158 - uberon - homologous_to - homologous_to VBO calls this homologous_to shares ancestor with @@ -3607,19 +2276,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - lactation SubClassOf 'only in taxon' some 'Mammalia' - x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria - - - - RO:0002160 - uberon - only_in_taxon - only_in_taxon only in taxon @@ -3638,30 +2298,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - - - - - - - - - - - - - - - - - - - - - @@ -3682,53 +2318,16 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. - - - - - RO:0002162 - uberon - in_taxon - in_taxon Connects a biological entity to its taxon of origin. in taxon @@ -3740,14 +2339,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. - - - Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) - spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern @@ -3765,14 +2359,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b - - RO:0002170 - uberon - connected_to - connected_to - connected to connected to https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern @@ -3785,15 +2372,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - The M8 connects Glasgow and Edinburgh - a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system. - - RO:0002176 - uberon - connects - connects - connects connects https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern @@ -3808,28 +2387,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. - attached to part of (anatomical structure to anatomical structure) - RO:0002177 - uberon - attaches_to_part_of - attaches_to_part_of - attached to part of attached to part of - - - - - - - - true - @@ -3839,12 +2399,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy. Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure - - RO:0002178 - uberon - supplies - supplies - supplies supplies @@ -3856,12 +2410,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure. Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure - - RO:0002179 - uberon - drains - drains - drains drains @@ -3871,14 +2419,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. - For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. - RO:0002180 external - uberon has_component has_component @@ -3898,18 +2442,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y - - - - - RO:0002202 - uberon - develops_from - develops_from This is the transitive form of the develops from relation - develops from develops from @@ -3922,17 +2456,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of develops from - - - - RO:0002203 - uberon - develops_into - develops_into - develops into develops into @@ -3949,10 +2474,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - 'neural crest cell' SubClassOf expresses some 'Wnt1 gene' - x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process - expressed in @@ -3979,19 +2501,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. - - - FBbt - - RO:0002207 has developmental precursor - uberon - directly_develops_from - directly_develops_from TODO - add child relations from DOS - directly develops from directly develops from @@ -4001,9 +2513,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of directly develops from - developmental precursor of directly develops into @@ -4031,14 +2541,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. - - - - - GO - Regulation precludes parthood; the regulatory process may not be within the regulated process. - regulates (processual) - false RO:0002211 external regulates @@ -4063,9 +2565,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. - - - negatively regulates (process to process) RO:0002212 external @@ -4096,10 +2595,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. - - - positively regulates (process to process) - RO:0002213 external positively_regulates @@ -4119,17 +2614,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) - osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. - - has function realized in - - - For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". RO:0002215 external - uberon capable_of capable_of @@ -4144,31 +2631,15 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. - - has function in RO:0002216 external - uberon capable_of_part_of capable_of_part_of capable of part of capable of part of - - - - - - - - true - @@ -4177,15 +2648,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x - - - RO:0002219 - uberon - surrounded_by - surrounded_by - surrounded by surrounded by @@ -4197,18 +2660,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. - The epidermis layer of a vertebrate is adjacent to the dermis. - The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. - The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. - x adjacent to y if and only if x and y share a boundary. This relation acts as a join point with BSPO - - RO:0002220 external - uberon adjacent_to @@ -4217,12 +2672,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.adjacent to adjacent to - - - - A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. - - @@ -4230,16 +2679,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of surrounded by - - - RO:0002221 - uberon - surrounds - surrounds - surrounds surrounds @@ -4250,11 +2691,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. - https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to @@ -4268,17 +2704,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of starts with - - Chris Mungall - Allen - RO:0002223 - uberon - starts - starts - starts starts @@ -4290,15 +2717,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor - x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - - Chris Mungall - started by RO:0002224 external - uberon starts_with starts_with @@ -4316,14 +2737,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x develops from part of y if and only if there exists some z such that x develops from z and z is part of y - - RO:0002225 - uberon - develops_from_part_of - develops_from_part_of - develops from part of develops from part of @@ -4338,16 +2752,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x develops_in y if x is located in y whilst x is developing - - EHDAA2 - Jonathan Bard, EHDAA2 - RO:0002226 - uberon - develops_in - develops_in - develops in develops in @@ -4359,16 +2764,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of ends with - - Chris Mungall - RO:0002229 - uberon - ends - ends - ends ends @@ -4380,14 +2777,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - - Chris Mungall - finished by RO:0002230 external - uberon ends_with ends_with @@ -4407,10 +2799,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y - - starts with process that occurs in RO:0002231 external has_start_location @@ -4432,10 +2821,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y - - ends with process that occurs in RO:0002232 external has_end_location @@ -4457,10 +2843,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. - - consumes RO:0002233 external has_input @@ -4485,10 +2868,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. - - produces RO:0002234 external has_output @@ -4510,13 +2890,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1. b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t. - - RO:0002252 - uberon - connecting_branch_of - connecting_branch_of connecting branch of @@ -4528,7 +2902,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of connecting branch of - has connecting branch @@ -4546,15 +2919,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] - x has developmental contribution from y iff x has some part z such that z develops from y - - RO:0002254 - uberon - has_developmental_contribution_from - has_developmental_contribution_from - has developmental contribution from has developmental contribution from @@ -4569,9 +2934,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of has developmental contribution from - developmentally contributes to @@ -4585,21 +2948,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T - - - - induced by - - Developmental Biology, Gilbert, 8th edition, figure 6.5(F) - GO:0001759 - We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm] - RO:0002256 - uberon - developmentally_induced_by - developmentally_induced_by - developmentally induced by developmentally induced by @@ -4610,9 +2959,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Inverse of developmentally induced by - developmentally induces @@ -4625,11 +2972,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false - - In general you should not use this relation to make assertions - use one of the more specific relations below this one This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from developmentally preceded by @@ -4644,7 +2988,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. acts upstream of @@ -4661,7 +3004,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects @@ -4675,16 +3017,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage - - replaces - RO:0002285 - uberon - developmentally_replaces - developmentally_replaces - developmentally replaces developmentally replaces @@ -4694,9 +3028,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Inverse of developmentally preceded by - developmentally succeeded by @@ -4710,9 +3042,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue - - part of developmental precursor of @@ -4722,9 +3051,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process. - expresses @@ -4736,10 +3063,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. - RO:0002295 external results_in_developmental_progression_of @@ -4756,11 +3081,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - every flower development (GO:0009908) results in development of some flower (PO:0009046) - p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. - - http://www.geneontology.org/GO.doc.development.shtml RO:0002296 external results_in_development_of @@ -4780,11 +3101,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. - every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) - - - GOC:mtg_berkeley_2013 RO:0002297 external results_in_formation_of @@ -4793,7 +3109,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. results_in_formation_of results in formation of - results in formation of + results in formation of anatomical entity @@ -4803,12 +3119,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. - tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) - The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. - - GOC:mtg_berkeley_2013 RO:0002298 external results_in_morphogenesis_of @@ -4827,12 +3138,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process - bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) - The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. - - GOC:mtg_berkeley_2013 RO:0002299 external results_in_maturation_of @@ -4852,8 +3158,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. - - RO:0002304 external causally_upstream_of,_positive_effect @@ -4874,7 +3178,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. - RO:0002305 external causally_upstream_of,_negative_effect @@ -4891,32 +3194,15 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of characteristic of part of - - inheres in part of - - characteristic of part of - - - - - - - - true - @@ -4926,10 +3212,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity - - GOC:mtg_berkeley_2013 RO:0002315 external results_in_acquisition_of_features_of @@ -4947,8 +3230,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A relationship that holds via some environmental process - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. evolutionarily related to @@ -4958,9 +3239,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A mereological relationship or a topological relationship - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships - mereotopologically related to @@ -4970,8 +3248,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A relationship that holds between entities participating in some developmental process (GO:0032502) - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development developmentally related to @@ -4990,15 +3266,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - a particular instances of akt-2 enables some instance of protein kinase activity c enables p iff c is capable of p and c acts to execute p. - - catalyzes - executes - has - is catalyzing - is executing - This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. enables https://wiki.geneontology.org/Enables @@ -5010,13 +3278,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. - - This is a grouping relation that collects relations used for the purpose of connecting structure and function - RO:0002328 - uberon - functionally_related_to - functionally_related_to - functionally related to functionally related to @@ -5026,24 +3287,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - this relation holds between c and p when c is part of some c', and c' is capable of p. - - false part of structure that is capable of - - - - - - - - true - @@ -5053,8 +3299,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts. - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism genomically related to @@ -5074,9 +3318,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. c involved_in p if and only if c enables some process p', and p' is part of p - - actively involved in - enables part of involved in https://wiki.geneontology.org/Involved_in @@ -5089,11 +3330,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid p regulates levels of c if p regulates some amount (PATO:0000070) of c - - - regulates levels of (process to entity) RO:0002332 external regulates_levels_of @@ -5110,7 +3347,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of enables - enabled by https://wiki.geneontology.org/Enabled_by @@ -5126,8 +3362,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of regulates - - regulated by (processual) RO:0002334 external regulated_by @@ -5144,7 +3378,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of negatively regulates - RO:0002335 external negatively_regulated_by @@ -5161,7 +3394,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of positively regulates - RO:0002336 external positively_regulated_by @@ -5179,8 +3411,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A relationship that holds via some process of localization - - Do not use this relation directly. It is a grouping relation. related via localization to @@ -5195,7 +3425,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. - RO:0002338 external has_target_start_location @@ -5218,7 +3447,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. - RO:0002339 external has_target_end_location @@ -5237,7 +3465,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l - RO:0002341 external results_in_transport_along @@ -5254,7 +3481,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. - RO:0002342 external results_in_transport_across @@ -5271,8 +3497,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - 'pollen tube growth' results_in growth_of some 'pollen tube' - RO:0002343 external results_in_growth_of @@ -5287,8 +3511,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) - RO:0002344 external results_in_transport_to_from_or_in @@ -5304,12 +3526,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - An organism that is a member of a population of organisms is member of is a mereological relation between a item and a collection. - is member of - member part of - SIO - member of @@ -5321,13 +3538,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. has member is a mereological relation between a collection and an item. - SIO - - RO:0002351 - uberon - has_member - has_member - has member has member @@ -5339,14 +3549,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of has input - - RO:0002352 - uberon - input_of - input_of - input of input of @@ -5358,10 +3562,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of has output - RO:0002353 external - uberon output_of @@ -5376,7 +3578,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - formed as result of @@ -5386,8 +3587,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - http://neurolex.org/wiki/Property:DendriteLocation has dendrite location @@ -5400,14 +3599,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a - - attached to (anatomical structure to anatomical structure) - RO:0002371 - uberon - attaches_to - attaches_to - attached to attached to @@ -5420,13 +3612,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. - - Wikipedia:Insertion_(anatomy) - RO:0002372 - uberon - has_muscle_origin - has_muscle_origin - has muscle origin has muscle origin @@ -5446,13 +3631,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. - - Wikipedia:Insertion_(anatomy) - RO:0002373 - uberon - has_muscle_insertion - has_muscle_insertion - has muscle insertion has muscle insertion @@ -5471,12 +3649,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships - This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) - in branching relationship with https://github.com/obophenotype/uberon/issues/170 @@ -5489,23 +3662,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Deschutes River tributary_of Columbia River - inferior epigastric vein tributary_of external iliac vein - x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. - - drains into - drains to - tributary channel of - http://en.wikipedia.org/wiki/Tributary - http://www.medindia.net/glossary/venous_tributary.htm - This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries) - RO:0002376 - uberon - tributary_of - tributary_of - tributary of tributary of http://en.wikipedia.org/wiki/Tributary @@ -5523,10 +3681,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location - - This relation is added for formal completeness. It is unlikely to be used in many practical scenarios spatially coextensive with @@ -5544,15 +3699,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y - - RO:0002380 - uberon - branching_part_of - branching_part_of - branching part of branching part of FMA:85994 @@ -5566,9 +3714,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). - has developmental potential involving @@ -5578,14 +3724,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y - - RO:0002385 - uberon - has_potential_to_developmentally_contribute_to - has_potential_to_developmentally_contribute_to - has potential to developmentally contribute to has potential to developmentally contribute to @@ -5595,9 +3734,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y - has potential to developmentally induce @@ -5607,14 +3744,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x has the potential to develop into y iff x develops into y or if x is capable of developing into y - - RO:0002387 - uberon - has_potential_to_develop_into - has_potential_to_develop_into - has potential to develop into has potential to develop into @@ -5624,9 +3754,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y - has potential to directly develop into @@ -5638,9 +3766,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of upstream of - RO:0002404 external causally_downstream_of @@ -5657,8 +3783,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - RO:0002405 external immediately_causally_downstream_of @@ -5692,9 +3816,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. - - indirectly activates - indirectly positively regulates https://wiki.geneontology.org/Indirectly_positively_regulates @@ -5720,9 +3841,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. - - indirectly inhibits - indirectly negatively regulates https://wiki.geneontology.org/Indirectly_negatively_regulates @@ -5748,8 +3866,6 @@ For the second, we consider a relationship to be regulatory if the system in whi For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to @@ -5768,7 +3884,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. - RO:0002411 external causally_upstream_of @@ -5787,8 +3902,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. - - RO:0002412 external immediately_causally_upstream_of @@ -5807,8 +3920,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 - - influences (processual) RO:0002418 external affects @@ -5825,8 +3936,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different inverse of causally upstream of or within - - RO:0002427 external causally_downstream_of_or_within @@ -5851,7 +3960,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' regulates some p - involved in regulation of @@ -5870,8 +3978,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' positively regulates some p - - involved in positive regulation of @@ -5890,7 +3996,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' negatively regulates some p - involved in negative regulation of @@ -5905,8 +4010,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union - - involved in or reguates involved in or involved in regulation of @@ -5917,28 +4020,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - - executes activity in enables activity in is active in https://wiki.geneontology.org/Is_active_in - - - - - - - - true - @@ -5954,11 +4041,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. - - RO:0002433 - uberon - contributes_to_morphology_of - contributes_to_morphology_of contributes to morphology of @@ -5973,13 +4055,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different A relationship that holds between two entities in which the processes executed by the two entities are causally connected. This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. Considering relabeling as 'pairwise interacts with' - - Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. in pairwise interaction with interacts with http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ - http://purl.obolibrary.org/obo/MI_0914 @@ -5990,12 +4069,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. - - binds - molecularly binds with molecularly interacts with - http://purl.obolibrary.org/obo/MI_0915 @@ -6005,8 +4080,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different Axiomatization to GO to be added later - - An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. phosphorylates @@ -6027,8 +4100,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. - - molecularly controls directly regulates activity of @@ -6048,9 +4119,6 @@ A and B can be physically interacting but not necessarily. Immediately upstream The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. - - - directly inhibits molecularly decreases activity of directly negatively regulates activity of @@ -6070,9 +4138,6 @@ For example, A and B may be gene products and binding of B by A negatively regul The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. - - - directly activates molecularly increases activity of directly positively regulates activity of @@ -6082,8 +4147,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. helper property (not for use in curation) @@ -6095,16 +4158,8 @@ For example, A and B may be gene products and binding of B by A positively regul - 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. - - - - RO:0002473 - uberon - composed_primarily_of - composed_primarily_of composed primarily of @@ -6115,24 +4170,10 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. - has part that occurs in - - - - - - - - true - @@ -6140,7 +4181,6 @@ For example, A and B may be gene products and binding of B by A positively regul - is kinase activity @@ -6152,7 +4192,6 @@ For example, A and B may be gene products and binding of B by A positively regul See notes for inverse relation - receives input from @@ -6163,7 +4202,6 @@ For example, A and B may be gene products and binding of B by A positively regul This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. - sends output to @@ -6174,8 +4212,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. relation between physical entity and a process or stage @@ -6191,11 +4227,6 @@ For example, A and B may be gene products and binding of B by A positively regul x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). - - RO:0002488 - uberon - existence_starts_during - existence_starts_during existence starts during @@ -6206,11 +4237,6 @@ For example, A and B may be gene products and binding of B by A positively regul x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). - - RO:0002489 - uberon - existence_starts_with - existence_starts_with existence starts with @@ -6221,7 +4247,6 @@ For example, A and B may be gene products and binding of B by A positively regul x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence overlaps @@ -6234,12 +4259,7 @@ For example, A and B may be gene products and binding of B by A positively regul x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) - - RO:0002491 exists during - uberon - existence_starts_and_ends_during - existence_starts_and_ends_during The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts and ends during @@ -6255,23 +4275,10 @@ For example, A and B may be gene products and binding of B by A positively regul - Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). - - RO:0002492 - ceases_to_exist_during - uberon - existence_ends_during - existence_ends_during The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during - - - - Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. - https://orcid.org/0000-0002-6601-2165 - @@ -6280,11 +4287,6 @@ For example, A and B may be gene products and binding of B by A positively regul x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). - - RO:0002493 - uberon - existence_ends_with - existence_ends_with The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends with @@ -6297,11 +4299,6 @@ For example, A and B may be gene products and binding of B by A positively regul x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships - - RO:0002494 - uberon - transformation_of - transformation_of transformation of @@ -6313,12 +4310,6 @@ For example, A and B may be gene products and binding of B by A positively regul x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t - - - RO:0002495 - uberon - immediate_transformation_of - immediate_transformation_of immediate transformation of @@ -6349,11 +4340,6 @@ For example, A and B may be gene products and binding of B by A positively regul x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). - - RO:0002496 - uberon - existence_starts_during_or_after - existence_starts_during_or_after The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts during or after @@ -6385,11 +4371,6 @@ For example, A and B may be gene products and binding of B by A positively regul x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. - - RO:0002497 - uberon - existence_ends_during_or_before - existence_ends_during_or_before The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during or before @@ -6402,7 +4383,6 @@ For example, A and B may be gene products and binding of B by A positively regul A relationship between a material entity and a process where the material entity has some causal role that influences the process - causal agent in process @@ -6415,9 +4395,6 @@ For example, A and B may be gene products and binding of B by A positively regul p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. - - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes @@ -6426,7 +4403,6 @@ For example, A and B may be gene products and binding of B by A positively regul - depends on @@ -6440,9 +4416,6 @@ For example, A and B may be gene products and binding of B by A positively regul The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch - - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between entities @@ -6456,18 +4429,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - - Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. - - has supporting framework - The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). - RO:0002551 - uberon - has_skeleton - has_skeleton has skeleton @@ -6484,9 +4447,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - causally influenced by (entity-centric) causally influenced by @@ -6496,7 +4456,6 @@ For example, A and B may be gene products and binding of B by A positively regul - interaction relation helper property http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ @@ -6508,7 +4467,6 @@ For example, A and B may be gene products and binding of B by A positively regul - molecular interaction relation helper property @@ -6519,8 +4477,6 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - - RO:0002565 external results_in_movement_of @@ -6550,10 +4506,6 @@ For example, A and B may be gene products and binding of B by A positively regul The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). - - - - causally influences (entity-centric) causally influences @@ -6566,8 +4518,6 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between elements of a musculoskeletal system or its analogs. - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. biomechanically related to @@ -6578,12 +4528,6 @@ For example, A and B may be gene products and binding of B by A positively regul m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. - - Wikipedia:Antagonist_(muscle) - RO:0002568 - uberon - has_muscle_antagonist - has_muscle_antagonist has muscle antagonist @@ -6596,13 +4540,8 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of branching part of - - RO:0002569 - uberon - has_branching_part - has_branching_part has branching part @@ -6615,14 +4554,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. - - UBERON:cjm - This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. - RO:0002570 - uberon - conduit_for - conduit_for conduit for @@ -6634,13 +4566,7 @@ For example, A and B may be gene products and binding of B by A positively regul x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - - - RO:0002571 - uberon - lumen_of - lumen_of lumen of @@ -6652,12 +4578,7 @@ For example, A and B may be gene products and binding of B by A positively regul s is luminal space of x iff s is lumen_of x and s is an immaterial entity - - RO:0002572 - uberon - luminal_space_of - luminal_space_of luminal space of @@ -6670,12 +4591,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has skeleton - - RO:0002576 - uberon - skeleton_of - skeleton_of skeleton of @@ -6687,10 +4603,6 @@ For example, A and B may be gene products and binding of B by A positively regul p directly regulates q iff p is immediately causally upstream of q and p regulates q. - - - directly regulates (processual) - RO:0002578 external directly_regulates @@ -6712,9 +4624,7 @@ For example, A and B may be gene products and binding of B by A positively regul - gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p - has part structure that is capable of @@ -6784,8 +4694,6 @@ For example, A and B may be gene products and binding of B by A positively regul A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - - causal relation between material entity and a process @@ -6799,9 +4707,7 @@ For example, A and B may be gene products and binding of B by A positively regul - pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. - capable of regulating @@ -6816,7 +4722,6 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. - capable of negatively regulating @@ -6830,9 +4735,7 @@ For example, A and B may be gene products and binding of B by A positively regul - renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. - capable of positively regulating @@ -6843,7 +4746,6 @@ For example, A and B may be gene products and binding of B by A positively regul Inverse of 'causal agent in process' - RO:0002608 external process_has_causal_agent @@ -6859,9 +4761,6 @@ For example, A and B may be gene products and binding of B by A positively regul p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. - - directly positively regulates (process to process) - RO:0002629 external directly_positively_regulates @@ -6881,8 +4780,6 @@ For example, A and B may be gene products and binding of B by A positively regul p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. - - directly negatively regulates (process to process) RO:0002630 external @@ -6909,12 +4806,9 @@ For example, A and B may be gene products and binding of B by A positively regul - a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. - RO:0003000 external - uberon produces produces @@ -6930,12 +4824,9 @@ For example, A and B may be gene products and binding of B by A positively regul - a produced_by b iff some process that occurs_in b has_output a. - RO:0003001 external - uberon produced_by produced_by @@ -7042,7 +4933,6 @@ For example, A and B may be gene products and binding of B by A positively regul - 2018-01-26T23:49:30Z @@ -7080,7 +4970,6 @@ For example, A and B may be gene products and binding of B by A positively regul c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive - 2018-01-26T23:53:14Z @@ -7127,7 +5016,6 @@ For example, A and B may be gene products and binding of B by A positively regul - 2018-03-13T23:55:19Z causally upstream of or within, positive effect @@ -7143,7 +5031,6 @@ For example, A and B may be gene products and binding of B by A positively regul The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. - regulates activity of @@ -7391,7 +5278,6 @@ For example, A and B may be gene products and binding of B by A positively regul - 'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)') A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. @@ -7411,7 +5297,6 @@ For example, A and B may be gene products and binding of B by A positively regul - 'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor') A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. @@ -7433,12 +5318,7 @@ For example, A and B may be gene products and binding of B by A positively regul - A diagnostic testing device utilizes a specimen. X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. - - - A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. - See github ticket https://github.com/oborel/obo-relations/issues/497 2021-11-08T12:00:00Z utilizes device utilizes material @@ -7564,7 +5444,6 @@ For example, A and B may be gene products and binding of B by A positively regul - x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y. @@ -7584,8 +5463,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - carries uberon channel_for @@ -7597,7 +5474,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uberon channels_from channels_from @@ -7608,7 +5484,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uberon channels_into channels_into @@ -7619,10 +5494,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y. uberon distally_connected_to @@ -7641,11 +5514,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y uberon extends_fibers_into @@ -7675,11 +5543,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - @@ -7707,7 +5570,6 @@ For example, A and B may be gene products and binding of B by A positively regul - x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y. uberon @@ -7736,7 +5598,6 @@ For example, A and B may be gene products and binding of B by A positively regul - x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y. @@ -7790,7 +5651,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uberon transitively_anteriorly_connected_to transitively anteriorly connected to @@ -7802,7 +5662,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uberon transitively_distally_connected_to transitively distally connected to @@ -7814,7 +5673,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uberon transitively_proximally_connected_to transitively proximally connected to @@ -8024,13 +5882,14 @@ For example, A and B may be gene products and binding of B by A positively regul - Any fibroblast that is deriived from the neural crest. - fibroblast neural crest derived + Any fibroblast that is derived from the neural crest. + fibroblast neural crest derived + neural crest derived fibroblast - Any fibroblast that is deriived from the neural crest. + Any fibroblast that is derived from the neural crest. https://orcid.org/0000-0001-5208-3432 @@ -13529,15 +11388,21 @@ radial glial cells acting as neural progenitors throughout life. - - - - - - + + camera type eye photoreceptor cell camera-type eye photoreceptor cell + + + + + + + + + https://github.com/obophenotype/cell-ontology/issues/2245 + @@ -14862,32 +12727,32 @@ plexiform layer. - - + + A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer - + - + - + PMID:12382326 - + PMID:12382326 @@ -23472,7 +21337,6 @@ plexiform layer. - GC_ID:1 PMID:15371245 ncbi_taxonomy @@ -23486,7 +21350,6 @@ plexiform layer. - GC_ID:1 Mus mice @@ -23505,7 +21368,7 @@ plexiform layer. mice - + @@ -23520,7 +21383,6 @@ plexiform layer. - NCBITaxon:85055 GC_ID:1 house mouse @@ -23548,7 +21410,6 @@ plexiform layer. - GC_ID:1 ncbi_taxonomy NCBITaxon:117570 @@ -23561,7 +21422,6 @@ plexiform layer. - NCBITaxon:40673 GC_ID:1 bony vertebrates @@ -23601,7 +21461,6 @@ plexiform layer. - GC_ID:1 ncbi_taxonomy NCBITaxon:1338369 @@ -23614,7 +21473,6 @@ plexiform layer. - GC_ID:1 PMID:11743200 PMID:11791233 @@ -23636,7 +21494,6 @@ plexiform layer. - GC_ID:1 mice and others ncbi_taxonomy @@ -23663,7 +21520,6 @@ plexiform layer. - GC_ID:1 PMID:23020233 PMID:30257078 @@ -23727,7 +21583,6 @@ plexiform layer. - GC_ID:1 PMID:11214319 PMID:12082125 @@ -23744,7 +21599,6 @@ plexiform layer. - GC_ID:1 PMID:11214319 PMID:12082125 @@ -23767,7 +21621,6 @@ plexiform layer. - GC_ID:1 tetrapods ncbi_taxonomy @@ -23787,7 +21640,6 @@ plexiform layer. - GC_ID:1 amniotes ncbi_taxonomy @@ -23807,7 +21659,6 @@ plexiform layer. - GC_ID:1 Theria ncbi_taxonomy @@ -23827,7 +21678,6 @@ plexiform layer. - GC_ID:1 ncbi_taxonomy Fungi/Metazoa group @@ -23854,7 +21704,6 @@ plexiform layer. - GC_ID:1 metazoans multicellular animals @@ -23895,7 +21744,6 @@ plexiform layer. - GC_ID:1 ncbi_taxonomy NCBITaxon:33213 @@ -23908,7 +21756,6 @@ plexiform layer. - GC_ID:1 deuterostomes ncbi_taxonomy @@ -23928,7 +21775,6 @@ plexiform layer. - GC_ID:1 PMID:15019624 PMID:15371245 @@ -23943,7 +21789,6 @@ plexiform layer. - NCBITaxon:109679 GC_ID:1 ncbi_taxonomy @@ -23957,7 +21802,6 @@ plexiform layer. - GC_ID:1 mammals ncbi_taxonomy @@ -23984,7 +21828,6 @@ plexiform layer. - GC_ID:1 ncbi_taxonomy NCBITaxon:6072 @@ -23997,7 +21840,6 @@ plexiform layer. - GC_ID:1 chordates ncbi_taxonomy @@ -24024,7 +21866,6 @@ plexiform layer. - GC_ID:1 Vertebrata vertebrates @@ -24058,7 +21899,6 @@ plexiform layer. - GC_ID:1 Gnathostomata jawed vertebrates @@ -24085,7 +21925,6 @@ plexiform layer. - GC_ID:1 ncbi_taxonomy NCBITaxon:8287 @@ -24098,7 +21937,6 @@ plexiform layer. - GC_ID:1 Mus ncbi_taxonomy @@ -24118,7 +21956,6 @@ plexiform layer. - GC_ID:1 Craniata ncbi_taxonomy @@ -24138,7 +21975,6 @@ plexiform layer. - GC_ID:1 eutherian mammals placental mammals @@ -24186,7 +22022,6 @@ plexiform layer. - GC_ID:1 rodent ncbi_taxonomy @@ -24322,7 +22157,6 @@ plexiform layer. A branchiness quality inhering in a bearer by virtue of the bearer's having branches. - ramified ramiform quality @@ -24369,7 +22203,6 @@ plexiform layer. A morphological quality inhering in a bearer by virtue of the bearer's affording blocked passage or view. - quality blocked PATO:0000608 @@ -24435,7 +22268,6 @@ plexiform layer. A optical quality inhering in a bearer by virtue of the bearer's not being clear; not transmitting or reflecting light or radiant energy. - non-transparent quality clouding @@ -24459,7 +22291,6 @@ plexiform layer. A optical quality inhering in a bearer by virtue of the bearer's lacking opacity. - clear hyaline quality @@ -24755,7 +22586,6 @@ plexiform layer. A contractility quality inhering in a bearer by virtue of the bearer's ability of contracting or being contracted. - quality PATO:0001690 @@ -24777,7 +22607,6 @@ plexiform layer. A shape quality in a bearer by virtue of the bearer's curving inward. - quality PATO:0001857 @@ -24931,7 +22760,6 @@ plexiform layer. A complete three dimensional shape in which for every line connecting pair of points on the object is within the object. Or: a shape lacking cavities. Contrast: concave. - Image:http://upload.wikimedia.org/wikipedia/commons/0/06/Convex_polygon_illustration1.png quality PATO:0002007 @@ -24992,7 +22820,6 @@ plexiform layer. A concave quality inhering in a bearer by virtue of the bearer's curving inward on both sides or surfaces. - quality PATO:0002039 @@ -25630,7 +23457,6 @@ plexiform layer. PR:000001012 Category=gene. Requested by=CL. integrin alpha-M - @@ -25774,7 +23600,6 @@ plexiform layer. PR:000001024 Category=gene. Requested by=CL. neural cell adhesion molecule 1 - @@ -25859,7 +23684,6 @@ plexiform layer. PR:000001084 Category=gene. Requested by=CL. T-cell surface glycoprotein CD8 alpha chain - @@ -25988,7 +23812,6 @@ plexiform layer. PR:000001444 Category=gene. Requested by=CL. cadherin-5 - @@ -26021,7 +23844,6 @@ plexiform layer. PR:000001839 Category=gene. Requested by=CL. T-cell surface glycoprotein CD5 - @@ -26063,7 +23885,6 @@ plexiform layer. PR:000001869 Category=gene. Requested by=CL. interleukin-7 receptor subunit alpha - @@ -26128,7 +23949,6 @@ plexiform layer. PR:000001945 Category=gene. Requested by=CL. transferrin receptor protein 1 - @@ -26198,7 +24018,6 @@ plexiform layer. PR:000002112 Category=gene. Requested by=CL. vascular endothelial growth factor receptor 2 - @@ -26321,7 +24140,6 @@ plexiform layer. PR:000014841 Category=gene. sonic hedgehog protein - @@ -26363,7 +24181,6 @@ plexiform layer. PR:000016043 Category=gene. Requested by=CL. T-cell acute lymphocytic leukemia protein 1 - @@ -26618,11 +24435,10 @@ plexiform layer. - - + + - @@ -26630,9 +24446,6 @@ plexiform layer. An organ of sight that includes the camera-type eyeball and supporting structures such as the lacrimal apparatus, the conjunctiva, the eyelid. - A cavitated compound organ that transduces light waves into neural signals.[TAO] - The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] - FMA distinguishes Eye (subdivision of face) which has its parts an Eyeball (organ), as well as other structures, and the orbit of skull. MA includes eyelid, conjunctiva and lacrimal apparatus as part of MA:eye - consistent with FMA - so we can infer that MA:eye is more like FMA:eye than FMA:eyeball. For other AOs this distinction is less meaningful - e.g. ZFA has no eyelid; XAO has no eyelid, but it has conjuctiva, which is considered part of the xao:eye. GO considers eyelid development part of eye development. See also notes on optic nerve - XAO, AAO and BTO consider this part of the eye. MA considers the eye muscles part of the eye, whereas FMA has a class 'orbital content' for this eye AAO:0010340 BIRNLEX:1169 @@ -26663,16 +24476,6 @@ plexiform layer. camera-type eye - - - - - - - - - definitional - @@ -26680,31 +24483,6 @@ plexiform layer. GO:0043010 https://orcid.org/0000-0002-6601-2165 - - - - A cavitated compound organ that transduces light waves into neural signals.[TAO] - 2012-08-14 - TAO:0000107 - TAO - TAO:wd - - - - - The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] - 2012-09-17 - VHOG:0000275 - VHOG - DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007) - http://bgee.unil.ch/ - - - - - FMA distinguishes Eye (subdivision of face) which has its parts an Eyeball (organ), as well as other structures, and the orbit of skull. MA includes eyelid, conjunctiva and lacrimal apparatus as part of MA:eye - consistent with FMA - so we can infer that MA:eye is more like FMA:eye than FMA:eyeball. For other AOs this distinction is less meaningful - e.g. ZFA has no eyelid; XAO has no eyelid, but it has conjuctiva, which is considered part of the xao:eye. GO considers eyelid development part of eye development. See also notes on optic nerve - XAO, AAO and BTO consider this part of the eye. MA considers the eye muscles part of the eye, whereas FMA has a class 'orbital content' for this - FMA - @@ -26789,7 +24567,6 @@ plexiform layer. EHDAA2:0001824 EHDAA:500 EMAPA:35955 - FBbt:00005155 GAID:63 HAO:0000930 MA:0000017 @@ -26822,12 +24599,6 @@ plexiform layer. https://github.com/obophenotype/uberon/issues/549 https://orcid.org/0000-0002-6601-2165 - - - - FBbt:00005155 - - @@ -26913,8 +24684,6 @@ plexiform layer. Any hollow cylindrical anatomical structure containing a lumen through which substances are transported. - not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts) - tubular galen:Tube anatomical tube duct @@ -26948,10 +24717,6 @@ plexiform layer. The head is the anterior-most division of the body [GO]. - - Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO] - Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO] - Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG] AAO:0010335 AEO:0000106 BILA:0000115 @@ -26998,34 +24763,6 @@ plexiform layer. GO:0060322 Wikipedia:Head - - - - Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO] - 2012-06-20 - AAO:0010335 - AAO - AAO:BJB - - - - - Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO] - 2012-08-14 - TAO:0001114 - TAO - ZFIN:curator - - - - - Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG] - 2012-09-17 - VHOG:0001644 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.82 - http://bgee.unil.ch/ - @@ -27073,9 +24810,6 @@ plexiform layer. Multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer. - A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO] - a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP] - in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA. FMA:9581 GAID:19 MESH:D012704 @@ -27103,27 +24837,6 @@ plexiform layer. Wikipedia:Serous_membrane https://github.com/obophenotype/uberon/issues/86 - - - - A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO] - 2012-08-14 - TAO:0005425 - TAO - Wikipedia:Serous_membrane - - - - - a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP] - Wikipedia:Serous_membrane - - - - - in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA. - FMA - @@ -27219,10 +24932,8 @@ plexiform layer. Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. - in FMA, serosa is a wall UBERON:0009915 wall - EMAPA:25036 FMA:82482 galen:Wall wall of organ @@ -27238,12 +24949,6 @@ plexiform layer. Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. FMA:82482 - - - - in FMA, serosa is a wall - FMA - @@ -27279,7 +24984,6 @@ plexiform layer. CARO:0000003 EHDAA2:0003003 EMAPA:0 - FBbt:00007001 FMA:305751 FMA:67135 GAID:781 @@ -27307,12 +25011,6 @@ plexiform layer. Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. CARO:0000003 - - - - FBbt:00007001 - - @@ -27350,8 +25048,6 @@ plexiform layer. - Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. - CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4 BIRNLEX:4 CARO:0020004 EFO:0000634 @@ -27385,12 +25081,6 @@ plexiform layer. Wikipedia - - - - Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. - GO:0048513 - @@ -27412,8 +25102,6 @@ plexiform layer. A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity. FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction - Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball. - Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal. FMA:86140 uberon organ region with fixed fiat boundary @@ -27429,20 +25117,6 @@ plexiform layer. A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity. http://orcid.org/0000-0002-6601-2165 - - - - Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball. - FMA:86140 - 3 - - - - - Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal. - FMA:86140 - 1 - @@ -27475,7 +25149,6 @@ plexiform layer. A multicellular structure that is a part of an organ. - currently defined in a very broad sense, may be replaced by more specific classes in the future @@ -27632,7 +25305,6 @@ plexiform layer. - ncit:Death is an outcome XAO:0000437 XtroDO:0000085 uberon @@ -27647,12 +25319,6 @@ plexiform layer. End of the life of an organism. XAO:0000437 - - - - ncit:Death is an outcome - ncit - @@ -27781,12 +25447,9 @@ plexiform layer. - + The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm. merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube) - - (or external ectoderm) forms the following structures: Skin Epithelium of the mouth and nasal cavity saliavary glands, and glands of mouth and nasal cavity Enamel - as a side note dentin and dental pulp are formed from ectomesenchyme which is derived from ectoderm Epithelium of pineal and pituitary glands Lens and cornea of the eye Apical ectodermal ridge inducing development of the limb buds of the embryo. Sensory receptors in epidermis - BTO:0006242 EHDAA2:0001968 EHDAA:1494 EHDAA:350 @@ -27807,7 +25470,7 @@ plexiform layer. external ectoderm http://upload.wikimedia.org/wikipedia/commons/1/1d/Ectoderm.png - + @@ -27820,7 +25483,7 @@ plexiform layer. - + EHDAA2 @@ -27830,14 +25493,6 @@ plexiform layer. MGI:anna MP:0012532 - - - - BTO:0006242 - - - https://github.com/biopragmatics/biomappings - @@ -27871,7 +25526,6 @@ plexiform layer. Stage succeeding embryo, including mature structure. - In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997) BilaDO:0000003 OGES:000010 OGES:000014 @@ -27957,8 +25611,6 @@ plexiform layer. - the WBls class 'all stages' belongs here as it is the superclass of other WBls stages - we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage BILS:0000105 EFO:0000399 FBdv:00007012 @@ -28009,13 +25661,11 @@ plexiform layer. A stage at which the organism is a single cell produced by means of sexual reproduction. - As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG] BILS:0000106 BilaDO:0000005 EFO:0001322 EHDAA:27 FBdv:00005288 - IDOMAL:0000302 NCIT:C12601 PdumDv:0000100 VHOG:0000745 @@ -28041,24 +25691,6 @@ plexiform layer. A stage at which the organism is a single cell produced by means of sexual reproduction. Wikipedia:Zygote - - - - As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG] - 2012-09-17 - VHOG:0000745 - VHOG - ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107 - http://bgee.unil.ch/ - - - - - IDOMAL:0000302 - - - https://github.com/biopragmatics/biomappings - @@ -28206,7 +25838,7 @@ plexiform layer. - + @@ -28242,14 +25874,14 @@ plexiform layer. gastrula stage - + - + BILS @@ -28327,8 +25959,6 @@ plexiform layer. Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system. - - In zebrafish, the times of neurulation and segmentation overlap so extensively there is no distinct neurula period of development, such as occurs largely before segmentation in amphibian embryos. BILS:0000110 BilaDO:0000009 HsapDv:0000012 @@ -28415,7 +26045,6 @@ plexiform layer. A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. UBERON:0005163 CARO:0001001 - FBbt:00005099 NLX:147821 funiculus nerve fiber bundle @@ -28432,12 +26061,6 @@ plexiform layer. FBC:DOS FBbt:00005099 - - - - FBbt:00005099 - - @@ -28451,12 +26074,6 @@ plexiform layer. - - - - - - @@ -28497,24 +26114,7 @@ plexiform layer. - - - - - - - - - - - - - - - - - @@ -28528,11 +26128,6 @@ plexiform layer. The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks). - Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO] - Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG] - oral - some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives - in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips AAO:0010355 BTO:0001090 BTO:0004698 @@ -28541,7 +26136,6 @@ plexiform layer. EHDAA2:0001326 EHDAA:542 EMAPA:16262 - FBbt:00003126 FMA:49184 GAID:75 MA:0000341 @@ -28587,12 +26181,6 @@ plexiform layer. https://github.com/obophenotype/uberon/issues/661 http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg - - - - - the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts - @@ -28600,37 +26188,6 @@ plexiform layer. Wikipedia:Mouth https://github.com/obophenotype/uberon/wiki/The-digestive-tract - - - - Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO] - 2012-06-20 - AAO:0010355 - AAO - AAO:BJB - - - - - Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG] - 2012-09-17 - VHOG:0000812 - VHOG - DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008) - http://bgee.unil.ch/ - - - - - in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips - FMA - - - - - FBbt:00003126 - - @@ -28721,22 +26278,17 @@ plexiform layer. - + - - + + A fluid that is composed of blood plasma and erythrocytes. - This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid. - A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO] - Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO] - relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] - Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG] AAO:0000046 BTO:0000089 CALOHA:TS-0079 @@ -28771,34 +26323,34 @@ plexiform layer. blood - + - + - + - + CL:tm - + https://github.com/obophenotype/uberon/issues/1330 - + Bgee:AN @@ -28810,42 +26362,6 @@ plexiform layer. http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/9 - - - - A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO] - 2012-08-14 - TAO:0000007 - TAO - ZFIN:curator - - - - - Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO] - 2012-06-20 - AAO:0000046 - AAO - AAO:LAP - - - - - relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] - 2012-06-20 - AAO:0000046 - AAO - - - - - Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG] - 2012-09-17 - VHOG:0000224 - VHOG - DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006) - http://bgee.unil.ch/ - @@ -29009,14 +26525,11 @@ plexiform layer. consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77 - Anatomical system that consists of the muscles of the body.[VSAO] - we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA AAO:0000307 BILA:0000088 BTO:0001369 BTO:0001485 EFO:0000801 - EMAPA:35578 FMA:72954 MA:0002888 MAT:0000025 @@ -29044,21 +26557,6 @@ plexiform layer. The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified]. VSAO:0000033 - - - - Anatomical system that consists of the muscles of the body.[VSAO] - 2012-08-14 - VSAO:0000033 - VSAO - VSAO:curator - - - - - we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA - MA - @@ -29102,7 +26600,12 @@ plexiform layer. - + + + + + + @@ -29120,7 +26623,6 @@ plexiform layer. CARO:0000004 EHDAA2:0003004 EMAPA:35178 - FBbt:00007019 FMA:9669 HAO:0000004 MA:0002450 @@ -29144,28 +26646,12 @@ plexiform layer. organism substance - - - - - - - - - this relationship may be too strong and may be weakened in future - Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007019 - - @@ -29220,7 +26706,6 @@ plexiform layer. BILA:0000005 CARO:0000005 EHDAA2:0003005 - FBbt:00007017 FMA:5897 HAO:0000005 NCIT:C94478 @@ -29244,12 +26729,6 @@ plexiform layer. Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures. http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007017 - - @@ -29281,7 +26760,6 @@ plexiform layer. BILA:0000006 CARO:0000006 EHDAA2:0003006 - FBbt:00007016 FMA:67165 HAO:0000006 TAO:0001836 @@ -29299,12 +26777,6 @@ plexiform layer. Anatomical entity that has mass. http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007016 - - @@ -29322,7 +26794,6 @@ plexiform layer. BILA:0000007 CARO:0000007 EHDAA2:0003007 - FBbt:00007015 FMA:67112 HAO:0000007 TAO:0001835 @@ -29341,12 +26812,6 @@ plexiform layer. Anatomical entity that has no mass. http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007015 - - @@ -29389,10 +26854,8 @@ plexiform layer. EHDAA:392 EMAPA:16103 EV:0100000 - FBbt:00004856 FMA:7149 HAO:0000011 - IDOMAL:0002460 MA:0000003 NCIT:C12919 SCTID:278195005 @@ -29432,20 +26895,6 @@ plexiform layer. system GO:0048731 - - - - FBbt:00004856 - - - - - - IDOMAL:0002460 - - - https://github.com/biopragmatics/biomappings - @@ -29483,7 +26932,6 @@ plexiform layer. - organismal organism AAO:0010026 AEO:0000191 @@ -29498,7 +26946,6 @@ plexiform layer. EHDAA:1 EMAPA:25765 EV:0100016 - FBbt:00000001 FMA:256135 HAO:0000012 NCIT:C13041 @@ -29543,12 +26990,6 @@ plexiform layer. VHOG:0000671 WBbt:0007833 - - - - FBbt:00000001 - - @@ -29609,7 +27050,6 @@ plexiform layer. EFO:0000808 EHDAA2:0003032 EMAPA:36031 - FBbt:00007009 FMA:7153 HAO:0000032 MA:0002433 @@ -29652,12 +27092,6 @@ plexiform layer. CARO:DOS http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007009 - - @@ -29699,7 +27133,6 @@ plexiform layer. BILA:0000040 CARO:0000040 EHDAA2:0003040 - FBbt:00007013 FMA:63863 HAO:0000040 TAO:0000382 @@ -29725,12 +27158,6 @@ plexiform layer. Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue. http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007013 - - @@ -29749,7 +27176,6 @@ plexiform layer. - FBbt:00007277 VHOG:0001737 uberon UBERON:0000477 @@ -29763,12 +27189,6 @@ plexiform layer. Anatomical group whose component anatomical structures lie in close proximity to each other. FBbt:00007277 - - - - FBbt:00007277 - - @@ -29802,7 +27222,6 @@ plexiform layer. CARO:0000043 EHDAA2:0003043 EMAPA:35868 - FBbt:00007003 FMA:9637 HAO:0000043 MA:0003002 @@ -29838,12 +27257,6 @@ plexiform layer. Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. CARO:0000043 - - - - FBbt:00007003 - - @@ -29884,7 +27297,6 @@ plexiform layer. BILA:0000055 CARO:0000055 EHDAA2:0003055 - FBbt:00007010 HAO:0000055 TAO:0001488 TGMA:0001847 @@ -29911,12 +27323,6 @@ plexiform layer. CARO:0000055 http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007010 - - @@ -29955,7 +27361,7 @@ plexiform layer. - + @@ -29963,8 +27369,6 @@ plexiform layer. Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]. - The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG] - epithelial AAO:0000144 AAO:0010055 AEO:0000066 @@ -29974,7 +27378,6 @@ plexiform layer. CARO:0000066 EHDAA2:0003066 EMAPA:32738 - FBbt:00007005 FMA:9639 GAID:402 HAO:0000066 @@ -29999,14 +27402,14 @@ plexiform layer. epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg - + - + http://palaeos.com/metazoa/porifera/homoscleromorpha.html @@ -30016,22 +27419,6 @@ plexiform layer. Wikipedia:Epithelium http://orcid.org/0000-0001-9114-8737 - - - - The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG] - 2012-09-17 - VHOG:0000387 - VHOG - ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.59 - http://bgee.unil.ch/ - - - - - FBbt:00007005 - - @@ -30064,7 +27451,6 @@ plexiform layer. Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA]. - Unilaminar epithelium that consists of a single layer of squamous cells.[CARO] AAO:0010066 AEO:0000070 BILA:0000070 @@ -30096,16 +27482,6 @@ plexiform layer. Wikipedia:Simple_squamous_epithelium http://orcid.org/0000-0001-9114-8737 - - - - Unilaminar epithelium that consists of a single layer of squamous cells.[CARO] - 2012-06-20 - CARO:0000070 - CARO - FMA:45565 - http://orcid.org/0000-0001-9114-8737 - @@ -30182,7 +27558,6 @@ plexiform layer. Compound organ that contains one or more macroscopic anatomical spaces. - this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future AAO:0010016 AEO:0000072 BILA:0000072 @@ -30231,7 +27606,6 @@ plexiform layer. Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA]. consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable - Epithelium that consists of a single layer of epithelial cells.[CARO] AAO:0010062 AEO:0000073 BILA:0000073 @@ -30260,16 +27634,6 @@ plexiform layer. FMA:45561 http://orcid.org/0000-0001-9114-8737 - - - - Epithelium that consists of a single layer of epithelial cells.[CARO] - 2012-06-20 - CARO:0000073 - CARO - FMA:45561 - http://orcid.org/0000-0001-9114-8737 - @@ -30315,10 +27679,6 @@ plexiform layer. Subdivision of trunk that lies between the head and the abdomen. - note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest - - - EMAPA:35862 FMA:259209 MA:0000022 @@ -30392,8 +27752,6 @@ plexiform layer. Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. - embryonic - Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo AAO:0011035 AEO:0000169 BILA:0000056 @@ -30405,10 +27763,8 @@ plexiform layer. EHDAA2_RETIRED:0003236 EHDAA:38 EMAPA:16039 - FBbt:00000052 FMA:69068 GAID:963 - IDOMAL:0000646 MAT:0000226 MESH:D004622 MIAA:0000019 @@ -30444,26 +27800,6 @@ plexiform layer. GO:0009790 Wikipedia:Embryo - - - - Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo - ZFA - - - - - FBbt:00000052 - - - - - - IDOMAL:0000646 - - - https://github.com/biopragmatics/biomappings - @@ -30496,13 +27832,11 @@ plexiform layer. A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm. - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] embryonic tissue AAO:0000480 BILA:0000035 BTO:0000556 EMAPA:36033 - FBbt:00000110 FMA:69069 GAID:1303 MESH:D005855 @@ -30533,28 +27867,12 @@ plexiform layer. Wikipedia:Germ_layer https://github.com/obophenotype/uberon/issues/203 - - - - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - 2012-09-17 - VHOG:0001223 - VHOG - ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 - http://bgee.unil.ch/ - embryonic tissue FMA:69069 - - - - FBbt:00000110 - - @@ -30593,11 +27911,8 @@ plexiform layer. - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. - Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO] - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - ectodermal AAO:0000137 BILA:0000036 BTO:0000315 @@ -30606,7 +27921,6 @@ plexiform layer. EHDAA2:0000428 EMAPA:16069 EV:0100003 - FBbt:00000111 FMA:69070 GAID:1304 MAT:0000155 @@ -30631,14 +27945,14 @@ plexiform layer. ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -30647,31 +27961,6 @@ plexiform layer. Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. Wikipedia:Ectoderm - - - - Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO] - 2012-06-20 - AAO:0000137 - AAO - AAO:EJS - - - - - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - 2012-09-17 - VHOG:0000153 - VHOG - ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 - http://bgee.unil.ch/ - - - - - FBbt:00000111 - - @@ -30697,10 +27986,8 @@ plexiform layer. - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - endodermal AAO:0000139 BILA:0000038 BTO:0000800 @@ -30709,7 +27996,6 @@ plexiform layer. EHDAA2:0000436 EMAPA:16062 EV:0100005 - FBbt:00000125 FMA:69071 GAID:1305 MAT:0000175 @@ -30734,14 +28020,14 @@ plexiform layer. http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -30750,22 +28036,6 @@ plexiform layer. Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. Wikipedia:Endoderm - - - - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - 2012-09-17 - VHOG:0000154 - VHOG - ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 - http://bgee.unil.ch/ - - - - - FBbt:00000125 - - @@ -30792,13 +28062,9 @@ plexiform layer. - + The middle germ layer of the embryo, between the endoderm and ectoderm. - Primary germ layer that is the middle of the embryonic germ layers.[AAO] - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - mesodermal - sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates UBERON:0003263 AAO:0000304 BILA:0000037 @@ -30811,7 +28077,6 @@ plexiform layer. EHDAA:183 EMAPA:16083 EV:0100006 - FBbt:00000126 FMA:69072 GAID:522 MAT:0000174 @@ -30837,20 +28102,14 @@ plexiform layer. mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + - - sometimes not considered primary - - - - - + Bgee:AN @@ -30859,37 +28118,6 @@ plexiform layer. The middle germ layer of the embryo, between the endoderm and ectoderm. Wikipedia:Mesoderm - - - - Primary germ layer that is the middle of the embryonic germ layers.[AAO] - 2012-06-20 - AAO:0000304 - AAO - AAO:EJS - - - - - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - 2012-09-17 - VHOG:0000152 - VHOG - ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 - http://bgee.unil.ch/ - - - - - sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates - https://github.com/obophenotype/uberon/wiki/The-neural-crest - - - - - FBbt:00000126 - - @@ -30936,15 +28164,10 @@ plexiform layer. Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity. consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence - Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO] - the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx - stomodeal - This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity. stomodeal-hypophyseal primordium BTO:0004224 EHDAA2:0001929 EMAPA:16263 - FBbt:00000439 FMA:295846 NCIT:C34306 TAO:0001290 @@ -30977,34 +28200,12 @@ plexiform layer. http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/326 - - - - Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO] - 2012-08-14 - TAO:0001290 - TAO - ZFIN:curator - - - - - the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx - MP:0012522 - NCBITaxon:40674 - stomodeal-hypophyseal primordium XAO:0000269 - - - - FBbt:00000439 - - @@ -31069,7 +28270,6 @@ plexiform layer. - @@ -31084,7 +28284,7 @@ plexiform layer. - + @@ -31099,10 +28299,6 @@ plexiform layer. Cranial nerve fiber tract which is comprised of retinal ganglion cell axons running posterior medially towards the optic chiasm, at which some of the axons cross the midline and after which the structure is termed the optic tract. Transmits visual information from the retina to the brain[ZFA]. Do not classify under 'cranial nerve', as this is not a true nerve - should be classified as evaginated sensory afferent[ISBN:0471888893] - A collection of nerve cells that project visual information from the eyes to the brain. (Source: BioGlossary, www.Biology-Text.com)[TAO] - Fibrous, somatic sensory element covered by a fibrous connective-tissue sheath and is continuous with the layer of nerve cells on the inner surface of the eye.[AAO] - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup (reference 1); The (optic) stalk persists as the optic nerve (reference 2).[well established][VHOG] - (relaion to eye): MA, XAO, AAO and BTO consider this part of the eye. This is in contrast to GO, FMA, EHDAA2 (FMA has a class 'intra-ocular part of optic nerve' which represents the region of overlap). Relation to brain: part of diencephalon in EHDAA2, ZFA. In NIF, has the optic nerve root as part, which is a feature part of the diencphalon 2n optic nerve AAO:0010345 @@ -31150,14 +28346,14 @@ plexiform layer. cranial nerve II - + - + EHDAA2 @@ -31167,40 +28363,6 @@ plexiform layer. ISBN:0471209627 ISBN:0471888893 - - - - A collection of nerve cells that project visual information from the eyes to the brain. (Source: BioGlossary, www.Biology-Text.com)[TAO] - 2012-08-14 - TAO:0000435 - TAO - ZFIN:curator - - - - - Fibrous, somatic sensory element covered by a fibrous connective-tissue sheath and is continuous with the layer of nerve cells on the inner surface of the eye.[AAO] - 2012-06-20 - AAO:0010345 - AAO - AAO:EJS - - - - - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup (reference 1); The (optic) stalk persists as the optic nerve (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0000543 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429, http://medical-dictionary.thefreedictionary.com/optic+stalk - http://bgee.unil.ch/ - - - - - (relaion to eye): MA, XAO, AAO and BTO consider this part of the eye. This is in contrast to GO, FMA, EHDAA2 (FMA has a class 'intra-ocular part of optic nerve' which represents the region of overlap). Relation to brain: part of diencephalon in EHDAA2, ZFA. In NIF, has the optic nerve root as part, which is a feature part of the diencphalon - MA - @@ -31301,7 +28463,7 @@ plexiform layer. - + @@ -31330,11 +28492,6 @@ plexiform layer. - Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO] - Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO] - relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO] - As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG] - cardiac AAO:0010210 BILA:0000020 BTO:0000562 @@ -31378,14 +28535,14 @@ plexiform layer. https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb - + - + MA @@ -31395,42 +28552,6 @@ plexiform layer. Wikipedia:Heart http://orcid.org/0000-0002-6601-2165 - - - - Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO] - 2012-08-14 - TAO:0000114 - TAO - ZFIN:curator - - - - - Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO] - 2012-06-20 - AAO:0010210 - AAO - AAO:BJB - - - - - relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO] - 2012-06-20 - AAO:0010210 - AAO - - - - - As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG] - 2012-09-17 - VHOG:0000276 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481 - http://bgee.unil.ch/ - @@ -31463,13 +28584,7 @@ plexiform layer. - - - - - - - + @@ -31488,14 +28603,10 @@ plexiform layer. - + The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. requires review for applicability to invertebrate structures, e.g. synganglion - Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO] - Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO] - The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO) - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG] AAO:0010478 ABA:Brain BAMS:Br @@ -31511,7 +28622,6 @@ plexiform layer. EHDAA:6485 EMAPA:16894 EV:0100164 - FBbt:00005095 FMA:50801 GAID:571 HBA:4005 @@ -31551,11 +28661,11 @@ plexiform layer. https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb - + - + @@ -31568,13 +28678,13 @@ plexiform layer. - + FMA - + Bgee:AN @@ -31584,46 +28694,6 @@ plexiform layer. Wikipedia:Brain https://github.com/obophenotype/uberon/issues/300 - - - - Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO] - 2012-08-14 - TAO:0000008 - TAO - ZFIN:curator - - - - - Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO] - 2012-06-20 - AAO:0010478 - AAO - AAO:BJB - - - - - The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO) - http://neurolex.org/wiki/Cumbo_terms - - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0000157 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 - http://bgee.unil.ch/ - - - - - FBbt:00005095 - - @@ -31693,7 +28763,6 @@ plexiform layer. Any thin layer or plate. TODO - merge with cell layer? - laminar Wikipedia:Lamina_of_the_vertebral_arch laminar tissue uberon @@ -31749,8 +28818,6 @@ plexiform layer. A decussation of the diencephalon where the fibers of the optic nerve cross. - The point at which fibers of the optic nerves cross.[AAO] - The chiasm has been studied in great detail in some animals, while in others relatively little or nothing is known. Although there are some gross architectural features that are conserved within some animals, such as birds and fish, the general picture is one of diversity. This review will attempt to consider the key features of such diversity of chiasmatic organisation in vertebrates and the mechanisms that sculpt them from the limited literature that is available. However, as so much research has been undertaken on the structure and development of the chiasm in laboratory animals, any review must consider the information that has been gleaned from them and hope that future studies will determine whether the features revealed in these animals, and the underlying mechanisms that generate them, have a common vertebrate plan.[uncertain][VHOG] AAO:0010622 BAMS:DC BAMS:OC @@ -31801,25 +28868,6 @@ plexiform layer. Wikipedia:Optic_chiasm http://orcid.org/0000-0002-6601-2165 - - - - The point at which fibers of the optic nerves cross.[AAO] - 2012-06-20 - AAO:0010622 - AAO - AAO:DSM - - - - - The chiasm has been studied in great detail in some animals, while in others relatively little or nothing is known. Although there are some gross architectural features that are conserved within some animals, such as birds and fish, the general picture is one of diversity. This review will attempt to consider the key features of such diversity of chiasmatic organisation in vertebrates and the mechanisms that sculpt them from the limited literature that is available. However, as so much research has been undertaken on the structure and development of the chiasm in laboratory animals, any review must consider the information that has been gleaned from them and hope that future studies will determine whether the features revealed in these animals, and the underlying mechanisms that generate them, have a common vertebrate plan.[uncertain][VHOG] - 2012-09-17 - VHOG:0000190 - VHOG - DOI:10.1016/j.preteyeres.2005.04.005 Jeffery G, Erskine L, Variations in the architecture and development of the vertebrate optic chiasm. Progress in retinal and eye research (2005) - http://bgee.unil.ch/ - @@ -31881,9 +28929,9 @@ plexiform layer. - - - + + + @@ -31908,7 +28956,12 @@ plexiform layer. - + + + + + + @@ -31929,8 +28982,6 @@ plexiform layer. The transparent anterior portion of the fibrous coat of the eye that serves as the chief refractory structure. - corneal - Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals. In fish, and aquatic vertebrates in general, the cornea plays no role in focusing light, since it has virtually the same refractive index as water AAO:0010344 BTO:0000286 CALOHA:TS-0171 @@ -31964,46 +29015,36 @@ plexiform layer. cornea http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + - - - - - + MA - + MA - + FMA-isa - - - - - definitional - @@ -32037,6 +29078,7 @@ plexiform layer. + @@ -32063,10 +29105,7 @@ plexiform layer. A transparent and refractive lens located posterior to the iris. The lens of camera-type eye refracts light to be focused on the retina. - - The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] - This class excludes compound eye corneal lenses. AAO:0010348 BTO:0000723 CALOHA:TS-0545 @@ -32110,16 +29149,6 @@ plexiform layer. Wikipedia:Lens_(anatomy) http://orcid.org/0000-0002-6601-2165 - - - - The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] - 2012-09-17 - VHOG:0000169 - VHOG - DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007) - http://bgee.unil.ch/ - @@ -32190,16 +29219,13 @@ plexiform layer. - - - - + + + + The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. - The portion of the eye developing from the optic primordium and including the neural retina and the retinal pigment layer. Kimmel et al, 1995.[TAO] - The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] - retinal AAO:0010352 BAMS:R BIRNLEX:1153 @@ -32244,44 +29270,44 @@ plexiform layer. retina http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png - + - + - + - + - + FMA - + FMA - + FMA - + EHDAA2 @@ -32291,25 +29317,6 @@ plexiform layer. Wikipedia:Retina ZFIN:curator - - - - The portion of the eye developing from the optic primordium and including the neural retina and the retinal pigment layer. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000152 - TAO - ZFIN:curator - - - - - The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] - 2012-09-17 - VHOG:0000229 - VHOG - DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007) - http://bgee.unil.ch/ - @@ -32355,8 +29362,8 @@ plexiform layer. - - + + @@ -32364,17 +29371,12 @@ plexiform layer. An organ that detects light. - This class encompasses a variety of light-detecting structures from different phyla with no implication of homology, from the compound insect eye to the vertebrate camera-type eye (distinct classes are provided for each) - ocular - optic - Note that whilst this is classified as an organ, it is in fact more of a unit composed of different structures: in Drosophila, it includes the interommatidial bristle as a part; we consider here the vertebrate eye to include the eyeball/eye proper as a part, with the eye having as parts (when present): eyelids, conjuctiva, BILA:0000017 BTO:0000439 CALOHA:TS-0309 EFO:0000827 EV:0100336 - FBbt:00005162 GAID:69 MAT:0000140 MESH:D005123 @@ -32392,24 +29394,24 @@ plexiform layer. eye - + - + - + PMID:21062451 - + PMID:21062451 @@ -32418,12 +29420,6 @@ plexiform layer. An organ that detects light. https://orcid.org/0000-0002-6601-2165 - - - - FBbt:00005162 - - @@ -32450,8 +29446,6 @@ plexiform layer. Anatomical structure that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO]. - Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO] - Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO] articulation joint AEO:0000182 @@ -32496,24 +29490,6 @@ plexiform layer. Wikipedia:Joint http://dx.plos.org/10.1371/journal.pone.0051070 - - - - Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO] - 2012-08-14 - VSAO:0000101 - VSAO - PSPUB:0000170 - - - - - Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO] - 2012-08-14 - TAO:0000367 - TAO - TAO:pem - @@ -32584,16 +29560,11 @@ plexiform layer. Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes. - An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO] - digestive - many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class AAO:0000129 BILA:0000082 BTO:0000058 CALOHA:TS-1293 EFO:0000793 - EV:0100056 - FBbt:00005055 FMA:7152 GAID:278 MA:0002431 @@ -32630,27 +29601,6 @@ plexiform layer. NLM:alimentary+system Wikipedia:Digestive_system - - - - An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO] - 2012-06-20 - AAO:0000129 - AAO - AAO:BJB - - - - - many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class - MA - - - - - FBbt:00005055 - - @@ -32682,17 +29632,12 @@ plexiform layer. Organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP]. - the cardiovascular system and the lymphatic system are parts of the circulatory system - - Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO] - We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG] AAO:0000959 CALOHA:TS-2103 - MESH:D002319 VHOG:0001248 Wikipedia:Circulatory_system uberon @@ -32715,38 +29660,6 @@ plexiform layer. Wikipedia:Acoelomorpha - - - - - WBbt coelomocyte currently classified as circulating cell - - - - - Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO] - 2012-06-20 - AAO:0000959 - AAO - AAO:BJB - - - - - We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG] - 2012-09-17 - VHOG:0001248 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.493 - http://bgee.unil.ch/ - - - - - MESH:D002319 - - https://github.com/biopragmatics/biomappings - @@ -32774,12 +29687,8 @@ plexiform layer. A subdivision of the muscular system corresponding to a subdisivision of an organism. - - In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here. - AAO:0011066 BTO:0000887 EFO:0001949 - EMAPA:32715 EMAPA:35577 FMA:32558 MA:0000165 @@ -32815,12 +29724,6 @@ plexiform layer. Wikipedia:Muscular_system https://orcid.org/0000-0002-6601-2165 - - - - In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here. - FMA - @@ -32884,7 +29787,7 @@ plexiform layer. - + @@ -32892,11 +29795,6 @@ plexiform layer. The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]. - A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO] - Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO] - Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG] - nervous - neural AAO:0000324 BILA:0000079 BIRNLEX:844 @@ -32907,7 +29805,6 @@ plexiform layer. EHDAA:826 EMAPA:16469 EV:0100162 - FBbt:00005093 FMA:7157 GAID:466 MA:0000016 @@ -32939,14 +29836,14 @@ plexiform layer. http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -32961,40 +29858,6 @@ plexiform layer. Wikipedia:Nervous_system ZFIN:curator - - - - A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO] - 2012-08-14 - TAO:0000396 - TAO - ZFIN:curator - - - - - Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO] - 2012-06-20 - AAO:0000324 - AAO - AAO:BJB - - - - - Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG] - 2012-09-17 - VHOG:0000402 - VHOG - ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.117 - http://bgee.unil.ch/ - - - - - FBbt:00005093 - - @@ -33040,14 +29903,10 @@ plexiform layer. - + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. - Part of the nervous system which includes the brain and spinal cord.[AAO] - The brain and spinal cord. Kimmel et al, 1995.[TAO] - The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO). - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG] AAO:0000090 BAMS:CNS BILA:0000080 @@ -33060,7 +29919,6 @@ plexiform layer. EMAPA:16470 EMAPA:16754 EV:0100163 - FBbt:00005094 FMA:55675 GAID:570 MA:0000167 @@ -33089,7 +29947,7 @@ plexiform layer. central nervous system - + @@ -33103,7 +29961,7 @@ plexiform layer. - + Bgee:AN @@ -33120,46 +29978,6 @@ plexiform layer. Wikipedia:Acoelomorpha - - - - Part of the nervous system which includes the brain and spinal cord.[AAO] - 2012-06-20 - AAO:0000090 - AAO - AAO:BJB - - - - - The brain and spinal cord. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000012 - TAO - ZFIN:curator - - - - - The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO). - BIRNLEX:1099 - - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG] - 2012-09-17 - VHOG:0000293 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 (reference 1), ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 (reference 2), DOI:10.1016/j.cell.2007.02.040 Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud'homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007) (reference 3) - http://bgee.unil.ch/ - - - - - FBbt:00005094 - - @@ -33202,10 +30020,8 @@ plexiform layer. A group of axons linking two or more neuropils and having a common origin, termination[FBbt]. - White matter structure of CNS that contains axons that arise predominantly in one central nervous system part and terminate in another. Tracts are generally named by their region or origin followed by their region of primary termination, e.g., mammillothalamic tract contains axons that arise from neurons in the mammillary bodies and terminate in the thalamus. (CUMBO) BIRNLEX:1649 EV:0100304 - FBbt:00005100 FMA:83847 NLX:147822 axonal tract @@ -33228,18 +30044,6 @@ plexiform layer. http://flybrain.uni-freiburg.de/Flybrain/html/terms/terms.html https://github.com/obophenotype/uberon/issues/286 - - - - White matter structure of CNS that contains axons that arise predominantly in one central nervous system part and terminate in another. Tracts are generally named by their region or origin followed by their region of primary termination, e.g., mammillothalamic tract contains axons that arise from neurons in the mammillary bodies and terminate in the thalamus. (CUMBO) - http://neurolex.org/wiki/Cumbo_terms - - - - - FBbt:00005100 - - @@ -33361,15 +30165,12 @@ plexiform layer. Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information. - An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG] - note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs AAO:0000555 BAMS:SEN BILA:0000099 EFO:0000805 EHDAA2:0003094 EMAPA:16192 - FBbt:00007692 FMA:75259 MA:0002442 MAT:0000031 @@ -33403,22 +30204,6 @@ plexiform layer. Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information. Wikipedia:Sensory_system - - - - An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG] - 2012-09-17 - VHOG:0001674 - VHOG - DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) - http://bgee.unil.ch/ - - - - - FBbt:00007692 - - @@ -33477,7 +30262,6 @@ plexiform layer. BTO:0001886 EFO:0001652 EHDAA2:0003171 - FBbt:00005495 FMA:86589 MAT:0000482 NCIT:C34275 @@ -33511,12 +30295,6 @@ plexiform layer. FB:FBrf0089570 http://flybase.org/reports/FBrf0178740.html - - - - FBbt:00005495 - - @@ -33553,10 +30331,6 @@ plexiform layer. In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted]. - Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO] - The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG] - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] - The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium AAO:0010617 BTO:0001057 CALOHA:TS-2371 @@ -33568,7 +30342,6 @@ plexiform layer. EMAPA:16757 FMA:293882 MAT:0000069 - MESH:D054259 MIAA:0000069 NCIT:C34226 SCTID:362852000 @@ -33602,49 +30375,6 @@ plexiform layer. In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted]. Wikipedia:Neural_tube - - - - Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO] - 2012-06-20 - AAO:0010617 - AAO - AAO:JOR - - - - - The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG] - 2012-09-17 - VHOG:0000307 - VHOG - http://bgee.unil.ch/ - http://medical-dictionary.thefreedictionary.com/neural+tube - - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] - 2012-09-17 - VHOG:0000307 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 - http://bgee.unil.ch/ - - - - - The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium - GO:0021915 - - - - - MESH:D054259 - - - https://github.com/biopragmatics/biomappings - @@ -33675,7 +30405,6 @@ plexiform layer. BIRNLEX:6 CARO:0000000 EHDAA2:0002229 - FBbt:10000000 FMA:62955 HAO:0000000 MA:0000001 @@ -33699,12 +30428,6 @@ plexiform layer. FMA:62955 http://orcid.org/0000-0001-9114-8737 - - - - FBbt:10000000 - - @@ -33748,10 +30471,6 @@ plexiform layer. Muscle tissue which is unstriated, composed primarily of smooth muscle fibers surrounded by a reticulum of collagen and elastic fibers. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length[GO]. - A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO] - Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO] - (...) the first bilateral animals possessed only smooth muscles with the molecular repertoire necessary to build a striated muscle. (...) it is more parsimonious to regard striated muscle cells as a sister cell type to the smooth muscle cells. In this scenario, striated and smooth muscles would have arisen in the stem lineage that led to the Nephrozoa (i.e. all Bilateria exclusive the acoelomorphs) (Hejnol et al., 2009), from an 'acoel-like' smooth muscle, by segregation and divergence of functions and through differential recruitment of additional genes[well established][VHOG] - GO uses visceral and smooth interchangeably. However visceral can also be used in the sense of the viscera. Many fly annotations to smooth muscle terms. If we want to be inclusive of insects have to have a general definition of tissue that includes cells. AAO:0010244 AEO:0000141 BTO:0001260 @@ -33799,34 +30518,6 @@ plexiform layer. GO:0006939 Wikipedia:Smooth_muscle_tissue - - - - A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO] - 2012-08-14 - TAO:0005274 - TAO - ZFIN:curator - - - - - Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO] - 2012-06-20 - AAO:0010244 - AAO - AAO:CAM - - - - - (...) the first bilateral animals possessed only smooth muscles with the molecular repertoire necessary to build a striated muscle. (...) it is more parsimonious to regard striated muscle cells as a sister cell type to the smooth muscle cells. In this scenario, striated and smooth muscles would have arisen in the stem lineage that led to the Nephrozoa (i.e. all Bilateria exclusive the acoelomorphs) (Hejnol et al., 2009), from an 'acoel-like' smooth muscle, by segregation and divergence of functions and through differential recruitment of additional genes[well established][VHOG] - 2012-09-17 - VHOG:0001246 - VHOG - DOI:10.1002/jez.b.21416 Chiodin M, Achatz JG, Wanninger A, Martinez P, Molecular architecture of muscles in an acoel and its evolutionary implications. Journal of Experimental Zoology (2011) - http://bgee.unil.ch/ - @@ -33889,7 +30580,7 @@ plexiform layer. - + Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. Wikipedia: The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri). AEO:0000111 BTO:0002422 @@ -33914,14 +30605,14 @@ plexiform layer. mesothelium http://upload.wikimedia.org/wikipedia/commons/2/25/Mesothelium_peritoneal_wash_high_mag.jpg - + - + FMA @@ -33951,8 +30642,6 @@ plexiform layer. A major subdivision of an organism that is the entire part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. In vertebrares this includes the vertebral column.. - dorsal - In humans, called the back, a large posterior area of the human body, rising from the top of the buttocks to the back of the neck and the shoulders. It is the surface opposite to the chest, its height being defined by the vertebral column (commonly referred to as the spine or backbone) and its breadth being supported by the ribcage and shoulders. The spinal canal runs through the spine and provides nerves to the rest of the body BTO:0001713 CALOHA:TS-2223 EFO:0001405 @@ -34050,13 +30739,6 @@ plexiform layer. Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system. - - Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO] - Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO] - System that provides physical support to the organism.[AAO] - By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG] - skeletal - GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates AAO:0000566 BTO:0001486 CALOHA:TS-1320 @@ -34092,50 +30774,6 @@ plexiform layer. VSAO:0000027 http://dx.plos.org/10.1371/journal.pone.0051070 - - - - Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO] - 2012-08-14 - TAO:0000434 - TAO - TAO:wd - - - - - Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO] - 2012-08-14 - VSAO:0000027 - VSAO - GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 - PSPUB:0000170 - - - - - System that provides physical support to the organism.[AAO] - 2012-06-20 - AAO:0000566 - AAO - AAO:LAP - - - - - By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG] - 2012-09-17 - VHOG:0001254 - VHOG - DOI:10.1159/000324245 Donoghue PCJ, Sansom IJ, Origin and early evolution of vertebrate skeletonization. Microscopy research and technique (2002) - http://bgee.unil.ch/ - - - - - GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates - GO - @@ -34198,10 +30836,6 @@ plexiform layer. A subdivision of the head that has as parts the layers deep to the surface of the anterior surface, including the mouth, eyes, and nose (when present). In vertebrates, this includes the facial skeleton and structures superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, etc). - Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face. - The area that extends from the median ocellus to the oral foramen[HAO]. - facial - The face develops from outward growth of tissue located rostral to the cranium & pharynx. The lower jaw and most of the upper jaw are formed by growth of the first pharyngeal (branchial) arch. The upper incisor region and the nose and forehead (frontal region) are formed from tissue located rostral to the neural tube (frontonasal prominence) BTO:0003369 CALOHA:TS-2216 EMAPA:32763 @@ -34230,26 +30864,6 @@ plexiform layer. A subdivision of the head that has as parts the layers deep to the surface of the anterior surface, including the mouth, eyes, and nose (when present). In vertebrates, this includes the facial skeleton and structures superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, etc). http://orcid.org/0000-0002-6601-2165 - - - - Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face. - FMA:24728 - - - - - The area that extends from the median ocellus to the oral foramen[HAO]. - HAO:0000316 - http://api.hymao.org/api/ref/67791 - NCBITaxon:7399 - - - - - The face develops from outward growth of tissue located rostral to the cranium & pharynx. The lower jaw and most of the upper jaw are formed by growth of the first pharyngeal (branchial) arch. The upper incisor region and the nose and forehead (frontal region) are formed from tissue located rostral to the neural tube (frontonasal prominence) - vanat.cvm.umn.edu/TFFlectPDFs/LectFaceDevelop.pdf - @@ -34294,16 +30908,11 @@ plexiform layer. - + A tube extending from the mouth to the anus. - The alimentary or digestive tract, and associated organs.[TAO] - The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] - FMA also has a term 'gastrointestinal tract', but this includes the liver. - we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509 - we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this gut AAO:0010023 BILA:0000083 @@ -34312,10 +30921,8 @@ plexiform layer. EHDAA2:0000726 EHDAA:518 EMAPA:16247 - FBbt:00003125 FMA:45615 MA:0000917 - MESH:D041981 NCIT:C34082 TAO:0000112 TGMA:0001819 @@ -34337,14 +30944,14 @@ plexiform layer. digestive tract - + - + NCBIBook:NBK10107 @@ -34366,50 +30973,6 @@ plexiform layer. DOI:10.1371/journal.pone.0016309 - - - - The alimentary or digestive tract, and associated organs.[TAO] - 2012-08-14 - TAO:0000112 - TAO - ZFIN:curator - - - - - The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0000309 - VHOG - ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 - http://bgee.unil.ch/ - - - - - FMA also has a term 'gastrointestinal tract', but this includes the liver. - FMA - - - - - we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509 - MA - - - - - FBbt:00003125 - - - - - - MESH:D041981 - - https://github.com/biopragmatics/biomappings - @@ -34437,7 +31000,7 @@ plexiform layer. - + The ciliary muscle is a ring of smooth muscle in the middle layer of the eye that controls the eye's accommodation for viewing objects at varying distances and regulates the flow of aqueous humour through Schlemm's canal. [WP,unvetted]. BTO:0000654 @@ -34460,7 +31023,7 @@ plexiform layer. ciliary muscle http://upload.wikimedia.org/wikipedia/commons/2/28/Gray872.png - + @@ -34479,7 +31042,7 @@ plexiform layer. - + FMA @@ -34551,12 +31114,7 @@ plexiform layer. Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]. - Portion of tissue composed of contractile fibers.[TAO] - It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG] - muscular muscle - AAO:0011066 - EMAPA:32715 EMAPA:37474 EV:0100146 FMA:5022 @@ -34582,25 +31140,6 @@ plexiform layer. Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]. GO:0007517 - - - - Portion of tissue composed of contractile fibers.[TAO] - 2012-08-14 - TAO:0005145 - TAO - ZFIN:curator - - - - - It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG] - 2012-09-17 - VHOG:0001245 - VHOG - ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.75 - http://bgee.unil.ch/ - @@ -34620,7 +31159,8 @@ plexiform layer. - + + @@ -34640,12 +31180,6 @@ plexiform layer. A fold of skin that covers and protects part of the eyeball. Examples: upper eyelid, lower eyelid, nictitating membrane. - blepharic - palpebral - In humans the upper and lower eyelid consists of the following layers, starting anteriorly: (1) skin, (2) a layer of subcutaneous connective tissue, (3) a layer of striated muscle fibres of the orbicularis muscle, (4) a layer of submuscular connective tissue, (5) a fibrous layer, including the tarsal plates, (6) a layer of smooth muscle, (7) the palpebral conjunctiva. - Consider adding 'eye surface', like MA - FMA divides this into skin, fascia, conjunctiva - BTO:0002241 EHDAA2:0000487 EHDAA:9037 @@ -34672,14 +31206,14 @@ plexiform layer. eyelid https://upload.wikimedia.org/wikipedia/commons/8/84/Eye_makeup.jpg - + - + multiple @@ -34688,18 +31222,6 @@ plexiform layer. A fold of skin that covers and protects part of the eyeball. Examples: upper eyelid, lower eyelid, nictitating membrane. http://orcid.org/0000-0002-6601-2165 - - - - Consider adding 'eye surface', like MA - MA - - - - - FMA divides this into skin, fascia, conjunctiva - FMA - @@ -34738,8 +31260,6 @@ plexiform layer. The space in the eye, filled with aqueous humor, and bounded anteriorly by the cornea and a small portion of the sclera and posteriorly by a small portion of the ciliary body, the iris, and part of the crystalline lens. - The part of the eyeball between the cornea and the iris, filled with aqueous humor. [TFD][VHOG] - space in EHDAA2 - consider adding Cavity of anterior chamber of eyeball BTO:0002084 EHDAA2:0000129 EHDAA:9033 @@ -34779,22 +31299,6 @@ plexiform layer. MESH:A09.371.060.067 MP:0005205 - - - - The part of the eyeball between the cornea and the iris, filled with aqueous humor. [TFD][VHOG] - 2012-09-17 - VHOG:0001431 - VHOG - http://bgee.unil.ch/ - http://medical-dictionary.thefreedictionary.com/anterior+chamber - - - - - space in EHDAA2 - consider adding Cavity of anterior chamber of eyeball - EHDAA2 - @@ -34833,7 +31337,9 @@ plexiform layer. + + @@ -34867,7 +31373,6 @@ plexiform layer. The pigmented middle of the three concentric layers that make up an eye, consisting of the iris, ciliary body and choroid[WP,edited]. TODO - check child terms, isa vs partof. See also MA:0001284 ! tunica vasculosa plexus - uveal CALOHA:TS-2228 EMAPA:35901 FMA:58103 @@ -34974,7 +31479,7 @@ plexiform layer. - + @@ -34983,10 +31488,6 @@ plexiform layer. The adjustable membrane, composed of the stroma and pigmented epithelium, located just in front of the crystalline lens within the eye. - The opaque muscular contractile diaphragm suspended in the aqueous humour in front of the lens of the eye. The organ is perforated by the pupil and continues peripherally with the ciliary body. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] - The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] - iridial - The avian iris and ciliary body undergoes a transition from smooth-to-striated muscle during embryonic development [DOI:dx.doi.org/10.1006/dbio.1998.9019] AAO:0010347 BTO:0000653 CALOHA:TS-0491 @@ -35017,14 +31518,14 @@ plexiform layer. iris - + - + XAO @@ -35034,25 +31535,6 @@ plexiform layer. ISBN:0-683-40008-8 MP:0001322 - - - - The opaque muscular contractile diaphragm suspended in the aqueous humour in front of the lens of the eye. The organ is perforated by the pupil and continues peripherally with the ciliary body. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] - 2012-09-17 - VHOG:0000101 - VHOG - http://bgee.unil.ch/ - - - - - The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] - 2012-09-17 - VHOG:0000101 - VHOG - DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007) - http://bgee.unil.ch/ - @@ -35089,6 +31571,7 @@ plexiform layer. + @@ -35096,7 +31579,7 @@ plexiform layer. - + @@ -35105,9 +31588,6 @@ plexiform layer. The smooth stratified squamous epithelium that covers the outer surface of the cornea. - Portion of tissue comprised of four to six layers of nonkeratinized, stratified squamous cells and represents approximately 60% of the thickness of the cornea.[TAO] - In Humans: It consists of several layers of cells. The cells of the deepest layer are columnar; then follow two or three layers of polyhedral cells, the majority of which are prickle cells similar to those found in the stratum mucosum of the cuticle. Lastly, there are three or four layers of squamous cells, with flattened nuclei - In zebrafish: nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals BTO:0000287 CALOHA:TS-0173 EFO:0001917 @@ -35148,14 +31628,14 @@ plexiform layer. corneal epithelium http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png - + - + ISBN:0781772214 @@ -35166,15 +31646,6 @@ plexiform layer. MGI:smb MP:0006000 - - - - Portion of tissue comprised of four to six layers of nonkeratinized, stratified squamous cells and represents approximately 60% of the thickness of the cornea.[TAO] - 2012-08-14 - TAO:0002187 - TAO - ZFIN:ZDB-PUB-061010-3 - @@ -35251,16 +31722,16 @@ plexiform layer. - - + + + - - + @@ -35269,13 +31740,6 @@ plexiform layer. Opaque fibrous outer layer of the eyeball[ZFA,Kardong,WP]. - The sclera, also known as the white part of the eye, is the opaque (usually white, though certain animals, such as horses and lizards, can have black sclera), fibrous, protective, outer layer of the eye containing collagen and elastic fiber. It is derived from the neural crest. In children, it is thinner and shows some of the underlying pigment, appearing slightly blue. In the elderly, however, fatty deposits on the sclera can make it appear slightly yellow. The sclera forms the posterior five sixths of the connective tissue coat of the globe. It is continuous with the dura mater and the cornea, and maintains the shape of the globe, offering resistance to internal and external forces, and provides an attachment for the extraocular muscle insertions. The sclera is perforated by plenty of nerves and vessels passing through the posterior scleral foramen, the hole that is formed by the optic nerve. At the optic disk the outer two-thirds of the sclera continues with the dura mater (outer coat of the brain) via the dural sheath of the optic nerve. The inner third joins with some choroidal tissue to form a plate (lamina cribrosa) across the optic nerve with perforations through which the optic fibers (fasciculi). The thickness of the sclera varies from 1mm at the posterior pole to 0.3 mm just behind the rectus muscle insertions. The sclera's blood vessels are mainly on the surface, and together with the conjunctiva (which lies on top) This is a thin layer covering the sclera. Along with the vessels of the conjunctiva, those of the sclera renders the inflamed eye bright red. [WP,unvetted][Wikipedia:Sclera]. - The tough, usually white, outer coat of the eyeball, covering all the posterior surface and continuous anteriorly with the cornea. [TFD][VHOG] - scleral - in fish, reptiles and monotremes the connective tissue of the sclera is skeletal - continuous with the dura mater and the cornea; The sclera forms the posterior five-sixths of the connective tissue coat of the globe. - Majority derives from NC that surrounds optic cup of neurectoderm; a small temporal portion develops from the mesoderm that contributes to striated extra-ocular muscles and vascular endothelia[Rada&Johnson]. - Seko et al demonstrate chondrogenic potential and identify this as connective tissue[DOI:10.1371/journal.pone.0003709]. AAO:0010354 BTO:0001606 EMAPA:19027 @@ -35302,48 +31766,36 @@ plexiform layer. sclera http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + - - - - - + FMA - + ZFA - + ISBN:0781772214 - - - - - cjm - ISBN:0781772214 - Wikipedia - @@ -35351,22 +31803,6 @@ plexiform layer. Wikipedia:Sclera ZFIN:ZDB-PUB-050701-15 - - - - The sclera, also known as the white part of the eye, is the opaque (usually white, though certain animals, such as horses and lizards, can have black sclera), fibrous, protective, outer layer of the eye containing collagen and elastic fiber. It is derived from the neural crest. In children, it is thinner and shows some of the underlying pigment, appearing slightly blue. In the elderly, however, fatty deposits on the sclera can make it appear slightly yellow. The sclera forms the posterior five sixths of the connective tissue coat of the globe. It is continuous with the dura mater and the cornea, and maintains the shape of the globe, offering resistance to internal and external forces, and provides an attachment for the extraocular muscle insertions. The sclera is perforated by plenty of nerves and vessels passing through the posterior scleral foramen, the hole that is formed by the optic nerve. At the optic disk the outer two-thirds of the sclera continues with the dura mater (outer coat of the brain) via the dural sheath of the optic nerve. The inner third joins with some choroidal tissue to form a plate (lamina cribrosa) across the optic nerve with perforations through which the optic fibers (fasciculi). The thickness of the sclera varies from 1mm at the posterior pole to 0.3 mm just behind the rectus muscle insertions. The sclera's blood vessels are mainly on the surface, and together with the conjunctiva (which lies on top) This is a thin layer covering the sclera. Along with the vessels of the conjunctiva, those of the sclera renders the inflamed eye bright red. [WP,unvetted][Wikipedia:Sclera]. - Wikipedia:Sclera - - - - - The tough, usually white, outer coat of the eyeball, covering all the posterior surface and continuous anteriorly with the cornea. [TFD][VHOG] - 2012-09-17 - VHOG:0001274 - VHOG - http://bgee.unil.ch/ - http://medical-dictionary.thefreedictionary.com/sclera - @@ -35399,7 +31835,7 @@ plexiform layer. - + @@ -35408,7 +31844,6 @@ plexiform layer. The thickened portion of the vascular tunic, which lies between the choroid and the iris, composed of ciliary muscle and ciliary processes. - The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] AAO:0010341 BTO:0000260 CALOHA:TS-0694 @@ -35438,14 +31873,14 @@ plexiform layer. ciliary body http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + ISBN:0781772214 @@ -35456,16 +31891,6 @@ plexiform layer. MP:0005099 Wikipedia:Ciliary_body - - - - The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] - 2012-09-17 - VHOG:0000102 - VHOG - DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007) - http://bgee.unil.ch/ - @@ -35493,14 +31918,14 @@ plexiform layer. - + - + @@ -35529,8 +31954,6 @@ plexiform layer. Vascular layer containing connective tissue, of the eye lying between the retina and the sclera. The choroid provides oxygen and nourishment to the outer layers of the retina. Along with the ciliary body and iris, the choroid forms the uveal tract[WP]. check choroid vs choroid layer; check ZFA/TAO placement - no homology assertion in VHOG. Note this is entirely in the posterior region of eyeball in ZFA - choroidal - MP treats posterior uvea and optic choroid as distinct BTO:0001829 CALOHA:TS-2054 EMAPA:19077 @@ -35563,24 +31986,24 @@ plexiform layer. optic choroid http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + MA - + Wikipedia @@ -35595,12 +32018,6 @@ plexiform layer. Vascular layer containing connective tissue, of the eye lying between the retina and the sclera. The choroid provides oxygen and nourishment to the outer layers of the retina. Along with the ciliary body and iris, the choroid forms the uveal tract[WP]. Wikipedia:Choroid - - - - MP treats posterior uvea and optic choroid as distinct - MP - @@ -35674,13 +32091,19 @@ plexiform layer. + - + + + + + + @@ -35700,9 +32123,6 @@ plexiform layer. The lamellated connective tissue of the cornea between the Bowman and Descemet membranes. - Portion of tissue that is located basal to Bowman's layer and distal to Descemet's membrane and is comprised largely of connective tissue.[TAO] - relationship type change: subclass tissue (CARO:0000043) CHANGED TO: develops_from tissue (UBERON:0000479)[TAO] - relationship type change: subclass tissue (CARO:0000043) CHANGED TO: has_developmental_contribution_from tissue (UBERON:0000479)[TAO] substantia propria CALOHA:TS-1138 EFO:0002514 @@ -35729,18 +32149,6 @@ plexiform layer. substantia propria of cornea http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png - - - - - - - - - cjm - ISBN:0781772214 - Wikipedia - @@ -35749,31 +32157,6 @@ plexiform layer. MESH:A09.371.060.217.228 MP:0005300 - - - - Portion of tissue that is located basal to Bowman's layer and distal to Descemet's membrane and is comprised largely of connective tissue.[TAO] - 2012-08-14 - TAO:0002189 - TAO - ZFIN:ZDB-PUB-061010-3 - - - - - relationship type change: subclass tissue (CARO:0000043) CHANGED TO: develops_from tissue (UBERON:0000479)[TAO] - 2012-08-14 - TAO:0002189 - TAO - - - - - relationship type change: subclass tissue (CARO:0000043) CHANGED TO: has_developmental_contribution_from tissue (UBERON:0000479)[TAO] - 2012-08-14 - TAO:0002189 - TAO - @@ -35813,9 +32196,9 @@ plexiform layer. - - - + + + A double layer covering the ciliary body that produces aqueous humor. BTO:0001770 @@ -35835,15 +32218,15 @@ plexiform layer. ciliary epithelium - + - + - + @@ -35856,19 +32239,19 @@ plexiform layer. - + MA - + MP - + Wikipedia @@ -35901,6 +32284,7 @@ plexiform layer. + @@ -35915,7 +32299,6 @@ plexiform layer. Any of the layers that make up the retina[MP]. - MA does not treat internal/external limiting memranes as layers - these are classified as laminae. Here we follow other ontologies in grouping with other layers. MA also treats retinal pigment epithelium and neural retina epithelium as distinct from the layers. We follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers - these are also classified as layers, giving us over the usual 10 layers AAO:0010353 EMAPA:35742 FMA:58617 @@ -35940,12 +32323,6 @@ plexiform layer. Any of the layers that make up the retina[MP]. MP:0003727 - - - - MA does not treat internal/external limiting memranes as layers - these are classified as laminae. Here we follow other ontologies in grouping with other layers. MA also treats retinal pigment epithelium and neural retina epithelium as distinct from the layers. We follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers - these are also classified as layers, giving us over the usual 10 layers - MA - @@ -35983,7 +32360,6 @@ plexiform layer. - @@ -35991,7 +32367,7 @@ plexiform layer. - + @@ -36006,9 +32382,6 @@ plexiform layer. A monolayer of pigmented epithelium covering the neural retina; develops from the outer of the two layers of the optic cup[ZFA]. the pigmented cell layer just outside the neurosensory retina that nourishes retinal visual cells, and is firmly attached to the underlying choroid and overlying retinal visual cells[WP]. - A monolayer of pigmented epithelium covering the neural retina; develops from the outer of the two layers of the optic cup. Kimmel et al, 1995.[TAO] - The monolayer of pigmented epithelium covering the neural retina.[AAO] - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] AAO:0011096 BTO:0001177 CALOHA:TS-0869 @@ -36052,14 +32425,14 @@ plexiform layer. pigmented layer of retina http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png - + - + Wikipedia @@ -36069,34 +32442,6 @@ plexiform layer. Wikipedia:Retinal_pigment_epithelium ZFIN:curator - - - - A monolayer of pigmented epithelium covering the neural retina; develops from the outer of the two layers of the optic cup. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000144 - TAO - ZFIN:curator - - - - - The monolayer of pigmented epithelium covering the neural retina.[AAO] - 2012-06-20 - AAO:0011096 - AAO - ZFA:0000144 - - - - - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] - 2012-09-17 - VHOG:0000536 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 - http://bgee.unil.ch/ - @@ -36163,7 +32508,7 @@ plexiform layer. - + @@ -36171,8 +32516,6 @@ plexiform layer. The layer within the retina where the photoreceptor cell receptor segments reside. - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] - we follow MA and ZFA in subdividing this into inner and outer segments EMAPA:35686 FMA:58680 MA:0001308 @@ -36197,14 +32540,14 @@ plexiform layer. photoreceptor layer of retina http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png - + - + ZFA @@ -36214,22 +32557,6 @@ plexiform layer. Wikipedia:Layer_of_rods_and_cones ZFA:0000143 - - - - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] - 2012-09-17 - VHOG:0001165 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 - http://bgee.unil.ch/ - - - - - we follow MA and ZFA in subdividing this into inner and outer segments - MA - @@ -36377,7 +32704,12 @@ plexiform layer. - + + + + + + @@ -36392,7 +32724,6 @@ plexiform layer. The layer within the retina where the photoreceptor cell bodies reside. - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] outer nuclear layer BAMS:Ronl BTO:0005600 @@ -36424,33 +32755,12 @@ plexiform layer. outer nuclear layer of retina - - - - - - - - - soma - ZFA - The layer within the retina where the photoreceptor cell bodies reside. ZFA:0001464 - - - - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] - 2012-09-17 - VHOG:0001170 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 - http://bgee.unil.ch/ - @@ -36522,8 +32832,6 @@ plexiform layer. The layer within the retina where the bipolar cells synapse with the photoreceptor cells[ZFA]. Between the inner and outer nuclear layers, the outer plexiform layer (OPL) contains connections between the photoreceptors and bipolar and horizontal cells[GO]. - The layer within the retina where the bipolar cells synapse with the photoreceptor cells.[TAO] - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] external plexiform layer BAMS:Ropl BTO:0003174 @@ -36558,25 +32866,6 @@ plexiform layer. The layer within the retina where the bipolar cells synapse with the photoreceptor cells[ZFA]. Between the inner and outer nuclear layers, the outer plexiform layer (OPL) contains connections between the photoreceptors and bipolar and horizontal cells[GO]. ZFA:0001330 - - - - The layer within the retina where the bipolar cells synapse with the photoreceptor cells.[TAO] - 2012-08-14 - TAO:0001330 - TAO - ZFIN:curator - - - - - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] - 2012-09-17 - VHOG:0001171 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 - http://bgee.unil.ch/ - @@ -36667,8 +32956,6 @@ plexiform layer. Cytoarchitectural layer of retina containing closely packed cell bodies, the majority of which are bipolar cells (adapted from Wikipedia). - The layer of the retina composed of the cell bodies of bipolar cells, horizontal cells, and some of the cell bodies of amacrine cells[BTO:0003176]. - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] BAMS:Rinl BTO:0003176 EMAPA:19155 @@ -36708,22 +32995,6 @@ plexiform layer. Cytoarchitectural layer of retina containing closely packed cell bodies, the majority of which are bipolar cells (adapted from Wikipedia). NLX:93816 - - - - The layer of the retina composed of the cell bodies of bipolar cells, horizontal cells, and some of the cell bodies of amacrine cells[BTO:0003176]. - BTO:0003176 - - - - - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] - 2012-09-17 - VHOG:0001167 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 - http://bgee.unil.ch/ - @@ -36769,7 +33040,7 @@ plexiform layer. - + @@ -36790,9 +33061,6 @@ plexiform layer. Cytoarchitectural layer of retina that contains somata of retinal ganglion cells, bounded by the stratum opticum and the inner plexiform layer. - a layer of the retina that consists of retinal ganglion cells[WP]. innermost nuclear layer of the retina, which contains neurons that project axons through the optic nerve to the brain[Wikipedia:Ganglion_cell_layer]. - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] - NIFSTD class appears to be retired in nlx[http://neurolex.org/wiki/Nlx_anat_1005030] ganglion cell layer BAMS:Rgcl BTO:0003398 @@ -36828,7 +33096,7 @@ plexiform layer. ganglionic layer of retina http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png - + @@ -36841,7 +33109,7 @@ plexiform layer. - + FMA @@ -36850,28 +33118,6 @@ plexiform layer. Cytoarchitectural layer of retina that contains somata of retinal ganglion cells, bounded by the stratum opticum and the inner plexiform layer. NLX:36500 - - - - a layer of the retina that consists of retinal ganglion cells[WP]. innermost nuclear layer of the retina, which contains neurons that project axons through the optic nerve to the brain[Wikipedia:Ganglion_cell_layer]. - Wikipedia:Ganglion_cell_layer - - - - - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] - 2012-09-17 - VHOG:0001166 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 - http://bgee.unil.ch/ - - - - - NIFSTD class appears to be retired in nlx[http://neurolex.org/wiki/Nlx_anat_1005030] - NIF - @@ -36917,7 +33163,7 @@ plexiform layer. - + @@ -36943,7 +33189,6 @@ plexiform layer. Layer of the retina formed by expansion of the fibers of the optic nerve. - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] UBERON:0005888 nerve fiber layer DMBA:15652 @@ -36973,14 +33218,14 @@ plexiform layer. nerve fiber layer of retina - + - + FMA @@ -36990,16 +33235,6 @@ plexiform layer. ISBN:0-914294-08-3 MGI:smb - - - - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] - 2012-09-17 - VHOG:0001169 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 - http://bgee.unil.ch/ - @@ -37053,6 +33288,7 @@ plexiform layer. + @@ -37079,7 +33315,6 @@ plexiform layer. The row of fused Muller cell processes and astrocytes that separates the retinal nerve fiber layer from the vitreous[MP]. TODO - check frog/fish - Membrane on the apical surface of the retina. The retinal vasculature becomes adhered to the apical surface of the ILM by 30dpf[ZFIN:ZDB-PUB-071023-7, ZFIN:ZDB-PUB-120529-3]. ILM EMAPA:36519 FMA:58689 @@ -37117,12 +33352,6 @@ plexiform layer. The row of fused Muller cell processes and astrocytes that separates the retinal nerve fiber layer from the vitreous[MP]. MP:0010235 - - - - Membrane on the apical surface of the retina. The retinal vasculature becomes adhered to the apical surface of the ILM by 30dpf[ZFIN:ZDB-PUB-071023-7, ZFIN:ZDB-PUB-120529-3]. - ZFIN:ZDB-PUB-071023-7, ZFIN:ZDB-PUB-120529-3 - @@ -37228,10 +33457,6 @@ plexiform layer. Cytoarchitectural layer of the retina that is made up of a dense reticulum of fibrils formed by interlaced dendrites of retinal ganglion cells and cells of the inner nuclear layer (adapted from Wikipedia). - The inner plexiform layer (IPL) is positioned between the INL and the ganglion cell layer and contains the dendrites of RGCs and processes of bipolar and amacrine cells[GO][GO:0010842]. - The layer within the retina where the bipolar cells synapse with the dendrites of the ganglion cells.[TAO] - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] - http://neurolex.org/wiki/Nlx_anat_1005032 appears to be retired BAMS:Ripl BTO:0003175 EMAPA:35741 @@ -37270,31 +33495,6 @@ plexiform layer. Cytoarchitectural layer of the retina that is made up of a dense reticulum of fibrils formed by interlaced dendrites of retinal ganglion cells and cells of the inner nuclear layer (adapted from Wikipedia). NLX:20558 - - - - The inner plexiform layer (IPL) is positioned between the INL and the ganglion cell layer and contains the dendrites of RGCs and processes of bipolar and amacrine cells[GO][GO:0010842]. - GO:0010842 - - - - - The layer within the retina where the bipolar cells synapse with the dendrites of the ganglion cells.[TAO] - 2012-08-14 - TAO:0001329 - TAO - ZFIN:curator - - - - - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] - 2012-09-17 - VHOG:0001168 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 - http://bgee.unil.ch/ - @@ -37358,7 +33558,12 @@ plexiform layer. - + + + + + + @@ -37366,9 +33571,6 @@ plexiform layer. A thick watery refractive medium that fills the space between the lens and the cornea[WP]. - The fluid produced by the ciliary process in the eye and occupying the anterior and posterior chambers. It provides nourishment for the lens and cornea and maintains the ocular pressure, and hence the optical integrity of the eyeball. [TFD][VHOG] - (...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG] - FMA says A+P chambers, and MA states A chamber. ZFA states A chamber and tha it is produced primarily by dorsal ciliary epithelial cells.To be investigated across taxa. EHDAA2:0000139 EHDAA:10196 EMAPA:18232 @@ -37394,50 +33596,12 @@ plexiform layer. aqueous humor of eyeball http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - - - - - - - - - FMA def states A and P - located_in in EHDAA2 - VHOG - A thick watery refractive medium that fills the space between the lens and the cornea[WP]. Wikipedia:Aqueous_humor - - - - The fluid produced by the ciliary process in the eye and occupying the anterior and posterior chambers. It provides nourishment for the lens and cornea and maintains the ocular pressure, and hence the optical integrity of the eyeball. [TFD][VHOG] - 2012-09-17 - VHOG:0000548 - VHOG - http://bgee.unil.ch/ - http://medical-dictionary.thefreedictionary.com/aqueous+humour - - - - - (...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0000548 - VHOG - DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424 and p.426 and p.429 and Figure 12-24 - http://bgee.unil.ch/ - - - - - FMA says A+P chambers, and MA states A chamber. ZFA states A chamber and tha it is produced primarily by dorsal ciliary epithelial cells.To be investigated across taxa. - FMA - @@ -37492,7 +33656,6 @@ plexiform layer. EV:0100344 FMA:58822 MA:0001286 - MESH:D014822 NCIT:C13323 UMLS:C0229096 VHOG:0000795 @@ -37526,13 +33689,6 @@ plexiform layer. portion of vitreous humor FMA:67388 - - - - MESH:D014822 - - https://github.com/biopragmatics/biomappings - @@ -37584,6 +33740,7 @@ plexiform layer. + @@ -37591,7 +33748,12 @@ plexiform layer. - + + + + + + @@ -37615,23 +33777,12 @@ plexiform layer. vitreous body http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - - - - FMA - - - - - neural ectoderm of optic cup - ISBN:0781772214 - @@ -37763,8 +33914,8 @@ plexiform layer. - - + + @@ -37773,7 +33924,6 @@ plexiform layer. Any of the parts of the eye that lie in front of, or ventral to, the lens (inclusive). - EMAPA:36594 FMA:58865 MA:0002484 @@ -37797,26 +33947,16 @@ plexiform layer. anterior segment of eyeball http://upload.wikimedia.org/wikipedia/commons/b/ba/Cataract_in_human_eye.png - + - - - - - + FMA - - - - - cjm - @@ -37831,14 +33971,6 @@ plexiform layer. MESH:A09.371.060 MP:0005193 - - - - - ZFA - https://github.com/obophenotype/uberon/issues/378 - pending - @@ -37865,8 +33997,8 @@ plexiform layer. - - + + @@ -37896,26 +34028,16 @@ plexiform layer. posterior segment of eyeball http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - - - - - + FMA - - - - - cjm - @@ -37949,9 +34071,10 @@ plexiform layer. - - - + + + + @@ -37972,12 +34095,10 @@ plexiform layer. The mucous membrane that lines the inner surface of the eyelids and the front of the eyeball. - conjunctival AAO:0010343 BTO:0003415 CALOHA:TS-2232 EFO:0000374 - EMAPA:18233 EV:0100340 FMA:59011 GAID:898 @@ -38001,15 +34122,15 @@ plexiform layer. conjunctiva http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png - + - + - + @@ -38022,19 +34143,19 @@ plexiform layer. - + cjm - + MA - + ISBN:0781772214 @@ -38085,7 +34206,6 @@ plexiform layer. - @@ -38098,15 +34218,15 @@ plexiform layer. - + + + + + + The most anterior region of the brain including both the telencephalon and diencephalon. - Most anterior of the three regions of the brain consisting of the telencephalon and diencephalon.[AAO] - The most anterior region the brain including both the telencephalon and diencephalon. Kimmel et al, 1995.[TAO] - relationship loss: develops_from forebrain neural tube (TAO:0007041)[TAO] - In craniate embryos, neural expression of Distal-less-related genes is exclusively in the forebrain (...). Because the major neural expression domain of amphioxus AmphiDll is in the anterior three-fourths of the cerebral vesicle, we suggest that this region of the neural tube is homologous to parts of the craniate forebrain. This conclusion is strongly supported by three-dimensional, computer-assisted reconstruction of the neural tube of amphioxus based on serial transmission electron microscopy. At the neuroanatomical level, a number of detailed homologies are indicated between the anterior three-fourths of the amphioxus cerebral vesicle and the diencephalic region of the craniate forebrain. If one assumes that the amphioxus condition fairly represents the nervous system of the proximate ancestor of the craniates, one can suggest that they evolved from a creature that had the beginnings of a forebrain.[well established][VHOG] - prosencephalic FB AAO:0010147 BAMS:FB @@ -38145,16 +34265,6 @@ plexiform layer. forebrain http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg - - - - - - - - - definitional - @@ -38162,42 +34272,6 @@ plexiform layer. Wikipedia:Forebrain ZFIN:ZDB-PUB-961014-576 - - - - Most anterior of the three regions of the brain consisting of the telencephalon and diencephalon.[AAO] - 2012-06-20 - AAO:0010147 - AAO - AAO:BJB - - - - - The most anterior region the brain including both the telencephalon and diencephalon. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000109 - TAO - ZFIN:curator - - - - - relationship loss: develops_from forebrain neural tube (TAO:0007041)[TAO] - 2012-08-14 - TAO:0000109 - TAO - - - - - In craniate embryos, neural expression of Distal-less-related genes is exclusively in the forebrain (...). Because the major neural expression domain of amphioxus AmphiDll is in the anterior three-fourths of the cerebral vesicle, we suggest that this region of the neural tube is homologous to parts of the craniate forebrain. This conclusion is strongly supported by three-dimensional, computer-assisted reconstruction of the neural tube of amphioxus based on serial transmission electron microscopy. At the neuroanatomical level, a number of detailed homologies are indicated between the anterior three-fourths of the amphioxus cerebral vesicle and the diencephalic region of the craniate forebrain. If one assumes that the amphioxus condition fairly represents the nervous system of the proximate ancestor of the craniates, one can suggest that they evolved from a creature that had the beginnings of a forebrain.[well established][VHOG] - 2012-09-17 - VHOG:0000383 - VHOG - PMID:8787764 Holland ND, Panganiban G, Henyey EL, Holland LZ, Sequence and developmental expression of AmphiDll, an amphioxus Distal-less gene transcribed in the ectoderm, epidermis and nervous system: insights into evolution of craniate forebrain and neural crest. Development (1996) - http://bgee.unil.ch/ - @@ -38226,26 +34300,23 @@ plexiform layer. - - + + + + + + - + The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO]. developmental relationships need revised - - - Middle part of the brain composed of the optic tectum and penducular region.[AAO] - The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally. Kimmel et al, 1995.[TAO] - Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] - mesencephalic - part of brainstem in ABA - we reject this in favor of ISBN:0471888893 which has an implicit overlaps relationships MB AAO:0010149 BAMS:MES @@ -38288,24 +34359,14 @@ plexiform layer. midbrain http://upload.wikimedia.org/wikipedia/commons/f/f9/Human_brain_inferior_view_description.JPG - - - - - + - - definitional - - - - - + Bgee:AN @@ -38314,57 +34375,6 @@ plexiform layer. The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO]. GO:0030901 - - - - - ZFA - https://github.com/obophenotype/uberon/issues/378 - ABA - pending - - - - - - ZFA - ABA - pending - - - - - Middle part of the brain composed of the optic tectum and penducular region.[AAO] - 2012-06-20 - AAO:0010149 - AAO - AAO:BJB - - - - - The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000128 - TAO - ZFIN:curator - - - - - Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] - 2012-09-17 - VHOG:0000069 - VHOG - DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999) - http://bgee.unil.ch/ - - - - - part of brainstem in ABA - we reject this in favor of ISBN:0471888893 which has an implicit overlaps relationships - ABA - @@ -38400,7 +34410,6 @@ plexiform layer. - @@ -38408,23 +34417,25 @@ plexiform layer. - + + + + + + - + + + + + + The division of the forebrain that develops from the foremost primary cerebral vesicle. - - - - The more posterior and ventral of two forebrain neuromeres, the other being the telencephalon; major derivatives are the eye cups, the brain pretectal region, the thalamus, hypothalamus, and epithalamus (including the habenula and epiphysis). Kimmel et al, 1995.[TAO] - Unpaired part of the forebrain comprised of three major parts; the epithalamus, thalamus, and hypothalamus.[AAO] - Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] - diencephalic - in ABA, this is part of the brain stem DiE AAO:0010481 BAMS:DI @@ -38478,88 +34489,12 @@ plexiform layer. diencephalon http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg - - - - - - - - - - - - - definitional - - - - - - definitional - The division of the forebrain that develops from the foremost primary cerebral vesicle. Wikipedia:Diencephalon - - - - - ZFA - ABA - https://github.com/obophenotype/uberon/issues/378 - pending - - - - - - ABA - - - - - - not well differentiated from the cerebrum. (Ariens, p. 868) - PMID:8932866 - - - - - The more posterior and ventral of two forebrain neuromeres, the other being the telencephalon; major derivatives are the eye cups, the brain pretectal region, the thalamus, hypothalamus, and epithalamus (including the habenula and epiphysis). Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000101 - TAO - ZFIN:curator - - - - - Unpaired part of the forebrain comprised of three major parts; the epithalamus, thalamus, and hypothalamus.[AAO] - 2012-06-20 - AAO:0010481 - AAO - AAO:BJB - - - - - Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] - 2012-09-17 - VHOG:0000318 - VHOG - DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999) - http://bgee.unil.ch/ - - - - - in ABA, this is part of the brain stem - ABA - @@ -38619,6 +34554,7 @@ plexiform layer. + @@ -38651,9 +34587,6 @@ plexiform layer. Organ component of neuraxis that has as its parts the medullary reticular formation, inferior olivary complex and cochlear nuclear complex, among other structures[FMA]. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate[GO]. - Posterior portion of the hindbrain which controls respiration, heartbeat, digestion, and swallowing as well as some locomotor responses.[AAO] - The posterior region of the brain that is continuous with the spinal cord. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-17, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] - Classical anatomical studies subdivided the vertebrate rhombencephalon into pons and medulla oblongata. (...) The medulla oblongata appears therefore as a tagma, that is, a group of segmental units (pseudorhombomeres, in this case) sharing some morphological and molecular characteristics, and in some aspects different from the segmental units present in adjoining brain regions, pons and spinal cord.[well established][VHOG] bulb medulla AAO:0010486 @@ -38708,34 +34641,6 @@ plexiform layer. GO:0021550 Wikipedia:Bone_marrow_of_ovary_oblongata - - - - Posterior portion of the hindbrain which controls respiration, heartbeat, digestion, and swallowing as well as some locomotor responses.[AAO] - 2012-06-20 - AAO:0010486 - AAO - AAO:BJB - - - - - The posterior region of the brain that is continuous with the spinal cord. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-17, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] - 2012-09-17 - VHOG:0000181 - VHOG - http://bgee.unil.ch/ - - - - - Classical anatomical studies subdivided the vertebrate rhombencephalon into pons and medulla oblongata. (...) The medulla oblongata appears therefore as a tagma, that is, a group of segmental units (pseudorhombomeres, in this case) sharing some morphological and molecular characteristics, and in some aspects different from the segmental units present in adjoining brain regions, pons and spinal cord.[well established][VHOG] - 2012-09-17 - VHOG:0000181 - VHOG - DOI:10.1016/j.ydbio.2008.08.017 Marin F, Aroca P, Puelles L, Hox gene colinear expression in the avian medulla oblongata is correlated with pseudorhombomeric domains. Developmental Biology (2008) - http://bgee.unil.ch/ - @@ -38833,7 +34738,6 @@ plexiform layer. BM:Tel-OT DHBA:10589 DMBA:17785 - EMAPA:16678 EMAPA:35617 FMA:62046 GAID:735 @@ -38933,10 +34837,9 @@ plexiform layer. - + Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP]. - Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG] MTg tegmentum BAMS:MTg @@ -38950,7 +34853,6 @@ plexiform layer. HBA:9002 MA:0000212 MAT:0000452 - MESH:D013681 SCTID:362392007 TAO:0000160 UMLS:C0039441 @@ -38974,14 +34876,14 @@ plexiform layer. midbrain tegmentum http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray712.png - + - + ZFA @@ -38992,16 +34894,6 @@ plexiform layer. ISBN:0471888893 Wikipedia:Midbrain_tegmentum - - - - Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG] - 2012-09-17 - VHOG:0001367 - VHOG - DOI:10.1016/j.brainresbull.2005.05.001 Villar-Cheda B, Abalo XM, Anadon R, Rodicio MC, The tegmental proliferation region in the sea lamprey. Brain Research Bulletin (2005) - http://bgee.unil.ch/ - @@ -39016,13 +34908,6 @@ plexiform layer. tegmentum ISBN:0471888893 - - - - MESH:D013681 - - https://github.com/biopragmatics/biomappings - @@ -39161,14 +35046,15 @@ plexiform layer. + - - + + @@ -39181,7 +35067,7 @@ plexiform layer. - + @@ -39197,11 +35083,6 @@ plexiform layer. A vessel through which blood circulates in the body. consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus - Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG] - Any of the vessels through which blood circulates in the body.[AAO] - The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] - annelids have blood vessels, but this class is not applicable to annelids. - FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX vascular element AAO:0011004 AEO:0000207 @@ -39240,34 +35121,34 @@ plexiform layer. blood vessel http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg - + - + - + - + AEO - + EHDAA2 - + GO:0072360 @@ -39277,40 +35158,6 @@ plexiform layer. BTO:0001102 Wikipedia:Blood_vessel - - - - Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG] - 2012-09-17 - VHOG:0001250 - VHOG - http://bgee.unil.ch/ - - - - - Any of the vessels through which blood circulates in the body.[AAO] - 2012-06-20 - AAO:0011004 - AAO - AAO:EJS - - - - - The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] - 2012-09-17 - VHOG:0001250 - VHOG - DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006) - http://bgee.unil.ch/ - - - - - FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX - FMA - @@ -39361,7 +35208,6 @@ plexiform layer. - @@ -39471,7 +35317,6 @@ plexiform layer. A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA]. - endothelial BTO:0000393 CALOHA:TS-0278 EFO:0002548 @@ -39525,7 +35370,6 @@ plexiform layer. A nervous system structure composed primarily of nerve cell bodies (somas). May also include dendrites and the initial unmyelinated portion of axons. - Multi-tissue comprised of neurons, dendrites, axon terminals, glial cells, and capillaries.[TAO] AEO:0001012 EHDAA2:0003136 EHDAA2_RETIRED:0004658 @@ -39533,7 +35377,6 @@ plexiform layer. FMA:67242 HBA:4006 MA:0001112 - MESH:D066128 NCIT:C32695 TAO:0002197 UMLS:C0018220 @@ -39565,29 +35408,12 @@ plexiform layer. Wikipedia:Gray_matter http://orcid.org/0000-0002-6601-2165 - - - - Multi-tissue comprised of neurons, dendrites, axon terminals, glial cells, and capillaries.[TAO] - 2012-08-14 - TAO:0002197 - TAO - ZFIN:curator - EMAPA:37596 MA:th - - - - MESH:D066128 - - - https://github.com/biopragmatics/biomappings - @@ -39633,8 +35459,12 @@ plexiform layer. - - + + + + + + @@ -39647,18 +35477,10 @@ plexiform layer. - + The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA]. - - - Posterior part of the brain consisting of the cerebellum and medulla oblongata.[AAO] - The most posterior of the three principal regions of the brain, forming the rhombencephalon and all or most of the metencephalon. Kimmel et al, 1995.[TAO] - relationship loss: develops_from hindbrain neural tube (TAO:0007043)[TAO] - Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] - rhombencephalic - in MA, brainstem and hindbrain and part-of siblings under brain, consistent with FMA and NIF. See also notes for cerebellum. We weaken the relation in ABA to overlaps AAO:0010150 BAMS:HB BIRNLEX:942 @@ -39698,25 +35520,14 @@ plexiform layer. hindbrain http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg - - - - - + - - modified-source-relation - ABA - - - - - + Bgee:AN @@ -39727,69 +35538,12 @@ plexiform layer. ZFA:0000029 ZFIN:curator - - - - - ZFA - ABA - https://github.com/obophenotype/uberon/issues/378 - pending - - - - - - ABA - PMID:8932866 - - - - Posterior part of the brain consisting of the cerebellum and medulla oblongata.[AAO] - 2012-06-20 - AAO:0010150 - AAO - AAO:BJB - - - - - The most posterior of the three principal regions of the brain, forming the rhombencephalon and all or most of the metencephalon. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000029 - TAO - ZFIN:curator - - - - - relationship loss: develops_from hindbrain neural tube (TAO:0007043)[TAO] - 2012-08-14 - TAO:0000029 - TAO - - - - - Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] - 2012-09-17 - VHOG:0000070 - VHOG - DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999) - http://bgee.unil.ch/ - - - - - in MA, brainstem and hindbrain and part-of siblings under brain, consistent with FMA and NIF. See also notes for cerebellum. We weaken the relation in ABA to overlaps - MA - @@ -39837,7 +35591,6 @@ plexiform layer. An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face. see also: vascular system. Consider merging? - vascular BTO:0003718 FMA:69050 TAO:0005249 @@ -39895,16 +35648,11 @@ plexiform layer. Anatomical structure that is part of an embryo. - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO] - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO] - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO] - in FMA embryo is_a embryonic structure AAO:0000138 BILA:0000034 BTO:0000174 CALOHA:TS-2110 EFO:0000461 - FBbt:00004208 FMA:69067 GAID:407 MESH:D004628 @@ -39935,45 +35683,6 @@ plexiform layer. BTO:0000174 ZFIN:curator - - - - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO] - 2012-06-20 - AAO:0000138 - AAO - AAO:BJB - - - - - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO] - 2012-08-14 - TAO:0001105 - TAO - ZFIN:curator - - - - - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO] - 2012-08-14 - VSAO:0000178 - VSAO - ZFIN:curator - - - - - in FMA embryo is_a embryonic structure - FMA - - - - - FBbt:00004208 - - @@ -40030,8 +35739,6 @@ plexiform layer. An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen. - An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO] - general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs. AAO:0010386 BTO:0001491 EHDAA:512 @@ -40066,21 +35773,6 @@ plexiform layer. Wikipedia:Viscus https://github.com/obophenotype/mouse-anatomy-ontology/issues/14 - - - - An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO] - 2012-06-20 - AAO:0010386 - AAO - BTO:0001491 - - - - - general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs. - FMA - @@ -40137,21 +35829,15 @@ plexiform layer. The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA]. - Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO] - The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO] - The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO] - The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG] axial skeleton AAO:0000034 EFO:0000942 EHDAA2:0000161 EHDAA:5049 - EMAPA:17214 EMAPA:37721 FMA:71221 MA:0002986 MAT:0000148 - MESH:D013131 MIAA:0000148 TAO:0000317 VHOG:0000317 @@ -40177,43 +35863,6 @@ plexiform layer. https://sourceforge.net/tracker/?func=detail&aid=2983975&group_id=76834&atid=974957 https://sourceforge.net/tracker/?func=detail&atid=1205376&aid=2983977&group_id=76834 - - - - Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO] - 2012-08-14 - VSAO:0000093 - VSAO - PSPUB:0000170 - - - - - The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO] - 2012-06-20 - AAO:0000034 - AAO - AAO:LAP - - - - - The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO] - 2012-08-14 - TAO:0000317 - TAO - ZFIN:curator - - - - - The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG] - 2012-09-17 - VHOG:0000317 - VHOG - DOI:10.1186/1742-9994-8-4 Schilling N, Evolution of the axial system in craniates: morphology and function of the perivertebral musculature. Frontiers in Zoology (2011) - http://bgee.unil.ch/ - @@ -40227,13 +35876,6 @@ plexiform layer. EMAPA:37721 MA:th - - - - MESH:D013131 - - https://github.com/biopragmatics/biomappings - @@ -40248,10 +35890,6 @@ plexiform layer. Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present. - - - Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO] - Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO] AAO:0010339 BILA:0000116 BTO:0001493 @@ -40291,32 +35929,6 @@ plexiform layer. UBERONREF:0000006 Wikipedia:Torso - - - - - ZFA - https://github.com/obophenotype/uberon/issues/378 - pending - - - - - Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO] - 2012-06-20 - AAO:0010339 - AAO - AAO:BJB - - - - - Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO] - 2012-08-14 - TAO:0001115 - TAO - ZFIN:curator - @@ -40349,7 +35961,6 @@ plexiform layer. The sensory system subserving the sense of vision. - The sensory system used for sight.[AAO] UBERON:0007036 AAO:0000632 BILA:0000140 @@ -40379,15 +35990,6 @@ plexiform layer. The sensory system subserving the sense of vision. NIFSTD:FMAID_7191 - - - - The sensory system used for sight.[AAO] - 2012-06-20 - AAO:0000632 - AAO - AAO:EJS - @@ -40549,10 +36151,9 @@ plexiform layer. - + Vasculature that is part of the eye region. - not part of the eye in ZFA. Note this changed to a blood vessel in ZFA FMA:74743 SCTID:123846009 TAO:0007057 @@ -40572,14 +36173,14 @@ plexiform layer. https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb - + - + ISBN:0781772214 @@ -40589,12 +36190,6 @@ plexiform layer. OBOL:automatic https://sourceforge.net/tracker/?func=detail&aid=3489658&group_id=76834&atid=994726 - - - - not part of the eye in ZFA. Note this changed to a blood vessel in ZFA - ZFA - @@ -40638,7 +36233,12 @@ plexiform layer. - + + + + + + @@ -40648,9 +36248,6 @@ plexiform layer. Anatomical system that consists of the muscular and skeletal systems. - Anatomical system that provides locomotion and physical support to the organism.[AAO] - There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG] - musculoskeletal AAO:0010546 CALOHA:TS-1311 EMAPA:32714 @@ -40672,16 +36269,6 @@ plexiform layer. musculoskeletal system - - - - - - - - - check ctenophore - @@ -40690,25 +36277,6 @@ plexiform layer. VSAO:curator https://github.com/obophenotype/uberon/issues/77 - - - - Anatomical system that provides locomotion and physical support to the organism.[AAO] - 2012-06-20 - AAO:0010546 - AAO - AAO:EJS - - - - - There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG] - 2012-09-17 - VHOG:0001275 - VHOG - DOI:10.1002/jez.b.21246 Shearman RM, Burke AC, The lateral somitic frontier in ontogeny and phylogeny. Journal of Experimental Zoology (2009) - http://bgee.unil.ch/ - @@ -40750,7 +36318,6 @@ plexiform layer. The part of the coelemic cavity lumen that is enclosed by the walls of the thorax. - In many species, the diaphragm separates thoracic and abdominal cavities EMAPA:36497 FMA:7565 GAID:93 @@ -40817,21 +36384,28 @@ plexiform layer. - + - - + + + + + + + + + + + + Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO). TODO - add superclass to unify with VNC? - - Part of the central nervous system which descends from the hindbrain within the vertebral column.[AAO] - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG] AAO:0010151 BAMS:SP BAMS:Spinal @@ -40884,69 +36458,22 @@ plexiform layer. https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Spinal_Cord.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Spinal_Cord.glb - + - - - - - - - - - + ZFA - - - - - definitional - - - - - - definitional - Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO). BIRNLEX:1709 - - - - - ZFA - https://github.com/obophenotype/uberon/issues/378 - pending - - - - - Part of the central nervous system which descends from the hindbrain within the vertebral column.[AAO] - 2012-06-20 - AAO:0010151 - AAO - AAO:BJB - - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0000601 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 - http://bgee.unil.ch/ - @@ -41044,12 +36571,6 @@ plexiform layer. Stalk-like part of the brain that includes amongst its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,MP,generalized]. - - - - Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain.[TAO] - Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,adopted][ZFA:0001707]. - the stalk-like part of the brain that comprises the midbrain (aka mesencephalon), the pons (aka pons Varolii), and the medulla oblongata, and connects the cerebral hemispheres with the cervical spinal cord[MP] BAMS:BS BIRNLEX:1565 BTO:0000146 @@ -41096,48 +36617,6 @@ plexiform layer. Wikipedia:Brainstem ZFA:0001707 - - - - - we apply a strict definition - - - - - - ZFA - ABA - https://github.com/obophenotype/uberon/issues/378 - pending - - - - - - we apply a strict definition - - - - - Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain.[TAO] - 2012-08-14 - TAO:0002156 - TAO - ISBN:3764351209 - - - - - Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,adopted][ZFA:0001707]. - ZFA:0001707 - - - - - the stalk-like part of the brain that comprises the midbrain (aka mesencephalon), the pons (aka pons Varolii), and the medulla oblongata, and connects the cerebral hemispheres with the cervical spinal cord[MP] - MP:0005277 - @@ -41219,17 +36698,12 @@ plexiform layer. Neural tissue consisting of myelinated axons connecting grey matter areas of the central nervous system. - Cell part cluster consisting predominantly of neurites in the brain and the spinal cord[FMA:83929]. - Multi-tissue structure comprised largely of myelinated axons.[TAO] - The myelination of axons by glial cells was the last major step in the evolution of cells in the vertebrate nervous system, and white-matter tracts are key to the architecture of the mammalian brain.[well established][VHOG] - nlx_anat_101177 seems to have been lost in the transition from NIFGA to Neurolex AEO:0000139 AEO:0001011 EMAPA:35927 FMA:83929 HBA:9218 MA:0001135 - MESH:D066127 NCIT:C33892 NLX:412 NLXANAT:101177 @@ -41265,46 +36739,6 @@ plexiform layer. Wikipedia:White_matter https://orcid.org/0000-0002-6601-2165 - - - - Cell part cluster consisting predominantly of neurites in the brain and the spinal cord[FMA:83929]. - FMA:83929 - - - - - Multi-tissue structure comprised largely of myelinated axons.[TAO] - 2012-08-14 - TAO:0002142 - TAO - ZFIN:curator - - - - - The myelination of axons by glial cells was the last major step in the evolution of cells in the vertebrate nervous system, and white-matter tracts are key to the architecture of the mammalian brain.[well established][VHOG] - 2012-09-17 - VHOG:0001764 - VHOG - DOI:10.1038/nature09614 Nave KA, Myelination and support of axonal integrity by glia. Nature (2010) - http://bgee.unil.ch/ - - - - - nlx_anat_101177 seems to have been lost in the transition from NIFGA to Neurolex - NIF - https://github.com/SciCrunch/NIF-Ontology/issues/83 - - - - - MESH:D066127 - - - https://github.com/biopragmatics/biomappings - @@ -41361,7 +36795,12 @@ plexiform layer. - + + + + + + @@ -41369,15 +36808,11 @@ plexiform layer. The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities. - Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]. - The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]. - In mammals it forms the peritoneal, pleural, and pericardial cavities UBERON:0000169 body cavity AEO:0000186 BTO:0001707 EHDAA2:0000267 - FBbt:00005060 FMA:85006 NCIT:C25444 RETIRED_EHDAA2:0003186 @@ -41402,52 +36837,18 @@ plexiform layer. EDITOR_NOTE check the FMA placement here; ncit placement of body cavity here probably not correct coelemic cavity lumen - - - - - - - - - definitional - The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities. BTO:0001707 - - - - Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]. - 2012-09-12 - ZFA:0001438 - ZFA - ZFIN:curator - - - - - The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]. - 2012-09-12 - BTO:0001707 - BTO - BTO - body cavity BTO:0001707 - - - - FBbt:00005060 - - @@ -41504,6 +36905,7 @@ plexiform layer. + @@ -41511,21 +36913,9 @@ plexiform layer. - - - - - - - - - - - - - - - + + + @@ -41539,13 +36929,6 @@ plexiform layer. A flexible rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In some chordates, it persists throughout life as the main axial support of the body, while in most vertebrates it becomes the nucleus pulposus of the intervertebral disc. The notochord is found ventral to the neural tube. - Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO] - Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO] - Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO] - relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO] - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG] - notochordal - In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord. AAO:0000327 BTO:0001768 CALOHA:TS-0690 @@ -41580,15 +36963,15 @@ plexiform layer. notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + @@ -41607,19 +36990,19 @@ plexiform layer. - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -41632,51 +37015,6 @@ plexiform layer. https://github.com/obophenotype/uberon/issues/25 https://github.com/obophenotype/uberon/issues/271 - - - - Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO] - 2012-08-14 - VSAO:0000032 - VSAO - PSPUB:0000170 - - - - - Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000135 - TAO - ZFIN:curator - - - - - Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO] - 2012-06-20 - AAO:0000327 - AAO - AAO:LAP - - - - - relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO] - 2012-06-20 - AAO:0000327 - AAO - - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG] - 2012-09-17 - VHOG:0000199 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 - http://bgee.unil.ch/ - @@ -41704,18 +37042,10 @@ plexiform layer. - - + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. - EDITOR_NOTE currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk - Post-cranial axial segments which form sclerotome and dermomyotome.[AAO] - Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO] - relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO] - relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO] - relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO] - (...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG] - somitic mesodermal cluster AAO:0010569 AEO:0001015 @@ -41751,11 +37081,11 @@ plexiform layer. somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + @@ -41768,13 +37098,13 @@ plexiform layer. - + GOTAX:0000352 - + ZFA @@ -41790,58 +37120,6 @@ plexiform layer. PMID:17237766 - - - - Post-cranial axial segments which form sclerotome and dermomyotome.[AAO] - 2012-06-20 - AAO:0010569 - AAO - AAO:EJS - - - - - Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000155 - TAO - ZFIN:curator - - - - - relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO] - 2012-08-14 - TAO:0000155 - TAO - - - - - relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO] - 2012-08-14 - TAO:0000155 - TAO - - - - - relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO] - 2012-06-20 - AAO:0010569 - AAO - - - - - (...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0000191 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.40, DOI:10.1093/icb/43.1.137 Balavoine G, Adoutte A, The segmented urbilateria: a testable scenario. Integrative and Comparative Biology (2003) - http://bgee.unil.ch/ - @@ -41886,20 +37164,25 @@ plexiform layer. + - - - - - - + + + + + + + + + + + + + + + + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. - EDITOR_NOTE consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams). - - A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO] - Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO] - A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831] - We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG] AAO:0010578 BTO:0001764 CALOHA:TS-0676 @@ -41912,7 +37195,6 @@ plexiform layer. MIAA:0000066 NCIT:C34222 SCTID:361462002 - TAO:0000045 UMLS:C0027789 VHOG:0000057 Wikipedia:Neural_crest @@ -41932,66 +37214,45 @@ plexiform layer. http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - - - - - + - + - - - - - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - - Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells - ISBN:0073040584 - - - - - + BTO - + PMID:11523831 - - pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest - - - - - + PMID:11523831 @@ -42000,47 +37261,6 @@ plexiform layer. A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. MP:0009846 - - - - - ISBN:0073040584 - PMID:17377535 - - - - - A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000045 - TAO - ZFIN:curator - - - - - Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO] - 2012-06-20 - AAO:0010578 - AAO - AAO:EJS - - - - - A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831] - PMID:11523831 - - - - - We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG] - 2012-09-17 - VHOG:0000057 - VHOG - DOI:10.1111/j.1469-7580.2012.01495.x Hall BK, Gillis JA, Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues. J Anat (2012) - http://bgee.unil.ch/ - @@ -42082,9 +37302,6 @@ plexiform layer. Embryonic ectoderm that gives rise to nervous tissue. - (...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG] - neurectodermal - we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here AAO:0011074 BILA:0000039 CALOHA:TS-1212 @@ -42093,7 +37310,6 @@ plexiform layer. EHDAA:255 EMAPA:16073 EV:0100004 - FBbt:00001057 FMA:87657 MAT:0000176 MIAA:0000176 @@ -42122,22 +37338,6 @@ plexiform layer. Embryonic ectoderm that gives rise to nervous tissue. Wikipedia:Neuroectoderm - - - - (...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG] - 2012-09-17 - VHOG:0000150 - VHOG - DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) - http://bgee.unil.ch/ - - - - - FBbt:00001057 - - @@ -42172,10 +37372,6 @@ plexiform layer. Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance. - One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO] - Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO] - Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO] - MA also has set of connective tissues AAO:0000098 BTO:0000421 CALOHA:TS-2009 @@ -42216,40 +37412,6 @@ plexiform layer. http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/23 - - - - One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO] - 2012-06-20 - AAO:0000098 - AAO - AAO:LAP - - - - - Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO] - 2012-08-14 - TAO:0001641 - TAO - TAO:wd - - - - - Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO] - 2012-08-14 - VSAO:0000017 - VSAO - GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 - PSPUB:0000170 - - - - - MA also has set of connective tissues - MA - @@ -42313,8 +37475,6 @@ plexiform layer. Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]. - - One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO] AAO:0000306 AEO:0000122 CALOHA:TS-0642 @@ -42345,15 +37505,6 @@ plexiform layer. Wikipedia:Muscle_tissue https://sourceforge.net/tracker/index.php?func=detail&aid=2801266&group_id=36855&atid=440764 - - - - One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO] - 2012-06-20 - AAO:0000306 - AAO - AAO:LAP - @@ -42380,21 +37531,22 @@ plexiform layer. - + - + + + + + + Anatomical system that is involved in the production of hematopoietic cells. - Anatomical system that consists of the blood and blood forming tissues.[AAO] - Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG] - hematopoietic - In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes AAO:0011002 BTO:0000570 CALOHA:TS-0449 @@ -42432,57 +37584,22 @@ plexiform layer. hematopoietic system - + - - - - - + FMA - - - - - definitional - Anatomical system that is involved in the production of hematopoietic cells. Wikipedia:Haematopoiesis - - - - Anatomical system that consists of the blood and blood forming tissues.[AAO] - 2012-06-20 - AAO:0011002 - AAO - AAO:EJS - - - - - Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG] - 2012-09-17 - VHOG:0001624 - VHOG - DOI:10.1016/j.coph.2010.05.004 Ellett F, Lieschke GJ, Zebrafish as a model for vertebrate hematopoiesis. Current Opinion in Pharmacology (2010) - http://bgee.unil.ch/ - - - - - In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes - WP - @@ -42514,8 +37631,8 @@ plexiform layer. - - + + @@ -42541,11 +37658,11 @@ plexiform layer. iris epithelium - + - + @@ -42558,13 +37675,13 @@ plexiform layer. - + MA - + MP @@ -42638,7 +37755,6 @@ plexiform layer. In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA]. MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class - In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG] BTO:0004593 FMA:296704 MAT:0000067 @@ -42666,16 +37782,6 @@ plexiform layer. Wikipedia:Epiblast ZFIN:curator - - - - In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG] - 2012-09-17 - VHOG:0000243 - VHOG - DOI:10.1146/annurev.cellbio.042308.113344 Zorn AM, Wells JM, Vertebrate endoderm development and organ formation. Annual Review of Cell Developmental Biology (2009) - http://bgee.unil.ch/ - @@ -42714,16 +37820,13 @@ plexiform layer. - + Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic. Do not merge with neurogenic placode - Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons - The term placode or placodes also applies to developing organs such as teeth, mammary glands, hair follicles, feathers and scales. We include a separate parent class for this. to avoid confusion, we include neurogenic placode as a subclass ectodermal placode placode AAO:0010466 EFO:0001650 - FMA:293966 MAT:0000369 MIAA:0000369 XAO:0000305 @@ -42734,7 +37837,7 @@ plexiform layer. cranial placode - + @@ -42747,7 +37850,7 @@ plexiform layer. - + PMID:11523831 PMID:22512454 @@ -42761,12 +37864,6 @@ plexiform layer. https://orcid.org/0000-0002-6601-2165 https://sourceforge.net/p/obo/xenopus-anatomy-xao-term-requests/11/ - - - - Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons - PMID:11523831 - @@ -42850,6 +37947,7 @@ plexiform layer. + @@ -42952,7 +38050,7 @@ plexiform layer. - + @@ -42965,10 +38063,9 @@ plexiform layer. - + The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate. consider adding class for organizer. Consider adding separate class for isthmus as a structure - Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG] AAO:0011064 DMBA:16810 EHDAA2:0004395 @@ -42995,31 +38092,24 @@ plexiform layer. midbrain-hindbrain boundary - + - + - - ZFA - https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/106/ - - - - - + ZFA - + ZFA @@ -43028,16 +38118,6 @@ plexiform layer. The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate. GO:0021555 - - - - Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG] - 2012-09-17 - VHOG:0000649 - VHOG - DOI:10.1016/j.ydbio.2005.02.008 Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005) - http://bgee.unil.ch/ - @@ -43063,6 +38143,7 @@ plexiform layer. + @@ -43070,14 +38151,7 @@ plexiform layer. - - - - - - The portion of neural plate anterior to the mid-hindbrain junction. - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] AAO:0011084 TAO:0007016 VHOG:0001200 @@ -43094,16 +38168,6 @@ plexiform layer. The portion of neural plate anterior to the mid-hindbrain junction. XB:curator - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] - 2012-09-17 - VHOG:0001200 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 - http://bgee.unil.ch/ - @@ -43117,14 +38181,7 @@ plexiform layer. - - - - - - The portion of neural plate posterior to the mid-hindbrain junction. - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] TAO:0007017 VHOG:0001201 XAO:0000046 @@ -43140,16 +38197,6 @@ plexiform layer. The portion of neural plate posterior to the mid-hindbrain junction. XB:curator - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] - 2012-09-17 - VHOG:0001201 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 - http://bgee.unil.ch/ - @@ -43184,10 +38231,8 @@ plexiform layer. - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. - Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO] - It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG] AAO:0011086 EFO:0001982 EMAPA:16189 @@ -43209,14 +38254,14 @@ plexiform layer. presomitic mesoderm - + - + Bgee:AN @@ -43225,25 +38270,6 @@ plexiform layer. Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. ZFIN:curator - - - - Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000279 - TAO - ZFIN:curator - - - - - It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG] - 2012-09-17 - VHOG:0000559 - VHOG - DOI:10.1006/dbio.2001.0460 Schubert M, Holland LZ, Dale Stokes M and Holland ND, Three Amphoxius Wnt Genes (AmphiWnt3, AmphiWnt5, and AmphiWnt6) Associated with the Tail Bud: the Evolution of Somitogenesis in Chordates. Developmental Biology (2001) - http://bgee.unil.ch/ - @@ -43282,11 +38308,6 @@ plexiform layer. Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted]. - Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO] - Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO] - relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO] - Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG] - EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac ventral lateral plate mesoderm AAO:0011006 EFO:0003489 @@ -43319,48 +38340,6 @@ plexiform layer. Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted]. Wikipedia:Blood_island_of_umbilical_vesicle - - - - Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000094 - TAO - ZFIN:curator - - - - - Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO] - 2012-06-20 - AAO:0011006 - AAO - AAO:EJS - - - - - relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO] - 2012-08-14 - TAO:0000094 - TAO - - - - - Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0000085 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450, DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual Review of Cell and Developmental Biology (2006) - http://bgee.unil.ch/ - - - - - EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac - EHDAA2 - @@ -43399,7 +38378,6 @@ plexiform layer. The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord. - The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] AAO:0011017 EFO:0003647 TAO:0001204 @@ -43422,15 +38400,6 @@ plexiform layer. GO:0048318 Wikipedia:Chordamesoderm - - - - The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] - 2012-09-17 - VHOG:0000107 - VHOG - http://bgee.unil.ch/ - @@ -43458,7 +38427,8 @@ plexiform layer. - + + @@ -43472,7 +38442,6 @@ plexiform layer. Portion of tissue that is part of the anterior neural keel and will form the optic vesicle[ZFA]. A paired ectodermal placode that becomes invaginated to form the embryonic lens vesicles. - TODO - check that GO's optic placode is the same as ZFA's eye primordium; we may want to have separate term for ocular primordium precursor. XAO has both optic field and eye primordium. UBERON:0005060 AAO:0011038 EFO:0003541 @@ -43496,7 +38465,7 @@ plexiform layer. eye primordium - + @@ -43509,7 +38478,7 @@ plexiform layer. - + PMID:16496288 XAO @@ -43520,12 +38489,6 @@ plexiform layer. GO:0046619 ZFA:0000570 - - - - TODO - check that GO's optic placode is the same as ZFA's eye primordium; we may want to have separate term for ocular primordium precursor. XAO has both optic field and eye primordium. - GO - @@ -43565,8 +38528,8 @@ plexiform layer. - - + + @@ -43574,7 +38537,6 @@ plexiform layer. Multi-tissue structure that is comprised of neural and non-neural epithelial layers which will form the retina and retinal pigmented epithelium of the mature eye[ZFA]. double walled structured formed by expansion and invagination of the distal end of the optic vesicle that develops into the pigmented and sensory layers of the retina while the mouth of the optic cup eventually forms the pupil of the eye[MP]. - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG] BTO:0005351 EHDAA2:0001303 EHDAA:2912 @@ -43595,24 +38557,24 @@ plexiform layer. optic cup - + - + - + ZFA - + ZFA @@ -43623,16 +38585,6 @@ plexiform layer. Wikipedia:Optic_cup_(embryology) ZFA:0001202 - - - - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG] - 2012-09-17 - VHOG:0000167 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 - http://bgee.unil.ch/ - @@ -43676,8 +38628,9 @@ plexiform layer. + - + @@ -43691,9 +38644,6 @@ plexiform layer. A thickened portion of ectoderm which serves as the precursor to the lens. SOX2 and Pou2f1 are involved in its development[WP]. - Ectodermal primordium of the lens of the eye. Kimmel et al, 1995.[TAO] - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG] - Classical transplantation experiments using amphibian embryos suggested that the optic vesicle is the source of lens-inducing signals sufficient to generate lens tissues in competent ectoderm (reviewed in Grainger et al., 1996). More recent findings suggest a multistep model for lens induction. There is now good evidence that lens specification occurs at the neurula stage, before the optic vesicle contact the surface ectoderm, and that neural crest cell migration in the frontonasal region is required to restrict the position of the lens placode (Bailey et al., 2006) AAO:0011055 EFO:0003494 EHDAA2:0000982 @@ -43718,7 +38668,7 @@ plexiform layer. lens placode http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png - + @@ -43731,7 +38681,7 @@ plexiform layer. - + ZFA @@ -43741,31 +38691,6 @@ plexiform layer. Wikipedia:Lens_placode ZFIN:curator - - - - Ectodermal primordium of the lens of the eye. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000122 - TAO - ZFIN:curator - - - - - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG] - 2012-09-17 - VHOG:0000166 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 - http://bgee.unil.ch/ - - - - - Classical transplantation experiments using amphibian embryos suggested that the optic vesicle is the source of lens-inducing signals sufficient to generate lens tissues in competent ectoderm (reviewed in Grainger et al., 1996). More recent findings suggest a multistep model for lens induction. There is now good evidence that lens specification occurs at the neurula stage, before the optic vesicle contact the surface ectoderm, and that neural crest cell migration in the frontonasal region is required to restrict the position of the lens placode (Bailey et al., 2006) - NCBIBook:NBK53175 - @@ -43795,12 +38720,10 @@ plexiform layer. - - - + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. - The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO] - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] AAO:0011072 BTO:0001765 DHBA:10153 @@ -43809,7 +38732,6 @@ plexiform layer. EHDAA:902 EMAPA:35593 FMA:293879 - MESH:D054258 NCIT:C34225 RETIRED_EHDAA2:0001252 TAO:0000132 @@ -43829,34 +38751,34 @@ plexiform layer. neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -43868,33 +38790,6 @@ plexiform layer. Wikipedia:Neural_plate ZFIN:curator - - - - The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000132 - TAO - ZFIN:curator - - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] - 2012-09-17 - VHOG:0000068 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 - http://bgee.unil.ch/ - - - - - MESH:D054258 - - - https://github.com/biopragmatics/biomappings - @@ -43928,7 +38823,6 @@ plexiform layer. - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] AAO:0011082 TAO:0007037 VHOG:0001383 @@ -43944,16 +38838,6 @@ plexiform layer. lexical - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] - 2012-09-17 - VHOG:0001383 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 - http://bgee.unil.ch/ - @@ -43963,23 +38847,14 @@ plexiform layer. - - - - - - - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. - Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO] - Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG] - note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here) AAO:0010568 EFO:0003515 EMAPA:16183 @@ -44004,7 +38879,7 @@ plexiform layer. paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -44017,7 +38892,7 @@ plexiform layer. - + Bgee:AN @@ -44027,31 +38902,6 @@ plexiform layer. GO:0048339 https://github.com/obophenotype/uberon/issues/30 - - - - Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO] - 2012-06-20 - AAO:0010568 - AAO - AAO:EJS - - - - - Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG] - 2012-09-17 - VHOG:0000114 - VHOG - DOI:10.1002/dvdy.21177 Kusakabe R and Kuratani S. Evolutionary perspectives from development of mesodermal components in the lamprey. Developmental dynamics (2007) - http://bgee.unil.ch/ - - - - - note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here) - ZFA - @@ -44099,7 +38949,6 @@ plexiform layer. TODO - add grouping class for the anterior end of the neural tube at all stages - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] AAO:0011012 TAO:0007038 VHOG:0001384 @@ -44109,16 +38958,6 @@ plexiform layer. UBERON:0003080 anterior neural tube - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] - 2012-09-17 - VHOG:0001384 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 - http://bgee.unil.ch/ - @@ -44129,7 +38968,7 @@ plexiform layer. - + @@ -44143,10 +38982,6 @@ plexiform layer. Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]. - Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO] - The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] - A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG] - subclass of mesoderm in ZFA. UBERON:0006258 AAO:0010574 EHDAA2:0000919 @@ -44173,7 +39008,7 @@ plexiform layer. lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -44186,7 +39021,7 @@ plexiform layer. - + EHDAA2 VHOG @@ -44197,40 +39032,6 @@ plexiform layer. MP:0010117 Wikipedia:Lateral_plate_mesoderm - - - - Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO] - 2012-06-20 - AAO:0010574 - AAO - AAO:EJS - - - - - The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] - 2012-09-17 - VHOG:0000118 - VHOG - http://bgee.unil.ch/ - - - - - A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG] - 2012-09-17 - VHOG:0000118 - VHOG - DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) - http://bgee.unil.ch/ - - - - - subclass of mesoderm in ZFA. - ZFA - @@ -44270,20 +39071,17 @@ plexiform layer. - - + + - + Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. should probably be merged with heart rudiment. - Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO] - The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO] - relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO] AAO:0011044 BTO:0001887 NCIT:C34276 @@ -44298,15 +39096,15 @@ plexiform layer. heart primordium - + - + - + @@ -44319,19 +39117,19 @@ plexiform layer. - + ZFA - + ZFA - + XAO @@ -44340,32 +39138,6 @@ plexiform layer. Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. ZFIN:curator - - - - Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO] - 2012-08-14 - TAO:0000028 - TAO - ZFIN:curator - - - - - The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO] - 2012-06-20 - AAO:0011044 - AAO - XAO:curator - - - - - relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO] - 2012-08-14 - TAO:0000028 - TAO - @@ -44386,15 +39158,11 @@ plexiform layer. - - + + Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. - Skeletogenic portion of somites.[AAO] - The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG] - part_of somite in XAO AAO:0010571 AEO:0000212 - BTO:0006255 EHDAA2:0003439 EMAPA:31159 FMA:295652 @@ -44415,11 +39183,11 @@ plexiform layer. sclerotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + - + @@ -44438,13 +39206,13 @@ plexiform layer. - + VHOG:0000680 - + ZFA @@ -44455,39 +39223,6 @@ plexiform layer. XB:curator https://github.com/obophenotype/uberon/issues/316 - - - - Skeletogenic portion of somites.[AAO] - 2012-06-20 - AAO:0010571 - AAO - AAO:EJS - - - - - The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG] - 2012-09-17 - VHOG:0000680 - VHOG - DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) - http://bgee.unil.ch/ - - - - - part_of somite in XAO - XAO - - - - - BTO:0006255 - - - https://github.com/biopragmatics/biomappings - @@ -44529,8 +39264,6 @@ plexiform layer. The narrow, proximal portion of the optic vesicle which connects the embryonic eye and forebrain. - The evagination from the neural tube of the developing embryo which develops the optic cup at its extremity; the stalk persists as the optic nerve. [TFD][VHOG] - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG] AAO:0011077 EHDAA2:0001318 EHDAA:3816 @@ -44566,26 +39299,6 @@ plexiform layer. ISBN:0-914294-08-3 MP:0004268 - - - - The evagination from the neural tube of the developing embryo which develops the optic cup at its extremity; the stalk persists as the optic nerve. [TFD][VHOG] - 2012-09-17 - VHOG:0000223 - VHOG - http://bgee.unil.ch/ - http://medical-dictionary.thefreedictionary.com/optic+stalk - - - - - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG] - 2012-09-17 - VHOG:0000223 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 - http://bgee.unil.ch/ - @@ -44612,7 +39325,9 @@ plexiform layer. + + @@ -44626,9 +39341,6 @@ plexiform layer. Neural crest cells (NCCs) originating in the anterior part of the developing embryo and residing between the mid-diencephalon and the forming hindbrain; cranial NCCs migrate dorsolaterally to form the craniofacial mesenchyme that differentiates into various craniofacial cartilages and bones, cranial neurons, glia, and connective tissues of the face; these cells enter the pharyngeal pouches and arches where they give rise to thymic cells, bones of the middle ear and jaw (mandible), and the odontoblasts of the tooth primordia; like their counterparts in the trunk, cranial NCCs also contribute to the developing peripheral nervous system, along with the pigmented cell (i.e. melanocyte) lineage. - Anterior most portion of the neural crest. Migrates in three highly conserved streams: mandibular, hyoid and branchial.[AAO] - Neural crest that is part of the head.[TAO] - We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] AAO:0010580 EFO:0003645 EHDAA2:0004420 @@ -44658,34 +39370,6 @@ plexiform layer. Neural crest cells (NCCs) originating in the anterior part of the developing embryo and residing between the mid-diencephalon and the forming hindbrain; cranial NCCs migrate dorsolaterally to form the craniofacial mesenchyme that differentiates into various craniofacial cartilages and bones, cranial neurons, glia, and connective tissues of the face; these cells enter the pharyngeal pouches and arches where they give rise to thymic cells, bones of the middle ear and jaw (mandible), and the odontoblasts of the tooth primordia; like their counterparts in the trunk, cranial NCCs also contribute to the developing peripheral nervous system, along with the pigmented cell (i.e. melanocyte) lineage. MGI:anna - - - - Anterior most portion of the neural crest. Migrates in three highly conserved streams: mandibular, hyoid and branchial.[AAO] - 2012-06-20 - AAO:0010580 - AAO - AAO:EJS - - - - - Neural crest that is part of the head.[TAO] - 2012-08-14 - TAO:0001194 - TAO - ZFIN:curator - - - - - We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] - 2012-09-17 - VHOG:0000063 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 - http://bgee.unil.ch/ - @@ -44714,7 +39398,6 @@ plexiform layer. Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types. - this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs AAO:0010015 AEO:0000024 BILA:0000024 @@ -44778,9 +39461,6 @@ plexiform layer. Portion of tissue composed of mesenchymal cells (motile cells that develop from epthelia via an epithelial to mesenchymal transition) and surrounding extracellular material. Mesenchyme has different embryological origins in different metazoan taxa - in many invertebrates it derives in whole or part from ectoderm. In vertebrates it derives largely from mesoderm, and sometimes the terms are used interchangeably, e.g. lateral plate mesoderm/mesenchyme. the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense - A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO] - Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO] - mesenchymal AAO:0010427 AEO:0000145 BTO:0001393 @@ -44815,24 +39495,6 @@ plexiform layer. https://en.wikipedia.org/wiki/Mesenchyme https://github.com/obophenotype/uberon/issues/1641 - - - - A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000393 - TAO - ZFIN:curator - - - - - Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO] - 2012-06-20 - AAO:0010427 - AAO - AAO:EJS - @@ -44863,6 +39525,7 @@ plexiform layer. + @@ -44870,7 +39533,7 @@ plexiform layer. - + Mesenchyme that is part of a developing camera-type eye. TODO - change mesenchyme relationships to precursor_of EHDAA2:0000485 @@ -44882,14 +39545,14 @@ plexiform layer. UBERON:0003314 eye mesenchyme - + - + EHDAA2 @@ -44922,6 +39585,7 @@ plexiform layer. + @@ -44989,7 +39653,6 @@ plexiform layer. The regions of the brain that are largely or entirely composed of myelinated nerve cell axons and contain few or no neural cell bodies or dendrites. EMAPA:35187 - HBA:9218 MA:0000820 NCIT:C49334 UMLS:C1706995 @@ -45076,7 +39739,6 @@ plexiform layer. A portion of connective tissue that is part of a head [Automatically generated definition]. - EMAPA:16098 MA:0000577 adult head connective tissue adult head portion of connective tissue @@ -45206,8 +39868,6 @@ plexiform layer. Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature. - One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO] - FMA definition includes vasculature AAO:0000325 AEO:0000123 EHDAA2:0003123 @@ -45230,21 +39890,6 @@ plexiform layer. Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature. FMA:9642 - - - - One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO] - 2012-06-20 - AAO:0000325 - AAO - AAO:LAP - - - - - FMA definition includes vasculature - FMA - @@ -45300,7 +39945,6 @@ plexiform layer. An anatomical space that surrounded_by a neural tube. - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] UBERON:0005713 AAO:0011073 EHDAA2:0001269 @@ -45326,16 +39970,6 @@ plexiform layer. An anatomical space that surrounded_by a neural tube. OBOL:automatic - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] - 2012-09-17 - VHOG:0001119 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 - http://bgee.unil.ch/ - @@ -45392,7 +40026,6 @@ plexiform layer. A neural crest that has_potential_to_developmentally_contribute_to a midbrain. - We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] EFO:0003591 EHDAA2:0001101 EHDAA:360 @@ -45419,16 +40052,6 @@ plexiform layer. A neural crest that has_potential_to_developmentally_contribute_to a midbrain. OBOL:automatic - - - - We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] - 2012-09-17 - VHOG:0000796 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 - http://bgee.unil.ch/ - @@ -45466,7 +40089,6 @@ plexiform layer. A neural crest that has_potential_to_developmentally_contribute_to a diencephalon. - We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] EFO:0003573 EHDAA2:0000603 EMAPA:16518 @@ -45488,16 +40110,6 @@ plexiform layer. A neural crest that has_potential_to_developmentally_contribute_to a diencephalon. OBOL:automatic - - - - We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] - 2012-09-17 - VHOG:0000798 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 - http://bgee.unil.ch/ - @@ -45548,8 +40160,6 @@ plexiform layer. A neural crest that has_potential_to_developmentally_contribute_to a hindbrain. - Cranial neural crest that is part of the hindbrain.[TAO] - We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] EHDAA2:0001628 EHDAA:362 EMAPA:35747 @@ -45576,25 +40186,6 @@ plexiform layer. A neural crest that has_potential_to_developmentally_contribute_to a hindbrain. OBOL:automatic - - - - Cranial neural crest that is part of the hindbrain.[TAO] - 2012-08-14 - TAO:0007063 - TAO - ZFIN:curator - - - - - We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] - 2012-09-17 - VHOG:0001210 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 - http://bgee.unil.ch/ - @@ -45638,7 +40229,6 @@ plexiform layer. A neural crest that has_potential_to_developmentally_contribute_to a spinal cord. - We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)[well established][VHOG] EHDAA:696 EMAPA:16163 EMAPA:16881 @@ -45655,16 +40245,6 @@ plexiform layer. A neural crest that has_potential_to_developmentally_contribute_to a spinal cord. OBOL:automatic - - - - We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)[well established][VHOG] - 2012-09-17 - VHOG:0001006 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 - http://bgee.unil.ch/ - @@ -45747,10 +40327,9 @@ plexiform layer. - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults - (...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG] EHDAA:251 EMAPA:16088 NCIT:C34195 @@ -45763,14 +40342,14 @@ plexiform layer. intraembryonic coelom - + - + Wikipedia @@ -45780,16 +40359,6 @@ plexiform layer. MGI:anna MP:0012187 - - - - (...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG] - 2012-09-17 - VHOG:0000316 - VHOG - ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.166 - http://bgee.unil.ch/ - @@ -45822,7 +40391,6 @@ plexiform layer. Connective, non-functional supportive framework of a biological cell, tissue, or organ. Contrast with parenchyma. - stromal FMA:81494 NCIT:C67387 UMLS:C0927195 @@ -45862,7 +40430,6 @@ plexiform layer. - @@ -45875,10 +40442,9 @@ plexiform layer. - + The part of the retina that contains neurons and photoreceptor cells[GO]. - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] AAO:0011095 BTO:0000929 CALOHA:TS-0685 @@ -45907,14 +40473,14 @@ plexiform layer. retinal neural layer - + - + Bgee:AN @@ -45923,16 +40489,6 @@ plexiform layer. The part of the retina that contains neurons and photoreceptor cells[GO]. GO:0003407 - - - - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] - 2012-09-17 - VHOG:0000535 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 - http://bgee.unil.ch/ - @@ -45998,10 +40554,8 @@ plexiform layer. Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. - contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers AEO:0000114 EHDAA2:0003114 - FBbt:00007474 epithelial or endothelial tube uberon UBERON:0003914 @@ -46014,12 +40568,6 @@ plexiform layer. GO:0060562 PMID:12526790 - - - - FBbt:00007474 - - @@ -46097,6 +40645,7 @@ plexiform layer. + @@ -46117,7 +40666,6 @@ plexiform layer. The single layer of epithelial cells that lines the early neural tube and develops into the nervous system and into the neural crest cells. - As the cells adjacent to the lumen continue to divide, the migrating cells form a second layer around the original neural tube. This layer becomes progressively thicker as more cells are added to it from the germinal neuroepithelium. This new layer is called the mantle (or intermediate) zone, and the germinal epithelium is now called the ventricular zone (and, later, the ependyma)[NCBIBook:NBK10047] germinal neuroepithelial layer germinal neuroepithelium original neural tube @@ -46178,10 +40726,9 @@ plexiform layer. - + The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium. consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure - The layer of undifferentiated, proliferating cells that line the neural tube lumen ependymal layer EMAPA:17152 EMAPA:35362 @@ -46196,7 +40743,7 @@ plexiform layer. neural tube ventricular layer - + @@ -46209,7 +40756,7 @@ plexiform layer. - + NCBIBook:NBK10047 @@ -46219,12 +40766,6 @@ plexiform layer. MP:0009689 http://www.ncbi.nlm.nih.gov/books/NBK10047 - - - - The layer of undifferentiated, proliferating cells that line the neural tube lumen - MP:0009689 - @@ -46262,6 +40803,7 @@ plexiform layer. + @@ -46269,7 +40811,12 @@ plexiform layer. - + + + + + + @@ -46293,23 +40840,12 @@ plexiform layer. neural tube mantle layer - - - - NCBIBook:NBK10047 - - - - - by division - NCBIBook:NBK10047 - @@ -46336,6 +40872,7 @@ plexiform layer. + @@ -46343,7 +40880,12 @@ plexiform layer. - + + + + + + @@ -46360,16 +40902,6 @@ plexiform layer. neural tube marginal layer - - - - - - - - - forms from axons - @@ -46398,7 +40930,6 @@ plexiform layer. The subdivision of the face that includes the eye (eyeball plus adnexa such as eyelids) and the orbit of the skull and associated parts of the face such as the eyebrows, if present. note the FMA class is more narrow though, and is more like eye + muscles + vasculature. The FMA also has FMA:72951 orbital part of eye - in HP covers eyelid, eyebrow. FMA:260119 content of orbital part of eye eye region @@ -46418,12 +40949,6 @@ plexiform layer. The subdivision of the face that includes the eye (eyeball plus adnexa such as eyelids) and the orbit of the skull and associated parts of the face such as the eyebrows, if present. http://orcid.org/0000-0002-6601-2165 - - - - in HP covers eyelid, eyebrow. - HP:0000284 - @@ -46499,7 +41024,6 @@ plexiform layer. - FMA has both conduit and conduit space. In EHDAA2 this is a surface feature AEO:0000080 EHDAA2:0003080 FMA:242873 @@ -46521,12 +41045,6 @@ plexiform layer. Any tube, opening or passage that connects two distinct anatomical spaces. http://orcid.org/0000-0002-6601-2165 - - - - FMA has both conduit and conduit space. In EHDAA2 this is a surface feature - FMA - @@ -46571,7 +41089,6 @@ plexiform layer. An anatomical structure that develops (entirely or partially) from the mesoderm. - Grouping term for query purposes mesodermal derivative uberon UBERON:0004120 @@ -46615,7 +41132,6 @@ plexiform layer. An anatomical structure that develops (entirely or partially) from the ectoderm. - Grouping term for query purposes ectodermal deriviative uberon UBERON:0004121 @@ -46642,9 +41158,9 @@ plexiform layer. - - - + + + @@ -46652,7 +41168,6 @@ plexiform layer. The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup[GO]. Portion of tissue that is comprised of neuroepitheium which has pinched off from the anterior neural keel and will form the optic cup[ZFA]. - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles.[well established][VHOG] AAO:0011039 EHDAA2:0001320 EMAPA:16540 @@ -46677,34 +41192,34 @@ plexiform layer. optic vesicle http://upload.wikimedia.org/wikipedia/commons/e/e0/Gray863.png - + - + - + - + ZFA - + GO-def - + ZFA @@ -46714,16 +41229,6 @@ plexiform layer. GO:0003404 Wikipedia:Optic_vesicles - - - - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles.[well established][VHOG] - 2012-09-17 - VHOG:0000165 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 - http://bgee.unil.ch/ - @@ -46764,7 +41269,6 @@ plexiform layer. The first recognizable structure derived from the heart field. TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO - (In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG] EHDAA2:0000215 EMAPA:16106 VHOG:0000975 @@ -46783,16 +41287,6 @@ plexiform layer. The first recognizable structure derived from the heart field. GO:0003142 - - - - (In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG] - 2012-09-17 - VHOG:0000975 - VHOG - PMID:15611355 Gittenberger-de Groot AC, Bartelings MM, Deruiter MC, Poelmann RE, Basics of cardiac development for the understanding of congenital heart malformations. Pediatric Research (2005) - http://bgee.unil.ch/ - @@ -46818,12 +41312,12 @@ plexiform layer. + - - + + A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. - this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138] XAO:0004185 first heart field primary heart field @@ -46834,24 +41328,24 @@ plexiform layer. UBERON:0004140 primary heart field - + - + - + GO:0003128 - + https://orcid.org/0000-0003-3308-6245 @@ -46862,12 +41356,6 @@ plexiform layer. GOC:mtg_heart GOC:rl - - - - this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138] - GO - @@ -46910,9 +41398,8 @@ plexiform layer. - + An epithelial tube that will give rise to the mature heart. - the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube. AAO:0010411 EFO:0003526 EMAPA:32685 @@ -46930,14 +41417,14 @@ plexiform layer. heart tube - + - + ZFA-modified @@ -46947,12 +41434,6 @@ plexiform layer. GO:0003143 GOC:mtg_heart - - - - the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube. - MP:0012700 - @@ -46978,6 +41459,7 @@ plexiform layer. + @@ -47018,7 +41500,8 @@ plexiform layer. - + + @@ -47034,14 +41517,14 @@ plexiform layer. eye muscle - + - + MA @@ -47071,10 +41554,7 @@ plexiform layer. Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body. - - Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO] - skeletal AEO:0000168 EHDAA2:0001843 EHDAA:5047 @@ -47107,15 +41587,6 @@ plexiform layer. Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body. VSAO:0000026 - - - - Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO] - 2012-08-14 - VSAO:0000026 - VSAO - GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 - @@ -47130,7 +41601,6 @@ plexiform layer. A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube. - The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO] TAO:0000115 ZFA:0000115 heart cone @@ -47145,15 +41615,6 @@ plexiform layer. A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube. GO:0003313 - - - - The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO] - 2012-08-14 - TAO:0000115 - TAO - ZFIN:curator - @@ -47221,6 +41682,7 @@ plexiform layer. + @@ -47245,10 +41707,9 @@ plexiform layer. - + A transparent homogeneous acellular layer found between the substantia propria and the endothelial layer of the cornea[MP]. - Acellular anatomical structure composed of collagen, Descemet's membrane is secreted as a basement membrane of the corneal endothelium. Located between the stroma and the corneal endothelium, it is approximately 0.15 micrometer thick at 6 months post-fertilization.[ZFIN] EMAPA:18804 FMA:58309 GAID:894 @@ -47275,14 +41736,14 @@ plexiform layer. Descemet's membrane https://github.com/obophenotype/uberon/issues/15 - + - + Cline et al @@ -47298,16 +41759,6 @@ plexiform layer. MP:0004285 https://github.com/obophenotype/uberon/issues/15 - - - - Acellular anatomical structure composed of collagen, Descemet's membrane is secreted as a basement membrane of the corneal endothelium. Located between the stroma and the corneal endothelium, it is approximately 0.15 micrometer thick at 6 months post-fertilization.[ZFIN] - 2016-05-01 - TAO:0002157 - ZFIN - ZFIN:ZDB-PUB-061010-3 - https://orcid.org/0000-0001-9114-8737 - @@ -47374,6 +41825,7 @@ plexiform layer. + @@ -47387,8 +41839,6 @@ plexiform layer. A transparent homogeneous acellular layer, 6 to 9 um thick, lying between the basal lamina of the outer layer of stratified epithelium and the substantia propria of the cornea; it is considered to be a basement membrane. - Acellular anatomical structure that is the zone of collagen fibers adjacent the basement membrane of the corneal epithelium.[TAO] - Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals FMA:58273 MA:0001240 NCIT:C32226 @@ -47419,15 +41869,6 @@ plexiform layer. A transparent homogeneous acellular layer, 6 to 9 um thick, lying between the basal lamina of the outer layer of stratified epithelium and the substantia propria of the cornea; it is considered to be a basement membrane. ncithesaurus:Bowman_s_Membrane - - - - Acellular anatomical structure that is the zone of collagen fibers adjacent the basement membrane of the corneal epithelium.[TAO] - 2012-08-14 - TAO:0002155 - TAO - ZFIN:ZDB-PUB-061010-3 - @@ -47517,7 +41958,6 @@ plexiform layer. Sum of all sensory systems in an organism. - note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs FMA:78499 sense organ system uberon @@ -47583,18 +42023,14 @@ plexiform layer. Anatomical system that has as its parts the heart and blood vessels. - we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph. - The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG] AAO:0011001 BILA:0000016 BTO:0000088 CALOHA:TS-1297 EFO:0000791 - EHDAA2:0000216 EHDAA:394 EMAPA:16104 - EMAPA:16370 EV:0100017 FMA:7161 GAID:467 @@ -47628,16 +42064,6 @@ plexiform layer. Anatomical system that has as its parts the heart and blood vessels. BTO:0000088 - - - - The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG] - 2012-09-17 - VHOG:0000302 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.451 - http://bgee.unil.ch/ - @@ -47889,6 +42315,7 @@ plexiform layer. + @@ -47954,11 +42381,9 @@ plexiform layer. Organism at the gastrula stage. - We explicitly merge the NCITA terms here UBERON:0007012 BILA:0000060 BTO:0001403 - FBbt:00005317 FMA:293108 GAID:1302 MESH:D005775 @@ -47990,18 +42415,6 @@ plexiform layer. Wikipedia:Gastrula Wikipedia:Trilaminar_blastocyst - - - - We explicitly merge the NCITA terms here - NCIT - - - - - FBbt:00005317 - - @@ -48075,10 +42488,8 @@ plexiform layer. - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. - Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO] - Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO] AAO:0011129 TAO:0001890 VSAO:0000128 @@ -48091,14 +42502,14 @@ plexiform layer. skeletal element - + - + VSAO @@ -48107,24 +42518,6 @@ plexiform layer. Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. https://orcid.org/0000-0002-6601-2165 - - - - Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO] - 2012-08-14 - VSAO:0000128 - VSAO - PSPUB:0000170 - - - - - Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO] - 2012-08-14 - TAO:0001890 - TAO - TAO:VSAO_workshop - @@ -48143,7 +42536,7 @@ plexiform layer. - + @@ -48182,14 +42575,14 @@ plexiform layer. UBERON:0004770 articular system - + - + FMA @@ -48242,7 +42635,6 @@ plexiform layer. An endothelium that is part of the cardiovascular system. consider merging with 'endothelium' - Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] BTO:0001853 EMAPA:35201 GAID:519 @@ -48267,16 +42659,6 @@ plexiform layer. An endothelium that is part of the cardiovascular system. https://orcid.org/0000-0002-6601-2165 - - - - Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] - 2012-09-17 - VHOG:0001217 - VHOG - ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207 - http://bgee.unil.ch/ - @@ -48311,7 +42693,6 @@ plexiform layer. Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP]. - We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors visceral mesoderm AAO:0011102 BILA:0000044 @@ -48331,12 +42712,6 @@ plexiform layer. Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP]. Wikipedia:Lateral_plate_mesoderm#Division_into_layers - - - - We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors - BILA - @@ -48371,8 +42746,6 @@ plexiform layer. The central region of trunk mesoderm. This tissue forms the notochord. - Notochord rudiment[ZFIN:ZDB-PUB-961014-576]. - WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord. AAO:0000478 EFO:0003426 TAO:0000091 @@ -48393,12 +42766,6 @@ plexiform layer. The central region of trunk mesoderm. This tissue forms the notochord. https://orcid.org/0000-0002-6601-2165 - - - - Notochord rudiment[ZFIN:ZDB-PUB-961014-576]. - ZFIN:ZDB-PUB-961014-576 - @@ -48431,7 +42798,6 @@ plexiform layer. Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts. - FBbt:00005811 joint uberon UBERON:0004905 @@ -48444,12 +42810,6 @@ plexiform layer. Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts. http://orcid.org/0000-0002-6601-2165 - - - - FBbt:00005811 - - @@ -48481,9 +42841,7 @@ plexiform layer. A proximal-distal subdivision of the digestive tract. - intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct. - FBbt:00100315 FMA:71131 uberon alimentary system subdivision @@ -48502,12 +42860,6 @@ plexiform layer. A proximal-distal subdivision of the digestive tract. http://orcid.org/0000-0002-6601-2165 - - - - FBbt:00100315 - - @@ -48572,7 +42924,6 @@ plexiform layer. The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds. - The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]. AAO:0011071 EMAPA:35594 FMA:295624 @@ -48594,12 +42945,6 @@ plexiform layer. Wikipedia:Neural_groove http://orcid.org/0000-0002-6601-2165 - - - - The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]. - Wikipedia:Neural_groove - @@ -48615,6 +42960,7 @@ plexiform layer. + @@ -48622,14 +42968,7 @@ plexiform layer. - - - - - - One of the two elevated edges of the neural groove[GO,MP]. - In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]. EHDAA2:0001249 FMA:295618 NCIT:C34223 @@ -48652,12 +42991,6 @@ plexiform layer. MP:0011256 Wikipedia:Neural_fold - - - - In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]. - Wikipedia:Neural_fold - @@ -48684,7 +43017,6 @@ plexiform layer. A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN]. - An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO] EFO:0003498 TAO:0000133 ZFA:0000133 @@ -48701,15 +43033,6 @@ plexiform layer. GO:0014024 ZFA:0000133 - - - - An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000133 - TAO - ZFIN:curator - @@ -48732,8 +43055,6 @@ plexiform layer. An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm[GO]. consder adding placodal ectoderm as a distinct class? Also place placodal ectoderm as develops_from ectoderm; need to check taxon-appropriateness - With the exception of the adenohypophysis, homologues of the nonneurogenic placodes (e.g. placodes giving rise to the teeth, hair follicles and lens), appear to be lacking in invertebrate chordates. - in GO, covers optic, otic, olfactory, mammary, hair, tooth, sebaceous - and also insect structures AEO:0000218 uberon epithelial placode @@ -48746,13 +43067,6 @@ plexiform layer. An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm[GO]. GO:0060788 - - - - in GO, covers optic, otic, olfactory, mammary, hair, tooth, sebaceous - and also insect structures - GO - https://github.com/geneontology/go-ontology/issues/12223#issuecomment-215692347 - @@ -48779,8 +43093,6 @@ plexiform layer. Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO]. - in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila - EMAPA:32715 FMA:30316 musculus uberon @@ -48833,10 +43145,8 @@ plexiform layer. A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part. - we go with the FMA classification rather than the CARO one. FMA def: 'Anatomical cluster which has as direct parts cell parts from two or more cells.' AAO:0011000 CARO:0001000 - FBbt:00007060 FMA:83115 multi-cell-component structure multi-cell-part structure @@ -48852,19 +43162,6 @@ plexiform layer. A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part. CARO:0001000 - - - - we go with the FMA classification rather than the CARO one. FMA def: 'Anatomical cluster which has as direct parts cell parts from two or more cells.' - CARO - FMA - - - - - FBbt:00007060 - - @@ -49116,9 +43413,8 @@ plexiform layer. - + Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells. - Mesoderm that will give rise, along with cranial neural crest cells, to connective tissue, bone and musculature in the head. (Source: BioGlossary, www.Biology-Text.com)[TAO] EFO:0003492 EHDAA2:0000732 EHDAA:179 @@ -49138,14 +43434,14 @@ plexiform layer. head mesenchyme - + - + EHDAA2 @@ -49155,15 +43451,6 @@ plexiform layer. ISBN:0683400088 MP:0011260 - - - - Mesoderm that will give rise, along with cranial neural crest cells, to connective tissue, bone and musculature in the head. (Source: BioGlossary, www.Biology-Text.com)[TAO] - 2012-08-14 - TAO:0000113 - TAO - ZFIN:curator - @@ -49212,7 +43499,7 @@ plexiform layer. - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -49228,14 +43515,14 @@ plexiform layer. trunk mesenchyme - + - + EHDAA2 @@ -49256,14 +43543,14 @@ plexiform layer. - - + + + + + + The posterior part of the developing vertebrate hindbrain or the corresponding part of the adult brain composed of the medulla oblongata and a portion of the fourth ventricle; as well as the glossopharyngeal nerve (CN IX), vagus nerve (CN X), accessory nerve (CN XI), hypoglossal nerve (CN XII), and a portion of the vestibulocochlear nerve (CN VIII).[BTO,WP]. - - The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG] - The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] - the terms metencephalon and myelencephalon are only meaningful in mammals and birds - Neuroanatomy of the Zebrafish Brain. Note that its not clear if this refers to the developing medulla oblongata - MA (adult) has two distinct classes BTO:0000758 CALOHA:TS-0607 CALOHA:TS-2365 @@ -49273,7 +43560,6 @@ plexiform layer. EMAPA:17082 HBA:9512 MA:0000205 - MESH:D054024 VHOG:0000456 Wikipedia:Myelencephalon uberon @@ -49283,16 +43569,6 @@ plexiform layer. myelencephalon http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg - - - - - - - - - definitional - @@ -49300,34 +43576,6 @@ plexiform layer. BTO:0000758 Wikipedia:Myelencephalon - - - - The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG] - 2012-09-17 - VHOG:0000456 - VHOG - http://bgee.unil.ch/ - http://medical-dictionary.thefreedictionary.com/myelencephalon - - - - - The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0000456 - VHOG - ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500 - http://bgee.unil.ch/ - - - - - MESH:D054024 - - - https://github.com/biopragmatics/biomappings - @@ -49421,7 +43669,6 @@ plexiform layer. An array of photoreceptors and any supporting cells found in an eye. - FBbt:00004200 light-sensitive tissue uberon UBERON:0005388 @@ -49433,12 +43680,6 @@ plexiform layer. An array of photoreceptors and any supporting cells found in an eye. https://orcid.org/0000-0002-6601-2165 - - - - FBbt:00004200 - - @@ -49459,7 +43700,6 @@ plexiform layer. A transparent structure that is part of a visual sense organ, the function of which is to direct or focus light onto a photoreceptor array. - directing or focusing light onto light receptors lens uberon UBERON:0005389 @@ -49491,7 +43731,6 @@ plexiform layer. AEO:0000125 CALOHA:TS-2122 EHDAA2:0003125 - FBbt:00007006 FMA:292313 MIAA:0000019 uberon @@ -49502,12 +43741,6 @@ plexiform layer. developing anatomical structure - - - - FBbt:00007006 - - @@ -49532,6 +43765,7 @@ plexiform layer. + @@ -49545,7 +43779,6 @@ plexiform layer. Portion of tissue that is the outer layer of the optic cup and will become the retinal pigmented epithelium. - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] EHDAA2:0001306 EMAPA:16677 TAO:0000064 @@ -49571,16 +43804,6 @@ plexiform layer. Portion of tissue that is the outer layer of the optic cup and will become the retinal pigmented epithelium. ZFIN:curator - - - - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] - 2012-09-17 - VHOG:0000492 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 - http://bgee.unil.ch/ - @@ -49642,6 +43865,7 @@ plexiform layer. + @@ -49655,7 +43879,6 @@ plexiform layer. Portion of tissue that is the inner layer of the optic cup and will become the neural retina. - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] EHDAA2:0001304 EMAPA:16675 TAO:0001071 @@ -49681,16 +43904,6 @@ plexiform layer. Portion of tissue that is the inner layer of the optic cup and will become the neural retina. ZFIN:curator - - - - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] - 2012-09-17 - VHOG:0000490 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 - http://bgee.unil.ch/ - @@ -49735,6 +43948,7 @@ plexiform layer. + @@ -49742,9 +43956,6 @@ plexiform layer. Portion of tissue that gives rise to the lens. - A vesicle formed from the lens pit of the embryo, developing into the crystalline lens. [TFD][VHOG] - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG] - the lens of zebrafish (and other teleosts) forms from delamination of cells from the lens placode; thus, there is no formation of a hollow lens vesicle, in contrast to the situation in mammals and birds (Glass and Dahm, 2004) [PMID:16496288] The lens of the zebrafish forms by delamination of lens placodal cells and not through invagination. This results in a solid spherical mass as opposed to a hollow lens vesicle. Detachment of the solid lens vesicle of zebrafish at 24b26 hpf is accomplished in part by apoptosis, similar to mammals EHDAA2:0000983 EHDAA:4737 EMAPA:17163 @@ -49770,32 +43981,6 @@ plexiform layer. ZFIN:curator https://sourceforge.net/tracker/?func=detail&atid=994726&aid=3514998&group_id=76834 - - - - A vesicle formed from the lens pit of the embryo, developing into the crystalline lens. [TFD][VHOG] - 2012-09-17 - VHOG:0001163 - VHOG - http://bgee.unil.ch/ - http://medical-dictionary.thefreedictionary.com/lens+vesicle - - - - - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG] - 2012-09-17 - VHOG:0001163 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 - http://bgee.unil.ch/ - - - - - the lens of zebrafish (and other teleosts) forms from delamination of cells from the lens placode; thus, there is no formation of a hollow lens vesicle, in contrast to the situation in mammals and birds (Glass and Dahm, 2004) [PMID:16496288] The lens of the zebrafish forms by delamination of lens placodal cells and not through invagination. This results in a solid spherical mass as opposed to a hollow lens vesicle. Detachment of the solid lens vesicle of zebrafish at 24b26 hpf is accomplished in part by apoptosis, similar to mammals - ZFA - @@ -49836,8 +44021,9 @@ plexiform layer. + - + Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea. TAO:0002188 ZFA:0001688 @@ -49845,7 +44031,7 @@ plexiform layer. UBERON:0005427 corneal primordium - + @@ -49864,7 +44050,7 @@ plexiform layer. - + ZFA @@ -49887,9 +44073,8 @@ plexiform layer. - + Multi-tissue structure that arises from the heart rudiment and will become the heart tube. - BTO:0006179 EHDAA2:0001512 EHDAA:424 EHDAA:436 @@ -49906,14 +44091,14 @@ plexiform layer. primitive heart tube - + - + ZFA @@ -49922,14 +44107,6 @@ plexiform layer. Multi-tissue structure that arises from the heart rudiment and will become the heart tube. ZFA:0000149 - - - - BTO:0006179 - - - https://github.com/biopragmatics/biomappings - @@ -49956,7 +44133,6 @@ plexiform layer. - A depression in the front of the vitreous body, lodging the lens. [adapted_from_the_definition_of_the_hyaloid_fossa] EHDAA2:0000789 EHDAA:4733 EMAPA:17302 @@ -49967,16 +44143,6 @@ plexiform layer. UBERON:0005606 hyaloid cavity - - - - A depression in the front of the vitreous body, lodging the lens. [adapted_from_the_definition_of_the_hyaloid_fossa] - 2012-09-17 - VHOG:0001477 - VHOG - http://bgee.unil.ch/ - http://medical-dictionary.thefreedictionary.com/hyaloid+fossa - @@ -50056,7 +44222,6 @@ plexiform layer. An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina. - this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell. AAO:0010596 FMA:63872 @@ -50124,7 +44289,7 @@ plexiform layer. - + A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 @@ -50134,7 +44299,7 @@ plexiform layer. UBERON:0005856 developing mesenchymal condensation - + @@ -50153,7 +44318,7 @@ plexiform layer. - + AEO-modified-relation @@ -50209,10 +44374,16 @@ plexiform layer. + - - - + + + + + + + + A serous sac which is the aggregate of the conjunctiva plus the conjunctival space. EMAPA:18233 FMA:20291 @@ -50223,18 +44394,14 @@ plexiform layer. UBERON:0005908 conjunctival sac - + - + - - - - @@ -50244,21 +44411,15 @@ plexiform layer. - + FMA - + HPO:pr - - - - - MA - @@ -50298,10 +44459,8 @@ plexiform layer. Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified]. - Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO] AAO:0000963 EMAPA:17214 - EMAPA:18043 MA:0000308 NCIT:C32172 SCTID:361725000 @@ -50329,15 +44488,6 @@ plexiform layer. https://github.com/obophenotype/uberon/issues/44 https://github.com/obophenotype/uberon/wiki/The-axial-skeleton - - - - Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO] - 2012-08-14 - VSAO:0000056 - VSAO - PSPUB:0000170 - @@ -50378,7 +44528,6 @@ plexiform layer. A threadlike extension of a nerve cell and consists of an axon and myelin sheath (if it is myelinated) in the nervous system. There are nerve fibers in the central nervous system and peripheral nervous system. A nerve fiber may be myelinated and/or unmyelinated. In the central nervous system (CNS), myelin by oligodendroglia cells is formed. Schwann cells form myelin in the peripheral nervous system (PNS). Schwann cells also make a thin covering in an axon without myelin (in the PNS). A peripheral nerve fiber contains an axon, myelin sheath, schwann cells and its endoneurium. There are no endoneurium and schwann cells in the central nervous system. - neurofibrous BAMS:nfi FMA:5914 MESH:D009412 @@ -50469,7 +44618,6 @@ plexiform layer. - http://www1.pbrc.hawaii.edu/~danh/MyelinEvolution/evolution.html, http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=6134604, Wikipedia:Myelin#Invertebrate_myelin FMA:5915 GAID:745 MESH:D009413 @@ -50511,7 +44659,7 @@ plexiform layer. - + @@ -50534,14 +44682,14 @@ plexiform layer. future diencephalon - + - + EHDAA2 @@ -50577,7 +44725,6 @@ plexiform layer. The embryonic precursor of the brain. - The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO) BAMS:Enc BTO:0004726 EFO:0003431 @@ -50606,12 +44753,6 @@ plexiform layer. The embryonic precursor of the brain. NLX:94995 - - - - The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO) - http://neurolex.org/wiki/Cumbo_terms - @@ -50724,7 +44865,7 @@ plexiform layer. - + @@ -50748,14 +44889,14 @@ plexiform layer. future spinal cord - + - + EHDAA2 @@ -50792,10 +44933,9 @@ plexiform layer. - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB - The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG] EHDAA2:0001278 EHDAA:264 EMAPA:16101 @@ -50807,7 +44947,7 @@ plexiform layer. notochordal plate - + @@ -50820,7 +44960,7 @@ plexiform layer. - + EHDAA2 @@ -50829,15 +44969,6 @@ plexiform layer. The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. VHOG:0001212 - - - - The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG] - 2012-09-17 - VHOG:0001212 - VHOG - http://bgee.unil.ch/ - @@ -50857,7 +44988,7 @@ plexiform layer. - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -50874,14 +45005,14 @@ plexiform layer. The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -50918,6 +45049,7 @@ plexiform layer. + @@ -50995,7 +45127,6 @@ plexiform layer. Body substance in a liquid or semi-solid state in the eyeball which serves to refract light. - ocular refraction MA:0001911 uberon UBERON:0006312 @@ -51079,10 +45210,6 @@ plexiform layer. The pharynx is the part of the digestive system immediately posterior to the mouth[GO]. - currently this is an extremely generic class, encompassing both protostomes and deuterostomes. - 2023-04-20 - branchial - pharyngeal MAT:0000049 MESH:D010614 MIAA:0000049 @@ -51439,7 +45566,6 @@ plexiform layer. An epithelium characterised by its most superficial layer consisting of squamous epithelial cells. - FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium BTO:0002072 NCIT:C12848 SCTID:40118003 @@ -51455,12 +45581,6 @@ plexiform layer. An epithelium characterised by its most superficial layer consisting of squamous epithelial cells. Wikipedia:Squamous_epithelium - - - - FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium - FBbt - @@ -51535,12 +45655,6 @@ plexiform layer. Old definition: 'Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.' Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism. anatomical surface - - - - - via morphological boundary in CARO - @@ -51559,6 +45673,7 @@ plexiform layer. + @@ -51733,7 +45848,6 @@ plexiform layer. - The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis BILA:0000084 NCIT:C34268 SCTID:360394002 @@ -51749,12 +45863,6 @@ plexiform layer. UBERON:0007026 presumptive gut - - - - The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis - NCBIBook:NBK10107 - @@ -51785,10 +45893,13 @@ plexiform layer. - + + + + + + A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]. - note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis - SPD:0000130 TADS:0000147 http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg dorsal tube @@ -51800,16 +45911,6 @@ plexiform layer. Gene notes: Bmp, Nkx, Gata primary circulatory organ - - - - - - - - - GO uses blood circulation generically to include the haemolymphatic fluid of arthropods - @@ -51848,7 +45949,6 @@ plexiform layer. An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. - An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO] EFO:0003497 TAO:0000131 ZFA:0000131 @@ -51864,15 +45964,6 @@ plexiform layer. An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. ZFIN:ZDB-PUB-961014-576 - - - - An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000131 - TAO - ZFIN:curator - @@ -51897,6 +45988,7 @@ plexiform layer. + @@ -51962,8 +46054,8 @@ plexiform layer. - - + + @@ -51972,7 +46064,6 @@ plexiform layer. The rhombencephalon (or hindbrain) is a developmental categorization of portions of the central nervous system in vertebrates. The rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. In the human embryo eight rhombomeres can be distinguished, from caudal to rostral: Rh7-Rh1 and the isthmus (the most rostral rhombomere). A rare disease of the rhombencephalon, 'rhombencephalosynapsis' is characterized by a missing vermis resulting in a fused cerebellum. Patients generally present with cerebellar ataxia. The caudal rhombencephalon has been generally considered as the initiation site for neural tube closure. TODO - unify naming conventions - The embryonic rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. Rhombomeres Rh7-Rh4 form the myelencephalon that will give the medulla oblongata. Rhombomeres Rh3-Rh1 form the metencephalon that will form the pons and the cerebellum[NPX:PDR]. BAMS:HB CALOHA:TS-2118 EFO:0003440 @@ -51990,24 +46081,24 @@ plexiform layer. presumptive hindbrain - + - + - + XAO-abduced - + cjm @@ -52016,12 +46107,6 @@ plexiform layer. The rhombencephalon (or hindbrain) is a developmental categorization of portions of the central nervous system in vertebrates. The rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. In the human embryo eight rhombomeres can be distinguished, from caudal to rostral: Rh7-Rh1 and the isthmus (the most rostral rhombomere). A rare disease of the rhombencephalon, 'rhombencephalosynapsis' is characterized by a missing vermis resulting in a fused cerebellum. Patients generally present with cerebellar ataxia. The caudal rhombencephalon has been generally considered as the initiation site for neural tube closure. Wikipedia:Rhombencephalon - - - - The embryonic rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. Rhombomeres Rh7-Rh4 form the myelencephalon that will give the medulla oblongata. Rhombomeres Rh3-Rh1 form the metencephalon that will form the pons and the cerebellum[NPX:PDR]. - NPX:PDR - @@ -52064,7 +46149,7 @@ plexiform layer. - + @@ -52083,14 +46168,14 @@ plexiform layer. presumptive midbrain hindbrain boundary - + - + ZFA @@ -52129,7 +46214,12 @@ plexiform layer. - + + + + + + @@ -52146,17 +46236,6 @@ plexiform layer. presumptive segmental plate - - - - - - - - - https://github.com/obophenotype/uberon/wiki/The-neural-crest - EDHAA2 - @@ -52208,7 +46287,6 @@ plexiform layer. A presumptive structure that has the potential to develop into a neural plate. consider merging - Region of the gastrula which gives rise to the neural plate.[TAO] EFO:0003424 TAO:0000063 ZFA:0000063 @@ -52225,15 +46303,6 @@ plexiform layer. A presumptive structure that has the potential to develop into a neural plate. OBOL:automatic - - - - Region of the gastrula which gives rise to the neural plate.[TAO] - 2012-08-14 - TAO:0000063 - TAO - ZFIN:curator - @@ -52252,7 +46321,7 @@ plexiform layer. - + @@ -52278,7 +46347,7 @@ plexiform layer. presumptive paraxial mesoderm - + @@ -52294,7 +46363,7 @@ plexiform layer. - + https://github.com/obophenotype/uberon/issues/1277 @@ -52376,7 +46445,7 @@ plexiform layer. - + A neural decussation that is part of a diencephalon. FMA:62446 diencephalon decussation @@ -52384,7 +46453,7 @@ plexiform layer. UBERON:0007425 decussation of diencephalon - + @@ -52397,7 +46466,7 @@ plexiform layer. - + Obol @@ -52472,7 +46541,7 @@ plexiform layer. - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -52480,7 +46549,7 @@ plexiform layer. UBERON:0007524 dense mesenchyme tissue - + @@ -52493,7 +46562,7 @@ plexiform layer. - + AEO @@ -52553,7 +46622,6 @@ plexiform layer. - MA does treat internal/external limiting membranes as layers - these are classified as laminae. We do not follow this convention. However, we do following MA is grouping these terms together MA:0001318 SCTID:280667001 retina lamina @@ -52568,12 +46636,6 @@ plexiform layer. UBERON - - - - MA does treat internal/external limiting membranes as layers - these are classified as laminae. We do not follow this convention. However, we do following MA is grouping these terms together - MA - @@ -52679,7 +46741,6 @@ plexiform layer. AEO:0000170 EFO:0001649 EHDAA2:0003170 - FBbt:00005426 Wikipedia:Anlage_(biology) developmental field uberon @@ -52709,12 +46770,6 @@ plexiform layer. FBbt:00005426 http://flybase.org/reports/FBrf0178740.html - - - - FBbt:00005426 - - @@ -52739,7 +46794,7 @@ plexiform layer. - + An axon tract that is part of a brain. the NIFSTD class 'nerve tract' is classified under 'regional part of brain', so it may seem like it belongs here, but actually includes spinal cord tracts FMA:83848 @@ -52749,14 +46804,14 @@ plexiform layer. UBERON:0007702 tract of brain - + - + cjm @@ -52784,12 +46839,10 @@ plexiform layer. - + Anatomical system that consists of all blood and lymph vessels. consider merging with vasculature - The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]. - in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system BTO:0001085 CALOHA:TS-2053 EHDAA2:0004520 @@ -52803,14 +46856,14 @@ plexiform layer. vascular system - + - + MA @@ -52819,18 +46872,6 @@ plexiform layer. Anatomical system that consists of all blood and lymph vessels. http://orcid.org/0000-0002-6601-2165 - - - - The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]. - ncithesaurus:Vascular_System - - - - - in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system - MA - @@ -52943,7 +46984,7 @@ plexiform layer. - + @@ -52960,14 +47001,14 @@ plexiform layer. UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -53063,8 +47104,13 @@ plexiform layer. - - + + + + + + + TODO - developmental relationships for lines TAO:0007044 ZFA:0007044 @@ -53074,27 +47120,16 @@ plexiform layer. UBERON:0009615 midbrain hindbrain boundary neural plate - + - - - - - + ZFA - - - - - https://github.com/obophenotype/uberon/issues/438 - Bgee:AN - @@ -53125,14 +47160,14 @@ plexiform layer. - + - + @@ -53157,24 +47192,24 @@ plexiform layer. presumptive midbrain - + - + - + ZFA - + ZFA @@ -53220,7 +47255,7 @@ plexiform layer. - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -53228,14 +47263,14 @@ plexiform layer. UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -53256,8 +47291,9 @@ plexiform layer. + - + EFO:0003704 TAO:0005041 ZFA:0005041 @@ -53267,14 +47303,14 @@ plexiform layer. anterior lateral plate mesoderm - + - + ZFA @@ -53328,16 +47364,16 @@ plexiform layer. - + - + EHDAA2:0001315 EHDAA:1122 uberon UBERON:0009920 optic neural crest - + @@ -53350,7 +47386,7 @@ plexiform layer. - + EHDAA2 @@ -53388,7 +47424,6 @@ plexiform layer. CARO:0010000 - FBbt:00100313 multicellular structure uberon UBERON:0010000 @@ -53402,12 +47437,6 @@ plexiform layer. An anatomical structure that has more than one cell as a part. CARO:0010000 - - - - FBbt:00100313 - - @@ -53490,7 +47519,8 @@ plexiform layer. - + + @@ -53498,8 +47528,6 @@ plexiform layer. The core globe-shaped component of the camera-type eye. - See notes for camera-type eye - FMA:12513 MIAA:0000283 SCTID:244486005 @@ -53515,14 +47543,14 @@ plexiform layer. eyeball of camera-type eye - + - + FMA @@ -53563,8 +47591,8 @@ plexiform layer. - - + + Portion of tissue that is dorsolateral to the floor plate and part of the midbrain. DHBA:12322 EFO:0003567 @@ -53578,11 +47606,11 @@ plexiform layer. midbrain basal plate - + - + @@ -53595,13 +47623,13 @@ plexiform layer. - + EHDAA2 - + ZFA @@ -53628,8 +47656,9 @@ plexiform layer. + - + Portion of neural tube that gives rise to the midbrain. we follow ZFA in temporally dividing midbrain NT from presumptive midbrain, but in future this may be collapsed TAO:0007039 @@ -53638,14 +47667,14 @@ plexiform layer. UBERON:0010286 midbrain neural tube - + - + ZFA @@ -53672,7 +47701,12 @@ plexiform layer. - + + + + + + @@ -53680,7 +47714,6 @@ plexiform layer. Developing anatomical structure that develops into the eyeball and associated structures. - Multi-tissue structure that consists of the structures that develop into the retina and lens.[TAO] TAO:0002201 ZFA:0001678 future eye @@ -53688,31 +47721,12 @@ plexiform layer. UBERON:0010312 immature eye - - - - - - - - - definitional - Developing anatomical structure that develops into the eyeball and associated structures. ZFA:0001678 - - - - Multi-tissue structure that consists of the structures that develop into the retina and lens.[TAO] - 2012-08-14 - TAO:0002201 - TAO - ZFIN:curator - @@ -53739,7 +47753,6 @@ plexiform layer. An anatomical structure that develops from the neural crest. - Grouping term for query purposes uberon UBERON:0010313 @@ -53776,7 +47789,6 @@ plexiform layer. An anatomical structure that has some part that develops from the neural crest. - Grouping term for query purposes uberon UBERON:0010314 @@ -53851,18 +47863,13 @@ plexiform layer. + - - - - - - The integrated unit (of the eye) that consists of the conjunctiva, the corneal surface, and the ocular mucosal adnexa including the lid margins and the meibomian gland openings, the lacrimal glands and the lacrimal drainage system, all which are critical to maintain ocular surface integrity and provide protection from external antigens and pathogenic microorganisms. EMAPA:35336 MA:0002486 @@ -53893,6 +47900,7 @@ plexiform layer. + @@ -53969,10 +47977,9 @@ plexiform layer. - - + + Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. - Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO] FMA:23879 SCTID:129140006 VSAO:0000042 @@ -53983,11 +47990,11 @@ plexiform layer. subdivision of skeleton - + - + @@ -54000,13 +48007,13 @@ plexiform layer. - + UBERONREF:0000003 - + VSAO @@ -54016,16 +48023,6 @@ plexiform layer. UBERONREF:0000003 https://orcid.org/0000-0002-6601-2165 - - - - Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO] - 2012-08-14 - VSAO:0000042 - incorrect - VSAO - VSAO:curator - @@ -54077,7 +48074,7 @@ plexiform layer. - + Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system FMA:302077 @@ -54087,7 +48084,7 @@ plexiform layer. postcranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton - + @@ -54100,7 +48097,7 @@ plexiform layer. - + cjm @@ -54133,6 +48130,7 @@ plexiform layer. + @@ -54185,7 +48183,6 @@ plexiform layer. - FBbt:00007330 FMA:67509 SCTID:91690000 uberon @@ -54207,21 +48204,15 @@ plexiform layer. A subdivision of an anatomical system. http://orcid.org/0000-0002-6601-2165 - - - - FBbt:00007330 - - + - - Muscles within the eye (bulbus oculi).[AAO] + AAO:0010038 EMAPA:18808 FMA:49150 @@ -54231,25 +48222,16 @@ plexiform layer. UBERON:0011222 intra-ocular muscle - + - + EMAPA - - - - Muscles within the eye (bulbus oculi).[AAO] - 2012-06-20 - AAO:0010038 - AAO - AAO:EJS - @@ -54508,7 +48490,8 @@ plexiform layer. - + + @@ -54550,7 +48533,7 @@ plexiform layer. anterior uvea - + @@ -54563,7 +48546,7 @@ plexiform layer. - + MP @@ -54612,7 +48595,6 @@ plexiform layer. The aggregate of the coelemic cavity lumen plus the membranes that line the lumen. EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining. - coelomic EHDAA2:0004731 Wikipedia:Coelom enterocoelom @@ -54696,6 +48678,7 @@ plexiform layer. + @@ -54920,10 +48903,8 @@ plexiform layer. The region of the organism associated with the visceral organs. - Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]. AEO:0000103 BTO:0001489 - EMAPA:36031 FMA:231424 uberon body @@ -54944,12 +48925,6 @@ plexiform layer. The region of the organism associated with the visceral organs. AEO:0000103 - - - - Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]. - FMA:231424 - @@ -54965,6 +48940,42 @@ plexiform layer. + + + + + + + + + + + + + + + + + Mesenchyme that develops_from the neural crest[Automatically generated definition]. + EMAPA:32735 + FMA:293883 + mesenchyme from neural crest + neural crest derived mesenchyme + neural crest mesenchyme + uberon + UBERON:0014387 + mesenchyme derived from neural crest + + + + + Mesenchyme that develops_from the neural crest[Automatically generated definition]. + OBOL:automatic + https://github.com/obophenotype/uberon/issues/248 + + + + @@ -55062,7 +49073,6 @@ plexiform layer. An anatomical group whose component structures share a common function. AEO:0000093 - FBbt:00007278 uberon UBERON:0015203 non-connected functional system @@ -55076,36 +49086,13 @@ plexiform layer. FBC:DOS FBbt:00007278 - - - - FBbt:00007278 - - - - - - - - - - - - - - - - - - - @@ -55113,7 +49100,6 @@ plexiform layer. Any structure that is placed on one side of the left-right axis of a bilaterian. - This class is primarily to implement taxon constraints. It may be removed in the future. uberon UBERON:0015212 @@ -55147,7 +49133,6 @@ plexiform layer. A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile. heart - SPD:0000130 cardiac pump heart or heart like organ circulatory vessel @@ -55221,6 +49206,7 @@ plexiform layer. + @@ -55347,7 +49333,7 @@ plexiform layer. - + @@ -55370,7 +49356,7 @@ plexiform layer. UBERON:0016887 entire extraembryonic component - + @@ -55383,7 +49369,7 @@ plexiform layer. - + AEO @@ -55406,6 +49392,8 @@ plexiform layer. + + @@ -55723,12 +49711,6 @@ plexiform layer. - - - - - - @@ -55856,7 +49838,6 @@ plexiform layer. CARO:0020000 - FBbt:00007276 uberon UBERON:0034923 @@ -55874,12 +49855,6 @@ plexiform layer. Material anatomical entity consisting of multiple anatomical structures that are not connected to each other. CARO:0020000 - - - - FBbt:00007276 - - @@ -56154,7 +50129,6 @@ plexiform layer. - example to be eventually removed example to be eventually removed @@ -56163,9 +50137,7 @@ plexiform layer. - failed exploratory term The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job - Person:Alan Ruttenberg failed exploratory term @@ -56174,7 +50146,6 @@ plexiform layer. - metadata complete Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. metadata complete @@ -56184,7 +50155,6 @@ plexiform layer. - organizational term Term created to ease viewing/sort terms for development purpose, and will not be included in a release organizational term @@ -56194,7 +50164,6 @@ plexiform layer. - ready for release Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release @@ -56204,7 +50173,6 @@ plexiform layer. - metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete @@ -56214,7 +50182,6 @@ plexiform layer. - uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated @@ -56224,7 +50191,6 @@ plexiform layer. - pending final vetting All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting @@ -56234,7 +50200,6 @@ plexiform layer. - placeholder removed placeholder removed @@ -56243,7 +50208,6 @@ plexiform layer. - terms merged An editor note should explain what were the merged terms and the reason for the merge. terms merged @@ -56253,7 +50217,6 @@ plexiform layer. - term imported This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. term imported @@ -56263,7 +50226,6 @@ plexiform layer. - term split This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. term split @@ -56273,10 +50235,7 @@ plexiform layer. - universal Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. - Alan Ruttenberg - A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf universal @@ -56285,10 +50244,8 @@ plexiform layer. - defined class A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. - Alan Ruttenberg defined class @@ -56297,10 +50254,8 @@ plexiform layer. - named class expression A named class expression is a logical expression that is given a name. The name can be used in place of the expression. named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions - Alan Ruttenberg named class expression @@ -56309,10 +50264,7 @@ plexiform layer. - to be replaced with external ontology term Terms with this status should eventually replaced with a term from another ontology. - Alan Ruttenberg - group:OBI to be replaced with external ontology term @@ -56321,10 +50273,7 @@ plexiform layer. - requires discussion A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. - Alan Ruttenberg - group:OBI requires discussion @@ -56335,9 +50284,7 @@ plexiform layer. The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. - https://github.com/information-artifact-ontology/ontology-metadata/issues/77 - https://orcid.org/0000-0001-5208-3432 out of scope @@ -56351,42 +50298,6 @@ plexiform layer. /////////////////////////////////////////////////////////////////////////////////////// --> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -56448,46 +50359,34 @@ plexiform layer. /////////////////////////////////////////////////////////////////////////////////////// --> - - - - - - - - - - - - - + - + - + - + - + - + - + - + - + - + @@ -56514,8 +50413,8 @@ plexiform layer. - - + + @@ -56525,7 +50424,7 @@ plexiform layer. - + @@ -56535,7 +50434,7 @@ plexiform layer. - + @@ -56552,67 +50451,8 @@ plexiform layer. - - - - - - - - - - true - GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' - involved in BP - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + @@ -56630,8 +50470,8 @@ plexiform layer. - - + + @@ -56641,8 +50481,8 @@ plexiform layer. - - + + @@ -56652,8 +50492,8 @@ plexiform layer. - - + + @@ -56670,8 +50510,8 @@ plexiform layer. - - + + @@ -56688,8 +50528,8 @@ plexiform layer. - - + + @@ -56699,8 +50539,8 @@ plexiform layer. - - + + @@ -56710,8 +50550,8 @@ plexiform layer. - - + + @@ -56728,8 +50568,8 @@ plexiform layer. - - + + @@ -56746,8 +50586,8 @@ plexiform layer. - - + + @@ -56757,8 +50597,8 @@ plexiform layer. - - + + @@ -56768,8 +50608,8 @@ plexiform layer. - - + + @@ -56786,8 +50626,8 @@ plexiform layer. - - + + @@ -56804,8 +50644,8 @@ plexiform layer. - - + + @@ -56815,8 +50655,8 @@ plexiform layer. - - + + @@ -56831,8 +50671,8 @@ plexiform layer. - - + + @@ -56849,8 +50689,8 @@ plexiform layer. - - + + @@ -56860,8 +50700,8 @@ plexiform layer. - - + + @@ -56876,8 +50716,8 @@ plexiform layer. - - + + @@ -56894,8 +50734,8 @@ plexiform layer. - - + + @@ -56905,8 +50745,8 @@ plexiform layer. - - + + @@ -56921,8 +50761,8 @@ plexiform layer. - - + + @@ -56939,8 +50779,8 @@ plexiform layer. - - + + @@ -56950,8 +50790,8 @@ plexiform layer. - - + + @@ -56966,8 +50806,8 @@ plexiform layer. - - + + @@ -56984,8 +50824,8 @@ plexiform layer. - - + + @@ -56995,8 +50835,8 @@ plexiform layer. - - + + @@ -57011,8 +50851,8 @@ plexiform layer. - - + + @@ -57072,8 +50912,8 @@ plexiform layer. - - + + @@ -57083,8 +50923,8 @@ plexiform layer. - - + + @@ -57099,8 +50939,8 @@ plexiform layer. - - + + @@ -57115,9 +50955,9 @@ plexiform layer. - - - + + + @@ -57127,8 +50967,8 @@ plexiform layer. - - + + @@ -57142,9 +50982,9 @@ plexiform layer. - - - + + + @@ -57159,9 +50999,9 @@ plexiform layer. - - - + + + @@ -57171,8 +51011,8 @@ plexiform layer. - - + + @@ -57186,7 +51026,7 @@ plexiform layer. - + diff --git a/src/ontology/subsets/eye_upper_slim.tsv b/src/ontology/subsets/eye_upper_slim.tsv index 4b5094794..6ab8a4e93 100644 --- a/src/ontology/subsets/eye_upper_slim.tsv +++ b/src/ontology/subsets/eye_upper_slim.tsv @@ -1,320 +1,317 @@ ?x ?label -_:B0eeff062X2D4c9fX2D4f5fX2D85faX2D91dcf1dacab2genid1015 -_:B0eeff062X2D4c9fX2D4f5fX2D85faX2D91dcf1dacab2genid1023 -_:B0eeff062X2D4c9fX2D4f5fX2D85faX2D91dcf1dacab2genid1030 -_:B0eeff062X2D4c9fX2D4f5fX2D85faX2D91dcf1dacab2genid1037 -_:B0eeff062X2D4c9fX2D4f5fX2D85faX2D91dcf1dacab2genid1043 -_:B0eeff062X2D4c9fX2D4f5fX2D85faX2D91dcf1dacab2genid1053 -_:B0eeff062X2D4c9fX2D4f5fX2D85faX2D91dcf1dacab2genid1068 -_:B0eeff062X2D4c9fX2D4f5fX2D85faX2D91dcf1dacab2genid1074 -_:B0eeff062X2D4c9fX2D4f5fX2D85faX2D91dcf1dacab2genid1081 -_:B0eeff062X2D4c9fX2D4f5fX2D85faX2D91dcf1dacab2genid1087 -_:B0eeff062X2D4c9fX2D4f5fX2D85faX2D91dcf1dacab2genid1093 -_:B0eeff062X2D4c9fX2D4f5fX2D85faX2D91dcf1dacab2genid1100 -_:B0eeff062X2D4c9fX2D4f5fX2D85faX2D91dcf1dacab2genid1107 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+_:B4f14f866X2Da756X2D48e6X2D9c37X2D1d31e14ff4c3genid973 +_:B4f14f866X2Da756X2D48e6X2D9c37X2D1d31e14ff4c3genid980 +_:B4f14f866X2Da756X2D48e6X2D9c37X2D1d31e14ff4c3genid986 +_:B4f14f866X2Da756X2D48e6X2D9c37X2D1d31e14ff4c3genid996 "continuant" "occurrent" "independent continuant" @@ -323,7 +320,7 @@ _:B0eeff062X2D4c9fX2D4f5fX2D85faX2D91dcf1dacab2genid966 "material entity" "immaterial entity" "cell" - "fibroblast neural crest derived" + "neural crest derived fibroblast" "neuronal receptor cell" "early embryonic cell (metazoa)" "migratory cranial neural crest cell" @@ -1202,6 +1199,7 @@ _:B0eeff062X2D4c9fX2D4f5fX2D85faX2D91dcf1dacab2genid966 "anatomical conduit space" "main body axis" "body proper" + "mesenchyme derived from neural crest" "thoracic skeleton" "primordial vasculature" "non-connected functional system" diff --git a/src/ontology/subsets/general_cell_types_upper_slim.json b/src/ontology/subsets/general_cell_types_upper_slim.json index 423bc976d..1f330c5ba 100644 --- a/src/ontology/subsets/general_cell_types_upper_slim.json +++ b/src/ontology/subsets/general_cell_types_upper_slim.json @@ -4,9 +4,9 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-02-13" + "val" : "2024-04-05" } ], - "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-02-13/subsets/general_cell_types_upper_slim.owl" + "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-04-05/subsets/general_cell_types_upper_slim.owl" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/BFO_0000002", @@ -78,18 +78,6 @@ "val" : "BFO:0000050" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "is part of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my brain is part of my body (continuant parthood, two material entities)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this day is part of this year (occurrent parthood)" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." }, { @@ -98,42 +86,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "part_of" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000002" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000003" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000004" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000017" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000019" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000020" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000031" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "part_of" @@ -164,18 +122,6 @@ "val" : "BFO:0000051" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has part" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my body has part my brain (continuant parthood, two material entities)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this year has part this day (occurrent parthood)" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." }, { @@ -184,21 +130,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has_part" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_part" @@ -217,26 +154,11 @@ "val" : "BFO:0000062" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "preceded by" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is preceded by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "preceded_by" - }, { - "pred" : "http://purl.org/dc/terms/source", - "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "preceded_by" @@ -255,14 +177,8 @@ "val" : "BFO:0000063" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "precedes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "precedes" @@ -282,26 +198,11 @@ "val" : "BFO:0000066" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "occurs in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "occurs_in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "unfolds in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "unfolds_in" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "occurs_in" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Occurs_in" @@ -315,412 +216,12 @@ "definition" : { "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" }, - "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ], - "xrefs" : [ { - "val" : "BFO:0000067" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "site of" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "contains_process" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - } ] + "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000141", "lbl" : "immaterial entity", "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000096", - "lbl" : "anterior to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000096" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "anterior_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000097", - "lbl" : "distal to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000097" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "distal_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000098", - "lbl" : "dorsal to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000098" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dorsal_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000099", - "lbl" : "posterior to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000099" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "posterior_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000100", - "lbl" : "proximal to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000100" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "proximal_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000102", - "lbl" : "ventral to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000102" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "ventral_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000107", - "lbl" : "deep to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000107" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "deep_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000108", - "lbl" : "superficial to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000108" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "superficial_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000120", - "lbl" : "in left side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000120" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_left_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000121", - "lbl" : "in right side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000121" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_right_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000122", - "lbl" : "in posterior side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000122" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_posterior_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000123", - "lbl" : "in anterior side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000123" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_anterior_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000124", - "lbl" : "in proximal side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000124" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_proximal_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "lbl" : "in lateral side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000126" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_lateral_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001100", - "lbl" : "in superficial part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001100" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_superficial_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001101", - "lbl" : "in deep part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001101" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_deep_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001106", - "lbl" : "proximalmost part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001106" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "proximalmost_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001107", - "lbl" : "immediately deep to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001107" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "immediately_deep_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001108", - "lbl" : "distalmost part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001108" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "distalmost_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001113", - "lbl" : "preaxialmost part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001113" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "preaxialmost_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001115", - "lbl" : "postaxialmost part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001115" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "postaxialmost_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0005001", - "lbl" : "intersects midsagittal plane of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0005001" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "intersects_midsagittal_plane_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0015014", - "lbl" : "immediately superficial to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0015014" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "immediately_superficial_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0015101", - "lbl" : "in dorsal side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0015101" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_dorsal_side_of" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000000", "lbl" : "cell", @@ -10199,13 +9700,7 @@ }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000002", "lbl" : "example to be eventually removed", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "example to be eventually removed" - } ] - } + "type" : "INDIVIDUAL" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000028", "lbl" : "symbol", @@ -10217,14 +9712,7 @@ "meta" : { "definition" : { "val" : "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "failed exploratory term" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person:Alan Ruttenberg" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000115", @@ -10235,20 +9723,8 @@ "val" : "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "definition" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2012-04-05: \nBarry Smith\n\nThe official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. \n\nOn the specifics of the proposed definition:\n\nWe don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Daniel Schober" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" } ] } }, { @@ -10258,32 +9734,7 @@ "meta" : { "definition" : { "val" : "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology." - }, - "xrefs" : [ { - "val" : "IAO:0000116" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "editor note" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Daniel Schober" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "editor_note" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000120", @@ -10292,11 +9743,7 @@ "meta" : { "definition" : { "val" : "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "metadata complete" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000121", @@ -10305,11 +9752,7 @@ "meta" : { "definition" : { "val" : "Term created to ease viewing/sort terms for development purpose, and will not be included in a release" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "organizational term" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000122", @@ -10318,11 +9761,7 @@ "meta" : { "definition" : { "val" : "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\"" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "ready for release" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000123", @@ -10331,11 +9770,7 @@ "meta" : { "definition" : { "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "metadata incomplete" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000124", @@ -10344,11 +9779,7 @@ "meta" : { "definition" : { "val" : "Nothing done yet beyond assigning a unique class ID and proposing a preferred term." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "uncurated" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000125", @@ -10357,31 +9788,18 @@ "meta" : { "definition" : { "val" : "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "pending final vetting" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000226", "lbl" : "placeholder removed", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "placeholder removed" - } ] - } + "type" : "INDIVIDUAL" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000227", "lbl" : "terms merged", "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "terms merged" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "An editor note should explain what were the merged terms and the reason for the merge." } ] @@ -10392,9 +9810,6 @@ "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "term imported" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use." } ] @@ -10405,9 +9820,6 @@ "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "term split" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created." } ] @@ -10419,17 +9831,7 @@ "meta" : { "definition" : { "val" : "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has obsolescence reason" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Melanie Courtot" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000233", @@ -10444,29 +9846,8 @@ "val" : "IAO:0000233" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "term tracker item" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_class_level", - "val" : "true" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", "val" : "true" @@ -10481,17 +9862,8 @@ "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "universal" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf" } ] } }, { @@ -10503,14 +9875,8 @@ "val" : "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "defined class" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" } ] } }, { @@ -10522,14 +9888,8 @@ "val" : "A named class expression is a logical expression that is given a name. The name can be used in place of the expression." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "named class expression" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" } ] } }, { @@ -10539,17 +9899,7 @@ "meta" : { "definition" : { "val" : "Terms with this status should eventually replaced with a term from another ontology." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "to be replaced with external ontology term" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "group:OBI" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000424", @@ -10558,17 +9908,7 @@ "meta" : { "definition" : { "val" : "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "expand expression to" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "ObjectProperty: RO_0002104\nLabel: has plasma membrane part\nAnnotations: IAO_0000424 \"http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\"\n" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000428", @@ -10577,17 +9917,7 @@ "meta" : { "definition" : { "val" : "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "requires discussion" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "group:OBI" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000700", @@ -10601,20 +9931,8 @@ "val" : "IAO:0000700" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has ontology root term" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Nicolas Matentzoglu" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_class_level", - "val" : "true" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", "val" : "true" @@ -10631,20 +9949,7 @@ "definition" : { "val" : "Use on obsolete terms, relating the term to another term that can be used as a substitute" }, - "comments" : [ "Add as annotation triples in the granting ontology" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "term replaced by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person:Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Person:Alan Ruttenberg" - } ] + "comments" : [ "Add as annotation triples in the granting ontology" ] } }, { "id" : "http://purl.obolibrary.org/obo/NCBITaxon_1", @@ -10679,9 +9984,6 @@ "val" : "PMID:15371245" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_family" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -10696,7 +9998,7 @@ "pred" : "hasExactSynonym", "val" : "Mus" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003003", + "synonymType" : "http://purl.obolibrary.org/obo/ncbitaxon#genbank_common_name", "pred" : "hasExactSynonym", "val" : "mice" }, { @@ -10708,9 +10010,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_genus" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -10733,9 +10032,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_species" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "NCBITaxon:85055" }, { @@ -10752,9 +10048,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -10773,9 +10066,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "NCBITaxon:40673" }, { @@ -10810,9 +10100,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -10835,9 +10122,6 @@ "val" : "PMID:11791233" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -10860,9 +10144,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_suborder" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -10909,9 +10190,6 @@ "val" : "PMID:30257078" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_superkingdom" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -10933,9 +10211,6 @@ "val" : "PMID:15522813" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_superorder" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -10960,9 +10235,6 @@ "val" : "PMID:15522813" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -10981,9 +10253,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11002,9 +10271,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11023,9 +10289,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11048,9 +10311,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11081,9 +10341,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_kingdom" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11097,9 +10354,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11118,9 +10372,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11138,9 +10389,6 @@ "val" : "PMID:15371245" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11154,9 +10402,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_subfamily" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "NCBITaxon:109679" }, { @@ -11182,9 +10427,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_class" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11198,9 +10440,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11223,9 +10462,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_phylum" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11252,9 +10488,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11277,9 +10510,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11293,9 +10523,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_superclass" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11314,9 +10541,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_subgenus" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11335,9 +10559,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_subphylum" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11372,9 +10593,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11397,9 +10615,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_order" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11415,15 +10630,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/77" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", - "val" : "https://orcid.org/0000-0001-5208-3432" } ] } }, { @@ -11435,9 +10644,6 @@ "val" : "Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'part disjoint with' 'defined by construct' \"\"\"\n PREFIX owl: \n PREFIX : some (\n and some (\n and some (\n and some ?Y)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { @@ -15399,33 +14126,9 @@ "definition" : { "val" : "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " }, - "xrefs" : [ { - "val" : "RO:0002103" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that part_of some ( that has_part some ( that some Y?)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "synapsed_by" } ] } }, { @@ -15437,29 +14140,8 @@ "val" : "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9990-8331" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-1617-8244" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19243617" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( and some ?Y)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] } }, { @@ -15471,26 +14153,8 @@ "val" : "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. " }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "synapsed in" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (\n http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some (\n http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { @@ -15502,20 +14166,8 @@ "val" : "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "synapses in" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that some ( that some Y?)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { @@ -15528,23 +14180,8 @@ }, "comments" : [ "N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part some (\n ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( \n\t‘synapse ; GO:0045202’ that has_part some (\n\t ‘post-synaptic membrane ; GO:0045211’ that part_of some N2))))" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that part_of some ( that some ( that some Y?)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { @@ -15556,23 +14193,8 @@ "val" : "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has synapse in" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that some Y?)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { @@ -15588,20 +14210,11 @@ "val" : "RO:0002131" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "overlaps" @@ -15614,26 +14227,7 @@ "meta" : { "definition" : { "val" : "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has fasciculating component" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", - "val" : "(forall (?x ?y) \n\t(iff \n\t\t(has_fasciculating_neuron_projection ?x ?y)\n\t\t(exists (?nps ?npbs)\t\t\n\t\t\t(and \n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?x)\n\t\t\t\t(\"neuron projection ; GO0043005\" ?y)\n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n\t\t\t\t(part_of ?nps ?y)\n\t\t\t\t(part_of ?npbs ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))\n\n\n" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002134", @@ -15643,30 +14237,9 @@ "definition" : { "val" : "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." }, - "xrefs" : [ { - "val" : "RO:0002134" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that ( some ( that some Y?)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "innervates" } ] } }, { @@ -15677,31 +14250,7 @@ "definition" : { "val" : "X continuous_with Y if and only if X and Y share a fiat boundary." }, - "xrefs" : [ { - "val" : "RO:0002150" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "connected to" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "continuous_with" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "FMA:85972" } ] @@ -15714,23 +14263,7 @@ "definition" : { "val" : "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." }, - "comments" : [ "VBO calls this homologous_to" ], - "xrefs" : [ { - "val" : "RO:0002158" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Consider obsoleting and merging with child relation, 'in homology relationship with'" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "homologous_to" - } ] + "comments" : [ "VBO calls this homologous_to" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -15740,33 +14273,9 @@ "definition" : { "val" : "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." }, - "xrefs" : [ { - "val" : "RO:0002160" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "lactation SubClassOf 'only in taxon' some 'Mammalia'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "only_in_taxon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" @@ -15774,48 +14283,15 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002161", - "lbl" : "never_in_taxon", + "lbl" : "never in taxon", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL." }, - "xrefs" : [ { - "val" : "RO:0002161" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "tooth SubClassOf 'never in taxon' value 'Aves'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", - "val" : "Class: EquivalentTo: ?X and (RO_0002162 some ?Y)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", - "val" : "Class: ?X DisjointWith: RO_0002162 some ?Y " - }, { "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_class_level", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "never_in_taxon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" @@ -15831,31 +14307,7 @@ }, "comments" : [ "Connects a biological entity to its taxon of origin." ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002162" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9227-417X" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_taxon" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] @@ -15870,26 +14322,11 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" @@ -15903,22 +14340,7 @@ "definition" : { "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" }, - "xrefs" : [ { - "val" : "RO:0002170" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "connected_to" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" }, { @@ -15928,42 +14350,16 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002175", - "lbl" : "present_in_taxon", + "lbl" : "present in taxon", "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S" }, "comments" : [ "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "applicable for taxon" - } ], - "xrefs" : [ { - "val" : "RO:0002175" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_class_level", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "present_in_taxon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" @@ -15977,25 +14373,7 @@ "definition" : { "val" : "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." }, - "xrefs" : [ { - "val" : "RO:0002176" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The M8 connects Glasgow and Edinburgh" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "connects" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" }, { @@ -16010,20 +14388,7 @@ "meta" : { "definition" : { "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." - }, - "xrefs" : [ { - "val" : "RO:0002177" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "attached to part of (anatomical structure to anatomical structure)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "attaches_to_part_of" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002178", @@ -16033,21 +14398,9 @@ "definition" : { "val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." }, - "xrefs" : [ { - "val" : "RO:0002178" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "supplies" } ] } }, { @@ -16058,21 +14411,9 @@ "definition" : { "val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." }, - "xrefs" : [ { - "val" : "RO:0002179" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "drains" } ] } }, { @@ -16088,23 +14429,11 @@ "val" : "RO:0002180" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_component" @@ -16121,32 +14450,7 @@ "definition" : { "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" }, - "comments" : [ "This is the transitive form of the develops from relation" ], - "xrefs" : [ { - "val" : "RO:0002202" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9114-8737" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-1980-3228" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "develops_from" - } ] + "comments" : [ "This is the transitive form of the develops from relation" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002203", @@ -16156,29 +14460,7 @@ "definition" : { "val" : "inverse of develops from" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "xrefs" : [ { - "val" : "RO:0002203" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-1980-3228" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "develops_into" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002206", @@ -16187,17 +14469,7 @@ "meta" : { "definition" : { "val" : "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002207", @@ -16211,31 +14483,6 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "has developmental precursor" - } ], - "xrefs" : [ { - "val" : "RO:0002207" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "FBbt" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002202" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "directly_develops_from" } ] } }, { @@ -16246,14 +14493,7 @@ "definition" : { "val" : "inverse of directly develops from" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "developmental precursor of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002211", @@ -16268,30 +14508,6 @@ "val" : "RO:0002211" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-7476-6306" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-3837-8864" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GO" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Regulation precludes parthood; the regulatory process may not be within the regulated process." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "regulates (processual)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "false" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16312,15 +14528,6 @@ "val" : "RO:0002212" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "negatively regulates (process to process)" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002211" }, { @@ -16344,18 +14551,6 @@ "val" : "RO:0002213" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "positively regulates (process to process)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002211" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16376,32 +14571,8 @@ "val" : "RO:0002215" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "osteoclast SubClassOf 'capable of' some 'bone resorption'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has function realized in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20123131" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/21208450" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "capable_of" @@ -16419,17 +14590,8 @@ "val" : "RO:0002216" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has function in" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "capable_of_part_of" @@ -16445,26 +14607,7 @@ "meta" : { "definition" : { "val" : "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" - }, - "xrefs" : [ { - "val" : "RO:0002219" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "surrounded_by" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002220", @@ -16479,35 +14622,11 @@ "val" : "RO:0002220" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The epidermis layer of a vertebrate is adjacent to the dermis." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This relation acts as a join point with BSPO" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "adjacent_to" @@ -16521,26 +14640,7 @@ "definition" : { "val" : "inverse of surrounded by" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "xrefs" : [ { - "val" : "RO:0002221" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "surrounds" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002222", @@ -16548,23 +14648,7 @@ "type" : "PROPERTY", "meta" : { "comments" : [ "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations." ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://en.wikipedia.org/wiki/Allen%27s_interval_algebra" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." - }, { - "pred" : "http://purl.org/dc/terms/source", - "val" : "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002223", @@ -16574,29 +14658,7 @@ "definition" : { "val" : "inverse of starts with" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002223" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Allen" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "starts" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002224", @@ -16611,26 +14673,8 @@ "val" : "RO:0002224" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "started by" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "starts_with" @@ -16643,23 +14687,7 @@ "meta" : { "definition" : { "val" : "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" - }, - "xrefs" : [ { - "val" : "RO:0002225" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "develops_from_part_of" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002226", @@ -16668,29 +14696,7 @@ "meta" : { "definition" : { "val" : "x develops_in y if x is located in y whilst x is developing" - }, - "xrefs" : [ { - "val" : "RO:0002226" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "EHDAA2" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Jonathan Bard, EHDAA2" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "develops_in" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002229", @@ -16700,26 +14706,7 @@ "definition" : { "val" : "inverse of ends with" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002229" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "ends" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002230", @@ -16734,23 +14721,8 @@ "val" : "RO:0002230" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "finished by" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "ends_with" @@ -16769,15 +14741,6 @@ "val" : "RO:0002231" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "starts with process that occurs in" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16798,15 +14761,6 @@ "val" : "RO:0002232" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "ends with process that occurs in" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16827,15 +14781,6 @@ "val" : "RO:0002233" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "consumes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16859,15 +14804,6 @@ "val" : "RO:0002234" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "produces" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16886,22 +14822,7 @@ "definition" : { "val" : "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." }, - "xrefs" : [ { - "val" : "RO:0002252" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004036", - "val" : "http://purl.obolibrary.org/obo/BFO_0000050" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "connecting_branch_of" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/issues/2212" } ] @@ -16914,11 +14835,7 @@ "definition" : { "val" : "inverse of connecting branch of" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004036", - "val" : "http://purl.obolibrary.org/obo/BFO_0000051" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002254", @@ -16927,26 +14844,7 @@ "meta" : { "definition" : { "val" : "x has developmental contribution from y iff x has some part z such that z develops from y" - }, - "xrefs" : [ { - "val" : "RO:0002254" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_developmental_contribution_from" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002255", @@ -16956,14 +14854,7 @@ "definition" : { "val" : "inverse of has developmental contribution from" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002256", @@ -16972,44 +14863,7 @@ "meta" : { "definition" : { "val" : "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" - }, - "xrefs" : [ { - "val" : "RO:0002256" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9114-8737" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "induced by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GO:0001759" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "developmentally_induced_by" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002257", @@ -17018,14 +14872,7 @@ "meta" : { "definition" : { "val" : "Inverse of developmentally induced by" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002258", @@ -17037,17 +14884,8 @@ }, "comments" : [ "This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "false" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "In general you should not use this relation to make assertions - use one of the more specific relations below this one" } ] } }, { @@ -17060,9 +14898,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of" } ] @@ -17081,9 +14916,6 @@ "val" : "affects" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within" } ] @@ -17096,27 +14928,9 @@ "definition" : { "val" : "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" }, - "xrefs" : [ { - "val" : "RO:0002285" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "replaces" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "developmentally_replaces" } ] } }, { @@ -17126,31 +14940,12 @@ "meta" : { "definition" : { "val" : "Inverse of developmentally preceded by" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002287", "lbl" : "part of developmental precursor of", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002292", "lbl" : "expresses", @@ -17158,14 +14953,7 @@ "meta" : { "definition" : { "val" : "y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002295", @@ -17179,14 +14967,8 @@ "val" : "RO:0002295" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" @@ -17211,18 +14993,6 @@ "val" : "RO:0002296" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "every flower development (GO:0009908) results in development of some flower (PO:0009046)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.geneontology.org/GO.doc.development.shtml" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17232,7 +15002,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -17240,21 +15010,6 @@ "val" : "RO:0002297" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:mtg_berkeley_2013" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17275,21 +15030,6 @@ "val" : "RO:0002298" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:mtg_berkeley_2013" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17310,21 +15050,6 @@ "val" : "RO:0002299" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:mtg_berkeley_2013" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17346,12 +15071,6 @@ "val" : "RO:0002304" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002411" - }, { - "pred" : "http://purl.org/dc/terms/creator", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17377,9 +15096,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002411" - }, { - "pred" : "http://purl.org/dc/terms/creator", - "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" @@ -17402,18 +15118,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "inheres in part of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" @@ -17432,15 +15136,6 @@ "val" : "RO:0002315" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:mtg_berkeley_2013" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17455,14 +15150,7 @@ "meta" : { "definition" : { "val" : "A relationship that holds via some environmental process" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002323", @@ -17471,17 +15159,7 @@ "meta" : { "definition" : { "val" : "A mereological relationship or a topological relationship" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002324", @@ -17490,14 +15168,7 @@ "meta" : { "definition" : { "val" : "A relationship that holds between entities participating in some developmental process (GO:0032502)" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002327", @@ -17509,30 +15180,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a particular instances of akt-2 enables some instance of protein kinase activity" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "catalyzes" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "executes" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is catalyzing" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is executing" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Enables" } ] @@ -17544,23 +15191,7 @@ "meta" : { "definition" : { "val" : "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." - }, - "xrefs" : [ { - "val" : "RO:0002328" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This is a grouping relation that collects relations used for the purpose of connecting structure and function" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "functionally_related_to" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002329", @@ -17569,14 +15200,7 @@ "meta" : { "definition" : { "val" : "this relation holds between c and p when c is part of some c', and c' is capable of p." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "false" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002330", @@ -17585,14 +15209,7 @@ "meta" : { "definition" : { "val" : "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002331", @@ -17603,15 +15220,6 @@ "val" : "c involved_in p if and only if c enables some process p', and p' is part of p" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "actively involved in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "enables part of" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Involved_in" } ] @@ -17628,18 +15236,6 @@ "val" : "RO:0002332" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "regulates levels of (process to entity)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17657,9 +15253,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Enabled_by" } ] @@ -17677,12 +15270,6 @@ "val" : "RO:0002334" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "regulated by (processual)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17703,9 +15290,6 @@ "val" : "RO:0002335" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17726,9 +15310,6 @@ "val" : "RO:0002336" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17743,14 +15324,7 @@ "meta" : { "definition" : { "val" : "A relationship that holds via some process of localization" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is a grouping relation." - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002338", @@ -17765,9 +15339,6 @@ "val" : "RO:0002338" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17788,9 +15359,6 @@ "val" : "RO:0002339" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17810,9 +15378,6 @@ "val" : "RO:0002341" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17833,9 +15398,6 @@ "val" : "RO:0002342" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17852,12 +15414,6 @@ "val" : "RO:0002343" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'pollen tube growth' results_in growth_of some 'pollen tube'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17874,12 +15430,6 @@ "val" : "RO:0002344" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17894,23 +15444,7 @@ "meta" : { "definition" : { "val" : "is member of is a mereological relation between a item and a collection." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "An organism that is a member of a population of organisms" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is member of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "member part of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "SIO" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002351", @@ -17919,23 +15453,7 @@ "meta" : { "definition" : { "val" : "has member is a mereological relation between a collection and an item." - }, - "xrefs" : [ { - "val" : "RO:0002351" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "SIO" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_member" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002352", @@ -17945,20 +15463,7 @@ "definition" : { "val" : "inverse of has input" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002352" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "input_of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002353", @@ -17973,14 +15478,8 @@ "val" : "RO:0002353" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "output_of" @@ -17989,26 +15488,11 @@ }, { "id" : "http://purl.obolibrary.org/obo/RO_0002354", "lbl" : "formed as result of", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002360", "lbl" : "has dendrite location", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.org/dc/terms/source", - "val" : "http://neurolex.org/wiki/Property:DendriteLocation" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002371", "lbl" : "attached to", @@ -18017,23 +15501,7 @@ "definition" : { "val" : "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002371" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "attached to (anatomical structure to anatomical structure)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "attaches_to" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002372", @@ -18043,22 +15511,7 @@ "definition" : { "val" : "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." }, - "xrefs" : [ { - "val" : "RO:0002372" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Wikipedia:Insertion_(anatomy)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_muscle_origin" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://dbpedia.org/property/origin" } ] @@ -18071,22 +15524,7 @@ "definition" : { "val" : "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." }, - "xrefs" : [ { - "val" : "RO:0002373" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Wikipedia:Insertion_(anatomy)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_muscle_insertion" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://dbpedia.org/property/insertion" } ] @@ -18100,21 +15538,6 @@ "val" : "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004036", - "val" : "http://purl.obolibrary.org/obo/BFO_0000050" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png" }, { @@ -18131,46 +15554,7 @@ "val" : "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002376" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Deschutes River tributary_of Columbia River" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "inferior epigastric vein tributary_of external iliac vein" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "drains into" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "drains to" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "tributary channel of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://en.wikipedia.org/wiki/Tributary" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.medindia.net/glossary/venous_tributary.htm" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "tributary_of" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://dbpedia.org/ontology/drainsTo" }, { @@ -18185,17 +15569,7 @@ "meta" : { "definition" : { "val" : "x spatially_coextensive_with y if and inly if x and y have the same location" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A lump of clay and a statue" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002380", @@ -18206,22 +15580,7 @@ "val" : "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002380" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "branching_part_of" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/issues/2212" }, { @@ -18236,14 +15595,7 @@ "meta" : { "definition" : { "val" : "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002385", @@ -18252,23 +15604,7 @@ "meta" : { "definition" : { "val" : "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" - }, - "xrefs" : [ { - "val" : "RO:0002385" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_potential_to_developmentally_contribute_to" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002386", @@ -18277,14 +15613,7 @@ "meta" : { "definition" : { "val" : "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002387", @@ -18293,23 +15622,7 @@ "meta" : { "definition" : { "val" : "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" - }, - "xrefs" : [ { - "val" : "RO:0002387" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_potential_to_develop_into" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002388", @@ -18318,14 +15631,7 @@ "meta" : { "definition" : { "val" : "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002404", @@ -18339,12 +15645,6 @@ "val" : "RO:0002404" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -18361,12 +15661,6 @@ "val" : "RO:0002405" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -18383,15 +15677,6 @@ "val" : "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "indirectly activates" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002579", - "val" : "http://purl.obolibrary.org/obo/RO_0002213" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Indirectly_positively_regulates" } ] @@ -18405,15 +15690,6 @@ "val" : "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "indirectly inhibits" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002579", - "val" : "http://purl.obolibrary.org/obo/RO_0002212" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Indirectly_negatively_regulates" } ] @@ -18430,12 +15706,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." } ] } }, { @@ -18451,9 +15721,6 @@ "val" : "RO:0002411" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -18473,12 +15740,6 @@ "val" : "RO:0002412" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002411" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -18504,12 +15765,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "influences (processual)" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" @@ -18531,12 +15786,6 @@ "val" : "RO:0002427" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -18551,11 +15800,7 @@ "meta" : { "definition" : { "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002429", @@ -18564,14 +15809,7 @@ "meta" : { "definition" : { "val" : "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002428" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002430", @@ -18582,9 +15820,6 @@ "val" : "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002428" } ] @@ -18600,12 +15835,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "OWL does not allow defining object properties via a Union" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "involved in or reguates" } ] } }, { @@ -18623,15 +15852,6 @@ "val" : "enables activity in" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A protein that enables activity in a cytosol." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "executes activity in" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Is_active_in" } ] @@ -18643,20 +15863,7 @@ "meta" : { "definition" : { "val" : "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." - }, - "xrefs" : [ { - "val" : "RO:0002433" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "contributes_to_morphology_of" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002434", @@ -18677,18 +15884,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Considering relabeling as 'pairwise interacts with'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" - }, { - "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", - "val" : "http://purl.obolibrary.org/obo/MI_0914" } ] } }, { @@ -18700,20 +15898,8 @@ "val" : "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "binds" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "molecularly binds with" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ECO_0000353" - }, { - "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", - "val" : "http://purl.obolibrary.org/obo/MI_0915" } ] } }, { @@ -18724,12 +15910,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Axiomatization to GO to be added later" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." } ] } }, { @@ -18743,13 +15923,6 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "molecularly controls" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" } ] } }, { @@ -18763,16 +15936,6 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "molecularly decreases activity of" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "directly inhibits" } ] } }, { @@ -18786,31 +15949,12 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "molecularly increases activity of" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "directly activates" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002464", "lbl" : "helper property (not for use in curation)", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002473", "lbl" : "composed primarily of", @@ -18819,29 +15963,7 @@ "definition" : { "val" : "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002473" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "composed_primarily_of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002479", @@ -18851,22 +15973,12 @@ "definition" : { "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002481", "lbl" : "is kinase activity", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002485", "lbl" : "receives input from", @@ -18875,9 +15987,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "See notes for inverse relation" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { @@ -18888,24 +15997,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002487", "lbl" : "relation between physical entity and a process or stage", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage." - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002488", "lbl" : "existence starts during", @@ -18913,20 +16010,7 @@ "meta" : { "definition" : { "val" : "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." - }, - "xrefs" : [ { - "val" : "RO:0002488" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_starts_during" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002489", @@ -18935,20 +16019,7 @@ "meta" : { "definition" : { "val" : "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." - }, - "xrefs" : [ { - "val" : "RO:0002489" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_starts_with" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002490", @@ -18958,11 +16029,7 @@ "definition" : { "val" : "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002491", @@ -18976,19 +16043,6 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "exists during" - } ], - "xrefs" : [ { - "val" : "RO:0002491" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_starts_and_ends_during" } ] } }, { @@ -18999,24 +16053,7 @@ "definition" : { "val" : "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "ceases_to_exist_during" - } ], - "xrefs" : [ { - "val" : "RO:0002492" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_ends_during" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002493", @@ -19026,20 +16063,7 @@ "definition" : { "val" : "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "xrefs" : [ { - "val" : "RO:0002493" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_ends_with" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002494", @@ -19048,20 +16072,7 @@ "meta" : { "definition" : { "val" : "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" - }, - "xrefs" : [ { - "val" : "RO:0002494" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "transformation_of" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002495", @@ -19070,23 +16081,7 @@ "meta" : { "definition" : { "val" : "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" - }, - "xrefs" : [ { - "val" : "RO:0002495" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002494" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "immediate_transformation_of" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002496", @@ -19096,20 +16091,7 @@ "definition" : { "val" : "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "xrefs" : [ { - "val" : "RO:0002496" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_starts_during_or_after" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002497", @@ -19119,20 +16101,7 @@ "definition" : { "val" : "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "xrefs" : [ { - "val" : "RO:0002497" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_ends_during_or_before" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002500", @@ -19141,11 +16110,7 @@ "meta" : { "definition" : { "val" : "A relationship between a material entity and a process where the material entity has some causal role that influences the process" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002501", @@ -19154,17 +16119,7 @@ "meta" : { "definition" : { "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002502", @@ -19172,9 +16127,6 @@ "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/BFO_0000169" } ] @@ -19187,15 +16139,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." } ] } }, { @@ -19205,55 +16148,18 @@ "meta" : { "definition" : { "val" : "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." - }, - "xrefs" : [ { - "val" : "RO:0002551" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has supporting framework" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_skeleton" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002559", "lbl" : "causally influenced by", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "causally influenced by (entity-centric)" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002563", "lbl" : "interaction relation helper property", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29" }, { @@ -19264,13 +16170,7 @@ }, { "id" : "http://purl.obolibrary.org/obo/RO_0002564", "lbl" : "molecular interaction relation helper property", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002565", "lbl" : "results in movement of", @@ -19284,11 +16184,6 @@ "val" : "RO:0002565" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -19303,20 +16198,7 @@ "meta" : { "definition" : { "val" : "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "causally influences (entity-centric)" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002567", @@ -19325,14 +16207,7 @@ "meta" : { "definition" : { "val" : "A relation that holds between elements of a musculoskeletal system or its analogs." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002568", @@ -19341,23 +16216,7 @@ "meta" : { "definition" : { "val" : "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." - }, - "xrefs" : [ { - "val" : "RO:0002568" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Wikipedia:Antagonist_(muscle)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_muscle_antagonist" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002569", @@ -19367,20 +16226,7 @@ "definition" : { "val" : "inverse of branching part of" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002569" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_branching_part" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002570", @@ -19390,26 +16236,7 @@ "definition" : { "val" : "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002570" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "UBERON:cjm" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "conduit_for" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002571", @@ -19419,23 +16246,7 @@ "definition" : { "val" : "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002571" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "lumen_of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002572", @@ -19445,20 +16256,7 @@ "definition" : { "val" : "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002572" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "luminal_space_of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002576", @@ -19468,20 +16266,7 @@ "definition" : { "val" : "inverse of has skeleton" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "xrefs" : [ { - "val" : "RO:0002576" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "skeleton_of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002578", @@ -19496,18 +16281,6 @@ "val" : "RO:0002578" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "directly regulates (processual)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002211" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -19515,24 +16288,6 @@ "val" : "directly_regulates" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002581", - "lbl" : "is a defining property chain axiom", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002582", - "lbl" : "is a defining property chain axiom where second argument is reflexive", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R." - } - } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002584", "lbl" : "has part structure that is capable of", @@ -19540,14 +16295,7 @@ "meta" : { "definition" : { "val" : "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002586", @@ -19621,12 +16369,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] } }, { @@ -19636,14 +16378,7 @@ "meta" : { "definition" : { "val" : "Holds between c and p if and only if c is capable of some activity a, and a regulates p." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "pyrethroid -> growth" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002597", @@ -19652,11 +16387,7 @@ "meta" : { "definition" : { "val" : "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002598", @@ -19665,14 +16396,7 @@ "meta" : { "definition" : { "val" : "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "renin -> arteriolar smooth muscle contraction" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002608", @@ -19686,9 +16410,6 @@ "val" : "RO:0002608" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -19709,15 +16430,6 @@ "val" : "RO:0002629" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "directly positively regulates (process to process)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002578" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -19741,12 +16453,6 @@ "val" : "RO:0002630" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "directly negatively regulates (process to process)" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002578" }, { @@ -19774,17 +16480,8 @@ "val" : "RO:0003000" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9114-8737" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "produces" @@ -19803,17 +16500,8 @@ "val" : "RO:0003001" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9114-8737" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "produced_by" @@ -19922,9 +16610,6 @@ "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002264" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { @@ -19965,9 +16650,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002263" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { @@ -20026,9 +16708,6 @@ "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002418" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { @@ -20059,11 +16738,7 @@ "meta" : { "definition" : { "val" : "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0012000", @@ -20325,9 +17000,6 @@ "xrefs" : [ "PMID:19243617" ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" - }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1617-8244" }, { @@ -20345,9 +17017,6 @@ "xrefs" : [ "PMID:19243617" ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" - }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1617-8244" }, { @@ -20368,21 +17037,6 @@ "val" : "utilizes" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A diagnostic testing device utilizes a specimen." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9625-1899" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-2620-0345" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "See github ticket https://github.com/oborel/obo-relations/issues/497" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-11-08T12:00:00Z" } ] @@ -20568,8 +17222,6 @@ "val" : "EHDAA:500" }, { "val" : "EMAPA:35955" - }, { - "val" : "FBbt:00005155" }, { "val" : "GAID:63" }, { @@ -20617,12 +17269,6 @@ "val" : "galen:Tube" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts)" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "tubular" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -20687,15 +17333,6 @@ "val" : "galen:Tendon" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Dense regular connective tissue that connects muscle to bone.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Phylogenetically, tendinous tissue first appears in the invertebrate chordate Branchiostoma as myosepta. This two-dimensional array of collagen fibers is highly organized, with fibers running along two primary axes. In hagfish the first linear tendons appear and the myosepta have developed specialized regions with unidirectional fiber orientation - a linear tendon within the flat sheet of myoseptum.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in FMA, tendon is an organ component that with parts dense-irregular-connective-tissue of tendon and dense-irregular-connective-tissue of tendon sheath; we follow VSAO in making it a subtype of the former. In VSAO tendons connect muscle to bone; in WP the def states integument (e.g. auricular muscles) - but JB confirms this is not actually tendon but aponeurosis" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -20730,8 +17367,6 @@ } ], "xrefs" : [ { "val" : "AAO:0011123" - }, { - "val" : "FBbt:00100314" }, { "val" : "FMA:30320" }, { @@ -20752,12 +17387,6 @@ "val" : "galen:Duct" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -20785,16 +17414,11 @@ "xrefs" : [ "FMA:82482" ] } ], "xrefs" : [ { - "val" : "EMAPA:25036" - }, { "val" : "FMA:82482" }, { "val" : "galen:Wall" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in FMA, serosa is a wall" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0009915" }, { @@ -20832,8 +17456,6 @@ "val" : "EHDAA2:0003003" }, { "val" : "EMAPA:0" - }, { - "val" : "FBbt:00007001" }, { "val" : "FMA:305751" }, { @@ -20933,12 +17555,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -20973,12 +17589,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -21017,9 +17627,6 @@ "val" : "SCTID:91717005" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "currently defined in a very broad sense, may be replaced by more specific classes in the future" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { @@ -21150,9 +17757,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "ncit:Death is an outcome" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -21230,9 +17834,6 @@ "val" : "WBls:0000103" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -21349,12 +17950,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "the WBls class 'all stages' belongs here as it is the superclass of other WBls stages" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -21407,8 +18002,6 @@ "val" : "EHDAA:27" }, { "val" : "FBdv:00005288" - }, { - "val" : "IDOMAL:0000302" }, { "val" : "NCIT:C12601" }, { @@ -21423,9 +18016,6 @@ "val" : "ZFS:0000001" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -21603,12 +18193,6 @@ "val" : "XAO:1000006" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002174", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7955" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In zebrafish, the times of neurulation and segmentation overlap so extensively there is no distinct neurula period of development, such as occurs largely before segmentation in amphibian embryos." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -21741,8 +18325,6 @@ "val" : "EHDAA:542" }, { "val" : "EMAPA:16262" - }, { - "val" : "FBbt:00003126" }, { "val" : "FMA:49184" }, { @@ -21785,21 +18367,6 @@ "val" : "http://purl.obolibrary.org/obo/uberon/images/lamprey_sucker_rosava_3238889218.jpg" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "oral" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -21907,8 +18474,6 @@ "val" : "BTO:0001485" }, { "val" : "EFO:0000801" - }, { - "val" : "EMAPA:35578" }, { "val" : "FMA:72954" }, { @@ -21931,12 +18496,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system that consists of the muscles of the body.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -21987,8 +18546,6 @@ "val" : "EHDAA2:0003004" }, { "val" : "EMAPA:35178" - }, { - "val" : "FBbt:00007019" }, { "val" : "FMA:9669" }, { @@ -22061,8 +18618,6 @@ "val" : "CARO:0000005" }, { "val" : "EHDAA2:0003005" - }, { - "val" : "FBbt:00007017" }, { "val" : "FMA:5897" }, { @@ -22116,8 +18671,6 @@ "val" : "CARO:0000006" }, { "val" : "EHDAA2:0003006" - }, { - "val" : "FBbt:00007016" }, { "val" : "FMA:67165" }, { @@ -22168,8 +18721,6 @@ "val" : "CARO:0000007" }, { "val" : "EHDAA2:0003007" - }, { - "val" : "FBbt:00007015" }, { "val" : "FMA:67112" }, { @@ -22248,14 +18799,10 @@ "val" : "EMAPA:16103" }, { "val" : "EV:0100000" - }, { - "val" : "FBbt:00004856" }, { "val" : "FMA:7149" }, { "val" : "HAO:0000011" - }, { - "val" : "IDOMAL:0002460" }, { "val" : "MA:0000003" }, { @@ -22364,8 +18911,6 @@ "val" : "EMAPA:25765" }, { "val" : "EV:0100016" - }, { - "val" : "FBbt:00000001" }, { "val" : "FMA:256135" }, { @@ -22407,9 +18952,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "organismal" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -22459,8 +19001,6 @@ "val" : "EHDAA2:0003032" }, { "val" : "EMAPA:36031" - }, { - "val" : "FBbt:00007009" }, { "val" : "FMA:7153" }, { @@ -22535,8 +19075,6 @@ "val" : "CARO:0000040" }, { "val" : "EHDAA2:0003040" - }, { - "val" : "FBbt:00007013" }, { "val" : "FMA:63863" }, { @@ -22575,8 +19113,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "xrefs" : [ { - "val" : "FBbt:00007277" - }, { "val" : "VHOG:0001737" } ], "basicPropertyValues" : [ { @@ -22630,8 +19166,6 @@ "val" : "EHDAA2:0003042" }, { "val" : "EHDAA:46" - }, { - "val" : "FBbt:00005835" }, { "val" : "FMA:85537" }, { @@ -22698,8 +19232,6 @@ "val" : "EHDAA2:0003043" }, { "val" : "EMAPA:35868" - }, { - "val" : "FBbt:00007003" }, { "val" : "FMA:9637" }, { @@ -22770,8 +19302,6 @@ "val" : "CARO:0000055" }, { "val" : "EHDAA2:0003055" - }, { - "val" : "FBbt:00007010" }, { "val" : "HAO:0000055" }, { @@ -22836,8 +19366,6 @@ "val" : "EHDAA2:0003066" }, { "val" : "EMAPA:32738" - }, { - "val" : "FBbt:00007005" }, { "val" : "FMA:9639" }, { @@ -22866,12 +19394,6 @@ "val" : "ZFA:0001486" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "epithelial" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -22929,9 +19451,6 @@ "val" : "ZFA:0001494" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Epithelium that consists of more than one layer of epithelial cells.[CARO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -22988,9 +19507,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Epithelium that consists of a single layer of epithelial cells.[CARO]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -23040,14 +19556,10 @@ "val" : "EHDAA:38" }, { "val" : "EMAPA:16039" - }, { - "val" : "FBbt:00000052" }, { "val" : "FMA:69068" }, { "val" : "GAID:963" - }, { - "val" : "IDOMAL:0000646" }, { "val" : "MAT:0000226" }, { @@ -23074,12 +19586,6 @@ "val" : "http://neurolex.org/wiki/Category:Embryonic_organism" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "embryonic" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -23128,8 +19634,6 @@ "val" : "BTO:0000556" }, { "val" : "EMAPA:36033" - }, { - "val" : "FBbt:00000110" }, { "val" : "FMA:69069" }, { @@ -23156,9 +19660,6 @@ "val" : "ZFA:0001122" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -23194,8 +19695,6 @@ "val" : "EMAPA:16069" }, { "val" : "EV:0100003" - }, { - "val" : "FBbt:00000111" }, { "val" : "FMA:69070" }, { @@ -23226,15 +19725,6 @@ "val" : "ZFA:0000016" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "ectodermal" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -23274,8 +19764,6 @@ "val" : "EMAPA:16062" }, { "val" : "EV:0100005" - }, { - "val" : "FBbt:00000125" }, { "val" : "FMA:69071" }, { @@ -23304,12 +19792,6 @@ "val" : "ZFA:0000017" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "endodermal" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -23364,8 +19846,6 @@ "val" : "EMAPA:16083" }, { "val" : "EV:0100006" - }, { - "val" : "FBbt:00000126" }, { "val" : "FMA:69072" }, { @@ -23396,18 +19876,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Primary germ layer that is the middle of the embryonic germ layers.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "mesodermal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0003263" @@ -23467,8 +19935,6 @@ "val" : "EHDAA2:0001929" }, { "val" : "EMAPA:16263" - }, { - "val" : "FBbt:00000439" }, { "val" : "FMA:295846" }, { @@ -23489,18 +19955,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "stomodeal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -23542,8 +19996,6 @@ "val" : "EMAPA:35306" }, { "val" : "EV:0100128" - }, { - "val" : "FBbt:00005068" }, { "val" : "FMA:9668" }, { @@ -23570,15 +20022,6 @@ "val" : "ZFA:0001158" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "endocrine" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -23611,8 +20054,6 @@ "val" : "EFO:0000827" }, { "val" : "EV:0100336" - }, { - "val" : "FBbt:00005162" }, { "val" : "GAID:69" }, { @@ -23625,20 +20066,8 @@ "val" : "Wikipedia:Eye" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This class encompasses a variety of light-detecting structures from different phyla with no implication of homology, from the compound insect eye to the vertebrate camera-type eye (distinct classes are provided for each)" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "ocular" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "optic" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000010", - "val" : "Note that whilst this is classified as an organ, it is in fact more of a unit composed of different structures: in Drosophila, it includes the interommatidial bristle as a part; we consider here the vertebrate eye to include the eyeball/eye proper as a part, with the eye having as parts (when present): eyelids, conjuctiva," }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -23718,12 +20147,6 @@ "val" : "galen:Joint" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -23761,10 +20184,6 @@ "val" : "CALOHA:TS-1293" }, { "val" : "EFO:0000793" - }, { - "val" : "EV:0100056" - }, { - "val" : "FBbt:00005055" }, { "val" : "FMA:7152" }, { @@ -23799,15 +20218,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "digestive" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -23833,17 +20243,12 @@ "val" : "AAO:0000959" }, { "val" : "CALOHA:TS-2103" - }, { - "val" : "MESH:D002319" }, { "val" : "VHOG:0001248" }, { "val" : "Wikipedia:Circulatory_system" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "the cardiovascular system and the lymphatic system are parts of the circulatory system" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_147099" }, { @@ -23852,18 +20257,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6157" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002174", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6231" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -23915,13 +20311,9 @@ "val" : "musculature system" } ], "xrefs" : [ { - "val" : "AAO:0011066" - }, { "val" : "BTO:0000887" }, { "val" : "EFO:0001949" - }, { - "val" : "EMAPA:32715" }, { "val" : "EMAPA:35577" }, { @@ -23944,12 +20336,6 @@ "val" : "ZFA:0000548" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0001474" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -24001,8 +20387,6 @@ "val" : "EMAPA:16469" }, { "val" : "EV:0100162" - }, { - "val" : "FBbt:00005093" }, { "val" : "FMA:7157" }, { @@ -24042,21 +20426,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "nervous" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "neural" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -24120,8 +20489,6 @@ "val" : "EMAPA:16754" }, { "val" : "EV:0100163" - }, { - "val" : "FBbt:00005094" }, { "val" : "FMA:55675" }, { @@ -24157,18 +20524,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Part of the nervous system which includes the brain and spinal cord.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The brain and spinal cord. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO)." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -24233,8 +20588,6 @@ "val" : "EHDAA2:0003094" }, { "val" : "EMAPA:16192" - }, { - "val" : "FBbt:00007692" }, { "val" : "FMA:75259" }, { @@ -24257,12 +20610,6 @@ "val" : "ZFA:0000282" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -24314,8 +20661,6 @@ "val" : "FMA:293882" }, { "val" : "MAT:0000069" - }, { - "val" : "MESH:D054259" }, { "val" : "MIAA:0000069" }, { @@ -24338,18 +20683,6 @@ "val" : "neuronames:1365" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -24381,8 +20714,6 @@ "val" : "CARO:0000000" }, { "val" : "EHDAA2:0002229" - }, { - "val" : "FBbt:10000000" }, { "val" : "FMA:62955" }, { @@ -24596,15 +20927,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "This result implies the following views in terms of evolutionary differentiation: (1) Arthropod striated muscle and vertebrate skeletal and cardiac muscles share a common ancestor. In other words, they did not evolve independently (...) (5) The divergence of vertebrate skeletal and cardiac muscles/vertebrate smooth muscle and nonmuscle is at least before that of vertebrates/arthropods. In other words, emergence of skeletal and cardiac musle type tissues preceded the vertebrate/arthropod divergence (ca. 700 MYA).[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -24667,27 +20989,6 @@ "val" : "ZFA:0000434" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0001016" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "System that provides physical support to the organism.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "skeletal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -24771,30 +21072,6 @@ "val" : "galen:Bone" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0001015" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0001630" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0002385" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Skeletal element that is composed of bone tissue.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -24847,14 +21124,10 @@ "val" : "EHDAA:518" }, { "val" : "EMAPA:16247" - }, { - "val" : "FBbt:00003125" }, { "val" : "FMA:45615" }, { "val" : "MA:0000917" - }, { - "val" : "MESH:D041981" }, { "val" : "NCIT:C34082" }, { @@ -24881,21 +21154,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The alimentary or digestive tract, and associated organs.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "FMA also has a term 'gastrointestinal tract', but this includes the liver." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000013", - "val" : "we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -24917,10 +21175,6 @@ "xrefs" : [ "ZFA:0005145" ] } ], "xrefs" : [ { - "val" : "AAO:0011066" - }, { - "val" : "EMAPA:32715" - }, { "val" : "EMAPA:37474" }, { "val" : "EV:0100146" @@ -24944,15 +21198,6 @@ "val" : "galen:Muscle" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of tissue composed of contractile fibers.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "muscular" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -24997,9 +21242,6 @@ "val" : "galen:StriatedMuscle" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Voluntary muscle tissue arranged in bundles of fibers.[AAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -25045,8 +21287,6 @@ "val" : "CALOHA:TS-2110" }, { "val" : "EFO:0000461" - }, { - "val" : "FBbt:00004208" }, { "val" : "FMA:69067" }, { @@ -25071,18 +21311,6 @@ "val" : "ZFA:0001105" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in FMA embryo is_a embryonic structure" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -25152,18 +21380,6 @@ "val" : "galen:Trunk" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000026" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000033" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -25214,9 +21430,6 @@ "val" : "http://uri.neuinfo.org/nif/nifstd/FMAID_7191" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The sensory system used for sight.[AAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0007036" }, { @@ -25305,15 +21518,6 @@ "val" : "XAO:0000168" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system that provides locomotion and physical support to the organism.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "musculoskeletal" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -25388,27 +21592,6 @@ "val" : "http://evolution.berkeley.edu/evolibrary/images/history/notochords.jpg" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "notochordal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -25495,32 +21678,8 @@ "val" : "ZFA:0000155" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "EDITOR_NOTE currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7712" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Post-cranial axial segments which form sclerotome and dermomyotome.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "somitic" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -25618,8 +21777,6 @@ "val" : "NCIT:C34222" }, { "val" : "SCTID:361462002" - }, { - "val" : "TAO:0000045" }, { "val" : "UMLS:C0027789" }, { @@ -25634,24 +21791,6 @@ "val" : "neuronames:1366" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "EDITOR_NOTE consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams)." - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002174", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_117565" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -25710,8 +21849,6 @@ "val" : "EMAPA:16073" }, { "val" : "EV:0100004" - }, { - "val" : "FBbt:00001057" }, { "val" : "FMA:87657" }, { @@ -25734,15 +21871,6 @@ "val" : "ZFA:0001120" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "neurectodermal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000013", - "val" : "we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -25942,12 +22070,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000009", - "val" : "In adults, marrow in large bones produces new blood cells[Wikipedia:Bone_marrow]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26020,18 +22142,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "MA also has set of connective tissues" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26088,12 +22198,6 @@ "val" : "galen:MuscleTissue" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0003714" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -26178,18 +22282,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system that consists of the blood and blood forming tissues.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "hematopoietic" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26239,9 +22331,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26308,9 +22397,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "see https://github.com/obophenotype/uberon/issues/27" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26352,14 +22438,8 @@ "val" : "EHDAA2:0003096" }, { "val" : "EHDAA:2161" - }, { - "val" : "EHDAA:4475" - }, { - "val" : "EHDAA:6522" }, { "val" : "EMAPA:18425" - }, { - "val" : "FBbt:00100317" }, { "val" : "FMA:7146" }, { @@ -26386,12 +22466,6 @@ "val" : "galen:Gland" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0001434" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "glandular" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -26446,9 +22520,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26542,12 +22613,6 @@ "val" : "ZFA:0000279" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -26609,21 +22674,6 @@ "val" : "ZFA:0000094" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -26659,9 +22709,6 @@ "val" : "ZFA:0001204" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -26704,8 +22751,6 @@ "val" : "EMAPA:35593" }, { "val" : "FMA:293879" - }, { - "val" : "MESH:D054258" }, { "val" : "NCIT:C34225" }, { @@ -26726,12 +22771,6 @@ "val" : "neuronames:1362" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -26791,15 +22830,6 @@ "val" : "ZFA:0000255" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -26867,18 +22897,6 @@ "val" : "ZFA:0000121" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "subclass of mesoderm in ZFA." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0006258" }, { @@ -26962,12 +22980,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The term 'myotome' is also used to describe the muscles served by a single nerve root / spinal segment - consider adding new class, myomere." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of the somites giving rise to body wall muscle masses. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "In all vertebrates, the skeletal muscle of the body axis is chiefly derived from an early embryonic compartment, known as the myotome.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27016,9 +23028,6 @@ "val" : "ZFA:0000496" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -27081,15 +23090,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "mesenchymal" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27129,9 +23129,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27154,13 +23151,8 @@ "val" : "AEO:0000114" }, { "val" : "EHDAA2:0003114" - }, { - "val" : "FBbt:00007474" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -27215,9 +23207,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "FMA has both conduit and conduit space. In EHDAA2 this is a surface feature" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27239,9 +23228,6 @@ "xrefs" : [ "FBbt:00025998" ] } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Grouping term for query purposes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -27262,9 +23248,6 @@ "xrefs" : [ "FBbt:00025990" ] } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Grouping term for query purposes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -27318,17 +23301,8 @@ "val" : "galen:Skeleton" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000383" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "skeletal" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27378,21 +23352,6 @@ "val" : "ZFA:0001513" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of somites that gives rise to dermis and muscles.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "all but the sclerotome of a mesodermal somite; the primordium of skeletal muscle and, perhaps, of the dermis." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -27416,9 +23375,6 @@ "val" : "FMA:78499" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -27512,8 +23468,6 @@ "val" : "BILA:0000060" }, { "val" : "BTO:0001403" - }, { - "val" : "FBbt:00005317" }, { "val" : "FMA:293108" }, { @@ -27536,9 +23490,6 @@ "val" : "Wikipedia:Trilaminar_blastocyst" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "We explicitly merge the NCITA terms here" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0007012" }, { @@ -27570,9 +23521,6 @@ "val" : "ZFA:0005619" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -27601,12 +23549,6 @@ "val" : "galen:SkeletalStructure" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -27688,12 +23630,6 @@ "val" : "ZFA:0000091" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Notochord rudiment[ZFIN:ZDB-PUB-961014-576]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -27712,9 +23648,6 @@ "pred" : "hasNarrowSynonym", "val" : "joint" } ], - "xrefs" : [ { - "val" : "FBbt:00005811" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27750,14 +23683,9 @@ "xrefs" : [ "FMA:71131" ] } ], "xrefs" : [ { - "val" : "FBbt:00100315" - }, { "val" : "FMA:71131" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct." - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { @@ -27812,9 +23740,6 @@ "val" : "neuronames:1363" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -27852,9 +23777,6 @@ "val" : "neuronames:1364" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -27882,9 +23804,6 @@ "val" : "ZFA:0000133" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -27910,14 +23829,9 @@ "val" : "muscle element" } ], "xrefs" : [ { - "val" : "EMAPA:32715" - }, { "val" : "FMA:30316" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -28010,9 +23924,6 @@ "pred" : "hasExactSynonym", "val" : "light-sensitive tissue" } ], - "xrefs" : [ { - "val" : "FBbt:00004200" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28041,8 +23952,6 @@ "val" : "CALOHA:TS-2122" }, { "val" : "EHDAA2:0003125" - }, { - "val" : "FBbt:00007006" }, { "val" : "FMA:292313" }, { @@ -28128,9 +24037,6 @@ "val" : "Wikipedia:Basement_membrane" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell." - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_80999" }, { @@ -28164,9 +24070,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO - check ordering; awaiting confirmation from JB" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28404,9 +24307,6 @@ "val" : "UMLS:C1514442" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -28436,16 +24336,11 @@ "xrefs" : [ "FBbt:00003154" ] } ], "xrefs" : [ { - "val" : "SPD:0000130" - }, { "val" : "TADS:0000147" }, { "val" : "http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -28473,9 +24368,6 @@ "val" : "ZFA:0000131" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -28537,9 +24429,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider merging" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Region of the gastrula which gives rise to the neural plate.[TAO]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28680,12 +24569,6 @@ "val" : "XAO:0004030" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Regular connective tissue, the intercellular matrix of which consists predominantly of collagen fiber bundles arranged in parallel arrays.[FMA]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -28756,8 +24639,6 @@ } ], "xrefs" : [ { "val" : "CARO:0010000" - }, { - "val" : "FBbt:00100313" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", @@ -28792,6 +24673,21 @@ "val" : "uberon" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0010314", + "lbl" : "structure with developmental contribution from neural crest", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An anatomical structure that has some part that develops from the neural crest.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/UBERON_0010316", "lbl" : "germ layer / neural crest", @@ -28854,8 +24750,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "xrefs" : [ { - "val" : "FBbt:00007330" - }, { "val" : "FMA:67509" }, { "val" : "SCTID:91690000" @@ -28949,9 +24843,6 @@ "val" : "Wikipedia:Dense_irregular_connective_tissue" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Tissue characterized by a thick, random arrangement of collagen and elastin fibers with very few cells. The majority of the cells are fibroblasts, but mast cells and macrophages may also be seen. It is found in the dermis, periosteum, perichondrium, capsules of organs and sheaths of nerves and muscles[NCIT]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -28977,9 +24868,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "our OWL definition states that this is differentiated from other connective tissue types by virtue of the fact that the collage fiber component predominates, as opposed to cells and fluid." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -29000,9 +24888,6 @@ "val" : "NIF_Subcellular:sao7547390221" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "the FMA class specifically refers to ureter" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -29039,9 +24924,6 @@ "val" : "Wikipedia:Epimysium" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000009", - "val" : "The Epimysium also protects muscles from friction against other muscles and bones" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -29084,9 +24966,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_147099" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "coelomic" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -29132,9 +25011,6 @@ "val" : "UMLS:C0229619" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "Bone marrow in humans, kidney interstitium in Danio, within a stroma of reticuloendothelial tissue" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -29218,15 +25094,10 @@ "val" : "AEO:0000103" }, { "val" : "BTO:0001489" - }, { - "val" : "EMAPA:36031" }, { "val" : "FMA:231424" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -29303,8 +25174,6 @@ }, "xrefs" : [ { "val" : "AEO:0000093" - }, { - "val" : "FBbt:00007278" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -29339,9 +25208,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This class is primarily to implement taxon constraints. It may be removed in the future." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -29372,9 +25238,6 @@ "pred" : "hasRelatedSynonym", "val" : "cardiac structure" } ], - "xrefs" : [ { - "val" : "SPD:0000130" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -29520,8 +25383,6 @@ "val" : "EHDAA2:0001842" }, { "val" : "EMAPA:35578" - }, { - "val" : "MA:0000165" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", @@ -29593,8 +25454,6 @@ "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], "xrefs" : [ { "val" : "CARO:0020000" - }, { - "val" : "FBbt:00007276" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", @@ -30062,120 +25921,6 @@ "val" : "uberon" } ] } - }, { - "id" : "http://purl.org/dc/elements/1.1/creator", - "lbl" : "creator", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/elements/1.1/creator" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-creator" - } ] - } - }, { - "id" : "http://purl.org/dc/elements/1.1/description", - "lbl" : "description", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/elements/1.1/description" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-description" - } ] - } - }, { - "id" : "http://purl.org/dc/elements/1.1/title", - "lbl" : "title", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/elements/1.1/title" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-title" - } ] - } - }, { - "id" : "http://purl.org/dc/terms/contributor", - "lbl" : "contributor", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/terms/contributor" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-contributor" - } ] - } - }, { - "id" : "http://purl.org/dc/terms/date", - "lbl" : "date", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/terms/date" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dcterms-date" - } ] - } - }, { - "id" : "http://purl.org/dc/terms/license", - "lbl" : "license", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/terms/license" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dcterms-license" - } ] - } }, { "id" : "http://www.geneontology.org/formats/oboInOwl#SubsetProperty", "lbl" : "subset_property", @@ -30209,9 +25954,6 @@ "val" : "An alternative label for a class or property which has a more general meaning than the preferred name/primary label." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/18" }, { @@ -30232,9 +25974,6 @@ "val" : "An alternative label for a class or property which has the exact same meaning than the preferred name/primary label." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/20" }, { @@ -30251,9 +25990,6 @@ "val" : "An alternative label for a class or property which has a more specific meaning than the preferred name/primary label." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/19" }, { @@ -30274,9 +26010,6 @@ "val" : "An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/21" }, { @@ -30309,35 +26042,10 @@ "val" : "http://www.w3.org/2000/01/rdf-schema#seeAlso" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "seeAlso" } ] } - }, { - "id" : "http://xmlns.com/foaf/0.1/depiction", - "lbl" : "depiction", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://xmlns.com/foaf/0.1/depiction" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "depiction" - } ] - } } ], "edges" : [ { "sub" : "http://purl.obolibrary.org/obo/BFO_0000004", @@ -35356,17 +31064,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0004921", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts" - } ] - } - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0001106", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0001555" + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004921" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -35410,13 +31108,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000463", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000468", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "this relationship may be too strong and may be weakened in future" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000468" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000463", "pred" : "http://purl.obolibrary.org/obo/RO_0000086", @@ -35620,13 +31312,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000926", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000923", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "sometimes not considered primary" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000923" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000926", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -36045,13 +31731,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002204", "pred" : "http://purl.obolibrary.org/obo/RO_0002254", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000926", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "check ctenophore" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000926" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002204", "pred" : "http://purl.obolibrary.org/obo/RO_0002492", @@ -36076,6 +31756,10 @@ "val" : "VSAO" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", "pred" : "is_a", @@ -36084,14 +31768,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0011137" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000098", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0001555" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000102", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0001049" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -36188,6 +31864,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010314" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "is_a", @@ -36208,16 +31888,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_89593", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "ISBN:0073040584" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_89593" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -36241,13 +31912,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "http://purl.obolibrary.org/obo/RO_0002473", - "obj" : "http://purl.obolibrary.org/obo/CL_0000333", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/CL_0000333" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "http://purl.obolibrary.org/obo/RO_0002488", @@ -36302,6 +31967,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002371", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000479" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0002371", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002371", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -36388,13 +32057,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002390", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0003061", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "definitional" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0003061" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002405", "pred" : "is_a", @@ -36571,10 +32234,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0003077", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0015212" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0003077", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000922" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003077", "pred" : "http://purl.obolibrary.org/obo/RO_0002488", @@ -36844,19 +32503,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004755", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/CL_0007001", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#date_retrieved", - "val" : "2012-08-14" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#external_class", - "val" : "VSAO:0000015" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "VSAO" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/CL_0007001" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004765", "pred" : "is_a", @@ -36968,14 +32615,14 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005062", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0015212" + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010371" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005062", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0005061" + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0015212" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005062", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000126", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0005061" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005068", @@ -37206,13 +32853,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006984", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0010199", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "via morphological boundary in CARO" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010199" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007010", "pred" : "is_a", @@ -37256,13 +32897,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007100", "pred" : "http://purl.obolibrary.org/obo/RO_0002215", - "obj" : "http://purl.obolibrary.org/obo/GO_0008015", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "GO uses blood circulation generically to include the haemolymphatic fluid of arthropods" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/GO_0008015" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007135", "pred" : "is_a", @@ -37278,16 +32913,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007282", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0009618", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#consistent_with", - "val" : "https://github.com/obophenotype/uberon/wiki/The-neural-crest" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "EDHAA2" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0009618" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007282", "pred" : "http://purl.obolibrary.org/obo/RO_0002387", @@ -37458,6 +33084,14 @@ "val" : "CARO" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0010314", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0010314", + "pred" : "http://purl.obolibrary.org/obo/RO_0002254", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0002342" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0010316", "pred" : "is_a", @@ -37580,6 +33214,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0011860", "pred" : "http://purl.obolibrary.org/obo/RO_0002473", "obj" : "http://purl.obolibrary.org/obo/GO_0098643" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0011899", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0011899", "pred" : "is_a", @@ -37622,6 +33260,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0011997", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0012429", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0012429", "pred" : "is_a", @@ -37746,10 +33388,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0015212", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0015212", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000465" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0015212", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -39106,10 +34744,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000057" - }, { - "sub" : "http://purl.obolibrary.org/obo/uberon/core#anteriorly_connected_to", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BSPO_0000099" }, { "sub" : "http://purl.obolibrary.org/obo/uberon/core#anteriorly_connected_to", "pred" : "subPropertyOf", @@ -39118,10 +34752,6 @@ "sub" : "http://purl.obolibrary.org/obo/uberon/core#anteriorly_connected_to", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/uberon/core#transitively_anteriorly_connected_to" - }, { - "sub" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BSPO_0000100" }, { "sub" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", "pred" : "subPropertyOf", @@ -39138,18 +34768,10 @@ "sub" : "http://purl.obolibrary.org/obo/uberon/core#layer_part_of", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000050" - }, { - "sub" : "http://purl.obolibrary.org/obo/uberon/core#posteriorly_connected_to", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BSPO_0000096" }, { "sub" : "http://purl.obolibrary.org/obo/uberon/core#posteriorly_connected_to", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002170" - }, { - "sub" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BSPO_0000097" }, { "sub" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to", "pred" : "subPropertyOf", @@ -39366,10 +34988,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012001", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012005" - }, { - "sub" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", - "pred" : "inverseOf", - "obj" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to" } ], "logicalDefinitionAxioms" : [ { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000006", @@ -41170,13 +36788,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002082", "fillerId" : "http://purl.obolibrary.org/obo/GO_0040016" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0000165", - "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0004921" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BSPO_0001106", - "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0001555" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0000307", "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000468" ], @@ -41513,6 +37124,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0000086", "fillerId" : "http://purl.obolibrary.org/obo/PATO_0001993" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0010314", + "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002254", + "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0002342" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0010371", "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000483" ], @@ -41567,13 +37185,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002473", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0002530" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0015212", - "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0000465" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0016879", "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0006598" ], @@ -41887,7 +37498,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002551", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061", "http://purl.obolibrary.org/obo/UBERON_0000475" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002566", @@ -41949,10 +37560,6 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0019000", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/uberon/core#channel_for", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0004111" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000463" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] @@ -41984,21 +37591,12 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002287", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002210" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002329", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002215" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002496" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002497" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002479", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/BFO_0000066" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/RO_0000057" ] @@ -42017,24 +37615,12 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000066", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000066", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002314", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0000052", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0001025", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0001025", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002005", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002005", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002005", "http://purl.obolibrary.org/obo/RO_0002380" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002100", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002100", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/uberon/core#extends_fibers_into", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002100", "http://purl.obolibrary.org/obo/RO_0013001" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002102", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002102", "http://purl.obolibrary.org/obo/BFO_0000050" ] @@ -42050,24 +37636,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002131", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002131", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002134", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002134", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002150", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002170", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002176", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002178", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002202", "http://purl.obolibrary.org/obo/RO_0002162" ] @@ -42104,9 +37675,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0019002", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002213", "http://purl.obolibrary.org/obo/RO_0019002" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002216", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002215", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002215", "http://purl.obolibrary.org/obo/RO_0002162" ] @@ -42155,9 +37723,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002254", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002256", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002258", "http://purl.obolibrary.org/obo/RO_0002496" ] @@ -42179,9 +37744,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004031", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/BFO_0000051" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002432", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/BFO_0000066" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002327", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002017" ] @@ -42245,15 +37807,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002339", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002339", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002177", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002371", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002371", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002387", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002407", "http://purl.obolibrary.org/obo/RO_0002629" ] @@ -42266,15 +37819,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002488", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002488", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002488", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002492", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002492", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002492", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002496", "http://purl.obolibrary.org/obo/BFO_0000050" ] @@ -42293,9 +37840,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002497", "http://purl.obolibrary.org/obo/RO_0002082" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/uberon/core#indirectly_supplies", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002569", "http://purl.obolibrary.org/obo/RO_0002178" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/uberon/core#indirectly_supplies", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002569", "http://purl.obolibrary.org/obo/uberon/core#indirectly_supplies" ] @@ -42314,12 +37858,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002630", "http://purl.obolibrary.org/obo/RO_0002630" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0003000", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0003001", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0013001", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0013001", "http://purl.obolibrary.org/obo/BFO_0000050" ] diff --git a/src/ontology/subsets/general_cell_types_upper_slim.obo b/src/ontology/subsets/general_cell_types_upper_slim.obo index bf1c7bcd8..e08277a75 100644 --- a/src/ontology/subsets/general_cell_types_upper_slim.obo +++ b/src/ontology/subsets/general_cell_types_upper_slim.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: cl/releases/2024-02-13/subsets/general_cell_types_upper_slim.owl +data-version: cl/releases/2024-04-05/subsets/general_cell_types_upper_slim.owl subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -88,7 +88,7 @@ synonymtypedef: synonym "" synonymtypedef: SYSTEMATIC "" synonymtypedef: systematic_synonym "" ontology: cl/subsets/general_cell_types_upper_slim -property_value: owl:versionInfo "2024-02-13" xsd:string +property_value: owl:versionInfo "2024-04-05" xsd:string [Term] id: BFO:0000002 @@ -159,7 +159,7 @@ is_a: UBERON:0000061 ! anatomical structure disjoint_from: GO:0031012 ! extracellular matrix disjoint_from: GO:0032991 ! protein-containing complex disjoint_from: GO:0043226 ! organelle -relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms +relationship: RO:0002160 NCBITaxon:131567 ! only in taxon cellular organisms [Term] id: CL:0000006 @@ -193,8 +193,8 @@ is_a: CL:0011115 ! precursor cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0017145 ! stem cell division relationship: capable_of GO:0017145 ! stem cell division -relationship: in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000037 @@ -244,8 +244,8 @@ relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surfac relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -relationship: develops_from CL:0000566 ! angioblastic mesenchymal cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000566 ! develops from angioblastic mesenchymal cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000039 @@ -277,11 +277,11 @@ intersection_of: has_part CL:0017503 ! basophilic cytoplasm intersection_of: has_part GO:0000791 ! euchromatin intersection_of: has_part GO:0005730 ! nucleolus intersection_of: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M -relationship: develops_from CL:0002009 ! macrophage dendritic cell progenitor relationship: has_part CL:0017503 ! basophilic cytoplasm relationship: has_part GO:0000791 ! euchromatin relationship: has_part GO:0005730 ! nucleolus relationship: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M +relationship: RO:0002202 CL:0002009 ! develops from macrophage dendritic cell progenitor [Term] id: CL:0000048 @@ -317,7 +317,7 @@ xref: BTO:0004730 is_a: CL:0002032 {is_inferred="true"} ! hematopoietic oligopotent progenitor cell disjoint_from: CL:0000051 ! common lymphoid progenitor disjoint_from: CL:0000557 ! granulocyte monocyte progenitor cell -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000051 @@ -340,7 +340,7 @@ is_a: CL:0011026 ! progenitor cell intersection_of: CL:0002032 ! hematopoietic oligopotent progenitor cell intersection_of: capable_of GO:0030098 ! lymphocyte differentiation relationship: capable_of GO:0030098 ! lymphocyte differentiation -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000052 @@ -387,8 +387,8 @@ xref: FMA:63877 xref: NCIT:C12482 xref: VHOG:0001482 is_a: CL:0002320 ! connective tissue cell -relationship: develops_from CL:0000134 ! mesenchymal stem cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000066 @@ -407,8 +407,8 @@ xref: WBbt:0003672 is_a: CL:0000000 ! cell disjoint_from: CL:0000738 ! leukocyte relationship: part_of UBERON:0000483 ! epithelium -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000075 @@ -417,7 +417,7 @@ def: "A columnar/cuboidal epithelial cell is a cell usually found in a two dimen subset: cellxgene_subset subset: human_reference_atlas is_a: CL:0000066 ! epithelial cell -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000081 @@ -454,8 +454,8 @@ intersection_of: CL:0000542 ! lymphocyte intersection_of: capable_of GO:0002456 ! T cell mediated immunity disjoint_from: CL:0000945 ! lymphocyte of B lineage relationship: capable_of GO:0002456 ! T cell mediated immunity -relationship: develops_from CL:0000827 ! pro-T cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000827 ! develops from pro-T cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000092 @@ -483,7 +483,6 @@ intersection_of: part_of UBERON:0001474 ! bone element intersection_of: RO:0002104 PR:000001954 ! has plasma membrane part tumor necrosis factor receptor superfamily member 11A intersection_of: RO:0002104 PR:000002062 ! has plasma membrane part macrophage colony-stimulating factor 1 receptor relationship: capable_of GO:0045453 ! bone resorption -relationship: develops_from CL:0000576 ! monocyte relationship: has_part PR:000001850 ! cathepsin K relationship: has_part PR:000001937 ! tartrate-resistant acid phosphatase type 5 relationship: has_part PR:000001944 ! transcription factor PU.1 @@ -491,6 +490,7 @@ relationship: has_part PR:000007597 ! protein c-Fos relationship: has_part PR:000011178 ! nuclear factor NF-kappa-B p100 subunit relationship: RO:0002104 PR:000001954 ! has plasma membrane part tumor necrosis factor receptor superfamily member 11A relationship: RO:0002104 PR:000002062 ! has plasma membrane part macrophage colony-stimulating factor 1 receptor +relationship: RO:0002202 CL:0000576 ! develops from monocyte [Term] id: CL:0000094 @@ -523,17 +523,17 @@ relationship: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon relationship: CL:4030046 PR:000001024 ! lacks_plasma_membrane_part neural cell adhesion molecule 1 relationship: CL:4030046 PR:000001084 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD8 alpha chain relationship: has_part GO:0030141 ! secretory granule -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M relationship: RO:0002104 PR:000001332 ! has plasma membrane part carcinoembryonic antigen-related cell adhesion molecule 8 relationship: RO:0002104 PR:000001969 ! has plasma membrane part urokinase plasminogen activator surface receptor +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000095 name: neuron associated cell subset: cellxgene_subset is_a: CL:0002319 ! neural cell -relationship: develops_from CL:0000133 ! neurectodermal cell +relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell [Term] id: CL:0000100 @@ -547,7 +547,7 @@ xref: FBbt:00005123 xref: FMA:83617 xref: WBbt:0005409 is_a: CL:0000527 ! efferent neuron -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000101 @@ -574,7 +574,7 @@ is_a: CL:0000518 {is_inferred="true"} ! phagocyte (sensu Vertebrata) is_a: CL:0000842 ! mononuclear cell intersection_of: CL:0000518 ! phagocyte (sensu Vertebrata) intersection_of: bearer_of PATO:0001407 ! mononucleate -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000125 @@ -637,8 +637,8 @@ xref: CALOHA:TS-0012 xref: FMA:63880 is_a: CL:0000325 ! stuff accumulating cell is_a: CL:0002320 ! connective tissue cell -relationship: develops_from CL:0000134 ! mesenchymal stem cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000145 @@ -677,11 +677,11 @@ xref: MESH:D008544 xref: VHOG:0001679 is_a: CL:0000147 ! pigment cell intersection_of: CL:0000147 ! pigment cell -intersection_of: develops_from CL:0000541 ! melanoblast intersection_of: has_part GO:0042470 ! melanosome -relationship: develops_from CL:0000541 ! melanoblast +intersection_of: RO:0002202 CL:0000541 ! develops from melanoblast relationship: has_part GO:0042470 ! melanosome -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000541 ! develops from melanoblast +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000149 @@ -723,7 +723,7 @@ synonym: "endocrinocyte" EXACT [] xref: FMA:83809 is_a: CL:0000151 ! secretory cell relationship: part_of UBERON:0000949 ! endocrine system -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000183 @@ -747,8 +747,8 @@ xref: FMA:67328 xref: WBbt:0003675 is_a: CL:0000183 ! contractile cell is_a: CL:0000393 ! electrically responsive cell -relationship: develops_from CL:0000056 ! myoblast -property_value: depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI +relationship: RO:0002202 CL:0000056 ! develops from myoblast +property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI [Term] id: CL:0000188 @@ -765,7 +765,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001134 ! skeletal muscle tissue relationship: part_of UBERON:0001134 ! skeletal muscle tissue -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000192 @@ -783,8 +783,8 @@ xref: CALOHA:TS-2159 xref: FMA:14072 is_a: CL:0008000 ! non-striated muscle cell is_a: CL:0008007 ! visceral muscle cell -relationship: develops_from CL:0000514 ! smooth muscle myoblast -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000514 ! develops from smooth muscle myoblast +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000197 @@ -811,7 +811,7 @@ is_a: CL:0000006 {is_inferred="true"} ! neuronal receptor cell intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0050962 ! detection of light stimulus involved in sensory perception relationship: capable_of GO:0050962 ! detection of light stimulus involved in sensory perception -property_value: depiction "https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg" xsd:anyURI [Term] id: CL:0000211 @@ -918,8 +918,8 @@ intersection_of: capable_of GO:0002504 ! antigen processing and presentation of intersection_of: capable_of GO:0006909 ! phagocytosis intersection_of: capable_of GO:0031268 ! pseudopodium organization relationship: capable_of GO:0031268 ! pseudopodium organization -relationship: develops_from CL:0000576 ! monocyte -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000576 ! develops from monocyte +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000236 @@ -941,7 +941,7 @@ is_a: CL:0000945 {is_inferred="true"} ! lymphocyte of B lineage intersection_of: CL:0000945 ! lymphocyte of B lineage intersection_of: capable_of GO:0019724 ! B cell mediated immunity relationship: capable_of GO:0019724 ! B cell mediated immunity -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000255 @@ -950,8 +950,8 @@ subset: cellxgene_subset xref: MESH:D005057 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell -intersection_of: only_in_taxon NCBITaxon:2759 ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +intersection_of: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota [Term] id: CL:0000325 @@ -973,7 +973,7 @@ xref: FMA:86667 is_a: CL:0000219 ! motile cell is_a: CL:0011012 ! neural crest cell is_a: CL:0011026 ! progenitor cell -relationship: develops_from CL:0007004 ! premigratory neural crest cell +relationship: RO:0002202 CL:0007004 ! develops from premigratory neural crest cell [Term] id: CL:0000349 @@ -1013,8 +1013,8 @@ is_a: CL:0000007 ! early embryonic cell (metazoa) is_a: CL:0000255 ! eukaryotic cell is_a: CL:0010017 ! zygote intersection_of: CL:0010017 ! zygote -intersection_of: only_in_taxon NCBITaxon:33208 ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +intersection_of: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa [Term] id: CL:0000393 @@ -1065,7 +1065,7 @@ relationship: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon relationship: CL:4030046 PR:000001024 ! lacks_plasma_membrane_part neural cell adhesion molecule 1 relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-spanning 4-domains subfamily A member 1 relationship: has_part GO:0042613 ! MHC class II protein complex -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000473 @@ -1083,8 +1083,8 @@ subset: human_reference_atlas xref: BTO:0002064 xref: FMA:83624 is_a: CL:0002320 ! connective tissue cell -relationship: develops_from CL:0000134 ! mesenchymal stem cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000513 @@ -1097,8 +1097,8 @@ xref: FMA:84797 is_a: CL:0002494 ! cardiocyte is_a: CL:0010021 ! cardiac myoblast intersection_of: CL:0000056 ! myoblast -intersection_of: develops_into CL:0000746 ! cardiac muscle cell intersection_of: part_of UBERON:0001133 ! cardiac muscle tissue +intersection_of: RO:0002203 CL:0000746 ! develops into cardiac muscle cell relationship: part_of UBERON:0001133 ! cardiac muscle tissue [Term] @@ -1111,8 +1111,8 @@ synonym: "satellite cell" RELATED [] xref: FMA:84798 is_a: CL:0000056 ! myoblast intersection_of: CL:0000056 ! myoblast -intersection_of: develops_into CL:0000192 ! smooth muscle cell -relationship: develops_into CL:0000192 ! smooth muscle cell +intersection_of: RO:0002203 CL:0000192 ! develops into smooth muscle cell +relationship: RO:0002203 CL:0000192 ! develops into smooth muscle cell [Term] id: CL:0000515 @@ -1123,9 +1123,9 @@ xref: FMA:84799 is_a: CL:0000056 ! myoblast is_a: CL:0011026 ! progenitor cell intersection_of: CL:0000056 ! myoblast -intersection_of: develops_into CL:0008002 ! skeletal muscle fiber -relationship: develops_from CL:0000355 ! multi-potent skeletal muscle stem cell -relationship: develops_into CL:0008002 ! skeletal muscle fiber +intersection_of: RO:0002203 CL:0008002 ! develops into skeletal muscle fiber +relationship: RO:0002202 CL:0000355 ! develops from multi-potent skeletal muscle stem cell +relationship: RO:0002203 CL:0008002 ! develops into skeletal muscle fiber [Term] id: CL:0000518 @@ -1133,7 +1133,7 @@ name: phagocyte (sensu Vertebrata) def: "A phagocyte in vertebrates that is able to phagocytosis." [GOC:tfm] is_a: CL:0000234 ! phagocyte is_a: CL:0000255 ! eukaryotic cell -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata [Term] id: CL:0000526 @@ -1143,7 +1143,7 @@ subset: human_reference_atlas synonym: "input neuron" EXACT [] xref: FMA:87653 is_a: CL:0000540 ! neuron -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000527 @@ -1171,8 +1171,8 @@ is_a: CL:0000393 ! electrically responsive cell is_a: CL:0000404 ! electrically signaling cell is_a: CL:0002319 ! neural cell relationship: capable_of GO:0019226 ! transmission of nerve impulse -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://www.swissbiopics.org/api/image/Neuron_cells.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Neuron_cells.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000541 @@ -1183,7 +1183,7 @@ xref: BTO:0003217 xref: FMA:83377 is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0011026 ! progenitor cell -relationship: develops_from CL:0000333 ! migratory neural crest cell +relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell [Term] id: CL:0000542 @@ -1206,10 +1206,10 @@ intersection_of: has_part CL:0017500 ! neutrophillic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin disjoint_from: CL:0000766 ! myeloid leukocyte relationship: bearer_of PATO:0040072 ! high nuclear/cytoplasmic ratio -relationship: develops_from CL:0000051 ! common lymphoid progenitor relationship: has_part CL:0017500 ! neutrophillic cytoplasm relationship: has_part GO:0000792 ! heterochromatin -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000051 ! develops from common lymphoid progenitor +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000557 @@ -1245,8 +1245,8 @@ relationship: CL:4030045 PR:000007857 ! lacks_part erythroid transcription facto relationship: CL:4030045 PR:000007858 ! lacks_part endothelial transcription factor GATA-2 relationship: has_part PR:000001944 ! transcription factor PU.1 relationship: has_part PR:000005307 ! CCAAT/enhancer-binding protein alpha -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002104 PR:000001865 ! has plasma membrane part interleukin-3 receptor class 2 alpha chain +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000559 @@ -1264,10 +1264,10 @@ intersection_of: CL:0002194 ! monopoietic cell intersection_of: capable_of GO:0030224 ! monocyte differentiation intersection_of: has_part GO:0042582 ! azurophil granule intersection_of: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M -relationship: develops_from CL:0000040 ! monoblast relationship: has_part GO:0042582 ! azurophil granule -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M +relationship: RO:0002202 CL:0000040 ! develops from monoblast +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000566 @@ -1283,10 +1283,10 @@ intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: RO:0002104 PR:000001444 ! has plasma membrane part cadherin-5 intersection_of: RO:0002104 PR:000002112 ! has plasma membrane part vascular endothelial growth factor receptor 2 intersection_of: RO:0002104 PR:000016043 ! has plasma membrane part T-cell acute lymphocytic leukemia protein 1 -relationship: develops_from CL:0000134 ! mesenchymal stem cell relationship: RO:0002104 PR:000001444 ! has plasma membrane part cadherin-5 relationship: RO:0002104 PR:000002112 ! has plasma membrane part vascular endothelial growth factor receptor 2 relationship: RO:0002104 PR:000016043 ! has plasma membrane part T-cell acute lymphocytic leukemia protein 1 +relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell [Term] id: CL:0000576 @@ -1311,8 +1311,8 @@ intersection_of: capable_of GO:0043011 ! myeloid dendritic cell differentiation relationship: capable_of GO:0030225 ! macrophage differentiation relationship: capable_of GO:0030316 ! osteoclast differentiation relationship: capable_of GO:0043011 ! myeloid dendritic cell differentiation -relationship: develops_from CL:0000559 ! promonocyte -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000559 ! develops from promonocyte +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000623 @@ -1343,8 +1343,8 @@ relationship: capable_of GO:0002228 ! natural killer cell mediated immunity relationship: capable_of GO:0050776 ! regulation of immune response relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-spanning 4-domains subfamily A member 1 relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule -relationship: develops_from CL:0000825 ! pro-NK cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000825 ! develops from pro-NK cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000680 @@ -1353,9 +1353,9 @@ def: "A non-terminally differentiated cell that is capable of developing into a subset: cellxgene_subset is_a: CL:0000055 ! non-terminally differentiated cell intersection_of: CL:0011115 ! precursor cell -intersection_of: develops_into CL:0000187 ! muscle cell -relationship: develops_from CL:0000222 ! mesodermal cell -relationship: develops_into CL:0000187 ! muscle cell +intersection_of: RO:0002203 CL:0000187 ! develops into muscle cell +relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell +relationship: RO:0002203 CL:0000187 ! develops into muscle cell [Term] id: CL:0000723 @@ -1405,10 +1405,10 @@ intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0002505 ! nucleated intersection_of: capable_of GO:0001667 ! ameboidal-type cell migration relationship: capable_of GO:0001667 ! ameboidal-type cell migration -relationship: develops_from CL:0000037 ! hematopoietic stem cell -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0002405 ! immune system -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002202 CL:0000037 ! develops from hematopoietic stem cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000746 @@ -1436,9 +1436,9 @@ intersection_of: has_part GO:0030017 ! sarcomere intersection_of: part_of UBERON:0007100 ! primary circulatory organ intersection_of: participates_in GO:0060047 ! heart contraction relationship: bearer_of PATO:0002478 ! transversely striated -relationship: develops_from CL:0000513 ! cardiac muscle myoblast relationship: participates_in GO:0060047 ! heart contraction -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000513 ! develops from cardiac muscle myoblast +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000763 @@ -1450,8 +1450,8 @@ xref: CALOHA:TS-0647 xref: MESH:D022423 is_a: CL:0000988 {is_inferred="true"} ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell -intersection_of: develops_from CL:0000049 ! common myeloid progenitor -relationship: develops_from CL:0000049 ! common myeloid progenitor +intersection_of: RO:0002202 CL:0000049 ! develops from common myeloid progenitor +relationship: RO:0002202 CL:0000049 ! develops from common myeloid progenitor [Term] id: CL:0000766 @@ -1461,7 +1461,7 @@ subset: cellxgene_subset is_a: CL:0000738 {is_inferred="true"} ! leukocyte is_a: CL:0000763 ! myeloid cell intersection_of: CL:0000738 ! leukocyte -intersection_of: develops_from CL:0000049 ! common myeloid progenitor +intersection_of: RO:0002202 CL:0000049 ! develops from common myeloid progenitor [Term] id: CL:0000775 @@ -1490,9 +1490,9 @@ is_a: CL:0000094 {is_inferred="true"} ! granulocyte intersection_of: CL:0000094 ! granulocyte intersection_of: RO:0002104 PR:000001479 ! has plasma membrane part low affinity immunoglobulin gamma Fc region receptor II intersection_of: RO:0002104 PR:000001879 ! has plasma membrane part leukosialin -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002104 PR:000001479 ! has plasma membrane part low affinity immunoglobulin gamma Fc region receptor II relationship: RO:0002104 PR:000001879 ! has plasma membrane part leukosialin +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000782 @@ -1509,9 +1509,9 @@ is_a: CL:0000766 ! myeloid leukocyte is_a: CL:0000990 {is_inferred="true"} ! conventional dendritic cell intersection_of: CL:0000990 ! conventional dendritic cell intersection_of: CL:4030046 PR:000001865 ! lacks_plasma_membrane_part interleukin-3 receptor class 2 alpha chain -intersection_of: develops_from CL:0000763 ! myeloid cell +intersection_of: RO:0002202 CL:0000763 ! develops from myeloid cell relationship: CL:4030046 PR:000001865 ! lacks_plasma_membrane_part interleukin-3 receptor class 2 alpha chain -relationship: develops_from CL:0000763 ! myeloid cell +relationship: RO:0002202 CL:0000763 ! develops from myeloid cell [Term] id: CL:0000825 @@ -1534,11 +1534,11 @@ intersection_of: RO:0002104 PR:000001381 ! has plasma membrane part interleukin- intersection_of: RO:0002104 PR:000001898 ! has plasma membrane part neprilysin relationship: CL:4030046 PR:000001874 ! lacks_plasma_membrane_part KLRB1-like protein relationship: CL:4030046 PR:000002065 ! lacks_plasma_membrane_part mast/stem cell growth factor receptor -relationship: develops_from CL:0000051 ! common lymphoid progenitor relationship: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule relationship: RO:0002104 PR:000001015 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RA relationship: RO:0002104 PR:000001381 ! has plasma membrane part interleukin-2 receptor subunit beta relationship: RO:0002104 PR:000001898 ! has plasma membrane part neprilysin +relationship: RO:0002202 CL:0000051 ! develops from common lymphoid progenitor [Term] id: CL:0000826 @@ -1563,11 +1563,11 @@ intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: has_part PR:000001903 ! paired box protein PAX-5 intersection_of: has_part PR:000006611 ! DNA nucleotidylexotransferase intersection_of: participates_in GO:0033152 ! immunoglobulin V(D)J recombination -relationship: develops_from CL:0000051 ! common lymphoid progenitor relationship: has_part PR:000001903 ! paired box protein PAX-5 relationship: has_part PR:000006611 ! DNA nucleotidylexotransferase relationship: participates_in GO:0033152 ! immunoglobulin V(D)J recombination -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000051 ! develops from common lymphoid progenitor +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000827 @@ -1583,7 +1583,7 @@ is_a: CL:0000838 {is_inferred="true"} ! lymphoid lineage restricted progenitor c intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: capable_of GO:0030217 ! T cell differentiation relationship: capable_of GO:0030217 ! T cell differentiation -relationship: develops_from CL:0000051 ! common lymphoid progenitor +relationship: RO:0002202 CL:0000051 ! develops from common lymphoid progenitor [Term] id: CL:0000837 @@ -1630,9 +1630,9 @@ relationship: CL:4030046 PR:000001869 ! lacks_plasma_membrane_part interleukin-7 relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -relationship: develops_from CL:0000037 ! hematopoietic stem cell -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule +relationship: RO:0002202 CL:0000037 ! develops from hematopoietic stem cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000838 @@ -1667,7 +1667,7 @@ is_a: CL:0011026 ! progenitor cell intersection_of: CL:0002031 ! hematopoietic lineage restricted progenitor cell intersection_of: capable_of GO:0030099 ! myeloid cell differentiation relationship: capable_of GO:0030099 ! myeloid cell differentiation -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000842 @@ -1692,8 +1692,8 @@ def: "A lymphocyte of B lineage with the commitment to express an immunoglobulin comment: Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells). Lymphocytes of B cell lineage can be distinguished from those of T cell lineage by their lack of CD3e (as part of the T cell receptor complex). subset: human_reference_atlas is_a: CL:0000542 {is_inferred="true"} ! lymphocyte -relationship: develops_from CL:0000826 ! pro-B cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000826 ! develops from pro-B cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000988 @@ -1727,8 +1727,8 @@ xref: FMA:84191 is_a: CL:0000451 {is_inferred="true"} ! dendritic cell intersection_of: CL:0000451 ! dendritic cell intersection_of: RO:0015015 PR:000001013 ! has high plasma membrane amount integrin alpha-X -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0015015 PR:000001013 ! has high plasma membrane amount integrin alpha-X +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0001012 @@ -1745,9 +1745,9 @@ subset: human_reference_atlas is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001474 ! bone element -relationship: dc-contributor https://orcid.org/0000-0001-9990-8331 relationship: part_of UBERON:0001474 ! bone element -relationship: present_in_taxon NCBITaxon:9606 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2011-11-16T04:28:16Z [Term] @@ -1781,7 +1781,7 @@ relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surfac relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:27Z [Term] @@ -1801,9 +1801,9 @@ relationship: capable_of GO:0001816 ! cytokine production relationship: capable_of GO:0045087 ! innate immune response relationship: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule relationship: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon -relationship: dc-contributor https://orcid.org/0000-0001-9990-8331 -relationship: present_in_taxon NCBITaxon:9606 -property_value: dcterms-date "2017-01-30T20:20:48Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 +property_value: http://purl.org/dc/terms/date "2017-01-30T20:20:48Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0001067 @@ -1814,9 +1814,9 @@ is_a: CL:0001065 ! innate lymphoid cell intersection_of: CL:0001065 ! innate lymphoid cell intersection_of: capable_of GO:0032609 ! type II interferon production relationship: capable_of GO:0032609 ! type II interferon production -relationship: dc-contributor https://orcid.org/0000-0001-9990-8331 -relationship: present_in_taxon NCBITaxon:9606 -property_value: dcterms-date "2017-01-30T20:42:44Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 +property_value: http://purl.org/dc/terms/date "2017-01-30T20:42:44Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0002009 @@ -1832,8 +1832,8 @@ intersection_of: capable_of GO:0030224 ! monocyte differentiation intersection_of: capable_of GO:0043011 ! myeloid dendritic cell differentiation relationship: capable_of GO:0030224 ! monocyte differentiation relationship: capable_of GO:0043011 ! myeloid dendritic cell differentiation -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000557 ! granulocyte monocyte progenitor cell +relationship: RO:0002202 CL:0000557 ! develops from granulocyte monocyte progenitor cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-19T02:51:58Z [Term] @@ -1846,8 +1846,8 @@ intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001400 ! unipotent disjoint_from: CL:0002032 ! hematopoietic oligopotent progenitor cell relationship: bearer_of PATO:0001400 ! unipotent -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002032 ! hematopoietic oligopotent progenitor cell +relationship: RO:0002202 CL:0002032 ! develops from hematopoietic oligopotent progenitor cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:20Z [Term] @@ -1860,8 +1860,8 @@ is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001401 ! oligopotent relationship: bearer_of PATO:0001401 ! oligopotent -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000837 ! hematopoietic multipotent progenitor cell +relationship: RO:0002202 CL:0000837 ! develops from hematopoietic multipotent progenitor cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:27Z [Term] @@ -1871,9 +1871,9 @@ def: "An epithelial cell derived from ectoderm." [FMA:69074, GOC:tfm] xref: FMA:69074 is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell -intersection_of: develops_from CL:0000221 ! ectodermal cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000221 ! ectodermal cell +intersection_of: RO:0002202 CL:0000221 ! develops from ectodermal cell +relationship: RO:0002202 CL:0000221 ! develops from ectodermal cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T03:38:22Z [Term] @@ -1888,8 +1888,8 @@ xref: MESH:D001854 is_a: CL:0001035 {is_inferred="true"} ! bone cell intersection_of: CL:0001035 ! bone cell intersection_of: part_of UBERON:0002371 ! bone marrow -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002371 ! bone marrow +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-07-22T04:48:15Z [Term] @@ -1901,7 +1901,7 @@ is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor ce intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: capable_of GO:0030224 ! monocyte differentiation relationship: capable_of GO:0030224 ! monocyte differentiation -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-30T01:27:48Z [Term] @@ -1913,7 +1913,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0002505 ! nucleated relationship: bearer_of PATO:0002505 ! nucleated -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T03:32:33Z [Term] @@ -1926,8 +1926,8 @@ xref: FMA:70333 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001016 ! nervous system -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001016 ! nervous system +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T01:34:57Z [Term] @@ -1941,8 +1941,8 @@ xref: MESH:D003239 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0002384 ! connective tissue -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002384 ! connective tissue +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T03:01:54Z [Term] @@ -1953,7 +1953,7 @@ xref: CALOHA:TS-0263 xref: FMA:82840 xref: WBbt:0007028 is_a: CL:0000000 ! cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T03:39:21Z [Term] @@ -1970,7 +1970,7 @@ intersection_of: bearer_of PATO:0001908 ! multinucleate intersection_of: bearer_of PATO:0002478 ! transversely striated intersection_of: has_part GO:0030017 ! sarcomere relationship: bearer_of PATO:0002478 ! transversely striated -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-24T01:13:01Z [Term] @@ -1986,8 +1986,8 @@ xref: FMA:84791 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0007100 ! primary circulatory organ -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0007100 ! primary circulatory organ +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T09:37:22Z [Term] @@ -1997,7 +1997,7 @@ def: "Cell that has the potential to form a skeletal cell type (e.g. cells in pe comment: Needs logical definition. Should be capable_of skeletal system morphogenesis? or skeletal tissue development? needs to be added to GO. NOTES:a cell type of the early embryo (see also: mesenchymal cells) that will give rise to mineralized connective tissue. Scleroblasts can differentiate into osteoblasts (bone-forming cells), chondroblasts (cartilage-forming cells), odontoblasts (dentin-forming cells), ameloblasts (enamel-forming cells). The mesenchymal cells developing into osteoblasts and chondroblasts are derived from the mesoderm. Those developing into odontoblasts are neural crest cells. Those developing into ameloblasts are derived from the ectoderm. (http://www.copewithcytokines.de/cope.cgi?key=scleroblasts) synonym: "scleroblast" EXACT [GO_REF:0000034] is_a: CL:0000000 ! cell -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-15T02:51:27Z [Term] @@ -2005,9 +2005,9 @@ id: CL:0007004 name: premigratory neural crest cell def: "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells." [UBERONREF:0000002] is_a: CL:0011012 ! neural crest cell -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 -relationship: develops_from CL:0000133 ! neurectodermal cell relationship: part_of UBERON:0002342 ! neural crest +relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-27T08:27:35Z [Term] @@ -2036,7 +2036,7 @@ intersection_of: bearer_of PATO:0001908 ! multinucleate intersection_of: bearer_of PATO:0002478 ! transversely striated intersection_of: has_part GO:0030017 ! sarcomere intersection_of: part_of UBERON:0001134 ! skeletal muscle tissue -relationship: develops_from CL:0000515 ! skeletal muscle myoblast +relationship: RO:0002202 CL:0000515 ! develops from skeletal muscle myoblast [Term] id: CL:0008007 @@ -2058,7 +2058,7 @@ synonym: "mesenchyme cell" EXACT [] is_a: CL:0000219 ! motile cell relationship: capable_of GO:0016477 ! cell migration relationship: part_of UBERON:0003104 ! mesenchyme -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0009004 @@ -2077,7 +2077,7 @@ name: zygote def: "A zygote in a plant or an animal." [] xref: MESH:D015053 is_a: CL:0000000 ! cell -relationship: seeAlso https://github.com/obophenotype/cell-ontology/issues/786 +property_value: seeAlso https://github.com/obophenotype/cell-ontology/issues/786 [Term] id: CL:0010021 @@ -2085,8 +2085,8 @@ name: cardiac myoblast xref: MESH:D032386 is_a: CL:0000056 ! myoblast intersection_of: CL:0000056 ! myoblast -intersection_of: develops_into CL:0000746 ! cardiac muscle cell -relationship: develops_into CL:0000746 ! cardiac muscle cell +intersection_of: RO:0002203 CL:0000746 ! develops into cardiac muscle cell +relationship: RO:0002203 CL:0000746 ! develops into cardiac muscle cell [Term] id: CL:0011012 @@ -2103,9 +2103,9 @@ def: "A precursor cell that has a tendency to differentiate into a specific type subset: cellxgene_subset is_a: CL:0011115 ! precursor cell intersection_of: CL:0011115 ! precursor cell -intersection_of: develops_from CL:0000034 ! stem cell -relationship: dc-contributor https://orcid.org/0000-0001-5208-3432 -relationship: develops_from CL:0000034 ! stem cell +intersection_of: RO:0002202 CL:0000034 ! develops from stem cell +relationship: RO:0002202 CL:0000034 ! develops from stem cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011115 @@ -2126,7 +2126,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0070046 ! neutrophillic relationship: bearer_of PATO:0070046 ! neutrophillic -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-05-25T01:36:34Z [Term] @@ -2137,7 +2137,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0002094 ! basophilic relationship: bearer_of PATO:0002094 ! basophilic -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-22T04:24:54Z [Term] @@ -2228,7 +2228,7 @@ namespace: biological_process def: "A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities." [GOC:dph, GOC:go_curators, GOC:tb, ISBN:978-0-07-139011-8] comment: Action potentials typically propagate across excitable membranes. This class covers both action potentials that propagate and those that fail to do so. is_a: GO:0042391 ! regulation of membrane potential -relationship: never_in_taxon NCBITaxon:4895 +property_value: RO:0002161 NCBITaxon:4895 [Term] id: GO:0001667 @@ -2304,8 +2304,8 @@ def: "A multicellular organismal process by which exposure to an activating fact subset: goslim_pir is_a: GO:0009987 ! cellular process is_a: GO:0032501 ! multicellular organismal process -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24416" xsd:anyURI [Term] @@ -2419,8 +2419,8 @@ synonym: "acquired immune response" EXACT [ISBN:068340007X] synonym: "immune memory response" EXACT [GOC:add] xref: Wikipedia:Adaptive_immune_system is_a: GO:0006955 ! immune response -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0002252 @@ -2455,7 +2455,7 @@ subset: goslim_mouse subset: goslim_pir xref: Wikipedia:Immune_system is_a: GO:0008150 ! biological_process -relationship: never_in_taxon NCBITaxon:4895 +property_value: RO:0002161 NCBITaxon:4895 [Term] id: GO:0002377 @@ -2499,9 +2499,9 @@ synonym: "leukocyte immune effector process" EXACT [] is_a: GO:0002252 ! immune effector process intersection_of: GO:0002376 ! immune system process intersection_of: process_has_causal_agent CL:0000738 ! leukocyte -relationship: in_taxon NCBITaxon:7742 {all_only="true"} ! Vertebrata -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: process_has_causal_agent CL:0000738 ! leukocyte +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 {all_only="true"} ! in taxon Vertebrata [Term] id: GO:0002449 @@ -2699,8 +2699,8 @@ namespace: cellular_component def: "A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures." [GOC:dos, GOC:mah, ISBN:0721639976, PMID:19693541, PMID:21421911] xref: Wikipedia:Collagen is_a: GO:0032991 ! protein-containing complex -relationship: in_taxon NCBITaxon:33208 {all_only="true", source="PMID:12382326"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 {source="PMID:12382326"} ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 {source="PMID:12382326"} ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true", source="PMID:12382326"} ! in taxon Metazoa [Term] id: GO:0005587 @@ -2766,8 +2766,8 @@ xref: NIF_Subcellular:sao1702920020 xref: Wikipedia:Cell_nucleus is_a: GO:0043231 ! intracellular membrane-bounded organelle disjoint_from: GO:0005737 ! cytoplasm -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota [Term] id: GO:0005694 @@ -2836,7 +2836,7 @@ subset: goslim_plant xref: NIF_Subcellular:sao585356902 xref: Wikipedia:Lysosome is_a: GO:0000323 ! lytic vacuole -relationship: never_in_taxon NCBITaxon:4751 +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0005766 @@ -3051,7 +3051,7 @@ namespace: biological_process def: "A vesicle-mediated transport process that results in the engulfment of external particulate material by phagocytes and their delivery to the lysosome. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles." [ISBN:0198506732] xref: Wikipedia:Phagocytosis is_a: GO:0006897 ! endocytosis -relationship: never_in_taxon NCBITaxon:4751 +property_value: RO:0002161 NCBITaxon:4751 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24907" xsd:anyURI [Term] @@ -3465,8 +3465,8 @@ namespace: biological_process def: "The process whose specific outcome is the progression of an embryo over time, from zygote formation until the end of the embryonic life stage. The end of the embryonic life stage is organism-specific and may be somewhat arbitrary; for mammals it is usually considered to be birth, for insects the hatching of the first instar larva from the eggshell." [GOC:go_curators, GOC:isa_complete, GOC:mtg_sensu] synonym: "embryogenesis" BROAD [] is_a: GO:0009790 ! embryo development -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0009888 @@ -3479,14 +3479,14 @@ xref: Wikipedia:Histogenesis is_a: GO:0048856 ! anatomical structure development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0000479 ! tissue -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: never_in_taxon NCBITaxon:147554 -relationship: never_in_taxon NCBITaxon:33630 -relationship: never_in_taxon NCBITaxon:33682 -relationship: never_in_taxon NCBITaxon:38254 -relationship: never_in_taxon NCBITaxon:4891 -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota relationship: results_in_development_of UBERON:0000479 ! tissue +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota +property_value: RO:0002161 NCBITaxon:147554 +property_value: RO:0002161 NCBITaxon:33630 +property_value: RO:0002161 NCBITaxon:33682 +property_value: RO:0002161 NCBITaxon:38254 +property_value: RO:0002161 NCBITaxon:4891 [Term] id: GO:0009914 @@ -3697,7 +3697,7 @@ namespace: biological_process def: "The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues." [GOC:cjm, GOC:dph, GOC:ems, GOC:pf, Wikipedia:Cell_migration] xref: Wikipedia:Cell_migration is_a: GO:0048870 ! cell motility -relationship: never_in_taxon NCBITaxon:4890 +property_value: RO:0002161 NCBITaxon:4890 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24787" xsd:anyURI [Term] @@ -3871,7 +3871,7 @@ subset: goslim_drosophila subset: goslim_flybase_ribbon xref: Wikipedia:Cell_junction is_a: GO:0110165 ! cellular anatomical entity -relationship: never_in_taxon NCBITaxon:4751 +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0030097 @@ -3938,8 +3938,8 @@ def: "A small subcellular vesicle, surrounded by a membrane, that is formed from comment: Note that the term 'secretory vesicle' is sometimes used in this sense, but can also mean 'transport vesicle ; GO:0030133'. synonym: "secretory vesicle" BROAD [] is_a: GO:0099503 ! secretory vesicle -relationship: never_in_taxon NCBITaxon:4890 relationship: part_of GO:0012505 ! endomembrane system +property_value: RO:0002161 NCBITaxon:4890 [Term] id: GO:0030154 @@ -4159,10 +4159,10 @@ subset: goslim_pir synonym: "organismal physiological process" EXACT [] synonym: "single-multicellular organism process" RELATED [] is_a: GO:0008150 ! biological_process -relationship: never_in_taxon NCBITaxon:2 -relationship: never_in_taxon NCBITaxon:2157 -relationship: never_in_taxon NCBITaxon:4896 -relationship: never_in_taxon NCBITaxon:4932 +property_value: RO:0002161 NCBITaxon:2 +property_value: RO:0002161 NCBITaxon:2157 +property_value: RO:0002161 NCBITaxon:4896 +property_value: RO:0002161 NCBITaxon:4932 created_by: jl creation_date: 2012-09-19T16:07:47Z @@ -4320,7 +4320,7 @@ def: "Self-propelled movement of a cell or organism from one location to another subset: goslim_chembl subset: goslim_pir is_a: GO:0008150 ! biological_process -relationship: never_in_taxon NCBITaxon:451864 +property_value: RO:0002161 NCBITaxon:451864 [Term] id: GO:0040016 @@ -4358,11 +4358,11 @@ namespace: cellular_component def: "A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells." [GOC:jl, PMID:11584301] xref: Wikipedia:Melanosome is_a: GO:0048770 ! pigment granule -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: never_in_taxon NCBITaxon:4895 -relationship: never_in_taxon NCBITaxon:6237 {source="GOC:kmv"} -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa relationship: part_of CL:0000148 ! melanocyte +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa +property_value: RO:0002161 NCBITaxon:4895 +property_value: RO:0002161 NCBITaxon:6237 {source="GOC:kmv"} [Term] id: GO:0042582 @@ -4430,8 +4430,8 @@ name: chordate embryonic development namespace: biological_process def: "The process whose specific outcome is the progression of the embryo over time, from zygote formation through a stage including a notochord and neural tube until birth or egg hatching." [GOC:mtg_sensu] is_a: GO:0009792 ! embryo development ending in birth or egg hatching -relationship: in_taxon NCBITaxon:7711 {all_only="true"} ! Chordata -relationship: only_in_taxon NCBITaxon:7711 ! Chordata +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {all_only="true"} ! in taxon Chordata [Term] id: GO:0043011 @@ -4603,7 +4603,7 @@ synonym: "interspecies interaction" EXACT [] synonym: "interspecies interaction between organisms" EXACT [] synonym: "interspecies interaction with other organisms" EXACT [] is_a: GO:0008150 ! biological_process -relationship: never_in_taxon NCBITaxon:4895 +property_value: RO:0002161 NCBITaxon:4895 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20191" xsd:anyURI [Term] @@ -4635,8 +4635,8 @@ synonym: "synaptic junction" EXACT [] xref: NIF_Subcellular:sao914572699 xref: Wikipedia:Chemical_synapse is_a: GO:0030054 ! cell junction -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0045321 @@ -4651,8 +4651,8 @@ is_a: GO:0002376 ! immune system process intersection_of: GO:0001775 ! cell activation intersection_of: has_primary_input CL:0000738 ! leukocyte relationship: has_primary_input CL:0000738 ! leukocyte -relationship: in_taxon NCBITaxon:7742 {all_only="true"} ! Vertebrata -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 {all_only="true"} ! in taxon Vertebrata [Term] id: GO:0045453 @@ -5007,8 +5007,8 @@ is_a: GO:0003008 ! system process intersection_of: GO:0003008 ! system process intersection_of: has_participant UBERON:0001016 ! nervous system relationship: has_participant UBERON:0001016 ! nervous system -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13824" xsd:anyURI [Term] @@ -5276,8 +5276,8 @@ name: collagen-containing extracellular matrix namespace: cellular_component def: "An extracellular matrix consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that provides not only essential physical scaffolding for the cellular constituents but can also initiate crucial biochemical and biomechanical cues required for tissue morphogenesis, differentiation and homeostasis. The components are secreted by cells in the vicinity and form a sheet underlying or overlying cells such as endothelial and epithelial cells." [GOC:BHF, GOC:rph, PMID:21123617] is_a: GO:0031012 ! extracellular matrix -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa created_by: dph creation_date: 2018-04-13T12:47:21Z @@ -5632,9 +5632,9 @@ subset: goslim_synapse is_a: GO:0007267 ! cell-cell signaling intersection_of: GO:0007267 ! cell-cell signaling intersection_of: occurs_in GO:0045202 ! synapse -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa relationship: occurs_in GO:0045202 ! synapse -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0099537 @@ -5816,18 +5816,16 @@ namespace: ncbi_taxonomy xref: GC_ID:1 xref: PMID:15371245 is_a: NCBITaxon:337687 ! Muroidea -property_value: has_rank NCBITaxon:family [Term] id: NCBITaxon:10088 name: Mus namespace: ncbi_taxonomy -synonym: "mice" EXACT OMO:0003003 [] +synonym: "mice" EXACT genbank_common_name [] synonym: "mouse" EXACT OMO:0003003 [] synonym: "Mus" EXACT scientific_name [] xref: GC_ID:1 is_a: NCBITaxon:39107 ! Murinae -property_value: has_rank NCBITaxon:genus [Term] id: NCBITaxon:10090 @@ -5838,7 +5836,6 @@ synonym: "house mouse" EXACT genbank_common_name [] synonym: "mouse" EXACT OMO:0003003 [] xref: GC_ID:1 is_a: NCBITaxon:862507 ! Mus -property_value: has_rank NCBITaxon:species [Term] id: NCBITaxon:117570 @@ -5846,7 +5843,6 @@ name: Teleostomi namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:7776 ! Gnathostomata -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:117571 @@ -5856,7 +5852,6 @@ alt_id: NCBITaxon:40673 synonym: "bony vertebrates" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:117570 ! Teleostomi -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:131567 @@ -5872,7 +5867,6 @@ name: Dipnotetrapodomorpha namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:8287 ! Sarcopterygii -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:1437010 @@ -5883,7 +5877,6 @@ xref: GC_ID:1 xref: PMID:11743200 xref: PMID:11791233 is_a: NCBITaxon:9347 ! Eutheria -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:1963758 @@ -5893,7 +5886,6 @@ synonym: "mice and others" EXACT genbank_common_name [] synonym: "Sciurognathi" RELATED in_part [] xref: GC_ID:1 is_a: NCBITaxon:9989 ! Rodentia -property_value: has_rank NCBITaxon:suborder [Term] id: NCBITaxon:2759 @@ -5910,7 +5902,6 @@ xref: GC_ID:1 xref: PMID:23020233 xref: PMID:30257078 is_a: NCBITaxon:131567 ! cellular organisms -property_value: has_rank NCBITaxon:superkingdom [Term] id: NCBITaxon:314146 @@ -5922,7 +5913,6 @@ xref: PMID:12082125 xref: PMID:12878460 xref: PMID:15522813 is_a: NCBITaxon:1437010 ! Boreoeutheria -property_value: has_rank NCBITaxon:superorder [Term] id: NCBITaxon:314147 @@ -5934,7 +5924,6 @@ xref: PMID:11214319 xref: PMID:12082125 xref: PMID:15522813 is_a: NCBITaxon:314146 ! Euarchontoglires -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:32523 @@ -5943,7 +5932,6 @@ namespace: ncbi_taxonomy synonym: "tetrapods" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:1338369 ! Dipnotetrapodomorpha -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:32524 @@ -5952,7 +5940,6 @@ namespace: ncbi_taxonomy synonym: "amniotes" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:32523 ! Tetrapoda -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:32525 @@ -5961,7 +5948,6 @@ namespace: ncbi_taxonomy synonym: "Theria" EXACT scientific_name [] xref: GC_ID:1 is_a: NCBITaxon:40674 ! Mammalia -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:33154 @@ -5971,7 +5957,6 @@ synonym: "Fungi/Metazoa group" RELATED synonym [] synonym: "opisthokonts" RELATED synonym [] xref: GC_ID:1 is_a: NCBITaxon:2759 ! Eukaryota -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:33208 @@ -5983,7 +5968,6 @@ synonym: "metazoans" EXACT genbank_common_name [] synonym: "multicellular animals" EXACT OMO:0003003 [] xref: GC_ID:1 is_a: NCBITaxon:33154 ! Opisthokonta -property_value: has_rank NCBITaxon:kingdom [Term] id: NCBITaxon:33213 @@ -5991,7 +5975,6 @@ name: Bilateria namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:6072 ! Eumetazoa -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:33511 @@ -6000,7 +5983,6 @@ namespace: ncbi_taxonomy synonym: "deuterostomes" EXACT OMO:0003003 [] xref: GC_ID:1 is_a: NCBITaxon:33213 ! Bilateria -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:337687 @@ -6010,7 +5992,6 @@ xref: GC_ID:1 xref: PMID:15019624 xref: PMID:15371245 is_a: NCBITaxon:1963758 ! Myomorpha -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:39107 @@ -6019,7 +6000,6 @@ namespace: ncbi_taxonomy alt_id: NCBITaxon:109679 xref: GC_ID:1 is_a: NCBITaxon:10066 ! Muridae -property_value: has_rank NCBITaxon:subfamily [Term] id: NCBITaxon:40674 @@ -6029,7 +6009,6 @@ synonym: "mammals" EXACT genbank_common_name [] synonym: "mammals" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:32524 ! Amniota -property_value: has_rank NCBITaxon:class [Term] id: NCBITaxon:6072 @@ -6037,7 +6016,6 @@ name: Eumetazoa namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:33208 ! Metazoa -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:7711 @@ -6047,7 +6025,6 @@ synonym: "chordates" EXACT genbank_common_name [] synonym: "chordates" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:33511 ! Deuterostomia -property_value: has_rank NCBITaxon:phylum [Term] id: NCBITaxon:7742 @@ -6058,7 +6035,6 @@ synonym: "vertebrates" EXACT genbank_common_name [] synonym: "vertebrates" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:89593 ! Craniata -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:7776 @@ -6068,7 +6044,6 @@ synonym: "Gnathostomata" EXACT scientific_name [] synonym: "jawed vertebrates" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:7742 ! Vertebrata -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:8287 @@ -6076,7 +6051,6 @@ name: Sarcopterygii namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:117571 ! Euteleostomi -property_value: has_rank NCBITaxon:superclass [Term] id: NCBITaxon:862507 @@ -6085,7 +6059,6 @@ namespace: ncbi_taxonomy synonym: "Mus" EXACT scientific_name [] xref: GC_ID:1 is_a: NCBITaxon:10088 ! Mus -property_value: has_rank NCBITaxon:subgenus [Term] id: NCBITaxon:89593 @@ -6094,7 +6067,6 @@ namespace: ncbi_taxonomy synonym: "Craniata" EXACT scientific_name [] xref: GC_ID:1 is_a: NCBITaxon:7711 ! Chordata -property_value: has_rank NCBITaxon:subphylum [Term] id: NCBITaxon:9347 @@ -6107,7 +6079,6 @@ synonym: "placentals" EXACT genbank_common_name [] synonym: "placentals" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:32525 ! Theria -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:9989 @@ -6117,7 +6088,6 @@ synonym: "rodent" EXACT genbank_common_name [] synonym: "rodents" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:314147 ! Glires -property_value: has_rank NCBITaxon:order [Term] id: PATO:0000001 @@ -6309,7 +6279,6 @@ comment: This refers to the disposition of the bearer. subset: disposition_slim subset: value_slim is_a: PATO:0001579 ! contractility -property_value: RO:0002604 PATO:0001691 [Term] id: PATO:0001873 @@ -6378,7 +6347,6 @@ subset: attribute_slim xref: Image:http\://upload.wikimedia.org/wikipedia/commons/0/06/Convex_polygon_illustration1.png is_a: PATO:0002266 ! 3-D shape relationship: RO:0015011 PATO:0002006 ! has cross section 2-D shape -property_value: RO:0002604 PATO:0002008 [Term] id: PATO:0002014 @@ -6395,7 +6363,7 @@ namespace: quality def: "A quality inhering in a bearer by virtue of the bearer's having an empty space or cavity within." [url:http\://www.merriam-webster.com/dictionary/hollow] subset: value_slim is_a: PATO:0002014 ! structure, cavities -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-09-18T02:19:20Z [Term] @@ -6407,7 +6375,7 @@ subset: disposition_slim subset: mpath_slim subset: value_slim is_a: PATO:0070045 ! anatomical histological quality -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-10-05T12:05:23Z [Term] @@ -6417,7 +6385,7 @@ namespace: quality def: "A quality inhering in a bearer by virtue of its constitution." [PATOC:GVG] subset: attribute_slim is_a: PATO:0001018 ! physical quality -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-03-15T04:35:27Z [Term] @@ -6427,7 +6395,7 @@ namespace: quality def: "A cylindrical shape quality inhering in a bearer by virtue of the bearer's being imperfectly cylindrical or approximately cylindrical." [url:http\://www.thefreedictionary.com/Subcylindrical] subset: value_slim is_a: PATO:0001873 ! cylindrical -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-07-13T04:22:30Z [Term] @@ -6436,7 +6404,7 @@ name: 3-D shape namespace: quality def: "A shape that inheres in a 3 dimensional entity." [PATOC:OREGON] is_a: PATO:0000052 ! shape -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-10-05T12:31:16Z [Term] @@ -6449,7 +6417,7 @@ synonym: "tube-shaped" EXACT [] synonym: "tubulate" EXACT [] is_a: PATO:0001873 ! cylindrical is_a: PATO:0002078 ! hollow -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-06-08T06:33:50Z [Term] @@ -6460,7 +6428,7 @@ def: "A convex 3-D shape quality inhering in a bearer by virtue of the bearer's comment: Note that a fiber shaped object may take any circuitous or straight path through space (think of a length of string or rope). subset: value_slim is_a: PATO:0002226 ! subcylindrical -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-09-09T04:50:10Z [Term] @@ -6470,7 +6438,7 @@ namespace: quality def: "A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt" [wiktionary:superellipse] synonym: "Lamé curve" EXACT [] is_a: PATO:0002006 ! 2-D shape -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-10-12T12:45:16Z [Term] @@ -6482,7 +6450,7 @@ subset: cell_quality subset: mpath_slim subset: value_slim is_a: PATO:0001410 ! striated -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2013-09-15T12:29:15Z [Term] @@ -6493,7 +6461,7 @@ def: "A nucleate quality inhering in a bearer by virtue of the bearer's having o subset: mpath_slim subset: value_slim is_a: PATO:0001404 ! nucleate quality -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2013-10-21T05:44:34Z [Term] @@ -6502,7 +6470,7 @@ name: disconnected namespace: quality def: "A structural quality inhering in the bearer by virtue of the bearer consisting of multiple structures lacking any physical connection to each other." [GOC:dos] is_a: PATO:0000141 ! structure -relationship: dc-contributor https://orcid.org/0000-0002-7073-9172 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2014-12-12T08:43:17Z [Term] @@ -6621,7 +6589,6 @@ synonym: "T200" BROAD [PRO:DNx] xref: IUPHARobj:1852 xref: PIRSF:PIRSF002004 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P08575 [Term] id: PR:000001012 @@ -6640,7 +6607,6 @@ synonym: "leukocyte adhesion receptor MO1" EXACT [] synonym: "neutrophil adherence receptor" EXACT [] xref: IUPHARobj:2452 is_a: PR:000001005 ! integrin alpha with A domain -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P11215 [Term] id: PR:000001013 @@ -6657,7 +6623,6 @@ synonym: "leukocyte adhesion glycoprotein p150,95 alpha chain" EXACT [] synonym: "leukocyte adhesion receptor p150,95" EXACT [] xref: IUPHARobj:2454 is_a: PR:000001005 ! integrin alpha with A domain -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P20702 [Term] id: PR:000001015 @@ -6668,7 +6633,6 @@ comment: Category=sequence. Requested by=CL. Note: This isoform includes the reg synonym: "CD45RA" EXACT [] synonym: "PTPRC/iso:CD45RA" EXACT PRO-short-label [PRO:DNx] is_a: PR:000050216 ! receptor-type tyrosine-protein phosphatase C isoform CD45R -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P08575-8 [Term] id: PR:000001018 @@ -6724,7 +6688,6 @@ synonym: "NCAM-1" EXACT [] synonym: "NCAM1" EXACT PRO-short-label [PRO:DNx] xref: IUPHARobj:2769 is_a: PR:000001023 ! neural cell adhesion molecule NCAM -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P13591 [Term] id: PR:000001083 @@ -6761,7 +6724,6 @@ synonym: "MAL" RELATED Gene-based [] synonym: "T-cell surface glycoprotein Lyt-2" EXACT [] synonym: "T-lymphocyte differentiation antigen T8/Leu-2" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P01732 [Term] id: PR:000001289 @@ -6806,7 +6768,6 @@ synonym: "CEACAM8" EXACT PRO-short-label [PRO:DNx] synonym: "CGM6" RELATED Gene-based [] synonym: "non-specific cross-reacting antigen NCA-95" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P31997 [Term] id: PR:000001355 @@ -6834,7 +6795,6 @@ synonym: "p70-75" EXACT [] synonym: "p75" BROAD [PRO:DNx] xref: IUPHARobj:1696 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P14784 [Term] id: PR:000001444 @@ -6848,7 +6808,6 @@ synonym: "CDH5" EXACT PRO-short-label [PRO:DNx] synonym: "vascular endothelial cadherin" EXACT [] synonym: "VE-cadherin" EXACT [] is_a: PR:000001327 ! cadherin -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P33151 [Term] id: PR:000001479 @@ -6900,7 +6859,6 @@ synonym: "lymphocyte antigen 1" EXACT [] synonym: "lymphocyte antigen T1/Leu-1" EXACT [] synonym: "Lyt-1" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P06127 [Term] id: PR:000001850 @@ -6916,7 +6874,6 @@ synonym: "CTSO" RELATED Gene-based [] synonym: "CTSO2" RELATED Gene-based [] xref: IUPHARobj:2350 is_a: PR:000040662 ! cathepsin-like protease -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P43235 [Term] id: PR:000001865 @@ -6952,7 +6909,6 @@ synonym: "IL7R" EXACT PRO-short-label [PRO:DNx] xref: IUPHARobj:1698 xref: PIRSF:PIRSF001960 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P16871 [Term] id: PR:000001874 @@ -6980,7 +6936,6 @@ synonym: "sialophorin" EXACT [] synonym: "SPN" EXACT PRO-short-label [PRO:DNx] xref: PIRSF:PIRSF001994 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P16150 [Term] id: PR:000001889 @@ -7015,7 +6970,6 @@ synonym: "skin fibroblast elastase" EXACT [] xref: IUPHARobj:1611 xref: PIRSF:PIRSF501074 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P08473 [Term] id: PR:000001903 @@ -7028,7 +6982,6 @@ synonym: "BSAP" EXACT [] synonym: "Pax-5" RELATED Gene-based [] synonym: "PAX5" EXACT PRO-short-label [PRO:DNx] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q02548 [Term] id: PR:000001937 @@ -7045,7 +6998,6 @@ synonym: "TrATPase" EXACT [] synonym: "type 5 acid phosphatase" EXACT [] xref: PIRSF:PIRSF000898 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P13686 [Term] id: PR:000001944 @@ -7059,7 +7011,6 @@ synonym: "Sfpi-1" RELATED Gene-based [] synonym: "Sfpi1" RELATED Gene-based [] synonym: "SPI1" EXACT PRO-short-label [PRO:DNx] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P17947 [Term] id: PR:000001954 @@ -7076,7 +7027,6 @@ synonym: "TNFRSF11A" EXACT PRO-short-label [PRO:DNx] xref: IUPHARobj:1881 xref: PIRSF:PIRSF038806 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q9Y6Q6 [Term] id: PR:000001969 @@ -7093,7 +7043,6 @@ synonym: "UPAR" RELATED Gene-based [] synonym: "uPAR" EXACT [] xref: PIRSF:PIRSF002022 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q03405 [Term] id: PR:000001971 @@ -7122,7 +7071,6 @@ synonym: "proto-oncogene c-Fms" EXACT [] xref: IUPHARobj:1806 xref: PIRSF:PIRSF500947 is_a: PR:000001810 ! CSF-1/PDGF receptor-type tyrosine-protein kinase -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P07333 [Term] id: PR:000002065 @@ -7158,7 +7106,6 @@ synonym: "VEGFR-2" EXACT [] synonym: "VEGFR2" RELATED Gene-based [] xref: IUPHARobj:1813 is_a: PR:000001971 ! vascular endothelial growth factor receptor -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P35968 [Term] id: PR:000002976 @@ -7201,7 +7148,6 @@ synonym: "C/EBP alpha" EXACT [] synonym: "CEBP" RELATED Gene-based [] synonym: "CEBPA" EXACT PRO-short-label [PRO:DNx] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P49715 [Term] id: PR:000006611 @@ -7215,7 +7161,6 @@ synonym: "terminal addition enzyme" EXACT [] synonym: "terminal deoxynucleotidyltransferase" EXACT [] synonym: "terminal transferase" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P04053 [Term] id: PR:000007597 @@ -7230,7 +7175,6 @@ synonym: "G0S7" RELATED Gene-based [] synonym: "proto-oncogene protein c-fos" EXACT [] synonym: "transcription factor AP-1 subunit c-Fos" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P01100 [Term] id: PR:000007857 @@ -7247,7 +7191,6 @@ synonym: "GF-1" RELATED [] synonym: "GF1" RELATED Gene-based [] synonym: "NF-E1 DNA-binding protein" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P15976 [Term] id: PR:000007858 @@ -7258,7 +7201,6 @@ comment: Category=gene. Requested by=CL. synonym: "GATA-binding protein 2" EXACT [] synonym: "GATA2" EXACT PRO-short-label [PRO:DNx] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P23769 [Term] id: PR:000011178 @@ -7275,7 +7217,6 @@ synonym: "NFKB2" EXACT PRO-short-label [PRO:DNx] synonym: "nuclear factor of kappa light polypeptide gene enhancer in B-cells 2" EXACT [] synonym: "oncogene Lyt-10" EXACT [] is_a: PR:000001753 ! transcription factor NF-kappa-B subunit -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q00653 [Term] id: PR:000014841 @@ -7289,7 +7230,6 @@ synonym: "SHH" EXACT PRO-short-label [PRO:DNx] synonym: "Shh unprocessed N-terminal signaling and C-terminal autoprocessing domains" EXACT [] synonym: "ShhNC" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q15465 [Term] id: PR:000016043 @@ -7307,7 +7247,6 @@ synonym: "TAL-1" EXACT [] synonym: "TAL1" EXACT PRO-short-label [PRO:DNx] synonym: "TCL5" RELATED Gene-based [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P17542 [Term] id: PR:000025796 @@ -7325,8 +7264,8 @@ def: "A protein that is encoded in the genome of Mus musculus." [PRO:DAN] synonym: "mouse protein" EXACT PRO-short-label [PRO:DAN] is_a: PR:000036194 ! eukaryotic protein intersection_of: PR:000000001 ! protein -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus -relationship: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus +relationship: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:000036194 @@ -7336,8 +7275,8 @@ def: "A protein that is encoded in the genome of some Eukaryota." [PRO:DAN] synonym: "Eukaryota protein" EXACT [PRO:DAN] is_a: PR:000000001 ! protein intersection_of: PR:000000001 ! protein -intersection_of: only_in_taxon NCBITaxon:2759 ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +intersection_of: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota [Term] id: PR:000040662 @@ -7348,7 +7287,7 @@ comment: Category=family. synonym: "cathepsin" NARROW [PRO:DAN] synonym: "fam:CTS" EXACT PRO-short-label [PRO:DNx] is_a: PR:000036194 ! eukaryotic protein -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa [Term] id: PR:000050216 @@ -7384,9 +7323,9 @@ subset: common_anatomy subset: upper_level xref: BFO:0000003 disjoint_from: UBERON:0001062 ! anatomical entity -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000020 @@ -7411,7 +7350,6 @@ xref: CALOHA:TS-2043 xref: EHDAA2:0001824 xref: EHDAA:500 xref: EMAPA:35955 -xref: FBbt:00005155 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: GAID:63 xref: HAO:0000930 xref: MA:0000017 @@ -7426,7 +7364,7 @@ intersection_of: UBERON:0000062 ! organ intersection_of: capable_of GO:0050906 ! detection of stimulus involved in sensory perception relationship: capable_of GO:0050906 ! detection of stimulus involved in sensory perception relationship: part_of UBERON:0001032 ! sensory system -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" xsd:anyURI [Term] id: UBERON:0000025 @@ -7438,11 +7376,9 @@ synonym: "duct" NARROW [] xref: galen:Tube is_a: UBERON:0004111 ! anatomical conduit intersection_of: UBERON:0004111 ! anatomical conduit -intersection_of: has_quality PATO:0002299 ! tubular +intersection_of: RO:0000086 PATO:0002299 ! has quality tubular relationship: has_part UBERON:0013522 ! subdivision of tube -relationship: has_quality PATO:0002299 ! tubular -property_value: IAO:0000232 "not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts)" xsd:string -property_value: UBPROP:0000007 "tubular" xsd:string +relationship: RO:0000086 PATO:0002299 ! has quality tubular [Term] id: UBERON:0000043 @@ -7473,15 +7409,12 @@ xref: Wikipedia:Tendon xref: XAO:0000173 xref: ZFA:0005647 is_a: UBERON:0007846 {source="VSAO"} ! dense regular connective tissue -relationship: connects UBERON:0001474 ! bone element -relationship: connects UBERON:0001630 ! muscle organ relationship: has_part CL:0000327 {source="AEO"} ! extracellular matrix secreting cell -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0002204 {source="OG"} ! musculoskeletal system -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Dense regular connective tissue that connects muscle to bone.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000073", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000003 "Phylogenetically, tendinous tissue first appears in the invertebrate chordate Branchiostoma as myosepta. This two-dimensional array of collagen fibers is highly organized, with fibers running along two primary axes. In hagfish the first linear tendons appear and the myosepta have developed specialized regions with unidirectional fiber orientation - a linear tendon within the flat sheet of myoseptum.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001286", ontology="VHOG", source="DOI:10.1016/S1095-6433(02)00241-6 Summers AP, Koob TJ, The evolution of tendon - morphology and material properties. Comparative Biochemistry and Physiology-Part A: Molecular and Integrative Physiology (2002)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "in FMA, tendon is an organ component that with parts dense-irregular-connective-tissue of tendon and dense-irregular-connective-tissue of tendon sheath; we follow VSAO in making it a subtype of the former. In VSAO tendons connect muscle to bone; in WP the def states integument (e.g. auricular muscles) - but JB confirms this is not actually tendon but aponeurosis" xsd:string {external_ontology="FMA"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002176 UBERON:0001474 ! connects bone element +relationship: RO:0002176 UBERON:0001630 ! connects muscle organ +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg" xsd:anyURI [Term] id: UBERON:0000058 @@ -7494,7 +7427,6 @@ synonym: "ducts" RELATED OMO:0003004 [XAO:0004000] synonym: "exocrine duct" NARROW [] synonym: "exocrine gland duct" NARROW [] xref: AAO:0011123 -xref: FBbt:00100314 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:30320 xref: galen:Duct xref: NCIT:C12948 @@ -7506,11 +7438,9 @@ xref: XAO:0004000 xref: ZFA:0005171 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000063 ! organ subunit -relationship: conduit_for UBERON:0000463 ! organism substance relationship: has_part UBERON:0034969 ! epithelial layer of duct -relationship: has_quality PATO:0002299 ! tubular -property_value: UBPROP:0000001 "A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171]." xsd:string {source="ZFA:0005171"} -property_value: UBPROP:0000012 "Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here." xsd:string +relationship: RO:0000086 PATO:0002299 ! has quality tubular +relationship: RO:0002570 UBERON:0000463 ! conduit for organism substance [Term] id: UBERON:0000060 @@ -7522,13 +7452,11 @@ subset: upper_level synonym: "organ wall" RELATED [FMA:82482] synonym: "wall" BROAD [] synonym: "wall of organ" EXACT [FMA:82482] -xref: EMAPA:25036 xref: FMA:82482 xref: galen:Wall is_a: UBERON:0000064 ! organ part relationship: adjacent_to UBERON:0002553 ! anatomical cavity relationship: has_part UBERON:0004923 ! organ component layer -property_value: UBPROP:0000012 "in FMA, serosa is a wall" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0000061 @@ -7545,7 +7473,6 @@ xref: BILA:0000003 xref: CARO:0000003 xref: EHDAA2:0003003 xref: EMAPA:0 -xref: FBbt:00007001 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:305751 xref: FMA:67135 xref: GAID:781 @@ -7560,10 +7487,10 @@ xref: VHOG:0001759 xref: XAO:0003000 xref: ZFA:0000037 is_a: UBERON:0000465 ! material anatomical entity -relationship: existence_ends_during_or_before UBERON:0000071 ! death stage -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0002497 UBERON:0000071 ! existence ends during or before death stage +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000062 @@ -7590,14 +7517,12 @@ xref: Wikipedia:Organ_(anatomy) is_a: UBERON:0010000 ! multicellular anatomical structure disjoint_from: UBERON:0034921 ! multi organ part structure relationship: capable_of GO:0008150 ! biological_process -relationship: has_boundary UBERON:0006984 ! anatomical surface -relationship: never_in_taxon NCBITaxon:110815 {source="Wikipedia"} relationship: part_of UBERON:0000467 ! anatomical system -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: UBPROP:0000001 "Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." xsd:string {source="GO:0048513"} -property_value: UBPROP:0000012 "CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4" xsd:string +relationship: RO:0002002 UBERON:0006984 ! has 2D boundary anatomical surface +property_value: RO:0002161 NCBITaxon:110815 {source="Wikipedia"} +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000063 @@ -7610,9 +7535,7 @@ synonym: "organ segment" RELATED [FMA:86140] synonym: "segment of organ" RELATED [FMA:86140] xref: FMA:86140 is_a: UBERON:0000064 ! organ part -property_value: editor_note "FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction" xsd:string -property_value: UBPROP:0000001 "Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball." xsd:string {source="FMA:86140", version="3"} -property_value: UBPROP:0000001 "Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal." xsd:string {source="FMA:86140", version="1"} +property_value: IAO:0000116 "FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction" xsd:string [Term] id: UBERON:0000064 @@ -7633,10 +7556,9 @@ xref: SCTID:113343008 xref: SCTID:91717005 is_a: UBERON:0010000 ! multicellular anatomical structure relationship: part_of UBERON:0000062 ! organ -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: IAO:0000232 "currently defined in a very broad sense, may be replaced by more specific classes in the future" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000066 @@ -7685,7 +7607,7 @@ is_a: UBERON:0000105 ! life cycle stage disjoint_from: UBERON:0000092 ! post-embryonic stage relationship: precedes UBERON:0000066 ! fully formed stage relationship: precedes UBERON:0000092 ! post-embryonic stage -relationship: simultaneous_with GO:0009790 ! embryo development +relationship: RO:0002082 GO:0009790 ! simultaneous with embryo development [Term] id: UBERON:0000071 @@ -7698,11 +7620,10 @@ xref: XAO:0000437 xref: XtroDO:0000085 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage -relationship: ends UBERON:0000104 ! life cycle -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: UBPROP:0000012 "ncit:Death is an outcome" xsd:string {external_ontology="ncit"} +relationship: RO:0002229 UBERON:0000104 ! ends life cycle +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000075 @@ -7719,9 +7640,9 @@ xref: NCIT:C34076 xref: SCTID:118966000 xref: UMLS:C1519343 {source="ncithesaurus:Skeletal_System_Part"} is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision -relationship: composed_primarily_of UBERON:0004765 ! skeletal element -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0001434 ! skeletal system +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002473 UBERON:0004765 ! composed primarily of skeletal element [Term] id: UBERON:0000092 @@ -7741,9 +7662,8 @@ xref: WBls:0000103 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage relationship: preceded_by UBERON:0000068 ! embryo stage -relationship: simultaneous_with GO:0009791 ! post-embryonic development +relationship: RO:0002082 GO:0009791 ! simultaneous with post-embryonic development property_value: seeAlso "https://github.com/obophenotype/uberon/issues/344" xsd:anyURI -property_value: UBPROP:0000008 "In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)" xsd:string [Term] id: UBERON:0000104 @@ -7765,9 +7685,9 @@ is_a: BFO:0000003 ! occurrent is_a: UBERON:0000000 ! processual entity relationship: ends_with UBERON:0000071 ! death stage relationship: has_part UBERON:0000105 ! life cycle stage -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 property_value: seeAlso "https://github.com/obophenotype/uberon/issues/532" xsd:anyURI [Term] @@ -7796,12 +7716,10 @@ xref: ZFS:0000000 xref: ZFS:0100000 is_a: UBERON:0000000 ! processual entity relationship: part_of UBERON:0000104 ! life cycle -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: editor_note "this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here" xsd:string -property_value: UBPROP:0000012 "the WBls class 'all stages' belongs here as it is the superclass of other WBls stages" xsd:string -property_value: UBPROP:0000012 "we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage" xsd:string +property_value: IAO:0000116 "this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000106 @@ -7821,7 +7739,6 @@ xref: BILS:0000106 xref: EFO:0001322 xref: EHDAA:27 xref: FBdv:00005288 -xref: IDOMAL:0000302 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C12601 xref: PdumDv:0000100 xref: VHOG:0000745 @@ -7831,9 +7748,8 @@ xref: ZFS:0000001 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage -relationship: seeAlso EMAPA:16033 -relationship: starts UBERON:0000104 ! life cycle -property_value: UBPROP:0000003 "As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000745", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107", source="http://bgee.unil.ch/"} +relationship: RO:0002223 UBERON:0000104 ! starts life cycle +property_value: seeAlso EMAPA:16033 [Term] id: UBERON:0000107 @@ -7856,10 +7772,10 @@ xref: ZFS:0000046 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage intersection_of: UBERON:0000105 ! life cycle stage -intersection_of: simultaneous_with GO:0040016 ! embryonic cleavage +intersection_of: RO:0002082 GO:0040016 ! simultaneous with embryonic cleavage relationship: immediately_preceded_by UBERON:0000106 ! zygote stage relationship: part_of UBERON:0000068 ! embryo stage -relationship: simultaneous_with GO:0040016 ! embryonic cleavage +relationship: RO:0002082 GO:0040016 ! simultaneous with embryonic cleavage [Term] id: UBERON:0000108 @@ -7883,8 +7799,8 @@ is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000107 ! cleavage stage -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI -property_value: editor_note "consider adding a preceding stage 'morula stage' as part of cleavage" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI +property_value: IAO:0000116 "consider adding a preceding stage 'morula stage' as part of cleavage" xsd:string [Term] id: UBERON:0000109 @@ -7911,10 +7827,10 @@ xref: XAO:1000005 xref: ZFS:0000047 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000108 {source="BILS"} ! blastula stage -relationship: simultaneous_with GO:0007369 ! gastrulation +relationship: RO:0002082 GO:0007369 ! simultaneous with gastrulation +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0000110 @@ -7928,14 +7844,12 @@ xref: MmusDv:0000017 xref: XAO:1000006 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000109 ! gastrula stage -relationship: simultaneous_with GO:0001841 ! neural tube formation -property_value: RO:0002174 NCBITaxon:7955 +relationship: RO:0002082 GO:0001841 ! simultaneous with neural tube formation +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa property_value: seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/343" xsd:anyURI -property_value: UBPROP:0000008 "In zebrafish, the times of neurulation and segmentation overlap so extensively there is no distinct neurula period of development, such as occurs largely before segmentation in amphibian embryos." xsd:string [Term] id: UBERON:0000111 @@ -7952,9 +7866,9 @@ xref: OGES:000032 xref: Wikipedia:Organogenesis is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000068 ! embryo stage -relationship: simultaneous_with GO:0048513 ! animal organ development +relationship: RO:0002082 GO:0048513 ! simultaneous with animal organ development +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa property_value: seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/533" xsd:anyURI @@ -7990,7 +7904,6 @@ xref: EFO:0000825 xref: EHDAA2:0001326 xref: EHDAA:542 xref: EMAPA:16262 -xref: FBbt:00003126 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:49184 xref: GAID:75 xref: galen:Mouth @@ -8011,19 +7924,11 @@ xref: Wikipedia:Mouth xref: XAO:0003029 xref: ZFA:0000547 xref: ZFA:0000590 -is_a: UBERON:0004921 {notes="the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts"} ! subdivision of digestive tract -intersection_of: UBERON:0004921 ! subdivision of digestive tract -intersection_of: proximalmost_part_of UBERON:0001555 ! digestive tract -relationship: develops_from UBERON:0035804 ! future mouth -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: proximalmost_part_of UBERON:0001555 ! digestive tract -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI +is_a: UBERON:0004921 ! subdivision of digestive tract +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002202 UBERON:0035804 ! develops from future mouth +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/661" xsd:anyURI -property_value: UBPROP:0000001 "Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010355", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000812", ontology="VHOG", source="DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "oral" xsd:string -property_value: UBPROP:0000011 "some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives" xsd:string -property_value: UBPROP:0000012 "in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0000307 @@ -8042,11 +7947,11 @@ xref: OGEM:000006 xref: Wikipedia:Blastula is_a: UBERON:0000922 ! embryo intersection_of: UBERON:0000468 ! multicellular organism -intersection_of: existence_starts_and_ends_during UBERON:0000108 ! blastula stage -relationship: develops_from UBERON:0007010 ! cleaving embryo -relationship: existence_starts_and_ends_during UBERON:0000108 ! blastula stage -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI -property_value: editor_note "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" xsd:string +intersection_of: RO:0002491 UBERON:0000108 ! existence starts and ends during blastula stage +relationship: RO:0002202 UBERON:0007010 ! develops from cleaving embryo +relationship: RO:0002491 UBERON:0000108 ! existence starts and ends during blastula stage +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI +property_value: IAO:0000116 "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" xsd:string [Term] id: UBERON:0000383 @@ -8069,7 +7974,6 @@ xref: BILA:0000088 xref: BTO:0001369 xref: BTO:0001485 xref: EFO:0000801 -xref: EMAPA:35578 xref: FMA:72954 xref: MA:0002888 xref: MAT:0000025 @@ -8078,15 +7982,13 @@ xref: VSAO:0000033 xref: XAO:0004042 is_a: UBERON:0011216 ! organ system subdivision intersection_of: UBERON:0011216 ! organ system subdivision -intersection_of: composed_primarily_of UBERON:0001015 ! musculature +intersection_of: RO:0002473 UBERON:0001015 ! composed primarily of musculature relationship: capable_of GO:0003012 ! muscle system process -relationship: composed_primarily_of UBERON:0001015 ! musculature -relationship: never_in_taxon NCBITaxon:6040 -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: present_in_taxon NCBITaxon:9606 -property_value: editor_note "consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77" xsd:string -property_value: UBPROP:0000001 "Anatomical system that consists of the muscles of the body.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000033", ontology="VSAO", source="VSAO:curator"} -property_value: UBPROP:0000012 "we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA" xsd:string {external_ontology="MA"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002473 UBERON:0001015 ! composed primarily of musculature +property_value: IAO:0000116 "consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77" xsd:string +property_value: RO:0002161 NCBITaxon:6040 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000463 @@ -8108,7 +8010,6 @@ xref: CALOHA:TS-2101 xref: CARO:0000004 xref: EHDAA2:0003004 xref: EMAPA:35178 -xref: FBbt:00007019 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9669 xref: galen:BodySubstance xref: HAO:0000004 @@ -8121,11 +8022,11 @@ xref: VHOG:0001726 xref: XAO:0004001 xref: ZFA:0001487 is_a: UBERON:0000465 ! material anatomical entity -relationship: has_quality PATO:0002198 ! quality of a substance -relationship: part_of UBERON:0000468 {notes="this relationship may be too strong and may be weakened in future"} ! multicellular organism -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: part_of UBERON:0000468 ! multicellular organism +relationship: RO:0000086 PATO:0002198 ! has quality quality of a substance +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000464 @@ -8143,7 +8044,6 @@ xref: AEO:0000005 xref: BILA:0000005 xref: CARO:0000005 xref: EHDAA2:0003005 -xref: FBbt:00007017 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:5897 xref: HAO:0000005 xref: NCIT:C94478 @@ -8154,10 +8054,10 @@ xref: VHOG:0001728 xref: XAO:0003190 xref: ZFA:0001643 is_a: UBERON:0000466 ! immaterial anatomical entity -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -relationship: surrounded_by UBERON:0000061 ! anatomical structure +relationship: RO:0002219 UBERON:0000061 ! surrounded by anatomical structure +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000465 @@ -8171,7 +8071,6 @@ xref: AEO:0000006 xref: BILA:0000006 xref: CARO:0000006 xref: EHDAA2:0003006 -xref: FBbt:00007016 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67165 xref: HAO:0000006 xref: TAO:0001836 @@ -8180,9 +8079,9 @@ xref: VHOG:0001721 is_a: BFO:0000040 ! material entity is_a: UBERON:0001062 ! anatomical entity disjoint_from: UBERON:0000466 ! immaterial anatomical entity -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000466 @@ -8197,7 +8096,6 @@ xref: AEO:0000007 xref: BILA:0000007 xref: CARO:0000007 xref: EHDAA2:0003007 -xref: FBbt:00007015 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67112 xref: HAO:0000007 xref: TAO:0001835 @@ -8205,9 +8103,9 @@ xref: TGMA:0001827 xref: VHOG:0001727 is_a: BFO:0000141 ! immaterial entity is_a: UBERON:0001062 ! anatomical entity -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000467 @@ -8235,11 +8133,9 @@ xref: EHDAA2:0003011 xref: EHDAA:392 xref: EMAPA:16103 xref: EV:0100000 -xref: FBbt:00004856 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7149 xref: galen:AnatomicalSystem xref: HAO:0000011 -xref: IDOMAL:0002460 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: MA:0000003 xref: NCIT:C12919 xref: SCTID:278195005 @@ -8255,11 +8151,11 @@ xref: ZFA:0001439 is_a: UBERON:0000061 ! anatomical structure relationship: has_part UBERON:0000062 ! organ relationship: part_of UBERON:0000468 ! multicellular organism -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -relationship: present_in_taxon NCBITaxon:9606 -relationship: seeAlso EHDAA2:0001330 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:9606 +property_value: seeAlso EHDAA2:0001330 [Term] id: UBERON:0000468 @@ -8290,7 +8186,6 @@ xref: EHDAA2:0003191 xref: EHDAA:1 xref: EMAPA:25765 xref: EV:0100016 -xref: FBbt:00000001 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:256135 xref: galen:Organism xref: HAO:0000012 @@ -8306,11 +8201,10 @@ xref: Wikipedia:Multi-cellular_organism xref: XAO:0003004 xref: ZFA:0001094 is_a: UBERON:0010000 ! multicellular anatomical structure -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: editor_note "TODO - split body and mc organism? body continues after death stage" xsd:string -property_value: UBPROP:0000007 "organismal" xsd:string +property_value: IAO:0000116 "TODO - split body and mc organism? body continues after death stage" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000475 @@ -8335,7 +8229,6 @@ xref: CARO:0000032 xref: EFO:0000808 xref: EHDAA2:0003032 xref: EMAPA:36031 -xref: FBbt:00007009 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7153 xref: galen:BodyPart xref: HAO:0000032 @@ -8353,10 +8246,10 @@ xref: XAO:0003013 xref: ZFA:0001308 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure relationship: part_of UBERON:0000468 ! multicellular organism -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: editor_note "Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency" xsd:string +property_value: IAO:0000116 "Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000476 @@ -8371,7 +8264,6 @@ xref: AEO:0000040 xref: BILA:0000040 xref: CARO:0000040 xref: EHDAA2:0003040 -xref: FBbt:00007013 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:63863 xref: HAO:0000040 xref: TAO:0000382 @@ -8380,9 +8272,9 @@ xref: XAO:0003162 xref: ZFA:0000382 is_a: UBERON:0000061 ! anatomical structure disjoint_from: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000477 @@ -8391,12 +8283,11 @@ namespace: uberon def: "Anatomical group whose component anatomical structures lie in close proximity to each other." [FBbt:00007277] subset: common_anatomy subset: upper_level -xref: FBbt:00007277 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: VHOG:0001737 is_a: UBERON:0034923 ! disconnected anatomical group -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000478 @@ -8417,7 +8308,6 @@ xref: CALOHA:TS-2119 xref: CARO:0000042 xref: EHDAA2:0003042 xref: EHDAA:46 -xref: FBbt:00005835 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:85537 xref: HAO:0000042 xref: NCIT:C34055 @@ -8453,7 +8343,6 @@ xref: CALOHA:TS-2090 xref: CARO:0000043 xref: EHDAA2:0003043 xref: EMAPA:35868 -xref: FBbt:00007003 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9637 xref: galen:Tissue xref: HAO:0000043 @@ -8470,10 +8359,10 @@ xref: ZFA:0001477 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure relationship: has_part GO:0031012 ! extracellular matrix relationship: part_of UBERON:0000468 ! multicellular organism -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: editor_note "changed label and definition to reflect CARO2" xsd:string +property_value: IAO:0000116 "changed label and definition to reflect CARO2" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000481 @@ -8488,7 +8377,6 @@ xref: AEO:0000055 xref: BILA:0000055 xref: CARO:0000055 xref: EHDAA2:0003055 -xref: FBbt:00007010 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: HAO:0000055 xref: TAO:0001488 xref: TGMA:0001847 @@ -8497,9 +8385,9 @@ xref: XAO:0003037 xref: ZFA:0001488 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure relationship: has_part UBERON:0000479 ! tissue -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000483 @@ -8521,7 +8409,6 @@ xref: CALOHA:TS-0288 xref: CARO:0000066 xref: EHDAA2:0003066 xref: EMAPA:32738 -xref: FBbt:00007005 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9639 xref: GAID:402 xref: HAO:0000066 @@ -8538,16 +8425,14 @@ xref: ZFA:0001486 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue -intersection_of: composed_primarily_of CL:0000066 ! epithelial cell +intersection_of: RO:0002473 CL:0000066 ! composed primarily of epithelial cell union_of: UBERON:0000486 ! multilaminar epithelium union_of: UBERON:0000490 ! unilaminar epithelium -relationship: composed_primarily_of CL:0000066 ! epithelial cell relationship: has_part GO:0005911 ! cell-cell junction relationship: has_part UBERON:0005769 ! basement membrane of epithelium -relationship: only_in_taxon NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! Metazoa -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI -property_value: UBPROP:0000003 "The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000387", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.59", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "epithelial" xsd:string +relationship: RO:0002160 NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! only in taxon Metazoa +relationship: RO:0002473 CL:0000066 ! composed primarily of epithelial cell +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI [Term] id: UBERON:0000486 @@ -8574,7 +8459,6 @@ xref: Wikipedia:Stratified_epithelium xref: XAO:0004006 xref: ZFA:0001494 is_a: UBERON:0000483 ! epithelium -property_value: UBPROP:0000001 "Epithelium that consists of more than one layer of epithelial cells.[CARO]" xsd:string {date_retrieved="2012-06-20", external_class="CARO:0000069", ontology="CARO", source="FMA:45562", source="http://orcid.org/0000-0001-9114-8737"} [Term] id: UBERON:0000490 @@ -8599,8 +8483,7 @@ xref: UMLS:C0682574 {source="ncithesaurus:Simple_Epithelium"} xref: XAO:0004007 xref: ZFA:0001495 is_a: UBERON:0000483 ! epithelium -property_value: editor_note "consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable" xsd:string -property_value: UBPROP:0000001 "Epithelium that consists of a single layer of epithelial cells.[CARO]" xsd:string {date_retrieved="2012-06-20", external_class="CARO:0000073", ontology="CARO", source="FMA:45561", source="http://orcid.org/0000-0001-9114-8737"} +property_value: IAO:0000116 "consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable" xsd:string [Term] id: UBERON:0000922 @@ -8625,11 +8508,9 @@ xref: EHDAA2:0000002 xref: EHDAA2_RETIRED:0003236 xref: EHDAA:38 xref: EMAPA:16039 -xref: FBbt:00000052 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69068 xref: GAID:963 xref: http://neurolex.org/wiki/Category\:Embryonic_organism -xref: IDOMAL:0000646 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: MAT:0000226 xref: MESH:D004622 xref: MIAA:0000019 @@ -8643,14 +8524,12 @@ xref: XAO:0000113 xref: ZFA:0000103 is_a: UBERON:0000468 ! multicellular organism intersection_of: UBERON:0000468 ! multicellular organism -intersection_of: existence_ends_with UBERON:0000068 ! embryo stage -intersection_of: existence_starts_with UBERON:0000068 ! embryo stage -relationship: existence_ends_with UBERON:0000068 ! embryo stage -relationship: existence_starts_with UBERON:0000068 ! embryo stage -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" xsd:anyURI +intersection_of: RO:0002489 UBERON:0000068 ! existence starts with embryo stage +intersection_of: RO:0002493 UBERON:0000068 ! existence ends with embryo stage +relationship: RO:0002489 UBERON:0000068 ! existence starts with embryo stage +relationship: RO:0002493 UBERON:0000068 ! existence ends with embryo stage +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/503" xsd:anyURI -property_value: UBPROP:0000007 "embryonic" xsd:string -property_value: UBPROP:0000012 "Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo" xsd:string {external_ontology="ZFA"} [Term] id: UBERON:0000923 @@ -8669,7 +8548,6 @@ xref: AAO:0000480 xref: BILA:0000035 xref: BTO:0000556 xref: EMAPA:36033 -xref: FBbt:00000110 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69069 xref: GAID:1303 xref: MESH:D005855 @@ -8683,8 +8561,7 @@ xref: Wikipedia:Germ_layer xref: XAO:0003011 xref: ZFA:0001122 is_a: UBERON:0010316 ! germ layer / neural crest -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001223", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0000924 @@ -8704,7 +8581,6 @@ xref: EFO:0000414 xref: EHDAA2:0000428 xref: EMAPA:16069 xref: EV:0100003 -xref: FBbt:00000111 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69070 xref: GAID:1304 xref: MAT:0000155 @@ -8721,11 +8597,8 @@ xref: XAO:0000001 xref: ZFA:0000016 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000221 ! ectodermal cell -relationship: immediate_transformation_of UBERON:0006601 {source="Bgee:AN"} ! presumptive ectoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png" xsd:anyURI -property_value: UBPROP:0000001 "Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000137", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000153", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "ectodermal" xsd:string +relationship: RO:0002495 UBERON:0006601 {source="Bgee:AN"} ! immediate transformation of presumptive ectoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png" xsd:anyURI [Term] id: UBERON:0000925 @@ -8745,7 +8618,6 @@ xref: EFO:0002545 xref: EHDAA2:0000436 xref: EMAPA:16062 xref: EV:0100005 -xref: FBbt:00000125 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69071 xref: GAID:1305 xref: MAT:0000175 @@ -8761,11 +8633,9 @@ xref: XAO:0000090 xref: ZFA:0000017 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000223 ! endodermal cell -relationship: immediate_transformation_of UBERON:0006595 {source="Bgee:AN"} ! presumptive endoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png" xsd:anyURI -property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000154", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "endodermal" xsd:string +relationship: RO:0002495 UBERON:0006595 {source="Bgee:AN"} ! immediate transformation of presumptive endoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png" xsd:anyURI [Term] id: UBERON:0000926 @@ -8791,7 +8661,6 @@ xref: EHDAA:160 xref: EHDAA:183 xref: EMAPA:16083 xref: EV:0100006 -xref: FBbt:00000126 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69072 xref: GAID:522 xref: MAT:0000174 @@ -8805,15 +8674,11 @@ xref: VHOG:0000152 xref: Wikipedia:Mesoderm xref: XAO:0000050 xref: ZFA:0000041 -is_a: UBERON:0000923 {notes="sometimes not considered primary"} ! germ layer +is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000222 ! mesodermal cell -relationship: immediate_transformation_of UBERON:0006603 {source="Bgee:AN"} ! presumptive mesoderm -relationship: never_in_taxon NCBITaxon:6040 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" xsd:anyURI -property_value: UBPROP:0000001 "Primary germ layer that is the middle of the embryonic germ layers.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000304", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000152", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "mesodermal" xsd:string -property_value: UBPROP:0000008 "sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates" xsd:string {source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} +relationship: RO:0002495 UBERON:0006603 {source="Bgee:AN"} ! immediate transformation of presumptive mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" xsd:anyURI +property_value: RO:0002161 NCBITaxon:6040 [Term] id: UBERON:0000930 @@ -8835,7 +8700,6 @@ synonym: "stomodeal-hypophyseal primordium" BROAD [XAO:0000269] xref: BTO:0004224 xref: EHDAA2:0001929 xref: EMAPA:16263 -xref: FBbt:00000439 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:295846 xref: NCIT:C34306 xref: TAO:0001290 @@ -8845,15 +8709,11 @@ xref: Wikipedia:Stomodeum xref: XAO:0000269 xref: ZFA:0001290 is_a: UBERON:0013522 ! subdivision of tube -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000924 ! ectoderm relationship: part_of UBERON:0035804 ! future mouth -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI -property_value: editor_note "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" xsd:string -property_value: UBPROP:0000001 "Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001290", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx" xsd:string {source="MP:0012522", taxon="NCBITaxon:40674"} -property_value: UBPROP:0000007 "stomodeal" xsd:string -property_value: UBPROP:0000008 "This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity." xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI +property_value: IAO:0000116 "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" xsd:string [Term] id: UBERON:0000949 @@ -8873,7 +8733,6 @@ xref: EFO:0002969 xref: EHDAA2:0002224 xref: EMAPA:35306 xref: EV:0100128 -xref: FBbt:00005068 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9668 xref: GAID:439 xref: MA:0000012 @@ -8896,12 +8755,9 @@ disjoint_from: UBERON:0002330 ! exocrine system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0004456 ! entire sense organ system -relationship: composed_primarily_of UBERON:0002368 ! endocrine gland -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: UBPROP:0000001 "Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010279", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000098", ontology="VHOG", source="DOI:10.1073/pnas.0812138106 Markov GV, Tavares R, Dauphin-Villemant C, Demeneix BA, Baker ME, Laudet V, Independent elaboration of steroid hormone signaling pathways in metazoans. PNAS (2009)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "endocrine" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002473 UBERON:0002368 ! composed primarily of endocrine gland +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage [Term] id: UBERON:0000970 @@ -8921,7 +8777,6 @@ xref: BTO:0000439 xref: CALOHA:TS-0309 xref: EFO:0000827 xref: EV:0100336 -xref: FBbt:00005162 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: GAID:69 xref: MAT:0000140 xref: MESH:D005123 @@ -8932,11 +8787,7 @@ relationship: capable_of GO:0009584 ! detection of visible light relationship: has_part CL:0000149 {source="PMID:21062451"} ! visual pigment cell relationship: has_part CL:0000210 {source="PMID:21062451"} ! photoreceptor cell relationship: part_of UBERON:0002104 ! visual system -relationship: present_in_taxon NCBITaxon:9606 -property_value: IAO:0000232 "This class encompasses a variety of light-detecting structures from different phyla with no implication of homology, from the compound insect eye to the vertebrate camera-type eye (distinct classes are provided for each)" xsd:string -property_value: UBPROP:0000007 "ocular" xsd:string -property_value: UBPROP:0000007 "optic" xsd:string -property_value: UBPROP:0000010 "Note that whilst this is classified as an organ, it is in fact more of a unit composed of different structures: in Drosophila, it includes the interommatidial bristle as a part; we consider here the vertebrate eye to include the eyeball/eye proper as a part, with the eye having as parts (when present): eyelids, conjuctiva," xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000982 @@ -8976,10 +8827,8 @@ xref: XAO:0000171 xref: ZFA:0001596 is_a: UBERON:0004905 ! articulation disjoint_from: UBERON:0001474 ! bone element -relationship: connects UBERON:0004765 ! skeletal element -relationship: contributes_to_morphology_of UBERON:0001434 ! skeletal system -property_value: UBPROP:0000001 "Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000101", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000367", ontology="TAO", source="TAO:pem"} +relationship: RO:0002176 UBERON:0004765 ! connects skeletal element +relationship: RO:0002433 UBERON:0001434 ! contributes to morphology of skeletal system [Term] id: UBERON:0001007 @@ -9000,8 +8849,6 @@ xref: BILA:0000082 xref: BTO:0000058 xref: CALOHA:TS-1293 xref: EFO:0000793 -xref: EV:0100056 -xref: FBbt:00005055 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7152 xref: GAID:278 xref: galen:DigestiveSystem @@ -9029,11 +8876,8 @@ disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0022600 ! digestive system process -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000129", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000007 "digestive" xsd:string -property_value: UBPROP:0000012 "many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class" xsd:string {external_ontology="MA"} +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001009 @@ -9045,7 +8889,6 @@ subset: uberon_slim synonym: "systema cardiovasculare" RELATED OMO:0003011 [Wikipedia:Circulatory_system] xref: AAO:0000959 xref: CALOHA:TS-2103 -xref: MESH:D002319 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: VHOG:0001248 xref: Wikipedia:Circulatory_system is_a: UBERON:0000467 ! anatomical system @@ -9057,17 +8900,13 @@ disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0003013 ! circulatory system process -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} -relationship: never_in_taxon NCBITaxon:6073 -relationship: never_in_taxon NCBITaxon:6157 -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI -property_value: IAO:0000232 "the cardiovascular system and the lymphatic system are parts of the circulatory system" xsd:string -property_value: RO:0002174 NCBITaxon:6231 {notes="WBbt coelomocyte currently classified as circulating cell"} -property_value: UBPROP:0000001 "Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000959", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001248", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.493", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} +property_value: RO:0002161 NCBITaxon:6073 +property_value: RO:0002161 NCBITaxon:6157 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001015 @@ -9087,10 +8926,8 @@ synonym: "musculature system" RELATED [] synonym: "musculi" EXACT OMO:0003011 [FMA:32558, FMA:TA] synonym: "set of muscles" EXACT [FMA:32558] synonym: "set of skeletal muscles" EXACT [MA:0000165] -xref: AAO:0011066 xref: BTO:0000887 xref: EFO:0001949 -xref: EMAPA:32715 xref: EMAPA:35577 xref: FMA:32558 xref: MA:0000165 @@ -9102,11 +8939,9 @@ xref: WBbt:0005737 xref: Wikipedia:Muscular_system xref: ZFA:0000548 is_a: UBERON:0011216 ! organ system subdivision -relationship: composed_primarily_of UBERON:0001630 ! muscle organ relationship: part_of UBERON:0000383 ! musculature of body -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png" xsd:anyURI -property_value: RO:0002171 UBERON:0001474 -property_value: UBPROP:0000012 "In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here." xsd:string {external_ontology="FMA"} +relationship: RO:0002473 UBERON:0001630 ! composed primarily of muscle organ +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png" xsd:anyURI [Term] id: UBERON:0001016 @@ -9132,7 +8967,6 @@ xref: EHDAA2:0001246 xref: EHDAA:826 xref: EMAPA:16469 xref: EV:0100162 -xref: FBbt:00005093 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7157 xref: GAID:466 xref: MA:0000016 @@ -9157,20 +8991,15 @@ disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0050877 ! nervous system process -relationship: composed_primarily_of CL:0002319 ! neural cell -relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: has_part CL:0000540 ! neuron -relationship: immediate_transformation_of UBERON:0016880 {source="Bgee:AN"} ! future nervous system -relationship: never_in_taxon NCBITaxon:6040 -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI -property_value: UBPROP:0000001 "A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000396", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000324", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000402", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.117", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "nervous" xsd:string -property_value: UBPROP:0000007 "neural" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002473 CL:0002319 ! composed primarily of neural cell +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +relationship: RO:0002495 UBERON:0016880 {source="Bgee:AN"} ! immediate transformation of future nervous system +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI +property_value: RO:0002161 NCBITaxon:6040 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001017 @@ -9199,7 +9028,6 @@ xref: EHDAA:828 xref: EMAPA:16470 xref: EMAPA:16754 xref: EV:0100163 -xref: FBbt:00005094 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:55675 xref: GAID:570 xref: MA:0000167 @@ -9216,15 +9044,11 @@ xref: XAO:0000215 xref: ZFA:0000012 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0011216 {source="FBbt", source="cjm"} ! organ system subdivision -relationship: immediate_transformation_of UBERON:0016879 {source="Bgee:AN"} ! future central nervous system -relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0001016 ! nervous system -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "Part of the nervous system which includes the brain and spinal cord.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000090", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "The brain and spinal cord. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000012", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO)." xsd:string {source="BIRNLEX:1099"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000293", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 (reference 1), ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 (reference 2), DOI:10.1016/j.cell.2007.02.040 Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud'homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007) (reference 3)", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002495 UBERON:0016879 {source="Bgee:AN"} ! immediate transformation of future central nervous system +property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001032 @@ -9249,7 +9073,6 @@ xref: BILA:0000099 xref: EFO:0000805 xref: EHDAA2:0003094 xref: EMAPA:16192 -xref: FBbt:00007692 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:75259 xref: MA:0002442 xref: MAT:0000031 @@ -9264,9 +9087,7 @@ is_a: UBERON:0015203 ! non-connected functional system relationship: capable_of_part_of GO:0007600 ! sensory perception relationship: overlaps UBERON:0001016 ! nervous system relationship: part_of UBERON:0004456 ! entire sense organ system -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" xsd:anyURI -property_value: UBPROP:0000003 "An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001674", ontology="VHOG", source="DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" xsd:anyURI [Term] id: UBERON:0001049 @@ -9290,7 +9111,6 @@ xref: EMAPA:16164 xref: EMAPA:16757 xref: FMA:293882 xref: MAT:0000069 -xref: MESH:D054259 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: MIAA:0000069 xref: NCIT:C34226 xref: neuronames:1365 @@ -9305,12 +9125,8 @@ is_a: UBERON:0003914 {source="EHDAA2"} ! epithelial tube is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0016879 ! future central nervous system -relationship: develops_from UBERON:0005068 ! neural rod -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010617", ontology="AAO", source="AAO:JOR"} -property_value: UBPROP:0000001 "The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000307", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/neural+tube"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000307", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000011 "The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium" xsd:string {source="GO:0021915"} +relationship: RO:0002202 UBERON:0005068 ! develops from neural rod +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0001062 @@ -9326,7 +9142,6 @@ xref: BILA:0000000 xref: BIRNLEX:6 xref: CARO:0000000 xref: EHDAA2:0002229 -xref: FBbt:10000000 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:62955 xref: HAO:0000000 xref: MA:0000001 @@ -9337,9 +9152,9 @@ xref: UMLS:C1515976 {source="ncithesaurus:Anatomic_Structure_System_or_Substance xref: WBbt:0000100 xref: XAO:0000000 xref: ZFA:0100000 -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0001133 @@ -9390,10 +9205,10 @@ is_a: UBERON:8600006 ! visceral striated muscle tissue intersection_of: UBERON:0002036 ! striated muscle tissue intersection_of: has_part CL:0000746 ! cardiac muscle cell disjoint_from: UBERON:0001134 ! skeletal muscle tissue -relationship: composed_primarily_of CL:0000746 ! cardiac muscle cell relationship: has_part CL:0000746 ! cardiac muscle cell relationship: part_of UBERON:0007100 ! primary circulatory organ -property_value: editor_note "check relationship with myocardium. part_of in MA - but we also have a more specific class 'cardiac muscle tissue of myocardium'. Check ncit" xsd:string +relationship: RO:0002473 CL:0000746 ! composed primarily of cardiac muscle cell +property_value: IAO:0000116 "check relationship with myocardium. part_of in MA - but we also have a more specific class 'cardiac muscle tissue of myocardium'. Check ncit" xsd:string [Term] id: UBERON:0001134 @@ -9415,15 +9230,12 @@ xref: UMLS:C0242692 {source="ncithesaurus:Skeletal_Muscle_Tissue"} xref: Wikipedia:Skeletal_striated_muscle is_a: UBERON:0002036 ! striated muscle tissue intersection_of: UBERON:0002385 ! muscle tissue -intersection_of: composed_primarily_of CL:0008002 ! skeletal muscle fiber -relationship: composed_primarily_of CL:0008002 ! skeletal muscle fiber -relationship: develops_from UBERON:0003082 ! myotome +intersection_of: RO:0002473 CL:0008002 ! composed primarily of skeletal muscle fiber relationship: part_of UBERON:0014892 ! skeletal muscle organ, vertebrate -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/c/c0/Skeletal_muscle.jpg" xsd:anyURI -property_value: editor_note "TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle." xsd:string -property_value: UBPROP:0000001 "Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005277", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA]" xsd:string {external_class="FMA:14069", ontology="FMA"} -property_value: UBPROP:0000003 "This result implies the following views in terms of evolutionary differentiation: (1) Arthropod striated muscle and vertebrate skeletal and cardiac muscles share a common ancestor. In other words, they did not evolve independently (...) (5) The divergence of vertebrate skeletal and cardiac muscles/vertebrate smooth muscle and nonmuscle is at least before that of vertebrates/arthropods. In other words, emergence of skeletal and cardiac musle type tissues preceded the vertebrate/arthropod divergence (ca. 700 MYA).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000319", ontology="VHOG", source="PMID:10368962 Oota S, Saitou N, Phylogenetic relationship of muscle tissues deduced from superimposition of gene trees. Mol Biol Evol (1999)", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003082 ! develops from myotome +relationship: RO:0002473 CL:0008002 ! composed primarily of skeletal muscle fiber +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/c/c0/Skeletal_muscle.jpg" xsd:anyURI +property_value: IAO:0000116 "TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle." xsd:string [Term] id: UBERON:0001434 @@ -9462,18 +9274,11 @@ disjoint_from: UBERON:0002330 ! exocrine system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0004456 ! entire sense organ system -relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: has_part UBERON:0004288 ! skeleton relationship: has_part UBERON:0004770 ! articular system relationship: part_of UBERON:0002204 ! musculoskeletal system -property_value: RO:0002171 UBERON:0001016 +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/The-skeletal-system" xsd:anyURI -property_value: UBPROP:0000001 "Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000434", ontology="TAO", source="TAO:wd"} -property_value: UBPROP:0000001 "Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000027", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "System that provides physical support to the organism.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000566", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000003 "By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001254", ontology="VHOG", source="DOI:10.1159/000324245 Donoghue PCJ, Sansom IJ, Origin and early evolution of vertebrate skeletonization. Microscopy research and technique (2002)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "skeletal" xsd:string -property_value: UBPROP:0000012 "GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates" xsd:string {external_ontology="GO"} [Term] id: UBERON:0001474 @@ -9516,19 +9321,11 @@ xref: XAO:0000169 xref: ZFA:0001514 is_a: UBERON:0004765 ! skeletal element intersection_of: UBERON:0004765 ! skeletal element -intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue +intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue disjoint_from: UBERON:0001630 ! muscle organ disjoint_from: UBERON:0005090 ! muscle structure -relationship: composed_primarily_of UBERON:0002481 {source="VSAO-modified"} ! bone tissue -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata -property_value: RO:0002171 UBERON:0001015 -property_value: RO:0002171 UBERON:0001630 -property_value: RO:0002171 UBERON:0002385 -property_value: UBPROP:0000001 "Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000047", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000001 "Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001514", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Skeletal element that is composed of bone tissue.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000057", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000002 "relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000047", ontology="AAO"} -property_value: UBPROP:0000003 "The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001190", ontology="VHOG", source="DOI:10.1159/000324245 Murdock DJ, Donoghue PC, Evolutionary Origins of Animal Skeletal Biomineralization. Cells Tissues Organs (2011)", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002473 UBERON:0002481 {source="VSAO-modified"} ! composed primarily of bone tissue [Term] id: UBERON:0001555 @@ -9552,11 +9349,9 @@ xref: BTO:0000545 xref: EHDAA2:0000726 xref: EHDAA:518 xref: EMAPA:16247 -xref: FBbt:00003125 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45615 xref: galen:AlimentaryTract xref: MA:0000917 -xref: MESH:D041981 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: NCIT:C34082 xref: TAO:0000112 xref: TGMA:0001819 @@ -9565,18 +9360,13 @@ xref: VHOG:0000309 xref: WBbt:0005743 xref: ZFA:0000112 is_a: UBERON:0000025 ! tube -relationship: connects UBERON:0000165 ! mouth -relationship: immediate_transformation_of UBERON:0007026 {source="NCBIBook:NBK10107"} ! presumptive gut -relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} -relationship: never_in_taxon NCBITaxon:41324 {source="DOI:10.1371/journal.pone.0016309"} -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0001007 ! digestive system -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "The alimentary or digestive tract, and associated organs.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000112", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000309", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "FMA also has a term 'gastrointestinal tract', but this includes the liver." xsd:string {external_ontology="FMA"} -property_value: UBPROP:0000012 "we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509" xsd:string {external_ontology="MA"} -property_value: UBPROP:0000013 "we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002176 UBERON:0000165 ! connects mouth +relationship: RO:0002495 UBERON:0007026 {source="NCBIBook:NBK10107"} ! immediate transformation of presumptive gut +property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} +property_value: RO:0002161 NCBITaxon:41324 {source="DOI:10.1371/journal.pone.0016309"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001630 @@ -9588,8 +9378,6 @@ subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "muscle" BROAD [ZFA:0005145] -xref: AAO:0011066 -xref: EMAPA:32715 xref: EMAPA:37474 {source="MA:th"} xref: EV:0100146 xref: FMA:5022 @@ -9604,12 +9392,9 @@ xref: ZFA:0005145 is_a: UBERON:0000062 ! organ is_a: UBERON:0005090 ! muscle structure intersection_of: UBERON:0000062 ! organ -intersection_of: composed_primarily_of UBERON:0002385 ! muscle tissue -relationship: composed_primarily_of UBERON:0002385 ! muscle tissue +intersection_of: RO:0002473 UBERON:0002385 ! composed primarily of muscle tissue relationship: part_of UBERON:0001015 ! musculature -property_value: UBPROP:0000001 "Portion of tissue composed of contractile fibers.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005145", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001245", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.75", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "muscular" xsd:string +relationship: RO:0002473 UBERON:0002385 ! composed primarily of muscle tissue [Term] id: UBERON:0002036 @@ -9633,9 +9418,8 @@ xref: WBbt:0005779 xref: Wikipedia:Striated_muscle is_a: UBERON:0002385 ! muscle tissue intersection_of: UBERON:0002385 ! muscle tissue -intersection_of: composed_primarily_of CL:0000737 ! striated muscle cell -relationship: composed_primarily_of CL:0000737 ! striated muscle cell -property_value: UBPROP:0000001 "Voluntary muscle tissue arranged in bundles of fibers.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010762", ontology="AAO", source="AAO:CAM"} +intersection_of: RO:0002473 CL:0000737 ! composed primarily of striated muscle cell +relationship: RO:0002473 CL:0000737 ! composed primarily of striated muscle cell [Term] id: UBERON:0002050 @@ -9655,7 +9439,6 @@ xref: BILA:0000034 xref: BTO:0000174 xref: CALOHA:TS-2110 xref: EFO:0000461 -xref: FBbt:00004208 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69067 xref: GAID:407 xref: MESH:D004628 @@ -9671,10 +9454,6 @@ is_a: UBERON:0005423 ! developing anatomical structure intersection_of: UBERON:0005423 ! developing anatomical structure intersection_of: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0000922 ! embryo -property_value: UBPROP:0000001 "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000138", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001105", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000178", ontology="VSAO", source="ZFIN:curator"} -property_value: UBPROP:0000012 "in FMA embryo is_a embryonic structure" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0002100 @@ -9710,10 +9489,6 @@ xref: XAO:0003025 xref: ZFA:0001115 is_a: UBERON:0011676 ! subdivision of organism along main body axis relationship: part_of UBERON:0013702 ! body proper -property_value: RO:0002171 UBERON:0000026 {exceptions="ZFA", source="https://github.com/obophenotype/uberon/issues/378", status="pending"} -property_value: RO:0002171 UBERON:0000033 -property_value: UBPROP:0000001 "Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010339", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001115", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0002104 @@ -9741,7 +9516,6 @@ xref: XAO:0003198 xref: ZFA:0001127 is_a: UBERON:0001032 ! sensory system relationship: capable_of_part_of GO:0007601 ! visual perception -property_value: UBPROP:0000001 "The sensory system used for sight.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000632", ontology="AAO", source="AAO:EJS"} [Term] id: UBERON:0002193 @@ -9757,7 +9531,7 @@ xref: EMAPA:18765 xref: FMA:74562 xref: MA:0000013 is_a: UBERON:0000467 {source="MA"} ! anatomical system -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria [Term] id: UBERON:0002204 @@ -9787,13 +9561,10 @@ disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of_part_of GO:0040011 ! locomotion -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: has_developmental_contribution_from UBERON:0000926 {notes="check ctenophore"} ! mesoderm relationship: has_part UBERON:0000383 ! musculature of body relationship: has_part UBERON:0001434 ! skeletal system -property_value: UBPROP:0000001 "Anatomical system that provides locomotion and physical support to the organism.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010546", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001275", ontology="VHOG", source="DOI:10.1002/jez.b.21246 Shearman RM, Burke AC, The lateral somitic frontier in ontogeny and phylogeny. Journal of Experimental Zoology (2009)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "musculoskeletal" xsd:string +relationship: RO:0002254 UBERON:0000926 ! has developmental contribution from mesoderm +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage [Term] id: UBERON:0002328 @@ -9831,23 +9602,15 @@ xref: XAO:0000055 xref: ZFA:0000135 is_a: UBERON:0000062 {source="PMID:15890825"} ! organ is_a: UBERON:0000481 {source="VSAO"} ! multi-tissue structure +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004121 ! ectoderm-derived structure -relationship: develops_from UBERON:0004880 {source="ZFA"} ! chordamesoderm -relationship: develops_from UBERON:0006267 {source="EHDAA2"} ! notochordal plate -relationship: dorsal_to UBERON:0001555 ! digestive tract -relationship: existence_starts_during UBERON:0000068 ! embryo stage -relationship: only_in_taxon NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! Chordata relationship: part_of UBERON:0011137 ! axial skeletal system relationship: produces PR:000014841 ! sonic hedgehog protein -relationship: ventral_to UBERON:0001049 ! neural tube -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000032", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000135", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000327", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000002 "relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000327", ontology="AAO"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000199", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "notochordal" xsd:string -property_value: UBPROP:0000011 "In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord." xsd:string +relationship: RO:0002160 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! only in taxon Chordata +relationship: RO:0002202 UBERON:0004880 {source="ZFA"} ! develops from chordamesoderm +relationship: RO:0002202 UBERON:0006267 {source="EHDAA2"} ! develops from notochordal plate +relationship: RO:0002488 UBERON:0000068 ! existence starts during embryo stage +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0002329 @@ -9886,18 +9649,10 @@ xref: XAO:0000058 xref: ZFA:0000155 is_a: UBERON:0005423 ! developing anatomical structure is_a: UBERON:0007503 {source="EHDAA2"} ! epithelial vesicle -relationship: develops_from UBERON:0003059 {source="ZFA"} ! presomitic mesoderm -relationship: never_in_taxon NCBITaxon:7712 {source="PMID:17237766"} -relationship: only_in_taxon NCBITaxon:7711 {source="GOTAX:0000352"} ! Chordata -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: IAO:0000232 "EDITOR_NOTE currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk" xsd:string -property_value: UBPROP:0000001 "Post-cranial axial segments which form sclerotome and dermomyotome.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010569", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000001 "Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000155", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000002 "relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000155", ontology="TAO"} -property_value: UBPROP:0000002 "relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000155", ontology="TAO"} -property_value: UBPROP:0000002 "relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010569", ontology="AAO"} -property_value: UBPROP:0000003 "(...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000191", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.40, DOI:10.1093/icb/43.1.137 Balavoine G, Adoutte A, The segmented urbilateria: a testable scenario. Integrative and Comparative Biology (2003)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "somitic" xsd:string +relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata +relationship: RO:0002202 UBERON:0003059 {source="ZFA"} ! develops from presomitic mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: RO:0002161 NCBITaxon:7712 {source="PMID:17237766"} [Term] id: UBERON:0002330 @@ -9921,9 +9676,9 @@ is_a: UBERON:0000467 ! anatomical system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0004456 ! entire sense organ system -relationship: composed_primarily_of UBERON:0002365 ! exocrine gland -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002473 UBERON:0002365 ! composed primarily of exocrine gland +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage [Term] id: UBERON:0002342 @@ -9950,28 +9705,22 @@ xref: MIAA:0000066 xref: NCIT:C34222 xref: neuronames:1366 xref: SCTID:361462002 -xref: TAO:0000045 xref: UMLS:C0027789 {source="ncithesaurus:Neural_Crest"} xref: VHOG:0000057 xref: Wikipedia:Neural_crest xref: XAO:0000048 xref: ZFA:0000045 is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0010316 ! germ layer / neural crest -relationship: composed_primarily_of CL:0000333 {notes="pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! migratory neural crest cell -relationship: develops_from UBERON:0003075 {source="BTO"} ! neural plate -relationship: develops_from UBERON:0005062 {source="PMID:11523831"} ! neural fold -relationship: existence_starts_during UBERON:0000110 {source="PMID:11523831"} ! neurula stage -relationship: only_in_taxon NCBITaxon:89593 {notes="Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells", source="ISBN:0073040584"} ! Craniata relationship: part_of UBERON:0002346 {source="XAO", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! neurectoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI -property_value: IAO:0000232 "EDITOR_NOTE consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams)." xsd:string -property_value: RO:0002174 NCBITaxon:117565 {source="ISBN:0073040584", source="PMID:17377535"} -property_value: UBPROP:0000001 "A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000045", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010578", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831]" xsd:string {source="PMID:11523831"} -property_value: UBPROP:0000003 "We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000057", ontology="VHOG", source="DOI:10.1111/j.1469-7580.2012.01495.x Hall BK, Gillis JA, Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues. J Anat (2012)", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata +relationship: RO:0002202 UBERON:0003075 {source="BTO"} ! develops from neural plate +relationship: RO:0002202 UBERON:0005062 {source="PMID:11523831"} ! develops from neural fold +relationship: RO:0002473 CL:0000333 ! composed primarily of migratory neural crest cell +relationship: RO:0002488 UBERON:0000110 {source="PMID:11523831"} ! existence starts during neurula stage +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI [Term] id: UBERON:0002346 @@ -9994,7 +9743,6 @@ xref: EHDAA:1498 xref: EHDAA:255 xref: EMAPA:16073 xref: EV:0100004 -xref: FBbt:00001057 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:87657 xref: MAT:0000176 xref: MIAA:0000176 @@ -10008,9 +9756,6 @@ xref: ZFA:0001120 is_a: UBERON:0000923 ! germ layer is_a: UBERON:0004121 ! ectoderm-derived structure relationship: has_part CL:0000133 ! neurectodermal cell -property_value: UBPROP:0000003 "(...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000150", ontology="VHOG", source="DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "neurectodermal" xsd:string -property_value: UBPROP:0000013 "we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here" xsd:string [Term] id: UBERON:0002365 @@ -10041,7 +9786,7 @@ intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0002330 ! exocrine system relationship: has_part UBERON:0000058 ! duct relationship: part_of UBERON:0002330 ! exocrine system -property_value: editor_note "Currently this is logically defined by the system it belongs to, but a better system may be base this on presence/absence of ducts. However, the dual nature of the liver should be taken into consideration here. Consider adding subclasses" xsd:string +property_value: IAO:0000116 "Currently this is logically defined by the system it belongs to, but a better system may be base this on presence/absence of ducts. However, the dual nature of the liver should be taken into consideration here. Consider adding subclasses" xsd:string [Term] id: UBERON:0002368 @@ -10073,7 +9818,7 @@ intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0000949 ! endocrine system relationship: capable_of GO:0046879 ! hormone secretion relationship: part_of UBERON:0000949 ! endocrine system -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/da/Illu_endocrine_system.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/da/Illu_endocrine_system.png" xsd:anyURI [Term] id: UBERON:0002371 @@ -10109,6 +9854,7 @@ xref: VHOG:0001218 xref: Wikipedia:Bone_marrow xref: XAO:0000123 is_a: UBERON:0000479 ! tissue +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000479 ! tissue intersection_of: has_part UBERON:0012429 ! hematopoietic tissue intersection_of: part_of UBERON:0001474 ! bone element @@ -10117,12 +9863,10 @@ relationship: has_part UBERON:0012429 ! hematopoietic tissue relationship: part_of UBERON:0001474 ! bone element relationship: part_of UBERON:0002390 {source="FMA", source="MA"} ! hematopoietic system relationship: part_of UBERON:0002405 ! immune system -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg" xsd:anyURI -property_value: editor_note "consider placement of NCIT:C53466 medullary bone" xsd:string -property_value: editor_note "TODO - create superclass for bone marrow / head kidney. both are portions of tissue in the hematopoetic system. also consider adding as subclass of zone of bone organ for consistency with FMA. See also: Leydig and epigonal organs" xsd:string -property_value: UBPROP:0000003 "The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001218", ontology="VHOG", source="DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood Cells and Blood Cell Development in the Animal Kingdom. Annual Review of Cell and Developmental Biology (2006)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000009 "In adults, marrow in large bones produces new blood cells[Wikipedia:Bone_marrow]" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg" xsd:anyURI +property_value: IAO:0000116 "consider placement of NCIT:C53466 medullary bone" xsd:string +property_value: IAO:0000116 "TODO - create superclass for bone marrow / head kidney. both are portions of tissue in the hematopoetic system. also consider adding as subclass of zone of bone organ for consistency with FMA. See also: Leydig and epigonal organs" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002384 @@ -10156,12 +9900,8 @@ xref: VSAO:0000017 xref: XAO:0001017 xref: ZFA:0001632 is_a: UBERON:0000479 ! tissue -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000098", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000001 "Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001641", ontology="TAO", source="TAO:wd"} -property_value: UBPROP:0000001 "Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000017", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} -property_value: UBPROP:0000012 "MA also has set of connective tissues" xsd:string {external_ontology="MA"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002385 @@ -10189,13 +9929,11 @@ xref: Wikipedia:Muscle_tissue is_a: UBERON:0000479 ! tissue is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000479 ! tissue -intersection_of: composed_primarily_of CL:0000187 ! muscle cell +intersection_of: RO:0002473 CL:0000187 ! composed primarily of muscle cell relationship: capable_of GO:0006936 ! muscle contraction -relationship: composed_primarily_of CL:0000187 ! muscle cell -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0001015 ! musculature -property_value: RO:0002171 UBERON:0003714 -property_value: UBPROP:0000001 "One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000306", ontology="AAO", source="AAO:LAP"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002473 CL:0000187 ! composed primarily of muscle cell [Term] id: UBERON:0002390 @@ -10239,14 +9977,10 @@ is_a: UBERON:0000467 ! anatomical system is_a: UBERON:0004120 ! mesoderm-derived structure disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0004456 ! entire sense organ system -relationship: develops_from UBERON:0003061 {evidence="definitional"} ! blood island -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0002193 {source="FMA"} ! hemolymphoid system -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "Anatomical system that consists of the blood and blood forming tissues.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011002", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001624", ontology="VHOG", source="DOI:10.1016/j.coph.2010.05.004 Ellett F, Lieschke GJ, Zebrafish as a model for vertebrate hematopoiesis. Current Opinion in Pharmacology (2010)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "hematopoietic" xsd:string -property_value: UBPROP:0000008 "In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes" xsd:string {source="WP"} +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002202 UBERON:0003061 ! develops from blood island +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002405 @@ -10275,10 +10009,9 @@ xref: ZFA:0001159 is_a: UBERON:0015203 ! non-connected functional system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0002376 ! immune system process -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: present_in_taxon NCBITaxon:9606 relationship: protects UBERON:0000468 ! multicellular organism -property_value: UBPROP:0000003 "The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001247", ontology="VHOG", source="PMID:21046016 Dzik JM, The ancestry and cumulative evolution of immune reactions. Acta biochimica Polonica (2010)", source="http://bgee.unil.ch/"} +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002481 @@ -10307,10 +10040,9 @@ xref: XAO:0004040 xref: ZFA:0005621 is_a: UBERON:0004755 {source="VSAO"} ! skeletal tissue disjoint_from: UBERON:0005090 ! muscle structure -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0001474 ! bone element -property_value: editor_note "see https://github.com/obophenotype/uberon/issues/27" xsd:string -property_value: UBPROP:0000001 "Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000047", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +property_value: IAO:0000116 "see https://github.com/obophenotype/uberon/issues/27" xsd:string [Term] id: UBERON:0002530 @@ -10329,10 +10061,7 @@ xref: BTO:0000522 xref: EFO:0000797 xref: EHDAA2:0003096 xref: EHDAA:2161 -xref: EHDAA:4475 -xref: EHDAA:6522 xref: EMAPA:18425 -xref: FBbt:00100317 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7146 xref: FMA:86294 xref: galen:Gland @@ -10347,11 +10076,9 @@ xref: Wikipedia:Gland xref: WikipediaCategory:Glands is_a: UBERON:0000062 ! organ relationship: capable_of GO:0046903 ! secretion -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: produces UBERON:0000463 ! organism substance -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/a1/Gray1026.png" xsd:anyURI -property_value: RO:0002171 UBERON:0001434 -property_value: UBPROP:0000007 "glandular" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/a1/Gray1026.png" xsd:anyURI [Term] id: UBERON:0002532 @@ -10375,9 +10102,8 @@ xref: VHOG:0000243 xref: Wikipedia:Epiblast is_a: UBERON:0002050 ! embryonic structure relationship: has_part CL:0000352 ! epiblast cell -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" xsd:anyURI -property_value: editor_note "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" xsd:string -property_value: UBPROP:0000003 "In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000243", ontology="VHOG", source="DOI:10.1146/annurev.cellbio.042308.113344 Zorn AM, Wells JM, Vertebrate endoderm development and organ formation. Annual Review of Cell Developmental Biology (2009)", source="http://bgee.unil.ch/"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" xsd:anyURI +property_value: IAO:0000116 "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" xsd:string [Term] id: UBERON:0002553 @@ -10393,7 +10119,7 @@ xref: galen:Cavity xref: MA:0002447 xref: NCIT:C34007 is_a: UBERON:0000464 ! anatomical space -relationship: location_of UBERON:0000463 ! organism substance +relationship: RO:0001015 UBERON:0000463 ! location of organism substance [Term] id: UBERON:0003059 @@ -10419,13 +10145,11 @@ xref: XAO:0000057 xref: ZFA:0000279 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0005423 ! developing anatomical structure -intersection_of: has_potential_to_develop_into UBERON:0002329 ! somite -intersection_of: immediate_transformation_of UBERON:0007282 ! presumptive segmental plate -relationship: has_potential_to_develop_into UBERON:0002329 ! somite -relationship: immediate_transformation_of UBERON:0007282 {source="Bgee:AN"} ! presumptive segmental plate +intersection_of: RO:0002387 UBERON:0002329 ! has potential to develop into somite +intersection_of: RO:0002495 UBERON:0007282 ! immediate transformation of presumptive segmental plate relationship: part_of UBERON:0003077 ! paraxial mesoderm -property_value: UBPROP:0000001 "Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000279", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000559", ontology="VHOG", source="DOI:10.1006/dbio.2001.0460 Schubert M, Holland LZ, Dale Stokes M and Holland ND, Three Amphoxius Wnt Genes (AmphiWnt3, AmphiWnt5, and AmphiWnt6) Associated with the Tail Bud: the Evolution of Somitogenesis in Chordates. Developmental Biology (2001)", source="http://bgee.unil.ch/"} +relationship: RO:0002387 UBERON:0002329 ! has potential to develop into somite +relationship: RO:0002495 UBERON:0007282 {source="Bgee:AN"} ! immediate transformation of presumptive segmental plate [Term] id: UBERON:0003061 @@ -10455,13 +10179,8 @@ xref: Wikipedia:Blood_island_of_umbilical_vesicle xref: XAO:0000067 xref: ZFA:0000094 is_a: UBERON:0006598 ! presumptive structure -relationship: develops_from UBERON:0003081 ! lateral plate mesoderm -relationship: has_potential_to_develop_into UBERON:0002390 ! hematopoietic system -property_value: UBPROP:0000001 "Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000094", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011006", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000002 "relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000094", ontology="TAO"} -property_value: UBPROP:0000003 "Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000085", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450, DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual Review of Cell and Developmental Biology (2006)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac" xsd:string {external_ontology="EHDAA2"} +relationship: RO:0002202 UBERON:0003081 ! develops from lateral plate mesoderm +relationship: RO:0002387 UBERON:0002390 ! has potential to develop into hematopoietic system [Term] id: UBERON:0003068 @@ -10479,11 +10198,10 @@ xref: Wikipedia:Chordamesoderm xref: XAO:0000205 xref: ZFA:0001204 is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0000926 ! mesoderm -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0000926 ! mesoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000107", ontology="VHOG", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002202 UBERON:0000926 ! develops from mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003075 @@ -10503,7 +10221,6 @@ xref: EHDAA:346 xref: EHDAA:902 xref: EMAPA:35593 xref: FMA:293879 -xref: MESH:D054258 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C34225 xref: neuronames:1362 xref: RETIRED_EHDAA2:0001252 @@ -10516,12 +10233,10 @@ xref: ZFA:0000132 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0016879 ! future central nervous system -relationship: developmentally_induced_by UBERON:0002328 {source="Wikipedia"} ! notochord -relationship: immediate_transformation_of UBERON:0007284 {source="Bgee:AN"} ! presumptive neural plate -relationship: only_in_taxon NCBITaxon:7711 {source="GOTAX:0000352"} ! Chordata -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI -property_value: UBPROP:0000001 "The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000132", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000068", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata +relationship: RO:0002256 UBERON:0002328 {source="Wikipedia"} ! developmentally induced by notochord +relationship: RO:0002495 UBERON:0007284 {source="Bgee:AN"} ! immediate transformation of presumptive neural plate +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI [Term] id: UBERON:0003077 @@ -10550,13 +10265,9 @@ xref: ZFA:0000255 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue is_a: UBERON:0015212 ! lateral structure -relationship: existence_starts_during UBERON:0000109 ! gastrula stage -relationship: immediate_transformation_of UBERON:0007285 {source="Bgee:AN"} ! presumptive paraxial mesoderm -relationship: in_lateral_side_of UBERON:0000922 ! embryo -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010568", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000114", ontology="VHOG", source="DOI:10.1002/dvdy.21177 Kusakabe R and Kuratani S. Evolutionary perspectives from development of mesodermal components in the lamprey. Developmental dynamics (2007)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here)" xsd:string {external_ontology="ZFA"} +relationship: RO:0002488 UBERON:0000109 ! existence starts during gastrula stage +relationship: RO:0002495 UBERON:0007285 {source="Bgee:AN"} ! immediate transformation of presumptive paraxial mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003081 @@ -10588,14 +10299,10 @@ is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0000926 {source="EHDAA2", source="VHOG"} ! mesoderm -relationship: surrounds UBERON:0003887 ! intraembryonic coelom -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010574", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000001 "The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000118", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000118", ontology="VHOG", source="DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "subclass of mesoderm in ZFA." xsd:string {external_ontology="ZFA"} +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002221 UBERON:0003887 ! surrounds intraembryonic coelom +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003082 @@ -10630,12 +10337,10 @@ xref: Wikipedia:Myotome xref: XAO:0000315 xref: ZFA:0001056 is_a: UBERON:0017650 {source="AEO"} ! developing mesenchymal structure -relationship: contributes_to_morphology_of UBERON:0001630 ! muscle organ -relationship: develops_from UBERON:0004290 {source="EHDAA2-abduced"} ! dermomyotome -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI -property_value: editor_note "The term 'myotome' is also used to describe the muscles served by a single nerve root / spinal segment - consider adding new class, myomere." xsd:string -property_value: UBPROP:0000001 "Portion of the somites giving rise to body wall muscle masses. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001056", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "In all vertebrates, the skeletal muscle of the body axis is chiefly derived from an early embryonic compartment, known as the myotome.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001244", ontology="VHOG", source="DOI:10.1038/sj.embor.embor920 Hollway GE, Currie PD, Myotome meanderings. Cellular morphogenesis and the making of muscle. EMBO Rep.(2003)", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0004290 {source="EHDAA2-abduced"} ! develops from dermomyotome +relationship: RO:0002433 UBERON:0001630 ! contributes to morphology of muscle organ +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI +property_value: IAO:0000116 "The term 'myotome' is also used to describe the muscles served by a single nerve root / spinal segment - consider adding new class, myomere." xsd:string [Term] id: UBERON:0003103 @@ -10658,7 +10363,6 @@ xref: VHOG:0001723 xref: XAO:0003041 xref: ZFA:0000496 is_a: UBERON:0000062 ! organ -property_value: IAO:0000232 "this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs" xsd:string [Term] id: UBERON:0003104 @@ -10688,15 +10392,12 @@ xref: XAO:0003046 xref: ZFA:0000393 is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue -intersection_of: composed_primarily_of CL:0008019 ! mesenchymal cell -relationship: composed_primarily_of CL:0008019 ! mesenchymal cell -relationship: functionally_related_to GO:0032502 ! developmental process -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI -property_value: editor_note "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" xsd:string -property_value: UBPROP:0000001 "A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000393", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010427", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000007 "mesenchymal" xsd:string +intersection_of: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002328 GO:0032502 ! functionally related to developmental process +relationship: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI +property_value: IAO:0000116 "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" xsd:string [Term] id: UBERON:0003887 @@ -10712,10 +10413,9 @@ xref: UMLS:C1512940 {source="ncithesaurus:Intraembryonic_Coelom"} xref: VHOG:0000316 xref: Wikipedia:Intraembryonic_coelom is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0003081 {source="Wikipedia"} ! lateral plate mesoderm relationship: part_of UBERON:0011997 ! coelom -property_value: editor_note "consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults" xsd:string -property_value: UBPROP:0000003 "(...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000316", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.166", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003081 {source="Wikipedia"} ! develops from lateral plate mesoderm +property_value: IAO:0000116 "consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults" xsd:string [Term] id: UBERON:0003914 @@ -10725,12 +10425,10 @@ def: "Epithelial tubes transport gases, liquids and cells from one site to anoth synonym: "epithelial or endothelial tube" EXACT [] xref: AEO:0000114 xref: EHDAA2:0003114 -xref: FBbt:00007474 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000025 ! tube is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium -intersection_of: has_quality PATO:0002299 ! tubular -property_value: IAO:0000232 "contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers" xsd:string +intersection_of: RO:0000086 PATO:0002299 ! has quality tubular [Term] id: UBERON:0004111 @@ -10750,15 +10448,14 @@ xref: SCTID:346902003 xref: Wikipedia:Foramen is_a: UBERON:0010000 ! multicellular anatomical structure intersection_of: UBERON:0010000 ! multicellular anatomical structure -intersection_of: conduit_for UBERON:0000061 ! anatomical structure intersection_of: has_part UBERON:0013686 ! anatomical conduit space -relationship: conduit_for UBERON:0000061 ! anatomical structure -relationship: connects UBERON:0000464 {cardinality="2"} ! anatomical space +intersection_of: RO:0002570 UBERON:0000061 ! conduit for anatomical structure relationship: has_part UBERON:0013686 ! anatomical conduit space -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: UBPROP:0000012 "FMA has both conduit and conduit space. In EHDAA2 this is a surface feature" xsd:string {external_ontology="FMA"} +relationship: RO:0002176 UBERON:0000464 {cardinality="2"} ! connects anatomical space +relationship: RO:0002570 UBERON:0000061 ! conduit for anatomical structure +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0004120 @@ -10769,9 +10466,8 @@ subset: grouping_class synonym: "mesodermal derivative" EXACT [FBbt:00025998] is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: develops_from UBERON:0000926 ! mesoderm -relationship: develops_from UBERON:0000926 ! mesoderm -property_value: IAO:0000232 "Grouping term for query purposes" xsd:string +intersection_of: RO:0002202 UBERON:0000926 ! develops from mesoderm +relationship: RO:0002202 UBERON:0000926 ! develops from mesoderm [Term] id: UBERON:0004121 @@ -10782,9 +10478,8 @@ subset: grouping_class synonym: "ectodermal deriviative" EXACT [FBbt:00025990] is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: develops_from UBERON:0000924 ! ectoderm -relationship: develops_from UBERON:0000924 ! ectoderm -property_value: IAO:0000232 "Grouping term for query purposes" xsd:string +intersection_of: RO:0002202 UBERON:0000924 ! develops from ectoderm +relationship: RO:0002202 UBERON:0000924 ! develops from ectoderm [Term] id: UBERON:0004288 @@ -10814,13 +10509,10 @@ xref: Wikipedia:Skeleton xref: XAO:0004053 is_a: UBERON:0034925 ! anatomical collection disjoint_from: UBERON:0004770 ! articular system -relationship: has_member UBERON:0004765 ! skeletal element relationship: part_of UBERON:0001434 ! skeletal system -relationship: present_in_taxon NCBITaxon:9606 -property_value: RO:0002171 UBERON:0000383 +relationship: RO:0002351 UBERON:0004765 ! has member skeletal element +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/The-skeletal-system" xsd:anyURI -property_value: UBPROP:0000001 "Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000026", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070"} -property_value: UBPROP:0000007 "skeletal" xsd:string [Term] id: UBERON:0004290 @@ -10841,13 +10533,8 @@ xref: VHOG:0000676 xref: ZFA:0001513 is_a: UBERON:0000486 {source="AEO"} ! multilaminar epithelium is_a: UBERON:0016888 {source="AEO"} ! transitional anatomical structure -relationship: develops_from UBERON:0002329 {source="EHDAA2", source="ZFA"} ! somite relationship: has_part CL:0000075 ! columnar/cuboidal epithelial cell -property_value: UBPROP:0000001 "all but the sclerotome of a mesodermal somite; the primordium of skeletal muscle and, perhaps, of the dermis." xsd:string {source="http://medical-dictionary.thefreedictionary.com/dermomyotome"} -property_value: UBPROP:0000001 "Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768]." xsd:string {source="http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768"} -property_value: UBPROP:0000001 "Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001513", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Portion of somites that gives rise to dermis and muscles.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010572", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000676", ontology="VHOG", source="DOI:10.1111/j.1525-142X.2006.05079.x Devoto SH, Stoiber W, Hammond CL, Steinbacher P, Haslett JR, Barresi MJF, Patterson SE, Adiarte EG and Hughes SM, Generality of vertebrate developmental patterns: evidence for a dermomyotome in fish. Evolution and Development (2006)", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0002329 {source="EHDAA2", source="ZFA"} ! develops from somite [Term] id: UBERON:0004456 @@ -10858,9 +10545,8 @@ subset: uberon_slim synonym: "sense organ system" EXACT [FMA:78499] xref: FMA:78499 is_a: UBERON:0000467 ! anatomical system -relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: overlaps UBERON:0001016 ! nervous system -property_value: UBPROP:0000012 "note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs" xsd:string +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage [Term] id: UBERON:0004716 @@ -10877,12 +10563,12 @@ xref: NCIT:C34131 xref: UMLS:C1516779 {source="ncithesaurus:Conceptus"} xref: Wikipedia:Conceptus is_a: UBERON:0000061 ! anatomical structure -relationship: develops_from CL:0000365 ! animal zygote -relationship: existence_ends_with UBERON:0000068 ! embryo stage -relationship: existence_starts_with UBERON:0000068 ! embryo stage relationship: has_part UBERON:0002050 ! embryonic structure relationship: has_part UBERON:0016887 ! entire extraembryonic component -property_value: editor_note "EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus" xsd:string +relationship: RO:0002202 CL:0000365 ! develops from animal zygote +relationship: RO:0002489 UBERON:0000068 ! existence starts with embryo stage +relationship: RO:0002493 UBERON:0000068 ! existence ends with embryo stage +property_value: IAO:0000116 "EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus" xsd:string [Term] id: UBERON:0004734 @@ -10902,7 +10588,6 @@ synonym: "trilaminar disk" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "trilaminar germ" RELATED [https://orcid.org/0000-0002-6601-2165] xref: BILA:0000060 xref: BTO:0001403 -xref: FBbt:00005317 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:293108 xref: GAID:1302 xref: MESH:D005775 @@ -10915,10 +10600,9 @@ xref: Wikipedia:Gastrula xref: Wikipedia:Trilaminar_blastocyst is_a: UBERON:0000922 ! embryo intersection_of: UBERON:0000468 ! multicellular organism -intersection_of: existence_starts_and_ends_during UBERON:0000109 ! gastrula stage -relationship: develops_from UBERON:0000307 ! blastula -relationship: existence_starts_and_ends_during UBERON:0000109 ! gastrula stage -property_value: UBPROP:0000012 "We explicitly merge the NCITA terms here" xsd:string {external_ontology="NCIT"} +intersection_of: RO:0002491 UBERON:0000109 ! existence starts and ends during gastrula stage +relationship: RO:0002202 UBERON:0000307 ! develops from blastula +relationship: RO:0002491 UBERON:0000109 ! existence starts and ends during gastrula stage [Term] id: UBERON:0004755 @@ -10933,9 +10617,8 @@ xref: VSAO:0000015 xref: XAO:0004038 xref: ZFA:0005619 is_a: UBERON:0002384 {source="VSAO"} ! connective tissue -relationship: develops_from CL:0007001 {date_retrieved="2012-08-14", external_class="VSAO:0000015", source="VSAO"} ! skeletogenic cell relationship: part_of UBERON:0004765 ! skeletal element -property_value: UBPROP:0000001 "A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000015", notes="taken from version of VSAO used in TAO and used directly in Uberon", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} +relationship: RO:0002202 CL:0007001 ! develops from skeletogenic cell [Term] id: UBERON:0004765 @@ -10952,8 +10635,6 @@ xref: XAO:0004012 xref: ZFA:0005494 is_a: UBERON:0000062 ! organ relationship: part_of UBERON:0001434 {source="VSAO"} ! skeletal system -property_value: UBPROP:0000001 "Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000128", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001890", ontology="TAO", source="TAO:VSAO_workshop"} [Term] id: UBERON:0004770 @@ -10971,12 +10652,12 @@ xref: SCTID:361827000 xref: VSAO:0000181 is_a: UBERON:0034925 ! anatomical collection intersection_of: UBERON:0034925 ! anatomical collection -intersection_of: has_member UBERON:0000982 ! skeletal joint -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: functionally_related_to GO:0040011 ! locomotion -relationship: has_member UBERON:0000982 ! skeletal joint -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +intersection_of: RO:0002351 UBERON:0000982 ! has member skeletal joint relationship: part_of UBERON:0001434 {source="FMA"} ! skeletal system +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002328 GO:0040011 ! functionally related to locomotion +relationship: RO:0002351 UBERON:0000982 ! has member skeletal joint +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage [Term] id: UBERON:0004880 @@ -10994,10 +10675,8 @@ xref: EFO:0003426 xref: TAO:0000091 xref: ZFA:0000091 is_a: UBERON:0002050 ! embryonic structure -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0003068 ! axial mesoderm -property_value: UBPROP:0000001 "Notochord rudiment[ZFIN:ZDB-PUB-961014-576]." xsd:string {source="ZFIN:ZDB-PUB-961014-576"} -property_value: UBPROP:0000012 "WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord." xsd:string +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata [Term] id: UBERON:0004905 @@ -11006,7 +10685,6 @@ namespace: uberon def: "Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts." [http://orcid.org/0000-0002-6601-2165] subset: grouping_class synonym: "joint" NARROW [] -xref: FBbt:00005811 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0034921 ! multi organ part structure relationship: part_of UBERON:0004770 ! articular system @@ -11022,15 +10700,13 @@ synonym: "gut section" RELATED [FBbt:00100315] synonym: "intestinal tract" RELATED [] synonym: "segment of intestinal tract" RELATED [] synonym: "subdivision of alimentary system" RELATED [FMA:71131] -xref: FBbt:00100315 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:71131 is_a: UBERON:0013522 ! subdivision of tube intersection_of: UBERON:0013522 ! subdivision of tube intersection_of: subdivision_of UBERON:0001555 ! digestive tract relationship: part_of UBERON:0001555 ! digestive tract -relationship: present_in_taxon NCBITaxon:9606 relationship: subdivision_of UBERON:0001555 ! digestive tract -property_value: IAO:0000232 "intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct." xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004923 @@ -11040,8 +10716,8 @@ def: "A part of a wall of an organ that forms a layer." [http://orcid.org/0000-0 subset: upper_level xref: FMA:82485 is_a: UBERON:0000064 ! organ part -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000060 ! anatomical wall +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0005061 @@ -11059,7 +10735,6 @@ xref: Wikipedia:Neural_groove xref: XAO:0000248 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0003075 ! neural plate -property_value: UBPROP:0000001 "The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]." xsd:string {source="Wikipedia:Neural_groove"} [Term] id: UBERON:0005062 @@ -11079,10 +10754,9 @@ xref: XAO:0004087 is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0005157 ! epithelial fold is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0015212 ! lateral structure -relationship: in_lateral_side_of UBERON:0005061 ! neural groove relationship: part_of UBERON:0005061 ! neural groove -property_value: UBPROP:0000001 "In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]." xsd:string {source="Wikipedia:Neural_fold"} [Term] id: UBERON:0005068 @@ -11095,8 +10769,7 @@ xref: EFO:0003498 xref: TAO:0000133 xref: ZFA:0000133 is_a: UBERON:0016879 ! future central nervous system -relationship: develops_from UBERON:0007135 ! neural keel -property_value: UBPROP:0000001 "An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000133", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002202 UBERON:0007135 ! develops from neural keel [Term] id: UBERON:0005090 @@ -11106,12 +10779,10 @@ def: "Muscle structures are contractile cells, tissues or organs that are found synonym: "muscle" RELATED [] synonym: "muscle element" RELATED [] synonym: "musculus" EXACT [FMA:30316] -xref: EMAPA:32715 xref: FMA:30316 is_a: UBERON:0000061 ! anatomical structure relationship: has_part CL:0000187 ! muscle cell -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: IAO:0000232 "in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0005157 @@ -11164,14 +10835,13 @@ name: photoreceptor array namespace: uberon def: "An array of photoreceptors and any supporting cells found in an eye." [https://orcid.org/0000-0002-6601-2165] synonym: "light-sensitive tissue" EXACT [] -xref: FBbt:00004200 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0004923 ! organ component layer intersection_of: UBERON:0004923 ! organ component layer -intersection_of: composed_primarily_of CL:0000210 ! photoreceptor cell intersection_of: part_of UBERON:0000970 ! eye -relationship: composed_primarily_of CL:0000210 ! photoreceptor cell +intersection_of: RO:0002473 CL:0000210 ! composed primarily of photoreceptor cell relationship: part_of UBERON:0000970 ! eye relationship: part_of UBERON:0001016 ! nervous system +relationship: RO:0002473 CL:0000210 ! composed primarily of photoreceptor cell [Term] id: UBERON:0005423 @@ -11184,14 +10854,13 @@ synonym: "developmental tissue" RELATED [MIAA:0000019] xref: AEO:0000125 xref: CALOHA:TS-2122 xref: EHDAA2:0003125 -xref: FBbt:00007006 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:292313 xref: MIAA:0000019 is_a: UBERON:0000465 ! material anatomical entity relationship: capable_of GO:0032502 ! developmental process -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0005764 @@ -11204,9 +10873,9 @@ is_a: UBERON:0000476 ! acellular anatomical structure intersection_of: UBERON:0000476 ! acellular anatomical structure intersection_of: bounding_layer_of UBERON:0000061 ! anatomical structure relationship: bounding_layer_of UBERON:0000061 ! anatomical structure -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0005769 @@ -11226,12 +10895,11 @@ xref: Wikipedia:Basement_membrane is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005764 {source="FMA"} ! acellular membrane relationship: adjacent_to CL:0000066 ! epithelial cell -relationship: composed_primarily_of GO:0005604 ! basement membrane relationship: has_part GO:0005587 ! collagen type IV trimer -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa relationship: part_of UBERON:0000483 ! epithelium -relationship: present_in_taxon NCBITaxon:80999 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} -property_value: IAO:0000232 "this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell." xsd:string +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002473 GO:0005604 ! composed primarily of basement membrane +property_value: RO:0002175 NCBITaxon:80999 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} [Term] id: UBERON:0006267 @@ -11249,9 +10917,8 @@ is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium -relationship: develops_from UBERON:0006268 {source="EHDAA2"} ! notochordal process -property_value: editor_note "TODO - check ordering; awaiting confirmation from JB" xsd:string -property_value: UBPROP:0000001 "The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001212", ontology="VHOG", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0006268 {source="EHDAA2"} ! develops from notochordal process +property_value: IAO:0000116 "TODO - check ordering; awaiting confirmation from JB" xsd:string [Term] id: UBERON:0006268 @@ -11270,8 +10937,8 @@ xref: NCIT:C34232 xref: UMLS:C1518430 {source="ncithesaurus:Notochordal_Process"} xref: VHOG:0001213 is_a: UBERON:0005423 ! developing anatomical structure -relationship: develops_from UBERON:0000924 {source="EHDAA2"} ! ectoderm -relationship: only_in_taxon NCBITaxon:7711 ! Chordata +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002202 UBERON:0000924 {source="EHDAA2"} ! develops from ectoderm [Term] id: UBERON:0006595 @@ -11285,11 +10952,11 @@ xref: TAO:0000416 xref: ZFA:0000416 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0000925 ! endoderm intersection_of: part_of UBERON:0000307 ! blastula -relationship: has_potential_to_develop_into UBERON:0000925 ! endoderm -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +intersection_of: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm relationship: part_of UBERON:0000307 ! blastula +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm [Term] id: UBERON:0006598 @@ -11303,10 +10970,10 @@ xref: TAO:0001116 xref: ZFA:0001116 is_a: UBERON:0002050 ! embryonic structure intersection_of: UBERON:0005423 ! developing anatomical structure -intersection_of: has_potential_to_develop_into UBERON:0000061 ! anatomical structure intersection_of: part_of UBERON:0000922 ! embryo -relationship: has_potential_to_develop_into UBERON:0000061 ! anatomical structure -property_value: editor_note "Consider merging with anlage" xsd:string +intersection_of: RO:0002387 UBERON:0000061 ! has potential to develop into anatomical structure +relationship: RO:0002387 UBERON:0000061 ! has potential to develop into anatomical structure +property_value: IAO:0000116 "Consider merging with anlage" xsd:string [Term] id: UBERON:0006601 @@ -11322,11 +10989,11 @@ xref: XAO:0004132 xref: ZFA:0001376 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0000924 ! ectoderm intersection_of: part_of UBERON:0000307 ! blastula -relationship: has_potential_to_develop_into UBERON:0000924 ! ectoderm -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +intersection_of: RO:0002387 UBERON:0000924 ! has potential to develop into ectoderm relationship: part_of UBERON:0000307 ! blastula +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002387 UBERON:0000924 ! has potential to develop into ectoderm [Term] id: UBERON:0006603 @@ -11340,11 +11007,11 @@ xref: TAO:0001377 xref: ZFA:0001377 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0000926 ! mesoderm intersection_of: part_of UBERON:0000307 ! blastula -relationship: has_potential_to_develop_into UBERON:0000926 ! mesoderm -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +intersection_of: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm relationship: part_of UBERON:0000307 ! blastula +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm [Term] id: UBERON:0006984 @@ -11359,7 +11026,7 @@ xref: EHDAA2_RETIRED:0003192 xref: FMA:24137 xref: NCIT:C34022 xref: UMLS:C1515977 {source="ncithesaurus:Anatomic_Surface"} -is_a: UBERON:0010199 {notes="via morphological boundary in CARO"} ! bona-fide anatomical boundary +is_a: UBERON:0010199 ! bona-fide anatomical boundary [Term] id: UBERON:0007010 @@ -11369,10 +11036,10 @@ def: "Organism at the cleavage stage." [OBOL:automatic] xref: BILA:0000058 is_a: UBERON:0000922 ! embryo intersection_of: UBERON:0000468 ! multicellular organism -intersection_of: existence_ends_with UBERON:0000107 ! cleavage stage -intersection_of: existence_starts_with UBERON:0000107 ! cleavage stage -relationship: existence_ends_with UBERON:0000107 ! cleavage stage -relationship: existence_starts_with UBERON:0000107 ! cleavage stage +intersection_of: RO:0002489 UBERON:0000107 ! existence starts with cleavage stage +intersection_of: RO:0002493 UBERON:0000107 ! existence ends with cleavage stage +relationship: RO:0002489 UBERON:0000107 ! existence starts with cleavage stage +relationship: RO:0002493 UBERON:0000107 ! existence ends with cleavage stage [Term] id: UBERON:0007026 @@ -11391,12 +11058,11 @@ xref: SCTID:360394002 xref: UMLS:C1514442 {source="ncithesaurus:Primordial_Gut"} is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001555 ! digestive tract -relationship: existence_starts_during UBERON:0000109 ! gastrula stage -relationship: has_developmental_contribution_from UBERON:0000925 ! endoderm -relationship: has_developmental_contribution_from UBERON:0000926 ! mesoderm -relationship: has_potential_to_develop_into UBERON:0001555 ! digestive tract -property_value: UBPROP:0000011 "The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis" xsd:string {source="NCBIBook:NBK10107"} +intersection_of: RO:0002387 UBERON:0001555 ! has potential to develop into digestive tract +relationship: RO:0002254 UBERON:0000925 ! has developmental contribution from endoderm +relationship: RO:0002254 UBERON:0000926 ! has developmental contribution from mesoderm +relationship: RO:0002387 UBERON:0001555 ! has potential to develop into digestive tract +relationship: RO:0002488 UBERON:0000109 ! existence starts during gastrula stage [Term] id: UBERON:0007100 @@ -11409,14 +11075,12 @@ synonym: "adult heart" RELATED [FBbt:00003154] synonym: "dorsal tube" NARROW [Wikipedia:Heart] synonym: "heart" NARROW [GO:0007507] xref: http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg -xref: SPD:0000130 xref: TADS:0000147 is_a: UBERON:0015228 ! circulatory organ intersection_of: UBERON:0015228 ! circulatory organ intersection_of: capable_of GO:0008015 ! blood circulation -relationship: capable_of GO:0008015 {notes="GO uses blood circulation generically to include the haemolymphatic fluid of arthropods"} ! blood circulation +relationship: capable_of GO:0008015 ! blood circulation relationship: has_part CL:0002494 ! cardiocyte -property_value: UBPROP:0000008 "note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis" xsd:string [Term] id: UBERON:0007135 @@ -11429,8 +11093,7 @@ xref: EFO:0003497 xref: TAO:0000131 xref: ZFA:0000131 is_a: UBERON:0016879 ! future central nervous system -relationship: develops_from UBERON:0003075 ! neural plate -property_value: UBPROP:0000001 "An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000131", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002202 UBERON:0003075 ! develops from neural plate [Term] id: UBERON:0007282 @@ -11444,9 +11107,9 @@ xref: TAO:0000053 xref: ZFA:0000053 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0003059 ! presomitic mesoderm -relationship: develops_from UBERON:0009618 {consistent_with="https://github.com/obophenotype/uberon/wiki/The-neural-crest", source="EDHAA2"} ! trunk paraxial mesoderm -relationship: has_potential_to_develop_into UBERON:0003059 ! presomitic mesoderm +intersection_of: RO:0002387 UBERON:0003059 ! has potential to develop into presomitic mesoderm +relationship: RO:0002202 UBERON:0009618 ! develops from trunk paraxial mesoderm +relationship: RO:0002387 UBERON:0003059 ! has potential to develop into presomitic mesoderm [Term] id: UBERON:0007284 @@ -11461,12 +11124,11 @@ xref: TAO:0000063 xref: ZFA:0000063 is_a: UBERON:0016879 ! future central nervous system intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0003075 ! neural plate -relationship: develops_from UBERON:0002346 ! neurectoderm -relationship: has_potential_to_develop_into UBERON:0003075 ! neural plate +intersection_of: RO:0002387 UBERON:0003075 ! has potential to develop into neural plate relationship: part_of UBERON:0004734 ! gastrula -property_value: editor_note "consider merging" xsd:string -property_value: UBPROP:0000001 "Region of the gastrula which gives rise to the neural plate.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000063", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002202 UBERON:0002346 ! develops from neurectoderm +relationship: RO:0002387 UBERON:0003075 ! has potential to develop into neural plate +property_value: IAO:0000116 "consider merging" xsd:string [Term] id: UBERON:0007285 @@ -11482,10 +11144,10 @@ xref: XAO:0004134 xref: ZFA:0000591 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 {source="https://github.com/obophenotype/uberon/issues/1277"} ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0003077 {source="https://github.com/obophenotype/uberon/issues/1277"} ! paraxial mesoderm intersection_of: part_of UBERON:0000307 {source="https://github.com/obophenotype/uberon/issues/1277"} ! blastula -relationship: has_potential_to_develop_into UBERON:0003077 ! paraxial mesoderm +intersection_of: RO:0002387 UBERON:0003077 {source="https://github.com/obophenotype/uberon/issues/1277"} ! has potential to develop into paraxial mesoderm relationship: part_of UBERON:0000307 ! blastula +relationship: RO:0002387 UBERON:0003077 ! has potential to develop into paraxial mesoderm [Term] id: UBERON:0007503 @@ -11518,7 +11180,7 @@ disjoint_from: UBERON:0011821 ! irregular connective tissue relationship: has_part CL:0000057 ! fibroblast relationship: has_part GO:0071953 ! elastic fiber relationship: has_part UBERON:0011860 ! collection of collagen fibrils -property_value: editor_note "the connective tissue hierarchy largely follows FMA with definitions from VSAO. Note that in FMA, loose-CT is irregular-CT. This means regular-CT is necessarily equivalent to dense-regular-CT (assuming a JEPD classification)." xsd:string +property_value: IAO:0000116 "the connective tissue hierarchy largely follows FMA with definitions from VSAO. Note that in FMA, loose-CT is irregular-CT. This means regular-CT is necessarily equivalent to dense-regular-CT (assuming a JEPD classification)." xsd:string [Term] id: UBERON:0007846 @@ -11540,10 +11202,8 @@ xref: XAO:0004030 is_a: UBERON:0007845 {source="FMA"} ! regular connective tissue is_a: UBERON:0011823 {source="ncithesaurus"} ! dense connective tissue intersection_of: UBERON:0007845 ! regular connective tissue -intersection_of: composed_primarily_of UBERON:0011860 ! collection of collagen fibrils intersection_of: has_part GO:0071953 ! elastic fiber -property_value: UBPROP:0000001 "Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000050", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "Regular connective tissue, the intercellular matrix of which consists predominantly of collagen fiber bundles arranged in parallel arrays.[FMA]" xsd:string {date_retrieved="2012-08-29", external_class="FMA:64781", ontology="FMA"} +intersection_of: RO:0002473 UBERON:0011860 ! composed primarily of collection of collagen fibrils [Term] id: UBERON:0009142 @@ -11555,10 +11215,10 @@ xref: EHDAA2:0001113 xref: EHDAA:177 xref: EMAPA:16097 is_a: UBERON:0000477 ! anatomical cluster -relationship: composed_primarily_of UBERON:0003104 ! mesenchyme -relationship: has_developmental_contribution_from UBERON:0000926 {source="EHDAA2"} ! mesoderm relationship: part_of UBERON:0000922 ! embryo -property_value: editor_note "consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)" xsd:string +relationship: RO:0002254 UBERON:0000926 {source="EHDAA2"} ! has developmental contribution from mesoderm +relationship: RO:0002473 UBERON:0003104 ! composed primarily of mesenchyme +property_value: IAO:0000116 "consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)" xsd:string [Term] id: UBERON:0009618 @@ -11580,15 +11240,14 @@ subset: common_anatomy subset: upper_level synonym: "multicellular structure" EXACT [FBbt:00100313] xref: CARO:0010000 -xref: FBbt:00100313 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: has_quality PATO:0001993 ! multicellular +intersection_of: RO:0000086 PATO:0001993 ! has quality multicellular relationship: has_part CL:0000000 ! cell -relationship: has_quality PATO:0001993 ! multicellular -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0000086 PATO:0001993 ! has quality multicellular +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0010199 @@ -11600,13 +11259,24 @@ subset: upper_level xref: CARO:0001004 is_a: UBERON:0000466 {source="CARO"} ! immaterial anatomical entity +[Term] +id: UBERON:0010314 +name: structure with developmental contribution from neural crest +namespace: uberon +def: "An anatomical structure that has some part that develops from the neural crest." [https://orcid.org/0000-0002-6601-2165] +subset: grouping_class +is_a: UBERON:0000061 ! anatomical structure +intersection_of: UBERON:0000061 ! anatomical structure +intersection_of: RO:0002254 UBERON:0002342 ! has developmental contribution from neural crest +relationship: RO:0002254 UBERON:0002342 ! has developmental contribution from neural crest + [Term] id: UBERON:0010316 name: germ layer / neural crest namespace: uberon is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0005291 ! embryonic tissue -relationship: develops_from UBERON:0002532 ! epiblast (generic) +relationship: RO:0002202 UBERON:0002532 ! develops from epiblast (generic) [Term] id: UBERON:0010371 @@ -11618,8 +11288,8 @@ xref: FMA:69064 is_a: UBERON:0000483 ! epithelium is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000483 ! epithelium -intersection_of: develops_from UBERON:0000924 ! ectoderm -relationship: composed_primarily_of CL:0002077 ! ecto-epithelial cell +intersection_of: RO:0002202 UBERON:0000924 ! develops from ectoderm +relationship: RO:0002473 CL:0002077 ! composed primarily of ecto-epithelial cell [Term] id: UBERON:0011137 @@ -11639,15 +11309,14 @@ def: "A subdivision of an anatomical system." [http://orcid.org/0000-0002-6601-2 subset: common_anatomy subset: human_reference_atlas subset: upper_level -xref: FBbt:00007330 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67509 xref: SCTID:91690000 is_a: UBERON:0010000 {source="FBbt"} ! multicellular anatomical structure relationship: part_of UBERON:0000467 ! anatomical system -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0011676 @@ -11660,7 +11329,7 @@ synonym: "body segment" RELATED [] synonym: "main body segment" RELATED [] is_a: UBERON:0000475 ! organism subdivision relationship: part_of UBERON:0013701 ! main body axis -property_value: editor_note "Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem" xsd:string +property_value: IAO:0000116 "Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem" xsd:string [Term] id: UBERON:0011821 @@ -11684,10 +11353,9 @@ xref: Wikipedia:Dense_irregular_connective_tissue is_a: UBERON:0011821 {source="FMA"} ! irregular connective tissue is_a: UBERON:0011823 ! dense connective tissue intersection_of: UBERON:0011821 ! irregular connective tissue -intersection_of: composed_primarily_of UBERON:0011860 ! collection of collagen fibrils intersection_of: has_part GO:0071953 ! elastic fiber +intersection_of: RO:0002473 UBERON:0011860 ! composed primarily of collection of collagen fibrils relationship: has_part GO:0071953 ! elastic fiber -property_value: UBPROP:0000001 "Tissue characterized by a thick, random arrangement of collagen and elastin fibers with very few cells. The majority of the cells are fibroblasts, but mast cells and macrophages may also be seen. It is found in the dermis, periosteum, perichondrium, capsules of organs and sheaths of nerves and muscles[NCIT]" xsd:string {date_retrieved="2012-08-29", external_class="ncithesaurus:Irregular_Dense_Connective_Tissue", ontology="NCIT"} [Term] id: UBERON:0011823 @@ -11701,10 +11369,9 @@ xref: Wikipedia:Dense_connective_tissue is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002384 ! connective tissue intersection_of: UBERON:0002384 ! connective tissue -intersection_of: composed_primarily_of UBERON:0011860 ! collection of collagen fibrils -relationship: composed_primarily_of UBERON:0011860 ! collection of collagen fibrils -property_value: editor_note "our OWL definition states that this is differentiated from other connective tissue types by virtue of the fact that the collage fiber component predominates, as opposed to cells and fluid." xsd:string -property_value: UBPROP:0000001 "Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT]" xsd:string {date_retrieved="2012-08-29", external_class="ncithesaurus:Dense_Connective_Tissue", ontology="NCIT"} +intersection_of: RO:0002473 UBERON:0011860 ! composed primarily of collection of collagen fibrils +relationship: RO:0002473 UBERON:0011860 ! composed primarily of collection of collagen fibrils +property_value: IAO:0000116 "our OWL definition states that this is differentiated from other connective tissue types by virtue of the fact that the collage fiber component predominates, as opposed to cells and fluid." xsd:string [Term] id: UBERON:0011860 @@ -11716,10 +11383,9 @@ xref: NCIT:C32339 xref: NIF_Subcellular:sao7547390221 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000476 {source="ZFA"} ! acellular anatomical structure -relationship: composed_primarily_of GO:0005581 ! collagen trimer -relationship: composed_primarily_of GO:0098643 ! banded collagen fibril -relationship: seeAlso UBERON:0007377 -property_value: UBPROP:0000012 "the FMA class specifically refers to ureter" xsd:string {external_ontology="FMA"} +relationship: RO:0002473 GO:0005581 ! composed primarily of collagen trimer +relationship: RO:0002473 GO:0098643 ! composed primarily of banded collagen fibril +property_value: seeAlso UBERON:0007377 [Term] id: UBERON:0011899 @@ -11732,11 +11398,11 @@ xref: FMA:9726 xref: NCIT:C32527 xref: UMLS:C0504096 {source="ncithesaurus:Epimysium"} xref: Wikipedia:Epimysium +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0011822 {source="FMA"} ! dense irregular connective tissue relationship: bounding_layer_of UBERON:0014892 ! skeletal muscle organ, vertebrate -relationship: continuous_with UBERON:0000043 ! tendon relationship: part_of UBERON:0001134 {source="FMA"} ! skeletal muscle tissue -property_value: UBPROP:0000009 "The Epimysium also protects muscles from friction against other muscles and bones" xsd:string +relationship: RO:0002150 UBERON:0000043 ! continuous with tendon [Term] id: UBERON:0011997 @@ -11751,10 +11417,9 @@ synonym: "schizocoelom" NARROW [] xref: EHDAA2:0004731 xref: Wikipedia:Coelom is_a: UBERON:0000481 {source="EHDAA2"} ! multi-tissue structure -relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -property_value: editor_note "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." xsd:string -property_value: UBPROP:0000007 "coelomic" xsd:string +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +property_value: IAO:0000116 "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." xsd:string +property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} [Term] id: UBERON:0012429 @@ -11770,12 +11435,12 @@ xref: CALOHA:TS-2142 xref: FMA:14073 xref: NCIT:C13051 xref: UMLS:C0229619 {source="ncithesaurus:Hematopoietic_Tissue"} +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0034769 {source="FMA"} ! lymphomyeloid tissue intersection_of: UBERON:0000479 ! tissue intersection_of: site_of GO:0030097 ! hemopoiesis relationship: part_of UBERON:0002390 {source="defitional"} ! hematopoietic system relationship: site_of GO:0030097 ! hemopoiesis -property_value: UBPROP:0000008 "Bone marrow in humans, kidney interstitium in Danio, within a stroma of reticuloendothelial tissue" xsd:string [Term] id: UBERON:0013522 @@ -11796,11 +11461,11 @@ subset: common_anatomy synonym: "foramen space" NARROW [] xref: FMA:9338 is_a: UBERON:0000464 {source="FMA"} ! anatomical space -relationship: connects UBERON:0000464 {cardinality="2"} ! anatomical space -relationship: luminal_space_of UBERON:0004111 ! anatomical conduit -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0002176 UBERON:0000464 {cardinality="2"} ! connects anatomical space +relationship: RO:0002572 UBERON:0004111 ! luminal space of anatomical conduit +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0013701 @@ -11809,7 +11474,7 @@ namespace: uberon def: "A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages." [https://orcid.org/0000-0002-6601-2165] subset: non_informative is_a: UBERON:0000475 ! organism subdivision -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0013702 @@ -11821,11 +11486,9 @@ synonym: "body" RELATED [AEO:0000103] synonym: "whole body" RELATED [BTO:0001489] xref: AEO:0000103 xref: BTO:0001489 -xref: EMAPA:36031 xref: FMA:231424 is_a: UBERON:0000475 {source="AEO"} ! organism subdivision relationship: part_of UBERON:0013701 ! main body axis -property_value: UBPROP:0000001 "Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]." xsd:string {source="FMA:231424"} [Term] id: UBERON:0014892 @@ -11855,17 +11518,17 @@ xref: XAO:0000174 xref: ZFA:0005277 is_a: UBERON:0001630 ! muscle organ intersection_of: UBERON:0001630 ! muscle organ -intersection_of: composed_primarily_of UBERON:0001134 ! skeletal muscle tissue -intersection_of: develops_from UBERON:0003082 ! myotome -intersection_of: surrounded_by UBERON:0011899 ! epimysium -intersection_of: synapsed_by CL:0000100 ! motor neuron -relationship: composed_primarily_of UBERON:0001134 ! skeletal muscle tissue -relationship: develops_from UBERON:0003082 ! myotome -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +intersection_of: RO:0002103 CL:0000100 ! synapsed by motor neuron +intersection_of: RO:0002202 UBERON:0003082 ! develops from myotome +intersection_of: RO:0002219 UBERON:0011899 ! surrounded by epimysium +intersection_of: RO:0002473 UBERON:0001134 ! composed primarily of skeletal muscle tissue relationship: part_of UBERON:0018254 ! skeletal musculature -relationship: present_in_taxon NCBITaxon:9606 -relationship: surrounded_by UBERON:0011899 ! epimysium -relationship: synapsed_by CL:0000100 ! motor neuron +relationship: RO:0002103 CL:0000100 ! synapsed by motor neuron +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002202 UBERON:0003082 ! develops from myotome +relationship: RO:0002219 UBERON:0011899 ! surrounded by epimysium +relationship: RO:0002473 UBERON:0001134 ! composed primarily of skeletal muscle tissue +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0015203 @@ -11873,7 +11536,6 @@ name: non-connected functional system namespace: uberon def: "An anatomical group whose component structures share a common function." [AEO:0000093, AEO:JB, FBbt:00007278, FBC:DOS] xref: AEO:0000093 -xref: FBbt:00007278 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0034923 ! disconnected anatomical group [Term] @@ -11884,8 +11546,8 @@ def: "A non-connected functional system that is composed primarily of a gland." xref: EHDAA2:0002223 is_a: UBERON:0015203 ! non-connected functional system intersection_of: UBERON:0015203 ! non-connected functional system -intersection_of: composed_primarily_of UBERON:0002530 ! gland -relationship: composed_primarily_of UBERON:0002530 ! gland +intersection_of: RO:0002473 UBERON:0002530 ! composed primarily of gland +relationship: RO:0002473 UBERON:0002530 ! composed primarily of gland [Term] id: UBERON:0015212 @@ -11895,11 +11557,7 @@ def: "Any structure that is placed on one side of the left-right axis of a bilat subset: grouping_class subset: non_informative is_a: UBERON:0000061 ! anatomical structure -intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: in_lateral_side_of UBERON:0000465 ! material anatomical entity -relationship: in_lateral_side_of UBERON:0000465 ! material anatomical entity -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -property_value: IAO:0000232 "This class is primarily to implement taxon constraints. It may be removed in the future." xsd:string +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria [Term] id: UBERON:0015228 @@ -11912,10 +11570,9 @@ synonym: "cardiac structure" RELATED [] synonym: "circulatory vessel" NARROW [] synonym: "heart" BROAD [] synonym: "heart or heart like organ" EXACT [] -xref: SPD:0000130 is_a: UBERON:0003103 ! compound organ -relationship: has_quality PATO:0001690 ! contractile relationship: part_of UBERON:0001009 ! circulatory system +relationship: RO:0000086 PATO:0001690 ! has quality contractile [Term] id: UBERON:0015757 @@ -11935,10 +11592,10 @@ synonym: "future CNS" EXACT [] synonym: "presumptive central nervous system" EXACT [] is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001017 ! central nervous system -relationship: develops_from UBERON:0000924 ! ectoderm -relationship: has_potential_to_develop_into UBERON:0001017 ! central nervous system +intersection_of: RO:0002387 UBERON:0001017 ! has potential to develop into central nervous system relationship: part_of UBERON:0016880 ! future nervous system +relationship: RO:0002202 UBERON:0000924 ! develops from ectoderm +relationship: RO:0002387 UBERON:0001017 ! has potential to develop into central nervous system [Term] id: UBERON:0016880 @@ -11950,9 +11607,9 @@ synonym: "presumptive nervous system" EXACT [AAO:0000477] xref: AAO:0000477 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001016 ! nervous system -relationship: existence_starts_during_or_after UBERON:0000111 ! organogenesis stage -relationship: has_potential_to_develop_into UBERON:0001016 ! nervous system +intersection_of: RO:0002387 UBERON:0001016 ! has potential to develop into nervous system +relationship: RO:0002387 UBERON:0001016 ! has potential to develop into nervous system +relationship: RO:0002496 UBERON:0000111 ! existence starts during or after organogenesis stage [Term] id: UBERON:0016887 @@ -11966,8 +11623,8 @@ xref: EHDAA2:0000003 xref: EMAPA:16042 is_a: UBERON:0000481 {source="AEO"} ! multi-tissue structure relationship: adjacent_to UBERON:0002050 ! embryonic structure -relationship: existence_starts_and_ends_during UBERON:0000068 ! embryo stage relationship: part_of UBERON:0004716 {source="AEO"} ! conceptus +relationship: RO:0002491 UBERON:0000068 ! existence starts and ends during embryo stage [Term] id: UBERON:0016888 @@ -11985,8 +11642,8 @@ def: "A mesenchyme-derived anatomical entity undergoing a transtion to become an xref: AEO:0001016 is_a: UBERON:0005423 ! developing anatomical structure intersection_of: UBERON:0005423 ! developing anatomical structure -intersection_of: composed_primarily_of UBERON:0003104 ! mesenchyme -relationship: composed_primarily_of UBERON:0003104 ! mesenchyme +intersection_of: RO:0002473 UBERON:0003104 ! composed primarily of mesenchyme +relationship: RO:0002473 UBERON:0003104 ! composed primarily of mesenchyme [Term] id: UBERON:0018254 @@ -11996,12 +11653,11 @@ subset: grouping_class subset: human_reference_atlas xref: EHDAA2:0001842 xref: EMAPA:35578 -xref: MA:0000165 is_a: UBERON:0000061 ! anatomical structure -relationship: composed_primarily_of UBERON:0014892 ! skeletal muscle organ, vertebrate relationship: part_of UBERON:0000383 {source="MA"} ! musculature of body -relationship: present_in_taxon NCBITaxon:9606 -property_value: editor_note "Added for consistency with MA EMAPA and EHDAA2. See https://github.com/obophenotype/mouse-anatomy-ontology/issues/104" xsd:string +relationship: RO:0002473 UBERON:0014892 ! composed primarily of skeletal muscle organ, vertebrate +property_value: IAO:0000116 "Added for consistency with MA EMAPA and EHDAA2. See https://github.com/obophenotype/mouse-anatomy-ontology/issues/104" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0034769 @@ -12020,10 +11676,10 @@ subset: common_anatomy synonym: "anatomical cluster" RELATED [CARO:0020001] xref: CARO:0020001 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure -relationship: composed_primarily_of UBERON:0000064 ! organ part -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0002473 UBERON:0000064 ! composed primarily of organ part +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0034923 @@ -12032,14 +11688,13 @@ namespace: uberon def: "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other." [CARO:0020000] subset: common_anatomy xref: CARO:0020000 -xref: FBbt:00007276 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000465 {source="CARO"} ! material anatomical entity -relationship: composed_primarily_of UBERON:0000061 ! anatomical structure relationship: has_component UBERON:0000061 {minCardinality="2"} ! anatomical structure -relationship: has_quality PATO:0010001 ! disconnected -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0000086 PATO:0010001 ! has quality disconnected +relationship: RO:0002473 UBERON:0000061 ! composed primarily of anatomical structure +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0034925 @@ -12048,11 +11703,11 @@ namespace: uberon def: "A collection of anatomical structures that are alike in terms of their morphology or developmental origin." [http://orcid.org/0000-0002-6601-2165] subset: common_anatomy is_a: UBERON:0000465 ! material anatomical entity -relationship: has_member UBERON:0000061 ! anatomical structure -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: editor_note "resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected" xsd:string +relationship: RO:0002351 UBERON:0000061 ! has member anatomical structure +property_value: IAO:0000116 "resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0034969 @@ -12088,9 +11743,9 @@ def: "A muscle tissue that is associated with soft internal organs (viscera)." [ comment: It is quite common to refer to visceral muscles as smooth muscles, by analogy with vertebrates; however, most visceral muscles in arthropods are actually striated. {xref="https://en.wikipedia.org/wiki/Smooth_muscle", xref="FBbt:00005070", comment="PMID:8720463"} synonym: "visceral muscle" EXACT [] {comment="BTO:0002780"} is_a: UBERON:0002385 ! muscle tissue -relationship: composed_primarily_of CL:0008007 ! visceral muscle cell -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -property_value: dcterms-date "2023-02-16T10:17:46Z" xsd:dateTime +relationship: RO:0002473 CL:0008007 ! composed primarily of visceral muscle cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-02-16T10:17:46Z" xsd:dateTime [Term] id: UBERON:8600006 @@ -12100,8 +11755,14 @@ def: "A striated muscle tissue that is associated with soft internal organs (vis synonym: "striated visceral muscle tissue" EXACT [] is_a: UBERON:0002036 ! striated muscle tissue is_a: UBERON:8600004 ! visceral muscle tissue -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -property_value: dcterms-date "2023-02-16T10:34:43Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-02-16T10:34:43Z" xsd:dateTime + +[Typedef] +id: BFO:0000067 +name: contains process +def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] +comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant [Typedef] id: CL:4030044 @@ -12122,11 +11783,6 @@ id: RO:0000052 name: characteristic of def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." [] comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. -property_value: IAO:0000111 "inheres in" xsd:string -property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string -property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string -property_value: IAO:0000118 "inheres_in" xsd:string -property_value: RO:0001900 RO:0001901 is_functional: true is_a: RO:0002314 ! characteristic of part of inverse_of: bearer_of ! bearer of @@ -12136,10 +11792,7 @@ id: RO:0000079 name: function of def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. -property_value: editor_note "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string -property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string -property_value: IAO:0000118 "function_of" xsd:string -property_value: IAO:0000118 "is function of" xsd:string +property_value: IAO:0000116 "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string is_a: RO:0000052 ! characteristic of inverse_of: RO:0000085 ! has function @@ -12148,22 +11801,16 @@ id: RO:0000080 name: quality of def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. -property_value: editor_note "A quality inheres in its bearer at all times for which the quality exists." xsd:string -property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string -property_value: IAO:0000118 "is quality of" xsd:string -property_value: IAO:0000118 "quality_of" xsd:string +property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string is_a: RO:0000052 ! characteristic of -inverse_of: has_quality ! has quality +inverse_of: RO:0000086 ! has quality [Typedef] id: RO:0000081 name: role of def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. -property_value: editor_note "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string -property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string -property_value: IAO:0000118 "is role of" xsd:string -property_value: IAO:0000118 "role_of" xsd:string +property_value: IAO:0000116 "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string is_a: RO:0000052 ! characteristic of inverse_of: RO:0000087 ! has role @@ -12171,19 +11818,22 @@ inverse_of: RO:0000087 ! has role id: RO:0000085 name: has function def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] -property_value: editor_note "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string -property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string -property_value: IAO:0000118 "has_function" xsd:string +property_value: IAO:0000116 "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string domain: BFO:0000004 ! independent continuant is_a: bearer_of ! bearer of +[Typedef] +id: RO:0000086 +name: has quality +def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] +property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string +is_a: bearer_of ! bearer of + [Typedef] id: RO:0000087 name: has role def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] -property_value: editor_note "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string -property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string -property_value: IAO:0000118 "has_role" xsd:string +property_value: IAO:0000116 "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string domain: BFO:0000004 ! independent continuant is_a: bearer_of ! bearer of @@ -12208,12 +11858,7 @@ id: RO:0001000 name: derives from def: "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" [] subset: ro-eco -property_value: editor_note "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." xsd:string -property_value: IAO:0000112 "this cell derives from this parent cell (cell division)" xsd:string -property_value: IAO:0000112 "this nucleus derives from this parent nucleus (nuclear division)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000118 "derives_from" xsd:string -property_value: IAO:0000232 "This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations." xsd:string +property_value: IAO:0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." xsd:string inverse_of: RO:0001001 ! derives into [Typedef] @@ -12221,33 +11866,57 @@ id: RO:0001001 name: derives into def: "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" [] subset: ro-eco -property_value: editor_note "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." xsd:string -property_value: IAO:0000112 "this parent cell derives into this cell (cell division)" xsd:string -property_value: IAO:0000112 "this parent nucleus derives into this nucleus (nuclear division)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000118 "derives_into" xsd:string +property_value: IAO:0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." xsd:string + +[Typedef] +id: RO:0001015 +name: location of +def: "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" [] +property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +is_transitive: true +inverse_of: RO:0001025 ! located in + +[Typedef] +id: RO:0001025 +name: located in +def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +property_value: IAO:0000116 "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" xsd:string +property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Located_in" xsd:anyURI +domain: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +range: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +is_transitive: true +transitive_over: part_of ! part of [Typedef] id: RO:0002000 name: 2D boundary of def: "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" [] -property_value: editor_note "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string -property_value: editor_note "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string -property_value: IAO:0000112 "the surface of my skin is a 2D boundary of my body" xsd:string -property_value: IAO:0000118 "2D_boundary_of" xsd:string -property_value: IAO:0000118 "boundary of" xsd:string -property_value: IAO:0000118 "is 2D boundary of" xsd:string -property_value: IAO:0000118 "is boundary of" xsd:string -property_value: IAO:0000118 "surface of" xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string +is_a: RO:0002323 ! mereotopologically related to +inverse_of: RO:0002002 ! has 2D boundary + +[Typedef] +id: RO:0002002 +name: has 2D boundary +def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000141 ! immaterial entity is_a: RO:0002323 ! mereotopologically related to -inverse_of: has_boundary ! has 2D boundary + +[Typedef] +id: RO:0002005 +name: innervated_by +domain: UBERON:0000061 ! anatomical structure +inverse_of: RO:0002134 ! innervates [Typedef] id: RO:0002006 name: has synaptic terminal of -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: overlaps ! overlaps inverse_of: RO:0002130 ! has synaptic terminal in @@ -12329,16 +11998,23 @@ id: RO:0002081 name: before or simultaneous with comment: Primitive instance level timing relation between events subset: ro-eco -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000118 "<=" xsd:string is_a: RO:0002222 ! temporally related to +[Typedef] +id: RO:0002082 +name: simultaneous with +def: "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." [] +comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) +subset: ro-eco +is_symmetric: true +is_transitive: true +is_a: RO:0002081 ! before or simultaneous with + [Typedef] id: RO:0002086 name: ends after comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) subset: ro-eco -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string is_transitive: true is_a: RO:0002222 ! temporally related to @@ -12346,25 +12022,16 @@ is_a: RO:0002222 ! temporally related to id: RO:0002100 name: has soma location def: "Relation between a neuron and a material anatomical entity that its soma is part of." [] -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron range: UBERON:0000465 ! material anatomical entity is_a: overlaps ! overlaps -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] [Typedef] id: RO:0002101 name: fasciculates with def: "relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.\n" [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "fasciculates with" xsd:string -property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: overlaps ! overlaps inverse_of: RO:0002132 ! has fasciculating neuron projection @@ -12373,27 +12040,23 @@ inverse_of: RO:0002132 ! has fasciculating neuron projection id: RO:0002102 name: axon synapses in def: "Relation between a neuron and some structure its axon forms (chemical) synapses in." [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: RO:0002113 ! has presynaptic terminal in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "BFO_0000051 some (\n GO_0030424 and BFO_0000051 some (\n GO_0042734 and BFO_0000050 some (\n GO_0045202 and BFO_0000050 some ?Y)))" [] +[Typedef] +id: RO:0002103 +name: synapsed by +def: "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " [] +is_a: RO:0002485 ! receives input from +inverse_of: RO:0002120 ! synapsed to +expand_expression_to: "BFO_0000051 some (GO_0045211 that part_of some (GO_0045202 that has_part some (GO_0042734 that BFO_0000050 some Y?)))" [] + [Typedef] id: RO:0002104 name: has plasma membrane part def: "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part." [] -property_value: IAO:0000112 "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9990-8331 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 -property_value: RO:0001900 RO:0001901 domain: UBERON:0000465 ! material anatomical entity range: UBERON:0000465 ! material anatomical entity is_a: has_part ! has part @@ -12403,29 +12066,19 @@ expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] id: RO:0002110 name: has postsynaptic terminal in def: "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. " [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "synapsed in" xsd:string -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: RO:0002130 ! has synaptic terminal in inverse_of: RO:0002113 ! has presynaptic terminal in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (\n http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some (\n http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))" [] [Typedef] id: RO:0002113 name: has presynaptic terminal in def: "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input." [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000118 "synapses in" xsd:string -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: RO:0002130 ! has synaptic terminal in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000050 some Y?)" [] [Typedef] @@ -12433,11 +12086,6 @@ id: RO:0002120 name: synapsed to def: " Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.\n " [] comment: N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part some (\n ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( \n ‘synapse ; GO:0045202’ that has_part some (\n ‘post-synaptic membrane ; GO:0045211’ that part_of some N2)))) -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 is_a: RO:0002486 ! sends output to expand_expression_to: "BFO_0000051 some (GO_0042734 that part_of some (GO_0045202 that BFO_0000051 some (GO_0045211 that BFO_0000050 some Y?)))" [] @@ -12445,103 +12093,270 @@ expand_expression_to: "BFO_0000051 some (GO_0042734 that part_of some (GO_004520 id: RO:0002130 name: has synaptic terminal in def: "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "has synapse in" xsd:string -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: overlaps ! overlaps -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "RO_0002131 some (GO_0045202 that BFO_0000050 some Y?)" [] [Typedef] id: RO:0002132 name: has fasciculating neuron projection def: "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "has fasciculating component" xsd:string -property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string -property_value: RO:0001900 RO:0001901 is_a: overlaps ! overlaps +[Typedef] +id: RO:0002134 +name: innervates +def: "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." [] +transitive_over: part_of ! part of +expand_expression_to: "RO_0002132 some (GO_0043005 that (RO_0002131 some (GO_0045202 that BFO_0000050 some Y?)))" [] + +[Typedef] +id: RO:0002150 +name: continuous with +def: "X continuous_with Y if and only if X and Y share a fiat boundary." [] +property_value: seeAlso "FMA:85972" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000004 ! independent continuant +is_symmetric: true +is_a: RO:0002323 ! mereotopologically related to + +[Typedef] +id: RO:0002158 +name: shares ancestor with +def: "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." [] +comment: VBO calls this homologous_to +is_symmetric: true +is_transitive: true +is_a: RO:0002320 ! evolutionarily related to + +[Typedef] +id: RO:0002160 +name: only in taxon +def: "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." [] +property_value: IAO:0000116 "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" xsd:string +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints +is_a: RO:0002162 ! in taxon + +[Typedef] +id: RO:0002162 +name: in taxon +def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." [] +comment: Connects a biological entity to its taxon of origin. +subset: ro-eco +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints +holds_over_chain: capable_of RO:0002162 +holds_over_chain: extends_fibers_into RO:0002162 +holds_over_chain: has_part RO:0002162 +holds_over_chain: part_of RO:0002162 +holds_over_chain: results_in_developmental_progression_of RO:0002162 +holds_over_chain: RO:0002202 RO:0002162 +holds_over_chain: RO:0002206 RO:0002162 +holds_over_chain: RO:0002225 RO:0002162 +holds_over_chain: RO:0002254 RO:0002162 +is_a: RO:0002320 ! evolutionarily related to + [Typedef] id: RO:0002163 name: spatially disjoint from def: "A is spatially_disjoint_from B if and only if they have no parts in common" [] subset: ro-eco -property_value: editor_note "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" xsd:anyURI is_a: RO:0002323 ! mereotopologically related to expand_expression_to: "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" [] +[Typedef] +id: RO:0002170 +name: connected to +def: "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" [] +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI +is_a: RO:0002323 ! mereotopologically related to + +[Typedef] +id: RO:0002176 +name: connects +def: "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." [] +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI +domain: BFO:0000004 ! independent continuant +is_a: RO:0002323 ! mereotopologically related to + +[Typedef] +id: RO:0002177 +name: attached to part of +def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000061 ! anatomical structure +is_a: RO:0002323 ! mereotopologically related to +is_a: RO:0002567 ! biomechanically related to + +[Typedef] +id: RO:0002178 +name: supplies +def: "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." [] +property_value: IAO:0000116 "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" xsd:string +is_a: RO:0002170 ! connected to + +[Typedef] +id: RO:0002179 +name: drains +def: "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." [] +property_value: IAO:0000116 "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" xsd:string +is_a: RO:0002170 ! connected to + +[Typedef] +id: RO:0002202 +name: develops from +def: "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" [] +comment: This is the transitive form of the develops from relation +domain: BFO:0000004 ! independent continuant +range: BFO:0000004 ! independent continuant +is_transitive: true +is_a: RO:0002254 ! has developmental contribution from +is_a: RO:0002258 ! developmentally preceded by +inverse_of: RO:0002203 ! develops into + +[Typedef] +id: RO:0002203 +name: develops into +def: "inverse of develops from" [] +subset: RO:0002259 +is_transitive: true +is_a: RO:0002286 ! developmentally succeeded by +is_a: RO:0002387 ! has potential to develop into +is_a: RO:0002388 ! has potential to directly develop into + [Typedef] id: RO:0002206 name: expressed in def: "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" [] -property_value: IAO:0000112 "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000002 ! continuant range: UBERON:0000465 ! material anatomical entity is_a: RO:0002330 ! genomically related to inverse_of: RO:0002292 ! expresses -transitive_over: part_of ! part_of +transitive_over: part_of ! part of + +[Typedef] +id: RO:0002207 +name: directly develops from +def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] +comment: TODO - add child relations from DOS +synonym: "has developmental precursor" EXACT [] +is_a: RO:0002202 ! develops from +inverse_of: RO:0002210 ! directly develops into [Typedef] id: RO:0002210 name: directly develops into def: "inverse of directly develops from" [] subset: RO:0002259 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000118 "developmental precursor of" xsd:string -is_a: develops_into ! develops into +is_a: RO:0002203 ! develops into + +[Typedef] +id: RO:0002219 +name: surrounded by +def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" [] +is_a: adjacent_to ! adjacent to +inverse_of: RO:0002221 ! surrounds + +[Typedef] +id: RO:0002221 +name: surrounds +def: "inverse of surrounded by" [] +subset: RO:0002259 +is_a: adjacent_to ! adjacent to [Typedef] id: RO:0002222 name: temporally related to comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. subset: ro-eco -property_value: http://purl.org/dc/terms/source "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" xsd:anyURI -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent +[Typedef] +id: RO:0002223 +name: starts +def: "inverse of starts with" [] +subset: ro-eco +is_a: part_of ! part of +is_a: RO:0002222 ! temporally related to +inverse_of: starts_with ! starts with + +[Typedef] +id: RO:0002225 +name: develops from part of +def: "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" [] +holds_over_chain: RO:0002207 part_of +is_a: RO:0002202 ! develops from + +[Typedef] +id: RO:0002226 +name: develops in +def: "x develops_in y if x is located in y whilst x is developing" [] +domain: UBERON:0001062 ! anatomical entity +holds_over_chain: RO:0002207 RO:0001025 +is_a: RO:0002258 ! developmentally preceded by + +[Typedef] +id: RO:0002229 +name: ends +def: "inverse of ends with" [] +subset: ro-eco +is_a: part_of ! part of +is_a: RO:0002222 ! temporally related to +inverse_of: ends_with ! ends with + +[Typedef] +id: RO:0002252 +name: connecting branch of +def: "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." [] +property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 +is_a: RO:0002170 ! connected to +is_a: RO:0002375 ! in branching relationship with +inverse_of: RO:0002253 ! has connecting branch + [Typedef] id: RO:0002253 name: has connecting branch def: "inverse of connecting branch of" [] subset: RO:0002259 -property_value: RO:0004036 BFO:0000051 is_a: RO:0002375 ! in branching relationship with +[Typedef] +id: RO:0002254 +name: has developmental contribution from +def: "x has developmental contribution from y iff x has some part z such that z develops from y" [] +domain: UBERON:0001062 ! anatomical entity +range: UBERON:0001062 ! anatomical entity +holds_over_chain: has_part RO:0002202 +is_a: RO:0002258 ! developmentally preceded by +inverse_of: RO:0002255 ! developmentally contributes to + [Typedef] id: RO:0002255 name: developmentally contributes to def: "inverse of has developmental contribution from" [] subset: RO:0002259 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -holds_over_chain: develops_into part_of -is_a: has_potential_to_developmentally_contribute_to ! has potential to developmentally contribute to +holds_over_chain: RO:0002203 part_of is_a: RO:0002286 ! developmentally succeeded by +is_a: RO:0002385 ! has potential to developmentally contribute to + +[Typedef] +id: RO:0002256 +name: developmentally induced by +def: "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" [] +domain: UBERON:0000465 ! material anatomical entity +range: UBERON:0000465 ! material anatomical entity +is_a: RO:0002258 ! developmentally preceded by +inverse_of: RO:0002257 ! developmentally induces [Typedef] id: RO:0002257 name: developmentally induces def: "Inverse of developmentally induced by" [] -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002286 ! developmentally succeeded by is_a: RO:0002386 ! has potential to developmentally induce @@ -12550,10 +12365,7 @@ id: RO:0002258 name: developmentally preceded by def: "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p" [] comment: This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from -property_value: editor_note "false" xsd:boolean -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string +property_value: IAO:0000116 "false" xsd:boolean domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant is_a: RO:0002324 ! developmentally related to @@ -12564,7 +12376,6 @@ id: RO:0002263 name: acts upstream of def: "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: IAO:0000112 "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." xsd:string property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of holds_over_chain: RO:0002327 causally_upstream_of is_a: RO:0002264 ! acts upstream of or within @@ -12575,25 +12386,26 @@ name: acts upstream of or within def: "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term synonym: "affects" RELATED [] -property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within" xsd:anyURI holds_over_chain: RO:0002327 causally_upstream_of_or_within is_a: RO:0002500 ! causal agent in process +[Typedef] +id: RO:0002285 +name: developmentally replaces +def: "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" [] +property_value: IAO:0000116 "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" xsd:string +is_a: RO:0002258 ! developmentally preceded by + [Typedef] id: RO:0002286 name: developmentally succeeded by def: "Inverse of developmentally preceded by" [] -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002384 ! has developmental potential involving [Typedef] id: RO:0002287 name: part of developmental precursor of -property_value: IAO:0000112 "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: part_of RO:0002210 is_a: RO:0002286 ! developmentally succeeded by @@ -12601,80 +12413,58 @@ is_a: RO:0002286 ! developmentally succeeded by id: RO:0002292 name: expresses def: "y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." [] -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002330 ! genomically related to [Typedef] id: RO:0002314 name: characteristic of part of def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." [] -property_value: editor_note "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "inheres in part of" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: RO:0000052 part_of {RO:0002582="true"} is_a: RO:0002502 ! depends on -transitive_over: part_of ! part_of +transitive_over: part_of ! part of [Typedef] id: RO:0002320 name: evolutionarily related to def: "A relationship that holds via some environmental process" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." xsd:string [Typedef] id: RO:0002323 name: mereotopologically related to def: "A mereological relationship or a topological relationship" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string -property_value: RO:0001900 RO:0001901 [Typedef] id: RO:0002324 name: developmentally related to def: "A relationship that holds between entities participating in some developmental process (GO:0032502)" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" xsd:string [Typedef] id: RO:0002327 name: enables def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "catalyzes" xsd:string -property_value: IAO:0000118 "executes" xsd:string -property_value: IAO:0000118 "has" xsd:string -property_value: IAO:0000118 "is catalyzing" xsd:string -property_value: IAO:0000118 "is executing" xsd:string -property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string property_value: seeAlso "https://wiki.geneontology.org/Enables" xsd:anyURI is_a: capable_of ! capable of inverse_of: RO:0002333 ! enabled by transitive_over: has_part ! has part transitive_over: RO:0002017 ! has component activity +[Typedef] +id: RO:0002328 +name: functionally related to +def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] + [Typedef] id: RO:0002329 name: part of structure that is capable of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "false" xsd:boolean -holds_over_chain: part_of capable_of {RO:0002581="true"} -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002330 name: genomically related to def: "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant @@ -12682,31 +12472,25 @@ range: BFO:0000002 ! continuant id: RO:0002331 name: involved in def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "actively involved in" xsd:string -property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Involved_in" xsd:anyURI holds_over_chain: RO:0002327 part_of is_a: participates_in ! participates in is_a: RO:0002431 ! involved in or involved in regulation of -transitive_over: part_of ! part_of +transitive_over: part_of ! part of [Typedef] id: RO:0002333 name: enabled by def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso "https://wiki.geneontology.org/Enabled_by" xsd:anyURI -is_a: functionally_related_to ! functionally related to is_a: has_participant ! has participant +is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002337 name: related via localization to def: "A relationship that holds via some process of localization" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is a grouping relation." xsd:string domain: BFO:0000015 ! process range: BFO:0000002 ! continuant @@ -12714,84 +12498,134 @@ range: BFO:0000002 ! continuant id: RO:0002350 name: member of def: "is member of is a mereological relation between a item and a collection." [] -property_value: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string -property_value: IAO:0000118 "is member of" xsd:string -property_value: IAO:0000118 "member part of" xsd:string -property_value: IAO:0000119 "SIO" xsd:string -property_value: RO:0001900 RO:0001901 -is_a: part_of ! part_of -inverse_of: has_member ! has member +is_a: part_of ! part of +inverse_of: RO:0002351 ! has member + +[Typedef] +id: RO:0002351 +name: has member +def: "has member is a mereological relation between a collection and an item." [] +is_a: has_part ! has part + +[Typedef] +id: RO:0002352 +name: input of +def: "inverse of has input" [] +subset: ro-eco +subset: RO:0002259 +is_a: participates_in ! participates in +is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002354 name: formed as result of -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: output_of ! output of [Typedef] id: RO:0002360 name: has dendrite location -property_value: http://purl.org/dc/terms/source "http://neurolex.org/wiki/Property:DendriteLocation" xsd:anyURI -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps [Typedef] -id: RO:0002375 -name: in branching relationship with -def: "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" xsd:string -property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string -property_value: RO:0004036 BFO:0000050 -property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png -property_value: seeAlso "https://github.com/obophenotype/uberon/issues/170" xsd:anyURI -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: RO:0002323 ! mereotopologically related to +id: RO:0002371 +name: attached to +def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] +subset: ro-eco +is_symmetric: true +is_a: RO:0002170 ! connected to +is_a: RO:0002177 ! attached to part of [Typedef] -id: RO:0002379 -name: spatially coextensive with -def: "x spatially_coextensive_with y if and inly if x and y have the same location" [] -property_value: IAO:0000112 "A lump of clay and a statue" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" xsd:string +id: RO:0002372 +name: has muscle origin +def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] +property_value: seeAlso http://dbpedia.org/property/origin +domain: UBERON:0000061 {comment="We need to import uberon muscle to create a stricter domain constraint"} ! anatomical structure +is_a: RO:0002371 ! attached to +is_a: RO:0002567 ! biomechanically related to + +[Typedef] +id: RO:0002373 +name: has muscle insertion +def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] +property_value: seeAlso http://dbpedia.org/property/insertion +domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} ! anatomical structure +is_a: RO:0002371 ! attached to +is_a: RO:0002567 ! biomechanically related to + +[Typedef] +id: RO:0002375 +name: in branching relationship with +def: "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." [] +property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png +property_value: seeAlso "https://github.com/obophenotype/uberon/issues/170" xsd:anyURI +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002323 ! mereotopologically related to + +[Typedef] +id: RO:0002376 +name: tributary of +def: "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." [] +subset: ro-eco +property_value: seeAlso http://dbpedia.org/ontology/drainsTo +property_value: seeAlso "http://en.wikipedia.org/wiki/Tributary" xsd:anyURI +is_a: RO:0002170 ! connected to +is_a: RO:0002375 ! in branching relationship with + +[Typedef] +id: RO:0002379 +name: spatially coextensive with +def: "x spatially_coextensive_with y if and inly if x and y have the same location" [] is_a: overlaps ! overlaps +[Typedef] +id: RO:0002380 +name: branching part of +def: "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" [] +subset: ro-eco +property_value: seeAlso "FMA:85994" xsd:string +property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 +is_a: part_of ! part of +is_a: RO:0002375 ! in branching relationship with +inverse_of: RO:0002569 ! has branching part + [Typedef] id: RO:0002384 name: has developmental potential involving def: "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: UBERON:0001062 ! anatomical entity range: UBERON:0001062 ! anatomical entity is_a: RO:0002324 ! developmentally related to +[Typedef] +id: RO:0002385 +name: has potential to developmentally contribute to +def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] +is_a: RO:0002384 ! has developmental potential involving + [Typedef] id: RO:0002386 name: has potential to developmentally induce def: "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002384 ! has developmental potential involving + +[Typedef] +id: RO:0002387 +name: has potential to develop into +def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] is_a: RO:0002384 ! has developmental potential involving [Typedef] id: RO:0002388 name: has potential to directly develop into def: "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: has_potential_to_develop_into ! has potential to develop into +is_a: RO:0002387 ! has potential to develop into [Typedef] id: RO:0002407 name: indirectly positively regulates def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "indirectly activates" xsd:string -property_value: RO:0002579 RO:0002213 property_value: seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates" xsd:anyURI holds_over_chain: directly_positively_regulates directly_positively_regulates holds_over_chain: directly_positively_regulates RO:0002407 @@ -12805,9 +12639,6 @@ transitive_over: directly_positively_regulates ! directly positively regulates id: RO:0002409 name: indirectly negatively regulates def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "indirectly inhibits" xsd:string -property_value: RO:0002579 RO:0002212 property_value: seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates" xsd:anyURI holds_over_chain: directly_negatively_regulates directly_negatively_regulates holds_over_chain: directly_negatively_regulates RO:0002409 @@ -12820,15 +12651,12 @@ transitive_over: directly_negatively_regulates ! directly negatively regulates id: RO:0002410 name: causally related to def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] -property_value: editor_note "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string [Typedef] id: RO:0002428 name: involved in regulation of def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002327 regulates holds_over_chain: RO:0002331 regulates is_a: RO:0002263 ! acts upstream of @@ -12838,8 +12666,6 @@ is_a: RO:0002431 ! involved in or involved in regulation of id: RO:0002429 name: involved in positive regulation of def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0004049 RO:0002428 holds_over_chain: RO:0002327 positively_regulates holds_over_chain: RO:0002331 positively_regulates is_a: RO:0002428 ! involved in regulation of @@ -12848,7 +12674,6 @@ is_a: RO:0002428 ! involved in regulation of id: RO:0002430 name: involved in negative regulation of def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002428 holds_over_chain: RO:0002327 negatively_regulates holds_over_chain: RO:0002331 negatively_regulates @@ -12858,11 +12683,9 @@ is_a: RO:0002428 ! involved in regulation of id: RO:0002431 name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] -property_value: editor_note "OWL does not allow defining object properties via a Union" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "involved in or reguates" xsd:string -is_a: functionally_related_to ! functionally related to +property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string is_a: RO:0002264 ! acts upstream of or within +is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process [Typedef] @@ -12870,12 +12693,14 @@ id: RO:0002432 name: is active in def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [https://orcid.org/0000-0002-6601-2165, https://orcid.org/0000-0002-7073-9172] synonym: "enables activity in" EXACT [] -property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "executes activity in" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Is_active_in" xsd:anyURI -holds_over_chain: RO:0002327 occurs_in {RO:0002581="true"} -is_a: functionally_related_to ! functionally related to +is_a: overlaps ! overlaps +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002433 +name: contributes to morphology of +def: "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." [] is_a: overlaps ! overlaps [Typedef] @@ -12884,11 +12709,8 @@ name: interacts with def: "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." [] subset: ro-eco synonym: "in pairwise interaction with" EXACT [] -property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0914" xsd:anyURI -property_value: editor_note "Considering relabeling as 'pairwise interacts with'" xsd:anyURI -property_value: editor_note "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string +property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI +property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity @@ -12898,10 +12720,6 @@ is_symmetric: true id: RO:0002436 name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] -property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0915" xsd:anyURI -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "binds" xsd:string -property_value: IAO:0000118 "molecularly binds with" xsd:string property_value: seeAlso ECO:0000353 is_symmetric: true is_a: RO:0002434 ! interacts with @@ -12909,9 +12727,7 @@ is_a: RO:0002434 ! interacts with [Typedef] id: RO:0002447 name: phosphorylates -property_value: editor_note "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string +property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string is_a: RO:0002436 ! molecularly interacts with [Typedef] @@ -12919,8 +12735,6 @@ id: RO:0002448 name: directly regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." [] synonym: "molecularly controls" EXACT [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002436 ! molecularly interacts with @@ -12931,9 +12745,6 @@ id: RO:0002449 name: directly negatively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] synonym: "molecularly decreases activity of" EXACT [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 -property_value: IAO:0000118 "directly inhibits" xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002448 ! directly regulates activity of @@ -12943,9 +12754,6 @@ id: RO:0002450 name: directly positively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] synonym: "molecularly increases activity of" EXACT [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 -property_value: IAO:0000118 "directly activates" xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002448 ! directly regulates activity of @@ -12953,61 +12761,136 @@ is_a: RO:0002448 ! directly regulates activity of [Typedef] id: RO:0002464 name: helper property (not for use in curation) -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string + +[Typedef] +id: RO:0002473 +name: composed primarily of +def: "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." [] +subset: ro-eco +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: has_part ! has part [Typedef] id: RO:0002479 name: has part that occurs in def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] subset: ro-eco -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant -holds_over_chain: has_part occurs_in {RO:0002581="true"} [Typedef] id: RO:0002481 name: is kinase activity -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002564 ! molecular interaction relation helper property [Typedef] id: RO:0002485 name: receives input from -property_value: editor_note "See notes for inverse relation" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: connected_to ! connected to +property_value: IAO:0000116 "See notes for inverse relation" xsd:string +is_a: RO:0002170 ! connected to inverse_of: RO:0002486 ! sends output to [Typedef] id: RO:0002486 name: sends output to -property_value: editor_note "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: connected_to ! connected to +property_value: IAO:0000116 "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." xsd:string +is_a: RO:0002170 ! connected to [Typedef] id: RO:0002487 name: relation between physical entity and a process or stage -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage." xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000003 ! occurrent +[Typedef] +id: RO:0002488 +name: existence starts during +def: "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." [] +is_a: RO:0002490 ! existence overlaps +is_a: RO:0002496 ! existence starts during or after +transitive_over: part_of ! part of + +[Typedef] +id: RO:0002489 +name: existence starts with +def: "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." [] +is_a: RO:0002488 ! existence starts during + [Typedef] id: RO:0002490 name: existence overlaps def: "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" [] comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002487 ! relation between physical entity and a process or stage +[Typedef] +id: RO:0002491 +name: existence starts and ends during +def: "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +synonym: "exists during" EXACT [] +is_a: RO:0002488 ! existence starts during +is_a: RO:0002492 ! existence ends during + +[Typedef] +id: RO:0002492 +name: existence ends during +def: "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +is_a: RO:0002490 ! existence overlaps +is_a: RO:0002497 ! existence ends during or before +transitive_over: part_of ! part of + +[Typedef] +id: RO:0002493 +name: existence ends with +def: "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +is_a: RO:0002492 ! existence ends during + +[Typedef] +id: RO:0002494 +name: transformation of +def: "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" [] +is_transitive: true +is_a: RO:0002202 ! develops from + +[Typedef] +id: RO:0002495 +name: immediate transformation of +def: "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" [] +is_a: RO:0002207 ! directly develops from +is_a: RO:0002494 ! transformation of + +[Typedef] +id: RO:0002496 +name: existence starts during or after +def: "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +holds_over_chain: part_of RO:0002496 +holds_over_chain: RO:0002258 RO:0002496 +is_a: RO:0002487 ! relation between physical entity and a process or stage +transitive_over: part_of ! part of +transitive_over: preceded_by ! preceded by +transitive_over: RO:0002082 ! simultaneous with + +[Typedef] +id: RO:0002497 +name: existence ends during or before +def: "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +holds_over_chain: part_of RO:0002497 +holds_over_chain: RO:0002286 RO:0002497 +is_a: RO:0002487 ! relation between physical entity and a process or stage +transitive_over: part_of ! part of +transitive_over: precedes ! precedes +transitive_over: RO:0002082 ! simultaneous with + [Typedef] id: RO:0002500 name: causal agent in process def: "A relationship between a material entity and a process where the material entity has some causal role that influences the process" [] -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_a: RO:0002595 ! causal relation between material entity and a process inverse_of: process_has_causal_agent ! process has causal agent @@ -13015,9 +12898,6 @@ inverse_of: process_has_causal_agent ! process has causal agent id: RO:0002501 name: causal relation between processes def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent is_a: RO:0002410 ! causally related to @@ -13025,33 +12905,35 @@ is_a: RO:0002410 ! causally related to [Typedef] id: RO:0002502 name: depends on -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso BFO:0000169 [Typedef] id: RO:0002506 name: causal relation between entities -property_value: editor_note "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: IAO:0000116 "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant is_a: RO:0002410 ! causally related to +[Typedef] +id: RO:0002551 +name: has skeleton +def: "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." [] +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000465 {IAO:0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} ! material anatomical entity +is_a: has_part ! has part +inverse_of: RO:0002576 ! skeleton of +is_asymmetric: true + [Typedef] id: RO:0002559 name: causally influenced by -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string is_a: RO:0002506 ! causal relation between entities inverse_of: RO:0002566 ! causally influences [Typedef] id: RO:0002563 name: interaction relation helper property -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29 property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI is_a: RO:0002464 ! helper property (not for use in curation) @@ -13059,17 +12941,12 @@ is_a: RO:0002464 ! helper property (not for use in curation) [Typedef] id: RO:0002564 name: molecular interaction relation helper property -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002563 ! interaction relation helper property [Typedef] id: RO:0002566 name: causally influences def: "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant is_a: RO:0002506 ! causal relation between entities @@ -13078,20 +12955,66 @@ is_a: RO:0002506 ! causal relation between entities id: RO:0002567 name: biomechanically related to def: "A relation that holds between elements of a musculoskeletal system or its analogs." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string domain: UBERON:0000061 ! anatomical structure range: UBERON:0000061 ! anatomical structure -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002568 +name: has muscle antagonist +def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] +is_a: RO:0002567 ! biomechanically related to + +[Typedef] +id: RO:0002569 +name: has branching part +def: "inverse of branching part of" [] +subset: ro-eco +subset: RO:0002259 +is_transitive: true +is_a: has_part ! has part +is_a: RO:0002375 ! in branching relationship with + +[Typedef] +id: RO:0002570 +name: conduit for +def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] +subset: ro-eco +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: overlaps ! overlaps + +[Typedef] +id: RO:0002571 +name: lumen of +def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] +subset: ro-eco +range: BFO:0000040 ! material entity +is_a: part_of ! part of + +[Typedef] +id: RO:0002572 +name: luminal space of +def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" [] +subset: ro-eco +domain: BFO:0000141 ! immaterial entity +is_a: RO:0002571 ! lumen of + +[Typedef] +id: RO:0002576 +name: skeleton of +def: "inverse of has skeleton" [] +subset: RO:0002259 +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000061 ! anatomical structure +is_a: part_of ! part of [Typedef] id: RO:0002584 name: has part structure that is capable of def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" [] -property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: has_part capable_of -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to is_a: RO:0002595 ! causal relation between material entity and a process [Typedef] @@ -13104,9 +13027,7 @@ is_a: has_input ! has input id: RO:0002595 name: causal relation between material entity and a process def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." [] -property_value: editor_note "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000040 ! material entity range: BFO:0000015 ! process is_a: RO:0002410 ! causally related to @@ -13115,8 +13036,6 @@ is_a: RO:0002410 ! causally related to id: RO:0002596 name: capable of regulating def: "Holds between c and p if and only if c is capable of some activity a, and a regulates p." [] -property_value: IAO:0000112 "pyrethroid -> growth" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations holds_over_chain: capable_of regulates is_a: RO:0002500 ! causal agent in process @@ -13124,7 +13043,6 @@ is_a: RO:0002500 ! causal agent in process id: RO:0002597 name: capable of negatively regulating def: "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." [] -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations holds_over_chain: capable_of negatively_regulates is_a: RO:0002596 ! capable of regulating @@ -13132,8 +13050,6 @@ is_a: RO:0002596 ! capable of regulating id: RO:0002598 name: capable of positively regulating def: "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." [] -property_value: IAO:0000112 "renin -> arteriolar smooth muscle contraction" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations holds_over_chain: capable_of positively_regulates is_a: RO:0002596 ! capable of regulating @@ -13142,7 +13058,7 @@ id: RO:0004031 name: enables subfunction def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] holds_over_chain: RO:0002327 has_part -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z @@ -13150,7 +13066,6 @@ creation_date: 2018-01-25T23:20:13Z id: RO:0004032 name: acts upstream of or within, positive effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: RO:0004049 RO:0002264 property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0004047 is_a: RO:0002264 ! acts upstream of or within @@ -13173,7 +13088,6 @@ id: RO:0004034 name: acts upstream of, positive effect def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: RO:0004049 RO:0002263 property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 causally_upstream_of,_positive_effect is_a: RO:0002263 ! acts upstream of @@ -13206,7 +13120,6 @@ creation_date: 2018-03-13T23:55:05Z [Typedef] id: RO:0004047 name: causally upstream of or within, positive effect -property_value: RO:0004049 RO:0002418 property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect is_a: causally_upstream_of_or_within ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 @@ -13216,7 +13129,6 @@ creation_date: 2018-03-13T23:55:19Z id: RO:0011002 name: regulates activity of def: "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." [] -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002566 ! causally influences @@ -13271,7 +13183,7 @@ name: has synaptic IO in region def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region." [] synonym: "has synaptic input or output in" EXACT [] is_a: RO:0002130 ! has synaptic terminal in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:26:52Z @@ -13284,7 +13196,7 @@ synonym: "has sensory terminal in" EXACT [] synonym: "has sensory terminal location" EXACT [] domain: CL:0000101 ! sensory neuron is_a: RO:0002360 ! has dendrite location -transitive_over: part_of ! part_of +transitive_over: part_of ! part of created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-20T12:10:09Z @@ -13327,9 +13239,8 @@ comment: Example: a spherical object has the quality of being spherical, and the id: RO:0015015 name: has high plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: dc-contributor https://orcid.org/0000-0003-1617-8244 -property_value: dc-contributor https://orcid.org/0000-0003-1940-6740 -property_value: IAO:0000112 "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part @@ -13337,9 +13248,8 @@ is_a: RO:0002104 ! has plasma membrane part id: RO:0015016 name: has low plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: dc-contributor https://orcid.org/0000-0003-1617-8244 -property_value: dc-contributor https://orcid.org/0000-0003-1940-6740 -property_value: IAO:0000112 "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part @@ -13348,11 +13258,6 @@ id: RO:0017001 name: device utilizes material def: "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." [] synonym: "utilizes" BROAD [] -property_value: IAO:0000112 "A diagnostic testing device utilizes a specimen." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 -property_value: IAO:0000117 https://orcid.org/0000-0003-2620-0345 -property_value: IAO:0000232 "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." xsd:string -property_value: IAO:0000232 "See github ticket https://github.com/oborel/obo-relations/issues/497" xsd:string holds_over_chain: capable_of has_input creation_date: 2021-11-08T12:00:00Z @@ -13373,65 +13278,24 @@ creation_date: 2020-06-08T17:21:33Z id: adjacent_to name: adjacent to namespace: external -namespace: uberon def: "x adjacent to y if and only if x and y share a boundary." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002220 -property_value: editor_note "This relation acts as a join point with BSPO" xsd:string -property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} -property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string -property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string -property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000004 ! independent continuant is_a: RO:0002163 ! spatially disjoint from -[Typedef] -id: anterior_to -name: anterior to -namespace: uberon -xref: BSPO:0000096 - [Typedef] id: anteriorly_connected_to name: anteriorly connected to namespace: uberon def: "x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] -is_a: connected_to ! connected to -is_a: posterior_to ! posterior to +is_a: RO:0002170 ! connected to is_a: transitively_anteriorly_connected_to ! transitively anteriorly connected to -[Typedef] -id: attaches_to -name: attached to -namespace: uberon -def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] -subset: ro-eco -xref: RO:0002371 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000589 "attached to (anatomical structure to anatomical structure)" xsd:string -is_symmetric: true -is_a: attaches_to_part_of ! attached to part of -is_a: connected_to ! connected to - -[Typedef] -id: attaches_to_part_of -name: attached to part of -namespace: uberon -def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] -xref: RO:0002177 -property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string -domain: UBERON:0000061 ! anatomical structure -range: UBERON:0000061 ! anatomical structure -holds_over_chain: attaches_to part_of {RO:0002582="true"} -is_a: RO:0002323 ! mereotopologically related to -is_a: RO:0002567 ! biomechanically related to - [Typedef] id: bearer_of name: bearer of @@ -13439,13 +13303,7 @@ name: has characteristic namespace: external def: "Inverse of characteristic_of" [] xref: RO:0000053 -property_value: editor_note "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string -property_value: IAO:0000111 "bearer of" xsd:string -property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string -property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string -property_value: IAO:0000118 "bearer_of" xsd:string -property_value: IAO:0000118 "is bearer of" xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string range: BFO:0000020 ! specifically dependent continuant is_inverse_functional: true @@ -13453,45 +13311,20 @@ is_inverse_functional: true id: bounding_layer_of name: bounding layer of namespace: external -namespace: uberon def: "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000" [] comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. subset: ro-eco xref: RO:0002007 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 range: BFO:0000040 ! material entity -is_a: part_of ! part_of - -[Typedef] -id: branching_part_of -name: branching part of -namespace: uberon -def: "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" [] -subset: ro-eco -xref: RO:0002380 -property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso "FMA:85994" xsd:string -property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 -is_a: part_of ! part_of -is_a: RO:0002375 ! in branching relationship with -inverse_of: has_branching_part ! has branching part +is_a: part_of ! part of [Typedef] id: capable_of name: capable of namespace: external -namespace: uberon def: "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " [] subset: ro-eco xref: RO:0002215 -property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string -property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "has function realized in" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 -property_value: IAO:0000232 "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000015 ! process is_a: capable_of_part_of ! capable of part of @@ -13500,14 +13333,10 @@ is_a: capable_of_part_of ! capable of part of id: capable_of_part_of name: capable of part of namespace: external -namespace: uberon def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] xref: RO:0002216 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "has function in" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: capable_of part_of {RO:0002582="true"} -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process [Typedef] @@ -13516,8 +13345,6 @@ name: causally downstream of namespace: external def: "inverse of upstream of" [] xref: RO:0002404 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of_or_within ! causally downstream of or within is_a: preceded_by ! preceded by inverse_of: causally_upstream_of ! causally upstream of @@ -13529,8 +13356,6 @@ namespace: external def: "inverse of causally upstream of or within" [] subset: RO:0002259 xref: RO:0002427 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_transitive: true is_a: RO:0002501 ! causal relation between processes @@ -13542,7 +13367,6 @@ def: "p is causally upstream of q iff p is causally related to q, the end of p p subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002411 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within is_a: precedes ! precedes @@ -13555,7 +13379,6 @@ def: "p is causally upstream of, negative effect q iff p is casually upstream of subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 -property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_negative_effect is_a: causally_upstream_of ! causally upstream of @@ -13570,8 +13393,6 @@ comment: holds between x and y if and only if x is causally upstream of y and th subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002304 -property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 -property_value: RO:0004049 RO:0002411 property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_positive_effect is_a: causally_upstream_of ! causally upstream of is_a: RO:0004047 ! causally upstream of or within, positive effect @@ -13583,9 +13404,7 @@ namespace: external def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] synonym: "affects" RELATED [] xref: RO:0002418 -property_value: editor_note "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "influences (processual)" xsd:string +property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string is_transitive: true is_a: RO:0002501 ! causal relation between processes inverse_of: causally_downstream_of_or_within ! causally downstream of or within @@ -13595,510 +13414,81 @@ id: channel_for name: channel for namespace: uberon synonym: "carries" BROAD [] -domain: UBERON:0004111 ! anatomical conduit -range: UBERON:0000463 ! organism substance [Typedef] id: channels_from name: channels_from namespace: uberon -is_transitive: true [Typedef] id: channels_into name: channels_into namespace: uberon -is_transitive: true [Typedef] -id: composed_primarily_of -name: composed primarily of -namespace: uberon -def: "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." [] -subset: ro-eco -xref: RO:0002473 -property_value: IAO:0000112 "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: RO:0001900 RO:0001901 -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: has_part ! has part +id: directly_negatively_regulates +name: directly negatively regulates +namespace: external +def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0002630 +property_value: RO:0004050 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates" xsd:anyURI +is_a: directly_regulates ! directly regulates +is_a: negatively_regulates ! negatively regulates [Typedef] -id: conduit_for -name: conduit for -namespace: uberon -def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] -subset: ro-eco -xref: RO:0002570 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "UBERON:cjm" xsd:string -property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: overlaps ! overlaps +id: directly_positively_regulates +name: directly positively regulates +namespace: external +def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0002629 +property_value: seeAlso "https://wiki.geneontology.org/Directly_positively_regulates" xsd:anyURI +is_a: directly_regulates ! directly regulates +is_a: positively_regulates ! positively regulates [Typedef] -id: connected_to -name: connected to -namespace: uberon -def: "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" [] -xref: RO:0002170 -property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI -property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI -is_a: RO:0002323 ! mereotopologically related to +id: directly_regulates +name: directly regulates +namespace: external +def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0002578 +is_a: immediately_causally_upstream_of ! immediately causally upstream of +is_a: regulates ! regulates [Typedef] -id: connecting_branch_of -name: connecting branch of -namespace: uberon -def: "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." [] -xref: RO:0002252 -property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." xsd:string -property_value: RO:0004036 BFO:0000050 -property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 -is_a: connected_to ! connected to -is_a: RO:0002375 ! in branching relationship with -inverse_of: RO:0002253 ! has connecting branch - -[Typedef] -id: connects -name: connects -namespace: uberon -def: "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." [] -xref: RO:0002176 -property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string -property_value: IAO:0000112 "The M8 connects Glasgow and Edinburgh" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI -property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI -domain: BFO:0000004 ! independent continuant -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: contains_process -name: contains process -namespace: uberon -def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] -comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant -xref: BFO:0000067 -property_value: IAO:0000111 "site of" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - -[Typedef] -id: continuous_with -name: continuous with -namespace: uberon -def: "X continuous_with Y if and only if X and Y share a fiat boundary." [] -xref: RO:0002150 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "connected to" xsd:string -property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string -property_value: RO:0001900 RO:0001901 -property_value: seeAlso "FMA:85972" xsd:string -domain: BFO:0000004 ! independent continuant -range: BFO:0000004 ! independent continuant -is_symmetric: true -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: contributes_to_morphology_of -name: contributes to morphology of -namespace: uberon -def: "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." [] -xref: RO:0002433 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: overlaps ! overlaps - -[Typedef] -id: dc-contributor -name: contributor -namespace: uberon -xref: http://purl.org/dc/terms/contributor -is_metadata_tag: true - -[Typedef] -id: dc-creator -name: creator -namespace: uberon -xref: http://purl.org/dc/elements/1.1/creator -is_metadata_tag: true - -[Typedef] -id: dc-description -name: description -namespace: uberon -xref: http://purl.org/dc/elements/1.1/description -is_metadata_tag: true - -[Typedef] -id: dc-title -name: title -namespace: uberon -xref: http://purl.org/dc/elements/1.1/title -is_metadata_tag: true - -[Typedef] -id: dcterms-date -name: date -namespace: uberon -xref: http://purl.org/dc/terms/date -is_metadata_tag: true - -[Typedef] -id: dcterms-license -name: license -namespace: uberon -xref: http://purl.org/dc/terms/license -is_metadata_tag: true - -[Typedef] -id: deep_to -name: deep to -namespace: uberon -xref: BSPO:0000107 - -[Typedef] -id: depiction -name: depiction -namespace: uberon -xref: http://xmlns.com/foaf/0.1/depiction -is_metadata_tag: true - -[Typedef] -id: developmentally_induced_by -name: developmentally induced by -namespace: uberon -def: "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" [] -xref: RO:0002256 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "induced by" xsd:string -property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string -property_value: IAO:0000119 "GO:0001759" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 -property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string -domain: UBERON:0000465 ! material anatomical entity -range: UBERON:0000465 ! material anatomical entity -is_a: RO:0002258 ! developmentally preceded by -inverse_of: RO:0002257 ! developmentally induces - -[Typedef] -id: developmentally_replaces -name: developmentally replaces -namespace: uberon -def: "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" [] -xref: RO:0002285 -property_value: editor_note "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "replaces" xsd:string -is_a: RO:0002258 ! developmentally preceded by - -[Typedef] -id: develops_from -name: develops from -namespace: uberon -def: "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" [] -comment: This is the transitive form of the develops from relation -xref: RO:0002202 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 -domain: BFO:0000004 ! independent continuant -range: BFO:0000004 ! independent continuant -is_transitive: true -is_a: has_developmental_contribution_from ! has developmental contribution from -is_a: RO:0002258 ! developmentally preceded by -inverse_of: develops_into ! develops into - -[Typedef] -id: develops_from_part_of -name: develops from part of -namespace: uberon -def: "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" [] -xref: RO:0002225 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -holds_over_chain: directly_develops_from part_of -is_a: develops_from ! develops from - -[Typedef] -id: develops_in -name: develops in -namespace: uberon -def: "x develops_in y if x is located in y whilst x is developing" [] -xref: RO:0002226 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "EHDAA2" xsd:string -property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string -domain: UBERON:0001062 ! anatomical entity -holds_over_chain: directly_develops_from located_in -is_a: RO:0002258 ! developmentally preceded by - -[Typedef] -id: develops_into -name: develops into -namespace: uberon -def: "inverse of develops from" [] -subset: RO:0002259 -xref: RO:0002203 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 -is_transitive: true -is_a: has_potential_to_develop_into ! has potential to develop into -is_a: RO:0002286 ! developmentally succeeded by -is_a: RO:0002388 ! has potential to directly develop into - -[Typedef] -id: directly_develops_from -name: directly develops from -namespace: uberon -def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] -comment: TODO - add child relations from DOS -synonym: "has developmental precursor" EXACT [] -xref: RO:0002207 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000119 "FBbt" xsd:string -property_value: RO:0002575 RO:0002202 -is_a: develops_from ! develops from -inverse_of: RO:0002210 ! directly develops into - -[Typedef] -id: directly_negatively_regulates -name: directly negatively regulates -namespace: external -def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -xref: RO:0002630 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string -property_value: RO:0004050 RO:0002578 -property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates" xsd:anyURI -is_a: directly_regulates ! directly regulates -is_a: negatively_regulates ! negatively regulates - -[Typedef] -id: directly_positively_regulates -name: directly positively regulates -namespace: external -def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -xref: RO:0002629 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string -property_value: RO:0004049 RO:0002578 -property_value: seeAlso "https://wiki.geneontology.org/Directly_positively_regulates" xsd:anyURI -is_a: directly_regulates ! directly regulates -is_a: positively_regulates ! positively regulates - -[Typedef] -id: directly_regulates -name: directly regulates -namespace: external -def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -xref: RO:0002578 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly regulates (processual)" xsd:string -property_value: RO:0002575 RO:0002211 -is_a: immediately_causally_upstream_of ! immediately causally upstream of -is_a: regulates ! regulates - -[Typedef] -id: distal_to -name: distal to -namespace: uberon -xref: BSPO:0000097 - -[Typedef] -id: distally_connected_to -name: distally connected to +id: distally_connected_to +name: distally connected to namespace: uberon def: "x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] -is_a: connected_to ! connected to -is_a: proximal_to ! proximal to +is_a: RO:0002170 ! connected to is_a: transitively_distally_connected_to ! transitively distally connected to -inverse_of: proximally_connected_to ! proximally connected to - -[Typedef] -id: distalmost_part_of -name: distalmost part of -namespace: uberon -xref: BSPO:0001108 - -[Typedef] -id: dorsal_to -name: dorsal to -namespace: uberon -xref: BSPO:0000098 - -[Typedef] -id: drains -name: drains -namespace: uberon -def: "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." [] -xref: RO:0002179 -property_value: editor_note "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 -is_a: connected_to ! connected to - -[Typedef] -id: editor_note -name: editor note -namespace: uberon -def: "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology." [] -xref: IAO:0000116 -property_value: IAO:0000111 "editor note" xsd:string -property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000117 "PERSON:Daniel Schober" xsd:string -property_value: IAO:0000119 "GROUP:OBI:" xsd:string -is_metadata_tag: true - -[Typedef] -id: ends -name: ends -namespace: uberon -def: "inverse of ends with" [] -subset: ro-eco -xref: RO:0002229 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: part_of ! part_of -is_a: RO:0002222 ! temporally related to -inverse_of: ends_with ! ends with [Typedef] id: ends_with name: ends with namespace: external -namespace: uberon def: "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002230 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "finished by" xsd:string is_transitive: true is_a: has_part ! has part is_a: RO:0002222 ! temporally related to -[Typedef] -id: existence_ends_during -name: existence ends during -namespace: uberon -def: "Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely." [https://orcid.org/0000-0002-6601-2165] -def: "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -synonym: "ceases_to_exist_during" EXACT [] -xref: RO:0002492 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_ends_during_or_before ! existence ends during or before -is_a: RO:0002490 ! existence overlaps -transitive_over: part_of ! part_of - -[Typedef] -id: existence_ends_during_or_before -name: existence ends during or before -namespace: uberon -def: "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -xref: RO:0002497 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -holds_over_chain: part_of existence_ends_during_or_before -holds_over_chain: RO:0002286 existence_ends_during_or_before -is_a: RO:0002487 ! relation between physical entity and a process or stage -transitive_over: part_of ! part_of -transitive_over: precedes ! precedes -transitive_over: simultaneous_with ! simultaneous with - -[Typedef] -id: existence_ends_with -name: existence ends with -namespace: uberon -def: "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -xref: RO:0002493 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_ends_during ! existence ends during - -[Typedef] -id: existence_starts_and_ends_during -name: existence starts and ends during -namespace: uberon -def: "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -synonym: "exists during" EXACT [] -xref: RO:0002491 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_ends_during ! existence ends during -is_a: existence_starts_during ! existence starts during - -[Typedef] -id: existence_starts_during -name: existence starts during -namespace: uberon -def: "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." [] -xref: RO:0002488 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_starts_during_or_after ! existence starts during or after -is_a: RO:0002490 ! existence overlaps -transitive_over: part_of ! part_of - -[Typedef] -id: existence_starts_during_or_after -name: existence starts during or after -namespace: uberon -def: "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -xref: RO:0002496 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -holds_over_chain: part_of existence_starts_during_or_after -holds_over_chain: RO:0002258 existence_starts_during_or_after -is_a: RO:0002487 ! relation between physical entity and a process or stage -transitive_over: part_of ! part_of -transitive_over: preceded_by ! preceded by -transitive_over: simultaneous_with ! simultaneous with - -[Typedef] -id: existence_starts_with -name: existence starts with -namespace: uberon -def: "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." [] -xref: RO:0002489 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_starts_during ! existence starts during - [Typedef] id: extends_fibers_into name: extends_fibers_into namespace: uberon def: "X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y" [https://orcid.org/0000-0002-7073-9172] -holds_over_chain: RO:0002100 RO:0013001 -is_symmetric: true -is_a: connected_to ! connected to +is_a: RO:0002170 ! connected to [Typedef] id: filtered_through @@ -14107,75 +13497,17 @@ namespace: uberon def: "Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity." [] comment: Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed -[Typedef] -id: functionally_related_to -name: functionally related to -namespace: uberon -def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] -xref: RO:0002328 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string - -[Typedef] -id: has_boundary -name: has 2D boundary -namespace: uberon -def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] -xref: RO:0002002 -property_value: editor_note "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string -property_value: editor_note "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string -property_value: IAO:0000112 "my body has 2D boundary the surface of my skin" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "has boundary" xsd:string -property_value: IAO:0000118 "has_2D_boundary" xsd:string -property_value: RO:0001900 RO:0001901 -domain: BFO:0000040 ! material entity -range: BFO:0000141 ! immaterial entity -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: has_branching_part -name: has branching part -namespace: uberon -def: "inverse of branching part of" [] -subset: ro-eco -subset: RO:0002259 -xref: RO:0002569 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_transitive: true -is_a: has_part ! has part -is_a: RO:0002375 ! in branching relationship with - [Typedef] id: has_component name: has component namespace: external -namespace: uberon def: "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] subset: ro-eco xref: RO:0002180 -property_value: editor_note "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency is_a: has_part ! has part -[Typedef] -id: has_developmental_contribution_from -name: has developmental contribution from -namespace: uberon -def: "x has developmental contribution from y iff x has some part z such that z develops from y" [] -xref: RO:0002254 -property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: UBERON:0001062 ! anatomical entity -range: UBERON:0001062 ! anatomical entity -holds_over_chain: has_part develops_from -is_a: RO:0002258 ! developmentally preceded by -inverse_of: RO:0002255 ! developmentally contributes to - [Typedef] id: has_end_location name: has end location @@ -14183,9 +13515,6 @@ namespace: external def: "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" [] subset: ro-eco xref: RO:0002232 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "ends with process that occurs in" xsd:string domain: BFO:0000015 ! process range: BFO:0000004 ! independent continuant holds_over_chain: ends_with occurs_in @@ -14209,14 +13538,11 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002233 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "consumes" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Has_input" xsd:anyURI domain: BFO:0000015 ! process holds_over_chain: starts_with has_input is_a: has_participant ! has participant -inverse_of: input_of ! input of +inverse_of: RO:0002352 ! input of [Typedef] id: has_low_plasma_membrane_amount @@ -14226,52 +13552,6 @@ property_value: term_tracker_item https://github.com/obophenotype/cell-ontology/ is_obsolete: true replaced_by: RO:0015016 -[Typedef] -id: has_member -name: has member -namespace: uberon -def: "has member is a mereological relation between a collection and an item." [] -xref: RO:0002351 -property_value: IAO:0000119 "SIO" xsd:string -property_value: RO:0001900 RO:0001901 -is_a: has_part ! has part - -[Typedef] -id: has_muscle_antagonist -name: has muscle antagonist -namespace: uberon -def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] -xref: RO:0002568 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "Wikipedia:Antagonist_(muscle)" xsd:string -is_a: RO:0002567 ! biomechanically related to - -[Typedef] -id: has_muscle_insertion -name: has muscle insertion -namespace: uberon -def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] -xref: RO:0002373 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string -property_value: seeAlso http://dbpedia.org/property/insertion -domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} ! anatomical structure -is_a: attaches_to ! attached to -is_a: RO:0002567 ! biomechanically related to - -[Typedef] -id: has_muscle_origin -name: has muscle origin -namespace: uberon -def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] -xref: RO:0002372 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string -property_value: seeAlso http://dbpedia.org/property/origin -domain: UBERON:0000061 {comment="We need to import uberon muscle to create a stricter domain constraint"} ! anatomical structure -is_a: attaches_to ! attached to -is_a: RO:0002567 ! biomechanically related to - [Typedef] id: has_negative_regulatory_component_activity name: has negative regulatory component activity @@ -14289,13 +13569,9 @@ id: has_ontology_root_term name: has ontology root term name: preferred_root namespace: external -namespace: uberon def: "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root." [] xref: IAO:0000700 -property_value: IAO:0000111 "has ontology root term" xsd:string -property_value: IAO:0000117 "Nicolas Matentzoglu" xsd:string is_metadata_tag: true -is_class_level: true [Typedef] id: has_output @@ -14307,9 +13583,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002234 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "produces" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Has_output" xsd:anyURI holds_over_chain: ends_with has_output is_a: has_participant ! has participant @@ -14321,62 +13594,29 @@ name: has part name: has_part namespace: external namespace: quality -namespace: uberon def: "a core relation that holds between a whole and its part" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000051 -property_value: editor_note "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string -property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string -property_value: IAO:0000111 "has part" xsd:string -property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string -property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string -property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string -property_value: IAO:0000118 "has_part" xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string is_transitive: true is_a: overlaps ! overlaps [Typedef] -id: has_participant -name: has participant -namespace: external -def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] -xref: RO:0000057 -property_value: editor_note "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string -property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string -property_value: IAO:0000111 "has participant" xsd:string -property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string -property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string -property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string -property_value: IAO:0000118 "has_participant" xsd:string -domain: BFO:0000003 ! occurrent -range: BFO:0000002 ! continuant -holds_over_chain: has_part has_participant - -[Typedef] -id: has_potential_to_develop_into -name: has potential to develop into -namespace: uberon -def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] -xref: RO:0002387 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: RO:0002384 ! has developmental potential involving - -[Typedef] -id: has_potential_to_developmentally_contribute_to -name: has potential to developmentally contribute to -namespace: uberon -def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] -xref: RO:0002385 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: RO:0002384 ! has developmental potential involving - -[Typedef] +id: has_participant +name: has participant +namespace: external +def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] +xref: RO:0000057 +property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string +domain: BFO:0000003 ! occurrent +range: BFO:0000002 ! continuant +holds_over_chain: has_part has_participant + +[Typedef] id: has_primary_input name: has primary input namespace: external @@ -14411,17 +13651,6 @@ is_a: has_primary_input_or_output ! has primary input or output created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z -[Typedef] -id: has_quality -name: has quality -namespace: uberon -def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] -xref: RO:0000086 -property_value: editor_note "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string -property_value: IAO:0000112 "this apple has quality this red color" xsd:string -property_value: IAO:0000118 "has_quality" xsd:string -is_a: bearer_of ! bearer of - [Typedef] id: has_regulatory_component_activity name: has regulatory component activity @@ -14433,23 +13662,6 @@ is_a: RO:0002017 ! has component activity created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z -[Typedef] -id: has_skeleton -name: has skeleton -namespace: uberon -def: "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." [] -xref: RO:0002551 -property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "has supporting framework" xsd:string -property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string -domain: UBERON:0000061 ! anatomical structure -domain: UBERON:0000475 ! organism subdivision -range: UBERON:0000465 {IAO:0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} ! material anatomical entity -is_a: has_part ! has part -inverse_of: skeleton_of ! skeleton of -is_asymmetric: true - [Typedef] id: has_small_molecule_activator name: has small molecule activator @@ -14468,9 +13680,6 @@ namespace: external def: "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y" [] subset: ro-eco xref: RO:0002231 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "starts with process that occurs in" xsd:string domain: BFO:0000015 ! process range: BFO:0000004 ! independent continuant holds_over_chain: starts_with occurs_in @@ -14485,9 +13694,8 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002339 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of [Typedef] id: has_target_start_location @@ -14498,41 +13706,14 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002338 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in -transitive_over: part_of ! part_of - -[Typedef] -id: homologous_to -name: shares ancestor with -namespace: uberon -def: "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." [] -comment: VBO calls this homologous_to -xref: RO:0002158 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000232 "Consider obsoleting and merging with child relation, 'in homology relationship with'" xsd:string -is_symmetric: true -is_transitive: true -is_a: RO:0002320 ! evolutionarily related to - -[Typedef] -id: immediate_transformation_of -name: immediate transformation of -namespace: uberon -def: "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" [] -xref: RO:0002495 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0002575 RO:0002494 -is_a: directly_develops_from ! directly develops from -is_a: transformation_of ! transformation of +transitive_over: part_of ! part of [Typedef] id: immediately_causally_downstream_of name: immediately causally downstream of namespace: external xref: RO:0002405 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of ! causally downstream of is_a: immediately_preceded_by ! immediately preceded by inverse_of: immediately_causally_upstream_of ! immediately causally upstream of @@ -14543,26 +13724,15 @@ name: immediately causally upstream of namespace: external def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] xref: RO:0002412 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: immediately_precedes ! immediately precedes -[Typedef] -id: immediately_deep_to -name: immediately deep to -namespace: uberon -xref: BSPO:0001107 - [Typedef] id: immediately_preceded_by name: immediately preceded by namespace: external -namespace: uberon comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) xref: RO:0002087 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000118 "starts_at_end_of" xsd:string holds_over_chain: starts_with ends_with is_a: preceded_by ! preceded by inverse_of: immediately_precedes ! immediately precedes @@ -14574,228 +13744,22 @@ namespace: external comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) subset: ro-eco xref: RO:0002090 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "ends_at_start_of" xsd:string -property_value: IAO:0000118 "meets" xsd:string -property_value: RO:0002575 BFO:0000063 holds_over_chain: ends_with starts_with is_a: precedes ! precedes -[Typedef] -id: immediately_superficial_to -name: immediately superficial to -namespace: uberon -xref: BSPO:0015014 - -[Typedef] -id: in_anterior_side_of -name: in anterior side of -namespace: uberon -xref: BSPO:0000123 - -[Typedef] -id: in_deep_part_of -name: in deep part of -namespace: uberon -xref: BSPO:0001101 - -[Typedef] -id: in_dorsal_side_of -name: in dorsal side of -namespace: uberon -xref: BSPO:0015101 - -[Typedef] -id: in_lateral_side_of -name: in lateral side of -namespace: uberon -xref: BSPO:0000126 - -[Typedef] -id: in_left_side_of -name: in left side of -namespace: uberon -xref: BSPO:0000120 - -[Typedef] -id: in_posterior_side_of -name: in posterior side of -namespace: uberon -xref: BSPO:0000122 - -[Typedef] -id: in_proximal_side_of -name: in proximal side of -namespace: uberon -xref: BSPO:0000124 - -[Typedef] -id: in_right_side_of -name: in right side of -namespace: uberon -xref: BSPO:0000121 - -[Typedef] -id: in_superficial_part_of -name: in superficial part of -namespace: uberon -xref: BSPO:0001100 - -[Typedef] -id: in_taxon -name: in taxon -namespace: uberon -def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." [] -comment: Connects a biological entity to its taxon of origin. -subset: ro-eco -xref: RO:0002162 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9227-417X -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -holds_over_chain: attaches_to in_taxon -holds_over_chain: capable_of in_taxon -holds_over_chain: connected_to in_taxon -holds_over_chain: connects in_taxon -holds_over_chain: continuous_with in_taxon -holds_over_chain: developmentally_induced_by in_taxon -holds_over_chain: develops_from in_taxon -holds_over_chain: develops_from_part_of in_taxon -holds_over_chain: existence_ends_during in_taxon -holds_over_chain: existence_starts_during in_taxon -holds_over_chain: extends_fibers_into in_taxon -holds_over_chain: has_developmental_contribution_from in_taxon -holds_over_chain: has_part in_taxon -holds_over_chain: has_potential_to_develop_into in_taxon -holds_over_chain: innervated_by in_taxon -holds_over_chain: overlaps in_taxon -holds_over_chain: part_of in_taxon -holds_over_chain: produced_by in_taxon -holds_over_chain: produces in_taxon -holds_over_chain: results_in_developmental_progression_of in_taxon -holds_over_chain: RO:0002206 in_taxon -holds_over_chain: supplies in_taxon -is_a: RO:0002320 ! evolutionarily related to - [Typedef] id: indirectly_supplies name: indirectly_supplies namespace: uberon def: "a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s." [] -property_value: editor_note "add to RO" xsd:string -holds_over_chain: has_branching_part indirectly_supplies -holds_over_chain: has_branching_part supplies -is_transitive: true - -[Typedef] -id: innervated_by -name: innervated_by -namespace: uberon -xref: RO:0002005 -property_value: http://purl.org/spar/cito/citesAsAuthority "http://www.ncbi.nlm.nih.gov/pubmed/22402613" xsd:anyURI -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -domain: UBERON:0000061 ! anatomical structure -inverse_of: innervates ! innervates -transitive_over: branching_part_of ! branching part of - -[Typedef] -id: innervates -name: innervates -namespace: uberon -def: "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." [] -xref: RO:0002134 -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 -transitive_over: part_of ! part_of -expand_expression_to: "RO_0002132 some (GO_0043005 that (RO_0002131 some (GO_0045202 that BFO_0000050 some Y?)))" [] - -[Typedef] -id: input_of -name: input of -namespace: uberon -def: "inverse of has input" [] -subset: ro-eco -subset: RO:0002259 -xref: RO:0002352 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: functionally_related_to ! functionally related to -is_a: participates_in ! participates in - -[Typedef] -id: intersects_midsagittal_plane_of -name: intersects midsagittal plane of -namespace: uberon -xref: BSPO:0005001 +property_value: IAO:0000116 "add to RO" xsd:string +holds_over_chain: RO:0002569 indirectly_supplies [Typedef] id: layer_part_of name: layer part of namespace: uberon -is_a: part_of ! part_of - -[Typedef] -id: located_in -name: located in -namespace: uberon -def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -xref: RO:0001025 -property_value: editor_note "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" xsd:string -property_value: editor_note "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:located_in" xsd:string -property_value: IAO:0000111 "located in" xsd:string -property_value: IAO:0000112 "my brain is located in my head" xsd:string -property_value: IAO:0000112 "this rat is located in this cage" xsd:string -property_value: IAO:0000118 "located_in" xsd:string -property_value: RO:0001900 RO:0001901 -property_value: seeAlso "https://wiki.geneontology.org/Located_in" xsd:anyURI -domain: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant -range: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant -is_transitive: true -transitive_over: part_of ! part_of - -[Typedef] -id: location_of -name: location of -namespace: uberon -def: "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" [] -xref: RO:0001015 -property_value: editor_note "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: IAO:0000111 "is location of" xsd:string -property_value: IAO:0000112 "my head is the location of my brain" xsd:string -property_value: IAO:0000112 "this cage is the location of this rat" xsd:string -property_value: IAO:0000118 "location_of" xsd:string -property_value: RO:0001900 RO:0001901 -is_transitive: true -inverse_of: located_in ! located in - -[Typedef] -id: lumen_of -name: lumen of -namespace: uberon -def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] -subset: ro-eco -xref: RO:0002571 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 https://orcid.org/0000-0002-6601-2165 -range: BFO:0000040 ! material entity -is_a: part_of ! part_of - -[Typedef] -id: luminal_space_of -name: luminal space of -namespace: uberon -def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" [] -subset: ro-eco -xref: RO:0002572 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: BFO:0000141 ! immaterial entity -is_a: lumen_of ! lumen of +is_a: part_of ! part of [Typedef] id: negatively_regulated_by @@ -14804,7 +13768,6 @@ namespace: external def: "inverse of negatively regulates" [] subset: RO:0002259 xref: RO:0002335 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -14816,9 +13779,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002212 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002211 holds_over_chain: ends_with negatively_regulates is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect @@ -14831,30 +13791,11 @@ name: negatively regulates characteristic namespace: gene_ontology def: "A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C." [] xref: RO:0019002 -property_value: dc-contributor https://orcid.org/0000-0002-8688-6599 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 holds_over_chain: negatively_regulates positively_regulates_characteristic holds_over_chain: positively_regulates negatively_regulates_characteristic is_a: regulates_characteristic ! regulates characteristic -[Typedef] -id: never_in_taxon -name: never in taxon -name: never_in_taxon -namespace: uberon -def: "S never_in_taxon T iff: S SubClassOf in_taxon only not T." [PMID:20973947] -def: "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL." [] -xref: RO:0002161 -property_value: IAO:0000112 "tooth SubClassOf 'never in taxon' value 'Aves'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 -property_value: OMO:0002000 "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" xsd:string -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -expand_assertion_to: "Class: EquivalentTo: ?X and (RO_0002162 some ?Y)" [] -expand_assertion_to: "Class: ?X DisjointWith: RO_0002162 some ?Y " [] -is_metadata_tag: true -is_class_level: true - [Typedef] id: occurs_in name: occurs in @@ -14865,64 +13806,38 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000066 -property_value: IAO:0000111 "occurs in" xsd:string -property_value: IAO:0000118 "occurs_in" xsd:string -property_value: IAO:0000118 "unfolds in" xsd:string -property_value: IAO:0000118 "unfolds_in" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl property_value: seeAlso "https://wiki.geneontology.org/Occurs_in" xsd:anyURI domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant holds_over_chain: part_of occurs_in -inverse_of: contains_process ! contains process -transitive_over: part_of ! part_of - -[Typedef] -id: only_in_taxon -name: only in taxon -namespace: uberon -def: "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." [] -xref: RO:0002160 -property_value: editor_note "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" xsd:string -property_value: IAO:0000112 "lactation SubClassOf 'only in taxon' some 'Mammalia'" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -is_a: in_taxon ! in taxon +inverse_of: BFO:0000067 ! contains process +transitive_over: part_of ! part of [Typedef] id: output_of name: output of namespace: external -namespace: uberon def: "inverse of has output" [] subset: ro-eco subset: RO:0002259 xref: RO:0002353 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: functionally_related_to ! functionally related to is_a: participates_in ! participates in +is_a: RO:0002328 ! functionally related to [Typedef] id: overlaps name: overlaps namespace: external -namespace: uberon def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002131 -property_value: IAO:0000114 IAO:0000125 -property_value: RO:0001900 RO:0001901 holds_over_chain: has_part overlaps -holds_over_chain: has_part part_of {RO:0002582="true"} holds_over_chain: part_of part_of is_symmetric: true is_a: RO:0002323 ! mereotopologically related to -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] [Typedef] @@ -14931,29 +13846,15 @@ name: part of name: part_of namespace: external namespace: quality -namespace: uberon def: "a core relation that holds between a part and its whole" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000050 -property_value: editor_note "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string -property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string -property_value: IAO:0000111 "is part of" xsd:string -property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string -property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string -property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string -property_value: IAO:0000118 "part_of" xsd:string -property_value: RO:0001900 RO:0001901 -property_value: RO:0040042 BFO:0000002 -property_value: RO:0040042 BFO:0000003 -property_value: RO:0040042 BFO:0000004 -property_value: RO:0040042 BFO:0000017 -property_value: RO:0040042 BFO:0000019 -property_value: RO:0040042 BFO:0000020 -property_value: RO:0040042 BFO:0000031 +property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string @@ -14966,14 +13867,8 @@ inverse_of: has_part ! has part id: participates_in name: participates in namespace: external -namespace: uberon def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] xref: RO:0000056 -property_value: IAO:0000111 "participates in" xsd:string -property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string -property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string -property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string -property_value: IAO:0000118 "participates_in" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000003 ! occurrent inverse_of: has_participant ! has participant @@ -14985,7 +13880,6 @@ namespace: external def: "inverse of positively regulates" [] subset: RO:0002259 xref: RO:0002336 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -14997,10 +13891,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002213 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "positively regulates (process to process)" xsd:string -property_value: RO:0004049 RO:0002211 holds_over_chain: ends_with positively_regulates holds_over_chain: negatively_regulates negatively_regulates is_transitive: true @@ -15014,49 +13904,25 @@ name: positively regulates characteristic namespace: gene_ontology def: "A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C." [] xref: RO:0019001 -property_value: dc-contributor https://orcid.org/0000-0002-8688-6599 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 holds_over_chain: positively_regulates positively_regulates_characteristic is_a: regulates_characteristic ! regulates characteristic -[Typedef] -id: postaxialmost_part_of -name: postaxialmost part of -namespace: uberon -xref: BSPO:0001115 - -[Typedef] -id: posterior_to -name: posterior to -namespace: uberon -xref: BSPO:0000099 - [Typedef] id: posteriorly_connected_to name: posteriorly connected to namespace: uberon def: "x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] -is_a: anterior_to ! anterior to -is_a: connected_to ! connected to - -[Typedef] -id: preaxialmost_part_of -name: preaxialmost part of -namespace: uberon -xref: BSPO:0001113 +is_a: RO:0002170 ! connected to [Typedef] id: preceded_by name: preceded by namespace: external -namespace: uberon def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000062 -property_value: editor_note "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string -property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string -property_value: IAO:0000111 "preceded by" xsd:string -property_value: IAO:0000118 "is preceded by" xsd:string -property_value: IAO:0000118 "preceded_by" xsd:string +property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent holds_over_chain: part_of preceded_by @@ -15068,53 +13934,30 @@ inverse_of: precedes ! precedes id: precedes name: precedes namespace: external -namespace: uberon def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000063 -property_value: IAO:0000111 "precedes" xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent holds_over_chain: part_of precedes is_transitive: true is_a: RO:0002222 ! temporally related to -[Typedef] -id: present_in_taxon -name: present in taxon -name: present_in_taxon -namespace: uberon -def: "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S" [] -def: "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S." [https://orcid.org/0000-0002-6601-2165] -comment: The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology. -synonym: "applicable for taxon" EXACT [] -xref: RO:0002175 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: OMO:0002000 "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" xsd:string -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -is_metadata_tag: true -is_class_level: true - [Typedef] id: process_has_causal_agent name: process has causal agent namespace: external def: "Inverse of 'causal agent in process'" [] xref: RO:0002608 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_a: RO:0002410 ! causally related to [Typedef] id: produced_by name: produced by namespace: external -namespace: uberon def: "a produced_by b iff some process that occurs_in b has_output a." [] subset: ro-eco xref: RO:0003001 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity @@ -15122,13 +13965,10 @@ range: BFO:0000040 ! material entity id: produces name: produces namespace: external -namespace: uberon def: "a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix." [] comment: Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. subset: ro-eco xref: RO:0003000 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity inverse_of: produced_by ! produced by @@ -15138,27 +13978,14 @@ id: protects name: protects namespace: uberon -[Typedef] -id: proximal_to -name: proximal to -namespace: uberon -xref: BSPO:0000100 - [Typedef] id: proximally_connected_to name: proximally connected to namespace: uberon def: "x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] -is_a: connected_to ! connected to -is_a: distal_to ! distal to +is_a: RO:0002170 ! connected to is_a: transitively_proximally_connected_to ! transitively proximally connected to -[Typedef] -id: proximalmost_part_of -name: proximalmost part of -namespace: uberon -xref: BSPO:0001106 - [Typedef] id: regulated_by name: regulated by @@ -15166,8 +13993,6 @@ namespace: external def: "inverse of regulates" [] subset: RO:0002259 xref: RO:0002334 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000589 "regulated by (processual)" xsd:string domain: BFO:0000015 ! process range: BFO:0000015 ! process is_transitive: true @@ -15182,14 +14007,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 -property_value: IAO:0000117 https://orcid.org/0000-0001-7476-6306 -property_value: IAO:0000117 https://orcid.org/0000-0002-3837-8864 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GO" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string -property_value: IAO:0000589 "regulates (processual)" xsd:string -property_value: IAO:0000600 "false" xsd:boolean domain: BFO:0000015 ! process range: BFO:0000015 ! process holds_over_chain: directly_regulates directly_regulates @@ -15205,7 +14022,7 @@ name: regulates characteristic namespace: gene_ontology def: "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C." [] xref: RO:0019000 -property_value: dc-contributor https://orcid.org/0000-0002-8688-6599 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 domain: BFO:0000015 ! process range: PATO:0000001 ! quality holds_over_chain: regulates regulates_characteristic @@ -15217,13 +14034,9 @@ name: regulates levels of namespace: external def: "p regulates levels of c if p regulates some amount (PATO:0000070) of c" [] xref: RO:0002332 -property_value: IAO:0000112 "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "regulates levels of (process to entity)" xsd:string domain: BFO:0000015 ! process range: BFO:0000040 ! material entity -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to [Typedef] id: results_in_acquisition_of_features_of @@ -15234,9 +14047,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002315 -property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string range: UBERON:0000061 ! anatomical structure is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -15271,10 +14081,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002296 -property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "http://www.geneontology.org/GO.doc.development.shtml" xsd:anyURI is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -15284,9 +14090,7 @@ name: results in developmental progression of namespace: external def: "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." [] xref: RO:0002295 -property_value: editor_note "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000116 "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string property_value: seeAlso Ontology:extensions domain: GO:0008150 ! biological_process range: UBERON:0001062 ! anatomical entity @@ -15318,16 +14122,12 @@ is_a: has_participant ! has participant [Typedef] id: results_in_formation_of name: results in formation of +name: results in formation of anatomical entity namespace: external subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002297 -property_value: IAO:0000112 "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." xsd:string -property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of inverse_of: RO:0002354 ! formed as result of @@ -15349,8 +14149,6 @@ id: results_in_growth_of name: results in growth of namespace: external xref: RO:0002343 -property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -15363,11 +14161,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002299 -property_value: IAO:0000112 " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" xsd:string -property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -15380,11 +14173,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002298 -property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." xsd:string -property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -15397,8 +14185,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002565 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure [Typedef] @@ -15417,7 +14203,6 @@ namespace: external def: "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002342 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in is_a: RO:0002021 ! occurs across @@ -15427,7 +14212,6 @@ name: results in transport along namespace: external def: "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " [] xref: RO:0002341 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002337 ! related via localization to [Typedef] @@ -15435,36 +14219,13 @@ id: results_in_transport_to_from_or_in name: results in transport to from or in namespace: external xref: RO:0002344 -property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002337 ! related via localization to -[Typedef] -id: seeAlso -name: see also -namespace: uberon -xref: http://www.w3.org/2000/01/rdf-schema#seeAlso -is_metadata_tag: true - [Typedef] id: sexually_homologous_to name: sexually_homologous_to namespace: uberon -is_a: homologous_to ! shares ancestor with - -[Typedef] -id: simultaneous_with -name: simultaneous with -namespace: uberon -def: "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." [] -comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) -subset: ro-eco -xref: RO:0002082 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -is_symmetric: true -is_transitive: true -is_a: RO:0002081 ! before or simultaneous with +is_a: RO:0002158 ! shares ancestor with [Typedef] id: site_of @@ -15473,46 +14234,13 @@ namespace: uberon def: "c site_of p if c is the bearer of a disposition that is realized by a process that has p as part." [] synonym: "capable_of_has_part" RELATED [] -[Typedef] -id: skeleton_of -name: skeleton of -namespace: uberon -def: "inverse of has skeleton" [] -subset: RO:0002259 -xref: RO:0002576 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: UBERON:0000061 ! anatomical structure -range: UBERON:0000061 ! anatomical structure -is_a: part_of ! part_of - -[Typedef] -id: starts -name: starts -namespace: uberon -def: "inverse of starts with" [] -subset: ro-eco -xref: RO:0002223 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "Allen" xsd:string -is_a: part_of ! part_of -is_a: RO:0002222 ! temporally related to -inverse_of: starts_with ! starts with - [Typedef] id: starts_with name: starts with namespace: external -namespace: uberon def: "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002224 -property_value: IAO:0000112 "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "started by" xsd:string is_transitive: true is_a: has_part ! has part is_a: RO:0002222 ! temporally related to @@ -15523,139 +14251,36 @@ name: subdivision of namespace: uberon comment: placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B -[Typedef] -id: superficial_to -name: superficial to -namespace: uberon -xref: BSPO:0000108 - -[Typedef] -id: supplies -name: supplies -namespace: uberon -def: "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." [] -xref: RO:0002178 -property_value: editor_note "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 -is_a: connected_to ! connected to - -[Typedef] -id: surrounded_by -name: surrounded by -namespace: uberon -def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" [] -xref: RO:0002219 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0001900 RO:0001901 -is_a: adjacent_to ! adjacent to -inverse_of: surrounds ! surrounds - -[Typedef] -id: surrounds -name: surrounds -namespace: uberon -def: "inverse of surrounded by" [] -subset: RO:0002259 -xref: RO:0002221 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0001900 RO:0001901 -is_a: adjacent_to ! adjacent to - -[Typedef] -id: synapsed_by -name: synapsed by -namespace: uberon -def: "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " [] -xref: RO:0002103 -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 -is_a: RO:0002485 ! receives input from -inverse_of: RO:0002120 ! synapsed to -expand_expression_to: "BFO_0000051 some (GO_0045211 that part_of some (GO_0045202 that has_part some (GO_0042734 that BFO_0000050 some Y?)))" [] - [Typedef] id: term_tracker_item name: term tracker item namespace: external -namespace: uberon def: "An IRI or similar locator for a request or discussion of an ontology term." [] comment: The 'tracker item' can associate a tracker with a specific ontology term. xref: IAO:0000233 -property_value: IAO:0000111 "term tracker item" xsd:string -property_value: IAO:0000112 "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" xsd:string -property_value: IAO:0000119 "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" xsd:string is_metadata_tag: true -is_class_level: true - -[Typedef] -id: transformation_of -name: transformation of -namespace: uberon -def: "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" [] -xref: RO:0002494 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_transitive: true -is_a: develops_from ! develops from [Typedef] id: transitively_anteriorly_connected_to name: transitively anteriorly connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI -is_transitive: true [Typedef] id: transitively_distally_connected_to name: transitively distally connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI -is_transitive: true [Typedef] id: transitively_proximally_connected_to name: transitively proximally connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI -is_transitive: true - -[Typedef] -id: tributary_of -name: tributary of -namespace: uberon -def: "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." [] -subset: ro-eco -xref: RO:0002376 -property_value: IAO:0000112 "Deschutes River tributary_of Columbia River" xsd:string -property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "drains into" xsd:string -property_value: IAO:0000118 "drains to" xsd:string -property_value: IAO:0000118 "tributary channel of" xsd:string -property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Tributary" xsd:string -property_value: IAO:0000119 "http://www.medindia.net/glossary/venous_tributary.htm" xsd:string -property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" xsd:anyURI -property_value: seeAlso http://dbpedia.org/ontology/drainsTo -property_value: seeAlso "http://en.wikipedia.org/wiki/Tributary" xsd:anyURI -is_a: connected_to ! connected to -is_a: RO:0002375 ! in branching relationship with [Typedef] id: trunk_part_of name: trunk_part_of namespace: uberon -is_a: part_of ! part_of - -[Typedef] -id: ventral_to -name: ventral to -namespace: uberon -xref: BSPO:0000102 +is_a: part_of ! part of diff --git a/src/ontology/subsets/general_cell_types_upper_slim.owl b/src/ontology/subsets/general_cell_types_upper_slim.owl index 48fbe975e..8532201d2 100644 --- a/src/ontology/subsets/general_cell_types_upper_slim.owl +++ b/src/ontology/subsets/general_cell_types_upper_slim.owl @@ -10,28 +10,21 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" - xmlns:cito="http://purl.org/spar/cito/" xmlns:core="http://purl.obolibrary.org/obo/uberon/core#" xmlns:foaf="http://xmlns.com/foaf/0.1/" - xmlns:obo2="http://www.geneontology.org/formats/oboInOwl#http://purl.obolibrary.org/obo/" xmlns:pato="http://purl.obolibrary.org/obo/pato#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" - xmlns:skos="http://www.w3.org/2004/02/skos/core#" xmlns:swrl="http://www.w3.org/2003/11/swrl#" - xmlns:sssom="https://w3id.org/sssom/" - xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#" xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:terms="http://purl.org/dc/terms/" - xmlns:vocab="https://w3id.org/semapv/vocab/" - xmlns:terms1="http://www.geneontology.org/formats/oboInOwl#http://purl.org/dc/terms/" xmlns:uberon="http://purl.obolibrary.org/obo/uberon#" xmlns:ubprop="http://purl.obolibrary.org/obo/ubprop#" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - 2024-02-13 + + 2024-04-05 @@ -55,29 +48,9 @@ - - - - - - - - - - - - - - - - - - - definition - The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith @@ -99,8 +72,6 @@ We don't have definitions of 'meaning' or 'expression' Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition @@ -110,72 +81,28 @@ We also have the outstanding issue of how to aim different definitions to differ - editor note - An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obofoundry.org/obo/obi> - IAO:0000116 - uberon - editor_note - true - editor_note - editor note editor note - - - - - - - - - - - - - - - - - - - has obsolescence reason Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. - PERSON:Alan Ruttenberg - PERSON:Melanie Courtot has obsolescence reason - - - - - - - term tracker item - the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ - An IRI or similar locator for a request or discussion of an ontology term. - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg IAO:0000233 external - uberon term_tracker_item - true true term_tracker_item The 'tracker item' can associate a tracker with a specific ontology term. @@ -185,63 +112,23 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - - expand expression to - ObjectProperty: RO_0002104 -Label: has plasma membrane part -Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" - A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones - Chris Mungall expand expression to expand expression to - - - - - - - - - - - - - - - - - - - - - - - - - has ontology root term Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. - Nicolas Matentzoglu IAO:0000700 external - uberon has_ontology_root_term - true true has_ontology_root_term has ontology root term @@ -251,20 +138,10 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - - - - - - - term replaced by - Use on obsolete terms, relating the term to another term that can be used as a substitute - Person:Alan Ruttenberg - Person:Alan Ruttenberg Add as annotation triples in the granting ontology term replaced by term replaced by @@ -275,24 +152,6 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - 'part disjoint with' 'defined by construct' """ - PREFIX owl: <http://www.w3.org/2002/07/owl#> - PREFIX : <http://example.org/ - CONSTRUCT { - [ - a owl:Restriction ; - owl:onProperty :part_of ; - owl:someValuesFrom ?a ; - owl:disjointWith [ - a owl:Restriction ; - owl:onProperty :part_of ; - owl:someValuesFrom ?b - ] - ] - } - WHERE { - ?a :part_disjoint_with ?b . - } Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. @@ -305,11 +164,9 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation) A synonym type for describing abbreviations or initalisms - 2023-03-03 abbreviation @@ -335,11 +192,9 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form) A synonym type for describing pluralization synonyms - 2023-03-03 plural form @@ -354,23 +209,10 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - - - - - - - tooth SubClassOf 'never in taxon' value 'Aves' - S never_in_taxon T iff: S SubClassOf in_taxon only not T. x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL. - - - - Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: ?X and (RO_0002162 some ?Y) - Class: ?X DisjointWith: RO_0002162 some ?Y PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> @@ -394,34 +236,9 @@ CONSTRUCT { WHERE { ?x never_in_taxon: ?taxon . } - RO:0002161 - uberon - never_in_taxon - true - true - never_in_taxon never in taxon - never_in_taxon - - - - S never_in_taxon T iff: S SubClassOf in_taxon only not T. - PMID:20973947 - - - - - - - - - - - - - @@ -429,9 +246,6 @@ WHERE { S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S - S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S. - - PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> @@ -456,24 +270,10 @@ WHERE { )) as ?witness) BIND(CONCAT(STR(?x), " in taxon ", STR(?taxon)) AS ?label) } - RO:0002175 - applicable for taxon - uberon - present_in_taxon - true - true - present_in_taxon The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology. present in taxon - present_in_taxon - - - - S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S. - https://orcid.org/0000-0002-6601-2165 - @@ -485,60 +285,6 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL - is a defining property chain axiom - - - - - - - - If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. - is a defining property chain axiom where second argument is reflexive - - - - - - - - - - - - - - - - - - - - - - @@ -549,126 +295,6 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -927,12 +553,6 @@ WHERE { - - - - - - @@ -1363,14 +983,7 @@ WHERE { - - http://purl.org/dc/elements/1.1/creator - uberon - dc-creator - true - dc-creator - creator - + @@ -1382,14 +995,7 @@ WHERE { - - http://purl.org/dc/elements/1.1/description - uberon - dc-description - true - dc-description - description - + @@ -1401,71 +1007,25 @@ WHERE { - - http://purl.org/dc/elements/1.1/title - uberon - dc-title - true - dc-title - title - + - - http://purl.org/dc/terms/contributor - uberon - dc-contributor - true - dc-contributor - contributor - - - - - - - - - - - - - + - - http://purl.org/dc/terms/date - uberon - dcterms-date - true - dcterms-date - date - + - - http://purl.org/dc/terms/license - uberon - dcterms-license - true - dcterms-license - license - - - - - - - + @@ -1475,18 +1035,6 @@ WHERE { - - - - - - - - - - - - @@ -1503,18 +1051,6 @@ WHERE { - - - - - - - - - - - - @@ -1523,18 +1059,6 @@ WHERE { - - - - - - - - - - - - @@ -1551,66 +1075,6 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -1623,7 +1087,6 @@ WHERE { An alternative label for a class or property which has a more general meaning than the preferred name/primary label. - https://github.com/information-artifact-ontology/ontology-metadata/issues/18 has broad synonym has_broad_synonym @@ -1644,7 +1107,6 @@ WHERE { An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. - https://github.com/information-artifact-ontology/ontology-metadata/issues/20 has exact synonym has_exact_synonym @@ -1657,7 +1119,6 @@ WHERE { An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. - https://github.com/information-artifact-ontology/ontology-metadata/issues/19 has narrow synonym has_narrow_synonym @@ -1678,7 +1139,6 @@ WHERE { An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. - https://github.com/information-artifact-ontology/ontology-metadata/issues/21 has related synonym has_related_synonym @@ -1687,12 +1147,6 @@ WHERE { - - - - - - @@ -1717,30 +1171,6 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - - - @@ -1753,72 +1183,12 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -1833,60 +1203,6 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -1903,9 +1219,6 @@ WHERE { http://www.w3.org/2000/01/rdf-schema#seeAlso - uberon - seeAlso - true seeAlso see also @@ -1918,63 +1231,9 @@ WHERE { - - - - - - - - http://xmlns.com/foaf/0.1/depiction - uberon - depiction - true - depiction - depiction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + @@ -1995,29 +1254,15 @@ WHERE { - is part of - my brain is part of my body (continuant parthood, two material entities) - my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) - this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. - part_of - - - - - - - - BFO:0000050 external quality - uberon part_of @@ -2040,22 +1285,15 @@ A continuant cannot be part of an occurrent: use 'participates in'. An - has part - my body has part my brain (continuant parthood, two material entities) - my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) - this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. - has_part - BFO:0000051 external quality - uberon has_part @@ -2080,15 +1318,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. - preceded by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. - is preceded by - preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 external - uberon preceded_by preceded_by @@ -2109,11 +1342,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. - precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. BFO:0000063 external - uberon precedes precedes @@ -2137,11 +1368,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - occurs_in - unfolds in - unfolds_in BFO:0000066 external occurs_in @@ -2150,7 +1377,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. occurs_in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant - occurs in occurs in https://wiki.geneontology.org/Occurs_in @@ -2161,308 +1387,13 @@ A continuant cannot have an occurrent as part: use 'participates in'. - site of [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - BFO:0000067 - uberon - contains_process - contains_process Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant - - contains process contains process - - - - BSPO:0000096 - uberon - anterior_to - anterior_to - anterior to - - - - - - - - BSPO:0000097 - uberon - distal_to - distal_to - distal to - - - - - - - - BSPO:0000098 - uberon - dorsal_to - dorsal_to - dorsal to - - - - - - - - BSPO:0000099 - uberon - posterior_to - posterior_to - posterior to - - - - - - - - BSPO:0000100 - uberon - proximal_to - proximal_to - proximal to - - - - - - - - BSPO:0000102 - uberon - ventral_to - ventral_to - ventral to - - - - - - - - BSPO:0000107 - uberon - deep_to - deep_to - deep to - - - - - - - - BSPO:0000108 - uberon - superficial_to - superficial_to - superficial to - - - - - - - - BSPO:0000120 - uberon - in_left_side_of - in_left_side_of - in left side of - - - - - - - - BSPO:0000121 - uberon - in_right_side_of - in_right_side_of - in right side of - - - - - - - - BSPO:0000122 - uberon - in_posterior_side_of - in_posterior_side_of - in posterior side of - - - - - - - - BSPO:0000123 - uberon - in_anterior_side_of - in_anterior_side_of - in anterior side of - - - - - - - - BSPO:0000124 - uberon - in_proximal_side_of - in_proximal_side_of - in proximal side of - - - - - - - - BSPO:0000126 - uberon - in_lateral_side_of - in_lateral_side_of - in lateral side of - - - - - - - - BSPO:0001100 - uberon - in_superficial_part_of - in_superficial_part_of - in superficial part of - - - - - - - - BSPO:0001101 - uberon - in_deep_part_of - in_deep_part_of - in deep part of - - - - - - - - BSPO:0001106 - uberon - proximalmost_part_of - proximalmost_part_of - proximalmost part of - - - - - - - - BSPO:0001107 - uberon - immediately_deep_to - immediately_deep_to - immediately deep to - - - - - - - - BSPO:0001108 - uberon - distalmost_part_of - distalmost_part_of - distalmost part of - - - - - - - - BSPO:0001113 - uberon - preaxialmost_part_of - preaxialmost_part_of - preaxialmost part of - - - - - - - - BSPO:0001115 - uberon - postaxialmost_part_of - postaxialmost_part_of - postaxialmost part of - - - - - - - - BSPO:0005001 - uberon - intersects_midsagittal_plane_of - intersects_midsagittal_plane_of - intersects midsagittal plane of - - - - - - - - BSPO:0015014 - uberon - immediately_superficial_to - immediately_superficial_to - immediately superficial to - - - - - - - - BSPO:0015101 - uberon - in_dorsal_side_of - in_dorsal_side_of - in dorsal side of - - - - @@ -2522,12 +1453,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - inheres in - this fragility is a characteristic of this vase - this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. - inheres_in - Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of @@ -2539,14 +1465,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - bearer of - this apple is bearer of this red color - this vase is bearer of this fragility Inverse of characteristic_of A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. - bearer_of - is bearer of - RO:0000053 external bearer_of @@ -2563,15 +1483,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. - participates in - this blood clot participates in this blood coagulation - this input material (or this output material) participates in this process - this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process - participates_in RO:0000056 external - uberon participates_in participates_in participates in @@ -2589,14 +1503,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - has participant - this blood coagulation has participant this blood clot - this investigation has participant this investigator - this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. - has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 external has_participant @@ -2612,11 +1520,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. - function_of - is function of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. function of @@ -2628,11 +1533,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. - is quality of - quality_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. quality of @@ -2644,11 +1546,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. - is role of - role_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. role of @@ -2660,10 +1559,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. - has_function has function @@ -2673,15 +1570,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. - has_quality - RO:0000086 - uberon - has_quality - has_quality - has quality has quality @@ -2692,10 +1582,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. - has_role has role @@ -2729,13 +1617,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this cell derives from this parent cell (cell division) - this nucleus derives from this parent nucleus (nuclear division) - a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. - derives_from - This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. derives from @@ -2745,12 +1628,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this parent cell derives into this cell (cell division) - this parent nucleus derives into this nucleus (nuclear division) - a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. - derives_into derives into @@ -2762,18 +1641,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - is location of - my head is the location of my brain - this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - location_of - - RO:0001015 - uberon - location_of - location_of - location of location of @@ -2789,21 +1658,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. - located in - my brain is located in my head - this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - located_in - - http://www.obofoundry.org/ro/#OBO_REL:located_in - RO:0001025 - uberon - located_in - located_in - located in located in https://wiki.geneontology.org/Located_in @@ -2827,16 +1685,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. - the surface of my skin is a 2D boundary of my body a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - 2D_boundary_of - boundary of - is 2D boundary of - is boundary of - surface of - 2D boundary of @@ -2848,19 +1699,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. - my body has 2D boundary the surface of my skin a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - - has boundary - has_2D_boundary - - RO:0002002 - uberon - has_boundary - has_boundary - has 2D boundary has 2D boundary @@ -2871,17 +1712,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - http://www.ncbi.nlm.nih.gov/pubmed/22402613 - RO:0002005 - uberon - innervated_by - innervated_by - innervated_by innervated_by @@ -2892,8 +1722,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - has synaptic terminal of @@ -2913,10 +1741,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - RO:0002007 external - uberon bounding_layer_of bounding_layer_of @@ -3095,8 +1921,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland - <= Primitive instance level timing relation between events before or simultaneous with @@ -3111,15 +1935,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time. - - David Osumi-Sutherland - RO:0002082 - uberon - simultaneous_with - simultaneous_with t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) - simultaneous with simultaneous with @@ -3130,7 +1947,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after @@ -3147,11 +1963,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland - starts_at_end_of RO:0002087 external - uberon immediately_preceded_by immediately_preceded_by X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) @@ -3169,11 +1982,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - - David Osumi-Sutherland - ends_at_start_of - meets - RO:0002090 external immediately_precedes @@ -3196,12 +2004,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between a neuron and a material anatomical entity that its soma is part of. - <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) - has soma location @@ -3213,33 +2018,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. - - fasciculates with - (forall (?x ?y) - (iff - (fasciculates_with ?x ?y) - (exists (?nps ?npbs) - (and - ("neuron ; CL_0000540" ?x) - ("neuron projection bundle ; CARO_0001001" ?y) - ("neuron projection segment ; CARO_0001502" ?nps) - ("neuron projection bundle segment ; CARO_0001500' " ?npbs) - (part_of ?npbs ?y) - (part_of ?nps ?x) - (part_of ?nps ?npbs) - (forall (?npbss) - (if - (and - ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) - (part_of ?npbss ?npbs) - ) - (overlaps ?nps ?npbss) - )))))) - - fasciculates with @@ -3254,16 +2034,11 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between a neuron and some structure its axon forms (chemical) synapses in. - - <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y))) - - axon synapses in @@ -3285,18 +2060,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. - - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) - - - RO:0002103 - uberon - synapsed_by - synapsed_by - synapsed by synapsed by @@ -3308,15 +2073,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] - Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. - - - - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) - has plasma membrane part @@ -3332,16 +2090,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. - - - synapsed in http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)) - - has postsynaptic terminal in @@ -3356,12 +2108,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. - synapses in <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) - - has presynaptic terminal in @@ -3382,14 +2130,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. - - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) - - N1 synapsed_to some N2 Expands to: N1 SubclassOf ( @@ -3411,13 +2154,8 @@ N1 SubclassOf ( - A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. - - has synapse in <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) - - has synaptic terminal in @@ -3432,10 +2170,6 @@ N1 SubclassOf ( - - - - @@ -3444,13 +2178,10 @@ N1 SubclassOf ( - x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) - RO:0002131 external - uberon overlaps @@ -3459,15 +2190,6 @@ N1 SubclassOf ( overlaps overlaps - - - - - - - - true - @@ -3486,35 +2208,7 @@ N1 SubclassOf ( - The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. - - has fasciculating component - (forall (?x ?y) - (iff - (has_fasciculating_neuron_projection ?x ?y) - (exists (?nps ?npbs) - (and - ("neuron projection bundle ; CARO_0001001" ?x) - ("neuron projection ; GO0043005" ?y) - ("neuron projection segment ; CARO_0001502" ?nps) - ("neuron projection bundle segment ; CARO_0001500" ?npbs) - (part_of ?nps ?y) - (part_of ?npbs ?x) - (part_of ?nps ?npbs) - (forall (?npbss) - (if - (and - ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) - (part_of ?npbss ?npbs) - ) - (overlaps ?nps ?npbss) - )))))) - - - - - has fasciculating neuron projection @@ -3527,19 +2221,10 @@ N1 SubclassOf ( - Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - <http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) - - - RO:0002134 - uberon - innervates - innervates - innervates innervates @@ -3552,17 +2237,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - X continuous_with Y if and only if X and Y share a fiat boundary. - - connected to - The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) - - RO:0002150 - uberon - continuous_with - continuous_with - continuous with continuous with FMA:85972 @@ -3575,13 +2250,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a. - Consider obsoleting and merging with child relation, 'in homology relationship with' - RO:0002158 - uberon - homologous_to - homologous_to VBO calls this homologous_to shares ancestor with @@ -3592,19 +2261,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - lactation SubClassOf 'only in taxon' some 'Mammalia' - x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria - - - - RO:0002160 - uberon - only_in_taxon - only_in_taxon only in taxon @@ -3623,30 +2283,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - - - - - - - - - - - - - - - - - - - - - @@ -3667,53 +2303,16 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. - - - - - RO:0002162 - uberon - in_taxon - in_taxon Connects a biological entity to its taxon of origin. in taxon @@ -3725,14 +2324,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. - - - Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) - spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern @@ -3750,14 +2344,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b - - RO:0002170 - uberon - connected_to - connected_to - connected to connected to https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern @@ -3770,15 +2357,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - The M8 connects Glasgow and Edinburgh - a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system. - - RO:0002176 - uberon - connects - connects - connects connects https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern @@ -3793,28 +2372,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. - attached to part of (anatomical structure to anatomical structure) - RO:0002177 - uberon - attaches_to_part_of - attaches_to_part_of - attached to part of attached to part of - - - - - - - - true - @@ -3824,12 +2384,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy. Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure - - RO:0002178 - uberon - supplies - supplies - supplies supplies @@ -3841,12 +2395,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure. Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure - - RO:0002179 - uberon - drains - drains - drains drains @@ -3856,14 +2404,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. - For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. - RO:0002180 external - uberon has_component has_component @@ -3883,18 +2427,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y - - - - - RO:0002202 - uberon - develops_from - develops_from This is the transitive form of the develops from relation - develops from develops from @@ -3907,17 +2441,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of develops from - - - - RO:0002203 - uberon - develops_into - develops_into - develops into develops into @@ -3934,10 +2459,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - 'neural crest cell' SubClassOf expresses some 'Wnt1 gene' - x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process - expressed in @@ -3964,19 +2486,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. - - - FBbt - - RO:0002207 has developmental precursor - uberon - directly_develops_from - directly_develops_from TODO - add child relations from DOS - directly develops from directly develops from @@ -3986,9 +2498,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of directly develops from - developmental precursor of directly develops into @@ -4016,14 +2526,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. - - - - - GO - Regulation precludes parthood; the regulatory process may not be within the regulated process. - regulates (processual) - false RO:0002211 external regulates @@ -4048,9 +2550,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. - - - negatively regulates (process to process) RO:0002212 external @@ -4081,10 +2580,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. - - - positively regulates (process to process) - RO:0002213 external positively_regulates @@ -4104,17 +2599,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) - osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. - - has function realized in - - - For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". RO:0002215 external - uberon capable_of capable_of @@ -4129,31 +2616,15 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. - - has function in RO:0002216 external - uberon capable_of_part_of capable_of_part_of capable of part of capable of part of - - - - - - - - true - @@ -4162,15 +2633,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x - - - RO:0002219 - uberon - surrounded_by - surrounded_by - surrounded by surrounded by @@ -4182,18 +2645,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. - The epidermis layer of a vertebrate is adjacent to the dermis. - The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. - The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. - x adjacent to y if and only if x and y share a boundary. This relation acts as a join point with BSPO - - RO:0002220 external - uberon adjacent_to @@ -4202,12 +2657,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.adjacent to adjacent to - - - - A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. - - @@ -4215,16 +2664,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of surrounded by - - - RO:0002221 - uberon - surrounds - surrounds - surrounds surrounds @@ -4235,11 +2676,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. - https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to @@ -4253,17 +2689,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of starts with - - Chris Mungall - Allen - RO:0002223 - uberon - starts - starts - starts starts @@ -4275,15 +2702,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor - x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - - Chris Mungall - started by RO:0002224 external - uberon starts_with starts_with @@ -4301,14 +2722,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x develops from part of y if and only if there exists some z such that x develops from z and z is part of y - - RO:0002225 - uberon - develops_from_part_of - develops_from_part_of - develops from part of develops from part of @@ -4323,16 +2737,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x develops_in y if x is located in y whilst x is developing - - EHDAA2 - Jonathan Bard, EHDAA2 - RO:0002226 - uberon - develops_in - develops_in - develops in develops in @@ -4344,16 +2749,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of ends with - - Chris Mungall - RO:0002229 - uberon - ends - ends - ends ends @@ -4365,14 +2762,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - - Chris Mungall - finished by RO:0002230 external - uberon ends_with ends_with @@ -4392,10 +2784,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y - - starts with process that occurs in RO:0002231 external has_start_location @@ -4417,10 +2806,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y - - ends with process that occurs in RO:0002232 external has_end_location @@ -4442,10 +2828,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. - - consumes RO:0002233 external has_input @@ -4470,10 +2853,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. - - produces RO:0002234 external has_output @@ -4495,13 +2875,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1. b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t. - - RO:0002252 - uberon - connecting_branch_of - connecting_branch_of connecting branch of @@ -4513,7 +2887,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of connecting branch of - has connecting branch @@ -4531,15 +2904,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] - x has developmental contribution from y iff x has some part z such that z develops from y - - RO:0002254 - uberon - has_developmental_contribution_from - has_developmental_contribution_from - has developmental contribution from has developmental contribution from @@ -4554,9 +2919,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of has developmental contribution from - developmentally contributes to @@ -4570,21 +2933,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T - - - - induced by - - Developmental Biology, Gilbert, 8th edition, figure 6.5(F) - GO:0001759 - We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm] - RO:0002256 - uberon - developmentally_induced_by - developmentally_induced_by - developmentally induced by developmentally induced by @@ -4595,9 +2944,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Inverse of developmentally induced by - developmentally induces @@ -4610,11 +2957,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false - - In general you should not use this relation to make assertions - use one of the more specific relations below this one This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from developmentally preceded by @@ -4629,7 +2973,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. acts upstream of @@ -4646,7 +2989,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects @@ -4660,16 +3002,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage - - replaces - RO:0002285 - uberon - developmentally_replaces - developmentally_replaces - developmentally replaces developmentally replaces @@ -4679,9 +3013,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Inverse of developmentally preceded by - developmentally succeeded by @@ -4695,9 +3027,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue - - part of developmental precursor of @@ -4707,9 +3036,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process. - expresses @@ -4721,10 +3048,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. - RO:0002295 external results_in_developmental_progression_of @@ -4741,11 +3066,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - every flower development (GO:0009908) results in development of some flower (PO:0009046) - p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. - - http://www.geneontology.org/GO.doc.development.shtml RO:0002296 external results_in_development_of @@ -4765,11 +3086,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. - every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) - - - GOC:mtg_berkeley_2013 RO:0002297 external results_in_formation_of @@ -4778,7 +3094,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. results_in_formation_of results in formation of - results in formation of + results in formation of anatomical entity @@ -4788,12 +3104,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. - tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) - The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. - - GOC:mtg_berkeley_2013 RO:0002298 external results_in_morphogenesis_of @@ -4812,12 +3123,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process - bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) - The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. - - GOC:mtg_berkeley_2013 RO:0002299 external results_in_maturation_of @@ -4837,8 +3143,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. - - RO:0002304 external causally_upstream_of,_positive_effect @@ -4859,7 +3163,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. - RO:0002305 external causally_upstream_of,_negative_effect @@ -4876,32 +3179,15 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of characteristic of part of - - inheres in part of - - characteristic of part of - - - - - - - - true - @@ -4911,10 +3197,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity - - GOC:mtg_berkeley_2013 RO:0002315 external results_in_acquisition_of_features_of @@ -4932,8 +3215,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A relationship that holds via some environmental process - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. evolutionarily related to @@ -4943,9 +3224,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A mereological relationship or a topological relationship - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships - mereotopologically related to @@ -4955,8 +3233,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A relationship that holds between entities participating in some developmental process (GO:0032502) - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development developmentally related to @@ -4975,15 +3251,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - a particular instances of akt-2 enables some instance of protein kinase activity c enables p iff c is capable of p and c acts to execute p. - - catalyzes - executes - has - is catalyzing - is executing - This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. enables https://wiki.geneontology.org/Enables @@ -4995,13 +3263,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. - - This is a grouping relation that collects relations used for the purpose of connecting structure and function - RO:0002328 - uberon - functionally_related_to - functionally_related_to - functionally related to functionally related to @@ -5011,24 +3272,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - this relation holds between c and p when c is part of some c', and c' is capable of p. - - false part of structure that is capable of - - - - - - - - true - @@ -5038,8 +3284,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts. - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism genomically related to @@ -5059,9 +3303,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. c involved_in p if and only if c enables some process p', and p' is part of p - - actively involved in - enables part of involved in https://wiki.geneontology.org/Involved_in @@ -5074,11 +3315,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid p regulates levels of c if p regulates some amount (PATO:0000070) of c - - - regulates levels of (process to entity) RO:0002332 external regulates_levels_of @@ -5095,7 +3332,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of enables - enabled by https://wiki.geneontology.org/Enabled_by @@ -5111,8 +3347,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of regulates - - regulated by (processual) RO:0002334 external regulated_by @@ -5129,7 +3363,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of negatively regulates - RO:0002335 external negatively_regulated_by @@ -5146,7 +3379,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of positively regulates - RO:0002336 external positively_regulated_by @@ -5164,8 +3396,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A relationship that holds via some process of localization - - Do not use this relation directly. It is a grouping relation. related via localization to @@ -5180,7 +3410,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. - RO:0002338 external has_target_start_location @@ -5203,7 +3432,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. - RO:0002339 external has_target_end_location @@ -5222,7 +3450,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l - RO:0002341 external results_in_transport_along @@ -5239,7 +3466,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. - RO:0002342 external results_in_transport_across @@ -5256,8 +3482,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - 'pollen tube growth' results_in growth_of some 'pollen tube' - RO:0002343 external results_in_growth_of @@ -5272,8 +3496,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) - RO:0002344 external results_in_transport_to_from_or_in @@ -5289,12 +3511,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - An organism that is a member of a population of organisms is member of is a mereological relation between a item and a collection. - is member of - member part of - SIO - member of @@ -5306,13 +3523,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. has member is a mereological relation between a collection and an item. - SIO - - RO:0002351 - uberon - has_member - has_member - has member has member @@ -5324,14 +3534,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of has input - - RO:0002352 - uberon - input_of - input_of - input of input of @@ -5343,10 +3547,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of has output - RO:0002353 external - uberon output_of @@ -5361,7 +3563,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - formed as result of @@ -5371,8 +3572,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - http://neurolex.org/wiki/Property:DendriteLocation has dendrite location @@ -5385,14 +3584,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a - - attached to (anatomical structure to anatomical structure) - RO:0002371 - uberon - attaches_to - attaches_to - attached to attached to @@ -5405,13 +3597,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. - - Wikipedia:Insertion_(anatomy) - RO:0002372 - uberon - has_muscle_origin - has_muscle_origin - has muscle origin has muscle origin @@ -5431,13 +3616,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. - - Wikipedia:Insertion_(anatomy) - RO:0002373 - uberon - has_muscle_insertion - has_muscle_insertion - has muscle insertion has muscle insertion @@ -5456,12 +3634,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships - This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) - in branching relationship with https://github.com/obophenotype/uberon/issues/170 @@ -5474,23 +3647,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Deschutes River tributary_of Columbia River - inferior epigastric vein tributary_of external iliac vein - x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. - - drains into - drains to - tributary channel of - http://en.wikipedia.org/wiki/Tributary - http://www.medindia.net/glossary/venous_tributary.htm - This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries) - RO:0002376 - uberon - tributary_of - tributary_of - tributary of tributary of http://en.wikipedia.org/wiki/Tributary @@ -5508,10 +3666,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location - - This relation is added for formal completeness. It is unlikely to be used in many practical scenarios spatially coextensive with @@ -5523,15 +3678,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y - - RO:0002380 - uberon - branching_part_of - branching_part_of - branching part of branching part of FMA:85994 @@ -5545,9 +3693,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). - has developmental potential involving @@ -5557,14 +3703,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y - - RO:0002385 - uberon - has_potential_to_developmentally_contribute_to - has_potential_to_developmentally_contribute_to - has potential to developmentally contribute to has potential to developmentally contribute to @@ -5574,9 +3713,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y - has potential to developmentally induce @@ -5586,14 +3723,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x has the potential to develop into y iff x develops into y or if x is capable of developing into y - - RO:0002387 - uberon - has_potential_to_develop_into - has_potential_to_develop_into - has potential to develop into has potential to develop into @@ -5603,9 +3733,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y - has potential to directly develop into @@ -5617,9 +3745,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of upstream of - RO:0002404 external causally_downstream_of @@ -5636,8 +3762,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - RO:0002405 external immediately_causally_downstream_of @@ -5671,9 +3795,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. - - indirectly activates - indirectly positively regulates https://wiki.geneontology.org/Indirectly_positively_regulates @@ -5699,9 +3820,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. - - indirectly inhibits - indirectly negatively regulates https://wiki.geneontology.org/Indirectly_negatively_regulates @@ -5727,8 +3845,6 @@ For the second, we consider a relationship to be regulatory if the system in whi For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to @@ -5747,7 +3863,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. - RO:0002411 external causally_upstream_of @@ -5766,8 +3881,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. - - RO:0002412 external immediately_causally_upstream_of @@ -5786,8 +3899,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 - - influences (processual) RO:0002418 external affects @@ -5804,8 +3915,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different inverse of causally upstream of or within - - RO:0002427 external causally_downstream_of_or_within @@ -5830,7 +3939,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' regulates some p - involved in regulation of @@ -5849,8 +3957,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' positively regulates some p - - involved in positive regulation of @@ -5869,7 +3975,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' negatively regulates some p - involved in negative regulation of @@ -5884,8 +3989,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union - - involved in or reguates involved in or involved in regulation of @@ -5896,28 +3999,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - - executes activity in enables activity in is active in https://wiki.geneontology.org/Is_active_in - - - - - - - - true - @@ -5933,11 +4020,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. - - RO:0002433 - uberon - contributes_to_morphology_of - contributes_to_morphology_of contributes to morphology of @@ -5952,13 +4034,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different A relationship that holds between two entities in which the processes executed by the two entities are causally connected. This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. Considering relabeling as 'pairwise interacts with' - - Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. in pairwise interaction with interacts with http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ - http://purl.obolibrary.org/obo/MI_0914 @@ -5969,12 +4048,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. - - binds - molecularly binds with molecularly interacts with - http://purl.obolibrary.org/obo/MI_0915 @@ -5984,8 +4059,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different Axiomatization to GO to be added later - - An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. phosphorylates @@ -6006,8 +4079,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. - - molecularly controls directly regulates activity of @@ -6027,9 +4098,6 @@ A and B can be physically interacting but not necessarily. Immediately upstream The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. - - - directly inhibits molecularly decreases activity of directly negatively regulates activity of @@ -6049,9 +4117,6 @@ For example, A and B may be gene products and binding of B by A negatively regul The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. - - - directly activates molecularly increases activity of directly positively regulates activity of @@ -6061,8 +4126,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. helper property (not for use in curation) @@ -6074,16 +4137,8 @@ For example, A and B may be gene products and binding of B by A positively regul - 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. - - - - RO:0002473 - uberon - composed_primarily_of - composed_primarily_of composed primarily of @@ -6094,24 +4149,10 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. - has part that occurs in - - - - - - - - true - @@ -6119,7 +4160,6 @@ For example, A and B may be gene products and binding of B by A positively regul - is kinase activity @@ -6131,7 +4171,6 @@ For example, A and B may be gene products and binding of B by A positively regul See notes for inverse relation - receives input from @@ -6142,7 +4181,6 @@ For example, A and B may be gene products and binding of B by A positively regul This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. - sends output to @@ -6153,8 +4191,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. relation between physical entity and a process or stage @@ -6170,11 +4206,6 @@ For example, A and B may be gene products and binding of B by A positively regul x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). - - RO:0002488 - uberon - existence_starts_during - existence_starts_during existence starts during @@ -6185,11 +4216,6 @@ For example, A and B may be gene products and binding of B by A positively regul x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). - - RO:0002489 - uberon - existence_starts_with - existence_starts_with existence starts with @@ -6200,7 +4226,6 @@ For example, A and B may be gene products and binding of B by A positively regul x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence overlaps @@ -6213,12 +4238,7 @@ For example, A and B may be gene products and binding of B by A positively regul x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) - - RO:0002491 exists during - uberon - existence_starts_and_ends_during - existence_starts_and_ends_during The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts and ends during @@ -6234,23 +4254,10 @@ For example, A and B may be gene products and binding of B by A positively regul - Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). - - RO:0002492 - ceases_to_exist_during - uberon - existence_ends_during - existence_ends_during The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during - - - - Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. - https://orcid.org/0000-0002-6601-2165 - @@ -6259,11 +4266,6 @@ For example, A and B may be gene products and binding of B by A positively regul x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). - - RO:0002493 - uberon - existence_ends_with - existence_ends_with The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends with @@ -6276,11 +4278,6 @@ For example, A and B may be gene products and binding of B by A positively regul x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships - - RO:0002494 - uberon - transformation_of - transformation_of transformation of @@ -6292,12 +4289,6 @@ For example, A and B may be gene products and binding of B by A positively regul x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t - - - RO:0002495 - uberon - immediate_transformation_of - immediate_transformation_of immediate transformation of @@ -6328,11 +4319,6 @@ For example, A and B may be gene products and binding of B by A positively regul x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). - - RO:0002496 - uberon - existence_starts_during_or_after - existence_starts_during_or_after The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts during or after @@ -6364,11 +4350,6 @@ For example, A and B may be gene products and binding of B by A positively regul x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. - - RO:0002497 - uberon - existence_ends_during_or_before - existence_ends_during_or_before The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during or before @@ -6381,7 +4362,6 @@ For example, A and B may be gene products and binding of B by A positively regul A relationship between a material entity and a process where the material entity has some causal role that influences the process - causal agent in process @@ -6394,9 +4374,6 @@ For example, A and B may be gene products and binding of B by A positively regul p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. - - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes @@ -6405,7 +4382,6 @@ For example, A and B may be gene products and binding of B by A positively regul - depends on @@ -6419,9 +4395,6 @@ For example, A and B may be gene products and binding of B by A positively regul The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch - - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between entities @@ -6435,17 +4408,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. - - has supporting framework - The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). - RO:0002551 - uberon - has_skeleton - has_skeleton has skeleton @@ -6462,9 +4426,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - causally influenced by (entity-centric) causally influenced by @@ -6474,7 +4435,6 @@ For example, A and B may be gene products and binding of B by A positively regul - interaction relation helper property http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ @@ -6486,7 +4446,6 @@ For example, A and B may be gene products and binding of B by A positively regul - molecular interaction relation helper property @@ -6497,8 +4456,6 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - - RO:0002565 external results_in_movement_of @@ -6528,10 +4485,6 @@ For example, A and B may be gene products and binding of B by A positively regul The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). - - - - causally influences (entity-centric) causally influences @@ -6544,8 +4497,6 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between elements of a musculoskeletal system or its analogs. - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. biomechanically related to @@ -6556,12 +4507,6 @@ For example, A and B may be gene products and binding of B by A positively regul m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. - - Wikipedia:Antagonist_(muscle) - RO:0002568 - uberon - has_muscle_antagonist - has_muscle_antagonist has muscle antagonist @@ -6574,13 +4519,8 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of branching part of - - RO:0002569 - uberon - has_branching_part - has_branching_part has branching part @@ -6593,14 +4533,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. - - UBERON:cjm - This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. - RO:0002570 - uberon - conduit_for - conduit_for conduit for @@ -6612,13 +4545,7 @@ For example, A and B may be gene products and binding of B by A positively regul x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - - - RO:0002571 - uberon - lumen_of - lumen_of lumen of @@ -6630,12 +4557,7 @@ For example, A and B may be gene products and binding of B by A positively regul s is luminal space of x iff s is lumen_of x and s is an immaterial entity - - RO:0002572 - uberon - luminal_space_of - luminal_space_of luminal space of @@ -6648,12 +4570,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has skeleton - - RO:0002576 - uberon - skeleton_of - skeleton_of skeleton of @@ -6665,10 +4582,6 @@ For example, A and B may be gene products and binding of B by A positively regul p directly regulates q iff p is immediately causally upstream of q and p regulates q. - - - directly regulates (processual) - RO:0002578 external directly_regulates @@ -6690,9 +4603,7 @@ For example, A and B may be gene products and binding of B by A positively regul - gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p - has part structure that is capable of @@ -6762,8 +4673,6 @@ For example, A and B may be gene products and binding of B by A positively regul A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - - causal relation between material entity and a process @@ -6777,9 +4686,7 @@ For example, A and B may be gene products and binding of B by A positively regul - pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. - capable of regulating @@ -6794,7 +4701,6 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. - capable of negatively regulating @@ -6808,9 +4714,7 @@ For example, A and B may be gene products and binding of B by A positively regul - renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. - capable of positively regulating @@ -6821,7 +4725,6 @@ For example, A and B may be gene products and binding of B by A positively regul Inverse of 'causal agent in process' - RO:0002608 external process_has_causal_agent @@ -6837,9 +4740,6 @@ For example, A and B may be gene products and binding of B by A positively regul p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. - - directly positively regulates (process to process) - RO:0002629 external directly_positively_regulates @@ -6859,8 +4759,6 @@ For example, A and B may be gene products and binding of B by A positively regul p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. - - directly negatively regulates (process to process) RO:0002630 external @@ -6887,12 +4785,9 @@ For example, A and B may be gene products and binding of B by A positively regul - a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. - RO:0003000 external - uberon produces produces @@ -6908,12 +4803,9 @@ For example, A and B may be gene products and binding of B by A positively regul - a produced_by b iff some process that occurs_in b has_output a. - RO:0003001 external - uberon produced_by produced_by @@ -7020,7 +4912,6 @@ For example, A and B may be gene products and binding of B by A positively regul - 2018-01-26T23:49:30Z @@ -7058,7 +4949,6 @@ For example, A and B may be gene products and binding of B by A positively regul c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive - 2018-01-26T23:53:14Z @@ -7105,7 +4995,6 @@ For example, A and B may be gene products and binding of B by A positively regul - 2018-03-13T23:55:19Z causally upstream of or within, positive effect @@ -7121,7 +5010,6 @@ For example, A and B may be gene products and binding of B by A positively regul The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. - regulates activity of @@ -7369,7 +5257,6 @@ For example, A and B may be gene products and binding of B by A positively regul - 'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)') A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. @@ -7389,7 +5276,6 @@ For example, A and B may be gene products and binding of B by A positively regul - 'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor') A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. @@ -7411,12 +5297,7 @@ For example, A and B may be gene products and binding of B by A positively regul - A diagnostic testing device utilizes a specimen. X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. - - - A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. - See github ticket https://github.com/oborel/obo-relations/issues/497 2021-11-08T12:00:00Z utilizes device utilizes material @@ -7542,7 +5423,6 @@ For example, A and B may be gene products and binding of B by A positively regul - x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y. @@ -7562,8 +5442,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - carries uberon channel_for @@ -7575,7 +5453,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uberon channels_from channels_from @@ -7586,7 +5463,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uberon channels_into channels_into @@ -7597,10 +5473,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y. uberon distally_connected_to @@ -7619,11 +5493,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y uberon extends_fibers_into @@ -7653,11 +5522,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - @@ -7685,7 +5549,6 @@ For example, A and B may be gene products and binding of B by A positively regul - x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y. uberon @@ -7714,7 +5577,6 @@ For example, A and B may be gene products and binding of B by A positively regul - x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y. @@ -7768,7 +5630,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uberon transitively_anteriorly_connected_to transitively anteriorly connected to @@ -7780,7 +5641,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uberon transitively_distally_connected_to transitively distally connected to @@ -7792,7 +5652,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uberon transitively_proximally_connected_to transitively proximally connected to @@ -15450,32 +13309,32 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer - + - + - + PMID:12382326 - + PMID:12382326 @@ -23691,7 +21550,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 PMID:15371245 ncbi_taxonomy @@ -23705,7 +21563,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 Mus mice @@ -23724,7 +21581,7 @@ For example, A and B may be gene products and binding of B by A positively regul mice - + @@ -23739,7 +21596,6 @@ For example, A and B may be gene products and binding of B by A positively regul - NCBITaxon:85055 GC_ID:1 house mouse @@ -23767,7 +21623,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 ncbi_taxonomy NCBITaxon:117570 @@ -23780,7 +21635,6 @@ For example, A and B may be gene products and binding of B by A positively regul - NCBITaxon:40673 GC_ID:1 bony vertebrates @@ -23820,7 +21674,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 ncbi_taxonomy NCBITaxon:1338369 @@ -23833,7 +21686,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 PMID:11743200 PMID:11791233 @@ -23855,7 +21707,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 mice and others ncbi_taxonomy @@ -23882,7 +21733,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 PMID:23020233 PMID:30257078 @@ -23946,7 +21796,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 PMID:11214319 PMID:12082125 @@ -23963,7 +21812,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 PMID:11214319 PMID:12082125 @@ -23986,7 +21834,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 tetrapods ncbi_taxonomy @@ -24006,7 +21853,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 amniotes ncbi_taxonomy @@ -24026,7 +21872,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 Theria ncbi_taxonomy @@ -24046,7 +21891,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 ncbi_taxonomy Fungi/Metazoa group @@ -24073,7 +21917,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 metazoans multicellular animals @@ -24114,7 +21957,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 ncbi_taxonomy NCBITaxon:33213 @@ -24127,7 +21969,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 deuterostomes ncbi_taxonomy @@ -24147,7 +21988,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 PMID:15019624 PMID:15371245 @@ -24162,7 +22002,6 @@ For example, A and B may be gene products and binding of B by A positively regul - NCBITaxon:109679 GC_ID:1 ncbi_taxonomy @@ -24176,7 +22015,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 mammals ncbi_taxonomy @@ -24203,7 +22041,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 ncbi_taxonomy NCBITaxon:6072 @@ -24216,7 +22053,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 chordates ncbi_taxonomy @@ -24243,7 +22079,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 Vertebrata vertebrates @@ -24277,7 +22112,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 Gnathostomata jawed vertebrates @@ -24304,7 +22138,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 ncbi_taxonomy NCBITaxon:8287 @@ -24317,7 +22150,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 Mus ncbi_taxonomy @@ -24337,7 +22169,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 Craniata ncbi_taxonomy @@ -24357,7 +22188,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 eutherian mammals placental mammals @@ -24405,7 +22235,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 rodent ncbi_taxonomy @@ -24807,7 +22636,6 @@ For example, A and B may be gene products and binding of B by A positively regul A contractility quality inhering in a bearer by virtue of the bearer's ability of contracting or being contracted. - quality PATO:0001690 @@ -24963,7 +22791,6 @@ For example, A and B may be gene products and binding of B by A positively regul A complete three dimensional shape in which for every line connecting pair of points on the object is within the object. Or: a shape lacking cavities. Contrast: concave. - Image:http://upload.wikimedia.org/wikipedia/commons/0/06/Convex_polygon_illustration1.png quality PATO:0002007 @@ -25490,7 +23317,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001006 Category=gene. Requested by=CL. receptor-type tyrosine-protein phosphatase C - @@ -25540,7 +23366,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001012 Category=gene. Requested by=CL. integrin alpha-M - @@ -25587,7 +23412,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001013 Category=gene. Requested by=CL. integrin alpha-X - @@ -25622,7 +23446,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001015 Category=sequence. Requested by=CL. Note: This isoform includes the region encoded by the variable exon 4(A), and lacks the region encoded by exons 5(B) and 6(C). receptor-type tyrosine-protein phosphatase C isoform CD45RA - @@ -25756,7 +23579,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001024 Category=gene. Requested by=CL. neural cell adhesion molecule 1 - @@ -25841,7 +23663,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001084 Category=gene. Requested by=CL. T-cell surface glycoprotein CD8 alpha chain - @@ -25971,7 +23792,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001332 Category=gene. Requested by=CL. carcinoembryonic antigen-related cell adhesion molecule 8 - @@ -26034,7 +23854,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001381 Category=gene. Requested by=CL. interleukin-2 receptor subunit beta - @@ -26078,7 +23897,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001444 Category=gene. Requested by=CL. cadherin-5 - @@ -26200,7 +24018,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001839 Category=gene. Requested by=CL. T-cell surface glycoprotein CD5 - @@ -26240,7 +24057,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001850 Category=gene. Requested by=CL. cathepsin K - @@ -26337,7 +24153,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001869 Category=gene. Requested by=CL. interleukin-7 receptor subunit alpha - @@ -26394,7 +24209,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001879 Category=gene. Requested by=CL. leukosialin - @@ -26471,7 +24285,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001898 Category=gene. Requested by=CL. neprilysin - @@ -26508,7 +24321,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001903 Category=gene. Requested by=CL. paired box protein PAX-5 - @@ -26549,7 +24361,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001937 Category=gene. Requested by=CL. tartrate-resistant acid phosphatase type 5 - @@ -26593,7 +24404,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001944 Category=gene. Requested by=CL. transcription factor PU.1 - @@ -26640,7 +24450,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001954 Category=gene. Requested by=CL. tumor necrosis factor receptor superfamily member 11A - @@ -26681,7 +24490,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001969 Category=gene. Requested by=CL. urokinase plasminogen activator surface receptor - @@ -26751,7 +24559,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000002062 Category=gene. Requested by=CL. macrophage colony-stimulating factor 1 receptor - @@ -26847,7 +24654,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000002112 Category=gene. Requested by=CL. vascular endothelial growth factor receptor 2 - @@ -26968,7 +24774,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000005307 Category=gene. Requested by=CL. CCAAT/enhancer-binding protein alpha - @@ -27006,7 +24811,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000006611 Category=gene. Requested by=CL. DNA nucleotidylexotransferase - @@ -27045,7 +24849,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000007597 Category=gene. Requested by=CL. protein c-Fos - @@ -27086,7 +24889,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000007857 Category=gene. Requested by=CL. erythroid transcription factor - @@ -27127,7 +24929,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000007858 Category=gene. Requested by=CL. endothelial transcription factor GATA-2 - @@ -27162,7 +24963,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000011178 Category=gene. Requested by=CL. nuclear factor NF-kappa-B p100 subunit - @@ -27200,7 +25000,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000014841 Category=gene. sonic hedgehog protein - @@ -27242,7 +25041,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000016043 Category=gene. Requested by=CL. T-cell acute lymphocytic leukemia protein 1 - @@ -27575,7 +25373,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA2:0001824 EHDAA:500 EMAPA:35955 - FBbt:00005155 GAID:63 HAO:0000930 MA:0000017 @@ -27608,12 +25405,6 @@ For example, A and B may be gene products and binding of B by A positively regul https://github.com/obophenotype/uberon/issues/549 https://orcid.org/0000-0002-6601-2165 - - - - FBbt:00005155 - - @@ -27699,8 +25490,6 @@ For example, A and B may be gene products and binding of B by A positively regul Any hollow cylindrical anatomical structure containing a lumen through which substances are transported. - not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts) - tubular galen:Tube anatomical tube duct @@ -27721,8 +25510,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -27742,9 +25531,6 @@ For example, A and B may be gene products and binding of B by A positively regul Dense regular connective tissue that connects muscle to bone[VSAO]. - Dense regular connective tissue that connects muscle to bone.[VSAO] - Phylogenetically, tendinous tissue first appears in the invertebrate chordate Branchiostoma as myosepta. This two-dimensional array of collagen fibers is highly organized, with fibers running along two primary axes. In hagfish the first linear tendons appear and the myosepta have developed specialized regions with unidirectional fiber orientation - a linear tendon within the flat sheet of myoseptum.[well established][VHOG] - in FMA, tendon is an organ component that with parts dense-irregular-connective-tissue of tendon and dense-irregular-connective-tissue of tendon sheath; we follow VSAO in making it a subtype of the former. In VSAO tendons connect muscle to bone; in WP the def states integument (e.g. auricular muscles) - but JB confirms this is not actually tendon but aponeurosis AEO:0000091 BTO:0001356 CALOHA:TS-1021 @@ -27773,11 +25559,11 @@ For example, A and B may be gene products and binding of B by A positively regul tendon http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg - + - + @@ -27790,13 +25576,13 @@ For example, A and B may be gene products and binding of B by A positively regul - + OG - + AEO @@ -27808,31 +25594,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Tendon http://dx.plos.org/10.1371/journal.pone.0051070 - - - - Dense regular connective tissue that connects muscle to bone.[VSAO] - 2012-08-14 - VSAO:0000073 - VSAO - PSPUB:0000170 - - - - - Phylogenetically, tendinous tissue first appears in the invertebrate chordate Branchiostoma as myosepta. This two-dimensional array of collagen fibers is highly organized, with fibers running along two primary axes. In hagfish the first linear tendons appear and the myosepta have developed specialized regions with unidirectional fiber orientation - a linear tendon within the flat sheet of myoseptum.[well established][VHOG] - 2012-09-17 - VHOG:0001286 - VHOG - DOI:10.1016/S1095-6433(02)00241-6 Summers AP, Koob TJ, The evolution of tendon - morphology and material properties. Comparative Biochemistry and Physiology-Part A: Molecular and Integrative Physiology (2002) - http://bgee.unil.ch/ - - - - - in FMA, tendon is an organ component that with parts dense-irregular-connective-tissue of tendon and dense-irregular-connective-tissue of tendon sheath; we follow VSAO in making it a subtype of the former. In VSAO tendons connect muscle to bone; in WP the def states integument (e.g. auricular muscles) - but JB confirms this is not actually tendon but aponeurosis - FMA - @@ -27879,10 +25640,7 @@ For example, A and B may be gene products and binding of B by A positively regul A tubular structure that transports secreted or excreted substances. - A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171]. - Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here. AAO:0011123 - FBbt:00100314 FMA:30320 NCIT:C12948 SCTID:91726008 @@ -27908,18 +25666,6 @@ For example, A and B may be gene products and binding of B by A positively regul http://orcid.org/0000-0002-6601-2165 http://www.siumed.edu/~dking2/intro/glands.htm#ducts - - - - A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171]. - ZFA:0005171 - - - - - FBbt:00100314 - - @@ -27953,10 +25699,8 @@ For example, A and B may be gene products and binding of B by A positively regul Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. - in FMA, serosa is a wall UBERON:0009915 wall - EMAPA:25036 FMA:82482 galen:Wall wall of organ @@ -27972,12 +25716,6 @@ For example, A and B may be gene products and binding of B by A positively regul Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. FMA:82482 - - - - in FMA, serosa is a wall - FMA - @@ -28013,7 +25751,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0000003 EHDAA2:0003003 EMAPA:0 - FBbt:00007001 FMA:305751 FMA:67135 GAID:781 @@ -28041,12 +25778,6 @@ For example, A and B may be gene products and binding of B by A positively regul Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. CARO:0000003 - - - - FBbt:00007001 - - @@ -28084,8 +25815,6 @@ For example, A and B may be gene products and binding of B by A positively regul - Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. - CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4 BIRNLEX:4 CARO:0020004 EFO:0000634 @@ -28119,12 +25848,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia - - - - Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. - GO:0048513 - @@ -28146,8 +25869,6 @@ For example, A and B may be gene products and binding of B by A positively regul A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity. FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction - Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball. - Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal. FMA:86140 uberon organ region with fixed fiat boundary @@ -28163,20 +25884,6 @@ For example, A and B may be gene products and binding of B by A positively regul A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity. http://orcid.org/0000-0002-6601-2165 - - - - Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball. - FMA:86140 - 3 - - - - - Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal. - FMA:86140 - 1 - @@ -28209,7 +25916,6 @@ For example, A and B may be gene products and binding of B by A positively regul A multicellular structure that is a part of an organ. - currently defined in a very broad sense, may be replaced by more specific classes in the future @@ -28366,7 +26072,6 @@ For example, A and B may be gene products and binding of B by A positively regul - ncit:Death is an outcome XAO:0000437 XtroDO:0000085 uberon @@ -28381,12 +26086,6 @@ For example, A and B may be gene products and binding of B by A positively regul End of the life of an organism. XAO:0000437 - - - - ncit:Death is an outcome - ncit - @@ -28472,7 +26171,6 @@ For example, A and B may be gene products and binding of B by A positively regul Stage succeeding embryo, including mature structure. - In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997) BilaDO:0000003 OGES:000010 OGES:000014 @@ -28558,8 +26256,6 @@ For example, A and B may be gene products and binding of B by A positively regul - the WBls class 'all stages' belongs here as it is the superclass of other WBls stages - we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage BILS:0000105 EFO:0000399 FBdv:00007012 @@ -28610,13 +26306,11 @@ For example, A and B may be gene products and binding of B by A positively regul A stage at which the organism is a single cell produced by means of sexual reproduction. - As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG] BILS:0000106 BilaDO:0000005 EFO:0001322 EHDAA:27 FBdv:00005288 - IDOMAL:0000302 NCIT:C12601 PdumDv:0000100 VHOG:0000745 @@ -28642,24 +26336,6 @@ For example, A and B may be gene products and binding of B by A positively regul A stage at which the organism is a single cell produced by means of sexual reproduction. Wikipedia:Zygote - - - - As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG] - 2012-09-17 - VHOG:0000745 - VHOG - ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107 - http://bgee.unil.ch/ - - - - - IDOMAL:0000302 - - - https://github.com/biopragmatics/biomappings - @@ -28807,7 +26483,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -28843,14 +26519,14 @@ For example, A and B may be gene products and binding of B by A positively regul gastrula stage - + - + BILS @@ -28928,8 +26604,6 @@ For example, A and B may be gene products and binding of B by A positively regul Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system. - - In zebrafish, the times of neurulation and segmentation overlap so extensively there is no distinct neurula period of development, such as occurs largely before segmentation in amphibian embryos. BILS:0000110 BilaDO:0000009 HsapDv:0000012 @@ -29000,24 +26674,7 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - @@ -29031,11 +26688,6 @@ For example, A and B may be gene products and binding of B by A positively regul The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks). - Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO] - Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG] - oral - some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives - in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips AAO:0010355 BTO:0001090 BTO:0004698 @@ -29044,7 +26696,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA2:0001326 EHDAA:542 EMAPA:16262 - FBbt:00003126 FMA:49184 GAID:75 MA:0000341 @@ -29090,12 +26741,6 @@ For example, A and B may be gene products and binding of B by A positively regul https://github.com/obophenotype/uberon/issues/661 http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg - - - - - the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts - @@ -29103,37 +26748,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Mouth https://github.com/obophenotype/uberon/wiki/The-digestive-tract - - - - Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO] - 2012-06-20 - AAO:0010355 - AAO - AAO:BJB - - - - - Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG] - 2012-09-17 - VHOG:0000812 - VHOG - DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008) - http://bgee.unil.ch/ - - - - - in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips - FMA - - - - - FBbt:00003126 - - @@ -29315,14 +26929,11 @@ For example, A and B may be gene products and binding of B by A positively regul consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77 - Anatomical system that consists of the muscles of the body.[VSAO] - we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA AAO:0000307 BILA:0000088 BTO:0001369 BTO:0001485 EFO:0000801 - EMAPA:35578 FMA:72954 MA:0002888 MAT:0000025 @@ -29350,21 +26961,6 @@ For example, A and B may be gene products and binding of B by A positively regul The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified]. VSAO:0000033 - - - - Anatomical system that consists of the muscles of the body.[VSAO] - 2012-08-14 - VSAO:0000033 - VSAO - VSAO:curator - - - - - we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA - MA - @@ -29408,7 +27004,12 @@ For example, A and B may be gene products and binding of B by A positively regul - + + + + + + @@ -29426,7 +27027,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0000004 EHDAA2:0003004 EMAPA:35178 - FBbt:00007019 FMA:9669 HAO:0000004 MA:0002450 @@ -29450,28 +27050,12 @@ For example, A and B may be gene products and binding of B by A positively regul organism substance - - - - - - - - - this relationship may be too strong and may be weakened in future - Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007019 - - @@ -29526,7 +27110,6 @@ For example, A and B may be gene products and binding of B by A positively regul BILA:0000005 CARO:0000005 EHDAA2:0003005 - FBbt:00007017 FMA:5897 HAO:0000005 NCIT:C94478 @@ -29550,12 +27133,6 @@ For example, A and B may be gene products and binding of B by A positively regul Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures. http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007017 - - @@ -29587,7 +27164,6 @@ For example, A and B may be gene products and binding of B by A positively regul BILA:0000006 CARO:0000006 EHDAA2:0003006 - FBbt:00007016 FMA:67165 HAO:0000006 TAO:0001836 @@ -29605,12 +27181,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical entity that has mass. http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007016 - - @@ -29628,7 +27198,6 @@ For example, A and B may be gene products and binding of B by A positively regul BILA:0000007 CARO:0000007 EHDAA2:0003007 - FBbt:00007015 FMA:67112 HAO:0000007 TAO:0001835 @@ -29647,12 +27216,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical entity that has no mass. http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007015 - - @@ -29695,10 +27258,8 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA:392 EMAPA:16103 EV:0100000 - FBbt:00004856 FMA:7149 HAO:0000011 - IDOMAL:0002460 MA:0000003 NCIT:C12919 SCTID:278195005 @@ -29738,20 +27299,6 @@ For example, A and B may be gene products and binding of B by A positively regul system GO:0048731 - - - - FBbt:00004856 - - - - - - IDOMAL:0002460 - - - https://github.com/biopragmatics/biomappings - @@ -29789,7 +27336,6 @@ For example, A and B may be gene products and binding of B by A positively regul - organismal organism AAO:0010026 AEO:0000191 @@ -29804,7 +27350,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA:1 EMAPA:25765 EV:0100016 - FBbt:00000001 FMA:256135 HAO:0000012 NCIT:C13041 @@ -29849,12 +27394,6 @@ For example, A and B may be gene products and binding of B by A positively regul VHOG:0000671 WBbt:0007833 - - - - FBbt:00000001 - - @@ -29915,7 +27454,6 @@ For example, A and B may be gene products and binding of B by A positively regul EFO:0000808 EHDAA2:0003032 EMAPA:36031 - FBbt:00007009 FMA:7153 HAO:0000032 MA:0002433 @@ -29958,12 +27496,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:DOS http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007009 - - @@ -30005,7 +27537,6 @@ For example, A and B may be gene products and binding of B by A positively regul BILA:0000040 CARO:0000040 EHDAA2:0003040 - FBbt:00007013 FMA:63863 HAO:0000040 TAO:0000382 @@ -30031,12 +27562,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue. http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007013 - - @@ -30055,7 +27580,6 @@ For example, A and B may be gene products and binding of B by A positively regul - FBbt:00007277 VHOG:0001737 uberon UBERON:0000477 @@ -30069,12 +27593,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical group whose component anatomical structures lie in close proximity to each other. FBbt:00007277 - - - - FBbt:00007277 - - @@ -30107,7 +27625,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0000042 EHDAA2:0003042 EHDAA:46 - FBbt:00005835 FMA:85537 HAO:0000042 NCIT:C34055 @@ -30137,12 +27654,6 @@ For example, A and B may be gene products and binding of B by A positively regul http://orcid.org/0000-0001-9114-8737 https://cedar.bio.indiana.edu/trac/env/ontologies/ticket/279 - - - - FBbt:00005835 - - @@ -30189,7 +27700,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0000043 EHDAA2:0003043 EMAPA:35868 - FBbt:00007003 FMA:9637 HAO:0000043 MA:0003002 @@ -30225,12 +27735,6 @@ For example, A and B may be gene products and binding of B by A positively regul Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. CARO:0000043 - - - - FBbt:00007003 - - @@ -30271,7 +27775,6 @@ For example, A and B may be gene products and binding of B by A positively regul BILA:0000055 CARO:0000055 EHDAA2:0003055 - FBbt:00007010 HAO:0000055 TAO:0001488 TGMA:0001847 @@ -30298,12 +27801,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0000055 http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007010 - - @@ -30350,7 +27847,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -30358,8 +27855,6 @@ For example, A and B may be gene products and binding of B by A positively regul Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]. - The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG] - epithelial AAO:0000144 AAO:0010055 AEO:0000066 @@ -30369,7 +27864,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0000066 EHDAA2:0003066 EMAPA:32738 - FBbt:00007005 FMA:9639 GAID:402 HAO:0000066 @@ -30394,14 +27888,14 @@ For example, A and B may be gene products and binding of B by A positively regul epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg - + - + http://palaeos.com/metazoa/porifera/homoscleromorpha.html @@ -30411,22 +27905,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Epithelium http://orcid.org/0000-0001-9114-8737 - - - - The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG] - 2012-09-17 - VHOG:0000387 - VHOG - ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.59 - http://bgee.unil.ch/ - - - - - FBbt:00007005 - - @@ -30447,7 +27925,6 @@ For example, A and B may be gene products and binding of B by A positively regul Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA]. - Epithelium that consists of more than one layer of epithelial cells.[CARO] AAO:0010059 AEO:0000069 BILA:0000069 @@ -30479,16 +27956,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Stratified_epithelium http://orcid.org/0000-0001-9114-8737 - - - - Epithelium that consists of more than one layer of epithelial cells.[CARO] - 2012-06-20 - CARO:0000069 - CARO - FMA:45562 - http://orcid.org/0000-0001-9114-8737 - @@ -30510,7 +27977,6 @@ For example, A and B may be gene products and binding of B by A positively regul Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA]. consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable - Epithelium that consists of a single layer of epithelial cells.[CARO] AAO:0010062 AEO:0000073 BILA:0000073 @@ -30539,16 +28005,6 @@ For example, A and B may be gene products and binding of B by A positively regul FMA:45561 http://orcid.org/0000-0001-9114-8737 - - - - Epithelium that consists of a single layer of epithelial cells.[CARO] - 2012-06-20 - CARO:0000073 - CARO - FMA:45561 - http://orcid.org/0000-0001-9114-8737 - @@ -30603,8 +28059,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. - embryonic - Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo AAO:0011035 AEO:0000169 BILA:0000056 @@ -30616,10 +28070,8 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA2_RETIRED:0003236 EHDAA:38 EMAPA:16039 - FBbt:00000052 FMA:69068 GAID:963 - IDOMAL:0000646 MAT:0000226 MESH:D004622 MIAA:0000019 @@ -30655,26 +28107,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0009790 Wikipedia:Embryo - - - - Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo - ZFA - - - - - FBbt:00000052 - - - - - - IDOMAL:0000646 - - - https://github.com/biopragmatics/biomappings - @@ -30707,13 +28139,11 @@ For example, A and B may be gene products and binding of B by A positively regul A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm. - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] embryonic tissue AAO:0000480 BILA:0000035 BTO:0000556 EMAPA:36033 - FBbt:00000110 FMA:69069 GAID:1303 MESH:D005855 @@ -30744,28 +28174,12 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Germ_layer https://github.com/obophenotype/uberon/issues/203 - - - - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - 2012-09-17 - VHOG:0001223 - VHOG - ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 - http://bgee.unil.ch/ - embryonic tissue FMA:69069 - - - - FBbt:00000110 - - @@ -30804,11 +28218,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. - Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO] - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - ectodermal AAO:0000137 BILA:0000036 BTO:0000315 @@ -30817,7 +28228,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA2:0000428 EMAPA:16069 EV:0100003 - FBbt:00000111 FMA:69070 GAID:1304 MAT:0000155 @@ -30842,14 +28252,14 @@ For example, A and B may be gene products and binding of B by A positively regul ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -30858,31 +28268,6 @@ For example, A and B may be gene products and binding of B by A positively regul Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. Wikipedia:Ectoderm - - - - Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO] - 2012-06-20 - AAO:0000137 - AAO - AAO:EJS - - - - - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - 2012-09-17 - VHOG:0000153 - VHOG - ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 - http://bgee.unil.ch/ - - - - - FBbt:00000111 - - @@ -30908,10 +28293,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - endodermal AAO:0000139 BILA:0000038 BTO:0000800 @@ -30920,7 +28303,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA2:0000436 EMAPA:16062 EV:0100005 - FBbt:00000125 FMA:69071 GAID:1305 MAT:0000175 @@ -30945,14 +28327,14 @@ For example, A and B may be gene products and binding of B by A positively regul http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -30961,22 +28343,6 @@ For example, A and B may be gene products and binding of B by A positively regul Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. Wikipedia:Endoderm - - - - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - 2012-09-17 - VHOG:0000154 - VHOG - ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 - http://bgee.unil.ch/ - - - - - FBbt:00000125 - - @@ -31003,13 +28369,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + The middle germ layer of the embryo, between the endoderm and ectoderm. - Primary germ layer that is the middle of the embryonic germ layers.[AAO] - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - mesodermal - sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates UBERON:0003263 AAO:0000304 BILA:0000037 @@ -31022,7 +28384,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA:183 EMAPA:16083 EV:0100006 - FBbt:00000126 FMA:69072 GAID:522 MAT:0000174 @@ -31048,20 +28409,14 @@ For example, A and B may be gene products and binding of B by A positively regul mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + - - sometimes not considered primary - - - - - + Bgee:AN @@ -31070,37 +28425,6 @@ For example, A and B may be gene products and binding of B by A positively regul The middle germ layer of the embryo, between the endoderm and ectoderm. Wikipedia:Mesoderm - - - - Primary germ layer that is the middle of the embryonic germ layers.[AAO] - 2012-06-20 - AAO:0000304 - AAO - AAO:EJS - - - - - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - 2012-09-17 - VHOG:0000152 - VHOG - ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 - http://bgee.unil.ch/ - - - - - sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates - https://github.com/obophenotype/uberon/wiki/The-neural-crest - - - - - FBbt:00000126 - - @@ -31147,15 +28471,10 @@ For example, A and B may be gene products and binding of B by A positively regul Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity. consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence - Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO] - the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx - stomodeal - This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity. stomodeal-hypophyseal primordium BTO:0004224 EHDAA2:0001929 EMAPA:16263 - FBbt:00000439 FMA:295846 NCIT:C34306 TAO:0001290 @@ -31188,34 +28507,12 @@ For example, A and B may be gene products and binding of B by A positively regul http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/326 - - - - Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO] - 2012-08-14 - TAO:0001290 - TAO - ZFIN:curator - - - - - the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx - MP:0012522 - NCBITaxon:40674 - stomodeal-hypophyseal primordium XAO:0000269 - - - - FBbt:00000439 - - @@ -31294,16 +28591,12 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity. - Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO] - Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG] - endocrine AAO:0010279 CALOHA:TS-1301 EFO:0002969 EHDAA2:0002224 EMAPA:35306 EV:0100128 - FBbt:00005068 FMA:9668 GAID:439 MA:0000012 @@ -31334,31 +28627,6 @@ For example, A and B may be gene products and binding of B by A positively regul NLM:endocrine+system Wikipedia:Endocrine_system - - - - Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO] - 2012-06-20 - AAO:0010279 - AAO - AAO:BJB - - - - - Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG] - 2012-09-17 - VHOG:0000098 - VHOG - DOI:10.1073/pnas.0812138106 Markov GV, Tavares R, Dauphin-Villemant C, Demeneix BA, Baker ME, Laudet V, Independent elaboration of steroid hormone signaling pathways in metazoans. PNAS (2009) - http://bgee.unil.ch/ - - - - - FBbt:00005068 - - @@ -31384,8 +28652,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -31393,17 +28661,12 @@ For example, A and B may be gene products and binding of B by A positively regul An organ that detects light. - This class encompasses a variety of light-detecting structures from different phyla with no implication of homology, from the compound insect eye to the vertebrate camera-type eye (distinct classes are provided for each) - ocular - optic - Note that whilst this is classified as an organ, it is in fact more of a unit composed of different structures: in Drosophila, it includes the interommatidial bristle as a part; we consider here the vertebrate eye to include the eyeball/eye proper as a part, with the eye having as parts (when present): eyelids, conjuctiva, BILA:0000017 BTO:0000439 CALOHA:TS-0309 EFO:0000827 EV:0100336 - FBbt:00005162 GAID:69 MAT:0000140 MESH:D005123 @@ -31421,24 +28684,24 @@ For example, A and B may be gene products and binding of B by A positively regul eye - + - + - + PMID:21062451 - + PMID:21062451 @@ -31447,12 +28710,6 @@ For example, A and B may be gene products and binding of B by A positively regul An organ that detects light. https://orcid.org/0000-0002-6601-2165 - - - - FBbt:00005162 - - @@ -31480,8 +28737,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical structure that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO]. - Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO] - Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO] articulation joint AEO:0000182 @@ -31526,24 +28781,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Joint http://dx.plos.org/10.1371/journal.pone.0051070 - - - - Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO] - 2012-08-14 - VSAO:0000101 - VSAO - PSPUB:0000170 - - - - - Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO] - 2012-08-14 - TAO:0000367 - TAO - TAO:pem - @@ -31616,16 +28853,11 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes. - An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO] - digestive - many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class AAO:0000129 BILA:0000082 BTO:0000058 CALOHA:TS-1293 EFO:0000793 - EV:0100056 - FBbt:00005055 FMA:7152 GAID:278 MA:0002431 @@ -31662,27 +28894,6 @@ For example, A and B may be gene products and binding of B by A positively regul NLM:alimentary+system Wikipedia:Digestive_system - - - - An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO] - 2012-06-20 - AAO:0000129 - AAO - AAO:BJB - - - - - many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class - MA - - - - - FBbt:00005055 - - @@ -31716,17 +28927,12 @@ For example, A and B may be gene products and binding of B by A positively regul Organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP]. - the cardiovascular system and the lymphatic system are parts of the circulatory system - - Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO] - We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG] AAO:0000959 CALOHA:TS-2103 - MESH:D002319 VHOG:0001248 Wikipedia:Circulatory_system uberon @@ -31749,38 +28955,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Acoelomorpha - - - - - WBbt coelomocyte currently classified as circulating cell - - - - - Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO] - 2012-06-20 - AAO:0000959 - AAO - AAO:BJB - - - - - We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG] - 2012-09-17 - VHOG:0001248 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.493 - http://bgee.unil.ch/ - - - - - MESH:D002319 - - https://github.com/biopragmatics/biomappings - @@ -31808,12 +28982,8 @@ For example, A and B may be gene products and binding of B by A positively regul A subdivision of the muscular system corresponding to a subdisivision of an organism. - - In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here. - AAO:0011066 BTO:0000887 EFO:0001949 - EMAPA:32715 EMAPA:35577 FMA:32558 MA:0000165 @@ -31849,12 +29019,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Muscular_system https://orcid.org/0000-0002-6601-2165 - - - - In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here. - FMA - @@ -31918,7 +29082,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -31928,11 +29092,6 @@ For example, A and B may be gene products and binding of B by A positively regul The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]. - A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO] - Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO] - Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG] - nervous - neural AAO:0000324 BILA:0000079 BIRNLEX:844 @@ -31943,7 +29102,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA:826 EMAPA:16469 EV:0100162 - FBbt:00005093 FMA:7157 GAID:466 MA:0000016 @@ -31975,14 +29133,14 @@ For example, A and B may be gene products and binding of B by A positively regul http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -31997,40 +29155,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Nervous_system ZFIN:curator - - - - A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO] - 2012-08-14 - TAO:0000396 - TAO - ZFIN:curator - - - - - Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO] - 2012-06-20 - AAO:0000324 - AAO - AAO:BJB - - - - - Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG] - 2012-09-17 - VHOG:0000402 - VHOG - ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.117 - http://bgee.unil.ch/ - - - - - FBbt:00005093 - - @@ -32076,14 +29200,10 @@ For example, A and B may be gene products and binding of B by A positively regul - + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. - Part of the nervous system which includes the brain and spinal cord.[AAO] - The brain and spinal cord. Kimmel et al, 1995.[TAO] - The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO). - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG] AAO:0000090 BAMS:CNS BILA:0000080 @@ -32096,7 +29216,6 @@ For example, A and B may be gene products and binding of B by A positively regul EMAPA:16470 EMAPA:16754 EV:0100163 - FBbt:00005094 FMA:55675 GAID:570 MA:0000167 @@ -32125,7 +29244,7 @@ For example, A and B may be gene products and binding of B by A positively regul central nervous system - + @@ -32139,7 +29258,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + Bgee:AN @@ -32156,46 +29275,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Acoelomorpha - - - - Part of the nervous system which includes the brain and spinal cord.[AAO] - 2012-06-20 - AAO:0000090 - AAO - AAO:BJB - - - - - The brain and spinal cord. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000012 - TAO - ZFIN:curator - - - - - The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO). - BIRNLEX:1099 - - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG] - 2012-09-17 - VHOG:0000293 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 (reference 1), ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 (reference 2), DOI:10.1016/j.cell.2007.02.040 Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud'homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007) (reference 3) - http://bgee.unil.ch/ - - - - - FBbt:00005094 - - @@ -32255,15 +29334,12 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information. - An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG] - note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs AAO:0000555 BAMS:SEN BILA:0000099 EFO:0000805 EHDAA2:0003094 EMAPA:16192 - FBbt:00007692 FMA:75259 MA:0002442 MAT:0000031 @@ -32297,22 +29373,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information. Wikipedia:Sensory_system - - - - An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG] - 2012-09-17 - VHOG:0001674 - VHOG - DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) - http://bgee.unil.ch/ - - - - - FBbt:00007692 - - @@ -32370,10 +29430,6 @@ For example, A and B may be gene products and binding of B by A positively regul In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted]. - Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO] - The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG] - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] - The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium AAO:0010617 BTO:0001057 CALOHA:TS-2371 @@ -32385,7 +29441,6 @@ For example, A and B may be gene products and binding of B by A positively regul EMAPA:16757 FMA:293882 MAT:0000069 - MESH:D054259 MIAA:0000069 NCIT:C34226 SCTID:362852000 @@ -32419,49 +29474,6 @@ For example, A and B may be gene products and binding of B by A positively regul In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted]. Wikipedia:Neural_tube - - - - Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO] - 2012-06-20 - AAO:0010617 - AAO - AAO:JOR - - - - - The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG] - 2012-09-17 - VHOG:0000307 - VHOG - http://bgee.unil.ch/ - http://medical-dictionary.thefreedictionary.com/neural+tube - - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] - 2012-09-17 - VHOG:0000307 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 - http://bgee.unil.ch/ - - - - - The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium - GO:0021915 - - - - - MESH:D054259 - - - https://github.com/biopragmatics/biomappings - @@ -32492,7 +29504,6 @@ For example, A and B may be gene products and binding of B by A positively regul BIRNLEX:6 CARO:0000000 EHDAA2:0002229 - FBbt:10000000 FMA:62955 HAO:0000000 MA:0000001 @@ -32516,12 +29527,6 @@ For example, A and B may be gene products and binding of B by A positively regul FMA:62955 http://orcid.org/0000-0001-9114-8737 - - - - FBbt:10000000 - - @@ -32781,9 +29786,6 @@ For example, A and B may be gene products and binding of B by A positively regul Muscle tissue that consists primarily of skeletal muscle fibers. TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle. - Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO] - Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA] - This result implies the following views in terms of evolutionary differentiation: (1) Arthropod striated muscle and vertebrate skeletal and cardiac muscles share a common ancestor. In other words, they did not evolve independently (...) (5) The divergence of vertebrate skeletal and cardiac muscles/vertebrate smooth muscle and nonmuscle is at least before that of vertebrates/arthropods. In other words, emergence of skeletal and cardiac musle type tissues preceded the vertebrate/arthropod divergence (ca. 700 MYA).[well established][VHOG] skeletal muscle EMAPA:32716 FMA:14069 @@ -32808,32 +29810,6 @@ For example, A and B may be gene products and binding of B by A positively regul Muscle tissue that consists primarily of skeletal muscle fibers. https://github.com/obophenotype/uberon/issues/324 - - - - Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO] - 2012-08-14 - TAO:0005277 - TAO - ZFIN:curator - - - - - Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA] - FMA:14069 - FMA - - - - - This result implies the following views in terms of evolutionary differentiation: (1) Arthropod striated muscle and vertebrate skeletal and cardiac muscles share a common ancestor. In other words, they did not evolve independently (...) (5) The divergence of vertebrate skeletal and cardiac muscles/vertebrate smooth muscle and nonmuscle is at least before that of vertebrates/arthropods. In other words, emergence of skeletal and cardiac musle type tissues preceded the vertebrate/arthropod divergence (ca. 700 MYA).[well established][VHOG] - 2012-09-17 - VHOG:0000319 - VHOG - PMID:10368962 Oota S, Saitou N, Phylogenetic relationship of muscle tissues deduced from superimposition of gene trees. Mol Biol Evol (1999) - http://bgee.unil.ch/ - @@ -32905,13 +29881,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system. - - Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO] - Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO] - System that provides physical support to the organism.[AAO] - By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG] - skeletal - GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates AAO:0000566 BTO:0001486 CALOHA:TS-1320 @@ -32947,50 +29916,6 @@ For example, A and B may be gene products and binding of B by A positively regul VSAO:0000027 http://dx.plos.org/10.1371/journal.pone.0051070 - - - - Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO] - 2012-08-14 - TAO:0000434 - TAO - TAO:wd - - - - - Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO] - 2012-08-14 - VSAO:0000027 - VSAO - GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 - PSPUB:0000170 - - - - - System that provides physical support to the organism.[AAO] - 2012-06-20 - AAO:0000566 - AAO - AAO:LAP - - - - - By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG] - 2012-09-17 - VHOG:0001254 - VHOG - DOI:10.1159/000324245 Donoghue PCJ, Sansom IJ, Origin and early evolution of vertebrate skeletonization. Microscopy research and technique (2002) - http://bgee.unil.ch/ - - - - - GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates - GO - @@ -33033,18 +29958,10 @@ For example, A and B may be gene products and binding of B by A positively regul - + Skeletal element that is composed of bone tissue. - - - - Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO] - Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO] - Skeletal element that is composed of bone tissue.[VSAO] - relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] - The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG] AAO:0000047 AEO:0000082 BTO:0000140 @@ -33083,14 +30000,14 @@ For example, A and B may be gene products and binding of B by A positively regul bone element - + - + VSAO-modified @@ -33103,51 +30020,6 @@ For example, A and B may be gene products and binding of B by A positively regul http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/277 - - - - Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO] - 2012-06-20 - AAO:0000047 - AAO - AAO:LAP - - - - - Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO] - 2012-08-14 - TAO:0001514 - TAO - ZFIN:curator - - - - - Skeletal element that is composed of bone tissue.[VSAO] - 2012-08-14 - VSAO:0000057 - VSAO - PSPUB:0000170 - - - - - relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] - 2012-06-20 - AAO:0000047 - AAO - - - - - The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG] - 2012-09-17 - VHOG:0001190 - VHOG - DOI:10.1159/000324245 Murdock DJ, Donoghue PC, Evolutionary Origins of Animal Skeletal Biomineralization. Cells Tissues Organs (2011) - http://bgee.unil.ch/ - @@ -33201,16 +30073,11 @@ For example, A and B may be gene products and binding of B by A positively regul - + A tube extending from the mouth to the anus. - The alimentary or digestive tract, and associated organs.[TAO] - The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] - FMA also has a term 'gastrointestinal tract', but this includes the liver. - we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509 - we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this gut AAO:0010023 BILA:0000083 @@ -33219,10 +30086,8 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA2:0000726 EHDAA:518 EMAPA:16247 - FBbt:00003125 FMA:45615 MA:0000917 - MESH:D041981 NCIT:C34082 TAO:0000112 TGMA:0001819 @@ -33244,14 +30109,14 @@ For example, A and B may be gene products and binding of B by A positively regul digestive tract - + - + NCBIBook:NBK10107 @@ -33273,50 +30138,6 @@ For example, A and B may be gene products and binding of B by A positively regul DOI:10.1371/journal.pone.0016309 - - - - The alimentary or digestive tract, and associated organs.[TAO] - 2012-08-14 - TAO:0000112 - TAO - ZFIN:curator - - - - - The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0000309 - VHOG - ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 - http://bgee.unil.ch/ - - - - - FMA also has a term 'gastrointestinal tract', but this includes the liver. - FMA - - - - - we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509 - MA - - - - - FBbt:00003125 - - - - - - MESH:D041981 - - https://github.com/biopragmatics/biomappings - @@ -33367,12 +30188,7 @@ For example, A and B may be gene products and binding of B by A positively regul Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]. - Portion of tissue composed of contractile fibers.[TAO] - It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG] - muscular muscle - AAO:0011066 - EMAPA:32715 EMAPA:37474 EV:0100146 FMA:5022 @@ -33398,25 +30214,6 @@ For example, A and B may be gene products and binding of B by A positively regul Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]. GO:0007517 - - - - Portion of tissue composed of contractile fibers.[TAO] - 2012-08-14 - TAO:0005145 - TAO - ZFIN:curator - - - - - It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG] - 2012-09-17 - VHOG:0001245 - VHOG - ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.75 - http://bgee.unil.ch/ - @@ -33454,7 +30251,6 @@ For example, A and B may be gene products and binding of B by A positively regul Muscle tissue that contains fibers that are divided by transverse bands into striations. - Voluntary muscle tissue arranged in bundles of fibers.[AAO] AAO:0010762 AEO:0000140 CALOHA:TS-2047 @@ -33482,15 +30278,6 @@ For example, A and B may be gene products and binding of B by A positively regul GOC:dph GOC:mtg_muscle - - - - Voluntary muscle tissue arranged in bundles of fibers.[AAO] - 2012-06-20 - AAO:0010762 - AAO - AAO:CAM - @@ -33522,16 +30309,11 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical structure that is part of an embryo. - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO] - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO] - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO] - in FMA embryo is_a embryonic structure AAO:0000138 BILA:0000034 BTO:0000174 CALOHA:TS-2110 EFO:0000461 - FBbt:00004208 FMA:69067 GAID:407 MESH:D004628 @@ -33562,45 +30344,6 @@ For example, A and B may be gene products and binding of B by A positively regul BTO:0000174 ZFIN:curator - - - - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO] - 2012-06-20 - AAO:0000138 - AAO - AAO:BJB - - - - - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO] - 2012-08-14 - TAO:0001105 - TAO - ZFIN:curator - - - - - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO] - 2012-08-14 - VSAO:0000178 - VSAO - ZFIN:curator - - - - - in FMA embryo is_a embryonic structure - FMA - - - - - FBbt:00004208 - - @@ -33646,10 +30389,6 @@ For example, A and B may be gene products and binding of B by A positively regul Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present. - - - Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO] - Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO] AAO:0010339 BILA:0000116 BTO:0001493 @@ -33689,32 +30428,6 @@ For example, A and B may be gene products and binding of B by A positively regul UBERONREF:0000006 Wikipedia:Torso - - - - - ZFA - https://github.com/obophenotype/uberon/issues/378 - pending - - - - - Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO] - 2012-06-20 - AAO:0010339 - AAO - AAO:BJB - - - - - Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO] - 2012-08-14 - TAO:0001115 - TAO - ZFIN:curator - @@ -33747,7 +30460,6 @@ For example, A and B may be gene products and binding of B by A positively regul The sensory system subserving the sense of vision. - The sensory system used for sight.[AAO] UBERON:0007036 AAO:0000632 BILA:0000140 @@ -33777,15 +30489,6 @@ For example, A and B may be gene products and binding of B by A positively regul The sensory system subserving the sense of vision. NIFSTD:FMAID_7191 - - - - The sensory system used for sight.[AAO] - 2012-06-20 - AAO:0000632 - AAO - AAO:EJS - @@ -33861,7 +30564,12 @@ For example, A and B may be gene products and binding of B by A positively regul - + + + + + + @@ -33873,9 +30581,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that consists of the muscular and skeletal systems. - Anatomical system that provides locomotion and physical support to the organism.[AAO] - There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG] - musculoskeletal AAO:0010546 CALOHA:TS-1311 EMAPA:32714 @@ -33897,16 +30602,6 @@ For example, A and B may be gene products and binding of B by A positively regul musculoskeletal system - - - - - - - - - check ctenophore - @@ -33915,25 +30610,6 @@ For example, A and B may be gene products and binding of B by A positively regul VSAO:curator https://github.com/obophenotype/uberon/issues/77 - - - - Anatomical system that provides locomotion and physical support to the organism.[AAO] - 2012-06-20 - AAO:0010546 - AAO - AAO:EJS - - - - - There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG] - 2012-09-17 - VHOG:0001275 - VHOG - DOI:10.1002/jez.b.21246 Shearman RM, Burke AC, The lateral somitic frontier in ontogeny and phylogeny. Journal of Experimental Zoology (2009) - http://bgee.unil.ch/ - @@ -33948,6 +30624,7 @@ For example, A and B may be gene products and binding of B by A positively regul + @@ -33955,21 +30632,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - + + + @@ -33983,13 +30648,6 @@ For example, A and B may be gene products and binding of B by A positively regul A flexible rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In some chordates, it persists throughout life as the main axial support of the body, while in most vertebrates it becomes the nucleus pulposus of the intervertebral disc. The notochord is found ventral to the neural tube. - Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO] - Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO] - Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO] - relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO] - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG] - notochordal - In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord. AAO:0000327 BTO:0001768 CALOHA:TS-0690 @@ -34024,15 +30682,15 @@ For example, A and B may be gene products and binding of B by A positively regul notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + @@ -34051,19 +30709,19 @@ For example, A and B may be gene products and binding of B by A positively regul - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -34076,51 +30734,6 @@ For example, A and B may be gene products and binding of B by A positively regul https://github.com/obophenotype/uberon/issues/25 https://github.com/obophenotype/uberon/issues/271 - - - - Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO] - 2012-08-14 - VSAO:0000032 - VSAO - PSPUB:0000170 - - - - - Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000135 - TAO - ZFIN:curator - - - - - Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO] - 2012-06-20 - AAO:0000327 - AAO - AAO:LAP - - - - - relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO] - 2012-06-20 - AAO:0000327 - AAO - - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG] - 2012-09-17 - VHOG:0000199 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 - http://bgee.unil.ch/ - @@ -34148,18 +30761,10 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. - EDITOR_NOTE currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk - Post-cranial axial segments which form sclerotome and dermomyotome.[AAO] - Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO] - relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO] - relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO] - relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO] - (...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG] - somitic mesodermal cluster AAO:0010569 AEO:0001015 @@ -34195,11 +30800,11 @@ For example, A and B may be gene products and binding of B by A positively regul somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + @@ -34212,13 +30817,13 @@ For example, A and B may be gene products and binding of B by A positively regul - + GOTAX:0000352 - + ZFA @@ -34234,58 +30839,6 @@ For example, A and B may be gene products and binding of B by A positively regul PMID:17237766 - - - - Post-cranial axial segments which form sclerotome and dermomyotome.[AAO] - 2012-06-20 - AAO:0010569 - AAO - AAO:EJS - - - - - Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000155 - TAO - ZFIN:curator - - - - - relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO] - 2012-08-14 - TAO:0000155 - TAO - - - - - relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO] - 2012-08-14 - TAO:0000155 - TAO - - - - - relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO] - 2012-06-20 - AAO:0010569 - AAO - - - - - (...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0000191 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.40, DOI:10.1093/icb/43.1.137 Balavoine G, Adoutte A, The segmented urbilateria: a testable scenario. Integrative and Comparative Biology (2003) - http://bgee.unil.ch/ - @@ -34394,20 +30947,25 @@ For example, A and B may be gene products and binding of B by A positively regul + - - - - - - + + + + + + + + + + + + + + + + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. - EDITOR_NOTE consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams). - - A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO] - Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO] - A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831] - We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG] AAO:0010578 BTO:0001764 CALOHA:TS-0676 @@ -34420,7 +30978,6 @@ For example, A and B may be gene products and binding of B by A positively regul MIAA:0000066 NCIT:C34222 SCTID:361462002 - TAO:0000045 UMLS:C0027789 VHOG:0000057 Wikipedia:Neural_crest @@ -34440,66 +30997,45 @@ For example, A and B may be gene products and binding of B by A positively regul http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - - - - - + - + - - - - - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - - Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells - ISBN:0073040584 - - - - - + BTO - + PMID:11523831 - - pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest - - - - - + PMID:11523831 @@ -34508,47 +31044,6 @@ For example, A and B may be gene products and binding of B by A positively regul A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. MP:0009846 - - - - - ISBN:0073040584 - PMID:17377535 - - - - - A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000045 - TAO - ZFIN:curator - - - - - Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO] - 2012-06-20 - AAO:0010578 - AAO - AAO:EJS - - - - - A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831] - PMID:11523831 - - - - - We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG] - 2012-09-17 - VHOG:0000057 - VHOG - DOI:10.1111/j.1469-7580.2012.01495.x Hall BK, Gillis JA, Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues. J Anat (2012) - http://bgee.unil.ch/ - @@ -34590,9 +31085,6 @@ For example, A and B may be gene products and binding of B by A positively regul Embryonic ectoderm that gives rise to nervous tissue. - (...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG] - neurectodermal - we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here AAO:0011074 BILA:0000039 CALOHA:TS-1212 @@ -34601,7 +31093,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA:255 EMAPA:16073 EV:0100004 - FBbt:00001057 FMA:87657 MAT:0000176 MIAA:0000176 @@ -34630,22 +31121,6 @@ For example, A and B may be gene products and binding of B by A positively regul Embryonic ectoderm that gives rise to nervous tissue. Wikipedia:Neuroectoderm - - - - (...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG] - 2012-09-17 - VHOG:0000150 - VHOG - DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) - http://bgee.unil.ch/ - - - - - FBbt:00001057 - - @@ -34854,13 +31329,14 @@ For example, A and B may be gene products and binding of B by A positively regul + - + @@ -34883,8 +31359,6 @@ For example, A and B may be gene products and binding of B by A positively regul TODO - create superclass for bone marrow / head kidney. both are portions of tissue in the hematopoetic system. also consider adding as subclass of zone of bone organ for consistency with FMA. See also: Leydig and epigonal organs consider placement of NCIT:C53466 medullary bone - The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG] - In adults, marrow in large bones produces new blood cells[Wikipedia:Bone_marrow] AAO:0011007 BTO:0000141 BTO:0000829 @@ -34918,14 +31392,14 @@ For example, A and B may be gene products and binding of B by A positively regul bone marrow http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg - + - + FMA MA @@ -34936,16 +31410,6 @@ For example, A and B may be gene products and binding of B by A positively regul MGI:cwg MP:0002397 - - - - The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG] - 2012-09-17 - VHOG:0001218 - VHOG - DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood Cells and Blood Cell Development in the Animal Kingdom. Annual Review of Cell and Developmental Biology (2006) - http://bgee.unil.ch/ - @@ -34989,10 +31453,6 @@ For example, A and B may be gene products and binding of B by A positively regul Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance. - One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO] - Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO] - Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO] - MA also has set of connective tissues AAO:0000098 BTO:0000421 CALOHA:TS-2009 @@ -35033,40 +31493,6 @@ For example, A and B may be gene products and binding of B by A positively regul http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/23 - - - - One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO] - 2012-06-20 - AAO:0000098 - AAO - AAO:LAP - - - - - Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO] - 2012-08-14 - TAO:0001641 - TAO - TAO:wd - - - - - Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO] - 2012-08-14 - VSAO:0000017 - VSAO - GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 - PSPUB:0000170 - - - - - MA also has set of connective tissues - MA - @@ -35129,8 +31555,6 @@ For example, A and B may be gene products and binding of B by A positively regul Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]. - - One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO] AAO:0000306 AEO:0000122 CALOHA:TS-0642 @@ -35161,15 +31585,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Muscle_tissue https://sourceforge.net/tracker/index.php?func=detail&aid=2801266&group_id=36855&atid=440764 - - - - One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO] - 2012-06-20 - AAO:0000306 - AAO - AAO:LAP - @@ -35196,22 +31611,23 @@ For example, A and B may be gene products and binding of B by A positively regul - + - + + + + + + Anatomical system that is involved in the production of hematopoietic cells. - Anatomical system that consists of the blood and blood forming tissues.[AAO] - Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG] - hematopoietic - In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes AAO:0011002 BTO:0000570 CALOHA:TS-0449 @@ -35249,57 +31665,22 @@ For example, A and B may be gene products and binding of B by A positively regul hematopoietic system - + - - - - - + FMA - - - - - definitional - Anatomical system that is involved in the production of hematopoietic cells. Wikipedia:Haematopoiesis - - - - Anatomical system that consists of the blood and blood forming tissues.[AAO] - 2012-06-20 - AAO:0011002 - AAO - AAO:EJS - - - - - Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG] - 2012-09-17 - VHOG:0001624 - VHOG - DOI:10.1016/j.coph.2010.05.004 Ellett F, Lieschke GJ, Zebrafish as a model for vertebrate hematopoiesis. Current Opinion in Pharmacology (2010) - http://bgee.unil.ch/ - - - - - In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes - WP - @@ -35340,7 +31721,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies. - The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG] AAO:0011003 BILA:0000104 BTO:0005810 @@ -35370,16 +31750,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies. Wikipedia:Immune_system - - - - The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG] - 2012-09-17 - VHOG:0001247 - VHOG - PMID:21046016 Dzik JM, The ancestry and cumulative evolution of immune reactions. Acta biochimica Polonica (2010) - http://bgee.unil.ch/ - @@ -35408,7 +31778,6 @@ For example, A and B may be gene products and binding of B by A positively regul Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts. see https://github.com/obophenotype/uberon/issues/27 - Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO] CALOHA:TS-2011 EMAPA:35179 FMA:224804 @@ -35448,16 +31817,6 @@ For example, A and B may be gene products and binding of B by A positively regul VSAO:0000047 http://dx.plos.org/10.1371/journal.pone.0051070 - - - - Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO] - 2012-08-14 - VSAO:0000047 - VSAO - GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 - PSPUB:0000170 - @@ -35514,18 +31873,13 @@ For example, A and B may be gene products and binding of B by A positively regul An organ that functions as a secretory or excretory organ. - - glandular AAO:0000212 AEO:0000096 BTO:0000522 EFO:0000797 EHDAA2:0003096 EHDAA:2161 - EHDAA:4475 - EHDAA:6522 EMAPA:18425 - FBbt:00100317 FMA:7146 FMA:86294 HAO:0000375 @@ -35556,12 +31910,6 @@ For example, A and B may be gene products and binding of B by A positively regul MGI:csmith MP:0002163 - - - - FBbt:00100317 - - @@ -35603,7 +31951,6 @@ For example, A and B may be gene products and binding of B by A positively regul In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA]. MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class - In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG] BTO:0004593 FMA:296704 MAT:0000067 @@ -35631,16 +31978,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Epiblast ZFIN:curator - - - - In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG] - 2012-09-17 - VHOG:0000243 - VHOG - DOI:10.1146/annurev.cellbio.042308.113344 Zorn AM, Wells JM, Vertebrate endoderm development and organ formation. Annual Review of Cell Developmental Biology (2009) - http://bgee.unil.ch/ - @@ -35738,10 +32075,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. - Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO] - It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG] AAO:0011086 EFO:0001982 EMAPA:16189 @@ -35763,14 +32098,14 @@ For example, A and B may be gene products and binding of B by A positively regul presomitic mesoderm - + - + Bgee:AN @@ -35779,25 +32114,6 @@ For example, A and B may be gene products and binding of B by A positively regul Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. ZFIN:curator - - - - Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000279 - TAO - ZFIN:curator - - - - - It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG] - 2012-09-17 - VHOG:0000559 - VHOG - DOI:10.1006/dbio.2001.0460 Schubert M, Holland LZ, Dale Stokes M and Holland ND, Three Amphoxius Wnt Genes (AmphiWnt3, AmphiWnt5, and AmphiWnt6) Associated with the Tail Bud: the Evolution of Somitogenesis in Chordates. Developmental Biology (2001) - http://bgee.unil.ch/ - @@ -35836,11 +32152,6 @@ For example, A and B may be gene products and binding of B by A positively regul Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted]. - Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO] - Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO] - relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO] - Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG] - EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac ventral lateral plate mesoderm AAO:0011006 EFO:0003489 @@ -35873,48 +32184,6 @@ For example, A and B may be gene products and binding of B by A positively regul Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted]. Wikipedia:Blood_island_of_umbilical_vesicle - - - - Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000094 - TAO - ZFIN:curator - - - - - Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO] - 2012-06-20 - AAO:0011006 - AAO - AAO:EJS - - - - - relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO] - 2012-08-14 - TAO:0000094 - TAO - - - - - Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0000085 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450, DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual Review of Cell and Developmental Biology (2006) - http://bgee.unil.ch/ - - - - - EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac - EHDAA2 - @@ -35953,7 +32222,6 @@ For example, A and B may be gene products and binding of B by A positively regul The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord. - The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] AAO:0011017 EFO:0003647 TAO:0001204 @@ -35976,15 +32244,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0048318 Wikipedia:Chordamesoderm - - - - The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] - 2012-09-17 - VHOG:0000107 - VHOG - http://bgee.unil.ch/ - @@ -36000,12 +32259,10 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. - The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO] - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] AAO:0011072 BTO:0001765 DHBA:10153 @@ -36014,7 +32271,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA:902 EMAPA:35593 FMA:293879 - MESH:D054258 NCIT:C34225 RETIRED_EHDAA2:0001252 TAO:0000132 @@ -36034,34 +32290,34 @@ For example, A and B may be gene products and binding of B by A positively regul neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -36073,33 +32329,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Neural_plate ZFIN:curator - - - - The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000132 - TAO - ZFIN:curator - - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] - 2012-09-17 - VHOG:0000068 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 - http://bgee.unil.ch/ - - - - - MESH:D054258 - - - https://github.com/biopragmatics/biomappings - @@ -36122,23 +32351,14 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. - Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO] - Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG] - note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here) AAO:0010568 EFO:0003515 EMAPA:16183 @@ -36163,7 +32383,7 @@ For example, A and B may be gene products and binding of B by A positively regul paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -36176,7 +32396,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + Bgee:AN @@ -36186,31 +32406,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0048339 https://github.com/obophenotype/uberon/issues/30 - - - - Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO] - 2012-06-20 - AAO:0010568 - AAO - AAO:EJS - - - - - Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG] - 2012-09-17 - VHOG:0000114 - VHOG - DOI:10.1002/dvdy.21177 Kusakabe R and Kuratani S. Evolutionary perspectives from development of mesodermal components in the lamprey. Developmental dynamics (2007) - http://bgee.unil.ch/ - - - - - note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here) - ZFA - @@ -36248,7 +32443,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -36262,10 +32457,6 @@ For example, A and B may be gene products and binding of B by A positively regul Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]. - Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO] - The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] - A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG] - subclass of mesoderm in ZFA. UBERON:0006258 AAO:0010574 EHDAA2:0000919 @@ -36292,7 +32483,7 @@ For example, A and B may be gene products and binding of B by A positively regul lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -36305,7 +32496,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + EHDAA2 VHOG @@ -36316,40 +32507,6 @@ For example, A and B may be gene products and binding of B by A positively regul MP:0010117 Wikipedia:Lateral_plate_mesoderm - - - - Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO] - 2012-06-20 - AAO:0010574 - AAO - AAO:EJS - - - - - The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] - 2012-09-17 - VHOG:0000118 - VHOG - http://bgee.unil.ch/ - - - - - A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG] - 2012-09-17 - VHOG:0000118 - VHOG - DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) - http://bgee.unil.ch/ - - - - - subclass of mesoderm in ZFA. - ZFA - @@ -36389,7 +32546,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -36398,8 +32555,6 @@ For example, A and B may be gene products and binding of B by A positively regul A transitional population of migrating mesenchymal cells that derive from somites and that will become muscle cells. The term 'myotome' is also used to describe the muscles served by a single nerve root / spinal segment - consider adding new class, myomere. - Portion of the somites giving rise to body wall muscle masses. Kimmel et al, 1995.[TAO] - In all vertebrates, the skeletal muscle of the body axis is chiefly derived from an early embryonic compartment, known as the myotome.[well established][VHOG] AAO:0011067 AEO:0001018 BTO:0000742 @@ -36432,7 +32587,7 @@ For example, A and B may be gene products and binding of B by A positively regul myotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + @@ -36445,7 +32600,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + EHDAA2-abduced @@ -36454,25 +32609,6 @@ For example, A and B may be gene products and binding of B by A positively regul A transitional population of migrating mesenchymal cells that derive from somites and that will become muscle cells. AEO:0001018 - - - - Portion of the somites giving rise to body wall muscle masses. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0001056 - TAO - ZFIN:curator - - - - - In all vertebrates, the skeletal muscle of the body axis is chiefly derived from an early embryonic compartment, known as the myotome.[well established][VHOG] - 2012-09-17 - VHOG:0001244 - VHOG - DOI:10.1038/sj.embor.embor920 Hollway GE, Currie PD, Myotome meanderings. Cellular morphogenesis and the making of muscle. EMBO Rep.(2003) - http://bgee.unil.ch/ - @@ -36501,7 +32637,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types. - this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs AAO:0010015 AEO:0000024 BILA:0000024 @@ -36565,9 +32700,6 @@ For example, A and B may be gene products and binding of B by A positively regul Portion of tissue composed of mesenchymal cells (motile cells that develop from epthelia via an epithelial to mesenchymal transition) and surrounding extracellular material. Mesenchyme has different embryological origins in different metazoan taxa - in many invertebrates it derives in whole or part from ectoderm. In vertebrates it derives largely from mesoderm, and sometimes the terms are used interchangeably, e.g. lateral plate mesoderm/mesenchyme. the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense - A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO] - Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO] - mesenchymal AAO:0010427 AEO:0000145 BTO:0001393 @@ -36602,24 +32734,6 @@ For example, A and B may be gene products and binding of B by A positively regul https://en.wikipedia.org/wiki/Mesenchyme https://github.com/obophenotype/uberon/issues/1641 - - - - A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000393 - TAO - ZFIN:curator - - - - - Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO] - 2012-06-20 - AAO:0010427 - AAO - AAO:EJS - @@ -36646,10 +32760,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults - (...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG] EHDAA:251 EMAPA:16088 NCIT:C34195 @@ -36662,14 +32775,14 @@ For example, A and B may be gene products and binding of B by A positively regul intraembryonic coelom - + - + Wikipedia @@ -36679,16 +32792,6 @@ For example, A and B may be gene products and binding of B by A positively regul MGI:anna MP:0012187 - - - - (...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG] - 2012-09-17 - VHOG:0000316 - VHOG - ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.166 - http://bgee.unil.ch/ - @@ -36721,10 +32824,8 @@ For example, A and B may be gene products and binding of B by A positively regul Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. - contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers AEO:0000114 EHDAA2:0003114 - FBbt:00007474 epithelial or endothelial tube uberon UBERON:0003914 @@ -36737,12 +32838,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0060562 PMID:12526790 - - - - FBbt:00007474 - - @@ -36788,7 +32883,6 @@ For example, A and B may be gene products and binding of B by A positively regul - FMA has both conduit and conduit space. In EHDAA2 this is a surface feature AEO:0000080 EHDAA2:0003080 FMA:242873 @@ -36810,12 +32904,6 @@ For example, A and B may be gene products and binding of B by A positively regul Any tube, opening or passage that connects two distinct anatomical spaces. http://orcid.org/0000-0002-6601-2165 - - - - FMA has both conduit and conduit space. In EHDAA2 this is a surface feature - FMA - @@ -36860,7 +32948,6 @@ For example, A and B may be gene products and binding of B by A positively regul An anatomical structure that develops (entirely or partially) from the mesoderm. - Grouping term for query purposes mesodermal derivative uberon UBERON:0004120 @@ -36904,7 +32991,6 @@ For example, A and B may be gene products and binding of B by A positively regul An anatomical structure that develops (entirely or partially) from the ectoderm. - Grouping term for query purposes ectodermal deriviative uberon UBERON:0004121 @@ -36944,10 +33030,7 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body. - - Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO] - skeletal AEO:0000168 EHDAA2:0001843 EHDAA:5047 @@ -36980,15 +33063,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body. VSAO:0000026 - - - - Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO] - 2012-08-14 - VSAO:0000026 - VSAO - GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 - @@ -37003,13 +33077,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + The bilaminar epithelium formed from the myotome and dermatome. - Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768]. - Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO] - Portion of somites that gives rise to dermis and muscles.[AAO] - all but the sclerotome of a mesodermal somite; the primordium of skeletal muscle and, perhaps, of the dermis. - Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic.[well established][VHOG] AAO:0010572 AEO:0000214 EHDAA2:0003259 @@ -37026,7 +33095,7 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0004290 dermomyotome - + @@ -37045,7 +33114,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + EHDAA2 ZFA @@ -37055,46 +33124,6 @@ For example, A and B may be gene products and binding of B by A positively regul The bilaminar epithelium formed from the myotome and dermatome. AEO:0000214 - - - - Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768]. - http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768 - - - - - Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO] - 2012-08-14 - TAO:0001513 - TAO - ZFIN:curator - - - - - Portion of somites that gives rise to dermis and muscles.[AAO] - 2012-06-20 - AAO:0010572 - AAO - AAO:EJS - - - - - all but the sclerotome of a mesodermal somite; the primordium of skeletal muscle and, perhaps, of the dermis. - http://medical-dictionary.thefreedictionary.com/dermomyotome - - - - - Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic.[well established][VHOG] - 2012-09-17 - VHOG:0000676 - VHOG - DOI:10.1111/j.1525-142X.2006.05079.x Devoto SH, Stoiber W, Hammond CL, Steinbacher P, Haslett JR, Barresi MJF, Patterson SE, Adiarte EG and Hughes SM, Generality of vertebrate developmental patterns: evidence for a dermomyotome in fish. Evolution and Development (2006) - http://bgee.unil.ch/ - @@ -37134,7 +33163,6 @@ For example, A and B may be gene products and binding of B by A positively regul Sum of all sensory systems in an organism. - note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs FMA:78499 sense organ system uberon @@ -37250,11 +33278,9 @@ For example, A and B may be gene products and binding of B by A positively regul Organism at the gastrula stage. - We explicitly merge the NCITA terms here UBERON:0007012 BILA:0000060 BTO:0001403 - FBbt:00005317 FMA:293108 GAID:1302 MESH:D005775 @@ -37286,18 +33312,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Gastrula Wikipedia:Trilaminar_blastocyst - - - - We explicitly merge the NCITA terms here - NCIT - - - - - FBbt:00005317 - - @@ -37377,9 +33391,13 @@ For example, A and B may be gene products and binding of B by A positively regul - + + + + + + A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]. - A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO] EMAPA:37744 MA:0003047 SCTID:309311006 @@ -37391,24 +33409,12 @@ For example, A and B may be gene products and binding of B by A positively regul Four classes of mineralized tissues are found in vertebrates: bone, cartilage, dentine, and enamel. We think of cartilage and bone as skeletal tissues and of enamel and dentine as dental tissues, but enamel and dentine arose evolutionarily together with bone as skeletal tissues in the dermal skeleton (exoskeleton) of early vertebrates. Scales and teeth of sharks are examples of dermal skeletal elements that are still composed of the three ancient components-enamel, dentine, and bone. Cartilage, on the other hand, provided the basis for the second vertebrate skeletal system, the endoskeleton (Smith and Hall, 1990; Hall, 1998a,b). some invertebrate skeletal tissues have surprisingly bone-like features. Examples include chondrocytes interconnected by cell processes in cephalopod cartilages (Cole and Hall, 2004a,b), and the calcium phosphate layer in the shells of brachiopods (Rodland et al., 2003). However, neither bone nor mineralized cartilage have been found in invertebrates. Editors notes: TODO - develops_from skeletal tissue - - - - VSAO - - - - - 2012-08-14 - VSAO:0000015 - VSAO - @@ -37419,17 +33425,6 @@ For example, A and B may be gene products and binding of B by A positively regul http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/134 - - - - A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO] - 2012-08-14 - VSAO:0000015 - taken from version of VSAO used in TAO and used directly in Uberon - VSAO - GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 - PSPUB:0000170 - @@ -37443,10 +33438,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. - Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO] - Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO] AAO:0011129 TAO:0001890 VSAO:0000128 @@ -37459,14 +33452,14 @@ For example, A and B may be gene products and binding of B by A positively regul skeletal element - + - + VSAO @@ -37475,24 +33468,6 @@ For example, A and B may be gene products and binding of B by A positively regul Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. https://orcid.org/0000-0002-6601-2165 - - - - Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO] - 2012-08-14 - VSAO:0000128 - VSAO - PSPUB:0000170 - - - - - Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO] - 2012-08-14 - TAO:0001890 - TAO - TAO:VSAO_workshop - @@ -37511,7 +33486,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -37550,14 +33525,14 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0004770 articular system - + - + FMA @@ -37604,8 +33579,6 @@ For example, A and B may be gene products and binding of B by A positively regul The central region of trunk mesoderm. This tissue forms the notochord. - Notochord rudiment[ZFIN:ZDB-PUB-961014-576]. - WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord. AAO:0000478 EFO:0003426 TAO:0000091 @@ -37626,12 +33599,6 @@ For example, A and B may be gene products and binding of B by A positively regul The central region of trunk mesoderm. This tissue forms the notochord. https://orcid.org/0000-0002-6601-2165 - - - - Notochord rudiment[ZFIN:ZDB-PUB-961014-576]. - ZFIN:ZDB-PUB-961014-576 - @@ -37664,7 +33631,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts. - FBbt:00005811 joint uberon UBERON:0004905 @@ -37677,12 +33643,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts. http://orcid.org/0000-0002-6601-2165 - - - - FBbt:00005811 - - @@ -37714,9 +33674,7 @@ For example, A and B may be gene products and binding of B by A positively regul A proximal-distal subdivision of the digestive tract. - intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct. - FBbt:00100315 FMA:71131 uberon alimentary system subdivision @@ -37735,12 +33693,6 @@ For example, A and B may be gene products and binding of B by A positively regul A proximal-distal subdivision of the digestive tract. http://orcid.org/0000-0002-6601-2165 - - - - FBbt:00100315 - - @@ -37805,7 +33757,6 @@ For example, A and B may be gene products and binding of B by A positively regul The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds. - The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]. AAO:0011071 EMAPA:35594 FMA:295624 @@ -37827,12 +33778,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Neural_groove http://orcid.org/0000-0002-6601-2165 - - - - The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]. - Wikipedia:Neural_groove - @@ -37848,6 +33793,7 @@ For example, A and B may be gene products and binding of B by A positively regul + @@ -37855,14 +33801,7 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - One of the two elevated edges of the neural groove[GO,MP]. - In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]. EHDAA2:0001249 FMA:295618 NCIT:C34223 @@ -37885,12 +33824,6 @@ For example, A and B may be gene products and binding of B by A positively regul MP:0011256 Wikipedia:Neural_fold - - - - In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]. - Wikipedia:Neural_fold - @@ -37917,7 +33850,6 @@ For example, A and B may be gene products and binding of B by A positively regul A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN]. - An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO] EFO:0003498 TAO:0000133 ZFA:0000133 @@ -37934,15 +33866,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0014024 ZFA:0000133 - - - - An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000133 - TAO - ZFIN:curator - @@ -37969,8 +33892,6 @@ For example, A and B may be gene products and binding of B by A positively regul Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO]. - in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila - EMAPA:32715 FMA:30316 musculus uberon @@ -38038,7 +33959,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -38054,14 +33975,14 @@ For example, A and B may be gene products and binding of B by A positively regul trunk mesenchyme - + - + EHDAA2 @@ -38163,7 +34084,6 @@ For example, A and B may be gene products and binding of B by A positively regul An array of photoreceptors and any supporting cells found in an eye. - FBbt:00004200 light-sensitive tissue uberon UBERON:0005388 @@ -38175,12 +34095,6 @@ For example, A and B may be gene products and binding of B by A positively regul An array of photoreceptors and any supporting cells found in an eye. https://orcid.org/0000-0002-6601-2165 - - - - FBbt:00004200 - - @@ -38200,7 +34114,6 @@ For example, A and B may be gene products and binding of B by A positively regul AEO:0000125 CALOHA:TS-2122 EHDAA2:0003125 - FBbt:00007006 FMA:292313 MIAA:0000019 uberon @@ -38211,12 +34124,6 @@ For example, A and B may be gene products and binding of B by A positively regul developing anatomical structure - - - - FBbt:00007006 - - @@ -38302,7 +34209,6 @@ For example, A and B may be gene products and binding of B by A positively regul An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina. - this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell. AAO:0010596 FMA:63872 @@ -38372,10 +34278,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB - The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG] EHDAA2:0001278 EHDAA:264 EMAPA:16101 @@ -38387,7 +34292,7 @@ For example, A and B may be gene products and binding of B by A positively regul notochordal plate - + @@ -38400,7 +34305,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + EHDAA2 @@ -38409,15 +34314,6 @@ For example, A and B may be gene products and binding of B by A positively regul The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. VHOG:0001212 - - - - The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG] - 2012-09-17 - VHOG:0001212 - VHOG - http://bgee.unil.ch/ - @@ -38437,7 +34333,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -38454,14 +34350,14 @@ For example, A and B may be gene products and binding of B by A positively regul The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -38725,12 +34621,6 @@ For example, A and B may be gene products and binding of B by A positively regul Old definition: 'Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.' Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism. anatomical surface - - - - - via morphological boundary in CARO - @@ -38831,7 +34721,6 @@ For example, A and B may be gene products and binding of B by A positively regul - The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis BILA:0000084 NCIT:C34268 SCTID:360394002 @@ -38847,12 +34736,6 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0007026 presumptive gut - - - - The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis - NCBIBook:NBK10107 - @@ -38883,10 +34766,13 @@ For example, A and B may be gene products and binding of B by A positively regul - + + + + + + A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]. - note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis - SPD:0000130 TADS:0000147 http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg dorsal tube @@ -38898,16 +34784,6 @@ For example, A and B may be gene products and binding of B by A positively regul Gene notes: Bmp, Nkx, Gata primary circulatory organ - - - - - - - - - GO uses blood circulation generically to include the haemolymphatic fluid of arthropods - @@ -38946,7 +34822,6 @@ For example, A and B may be gene products and binding of B by A positively regul An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. - An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO] EFO:0003497 TAO:0000131 ZFA:0000131 @@ -38962,15 +34837,6 @@ For example, A and B may be gene products and binding of B by A positively regul An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. ZFIN:ZDB-PUB-961014-576 - - - - An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000131 - TAO - ZFIN:curator - @@ -38995,7 +34861,12 @@ For example, A and B may be gene products and binding of B by A positively regul - + + + + + + @@ -39012,17 +34883,6 @@ For example, A and B may be gene products and binding of B by A positively regul presumptive segmental plate - - - - - - - - - https://github.com/obophenotype/uberon/wiki/The-neural-crest - EDHAA2 - @@ -39074,7 +34934,6 @@ For example, A and B may be gene products and binding of B by A positively regul A presumptive structure that has the potential to develop into a neural plate. consider merging - Region of the gastrula which gives rise to the neural plate.[TAO] EFO:0003424 TAO:0000063 ZFA:0000063 @@ -39091,15 +34950,6 @@ For example, A and B may be gene products and binding of B by A positively regul A presumptive structure that has the potential to develop into a neural plate. OBOL:automatic - - - - Region of the gastrula which gives rise to the neural plate.[TAO] - 2012-08-14 - TAO:0000063 - TAO - ZFIN:curator - @@ -39118,7 +34968,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -39144,7 +34994,7 @@ For example, A and B may be gene products and binding of B by A positively regul presumptive paraxial mesoderm - + @@ -39160,7 +35010,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + https://github.com/obophenotype/uberon/issues/1277 @@ -39209,7 +35059,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -39217,7 +35067,7 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0007524 dense mesenchyme tissue - + @@ -39230,7 +35080,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + AEO @@ -39309,8 +35159,6 @@ For example, A and B may be gene products and binding of B by A positively regul Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts). - Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).[VSAO] - Regular connective tissue, the intercellular matrix of which consists predominantly of collagen fiber bundles arranged in parallel arrays.[FMA] FMA:64781 NCIT:C33453 SCTID:22560007 @@ -39348,24 +35196,6 @@ For example, A and B may be gene products and binding of B by A positively regul VSAO:0000050 http://dx.plos.org/10.1371/journal.pone.0051070 - - - - Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).[VSAO] - 2012-08-14 - VSAO:0000050 - VSAO - GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 - PSPUB:0000170 - - - - - Regular connective tissue, the intercellular matrix of which consists predominantly of collagen fiber bundles arranged in parallel arrays.[FMA] - 2012-08-29 - FMA:64781 - FMA - @@ -39409,7 +35239,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -39426,14 +35256,14 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -39455,7 +35285,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -39463,14 +35293,14 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -39520,7 +35350,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0010000 - FBbt:00100313 multicellular structure uberon UBERON:0010000 @@ -39534,12 +35363,6 @@ For example, A and B may be gene products and binding of B by A positively regul An anatomical structure that has more than one cell as a part. CARO:0010000 - - - - FBbt:00100313 - - @@ -39576,6 +35399,42 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + + + + + + + + + + + + An anatomical structure that has some part that develops from the neural crest. + uberon + UBERON:0010314 + + structure with developmental contribution from neural crest + + + + + An anatomical structure that has some part that develops from the neural crest. + https://orcid.org/0000-0002-6601-2165 + + + + @@ -39679,7 +35538,6 @@ For example, A and B may be gene products and binding of B by A positively regul - FBbt:00007330 FMA:67509 SCTID:91690000 uberon @@ -39701,12 +35559,6 @@ For example, A and B may be gene products and binding of B by A positively regul A subdivision of an anatomical system. http://orcid.org/0000-0002-6601-2165 - - - - FBbt:00007330 - - @@ -39791,7 +35643,6 @@ For example, A and B may be gene products and binding of B by A positively regul Irregular connective tissue is an irregular connective tissue, the intercellular matrix of which contains a dense irregular network of collagen and elastic fiber bundles. Examples: connective tissue of peritoneum, connective tissue of fibrous pericardium. - Tissue characterized by a thick, random arrangement of collagen and elastin fibers with very few cells. The majority of the cells are fibroblasts, but mast cells and macrophages may also be seen. It is found in the dermis, periosteum, perichondrium, capsules of organs and sheaths of nerves and muscles[NCIT] FMA:20109 NCIT:C32882 UMLS:C0738366 @@ -39815,14 +35666,6 @@ For example, A and B may be gene products and binding of B by A positively regul FMA:20109 Wikipedia:Dense_irregular_connective_tissue - - - - Tissue characterized by a thick, random arrangement of collagen and elastin fibers with very few cells. The majority of the cells are fibroblasts, but mast cells and macrophages may also be seen. It is found in the dermis, periosteum, perichondrium, capsules of organs and sheaths of nerves and muscles[NCIT] - 2012-08-29 - ncithesaurus:Irregular_Dense_Connective_Tissue - NCIT - @@ -39862,7 +35705,6 @@ For example, A and B may be gene products and binding of B by A positively regul Dense connective tissue is mainly composed of collagen type I. Crowded between the collagen fibers are rows of fibroblasts, fiber-forming cells, that manufacture the fibers. Dense connective tissue forms strong, rope-like structures such as tendons and ligaments. Tendons attach skeletal muscles to bones; ligaments connect bones to bones at joints. Ligaments are more stretchy and contain more elastic fibers than tendons. Dense connective tissue also make up the lower layers of the skin (dermis), where it is arranged in sheets. our OWL definition states that this is differentiated from other connective tissue types by virtue of the fact that the collage fiber component predominates, as opposed to cells and fluid. - Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT] AAO:0000121 NCIT:C32450 UMLS:C1511770 @@ -39877,14 +35719,6 @@ For example, A and B may be gene products and binding of B by A positively regul Dense connective tissue is mainly composed of collagen type I. Crowded between the collagen fibers are rows of fibroblasts, fiber-forming cells, that manufacture the fibers. Dense connective tissue forms strong, rope-like structures such as tendons and ligaments. Tendons attach skeletal muscles to bones; ligaments connect bones to bones at joints. Ligaments are more stretchy and contain more elastic fibers than tendons. Dense connective tissue also make up the lower layers of the skin (dermis), where it is arranged in sheets. Wikipedia:Dense_connective_tissue - - - - Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT] - 2012-08-29 - ncithesaurus:Dense_Connective_Tissue - NCIT - @@ -39911,7 +35745,6 @@ For example, A and B may be gene products and binding of B by A positively regul - the FMA class specifically refers to ureter FMA:63212 MESH:D024022 NCIT:C32339 @@ -39927,20 +35760,15 @@ For example, A and B may be gene products and binding of B by A positively regul ZFA - - - - the FMA class specifically refers to ureter - FMA - + - + @@ -39954,7 +35782,6 @@ For example, A and B may be gene products and binding of B by A positively regul Epimysium is a layer of connective tissue which ensheaths the entire muscle. It is composed of dense irregular connective tissue. It is continuous with fascia and other connective tissue wrappings of muscle including the endomysium, and perimysium. It is also continuous with tendons where it becomes thicker and collagenous. - The Epimysium also protects muscles from friction against other muscles and bones FMA:9726 NCIT:C32527 UMLS:C0504096 @@ -39965,7 +35792,7 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0011899 epimysium - + @@ -39978,7 +35805,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + FMA @@ -40022,7 +35849,6 @@ For example, A and B may be gene products and binding of B by A positively regul The aggregate of the coelemic cavity lumen plus the membranes that line the lumen. EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining. - coelomic EHDAA2:0004731 Wikipedia:Coelom enterocoelom @@ -40083,8 +35909,9 @@ For example, A and B may be gene products and binding of B by A positively regul + - + @@ -40092,7 +35919,6 @@ For example, A and B may be gene products and binding of B by A positively regul Blood-forming tissue, consisting of reticular fibers and cells. - Bone marrow in humans, kidney interstitium in Danio, within a stroma of reticuloendothelial tissue CALOHA:TS-2142 FMA:14073 NCIT:C13051 @@ -40106,7 +35932,7 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0012429 hematopoietic tissue - + @@ -40119,7 +35945,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + defitional @@ -40282,10 +36108,8 @@ For example, A and B may be gene products and binding of B by A positively regul The region of the organism associated with the visceral organs. - Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]. AEO:0000103 BTO:0001489 - EMAPA:36031 FMA:231424 uberon body @@ -40306,12 +36130,6 @@ For example, A and B may be gene products and binding of B by A positively regul The region of the organism associated with the visceral organs. AEO:0000103 - - - - Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]. - FMA:231424 - @@ -40432,7 +36250,6 @@ For example, A and B may be gene products and binding of B by A positively regul An anatomical group whose component structures share a common function. AEO:0000093 - FBbt:00007278 uberon UBERON:0015203 non-connected functional system @@ -40446,12 +36263,6 @@ For example, A and B may be gene products and binding of B by A positively regul FBC:DOS FBbt:00007278 - - - - FBbt:00007278 - - @@ -40494,24 +36305,7 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - @@ -40519,7 +36313,6 @@ For example, A and B may be gene products and binding of B by A positively regul Any structure that is placed on one side of the left-right axis of a bilaterian. - This class is primarily to implement taxon constraints. It may be removed in the future. uberon UBERON:0015212 @@ -40553,7 +36346,6 @@ For example, A and B may be gene products and binding of B by A positively regul A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile. heart - SPD:0000130 cardiac pump heart or heart like organ circulatory vessel @@ -40701,7 +36493,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -40724,7 +36516,7 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0016887 entire extraembryonic component - + @@ -40737,7 +36529,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + AEO @@ -40823,7 +36615,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -40834,21 +36626,20 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA2:0001842 EMAPA:35578 - MA:0000165 uberon UBERON:0018254 skeletal musculature - + - + MA @@ -40943,7 +36734,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0020000 - FBbt:00007276 uberon UBERON:0034923 @@ -40961,12 +36751,6 @@ For example, A and B may be gene products and binding of B by A positively regul Material anatomical entity consisting of multiple anatomical structures that are not connected to each other. CARO:0020000 - - - - FBbt:00007276 - - @@ -41156,7 +36940,6 @@ For example, A and B may be gene products and binding of B by A positively regul - example to be eventually removed example to be eventually removed @@ -41165,9 +36948,7 @@ For example, A and B may be gene products and binding of B by A positively regul - failed exploratory term The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job - Person:Alan Ruttenberg failed exploratory term @@ -41176,7 +36957,6 @@ For example, A and B may be gene products and binding of B by A positively regul - metadata complete Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. metadata complete @@ -41186,7 +36966,6 @@ For example, A and B may be gene products and binding of B by A positively regul - organizational term Term created to ease viewing/sort terms for development purpose, and will not be included in a release organizational term @@ -41196,7 +36975,6 @@ For example, A and B may be gene products and binding of B by A positively regul - ready for release Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release @@ -41206,7 +36984,6 @@ For example, A and B may be gene products and binding of B by A positively regul - metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete @@ -41216,7 +36993,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated @@ -41226,7 +37002,6 @@ For example, A and B may be gene products and binding of B by A positively regul - pending final vetting All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting @@ -41236,7 +37011,6 @@ For example, A and B may be gene products and binding of B by A positively regul - placeholder removed placeholder removed @@ -41245,7 +37019,6 @@ For example, A and B may be gene products and binding of B by A positively regul - terms merged An editor note should explain what were the merged terms and the reason for the merge. terms merged @@ -41255,7 +37028,6 @@ For example, A and B may be gene products and binding of B by A positively regul - term imported This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. term imported @@ -41265,7 +37037,6 @@ For example, A and B may be gene products and binding of B by A positively regul - term split This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. term split @@ -41275,10 +37046,7 @@ For example, A and B may be gene products and binding of B by A positively regul - universal Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. - Alan Ruttenberg - A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf universal @@ -41287,10 +37055,8 @@ For example, A and B may be gene products and binding of B by A positively regul - defined class A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. - Alan Ruttenberg defined class @@ -41299,10 +37065,8 @@ For example, A and B may be gene products and binding of B by A positively regul - named class expression A named class expression is a logical expression that is given a name. The name can be used in place of the expression. named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions - Alan Ruttenberg named class expression @@ -41311,10 +37075,7 @@ For example, A and B may be gene products and binding of B by A positively regul - to be replaced with external ontology term Terms with this status should eventually replaced with a term from another ontology. - Alan Ruttenberg - group:OBI to be replaced with external ontology term @@ -41323,10 +37084,7 @@ For example, A and B may be gene products and binding of B by A positively regul - requires discussion A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. - Alan Ruttenberg - group:OBI requires discussion @@ -41337,9 +37095,7 @@ For example, A and B may be gene products and binding of B by A positively regul The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. - https://github.com/information-artifact-ontology/ontology-metadata/issues/77 - https://orcid.org/0000-0001-5208-3432 out of scope @@ -41395,24 +37151,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - @@ -41454,46 +37192,34 @@ For example, A and B may be gene products and binding of B by A positively regul /////////////////////////////////////////////////////////////////////////////////////// --> - - - - + - - - - - - - - - - + - + - + - + - + - + - + - + - + @@ -41520,8 +37246,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41531,7 +37257,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -41541,7 +37267,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -41558,67 +37284,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - true - GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' - involved in BP - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + @@ -41636,8 +37303,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41647,8 +37314,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41658,8 +37325,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41676,8 +37343,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41694,8 +37361,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41705,8 +37372,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41716,8 +37383,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41734,8 +37401,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41752,8 +37419,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41763,8 +37430,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41774,8 +37441,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41792,8 +37459,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41810,8 +37477,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41821,8 +37488,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41837,8 +37504,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41855,8 +37522,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41866,8 +37533,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41882,8 +37549,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41900,8 +37567,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41911,8 +37578,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41927,8 +37594,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41945,8 +37612,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41956,8 +37623,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41972,8 +37639,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41990,8 +37657,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -42001,8 +37668,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -42017,8 +37684,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -42078,8 +37745,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -42089,8 +37756,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -42105,8 +37772,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -42121,9 +37788,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + @@ -42133,8 +37800,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -42148,9 +37815,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + @@ -42165,9 +37832,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + @@ -42177,8 +37844,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -42192,7 +37859,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + diff --git a/src/ontology/subsets/general_cell_types_upper_slim.tsv b/src/ontology/subsets/general_cell_types_upper_slim.tsv index a0a6dd677..6d53c2d02 100644 --- a/src/ontology/subsets/general_cell_types_upper_slim.tsv +++ b/src/ontology/subsets/general_cell_types_upper_slim.tsv @@ -1,275 +1,273 @@ ?x ?label -_:B9ac295d7X2Ded0bX2D4368X2D889cX2D7714613be411genid1047 -_:B9ac295d7X2Ded0bX2D4368X2D889cX2D7714613be411genid1054 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a/src/ontology/subsets/kidney_upper_slim.json b/src/ontology/subsets/kidney_upper_slim.json index 84c2067cc..f32433dec 100644 --- a/src/ontology/subsets/kidney_upper_slim.json +++ b/src/ontology/subsets/kidney_upper_slim.json @@ -4,9 +4,9 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-02-13" + "val" : "2024-04-05" } ], - "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-02-13/subsets/kidney_upper_slim.owl" + "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-04-05/subsets/kidney_upper_slim.owl" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/BFO_0000002", @@ -78,18 +78,6 @@ "val" : "BFO:0000050" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "is part of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my brain is part of my body (continuant parthood, two material entities)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this day is part of this year (occurrent parthood)" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." }, { @@ -98,42 +86,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "part_of" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000002" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000003" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000004" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000017" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000019" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000020" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000031" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "part_of" @@ -164,18 +122,6 @@ "val" : "BFO:0000051" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has part" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my body has part my brain (continuant parthood, two material entities)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this year has part this day (occurrent parthood)" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." }, { @@ -184,21 +130,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has_part" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_part" @@ -217,26 +154,11 @@ "val" : "BFO:0000062" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "preceded by" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is preceded by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "preceded_by" - }, { - "pred" : "http://purl.org/dc/terms/source", - "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "preceded_by" @@ -255,14 +177,8 @@ "val" : "BFO:0000063" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "precedes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "precedes" @@ -282,26 +198,11 @@ "val" : "BFO:0000066" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "occurs in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "occurs_in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "unfolds in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "unfolds_in" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "occurs_in" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Occurs_in" @@ -315,412 +216,12 @@ "definition" : { "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" }, - "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ], - "xrefs" : [ { - "val" : "BFO:0000067" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "site of" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "contains_process" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - } ] + "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000141", "lbl" : "immaterial entity", "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000096", - "lbl" : "anterior to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000096" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "anterior_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000097", - "lbl" : "distal to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000097" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "distal_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000098", - "lbl" : "dorsal to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000098" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dorsal_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000099", - "lbl" : "posterior to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000099" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "posterior_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000100", - "lbl" : "proximal to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000100" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "proximal_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000102", - "lbl" : "ventral to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000102" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "ventral_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000107", - "lbl" : "deep to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000107" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "deep_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000108", - "lbl" : "superficial to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000108" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "superficial_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000120", - "lbl" : "in left side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000120" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_left_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000121", - "lbl" : "in right side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000121" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_right_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000122", - "lbl" : "in posterior side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000122" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_posterior_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000123", - "lbl" : "in anterior side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000123" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_anterior_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000124", - "lbl" : "in proximal side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000124" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_proximal_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "lbl" : "in lateral side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000126" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_lateral_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001100", - "lbl" : "in superficial part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001100" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_superficial_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001101", - "lbl" : "in deep part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001101" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_deep_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001106", - "lbl" : "proximalmost part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001106" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "proximalmost_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001107", - "lbl" : "immediately deep to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001107" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "immediately_deep_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001108", - "lbl" : "distalmost part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001108" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "distalmost_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001113", - "lbl" : "preaxialmost part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001113" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "preaxialmost_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001115", - "lbl" : "postaxialmost part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001115" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "postaxialmost_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0005001", - "lbl" : "intersects midsagittal plane of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0005001" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "intersects_midsagittal_plane_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0015014", - "lbl" : "immediately superficial to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0015014" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "immediately_superficial_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0015101", - "lbl" : "in dorsal side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0015101" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_dorsal_side_of" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000000", "lbl" : "cell", @@ -3018,7 +2519,8 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A cell that is part of a renal medulla." + "val" : "A cell that is part of a renal medulla.", + "xrefs" : [ "PMID:22343825" ] }, "xrefs" : [ { "val" : "KUPO:0001017" @@ -3123,6 +2625,10 @@ "lbl" : "kidney interstitial fibroblast", "type" : "CLASS", "meta" : { + "definition" : { + "val" : "A fibroblast that is part of an interstitial compartment of a kidney.", + "xrefs" : [ "PMID:10559635" ] + }, "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "KUPO:0001102" @@ -3174,6 +2680,10 @@ "lbl" : "kidney blood vessel cell", "type" : "CLASS", "meta" : { + "definition" : { + "val" : "A blood vessel cell that is part of a kidney.", + "xrefs" : [ "PMID:34843404" ] + }, "xrefs" : [ { "val" : "KUPO:0001014" } ] @@ -11124,13 +10634,7 @@ }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000002", "lbl" : "example to be eventually removed", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "example to be eventually removed" - } ] - } + "type" : "INDIVIDUAL" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000028", "lbl" : "symbol", @@ -11142,14 +10646,7 @@ "meta" : { "definition" : { "val" : "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "failed exploratory term" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person:Alan Ruttenberg" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000115", @@ -11160,20 +10657,8 @@ "val" : "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "definition" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2012-04-05: \nBarry Smith\n\nThe official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. \n\nOn the specifics of the proposed definition:\n\nWe don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Daniel Schober" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" } ] } }, { @@ -11183,32 +10668,7 @@ "meta" : { "definition" : { "val" : "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology." - }, - "xrefs" : [ { - "val" : "IAO:0000116" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "editor note" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Daniel Schober" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "editor_note" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000120", @@ -11217,11 +10677,7 @@ "meta" : { "definition" : { "val" : "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "metadata complete" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000121", @@ -11230,11 +10686,7 @@ "meta" : { "definition" : { "val" : "Term created to ease viewing/sort terms for development purpose, and will not be included in a release" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "organizational term" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000122", @@ -11243,11 +10695,7 @@ "meta" : { "definition" : { "val" : "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\"" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "ready for release" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000123", @@ -11256,11 +10704,7 @@ "meta" : { "definition" : { "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "metadata incomplete" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000124", @@ -11269,11 +10713,7 @@ "meta" : { "definition" : { "val" : "Nothing done yet beyond assigning a unique class ID and proposing a preferred term." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "uncurated" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000125", @@ -11282,31 +10722,18 @@ "meta" : { "definition" : { "val" : "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "pending final vetting" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000226", "lbl" : "placeholder removed", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "placeholder removed" - } ] - } + "type" : "INDIVIDUAL" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000227", "lbl" : "terms merged", "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "terms merged" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "An editor note should explain what were the merged terms and the reason for the merge." } ] @@ -11317,9 +10744,6 @@ "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "term imported" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use." } ] @@ -11330,9 +10754,6 @@ "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "term split" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created." } ] @@ -11344,17 +10765,7 @@ "meta" : { "definition" : { "val" : "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has obsolescence reason" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Melanie Courtot" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000233", @@ -11369,29 +10780,8 @@ "val" : "IAO:0000233" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "term tracker item" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_class_level", - "val" : "true" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", "val" : "true" @@ -11406,17 +10796,8 @@ "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "universal" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf" } ] } }, { @@ -11428,14 +10809,8 @@ "val" : "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "defined class" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" } ] } }, { @@ -11447,14 +10822,8 @@ "val" : "A named class expression is a logical expression that is given a name. The name can be used in place of the expression." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "named class expression" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" } ] } }, { @@ -11464,17 +10833,7 @@ "meta" : { "definition" : { "val" : "Terms with this status should eventually replaced with a term from another ontology." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "to be replaced with external ontology term" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "group:OBI" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000424", @@ -11483,17 +10842,7 @@ "meta" : { "definition" : { "val" : "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "expand expression to" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "ObjectProperty: RO_0002104\nLabel: has plasma membrane part\nAnnotations: IAO_0000424 \"http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\"\n" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000428", @@ -11502,17 +10851,7 @@ "meta" : { "definition" : { "val" : "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "requires discussion" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "group:OBI" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000700", @@ -11526,20 +10865,8 @@ "val" : "IAO:0000700" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has ontology root term" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Nicolas Matentzoglu" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_class_level", - "val" : "true" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", "val" : "true" @@ -11556,20 +10883,7 @@ "definition" : { "val" : "Use on obsolete terms, relating the term to another term that can be used as a substitute" }, - "comments" : [ "Add as annotation triples in the granting ontology" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "term replaced by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person:Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Person:Alan Ruttenberg" - } ] + "comments" : [ "Add as annotation triples in the granting ontology" ] } }, { "id" : "http://purl.obolibrary.org/obo/NCBITaxon_1", @@ -11604,9 +10918,6 @@ "val" : "PMID:15371245" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_family" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11621,7 +10932,7 @@ "pred" : "hasExactSynonym", "val" : "Mus" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003003", + "synonymType" : "http://purl.obolibrary.org/obo/ncbitaxon#genbank_common_name", "pred" : "hasExactSynonym", "val" : "mice" }, { @@ -11633,9 +10944,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_genus" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11658,9 +10966,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_species" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "NCBITaxon:85055" }, { @@ -11677,9 +10982,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11698,9 +11000,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "NCBITaxon:40673" }, { @@ -11735,9 +11034,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11760,9 +11056,6 @@ "val" : "PMID:11791233" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11785,9 +11078,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_suborder" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11834,9 +11124,6 @@ "val" : "PMID:30257078" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_superkingdom" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11858,9 +11145,6 @@ "val" : "PMID:15522813" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_superorder" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11885,9 +11169,6 @@ "val" : "PMID:15522813" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11906,9 +11187,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11927,9 +11205,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11948,9 +11223,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11973,9 +11245,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -12006,9 +11275,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_kingdom" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -12022,9 +11288,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -12043,9 +11306,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -12063,9 +11323,6 @@ "val" : "PMID:15371245" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -12079,9 +11336,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_subfamily" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "NCBITaxon:109679" }, { @@ -12107,9 +11361,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_class" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -12123,9 +11374,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -12148,9 +11396,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_phylum" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -12177,9 +11422,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -12202,9 +11444,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -12218,9 +11457,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_superclass" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -12239,9 +11475,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_subgenus" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -12260,9 +11493,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_subphylum" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -12297,9 +11527,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -12322,9 +11549,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_order" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -12340,15 +11564,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/77" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", - "val" : "https://orcid.org/0000-0001-5208-3432" } ] } }, { @@ -12360,9 +11578,6 @@ "val" : "Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'part disjoint with' 'defined by construct' \"\"\"\n PREFIX owl: \n PREFIX : some (\n and some (\n and some (\n and some ?Y)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { @@ -15493,33 +14274,9 @@ "definition" : { "val" : "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " }, - "xrefs" : [ { - "val" : "RO:0002103" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that part_of some ( that has_part some ( that some Y?)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "synapsed_by" } ] } }, { @@ -15531,29 +14288,8 @@ "val" : "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9990-8331" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-1617-8244" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19243617" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( and some ?Y)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] } }, { @@ -15565,26 +14301,8 @@ "val" : "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. " }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "synapsed in" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (\n http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some (\n http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { @@ -15596,20 +14314,8 @@ "val" : "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "synapses in" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that some ( that some Y?)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { @@ -15622,23 +14328,8 @@ }, "comments" : [ "N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part some (\n ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( \n\t‘synapse ; GO:0045202’ that has_part some (\n\t ‘post-synaptic membrane ; GO:0045211’ that part_of some N2))))" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that part_of some ( that some ( that some Y?)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { @@ -15650,23 +14341,8 @@ "val" : "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has synapse in" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that some Y?)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { @@ -15682,20 +14358,11 @@ "val" : "RO:0002131" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "overlaps" @@ -15708,26 +14375,7 @@ "meta" : { "definition" : { "val" : "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has fasciculating component" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", - "val" : "(forall (?x ?y) \n\t(iff \n\t\t(has_fasciculating_neuron_projection ?x ?y)\n\t\t(exists (?nps ?npbs)\t\t\n\t\t\t(and \n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?x)\n\t\t\t\t(\"neuron projection ; GO0043005\" ?y)\n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n\t\t\t\t(part_of ?nps ?y)\n\t\t\t\t(part_of ?npbs ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))\n\n\n" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002134", @@ -15737,30 +14385,9 @@ "definition" : { "val" : "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." }, - "xrefs" : [ { - "val" : "RO:0002134" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that ( some ( that some Y?)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "innervates" } ] } }, { @@ -15771,31 +14398,7 @@ "definition" : { "val" : "X continuous_with Y if and only if X and Y share a fiat boundary." }, - "xrefs" : [ { - "val" : "RO:0002150" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "connected to" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "continuous_with" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "FMA:85972" } ] @@ -15808,23 +14411,7 @@ "definition" : { "val" : "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." }, - "comments" : [ "VBO calls this homologous_to" ], - "xrefs" : [ { - "val" : "RO:0002158" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Consider obsoleting and merging with child relation, 'in homology relationship with'" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "homologous_to" - } ] + "comments" : [ "VBO calls this homologous_to" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -15834,33 +14421,9 @@ "definition" : { "val" : "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." }, - "xrefs" : [ { - "val" : "RO:0002160" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "lactation SubClassOf 'only in taxon' some 'Mammalia'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "only_in_taxon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" @@ -15868,48 +14431,15 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002161", - "lbl" : "never_in_taxon", + "lbl" : "never in taxon", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL." }, - "xrefs" : [ { - "val" : "RO:0002161" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "tooth SubClassOf 'never in taxon' value 'Aves'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", - "val" : "Class: EquivalentTo: ?X and (RO_0002162 some ?Y)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", - "val" : "Class: ?X DisjointWith: RO_0002162 some ?Y " - }, { "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_class_level", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "never_in_taxon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" @@ -15925,31 +14455,7 @@ }, "comments" : [ "Connects a biological entity to its taxon of origin." ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002162" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9227-417X" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_taxon" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] @@ -15964,26 +14470,11 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" @@ -15997,22 +14488,7 @@ "definition" : { "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" }, - "xrefs" : [ { - "val" : "RO:0002170" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "connected_to" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" }, { @@ -16022,42 +14498,16 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002175", - "lbl" : "present_in_taxon", + "lbl" : "present in taxon", "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S" }, "comments" : [ "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "applicable for taxon" - } ], - "xrefs" : [ { - "val" : "RO:0002175" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_class_level", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "present_in_taxon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" @@ -16071,25 +14521,7 @@ "definition" : { "val" : "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." }, - "xrefs" : [ { - "val" : "RO:0002176" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The M8 connects Glasgow and Edinburgh" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "connects" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" }, { @@ -16104,20 +14536,7 @@ "meta" : { "definition" : { "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." - }, - "xrefs" : [ { - "val" : "RO:0002177" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "attached to part of (anatomical structure to anatomical structure)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "attaches_to_part_of" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002178", @@ -16127,21 +14546,9 @@ "definition" : { "val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." }, - "xrefs" : [ { - "val" : "RO:0002178" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "supplies" } ] } }, { @@ -16152,21 +14559,9 @@ "definition" : { "val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." }, - "xrefs" : [ { - "val" : "RO:0002179" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "drains" } ] } }, { @@ -16182,23 +14577,11 @@ "val" : "RO:0002180" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_component" @@ -16215,32 +14598,7 @@ "definition" : { "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" }, - "comments" : [ "This is the transitive form of the develops from relation" ], - "xrefs" : [ { - "val" : "RO:0002202" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9114-8737" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-1980-3228" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "develops_from" - } ] + "comments" : [ "This is the transitive form of the develops from relation" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002203", @@ -16250,29 +14608,7 @@ "definition" : { "val" : "inverse of develops from" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "xrefs" : [ { - "val" : "RO:0002203" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-1980-3228" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "develops_into" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002206", @@ -16281,17 +14617,7 @@ "meta" : { "definition" : { "val" : "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002207", @@ -16305,31 +14631,6 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "has developmental precursor" - } ], - "xrefs" : [ { - "val" : "RO:0002207" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "FBbt" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002202" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "directly_develops_from" } ] } }, { @@ -16340,14 +14641,7 @@ "definition" : { "val" : "inverse of directly develops from" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "developmental precursor of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002211", @@ -16362,30 +14656,6 @@ "val" : "RO:0002211" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-7476-6306" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-3837-8864" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GO" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Regulation precludes parthood; the regulatory process may not be within the regulated process." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "regulates (processual)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "false" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16406,15 +14676,6 @@ "val" : "RO:0002212" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "negatively regulates (process to process)" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002211" }, { @@ -16438,18 +14699,6 @@ "val" : "RO:0002213" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "positively regulates (process to process)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002211" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16470,32 +14719,8 @@ "val" : "RO:0002215" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "osteoclast SubClassOf 'capable of' some 'bone resorption'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has function realized in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20123131" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/21208450" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "capable_of" @@ -16513,17 +14738,8 @@ "val" : "RO:0002216" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has function in" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "capable_of_part_of" @@ -16539,26 +14755,7 @@ "meta" : { "definition" : { "val" : "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" - }, - "xrefs" : [ { - "val" : "RO:0002219" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "surrounded_by" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002220", @@ -16573,35 +14770,11 @@ "val" : "RO:0002220" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The epidermis layer of a vertebrate is adjacent to the dermis." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This relation acts as a join point with BSPO" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "adjacent_to" @@ -16615,26 +14788,7 @@ "definition" : { "val" : "inverse of surrounded by" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "xrefs" : [ { - "val" : "RO:0002221" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "surrounds" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002222", @@ -16642,23 +14796,7 @@ "type" : "PROPERTY", "meta" : { "comments" : [ "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations." ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://en.wikipedia.org/wiki/Allen%27s_interval_algebra" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." - }, { - "pred" : "http://purl.org/dc/terms/source", - "val" : "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002223", @@ -16668,29 +14806,7 @@ "definition" : { "val" : "inverse of starts with" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002223" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Allen" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "starts" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002224", @@ -16705,26 +14821,8 @@ "val" : "RO:0002224" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "started by" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "starts_with" @@ -16737,23 +14835,7 @@ "meta" : { "definition" : { "val" : "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" - }, - "xrefs" : [ { - "val" : "RO:0002225" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "develops_from_part_of" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002226", @@ -16762,29 +14844,7 @@ "meta" : { "definition" : { "val" : "x develops_in y if x is located in y whilst x is developing" - }, - "xrefs" : [ { - "val" : "RO:0002226" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "EHDAA2" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Jonathan Bard, EHDAA2" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "develops_in" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002229", @@ -16794,26 +14854,7 @@ "definition" : { "val" : "inverse of ends with" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002229" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "ends" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002230", @@ -16828,23 +14869,8 @@ "val" : "RO:0002230" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "finished by" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "ends_with" @@ -16863,15 +14889,6 @@ "val" : "RO:0002231" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "starts with process that occurs in" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16892,15 +14909,6 @@ "val" : "RO:0002232" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "ends with process that occurs in" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16921,15 +14929,6 @@ "val" : "RO:0002233" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "consumes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16953,15 +14952,6 @@ "val" : "RO:0002234" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "produces" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16980,22 +14970,7 @@ "definition" : { "val" : "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." }, - "xrefs" : [ { - "val" : "RO:0002252" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004036", - "val" : "http://purl.obolibrary.org/obo/BFO_0000050" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "connecting_branch_of" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/issues/2212" } ] @@ -17008,11 +14983,7 @@ "definition" : { "val" : "inverse of connecting branch of" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004036", - "val" : "http://purl.obolibrary.org/obo/BFO_0000051" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002254", @@ -17021,26 +14992,7 @@ "meta" : { "definition" : { "val" : "x has developmental contribution from y iff x has some part z such that z develops from y" - }, - "xrefs" : [ { - "val" : "RO:0002254" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_developmental_contribution_from" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002255", @@ -17050,14 +15002,7 @@ "definition" : { "val" : "inverse of has developmental contribution from" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002256", @@ -17066,44 +15011,7 @@ "meta" : { "definition" : { "val" : "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" - }, - "xrefs" : [ { - "val" : "RO:0002256" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9114-8737" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "induced by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GO:0001759" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "developmentally_induced_by" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002257", @@ -17112,14 +15020,7 @@ "meta" : { "definition" : { "val" : "Inverse of developmentally induced by" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002258", @@ -17131,17 +15032,8 @@ }, "comments" : [ "This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "false" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "In general you should not use this relation to make assertions - use one of the more specific relations below this one" } ] } }, { @@ -17154,9 +15046,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of" } ] @@ -17175,9 +15064,6 @@ "val" : "affects" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within" } ] @@ -17190,27 +15076,9 @@ "definition" : { "val" : "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" }, - "xrefs" : [ { - "val" : "RO:0002285" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "replaces" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "developmentally_replaces" } ] } }, { @@ -17220,31 +15088,12 @@ "meta" : { "definition" : { "val" : "Inverse of developmentally preceded by" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002287", "lbl" : "part of developmental precursor of", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002292", "lbl" : "expresses", @@ -17252,14 +15101,7 @@ "meta" : { "definition" : { "val" : "y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002295", @@ -17273,14 +15115,8 @@ "val" : "RO:0002295" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" @@ -17305,18 +15141,6 @@ "val" : "RO:0002296" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "every flower development (GO:0009908) results in development of some flower (PO:0009046)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.geneontology.org/GO.doc.development.shtml" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17326,7 +15150,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -17334,21 +15158,6 @@ "val" : "RO:0002297" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:mtg_berkeley_2013" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17369,21 +15178,6 @@ "val" : "RO:0002298" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:mtg_berkeley_2013" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17404,21 +15198,6 @@ "val" : "RO:0002299" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:mtg_berkeley_2013" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17440,12 +15219,6 @@ "val" : "RO:0002304" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002411" - }, { - "pred" : "http://purl.org/dc/terms/creator", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17471,9 +15244,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002411" - }, { - "pred" : "http://purl.org/dc/terms/creator", - "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" @@ -17496,18 +15266,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "inheres in part of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" @@ -17526,15 +15284,6 @@ "val" : "RO:0002315" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:mtg_berkeley_2013" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17549,14 +15298,7 @@ "meta" : { "definition" : { "val" : "A relationship that holds via some environmental process" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002323", @@ -17565,17 +15307,7 @@ "meta" : { "definition" : { "val" : "A mereological relationship or a topological relationship" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002324", @@ -17584,14 +15316,7 @@ "meta" : { "definition" : { "val" : "A relationship that holds between entities participating in some developmental process (GO:0032502)" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002327", @@ -17603,30 +15328,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a particular instances of akt-2 enables some instance of protein kinase activity" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "catalyzes" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "executes" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is catalyzing" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is executing" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Enables" } ] @@ -17638,23 +15339,7 @@ "meta" : { "definition" : { "val" : "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." - }, - "xrefs" : [ { - "val" : "RO:0002328" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This is a grouping relation that collects relations used for the purpose of connecting structure and function" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "functionally_related_to" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002329", @@ -17663,14 +15348,7 @@ "meta" : { "definition" : { "val" : "this relation holds between c and p when c is part of some c', and c' is capable of p." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "false" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002330", @@ -17679,14 +15357,7 @@ "meta" : { "definition" : { "val" : "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002331", @@ -17697,15 +15368,6 @@ "val" : "c involved_in p if and only if c enables some process p', and p' is part of p" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "actively involved in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "enables part of" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Involved_in" } ] @@ -17722,18 +15384,6 @@ "val" : "RO:0002332" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "regulates levels of (process to entity)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17751,9 +15401,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Enabled_by" } ] @@ -17771,12 +15418,6 @@ "val" : "RO:0002334" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "regulated by (processual)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17797,9 +15438,6 @@ "val" : "RO:0002335" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17820,9 +15458,6 @@ "val" : "RO:0002336" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17837,14 +15472,7 @@ "meta" : { "definition" : { "val" : "A relationship that holds via some process of localization" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is a grouping relation." - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002338", @@ -17859,9 +15487,6 @@ "val" : "RO:0002338" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17882,9 +15507,6 @@ "val" : "RO:0002339" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17904,9 +15526,6 @@ "val" : "RO:0002341" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17927,9 +15546,6 @@ "val" : "RO:0002342" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17946,12 +15562,6 @@ "val" : "RO:0002343" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'pollen tube growth' results_in growth_of some 'pollen tube'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17968,12 +15578,6 @@ "val" : "RO:0002344" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17988,23 +15592,7 @@ "meta" : { "definition" : { "val" : "is member of is a mereological relation between a item and a collection." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "An organism that is a member of a population of organisms" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is member of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "member part of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "SIO" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002351", @@ -18013,23 +15601,7 @@ "meta" : { "definition" : { "val" : "has member is a mereological relation between a collection and an item." - }, - "xrefs" : [ { - "val" : "RO:0002351" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "SIO" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_member" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002352", @@ -18039,20 +15611,7 @@ "definition" : { "val" : "inverse of has input" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002352" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "input_of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002353", @@ -18067,14 +15626,8 @@ "val" : "RO:0002353" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "output_of" @@ -18083,26 +15636,11 @@ }, { "id" : "http://purl.obolibrary.org/obo/RO_0002354", "lbl" : "formed as result of", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002360", "lbl" : "has dendrite location", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.org/dc/terms/source", - "val" : "http://neurolex.org/wiki/Property:DendriteLocation" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002371", "lbl" : "attached to", @@ -18111,23 +15649,7 @@ "definition" : { "val" : "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002371" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "attached to (anatomical structure to anatomical structure)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "attaches_to" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002372", @@ -18137,22 +15659,7 @@ "definition" : { "val" : "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." }, - "xrefs" : [ { - "val" : "RO:0002372" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Wikipedia:Insertion_(anatomy)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_muscle_origin" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://dbpedia.org/property/origin" } ] @@ -18165,22 +15672,7 @@ "definition" : { "val" : "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." }, - "xrefs" : [ { - "val" : "RO:0002373" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Wikipedia:Insertion_(anatomy)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_muscle_insertion" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://dbpedia.org/property/insertion" } ] @@ -18194,21 +15686,6 @@ "val" : "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004036", - "val" : "http://purl.obolibrary.org/obo/BFO_0000050" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png" }, { @@ -18225,46 +15702,7 @@ "val" : "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002376" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Deschutes River tributary_of Columbia River" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "inferior epigastric vein tributary_of external iliac vein" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "drains into" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "drains to" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "tributary channel of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://en.wikipedia.org/wiki/Tributary" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.medindia.net/glossary/venous_tributary.htm" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "tributary_of" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://dbpedia.org/ontology/drainsTo" }, { @@ -18279,17 +15717,7 @@ "meta" : { "definition" : { "val" : "x spatially_coextensive_with y if and inly if x and y have the same location" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A lump of clay and a statue" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002380", @@ -18300,22 +15728,7 @@ "val" : "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002380" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "branching_part_of" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/issues/2212" }, { @@ -18330,14 +15743,7 @@ "meta" : { "definition" : { "val" : "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002385", @@ -18346,23 +15752,7 @@ "meta" : { "definition" : { "val" : "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" - }, - "xrefs" : [ { - "val" : "RO:0002385" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_potential_to_developmentally_contribute_to" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002386", @@ -18371,14 +15761,7 @@ "meta" : { "definition" : { "val" : "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002387", @@ -18387,23 +15770,7 @@ "meta" : { "definition" : { "val" : "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" - }, - "xrefs" : [ { - "val" : "RO:0002387" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_potential_to_develop_into" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002388", @@ -18412,14 +15779,7 @@ "meta" : { "definition" : { "val" : "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002404", @@ -18433,12 +15793,6 @@ "val" : "RO:0002404" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -18455,12 +15809,6 @@ "val" : "RO:0002405" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -18477,15 +15825,6 @@ "val" : "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "indirectly activates" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002579", - "val" : "http://purl.obolibrary.org/obo/RO_0002213" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Indirectly_positively_regulates" } ] @@ -18499,15 +15838,6 @@ "val" : "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "indirectly inhibits" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002579", - "val" : "http://purl.obolibrary.org/obo/RO_0002212" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Indirectly_negatively_regulates" } ] @@ -18524,12 +15854,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." } ] } }, { @@ -18545,9 +15869,6 @@ "val" : "RO:0002411" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -18567,12 +15888,6 @@ "val" : "RO:0002412" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002411" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -18598,12 +15913,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "influences (processual)" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" @@ -18625,12 +15934,6 @@ "val" : "RO:0002427" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -18645,11 +15948,7 @@ "meta" : { "definition" : { "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002429", @@ -18658,14 +15957,7 @@ "meta" : { "definition" : { "val" : "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002428" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002430", @@ -18676,9 +15968,6 @@ "val" : "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002428" } ] @@ -18694,12 +15983,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "OWL does not allow defining object properties via a Union" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "involved in or reguates" } ] } }, { @@ -18717,15 +16000,6 @@ "val" : "enables activity in" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A protein that enables activity in a cytosol." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "executes activity in" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Is_active_in" } ] @@ -18737,20 +16011,7 @@ "meta" : { "definition" : { "val" : "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." - }, - "xrefs" : [ { - "val" : "RO:0002433" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "contributes_to_morphology_of" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002434", @@ -18771,18 +16032,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Considering relabeling as 'pairwise interacts with'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" - }, { - "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", - "val" : "http://purl.obolibrary.org/obo/MI_0914" } ] } }, { @@ -18794,20 +16046,8 @@ "val" : "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "binds" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "molecularly binds with" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ECO_0000353" - }, { - "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", - "val" : "http://purl.obolibrary.org/obo/MI_0915" } ] } }, { @@ -18818,12 +16058,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Axiomatization to GO to be added later" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." } ] } }, { @@ -18837,13 +16071,6 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "molecularly controls" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" } ] } }, { @@ -18857,16 +16084,6 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "molecularly decreases activity of" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "directly inhibits" } ] } }, { @@ -18880,31 +16097,12 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "molecularly increases activity of" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "directly activates" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002464", "lbl" : "helper property (not for use in curation)", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002473", "lbl" : "composed primarily of", @@ -18913,29 +16111,7 @@ "definition" : { "val" : "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002473" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "composed_primarily_of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002479", @@ -18945,22 +16121,12 @@ "definition" : { "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002481", "lbl" : "is kinase activity", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002485", "lbl" : "receives input from", @@ -18969,9 +16135,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "See notes for inverse relation" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { @@ -18982,24 +16145,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002487", "lbl" : "relation between physical entity and a process or stage", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage." - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002488", "lbl" : "existence starts during", @@ -19007,20 +16158,7 @@ "meta" : { "definition" : { "val" : "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." - }, - "xrefs" : [ { - "val" : "RO:0002488" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_starts_during" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002489", @@ -19029,20 +16167,7 @@ "meta" : { "definition" : { "val" : "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." - }, - "xrefs" : [ { - "val" : "RO:0002489" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_starts_with" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002490", @@ -19052,11 +16177,7 @@ "definition" : { "val" : "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002491", @@ -19070,19 +16191,6 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "exists during" - } ], - "xrefs" : [ { - "val" : "RO:0002491" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_starts_and_ends_during" } ] } }, { @@ -19093,24 +16201,7 @@ "definition" : { "val" : "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "ceases_to_exist_during" - } ], - "xrefs" : [ { - "val" : "RO:0002492" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_ends_during" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002493", @@ -19120,20 +16211,7 @@ "definition" : { "val" : "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "xrefs" : [ { - "val" : "RO:0002493" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_ends_with" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002494", @@ -19142,20 +16220,7 @@ "meta" : { "definition" : { "val" : "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" - }, - "xrefs" : [ { - "val" : "RO:0002494" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "transformation_of" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002495", @@ -19164,23 +16229,7 @@ "meta" : { "definition" : { "val" : "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" - }, - "xrefs" : [ { - "val" : "RO:0002495" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002494" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "immediate_transformation_of" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002496", @@ -19190,20 +16239,7 @@ "definition" : { "val" : "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "xrefs" : [ { - "val" : "RO:0002496" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_starts_during_or_after" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002497", @@ -19213,20 +16249,7 @@ "definition" : { "val" : "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "xrefs" : [ { - "val" : "RO:0002497" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_ends_during_or_before" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002500", @@ -19235,11 +16258,7 @@ "meta" : { "definition" : { "val" : "A relationship between a material entity and a process where the material entity has some causal role that influences the process" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002501", @@ -19248,17 +16267,7 @@ "meta" : { "definition" : { "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002502", @@ -19266,9 +16275,6 @@ "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/BFO_0000169" } ] @@ -19281,15 +16287,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." } ] } }, { @@ -19299,55 +16296,18 @@ "meta" : { "definition" : { "val" : "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." - }, - "xrefs" : [ { - "val" : "RO:0002551" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has supporting framework" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_skeleton" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002559", "lbl" : "causally influenced by", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "causally influenced by (entity-centric)" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002563", "lbl" : "interaction relation helper property", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29" }, { @@ -19358,13 +16318,7 @@ }, { "id" : "http://purl.obolibrary.org/obo/RO_0002564", "lbl" : "molecular interaction relation helper property", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002565", "lbl" : "results in movement of", @@ -19378,11 +16332,6 @@ "val" : "RO:0002565" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -19397,20 +16346,7 @@ "meta" : { "definition" : { "val" : "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "causally influences (entity-centric)" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002567", @@ -19419,14 +16355,7 @@ "meta" : { "definition" : { "val" : "A relation that holds between elements of a musculoskeletal system or its analogs." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002568", @@ -19435,23 +16364,7 @@ "meta" : { "definition" : { "val" : "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." - }, - "xrefs" : [ { - "val" : "RO:0002568" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Wikipedia:Antagonist_(muscle)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_muscle_antagonist" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002569", @@ -19461,20 +16374,7 @@ "definition" : { "val" : "inverse of branching part of" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002569" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_branching_part" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002570", @@ -19484,26 +16384,7 @@ "definition" : { "val" : "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002570" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "UBERON:cjm" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "conduit_for" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002571", @@ -19513,23 +16394,7 @@ "definition" : { "val" : "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002571" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "lumen_of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002572", @@ -19539,20 +16404,7 @@ "definition" : { "val" : "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002572" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "luminal_space_of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002576", @@ -19562,20 +16414,7 @@ "definition" : { "val" : "inverse of has skeleton" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "xrefs" : [ { - "val" : "RO:0002576" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "skeleton_of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002578", @@ -19590,18 +16429,6 @@ "val" : "RO:0002578" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "directly regulates (processual)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002211" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -19609,24 +16436,6 @@ "val" : "directly_regulates" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002581", - "lbl" : "is a defining property chain axiom", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002582", - "lbl" : "is a defining property chain axiom where second argument is reflexive", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R." - } - } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002584", "lbl" : "has part structure that is capable of", @@ -19634,14 +16443,7 @@ "meta" : { "definition" : { "val" : "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002586", @@ -19715,12 +16517,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] } }, { @@ -19730,14 +16526,7 @@ "meta" : { "definition" : { "val" : "Holds between c and p if and only if c is capable of some activity a, and a regulates p." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "pyrethroid -> growth" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002597", @@ -19746,11 +16535,7 @@ "meta" : { "definition" : { "val" : "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002598", @@ -19759,14 +16544,7 @@ "meta" : { "definition" : { "val" : "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "renin -> arteriolar smooth muscle contraction" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002608", @@ -19780,9 +16558,6 @@ "val" : "RO:0002608" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -19803,15 +16578,6 @@ "val" : "RO:0002629" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "directly positively regulates (process to process)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002578" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -19835,12 +16601,6 @@ "val" : "RO:0002630" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "directly negatively regulates (process to process)" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002578" }, { @@ -19868,17 +16628,8 @@ "val" : "RO:0003000" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9114-8737" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "produces" @@ -19897,17 +16648,8 @@ "val" : "RO:0003001" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9114-8737" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "produced_by" @@ -20016,9 +16758,6 @@ "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002264" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { @@ -20059,9 +16798,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002263" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { @@ -20120,9 +16856,6 @@ "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002418" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { @@ -20153,11 +16886,7 @@ "meta" : { "definition" : { "val" : "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0012000", @@ -20419,9 +17148,6 @@ "xrefs" : [ "PMID:19243617" ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" - }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1617-8244" }, { @@ -20439,9 +17165,6 @@ "xrefs" : [ "PMID:19243617" ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" - }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1617-8244" }, { @@ -20462,21 +17185,6 @@ "val" : "utilizes" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A diagnostic testing device utilizes a specimen." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9625-1899" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-2620-0345" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "See github ticket https://github.com/oborel/obo-relations/issues/497" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-11-08T12:00:00Z" } ] @@ -20619,12 +17327,6 @@ "val" : "galen:Tube" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts)" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "tubular" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -20672,8 +17374,6 @@ "val" : "EMAPA:37283" }, { "val" : "EV:0100155" - }, { - "val" : "FBbt:00007000" }, { "val" : "HAO:0000144" }, { @@ -20694,18 +17394,6 @@ "val" : "XAO:0000218" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "An appendage is an external body part, or natural prolongation, that protrudes from an organism's body, such as a vertebrate's limbs[BILA][BILA:0000018]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organ or organ part that is attached to the body of an organism. For example a limb[GO, modified][GO:0048736]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "appendicular" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "this is currently a subtype of organism subdivision - which would exclude feathers" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -20789,24 +17477,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical structure consisting of long narrow duct which carries urine from the kidney to the urinary bladder.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The duct of amniotes that carries urine from a metanephric kidney to the urinary bladder. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "ureteral" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "ureteric" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000010", - "val" : "in humans, consists of adventitial, muscular and mucoa layers" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -20863,12 +17533,6 @@ "val" : "galen:Urethra" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "urethral" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In human males, the urethra travels through the penis, and carries semen as well as urine. In females, the urethra is shorter and emerges above the vaginal opening." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -20903,8 +17567,6 @@ } ], "xrefs" : [ { "val" : "AAO:0011123" - }, { - "val" : "FBbt:00100314" }, { "val" : "FMA:30320" }, { @@ -20925,12 +17587,6 @@ "val" : "galen:Duct" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -20958,16 +17614,11 @@ "xrefs" : [ "FMA:82482" ] } ], "xrefs" : [ { - "val" : "EMAPA:25036" - }, { "val" : "FMA:82482" }, { "val" : "galen:Wall" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in FMA, serosa is a wall" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0009915" }, { @@ -21005,8 +17656,6 @@ "val" : "EHDAA2:0003003" }, { "val" : "EMAPA:0" - }, { - "val" : "FBbt:00007001" }, { "val" : "FMA:305751" }, { @@ -21106,12 +17755,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -21146,12 +17789,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -21190,9 +17827,6 @@ "val" : "SCTID:91717005" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "currently defined in a very broad sense, may be replaced by more specific classes in the future" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { @@ -21323,9 +17957,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "ncit:Death is an outcome" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -21411,9 +18042,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "ZFA - The multi-tissue structure where the glomerular basement membrane supported by mesonephric podocytes filters blood from the glomerular capillaries. GUDMAP: 'Together, the Bowman's capsule and the glomerulus comprise the definitive renal corpuscle.' - here the glomerulus is part of the capsule?" }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0001-9114-8737" @@ -21555,24 +18183,6 @@ "val" : "ZFA:0000529" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A kidney formed of nephric tubules arising in the middle region of the nephric ridge; a transient embryonic stage that replaces the pronephros, but is itself replaced by the adult metanephros [in mammals; in fishes and amphibians it is the adult kidney]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organ that is the definitive adult kidney. It replaces the earlier pronephros, which degenerates as the mesonephros becomes functional in feeding stage tadpoles.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates. (...) In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "mesonephric" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In mammals, the mesonephros is the second of the three embryonic kidneys to be established and exists only transiently. In fish and amphibians, the mesonephros will form the mature kidney" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000009", - "val" : "By contrast to the pronephros, the histological features of the mammalian mesonephros, with its primitive glomeruli, suggest that it probably functions as a primitive kidney, and is involved in the production of much of the amniotic fluid. Within the two mesonephroi, one located on either side of the dorsal mesentery of the hindgut, a substantial number (in the region of about 40 or more) of cranio-caudally segmented mesonephric tubules are formed. It has, however, been suggested that only the most rostrally located 4-6 pairs of mesonephric tubules drain into the mesonephric portion of the nephric duct. This is now seen to extend along the length of the mesonephroi, being located towards their lateral sides. The mesonephros is also retained over a considerably longer period than the pronephros, but gradually undergoes regression in a cranio-caudal direction. While the rostral part displays clear evidence of regression its more caudal part appears to display evidence of functional activity. Within the medial part of the mesonephros, vesicles are formed, although no glomeruli are formed there in this species. It is, however, difficult to believe that the relatively enormous mesonephroi do not have an excretory role in the mouse, only serving as a base for gonadal differentiation. In the human embryo, the medial part of the mesonephric tubules enlarges, become invaginated by capillaries, and form glomeruli. These then take on an excretory role. In the mouse, the mesonephric ducts appear to be patent throughout their length[GUDMAP, modified]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -21639,18 +18249,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO check developmental relationships" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A kidney formed of nephric tubules arising in the posterior region of the nephric ridge and drained by a ureter; replaces the embryonic pronephros and mesonephros [in mammals]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "metanephric" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "During the fifth week of gestation, the mesonephric duct develops an outpouching, the ureteric bud, near its attachment to the cloaca. This bud, also called the metanephrogenic diverticulum, grows posteriorly and towards the head of the embryo. The elongated stalk of the ureteric bud, the metanephric duct, later forms the ureter. As the cranial end of the bud extends into the intermediate mesoderm, it undergoes a series of branchings to form the collecting duct system of the kidney. It also forms the major and minor calyces and the renal pelvis" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -21692,12 +18290,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO check" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Any of the renal tubules composing the mesonephros. In mammals they function as excretory structures during the early embryonic development but are later incorporated into the reproductive system. [TFD][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -21765,15 +18357,6 @@ "val" : "Wikipedia:Ureteric_bud" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts. [Embryology, See_Dudek_RW_and_Fix_JD, Third_Edition_(2004)_Philadelphia:_Lippincott_William_and_Wilkins, p.137][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts[VHOG:0000541]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -21813,9 +18396,6 @@ "val" : "WBls:0000103" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -21932,12 +18512,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "the WBls class 'all stages' belongs here as it is the superclass of other WBls stages" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -21990,8 +18564,6 @@ "val" : "EHDAA:27" }, { "val" : "FBdv:00005288" - }, { - "val" : "IDOMAL:0000302" }, { "val" : "NCIT:C12601" }, { @@ -22006,9 +18578,6 @@ "val" : "ZFS:0000001" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -22186,12 +18755,6 @@ "val" : "XAO:1000006" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002174", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7955" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In zebrafish, the times of neurulation and segmentation overlap so extensively there is no distinct neurula period of development, such as occurs largely before segmentation in amphibian embryos." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -22309,9 +18872,6 @@ "val" : "NCIT:C12749" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A thin sheet or layer of pliable tissue, serving as a covering or envelope of a part, as the lining of a cavity, as a partition or septum, or to connect two structures." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -22346,9 +18906,6 @@ "val" : "SCTID:91837002" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in FMA, this is an anatomical conduit *space*, rather than anatomical conduit" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -22397,27 +18954,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "adding df link to embryonic cloaca leads to a cycle in uberon-simple, as cloaca is a suberclass of embryonic cloaca" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9369" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A common passage for fecal, urinary, and reproductive discharge in most lower vertebrates as well as the terminal end of the hindgut before division into rectum, bladder, and genital primordia in mammalian embryos. [TFD][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical structure which is the common receptacle for the alimentary canal, Wolffian ducts, oviducts, and the bladder.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "A cloaca is apparently a primitive vertebrate feature because it occurs in most primitive gnathostomes and persists in the embryos of almost all vertebrates.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "cloacal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "Human beings only have an embryonic cloaca, which is split up into separate tracts during the development of the urinary and reproductive organs" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "hindgut endoderm and proctodeal ectoderm." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -22448,9 +18984,6 @@ "val" : "Wikipedia:Cloaca_(embryology)" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "this class represents the embryonic form of the cloaca, as found in both mammals and non-mammals." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -22502,15 +19035,6 @@ "val" : "Wikipedia:Definitive_urogenital_sinus" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The ventral part of the cloaca after its separation from the rectum, giving rise to the lower part of the bladder in both sexes, to the prostatic portion of the male urethra, and to the urethra and vestibule in the female. [TFD][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "In mammals the lowly monotremes still have a cloaca. Higher types have done away with this structure and have a separate anal outlet for the rectum. The monotreme cloaca shows the initiation of this subdivision. The cloaca has such includes only the distal part, roughly comparable to the proctodeum. The more proximal part is divided into (1) a large dorsal passage into which the intestine opens, the coprodeum, and (2) a ventral portion, the urodeum with which the bladder connects. (...) the development of the placental mammals recapitulates in many respects the phylogenetic story. In the sexually indifferent stage of placental mammal there is a cloaca. While the indifferent stage still persists, a septum develops, and extends out to the closing membrane. This divides the cloaca into two chambers: a coprodeum continuous with the gut above, and a urodeum or urogenital sinus below.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000013", - "val" : "the term 'urogenital sinus' may refer to the primitive urogenital sinus present as a transient developmental structure in most mammals or it may refer to a condition in which an unseptated cloaca persists in animals longer than normal" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -22601,8 +19125,6 @@ "val" : "EHDAA:542" }, { "val" : "EMAPA:16262" - }, { - "val" : "FBbt:00003126" }, { "val" : "FMA:49184" }, { @@ -22645,21 +19167,6 @@ "val" : "http://purl.obolibrary.org/obo/uberon/images/lamprey_sucker_rosava_3238889218.jpg" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "oral" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -22786,23 +19293,8 @@ "val" : "galen:Blood" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid." - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -22894,10 +19386,6 @@ "xrefs" : [ "Wikipedia:Parenchyma" ] }, "xrefs" : [ { - "val" : "BTO:0000999" - }, { - "val" : "BTO:0001539" - }, { "val" : "EHDAA:3015" }, { "val" : "EHDAA:3905" @@ -22931,15 +19419,6 @@ "val" : "Wikipedia:Parenchyma" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "parenchymal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "Early in development the mammalian embryo has three distinct layers: ectoderm (external layer), endoderm (internal layer) and in between those two layers the middle layer or mesoderm. The parenchyma of most organs is of ectodermal (brain, skin) or endodermal origin (lungs, gastrointestinal tract, liver, pancreas). The parenchyma of a few organs (spleen, kidneys, heart) is of mesodermal origin. The stroma of all organs is of mesodermal origin" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "the FMA definition is more restrictive, and limits this to solid organs. This would seem to cause problems for the lung parenchyma, except FMA classifies Lung as solid rather than cavitated" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -23029,9 +19508,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000010", - "val" : "The renal medulla is split up into a number of sections, known as the renal pyramids. Blood enters into the kidney via the renal artery, which then splits up to form the arcuate arterioles. The arcuate arterioles each in turn branch into interlobular arterioles, which finally reach the glomeruli. At the glomerulus the blood reaches a highly disfavourable pressure gradient and a large exchange surface area, which forces the serum portion of the blood out of the vessel into the renal tubules. Flow continues through the renal tubules, including the proximal tubule, the Loop of Henle, and finally leaves the kidney by means of the collecting duct, leading to the renal ureter. The renal medulla contains the structures of the nephrons responsible for maintaining the salt and water balance of the blood. The renal medulla is hypertonic to the filtrate in the nephron and aids in the reabsorption of water" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -23103,8 +19579,6 @@ "val" : "BTO:0001485" }, { "val" : "EFO:0000801" - }, { - "val" : "EMAPA:35578" }, { "val" : "FMA:72954" }, { @@ -23127,12 +19601,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system that consists of the muscles of the body.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -23183,8 +19651,6 @@ "val" : "EHDAA2:0003004" }, { "val" : "EMAPA:35178" - }, { - "val" : "FBbt:00007019" }, { "val" : "FMA:9669" }, { @@ -23257,8 +19723,6 @@ "val" : "CARO:0000005" }, { "val" : "EHDAA2:0003005" - }, { - "val" : "FBbt:00007017" }, { "val" : "FMA:5897" }, { @@ -23312,8 +19776,6 @@ "val" : "CARO:0000006" }, { "val" : "EHDAA2:0003006" - }, { - "val" : "FBbt:00007016" }, { "val" : "FMA:67165" }, { @@ -23364,8 +19826,6 @@ "val" : "CARO:0000007" }, { "val" : "EHDAA2:0003007" - }, { - "val" : "FBbt:00007015" }, { "val" : "FMA:67112" }, { @@ -23444,14 +19904,10 @@ "val" : "EMAPA:16103" }, { "val" : "EV:0100000" - }, { - "val" : "FBbt:00004856" }, { "val" : "FMA:7149" }, { "val" : "HAO:0000011" - }, { - "val" : "IDOMAL:0002460" }, { "val" : "MA:0000003" }, { @@ -23560,8 +20016,6 @@ "val" : "EMAPA:25765" }, { "val" : "EV:0100016" - }, { - "val" : "FBbt:00000001" }, { "val" : "FMA:256135" }, { @@ -23603,9 +20057,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "organismal" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -23649,9 +20100,6 @@ "val" : "ZFA:0001489" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -23700,8 +20148,6 @@ "val" : "EHDAA2:0003032" }, { "val" : "EMAPA:36031" - }, { - "val" : "FBbt:00007009" }, { "val" : "FMA:7153" }, { @@ -23776,8 +20222,6 @@ "val" : "CARO:0000040" }, { "val" : "EHDAA2:0003040" - }, { - "val" : "FBbt:00007013" }, { "val" : "FMA:63863" }, { @@ -23816,8 +20260,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "xrefs" : [ { - "val" : "FBbt:00007277" - }, { "val" : "VHOG:0001737" } ], "basicPropertyValues" : [ { @@ -23874,8 +20316,6 @@ "val" : "EHDAA2:0003043" }, { "val" : "EMAPA:35868" - }, { - "val" : "FBbt:00007003" }, { "val" : "FMA:9637" }, { @@ -23946,8 +20386,6 @@ "val" : "CARO:0000055" }, { "val" : "EHDAA2:0003055" - }, { - "val" : "FBbt:00007010" }, { "val" : "HAO:0000055" }, { @@ -24012,8 +20450,6 @@ "val" : "EHDAA2:0003066" }, { "val" : "EMAPA:32738" - }, { - "val" : "FBbt:00007005" }, { "val" : "FMA:9639" }, { @@ -24042,12 +20478,6 @@ "val" : "ZFA:0001486" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "epithelial" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -24095,8 +20525,6 @@ "val" : "CARO:0000068" }, { "val" : "EHDAA2_RETIRED:0003068" - }, { - "val" : "FBbt:00007027" }, { "val" : "FMA:45567" }, { @@ -24173,9 +20601,6 @@ "val" : "ZFA:0001498" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Unilaminar epithelium that consists of a single layer of squamous cells.[CARO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -24229,9 +20654,6 @@ "val" : "ZFA:0001490" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -24288,9 +20710,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Epithelium that consists of a single layer of epithelial cells.[CARO]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -24333,18 +20752,6 @@ "val" : "Wikipedia:Thorax" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000026" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000033" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0002417" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -24409,12 +20816,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "abdominal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "celiac" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -24464,14 +20865,10 @@ "val" : "EHDAA:38" }, { "val" : "EMAPA:16039" - }, { - "val" : "FBbt:00000052" }, { "val" : "FMA:69068" }, { "val" : "GAID:963" - }, { - "val" : "IDOMAL:0000646" }, { "val" : "MAT:0000226" }, { @@ -24498,12 +20895,6 @@ "val" : "http://neurolex.org/wiki/Category:Embryonic_organism" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "embryonic" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -24552,8 +20943,6 @@ "val" : "BTO:0000556" }, { "val" : "EMAPA:36033" - }, { - "val" : "FBbt:00000110" }, { "val" : "FMA:69069" }, { @@ -24580,9 +20969,6 @@ "val" : "ZFA:0001122" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -24618,8 +21004,6 @@ "val" : "EMAPA:16069" }, { "val" : "EV:0100003" - }, { - "val" : "FBbt:00000111" }, { "val" : "FMA:69070" }, { @@ -24650,15 +21034,6 @@ "val" : "ZFA:0000016" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "ectodermal" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -24698,8 +21073,6 @@ "val" : "EMAPA:16062" }, { "val" : "EV:0100005" - }, { - "val" : "FBbt:00000125" }, { "val" : "FMA:69071" }, { @@ -24728,12 +21101,6 @@ "val" : "ZFA:0000017" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "endodermal" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -24788,8 +21155,6 @@ "val" : "EMAPA:16083" }, { "val" : "EV:0100006" - }, { - "val" : "FBbt:00000126" }, { "val" : "FMA:69072" }, { @@ -24820,18 +21185,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Primary germ layer that is the middle of the embryonic germ layers.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "mesodermal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0003263" @@ -24891,8 +21244,6 @@ "val" : "EHDAA2:0001929" }, { "val" : "EMAPA:16263" - }, { - "val" : "FBbt:00000439" }, { "val" : "FMA:295846" }, { @@ -24913,18 +21264,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "stomodeal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -24968,8 +21307,6 @@ "val" : "EHDAA2:0000121" }, { "val" : "EMAPA:25038" - }, { - "val" : "FBbt:00000123" }, { "val" : "NCIT:C34278" }, { @@ -24988,15 +21325,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "removed WBbt:0006795 'proctodeum' - junction between the alimentary and genital tracts in the male." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "An inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "proctodeal" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -25090,21 +21418,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "cardiac" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -25139,9 +21452,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO - merge with cell layer?" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "laminar" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -25171,12 +21481,6 @@ "val" : "galen:Medulla" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "this class is used in a very general sense" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "medullary" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -25255,12 +21559,6 @@ "val" : "galen:Joint" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -25328,8 +21626,6 @@ "val" : "EMAPA:17381" }, { "val" : "EV:0100100" - }, { - "val" : "FBbt:00004857" }, { "val" : "FMA:7160" }, { @@ -25340,8 +21636,6 @@ "val" : "HAO:0000895" }, { "val" : "MA:0000326" - }, { - "val" : "MESH:D005835" }, { "val" : "MIAA:0000305" }, { @@ -25369,15 +21663,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system which consists of organs and tissues associated with sexual reproduction of the organism.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Arguably, one of the most important aspects of urbilaterian organogenesis would have been gonadogenesis, since Urbilateria must have successfully generated gametes and developed a strategy for extrusion and fertilization, in order to be the ancestor of all living Bilateria.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000202", - "val" : "http://purl.obolibrary.org/obo/FMA_75572" }, { "pred" : "http://purl.org/dc/terms/date", "val" : "2022-06-10T18:22:34Z" @@ -25418,8 +21703,6 @@ "val" : "BTO:0000534" }, { "val" : "EMAPA:17383" - }, { - "val" : "FBbt:00004858" }, { "val" : "FMA:18250" }, { @@ -25450,21 +21733,6 @@ "val" : "ZFA:0000413" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "gonadal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "FMA xref is a 'general anatomical term'" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -25502,10 +21770,6 @@ "val" : "CALOHA:TS-1293" }, { "val" : "EFO:0000793" - }, { - "val" : "EV:0100056" - }, { - "val" : "FBbt:00005055" }, { "val" : "FMA:7152" }, { @@ -25540,15 +21804,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "digestive" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -25610,8 +21865,6 @@ "val" : "EMAPA:17366" }, { "val" : "EV:0100095" - }, { - "val" : "FBbt:00005056" }, { "val" : "FMA:7159" }, { @@ -25656,18 +21909,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Evolution of vertebrate renal anatomy appears quite conservative when compared, for example, to evolution of respiratory and cardiovascular systems in vertebrates. Major anatomical changes in vertebrates kidneys separate those of birds and mammals from kidneys of lower vertebrates. General increase in animal size from fish to mammals is reflected by an increase in total number of nephrons per kidney, rather than by constant change in tubular dimensions.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "This definition is inclusive of the organs of the vertebrate renal system, as well as the Malpighian tubules of insects, and allows for future incorporation of structures such as the antennal glands of crustaceans" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -25693,17 +21934,12 @@ "val" : "AAO:0000959" }, { "val" : "CALOHA:TS-2103" - }, { - "val" : "MESH:D002319" }, { "val" : "VHOG:0001248" }, { "val" : "Wikipedia:Circulatory_system" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "the cardiovascular system and the lymphatic system are parts of the circulatory system" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_147099" }, { @@ -25712,18 +21948,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6157" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002174", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6231" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -25775,13 +22002,9 @@ "val" : "musculature system" } ], "xrefs" : [ { - "val" : "AAO:0011066" - }, { "val" : "BTO:0000887" }, { "val" : "EFO:0001949" - }, { - "val" : "EMAPA:32715" }, { "val" : "EMAPA:35577" }, { @@ -25804,12 +22027,6 @@ "val" : "ZFA:0000548" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0001474" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -25861,8 +22078,6 @@ "val" : "EMAPA:16469" }, { "val" : "EV:0100162" - }, { - "val" : "FBbt:00005093" }, { "val" : "FMA:7157" }, { @@ -25902,21 +22117,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "nervous" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "neural" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -25980,8 +22180,6 @@ "val" : "EMAPA:16754" }, { "val" : "EV:0100163" - }, { - "val" : "FBbt:00005094" }, { "val" : "FMA:55675" }, { @@ -26017,18 +22215,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Part of the nervous system which includes the brain and spinal cord.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The brain and spinal cord. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO)." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26067,8 +22253,6 @@ "val" : "EHDAA:520" }, { "val" : "EMAPA:16548" - }, { - "val" : "FBbt:00005379" }, { "val" : "FMA:45616" }, { @@ -26091,12 +22275,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. In vertebrates the term may refer to a developmental structure" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The anterior portion of the primitive digestive tube of the embryo that lies cephalic to the junction of the yolk stalk, consists of endodermal tissue, and gives rise to the the pharynx, lower respiratory system, esophagus, stomach, duodenum proximal to the biliary tract, liver, pancreas, biliary tract, and gall bladder." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26133,8 +22311,6 @@ "val" : "EHDAA:983" }, { "val" : "EMAPA:16255" - }, { - "val" : "FBbt:00005383" }, { "val" : "FMA:45617" }, { @@ -26157,15 +22333,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. We may explicitly make this a developmental class" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In humans: originates from the foregut at the opening of the bile duct into the duodenum and continues through the small intestine and much of the large intestine until the transition to the hindgut about two-thirds of the way through the transverse colon" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in FMA this represents an embryonic region." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26202,8 +22369,6 @@ "val" : "EHDAA:975" }, { "val" : "EMAPA:16715" - }, { - "val" : "FBbt:00005384" }, { "val" : "FMA:45618" }, { @@ -26226,15 +22391,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future (vertebrates have some contribution from NC - https://github.com/obophenotype/uberon/wiki/The-neural-crest). We may explicitly make this a developmental class" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "the caudal portion of the primitive digestive tube of the embryo" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in FMA this class has no children. In MA it has a single child hindgut epithelium" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26280,8 +22436,6 @@ "val" : "EFO:0001652" }, { "val" : "EHDAA2:0003171" - }, { - "val" : "FBbt:00005495" }, { "val" : "FMA:86589" }, { @@ -26344,8 +22498,6 @@ "val" : "FMA:293882" }, { "val" : "MAT:0000069" - }, { - "val" : "MESH:D054259" }, { "val" : "MIAA:0000069" }, { @@ -26368,18 +22520,6 @@ "val" : "neuronames:1365" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -26411,8 +22551,6 @@ "val" : "CARO:0000000" }, { "val" : "EHDAA2:0002229" - }, { - "val" : "FBbt:10000000" }, { "val" : "FMA:62955" }, { @@ -26517,12 +22655,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Trunk of systemic vein which is formed by the union of the right common iliac vein and the left common iliac vein and terminates in the right atrium[FMA]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Phylogenetic modifications within this basic pattern of arteries and veins are largely correlated with functional changes. In the transition from water to land, gills gave way to lungs, accompanied by the establishment of a pulmonary circulation. In some fishes and certainly in tetrapods, the cardinal veins become less involved in blood return. Instead, the composite, prominent postcava (posterior vena cava) arose to drain the posterior part of the body and the precava (anterior vena cava) developed to drain the anterior part of the body.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26573,9 +22705,6 @@ "val" : "galen:Urine" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "kidney excreta from some taxa (e.g. in aves) may not be liquid" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -26637,12 +22766,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The renal veins are veins that drain the kidney. They connect the kidney to the inferior vena cava. It is usually singular to each kidney, except in the condition 'multiple renal veins'. It also divides into 2 divisions upon entering the kidney: the anterior branch which receives blood from the anterior portion of the kidney and, the posterior branch which receives blood from the posterior portion. Often, each renal vein will have a branch that receives blood from the ureter. [WP,unvetted][Wikipedia:Renal_vein]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in EHDAA2, the renal vein is part of the kidney" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26768,9 +22891,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000010", - "val" : "In the adult metanephros, it forms a continuous smooth outer zone with a number of projections that extend down between the pyramids. It contains the renal corpuscles and the renal tubules except for parts of the loop of Henle which descend into the renal medulla. It also contains blood vessels and cortical collecting ducts. The renal cortex is the part of the kidney where ultrafiltration occurs.[WP]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26861,15 +22981,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A mass of arterial capillaries enveloped in a capsule and attached to a tubule in the kidney[BTO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A tuft of capillaries found in a Bowman's capsule in which waste products are filtered from the blood and urine formation is initiated. Paired highly vascularized structures of the pronephros, responsible for blood filtration.[XAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The part of the nephron that filters blood.[TAO]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26966,15 +23077,6 @@ "val" : "ZFA:0005310" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical structure found in the kidney consisting of an expanded end of a kidney tubule surrounding a glomerulus and is the major site of filtration.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000009", - "val" : "Fluids from blood in the glomerulus are collected in the Bowman's capsule and further processed along the nephron to form urine. This process is known as ultrafiltration[WP]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "One fold of the S-shaped body gives rise to Bowman's capsule[GUDMAP]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -27041,9 +23143,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "note that in ISBN:0073040584 (Vertebrates, Kardong), the uriniferous tubule contains the nephron, so we have a separate class, rather than using a synonym, as in MA" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0004210" @@ -27132,12 +23231,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Renal duct that collects the output from renal tubules.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in ISBN:0073040584 (Vertebrates, Kardong), the nephron is adjacent to the collecting tubule, consistent with FMA, but not GO. Wikipedia says: Many sources include the connecting tubule as part of the collecting duct system. However, the embryological origin is more similar to the nephron than it is to the rest of the collecting duct (which derives from the ureteric bud), and other sources therefore classify the connecting tubule with the nephron" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27172,8 +23265,6 @@ "val" : "CALOHA:TS-2005" }, { "val" : "EV:0100082" - }, { - "val" : "FBbt:00047153" }, { "val" : "FMA:15711" }, { @@ -27200,12 +23291,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "anal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27289,26 +23374,8 @@ "val" : "galen:UrinaryBladder" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_8782" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A saccular organ in which urine accumulates before discharge from the body. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical structure which consists of a membranous sac used to temporarily store urine until it is excreted from the body.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "In tetrapods, the urinary bladder arises as an outpocketing of the cloaca. (...) The tetrapod urinary bladder appears first among amphibians and is present in Sphenodon, turtles, most lizards, ostriches among birds, and all mammals.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "vesical" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "The urinary bladder evolved in tetrapods. Birds to not possess a true urinary bladder, although Palaeognathae have an undifferentiated cloacal outpocketing that serves a similar function[https://github.com/obophenotype/uberon/issues/454]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27355,12 +23422,6 @@ "val" : "VSAO:0000304" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "this class describes the subdivision of the limb/fin, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831). See also comments on obo-anatomy mail list. Note that even though the class includes soft tissue it is more restrictive than 'pelvis' which also includes structures in cavities etc. TODO this needs to be better documented" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Subdivision of lower limb or fin which links the limb/fin to the body[FMA,modified]. There is only one instance of the pelvic girdle region per organism.[VSAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -27427,12 +23488,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Functional unit of the kidney that filters waste.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In the avian kidney, three types of nephron are identified: mammalian-type nephrons with long and short loops of Henle, and reptilian type nephrons (Gambaryan, 1992)" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27508,9 +23563,6 @@ "val" : "ZFA:0005290" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Renal tubule that connects to the renal corpuscle.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -27568,21 +23620,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "the definitions of some kidney parts (e.g. proximal straight tubule) refer to Henle's loop, even in species where this may not be present. Requires review." - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002174", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_8353" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_8782" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A highly specialized segment of the mammalian kidney tubules, that dips into the medulla. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, p.648, see_Liem_KF][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "The structure differs considerably between species; there is a definite physical loop of Henle in the mammalian and avian renal systems but this seems to be absent in Xenopus. However, homologs of some, but not all, molecular markers (e.g. cldn8 and clcnk) of the mammalian loop of Henle were found to be present in the pronephros of the frog larva ." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000009", - "val" : "The loop of Henle plays an important role in creating a concentration gradient in the medulla of the kidney. It is involved in reabsorption of filtered water and ions including sodium, potassium and calcium, and independently regulates both the volume and osmolarity of body fluids." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27696,9 +23736,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of the renal tubule which is just posterior to the proximal convoluted tubule.[TAO]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0005166" @@ -27756,12 +23793,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "a portion of kidney nephron between the loop of Henle and the collecting duct system[Wikipedia:Distal_convoluted_tubule]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000009", - "val" : "in humans it is responsible for the reabsorption of about 5% of filtered sodium via the thiazide-sensitive Na-Cl symporter." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27871,9 +23902,6 @@ "val" : "WBbt:0006919" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -27938,27 +23966,6 @@ "val" : "ZFA:0000434" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0001016" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "System that provides physical support to the organism.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "skeletal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -28052,14 +24059,10 @@ "val" : "EHDAA:518" }, { "val" : "EMAPA:16247" - }, { - "val" : "FBbt:00003125" }, { "val" : "FMA:45615" }, { "val" : "MA:0000917" - }, { - "val" : "MESH:D041981" }, { "val" : "NCIT:C34082" }, { @@ -28086,21 +24089,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The alimentary or digestive tract, and associated organs.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "FMA also has a term 'gastrointestinal tract', but this includes the liver." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000013", - "val" : "we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28149,10 +24137,6 @@ "xrefs" : [ "ZFA:0005145" ] } ], "xrefs" : [ { - "val" : "AAO:0011066" - }, { - "val" : "EMAPA:32715" - }, { "val" : "EMAPA:37474" }, { "val" : "EV:0100146" @@ -28176,15 +24160,6 @@ "val" : "galen:Muscle" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of tissue composed of contractile fibers.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "muscular" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -28227,8 +24202,6 @@ "val" : "CALOHA:TS-0054" }, { "val" : "EFO:0000814" - }, { - "val" : "EHDAA2:0000143" }, { "val" : "EHDAA2:0003253" }, { @@ -28269,21 +24242,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Note that in FMA an artery is a tree, whereas AEO/JB defines it as a tube; FMA includes a separate class for what it calls the trunk. Classification in this ontology may currently (Jan 2012) represent a mix of both schemes, although we are gradually revising in the direction of the AEO scheme." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Part of the circulatory system composed of blood vessels which carry oxygenated blood away from the heart to the rest of the body.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "arterial" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "Some arthropods have primitive arterial systems but this term refers to arteries in a true closed circulatory system." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000202", - "val" : "http://purl.obolibrary.org/obo/FMA_63812" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28373,18 +24331,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO - check with MA - vein vs venous blood vessel" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Part of the circulatory system composed of blood vessels which carry blood from other organs, tissues, and cells to the heart.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "venous" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000202", - "val" : "http://purl.obolibrary.org/obo/FMA_63814" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28423,12 +24369,6 @@ "val" : "galen:Cortex" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "cortical" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "this class is used more generically than in FMA, and includes e.g. cortex of hair" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -28534,9 +24474,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Multi-tissue structure part of the blood vasculature formed by the anastomosis of capillaries. Venules carry blood toward the heart.[TAO]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28589,12 +24526,6 @@ "val" : "ZFA:0005255" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Multi-tissue structure part of the blood vasculature, feeds into capillaries. Arterioles carry blood away from the heart.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Small, terminal branch of an artery which generally connects to capillaries.[AAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -28685,21 +24616,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Any of the vessels through which blood circulates in the body.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "annelids have blood vessels, but this class is not applicable to annelids." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28766,15 +24682,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Any of the tiny blood vessels connecting the arterioles to the venules.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000010", - "val" : "capillaries lack tunica media and tunica adventitia; only the endothelial wall of the tunica intima belongs" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28821,9 +24728,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "endothelial" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28859,9 +24763,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "vascular" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28911,8 +24812,6 @@ "val" : "CALOHA:TS-2110" }, { "val" : "EFO:0000461" - }, { - "val" : "FBbt:00004208" }, { "val" : "FMA:69067" }, { @@ -28937,18 +24836,6 @@ "val" : "ZFA:0001105" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in FMA embryo is_a embryonic structure" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -29011,12 +24898,6 @@ "val" : "XAO:0003034" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -29084,15 +24965,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Right cardiac chamber which is continuous with the superior vena cava and inferior vena cava.[FMA]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000006", - "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -29184,15 +25056,6 @@ "val" : "galen:Atrium" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "One of four heart chambers.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "One of two chambers of the heart which receive blood from the veins and forces it by muscular contration to the ventricle.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -29224,8 +25087,6 @@ "val" : "EHDAA2:0000161" }, { "val" : "EHDAA:5049" - }, { - "val" : "EMAPA:17214" }, { "val" : "EMAPA:37721" }, { @@ -29234,8 +25095,6 @@ "val" : "MA:0002986" }, { "val" : "MAT:0000148" - }, { - "val" : "MESH:D013131" }, { "val" : "MIAA:0000148" }, { @@ -29250,18 +25109,6 @@ "val" : "ZFA:0000317" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -29316,8 +25163,6 @@ "val" : "SCTID:322050006" }, { "val" : "UMLS:C0222646" - }, { - "val" : "VHOG:0001666" }, { "val" : "VSAO:0000076" }, { @@ -29328,18 +25173,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Skeletal subdivision consisting of all the skeletal elements in the pectoral and pelvic appendage complexes.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Skeletal system that consists of the paired fins (pectoral or pelvic fins).[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The pectoral and pelvic girdles, which articulate with the axial skeleton, together with their associated limbs, the forelimbs and hind limbs, form the appendicular skeleton.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "ontologies differ in whether they treat the term appendicular skeleton as being the entire set of bones in the limbs, or whether the fore and hind limbs/fins are treated as seperate appendicular skeletons. Here we follow FMA, and treat the appendicular skeleton as the sum total of skeletal elements in the organism (this is evidenced by the fact that in FMA, skeleton of left/right upper/lower limb is part_of a appendicular skeleton, and subtypes of 'subdivision of appendicular skeleton'). We have separate classes such as 'skeleton of limb', and 'skeleton of hindlimb' for the 4 parts of the appendicular skeleton. In future the ZFA/TAO classes may be moved." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -29416,18 +25249,6 @@ "val" : "galen:Trunk" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000026" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000033" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -29438,8 +25259,8 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A paired organ of the urinary tract which has the production of urine as its primary function.", - "xrefs" : [ "Wikipedia:Kidney", "http://anatomy.uams.edu/anatomyhtml/kidney.html" ] + "val" : "A paired organ of the urinary tract that produces urine and maintains bodily fluid homeostasis, blood pressure, pH levels, red blood cell production and skeleton mineralization.", + "xrefs" : [ "PMID:25140012", "PMID:35003210", "Wikipedia:Kidney", "http://anatomy.uams.edu/anatomyhtml/kidney.html", "https://www.kidney.org/kidneydisease/top-5-jobs-kidneys-do" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#major_organ", "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { @@ -29454,28 +25275,14 @@ "val" : "BTO:0000671" }, { "val" : "CALOHA:TS-0510" - }, { - "val" : "EFO:0000929" - }, { - "val" : "EMAPA:17373" - }, { - "val" : "EV:0100096" - }, { - "val" : "FMA:7203" }, { "val" : "GAID:423" - }, { - "val" : "MA:0000368" }, { "val" : "MAT:0000119" }, { "val" : "MESH:D007668" }, { "val" : "MIAA:0000119" - }, { - "val" : "NCIT:C12415" - }, { - "val" : "SCTID:181414000" }, { "val" : "UMLS:C0022646" }, { @@ -29486,20 +25293,14 @@ "val" : "galen:Kidney" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000160" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "One of either of a pair of structures lying on either side of the dorsal aorta in which fluid balance is regulated and waste is excreted out in the form of urine.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "renal" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-7655-4833" }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000202", - "val" : "http://purl.obolibrary.org/obo/FMA_264815" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-2804-127X" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -29549,8 +25350,6 @@ "val" : "FMA:72170" }, { "val" : "MAT:0000117" - }, { - "val" : "MESH:D060910" }, { "val" : "MIAA:0000117" }, { @@ -29571,21 +25370,6 @@ "val" : "ZFA:0000151" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A kidney formed of nephric tubules arising in the anterior region of the nephric ridge; forms only as a transient embryonic structure. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.748][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organ that serves as a transient kidney, providing osmoregulation during early developmental stages and then degenerating during metamorphosis.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The embryonic kidney, present at the level of the third somite, is composed of two glomeruli fused at the midline, two pronephric tubules, and paired bilateral pronephric ducts that modify the composition of the blood filtrate before delivering it to the cloaca for excretion.Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "pronephric" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0005794" }, { @@ -29724,15 +25508,6 @@ "val" : "XAO:0000168" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system that provides locomotion and physical support to the organism.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "musculoskeletal" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -29792,9 +25567,6 @@ "val" : "Wikipedia:Thoracic_cavity" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In many species, the diaphragm separates thoracic and abdominal cavities" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -29865,8 +25637,6 @@ "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], "xrefs" : [ { "val" : "BTO:0002494" - }, { - "val" : "EMAPA:28248" }, { "val" : "EMAPA:36561" }, { @@ -29883,12 +25653,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "mesangial" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "WP considers this the same as glomerular mesangium. In MA, glomerular and extraglomerular are distingsuished. FMA class has no definition and is a type of stroma, which is inconsistent with our classification of this here." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -29973,8 +25737,6 @@ "val" : "BTO:0001707" }, { "val" : "EHDAA2:0000267" - }, { - "val" : "FBbt:00005060" }, { "val" : "FMA:85006" }, { @@ -29993,15 +25755,6 @@ "val" : "galen:BodyCavity" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In mammals it forms the peritoneal, pleural, and pericardial cavities" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0000169" }, { @@ -30079,27 +25832,6 @@ "val" : "http://evolution.berkeley.edu/evolibrary/images/history/notochords.jpg" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "notochordal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -30186,32 +25918,8 @@ "val" : "ZFA:0000155" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "EDITOR_NOTE currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7712" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Post-cranial axial segments which form sclerotome and dermomyotome.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "somitic" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -30250,9 +25958,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "not part of a nephron or distal tubule in MA and FMA" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -30308,8 +26013,6 @@ "val" : "NCIT:C34222" }, { "val" : "SCTID:361462002" - }, { - "val" : "TAO:0000045" }, { "val" : "UMLS:C0027789" }, { @@ -30324,24 +26027,6 @@ "val" : "neuronames:1366" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "EDITOR_NOTE consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams)." - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002174", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_117565" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -30400,8 +26085,6 @@ "val" : "EMAPA:16073" }, { "val" : "EV:0100004" - }, { - "val" : "FBbt:00001057" }, { "val" : "FMA:87657" }, { @@ -30424,15 +26107,6 @@ "val" : "ZFA:0001120" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "neurectodermal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000013", - "val" : "we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -30496,12 +26170,6 @@ "val" : "galen:Pelvis" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "pelvic" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "MA and FMA differ in what they consider to be parts of the pelvis. MA includes ureter, urethra, urinary bladder, reproductive organs" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -30570,18 +26238,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "MA also has set of connective tissues" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -30638,12 +26294,6 @@ "val" : "galen:MuscleTissue" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0003714" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -30728,18 +26378,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system that consists of the blood and blood forming tissues.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "hematopoietic" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -30834,9 +26472,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -30930,12 +26565,6 @@ "val" : "ZFA:0000279" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -30968,8 +26597,6 @@ } ], "xrefs" : [ { "val" : "AAO:0011088" - }, { - "val" : "BTO:0005991" }, { "val" : "NCIT:C34279" }, { @@ -30978,8 +26605,6 @@ "val" : "TAO:0000150" }, { "val" : "UMLS:C1283945" - }, { - "val" : "VHOG:0000082" }, { "val" : "Wikipedia:Pronephric_duct" }, { @@ -30988,15 +26613,6 @@ "val" : "ZFA:0000150" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Duct of the embryonic kidney, present bilaterally ventral to the somites and leading to the anal region where it empties separately from, and just posterior to the anus. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -31058,21 +26674,6 @@ "val" : "ZFA:0000094" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -31134,15 +26735,6 @@ "val" : "ZFA:0001206" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Mesoderm between somite and lateral plate. Traditionally thought to give rise to the urogenital system.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...)the mesoderm of a developing vertebrate transitionally differentiates into the following sub-types: Chordamesoderm (also known as axial mesoderm) which later on gives rise to notochord in all chordates, Paraxial mesoderm, Intermediate mesoderm, Lateral plate mesoderm (reference 1); The mesoderm is present in Bilateria, therefore they are sometimes called triploblasts. Ectoderm and endoderm are usually organized as epithelial layers, while mesoderm can be epithelial or a compact, three-dimensional tissue.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm')." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -31181,9 +26773,6 @@ "val" : "ZFA:0001204" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -31224,14 +26813,10 @@ } ], "xrefs" : [ { "val" : "AAO:0000637" - }, { - "val" : "BTO:0005990" }, { "val" : "EHDAA2:0001243" }, { "val" : "EHDAA:1590" - }, { - "val" : "EMAPA:16577" }, { "val" : "GAID:1315" }, { @@ -31244,8 +26829,6 @@ "val" : "TAO:0000546" }, { "val" : "UMLS:C0043204" - }, { - "val" : "VHOG:0000082" }, { "val" : "Wikipedia:Mesonephric_duct" }, { @@ -31259,18 +26842,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO - mesonephric portion of the nephric duct" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical structure consisting of either of a pair of longitudinal ducts which carry urine and in males, sperm, to the cloaca.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "In the male the Wolffian duct persists, and forms for example the epididymis, the ductus deferens, the ejaculatory duct, seminal vesicle and efferent ducts." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -31314,8 +26885,6 @@ "val" : "EMAPA:35593" }, { "val" : "FMA:293879" - }, { - "val" : "MESH:D054258" }, { "val" : "NCIT:C34225" }, { @@ -31336,12 +26905,6 @@ "val" : "neuronames:1362" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -31401,15 +26964,6 @@ "val" : "ZFA:0000255" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -31477,18 +27031,6 @@ "val" : "ZFA:0000121" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "subclass of mesoderm in ZFA." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0006258" }, { @@ -31535,15 +27077,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "should probably be merged with heart rudiment." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -31574,8 +27107,6 @@ "val" : "AAO:0010571" }, { "val" : "AEO:0000212" - }, { - "val" : "BTO:0006255" }, { "val" : "EHDAA2:0003439" }, { @@ -31598,15 +27129,6 @@ "val" : "ZFA:0001080" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Skeletogenic portion of somites.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "part_of somite in XAO" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -31654,9 +27176,6 @@ "val" : "ZFA:0000496" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -31719,15 +27238,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "mesenchymal" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -31761,8 +27271,6 @@ "val" : "genitalia" } ], "xrefs" : [ { - "val" : "EMAPA:17381" - }, { "val" : "EMAPA:37731" }, { "val" : "MA:0001752" @@ -31780,9 +27288,6 @@ "val" : "WBbt:0008422" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "GO uses genitalia for the singular organ" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -31833,12 +27338,6 @@ "val" : "Wikipedia:Metanephric_blastema" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A mass of intermediate mesodermal cells around the distal end of the ureteric bud that gives rise to nephrons in the metanephric kidney. [TFD][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "When the ureteric buds emerge from the nephric duct, they enter the metanephrogenic mesenchyme. The ureteric buds induce this mesenchymal tissue to condense around them and differentiate into the nephrons of the mammalian kidney. As this mesenchyme differentiates, it tells the ureteric bud to branch and grow.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -31919,9 +27418,6 @@ "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "UBERON:0012254" } ] } }, { @@ -31997,8 +27493,6 @@ "xrefs" : [ "OBOL:automatic" ] } ], "xrefs" : [ { - "val" : "EMAPA:28457" - }, { "val" : "MA:0001682" }, { "val" : "TAO:0005306" @@ -32225,9 +27719,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -32255,9 +27746,6 @@ "val" : "UMLS:C0927195" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "stromal" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -32279,13 +27767,8 @@ "val" : "AEO:0000114" }, { "val" : "EHDAA2:0003114" - }, { - "val" : "FBbt:00007474" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -32498,9 +27981,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "FMA has both conduit and conduit space. In EHDAA2 this is a surface feature" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -32522,9 +28002,6 @@ "xrefs" : [ "FBbt:00025998" ] } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Grouping term for query purposes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -32545,9 +28022,6 @@ "xrefs" : [ "FBbt:00025990" ] } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Grouping term for query purposes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -32621,21 +28095,6 @@ "val" : "galen:GenitoUrinarySystem" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship type change: differentiates_from intermediate mesoderm (AAO:0010575) CHANGED TO: develops_from intermediate mesoderm (UBERON:0003064)[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Kidneys and gonads (of vertebrates) develop from adjacent tissues, and after the excretory or urinary ducts have developed, the reproductive system usually taps into them or their derivatives.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "genitourinary" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "urogenital" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -32713,9 +28172,6 @@ "val" : "MESH:D007686" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0012424" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -32784,9 +28240,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -32828,9 +28281,6 @@ "val" : "XAO:0004185" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -32874,9 +28324,6 @@ "val" : "ZFA:0000360" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33070,8 +28517,6 @@ } ], "xrefs" : [ { "val" : "EMAPA:27756" - }, { - "val" : "VO:0010896" }, { "val" : "ZFA:0005589" } ], @@ -33161,12 +28606,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "not the same as FMA:50609 Pyramid (which is a volume / dimensional entity)" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000202", - "val" : "http://purl.obolibrary.org/obo/FMA_74268" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0002449" @@ -33380,9 +28819,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Capillary that is part of the renal glomerulus. Glomerular capillary endothelial membranes in zebrafish normally have a fenestrated morphology that is visible at the ultrastructural level.[TAO]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -33437,17 +28873,8 @@ "val" : "galen:Skeleton" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000383" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "skeletal" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -33480,9 +28907,6 @@ "val" : "ZFA:0000115" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33510,8 +28934,6 @@ "val" : "EMAPA:16072" }, { "val" : "FMA:293110" - }, { - "val" : "MESH:D054240" }, { "val" : "NCIT:C28402" }, { @@ -33524,15 +28946,6 @@ "val" : "Wikipedia:Primitive_streak" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002174", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_32443" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) the blastopore equivalent of chordates (germ ring in fish, marginal zone/blastopore lip in frog and node/primitive streak in chick and mouse) (...) (reference 1); Indeed, the primitive streak has been considered the homologue of the blastopore since the 1870s (reference 2).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "VHOG includes a very broad grouping here based on http://www.ncbi.nlm.nih.gov/pubmed/9609826" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -33569,14 +28982,10 @@ "val" : "CALOHA:TS-1297" }, { "val" : "EFO:0000791" - }, { - "val" : "EHDAA2:0000216" }, { "val" : "EHDAA:394" }, { "val" : "EMAPA:16104" - }, { - "val" : "EMAPA:16370" }, { "val" : "EV:0100017" }, { @@ -33611,14 +29020,8 @@ "val" : "ZFA:0000010" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph." - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -33700,9 +29103,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -33744,9 +29144,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -34008,8 +29405,6 @@ "val" : "BILA:0000060" }, { "val" : "BTO:0001403" - }, { - "val" : "FBbt:00005317" }, { "val" : "FMA:293108" }, { @@ -34032,9 +29427,6 @@ "val" : "Wikipedia:Trilaminar_blastocyst" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "We explicitly merge the NCITA terms here" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0007012" }, { @@ -34066,12 +29458,6 @@ "val" : "galen:SkeletalStructure" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34239,9 +29625,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider merging with 'endothelium'" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -34281,9 +29664,6 @@ "val" : "XAO:0000276" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34315,12 +29695,6 @@ "val" : "Wikipedia:Somatopleure" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "Gives rise to the paired appendages in jawed vertebrates. a persistent somatopleure through the redistribution and expansion of the lateral plate mesoderm is a synapomorphy for gnathostomes and a critical step in generating a novel developmental module with dramatic evolutionary potentia (Tulenko et al. 2012) http://burkelab.research.wesleyan.edu/current-projects/lamprey/" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "sources differ as to whether this is part-of or develops-from the LPM" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -34394,9 +29768,6 @@ "val" : "Wikipedia:Urogenital_folds" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000013", - "val" : "Less commonly, urogenital fold refers to the fold in the mesonephros which is the precursor of e.g. the suspensory ligament of the ovary. This is the case in older versions of Gray's anatomy[WP]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34437,12 +29808,6 @@ "val" : "ZFA:0000091" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Notochord rudiment[ZFIN:ZDB-PUB-961014-576]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34461,9 +29826,6 @@ "pred" : "hasNarrowSynonym", "val" : "joint" } ], - "xrefs" : [ { - "val" : "FBbt:00005811" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -34499,14 +29861,9 @@ "xrefs" : [ "FMA:71131" ] } ], "xrefs" : [ { - "val" : "FBbt:00100315" - }, { "val" : "FMA:71131" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct." - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { @@ -34561,9 +29918,6 @@ "val" : "neuronames:1363" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34601,9 +29955,6 @@ "val" : "neuronames:1364" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34631,9 +29982,6 @@ "val" : "ZFA:0000133" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34687,14 +30035,9 @@ "val" : "muscle element" } ], "xrefs" : [ { - "val" : "EMAPA:32715" - }, { "val" : "FMA:30316" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -35008,9 +30351,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "interstital" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -35254,12 +30594,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000009", - "val" : "The interstitium is necessarily involved in all intrarenal exchange processes since the reabsorption and secretion of fluid and solutes implicates a transit across the interstitial compartment." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000010", - "val" : "The fibroblasts in the interstitium provide the 'skeleton' of the tissue and maintain the three-dimensional architecture of the tissue." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -35349,8 +30683,6 @@ "val" : "CALOHA:TS-2122" }, { "val" : "EHDAA2:0003125" - }, { - "val" : "FBbt:00007006" }, { "val" : "FMA:292313" }, { @@ -35390,8 +30722,6 @@ "xrefs" : [ "EMAPA:16208" ] } ], "xrefs" : [ { - "val" : "BTO:0006179" - }, { "val" : "EHDAA2:0001512" }, { "val" : "EHDAA:424" @@ -35462,12 +30792,6 @@ "val" : "ZFA:0001262" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Immature reproductive tissue that has not undergone final maturation into either testis or ovary.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "this is a very broad grouping class" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -35514,9 +30838,6 @@ "val" : "ZFA:0000067" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of tissue that consists of the mesenchymal precursor to the pronephric kidney and that begins to separate from the intermediate mesoderm at NF stage 21 and epithelializes by NF stage 30.[AAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -35542,15 +30863,10 @@ } ], "xrefs" : [ { "val" : "EMAPA:28239" - }, { - "val" : "SCTID:362217000" }, { "val" : "Wikipedia:Glomerulus" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "...Soon afterwards, endothelial cells invade to make a capillary knot-like outgrowth, the glomerular tuft, which goes on to form the glomerulus" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -35666,9 +30982,6 @@ "val" : "Wikipedia:Basement_membrane" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell." - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_80999" }, { @@ -35707,8 +31020,6 @@ "val" : "FMA:74274" }, { "val" : "MA:0001659" - }, { - "val" : "MESH:D050533" }, { "val" : "NCIT:C32683" }, { @@ -35723,9 +31034,6 @@ "val" : "ZFA:0005285" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Membrane between the mesonephric podocytes and the renal glomerular capillaries. It is a trilaminar structure composed of the fused basement membranes of the glomerular capillaries and basement membrane of the podocytes. The capillary membranes touch the GBM at contact points that are separated by pores. The membrane is semi-permeable allowing water and small molecules to pass into the renal capsular space.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -35810,8 +31118,6 @@ "val" : "AAO:0000963" }, { "val" : "EMAPA:17214" - }, { - "val" : "EMAPA:18043" }, { "val" : "MA:0000308" }, { @@ -35830,9 +31136,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -35885,12 +31188,6 @@ "val" : "Wikipedia:Cloacal_membrane" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A membrane that separates the proctodeum and the hindgut in the early embryo. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.497, see_Kardong_KV][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "In mammals, the cloaca exists as an embryonic structure that undergoes septation to become distinct urethral, anal, and genital orifices.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -35924,9 +31221,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO - check ordering; awaiting confirmation from JB" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -36103,9 +31397,6 @@ "val" : "ZFA:0005289" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in ZFA this is defined as part of mesonephros" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -36308,14 +31599,9 @@ "val" : "terminal section of digestive tract" } ], "xrefs" : [ { - "val" : "FBbt:00005756" - }, { "val" : "WBbt:0005773" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "this class is the superclass of 'rectum', which is currently reserved for the vertebrate structure. May be merged in future." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -36368,9 +31654,6 @@ "val" : "Wikipedia:Squamous_epithelium" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -36541,9 +31824,6 @@ "val" : "UMLS:C1514442" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -36573,16 +31853,11 @@ "xrefs" : [ "FBbt:00003154" ] } ], "xrefs" : [ { - "val" : "SPD:0000130" - }, { "val" : "TADS:0000147" }, { "val" : "http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -36610,9 +31885,6 @@ "val" : "ZFA:0000131" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -36674,9 +31946,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider merging" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Region of the gastrula which gives rise to the neural plate.[TAO]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -36874,9 +32143,6 @@ "val" : "FMA:17692" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "consider moving MA:0000377 renal tubule here, as it includes the various segments (proximal etc) as subclasses, not parts" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -36929,8 +32195,6 @@ "val" : "EFO:0001649" }, { "val" : "EHDAA2:0003170" - }, { - "val" : "FBbt:00005426" }, { "val" : "Wikipedia:Anlage_(biology)" } ], @@ -36970,12 +32234,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -37021,12 +32279,6 @@ "val" : "VSAO:0000303" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "this encompasses non-skeletal tissue" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There are only two instances of appendage girdle regions per organism.[VSAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0007824" }, { @@ -37102,21 +32354,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "need to resolve whether this is a paired structure or a single belt (Paired in FMA - implicitly paired in VSAO)" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical cluster by which the hind limbs are supported and attached to the vertebral column.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical cluster that consists of the paired basipterygia which support the pelvic fin.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Girdle skeleton consisting of a set of bones linking the axial series to the hindlimb/fin skeleton and offering anchoring areas for hindlimb/fin and caudal musculature.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "Note that the VSAO and many ontologies use the label 'pelvic girdle' to denote the skeletal region specifically. We place the EHDAA2 class here, note that this includes the pre-cartilage condensation as parts" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -37314,9 +32551,6 @@ "xrefs" : [ "OBOL:automatic", "https://orcid.org/0000-0002-6601-2165" ] } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "this class groups vertebrate nephron tubules with analagous structures such as insect Malpighian tubules" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -37416,9 +32650,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "FMA only has the set term" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -37496,9 +32727,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "todo - add has_part relationships." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "human kidneys have multilobar (multipyramidal) architecture while mice and rats have unilobar (unipyramidal) kidneys" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -37524,8 +32752,6 @@ } ], "xrefs" : [ { "val" : "CARO:0010000" - }, { - "val" : "FBbt:00100313" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", @@ -37605,9 +32831,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Grouping term for query purposes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -37713,9 +32936,6 @@ "val" : "presumptive nephron" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "EHDAA2 treats this as already having a tubular structure, but in the ZFA representation this is a cluster of cells" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -37772,15 +32992,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical group that consists of the soft and skeletal tissues of the appendicular region of the body and the appendage proper.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000005", - "val" : "It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "note that the FMA uses the term 'limb' to refer to the entire appendage complex (free limb plus girdle region)" }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0001-9114-8737" @@ -37839,15 +33050,6 @@ "val" : "VSAO:0000215" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0010708" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Appendage girdle complex that when present, encompasses the pelvic appendage and the pelvic girdle.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region). Note the MA class 'hindlimb' may also belong here" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -37871,15 +33073,6 @@ "val" : "VSAO:0000302" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Skeletal subdivision that is part of the appendage girdle region.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: part_of subdivision of skeleton (UBERON:0010912)[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: proximally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -37911,9 +33104,6 @@ "val" : "VSAO:0000042" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -38004,8 +33194,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "xrefs" : [ { - "val" : "FBbt:00007330" - }, { "val" : "FMA:67509" }, { "val" : "SCTID:91690000" @@ -38038,15 +33226,10 @@ }, "xrefs" : [ { "val" : "FMA:7484" - }, { - "val" : "VHOG:0001666" }, { "val" : "VSAO:0000306" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Skeletal system which consists of the appendicular skeleton plus associated joints.[VSAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -38173,9 +33356,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_147099" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "coelomic" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -38341,9 +33521,6 @@ "val" : "Wikipedia:Urethral_groove" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In humans, the urethral groove is a temporary linear indentation on the underside (ventral side) of the male penis during embryonic development. It typically appears around 8 weeks of gestation and becomes closed into a normal male urethra by the 12th week" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -38427,15 +33604,10 @@ "val" : "AEO:0000103" }, { "val" : "BTO:0001489" - }, { - "val" : "EMAPA:36031" }, { "val" : "FMA:231424" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -38463,8 +33635,6 @@ "xrefs" : [ "FMA:83067" ] } ], "xrefs" : [ { - "val" : "BTO:0006187" - }, { "val" : "FMA:83067" } ], "basicPropertyValues" : [ { @@ -38570,9 +33740,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This class is primarily to implement taxon constraints. It may be removed in the future." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -38603,9 +33770,6 @@ "pred" : "hasRelatedSynonym", "val" : "cardiac structure" } ], - "xrefs" : [ { - "val" : "SPD:0000130" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -38797,8 +33961,6 @@ "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], "xrefs" : [ { "val" : "CARO:0020000" - }, { - "val" : "FBbt:00007276" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", @@ -39034,9 +34196,6 @@ "val" : "microvessel" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "microvascular" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "http://orcid.org/0000-0002-2825-0621" }, { @@ -39057,9 +34216,6 @@ "xrefs" : [ "GO:0007588" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], - "xrefs" : [ { - "val" : "BTO:0006338" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" @@ -39428,120 +34584,6 @@ "val" : "uberon" } ] } - }, { - "id" : "http://purl.org/dc/elements/1.1/creator", - "lbl" : "creator", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/elements/1.1/creator" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-creator" - } ] - } - }, { - "id" : "http://purl.org/dc/elements/1.1/description", - "lbl" : "description", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/elements/1.1/description" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-description" - } ] - } - }, { - "id" : "http://purl.org/dc/elements/1.1/title", - "lbl" : "title", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/elements/1.1/title" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-title" - } ] - } - }, { - "id" : "http://purl.org/dc/terms/contributor", - "lbl" : "contributor", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/terms/contributor" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-contributor" - } ] - } - }, { - "id" : "http://purl.org/dc/terms/date", - "lbl" : "date", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/terms/date" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dcterms-date" - } ] - } - }, { - "id" : "http://purl.org/dc/terms/license", - "lbl" : "license", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/terms/license" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dcterms-license" - } ] - } }, { "id" : "http://www.geneontology.org/formats/oboInOwl#SubsetProperty", "lbl" : "subset_property", @@ -39575,9 +34617,6 @@ "val" : "An alternative label for a class or property which has a more general meaning than the preferred name/primary label." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/18" }, { @@ -39598,9 +34637,6 @@ "val" : "An alternative label for a class or property which has the exact same meaning than the preferred name/primary label." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/20" }, { @@ -39617,9 +34653,6 @@ "val" : "An alternative label for a class or property which has a more specific meaning than the preferred name/primary label." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/19" }, { @@ -39640,9 +34673,6 @@ "val" : "An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/21" }, { @@ -39675,35 +34705,10 @@ "val" : "http://www.w3.org/2000/01/rdf-schema#seeAlso" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "seeAlso" } ] } - }, { - "id" : "http://xmlns.com/foaf/0.1/depiction", - "lbl" : "depiction", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://xmlns.com/foaf/0.1/depiction" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "depiction" - } ] - } } ], "edges" : [ { "sub" : "http://purl.obolibrary.org/obo/BFO_0000004", @@ -44677,10 +39682,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000056", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0036295" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000056", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000468" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000056", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -44726,16 +39727,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000057", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000164", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "pelvic part of UG sinus gives rise to prostatic and membranous parts of urethra" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "Wikipedia" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000164" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000057", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -44952,13 +39944,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000081", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0003220", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "definitional" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0003220" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000081", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -45013,10 +39999,6 @@ "val" : "EHDAA2" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000084", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0012275" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000084", "pred" : "is_a", @@ -45324,17 +40306,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0004921", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts" - } ] - } - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0001106", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0001555" + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004921" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -45476,13 +40448,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000463", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000468", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "this relationship may be too strong and may be weakened in future" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000468" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000463", "pred" : "http://purl.obolibrary.org/obo/RO_0000086", @@ -45742,13 +40708,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000926", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000923", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "sometimes not considered primary" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000923" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000926", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -46296,13 +41256,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001231", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0003918", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "checkme" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0003918" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001231", "pred" : "http://purl.obolibrary.org/obo/RO_0002433", @@ -46314,16 +41268,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001232", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0001285", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "checkme" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "GO" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0001285" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001232", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -46344,10 +41289,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001245", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001555" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0001245", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0001108", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0001555" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001245", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -46383,13 +41324,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001255", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000164", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "upper part of UG sinus" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000164" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001271", "pred" : "is_a", @@ -46406,10 +41341,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001271", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0010709" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0001271", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0002355" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001271", "pred" : "http://purl.obolibrary.org/obo/RO_0002551", @@ -46431,13 +41362,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001285", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0004208", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "definitional" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004208" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001285", "pred" : "http://purl.obolibrary.org/obo/RO_0002433", @@ -46473,16 +41398,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001287", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0004134", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "MA uses subclass" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "GOC:mtg_kidney_jan10" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004134" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001287", "pred" : "http://purl.obolibrary.org/obo/RO_0002150", @@ -46578,16 +41494,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001290", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0004134", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "MA uses subclass" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "GOC:mtg_kidney_jan10" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004134" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001290", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -46671,13 +41578,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001353", "pred" : "http://purl.obolibrary.org/obo/RO_0002254", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000931", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "cjm" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000931" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001434", "pred" : "is_a", @@ -46876,6 +41777,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000055" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -47013,10 +41918,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002078", "pred" : "http://purl.obolibrary.org/obo/RO_0002170", "obj" : "http://purl.obolibrary.org/obo/UBERON_0004537" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0002081", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002081", "pred" : "is_a", @@ -47095,10 +41996,6 @@ "val" : "FMA" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0002113", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000468" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002113", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -47106,13 +42003,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002113", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0003918", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "definitional" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0003918" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002113", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -47204,13 +42095,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002204", "pred" : "http://purl.obolibrary.org/obo/RO_0002254", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000926", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "check ctenophore" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000926" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002204", "pred" : "http://purl.obolibrary.org/obo/RO_0002492", @@ -47271,6 +42156,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002319", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000119" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0002319", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002319", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -47295,6 +42184,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002321", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0003891" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0002321", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002321", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -47326,13 +42219,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002323", "pred" : "http://purl.obolibrary.org/obo/RO_0002494", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0003886", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "definitional" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0003886" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002323", "pred" : "http://purl.obolibrary.org/obo/RO_0002572", @@ -47357,6 +42244,10 @@ "val" : "VSAO" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", "pred" : "is_a", @@ -47365,14 +42256,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0011137" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000098", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0001555" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000102", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0001049" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -47473,6 +42356,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010314" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "is_a", @@ -47493,16 +42380,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_89593", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "ISBN:0073040584" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_89593" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -47526,13 +42404,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "http://purl.obolibrary.org/obo/RO_0002473", - "obj" : "http://purl.obolibrary.org/obo/CL_0000333", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/CL_0000333" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "http://purl.obolibrary.org/obo/RO_0002488", @@ -47624,13 +42496,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002390", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0003061", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "definitional" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0003061" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002417", "pred" : "is_a", @@ -47805,10 +42671,6 @@ "val" : "GO" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0003074", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0012275" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003074", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -47883,10 +42745,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0003077", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0015212" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0003077", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000922" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003077", "pred" : "http://purl.obolibrary.org/obo/RO_0002488", @@ -48354,6 +43212,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004140", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0002050" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004140", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004140", "pred" : "is_a", @@ -48408,6 +43270,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004151", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000064" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004151", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004151", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -48420,6 +43286,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004188", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0004211" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004188", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0012275" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004188", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -48987,14 +43857,14 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005062", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0015212" + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010371" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005062", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0005061" + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0015212" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005062", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000126", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0005061" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005068", @@ -49080,6 +43950,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0005103", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0004819" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0005103", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0012275" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005103", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -49290,6 +44164,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0005721", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000926" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0005721", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005721", "pred" : "is_a", @@ -49402,6 +44280,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", "pred" : "http://purl.obolibrary.org/obo/RO_0002473", "obj" : "http://purl.obolibrary.org/obo/GO_0005604" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0005777", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005777", "pred" : "is_a", @@ -49742,13 +44624,11 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006984", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0010199", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "via morphological boundary in CARO" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010199" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0007005", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007005", "pred" : "is_a", @@ -49812,13 +44692,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007100", "pred" : "http://purl.obolibrary.org/obo/RO_0002215", - "obj" : "http://purl.obolibrary.org/obo/GO_0008015", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "GO uses blood circulation generically to include the haemolymphatic fluid of arthropods" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/GO_0008015" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007135", "pred" : "is_a", @@ -49834,16 +44708,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007282", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0009618", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#consistent_with", - "val" : "https://github.com/obophenotype/uberon/wiki/The-neural-crest" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "EDHAA2" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0009618" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007282", "pred" : "http://purl.obolibrary.org/obo/RO_0002387", @@ -50043,6 +44908,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0007823", "pred" : "http://purl.obolibrary.org/obo/RO_0002551", "obj" : "http://purl.obolibrary.org/obo/UBERON_0010719" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0007832", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007832", "pred" : "is_a", @@ -50197,6 +45066,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0009856", "pred" : "http://purl.obolibrary.org/obo/RO_0000086", "obj" : "http://purl.obolibrary.org/obo/PATO_0001987" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0009881", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0009881", "pred" : "is_a", @@ -50313,6 +45186,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0010371", "pred" : "http://purl.obolibrary.org/obo/RO_0002473", "obj" : "http://purl.obolibrary.org/obo/CL_0002077" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0010377", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0010377", "pred" : "is_a", @@ -50423,10 +45300,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0010707", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0015212" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0010707", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000468" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0010707", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -50557,16 +45430,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0011143", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/UBERON_0002113" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0011143", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0001008", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "FMA-abduced-lr" - } ] - } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0011216", "pred" : "is_a", @@ -50831,10 +45694,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0015212", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0015212", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000465" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0015212", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -51011,8 +45870,8 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0004151" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0035554", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000121", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000948" + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0015212" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0035804", "pred" : "is_a", @@ -52239,10 +47098,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000057" - }, { - "sub" : "http://purl.obolibrary.org/obo/uberon/core#anteriorly_connected_to", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BSPO_0000099" }, { "sub" : "http://purl.obolibrary.org/obo/uberon/core#anteriorly_connected_to", "pred" : "subPropertyOf", @@ -52251,10 +47106,6 @@ "sub" : "http://purl.obolibrary.org/obo/uberon/core#anteriorly_connected_to", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/uberon/core#transitively_anteriorly_connected_to" - }, { - "sub" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BSPO_0000100" }, { "sub" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", "pred" : "subPropertyOf", @@ -52271,18 +47122,10 @@ "sub" : "http://purl.obolibrary.org/obo/uberon/core#layer_part_of", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000050" - }, { - "sub" : "http://purl.obolibrary.org/obo/uberon/core#posteriorly_connected_to", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BSPO_0000096" }, { "sub" : "http://purl.obolibrary.org/obo/uberon/core#posteriorly_connected_to", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002170" - }, { - "sub" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BSPO_0000097" }, { "sub" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to", "pred" : "subPropertyOf", @@ -52499,10 +47342,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012001", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012005" - }, { - "sub" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", - "pred" : "inverseOf", - "obj" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to" } ], "logicalDefinitionAxioms" : [ { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000034", @@ -53285,7 +48124,7 @@ } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_1000854", - "genusIds" : [ "http://purl.obolibrary.org/obo/CL_1000504" ], + "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0003517" @@ -54364,13 +49203,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002082", "fillerId" : "http://purl.obolibrary.org/obo/GO_0040016" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0000165", - "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0004921" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BSPO_0001106", - "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0001555" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0000174", "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000463" ], @@ -54521,13 +49353,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0001285" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0001245", - "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000161" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BSPO_0001108", - "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0001555" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0001271", "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0007823" ], @@ -54626,13 +49451,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0001025", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0002323" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0002078", - "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0002081" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BSPO_0000121", - "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0000948" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0002201", "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0002049" ], @@ -55359,13 +50177,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002387", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0002049" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0015212", - "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0000465" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0016879", "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0006598" ], @@ -55401,13 +50212,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0000362" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0035554", - "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0004151" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BSPO_0000121", - "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0000948" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_8450002", "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000467" ], @@ -55598,12 +50402,6 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0002177", "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002178", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001637" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002179", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001638" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002202", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], @@ -55726,8 +50524,8 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002551", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061", "http://purl.obolibrary.org/obo/UBERON_0000475" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465", "http://purl.obolibrary.org/obo/UBERON_0010912" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002566", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], @@ -55785,10 +50583,6 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0019000", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/uberon/core#channel_for", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0004111" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000463" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] @@ -55820,21 +50614,12 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002287", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002210" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002329", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002215" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002496" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002497" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002479", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/BFO_0000066" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/RO_0000057" ] @@ -55853,24 +50638,12 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000066", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000066", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002314", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0000052", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0001025", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0001025", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002005", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002005", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002005", "http://purl.obolibrary.org/obo/RO_0002380" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002100", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002100", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/uberon/core#extends_fibers_into", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002100", "http://purl.obolibrary.org/obo/RO_0013001" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002102", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002102", "http://purl.obolibrary.org/obo/BFO_0000050" ] @@ -55886,24 +50659,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002131", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002131", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002134", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002134", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002150", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002170", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002176", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002178", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002202", "http://purl.obolibrary.org/obo/RO_0002162" ] @@ -55940,9 +50698,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0019002", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002213", "http://purl.obolibrary.org/obo/RO_0019002" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002216", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002215", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002215", "http://purl.obolibrary.org/obo/RO_0002162" ] @@ -55991,9 +50746,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002254", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002256", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002258", "http://purl.obolibrary.org/obo/RO_0002496" ] @@ -56015,9 +50767,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004031", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/BFO_0000051" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002432", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/BFO_0000066" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002327", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002017" ] @@ -56081,15 +50830,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002339", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002339", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002177", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002371", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002371", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002387", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002407", "http://purl.obolibrary.org/obo/RO_0002629" ] @@ -56102,15 +50842,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002488", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002488", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002488", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002492", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002492", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002492", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002496", "http://purl.obolibrary.org/obo/BFO_0000050" ] @@ -56129,9 +50863,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002497", "http://purl.obolibrary.org/obo/RO_0002082" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/uberon/core#indirectly_supplies", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002569", "http://purl.obolibrary.org/obo/RO_0002178" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/uberon/core#indirectly_supplies", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002569", "http://purl.obolibrary.org/obo/uberon/core#indirectly_supplies" ] @@ -56150,12 +50881,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002630", "http://purl.obolibrary.org/obo/RO_0002630" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0003000", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0003001", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0013001", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0013001", "http://purl.obolibrary.org/obo/BFO_0000050" ] diff --git a/src/ontology/subsets/kidney_upper_slim.obo b/src/ontology/subsets/kidney_upper_slim.obo index 161bb5549..39727a2fa 100644 --- a/src/ontology/subsets/kidney_upper_slim.obo +++ b/src/ontology/subsets/kidney_upper_slim.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: cl/releases/2024-02-13/subsets/kidney_upper_slim.owl +data-version: cl/releases/2024-04-05/subsets/kidney_upper_slim.owl subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -88,7 +88,7 @@ synonymtypedef: synonym "" synonymtypedef: SYSTEMATIC "" synonymtypedef: systematic_synonym "" ontology: cl/subsets/kidney_upper_slim -property_value: owl:versionInfo "2024-02-13" xsd:string +property_value: owl:versionInfo "2024-04-05" xsd:string [Term] id: BFO:0000002 @@ -159,7 +159,7 @@ is_a: UBERON:0000061 ! anatomical structure disjoint_from: GO:0031012 ! extracellular matrix disjoint_from: GO:0032991 ! protein-containing complex disjoint_from: GO:0043226 ! organelle -relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms +relationship: RO:0002160 NCBITaxon:131567 ! only in taxon cellular organisms [Term] id: CL:0000007 @@ -182,8 +182,8 @@ is_a: CL:0011115 ! precursor cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0017145 ! stem cell division relationship: capable_of GO:0017145 ! stem cell division -relationship: in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000037 @@ -233,8 +233,8 @@ relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surfac relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -relationship: develops_from CL:0000566 ! angioblastic mesenchymal cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000566 ! develops from angioblastic mesenchymal cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000038 @@ -251,7 +251,7 @@ synonym: "erythroid stem cell" RELATED [] xref: BTO:0004911 is_a: CL:0000764 ! erythroid lineage cell is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor cell -relationship: develops_from CL:0000050 ! megakaryocyte-erythroid progenitor cell +relationship: RO:0002202 CL:0000050 ! develops from megakaryocyte-erythroid progenitor cell [Term] id: CL:0000039 @@ -296,7 +296,7 @@ synonym: "pluripotent stem cell (bone marrow)" RELATED [ISBN:0878932437] xref: BTO:0004730 is_a: CL:0002032 {is_inferred="true"} ! hematopoietic oligopotent progenitor cell disjoint_from: CL:0000050 ! megakaryocyte-erythroid progenitor cell -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000050 @@ -320,7 +320,7 @@ intersection_of: capable_of GO:0030218 ! erythrocyte differentiation intersection_of: capable_of GO:0030219 ! megakaryocyte differentiation relationship: capable_of GO:0030218 ! erythrocyte differentiation relationship: capable_of GO:0030219 ! megakaryocyte differentiation -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000052 @@ -367,8 +367,8 @@ xref: FMA:63877 xref: NCIT:C12482 xref: VHOG:0001482 is_a: CL:0002320 ! connective tissue cell -relationship: develops_from CL:0000134 ! mesenchymal stem cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000064 @@ -399,8 +399,8 @@ xref: FMA:66768 xref: WBbt:0003672 is_a: CL:0000000 ! cell relationship: part_of UBERON:0000483 ! epithelium -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000067 @@ -434,9 +434,9 @@ is_a: CL:0000076 {is_inferred="true"} ! squamous epithelial cell is_a: CL:0002139 ! endothelial cell of vascular tree intersection_of: CL:0000076 ! squamous epithelial cell intersection_of: part_of UBERON:0004638 ! blood vessel endothelium -relationship: develops_from CL:0002546 ! embryonic blood vessel endothelial progenitor cell relationship: part_of UBERON:0004638 ! blood vessel endothelium -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0002546 ! develops from embryonic blood vessel endothelial progenitor cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000072 @@ -451,7 +451,7 @@ def: "A columnar/cuboidal epithelial cell is a cell usually found in a two dimen subset: cellxgene_subset subset: human_reference_atlas is_a: CL:0000066 ! epithelial cell -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000076 @@ -486,7 +486,7 @@ xref: CALOHA:TS-0278 xref: FMA:66772 is_a: CL:0000213 ! lining cell is_a: CL:0002078 ! meso-epithelial cell -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000133 @@ -562,8 +562,8 @@ xref: FMA:67328 xref: WBbt:0003675 is_a: CL:0000183 ! contractile cell is_a: CL:0000393 ! electrically responsive cell -relationship: develops_from CL:0000056 ! myoblast -property_value: depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI +relationship: RO:0002202 CL:0000056 ! develops from myoblast +property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI [Term] id: CL:0000192 @@ -581,8 +581,8 @@ xref: CALOHA:TS-2159 xref: FMA:14072 is_a: CL:0008000 ! non-striated muscle cell is_a: CL:0008007 ! visceral muscle cell -relationship: develops_from CL:0000514 ! smooth muscle myoblast -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000514 ! develops from smooth muscle myoblast +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000211 @@ -665,8 +665,8 @@ intersection_of: CL:4030046 PR:000001945 ! lacks_plasma_membrane_part transferri relationship: bearer_of PATO:0002039 ! biconcave relationship: CL:4030045 GO:0005840 ! lacks_part ribosome relationship: CL:4030046 PR:000001945 ! lacks_plasma_membrane_part transferrin receptor protein 1 -relationship: develops_from CL:0000558 ! reticulocyte -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000558 ! develops from reticulocyte +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000239 @@ -681,8 +681,8 @@ subset: cellxgene_subset xref: MESH:D005057 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell -intersection_of: only_in_taxon NCBITaxon:2759 ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +intersection_of: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota [Term] id: CL:0000329 @@ -700,7 +700,7 @@ xref: FMA:86667 is_a: CL:0000219 ! motile cell is_a: CL:0011012 ! neural crest cell is_a: CL:0011026 ! progenitor cell -relationship: develops_from CL:0007004 ! premigratory neural crest cell +relationship: RO:0002202 CL:0007004 ! develops from premigratory neural crest cell [Term] id: CL:0000335 @@ -726,8 +726,8 @@ is_a: CL:0000007 ! early embryonic cell (metazoa) is_a: CL:0000255 ! eukaryotic cell is_a: CL:0010017 ! zygote intersection_of: CL:0010017 ! zygote -intersection_of: only_in_taxon NCBITaxon:33208 ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +intersection_of: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa [Term] id: CL:0000393 @@ -751,8 +751,8 @@ synonym: "satellite cell" RELATED [] xref: FMA:84798 is_a: CL:0000056 ! myoblast intersection_of: CL:0000056 ! myoblast -intersection_of: develops_into CL:0000192 ! smooth muscle cell -relationship: develops_into CL:0000192 ! smooth muscle cell +intersection_of: RO:0002203 CL:0000192 ! develops into smooth muscle cell +relationship: RO:0002203 CL:0000192 ! develops into smooth muscle cell [Term] id: CL:0000540 @@ -773,8 +773,8 @@ is_a: CL:0000393 ! electrically responsive cell is_a: CL:0000404 ! electrically signaling cell is_a: CL:0002319 ! neural cell relationship: capable_of GO:0019226 ! transmission of nerve impulse -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://www.swissbiopics.org/api/image/Neuron_cells.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Neuron_cells.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000547 @@ -817,10 +817,10 @@ relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-span relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD5 relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G -relationship: develops_from CL:0000038 ! erythroid progenitor cell relationship: has_part CL:0017503 ! basophilic cytoplasm relationship: has_part GO:0005730 ! nucleolus relationship: RO:0002104 PR:000001945 ! has plasma membrane part transferrin receptor protein 1 +relationship: RO:0002202 CL:0000038 ! develops from erythroid progenitor cell [Term] id: CL:0000549 @@ -858,10 +858,10 @@ intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017504 ! polychromatophilic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin intersection_of: RO:0002104 PR:000001945 ! has plasma membrane part transferrin receptor protein 1 -relationship: develops_from CL:0000549 ! basophilic erythroblast relationship: has_part CL:0017504 ! polychromatophilic cytoplasm relationship: has_part GO:0000792 ! heterochromatin relationship: RO:0002104 PR:000001945 ! has plasma membrane part transferrin receptor protein 1 +relationship: RO:0002202 CL:0000549 ! develops from basophilic erythroblast [Term] id: CL:0000552 @@ -877,9 +877,9 @@ is_a: CL:0000765 {is_inferred="true"} ! erythroblast intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017502 ! acidophilic cytoplasm intersection_of: participates_in GO:0030263 ! apoptotic chromosome condensation -relationship: develops_from CL:0000550 ! polychromatophilic erythroblast relationship: has_part CL:0017502 ! acidophilic cytoplasm relationship: participates_in GO:0030263 ! apoptotic chromosome condensation +relationship: RO:0002202 CL:0000550 ! develops from polychromatophilic erythroblast [Term] id: CL:0000553 @@ -933,8 +933,8 @@ relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surfac relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -relationship: develops_from CL:0000050 ! megakaryocyte-erythroid progenitor cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000050 ! develops from megakaryocyte-erythroid progenitor cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000556 @@ -953,8 +953,8 @@ xref: FMA:83555 is_a: CL:0000763 {is_inferred="true"} ! myeloid cell disjoint_from: CL:0000764 ! erythroid lineage cell relationship: bearer_of PATO:0001393 ! euploid -relationship: develops_from CL:0000553 ! megakaryocyte progenitor cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000553 ! develops from megakaryocyte progenitor cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000558 @@ -993,8 +993,8 @@ relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-span relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD5 relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G -relationship: develops_from CL:0000552 ! orthochromatic erythroblast relationship: RO:0002104 PR:000001945 ! has plasma membrane part transferrin receptor protein 1 +relationship: RO:0002202 CL:0000552 ! develops from orthochromatic erythroblast [Term] id: CL:0000566 @@ -1010,10 +1010,10 @@ intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: RO:0002104 PR:000001444 ! has plasma membrane part cadherin-5 intersection_of: RO:0002104 PR:000002112 ! has plasma membrane part vascular endothelial growth factor receptor 2 intersection_of: RO:0002104 PR:000016043 ! has plasma membrane part T-cell acute lymphocytic leukemia protein 1 -relationship: develops_from CL:0000134 ! mesenchymal stem cell relationship: RO:0002104 PR:000001444 ! has plasma membrane part cadherin-5 relationship: RO:0002104 PR:000002112 ! has plasma membrane part vascular endothelial growth factor receptor 2 relationship: RO:0002104 PR:000016043 ! has plasma membrane part T-cell acute lymphocytic leukemia protein 1 +relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell [Term] id: CL:0000586 @@ -1052,7 +1052,7 @@ intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0002001 ! renin secretion into blood stream intersection_of: part_of UBERON:0002113 ! kidney relationship: capable_of GO:0002001 ! renin secretion into blood stream -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000650 @@ -1066,7 +1066,7 @@ xref: CALOHA:TS-0617 xref: FMA:70972 xref: MESH:D050527 is_a: CL:0000669 ! pericyte -relationship: develops_from CL:0000134 ! mesenchymal stem cell +relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell [Term] id: CL:0000666 @@ -1094,7 +1094,7 @@ is_a: CL:0000183 ! contractile cell is_a: CL:0000630 ! supporting cell is_a: CL:0002320 ! connective tissue cell is_a: CL:0008034 ! mural cell -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000680 @@ -1103,9 +1103,9 @@ def: "A non-terminally differentiated cell that is capable of developing into a subset: cellxgene_subset is_a: CL:0000055 ! non-terminally differentiated cell intersection_of: CL:0011115 ! precursor cell -intersection_of: develops_into CL:0000187 ! muscle cell -relationship: develops_from CL:0000222 ! mesodermal cell -relationship: develops_into CL:0000187 ! muscle cell +intersection_of: RO:0002203 CL:0000187 ! develops into muscle cell +relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell +relationship: RO:0002203 CL:0000187 ! develops into muscle cell [Term] id: CL:0000723 @@ -1128,8 +1128,8 @@ xref: CALOHA:TS-0647 xref: MESH:D022423 is_a: CL:0000988 {is_inferred="true"} ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell -intersection_of: develops_from CL:0000049 ! common myeloid progenitor -relationship: develops_from CL:0000049 ! common myeloid progenitor +intersection_of: RO:0002202 CL:0000049 ! develops from common myeloid progenitor +relationship: RO:0002202 CL:0000049 ! develops from common myeloid progenitor [Term] id: CL:0000764 @@ -1143,7 +1143,7 @@ xref: CALOHA:TS-0290 xref: FMA:62845 xref: FMA:83516 is_a: CL:0000763 ! myeloid cell -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000765 @@ -1186,8 +1186,8 @@ relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-span relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD5 relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G -relationship: develops_from CL:0000547 ! proerythroblast relationship: has_part GO:0005634 ! nucleus +relationship: RO:0002202 CL:0000547 ! develops from proerythroblast [Term] id: CL:0000837 @@ -1234,9 +1234,9 @@ relationship: CL:4030046 PR:000001869 ! lacks_plasma_membrane_part interleukin-7 relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -relationship: develops_from CL:0000037 ! hematopoietic stem cell -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule +relationship: RO:0002202 CL:0000037 ! develops from hematopoietic stem cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000839 @@ -1254,7 +1254,7 @@ is_a: CL:0011026 ! progenitor cell intersection_of: CL:0002031 ! hematopoietic lineage restricted progenitor cell intersection_of: capable_of GO:0030099 ! myeloid cell differentiation relationship: capable_of GO:0030099 ! myeloid cell differentiation -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000988 @@ -1280,8 +1280,8 @@ intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001400 ! unipotent disjoint_from: CL:0002032 ! hematopoietic oligopotent progenitor cell relationship: bearer_of PATO:0001400 ! unipotent -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002032 ! hematopoietic oligopotent progenitor cell +relationship: RO:0002202 CL:0002032 ! develops from hematopoietic oligopotent progenitor cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:20Z [Term] @@ -1294,8 +1294,8 @@ is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001401 ! oligopotent relationship: bearer_of PATO:0001401 ! oligopotent -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000837 ! hematopoietic multipotent progenitor cell +relationship: RO:0002202 CL:0000837 ! develops from hematopoietic multipotent progenitor cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:27Z [Term] @@ -1305,9 +1305,9 @@ def: "An epithelial cell derived from ectoderm." [FMA:69074, GOC:tfm] xref: FMA:69074 is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell -intersection_of: develops_from CL:0000221 ! ectodermal cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000221 ! ectodermal cell +intersection_of: RO:0002202 CL:0000221 ! develops from ectodermal cell +relationship: RO:0002202 CL:0000221 ! develops from ectodermal cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T03:38:22Z [Term] @@ -1318,9 +1318,9 @@ synonym: "epithelial mesenchymal cell" EXACT [] xref: FMA:69076 is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell -intersection_of: develops_from CL:0000222 ! mesodermal cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000222 ! mesodermal cell +intersection_of: RO:0002202 CL:0000222 ! develops from mesodermal cell +relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T03:49:14Z [Term] @@ -1335,7 +1335,7 @@ xref: BTO:0001854 xref: CALOHA:TS-1106 xref: FMA:67755 is_a: CL:0000115 ! endothelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T02:06:40Z [Term] @@ -1352,8 +1352,8 @@ is_a: CL:1000618 {is_inferred="true"} ! juxtaglomerular complex cell is_a: CL:1001318 ! renal interstitial pericyte intersection_of: CL:0002320 ! connective tissue cell intersection_of: part_of UBERON:0002321 ! extraglomerular mesangium -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002321 ! extraglomerular mesangium +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T02:20:55Z [Term] @@ -1369,7 +1369,7 @@ is_a: CL:0000666 ! fenestrated cell is_a: CL:1000746 ! glomerular cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0000074 ! renal glomerulus -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-26T10:59:44Z [Term] @@ -1381,7 +1381,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0002505 ! nucleated relationship: bearer_of PATO:0002505 ! nucleated -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T03:32:33Z [Term] @@ -1416,7 +1416,7 @@ is_a: CL:1000615 ! kidney cortex tubule cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0004134 ! proximal tubule relationship: part_of UBERON:0004134 ! proximal tubule -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0002319 @@ -1428,8 +1428,8 @@ xref: FMA:70333 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001016 ! nervous system -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001016 ! nervous system +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T01:34:57Z [Term] @@ -1443,8 +1443,8 @@ xref: MESH:D003239 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0002384 ! connective tissue -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002384 ! connective tissue +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T03:01:54Z [Term] @@ -1455,7 +1455,7 @@ xref: CALOHA:TS-0263 xref: FMA:82840 xref: WBbt:0007028 is_a: CL:0000000 ! cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T03:39:21Z [Term] @@ -1471,8 +1471,8 @@ xref: FMA:84791 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0007100 ! primary circulatory organ -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0007100 ! primary circulatory organ +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T09:37:22Z [Term] @@ -1485,7 +1485,7 @@ is_a: CL:0000066 ! epithelial cell is_a: CL:1000497 {is_inferred="true"} ! kidney cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0002113 ! kidney -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-08T10:46:34Z [Term] @@ -1494,7 +1494,7 @@ name: embryonic blood vessel endothelial progenitor cell def: "An endothelial progenitor cell that participates in angiogenesis during development." [GOC:tfm] comment: See CL:0002619. is_a: CL:0000222 ! mesodermal cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T04:20:39Z [Term] @@ -1514,8 +1514,8 @@ def: "A cell that is part of a cortex of kidney." [] is_a: CL:1000497 ! kidney cell intersection_of: CL:1000497 ! kidney cell intersection_of: part_of UBERON:0001225 ! cortex of kidney -relationship: dc-contributor https://orcid.org/0000-0002-0956-8634 relationship: part_of UBERON:0001225 ! cortex of kidney +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0956-8634 creation_date: 2011-10-25T03:49:41Z [Term] @@ -1531,9 +1531,9 @@ id: CL:0007004 name: premigratory neural crest cell def: "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells." [UBERONREF:0000002] is_a: CL:0011012 ! neural crest cell -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 -relationship: develops_from CL:0000133 ! neurectodermal cell relationship: part_of UBERON:0002342 ! neural crest +relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-27T08:27:35Z [Term] @@ -1569,7 +1569,7 @@ synonym: "mesenchyme cell" EXACT [] is_a: CL:0000219 ! motile cell relationship: capable_of GO:0016477 ! cell migration relationship: part_of UBERON:0003104 ! mesenchyme -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0008034 @@ -1579,8 +1579,8 @@ subset: added_for_HCA subset: cellxgene_subset subset: human_reference_atlas is_a: CL:4033054 ! perivascular cell -relationship: dc-contributor https://orcid.org/0000-0002-7073-9172 -relationship: present_in_taxon NCBITaxon:9606 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2020-02-29T17:33:55Z [Term] @@ -1589,7 +1589,7 @@ name: zygote def: "A zygote in a plant or an animal." [] xref: MESH:D015053 is_a: CL:0000000 ! cell -relationship: seeAlso https://github.com/obophenotype/cell-ontology/issues/786 +property_value: seeAlso https://github.com/obophenotype/cell-ontology/issues/786 [Term] id: CL:0011012 @@ -1606,9 +1606,9 @@ def: "A precursor cell that has a tendency to differentiate into a specific type subset: cellxgene_subset is_a: CL:0011115 ! precursor cell intersection_of: CL:0011115 ! precursor cell -intersection_of: develops_from CL:0000034 ! stem cell -relationship: dc-contributor https://orcid.org/0000-0001-5208-3432 -relationship: develops_from CL:0000034 ! stem cell +intersection_of: RO:0002202 CL:0000034 ! develops from stem cell +relationship: RO:0002202 CL:0000034 ! develops from stem cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011115 @@ -1630,7 +1630,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0002418 ! acidophilic relationship: bearer_of PATO:0002418 ! acidophilic -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-22T04:23:25Z [Term] @@ -1641,7 +1641,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0002094 ! basophilic relationship: bearer_of PATO:0002094 ! basophilic -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-22T04:24:54Z [Term] @@ -1652,7 +1652,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0070047 ! polychromatophilic relationship: bearer_of PATO:0070047 ! polychromatophilic -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-28T04:25:23Z [Term] @@ -1696,7 +1696,7 @@ is_a: CL:1000449 ! epithelial cell of nephron is_a: CL:1001225 {is_inferred="true"} ! kidney collecting duct cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001232 ! collecting duct of renal tubule -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000494 @@ -1740,7 +1740,7 @@ relationship: part_of UBERON:0005215 ! kidney interstitium [Term] id: CL:1000504 name: kidney medulla cell -def: "A cell that is part of a renal medulla." [] +def: "A cell that is part of a renal medulla." [PMID:22343825] xref: KUPO:0001017 is_a: CL:1000497 ! kidney cell intersection_of: CL:1000497 ! kidney cell @@ -1838,6 +1838,7 @@ relationship: part_of UBERON:0002303 ! juxtaglomerular apparatus [Term] id: CL:1000692 name: kidney interstitial fibroblast +def: "A fibroblast that is part of an interstitial compartment of a kidney." [PMID:10559635] subset: cellxgene_subset subset: human_reference_atlas xref: KUPO:0001102 @@ -1845,7 +1846,7 @@ is_a: CL:0000057 ! fibroblast is_a: CL:1000500 ! kidney interstitial cell intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0005215 ! kidney interstitium -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000746 @@ -1868,7 +1869,7 @@ is_a: CL:1000615 ! kidney cortex tubule cell intersection_of: CL:1000494 ! nephron tubule epithelial cell intersection_of: part_of UBERON:0005097 ! renal connecting tubule relationship: part_of UBERON:0005097 ! renal connecting tubule -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000849 @@ -1881,15 +1882,16 @@ is_a: CL:0002305 {is_inferred="true"} ! epithelial cell of distal tubule intersection_of: CL:0002305 ! epithelial cell of distal tubule intersection_of: part_of UBERON:0001292 ! distal convoluted tubule relationship: part_of UBERON:0001292 ! distal convoluted tubule -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000854 name: kidney blood vessel cell +def: "A blood vessel cell that is part of a kidney." [PMID:34843404] xref: KUPO:0001014 is_a: CL:0002584 ! renal cortical epithelial cell is_a: CL:1000504 {is_inferred="true"} ! kidney medulla cell -intersection_of: CL:1000504 ! kidney medulla cell +intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0003517 ! kidney blood vessel relationship: part_of UBERON:0003517 ! kidney blood vessel relationship: participates_in GO:0008015 ! blood circulation @@ -1981,7 +1983,7 @@ is_a: CL:0000669 {is_inferred="true"} ! pericyte is_a: CL:1000500 ! kidney interstitial cell intersection_of: CL:0000669 ! pericyte intersection_of: part_of UBERON:0005215 ! kidney interstitium -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4030031 @@ -1991,7 +1993,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0005169 ! interstitial tissue relationship: part_of UBERON:0005169 ! interstitial tissue -property_value: dcterms-date "2022-11-30T14:35:08Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2022-11-30T14:35:08Z" xsd:dateTime [Term] id: CL:4033054 @@ -2001,8 +2003,8 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: adjacent_to UBERON:0002049 ! vasculature relationship: adjacent_to UBERON:0002049 ! vasculature -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -property_value: dcterms-date "2023-08-22T13:40:28Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-08-22T13:40:28Z" xsd:dateTime [Term] id: GO:0000003 @@ -2053,8 +2055,8 @@ is_a: GO:0007049 ! cell cycle intersection_of: GO:0007049 ! cell cycle intersection_of: has_part GO:0140014 ! mitotic nuclear division relationship: has_part GO:0140014 ! mitotic nuclear division -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota [Term] id: GO:0000280 @@ -2106,7 +2108,7 @@ namespace: biological_process def: "A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities." [GOC:dph, GOC:go_curators, GOC:tb, ISBN:978-0-07-139011-8] comment: Action potentials typically propagate across excitable membranes. This class covers both action potentials that propagate and those that fail to do so. is_a: GO:0042391 ! regulation of membrane potential -relationship: never_in_taxon NCBITaxon:4895 +property_value: RO:0002161 NCBITaxon:4895 [Term] id: GO:0001578 @@ -2314,7 +2316,7 @@ subset: goslim_mouse subset: goslim_pir xref: Wikipedia:Immune_system is_a: GO:0008150 ! biological_process -relationship: never_in_taxon NCBITaxon:4895 +property_value: RO:0002161 NCBITaxon:4895 [Term] id: GO:0003008 @@ -2492,8 +2494,8 @@ namespace: cellular_component def: "A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures." [GOC:dos, GOC:mah, ISBN:0721639976, PMID:19693541, PMID:21421911] xref: Wikipedia:Collagen is_a: GO:0032991 ! protein-containing complex -relationship: in_taxon NCBITaxon:33208 {all_only="true", source="PMID:12382326"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 {source="PMID:12382326"} ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 {source="PMID:12382326"} ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true", source="PMID:12382326"} ! in taxon Metazoa [Term] id: GO:0005587 @@ -2574,8 +2576,8 @@ xref: NIF_Subcellular:sao1702920020 xref: Wikipedia:Cell_nucleus is_a: GO:0043231 ! intracellular membrane-bounded organelle disjoint_from: GO:0005737 ! cytoplasm -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota [Term] id: GO:0005694 @@ -2674,10 +2676,10 @@ synonym: "Golgi ribbon" NARROW [] xref: NIF_Subcellular:sao451912436 xref: Wikipedia:Golgi_apparatus is_a: GO:0043231 ! intracellular membrane-bounded organelle -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota relationship: part_of GO:0005737 ! cytoplasm relationship: part_of GO:0012505 ! endomembrane system +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota [Term] id: GO:0005798 @@ -2812,14 +2814,14 @@ is_a: GO:0043227 ! membrane-bounded organelle is_a: GO:0120025 ! plasma membrane bounded cell projection is_a: PR:000050567 ! protein-containing material entity relationship: has_part GO:0030990 ! intraciliary transport particle -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: never_in_taxon NCBITaxon:3176 -relationship: never_in_taxon NCBITaxon:3312 -relationship: never_in_taxon NCBITaxon:3378 -relationship: never_in_taxon NCBITaxon:3398 -relationship: never_in_taxon NCBITaxon:4890 -relationship: never_in_taxon NCBITaxon:5782 -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota +property_value: RO:0002161 NCBITaxon:3176 +property_value: RO:0002161 NCBITaxon:3312 +property_value: RO:0002161 NCBITaxon:3378 +property_value: RO:0002161 NCBITaxon:3398 +property_value: RO:0002161 NCBITaxon:4890 +property_value: RO:0002161 NCBITaxon:5782 [Term] id: GO:0005930 @@ -2986,11 +2988,11 @@ synonym: "type I programmed cell death" NARROW [] xref: Wikipedia:Apoptosis is_a: GO:0012501 ! programmed cell death relationship: ends_with GO:0097194 ! execution phase of apoptosis -relationship: in_taxon NCBITaxon:33154 {all_only="true"} ! Opisthokonta -relationship: never_in_taxon NCBITaxon:2 -relationship: never_in_taxon NCBITaxon:4896 -relationship: only_in_taxon NCBITaxon:33154 ! Opisthokonta +relationship: RO:0002160 NCBITaxon:33154 ! only in taxon Opisthokonta +relationship: RO:0002162 NCBITaxon:33154 {all_only="true"} ! in taxon Opisthokonta relationship: starts_with GO:0097190 ! apoptotic signaling pathway +property_value: RO:0002161 NCBITaxon:2 +property_value: RO:0002161 NCBITaxon:4896 [Term] id: GO:0006921 @@ -3492,8 +3494,8 @@ namespace: biological_process def: "The process whose specific outcome is the progression of an embryo over time, from zygote formation until the end of the embryonic life stage. The end of the embryonic life stage is organism-specific and may be somewhat arbitrary; for mammals it is usually considered to be birth, for insects the hatching of the first instar larva from the eggshell." [GOC:go_curators, GOC:isa_complete, GOC:mtg_sensu] synonym: "embryogenesis" BROAD [] is_a: GO:0009790 ! embryo development -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0009888 @@ -3506,14 +3508,14 @@ xref: Wikipedia:Histogenesis is_a: GO:0048856 ! anatomical structure development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0000479 ! tissue -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: never_in_taxon NCBITaxon:147554 -relationship: never_in_taxon NCBITaxon:33630 -relationship: never_in_taxon NCBITaxon:33682 -relationship: never_in_taxon NCBITaxon:38254 -relationship: never_in_taxon NCBITaxon:4891 -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota relationship: results_in_development_of UBERON:0000479 ! tissue +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota +property_value: RO:0002161 NCBITaxon:147554 +property_value: RO:0002161 NCBITaxon:33630 +property_value: RO:0002161 NCBITaxon:33682 +property_value: RO:0002161 NCBITaxon:38254 +property_value: RO:0002161 NCBITaxon:4891 [Term] id: GO:0009987 @@ -3743,7 +3745,7 @@ namespace: biological_process def: "The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues." [GOC:cjm, GOC:dph, GOC:ems, GOC:pf, Wikipedia:Cell_migration] xref: Wikipedia:Cell_migration is_a: GO:0048870 ! cell motility -relationship: never_in_taxon NCBITaxon:4890 +property_value: RO:0002161 NCBITaxon:4890 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24787" xsd:anyURI [Term] @@ -3993,7 +3995,7 @@ subset: goslim_drosophila subset: goslim_flybase_ribbon xref: Wikipedia:Cell_junction is_a: GO:0110165 ! cellular anatomical entity -relationship: never_in_taxon NCBITaxon:4751 +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0030097 @@ -4261,10 +4263,10 @@ subset: goslim_pir synonym: "organismal physiological process" EXACT [] synonym: "single-multicellular organism process" RELATED [] is_a: GO:0008150 ! biological_process -relationship: never_in_taxon NCBITaxon:2 -relationship: never_in_taxon NCBITaxon:2157 -relationship: never_in_taxon NCBITaxon:4896 -relationship: never_in_taxon NCBITaxon:4932 +property_value: RO:0002161 NCBITaxon:2 +property_value: RO:0002161 NCBITaxon:2157 +property_value: RO:0002161 NCBITaxon:4896 +property_value: RO:0002161 NCBITaxon:4932 created_by: jl creation_date: 2012-09-19T16:07:47Z @@ -4517,7 +4519,7 @@ def: "Self-propelled movement of a cell or organism from one location to another subset: goslim_chembl subset: goslim_pir is_a: GO:0008150 ! biological_process -relationship: never_in_taxon NCBITaxon:451864 +property_value: RO:0002161 NCBITaxon:451864 [Term] id: GO:0040016 @@ -4553,16 +4555,16 @@ intersection_of: GO:0006810 ! transport intersection_of: has_primary_input GO:0032991 ! protein-containing complex intersection_of: occurs_in GO:0005929 ! cilium intersection_of: results_in_transport_along GO:0005874 ! microtubule -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: never_in_taxon NCBITaxon:3176 -relationship: never_in_taxon NCBITaxon:3312 -relationship: never_in_taxon NCBITaxon:3378 -relationship: never_in_taxon NCBITaxon:3398 -relationship: never_in_taxon NCBITaxon:4890 -relationship: never_in_taxon NCBITaxon:5782 relationship: occurs_in GO:0005929 ! cilium -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota relationship: part_of GO:0044782 ! cilium organization +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota +property_value: RO:0002161 NCBITaxon:3176 +property_value: RO:0002161 NCBITaxon:3312 +property_value: RO:0002161 NCBITaxon:3378 +property_value: RO:0002161 NCBITaxon:3398 +property_value: RO:0002161 NCBITaxon:4890 +property_value: RO:0002161 NCBITaxon:5782 [Term] id: GO:0042391 @@ -4613,8 +4615,8 @@ name: chordate embryonic development namespace: biological_process def: "The process whose specific outcome is the progression of the embryo over time, from zygote formation through a stage including a notochord and neural tube until birth or egg hatching." [GOC:mtg_sensu] is_a: GO:0009792 ! embryo development ending in birth or egg hatching -relationship: in_taxon NCBITaxon:7711 {all_only="true"} ! Chordata -relationship: only_in_taxon NCBITaxon:7711 ! Chordata +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {all_only="true"} ! in taxon Chordata [Term] id: GO:0043073 @@ -4845,9 +4847,9 @@ is_a: GO:0006996 ! organelle organization is_a: GO:0120036 ! plasma membrane bounded cell projection organization intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0005929 ! cilium -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota relationship: results_in_organization_of GO:0005929 ! cilium +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota created_by: jl creation_date: 2013-03-27T15:09:58Z @@ -4879,8 +4881,8 @@ synonym: "synaptic junction" EXACT [] xref: NIF_Subcellular:sao914572699 xref: Wikipedia:Chemical_synapse is_a: GO:0030054 ! cell junction -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0046903 @@ -5163,8 +5165,8 @@ is_a: GO:0003008 ! system process intersection_of: GO:0003008 ! system process intersection_of: has_participant UBERON:0001016 ! nervous system relationship: has_participant UBERON:0001016 ! nervous system -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13824" xsd:anyURI [Term] @@ -5303,8 +5305,8 @@ is_a: GO:0051179 ! localization intersection_of: GO:0051179 ! localization intersection_of: has_primary_input GO:0043226 ! organelle relationship: has_primary_input GO:0043226 ! organelle -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19809" xsd:anyURI [Term] @@ -5352,10 +5354,10 @@ synonym: "positioning within cell" NARROW [] is_a: GO:0051234 ! establishment of localization intersection_of: GO:0051234 ! establishment of localization intersection_of: occurs_in CL:0000000 ! cell -relationship: in_taxon NCBITaxon:131567 {all_only="true"} ! cellular organisms relationship: occurs_in CL:0000000 ! cell -relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms relationship: part_of GO:0051641 ! cellular localization +relationship: RO:0002160 NCBITaxon:131567 ! only in taxon cellular organisms +relationship: RO:0002162 NCBITaxon:131567 {all_only="true"} ! in taxon cellular organisms [Term] id: GO:0051650 @@ -5447,15 +5449,15 @@ relationship: has_part GO:0035735 ! intraciliary transport involved in cilium as relationship: has_part GO:0061512 ! protein localization to cilium relationship: has_part GO:0097712 ! vesicle targeting, trans-Golgi to periciliary membrane compartment relationship: has_part GO:1905349 ! ciliary transition zone assembly -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: never_in_taxon NCBITaxon:3176 -relationship: never_in_taxon NCBITaxon:3312 -relationship: never_in_taxon NCBITaxon:3378 -relationship: never_in_taxon NCBITaxon:3398 -relationship: never_in_taxon NCBITaxon:4890 -relationship: never_in_taxon NCBITaxon:5782 relationship: results_in_assembly_of GO:0005929 ! cilium +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota relationship: starts_with GO:0097711 ! ciliary basal body-plasma membrane docking +property_value: RO:0002161 NCBITaxon:3176 +property_value: RO:0002161 NCBITaxon:3312 +property_value: RO:0002161 NCBITaxon:3378 +property_value: RO:0002161 NCBITaxon:3398 +property_value: RO:0002161 NCBITaxon:4890 +property_value: RO:0002161 NCBITaxon:5782 [Term] id: GO:0060429 @@ -5500,14 +5502,14 @@ is_a: GO:0033365 ! protein localization to organelle intersection_of: GO:0008104 ! protein localization intersection_of: has_target_end_location GO:0005929 ! cilium relationship: has_target_end_location GO:0005929 ! cilium -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: never_in_taxon NCBITaxon:3176 -relationship: never_in_taxon NCBITaxon:3312 -relationship: never_in_taxon NCBITaxon:3378 -relationship: never_in_taxon NCBITaxon:3398 -relationship: never_in_taxon NCBITaxon:4890 -relationship: never_in_taxon NCBITaxon:5782 -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota +property_value: RO:0002161 NCBITaxon:3176 +property_value: RO:0002161 NCBITaxon:3312 +property_value: RO:0002161 NCBITaxon:3378 +property_value: RO:0002161 NCBITaxon:3398 +property_value: RO:0002161 NCBITaxon:4890 +property_value: RO:0002161 NCBITaxon:5782 created_by: dph creation_date: 2013-03-22T15:41:44Z @@ -5517,8 +5519,8 @@ name: collagen-containing extracellular matrix namespace: cellular_component def: "An extracellular matrix consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that provides not only essential physical scaffolding for the cellular constituents but can also initiate crucial biochemical and biomechanical cues required for tissue morphogenesis, differentiation and homeostasis. The components are secreted by cells in the vicinity and form a sheet underlying or overlying cells such as endothelial and epithelial cells." [GOC:BHF, GOC:rph, PMID:21123617] is_a: GO:0031012 ! extracellular matrix -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa created_by: dph creation_date: 2018-04-13T12:47:21Z @@ -6053,9 +6055,9 @@ subset: goslim_synapse is_a: GO:0007267 ! cell-cell signaling intersection_of: GO:0007267 ! cell-cell signaling intersection_of: occurs_in GO:0045202 ! synapse -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa relationship: occurs_in GO:0045202 ! synapse -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0099537 @@ -6282,18 +6284,16 @@ namespace: ncbi_taxonomy xref: GC_ID:1 xref: PMID:15371245 is_a: NCBITaxon:337687 ! Muroidea -property_value: has_rank NCBITaxon:family [Term] id: NCBITaxon:10088 name: Mus namespace: ncbi_taxonomy -synonym: "mice" EXACT OMO:0003003 [] +synonym: "mice" EXACT genbank_common_name [] synonym: "mouse" EXACT OMO:0003003 [] synonym: "Mus" EXACT scientific_name [] xref: GC_ID:1 is_a: NCBITaxon:39107 ! Murinae -property_value: has_rank NCBITaxon:genus [Term] id: NCBITaxon:10090 @@ -6304,7 +6304,6 @@ synonym: "house mouse" EXACT genbank_common_name [] synonym: "mouse" EXACT OMO:0003003 [] xref: GC_ID:1 is_a: NCBITaxon:862507 ! Mus -property_value: has_rank NCBITaxon:species [Term] id: NCBITaxon:117570 @@ -6312,7 +6311,6 @@ name: Teleostomi namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:7776 ! Gnathostomata -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:117571 @@ -6322,7 +6320,6 @@ alt_id: NCBITaxon:40673 synonym: "bony vertebrates" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:117570 ! Teleostomi -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:131567 @@ -6338,7 +6335,6 @@ name: Dipnotetrapodomorpha namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:8287 ! Sarcopterygii -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:1437010 @@ -6349,7 +6345,6 @@ xref: GC_ID:1 xref: PMID:11743200 xref: PMID:11791233 is_a: NCBITaxon:9347 ! Eutheria -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:1963758 @@ -6359,7 +6354,6 @@ synonym: "mice and others" EXACT genbank_common_name [] synonym: "Sciurognathi" RELATED in_part [] xref: GC_ID:1 is_a: NCBITaxon:9989 ! Rodentia -property_value: has_rank NCBITaxon:suborder [Term] id: NCBITaxon:2759 @@ -6376,7 +6370,6 @@ xref: GC_ID:1 xref: PMID:23020233 xref: PMID:30257078 is_a: NCBITaxon:131567 ! cellular organisms -property_value: has_rank NCBITaxon:superkingdom [Term] id: NCBITaxon:314146 @@ -6388,7 +6381,6 @@ xref: PMID:12082125 xref: PMID:12878460 xref: PMID:15522813 is_a: NCBITaxon:1437010 ! Boreoeutheria -property_value: has_rank NCBITaxon:superorder [Term] id: NCBITaxon:314147 @@ -6400,7 +6392,6 @@ xref: PMID:11214319 xref: PMID:12082125 xref: PMID:15522813 is_a: NCBITaxon:314146 ! Euarchontoglires -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:32523 @@ -6409,7 +6400,6 @@ namespace: ncbi_taxonomy synonym: "tetrapods" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:1338369 ! Dipnotetrapodomorpha -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:32524 @@ -6418,7 +6408,6 @@ namespace: ncbi_taxonomy synonym: "amniotes" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:32523 ! Tetrapoda -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:32525 @@ -6427,7 +6416,6 @@ namespace: ncbi_taxonomy synonym: "Theria" EXACT scientific_name [] xref: GC_ID:1 is_a: NCBITaxon:40674 ! Mammalia -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:33154 @@ -6437,7 +6425,6 @@ synonym: "Fungi/Metazoa group" RELATED synonym [] synonym: "opisthokonts" RELATED synonym [] xref: GC_ID:1 is_a: NCBITaxon:2759 ! Eukaryota -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:33208 @@ -6449,7 +6436,6 @@ synonym: "metazoans" EXACT genbank_common_name [] synonym: "multicellular animals" EXACT OMO:0003003 [] xref: GC_ID:1 is_a: NCBITaxon:33154 ! Opisthokonta -property_value: has_rank NCBITaxon:kingdom [Term] id: NCBITaxon:33213 @@ -6457,7 +6443,6 @@ name: Bilateria namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:6072 ! Eumetazoa -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:33511 @@ -6466,7 +6451,6 @@ namespace: ncbi_taxonomy synonym: "deuterostomes" EXACT OMO:0003003 [] xref: GC_ID:1 is_a: NCBITaxon:33213 ! Bilateria -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:337687 @@ -6476,7 +6460,6 @@ xref: GC_ID:1 xref: PMID:15019624 xref: PMID:15371245 is_a: NCBITaxon:1963758 ! Myomorpha -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:39107 @@ -6485,7 +6468,6 @@ namespace: ncbi_taxonomy alt_id: NCBITaxon:109679 xref: GC_ID:1 is_a: NCBITaxon:10066 ! Muridae -property_value: has_rank NCBITaxon:subfamily [Term] id: NCBITaxon:40674 @@ -6495,7 +6477,6 @@ synonym: "mammals" EXACT genbank_common_name [] synonym: "mammals" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:32524 ! Amniota -property_value: has_rank NCBITaxon:class [Term] id: NCBITaxon:6072 @@ -6503,7 +6484,6 @@ name: Eumetazoa namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:33208 ! Metazoa -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:7711 @@ -6513,7 +6493,6 @@ synonym: "chordates" EXACT genbank_common_name [] synonym: "chordates" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:33511 ! Deuterostomia -property_value: has_rank NCBITaxon:phylum [Term] id: NCBITaxon:7742 @@ -6524,7 +6503,6 @@ synonym: "vertebrates" EXACT genbank_common_name [] synonym: "vertebrates" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:89593 ! Craniata -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:7776 @@ -6534,7 +6512,6 @@ synonym: "Gnathostomata" EXACT scientific_name [] synonym: "jawed vertebrates" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:7742 ! Vertebrata -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:8287 @@ -6542,7 +6519,6 @@ name: Sarcopterygii namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:117571 ! Euteleostomi -property_value: has_rank NCBITaxon:superclass [Term] id: NCBITaxon:862507 @@ -6551,7 +6527,6 @@ namespace: ncbi_taxonomy synonym: "Mus" EXACT scientific_name [] xref: GC_ID:1 is_a: NCBITaxon:10088 ! Mus -property_value: has_rank NCBITaxon:subgenus [Term] id: NCBITaxon:89593 @@ -6560,7 +6535,6 @@ namespace: ncbi_taxonomy synonym: "Craniata" EXACT scientific_name [] xref: GC_ID:1 is_a: NCBITaxon:7711 ! Chordata -property_value: has_rank NCBITaxon:subphylum [Term] id: NCBITaxon:9347 @@ -6573,7 +6547,6 @@ synonym: "placentals" EXACT genbank_common_name [] synonym: "placentals" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:32525 ! Theria -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:9989 @@ -6583,7 +6556,6 @@ synonym: "rodent" EXACT genbank_common_name [] synonym: "rodents" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:314147 ! Glires -property_value: has_rank NCBITaxon:order [Term] id: PATO:0000001 @@ -6634,7 +6606,6 @@ subset: value_slim synonym: "ramified" EXACT [] synonym: "ramiform" EXACT [] is_a: PATO:0002009 ! branchiness -property_value: RO:0002604 PATO:0000414 [Term] id: PATO:0000411 @@ -6794,7 +6765,6 @@ comment: This refers to the disposition of the bearer. subset: disposition_slim subset: value_slim is_a: PATO:0001579 ! contractility -property_value: RO:0002604 PATO:0001691 [Term] id: PATO:0001857 @@ -6804,7 +6774,6 @@ def: "A shape quality in a bearer by virtue of the bearer's curving inward." [Wo subset: cell_quality subset: value_slim is_a: PATO:0002005 ! concavity -property_value: RO:0002604 PATO:0001355 [Term] id: PATO:0001873 @@ -6881,7 +6850,6 @@ subset: attribute_slim xref: Image:http\://upload.wikimedia.org/wikipedia/commons/0/06/Convex_polygon_illustration1.png is_a: PATO:0002266 ! 3-D shape relationship: RO:0015011 PATO:0002006 ! has cross section 2-D shape -property_value: RO:0002604 PATO:0002008 [Term] id: PATO:0002009 @@ -6907,7 +6875,6 @@ namespace: quality def: "A concave quality inhering in a bearer by virtue of the bearer's curving inward on both sides or surfaces." [PATOC:GVG] subset: value_slim is_a: PATO:0001857 ! concave -property_value: RO:0002604 PATO:0002040 [Term] id: PATO:0002045 @@ -6919,7 +6886,7 @@ synonym: "dendriform" EXACT [] synonym: "dendroid" EXACT [] synonym: "dendroidal" EXACT [] is_a: PATO:0000402 ! branched -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-02-15T08:11:41Z [Term] @@ -6929,7 +6896,7 @@ namespace: quality def: "A quality inhering in a bearer by virtue of the bearer's having an empty space or cavity within." [url:http\://www.merriam-webster.com/dictionary/hollow] subset: value_slim is_a: PATO:0002014 ! structure, cavities -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-09-18T02:19:20Z [Term] @@ -6941,7 +6908,7 @@ subset: disposition_slim subset: mpath_slim subset: value_slim is_a: PATO:0070045 ! anatomical histological quality -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-10-05T12:05:23Z [Term] @@ -6952,7 +6919,7 @@ def: "A quality inhering in a bearer by virtue of the bearer's processing the fo subset: mpath_slim subset: value_slim is_a: PATO:0000141 ! structure -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-10-06T04:37:14Z [Term] @@ -6962,7 +6929,7 @@ namespace: quality def: "A quality inhering in a bearer by virtue of its constitution." [PATOC:GVG] subset: attribute_slim is_a: PATO:0001018 ! physical quality -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-03-15T04:35:27Z [Term] @@ -6972,7 +6939,7 @@ namespace: quality def: "A cylindrical shape quality inhering in a bearer by virtue of the bearer's being imperfectly cylindrical or approximately cylindrical." [url:http\://www.thefreedictionary.com/Subcylindrical] subset: value_slim is_a: PATO:0001873 ! cylindrical -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-07-13T04:22:30Z [Term] @@ -6981,7 +6948,7 @@ name: 3-D shape namespace: quality def: "A shape that inheres in a 3 dimensional entity." [PATOC:OREGON] is_a: PATO:0000052 ! shape -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-10-05T12:31:16Z [Term] @@ -6994,7 +6961,7 @@ synonym: "tube-shaped" EXACT [] synonym: "tubulate" EXACT [] is_a: PATO:0001873 ! cylindrical is_a: PATO:0002078 ! hollow -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-06-08T06:33:50Z [Term] @@ -7005,7 +6972,7 @@ def: "A convex 3-D shape quality inhering in a bearer by virtue of the bearer's comment: Note that a fiber shaped object may take any circuitous or straight path through space (think of a length of string or rope). subset: value_slim is_a: PATO:0002226 ! subcylindrical -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-09-09T04:50:10Z [Term] @@ -7015,7 +6982,7 @@ namespace: quality def: "A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt" [wiktionary:superellipse] synonym: "Lamé curve" EXACT [] is_a: PATO:0002006 ! 2-D shape -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-10-12T12:45:16Z [Term] @@ -7028,7 +6995,7 @@ subset: mpath_slim subset: value_slim synonym: "eosinophilic" EXACT [] is_a: PATO:0070045 ! anatomical histological quality -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2012-12-17T03:01:19Z [Term] @@ -7038,7 +7005,7 @@ namespace: quality def: "A structure quality inhering in a bearer by virtue of the bearer's being capable of swelling or stretching." [PATOC:WD] subset: value_slim is_a: PATO:0015008 ! distensibility -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2013-09-15T11:48:26Z [Term] @@ -7049,7 +7016,7 @@ def: "A nucleate quality inhering in a bearer by virtue of the bearer's having o subset: mpath_slim subset: value_slim is_a: PATO:0001404 ! nucleate quality -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2013-10-21T05:44:34Z [Term] @@ -7058,7 +7025,7 @@ name: disconnected namespace: quality def: "A structural quality inhering in the bearer by virtue of the bearer consisting of multiple structures lacking any physical connection to each other." [GOC:dos] is_a: PATO:0000141 ! structure -relationship: dc-contributor https://orcid.org/0000-0002-7073-9172 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2014-12-12T08:43:17Z [Term] @@ -7186,7 +7153,6 @@ synonym: "leukocyte adhesion receptor MO1" EXACT [] synonym: "neutrophil adherence receptor" EXACT [] xref: IUPHARobj:2452 is_a: PR:000001005 ! integrin alpha with A domain -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P11215 [Term] id: PR:000001018 @@ -7242,7 +7208,6 @@ synonym: "NCAM-1" EXACT [] synonym: "NCAM1" EXACT PRO-short-label [PRO:DNx] xref: IUPHARobj:2769 is_a: PR:000001023 ! neural cell adhesion molecule NCAM -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P13591 [Term] id: PR:000001083 @@ -7279,7 +7244,6 @@ synonym: "MAL" RELATED Gene-based [] synonym: "T-cell surface glycoprotein Lyt-2" EXACT [] synonym: "T-lymphocyte differentiation antigen T8/Leu-2" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P01732 [Term] id: PR:000001289 @@ -7323,7 +7287,6 @@ synonym: "CDH5" EXACT PRO-short-label [PRO:DNx] synonym: "vascular endothelial cadherin" EXACT [] synonym: "VE-cadherin" EXACT [] is_a: PR:000001327 ! cadherin -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P33151 [Term] id: PR:000001839 @@ -7338,7 +7301,6 @@ synonym: "lymphocyte antigen 1" EXACT [] synonym: "lymphocyte antigen T1/Leu-1" EXACT [] synonym: "Lyt-1" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P06127 [Term] id: PR:000001869 @@ -7356,7 +7318,6 @@ synonym: "IL7R" EXACT PRO-short-label [PRO:DNx] xref: IUPHARobj:1698 xref: PIRSF:PIRSF001960 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P16871 [Term] id: PR:000001889 @@ -7385,7 +7346,6 @@ synonym: "TFRC" EXACT PRO-short-label [PRO:DNx] synonym: "TR" RELATED [] synonym: "Trfr" RELATED Gene-based [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P02786 [Term] id: PR:000001971 @@ -7414,7 +7374,6 @@ synonym: "VEGFR-2" EXACT [] synonym: "VEGFR2" RELATED Gene-based [] xref: IUPHARobj:1813 is_a: PR:000001971 ! vascular endothelial growth factor receptor -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P35968 [Term] id: PR:000002976 @@ -7457,7 +7416,6 @@ synonym: "angiotensinogenase" RELATED [] synonym: "REN" EXACT PRO-short-label [PRO:DNx] xref: IUPHARobj:2413 is_a: PR:000050025 ! angiotensinogenase -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P00797 [Term] id: PR:000014841 @@ -7471,7 +7429,6 @@ synonym: "SHH" EXACT PRO-short-label [PRO:DNx] synonym: "Shh unprocessed N-terminal signaling and C-terminal autoprocessing domains" EXACT [] synonym: "ShhNC" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q15465 [Term] id: PR:000016043 @@ -7489,7 +7446,6 @@ synonym: "TAL-1" EXACT [] synonym: "TAL1" EXACT PRO-short-label [PRO:DNx] synonym: "TCL5" RELATED Gene-based [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P17542 [Term] id: PR:000025796 @@ -7507,8 +7463,8 @@ def: "A protein that is encoded in the genome of Mus musculus." [PRO:DAN] synonym: "mouse protein" EXACT PRO-short-label [PRO:DAN] is_a: PR:000036194 ! eukaryotic protein intersection_of: PR:000000001 ! protein -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus -relationship: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus +relationship: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:000036194 @@ -7518,8 +7474,8 @@ def: "A protein that is encoded in the genome of some Eukaryota." [PRO:DAN] synonym: "Eukaryota protein" EXACT [PRO:DAN] is_a: PR:000000001 ! protein intersection_of: PR:000000001 ! protein -intersection_of: only_in_taxon NCBITaxon:2759 ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +intersection_of: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota [Term] id: PR:000050025 @@ -7554,9 +7510,9 @@ subset: common_anatomy subset: upper_level xref: BFO:0000003 disjoint_from: UBERON:0001062 ! anatomical entity -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000025 @@ -7568,11 +7524,9 @@ synonym: "duct" NARROW [] xref: galen:Tube is_a: UBERON:0004111 ! anatomical conduit intersection_of: UBERON:0004111 ! anatomical conduit -intersection_of: has_quality PATO:0002299 ! tubular +intersection_of: RO:0000086 PATO:0002299 ! has quality tubular relationship: has_part UBERON:0013522 ! subdivision of tube -relationship: has_quality PATO:0002299 ! tubular -property_value: IAO:0000232 "not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts)" xsd:string -property_value: UBPROP:0000007 "tubular" xsd:string +relationship: RO:0000086 PATO:0002299 ! has quality tubular [Term] id: UBERON:0000026 @@ -7594,7 +7548,6 @@ xref: EFO:0000799 xref: EHDAA2:0003193 xref: EMAPA:37283 {source="MA:th"} xref: EV:0100155 -xref: FBbt:00007000 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: HAO:0000144 xref: MAT:0000023 xref: MESH:D005121 @@ -7605,11 +7558,7 @@ xref: VSAO:0000075 xref: Wikipedia:Appendage xref: XAO:0000218 is_a: UBERON:0000475 ! organism subdivision -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: UBPROP:0000001 "An appendage is an external body part, or natural prolongation, that protrudes from an organism's body, such as a vertebrate's limbs[BILA][BILA:0000018]." xsd:string {source="BILA:0000018"} -property_value: UBPROP:0000001 "Organ or organ part that is attached to the body of an organism. For example a limb[GO, modified][GO:0048736]." xsd:string {source="GO:0048736"} -property_value: UBPROP:0000007 "appendicular" xsd:string -property_value: UBPROP:0000008 "this is currently a subtype of organism subdivision - which would exclude feathers" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0000055 @@ -7621,7 +7570,7 @@ subset: human_reference_atlas subset: pheno_slim is_a: UBERON:0004111 ! anatomical conduit relationship: channel_for UBERON:0006314 ! bodily fluid -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000056 @@ -7663,17 +7612,10 @@ is_a: UBERON:0015212 ! lateral structure relationship: channel_for UBERON:0001088 ! urine relationship: channels_from UBERON:0001224 ! renal pelvis relationship: channels_into UBERON:0001255 ! urinary bladder -relationship: develops_from UBERON:0005081 {source="GO"} ! ureter ureteric bud -relationship: in_lateral_side_of UBERON:0000468 ! multicellular organism relationship: part_of UBERON:0036295 ! renal pelvis/ureter -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg" xsd:anyURI -property_value: UBPROP:0000001 "Anatomical structure consisting of long narrow duct which carries urine from the kidney to the urinary bladder.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010254", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "The duct of amniotes that carries urine from a metanephric kidney to the urinary bladder. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000605", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000605", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "ureteral" xsd:string -property_value: UBPROP:0000007 "ureteric" xsd:string -property_value: UBPROP:0000010 "in humans, consists of adventitial, muscular and mucoa layers" xsd:string +relationship: RO:0002202 UBERON:0005081 {source="GO"} ! develops from ureter ureteric bud +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000057 @@ -7709,13 +7651,11 @@ is_a: UBERON:0004120 ! mesoderm-derived structure relationship: capable_of_part_of GO:0060073 ! micturition relationship: channel_for UBERON:0001088 ! urine relationship: channels_from UBERON:0001255 ! urinary bladder -relationship: continuous_with UBERON:0001255 ! urinary bladder -relationship: develops_from UBERON:0000164 {notes="pelvic part of UG sinus gives rise to prostatic and membranous parts of urethra", source="Wikipedia"} ! primitive urogenital sinus -relationship: develops_from UBERON:0013241 {source="Wikipedia"} ! embryonic urethral groove relationship: part_of UBERON:0001556 ! lower urinary tract -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png" xsd:anyURI -property_value: UBPROP:0000007 "urethral" xsd:string -property_value: UBPROP:0000008 "In human males, the urethra travels through the penis, and carries semen as well as urine. In females, the urethra is shorter and emerges above the vaginal opening." xsd:string +relationship: RO:0002150 UBERON:0001255 ! continuous with urinary bladder +relationship: RO:0002202 UBERON:0000164 ! develops from primitive urogenital sinus +relationship: RO:0002202 UBERON:0013241 {source="Wikipedia"} ! develops from embryonic urethral groove +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png" xsd:anyURI [Term] id: UBERON:0000058 @@ -7728,7 +7668,6 @@ synonym: "ducts" RELATED OMO:0003004 [XAO:0004000] synonym: "exocrine duct" NARROW [] synonym: "exocrine gland duct" NARROW [] xref: AAO:0011123 -xref: FBbt:00100314 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:30320 xref: galen:Duct xref: NCIT:C12948 @@ -7740,11 +7679,9 @@ xref: XAO:0004000 xref: ZFA:0005171 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000063 ! organ subunit -relationship: conduit_for UBERON:0000463 ! organism substance relationship: has_part UBERON:0034969 ! epithelial layer of duct -relationship: has_quality PATO:0002299 ! tubular -property_value: UBPROP:0000001 "A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171]." xsd:string {source="ZFA:0005171"} -property_value: UBPROP:0000012 "Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here." xsd:string +relationship: RO:0000086 PATO:0002299 ! has quality tubular +relationship: RO:0002570 UBERON:0000463 ! conduit for organism substance [Term] id: UBERON:0000060 @@ -7756,13 +7693,11 @@ subset: upper_level synonym: "organ wall" RELATED [FMA:82482] synonym: "wall" BROAD [] synonym: "wall of organ" EXACT [FMA:82482] -xref: EMAPA:25036 xref: FMA:82482 xref: galen:Wall is_a: UBERON:0000064 ! organ part relationship: adjacent_to UBERON:0002553 ! anatomical cavity relationship: has_part UBERON:0004923 ! organ component layer -property_value: UBPROP:0000012 "in FMA, serosa is a wall" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0000061 @@ -7779,7 +7714,6 @@ xref: BILA:0000003 xref: CARO:0000003 xref: EHDAA2:0003003 xref: EMAPA:0 -xref: FBbt:00007001 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:305751 xref: FMA:67135 xref: GAID:781 @@ -7794,10 +7728,10 @@ xref: VHOG:0001759 xref: XAO:0003000 xref: ZFA:0000037 is_a: UBERON:0000465 ! material anatomical entity -relationship: existence_ends_during_or_before UBERON:0000071 ! death stage -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0002497 UBERON:0000071 ! existence ends during or before death stage +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000062 @@ -7824,14 +7758,12 @@ xref: Wikipedia:Organ_(anatomy) is_a: UBERON:0010000 ! multicellular anatomical structure disjoint_from: UBERON:0034921 ! multi organ part structure relationship: capable_of GO:0008150 ! biological_process -relationship: has_boundary UBERON:0006984 ! anatomical surface -relationship: never_in_taxon NCBITaxon:110815 {source="Wikipedia"} relationship: part_of UBERON:0000467 ! anatomical system -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: UBPROP:0000001 "Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." xsd:string {source="GO:0048513"} -property_value: UBPROP:0000012 "CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4" xsd:string +relationship: RO:0002002 UBERON:0006984 ! has 2D boundary anatomical surface +property_value: RO:0002161 NCBITaxon:110815 {source="Wikipedia"} +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000063 @@ -7844,9 +7776,7 @@ synonym: "organ segment" RELATED [FMA:86140] synonym: "segment of organ" RELATED [FMA:86140] xref: FMA:86140 is_a: UBERON:0000064 ! organ part -property_value: editor_note "FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction" xsd:string -property_value: UBPROP:0000001 "Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball." xsd:string {source="FMA:86140", version="3"} -property_value: UBPROP:0000001 "Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal." xsd:string {source="FMA:86140", version="1"} +property_value: IAO:0000116 "FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction" xsd:string [Term] id: UBERON:0000064 @@ -7867,10 +7797,9 @@ xref: SCTID:113343008 xref: SCTID:91717005 is_a: UBERON:0010000 ! multicellular anatomical structure relationship: part_of UBERON:0000062 ! organ -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: IAO:0000232 "currently defined in a very broad sense, may be replaced by more specific classes in the future" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000066 @@ -7919,7 +7848,7 @@ is_a: UBERON:0000105 ! life cycle stage disjoint_from: UBERON:0000092 ! post-embryonic stage relationship: precedes UBERON:0000066 ! fully formed stage relationship: precedes UBERON:0000092 ! post-embryonic stage -relationship: simultaneous_with GO:0009790 ! embryo development +relationship: RO:0002082 GO:0009790 ! simultaneous with embryo development [Term] id: UBERON:0000071 @@ -7932,11 +7861,10 @@ xref: XAO:0000437 xref: XtroDO:0000085 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage -relationship: ends UBERON:0000104 ! life cycle -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: UBPROP:0000012 "ncit:Death is an outcome" xsd:string {external_ontology="ncit"} +relationship: RO:0002229 UBERON:0000104 ! ends life cycle +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000074 @@ -7972,14 +7900,13 @@ xref: Wikipedia:Glomerulus xref: ZFA:0001288 is_a: UBERON:0000064 ! organ part is_a: UBERON:0004120 ! mesoderm-derived structure -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 -relationship: develops_from UBERON:0005749 ! glomerular tuft relationship: part_of UBERON:0001229 {source="FMA", source="MA"} ! renal corpuscle -relationship: present_in_taxon NCBITaxon:9606 -relationship: surrounded_by UBERON:0001230 ! glomerular capsule -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg" xsd:anyURI -property_value: UBPROP:0000012 "ZFA - The multi-tissue structure where the glomerular basement membrane supported by mesonephric podocytes filters blood from the glomerular capillaries. GUDMAP: 'Together, the Bowman's capsule and the glomerulus comprise the definitive renal corpuscle.' - here the glomerulus is part of the capsule?" xsd:string {external_ontology="ZFA"} +relationship: RO:0002202 UBERON:0005749 ! develops from glomerular tuft +relationship: RO:0002219 UBERON:0001230 ! surrounded by glomerular capsule +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2009-06-18T09:26:37Z [Term] @@ -7997,9 +7924,9 @@ xref: NCIT:C34076 xref: SCTID:118966000 xref: UMLS:C1519343 {source="ncithesaurus:Skeletal_System_Part"} is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision -relationship: composed_primarily_of UBERON:0004765 ! skeletal element -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0001434 ! skeletal system +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002473 UBERON:0004765 ! composed primarily of skeletal element [Term] id: UBERON:0000080 @@ -8040,14 +7967,8 @@ xref: XAO:0000141 xref: ZFA:0000529 is_a: UBERON:0002113 ! kidney is_a: UBERON:0004120 ! mesoderm-derived structure -relationship: develops_from UBERON:0002120 ! pronephros -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray986.png" xsd:anyURI -property_value: UBPROP:0000001 "A kidney formed of nephric tubules arising in the middle region of the nephric ridge; a transient embryonic stage that replaces the pronephros, but is itself replaced by the adult metanephros [in mammals; in fishes and amphibians it is the adult kidney]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000038", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000001 "Organ that is the definitive adult kidney. It replaces the earlier pronephros, which degenerates as the mesonephros becomes functional in feeding stage tadpoles.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010384", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates. (...) In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000038", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "mesonephric" xsd:string -property_value: UBPROP:0000008 "In mammals, the mesonephros is the second of the three embryonic kidneys to be established and exists only transiently. In fish and amphibians, the mesonephros will form the mature kidney" xsd:string -property_value: UBPROP:0000009 "By contrast to the pronephros, the histological features of the mammalian mesonephros, with its primitive glomeruli, suggest that it probably functions as a primitive kidney, and is involved in the production of much of the amniotic fluid. Within the two mesonephroi, one located on either side of the dorsal mesentery of the hindgut, a substantial number (in the region of about 40 or more) of cranio-caudally segmented mesonephric tubules are formed. It has, however, been suggested that only the most rostrally located 4-6 pairs of mesonephric tubules drain into the mesonephric portion of the nephric duct. This is now seen to extend along the length of the mesonephroi, being located towards their lateral sides. The mesonephros is also retained over a considerably longer period than the pronephros, but gradually undergoes regression in a cranio-caudal direction. While the rostral part displays clear evidence of regression its more caudal part appears to display evidence of functional activity. Within the medial part of the mesonephros, vesicles are formed, although no glomeruli are formed there in this species. It is, however, difficult to believe that the relatively enormous mesonephroi do not have an excretory role in the mouse, only serving as a base for gonadal differentiation. In the human embryo, the medial part of the mesonephric tubules enlarges, become invaginated by capillaries, and form glomeruli. These then take on an excretory role. In the mouse, the mesonephric ducts appear to be patent throughout their length[GUDMAP, modified]" xsd:string +relationship: RO:0002202 UBERON:0002120 ! develops from pronephros +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray986.png" xsd:anyURI [Term] id: UBERON:0000081 @@ -8075,16 +7996,12 @@ xref: VHOG:0000039 xref: Wikipedia:Metanephros#Metanephros is_a: UBERON:0002113 ! kidney is_a: UBERON:0004120 ! mesoderm-derived structure -relationship: developmentally_replaces UBERON:0000080 {source="ISBN:9780878932504"} ! mesonephros -relationship: develops_from UBERON:0003220 {evidence="definitional"} ! metanephric mesenchyme -relationship: develops_from UBERON:0005080 {source="GO"} ! metanephric ureteric bud -relationship: develops_from UBERON:0005753 ! caudal part of nephrogenic cord -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -property_value: editor_note "TODO check developmental relationships" xsd:string -property_value: UBPROP:0000001 "A kidney formed of nephric tubules arising in the posterior region of the nephric ridge and drained by a ureter; replaces the embryonic pronephros and mesonephros [in mammals]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000039", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000039", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "metanephric" xsd:string -property_value: UBPROP:0000011 "During the fifth week of gestation, the mesonephric duct develops an outpouching, the ureteric bud, near its attachment to the cloaca. This bud, also called the metanephrogenic diverticulum, grows posteriorly and towards the head of the embryo. The elongated stalk of the ureteric bud, the metanephric duct, later forms the ureter. As the cranial end of the bud extends into the intermediate mesoderm, it undergoes a series of branchings to form the collecting duct system of the kidney. It also forms the major and minor calyces and the renal pelvis" xsd:string +relationship: RO:0002202 UBERON:0003220 ! develops from metanephric mesenchyme +relationship: RO:0002202 UBERON:0005080 {source="GO"} ! develops from metanephric ureteric bud +relationship: RO:0002202 UBERON:0005753 ! develops from caudal part of nephrogenic cord +relationship: RO:0002285 UBERON:0000080 {source="ISBN:9780878932504"} ! developmentally replaces mesonephros +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +property_value: IAO:0000116 "TODO check developmental relationships" xsd:string [Term] id: UBERON:0000083 @@ -8104,9 +8021,7 @@ is_a: UBERON:0005103 ! mesonephric epithelium is_a: UBERON:0006555 ! excretory tube intersection_of: UBERON:0003914 ! epithelial tube intersection_of: part_of UBERON:0000080 ! mesonephros -property_value: editor_note "TODO check" xsd:string -property_value: UBPROP:0000001 "Any of the renal tubules composing the mesonephros. In mammals they function as excretory structures during the early embryonic development but are later incorporated into the reproductive system. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000500", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/mesonephric+tubule"} -property_value: UBPROP:0000003 "As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000500", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639", source="http://bgee.unil.ch/"} +property_value: IAO:0000116 "TODO check" xsd:string [Term] id: UBERON:0000084 @@ -8133,14 +8048,10 @@ xref: VHOG:0000541 xref: Wikipedia:Ureteric_bud is_a: UBERON:0000083 ! mesonephric tubule is_a: UBERON:0007499 {source="EHDAA2"} ! epithelial sac -is_a: UBERON:0012275 ! meso-epithelium is_a: UBERON:0034969 ! epithelial layer of duct -relationship: developmentally_induced_by UBERON:0003220 {source="ISBN:9780878932504"} ! metanephric mesenchyme -relationship: develops_from UBERON:0003074 {source="EHDAA2"} ! mesonephric duct relationship: part_of UBERON:0003074 ! mesonephric duct -property_value: UBPROP:0000001 "Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts. [Embryology, See_Dudek_RW_and_Fix_JD, Third_Edition_(2004)_Philadelphia:_Lippincott_William_and_Wilkins, p.137][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000541", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000001 "Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts[VHOG:0000541]." xsd:string {source="VHOG:0000541"} -property_value: UBPROP:0000003 "The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000541", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003074 {source="EHDAA2"} ! develops from mesonephric duct +relationship: RO:0002256 UBERON:0003220 {source="ISBN:9780878932504"} ! developmentally induced by metanephric mesenchyme [Term] id: UBERON:0000092 @@ -8160,9 +8071,8 @@ xref: WBls:0000103 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage relationship: preceded_by UBERON:0000068 ! embryo stage -relationship: simultaneous_with GO:0009791 ! post-embryonic development +relationship: RO:0002082 GO:0009791 ! simultaneous with post-embryonic development property_value: seeAlso "https://github.com/obophenotype/uberon/issues/344" xsd:anyURI -property_value: UBPROP:0000008 "In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)" xsd:string [Term] id: UBERON:0000104 @@ -8184,9 +8094,9 @@ is_a: BFO:0000003 ! occurrent is_a: UBERON:0000000 ! processual entity relationship: ends_with UBERON:0000071 ! death stage relationship: has_part UBERON:0000105 ! life cycle stage -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 property_value: seeAlso "https://github.com/obophenotype/uberon/issues/532" xsd:anyURI [Term] @@ -8215,12 +8125,10 @@ xref: ZFS:0000000 xref: ZFS:0100000 is_a: UBERON:0000000 ! processual entity relationship: part_of UBERON:0000104 ! life cycle -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: editor_note "this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here" xsd:string -property_value: UBPROP:0000012 "the WBls class 'all stages' belongs here as it is the superclass of other WBls stages" xsd:string -property_value: UBPROP:0000012 "we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage" xsd:string +property_value: IAO:0000116 "this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000106 @@ -8240,7 +8148,6 @@ xref: BILS:0000106 xref: EFO:0001322 xref: EHDAA:27 xref: FBdv:00005288 -xref: IDOMAL:0000302 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C12601 xref: PdumDv:0000100 xref: VHOG:0000745 @@ -8250,9 +8157,8 @@ xref: ZFS:0000001 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage -relationship: seeAlso EMAPA:16033 -relationship: starts UBERON:0000104 ! life cycle -property_value: UBPROP:0000003 "As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000745", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107", source="http://bgee.unil.ch/"} +relationship: RO:0002223 UBERON:0000104 ! starts life cycle +property_value: seeAlso EMAPA:16033 [Term] id: UBERON:0000107 @@ -8275,10 +8181,10 @@ xref: ZFS:0000046 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage intersection_of: UBERON:0000105 ! life cycle stage -intersection_of: simultaneous_with GO:0040016 ! embryonic cleavage +intersection_of: RO:0002082 GO:0040016 ! simultaneous with embryonic cleavage relationship: immediately_preceded_by UBERON:0000106 ! zygote stage relationship: part_of UBERON:0000068 ! embryo stage -relationship: simultaneous_with GO:0040016 ! embryonic cleavage +relationship: RO:0002082 GO:0040016 ! simultaneous with embryonic cleavage [Term] id: UBERON:0000108 @@ -8302,8 +8208,8 @@ is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000107 ! cleavage stage -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI -property_value: editor_note "consider adding a preceding stage 'morula stage' as part of cleavage" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI +property_value: IAO:0000116 "consider adding a preceding stage 'morula stage' as part of cleavage" xsd:string [Term] id: UBERON:0000109 @@ -8330,10 +8236,10 @@ xref: XAO:1000005 xref: ZFS:0000047 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000108 {source="BILS"} ! blastula stage -relationship: simultaneous_with GO:0007369 ! gastrulation +relationship: RO:0002082 GO:0007369 ! simultaneous with gastrulation +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0000110 @@ -8347,14 +8253,12 @@ xref: MmusDv:0000017 xref: XAO:1000006 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000109 ! gastrula stage -relationship: simultaneous_with GO:0001841 ! neural tube formation -property_value: RO:0002174 NCBITaxon:7955 +relationship: RO:0002082 GO:0001841 ! simultaneous with neural tube formation +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa property_value: seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/343" xsd:anyURI -property_value: UBPROP:0000008 "In zebrafish, the times of neurulation and segmentation overlap so extensively there is no distinct neurula period of development, such as occurs largely before segmentation in amphibian embryos." xsd:string [Term] id: UBERON:0000111 @@ -8371,9 +8275,9 @@ xref: OGES:000032 xref: Wikipedia:Organogenesis is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000068 ! embryo stage -relationship: simultaneous_with GO:0048513 ! animal organ development +relationship: RO:0002082 GO:0048513 ! simultaneous with animal organ development +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa property_value: seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/533" xsd:anyURI @@ -8389,14 +8293,14 @@ synonym: "layer of cells" EXACT [] synonym: "sheath of cells" RELATED [] xref: NCIT:C66831 is_a: UBERON:0000957 ! lamina -property_value: editor_note "consider adding to caro" xsd:string +property_value: IAO:0000116 "consider adding to caro" xsd:string [Term] id: UBERON:0000154 name: posterior region of body namespace: uberon is_a: UBERON:0000475 ! organism subdivision -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria [Term] id: UBERON:0000158 @@ -8410,7 +8314,6 @@ xref: MESH:D008566 xref: NCIT:C12749 is_a: UBERON:0004923 ! organ component layer relationship: bounding_layer_of UBERON:0000064 ! organ part -property_value: UBPROP:0000001 "A thin sheet or layer of pliable tissue, serving as a covering or envelope of a part, as the lining of a cavity, as a partition or septum, or to connect two structures." xsd:string {source="ncithesaurus:Membrane"} [Term] id: UBERON:0000161 @@ -8424,7 +8327,6 @@ synonym: "ostium" BROAD [] xref: FMA:3724 xref: SCTID:91837002 is_a: UBERON:0004111 ! anatomical conduit -property_value: UBPROP:0000012 "in FMA, this is an anatomical conduit *space*, rather than anatomical conduit" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0000162 @@ -8445,17 +8347,10 @@ xref: Wikipedia:Cloaca xref: XAO:0000244 xref: ZFA:0005781 is_a: UBERON:0013522 ! subdivision of tube -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0001555 {source="ZFA"} ! digestive tract relationship: part_of UBERON:0004122 {source="AAO"} ! genitourinary system -relationship: present_in_taxon NCBITaxon:9369 {notes="most adult placentals have no trace of a cloaca. However, the tenrecs and golden moles, small placental mammals native to Africa, retain a cloaca as adults."} -property_value: editor_note "adding df link to embryonic cloaca leads to a cycle in uberon-simple, as cloaca is a suberclass of embryonic cloaca" xsd:string -property_value: UBPROP:0000001 "A common passage for fecal, urinary, and reproductive discharge in most lower vertebrates as well as the terminal end of the hindgut before division into rectum, bladder, and genital primordia in mammalian embryos. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001186", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/cloaca"} -property_value: UBPROP:0000001 "Anatomical structure which is the common receptacle for the alimentary canal, Wolffian ducts, oviducts, and the bladder.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000095", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "A cloaca is apparently a primitive vertebrate feature because it occurs in most primitive gnathostomes and persists in the embryos of almost all vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001186", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.572", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "cloacal" xsd:string -property_value: UBPROP:0000008 "Human beings only have an embryonic cloaca, which is split up into separate tracts during the development of the urinary and reproductive organs" xsd:string -property_value: UBPROP:0000011 "hindgut endoderm and proctodeal ectoderm." xsd:string {source="WP"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +property_value: IAO:0000116 "adding df link to embryonic cloaca leads to a cycle in uberon-simple, as cloaca is a suberclass of embryonic cloaca" xsd:string [Term] id: UBERON:0000163 @@ -8469,11 +8364,10 @@ xref: EHDAA:4895 xref: EMAPA:27573 xref: Wikipedia:Cloaca_(embryology) is_a: UBERON:0000162 ! cloaca -relationship: has_developmental_contribution_from UBERON:0003064 ! intermediate mesoderm relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0001008 {source="EHDAA2"} ! renal system relationship: part_of UBERON:0012361 {source="EHDAA2"} ! internal anal region -property_value: IAO:0000232 "this class represents the embryonic form of the cloaca, as found in both mammals and non-mammals." xsd:string +relationship: RO:0002254 UBERON:0003064 ! has developmental contribution from intermediate mesoderm [Term] id: UBERON:0000164 @@ -8495,14 +8389,11 @@ xref: UMLS:C0231057 {source="ncithesaurus:Urogenital_Sinus"} xref: VHOG:0000414 xref: Wikipedia:Definitive_urogenital_sinus is_a: UBERON:0002050 ! embryonic structure -relationship: contributes_to_morphology_of UBERON:0000163 ! embryonic cloaca -relationship: develops_from UBERON:0003064 ! intermediate mesoderm -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0000163 {source="MP-def"} ! embryonic cloaca -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png" xsd:anyURI -property_value: UBPROP:0000001 "The ventral part of the cloaca after its separation from the rectum, giving rise to the lower part of the bladder in both sexes, to the prostatic portion of the male urethra, and to the urethra and vestibule in the female. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000414", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/urogenital+sinus"} -property_value: UBPROP:0000003 "In mammals the lowly monotremes still have a cloaca. Higher types have done away with this structure and have a separate anal outlet for the rectum. The monotreme cloaca shows the initiation of this subdivision. The cloaca has such includes only the distal part, roughly comparable to the proctodeum. The more proximal part is divided into (1) a large dorsal passage into which the intestine opens, the coprodeum, and (2) a ventral portion, the urodeum with which the bladder connects. (...) the development of the placental mammals recapitulates in many respects the phylogenetic story. In the sexually indifferent stage of placental mammal there is a cloaca. While the indifferent stage still persists, a septum develops, and extends out to the closing membrane. This divides the cloaca into two chambers: a coprodeum continuous with the gut above, and a urodeum or urogenital sinus below.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000414", ontology="VHOG", source="ISBN:978-0721676678 Romer AS, Vertebrate body (1970)p.388-89 and Figure 300", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000013 "the term 'urogenital sinus' may refer to the primitive urogenital sinus present as a transient developmental structure in most mammals or it may refer to a condition in which an unseptated cloaca persists in animals longer than normal" xsd:string {source="MP"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002202 UBERON:0003064 ! develops from intermediate mesoderm +relationship: RO:0002433 UBERON:0000163 ! contributes to morphology of embryonic cloaca +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png" xsd:anyURI [Term] id: UBERON:0000165 @@ -8536,7 +8427,6 @@ xref: EFO:0000825 xref: EHDAA2:0001326 xref: EHDAA:542 xref: EMAPA:16262 -xref: FBbt:00003126 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:49184 xref: GAID:75 xref: galen:Mouth @@ -8557,19 +8447,11 @@ xref: Wikipedia:Mouth xref: XAO:0003029 xref: ZFA:0000547 xref: ZFA:0000590 -is_a: UBERON:0004921 {notes="the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts"} ! subdivision of digestive tract -intersection_of: UBERON:0004921 ! subdivision of digestive tract -intersection_of: proximalmost_part_of UBERON:0001555 ! digestive tract -relationship: develops_from UBERON:0035804 ! future mouth -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: proximalmost_part_of UBERON:0001555 ! digestive tract -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI +is_a: UBERON:0004921 ! subdivision of digestive tract +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002202 UBERON:0035804 ! develops from future mouth +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/661" xsd:anyURI -property_value: UBPROP:0000001 "Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010355", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000812", ontology="VHOG", source="DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "oral" xsd:string -property_value: UBPROP:0000011 "some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives" xsd:string -property_value: UBPROP:0000012 "in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0000174 @@ -8632,15 +8514,10 @@ is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000179 ! haemolymphatic fluid relationship: has_part CL:0000232 {source="CL:tm"} ! erythrocyte relationship: has_part UBERON:0001969 ! blood plasma -relationship: immediate_transformation_of UBERON:0006596 {source="Bgee:AN"} ! presumptive blood -relationship: located_in UBERON:0002049 {source="https://github.com/obophenotype/uberon/issues/1330"} ! vasculature relationship: part_of UBERON:0002390 ! hematopoietic system -relationship: present_in_taxon NCBITaxon:9606 -property_value: IAO:0000232 "This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid." xsd:string -property_value: UBPROP:0000001 "A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000007", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000046", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000002 "relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000046", ontology="AAO"} -property_value: UBPROP:0000003 "Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000224", ontology="VHOG", source="DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006) ", source="http://bgee.unil.ch/"} +relationship: RO:0001025 UBERON:0002049 {source="https://github.com/obophenotype/uberon/issues/1330"} ! located in vasculature +relationship: RO:0002495 UBERON:0006596 {source="Bgee:AN"} ! immediate transformation of presumptive blood +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000179 @@ -8653,9 +8530,9 @@ xref: CARO:0000081 is_a: UBERON:0006314 ! bodily fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: part_of UBERON:0002193 ! hemolymphoid system -relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0002193 ! hemolymphoid system +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 creation_date: 2009-04-08T04:38:19Z [Term] @@ -8675,19 +8552,17 @@ xref: OGEM:000006 xref: Wikipedia:Blastula is_a: UBERON:0000922 ! embryo intersection_of: UBERON:0000468 ! multicellular organism -intersection_of: existence_starts_and_ends_during UBERON:0000108 ! blastula stage -relationship: develops_from UBERON:0007010 ! cleaving embryo -relationship: existence_starts_and_ends_during UBERON:0000108 ! blastula stage -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI -property_value: editor_note "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" xsd:string +intersection_of: RO:0002491 UBERON:0000108 ! existence starts and ends during blastula stage +relationship: RO:0002202 UBERON:0007010 ! develops from cleaving embryo +relationship: RO:0002491 UBERON:0000108 ! existence starts and ends during blastula stage +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI +property_value: IAO:0000116 "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" xsd:string [Term] id: UBERON:0000353 name: parenchyma namespace: uberon def: "Functional part of an organ in the body. This is in contrast to the stroma, which refers to the structural tissue of organs, being exactly, connective tissues." [Wikipedia:Parenchyma] -xref: BTO:0000999 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} -xref: BTO:0001539 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: EHDAA:3015 xref: EHDAA:3905 xref: EHDAA:3999 @@ -8707,10 +8582,7 @@ xref: Wikipedia:Parenchyma is_a: UBERON:0000064 ! organ part disjoint_from: UBERON:0003891 ! stroma relationship: capable_of GO:0032501 ! multicellular organismal process -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: UBPROP:0000007 "parenchymal" xsd:string -property_value: UBPROP:0000011 "Early in development the mammalian embryo has three distinct layers: ectoderm (external layer), endoderm (internal layer) and in between those two layers the middle layer or mesoderm. The parenchyma of most organs is of ectodermal (brain, skin) or endodermal origin (lungs, gastrointestinal tract, liver, pancreas). The parenchyma of a few organs (spleen, kidneys, heart) is of mesodermal origin. The stroma of all organs is of mesodermal origin" xsd:string {source="WP"} -property_value: UBPROP:0000012 "the FMA definition is more restrictive, and limits this to solid organs. This would seem to cause problems for the lung parenchyma, except FMA classifies Lung as solid rather than cavitated" xsd:string {external_ontology="FMA"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0000362 @@ -8745,16 +8617,15 @@ is_a: UBERON:0000958 ! medulla of organ intersection_of: UBERON:0000958 ! medulla of organ intersection_of: part_of UBERON:0002113 ! kidney relationship: capable_of_part_of GO:0070295 ! renal water absorption -relationship: contributes_to_morphology_of UBERON:0002113 ! kidney relationship: has_part UBERON:0004200 ! kidney pyramid relationship: part_of UBERON:0002113 ! kidney -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" xsd:anyURI -property_value: UBPROP:0000010 "The renal medulla is split up into a number of sections, known as the renal pyramids. Blood enters into the kidney via the renal artery, which then splits up to form the arcuate arterioles. The arcuate arterioles each in turn branch into interlobular arterioles, which finally reach the glomeruli. At the glomerulus the blood reaches a highly disfavourable pressure gradient and a large exchange surface area, which forces the serum portion of the blood out of the vessel into the renal tubules. Flow continues through the renal tubules, including the proximal tubule, the Loop of Henle, and finally leaves the kidney by means of the collecting duct, leading to the renal ureter. The renal medulla contains the structures of the nephrons responsible for maintaining the salt and water balance of the blood. The renal medulla is hypertonic to the filtrate in the nephron and aids in the reabsorption of water" xsd:string +relationship: RO:0002433 UBERON:0002113 ! contributes to morphology of kidney +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000383 @@ -8777,7 +8648,6 @@ xref: BILA:0000088 xref: BTO:0001369 xref: BTO:0001485 xref: EFO:0000801 -xref: EMAPA:35578 xref: FMA:72954 xref: MA:0002888 xref: MAT:0000025 @@ -8786,15 +8656,13 @@ xref: VSAO:0000033 xref: XAO:0004042 is_a: UBERON:0011216 ! organ system subdivision intersection_of: UBERON:0011216 ! organ system subdivision -intersection_of: composed_primarily_of UBERON:0001015 ! musculature +intersection_of: RO:0002473 UBERON:0001015 ! composed primarily of musculature relationship: capable_of GO:0003012 ! muscle system process -relationship: composed_primarily_of UBERON:0001015 ! musculature -relationship: never_in_taxon NCBITaxon:6040 -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: present_in_taxon NCBITaxon:9606 -property_value: editor_note "consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77" xsd:string -property_value: UBPROP:0000001 "Anatomical system that consists of the muscles of the body.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000033", ontology="VSAO", source="VSAO:curator"} -property_value: UBPROP:0000012 "we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA" xsd:string {external_ontology="MA"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002473 UBERON:0001015 ! composed primarily of musculature +property_value: IAO:0000116 "consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77" xsd:string +property_value: RO:0002161 NCBITaxon:6040 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000463 @@ -8816,7 +8684,6 @@ xref: CALOHA:TS-2101 xref: CARO:0000004 xref: EHDAA2:0003004 xref: EMAPA:35178 -xref: FBbt:00007019 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9669 xref: galen:BodySubstance xref: HAO:0000004 @@ -8829,11 +8696,11 @@ xref: VHOG:0001726 xref: XAO:0004001 xref: ZFA:0001487 is_a: UBERON:0000465 ! material anatomical entity -relationship: has_quality PATO:0002198 ! quality of a substance -relationship: part_of UBERON:0000468 {notes="this relationship may be too strong and may be weakened in future"} ! multicellular organism -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: part_of UBERON:0000468 ! multicellular organism +relationship: RO:0000086 PATO:0002198 ! has quality quality of a substance +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000464 @@ -8851,7 +8718,6 @@ xref: AEO:0000005 xref: BILA:0000005 xref: CARO:0000005 xref: EHDAA2:0003005 -xref: FBbt:00007017 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:5897 xref: HAO:0000005 xref: NCIT:C94478 @@ -8862,10 +8728,10 @@ xref: VHOG:0001728 xref: XAO:0003190 xref: ZFA:0001643 is_a: UBERON:0000466 ! immaterial anatomical entity -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -relationship: surrounded_by UBERON:0000061 ! anatomical structure +relationship: RO:0002219 UBERON:0000061 ! surrounded by anatomical structure +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000465 @@ -8879,7 +8745,6 @@ xref: AEO:0000006 xref: BILA:0000006 xref: CARO:0000006 xref: EHDAA2:0003006 -xref: FBbt:00007016 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67165 xref: HAO:0000006 xref: TAO:0001836 @@ -8888,9 +8753,9 @@ xref: VHOG:0001721 is_a: BFO:0000040 ! material entity is_a: UBERON:0001062 ! anatomical entity disjoint_from: UBERON:0000466 ! immaterial anatomical entity -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000466 @@ -8905,7 +8770,6 @@ xref: AEO:0000007 xref: BILA:0000007 xref: CARO:0000007 xref: EHDAA2:0003007 -xref: FBbt:00007015 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67112 xref: HAO:0000007 xref: TAO:0001835 @@ -8913,9 +8777,9 @@ xref: TGMA:0001827 xref: VHOG:0001727 is_a: BFO:0000141 ! immaterial entity is_a: UBERON:0001062 ! anatomical entity -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000467 @@ -8943,11 +8807,9 @@ xref: EHDAA2:0003011 xref: EHDAA:392 xref: EMAPA:16103 xref: EV:0100000 -xref: FBbt:00004856 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7149 xref: galen:AnatomicalSystem xref: HAO:0000011 -xref: IDOMAL:0002460 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: MA:0000003 xref: NCIT:C12919 xref: SCTID:278195005 @@ -8963,11 +8825,11 @@ xref: ZFA:0001439 is_a: UBERON:0000061 ! anatomical structure relationship: has_part UBERON:0000062 ! organ relationship: part_of UBERON:0000468 ! multicellular organism -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -relationship: present_in_taxon NCBITaxon:9606 -relationship: seeAlso EHDAA2:0001330 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:9606 +property_value: seeAlso EHDAA2:0001330 [Term] id: UBERON:0000468 @@ -8998,7 +8860,6 @@ xref: EHDAA2:0003191 xref: EHDAA:1 xref: EMAPA:25765 xref: EV:0100016 -xref: FBbt:00000001 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:256135 xref: galen:Organism xref: HAO:0000012 @@ -9014,11 +8875,10 @@ xref: Wikipedia:Multi-cellular_organism xref: XAO:0003004 xref: ZFA:0001094 is_a: UBERON:0010000 ! multicellular anatomical structure -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: editor_note "TODO - split body and mc organism? body continues after death stage" xsd:string -property_value: UBPROP:0000007 "organismal" xsd:string +property_value: IAO:0000116 "TODO - split body and mc organism? body continues after death stage" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000471 @@ -9039,7 +8899,6 @@ xref: XAO:0003039 xref: ZFA:0001489 is_a: UBERON:0000481 ! multi-tissue structure relationship: part_of UBERON:0003103 ! compound organ -property_value: IAO:0000232 "this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future" xsd:string [Term] id: UBERON:0000475 @@ -9064,7 +8923,6 @@ xref: CARO:0000032 xref: EFO:0000808 xref: EHDAA2:0003032 xref: EMAPA:36031 -xref: FBbt:00007009 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7153 xref: galen:BodyPart xref: HAO:0000032 @@ -9082,10 +8940,10 @@ xref: XAO:0003013 xref: ZFA:0001308 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure relationship: part_of UBERON:0000468 ! multicellular organism -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: editor_note "Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency" xsd:string +property_value: IAO:0000116 "Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000476 @@ -9100,7 +8958,6 @@ xref: AEO:0000040 xref: BILA:0000040 xref: CARO:0000040 xref: EHDAA2:0003040 -xref: FBbt:00007013 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:63863 xref: HAO:0000040 xref: TAO:0000382 @@ -9109,9 +8966,9 @@ xref: XAO:0003162 xref: ZFA:0000382 is_a: UBERON:0000061 ! anatomical structure disjoint_from: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000477 @@ -9120,12 +8977,11 @@ namespace: uberon def: "Anatomical group whose component anatomical structures lie in close proximity to each other." [FBbt:00007277] subset: common_anatomy subset: upper_level -xref: FBbt:00007277 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: VHOG:0001737 is_a: UBERON:0034923 ! disconnected anatomical group -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000479 @@ -9147,7 +9003,6 @@ xref: CALOHA:TS-2090 xref: CARO:0000043 xref: EHDAA2:0003043 xref: EMAPA:35868 -xref: FBbt:00007003 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9637 xref: galen:Tissue xref: HAO:0000043 @@ -9164,10 +9019,10 @@ xref: ZFA:0001477 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure relationship: has_part GO:0031012 ! extracellular matrix relationship: part_of UBERON:0000468 ! multicellular organism -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: editor_note "changed label and definition to reflect CARO2" xsd:string +property_value: IAO:0000116 "changed label and definition to reflect CARO2" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000481 @@ -9182,7 +9037,6 @@ xref: AEO:0000055 xref: BILA:0000055 xref: CARO:0000055 xref: EHDAA2:0003055 -xref: FBbt:00007010 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: HAO:0000055 xref: TAO:0001488 xref: TGMA:0001847 @@ -9191,9 +9045,9 @@ xref: XAO:0003037 xref: ZFA:0001488 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure relationship: has_part UBERON:0000479 ! tissue -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000483 @@ -9215,7 +9069,6 @@ xref: CALOHA:TS-0288 xref: CARO:0000066 xref: EHDAA2:0003066 xref: EMAPA:32738 -xref: FBbt:00007005 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9639 xref: GAID:402 xref: HAO:0000066 @@ -9232,14 +9085,12 @@ xref: ZFA:0001486 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue -intersection_of: composed_primarily_of CL:0000066 ! epithelial cell -relationship: composed_primarily_of CL:0000066 ! epithelial cell +intersection_of: RO:0002473 CL:0000066 ! composed primarily of epithelial cell relationship: has_part GO:0005911 ! cell-cell junction relationship: has_part UBERON:0005769 ! basement membrane of epithelium -relationship: only_in_taxon NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! Metazoa -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI -property_value: UBPROP:0000003 "The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000387", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.59", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "epithelial" xsd:string +relationship: RO:0002160 NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! only in taxon Metazoa +relationship: RO:0002473 CL:0000066 ! composed primarily of epithelial cell +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI [Term] id: UBERON:0000485 @@ -9258,7 +9109,6 @@ xref: AEO:0000068 xref: BILA:0000068 xref: CARO:0000068 xref: EHDAA2_RETIRED:0003068 -xref: FBbt:00007027 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45567 xref: HAO:0000068 xref: NCIT:C33552 @@ -9270,7 +9120,7 @@ xref: XAO:0004008 xref: ZFA:0001496 is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0012274 ! columnar epithelium -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray1059.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray1059.png" xsd:anyURI [Term] id: UBERON:0000487 @@ -9299,8 +9149,7 @@ is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0006914 ! squamous epithelium intersection_of: UBERON:0000490 ! unilaminar epithelium intersection_of: has_part CL:0000076 ! squamous epithelial cell -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Unilaminar epithelium that consists of a single layer of squamous cells.[CARO]" xsd:string {date_retrieved="2012-06-20", external_class="CARO:0000070", ontology="CARO", source="FMA:45565", source="http://orcid.org/0000-0001-9114-8737"} +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI [Term] id: UBERON:0000489 @@ -9327,7 +9176,6 @@ is_a: UBERON:0003103 ! compound organ intersection_of: UBERON:0003103 ! compound organ intersection_of: has_part UBERON:0002553 ! anatomical cavity relationship: has_part UBERON:0002553 ! anatomical cavity -property_value: IAO:0000232 "this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future" xsd:string [Term] id: UBERON:0000490 @@ -9352,8 +9200,7 @@ xref: UMLS:C0682574 {source="ncithesaurus:Simple_Epithelium"} xref: XAO:0004007 xref: ZFA:0001495 is_a: UBERON:0000483 ! epithelium -property_value: editor_note "consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable" xsd:string -property_value: UBPROP:0000001 "Epithelium that consists of a single layer of epithelial cells.[CARO]" xsd:string {date_retrieved="2012-06-20", external_class="CARO:0000073", ontology="CARO", source="FMA:45561", source="http://orcid.org/0000-0001-9114-8737"} +property_value: IAO:0000116 "consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable" xsd:string [Term] id: UBERON:0000915 @@ -9373,12 +9220,8 @@ xref: Wikipedia:Thorax is_a: UBERON:0009569 {source="FMA"} ! subdivision of trunk is_a: UBERON:0011676 ! subdivision of organism along main body axis intersection_of: UBERON:0011676 ! subdivision of organism along main body axis -intersection_of: has_skeleton UBERON:0014477 ! thoracic skeleton -relationship: has_skeleton UBERON:0014477 ! thoracic skeleton -property_value: IAO:0000232 "note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest" xsd:string -property_value: RO:0002171 UBERON:0000026 -property_value: RO:0002171 UBERON:0000033 -property_value: RO:0002171 UBERON:0002417 +intersection_of: RO:0002551 UBERON:0014477 ! has skeleton thoracic skeleton +relationship: RO:0002551 UBERON:0014477 ! has skeleton thoracic skeleton [Term] id: UBERON:0000916 @@ -9408,11 +9251,9 @@ xref: MIAA:0000298 xref: SCTID:302553009 xref: Wikipedia:Abdomen is_a: UBERON:0009569 ! subdivision of trunk -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0002417 {source="MA"} ! abdominal segment of trunk -property_value: editor_note "Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class" xsd:string -property_value: UBPROP:0000007 "abdominal" xsd:string -property_value: UBPROP:0000007 "celiac" xsd:string +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +property_value: IAO:0000116 "Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class" xsd:string [Term] id: UBERON:0000922 @@ -9437,11 +9278,9 @@ xref: EHDAA2:0000002 xref: EHDAA2_RETIRED:0003236 xref: EHDAA:38 xref: EMAPA:16039 -xref: FBbt:00000052 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69068 xref: GAID:963 xref: http://neurolex.org/wiki/Category\:Embryonic_organism -xref: IDOMAL:0000646 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: MAT:0000226 xref: MESH:D004622 xref: MIAA:0000019 @@ -9455,14 +9294,12 @@ xref: XAO:0000113 xref: ZFA:0000103 is_a: UBERON:0000468 ! multicellular organism intersection_of: UBERON:0000468 ! multicellular organism -intersection_of: existence_ends_with UBERON:0000068 ! embryo stage -intersection_of: existence_starts_with UBERON:0000068 ! embryo stage -relationship: existence_ends_with UBERON:0000068 ! embryo stage -relationship: existence_starts_with UBERON:0000068 ! embryo stage -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" xsd:anyURI +intersection_of: RO:0002489 UBERON:0000068 ! existence starts with embryo stage +intersection_of: RO:0002493 UBERON:0000068 ! existence ends with embryo stage +relationship: RO:0002489 UBERON:0000068 ! existence starts with embryo stage +relationship: RO:0002493 UBERON:0000068 ! existence ends with embryo stage +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/503" xsd:anyURI -property_value: UBPROP:0000007 "embryonic" xsd:string -property_value: UBPROP:0000012 "Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo" xsd:string {external_ontology="ZFA"} [Term] id: UBERON:0000923 @@ -9481,7 +9318,6 @@ xref: AAO:0000480 xref: BILA:0000035 xref: BTO:0000556 xref: EMAPA:36033 -xref: FBbt:00000110 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69069 xref: GAID:1303 xref: MESH:D005855 @@ -9495,8 +9331,7 @@ xref: Wikipedia:Germ_layer xref: XAO:0003011 xref: ZFA:0001122 is_a: UBERON:0010316 ! germ layer / neural crest -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001223", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0000924 @@ -9516,7 +9351,6 @@ xref: EFO:0000414 xref: EHDAA2:0000428 xref: EMAPA:16069 xref: EV:0100003 -xref: FBbt:00000111 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69070 xref: GAID:1304 xref: MAT:0000155 @@ -9533,11 +9367,8 @@ xref: XAO:0000001 xref: ZFA:0000016 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000221 ! ectodermal cell -relationship: immediate_transformation_of UBERON:0006601 {source="Bgee:AN"} ! presumptive ectoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png" xsd:anyURI -property_value: UBPROP:0000001 "Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000137", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000153", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "ectodermal" xsd:string +relationship: RO:0002495 UBERON:0006601 {source="Bgee:AN"} ! immediate transformation of presumptive ectoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png" xsd:anyURI [Term] id: UBERON:0000925 @@ -9557,7 +9388,6 @@ xref: EFO:0002545 xref: EHDAA2:0000436 xref: EMAPA:16062 xref: EV:0100005 -xref: FBbt:00000125 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69071 xref: GAID:1305 xref: MAT:0000175 @@ -9573,11 +9403,9 @@ xref: XAO:0000090 xref: ZFA:0000017 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000223 ! endodermal cell -relationship: immediate_transformation_of UBERON:0006595 {source="Bgee:AN"} ! presumptive endoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png" xsd:anyURI -property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000154", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "endodermal" xsd:string +relationship: RO:0002495 UBERON:0006595 {source="Bgee:AN"} ! immediate transformation of presumptive endoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png" xsd:anyURI [Term] id: UBERON:0000926 @@ -9603,7 +9431,6 @@ xref: EHDAA:160 xref: EHDAA:183 xref: EMAPA:16083 xref: EV:0100006 -xref: FBbt:00000126 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69072 xref: GAID:522 xref: MAT:0000174 @@ -9617,15 +9444,11 @@ xref: VHOG:0000152 xref: Wikipedia:Mesoderm xref: XAO:0000050 xref: ZFA:0000041 -is_a: UBERON:0000923 {notes="sometimes not considered primary"} ! germ layer +is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000222 ! mesodermal cell -relationship: immediate_transformation_of UBERON:0006603 {source="Bgee:AN"} ! presumptive mesoderm -relationship: never_in_taxon NCBITaxon:6040 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" xsd:anyURI -property_value: UBPROP:0000001 "Primary germ layer that is the middle of the embryonic germ layers.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000304", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000152", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "mesodermal" xsd:string -property_value: UBPROP:0000008 "sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates" xsd:string {source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} +relationship: RO:0002495 UBERON:0006603 {source="Bgee:AN"} ! immediate transformation of presumptive mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" xsd:anyURI +property_value: RO:0002161 NCBITaxon:6040 [Term] id: UBERON:0000930 @@ -9647,7 +9470,6 @@ synonym: "stomodeal-hypophyseal primordium" BROAD [XAO:0000269] xref: BTO:0004224 xref: EHDAA2:0001929 xref: EMAPA:16263 -xref: FBbt:00000439 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:295846 xref: NCIT:C34306 xref: TAO:0001290 @@ -9657,15 +9479,11 @@ xref: Wikipedia:Stomodeum xref: XAO:0000269 xref: ZFA:0001290 is_a: UBERON:0013522 ! subdivision of tube -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000924 ! ectoderm relationship: part_of UBERON:0035804 ! future mouth -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI -property_value: editor_note "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" xsd:string -property_value: UBPROP:0000001 "Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001290", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx" xsd:string {source="MP:0012522", taxon="NCBITaxon:40674"} -property_value: UBPROP:0000007 "stomodeal" xsd:string -property_value: UBPROP:0000008 "This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity." xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI +property_value: IAO:0000116 "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" xsd:string [Term] id: UBERON:0000931 @@ -9681,7 +9499,6 @@ synonym: "proctodaeum" EXACT [] xref: AAO:0011087 xref: EHDAA2:0000121 xref: EMAPA:25038 -xref: FBbt:00000123 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: NCIT:C34278 xref: TAO:0000066 xref: UMLS:C0231054 {source="ncithesaurus:Proctodeum"} @@ -9690,16 +9507,13 @@ xref: Wikipedia:Proctodeum xref: XAO:0001019 xref: ZFA:0000066 is_a: UBERON:0016566 {source="EHDAA2"} ! pit -relationship: develops_from UBERON:0000924 ! ectoderm -relationship: has_potential_to_develop_into UBERON:0001353 ! anal region -relationship: located_in UBERON:0012469 {source="EHDAA2"} ! external anal region -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0007026 ! presumptive gut -property_value: editor_note "removed WBbt:0006795 'proctodeum' - junction between the alimentary and genital tracts in the male." xsd:string +relationship: RO:0001025 UBERON:0012469 {source="EHDAA2"} ! located in external anal region +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002202 UBERON:0000924 ! develops from ectoderm +relationship: RO:0002387 UBERON:0001353 ! has potential to develop into anal region +property_value: IAO:0000116 "removed WBbt:0006795 'proctodeum' - junction between the alimentary and genital tracts in the male." xsd:string property_value: seeAlso "https://github.com/obophenotype/uberon/issues/685" xsd:anyURI -property_value: UBPROP:0000001 "An inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000066", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011087", ontology="AAO", source="ZFA:0000066"} -property_value: UBPROP:0000007 "proctodeal" xsd:string [Term] id: UBERON:0000948 @@ -9748,22 +9562,17 @@ is_a: UBERON:0007100 ! primary circulatory organ is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0007100 ! primary circulatory organ intersection_of: has_part UBERON:0004151 ! cardiac chamber -relationship: contributes_to_morphology_of UBERON:0004535 ! cardiovascular system -relationship: develops_from UBERON:0004141 ! heart tube relationship: has_part UBERON:0004151 ! cardiac chamber -relationship: never_in_taxon NCBITaxon:6239 -relationship: never_in_taxon NCBITaxon:7227 -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0015410 {source="MA"} ! heart plus pericardium -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI -property_value: UBPROP:0000001 "Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000114", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010210", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000002 "relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010210", ontology="AAO"} -property_value: UBPROP:0000003 "As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000276", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "cardiac" xsd:string +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002202 UBERON:0004141 ! develops from heart tube +relationship: RO:0002433 UBERON:0004535 ! contributes to morphology of cardiovascular system +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI +property_value: RO:0002161 NCBITaxon:6239 +property_value: RO:0002161 NCBITaxon:7227 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000957 @@ -9777,11 +9586,10 @@ synonym: "laminar tissue" EXACT [] xref: Wikipedia:Lamina_of_the_vertebral_arch is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue -intersection_of: has_quality PATO:0002124 ! laminar -relationship: has_quality PATO:0002124 ! laminar -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/80/Laminaarcusvertebrae.png" xsd:anyURI -property_value: editor_note "TODO - merge with cell layer?" xsd:string -property_value: UBPROP:0000007 "laminar" xsd:string +intersection_of: RO:0000086 PATO:0002124 ! has quality laminar +relationship: RO:0000086 PATO:0002124 ! has quality laminar +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/80/Laminaarcusvertebrae.png" xsd:anyURI +property_value: IAO:0000116 "TODO - merge with cell layer?" xsd:string [Term] id: UBERON:0000958 @@ -9793,10 +9601,8 @@ synonym: "medulla" EXACT [FMA:61108] xref: FMA:61108 xref: galen:Medulla is_a: UBERON:0000471 ! compound organ component -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: surrounded_by UBERON:0001851 ! cortex -property_value: IAO:0000232 "this class is used in a very general sense" xsd:string -property_value: UBPROP:0000007 "medullary" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002219 UBERON:0001851 ! surrounded by cortex [Term] id: UBERON:0000982 @@ -9835,10 +9641,8 @@ xref: Wikipedia:Joint xref: XAO:0000171 xref: ZFA:0001596 is_a: UBERON:0004905 ! articulation -relationship: connects UBERON:0004765 ! skeletal element -relationship: contributes_to_morphology_of UBERON:0001434 ! skeletal system -property_value: UBPROP:0000001 "Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000101", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000367", ontology="TAO", source="TAO:pem"} +relationship: RO:0002176 UBERON:0004765 ! connects skeletal element +relationship: RO:0002433 UBERON:0001434 ! contributes to morphology of skeletal system [Term] id: UBERON:0000990 @@ -9869,13 +9673,11 @@ xref: EHDAA2:0001603 xref: EHDAA:5923 xref: EMAPA:17381 xref: EV:0100100 -xref: FBbt:00004857 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7160 xref: GAID:363 xref: HAO:0000374 xref: HAO:0000895 xref: MA:0000326 -xref: MESH:D005835 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: MIAA:0000305 xref: NCIT:C12841 xref: SCTID:278875001 @@ -9897,15 +9699,12 @@ disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:8450002 ! excretory system relationship: capable_of_part_of GO:0000003 ! reproduction -relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: has_part UBERON:0000991 ! gonad -relationship: present_in_taxon NCBITaxon:9606 -property_value: dcterms-date "2022-06-10T18:22:34Z" xsd:dateTime -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/52/Penis.svg" xsd:anyURI -property_value: editor_note "consider splitting genitalia from reproductive system" xsd:string -property_value: UBPROP:0000001 "Anatomical system which consists of organs and tissues associated with sexual reproduction of the organism.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010258", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "Arguably, one of the most important aspects of urbilaterian organogenesis would have been gonadogenesis, since Urbilateria must have successfully generated gametes and developed a strategy for extrusion and fertilization, in order to be the ancestor of all living Bilateria.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000182", ontology="VHOG", source="PMID:21672850 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across Bilateria. Integrative and Comparative Biology (2007)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000202 FMA:75572 +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +property_value: http://purl.org/dc/terms/date "2022-06-10T18:22:34Z" xsd:dateTime +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/52/Penis.svg" xsd:anyURI +property_value: IAO:0000116 "consider splitting genitalia from reproductive system" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000991 @@ -9924,7 +9723,6 @@ xref: BILA:0000123 xref: BSA:0000079 xref: BTO:0000534 xref: EMAPA:17383 -xref: FBbt:00004858 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:18250 xref: GAID:368 xref: HAO:0000379 @@ -9942,14 +9740,9 @@ xref: ZFA:0000413 is_a: UBERON:0003133 ! reproductive organ intersection_of: UBERON:0003133 ! reproductive organ intersection_of: has_part CL:0000586 ! germ cell -relationship: contains_process GO:0007276 ! gamete generation -relationship: develops_from UBERON:0005564 ! gonad primordium +relationship: BFO:0000067 GO:0007276 ! contains process gamete generation relationship: has_part CL:0000586 ! germ cell -property_value: UBPROP:0000001 "Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000213", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000413", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000397", ontology="VHOG", source="DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T, Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "gonadal" xsd:string -property_value: UBPROP:0000012 "FMA xref is a 'general anatomical term'" xsd:string {external_ontology="FMA"} +relationship: RO:0002202 UBERON:0005564 ! develops from gonad primordium [Term] id: UBERON:0001007 @@ -9970,8 +9763,6 @@ xref: BILA:0000082 xref: BTO:0000058 xref: CALOHA:TS-1293 xref: EFO:0000793 -xref: EV:0100056 -xref: FBbt:00005055 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7152 xref: GAID:278 xref: galen:DigestiveSystem @@ -9997,11 +9788,8 @@ disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:8450002 ! excretory system relationship: capable_of GO:0022600 ! digestive system process -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000129", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000007 "digestive" xsd:string -property_value: UBPROP:0000012 "many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class" xsd:string {external_ontology="MA"} +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001008 @@ -10031,7 +9819,6 @@ xref: EHDAA2:0001601 xref: EHDAA:5901 xref: EMAPA:17366 xref: EV:0100095 -xref: FBbt:00005056 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7159 xref: GAID:391 xref: galen:UrinaryTract @@ -10053,15 +9840,11 @@ is_a: UBERON:8450002 ! excretory system intersection_of: UBERON:8450002 ! excretory system intersection_of: capable_of GO:0097254 ! renal tubular secretion relationship: capable_of GO:0097254 ! renal tubular secretion -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: never_in_taxon NCBITaxon:110815 {source="Wikipedia"} -relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010257", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "Evolution of vertebrate renal anatomy appears quite conservative when compared, for example, to evolution of respiratory and cardiovascular systems in vertebrates. Major anatomical changes in vertebrates kidneys separate those of birds and mammals from kidneys of lower vertebrates. General increase in animal size from fish to mammals is reflected by an increase in total number of nephrons per kidney, rather than by constant change in tubular dimensions.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000723", ontology="VHOG", source="ISBN:978-3540428541 Kapoor BG, Bhavna Khanna, Ichthyology Handbook (2004) p.406", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels" xsd:string {source="GO"} -property_value: UBPROP:0000008 "This definition is inclusive of the organs of the vertebrate renal system, as well as the Malpighian tubules of insects, and allows for future incorporation of structures such as the antennal glands of crustaceans" xsd:string {source="DOI:10.1371/journal.pone.0099864"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +property_value: RO:0002161 NCBITaxon:110815 {source="Wikipedia"} +property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001009 @@ -10073,7 +9856,6 @@ subset: uberon_slim synonym: "systema cardiovasculare" RELATED OMO:0003011 [Wikipedia:Circulatory_system] xref: AAO:0000959 xref: CALOHA:TS-2103 -xref: MESH:D002319 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: VHOG:0001248 xref: Wikipedia:Circulatory_system is_a: UBERON:0000467 ! anatomical system @@ -10083,17 +9865,13 @@ disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:8450002 ! excretory system relationship: capable_of GO:0003013 ! circulatory system process -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} -relationship: never_in_taxon NCBITaxon:6073 -relationship: never_in_taxon NCBITaxon:6157 -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI -property_value: IAO:0000232 "the cardiovascular system and the lymphatic system are parts of the circulatory system" xsd:string -property_value: RO:0002174 NCBITaxon:6231 {notes="WBbt coelomocyte currently classified as circulating cell"} -property_value: UBPROP:0000001 "Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000959", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001248", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.493", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} +property_value: RO:0002161 NCBITaxon:6073 +property_value: RO:0002161 NCBITaxon:6157 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001015 @@ -10113,10 +9891,8 @@ synonym: "musculature system" RELATED [] synonym: "musculi" EXACT OMO:0003011 [FMA:32558, FMA:TA] synonym: "set of muscles" EXACT [FMA:32558] synonym: "set of skeletal muscles" EXACT [MA:0000165] -xref: AAO:0011066 xref: BTO:0000887 xref: EFO:0001949 -xref: EMAPA:32715 xref: EMAPA:35577 xref: FMA:32558 xref: MA:0000165 @@ -10128,11 +9904,9 @@ xref: WBbt:0005737 xref: Wikipedia:Muscular_system xref: ZFA:0000548 is_a: UBERON:0011216 ! organ system subdivision -relationship: composed_primarily_of UBERON:0001630 ! muscle organ relationship: part_of UBERON:0000383 ! musculature of body -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png" xsd:anyURI -property_value: RO:0002171 UBERON:0001474 -property_value: UBPROP:0000012 "In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here." xsd:string {external_ontology="FMA"} +relationship: RO:0002473 UBERON:0001630 ! composed primarily of muscle organ +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png" xsd:anyURI [Term] id: UBERON:0001016 @@ -10158,7 +9932,6 @@ xref: EHDAA2:0001246 xref: EHDAA:826 xref: EMAPA:16469 xref: EV:0100162 -xref: FBbt:00005093 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7157 xref: GAID:466 xref: MA:0000016 @@ -10181,20 +9954,15 @@ disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:8450002 ! excretory system relationship: capable_of GO:0050877 ! nervous system process -relationship: composed_primarily_of CL:0002319 ! neural cell -relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: has_part CL:0000540 ! neuron -relationship: immediate_transformation_of UBERON:0016880 {source="Bgee:AN"} ! future nervous system -relationship: never_in_taxon NCBITaxon:6040 -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI -property_value: UBPROP:0000001 "A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000396", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000324", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000402", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.117", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "nervous" xsd:string -property_value: UBPROP:0000007 "neural" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002473 CL:0002319 ! composed primarily of neural cell +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +relationship: RO:0002495 UBERON:0016880 {source="Bgee:AN"} ! immediate transformation of future nervous system +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI +property_value: RO:0002161 NCBITaxon:6040 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001017 @@ -10223,7 +9991,6 @@ xref: EHDAA:828 xref: EMAPA:16470 xref: EMAPA:16754 xref: EV:0100163 -xref: FBbt:00005094 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:55675 xref: GAID:570 xref: MA:0000167 @@ -10240,15 +10007,11 @@ xref: XAO:0000215 xref: ZFA:0000012 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0011216 {source="FBbt", source="cjm"} ! organ system subdivision -relationship: immediate_transformation_of UBERON:0016879 {source="Bgee:AN"} ! future central nervous system -relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0001016 ! nervous system -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "Part of the nervous system which includes the brain and spinal cord.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000090", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "The brain and spinal cord. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000012", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO)." xsd:string {source="BIRNLEX:1099"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000293", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 (reference 1), ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 (reference 2), DOI:10.1016/j.cell.2007.02.040 Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud'homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007) (reference 3)", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002495 UBERON:0016879 {source="Bgee:AN"} ! immediate transformation of future central nervous system +property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001041 @@ -10266,7 +10029,6 @@ xref: BTO:0000507 xref: EHDAA2:0000557 xref: EHDAA:520 xref: EMAPA:16548 -xref: FBbt:00005379 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45616 xref: MA:0001526 xref: NCIT:C34180 @@ -10277,10 +10039,8 @@ xref: VHOG:0000285 xref: Wikipedia:Foregut xref: XAO:0000232 is_a: UBERON:0004921 ! subdivision of digestive tract -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/9a/Gray27.png" xsd:anyURI -property_value: editor_note "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. In vertebrates the term may refer to a developmental structure" xsd:string -property_value: UBPROP:0000001 "The anterior portion of the primitive digestive tube of the embryo that lies cephalic to the junction of the yolk stalk, consists of endodermal tissue, and gives rise to the the pharynx, lower respiratory system, esophagus, stomach, duodenum proximal to the biliary tract, liver, pancreas, biliary tract, and gall bladder." xsd:string {source="MP:0000474"} -property_value: UBPROP:0000003 "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000285", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11", source="http://bgee.unil.ch/"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/9a/Gray27.png" xsd:anyURI +property_value: IAO:0000116 "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. In vertebrates the term may refer to a developmental structure" xsd:string [Term] id: UBERON:0001045 @@ -10298,7 +10058,6 @@ xref: EFO:0001950 xref: EHDAA2:0001185 xref: EHDAA:983 xref: EMAPA:16255 -xref: FBbt:00005383 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45617 xref: MA:0001564 xref: NCIT:C34210 @@ -10310,11 +10069,8 @@ xref: Wikipedia:Midgut xref: XAO:0000103 is_a: UBERON:0004921 ! subdivision of digestive tract relationship: proximally_connected_to UBERON:0001041 ! foregut -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/3d/Illu_small_intestine.jpg" xsd:anyURI -property_value: editor_note "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. We may explicitly make this a developmental class" xsd:string -property_value: UBPROP:0000003 "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000290", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "In humans: originates from the foregut at the opening of the bile duct into the duodenum and continues through the small intestine and much of the large intestine until the transition to the hindgut about two-thirds of the way through the transverse colon" xsd:string {source="WP"} -property_value: UBPROP:0000012 "in FMA this represents an embryonic region." xsd:string {external_ontology="FMA"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3d/Illu_small_intestine.jpg" xsd:anyURI +property_value: IAO:0000116 "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. We may explicitly make this a developmental class" xsd:string [Term] id: UBERON:0001046 @@ -10331,7 +10087,6 @@ xref: BTO:0000510 xref: EHDAA2:0000779 xref: EHDAA:975 xref: EMAPA:16715 -xref: FBbt:00005384 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45618 xref: MA:0001527 xref: NCIT:C34188 @@ -10342,13 +10097,10 @@ xref: VHOG:0000459 xref: Wikipedia:Hindgut xref: XAO:0000104 is_a: UBERON:0004921 ! subdivision of digestive tract -relationship: develops_from UBERON:0003104 {source="Wikipedia"} ! mesenchyme relationship: proximally_connected_to UBERON:0001045 ! midgut -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray472.png" xsd:anyURI -property_value: editor_note "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future (vertebrates have some contribution from NC - https://github.com/obophenotype/uberon/wiki/The-neural-crest). We may explicitly make this a developmental class" xsd:string -property_value: UBPROP:0000001 "the caudal portion of the primitive digestive tube of the embryo" xsd:string {source="MP:0008786"} -property_value: UBPROP:0000003 "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000459", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "in FMA this class has no children. In MA it has a single child hindgut epithelium" xsd:string {external_ontology="FMA"} +relationship: RO:0002202 UBERON:0003104 {source="Wikipedia"} ! develops from mesenchyme +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray472.png" xsd:anyURI +property_value: IAO:0000116 "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future (vertebrates have some contribution from NC - https://github.com/obophenotype/uberon/wiki/The-neural-crest). We may explicitly make this a developmental class" xsd:string [Term] id: UBERON:0001048 @@ -10367,7 +10119,6 @@ xref: AEO:0000171 xref: BTO:0001886 xref: EFO:0001652 xref: EHDAA2:0003171 -xref: FBbt:00005495 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:86589 xref: MAT:0000482 xref: NCIT:C34275 @@ -10399,7 +10150,6 @@ xref: EMAPA:16164 xref: EMAPA:16757 xref: FMA:293882 xref: MAT:0000069 -xref: MESH:D054259 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: MIAA:0000069 xref: NCIT:C34226 xref: neuronames:1365 @@ -10414,12 +10164,8 @@ is_a: UBERON:0003914 {source="EHDAA2"} ! epithelial tube is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0016879 ! future central nervous system -relationship: develops_from UBERON:0005068 ! neural rod -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010617", ontology="AAO", source="AAO:JOR"} -property_value: UBPROP:0000001 "The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000307", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/neural+tube"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000307", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000011 "The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium" xsd:string {source="GO:0021915"} +relationship: RO:0002202 UBERON:0005068 ! develops from neural rod +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0001062 @@ -10435,7 +10181,6 @@ xref: BILA:0000000 xref: BIRNLEX:6 xref: CARO:0000000 xref: EHDAA2:0002229 -xref: FBbt:10000000 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:62955 xref: HAO:0000000 xref: MA:0000001 @@ -10446,9 +10191,9 @@ xref: UMLS:C1515976 {source="ncithesaurus:Anatomic_Structure_System_or_Substance xref: WBbt:0000100 xref: XAO:0000000 xref: ZFA:0100000 -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0001072 @@ -10481,13 +10226,11 @@ xref: Wikipedia:Inferior_vena_cava xref: XAO:0000388 is_a: UBERON:0004087 ! vena cava intersection_of: UBERON:0004087 ! vena cava -intersection_of: drains UBERON:0000154 ! posterior region of body -relationship: connected_to UBERON:0002078 ! right cardiac atrium -relationship: drains UBERON:0000154 ! posterior region of body -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray577.png" xsd:anyURI -property_value: UBPROP:0000001 "Trunk of systemic vein which is formed by the union of the right common iliac vein and the left common iliac vein and terminates in the right atrium[FMA]." xsd:string {source="FMA:10951"} -property_value: UBPROP:0000003 "Phylogenetic modifications within this basic pattern of arteries and veins are largely correlated with functional changes. In the transition from water to land, gills gave way to lungs, accompanied by the establishment of a pulmonary circulation. In some fishes and certainly in tetrapods, the cardinal veins become less involved in blood return. Instead, the composite, prominent postcava (posterior vena cava) arose to drain the posterior part of the body and the precava (anterior vena cava) developed to drain the anterior part of the body.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001194", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.454-455", source="http://bgee.unil.ch/"} +intersection_of: RO:0002179 UBERON:0000154 ! drains posterior region of body +relationship: RO:0002170 UBERON:0002078 ! connected to right cardiac atrium +relationship: RO:0002179 UBERON:0000154 ! drains posterior region of body +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray577.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001088 @@ -10516,7 +10259,6 @@ is_a: UBERON:0000174 ! excreta intersection_of: UBERON:0000174 ! excreta intersection_of: produced_by UBERON:0002113 ! kidney relationship: produced_by UBERON:0002113 ! kidney -property_value: UBPROP:0000008 "kidney excreta from some taxa (e.g. in aves) may not be liquid" xsd:string [Term] id: UBERON:0001140 @@ -10545,15 +10287,13 @@ xref: UMLS:C0035092 {source="ncithesaurus:Renal_Vein"} xref: Wikipedia:Renal_vein is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein -intersection_of: drains UBERON:0002113 ! kidney -relationship: drains UBERON:0002113 ! kidney -relationship: present_in_taxon NCBITaxon:9606 -relationship: tributary_of UBERON:0001072 ! posterior vena cava -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI -property_value: UBPROP:0000001 "The renal veins are veins that drain the kidney. They connect the kidney to the inferior vena cava. It is usually singular to each kidney, except in the condition 'multiple renal veins'. It also divides into 2 divisions upon entering the kidney: the anterior branch which receives blood from the anterior portion of the kidney and, the posterior branch which receives blood from the posterior portion. Often, each renal vein will have a branch that receives blood from the ureter. [WP,unvetted][Wikipedia:Renal_vein]." xsd:string {source="Wikipedia:Renal_vein"} -property_value: UBPROP:0000012 "in EHDAA2, the renal vein is part of the kidney" xsd:string {external_ontology="EHDAA2"} +intersection_of: RO:0002179 UBERON:0002113 ! drains kidney +relationship: RO:0002179 UBERON:0002113 ! drains kidney +relationship: RO:0002376 UBERON:0001072 ! tributary of posterior vena cava +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001224 @@ -10585,12 +10325,12 @@ disjoint_from: UBERON:0002355 ! pelvic region of trunk relationship: channel_for UBERON:0001088 ! urine relationship: channels_from UBERON:0002113 ! kidney relationship: channels_into UBERON:0000056 ! ureter -relationship: continuous_with UBERON:0000056 {source="FMA"} ! ureter -relationship: contributes_to_morphology_of UBERON:0000056 ! ureter relationship: part_of UBERON:0002113 {source="MA"} ! kidney relationship: part_of UBERON:0036295 ! renal pelvis/ureter -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/c/c0/Illu_kidney2.jpg" xsd:anyURI +relationship: RO:0002150 UBERON:0000056 {source="FMA"} ! continuous with ureter +relationship: RO:0002433 UBERON:0000056 ! contributes to morphology of ureter +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/c/c0/Illu_kidney2.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001225 @@ -10618,15 +10358,14 @@ xref: Wikipedia:Renal_cortex is_a: UBERON:0001851 ! cortex intersection_of: UBERON:0001851 ! cortex intersection_of: part_of UBERON:0002113 ! kidney -relationship: contributes_to_morphology_of UBERON:0002113 ! kidney relationship: part_of UBERON:0008987 {source="FMA"} ! renal parenchyma -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" xsd:anyURI -property_value: UBPROP:0000010 "In the adult metanephros, it forms a continuous smooth outer zone with a number of projections that extend down between the pyramids. It contains the renal corpuscles and the renal tubules except for parts of the loop of Henle which descend into the renal medulla. It also contains blood vessels and cortical collecting ducts. The renal cortex is the part of the kidney where ultrafiltration occurs.[WP]" xsd:string +relationship: RO:0002433 UBERON:0002113 ! contributes to morphology of kidney +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001229 @@ -10659,15 +10398,12 @@ xref: VHOG:0001262 xref: Wikipedia:Renal_corpuscle xref: ZFA:0005281 is_a: UBERON:0000063 ! organ subunit -relationship: contributes_to_morphology_of UBERON:0001225 ! cortex of kidney -relationship: contributes_to_morphology_of UBERON:0001285 ! nephron relationship: part_of UBERON:0001225 ! cortex of kidney relationship: part_of UBERON:0001285 {source="MA", source="ZFA"} ! nephron -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg" xsd:anyURI -property_value: UBPROP:0000001 "A mass of arterial capillaries enveloped in a capsule and attached to a tubule in the kidney[BTO]" xsd:string {date_retrieved="2012-11-28", external_class="BTO:0000333", ontology="BTO", source="BTO:curator"} -property_value: UBPROP:0000001 "A tuft of capillaries found in a Bowman's capsule in which waste products are filtered from the blood and urine formation is initiated. Paired highly vascularized structures of the pronephros, responsible for blood filtration.[XAO]" xsd:string {date_retrieved="2012-11-28", external_class="XAO:0000146", ontology="XAO", source="XAO:curator"} -property_value: UBPROP:0000001 "The part of the nephron that filters blood.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005281", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002433 UBERON:0001225 ! contributes to morphology of cortex of kidney +relationship: RO:0002433 UBERON:0001285 ! contributes to morphology of nephron +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001230 @@ -10705,13 +10441,10 @@ xref: ZFA:0005254 xref: ZFA:0005310 is_a: UBERON:0000064 ! organ part relationship: capable_of_part_of GO:0003094 {source="Wikipedia"} ! glomerular filtration -relationship: contributes_to_morphology_of UBERON:0001229 ! renal corpuscle -relationship: develops_from UBERON:0004199 ! S-shaped body relationship: part_of UBERON:0001229 ! renal corpuscle -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg" xsd:anyURI -property_value: UBPROP:0000001 "Anatomical structure found in the kidney consisting of an expanded end of a kidney tubule surrounding a glomerulus and is the major site of filtration.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010526", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000009 "Fluids from blood in the glomerulus are collected in the Bowman's capsule and further processed along the nephron to form urine. This process is known as ultrafiltration[WP]." xsd:string -property_value: UBPROP:0000011 "One fold of the S-shaped body gives rise to Bowman's capsule[GUDMAP]" xsd:string +relationship: RO:0002202 UBERON:0004199 ! develops from S-shaped body +relationship: RO:0002433 UBERON:0001229 ! contributes to morphology of renal corpuscle +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg" xsd:anyURI [Term] id: UBERON:0001231 @@ -10747,11 +10480,10 @@ is_a: UBERON:0004211 ! nephron epithelium is_a: UBERON:0009773 {source="GO"} ! renal tubule intersection_of: UBERON:0003914 {source="GO", source="MA", source="ZFA"} ! epithelial tube intersection_of: part_of UBERON:0001285 {source="GO", source="MA", source="ZFA"} ! nephron -relationship: contributes_to_morphology_of UBERON:0001285 ! nephron -relationship: develops_from UBERON:0003918 {notes="checkme"} ! kidney mesenchyme relationship: has_part CL:0005009 {source="ZFA"} ! renal principal cell -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000012 "note that in ISBN:0073040584 (Vertebrates, Kardong), the uriniferous tubule contains the nephron, so we have a separate class, rather than using a synonym, as in MA" xsd:string {external_ontology="MA"} +relationship: RO:0002202 UBERON:0003918 ! develops from kidney mesenchyme +relationship: RO:0002433 UBERON:0001285 ! contributes to morphology of nephron +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001232 @@ -10786,12 +10518,10 @@ xref: TAO:0005294 xref: Wikipedia:Collecting_tubule xref: ZFA:0005294 is_a: UBERON:0006555 ! excretory tube -relationship: contributes_to_morphology_of UBERON:0002113 ! kidney -relationship: part_of UBERON:0001285 {notes="checkme", source="GO"} ! nephron +relationship: part_of UBERON:0001285 ! nephron relationship: part_of UBERON:0004100 ! renal collecting system -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "Renal duct that collects the output from renal tubules.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005294", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000012 "in ISBN:0073040584 (Vertebrates, Kardong), the nephron is adjacent to the collecting tubule, consistent with FMA, but not GO. Wikipedia says: Many sources include the connecting tubule as part of the collecting duct system. However, the embryological origin is more similar to the nephron than it is to the rest of the collecting duct (which derives from the ureteric bud), and other sources therefore classify the connecting tubule with the nephron" xsd:string {external_ontology="FMA"} +relationship: RO:0002433 UBERON:0002113 ! contributes to morphology of kidney +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001245 @@ -10808,7 +10538,6 @@ synonym: "proctodeum" RELATED [] xref: BTO:0001680 xref: CALOHA:TS-2005 xref: EV:0100082 -xref: FBbt:00047153 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:15711 xref: GAID:312 xref: galen:Anus @@ -10822,16 +10551,11 @@ xref: WBbt:0005364 xref: Wikipedia:Anus is_a: UBERON:0000161 ! orifice is_a: UBERON:0004121 ! ectoderm-derived structure -intersection_of: UBERON:0000161 ! orifice -intersection_of: distalmost_part_of UBERON:0001555 ! digestive tract -relationship: develops_from UBERON:0000931 ! proctodeum -relationship: distalmost_part_of UBERON:0001555 ! digestive tract relationship: part_of UBERON:0001555 ! digestive tract -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/65/Protovsdeuterostomes.svg" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/75/Anorectum.gif" xsd:anyURI -property_value: UBPROP:0000007 "anal" xsd:string -property_value: UBPROP:0000008 "In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html" xsd:string +relationship: RO:0002202 UBERON:0000931 ! develops from proctodeum +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/65/Protovsdeuterostomes.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/75/Anorectum.gif" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001255 @@ -10872,18 +10596,12 @@ xref: XAO:0000154 is_a: UBERON:0002075 ! viscus is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0018707 {source="BTO"} ! bladder organ -relationship: develops_from UBERON:0000164 {notes="upper part of UG sinus"} ! primitive urogenital sinus -relationship: never_in_taxon NCBITaxon:8782 {editor="https://orcid.org/0000-0003-3308-6245", id="GOTAX:0010073", source="https://github.com/obophenotype/uberon/issues/454"} relationship: part_of UBERON:0001556 {source="FMA"} ! lower urinary tract -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Urinary_Bladder.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urinary_Bladder.glb" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg" xsd:anyURI -property_value: UBPROP:0000001 "A saccular organ in which urine accumulates before discharge from the body. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000740", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000001 "Anatomical structure which consists of a membranous sac used to temporarily store urine until it is excreted from the body.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000623", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "In tetrapods, the urinary bladder arises as an outpocketing of the cloaca. (...) The tetrapod urinary bladder appears first among amphibians and is present in Sphenodon, turtles, most lizards, ostriches among birds, and all mammals.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000740", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.577-78", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "vesical" xsd:string -property_value: UBPROP:0000008 "The urinary bladder evolved in tetrapods. Birds to not possess a true urinary bladder, although Palaeognathae have an undifferentiated cloacal outpocketing that serves a similar function[https://github.com/obophenotype/uberon/issues/454]" xsd:string +relationship: RO:0002202 UBERON:0000164 ! develops from primitive urogenital sinus +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Urinary_Bladder.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urinary_Bladder.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001271 @@ -10905,12 +10623,9 @@ is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0007823 ! appendage girdle region intersection_of: part_of UBERON:0010709 ! pelvic complex disjoint_from: UBERON:0007832 ! pelvic girdle skeleton -relationship: has_skeleton UBERON:0007832 ! pelvic girdle skeleton -relationship: in_lateral_side_of UBERON:0002355 ! pelvic region of trunk relationship: part_of UBERON:0002355 ! pelvic region of trunk relationship: part_of UBERON:0010709 ! pelvic complex -property_value: IAO:0000232 "this class describes the subdivision of the limb/fin, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831). See also comments on obo-anatomy mail list. Note that even though the class includes soft tissue it is more restrictive than 'pelvis' which also includes structures in cavities etc. TODO this needs to be better documented" xsd:string -property_value: UBPROP:0000001 "Subdivision of lower limb or fin which links the limb/fin to the body[FMA,modified]. There is only one instance of the pelvic girdle region per organism.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000304", ontology="VSAO", source="https://orcid.org/0000-0002-6601-2165"} +relationship: RO:0002551 UBERON:0007832 ! has skeleton pelvic girdle skeleton [Term] id: UBERON:0001285 @@ -10940,15 +10655,13 @@ xref: UMLS:C0027713 {source="ncithesaurus:Nephron"} xref: Wikipedia:Nephron xref: ZFA:0005282 is_a: UBERON:0000064 ! organ part -relationship: contributes_to_morphology_of UBERON:0002113 ! kidney -relationship: develops_from UBERON:0004208 {evidence="definitional"} ! nephrogenic mesenchyme -relationship: immediate_transformation_of UBERON:0010532 {source="Bgee:AN"} ! primitive nephron relationship: part_of UBERON:0007684 {source="FMA"} ! uriniferous tubule -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI -property_value: editor_note "kidney terms require review for cross-vertebrate compatibility and developmental relationships." xsd:string -property_value: UBPROP:0000001 "Functional unit of the kidney that filters waste.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002153", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000008 "In the avian kidney, three types of nephron are identified: mammalian-type nephrons with long and short loops of Henle, and reptilian type nephrons (Gambaryan, 1992)" xsd:string {source="GO"} +relationship: RO:0002202 UBERON:0004208 ! develops from nephrogenic mesenchyme +relationship: RO:0002433 UBERON:0002113 ! contributes to morphology of kidney +relationship: RO:0002495 UBERON:0010532 {source="Bgee:AN"} ! immediate transformation of primitive nephron +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: IAO:0000116 "kidney terms require review for cross-vertebrate compatibility and developmental relationships." xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001287 @@ -10981,13 +10694,12 @@ xref: ZFA:0005290 is_a: UBERON:0006534 {source="MA"} ! renal convoluted tubule is_a: UBERON:0006853 ! renal cortex tubule is_a: UBERON:0012275 ! meso-epithelium -relationship: continuous_with UBERON:0001230 {source="GO"} ! glomerular capsule -relationship: continuous_with UBERON:0001290 ! proximal straight tubule -relationship: contributes_to_morphology_of UBERON:0001231 ! nephron tubule -relationship: develops_from UBERON:0003220 {source="Wikipedia"} ! metanephric mesenchyme -relationship: part_of UBERON:0004134 {notes="MA uses subclass", source="GOC:mtg_kidney_jan10"} ! proximal tubule -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI -property_value: UBPROP:0000001 "Renal tubule that connects to the renal corpuscle.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005290", ontology="TAO", source="ZFIN:curator"} +relationship: part_of UBERON:0004134 ! proximal tubule +relationship: RO:0002150 UBERON:0001230 {source="GO"} ! continuous with glomerular capsule +relationship: RO:0002150 UBERON:0001290 ! continuous with proximal straight tubule +relationship: RO:0002202 UBERON:0003220 {source="Wikipedia"} ! develops from metanephric mesenchyme +relationship: RO:0002433 UBERON:0001231 ! contributes to morphology of nephron tubule +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI [Term] id: UBERON:0001288 @@ -11013,18 +10725,14 @@ xref: VHOG:0001270 xref: Wikipedia:Loop_of_Henle is_a: UBERON:0007685 ! region of nephron tubule intersection_of: UBERON:0007685 ! region of nephron tubule -intersection_of: continuous_with UBERON:0001287 ! proximal convoluted tubule -intersection_of: continuous_with UBERON:0001292 ! distal convoluted tubule -relationship: continuous_with UBERON:0001287 ! proximal convoluted tubule -relationship: continuous_with UBERON:0001292 ! distal convoluted tubule -relationship: contributes_to_morphology_of UBERON:0001231 ! nephron tubule -relationship: present_in_taxon NCBITaxon:8782 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI -property_value: editor_note "the definitions of some kidney parts (e.g. proximal straight tubule) refer to Henle's loop, even in species where this may not be present. Requires review." xsd:string -property_value: RO:0002174 NCBITaxon:8353 -property_value: UBPROP:0000001 "A highly specialized segment of the mammalian kidney tubules, that dips into the medulla. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, p.648, see_Liem_KF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001270", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "The structure differs considerably between species; there is a definite physical loop of Henle in the mammalian and avian renal systems but this seems to be absent in Xenopus. However, homologs of some, but not all, molecular markers (e.g. cldn8 and clcnk) of the mammalian loop of Henle were found to be present in the pronephros of the frog larva ." xsd:string {source="DOI:10.1371/journal.pone.0099864"} -property_value: UBPROP:0000009 "The loop of Henle plays an important role in creating a concentration gradient in the medulla of the kidney. It is involved in reabsorption of filtered water and ions including sodium, potassium and calcium, and independently regulates both the volume and osmolarity of body fluids." xsd:string {source="DOI:10.1371/journal.pone.0099864"} +intersection_of: RO:0002150 UBERON:0001287 ! continuous with proximal convoluted tubule +intersection_of: RO:0002150 UBERON:0001292 ! continuous with distal convoluted tubule +relationship: RO:0002150 UBERON:0001287 ! continuous with proximal convoluted tubule +relationship: RO:0002150 UBERON:0001292 ! continuous with distal convoluted tubule +relationship: RO:0002433 UBERON:0001231 ! contributes to morphology of nephron tubule +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: IAO:0000116 "the definitions of some kidney parts (e.g. proximal straight tubule) refer to Henle's loop, even in species where this may not be present. Requires review." xsd:string +property_value: RO:0002175 NCBITaxon:8782 [Term] id: UBERON:0001289 @@ -11045,10 +10753,10 @@ xref: SCTID:245350001 xref: UMLS:C0227657 {source="ncithesaurus:Descending_Limb_of_the_Henle_s_Loop"} xref: Wikipedia:Descending_limb_of_loop_of_henle is_a: UBERON:0007685 {source="FMA"} ! region of nephron tubule -relationship: contributes_to_morphology_of UBERON:0001288 ! loop of Henle relationship: part_of UBERON:0001288 {source="FMA"} ! loop of Henle -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +relationship: RO:0002433 UBERON:0001288 ! contributes to morphology of loop of Henle +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001290 @@ -11076,14 +10784,13 @@ xref: Wikipedia:Proximal_straight_tubule xref: ZFA:0005291 is_a: UBERON:0006853 ! renal cortex tubule is_a: UBERON:0009035 {source="MA"} ! renal straight tubule -relationship: continuous_with UBERON:0001287 ! proximal convoluted tubule -relationship: continuous_with UBERON:0005096 ! descending thin limb relationship: part_of UBERON:0001289 {source="MA"} ! descending limb of loop of Henle -relationship: part_of UBERON:0004134 {notes="MA uses subclass", source="GOC:mtg_kidney_jan10"} ! proximal tubule +relationship: part_of UBERON:0004134 ! proximal tubule relationship: part_of UBERON:0006542 {source="MA"} ! outer medulla outer stripe loop of Henle -relationship: present_in_taxon NCBITaxon:9606 -property_value: editor_note "TODO - is S3 exactly coincident with PST? todo - ensure relationships work across species (loop of Henle)" xsd:string -property_value: UBPROP:0000001 "Portion of the renal tubule which is just posterior to the proximal convoluted tubule.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005291", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002150 UBERON:0001287 ! continuous with proximal convoluted tubule +relationship: RO:0002150 UBERON:0005096 ! continuous with descending thin limb +property_value: IAO:0000116 "TODO - is S3 exactly coincident with PST? todo - ensure relationships work across species (loop of Henle)" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001292 @@ -11109,13 +10816,11 @@ xref: Wikipedia:Distal_convoluted_tubule is_a: UBERON:0006534 {source="MA"} ! renal convoluted tubule is_a: UBERON:0006853 ! renal cortex tubule is_a: UBERON:0012275 ! meso-epithelium -relationship: contributes_to_morphology_of UBERON:0001231 ! nephron tubule -relationship: develops_from UBERON:0003220 ! metanephric mesenchyme relationship: part_of UBERON:0004135 {source="EMAPA", source="GO", source="MA-modified-from-isa"} ! distal tubule -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/2/21/Kidney_nephron.png" xsd:anyURI -property_value: UBPROP:0000001 "a portion of kidney nephron between the loop of Henle and the collecting duct system[Wikipedia:Distal_convoluted_tubule]." xsd:string {source="Wikipedia:Distal_convoluted_tubule"} -property_value: UBPROP:0000009 "in humans it is responsible for the reabsorption of about 5% of filtered sodium via the thiazide-sensitive Na-Cl symporter." xsd:string +relationship: RO:0002202 UBERON:0003220 ! develops from metanephric mesenchyme +relationship: RO:0002433 UBERON:0001231 ! contributes to morphology of nephron tubule +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/21/Kidney_nephron.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001293 @@ -11137,8 +10842,8 @@ xref: EMAPA:28310 xref: FMA:17733 xref: MA:0001653 is_a: UBERON:0000064 ! organ part -relationship: contributes_to_morphology_of UBERON:0000362 ! renal medulla relationship: part_of UBERON:0000362 ! renal medulla +relationship: RO:0002433 UBERON:0000362 ! contributes to morphology of renal medulla [Term] id: UBERON:0001353 @@ -11163,11 +10868,10 @@ xref: UMLS:C0230120 {source="ncithesaurus:Anal_Region"} xref: VHOG:0000395 xref: WBbt:0006919 is_a: UBERON:0000475 ! organism subdivision -relationship: has_developmental_contribution_from UBERON:0000931 {evidence="cjm"} ! proctodeum relationship: overlaps UBERON:0006866 ! terminal part of digestive tract -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray408.png" xsd:anyURI +relationship: RO:0002254 UBERON:0000931 ! has developmental contribution from proctodeum +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray408.png" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/507" xsd:anyURI -property_value: UBPROP:0000003 "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000395", ontology="VHOG", source="ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11", source="http://bgee.unil.ch/"} [Term] id: UBERON:0001434 @@ -11203,18 +10907,11 @@ intersection_of: has_part UBERON:0004770 ! articular system disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:8450002 ! excretory system -relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: has_part UBERON:0004288 ! skeleton relationship: has_part UBERON:0004770 ! articular system relationship: part_of UBERON:0002204 ! musculoskeletal system -property_value: RO:0002171 UBERON:0001016 +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/The-skeletal-system" xsd:anyURI -property_value: UBPROP:0000001 "Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000434", ontology="TAO", source="TAO:wd"} -property_value: UBPROP:0000001 "Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000027", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "System that provides physical support to the organism.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000566", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000003 "By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001254", ontology="VHOG", source="DOI:10.1159/000324245 Donoghue PCJ, Sansom IJ, Origin and early evolution of vertebrate skeletonization. Microscopy research and technique (2002)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "skeletal" xsd:string -property_value: UBPROP:0000012 "GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates" xsd:string {external_ontology="GO"} [Term] id: UBERON:0001552 @@ -11232,10 +10929,10 @@ xref: MA:0002583 xref: Wikipedia:Arcuate_arteries_of_the_kidney is_a: UBERON:0001637 ! artery is_a: UBERON:0003644 ! kidney arterial blood vessel -relationship: connecting_branch_of UBERON:0009885 ! interlobar artery relationship: part_of UBERON:0001225 {source="MA"} ! cortex of kidney -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/87/2610_The_Kidney.jpg" xsd:anyURI +relationship: RO:0002252 UBERON:0009885 ! connecting branch of interlobar artery +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/87/2610_The_Kidney.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001555 @@ -11259,11 +10956,9 @@ xref: BTO:0000545 xref: EHDAA2:0000726 xref: EHDAA:518 xref: EMAPA:16247 -xref: FBbt:00003125 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45615 xref: galen:AlimentaryTract xref: MA:0000917 -xref: MESH:D041981 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: NCIT:C34082 xref: TAO:0000112 xref: TGMA:0001819 @@ -11272,18 +10967,13 @@ xref: VHOG:0000309 xref: WBbt:0005743 xref: ZFA:0000112 is_a: UBERON:0000025 ! tube -relationship: connects UBERON:0000165 ! mouth -relationship: immediate_transformation_of UBERON:0007026 {source="NCBIBook:NBK10107"} ! presumptive gut -relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} -relationship: never_in_taxon NCBITaxon:41324 {source="DOI:10.1371/journal.pone.0016309"} -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0001007 ! digestive system -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "The alimentary or digestive tract, and associated organs.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000112", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000309", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "FMA also has a term 'gastrointestinal tract', but this includes the liver." xsd:string {external_ontology="FMA"} -property_value: UBPROP:0000012 "we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509" xsd:string {external_ontology="MA"} -property_value: UBPROP:0000013 "we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002176 UBERON:0000165 ! connects mouth +relationship: RO:0002495 UBERON:0007026 {source="NCBIBook:NBK10107"} ! immediate transformation of presumptive gut +property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} +property_value: RO:0002161 NCBITaxon:41324 {source="DOI:10.1371/journal.pone.0016309"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001556 @@ -11301,7 +10991,7 @@ is_a: UBERON:0011216 ! organ system subdivision relationship: has_part UBERON:0000057 ! urethra relationship: has_part UBERON:0001255 ! urinary bladder relationship: part_of UBERON:0001008 ! renal system -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001630 @@ -11313,8 +11003,6 @@ subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "muscle" BROAD [ZFA:0005145] -xref: AAO:0011066 -xref: EMAPA:32715 xref: EMAPA:37474 {source="MA:th"} xref: EV:0100146 xref: FMA:5022 @@ -11329,12 +11017,9 @@ xref: ZFA:0005145 is_a: UBERON:0000062 ! organ is_a: UBERON:0005090 ! muscle structure intersection_of: UBERON:0000062 ! organ -intersection_of: composed_primarily_of UBERON:0002385 ! muscle tissue -relationship: composed_primarily_of UBERON:0002385 ! muscle tissue +intersection_of: RO:0002473 UBERON:0002385 ! composed primarily of muscle tissue relationship: part_of UBERON:0001015 ! musculature -property_value: UBPROP:0000001 "Portion of tissue composed of contractile fibers.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005145", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001245", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.75", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "muscular" xsd:string +relationship: RO:0002473 UBERON:0002385 ! composed primarily of muscle tissue [Term] id: UBERON:0001637 @@ -11355,7 +11040,6 @@ xref: AEO:0000208 xref: BTO:0000573 xref: CALOHA:TS-0054 xref: EFO:0000814 -xref: EHDAA2:0000143 xref: EHDAA2:0003253 xref: EMAPA:35147 xref: EV:0100026 @@ -11376,12 +11060,7 @@ xref: XAO:0000114 xref: ZFA:0000005 is_a: UBERON:0003509 ! arterial blood vessel relationship: channels_from UBERON:0000948 ! heart -property_value: editor_note "Note that in FMA an artery is a tree, whereas AEO/JB defines it as a tube; FMA includes a separate class for what it calls the trunk. Classification in this ontology may currently (Jan 2012) represent a mix of both schemes, although we are gradually revising in the direction of the AEO scheme." xsd:string -property_value: UBPROP:0000001 "Part of the circulatory system composed of blood vessels which carry oxygenated blood away from the heart to the rest of the body.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010211", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001251", ontology="VHOG", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "arterial" xsd:string -property_value: UBPROP:0000012 "Some arthropods have primitive arterial systems but this term refers to arteries in a true closed circulatory system." xsd:string -property_value: UBPROP:0000202 FMA:63812 +property_value: IAO:0000116 "Note that in FMA an artery is a tree, whereas AEO/JB defines it as a tube; FMA includes a separate class for what it calls the trunk. Classification in this ontology may currently (Jan 2012) represent a mix of both schemes, although we are gradually revising in the direction of the AEO scheme." xsd:string [Term] id: UBERON:0001638 @@ -11426,12 +11105,8 @@ intersection_of: UBERON:0003920 ! venous blood vessel intersection_of: channel_for UBERON:0013756 ! venous blood relationship: channel_for UBERON:0013756 ! venous blood relationship: channels_from UBERON:0001982 ! capillary -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c2/Venous_system_en.svg" xsd:anyURI -property_value: editor_note "TODO - check with MA - vein vs venous blood vessel" xsd:string -property_value: UBPROP:0000001 "Part of the circulatory system composed of blood vessels which carry blood from other organs, tissues, and cells to the heart.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010212", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001743", ontology="VHOG", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "venous" xsd:string -property_value: UBPROP:0000202 FMA:63814 +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c2/Venous_system_en.svg" xsd:anyURI +property_value: IAO:0000116 "TODO - check with MA - vein vs venous blood vessel" xsd:string [Term] id: UBERON:0001851 @@ -11450,8 +11125,6 @@ xref: galen:Cortex xref: Wikipedia:Cortex_(anatomy) is_a: UBERON:0000064 ! organ part relationship: bounding_layer_of UBERON:0000062 ! organ -property_value: UBPROP:0000007 "cortical" xsd:string -property_value: UBPROP:0000012 "this class is used more generically than in FMA, and includes e.g. cortex of hair" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0001969 @@ -11482,12 +11155,12 @@ is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000179 ! haemolymphatic fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: has_part GO:0005577 ! fibrinogen complex -intersection_of: has_quality PATO:0001548 ! quality of a liquid intersection_of: part_of UBERON:0000178 ! blood -intersection_of: surrounds CL:0000232 ! erythrocyte +intersection_of: RO:0000086 PATO:0001548 ! has quality quality of a liquid +intersection_of: RO:0002221 CL:0000232 ! surrounds erythrocyte relationship: has_part GO:0005577 ! fibrinogen complex relationship: part_of UBERON:0000178 ! blood -relationship: surrounds CL:0000232 ! erythrocyte +relationship: RO:0002221 CL:0000232 ! surrounds erythrocyte [Term] id: UBERON:0001979 @@ -11513,11 +11186,10 @@ xref: Wikipedia:Venule xref: ZFA:0005315 is_a: UBERON:0003920 ! venous blood vessel is_a: UBERON:8410081 ! blood microvessel -relationship: connects UBERON:0001638 ! vein -relationship: connects UBERON:0001982 ! capillary -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/d/da/Illu_capillary.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Multi-tissue structure part of the blood vasculature formed by the anastomosis of capillaries. Venules carry blood toward the heart.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005315", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002176 UBERON:0001638 ! connects vein +relationship: RO:0002176 UBERON:0001982 ! connects capillary +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/da/Illu_capillary.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001980 @@ -11544,14 +11216,12 @@ xref: ZFA:0005255 is_a: UBERON:0003509 {source="MA"} ! arterial blood vessel is_a: UBERON:8410081 ! blood microvessel intersection_of: UBERON:0001981 ! blood vessel -intersection_of: connects UBERON:0001637 ! artery -intersection_of: connects UBERON:0001982 ! capillary -relationship: connects UBERON:0001637 ! artery -relationship: connects UBERON:0001982 ! capillary -relationship: contributes_to_morphology_of UBERON:0001637 ! artery -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/d/da/Illu_capillary.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Multi-tissue structure part of the blood vasculature, feeds into capillaries. Arterioles carry blood away from the heart.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002138", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Small, terminal branch of an artery which generally connects to capillaries.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010253", ontology="AAO", source="AAO:BJB"} +intersection_of: RO:0002176 UBERON:0001637 ! connects artery +intersection_of: RO:0002176 UBERON:0001982 ! connects capillary +relationship: RO:0002176 UBERON:0001637 ! connects artery +relationship: RO:0002176 UBERON:0001982 ! connects capillary +relationship: RO:0002433 UBERON:0001637 ! contributes to morphology of artery +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/da/Illu_capillary.jpg" xsd:anyURI [Term] id: UBERON:0001981 @@ -11593,22 +11263,18 @@ xref: XAO:0001011 xref: ZFA:0005314 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000055 ! vessel +is_a: UBERON:0004120 ! mesoderm-derived structure relationship: capable_of_part_of GO:0008015 ! blood circulation relationship: channel_for UBERON:0000178 ! blood -relationship: develops_from UBERON:0004872 ! splanchnic layer of lateral plate mesoderm -relationship: develops_from UBERON:0006965 {source="GO:0072360"} ! vascular cord relationship: has_part CL:0000071 {source="AEO"} ! blood vessel endothelial cell relationship: has_part UBERON:0007500 {source="EHDAA2"} ! epithelial tube open at both ends -relationship: has_quality PATO:0002045 ! dendritic relationship: part_of UBERON:0004537 ! blood vasculature -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI -property_value: editor_note "consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus" xsd:string -property_value: UBPROP:0000001 "Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001250", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000001 "Any of the vessels through which blood circulates in the body.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011004", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001250", ontology="VHOG", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "annelids have blood vessels, but this class is not applicable to annelids." xsd:string -property_value: UBPROP:0000012 "FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX" xsd:string {external_ontology="FMA"} +relationship: RO:0000086 PATO:0002045 ! has quality dendritic +relationship: RO:0002202 UBERON:0004872 ! develops from splanchnic layer of lateral plate mesoderm +relationship: RO:0002202 UBERON:0006965 {source="GO:0072360"} ! develops from vascular cord +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: IAO:0000116 "consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001982 @@ -11641,17 +11307,14 @@ xref: XAO:0000116 xref: ZFA:0005250 is_a: UBERON:8410081 ! blood microvessel intersection_of: UBERON:8410081 ! blood microvessel -intersection_of: connects UBERON:0001979 ! venule -intersection_of: connects UBERON:0001980 ! arteriole -relationship: connects UBERON:0001979 ! venule -relationship: connects UBERON:0001980 ! arteriole -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/A_red_blood_cell_in_a_capillary,_pancreatic_tissue_-_TEM.jpg" xsd:anyURI -property_value: editor_note "not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element" xsd:string +intersection_of: RO:0002176 UBERON:0001979 ! connects venule +intersection_of: RO:0002176 UBERON:0001980 ! connects arteriole +relationship: RO:0002176 UBERON:0001979 ! connects venule +relationship: RO:0002176 UBERON:0001980 ! connects arteriole +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/A_red_blood_cell_in_a_capillary,_pancreatic_tissue_-_TEM.jpg" xsd:anyURI +property_value: IAO:0000116 "not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element" xsd:string +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/uberon/issues/2186" xsd:string -property_value: UBPROP:0000001 "Any of the tiny blood vessels connecting the arterioles to the venules.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010252", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001253", ontology="VHOG", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000010 "capillaries lack tunica media and tunica adventitia; only the endothelial wall of the tunica intima belongs" xsd:string [Term] id: UBERON:0001986 @@ -11675,11 +11338,10 @@ xref: UMLS:C0014257 {source="ncithesaurus:Endothelium"} is_a: UBERON:0000487 {source="FMA-text-def", source="https://github.com/obophenotype/uberon/issues/225"} ! simple squamous epithelium is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0000483 ! epithelium -intersection_of: composed_primarily_of CL:0000115 ! endothelial cell -relationship: composed_primarily_of CL:0000115 ! endothelial cell -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000007 "endothelial" xsd:string +intersection_of: RO:0002473 CL:0000115 ! composed primarily of endothelial cell +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002473 CL:0000115 ! composed primarily of endothelial cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002049 @@ -11696,13 +11358,12 @@ xref: FMA:69050 xref: TAO:0005249 xref: ZFA:0005249 is_a: UBERON:0000477 {source="FMA"} ! anatomical cluster -relationship: composed_primarily_of UBERON:0000055 ! vessel relationship: has_part UBERON:0000179 ! haemolymphatic fluid relationship: part_of UBERON:0007798 ! vascular system -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI -property_value: editor_note "see also: vascular system. Consider merging?" xsd:string -property_value: UBPROP:0000007 "vascular" xsd:string +relationship: RO:0002473 UBERON:0000055 ! composed primarily of vessel +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: IAO:0000116 "see also: vascular system. Consider merging?" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002050 @@ -11722,7 +11383,6 @@ xref: BILA:0000034 xref: BTO:0000174 xref: CALOHA:TS-2110 xref: EFO:0000461 -xref: FBbt:00004208 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69067 xref: GAID:407 xref: MESH:D004628 @@ -11738,10 +11398,6 @@ is_a: UBERON:0005423 ! developing anatomical structure intersection_of: UBERON:0005423 ! developing anatomical structure intersection_of: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0000922 ! embryo -property_value: UBPROP:0000001 "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000138", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001105", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000178", ontology="VSAO", source="ZFIN:curator"} -property_value: UBPROP:0000012 "in FMA embryo is_a embryonic structure" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0002075 @@ -11772,10 +11428,8 @@ xref: Wikipedia:Viscus xref: XAO:0003034 is_a: UBERON:0005177 ! trunk region element intersection_of: UBERON:0000062 ! organ -intersection_of: located_in UBERON:0002323 ! coelemic cavity lumen -relationship: located_in UBERON:0002323 ! coelemic cavity lumen -property_value: UBPROP:0000001 "An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010386", ontology="AAO", source="BTO:0001491"} -property_value: UBPROP:0000012 "general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs." xsd:string {external_ontology="FMA"} +intersection_of: RO:0001025 UBERON:0002323 ! located in coelemic cavity lumen +relationship: RO:0001025 UBERON:0002323 ! located in coelemic cavity lumen [Term] id: UBERON:0002078 @@ -11806,16 +11460,11 @@ xref: Wikipedia:Right_atrium xref: XAO:0003192 is_a: UBERON:0002081 ! cardiac atrium is_a: UBERON:0035554 ! right cardiac chamber -intersection_of: UBERON:0002081 ! cardiac atrium -intersection_of: in_right_side_of UBERON:0000948 ! heart -relationship: connected_to UBERON:0004537 ! blood vasculature -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI -property_value: UBPROP:0000001 "Right cardiac chamber which is continuous with the superior vena cava and inferior vena cava.[FMA]" xsd:string {source="FMA:7096"} -property_value: UBPROP:0000003 "The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000328", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +relationship: RO:0002170 UBERON:0004537 ! connected to blood vasculature +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002081 @@ -11853,13 +11502,9 @@ xref: UMLS:C0018792 {source="ncithesaurus:Cardiac_Atrium"} xref: VHOG:0000175 xref: Wikipedia:Heart_atrium xref: ZFA:0000471 -is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004151 ! cardiac chamber -relationship: contributes_to_morphology_of UBERON:0000948 ! heart -relationship: immediate_transformation_of UBERON:0010227 ! future cardiac atrium -property_value: UBPROP:0000001 "One of four heart chambers.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000471", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "One of two chambers of the heart which receive blood from the veins and forces it by muscular contration to the ventricle.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010246", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000175", ontology="VHOG", source="ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.428", source="http://bgee.unil.ch/"} +relationship: RO:0002433 UBERON:0000948 ! contributes to morphology of heart +relationship: RO:0002495 UBERON:0010227 ! immediate transformation of future cardiac atrium [Term] id: UBERON:0002090 @@ -11877,12 +11522,10 @@ xref: AAO:0000034 xref: EFO:0000942 xref: EHDAA2:0000161 xref: EHDAA:5049 -xref: EMAPA:17214 xref: EMAPA:37721 {source="MA:th"} xref: FMA:71221 xref: MA:0002986 xref: MAT:0000148 -xref: MESH:D013131 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: MIAA:0000148 xref: TAO:0000317 xref: VHOG:0000317 @@ -11890,14 +11533,10 @@ xref: VSAO:0000093 xref: XAO:0003073 xref: ZFA:0000317 is_a: UBERON:0010912 ! subdivision of skeleton -relationship: develops_from UBERON:0003089 ! sclerotome relationship: part_of UBERON:0005944 ! axial skeleton plus cranial skeleton relationship: part_of UBERON:0011138 ! postcranial axial skeletal system +relationship: RO:0002202 UBERON:0003089 ! develops from sclerotome property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" xsd:anyURI -property_value: UBPROP:0000001 "Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000093", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000034", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000001 "The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000317", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000317", ontology="VHOG", source="DOI:10.1186/1742-9994-8-4 Schilling N, Evolution of the axial system in craniates: morphology and function of the perivertebral musculature. Frontiers in Zoology (2011)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0002091 @@ -11923,22 +11562,17 @@ xref: MIAA:0000278 xref: NCIT:C49477 xref: SCTID:322050006 xref: UMLS:C0222646 {source="ncithesaurus:Appendicular_Skeleton"} -xref: VHOG:0001666 xref: VSAO:0000076 xref: Wikipedia:Appendicular_skeleton xref: XAO:0003166 is_a: UBERON:0010912 ! subdivision of skeleton -relationship: contributes_to_morphology_of UBERON:0001434 ! skeletal system -relationship: only_in_taxon NCBITaxon:7776 ! Gnathostomata relationship: overlaps UBERON:0000026 ! appendage relationship: part_of UBERON:0011249 ! appendicular skeletal system -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/7c/Appendicular_skeleton_diagram.svg" xsd:anyURI +relationship: RO:0002160 NCBITaxon:7776 ! only in taxon Gnathostomata +relationship: RO:0002433 UBERON:0001434 ! contributes to morphology of skeletal system +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7c/Appendicular_skeleton_diagram.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton" xsd:anyURI -property_value: UBPROP:0000001 "Skeletal subdivision consisting of all the skeletal elements in the pectoral and pelvic appendage complexes.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000076", ontology="VSAO", source="PSPUB:0000170", source="https://orcid.org/0000-0002-6601-2165"} -property_value: UBPROP:0000001 "Skeletal system that consists of the paired fins (pectoral or pelvic fins).[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000027", ontology="TAO", source="TAO:wd"} -property_value: UBPROP:0000001 "The pectoral and pelvic girdles, which articulate with the axial skeleton, together with their associated limbs, the forelimbs and hind limbs, form the appendicular skeleton.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000747", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000012 "ontologies differ in whether they treat the term appendicular skeleton as being the entire set of bones in the limbs, or whether the fore and hind limbs/fins are treated as seperate appendicular skeletons. Here we follow FMA, and treat the appendicular skeleton as the sum total of skeletal elements in the organism (this is evidenced by the fact that in FMA, skeleton of left/right upper/lower limb is part_of a appendicular skeleton, and subtypes of 'subdivision of appendicular skeleton'). We have separate classes such as 'skeleton of limb', and 'skeleton of hindlimb' for the 4 parts of the appendicular skeleton. In future the ZFA/TAO classes may be moved." xsd:string {external_ontology="FMA"} [Term] id: UBERON:0002100 @@ -11974,16 +11608,12 @@ xref: XAO:0003025 xref: ZFA:0001115 is_a: UBERON:0011676 ! subdivision of organism along main body axis relationship: part_of UBERON:0013702 ! body proper -property_value: RO:0002171 UBERON:0000026 {exceptions="ZFA", source="https://github.com/obophenotype/uberon/issues/378", status="pending"} -property_value: RO:0002171 UBERON:0000033 -property_value: UBPROP:0000001 "Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010339", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001115", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0002113 name: kidney namespace: uberon -def: "A paired organ of the urinary tract which has the production of urine as its primary function." [http://anatomy.uams.edu/anatomyhtml/kidney.html, Wikipedia:Kidney] +def: "A paired organ of the urinary tract that produces urine and maintains bodily fluid homeostasis, blood pressure, pH levels, red blood cell production and skeleton mineralization." [http://anatomy.uams.edu/anatomyhtml/kidney.html, https://www.kidney.org/kidneydisease/top-5-jobs-kidneys-do, PMID:25140012, PMID:35003210, Wikipedia:Kidney] subset: efo_slim subset: human_reference_atlas subset: major_organ @@ -11995,35 +11625,25 @@ synonym: "reniculate kidney" NARROW SENSU [Wikipedia:Reniculate_kidney] xref: AAO:0000250 xref: BTO:0000671 xref: CALOHA:TS-0510 -xref: EFO:0000929 -xref: EMAPA:17373 -xref: EV:0100096 -xref: FMA:7203 xref: GAID:423 xref: galen:Kidney -xref: MA:0000368 xref: MAT:0000119 xref: MESH:D007668 xref: MIAA:0000119 -xref: NCIT:C12415 -xref: SCTID:181414000 xref: UMLS:C0022646 {source="ncithesaurus:Kidney"} xref: Wikipedia:Kidney xref: XAO:0003267 is_a: UBERON:0000489 ! cavitated compound organ is_a: UBERON:0005172 ! abdomen element is_a: UBERON:0015212 ! lateral structure -relationship: contributes_to_morphology_of UBERON:0001008 ! renal system -relationship: develops_from UBERON:0003918 {evidence="definitional"} ! kidney mesenchyme -relationship: develops_from UBERON:0005095 ! kidney rudiment -relationship: in_lateral_side_of UBERON:0000468 ! multicellular organism -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0011143 {source="FMA"} ! upper urinary tract -relationship: present_in_taxon NCBITaxon:9606 -property_value: RO:0002171 UBERON:0000160 -property_value: UBPROP:0000001 "One of either of a pair of structures lying on either side of the dorsal aorta in which fluid balance is regulated and waste is excreted out in the form of urine.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000250", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000007 "renal" xsd:string -property_value: UBPROP:0000202 FMA:264815 +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002202 UBERON:0003918 ! develops from kidney mesenchyme +relationship: RO:0002202 UBERON:0005095 ! develops from kidney rudiment +relationship: RO:0002433 UBERON:0001008 ! contributes to morphology of renal system +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7655-4833 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2804-127X +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002120 @@ -12047,7 +11667,6 @@ xref: EHDAA:1017 xref: EMAPA:16579 xref: FMA:72170 xref: MAT:0000117 -xref: MESH:D060910 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: MIAA:0000117 xref: NCIT:C34280 xref: SCTID:308804007 @@ -12060,14 +11679,9 @@ xref: ZFA:0000151 is_a: UBERON:0002113 {source="GO"} ! kidney is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005423 ! developing anatomical structure -relationship: develops_from UBERON:0005721 {source="ZFA"} ! pronephric mesoderm -relationship: develops_from UBERON:0005754 ! rostral part of nephrogenic cord -relationship: located_in UBERON:0003887 {source="OG"} ! intraembryonic coelom -property_value: UBPROP:0000001 "A kidney formed of nephric tubules arising in the anterior region of the nephric ridge; forms only as a transient embryonic structure. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.748][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000037", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000001 "Organ that serves as a transient kidney, providing osmoregulation during early developmental stages and then degenerating during metamorphosis.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011089", ontology="AAO", source="XAO:curator"} -property_value: UBPROP:0000001 "The embryonic kidney, present at the level of the third somite, is composed of two glomeruli fused at the midline, two pronephric tubules, and paired bilateral pronephric ducts that modify the composition of the blood filtrate before delivering it to the cloaca for excretion.Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000151", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000037", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.637", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "pronephric" xsd:string +relationship: RO:0001025 UBERON:0003887 {source="OG"} ! located in intraembryonic coelom +relationship: RO:0002202 UBERON:0005721 {source="ZFA"} ! develops from pronephric mesoderm +relationship: RO:0002202 UBERON:0005754 ! develops from rostral part of nephrogenic cord [Term] id: UBERON:0002193 @@ -12083,7 +11697,7 @@ xref: EMAPA:18765 xref: FMA:74562 xref: MA:0000013 is_a: UBERON:0000467 {source="MA"} ! anatomical system -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria [Term] id: UBERON:0002201 @@ -12132,13 +11746,10 @@ is_a: UBERON:0000467 ! anatomical system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:8450002 ! excretory system relationship: capable_of_part_of GO:0040011 ! locomotion -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: has_developmental_contribution_from UBERON:0000926 {notes="check ctenophore"} ! mesoderm relationship: has_part UBERON:0000383 ! musculature of body relationship: has_part UBERON:0001434 ! skeletal system -property_value: UBPROP:0000001 "Anatomical system that provides locomotion and physical support to the organism.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010546", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001275", ontology="VHOG", source="DOI:10.1002/jez.b.21246 Shearman RM, Burke AC, The lateral somitic frontier in ontogeny and phylogeny. Journal of Experimental Zoology (2009)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "musculoskeletal" xsd:string +relationship: RO:0002254 UBERON:0000926 ! has developmental contribution from mesoderm +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage [Term] id: UBERON:0002224 @@ -12165,13 +11776,12 @@ xref: UMLS:C0230139 {source="ncithesaurus:Thoracic_Cavity"} xref: Wikipedia:Thoracic_cavity is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0000915 ! thoracic segment of trunk intersection_of: part_of UBERON:0002323 ! coelemic cavity lumen -relationship: luminal_space_of UBERON:0000915 ! thoracic segment of trunk +intersection_of: RO:0002572 UBERON:0000915 ! luminal space of thoracic segment of trunk relationship: part_of UBERON:0002323 ! coelemic cavity lumen -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI -property_value: UBPROP:0000008 "In many species, the diaphragm separates thoracic and abdominal cavities" xsd:string +relationship: RO:0002572 UBERON:0000915 ! luminal space of thoracic segment of trunk +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI [Term] id: UBERON:0002303 @@ -12200,7 +11810,7 @@ relationship: has_part CL:0000648 ! kidney granular cell relationship: has_part CL:0002173 ! extraglomerular mesangial cell relationship: has_part UBERON:0002335 ! macula densa relationship: part_of UBERON:0001225 {source="MA"} ! cortex of kidney -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002319 @@ -12211,7 +11821,6 @@ subset: human_reference_atlas subset: pheno_slim subset: uberon_slim xref: BTO:0002494 -xref: EMAPA:28248 xref: EMAPA:36561 {source="MA:th"} xref: FMA:84139 xref: MA:0002617 @@ -12219,17 +11828,16 @@ xref: NCIT:C33101 xref: UMLS:C0017655 {source="ncithesaurus:Mesangium"} xref: Wikipedia:Mesangium is_a: UBERON:0000119 ! cell layer +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000119 ! cell layer -intersection_of: composed_primarily_of CL:0000650 ! mesangial cell -intersection_of: located_in UBERON:0005777 ! glomerular basement membrane -relationship: composed_primarily_of CL:0000650 ! mesangial cell -relationship: located_in UBERON:0005777 ! glomerular basement membrane +intersection_of: RO:0001025 UBERON:0005777 ! located in glomerular basement membrane +intersection_of: RO:0002473 CL:0000650 ! composed primarily of mesangial cell relationship: part_of UBERON:0000074 ! renal glomerulus relationship: part_of UBERON:0005215 ! kidney interstitium -relationship: present_in_taxon NCBITaxon:9606 -relationship: surrounds UBERON:0004212 ! glomerular capillary -property_value: UBPROP:0000007 "mesangial" xsd:string -property_value: UBPROP:0000012 "WP considers this the same as glomerular mesangium. In MA, glomerular and extraglomerular are distingsuished. FMA class has no definition and is a type of stroma, which is inconsistent with our classification of this here." xsd:string {external_ontology="MA"} +relationship: RO:0001025 UBERON:0005777 ! located in glomerular basement membrane +relationship: RO:0002221 UBERON:0004212 ! surrounds glomerular capillary +relationship: RO:0002473 CL:0000650 ! composed primarily of mesangial cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002321 @@ -12242,6 +11850,7 @@ xref: EMAPA:28278 xref: FMA:84141 xref: MA:0002602 is_a: UBERON:0003891 ! stroma +is_a: UBERON:0004120 ! mesoderm-derived structure relationship: overlaps UBERON:0000074 ! renal glomerulus relationship: part_of UBERON:0002303 {source="MA"} ! juxtaglomerular apparatus relationship: part_of UBERON:0002319 {source="MA"} ! mesangium @@ -12268,7 +11877,6 @@ synonym: "ventral body cavity" NARROW [NCBITaxon:7742] xref: AEO:0000186 xref: BTO:0001707 xref: EHDAA2:0000267 -xref: FBbt:00005060 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:85006 xref: galen:BodyCavity xref: NCIT:C25444 @@ -12278,11 +11886,8 @@ xref: TAO:0001438 xref: UMLS:C0333343 {source="ncithesaurus:Cavity"} xref: ZFA:0001438 is_a: UBERON:0002553 ! anatomical cavity -relationship: luminal_space_of UBERON:0011997 ! coelom -relationship: transformation_of UBERON:0003886 {evidence="definitional"} ! future coelemic cavity lumen -property_value: UBPROP:0000001 "Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]." xsd:string {date_retrieved="2012-09-12", external_class="ZFA:0001438", ontology="ZFA", source="ZFIN:curator"} -property_value: UBPROP:0000001 "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]." xsd:string {date_retrieved="2012-09-12", external_class="BTO:0001707", ontology="BTO", source="BTO"} -property_value: UBPROP:0000008 "In mammals it forms the peritoneal, pleural, and pericardial cavities" xsd:string +relationship: RO:0002494 UBERON:0003886 ! transformation of future coelemic cavity lumen +relationship: RO:0002572 UBERON:0011997 ! luminal space of coelom [Term] id: UBERON:0002328 @@ -12320,23 +11925,15 @@ xref: XAO:0000055 xref: ZFA:0000135 is_a: UBERON:0000062 {source="PMID:15890825"} ! organ is_a: UBERON:0000481 {source="VSAO"} ! multi-tissue structure +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004121 ! ectoderm-derived structure -relationship: develops_from UBERON:0004880 {source="ZFA"} ! chordamesoderm -relationship: develops_from UBERON:0006267 {source="EHDAA2"} ! notochordal plate -relationship: dorsal_to UBERON:0001555 ! digestive tract -relationship: existence_starts_during UBERON:0000068 ! embryo stage -relationship: only_in_taxon NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! Chordata relationship: part_of UBERON:0011137 ! axial skeletal system relationship: produces PR:000014841 ! sonic hedgehog protein -relationship: ventral_to UBERON:0001049 ! neural tube -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000032", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000135", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000327", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000002 "relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000327", ontology="AAO"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000199", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "notochordal" xsd:string -property_value: UBPROP:0000011 "In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord." xsd:string +relationship: RO:0002160 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! only in taxon Chordata +relationship: RO:0002202 UBERON:0004880 {source="ZFA"} ! develops from chordamesoderm +relationship: RO:0002202 UBERON:0006267 {source="EHDAA2"} ! develops from notochordal plate +relationship: RO:0002488 UBERON:0000068 ! existence starts during embryo stage +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0002329 @@ -12375,18 +11972,10 @@ xref: XAO:0000058 xref: ZFA:0000155 is_a: UBERON:0005423 ! developing anatomical structure is_a: UBERON:0007503 {source="EHDAA2"} ! epithelial vesicle -relationship: develops_from UBERON:0003059 {source="ZFA"} ! presomitic mesoderm -relationship: never_in_taxon NCBITaxon:7712 {source="PMID:17237766"} -relationship: only_in_taxon NCBITaxon:7711 {source="GOTAX:0000352"} ! Chordata -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: IAO:0000232 "EDITOR_NOTE currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk" xsd:string -property_value: UBPROP:0000001 "Post-cranial axial segments which form sclerotome and dermomyotome.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010569", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000001 "Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000155", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000002 "relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000155", ontology="TAO"} -property_value: UBPROP:0000002 "relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000155", ontology="TAO"} -property_value: UBPROP:0000002 "relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010569", ontology="AAO"} -property_value: UBPROP:0000003 "(...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000191", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.40, DOI:10.1093/icb/43.1.137 Balavoine G, Adoutte A, The segmented urbilateria: a testable scenario. Integrative and Comparative Biology (2003)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "somitic" xsd:string +relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata +relationship: RO:0002202 UBERON:0003059 {source="ZFA"} ! develops from presomitic mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: RO:0002161 NCBITaxon:7712 {source="PMID:17237766"} [Term] id: UBERON:0002335 @@ -12407,8 +11996,7 @@ xref: Wikipedia:Macula_densa is_a: UBERON:0004211 ! nephron epithelium relationship: part_of UBERON:0002303 {source="MA"} ! juxtaglomerular apparatus relationship: part_of UBERON:0004135 {source="GO"} ! distal tubule -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000012 "not part of a nephron or distal tubule in MA and FMA" xsd:string {external_ontology="MA"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002342 @@ -12435,28 +12023,22 @@ xref: MIAA:0000066 xref: NCIT:C34222 xref: neuronames:1366 xref: SCTID:361462002 -xref: TAO:0000045 xref: UMLS:C0027789 {source="ncithesaurus:Neural_Crest"} xref: VHOG:0000057 xref: Wikipedia:Neural_crest xref: XAO:0000048 xref: ZFA:0000045 is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0010316 ! germ layer / neural crest -relationship: composed_primarily_of CL:0000333 {notes="pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! migratory neural crest cell -relationship: develops_from UBERON:0003075 {source="BTO"} ! neural plate -relationship: develops_from UBERON:0005062 {source="PMID:11523831"} ! neural fold -relationship: existence_starts_during UBERON:0000110 {source="PMID:11523831"} ! neurula stage -relationship: only_in_taxon NCBITaxon:89593 {notes="Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells", source="ISBN:0073040584"} ! Craniata relationship: part_of UBERON:0002346 {source="XAO", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! neurectoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI -property_value: IAO:0000232 "EDITOR_NOTE consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams)." xsd:string -property_value: RO:0002174 NCBITaxon:117565 {source="ISBN:0073040584", source="PMID:17377535"} -property_value: UBPROP:0000001 "A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000045", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010578", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831]" xsd:string {source="PMID:11523831"} -property_value: UBPROP:0000003 "We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000057", ontology="VHOG", source="DOI:10.1111/j.1469-7580.2012.01495.x Hall BK, Gillis JA, Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues. J Anat (2012)", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata +relationship: RO:0002202 UBERON:0003075 {source="BTO"} ! develops from neural plate +relationship: RO:0002202 UBERON:0005062 {source="PMID:11523831"} ! develops from neural fold +relationship: RO:0002473 CL:0000333 ! composed primarily of migratory neural crest cell +relationship: RO:0002488 UBERON:0000110 {source="PMID:11523831"} ! existence starts during neurula stage +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI [Term] id: UBERON:0002346 @@ -12479,7 +12061,6 @@ xref: EHDAA:1498 xref: EHDAA:255 xref: EMAPA:16073 xref: EV:0100004 -xref: FBbt:00001057 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:87657 xref: MAT:0000176 xref: MIAA:0000176 @@ -12493,9 +12074,6 @@ xref: ZFA:0001120 is_a: UBERON:0000923 ! germ layer is_a: UBERON:0004121 ! ectoderm-derived structure relationship: has_part CL:0000133 ! neurectodermal cell -property_value: UBPROP:0000003 "(...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000150", ontology="VHOG", source="DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "neurectodermal" xsd:string -property_value: UBPROP:0000013 "we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here" xsd:string [Term] id: UBERON:0002355 @@ -12527,8 +12105,6 @@ xref: Wikipedia:Pelvis is_a: UBERON:0000475 ! organism subdivision relationship: has_part UBERON:0007832 ! pelvic girdle skeleton relationship: part_of UBERON:0002417 ! abdominal segment of trunk -property_value: UBPROP:0000007 "pelvic" xsd:string -property_value: UBPROP:0000012 "MA and FMA differ in what they consider to be parts of the pelvis. MA includes ureter, urethra, urinary bladder, reproductive organs" xsd:string {external_ontology="MA"} [Term] id: UBERON:0002384 @@ -12562,12 +12138,8 @@ xref: VSAO:0000017 xref: XAO:0001017 xref: ZFA:0001632 is_a: UBERON:0000479 ! tissue -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000098", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000001 "Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001641", ontology="TAO", source="TAO:wd"} -property_value: UBPROP:0000001 "Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000017", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} -property_value: UBPROP:0000012 "MA also has set of connective tissues" xsd:string {external_ontology="MA"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002385 @@ -12595,13 +12167,11 @@ xref: Wikipedia:Muscle_tissue is_a: UBERON:0000479 ! tissue is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000479 ! tissue -intersection_of: composed_primarily_of CL:0000187 ! muscle cell +intersection_of: RO:0002473 CL:0000187 ! composed primarily of muscle cell relationship: capable_of GO:0006936 ! muscle contraction -relationship: composed_primarily_of CL:0000187 ! muscle cell -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0001015 ! musculature -property_value: RO:0002171 UBERON:0003714 -property_value: UBPROP:0000001 "One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000306", ontology="AAO", source="AAO:LAP"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002473 CL:0000187 ! composed primarily of muscle cell [Term] id: UBERON:0002390 @@ -12644,14 +12214,10 @@ xref: ZFA:0005023 is_a: UBERON:0000467 ! anatomical system is_a: UBERON:0004120 ! mesoderm-derived structure disjoint_from: UBERON:8450002 ! excretory system -relationship: develops_from UBERON:0003061 {evidence="definitional"} ! blood island -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0002193 {source="FMA"} ! hemolymphoid system -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "Anatomical system that consists of the blood and blood forming tissues.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011002", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001624", ontology="VHOG", source="DOI:10.1016/j.coph.2010.05.004 Ellett F, Lieschke GJ, Zebrafish as a model for vertebrate hematopoiesis. Current Opinion in Pharmacology (2010)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "hematopoietic" xsd:string -property_value: UBPROP:0000008 "In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes" xsd:string {source="WP"} +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002202 UBERON:0003061 ! develops from blood island +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002417 @@ -12692,9 +12258,8 @@ xref: VHOG:0000243 xref: Wikipedia:Epiblast is_a: UBERON:0002050 ! embryonic structure relationship: has_part CL:0000352 ! epiblast cell -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" xsd:anyURI -property_value: editor_note "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" xsd:string -property_value: UBPROP:0000003 "In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000243", ontology="VHOG", source="DOI:10.1146/annurev.cellbio.042308.113344 Zorn AM, Wells JM, Vertebrate endoderm development and organ formation. Annual Review of Cell Developmental Biology (2009)", source="http://bgee.unil.ch/"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" xsd:anyURI +property_value: IAO:0000116 "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" xsd:string [Term] id: UBERON:0002553 @@ -12710,7 +12275,7 @@ xref: galen:Cavity xref: MA:0002447 xref: NCIT:C34007 is_a: UBERON:0000464 ! anatomical space -relationship: location_of UBERON:0000463 ! organism substance +relationship: RO:0001015 UBERON:0000463 ! location of organism substance [Term] id: UBERON:0003059 @@ -12736,13 +12301,11 @@ xref: XAO:0000057 xref: ZFA:0000279 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0005423 ! developing anatomical structure -intersection_of: has_potential_to_develop_into UBERON:0002329 ! somite -intersection_of: immediate_transformation_of UBERON:0007282 ! presumptive segmental plate -relationship: has_potential_to_develop_into UBERON:0002329 ! somite -relationship: immediate_transformation_of UBERON:0007282 {source="Bgee:AN"} ! presumptive segmental plate +intersection_of: RO:0002387 UBERON:0002329 ! has potential to develop into somite +intersection_of: RO:0002495 UBERON:0007282 ! immediate transformation of presumptive segmental plate relationship: part_of UBERON:0003077 ! paraxial mesoderm -property_value: UBPROP:0000001 "Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000279", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000559", ontology="VHOG", source="DOI:10.1006/dbio.2001.0460 Schubert M, Holland LZ, Dale Stokes M and Holland ND, Three Amphoxius Wnt Genes (AmphiWnt3, AmphiWnt5, and AmphiWnt6) Associated with the Tail Bud: the Evolution of Somitogenesis in Chordates. Developmental Biology (2001)", source="http://bgee.unil.ch/"} +relationship: RO:0002387 UBERON:0002329 ! has potential to develop into somite +relationship: RO:0002495 UBERON:0007282 {source="Bgee:AN"} ! immediate transformation of presumptive segmental plate [Term] id: UBERON:0003060 @@ -12755,23 +12318,18 @@ synonym: "archinephric duct" RELATED [VHOG:0000082] synonym: "ductus pronephricus" RELATED OMO:0003011 [Wikipedia:Pronephric_duct] synonym: "pronephric ducts" RELATED OMO:0003004 [ZFA:0000150] xref: AAO:0011088 -xref: BTO:0005991 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C34279 xref: SCTID:361406002 xref: TAO:0000150 xref: UMLS:C1283945 {source="ncithesaurus:Pronephric_Duct"} -xref: VHOG:0000082 xref: Wikipedia:Pronephric_duct xref: XAO:0000063 xref: ZFA:0000150 is_a: UBERON:0009201 {source="GO"} ! nephric duct is_a: UBERON:0012275 ! meso-epithelium -relationship: develops_from UBERON:0003064 {source="Wikipedia"} ! intermediate mesoderm -relationship: develops_from UBERON:0005721 {source="XAO"} ! pronephric mesoderm relationship: part_of UBERON:0002120 ! pronephros -property_value: UBPROP:0000001 "Duct of the embryonic kidney, present bilaterally ventral to the somites and leading to the anal region where it empties separately from, and just posterior to the anus. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000150", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000082", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "(...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000082", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.686", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003064 {source="Wikipedia"} ! develops from intermediate mesoderm +relationship: RO:0002202 UBERON:0005721 {source="XAO"} ! develops from pronephric mesoderm [Term] id: UBERON:0003061 @@ -12801,13 +12359,8 @@ xref: Wikipedia:Blood_island_of_umbilical_vesicle xref: XAO:0000067 xref: ZFA:0000094 is_a: UBERON:0006598 ! presumptive structure -relationship: develops_from UBERON:0003081 ! lateral plate mesoderm -relationship: has_potential_to_develop_into UBERON:0002390 ! hematopoietic system -property_value: UBPROP:0000001 "Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000094", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011006", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000002 "relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000094", ontology="TAO"} -property_value: UBPROP:0000003 "Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000085", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450, DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual Review of Cell and Developmental Biology (2006)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac" xsd:string {external_ontology="EHDAA2"} +relationship: RO:0002202 UBERON:0003081 ! develops from lateral plate mesoderm +relationship: RO:0002387 UBERON:0002390 ! has potential to develop into hematopoietic system [Term] id: UBERON:0003064 @@ -12837,13 +12390,10 @@ xref: ZFA:0001206 is_a: UBERON:0002050 ! embryonic structure relationship: adjacent_to UBERON:0003077 ! paraxial mesoderm relationship: adjacent_to UBERON:0003081 ! lateral plate mesoderm -relationship: develops_from UBERON:0000926 {source="XAO"} ! mesoderm relationship: part_of UBERON:0000926 {source="AAO"} ! mesoderm relationship: part_of UBERON:0005256 {source="EMAPA"} ! trunk mesenchyme -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "Mesoderm between somite and lateral plate. Traditionally thought to give rise to the urogenital system.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010575", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "(...)the mesoderm of a developing vertebrate transitionally differentiates into the following sub-types: Chordamesoderm (also known as axial mesoderm) which later on gives rise to notochord in all chordates, Paraxial mesoderm, Intermediate mesoderm, Lateral plate mesoderm (reference 1); The mesoderm is present in Bilateria, therefore they are sometimes called triploblasts. Ectoderm and endoderm are usually organized as epithelial layers, while mesoderm can be epithelial or a compact, three-dimensional tissue.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000087", ontology="VHOG", source="Wikipedia:Mesoderm, ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.43", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm')." xsd:string {external_ontology="ZFA"} +relationship: RO:0002202 UBERON:0000926 {source="XAO"} ! develops from mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003068 @@ -12861,11 +12411,10 @@ xref: Wikipedia:Chordamesoderm xref: XAO:0000205 xref: ZFA:0001204 is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0000926 ! mesoderm -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0000926 ! mesoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000107", ontology="VHOG", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002202 UBERON:0000926 ! develops from mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003074 @@ -12881,32 +12430,24 @@ synonym: "Leydig's duct" RELATED [Wikipedia:Wolffian_duct] synonym: "renal duct" RELATED [] synonym: "Wolffian duct" EXACT [GOC:yaf, Wikipedia:Wolffian_duct, ZFA:0000546] xref: AAO:0000637 -xref: BTO:0005990 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: EHDAA2:0001243 xref: EHDAA:1590 -xref: EMAPA:16577 xref: GAID:1315 xref: MESH:D014928 xref: NCIT:C26469 xref: SCTID:308800003 xref: TAO:0000546 xref: UMLS:C0043204 {source="ncithesaurus:Mesonephric_Duct"} -xref: VHOG:0000082 xref: Wikipedia:Mesonephric_duct xref: XAO:0000242 xref: ZFA:0000546 is_a: UBERON:0000083 ! mesonephric tubule is_a: UBERON:0009201 {source="GO"} ! nephric duct -is_a: UBERON:0012275 ! meso-epithelium -relationship: develops_from UBERON:0003060 ! pronephric duct -relationship: develops_from UBERON:0005792 {source="EHDAA2"} ! nephric ridge -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png" xsd:anyURI -property_value: editor_note "Consider adding subclasses for male and female specific variants" xsd:string -property_value: editor_note "TODO - mesonephric portion of the nephric duct" xsd:string -property_value: UBPROP:0000001 "Anatomical structure consisting of either of a pair of longitudinal ducts which carry urine and in males, sperm, to the cloaca.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000637", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000082", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "(...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000082", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.686", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000011 "In the male the Wolffian duct persists, and forms for example the epididymis, the ductus deferens, the ejaculatory duct, seminal vesicle and efferent ducts." xsd:string +relationship: RO:0002202 UBERON:0003060 ! develops from pronephric duct +relationship: RO:0002202 UBERON:0005792 {source="EHDAA2"} ! develops from nephric ridge +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png" xsd:anyURI +property_value: IAO:0000116 "Consider adding subclasses for male and female specific variants" xsd:string +property_value: IAO:0000116 "TODO - mesonephric portion of the nephric duct" xsd:string [Term] id: UBERON:0003075 @@ -12926,7 +12467,6 @@ xref: EHDAA:346 xref: EHDAA:902 xref: EMAPA:35593 xref: FMA:293879 -xref: MESH:D054258 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C34225 xref: neuronames:1362 xref: RETIRED_EHDAA2:0001252 @@ -12939,12 +12479,10 @@ xref: ZFA:0000132 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0016879 ! future central nervous system -relationship: developmentally_induced_by UBERON:0002328 {source="Wikipedia"} ! notochord -relationship: immediate_transformation_of UBERON:0007284 {source="Bgee:AN"} ! presumptive neural plate -relationship: only_in_taxon NCBITaxon:7711 {source="GOTAX:0000352"} ! Chordata -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI -property_value: UBPROP:0000001 "The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000132", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000068", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata +relationship: RO:0002256 UBERON:0002328 {source="Wikipedia"} ! developmentally induced by notochord +relationship: RO:0002495 UBERON:0007284 {source="Bgee:AN"} ! immediate transformation of presumptive neural plate +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI [Term] id: UBERON:0003077 @@ -12973,13 +12511,9 @@ xref: ZFA:0000255 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue is_a: UBERON:0015212 ! lateral structure -relationship: existence_starts_during UBERON:0000109 ! gastrula stage -relationship: immediate_transformation_of UBERON:0007285 {source="Bgee:AN"} ! presumptive paraxial mesoderm -relationship: in_lateral_side_of UBERON:0000922 ! embryo -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010568", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000114", ontology="VHOG", source="DOI:10.1002/dvdy.21177 Kusakabe R and Kuratani S. Evolutionary perspectives from development of mesodermal components in the lamprey. Developmental dynamics (2007)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here)" xsd:string {external_ontology="ZFA"} +relationship: RO:0002488 UBERON:0000109 ! existence starts during gastrula stage +relationship: RO:0002495 UBERON:0007285 {source="Bgee:AN"} ! immediate transformation of presumptive paraxial mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003081 @@ -13011,14 +12545,10 @@ is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0000926 {source="EHDAA2", source="VHOG"} ! mesoderm -relationship: surrounds UBERON:0003887 ! intraembryonic coelom -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010574", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000001 "The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000118", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000118", ontology="VHOG", source="DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "subclass of mesoderm in ZFA." xsd:string {external_ontology="ZFA"} +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002221 UBERON:0003887 ! surrounds intraembryonic coelom +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003084 @@ -13036,14 +12566,11 @@ xref: UMLS:C1514450 {source="ncithesaurus:Primordium_of_the_Heart"} xref: XAO:0000336 xref: ZFA:0000028 is_a: UBERON:0001048 {source="Obol"} ! primordium -relationship: develops_from UBERON:0003081 {source="ZFA"} ! lateral plate mesoderm -relationship: develops_from UBERON:0004140 ! primary heart field -relationship: develops_from UBERON:0007005 {source="XAO"} ! cardiogenic splanchnic mesoderm relationship: part_of UBERON:0004535 {source="ZFA"} ! cardiovascular system -property_value: editor_note "should probably be merged with heart rudiment." xsd:string -property_value: UBPROP:0000001 "Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000028", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011044", ontology="AAO", source="XAO:curator"} -property_value: UBPROP:0000002 "relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000028", ontology="TAO"} +relationship: RO:0002202 UBERON:0003081 {source="ZFA"} ! develops from lateral plate mesoderm +relationship: RO:0002202 UBERON:0004140 ! develops from primary heart field +relationship: RO:0002202 UBERON:0007005 {source="XAO"} ! develops from cardiogenic splanchnic mesoderm +property_value: IAO:0000116 "should probably be merged with heart rudiment." xsd:string [Term] id: UBERON:0003089 @@ -13057,7 +12584,6 @@ synonym: "sclerotomes" EXACT OMO:0003004 [TAO:0001080] synonym: "sclerotomus" RELATED OMO:0003011 [Wikipedia:Sclerotome] xref: AAO:0010571 xref: AEO:0000212 -xref: BTO:0006255 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: EHDAA2:0003439 xref: EMAPA:31159 xref: FMA:295652 @@ -13070,12 +12596,9 @@ xref: XAO:0000397 xref: ZFA:0001080 is_a: UBERON:0005856 {source="EHDAA2"} ! developing mesenchymal condensation is_a: UBERON:0007530 {source="EHDAA2"} ! migrating mesenchyme population -relationship: develops_from UBERON:0002329 {source="ZFA"} ! somite -relationship: only_in_taxon NCBITaxon:7742 {source="VHOG:0000680"} ! Vertebrata -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI -property_value: UBPROP:0000001 "Skeletogenic portion of somites.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010571", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000680", ontology="VHOG", source="DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "part_of somite in XAO" xsd:string {external_ontology="XAO"} +relationship: RO:0002160 NCBITaxon:7742 {source="VHOG:0000680"} ! only in taxon Vertebrata +relationship: RO:0002202 UBERON:0002329 {source="ZFA"} ! develops from somite +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI [Term] id: UBERON:0003103 @@ -13098,7 +12621,6 @@ xref: VHOG:0001723 xref: XAO:0003041 xref: ZFA:0000496 is_a: UBERON:0000062 ! organ -property_value: IAO:0000232 "this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs" xsd:string [Term] id: UBERON:0003104 @@ -13128,15 +12650,12 @@ xref: XAO:0003046 xref: ZFA:0000393 is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue -intersection_of: composed_primarily_of CL:0008019 ! mesenchymal cell -relationship: composed_primarily_of CL:0008019 ! mesenchymal cell -relationship: functionally_related_to GO:0032502 ! developmental process -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI -property_value: editor_note "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" xsd:string -property_value: UBPROP:0000001 "A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000393", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010427", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000007 "mesenchymal" xsd:string +intersection_of: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002328 GO:0032502 ! functionally related to developmental process +relationship: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI +property_value: IAO:0000116 "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" xsd:string [Term] id: UBERON:0003133 @@ -13150,7 +12669,6 @@ synonym: "genital organ" EXACT [] synonym: "genitalia" RELATED OMO:0003004 [] synonym: "reproductive system organ" EXACT [] synonym: "sex organ" EXACT [] -xref: EMAPA:17381 xref: EMAPA:37731 {source="MA:th"} xref: MA:0001752 xref: MESH:D005835 @@ -13164,7 +12682,6 @@ is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0000062 ! organ intersection_of: capable_of_part_of GO:0000003 ! reproduction relationship: capable_of_part_of GO:0000003 ! reproduction -property_value: UBPROP:0000012 "GO uses genitalia for the singular organ" xsd:string {external_ontology="GO"} [Term] id: UBERON:0003220 @@ -13190,12 +12707,10 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: has_potential_to_develop_into UBERON:0000081 ! metanephros -relationship: developmentally_induced_by UBERON:0000084 {source="ISBN:9780878932504"} ! ureteric bud -relationship: develops_from UBERON:0003074 ! mesonephric duct -relationship: has_potential_to_develop_into UBERON:0000081 ! metanephros -property_value: UBPROP:0000001 "A mass of intermediate mesodermal cells around the distal end of the ureteric bud that gives rise to nephrons in the metanephric kidney. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000540", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/metanephric+mesenchyme"} -property_value: UBPROP:0000003 "When the ureteric buds emerge from the nephric duct, they enter the metanephrogenic mesenchyme. The ureteric buds induce this mesenchymal tissue to condense around them and differentiate into the nephrons of the mammalian kidney. As this mesenchyme differentiates, it tells the ureteric bud to branch and grow.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000540", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.462", source="http://bgee.unil.ch/"} +intersection_of: RO:0002387 UBERON:0000081 ! has potential to develop into metanephros +relationship: RO:0002202 UBERON:0003074 ! develops from mesonephric duct +relationship: RO:0002256 UBERON:0000084 {source="ISBN:9780878932504"} ! developmentally induced by ureteric bud +relationship: RO:0002387 UBERON:0000081 ! has potential to develop into metanephros [Term] id: UBERON:0003479 @@ -13216,7 +12731,7 @@ xref: MA:0001903 is_a: UBERON:0001638 ! vein is_a: UBERON:0003519 ! thoracic cavity blood vessel intersection_of: UBERON:0001638 ! vein -intersection_of: located_in UBERON:0002224 ! thoracic cavity +intersection_of: RO:0001025 UBERON:0002224 ! located in thoracic cavity [Term] id: UBERON:0003497 @@ -13229,7 +12744,6 @@ is_a: UBERON:0003835 ! abdominal segment blood vessel intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0000916 ! abdomen relationship: part_of UBERON:0000916 ! abdomen -property_value: seeAlso "UBERON:0012254" xsd:string {notes="abdominal aorta artery"} [Term] id: UBERON:0003509 @@ -13270,7 +12784,6 @@ subset: pheno_slim subset: vertebrate_core synonym: "blood vessel of kidney" EXACT [OBOL:automatic] synonym: "renal blood vessel" EXACT [OBOL:automatic] -xref: EMAPA:28457 xref: MA:0001682 xref: TAO:0005306 xref: ZFA:0005306 @@ -13278,7 +12791,7 @@ is_a: UBERON:0003497 ! abdomen blood vessel intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0002113 ! kidney relationship: part_of UBERON:0006544 ! kidney vasculature -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003519 @@ -13298,8 +12811,8 @@ xref: EMAPA:37240 {source="MA:th"} xref: MA:0000554 is_a: UBERON:0001981 ! blood vessel intersection_of: UBERON:0001981 ! blood vessel -intersection_of: located_in UBERON:0002224 ! thoracic cavity -relationship: located_in UBERON:0002224 ! thoracic cavity +intersection_of: RO:0001025 UBERON:0002224 ! located in thoracic cavity +relationship: RO:0001025 UBERON:0002224 ! located in thoracic cavity [Term] id: UBERON:0003527 @@ -13321,7 +12834,7 @@ is_a: UBERON:0001982 ! capillary is_a: UBERON:0003517 ! kidney blood vessel intersection_of: UBERON:0001982 ! capillary intersection_of: part_of UBERON:0002113 ! kidney -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003644 @@ -13362,11 +12875,11 @@ synonym: "body cavity precursor" RELATED [] synonym: "future coelomic cavity lumen" EXACT [] is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: has_potential_to_develop_into UBERON:0002323 ! coelemic cavity lumen -relationship: existence_ends_during UBERON:0000111 ! organogenesis stage -relationship: existence_starts_during UBERON:0000109 ! gastrula stage -relationship: has_potential_to_develop_into UBERON:0002323 ! coelemic cavity lumen +intersection_of: RO:0002387 UBERON:0002323 ! has potential to develop into coelemic cavity lumen relationship: part_of UBERON:0000926 ! mesoderm +relationship: RO:0002387 UBERON:0002323 ! has potential to develop into coelemic cavity lumen +relationship: RO:0002488 UBERON:0000109 ! existence starts during gastrula stage +relationship: RO:0002492 UBERON:0000111 ! existence ends during organogenesis stage [Term] id: UBERON:0003887 @@ -13382,10 +12895,9 @@ xref: UMLS:C1512940 {source="ncithesaurus:Intraembryonic_Coelom"} xref: VHOG:0000316 xref: Wikipedia:Intraembryonic_coelom is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0003081 {source="Wikipedia"} ! lateral plate mesoderm relationship: part_of UBERON:0011997 ! coelom -property_value: editor_note "consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults" xsd:string -property_value: UBPROP:0000003 "(...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000316", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.166", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003081 {source="Wikipedia"} ! develops from lateral plate mesoderm +property_value: IAO:0000116 "consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults" xsd:string [Term] id: UBERON:0003891 @@ -13398,9 +12910,8 @@ xref: FMA:81494 xref: NCIT:C67387 xref: UMLS:C0927195 {source="ncithesaurus:Stroma_Connective_Tissue"} is_a: UBERON:0000064 ! organ part -relationship: composed_primarily_of UBERON:0002384 ! connective tissue -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: UBPROP:0000007 "stromal" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002473 UBERON:0002384 ! composed primarily of connective tissue [Term] id: UBERON:0003914 @@ -13410,12 +12921,10 @@ def: "Epithelial tubes transport gases, liquids and cells from one site to anoth synonym: "epithelial or endothelial tube" EXACT [] xref: AEO:0000114 xref: EHDAA2:0003114 -xref: FBbt:00007474 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000025 ! tube is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium -intersection_of: has_quality PATO:0002299 ! tubular -property_value: IAO:0000232 "contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers" xsd:string +intersection_of: RO:0000086 PATO:0002299 ! has quality tubular [Term] id: UBERON:0003918 @@ -13426,9 +12935,9 @@ subset: pheno_slim synonym: "mesenchyme of kidney" EXACT [] is_a: UBERON:0003104 ! mesenchyme intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: has_potential_to_develop_into UBERON:0002113 ! kidney -relationship: has_potential_to_develop_into UBERON:0002113 ! kidney -property_value: editor_note "check this" xsd:string +intersection_of: RO:0002387 UBERON:0002113 ! has potential to develop into kidney +relationship: RO:0002387 UBERON:0002113 ! has potential to develop into kidney +property_value: IAO:0000116 "check this" xsd:string [Term] id: UBERON:0003920 @@ -13446,7 +12955,7 @@ is_a: UBERON:0001981 ! blood vessel intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0004582 ! venous system relationship: part_of UBERON:0004582 ! venous system -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004087 @@ -13469,10 +12978,10 @@ xref: UMLS:C0042460 {source="ncithesaurus:Vena_Cava"} xref: Wikipedia:Venae_cavae is_a: UBERON:0003479 ! thoracic cavity vein is_a: UBERON:0013768 ! great vessel of heart -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/35/Relations_of_the_aorta,_trachea,_esophagus_and_other_heart_structures.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/7/7c/Heart_numlabels.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/35/Relations_of_the_aorta,_trachea,_esophagus_and_other_heart_structures.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/7c/Heart_numlabels.png" xsd:anyURI [Term] id: UBERON:0004100 @@ -13489,8 +12998,8 @@ xref: SCTID:279371005 xref: Wikipedia:Collecting_duct_system is_a: UBERON:0000467 ! anatomical system relationship: part_of UBERON:0002113 ! kidney -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004111 @@ -13510,15 +13019,14 @@ xref: SCTID:346902003 xref: Wikipedia:Foramen is_a: UBERON:0010000 ! multicellular anatomical structure intersection_of: UBERON:0010000 ! multicellular anatomical structure -intersection_of: conduit_for UBERON:0000061 ! anatomical structure intersection_of: has_part UBERON:0013686 ! anatomical conduit space -relationship: conduit_for UBERON:0000061 ! anatomical structure -relationship: connects UBERON:0000464 {cardinality="2"} ! anatomical space +intersection_of: RO:0002570 UBERON:0000061 ! conduit for anatomical structure relationship: has_part UBERON:0013686 ! anatomical conduit space -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: UBPROP:0000012 "FMA has both conduit and conduit space. In EHDAA2 this is a surface feature" xsd:string {external_ontology="FMA"} +relationship: RO:0002176 UBERON:0000464 {cardinality="2"} ! connects anatomical space +relationship: RO:0002570 UBERON:0000061 ! conduit for anatomical structure +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0004120 @@ -13529,9 +13037,8 @@ subset: grouping_class synonym: "mesodermal derivative" EXACT [FBbt:00025998] is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: develops_from UBERON:0000926 ! mesoderm -relationship: develops_from UBERON:0000926 ! mesoderm -property_value: IAO:0000232 "Grouping term for query purposes" xsd:string +intersection_of: RO:0002202 UBERON:0000926 ! develops from mesoderm +relationship: RO:0002202 UBERON:0000926 ! develops from mesoderm [Term] id: UBERON:0004121 @@ -13542,9 +13049,8 @@ subset: grouping_class synonym: "ectodermal deriviative" EXACT [FBbt:00025990] is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: develops_from UBERON:0000924 ! ectoderm -relationship: develops_from UBERON:0000924 ! ectoderm -property_value: IAO:0000232 "Grouping term for query purposes" xsd:string +intersection_of: RO:0002202 UBERON:0000924 ! develops from ectoderm +relationship: RO:0002202 UBERON:0000924 ! develops from ectoderm [Term] id: UBERON:0004122 @@ -13580,14 +13086,9 @@ is_a: UBERON:0000467 ! anatomical system intersection_of: UBERON:0000467 ! anatomical system intersection_of: has_part UBERON:0000990 ! reproductive system intersection_of: has_part UBERON:0001008 ! renal system -relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: has_part UBERON:0000990 ! reproductive system relationship: has_part UBERON:0001008 ! renal system -property_value: UBPROP:0000001 "Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000624", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000002 "relationship type change: differentiates_from intermediate mesoderm (AAO:0010575) CHANGED TO: develops_from intermediate mesoderm (UBERON:0003064)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000624", ontology="AAO"} -property_value: UBPROP:0000003 "Kidneys and gonads (of vertebrates) develop from adjacent tissues, and after the excretory or urinary ducts have developed, the reproductive system usually taps into them or their derivatives.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000286", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.633", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "genitourinary" xsd:string -property_value: UBPROP:0000007 "urogenital" xsd:string +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage [Term] id: UBERON:0004134 @@ -13604,10 +13105,10 @@ xref: EMAPA:28281 xref: MA:0002611 xref: MESH:D007687 is_a: UBERON:0006853 ! renal cortex tubule -relationship: continuous_with UBERON:0001230 {source="GO"} ! glomerular capsule -relationship: continuous_with UBERON:0001289 {source="GO"} ! descending limb of loop of Henle -relationship: present_in_taxon NCBITaxon:9606 -property_value: editor_note "TODO - ensure definition works across species." xsd:string +relationship: RO:0002150 UBERON:0001230 {source="GO"} ! continuous with glomerular capsule +relationship: RO:0002150 UBERON:0001289 {source="GO"} ! continuous with descending limb of loop of Henle +property_value: IAO:0000116 "TODO - ensure definition works across species." xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004135 @@ -13622,7 +13123,6 @@ xref: EMAPA:28387 xref: MA:0002633 xref: MESH:D007686 is_a: UBERON:0007685 ! region of nephron tubule -property_value: RO:0002171 UBERON:0012424 [Term] id: UBERON:0004136 @@ -13634,7 +13134,7 @@ synonym: "tubulus attenuatus" EXACT [FMA:17718] xref: FMA:17718 is_a: UBERON:0007685 ! region of nephron tubule relationship: part_of UBERON:0001288 {source="FMA"} ! loop of Henle -property_value: editor_note "TODO - check for applicability across species" xsd:string +property_value: IAO:0000116 "TODO - check for applicability across species" xsd:string [Term] id: UBERON:0004139 @@ -13650,9 +13150,8 @@ xref: EHDAA2:0000215 xref: EMAPA:16106 xref: VHOG:0000975 is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0003084 ! heart primordium -property_value: editor_note "TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO" xsd:string -property_value: UBPROP:0000003 "(In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000975", ontology="VHOG", source="PMID:15611355 Gittenberger-de Groot AC, Bartelings MM, Deruiter MC, Poelmann RE, Basics of cardiac development for the understanding of congenital heart malformations. Pediatric Research (2005)", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003084 ! develops from heart primordium +property_value: IAO:0000116 "TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO" xsd:string [Term] id: UBERON:0004140 @@ -13666,11 +13165,11 @@ synonym: "PHF" RELATED OMO:0003000 [XAO:0004185] synonym: "primary heart field" EXACT [PMID:17276708, XAO:0004185] xref: XAO:0004185 is_a: UBERON:0002050 ! embryonic structure +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007688 ! anlage relationship: part_of UBERON:0003081 {source="GO:0003128"} ! lateral plate mesoderm relationship: part_of UBERON:0036146 {source="https://orcid.org/0000-0003-3308-6245"} ! cardiopharyngeal field -property_value: UBPROP:0000012 "this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138]" xsd:string {external_ontology="GO"} [Term] id: UBERON:0004141 @@ -13693,8 +13192,7 @@ xref: ZFA:0000360 is_a: UBERON:0003914 ! epithelial tube is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0012275 ! meso-epithelium -relationship: immediate_transformation_of UBERON:0005498 {source="ZFA-modified"} ! primitive heart tube -property_value: UBPROP:0000001 "the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube." xsd:string {source="MP:0012700"} +relationship: RO:0002495 UBERON:0005498 {source="ZFA-modified"} ! immediate transformation of primitive heart tube [Term] id: UBERON:0004151 @@ -13707,6 +13205,7 @@ synonym: "heart chamber" EXACT [] xref: FMA:7095 xref: SCTID:276456008 is_a: UBERON:0000064 ! organ part +is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0000948 ! heart [Term] @@ -13739,11 +13238,12 @@ xref: BTO:0001515 xref: EMAPA:35458 xref: MA:0002847 is_a: UBERON:0004211 ! nephron epithelium +is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000074 ! renal glomerulus relationship: part_of UBERON:0000074 ! renal glomerulus -relationship: present_in_taxon NCBITaxon:9606 -property_value: editor_note "TODO - check - GO says outer, BTO says inner. Make this a superclass" xsd:string +property_value: IAO:0000116 "TODO - check - GO says outer, BTO says inner. Make this a superclass" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004190 @@ -13760,7 +13260,7 @@ is_a: UBERON:0006544 ! kidney vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: part_of UBERON:0000074 ! renal glomerulus relationship: part_of UBERON:0000074 ! renal glomerulus -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004198 @@ -13772,8 +13272,8 @@ synonym: "CSB" EXACT OMO:0003000 [] xref: EMAPA:27681 xref: ZFA:0005588 is_a: UBERON:0005423 ! developing anatomical structure -relationship: develops_from UBERON:0004209 {source="ZFA"} ! renal vesicle relationship: part_of UBERON:0010532 {source="cjm"} ! primitive nephron +relationship: RO:0002202 UBERON:0004209 {source="ZFA"} ! develops from renal vesicle [Term] id: UBERON:0004199 @@ -13784,12 +13284,11 @@ subset: pheno_slim synonym: "SSB" EXACT OMO:0003000 [] synonym: "stage II nephron" EXACT [http://www.gudmap.org/Organ_Summaries/Metanephros/Renal_vesicle.html] xref: EMAPA:27756 -xref: VO:0010896 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: ZFA:0005589 is_a: UBERON:0005423 ! developing anatomical structure -relationship: develops_from UBERON:0004198 {source="GO"} ! comma-shaped body relationship: part_of UBERON:0010532 {source="cjm"} ! primitive nephron -property_value: editor_note "TODO" xsd:string +relationship: RO:0002202 UBERON:0004198 {source="GO"} ! develops from comma-shaped body +property_value: IAO:0000116 "TODO" xsd:string [Term] id: UBERON:0004200 @@ -13821,16 +13320,14 @@ xref: UMLS:C0227629 {source="ncithesaurus:Renal_Pyramid"} xref: UMLS:C1514613 {source="ncithesaurus:Pyramid_of_Malpighi"} xref: Wikipedia:Renal_pyramids is_a: UBERON:0000064 ! organ part -relationship: contributes_to_morphology_of UBERON:0000362 ! renal medulla relationship: part_of UBERON:0000362 ! renal medulla -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI -property_value: UBPROP:0000012 "not the same as FMA:50609 Pyramid (which is a volume / dimensional entity)" xsd:string {external_ontology="FMA"} -property_value: UBPROP:0000202 FMA:74268 +relationship: RO:0002433 UBERON:0000362 ! contributes to morphology of renal medulla +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004202 @@ -13849,9 +13346,9 @@ xref: EMAPA:29663 xref: FMA:76662 xref: MA:0002629 is_a: UBERON:0010000 ! multicellular anatomical structure -relationship: contributes_to_morphology_of UBERON:0001293 ! outer medulla of kidney relationship: part_of UBERON:0001293 ! outer medulla of kidney -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002433 UBERON:0001293 ! contributes to morphology of outer medulla of kidney +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004208 @@ -13863,8 +13360,8 @@ synonym: "mesenchyme of nephron" EXACT [OBOL:automatic] synonym: "nephron mesenchyme" EXACT [OBOL:automatic] is_a: UBERON:0003104 ! mesenchyme intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: has_potential_to_develop_into UBERON:0001285 ! nephron -relationship: has_potential_to_develop_into UBERON:0001285 ! nephron +intersection_of: RO:0002387 UBERON:0001285 ! has potential to develop into nephron +relationship: RO:0002387 UBERON:0001285 ! has potential to develop into nephron [Term] id: UBERON:0004209 @@ -13873,11 +13370,11 @@ namespace: uberon def: "The renal vesicle is the primordial structure of the nephron epithelium, and is formed by the condensation of mesenchymal cells." [GO:0072077] synonym: "stage I nephron" EXACT [http://www.gudmap.org/Organ_Summaries/Metanephros/Renal_vesicle.html, ZFA:0005586] is_a: UBERON:0007503 {source="EHDAA2"} ! epithelial vesicle -relationship: developmentally_induced_by UBERON:0000084 ! ureteric bud -relationship: develops_from UBERON:0004208 ! nephrogenic mesenchyme -relationship: has_potential_to_develop_into UBERON:0004211 ! nephron epithelium relationship: part_of UBERON:0010536 ! nephron progenitor -property_value: editor_note "note that this class includes both metanephric and mesonephric vesicles - ZFA and EHDAA2 associations are placed with these classes. TODO - make a more specific develops_from relationship - see UBERON:0005107 ! metanephric cap" xsd:string +relationship: RO:0002202 UBERON:0004208 ! develops from nephrogenic mesenchyme +relationship: RO:0002256 UBERON:0000084 ! developmentally induced by ureteric bud +relationship: RO:0002387 UBERON:0004211 ! has potential to develop into nephron epithelium +property_value: IAO:0000116 "note that this class includes both metanephric and mesonephric vesicles - ZFA and EHDAA2 associations are placed with these classes. TODO - make a more specific develops_from relationship - see UBERON:0005107 ! metanephric cap" xsd:string [Term] id: UBERON:0004211 @@ -13919,11 +13416,10 @@ xref: ZFA:0005284 is_a: UBERON:0003527 ! kidney capillary intersection_of: UBERON:0001982 ! capillary intersection_of: part_of UBERON:0000074 ! renal glomerulus -relationship: connected_to UBERON:0004639 ! renal afferent arteriole -relationship: contributes_to_morphology_of UBERON:0000074 ! renal glomerulus relationship: part_of UBERON:0004190 {source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! renal glomerulus vasculature -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "Capillary that is part of the renal glomerulus. Glomerular capillary endothelial membranes in zebrafish normally have a fenestrated morphology that is visible at the ultrastructural level.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005284", ontology="TAO", source="ZFIN:ZDB-PUB-000824-1", source="ZFIN:curator"} +relationship: RO:0002170 UBERON:0004639 ! connected to renal afferent arteriole +relationship: RO:0002433 UBERON:0000074 ! contributes to morphology of renal glomerulus +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004288 @@ -13953,13 +13449,10 @@ xref: Wikipedia:Skeleton xref: XAO:0004053 is_a: UBERON:0034925 ! anatomical collection disjoint_from: UBERON:0004770 ! articular system -relationship: has_member UBERON:0004765 ! skeletal element relationship: part_of UBERON:0001434 ! skeletal system -relationship: present_in_taxon NCBITaxon:9606 -property_value: RO:0002171 UBERON:0000383 +relationship: RO:0002351 UBERON:0004765 ! has member skeletal element +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/The-skeletal-system" xsd:anyURI -property_value: UBPROP:0000001 "Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000026", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070"} -property_value: UBPROP:0000007 "skeletal" xsd:string [Term] id: UBERON:0004291 @@ -13971,8 +13464,7 @@ synonym: "rudimentary heart" EXACT [ZFA:0000115] xref: TAO:0000115 xref: ZFA:0000115 is_a: UBERON:0012275 ! meso-epithelium -relationship: develops_from UBERON:0004139 ! cardiogenic plate -property_value: UBPROP:0000001 "The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000115", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002202 UBERON:0004139 ! develops from cardiogenic plate [Term] id: UBERON:0004341 @@ -13986,7 +13478,6 @@ xref: EHDAA2:0001525 xref: EHDAA:185 xref: EMAPA:16072 xref: FMA:293110 -xref: MESH:D054240 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C28402 xref: SCTID:361438007 xref: UMLS:C0033153 {source="ncithesaurus:Primitive_Streak"} @@ -13994,12 +13485,9 @@ xref: VHOG:0001202 xref: Wikipedia:Primitive_streak is_a: UBERON:0000485 {source="EHDAA2"} ! simple columnar epithelium is_a: UBERON:0005291 ! embryonic tissue -relationship: has_potential_to_develop_into UBERON:0000925 ! endoderm -relationship: has_potential_to_develop_into UBERON:0000926 ! mesoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Gray13.png" xsd:anyURI -property_value: RO:0002174 NCBITaxon:32443 -property_value: UBPROP:0000003 "(...) the blastopore equivalent of chordates (germ ring in fish, marginal zone/blastopore lip in frog and node/primitive streak in chick and mouse) (...) (reference 1); Indeed, the primitive streak has been considered the homologue of the blastopore since the 1870s (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001202", ontology="VHOG", source="PMID:9609826 Wu LH, Lengyel JA, Role of caudal in hindgut specification and gastrulation suggests homology between Drosophila amnioproctodeal invagination and vertebrate blastopore. Development (1998), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.139", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "VHOG includes a very broad grouping here based on http://www.ncbi.nlm.nih.gov/pubmed/9609826" xsd:string {external_ontology="VHOG"} +relationship: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm +relationship: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Gray13.png" xsd:anyURI [Term] id: UBERON:0004535 @@ -14018,10 +13506,8 @@ xref: BILA:0000016 xref: BTO:0000088 xref: CALOHA:TS-1297 xref: EFO:0000791 -xref: EHDAA2:0000216 xref: EHDAA:394 xref: EMAPA:16104 -xref: EMAPA:16370 xref: EV:0100017 xref: FMA:7161 xref: GAID:467 @@ -14047,9 +13533,7 @@ intersection_of: part_of UBERON:0001009 ! circulatory system relationship: has_part UBERON:0000948 ! heart relationship: has_part UBERON:0001981 ! blood vessel relationship: part_of UBERON:0001009 ! circulatory system -relationship: present_in_taxon NCBITaxon:9606 -property_value: IAO:0000232 "we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph." xsd:string -property_value: UBPROP:0000003 "The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000302", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.451", source="http://bgee.unil.ch/"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004537 @@ -14067,11 +13551,11 @@ xref: ZFA:0001079 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature -intersection_of: composed_primarily_of UBERON:0001981 ! blood vessel -relationship: composed_primarily_of UBERON:0001981 ! blood vessel -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +intersection_of: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel +relationship: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004572 @@ -14090,9 +13574,8 @@ xref: SCTID:362030008 xref: VHOG:0000273 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0007798 {source="MA"} ! vascular system -relationship: has_member UBERON:0001637 ! artery -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000003 "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000273", ontology="VHOG", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005)", source="http://bgee.unil.ch/"} +relationship: RO:0002351 UBERON:0001637 ! has member artery +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004582 @@ -14112,9 +13595,8 @@ xref: UMLS:C1267406 {source="ncithesaurus:Venous_System"} xref: VHOG:0000277 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0007798 {source="MA"} ! vascular system -relationship: composed_primarily_of UBERON:0001638 ! vein -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000003 "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000277", ontology="VHOG", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005)", source="http://bgee.unil.ch/"} +relationship: RO:0002473 UBERON:0001638 ! composed primarily of vein +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004638 @@ -14136,7 +13618,7 @@ is_a: UBERON:0004852 ! cardiovascular system endothelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0001981 ! blood vessel relationship: part_of UBERON:0001981 ! blood vessel -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004639 @@ -14164,12 +13646,12 @@ is_a: UBERON:0001637 ! artery is_a: UBERON:0001980 ! arteriole is_a: UBERON:0003644 ! kidney arterial blood vessel relationship: capable_of GO:0003093 {source="Wikipedia"} ! regulation of glomerular filtration -relationship: connecting_branch_of UBERON:0004723 ! interlobular artery -relationship: contributes_to_morphology_of UBERON:0001229 ! renal corpuscle relationship: part_of UBERON:0001229 ! renal corpuscle -relationship: present_in_taxon NCBITaxon:9606 -relationship: supplies UBERON:0001285 ! nephron -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +relationship: RO:0002178 UBERON:0001285 ! supplies nephron +relationship: RO:0002252 UBERON:0004723 ! connecting branch of interlobular artery +relationship: RO:0002433 UBERON:0001229 ! contributes to morphology of renal corpuscle +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004716 @@ -14186,12 +13668,12 @@ xref: NCIT:C34131 xref: UMLS:C1516779 {source="ncithesaurus:Conceptus"} xref: Wikipedia:Conceptus is_a: UBERON:0000061 ! anatomical structure -relationship: develops_from CL:0000365 ! animal zygote -relationship: existence_ends_with UBERON:0000068 ! embryo stage -relationship: existence_starts_with UBERON:0000068 ! embryo stage relationship: has_part UBERON:0002050 ! embryonic structure relationship: has_part UBERON:0016887 ! entire extraembryonic component -property_value: editor_note "EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus" xsd:string +relationship: RO:0002202 CL:0000365 ! develops from animal zygote +relationship: RO:0002489 UBERON:0000068 ! existence starts with embryo stage +relationship: RO:0002493 UBERON:0000068 ! existence ends with embryo stage +property_value: IAO:0000116 "EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus" xsd:string [Term] id: UBERON:0004723 @@ -14216,9 +13698,9 @@ xref: UMLS:C1512856 {source="ncithesaurus:Interlobular_Artery"} xref: Wikipedia:Interlobular_arteries is_a: UBERON:0003644 ! kidney arterial blood vessel disjoint_from: UBERON:0009885 {source="Wikipedia:Renal_circulation"} ! interlobar artery -relationship: connected_to UBERON:0001552 ! kidney arcuate artery -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +relationship: RO:0002170 UBERON:0001552 ! connected to kidney arcuate artery +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004734 @@ -14238,7 +13720,6 @@ synonym: "trilaminar disk" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "trilaminar germ" RELATED [https://orcid.org/0000-0002-6601-2165] xref: BILA:0000060 xref: BTO:0001403 -xref: FBbt:00005317 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:293108 xref: GAID:1302 xref: MESH:D005775 @@ -14251,10 +13732,9 @@ xref: Wikipedia:Gastrula xref: Wikipedia:Trilaminar_blastocyst is_a: UBERON:0000922 ! embryo intersection_of: UBERON:0000468 ! multicellular organism -intersection_of: existence_starts_and_ends_during UBERON:0000109 ! gastrula stage -relationship: develops_from UBERON:0000307 ! blastula -relationship: existence_starts_and_ends_during UBERON:0000109 ! gastrula stage -property_value: UBPROP:0000012 "We explicitly merge the NCITA terms here" xsd:string {external_ontology="NCIT"} +intersection_of: RO:0002491 UBERON:0000109 ! existence starts and ends during gastrula stage +relationship: RO:0002202 UBERON:0000307 ! develops from blastula +relationship: RO:0002491 UBERON:0000109 ! existence starts and ends during gastrula stage [Term] id: UBERON:0004765 @@ -14271,8 +13751,6 @@ xref: XAO:0004012 xref: ZFA:0005494 is_a: UBERON:0000062 ! organ relationship: part_of UBERON:0001434 {source="VSAO"} ! skeletal system -property_value: UBPROP:0000001 "Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000128", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001890", ontology="TAO", source="TAO:VSAO_workshop"} [Term] id: UBERON:0004770 @@ -14290,12 +13768,12 @@ xref: SCTID:361827000 xref: VSAO:0000181 is_a: UBERON:0034925 ! anatomical collection intersection_of: UBERON:0034925 ! anatomical collection -intersection_of: has_member UBERON:0000982 ! skeletal joint -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: functionally_related_to GO:0040011 ! locomotion -relationship: has_member UBERON:0000982 ! skeletal joint -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +intersection_of: RO:0002351 UBERON:0000982 ! has member skeletal joint relationship: part_of UBERON:0001434 {source="FMA"} ! skeletal system +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002328 GO:0040011 ! functionally related to locomotion +relationship: RO:0002351 UBERON:0000982 ! has member skeletal joint +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage [Term] id: UBERON:0004810 @@ -14314,9 +13792,9 @@ intersection_of: UBERON:0000483 ! epithelium intersection_of: adjacent_to UBERON:0000464 ! anatomical space intersection_of: part_of UBERON:0001231 ! nephron tubule relationship: adjacent_to UBERON:0000464 ! anatomical space -relationship: contributes_to_morphology_of UBERON:0001231 ! nephron tubule relationship: part_of UBERON:0001231 ! nephron tubule -property_value: editor_note "See https://github.com/obophenotype/uberon/issues/1305" xsd:string +relationship: RO:0002433 UBERON:0001231 ! contributes to morphology of nephron tubule +property_value: IAO:0000116 "See https://github.com/obophenotype/uberon/issues/1305" xsd:string [Term] id: UBERON:0004819 @@ -14335,8 +13813,8 @@ xref: MA:0002846 is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002113 ! kidney -relationship: contributes_to_morphology_of UBERON:0002113 ! kidney relationship: part_of UBERON:0002113 ! kidney +relationship: RO:0002433 UBERON:0002113 ! contributes to morphology of kidney [Term] id: UBERON:0004852 @@ -14361,8 +13839,7 @@ is_a: UBERON:0001986 ! endothelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0004535 ! cardiovascular system relationship: part_of UBERON:0004535 ! cardiovascular system -property_value: editor_note "consider merging with 'endothelium'" xsd:string -property_value: UBPROP:0000003 "Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001217", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207", source="http://bgee.unil.ch/"} +property_value: IAO:0000116 "consider merging with 'endothelium'" xsd:string [Term] id: UBERON:0004872 @@ -14380,7 +13857,6 @@ xref: Wikipedia:Lateral_plate_mesoderm#Division_into_layers xref: XAO:0000276 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0003081 ! lateral plate mesoderm -property_value: UBPROP:0000012 "We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors" xsd:string {external_ontology="BILA"} [Term] id: UBERON:0004874 @@ -14398,9 +13874,7 @@ xref: Wikipedia:Somatopleure is_a: UBERON:0002050 ! embryonic structure relationship: overlaps UBERON:0000924 ! ectoderm relationship: part_of UBERON:0003081 {source="EHDAA2"} ! lateral plate mesoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png" xsd:anyURI -property_value: UBPROP:0000011 "Gives rise to the paired appendages in jawed vertebrates. a persistent somatopleure through the redistribution and expansion of the lateral plate mesoderm is a synapomorphy for gnathostomes and a critical step in generating a novel developmental module with dramatic evolutionary potentia (Tulenko et al. 2012) http://burkelab.research.wesleyan.edu/current-projects/lamprey/" xsd:string -property_value: UBPROP:0000012 "sources differ as to whether this is part-of or develops-from the LPM" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png" xsd:anyURI [Term] id: UBERON:0004875 @@ -14415,7 +13889,7 @@ xref: SCTID:361405003 xref: UMLS:C1283944 {source="ncithesaurus:Nephrogenic_Cord"} xref: Wikipedia:Nephrogenic_cord is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0004876 ! urogenital fold +relationship: RO:0002202 UBERON:0004876 ! develops from urogenital fold [Term] id: UBERON:0004876 @@ -14431,11 +13905,10 @@ xref: EMAPA:30888 xref: FMA:321919 xref: Wikipedia:Urogenital_folds is_a: UBERON:0006598 ! presumptive structure -relationship: develops_from UBERON:0003064 {source="Wikipedia"} ! intermediate mesoderm -relationship: develops_from UBERON:0012292 {source="EHDAA2"} ! embryonic cloacal fold -relationship: has_potential_to_develop_into UBERON:0004176 ! external genitalia relationship: part_of UBERON:0009196 {source="EHDAA2"} ! indifferent external genitalia -property_value: UBPROP:0000013 "Less commonly, urogenital fold refers to the fold in the mesonephros which is the precursor of e.g. the suspensory ligament of the ovary. This is the case in older versions of Gray's anatomy[WP]" xsd:string +relationship: RO:0002202 UBERON:0003064 {source="Wikipedia"} ! develops from intermediate mesoderm +relationship: RO:0002202 UBERON:0012292 {source="EHDAA2"} ! develops from embryonic cloacal fold +relationship: RO:0002387 UBERON:0004176 ! has potential to develop into external genitalia [Term] id: UBERON:0004880 @@ -14453,10 +13926,8 @@ xref: EFO:0003426 xref: TAO:0000091 xref: ZFA:0000091 is_a: UBERON:0002050 ! embryonic structure -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0003068 ! axial mesoderm -property_value: UBPROP:0000001 "Notochord rudiment[ZFIN:ZDB-PUB-961014-576]." xsd:string {source="ZFIN:ZDB-PUB-961014-576"} -property_value: UBPROP:0000012 "WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord." xsd:string +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata [Term] id: UBERON:0004905 @@ -14465,7 +13936,6 @@ namespace: uberon def: "Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts." [http://orcid.org/0000-0002-6601-2165] subset: grouping_class synonym: "joint" NARROW [] -xref: FBbt:00005811 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0034921 ! multi organ part structure relationship: part_of UBERON:0004770 ! articular system @@ -14481,15 +13951,13 @@ synonym: "gut section" RELATED [FBbt:00100315] synonym: "intestinal tract" RELATED [] synonym: "segment of intestinal tract" RELATED [] synonym: "subdivision of alimentary system" RELATED [FMA:71131] -xref: FBbt:00100315 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:71131 is_a: UBERON:0013522 ! subdivision of tube intersection_of: UBERON:0013522 ! subdivision of tube intersection_of: subdivision_of UBERON:0001555 ! digestive tract relationship: part_of UBERON:0001555 ! digestive tract -relationship: present_in_taxon NCBITaxon:9606 relationship: subdivision_of UBERON:0001555 ! digestive tract -property_value: IAO:0000232 "intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct." xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004923 @@ -14499,8 +13967,8 @@ def: "A part of a wall of an organ that forms a layer." [http://orcid.org/0000-0 subset: upper_level xref: FMA:82485 is_a: UBERON:0000064 ! organ part -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000060 ! anatomical wall +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0005061 @@ -14518,7 +13986,6 @@ xref: Wikipedia:Neural_groove xref: XAO:0000248 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0003075 ! neural plate -property_value: UBPROP:0000001 "The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]." xsd:string {source="Wikipedia:Neural_groove"} [Term] id: UBERON:0005062 @@ -14538,10 +14005,9 @@ xref: XAO:0004087 is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0005157 ! epithelial fold is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0015212 ! lateral structure -relationship: in_lateral_side_of UBERON:0005061 ! neural groove relationship: part_of UBERON:0005061 ! neural groove -property_value: UBPROP:0000001 "In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]." xsd:string {source="Wikipedia:Neural_fold"} [Term] id: UBERON:0005068 @@ -14554,8 +14020,7 @@ xref: EFO:0003498 xref: TAO:0000133 xref: ZFA:0000133 is_a: UBERON:0016879 ! future central nervous system -relationship: develops_from UBERON:0007135 ! neural keel -property_value: UBPROP:0000001 "An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000133", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002202 UBERON:0007135 ! develops from neural keel [Term] id: UBERON:0005080 @@ -14564,8 +14029,8 @@ namespace: uberon def: "The portion of the ureteric bud tube that contributes to the morphogenesis of the metanephros[GO]." [GO:0035502] is_a: UBERON:0000084 ! ureteric bud intersection_of: UBERON:0000084 ! ureteric bud -intersection_of: has_potential_to_develop_into UBERON:0000081 ! metanephros -relationship: has_potential_to_develop_into UBERON:0000081 ! metanephros +intersection_of: RO:0002387 UBERON:0000081 ! has potential to develop into metanephros +relationship: RO:0002387 UBERON:0000081 ! has potential to develop into metanephros [Term] id: UBERON:0005081 @@ -14574,8 +14039,8 @@ namespace: uberon def: "The portion of the ureteric bud that contributes to the morphogenesis of the ureter. The ureter ureteric bud is the initial structure that forms the ureter[GO]." [GO:0035503] is_a: UBERON:0000084 ! ureteric bud intersection_of: UBERON:0000084 ! ureteric bud -intersection_of: has_potential_to_develop_into UBERON:0000056 ! ureter -relationship: has_potential_to_develop_into UBERON:0000056 ! ureter +intersection_of: RO:0002387 UBERON:0000056 ! has potential to develop into ureter +relationship: RO:0002387 UBERON:0000056 ! has potential to develop into ureter [Term] id: UBERON:0005090 @@ -14585,12 +14050,10 @@ def: "Muscle structures are contractile cells, tissues or organs that are found synonym: "muscle" RELATED [] synonym: "muscle element" RELATED [] synonym: "musculus" EXACT [FMA:30316] -xref: EMAPA:32715 xref: FMA:30316 is_a: UBERON:0000061 ! anatomical structure relationship: has_part CL:0000187 ! muscle cell -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: IAO:0000232 "in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0005095 @@ -14599,8 +14062,8 @@ namespace: uberon def: "Missing definition for term UBERON:0005095. Please replace it using linked reference." [GO:0072003] synonym: "kidney anlage" RELATED [GOC:mtg_kidney_jan10] is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0007687 {source="GO"} ! kidney field -property_value: editor_note "class added for consistency with GO - consider merging with kidney mesenchyme." xsd:string +relationship: RO:0002202 UBERON:0007687 {source="GO"} ! develops from kidney field +property_value: IAO:0000116 "class added for consistency with GO - consider merging with kidney mesenchyme." xsd:string [Term] id: UBERON:0005096 @@ -14627,8 +14090,8 @@ xref: Wikipedia:Descending_limb_of_loop_of_Henle is_a: UBERON:0000064 ! organ part relationship: part_of UBERON:0001289 ! descending limb of loop of Henle relationship: part_of UBERON:0004136 ! intermediate tubule -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/uberon/issues/2276" xsd:string [Term] @@ -14648,9 +14111,9 @@ xref: MA:0002610 xref: Wikipedia:Connecting_tubule is_a: UBERON:0007685 ! region of nephron tubule is_a: UBERON:0012275 ! meso-epithelium -relationship: develops_from UBERON:0003220 {source="Wikipedia"} ! metanephric mesenchyme -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +relationship: RO:0002202 UBERON:0003220 {source="Wikipedia"} ! develops from metanephric mesenchyme +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0005103 @@ -14658,6 +14121,7 @@ name: mesonephric epithelium namespace: uberon def: "An epithelium that is part of a mesonephros [Automatically generated definition]." [OBOL:automatic] is_a: UBERON:0004819 ! kidney epithelium +is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000080 ! mesonephros relationship: part_of UBERON:0000080 ! mesonephros @@ -14701,9 +14165,9 @@ xref: SCTID:245434005 xref: UMLS:C0227658 {source="ncithesaurus:Ascending_Limb_of_the_Henle_s_Loop"} xref: Wikipedia:Ascending_limb_of_loop_of_Henle is_a: UBERON:0004135 ! distal tubule -relationship: contributes_to_morphology_of UBERON:0001288 ! loop of Henle relationship: part_of UBERON:0001288 ! loop of Henle -property_value: editor_note "TODO - thick/thin check. Also relationship to distal tubule. We need a home for MA:0002634-renal straight tubule" xsd:string +relationship: RO:0002433 UBERON:0001288 ! contributes to morphology of loop of Henle +property_value: IAO:0000116 "TODO - thick/thin check. Also relationship to distal tubule. We need a home for MA:0002634-renal straight tubule" xsd:string [Term] id: UBERON:0005167 @@ -14734,9 +14198,8 @@ synonym: "interstitium" EXACT [] xref: FMA:86301 xref: SCTID:85293002 is_a: UBERON:0003891 {source="FMA"} ! stroma -relationship: present_in_taxon NCBITaxon:9606 -property_value: editor_note "specify differentia from stroma" xsd:string -property_value: UBPROP:0000007 "interstital" xsd:string +property_value: IAO:0000116 "specify differentia from stroma" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0005172 @@ -14794,8 +14257,8 @@ xref: MA:0000557 is_a: UBERON:0002075 ! viscus is_a: UBERON:0005181 ! thoracic segment organ intersection_of: UBERON:0000062 ! organ -intersection_of: located_in UBERON:0002224 ! thoracic cavity -relationship: located_in UBERON:0002224 ! thoracic cavity +intersection_of: RO:0001025 UBERON:0002224 ! located in thoracic cavity +relationship: RO:0001025 UBERON:0002224 ! located in thoracic cavity [Term] id: UBERON:0005179 @@ -14868,13 +14331,11 @@ xref: SCTID:362210003 is_a: UBERON:0005169 ! interstitial tissue intersection_of: UBERON:0005169 ! interstitial tissue intersection_of: part_of UBERON:0002113 ! kidney -relationship: composed_primarily_of CL:1000692 ! kidney interstitial fibroblast -relationship: contributes_to_morphology_of UBERON:0002113 ! kidney relationship: part_of UBERON:0002113 ! kidney -relationship: present_in_taxon NCBITaxon:9606 -property_value: editor_note "See https://sourceforge.net/p/geneontology/ontology-requests/10941/" xsd:string -property_value: UBPROP:0000009 "The interstitium is necessarily involved in all intrarenal exchange processes since the reabsorption and secretion of fluid and solutes implicates a transit across the interstitial compartment." xsd:string -property_value: UBPROP:0000010 "The fibroblasts in the interstitium provide the 'skeleton' of the tissue and maintain the three-dimensional architecture of the tissue." xsd:string +relationship: RO:0002433 UBERON:0002113 ! contributes to morphology of kidney +relationship: RO:0002473 CL:1000692 ! composed primarily of kidney interstitial fibroblast +property_value: IAO:0000116 "See https://sourceforge.net/p/geneontology/ontology-requests/10941/" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0005256 @@ -14925,14 +14386,13 @@ synonym: "developmental tissue" RELATED [MIAA:0000019] xref: AEO:0000125 xref: CALOHA:TS-2122 xref: EHDAA2:0003125 -xref: FBbt:00007006 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:292313 xref: MIAA:0000019 is_a: UBERON:0000465 ! material anatomical entity relationship: capable_of GO:0032502 ! developmental process -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0005498 @@ -14942,7 +14402,6 @@ def: "Multi-tissue structure that arises from the heart rudiment and will become subset: vertebrate_core synonym: "early primitive heart tube" NARROW [EMAPA:16208] synonym: "primitive heart tube" EXACT [EMAPA:16215] -xref: BTO:0006179 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: EHDAA2:0001512 xref: EHDAA:424 xref: EHDAA:436 @@ -14954,8 +14413,8 @@ xref: Wikipedia:Primitive_heart_tube xref: ZFA:0000149 is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004120 ! mesoderm-derived structure -relationship: develops_from UBERON:0004291 {source="ZFA"} ! heart rudiment relationship: part_of UBERON:0000922 ! embryo +relationship: RO:0002202 UBERON:0004291 {source="ZFA"} ! develops from heart rudiment [Term] id: UBERON:0005564 @@ -14978,10 +14437,8 @@ xref: TAO:0001262 xref: WBbt:0008366 xref: ZFA:0001262 is_a: UBERON:0001048 {source="Obol"} ! primordium -relationship: has_potential_to_develop_into UBERON:0000991 ! gonad relationship: part_of UBERON:0000990 {source="ZFA"} ! reproductive system -property_value: UBPROP:0000001 "Immature reproductive tissue that has not undergone final maturation into either testis or ovary.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001262", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000008 "this is a very broad grouping class" xsd:string +relationship: RO:0002387 UBERON:0000991 ! has potential to develop into gonad [Term] id: UBERON:0005721 @@ -15001,13 +14458,13 @@ xref: VHOG:0001239 xref: XAO:0000264 xref: ZFA:0000067 is_a: UBERON:0000926 ! mesoderm +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0000926 ! mesoderm -intersection_of: has_potential_to_develop_into UBERON:0002120 ! pronephros -relationship: has_potential_to_develop_into UBERON:0002120 ! pronephros -relationship: immediate_transformation_of UBERON:0007297 {source="Bgee:AN"} ! presumptive pronephric mesoderm +intersection_of: RO:0002387 UBERON:0002120 ! has potential to develop into pronephros relationship: part_of UBERON:0003064 {source="ZFA"} ! intermediate mesoderm -property_value: UBPROP:0000001 "Portion of tissue that consists of the mesenchymal precursor to the pronephric kidney and that begins to separate from the intermediate mesoderm at NF stage 21 and epithelializes by NF stage 30.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011090", ontology="AAO", source="XAO:curator"} +relationship: RO:0002387 UBERON:0002120 ! has potential to develop into pronephros +relationship: RO:0002495 UBERON:0007297 {source="Bgee:AN"} ! immediate transformation of presumptive pronephric mesoderm [Term] id: UBERON:0005749 @@ -15018,14 +14475,12 @@ subset: pheno_slim synonym: "glomerular capillary tuft" RELATED [] synonym: "glomerulus" RELATED INCONSISTENT [EMAPA:28239] xref: EMAPA:28239 -xref: SCTID:362217000 xref: Wikipedia:Glomerulus is_a: UBERON:0000064 ! organ part is_a: UBERON:0004120 ! mesoderm-derived structure relationship: capable_of_part_of GO:0003094 ! glomerular filtration -relationship: develops_from UBERON:0003220 {source="Wikipedia"} ! metanephric mesenchyme relationship: part_of UBERON:0001230 ! glomerular capsule -property_value: UBPROP:0000011 "...Soon afterwards, endothelial cells invade to make a capillary knot-like outgrowth, the glomerular tuft, which goes on to form the glomerulus" xsd:string {source="GudMap"} +relationship: RO:0002202 UBERON:0003220 {source="Wikipedia"} ! develops from metanephric mesenchyme [Term] id: UBERON:0005753 @@ -15058,9 +14513,9 @@ is_a: UBERON:0000476 ! acellular anatomical structure intersection_of: UBERON:0000476 ! acellular anatomical structure intersection_of: bounding_layer_of UBERON:0000061 ! anatomical structure relationship: bounding_layer_of UBERON:0000061 ! anatomical structure -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0005769 @@ -15080,12 +14535,11 @@ xref: Wikipedia:Basement_membrane is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005764 {source="FMA"} ! acellular membrane relationship: adjacent_to CL:0000066 ! epithelial cell -relationship: composed_primarily_of GO:0005604 ! basement membrane relationship: has_part GO:0005587 ! collagen type IV trimer -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa relationship: part_of UBERON:0000483 ! epithelium -relationship: present_in_taxon NCBITaxon:80999 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} -property_value: IAO:0000232 "this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell." xsd:string +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002473 GO:0005604 ! composed primarily of basement membrane +property_value: RO:0002175 NCBITaxon:80999 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} [Term] id: UBERON:0005777 @@ -15101,20 +14555,19 @@ xref: EMAPA:28251 xref: EMAPA:30965 xref: FMA:74274 xref: MA:0001659 -xref: MESH:D050533 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C32683 xref: SCTID:243897006 xref: TAO:0005285 xref: UMLS:C0599297 {source="ncithesaurus:Glomerular_Basement_Membrane"} xref: Wikipedia:Glomerular_basement_membrane xref: ZFA:0005285 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005769 ! basement membrane of epithelium intersection_of: UBERON:0005769 ! basement membrane of epithelium intersection_of: part_of UBERON:0000074 ! renal glomerulus relationship: capable_of GO:0003094 ! glomerular filtration relationship: part_of UBERON:0004188 {is_inferred="true", source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! glomerular epithelium -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/de/PhysiologieGlom%C3%A9rulaire.png" xsd:anyURI -property_value: UBPROP:0000001 "Membrane between the mesonephric podocytes and the renal glomerular capillaries. It is a trilaminar structure composed of the fused basement membranes of the glomerular capillaries and basement membrane of the podocytes. The capillary membranes touch the GBM at contact points that are separated by pores. The membrane is semi-permeable allowing water and small molecules to pass into the renal capsular space.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005285", ontology="TAO", source="ZFIN:ZDB-PUB-000824-1"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/de/PhysiologieGlom%C3%A9rulaire.png" xsd:anyURI [Term] id: UBERON:0005792 @@ -15129,7 +14582,7 @@ xref: VHOG:0001240 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0001008 ! renal system relationship: part_of UBERON:0004122 ! genitourinary system -property_value: editor_note "TODO - check ridge vs cord vs nephrogenic cord vs blastema" xsd:string +property_value: IAO:0000116 "TODO - check ridge vs cord vs nephrogenic cord vs blastema" xsd:string [Term] id: UBERON:0005856 @@ -15142,7 +14595,7 @@ xref: EHDAA2_RETIRED:0003148 xref: EHDAA:8979 is_a: UBERON:0007524 {source="AEO"} ! dense mesenchyme tissue is_a: UBERON:0011585 {source="cjm"} ! cell condensation -relationship: composed_primarily_of CL:0000335 {source="AEO-modified-relation"} ! mesenchyme condensation cell +relationship: RO:0002473 CL:0000335 {source="AEO-modified-relation"} ! composed primarily of mesenchyme condensation cell [Term] id: UBERON:0005944 @@ -15155,7 +14608,6 @@ subset: uberon_slim synonym: "skeleton axiale" RELATED OMO:0003011 [Wikipedia:Axial_skeleton] xref: AAO:0000963 xref: EMAPA:17214 -xref: EMAPA:18043 xref: MA:0000308 xref: NCIT:C32172 xref: SCTID:361725000 @@ -15164,13 +14616,12 @@ xref: VSAO:0000056 xref: Wikipedia:Axial_skeleton xref: XAO:0004011 is_a: UBERON:0010912 ! subdivision of skeleton -relationship: contributes_to_morphology_of UBERON:0001434 ! skeletal system -relationship: develops_from UBERON:0003089 ! sclerotome relationship: part_of UBERON:0011137 ! axial skeletal system -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg" xsd:anyURI +relationship: RO:0002202 UBERON:0003089 ! develops from sclerotome +relationship: RO:0002433 UBERON:0001434 ! contributes to morphology of skeletal system +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" xsd:anyURI -property_value: UBPROP:0000001 "Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000056", ontology="VSAO", source="PSPUB:0000170"} [Term] id: UBERON:0006217 @@ -15192,14 +14643,12 @@ xref: UMLS:C0231056 {source="ncithesaurus:Cloacal_Membrane"} xref: VHOG:0001198 xref: Wikipedia:Cloacal_membrane is_a: UBERON:0000158 ! membranous layer -relationship: contributes_to_morphology_of UBERON:0000163 ! embryonic cloaca -relationship: develops_from UBERON:0004341 {source="Wikipedia"} ! primitive streak -relationship: has_developmental_contribution_from UBERON:0000924 ! ectoderm -relationship: has_developmental_contribution_from UBERON:0000925 ! endoderm relationship: part_of UBERON:0000163 ! embryonic cloaca -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray991.png" xsd:anyURI -property_value: UBPROP:0000001 "A membrane that separates the proctodeum and the hindgut in the early embryo. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.497, see_Kardong_KV][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001198", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "In mammals, the cloaca exists as an embryonic structure that undergoes septation to become distinct urethral, anal, and genital orifices.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001198", ontology="VHOG", source="PMID:11830557 De Santa Barbara P, Roberts DJ, Tail gut endoderm and gut/genitourinary/tail development: a new tissue-specific role for Hoxa13. Development (2002)", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0004341 {source="Wikipedia"} ! develops from primitive streak +relationship: RO:0002254 UBERON:0000924 ! has developmental contribution from ectoderm +relationship: RO:0002254 UBERON:0000925 ! has developmental contribution from endoderm +relationship: RO:0002433 UBERON:0000163 ! contributes to morphology of embryonic cloaca +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray991.png" xsd:anyURI [Term] id: UBERON:0006267 @@ -15217,9 +14666,8 @@ is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium -relationship: develops_from UBERON:0006268 {source="EHDAA2"} ! notochordal process -property_value: editor_note "TODO - check ordering; awaiting confirmation from JB" xsd:string -property_value: UBPROP:0000001 "The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001212", ontology="VHOG", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0006268 {source="EHDAA2"} ! develops from notochordal process +property_value: IAO:0000116 "TODO - check ordering; awaiting confirmation from JB" xsd:string [Term] id: UBERON:0006268 @@ -15238,8 +14686,8 @@ xref: NCIT:C34232 xref: UMLS:C1518430 {source="ncithesaurus:Notochordal_Process"} xref: VHOG:0001213 is_a: UBERON:0005423 ! developing anatomical structure -relationship: develops_from UBERON:0000924 {source="EHDAA2"} ! ectoderm -relationship: only_in_taxon NCBITaxon:7711 ! Chordata +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002202 UBERON:0000924 {source="EHDAA2"} ! develops from ectoderm [Term] id: UBERON:0006314 @@ -15258,8 +14706,8 @@ xref: MESH:D001826 xref: Wikipedia:Body_fluid is_a: UBERON:0000463 ! organism substance intersection_of: UBERON:0000463 ! organism substance -intersection_of: has_quality PATO:0001548 ! quality of a liquid -relationship: has_quality PATO:0001548 ! quality of a liquid +intersection_of: RO:0000086 PATO:0001548 ! has quality quality of a liquid +relationship: RO:0000086 PATO:0001548 ! has quality quality of a liquid [Term] id: UBERON:0006534 @@ -15304,7 +14752,7 @@ is_a: UBERON:0006876 ! vasculature of organ intersection_of: UBERON:0002049 ! vasculature intersection_of: part_of UBERON:0002113 ! kidney relationship: part_of UBERON:0002113 ! kidney -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0006553 @@ -15317,7 +14765,6 @@ is_a: UBERON:0000058 ! duct intersection_of: UBERON:0000058 ! duct intersection_of: part_of UBERON:0002113 ! kidney relationship: part_of UBERON:0002113 ! kidney -property_value: UBPROP:0000012 "in ZFA this is defined as part of mesonephros" xsd:string {external_ontology="ZFA"} [Term] id: UBERON:0006555 @@ -15341,11 +14788,11 @@ xref: TAO:0000416 xref: ZFA:0000416 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0000925 ! endoderm intersection_of: part_of UBERON:0000307 ! blastula -relationship: has_potential_to_develop_into UBERON:0000925 ! endoderm -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +intersection_of: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm relationship: part_of UBERON:0000307 ! blastula +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm [Term] id: UBERON:0006596 @@ -15359,8 +14806,8 @@ xref: TAO:0000568 xref: ZFA:0000568 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0000178 ! blood -relationship: has_potential_to_develop_into UBERON:0000178 ! blood +intersection_of: RO:0002387 UBERON:0000178 ! has potential to develop into blood +relationship: RO:0002387 UBERON:0000178 ! has potential to develop into blood [Term] id: UBERON:0006598 @@ -15374,10 +14821,10 @@ xref: TAO:0001116 xref: ZFA:0001116 is_a: UBERON:0002050 ! embryonic structure intersection_of: UBERON:0005423 ! developing anatomical structure -intersection_of: has_potential_to_develop_into UBERON:0000061 ! anatomical structure intersection_of: part_of UBERON:0000922 ! embryo -relationship: has_potential_to_develop_into UBERON:0000061 ! anatomical structure -property_value: editor_note "Consider merging with anlage" xsd:string +intersection_of: RO:0002387 UBERON:0000061 ! has potential to develop into anatomical structure +relationship: RO:0002387 UBERON:0000061 ! has potential to develop into anatomical structure +property_value: IAO:0000116 "Consider merging with anlage" xsd:string [Term] id: UBERON:0006601 @@ -15393,11 +14840,11 @@ xref: XAO:0004132 xref: ZFA:0001376 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0000924 ! ectoderm intersection_of: part_of UBERON:0000307 ! blastula -relationship: has_potential_to_develop_into UBERON:0000924 ! ectoderm -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +intersection_of: RO:0002387 UBERON:0000924 ! has potential to develop into ectoderm relationship: part_of UBERON:0000307 ! blastula +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002387 UBERON:0000924 ! has potential to develop into ectoderm [Term] id: UBERON:0006603 @@ -15411,11 +14858,11 @@ xref: TAO:0001377 xref: ZFA:0001377 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0000926 ! mesoderm intersection_of: part_of UBERON:0000307 ! blastula -relationship: has_potential_to_develop_into UBERON:0000926 ! mesoderm -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +intersection_of: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm relationship: part_of UBERON:0000307 ! blastula +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm [Term] id: UBERON:0006853 @@ -15439,12 +14886,10 @@ def: "The distalmost portion of the digestive tract, derived from the hindgut, a synonym: "rectal part of digestive tract" RELATED [] synonym: "rectum" NARROW [FBbt:00005756] synonym: "terminal section of digestive tract" RELATED [] -xref: FBbt:00005756 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: WBbt:0005773 is_a: UBERON:0004921 ! subdivision of digestive tract -relationship: continuous_with UBERON:0001245 ! anus -relationship: develops_from UBERON:0001046 ! hindgut -property_value: IAO:0000232 "this class is the superclass of 'rectum', which is currently reserved for the vertebrate structure. May be merged in future." xsd:string +relationship: RO:0002150 UBERON:0001245 ! continuous with anus +relationship: RO:0002202 UBERON:0001046 ! develops from hindgut [Term] id: UBERON:0006876 @@ -15474,7 +14919,6 @@ is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: has_part CL:0000076 ! squamous epithelial cell relationship: has_part CL:0000076 ! squamous epithelial cell -property_value: UBPROP:0000012 "FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium" xsd:string {external_ontology="FBbt"} [Term] id: UBERON:0006965 @@ -15505,7 +14949,7 @@ xref: EHDAA2_RETIRED:0003192 xref: FMA:24137 xref: NCIT:C34022 xref: UMLS:C1515977 {source="ncithesaurus:Anatomic_Surface"} -is_a: UBERON:0010199 {notes="via morphological boundary in CARO"} ! bona-fide anatomical boundary +is_a: UBERON:0010199 ! bona-fide anatomical boundary [Term] id: UBERON:0007005 @@ -15528,13 +14972,14 @@ xref: FMA:293143 xref: SCTID:360387000 xref: VHOG:0001641 xref: XAO:0000235 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue -relationship: developmentally_induced_by UBERON:0009881 ! anterior lateral plate mesoderm -relationship: develops_from UBERON:0004872 ! splanchnic layer of lateral plate mesoderm relationship: part_of UBERON:0004140 ! primary heart field relationship: part_of UBERON:0009881 ! anterior lateral plate mesoderm -property_value: editor_note "consider FBbt:00005541 ! cardiogenic mesoderm" xsd:string -property_value: editor_note "review EHDAA2 placement" xsd:string +relationship: RO:0002202 UBERON:0004872 ! develops from splanchnic layer of lateral plate mesoderm +relationship: RO:0002256 UBERON:0009881 ! developmentally induced by anterior lateral plate mesoderm +property_value: IAO:0000116 "consider FBbt:00005541 ! cardiogenic mesoderm" xsd:string +property_value: IAO:0000116 "review EHDAA2 placement" xsd:string [Term] id: UBERON:0007010 @@ -15544,10 +14989,10 @@ def: "Organism at the cleavage stage." [OBOL:automatic] xref: BILA:0000058 is_a: UBERON:0000922 ! embryo intersection_of: UBERON:0000468 ! multicellular organism -intersection_of: existence_ends_with UBERON:0000107 ! cleavage stage -intersection_of: existence_starts_with UBERON:0000107 ! cleavage stage -relationship: existence_ends_with UBERON:0000107 ! cleavage stage -relationship: existence_starts_with UBERON:0000107 ! cleavage stage +intersection_of: RO:0002489 UBERON:0000107 ! existence starts with cleavage stage +intersection_of: RO:0002493 UBERON:0000107 ! existence ends with cleavage stage +relationship: RO:0002489 UBERON:0000107 ! existence starts with cleavage stage +relationship: RO:0002493 UBERON:0000107 ! existence ends with cleavage stage [Term] id: UBERON:0007026 @@ -15566,12 +15011,11 @@ xref: SCTID:360394002 xref: UMLS:C1514442 {source="ncithesaurus:Primordial_Gut"} is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001555 ! digestive tract -relationship: existence_starts_during UBERON:0000109 ! gastrula stage -relationship: has_developmental_contribution_from UBERON:0000925 ! endoderm -relationship: has_developmental_contribution_from UBERON:0000926 ! mesoderm -relationship: has_potential_to_develop_into UBERON:0001555 ! digestive tract -property_value: UBPROP:0000011 "The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis" xsd:string {source="NCBIBook:NBK10107"} +intersection_of: RO:0002387 UBERON:0001555 ! has potential to develop into digestive tract +relationship: RO:0002254 UBERON:0000925 ! has developmental contribution from endoderm +relationship: RO:0002254 UBERON:0000926 ! has developmental contribution from mesoderm +relationship: RO:0002387 UBERON:0001555 ! has potential to develop into digestive tract +relationship: RO:0002488 UBERON:0000109 ! existence starts during gastrula stage [Term] id: UBERON:0007100 @@ -15584,14 +15028,12 @@ synonym: "adult heart" RELATED [FBbt:00003154] synonym: "dorsal tube" NARROW [Wikipedia:Heart] synonym: "heart" NARROW [GO:0007507] xref: http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg -xref: SPD:0000130 xref: TADS:0000147 is_a: UBERON:0015228 ! circulatory organ intersection_of: UBERON:0015228 ! circulatory organ intersection_of: capable_of GO:0008015 ! blood circulation -relationship: capable_of GO:0008015 {notes="GO uses blood circulation generically to include the haemolymphatic fluid of arthropods"} ! blood circulation +relationship: capable_of GO:0008015 ! blood circulation relationship: has_part CL:0002494 ! cardiocyte -property_value: UBPROP:0000008 "note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis" xsd:string [Term] id: UBERON:0007135 @@ -15604,8 +15046,7 @@ xref: EFO:0003497 xref: TAO:0000131 xref: ZFA:0000131 is_a: UBERON:0016879 ! future central nervous system -relationship: develops_from UBERON:0003075 ! neural plate -property_value: UBPROP:0000001 "An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000131", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002202 UBERON:0003075 ! develops from neural plate [Term] id: UBERON:0007282 @@ -15619,9 +15060,9 @@ xref: TAO:0000053 xref: ZFA:0000053 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0003059 ! presomitic mesoderm -relationship: develops_from UBERON:0009618 {consistent_with="https://github.com/obophenotype/uberon/wiki/The-neural-crest", source="EDHAA2"} ! trunk paraxial mesoderm -relationship: has_potential_to_develop_into UBERON:0003059 ! presomitic mesoderm +intersection_of: RO:0002387 UBERON:0003059 ! has potential to develop into presomitic mesoderm +relationship: RO:0002202 UBERON:0009618 ! develops from trunk paraxial mesoderm +relationship: RO:0002387 UBERON:0003059 ! has potential to develop into presomitic mesoderm [Term] id: UBERON:0007284 @@ -15636,12 +15077,11 @@ xref: TAO:0000063 xref: ZFA:0000063 is_a: UBERON:0016879 ! future central nervous system intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0003075 ! neural plate -relationship: develops_from UBERON:0002346 ! neurectoderm -relationship: has_potential_to_develop_into UBERON:0003075 ! neural plate +intersection_of: RO:0002387 UBERON:0003075 ! has potential to develop into neural plate relationship: part_of UBERON:0004734 ! gastrula -property_value: editor_note "consider merging" xsd:string -property_value: UBPROP:0000001 "Region of the gastrula which gives rise to the neural plate.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000063", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002202 UBERON:0002346 ! develops from neurectoderm +relationship: RO:0002387 UBERON:0003075 ! has potential to develop into neural plate +property_value: IAO:0000116 "consider merging" xsd:string [Term] id: UBERON:0007285 @@ -15657,10 +15097,10 @@ xref: XAO:0004134 xref: ZFA:0000591 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 {source="https://github.com/obophenotype/uberon/issues/1277"} ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0003077 {source="https://github.com/obophenotype/uberon/issues/1277"} ! paraxial mesoderm intersection_of: part_of UBERON:0000307 {source="https://github.com/obophenotype/uberon/issues/1277"} ! blastula -relationship: has_potential_to_develop_into UBERON:0003077 ! paraxial mesoderm +intersection_of: RO:0002387 UBERON:0003077 {source="https://github.com/obophenotype/uberon/issues/1277"} ! has potential to develop into paraxial mesoderm relationship: part_of UBERON:0000307 ! blastula +relationship: RO:0002387 UBERON:0003077 ! has potential to develop into paraxial mesoderm [Term] id: UBERON:0007297 @@ -15674,8 +15114,8 @@ xref: TAO:0001070 xref: ZFA:0001070 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0005721 ! pronephric mesoderm -relationship: has_potential_to_develop_into UBERON:0005721 ! pronephric mesoderm +intersection_of: RO:0002387 UBERON:0005721 ! has potential to develop into pronephric mesoderm +relationship: RO:0002387 UBERON:0005721 ! has potential to develop into pronephric mesoderm [Term] id: UBERON:0007499 @@ -15687,7 +15127,7 @@ xref: EHDAA2:0003115 is_a: UBERON:0003914 {source="AEO"} ! epithelial tube is_a: UBERON:0009856 ! sac intersection_of: UBERON:0000483 ! epithelium -intersection_of: has_quality PATO:0001987 ! saccular +intersection_of: RO:0000086 PATO:0001987 ! has quality saccular [Term] id: UBERON:0007500 @@ -15728,7 +15168,7 @@ is_a: UBERON:0003104 ! mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: participates_in GO:0016477 ! cell migration relationship: participates_in GO:0016477 ! cell migration -property_value: editor_note "this class will be an important part of the NC reorganization" xsd:string +property_value: IAO:0000116 "this class will be an important part of the NC reorganization" xsd:string [Term] id: UBERON:0007684 @@ -15751,7 +15191,6 @@ synonym: "renal tubule region" EXACT [FMA:17692] xref: FMA:17692 is_a: UBERON:0001231 ! nephron tubule relationship: part_of UBERON:0001231 ! nephron tubule -property_value: UBPROP:0000012 "consider moving MA:0000377 renal tubule here, as it includes the various segments (proximal etc) as subclasses, not parts" xsd:string {external_ontology="MA"} [Term] id: UBERON:0007687 @@ -15763,8 +15202,8 @@ is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0006598 ! presumptive structure is_a: UBERON:0007688 ! anlage intersection_of: UBERON:0007688 ! anlage -intersection_of: has_potential_to_develop_into UBERON:0002113 ! kidney -relationship: has_potential_to_develop_into UBERON:0002113 ! kidney +intersection_of: RO:0002387 UBERON:0002113 ! has potential to develop into kidney +relationship: RO:0002387 UBERON:0002113 ! has potential to develop into kidney [Term] id: UBERON:0007688 @@ -15779,7 +15218,6 @@ synonym: "organ field" RELATED [] xref: AEO:0000170 xref: EFO:0001649 xref: EHDAA2:0003170 -xref: FBbt:00005426 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: Wikipedia:Anlage_(biology) is_a: UBERON:0000479 {source="FBbt"} ! tissue is_a: UBERON:0005423 {source="AEO", source="FBbt"} ! developing anatomical structure @@ -15800,10 +15238,8 @@ xref: NCIT:C33854 xref: UMLS:C0489903 {source="ncithesaurus:Vascular_System"} is_a: UBERON:0000467 ! anatomical system relationship: part_of UBERON:0004535 {source="MA"} ! cardiovascular system -relationship: present_in_taxon NCBITaxon:9606 -property_value: editor_note "consider merging with vasculature" xsd:string -property_value: UBPROP:0000001 "The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]." xsd:string {source="ncithesaurus:Vascular_System"} -property_value: UBPROP:0000012 "in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system" xsd:string {external_ontology="MA"} +property_value: IAO:0000116 "consider merging with vasculature" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0007823 @@ -15822,12 +15258,10 @@ xref: FMA:24874 xref: VSAO:0000303 is_a: UBERON:0000475 ! organism subdivision intersection_of: UBERON:0000475 ! organism subdivision -intersection_of: has_skeleton UBERON:0010719 ! girdle skeleton -relationship: has_skeleton UBERON:0010719 ! girdle skeleton -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +intersection_of: RO:0002551 UBERON:0010719 ! has skeleton girdle skeleton relationship: part_of UBERON:0010707 ! appendage girdle complex -property_value: IAO:0000232 "this encompasses non-skeletal tissue" xsd:string -property_value: UBPROP:0000001 "An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There are only two instances of appendage girdle regions per organism.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000303", ontology="VSAO", source="https://orcid.org/0000-0002-6601-2165"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002551 UBERON:0010719 ! has skeleton girdle skeleton [Term] id: UBERON:0007832 @@ -15858,21 +15292,17 @@ xref: VSAO:0000155 xref: Wikipedia:Pelvis xref: XAO:0003064 xref: ZFA:0000565 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010719 ! girdle skeleton intersection_of: UBERON:0010912 ! subdivision of skeleton intersection_of: part_of UBERON:0001271 ! pelvic girdle region -intersection_of: skeleton_of UBERON:0001271 ! pelvic girdle region -relationship: develops_from UBERON:0010377 {source="PMID:21455939"} ! mesenchyme from somatopleure +intersection_of: RO:0002576 UBERON:0001271 ! skeleton of pelvic girdle region relationship: part_of UBERON:0001271 ! pelvic girdle region relationship: part_of UBERON:0012476 ! skeleton of pelvic complex -relationship: skeleton_of UBERON:0001271 ! pelvic girdle region -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png" xsd:anyURI -property_value: editor_note "need to resolve whether this is a paired structure or a single belt (Paired in FMA - implicitly paired in VSAO)" xsd:string -property_value: UBPROP:0000001 "Anatomical cluster by which the hind limbs are supported and attached to the vertebral column.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000426", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000001 "Anatomical cluster that consists of the paired basipterygia which support the pelvic fin.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000565", ontology="TAO", source="TAO:wd"} -property_value: UBPROP:0000001 "Girdle skeleton consisting of a set of bones linking the axial series to the hindlimb/fin skeleton and offering anchoring areas for hindlimb/fin and caudal musculature.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000155", ontology="VSAO", source="https://orcid.org/0000-0002-6601-2165"} -property_value: UBPROP:0000003 "The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000305", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.333", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "Note that the VSAO and many ontologies use the label 'pelvic girdle' to denote the skeletal region specifically. We place the EHDAA2 class here, note that this includes the pre-cartilage condensation as parts" xsd:string {external_ontology="VSAO"} +relationship: RO:0002202 UBERON:0010377 {source="PMID:21455939"} ! develops from mesenchyme from somatopleure +relationship: RO:0002576 UBERON:0001271 ! skeleton of pelvic girdle region +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png" xsd:anyURI +property_value: IAO:0000116 "need to resolve whether this is a paired structure or a single belt (Paired in FMA - implicitly paired in VSAO)" xsd:string [Term] id: UBERON:0008987 @@ -15912,10 +15342,10 @@ xref: EHDAA2:0001113 xref: EHDAA:177 xref: EMAPA:16097 is_a: UBERON:0000477 ! anatomical cluster -relationship: composed_primarily_of UBERON:0003104 ! mesenchyme -relationship: has_developmental_contribution_from UBERON:0000926 {source="EHDAA2"} ! mesoderm relationship: part_of UBERON:0000922 ! embryo -property_value: editor_note "consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)" xsd:string +relationship: RO:0002254 UBERON:0000926 {source="EHDAA2"} ! has developmental contribution from mesoderm +relationship: RO:0002473 UBERON:0003104 ! composed primarily of mesenchyme +property_value: IAO:0000116 "consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)" xsd:string [Term] id: UBERON:0009196 @@ -15975,8 +15405,7 @@ synonym: "renal tubule (generic)" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "tubule of excretory system" EXACT [https://orcid.org/0000-0002-6601-2165, OBOL:automatic] is_a: UBERON:0003914 ! epithelial tube is_a: UBERON:0006555 ! excretory tube -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -property_value: IAO:0000232 "this class groups vertebrate nephron tubules with analagous structures such as insect Malpighian tubules" xsd:string +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria [Term] id: UBERON:0009856 @@ -15987,8 +15416,8 @@ synonym: "pouch" EXACT [] xref: galen:Diverticulum is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: has_quality PATO:0001987 ! saccular -relationship: has_quality PATO:0001987 ! saccular +intersection_of: RO:0000086 PATO:0001987 ! has quality saccular +relationship: RO:0000086 PATO:0001987 ! has quality saccular [Term] id: UBERON:0009881 @@ -15999,6 +15428,7 @@ synonym: "ALPM" EXACT [ZFA:0005041] xref: EFO:0003704 xref: TAO:0005041 xref: ZFA:0005041 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue relationship: part_of UBERON:0003081 {source="ZFA"} ! lateral plate mesoderm @@ -16022,11 +15452,10 @@ xref: SCTID:62802007 xref: Wikipedia:Interlobar_arteries is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0009913 ! renal lobe -relationship: present_in_taxon NCBITaxon:9606 -relationship: supplies UBERON:0009913 ! renal lobe -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI -property_value: UBPROP:0000012 "FMA only has the set term" xsd:string {external_ontology="FMA"} +intersection_of: RO:0002178 UBERON:0009913 ! supplies renal lobe +relationship: RO:0002178 UBERON:0009913 ! supplies renal lobe +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0009912 @@ -16057,11 +15486,10 @@ xref: Wikipedia:Renal_lobe is_a: UBERON:0009912 ! anatomical lobe intersection_of: UBERON:0009912 ! anatomical lobe intersection_of: part_of UBERON:0002113 ! kidney -relationship: contributes_to_morphology_of UBERON:0002113 ! kidney relationship: part_of UBERON:0002113 ! kidney -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI -property_value: editor_note "todo - add has_part relationships." xsd:string -property_value: UBPROP:0000008 "human kidneys have multilobar (multipyramidal) architecture while mice and rats have unilobar (unipyramidal) kidneys" xsd:string {source="MP"} +relationship: RO:0002433 UBERON:0002113 ! contributes to morphology of kidney +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI +property_value: IAO:0000116 "todo - add has_part relationships." xsd:string [Term] id: UBERON:0010000 @@ -16072,15 +15500,14 @@ subset: common_anatomy subset: upper_level synonym: "multicellular structure" EXACT [FBbt:00100313] xref: CARO:0010000 -xref: FBbt:00100313 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: has_quality PATO:0001993 ! multicellular +intersection_of: RO:0000086 PATO:0001993 ! has quality multicellular relationship: has_part CL:0000000 ! cell -relationship: has_quality PATO:0001993 ! multicellular -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0000086 PATO:0001993 ! has quality multicellular +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0010199 @@ -16104,8 +15531,8 @@ xref: FMA:71005 xref: TAO:0002228 xref: ZFA:0001718 is_a: UBERON:0006598 ! presumptive structure -relationship: has_potential_to_develop_into UBERON:0002081 ! cardiac atrium relationship: part_of UBERON:0004141 {source="ZFA"} ! heart tube +relationship: RO:0002387 UBERON:0002081 ! has potential to develop into cardiac atrium [Term] id: UBERON:0010314 @@ -16115,9 +15542,8 @@ def: "An anatomical structure that has some part that develops from the neural c subset: grouping_class is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: has_developmental_contribution_from UBERON:0002342 ! neural crest -relationship: has_developmental_contribution_from UBERON:0002342 ! neural crest -property_value: IAO:0000232 "Grouping term for query purposes" xsd:string +intersection_of: RO:0002254 UBERON:0002342 ! has developmental contribution from neural crest +relationship: RO:0002254 UBERON:0002342 ! has developmental contribution from neural crest [Term] id: UBERON:0010316 @@ -16125,7 +15551,7 @@ name: germ layer / neural crest namespace: uberon is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0005291 ! embryonic tissue -relationship: develops_from UBERON:0002532 ! epiblast (generic) +relationship: RO:0002202 UBERON:0002532 ! develops from epiblast (generic) [Term] id: UBERON:0010371 @@ -16137,8 +15563,8 @@ xref: FMA:69064 is_a: UBERON:0000483 ! epithelium is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000483 ! epithelium -intersection_of: develops_from UBERON:0000924 ! ectoderm -relationship: composed_primarily_of CL:0002077 ! ecto-epithelial cell +intersection_of: RO:0002202 UBERON:0000924 ! develops from ectoderm +relationship: RO:0002473 CL:0002077 ! composed primarily of ecto-epithelial cell [Term] id: UBERON:0010377 @@ -16146,14 +15572,15 @@ name: mesenchyme from somatopleure namespace: uberon def: "Mesenchyme that develops_from a somatopleure." [OBOL:automatic] xref: EHDAA2:0001120 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: develops_from UBERON:0004874 ! somatopleure intersection_of: part_of UBERON:0000922 ! embryo -relationship: develops_from UBERON:0004874 ! somatopleure +intersection_of: RO:0002202 UBERON:0004874 ! develops from somatopleure relationship: part_of UBERON:0009142 {source="EHDAA2"} ! entire embryonic mesenchyme -property_value: editor_note "the way this class is defined also includes extraembryonic mesenchyme such as the amniotic mesenchyme; in future this may be restricted to embryonic derivatives" xsd:string +relationship: RO:0002202 UBERON:0004874 ! develops from somatopleure +property_value: IAO:0000116 "the way this class is defined also includes extraembryonic mesenchyme such as the amniotic mesenchyme; in future this may be restricted to embryonic derivatives" xsd:string [Term] id: UBERON:0010523 @@ -16179,18 +15606,17 @@ synonym: "primitive nephron" BROAD [] is_a: UBERON:0003914 {source="EHDAA2-inferred"} ! epithelial tube is_a: UBERON:0004819 ! kidney epithelium is_a: UBERON:0006555 ! excretory tube -relationship: develops_from UBERON:0004209 {source="EHDAA2"} ! renal vesicle -relationship: has_potential_to_develop_into UBERON:0001285 ! nephron -relationship: located_in UBERON:0003918 ! kidney mesenchyme -property_value: UBPROP:0000012 "EHDAA2 treats this as already having a tubular structure, but in the ZFA representation this is a cluster of cells" xsd:string {external_ontology="EHDAA2"} +relationship: RO:0001025 UBERON:0003918 ! located in kidney mesenchyme +relationship: RO:0002202 UBERON:0004209 {source="EHDAA2"} ! develops from renal vesicle +relationship: RO:0002387 UBERON:0001285 ! has potential to develop into nephron [Term] id: UBERON:0010536 name: nephron progenitor namespace: uberon is_a: UBERON:0000479 {source="ZFA"} ! tissue -relationship: has_potential_to_develop_into UBERON:0001285 ! nephron relationship: part_of UBERON:0003918 {source="cjm"} ! kidney mesenchyme +relationship: RO:0002387 UBERON:0001285 ! has potential to develop into nephron [Term] id: UBERON:0010707 @@ -16208,14 +15634,10 @@ xref: FMA:7182 xref: VSAO:0000214 is_a: UBERON:0000475 ! organism subdivision is_a: UBERON:0015212 ! lateral structure -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 -relationship: functionally_related_to GO:0040011 ! locomotion -relationship: in_lateral_side_of UBERON:0000468 ! multicellular organism -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata -property_value: editor_note "It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO]" xsd:string -property_value: UBPROP:0000001 "Anatomical group that consists of the soft and skeletal tissues of the appendicular region of the body and the appendage proper.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000214", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070"} -property_value: UBPROP:0000005 "It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO]" xsd:string {date_retrieved="2012-09-06", external_class="VSAO:0000214", ontology="VSAO", source="Curator"} -property_value: UBPROP:0000012 "note that the FMA uses the term 'limb' to refer to the entire appendage complex (free limb plus girdle region)" xsd:string {external_ontology="FMA"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002328 GO:0040011 ! functionally related to locomotion +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: IAO:0000116 "It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO]" xsd:string creation_date: 2012-04-23T10:46:51Z [Term] @@ -16238,10 +15660,7 @@ is_a: UBERON:0010707 ! appendage girdle complex intersection_of: UBERON:0010707 ! appendage girdle complex intersection_of: has_part UBERON:0001271 ! pelvic girdle region relationship: has_part UBERON:0001271 ! pelvic girdle region -relationship: has_skeleton UBERON:0012476 ! skeleton of pelvic complex -property_value: RO:0002171 UBERON:0010708 -property_value: UBPROP:0000001 "Appendage girdle complex that when present, encompasses the pelvic appendage and the pelvic girdle.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000215", ontology="VSAO", source="VSAO:MAH"} -property_value: UBPROP:0000012 "note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region). Note the MA class 'hindlimb' may also belong here" xsd:string {external_ontology="FMA"} +relationship: RO:0002551 UBERON:0012476 ! has skeleton skeleton of pelvic complex [Term] id: UBERON:0010719 @@ -16253,14 +15672,11 @@ xref: AAO:0010686 xref: VSAO:0000302 is_a: UBERON:0010912 ! subdivision of skeleton intersection_of: UBERON:0010912 ! subdivision of skeleton -intersection_of: skeleton_of UBERON:0007823 ! appendage girdle region +intersection_of: RO:0002576 UBERON:0007823 ! skeleton of appendage girdle region relationship: part_of UBERON:0002091 ! appendicular skeleton relationship: part_of UBERON:0007823 ! appendage girdle region relationship: proximally_connected_to UBERON:0002090 ! postcranial axial skeleton -relationship: skeleton_of UBERON:0007823 ! appendage girdle region -property_value: UBPROP:0000001 "Skeletal subdivision that is part of the appendage girdle region.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000302", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070"} -property_value: UBPROP:0000002 "relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: part_of subdivision of skeleton (UBERON:0010912)[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000302", ontology="VSAO"} -property_value: UBPROP:0000002 "relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: proximally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000302", ontology="VSAO"} +relationship: RO:0002576 UBERON:0007823 ! skeleton of appendage girdle region [Term] id: UBERON:0010912 @@ -16276,7 +15692,6 @@ xref: VSAO:0000042 is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision relationship: part_of UBERON:0000075 {source="UBERONREF:0000003"} ! subdivision of skeletal system relationship: part_of UBERON:0004288 {source="VSAO"} ! skeleton -property_value: UBPROP:0000001 "Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000042", notes="incorrect", ontology="VSAO", source="VSAO:curator"} [Term] id: UBERON:0011137 @@ -16297,7 +15712,7 @@ synonym: "axial skeletal system" BROAD [https://github.com/obophenotype/uberon/w synonym: "post-cranial axial skeletal system" EXACT [] xref: FMA:302077 is_a: UBERON:0000075 {source="FMA"} ! subdivision of skeletal system -relationship: develops_from UBERON:0003089 {source="cjm"} ! sclerotome +relationship: RO:0002202 UBERON:0003089 {source="cjm"} ! develops from sclerotome property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" xsd:anyURI [Term] @@ -16315,9 +15730,8 @@ is_a: UBERON:0011216 ! organ system subdivision is_a: UBERON:0015212 ! lateral structure relationship: has_part UBERON:0000056 ! ureter relationship: has_part UBERON:0002113 ! kidney -relationship: in_lateral_side_of UBERON:0001008 {source="FMA-abduced-lr"} ! renal system relationship: part_of UBERON:0001008 {source="FMA"} ! renal system -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0011216 @@ -16327,15 +15741,14 @@ def: "A subdivision of an anatomical system." [http://orcid.org/0000-0002-6601-2 subset: common_anatomy subset: human_reference_atlas subset: upper_level -xref: FBbt:00007330 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67509 xref: SCTID:91690000 is_a: UBERON:0010000 {source="FBbt"} ! multicellular anatomical structure relationship: part_of UBERON:0000467 ! anatomical system -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0011249 @@ -16343,13 +15756,11 @@ name: appendicular skeletal system namespace: uberon def: "Subdivision of the skeletal system which consists of the appendicular skeleton plus associated joints." [https://orcid.org/0000-0002-6601-2165] xref: FMA:7484 -xref: VHOG:0001666 xref: VSAO:0000306 is_a: UBERON:0000075 ! subdivision of skeletal system relationship: has_part UBERON:0000982 ! skeletal joint relationship: has_part UBERON:0002091 ! appendicular skeleton property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton" xsd:anyURI -property_value: UBPROP:0000001 "Skeletal system which consists of the appendicular skeleton plus associated joints.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000306", ontology="VSAO", source="https://orcid.org/0000-0002-6601-2165"} [Term] id: UBERON:0011585 @@ -16359,7 +15770,7 @@ def: "Anatomical structure that is an aggregation of similar cells from which ca xref: VSAO:0000006 xref: XAO:0004021 is_a: UBERON:0000061 {source="VSAO"} ! anatomical structure -property_value: editor_note "consider obsoleting, coordinate with VSAO" xsd:string +property_value: IAO:0000116 "consider obsoleting, coordinate with VSAO" xsd:string [Term] id: UBERON:0011676 @@ -16372,7 +15783,7 @@ synonym: "body segment" RELATED [] synonym: "main body segment" RELATED [] is_a: UBERON:0000475 ! organism subdivision relationship: part_of UBERON:0013701 ! main body axis -property_value: editor_note "Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem" xsd:string +property_value: IAO:0000116 "Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem" xsd:string [Term] id: UBERON:0011695 @@ -16403,10 +15814,9 @@ synonym: "schizocoelom" NARROW [] xref: EHDAA2:0004731 xref: Wikipedia:Coelom is_a: UBERON:0000481 {source="EHDAA2"} ! multi-tissue structure -relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -property_value: editor_note "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." xsd:string -property_value: UBPROP:0000007 "coelomic" xsd:string +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +property_value: IAO:0000116 "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." xsd:string +property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} [Term] id: UBERON:0012274 @@ -16428,7 +15838,7 @@ xref: FMA:86452 is_a: UBERON:0000483 ! epithelium is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000483 ! epithelium -intersection_of: develops_from UBERON:0000926 ! mesoderm +intersection_of: RO:0002202 UBERON:0000926 ! develops from mesoderm [Term] id: UBERON:0012292 @@ -16474,10 +15884,10 @@ synonym: "skeleton of posterior limb/fin and girdle" RELATED [https://orcid.org/ xref: FMA:24140 is_a: UBERON:0010912 ! subdivision of skeleton intersection_of: UBERON:0010912 ! subdivision of skeleton -intersection_of: skeleton_of UBERON:0010709 ! pelvic complex +intersection_of: RO:0002576 UBERON:0010709 ! skeleton of pelvic complex relationship: part_of UBERON:0002091 ! appendicular skeleton relationship: part_of UBERON:0010709 {source="FMA"} ! pelvic complex -relationship: skeleton_of UBERON:0010709 ! pelvic complex +relationship: RO:0002576 UBERON:0010709 ! skeleton of pelvic complex [Term] id: UBERON:0013241 @@ -16490,8 +15900,7 @@ synonym: "urethral sulcus" EXACT [] xref: SCTID:361531004 xref: Wikipedia:Urethral_groove is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0004876 {source="Wikipedia"} ! urogenital fold -property_value: UBPROP:0000008 "In humans, the urethral groove is a temporary linear indentation on the underside (ventral side) of the male penis during embryonic development. It typically appears around 8 weeks of gestation and becomes closed into a normal male urethra by the 12th week" xsd:string {source="Wikipedia:Urethral_groove"} +relationship: RO:0002202 UBERON:0004876 {source="Wikipedia"} ! develops from urogenital fold [Term] id: UBERON:0013522 @@ -16512,11 +15921,11 @@ subset: common_anatomy synonym: "foramen space" NARROW [] xref: FMA:9338 is_a: UBERON:0000464 {source="FMA"} ! anatomical space -relationship: connects UBERON:0000464 {cardinality="2"} ! anatomical space -relationship: luminal_space_of UBERON:0004111 ! anatomical conduit -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0002176 UBERON:0000464 {cardinality="2"} ! connects anatomical space +relationship: RO:0002572 UBERON:0004111 ! luminal space of anatomical conduit +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0013701 @@ -16525,7 +15934,7 @@ namespace: uberon def: "A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages." [https://orcid.org/0000-0002-6601-2165] subset: non_informative is_a: UBERON:0000475 ! organism subdivision -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0013702 @@ -16537,11 +15946,9 @@ synonym: "body" RELATED [AEO:0000103] synonym: "whole body" RELATED [BTO:0001489] xref: AEO:0000103 xref: BTO:0001489 -xref: EMAPA:36031 xref: FMA:231424 is_a: UBERON:0000475 {source="AEO"} ! organism subdivision relationship: part_of UBERON:0013701 ! main body axis -property_value: UBPROP:0000001 "Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]." xsd:string {source="FMA:231424"} [Term] id: UBERON:0013756 @@ -16551,12 +15958,11 @@ def: "A blood that is part of a vein." [OBOL:automatic] synonym: "blood in vein" EXACT [FMA:83067] synonym: "portion of venous blood" EXACT [FMA:83067] synonym: "venous blood" EXACT [FMA:83067] -xref: BTO:0006187 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: FMA:83067 is_a: UBERON:0000178 ! blood intersection_of: UBERON:0000178 ! blood -intersection_of: located_in UBERON:0001638 ! vein -relationship: located_in UBERON:0001638 ! vein +intersection_of: RO:0001025 UBERON:0001638 ! located in vein +relationship: RO:0001025 UBERON:0001638 ! located in vein [Term] id: UBERON:0013768 @@ -16588,7 +15994,7 @@ xref: Wikipedia:Thoracic_skeleton is_a: UBERON:0010912 ! subdivision of skeleton relationship: part_of UBERON:0000915 ! thoracic segment of trunk relationship: part_of UBERON:0002090 ! postcranial axial skeleton -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0014903 @@ -16600,9 +16006,9 @@ xref: TAO:0005076 xref: ZFA:0005076 is_a: UBERON:0001048 ! primordium intersection_of: UBERON:0001048 ! primordium -intersection_of: has_potential_to_develop_into UBERON:0002049 ! vasculature -relationship: has_potential_to_develop_into UBERON:0002049 ! vasculature +intersection_of: RO:0002387 UBERON:0002049 ! has potential to develop into vasculature relationship: part_of UBERON:0011695 ! embryonic cardiovascular system +relationship: RO:0002387 UBERON:0002049 ! has potential to develop into vasculature [Term] id: UBERON:0015212 @@ -16612,11 +16018,7 @@ def: "Any structure that is placed on one side of the left-right axis of a bilat subset: grouping_class subset: non_informative is_a: UBERON:0000061 ! anatomical structure -intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: in_lateral_side_of UBERON:0000465 ! material anatomical entity -relationship: in_lateral_side_of UBERON:0000465 ! material anatomical entity -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -property_value: IAO:0000232 "This class is primarily to implement taxon constraints. It may be removed in the future." xsd:string +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria [Term] id: UBERON:0015228 @@ -16629,10 +16031,9 @@ synonym: "cardiac structure" RELATED [] synonym: "circulatory vessel" NARROW [] synonym: "heart" BROAD [] synonym: "heart or heart like organ" EXACT [] -xref: SPD:0000130 is_a: UBERON:0003103 ! compound organ -relationship: has_quality PATO:0001690 ! contractile relationship: part_of UBERON:0001009 ! circulatory system +relationship: RO:0000086 PATO:0001690 ! has quality contractile [Term] id: UBERON:0015410 @@ -16644,7 +16045,7 @@ xref: EMAPA:37597 {source="MA:th"} xref: MA:0002449 is_a: UBERON:0005178 {source="MA"} ! thoracic cavity element relationship: part_of UBERON:0004535 ! cardiovascular system -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0016566 @@ -16665,10 +16066,10 @@ synonym: "future CNS" EXACT [] synonym: "presumptive central nervous system" EXACT [] is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001017 ! central nervous system -relationship: develops_from UBERON:0000924 ! ectoderm -relationship: has_potential_to_develop_into UBERON:0001017 ! central nervous system +intersection_of: RO:0002387 UBERON:0001017 ! has potential to develop into central nervous system relationship: part_of UBERON:0016880 ! future nervous system +relationship: RO:0002202 UBERON:0000924 ! develops from ectoderm +relationship: RO:0002387 UBERON:0001017 ! has potential to develop into central nervous system [Term] id: UBERON:0016880 @@ -16680,9 +16081,9 @@ synonym: "presumptive nervous system" EXACT [AAO:0000477] xref: AAO:0000477 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001016 ! nervous system -relationship: existence_starts_during_or_after UBERON:0000111 ! organogenesis stage -relationship: has_potential_to_develop_into UBERON:0001016 ! nervous system +intersection_of: RO:0002387 UBERON:0001016 ! has potential to develop into nervous system +relationship: RO:0002387 UBERON:0001016 ! has potential to develop into nervous system +relationship: RO:0002496 UBERON:0000111 ! existence starts during or after organogenesis stage [Term] id: UBERON:0016887 @@ -16696,8 +16097,8 @@ xref: EHDAA2:0000003 xref: EMAPA:16042 is_a: UBERON:0000481 {source="AEO"} ! multi-tissue structure relationship: adjacent_to UBERON:0002050 ! embryonic structure -relationship: existence_starts_and_ends_during UBERON:0000068 ! embryo stage relationship: part_of UBERON:0004716 {source="AEO"} ! conceptus +relationship: RO:0002491 UBERON:0000068 ! existence starts and ends during embryo stage [Term] id: UBERON:0018707 @@ -16708,8 +16109,8 @@ synonym: "bladder" NARROW [BTO:0000123] xref: BTO:0000123 is_a: UBERON:0000489 ! cavitated compound organ is_a: UBERON:0009856 ! sac -relationship: has_quality PATO:0002468 ! distensible -relationship: location_of UBERON:0000463 ! organism substance +relationship: RO:0000086 PATO:0002468 ! has quality distensible +relationship: RO:0001015 UBERON:0000463 ! location of organism substance [Term] id: UBERON:0034921 @@ -16720,10 +16121,10 @@ subset: common_anatomy synonym: "anatomical cluster" RELATED [CARO:0020001] xref: CARO:0020001 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure -relationship: composed_primarily_of UBERON:0000064 ! organ part -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0002473 UBERON:0000064 ! composed primarily of organ part +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0034923 @@ -16732,14 +16133,13 @@ namespace: uberon def: "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other." [CARO:0020000] subset: common_anatomy xref: CARO:0020000 -xref: FBbt:00007276 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000465 {source="CARO"} ! material anatomical entity -relationship: composed_primarily_of UBERON:0000061 ! anatomical structure relationship: has_component UBERON:0000061 {minCardinality="2"} ! anatomical structure -relationship: has_quality PATO:0010001 ! disconnected -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0000086 PATO:0010001 ! has quality disconnected +relationship: RO:0002473 UBERON:0000061 ! composed primarily of anatomical structure +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0034925 @@ -16748,11 +16148,11 @@ namespace: uberon def: "A collection of anatomical structures that are alike in terms of their morphology or developmental origin." [http://orcid.org/0000-0002-6601-2165] subset: common_anatomy is_a: UBERON:0000465 ! material anatomical entity -relationship: has_member UBERON:0000061 ! anatomical structure -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: editor_note "resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected" xsd:string +relationship: RO:0002351 UBERON:0000061 ! has member anatomical structure +property_value: IAO:0000116 "resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0034969 @@ -16798,9 +16198,7 @@ def: "Any chamber of the right side of the heart." [http://orcid.org/0000-0002-6 xref: FMA:7165 xref: SCTID:362007002 is_a: UBERON:0004151 ! cardiac chamber -intersection_of: UBERON:0004151 ! cardiac chamber -intersection_of: in_right_side_of UBERON:0000948 ! heart -relationship: in_right_side_of UBERON:0000948 ! heart +is_a: UBERON:0015212 ! lateral structure [Term] id: UBERON:0035804 @@ -16835,9 +16233,9 @@ xref: AAO:0010270 xref: ZFA:0005594 is_a: UBERON:0000465 ! material anatomical entity relationship: bounding_layer_of UBERON:0000061 ! anatomical structure -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0036295 @@ -16850,7 +16248,7 @@ synonym: "renal pelvis plus ureter" EXACT [] xref: NCIT:C54419 is_a: UBERON:0000477 ! anatomical cluster relationship: part_of UBERON:0011143 {source="NCIT"} ! upper urinary tract -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:8410081 @@ -16862,7 +16260,6 @@ synonym: "microvessel" BROAD [] is_a: UBERON:0001981 ! blood vessel is_a: UBERON:0010523 ! microcirculatory vessel property_value: seeAlso "https://github.com/obophenotype/uberon/issues/2186" xsd:string -property_value: UBPROP:0000007 "microvascular" xsd:string created_by: http://orcid.org/0000-0002-2825-0621 [Term] @@ -16871,12 +16268,11 @@ name: excretory system namespace: uberon def: "An anatomical system that eliminates waste products that arise as a result of metabolic activity." [GO:0007588] subset: human_reference_atlas -xref: BTO:0006338 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} is_a: UBERON:0000467 ! anatomical system intersection_of: UBERON:0000467 ! anatomical system intersection_of: capable_of GO:0046903 ! secretion relationship: capable_of GO:0046903 ! secretion -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 created_by: http://orcid.org/0000-0002-6095-8718 creation_date: 2022-05-25T18:21:29Z @@ -16888,9 +16284,15 @@ def: "A muscle tissue that is associated with soft internal organs (viscera)." [ comment: It is quite common to refer to visceral muscles as smooth muscles, by analogy with vertebrates; however, most visceral muscles in arthropods are actually striated. {xref="https://en.wikipedia.org/wiki/Smooth_muscle", xref="FBbt:00005070", comment="PMID:8720463"} synonym: "visceral muscle" EXACT [] {comment="BTO:0002780"} is_a: UBERON:0002385 ! muscle tissue -relationship: composed_primarily_of CL:0008007 ! visceral muscle cell -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -property_value: dcterms-date "2023-02-16T10:17:46Z" xsd:dateTime +relationship: RO:0002473 CL:0008007 ! composed primarily of visceral muscle cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-02-16T10:17:46Z" xsd:dateTime + +[Typedef] +id: BFO:0000067 +name: contains process +def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] +comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant [Typedef] id: CL:4030044 @@ -16911,11 +16313,6 @@ id: RO:0000052 name: characteristic of def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." [] comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. -property_value: IAO:0000111 "inheres in" xsd:string -property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string -property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string -property_value: IAO:0000118 "inheres_in" xsd:string -property_value: RO:0001900 RO:0001901 is_functional: true is_a: RO:0002314 ! characteristic of part of inverse_of: bearer_of ! bearer of @@ -16925,10 +16322,7 @@ id: RO:0000079 name: function of def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. -property_value: editor_note "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string -property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string -property_value: IAO:0000118 "function_of" xsd:string -property_value: IAO:0000118 "is function of" xsd:string +property_value: IAO:0000116 "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string is_a: RO:0000052 ! characteristic of inverse_of: RO:0000085 ! has function @@ -16937,22 +16331,16 @@ id: RO:0000080 name: quality of def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. -property_value: editor_note "A quality inheres in its bearer at all times for which the quality exists." xsd:string -property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string -property_value: IAO:0000118 "is quality of" xsd:string -property_value: IAO:0000118 "quality_of" xsd:string +property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string is_a: RO:0000052 ! characteristic of -inverse_of: has_quality ! has quality +inverse_of: RO:0000086 ! has quality [Typedef] id: RO:0000081 name: role of def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. -property_value: editor_note "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string -property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string -property_value: IAO:0000118 "is role of" xsd:string -property_value: IAO:0000118 "role_of" xsd:string +property_value: IAO:0000116 "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string is_a: RO:0000052 ! characteristic of inverse_of: RO:0000087 ! has role @@ -16960,19 +16348,22 @@ inverse_of: RO:0000087 ! has role id: RO:0000085 name: has function def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] -property_value: editor_note "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string -property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string -property_value: IAO:0000118 "has_function" xsd:string +property_value: IAO:0000116 "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string domain: BFO:0000004 ! independent continuant is_a: bearer_of ! bearer of +[Typedef] +id: RO:0000086 +name: has quality +def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] +property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string +is_a: bearer_of ! bearer of + [Typedef] id: RO:0000087 name: has role def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] -property_value: editor_note "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string -property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string -property_value: IAO:0000118 "has_role" xsd:string +property_value: IAO:0000116 "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string domain: BFO:0000004 ! independent continuant is_a: bearer_of ! bearer of @@ -16997,12 +16388,7 @@ id: RO:0001000 name: derives from def: "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" [] subset: ro-eco -property_value: editor_note "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." xsd:string -property_value: IAO:0000112 "this cell derives from this parent cell (cell division)" xsd:string -property_value: IAO:0000112 "this nucleus derives from this parent nucleus (nuclear division)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000118 "derives_from" xsd:string -property_value: IAO:0000232 "This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations." xsd:string +property_value: IAO:0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." xsd:string inverse_of: RO:0001001 ! derives into [Typedef] @@ -17010,33 +16396,57 @@ id: RO:0001001 name: derives into def: "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" [] subset: ro-eco -property_value: editor_note "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." xsd:string -property_value: IAO:0000112 "this parent cell derives into this cell (cell division)" xsd:string -property_value: IAO:0000112 "this parent nucleus derives into this nucleus (nuclear division)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000118 "derives_into" xsd:string +property_value: IAO:0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." xsd:string + +[Typedef] +id: RO:0001015 +name: location of +def: "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" [] +property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +is_transitive: true +inverse_of: RO:0001025 ! located in + +[Typedef] +id: RO:0001025 +name: located in +def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +property_value: IAO:0000116 "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" xsd:string +property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Located_in" xsd:anyURI +domain: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +range: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +is_transitive: true +transitive_over: part_of ! part of [Typedef] id: RO:0002000 name: 2D boundary of def: "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" [] -property_value: editor_note "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string -property_value: editor_note "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string -property_value: IAO:0000112 "the surface of my skin is a 2D boundary of my body" xsd:string -property_value: IAO:0000118 "2D_boundary_of" xsd:string -property_value: IAO:0000118 "boundary of" xsd:string -property_value: IAO:0000118 "is 2D boundary of" xsd:string -property_value: IAO:0000118 "is boundary of" xsd:string -property_value: IAO:0000118 "surface of" xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string +is_a: RO:0002323 ! mereotopologically related to +inverse_of: RO:0002002 ! has 2D boundary + +[Typedef] +id: RO:0002002 +name: has 2D boundary +def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000141 ! immaterial entity is_a: RO:0002323 ! mereotopologically related to -inverse_of: has_boundary ! has 2D boundary + +[Typedef] +id: RO:0002005 +name: innervated_by +domain: UBERON:0000061 ! anatomical structure +inverse_of: RO:0002134 ! innervates [Typedef] id: RO:0002006 name: has synaptic terminal of -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: overlaps ! overlaps inverse_of: RO:0002130 ! has synaptic terminal in @@ -17118,16 +16528,23 @@ id: RO:0002081 name: before or simultaneous with comment: Primitive instance level timing relation between events subset: ro-eco -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000118 "<=" xsd:string is_a: RO:0002222 ! temporally related to +[Typedef] +id: RO:0002082 +name: simultaneous with +def: "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." [] +comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) +subset: ro-eco +is_symmetric: true +is_transitive: true +is_a: RO:0002081 ! before or simultaneous with + [Typedef] id: RO:0002086 name: ends after comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) subset: ro-eco -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string is_transitive: true is_a: RO:0002222 ! temporally related to @@ -17135,25 +16552,16 @@ is_a: RO:0002222 ! temporally related to id: RO:0002100 name: has soma location def: "Relation between a neuron and a material anatomical entity that its soma is part of." [] -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron range: UBERON:0000465 ! material anatomical entity is_a: overlaps ! overlaps -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] [Typedef] id: RO:0002101 name: fasciculates with def: "relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.\n" [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "fasciculates with" xsd:string -property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: overlaps ! overlaps inverse_of: RO:0002132 ! has fasciculating neuron projection @@ -17162,27 +16570,23 @@ inverse_of: RO:0002132 ! has fasciculating neuron projection id: RO:0002102 name: axon synapses in def: "Relation between a neuron and some structure its axon forms (chemical) synapses in." [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: RO:0002113 ! has presynaptic terminal in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "BFO_0000051 some (\n GO_0030424 and BFO_0000051 some (\n GO_0042734 and BFO_0000050 some (\n GO_0045202 and BFO_0000050 some ?Y)))" [] +[Typedef] +id: RO:0002103 +name: synapsed by +def: "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " [] +is_a: RO:0002485 ! receives input from +inverse_of: RO:0002120 ! synapsed to +expand_expression_to: "BFO_0000051 some (GO_0045211 that part_of some (GO_0045202 that has_part some (GO_0042734 that BFO_0000050 some Y?)))" [] + [Typedef] id: RO:0002104 name: has plasma membrane part def: "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part." [] -property_value: IAO:0000112 "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9990-8331 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 -property_value: RO:0001900 RO:0001901 domain: UBERON:0000465 ! material anatomical entity range: UBERON:0000465 ! material anatomical entity is_a: has_part ! has part @@ -17192,29 +16596,19 @@ expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] id: RO:0002110 name: has postsynaptic terminal in def: "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. " [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "synapsed in" xsd:string -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: RO:0002130 ! has synaptic terminal in inverse_of: RO:0002113 ! has presynaptic terminal in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (\n http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some (\n http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))" [] [Typedef] id: RO:0002113 name: has presynaptic terminal in def: "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input." [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000118 "synapses in" xsd:string -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: RO:0002130 ! has synaptic terminal in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000050 some Y?)" [] [Typedef] @@ -17222,11 +16616,6 @@ id: RO:0002120 name: synapsed to def: " Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.\n " [] comment: N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part some (\n ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( \n ‘synapse ; GO:0045202’ that has_part some (\n ‘post-synaptic membrane ; GO:0045211’ that part_of some N2)))) -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 is_a: RO:0002486 ! sends output to expand_expression_to: "BFO_0000051 some (GO_0042734 that part_of some (GO_0045202 that BFO_0000051 some (GO_0045211 that BFO_0000050 some Y?)))" [] @@ -17234,103 +16623,270 @@ expand_expression_to: "BFO_0000051 some (GO_0042734 that part_of some (GO_004520 id: RO:0002130 name: has synaptic terminal in def: "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "has synapse in" xsd:string -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: overlaps ! overlaps -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "RO_0002131 some (GO_0045202 that BFO_0000050 some Y?)" [] [Typedef] id: RO:0002132 name: has fasciculating neuron projection def: "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "has fasciculating component" xsd:string -property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string -property_value: RO:0001900 RO:0001901 is_a: overlaps ! overlaps +[Typedef] +id: RO:0002134 +name: innervates +def: "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." [] +transitive_over: part_of ! part of +expand_expression_to: "RO_0002132 some (GO_0043005 that (RO_0002131 some (GO_0045202 that BFO_0000050 some Y?)))" [] + +[Typedef] +id: RO:0002150 +name: continuous with +def: "X continuous_with Y if and only if X and Y share a fiat boundary." [] +property_value: seeAlso "FMA:85972" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000004 ! independent continuant +is_symmetric: true +is_a: RO:0002323 ! mereotopologically related to + +[Typedef] +id: RO:0002158 +name: shares ancestor with +def: "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." [] +comment: VBO calls this homologous_to +is_symmetric: true +is_transitive: true +is_a: RO:0002320 ! evolutionarily related to + +[Typedef] +id: RO:0002160 +name: only in taxon +def: "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." [] +property_value: IAO:0000116 "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" xsd:string +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints +is_a: RO:0002162 ! in taxon + +[Typedef] +id: RO:0002162 +name: in taxon +def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." [] +comment: Connects a biological entity to its taxon of origin. +subset: ro-eco +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints +holds_over_chain: capable_of RO:0002162 +holds_over_chain: extends_fibers_into RO:0002162 +holds_over_chain: has_part RO:0002162 +holds_over_chain: part_of RO:0002162 +holds_over_chain: results_in_developmental_progression_of RO:0002162 +holds_over_chain: RO:0002202 RO:0002162 +holds_over_chain: RO:0002206 RO:0002162 +holds_over_chain: RO:0002225 RO:0002162 +holds_over_chain: RO:0002254 RO:0002162 +is_a: RO:0002320 ! evolutionarily related to + [Typedef] id: RO:0002163 name: spatially disjoint from def: "A is spatially_disjoint_from B if and only if they have no parts in common" [] subset: ro-eco -property_value: editor_note "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" xsd:anyURI is_a: RO:0002323 ! mereotopologically related to expand_expression_to: "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" [] +[Typedef] +id: RO:0002170 +name: connected to +def: "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" [] +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI +is_a: RO:0002323 ! mereotopologically related to + +[Typedef] +id: RO:0002176 +name: connects +def: "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." [] +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI +domain: BFO:0000004 ! independent continuant +is_a: RO:0002323 ! mereotopologically related to + +[Typedef] +id: RO:0002177 +name: attached to part of +def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000061 ! anatomical structure +is_a: RO:0002323 ! mereotopologically related to +is_a: RO:0002567 ! biomechanically related to + +[Typedef] +id: RO:0002178 +name: supplies +def: "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." [] +property_value: IAO:0000116 "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" xsd:string +is_a: RO:0002170 ! connected to + +[Typedef] +id: RO:0002179 +name: drains +def: "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." [] +property_value: IAO:0000116 "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" xsd:string +is_a: RO:0002170 ! connected to + +[Typedef] +id: RO:0002202 +name: develops from +def: "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" [] +comment: This is the transitive form of the develops from relation +domain: BFO:0000004 ! independent continuant +range: BFO:0000004 ! independent continuant +is_transitive: true +is_a: RO:0002254 ! has developmental contribution from +is_a: RO:0002258 ! developmentally preceded by +inverse_of: RO:0002203 ! develops into + +[Typedef] +id: RO:0002203 +name: develops into +def: "inverse of develops from" [] +subset: RO:0002259 +is_transitive: true +is_a: RO:0002286 ! developmentally succeeded by +is_a: RO:0002387 ! has potential to develop into +is_a: RO:0002388 ! has potential to directly develop into + [Typedef] id: RO:0002206 name: expressed in def: "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" [] -property_value: IAO:0000112 "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000002 ! continuant range: UBERON:0000465 ! material anatomical entity is_a: RO:0002330 ! genomically related to inverse_of: RO:0002292 ! expresses -transitive_over: part_of ! part_of +transitive_over: part_of ! part of + +[Typedef] +id: RO:0002207 +name: directly develops from +def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] +comment: TODO - add child relations from DOS +synonym: "has developmental precursor" EXACT [] +is_a: RO:0002202 ! develops from +inverse_of: RO:0002210 ! directly develops into [Typedef] id: RO:0002210 name: directly develops into def: "inverse of directly develops from" [] subset: RO:0002259 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000118 "developmental precursor of" xsd:string -is_a: develops_into ! develops into +is_a: RO:0002203 ! develops into + +[Typedef] +id: RO:0002219 +name: surrounded by +def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" [] +is_a: adjacent_to ! adjacent to +inverse_of: RO:0002221 ! surrounds + +[Typedef] +id: RO:0002221 +name: surrounds +def: "inverse of surrounded by" [] +subset: RO:0002259 +is_a: adjacent_to ! adjacent to [Typedef] id: RO:0002222 name: temporally related to comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. subset: ro-eco -property_value: http://purl.org/dc/terms/source "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" xsd:anyURI -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent +[Typedef] +id: RO:0002223 +name: starts +def: "inverse of starts with" [] +subset: ro-eco +is_a: part_of ! part of +is_a: RO:0002222 ! temporally related to +inverse_of: starts_with ! starts with + +[Typedef] +id: RO:0002225 +name: develops from part of +def: "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" [] +holds_over_chain: RO:0002207 part_of +is_a: RO:0002202 ! develops from + +[Typedef] +id: RO:0002226 +name: develops in +def: "x develops_in y if x is located in y whilst x is developing" [] +domain: UBERON:0001062 ! anatomical entity +holds_over_chain: RO:0002207 RO:0001025 +is_a: RO:0002258 ! developmentally preceded by + +[Typedef] +id: RO:0002229 +name: ends +def: "inverse of ends with" [] +subset: ro-eco +is_a: part_of ! part of +is_a: RO:0002222 ! temporally related to +inverse_of: ends_with ! ends with + +[Typedef] +id: RO:0002252 +name: connecting branch of +def: "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." [] +property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 +is_a: RO:0002170 ! connected to +is_a: RO:0002375 ! in branching relationship with +inverse_of: RO:0002253 ! has connecting branch + [Typedef] id: RO:0002253 name: has connecting branch def: "inverse of connecting branch of" [] subset: RO:0002259 -property_value: RO:0004036 BFO:0000051 is_a: RO:0002375 ! in branching relationship with +[Typedef] +id: RO:0002254 +name: has developmental contribution from +def: "x has developmental contribution from y iff x has some part z such that z develops from y" [] +domain: UBERON:0001062 ! anatomical entity +range: UBERON:0001062 ! anatomical entity +holds_over_chain: has_part RO:0002202 +is_a: RO:0002258 ! developmentally preceded by +inverse_of: RO:0002255 ! developmentally contributes to + [Typedef] id: RO:0002255 name: developmentally contributes to def: "inverse of has developmental contribution from" [] subset: RO:0002259 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -holds_over_chain: develops_into part_of -is_a: has_potential_to_developmentally_contribute_to ! has potential to developmentally contribute to +holds_over_chain: RO:0002203 part_of is_a: RO:0002286 ! developmentally succeeded by +is_a: RO:0002385 ! has potential to developmentally contribute to + +[Typedef] +id: RO:0002256 +name: developmentally induced by +def: "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" [] +domain: UBERON:0000465 ! material anatomical entity +range: UBERON:0000465 ! material anatomical entity +is_a: RO:0002258 ! developmentally preceded by +inverse_of: RO:0002257 ! developmentally induces [Typedef] id: RO:0002257 name: developmentally induces def: "Inverse of developmentally induced by" [] -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002286 ! developmentally succeeded by is_a: RO:0002386 ! has potential to developmentally induce @@ -17339,10 +16895,7 @@ id: RO:0002258 name: developmentally preceded by def: "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p" [] comment: This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from -property_value: editor_note "false" xsd:boolean -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string +property_value: IAO:0000116 "false" xsd:boolean domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant is_a: RO:0002324 ! developmentally related to @@ -17353,7 +16906,6 @@ id: RO:0002263 name: acts upstream of def: "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: IAO:0000112 "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." xsd:string property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of holds_over_chain: RO:0002327 causally_upstream_of is_a: RO:0002264 ! acts upstream of or within @@ -17364,25 +16916,26 @@ name: acts upstream of or within def: "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term synonym: "affects" RELATED [] -property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within" xsd:anyURI holds_over_chain: RO:0002327 causally_upstream_of_or_within is_a: RO:0002500 ! causal agent in process +[Typedef] +id: RO:0002285 +name: developmentally replaces +def: "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" [] +property_value: IAO:0000116 "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" xsd:string +is_a: RO:0002258 ! developmentally preceded by + [Typedef] id: RO:0002286 name: developmentally succeeded by def: "Inverse of developmentally preceded by" [] -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002384 ! has developmental potential involving [Typedef] id: RO:0002287 name: part of developmental precursor of -property_value: IAO:0000112 "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: part_of RO:0002210 is_a: RO:0002286 ! developmentally succeeded by @@ -17390,80 +16943,58 @@ is_a: RO:0002286 ! developmentally succeeded by id: RO:0002292 name: expresses def: "y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." [] -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002330 ! genomically related to [Typedef] id: RO:0002314 name: characteristic of part of def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." [] -property_value: editor_note "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "inheres in part of" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: RO:0000052 part_of {RO:0002582="true"} is_a: RO:0002502 ! depends on -transitive_over: part_of ! part_of +transitive_over: part_of ! part of [Typedef] id: RO:0002320 name: evolutionarily related to def: "A relationship that holds via some environmental process" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." xsd:string [Typedef] id: RO:0002323 name: mereotopologically related to def: "A mereological relationship or a topological relationship" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string -property_value: RO:0001900 RO:0001901 [Typedef] id: RO:0002324 name: developmentally related to def: "A relationship that holds between entities participating in some developmental process (GO:0032502)" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" xsd:string [Typedef] id: RO:0002327 name: enables def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "catalyzes" xsd:string -property_value: IAO:0000118 "executes" xsd:string -property_value: IAO:0000118 "has" xsd:string -property_value: IAO:0000118 "is catalyzing" xsd:string -property_value: IAO:0000118 "is executing" xsd:string -property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string property_value: seeAlso "https://wiki.geneontology.org/Enables" xsd:anyURI is_a: capable_of ! capable of inverse_of: RO:0002333 ! enabled by transitive_over: has_part ! has part transitive_over: RO:0002017 ! has component activity +[Typedef] +id: RO:0002328 +name: functionally related to +def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] + [Typedef] id: RO:0002329 name: part of structure that is capable of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "false" xsd:boolean -holds_over_chain: part_of capable_of {RO:0002581="true"} -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002330 name: genomically related to def: "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant @@ -17471,31 +17002,25 @@ range: BFO:0000002 ! continuant id: RO:0002331 name: involved in def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "actively involved in" xsd:string -property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Involved_in" xsd:anyURI holds_over_chain: RO:0002327 part_of is_a: participates_in ! participates in is_a: RO:0002431 ! involved in or involved in regulation of -transitive_over: part_of ! part_of +transitive_over: part_of ! part of [Typedef] id: RO:0002333 name: enabled by def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso "https://wiki.geneontology.org/Enabled_by" xsd:anyURI -is_a: functionally_related_to ! functionally related to is_a: has_participant ! has participant +is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002337 name: related via localization to def: "A relationship that holds via some process of localization" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is a grouping relation." xsd:string domain: BFO:0000015 ! process range: BFO:0000002 ! continuant @@ -17503,84 +17028,134 @@ range: BFO:0000002 ! continuant id: RO:0002350 name: member of def: "is member of is a mereological relation between a item and a collection." [] -property_value: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string -property_value: IAO:0000118 "is member of" xsd:string -property_value: IAO:0000118 "member part of" xsd:string -property_value: IAO:0000119 "SIO" xsd:string -property_value: RO:0001900 RO:0001901 -is_a: part_of ! part_of -inverse_of: has_member ! has member +is_a: part_of ! part of +inverse_of: RO:0002351 ! has member [Typedef] -id: RO:0002354 -name: formed as result of -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: output_of ! output of +id: RO:0002351 +name: has member +def: "has member is a mereological relation between a collection and an item." [] +is_a: has_part ! has part [Typedef] -id: RO:0002360 +id: RO:0002352 +name: input of +def: "inverse of has input" [] +subset: ro-eco +subset: RO:0002259 +is_a: participates_in ! participates in +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002354 +name: formed as result of +is_a: output_of ! output of + +[Typedef] +id: RO:0002360 name: has dendrite location -property_value: http://purl.org/dc/terms/source "http://neurolex.org/wiki/Property:DendriteLocation" xsd:anyURI -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps +[Typedef] +id: RO:0002371 +name: attached to +def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] +subset: ro-eco +is_symmetric: true +is_a: RO:0002170 ! connected to +is_a: RO:0002177 ! attached to part of + +[Typedef] +id: RO:0002372 +name: has muscle origin +def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] +property_value: seeAlso http://dbpedia.org/property/origin +domain: UBERON:0000061 {comment="We need to import uberon muscle to create a stricter domain constraint"} ! anatomical structure +is_a: RO:0002371 ! attached to +is_a: RO:0002567 ! biomechanically related to + +[Typedef] +id: RO:0002373 +name: has muscle insertion +def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] +property_value: seeAlso http://dbpedia.org/property/insertion +domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} ! anatomical structure +is_a: RO:0002371 ! attached to +is_a: RO:0002567 ! biomechanically related to + [Typedef] id: RO:0002375 name: in branching relationship with def: "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" xsd:string -property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string -property_value: RO:0004036 BFO:0000050 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png property_value: seeAlso "https://github.com/obophenotype/uberon/issues/170" xsd:anyURI domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002323 ! mereotopologically related to +[Typedef] +id: RO:0002376 +name: tributary of +def: "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." [] +subset: ro-eco +property_value: seeAlso http://dbpedia.org/ontology/drainsTo +property_value: seeAlso "http://en.wikipedia.org/wiki/Tributary" xsd:anyURI +is_a: RO:0002170 ! connected to +is_a: RO:0002375 ! in branching relationship with + [Typedef] id: RO:0002379 name: spatially coextensive with def: "x spatially_coextensive_with y if and inly if x and y have the same location" [] -property_value: IAO:0000112 "A lump of clay and a statue" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" xsd:string is_a: overlaps ! overlaps +[Typedef] +id: RO:0002380 +name: branching part of +def: "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" [] +subset: ro-eco +property_value: seeAlso "FMA:85994" xsd:string +property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 +is_a: part_of ! part of +is_a: RO:0002375 ! in branching relationship with +inverse_of: RO:0002569 ! has branching part + [Typedef] id: RO:0002384 name: has developmental potential involving def: "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: UBERON:0001062 ! anatomical entity range: UBERON:0001062 ! anatomical entity is_a: RO:0002324 ! developmentally related to +[Typedef] +id: RO:0002385 +name: has potential to developmentally contribute to +def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] +is_a: RO:0002384 ! has developmental potential involving + [Typedef] id: RO:0002386 name: has potential to developmentally induce def: "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002384 ! has developmental potential involving + +[Typedef] +id: RO:0002387 +name: has potential to develop into +def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] is_a: RO:0002384 ! has developmental potential involving [Typedef] id: RO:0002388 name: has potential to directly develop into def: "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: has_potential_to_develop_into ! has potential to develop into +is_a: RO:0002387 ! has potential to develop into [Typedef] id: RO:0002407 name: indirectly positively regulates def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "indirectly activates" xsd:string -property_value: RO:0002579 RO:0002213 property_value: seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates" xsd:anyURI holds_over_chain: directly_positively_regulates directly_positively_regulates holds_over_chain: directly_positively_regulates RO:0002407 @@ -17594,9 +17169,6 @@ transitive_over: directly_positively_regulates ! directly positively regulates id: RO:0002409 name: indirectly negatively regulates def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "indirectly inhibits" xsd:string -property_value: RO:0002579 RO:0002212 property_value: seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates" xsd:anyURI holds_over_chain: directly_negatively_regulates directly_negatively_regulates holds_over_chain: directly_negatively_regulates RO:0002409 @@ -17609,15 +17181,12 @@ transitive_over: directly_negatively_regulates ! directly negatively regulates id: RO:0002410 name: causally related to def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] -property_value: editor_note "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string [Typedef] id: RO:0002428 name: involved in regulation of def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002327 regulates holds_over_chain: RO:0002331 regulates is_a: RO:0002263 ! acts upstream of @@ -17627,8 +17196,6 @@ is_a: RO:0002431 ! involved in or involved in regulation of id: RO:0002429 name: involved in positive regulation of def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0004049 RO:0002428 holds_over_chain: RO:0002327 positively_regulates holds_over_chain: RO:0002331 positively_regulates is_a: RO:0002428 ! involved in regulation of @@ -17637,7 +17204,6 @@ is_a: RO:0002428 ! involved in regulation of id: RO:0002430 name: involved in negative regulation of def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002428 holds_over_chain: RO:0002327 negatively_regulates holds_over_chain: RO:0002331 negatively_regulates @@ -17647,11 +17213,9 @@ is_a: RO:0002428 ! involved in regulation of id: RO:0002431 name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] -property_value: editor_note "OWL does not allow defining object properties via a Union" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "involved in or reguates" xsd:string -is_a: functionally_related_to ! functionally related to +property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string is_a: RO:0002264 ! acts upstream of or within +is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process [Typedef] @@ -17659,12 +17223,14 @@ id: RO:0002432 name: is active in def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [https://orcid.org/0000-0002-6601-2165, https://orcid.org/0000-0002-7073-9172] synonym: "enables activity in" EXACT [] -property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "executes activity in" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Is_active_in" xsd:anyURI -holds_over_chain: RO:0002327 occurs_in {RO:0002581="true"} -is_a: functionally_related_to ! functionally related to +is_a: overlaps ! overlaps +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002433 +name: contributes to morphology of +def: "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." [] is_a: overlaps ! overlaps [Typedef] @@ -17673,11 +17239,8 @@ name: interacts with def: "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." [] subset: ro-eco synonym: "in pairwise interaction with" EXACT [] -property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0914" xsd:anyURI -property_value: editor_note "Considering relabeling as 'pairwise interacts with'" xsd:anyURI -property_value: editor_note "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string +property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI +property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity @@ -17687,10 +17250,6 @@ is_symmetric: true id: RO:0002436 name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] -property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0915" xsd:anyURI -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "binds" xsd:string -property_value: IAO:0000118 "molecularly binds with" xsd:string property_value: seeAlso ECO:0000353 is_symmetric: true is_a: RO:0002434 ! interacts with @@ -17698,9 +17257,7 @@ is_a: RO:0002434 ! interacts with [Typedef] id: RO:0002447 name: phosphorylates -property_value: editor_note "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string +property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string is_a: RO:0002436 ! molecularly interacts with [Typedef] @@ -17708,8 +17265,6 @@ id: RO:0002448 name: directly regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." [] synonym: "molecularly controls" EXACT [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002436 ! molecularly interacts with @@ -17720,9 +17275,6 @@ id: RO:0002449 name: directly negatively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] synonym: "molecularly decreases activity of" EXACT [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 -property_value: IAO:0000118 "directly inhibits" xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002448 ! directly regulates activity of @@ -17732,9 +17284,6 @@ id: RO:0002450 name: directly positively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] synonym: "molecularly increases activity of" EXACT [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 -property_value: IAO:0000118 "directly activates" xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002448 ! directly regulates activity of @@ -17742,61 +17291,136 @@ is_a: RO:0002448 ! directly regulates activity of [Typedef] id: RO:0002464 name: helper property (not for use in curation) -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string + +[Typedef] +id: RO:0002473 +name: composed primarily of +def: "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." [] +subset: ro-eco +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: has_part ! has part [Typedef] id: RO:0002479 name: has part that occurs in def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] subset: ro-eco -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant -holds_over_chain: has_part occurs_in {RO:0002581="true"} [Typedef] id: RO:0002481 name: is kinase activity -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002564 ! molecular interaction relation helper property [Typedef] id: RO:0002485 name: receives input from -property_value: editor_note "See notes for inverse relation" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: connected_to ! connected to +property_value: IAO:0000116 "See notes for inverse relation" xsd:string +is_a: RO:0002170 ! connected to inverse_of: RO:0002486 ! sends output to [Typedef] id: RO:0002486 name: sends output to -property_value: editor_note "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: connected_to ! connected to +property_value: IAO:0000116 "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." xsd:string +is_a: RO:0002170 ! connected to [Typedef] id: RO:0002487 name: relation between physical entity and a process or stage -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage." xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000003 ! occurrent +[Typedef] +id: RO:0002488 +name: existence starts during +def: "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." [] +is_a: RO:0002490 ! existence overlaps +is_a: RO:0002496 ! existence starts during or after +transitive_over: part_of ! part of + +[Typedef] +id: RO:0002489 +name: existence starts with +def: "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." [] +is_a: RO:0002488 ! existence starts during + [Typedef] id: RO:0002490 name: existence overlaps def: "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" [] comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002487 ! relation between physical entity and a process or stage +[Typedef] +id: RO:0002491 +name: existence starts and ends during +def: "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +synonym: "exists during" EXACT [] +is_a: RO:0002488 ! existence starts during +is_a: RO:0002492 ! existence ends during + +[Typedef] +id: RO:0002492 +name: existence ends during +def: "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +is_a: RO:0002490 ! existence overlaps +is_a: RO:0002497 ! existence ends during or before +transitive_over: part_of ! part of + +[Typedef] +id: RO:0002493 +name: existence ends with +def: "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +is_a: RO:0002492 ! existence ends during + +[Typedef] +id: RO:0002494 +name: transformation of +def: "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" [] +is_transitive: true +is_a: RO:0002202 ! develops from + +[Typedef] +id: RO:0002495 +name: immediate transformation of +def: "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" [] +is_a: RO:0002207 ! directly develops from +is_a: RO:0002494 ! transformation of + +[Typedef] +id: RO:0002496 +name: existence starts during or after +def: "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +holds_over_chain: part_of RO:0002496 +holds_over_chain: RO:0002258 RO:0002496 +is_a: RO:0002487 ! relation between physical entity and a process or stage +transitive_over: part_of ! part of +transitive_over: preceded_by ! preceded by +transitive_over: RO:0002082 ! simultaneous with + +[Typedef] +id: RO:0002497 +name: existence ends during or before +def: "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +holds_over_chain: part_of RO:0002497 +holds_over_chain: RO:0002286 RO:0002497 +is_a: RO:0002487 ! relation between physical entity and a process or stage +transitive_over: part_of ! part of +transitive_over: precedes ! precedes +transitive_over: RO:0002082 ! simultaneous with + [Typedef] id: RO:0002500 name: causal agent in process def: "A relationship between a material entity and a process where the material entity has some causal role that influences the process" [] -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_a: RO:0002595 ! causal relation between material entity and a process inverse_of: process_has_causal_agent ! process has causal agent @@ -17804,9 +17428,6 @@ inverse_of: process_has_causal_agent ! process has causal agent id: RO:0002501 name: causal relation between processes def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent is_a: RO:0002410 ! causally related to @@ -17814,33 +17435,35 @@ is_a: RO:0002410 ! causally related to [Typedef] id: RO:0002502 name: depends on -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso BFO:0000169 [Typedef] id: RO:0002506 name: causal relation between entities -property_value: editor_note "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: IAO:0000116 "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant is_a: RO:0002410 ! causally related to +[Typedef] +id: RO:0002551 +name: has skeleton +def: "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." [] +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000465 {IAO:0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} ! material anatomical entity +is_a: has_part ! has part +inverse_of: RO:0002576 ! skeleton of +is_asymmetric: true + [Typedef] id: RO:0002559 name: causally influenced by -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string is_a: RO:0002506 ! causal relation between entities inverse_of: RO:0002566 ! causally influences [Typedef] id: RO:0002563 name: interaction relation helper property -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29 property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI is_a: RO:0002464 ! helper property (not for use in curation) @@ -17848,17 +17471,12 @@ is_a: RO:0002464 ! helper property (not for use in curation) [Typedef] id: RO:0002564 name: molecular interaction relation helper property -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002563 ! interaction relation helper property [Typedef] id: RO:0002566 name: causally influences def: "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant is_a: RO:0002506 ! causal relation between entities @@ -17867,20 +17485,66 @@ is_a: RO:0002506 ! causal relation between entities id: RO:0002567 name: biomechanically related to def: "A relation that holds between elements of a musculoskeletal system or its analogs." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string domain: UBERON:0000061 ! anatomical structure range: UBERON:0000061 ! anatomical structure -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002568 +name: has muscle antagonist +def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] +is_a: RO:0002567 ! biomechanically related to + +[Typedef] +id: RO:0002569 +name: has branching part +def: "inverse of branching part of" [] +subset: ro-eco +subset: RO:0002259 +is_transitive: true +is_a: has_part ! has part +is_a: RO:0002375 ! in branching relationship with + +[Typedef] +id: RO:0002570 +name: conduit for +def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] +subset: ro-eco +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: overlaps ! overlaps + +[Typedef] +id: RO:0002571 +name: lumen of +def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] +subset: ro-eco +range: BFO:0000040 ! material entity +is_a: part_of ! part of + +[Typedef] +id: RO:0002572 +name: luminal space of +def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" [] +subset: ro-eco +domain: BFO:0000141 ! immaterial entity +is_a: RO:0002571 ! lumen of + +[Typedef] +id: RO:0002576 +name: skeleton of +def: "inverse of has skeleton" [] +subset: RO:0002259 +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000061 ! anatomical structure +is_a: part_of ! part of [Typedef] id: RO:0002584 name: has part structure that is capable of def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" [] -property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: has_part capable_of -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to is_a: RO:0002595 ! causal relation between material entity and a process [Typedef] @@ -17893,9 +17557,7 @@ is_a: has_input ! has input id: RO:0002595 name: causal relation between material entity and a process def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." [] -property_value: editor_note "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000040 ! material entity range: BFO:0000015 ! process is_a: RO:0002410 ! causally related to @@ -17904,8 +17566,6 @@ is_a: RO:0002410 ! causally related to id: RO:0002596 name: capable of regulating def: "Holds between c and p if and only if c is capable of some activity a, and a regulates p." [] -property_value: IAO:0000112 "pyrethroid -> growth" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations holds_over_chain: capable_of regulates is_a: RO:0002500 ! causal agent in process @@ -17913,7 +17573,6 @@ is_a: RO:0002500 ! causal agent in process id: RO:0002597 name: capable of negatively regulating def: "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." [] -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations holds_over_chain: capable_of negatively_regulates is_a: RO:0002596 ! capable of regulating @@ -17921,8 +17580,6 @@ is_a: RO:0002596 ! capable of regulating id: RO:0002598 name: capable of positively regulating def: "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." [] -property_value: IAO:0000112 "renin -> arteriolar smooth muscle contraction" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations holds_over_chain: capable_of positively_regulates is_a: RO:0002596 ! capable of regulating @@ -17931,7 +17588,7 @@ id: RO:0004031 name: enables subfunction def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] holds_over_chain: RO:0002327 has_part -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z @@ -17939,7 +17596,6 @@ creation_date: 2018-01-25T23:20:13Z id: RO:0004032 name: acts upstream of or within, positive effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: RO:0004049 RO:0002264 property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0004047 is_a: RO:0002264 ! acts upstream of or within @@ -17962,7 +17618,6 @@ id: RO:0004034 name: acts upstream of, positive effect def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: RO:0004049 RO:0002263 property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 causally_upstream_of,_positive_effect is_a: RO:0002263 ! acts upstream of @@ -17995,7 +17650,6 @@ creation_date: 2018-03-13T23:55:05Z [Typedef] id: RO:0004047 name: causally upstream of or within, positive effect -property_value: RO:0004049 RO:0002418 property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect is_a: causally_upstream_of_or_within ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 @@ -18005,7 +17659,6 @@ creation_date: 2018-03-13T23:55:19Z id: RO:0011002 name: regulates activity of def: "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." [] -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002566 ! causally influences @@ -18060,7 +17713,7 @@ name: has synaptic IO in region def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region." [] synonym: "has synaptic input or output in" EXACT [] is_a: RO:0002130 ! has synaptic terminal in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:26:52Z @@ -18072,7 +17725,7 @@ synonym: "has sensory dendrite location" EXACT [] synonym: "has sensory terminal in" EXACT [] synonym: "has sensory terminal location" EXACT [] is_a: RO:0002360 ! has dendrite location -transitive_over: part_of ! part_of +transitive_over: part_of ! part of created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-20T12:10:09Z @@ -18115,9 +17768,8 @@ comment: Example: a spherical object has the quality of being spherical, and the id: RO:0015015 name: has high plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: dc-contributor https://orcid.org/0000-0003-1617-8244 -property_value: dc-contributor https://orcid.org/0000-0003-1940-6740 -property_value: IAO:0000112 "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part @@ -18125,9 +17777,8 @@ is_a: RO:0002104 ! has plasma membrane part id: RO:0015016 name: has low plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: dc-contributor https://orcid.org/0000-0003-1617-8244 -property_value: dc-contributor https://orcid.org/0000-0003-1940-6740 -property_value: IAO:0000112 "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part @@ -18136,11 +17787,6 @@ id: RO:0017001 name: device utilizes material def: "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." [] synonym: "utilizes" BROAD [] -property_value: IAO:0000112 "A diagnostic testing device utilizes a specimen." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 -property_value: IAO:0000117 https://orcid.org/0000-0003-2620-0345 -property_value: IAO:0000232 "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." xsd:string -property_value: IAO:0000232 "See github ticket https://github.com/oborel/obo-relations/issues/497" xsd:string holds_over_chain: capable_of has_input creation_date: 2021-11-08T12:00:00Z @@ -18161,65 +17807,24 @@ creation_date: 2020-06-08T17:21:33Z id: adjacent_to name: adjacent to namespace: external -namespace: uberon def: "x adjacent to y if and only if x and y share a boundary." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002220 -property_value: editor_note "This relation acts as a join point with BSPO" xsd:string -property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} -property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string -property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string -property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000004 ! independent continuant is_a: RO:0002163 ! spatially disjoint from -[Typedef] -id: anterior_to -name: anterior to -namespace: uberon -xref: BSPO:0000096 - [Typedef] id: anteriorly_connected_to name: anteriorly connected to namespace: uberon def: "x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] -is_a: connected_to ! connected to -is_a: posterior_to ! posterior to +is_a: RO:0002170 ! connected to is_a: transitively_anteriorly_connected_to ! transitively anteriorly connected to -[Typedef] -id: attaches_to -name: attached to -namespace: uberon -def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] -subset: ro-eco -xref: RO:0002371 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000589 "attached to (anatomical structure to anatomical structure)" xsd:string -is_symmetric: true -is_a: attaches_to_part_of ! attached to part of -is_a: connected_to ! connected to - -[Typedef] -id: attaches_to_part_of -name: attached to part of -namespace: uberon -def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] -xref: RO:0002177 -property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string -domain: UBERON:0000061 ! anatomical structure -range: UBERON:0000061 ! anatomical structure -holds_over_chain: attaches_to part_of {RO:0002582="true"} -is_a: RO:0002323 ! mereotopologically related to -is_a: RO:0002567 ! biomechanically related to - [Typedef] id: bearer_of name: bearer of @@ -18227,13 +17832,7 @@ name: has characteristic namespace: external def: "Inverse of characteristic_of" [] xref: RO:0000053 -property_value: editor_note "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string -property_value: IAO:0000111 "bearer of" xsd:string -property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string -property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string -property_value: IAO:0000118 "bearer_of" xsd:string -property_value: IAO:0000118 "is bearer of" xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string range: BFO:0000020 ! specifically dependent continuant is_inverse_functional: true @@ -18241,45 +17840,20 @@ is_inverse_functional: true id: bounding_layer_of name: bounding layer of namespace: external -namespace: uberon def: "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000" [] comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. subset: ro-eco xref: RO:0002007 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 range: BFO:0000040 ! material entity -is_a: part_of ! part_of - -[Typedef] -id: branching_part_of -name: branching part of -namespace: uberon -def: "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" [] -subset: ro-eco -xref: RO:0002380 -property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso "FMA:85994" xsd:string -property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 -is_a: part_of ! part_of -is_a: RO:0002375 ! in branching relationship with -inverse_of: has_branching_part ! has branching part +is_a: part_of ! part of [Typedef] id: capable_of name: capable of namespace: external -namespace: uberon def: "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " [] subset: ro-eco xref: RO:0002215 -property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string -property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "has function realized in" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 -property_value: IAO:0000232 "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000015 ! process is_a: capable_of_part_of ! capable of part of @@ -18288,14 +17862,10 @@ is_a: capable_of_part_of ! capable of part of id: capable_of_part_of name: capable of part of namespace: external -namespace: uberon def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] xref: RO:0002216 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "has function in" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: capable_of part_of {RO:0002582="true"} -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process [Typedef] @@ -18304,8 +17874,6 @@ name: causally downstream of namespace: external def: "inverse of upstream of" [] xref: RO:0002404 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of_or_within ! causally downstream of or within is_a: preceded_by ! preceded by inverse_of: causally_upstream_of ! causally upstream of @@ -18317,8 +17885,6 @@ namespace: external def: "inverse of causally upstream of or within" [] subset: RO:0002259 xref: RO:0002427 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_transitive: true is_a: RO:0002501 ! causal relation between processes @@ -18330,7 +17896,6 @@ def: "p is causally upstream of q iff p is causally related to q, the end of p p subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002411 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within is_a: precedes ! precedes @@ -18343,7 +17908,6 @@ def: "p is causally upstream of, negative effect q iff p is casually upstream of subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 -property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_negative_effect is_a: causally_upstream_of ! causally upstream of @@ -18358,8 +17922,6 @@ comment: holds between x and y if and only if x is causally upstream of y and th subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002304 -property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 -property_value: RO:0004049 RO:0002411 property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_positive_effect is_a: causally_upstream_of ! causally upstream of is_a: RO:0004047 ! causally upstream of or within, positive effect @@ -18371,9 +17933,7 @@ namespace: external def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] synonym: "affects" RELATED [] xref: RO:0002418 -property_value: editor_note "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "influences (processual)" xsd:string +property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string is_transitive: true is_a: RO:0002501 ! causal relation between processes inverse_of: causally_downstream_of_or_within ! causally downstream of or within @@ -18383,511 +17943,81 @@ id: channel_for name: channel for namespace: uberon synonym: "carries" BROAD [] -domain: UBERON:0004111 ! anatomical conduit -range: UBERON:0000463 ! organism substance [Typedef] id: channels_from name: channels_from namespace: uberon -is_transitive: true [Typedef] id: channels_into name: channels_into namespace: uberon -is_transitive: true [Typedef] -id: composed_primarily_of -name: composed primarily of -namespace: uberon -def: "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." [] -subset: ro-eco -xref: RO:0002473 -property_value: IAO:0000112 "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: RO:0001900 RO:0001901 -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: has_part ! has part +id: directly_negatively_regulates +name: directly negatively regulates +namespace: external +def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0002630 +property_value: RO:0004050 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates" xsd:anyURI +is_a: directly_regulates ! directly regulates +is_a: negatively_regulates ! negatively regulates [Typedef] -id: conduit_for -name: conduit for -namespace: uberon -def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] -subset: ro-eco -xref: RO:0002570 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "UBERON:cjm" xsd:string -property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: overlaps ! overlaps +id: directly_positively_regulates +name: directly positively regulates +namespace: external +def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0002629 +property_value: seeAlso "https://wiki.geneontology.org/Directly_positively_regulates" xsd:anyURI +is_a: directly_regulates ! directly regulates +is_a: positively_regulates ! positively regulates [Typedef] -id: connected_to -name: connected to -namespace: uberon -def: "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" [] -xref: RO:0002170 -property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI -property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: connecting_branch_of -name: connecting branch of -namespace: uberon -def: "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." [] -xref: RO:0002252 -property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." xsd:string -property_value: RO:0004036 BFO:0000050 -property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 -is_a: connected_to ! connected to -is_a: RO:0002375 ! in branching relationship with -inverse_of: RO:0002253 ! has connecting branch - -[Typedef] -id: connects -name: connects -namespace: uberon -def: "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." [] -xref: RO:0002176 -property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string -property_value: IAO:0000112 "The M8 connects Glasgow and Edinburgh" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI -property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI -domain: BFO:0000004 ! independent continuant -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: contains_process -name: contains process -namespace: uberon -def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] -comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant -xref: BFO:0000067 -property_value: IAO:0000111 "site of" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - -[Typedef] -id: continuous_with -name: continuous with -namespace: uberon -def: "X continuous_with Y if and only if X and Y share a fiat boundary." [] -xref: RO:0002150 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "connected to" xsd:string -property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string -property_value: RO:0001900 RO:0001901 -property_value: seeAlso "FMA:85972" xsd:string -domain: BFO:0000004 ! independent continuant -range: BFO:0000004 ! independent continuant -is_symmetric: true -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: contributes_to_morphology_of -name: contributes to morphology of -namespace: uberon -def: "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." [] -xref: RO:0002433 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: overlaps ! overlaps - -[Typedef] -id: dc-contributor -name: contributor -namespace: uberon -xref: http://purl.org/dc/terms/contributor -is_metadata_tag: true - -[Typedef] -id: dc-creator -name: creator -namespace: uberon -xref: http://purl.org/dc/elements/1.1/creator -is_metadata_tag: true - -[Typedef] -id: dc-description -name: description -namespace: uberon -xref: http://purl.org/dc/elements/1.1/description -is_metadata_tag: true - -[Typedef] -id: dc-title -name: title -namespace: uberon -xref: http://purl.org/dc/elements/1.1/title -is_metadata_tag: true - -[Typedef] -id: dcterms-date -name: date -namespace: uberon -xref: http://purl.org/dc/terms/date -is_metadata_tag: true - -[Typedef] -id: dcterms-license -name: license -namespace: uberon -xref: http://purl.org/dc/terms/license -is_metadata_tag: true - -[Typedef] -id: deep_to -name: deep to -namespace: uberon -xref: BSPO:0000107 - -[Typedef] -id: depiction -name: depiction -namespace: uberon -xref: http://xmlns.com/foaf/0.1/depiction -is_metadata_tag: true - -[Typedef] -id: developmentally_induced_by -name: developmentally induced by -namespace: uberon -def: "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" [] -xref: RO:0002256 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "induced by" xsd:string -property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string -property_value: IAO:0000119 "GO:0001759" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 -property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string -domain: UBERON:0000465 ! material anatomical entity -range: UBERON:0000465 ! material anatomical entity -is_a: RO:0002258 ! developmentally preceded by -inverse_of: RO:0002257 ! developmentally induces - -[Typedef] -id: developmentally_replaces -name: developmentally replaces -namespace: uberon -def: "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" [] -xref: RO:0002285 -property_value: editor_note "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "replaces" xsd:string -is_a: RO:0002258 ! developmentally preceded by - -[Typedef] -id: develops_from -name: develops from -namespace: uberon -def: "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" [] -comment: This is the transitive form of the develops from relation -xref: RO:0002202 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 -domain: BFO:0000004 ! independent continuant -range: BFO:0000004 ! independent continuant -is_transitive: true -is_a: has_developmental_contribution_from ! has developmental contribution from -is_a: RO:0002258 ! developmentally preceded by -inverse_of: develops_into ! develops into - -[Typedef] -id: develops_from_part_of -name: develops from part of -namespace: uberon -def: "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" [] -xref: RO:0002225 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -holds_over_chain: directly_develops_from part_of -is_a: develops_from ! develops from - -[Typedef] -id: develops_in -name: develops in -namespace: uberon -def: "x develops_in y if x is located in y whilst x is developing" [] -xref: RO:0002226 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "EHDAA2" xsd:string -property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string -domain: UBERON:0001062 ! anatomical entity -holds_over_chain: directly_develops_from located_in -is_a: RO:0002258 ! developmentally preceded by - -[Typedef] -id: develops_into -name: develops into -namespace: uberon -def: "inverse of develops from" [] -subset: RO:0002259 -xref: RO:0002203 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 -is_transitive: true -is_a: has_potential_to_develop_into ! has potential to develop into -is_a: RO:0002286 ! developmentally succeeded by -is_a: RO:0002388 ! has potential to directly develop into - -[Typedef] -id: directly_develops_from -name: directly develops from -namespace: uberon -def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] -comment: TODO - add child relations from DOS -synonym: "has developmental precursor" EXACT [] -xref: RO:0002207 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000119 "FBbt" xsd:string -property_value: RO:0002575 RO:0002202 -is_a: develops_from ! develops from -inverse_of: RO:0002210 ! directly develops into - -[Typedef] -id: directly_negatively_regulates -name: directly negatively regulates -namespace: external -def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -xref: RO:0002630 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string -property_value: RO:0004050 RO:0002578 -property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates" xsd:anyURI -is_a: directly_regulates ! directly regulates -is_a: negatively_regulates ! negatively regulates - -[Typedef] -id: directly_positively_regulates -name: directly positively regulates -namespace: external -def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -xref: RO:0002629 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string -property_value: RO:0004049 RO:0002578 -property_value: seeAlso "https://wiki.geneontology.org/Directly_positively_regulates" xsd:anyURI -is_a: directly_regulates ! directly regulates -is_a: positively_regulates ! positively regulates - -[Typedef] -id: directly_regulates -name: directly regulates -namespace: external -def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -xref: RO:0002578 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly regulates (processual)" xsd:string -property_value: RO:0002575 RO:0002211 -is_a: immediately_causally_upstream_of ! immediately causally upstream of -is_a: regulates ! regulates - -[Typedef] -id: distal_to -name: distal to -namespace: uberon -xref: BSPO:0000097 - -[Typedef] -id: distally_connected_to -name: distally connected to +id: directly_regulates +name: directly regulates +namespace: external +def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0002578 +is_a: immediately_causally_upstream_of ! immediately causally upstream of +is_a: regulates ! regulates + +[Typedef] +id: distally_connected_to +name: distally connected to namespace: uberon def: "x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] -is_a: connected_to ! connected to -is_a: proximal_to ! proximal to +is_a: RO:0002170 ! connected to is_a: transitively_distally_connected_to ! transitively distally connected to -inverse_of: proximally_connected_to ! proximally connected to - -[Typedef] -id: distalmost_part_of -name: distalmost part of -namespace: uberon -xref: BSPO:0001108 - -[Typedef] -id: dorsal_to -name: dorsal to -namespace: uberon -xref: BSPO:0000098 - -[Typedef] -id: drains -name: drains -namespace: uberon -def: "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." [] -xref: RO:0002179 -property_value: editor_note "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 -domain: UBERON:0001638 ! vein -is_a: connected_to ! connected to - -[Typedef] -id: editor_note -name: editor note -namespace: uberon -def: "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology." [] -xref: IAO:0000116 -property_value: IAO:0000111 "editor note" xsd:string -property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000117 "PERSON:Daniel Schober" xsd:string -property_value: IAO:0000119 "GROUP:OBI:" xsd:string -is_metadata_tag: true - -[Typedef] -id: ends -name: ends -namespace: uberon -def: "inverse of ends with" [] -subset: ro-eco -xref: RO:0002229 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: part_of ! part_of -is_a: RO:0002222 ! temporally related to -inverse_of: ends_with ! ends with [Typedef] id: ends_with name: ends with namespace: external -namespace: uberon def: "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002230 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "finished by" xsd:string is_transitive: true is_a: has_part ! has part is_a: RO:0002222 ! temporally related to -[Typedef] -id: existence_ends_during -name: existence ends during -namespace: uberon -def: "Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely." [https://orcid.org/0000-0002-6601-2165] -def: "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -synonym: "ceases_to_exist_during" EXACT [] -xref: RO:0002492 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_ends_during_or_before ! existence ends during or before -is_a: RO:0002490 ! existence overlaps -transitive_over: part_of ! part_of - -[Typedef] -id: existence_ends_during_or_before -name: existence ends during or before -namespace: uberon -def: "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -xref: RO:0002497 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -holds_over_chain: part_of existence_ends_during_or_before -holds_over_chain: RO:0002286 existence_ends_during_or_before -is_a: RO:0002487 ! relation between physical entity and a process or stage -transitive_over: part_of ! part_of -transitive_over: precedes ! precedes -transitive_over: simultaneous_with ! simultaneous with - -[Typedef] -id: existence_ends_with -name: existence ends with -namespace: uberon -def: "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -xref: RO:0002493 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_ends_during ! existence ends during - -[Typedef] -id: existence_starts_and_ends_during -name: existence starts and ends during -namespace: uberon -def: "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -synonym: "exists during" EXACT [] -xref: RO:0002491 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_ends_during ! existence ends during -is_a: existence_starts_during ! existence starts during - -[Typedef] -id: existence_starts_during -name: existence starts during -namespace: uberon -def: "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." [] -xref: RO:0002488 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_starts_during_or_after ! existence starts during or after -is_a: RO:0002490 ! existence overlaps -transitive_over: part_of ! part_of - -[Typedef] -id: existence_starts_during_or_after -name: existence starts during or after -namespace: uberon -def: "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -xref: RO:0002496 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -holds_over_chain: part_of existence_starts_during_or_after -holds_over_chain: RO:0002258 existence_starts_during_or_after -is_a: RO:0002487 ! relation between physical entity and a process or stage -transitive_over: part_of ! part_of -transitive_over: preceded_by ! preceded by -transitive_over: simultaneous_with ! simultaneous with - -[Typedef] -id: existence_starts_with -name: existence starts with -namespace: uberon -def: "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." [] -xref: RO:0002489 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_starts_during ! existence starts during - [Typedef] id: extends_fibers_into name: extends_fibers_into namespace: uberon def: "X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y" [https://orcid.org/0000-0002-7073-9172] -holds_over_chain: RO:0002100 RO:0013001 -is_symmetric: true -is_a: connected_to ! connected to +is_a: RO:0002170 ! connected to [Typedef] id: filtered_through @@ -18896,75 +18026,17 @@ namespace: uberon def: "Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity." [] comment: Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed -[Typedef] -id: functionally_related_to -name: functionally related to -namespace: uberon -def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] -xref: RO:0002328 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string - -[Typedef] -id: has_boundary -name: has 2D boundary -namespace: uberon -def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] -xref: RO:0002002 -property_value: editor_note "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string -property_value: editor_note "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string -property_value: IAO:0000112 "my body has 2D boundary the surface of my skin" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "has boundary" xsd:string -property_value: IAO:0000118 "has_2D_boundary" xsd:string -property_value: RO:0001900 RO:0001901 -domain: BFO:0000040 ! material entity -range: BFO:0000141 ! immaterial entity -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: has_branching_part -name: has branching part -namespace: uberon -def: "inverse of branching part of" [] -subset: ro-eco -subset: RO:0002259 -xref: RO:0002569 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_transitive: true -is_a: has_part ! has part -is_a: RO:0002375 ! in branching relationship with - [Typedef] id: has_component name: has component namespace: external -namespace: uberon def: "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] subset: ro-eco xref: RO:0002180 -property_value: editor_note "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency is_a: has_part ! has part -[Typedef] -id: has_developmental_contribution_from -name: has developmental contribution from -namespace: uberon -def: "x has developmental contribution from y iff x has some part z such that z develops from y" [] -xref: RO:0002254 -property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: UBERON:0001062 ! anatomical entity -range: UBERON:0001062 ! anatomical entity -holds_over_chain: has_part develops_from -is_a: RO:0002258 ! developmentally preceded by -inverse_of: RO:0002255 ! developmentally contributes to - [Typedef] id: has_end_location name: has end location @@ -18972,9 +18044,6 @@ namespace: external def: "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" [] subset: ro-eco xref: RO:0002232 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "ends with process that occurs in" xsd:string domain: BFO:0000015 ! process range: BFO:0000004 ! independent continuant holds_over_chain: ends_with occurs_in @@ -18998,14 +18067,11 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002233 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "consumes" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Has_input" xsd:anyURI domain: BFO:0000015 ! process holds_over_chain: starts_with has_input is_a: has_participant ! has participant -inverse_of: input_of ! input of +inverse_of: RO:0002352 ! input of [Typedef] id: has_low_plasma_membrane_amount @@ -19015,52 +18081,6 @@ property_value: term_tracker_item https://github.com/obophenotype/cell-ontology/ is_obsolete: true replaced_by: RO:0015016 -[Typedef] -id: has_member -name: has member -namespace: uberon -def: "has member is a mereological relation between a collection and an item." [] -xref: RO:0002351 -property_value: IAO:0000119 "SIO" xsd:string -property_value: RO:0001900 RO:0001901 -is_a: has_part ! has part - -[Typedef] -id: has_muscle_antagonist -name: has muscle antagonist -namespace: uberon -def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] -xref: RO:0002568 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "Wikipedia:Antagonist_(muscle)" xsd:string -is_a: RO:0002567 ! biomechanically related to - -[Typedef] -id: has_muscle_insertion -name: has muscle insertion -namespace: uberon -def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] -xref: RO:0002373 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string -property_value: seeAlso http://dbpedia.org/property/insertion -domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} ! anatomical structure -is_a: attaches_to ! attached to -is_a: RO:0002567 ! biomechanically related to - -[Typedef] -id: has_muscle_origin -name: has muscle origin -namespace: uberon -def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] -xref: RO:0002372 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string -property_value: seeAlso http://dbpedia.org/property/origin -domain: UBERON:0000061 {comment="We need to import uberon muscle to create a stricter domain constraint"} ! anatomical structure -is_a: attaches_to ! attached to -is_a: RO:0002567 ! biomechanically related to - [Typedef] id: has_negative_regulatory_component_activity name: has negative regulatory component activity @@ -19078,13 +18098,9 @@ id: has_ontology_root_term name: has ontology root term name: preferred_root namespace: external -namespace: uberon def: "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root." [] xref: IAO:0000700 -property_value: IAO:0000111 "has ontology root term" xsd:string -property_value: IAO:0000117 "Nicolas Matentzoglu" xsd:string is_metadata_tag: true -is_class_level: true [Typedef] id: has_output @@ -19096,9 +18112,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002234 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "produces" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Has_output" xsd:anyURI holds_over_chain: ends_with has_output is_a: has_participant ! has participant @@ -19110,62 +18123,29 @@ name: has part name: has_part namespace: external namespace: quality -namespace: uberon def: "a core relation that holds between a whole and its part" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000051 -property_value: editor_note "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string -property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string -property_value: IAO:0000111 "has part" xsd:string -property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string -property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string -property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string -property_value: IAO:0000118 "has_part" xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string is_transitive: true is_a: overlaps ! overlaps [Typedef] -id: has_participant -name: has participant -namespace: external -def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] -xref: RO:0000057 -property_value: editor_note "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string -property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string -property_value: IAO:0000111 "has participant" xsd:string -property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string -property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string -property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string -property_value: IAO:0000118 "has_participant" xsd:string -domain: BFO:0000003 ! occurrent -range: BFO:0000002 ! continuant -holds_over_chain: has_part has_participant - -[Typedef] -id: has_potential_to_develop_into -name: has potential to develop into -namespace: uberon -def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] -xref: RO:0002387 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: RO:0002384 ! has developmental potential involving - -[Typedef] -id: has_potential_to_developmentally_contribute_to -name: has potential to developmentally contribute to -namespace: uberon -def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] -xref: RO:0002385 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: RO:0002384 ! has developmental potential involving - -[Typedef] +id: has_participant +name: has participant +namespace: external +def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] +xref: RO:0000057 +property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string +domain: BFO:0000003 ! occurrent +range: BFO:0000002 ! continuant +holds_over_chain: has_part has_participant + +[Typedef] id: has_primary_input name: has primary input namespace: external @@ -19200,17 +18180,6 @@ is_a: has_primary_input_or_output ! has primary input or output created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z -[Typedef] -id: has_quality -name: has quality -namespace: uberon -def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] -xref: RO:0000086 -property_value: editor_note "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string -property_value: IAO:0000112 "this apple has quality this red color" xsd:string -property_value: IAO:0000118 "has_quality" xsd:string -is_a: bearer_of ! bearer of - [Typedef] id: has_regulatory_component_activity name: has regulatory component activity @@ -19222,24 +18191,6 @@ is_a: RO:0002017 ! has component activity created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z -[Typedef] -id: has_skeleton -name: has skeleton -namespace: uberon -def: "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." [] -xref: RO:0002551 -property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "has supporting framework" xsd:string -property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string -domain: UBERON:0000061 ! anatomical structure -domain: UBERON:0000475 ! organism subdivision -range: UBERON:0000465 {IAO:0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} ! material anatomical entity -range: UBERON:0010912 ! subdivision of skeleton -is_a: has_part ! has part -inverse_of: skeleton_of ! skeleton of -is_asymmetric: true - [Typedef] id: has_small_molecule_activator name: has small molecule activator @@ -19258,9 +18209,6 @@ namespace: external def: "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y" [] subset: ro-eco xref: RO:0002231 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "starts with process that occurs in" xsd:string domain: BFO:0000015 ! process range: BFO:0000004 ! independent continuant holds_over_chain: starts_with occurs_in @@ -19275,9 +18223,8 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002339 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of [Typedef] id: has_target_start_location @@ -19288,41 +18235,14 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002338 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in -transitive_over: part_of ! part_of - -[Typedef] -id: homologous_to -name: shares ancestor with -namespace: uberon -def: "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." [] -comment: VBO calls this homologous_to -xref: RO:0002158 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000232 "Consider obsoleting and merging with child relation, 'in homology relationship with'" xsd:string -is_symmetric: true -is_transitive: true -is_a: RO:0002320 ! evolutionarily related to - -[Typedef] -id: immediate_transformation_of -name: immediate transformation of -namespace: uberon -def: "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" [] -xref: RO:0002495 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0002575 RO:0002494 -is_a: directly_develops_from ! directly develops from -is_a: transformation_of ! transformation of +transitive_over: part_of ! part of [Typedef] id: immediately_causally_downstream_of name: immediately causally downstream of namespace: external xref: RO:0002405 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of ! causally downstream of is_a: immediately_preceded_by ! immediately preceded by inverse_of: immediately_causally_upstream_of ! immediately causally upstream of @@ -19333,26 +18253,15 @@ name: immediately causally upstream of namespace: external def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] xref: RO:0002412 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: immediately_precedes ! immediately precedes -[Typedef] -id: immediately_deep_to -name: immediately deep to -namespace: uberon -xref: BSPO:0001107 - [Typedef] id: immediately_preceded_by name: immediately preceded by namespace: external -namespace: uberon comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) xref: RO:0002087 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000118 "starts_at_end_of" xsd:string holds_over_chain: starts_with ends_with is_a: preceded_by ! preceded by inverse_of: immediately_precedes ! immediately precedes @@ -19364,228 +18273,22 @@ namespace: external comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) subset: ro-eco xref: RO:0002090 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "ends_at_start_of" xsd:string -property_value: IAO:0000118 "meets" xsd:string -property_value: RO:0002575 BFO:0000063 holds_over_chain: ends_with starts_with is_a: precedes ! precedes -[Typedef] -id: immediately_superficial_to -name: immediately superficial to -namespace: uberon -xref: BSPO:0015014 - -[Typedef] -id: in_anterior_side_of -name: in anterior side of -namespace: uberon -xref: BSPO:0000123 - -[Typedef] -id: in_deep_part_of -name: in deep part of -namespace: uberon -xref: BSPO:0001101 - -[Typedef] -id: in_dorsal_side_of -name: in dorsal side of -namespace: uberon -xref: BSPO:0015101 - -[Typedef] -id: in_lateral_side_of -name: in lateral side of -namespace: uberon -xref: BSPO:0000126 - -[Typedef] -id: in_left_side_of -name: in left side of -namespace: uberon -xref: BSPO:0000120 - -[Typedef] -id: in_posterior_side_of -name: in posterior side of -namespace: uberon -xref: BSPO:0000122 - -[Typedef] -id: in_proximal_side_of -name: in proximal side of -namespace: uberon -xref: BSPO:0000124 - -[Typedef] -id: in_right_side_of -name: in right side of -namespace: uberon -xref: BSPO:0000121 - -[Typedef] -id: in_superficial_part_of -name: in superficial part of -namespace: uberon -xref: BSPO:0001100 - -[Typedef] -id: in_taxon -name: in taxon -namespace: uberon -def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." [] -comment: Connects a biological entity to its taxon of origin. -subset: ro-eco -xref: RO:0002162 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9227-417X -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -holds_over_chain: attaches_to in_taxon -holds_over_chain: capable_of in_taxon -holds_over_chain: connected_to in_taxon -holds_over_chain: connects in_taxon -holds_over_chain: continuous_with in_taxon -holds_over_chain: developmentally_induced_by in_taxon -holds_over_chain: develops_from in_taxon -holds_over_chain: develops_from_part_of in_taxon -holds_over_chain: existence_ends_during in_taxon -holds_over_chain: existence_starts_during in_taxon -holds_over_chain: extends_fibers_into in_taxon -holds_over_chain: has_developmental_contribution_from in_taxon -holds_over_chain: has_part in_taxon -holds_over_chain: has_potential_to_develop_into in_taxon -holds_over_chain: innervated_by in_taxon -holds_over_chain: overlaps in_taxon -holds_over_chain: part_of in_taxon -holds_over_chain: produced_by in_taxon -holds_over_chain: produces in_taxon -holds_over_chain: results_in_developmental_progression_of in_taxon -holds_over_chain: RO:0002206 in_taxon -holds_over_chain: supplies in_taxon -is_a: RO:0002320 ! evolutionarily related to - [Typedef] id: indirectly_supplies name: indirectly_supplies namespace: uberon def: "a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s." [] -property_value: editor_note "add to RO" xsd:string -holds_over_chain: has_branching_part indirectly_supplies -holds_over_chain: has_branching_part supplies -is_transitive: true - -[Typedef] -id: innervated_by -name: innervated_by -namespace: uberon -xref: RO:0002005 -property_value: http://purl.org/spar/cito/citesAsAuthority "http://www.ncbi.nlm.nih.gov/pubmed/22402613" xsd:anyURI -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -domain: UBERON:0000061 ! anatomical structure -inverse_of: innervates ! innervates -transitive_over: branching_part_of ! branching part of - -[Typedef] -id: innervates -name: innervates -namespace: uberon -def: "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." [] -xref: RO:0002134 -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 -transitive_over: part_of ! part_of -expand_expression_to: "RO_0002132 some (GO_0043005 that (RO_0002131 some (GO_0045202 that BFO_0000050 some Y?)))" [] - -[Typedef] -id: input_of -name: input of -namespace: uberon -def: "inverse of has input" [] -subset: ro-eco -subset: RO:0002259 -xref: RO:0002352 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: functionally_related_to ! functionally related to -is_a: participates_in ! participates in - -[Typedef] -id: intersects_midsagittal_plane_of -name: intersects midsagittal plane of -namespace: uberon -xref: BSPO:0005001 +property_value: IAO:0000116 "add to RO" xsd:string +holds_over_chain: RO:0002569 indirectly_supplies [Typedef] id: layer_part_of name: layer part of namespace: uberon -is_a: part_of ! part_of - -[Typedef] -id: located_in -name: located in -namespace: uberon -def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -xref: RO:0001025 -property_value: editor_note "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" xsd:string -property_value: editor_note "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:located_in" xsd:string -property_value: IAO:0000111 "located in" xsd:string -property_value: IAO:0000112 "my brain is located in my head" xsd:string -property_value: IAO:0000112 "this rat is located in this cage" xsd:string -property_value: IAO:0000118 "located_in" xsd:string -property_value: RO:0001900 RO:0001901 -property_value: seeAlso "https://wiki.geneontology.org/Located_in" xsd:anyURI -domain: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant -range: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant -is_transitive: true -transitive_over: part_of ! part_of - -[Typedef] -id: location_of -name: location of -namespace: uberon -def: "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" [] -xref: RO:0001015 -property_value: editor_note "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: IAO:0000111 "is location of" xsd:string -property_value: IAO:0000112 "my head is the location of my brain" xsd:string -property_value: IAO:0000112 "this cage is the location of this rat" xsd:string -property_value: IAO:0000118 "location_of" xsd:string -property_value: RO:0001900 RO:0001901 -is_transitive: true -inverse_of: located_in ! located in - -[Typedef] -id: lumen_of -name: lumen of -namespace: uberon -def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] -subset: ro-eco -xref: RO:0002571 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 https://orcid.org/0000-0002-6601-2165 -range: BFO:0000040 ! material entity -is_a: part_of ! part_of - -[Typedef] -id: luminal_space_of -name: luminal space of -namespace: uberon -def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" [] -subset: ro-eco -xref: RO:0002572 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: BFO:0000141 ! immaterial entity -is_a: lumen_of ! lumen of +is_a: part_of ! part of [Typedef] id: negatively_regulated_by @@ -19594,7 +18297,6 @@ namespace: external def: "inverse of negatively regulates" [] subset: RO:0002259 xref: RO:0002335 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -19606,9 +18308,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002212 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002211 holds_over_chain: ends_with negatively_regulates is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect @@ -19621,30 +18320,11 @@ name: negatively regulates characteristic namespace: gene_ontology def: "A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C." [] xref: RO:0019002 -property_value: dc-contributor https://orcid.org/0000-0002-8688-6599 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 holds_over_chain: negatively_regulates positively_regulates_characteristic holds_over_chain: positively_regulates negatively_regulates_characteristic is_a: regulates_characteristic ! regulates characteristic -[Typedef] -id: never_in_taxon -name: never in taxon -name: never_in_taxon -namespace: uberon -def: "S never_in_taxon T iff: S SubClassOf in_taxon only not T." [PMID:20973947] -def: "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL." [] -xref: RO:0002161 -property_value: IAO:0000112 "tooth SubClassOf 'never in taxon' value 'Aves'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 -property_value: OMO:0002000 "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" xsd:string -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -expand_assertion_to: "Class: EquivalentTo: ?X and (RO_0002162 some ?Y)" [] -expand_assertion_to: "Class: ?X DisjointWith: RO_0002162 some ?Y " [] -is_metadata_tag: true -is_class_level: true - [Typedef] id: occurs_in name: occurs in @@ -19655,64 +18335,38 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000066 -property_value: IAO:0000111 "occurs in" xsd:string -property_value: IAO:0000118 "occurs_in" xsd:string -property_value: IAO:0000118 "unfolds in" xsd:string -property_value: IAO:0000118 "unfolds_in" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl property_value: seeAlso "https://wiki.geneontology.org/Occurs_in" xsd:anyURI domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant holds_over_chain: part_of occurs_in -inverse_of: contains_process ! contains process -transitive_over: part_of ! part_of - -[Typedef] -id: only_in_taxon -name: only in taxon -namespace: uberon -def: "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." [] -xref: RO:0002160 -property_value: editor_note "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" xsd:string -property_value: IAO:0000112 "lactation SubClassOf 'only in taxon' some 'Mammalia'" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -is_a: in_taxon ! in taxon +inverse_of: BFO:0000067 ! contains process +transitive_over: part_of ! part of [Typedef] id: output_of name: output of namespace: external -namespace: uberon def: "inverse of has output" [] subset: ro-eco subset: RO:0002259 xref: RO:0002353 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: functionally_related_to ! functionally related to is_a: participates_in ! participates in +is_a: RO:0002328 ! functionally related to [Typedef] id: overlaps name: overlaps namespace: external -namespace: uberon def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002131 -property_value: IAO:0000114 IAO:0000125 -property_value: RO:0001900 RO:0001901 holds_over_chain: has_part overlaps -holds_over_chain: has_part part_of {RO:0002582="true"} holds_over_chain: part_of part_of is_symmetric: true is_a: RO:0002323 ! mereotopologically related to -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] [Typedef] @@ -19721,29 +18375,15 @@ name: part of name: part_of namespace: external namespace: quality -namespace: uberon def: "a core relation that holds between a part and its whole" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000050 -property_value: editor_note "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string -property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string -property_value: IAO:0000111 "is part of" xsd:string -property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string -property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string -property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string -property_value: IAO:0000118 "part_of" xsd:string -property_value: RO:0001900 RO:0001901 -property_value: RO:0040042 BFO:0000002 -property_value: RO:0040042 BFO:0000003 -property_value: RO:0040042 BFO:0000004 -property_value: RO:0040042 BFO:0000017 -property_value: RO:0040042 BFO:0000019 -property_value: RO:0040042 BFO:0000020 -property_value: RO:0040042 BFO:0000031 +property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string @@ -19756,14 +18396,8 @@ inverse_of: has_part ! has part id: participates_in name: participates in namespace: external -namespace: uberon def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] xref: RO:0000056 -property_value: IAO:0000111 "participates in" xsd:string -property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string -property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string -property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string -property_value: IAO:0000118 "participates_in" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000003 ! occurrent inverse_of: has_participant ! has participant @@ -19775,7 +18409,6 @@ namespace: external def: "inverse of positively regulates" [] subset: RO:0002259 xref: RO:0002336 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -19787,10 +18420,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002213 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "positively regulates (process to process)" xsd:string -property_value: RO:0004049 RO:0002211 holds_over_chain: ends_with positively_regulates holds_over_chain: negatively_regulates negatively_regulates is_transitive: true @@ -19804,49 +18433,25 @@ name: positively regulates characteristic namespace: gene_ontology def: "A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C." [] xref: RO:0019001 -property_value: dc-contributor https://orcid.org/0000-0002-8688-6599 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 holds_over_chain: positively_regulates positively_regulates_characteristic is_a: regulates_characteristic ! regulates characteristic -[Typedef] -id: postaxialmost_part_of -name: postaxialmost part of -namespace: uberon -xref: BSPO:0001115 - -[Typedef] -id: posterior_to -name: posterior to -namespace: uberon -xref: BSPO:0000099 - [Typedef] id: posteriorly_connected_to name: posteriorly connected to namespace: uberon def: "x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] -is_a: anterior_to ! anterior to -is_a: connected_to ! connected to - -[Typedef] -id: preaxialmost_part_of -name: preaxialmost part of -namespace: uberon -xref: BSPO:0001113 +is_a: RO:0002170 ! connected to [Typedef] id: preceded_by name: preceded by namespace: external -namespace: uberon def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000062 -property_value: editor_note "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string -property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string -property_value: IAO:0000111 "preceded by" xsd:string -property_value: IAO:0000118 "is preceded by" xsd:string -property_value: IAO:0000118 "preceded_by" xsd:string +property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent holds_over_chain: part_of preceded_by @@ -19858,53 +18463,30 @@ inverse_of: precedes ! precedes id: precedes name: precedes namespace: external -namespace: uberon def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000063 -property_value: IAO:0000111 "precedes" xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent holds_over_chain: part_of precedes is_transitive: true is_a: RO:0002222 ! temporally related to -[Typedef] -id: present_in_taxon -name: present in taxon -name: present_in_taxon -namespace: uberon -def: "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S" [] -def: "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S." [https://orcid.org/0000-0002-6601-2165] -comment: The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology. -synonym: "applicable for taxon" EXACT [] -xref: RO:0002175 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: OMO:0002000 "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" xsd:string -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -is_metadata_tag: true -is_class_level: true - [Typedef] id: process_has_causal_agent name: process has causal agent namespace: external def: "Inverse of 'causal agent in process'" [] xref: RO:0002608 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_a: RO:0002410 ! causally related to [Typedef] id: produced_by name: produced by namespace: external -namespace: uberon def: "a produced_by b iff some process that occurs_in b has_output a." [] subset: ro-eco xref: RO:0003001 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity @@ -19912,13 +18494,10 @@ range: BFO:0000040 ! material entity id: produces name: produces namespace: external -namespace: uberon def: "a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix." [] comment: Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. subset: ro-eco xref: RO:0003000 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity inverse_of: produced_by ! produced by @@ -19928,27 +18507,14 @@ id: protects name: protects namespace: uberon -[Typedef] -id: proximal_to -name: proximal to -namespace: uberon -xref: BSPO:0000100 - [Typedef] id: proximally_connected_to name: proximally connected to namespace: uberon def: "x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] -is_a: connected_to ! connected to -is_a: distal_to ! distal to +is_a: RO:0002170 ! connected to is_a: transitively_proximally_connected_to ! transitively proximally connected to -[Typedef] -id: proximalmost_part_of -name: proximalmost part of -namespace: uberon -xref: BSPO:0001106 - [Typedef] id: regulated_by name: regulated by @@ -19956,8 +18522,6 @@ namespace: external def: "inverse of regulates" [] subset: RO:0002259 xref: RO:0002334 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000589 "regulated by (processual)" xsd:string domain: BFO:0000015 ! process range: BFO:0000015 ! process is_transitive: true @@ -19972,14 +18536,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 -property_value: IAO:0000117 https://orcid.org/0000-0001-7476-6306 -property_value: IAO:0000117 https://orcid.org/0000-0002-3837-8864 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GO" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string -property_value: IAO:0000589 "regulates (processual)" xsd:string -property_value: IAO:0000600 "false" xsd:boolean domain: BFO:0000015 ! process range: BFO:0000015 ! process holds_over_chain: directly_regulates directly_regulates @@ -19995,7 +18551,7 @@ name: regulates characteristic namespace: gene_ontology def: "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C." [] xref: RO:0019000 -property_value: dc-contributor https://orcid.org/0000-0002-8688-6599 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 domain: BFO:0000015 ! process range: PATO:0000001 ! quality holds_over_chain: regulates regulates_characteristic @@ -20007,13 +18563,9 @@ name: regulates levels of namespace: external def: "p regulates levels of c if p regulates some amount (PATO:0000070) of c" [] xref: RO:0002332 -property_value: IAO:0000112 "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "regulates levels of (process to entity)" xsd:string domain: BFO:0000015 ! process range: BFO:0000040 ! material entity -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to [Typedef] id: results_in_acquisition_of_features_of @@ -20024,9 +18576,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002315 -property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string range: UBERON:0000061 ! anatomical structure is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -20061,10 +18610,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002296 -property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "http://www.geneontology.org/GO.doc.development.shtml" xsd:anyURI is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -20074,9 +18619,7 @@ name: results in developmental progression of namespace: external def: "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." [] xref: RO:0002295 -property_value: editor_note "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000116 "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string property_value: seeAlso Ontology:extensions domain: GO:0008150 ! biological_process range: UBERON:0001062 ! anatomical entity @@ -20108,16 +18651,12 @@ is_a: has_participant ! has participant [Typedef] id: results_in_formation_of name: results in formation of +name: results in formation of anatomical entity namespace: external subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002297 -property_value: IAO:0000112 "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." xsd:string -property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of inverse_of: RO:0002354 ! formed as result of @@ -20139,8 +18678,6 @@ id: results_in_growth_of name: results in growth of namespace: external xref: RO:0002343 -property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -20153,11 +18690,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002299 -property_value: IAO:0000112 " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" xsd:string -property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -20170,11 +18702,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002298 -property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." xsd:string -property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -20187,8 +18714,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002565 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure [Typedef] @@ -20207,7 +18732,6 @@ namespace: external def: "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002342 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in is_a: RO:0002021 ! occurs across @@ -20217,7 +18741,6 @@ name: results in transport along namespace: external def: "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " [] xref: RO:0002341 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002337 ! related via localization to [Typedef] @@ -20225,36 +18748,13 @@ id: results_in_transport_to_from_or_in name: results in transport to from or in namespace: external xref: RO:0002344 -property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002337 ! related via localization to -[Typedef] -id: seeAlso -name: see also -namespace: uberon -xref: http://www.w3.org/2000/01/rdf-schema#seeAlso -is_metadata_tag: true - [Typedef] id: sexually_homologous_to name: sexually_homologous_to namespace: uberon -is_a: homologous_to ! shares ancestor with - -[Typedef] -id: simultaneous_with -name: simultaneous with -namespace: uberon -def: "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." [] -comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) -subset: ro-eco -xref: RO:0002082 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -is_symmetric: true -is_transitive: true -is_a: RO:0002081 ! before or simultaneous with +is_a: RO:0002158 ! shares ancestor with [Typedef] id: site_of @@ -20263,46 +18763,13 @@ namespace: uberon def: "c site_of p if c is the bearer of a disposition that is realized by a process that has p as part." [] synonym: "capable_of_has_part" RELATED [] -[Typedef] -id: skeleton_of -name: skeleton of -namespace: uberon -def: "inverse of has skeleton" [] -subset: RO:0002259 -xref: RO:0002576 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: UBERON:0000061 ! anatomical structure -range: UBERON:0000061 ! anatomical structure -is_a: part_of ! part_of - -[Typedef] -id: starts -name: starts -namespace: uberon -def: "inverse of starts with" [] -subset: ro-eco -xref: RO:0002223 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "Allen" xsd:string -is_a: part_of ! part_of -is_a: RO:0002222 ! temporally related to -inverse_of: starts_with ! starts with - [Typedef] id: starts_with name: starts with namespace: external -namespace: uberon def: "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002224 -property_value: IAO:0000112 "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "started by" xsd:string is_transitive: true is_a: has_part ! has part is_a: RO:0002222 ! temporally related to @@ -20313,140 +18780,36 @@ name: subdivision of namespace: uberon comment: placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B -[Typedef] -id: superficial_to -name: superficial to -namespace: uberon -xref: BSPO:0000108 - -[Typedef] -id: supplies -name: supplies -namespace: uberon -def: "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." [] -xref: RO:0002178 -property_value: editor_note "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 -domain: UBERON:0001637 ! artery -is_a: connected_to ! connected to - -[Typedef] -id: surrounded_by -name: surrounded by -namespace: uberon -def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" [] -xref: RO:0002219 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0001900 RO:0001901 -is_a: adjacent_to ! adjacent to -inverse_of: surrounds ! surrounds - -[Typedef] -id: surrounds -name: surrounds -namespace: uberon -def: "inverse of surrounded by" [] -subset: RO:0002259 -xref: RO:0002221 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0001900 RO:0001901 -is_a: adjacent_to ! adjacent to - -[Typedef] -id: synapsed_by -name: synapsed by -namespace: uberon -def: "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " [] -xref: RO:0002103 -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 -is_a: RO:0002485 ! receives input from -inverse_of: RO:0002120 ! synapsed to -expand_expression_to: "BFO_0000051 some (GO_0045211 that part_of some (GO_0045202 that has_part some (GO_0042734 that BFO_0000050 some Y?)))" [] - [Typedef] id: term_tracker_item name: term tracker item namespace: external -namespace: uberon def: "An IRI or similar locator for a request or discussion of an ontology term." [] comment: The 'tracker item' can associate a tracker with a specific ontology term. xref: IAO:0000233 -property_value: IAO:0000111 "term tracker item" xsd:string -property_value: IAO:0000112 "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" xsd:string -property_value: IAO:0000119 "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" xsd:string is_metadata_tag: true -is_class_level: true - -[Typedef] -id: transformation_of -name: transformation of -namespace: uberon -def: "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" [] -xref: RO:0002494 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_transitive: true -is_a: develops_from ! develops from [Typedef] id: transitively_anteriorly_connected_to name: transitively anteriorly connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI -is_transitive: true [Typedef] id: transitively_distally_connected_to name: transitively distally connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI -is_transitive: true [Typedef] id: transitively_proximally_connected_to name: transitively proximally connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI -is_transitive: true - -[Typedef] -id: tributary_of -name: tributary of -namespace: uberon -def: "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." [] -subset: ro-eco -xref: RO:0002376 -property_value: IAO:0000112 "Deschutes River tributary_of Columbia River" xsd:string -property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "drains into" xsd:string -property_value: IAO:0000118 "drains to" xsd:string -property_value: IAO:0000118 "tributary channel of" xsd:string -property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Tributary" xsd:string -property_value: IAO:0000119 "http://www.medindia.net/glossary/venous_tributary.htm" xsd:string -property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" xsd:anyURI -property_value: seeAlso http://dbpedia.org/ontology/drainsTo -property_value: seeAlso "http://en.wikipedia.org/wiki/Tributary" xsd:anyURI -is_a: connected_to ! connected to -is_a: RO:0002375 ! in branching relationship with [Typedef] id: trunk_part_of name: trunk_part_of namespace: uberon -is_a: part_of ! part_of - -[Typedef] -id: ventral_to -name: ventral to -namespace: uberon -xref: BSPO:0000102 +is_a: part_of ! part of diff --git a/src/ontology/subsets/kidney_upper_slim.owl b/src/ontology/subsets/kidney_upper_slim.owl index a3abeb5aa..4dc7611c9 100644 --- a/src/ontology/subsets/kidney_upper_slim.owl +++ b/src/ontology/subsets/kidney_upper_slim.owl @@ -10,28 +10,21 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" - xmlns:cito="http://purl.org/spar/cito/" xmlns:core="http://purl.obolibrary.org/obo/uberon/core#" xmlns:foaf="http://xmlns.com/foaf/0.1/" - xmlns:obo2="http://www.geneontology.org/formats/oboInOwl#http://purl.obolibrary.org/obo/" xmlns:pato="http://purl.obolibrary.org/obo/pato#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" - xmlns:skos="http://www.w3.org/2004/02/skos/core#" xmlns:swrl="http://www.w3.org/2003/11/swrl#" - xmlns:sssom="https://w3id.org/sssom/" - xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#" xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:terms="http://purl.org/dc/terms/" - xmlns:vocab="https://w3id.org/semapv/vocab/" - xmlns:terms1="http://www.geneontology.org/formats/oboInOwl#http://purl.org/dc/terms/" xmlns:uberon="http://purl.obolibrary.org/obo/uberon#" xmlns:ubprop="http://purl.obolibrary.org/obo/ubprop#" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - 2024-02-13 + + 2024-04-05 @@ -55,29 +48,9 @@ - - - - - - - - - - - - - - - - - - - definition - The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith @@ -99,8 +72,6 @@ We don't have definitions of 'meaning' or 'expression' Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition @@ -110,72 +81,28 @@ We also have the outstanding issue of how to aim different definitions to differ - editor note - An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obofoundry.org/obo/obi> - IAO:0000116 - uberon - editor_note - true - editor_note - editor note editor note - - - - - - - - - - - - - - - - - - - has obsolescence reason Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. - PERSON:Alan Ruttenberg - PERSON:Melanie Courtot has obsolescence reason - - - - - - - term tracker item - the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ - An IRI or similar locator for a request or discussion of an ontology term. - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg IAO:0000233 external - uberon term_tracker_item - true true term_tracker_item The 'tracker item' can associate a tracker with a specific ontology term. @@ -185,63 +112,23 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - - expand expression to - ObjectProperty: RO_0002104 -Label: has plasma membrane part -Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" - A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones - Chris Mungall expand expression to expand expression to - - - - - - - - - - - - - - - - - - - - - - - - - has ontology root term Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. - Nicolas Matentzoglu IAO:0000700 external - uberon has_ontology_root_term - true true has_ontology_root_term has ontology root term @@ -251,20 +138,10 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - - - - - - - term replaced by - Use on obsolete terms, relating the term to another term that can be used as a substitute - Person:Alan Ruttenberg - Person:Alan Ruttenberg Add as annotation triples in the granting ontology term replaced by term replaced by @@ -275,24 +152,6 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - 'part disjoint with' 'defined by construct' """ - PREFIX owl: <http://www.w3.org/2002/07/owl#> - PREFIX : <http://example.org/ - CONSTRUCT { - [ - a owl:Restriction ; - owl:onProperty :part_of ; - owl:someValuesFrom ?a ; - owl:disjointWith [ - a owl:Restriction ; - owl:onProperty :part_of ; - owl:someValuesFrom ?b - ] - ] - } - WHERE { - ?a :part_disjoint_with ?b . - } Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. @@ -305,11 +164,9 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation) A synonym type for describing abbreviations or initalisms - 2023-03-03 abbreviation @@ -335,11 +192,9 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form) A synonym type for describing pluralization synonyms - 2023-03-03 plural form @@ -354,23 +209,10 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - - - - - - - tooth SubClassOf 'never in taxon' value 'Aves' - S never_in_taxon T iff: S SubClassOf in_taxon only not T. x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL. - - - - Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: ?X and (RO_0002162 some ?Y) - Class: ?X DisjointWith: RO_0002162 some ?Y PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> @@ -394,34 +236,9 @@ CONSTRUCT { WHERE { ?x never_in_taxon: ?taxon . } - RO:0002161 - uberon - never_in_taxon - true - true - never_in_taxon never in taxon - never_in_taxon - - - - S never_in_taxon T iff: S SubClassOf in_taxon only not T. - PMID:20973947 - - - - - - - - - - - - - @@ -429,9 +246,6 @@ WHERE { S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S - S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S. - - PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> @@ -456,24 +270,10 @@ WHERE { )) as ?witness) BIND(CONCAT(STR(?x), " in taxon ", STR(?taxon)) AS ?label) } - RO:0002175 - applicable for taxon - uberon - present_in_taxon - true - true - present_in_taxon The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology. present in taxon - present_in_taxon - - - - S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S. - https://orcid.org/0000-0002-6601-2165 - @@ -485,60 +285,6 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL - is a defining property chain axiom - - - - - - - - If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. - is a defining property chain axiom where second argument is reflexive - - - - - - - - - - - - - - - - - - - - - - @@ -549,126 +295,6 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -927,12 +553,6 @@ WHERE { - - - - - - @@ -1363,14 +983,7 @@ WHERE { - - http://purl.org/dc/elements/1.1/creator - uberon - dc-creator - true - dc-creator - creator - + @@ -1382,14 +995,7 @@ WHERE { - - http://purl.org/dc/elements/1.1/description - uberon - dc-description - true - dc-description - description - + @@ -1401,71 +1007,25 @@ WHERE { - - http://purl.org/dc/elements/1.1/title - uberon - dc-title - true - dc-title - title - + - - http://purl.org/dc/terms/contributor - uberon - dc-contributor - true - dc-contributor - contributor - - - - - - - - - - - - - + - - http://purl.org/dc/terms/date - uberon - dcterms-date - true - dcterms-date - date - + - - http://purl.org/dc/terms/license - uberon - dcterms-license - true - dcterms-license - license - - - - - - - + @@ -1475,18 +1035,6 @@ WHERE { - - - - - - - - - - - - @@ -1503,18 +1051,6 @@ WHERE { - - - - - - - - - - - - @@ -1523,18 +1059,6 @@ WHERE { - - - - - - - - - - - - @@ -1551,66 +1075,6 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -1623,7 +1087,6 @@ WHERE { An alternative label for a class or property which has a more general meaning than the preferred name/primary label. - https://github.com/information-artifact-ontology/ontology-metadata/issues/18 has broad synonym has_broad_synonym @@ -1644,7 +1107,6 @@ WHERE { An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. - https://github.com/information-artifact-ontology/ontology-metadata/issues/20 has exact synonym has_exact_synonym @@ -1657,7 +1119,6 @@ WHERE { An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. - https://github.com/information-artifact-ontology/ontology-metadata/issues/19 has narrow synonym has_narrow_synonym @@ -1678,7 +1139,6 @@ WHERE { An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. - https://github.com/information-artifact-ontology/ontology-metadata/issues/21 has related synonym has_related_synonym @@ -1687,12 +1147,6 @@ WHERE { - - - - - - @@ -1717,30 +1171,6 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - - - @@ -1753,72 +1183,12 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -1833,60 +1203,6 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -1903,9 +1219,6 @@ WHERE { http://www.w3.org/2000/01/rdf-schema#seeAlso - uberon - seeAlso - true seeAlso see also @@ -1918,63 +1231,9 @@ WHERE { - - - - - - - - http://xmlns.com/foaf/0.1/depiction - uberon - depiction - true - depiction - depiction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + @@ -1995,29 +1254,15 @@ WHERE { - is part of - my brain is part of my body (continuant parthood, two material entities) - my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) - this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. - part_of - - - - - - - - BFO:0000050 external quality - uberon part_of @@ -2040,22 +1285,15 @@ A continuant cannot be part of an occurrent: use 'participates in'. An - has part - my body has part my brain (continuant parthood, two material entities) - my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) - this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. - has_part - BFO:0000051 external quality - uberon has_part @@ -2080,15 +1318,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. - preceded by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. - is preceded by - preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 external - uberon preceded_by preceded_by @@ -2109,11 +1342,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. - precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. BFO:0000063 external - uberon precedes precedes @@ -2137,11 +1368,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - occurs_in - unfolds in - unfolds_in BFO:0000066 external occurs_in @@ -2150,7 +1377,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. occurs_in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant - occurs in occurs in https://wiki.geneontology.org/Occurs_in @@ -2161,308 +1387,13 @@ A continuant cannot have an occurrent as part: use 'participates in'. - site of [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - BFO:0000067 - uberon - contains_process - contains_process Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant - - contains process contains process - - - - BSPO:0000096 - uberon - anterior_to - anterior_to - anterior to - - - - - - - - BSPO:0000097 - uberon - distal_to - distal_to - distal to - - - - - - - - BSPO:0000098 - uberon - dorsal_to - dorsal_to - dorsal to - - - - - - - - BSPO:0000099 - uberon - posterior_to - posterior_to - posterior to - - - - - - - - BSPO:0000100 - uberon - proximal_to - proximal_to - proximal to - - - - - - - - BSPO:0000102 - uberon - ventral_to - ventral_to - ventral to - - - - - - - - BSPO:0000107 - uberon - deep_to - deep_to - deep to - - - - - - - - BSPO:0000108 - uberon - superficial_to - superficial_to - superficial to - - - - - - - - BSPO:0000120 - uberon - in_left_side_of - in_left_side_of - in left side of - - - - - - - - BSPO:0000121 - uberon - in_right_side_of - in_right_side_of - in right side of - - - - - - - - BSPO:0000122 - uberon - in_posterior_side_of - in_posterior_side_of - in posterior side of - - - - - - - - BSPO:0000123 - uberon - in_anterior_side_of - in_anterior_side_of - in anterior side of - - - - - - - - BSPO:0000124 - uberon - in_proximal_side_of - in_proximal_side_of - in proximal side of - - - - - - - - BSPO:0000126 - uberon - in_lateral_side_of - in_lateral_side_of - in lateral side of - - - - - - - - BSPO:0001100 - uberon - in_superficial_part_of - in_superficial_part_of - in superficial part of - - - - - - - - BSPO:0001101 - uberon - in_deep_part_of - in_deep_part_of - in deep part of - - - - - - - - BSPO:0001106 - uberon - proximalmost_part_of - proximalmost_part_of - proximalmost part of - - - - - - - - BSPO:0001107 - uberon - immediately_deep_to - immediately_deep_to - immediately deep to - - - - - - - - BSPO:0001108 - uberon - distalmost_part_of - distalmost_part_of - distalmost part of - - - - - - - - BSPO:0001113 - uberon - preaxialmost_part_of - preaxialmost_part_of - preaxialmost part of - - - - - - - - BSPO:0001115 - uberon - postaxialmost_part_of - postaxialmost_part_of - postaxialmost part of - - - - - - - - BSPO:0005001 - uberon - intersects_midsagittal_plane_of - intersects_midsagittal_plane_of - intersects midsagittal plane of - - - - - - - - BSPO:0015014 - uberon - immediately_superficial_to - immediately_superficial_to - immediately superficial to - - - - - - - - BSPO:0015101 - uberon - in_dorsal_side_of - in_dorsal_side_of - in dorsal side of - - - - @@ -2522,12 +1453,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - inheres in - this fragility is a characteristic of this vase - this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. - inheres_in - Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of @@ -2539,14 +1465,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - bearer of - this apple is bearer of this red color - this vase is bearer of this fragility Inverse of characteristic_of A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. - bearer_of - is bearer of - RO:0000053 external bearer_of @@ -2563,15 +1483,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. - participates in - this blood clot participates in this blood coagulation - this input material (or this output material) participates in this process - this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process - participates_in RO:0000056 external - uberon participates_in participates_in participates in @@ -2589,14 +1503,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - has participant - this blood coagulation has participant this blood clot - this investigation has participant this investigator - this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. - has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 external has_participant @@ -2612,11 +1520,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. - function_of - is function of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. function of @@ -2628,11 +1533,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. - is quality of - quality_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. quality of @@ -2644,11 +1546,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. - is role of - role_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. role of @@ -2660,10 +1559,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. - has_function has function @@ -2673,15 +1570,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. - has_quality - RO:0000086 - uberon - has_quality - has_quality - has quality has quality @@ -2692,10 +1582,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. - has_role has role @@ -2729,13 +1617,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this cell derives from this parent cell (cell division) - this nucleus derives from this parent nucleus (nuclear division) - a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. - derives_from - This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. derives from @@ -2745,12 +1628,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this parent cell derives into this cell (cell division) - this parent nucleus derives into this nucleus (nuclear division) - a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. - derives_into derives into @@ -2762,18 +1641,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - is location of - my head is the location of my brain - this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - location_of - - RO:0001015 - uberon - location_of - location_of - location of location of @@ -2789,21 +1658,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. - located in - my brain is located in my head - this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - located_in - - http://www.obofoundry.org/ro/#OBO_REL:located_in - RO:0001025 - uberon - located_in - located_in - located in located in https://wiki.geneontology.org/Located_in @@ -2827,16 +1685,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. - the surface of my skin is a 2D boundary of my body a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - 2D_boundary_of - boundary of - is 2D boundary of - is boundary of - surface of - 2D boundary of @@ -2848,19 +1699,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. - my body has 2D boundary the surface of my skin a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - - has boundary - has_2D_boundary - - RO:0002002 - uberon - has_boundary - has_boundary - has 2D boundary has 2D boundary @@ -2871,17 +1712,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - http://www.ncbi.nlm.nih.gov/pubmed/22402613 - RO:0002005 - uberon - innervated_by - innervated_by - innervated_by innervated_by @@ -2892,8 +1722,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - has synaptic terminal of @@ -2924,10 +1752,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - RO:0002007 external - uberon bounding_layer_of bounding_layer_of @@ -3106,8 +1932,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland - <= Primitive instance level timing relation between events before or simultaneous with @@ -3122,15 +1946,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time. - - David Osumi-Sutherland - RO:0002082 - uberon - simultaneous_with - simultaneous_with t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) - simultaneous with simultaneous with @@ -3141,7 +1958,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after @@ -3158,11 +1974,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland - starts_at_end_of RO:0002087 external - uberon immediately_preceded_by immediately_preceded_by X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) @@ -3180,11 +1993,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - - David Osumi-Sutherland - ends_at_start_of - meets - RO:0002090 external immediately_precedes @@ -3207,12 +2015,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between a neuron and a material anatomical entity that its soma is part of. - <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) - has soma location @@ -3224,33 +2029,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. - - fasciculates with - (forall (?x ?y) - (iff - (fasciculates_with ?x ?y) - (exists (?nps ?npbs) - (and - ("neuron ; CL_0000540" ?x) - ("neuron projection bundle ; CARO_0001001" ?y) - ("neuron projection segment ; CARO_0001502" ?nps) - ("neuron projection bundle segment ; CARO_0001500' " ?npbs) - (part_of ?npbs ?y) - (part_of ?nps ?x) - (part_of ?nps ?npbs) - (forall (?npbss) - (if - (and - ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) - (part_of ?npbss ?npbs) - ) - (overlaps ?nps ?npbss) - )))))) - - fasciculates with @@ -3265,16 +2045,11 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between a neuron and some structure its axon forms (chemical) synapses in. - - <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y))) - - axon synapses in @@ -3296,18 +2071,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. - - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) - - - RO:0002103 - uberon - synapsed_by - synapsed_by - synapsed by synapsed by @@ -3319,15 +2084,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] - Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. - - - - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) - has plasma membrane part @@ -3343,16 +2101,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. - - - synapsed in http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)) - - has postsynaptic terminal in @@ -3367,12 +2119,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. - synapses in <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) - - has presynaptic terminal in @@ -3393,14 +2141,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. - - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) - - N1 synapsed_to some N2 Expands to: N1 SubclassOf ( @@ -3422,13 +2165,8 @@ N1 SubclassOf ( - A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. - - has synapse in <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) - - has synaptic terminal in @@ -3443,10 +2181,6 @@ N1 SubclassOf ( - - - - @@ -3455,13 +2189,10 @@ N1 SubclassOf ( - x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) - RO:0002131 external - uberon overlaps @@ -3470,15 +2201,6 @@ N1 SubclassOf ( overlaps overlaps - - - - - - - - true - @@ -3497,35 +2219,7 @@ N1 SubclassOf ( - The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. - - has fasciculating component - (forall (?x ?y) - (iff - (has_fasciculating_neuron_projection ?x ?y) - (exists (?nps ?npbs) - (and - ("neuron projection bundle ; CARO_0001001" ?x) - ("neuron projection ; GO0043005" ?y) - ("neuron projection segment ; CARO_0001502" ?nps) - ("neuron projection bundle segment ; CARO_0001500" ?npbs) - (part_of ?nps ?y) - (part_of ?npbs ?x) - (part_of ?nps ?npbs) - (forall (?npbss) - (if - (and - ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) - (part_of ?npbss ?npbs) - ) - (overlaps ?nps ?npbss) - )))))) - - - - - has fasciculating neuron projection @@ -3538,19 +2232,10 @@ N1 SubclassOf ( - Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - <http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) - - - RO:0002134 - uberon - innervates - innervates - innervates innervates @@ -3563,17 +2248,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - X continuous_with Y if and only if X and Y share a fiat boundary. - - connected to - The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) - - RO:0002150 - uberon - continuous_with - continuous_with - continuous with continuous with FMA:85972 @@ -3586,13 +2261,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a. - Consider obsoleting and merging with child relation, 'in homology relationship with' - RO:0002158 - uberon - homologous_to - homologous_to VBO calls this homologous_to shares ancestor with @@ -3603,19 +2272,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - lactation SubClassOf 'only in taxon' some 'Mammalia' - x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria - - - - RO:0002160 - uberon - only_in_taxon - only_in_taxon only in taxon @@ -3634,30 +2294,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - - - - - - - - - - - - - - - - - - - - - @@ -3678,53 +2314,16 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. - - - - - RO:0002162 - uberon - in_taxon - in_taxon Connects a biological entity to its taxon of origin. in taxon @@ -3736,14 +2335,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. - - - Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) - spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern @@ -3761,14 +2355,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b - - RO:0002170 - uberon - connected_to - connected_to - connected to connected to https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern @@ -3781,15 +2368,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - The M8 connects Glasgow and Edinburgh - a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system. - - RO:0002176 - uberon - connects - connects - connects connects https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern @@ -3804,28 +2383,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. - attached to part of (anatomical structure to anatomical structure) - RO:0002177 - uberon - attaches_to_part_of - attaches_to_part_of - attached to part of attached to part of - - - - - - - - true - @@ -3833,15 +2393,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy. Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure - - RO:0002178 - uberon - supplies - supplies - supplies supplies @@ -3851,15 +2404,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure. Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure - - RO:0002179 - uberon - drains - drains - drains drains @@ -3869,14 +2415,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. - For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. - RO:0002180 external - uberon has_component has_component @@ -3896,18 +2438,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y - - - - - RO:0002202 - uberon - develops_from - develops_from This is the transitive form of the develops from relation - develops from develops from @@ -3920,17 +2452,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of develops from - - - - RO:0002203 - uberon - develops_into - develops_into - develops into develops into @@ -3947,10 +2470,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - 'neural crest cell' SubClassOf expresses some 'Wnt1 gene' - x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process - expressed in @@ -3977,19 +2497,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. - - - FBbt - - RO:0002207 has developmental precursor - uberon - directly_develops_from - directly_develops_from TODO - add child relations from DOS - directly develops from directly develops from @@ -3999,9 +2509,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of directly develops from - developmental precursor of directly develops into @@ -4029,14 +2537,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. - - - - - GO - Regulation precludes parthood; the regulatory process may not be within the regulated process. - regulates (processual) - false RO:0002211 external regulates @@ -4061,9 +2561,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. - - - negatively regulates (process to process) RO:0002212 external @@ -4094,10 +2591,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. - - - positively regulates (process to process) - RO:0002213 external positively_regulates @@ -4117,17 +2610,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) - osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. - - has function realized in - - - For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". RO:0002215 external - uberon capable_of capable_of @@ -4142,31 +2627,15 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. - - has function in RO:0002216 external - uberon capable_of_part_of capable_of_part_of capable of part of capable of part of - - - - - - - - true - @@ -4175,15 +2644,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x - - - RO:0002219 - uberon - surrounded_by - surrounded_by - surrounded by surrounded by @@ -4195,18 +2656,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. - The epidermis layer of a vertebrate is adjacent to the dermis. - The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. - The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. - x adjacent to y if and only if x and y share a boundary. This relation acts as a join point with BSPO - - RO:0002220 external - uberon adjacent_to @@ -4215,12 +2668,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.adjacent to adjacent to - - - - A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. - - @@ -4228,16 +2675,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of surrounded by - - - RO:0002221 - uberon - surrounds - surrounds - surrounds surrounds @@ -4248,11 +2687,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. - https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to @@ -4266,17 +2700,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of starts with - - Chris Mungall - Allen - RO:0002223 - uberon - starts - starts - starts starts @@ -4288,15 +2713,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor - x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - - Chris Mungall - started by RO:0002224 external - uberon starts_with starts_with @@ -4314,14 +2733,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x develops from part of y if and only if there exists some z such that x develops from z and z is part of y - - RO:0002225 - uberon - develops_from_part_of - develops_from_part_of - develops from part of develops from part of @@ -4336,16 +2748,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x develops_in y if x is located in y whilst x is developing - - EHDAA2 - Jonathan Bard, EHDAA2 - RO:0002226 - uberon - develops_in - develops_in - develops in develops in @@ -4357,16 +2760,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of ends with - - Chris Mungall - RO:0002229 - uberon - ends - ends - ends ends @@ -4378,14 +2773,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - - Chris Mungall - finished by RO:0002230 external - uberon ends_with ends_with @@ -4405,10 +2795,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y - - starts with process that occurs in RO:0002231 external has_start_location @@ -4430,10 +2817,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y - - ends with process that occurs in RO:0002232 external has_end_location @@ -4455,10 +2839,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. - - consumes RO:0002233 external has_input @@ -4483,10 +2864,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. - - produces RO:0002234 external has_output @@ -4508,13 +2886,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1. b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t. - - RO:0002252 - uberon - connecting_branch_of - connecting_branch_of connecting branch of @@ -4526,7 +2898,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of connecting branch of - has connecting branch @@ -4544,15 +2915,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] - x has developmental contribution from y iff x has some part z such that z develops from y - - RO:0002254 - uberon - has_developmental_contribution_from - has_developmental_contribution_from - has developmental contribution from has developmental contribution from @@ -4567,9 +2930,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of has developmental contribution from - developmentally contributes to @@ -4583,21 +2944,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T - - - - induced by - - Developmental Biology, Gilbert, 8th edition, figure 6.5(F) - GO:0001759 - We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm] - RO:0002256 - uberon - developmentally_induced_by - developmentally_induced_by - developmentally induced by developmentally induced by @@ -4608,9 +2955,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Inverse of developmentally induced by - developmentally induces @@ -4623,11 +2968,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false - - In general you should not use this relation to make assertions - use one of the more specific relations below this one This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from developmentally preceded by @@ -4642,7 +2984,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. acts upstream of @@ -4659,7 +3000,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects @@ -4673,16 +3013,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage - - replaces - RO:0002285 - uberon - developmentally_replaces - developmentally_replaces - developmentally replaces developmentally replaces @@ -4692,9 +3024,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Inverse of developmentally preceded by - developmentally succeeded by @@ -4708,9 +3038,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue - - part of developmental precursor of @@ -4720,9 +3047,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process. - expresses @@ -4734,10 +3059,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. - RO:0002295 external results_in_developmental_progression_of @@ -4754,11 +3077,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - every flower development (GO:0009908) results in development of some flower (PO:0009046) - p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. - - http://www.geneontology.org/GO.doc.development.shtml RO:0002296 external results_in_development_of @@ -4778,11 +3097,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. - every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) - - - GOC:mtg_berkeley_2013 RO:0002297 external results_in_formation_of @@ -4791,7 +3105,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. results_in_formation_of results in formation of - results in formation of + results in formation of anatomical entity @@ -4801,12 +3115,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. - tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) - The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. - - GOC:mtg_berkeley_2013 RO:0002298 external results_in_morphogenesis_of @@ -4825,12 +3134,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process - bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) - The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. - - GOC:mtg_berkeley_2013 RO:0002299 external results_in_maturation_of @@ -4850,8 +3154,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. - - RO:0002304 external causally_upstream_of,_positive_effect @@ -4872,7 +3174,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. - RO:0002305 external causally_upstream_of,_negative_effect @@ -4889,32 +3190,15 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of characteristic of part of - - inheres in part of - - characteristic of part of - - - - - - - - true - @@ -4924,10 +3208,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity - - GOC:mtg_berkeley_2013 RO:0002315 external results_in_acquisition_of_features_of @@ -4945,8 +3226,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A relationship that holds via some environmental process - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. evolutionarily related to @@ -4956,9 +3235,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A mereological relationship or a topological relationship - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships - mereotopologically related to @@ -4968,8 +3244,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A relationship that holds between entities participating in some developmental process (GO:0032502) - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development developmentally related to @@ -4988,15 +3262,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - a particular instances of akt-2 enables some instance of protein kinase activity c enables p iff c is capable of p and c acts to execute p. - - catalyzes - executes - has - is catalyzing - is executing - This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. enables https://wiki.geneontology.org/Enables @@ -5008,13 +3274,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. - - This is a grouping relation that collects relations used for the purpose of connecting structure and function - RO:0002328 - uberon - functionally_related_to - functionally_related_to - functionally related to functionally related to @@ -5024,24 +3283,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - this relation holds between c and p when c is part of some c', and c' is capable of p. - - false part of structure that is capable of - - - - - - - - true - @@ -5051,8 +3295,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts. - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism genomically related to @@ -5072,9 +3314,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. c involved_in p if and only if c enables some process p', and p' is part of p - - actively involved in - enables part of involved in https://wiki.geneontology.org/Involved_in @@ -5087,11 +3326,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid p regulates levels of c if p regulates some amount (PATO:0000070) of c - - - regulates levels of (process to entity) RO:0002332 external regulates_levels_of @@ -5108,7 +3343,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of enables - enabled by https://wiki.geneontology.org/Enabled_by @@ -5124,8 +3358,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of regulates - - regulated by (processual) RO:0002334 external regulated_by @@ -5142,7 +3374,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of negatively regulates - RO:0002335 external negatively_regulated_by @@ -5159,7 +3390,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of positively regulates - RO:0002336 external positively_regulated_by @@ -5177,8 +3407,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A relationship that holds via some process of localization - - Do not use this relation directly. It is a grouping relation. related via localization to @@ -5193,7 +3421,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. - RO:0002338 external has_target_start_location @@ -5216,7 +3443,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. - RO:0002339 external has_target_end_location @@ -5235,7 +3461,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l - RO:0002341 external results_in_transport_along @@ -5252,7 +3477,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. - RO:0002342 external results_in_transport_across @@ -5269,8 +3493,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - 'pollen tube growth' results_in growth_of some 'pollen tube' - RO:0002343 external results_in_growth_of @@ -5285,8 +3507,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) - RO:0002344 external results_in_transport_to_from_or_in @@ -5302,12 +3522,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - An organism that is a member of a population of organisms is member of is a mereological relation between a item and a collection. - is member of - member part of - SIO - member of @@ -5319,13 +3534,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. has member is a mereological relation between a collection and an item. - SIO - - RO:0002351 - uberon - has_member - has_member - has member has member @@ -5337,14 +3545,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of has input - - RO:0002352 - uberon - input_of - input_of - input of input of @@ -5356,10 +3558,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of has output - RO:0002353 external - uberon output_of @@ -5374,7 +3574,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - formed as result of @@ -5384,8 +3583,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - http://neurolex.org/wiki/Property:DendriteLocation has dendrite location @@ -5398,14 +3595,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a - - attached to (anatomical structure to anatomical structure) - RO:0002371 - uberon - attaches_to - attaches_to - attached to attached to @@ -5418,13 +3608,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. - - Wikipedia:Insertion_(anatomy) - RO:0002372 - uberon - has_muscle_origin - has_muscle_origin - has muscle origin has muscle origin @@ -5444,13 +3627,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. - - Wikipedia:Insertion_(anatomy) - RO:0002373 - uberon - has_muscle_insertion - has_muscle_insertion - has muscle insertion has muscle insertion @@ -5469,12 +3645,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships - This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) - in branching relationship with https://github.com/obophenotype/uberon/issues/170 @@ -5487,23 +3658,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Deschutes River tributary_of Columbia River - inferior epigastric vein tributary_of external iliac vein - x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. - - drains into - drains to - tributary channel of - http://en.wikipedia.org/wiki/Tributary - http://www.medindia.net/glossary/venous_tributary.htm - This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries) - RO:0002376 - uberon - tributary_of - tributary_of - tributary of tributary of http://en.wikipedia.org/wiki/Tributary @@ -5521,10 +3677,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location - - This relation is added for formal completeness. It is unlikely to be used in many practical scenarios spatially coextensive with @@ -5542,15 +3695,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y - - RO:0002380 - uberon - branching_part_of - branching_part_of - branching part of branching part of FMA:85994 @@ -5564,9 +3710,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). - has developmental potential involving @@ -5576,14 +3720,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y - - RO:0002385 - uberon - has_potential_to_developmentally_contribute_to - has_potential_to_developmentally_contribute_to - has potential to developmentally contribute to has potential to developmentally contribute to @@ -5593,9 +3730,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y - has potential to developmentally induce @@ -5605,14 +3740,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x has the potential to develop into y iff x develops into y or if x is capable of developing into y - - RO:0002387 - uberon - has_potential_to_develop_into - has_potential_to_develop_into - has potential to develop into has potential to develop into @@ -5622,9 +3750,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y - has potential to directly develop into @@ -5636,9 +3762,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of upstream of - RO:0002404 external causally_downstream_of @@ -5655,8 +3779,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - RO:0002405 external immediately_causally_downstream_of @@ -5690,9 +3812,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. - - indirectly activates - indirectly positively regulates https://wiki.geneontology.org/Indirectly_positively_regulates @@ -5718,9 +3837,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. - - indirectly inhibits - indirectly negatively regulates https://wiki.geneontology.org/Indirectly_negatively_regulates @@ -5746,8 +3862,6 @@ For the second, we consider a relationship to be regulatory if the system in whi For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to @@ -5766,7 +3880,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. - RO:0002411 external causally_upstream_of @@ -5785,8 +3898,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. - - RO:0002412 external immediately_causally_upstream_of @@ -5805,8 +3916,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 - - influences (processual) RO:0002418 external affects @@ -5823,8 +3932,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different inverse of causally upstream of or within - - RO:0002427 external causally_downstream_of_or_within @@ -5849,7 +3956,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' regulates some p - involved in regulation of @@ -5868,8 +3974,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' positively regulates some p - - involved in positive regulation of @@ -5888,7 +3992,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' negatively regulates some p - involved in negative regulation of @@ -5903,8 +4006,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union - - involved in or reguates involved in or involved in regulation of @@ -5915,28 +4016,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - - executes activity in enables activity in is active in https://wiki.geneontology.org/Is_active_in - - - - - - - - true - @@ -5952,11 +4037,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. - - RO:0002433 - uberon - contributes_to_morphology_of - contributes_to_morphology_of contributes to morphology of @@ -5971,13 +4051,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different A relationship that holds between two entities in which the processes executed by the two entities are causally connected. This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. Considering relabeling as 'pairwise interacts with' - - Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. in pairwise interaction with interacts with http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ - http://purl.obolibrary.org/obo/MI_0914 @@ -5988,12 +4065,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. - - binds - molecularly binds with molecularly interacts with - http://purl.obolibrary.org/obo/MI_0915 @@ -6003,8 +4076,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different Axiomatization to GO to be added later - - An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. phosphorylates @@ -6025,8 +4096,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. - - molecularly controls directly regulates activity of @@ -6046,9 +4115,6 @@ A and B can be physically interacting but not necessarily. Immediately upstream The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. - - - directly inhibits molecularly decreases activity of directly negatively regulates activity of @@ -6068,9 +4134,6 @@ For example, A and B may be gene products and binding of B by A negatively regul The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. - - - directly activates molecularly increases activity of directly positively regulates activity of @@ -6080,8 +4143,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. helper property (not for use in curation) @@ -6093,16 +4154,8 @@ For example, A and B may be gene products and binding of B by A positively regul - 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. - - - - RO:0002473 - uberon - composed_primarily_of - composed_primarily_of composed primarily of @@ -6113,24 +4166,10 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. - has part that occurs in - - - - - - - - true - @@ -6138,7 +4177,6 @@ For example, A and B may be gene products and binding of B by A positively regul - is kinase activity @@ -6150,7 +4188,6 @@ For example, A and B may be gene products and binding of B by A positively regul See notes for inverse relation - receives input from @@ -6161,7 +4198,6 @@ For example, A and B may be gene products and binding of B by A positively regul This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. - sends output to @@ -6172,8 +4208,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. relation between physical entity and a process or stage @@ -6189,11 +4223,6 @@ For example, A and B may be gene products and binding of B by A positively regul x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). - - RO:0002488 - uberon - existence_starts_during - existence_starts_during existence starts during @@ -6204,11 +4233,6 @@ For example, A and B may be gene products and binding of B by A positively regul x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). - - RO:0002489 - uberon - existence_starts_with - existence_starts_with existence starts with @@ -6219,7 +4243,6 @@ For example, A and B may be gene products and binding of B by A positively regul x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence overlaps @@ -6232,12 +4255,7 @@ For example, A and B may be gene products and binding of B by A positively regul x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) - - RO:0002491 exists during - uberon - existence_starts_and_ends_during - existence_starts_and_ends_during The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts and ends during @@ -6253,23 +4271,10 @@ For example, A and B may be gene products and binding of B by A positively regul - Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). - - RO:0002492 - ceases_to_exist_during - uberon - existence_ends_during - existence_ends_during The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during - - - - Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. - https://orcid.org/0000-0002-6601-2165 - @@ -6278,11 +4283,6 @@ For example, A and B may be gene products and binding of B by A positively regul x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). - - RO:0002493 - uberon - existence_ends_with - existence_ends_with The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends with @@ -6295,11 +4295,6 @@ For example, A and B may be gene products and binding of B by A positively regul x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships - - RO:0002494 - uberon - transformation_of - transformation_of transformation of @@ -6311,12 +4306,6 @@ For example, A and B may be gene products and binding of B by A positively regul x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t - - - RO:0002495 - uberon - immediate_transformation_of - immediate_transformation_of immediate transformation of @@ -6347,11 +4336,6 @@ For example, A and B may be gene products and binding of B by A positively regul x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). - - RO:0002496 - uberon - existence_starts_during_or_after - existence_starts_during_or_after The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts during or after @@ -6383,11 +4367,6 @@ For example, A and B may be gene products and binding of B by A positively regul x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. - - RO:0002497 - uberon - existence_ends_during_or_before - existence_ends_during_or_before The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during or before @@ -6400,7 +4379,6 @@ For example, A and B may be gene products and binding of B by A positively regul A relationship between a material entity and a process where the material entity has some causal role that influences the process - causal agent in process @@ -6413,9 +4391,6 @@ For example, A and B may be gene products and binding of B by A positively regul p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. - - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes @@ -6424,7 +4399,6 @@ For example, A and B may be gene products and binding of B by A positively regul - depends on @@ -6438,9 +4412,6 @@ For example, A and B may be gene products and binding of B by A positively regul The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch - - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between entities @@ -6454,18 +4425,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - - Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. - - has supporting framework - The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). - RO:0002551 - uberon - has_skeleton - has_skeleton has skeleton @@ -6482,9 +4443,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - causally influenced by (entity-centric) causally influenced by @@ -6494,7 +4452,6 @@ For example, A and B may be gene products and binding of B by A positively regul - interaction relation helper property http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ @@ -6506,7 +4463,6 @@ For example, A and B may be gene products and binding of B by A positively regul - molecular interaction relation helper property @@ -6517,8 +4473,6 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - - RO:0002565 external results_in_movement_of @@ -6548,10 +4502,6 @@ For example, A and B may be gene products and binding of B by A positively regul The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). - - - - causally influences (entity-centric) causally influences @@ -6564,8 +4514,6 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between elements of a musculoskeletal system or its analogs. - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. biomechanically related to @@ -6576,12 +4524,6 @@ For example, A and B may be gene products and binding of B by A positively regul m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. - - Wikipedia:Antagonist_(muscle) - RO:0002568 - uberon - has_muscle_antagonist - has_muscle_antagonist has muscle antagonist @@ -6594,13 +4536,8 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of branching part of - - RO:0002569 - uberon - has_branching_part - has_branching_part has branching part @@ -6613,14 +4550,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. - - UBERON:cjm - This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. - RO:0002570 - uberon - conduit_for - conduit_for conduit for @@ -6632,13 +4562,7 @@ For example, A and B may be gene products and binding of B by A positively regul x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - - - RO:0002571 - uberon - lumen_of - lumen_of lumen of @@ -6650,12 +4574,7 @@ For example, A and B may be gene products and binding of B by A positively regul s is luminal space of x iff s is lumen_of x and s is an immaterial entity - - RO:0002572 - uberon - luminal_space_of - luminal_space_of luminal space of @@ -6668,12 +4587,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has skeleton - - RO:0002576 - uberon - skeleton_of - skeleton_of skeleton of @@ -6685,10 +4599,6 @@ For example, A and B may be gene products and binding of B by A positively regul p directly regulates q iff p is immediately causally upstream of q and p regulates q. - - - directly regulates (processual) - RO:0002578 external directly_regulates @@ -6710,9 +4620,7 @@ For example, A and B may be gene products and binding of B by A positively regul - gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p - has part structure that is capable of @@ -6782,8 +4690,6 @@ For example, A and B may be gene products and binding of B by A positively regul A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - - causal relation between material entity and a process @@ -6797,9 +4703,7 @@ For example, A and B may be gene products and binding of B by A positively regul - pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. - capable of regulating @@ -6814,7 +4718,6 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. - capable of negatively regulating @@ -6828,9 +4731,7 @@ For example, A and B may be gene products and binding of B by A positively regul - renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. - capable of positively regulating @@ -6841,7 +4742,6 @@ For example, A and B may be gene products and binding of B by A positively regul Inverse of 'causal agent in process' - RO:0002608 external process_has_causal_agent @@ -6857,9 +4757,6 @@ For example, A and B may be gene products and binding of B by A positively regul p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. - - directly positively regulates (process to process) - RO:0002629 external directly_positively_regulates @@ -6879,8 +4776,6 @@ For example, A and B may be gene products and binding of B by A positively regul p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. - - directly negatively regulates (process to process) RO:0002630 external @@ -6907,12 +4802,9 @@ For example, A and B may be gene products and binding of B by A positively regul - a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. - RO:0003000 external - uberon produces produces @@ -6928,12 +4820,9 @@ For example, A and B may be gene products and binding of B by A positively regul - a produced_by b iff some process that occurs_in b has_output a. - RO:0003001 external - uberon produced_by produced_by @@ -7040,7 +4929,6 @@ For example, A and B may be gene products and binding of B by A positively regul - 2018-01-26T23:49:30Z @@ -7078,7 +4966,6 @@ For example, A and B may be gene products and binding of B by A positively regul c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive - 2018-01-26T23:53:14Z @@ -7125,7 +5012,6 @@ For example, A and B may be gene products and binding of B by A positively regul - 2018-03-13T23:55:19Z causally upstream of or within, positive effect @@ -7141,7 +5027,6 @@ For example, A and B may be gene products and binding of B by A positively regul The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. - regulates activity of @@ -7388,7 +5273,6 @@ For example, A and B may be gene products and binding of B by A positively regul - 'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)') A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. @@ -7408,7 +5292,6 @@ For example, A and B may be gene products and binding of B by A positively regul - 'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor') A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. @@ -7430,12 +5313,7 @@ For example, A and B may be gene products and binding of B by A positively regul - A diagnostic testing device utilizes a specimen. X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. - - - A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. - See github ticket https://github.com/oborel/obo-relations/issues/497 2021-11-08T12:00:00Z utilizes device utilizes material @@ -7561,7 +5439,6 @@ For example, A and B may be gene products and binding of B by A positively regul - x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y. @@ -7581,8 +5458,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - carries uberon channel_for @@ -7594,7 +5469,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uberon channels_from channels_from @@ -7605,7 +5479,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uberon channels_into channels_into @@ -7616,10 +5489,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y. uberon distally_connected_to @@ -7638,11 +5509,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y uberon extends_fibers_into @@ -7672,11 +5538,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - @@ -7704,7 +5565,6 @@ For example, A and B may be gene products and binding of B by A positively regul - x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y. uberon @@ -7733,7 +5593,6 @@ For example, A and B may be gene products and binding of B by A positively regul - x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y. @@ -7787,7 +5646,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uberon transitively_anteriorly_connected_to transitively anteriorly connected to @@ -7799,7 +5657,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uberon transitively_distally_connected_to transitively distally connected to @@ -7811,7 +5668,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uberon transitively_proximally_connected_to transitively proximally connected to @@ -12806,6 +10662,12 @@ For example, A and B may be gene products and binding of B by A positively regul KUPO:0001017 kidney medulla cell + + + + A cell that is part of a renal medulla. + PMID:22343825 + @@ -13081,12 +10943,19 @@ For example, A and B may be gene products and binding of B by A positively regul + A fibroblast that is part of an interstitial compartment of a kidney. KUPO:0001102 kidney interstitial fibroblast + + + + A fibroblast that is part of an interstitial compartment of a kidney. + PMID:10559635 + @@ -13204,7 +11073,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -13226,6 +11095,7 @@ For example, A and B may be gene products and binding of B by A positively regul + A blood vessel cell that is part of a kidney. KUPO:0001014 kidney blood vessel cell @@ -13235,6 +11105,12 @@ For example, A and B may be gene products and binding of B by A positively regul true + + + + A blood vessel cell that is part of a kidney. + PMID:34843404 + @@ -14910,32 +12786,32 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer - + - + - + PMID:12382326 - + PMID:12382326 @@ -25001,7 +22877,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 PMID:15371245 ncbi_taxonomy @@ -25015,7 +22890,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 Mus mice @@ -25034,7 +22908,7 @@ For example, A and B may be gene products and binding of B by A positively regul mice - + @@ -25049,7 +22923,6 @@ For example, A and B may be gene products and binding of B by A positively regul - NCBITaxon:85055 GC_ID:1 house mouse @@ -25077,7 +22950,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 ncbi_taxonomy NCBITaxon:117570 @@ -25090,7 +22962,6 @@ For example, A and B may be gene products and binding of B by A positively regul - NCBITaxon:40673 GC_ID:1 bony vertebrates @@ -25130,7 +23001,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 ncbi_taxonomy NCBITaxon:1338369 @@ -25143,7 +23013,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 PMID:11743200 PMID:11791233 @@ -25165,7 +23034,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 mice and others ncbi_taxonomy @@ -25192,7 +23060,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 PMID:23020233 PMID:30257078 @@ -25256,7 +23123,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 PMID:11214319 PMID:12082125 @@ -25273,7 +23139,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 PMID:11214319 PMID:12082125 @@ -25296,7 +23161,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 tetrapods ncbi_taxonomy @@ -25316,7 +23180,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 amniotes ncbi_taxonomy @@ -25336,7 +23199,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 Theria ncbi_taxonomy @@ -25356,7 +23218,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 ncbi_taxonomy Fungi/Metazoa group @@ -25383,7 +23244,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 metazoans multicellular animals @@ -25424,7 +23284,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 ncbi_taxonomy NCBITaxon:33213 @@ -25437,7 +23296,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 deuterostomes ncbi_taxonomy @@ -25457,7 +23315,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 PMID:15019624 PMID:15371245 @@ -25472,7 +23329,6 @@ For example, A and B may be gene products and binding of B by A positively regul - NCBITaxon:109679 GC_ID:1 ncbi_taxonomy @@ -25486,7 +23342,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 mammals ncbi_taxonomy @@ -25513,7 +23368,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 ncbi_taxonomy NCBITaxon:6072 @@ -25526,7 +23380,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 chordates ncbi_taxonomy @@ -25553,7 +23406,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 Vertebrata vertebrates @@ -25587,7 +23439,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 Gnathostomata jawed vertebrates @@ -25614,7 +23465,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 ncbi_taxonomy NCBITaxon:8287 @@ -25627,7 +23477,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 Mus ncbi_taxonomy @@ -25647,7 +23496,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 Craniata ncbi_taxonomy @@ -25667,7 +23515,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 eutherian mammals placental mammals @@ -25715,7 +23562,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 rodent ncbi_taxonomy @@ -25831,7 +23677,6 @@ For example, A and B may be gene products and binding of B by A positively regul A branchiness quality inhering in a bearer by virtue of the bearer's having branches. - ramified ramiform quality @@ -26158,7 +24003,6 @@ For example, A and B may be gene products and binding of B by A positively regul A contractility quality inhering in a bearer by virtue of the bearer's ability of contracting or being contracted. - quality PATO:0001690 @@ -26180,7 +24024,6 @@ For example, A and B may be gene products and binding of B by A positively regul A shape quality in a bearer by virtue of the bearer's curving inward. - quality PATO:0001857 @@ -26354,7 +24197,6 @@ For example, A and B may be gene products and binding of B by A positively regul A complete three dimensional shape in which for every line connecting pair of points on the object is within the object. Or: a shape lacking cavities. Contrast: concave. - Image:http://upload.wikimedia.org/wikipedia/commons/0/06/Convex_polygon_illustration1.png quality PATO:0002007 @@ -26415,7 +24257,6 @@ For example, A and B may be gene products and binding of B by A positively regul A concave quality inhering in a bearer by virtue of the bearer's curving inward on both sides or surfaces. - quality PATO:0002039 @@ -27009,7 +24850,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001012 Category=gene. Requested by=CL. integrin alpha-M - @@ -27153,7 +24993,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001024 Category=gene. Requested by=CL. neural cell adhesion molecule 1 - @@ -27238,7 +25077,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001084 Category=gene. Requested by=CL. T-cell surface glycoprotein CD8 alpha chain - @@ -27367,7 +25205,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001444 Category=gene. Requested by=CL. cadherin-5 - @@ -27400,7 +25237,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001839 Category=gene. Requested by=CL. T-cell surface glycoprotein CD5 - @@ -27442,7 +25278,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001869 Category=gene. Requested by=CL. interleukin-7 receptor subunit alpha - @@ -27507,7 +25342,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001945 Category=gene. Requested by=CL. transferrin receptor protein 1 - @@ -27577,7 +25411,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000002112 Category=gene. Requested by=CL. vascular endothelial growth factor receptor 2 - @@ -27698,7 +25531,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000013883 Category=gene. renin - @@ -27730,7 +25562,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000014841 Category=gene. sonic hedgehog protein - @@ -27772,7 +25603,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000016043 Category=gene. Requested by=CL. T-cell acute lymphocytic leukemia protein 1 - @@ -28055,8 +25885,6 @@ For example, A and B may be gene products and binding of B by A positively regul Any hollow cylindrical anatomical structure containing a lumen through which substances are transported. - not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts) - tubular galen:Tube anatomical tube duct @@ -28084,10 +25912,6 @@ For example, A and B may be gene products and binding of B by A positively regul Major subdivision of an organism that protrudes from the body[DOS, CARO]. - An appendage is an external body part, or natural prolongation, that protrudes from an organism's body, such as a vertebrate's limbs[BILA][BILA:0000018]. - Organ or organ part that is attached to the body of an organism. For example a limb[GO, modified][GO:0048736]. - appendicular - this is currently a subtype of organism subdivision - which would exclude feathers AEO:0000193 BILA:0000018 BTO:0001492 @@ -28096,7 +25920,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA2:0003193 EMAPA:37283 EV:0100155 - FBbt:00007000 HAO:0000144 MAT:0000023 MESH:D005121 @@ -28123,30 +25946,12 @@ For example, A and B may be gene products and binding of B by A positively regul Major subdivision of an organism that protrudes from the body[DOS, CARO]. CARO:DOS - - - - An appendage is an external body part, or natural prolongation, that protrudes from an organism's body, such as a vertebrate's limbs[BILA][BILA:0000018]. - BILA:0000018 - - - - - Organ or organ part that is attached to the body of an organism. For example a limb[GO, modified][GO:0048736]. - GO:0048736 - EMAPA:37283 MA:th - - - - FBbt:00007000 - - @@ -28216,13 +26021,7 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - + @@ -28243,12 +26042,6 @@ For example, A and B may be gene products and binding of B by A positively regul Muscular duct that propels urine from the kidneys to the urinary bladder, or related organs. - Anatomical structure consisting of long narrow duct which carries urine from the kidney to the urinary bladder.[AAO] - The duct of amniotes that carries urine from a metanephric kidney to the urinary bladder. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] - The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG] - ureteral - ureteric - in humans, consists of adventitial, muscular and mucoa layers AAO:0010254 BTO:0001409 CALOHA:TS-1084 @@ -28282,14 +26075,14 @@ For example, A and B may be gene products and binding of B by A positively regul ureter https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg - + - + GO @@ -28299,34 +26092,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0090189 Wikipedia:Ureter - - - - Anatomical structure consisting of long narrow duct which carries urine from the kidney to the urinary bladder.[AAO] - 2012-06-20 - AAO:0010254 - AAO - AAO:BJB - - - - - The duct of amniotes that carries urine from a metanephric kidney to the urinary bladder. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] - 2012-09-17 - VHOG:0000605 - VHOG - http://bgee.unil.ch/ - - - - - The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG] - 2012-09-17 - VHOG:0000605 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543 - http://bgee.unil.ch/ - @@ -28361,8 +26126,13 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + + + + + + @@ -28382,8 +26152,6 @@ For example, A and B may be gene products and binding of B by A positively regul The fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening. - urethral - In human males, the urethra travels through the penis, and carries semen as well as urine. In females, the urethra is shorter and emerges above the vaginal opening. BTO:0001426 CALOHA:TS-1132 EFO:0000931 @@ -28412,25 +26180,14 @@ For example, A and B may be gene products and binding of B by A positively regul urethra https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png - - - - - + - - pelvic part of UG sinus gives rise to prostatic and membranous parts of urethra - Wikipedia - - - - - + Wikipedia @@ -28473,10 +26230,7 @@ For example, A and B may be gene products and binding of B by A positively regul A tubular structure that transports secreted or excreted substances. - A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171]. - Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here. AAO:0011123 - FBbt:00100314 FMA:30320 NCIT:C12948 SCTID:91726008 @@ -28502,18 +26256,6 @@ For example, A and B may be gene products and binding of B by A positively regul http://orcid.org/0000-0002-6601-2165 http://www.siumed.edu/~dking2/intro/glands.htm#ducts - - - - A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171]. - ZFA:0005171 - - - - - FBbt:00100314 - - @@ -28547,10 +26289,8 @@ For example, A and B may be gene products and binding of B by A positively regul Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. - in FMA, serosa is a wall UBERON:0009915 wall - EMAPA:25036 FMA:82482 galen:Wall wall of organ @@ -28566,12 +26306,6 @@ For example, A and B may be gene products and binding of B by A positively regul Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. FMA:82482 - - - - in FMA, serosa is a wall - FMA - @@ -28607,7 +26341,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0000003 EHDAA2:0003003 EMAPA:0 - FBbt:00007001 FMA:305751 FMA:67135 GAID:781 @@ -28635,12 +26368,6 @@ For example, A and B may be gene products and binding of B by A positively regul Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. CARO:0000003 - - - - FBbt:00007001 - - @@ -28678,8 +26405,6 @@ For example, A and B may be gene products and binding of B by A positively regul - Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. - CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4 BIRNLEX:4 CARO:0020004 EFO:0000634 @@ -28713,12 +26438,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia - - - - Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. - GO:0048513 - @@ -28740,8 +26459,6 @@ For example, A and B may be gene products and binding of B by A positively regul A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity. FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction - Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball. - Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal. FMA:86140 uberon organ region with fixed fiat boundary @@ -28757,20 +26474,6 @@ For example, A and B may be gene products and binding of B by A positively regul A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity. http://orcid.org/0000-0002-6601-2165 - - - - Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball. - FMA:86140 - 3 - - - - - Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal. - FMA:86140 - 1 - @@ -28803,7 +26506,6 @@ For example, A and B may be gene products and binding of B by A positively regul A multicellular structure that is a part of an organ. - currently defined in a very broad sense, may be replaced by more specific classes in the future @@ -28960,7 +26662,6 @@ For example, A and B may be gene products and binding of B by A positively regul - ncit:Death is an outcome XAO:0000437 XtroDO:0000085 uberon @@ -28975,12 +26676,6 @@ For example, A and B may be gene products and binding of B by A positively regul End of the life of an organism. XAO:0000437 - - - - ncit:Death is an outcome - ncit - @@ -28989,7 +26684,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -29004,7 +26699,6 @@ For example, A and B may be gene products and binding of B by A positively regul A capillary tuft which forms a close network with the visceral epithelium (podocytes) and the mesangium to form the filtration barrier and is surrounded by Bowman's capsule in nephrons of the vertebrate kidney[GO]. - ZFA - The multi-tissue structure where the glomerular basement membrane supported by mesonephric podocytes filters blood from the glomerular capillaries. GUDMAP: 'Together, the Bowman's capsule and the glomerulus comprise the definitive renal corpuscle.' - here the glomerulus is part of the capsule? 2009-06-18T09:26:37Z glomerulus @@ -29040,14 +26734,14 @@ For example, A and B may be gene products and binding of B by A positively regul http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg - + - + FMA MA @@ -29058,12 +26752,6 @@ For example, A and B may be gene products and binding of B by A positively regul MP:0005325 Wikipedia:Glomerulus - - - - ZFA - The multi-tissue structure where the glomerular basement membrane supported by mesonephric podocytes filters blood from the glomerular capillaries. GUDMAP: 'Together, the Bowman's capsule and the glomerulus comprise the definitive renal corpuscle.' - here the glomerulus is part of the capsule? - ZFA - @@ -29199,12 +26887,6 @@ For example, A and B may be gene products and binding of B by A positively regul The second stage of the kidney. It serves as the main excretory organ of aquatic vertebrates and as a temporary embryonic kidney in higher vertebrates. It is composed of the mesonephric duct (also called the Wolffian duct), mesonephric tubules, and associated capillary tufts. A single tubule and its associated capillary tuft is called a mesonephric excretory unit; these units are similar in structure and function to nephrons of the adult kidney. The mesonephros is derived from intermediate mesoderm in the vertebrate embryo. - A kidney formed of nephric tubules arising in the middle region of the nephric ridge; a transient embryonic stage that replaces the pronephros, but is itself replaced by the adult metanephros [in mammals; in fishes and amphibians it is the adult kidney]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG] - Organ that is the definitive adult kidney. It replaces the earlier pronephros, which degenerates as the mesonephros becomes functional in feeding stage tadpoles.[AAO] - As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates. (...) In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG] - mesonephric - In mammals, the mesonephros is the second of the three embryonic kidneys to be established and exists only transiently. In fish and amphibians, the mesonephros will form the mature kidney - By contrast to the pronephros, the histological features of the mammalian mesonephros, with its primitive glomeruli, suggest that it probably functions as a primitive kidney, and is involved in the production of much of the amniotic fluid. Within the two mesonephroi, one located on either side of the dorsal mesentery of the hindgut, a substantial number (in the region of about 40 or more) of cranio-caudally segmented mesonephric tubules are formed. It has, however, been suggested that only the most rostrally located 4-6 pairs of mesonephric tubules drain into the mesonephric portion of the nephric duct. This is now seen to extend along the length of the mesonephroi, being located towards their lateral sides. The mesonephros is also retained over a considerably longer period than the pronephros, but gradually undergoes regression in a cranio-caudal direction. While the rostral part displays clear evidence of regression its more caudal part appears to display evidence of functional activity. Within the medial part of the mesonephros, vesicles are formed, although no glomeruli are formed there in this species. It is, however, difficult to believe that the relatively enormous mesonephroi do not have an excretory role in the mouse, only serving as a base for gonadal differentiation. In the human embryo, the medial part of the mesonephric tubules enlarges, become invaginated by capillaries, and form glomeruli. These then take on an excretory role. In the mouse, the mesonephric ducts appear to be patent throughout their length[GUDMAP, modified] AAO:0010384 BTO:0001542 CALOHA:TS-0624 @@ -29249,34 +26931,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0001823 Wikipedia:Mesonephros - - - - A kidney formed of nephric tubules arising in the middle region of the nephric ridge; a transient embryonic stage that replaces the pronephros, but is itself replaced by the adult metanephros [in mammals; in fishes and amphibians it is the adult kidney]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG] - 2012-09-17 - VHOG:0000038 - VHOG - http://bgee.unil.ch/ - - - - - Organ that is the definitive adult kidney. It replaces the earlier pronephros, which degenerates as the mesonephros becomes functional in feeding stage tadpoles.[AAO] - 2012-06-20 - AAO:0010384 - AAO - AAO:BJB - - - - - As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates. (...) In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG] - 2012-09-17 - VHOG:0000038 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639 - http://bgee.unil.ch/ - @@ -29344,15 +26998,20 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + + + + + + - + @@ -29361,10 +27020,6 @@ For example, A and B may be gene products and binding of B by A positively regul In mammals, the metanephros is the excretory organ of the fetus, which develops into the mature kidney and is formed from the rear portion of the nephrogenic cord. The metanephros is an endocrine and metabolic organ that filters the blood and excretes the end products of body metabolism in the form of urine[GO]. TODO check developmental relationships - A kidney formed of nephric tubules arising in the posterior region of the nephric ridge and drained by a ureter; replaces the embryonic pronephros and mesonephros [in mammals]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG] - The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes.[well established][VHOG] - metanephric - During the fifth week of gestation, the mesonephric duct develops an outpouching, the ureteric bud, near its attachment to the cloaca. This bud, also called the metanephrogenic diverticulum, grows posteriorly and towards the head of the embryo. The elongated stalk of the ureteric bud, the metanephric duct, later forms the ureter. As the cranial end of the bud extends into the intermediate mesoderm, it undergoes a series of branchings to form the collecting duct system of the kidney. It also forms the major and minor calyces and the renal pelvis BTO:0001543 EHDAA2:0001137 EHDAA:3089 @@ -29388,34 +27043,24 @@ For example, A and B may be gene products and binding of B by A positively regul metanephros - - - - - + - + - - definitional - - - - - + GO - + ISBN:9780878932504 @@ -29425,25 +27070,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0001656 Wikipedia:Metanephros#Metanephros - - - - A kidney formed of nephric tubules arising in the posterior region of the nephric ridge and drained by a ureter; replaces the embryonic pronephros and mesonephros [in mammals]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG] - 2012-09-17 - VHOG:0000039 - VHOG - http://bgee.unil.ch/ - - - - - The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes.[well established][VHOG] - 2012-09-17 - VHOG:0000039 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543 - http://bgee.unil.ch/ - @@ -29502,8 +27128,6 @@ For example, A and B may be gene products and binding of B by A positively regul A mesonephric tubule is an epithelial tube that is part of the mesonephros[GO]. Genital ridge that is next to the mesonephros[WP]. TODO check - Any of the renal tubules composing the mesonephros. In mammals they function as excretory structures during the early embryonic development but are later incorporated into the reproductive system. [TFD][VHOG] - As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates.[well established][VHOG] AAO:0010389 EHDAA2:0001134 EMAPA:16747 @@ -29522,26 +27146,6 @@ For example, A and B may be gene products and binding of B by A positively regul A mesonephric tubule is an epithelial tube that is part of the mesonephros[GO]. Genital ridge that is next to the mesonephros[WP]. Wikipedia:Mesonephric_tubules - - - - Any of the renal tubules composing the mesonephros. In mammals they function as excretory structures during the early embryonic development but are later incorporated into the reproductive system. [TFD][VHOG] - 2012-09-17 - VHOG:0000500 - VHOG - http://bgee.unil.ch/ - http://medical-dictionary.thefreedictionary.com/mesonephric+tubule - - - - - As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates.[well established][VHOG] - 2012-09-17 - VHOG:0000500 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639 - http://bgee.unil.ch/ - @@ -29564,7 +27168,6 @@ For example, A and B may be gene products and binding of B by A positively regul - @@ -29572,12 +27175,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + An epithelial swelling on the Wolffian duct that elongates to invade the adjacent metanephric mesenchyme[MP]. - Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts. [Embryology, See_Dudek_RW_and_Fix_JD, Third_Edition_(2004)_Philadelphia:_Lippincott_William_and_Wilkins, p.137][VHOG] - Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts[VHOG:0000541]. - The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG] BTO:0001646 EHDAA2:0002140 EHDAA:3091 @@ -29600,11 +27200,11 @@ For example, A and B may be gene products and binding of B by A positively regul ureteric bud - + - + @@ -29617,13 +27217,13 @@ For example, A and B may be gene products and binding of B by A positively regul - + EHDAA2 - + ISBN:9780878932504 @@ -29633,31 +27233,6 @@ For example, A and B may be gene products and binding of B by A positively regul MP:0010979 PMID:19828308 - - - - Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts. [Embryology, See_Dudek_RW_and_Fix_JD, Third_Edition_(2004)_Philadelphia:_Lippincott_William_and_Wilkins, p.137][VHOG] - 2012-09-17 - VHOG:0000541 - VHOG - http://bgee.unil.ch/ - - - - - Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts[VHOG:0000541]. - VHOG:0000541 - - - - - The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG] - 2012-09-17 - VHOG:0000541 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543 - http://bgee.unil.ch/ - @@ -29723,7 +27298,6 @@ For example, A and B may be gene products and binding of B by A positively regul Stage succeeding embryo, including mature structure. - In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997) BilaDO:0000003 OGES:000010 OGES:000014 @@ -29809,8 +27383,6 @@ For example, A and B may be gene products and binding of B by A positively regul - the WBls class 'all stages' belongs here as it is the superclass of other WBls stages - we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage BILS:0000105 EFO:0000399 FBdv:00007012 @@ -29861,13 +27433,11 @@ For example, A and B may be gene products and binding of B by A positively regul A stage at which the organism is a single cell produced by means of sexual reproduction. - As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG] BILS:0000106 BilaDO:0000005 EFO:0001322 EHDAA:27 FBdv:00005288 - IDOMAL:0000302 NCIT:C12601 PdumDv:0000100 VHOG:0000745 @@ -29893,24 +27463,6 @@ For example, A and B may be gene products and binding of B by A positively regul A stage at which the organism is a single cell produced by means of sexual reproduction. Wikipedia:Zygote - - - - As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG] - 2012-09-17 - VHOG:0000745 - VHOG - ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107 - http://bgee.unil.ch/ - - - - - IDOMAL:0000302 - - - https://github.com/biopragmatics/biomappings - @@ -30058,7 +27610,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -30094,14 +27646,14 @@ For example, A and B may be gene products and binding of B by A positively regul gastrula stage - + - + BILS @@ -30179,8 +27731,6 @@ For example, A and B may be gene products and binding of B by A positively regul Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system. - - In zebrafish, the times of neurulation and segmentation overlap so extensively there is no distinct neurula period of development, such as occurs largely before segmentation in amphibian embryos. BILS:0000110 BilaDO:0000009 HsapDv:0000012 @@ -30306,7 +27856,6 @@ For example, A and B may be gene products and binding of B by A positively regul - A thin sheet or layer of pliable tissue, serving as a covering or envelope of a part, as the lining of a cavity, as a partition or septum, or to connect two structures. membrane FMA:30322 FMA:82500 @@ -30317,12 +27866,6 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0000158 membranous layer - - - - A thin sheet or layer of pliable tissue, serving as a covering or envelope of a part, as the lining of a cavity, as a partition or septum, or to connect two structures. - ncithesaurus:Membrane - @@ -30337,7 +27880,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical conduit that connects two adjacent body spaces (or a body space with the space surrounding the organism)[FMA,modified]. - in FMA, this is an anatomical conduit *space*, rather than anatomical conduit anatomical ostium ostium FMA:3724 @@ -30354,12 +27896,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical conduit that connects two adjacent body spaces (or a body space with the space surrounding the organism)[FMA,modified]. FMA:3724 - - - - in FMA, this is an anatomical conduit *space*, rather than anatomical conduit - FMA - @@ -30379,8 +27915,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -30389,13 +27925,6 @@ For example, A and B may be gene products and binding of B by A positively regul Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures. adding df link to embryonic cloaca leads to a cycle in uberon-simple, as cloaca is a suberclass of embryonic cloaca - - A common passage for fecal, urinary, and reproductive discharge in most lower vertebrates as well as the terminal end of the hindgut before division into rectum, bladder, and genital primordia in mammalian embryos. [TFD][VHOG] - Anatomical structure which is the common receptacle for the alimentary canal, Wolffian ducts, oviducts, and the bladder.[AAO] - A cloaca is apparently a primitive vertebrate feature because it occurs in most primitive gnathostomes and persists in the embryos of almost all vertebrates.[well established][VHOG] - cloacal - Human beings only have an embryonic cloaca, which is split up into separate tracts during the development of the urinary and reproductive organs - hindgut endoderm and proctodeal ectoderm. AAO:0000095 GAID:1206 MESH:D002988 @@ -30413,24 +27942,24 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0000162 cloaca - + - + - + ZFA - + AAO @@ -30440,47 +27969,6 @@ For example, A and B may be gene products and binding of B by A positively regul ISBN:0073040584 Wikipedia:Cloaca - - - - - most adult placentals have no trace of a cloaca. However, the tenrecs and golden moles, small placental mammals native to Africa, retain a cloaca as adults. - - - - - A common passage for fecal, urinary, and reproductive discharge in most lower vertebrates as well as the terminal end of the hindgut before division into rectum, bladder, and genital primordia in mammalian embryos. [TFD][VHOG] - 2012-09-17 - VHOG:0001186 - VHOG - http://bgee.unil.ch/ - http://medical-dictionary.thefreedictionary.com/cloaca - - - - - Anatomical structure which is the common receptacle for the alimentary canal, Wolffian ducts, oviducts, and the bladder.[AAO] - 2012-06-20 - AAO:0000095 - AAO - AAO:BJB - - - - - A cloaca is apparently a primitive vertebrate feature because it occurs in most primitive gnathostomes and persists in the embryos of almost all vertebrates.[well established][VHOG] - 2012-09-17 - VHOG:0001186 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.572 - http://bgee.unil.ch/ - - - - - hindgut endoderm and proctodeal ectoderm. - WP - @@ -30512,8 +28000,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -30521,7 +28009,6 @@ For example, A and B may be gene products and binding of B by A positively regul Endoderm-lined chamber that develops as pouch-like dilation of the caudal end of the hindgut and receives the allantois ventrally and two mesonephric ducts laterally; caudally it ends blindly at the cloacal membrane formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm[MP]. - this class represents the embryonic form of the cloaca, as found in both mammals and non-mammals. EHDAA2:0000256 EHDAA:4895 EMAPA:27573 @@ -30532,24 +28019,24 @@ For example, A and B may be gene products and binding of B by A positively regul embryonic cloaca - + - + - + EHDAA2 - + EHDAA2 @@ -30572,7 +28059,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -30592,9 +28079,6 @@ For example, A and B may be gene products and binding of B by A positively regul The ventral part of the cloaca remaining after septation of the rectum, which further develops into part of the bladder, part of the prostatic part of the male urethra and the urethra and vestibule in females. - The ventral part of the cloaca after its separation from the rectum, giving rise to the lower part of the bladder in both sexes, to the prostatic portion of the male urethra, and to the urethra and vestibule in the female. [TFD][VHOG] - In mammals the lowly monotremes still have a cloaca. Higher types have done away with this structure and have a separate anal outlet for the rectum. The monotreme cloaca shows the initiation of this subdivision. The cloaca has such includes only the distal part, roughly comparable to the proctodeum. The more proximal part is divided into (1) a large dorsal passage into which the intestine opens, the coprodeum, and (2) a ventral portion, the urodeum with which the bladder connects. (...) the development of the placental mammals recapitulates in many respects the phylogenetic story. In the sexually indifferent stage of placental mammal there is a cloaca. While the indifferent stage still persists, a septum develops, and extends out to the closing membrane. This divides the cloaca into two chambers: a coprodeum continuous with the gut above, and a urodeum or urogenital sinus below.[well established][VHOG] - the term 'urogenital sinus' may refer to the primitive urogenital sinus present as a transient developmental structure in most mammals or it may refer to a condition in which an unseptated cloaca persists in animals longer than normal urogenital sinus EHDAA2:0004060 EHDAA:5029 @@ -30614,14 +28098,14 @@ For example, A and B may be gene products and binding of B by A positively regul primitive urogenital sinus http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png - + - + MP-def @@ -30631,32 +28115,6 @@ For example, A and B may be gene products and binding of B by A positively regul ISBN:0-683-40008-8 MP:0010116 - - - - The ventral part of the cloaca after its separation from the rectum, giving rise to the lower part of the bladder in both sexes, to the prostatic portion of the male urethra, and to the urethra and vestibule in the female. [TFD][VHOG] - 2012-09-17 - VHOG:0000414 - VHOG - http://bgee.unil.ch/ - http://medical-dictionary.thefreedictionary.com/urogenital+sinus - - - - - In mammals the lowly monotremes still have a cloaca. Higher types have done away with this structure and have a separate anal outlet for the rectum. The monotreme cloaca shows the initiation of this subdivision. The cloaca has such includes only the distal part, roughly comparable to the proctodeum. The more proximal part is divided into (1) a large dorsal passage into which the intestine opens, the coprodeum, and (2) a ventral portion, the urodeum with which the bladder connects. (...) the development of the placental mammals recapitulates in many respects the phylogenetic story. In the sexually indifferent stage of placental mammal there is a cloaca. While the indifferent stage still persists, a septum develops, and extends out to the closing membrane. This divides the cloaca into two chambers: a coprodeum continuous with the gut above, and a urodeum or urogenital sinus below.[well established][VHOG] - 2012-09-17 - VHOG:0000414 - VHOG - ISBN:978-0721676678 Romer AS, Vertebrate body (1970)p.388-89 and Figure 300 - http://bgee.unil.ch/ - - - - - the term 'urogenital sinus' may refer to the primitive urogenital sinus present as a transient developmental structure in most mammals or it may refer to a condition in which an unseptated cloaca persists in animals longer than normal - MP - @@ -30693,24 +28151,7 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - @@ -30724,11 +28165,6 @@ For example, A and B may be gene products and binding of B by A positively regul The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks). - Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO] - Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG] - oral - some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives - in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips AAO:0010355 BTO:0001090 BTO:0004698 @@ -30737,7 +28173,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA2:0001326 EHDAA:542 EMAPA:16262 - FBbt:00003126 FMA:49184 GAID:75 MA:0000341 @@ -30783,12 +28218,6 @@ For example, A and B may be gene products and binding of B by A positively regul https://github.com/obophenotype/uberon/issues/661 http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg - - - - - the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts - @@ -30796,37 +28225,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Mouth https://github.com/obophenotype/uberon/wiki/The-digestive-tract - - - - Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO] - 2012-06-20 - AAO:0010355 - AAO - AAO:BJB - - - - - Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG] - 2012-09-17 - VHOG:0000812 - VHOG - DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008) - http://bgee.unil.ch/ - - - - - in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips - FMA - - - - - FBbt:00003126 - - @@ -30983,22 +28381,17 @@ For example, A and B may be gene products and binding of B by A positively regul - + - - + + A fluid that is composed of blood plasma and erythrocytes. - This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid. - A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO] - Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO] - relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] - Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG] AAO:0000046 BTO:0000089 CALOHA:TS-0079 @@ -31033,34 +28426,34 @@ For example, A and B may be gene products and binding of B by A positively regul blood - + - + - + - + CL:tm - + https://github.com/obophenotype/uberon/issues/1330 - + Bgee:AN @@ -31072,42 +28465,6 @@ For example, A and B may be gene products and binding of B by A positively regul http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/9 - - - - A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO] - 2012-08-14 - TAO:0000007 - TAO - ZFIN:curator - - - - - Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO] - 2012-06-20 - AAO:0000046 - AAO - AAO:LAP - - - - - relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] - 2012-06-20 - AAO:0000046 - AAO - - - - - Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG] - 2012-09-17 - VHOG:0000224 - VHOG - DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006) - http://bgee.unil.ch/ - @@ -31252,11 +28609,6 @@ For example, A and B may be gene products and binding of B by A positively regul Functional part of an organ in the body. This is in contrast to the stroma, which refers to the structural tissue of organs, being exactly, connective tissues. - parenchymal - Early in development the mammalian embryo has three distinct layers: ectoderm (external layer), endoderm (internal layer) and in between those two layers the middle layer or mesoderm. The parenchyma of most organs is of ectodermal (brain, skin) or endodermal origin (lungs, gastrointestinal tract, liver, pancreas). The parenchyma of a few organs (spleen, kidneys, heart) is of mesodermal origin. The stroma of all organs is of mesodermal origin - the FMA definition is more restrictive, and limits this to solid organs. This would seem to cause problems for the lung parenchyma, except FMA classifies Lung as solid rather than cavitated - BTO:0000999 - BTO:0001539 EHDAA:3015 EHDAA:3905 EHDAA:3999 @@ -31283,34 +28635,6 @@ For example, A and B may be gene products and binding of B by A positively regul Functional part of an organ in the body. This is in contrast to the stroma, which refers to the structural tissue of organs, being exactly, connective tissues. Wikipedia:Parenchyma - - - - Early in development the mammalian embryo has three distinct layers: ectoderm (external layer), endoderm (internal layer) and in between those two layers the middle layer or mesoderm. The parenchyma of most organs is of ectodermal (brain, skin) or endodermal origin (lungs, gastrointestinal tract, liver, pancreas). The parenchyma of a few organs (spleen, kidneys, heart) is of mesodermal origin. The stroma of all organs is of mesodermal origin - WP - - - - - the FMA definition is more restrictive, and limits this to solid organs. This would seem to cause problems for the lung parenchyma, except FMA classifies Lung as solid rather than cavitated - FMA - - - - - BTO:0000999 - - - https://github.com/biopragmatics/biomappings - - - - - BTO:0001539 - - - https://github.com/biopragmatics/biomappings - @@ -31361,7 +28685,6 @@ For example, A and B may be gene products and binding of B by A positively regul The inner portion of the kidney consisting of the renal pyramids. - The renal medulla is split up into a number of sections, known as the renal pyramids. Blood enters into the kidney via the renal artery, which then splits up to form the arcuate arterioles. The arcuate arterioles each in turn branch into interlobular arterioles, which finally reach the glomeruli. At the glomerulus the blood reaches a highly disfavourable pressure gradient and a large exchange surface area, which forces the serum portion of the blood out of the vessel into the renal tubules. Flow continues through the renal tubules, including the proximal tubule, the Loop of Henle, and finally leaves the kidney by means of the collecting duct, leading to the renal ureter. The renal medulla contains the structures of the nephrons responsible for maintaining the salt and water balance of the blood. The renal medulla is hypertonic to the filtrate in the nephron and aids in the reabsorption of water BTO:0001167 CALOHA:TS-1157 EMAPA:19279 @@ -31518,14 +28841,11 @@ For example, A and B may be gene products and binding of B by A positively regul consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77 - Anatomical system that consists of the muscles of the body.[VSAO] - we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA AAO:0000307 BILA:0000088 BTO:0001369 BTO:0001485 EFO:0000801 - EMAPA:35578 FMA:72954 MA:0002888 MAT:0000025 @@ -31553,21 +28873,6 @@ For example, A and B may be gene products and binding of B by A positively regul The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified]. VSAO:0000033 - - - - Anatomical system that consists of the muscles of the body.[VSAO] - 2012-08-14 - VSAO:0000033 - VSAO - VSAO:curator - - - - - we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA - MA - @@ -31611,7 +28916,12 @@ For example, A and B may be gene products and binding of B by A positively regul - + + + + + + @@ -31629,7 +28939,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0000004 EHDAA2:0003004 EMAPA:35178 - FBbt:00007019 FMA:9669 HAO:0000004 MA:0002450 @@ -31653,28 +28962,12 @@ For example, A and B may be gene products and binding of B by A positively regul organism substance - - - - - - - - - this relationship may be too strong and may be weakened in future - Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007019 - - @@ -31729,7 +29022,6 @@ For example, A and B may be gene products and binding of B by A positively regul BILA:0000005 CARO:0000005 EHDAA2:0003005 - FBbt:00007017 FMA:5897 HAO:0000005 NCIT:C94478 @@ -31753,12 +29045,6 @@ For example, A and B may be gene products and binding of B by A positively regul Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures. http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007017 - - @@ -31790,7 +29076,6 @@ For example, A and B may be gene products and binding of B by A positively regul BILA:0000006 CARO:0000006 EHDAA2:0003006 - FBbt:00007016 FMA:67165 HAO:0000006 TAO:0001836 @@ -31808,12 +29093,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical entity that has mass. http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007016 - - @@ -31831,7 +29110,6 @@ For example, A and B may be gene products and binding of B by A positively regul BILA:0000007 CARO:0000007 EHDAA2:0003007 - FBbt:00007015 FMA:67112 HAO:0000007 TAO:0001835 @@ -31850,12 +29128,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical entity that has no mass. http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007015 - - @@ -31898,10 +29170,8 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA:392 EMAPA:16103 EV:0100000 - FBbt:00004856 FMA:7149 HAO:0000011 - IDOMAL:0002460 MA:0000003 NCIT:C12919 SCTID:278195005 @@ -31941,20 +29211,6 @@ For example, A and B may be gene products and binding of B by A positively regul system GO:0048731 - - - - FBbt:00004856 - - - - - - IDOMAL:0002460 - - - https://github.com/biopragmatics/biomappings - @@ -31992,7 +29248,6 @@ For example, A and B may be gene products and binding of B by A positively regul - organismal organism AAO:0010026 AEO:0000191 @@ -32007,7 +29262,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA:1 EMAPA:25765 EV:0100016 - FBbt:00000001 FMA:256135 HAO:0000012 NCIT:C13041 @@ -32052,12 +29306,6 @@ For example, A and B may be gene products and binding of B by A positively regul VHOG:0000671 WBbt:0007833 - - - - FBbt:00000001 - - @@ -32105,7 +29353,6 @@ For example, A and B may be gene products and binding of B by A positively regul Multi-tissue structure that is part of a compound organ. - this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future AAO:0010017 AEO:0000019 BILA:0000019 @@ -32163,7 +29410,6 @@ For example, A and B may be gene products and binding of B by A positively regul EFO:0000808 EHDAA2:0003032 EMAPA:36031 - FBbt:00007009 FMA:7153 HAO:0000032 MA:0002433 @@ -32206,12 +29452,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:DOS http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007009 - - @@ -32253,7 +29493,6 @@ For example, A and B may be gene products and binding of B by A positively regul BILA:0000040 CARO:0000040 EHDAA2:0003040 - FBbt:00007013 FMA:63863 HAO:0000040 TAO:0000382 @@ -32279,12 +29518,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue. http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007013 - - @@ -32303,7 +29536,6 @@ For example, A and B may be gene products and binding of B by A positively regul - FBbt:00007277 VHOG:0001737 uberon UBERON:0000477 @@ -32317,12 +29549,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical group whose component anatomical structures lie in close proximity to each other. FBbt:00007277 - - - - FBbt:00007277 - - @@ -32356,7 +29582,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0000043 EHDAA2:0003043 EMAPA:35868 - FBbt:00007003 FMA:9637 HAO:0000043 MA:0003002 @@ -32392,12 +29617,6 @@ For example, A and B may be gene products and binding of B by A positively regul Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. CARO:0000043 - - - - FBbt:00007003 - - @@ -32438,7 +29657,6 @@ For example, A and B may be gene products and binding of B by A positively regul BILA:0000055 CARO:0000055 EHDAA2:0003055 - FBbt:00007010 HAO:0000055 TAO:0001488 TGMA:0001847 @@ -32465,12 +29683,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0000055 http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007010 - - @@ -32509,7 +29721,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -32517,8 +29729,6 @@ For example, A and B may be gene products and binding of B by A positively regul Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]. - The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG] - epithelial AAO:0000144 AAO:0010055 AEO:0000066 @@ -32528,7 +29738,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0000066 EHDAA2:0003066 EMAPA:32738 - FBbt:00007005 FMA:9639 GAID:402 HAO:0000066 @@ -32553,14 +29762,14 @@ For example, A and B may be gene products and binding of B by A positively regul epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg - + - + http://palaeos.com/metazoa/porifera/homoscleromorpha.html @@ -32570,22 +29779,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Epithelium http://orcid.org/0000-0001-9114-8737 - - - - The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG] - 2012-09-17 - VHOG:0000387 - VHOG - ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.59 - http://bgee.unil.ch/ - - - - - FBbt:00007005 - - @@ -32614,7 +29807,6 @@ For example, A and B may be gene products and binding of B by A positively regul BILA:0000068 CARO:0000068 EHDAA2_RETIRED:0003068 - FBbt:00007027 FMA:45567 HAO:0000068 NCIT:C33552 @@ -32654,12 +29846,6 @@ For example, A and B may be gene products and binding of B by A positively regul columnar epithlium AEO:0000068 - - - - FBbt:00007027 - - @@ -32693,7 +29879,6 @@ For example, A and B may be gene products and binding of B by A positively regul Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA]. - Unilaminar epithelium that consists of a single layer of squamous cells.[CARO] AAO:0010066 AEO:0000070 BILA:0000070 @@ -32725,16 +29910,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Simple_squamous_epithelium http://orcid.org/0000-0001-9114-8737 - - - - Unilaminar epithelium that consists of a single layer of squamous cells.[CARO] - 2012-06-20 - CARO:0000070 - CARO - FMA:45565 - http://orcid.org/0000-0001-9114-8737 - @@ -32773,7 +29948,6 @@ For example, A and B may be gene products and binding of B by A positively regul Compound organ that contains one or more macroscopic anatomical spaces. - this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future AAO:0010016 AEO:0000072 BILA:0000072 @@ -32822,7 +29996,6 @@ For example, A and B may be gene products and binding of B by A positively regul Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA]. consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable - Epithelium that consists of a single layer of epithelial cells.[CARO] AAO:0010062 AEO:0000073 BILA:0000073 @@ -32851,16 +30024,6 @@ For example, A and B may be gene products and binding of B by A positively regul FMA:45561 http://orcid.org/0000-0001-9114-8737 - - - - Epithelium that consists of a single layer of epithelial cells.[CARO] - 2012-06-20 - CARO:0000073 - CARO - FMA:45561 - http://orcid.org/0000-0001-9114-8737 - @@ -32906,10 +30069,6 @@ For example, A and B may be gene products and binding of B by A positively regul Subdivision of trunk that lies between the head and the abdomen. - note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest - - - EMAPA:35862 FMA:259209 MA:0000022 @@ -32955,7 +30114,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -32964,8 +30123,6 @@ For example, A and B may be gene products and binding of B by A positively regul The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column. Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class - abdominal - celiac BTO:0000020 CALOHA:TS-0001 EFO:0000968 @@ -32992,14 +30149,14 @@ For example, A and B may be gene products and binding of B by A positively regul abdomen - + - + MA @@ -33055,8 +30212,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. - embryonic - Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo AAO:0011035 AEO:0000169 BILA:0000056 @@ -33068,10 +30223,8 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA2_RETIRED:0003236 EHDAA:38 EMAPA:16039 - FBbt:00000052 FMA:69068 GAID:963 - IDOMAL:0000646 MAT:0000226 MESH:D004622 MIAA:0000019 @@ -33107,26 +30260,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0009790 Wikipedia:Embryo - - - - Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo - ZFA - - - - - FBbt:00000052 - - - - - - IDOMAL:0000646 - - - https://github.com/biopragmatics/biomappings - @@ -33159,13 +30292,11 @@ For example, A and B may be gene products and binding of B by A positively regul A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm. - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] embryonic tissue AAO:0000480 BILA:0000035 BTO:0000556 EMAPA:36033 - FBbt:00000110 FMA:69069 GAID:1303 MESH:D005855 @@ -33196,28 +30327,12 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Germ_layer https://github.com/obophenotype/uberon/issues/203 - - - - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - 2012-09-17 - VHOG:0001223 - VHOG - ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 - http://bgee.unil.ch/ - embryonic tissue FMA:69069 - - - - FBbt:00000110 - - @@ -33256,11 +30371,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. - Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO] - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - ectodermal AAO:0000137 BILA:0000036 BTO:0000315 @@ -33269,7 +30381,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA2:0000428 EMAPA:16069 EV:0100003 - FBbt:00000111 FMA:69070 GAID:1304 MAT:0000155 @@ -33294,14 +30405,14 @@ For example, A and B may be gene products and binding of B by A positively regul ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -33310,31 +30421,6 @@ For example, A and B may be gene products and binding of B by A positively regul Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. Wikipedia:Ectoderm - - - - Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO] - 2012-06-20 - AAO:0000137 - AAO - AAO:EJS - - - - - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - 2012-09-17 - VHOG:0000153 - VHOG - ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 - http://bgee.unil.ch/ - - - - - FBbt:00000111 - - @@ -33360,10 +30446,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - endodermal AAO:0000139 BILA:0000038 BTO:0000800 @@ -33372,7 +30456,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA2:0000436 EMAPA:16062 EV:0100005 - FBbt:00000125 FMA:69071 GAID:1305 MAT:0000175 @@ -33397,14 +30480,14 @@ For example, A and B may be gene products and binding of B by A positively regul http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -33413,22 +30496,6 @@ For example, A and B may be gene products and binding of B by A positively regul Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. Wikipedia:Endoderm - - - - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - 2012-09-17 - VHOG:0000154 - VHOG - ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 - http://bgee.unil.ch/ - - - - - FBbt:00000125 - - @@ -33455,13 +30522,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + The middle germ layer of the embryo, between the endoderm and ectoderm. - Primary germ layer that is the middle of the embryonic germ layers.[AAO] - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - mesodermal - sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates UBERON:0003263 AAO:0000304 BILA:0000037 @@ -33474,7 +30537,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA:183 EMAPA:16083 EV:0100006 - FBbt:00000126 FMA:69072 GAID:522 MAT:0000174 @@ -33500,20 +30562,14 @@ For example, A and B may be gene products and binding of B by A positively regul mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + - - sometimes not considered primary - - - - - + Bgee:AN @@ -33522,37 +30578,6 @@ For example, A and B may be gene products and binding of B by A positively regul The middle germ layer of the embryo, between the endoderm and ectoderm. Wikipedia:Mesoderm - - - - Primary germ layer that is the middle of the embryonic germ layers.[AAO] - 2012-06-20 - AAO:0000304 - AAO - AAO:EJS - - - - - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - 2012-09-17 - VHOG:0000152 - VHOG - ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 - http://bgee.unil.ch/ - - - - - sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates - https://github.com/obophenotype/uberon/wiki/The-neural-crest - - - - - FBbt:00000126 - - @@ -33599,15 +30624,10 @@ For example, A and B may be gene products and binding of B by A positively regul Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity. consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence - Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO] - the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx - stomodeal - This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity. stomodeal-hypophyseal primordium BTO:0004224 EHDAA2:0001929 EMAPA:16263 - FBbt:00000439 FMA:295846 NCIT:C34306 TAO:0001290 @@ -33640,34 +30660,12 @@ For example, A and B may be gene products and binding of B by A positively regul http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/326 - - - - Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO] - 2012-08-14 - TAO:0001290 - TAO - ZFIN:curator - - - - - the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx - MP:0012522 - NCBITaxon:40674 - stomodeal-hypophyseal primordium XAO:0000269 - - - - FBbt:00000439 - - @@ -33724,7 +30722,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -33745,13 +30743,9 @@ For example, A and B may be gene products and binding of B by A positively regul Inward fold on the surface of the embryonic ectoderm that develops into an ectodermal terminal part of the digestive tract. removed WBbt:0006795 'proctodeum' - junction between the alimentary and genital tracts in the male. - An inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[TAO] - Inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[AAO] - proctodeal AAO:0011087 EHDAA2:0000121 EMAPA:25038 - FBbt:00000123 NCIT:C34278 TAO:0000066 UMLS:C0231054 @@ -33770,7 +30764,7 @@ For example, A and B may be gene products and binding of B by A positively regul proctodeum https://github.com/obophenotype/uberon/issues/685 - + @@ -33783,7 +30777,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + EHDAA2 @@ -33794,30 +30788,6 @@ For example, A and B may be gene products and binding of B by A positively regul https://github.com/obophenotype/uberon/issues/685 https://sourceforge.net/p/fbbtdv/tickets/52 - - - - An inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[TAO] - 2012-08-14 - TAO:0000066 - TAO - ZFIN:curator - - - - - Inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[AAO] - 2012-06-20 - AAO:0011087 - AAO - ZFA:0000066 - - - - - FBbt:00000123 - - @@ -33863,7 +30833,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -33892,11 +30862,6 @@ For example, A and B may be gene products and binding of B by A positively regul - Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO] - Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO] - relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO] - As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG] - cardiac AAO:0010210 BILA:0000020 BTO:0000562 @@ -33940,14 +30905,14 @@ For example, A and B may be gene products and binding of B by A positively regul https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb - + - + MA @@ -33957,42 +30922,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Heart http://orcid.org/0000-0002-6601-2165 - - - - Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO] - 2012-08-14 - TAO:0000114 - TAO - ZFIN:curator - - - - - Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO] - 2012-06-20 - AAO:0010210 - AAO - AAO:BJB - - - - - relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO] - 2012-06-20 - AAO:0010210 - AAO - - - - - As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG] - 2012-09-17 - VHOG:0000276 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481 - http://bgee.unil.ch/ - @@ -34043,7 +30972,6 @@ For example, A and B may be gene products and binding of B by A positively regul Any thin layer or plate. TODO - merge with cell layer? - laminar Wikipedia:Lamina_of_the_vertebral_arch laminar tissue uberon @@ -34080,8 +31008,6 @@ For example, A and B may be gene products and binding of B by A positively regul Middle part of an organ, surrounded by the cortex. - this class is used in a very general sense - medullary FMA:61108 galen:Medulla medulla @@ -34122,8 +31048,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical structure that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO]. - Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO] - Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO] articulation joint AEO:0000182 @@ -34168,24 +31092,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Joint http://dx.plos.org/10.1371/journal.pone.0051070 - - - - Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO] - 2012-08-14 - VSAO:0000101 - VSAO - PSPUB:0000170 - - - - - Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO] - 2012-08-14 - TAO:0000367 - TAO - TAO:pem - @@ -34264,9 +31170,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that has as its parts the organs concerned with reproduction. consider splitting genitalia from reproductive system - Anatomical system which consists of organs and tissues associated with sexual reproduction of the organism.[AAO] - Arguably, one of the most important aspects of urbilaterian organogenesis would have been gonadogenesis, since Urbilateria must have successfully generated gametes and developed a strategy for extrusion and fertilization, in order to be the ancestor of all living Bilateria.[well established][VHOG] - 2022-06-10T18:22:34Z AAO:0010258 BILA:0000103 @@ -34277,13 +31180,11 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA:5923 EMAPA:17381 EV:0100100 - FBbt:00004857 FMA:7160 GAID:363 HAO:0000374 HAO:0000895 MA:0000326 - MESH:D005835 MIAA:0000305 NCIT:C12841 SCTID:278875001 @@ -34320,38 +31221,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that has as its parts the organs concerned with reproduction. Wikipedia:Reproductive_system - - - - Anatomical system which consists of organs and tissues associated with sexual reproduction of the organism.[AAO] - 2012-06-20 - AAO:0010258 - AAO - AAO:BJB - - - - - Arguably, one of the most important aspects of urbilaterian organogenesis would have been gonadogenesis, since Urbilateria must have successfully generated gametes and developed a strategy for extrusion and fertilization, in order to be the ancestor of all living Bilateria.[well established][VHOG] - 2012-09-17 - VHOG:0000182 - VHOG - PMID:21672850 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across Bilateria. Integrative and Comparative Biology (2007) - http://bgee.unil.ch/ - - - - - FBbt:00004857 - - - - - - MESH:D005835 - - https://github.com/biopragmatics/biomappings - @@ -34432,17 +31301,11 @@ For example, A and B may be gene products and binding of B by A positively regul Reproductive organ that produces and releases eggs (ovary) or sperm (testis). - Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO] - The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO] - Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG] - gonadal - FMA xref is a 'general anatomical term' AAO:0000213 BILA:0000123 BSA:0000079 BTO:0000534 EMAPA:17383 - FBbt:00004858 FMA:18250 GAID:368 HAO:0000379 @@ -34477,46 +31340,6 @@ For example, A and B may be gene products and binding of B by A positively regul ZFA:0000413 ZFIN:curator - - - - Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO] - 2012-06-20 - AAO:0000213 - AAO - AAO:BJB - - - - - The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO] - 2012-08-14 - TAO:0000413 - TAO - ZFIN:curator - - - - - Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG] - 2012-09-17 - VHOG:0000397 - VHOG - DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T, Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009) - http://bgee.unil.ch/ - - - - - FMA xref is a 'general anatomical term' - FMA - - - - - FBbt:00004858 - - @@ -34568,16 +31391,11 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes. - An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO] - digestive - many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class AAO:0000129 BILA:0000082 BTO:0000058 CALOHA:TS-1293 EFO:0000793 - EV:0100056 - FBbt:00005055 FMA:7152 GAID:278 MA:0002431 @@ -34614,27 +31432,6 @@ For example, A and B may be gene products and binding of B by A positively regul NLM:alimentary+system Wikipedia:Digestive_system - - - - An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO] - 2012-06-20 - AAO:0000129 - AAO - AAO:BJB - - - - - many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class - MA - - - - - FBbt:00005055 - - @@ -34675,10 +31472,6 @@ For example, A and B may be gene products and binding of B by A positively regul - An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO] - Evolution of vertebrate renal anatomy appears quite conservative when compared, for example, to evolution of respiratory and cardiovascular systems in vertebrates. Major anatomical changes in vertebrates kidneys separate those of birds and mammals from kidneys of lower vertebrates. General increase in animal size from fish to mammals is reflected by an increase in total number of nephrons per kidney, rather than by constant change in tubular dimensions.[well established][VHOG] - In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels - This definition is inclusive of the organs of the vertebrate renal system, as well as the Malpighian tubules of insects, and allows for future incorporation of structures such as the antennal glands of crustaceans excretory system AAO:0010257 BILA:0000015 @@ -34690,7 +31483,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA:5901 EMAPA:17366 EV:0100095 - FBbt:00005056 FMA:7159 GAID:391 MA:0000325 @@ -34743,43 +31535,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Acoelomorpha - - - - An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO] - 2012-06-20 - AAO:0010257 - AAO - AAO:BJB - - - - - Evolution of vertebrate renal anatomy appears quite conservative when compared, for example, to evolution of respiratory and cardiovascular systems in vertebrates. Major anatomical changes in vertebrates kidneys separate those of birds and mammals from kidneys of lower vertebrates. General increase in animal size from fish to mammals is reflected by an increase in total number of nephrons per kidney, rather than by constant change in tubular dimensions.[well established][VHOG] - 2012-09-17 - VHOG:0000723 - VHOG - ISBN:978-3540428541 Kapoor BG, Bhavna Khanna, Ichthyology Handbook (2004) p.406 - http://bgee.unil.ch/ - - - - - In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels - GO - - - - - This definition is inclusive of the organs of the vertebrate renal system, as well as the Malpighian tubules of insects, and allows for future incorporation of structures such as the antennal glands of crustaceans - DOI:10.1371/journal.pone.0099864 - - - - - FBbt:00005056 - - @@ -34835,17 +31590,12 @@ For example, A and B may be gene products and binding of B by A positively regul Organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP]. - the cardiovascular system and the lymphatic system are parts of the circulatory system - - Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO] - We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG] AAO:0000959 CALOHA:TS-2103 - MESH:D002319 VHOG:0001248 Wikipedia:Circulatory_system uberon @@ -34868,38 +31618,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Acoelomorpha - - - - - WBbt coelomocyte currently classified as circulating cell - - - - - Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO] - 2012-06-20 - AAO:0000959 - AAO - AAO:BJB - - - - - We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG] - 2012-09-17 - VHOG:0001248 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.493 - http://bgee.unil.ch/ - - - - - MESH:D002319 - - https://github.com/biopragmatics/biomappings - @@ -34927,12 +31645,8 @@ For example, A and B may be gene products and binding of B by A positively regul A subdivision of the muscular system corresponding to a subdisivision of an organism. - - In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here. - AAO:0011066 BTO:0000887 EFO:0001949 - EMAPA:32715 EMAPA:35577 FMA:32558 MA:0000165 @@ -34968,12 +31682,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Muscular_system https://orcid.org/0000-0002-6601-2165 - - - - In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here. - FMA - @@ -35037,7 +31745,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -35045,11 +31753,6 @@ For example, A and B may be gene products and binding of B by A positively regul The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]. - A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO] - Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO] - Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG] - nervous - neural AAO:0000324 BILA:0000079 BIRNLEX:844 @@ -35060,7 +31763,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA:826 EMAPA:16469 EV:0100162 - FBbt:00005093 FMA:7157 GAID:466 MA:0000016 @@ -35092,14 +31794,14 @@ For example, A and B may be gene products and binding of B by A positively regul http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -35114,40 +31816,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Nervous_system ZFIN:curator - - - - A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO] - 2012-08-14 - TAO:0000396 - TAO - ZFIN:curator - - - - - Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO] - 2012-06-20 - AAO:0000324 - AAO - AAO:BJB - - - - - Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG] - 2012-09-17 - VHOG:0000402 - VHOG - ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.117 - http://bgee.unil.ch/ - - - - - FBbt:00005093 - - @@ -35193,14 +31861,10 @@ For example, A and B may be gene products and binding of B by A positively regul - + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. - Part of the nervous system which includes the brain and spinal cord.[AAO] - The brain and spinal cord. Kimmel et al, 1995.[TAO] - The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO). - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG] AAO:0000090 BAMS:CNS BILA:0000080 @@ -35213,7 +31877,6 @@ For example, A and B may be gene products and binding of B by A positively regul EMAPA:16470 EMAPA:16754 EV:0100163 - FBbt:00005094 FMA:55675 GAID:570 MA:0000167 @@ -35242,7 +31905,7 @@ For example, A and B may be gene products and binding of B by A positively regul central nervous system - + @@ -35256,7 +31919,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + Bgee:AN @@ -35273,46 +31936,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Acoelomorpha - - - - Part of the nervous system which includes the brain and spinal cord.[AAO] - 2012-06-20 - AAO:0000090 - AAO - AAO:BJB - - - - - The brain and spinal cord. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000012 - TAO - ZFIN:curator - - - - - The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO). - BIRNLEX:1099 - - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG] - 2012-09-17 - VHOG:0000293 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 (reference 1), ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 (reference 2), DOI:10.1016/j.cell.2007.02.040 Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud'homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007) (reference 3) - http://bgee.unil.ch/ - - - - - FBbt:00005094 - - @@ -35355,15 +31978,12 @@ For example, A and B may be gene products and binding of B by A positively regul Anterior subdivision of a digestive tract. Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. In vertebrates the term may refer to a developmental structure - The anterior portion of the primitive digestive tube of the embryo that lies cephalic to the junction of the yolk stalk, consists of endodermal tissue, and gives rise to the the pharynx, lower respiratory system, esophagus, stomach, duodenum proximal to the biliary tract, liver, pancreas, biliary tract, and gall bladder. - The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] AAO:0011042 BILA:0000085 BTO:0000507 EHDAA2:0000557 EHDAA:520 EMAPA:16548 - FBbt:00005379 FMA:45616 MA:0001526 NCIT:C34180 @@ -35389,28 +32009,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anterior subdivision of a digestive tract. http://orcid.org/0000-0002-6601-2165 - - - - The anterior portion of the primitive digestive tube of the embryo that lies cephalic to the junction of the yolk stalk, consists of endodermal tissue, and gives rise to the the pharynx, lower respiratory system, esophagus, stomach, duodenum proximal to the biliary tract, liver, pancreas, biliary tract, and gall bladder. - MP:0000474 - - - - - The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0000285 - VHOG - ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 - http://bgee.unil.ch/ - - - - - FBbt:00005379 - - @@ -35446,16 +32044,12 @@ For example, A and B may be gene products and binding of B by A positively regul Middle subdivision of a digestive tract[CJM]. In vertebrates: The middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine[GO]. Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. We may explicitly make this a developmental class - The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] - In humans: originates from the foregut at the opening of the bile duct into the duodenum and continues through the small intestine and much of the large intestine until the transition to the hindgut about two-thirds of the way through the transverse colon - in FMA this represents an embryonic region. BILA:0000086 BTO:0000863 EFO:0001950 EHDAA2:0001185 EHDAA:983 EMAPA:16255 - FBbt:00005383 FMA:45617 MA:0001564 NCIT:C34210 @@ -35482,34 +32076,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0007494 Wikipedia:Midgut - - - - The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0000290 - VHOG - ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 - http://bgee.unil.ch/ - - - - - In humans: originates from the foregut at the opening of the bile duct into the duodenum and continues through the small intestine and much of the large intestine until the transition to the hindgut about two-thirds of the way through the transverse colon - WP - - - - - in FMA this represents an embryonic region. - FMA - - - - - FBbt:00005383 - - @@ -35530,7 +32096,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -35539,16 +32105,12 @@ For example, A and B may be gene products and binding of B by A positively regul The caudalmost subdivision of a digestive tract. Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future (vertebrates have some contribution from NC - https://github.com/obophenotype/uberon/wiki/The-neural-crest). We may explicitly make this a developmental class - the caudal portion of the primitive digestive tube of the embryo - The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] - in FMA this class has no children. In MA it has a single child hindgut epithelium AAO:0011052 BILA:0000087 BTO:0000510 EHDAA2:0000779 EHDAA:975 EMAPA:16715 - FBbt:00005384 FMA:45618 MA:0001527 NCIT:C34188 @@ -35567,14 +32129,14 @@ For example, A and B may be gene products and binding of B by A positively regul hindgut http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray472.png - + - + Wikipedia @@ -35583,34 +32145,6 @@ For example, A and B may be gene products and binding of B by A positively regul The caudalmost subdivision of a digestive tract. http://orcid.org/0000-0002-6601-2165 - - - - the caudal portion of the primitive digestive tube of the embryo - MP:0008786 - - - - - The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0000459 - VHOG - ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 - http://bgee.unil.ch/ - - - - - in FMA this class has no children. In MA it has a single child hindgut epithelium - FMA - - - - - FBbt:00005384 - - @@ -35642,7 +32176,6 @@ For example, A and B may be gene products and binding of B by A positively regul BTO:0001886 EFO:0001652 EHDAA2:0003171 - FBbt:00005495 FMA:86589 MAT:0000482 NCIT:C34275 @@ -35676,12 +32209,6 @@ For example, A and B may be gene products and binding of B by A positively regul FB:FBrf0089570 http://flybase.org/reports/FBrf0178740.html - - - - FBbt:00005495 - - @@ -35718,10 +32245,6 @@ For example, A and B may be gene products and binding of B by A positively regul In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted]. - Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO] - The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG] - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] - The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium AAO:0010617 BTO:0001057 CALOHA:TS-2371 @@ -35733,7 +32256,6 @@ For example, A and B may be gene products and binding of B by A positively regul EMAPA:16757 FMA:293882 MAT:0000069 - MESH:D054259 MIAA:0000069 NCIT:C34226 SCTID:362852000 @@ -35767,49 +32289,6 @@ For example, A and B may be gene products and binding of B by A positively regul In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted]. Wikipedia:Neural_tube - - - - Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO] - 2012-06-20 - AAO:0010617 - AAO - AAO:JOR - - - - - The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG] - 2012-09-17 - VHOG:0000307 - VHOG - http://bgee.unil.ch/ - http://medical-dictionary.thefreedictionary.com/neural+tube - - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] - 2012-09-17 - VHOG:0000307 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 - http://bgee.unil.ch/ - - - - - The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium - GO:0021915 - - - - - MESH:D054259 - - - https://github.com/biopragmatics/biomappings - @@ -35840,7 +32319,6 @@ For example, A and B may be gene products and binding of B by A positively regul BIRNLEX:6 CARO:0000000 EHDAA2:0002229 - FBbt:10000000 FMA:62955 HAO:0000000 MA:0000001 @@ -35864,12 +32342,6 @@ For example, A and B may be gene products and binding of B by A positively regul FMA:62955 http://orcid.org/0000-0001-9114-8737 - - - - FBbt:10000000 - - @@ -35908,8 +32380,6 @@ For example, A and B may be gene products and binding of B by A positively regul A vein that carries deoxygenated blood from the lower half of the body into the right atrium of the heart. - Trunk of systemic vein which is formed by the union of the right common iliac vein and the left common iliac vein and terminates in the right atrium[FMA]. - Phylogenetic modifications within this basic pattern of arteries and veins are largely correlated with functional changes. In the transition from water to land, gills gave way to lungs, accompanied by the establishment of a pulmonary circulation. In some fishes and certainly in tetrapods, the cardinal veins become less involved in blood return. Instead, the composite, prominent postcava (posterior vena cava) arose to drain the posterior part of the body and the precava (anterior vena cava) developed to drain the anterior part of the body.[well established][VHOG] AAO:0011083 BTO:0002682 EHDAA2:0000611 @@ -35946,22 +32416,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Inferior_vena_cava http://orcid.org/0000-0002-6601-2165 - - - - Trunk of systemic vein which is formed by the union of the right common iliac vein and the left common iliac vein and terminates in the right atrium[FMA]. - FMA:10951 - - - - - Phylogenetic modifications within this basic pattern of arteries and veins are largely correlated with functional changes. In the transition from water to land, gills gave way to lungs, accompanied by the establishment of a pulmonary circulation. In some fishes and certainly in tetrapods, the cardinal veins become less involved in blood return. Instead, the composite, prominent postcava (posterior vena cava) arose to drain the posterior part of the body and the precava (anterior vena cava) developed to drain the anterior part of the body.[well established][VHOG] - 2012-09-17 - VHOG:0001194 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.454-455 - http://bgee.unil.ch/ - @@ -36025,7 +32479,6 @@ For example, A and B may be gene products and binding of B by A positively regul Excretion that is the output of a kidney. - kidney excreta from some taxa (e.g. in aves) may not be liquid BTO:0001419 CALOHA:TS-1092 EFO:0001939 @@ -36093,8 +32546,6 @@ For example, A and B may be gene products and binding of B by A positively regul Either of the pair of major vessels which arise from the renal hilus and return blood from the kidneys, suprarenal gland and the ureter to the inferior vena cava. - The renal veins are veins that drain the kidney. They connect the kidney to the inferior vena cava. It is usually singular to each kidney, except in the condition 'multiple renal veins'. It also divides into 2 divisions upon entering the kidney: the anterior branch which receives blood from the anterior portion of the kidney and, the posterior branch which receives blood from the posterior portion. Often, each renal vein will have a branch that receives blood from the ureter. [WP,unvetted][Wikipedia:Renal_vein]. - in EHDAA2, the renal vein is part of the kidney BTO:0002681 EHDAA2:0001602 EHDAA:8722 @@ -36130,18 +32581,6 @@ For example, A and B may be gene products and binding of B by A positively regul MGI:csmith MP:0011323 - - - - The renal veins are veins that drain the kidney. They connect the kidney to the inferior vena cava. It is usually singular to each kidney, except in the condition 'multiple renal veins'. It also divides into 2 divisions upon entering the kidney: the anterior branch which receives blood from the anterior portion of the kidney and, the posterior branch which receives blood from the posterior portion. Often, each renal vein will have a branch that receives blood from the ureter. [WP,unvetted][Wikipedia:Renal_vein]. - Wikipedia:Renal_vein - - - - - in EHDAA2, the renal vein is part of the kidney - EHDAA2 - @@ -36175,14 +32614,14 @@ For example, A and B may be gene products and binding of B by A positively regul - + - + @@ -36234,24 +32673,24 @@ For example, A and B may be gene products and binding of B by A positively regul renal pelvis https://upload.wikimedia.org/wikipedia/commons/c/c0/Illu_kidney2.jpg - + - + - + MA - + FMA @@ -36297,7 +32736,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -36306,7 +32745,6 @@ For example, A and B may be gene products and binding of B by A positively regul Outer cortical portion of the kidney, between the renal capsule and the renal medulla. - In the adult metanephros, it forms a continuous smooth outer zone with a number of projections that extend down between the pyramids. It contains the renal corpuscles and the renal tubules except for parts of the loop of Henle which descend into the renal medulla. It also contains blood vessels and cortical collecting ducts. The renal cortex is the part of the kidney where ultrafiltration occurs.[WP] BTO:0001166 CALOHA:TS-0503 EMAPA:17952 @@ -36334,14 +32772,14 @@ For example, A and B may be gene products and binding of B by A positively regul https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg - + - + FMA @@ -36377,7 +32815,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -36392,9 +32830,6 @@ For example, A and B may be gene products and binding of B by A positively regul The structure containing the glomerular capsule and the glomerulus that serves as the initial blood-filtering component of a nephron. - A mass of arterial capillaries enveloped in a capsule and attached to a tubule in the kidney[BTO] - A tuft of capillaries found in a Bowman's capsule in which waste products are filtered from the blood and urine formation is initiated. Paired highly vascularized structures of the pronephros, responsible for blood filtration.[XAO] - The part of the nephron that filters blood.[TAO] BTO:0000333 CALOHA:TS-1317 EMAPA:28236 @@ -36425,14 +32860,14 @@ For example, A and B may be gene products and binding of B by A positively regul renal corpuscle https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg - + - + MA ZFA @@ -36443,33 +32878,6 @@ For example, A and B may be gene products and binding of B by A positively regul ISBN:0-683-40008-8 MP:0002827 - - - - A mass of arterial capillaries enveloped in a capsule and attached to a tubule in the kidney[BTO] - 2012-11-28 - BTO:0000333 - BTO - BTO:curator - - - - - A tuft of capillaries found in a Bowman's capsule in which waste products are filtered from the blood and urine formation is initiated. Paired highly vascularized structures of the pronephros, responsible for blood filtration.[XAO] - 2012-11-28 - XAO:0000146 - XAO - XAO:curator - - - - - The part of the nephron that filters blood.[TAO] - 2012-08-14 - TAO:0005281 - TAO - ZFIN:curator - @@ -36533,7 +32941,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -36541,9 +32949,6 @@ For example, A and B may be gene products and binding of B by A positively regul A cup-like sac at the expanded beginning of a tubular component of a nephron that contains the glomerulus. - Anatomical structure found in the kidney consisting of an expanded end of a kidney tubule surrounding a glomerulus and is the major site of filtration.[AAO] - Fluids from blood in the glomerulus are collected in the Bowman's capsule and further processed along the nephron to form urine. This process is known as ultrafiltration[WP]. - One fold of the S-shaped body gives rise to Bowman's capsule[GUDMAP] AAO:0010526 BTO:0002297 EMAPA:27973 @@ -36578,14 +32983,14 @@ For example, A and B may be gene products and binding of B by A positively regul glomerular capsule http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg - + - + Wikipedia @@ -36596,15 +33001,6 @@ For example, A and B may be gene products and binding of B by A positively regul MP:0002828 Wikipedia:Bowman%27s_capsule - - - - Anatomical structure found in the kidney consisting of an expanded end of a kidney tubule surrounding a glomerulus and is the major site of filtration.[AAO] - 2012-06-20 - AAO:0010526 - AAO - AAO:BJB - @@ -36684,11 +33080,16 @@ For example, A and B may be gene products and binding of B by A positively regul - + - - + + + + + + + @@ -36697,7 +33098,6 @@ For example, A and B may be gene products and binding of B by A positively regul An epithelial tube that is part of the nephron, the functional part of the kidney. - note that in ISBN:0073040584 (Vertebrates, Kardong), the uriniferous tubule contains the nephron, so we have a separate class, rather than using a synonym, as in MA UBERON:0004210 renal tubule BTO:0000343 @@ -36727,7 +33127,7 @@ For example, A and B may be gene products and binding of B by A positively regul nephron tubule - + @@ -36736,18 +33136,14 @@ For example, A and B may be gene products and binding of B by A positively regul - + - - - - - + GO MA ZFA @@ -36761,15 +33157,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + ZFA - - - - - checkme - @@ -36777,12 +33167,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0072078 Wikipedia:Renal_tubule - - - - note that in ISBN:0073040584 (Vertebrates, Kardong), the uriniferous tubule contains the nephron, so we have a separate class, rather than using a synonym, as in MA - MA - @@ -36808,7 +33192,12 @@ For example, A and B may be gene products and binding of B by A positively regul - + + + + + + @@ -36823,8 +33212,6 @@ For example, A and B may be gene products and binding of B by A positively regul The collecting duct is a portion of the nephron through which water flows, moving passively down its concentration gradient. - Renal duct that collects the output from renal tubules.[TAO] - in ISBN:0073040584 (Vertebrates, Kardong), the nephron is adjacent to the collecting tubule, consistent with FMA, but not GO. Wikipedia says: Many sources include the connecting tubule as part of the collecting duct system. However, the embryological origin is more similar to the nephron than it is to the rest of the collecting duct (which derives from the ureteric bud), and other sources therefore classify the connecting tubule with the nephron BTO:0000761 CALOHA:TS-0860 EMAPA:28407 @@ -36856,17 +33243,6 @@ For example, A and B may be gene products and binding of B by A positively regul collecting duct of renal tubule - - - - - - - - - checkme - GO - @@ -36874,21 +33250,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0072044 Wikipedia:Collecting_tubule - - - - Renal duct that collects the output from renal tubules.[TAO] - 2012-08-14 - TAO:0005294 - TAO - ZFIN:curator - - - - - in ISBN:0073040584 (Vertebrates, Kardong), the nephron is adjacent to the collecting tubule, consistent with FMA, but not GO. Wikipedia says: Many sources include the connecting tubule as part of the collecting duct system. However, the embryological origin is more similar to the nephron than it is to the rest of the collecting duct (which derives from the ureteric bud), and other sources therefore classify the connecting tubule with the nephron - FMA - @@ -36938,17 +33299,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - @@ -36957,12 +33307,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - @@ -36971,12 +33315,9 @@ For example, A and B may be gene products and binding of B by A positively regul Orifice at the opposite end of an animal's digestive tract from the mouth. Its function is to expel feces, unwanted semi-solid matter produced during digestion, which, depending on the type of animal, may be one or more of: matter which the animal cannot digest, such as bones; food material after all the nutrients have been extracted, for example cellulose or lignin; ingested matter which would be toxic if it remained in the digestive tract; and dead or excess gut bacteria and other endosymbionts. - anal - In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html BTO:0001680 CALOHA:TS-2005 EV:0100082 - FBbt:00047153 FMA:15711 GAID:312 MA:0000331 @@ -37008,12 +33349,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Anus ZFIN:curator - - - - FBbt:00047153 - - @@ -37029,16 +33364,15 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + + + + + + Distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP]. - - A saccular organ in which urine accumulates before discharge from the body. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] - Anatomical structure which consists of a membranous sac used to temporarily store urine until it is excreted from the body.[AAO] - In tetrapods, the urinary bladder arises as an outpocketing of the cloaca. (...) The tetrapod urinary bladder appears first among amphibians and is present in Sphenodon, turtles, most lizards, ostriches among birds, and all mammals.[well established][VHOG] - vesical - The urinary bladder evolved in tetrapods. Birds to not possess a true urinary bladder, although Palaeognathae have an undifferentiated cloacal outpocketing that serves a similar function[https://github.com/obophenotype/uberon/issues/454] bladder AAO:0000623 BTO:0001418 @@ -37077,14 +33411,10 @@ For example, A and B may be gene products and binding of B by A positively regul https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urinary_Bladder.glb https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg - + - - - - @@ -37094,15 +33424,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + FMA - - - - - upper part of UG sinus - @@ -37110,42 +33434,6 @@ For example, A and B may be gene products and binding of B by A positively regul MGI:anna Wikipedia:Urinary_bladder - - - - - https://orcid.org/0000-0003-3308-6245 - GOTAX:0010073 - https://github.com/obophenotype/uberon/issues/454 - - - - - A saccular organ in which urine accumulates before discharge from the body. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] - 2012-09-17 - VHOG:0000740 - VHOG - http://bgee.unil.ch/ - - - - - Anatomical structure which consists of a membranous sac used to temporarily store urine until it is excreted from the body.[AAO] - 2012-06-20 - AAO:0000623 - AAO - AAO:BJB - - - - - In tetrapods, the urinary bladder arises as an outpocketing of the cloaca. (...) The tetrapod urinary bladder appears first among amphibians and is present in Sphenodon, turtles, most lizards, ostriches among birds, and all mammals.[well established][VHOG] - 2012-09-17 - VHOG:0000740 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.577-78 - http://bgee.unil.ch/ - @@ -37208,12 +33496,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - @@ -37222,8 +33504,6 @@ For example, A and B may be gene products and binding of B by A positively regul The organism subdivision that includes the pelvic girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pelvic girdle regions. - this class describes the subdivision of the limb/fin, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831). See also comments on obo-anatomy mail list. Note that even though the class includes soft tissue it is more restrictive than 'pelvis' which also includes structures in cavities etc. TODO this needs to be better documented - Subdivision of lower limb or fin which links the limb/fin to the body[FMA,modified]. There is only one instance of the pelvic girdle region per organism.[VSAO] EMAPA:37862 FMA:16581 NCIT:C33291 @@ -37249,15 +33529,6 @@ For example, A and B may be gene products and binding of B by A positively regul https://groups.google.com/d/topic/obo-anatomy/h4R4xKmINrw/discussion https://orcid.org/0000-0002-6601-2165 - - - - Subdivision of lower limb or fin which links the limb/fin to the body[FMA,modified]. There is only one instance of the pelvic girdle region per organism.[VSAO] - 2012-08-14 - VSAO:0000304 - VSAO - https://orcid.org/0000-0002-6601-2165 - @@ -37283,20 +33554,23 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + + + + + + - + The basic functional unit of the kidney. its chief function is to regulate the concentration of water and soluble substances like sodium salts by filtering the blood, reabsorbing what is needed and excreting the rest as urine. A nephron eliminates wastes from the body, regulates blood volume and blood pressure, controls levels of electrolytes and metabolites, and regulates blood pH. Its functions are vital to life and are regulated by the endocrine system by hormones such as antidiuretic hormone, aldosterone, and parathyroid hormone.[WP]. kidney terms require review for cross-vertebrate compatibility and developmental relationships. - Functional unit of the kidney that filters waste.[TAO] - In the avian kidney, three types of nephron are identified: mammalian-type nephrons with long and short loops of Henle, and reptilian type nephrons (Gambaryan, 1992) BTO:0000924 CALOHA:TS-1312 EMAPA:28491 @@ -37324,34 +33598,24 @@ For example, A and B may be gene products and binding of B by A positively regul nephron http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + - - - - - + - + FMA - - definitional - - - - - + Bgee:AN @@ -37361,21 +33625,6 @@ For example, A and B may be gene products and binding of B by A positively regul PMID:9268568 Wikipedia:Nephron - - - - Functional unit of the kidney that filters waste.[TAO] - 2012-08-14 - TAO:0002153 - TAO - ZFIN:curator - - - - - In the avian kidney, three types of nephron are identified: mammalian-type nephrons with long and short loops of Henle, and reptilian type nephrons (Gambaryan, 1992) - GO - @@ -37411,15 +33660,20 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + + + + + + - + @@ -37427,7 +33681,6 @@ For example, A and B may be gene products and binding of B by A positively regul The proximal convoluted tubule is the most proximal portion of the proximal tubule and extends from the glomerular capsule to the proximal straight tubule. - Renal tubule that connects to the renal corpuscle.[TAO] CALOHA:TS-2198 EMAPA:28287 EV:0100388 @@ -37456,15 +33709,11 @@ For example, A and B may be gene products and binding of B by A positively regul proximal convoluted tubule http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - - - - - + - + @@ -37477,20 +33726,13 @@ For example, A and B may be gene products and binding of B by A positively regul - - MA uses subclass - GOC:mtg_kidney_jan10 - - - - - + GO - + Wikipedia @@ -37499,15 +33741,6 @@ For example, A and B may be gene products and binding of B by A positively regul The proximal convoluted tubule is the most proximal portion of the proximal tubule and extends from the glomerular capsule to the proximal straight tubule. GO:0072019 - - - - Renal tubule that connects to the renal corpuscle.[TAO] - 2012-08-14 - TAO:0005290 - TAO - ZFIN:curator - @@ -37581,11 +33814,7 @@ For example, A and B may be gene products and binding of B by A positively regul The section of the renal tubule in the kidney medulla with a hairpin bend; consists of a descending limb and an ascending limb, and is situated between the proximal convoluted tubule to the distal convoluted tubule; it functions to reabsorb water and ions from the urine. the definitions of some kidney parts (e.g. proximal straight tubule) refer to Henle's loop, even in species where this may not be present. Requires review. - - A highly specialized segment of the mammalian kidney tubules, that dips into the medulla. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, p.648, see_Liem_KF][VHOG] - The structure differs considerably between species; there is a definite physical loop of Henle in the mammalian and avian renal systems but this seems to be absent in Xenopus. However, homologs of some, but not all, molecular markers (e.g. cldn8 and clcnk) of the mammalian loop of Henle were found to be present in the pronephros of the frog larva . - The loop of Henle plays an important role in creating a concentration gradient in the medulla of the kidney. It is involved in reabsorption of filtered water and ions including sodium, potassium and calcium, and independently regulates both the volume and osmolarity of body fluids. BTO:0004608 EMAPA:19280 EV:0100390 @@ -37615,27 +33844,6 @@ For example, A and B may be gene products and binding of B by A positively regul MGI:csmith MP:0004755 - - - - A highly specialized segment of the mammalian kidney tubules, that dips into the medulla. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, p.648, see_Liem_KF][VHOG] - 2012-09-17 - VHOG:0001270 - VHOG - http://bgee.unil.ch/ - - - - - The structure differs considerably between species; there is a definite physical loop of Henle in the mammalian and avian renal systems but this seems to be absent in Xenopus. However, homologs of some, but not all, molecular markers (e.g. cldn8 and clcnk) of the mammalian loop of Henle were found to be present in the pronephros of the frog larva . - DOI:10.1371/journal.pone.0099864 - - - - - The loop of Henle plays an important role in creating a concentration gradient in the medulla of the kidney. It is involved in reabsorption of filtered water and ions including sodium, potassium and calcium, and independently regulates both the volume and osmolarity of body fluids. - DOI:10.1371/journal.pone.0099864 - @@ -37656,7 +33864,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -37683,7 +33891,7 @@ For example, A and B may be gene products and binding of B by A positively regul descending limb of loop of Henle http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + @@ -37696,7 +33904,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + FMA @@ -37720,9 +33928,14 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + + + + + + @@ -37738,7 +33951,6 @@ For example, A and B may be gene products and binding of B by A positively regul The proximal straight tubule is the part of the descending limb that extends from the proximal convoluted tubule to the descending thin tubule. TODO - is S3 exactly coincident with PST? todo - ensure relationships work across species (loop of Henle) - Portion of the renal tubule which is just posterior to the proximal convoluted tubule.[TAO] UBERON:0005166 BTO:0000055 EMAPA:29661 @@ -37762,15 +33974,11 @@ For example, A and B may be gene products and binding of B by A positively regul proximal straight tubule - + - - - - - + @@ -37783,20 +33991,13 @@ For example, A and B may be gene products and binding of B by A positively regul - + MA - - MA uses subclass - GOC:mtg_kidney_jan10 - - - - - + MA @@ -37805,15 +34006,6 @@ For example, A and B may be gene products and binding of B by A positively regul The proximal straight tubule is the part of the descending limb that extends from the proximal convoluted tubule to the descending thin tubule. GO:0072020 - - - - Portion of the renal tubule which is just posterior to the proximal convoluted tubule.[TAO] - 2012-08-14 - TAO:0005291 - TAO - ZFIN:curator - @@ -37847,7 +34039,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -37862,8 +34054,6 @@ For example, A and B may be gene products and binding of B by A positively regul The first segment of the nephron lying just downstream from the loop of Henle, immediately after the macula densa. - a portion of kidney nephron between the loop of Henle and the collecting duct system[Wikipedia:Distal_convoluted_tubule]. - in humans it is responsible for the reabsorption of about 5% of filtered sodium via the thiazide-sensitive Na-Cl symporter. EMAPA:28393 EV:0100389 FMA:17721 @@ -37885,7 +34075,7 @@ For example, A and B may be gene products and binding of B by A positively regul distal convoluted tubule https://upload.wikimedia.org/wikipedia/commons/2/21/Kidney_nephron.png - + @@ -37898,7 +34088,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + EMAPA GO MA-modified-from-isa @@ -37909,12 +34099,6 @@ For example, A and B may be gene products and binding of B by A positively regul The first segment of the nephron lying just downstream from the loop of Henle, immediately after the macula densa. GO:0072025 - - - - a portion of kidney nephron between the loop of Henle and the collecting duct system[Wikipedia:Distal_convoluted_tubule]. - Wikipedia:Distal_convoluted_tubule - @@ -38026,9 +34210,13 @@ For example, A and B may be gene products and binding of B by A positively regul - + + + + + + The anus and surrounding regions. Encompasses both internal and external regions, where present. - Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] EFO:0000847 EHDAA2:0000122 EHDAA:2931 @@ -38052,32 +34240,12 @@ For example, A and B may be gene products and binding of B by A positively regul https://github.com/obophenotype/uberon/issues/507 http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray408.png - - - - - - - - - cjm - The anus and surrounding regions. Encompasses both internal and external regions, where present. https://orcid.org/0000-0002-6601-2165 - - - - Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] - 2012-09-17 - VHOG:0000395 - VHOG - ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 - http://bgee.unil.ch/ - @@ -38134,13 +34302,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system. - - Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO] - Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO] - System that provides physical support to the organism.[AAO] - By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG] - skeletal - GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates AAO:0000566 BTO:0001486 CALOHA:TS-1320 @@ -38176,50 +34337,6 @@ For example, A and B may be gene products and binding of B by A positively regul VSAO:0000027 http://dx.plos.org/10.1371/journal.pone.0051070 - - - - Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO] - 2012-08-14 - TAO:0000434 - TAO - TAO:wd - - - - - Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO] - 2012-08-14 - VSAO:0000027 - VSAO - GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 - PSPUB:0000170 - - - - - System that provides physical support to the organism.[AAO] - 2012-06-20 - AAO:0000566 - AAO - AAO:LAP - - - - - By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG] - 2012-09-17 - VHOG:0001254 - VHOG - DOI:10.1159/000324245 Donoghue PCJ, Sansom IJ, Origin and early evolution of vertebrate skeletonization. Microscopy research and technique (2002) - http://bgee.unil.ch/ - - - - - GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates - GO - @@ -38246,7 +34363,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -38269,14 +34386,14 @@ For example, A and B may be gene products and binding of B by A positively regul kidney arcuate artery https://upload.wikimedia.org/wikipedia/commons/8/87/2610_The_Kidney.jpg - + - + MA @@ -38317,16 +34434,11 @@ For example, A and B may be gene products and binding of B by A positively regul - + A tube extending from the mouth to the anus. - The alimentary or digestive tract, and associated organs.[TAO] - The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] - FMA also has a term 'gastrointestinal tract', but this includes the liver. - we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509 - we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this gut AAO:0010023 BILA:0000083 @@ -38335,10 +34447,8 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA2:0000726 EHDAA:518 EMAPA:16247 - FBbt:00003125 FMA:45615 MA:0000917 - MESH:D041981 NCIT:C34082 TAO:0000112 TGMA:0001819 @@ -38360,14 +34470,14 @@ For example, A and B may be gene products and binding of B by A positively regul digestive tract - + - + NCBIBook:NBK10107 @@ -38389,50 +34499,6 @@ For example, A and B may be gene products and binding of B by A positively regul DOI:10.1371/journal.pone.0016309 - - - - The alimentary or digestive tract, and associated organs.[TAO] - 2012-08-14 - TAO:0000112 - TAO - ZFIN:curator - - - - - The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0000309 - VHOG - ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 - http://bgee.unil.ch/ - - - - - FMA also has a term 'gastrointestinal tract', but this includes the liver. - FMA - - - - - we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509 - MA - - - - - FBbt:00003125 - - - - - - MESH:D041981 - - https://github.com/biopragmatics/biomappings - @@ -38527,12 +34593,7 @@ For example, A and B may be gene products and binding of B by A positively regul Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]. - Portion of tissue composed of contractile fibers.[TAO] - It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG] - muscular muscle - AAO:0011066 - EMAPA:32715 EMAPA:37474 EV:0100146 FMA:5022 @@ -38558,25 +34619,6 @@ For example, A and B may be gene products and binding of B by A positively regul Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]. GO:0007517 - - - - Portion of tissue composed of contractile fibers.[TAO] - 2012-08-14 - TAO:0005145 - TAO - ZFIN:curator - - - - - It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG] - 2012-09-17 - VHOG:0001245 - VHOG - ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.75 - http://bgee.unil.ch/ - @@ -38604,17 +34646,11 @@ For example, A and B may be gene products and binding of B by A positively regul An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition]. Note that in FMA an artery is a tree, whereas AEO/JB defines it as a tube; FMA includes a separate class for what it calls the trunk. Classification in this ontology may currently (Jan 2012) represent a mix of both schemes, although we are gradually revising in the direction of the AEO scheme. - Part of the circulatory system composed of blood vessels which carry oxygenated blood away from the heart to the rest of the body.[AAO] - The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] - arterial - Some arthropods have primitive arterial systems but this term refers to arteries in a true closed circulatory system. - AAO:0010211 AEO:0000208 BTO:0000573 CALOHA:TS-0054 EFO:0000814 - EHDAA2:0000143 EHDAA2:0003253 EMAPA:35147 EV:0100026 @@ -38652,25 +34688,6 @@ For example, A and B may be gene products and binding of B by A positively regul An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition]. AEO:JB - - - - Part of the circulatory system composed of blood vessels which carry oxygenated blood away from the heart to the rest of the body.[AAO] - 2012-06-20 - AAO:0010211 - AAO - AAO:BJB - - - - - The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] - 2012-09-17 - VHOG:0001251 - VHOG - DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006) - http://bgee.unil.ch/ - @@ -38716,10 +34733,6 @@ For example, A and B may be gene products and binding of B by A positively regul Any of the tubular branching vessels that carry blood from the capillaries toward the heart. TODO - check with MA - vein vs venous blood vessel - Part of the circulatory system composed of blood vessels which carry blood from other organs, tissues, and cells to the heart.[AAO] - The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] - venous - venous subtree venous vessel AAO:0010212 @@ -38764,25 +34777,6 @@ For example, A and B may be gene products and binding of B by A positively regul Any of the tubular branching vessels that carry blood from the capillaries toward the heart. Wikipedia:Vein - - - - Part of the circulatory system composed of blood vessels which carry blood from other organs, tissues, and cells to the heart.[AAO] - 2012-06-20 - AAO:0010212 - AAO - AAO:BJB - - - - - The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] - 2012-09-17 - VHOG:0001743 - VHOG - DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006) - http://bgee.unil.ch/ - @@ -38823,8 +34817,6 @@ For example, A and B may be gene products and binding of B by A positively regul Outermost layer of an organ[WP]. - cortical - this class is used more generically than in FMA, and includes e.g. cortex of hair EFO:0000383 EHDAA:9344 FMA:61109 @@ -38845,12 +34837,6 @@ For example, A and B may be gene products and binding of B by A positively regul Outermost layer of an organ[WP]. Wikipedia:Cortex_(anatomy) - - - - this class is used more generically than in FMA, and includes e.g. cortex of hair - FMA - @@ -38977,7 +34963,6 @@ For example, A and B may be gene products and binding of B by A positively regul One of the minute vessels that collect deoxygenated blood from the capillary plexuses returns it to the veins. - Multi-tissue structure part of the blood vasculature formed by the anastomosis of capillaries. Venules carry blood toward the heart.[TAO] BTO:0002626 EMAPA:35917 FMA:63130 @@ -39007,15 +34992,6 @@ For example, A and B may be gene products and binding of B by A positively regul MESH:A07.231.432.952 MP:0004125 - - - - Multi-tissue structure part of the blood vasculature formed by the anastomosis of capillaries. Venules carry blood toward the heart.[TAO] - 2012-08-14 - TAO:0005315 - TAO - ZFIN:curator - @@ -39071,8 +35047,6 @@ For example, A and B may be gene products and binding of B by A positively regul The smallest division of the artery located between the muscular arteries and the capillaries[GO]. - Multi-tissue structure part of the blood vasculature, feeds into capillaries. Arterioles carry blood away from the heart.[TAO] - Small, terminal branch of an artery which generally connects to capillaries.[AAO] AAO:0010253 BTO:0001997 EMAPA:35146 @@ -39107,24 +35081,6 @@ For example, A and B may be gene products and binding of B by A positively regul The smallest division of the artery located between the muscular arteries and the capillaries[GO]. GO:0014830 - - - - Multi-tissue structure part of the blood vasculature, feeds into capillaries. Arterioles carry blood away from the heart.[TAO] - 2012-08-14 - TAO:0002138 - TAO - ZFIN:curator - - - - - Small, terminal branch of an artery which generally connects to capillaries.[AAO] - 2012-06-20 - AAO:0010253 - AAO - AAO:BJB - @@ -39146,14 +35102,15 @@ For example, A and B may be gene products and binding of B by A positively regul + - - + + @@ -39166,7 +35123,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -39182,11 +35139,6 @@ For example, A and B may be gene products and binding of B by A positively regul A vessel through which blood circulates in the body. consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus - Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG] - Any of the vessels through which blood circulates in the body.[AAO] - The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] - annelids have blood vessels, but this class is not applicable to annelids. - FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX vascular element AAO:0011004 AEO:0000207 @@ -39225,34 +35177,34 @@ For example, A and B may be gene products and binding of B by A positively regul blood vessel http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg - + - + - + - + AEO - + EHDAA2 - + GO:0072360 @@ -39262,40 +35214,6 @@ For example, A and B may be gene products and binding of B by A positively regul BTO:0001102 Wikipedia:Blood_vessel - - - - Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG] - 2012-09-17 - VHOG:0001250 - VHOG - http://bgee.unil.ch/ - - - - - Any of the vessels through which blood circulates in the body.[AAO] - 2012-06-20 - AAO:0011004 - AAO - AAO:EJS - - - - - The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] - 2012-09-17 - VHOG:0001250 - VHOG - DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006) - http://bgee.unil.ch/ - - - - - FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX - FMA - @@ -39364,9 +35282,6 @@ For example, A and B may be gene products and binding of B by A positively regul Any of the smallest blood vessels connecting arterioles with venules. not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element - Any of the tiny blood vessels connecting the arterioles to the venules.[AAO] - The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] - capillaries lack tunica media and tunica adventitia; only the endothelial wall of the tunica intima belongs AAO:0010252 BTO:0002045 CALOHA:TS-2006 @@ -39405,25 +35320,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Capillary https://github.com/obophenotype/uberon/issues/137 - - - - Any of the tiny blood vessels connecting the arterioles to the venules.[AAO] - 2012-06-20 - AAO:0010252 - AAO - AAO:BJB - - - - - The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] - 2012-09-17 - VHOG:0001253 - VHOG - DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006) - http://bgee.unil.ch/ - @@ -39463,7 +35359,6 @@ For example, A and B may be gene products and binding of B by A positively regul A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA]. - endothelial BTO:0000393 CALOHA:TS-0278 EFO:0002548 @@ -39531,7 +35426,6 @@ For example, A and B may be gene products and binding of B by A positively regul An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face. see also: vascular system. Consider merging? - vascular BTO:0003718 FMA:69050 TAO:0005249 @@ -39589,16 +35483,11 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical structure that is part of an embryo. - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO] - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO] - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO] - in FMA embryo is_a embryonic structure AAO:0000138 BILA:0000034 BTO:0000174 CALOHA:TS-2110 EFO:0000461 - FBbt:00004208 FMA:69067 GAID:407 MESH:D004628 @@ -39629,45 +35518,6 @@ For example, A and B may be gene products and binding of B by A positively regul BTO:0000174 ZFIN:curator - - - - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO] - 2012-06-20 - AAO:0000138 - AAO - AAO:BJB - - - - - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO] - 2012-08-14 - TAO:0001105 - TAO - ZFIN:curator - - - - - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO] - 2012-08-14 - VSAO:0000178 - VSAO - ZFIN:curator - - - - - in FMA embryo is_a embryonic structure - FMA - - - - - FBbt:00004208 - - @@ -39724,8 +35574,6 @@ For example, A and B may be gene products and binding of B by A positively regul An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen. - An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO] - general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs. AAO:0010386 BTO:0001491 EHDAA:512 @@ -39760,21 +35608,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Viscus https://github.com/obophenotype/mouse-anatomy-ontology/issues/14 - - - - An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO] - 2012-06-20 - AAO:0010386 - AAO - BTO:0001491 - - - - - general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs. - FMA - @@ -39811,17 +35644,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - @@ -39832,9 +35654,6 @@ For example, A and B may be gene products and binding of B by A positively regul A cardiac atrium that is in the right side of the heart. It receives deoxygenated blood. In mammals, this comes from the superior and inferior vena cava and the coronary sinus, and pumps it into the right ventricle through the tricuspid valve. - Right cardiac chamber which is continuous with the superior vena cava and inferior vena cava.[FMA] - The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG] - https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern AAO:0010248 BTO:0001703 EHDAA2:0000290 @@ -39871,22 +35690,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Right_atrium http://orcid.org/0000-0002-6601-2165 - - - - Right cardiac chamber which is continuous with the superior vena cava and inferior vena cava.[FMA] - FMA:7096 - - - - - The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG] - 2012-09-17 - VHOG:0000328 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 - http://bgee.unil.ch/ - @@ -39918,7 +35721,6 @@ For example, A and B may be gene products and binding of B by A positively regul - @@ -39933,9 +35735,6 @@ For example, A and B may be gene products and binding of B by A positively regul Cardiac chamber in which blood enters the heart. - One of four heart chambers.[TAO] - One of two chambers of the heart which receive blood from the veins and forces it by muscular contration to the ventricle.[AAO] - In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG] AAO:0010246 BTO:0000903 CALOHA:TS-0437 @@ -39978,34 +35777,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Heart_atrium http://orcid.org/0000-0002-6601-2165 - - - - One of four heart chambers.[TAO] - 2012-08-14 - TAO:0000471 - TAO - ZFIN:curator - - - - - One of two chambers of the heart which receive blood from the veins and forces it by muscular contration to the ventricle.[AAO] - 2012-06-20 - AAO:0010246 - AAO - AAO:BJB - - - - - In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG] - 2012-09-17 - VHOG:0000175 - VHOG - ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.428 - http://bgee.unil.ch/ - @@ -40062,21 +35833,15 @@ For example, A and B may be gene products and binding of B by A positively regul The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA]. - Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO] - The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO] - The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO] - The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG] axial skeleton AAO:0000034 EFO:0000942 EHDAA2:0000161 EHDAA:5049 - EMAPA:17214 EMAPA:37721 FMA:71221 MA:0002986 MAT:0000148 - MESH:D013131 MIAA:0000148 TAO:0000317 VHOG:0000317 @@ -40102,43 +35867,6 @@ For example, A and B may be gene products and binding of B by A positively regul https://sourceforge.net/tracker/?func=detail&aid=2983975&group_id=76834&atid=974957 https://sourceforge.net/tracker/?func=detail&atid=1205376&aid=2983977&group_id=76834 - - - - Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO] - 2012-08-14 - VSAO:0000093 - VSAO - PSPUB:0000170 - - - - - The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO] - 2012-06-20 - AAO:0000034 - AAO - AAO:LAP - - - - - The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO] - 2012-08-14 - TAO:0000317 - TAO - ZFIN:curator - - - - - The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG] - 2012-09-17 - VHOG:0000317 - VHOG - DOI:10.1186/1742-9994-8-4 Schilling N, Evolution of the axial system in craniates: morphology and function of the perivertebral musculature. Frontiers in Zoology (2011) - http://bgee.unil.ch/ - @@ -40152,13 +35880,6 @@ For example, A and B may be gene products and binding of B by A positively regul EMAPA:37721 MA:th - - - - MESH:D013131 - - https://github.com/biopragmatics/biomappings - @@ -40192,10 +35913,6 @@ For example, A and B may be gene products and binding of B by A positively regul Subdivision of skeleton which which consists of all the skeletal elements in in the pectoral and pelvic appendage complexes[cjm]. - Skeletal subdivision consisting of all the skeletal elements in the pectoral and pelvic appendage complexes.[VSAO] - Skeletal system that consists of the paired fins (pectoral or pelvic fins).[TAO] - The pectoral and pelvic girdles, which articulate with the axial skeleton, together with their associated limbs, the forelimbs and hind limbs, form the appendicular skeleton.[AAO] - ontologies differ in whether they treat the term appendicular skeleton as being the entire set of bones in the limbs, or whether the fore and hind limbs/fins are treated as seperate appendicular skeletons. Here we follow FMA, and treat the appendicular skeleton as the sum total of skeletal elements in the organism (this is evidenced by the fact that in FMA, skeleton of left/right upper/lower limb is part_of a appendicular skeleton, and subtypes of 'subdivision of appendicular skeleton'). We have separate classes such as 'skeleton of limb', and 'skeleton of hindlimb' for the 4 parts of the appendicular skeleton. In future the ZFA/TAO classes may be moved. AAO:0000747 EFO:0000951 EMAPA:32729 @@ -40206,7 +35923,6 @@ For example, A and B may be gene products and binding of B by A positively regul NCIT:C49477 SCTID:322050006 UMLS:C0222646 - VHOG:0001666 VSAO:0000076 Wikipedia:Appendicular_skeleton XAO:0003166 @@ -40233,40 +35949,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Appendicular_skeleton https://orcid.org/0000-0002-6601-2165 - - - - Skeletal subdivision consisting of all the skeletal elements in the pectoral and pelvic appendage complexes.[VSAO] - 2012-08-14 - VSAO:0000076 - VSAO - PSPUB:0000170 - https://orcid.org/0000-0002-6601-2165 - - - - - Skeletal system that consists of the paired fins (pectoral or pelvic fins).[TAO] - 2012-08-14 - TAO:0000027 - TAO - TAO:wd - - - - - The pectoral and pelvic girdles, which articulate with the axial skeleton, together with their associated limbs, the forelimbs and hind limbs, form the appendicular skeleton.[AAO] - 2012-06-20 - AAO:0000747 - AAO - AAO:LAP - - - - - ontologies differ in whether they treat the term appendicular skeleton as being the entire set of bones in the limbs, or whether the fore and hind limbs/fins are treated as seperate appendicular skeletons. Here we follow FMA, and treat the appendicular skeleton as the sum total of skeletal elements in the organism (this is evidenced by the fact that in FMA, skeleton of left/right upper/lower limb is part_of a appendicular skeleton, and subtypes of 'subdivision of appendicular skeleton'). We have separate classes such as 'skeleton of limb', and 'skeleton of hindlimb' for the 4 parts of the appendicular skeleton. In future the ZFA/TAO classes may be moved. - FMA - @@ -40306,10 +35988,6 @@ For example, A and B may be gene products and binding of B by A positively regul Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present. - - - Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO] - Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO] AAO:0010339 BILA:0000116 BTO:0001493 @@ -40349,32 +36027,6 @@ For example, A and B may be gene products and binding of B by A positively regul UBERONREF:0000006 Wikipedia:Torso - - - - - ZFA - https://github.com/obophenotype/uberon/issues/378 - pending - - - - - Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO] - 2012-06-20 - AAO:0010339 - AAO - AAO:BJB - - - - - Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO] - 2012-08-14 - TAO:0001115 - TAO - ZFIN:curator - @@ -40402,20 +36054,19 @@ For example, A and B may be gene products and binding of B by A positively regul - + - - + + - - + + - @@ -40428,26 +36079,17 @@ For example, A and B may be gene products and binding of B by A positively regul - A paired organ of the urinary tract which has the production of urine as its primary function. - + A paired organ of the urinary tract that produces urine and maintains bodily fluid homeostasis, blood pressure, pH levels, red blood cell production and skeleton mineralization. - One of either of a pair of structures lying on either side of the dorsal aorta in which fluid balance is regulated and waste is excreted out in the form of urine.[AAO] - renal - + + AAO:0000250 BTO:0000671 CALOHA:TS-0510 - EFO:0000929 - EMAPA:17373 - EV:0100096 - FMA:7203 GAID:423 - MA:0000368 MAT:0000119 MESH:D007668 MIAA:0000119 - NCIT:C12415 - SCTID:181414000 UMLS:C0022646 Wikipedia:Kidney XAO:0003267 @@ -40464,41 +36106,25 @@ For example, A and B may be gene products and binding of B by A positively regul kidney - + - - - - - + FMA - - - - - definitional - - A paired organ of the urinary tract which has the production of urine as its primary function. + A paired organ of the urinary tract that produces urine and maintains bodily fluid homeostasis, blood pressure, pH levels, red blood cell production and skeleton mineralization. + PMID:25140012 + PMID:35003210 Wikipedia:Kidney http://anatomy.uams.edu/anatomyhtml/kidney.html - - - - - One of either of a pair of structures lying on either side of the dorsal aorta in which fluid balance is regulated and waste is excreted out in the form of urine.[AAO] - 2012-06-20 - AAO:0000250 - AAO - AAO:BJB + https://www.kidney.org/kidneydisease/top-5-jobs-kidneys-do @@ -40522,8 +36148,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -40531,11 +36157,6 @@ For example, A and B may be gene products and binding of B by A positively regul In mammals, the pronephros is the first of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the pronephros is the fully functional embryonic kidney and is indispensible for larval life[GO]. - A kidney formed of nephric tubules arising in the anterior region of the nephric ridge; forms only as a transient embryonic structure. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.748][VHOG] - Organ that serves as a transient kidney, providing osmoregulation during early developmental stages and then degenerating during metamorphosis.[AAO] - The embryonic kidney, present at the level of the third somite, is composed of two glomeruli fused at the midline, two pronephric tubules, and paired bilateral pronephric ducts that modify the composition of the blood filtrate before delivering it to the cloaca for excretion.Kimmel et al, 1995.[TAO] - In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG] - pronephric UBERON:0005794 AAO:0011089 BTO:0001541 @@ -40545,7 +36166,6 @@ For example, A and B may be gene products and binding of B by A positively regul EMAPA:16579 FMA:72170 MAT:0000117 - MESH:D060910 MIAA:0000117 NCIT:C34280 SCTID:308804007 @@ -40567,11 +36187,11 @@ For example, A and B may be gene products and binding of B by A positively regul Once the more complex mesonephros forms the pronephros undergoes apoptosis in amphibians. In fishes the nephron degenerates but the organ remains and becomes a component of the immune system[Wikipedia:Pronephros]. // TODO - check developmental relationships. Note that we previously include the ZFA/XAO terms under the more specific 'pronephric kidney', but these are now merged. TODO GCI: relationship: capable_of GO:0030104 pronephros - + - + @@ -40584,13 +36204,13 @@ For example, A and B may be gene products and binding of B by A positively regul - + OG - + ZFA @@ -40600,51 +36220,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0048793 Wikipedia:Pronephros - - - - A kidney formed of nephric tubules arising in the anterior region of the nephric ridge; forms only as a transient embryonic structure. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.748][VHOG] - 2012-09-17 - VHOG:0000037 - VHOG - http://bgee.unil.ch/ - - - - - Organ that serves as a transient kidney, providing osmoregulation during early developmental stages and then degenerating during metamorphosis.[AAO] - 2012-06-20 - AAO:0011089 - AAO - XAO:curator - - - - - The embryonic kidney, present at the level of the third somite, is composed of two glomeruli fused at the midline, two pronephric tubules, and paired bilateral pronephric ducts that modify the composition of the blood filtrate before delivering it to the cloaca for excretion.Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000151 - TAO - ZFIN:curator - - - - - In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG] - 2012-09-17 - VHOG:0000037 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.637 - http://bgee.unil.ch/ - - - - - MESH:D060910 - - - https://github.com/biopragmatics/biomappings - @@ -40820,7 +36395,12 @@ For example, A and B may be gene products and binding of B by A positively regul - + + + + + + @@ -40830,9 +36410,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that consists of the muscular and skeletal systems. - Anatomical system that provides locomotion and physical support to the organism.[AAO] - There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG] - musculoskeletal AAO:0010546 CALOHA:TS-1311 EMAPA:32714 @@ -40854,16 +36431,6 @@ For example, A and B may be gene products and binding of B by A positively regul musculoskeletal system - - - - - - - - - check ctenophore - @@ -40872,25 +36439,6 @@ For example, A and B may be gene products and binding of B by A positively regul VSAO:curator https://github.com/obophenotype/uberon/issues/77 - - - - Anatomical system that provides locomotion and physical support to the organism.[AAO] - 2012-06-20 - AAO:0010546 - AAO - AAO:EJS - - - - - There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG] - 2012-09-17 - VHOG:0001275 - VHOG - DOI:10.1002/jez.b.21246 Shearman RM, Burke AC, The lateral somitic frontier in ontogeny and phylogeny. Journal of Experimental Zoology (2009) - http://bgee.unil.ch/ - @@ -40932,7 +36480,6 @@ For example, A and B may be gene products and binding of B by A positively regul The part of the coelemic cavity lumen that is enclosed by the walls of the thorax. - In many species, the diaphragm separates thoracic and abdominal cavities EMAPA:36497 FMA:7565 GAID:93 @@ -40991,7 +36538,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -41010,7 +36557,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + An anatomical structure which consists of juxtaglomerular cells, extraglomerular mesangial cells and the macula densa. The juxtaglomerular apparatus lies adjacent to the glomerulus and regulates kidney function by maintaining the blood flow to the kidney and the filtration rate[GO]. a microscopic structure in the kidney, which regulates the function of each nephron. The juxtaglomerular apparatus is named for its proximity to the glomerulus: it is found between the vascular pole of the renal corpuscle and the returning distal convoluted tubule of the same nephron. This location is critical to its function in regulating renal blood flow and glomerular filtration rate. The three cellular components of the apparatus are the macula densa, extraglomerular mesangial cells, and juxtaglomerular cells (also known as granular cells)[WP]. BTO:0005157 @@ -41032,24 +36579,24 @@ For example, A and B may be gene products and binding of B by A positively regul juxtaglomerular apparatus - + - + - + MA - + GO @@ -41099,6 +36646,7 @@ For example, A and B may be gene products and binding of B by A positively regul + @@ -41131,10 +36679,7 @@ For example, A and B may be gene products and binding of B by A positively regul The inner layer of the glomerulus, within the basement membrane surrounding the glomerular capillaries. - mesangial - WP considers this the same as glomerular mesangium. In MA, glomerular and extraglomerular are distingsuished. FMA class has no definition and is a type of stroma, which is inconsistent with our classification of this here. BTO:0002494 - EMAPA:28248 EMAPA:36561 FMA:84139 MA:0002617 @@ -41155,12 +36700,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Mesangium https://sourceforge.net/p/obo/foundational-model-of-anatomy-fma-requests/13/ - - - - WP considers this the same as glomerular mesangium. In MA, glomerular and extraglomerular are distingsuished. FMA class has no definition and is a type of stroma, which is inconsistent with our classification of this here. - MA - @@ -41180,8 +36719,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + + @@ -41198,24 +36738,24 @@ For example, A and B may be gene products and binding of B by A positively regul EDITOR_NOTE check MA part_ofs - should be spatially disjoint from renal glomerulus? extraglomerular mesangium - + - + - + MA - + MA @@ -41232,7 +36772,12 @@ For example, A and B may be gene products and binding of B by A positively regul - + + + + + + @@ -41240,15 +36785,11 @@ For example, A and B may be gene products and binding of B by A positively regul The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities. - Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]. - The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]. - In mammals it forms the peritoneal, pleural, and pericardial cavities UBERON:0000169 body cavity AEO:0000186 BTO:0001707 EHDAA2:0000267 - FBbt:00005060 FMA:85006 NCIT:C25444 RETIRED_EHDAA2:0003186 @@ -41273,52 +36814,18 @@ For example, A and B may be gene products and binding of B by A positively regul EDITOR_NOTE check the FMA placement here; ncit placement of body cavity here probably not correct coelemic cavity lumen - - - - - - - - - definitional - The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities. BTO:0001707 - - - - Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]. - 2012-09-12 - ZFA:0001438 - ZFA - ZFIN:curator - - - - - The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]. - 2012-09-12 - BTO:0001707 - BTO - BTO - body cavity BTO:0001707 - - - - FBbt:00005060 - - @@ -41375,6 +36882,7 @@ For example, A and B may be gene products and binding of B by A positively regul + @@ -41382,21 +36890,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - + + + @@ -41410,13 +36906,6 @@ For example, A and B may be gene products and binding of B by A positively regul A flexible rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In some chordates, it persists throughout life as the main axial support of the body, while in most vertebrates it becomes the nucleus pulposus of the intervertebral disc. The notochord is found ventral to the neural tube. - Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO] - Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO] - Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO] - relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO] - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG] - notochordal - In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord. AAO:0000327 BTO:0001768 CALOHA:TS-0690 @@ -41451,15 +36940,15 @@ For example, A and B may be gene products and binding of B by A positively regul notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + @@ -41478,19 +36967,19 @@ For example, A and B may be gene products and binding of B by A positively regul - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -41503,51 +36992,6 @@ For example, A and B may be gene products and binding of B by A positively regul https://github.com/obophenotype/uberon/issues/25 https://github.com/obophenotype/uberon/issues/271 - - - - Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO] - 2012-08-14 - VSAO:0000032 - VSAO - PSPUB:0000170 - - - - - Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000135 - TAO - ZFIN:curator - - - - - Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO] - 2012-06-20 - AAO:0000327 - AAO - AAO:LAP - - - - - relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO] - 2012-06-20 - AAO:0000327 - AAO - - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG] - 2012-09-17 - VHOG:0000199 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 - http://bgee.unil.ch/ - @@ -41575,18 +37019,10 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. - EDITOR_NOTE currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk - Post-cranial axial segments which form sclerotome and dermomyotome.[AAO] - Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO] - relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO] - relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO] - relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO] - (...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG] - somitic mesodermal cluster AAO:0010569 AEO:0001015 @@ -41622,11 +37058,11 @@ For example, A and B may be gene products and binding of B by A positively regul somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + @@ -41639,13 +37075,13 @@ For example, A and B may be gene products and binding of B by A positively regul - + GOTAX:0000352 - + ZFA @@ -41661,58 +37097,6 @@ For example, A and B may be gene products and binding of B by A positively regul PMID:17237766 - - - - Post-cranial axial segments which form sclerotome and dermomyotome.[AAO] - 2012-06-20 - AAO:0010569 - AAO - AAO:EJS - - - - - Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000155 - TAO - ZFIN:curator - - - - - relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO] - 2012-08-14 - TAO:0000155 - TAO - - - - - relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO] - 2012-08-14 - TAO:0000155 - TAO - - - - - relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO] - 2012-06-20 - AAO:0010569 - AAO - - - - - (...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0000191 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.40, DOI:10.1093/icb/43.1.137 Balavoine G, Adoutte A, The segmented urbilateria: a testable scenario. Integrative and Comparative Biology (2003) - http://bgee.unil.ch/ - @@ -41757,11 +37141,10 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + The macula densa is an area of specialized cells in the distal tubule that makes contact with the vascular pole of the glomerulus[GO]. - not part of a nephron or distal tubule in MA and FMA BTO:0003940 EMAPA:28399 FMA:86333 @@ -41777,24 +37160,24 @@ For example, A and B may be gene products and binding of B by A positively regul macula densa - + - + - + MA - + GO @@ -41804,12 +37187,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0072024 Wikipedia:Macula_densa - - - - not part of a nephron or distal tubule in MA and FMA - MA - @@ -41823,20 +37200,25 @@ For example, A and B may be gene products and binding of B by A positively regul + - - - - - - + + + + + + + + + + + + + + + + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. - EDITOR_NOTE consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams). - - A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO] - Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO] - A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831] - We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG] AAO:0010578 BTO:0001764 CALOHA:TS-0676 @@ -41849,7 +37231,6 @@ For example, A and B may be gene products and binding of B by A positively regul MIAA:0000066 NCIT:C34222 SCTID:361462002 - TAO:0000045 UMLS:C0027789 VHOG:0000057 Wikipedia:Neural_crest @@ -41869,66 +37250,45 @@ For example, A and B may be gene products and binding of B by A positively regul http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - - - - - + - + - - - - - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - - Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells - ISBN:0073040584 - - - - - + BTO - + PMID:11523831 - - pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest - - - - - + PMID:11523831 @@ -41937,47 +37297,6 @@ For example, A and B may be gene products and binding of B by A positively regul A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. MP:0009846 - - - - - ISBN:0073040584 - PMID:17377535 - - - - - A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000045 - TAO - ZFIN:curator - - - - - Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO] - 2012-06-20 - AAO:0010578 - AAO - AAO:EJS - - - - - A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831] - PMID:11523831 - - - - - We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG] - 2012-09-17 - VHOG:0000057 - VHOG - DOI:10.1111/j.1469-7580.2012.01495.x Hall BK, Gillis JA, Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues. J Anat (2012) - http://bgee.unil.ch/ - @@ -42019,9 +37338,6 @@ For example, A and B may be gene products and binding of B by A positively regul Embryonic ectoderm that gives rise to nervous tissue. - (...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG] - neurectodermal - we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here AAO:0011074 BILA:0000039 CALOHA:TS-1212 @@ -42030,7 +37346,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA:255 EMAPA:16073 EV:0100004 - FBbt:00001057 FMA:87657 MAT:0000176 MIAA:0000176 @@ -42059,22 +37374,6 @@ For example, A and B may be gene products and binding of B by A positively regul Embryonic ectoderm that gives rise to nervous tissue. Wikipedia:Neuroectoderm - - - - (...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG] - 2012-09-17 - VHOG:0000150 - VHOG - DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) - http://bgee.unil.ch/ - - - - - FBbt:00001057 - - @@ -42114,8 +37413,6 @@ For example, A and B may be gene products and binding of B by A positively regul The lower segment of the trunk, inferioposterior to the abdomen proper, in the transition area between the trunk and the lower limbs. - pelvic - MA and FMA differ in what they consider to be parts of the pelvis. MA includes ureter, urethra, urinary bladder, reproductive organs BTO:0001006 CALOHA:TS-2227 EFO:0002805 @@ -42150,12 +37447,6 @@ For example, A and B may be gene products and binding of B by A positively regul http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/720 - - - - MA and FMA differ in what they consider to be parts of the pelvis. MA includes ureter, urethra, urinary bladder, reproductive organs - MA - @@ -42196,10 +37487,6 @@ For example, A and B may be gene products and binding of B by A positively regul Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance. - One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO] - Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO] - Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO] - MA also has set of connective tissues AAO:0000098 BTO:0000421 CALOHA:TS-2009 @@ -42240,40 +37527,6 @@ For example, A and B may be gene products and binding of B by A positively regul http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/23 - - - - One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO] - 2012-06-20 - AAO:0000098 - AAO - AAO:LAP - - - - - Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO] - 2012-08-14 - TAO:0001641 - TAO - TAO:wd - - - - - Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO] - 2012-08-14 - VSAO:0000017 - VSAO - GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 - PSPUB:0000170 - - - - - MA also has set of connective tissues - MA - @@ -42336,8 +37589,6 @@ For example, A and B may be gene products and binding of B by A positively regul Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]. - - One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO] AAO:0000306 AEO:0000122 CALOHA:TS-0642 @@ -42368,15 +37619,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Muscle_tissue https://sourceforge.net/tracker/index.php?func=detail&aid=2801266&group_id=36855&atid=440764 - - - - One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO] - 2012-06-20 - AAO:0000306 - AAO - AAO:LAP - @@ -42403,21 +37645,22 @@ For example, A and B may be gene products and binding of B by A positively regul - + - + + + + + + Anatomical system that is involved in the production of hematopoietic cells. - Anatomical system that consists of the blood and blood forming tissues.[AAO] - Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG] - hematopoietic - In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes AAO:0011002 BTO:0000570 CALOHA:TS-0449 @@ -42455,57 +37698,22 @@ For example, A and B may be gene products and binding of B by A positively regul hematopoietic system - + - - - - - + FMA - - - - - definitional - Anatomical system that is involved in the production of hematopoietic cells. Wikipedia:Haematopoiesis - - - - Anatomical system that consists of the blood and blood forming tissues.[AAO] - 2012-06-20 - AAO:0011002 - AAO - AAO:EJS - - - - - Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG] - 2012-09-17 - VHOG:0001624 - VHOG - DOI:10.1016/j.coph.2010.05.004 Ellett F, Lieschke GJ, Zebrafish as a model for vertebrate hematopoiesis. Current Opinion in Pharmacology (2010) - http://bgee.unil.ch/ - - - - - In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes - WP - @@ -42591,7 +37799,6 @@ For example, A and B may be gene products and binding of B by A positively regul In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA]. MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class - In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG] BTO:0004593 FMA:296704 MAT:0000067 @@ -42619,16 +37826,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Epiblast ZFIN:curator - - - - In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG] - 2012-09-17 - VHOG:0000243 - VHOG - DOI:10.1146/annurev.cellbio.042308.113344 Zorn AM, Wells JM, Vertebrate endoderm development and organ formation. Annual Review of Cell Developmental Biology (2009) - http://bgee.unil.ch/ - @@ -42726,10 +37923,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. - Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO] - It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG] AAO:0011086 EFO:0001982 EMAPA:16189 @@ -42751,14 +37946,14 @@ For example, A and B may be gene products and binding of B by A positively regul presomitic mesoderm - + - + Bgee:AN @@ -42767,25 +37962,6 @@ For example, A and B may be gene products and binding of B by A positively regul Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. ZFIN:curator - - - - Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000279 - TAO - ZFIN:curator - - - - - It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG] - 2012-09-17 - VHOG:0000559 - VHOG - DOI:10.1006/dbio.2001.0460 Schubert M, Holland LZ, Dale Stokes M and Holland ND, Three Amphoxius Wnt Genes (AmphiWnt3, AmphiWnt5, and AmphiWnt6) Associated with the Tail Bud: the Evolution of Somitogenesis in Chordates. Developmental Biology (2001) - http://bgee.unil.ch/ - @@ -42818,19 +37994,14 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + In mammals, the pronephric duct is the predecessor of the Wolffian duct[WP]. - Duct of the embryonic kidney, present bilaterally ventral to the somites and leading to the anal region where it empties separately from, and just posterior to the anus. Kimmel et al, 1995.[TAO] - The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] - (...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG] AAO:0011088 - BTO:0005991 NCIT:C34279 SCTID:361406002 TAO:0000150 UMLS:C1283945 - VHOG:0000082 Wikipedia:Pronephric_duct XAO:0000063 ZFA:0000150 @@ -42843,11 +38014,11 @@ For example, A and B may be gene products and binding of B by A positively regul The pronephric duct collects the filtrate from the pronephric tubules and opens to the exterior of the pronephric kidney[GOC:mtg_kidney_jan10, PMID:15647339, XAO:0000063, ZFA:0000150] pronephric duct - + - + @@ -42860,13 +38031,13 @@ For example, A and B may be gene products and binding of B by A positively regul - + Wikipedia - + XAO @@ -42875,42 +38046,6 @@ For example, A and B may be gene products and binding of B by A positively regul In mammals, the pronephric duct is the predecessor of the Wolffian duct[WP]. Wikipedia:Pronephric_duct - - - - Duct of the embryonic kidney, present bilaterally ventral to the somites and leading to the anal region where it empties separately from, and just posterior to the anus. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000150 - TAO - ZFIN:curator - - - - - The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] - 2012-09-17 - VHOG:0000082 - VHOG - http://bgee.unil.ch/ - - - - - (...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG] - 2012-09-17 - VHOG:0000082 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.686 - http://bgee.unil.ch/ - - - - - BTO:0005991 - - - https://github.com/biopragmatics/biomappings - @@ -42957,11 +38092,6 @@ For example, A and B may be gene products and binding of B by A positively regul Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted]. - Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO] - Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO] - relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO] - Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG] - EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac ventral lateral plate mesoderm AAO:0011006 EFO:0003489 @@ -42994,48 +38124,6 @@ For example, A and B may be gene products and binding of B by A positively regul Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted]. Wikipedia:Blood_island_of_umbilical_vesicle - - - - Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000094 - TAO - ZFIN:curator - - - - - Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO] - 2012-06-20 - AAO:0011006 - AAO - AAO:EJS - - - - - relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO] - 2012-08-14 - TAO:0000094 - TAO - - - - - Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0000085 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450, DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual Review of Cell and Developmental Biology (2006) - http://bgee.unil.ch/ - - - - - EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac - EHDAA2 - @@ -43055,9 +38143,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + @@ -43071,9 +38159,6 @@ For example, A and B may be gene products and binding of B by A positively regul The intermediate mesoderm is located between the lateral mesoderm and the paraxial mesoderm. It develops into the kidney and gonads. - Mesoderm between somite and lateral plate. Traditionally thought to give rise to the urogenital system.[AAO] - (...)the mesoderm of a developing vertebrate transitionally differentiates into the following sub-types: Chordamesoderm (also known as axial mesoderm) which later on gives rise to notochord in all chordates, Paraxial mesoderm, Intermediate mesoderm, Lateral plate mesoderm (reference 1); The mesoderm is present in Bilateria, therefore they are sometimes called triploblasts. Ectoderm and endoderm are usually organized as epithelial layers, while mesoderm can be epithelial or a compact, three-dimensional tissue.[well established][VHOG] - all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). AAO:0010575 EMAPA:16056 EMAPA:16178 @@ -43099,34 +38184,34 @@ For example, A and B may be gene products and binding of B by A positively regul intermediate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + - + AAO - + EMAPA - + XAO @@ -43136,31 +38221,6 @@ For example, A and B may be gene products and binding of B by A positively regul GOC:curators Wikipedia:Intermediate_mesoderm - - - - Mesoderm between somite and lateral plate. Traditionally thought to give rise to the urogenital system.[AAO] - 2012-06-20 - AAO:0010575 - AAO - AAO:EJS - - - - - (...)the mesoderm of a developing vertebrate transitionally differentiates into the following sub-types: Chordamesoderm (also known as axial mesoderm) which later on gives rise to notochord in all chordates, Paraxial mesoderm, Intermediate mesoderm, Lateral plate mesoderm (reference 1); The mesoderm is present in Bilateria, therefore they are sometimes called triploblasts. Ectoderm and endoderm are usually organized as epithelial layers, while mesoderm can be epithelial or a compact, three-dimensional tissue.[well established][VHOG] - 2012-09-17 - VHOG:0000087 - VHOG - Wikipedia:Mesoderm, ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.43 - http://bgee.unil.ch/ - - - - - all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). - ZFA - @@ -43218,7 +38278,6 @@ For example, A and B may be gene products and binding of B by A positively regul The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord. - The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] AAO:0011017 EFO:0003647 TAO:0001204 @@ -43241,15 +38300,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0048318 Wikipedia:Chordamesoderm - - - - The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] - 2012-09-17 - VHOG:0000107 - VHOG - http://bgee.unil.ch/ - @@ -43264,33 +38314,25 @@ For example, A and B may be gene products and binding of B by A positively regul - - + Paired organ that connects the primitive kidney Wolffian body (or mesonephros) to the cloaca and serves as the anlage for certain male reproductive organs. the Wolffian duct is what remains of the pronephric duct after the atrophy of the pronephros[WP]. In Zebrafish: Duct of the adult kidney (mesonephros), present bilaterally ventral to the somites and leading to the cloacal chamber[ZFA]. Consider adding subclasses for male and female specific variants TODO - mesonephric portion of the nephric duct - Anatomical structure consisting of either of a pair of longitudinal ducts which carry urine and in males, sperm, to the cloaca.[AAO] - The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] - (...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG] - In the male the Wolffian duct persists, and forms for example the epididymis, the ductus deferens, the ejaculatory duct, seminal vesicle and efferent ducts. AAO:0000637 - BTO:0005990 EHDAA2:0001243 EHDAA:1590 - EMAPA:16577 GAID:1315 MESH:D014928 NCIT:C26469 SCTID:308800003 TAO:0000546 UMLS:C0043204 - VHOG:0000082 Wikipedia:Mesonephric_duct XAO:0000242 ZFA:0000546 @@ -43307,7 +38349,7 @@ For example, A and B may be gene products and binding of B by A positively regul mesonephric duct http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png - + @@ -43320,7 +38362,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + EHDAA2 @@ -43331,42 +38373,6 @@ For example, A and B may be gene products and binding of B by A positively regul ZFIN:curator https://github.com/obophenotype/uberon/issues/28 - - - - Anatomical structure consisting of either of a pair of longitudinal ducts which carry urine and in males, sperm, to the cloaca.[AAO] - 2012-06-20 - AAO:0000637 - AAO - AAO:BJB - - - - - The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] - 2012-09-17 - VHOG:0000082 - VHOG - http://bgee.unil.ch/ - - - - - (...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG] - 2012-09-17 - VHOG:0000082 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.686 - http://bgee.unil.ch/ - - - - - BTO:0005990 - - - https://github.com/biopragmatics/biomappings - @@ -43410,12 +38416,10 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. - The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO] - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] AAO:0011072 BTO:0001765 DHBA:10153 @@ -43424,7 +38428,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA:902 EMAPA:35593 FMA:293879 - MESH:D054258 NCIT:C34225 RETIRED_EHDAA2:0001252 TAO:0000132 @@ -43444,34 +38447,34 @@ For example, A and B may be gene products and binding of B by A positively regul neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -43483,33 +38486,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Neural_plate ZFIN:curator - - - - The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000132 - TAO - ZFIN:curator - - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] - 2012-09-17 - VHOG:0000068 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 - http://bgee.unil.ch/ - - - - - MESH:D054258 - - - https://github.com/biopragmatics/biomappings - @@ -43532,23 +38508,14 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. - Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO] - Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG] - note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here) AAO:0010568 EFO:0003515 EMAPA:16183 @@ -43573,7 +38540,7 @@ For example, A and B may be gene products and binding of B by A positively regul paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -43586,7 +38553,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + Bgee:AN @@ -43596,31 +38563,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0048339 https://github.com/obophenotype/uberon/issues/30 - - - - Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO] - 2012-06-20 - AAO:0010568 - AAO - AAO:EJS - - - - - Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG] - 2012-09-17 - VHOG:0000114 - VHOG - DOI:10.1002/dvdy.21177 Kusakabe R and Kuratani S. Evolutionary perspectives from development of mesodermal components in the lamprey. Developmental dynamics (2007) - http://bgee.unil.ch/ - - - - - note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here) - ZFA - @@ -43658,7 +38600,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -43672,10 +38614,6 @@ For example, A and B may be gene products and binding of B by A positively regul Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]. - Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO] - The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] - A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG] - subclass of mesoderm in ZFA. UBERON:0006258 AAO:0010574 EHDAA2:0000919 @@ -43702,7 +38640,7 @@ For example, A and B may be gene products and binding of B by A positively regul lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -43715,7 +38653,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + EHDAA2 VHOG @@ -43726,40 +38664,6 @@ For example, A and B may be gene products and binding of B by A positively regul MP:0010117 Wikipedia:Lateral_plate_mesoderm - - - - Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO] - 2012-06-20 - AAO:0010574 - AAO - AAO:EJS - - - - - The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] - 2012-09-17 - VHOG:0000118 - VHOG - http://bgee.unil.ch/ - - - - - A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG] - 2012-09-17 - VHOG:0000118 - VHOG - DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) - http://bgee.unil.ch/ - - - - - subclass of mesoderm in ZFA. - ZFA - @@ -43799,20 +38703,17 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + - + Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. should probably be merged with heart rudiment. - Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO] - The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO] - relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO] AAO:0011044 BTO:0001887 NCIT:C34276 @@ -43827,15 +38728,15 @@ For example, A and B may be gene products and binding of B by A positively regul heart primordium - + - + - + @@ -43848,19 +38749,19 @@ For example, A and B may be gene products and binding of B by A positively regul - + ZFA - + ZFA - + XAO @@ -43869,32 +38770,6 @@ For example, A and B may be gene products and binding of B by A positively regul Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. ZFIN:curator - - - - Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO] - 2012-08-14 - TAO:0000028 - TAO - ZFIN:curator - - - - - The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO] - 2012-06-20 - AAO:0011044 - AAO - XAO:curator - - - - - relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO] - 2012-08-14 - TAO:0000028 - TAO - @@ -43915,15 +38790,11 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. - Skeletogenic portion of somites.[AAO] - The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG] - part_of somite in XAO AAO:0010571 AEO:0000212 - BTO:0006255 EHDAA2:0003439 EMAPA:31159 FMA:295652 @@ -43944,11 +38815,11 @@ For example, A and B may be gene products and binding of B by A positively regul sclerotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + - + @@ -43967,13 +38838,13 @@ For example, A and B may be gene products and binding of B by A positively regul - + VHOG:0000680 - + ZFA @@ -43984,39 +38855,6 @@ For example, A and B may be gene products and binding of B by A positively regul XB:curator https://github.com/obophenotype/uberon/issues/316 - - - - Skeletogenic portion of somites.[AAO] - 2012-06-20 - AAO:0010571 - AAO - AAO:EJS - - - - - The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG] - 2012-09-17 - VHOG:0000680 - VHOG - DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) - http://bgee.unil.ch/ - - - - - part_of somite in XAO - XAO - - - - - BTO:0006255 - - - https://github.com/biopragmatics/biomappings - @@ -44045,7 +38883,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types. - this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs AAO:0010015 AEO:0000024 BILA:0000024 @@ -44109,9 +38946,6 @@ For example, A and B may be gene products and binding of B by A positively regul Portion of tissue composed of mesenchymal cells (motile cells that develop from epthelia via an epithelial to mesenchymal transition) and surrounding extracellular material. Mesenchyme has different embryological origins in different metazoan taxa - in many invertebrates it derives in whole or part from ectoderm. In vertebrates it derives largely from mesoderm, and sometimes the terms are used interchangeably, e.g. lateral plate mesoderm/mesenchyme. the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense - A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO] - Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO] - mesenchymal AAO:0010427 AEO:0000145 BTO:0001393 @@ -44146,24 +38980,6 @@ For example, A and B may be gene products and binding of B by A positively regul https://en.wikipedia.org/wiki/Mesenchyme https://github.com/obophenotype/uberon/issues/1641 - - - - A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000393 - TAO - ZFIN:curator - - - - - Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO] - 2012-06-20 - AAO:0010427 - AAO - AAO:EJS - @@ -44203,8 +39019,6 @@ For example, A and B may be gene products and binding of B by A positively regul An organ involved in reproduction. - GO uses genitalia for the singular organ - EMAPA:17381 EMAPA:37731 MA:0001752 MESH:D005835 @@ -44230,12 +39044,6 @@ For example, A and B may be gene products and binding of B by A positively regul An organ involved in reproduction. UBERON:xp - - - - GO uses genitalia for the singular organ - GO - @@ -44281,7 +39089,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -44289,8 +39097,6 @@ For example, A and B may be gene products and binding of B by A positively regul One of the two embryological structures that give rise to the kidney (the other is the ureteric bud). The metanephric blastema mostly develops into nephrons, but can also form parts of the collecting duct system.[WP]. Metanephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the metanephros[GO]. - A mass of intermediate mesodermal cells around the distal end of the ureteric bud that gives rise to nephrons in the metanephric kidney. [TFD][VHOG] - When the ureteric buds emerge from the nephric duct, they enter the metanephrogenic mesenchyme. The ureteric buds induce this mesenchymal tissue to condense around them and differentiate into the nephrons of the mammalian kidney. As this mesenchyme differentiates, it tells the ureteric bud to branch and grow.[well established][VHOG] EHDAA2:0004062 EHDAA:4041 EHDAA:5021 @@ -44309,14 +39115,14 @@ For example, A and B may be gene products and binding of B by A positively regul Genes: The positional specification of the metanephrogenic mesenchyme is negatively regulated by Foxc1 and Foxc2. Next the permanent kidney forming metanephrogenic mesenchyme is specified by Hox11 genes. The competence to respond to ureteric bud inducers is regulated by WT1. GDNF secretion restricted to posterior region by Robo2 and Sprouty1. The receptors for GDNF are synthesized in the nephric ducts and later in ureteric buds [ISBN:9780878932504 "Developmental Biology"] metanephric mesenchyme - + - + ISBN:9780878932504 @@ -44326,26 +39132,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0072075 Wikipedia:Metanephric_blastema - - - - A mass of intermediate mesodermal cells around the distal end of the ureteric bud that gives rise to nephrons in the metanephric kidney. [TFD][VHOG] - 2012-09-17 - VHOG:0000540 - VHOG - http://bgee.unil.ch/ - http://medical-dictionary.thefreedictionary.com/metanephric+mesenchyme - - - - - When the ureteric buds emerge from the nephric duct, they enter the metanephrogenic mesenchyme. The ureteric buds induce this mesenchymal tissue to condense around them and differentiate into the nephrons of the mammalian kidney. As this mesenchyme differentiates, it tells the ureteric bud to branch and grow.[well established][VHOG] - 2012-09-17 - VHOG:0000540 - VHOG - ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.462 - http://bgee.unil.ch/ - @@ -44501,7 +39287,6 @@ For example, A and B may be gene products and binding of B by A positively regul uberon UBERON:0003497 abdomen blood vessel - UBERON:0012254 @@ -44515,12 +39300,6 @@ For example, A and B may be gene products and binding of B by A positively regul blood vessel of abdomen OBOL:automatic - - - - UBERON:0012254 - abdominal aorta artery - @@ -44650,7 +39429,6 @@ For example, A and B may be gene products and binding of B by A positively regul A blood vessel that is part of a kidney [Automatically generated definition]. - EMAPA:28457 MA:0001682 TAO:0005306 ZFA:0005306 @@ -45032,10 +39810,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults - (...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG] EHDAA:251 EMAPA:16088 NCIT:C34195 @@ -45048,14 +39825,14 @@ For example, A and B may be gene products and binding of B by A positively regul intraembryonic coelom - + - + Wikipedia @@ -45065,16 +39842,6 @@ For example, A and B may be gene products and binding of B by A positively regul MGI:anna MP:0012187 - - - - (...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG] - 2012-09-17 - VHOG:0000316 - VHOG - ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.166 - http://bgee.unil.ch/ - @@ -45107,7 +39874,6 @@ For example, A and B may be gene products and binding of B by A positively regul Connective, non-functional supportive framework of a biological cell, tissue, or organ. Contrast with parenchyma. - stromal FMA:81494 NCIT:C67387 UMLS:C0927195 @@ -45149,10 +39915,8 @@ For example, A and B may be gene products and binding of B by A positively regul Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. - contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers AEO:0000114 EHDAA2:0003114 - FBbt:00007474 epithelial or endothelial tube uberon UBERON:0003914 @@ -45165,12 +39929,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0060562 PMID:12526790 - - - - FBbt:00007474 - - @@ -45414,7 +40172,6 @@ For example, A and B may be gene products and binding of B by A positively regul - FMA has both conduit and conduit space. In EHDAA2 this is a surface feature AEO:0000080 EHDAA2:0003080 FMA:242873 @@ -45436,12 +40193,6 @@ For example, A and B may be gene products and binding of B by A positively regul Any tube, opening or passage that connects two distinct anatomical spaces. http://orcid.org/0000-0002-6601-2165 - - - - FMA has both conduit and conduit space. In EHDAA2 this is a surface feature - FMA - @@ -45486,7 +40237,6 @@ For example, A and B may be gene products and binding of B by A positively regul An anatomical structure that develops (entirely or partially) from the mesoderm. - Grouping term for query purposes mesodermal derivative uberon UBERON:0004120 @@ -45530,7 +40280,6 @@ For example, A and B may be gene products and binding of B by A positively regul An anatomical structure that develops (entirely or partially) from the ectoderm. - Grouping term for query purposes ectodermal deriviative uberon UBERON:0004121 @@ -45590,11 +40339,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction. - Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.[AAO] - relationship type change: differentiates_from intermediate mesoderm (AAO:0010575) CHANGED TO: develops_from intermediate mesoderm (UBERON:0003064)[AAO] - Kidneys and gonads (of vertebrates) develop from adjacent tissues, and after the excretory or urinary ducts have developed, the reproductive system usually taps into them or their derivatives.[well established][VHOG] - genitourinary - urogenital AAO:0000624 BILA:0000122 BTO:0003091 @@ -45630,33 +40374,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction. VHOG:0000286 - - - - Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.[AAO] - 2012-06-20 - AAO:0000624 - AAO - AAO:EJS - - - - - relationship type change: differentiates_from intermediate mesoderm (AAO:0010575) CHANGED TO: develops_from intermediate mesoderm (UBERON:0003064)[AAO] - 2012-06-20 - AAO:0000624 - AAO - - - - - Kidneys and gonads (of vertebrates) develop from adjacent tissues, and after the excretory or urinary ducts have developed, the reproductive system usually taps into them or their derivatives.[well established][VHOG] - 2012-09-17 - VHOG:0000286 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.633 - http://bgee.unil.ch/ - @@ -45688,8 +40405,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + In mammals, the proximal tubule is a nephron tubule that connects Bowman's capsule to the loop of Henle. It has a brush border epithelial morphology[GO]. TODO - ensure definition works across species. @@ -45706,24 +40423,24 @@ For example, A and B may be gene products and binding of B by A positively regul proximal tubule - + - + - + GO - + GO @@ -45752,7 +40469,6 @@ For example, A and B may be gene products and binding of B by A positively regul The distal tubule is a nephron tubule that consists of the distal convoluted tubule and distal straight tubule segments. - BTO:0000482 CALOHA:TS-0504 EMAPA:28387 @@ -45783,7 +40499,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + The intermediate tubule is a nephron tubule that lies between the proximal and distal tubules. TODO - check for applicability across species FMA:17718 @@ -45793,14 +40509,14 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0004136 intermediate tubule - + - + FMA @@ -45830,7 +40546,6 @@ For example, A and B may be gene products and binding of B by A positively regul The first recognizable structure derived from the heart field. TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO - (In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG] EHDAA2:0000215 EMAPA:16106 VHOG:0000975 @@ -45849,16 +40564,6 @@ For example, A and B may be gene products and binding of B by A positively regul The first recognizable structure derived from the heart field. GO:0003142 - - - - (In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG] - 2012-09-17 - VHOG:0000975 - VHOG - PMID:15611355 Gittenberger-de Groot AC, Bartelings MM, Deruiter MC, Poelmann RE, Basics of cardiac development for the understanding of congenital heart malformations. Pediatric Research (2005) - http://bgee.unil.ch/ - @@ -45884,12 +40589,12 @@ For example, A and B may be gene products and binding of B by A positively regul + - - + + A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. - this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138] XAO:0004185 first heart field primary heart field @@ -45900,24 +40605,24 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0004140 primary heart field - + - + - + GO:0003128 - + https://orcid.org/0000-0003-3308-6245 @@ -45928,12 +40633,6 @@ For example, A and B may be gene products and binding of B by A positively regul GOC:mtg_heart GOC:rl - - - - this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138] - GO - @@ -45976,9 +40675,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + An epithelial tube that will give rise to the mature heart. - the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube. AAO:0010411 EFO:0003526 EMAPA:32685 @@ -45996,14 +40694,14 @@ For example, A and B may be gene products and binding of B by A positively regul heart tube - + - + ZFA-modified @@ -46013,12 +40711,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0003143 GOC:mtg_heart - - - - the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube. - MP:0012700 - @@ -46044,6 +40736,7 @@ For example, A and B may be gene products and binding of B by A positively regul + @@ -46110,6 +40803,7 @@ For example, A and B may be gene products and binding of B by A positively regul + @@ -46229,8 +40923,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + The comma-shaped body is the precursor structure to the S-shaped body that contributes to the morphogenesis of the nephron. EMAPA:27681 ZFA:0005588 @@ -46240,24 +40934,24 @@ For example, A and B may be gene products and binding of B by A positively regul comma-shaped body - + - + - + cjm - + ZFA @@ -46279,12 +40973,11 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + The S-shaped body is the successor of the comma-shaped body that contributes to the morphogenesis of the nephron. TODO EMAPA:27756 - VO:0010896 ZFA:0005589 SSB stage II nephron @@ -46293,24 +40986,24 @@ For example, A and B may be gene products and binding of B by A positively regul S-shaped body - + - + - + cjm - + GO @@ -46319,14 +41012,6 @@ For example, A and B may be gene products and binding of B by A positively regul The S-shaped body is the successor of the comma-shaped body that contributes to the morphogenesis of the nephron. GO:0072050 - - - - VO:0010896 - - - https://github.com/biopragmatics/biomappings - @@ -46360,8 +41045,6 @@ For example, A and B may be gene products and binding of B by A positively regul Kidney pyramids are the conical arrangements of tubules that constitute the renal medulla in a multi-lobed mammalian kidney; they contain the loops of Henle and the medullary collecting ducts. - not the same as FMA:50609 Pyramid (which is a volume / dimensional entity) - UBERON:0002449 UBERON:0005098 pyramid @@ -46402,12 +41085,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0072056 http://anatomy.uams.edu/anatomyhtml/kidney.html - - - - not the same as FMA:50609 Pyramid (which is a volume / dimensional entity) - FMA - @@ -46738,7 +41415,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -46753,7 +41430,6 @@ For example, A and B may be gene products and binding of B by A positively regul The small branching blood vessels in the kidney glomerulus that receives blood from the kidney afferent arterioles; these capillaries are under high pressure for filtering within the glomerulus. - Capillary that is part of the renal glomerulus. Glomerular capillary endothelial membranes in zebrafish normally have a fenestrated morphology that is visible at the ultrastructural level.[TAO] EMAPA:28245 FMA:274259 MA:0002587 @@ -46777,14 +41453,14 @@ For example, A and B may be gene products and binding of B by A positively regul glomerular capillary - + - + https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -46794,16 +41470,6 @@ For example, A and B may be gene products and binding of B by A positively regul MGI:csmith MP:0011320 - - - - Capillary that is part of the renal glomerulus. Glomerular capillary endothelial membranes in zebrafish normally have a fenestrated morphology that is visible at the ultrastructural level.[TAO] - 2012-08-14 - TAO:0005284 - TAO - ZFIN:ZDB-PUB-000824-1 - ZFIN:curator - @@ -46879,10 +41545,7 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body. - - Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO] - skeletal AEO:0000168 EHDAA2:0001843 EHDAA:5047 @@ -46915,15 +41578,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body. VSAO:0000026 - - - - Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO] - 2012-08-14 - VSAO:0000026 - VSAO - GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 - @@ -46938,7 +41592,6 @@ For example, A and B may be gene products and binding of B by A positively regul A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube. - The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO] TAO:0000115 ZFA:0000115 heart cone @@ -46953,15 +41606,6 @@ For example, A and B may be gene products and binding of B by A positively regul A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube. GO:0003313 - - - - The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO] - 2012-08-14 - TAO:0000115 - TAO - ZFIN:curator - @@ -46995,14 +41639,10 @@ For example, A and B may be gene products and binding of B by A positively regul The primitive streak is a structure that forms during the early stages of avian, reptilian and mammalian embryonic development[WP]. the midline ridge of the embryonic epiblast that later develops into mesoderm and endoderm[MP]. - - (...) the blastopore equivalent of chordates (germ ring in fish, marginal zone/blastopore lip in frog and node/primitive streak in chick and mouse) (...) (reference 1); Indeed, the primitive streak has been considered the homologue of the blastopore since the 1870s (reference 2).[well established][VHOG] - VHOG includes a very broad grouping here based on http://www.ncbi.nlm.nih.gov/pubmed/9609826 EHDAA2:0001525 EHDAA:185 EMAPA:16072 FMA:293110 - MESH:D054240 NCIT:C28402 SCTID:361438007 UMLS:C0033153 @@ -47029,30 +41669,6 @@ For example, A and B may be gene products and binding of B by A positively regul MP:0002231 Wikipedia:Primitive_streak - - - - (...) the blastopore equivalent of chordates (germ ring in fish, marginal zone/blastopore lip in frog and node/primitive streak in chick and mouse) (...) (reference 1); Indeed, the primitive streak has been considered the homologue of the blastopore since the 1870s (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0001202 - VHOG - PMID:9609826 Wu LH, Lengyel JA, Role of caudal in hindgut specification and gastrulation suggests homology between Drosophila amnioproctodeal invagination and vertebrate blastopore. Development (1998), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.139 - http://bgee.unil.ch/ - - - - - VHOG includes a very broad grouping here based on http://www.ncbi.nlm.nih.gov/pubmed/9609826 - VHOG - - - - - MESH:D054240 - - - https://github.com/biopragmatics/biomappings - @@ -47111,18 +41727,14 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that has as its parts the heart and blood vessels. - we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph. - The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG] AAO:0011001 BILA:0000016 BTO:0000088 CALOHA:TS-1297 EFO:0000791 - EHDAA2:0000216 EHDAA:394 EMAPA:16104 - EMAPA:16370 EV:0100017 FMA:7161 GAID:467 @@ -47156,16 +41768,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that has as its parts the heart and blood vessels. BTO:0000088 - - - - The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG] - 2012-09-17 - VHOG:0000302 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.451 - http://bgee.unil.ch/ - @@ -47253,7 +41855,6 @@ For example, A and B may be gene products and binding of B by A positively regul The part of the cardiovascular system consisting of all arteries. - The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] BTO:0004690 EHDAA2:0000143 EHDAA:396 @@ -47280,16 +41881,6 @@ For example, A and B may be gene products and binding of B by A positively regul The part of the cardiovascular system consisting of all arteries. https://orcid.org/0000-0002-6601-2165 - - - - The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] - 2012-09-17 - VHOG:0000273 - VHOG - DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005) - http://bgee.unil.ch/ - @@ -47306,7 +41897,6 @@ For example, A and B may be gene products and binding of B by A positively regul The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions. - The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] BTO:0004692 EHDAA2:0002171 EHDAA:486 @@ -47334,16 +41924,6 @@ For example, A and B may be gene products and binding of B by A positively regul The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions. https://orcid.org/0000-0002-6601-2165 - - - - The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] - 2012-09-17 - VHOG:0000277 - VHOG - DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005) - http://bgee.unil.ch/ - @@ -47424,7 +42004,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -47461,14 +42041,14 @@ For example, A and B may be gene products and binding of B by A positively regul renal afferent arteriole http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + - + Wikipedia @@ -47714,11 +42294,9 @@ For example, A and B may be gene products and binding of B by A positively regul Organism at the gastrula stage. - We explicitly merge the NCITA terms here UBERON:0007012 BILA:0000060 BTO:0001403 - FBbt:00005317 FMA:293108 GAID:1302 MESH:D005775 @@ -47750,18 +42328,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Gastrula Wikipedia:Trilaminar_blastocyst - - - - We explicitly merge the NCITA terms here - NCIT - - - - - FBbt:00005317 - - @@ -47835,10 +42401,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. - Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO] - Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO] AAO:0011129 TAO:0001890 VSAO:0000128 @@ -47851,14 +42415,14 @@ For example, A and B may be gene products and binding of B by A positively regul skeletal element - + - + VSAO @@ -47867,24 +42431,6 @@ For example, A and B may be gene products and binding of B by A positively regul Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. https://orcid.org/0000-0002-6601-2165 - - - - Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO] - 2012-08-14 - VSAO:0000128 - VSAO - PSPUB:0000170 - - - - - Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO] - 2012-08-14 - TAO:0001890 - TAO - TAO:VSAO_workshop - @@ -47903,7 +42449,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -47942,14 +42488,14 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0004770 articular system - + - + FMA @@ -48149,7 +42695,6 @@ For example, A and B may be gene products and binding of B by A positively regul An endothelium that is part of the cardiovascular system. consider merging with 'endothelium' - Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] BTO:0001853 EMAPA:35201 GAID:519 @@ -48174,16 +42719,6 @@ For example, A and B may be gene products and binding of B by A positively regul An endothelium that is part of the cardiovascular system. https://orcid.org/0000-0002-6601-2165 - - - - Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] - 2012-09-17 - VHOG:0001217 - VHOG - ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207 - http://bgee.unil.ch/ - @@ -48218,7 +42753,6 @@ For example, A and B may be gene products and binding of B by A positively regul Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP]. - We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors visceral mesoderm AAO:0011102 BILA:0000044 @@ -48238,12 +42772,6 @@ For example, A and B may be gene products and binding of B by A positively regul Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP]. Wikipedia:Lateral_plate_mesoderm#Division_into_layers - - - - We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors - BILA - @@ -48265,7 +42793,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -48273,8 +42801,6 @@ For example, A and B may be gene products and binding of B by A positively regul A structure created during embryogenesis when the lateral mesoderm splits into two layers - the outer (or somatic) layer becomes applied to the inner surface of the ectoderm, and with it forms the somatopleure.[WP]. - Gives rise to the paired appendages in jawed vertebrates. a persistent somatopleure through the redistribution and expansion of the lateral plate mesoderm is a synapomorphy for gnathostomes and a critical step in generating a novel developmental module with dramatic evolutionary potentia (Tulenko et al. 2012) http://burkelab.research.wesleyan.edu/current-projects/lamprey/ - sources differ as to whether this is part-of or develops-from the LPM EHDAA2:0001847 EHDAA:381 EMAPA:16180 @@ -48288,14 +42814,14 @@ For example, A and B may be gene products and binding of B by A positively regul somatopleure http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png - + - + EHDAA2 @@ -48361,9 +42887,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + @@ -48371,7 +42897,6 @@ For example, A and B may be gene products and binding of B by A positively regul One of of the pair of folds derived from the cloacal folds which give rise to a portion of the external genitalia; in male embryos they close over the urethral plate and fuse to form the spongy (penile) urethra and ventral aspect of the penis, not including the glans; failure of fusion of the urethral folds leads to hypospadias; in female embryos they fuse only anterior to the anus and form the labia minora[MP]. - Less commonly, urogenital fold refers to the fold in the mesonephros which is the precursor of e.g. the suspensory ligament of the ovary. This is the case in older versions of Gray's anatomy[WP] EHDAA2:0004022 EMAPA:30888 FMA:321919 @@ -48384,34 +42909,34 @@ For example, A and B may be gene products and binding of B by A positively regul urogenital fold - + - + - + - + EHDAA2 - + Wikipedia - + EHDAA2 @@ -48462,8 +42987,6 @@ For example, A and B may be gene products and binding of B by A positively regul The central region of trunk mesoderm. This tissue forms the notochord. - Notochord rudiment[ZFIN:ZDB-PUB-961014-576]. - WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord. AAO:0000478 EFO:0003426 TAO:0000091 @@ -48484,12 +43007,6 @@ For example, A and B may be gene products and binding of B by A positively regul The central region of trunk mesoderm. This tissue forms the notochord. https://orcid.org/0000-0002-6601-2165 - - - - Notochord rudiment[ZFIN:ZDB-PUB-961014-576]. - ZFIN:ZDB-PUB-961014-576 - @@ -48522,7 +43039,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts. - FBbt:00005811 joint uberon UBERON:0004905 @@ -48535,12 +43051,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts. http://orcid.org/0000-0002-6601-2165 - - - - FBbt:00005811 - - @@ -48572,9 +43082,7 @@ For example, A and B may be gene products and binding of B by A positively regul A proximal-distal subdivision of the digestive tract. - intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct. - FBbt:00100315 FMA:71131 uberon alimentary system subdivision @@ -48593,12 +43101,6 @@ For example, A and B may be gene products and binding of B by A positively regul A proximal-distal subdivision of the digestive tract. http://orcid.org/0000-0002-6601-2165 - - - - FBbt:00100315 - - @@ -48663,7 +43165,6 @@ For example, A and B may be gene products and binding of B by A positively regul The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds. - The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]. AAO:0011071 EMAPA:35594 FMA:295624 @@ -48685,12 +43186,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Neural_groove http://orcid.org/0000-0002-6601-2165 - - - - The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]. - Wikipedia:Neural_groove - @@ -48706,6 +43201,7 @@ For example, A and B may be gene products and binding of B by A positively regul + @@ -48713,14 +43209,7 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - One of the two elevated edges of the neural groove[GO,MP]. - In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]. EHDAA2:0001249 FMA:295618 NCIT:C34223 @@ -48743,12 +43232,6 @@ For example, A and B may be gene products and binding of B by A positively regul MP:0011256 Wikipedia:Neural_fold - - - - In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]. - Wikipedia:Neural_fold - @@ -48775,7 +43258,6 @@ For example, A and B may be gene products and binding of B by A positively regul A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN]. - An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO] EFO:0003498 TAO:0000133 ZFA:0000133 @@ -48792,15 +43274,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0014024 ZFA:0000133 - - - - An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000133 - TAO - ZFIN:curator - @@ -48897,8 +43370,6 @@ For example, A and B may be gene products and binding of B by A positively regul Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO]. - in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila - EMAPA:32715 FMA:30316 musculus uberon @@ -48926,7 +43397,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + Missing definition for term UBERON:0005095. Please replace it using linked reference. class added for consistency with GO - consider merging with kidney mesenchyme. uberon @@ -48934,14 +43405,14 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0005095 kidney rudiment - + - + GO @@ -49057,7 +43528,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + The connecting tubule is a tubular segment of the nephron; it connects the distal convoluted tubule to the collecting duct[GO]. BTO:0004539 @@ -49075,14 +43546,14 @@ For example, A and B may be gene products and binding of B by A positively regul renal connecting tubule http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + - + Wikipedia @@ -49129,6 +43600,7 @@ For example, A and B may be gene products and binding of B by A positively regul + @@ -49304,7 +43776,6 @@ For example, A and B may be gene products and binding of B by A positively regul Connective tissue between the cellular elements of a structure. specify differentia from stroma - interstital FMA:86301 SCTID:85293002 interstitium @@ -49735,8 +44206,6 @@ For example, A and B may be gene products and binding of B by A positively regul The interstitial compartment of the kidney, comprising the extravascular intertubular spaces of the renal parenchyma, with their attendant cellular elements and extracellular substances, bounded on all sides by epithelial and vascular basement membranes. See https://sourceforge.net/p/geneontology/ontology-requests/10941/ - The interstitium is necessarily involved in all intrarenal exchange processes since the reabsorption and secretion of fluid and solutes implicates a transit across the interstitial compartment. - The fibroblasts in the interstitium provide the 'skeleton' of the tissue and maintain the three-dimensional architecture of the tissue. EMAPA:28518 FMA:70983 MA:0002616 @@ -49815,7 +44284,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -49831,14 +44300,14 @@ For example, A and B may be gene products and binding of B by A positively regul trunk mesenchyme - + - + EHDAA2 @@ -49918,7 +44387,6 @@ For example, A and B may be gene products and binding of B by A positively regul AEO:0000125 CALOHA:TS-2122 EHDAA2:0003125 - FBbt:00007006 FMA:292313 MIAA:0000019 uberon @@ -49929,12 +44397,6 @@ For example, A and B may be gene products and binding of B by A positively regul developing anatomical structure - - - - FBbt:00007006 - - @@ -49955,9 +44417,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + Multi-tissue structure that arises from the heart rudiment and will become the heart tube. - BTO:0006179 EHDAA2:0001512 EHDAA:424 EHDAA:436 @@ -49974,14 +44435,14 @@ For example, A and B may be gene products and binding of B by A positively regul primitive heart tube - + - + ZFA @@ -49990,14 +44451,6 @@ For example, A and B may be gene products and binding of B by A positively regul Multi-tissue structure that arises from the heart rudiment and will become the heart tube. ZFA:0000149 - - - - BTO:0006179 - - - https://github.com/biopragmatics/biomappings - @@ -50017,7 +44470,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -50025,8 +44478,6 @@ For example, A and B may be gene products and binding of B by A positively regul Portion of tissue that gives rise to the immature gonad. - Immature reproductive tissue that has not undergone final maturation into either testis or ovary.[TAO] - this is a very broad grouping class EFO:0003651 EHDAA:5927 EMAPA:17204 @@ -50046,7 +44497,7 @@ For example, A and B may be gene products and binding of B by A positively regul gonad primordium - + @@ -50059,7 +44510,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + ZFA @@ -50068,15 +44519,6 @@ For example, A and B may be gene products and binding of B by A positively regul Portion of tissue that gives rise to the immature gonad. ZFA:0001262 - - - - Immature reproductive tissue that has not undergone final maturation into either testis or ovary.[TAO] - 2012-08-14 - TAO:0001262 - TAO - ZFIN:curator - @@ -50125,17 +44567,17 @@ For example, A and B may be gene products and binding of B by A positively regul + - + - + A mesoderm that has the potential to develop into a pronephros. - Portion of tissue that consists of the mesenchymal precursor to the pronephric kidney and that begins to separate from the intermediate mesoderm at NF stage 21 and epithelializes by NF stage 30.[AAO] AAO:0011090 EFO:0003479 TAO:0000067 @@ -50152,24 +44594,24 @@ For example, A and B may be gene products and binding of B by A positively regul the intermediate mesoderm of the chick embryo acquires its ability to form kidneys through its interactions with the paraxial mesoderm [ISBN:9780878932504 "Developmental Biology", PMID:10720431 "Signals from trunk paraxial mesoderm induce pronephros formation in chick intermediate mesoderm"]. These interactions induce the expression of TFs including Lim1, Pax2 and Pax6 that cause the intermediate mesoderm to form the kidney pronephric mesoderm - + - + - + ZFA - + Bgee:AN @@ -50178,15 +44620,6 @@ For example, A and B may be gene products and binding of B by A positively regul A mesoderm that has the potential to develop into a pronephros. OBOL:automatic - - - - Portion of tissue that consists of the mesenchymal precursor to the pronephric kidney and that begins to separate from the intermediate mesoderm at NF stage 21 and epithelializes by NF stage 30.[AAO] - 2012-06-20 - AAO:0011090 - AAO - XAO:curator - @@ -50225,7 +44658,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -50233,9 +44666,7 @@ For example, A and B may be gene products and binding of B by A positively regul The capillary loops of the kidney that normally function as a filtration unit[MP]. - ...Soon afterwards, endothelial cells invade to make a capillary knot-like outgrowth, the glomerular tuft, which goes on to form the glomerulus EMAPA:28239 - SCTID:362217000 Wikipedia:Glomerulus uberon glomerular capillary tuft @@ -50244,14 +44675,14 @@ For example, A and B may be gene products and binding of B by A positively regul glomerular tuft - + - + Wikipedia @@ -50262,12 +44693,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Glomerulus http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron - - - - ...Soon afterwards, endothelial cells invade to make a capillary knot-like outgrowth, the glomerular tuft, which goes on to form the glomerulus - GudMap - @@ -50430,7 +44855,6 @@ For example, A and B may be gene products and binding of B by A positively regul An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina. - this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell. AAO:0010596 FMA:63872 @@ -50507,8 +44931,9 @@ For example, A and B may be gene products and binding of B by A positively regul + - + @@ -50516,13 +44941,11 @@ For example, A and B may be gene products and binding of B by A positively regul The layer of extracellular matrix that lies between the endothelium of the glomerular capillaries and the podocytes of the inner or visceral layer of the Bowman capsule; it is a fusion of the endothelial cell and podocyte basal laminas and acts as a physical barrier and an ion-selective filter. - Membrane between the mesonephric podocytes and the renal glomerular capillaries. It is a trilaminar structure composed of the fused basement membranes of the glomerular capillaries and basement membrane of the podocytes. The capillary membranes touch the GBM at contact points that are separated by pores. The membrane is semi-permeable allowing water and small molecules to pass into the renal capsular space.[TAO] GBM EMAPA:28251 EMAPA:30965 FMA:74274 MA:0001659 - MESH:D050533 NCIT:C32683 SCTID:243897006 TAO:0005285 @@ -50538,14 +44961,14 @@ For example, A and B may be gene products and binding of B by A positively regul glomerular basement membrane http://upload.wikimedia.org/wikipedia/commons/d/de/PhysiologieGlom%C3%A9rulaire.png - + - + true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -50556,29 +44979,12 @@ For example, A and B may be gene products and binding of B by A positively regul MGI:anna MP:0011348 - - - - Membrane between the mesonephric podocytes and the renal glomerular capillaries. It is a trilaminar structure composed of the fused basement membranes of the glomerular capillaries and basement membrane of the podocytes. The capillary membranes touch the GBM at contact points that are separated by pores. The membrane is semi-permeable allowing water and small molecules to pass into the renal capsular space.[TAO] - 2012-08-14 - TAO:0005285 - TAO - ZFIN:ZDB-PUB-000824-1 - GBM - - - - MESH:D050533 - - - https://github.com/biopragmatics/biomappings - @@ -50647,7 +45053,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 @@ -50657,7 +45063,7 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0005856 developing mesenchymal condensation - + @@ -50676,7 +45082,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + AEO-modified-relation @@ -50718,10 +45124,8 @@ For example, A and B may be gene products and binding of B by A positively regul Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified]. - Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO] AAO:0000963 EMAPA:17214 - EMAPA:18043 MA:0000308 NCIT:C32172 SCTID:361725000 @@ -50749,15 +45153,6 @@ For example, A and B may be gene products and binding of B by A positively regul https://github.com/obophenotype/uberon/issues/44 https://github.com/obophenotype/uberon/wiki/The-axial-skeleton - - - - Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO] - 2012-08-14 - VSAO:0000056 - VSAO - PSPUB:0000170 - @@ -50784,7 +45179,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -50804,8 +45199,6 @@ For example, A and B may be gene products and binding of B by A positively regul The membrane that covers the embryonic cloaca, formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm; the urorectal septum joins the cloacal membrane and divides it into an anal membrane and a urogenital membrane; the point where the urorectal septum intersects the cloacal membrane is the future site of the perineal body; proliferation of mesoderm and ectoderm around the cloacal membrane produces primordial tissues of the external genitalia in both sexes: the genital tubercle, genital folds, and genital swellings. - A membrane that separates the proctodeum and the hindgut in the early embryo. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.497, see_Kardong_KV][VHOG] - In mammals, the cloaca exists as an embryonic structure that undergoes septation to become distinct urethral, anal, and genital orifices.[well established][VHOG] EHDAA2:0000257 EHDAA:214 EHDAA:2933 @@ -50825,14 +45218,14 @@ For example, A and B may be gene products and binding of B by A positively regul cloacal membrane http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray991.png - + - + Wikipedia @@ -50843,25 +45236,6 @@ For example, A and B may be gene products and binding of B by A positively regul MP:anna Wikipedia:Cloacal_membrane - - - - A membrane that separates the proctodeum and the hindgut in the early embryo. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.497, see_Kardong_KV][VHOG] - 2012-09-17 - VHOG:0001198 - VHOG - http://bgee.unil.ch/ - - - - - In mammals, the cloaca exists as an embryonic structure that undergoes septation to become distinct urethral, anal, and genital orifices.[well established][VHOG] - 2012-09-17 - VHOG:0001198 - VHOG - PMID:11830557 De Santa Barbara P, Roberts DJ, Tail gut endoderm and gut/genitourinary/tail development: a new tissue-specific role for Hoxa13. Development (2002) - http://bgee.unil.ch/ - @@ -50885,10 +45259,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB - The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG] EHDAA2:0001278 EHDAA:264 EMAPA:16101 @@ -50900,7 +45273,7 @@ For example, A and B may be gene products and binding of B by A positively regul notochordal plate - + @@ -50913,7 +45286,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + EHDAA2 @@ -50922,15 +45295,6 @@ For example, A and B may be gene products and binding of B by A positively regul The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. VHOG:0001212 - - - - The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG] - 2012-09-17 - VHOG:0001212 - VHOG - http://bgee.unil.ch/ - @@ -50950,7 +45314,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -50967,14 +45331,14 @@ For example, A and B may be gene products and binding of B by A positively regul The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -51190,7 +45554,6 @@ For example, A and B may be gene products and binding of B by A positively regul A tube in the kidney that collect and transport urine. - in ZFA this is defined as part of mesonephros TAO:0005289 ZFA:0005289 uberon @@ -51203,12 +45566,6 @@ For example, A and B may be gene products and binding of B by A positively regul A tube in the kidney that collect and transport urine. ZFIN:ZDB-PUB-071029-9 - - - - in ZFA this is defined as part of mesonephros - ZFA - @@ -51525,7 +45882,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + A region of nephron tubule that is part of a cortex of kidney. EMAPA:18976 MA:0002609 @@ -51535,14 +45892,14 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0006853 renal cortex tubule - + - + MA @@ -51583,8 +45940,6 @@ For example, A and B may be gene products and binding of B by A positively regul The distalmost portion of the digestive tract, derived from the hindgut, and terminating with the anus. - this class is the superclass of 'rectum', which is currently reserved for the vertebrate structure. May be merged in future. - FBbt:00005756 WBbt:0005773 rectum uberon @@ -51599,12 +45954,6 @@ For example, A and B may be gene products and binding of B by A positively regul The distalmost portion of the digestive tract, derived from the hindgut, and terminating with the anus. http://orcid.org/0000-0002-6601-2165 - - - - FBbt:00005756 - - @@ -51687,7 +46036,6 @@ For example, A and B may be gene products and binding of B by A positively regul An epithelium characterised by its most superficial layer consisting of squamous epithelial cells. - FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium BTO:0002072 NCIT:C12848 SCTID:40118003 @@ -51703,12 +46051,6 @@ For example, A and B may be gene products and binding of B by A positively regul An epithelium characterised by its most superficial layer consisting of squamous epithelial cells. Wikipedia:Squamous_epithelium - - - - FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium - FBbt - @@ -51783,12 +46125,6 @@ For example, A and B may be gene products and binding of B by A positively regul Old definition: 'Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.' Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism. anatomical surface - - - - - via morphological boundary in CARO - @@ -51807,6 +46143,7 @@ For example, A and B may be gene products and binding of B by A positively regul + @@ -51981,7 +46318,6 @@ For example, A and B may be gene products and binding of B by A positively regul - The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis BILA:0000084 NCIT:C34268 SCTID:360394002 @@ -51997,12 +46333,6 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0007026 presumptive gut - - - - The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis - NCBIBook:NBK10107 - @@ -52033,10 +46363,13 @@ For example, A and B may be gene products and binding of B by A positively regul - + + + + + + A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]. - note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis - SPD:0000130 TADS:0000147 http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg dorsal tube @@ -52048,16 +46381,6 @@ For example, A and B may be gene products and binding of B by A positively regul Gene notes: Bmp, Nkx, Gata primary circulatory organ - - - - - - - - - GO uses blood circulation generically to include the haemolymphatic fluid of arthropods - @@ -52096,7 +46419,6 @@ For example, A and B may be gene products and binding of B by A positively regul An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. - An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO] EFO:0003497 TAO:0000131 ZFA:0000131 @@ -52112,15 +46434,6 @@ For example, A and B may be gene products and binding of B by A positively regul An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. ZFIN:ZDB-PUB-961014-576 - - - - An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000131 - TAO - ZFIN:curator - @@ -52145,7 +46458,12 @@ For example, A and B may be gene products and binding of B by A positively regul - + + + + + + @@ -52162,17 +46480,6 @@ For example, A and B may be gene products and binding of B by A positively regul presumptive segmental plate - - - - - - - - - https://github.com/obophenotype/uberon/wiki/The-neural-crest - EDHAA2 - @@ -52224,7 +46531,6 @@ For example, A and B may be gene products and binding of B by A positively regul A presumptive structure that has the potential to develop into a neural plate. consider merging - Region of the gastrula which gives rise to the neural plate.[TAO] EFO:0003424 TAO:0000063 ZFA:0000063 @@ -52241,15 +46547,6 @@ For example, A and B may be gene products and binding of B by A positively regul A presumptive structure that has the potential to develop into a neural plate. OBOL:automatic - - - - Region of the gastrula which gives rise to the neural plate.[TAO] - 2012-08-14 - TAO:0000063 - TAO - ZFIN:curator - @@ -52268,7 +46565,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -52294,7 +46591,7 @@ For example, A and B may be gene products and binding of B by A positively regul presumptive paraxial mesoderm - + @@ -52310,7 +46607,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + https://github.com/obophenotype/uberon/issues/1277 @@ -52471,7 +46768,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -52479,7 +46776,7 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0007524 dense mesenchyme tissue - + @@ -52492,7 +46789,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + AEO @@ -52585,7 +46882,6 @@ For example, A and B may be gene products and binding of B by A positively regul - consider moving MA:0000377 renal tubule here, as it includes the various segments (proximal etc) as subclasses, not parts FMA:17692 renal tubule region uberon @@ -52593,12 +46889,6 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0007685 region of nephron tubule - - - - consider moving MA:0000377 renal tubule here, as it includes the various segments (proximal etc) as subclasses, not parts - MA - @@ -52670,7 +46960,6 @@ For example, A and B may be gene products and binding of B by A positively regul AEO:0000170 EFO:0001649 EHDAA2:0003170 - FBbt:00005426 Wikipedia:Anlage_(biology) developmental field uberon @@ -52700,12 +46989,6 @@ For example, A and B may be gene products and binding of B by A positively regul FBbt:00005426 http://flybase.org/reports/FBrf0178740.html - - - - FBbt:00005426 - - @@ -52713,12 +46996,10 @@ For example, A and B may be gene products and binding of B by A positively regul - + Anatomical system that consists of all blood and lymph vessels. consider merging with vasculature - The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]. - in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system BTO:0001085 CALOHA:TS-2053 EHDAA2:0004520 @@ -52732,14 +47013,14 @@ For example, A and B may be gene products and binding of B by A positively regul vascular system - + - + MA @@ -52748,18 +47029,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that consists of all blood and lymph vessels. http://orcid.org/0000-0002-6601-2165 - - - - The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]. - ncithesaurus:Vascular_System - - - - - in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system - MA - @@ -52803,8 +47072,6 @@ For example, A and B may be gene products and binding of B by A positively regul An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). - this encompasses non-skeletal tissue - An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There are only two instances of appendage girdle regions per organism.[VSAO] UBERON:0007824 girdle girdle region @@ -52826,15 +47093,6 @@ For example, A and B may be gene products and binding of B by A positively regul UBERONREF:0000003 https://orcid.org/0000-0002-6601-2165 - - - - An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There are only two instances of appendage girdle regions per organism.[VSAO] - 2012-08-14 - VSAO:0000303 - VSAO - https://orcid.org/0000-0002-6601-2165 - @@ -52886,6 +47144,7 @@ For example, A and B may be gene products and binding of B by A positively regul + @@ -52899,7 +47158,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -52908,11 +47167,6 @@ For example, A and B may be gene products and binding of B by A positively regul Skeletal subdivision consisting of a set of bones linking the axial series to the hindlimb zeugopodium and offering anchoring areas for hindlimb and caudal musculature. need to resolve whether this is a paired structure or a single belt (Paired in FMA - implicitly paired in VSAO) - Anatomical cluster by which the hind limbs are supported and attached to the vertebral column.[AAO] - Anatomical cluster that consists of the paired basipterygia which support the pelvic fin.[TAO] - Girdle skeleton consisting of a set of bones linking the axial series to the hindlimb/fin skeleton and offering anchoring areas for hindlimb/fin and caudal musculature.[VSAO] - The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin.[well established][VHOG] - Note that the VSAO and many ontologies use the label 'pelvic girdle' to denote the skeletal region specifically. We place the EHDAA2 class here, note that this includes the pre-cartilage condensation as parts AAO:0000426 AAO:0000768 EFO:0000947 @@ -52942,14 +47196,14 @@ For example, A and B may be gene products and binding of B by A positively regul pelvic girdle skeleton http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png - + - + PMID:21455939 @@ -52959,49 +47213,6 @@ For example, A and B may be gene products and binding of B by A positively regul VSAO:0000155 Wikipedia:Pelvis - - - - Anatomical cluster by which the hind limbs are supported and attached to the vertebral column.[AAO] - 2012-06-20 - AAO:0000426 - AAO - AAO:LAP - - - - - Anatomical cluster that consists of the paired basipterygia which support the pelvic fin.[TAO] - 2012-08-14 - TAO:0000565 - TAO - TAO:wd - - - - - Girdle skeleton consisting of a set of bones linking the axial series to the hindlimb/fin skeleton and offering anchoring areas for hindlimb/fin and caudal musculature.[VSAO] - 2012-08-14 - VSAO:0000155 - VSAO - https://orcid.org/0000-0002-6601-2165 - - - - - The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin.[well established][VHOG] - 2012-09-17 - VHOG:0000305 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.333 - http://bgee.unil.ch/ - - - - - Note that the VSAO and many ontologies use the label 'pelvic girdle' to denote the skeletal region specifically. We place the EHDAA2 class here, note that this includes the pre-cartilage condensation as parts - VSAO - @@ -53045,7 +47256,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + The functional tissue of the kidney, consisting of the nephrons. BTO:0003604 FMA:15574 @@ -53056,7 +47267,7 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0008987 renal parenchyma - + @@ -53069,7 +47280,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + FMA @@ -53139,7 +47350,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -53156,14 +47367,14 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -53282,7 +47493,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -53290,14 +47501,14 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -53327,7 +47538,6 @@ For example, A and B may be gene products and binding of B by A positively regul A renal tubule is a tube that filters, re-absorbs and secretes substances to rid an organism of waste and to play a role in fluid homeostasis. - this class groups vertebrate nephron tubules with analagous structures such as insect Malpighian tubules renal tubule (generic) tubule of excretory system uberon @@ -53395,8 +47605,9 @@ For example, A and B may be gene products and binding of B by A positively regul + - + EFO:0003704 TAO:0005041 ZFA:0005041 @@ -53406,14 +47617,14 @@ For example, A and B may be gene products and binding of B by A positively regul anterior lateral plate mesoderm - + - + ZFA @@ -53448,7 +47659,6 @@ For example, A and B may be gene products and binding of B by A positively regul An artery that supplies a renal lobe. - FMA only has the set term EMAPA:37091 FMA:71637 SCTID:62802007 @@ -53474,12 +47684,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Interlobar_arteries http://orcid.org/0000-0002-6601-2165 - - - - FMA only has the set term - FMA - @@ -53593,7 +47797,6 @@ For example, A and B may be gene products and binding of B by A positively regul The portion of a kidney consisting of a renal medullary pyramid and the renal cortex above it[MP]. It is composed of many renal lobules[WP]. todo - add has_part relationships. - human kidneys have multilobar (multipyramidal) architecture while mice and rats have unilobar (unipyramidal) kidneys FMA:17881 NCIT:C32894 UMLS:C0736382 @@ -53615,12 +47818,6 @@ For example, A and B may be gene products and binding of B by A positively regul MP:0011381 Wikipedia:Renal_lobe - - - - human kidneys have multilobar (multipyramidal) architecture while mice and rats have unilobar (unipyramidal) kidneys - MP - @@ -53688,7 +47885,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0010000 - FBbt:00100313 multicellular structure uberon UBERON:0010000 @@ -53702,12 +47898,6 @@ For example, A and B may be gene products and binding of B by A positively regul An anatomical structure that has more than one cell as a part. CARO:0010000 - - - - FBbt:00100313 - - @@ -53748,7 +47938,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -53766,14 +47956,14 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0010227 future cardiac atrium - + - + ZFA @@ -53825,7 +48015,6 @@ For example, A and B may be gene products and binding of B by A positively regul An anatomical structure that has some part that develops from the neural crest. - Grouping term for query purposes uberon UBERON:0010314 @@ -53914,9 +48103,10 @@ For example, A and B may be gene products and binding of B by A positively regul + - + @@ -53930,7 +48120,7 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0010377 mesenchyme from somatopleure - + @@ -53943,7 +48133,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + EHDAA2 @@ -53959,7 +48149,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses. MESH:D055806 TAO:0005251 @@ -53969,14 +48159,14 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0010523 microcirculatory vessel - + - + ZFA @@ -54009,7 +48199,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -54017,7 +48207,6 @@ For example, A and B may be gene products and binding of B by A positively regul An epithelial tube that is fated to become a nephron. - EHDAA2 treats this as already having a tubular structure, but in the ZFA representation this is a cluster of cells developing nephron primitive nephron future nephron @@ -54026,7 +48215,7 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0010532 primitive nephron - + @@ -54039,7 +48228,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + EHDAA2 @@ -54048,12 +48237,6 @@ For example, A and B may be gene products and binding of B by A positively regul An epithelial tube that is fated to become a nephron. http://orcid.org/0000-0002-6601-2165 - - - - EHDAA2 treats this as already having a tubular structure, but in the ZFA representation this is a cluster of cells - EHDAA2 - @@ -54061,7 +48244,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -54072,7 +48255,7 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0010536 nephron progenitor - + @@ -54085,7 +48268,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + cjm @@ -54096,12 +48279,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - @@ -54116,9 +48293,6 @@ For example, A and B may be gene products and binding of B by A positively regul An organism subdivision that includes both an appendage and its associated girdle region. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO] - Anatomical group that consists of the soft and skeletal tissues of the appendicular region of the body and the appendage proper.[VSAO] - It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO] - note that the FMA uses the term 'limb' to refer to the entire appendage complex (free limb plus girdle region) 2012-04-23T10:46:51Z EMAPA:37858 @@ -54141,30 +48315,6 @@ For example, A and B may be gene products and binding of B by A positively regul https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton https://orcid.org/0000-0002-6601-2165 - - - - Anatomical group that consists of the soft and skeletal tissues of the appendicular region of the body and the appendage proper.[VSAO] - 2012-08-14 - VSAO:0000214 - VSAO - GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 - - - - - It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO] - 2012-09-06 - VSAO:0000214 - VSAO - Curator - - - - - note that the FMA uses the term 'limb' to refer to the entire appendage complex (free limb plus girdle region) - FMA - @@ -54233,9 +48383,6 @@ For example, A and B may be gene products and binding of B by A positively regul Appendage girdle complex that when present, encompasses the pelvic appendicular skeleton and the pelvic girdle. - - Appendage girdle complex that when present, encompasses the pelvic appendage and the pelvic girdle.[VSAO] - note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region). Note the MA class 'hindlimb' may also belong here EMAPA:37863 FMA:7184 SCTID:416631005 @@ -54257,21 +48404,6 @@ For example, A and B may be gene products and binding of B by A positively regul Appendage girdle complex that when present, encompasses the pelvic appendicular skeleton and the pelvic girdle. VSAO:0000215 - - - - Appendage girdle complex that when present, encompasses the pelvic appendage and the pelvic girdle.[VSAO] - 2012-08-14 - VSAO:0000215 - VSAO - VSAO:MAH - - - - - note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region). Note the MA class 'hindlimb' may also belong here - FMA - @@ -54359,9 +48491,6 @@ For example, A and B may be gene products and binding of B by A positively regul The subdivision of the skeleton of either the pectoral or pelvic girdle. - Skeletal subdivision that is part of the appendage girdle region.[VSAO] - relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: part_of subdivision of skeleton (UBERON:0010912)[VSAO] - relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: proximally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO] AAO:0010686 VSAO:0000302 skeleton of girdle @@ -54375,31 +48504,6 @@ For example, A and B may be gene products and binding of B by A positively regul The subdivision of the skeleton of either the pectoral or pelvic girdle. https://orcid.org/0000-0002-6601-2165 - - - - Skeletal subdivision that is part of the appendage girdle region.[VSAO] - 2012-08-14 - VSAO:0000302 - VSAO - GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 - - - - - relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: part_of subdivision of skeleton (UBERON:0010912)[VSAO] - 2012-08-14 - VSAO:0000302 - VSAO - - - - - relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: proximally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO] - 2012-08-14 - VSAO:0000302 - VSAO - @@ -54407,10 +48511,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. - Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO] FMA:23879 SCTID:129140006 VSAO:0000042 @@ -54421,11 +48524,11 @@ For example, A and B may be gene products and binding of B by A positively regul subdivision of skeleton - + - + @@ -54438,13 +48541,13 @@ For example, A and B may be gene products and binding of B by A positively regul - + UBERONREF:0000003 - + VSAO @@ -54454,16 +48557,6 @@ For example, A and B may be gene products and binding of B by A positively regul UBERONREF:0000003 https://orcid.org/0000-0002-6601-2165 - - - - Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO] - 2012-08-14 - VSAO:0000042 - incorrect - VSAO - VSAO:curator - @@ -54515,7 +48608,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system FMA:302077 @@ -54525,7 +48618,7 @@ For example, A and B may be gene products and binding of B by A positively regul postcranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton - + @@ -54538,7 +48631,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + cjm @@ -54562,7 +48655,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -54575,7 +48668,6 @@ For example, A and B may be gene products and binding of B by A positively regul - Subdivision of urinary system which consists of the kidney and the ureters. FMA:45658 @@ -54588,26 +48680,16 @@ For example, A and B may be gene products and binding of B by A positively regul upper urinary tract - + - - - - - + FMA - - - - - FMA-abduced-lr - @@ -54632,7 +48714,6 @@ For example, A and B may be gene products and binding of B by A positively regul - FBbt:00007330 FMA:67509 SCTID:91690000 uberon @@ -54654,12 +48735,6 @@ For example, A and B may be gene products and binding of B by A positively regul A subdivision of an anatomical system. http://orcid.org/0000-0002-6601-2165 - - - - FBbt:00007330 - - @@ -54680,9 +48755,7 @@ For example, A and B may be gene products and binding of B by A positively regul Subdivision of the skeletal system which consists of the appendicular skeleton plus associated joints. - Skeletal system which consists of the appendicular skeleton plus associated joints.[VSAO] FMA:7484 - VHOG:0001666 VSAO:0000306 uberon UBERON:0011249 @@ -54695,15 +48768,6 @@ For example, A and B may be gene products and binding of B by A positively regul Subdivision of the skeletal system which consists of the appendicular skeleton plus associated joints. https://orcid.org/0000-0002-6601-2165 - - - - Skeletal system which consists of the appendicular skeleton plus associated joints.[VSAO] - 2012-08-14 - VSAO:0000306 - VSAO - https://orcid.org/0000-0002-6601-2165 - @@ -54820,7 +48884,6 @@ For example, A and B may be gene products and binding of B by A positively regul The aggregate of the coelemic cavity lumen plus the membranes that line the lumen. EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining. - coelomic EHDAA2:0004731 Wikipedia:Coelom enterocoelom @@ -54935,7 +48998,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -54950,14 +49013,14 @@ For example, A and B may be gene products and binding of B by A positively regul We presume this is distinct from AAO:0001003, an external integumentary structure - check with amphibian anatomy ontology developers. AO notes: the text def states mesenchymal swelling, EHDAA2 splits into mesenchymal and epithelial parts embryonic cloacal fold - + - + EHDAA2 @@ -54980,20 +49043,20 @@ For example, A and B may be gene products and binding of B by A positively regul - + EHDAA2:0004588 uberon UBERON:0012361 internal anal region - + - + EHDAA2 @@ -55003,20 +49066,20 @@ For example, A and B may be gene products and binding of B by A positively regul - + EHDAA2:0004589 uberon UBERON:0012469 external anal region - + - + EHDAA2 @@ -55043,7 +49106,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -55063,14 +49126,14 @@ For example, A and B may be gene products and binding of B by A positively regul skeleton of pelvic complex - + - + FMA @@ -55122,9 +49185,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + The precursor of the urethra. - In humans, the urethral groove is a temporary linear indentation on the underside (ventral side) of the male penis during embryonic development. It typically appears around 8 weeks of gestation and becomes closed into a normal male urethra by the 12th week SCTID:361531004 Wikipedia:Urethral_groove sulcus urethralis primarius @@ -55134,14 +49196,14 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0013241 embryonic urethral groove - + - + Wikipedia @@ -55150,12 +49212,6 @@ For example, A and B may be gene products and binding of B by A positively regul The precursor of the urethra. http://orcid.org/0000-0002-6601-2165 - - - - In humans, the urethral groove is a temporary linear indentation on the underside (ventral side) of the male penis during embryonic development. It typically appears around 8 weeks of gestation and becomes closed into a normal male urethra by the 12th week - Wikipedia:Urethral_groove - @@ -55281,10 +49337,8 @@ For example, A and B may be gene products and binding of B by A positively regul The region of the organism associated with the visceral organs. - Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]. AEO:0000103 BTO:0001489 - EMAPA:36031 FMA:231424 uberon body @@ -55305,12 +49359,6 @@ For example, A and B may be gene products and binding of B by A positively regul The region of the organism associated with the visceral organs. AEO:0000103 - - - - Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]. - FMA:231424 - @@ -55348,7 +49396,6 @@ For example, A and B may be gene products and binding of B by A positively regul A blood that is part of a vein. - BTO:0006187 FMA:83067 blood in vein portion of venous blood @@ -55363,14 +49410,6 @@ For example, A and B may be gene products and binding of B by A positively regul A blood that is part of a vein. OBOL:automatic - - - - BTO:0006187 - - - https://github.com/biopragmatics/biomappings - @@ -55511,24 +49550,7 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - @@ -55536,7 +49558,6 @@ For example, A and B may be gene products and binding of B by A positively regul Any structure that is placed on one side of the left-right axis of a bilaterian. - This class is primarily to implement taxon constraints. It may be removed in the future. uberon UBERON:0015212 @@ -55570,7 +49591,6 @@ For example, A and B may be gene products and binding of B by A positively regul A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile. heart - SPD:0000130 cardiac pump heart or heart like organ circulatory vessel @@ -55754,7 +49774,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -55777,7 +49797,7 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0016887 entire extraembryonic component - + @@ -55790,7 +49810,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + AEO @@ -55918,7 +49938,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0020000 - FBbt:00007276 uberon UBERON:0034923 @@ -55936,12 +49955,6 @@ For example, A and B may be gene products and binding of B by A positively regul Material anatomical entity consisting of multiple anatomical structures that are not connected to each other. CARO:0020000 - - - - FBbt:00007276 - - @@ -56082,24 +50095,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - + Any chamber of the right side of the heart. FMA:7165 SCTID:362007002 @@ -56217,7 +50214,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + The upper tract of the renal system. The renal pelvis is the large cavity in the middle of each kidney. Urine drains from each kidney through a long tube called the ureter, into the bladder, where it is stored until it is passed from the body through the urethra. NCIT:C54419 @@ -56228,14 +50225,14 @@ For example, A and B may be gene products and binding of B by A positively regul renal pelvis/ureter - + - + NCIT @@ -56253,7 +50250,6 @@ For example, A and B may be gene products and binding of B by A positively regul Any of the smallest blood vessels where blood circulates within organ tissues. Microvessels include terminal arterioles, metarterioles, capillaries, and venules (but exclude lymphatic capillaries). Arterioles carry oxygenated blood to the capillaries, and blood flows out of the capillaries through venules into veins. - microvascular http://orcid.org/0000-0002-2825-0621 microvasculature microvessel @@ -56297,7 +50293,6 @@ For example, A and B may be gene products and binding of B by A positively regul http://orcid.org/0000-0002-6095-8718 2022-05-25T18:21:29Z - BTO:0006338 uberon UBERON:8450002 @@ -56309,14 +50304,6 @@ For example, A and B may be gene products and binding of B by A positively regul An anatomical system that eliminates waste products that arise as a result of metabolic activity. GO:0007588 - - - - BTO:0006338 - - - https://github.com/biopragmatics/biomappings - @@ -56377,7 +50364,6 @@ For example, A and B may be gene products and binding of B by A positively regul - example to be eventually removed example to be eventually removed @@ -56386,9 +50372,7 @@ For example, A and B may be gene products and binding of B by A positively regul - failed exploratory term The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job - Person:Alan Ruttenberg failed exploratory term @@ -56397,7 +50381,6 @@ For example, A and B may be gene products and binding of B by A positively regul - metadata complete Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. metadata complete @@ -56407,7 +50390,6 @@ For example, A and B may be gene products and binding of B by A positively regul - organizational term Term created to ease viewing/sort terms for development purpose, and will not be included in a release organizational term @@ -56417,7 +50399,6 @@ For example, A and B may be gene products and binding of B by A positively regul - ready for release Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release @@ -56427,7 +50408,6 @@ For example, A and B may be gene products and binding of B by A positively regul - metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete @@ -56437,7 +50417,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated @@ -56447,7 +50426,6 @@ For example, A and B may be gene products and binding of B by A positively regul - pending final vetting All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting @@ -56457,7 +50435,6 @@ For example, A and B may be gene products and binding of B by A positively regul - placeholder removed placeholder removed @@ -56466,7 +50443,6 @@ For example, A and B may be gene products and binding of B by A positively regul - terms merged An editor note should explain what were the merged terms and the reason for the merge. terms merged @@ -56476,7 +50452,6 @@ For example, A and B may be gene products and binding of B by A positively regul - term imported This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. term imported @@ -56486,7 +50461,6 @@ For example, A and B may be gene products and binding of B by A positively regul - term split This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. term split @@ -56496,10 +50470,7 @@ For example, A and B may be gene products and binding of B by A positively regul - universal Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. - Alan Ruttenberg - A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf universal @@ -56508,10 +50479,8 @@ For example, A and B may be gene products and binding of B by A positively regul - defined class A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. - Alan Ruttenberg defined class @@ -56520,10 +50489,8 @@ For example, A and B may be gene products and binding of B by A positively regul - named class expression A named class expression is a logical expression that is given a name. The name can be used in place of the expression. named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions - Alan Ruttenberg named class expression @@ -56532,10 +50499,7 @@ For example, A and B may be gene products and binding of B by A positively regul - to be replaced with external ontology term Terms with this status should eventually replaced with a term from another ontology. - Alan Ruttenberg - group:OBI to be replaced with external ontology term @@ -56544,10 +50508,7 @@ For example, A and B may be gene products and binding of B by A positively regul - requires discussion A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. - Alan Ruttenberg - group:OBI requires discussion @@ -56558,9 +50519,7 @@ For example, A and B may be gene products and binding of B by A positively regul The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. - https://github.com/information-artifact-ontology/ontology-metadata/issues/77 - https://orcid.org/0000-0001-5208-3432 out of scope @@ -56574,24 +50533,6 @@ For example, A and B may be gene products and binding of B by A positively regul /////////////////////////////////////////////////////////////////////////////////////// --> - - - - - - - - - - - - - - - - - - @@ -56643,46 +50584,34 @@ For example, A and B may be gene products and binding of B by A positively regul /////////////////////////////////////////////////////////////////////////////////////// --> - - - - - - - - - - - - - + - + - + - + - + - + - + - + - + - + @@ -56709,8 +50638,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -56720,7 +50649,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -56730,7 +50659,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -56747,67 +50676,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - true - GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' - involved in BP - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + @@ -56825,8 +50695,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -56836,8 +50706,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -56847,8 +50717,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -56865,8 +50735,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -56883,8 +50753,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -56894,8 +50764,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -56905,8 +50775,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -56923,8 +50793,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -56941,8 +50811,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -56952,8 +50822,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -56963,8 +50833,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -56981,8 +50851,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -56999,8 +50869,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -57010,8 +50880,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -57026,8 +50896,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -57044,8 +50914,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -57055,8 +50925,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -57071,8 +50941,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -57089,8 +50959,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -57100,8 +50970,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -57116,8 +50986,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -57134,8 +51004,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -57145,8 +51015,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -57161,8 +51031,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -57179,8 +51049,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -57190,8 +51060,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -57206,8 +51076,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -57267,8 +51137,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -57278,8 +51148,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -57294,8 +51164,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -57310,9 +51180,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + @@ -57322,8 +51192,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -57337,9 +51207,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + @@ -57354,9 +51224,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + @@ -57366,8 +51236,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -57381,7 +51251,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + diff --git a/src/ontology/subsets/kidney_upper_slim.tsv b/src/ontology/subsets/kidney_upper_slim.tsv index 134b85af5..b82848970 100644 --- a/src/ontology/subsets/kidney_upper_slim.tsv +++ b/src/ontology/subsets/kidney_upper_slim.tsv @@ -1,373 +1,367 @@ ?x ?label -_:Be350484aX2D0263X2D4acdX2Da142X2D4091eb1e8e26genid1000 -_:Be350484aX2D0263X2D4acdX2Da142X2D4091eb1e8e26genid1011 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+_:B54f689ccX2D0367X2D4df3X2DaeacX2D9aa5d0817600genid890 +_:B54f689ccX2D0367X2D4df3X2DaeacX2D9aa5d0817600genid896 +_:B54f689ccX2D0367X2D4df3X2DaeacX2D9aa5d0817600genid903 +_:B54f689ccX2D0367X2D4df3X2DaeacX2D9aa5d0817600genid910 +_:B54f689ccX2D0367X2D4df3X2DaeacX2D9aa5d0817600genid916 +_:B54f689ccX2D0367X2D4df3X2DaeacX2D9aa5d0817600genid923 +_:B54f689ccX2D0367X2D4df3X2DaeacX2D9aa5d0817600genid929 +_:B54f689ccX2D0367X2D4df3X2DaeacX2D9aa5d0817600genid936 +_:B54f689ccX2D0367X2D4df3X2DaeacX2D9aa5d0817600genid943 +_:B54f689ccX2D0367X2D4df3X2DaeacX2D9aa5d0817600genid954 +_:B54f689ccX2D0367X2D4df3X2DaeacX2D9aa5d0817600genid964 +_:B54f689ccX2D0367X2D4df3X2DaeacX2D9aa5d0817600genid970 +_:B54f689ccX2D0367X2D4df3X2DaeacX2D9aa5d0817600genid976 +_:B54f689ccX2D0367X2D4df3X2DaeacX2D9aa5d0817600genid982 +_:B54f689ccX2D0367X2D4df3X2DaeacX2D9aa5d0817600genid988 +_:B54f689ccX2D0367X2D4df3X2DaeacX2D9aa5d0817600genid994 "continuant" "occurrent" "independent continuant" diff --git a/subsets/blood_and_immune_upper_slim.json b/subsets/blood_and_immune_upper_slim.json index f2b3e3a5d..fe2c37d13 100644 --- a/subsets/blood_and_immune_upper_slim.json +++ b/subsets/blood_and_immune_upper_slim.json @@ -4,9 +4,9 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-02-13" + "val" : "2024-04-05" } ], - "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-02-13/subsets/blood_and_immune_upper_slim.owl" + "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-04-05/subsets/blood_and_immune_upper_slim.owl" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/BFO_0000002", @@ -78,18 +78,6 @@ "val" : "BFO:0000050" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "is part of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my brain is part of my body (continuant parthood, two material entities)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this day is part of this year (occurrent parthood)" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." }, { @@ -98,42 +86,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "part_of" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000002" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000003" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000004" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000017" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000019" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000020" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000031" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "part_of" @@ -164,18 +122,6 @@ "val" : "BFO:0000051" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has part" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my body has part my brain (continuant parthood, two material entities)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this year has part this day (occurrent parthood)" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." }, { @@ -184,21 +130,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has_part" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_part" @@ -217,26 +154,11 @@ "val" : "BFO:0000062" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "preceded by" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is preceded by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "preceded_by" - }, { - "pred" : "http://purl.org/dc/terms/source", - "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "preceded_by" @@ -255,14 +177,8 @@ "val" : "BFO:0000063" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "precedes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "precedes" @@ -282,26 +198,11 @@ "val" : "BFO:0000066" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "occurs in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "occurs_in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "unfolds in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "unfolds_in" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "occurs_in" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Occurs_in" @@ -315,412 +216,12 @@ "definition" : { "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" }, - "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ], - "xrefs" : [ { - "val" : "BFO:0000067" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "site of" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "contains_process" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - } ] + "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000141", "lbl" : "immaterial entity", "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000096", - "lbl" : "anterior to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000096" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "anterior_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000097", - "lbl" : "distal to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000097" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "distal_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000098", - "lbl" : "dorsal to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000098" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dorsal_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000099", - "lbl" : "posterior to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000099" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "posterior_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000100", - "lbl" : "proximal to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000100" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "proximal_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000102", - "lbl" : "ventral to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000102" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "ventral_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000107", - "lbl" : "deep to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000107" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "deep_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000108", - "lbl" : "superficial to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000108" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "superficial_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000120", - "lbl" : "in left side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000120" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_left_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000121", - "lbl" : "in right side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000121" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_right_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000122", - "lbl" : "in posterior side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000122" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_posterior_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000123", - "lbl" : "in anterior side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000123" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_anterior_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000124", - "lbl" : "in proximal side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000124" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_proximal_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "lbl" : "in lateral side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000126" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_lateral_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001100", - "lbl" : "in superficial part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001100" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_superficial_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001101", - "lbl" : "in deep part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001101" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_deep_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001106", - "lbl" : "proximalmost part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001106" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "proximalmost_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001107", - "lbl" : "immediately deep to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001107" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "immediately_deep_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001108", - "lbl" : "distalmost part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001108" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "distalmost_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001113", - "lbl" : "preaxialmost part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001113" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "preaxialmost_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001115", - "lbl" : "postaxialmost part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001115" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "postaxialmost_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0005001", - "lbl" : "intersects midsagittal plane of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0005001" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "intersects_midsagittal_plane_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0015014", - "lbl" : "immediately superficial to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0015014" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "immediately_superficial_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0015101", - "lbl" : "in dorsal side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0015101" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_dorsal_side_of" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000000", "lbl" : "cell", @@ -14816,13 +14317,7 @@ }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000002", "lbl" : "example to be eventually removed", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "example to be eventually removed" - } ] - } + "type" : "INDIVIDUAL" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000028", "lbl" : "symbol", @@ -14834,14 +14329,7 @@ "meta" : { "definition" : { "val" : "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "failed exploratory term" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person:Alan Ruttenberg" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000115", @@ -14852,20 +14340,8 @@ "val" : "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "definition" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2012-04-05: \nBarry Smith\n\nThe official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. \n\nOn the specifics of the proposed definition:\n\nWe don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Daniel Schober" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" } ] } }, { @@ -14875,32 +14351,7 @@ "meta" : { "definition" : { "val" : "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology." - }, - "xrefs" : [ { - "val" : "IAO:0000116" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "editor note" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Daniel Schober" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "editor_note" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000120", @@ -14909,11 +14360,7 @@ "meta" : { "definition" : { "val" : "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "metadata complete" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000121", @@ -14922,11 +14369,7 @@ "meta" : { "definition" : { "val" : "Term created to ease viewing/sort terms for development purpose, and will not be included in a release" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "organizational term" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000122", @@ -14935,11 +14378,7 @@ "meta" : { "definition" : { "val" : "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\"" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "ready for release" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000123", @@ -14948,11 +14387,7 @@ "meta" : { "definition" : { "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "metadata incomplete" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000124", @@ -14961,11 +14396,7 @@ "meta" : { "definition" : { "val" : "Nothing done yet beyond assigning a unique class ID and proposing a preferred term." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "uncurated" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000125", @@ -14974,31 +14405,18 @@ "meta" : { "definition" : { "val" : "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "pending final vetting" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000226", "lbl" : "placeholder removed", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "placeholder removed" - } ] - } + "type" : "INDIVIDUAL" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000227", "lbl" : "terms merged", "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "terms merged" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "An editor note should explain what were the merged terms and the reason for the merge." } ] @@ -15009,9 +14427,6 @@ "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "term imported" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use." } ] @@ -15022,9 +14437,6 @@ "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "term split" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created." } ] @@ -15036,17 +14448,7 @@ "meta" : { "definition" : { "val" : "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has obsolescence reason" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Melanie Courtot" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000233", @@ -15061,29 +14463,8 @@ "val" : "IAO:0000233" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "term tracker item" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_class_level", - "val" : "true" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", "val" : "true" @@ -15098,17 +14479,8 @@ "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "universal" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf" } ] } }, { @@ -15120,14 +14492,8 @@ "val" : "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "defined class" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" } ] } }, { @@ -15139,14 +14505,8 @@ "val" : "A named class expression is a logical expression that is given a name. The name can be used in place of the expression." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "named class expression" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" } ] } }, { @@ -15156,17 +14516,7 @@ "meta" : { "definition" : { "val" : "Terms with this status should eventually replaced with a term from another ontology." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "to be replaced with external ontology term" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "group:OBI" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000424", @@ -15175,17 +14525,7 @@ "meta" : { "definition" : { "val" : "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "expand expression to" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "ObjectProperty: RO_0002104\nLabel: has plasma membrane part\nAnnotations: IAO_0000424 \"http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\"\n" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000428", @@ -15194,17 +14534,7 @@ "meta" : { "definition" : { "val" : "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "requires discussion" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "group:OBI" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000700", @@ -15218,20 +14548,8 @@ "val" : "IAO:0000700" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has ontology root term" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Nicolas Matentzoglu" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_class_level", - "val" : "true" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", "val" : "true" @@ -15248,20 +14566,7 @@ "definition" : { "val" : "Use on obsolete terms, relating the term to another term that can be used as a substitute" }, - "comments" : [ "Add as annotation triples in the granting ontology" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "term replaced by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person:Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Person:Alan Ruttenberg" - } ] + "comments" : [ "Add as annotation triples in the granting ontology" ] } }, { "id" : "http://purl.obolibrary.org/obo/NCBITaxon_1", @@ -15296,9 +14601,6 @@ "val" : "PMID:15371245" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_family" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15313,7 +14615,7 @@ "pred" : "hasExactSynonym", "val" : "Mus" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003003", + "synonymType" : "http://purl.obolibrary.org/obo/ncbitaxon#genbank_common_name", "pred" : "hasExactSynonym", "val" : "mice" }, { @@ -15325,9 +14627,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_genus" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15350,9 +14649,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_species" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "NCBITaxon:85055" }, { @@ -15369,9 +14665,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15390,9 +14683,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "NCBITaxon:40673" }, { @@ -15427,9 +14717,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15452,9 +14739,6 @@ "val" : "PMID:11791233" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15477,9 +14761,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_suborder" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15526,9 +14807,6 @@ "val" : "PMID:30257078" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_superkingdom" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15550,9 +14828,6 @@ "val" : "PMID:15522813" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_superorder" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15577,9 +14852,6 @@ "val" : "PMID:15522813" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15598,9 +14870,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15619,9 +14888,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15640,9 +14906,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15665,9 +14928,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15698,9 +14958,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_kingdom" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15714,9 +14971,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15735,9 +14989,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15755,9 +15006,6 @@ "val" : "PMID:15371245" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15771,9 +15019,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_subfamily" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "NCBITaxon:109679" }, { @@ -15799,9 +15044,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_class" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15815,9 +15057,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15840,9 +15079,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_phylum" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15869,9 +15105,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15894,9 +15127,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15910,9 +15140,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_superclass" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15931,9 +15158,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_subgenus" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15952,9 +15176,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_subphylum" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -15989,9 +15210,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -16014,9 +15232,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_order" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -16032,15 +15247,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/77" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", - "val" : "https://orcid.org/0000-0001-5208-3432" } ] } }, { @@ -16052,9 +15261,6 @@ "val" : "Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'part disjoint with' 'defined by construct' \"\"\"\n PREFIX owl: \n PREFIX : some (\n and some (\n and some (\n and some ?Y)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { @@ -21281,33 +19963,9 @@ "definition" : { "val" : "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " }, - "xrefs" : [ { - "val" : "RO:0002103" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that part_of some ( that has_part some ( that some Y?)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "synapsed_by" } ] } }, { @@ -21319,29 +19977,8 @@ "val" : "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9990-8331" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-1617-8244" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19243617" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( and some ?Y)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] } }, { @@ -21353,26 +19990,8 @@ "val" : "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. " }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "synapsed in" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (\n http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some (\n http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { @@ -21384,20 +20003,8 @@ "val" : "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "synapses in" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that some ( that some Y?)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { @@ -21410,23 +20017,8 @@ }, "comments" : [ "N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part some (\n ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( \n\t‘synapse ; GO:0045202’ that has_part some (\n\t ‘post-synaptic membrane ; GO:0045211’ that part_of some N2))))" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that part_of some ( that some ( that some Y?)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { @@ -21438,23 +20030,8 @@ "val" : "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has synapse in" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that some Y?)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { @@ -21470,20 +20047,11 @@ "val" : "RO:0002131" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "overlaps" @@ -21496,26 +20064,7 @@ "meta" : { "definition" : { "val" : "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has fasciculating component" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", - "val" : "(forall (?x ?y) \n\t(iff \n\t\t(has_fasciculating_neuron_projection ?x ?y)\n\t\t(exists (?nps ?npbs)\t\t\n\t\t\t(and \n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?x)\n\t\t\t\t(\"neuron projection ; GO0043005\" ?y)\n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n\t\t\t\t(part_of ?nps ?y)\n\t\t\t\t(part_of ?npbs ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))\n\n\n" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002134", @@ -21525,30 +20074,9 @@ "definition" : { "val" : "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." }, - "xrefs" : [ { - "val" : "RO:0002134" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that ( some ( that some Y?)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "innervates" } ] } }, { @@ -21559,31 +20087,7 @@ "definition" : { "val" : "X continuous_with Y if and only if X and Y share a fiat boundary." }, - "xrefs" : [ { - "val" : "RO:0002150" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "connected to" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "continuous_with" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "FMA:85972" } ] @@ -21596,23 +20100,7 @@ "definition" : { "val" : "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." }, - "comments" : [ "VBO calls this homologous_to" ], - "xrefs" : [ { - "val" : "RO:0002158" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Consider obsoleting and merging with child relation, 'in homology relationship with'" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "homologous_to" - } ] + "comments" : [ "VBO calls this homologous_to" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -21622,33 +20110,9 @@ "definition" : { "val" : "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." }, - "xrefs" : [ { - "val" : "RO:0002160" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "lactation SubClassOf 'only in taxon' some 'Mammalia'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "only_in_taxon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" @@ -21656,48 +20120,15 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002161", - "lbl" : "never_in_taxon", + "lbl" : "never in taxon", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL." }, - "xrefs" : [ { - "val" : "RO:0002161" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "tooth SubClassOf 'never in taxon' value 'Aves'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", - "val" : "Class: EquivalentTo: ?X and (RO_0002162 some ?Y)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", - "val" : "Class: ?X DisjointWith: RO_0002162 some ?Y " - }, { "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_class_level", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "never_in_taxon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" @@ -21713,31 +20144,7 @@ }, "comments" : [ "Connects a biological entity to its taxon of origin." ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002162" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9227-417X" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_taxon" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] @@ -21752,26 +20159,11 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" @@ -21785,22 +20177,7 @@ "definition" : { "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" }, - "xrefs" : [ { - "val" : "RO:0002170" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "connected_to" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" }, { @@ -21810,42 +20187,16 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002175", - "lbl" : "present_in_taxon", + "lbl" : "present in taxon", "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S" }, "comments" : [ "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "applicable for taxon" - } ], - "xrefs" : [ { - "val" : "RO:0002175" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_class_level", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "present_in_taxon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" @@ -21859,25 +20210,7 @@ "definition" : { "val" : "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." }, - "xrefs" : [ { - "val" : "RO:0002176" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The M8 connects Glasgow and Edinburgh" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "connects" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" }, { @@ -21892,20 +20225,7 @@ "meta" : { "definition" : { "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." - }, - "xrefs" : [ { - "val" : "RO:0002177" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "attached to part of (anatomical structure to anatomical structure)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "attaches_to_part_of" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002178", @@ -21915,21 +20235,9 @@ "definition" : { "val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." }, - "xrefs" : [ { - "val" : "RO:0002178" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "supplies" } ] } }, { @@ -21940,21 +20248,9 @@ "definition" : { "val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." }, - "xrefs" : [ { - "val" : "RO:0002179" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "drains" } ] } }, { @@ -21970,23 +20266,11 @@ "val" : "RO:0002180" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_component" @@ -22003,32 +20287,7 @@ "definition" : { "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" }, - "comments" : [ "This is the transitive form of the develops from relation" ], - "xrefs" : [ { - "val" : "RO:0002202" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9114-8737" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-1980-3228" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "develops_from" - } ] + "comments" : [ "This is the transitive form of the develops from relation" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002203", @@ -22038,29 +20297,7 @@ "definition" : { "val" : "inverse of develops from" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "xrefs" : [ { - "val" : "RO:0002203" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-1980-3228" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "develops_into" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002206", @@ -22069,17 +20306,7 @@ "meta" : { "definition" : { "val" : "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002207", @@ -22093,31 +20320,6 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "has developmental precursor" - } ], - "xrefs" : [ { - "val" : "RO:0002207" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "FBbt" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002202" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "directly_develops_from" } ] } }, { @@ -22128,14 +20330,7 @@ "definition" : { "val" : "inverse of directly develops from" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "developmental precursor of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002211", @@ -22150,30 +20345,6 @@ "val" : "RO:0002211" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-7476-6306" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-3837-8864" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GO" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Regulation precludes parthood; the regulatory process may not be within the regulated process." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "regulates (processual)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "false" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -22194,15 +20365,6 @@ "val" : "RO:0002212" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "negatively regulates (process to process)" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002211" }, { @@ -22226,18 +20388,6 @@ "val" : "RO:0002213" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "positively regulates (process to process)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002211" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -22258,32 +20408,8 @@ "val" : "RO:0002215" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "osteoclast SubClassOf 'capable of' some 'bone resorption'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has function realized in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20123131" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/21208450" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "capable_of" @@ -22301,17 +20427,8 @@ "val" : "RO:0002216" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has function in" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "capable_of_part_of" @@ -22327,26 +20444,7 @@ "meta" : { "definition" : { "val" : "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" - }, - "xrefs" : [ { - "val" : "RO:0002219" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "surrounded_by" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002220", @@ -22361,35 +20459,11 @@ "val" : "RO:0002220" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The epidermis layer of a vertebrate is adjacent to the dermis." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This relation acts as a join point with BSPO" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "adjacent_to" @@ -22403,26 +20477,7 @@ "definition" : { "val" : "inverse of surrounded by" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "xrefs" : [ { - "val" : "RO:0002221" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "surrounds" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002222", @@ -22430,23 +20485,7 @@ "type" : "PROPERTY", "meta" : { "comments" : [ "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations." ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://en.wikipedia.org/wiki/Allen%27s_interval_algebra" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." - }, { - "pred" : "http://purl.org/dc/terms/source", - "val" : "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002223", @@ -22456,29 +20495,7 @@ "definition" : { "val" : "inverse of starts with" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002223" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Allen" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "starts" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002224", @@ -22493,26 +20510,8 @@ "val" : "RO:0002224" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "started by" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "starts_with" @@ -22525,23 +20524,7 @@ "meta" : { "definition" : { "val" : "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" - }, - "xrefs" : [ { - "val" : "RO:0002225" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "develops_from_part_of" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002226", @@ -22550,29 +20533,7 @@ "meta" : { "definition" : { "val" : "x develops_in y if x is located in y whilst x is developing" - }, - "xrefs" : [ { - "val" : "RO:0002226" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "EHDAA2" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Jonathan Bard, EHDAA2" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "develops_in" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002229", @@ -22582,26 +20543,7 @@ "definition" : { "val" : "inverse of ends with" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002229" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "ends" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002230", @@ -22616,23 +20558,8 @@ "val" : "RO:0002230" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "finished by" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "ends_with" @@ -22651,15 +20578,6 @@ "val" : "RO:0002231" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "starts with process that occurs in" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -22680,15 +20598,6 @@ "val" : "RO:0002232" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "ends with process that occurs in" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -22709,15 +20618,6 @@ "val" : "RO:0002233" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "consumes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -22741,15 +20641,6 @@ "val" : "RO:0002234" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "produces" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -22768,22 +20659,7 @@ "definition" : { "val" : "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." }, - "xrefs" : [ { - "val" : "RO:0002252" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004036", - "val" : "http://purl.obolibrary.org/obo/BFO_0000050" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "connecting_branch_of" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/issues/2212" } ] @@ -22796,11 +20672,7 @@ "definition" : { "val" : "inverse of connecting branch of" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004036", - "val" : "http://purl.obolibrary.org/obo/BFO_0000051" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002254", @@ -22809,26 +20681,7 @@ "meta" : { "definition" : { "val" : "x has developmental contribution from y iff x has some part z such that z develops from y" - }, - "xrefs" : [ { - "val" : "RO:0002254" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_developmental_contribution_from" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002255", @@ -22838,14 +20691,7 @@ "definition" : { "val" : "inverse of has developmental contribution from" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002256", @@ -22854,44 +20700,7 @@ "meta" : { "definition" : { "val" : "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" - }, - "xrefs" : [ { - "val" : "RO:0002256" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9114-8737" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "induced by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GO:0001759" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "developmentally_induced_by" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002257", @@ -22900,14 +20709,7 @@ "meta" : { "definition" : { "val" : "Inverse of developmentally induced by" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002258", @@ -22919,17 +20721,8 @@ }, "comments" : [ "This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "false" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "In general you should not use this relation to make assertions - use one of the more specific relations below this one" } ] } }, { @@ -22942,9 +20735,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of" } ] @@ -22963,9 +20753,6 @@ "val" : "affects" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within" } ] @@ -22978,27 +20765,9 @@ "definition" : { "val" : "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" }, - "xrefs" : [ { - "val" : "RO:0002285" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "replaces" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "developmentally_replaces" } ] } }, { @@ -23008,31 +20777,12 @@ "meta" : { "definition" : { "val" : "Inverse of developmentally preceded by" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002287", "lbl" : "part of developmental precursor of", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002292", "lbl" : "expresses", @@ -23040,14 +20790,7 @@ "meta" : { "definition" : { "val" : "y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002295", @@ -23061,14 +20804,8 @@ "val" : "RO:0002295" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" @@ -23093,18 +20830,6 @@ "val" : "RO:0002296" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "every flower development (GO:0009908) results in development of some flower (PO:0009046)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.geneontology.org/GO.doc.development.shtml" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -23114,7 +20839,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -23122,21 +20847,6 @@ "val" : "RO:0002297" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:mtg_berkeley_2013" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -23157,21 +20867,6 @@ "val" : "RO:0002298" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:mtg_berkeley_2013" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -23192,21 +20887,6 @@ "val" : "RO:0002299" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:mtg_berkeley_2013" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -23228,12 +20908,6 @@ "val" : "RO:0002304" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002411" - }, { - "pred" : "http://purl.org/dc/terms/creator", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -23259,9 +20933,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002411" - }, { - "pred" : "http://purl.org/dc/terms/creator", - "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" @@ -23284,18 +20955,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "inheres in part of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" @@ -23314,15 +20973,6 @@ "val" : "RO:0002315" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:mtg_berkeley_2013" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -23337,14 +20987,7 @@ "meta" : { "definition" : { "val" : "A relationship that holds via some environmental process" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002323", @@ -23353,17 +20996,7 @@ "meta" : { "definition" : { "val" : "A mereological relationship or a topological relationship" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002324", @@ -23372,14 +21005,7 @@ "meta" : { "definition" : { "val" : "A relationship that holds between entities participating in some developmental process (GO:0032502)" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002327", @@ -23391,30 +21017,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a particular instances of akt-2 enables some instance of protein kinase activity" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "catalyzes" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "executes" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is catalyzing" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is executing" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Enables" } ] @@ -23426,23 +21028,7 @@ "meta" : { "definition" : { "val" : "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." - }, - "xrefs" : [ { - "val" : "RO:0002328" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This is a grouping relation that collects relations used for the purpose of connecting structure and function" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "functionally_related_to" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002329", @@ -23451,14 +21037,7 @@ "meta" : { "definition" : { "val" : "this relation holds between c and p when c is part of some c', and c' is capable of p." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "false" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002330", @@ -23467,14 +21046,7 @@ "meta" : { "definition" : { "val" : "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002331", @@ -23485,15 +21057,6 @@ "val" : "c involved_in p if and only if c enables some process p', and p' is part of p" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "actively involved in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "enables part of" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Involved_in" } ] @@ -23510,18 +21073,6 @@ "val" : "RO:0002332" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "regulates levels of (process to entity)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -23539,9 +21090,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Enabled_by" } ] @@ -23559,12 +21107,6 @@ "val" : "RO:0002334" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "regulated by (processual)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -23585,9 +21127,6 @@ "val" : "RO:0002335" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -23608,9 +21147,6 @@ "val" : "RO:0002336" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -23625,14 +21161,7 @@ "meta" : { "definition" : { "val" : "A relationship that holds via some process of localization" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is a grouping relation." - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002338", @@ -23647,9 +21176,6 @@ "val" : "RO:0002338" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -23670,9 +21196,6 @@ "val" : "RO:0002339" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -23692,9 +21215,6 @@ "val" : "RO:0002341" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -23715,9 +21235,6 @@ "val" : "RO:0002342" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -23734,12 +21251,6 @@ "val" : "RO:0002343" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'pollen tube growth' results_in growth_of some 'pollen tube'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -23756,12 +21267,6 @@ "val" : "RO:0002344" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -23776,23 +21281,7 @@ "meta" : { "definition" : { "val" : "is member of is a mereological relation between a item and a collection." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "An organism that is a member of a population of organisms" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is member of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "member part of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "SIO" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002351", @@ -23801,23 +21290,7 @@ "meta" : { "definition" : { "val" : "has member is a mereological relation between a collection and an item." - }, - "xrefs" : [ { - "val" : "RO:0002351" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "SIO" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_member" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002352", @@ -23827,20 +21300,7 @@ "definition" : { "val" : "inverse of has input" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002352" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "input_of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002353", @@ -23855,14 +21315,8 @@ "val" : "RO:0002353" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "output_of" @@ -23871,26 +21325,11 @@ }, { "id" : "http://purl.obolibrary.org/obo/RO_0002354", "lbl" : "formed as result of", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002360", "lbl" : "has dendrite location", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.org/dc/terms/source", - "val" : "http://neurolex.org/wiki/Property:DendriteLocation" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002371", "lbl" : "attached to", @@ -23899,23 +21338,7 @@ "definition" : { "val" : "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002371" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "attached to (anatomical structure to anatomical structure)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "attaches_to" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002372", @@ -23925,22 +21348,7 @@ "definition" : { "val" : "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." }, - "xrefs" : [ { - "val" : "RO:0002372" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Wikipedia:Insertion_(anatomy)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_muscle_origin" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://dbpedia.org/property/origin" } ] @@ -23953,22 +21361,7 @@ "definition" : { "val" : "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." }, - "xrefs" : [ { - "val" : "RO:0002373" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Wikipedia:Insertion_(anatomy)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_muscle_insertion" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://dbpedia.org/property/insertion" } ] @@ -23982,21 +21375,6 @@ "val" : "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004036", - "val" : "http://purl.obolibrary.org/obo/BFO_0000050" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png" }, { @@ -24013,46 +21391,7 @@ "val" : "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002376" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Deschutes River tributary_of Columbia River" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "inferior epigastric vein tributary_of external iliac vein" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "drains into" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "drains to" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "tributary channel of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://en.wikipedia.org/wiki/Tributary" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.medindia.net/glossary/venous_tributary.htm" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "tributary_of" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://dbpedia.org/ontology/drainsTo" }, { @@ -24067,17 +21406,7 @@ "meta" : { "definition" : { "val" : "x spatially_coextensive_with y if and inly if x and y have the same location" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A lump of clay and a statue" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002380", @@ -24088,22 +21417,7 @@ "val" : "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002380" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "branching_part_of" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/issues/2212" }, { @@ -24118,14 +21432,7 @@ "meta" : { "definition" : { "val" : "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002385", @@ -24134,23 +21441,7 @@ "meta" : { "definition" : { "val" : "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" - }, - "xrefs" : [ { - "val" : "RO:0002385" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_potential_to_developmentally_contribute_to" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002386", @@ -24159,14 +21450,7 @@ "meta" : { "definition" : { "val" : "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002387", @@ -24175,23 +21459,7 @@ "meta" : { "definition" : { "val" : "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" - }, - "xrefs" : [ { - "val" : "RO:0002387" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_potential_to_develop_into" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002388", @@ -24200,14 +21468,7 @@ "meta" : { "definition" : { "val" : "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002404", @@ -24221,12 +21482,6 @@ "val" : "RO:0002404" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -24243,12 +21498,6 @@ "val" : "RO:0002405" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -24265,15 +21514,6 @@ "val" : "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "indirectly activates" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002579", - "val" : "http://purl.obolibrary.org/obo/RO_0002213" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Indirectly_positively_regulates" } ] @@ -24287,15 +21527,6 @@ "val" : "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "indirectly inhibits" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002579", - "val" : "http://purl.obolibrary.org/obo/RO_0002212" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Indirectly_negatively_regulates" } ] @@ -24312,12 +21543,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." } ] } }, { @@ -24333,9 +21558,6 @@ "val" : "RO:0002411" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -24355,12 +21577,6 @@ "val" : "RO:0002412" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002411" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -24386,12 +21602,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "influences (processual)" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" @@ -24413,12 +21623,6 @@ "val" : "RO:0002427" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -24433,11 +21637,7 @@ "meta" : { "definition" : { "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002429", @@ -24446,14 +21646,7 @@ "meta" : { "definition" : { "val" : "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002428" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002430", @@ -24464,9 +21657,6 @@ "val" : "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002428" } ] @@ -24482,12 +21672,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "OWL does not allow defining object properties via a Union" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "involved in or reguates" } ] } }, { @@ -24505,15 +21689,6 @@ "val" : "enables activity in" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A protein that enables activity in a cytosol." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "executes activity in" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Is_active_in" } ] @@ -24525,20 +21700,7 @@ "meta" : { "definition" : { "val" : "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." - }, - "xrefs" : [ { - "val" : "RO:0002433" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "contributes_to_morphology_of" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002434", @@ -24559,18 +21721,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Considering relabeling as 'pairwise interacts with'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" - }, { - "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", - "val" : "http://purl.obolibrary.org/obo/MI_0914" } ] } }, { @@ -24582,20 +21735,8 @@ "val" : "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "binds" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "molecularly binds with" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ECO_0000353" - }, { - "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", - "val" : "http://purl.obolibrary.org/obo/MI_0915" } ] } }, { @@ -24606,12 +21747,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Axiomatization to GO to be added later" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." } ] } }, { @@ -24625,13 +21760,6 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "molecularly controls" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" } ] } }, { @@ -24645,16 +21773,6 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "molecularly decreases activity of" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "directly inhibits" } ] } }, { @@ -24668,31 +21786,12 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "molecularly increases activity of" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "directly activates" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002464", "lbl" : "helper property (not for use in curation)", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002473", "lbl" : "composed primarily of", @@ -24701,29 +21800,7 @@ "definition" : { "val" : "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002473" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "composed_primarily_of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002479", @@ -24733,22 +21810,12 @@ "definition" : { "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002481", "lbl" : "is kinase activity", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002485", "lbl" : "receives input from", @@ -24757,9 +21824,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "See notes for inverse relation" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { @@ -24770,24 +21834,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002487", "lbl" : "relation between physical entity and a process or stage", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage." - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002488", "lbl" : "existence starts during", @@ -24795,20 +21847,7 @@ "meta" : { "definition" : { "val" : "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." - }, - "xrefs" : [ { - "val" : "RO:0002488" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_starts_during" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002489", @@ -24817,20 +21856,7 @@ "meta" : { "definition" : { "val" : "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." - }, - "xrefs" : [ { - "val" : "RO:0002489" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_starts_with" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002490", @@ -24840,11 +21866,7 @@ "definition" : { "val" : "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002491", @@ -24858,19 +21880,6 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "exists during" - } ], - "xrefs" : [ { - "val" : "RO:0002491" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_starts_and_ends_during" } ] } }, { @@ -24881,24 +21890,7 @@ "definition" : { "val" : "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "ceases_to_exist_during" - } ], - "xrefs" : [ { - "val" : "RO:0002492" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_ends_during" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002493", @@ -24908,20 +21900,7 @@ "definition" : { "val" : "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "xrefs" : [ { - "val" : "RO:0002493" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_ends_with" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002494", @@ -24930,20 +21909,7 @@ "meta" : { "definition" : { "val" : "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" - }, - "xrefs" : [ { - "val" : "RO:0002494" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "transformation_of" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002495", @@ -24952,23 +21918,7 @@ "meta" : { "definition" : { "val" : "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" - }, - "xrefs" : [ { - "val" : "RO:0002495" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002494" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "immediate_transformation_of" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002496", @@ -24978,20 +21928,7 @@ "definition" : { "val" : "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "xrefs" : [ { - "val" : "RO:0002496" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_starts_during_or_after" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002497", @@ -25001,20 +21938,7 @@ "definition" : { "val" : "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "xrefs" : [ { - "val" : "RO:0002497" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_ends_during_or_before" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002500", @@ -25023,11 +21947,7 @@ "meta" : { "definition" : { "val" : "A relationship between a material entity and a process where the material entity has some causal role that influences the process" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002501", @@ -25036,17 +21956,7 @@ "meta" : { "definition" : { "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002502", @@ -25054,9 +21964,6 @@ "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/BFO_0000169" } ] @@ -25069,15 +21976,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." } ] } }, { @@ -25087,55 +21985,18 @@ "meta" : { "definition" : { "val" : "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." - }, - "xrefs" : [ { - "val" : "RO:0002551" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has supporting framework" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_skeleton" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002559", "lbl" : "causally influenced by", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "causally influenced by (entity-centric)" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002563", "lbl" : "interaction relation helper property", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29" }, { @@ -25146,13 +22007,7 @@ }, { "id" : "http://purl.obolibrary.org/obo/RO_0002564", "lbl" : "molecular interaction relation helper property", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002565", "lbl" : "results in movement of", @@ -25166,11 +22021,6 @@ "val" : "RO:0002565" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -25185,20 +22035,7 @@ "meta" : { "definition" : { "val" : "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "causally influences (entity-centric)" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002567", @@ -25207,14 +22044,7 @@ "meta" : { "definition" : { "val" : "A relation that holds between elements of a musculoskeletal system or its analogs." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002568", @@ -25223,23 +22053,7 @@ "meta" : { "definition" : { "val" : "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." - }, - "xrefs" : [ { - "val" : "RO:0002568" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Wikipedia:Antagonist_(muscle)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_muscle_antagonist" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002569", @@ -25249,20 +22063,7 @@ "definition" : { "val" : "inverse of branching part of" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002569" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_branching_part" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002570", @@ -25272,26 +22073,7 @@ "definition" : { "val" : "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002570" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "UBERON:cjm" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "conduit_for" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002571", @@ -25301,23 +22083,7 @@ "definition" : { "val" : "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002571" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "lumen_of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002572", @@ -25327,20 +22093,7 @@ "definition" : { "val" : "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002572" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "luminal_space_of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002576", @@ -25350,20 +22103,7 @@ "definition" : { "val" : "inverse of has skeleton" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "xrefs" : [ { - "val" : "RO:0002576" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "skeleton_of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002578", @@ -25378,18 +22118,6 @@ "val" : "RO:0002578" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "directly regulates (processual)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002211" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -25397,24 +22125,6 @@ "val" : "directly_regulates" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002581", - "lbl" : "is a defining property chain axiom", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002582", - "lbl" : "is a defining property chain axiom where second argument is reflexive", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R." - } - } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002584", "lbl" : "has part structure that is capable of", @@ -25422,14 +22132,7 @@ "meta" : { "definition" : { "val" : "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002586", @@ -25503,12 +22206,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] } }, { @@ -25518,14 +22215,7 @@ "meta" : { "definition" : { "val" : "Holds between c and p if and only if c is capable of some activity a, and a regulates p." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "pyrethroid -> growth" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002597", @@ -25534,11 +22224,7 @@ "meta" : { "definition" : { "val" : "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002598", @@ -25547,14 +22233,7 @@ "meta" : { "definition" : { "val" : "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "renin -> arteriolar smooth muscle contraction" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002608", @@ -25568,9 +22247,6 @@ "val" : "RO:0002608" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -25591,15 +22267,6 @@ "val" : "RO:0002629" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "directly positively regulates (process to process)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002578" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -25623,12 +22290,6 @@ "val" : "RO:0002630" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "directly negatively regulates (process to process)" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002578" }, { @@ -25656,17 +22317,8 @@ "val" : "RO:0003000" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9114-8737" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "produces" @@ -25685,17 +22337,8 @@ "val" : "RO:0003001" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9114-8737" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "produced_by" @@ -25804,9 +22447,6 @@ "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002264" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { @@ -25847,9 +22487,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002263" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { @@ -25908,9 +22545,6 @@ "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002418" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { @@ -25941,11 +22575,7 @@ "meta" : { "definition" : { "val" : "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0012000", @@ -26207,9 +22837,6 @@ "xrefs" : [ "PMID:19243617" ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" - }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1617-8244" }, { @@ -26227,9 +22854,6 @@ "xrefs" : [ "PMID:19243617" ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" - }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1617-8244" }, { @@ -26250,21 +22874,6 @@ "val" : "utilizes" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A diagnostic testing device utilizes a specimen." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9625-1899" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-2620-0345" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "See github ticket https://github.com/oborel/obo-relations/issues/497" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-11-08T12:00:00Z" } ] @@ -26407,12 +23016,6 @@ "val" : "galen:Tube" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts)" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "tubular" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -26458,16 +23061,11 @@ "xrefs" : [ "FMA:82482" ] } ], "xrefs" : [ { - "val" : "EMAPA:25036" - }, { "val" : "FMA:82482" }, { "val" : "galen:Wall" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in FMA, serosa is a wall" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0009915" }, { @@ -26505,8 +23103,6 @@ "val" : "EHDAA2:0003003" }, { "val" : "EMAPA:0" - }, { - "val" : "FBbt:00007001" }, { "val" : "FMA:305751" }, { @@ -26606,12 +23202,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26650,9 +23240,6 @@ "val" : "SCTID:91717005" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "currently defined in a very broad sense, may be replaced by more specific classes in the future" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { @@ -26783,9 +23370,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "ncit:Death is an outcome" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26863,9 +23447,6 @@ "val" : "WBls:0000103" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -26982,12 +23563,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "the WBls class 'all stages' belongs here as it is the superclass of other WBls stages" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27040,8 +23615,6 @@ "val" : "EHDAA:27" }, { "val" : "FBdv:00005288" - }, { - "val" : "IDOMAL:0000302" }, { "val" : "NCIT:C12601" }, { @@ -27056,9 +23629,6 @@ "val" : "ZFS:0000001" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -27236,12 +23806,6 @@ "val" : "XAO:1000006" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002174", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7955" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In zebrafish, the times of neurulation and segmentation overlap so extensively there is no distinct neurula period of development, such as occurs largely before segmentation in amphibian embryos." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -27374,8 +23938,6 @@ "val" : "EHDAA:542" }, { "val" : "EMAPA:16262" - }, { - "val" : "FBbt:00003126" }, { "val" : "FMA:49184" }, { @@ -27418,21 +23980,6 @@ "val" : "http://purl.obolibrary.org/obo/uberon/images/lamprey_sucker_rosava_3238889218.jpg" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "oral" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -27510,23 +24057,8 @@ "val" : "galen:Blood" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid." - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27659,8 +24191,6 @@ "val" : "BTO:0001485" }, { "val" : "EFO:0000801" - }, { - "val" : "EMAPA:35578" }, { "val" : "FMA:72954" }, { @@ -27683,12 +24213,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system that consists of the muscles of the body.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27739,8 +24263,6 @@ "val" : "EHDAA2:0003004" }, { "val" : "EMAPA:35178" - }, { - "val" : "FBbt:00007019" }, { "val" : "FMA:9669" }, { @@ -27813,8 +24335,6 @@ "val" : "CARO:0000005" }, { "val" : "EHDAA2:0003005" - }, { - "val" : "FBbt:00007017" }, { "val" : "FMA:5897" }, { @@ -27868,8 +24388,6 @@ "val" : "CARO:0000006" }, { "val" : "EHDAA2:0003006" - }, { - "val" : "FBbt:00007016" }, { "val" : "FMA:67165" }, { @@ -27920,8 +24438,6 @@ "val" : "CARO:0000007" }, { "val" : "EHDAA2:0003007" - }, { - "val" : "FBbt:00007015" }, { "val" : "FMA:67112" }, { @@ -28000,14 +24516,10 @@ "val" : "EMAPA:16103" }, { "val" : "EV:0100000" - }, { - "val" : "FBbt:00004856" }, { "val" : "FMA:7149" }, { "val" : "HAO:0000011" - }, { - "val" : "IDOMAL:0002460" }, { "val" : "MA:0000003" }, { @@ -28116,8 +24628,6 @@ "val" : "EMAPA:25765" }, { "val" : "EV:0100016" - }, { - "val" : "FBbt:00000001" }, { "val" : "FMA:256135" }, { @@ -28159,9 +24669,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "organismal" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28211,8 +24718,6 @@ "val" : "EHDAA2:0003032" }, { "val" : "EMAPA:36031" - }, { - "val" : "FBbt:00007009" }, { "val" : "FMA:7153" }, { @@ -28287,8 +24792,6 @@ "val" : "CARO:0000040" }, { "val" : "EHDAA2:0003040" - }, { - "val" : "FBbt:00007013" }, { "val" : "FMA:63863" }, { @@ -28327,8 +24830,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "xrefs" : [ { - "val" : "FBbt:00007277" - }, { "val" : "VHOG:0001737" } ], "basicPropertyValues" : [ { @@ -28385,8 +24886,6 @@ "val" : "EHDAA2:0003043" }, { "val" : "EMAPA:35868" - }, { - "val" : "FBbt:00007003" }, { "val" : "FMA:9637" }, { @@ -28457,8 +24956,6 @@ "val" : "CARO:0000055" }, { "val" : "EHDAA2:0003055" - }, { - "val" : "FBbt:00007010" }, { "val" : "HAO:0000055" }, { @@ -28523,8 +25020,6 @@ "val" : "EHDAA2:0003066" }, { "val" : "EMAPA:32738" - }, { - "val" : "FBbt:00007005" }, { "val" : "FMA:9639" }, { @@ -28553,12 +25048,6 @@ "val" : "ZFA:0001486" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "epithelial" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -28615,9 +25104,6 @@ "val" : "ZFA:0001498" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Unilaminar epithelium that consists of a single layer of squamous cells.[CARO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -28677,9 +25163,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Epithelium that consists of a single layer of epithelial cells.[CARO]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28722,18 +25205,6 @@ "val" : "Wikipedia:Thorax" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000026" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000033" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0002417" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -28782,14 +25253,10 @@ "val" : "EHDAA:38" }, { "val" : "EMAPA:16039" - }, { - "val" : "FBbt:00000052" }, { "val" : "FMA:69068" }, { "val" : "GAID:963" - }, { - "val" : "IDOMAL:0000646" }, { "val" : "MAT:0000226" }, { @@ -28816,12 +25283,6 @@ "val" : "http://neurolex.org/wiki/Category:Embryonic_organism" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "embryonic" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -28870,8 +25331,6 @@ "val" : "BTO:0000556" }, { "val" : "EMAPA:36033" - }, { - "val" : "FBbt:00000110" }, { "val" : "FMA:69069" }, { @@ -28898,9 +25357,6 @@ "val" : "ZFA:0001122" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -28936,8 +25392,6 @@ "val" : "EMAPA:16069" }, { "val" : "EV:0100003" - }, { - "val" : "FBbt:00000111" }, { "val" : "FMA:69070" }, { @@ -28968,15 +25422,6 @@ "val" : "ZFA:0000016" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "ectodermal" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -29016,8 +25461,6 @@ "val" : "EMAPA:16062" }, { "val" : "EV:0100005" - }, { - "val" : "FBbt:00000125" }, { "val" : "FMA:69071" }, { @@ -29046,12 +25489,6 @@ "val" : "ZFA:0000017" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "endodermal" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -29106,8 +25543,6 @@ "val" : "EMAPA:16083" }, { "val" : "EV:0100006" - }, { - "val" : "FBbt:00000126" }, { "val" : "FMA:69072" }, { @@ -29138,18 +25573,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Primary germ layer that is the middle of the embryonic germ layers.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "mesodermal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0003263" @@ -29209,8 +25632,6 @@ "val" : "EHDAA2:0001929" }, { "val" : "EMAPA:16263" - }, { - "val" : "FBbt:00000439" }, { "val" : "FMA:295846" }, { @@ -29231,18 +25652,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "stomodeal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -29336,21 +25745,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "cardiac" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -29439,12 +25833,6 @@ "val" : "galen:Joint" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -29482,10 +25870,6 @@ "val" : "CALOHA:TS-1293" }, { "val" : "EFO:0000793" - }, { - "val" : "EV:0100056" - }, { - "val" : "FBbt:00005055" }, { "val" : "FMA:7152" }, { @@ -29520,15 +25904,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "digestive" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -29554,17 +25929,12 @@ "val" : "AAO:0000959" }, { "val" : "CALOHA:TS-2103" - }, { - "val" : "MESH:D002319" }, { "val" : "VHOG:0001248" }, { "val" : "Wikipedia:Circulatory_system" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "the cardiovascular system and the lymphatic system are parts of the circulatory system" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_147099" }, { @@ -29573,18 +25943,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6157" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002174", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6231" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -29636,13 +25997,9 @@ "val" : "musculature system" } ], "xrefs" : [ { - "val" : "AAO:0011066" - }, { "val" : "BTO:0000887" }, { "val" : "EFO:0001949" - }, { - "val" : "EMAPA:32715" }, { "val" : "EMAPA:35577" }, { @@ -29665,12 +26022,6 @@ "val" : "ZFA:0000548" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0001474" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -29722,8 +26073,6 @@ "val" : "EMAPA:16469" }, { "val" : "EV:0100162" - }, { - "val" : "FBbt:00005093" }, { "val" : "FMA:7157" }, { @@ -29763,21 +26112,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "nervous" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "neural" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -29841,8 +26175,6 @@ "val" : "EMAPA:16754" }, { "val" : "EV:0100163" - }, { - "val" : "FBbt:00005094" }, { "val" : "FMA:55675" }, { @@ -29878,18 +26210,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Part of the nervous system which includes the brain and spinal cord.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The brain and spinal cord. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO)." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -29932,8 +26252,6 @@ "val" : "EFO:0001652" }, { "val" : "EHDAA2:0003171" - }, { - "val" : "FBbt:00005495" }, { "val" : "FMA:86589" }, { @@ -29996,8 +26314,6 @@ "val" : "FMA:293882" }, { "val" : "MAT:0000069" - }, { - "val" : "MESH:D054259" }, { "val" : "MIAA:0000069" }, { @@ -30020,18 +26336,6 @@ "val" : "neuronames:1365" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -30063,8 +26367,6 @@ "val" : "CARO:0000000" }, { "val" : "EHDAA2:0002229" - }, { - "val" : "FBbt:10000000" }, { "val" : "FMA:62955" }, { @@ -30154,27 +26456,6 @@ "val" : "ZFA:0000434" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0001016" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "System that provides physical support to the organism.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "skeletal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -30258,30 +26539,6 @@ "val" : "galen:Bone" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0001015" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0001630" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0002385" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Skeletal element that is composed of bone tissue.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -30334,14 +26591,10 @@ "val" : "EHDAA:518" }, { "val" : "EMAPA:16247" - }, { - "val" : "FBbt:00003125" }, { "val" : "FMA:45615" }, { "val" : "MA:0000917" - }, { - "val" : "MESH:D041981" }, { "val" : "NCIT:C34082" }, { @@ -30368,21 +26621,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The alimentary or digestive tract, and associated organs.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "FMA also has a term 'gastrointestinal tract', but this includes the liver." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000013", - "val" : "we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -30404,10 +26642,6 @@ "xrefs" : [ "ZFA:0005145" ] } ], "xrefs" : [ { - "val" : "AAO:0011066" - }, { - "val" : "EMAPA:32715" - }, { "val" : "EMAPA:37474" }, { "val" : "EV:0100146" @@ -30431,15 +26665,6 @@ "val" : "galen:Muscle" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of tissue composed of contractile fibers.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "muscular" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -30584,21 +26809,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Any of the vessels through which blood circulates in the body.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "annelids have blood vessels, but this class is not applicable to annelids." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -30642,9 +26852,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "endothelial" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -30680,9 +26887,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "vascular" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -30732,8 +26936,6 @@ "val" : "CALOHA:TS-2110" }, { "val" : "EFO:0000461" - }, { - "val" : "FBbt:00004208" }, { "val" : "FMA:69067" }, { @@ -30758,18 +26960,6 @@ "val" : "ZFA:0001105" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in FMA embryo is_a embryonic structure" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -30832,12 +27022,6 @@ "val" : "XAO:0003034" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -30869,8 +27053,6 @@ "val" : "EHDAA2:0000161" }, { "val" : "EHDAA:5049" - }, { - "val" : "EMAPA:17214" }, { "val" : "EMAPA:37721" }, { @@ -30879,8 +27061,6 @@ "val" : "MA:0002986" }, { "val" : "MAT:0000148" - }, { - "val" : "MESH:D013131" }, { "val" : "MIAA:0000148" }, { @@ -30895,18 +27075,6 @@ "val" : "ZFA:0000317" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -30979,18 +27147,6 @@ "val" : "galen:Trunk" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000026" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000033" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -31076,15 +27232,6 @@ "val" : "XAO:0000168" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system that provides locomotion and physical support to the organism.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "musculoskeletal" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -31144,9 +27291,6 @@ "val" : "Wikipedia:Thoracic_cavity" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In many species, the diaphragm separates thoracic and abdominal cavities" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -31213,8 +27357,6 @@ "val" : "BTO:0001707" }, { "val" : "EHDAA2:0000267" - }, { - "val" : "FBbt:00005060" }, { "val" : "FMA:85006" }, { @@ -31233,15 +27375,6 @@ "val" : "galen:BodyCavity" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In mammals it forms the peritoneal, pleural, and pericardial cavities" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0000169" }, { @@ -31319,27 +27452,6 @@ "val" : "http://evolution.berkeley.edu/evolibrary/images/history/notochords.jpg" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "notochordal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -31426,32 +27538,8 @@ "val" : "ZFA:0000155" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "EDITOR_NOTE currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7712" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Post-cranial axial segments which form sclerotome and dermomyotome.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "somitic" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -31510,8 +27598,6 @@ "val" : "NCIT:C34222" }, { "val" : "SCTID:361462002" - }, { - "val" : "TAO:0000045" }, { "val" : "UMLS:C0027789" }, { @@ -31526,24 +27612,6 @@ "val" : "neuronames:1366" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "EDITOR_NOTE consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams)." - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002174", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_117565" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -31602,8 +27670,6 @@ "val" : "EMAPA:16073" }, { "val" : "EV:0100004" - }, { - "val" : "FBbt:00001057" }, { "val" : "FMA:87657" }, { @@ -31626,15 +27692,6 @@ "val" : "ZFA:0001120" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "neurectodermal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000013", - "val" : "we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -31717,12 +27774,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000009", - "val" : "In adults, marrow in large bones produces new blood cells[Wikipedia:Bone_marrow]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -31795,18 +27846,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "MA also has set of connective tissues" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -31863,12 +27902,6 @@ "val" : "galen:MuscleTissue" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0003714" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -31953,18 +27986,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system that consists of the blood and blood forming tissues.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "hematopoietic" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -32014,9 +28035,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -32083,9 +28101,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "see https://github.com/obophenotype/uberon/issues/27" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -32138,9 +28153,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -32234,12 +28246,6 @@ "val" : "ZFA:0000279" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -32301,21 +28307,6 @@ "val" : "ZFA:0000094" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -32351,9 +28342,6 @@ "val" : "ZFA:0001204" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -32396,8 +28384,6 @@ "val" : "EMAPA:35593" }, { "val" : "FMA:293879" - }, { - "val" : "MESH:D054258" }, { "val" : "NCIT:C34225" }, { @@ -32418,12 +28404,6 @@ "val" : "neuronames:1362" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -32483,15 +28463,6 @@ "val" : "ZFA:0000255" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -32559,18 +28530,6 @@ "val" : "ZFA:0000121" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "subclass of mesoderm in ZFA." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0006258" }, { @@ -32617,15 +28576,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "should probably be merged with heart rudiment." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -32656,8 +28606,6 @@ "val" : "AAO:0010571" }, { "val" : "AEO:0000212" - }, { - "val" : "BTO:0006255" }, { "val" : "EHDAA2:0003439" }, { @@ -32680,15 +28628,6 @@ "val" : "ZFA:0001080" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Skeletogenic portion of somites.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "part_of somite in XAO" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -32736,9 +28675,6 @@ "val" : "ZFA:0000496" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -32801,15 +28737,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "mesenchymal" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -32871,9 +28798,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -32896,13 +28820,8 @@ "val" : "AEO:0000114" }, { "val" : "EHDAA2:0003114" - }, { - "val" : "FBbt:00007474" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -32957,9 +28876,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "FMA has both conduit and conduit space. In EHDAA2 this is a surface feature" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -32981,9 +28897,6 @@ "xrefs" : [ "FBbt:00025998" ] } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Grouping term for query purposes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33004,9 +28917,6 @@ "xrefs" : [ "FBbt:00025990" ] } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Grouping term for query purposes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33047,9 +28957,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -33091,9 +28998,6 @@ "val" : "XAO:0004185" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33137,9 +29041,6 @@ "val" : "ZFA:0000360" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33220,17 +29121,8 @@ "val" : "galen:Skeleton" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000383" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "skeletal" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -33263,9 +29155,6 @@ "val" : "ZFA:0000115" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33299,14 +29188,10 @@ "val" : "CALOHA:TS-1297" }, { "val" : "EFO:0000791" - }, { - "val" : "EHDAA2:0000216" }, { "val" : "EHDAA:394" }, { "val" : "EMAPA:16104" - }, { - "val" : "EMAPA:16370" }, { "val" : "EV:0100017" }, { @@ -33341,14 +29226,8 @@ "val" : "ZFA:0000010" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph." - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -33524,8 +29403,6 @@ "val" : "BILA:0000060" }, { "val" : "BTO:0001403" - }, { - "val" : "FBbt:00005317" }, { "val" : "FMA:293108" }, { @@ -33548,9 +29425,6 @@ "val" : "Wikipedia:Trilaminar_blastocyst" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "We explicitly merge the NCITA terms here" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0007012" }, { @@ -33582,9 +29456,6 @@ "val" : "ZFA:0005619" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33613,12 +29484,6 @@ "val" : "galen:SkeletalStructure" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33711,9 +29576,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider merging with 'endothelium'" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -33753,9 +29615,6 @@ "val" : "XAO:0000276" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33796,12 +29655,6 @@ "val" : "ZFA:0000091" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Notochord rudiment[ZFIN:ZDB-PUB-961014-576]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33820,9 +29673,6 @@ "pred" : "hasNarrowSynonym", "val" : "joint" } ], - "xrefs" : [ { - "val" : "FBbt:00005811" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -33858,14 +29708,9 @@ "xrefs" : [ "FMA:71131" ] } ], "xrefs" : [ { - "val" : "FBbt:00100315" - }, { "val" : "FMA:71131" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct." - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { @@ -33920,9 +29765,6 @@ "val" : "neuronames:1363" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33960,9 +29802,6 @@ "val" : "neuronames:1364" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33990,9 +29829,6 @@ "val" : "ZFA:0000133" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34018,14 +29854,9 @@ "val" : "muscle element" } ], "xrefs" : [ { - "val" : "EMAPA:32715" - }, { "val" : "FMA:30316" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34203,8 +30034,6 @@ "val" : "CALOHA:TS-2122" }, { "val" : "EHDAA2:0003125" - }, { - "val" : "FBbt:00007006" }, { "val" : "FMA:292313" }, { @@ -34244,8 +30073,6 @@ "xrefs" : [ "EMAPA:16208" ] } ], "xrefs" : [ { - "val" : "BTO:0006179" - }, { "val" : "EHDAA2:0001512" }, { "val" : "EHDAA:424" @@ -34335,9 +30162,6 @@ "val" : "Wikipedia:Basement_membrane" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell." - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_80999" }, { @@ -34391,8 +30215,6 @@ "val" : "AAO:0000963" }, { "val" : "EMAPA:17214" - }, { - "val" : "EMAPA:18043" }, { "val" : "MA:0000308" }, { @@ -34411,9 +30233,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -34451,9 +30270,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO - check ordering; awaiting confirmation from JB" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -34691,9 +30507,6 @@ "val" : "Wikipedia:Squamous_epithelium" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34864,9 +30677,6 @@ "val" : "UMLS:C1514442" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34896,16 +30706,11 @@ "xrefs" : [ "FBbt:00003154" ] } ], "xrefs" : [ { - "val" : "SPD:0000130" - }, { "val" : "TADS:0000147" }, { "val" : "http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34933,9 +30738,6 @@ "val" : "ZFA:0000131" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34997,9 +30799,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider merging" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Region of the gastrula which gives rise to the neural plate.[TAO]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -35145,8 +30944,6 @@ "val" : "EFO:0001649" }, { "val" : "EHDAA2:0003170" - }, { - "val" : "FBbt:00005426" }, { "val" : "Wikipedia:Anlage_(biology)" } ], @@ -35186,12 +30983,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -35311,8 +31102,6 @@ } ], "xrefs" : [ { "val" : "CARO:0010000" - }, { - "val" : "FBbt:00100313" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", @@ -35397,9 +31186,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Grouping term for query purposes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -35462,9 +31248,6 @@ "val" : "VSAO:0000042" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -35528,8 +31311,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "xrefs" : [ { - "val" : "FBbt:00007330" - }, { "val" : "FMA:67509" }, { "val" : "SCTID:91690000" @@ -35670,9 +31451,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_147099" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "coelomic" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -35742,9 +31520,6 @@ "val" : "UMLS:C0229619" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "Bone marrow in humans, kidney interstitium in Danio, within a stroma of reticuloendothelial tissue" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -35828,15 +31603,10 @@ "val" : "AEO:0000103" }, { "val" : "BTO:0001489" - }, { - "val" : "EMAPA:36031" }, { "val" : "FMA:231424" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -35909,8 +31679,6 @@ }, "xrefs" : [ { "val" : "AEO:0000093" - }, { - "val" : "FBbt:00007278" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -35928,9 +31696,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This class is primarily to implement taxon constraints. It may be removed in the future." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -35961,9 +31726,6 @@ "pred" : "hasRelatedSynonym", "val" : "cardiac structure" } ], - "xrefs" : [ { - "val" : "SPD:0000130" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -36148,8 +31910,6 @@ "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], "xrefs" : [ { "val" : "CARO:0020000" - }, { - "val" : "FBbt:00007276" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", @@ -36560,120 +32320,6 @@ "val" : "uberon" } ] } - }, { - "id" : "http://purl.org/dc/elements/1.1/creator", - "lbl" : "creator", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/elements/1.1/creator" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-creator" - } ] - } - }, { - "id" : "http://purl.org/dc/elements/1.1/description", - "lbl" : "description", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/elements/1.1/description" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-description" - } ] - } - }, { - "id" : "http://purl.org/dc/elements/1.1/title", - "lbl" : "title", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/elements/1.1/title" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-title" - } ] - } - }, { - "id" : "http://purl.org/dc/terms/contributor", - "lbl" : "contributor", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/terms/contributor" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-contributor" - } ] - } - }, { - "id" : "http://purl.org/dc/terms/date", - "lbl" : "date", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/terms/date" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dcterms-date" - } ] - } - }, { - "id" : "http://purl.org/dc/terms/license", - "lbl" : "license", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/terms/license" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dcterms-license" - } ] - } }, { "id" : "http://www.geneontology.org/formats/oboInOwl#SubsetProperty", "lbl" : "subset_property", @@ -36707,9 +32353,6 @@ "val" : "An alternative label for a class or property which has a more general meaning than the preferred name/primary label." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/18" }, { @@ -36730,9 +32373,6 @@ "val" : "An alternative label for a class or property which has the exact same meaning than the preferred name/primary label." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/20" }, { @@ -36749,9 +32389,6 @@ "val" : "An alternative label for a class or property which has a more specific meaning than the preferred name/primary label." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/19" }, { @@ -36772,9 +32409,6 @@ "val" : "An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/21" }, { @@ -36807,35 +32441,10 @@ "val" : "http://www.w3.org/2000/01/rdf-schema#seeAlso" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "seeAlso" } ] } - }, { - "id" : "http://xmlns.com/foaf/0.1/depiction", - "lbl" : "depiction", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://xmlns.com/foaf/0.1/depiction" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "depiction" - } ] - } } ], "edges" : [ { "sub" : "http://purl.obolibrary.org/obo/BFO_0000004", @@ -44294,17 +39903,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0004921", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts" - } ] - } - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0001106", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0001555" + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004921" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -44406,13 +40005,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000463", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000468", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "this relationship may be too strong and may be weakened in future" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000468" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000463", "pred" : "http://purl.obolibrary.org/obo/RO_0000086", @@ -44630,13 +40223,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000926", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000923", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "sometimes not considered primary" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000923" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000926", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -44978,6 +40565,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000055" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -45148,13 +40739,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002204", "pred" : "http://purl.obolibrary.org/obo/RO_0002254", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000926", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "check ctenophore" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000926" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002204", "pred" : "http://purl.obolibrary.org/obo/RO_0002492", @@ -45178,13 +40763,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002323", "pred" : "http://purl.obolibrary.org/obo/RO_0002494", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0003886", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "definitional" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0003886" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002323", "pred" : "http://purl.obolibrary.org/obo/RO_0002572", @@ -45209,6 +40788,10 @@ "val" : "VSAO" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", "pred" : "is_a", @@ -45217,14 +40800,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0011137" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000098", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0001555" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000102", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0001049" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -45301,6 +40876,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010314" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "is_a", @@ -45321,16 +40900,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_89593", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "ISBN:0073040584" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_89593" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -45354,13 +40924,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "http://purl.obolibrary.org/obo/RO_0002473", - "obj" : "http://purl.obolibrary.org/obo/CL_0000333", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/CL_0000333" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "http://purl.obolibrary.org/obo/RO_0002488", @@ -45387,6 +40951,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002371", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000479" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0002371", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002371", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -45473,13 +41041,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002390", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0003061", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "definitional" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0003061" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002405", "pred" : "is_a", @@ -45640,10 +41202,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0003077", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0015212" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0003077", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000922" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003077", "pred" : "http://purl.obolibrary.org/obo/RO_0002488", @@ -45891,6 +41449,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004140", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0002050" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004140", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004140", "pred" : "is_a", @@ -45945,6 +41507,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004151", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000064" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004151", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004151", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -46062,19 +41628,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004755", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/CL_0007001", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#date_retrieved", - "val" : "2012-08-14" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#external_class", - "val" : "VSAO:0000015" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "VSAO" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/CL_0007001" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004765", "pred" : "is_a", @@ -46202,14 +41756,14 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005062", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0015212" + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010371" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005062", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0005061" + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0015212" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005062", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000126", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0005061" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005068", @@ -46568,13 +42122,11 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006984", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0010199", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "via morphological boundary in CARO" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010199" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0007005", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007005", "pred" : "is_a", @@ -46638,13 +42190,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007100", "pred" : "http://purl.obolibrary.org/obo/RO_0002215", - "obj" : "http://purl.obolibrary.org/obo/GO_0008015", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "GO uses blood circulation generically to include the haemolymphatic fluid of arthropods" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/GO_0008015" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007135", "pred" : "is_a", @@ -46660,16 +42206,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007282", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0009618", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#consistent_with", - "val" : "https://github.com/obophenotype/uberon/wiki/The-neural-crest" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "EDHAA2" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0009618" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007282", "pred" : "http://purl.obolibrary.org/obo/RO_0002387", @@ -46835,6 +42372,10 @@ "val" : "EHDAA2" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0009881", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0009881", "pred" : "is_a", @@ -47067,6 +42608,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0012275", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0012429", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0012429", "pred" : "is_a", @@ -47179,10 +42724,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0015212", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0015212", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000465" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0015212", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -48509,10 +44050,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000057" - }, { - "sub" : "http://purl.obolibrary.org/obo/uberon/core#anteriorly_connected_to", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BSPO_0000099" }, { "sub" : "http://purl.obolibrary.org/obo/uberon/core#anteriorly_connected_to", "pred" : "subPropertyOf", @@ -48521,10 +44058,6 @@ "sub" : "http://purl.obolibrary.org/obo/uberon/core#anteriorly_connected_to", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/uberon/core#transitively_anteriorly_connected_to" - }, { - "sub" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BSPO_0000100" }, { "sub" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", "pred" : "subPropertyOf", @@ -48541,18 +44074,10 @@ "sub" : "http://purl.obolibrary.org/obo/uberon/core#layer_part_of", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000050" - }, { - "sub" : "http://purl.obolibrary.org/obo/uberon/core#posteriorly_connected_to", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BSPO_0000096" }, { "sub" : "http://purl.obolibrary.org/obo/uberon/core#posteriorly_connected_to", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002170" - }, { - "sub" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BSPO_0000097" }, { "sub" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to", "pred" : "subPropertyOf", @@ -48769,10 +44294,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012001", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012005" - }, { - "sub" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", - "pred" : "inverseOf", - "obj" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to" } ], "logicalDefinitionAxioms" : [ { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000034", @@ -51724,13 +47245,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002082", "fillerId" : "http://purl.obolibrary.org/obo/GO_0040016" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0000165", - "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0004921" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BSPO_0001106", - "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0001555" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0000179", "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000463" ], @@ -52212,13 +47726,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002387", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0002049" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0015212", - "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0000465" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0016879", "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0006598" ], @@ -52542,8 +48049,8 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002551", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061", "http://purl.obolibrary.org/obo/UBERON_0000475" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465", "http://purl.obolibrary.org/obo/UBERON_0010912" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002566", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], @@ -52601,10 +48108,6 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0019000", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/uberon/core#channel_for", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0004111" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000463" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] @@ -52636,21 +48139,12 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002287", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002210" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002329", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002215" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002496" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002497" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002479", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/BFO_0000066" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/RO_0000057" ] @@ -52669,24 +48163,12 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000066", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000066", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002314", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0000052", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0001025", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0001025", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002005", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002005", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002005", "http://purl.obolibrary.org/obo/RO_0002380" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002100", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002100", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/uberon/core#extends_fibers_into", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002100", "http://purl.obolibrary.org/obo/RO_0013001" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002102", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002102", "http://purl.obolibrary.org/obo/BFO_0000050" ] @@ -52702,24 +48184,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002131", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002131", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002134", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002134", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002150", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002170", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002176", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002178", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002202", "http://purl.obolibrary.org/obo/RO_0002162" ] @@ -52756,9 +48223,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0019002", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002213", "http://purl.obolibrary.org/obo/RO_0019002" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002216", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002215", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002215", "http://purl.obolibrary.org/obo/RO_0002162" ] @@ -52807,9 +48271,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002254", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002256", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002258", "http://purl.obolibrary.org/obo/RO_0002496" ] @@ -52831,9 +48292,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004031", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/BFO_0000051" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002432", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/BFO_0000066" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002327", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002017" ] @@ -52897,15 +48355,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002339", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002339", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002177", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002371", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002371", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002387", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002407", "http://purl.obolibrary.org/obo/RO_0002629" ] @@ -52918,15 +48367,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002488", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002488", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002488", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002492", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002492", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002492", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002496", "http://purl.obolibrary.org/obo/BFO_0000050" ] @@ -52945,9 +48388,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002497", "http://purl.obolibrary.org/obo/RO_0002082" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/uberon/core#indirectly_supplies", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002569", "http://purl.obolibrary.org/obo/RO_0002178" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/uberon/core#indirectly_supplies", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002569", "http://purl.obolibrary.org/obo/uberon/core#indirectly_supplies" ] @@ -52966,12 +48406,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002630", "http://purl.obolibrary.org/obo/RO_0002630" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0003000", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0003001", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0013001", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0013001", "http://purl.obolibrary.org/obo/BFO_0000050" ] diff --git a/subsets/blood_and_immune_upper_slim.obo b/subsets/blood_and_immune_upper_slim.obo index 35057603f..671299a14 100644 --- a/subsets/blood_and_immune_upper_slim.obo +++ b/subsets/blood_and_immune_upper_slim.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: cl/releases/2024-02-13/subsets/blood_and_immune_upper_slim.owl +data-version: cl/releases/2024-04-05/subsets/blood_and_immune_upper_slim.owl subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -88,7 +88,7 @@ synonymtypedef: synonym "" synonymtypedef: SYSTEMATIC "" synonymtypedef: systematic_synonym "" ontology: cl/subsets/blood_and_immune_upper_slim -property_value: owl:versionInfo "2024-02-13" xsd:string +property_value: owl:versionInfo "2024-04-05" xsd:string [Term] id: BFO:0000002 @@ -159,7 +159,7 @@ is_a: UBERON:0000061 ! anatomical structure disjoint_from: GO:0031012 ! extracellular matrix disjoint_from: GO:0032991 ! protein-containing complex disjoint_from: GO:0043226 ! organelle -relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms +relationship: RO:0002160 NCBITaxon:131567 ! only in taxon cellular organisms [Term] id: CL:0000007 @@ -182,8 +182,8 @@ is_a: CL:0011115 ! precursor cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0017145 ! stem cell division relationship: capable_of GO:0017145 ! stem cell division -relationship: in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000037 @@ -233,8 +233,8 @@ relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surfac relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -relationship: develops_from CL:0000566 ! angioblastic mesenchymal cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000566 ! develops from angioblastic mesenchymal cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000038 @@ -251,7 +251,7 @@ synonym: "erythroid stem cell" RELATED [] xref: BTO:0004911 is_a: CL:0000764 ! erythroid lineage cell is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor cell -relationship: develops_from CL:0000050 ! megakaryocyte-erythroid progenitor cell +relationship: RO:0002202 CL:0000050 ! develops from megakaryocyte-erythroid progenitor cell [Term] id: CL:0000040 @@ -273,11 +273,11 @@ intersection_of: has_part CL:0017503 ! basophilic cytoplasm intersection_of: has_part GO:0000791 ! euchromatin intersection_of: has_part GO:0005730 ! nucleolus intersection_of: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M -relationship: develops_from CL:0002009 ! macrophage dendritic cell progenitor relationship: has_part CL:0017503 ! basophilic cytoplasm relationship: has_part GO:0000791 ! euchromatin relationship: has_part GO:0005730 ! nucleolus relationship: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M +relationship: RO:0002202 CL:0002009 ! develops from macrophage dendritic cell progenitor [Term] id: CL:0000048 @@ -314,7 +314,7 @@ is_a: CL:0002032 {is_inferred="true"} ! hematopoietic oligopotent progenitor cel disjoint_from: CL:0000050 ! megakaryocyte-erythroid progenitor cell disjoint_from: CL:0000051 ! common lymphoid progenitor disjoint_from: CL:0000557 ! granulocyte monocyte progenitor cell -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000050 @@ -340,7 +340,7 @@ disjoint_from: CL:0000557 ! granulocyte monocyte progenitor cell disjoint_from: CL:0002009 ! macrophage dendritic cell progenitor relationship: capable_of GO:0030218 ! erythrocyte differentiation relationship: capable_of GO:0030219 ! megakaryocyte differentiation -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000051 @@ -363,7 +363,7 @@ is_a: CL:0011026 ! progenitor cell intersection_of: CL:0002032 ! hematopoietic oligopotent progenitor cell intersection_of: capable_of GO:0030098 ! lymphocyte differentiation relationship: capable_of GO:0030098 ! lymphocyte differentiation -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000052 @@ -410,8 +410,8 @@ xref: FMA:63877 xref: NCIT:C12482 xref: VHOG:0001482 is_a: CL:0002320 ! connective tissue cell -relationship: develops_from CL:0000134 ! mesenchymal stem cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000066 @@ -430,8 +430,8 @@ xref: WBbt:0003672 is_a: CL:0000000 ! cell disjoint_from: CL:0000738 ! leukocyte relationship: part_of UBERON:0000483 ! epithelium -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000071 @@ -444,9 +444,9 @@ is_a: CL:0000076 {is_inferred="true"} ! squamous epithelial cell is_a: CL:0002139 ! endothelial cell of vascular tree intersection_of: CL:0000076 ! squamous epithelial cell intersection_of: part_of UBERON:0004638 ! blood vessel endothelium -relationship: develops_from CL:0002546 ! embryonic blood vessel endothelial progenitor cell relationship: part_of UBERON:0004638 ! blood vessel endothelium -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0002546 ! develops from embryonic blood vessel endothelial progenitor cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000076 @@ -499,8 +499,8 @@ intersection_of: CL:0000542 ! lymphocyte intersection_of: capable_of GO:0002456 ! T cell mediated immunity disjoint_from: CL:0000945 ! lymphocyte of B lineage relationship: capable_of GO:0002456 ! T cell mediated immunity -relationship: develops_from CL:0000827 ! pro-T cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000827 ! develops from pro-T cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000092 @@ -528,7 +528,6 @@ intersection_of: part_of UBERON:0001474 ! bone element intersection_of: RO:0002104 PR:000001954 ! has plasma membrane part tumor necrosis factor receptor superfamily member 11A intersection_of: RO:0002104 PR:000002062 ! has plasma membrane part macrophage colony-stimulating factor 1 receptor relationship: capable_of GO:0045453 ! bone resorption -relationship: develops_from CL:0000576 ! monocyte relationship: has_part PR:000001850 ! cathepsin K relationship: has_part PR:000001937 ! tartrate-resistant acid phosphatase type 5 relationship: has_part PR:000001944 ! transcription factor PU.1 @@ -536,6 +535,7 @@ relationship: has_part PR:000007597 ! protein c-Fos relationship: has_part PR:000011178 ! nuclear factor NF-kappa-B p100 subunit relationship: RO:0002104 PR:000001954 ! has plasma membrane part tumor necrosis factor receptor superfamily member 11A relationship: RO:0002104 PR:000002062 ! has plasma membrane part macrophage colony-stimulating factor 1 receptor +relationship: RO:0002202 CL:0000576 ! develops from monocyte [Term] id: CL:0000094 @@ -568,10 +568,10 @@ relationship: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon relationship: CL:4030046 PR:000001024 ! lacks_plasma_membrane_part neural cell adhesion molecule 1 relationship: CL:4030046 PR:000001084 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD8 alpha chain relationship: has_part GO:0030141 ! secretory granule -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M relationship: RO:0002104 PR:000001332 ! has plasma membrane part carcinoembryonic antigen-related cell adhesion molecule 8 relationship: RO:0002104 PR:000001969 ! has plasma membrane part urokinase plasminogen activator surface receptor +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000097 @@ -611,13 +611,13 @@ relationship: capable_of GO:0002690 ! positive regulation of leukocyte chemotaxi relationship: capable_of GO:0002830 ! positive regulation of type 2 immune response relationship: capable_of GO:0030210 ! heparin biosynthetic process relationship: CL:4030046 PR:000001865 ! lacks_plasma_membrane_part interleukin-3 receptor class 2 alpha chain -relationship: develops_from CL:0000831 ! mast cell progenitor relationship: has_part GO:0030141 ! secretory granule -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002104 PR:000001255 ! has plasma membrane part C-C chemokine receptor type 3 relationship: RO:0002104 PR:000006169 ! has plasma membrane part cell surface glycoprotein CD200 receptor 3 +relationship: RO:0002202 CL:0000831 ! develops from mast cell progenitor relationship: RO:0015015 PR:000002065 ! has high plasma membrane amount mast/stem cell growth factor receptor relationship: RO:0015015 PR:000007431 ! has high plasma membrane amount high affinity immunoglobulin epsilon receptor subunit alpha +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000113 @@ -630,7 +630,7 @@ is_a: CL:0000518 {is_inferred="true"} ! phagocyte (sensu Vertebrata) is_a: CL:0000842 ! mononuclear cell intersection_of: CL:0000518 ! phagocyte (sensu Vertebrata) intersection_of: bearer_of PATO:0001407 ! mononucleate -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000115 @@ -645,7 +645,7 @@ xref: CALOHA:TS-0278 xref: FMA:66772 is_a: CL:0000213 ! lining cell is_a: CL:0002078 ! meso-epithelial cell -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000133 @@ -726,8 +726,8 @@ xref: FMA:67328 xref: WBbt:0003675 is_a: CL:0000183 ! contractile cell is_a: CL:0000393 ! electrically responsive cell -relationship: develops_from CL:0000056 ! myoblast -property_value: depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI +relationship: RO:0002202 CL:0000056 ! develops from myoblast +property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI [Term] id: CL:0000211 @@ -845,8 +845,8 @@ intersection_of: CL:4030046 PR:000001945 ! lacks_plasma_membrane_part transferri relationship: bearer_of PATO:0002039 ! biconcave relationship: CL:4030045 GO:0005840 ! lacks_part ribosome relationship: CL:4030046 PR:000001945 ! lacks_plasma_membrane_part transferrin receptor protein 1 -relationship: develops_from CL:0000558 ! reticulocyte -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000558 ! develops from reticulocyte +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000233 @@ -868,8 +868,8 @@ is_a: CL:0000458 ! serotonin secreting cell is_a: CL:0000763 {is_inferred="true"} ! myeloid cell relationship: bearer_of PATO:0001874 ! discoid relationship: capable_of_part_of GO:0007596 ! blood coagulation -relationship: develops_from CL:0000556 ! megakaryocyte -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000556 ! develops from megakaryocyte +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000234 @@ -909,8 +909,8 @@ intersection_of: capable_of GO:0002504 ! antigen processing and presentation of intersection_of: capable_of GO:0006909 ! phagocytosis intersection_of: capable_of GO:0031268 ! pseudopodium organization relationship: capable_of GO:0031268 ! pseudopodium organization -relationship: develops_from CL:0000576 ! monocyte -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000576 ! develops from monocyte +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000236 @@ -932,7 +932,7 @@ is_a: CL:0000945 {is_inferred="true"} ! lymphocyte of B lineage intersection_of: CL:0000945 ! lymphocyte of B lineage intersection_of: capable_of GO:0019724 ! B cell mediated immunity relationship: capable_of GO:0019724 ! B cell mediated immunity -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000255 @@ -941,8 +941,8 @@ subset: cellxgene_subset xref: MESH:D005057 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell -intersection_of: only_in_taxon NCBITaxon:2759 ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +intersection_of: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota [Term] id: CL:0000325 @@ -967,7 +967,7 @@ xref: FMA:86667 is_a: CL:0000219 ! motile cell is_a: CL:0011012 ! neural crest cell is_a: CL:0011026 ! progenitor cell -relationship: develops_from CL:0007004 ! premigratory neural crest cell +relationship: RO:0002202 CL:0007004 ! develops from premigratory neural crest cell [Term] id: CL:0000335 @@ -993,8 +993,8 @@ is_a: CL:0000007 ! early embryonic cell (metazoa) is_a: CL:0000255 ! eukaryotic cell is_a: CL:0010017 ! zygote intersection_of: CL:0010017 ! zygote -intersection_of: only_in_taxon NCBITaxon:33208 ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +intersection_of: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa [Term] id: CL:0000393 @@ -1045,7 +1045,7 @@ relationship: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon relationship: CL:4030046 PR:000001024 ! lacks_plasma_membrane_part neural cell adhesion molecule 1 relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-spanning 4-domains subfamily A member 1 relationship: has_part GO:0042613 ! MHC class II protein complex -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000457 @@ -1075,7 +1075,7 @@ name: phagocyte (sensu Vertebrata) def: "A phagocyte in vertebrates that is able to phagocytosis." [GOC:tfm] is_a: CL:0000234 ! phagocyte is_a: CL:0000255 ! eukaryotic cell -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata [Term] id: CL:0000540 @@ -1096,8 +1096,8 @@ is_a: CL:0000393 ! electrically responsive cell is_a: CL:0000404 ! electrically signaling cell is_a: CL:0002319 ! neural cell relationship: capable_of GO:0019226 ! transmission of nerve impulse -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://www.swissbiopics.org/api/image/Neuron_cells.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Neuron_cells.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000542 @@ -1120,10 +1120,10 @@ intersection_of: has_part CL:0017500 ! neutrophillic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin disjoint_from: CL:0000766 ! myeloid leukocyte relationship: bearer_of PATO:0040072 ! high nuclear/cytoplasmic ratio -relationship: develops_from CL:0000051 ! common lymphoid progenitor relationship: has_part CL:0017500 ! neutrophillic cytoplasm relationship: has_part GO:0000792 ! heterochromatin -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000051 ! develops from common lymphoid progenitor +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000547 @@ -1166,10 +1166,10 @@ relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-span relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD5 relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G -relationship: develops_from CL:0000038 ! erythroid progenitor cell relationship: has_part CL:0017503 ! basophilic cytoplasm relationship: has_part GO:0005730 ! nucleolus relationship: RO:0002104 PR:000001945 ! has plasma membrane part transferrin receptor protein 1 +relationship: RO:0002202 CL:0000038 ! develops from erythroid progenitor cell [Term] id: CL:0000549 @@ -1207,10 +1207,10 @@ intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017504 ! polychromatophilic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin intersection_of: RO:0002104 PR:000001945 ! has plasma membrane part transferrin receptor protein 1 -relationship: develops_from CL:0000549 ! basophilic erythroblast relationship: has_part CL:0017504 ! polychromatophilic cytoplasm relationship: has_part GO:0000792 ! heterochromatin relationship: RO:0002104 PR:000001945 ! has plasma membrane part transferrin receptor protein 1 +relationship: RO:0002202 CL:0000549 ! develops from basophilic erythroblast [Term] id: CL:0000552 @@ -1226,9 +1226,9 @@ is_a: CL:0000765 {is_inferred="true"} ! erythroblast intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017502 ! acidophilic cytoplasm intersection_of: participates_in GO:0030263 ! apoptotic chromosome condensation -relationship: develops_from CL:0000550 ! polychromatophilic erythroblast relationship: has_part CL:0017502 ! acidophilic cytoplasm relationship: participates_in GO:0030263 ! apoptotic chromosome condensation +relationship: RO:0002202 CL:0000550 ! develops from polychromatophilic erythroblast [Term] id: CL:0000553 @@ -1282,8 +1282,8 @@ relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surfac relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -relationship: develops_from CL:0000050 ! megakaryocyte-erythroid progenitor cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000050 ! develops from megakaryocyte-erythroid progenitor cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000556 @@ -1302,8 +1302,8 @@ xref: FMA:83555 is_a: CL:0000763 {is_inferred="true"} ! myeloid cell disjoint_from: CL:0000764 ! erythroid lineage cell relationship: bearer_of PATO:0001393 ! euploid -relationship: develops_from CL:0000553 ! megakaryocyte progenitor cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000553 ! develops from megakaryocyte progenitor cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000557 @@ -1339,8 +1339,8 @@ relationship: CL:4030045 PR:000007857 ! lacks_part erythroid transcription facto relationship: CL:4030045 PR:000007858 ! lacks_part endothelial transcription factor GATA-2 relationship: has_part PR:000001944 ! transcription factor PU.1 relationship: has_part PR:000005307 ! CCAAT/enhancer-binding protein alpha -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002104 PR:000001865 ! has plasma membrane part interleukin-3 receptor class 2 alpha chain +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000558 @@ -1379,8 +1379,8 @@ relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-span relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD5 relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G -relationship: develops_from CL:0000552 ! orthochromatic erythroblast relationship: RO:0002104 PR:000001945 ! has plasma membrane part transferrin receptor protein 1 +relationship: RO:0002202 CL:0000552 ! develops from orthochromatic erythroblast [Term] id: CL:0000559 @@ -1398,10 +1398,10 @@ intersection_of: CL:0002194 ! monopoietic cell intersection_of: capable_of GO:0030224 ! monocyte differentiation intersection_of: has_part GO:0042582 ! azurophil granule intersection_of: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M -relationship: develops_from CL:0000040 ! monoblast relationship: has_part GO:0042582 ! azurophil granule -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M +relationship: RO:0002202 CL:0000040 ! develops from monoblast +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000566 @@ -1417,10 +1417,10 @@ intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: RO:0002104 PR:000001444 ! has plasma membrane part cadherin-5 intersection_of: RO:0002104 PR:000002112 ! has plasma membrane part vascular endothelial growth factor receptor 2 intersection_of: RO:0002104 PR:000016043 ! has plasma membrane part T-cell acute lymphocytic leukemia protein 1 -relationship: develops_from CL:0000134 ! mesenchymal stem cell relationship: RO:0002104 PR:000001444 ! has plasma membrane part cadherin-5 relationship: RO:0002104 PR:000002112 ! has plasma membrane part vascular endothelial growth factor receptor 2 relationship: RO:0002104 PR:000016043 ! has plasma membrane part T-cell acute lymphocytic leukemia protein 1 +relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell [Term] id: CL:0000576 @@ -1445,8 +1445,8 @@ intersection_of: capable_of GO:0043011 ! myeloid dendritic cell differentiation relationship: capable_of GO:0030225 ! macrophage differentiation relationship: capable_of GO:0030316 ! osteoclast differentiation relationship: capable_of GO:0043011 ! myeloid dendritic cell differentiation -relationship: develops_from CL:0000559 ! promonocyte -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000559 ! develops from promonocyte +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000647 @@ -1468,9 +1468,9 @@ intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: bearer_of PATO:0001908 ! multinucleate intersection_of: participates_in GO:0002432 ! granuloma formation intersection_of: participates_in GO:0002544 ! chronic inflammatory response -relationship: develops_from CL:0000235 ! macrophage relationship: participates_in GO:0002432 ! granuloma formation relationship: participates_in GO:0002544 ! chronic inflammatory response +relationship: RO:0002202 CL:0000235 ! develops from macrophage [Term] id: CL:0000680 @@ -1479,9 +1479,9 @@ def: "A non-terminally differentiated cell that is capable of developing into a subset: cellxgene_subset is_a: CL:0000055 ! non-terminally differentiated cell intersection_of: CL:0011115 ! precursor cell -intersection_of: develops_into CL:0000187 ! muscle cell -relationship: develops_from CL:0000222 ! mesodermal cell -relationship: develops_into CL:0000187 ! muscle cell +intersection_of: RO:0002203 CL:0000187 ! develops into muscle cell +relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell +relationship: RO:0002203 CL:0000187 ! develops into muscle cell [Term] id: CL:0000723 @@ -1516,10 +1516,10 @@ intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0002505 ! nucleated intersection_of: capable_of GO:0001667 ! ameboidal-type cell migration relationship: capable_of GO:0001667 ! ameboidal-type cell migration -relationship: develops_from CL:0000037 ! hematopoietic stem cell -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0002405 ! immune system -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002202 CL:0000037 ! develops from hematopoietic stem cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000762 @@ -1533,7 +1533,7 @@ intersection_of: CL:0000763 ! myeloid cell intersection_of: bearer_of PATO:0001407 ! mononucleate intersection_of: capable_of GO:0007596 ! blood coagulation relationship: capable_of GO:0007596 ! blood coagulation -relationship: develops_from CL:0000828 ! thromboblast +relationship: RO:0002202 CL:0000828 ! develops from thromboblast [Term] id: CL:0000763 @@ -1545,8 +1545,8 @@ xref: CALOHA:TS-0647 xref: MESH:D022423 is_a: CL:0000988 {is_inferred="true"} ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell -intersection_of: develops_from CL:0000049 ! common myeloid progenitor -relationship: develops_from CL:0000049 ! common myeloid progenitor +intersection_of: RO:0002202 CL:0000049 ! develops from common myeloid progenitor +relationship: RO:0002202 CL:0000049 ! develops from common myeloid progenitor [Term] id: CL:0000764 @@ -1560,7 +1560,7 @@ xref: CALOHA:TS-0290 xref: FMA:62845 xref: FMA:83516 is_a: CL:0000763 ! myeloid cell -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000765 @@ -1603,8 +1603,8 @@ relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-span relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD5 relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G -relationship: develops_from CL:0000547 ! proerythroblast relationship: has_part GO:0005634 ! nucleus +relationship: RO:0002202 CL:0000547 ! develops from proerythroblast [Term] id: CL:0000766 @@ -1614,7 +1614,7 @@ subset: cellxgene_subset is_a: CL:0000738 {is_inferred="true"} ! leukocyte is_a: CL:0000763 ! myeloid cell intersection_of: CL:0000738 ! leukocyte -intersection_of: develops_from CL:0000049 ! common myeloid progenitor +intersection_of: RO:0002202 CL:0000049 ! develops from common myeloid progenitor [Term] id: CL:0000767 @@ -1638,12 +1638,12 @@ intersection_of: RO:0002104 PR:000001950 ! has plasma membrane part tumor necros intersection_of: RO:0015015 PR:000001255 ! has high plasma membrane amount C-C chemokine receptor type 3 intersection_of: RO:0015015 PR:000001865 ! has high plasma membrane amount interleukin-3 receptor class 2 alpha chain intersection_of: RO:0015015 PR:000007431 ! has high plasma membrane amount high affinity immunoglobulin epsilon receptor subunit alpha -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002104 PR:000001344 ! has plasma membrane part ectonucleotide pyrophosphatase/phosphodiesterase family member 3 relationship: RO:0002104 PR:000001950 ! has plasma membrane part tumor necrosis factor ligand superfamily member 5 relationship: RO:0015015 PR:000001255 ! has high plasma membrane amount C-C chemokine receptor type 3 relationship: RO:0015015 PR:000001865 ! has high plasma membrane amount interleukin-3 receptor class 2 alpha chain relationship: RO:0015015 PR:000007431 ! has high plasma membrane amount high affinity immunoglobulin epsilon receptor subunit alpha +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000771 @@ -1670,12 +1670,12 @@ intersection_of: RO:0002104 PR:000001255 ! has plasma membrane part C-C chemokin intersection_of: RO:0002104 PR:000001307 ! has plasma membrane part CD44 molecule intersection_of: RO:0002104 PR:000001343 ! has plasma membrane part CD69 molecule intersection_of: RO:0002104 PR:000005178 ! has plasma membrane part CD9 molecule -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002104 PR:000001254 ! has plasma membrane part C-C chemokine receptor type 1 relationship: RO:0002104 PR:000001255 ! has plasma membrane part C-C chemokine receptor type 3 relationship: RO:0002104 PR:000001307 ! has plasma membrane part CD44 molecule relationship: RO:0002104 PR:000001343 ! has plasma membrane part CD69 molecule relationship: RO:0002104 PR:000005178 ! has plasma membrane part CD9 molecule +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000775 @@ -1704,9 +1704,9 @@ is_a: CL:0000094 {is_inferred="true"} ! granulocyte intersection_of: CL:0000094 ! granulocyte intersection_of: RO:0002104 PR:000001479 ! has plasma membrane part low affinity immunoglobulin gamma Fc region receptor II intersection_of: RO:0002104 PR:000001879 ! has plasma membrane part leukosialin -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002104 PR:000001479 ! has plasma membrane part low affinity immunoglobulin gamma Fc region receptor II relationship: RO:0002104 PR:000001879 ! has plasma membrane part leukosialin +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000782 @@ -1723,9 +1723,9 @@ is_a: CL:0000766 ! myeloid leukocyte is_a: CL:0000990 {is_inferred="true"} ! conventional dendritic cell intersection_of: CL:0000990 ! conventional dendritic cell intersection_of: CL:4030046 PR:000001865 ! lacks_plasma_membrane_part interleukin-3 receptor class 2 alpha chain -intersection_of: develops_from CL:0000763 ! myeloid cell +intersection_of: RO:0002202 CL:0000763 ! develops from myeloid cell relationship: CL:4030046 PR:000001865 ! lacks_plasma_membrane_part interleukin-3 receptor class 2 alpha chain -relationship: develops_from CL:0000763 ! myeloid cell +relationship: RO:0002202 CL:0000763 ! develops from myeloid cell [Term] id: CL:0000784 @@ -1748,7 +1748,7 @@ is_a: CL:0000451 {is_inferred="true"} ! dendritic cell intersection_of: CL:0000451 ! dendritic cell intersection_of: capable_of GO:0032606 ! type I interferon production relationship: capable_of GO:0032606 ! type I interferon production -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000785 @@ -1769,8 +1769,8 @@ disjoint_from: CL:0000816 ! immature B cell disjoint_from: CL:0000817 ! precursor B cell disjoint_from: CL:0000818 ! transitional stage B cell relationship: capable_of GO:0042113 ! B cell activation -relationship: develops_from CL:0000818 ! transitional stage B cell relationship: output_of GO:0002335 ! mature B cell differentiation +relationship: RO:0002202 CL:0000818 ! develops from transitional stage B cell [Term] id: CL:0000786 @@ -1800,11 +1800,11 @@ intersection_of: RO:0002104 PR:000001935 ! has plasma membrane part syndecan-1 relationship: CL:4030046 GO:0019814 ! lacks_plasma_membrane_part immunoglobulin complex relationship: CL:4030046 GO:0042613 ! lacks_plasma_membrane_part MHC class II protein complex relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-spanning 4-domains subfamily A member 1 -relationship: develops_from CL:0000980 ! plasmablast relationship: has_part CL:0017508 ! cartwheel heterochromatin relationship: has_part GO:0005794 ! Golgi apparatus -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002104 PR:000001935 ! has plasma membrane part syndecan-1 +relationship: RO:0002202 CL:0000980 ! develops from plasmablast +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000789 @@ -1837,8 +1837,8 @@ synonym: "gd T cell" RELATED OMO:0003000 [] is_a: CL:0000084 {is_inferred="true"} ! T cell intersection_of: CL:0000084 ! T cell intersection_of: RO:0002104 GO:0042106 ! has plasma membrane part gamma-delta T cell receptor complex -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002104 GO:0042106 ! has plasma membrane part gamma-delta T cell receptor complex +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000816 @@ -1860,10 +1860,10 @@ intersection_of: RO:0002104 GO:0071753 ! has plasma membrane part IgM immunoglob intersection_of: RO:0002104 PR:000001289 ! has plasma membrane part membrane-spanning 4-domains subfamily A member 1 relationship: CL:4030044 GO:0045190 ! has_not_completed isotype switching relationship: CL:4030046 GO:0071738 ! lacks_plasma_membrane_part IgD immunoglobulin complex -relationship: develops_from CL:0000954 ! small pre-B-II cell -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002104 GO:0071753 ! has plasma membrane part IgM immunoglobulin complex relationship: RO:0002104 PR:000001289 ! has plasma membrane part membrane-spanning 4-domains subfamily A member 1 +relationship: RO:0002202 CL:0000954 ! develops from small pre-B-II cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000817 @@ -1880,8 +1880,8 @@ intersection_of: CL:4030046 GO:0071753 ! lacks_plasma_membrane_part IgM immunogl intersection_of: RO:0002104 PR:000001898 ! has plasma membrane part neprilysin disjoint_from: CL:0000826 ! pro-B cell relationship: CL:4030046 GO:0071753 ! lacks_plasma_membrane_part IgM immunoglobulin complex -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002104 PR:000001898 ! has plasma membrane part neprilysin +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000818 @@ -1905,12 +1905,12 @@ intersection_of: RO:0002104 PR:000001289 ! has plasma membrane part membrane-spa intersection_of: RO:0015015 PR:000001408 ! has high plasma membrane amount ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 intersection_of: RO:0015015 PR:000001932 ! has high plasma membrane amount signal transducer CD24 relationship: CL:4030044 GO:0002335 ! has_not_completed mature B cell differentiation -relationship: develops_from CL:0000816 ! immature B cell -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002104 GO:0071753 ! has plasma membrane part IgM immunoglobulin complex relationship: RO:0002104 PR:000001289 ! has plasma membrane part membrane-spanning 4-domains subfamily A member 1 +relationship: RO:0002202 CL:0000816 ! develops from immature B cell relationship: RO:0015015 PR:000001408 ! has high plasma membrane amount ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 relationship: RO:0015015 PR:000001932 ! has high plasma membrane amount signal transducer CD24 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000826 @@ -1935,11 +1935,11 @@ intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: has_part PR:000001903 ! paired box protein PAX-5 intersection_of: has_part PR:000006611 ! DNA nucleotidylexotransferase intersection_of: participates_in GO:0033152 ! immunoglobulin V(D)J recombination -relationship: develops_from CL:0000051 ! common lymphoid progenitor relationship: has_part PR:000001903 ! paired box protein PAX-5 relationship: has_part PR:000006611 ! DNA nucleotidylexotransferase relationship: participates_in GO:0033152 ! immunoglobulin V(D)J recombination -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000051 ! develops from common lymphoid progenitor +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000827 @@ -1955,7 +1955,7 @@ is_a: CL:0000838 {is_inferred="true"} ! lymphoid lineage restricted progenitor c intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: capable_of GO:0030217 ! T cell differentiation relationship: capable_of GO:0030217 ! T cell differentiation -relationship: develops_from CL:0000051 ! common lymphoid progenitor +relationship: RO:0002202 CL:0000051 ! develops from common lymphoid progenitor [Term] id: CL:0000828 @@ -1969,7 +1969,7 @@ intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: bearer_of PATO:0001407 ! mononucleate intersection_of: capable_of GO:0002574 ! thrombocyte differentiation relationship: capable_of GO:0002574 ! thrombocyte differentiation -relationship: develops_from CL:0000050 ! megakaryocyte-erythroid progenitor cell +relationship: RO:0002202 CL:0000050 ! develops from megakaryocyte-erythroid progenitor cell [Term] id: CL:0000831 @@ -2025,11 +2025,11 @@ relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte an relationship: CL:4030046 PR:000002979 ! lacks_plasma_membrane_part lymphocyte antigen 6A-2/6E-1 relationship: CL:4030046 PR:000002980 ! lacks_plasma_membrane_part lymphocyte antigen 6C2 relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -relationship: develops_from CL:0002028 ! basophil mast progenitor cell relationship: has_part PR:000007857 ! erythroid transcription factor relationship: has_part PR:000007858 ! endothelial transcription factor GATA-2 relationship: RO:0002104 PR:000005178 ! has plasma membrane part CD9 molecule relationship: RO:0002104 PR:000016401 ! has plasma membrane part transmembrane emp24 domain-containing protein 1 +relationship: RO:0002202 CL:0002028 ! develops from basophil mast progenitor cell relationship: RO:0015015 PR:000009143 ! has high plasma membrane amount integrin beta-7 relationship: RO:0015016 PR:000002065 ! has low plasma membrane amount mast/stem cell growth factor receptor relationship: RO:0015016 PR:000007431 ! has low plasma membrane amount high affinity immunoglobulin epsilon receptor subunit alpha @@ -2079,9 +2079,9 @@ relationship: CL:4030046 PR:000001869 ! lacks_plasma_membrane_part interleukin-7 relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -relationship: develops_from CL:0000037 ! hematopoietic stem cell -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule +relationship: RO:0002202 CL:0000037 ! develops from hematopoietic stem cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000838 @@ -2116,7 +2116,7 @@ is_a: CL:0011026 ! progenitor cell intersection_of: CL:0002031 ! hematopoietic lineage restricted progenitor cell intersection_of: capable_of GO:0030099 ! myeloid cell differentiation relationship: capable_of GO:0030099 ! myeloid cell differentiation -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000842 @@ -2159,8 +2159,8 @@ def: "A lymphocyte of B lineage with the commitment to express an immunoglobulin comment: Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells). Lymphocytes of B cell lineage can be distinguished from those of T cell lineage by their lack of CD3e (as part of the T cell receptor complex). subset: human_reference_atlas is_a: CL:0000542 {is_inferred="true"} ! lymphocyte -relationship: develops_from CL:0000826 ! pro-B cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000826 ! develops from pro-B cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000946 @@ -2229,10 +2229,10 @@ intersection_of: RO:0015015 PR:000001408 ! has high plasma membrane amount ADP-r intersection_of: RO:0015015 PR:000001963 ! has high plasma membrane amount CD27 molecule relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-spanning 4-domains subfamily A member 1 relationship: CL:4030046 PR:000001935 ! lacks_plasma_membrane_part syndecan-1 -relationship: develops_from CL:0000785 ! mature B cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000785 ! develops from mature B cell relationship: RO:0015015 PR:000001408 ! has high plasma membrane amount ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 relationship: RO:0015015 PR:000001963 ! has high plasma membrane amount CD27 molecule +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000988 @@ -2266,8 +2266,8 @@ xref: FMA:84191 is_a: CL:0000451 {is_inferred="true"} ! dendritic cell intersection_of: CL:0000451 ! dendritic cell intersection_of: RO:0015015 PR:000001013 ! has high plasma membrane amount integrin alpha-X -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0015015 PR:000001013 ! has high plasma membrane amount integrin alpha-X +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0001012 @@ -2284,9 +2284,9 @@ subset: human_reference_atlas is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001474 ! bone element -relationship: dc-contributor https://orcid.org/0000-0001-9990-8331 relationship: part_of UBERON:0001474 ! bone element -relationship: present_in_taxon NCBITaxon:9606 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2011-11-16T04:28:16Z [Term] @@ -2320,7 +2320,7 @@ relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surfac relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:27Z [Term] @@ -2340,9 +2340,9 @@ relationship: capable_of GO:0001816 ! cytokine production relationship: capable_of GO:0045087 ! innate immune response relationship: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule relationship: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon -relationship: dc-contributor https://orcid.org/0000-0001-9990-8331 -relationship: present_in_taxon NCBITaxon:9606 -property_value: dcterms-date "2017-01-30T20:20:48Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 +property_value: http://purl.org/dc/terms/date "2017-01-30T20:20:48Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0001200 @@ -2352,12 +2352,12 @@ comment: Types of B lineage lymphocytes include B cells and antibody secreting c is_a: CL:0000945 ! lymphocyte of B lineage intersection_of: CL:0000945 ! lymphocyte of B lineage intersection_of: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon -intersection_of: in_taxon NCBITaxon:40674 ! Mammalia intersection_of: RO:0002104 PR:000001002 ! has plasma membrane part CD19 molecule +intersection_of: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia relationship: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon -relationship: dc-contributor https://orcid.org/0000-0001-9990-8331 -relationship: in_taxon NCBITaxon:40674 ! Mammalia relationship: RO:0002104 PR:000001002 ! has plasma membrane part CD19 molecule +relationship: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 [Term] id: CL:0001201 @@ -2372,9 +2372,9 @@ is_a: CL:0000236 ! B cell is_a: CL:0001200 ! lymphocyte of B lineage, CD19-positive intersection_of: CL:0001200 ! lymphocyte of B lineage, CD19-positive intersection_of: capable_of GO:0019724 ! B cell mediated immunity -intersection_of: in_taxon NCBITaxon:40674 ! Mammalia intersection_of: RO:0002104 PR:000001002 ! has plasma membrane part CD19 molecule -relationship: dc-contributor https://orcid.org/0000-0001-9990-8331 +intersection_of: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 [Term] id: CL:0002009 @@ -2390,8 +2390,8 @@ intersection_of: capable_of GO:0030224 ! monocyte differentiation intersection_of: capable_of GO:0043011 ! myeloid dendritic cell differentiation relationship: capable_of GO:0030224 ! monocyte differentiation relationship: capable_of GO:0043011 ! myeloid dendritic cell differentiation -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000557 ! granulocyte monocyte progenitor cell +relationship: RO:0002202 CL:0000557 ! develops from granulocyte monocyte progenitor cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-19T02:51:58Z [Term] @@ -2417,12 +2417,12 @@ relationship: capable_of GO:0030221 ! basophil differentiation relationship: capable_of GO:0060374 ! mast cell differentiation relationship: CL:4030046 PR:000007431 ! lacks_plasma_membrane_part high affinity immunoglobulin epsilon receptor subunit alpha relationship: CL:4030046 PR:000016401 ! lacks_plasma_membrane_part transmembrane emp24 domain-containing protein 1 -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000557 ! granulocyte monocyte progenitor cell relationship: has_part PR:000005307 ! CCAAT/enhancer-binding protein alpha relationship: has_part PR:000007857 ! erythroid transcription factor relationship: has_part PR:000007858 ! endothelial transcription factor GATA-2 relationship: RO:0002104 PR:000001867 ! has plasma membrane part interleukin-5 receptor subunit alpha +relationship: RO:0002202 CL:0000557 ! develops from granulocyte monocyte progenitor cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-04-27T12:46:33Z [Term] @@ -2435,8 +2435,8 @@ intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001400 ! unipotent disjoint_from: CL:0002032 ! hematopoietic oligopotent progenitor cell relationship: bearer_of PATO:0001400 ! unipotent -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002032 ! hematopoietic oligopotent progenitor cell +relationship: RO:0002202 CL:0002032 ! develops from hematopoietic oligopotent progenitor cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:20Z [Term] @@ -2449,8 +2449,8 @@ is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001401 ! oligopotent relationship: bearer_of PATO:0001401 ! oligopotent -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000837 ! hematopoietic multipotent progenitor cell +relationship: RO:0002202 CL:0000837 ! develops from hematopoietic multipotent progenitor cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:27Z [Term] @@ -2460,9 +2460,9 @@ def: "An epithelial cell derived from ectoderm." [FMA:69074, GOC:tfm] xref: FMA:69074 is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell -intersection_of: develops_from CL:0000221 ! ectodermal cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000221 ! ectodermal cell +intersection_of: RO:0002202 CL:0000221 ! develops from ectodermal cell +relationship: RO:0002202 CL:0000221 ! develops from ectodermal cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T03:38:22Z [Term] @@ -2473,9 +2473,9 @@ synonym: "epithelial mesenchymal cell" EXACT [] xref: FMA:69076 is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell -intersection_of: develops_from CL:0000222 ! mesodermal cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000222 ! mesodermal cell +intersection_of: RO:0002202 CL:0000222 ! develops from mesodermal cell +relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T03:49:14Z [Term] @@ -2489,7 +2489,7 @@ is_a: CL:0000738 {is_inferred="true"} ! leukocyte intersection_of: CL:0000738 ! leukocyte intersection_of: CL:4030045 GO:0030141 ! lacks_part secretory granule relationship: CL:4030045 GO:0030141 ! lacks_part secretory granule -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-07-22T11:30:33Z [Term] @@ -2504,8 +2504,8 @@ xref: MESH:D001854 is_a: CL:0001035 {is_inferred="true"} ! bone cell intersection_of: CL:0001035 ! bone cell intersection_of: part_of UBERON:0002371 ! bone marrow -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002371 ! bone marrow +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-07-22T04:48:15Z [Term] @@ -2520,7 +2520,7 @@ xref: BTO:0001854 xref: CALOHA:TS-1106 xref: FMA:67755 is_a: CL:0000115 ! endothelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T02:06:40Z [Term] @@ -2533,7 +2533,7 @@ is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor ce intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: capable_of GO:0030851 ! granulocyte differentiation relationship: capable_of GO:0030851 ! granulocyte differentiation -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-30T12:54:27Z [Term] @@ -2545,7 +2545,7 @@ is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor ce intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: capable_of GO:0030224 ! monocyte differentiation relationship: capable_of GO:0030224 ! monocyte differentiation -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-30T01:27:48Z [Term] @@ -2557,7 +2557,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0002505 ! nucleated relationship: bearer_of PATO:0002505 ! nucleated -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T03:32:33Z [Term] @@ -2568,7 +2568,7 @@ is_a: CL:0000457 ! biogenic amine secreting cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0001821 ! histamine secretion relationship: capable_of GO:0001821 ! histamine secretion -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-10T03:04:42Z [Term] @@ -2581,8 +2581,8 @@ xref: FMA:70333 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001016 ! nervous system -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001016 ! nervous system +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T01:34:57Z [Term] @@ -2596,8 +2596,8 @@ xref: MESH:D003239 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0002384 ! connective tissue -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002384 ! connective tissue +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T03:01:54Z [Term] @@ -2608,7 +2608,7 @@ xref: CALOHA:TS-0263 xref: FMA:82840 xref: WBbt:0007028 is_a: CL:0000000 ! cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T03:39:21Z [Term] @@ -2624,7 +2624,7 @@ is_a: CL:0000084 {is_inferred="true"} ! T cell intersection_of: CL:0000084 ! T cell intersection_of: CL:4030044 GO:0045058 ! has_not_completed T cell selection relationship: CL:4030044 GO:0045058 ! has_not_completed T cell selection -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-10-12T01:56:17Z [Term] @@ -2640,8 +2640,8 @@ xref: FMA:84791 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0007100 ! primary circulatory organ -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0007100 ! primary circulatory organ +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T09:37:22Z [Term] @@ -2650,7 +2650,7 @@ name: embryonic blood vessel endothelial progenitor cell def: "An endothelial progenitor cell that participates in angiogenesis during development." [GOC:tfm] comment: See CL:0002619. is_a: CL:0000222 ! mesodermal cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T04:20:39Z [Term] @@ -2678,9 +2678,9 @@ relationship: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon relationship: CL:4030046 PR:000001084 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD8 alpha chain relationship: CL:4030046 PR:000001874 ! lacks_plasma_membrane_part KLRB1-like protein relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: RO:0002104 PR:000002065 ! has plasma membrane part mast/stem cell growth factor receptor relationship: RO:0002104 PR:000002979 ! has plasma membrane part lymphocyte antigen 6A-2/6E-1 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-08-29T10:08:02Z [Term] @@ -2690,7 +2690,7 @@ def: "Cell that has the potential to form a skeletal cell type (e.g. cells in pe comment: Needs logical definition. Should be capable_of skeletal system morphogenesis? or skeletal tissue development? needs to be added to GO. NOTES:a cell type of the early embryo (see also: mesenchymal cells) that will give rise to mineralized connective tissue. Scleroblasts can differentiate into osteoblasts (bone-forming cells), chondroblasts (cartilage-forming cells), odontoblasts (dentin-forming cells), ameloblasts (enamel-forming cells). The mesenchymal cells developing into osteoblasts and chondroblasts are derived from the mesoderm. Those developing into odontoblasts are neural crest cells. Those developing into ameloblasts are derived from the ectoderm. (http://www.copewithcytokines.de/cope.cgi?key=scleroblasts) synonym: "scleroblast" EXACT [GO_REF:0000034] is_a: CL:0000000 ! cell -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-15T02:51:27Z [Term] @@ -2698,9 +2698,9 @@ id: CL:0007004 name: premigratory neural crest cell def: "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells." [UBERONREF:0000002] is_a: CL:0011012 ! neural crest cell -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 -relationship: develops_from CL:0000133 ! neurectodermal cell relationship: part_of UBERON:0002342 ! neural crest +relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-27T08:27:35Z [Term] @@ -2720,7 +2720,7 @@ synonym: "mesenchyme cell" EXACT [] is_a: CL:0000219 ! motile cell relationship: capable_of GO:0016477 ! cell migration relationship: part_of UBERON:0003104 ! mesenchyme -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0010017 @@ -2728,7 +2728,7 @@ name: zygote def: "A zygote in a plant or an animal." [] xref: MESH:D015053 is_a: CL:0000000 ! cell -relationship: seeAlso https://github.com/obophenotype/cell-ontology/issues/786 +property_value: seeAlso https://github.com/obophenotype/cell-ontology/issues/786 [Term] id: CL:0011012 @@ -2745,9 +2745,9 @@ def: "A precursor cell that has a tendency to differentiate into a specific type subset: cellxgene_subset is_a: CL:0011115 ! precursor cell intersection_of: CL:0011115 ! precursor cell -intersection_of: develops_from CL:0000034 ! stem cell -relationship: dc-contributor https://orcid.org/0000-0001-5208-3432 -relationship: develops_from CL:0000034 ! stem cell +intersection_of: RO:0002202 CL:0000034 ! develops from stem cell +relationship: RO:0002202 CL:0000034 ! develops from stem cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011115 @@ -2793,7 +2793,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0070046 ! neutrophillic relationship: bearer_of PATO:0070046 ! neutrophillic -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-05-25T01:36:34Z [Term] @@ -2805,7 +2805,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0002418 ! acidophilic relationship: bearer_of PATO:0002418 ! acidophilic -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-22T04:23:25Z [Term] @@ -2816,7 +2816,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0002094 ! basophilic relationship: bearer_of PATO:0002094 ! basophilic -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-22T04:24:54Z [Term] @@ -2827,7 +2827,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0070047 ! polychromatophilic relationship: bearer_of PATO:0070047 ! polychromatophilic -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-28T04:25:23Z [Term] @@ -2835,7 +2835,7 @@ id: CL:0017508 name: cartwheel heterochromatin def: "Heterochromatin that is arranged in a carthwheel pattern." [GOC:tfm] is_a: GO:0000792 ! heterochromatin -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-28T04:28:35Z [Term] @@ -2860,8 +2860,8 @@ is_a: CL:0000080 ! circulating cell is_a: CL:0000842 ! mononuclear cell intersection_of: CL:0000842 ! mononuclear cell intersection_of: part_of UBERON:0000178 ! blood -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: part_of UBERON:0000178 ! blood +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-02-11T17:29:04Z [Term] @@ -2873,7 +2873,7 @@ is_a: CL:0000542 ! lymphocyte is_a: CL:2000001 ! peripheral blood mononuclear cell intersection_of: CL:0000542 ! lymphocyte intersection_of: part_of UBERON:0000178 ! blood -property_value: dcterms-date "2022-11-04T14:40:00Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2022-11-04T14:40:00Z" xsd:dateTime [Term] id: GO:0000278 @@ -2892,8 +2892,8 @@ is_a: GO:0007049 ! cell cycle intersection_of: GO:0007049 ! cell cycle intersection_of: has_part GO:0140014 ! mitotic nuclear division relationship: has_part GO:0140014 ! mitotic nuclear division -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota [Term] id: GO:0000280 @@ -2966,7 +2966,7 @@ namespace: biological_process def: "A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities." [GOC:dph, GOC:go_curators, GOC:tb, ISBN:978-0-07-139011-8] comment: Action potentials typically propagate across excitable membranes. This class covers both action potentials that propagate and those that fail to do so. is_a: GO:0042391 ! regulation of membrane potential -relationship: never_in_taxon NCBITaxon:4895 +property_value: RO:0002161 NCBITaxon:4895 [Term] id: GO:0001667 @@ -3063,8 +3063,8 @@ def: "A multicellular organismal process by which exposure to an activating fact subset: goslim_pir is_a: GO:0009987 ! cellular process is_a: GO:0032501 ! multicellular organismal process -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24416" xsd:anyURI [Term] @@ -3205,8 +3205,8 @@ synonym: "acquired immune response" EXACT [ISBN:068340007X] synonym: "immune memory response" EXACT [GOC:add] xref: Wikipedia:Adaptive_immune_system is_a: GO:0006955 ! immune response -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0002252 @@ -3325,7 +3325,7 @@ subset: goslim_mouse subset: goslim_pir xref: Wikipedia:Immune_system is_a: GO:0008150 ! biological_process -relationship: never_in_taxon NCBITaxon:4895 +property_value: RO:0002161 NCBITaxon:4895 [Term] id: GO:0002377 @@ -3398,9 +3398,9 @@ synonym: "leukocyte immune effector process" EXACT [] is_a: GO:0002252 ! immune effector process intersection_of: GO:0002376 ! immune system process intersection_of: process_has_causal_agent CL:0000738 ! leukocyte -relationship: in_taxon NCBITaxon:7742 {all_only="true"} ! Vertebrata -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: process_has_causal_agent CL:0000738 ! leukocyte +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 {all_only="true"} ! in taxon Vertebrata [Term] id: GO:0002449 @@ -3795,9 +3795,9 @@ def: "Any process that modulates the frequency, rate, or extent of an adaptive i is_a: GO:0002819 ! regulation of adaptive immune response intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0002460 ! adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains -relationship: in_taxon NCBITaxon:7776 {all_only="true"} ! Gnathostomata -relationship: only_in_taxon NCBITaxon:7776 ! Gnathostomata relationship: regulates GO:0002460 ! adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains +relationship: RO:0002160 NCBITaxon:7776 ! only in taxon Gnathostomata +relationship: RO:0002162 NCBITaxon:7776 {all_only="true"} ! in taxon Gnathostomata [Term] id: GO:0002824 @@ -3995,8 +3995,8 @@ namespace: cellular_component def: "A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures." [GOC:dos, GOC:mah, ISBN:0721639976, PMID:19693541, PMID:21421911] xref: Wikipedia:Collagen is_a: GO:0032991 ! protein-containing complex -relationship: in_taxon NCBITaxon:33208 {all_only="true", source="PMID:12382326"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 {source="PMID:12382326"} ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 {source="PMID:12382326"} ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true", source="PMID:12382326"} ! in taxon Metazoa [Term] id: GO:0005587 @@ -4077,8 +4077,8 @@ xref: NIF_Subcellular:sao1702920020 xref: Wikipedia:Cell_nucleus is_a: GO:0043231 ! intracellular membrane-bounded organelle disjoint_from: GO:0005737 ! cytoplasm -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota [Term] id: GO:0005694 @@ -4147,7 +4147,7 @@ subset: goslim_plant xref: NIF_Subcellular:sao585356902 xref: Wikipedia:Lysosome is_a: GO:0000323 ! lytic vacuole -relationship: never_in_taxon NCBITaxon:4751 +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0005766 @@ -4198,10 +4198,10 @@ synonym: "Golgi ribbon" NARROW [] xref: NIF_Subcellular:sao451912436 xref: Wikipedia:Golgi_apparatus is_a: GO:0043231 ! intracellular membrane-bounded organelle -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota relationship: part_of GO:0005737 ! cytoplasm relationship: part_of GO:0012505 ! endomembrane system +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota [Term] id: GO:0005840 @@ -4489,7 +4489,7 @@ namespace: biological_process def: "A vesicle-mediated transport process that results in the engulfment of external particulate material by phagocytes and their delivery to the lysosome. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles." [ISBN:0198506732] xref: Wikipedia:Phagocytosis is_a: GO:0006897 ! endocytosis -relationship: never_in_taxon NCBITaxon:4751 +property_value: RO:0002161 NCBITaxon:4751 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24907" xsd:anyURI [Term] @@ -4518,11 +4518,11 @@ synonym: "type I programmed cell death" NARROW [] xref: Wikipedia:Apoptosis is_a: GO:0012501 ! programmed cell death relationship: ends_with GO:0097194 ! execution phase of apoptosis -relationship: in_taxon NCBITaxon:33154 {all_only="true"} ! Opisthokonta -relationship: never_in_taxon NCBITaxon:2 -relationship: never_in_taxon NCBITaxon:4896 -relationship: only_in_taxon NCBITaxon:33154 ! Opisthokonta +relationship: RO:0002160 NCBITaxon:33154 ! only in taxon Opisthokonta +relationship: RO:0002162 NCBITaxon:33154 {all_only="true"} ! in taxon Opisthokonta relationship: starts_with GO:0097190 ! apoptotic signaling pathway +property_value: RO:0002161 NCBITaxon:2 +property_value: RO:0002161 NCBITaxon:4896 [Term] id: GO:0006921 @@ -4595,8 +4595,8 @@ subset: goslim_generic synonym: "inflammation" BROAD [] xref: Wikipedia:Inflammation is_a: GO:0006952 ! defense response -relationship: in_taxon NCBITaxon:7742 {all_only="true"} ! Vertebrata -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 {all_only="true"} ! in taxon Vertebrata [Term] id: GO:0006955 @@ -5033,8 +5033,8 @@ namespace: biological_process def: "The process whose specific outcome is the progression of an embryo over time, from zygote formation until the end of the embryonic life stage. The end of the embryonic life stage is organism-specific and may be somewhat arbitrary; for mammals it is usually considered to be birth, for insects the hatching of the first instar larva from the eggshell." [GOC:go_curators, GOC:isa_complete, GOC:mtg_sensu] synonym: "embryogenesis" BROAD [] is_a: GO:0009790 ! embryo development -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0009888 @@ -5047,14 +5047,14 @@ xref: Wikipedia:Histogenesis is_a: GO:0048856 ! anatomical structure development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0000479 ! tissue -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: never_in_taxon NCBITaxon:147554 -relationship: never_in_taxon NCBITaxon:33630 -relationship: never_in_taxon NCBITaxon:33682 -relationship: never_in_taxon NCBITaxon:38254 -relationship: never_in_taxon NCBITaxon:4891 -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota relationship: results_in_development_of UBERON:0000479 ! tissue +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota +property_value: RO:0002161 NCBITaxon:147554 +property_value: RO:0002161 NCBITaxon:33630 +property_value: RO:0002161 NCBITaxon:33682 +property_value: RO:0002161 NCBITaxon:38254 +property_value: RO:0002161 NCBITaxon:4891 [Term] id: GO:0009987 @@ -5301,7 +5301,7 @@ namespace: biological_process def: "The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues." [GOC:cjm, GOC:dph, GOC:ems, GOC:pf, Wikipedia:Cell_migration] xref: Wikipedia:Cell_migration is_a: GO:0048870 ! cell motility -relationship: never_in_taxon NCBITaxon:4890 +property_value: RO:0002161 NCBITaxon:4890 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24787" xsd:anyURI [Term] @@ -5573,7 +5573,7 @@ subset: goslim_drosophila subset: goslim_flybase_ribbon xref: Wikipedia:Cell_junction is_a: GO:0110165 ! cellular anatomical entity -relationship: never_in_taxon NCBITaxon:4751 +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0030097 @@ -5640,8 +5640,8 @@ def: "A small subcellular vesicle, surrounded by a membrane, that is formed from comment: Note that the term 'secretory vesicle' is sometimes used in this sense, but can also mean 'transport vesicle ; GO:0030133'. synonym: "secretory vesicle" BROAD [] is_a: GO:0099503 ! secretory vesicle -relationship: never_in_taxon NCBITaxon:4890 relationship: part_of GO:0012505 ! endomembrane system +property_value: RO:0002161 NCBITaxon:4890 [Term] id: GO:0030154 @@ -5843,8 +5843,8 @@ def: "Any process that modulates the frequency, rate or extent of cell migration is_a: GO:2000145 ! regulation of cell motility intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0016477 ! cell migration -relationship: never_in_taxon NCBITaxon:4890 relationship: regulates GO:0016477 ! cell migration +property_value: RO:0002161 NCBITaxon:4890 [Term] id: GO:0030335 @@ -6069,10 +6069,10 @@ subset: goslim_pir synonym: "organismal physiological process" EXACT [] synonym: "single-multicellular organism process" RELATED [] is_a: GO:0008150 ! biological_process -relationship: never_in_taxon NCBITaxon:2 -relationship: never_in_taxon NCBITaxon:2157 -relationship: never_in_taxon NCBITaxon:4896 -relationship: never_in_taxon NCBITaxon:4932 +property_value: RO:0002161 NCBITaxon:2 +property_value: RO:0002161 NCBITaxon:2157 +property_value: RO:0002161 NCBITaxon:4896 +property_value: RO:0002161 NCBITaxon:4932 created_by: jl creation_date: 2012-09-19T16:07:47Z @@ -6300,8 +6300,8 @@ subset: goslim_plant synonym: "growth pattern" RELATED [] synonym: "non-developmental growth" RELATED [GOC:mah] is_a: GO:0008150 ! biological_process -relationship: in_taxon NCBITaxon:131567 {all_only="true"} ! cellular organisms -relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms +relationship: RO:0002160 NCBITaxon:131567 ! only in taxon cellular organisms +relationship: RO:0002162 NCBITaxon:131567 {all_only="true"} ! in taxon cellular organisms [Term] id: GO:0040011 @@ -6311,7 +6311,7 @@ def: "Self-propelled movement of a cell or organism from one location to another subset: goslim_chembl subset: goslim_pir is_a: GO:0008150 ! biological_process -relationship: never_in_taxon NCBITaxon:451864 +property_value: RO:0002161 NCBITaxon:451864 [Term] id: GO:0040012 @@ -6452,8 +6452,8 @@ is_a: GO:0031099 ! regeneration is_a: GO:0048589 ! developmental growth intersection_of: GO:0031099 ! regeneration intersection_of: results_in_maturation_of UBERON:0000479 ! tissue -relationship: never_in_taxon NCBITaxon:4751 relationship: results_in_maturation_of UBERON:0000479 ! tissue +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0042330 @@ -6553,8 +6553,8 @@ name: chordate embryonic development namespace: biological_process def: "The process whose specific outcome is the progression of the embryo over time, from zygote formation through a stage including a notochord and neural tube until birth or egg hatching." [GOC:mtg_sensu] is_a: GO:0009792 ! embryo development ending in birth or egg hatching -relationship: in_taxon NCBITaxon:7711 {all_only="true"} ! Chordata -relationship: only_in_taxon NCBITaxon:7711 ! Chordata +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {all_only="true"} ! in taxon Chordata [Term] id: GO:0043011 @@ -6796,7 +6796,7 @@ synonym: "interspecies interaction" EXACT [] synonym: "interspecies interaction between organisms" EXACT [] synonym: "interspecies interaction with other organisms" EXACT [] is_a: GO:0008150 ! biological_process -relationship: never_in_taxon NCBITaxon:4895 +property_value: RO:0002161 NCBITaxon:4895 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20191" xsd:anyURI [Term] @@ -6854,8 +6854,8 @@ synonym: "synaptic junction" EXACT [] xref: NIF_Subcellular:sao914572699 xref: Wikipedia:Chemical_synapse is_a: GO:0030054 ! cell junction -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0045321 @@ -6870,8 +6870,8 @@ is_a: GO:0002376 ! immune system process intersection_of: GO:0001775 ! cell activation intersection_of: has_primary_input CL:0000738 ! leukocyte relationship: has_primary_input CL:0000738 ! leukocyte -relationship: in_taxon NCBITaxon:7742 {all_only="true"} ! Vertebrata -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 {all_only="true"} ! in taxon Vertebrata [Term] id: GO:0045453 @@ -7385,8 +7385,8 @@ is_a: GO:0003008 ! system process intersection_of: GO:0003008 ! system process intersection_of: has_participant UBERON:0001016 ! nervous system relationship: has_participant UBERON:0001016 ! nervous system -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13824" xsd:anyURI [Term] @@ -7426,9 +7426,9 @@ is_a: GO:0002376 ! immune system process is_a: GO:0016477 ! cell migration intersection_of: GO:0016477 ! cell migration intersection_of: results_in_movement_of CL:0000738 ! leukocyte -relationship: in_taxon NCBITaxon:7742 {all_only="true"} ! Vertebrata -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: results_in_movement_of CL:0000738 ! leukocyte +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 {all_only="true"} ! in taxon Vertebrata [Term] id: GO:0050920 @@ -7746,8 +7746,8 @@ name: collagen-containing extracellular matrix namespace: cellular_component def: "An extracellular matrix consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that provides not only essential physical scaffolding for the cellular constituents but can also initiate crucial biochemical and biomechanical cues required for tissue morphogenesis, differentiation and homeostasis. The components are secreted by cells in the vicinity and form a sheet underlying or overlying cells such as endothelial and epithelial cells." [GOC:BHF, GOC:rph, PMID:21123617] is_a: GO:0031012 ! extracellular matrix -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa created_by: dph creation_date: 2018-04-13T12:47:21Z @@ -8276,9 +8276,9 @@ subset: goslim_synapse is_a: GO:0007267 ! cell-cell signaling intersection_of: GO:0007267 ! cell-cell signaling intersection_of: occurs_in GO:0045202 ! synapse -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa relationship: occurs_in GO:0045202 ! synapse -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0099537 @@ -8579,18 +8579,16 @@ namespace: ncbi_taxonomy xref: GC_ID:1 xref: PMID:15371245 is_a: NCBITaxon:337687 ! Muroidea -property_value: has_rank NCBITaxon:family [Term] id: NCBITaxon:10088 name: Mus namespace: ncbi_taxonomy -synonym: "mice" EXACT OMO:0003003 [] +synonym: "mice" EXACT genbank_common_name [] synonym: "mouse" EXACT OMO:0003003 [] synonym: "Mus" EXACT scientific_name [] xref: GC_ID:1 is_a: NCBITaxon:39107 ! Murinae -property_value: has_rank NCBITaxon:genus [Term] id: NCBITaxon:10090 @@ -8601,7 +8599,6 @@ synonym: "house mouse" EXACT genbank_common_name [] synonym: "mouse" EXACT OMO:0003003 [] xref: GC_ID:1 is_a: NCBITaxon:862507 ! Mus -property_value: has_rank NCBITaxon:species [Term] id: NCBITaxon:117570 @@ -8609,7 +8606,6 @@ name: Teleostomi namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:7776 ! Gnathostomata -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:117571 @@ -8619,7 +8615,6 @@ alt_id: NCBITaxon:40673 synonym: "bony vertebrates" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:117570 ! Teleostomi -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:131567 @@ -8635,7 +8630,6 @@ name: Dipnotetrapodomorpha namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:8287 ! Sarcopterygii -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:1437010 @@ -8646,7 +8640,6 @@ xref: GC_ID:1 xref: PMID:11743200 xref: PMID:11791233 is_a: NCBITaxon:9347 ! Eutheria -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:1963758 @@ -8656,7 +8649,6 @@ synonym: "mice and others" EXACT genbank_common_name [] synonym: "Sciurognathi" RELATED in_part [] xref: GC_ID:1 is_a: NCBITaxon:9989 ! Rodentia -property_value: has_rank NCBITaxon:suborder [Term] id: NCBITaxon:2759 @@ -8673,7 +8665,6 @@ xref: GC_ID:1 xref: PMID:23020233 xref: PMID:30257078 is_a: NCBITaxon:131567 ! cellular organisms -property_value: has_rank NCBITaxon:superkingdom [Term] id: NCBITaxon:314146 @@ -8685,7 +8676,6 @@ xref: PMID:12082125 xref: PMID:12878460 xref: PMID:15522813 is_a: NCBITaxon:1437010 ! Boreoeutheria -property_value: has_rank NCBITaxon:superorder [Term] id: NCBITaxon:314147 @@ -8697,7 +8687,6 @@ xref: PMID:11214319 xref: PMID:12082125 xref: PMID:15522813 is_a: NCBITaxon:314146 ! Euarchontoglires -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:32523 @@ -8706,7 +8695,6 @@ namespace: ncbi_taxonomy synonym: "tetrapods" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:1338369 ! Dipnotetrapodomorpha -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:32524 @@ -8715,7 +8703,6 @@ namespace: ncbi_taxonomy synonym: "amniotes" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:32523 ! Tetrapoda -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:32525 @@ -8724,7 +8711,6 @@ namespace: ncbi_taxonomy synonym: "Theria" EXACT scientific_name [] xref: GC_ID:1 is_a: NCBITaxon:40674 ! Mammalia -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:33154 @@ -8734,7 +8720,6 @@ synonym: "Fungi/Metazoa group" RELATED synonym [] synonym: "opisthokonts" RELATED synonym [] xref: GC_ID:1 is_a: NCBITaxon:2759 ! Eukaryota -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:33208 @@ -8746,7 +8731,6 @@ synonym: "metazoans" EXACT genbank_common_name [] synonym: "multicellular animals" EXACT OMO:0003003 [] xref: GC_ID:1 is_a: NCBITaxon:33154 ! Opisthokonta -property_value: has_rank NCBITaxon:kingdom [Term] id: NCBITaxon:33213 @@ -8754,7 +8738,6 @@ name: Bilateria namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:6072 ! Eumetazoa -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:33511 @@ -8763,7 +8746,6 @@ namespace: ncbi_taxonomy synonym: "deuterostomes" EXACT OMO:0003003 [] xref: GC_ID:1 is_a: NCBITaxon:33213 ! Bilateria -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:337687 @@ -8773,7 +8755,6 @@ xref: GC_ID:1 xref: PMID:15019624 xref: PMID:15371245 is_a: NCBITaxon:1963758 ! Myomorpha -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:39107 @@ -8782,7 +8763,6 @@ namespace: ncbi_taxonomy alt_id: NCBITaxon:109679 xref: GC_ID:1 is_a: NCBITaxon:10066 ! Muridae -property_value: has_rank NCBITaxon:subfamily [Term] id: NCBITaxon:40674 @@ -8792,7 +8772,6 @@ synonym: "mammals" EXACT genbank_common_name [] synonym: "mammals" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:32524 ! Amniota -property_value: has_rank NCBITaxon:class [Term] id: NCBITaxon:6072 @@ -8800,7 +8779,6 @@ name: Eumetazoa namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:33208 ! Metazoa -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:7711 @@ -8810,7 +8788,6 @@ synonym: "chordates" EXACT genbank_common_name [] synonym: "chordates" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:33511 ! Deuterostomia -property_value: has_rank NCBITaxon:phylum [Term] id: NCBITaxon:7742 @@ -8821,7 +8798,6 @@ synonym: "vertebrates" EXACT genbank_common_name [] synonym: "vertebrates" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:89593 ! Craniata -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:7776 @@ -8831,7 +8807,6 @@ synonym: "Gnathostomata" EXACT scientific_name [] synonym: "jawed vertebrates" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:7742 ! Vertebrata -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:8287 @@ -8839,7 +8814,6 @@ name: Sarcopterygii namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:117571 ! Euteleostomi -property_value: has_rank NCBITaxon:superclass [Term] id: NCBITaxon:862507 @@ -8848,7 +8822,6 @@ namespace: ncbi_taxonomy synonym: "Mus" EXACT scientific_name [] xref: GC_ID:1 is_a: NCBITaxon:10088 ! Mus -property_value: has_rank NCBITaxon:subgenus [Term] id: NCBITaxon:89593 @@ -8857,7 +8830,6 @@ namespace: ncbi_taxonomy synonym: "Craniata" EXACT scientific_name [] xref: GC_ID:1 is_a: NCBITaxon:7711 ! Chordata -property_value: has_rank NCBITaxon:subphylum [Term] id: NCBITaxon:9347 @@ -8870,7 +8842,6 @@ synonym: "placentals" EXACT genbank_common_name [] synonym: "placentals" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:32525 ! Theria -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:9989 @@ -8880,7 +8851,6 @@ synonym: "rodent" EXACT genbank_common_name [] synonym: "rodents" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:314147 ! Glires -property_value: has_rank NCBITaxon:order [Term] id: PATO:0000001 @@ -8939,7 +8909,6 @@ subset: value_slim synonym: "ramified" EXACT [] synonym: "ramiform" EXACT [] is_a: PATO:0002009 ! branchiness -property_value: RO:0002604 PATO:0000414 [Term] id: PATO:0000411 @@ -9099,7 +9068,6 @@ def: "A quality inhering in a bearer by virtue of the bearer's lacking complete subset: value_slim synonym: "underdeveloped" RELATED [] is_a: PATO:0000261 ! maturity -property_value: RO:0002604 PATO:0001701 [Term] id: PATO:0001548 @@ -9129,7 +9097,6 @@ comment: This refers to the disposition of the bearer. subset: disposition_slim subset: value_slim is_a: PATO:0001579 ! contractility -property_value: RO:0002604 PATO:0001691 [Term] id: PATO:0001857 @@ -9139,7 +9106,6 @@ def: "A shape quality in a bearer by virtue of the bearer's curving inward." [Wo subset: cell_quality subset: value_slim is_a: PATO:0002005 ! concavity -property_value: RO:0002604 PATO:0001355 [Term] id: PATO:0001873 @@ -9227,7 +9193,6 @@ subset: attribute_slim xref: Image:http\://upload.wikimedia.org/wikipedia/commons/0/06/Convex_polygon_illustration1.png is_a: PATO:0002266 ! 3-D shape relationship: RO:0015011 PATO:0002006 ! has cross section 2-D shape -property_value: RO:0002604 PATO:0002008 [Term] id: PATO:0002009 @@ -9253,7 +9218,6 @@ namespace: quality def: "A concave quality inhering in a bearer by virtue of the bearer's curving inward on both sides or surfaces." [PATOC:GVG] subset: value_slim is_a: PATO:0001857 ! concave -property_value: RO:0002604 PATO:0002040 [Term] id: PATO:0002045 @@ -9265,7 +9229,7 @@ synonym: "dendriform" EXACT [] synonym: "dendroid" EXACT [] synonym: "dendroidal" EXACT [] is_a: PATO:0000402 ! branched -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-02-15T08:11:41Z [Term] @@ -9275,7 +9239,7 @@ namespace: quality def: "A quality inhering in a bearer by virtue of the bearer's having an empty space or cavity within." [url:http\://www.merriam-webster.com/dictionary/hollow] subset: value_slim is_a: PATO:0002014 ! structure, cavities -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-09-18T02:19:20Z [Term] @@ -9287,7 +9251,7 @@ subset: disposition_slim subset: mpath_slim subset: value_slim is_a: PATO:0070045 ! anatomical histological quality -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-10-05T12:05:23Z [Term] @@ -9297,7 +9261,7 @@ namespace: quality def: "A quality inhering in a bearer by virtue of its constitution." [PATOC:GVG] subset: attribute_slim is_a: PATO:0001018 ! physical quality -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-03-15T04:35:27Z [Term] @@ -9306,7 +9270,7 @@ name: 3-D shape namespace: quality def: "A shape that inheres in a 3 dimensional entity." [PATOC:OREGON] is_a: PATO:0000052 ! shape -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-10-05T12:31:16Z [Term] @@ -9319,7 +9283,7 @@ synonym: "tube-shaped" EXACT [] synonym: "tubulate" EXACT [] is_a: PATO:0001873 ! cylindrical is_a: PATO:0002078 ! hollow -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-06-08T06:33:50Z [Term] @@ -9329,7 +9293,7 @@ namespace: quality def: "A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt" [wiktionary:superellipse] synonym: "Lamé curve" EXACT [] is_a: PATO:0002006 ! 2-D shape -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-10-12T12:45:16Z [Term] @@ -9342,7 +9306,7 @@ subset: mpath_slim subset: value_slim synonym: "eosinophilic" EXACT [] is_a: PATO:0070045 ! anatomical histological quality -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2012-12-17T03:01:19Z [Term] @@ -9353,7 +9317,7 @@ def: "A nucleate quality inhering in a bearer by virtue of the bearer's having o subset: mpath_slim subset: value_slim is_a: PATO:0001404 ! nucleate quality -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2013-10-21T05:44:34Z [Term] @@ -9362,7 +9326,7 @@ name: disconnected namespace: quality def: "A structural quality inhering in the bearer by virtue of the bearer consisting of multiple structures lacking any physical connection to each other." [GOC:dos] is_a: PATO:0000141 ! structure -relationship: dc-contributor https://orcid.org/0000-0002-7073-9172 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2014-12-12T08:43:17Z [Term] @@ -9489,7 +9453,6 @@ synonym: "T200" BROAD [PRO:DNx] xref: IUPHARobj:1852 xref: PIRSF:PIRSF002004 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P08575 [Term] id: PR:000001012 @@ -9508,7 +9471,6 @@ synonym: "leukocyte adhesion receptor MO1" EXACT [] synonym: "neutrophil adherence receptor" EXACT [] xref: IUPHARobj:2452 is_a: PR:000001005 ! integrin alpha with A domain -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P11215 [Term] id: PR:000001013 @@ -9525,7 +9487,6 @@ synonym: "leukocyte adhesion glycoprotein p150,95 alpha chain" EXACT [] synonym: "leukocyte adhesion receptor p150,95" EXACT [] xref: IUPHARobj:2454 is_a: PR:000001005 ! integrin alpha with A domain -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P20702 [Term] id: PR:000001018 @@ -9581,7 +9542,6 @@ synonym: "NCAM-1" EXACT [] synonym: "NCAM1" EXACT PRO-short-label [PRO:DNx] xref: IUPHARobj:2769 is_a: PR:000001023 ! neural cell adhesion molecule NCAM -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P13591 [Term] id: PR:000001083 @@ -9618,7 +9578,6 @@ synonym: "MAL" RELATED Gene-based [] synonym: "T-cell surface glycoprotein Lyt-2" EXACT [] synonym: "T-lymphocyte differentiation antigen T8/Leu-2" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P01732 [Term] id: PR:000001094 @@ -9674,7 +9633,6 @@ synonym: "RANTES-R" EXACT [] synonym: "SCYAR1" RELATED Gene-based [] xref: IUPHARobj:58 is_a: PR:000001197 ! chemokine receptor CCR1/3/1L -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P32246 [Term] id: PR:000001255 @@ -9696,7 +9654,6 @@ synonym: "macrophage inflammatory protein 1-alpha receptor-like 2" EXACT [] synonym: "MIP-1 alpha RL2" EXACT [] xref: IUPHARobj:60 is_a: PR:000001197 ! chemokine receptor CCR1/3/1L -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P51677 [Term] id: PR:000001281 @@ -9779,7 +9736,6 @@ synonym: "CEACAM8" EXACT PRO-short-label [PRO:DNx] synonym: "CGM6" RELATED Gene-based [] synonym: "non-specific cross-reacting antigen NCA-95" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P31997 [Term] id: PR:000001343 @@ -9816,7 +9772,6 @@ synonym: "PDNP3" RELATED Gene-based [] synonym: "phosphodiesterase I beta" EXACT [] synonym: "phosphodiesterase I/nucleotide pyrophosphatase 3" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:O14638 [Term] id: PR:000001355 @@ -9855,7 +9810,6 @@ synonym: "NIM-R5 antigen" EXACT [] synonym: "T10" EXACT [] xref: IUPHARobj:2766 is_a: PR:000001281 ! ADP-ribosyl cyclase -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P28907 [Term] id: PR:000001444 @@ -9869,7 +9823,6 @@ synonym: "CDH5" EXACT PRO-short-label [PRO:DNx] synonym: "vascular endothelial cadherin" EXACT [] synonym: "VE-cadherin" EXACT [] is_a: PR:000001327 ! cadherin -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P33151 [Term] id: PR:000001479 @@ -9921,7 +9874,6 @@ synonym: "lymphocyte antigen 1" EXACT [] synonym: "lymphocyte antigen T1/Leu-1" EXACT [] synonym: "Lyt-1" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P06127 [Term] id: PR:000001850 @@ -9937,7 +9889,6 @@ synonym: "CTSO" RELATED Gene-based [] synonym: "CTSO2" RELATED Gene-based [] xref: IUPHARobj:2350 is_a: PR:000040662 ! cathepsin-like protease -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P43235 [Term] id: PR:000001861 @@ -9983,7 +9934,6 @@ synonym: "IL5RA" EXACT PRO-short-label [PRO:DNx] xref: IUPHARobj:1706 xref: PIRSF:PIRSF018419 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q01344 [Term] id: PR:000001869 @@ -10001,7 +9951,6 @@ synonym: "IL7R" EXACT PRO-short-label [PRO:DNx] xref: IUPHARobj:1698 xref: PIRSF:PIRSF001960 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P16871 [Term] id: PR:000001874 @@ -10029,7 +9978,6 @@ synonym: "sialophorin" EXACT [] synonym: "SPN" EXACT PRO-short-label [PRO:DNx] xref: PIRSF:PIRSF001994 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P16150 [Term] id: PR:000001889 @@ -10064,7 +10012,6 @@ synonym: "skin fibroblast elastase" EXACT [] xref: IUPHARobj:1611 xref: PIRSF:PIRSF501074 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P08473 [Term] id: PR:000001903 @@ -10077,7 +10024,6 @@ synonym: "BSAP" EXACT [] synonym: "Pax-5" RELATED Gene-based [] synonym: "PAX5" EXACT PRO-short-label [PRO:DNx] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q02548 [Term] id: PR:000001932 @@ -10096,7 +10042,6 @@ synonym: "R13-Ag" EXACT [] synonym: "small cell lung carcinoma cluster 4 antigen" EXACT [] synonym: "X62 heat stable antigen" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P25063 [Term] id: PR:000001935 @@ -10111,7 +10056,6 @@ synonym: "Synd-1" RELATED Gene-based [] synonym: "SYND1" EXACT [] xref: PIRSF:PIRSF015854 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P18827 [Term] id: PR:000001937 @@ -10128,7 +10072,6 @@ synonym: "TrATPase" EXACT [] synonym: "type 5 acid phosphatase" EXACT [] xref: PIRSF:PIRSF000898 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P13686 [Term] id: PR:000001944 @@ -10142,7 +10085,6 @@ synonym: "Sfpi-1" RELATED Gene-based [] synonym: "Sfpi1" RELATED Gene-based [] synonym: "SPI1" EXACT PRO-short-label [PRO:DNx] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P17947 [Term] id: PR:000001945 @@ -10159,7 +10101,6 @@ synonym: "TFRC" EXACT PRO-short-label [PRO:DNx] synonym: "TR" RELATED [] synonym: "Trfr" RELATED Gene-based [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P02786 [Term] id: PR:000001950 @@ -10193,7 +10134,6 @@ synonym: "TNFRSF11A" EXACT PRO-short-label [PRO:DNx] xref: IUPHARobj:1881 xref: PIRSF:PIRSF038806 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q9Y6Q6 [Term] id: PR:000001963 @@ -10226,7 +10166,6 @@ synonym: "UPAR" RELATED Gene-based [] synonym: "uPAR" EXACT [] xref: PIRSF:PIRSF002022 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q03405 [Term] id: PR:000001971 @@ -10255,7 +10194,6 @@ synonym: "proto-oncogene c-Fms" EXACT [] xref: IUPHARobj:1806 xref: PIRSF:PIRSF500947 is_a: PR:000001810 ! CSF-1/PDGF receptor-type tyrosine-protein kinase -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P07333 [Term] id: PR:000002065 @@ -10291,7 +10229,6 @@ synonym: "VEGFR-2" EXACT [] synonym: "VEGFR2" RELATED Gene-based [] xref: IUPHARobj:1813 is_a: PR:000001971 ! vascular endothelial growth factor receptor -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P35968 [Term] id: PR:000002976 @@ -10361,7 +10298,6 @@ synonym: "RAG1" EXACT PRO-short-label [PRO:DNx] synonym: "RING finger protein 74" EXACT [] synonym: "RNF74" RELATED Gene-based [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P15918 [Term] id: PR:000003460 @@ -10372,7 +10308,6 @@ comment: Category=gene. Requested by=CL. synonym: "RAG-2" EXACT [] synonym: "RAG2" EXACT PRO-short-label [PRO:DNx] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P55895 [Term] id: PR:000005178 @@ -10405,7 +10340,6 @@ synonym: "C/EBP alpha" EXACT [] synonym: "CEBP" RELATED Gene-based [] synonym: "CEBPA" EXACT PRO-short-label [PRO:DNx] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P49715 [Term] id: PR:000006169 @@ -10433,7 +10367,6 @@ synonym: "terminal addition enzyme" EXACT [] synonym: "terminal deoxynucleotidyltransferase" EXACT [] synonym: "terminal transferase" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P04053 [Term] id: PR:000007431 @@ -10448,7 +10381,6 @@ synonym: "FcERI" RELATED [] synonym: "IgE Fc receptor subunit alpha" EXACT [] xref: IUPHARobj:2933 is_a: PR:000001355 ! immunoglobulin gamma Fc receptor II/III/IV -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P12319 [Term] id: PR:000007597 @@ -10463,7 +10395,6 @@ synonym: "G0S7" RELATED Gene-based [] synonym: "proto-oncogene protein c-fos" EXACT [] synonym: "transcription factor AP-1 subunit c-Fos" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P01100 [Term] id: PR:000007857 @@ -10480,7 +10411,6 @@ synonym: "GF-1" RELATED [] synonym: "GF1" RELATED Gene-based [] synonym: "NF-E1 DNA-binding protein" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P15976 [Term] id: PR:000007858 @@ -10491,7 +10421,6 @@ comment: Category=gene. Requested by=CL. synonym: "GATA-binding protein 2" EXACT [] synonym: "GATA2" EXACT PRO-short-label [PRO:DNx] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P23769 [Term] id: PR:000009143 @@ -10505,7 +10434,6 @@ synonym: "ITGB7" EXACT PRO-short-label [PRO:DNx] synonym: "M290 IEL antigen" EXACT [] xref: IUPHARobj:2461 is_a: PR:000001861 ! integrin beta -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P26010 [Term] id: PR:000011178 @@ -10522,7 +10450,6 @@ synonym: "NFKB2" EXACT PRO-short-label [PRO:DNx] synonym: "nuclear factor of kappa light polypeptide gene enhancer in B-cells 2" EXACT [] synonym: "oncogene Lyt-10" EXACT [] is_a: PR:000001753 ! transcription factor NF-kappa-B subunit -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q00653 [Term] id: PR:000014841 @@ -10536,7 +10463,6 @@ synonym: "SHH" EXACT PRO-short-label [PRO:DNx] synonym: "Shh unprocessed N-terminal signaling and C-terminal autoprocessing domains" EXACT [] synonym: "ShhNC" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q15465 [Term] id: PR:000016043 @@ -10554,7 +10480,6 @@ synonym: "TAL-1" EXACT [] synonym: "TAL1" EXACT PRO-short-label [PRO:DNx] synonym: "TCL5" RELATED Gene-based [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P17542 [Term] id: PR:000016401 @@ -10570,7 +10495,6 @@ synonym: "p24gamma1" EXACT [] synonym: "putative T1/ST2 receptor-binding protein" EXACT [] synonym: "TMED1" EXACT PRO-short-label [PRO:DNx] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q13445 [Term] id: PR:000025796 @@ -10588,8 +10512,8 @@ def: "A protein that is encoded in the genome of Mus musculus." [PRO:DAN] synonym: "mouse protein" EXACT PRO-short-label [PRO:DAN] is_a: PR:000036194 ! eukaryotic protein intersection_of: PR:000000001 ! protein -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus -relationship: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus +relationship: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:000030035 @@ -10614,8 +10538,8 @@ def: "A protein that is encoded in the genome of some Eukaryota." [PRO:DAN] synonym: "Eukaryota protein" EXACT [PRO:DAN] is_a: PR:000000001 ! protein intersection_of: PR:000000001 ! protein -intersection_of: only_in_taxon NCBITaxon:2759 ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +intersection_of: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota [Term] id: PR:000040662 @@ -10626,7 +10550,7 @@ comment: Category=family. synonym: "cathepsin" NARROW [PRO:DAN] synonym: "fam:CTS" EXACT PRO-short-label [PRO:DNx] is_a: PR:000036194 ! eukaryotic protein -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa [Term] id: PR:000050567 @@ -10652,9 +10576,9 @@ subset: common_anatomy subset: upper_level xref: BFO:0000003 disjoint_from: UBERON:0001062 ! anatomical entity -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000025 @@ -10666,11 +10590,9 @@ synonym: "duct" NARROW [] xref: galen:Tube is_a: UBERON:0004111 ! anatomical conduit intersection_of: UBERON:0004111 ! anatomical conduit -intersection_of: has_quality PATO:0002299 ! tubular +intersection_of: RO:0000086 PATO:0002299 ! has quality tubular relationship: has_part UBERON:0013522 ! subdivision of tube -relationship: has_quality PATO:0002299 ! tubular -property_value: IAO:0000232 "not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts)" xsd:string -property_value: UBPROP:0000007 "tubular" xsd:string +relationship: RO:0000086 PATO:0002299 ! has quality tubular [Term] id: UBERON:0000055 @@ -10682,7 +10604,7 @@ subset: human_reference_atlas subset: pheno_slim is_a: UBERON:0004111 ! anatomical conduit relationship: channel_for UBERON:0006314 ! bodily fluid -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000060 @@ -10694,13 +10616,11 @@ subset: upper_level synonym: "organ wall" RELATED [FMA:82482] synonym: "wall" BROAD [] synonym: "wall of organ" EXACT [FMA:82482] -xref: EMAPA:25036 xref: FMA:82482 xref: galen:Wall is_a: UBERON:0000064 ! organ part relationship: adjacent_to UBERON:0002553 ! anatomical cavity relationship: has_part UBERON:0004923 ! organ component layer -property_value: UBPROP:0000012 "in FMA, serosa is a wall" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0000061 @@ -10717,7 +10637,6 @@ xref: BILA:0000003 xref: CARO:0000003 xref: EHDAA2:0003003 xref: EMAPA:0 -xref: FBbt:00007001 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:305751 xref: FMA:67135 xref: GAID:781 @@ -10732,10 +10651,10 @@ xref: VHOG:0001759 xref: XAO:0003000 xref: ZFA:0000037 is_a: UBERON:0000465 ! material anatomical entity -relationship: existence_ends_during_or_before UBERON:0000071 ! death stage -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0002497 UBERON:0000071 ! existence ends during or before death stage +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000062 @@ -10762,14 +10681,12 @@ xref: Wikipedia:Organ_(anatomy) is_a: UBERON:0010000 ! multicellular anatomical structure disjoint_from: UBERON:0034921 ! multi organ part structure relationship: capable_of GO:0008150 ! biological_process -relationship: has_boundary UBERON:0006984 ! anatomical surface -relationship: never_in_taxon NCBITaxon:110815 {source="Wikipedia"} relationship: part_of UBERON:0000467 ! anatomical system -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: UBPROP:0000001 "Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." xsd:string {source="GO:0048513"} -property_value: UBPROP:0000012 "CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4" xsd:string +relationship: RO:0002002 UBERON:0006984 ! has 2D boundary anatomical surface +property_value: RO:0002161 NCBITaxon:110815 {source="Wikipedia"} +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000064 @@ -10790,10 +10707,9 @@ xref: SCTID:113343008 xref: SCTID:91717005 is_a: UBERON:0010000 ! multicellular anatomical structure relationship: part_of UBERON:0000062 ! organ -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: IAO:0000232 "currently defined in a very broad sense, may be replaced by more specific classes in the future" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000066 @@ -10842,7 +10758,7 @@ is_a: UBERON:0000105 ! life cycle stage disjoint_from: UBERON:0000092 ! post-embryonic stage relationship: precedes UBERON:0000066 ! fully formed stage relationship: precedes UBERON:0000092 ! post-embryonic stage -relationship: simultaneous_with GO:0009790 ! embryo development +relationship: RO:0002082 GO:0009790 ! simultaneous with embryo development [Term] id: UBERON:0000071 @@ -10855,11 +10771,10 @@ xref: XAO:0000437 xref: XtroDO:0000085 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage -relationship: ends UBERON:0000104 ! life cycle -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: UBPROP:0000012 "ncit:Death is an outcome" xsd:string {external_ontology="ncit"} +relationship: RO:0002229 UBERON:0000104 ! ends life cycle +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000075 @@ -10876,9 +10791,9 @@ xref: NCIT:C34076 xref: SCTID:118966000 xref: UMLS:C1519343 {source="ncithesaurus:Skeletal_System_Part"} is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision -relationship: composed_primarily_of UBERON:0004765 ! skeletal element -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0001434 ! skeletal system +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002473 UBERON:0004765 ! composed primarily of skeletal element [Term] id: UBERON:0000092 @@ -10898,9 +10813,8 @@ xref: WBls:0000103 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage relationship: preceded_by UBERON:0000068 ! embryo stage -relationship: simultaneous_with GO:0009791 ! post-embryonic development +relationship: RO:0002082 GO:0009791 ! simultaneous with post-embryonic development property_value: seeAlso "https://github.com/obophenotype/uberon/issues/344" xsd:anyURI -property_value: UBPROP:0000008 "In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)" xsd:string [Term] id: UBERON:0000104 @@ -10922,9 +10836,9 @@ is_a: BFO:0000003 ! occurrent is_a: UBERON:0000000 ! processual entity relationship: ends_with UBERON:0000071 ! death stage relationship: has_part UBERON:0000105 ! life cycle stage -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 property_value: seeAlso "https://github.com/obophenotype/uberon/issues/532" xsd:anyURI [Term] @@ -10953,12 +10867,10 @@ xref: ZFS:0000000 xref: ZFS:0100000 is_a: UBERON:0000000 ! processual entity relationship: part_of UBERON:0000104 ! life cycle -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: editor_note "this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here" xsd:string -property_value: UBPROP:0000012 "the WBls class 'all stages' belongs here as it is the superclass of other WBls stages" xsd:string -property_value: UBPROP:0000012 "we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage" xsd:string +property_value: IAO:0000116 "this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000106 @@ -10978,7 +10890,6 @@ xref: BILS:0000106 xref: EFO:0001322 xref: EHDAA:27 xref: FBdv:00005288 -xref: IDOMAL:0000302 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C12601 xref: PdumDv:0000100 xref: VHOG:0000745 @@ -10988,9 +10899,8 @@ xref: ZFS:0000001 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage -relationship: seeAlso EMAPA:16033 -relationship: starts UBERON:0000104 ! life cycle -property_value: UBPROP:0000003 "As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000745", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107", source="http://bgee.unil.ch/"} +relationship: RO:0002223 UBERON:0000104 ! starts life cycle +property_value: seeAlso EMAPA:16033 [Term] id: UBERON:0000107 @@ -11013,10 +10923,10 @@ xref: ZFS:0000046 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage intersection_of: UBERON:0000105 ! life cycle stage -intersection_of: simultaneous_with GO:0040016 ! embryonic cleavage +intersection_of: RO:0002082 GO:0040016 ! simultaneous with embryonic cleavage relationship: immediately_preceded_by UBERON:0000106 ! zygote stage relationship: part_of UBERON:0000068 ! embryo stage -relationship: simultaneous_with GO:0040016 ! embryonic cleavage +relationship: RO:0002082 GO:0040016 ! simultaneous with embryonic cleavage [Term] id: UBERON:0000108 @@ -11040,8 +10950,8 @@ is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000107 ! cleavage stage -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI -property_value: editor_note "consider adding a preceding stage 'morula stage' as part of cleavage" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI +property_value: IAO:0000116 "consider adding a preceding stage 'morula stage' as part of cleavage" xsd:string [Term] id: UBERON:0000109 @@ -11068,10 +10978,10 @@ xref: XAO:1000005 xref: ZFS:0000047 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000108 {source="BILS"} ! blastula stage -relationship: simultaneous_with GO:0007369 ! gastrulation +relationship: RO:0002082 GO:0007369 ! simultaneous with gastrulation +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0000110 @@ -11085,14 +10995,12 @@ xref: MmusDv:0000017 xref: XAO:1000006 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000109 ! gastrula stage -relationship: simultaneous_with GO:0001841 ! neural tube formation -property_value: RO:0002174 NCBITaxon:7955 +relationship: RO:0002082 GO:0001841 ! simultaneous with neural tube formation +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa property_value: seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/343" xsd:anyURI -property_value: UBPROP:0000008 "In zebrafish, the times of neurulation and segmentation overlap so extensively there is no distinct neurula period of development, such as occurs largely before segmentation in amphibian embryos." xsd:string [Term] id: UBERON:0000111 @@ -11109,9 +11017,9 @@ xref: OGES:000032 xref: Wikipedia:Organogenesis is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000068 ! embryo stage -relationship: simultaneous_with GO:0048513 ! animal organ development +relationship: RO:0002082 GO:0048513 ! simultaneous with animal organ development +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa property_value: seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/533" xsd:anyURI @@ -11147,7 +11055,6 @@ xref: EFO:0000825 xref: EHDAA2:0001326 xref: EHDAA:542 xref: EMAPA:16262 -xref: FBbt:00003126 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:49184 xref: GAID:75 xref: galen:Mouth @@ -11168,19 +11075,11 @@ xref: Wikipedia:Mouth xref: XAO:0003029 xref: ZFA:0000547 xref: ZFA:0000590 -is_a: UBERON:0004921 {notes="the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts"} ! subdivision of digestive tract -intersection_of: UBERON:0004921 ! subdivision of digestive tract -intersection_of: proximalmost_part_of UBERON:0001555 ! digestive tract -relationship: develops_from UBERON:0035804 ! future mouth -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: proximalmost_part_of UBERON:0001555 ! digestive tract -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI +is_a: UBERON:0004921 ! subdivision of digestive tract +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002202 UBERON:0035804 ! develops from future mouth +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/661" xsd:anyURI -property_value: UBPROP:0000001 "Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010355", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000812", ontology="VHOG", source="DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "oral" xsd:string -property_value: UBPROP:0000011 "some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives" xsd:string -property_value: UBPROP:0000012 "in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0000178 @@ -11221,15 +11120,10 @@ is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000179 ! haemolymphatic fluid relationship: has_part CL:0000232 {source="CL:tm"} ! erythrocyte relationship: has_part UBERON:0001969 ! blood plasma -relationship: immediate_transformation_of UBERON:0006596 {source="Bgee:AN"} ! presumptive blood -relationship: located_in UBERON:0002049 {source="https://github.com/obophenotype/uberon/issues/1330"} ! vasculature relationship: part_of UBERON:0002390 ! hematopoietic system -relationship: present_in_taxon NCBITaxon:9606 -property_value: IAO:0000232 "This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid." xsd:string -property_value: UBPROP:0000001 "A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000007", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000046", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000002 "relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000046", ontology="AAO"} -property_value: UBPROP:0000003 "Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000224", ontology="VHOG", source="DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006) ", source="http://bgee.unil.ch/"} +relationship: RO:0001025 UBERON:0002049 {source="https://github.com/obophenotype/uberon/issues/1330"} ! located in vasculature +relationship: RO:0002495 UBERON:0006596 {source="Bgee:AN"} ! immediate transformation of presumptive blood +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000179 @@ -11242,9 +11136,9 @@ xref: CARO:0000081 is_a: UBERON:0006314 ! bodily fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: part_of UBERON:0002193 ! hemolymphoid system -relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0002193 ! hemolymphoid system +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 creation_date: 2009-04-08T04:38:19Z [Term] @@ -11264,11 +11158,11 @@ xref: OGEM:000006 xref: Wikipedia:Blastula is_a: UBERON:0000922 ! embryo intersection_of: UBERON:0000468 ! multicellular organism -intersection_of: existence_starts_and_ends_during UBERON:0000108 ! blastula stage -relationship: develops_from UBERON:0007010 ! cleaving embryo -relationship: existence_starts_and_ends_during UBERON:0000108 ! blastula stage -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI -property_value: editor_note "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" xsd:string +intersection_of: RO:0002491 UBERON:0000108 ! existence starts and ends during blastula stage +relationship: RO:0002202 UBERON:0007010 ! develops from cleaving embryo +relationship: RO:0002491 UBERON:0000108 ! existence starts and ends during blastula stage +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI +property_value: IAO:0000116 "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" xsd:string [Term] id: UBERON:0000383 @@ -11291,7 +11185,6 @@ xref: BILA:0000088 xref: BTO:0001369 xref: BTO:0001485 xref: EFO:0000801 -xref: EMAPA:35578 xref: FMA:72954 xref: MA:0002888 xref: MAT:0000025 @@ -11300,15 +11193,13 @@ xref: VSAO:0000033 xref: XAO:0004042 is_a: UBERON:0011216 ! organ system subdivision intersection_of: UBERON:0011216 ! organ system subdivision -intersection_of: composed_primarily_of UBERON:0001015 ! musculature +intersection_of: RO:0002473 UBERON:0001015 ! composed primarily of musculature relationship: capable_of GO:0003012 ! muscle system process -relationship: composed_primarily_of UBERON:0001015 ! musculature -relationship: never_in_taxon NCBITaxon:6040 -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: present_in_taxon NCBITaxon:9606 -property_value: editor_note "consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77" xsd:string -property_value: UBPROP:0000001 "Anatomical system that consists of the muscles of the body.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000033", ontology="VSAO", source="VSAO:curator"} -property_value: UBPROP:0000012 "we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA" xsd:string {external_ontology="MA"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002473 UBERON:0001015 ! composed primarily of musculature +property_value: IAO:0000116 "consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77" xsd:string +property_value: RO:0002161 NCBITaxon:6040 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000463 @@ -11330,7 +11221,6 @@ xref: CALOHA:TS-2101 xref: CARO:0000004 xref: EHDAA2:0003004 xref: EMAPA:35178 -xref: FBbt:00007019 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9669 xref: galen:BodySubstance xref: HAO:0000004 @@ -11343,11 +11233,11 @@ xref: VHOG:0001726 xref: XAO:0004001 xref: ZFA:0001487 is_a: UBERON:0000465 ! material anatomical entity -relationship: has_quality PATO:0002198 ! quality of a substance -relationship: part_of UBERON:0000468 {notes="this relationship may be too strong and may be weakened in future"} ! multicellular organism -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: part_of UBERON:0000468 ! multicellular organism +relationship: RO:0000086 PATO:0002198 ! has quality quality of a substance +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000464 @@ -11365,7 +11255,6 @@ xref: AEO:0000005 xref: BILA:0000005 xref: CARO:0000005 xref: EHDAA2:0003005 -xref: FBbt:00007017 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:5897 xref: HAO:0000005 xref: NCIT:C94478 @@ -11376,10 +11265,10 @@ xref: VHOG:0001728 xref: XAO:0003190 xref: ZFA:0001643 is_a: UBERON:0000466 ! immaterial anatomical entity -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -relationship: surrounded_by UBERON:0000061 ! anatomical structure +relationship: RO:0002219 UBERON:0000061 ! surrounded by anatomical structure +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000465 @@ -11393,7 +11282,6 @@ xref: AEO:0000006 xref: BILA:0000006 xref: CARO:0000006 xref: EHDAA2:0003006 -xref: FBbt:00007016 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67165 xref: HAO:0000006 xref: TAO:0001836 @@ -11402,9 +11290,9 @@ xref: VHOG:0001721 is_a: BFO:0000040 ! material entity is_a: UBERON:0001062 ! anatomical entity disjoint_from: UBERON:0000466 ! immaterial anatomical entity -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000466 @@ -11419,7 +11307,6 @@ xref: AEO:0000007 xref: BILA:0000007 xref: CARO:0000007 xref: EHDAA2:0003007 -xref: FBbt:00007015 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67112 xref: HAO:0000007 xref: TAO:0001835 @@ -11427,9 +11314,9 @@ xref: TGMA:0001827 xref: VHOG:0001727 is_a: BFO:0000141 ! immaterial entity is_a: UBERON:0001062 ! anatomical entity -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000467 @@ -11457,11 +11344,9 @@ xref: EHDAA2:0003011 xref: EHDAA:392 xref: EMAPA:16103 xref: EV:0100000 -xref: FBbt:00004856 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7149 xref: galen:AnatomicalSystem xref: HAO:0000011 -xref: IDOMAL:0002460 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: MA:0000003 xref: NCIT:C12919 xref: SCTID:278195005 @@ -11477,11 +11362,11 @@ xref: ZFA:0001439 is_a: UBERON:0000061 ! anatomical structure relationship: has_part UBERON:0000062 ! organ relationship: part_of UBERON:0000468 ! multicellular organism -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -relationship: present_in_taxon NCBITaxon:9606 -relationship: seeAlso EHDAA2:0001330 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:9606 +property_value: seeAlso EHDAA2:0001330 [Term] id: UBERON:0000468 @@ -11512,7 +11397,6 @@ xref: EHDAA2:0003191 xref: EHDAA:1 xref: EMAPA:25765 xref: EV:0100016 -xref: FBbt:00000001 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:256135 xref: galen:Organism xref: HAO:0000012 @@ -11528,11 +11412,10 @@ xref: Wikipedia:Multi-cellular_organism xref: XAO:0003004 xref: ZFA:0001094 is_a: UBERON:0010000 ! multicellular anatomical structure -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: editor_note "TODO - split body and mc organism? body continues after death stage" xsd:string -property_value: UBPROP:0000007 "organismal" xsd:string +property_value: IAO:0000116 "TODO - split body and mc organism? body continues after death stage" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000475 @@ -11557,7 +11440,6 @@ xref: CARO:0000032 xref: EFO:0000808 xref: EHDAA2:0003032 xref: EMAPA:36031 -xref: FBbt:00007009 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7153 xref: galen:BodyPart xref: HAO:0000032 @@ -11575,10 +11457,10 @@ xref: XAO:0003013 xref: ZFA:0001308 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure relationship: part_of UBERON:0000468 ! multicellular organism -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: editor_note "Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency" xsd:string +property_value: IAO:0000116 "Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000476 @@ -11593,7 +11475,6 @@ xref: AEO:0000040 xref: BILA:0000040 xref: CARO:0000040 xref: EHDAA2:0003040 -xref: FBbt:00007013 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:63863 xref: HAO:0000040 xref: TAO:0000382 @@ -11602,9 +11483,9 @@ xref: XAO:0003162 xref: ZFA:0000382 is_a: UBERON:0000061 ! anatomical structure disjoint_from: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000477 @@ -11613,12 +11494,11 @@ namespace: uberon def: "Anatomical group whose component anatomical structures lie in close proximity to each other." [FBbt:00007277] subset: common_anatomy subset: upper_level -xref: FBbt:00007277 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: VHOG:0001737 is_a: UBERON:0034923 ! disconnected anatomical group -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000479 @@ -11640,7 +11520,6 @@ xref: CALOHA:TS-2090 xref: CARO:0000043 xref: EHDAA2:0003043 xref: EMAPA:35868 -xref: FBbt:00007003 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9637 xref: galen:Tissue xref: HAO:0000043 @@ -11657,10 +11536,10 @@ xref: ZFA:0001477 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure relationship: has_part GO:0031012 ! extracellular matrix relationship: part_of UBERON:0000468 ! multicellular organism -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: editor_note "changed label and definition to reflect CARO2" xsd:string +property_value: IAO:0000116 "changed label and definition to reflect CARO2" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000481 @@ -11675,7 +11554,6 @@ xref: AEO:0000055 xref: BILA:0000055 xref: CARO:0000055 xref: EHDAA2:0003055 -xref: FBbt:00007010 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: HAO:0000055 xref: TAO:0001488 xref: TGMA:0001847 @@ -11684,9 +11562,9 @@ xref: XAO:0003037 xref: ZFA:0001488 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure relationship: has_part UBERON:0000479 ! tissue -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000483 @@ -11708,7 +11586,6 @@ xref: CALOHA:TS-0288 xref: CARO:0000066 xref: EHDAA2:0003066 xref: EMAPA:32738 -xref: FBbt:00007005 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9639 xref: GAID:402 xref: HAO:0000066 @@ -11725,14 +11602,12 @@ xref: ZFA:0001486 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue -intersection_of: composed_primarily_of CL:0000066 ! epithelial cell -relationship: composed_primarily_of CL:0000066 ! epithelial cell +intersection_of: RO:0002473 CL:0000066 ! composed primarily of epithelial cell relationship: has_part GO:0005911 ! cell-cell junction relationship: has_part UBERON:0005769 ! basement membrane of epithelium -relationship: only_in_taxon NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! Metazoa -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI -property_value: UBPROP:0000003 "The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000387", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.59", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "epithelial" xsd:string +relationship: RO:0002160 NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! only in taxon Metazoa +relationship: RO:0002473 CL:0000066 ! composed primarily of epithelial cell +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI [Term] id: UBERON:0000487 @@ -11761,8 +11636,7 @@ is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0006914 ! squamous epithelium intersection_of: UBERON:0000490 ! unilaminar epithelium intersection_of: has_part CL:0000076 ! squamous epithelial cell -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Unilaminar epithelium that consists of a single layer of squamous cells.[CARO]" xsd:string {date_retrieved="2012-06-20", external_class="CARO:0000070", ontology="CARO", source="FMA:45565", source="http://orcid.org/0000-0001-9114-8737"} +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI [Term] id: UBERON:0000490 @@ -11787,8 +11661,7 @@ xref: UMLS:C0682574 {source="ncithesaurus:Simple_Epithelium"} xref: XAO:0004007 xref: ZFA:0001495 is_a: UBERON:0000483 ! epithelium -property_value: editor_note "consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable" xsd:string -property_value: UBPROP:0000001 "Epithelium that consists of a single layer of epithelial cells.[CARO]" xsd:string {date_retrieved="2012-06-20", external_class="CARO:0000073", ontology="CARO", source="FMA:45561", source="http://orcid.org/0000-0001-9114-8737"} +property_value: IAO:0000116 "consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable" xsd:string [Term] id: UBERON:0000915 @@ -11808,12 +11681,8 @@ xref: Wikipedia:Thorax is_a: UBERON:0009569 {source="FMA"} ! subdivision of trunk is_a: UBERON:0011676 ! subdivision of organism along main body axis intersection_of: UBERON:0011676 ! subdivision of organism along main body axis -intersection_of: has_skeleton UBERON:0014477 ! thoracic skeleton -relationship: has_skeleton UBERON:0014477 ! thoracic skeleton -property_value: IAO:0000232 "note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest" xsd:string -property_value: RO:0002171 UBERON:0000026 -property_value: RO:0002171 UBERON:0000033 -property_value: RO:0002171 UBERON:0002417 +intersection_of: RO:0002551 UBERON:0014477 ! has skeleton thoracic skeleton +relationship: RO:0002551 UBERON:0014477 ! has skeleton thoracic skeleton [Term] id: UBERON:0000922 @@ -11838,11 +11707,9 @@ xref: EHDAA2:0000002 xref: EHDAA2_RETIRED:0003236 xref: EHDAA:38 xref: EMAPA:16039 -xref: FBbt:00000052 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69068 xref: GAID:963 xref: http://neurolex.org/wiki/Category\:Embryonic_organism -xref: IDOMAL:0000646 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: MAT:0000226 xref: MESH:D004622 xref: MIAA:0000019 @@ -11856,14 +11723,12 @@ xref: XAO:0000113 xref: ZFA:0000103 is_a: UBERON:0000468 ! multicellular organism intersection_of: UBERON:0000468 ! multicellular organism -intersection_of: existence_ends_with UBERON:0000068 ! embryo stage -intersection_of: existence_starts_with UBERON:0000068 ! embryo stage -relationship: existence_ends_with UBERON:0000068 ! embryo stage -relationship: existence_starts_with UBERON:0000068 ! embryo stage -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" xsd:anyURI +intersection_of: RO:0002489 UBERON:0000068 ! existence starts with embryo stage +intersection_of: RO:0002493 UBERON:0000068 ! existence ends with embryo stage +relationship: RO:0002489 UBERON:0000068 ! existence starts with embryo stage +relationship: RO:0002493 UBERON:0000068 ! existence ends with embryo stage +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/503" xsd:anyURI -property_value: UBPROP:0000007 "embryonic" xsd:string -property_value: UBPROP:0000012 "Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo" xsd:string {external_ontology="ZFA"} [Term] id: UBERON:0000923 @@ -11882,7 +11747,6 @@ xref: AAO:0000480 xref: BILA:0000035 xref: BTO:0000556 xref: EMAPA:36033 -xref: FBbt:00000110 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69069 xref: GAID:1303 xref: MESH:D005855 @@ -11896,8 +11760,7 @@ xref: Wikipedia:Germ_layer xref: XAO:0003011 xref: ZFA:0001122 is_a: UBERON:0010316 ! germ layer / neural crest -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001223", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0000924 @@ -11917,7 +11780,6 @@ xref: EFO:0000414 xref: EHDAA2:0000428 xref: EMAPA:16069 xref: EV:0100003 -xref: FBbt:00000111 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69070 xref: GAID:1304 xref: MAT:0000155 @@ -11934,11 +11796,8 @@ xref: XAO:0000001 xref: ZFA:0000016 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000221 ! ectodermal cell -relationship: immediate_transformation_of UBERON:0006601 {source="Bgee:AN"} ! presumptive ectoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png" xsd:anyURI -property_value: UBPROP:0000001 "Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000137", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000153", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "ectodermal" xsd:string +relationship: RO:0002495 UBERON:0006601 {source="Bgee:AN"} ! immediate transformation of presumptive ectoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png" xsd:anyURI [Term] id: UBERON:0000925 @@ -11958,7 +11817,6 @@ xref: EFO:0002545 xref: EHDAA2:0000436 xref: EMAPA:16062 xref: EV:0100005 -xref: FBbt:00000125 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69071 xref: GAID:1305 xref: MAT:0000175 @@ -11974,11 +11832,9 @@ xref: XAO:0000090 xref: ZFA:0000017 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000223 ! endodermal cell -relationship: immediate_transformation_of UBERON:0006595 {source="Bgee:AN"} ! presumptive endoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png" xsd:anyURI -property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000154", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "endodermal" xsd:string +relationship: RO:0002495 UBERON:0006595 {source="Bgee:AN"} ! immediate transformation of presumptive endoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png" xsd:anyURI [Term] id: UBERON:0000926 @@ -12004,7 +11860,6 @@ xref: EHDAA:160 xref: EHDAA:183 xref: EMAPA:16083 xref: EV:0100006 -xref: FBbt:00000126 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69072 xref: GAID:522 xref: MAT:0000174 @@ -12018,15 +11873,11 @@ xref: VHOG:0000152 xref: Wikipedia:Mesoderm xref: XAO:0000050 xref: ZFA:0000041 -is_a: UBERON:0000923 {notes="sometimes not considered primary"} ! germ layer +is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000222 ! mesodermal cell -relationship: immediate_transformation_of UBERON:0006603 {source="Bgee:AN"} ! presumptive mesoderm -relationship: never_in_taxon NCBITaxon:6040 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" xsd:anyURI -property_value: UBPROP:0000001 "Primary germ layer that is the middle of the embryonic germ layers.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000304", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000152", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "mesodermal" xsd:string -property_value: UBPROP:0000008 "sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates" xsd:string {source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} +relationship: RO:0002495 UBERON:0006603 {source="Bgee:AN"} ! immediate transformation of presumptive mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" xsd:anyURI +property_value: RO:0002161 NCBITaxon:6040 [Term] id: UBERON:0000930 @@ -12048,7 +11899,6 @@ synonym: "stomodeal-hypophyseal primordium" BROAD [XAO:0000269] xref: BTO:0004224 xref: EHDAA2:0001929 xref: EMAPA:16263 -xref: FBbt:00000439 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:295846 xref: NCIT:C34306 xref: TAO:0001290 @@ -12058,15 +11908,11 @@ xref: Wikipedia:Stomodeum xref: XAO:0000269 xref: ZFA:0001290 is_a: UBERON:0013522 ! subdivision of tube -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000924 ! ectoderm relationship: part_of UBERON:0035804 ! future mouth -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI -property_value: editor_note "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" xsd:string -property_value: UBPROP:0000001 "Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001290", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx" xsd:string {source="MP:0012522", taxon="NCBITaxon:40674"} -property_value: UBPROP:0000007 "stomodeal" xsd:string -property_value: UBPROP:0000008 "This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity." xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI +property_value: IAO:0000116 "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" xsd:string [Term] id: UBERON:0000948 @@ -12115,22 +11961,17 @@ is_a: UBERON:0007100 ! primary circulatory organ is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0007100 ! primary circulatory organ intersection_of: has_part UBERON:0004151 ! cardiac chamber -relationship: contributes_to_morphology_of UBERON:0004535 ! cardiovascular system -relationship: develops_from UBERON:0004141 ! heart tube relationship: has_part UBERON:0004151 ! cardiac chamber -relationship: never_in_taxon NCBITaxon:6239 -relationship: never_in_taxon NCBITaxon:7227 -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0015410 {source="MA"} ! heart plus pericardium -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI -property_value: UBPROP:0000001 "Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000114", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010210", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000002 "relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010210", ontology="AAO"} -property_value: UBPROP:0000003 "As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000276", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "cardiac" xsd:string +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002202 UBERON:0004141 ! develops from heart tube +relationship: RO:0002433 UBERON:0004535 ! contributes to morphology of cardiovascular system +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI +property_value: RO:0002161 NCBITaxon:6239 +property_value: RO:0002161 NCBITaxon:7227 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000982 @@ -12170,10 +12011,8 @@ xref: XAO:0000171 xref: ZFA:0001596 is_a: UBERON:0004905 ! articulation disjoint_from: UBERON:0001474 ! bone element -relationship: connects UBERON:0004765 ! skeletal element -relationship: contributes_to_morphology_of UBERON:0001434 ! skeletal system -property_value: UBPROP:0000001 "Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000101", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000367", ontology="TAO", source="TAO:pem"} +relationship: RO:0002176 UBERON:0004765 ! connects skeletal element +relationship: RO:0002433 UBERON:0001434 ! contributes to morphology of skeletal system [Term] id: UBERON:0001007 @@ -12194,8 +12033,6 @@ xref: BILA:0000082 xref: BTO:0000058 xref: CALOHA:TS-1293 xref: EFO:0000793 -xref: EV:0100056 -xref: FBbt:00005055 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7152 xref: GAID:278 xref: galen:DigestiveSystem @@ -12221,11 +12058,8 @@ disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system relationship: capable_of GO:0022600 ! digestive system process -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000129", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000007 "digestive" xsd:string -property_value: UBPROP:0000012 "many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class" xsd:string {external_ontology="MA"} +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001009 @@ -12237,7 +12071,6 @@ subset: uberon_slim synonym: "systema cardiovasculare" RELATED OMO:0003011 [Wikipedia:Circulatory_system] xref: AAO:0000959 xref: CALOHA:TS-2103 -xref: MESH:D002319 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: VHOG:0001248 xref: Wikipedia:Circulatory_system is_a: UBERON:0000467 ! anatomical system @@ -12247,17 +12080,13 @@ disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system relationship: capable_of GO:0003013 ! circulatory system process -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} -relationship: never_in_taxon NCBITaxon:6073 -relationship: never_in_taxon NCBITaxon:6157 -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI -property_value: IAO:0000232 "the cardiovascular system and the lymphatic system are parts of the circulatory system" xsd:string -property_value: RO:0002174 NCBITaxon:6231 {notes="WBbt coelomocyte currently classified as circulating cell"} -property_value: UBPROP:0000001 "Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000959", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001248", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.493", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} +property_value: RO:0002161 NCBITaxon:6073 +property_value: RO:0002161 NCBITaxon:6157 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001015 @@ -12277,10 +12106,8 @@ synonym: "musculature system" RELATED [] synonym: "musculi" EXACT OMO:0003011 [FMA:32558, FMA:TA] synonym: "set of muscles" EXACT [FMA:32558] synonym: "set of skeletal muscles" EXACT [MA:0000165] -xref: AAO:0011066 xref: BTO:0000887 xref: EFO:0001949 -xref: EMAPA:32715 xref: EMAPA:35577 xref: FMA:32558 xref: MA:0000165 @@ -12292,11 +12119,9 @@ xref: WBbt:0005737 xref: Wikipedia:Muscular_system xref: ZFA:0000548 is_a: UBERON:0011216 ! organ system subdivision -relationship: composed_primarily_of UBERON:0001630 ! muscle organ relationship: part_of UBERON:0000383 ! musculature of body -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png" xsd:anyURI -property_value: RO:0002171 UBERON:0001474 -property_value: UBPROP:0000012 "In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here." xsd:string {external_ontology="FMA"} +relationship: RO:0002473 UBERON:0001630 ! composed primarily of muscle organ +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png" xsd:anyURI [Term] id: UBERON:0001016 @@ -12322,7 +12147,6 @@ xref: EHDAA2:0001246 xref: EHDAA:826 xref: EMAPA:16469 xref: EV:0100162 -xref: FBbt:00005093 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7157 xref: GAID:466 xref: MA:0000016 @@ -12345,20 +12169,15 @@ disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system relationship: capable_of GO:0050877 ! nervous system process -relationship: composed_primarily_of CL:0002319 ! neural cell -relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: has_part CL:0000540 ! neuron -relationship: immediate_transformation_of UBERON:0016880 {source="Bgee:AN"} ! future nervous system -relationship: never_in_taxon NCBITaxon:6040 -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI -property_value: UBPROP:0000001 "A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000396", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000324", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000402", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.117", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "nervous" xsd:string -property_value: UBPROP:0000007 "neural" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002473 CL:0002319 ! composed primarily of neural cell +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +relationship: RO:0002495 UBERON:0016880 {source="Bgee:AN"} ! immediate transformation of future nervous system +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI +property_value: RO:0002161 NCBITaxon:6040 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001017 @@ -12387,7 +12206,6 @@ xref: EHDAA:828 xref: EMAPA:16470 xref: EMAPA:16754 xref: EV:0100163 -xref: FBbt:00005094 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:55675 xref: GAID:570 xref: MA:0000167 @@ -12404,15 +12222,11 @@ xref: XAO:0000215 xref: ZFA:0000012 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0011216 {source="FBbt", source="cjm"} ! organ system subdivision -relationship: immediate_transformation_of UBERON:0016879 {source="Bgee:AN"} ! future central nervous system -relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0001016 ! nervous system -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "Part of the nervous system which includes the brain and spinal cord.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000090", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "The brain and spinal cord. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000012", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO)." xsd:string {source="BIRNLEX:1099"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000293", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 (reference 1), ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 (reference 2), DOI:10.1016/j.cell.2007.02.040 Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud'homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007) (reference 3)", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002495 UBERON:0016879 {source="Bgee:AN"} ! immediate transformation of future central nervous system +property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001048 @@ -12431,7 +12245,6 @@ xref: AEO:0000171 xref: BTO:0001886 xref: EFO:0001652 xref: EHDAA2:0003171 -xref: FBbt:00005495 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:86589 xref: MAT:0000482 xref: NCIT:C34275 @@ -12463,7 +12276,6 @@ xref: EMAPA:16164 xref: EMAPA:16757 xref: FMA:293882 xref: MAT:0000069 -xref: MESH:D054259 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: MIAA:0000069 xref: NCIT:C34226 xref: neuronames:1365 @@ -12478,12 +12290,8 @@ is_a: UBERON:0003914 {source="EHDAA2"} ! epithelial tube is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0016879 ! future central nervous system -relationship: develops_from UBERON:0005068 ! neural rod -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010617", ontology="AAO", source="AAO:JOR"} -property_value: UBPROP:0000001 "The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000307", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/neural+tube"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000307", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000011 "The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium" xsd:string {source="GO:0021915"} +relationship: RO:0002202 UBERON:0005068 ! develops from neural rod +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0001062 @@ -12499,7 +12307,6 @@ xref: BILA:0000000 xref: BIRNLEX:6 xref: CARO:0000000 xref: EHDAA2:0002229 -xref: FBbt:10000000 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:62955 xref: HAO:0000000 xref: MA:0000001 @@ -12510,9 +12317,9 @@ xref: UMLS:C1515976 {source="ncithesaurus:Anatomic_Structure_System_or_Substance xref: WBbt:0000100 xref: XAO:0000000 xref: ZFA:0100000 -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0001434 @@ -12549,18 +12356,11 @@ disjoint_from: UBERON:0001474 ! bone element disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system -relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: has_part UBERON:0004288 ! skeleton relationship: has_part UBERON:0004770 ! articular system relationship: part_of UBERON:0002204 ! musculoskeletal system -property_value: RO:0002171 UBERON:0001016 +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/The-skeletal-system" xsd:anyURI -property_value: UBPROP:0000001 "Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000434", ontology="TAO", source="TAO:wd"} -property_value: UBPROP:0000001 "Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000027", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "System that provides physical support to the organism.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000566", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000003 "By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001254", ontology="VHOG", source="DOI:10.1159/000324245 Donoghue PCJ, Sansom IJ, Origin and early evolution of vertebrate skeletonization. Microscopy research and technique (2002)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "skeletal" xsd:string -property_value: UBPROP:0000012 "GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates" xsd:string {external_ontology="GO"} [Term] id: UBERON:0001474 @@ -12603,19 +12403,11 @@ xref: XAO:0000169 xref: ZFA:0001514 is_a: UBERON:0004765 ! skeletal element intersection_of: UBERON:0004765 ! skeletal element -intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue +intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue disjoint_from: UBERON:0001630 ! muscle organ disjoint_from: UBERON:0005090 ! muscle structure -relationship: composed_primarily_of UBERON:0002481 {source="VSAO-modified"} ! bone tissue -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata -property_value: RO:0002171 UBERON:0001015 -property_value: RO:0002171 UBERON:0001630 -property_value: RO:0002171 UBERON:0002385 -property_value: UBPROP:0000001 "Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000047", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000001 "Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001514", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Skeletal element that is composed of bone tissue.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000057", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000002 "relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000047", ontology="AAO"} -property_value: UBPROP:0000003 "The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001190", ontology="VHOG", source="DOI:10.1159/000324245 Murdock DJ, Donoghue PC, Evolutionary Origins of Animal Skeletal Biomineralization. Cells Tissues Organs (2011)", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002473 UBERON:0002481 {source="VSAO-modified"} ! composed primarily of bone tissue [Term] id: UBERON:0001555 @@ -12639,11 +12431,9 @@ xref: BTO:0000545 xref: EHDAA2:0000726 xref: EHDAA:518 xref: EMAPA:16247 -xref: FBbt:00003125 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45615 xref: galen:AlimentaryTract xref: MA:0000917 -xref: MESH:D041981 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: NCIT:C34082 xref: TAO:0000112 xref: TGMA:0001819 @@ -12652,18 +12442,13 @@ xref: VHOG:0000309 xref: WBbt:0005743 xref: ZFA:0000112 is_a: UBERON:0000025 ! tube -relationship: connects UBERON:0000165 ! mouth -relationship: immediate_transformation_of UBERON:0007026 {source="NCBIBook:NBK10107"} ! presumptive gut -relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} -relationship: never_in_taxon NCBITaxon:41324 {source="DOI:10.1371/journal.pone.0016309"} -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0001007 ! digestive system -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "The alimentary or digestive tract, and associated organs.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000112", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000309", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "FMA also has a term 'gastrointestinal tract', but this includes the liver." xsd:string {external_ontology="FMA"} -property_value: UBPROP:0000012 "we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509" xsd:string {external_ontology="MA"} -property_value: UBPROP:0000013 "we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002176 UBERON:0000165 ! connects mouth +relationship: RO:0002495 UBERON:0007026 {source="NCBIBook:NBK10107"} ! immediate transformation of presumptive gut +property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} +property_value: RO:0002161 NCBITaxon:41324 {source="DOI:10.1371/journal.pone.0016309"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001630 @@ -12675,8 +12460,6 @@ subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "muscle" BROAD [ZFA:0005145] -xref: AAO:0011066 -xref: EMAPA:32715 xref: EMAPA:37474 {source="MA:th"} xref: EV:0100146 xref: FMA:5022 @@ -12691,12 +12474,9 @@ xref: ZFA:0005145 is_a: UBERON:0000062 ! organ is_a: UBERON:0005090 ! muscle structure intersection_of: UBERON:0000062 ! organ -intersection_of: composed_primarily_of UBERON:0002385 ! muscle tissue -relationship: composed_primarily_of UBERON:0002385 ! muscle tissue +intersection_of: RO:0002473 UBERON:0002385 ! composed primarily of muscle tissue relationship: part_of UBERON:0001015 ! musculature -property_value: UBPROP:0000001 "Portion of tissue composed of contractile fibers.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005145", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001245", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.75", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "muscular" xsd:string +relationship: RO:0002473 UBERON:0002385 ! composed primarily of muscle tissue [Term] id: UBERON:0001969 @@ -12727,12 +12507,12 @@ is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000179 ! haemolymphatic fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: has_part GO:0005577 ! fibrinogen complex -intersection_of: has_quality PATO:0001548 ! quality of a liquid intersection_of: part_of UBERON:0000178 ! blood -intersection_of: surrounds CL:0000232 ! erythrocyte +intersection_of: RO:0000086 PATO:0001548 ! has quality quality of a liquid +intersection_of: RO:0002221 CL:0000232 ! surrounds erythrocyte relationship: has_part GO:0005577 ! fibrinogen complex relationship: part_of UBERON:0000178 ! blood -relationship: surrounds CL:0000232 ! erythrocyte +relationship: RO:0002221 CL:0000232 ! surrounds erythrocyte [Term] id: UBERON:0001981 @@ -12774,22 +12554,18 @@ xref: XAO:0001011 xref: ZFA:0005314 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000055 ! vessel +is_a: UBERON:0004120 ! mesoderm-derived structure relationship: capable_of_part_of GO:0008015 ! blood circulation relationship: channel_for UBERON:0000178 ! blood -relationship: develops_from UBERON:0004872 ! splanchnic layer of lateral plate mesoderm -relationship: develops_from UBERON:0006965 {source="GO:0072360"} ! vascular cord relationship: has_part CL:0000071 {source="AEO"} ! blood vessel endothelial cell relationship: has_part UBERON:0007500 {source="EHDAA2"} ! epithelial tube open at both ends -relationship: has_quality PATO:0002045 ! dendritic relationship: part_of UBERON:0004537 ! blood vasculature -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI -property_value: editor_note "consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus" xsd:string -property_value: UBPROP:0000001 "Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001250", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000001 "Any of the vessels through which blood circulates in the body.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011004", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001250", ontology="VHOG", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "annelids have blood vessels, but this class is not applicable to annelids." xsd:string -property_value: UBPROP:0000012 "FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX" xsd:string {external_ontology="FMA"} +relationship: RO:0000086 PATO:0002045 ! has quality dendritic +relationship: RO:0002202 UBERON:0004872 ! develops from splanchnic layer of lateral plate mesoderm +relationship: RO:0002202 UBERON:0006965 {source="GO:0072360"} ! develops from vascular cord +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: IAO:0000116 "consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001986 @@ -12813,11 +12589,10 @@ xref: UMLS:C0014257 {source="ncithesaurus:Endothelium"} is_a: UBERON:0000487 {source="FMA-text-def", source="https://github.com/obophenotype/uberon/issues/225"} ! simple squamous epithelium is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0000483 ! epithelium -intersection_of: composed_primarily_of CL:0000115 ! endothelial cell -relationship: composed_primarily_of CL:0000115 ! endothelial cell -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000007 "endothelial" xsd:string +intersection_of: RO:0002473 CL:0000115 ! composed primarily of endothelial cell +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002473 CL:0000115 ! composed primarily of endothelial cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002049 @@ -12834,13 +12609,12 @@ xref: FMA:69050 xref: TAO:0005249 xref: ZFA:0005249 is_a: UBERON:0000477 {source="FMA"} ! anatomical cluster -relationship: composed_primarily_of UBERON:0000055 ! vessel relationship: has_part UBERON:0000179 ! haemolymphatic fluid relationship: part_of UBERON:0007798 ! vascular system -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI -property_value: editor_note "see also: vascular system. Consider merging?" xsd:string -property_value: UBPROP:0000007 "vascular" xsd:string +relationship: RO:0002473 UBERON:0000055 ! composed primarily of vessel +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: IAO:0000116 "see also: vascular system. Consider merging?" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002050 @@ -12860,7 +12634,6 @@ xref: BILA:0000034 xref: BTO:0000174 xref: CALOHA:TS-2110 xref: EFO:0000461 -xref: FBbt:00004208 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69067 xref: GAID:407 xref: MESH:D004628 @@ -12876,10 +12649,6 @@ is_a: UBERON:0005423 ! developing anatomical structure intersection_of: UBERON:0005423 ! developing anatomical structure intersection_of: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0000922 ! embryo -property_value: UBPROP:0000001 "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000138", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001105", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000178", ontology="VSAO", source="ZFIN:curator"} -property_value: UBPROP:0000012 "in FMA embryo is_a embryonic structure" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0002075 @@ -12910,10 +12679,8 @@ xref: Wikipedia:Viscus xref: XAO:0003034 is_a: UBERON:0005177 ! trunk region element intersection_of: UBERON:0000062 ! organ -intersection_of: located_in UBERON:0002323 ! coelemic cavity lumen -relationship: located_in UBERON:0002323 ! coelemic cavity lumen -property_value: UBPROP:0000001 "An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010386", ontology="AAO", source="BTO:0001491"} -property_value: UBPROP:0000012 "general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs." xsd:string {external_ontology="FMA"} +intersection_of: RO:0001025 UBERON:0002323 ! located in coelemic cavity lumen +relationship: RO:0001025 UBERON:0002323 ! located in coelemic cavity lumen [Term] id: UBERON:0002090 @@ -12931,12 +12698,10 @@ xref: AAO:0000034 xref: EFO:0000942 xref: EHDAA2:0000161 xref: EHDAA:5049 -xref: EMAPA:17214 xref: EMAPA:37721 {source="MA:th"} xref: FMA:71221 xref: MA:0002986 xref: MAT:0000148 -xref: MESH:D013131 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: MIAA:0000148 xref: TAO:0000317 xref: VHOG:0000317 @@ -12944,14 +12709,10 @@ xref: VSAO:0000093 xref: XAO:0003073 xref: ZFA:0000317 is_a: UBERON:0010912 ! subdivision of skeleton -relationship: develops_from UBERON:0003089 ! sclerotome relationship: part_of UBERON:0005944 ! axial skeleton plus cranial skeleton relationship: part_of UBERON:0011138 ! postcranial axial skeletal system +relationship: RO:0002202 UBERON:0003089 ! develops from sclerotome property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" xsd:anyURI -property_value: UBPROP:0000001 "Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000093", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000034", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000001 "The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000317", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000317", ontology="VHOG", source="DOI:10.1186/1742-9994-8-4 Schilling N, Evolution of the axial system in craniates: morphology and function of the perivertebral musculature. Frontiers in Zoology (2011)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0002100 @@ -12987,10 +12748,6 @@ xref: XAO:0003025 xref: ZFA:0001115 is_a: UBERON:0011676 ! subdivision of organism along main body axis relationship: part_of UBERON:0013702 ! body proper -property_value: RO:0002171 UBERON:0000026 {exceptions="ZFA", source="https://github.com/obophenotype/uberon/issues/378", status="pending"} -property_value: RO:0002171 UBERON:0000033 -property_value: UBPROP:0000001 "Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010339", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001115", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0002193 @@ -13006,7 +12763,7 @@ xref: EMAPA:18765 xref: FMA:74562 xref: MA:0000013 is_a: UBERON:0000467 {source="MA"} ! anatomical system -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria [Term] id: UBERON:0002204 @@ -13034,13 +12791,10 @@ is_a: UBERON:0000467 ! anatomical system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system relationship: capable_of_part_of GO:0040011 ! locomotion -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: has_developmental_contribution_from UBERON:0000926 {notes="check ctenophore"} ! mesoderm relationship: has_part UBERON:0000383 ! musculature of body relationship: has_part UBERON:0001434 ! skeletal system -property_value: UBPROP:0000001 "Anatomical system that provides locomotion and physical support to the organism.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010546", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001275", ontology="VHOG", source="DOI:10.1002/jez.b.21246 Shearman RM, Burke AC, The lateral somitic frontier in ontogeny and phylogeny. Journal of Experimental Zoology (2009)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "musculoskeletal" xsd:string +relationship: RO:0002254 UBERON:0000926 ! has developmental contribution from mesoderm +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage [Term] id: UBERON:0002224 @@ -13067,13 +12821,12 @@ xref: UMLS:C0230139 {source="ncithesaurus:Thoracic_Cavity"} xref: Wikipedia:Thoracic_cavity is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0000915 ! thoracic segment of trunk intersection_of: part_of UBERON:0002323 ! coelemic cavity lumen -relationship: luminal_space_of UBERON:0000915 ! thoracic segment of trunk +intersection_of: RO:0002572 UBERON:0000915 ! luminal space of thoracic segment of trunk relationship: part_of UBERON:0002323 ! coelemic cavity lumen -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI -property_value: UBPROP:0000008 "In many species, the diaphragm separates thoracic and abdominal cavities" xsd:string +relationship: RO:0002572 UBERON:0000915 ! luminal space of thoracic segment of trunk +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI [Term] id: UBERON:0002323 @@ -13097,7 +12850,6 @@ synonym: "ventral body cavity" NARROW [NCBITaxon:7742] xref: AEO:0000186 xref: BTO:0001707 xref: EHDAA2:0000267 -xref: FBbt:00005060 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:85006 xref: galen:BodyCavity xref: NCIT:C25444 @@ -13107,11 +12859,8 @@ xref: TAO:0001438 xref: UMLS:C0333343 {source="ncithesaurus:Cavity"} xref: ZFA:0001438 is_a: UBERON:0002553 ! anatomical cavity -relationship: luminal_space_of UBERON:0011997 ! coelom -relationship: transformation_of UBERON:0003886 {evidence="definitional"} ! future coelemic cavity lumen -property_value: UBPROP:0000001 "Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]." xsd:string {date_retrieved="2012-09-12", external_class="ZFA:0001438", ontology="ZFA", source="ZFIN:curator"} -property_value: UBPROP:0000001 "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]." xsd:string {date_retrieved="2012-09-12", external_class="BTO:0001707", ontology="BTO", source="BTO"} -property_value: UBPROP:0000008 "In mammals it forms the peritoneal, pleural, and pericardial cavities" xsd:string +relationship: RO:0002494 UBERON:0003886 ! transformation of future coelemic cavity lumen +relationship: RO:0002572 UBERON:0011997 ! luminal space of coelom [Term] id: UBERON:0002328 @@ -13149,23 +12898,15 @@ xref: XAO:0000055 xref: ZFA:0000135 is_a: UBERON:0000062 {source="PMID:15890825"} ! organ is_a: UBERON:0000481 {source="VSAO"} ! multi-tissue structure +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004121 ! ectoderm-derived structure -relationship: develops_from UBERON:0004880 {source="ZFA"} ! chordamesoderm -relationship: develops_from UBERON:0006267 {source="EHDAA2"} ! notochordal plate -relationship: dorsal_to UBERON:0001555 ! digestive tract -relationship: existence_starts_during UBERON:0000068 ! embryo stage -relationship: only_in_taxon NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! Chordata relationship: part_of UBERON:0011137 ! axial skeletal system relationship: produces PR:000014841 ! sonic hedgehog protein -relationship: ventral_to UBERON:0001049 ! neural tube -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000032", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000135", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000327", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000002 "relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000327", ontology="AAO"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000199", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "notochordal" xsd:string -property_value: UBPROP:0000011 "In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord." xsd:string +relationship: RO:0002160 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! only in taxon Chordata +relationship: RO:0002202 UBERON:0004880 {source="ZFA"} ! develops from chordamesoderm +relationship: RO:0002202 UBERON:0006267 {source="EHDAA2"} ! develops from notochordal plate +relationship: RO:0002488 UBERON:0000068 ! existence starts during embryo stage +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0002329 @@ -13204,18 +12945,10 @@ xref: XAO:0000058 xref: ZFA:0000155 is_a: UBERON:0005423 ! developing anatomical structure is_a: UBERON:0007503 {source="EHDAA2"} ! epithelial vesicle -relationship: develops_from UBERON:0003059 {source="ZFA"} ! presomitic mesoderm -relationship: never_in_taxon NCBITaxon:7712 {source="PMID:17237766"} -relationship: only_in_taxon NCBITaxon:7711 {source="GOTAX:0000352"} ! Chordata -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: IAO:0000232 "EDITOR_NOTE currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk" xsd:string -property_value: UBPROP:0000001 "Post-cranial axial segments which form sclerotome and dermomyotome.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010569", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000001 "Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000155", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000002 "relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000155", ontology="TAO"} -property_value: UBPROP:0000002 "relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000155", ontology="TAO"} -property_value: UBPROP:0000002 "relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010569", ontology="AAO"} -property_value: UBPROP:0000003 "(...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000191", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.40, DOI:10.1093/icb/43.1.137 Balavoine G, Adoutte A, The segmented urbilateria: a testable scenario. Integrative and Comparative Biology (2003)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "somitic" xsd:string +relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata +relationship: RO:0002202 UBERON:0003059 {source="ZFA"} ! develops from presomitic mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: RO:0002161 NCBITaxon:7712 {source="PMID:17237766"} [Term] id: UBERON:0002342 @@ -13242,28 +12975,22 @@ xref: MIAA:0000066 xref: NCIT:C34222 xref: neuronames:1366 xref: SCTID:361462002 -xref: TAO:0000045 xref: UMLS:C0027789 {source="ncithesaurus:Neural_Crest"} xref: VHOG:0000057 xref: Wikipedia:Neural_crest xref: XAO:0000048 xref: ZFA:0000045 is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0010316 ! germ layer / neural crest -relationship: composed_primarily_of CL:0000333 {notes="pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! migratory neural crest cell -relationship: develops_from UBERON:0003075 {source="BTO"} ! neural plate -relationship: develops_from UBERON:0005062 {source="PMID:11523831"} ! neural fold -relationship: existence_starts_during UBERON:0000110 {source="PMID:11523831"} ! neurula stage -relationship: only_in_taxon NCBITaxon:89593 {notes="Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells", source="ISBN:0073040584"} ! Craniata relationship: part_of UBERON:0002346 {source="XAO", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! neurectoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI -property_value: IAO:0000232 "EDITOR_NOTE consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams)." xsd:string -property_value: RO:0002174 NCBITaxon:117565 {source="ISBN:0073040584", source="PMID:17377535"} -property_value: UBPROP:0000001 "A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000045", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010578", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831]" xsd:string {source="PMID:11523831"} -property_value: UBPROP:0000003 "We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000057", ontology="VHOG", source="DOI:10.1111/j.1469-7580.2012.01495.x Hall BK, Gillis JA, Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues. J Anat (2012)", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata +relationship: RO:0002202 UBERON:0003075 {source="BTO"} ! develops from neural plate +relationship: RO:0002202 UBERON:0005062 {source="PMID:11523831"} ! develops from neural fold +relationship: RO:0002473 CL:0000333 ! composed primarily of migratory neural crest cell +relationship: RO:0002488 UBERON:0000110 {source="PMID:11523831"} ! existence starts during neurula stage +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI [Term] id: UBERON:0002346 @@ -13286,7 +13013,6 @@ xref: EHDAA:1498 xref: EHDAA:255 xref: EMAPA:16073 xref: EV:0100004 -xref: FBbt:00001057 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:87657 xref: MAT:0000176 xref: MIAA:0000176 @@ -13300,9 +13026,6 @@ xref: ZFA:0001120 is_a: UBERON:0000923 ! germ layer is_a: UBERON:0004121 ! ectoderm-derived structure relationship: has_part CL:0000133 ! neurectodermal cell -property_value: UBPROP:0000003 "(...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000150", ontology="VHOG", source="DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "neurectodermal" xsd:string -property_value: UBPROP:0000013 "we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here" xsd:string [Term] id: UBERON:0002371 @@ -13338,6 +13061,7 @@ xref: VHOG:0001218 xref: Wikipedia:Bone_marrow xref: XAO:0000123 is_a: UBERON:0000479 ! tissue +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000479 ! tissue intersection_of: has_part UBERON:0012429 ! hematopoietic tissue intersection_of: part_of UBERON:0001474 ! bone element @@ -13346,12 +13070,10 @@ relationship: has_part UBERON:0012429 ! hematopoietic tissue relationship: part_of UBERON:0001474 ! bone element relationship: part_of UBERON:0002390 {source="FMA", source="MA"} ! hematopoietic system relationship: part_of UBERON:0002405 ! immune system -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg" xsd:anyURI -property_value: editor_note "consider placement of NCIT:C53466 medullary bone" xsd:string -property_value: editor_note "TODO - create superclass for bone marrow / head kidney. both are portions of tissue in the hematopoetic system. also consider adding as subclass of zone of bone organ for consistency with FMA. See also: Leydig and epigonal organs" xsd:string -property_value: UBPROP:0000003 "The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001218", ontology="VHOG", source="DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood Cells and Blood Cell Development in the Animal Kingdom. Annual Review of Cell and Developmental Biology (2006)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000009 "In adults, marrow in large bones produces new blood cells[Wikipedia:Bone_marrow]" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg" xsd:anyURI +property_value: IAO:0000116 "consider placement of NCIT:C53466 medullary bone" xsd:string +property_value: IAO:0000116 "TODO - create superclass for bone marrow / head kidney. both are portions of tissue in the hematopoetic system. also consider adding as subclass of zone of bone organ for consistency with FMA. See also: Leydig and epigonal organs" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002384 @@ -13385,12 +13107,8 @@ xref: VSAO:0000017 xref: XAO:0001017 xref: ZFA:0001632 is_a: UBERON:0000479 ! tissue -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000098", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000001 "Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001641", ontology="TAO", source="TAO:wd"} -property_value: UBPROP:0000001 "Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000017", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} -property_value: UBPROP:0000012 "MA also has set of connective tissues" xsd:string {external_ontology="MA"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002385 @@ -13418,13 +13136,11 @@ xref: Wikipedia:Muscle_tissue is_a: UBERON:0000479 ! tissue is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000479 ! tissue -intersection_of: composed_primarily_of CL:0000187 ! muscle cell +intersection_of: RO:0002473 CL:0000187 ! composed primarily of muscle cell relationship: capable_of GO:0006936 ! muscle contraction -relationship: composed_primarily_of CL:0000187 ! muscle cell -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0001015 ! musculature -property_value: RO:0002171 UBERON:0003714 -property_value: UBPROP:0000001 "One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000306", ontology="AAO", source="AAO:LAP"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002473 CL:0000187 ! composed primarily of muscle cell [Term] id: UBERON:0002390 @@ -13467,14 +13183,10 @@ xref: ZFA:0005023 is_a: UBERON:0000467 ! anatomical system is_a: UBERON:0004120 ! mesoderm-derived structure disjoint_from: UBERON:0002405 ! immune system -relationship: develops_from UBERON:0003061 {evidence="definitional"} ! blood island -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0002193 {source="FMA"} ! hemolymphoid system -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "Anatomical system that consists of the blood and blood forming tissues.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011002", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001624", ontology="VHOG", source="DOI:10.1016/j.coph.2010.05.004 Ellett F, Lieschke GJ, Zebrafish as a model for vertebrate hematopoiesis. Current Opinion in Pharmacology (2010)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "hematopoietic" xsd:string -property_value: UBPROP:0000008 "In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes" xsd:string {source="WP"} +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002202 UBERON:0003061 ! develops from blood island +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002405 @@ -13502,10 +13214,9 @@ xref: XAO:0003152 xref: ZFA:0001159 is_a: UBERON:0015203 ! non-connected functional system relationship: capable_of GO:0002376 ! immune system process -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: present_in_taxon NCBITaxon:9606 relationship: protects UBERON:0000468 ! multicellular organism -property_value: UBPROP:0000003 "The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001247", ontology="VHOG", source="PMID:21046016 Dzik JM, The ancestry and cumulative evolution of immune reactions. Acta biochimica Polonica (2010)", source="http://bgee.unil.ch/"} +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002481 @@ -13534,10 +13245,9 @@ xref: XAO:0004040 xref: ZFA:0005621 is_a: UBERON:0004755 {source="VSAO"} ! skeletal tissue disjoint_from: UBERON:0005090 ! muscle structure -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0001474 ! bone element -property_value: editor_note "see https://github.com/obophenotype/uberon/issues/27" xsd:string -property_value: UBPROP:0000001 "Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000047", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +property_value: IAO:0000116 "see https://github.com/obophenotype/uberon/issues/27" xsd:string [Term] id: UBERON:0002532 @@ -13561,9 +13271,8 @@ xref: VHOG:0000243 xref: Wikipedia:Epiblast is_a: UBERON:0002050 ! embryonic structure relationship: has_part CL:0000352 ! epiblast cell -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" xsd:anyURI -property_value: editor_note "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" xsd:string -property_value: UBPROP:0000003 "In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000243", ontology="VHOG", source="DOI:10.1146/annurev.cellbio.042308.113344 Zorn AM, Wells JM, Vertebrate endoderm development and organ formation. Annual Review of Cell Developmental Biology (2009)", source="http://bgee.unil.ch/"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" xsd:anyURI +property_value: IAO:0000116 "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" xsd:string [Term] id: UBERON:0002553 @@ -13579,7 +13288,7 @@ xref: galen:Cavity xref: MA:0002447 xref: NCIT:C34007 is_a: UBERON:0000464 ! anatomical space -relationship: location_of UBERON:0000463 ! organism substance +relationship: RO:0001015 UBERON:0000463 ! location of organism substance [Term] id: UBERON:0003059 @@ -13605,13 +13314,11 @@ xref: XAO:0000057 xref: ZFA:0000279 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0005423 ! developing anatomical structure -intersection_of: has_potential_to_develop_into UBERON:0002329 ! somite -intersection_of: immediate_transformation_of UBERON:0007282 ! presumptive segmental plate -relationship: has_potential_to_develop_into UBERON:0002329 ! somite -relationship: immediate_transformation_of UBERON:0007282 {source="Bgee:AN"} ! presumptive segmental plate +intersection_of: RO:0002387 UBERON:0002329 ! has potential to develop into somite +intersection_of: RO:0002495 UBERON:0007282 ! immediate transformation of presumptive segmental plate relationship: part_of UBERON:0003077 ! paraxial mesoderm -property_value: UBPROP:0000001 "Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000279", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000559", ontology="VHOG", source="DOI:10.1006/dbio.2001.0460 Schubert M, Holland LZ, Dale Stokes M and Holland ND, Three Amphoxius Wnt Genes (AmphiWnt3, AmphiWnt5, and AmphiWnt6) Associated with the Tail Bud: the Evolution of Somitogenesis in Chordates. Developmental Biology (2001)", source="http://bgee.unil.ch/"} +relationship: RO:0002387 UBERON:0002329 ! has potential to develop into somite +relationship: RO:0002495 UBERON:0007282 {source="Bgee:AN"} ! immediate transformation of presumptive segmental plate [Term] id: UBERON:0003061 @@ -13641,13 +13348,8 @@ xref: Wikipedia:Blood_island_of_umbilical_vesicle xref: XAO:0000067 xref: ZFA:0000094 is_a: UBERON:0006598 ! presumptive structure -relationship: develops_from UBERON:0003081 ! lateral plate mesoderm -relationship: has_potential_to_develop_into UBERON:0002390 ! hematopoietic system -property_value: UBPROP:0000001 "Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000094", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011006", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000002 "relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000094", ontology="TAO"} -property_value: UBPROP:0000003 "Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000085", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450, DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual Review of Cell and Developmental Biology (2006)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac" xsd:string {external_ontology="EHDAA2"} +relationship: RO:0002202 UBERON:0003081 ! develops from lateral plate mesoderm +relationship: RO:0002387 UBERON:0002390 ! has potential to develop into hematopoietic system [Term] id: UBERON:0003068 @@ -13665,11 +13367,10 @@ xref: Wikipedia:Chordamesoderm xref: XAO:0000205 xref: ZFA:0001204 is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0000926 ! mesoderm -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0000926 ! mesoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000107", ontology="VHOG", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002202 UBERON:0000926 ! develops from mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003075 @@ -13689,7 +13390,6 @@ xref: EHDAA:346 xref: EHDAA:902 xref: EMAPA:35593 xref: FMA:293879 -xref: MESH:D054258 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C34225 xref: neuronames:1362 xref: RETIRED_EHDAA2:0001252 @@ -13702,12 +13402,10 @@ xref: ZFA:0000132 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0016879 ! future central nervous system -relationship: developmentally_induced_by UBERON:0002328 {source="Wikipedia"} ! notochord -relationship: immediate_transformation_of UBERON:0007284 {source="Bgee:AN"} ! presumptive neural plate -relationship: only_in_taxon NCBITaxon:7711 {source="GOTAX:0000352"} ! Chordata -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI -property_value: UBPROP:0000001 "The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000132", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000068", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata +relationship: RO:0002256 UBERON:0002328 {source="Wikipedia"} ! developmentally induced by notochord +relationship: RO:0002495 UBERON:0007284 {source="Bgee:AN"} ! immediate transformation of presumptive neural plate +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI [Term] id: UBERON:0003077 @@ -13736,13 +13434,9 @@ xref: ZFA:0000255 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue is_a: UBERON:0015212 ! lateral structure -relationship: existence_starts_during UBERON:0000109 ! gastrula stage -relationship: immediate_transformation_of UBERON:0007285 {source="Bgee:AN"} ! presumptive paraxial mesoderm -relationship: in_lateral_side_of UBERON:0000922 ! embryo -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010568", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000114", ontology="VHOG", source="DOI:10.1002/dvdy.21177 Kusakabe R and Kuratani S. Evolutionary perspectives from development of mesodermal components in the lamprey. Developmental dynamics (2007)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here)" xsd:string {external_ontology="ZFA"} +relationship: RO:0002488 UBERON:0000109 ! existence starts during gastrula stage +relationship: RO:0002495 UBERON:0007285 {source="Bgee:AN"} ! immediate transformation of presumptive paraxial mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003081 @@ -13774,14 +13468,10 @@ is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0000926 {source="EHDAA2", source="VHOG"} ! mesoderm -relationship: surrounds UBERON:0003887 ! intraembryonic coelom -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010574", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000001 "The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000118", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000118", ontology="VHOG", source="DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "subclass of mesoderm in ZFA." xsd:string {external_ontology="ZFA"} +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002221 UBERON:0003887 ! surrounds intraembryonic coelom +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003084 @@ -13799,14 +13489,11 @@ xref: UMLS:C1514450 {source="ncithesaurus:Primordium_of_the_Heart"} xref: XAO:0000336 xref: ZFA:0000028 is_a: UBERON:0001048 {source="Obol"} ! primordium -relationship: develops_from UBERON:0003081 {source="ZFA"} ! lateral plate mesoderm -relationship: develops_from UBERON:0004140 ! primary heart field -relationship: develops_from UBERON:0007005 {source="XAO"} ! cardiogenic splanchnic mesoderm relationship: part_of UBERON:0004535 {source="ZFA"} ! cardiovascular system -property_value: editor_note "should probably be merged with heart rudiment." xsd:string -property_value: UBPROP:0000001 "Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000028", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011044", ontology="AAO", source="XAO:curator"} -property_value: UBPROP:0000002 "relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000028", ontology="TAO"} +relationship: RO:0002202 UBERON:0003081 {source="ZFA"} ! develops from lateral plate mesoderm +relationship: RO:0002202 UBERON:0004140 ! develops from primary heart field +relationship: RO:0002202 UBERON:0007005 {source="XAO"} ! develops from cardiogenic splanchnic mesoderm +property_value: IAO:0000116 "should probably be merged with heart rudiment." xsd:string [Term] id: UBERON:0003089 @@ -13820,7 +13507,6 @@ synonym: "sclerotomes" EXACT OMO:0003004 [TAO:0001080] synonym: "sclerotomus" RELATED OMO:0003011 [Wikipedia:Sclerotome] xref: AAO:0010571 xref: AEO:0000212 -xref: BTO:0006255 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: EHDAA2:0003439 xref: EMAPA:31159 xref: FMA:295652 @@ -13833,12 +13519,9 @@ xref: XAO:0000397 xref: ZFA:0001080 is_a: UBERON:0005856 {source="EHDAA2"} ! developing mesenchymal condensation is_a: UBERON:0007530 {source="EHDAA2"} ! migrating mesenchyme population -relationship: develops_from UBERON:0002329 {source="ZFA"} ! somite -relationship: only_in_taxon NCBITaxon:7742 {source="VHOG:0000680"} ! Vertebrata -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI -property_value: UBPROP:0000001 "Skeletogenic portion of somites.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010571", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000680", ontology="VHOG", source="DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "part_of somite in XAO" xsd:string {external_ontology="XAO"} +relationship: RO:0002160 NCBITaxon:7742 {source="VHOG:0000680"} ! only in taxon Vertebrata +relationship: RO:0002202 UBERON:0002329 {source="ZFA"} ! develops from somite +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI [Term] id: UBERON:0003103 @@ -13861,7 +13544,6 @@ xref: VHOG:0001723 xref: XAO:0003041 xref: ZFA:0000496 is_a: UBERON:0000062 ! organ -property_value: IAO:0000232 "this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs" xsd:string [Term] id: UBERON:0003104 @@ -13891,15 +13573,12 @@ xref: XAO:0003046 xref: ZFA:0000393 is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue -intersection_of: composed_primarily_of CL:0008019 ! mesenchymal cell -relationship: composed_primarily_of CL:0008019 ! mesenchymal cell -relationship: functionally_related_to GO:0032502 ! developmental process -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI -property_value: editor_note "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" xsd:string -property_value: UBPROP:0000001 "A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000393", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010427", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000007 "mesenchymal" xsd:string +intersection_of: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002328 GO:0032502 ! functionally related to developmental process +relationship: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI +property_value: IAO:0000116 "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" xsd:string [Term] id: UBERON:0003886 @@ -13912,11 +13591,11 @@ synonym: "body cavity precursor" RELATED [] synonym: "future coelomic cavity lumen" EXACT [] is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: has_potential_to_develop_into UBERON:0002323 ! coelemic cavity lumen -relationship: existence_ends_during UBERON:0000111 ! organogenesis stage -relationship: existence_starts_during UBERON:0000109 ! gastrula stage -relationship: has_potential_to_develop_into UBERON:0002323 ! coelemic cavity lumen +intersection_of: RO:0002387 UBERON:0002323 ! has potential to develop into coelemic cavity lumen relationship: part_of UBERON:0000926 ! mesoderm +relationship: RO:0002387 UBERON:0002323 ! has potential to develop into coelemic cavity lumen +relationship: RO:0002488 UBERON:0000109 ! existence starts during gastrula stage +relationship: RO:0002492 UBERON:0000111 ! existence ends during organogenesis stage [Term] id: UBERON:0003887 @@ -13932,10 +13611,9 @@ xref: UMLS:C1512940 {source="ncithesaurus:Intraembryonic_Coelom"} xref: VHOG:0000316 xref: Wikipedia:Intraembryonic_coelom is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0003081 {source="Wikipedia"} ! lateral plate mesoderm relationship: part_of UBERON:0011997 ! coelom -property_value: editor_note "consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults" xsd:string -property_value: UBPROP:0000003 "(...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000316", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.166", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003081 {source="Wikipedia"} ! develops from lateral plate mesoderm +property_value: IAO:0000116 "consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults" xsd:string [Term] id: UBERON:0003914 @@ -13945,12 +13623,10 @@ def: "Epithelial tubes transport gases, liquids and cells from one site to anoth synonym: "epithelial or endothelial tube" EXACT [] xref: AEO:0000114 xref: EHDAA2:0003114 -xref: FBbt:00007474 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000025 ! tube is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium -intersection_of: has_quality PATO:0002299 ! tubular -property_value: IAO:0000232 "contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers" xsd:string +intersection_of: RO:0000086 PATO:0002299 ! has quality tubular [Term] id: UBERON:0004111 @@ -13970,15 +13646,14 @@ xref: SCTID:346902003 xref: Wikipedia:Foramen is_a: UBERON:0010000 ! multicellular anatomical structure intersection_of: UBERON:0010000 ! multicellular anatomical structure -intersection_of: conduit_for UBERON:0000061 ! anatomical structure intersection_of: has_part UBERON:0013686 ! anatomical conduit space -relationship: conduit_for UBERON:0000061 ! anatomical structure -relationship: connects UBERON:0000464 {cardinality="2"} ! anatomical space +intersection_of: RO:0002570 UBERON:0000061 ! conduit for anatomical structure relationship: has_part UBERON:0013686 ! anatomical conduit space -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: UBPROP:0000012 "FMA has both conduit and conduit space. In EHDAA2 this is a surface feature" xsd:string {external_ontology="FMA"} +relationship: RO:0002176 UBERON:0000464 {cardinality="2"} ! connects anatomical space +relationship: RO:0002570 UBERON:0000061 ! conduit for anatomical structure +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0004120 @@ -13989,9 +13664,8 @@ subset: grouping_class synonym: "mesodermal derivative" EXACT [FBbt:00025998] is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: develops_from UBERON:0000926 ! mesoderm -relationship: develops_from UBERON:0000926 ! mesoderm -property_value: IAO:0000232 "Grouping term for query purposes" xsd:string +intersection_of: RO:0002202 UBERON:0000926 ! develops from mesoderm +relationship: RO:0002202 UBERON:0000926 ! develops from mesoderm [Term] id: UBERON:0004121 @@ -14002,9 +13676,8 @@ subset: grouping_class synonym: "ectodermal deriviative" EXACT [FBbt:00025990] is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: develops_from UBERON:0000924 ! ectoderm -relationship: develops_from UBERON:0000924 ! ectoderm -property_value: IAO:0000232 "Grouping term for query purposes" xsd:string +intersection_of: RO:0002202 UBERON:0000924 ! develops from ectoderm +relationship: RO:0002202 UBERON:0000924 ! develops from ectoderm [Term] id: UBERON:0004139 @@ -14020,9 +13693,8 @@ xref: EHDAA2:0000215 xref: EMAPA:16106 xref: VHOG:0000975 is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0003084 ! heart primordium -property_value: editor_note "TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO" xsd:string -property_value: UBPROP:0000003 "(In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000975", ontology="VHOG", source="PMID:15611355 Gittenberger-de Groot AC, Bartelings MM, Deruiter MC, Poelmann RE, Basics of cardiac development for the understanding of congenital heart malformations. Pediatric Research (2005)", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003084 ! develops from heart primordium +property_value: IAO:0000116 "TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO" xsd:string [Term] id: UBERON:0004140 @@ -14036,11 +13708,11 @@ synonym: "PHF" RELATED OMO:0003000 [XAO:0004185] synonym: "primary heart field" EXACT [PMID:17276708, XAO:0004185] xref: XAO:0004185 is_a: UBERON:0002050 ! embryonic structure +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007688 ! anlage relationship: part_of UBERON:0003081 {source="GO:0003128"} ! lateral plate mesoderm relationship: part_of UBERON:0036146 {source="https://orcid.org/0000-0003-3308-6245"} ! cardiopharyngeal field -property_value: UBPROP:0000012 "this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138]" xsd:string {external_ontology="GO"} [Term] id: UBERON:0004141 @@ -14063,8 +13735,7 @@ xref: ZFA:0000360 is_a: UBERON:0003914 ! epithelial tube is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0012275 ! meso-epithelium -relationship: immediate_transformation_of UBERON:0005498 {source="ZFA-modified"} ! primitive heart tube -property_value: UBPROP:0000001 "the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube." xsd:string {source="MP:0012700"} +relationship: RO:0002495 UBERON:0005498 {source="ZFA-modified"} ! immediate transformation of primitive heart tube [Term] id: UBERON:0004151 @@ -14077,6 +13748,7 @@ synonym: "heart chamber" EXACT [] xref: FMA:7095 xref: SCTID:276456008 is_a: UBERON:0000064 ! organ part +is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0000948 ! heart [Term] @@ -14107,13 +13779,10 @@ xref: Wikipedia:Skeleton xref: XAO:0004053 is_a: UBERON:0034925 ! anatomical collection disjoint_from: UBERON:0004770 ! articular system -relationship: has_member UBERON:0004765 ! skeletal element relationship: part_of UBERON:0001434 ! skeletal system -relationship: present_in_taxon NCBITaxon:9606 -property_value: RO:0002171 UBERON:0000383 +relationship: RO:0002351 UBERON:0004765 ! has member skeletal element +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/The-skeletal-system" xsd:anyURI -property_value: UBPROP:0000001 "Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000026", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070"} -property_value: UBPROP:0000007 "skeletal" xsd:string [Term] id: UBERON:0004291 @@ -14125,8 +13794,7 @@ synonym: "rudimentary heart" EXACT [ZFA:0000115] xref: TAO:0000115 xref: ZFA:0000115 is_a: UBERON:0012275 ! meso-epithelium -relationship: develops_from UBERON:0004139 ! cardiogenic plate -property_value: UBPROP:0000001 "The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000115", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002202 UBERON:0004139 ! develops from cardiogenic plate [Term] id: UBERON:0004535 @@ -14145,10 +13813,8 @@ xref: BILA:0000016 xref: BTO:0000088 xref: CALOHA:TS-1297 xref: EFO:0000791 -xref: EHDAA2:0000216 xref: EHDAA:394 xref: EMAPA:16104 -xref: EMAPA:16370 xref: EV:0100017 xref: FMA:7161 xref: GAID:467 @@ -14174,9 +13840,7 @@ intersection_of: part_of UBERON:0001009 ! circulatory system relationship: has_part UBERON:0000948 ! heart relationship: has_part UBERON:0001981 ! blood vessel relationship: part_of UBERON:0001009 ! circulatory system -relationship: present_in_taxon NCBITaxon:9606 -property_value: IAO:0000232 "we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph." xsd:string -property_value: UBPROP:0000003 "The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000302", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.451", source="http://bgee.unil.ch/"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004537 @@ -14194,11 +13858,11 @@ xref: ZFA:0001079 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature -intersection_of: composed_primarily_of UBERON:0001981 ! blood vessel -relationship: composed_primarily_of UBERON:0001981 ! blood vessel -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +intersection_of: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel +relationship: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004638 @@ -14220,7 +13884,7 @@ is_a: UBERON:0004852 ! cardiovascular system endothelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0001981 ! blood vessel relationship: part_of UBERON:0001981 ! blood vessel -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004716 @@ -14237,12 +13901,12 @@ xref: NCIT:C34131 xref: UMLS:C1516779 {source="ncithesaurus:Conceptus"} xref: Wikipedia:Conceptus is_a: UBERON:0000061 ! anatomical structure -relationship: develops_from CL:0000365 ! animal zygote -relationship: existence_ends_with UBERON:0000068 ! embryo stage -relationship: existence_starts_with UBERON:0000068 ! embryo stage relationship: has_part UBERON:0002050 ! embryonic structure relationship: has_part UBERON:0016887 ! entire extraembryonic component -property_value: editor_note "EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus" xsd:string +relationship: RO:0002202 CL:0000365 ! develops from animal zygote +relationship: RO:0002489 UBERON:0000068 ! existence starts with embryo stage +relationship: RO:0002493 UBERON:0000068 ! existence ends with embryo stage +property_value: IAO:0000116 "EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus" xsd:string [Term] id: UBERON:0004734 @@ -14262,7 +13926,6 @@ synonym: "trilaminar disk" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "trilaminar germ" RELATED [https://orcid.org/0000-0002-6601-2165] xref: BILA:0000060 xref: BTO:0001403 -xref: FBbt:00005317 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:293108 xref: GAID:1302 xref: MESH:D005775 @@ -14275,10 +13938,9 @@ xref: Wikipedia:Gastrula xref: Wikipedia:Trilaminar_blastocyst is_a: UBERON:0000922 ! embryo intersection_of: UBERON:0000468 ! multicellular organism -intersection_of: existence_starts_and_ends_during UBERON:0000109 ! gastrula stage -relationship: develops_from UBERON:0000307 ! blastula -relationship: existence_starts_and_ends_during UBERON:0000109 ! gastrula stage -property_value: UBPROP:0000012 "We explicitly merge the NCITA terms here" xsd:string {external_ontology="NCIT"} +intersection_of: RO:0002491 UBERON:0000109 ! existence starts and ends during gastrula stage +relationship: RO:0002202 UBERON:0000307 ! develops from blastula +relationship: RO:0002491 UBERON:0000109 ! existence starts and ends during gastrula stage [Term] id: UBERON:0004755 @@ -14293,9 +13955,8 @@ xref: VSAO:0000015 xref: XAO:0004038 xref: ZFA:0005619 is_a: UBERON:0002384 {source="VSAO"} ! connective tissue -relationship: develops_from CL:0007001 {date_retrieved="2012-08-14", external_class="VSAO:0000015", source="VSAO"} ! skeletogenic cell relationship: part_of UBERON:0004765 ! skeletal element -property_value: UBPROP:0000001 "A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000015", notes="taken from version of VSAO used in TAO and used directly in Uberon", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} +relationship: RO:0002202 CL:0007001 ! develops from skeletogenic cell [Term] id: UBERON:0004765 @@ -14312,8 +13973,6 @@ xref: XAO:0004012 xref: ZFA:0005494 is_a: UBERON:0000062 ! organ relationship: part_of UBERON:0001434 {source="VSAO"} ! skeletal system -property_value: UBPROP:0000001 "Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000128", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001890", ontology="TAO", source="TAO:VSAO_workshop"} [Term] id: UBERON:0004770 @@ -14331,12 +13990,12 @@ xref: SCTID:361827000 xref: VSAO:0000181 is_a: UBERON:0034925 ! anatomical collection intersection_of: UBERON:0034925 ! anatomical collection -intersection_of: has_member UBERON:0000982 ! skeletal joint -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: functionally_related_to GO:0040011 ! locomotion -relationship: has_member UBERON:0000982 ! skeletal joint -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +intersection_of: RO:0002351 UBERON:0000982 ! has member skeletal joint relationship: part_of UBERON:0001434 {source="FMA"} ! skeletal system +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002328 GO:0040011 ! functionally related to locomotion +relationship: RO:0002351 UBERON:0000982 ! has member skeletal joint +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage [Term] id: UBERON:0004852 @@ -14361,8 +14020,7 @@ is_a: UBERON:0001986 ! endothelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0004535 ! cardiovascular system relationship: part_of UBERON:0004535 ! cardiovascular system -property_value: editor_note "consider merging with 'endothelium'" xsd:string -property_value: UBPROP:0000003 "Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001217", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207", source="http://bgee.unil.ch/"} +property_value: IAO:0000116 "consider merging with 'endothelium'" xsd:string [Term] id: UBERON:0004872 @@ -14380,7 +14038,6 @@ xref: Wikipedia:Lateral_plate_mesoderm#Division_into_layers xref: XAO:0000276 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0003081 ! lateral plate mesoderm -property_value: UBPROP:0000012 "We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors" xsd:string {external_ontology="BILA"} [Term] id: UBERON:0004880 @@ -14398,10 +14055,8 @@ xref: EFO:0003426 xref: TAO:0000091 xref: ZFA:0000091 is_a: UBERON:0002050 ! embryonic structure -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0003068 ! axial mesoderm -property_value: UBPROP:0000001 "Notochord rudiment[ZFIN:ZDB-PUB-961014-576]." xsd:string {source="ZFIN:ZDB-PUB-961014-576"} -property_value: UBPROP:0000012 "WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord." xsd:string +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata [Term] id: UBERON:0004905 @@ -14410,7 +14065,6 @@ namespace: uberon def: "Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts." [http://orcid.org/0000-0002-6601-2165] subset: grouping_class synonym: "joint" NARROW [] -xref: FBbt:00005811 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0034921 ! multi organ part structure relationship: part_of UBERON:0004770 ! articular system @@ -14426,15 +14080,13 @@ synonym: "gut section" RELATED [FBbt:00100315] synonym: "intestinal tract" RELATED [] synonym: "segment of intestinal tract" RELATED [] synonym: "subdivision of alimentary system" RELATED [FMA:71131] -xref: FBbt:00100315 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:71131 is_a: UBERON:0013522 ! subdivision of tube intersection_of: UBERON:0013522 ! subdivision of tube intersection_of: subdivision_of UBERON:0001555 ! digestive tract relationship: part_of UBERON:0001555 ! digestive tract -relationship: present_in_taxon NCBITaxon:9606 relationship: subdivision_of UBERON:0001555 ! digestive tract -property_value: IAO:0000232 "intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct." xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004923 @@ -14444,8 +14096,8 @@ def: "A part of a wall of an organ that forms a layer." [http://orcid.org/0000-0 subset: upper_level xref: FMA:82485 is_a: UBERON:0000064 ! organ part -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000060 ! anatomical wall +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0005061 @@ -14463,7 +14115,6 @@ xref: Wikipedia:Neural_groove xref: XAO:0000248 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0003075 ! neural plate -property_value: UBPROP:0000001 "The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]." xsd:string {source="Wikipedia:Neural_groove"} [Term] id: UBERON:0005062 @@ -14483,10 +14134,9 @@ xref: XAO:0004087 is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0005157 ! epithelial fold is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0015212 ! lateral structure -relationship: in_lateral_side_of UBERON:0005061 ! neural groove relationship: part_of UBERON:0005061 ! neural groove -property_value: UBPROP:0000001 "In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]." xsd:string {source="Wikipedia:Neural_fold"} [Term] id: UBERON:0005068 @@ -14499,8 +14149,7 @@ xref: EFO:0003498 xref: TAO:0000133 xref: ZFA:0000133 is_a: UBERON:0016879 ! future central nervous system -relationship: develops_from UBERON:0007135 ! neural keel -property_value: UBPROP:0000001 "An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000133", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002202 UBERON:0007135 ! develops from neural keel [Term] id: UBERON:0005090 @@ -14510,12 +14159,10 @@ def: "Muscle structures are contractile cells, tissues or organs that are found synonym: "muscle" RELATED [] synonym: "muscle element" RELATED [] synonym: "musculus" EXACT [FMA:30316] -xref: EMAPA:32715 xref: FMA:30316 is_a: UBERON:0000061 ! anatomical structure relationship: has_part CL:0000187 ! muscle cell -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: IAO:0000232 "in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0005157 @@ -14552,8 +14199,8 @@ xref: MA:0000557 is_a: UBERON:0002075 ! viscus is_a: UBERON:0005181 ! thoracic segment organ intersection_of: UBERON:0000062 ! organ -intersection_of: located_in UBERON:0002224 ! thoracic cavity -relationship: located_in UBERON:0002224 ! thoracic cavity +intersection_of: RO:0001025 UBERON:0002224 ! located in thoracic cavity +relationship: RO:0001025 UBERON:0002224 ! located in thoracic cavity [Term] id: UBERON:0005181 @@ -14618,14 +14265,13 @@ synonym: "developmental tissue" RELATED [MIAA:0000019] xref: AEO:0000125 xref: CALOHA:TS-2122 xref: EHDAA2:0003125 -xref: FBbt:00007006 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:292313 xref: MIAA:0000019 is_a: UBERON:0000465 ! material anatomical entity relationship: capable_of GO:0032502 ! developmental process -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0005498 @@ -14635,7 +14281,6 @@ def: "Multi-tissue structure that arises from the heart rudiment and will become subset: vertebrate_core synonym: "early primitive heart tube" NARROW [EMAPA:16208] synonym: "primitive heart tube" EXACT [EMAPA:16215] -xref: BTO:0006179 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: EHDAA2:0001512 xref: EHDAA:424 xref: EHDAA:436 @@ -14647,8 +14292,8 @@ xref: Wikipedia:Primitive_heart_tube xref: ZFA:0000149 is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004120 ! mesoderm-derived structure -relationship: develops_from UBERON:0004291 {source="ZFA"} ! heart rudiment relationship: part_of UBERON:0000922 ! embryo +relationship: RO:0002202 UBERON:0004291 {source="ZFA"} ! develops from heart rudiment [Term] id: UBERON:0005764 @@ -14661,9 +14306,9 @@ is_a: UBERON:0000476 ! acellular anatomical structure intersection_of: UBERON:0000476 ! acellular anatomical structure intersection_of: bounding_layer_of UBERON:0000061 ! anatomical structure relationship: bounding_layer_of UBERON:0000061 ! anatomical structure -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0005769 @@ -14683,12 +14328,11 @@ xref: Wikipedia:Basement_membrane is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005764 {source="FMA"} ! acellular membrane relationship: adjacent_to CL:0000066 ! epithelial cell -relationship: composed_primarily_of GO:0005604 ! basement membrane relationship: has_part GO:0005587 ! collagen type IV trimer -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa relationship: part_of UBERON:0000483 ! epithelium -relationship: present_in_taxon NCBITaxon:80999 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} -property_value: IAO:0000232 "this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell." xsd:string +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002473 GO:0005604 ! composed primarily of basement membrane +property_value: RO:0002175 NCBITaxon:80999 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} [Term] id: UBERON:0005856 @@ -14701,7 +14345,7 @@ xref: EHDAA2_RETIRED:0003148 xref: EHDAA:8979 is_a: UBERON:0007524 {source="AEO"} ! dense mesenchyme tissue is_a: UBERON:0011585 {source="cjm"} ! cell condensation -relationship: composed_primarily_of CL:0000335 {source="AEO-modified-relation"} ! mesenchyme condensation cell +relationship: RO:0002473 CL:0000335 {source="AEO-modified-relation"} ! composed primarily of mesenchyme condensation cell [Term] id: UBERON:0005944 @@ -14714,7 +14358,6 @@ subset: uberon_slim synonym: "skeleton axiale" RELATED OMO:0003011 [Wikipedia:Axial_skeleton] xref: AAO:0000963 xref: EMAPA:17214 -xref: EMAPA:18043 xref: MA:0000308 xref: NCIT:C32172 xref: SCTID:361725000 @@ -14723,13 +14366,12 @@ xref: VSAO:0000056 xref: Wikipedia:Axial_skeleton xref: XAO:0004011 is_a: UBERON:0010912 ! subdivision of skeleton -relationship: contributes_to_morphology_of UBERON:0001434 ! skeletal system -relationship: develops_from UBERON:0003089 ! sclerotome relationship: part_of UBERON:0011137 ! axial skeletal system -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg" xsd:anyURI +relationship: RO:0002202 UBERON:0003089 ! develops from sclerotome +relationship: RO:0002433 UBERON:0001434 ! contributes to morphology of skeletal system +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" xsd:anyURI -property_value: UBPROP:0000001 "Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000056", ontology="VSAO", source="PSPUB:0000170"} [Term] id: UBERON:0006267 @@ -14747,9 +14389,8 @@ is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium -relationship: develops_from UBERON:0006268 {source="EHDAA2"} ! notochordal process -property_value: editor_note "TODO - check ordering; awaiting confirmation from JB" xsd:string -property_value: UBPROP:0000001 "The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001212", ontology="VHOG", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0006268 {source="EHDAA2"} ! develops from notochordal process +property_value: IAO:0000116 "TODO - check ordering; awaiting confirmation from JB" xsd:string [Term] id: UBERON:0006268 @@ -14768,8 +14409,8 @@ xref: NCIT:C34232 xref: UMLS:C1518430 {source="ncithesaurus:Notochordal_Process"} xref: VHOG:0001213 is_a: UBERON:0005423 ! developing anatomical structure -relationship: develops_from UBERON:0000924 {source="EHDAA2"} ! ectoderm -relationship: only_in_taxon NCBITaxon:7711 ! Chordata +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002202 UBERON:0000924 {source="EHDAA2"} ! develops from ectoderm [Term] id: UBERON:0006314 @@ -14788,8 +14429,8 @@ xref: MESH:D001826 xref: Wikipedia:Body_fluid is_a: UBERON:0000463 ! organism substance intersection_of: UBERON:0000463 ! organism substance -intersection_of: has_quality PATO:0001548 ! quality of a liquid -relationship: has_quality PATO:0001548 ! quality of a liquid +intersection_of: RO:0000086 PATO:0001548 ! has quality quality of a liquid +relationship: RO:0000086 PATO:0001548 ! has quality quality of a liquid [Term] id: UBERON:0006595 @@ -14803,11 +14444,11 @@ xref: TAO:0000416 xref: ZFA:0000416 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0000925 ! endoderm intersection_of: part_of UBERON:0000307 ! blastula -relationship: has_potential_to_develop_into UBERON:0000925 ! endoderm -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +intersection_of: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm relationship: part_of UBERON:0000307 ! blastula +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm [Term] id: UBERON:0006596 @@ -14821,8 +14462,8 @@ xref: TAO:0000568 xref: ZFA:0000568 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0000178 ! blood -relationship: has_potential_to_develop_into UBERON:0000178 ! blood +intersection_of: RO:0002387 UBERON:0000178 ! has potential to develop into blood +relationship: RO:0002387 UBERON:0000178 ! has potential to develop into blood [Term] id: UBERON:0006598 @@ -14836,10 +14477,10 @@ xref: TAO:0001116 xref: ZFA:0001116 is_a: UBERON:0002050 ! embryonic structure intersection_of: UBERON:0005423 ! developing anatomical structure -intersection_of: has_potential_to_develop_into UBERON:0000061 ! anatomical structure intersection_of: part_of UBERON:0000922 ! embryo -relationship: has_potential_to_develop_into UBERON:0000061 ! anatomical structure -property_value: editor_note "Consider merging with anlage" xsd:string +intersection_of: RO:0002387 UBERON:0000061 ! has potential to develop into anatomical structure +relationship: RO:0002387 UBERON:0000061 ! has potential to develop into anatomical structure +property_value: IAO:0000116 "Consider merging with anlage" xsd:string [Term] id: UBERON:0006601 @@ -14855,11 +14496,11 @@ xref: XAO:0004132 xref: ZFA:0001376 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0000924 ! ectoderm intersection_of: part_of UBERON:0000307 ! blastula -relationship: has_potential_to_develop_into UBERON:0000924 ! ectoderm -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +intersection_of: RO:0002387 UBERON:0000924 ! has potential to develop into ectoderm relationship: part_of UBERON:0000307 ! blastula +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002387 UBERON:0000924 ! has potential to develop into ectoderm [Term] id: UBERON:0006603 @@ -14873,11 +14514,11 @@ xref: TAO:0001377 xref: ZFA:0001377 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0000926 ! mesoderm intersection_of: part_of UBERON:0000307 ! blastula -relationship: has_potential_to_develop_into UBERON:0000926 ! mesoderm -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +intersection_of: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm relationship: part_of UBERON:0000307 ! blastula +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm [Term] id: UBERON:0006914 @@ -14893,7 +14534,6 @@ is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: has_part CL:0000076 ! squamous epithelial cell relationship: has_part CL:0000076 ! squamous epithelial cell -property_value: UBPROP:0000012 "FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium" xsd:string {external_ontology="FBbt"} [Term] id: UBERON:0006965 @@ -14924,7 +14564,7 @@ xref: EHDAA2_RETIRED:0003192 xref: FMA:24137 xref: NCIT:C34022 xref: UMLS:C1515977 {source="ncithesaurus:Anatomic_Surface"} -is_a: UBERON:0010199 {notes="via morphological boundary in CARO"} ! bona-fide anatomical boundary +is_a: UBERON:0010199 ! bona-fide anatomical boundary [Term] id: UBERON:0007005 @@ -14947,13 +14587,14 @@ xref: FMA:293143 xref: SCTID:360387000 xref: VHOG:0001641 xref: XAO:0000235 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue -relationship: developmentally_induced_by UBERON:0009881 ! anterior lateral plate mesoderm -relationship: develops_from UBERON:0004872 ! splanchnic layer of lateral plate mesoderm relationship: part_of UBERON:0004140 ! primary heart field relationship: part_of UBERON:0009881 ! anterior lateral plate mesoderm -property_value: editor_note "consider FBbt:00005541 ! cardiogenic mesoderm" xsd:string -property_value: editor_note "review EHDAA2 placement" xsd:string +relationship: RO:0002202 UBERON:0004872 ! develops from splanchnic layer of lateral plate mesoderm +relationship: RO:0002256 UBERON:0009881 ! developmentally induced by anterior lateral plate mesoderm +property_value: IAO:0000116 "consider FBbt:00005541 ! cardiogenic mesoderm" xsd:string +property_value: IAO:0000116 "review EHDAA2 placement" xsd:string [Term] id: UBERON:0007010 @@ -14963,10 +14604,10 @@ def: "Organism at the cleavage stage." [OBOL:automatic] xref: BILA:0000058 is_a: UBERON:0000922 ! embryo intersection_of: UBERON:0000468 ! multicellular organism -intersection_of: existence_ends_with UBERON:0000107 ! cleavage stage -intersection_of: existence_starts_with UBERON:0000107 ! cleavage stage -relationship: existence_ends_with UBERON:0000107 ! cleavage stage -relationship: existence_starts_with UBERON:0000107 ! cleavage stage +intersection_of: RO:0002489 UBERON:0000107 ! existence starts with cleavage stage +intersection_of: RO:0002493 UBERON:0000107 ! existence ends with cleavage stage +relationship: RO:0002489 UBERON:0000107 ! existence starts with cleavage stage +relationship: RO:0002493 UBERON:0000107 ! existence ends with cleavage stage [Term] id: UBERON:0007026 @@ -14985,12 +14626,11 @@ xref: SCTID:360394002 xref: UMLS:C1514442 {source="ncithesaurus:Primordial_Gut"} is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001555 ! digestive tract -relationship: existence_starts_during UBERON:0000109 ! gastrula stage -relationship: has_developmental_contribution_from UBERON:0000925 ! endoderm -relationship: has_developmental_contribution_from UBERON:0000926 ! mesoderm -relationship: has_potential_to_develop_into UBERON:0001555 ! digestive tract -property_value: UBPROP:0000011 "The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis" xsd:string {source="NCBIBook:NBK10107"} +intersection_of: RO:0002387 UBERON:0001555 ! has potential to develop into digestive tract +relationship: RO:0002254 UBERON:0000925 ! has developmental contribution from endoderm +relationship: RO:0002254 UBERON:0000926 ! has developmental contribution from mesoderm +relationship: RO:0002387 UBERON:0001555 ! has potential to develop into digestive tract +relationship: RO:0002488 UBERON:0000109 ! existence starts during gastrula stage [Term] id: UBERON:0007100 @@ -15003,14 +14643,12 @@ synonym: "adult heart" RELATED [FBbt:00003154] synonym: "dorsal tube" NARROW [Wikipedia:Heart] synonym: "heart" NARROW [GO:0007507] xref: http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg -xref: SPD:0000130 xref: TADS:0000147 is_a: UBERON:0015228 ! circulatory organ intersection_of: UBERON:0015228 ! circulatory organ intersection_of: capable_of GO:0008015 ! blood circulation -relationship: capable_of GO:0008015 {notes="GO uses blood circulation generically to include the haemolymphatic fluid of arthropods"} ! blood circulation +relationship: capable_of GO:0008015 ! blood circulation relationship: has_part CL:0002494 ! cardiocyte -property_value: UBPROP:0000008 "note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis" xsd:string [Term] id: UBERON:0007135 @@ -15023,8 +14661,7 @@ xref: EFO:0003497 xref: TAO:0000131 xref: ZFA:0000131 is_a: UBERON:0016879 ! future central nervous system -relationship: develops_from UBERON:0003075 ! neural plate -property_value: UBPROP:0000001 "An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000131", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002202 UBERON:0003075 ! develops from neural plate [Term] id: UBERON:0007282 @@ -15038,9 +14675,9 @@ xref: TAO:0000053 xref: ZFA:0000053 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0003059 ! presomitic mesoderm -relationship: develops_from UBERON:0009618 {consistent_with="https://github.com/obophenotype/uberon/wiki/The-neural-crest", source="EDHAA2"} ! trunk paraxial mesoderm -relationship: has_potential_to_develop_into UBERON:0003059 ! presomitic mesoderm +intersection_of: RO:0002387 UBERON:0003059 ! has potential to develop into presomitic mesoderm +relationship: RO:0002202 UBERON:0009618 ! develops from trunk paraxial mesoderm +relationship: RO:0002387 UBERON:0003059 ! has potential to develop into presomitic mesoderm [Term] id: UBERON:0007284 @@ -15055,12 +14692,11 @@ xref: TAO:0000063 xref: ZFA:0000063 is_a: UBERON:0016879 ! future central nervous system intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0003075 ! neural plate -relationship: develops_from UBERON:0002346 ! neurectoderm -relationship: has_potential_to_develop_into UBERON:0003075 ! neural plate +intersection_of: RO:0002387 UBERON:0003075 ! has potential to develop into neural plate relationship: part_of UBERON:0004734 ! gastrula -property_value: editor_note "consider merging" xsd:string -property_value: UBPROP:0000001 "Region of the gastrula which gives rise to the neural plate.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000063", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002202 UBERON:0002346 ! develops from neurectoderm +relationship: RO:0002387 UBERON:0003075 ! has potential to develop into neural plate +property_value: IAO:0000116 "consider merging" xsd:string [Term] id: UBERON:0007285 @@ -15076,10 +14712,10 @@ xref: XAO:0004134 xref: ZFA:0000591 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 {source="https://github.com/obophenotype/uberon/issues/1277"} ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0003077 {source="https://github.com/obophenotype/uberon/issues/1277"} ! paraxial mesoderm intersection_of: part_of UBERON:0000307 {source="https://github.com/obophenotype/uberon/issues/1277"} ! blastula -relationship: has_potential_to_develop_into UBERON:0003077 ! paraxial mesoderm +intersection_of: RO:0002387 UBERON:0003077 {source="https://github.com/obophenotype/uberon/issues/1277"} ! has potential to develop into paraxial mesoderm relationship: part_of UBERON:0000307 ! blastula +relationship: RO:0002387 UBERON:0003077 ! has potential to develop into paraxial mesoderm [Term] id: UBERON:0007500 @@ -15120,7 +14756,7 @@ is_a: UBERON:0003104 ! mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: participates_in GO:0016477 ! cell migration relationship: participates_in GO:0016477 ! cell migration -property_value: editor_note "this class will be an important part of the NC reorganization" xsd:string +property_value: IAO:0000116 "this class will be an important part of the NC reorganization" xsd:string [Term] id: UBERON:0007688 @@ -15135,7 +14771,6 @@ synonym: "organ field" RELATED [] xref: AEO:0000170 xref: EFO:0001649 xref: EHDAA2:0003170 -xref: FBbt:00005426 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: Wikipedia:Anlage_(biology) is_a: UBERON:0000479 {source="FBbt"} ! tissue is_a: UBERON:0005423 {source="AEO", source="FBbt"} ! developing anatomical structure @@ -15156,10 +14791,8 @@ xref: NCIT:C33854 xref: UMLS:C0489903 {source="ncithesaurus:Vascular_System"} is_a: UBERON:0000467 ! anatomical system relationship: part_of UBERON:0004535 {source="MA"} ! cardiovascular system -relationship: present_in_taxon NCBITaxon:9606 -property_value: editor_note "consider merging with vasculature" xsd:string -property_value: UBPROP:0000001 "The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]." xsd:string {source="ncithesaurus:Vascular_System"} -property_value: UBPROP:0000012 "in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system" xsd:string {external_ontology="MA"} +property_value: IAO:0000116 "consider merging with vasculature" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0009142 @@ -15171,10 +14804,10 @@ xref: EHDAA2:0001113 xref: EHDAA:177 xref: EMAPA:16097 is_a: UBERON:0000477 ! anatomical cluster -relationship: composed_primarily_of UBERON:0003104 ! mesenchyme -relationship: has_developmental_contribution_from UBERON:0000926 {source="EHDAA2"} ! mesoderm relationship: part_of UBERON:0000922 ! embryo -property_value: editor_note "consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)" xsd:string +relationship: RO:0002254 UBERON:0000926 {source="EHDAA2"} ! has developmental contribution from mesoderm +relationship: RO:0002473 UBERON:0003104 ! composed primarily of mesenchyme +property_value: IAO:0000116 "consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)" xsd:string [Term] id: UBERON:0009569 @@ -15208,6 +14841,7 @@ synonym: "ALPM" EXACT [ZFA:0005041] xref: EFO:0003704 xref: TAO:0005041 xref: ZFA:0005041 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue relationship: part_of UBERON:0003081 {source="ZFA"} ! lateral plate mesoderm @@ -15220,15 +14854,14 @@ subset: common_anatomy subset: upper_level synonym: "multicellular structure" EXACT [FBbt:00100313] xref: CARO:0010000 -xref: FBbt:00100313 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: has_quality PATO:0001993 ! multicellular +intersection_of: RO:0000086 PATO:0001993 ! has quality multicellular relationship: has_part CL:0000000 ! cell -relationship: has_quality PATO:0001993 ! multicellular -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0000086 PATO:0001993 ! has quality multicellular +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0010199 @@ -15257,12 +14890,12 @@ is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000463 ! organism substance intersection_of: UBERON:0000463 ! organism substance intersection_of: output_of GO:0007596 ! blood coagulation -relationship: develops_from UBERON:0000178 {source="BTO"} ! blood relationship: has_part CL:0000232 ! erythrocyte relationship: has_part CL:0000233 ! platelet relationship: has_part CL:0000738 ! leukocyte relationship: has_part GO:0005577 ! fibrinogen complex relationship: output_of GO:0007596 ! blood coagulation +relationship: RO:0002202 UBERON:0000178 {source="BTO"} ! develops from blood [Term] id: UBERON:0010314 @@ -15272,9 +14905,8 @@ def: "An anatomical structure that has some part that develops from the neural c subset: grouping_class is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: has_developmental_contribution_from UBERON:0002342 ! neural crest -relationship: has_developmental_contribution_from UBERON:0002342 ! neural crest -property_value: IAO:0000232 "Grouping term for query purposes" xsd:string +intersection_of: RO:0002254 UBERON:0002342 ! has developmental contribution from neural crest +relationship: RO:0002254 UBERON:0002342 ! has developmental contribution from neural crest [Term] id: UBERON:0010316 @@ -15282,7 +14914,7 @@ name: germ layer / neural crest namespace: uberon is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0005291 ! embryonic tissue -relationship: develops_from UBERON:0002532 ! epiblast (generic) +relationship: RO:0002202 UBERON:0002532 ! develops from epiblast (generic) [Term] id: UBERON:0010371 @@ -15294,8 +14926,8 @@ xref: FMA:69064 is_a: UBERON:0000483 ! epithelium is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000483 ! epithelium -intersection_of: develops_from UBERON:0000924 ! ectoderm -relationship: composed_primarily_of CL:0002077 ! ecto-epithelial cell +intersection_of: RO:0002202 UBERON:0000924 ! develops from ectoderm +relationship: RO:0002473 CL:0002077 ! composed primarily of ecto-epithelial cell [Term] id: UBERON:0010912 @@ -15311,7 +14943,6 @@ xref: VSAO:0000042 is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision relationship: part_of UBERON:0000075 {source="UBERONREF:0000003"} ! subdivision of skeletal system relationship: part_of UBERON:0004288 {source="VSAO"} ! skeleton -property_value: UBPROP:0000001 "Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000042", notes="incorrect", ontology="VSAO", source="VSAO:curator"} [Term] id: UBERON:0011137 @@ -15332,7 +14963,7 @@ synonym: "axial skeletal system" BROAD [https://github.com/obophenotype/uberon/w synonym: "post-cranial axial skeletal system" EXACT [] xref: FMA:302077 is_a: UBERON:0000075 {source="FMA"} ! subdivision of skeletal system -relationship: develops_from UBERON:0003089 {source="cjm"} ! sclerotome +relationship: RO:0002202 UBERON:0003089 {source="cjm"} ! develops from sclerotome property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" xsd:anyURI [Term] @@ -15343,15 +14974,14 @@ def: "A subdivision of an anatomical system." [http://orcid.org/0000-0002-6601-2 subset: common_anatomy subset: human_reference_atlas subset: upper_level -xref: FBbt:00007330 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67509 xref: SCTID:91690000 is_a: UBERON:0010000 {source="FBbt"} ! multicellular anatomical structure relationship: part_of UBERON:0000467 ! anatomical system -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0011585 @@ -15361,7 +14991,7 @@ def: "Anatomical structure that is an aggregation of similar cells from which ca xref: VSAO:0000006 xref: XAO:0004021 is_a: UBERON:0000061 {source="VSAO"} ! anatomical structure -property_value: editor_note "consider obsoleting, coordinate with VSAO" xsd:string +property_value: IAO:0000116 "consider obsoleting, coordinate with VSAO" xsd:string [Term] id: UBERON:0011676 @@ -15374,7 +15004,7 @@ synonym: "body segment" RELATED [] synonym: "main body segment" RELATED [] is_a: UBERON:0000475 ! organism subdivision relationship: part_of UBERON:0013701 ! main body axis -property_value: editor_note "Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem" xsd:string +property_value: IAO:0000116 "Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem" xsd:string [Term] id: UBERON:0011695 @@ -15405,10 +15035,9 @@ synonym: "schizocoelom" NARROW [] xref: EHDAA2:0004731 xref: Wikipedia:Coelom is_a: UBERON:0000481 {source="EHDAA2"} ! multi-tissue structure -relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -property_value: editor_note "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." xsd:string -property_value: UBPROP:0000007 "coelomic" xsd:string +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +property_value: IAO:0000116 "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." xsd:string +property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} [Term] id: UBERON:0012275 @@ -15421,7 +15050,7 @@ xref: FMA:86452 is_a: UBERON:0000483 ! epithelium is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000483 ! epithelium -intersection_of: develops_from UBERON:0000926 ! mesoderm +intersection_of: RO:0002202 UBERON:0000926 ! develops from mesoderm [Term] id: UBERON:0012429 @@ -15437,12 +15066,12 @@ xref: CALOHA:TS-2142 xref: FMA:14073 xref: NCIT:C13051 xref: UMLS:C0229619 {source="ncithesaurus:Hematopoietic_Tissue"} +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0034769 {source="FMA"} ! lymphomyeloid tissue intersection_of: UBERON:0000479 ! tissue intersection_of: site_of GO:0030097 ! hemopoiesis relationship: part_of UBERON:0002390 {source="defitional"} ! hematopoietic system relationship: site_of GO:0030097 ! hemopoiesis -property_value: UBPROP:0000008 "Bone marrow in humans, kidney interstitium in Danio, within a stroma of reticuloendothelial tissue" xsd:string [Term] id: UBERON:0013522 @@ -15463,11 +15092,11 @@ subset: common_anatomy synonym: "foramen space" NARROW [] xref: FMA:9338 is_a: UBERON:0000464 {source="FMA"} ! anatomical space -relationship: connects UBERON:0000464 {cardinality="2"} ! anatomical space -relationship: luminal_space_of UBERON:0004111 ! anatomical conduit -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0002176 UBERON:0000464 {cardinality="2"} ! connects anatomical space +relationship: RO:0002572 UBERON:0004111 ! luminal space of anatomical conduit +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0013701 @@ -15476,7 +15105,7 @@ namespace: uberon def: "A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages." [https://orcid.org/0000-0002-6601-2165] subset: non_informative is_a: UBERON:0000475 ! organism subdivision -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0013702 @@ -15488,11 +15117,9 @@ synonym: "body" RELATED [AEO:0000103] synonym: "whole body" RELATED [BTO:0001489] xref: AEO:0000103 xref: BTO:0001489 -xref: EMAPA:36031 xref: FMA:231424 is_a: UBERON:0000475 {source="AEO"} ! organism subdivision relationship: part_of UBERON:0013701 ! main body axis -property_value: UBPROP:0000001 "Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]." xsd:string {source="FMA:231424"} [Term] id: UBERON:0014477 @@ -15510,7 +15137,7 @@ xref: Wikipedia:Thoracic_skeleton is_a: UBERON:0010912 ! subdivision of skeleton relationship: part_of UBERON:0000915 ! thoracic segment of trunk relationship: part_of UBERON:0002090 ! postcranial axial skeleton -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0014903 @@ -15522,9 +15149,9 @@ xref: TAO:0005076 xref: ZFA:0005076 is_a: UBERON:0001048 ! primordium intersection_of: UBERON:0001048 ! primordium -intersection_of: has_potential_to_develop_into UBERON:0002049 ! vasculature -relationship: has_potential_to_develop_into UBERON:0002049 ! vasculature +intersection_of: RO:0002387 UBERON:0002049 ! has potential to develop into vasculature relationship: part_of UBERON:0011695 ! embryonic cardiovascular system +relationship: RO:0002387 UBERON:0002049 ! has potential to develop into vasculature [Term] id: UBERON:0015203 @@ -15532,7 +15159,6 @@ name: non-connected functional system namespace: uberon def: "An anatomical group whose component structures share a common function." [AEO:0000093, AEO:JB, FBbt:00007278, FBC:DOS] xref: AEO:0000093 -xref: FBbt:00007278 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0034923 ! disconnected anatomical group [Term] @@ -15543,11 +15169,7 @@ def: "Any structure that is placed on one side of the left-right axis of a bilat subset: grouping_class subset: non_informative is_a: UBERON:0000061 ! anatomical structure -intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: in_lateral_side_of UBERON:0000465 ! material anatomical entity -relationship: in_lateral_side_of UBERON:0000465 ! material anatomical entity -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -property_value: IAO:0000232 "This class is primarily to implement taxon constraints. It may be removed in the future." xsd:string +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria [Term] id: UBERON:0015228 @@ -15560,10 +15182,9 @@ synonym: "cardiac structure" RELATED [] synonym: "circulatory vessel" NARROW [] synonym: "heart" BROAD [] synonym: "heart or heart like organ" EXACT [] -xref: SPD:0000130 is_a: UBERON:0003103 ! compound organ -relationship: has_quality PATO:0001690 ! contractile relationship: part_of UBERON:0001009 ! circulatory system +relationship: RO:0000086 PATO:0001690 ! has quality contractile [Term] id: UBERON:0015410 @@ -15575,7 +15196,7 @@ xref: EMAPA:37597 {source="MA:th"} xref: MA:0002449 is_a: UBERON:0005178 {source="MA"} ! thoracic cavity element relationship: part_of UBERON:0004535 ! cardiovascular system -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0015757 @@ -15595,10 +15216,10 @@ synonym: "future CNS" EXACT [] synonym: "presumptive central nervous system" EXACT [] is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001017 ! central nervous system -relationship: develops_from UBERON:0000924 ! ectoderm -relationship: has_potential_to_develop_into UBERON:0001017 ! central nervous system +intersection_of: RO:0002387 UBERON:0001017 ! has potential to develop into central nervous system relationship: part_of UBERON:0016880 ! future nervous system +relationship: RO:0002202 UBERON:0000924 ! develops from ectoderm +relationship: RO:0002387 UBERON:0001017 ! has potential to develop into central nervous system [Term] id: UBERON:0016880 @@ -15610,9 +15231,9 @@ synonym: "presumptive nervous system" EXACT [AAO:0000477] xref: AAO:0000477 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001016 ! nervous system -relationship: existence_starts_during_or_after UBERON:0000111 ! organogenesis stage -relationship: has_potential_to_develop_into UBERON:0001016 ! nervous system +intersection_of: RO:0002387 UBERON:0001016 ! has potential to develop into nervous system +relationship: RO:0002387 UBERON:0001016 ! has potential to develop into nervous system +relationship: RO:0002496 UBERON:0000111 ! existence starts during or after organogenesis stage [Term] id: UBERON:0016887 @@ -15626,8 +15247,8 @@ xref: EHDAA2:0000003 xref: EMAPA:16042 is_a: UBERON:0000481 {source="AEO"} ! multi-tissue structure relationship: adjacent_to UBERON:0002050 ! embryonic structure -relationship: existence_starts_and_ends_during UBERON:0000068 ! embryo stage relationship: part_of UBERON:0004716 {source="AEO"} ! conceptus +relationship: RO:0002491 UBERON:0000068 ! existence starts and ends during embryo stage [Term] id: UBERON:0034769 @@ -15646,10 +15267,10 @@ subset: common_anatomy synonym: "anatomical cluster" RELATED [CARO:0020001] xref: CARO:0020001 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure -relationship: composed_primarily_of UBERON:0000064 ! organ part -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0002473 UBERON:0000064 ! composed primarily of organ part +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0034923 @@ -15658,14 +15279,13 @@ namespace: uberon def: "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other." [CARO:0020000] subset: common_anatomy xref: CARO:0020000 -xref: FBbt:00007276 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000465 {source="CARO"} ! material anatomical entity -relationship: composed_primarily_of UBERON:0000061 ! anatomical structure relationship: has_component UBERON:0000061 {minCardinality="2"} ! anatomical structure -relationship: has_quality PATO:0010001 ! disconnected -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0000086 PATO:0010001 ! has quality disconnected +relationship: RO:0002473 UBERON:0000061 ! composed primarily of anatomical structure +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0034925 @@ -15674,11 +15294,11 @@ namespace: uberon def: "A collection of anatomical structures that are alike in terms of their morphology or developmental origin." [http://orcid.org/0000-0002-6601-2165] subset: common_anatomy is_a: UBERON:0000465 ! material anatomical entity -relationship: has_member UBERON:0000061 ! anatomical structure -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: editor_note "resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected" xsd:string +relationship: RO:0002351 UBERON:0000061 ! has member anatomical structure +property_value: IAO:0000116 "resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0035804 @@ -15703,6 +15323,12 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007688 ! anlage +[Typedef] +id: BFO:0000067 +name: contains process +def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] +comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant + [Typedef] id: CL:4030044 name: has_not_completed @@ -15722,11 +15348,6 @@ id: RO:0000052 name: characteristic of def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." [] comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. -property_value: IAO:0000111 "inheres in" xsd:string -property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string -property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string -property_value: IAO:0000118 "inheres_in" xsd:string -property_value: RO:0001900 RO:0001901 is_functional: true is_a: RO:0002314 ! characteristic of part of inverse_of: bearer_of ! bearer of @@ -15736,10 +15357,7 @@ id: RO:0000079 name: function of def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. -property_value: editor_note "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string -property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string -property_value: IAO:0000118 "function_of" xsd:string -property_value: IAO:0000118 "is function of" xsd:string +property_value: IAO:0000116 "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string is_a: RO:0000052 ! characteristic of inverse_of: RO:0000085 ! has function @@ -15748,22 +15366,16 @@ id: RO:0000080 name: quality of def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. -property_value: editor_note "A quality inheres in its bearer at all times for which the quality exists." xsd:string -property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string -property_value: IAO:0000118 "is quality of" xsd:string -property_value: IAO:0000118 "quality_of" xsd:string +property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string is_a: RO:0000052 ! characteristic of -inverse_of: has_quality ! has quality +inverse_of: RO:0000086 ! has quality [Typedef] id: RO:0000081 name: role of def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. -property_value: editor_note "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string -property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string -property_value: IAO:0000118 "is role of" xsd:string -property_value: IAO:0000118 "role_of" xsd:string +property_value: IAO:0000116 "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string is_a: RO:0000052 ! characteristic of inverse_of: RO:0000087 ! has role @@ -15771,19 +15383,22 @@ inverse_of: RO:0000087 ! has role id: RO:0000085 name: has function def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] -property_value: editor_note "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string -property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string -property_value: IAO:0000118 "has_function" xsd:string +property_value: IAO:0000116 "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string domain: BFO:0000004 ! independent continuant is_a: bearer_of ! bearer of +[Typedef] +id: RO:0000086 +name: has quality +def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] +property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string +is_a: bearer_of ! bearer of + [Typedef] id: RO:0000087 name: has role def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] -property_value: editor_note "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string -property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string -property_value: IAO:0000118 "has_role" xsd:string +property_value: IAO:0000116 "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string domain: BFO:0000004 ! independent continuant is_a: bearer_of ! bearer of @@ -15808,12 +15423,7 @@ id: RO:0001000 name: derives from def: "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" [] subset: ro-eco -property_value: editor_note "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." xsd:string -property_value: IAO:0000112 "this cell derives from this parent cell (cell division)" xsd:string -property_value: IAO:0000112 "this nucleus derives from this parent nucleus (nuclear division)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000118 "derives_from" xsd:string -property_value: IAO:0000232 "This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations." xsd:string +property_value: IAO:0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." xsd:string inverse_of: RO:0001001 ! derives into [Typedef] @@ -15821,33 +15431,57 @@ id: RO:0001001 name: derives into def: "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" [] subset: ro-eco -property_value: editor_note "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." xsd:string -property_value: IAO:0000112 "this parent cell derives into this cell (cell division)" xsd:string -property_value: IAO:0000112 "this parent nucleus derives into this nucleus (nuclear division)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000118 "derives_into" xsd:string +property_value: IAO:0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." xsd:string + +[Typedef] +id: RO:0001015 +name: location of +def: "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" [] +property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +is_transitive: true +inverse_of: RO:0001025 ! located in + +[Typedef] +id: RO:0001025 +name: located in +def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +property_value: IAO:0000116 "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" xsd:string +property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Located_in" xsd:anyURI +domain: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +range: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +is_transitive: true +transitive_over: part_of ! part of [Typedef] id: RO:0002000 name: 2D boundary of def: "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" [] -property_value: editor_note "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string -property_value: editor_note "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string -property_value: IAO:0000112 "the surface of my skin is a 2D boundary of my body" xsd:string -property_value: IAO:0000118 "2D_boundary_of" xsd:string -property_value: IAO:0000118 "boundary of" xsd:string -property_value: IAO:0000118 "is 2D boundary of" xsd:string -property_value: IAO:0000118 "is boundary of" xsd:string -property_value: IAO:0000118 "surface of" xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string +is_a: RO:0002323 ! mereotopologically related to +inverse_of: RO:0002002 ! has 2D boundary + +[Typedef] +id: RO:0002002 +name: has 2D boundary +def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000141 ! immaterial entity is_a: RO:0002323 ! mereotopologically related to -inverse_of: has_boundary ! has 2D boundary + +[Typedef] +id: RO:0002005 +name: innervated_by +domain: UBERON:0000061 ! anatomical structure +inverse_of: RO:0002134 ! innervates [Typedef] id: RO:0002006 name: has synaptic terminal of -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: overlaps ! overlaps inverse_of: RO:0002130 ! has synaptic terminal in @@ -15929,16 +15563,23 @@ id: RO:0002081 name: before or simultaneous with comment: Primitive instance level timing relation between events subset: ro-eco -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000118 "<=" xsd:string is_a: RO:0002222 ! temporally related to +[Typedef] +id: RO:0002082 +name: simultaneous with +def: "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." [] +comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) +subset: ro-eco +is_symmetric: true +is_transitive: true +is_a: RO:0002081 ! before or simultaneous with + [Typedef] id: RO:0002086 name: ends after comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) subset: ro-eco -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string is_transitive: true is_a: RO:0002222 ! temporally related to @@ -15946,25 +15587,16 @@ is_a: RO:0002222 ! temporally related to id: RO:0002100 name: has soma location def: "Relation between a neuron and a material anatomical entity that its soma is part of." [] -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron range: UBERON:0000465 ! material anatomical entity is_a: overlaps ! overlaps -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] [Typedef] id: RO:0002101 name: fasciculates with def: "relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.\n" [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "fasciculates with" xsd:string -property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: overlaps ! overlaps inverse_of: RO:0002132 ! has fasciculating neuron projection @@ -15973,27 +15605,23 @@ inverse_of: RO:0002132 ! has fasciculating neuron projection id: RO:0002102 name: axon synapses in def: "Relation between a neuron and some structure its axon forms (chemical) synapses in." [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: RO:0002113 ! has presynaptic terminal in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "BFO_0000051 some (\n GO_0030424 and BFO_0000051 some (\n GO_0042734 and BFO_0000050 some (\n GO_0045202 and BFO_0000050 some ?Y)))" [] +[Typedef] +id: RO:0002103 +name: synapsed by +def: "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " [] +is_a: RO:0002485 ! receives input from +inverse_of: RO:0002120 ! synapsed to +expand_expression_to: "BFO_0000051 some (GO_0045211 that part_of some (GO_0045202 that has_part some (GO_0042734 that BFO_0000050 some Y?)))" [] + [Typedef] id: RO:0002104 name: has plasma membrane part def: "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part." [] -property_value: IAO:0000112 "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9990-8331 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 -property_value: RO:0001900 RO:0001901 domain: UBERON:0000465 ! material anatomical entity range: UBERON:0000465 ! material anatomical entity is_a: has_part ! has part @@ -16003,29 +15631,19 @@ expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] id: RO:0002110 name: has postsynaptic terminal in def: "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. " [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "synapsed in" xsd:string -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: RO:0002130 ! has synaptic terminal in inverse_of: RO:0002113 ! has presynaptic terminal in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (\n http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some (\n http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))" [] [Typedef] id: RO:0002113 name: has presynaptic terminal in def: "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input." [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000118 "synapses in" xsd:string -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: RO:0002130 ! has synaptic terminal in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000050 some Y?)" [] [Typedef] @@ -16033,11 +15651,6 @@ id: RO:0002120 name: synapsed to def: " Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.\n " [] comment: N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part some (\n ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( \n ‘synapse ; GO:0045202’ that has_part some (\n ‘post-synaptic membrane ; GO:0045211’ that part_of some N2)))) -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 is_a: RO:0002486 ! sends output to expand_expression_to: "BFO_0000051 some (GO_0042734 that part_of some (GO_0045202 that BFO_0000051 some (GO_0045211 that BFO_0000050 some Y?)))" [] @@ -16045,103 +15658,270 @@ expand_expression_to: "BFO_0000051 some (GO_0042734 that part_of some (GO_004520 id: RO:0002130 name: has synaptic terminal in def: "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "has synapse in" xsd:string -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: overlaps ! overlaps -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "RO_0002131 some (GO_0045202 that BFO_0000050 some Y?)" [] [Typedef] id: RO:0002132 name: has fasciculating neuron projection def: "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "has fasciculating component" xsd:string -property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string -property_value: RO:0001900 RO:0001901 is_a: overlaps ! overlaps +[Typedef] +id: RO:0002134 +name: innervates +def: "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." [] +transitive_over: part_of ! part of +expand_expression_to: "RO_0002132 some (GO_0043005 that (RO_0002131 some (GO_0045202 that BFO_0000050 some Y?)))" [] + +[Typedef] +id: RO:0002150 +name: continuous with +def: "X continuous_with Y if and only if X and Y share a fiat boundary." [] +property_value: seeAlso "FMA:85972" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000004 ! independent continuant +is_symmetric: true +is_a: RO:0002323 ! mereotopologically related to + +[Typedef] +id: RO:0002158 +name: shares ancestor with +def: "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." [] +comment: VBO calls this homologous_to +is_symmetric: true +is_transitive: true +is_a: RO:0002320 ! evolutionarily related to + +[Typedef] +id: RO:0002160 +name: only in taxon +def: "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." [] +property_value: IAO:0000116 "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" xsd:string +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints +is_a: RO:0002162 ! in taxon + +[Typedef] +id: RO:0002162 +name: in taxon +def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." [] +comment: Connects a biological entity to its taxon of origin. +subset: ro-eco +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints +holds_over_chain: capable_of RO:0002162 +holds_over_chain: extends_fibers_into RO:0002162 +holds_over_chain: has_part RO:0002162 +holds_over_chain: part_of RO:0002162 +holds_over_chain: results_in_developmental_progression_of RO:0002162 +holds_over_chain: RO:0002202 RO:0002162 +holds_over_chain: RO:0002206 RO:0002162 +holds_over_chain: RO:0002225 RO:0002162 +holds_over_chain: RO:0002254 RO:0002162 +is_a: RO:0002320 ! evolutionarily related to + [Typedef] id: RO:0002163 name: spatially disjoint from def: "A is spatially_disjoint_from B if and only if they have no parts in common" [] subset: ro-eco -property_value: editor_note "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" xsd:anyURI is_a: RO:0002323 ! mereotopologically related to expand_expression_to: "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" [] +[Typedef] +id: RO:0002170 +name: connected to +def: "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" [] +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI +is_a: RO:0002323 ! mereotopologically related to + +[Typedef] +id: RO:0002176 +name: connects +def: "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." [] +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI +domain: BFO:0000004 ! independent continuant +is_a: RO:0002323 ! mereotopologically related to + +[Typedef] +id: RO:0002177 +name: attached to part of +def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000061 ! anatomical structure +is_a: RO:0002323 ! mereotopologically related to +is_a: RO:0002567 ! biomechanically related to + +[Typedef] +id: RO:0002178 +name: supplies +def: "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." [] +property_value: IAO:0000116 "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" xsd:string +is_a: RO:0002170 ! connected to + +[Typedef] +id: RO:0002179 +name: drains +def: "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." [] +property_value: IAO:0000116 "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" xsd:string +is_a: RO:0002170 ! connected to + +[Typedef] +id: RO:0002202 +name: develops from +def: "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" [] +comment: This is the transitive form of the develops from relation +domain: BFO:0000004 ! independent continuant +range: BFO:0000004 ! independent continuant +is_transitive: true +is_a: RO:0002254 ! has developmental contribution from +is_a: RO:0002258 ! developmentally preceded by +inverse_of: RO:0002203 ! develops into + +[Typedef] +id: RO:0002203 +name: develops into +def: "inverse of develops from" [] +subset: RO:0002259 +is_transitive: true +is_a: RO:0002286 ! developmentally succeeded by +is_a: RO:0002387 ! has potential to develop into +is_a: RO:0002388 ! has potential to directly develop into + [Typedef] id: RO:0002206 name: expressed in def: "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" [] -property_value: IAO:0000112 "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000002 ! continuant range: UBERON:0000465 ! material anatomical entity is_a: RO:0002330 ! genomically related to inverse_of: RO:0002292 ! expresses -transitive_over: part_of ! part_of +transitive_over: part_of ! part of + +[Typedef] +id: RO:0002207 +name: directly develops from +def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] +comment: TODO - add child relations from DOS +synonym: "has developmental precursor" EXACT [] +is_a: RO:0002202 ! develops from +inverse_of: RO:0002210 ! directly develops into [Typedef] id: RO:0002210 name: directly develops into def: "inverse of directly develops from" [] subset: RO:0002259 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000118 "developmental precursor of" xsd:string -is_a: develops_into ! develops into +is_a: RO:0002203 ! develops into + +[Typedef] +id: RO:0002219 +name: surrounded by +def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" [] +is_a: adjacent_to ! adjacent to +inverse_of: RO:0002221 ! surrounds + +[Typedef] +id: RO:0002221 +name: surrounds +def: "inverse of surrounded by" [] +subset: RO:0002259 +is_a: adjacent_to ! adjacent to [Typedef] id: RO:0002222 name: temporally related to comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. subset: ro-eco -property_value: http://purl.org/dc/terms/source "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" xsd:anyURI -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent +[Typedef] +id: RO:0002223 +name: starts +def: "inverse of starts with" [] +subset: ro-eco +is_a: part_of ! part of +is_a: RO:0002222 ! temporally related to +inverse_of: starts_with ! starts with + +[Typedef] +id: RO:0002225 +name: develops from part of +def: "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" [] +holds_over_chain: RO:0002207 part_of +is_a: RO:0002202 ! develops from + +[Typedef] +id: RO:0002226 +name: develops in +def: "x develops_in y if x is located in y whilst x is developing" [] +domain: UBERON:0001062 ! anatomical entity +holds_over_chain: RO:0002207 RO:0001025 +is_a: RO:0002258 ! developmentally preceded by + +[Typedef] +id: RO:0002229 +name: ends +def: "inverse of ends with" [] +subset: ro-eco +is_a: part_of ! part of +is_a: RO:0002222 ! temporally related to +inverse_of: ends_with ! ends with + +[Typedef] +id: RO:0002252 +name: connecting branch of +def: "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." [] +property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 +is_a: RO:0002170 ! connected to +is_a: RO:0002375 ! in branching relationship with +inverse_of: RO:0002253 ! has connecting branch + [Typedef] id: RO:0002253 name: has connecting branch def: "inverse of connecting branch of" [] subset: RO:0002259 -property_value: RO:0004036 BFO:0000051 is_a: RO:0002375 ! in branching relationship with +[Typedef] +id: RO:0002254 +name: has developmental contribution from +def: "x has developmental contribution from y iff x has some part z such that z develops from y" [] +domain: UBERON:0001062 ! anatomical entity +range: UBERON:0001062 ! anatomical entity +holds_over_chain: has_part RO:0002202 +is_a: RO:0002258 ! developmentally preceded by +inverse_of: RO:0002255 ! developmentally contributes to + [Typedef] id: RO:0002255 name: developmentally contributes to def: "inverse of has developmental contribution from" [] subset: RO:0002259 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -holds_over_chain: develops_into part_of -is_a: has_potential_to_developmentally_contribute_to ! has potential to developmentally contribute to +holds_over_chain: RO:0002203 part_of is_a: RO:0002286 ! developmentally succeeded by +is_a: RO:0002385 ! has potential to developmentally contribute to + +[Typedef] +id: RO:0002256 +name: developmentally induced by +def: "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" [] +domain: UBERON:0000465 ! material anatomical entity +range: UBERON:0000465 ! material anatomical entity +is_a: RO:0002258 ! developmentally preceded by +inverse_of: RO:0002257 ! developmentally induces [Typedef] id: RO:0002257 name: developmentally induces def: "Inverse of developmentally induced by" [] -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002286 ! developmentally succeeded by is_a: RO:0002386 ! has potential to developmentally induce @@ -16150,10 +15930,7 @@ id: RO:0002258 name: developmentally preceded by def: "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p" [] comment: This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from -property_value: editor_note "false" xsd:boolean -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string +property_value: IAO:0000116 "false" xsd:boolean domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant is_a: RO:0002324 ! developmentally related to @@ -16164,7 +15941,6 @@ id: RO:0002263 name: acts upstream of def: "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: IAO:0000112 "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." xsd:string property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of holds_over_chain: RO:0002327 causally_upstream_of is_a: RO:0002264 ! acts upstream of or within @@ -16175,25 +15951,26 @@ name: acts upstream of or within def: "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term synonym: "affects" RELATED [] -property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within" xsd:anyURI holds_over_chain: RO:0002327 causally_upstream_of_or_within is_a: RO:0002500 ! causal agent in process +[Typedef] +id: RO:0002285 +name: developmentally replaces +def: "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" [] +property_value: IAO:0000116 "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" xsd:string +is_a: RO:0002258 ! developmentally preceded by + [Typedef] id: RO:0002286 name: developmentally succeeded by def: "Inverse of developmentally preceded by" [] -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002384 ! has developmental potential involving [Typedef] id: RO:0002287 name: part of developmental precursor of -property_value: IAO:0000112 "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: part_of RO:0002210 is_a: RO:0002286 ! developmentally succeeded by @@ -16201,80 +15978,58 @@ is_a: RO:0002286 ! developmentally succeeded by id: RO:0002292 name: expresses def: "y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." [] -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002330 ! genomically related to [Typedef] id: RO:0002314 name: characteristic of part of def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." [] -property_value: editor_note "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "inheres in part of" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: RO:0000052 part_of {RO:0002582="true"} is_a: RO:0002502 ! depends on -transitive_over: part_of ! part_of +transitive_over: part_of ! part of [Typedef] id: RO:0002320 name: evolutionarily related to def: "A relationship that holds via some environmental process" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." xsd:string [Typedef] id: RO:0002323 name: mereotopologically related to def: "A mereological relationship or a topological relationship" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string -property_value: RO:0001900 RO:0001901 [Typedef] id: RO:0002324 name: developmentally related to def: "A relationship that holds between entities participating in some developmental process (GO:0032502)" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" xsd:string [Typedef] id: RO:0002327 name: enables def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "catalyzes" xsd:string -property_value: IAO:0000118 "executes" xsd:string -property_value: IAO:0000118 "has" xsd:string -property_value: IAO:0000118 "is catalyzing" xsd:string -property_value: IAO:0000118 "is executing" xsd:string -property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string property_value: seeAlso "https://wiki.geneontology.org/Enables" xsd:anyURI is_a: capable_of ! capable of inverse_of: RO:0002333 ! enabled by transitive_over: has_part ! has part transitive_over: RO:0002017 ! has component activity +[Typedef] +id: RO:0002328 +name: functionally related to +def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] + [Typedef] id: RO:0002329 name: part of structure that is capable of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "false" xsd:boolean -holds_over_chain: part_of capable_of {RO:0002581="true"} -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002330 name: genomically related to def: "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant @@ -16282,31 +16037,25 @@ range: BFO:0000002 ! continuant id: RO:0002331 name: involved in def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "actively involved in" xsd:string -property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Involved_in" xsd:anyURI holds_over_chain: RO:0002327 part_of is_a: participates_in ! participates in is_a: RO:0002431 ! involved in or involved in regulation of -transitive_over: part_of ! part_of +transitive_over: part_of ! part of [Typedef] id: RO:0002333 name: enabled by def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso "https://wiki.geneontology.org/Enabled_by" xsd:anyURI -is_a: functionally_related_to ! functionally related to is_a: has_participant ! has participant +is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002337 name: related via localization to def: "A relationship that holds via some process of localization" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is a grouping relation." xsd:string domain: BFO:0000015 ! process range: BFO:0000002 ! continuant @@ -16314,84 +16063,134 @@ range: BFO:0000002 ! continuant id: RO:0002350 name: member of def: "is member of is a mereological relation between a item and a collection." [] -property_value: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string -property_value: IAO:0000118 "is member of" xsd:string -property_value: IAO:0000118 "member part of" xsd:string -property_value: IAO:0000119 "SIO" xsd:string -property_value: RO:0001900 RO:0001901 -is_a: part_of ! part_of -inverse_of: has_member ! has member +is_a: part_of ! part of +inverse_of: RO:0002351 ! has member + +[Typedef] +id: RO:0002351 +name: has member +def: "has member is a mereological relation between a collection and an item." [] +is_a: has_part ! has part + +[Typedef] +id: RO:0002352 +name: input of +def: "inverse of has input" [] +subset: ro-eco +subset: RO:0002259 +is_a: participates_in ! participates in +is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002354 name: formed as result of -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: output_of ! output of [Typedef] id: RO:0002360 name: has dendrite location -property_value: http://purl.org/dc/terms/source "http://neurolex.org/wiki/Property:DendriteLocation" xsd:anyURI -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps [Typedef] -id: RO:0002375 -name: in branching relationship with -def: "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" xsd:string -property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string -property_value: RO:0004036 BFO:0000050 -property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png -property_value: seeAlso "https://github.com/obophenotype/uberon/issues/170" xsd:anyURI -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: RO:0002323 ! mereotopologically related to +id: RO:0002371 +name: attached to +def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] +subset: ro-eco +is_symmetric: true +is_a: RO:0002170 ! connected to +is_a: RO:0002177 ! attached to part of [Typedef] -id: RO:0002379 -name: spatially coextensive with -def: "x spatially_coextensive_with y if and inly if x and y have the same location" [] -property_value: IAO:0000112 "A lump of clay and a statue" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" xsd:string -is_a: overlaps ! overlaps +id: RO:0002372 +name: has muscle origin +def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] +property_value: seeAlso http://dbpedia.org/property/origin +domain: UBERON:0000061 {comment="We need to import uberon muscle to create a stricter domain constraint"} ! anatomical structure +is_a: RO:0002371 ! attached to +is_a: RO:0002567 ! biomechanically related to + +[Typedef] +id: RO:0002373 +name: has muscle insertion +def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] +property_value: seeAlso http://dbpedia.org/property/insertion +domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} ! anatomical structure +is_a: RO:0002371 ! attached to +is_a: RO:0002567 ! biomechanically related to + +[Typedef] +id: RO:0002375 +name: in branching relationship with +def: "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." [] +property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png +property_value: seeAlso "https://github.com/obophenotype/uberon/issues/170" xsd:anyURI +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002323 ! mereotopologically related to + +[Typedef] +id: RO:0002376 +name: tributary of +def: "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." [] +subset: ro-eco +property_value: seeAlso http://dbpedia.org/ontology/drainsTo +property_value: seeAlso "http://en.wikipedia.org/wiki/Tributary" xsd:anyURI +is_a: RO:0002170 ! connected to +is_a: RO:0002375 ! in branching relationship with + +[Typedef] +id: RO:0002379 +name: spatially coextensive with +def: "x spatially_coextensive_with y if and inly if x and y have the same location" [] +is_a: overlaps ! overlaps + +[Typedef] +id: RO:0002380 +name: branching part of +def: "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" [] +subset: ro-eco +property_value: seeAlso "FMA:85994" xsd:string +property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 +is_a: part_of ! part of +is_a: RO:0002375 ! in branching relationship with +inverse_of: RO:0002569 ! has branching part [Typedef] id: RO:0002384 name: has developmental potential involving def: "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: UBERON:0001062 ! anatomical entity range: UBERON:0001062 ! anatomical entity is_a: RO:0002324 ! developmentally related to +[Typedef] +id: RO:0002385 +name: has potential to developmentally contribute to +def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] +is_a: RO:0002384 ! has developmental potential involving + [Typedef] id: RO:0002386 name: has potential to developmentally induce def: "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002384 ! has developmental potential involving + +[Typedef] +id: RO:0002387 +name: has potential to develop into +def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] is_a: RO:0002384 ! has developmental potential involving [Typedef] id: RO:0002388 name: has potential to directly develop into def: "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: has_potential_to_develop_into ! has potential to develop into +is_a: RO:0002387 ! has potential to develop into [Typedef] id: RO:0002407 name: indirectly positively regulates def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "indirectly activates" xsd:string -property_value: RO:0002579 RO:0002213 property_value: seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates" xsd:anyURI holds_over_chain: directly_positively_regulates directly_positively_regulates holds_over_chain: directly_positively_regulates RO:0002407 @@ -16405,9 +16204,6 @@ transitive_over: directly_positively_regulates ! directly positively regulates id: RO:0002409 name: indirectly negatively regulates def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "indirectly inhibits" xsd:string -property_value: RO:0002579 RO:0002212 property_value: seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates" xsd:anyURI holds_over_chain: directly_negatively_regulates directly_negatively_regulates holds_over_chain: directly_negatively_regulates RO:0002409 @@ -16420,15 +16216,12 @@ transitive_over: directly_negatively_regulates ! directly negatively regulates id: RO:0002410 name: causally related to def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] -property_value: editor_note "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string [Typedef] id: RO:0002428 name: involved in regulation of def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002327 regulates holds_over_chain: RO:0002331 regulates is_a: RO:0002263 ! acts upstream of @@ -16438,8 +16231,6 @@ is_a: RO:0002431 ! involved in or involved in regulation of id: RO:0002429 name: involved in positive regulation of def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0004049 RO:0002428 holds_over_chain: RO:0002327 positively_regulates holds_over_chain: RO:0002331 positively_regulates is_a: RO:0002428 ! involved in regulation of @@ -16448,7 +16239,6 @@ is_a: RO:0002428 ! involved in regulation of id: RO:0002430 name: involved in negative regulation of def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002428 holds_over_chain: RO:0002327 negatively_regulates holds_over_chain: RO:0002331 negatively_regulates @@ -16458,11 +16248,9 @@ is_a: RO:0002428 ! involved in regulation of id: RO:0002431 name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] -property_value: editor_note "OWL does not allow defining object properties via a Union" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "involved in or reguates" xsd:string -is_a: functionally_related_to ! functionally related to +property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string is_a: RO:0002264 ! acts upstream of or within +is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process [Typedef] @@ -16470,12 +16258,14 @@ id: RO:0002432 name: is active in def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [https://orcid.org/0000-0002-6601-2165, https://orcid.org/0000-0002-7073-9172] synonym: "enables activity in" EXACT [] -property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "executes activity in" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Is_active_in" xsd:anyURI -holds_over_chain: RO:0002327 occurs_in {RO:0002581="true"} -is_a: functionally_related_to ! functionally related to +is_a: overlaps ! overlaps +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002433 +name: contributes to morphology of +def: "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." [] is_a: overlaps ! overlaps [Typedef] @@ -16484,11 +16274,8 @@ name: interacts with def: "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." [] subset: ro-eco synonym: "in pairwise interaction with" EXACT [] -property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0914" xsd:anyURI -property_value: editor_note "Considering relabeling as 'pairwise interacts with'" xsd:anyURI -property_value: editor_note "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string +property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI +property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity @@ -16498,10 +16285,6 @@ is_symmetric: true id: RO:0002436 name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] -property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0915" xsd:anyURI -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "binds" xsd:string -property_value: IAO:0000118 "molecularly binds with" xsd:string property_value: seeAlso ECO:0000353 is_symmetric: true is_a: RO:0002434 ! interacts with @@ -16509,9 +16292,7 @@ is_a: RO:0002434 ! interacts with [Typedef] id: RO:0002447 name: phosphorylates -property_value: editor_note "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string +property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string is_a: RO:0002436 ! molecularly interacts with [Typedef] @@ -16519,8 +16300,6 @@ id: RO:0002448 name: directly regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." [] synonym: "molecularly controls" EXACT [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002436 ! molecularly interacts with @@ -16531,9 +16310,6 @@ id: RO:0002449 name: directly negatively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] synonym: "molecularly decreases activity of" EXACT [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 -property_value: IAO:0000118 "directly inhibits" xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002448 ! directly regulates activity of @@ -16543,9 +16319,6 @@ id: RO:0002450 name: directly positively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] synonym: "molecularly increases activity of" EXACT [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 -property_value: IAO:0000118 "directly activates" xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002448 ! directly regulates activity of @@ -16553,61 +16326,136 @@ is_a: RO:0002448 ! directly regulates activity of [Typedef] id: RO:0002464 name: helper property (not for use in curation) -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string + +[Typedef] +id: RO:0002473 +name: composed primarily of +def: "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." [] +subset: ro-eco +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: has_part ! has part [Typedef] id: RO:0002479 name: has part that occurs in def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] subset: ro-eco -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant -holds_over_chain: has_part occurs_in {RO:0002581="true"} [Typedef] id: RO:0002481 name: is kinase activity -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002564 ! molecular interaction relation helper property [Typedef] id: RO:0002485 name: receives input from -property_value: editor_note "See notes for inverse relation" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: connected_to ! connected to +property_value: IAO:0000116 "See notes for inverse relation" xsd:string +is_a: RO:0002170 ! connected to inverse_of: RO:0002486 ! sends output to [Typedef] id: RO:0002486 name: sends output to -property_value: editor_note "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: connected_to ! connected to +property_value: IAO:0000116 "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." xsd:string +is_a: RO:0002170 ! connected to [Typedef] id: RO:0002487 name: relation between physical entity and a process or stage -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage." xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000003 ! occurrent +[Typedef] +id: RO:0002488 +name: existence starts during +def: "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." [] +is_a: RO:0002490 ! existence overlaps +is_a: RO:0002496 ! existence starts during or after +transitive_over: part_of ! part of + +[Typedef] +id: RO:0002489 +name: existence starts with +def: "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." [] +is_a: RO:0002488 ! existence starts during + [Typedef] id: RO:0002490 name: existence overlaps def: "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" [] comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002487 ! relation between physical entity and a process or stage +[Typedef] +id: RO:0002491 +name: existence starts and ends during +def: "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +synonym: "exists during" EXACT [] +is_a: RO:0002488 ! existence starts during +is_a: RO:0002492 ! existence ends during + +[Typedef] +id: RO:0002492 +name: existence ends during +def: "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +is_a: RO:0002490 ! existence overlaps +is_a: RO:0002497 ! existence ends during or before +transitive_over: part_of ! part of + +[Typedef] +id: RO:0002493 +name: existence ends with +def: "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +is_a: RO:0002492 ! existence ends during + +[Typedef] +id: RO:0002494 +name: transformation of +def: "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" [] +is_transitive: true +is_a: RO:0002202 ! develops from + +[Typedef] +id: RO:0002495 +name: immediate transformation of +def: "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" [] +is_a: RO:0002207 ! directly develops from +is_a: RO:0002494 ! transformation of + +[Typedef] +id: RO:0002496 +name: existence starts during or after +def: "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +holds_over_chain: part_of RO:0002496 +holds_over_chain: RO:0002258 RO:0002496 +is_a: RO:0002487 ! relation between physical entity and a process or stage +transitive_over: part_of ! part of +transitive_over: preceded_by ! preceded by +transitive_over: RO:0002082 ! simultaneous with + +[Typedef] +id: RO:0002497 +name: existence ends during or before +def: "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +holds_over_chain: part_of RO:0002497 +holds_over_chain: RO:0002286 RO:0002497 +is_a: RO:0002487 ! relation between physical entity and a process or stage +transitive_over: part_of ! part of +transitive_over: precedes ! precedes +transitive_over: RO:0002082 ! simultaneous with + [Typedef] id: RO:0002500 name: causal agent in process def: "A relationship between a material entity and a process where the material entity has some causal role that influences the process" [] -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_a: RO:0002595 ! causal relation between material entity and a process inverse_of: process_has_causal_agent ! process has causal agent @@ -16615,9 +16463,6 @@ inverse_of: process_has_causal_agent ! process has causal agent id: RO:0002501 name: causal relation between processes def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent is_a: RO:0002410 ! causally related to @@ -16625,33 +16470,35 @@ is_a: RO:0002410 ! causally related to [Typedef] id: RO:0002502 name: depends on -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso BFO:0000169 [Typedef] id: RO:0002506 name: causal relation between entities -property_value: editor_note "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: IAO:0000116 "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant is_a: RO:0002410 ! causally related to +[Typedef] +id: RO:0002551 +name: has skeleton +def: "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." [] +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000465 {IAO:0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} ! material anatomical entity +is_a: has_part ! has part +inverse_of: RO:0002576 ! skeleton of +is_asymmetric: true + [Typedef] id: RO:0002559 name: causally influenced by -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string is_a: RO:0002506 ! causal relation between entities inverse_of: RO:0002566 ! causally influences [Typedef] id: RO:0002563 name: interaction relation helper property -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29 property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI is_a: RO:0002464 ! helper property (not for use in curation) @@ -16659,17 +16506,12 @@ is_a: RO:0002464 ! helper property (not for use in curation) [Typedef] id: RO:0002564 name: molecular interaction relation helper property -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002563 ! interaction relation helper property [Typedef] id: RO:0002566 name: causally influences def: "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant is_a: RO:0002506 ! causal relation between entities @@ -16678,20 +16520,66 @@ is_a: RO:0002506 ! causal relation between entities id: RO:0002567 name: biomechanically related to def: "A relation that holds between elements of a musculoskeletal system or its analogs." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string domain: UBERON:0000061 ! anatomical structure range: UBERON:0000061 ! anatomical structure -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002568 +name: has muscle antagonist +def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] +is_a: RO:0002567 ! biomechanically related to + +[Typedef] +id: RO:0002569 +name: has branching part +def: "inverse of branching part of" [] +subset: ro-eco +subset: RO:0002259 +is_transitive: true +is_a: has_part ! has part +is_a: RO:0002375 ! in branching relationship with + +[Typedef] +id: RO:0002570 +name: conduit for +def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] +subset: ro-eco +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: overlaps ! overlaps + +[Typedef] +id: RO:0002571 +name: lumen of +def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] +subset: ro-eco +range: BFO:0000040 ! material entity +is_a: part_of ! part of + +[Typedef] +id: RO:0002572 +name: luminal space of +def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" [] +subset: ro-eco +domain: BFO:0000141 ! immaterial entity +is_a: RO:0002571 ! lumen of + +[Typedef] +id: RO:0002576 +name: skeleton of +def: "inverse of has skeleton" [] +subset: RO:0002259 +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000061 ! anatomical structure +is_a: part_of ! part of [Typedef] id: RO:0002584 name: has part structure that is capable of def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" [] -property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: has_part capable_of -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to is_a: RO:0002595 ! causal relation between material entity and a process [Typedef] @@ -16704,9 +16592,7 @@ is_a: has_input ! has input id: RO:0002595 name: causal relation between material entity and a process def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." [] -property_value: editor_note "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000040 ! material entity range: BFO:0000015 ! process is_a: RO:0002410 ! causally related to @@ -16715,8 +16601,6 @@ is_a: RO:0002410 ! causally related to id: RO:0002596 name: capable of regulating def: "Holds between c and p if and only if c is capable of some activity a, and a regulates p." [] -property_value: IAO:0000112 "pyrethroid -> growth" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations holds_over_chain: capable_of regulates is_a: RO:0002500 ! causal agent in process @@ -16724,7 +16608,6 @@ is_a: RO:0002500 ! causal agent in process id: RO:0002597 name: capable of negatively regulating def: "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." [] -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations holds_over_chain: capable_of negatively_regulates is_a: RO:0002596 ! capable of regulating @@ -16732,8 +16615,6 @@ is_a: RO:0002596 ! capable of regulating id: RO:0002598 name: capable of positively regulating def: "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." [] -property_value: IAO:0000112 "renin -> arteriolar smooth muscle contraction" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations holds_over_chain: capable_of positively_regulates is_a: RO:0002596 ! capable of regulating @@ -16742,7 +16623,7 @@ id: RO:0004031 name: enables subfunction def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] holds_over_chain: RO:0002327 has_part -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z @@ -16750,7 +16631,6 @@ creation_date: 2018-01-25T23:20:13Z id: RO:0004032 name: acts upstream of or within, positive effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: RO:0004049 RO:0002264 property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0004047 is_a: RO:0002264 ! acts upstream of or within @@ -16773,7 +16653,6 @@ id: RO:0004034 name: acts upstream of, positive effect def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: RO:0004049 RO:0002263 property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 causally_upstream_of,_positive_effect is_a: RO:0002263 ! acts upstream of @@ -16806,7 +16685,6 @@ creation_date: 2018-03-13T23:55:05Z [Typedef] id: RO:0004047 name: causally upstream of or within, positive effect -property_value: RO:0004049 RO:0002418 property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect is_a: causally_upstream_of_or_within ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 @@ -16816,7 +16694,6 @@ creation_date: 2018-03-13T23:55:19Z id: RO:0011002 name: regulates activity of def: "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." [] -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002566 ! causally influences @@ -16871,7 +16748,7 @@ name: has synaptic IO in region def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region." [] synonym: "has synaptic input or output in" EXACT [] is_a: RO:0002130 ! has synaptic terminal in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:26:52Z @@ -16883,7 +16760,7 @@ synonym: "has sensory dendrite location" EXACT [] synonym: "has sensory terminal in" EXACT [] synonym: "has sensory terminal location" EXACT [] is_a: RO:0002360 ! has dendrite location -transitive_over: part_of ! part_of +transitive_over: part_of ! part of created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-20T12:10:09Z @@ -16926,9 +16803,8 @@ comment: Example: a spherical object has the quality of being spherical, and the id: RO:0015015 name: has high plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: dc-contributor https://orcid.org/0000-0003-1617-8244 -property_value: dc-contributor https://orcid.org/0000-0003-1940-6740 -property_value: IAO:0000112 "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part @@ -16936,9 +16812,8 @@ is_a: RO:0002104 ! has plasma membrane part id: RO:0015016 name: has low plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: dc-contributor https://orcid.org/0000-0003-1617-8244 -property_value: dc-contributor https://orcid.org/0000-0003-1940-6740 -property_value: IAO:0000112 "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part @@ -16947,11 +16822,6 @@ id: RO:0017001 name: device utilizes material def: "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." [] synonym: "utilizes" BROAD [] -property_value: IAO:0000112 "A diagnostic testing device utilizes a specimen." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 -property_value: IAO:0000117 https://orcid.org/0000-0003-2620-0345 -property_value: IAO:0000232 "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." xsd:string -property_value: IAO:0000232 "See github ticket https://github.com/oborel/obo-relations/issues/497" xsd:string holds_over_chain: capable_of has_input creation_date: 2021-11-08T12:00:00Z @@ -16972,65 +16842,24 @@ creation_date: 2020-06-08T17:21:33Z id: adjacent_to name: adjacent to namespace: external -namespace: uberon def: "x adjacent to y if and only if x and y share a boundary." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002220 -property_value: editor_note "This relation acts as a join point with BSPO" xsd:string -property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} -property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string -property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string -property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000004 ! independent continuant is_a: RO:0002163 ! spatially disjoint from -[Typedef] -id: anterior_to -name: anterior to -namespace: uberon -xref: BSPO:0000096 - [Typedef] id: anteriorly_connected_to name: anteriorly connected to namespace: uberon def: "x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] -is_a: connected_to ! connected to -is_a: posterior_to ! posterior to +is_a: RO:0002170 ! connected to is_a: transitively_anteriorly_connected_to ! transitively anteriorly connected to -[Typedef] -id: attaches_to -name: attached to -namespace: uberon -def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] -subset: ro-eco -xref: RO:0002371 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000589 "attached to (anatomical structure to anatomical structure)" xsd:string -is_symmetric: true -is_a: attaches_to_part_of ! attached to part of -is_a: connected_to ! connected to - -[Typedef] -id: attaches_to_part_of -name: attached to part of -namespace: uberon -def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] -xref: RO:0002177 -property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string -domain: UBERON:0000061 ! anatomical structure -range: UBERON:0000061 ! anatomical structure -holds_over_chain: attaches_to part_of {RO:0002582="true"} -is_a: RO:0002323 ! mereotopologically related to -is_a: RO:0002567 ! biomechanically related to - [Typedef] id: bearer_of name: bearer of @@ -17038,13 +16867,7 @@ name: has characteristic namespace: external def: "Inverse of characteristic_of" [] xref: RO:0000053 -property_value: editor_note "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string -property_value: IAO:0000111 "bearer of" xsd:string -property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string -property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string -property_value: IAO:0000118 "bearer_of" xsd:string -property_value: IAO:0000118 "is bearer of" xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string range: BFO:0000020 ! specifically dependent continuant is_inverse_functional: true @@ -17052,45 +16875,20 @@ is_inverse_functional: true id: bounding_layer_of name: bounding layer of namespace: external -namespace: uberon def: "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000" [] comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. subset: ro-eco xref: RO:0002007 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 range: BFO:0000040 ! material entity -is_a: part_of ! part_of - -[Typedef] -id: branching_part_of -name: branching part of -namespace: uberon -def: "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" [] -subset: ro-eco -xref: RO:0002380 -property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso "FMA:85994" xsd:string -property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 -is_a: part_of ! part_of -is_a: RO:0002375 ! in branching relationship with -inverse_of: has_branching_part ! has branching part +is_a: part_of ! part of [Typedef] id: capable_of name: capable of namespace: external -namespace: uberon def: "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " [] subset: ro-eco xref: RO:0002215 -property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string -property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "has function realized in" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 -property_value: IAO:0000232 "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000015 ! process is_a: capable_of_part_of ! capable of part of @@ -17099,14 +16897,10 @@ is_a: capable_of_part_of ! capable of part of id: capable_of_part_of name: capable of part of namespace: external -namespace: uberon def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] xref: RO:0002216 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "has function in" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: capable_of part_of {RO:0002582="true"} -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process [Typedef] @@ -17115,8 +16909,6 @@ name: causally downstream of namespace: external def: "inverse of upstream of" [] xref: RO:0002404 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of_or_within ! causally downstream of or within is_a: preceded_by ! preceded by inverse_of: causally_upstream_of ! causally upstream of @@ -17128,8 +16920,6 @@ namespace: external def: "inverse of causally upstream of or within" [] subset: RO:0002259 xref: RO:0002427 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_transitive: true is_a: RO:0002501 ! causal relation between processes @@ -17141,7 +16931,6 @@ def: "p is causally upstream of q iff p is causally related to q, the end of p p subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002411 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within is_a: precedes ! precedes @@ -17154,7 +16943,6 @@ def: "p is causally upstream of, negative effect q iff p is casually upstream of subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 -property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_negative_effect is_a: causally_upstream_of ! causally upstream of @@ -17169,8 +16957,6 @@ comment: holds between x and y if and only if x is causally upstream of y and th subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002304 -property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 -property_value: RO:0004049 RO:0002411 property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_positive_effect is_a: causally_upstream_of ! causally upstream of is_a: RO:0004047 ! causally upstream of or within, positive effect @@ -17182,9 +16968,7 @@ namespace: external def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] synonym: "affects" RELATED [] xref: RO:0002418 -property_value: editor_note "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "influences (processual)" xsd:string +property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string is_transitive: true is_a: RO:0002501 ! causal relation between processes inverse_of: causally_downstream_of_or_within ! causally downstream of or within @@ -17194,510 +16978,81 @@ id: channel_for name: channel for namespace: uberon synonym: "carries" BROAD [] -domain: UBERON:0004111 ! anatomical conduit -range: UBERON:0000463 ! organism substance [Typedef] id: channels_from name: channels_from namespace: uberon -is_transitive: true [Typedef] id: channels_into name: channels_into namespace: uberon -is_transitive: true [Typedef] -id: composed_primarily_of -name: composed primarily of -namespace: uberon -def: "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." [] -subset: ro-eco -xref: RO:0002473 -property_value: IAO:0000112 "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: RO:0001900 RO:0001901 -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: has_part ! has part +id: directly_negatively_regulates +name: directly negatively regulates +namespace: external +def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0002630 +property_value: RO:0004050 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates" xsd:anyURI +is_a: directly_regulates ! directly regulates +is_a: negatively_regulates ! negatively regulates [Typedef] -id: conduit_for -name: conduit for -namespace: uberon -def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] -subset: ro-eco -xref: RO:0002570 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "UBERON:cjm" xsd:string -property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: overlaps ! overlaps +id: directly_positively_regulates +name: directly positively regulates +namespace: external +def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0002629 +property_value: seeAlso "https://wiki.geneontology.org/Directly_positively_regulates" xsd:anyURI +is_a: directly_regulates ! directly regulates +is_a: positively_regulates ! positively regulates [Typedef] -id: connected_to -name: connected to -namespace: uberon -def: "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" [] -xref: RO:0002170 -property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI -property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI -is_a: RO:0002323 ! mereotopologically related to +id: directly_regulates +name: directly regulates +namespace: external +def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0002578 +is_a: immediately_causally_upstream_of ! immediately causally upstream of +is_a: regulates ! regulates [Typedef] -id: connecting_branch_of -name: connecting branch of -namespace: uberon -def: "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." [] -xref: RO:0002252 -property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." xsd:string -property_value: RO:0004036 BFO:0000050 -property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 -is_a: connected_to ! connected to -is_a: RO:0002375 ! in branching relationship with -inverse_of: RO:0002253 ! has connecting branch - -[Typedef] -id: connects -name: connects -namespace: uberon -def: "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." [] -xref: RO:0002176 -property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string -property_value: IAO:0000112 "The M8 connects Glasgow and Edinburgh" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI -property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI -domain: BFO:0000004 ! independent continuant -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: contains_process -name: contains process -namespace: uberon -def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] -comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant -xref: BFO:0000067 -property_value: IAO:0000111 "site of" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - -[Typedef] -id: continuous_with -name: continuous with -namespace: uberon -def: "X continuous_with Y if and only if X and Y share a fiat boundary." [] -xref: RO:0002150 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "connected to" xsd:string -property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string -property_value: RO:0001900 RO:0001901 -property_value: seeAlso "FMA:85972" xsd:string -domain: BFO:0000004 ! independent continuant -range: BFO:0000004 ! independent continuant -is_symmetric: true -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: contributes_to_morphology_of -name: contributes to morphology of -namespace: uberon -def: "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." [] -xref: RO:0002433 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: overlaps ! overlaps - -[Typedef] -id: dc-contributor -name: contributor -namespace: uberon -xref: http://purl.org/dc/terms/contributor -is_metadata_tag: true - -[Typedef] -id: dc-creator -name: creator -namespace: uberon -xref: http://purl.org/dc/elements/1.1/creator -is_metadata_tag: true - -[Typedef] -id: dc-description -name: description -namespace: uberon -xref: http://purl.org/dc/elements/1.1/description -is_metadata_tag: true - -[Typedef] -id: dc-title -name: title -namespace: uberon -xref: http://purl.org/dc/elements/1.1/title -is_metadata_tag: true - -[Typedef] -id: dcterms-date -name: date -namespace: uberon -xref: http://purl.org/dc/terms/date -is_metadata_tag: true - -[Typedef] -id: dcterms-license -name: license -namespace: uberon -xref: http://purl.org/dc/terms/license -is_metadata_tag: true - -[Typedef] -id: deep_to -name: deep to -namespace: uberon -xref: BSPO:0000107 - -[Typedef] -id: depiction -name: depiction -namespace: uberon -xref: http://xmlns.com/foaf/0.1/depiction -is_metadata_tag: true - -[Typedef] -id: developmentally_induced_by -name: developmentally induced by -namespace: uberon -def: "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" [] -xref: RO:0002256 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "induced by" xsd:string -property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string -property_value: IAO:0000119 "GO:0001759" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 -property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string -domain: UBERON:0000465 ! material anatomical entity -range: UBERON:0000465 ! material anatomical entity -is_a: RO:0002258 ! developmentally preceded by -inverse_of: RO:0002257 ! developmentally induces - -[Typedef] -id: developmentally_replaces -name: developmentally replaces -namespace: uberon -def: "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" [] -xref: RO:0002285 -property_value: editor_note "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "replaces" xsd:string -is_a: RO:0002258 ! developmentally preceded by - -[Typedef] -id: develops_from -name: develops from -namespace: uberon -def: "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" [] -comment: This is the transitive form of the develops from relation -xref: RO:0002202 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 -domain: BFO:0000004 ! independent continuant -range: BFO:0000004 ! independent continuant -is_transitive: true -is_a: has_developmental_contribution_from ! has developmental contribution from -is_a: RO:0002258 ! developmentally preceded by -inverse_of: develops_into ! develops into - -[Typedef] -id: develops_from_part_of -name: develops from part of -namespace: uberon -def: "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" [] -xref: RO:0002225 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -holds_over_chain: directly_develops_from part_of -is_a: develops_from ! develops from - -[Typedef] -id: develops_in -name: develops in -namespace: uberon -def: "x develops_in y if x is located in y whilst x is developing" [] -xref: RO:0002226 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "EHDAA2" xsd:string -property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string -domain: UBERON:0001062 ! anatomical entity -holds_over_chain: directly_develops_from located_in -is_a: RO:0002258 ! developmentally preceded by - -[Typedef] -id: develops_into -name: develops into -namespace: uberon -def: "inverse of develops from" [] -subset: RO:0002259 -xref: RO:0002203 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 -is_transitive: true -is_a: has_potential_to_develop_into ! has potential to develop into -is_a: RO:0002286 ! developmentally succeeded by -is_a: RO:0002388 ! has potential to directly develop into - -[Typedef] -id: directly_develops_from -name: directly develops from -namespace: uberon -def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] -comment: TODO - add child relations from DOS -synonym: "has developmental precursor" EXACT [] -xref: RO:0002207 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000119 "FBbt" xsd:string -property_value: RO:0002575 RO:0002202 -is_a: develops_from ! develops from -inverse_of: RO:0002210 ! directly develops into - -[Typedef] -id: directly_negatively_regulates -name: directly negatively regulates -namespace: external -def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -xref: RO:0002630 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string -property_value: RO:0004050 RO:0002578 -property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates" xsd:anyURI -is_a: directly_regulates ! directly regulates -is_a: negatively_regulates ! negatively regulates - -[Typedef] -id: directly_positively_regulates -name: directly positively regulates -namespace: external -def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -xref: RO:0002629 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string -property_value: RO:0004049 RO:0002578 -property_value: seeAlso "https://wiki.geneontology.org/Directly_positively_regulates" xsd:anyURI -is_a: directly_regulates ! directly regulates -is_a: positively_regulates ! positively regulates - -[Typedef] -id: directly_regulates -name: directly regulates -namespace: external -def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -xref: RO:0002578 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly regulates (processual)" xsd:string -property_value: RO:0002575 RO:0002211 -is_a: immediately_causally_upstream_of ! immediately causally upstream of -is_a: regulates ! regulates - -[Typedef] -id: distal_to -name: distal to -namespace: uberon -xref: BSPO:0000097 - -[Typedef] -id: distally_connected_to -name: distally connected to +id: distally_connected_to +name: distally connected to namespace: uberon def: "x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] -is_a: connected_to ! connected to -is_a: proximal_to ! proximal to +is_a: RO:0002170 ! connected to is_a: transitively_distally_connected_to ! transitively distally connected to -inverse_of: proximally_connected_to ! proximally connected to - -[Typedef] -id: distalmost_part_of -name: distalmost part of -namespace: uberon -xref: BSPO:0001108 - -[Typedef] -id: dorsal_to -name: dorsal to -namespace: uberon -xref: BSPO:0000098 - -[Typedef] -id: drains -name: drains -namespace: uberon -def: "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." [] -xref: RO:0002179 -property_value: editor_note "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 -is_a: connected_to ! connected to - -[Typedef] -id: editor_note -name: editor note -namespace: uberon -def: "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology." [] -xref: IAO:0000116 -property_value: IAO:0000111 "editor note" xsd:string -property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000117 "PERSON:Daniel Schober" xsd:string -property_value: IAO:0000119 "GROUP:OBI:" xsd:string -is_metadata_tag: true - -[Typedef] -id: ends -name: ends -namespace: uberon -def: "inverse of ends with" [] -subset: ro-eco -xref: RO:0002229 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: part_of ! part_of -is_a: RO:0002222 ! temporally related to -inverse_of: ends_with ! ends with [Typedef] id: ends_with name: ends with namespace: external -namespace: uberon def: "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002230 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "finished by" xsd:string is_transitive: true is_a: has_part ! has part is_a: RO:0002222 ! temporally related to -[Typedef] -id: existence_ends_during -name: existence ends during -namespace: uberon -def: "Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely." [https://orcid.org/0000-0002-6601-2165] -def: "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -synonym: "ceases_to_exist_during" EXACT [] -xref: RO:0002492 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_ends_during_or_before ! existence ends during or before -is_a: RO:0002490 ! existence overlaps -transitive_over: part_of ! part_of - -[Typedef] -id: existence_ends_during_or_before -name: existence ends during or before -namespace: uberon -def: "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -xref: RO:0002497 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -holds_over_chain: part_of existence_ends_during_or_before -holds_over_chain: RO:0002286 existence_ends_during_or_before -is_a: RO:0002487 ! relation between physical entity and a process or stage -transitive_over: part_of ! part_of -transitive_over: precedes ! precedes -transitive_over: simultaneous_with ! simultaneous with - -[Typedef] -id: existence_ends_with -name: existence ends with -namespace: uberon -def: "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -xref: RO:0002493 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_ends_during ! existence ends during - -[Typedef] -id: existence_starts_and_ends_during -name: existence starts and ends during -namespace: uberon -def: "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -synonym: "exists during" EXACT [] -xref: RO:0002491 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_ends_during ! existence ends during -is_a: existence_starts_during ! existence starts during - -[Typedef] -id: existence_starts_during -name: existence starts during -namespace: uberon -def: "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." [] -xref: RO:0002488 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_starts_during_or_after ! existence starts during or after -is_a: RO:0002490 ! existence overlaps -transitive_over: part_of ! part_of - -[Typedef] -id: existence_starts_during_or_after -name: existence starts during or after -namespace: uberon -def: "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -xref: RO:0002496 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -holds_over_chain: part_of existence_starts_during_or_after -holds_over_chain: RO:0002258 existence_starts_during_or_after -is_a: RO:0002487 ! relation between physical entity and a process or stage -transitive_over: part_of ! part_of -transitive_over: preceded_by ! preceded by -transitive_over: simultaneous_with ! simultaneous with - -[Typedef] -id: existence_starts_with -name: existence starts with -namespace: uberon -def: "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." [] -xref: RO:0002489 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_starts_during ! existence starts during - [Typedef] id: extends_fibers_into name: extends_fibers_into namespace: uberon def: "X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y" [https://orcid.org/0000-0002-7073-9172] -holds_over_chain: RO:0002100 RO:0013001 -is_symmetric: true -is_a: connected_to ! connected to +is_a: RO:0002170 ! connected to [Typedef] id: filtered_through @@ -17706,75 +17061,17 @@ namespace: uberon def: "Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity." [] comment: Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed -[Typedef] -id: functionally_related_to -name: functionally related to -namespace: uberon -def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] -xref: RO:0002328 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string - -[Typedef] -id: has_boundary -name: has 2D boundary -namespace: uberon -def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] -xref: RO:0002002 -property_value: editor_note "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string -property_value: editor_note "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string -property_value: IAO:0000112 "my body has 2D boundary the surface of my skin" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "has boundary" xsd:string -property_value: IAO:0000118 "has_2D_boundary" xsd:string -property_value: RO:0001900 RO:0001901 -domain: BFO:0000040 ! material entity -range: BFO:0000141 ! immaterial entity -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: has_branching_part -name: has branching part -namespace: uberon -def: "inverse of branching part of" [] -subset: ro-eco -subset: RO:0002259 -xref: RO:0002569 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_transitive: true -is_a: has_part ! has part -is_a: RO:0002375 ! in branching relationship with - [Typedef] id: has_component name: has component namespace: external -namespace: uberon def: "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] subset: ro-eco xref: RO:0002180 -property_value: editor_note "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency is_a: has_part ! has part -[Typedef] -id: has_developmental_contribution_from -name: has developmental contribution from -namespace: uberon -def: "x has developmental contribution from y iff x has some part z such that z develops from y" [] -xref: RO:0002254 -property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: UBERON:0001062 ! anatomical entity -range: UBERON:0001062 ! anatomical entity -holds_over_chain: has_part develops_from -is_a: RO:0002258 ! developmentally preceded by -inverse_of: RO:0002255 ! developmentally contributes to - [Typedef] id: has_end_location name: has end location @@ -17782,9 +17079,6 @@ namespace: external def: "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" [] subset: ro-eco xref: RO:0002232 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "ends with process that occurs in" xsd:string domain: BFO:0000015 ! process range: BFO:0000004 ! independent continuant holds_over_chain: ends_with occurs_in @@ -17808,14 +17102,11 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002233 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "consumes" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Has_input" xsd:anyURI domain: BFO:0000015 ! process holds_over_chain: starts_with has_input is_a: has_participant ! has participant -inverse_of: input_of ! input of +inverse_of: RO:0002352 ! input of [Typedef] id: has_low_plasma_membrane_amount @@ -17825,52 +17116,6 @@ property_value: term_tracker_item https://github.com/obophenotype/cell-ontology/ is_obsolete: true replaced_by: RO:0015016 -[Typedef] -id: has_member -name: has member -namespace: uberon -def: "has member is a mereological relation between a collection and an item." [] -xref: RO:0002351 -property_value: IAO:0000119 "SIO" xsd:string -property_value: RO:0001900 RO:0001901 -is_a: has_part ! has part - -[Typedef] -id: has_muscle_antagonist -name: has muscle antagonist -namespace: uberon -def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] -xref: RO:0002568 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "Wikipedia:Antagonist_(muscle)" xsd:string -is_a: RO:0002567 ! biomechanically related to - -[Typedef] -id: has_muscle_insertion -name: has muscle insertion -namespace: uberon -def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] -xref: RO:0002373 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string -property_value: seeAlso http://dbpedia.org/property/insertion -domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} ! anatomical structure -is_a: attaches_to ! attached to -is_a: RO:0002567 ! biomechanically related to - -[Typedef] -id: has_muscle_origin -name: has muscle origin -namespace: uberon -def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] -xref: RO:0002372 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string -property_value: seeAlso http://dbpedia.org/property/origin -domain: UBERON:0000061 {comment="We need to import uberon muscle to create a stricter domain constraint"} ! anatomical structure -is_a: attaches_to ! attached to -is_a: RO:0002567 ! biomechanically related to - [Typedef] id: has_negative_regulatory_component_activity name: has negative regulatory component activity @@ -17888,13 +17133,9 @@ id: has_ontology_root_term name: has ontology root term name: preferred_root namespace: external -namespace: uberon def: "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root." [] xref: IAO:0000700 -property_value: IAO:0000111 "has ontology root term" xsd:string -property_value: IAO:0000117 "Nicolas Matentzoglu" xsd:string is_metadata_tag: true -is_class_level: true [Typedef] id: has_output @@ -17906,9 +17147,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002234 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "produces" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Has_output" xsd:anyURI holds_over_chain: ends_with has_output is_a: has_participant ! has participant @@ -17920,62 +17158,29 @@ name: has part name: has_part namespace: external namespace: quality -namespace: uberon def: "a core relation that holds between a whole and its part" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000051 -property_value: editor_note "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string -property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string -property_value: IAO:0000111 "has part" xsd:string -property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string -property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string -property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string -property_value: IAO:0000118 "has_part" xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string is_transitive: true is_a: overlaps ! overlaps [Typedef] -id: has_participant -name: has participant -namespace: external -def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] -xref: RO:0000057 -property_value: editor_note "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string -property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string -property_value: IAO:0000111 "has participant" xsd:string -property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string -property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string -property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string -property_value: IAO:0000118 "has_participant" xsd:string -domain: BFO:0000003 ! occurrent -range: BFO:0000002 ! continuant -holds_over_chain: has_part has_participant - -[Typedef] -id: has_potential_to_develop_into -name: has potential to develop into -namespace: uberon -def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] -xref: RO:0002387 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: RO:0002384 ! has developmental potential involving - -[Typedef] -id: has_potential_to_developmentally_contribute_to -name: has potential to developmentally contribute to -namespace: uberon -def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] -xref: RO:0002385 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: RO:0002384 ! has developmental potential involving - -[Typedef] +id: has_participant +name: has participant +namespace: external +def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] +xref: RO:0000057 +property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string +domain: BFO:0000003 ! occurrent +range: BFO:0000002 ! continuant +holds_over_chain: has_part has_participant + +[Typedef] id: has_primary_input name: has primary input namespace: external @@ -18010,17 +17215,6 @@ is_a: has_primary_input_or_output ! has primary input or output created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z -[Typedef] -id: has_quality -name: has quality -namespace: uberon -def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] -xref: RO:0000086 -property_value: editor_note "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string -property_value: IAO:0000112 "this apple has quality this red color" xsd:string -property_value: IAO:0000118 "has_quality" xsd:string -is_a: bearer_of ! bearer of - [Typedef] id: has_regulatory_component_activity name: has regulatory component activity @@ -18032,24 +17226,6 @@ is_a: RO:0002017 ! has component activity created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z -[Typedef] -id: has_skeleton -name: has skeleton -namespace: uberon -def: "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." [] -xref: RO:0002551 -property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "has supporting framework" xsd:string -property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string -domain: UBERON:0000061 ! anatomical structure -domain: UBERON:0000475 ! organism subdivision -range: UBERON:0000465 {IAO:0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} ! material anatomical entity -range: UBERON:0010912 ! subdivision of skeleton -is_a: has_part ! has part -inverse_of: skeleton_of ! skeleton of -is_asymmetric: true - [Typedef] id: has_small_molecule_activator name: has small molecule activator @@ -18068,9 +17244,6 @@ namespace: external def: "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y" [] subset: ro-eco xref: RO:0002231 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "starts with process that occurs in" xsd:string domain: BFO:0000015 ! process range: BFO:0000004 ! independent continuant holds_over_chain: starts_with occurs_in @@ -18085,9 +17258,8 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002339 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of [Typedef] id: has_target_start_location @@ -18098,41 +17270,14 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002338 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in -transitive_over: part_of ! part_of - -[Typedef] -id: homologous_to -name: shares ancestor with -namespace: uberon -def: "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." [] -comment: VBO calls this homologous_to -xref: RO:0002158 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000232 "Consider obsoleting and merging with child relation, 'in homology relationship with'" xsd:string -is_symmetric: true -is_transitive: true -is_a: RO:0002320 ! evolutionarily related to - -[Typedef] -id: immediate_transformation_of -name: immediate transformation of -namespace: uberon -def: "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" [] -xref: RO:0002495 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0002575 RO:0002494 -is_a: directly_develops_from ! directly develops from -is_a: transformation_of ! transformation of +transitive_over: part_of ! part of [Typedef] id: immediately_causally_downstream_of name: immediately causally downstream of namespace: external xref: RO:0002405 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of ! causally downstream of is_a: immediately_preceded_by ! immediately preceded by inverse_of: immediately_causally_upstream_of ! immediately causally upstream of @@ -18143,26 +17288,15 @@ name: immediately causally upstream of namespace: external def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] xref: RO:0002412 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: immediately_precedes ! immediately precedes -[Typedef] -id: immediately_deep_to -name: immediately deep to -namespace: uberon -xref: BSPO:0001107 - [Typedef] id: immediately_preceded_by name: immediately preceded by namespace: external -namespace: uberon comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) xref: RO:0002087 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000118 "starts_at_end_of" xsd:string holds_over_chain: starts_with ends_with is_a: preceded_by ! preceded by inverse_of: immediately_precedes ! immediately precedes @@ -18174,228 +17308,22 @@ namespace: external comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) subset: ro-eco xref: RO:0002090 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "ends_at_start_of" xsd:string -property_value: IAO:0000118 "meets" xsd:string -property_value: RO:0002575 BFO:0000063 holds_over_chain: ends_with starts_with is_a: precedes ! precedes -[Typedef] -id: immediately_superficial_to -name: immediately superficial to -namespace: uberon -xref: BSPO:0015014 - -[Typedef] -id: in_anterior_side_of -name: in anterior side of -namespace: uberon -xref: BSPO:0000123 - -[Typedef] -id: in_deep_part_of -name: in deep part of -namespace: uberon -xref: BSPO:0001101 - -[Typedef] -id: in_dorsal_side_of -name: in dorsal side of -namespace: uberon -xref: BSPO:0015101 - -[Typedef] -id: in_lateral_side_of -name: in lateral side of -namespace: uberon -xref: BSPO:0000126 - -[Typedef] -id: in_left_side_of -name: in left side of -namespace: uberon -xref: BSPO:0000120 - -[Typedef] -id: in_posterior_side_of -name: in posterior side of -namespace: uberon -xref: BSPO:0000122 - -[Typedef] -id: in_proximal_side_of -name: in proximal side of -namespace: uberon -xref: BSPO:0000124 - -[Typedef] -id: in_right_side_of -name: in right side of -namespace: uberon -xref: BSPO:0000121 - -[Typedef] -id: in_superficial_part_of -name: in superficial part of -namespace: uberon -xref: BSPO:0001100 - -[Typedef] -id: in_taxon -name: in taxon -namespace: uberon -def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." [] -comment: Connects a biological entity to its taxon of origin. -subset: ro-eco -xref: RO:0002162 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9227-417X -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -holds_over_chain: attaches_to in_taxon -holds_over_chain: capable_of in_taxon -holds_over_chain: connected_to in_taxon -holds_over_chain: connects in_taxon -holds_over_chain: continuous_with in_taxon -holds_over_chain: developmentally_induced_by in_taxon -holds_over_chain: develops_from in_taxon -holds_over_chain: develops_from_part_of in_taxon -holds_over_chain: existence_ends_during in_taxon -holds_over_chain: existence_starts_during in_taxon -holds_over_chain: extends_fibers_into in_taxon -holds_over_chain: has_developmental_contribution_from in_taxon -holds_over_chain: has_part in_taxon -holds_over_chain: has_potential_to_develop_into in_taxon -holds_over_chain: innervated_by in_taxon -holds_over_chain: overlaps in_taxon -holds_over_chain: part_of in_taxon -holds_over_chain: produced_by in_taxon -holds_over_chain: produces in_taxon -holds_over_chain: results_in_developmental_progression_of in_taxon -holds_over_chain: RO:0002206 in_taxon -holds_over_chain: supplies in_taxon -is_a: RO:0002320 ! evolutionarily related to - [Typedef] id: indirectly_supplies name: indirectly_supplies namespace: uberon def: "a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s." [] -property_value: editor_note "add to RO" xsd:string -holds_over_chain: has_branching_part indirectly_supplies -holds_over_chain: has_branching_part supplies -is_transitive: true - -[Typedef] -id: innervated_by -name: innervated_by -namespace: uberon -xref: RO:0002005 -property_value: http://purl.org/spar/cito/citesAsAuthority "http://www.ncbi.nlm.nih.gov/pubmed/22402613" xsd:anyURI -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -domain: UBERON:0000061 ! anatomical structure -inverse_of: innervates ! innervates -transitive_over: branching_part_of ! branching part of - -[Typedef] -id: innervates -name: innervates -namespace: uberon -def: "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." [] -xref: RO:0002134 -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 -transitive_over: part_of ! part_of -expand_expression_to: "RO_0002132 some (GO_0043005 that (RO_0002131 some (GO_0045202 that BFO_0000050 some Y?)))" [] - -[Typedef] -id: input_of -name: input of -namespace: uberon -def: "inverse of has input" [] -subset: ro-eco -subset: RO:0002259 -xref: RO:0002352 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: functionally_related_to ! functionally related to -is_a: participates_in ! participates in - -[Typedef] -id: intersects_midsagittal_plane_of -name: intersects midsagittal plane of -namespace: uberon -xref: BSPO:0005001 +property_value: IAO:0000116 "add to RO" xsd:string +holds_over_chain: RO:0002569 indirectly_supplies [Typedef] id: layer_part_of name: layer part of namespace: uberon -is_a: part_of ! part_of - -[Typedef] -id: located_in -name: located in -namespace: uberon -def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -xref: RO:0001025 -property_value: editor_note "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" xsd:string -property_value: editor_note "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:located_in" xsd:string -property_value: IAO:0000111 "located in" xsd:string -property_value: IAO:0000112 "my brain is located in my head" xsd:string -property_value: IAO:0000112 "this rat is located in this cage" xsd:string -property_value: IAO:0000118 "located_in" xsd:string -property_value: RO:0001900 RO:0001901 -property_value: seeAlso "https://wiki.geneontology.org/Located_in" xsd:anyURI -domain: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant -range: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant -is_transitive: true -transitive_over: part_of ! part_of - -[Typedef] -id: location_of -name: location of -namespace: uberon -def: "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" [] -xref: RO:0001015 -property_value: editor_note "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: IAO:0000111 "is location of" xsd:string -property_value: IAO:0000112 "my head is the location of my brain" xsd:string -property_value: IAO:0000112 "this cage is the location of this rat" xsd:string -property_value: IAO:0000118 "location_of" xsd:string -property_value: RO:0001900 RO:0001901 -is_transitive: true -inverse_of: located_in ! located in - -[Typedef] -id: lumen_of -name: lumen of -namespace: uberon -def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] -subset: ro-eco -xref: RO:0002571 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 https://orcid.org/0000-0002-6601-2165 -range: BFO:0000040 ! material entity -is_a: part_of ! part_of - -[Typedef] -id: luminal_space_of -name: luminal space of -namespace: uberon -def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" [] -subset: ro-eco -xref: RO:0002572 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: BFO:0000141 ! immaterial entity -is_a: lumen_of ! lumen of +is_a: part_of ! part of [Typedef] id: negatively_regulated_by @@ -18404,7 +17332,6 @@ namespace: external def: "inverse of negatively regulates" [] subset: RO:0002259 xref: RO:0002335 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -18416,9 +17343,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002212 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002211 holds_over_chain: ends_with negatively_regulates is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect @@ -18431,30 +17355,11 @@ name: negatively regulates characteristic namespace: gene_ontology def: "A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C." [] xref: RO:0019002 -property_value: dc-contributor https://orcid.org/0000-0002-8688-6599 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 holds_over_chain: negatively_regulates positively_regulates_characteristic holds_over_chain: positively_regulates negatively_regulates_characteristic is_a: regulates_characteristic ! regulates characteristic -[Typedef] -id: never_in_taxon -name: never in taxon -name: never_in_taxon -namespace: uberon -def: "S never_in_taxon T iff: S SubClassOf in_taxon only not T." [PMID:20973947] -def: "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL." [] -xref: RO:0002161 -property_value: IAO:0000112 "tooth SubClassOf 'never in taxon' value 'Aves'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 -property_value: OMO:0002000 "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" xsd:string -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -expand_assertion_to: "Class: EquivalentTo: ?X and (RO_0002162 some ?Y)" [] -expand_assertion_to: "Class: ?X DisjointWith: RO_0002162 some ?Y " [] -is_metadata_tag: true -is_class_level: true - [Typedef] id: occurs_in name: occurs in @@ -18465,64 +17370,38 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000066 -property_value: IAO:0000111 "occurs in" xsd:string -property_value: IAO:0000118 "occurs_in" xsd:string -property_value: IAO:0000118 "unfolds in" xsd:string -property_value: IAO:0000118 "unfolds_in" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl property_value: seeAlso "https://wiki.geneontology.org/Occurs_in" xsd:anyURI domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant holds_over_chain: part_of occurs_in -inverse_of: contains_process ! contains process -transitive_over: part_of ! part_of - -[Typedef] -id: only_in_taxon -name: only in taxon -namespace: uberon -def: "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." [] -xref: RO:0002160 -property_value: editor_note "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" xsd:string -property_value: IAO:0000112 "lactation SubClassOf 'only in taxon' some 'Mammalia'" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -is_a: in_taxon ! in taxon +inverse_of: BFO:0000067 ! contains process +transitive_over: part_of ! part of [Typedef] id: output_of name: output of namespace: external -namespace: uberon def: "inverse of has output" [] subset: ro-eco subset: RO:0002259 xref: RO:0002353 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: functionally_related_to ! functionally related to is_a: participates_in ! participates in +is_a: RO:0002328 ! functionally related to [Typedef] id: overlaps name: overlaps namespace: external -namespace: uberon def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002131 -property_value: IAO:0000114 IAO:0000125 -property_value: RO:0001900 RO:0001901 holds_over_chain: has_part overlaps -holds_over_chain: has_part part_of {RO:0002582="true"} holds_over_chain: part_of part_of is_symmetric: true is_a: RO:0002323 ! mereotopologically related to -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] [Typedef] @@ -18531,29 +17410,15 @@ name: part of name: part_of namespace: external namespace: quality -namespace: uberon def: "a core relation that holds between a part and its whole" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000050 -property_value: editor_note "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string -property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string -property_value: IAO:0000111 "is part of" xsd:string -property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string -property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string -property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string -property_value: IAO:0000118 "part_of" xsd:string -property_value: RO:0001900 RO:0001901 -property_value: RO:0040042 BFO:0000002 -property_value: RO:0040042 BFO:0000003 -property_value: RO:0040042 BFO:0000004 -property_value: RO:0040042 BFO:0000017 -property_value: RO:0040042 BFO:0000019 -property_value: RO:0040042 BFO:0000020 -property_value: RO:0040042 BFO:0000031 +property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string @@ -18566,14 +17431,8 @@ inverse_of: has_part ! has part id: participates_in name: participates in namespace: external -namespace: uberon def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] xref: RO:0000056 -property_value: IAO:0000111 "participates in" xsd:string -property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string -property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string -property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string -property_value: IAO:0000118 "participates_in" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000003 ! occurrent inverse_of: has_participant ! has participant @@ -18585,7 +17444,6 @@ namespace: external def: "inverse of positively regulates" [] subset: RO:0002259 xref: RO:0002336 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -18597,10 +17455,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002213 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "positively regulates (process to process)" xsd:string -property_value: RO:0004049 RO:0002211 holds_over_chain: ends_with positively_regulates holds_over_chain: negatively_regulates negatively_regulates is_transitive: true @@ -18614,49 +17468,25 @@ name: positively regulates characteristic namespace: gene_ontology def: "A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C." [] xref: RO:0019001 -property_value: dc-contributor https://orcid.org/0000-0002-8688-6599 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 holds_over_chain: positively_regulates positively_regulates_characteristic is_a: regulates_characteristic ! regulates characteristic -[Typedef] -id: postaxialmost_part_of -name: postaxialmost part of -namespace: uberon -xref: BSPO:0001115 - -[Typedef] -id: posterior_to -name: posterior to -namespace: uberon -xref: BSPO:0000099 - [Typedef] id: posteriorly_connected_to name: posteriorly connected to namespace: uberon def: "x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] -is_a: anterior_to ! anterior to -is_a: connected_to ! connected to - -[Typedef] -id: preaxialmost_part_of -name: preaxialmost part of -namespace: uberon -xref: BSPO:0001113 +is_a: RO:0002170 ! connected to [Typedef] id: preceded_by name: preceded by namespace: external -namespace: uberon def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000062 -property_value: editor_note "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string -property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string -property_value: IAO:0000111 "preceded by" xsd:string -property_value: IAO:0000118 "is preceded by" xsd:string -property_value: IAO:0000118 "preceded_by" xsd:string +property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent holds_over_chain: part_of preceded_by @@ -18668,53 +17498,30 @@ inverse_of: precedes ! precedes id: precedes name: precedes namespace: external -namespace: uberon def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000063 -property_value: IAO:0000111 "precedes" xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent holds_over_chain: part_of precedes is_transitive: true is_a: RO:0002222 ! temporally related to -[Typedef] -id: present_in_taxon -name: present in taxon -name: present_in_taxon -namespace: uberon -def: "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S" [] -def: "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S." [https://orcid.org/0000-0002-6601-2165] -comment: The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology. -synonym: "applicable for taxon" EXACT [] -xref: RO:0002175 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: OMO:0002000 "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" xsd:string -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -is_metadata_tag: true -is_class_level: true - [Typedef] id: process_has_causal_agent name: process has causal agent namespace: external def: "Inverse of 'causal agent in process'" [] xref: RO:0002608 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_a: RO:0002410 ! causally related to [Typedef] id: produced_by name: produced by namespace: external -namespace: uberon def: "a produced_by b iff some process that occurs_in b has_output a." [] subset: ro-eco xref: RO:0003001 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity @@ -18722,13 +17529,10 @@ range: BFO:0000040 ! material entity id: produces name: produces namespace: external -namespace: uberon def: "a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix." [] comment: Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. subset: ro-eco xref: RO:0003000 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity inverse_of: produced_by ! produced by @@ -18738,27 +17542,14 @@ id: protects name: protects namespace: uberon -[Typedef] -id: proximal_to -name: proximal to -namespace: uberon -xref: BSPO:0000100 - [Typedef] id: proximally_connected_to name: proximally connected to namespace: uberon def: "x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] -is_a: connected_to ! connected to -is_a: distal_to ! distal to +is_a: RO:0002170 ! connected to is_a: transitively_proximally_connected_to ! transitively proximally connected to -[Typedef] -id: proximalmost_part_of -name: proximalmost part of -namespace: uberon -xref: BSPO:0001106 - [Typedef] id: regulated_by name: regulated by @@ -18766,8 +17557,6 @@ namespace: external def: "inverse of regulates" [] subset: RO:0002259 xref: RO:0002334 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000589 "regulated by (processual)" xsd:string domain: BFO:0000015 ! process range: BFO:0000015 ! process is_transitive: true @@ -18782,14 +17571,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 -property_value: IAO:0000117 https://orcid.org/0000-0001-7476-6306 -property_value: IAO:0000117 https://orcid.org/0000-0002-3837-8864 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GO" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string -property_value: IAO:0000589 "regulates (processual)" xsd:string -property_value: IAO:0000600 "false" xsd:boolean domain: BFO:0000015 ! process range: BFO:0000015 ! process holds_over_chain: directly_regulates directly_regulates @@ -18805,7 +17586,7 @@ name: regulates characteristic namespace: gene_ontology def: "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C." [] xref: RO:0019000 -property_value: dc-contributor https://orcid.org/0000-0002-8688-6599 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 domain: BFO:0000015 ! process range: PATO:0000001 ! quality holds_over_chain: regulates regulates_characteristic @@ -18817,13 +17598,9 @@ name: regulates levels of namespace: external def: "p regulates levels of c if p regulates some amount (PATO:0000070) of c" [] xref: RO:0002332 -property_value: IAO:0000112 "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "regulates levels of (process to entity)" xsd:string domain: BFO:0000015 ! process range: BFO:0000040 ! material entity -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to [Typedef] id: results_in_acquisition_of_features_of @@ -18834,9 +17611,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002315 -property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string range: UBERON:0000061 ! anatomical structure is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -18871,10 +17645,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002296 -property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "http://www.geneontology.org/GO.doc.development.shtml" xsd:anyURI is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -18884,9 +17654,7 @@ name: results in developmental progression of namespace: external def: "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." [] xref: RO:0002295 -property_value: editor_note "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000116 "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string property_value: seeAlso Ontology:extensions domain: GO:0008150 ! biological_process range: UBERON:0001062 ! anatomical entity @@ -18918,16 +17686,12 @@ is_a: has_participant ! has participant [Typedef] id: results_in_formation_of name: results in formation of +name: results in formation of anatomical entity namespace: external subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002297 -property_value: IAO:0000112 "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." xsd:string -property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of inverse_of: RO:0002354 ! formed as result of @@ -18949,8 +17713,6 @@ id: results_in_growth_of name: results in growth of namespace: external xref: RO:0002343 -property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -18963,11 +17725,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002299 -property_value: IAO:0000112 " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" xsd:string -property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -18980,11 +17737,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002298 -property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." xsd:string -property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -18997,8 +17749,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002565 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure [Typedef] @@ -19017,7 +17767,6 @@ namespace: external def: "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002342 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in is_a: RO:0002021 ! occurs across @@ -19027,7 +17776,6 @@ name: results in transport along namespace: external def: "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " [] xref: RO:0002341 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002337 ! related via localization to [Typedef] @@ -19035,36 +17783,13 @@ id: results_in_transport_to_from_or_in name: results in transport to from or in namespace: external xref: RO:0002344 -property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002337 ! related via localization to -[Typedef] -id: seeAlso -name: see also -namespace: uberon -xref: http://www.w3.org/2000/01/rdf-schema#seeAlso -is_metadata_tag: true - [Typedef] id: sexually_homologous_to name: sexually_homologous_to namespace: uberon -is_a: homologous_to ! shares ancestor with - -[Typedef] -id: simultaneous_with -name: simultaneous with -namespace: uberon -def: "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." [] -comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) -subset: ro-eco -xref: RO:0002082 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -is_symmetric: true -is_transitive: true -is_a: RO:0002081 ! before or simultaneous with +is_a: RO:0002158 ! shares ancestor with [Typedef] id: site_of @@ -19073,46 +17798,13 @@ namespace: uberon def: "c site_of p if c is the bearer of a disposition that is realized by a process that has p as part." [] synonym: "capable_of_has_part" RELATED [] -[Typedef] -id: skeleton_of -name: skeleton of -namespace: uberon -def: "inverse of has skeleton" [] -subset: RO:0002259 -xref: RO:0002576 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: UBERON:0000061 ! anatomical structure -range: UBERON:0000061 ! anatomical structure -is_a: part_of ! part_of - -[Typedef] -id: starts -name: starts -namespace: uberon -def: "inverse of starts with" [] -subset: ro-eco -xref: RO:0002223 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "Allen" xsd:string -is_a: part_of ! part_of -is_a: RO:0002222 ! temporally related to -inverse_of: starts_with ! starts with - [Typedef] id: starts_with name: starts with namespace: external -namespace: uberon def: "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002224 -property_value: IAO:0000112 "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "started by" xsd:string is_transitive: true is_a: has_part ! has part is_a: RO:0002222 ! temporally related to @@ -19123,139 +17815,36 @@ name: subdivision of namespace: uberon comment: placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B -[Typedef] -id: superficial_to -name: superficial to -namespace: uberon -xref: BSPO:0000108 - -[Typedef] -id: supplies -name: supplies -namespace: uberon -def: "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." [] -xref: RO:0002178 -property_value: editor_note "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 -is_a: connected_to ! connected to - -[Typedef] -id: surrounded_by -name: surrounded by -namespace: uberon -def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" [] -xref: RO:0002219 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0001900 RO:0001901 -is_a: adjacent_to ! adjacent to -inverse_of: surrounds ! surrounds - -[Typedef] -id: surrounds -name: surrounds -namespace: uberon -def: "inverse of surrounded by" [] -subset: RO:0002259 -xref: RO:0002221 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0001900 RO:0001901 -is_a: adjacent_to ! adjacent to - -[Typedef] -id: synapsed_by -name: synapsed by -namespace: uberon -def: "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " [] -xref: RO:0002103 -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 -is_a: RO:0002485 ! receives input from -inverse_of: RO:0002120 ! synapsed to -expand_expression_to: "BFO_0000051 some (GO_0045211 that part_of some (GO_0045202 that has_part some (GO_0042734 that BFO_0000050 some Y?)))" [] - [Typedef] id: term_tracker_item name: term tracker item namespace: external -namespace: uberon def: "An IRI or similar locator for a request or discussion of an ontology term." [] comment: The 'tracker item' can associate a tracker with a specific ontology term. xref: IAO:0000233 -property_value: IAO:0000111 "term tracker item" xsd:string -property_value: IAO:0000112 "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" xsd:string -property_value: IAO:0000119 "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" xsd:string is_metadata_tag: true -is_class_level: true - -[Typedef] -id: transformation_of -name: transformation of -namespace: uberon -def: "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" [] -xref: RO:0002494 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_transitive: true -is_a: develops_from ! develops from [Typedef] id: transitively_anteriorly_connected_to name: transitively anteriorly connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI -is_transitive: true [Typedef] id: transitively_distally_connected_to name: transitively distally connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI -is_transitive: true [Typedef] id: transitively_proximally_connected_to name: transitively proximally connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI -is_transitive: true - -[Typedef] -id: tributary_of -name: tributary of -namespace: uberon -def: "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." [] -subset: ro-eco -xref: RO:0002376 -property_value: IAO:0000112 "Deschutes River tributary_of Columbia River" xsd:string -property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "drains into" xsd:string -property_value: IAO:0000118 "drains to" xsd:string -property_value: IAO:0000118 "tributary channel of" xsd:string -property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Tributary" xsd:string -property_value: IAO:0000119 "http://www.medindia.net/glossary/venous_tributary.htm" xsd:string -property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" xsd:anyURI -property_value: seeAlso http://dbpedia.org/ontology/drainsTo -property_value: seeAlso "http://en.wikipedia.org/wiki/Tributary" xsd:anyURI -is_a: connected_to ! connected to -is_a: RO:0002375 ! in branching relationship with [Typedef] id: trunk_part_of name: trunk_part_of namespace: uberon -is_a: part_of ! part_of - -[Typedef] -id: ventral_to -name: ventral to -namespace: uberon -xref: BSPO:0000102 +is_a: part_of ! part of diff --git a/subsets/blood_and_immune_upper_slim.owl b/subsets/blood_and_immune_upper_slim.owl index d0c2dbd2b..75f5291d1 100644 --- a/subsets/blood_and_immune_upper_slim.owl +++ b/subsets/blood_and_immune_upper_slim.owl @@ -10,28 +10,21 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" - xmlns:cito="http://purl.org/spar/cito/" xmlns:core="http://purl.obolibrary.org/obo/uberon/core#" xmlns:foaf="http://xmlns.com/foaf/0.1/" - xmlns:obo2="http://www.geneontology.org/formats/oboInOwl#http://purl.obolibrary.org/obo/" xmlns:pato="http://purl.obolibrary.org/obo/pato#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" - xmlns:skos="http://www.w3.org/2004/02/skos/core#" xmlns:swrl="http://www.w3.org/2003/11/swrl#" - xmlns:sssom="https://w3id.org/sssom/" - xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#" xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:terms="http://purl.org/dc/terms/" - xmlns:vocab="https://w3id.org/semapv/vocab/" - xmlns:terms1="http://www.geneontology.org/formats/oboInOwl#http://purl.org/dc/terms/" xmlns:uberon="http://purl.obolibrary.org/obo/uberon#" xmlns:ubprop="http://purl.obolibrary.org/obo/ubprop#" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - 2024-02-13 + + 2024-04-05 @@ -55,29 +48,9 @@ - - - - - - - - - - - - - - - - - - - definition - The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith @@ -99,8 +72,6 @@ We don't have definitions of 'meaning' or 'expression' Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition @@ -110,72 +81,28 @@ We also have the outstanding issue of how to aim different definitions to differ - editor note - An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obofoundry.org/obo/obi> - IAO:0000116 - uberon - editor_note - true - editor_note - editor note editor note - - - - - - - - - - - - - - - - - - - has obsolescence reason Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. - PERSON:Alan Ruttenberg - PERSON:Melanie Courtot has obsolescence reason - - - - - - - term tracker item - the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ - An IRI or similar locator for a request or discussion of an ontology term. - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg IAO:0000233 external - uberon term_tracker_item - true true term_tracker_item The 'tracker item' can associate a tracker with a specific ontology term. @@ -185,63 +112,23 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - - expand expression to - ObjectProperty: RO_0002104 -Label: has plasma membrane part -Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" - A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones - Chris Mungall expand expression to expand expression to - - - - - - - - - - - - - - - - - - - - - - - - - has ontology root term Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. - Nicolas Matentzoglu IAO:0000700 external - uberon has_ontology_root_term - true true has_ontology_root_term has ontology root term @@ -251,20 +138,10 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - - - - - - - term replaced by - Use on obsolete terms, relating the term to another term that can be used as a substitute - Person:Alan Ruttenberg - Person:Alan Ruttenberg Add as annotation triples in the granting ontology term replaced by term replaced by @@ -275,24 +152,6 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - 'part disjoint with' 'defined by construct' """ - PREFIX owl: <http://www.w3.org/2002/07/owl#> - PREFIX : <http://example.org/ - CONSTRUCT { - [ - a owl:Restriction ; - owl:onProperty :part_of ; - owl:someValuesFrom ?a ; - owl:disjointWith [ - a owl:Restriction ; - owl:onProperty :part_of ; - owl:someValuesFrom ?b - ] - ] - } - WHERE { - ?a :part_disjoint_with ?b . - } Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. @@ -305,11 +164,9 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation) A synonym type for describing abbreviations or initalisms - 2023-03-03 abbreviation @@ -335,11 +192,9 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form) A synonym type for describing pluralization synonyms - 2023-03-03 plural form @@ -354,23 +209,10 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - - - - - - - tooth SubClassOf 'never in taxon' value 'Aves' - S never_in_taxon T iff: S SubClassOf in_taxon only not T. x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL. - - - - Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: ?X and (RO_0002162 some ?Y) - Class: ?X DisjointWith: RO_0002162 some ?Y PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> @@ -394,34 +236,9 @@ CONSTRUCT { WHERE { ?x never_in_taxon: ?taxon . } - RO:0002161 - uberon - never_in_taxon - true - true - never_in_taxon never in taxon - never_in_taxon - - - - S never_in_taxon T iff: S SubClassOf in_taxon only not T. - PMID:20973947 - - - - - - - - - - - - - @@ -429,9 +246,6 @@ WHERE { S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S - S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S. - - PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> @@ -456,24 +270,10 @@ WHERE { )) as ?witness) BIND(CONCAT(STR(?x), " in taxon ", STR(?taxon)) AS ?label) } - RO:0002175 - applicable for taxon - uberon - present_in_taxon - true - true - present_in_taxon The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology. present in taxon - present_in_taxon - - - - S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S. - https://orcid.org/0000-0002-6601-2165 - @@ -485,60 +285,6 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL - is a defining property chain axiom - - - - - - - - If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. - is a defining property chain axiom where second argument is reflexive - - - - - - - - - - - - - - - - - - - - - - @@ -549,126 +295,6 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -927,12 +553,6 @@ WHERE { - - - - - - @@ -1363,14 +983,7 @@ WHERE { - - http://purl.org/dc/elements/1.1/creator - uberon - dc-creator - true - dc-creator - creator - + @@ -1382,14 +995,7 @@ WHERE { - - http://purl.org/dc/elements/1.1/description - uberon - dc-description - true - dc-description - description - + @@ -1401,71 +1007,25 @@ WHERE { - - http://purl.org/dc/elements/1.1/title - uberon - dc-title - true - dc-title - title - + - - http://purl.org/dc/terms/contributor - uberon - dc-contributor - true - dc-contributor - contributor - - - - - - - - - - - - - + - - http://purl.org/dc/terms/date - uberon - dcterms-date - true - dcterms-date - date - + - - http://purl.org/dc/terms/license - uberon - dcterms-license - true - dcterms-license - license - - - - - - - + @@ -1475,18 +1035,6 @@ WHERE { - - - - - - - - - - - - @@ -1503,18 +1051,6 @@ WHERE { - - - - - - - - - - - - @@ -1523,18 +1059,6 @@ WHERE { - - - - - - - - - - - - @@ -1551,66 +1075,6 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -1623,7 +1087,6 @@ WHERE { An alternative label for a class or property which has a more general meaning than the preferred name/primary label. - https://github.com/information-artifact-ontology/ontology-metadata/issues/18 has broad synonym has_broad_synonym @@ -1644,7 +1107,6 @@ WHERE { An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. - https://github.com/information-artifact-ontology/ontology-metadata/issues/20 has exact synonym has_exact_synonym @@ -1657,7 +1119,6 @@ WHERE { An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. - https://github.com/information-artifact-ontology/ontology-metadata/issues/19 has narrow synonym has_narrow_synonym @@ -1678,7 +1139,6 @@ WHERE { An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. - https://github.com/information-artifact-ontology/ontology-metadata/issues/21 has related synonym has_related_synonym @@ -1687,12 +1147,6 @@ WHERE { - - - - - - @@ -1717,30 +1171,6 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - - - @@ -1753,72 +1183,12 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -1833,60 +1203,6 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -1903,9 +1219,6 @@ WHERE { http://www.w3.org/2000/01/rdf-schema#seeAlso - uberon - seeAlso - true seeAlso see also @@ -1918,63 +1231,9 @@ WHERE { - - - - - - - - http://xmlns.com/foaf/0.1/depiction - uberon - depiction - true - depiction - depiction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + @@ -1995,29 +1254,15 @@ WHERE { - is part of - my brain is part of my body (continuant parthood, two material entities) - my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) - this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. - part_of - - - - - - - - BFO:0000050 external quality - uberon part_of @@ -2040,22 +1285,15 @@ A continuant cannot be part of an occurrent: use 'participates in'. An - has part - my body has part my brain (continuant parthood, two material entities) - my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) - this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. - has_part - BFO:0000051 external quality - uberon has_part @@ -2080,15 +1318,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. - preceded by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. - is preceded by - preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 external - uberon preceded_by preceded_by @@ -2109,11 +1342,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. - precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. BFO:0000063 external - uberon precedes precedes @@ -2137,11 +1368,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - occurs_in - unfolds in - unfolds_in BFO:0000066 external occurs_in @@ -2150,7 +1377,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. occurs_in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant - occurs in occurs in https://wiki.geneontology.org/Occurs_in @@ -2161,308 +1387,13 @@ A continuant cannot have an occurrent as part: use 'participates in'. - site of [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - BFO:0000067 - uberon - contains_process - contains_process Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant - - contains process contains process - - - - BSPO:0000096 - uberon - anterior_to - anterior_to - anterior to - - - - - - - - BSPO:0000097 - uberon - distal_to - distal_to - distal to - - - - - - - - BSPO:0000098 - uberon - dorsal_to - dorsal_to - dorsal to - - - - - - - - BSPO:0000099 - uberon - posterior_to - posterior_to - posterior to - - - - - - - - BSPO:0000100 - uberon - proximal_to - proximal_to - proximal to - - - - - - - - BSPO:0000102 - uberon - ventral_to - ventral_to - ventral to - - - - - - - - BSPO:0000107 - uberon - deep_to - deep_to - deep to - - - - - - - - BSPO:0000108 - uberon - superficial_to - superficial_to - superficial to - - - - - - - - BSPO:0000120 - uberon - in_left_side_of - in_left_side_of - in left side of - - - - - - - - BSPO:0000121 - uberon - in_right_side_of - in_right_side_of - in right side of - - - - - - - - BSPO:0000122 - uberon - in_posterior_side_of - in_posterior_side_of - in posterior side of - - - - - - - - BSPO:0000123 - uberon - in_anterior_side_of - in_anterior_side_of - in anterior side of - - - - - - - - BSPO:0000124 - uberon - in_proximal_side_of - in_proximal_side_of - in proximal side of - - - - - - - - BSPO:0000126 - uberon - in_lateral_side_of - in_lateral_side_of - in lateral side of - - - - - - - - BSPO:0001100 - uberon - in_superficial_part_of - in_superficial_part_of - in superficial part of - - - - - - - - BSPO:0001101 - uberon - in_deep_part_of - in_deep_part_of - in deep part of - - - - - - - - BSPO:0001106 - uberon - proximalmost_part_of - proximalmost_part_of - proximalmost part of - - - - - - - - BSPO:0001107 - uberon - immediately_deep_to - immediately_deep_to - immediately deep to - - - - - - - - BSPO:0001108 - uberon - distalmost_part_of - distalmost_part_of - distalmost part of - - - - - - - - BSPO:0001113 - uberon - preaxialmost_part_of - preaxialmost_part_of - preaxialmost part of - - - - - - - - BSPO:0001115 - uberon - postaxialmost_part_of - postaxialmost_part_of - postaxialmost part of - - - - - - - - BSPO:0005001 - uberon - intersects_midsagittal_plane_of - intersects_midsagittal_plane_of - intersects midsagittal plane of - - - - - - - - BSPO:0015014 - uberon - immediately_superficial_to - immediately_superficial_to - immediately superficial to - - - - - - - - BSPO:0015101 - uberon - in_dorsal_side_of - in_dorsal_side_of - in dorsal side of - - - - @@ -2522,12 +1453,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - inheres in - this fragility is a characteristic of this vase - this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. - inheres_in - Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of @@ -2539,14 +1465,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - bearer of - this apple is bearer of this red color - this vase is bearer of this fragility Inverse of characteristic_of A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. - bearer_of - is bearer of - RO:0000053 external bearer_of @@ -2563,15 +1483,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. - participates in - this blood clot participates in this blood coagulation - this input material (or this output material) participates in this process - this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process - participates_in RO:0000056 external - uberon participates_in participates_in participates in @@ -2589,14 +1503,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - has participant - this blood coagulation has participant this blood clot - this investigation has participant this investigator - this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. - has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 external has_participant @@ -2612,11 +1520,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. - function_of - is function of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. function of @@ -2628,11 +1533,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. - is quality of - quality_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. quality of @@ -2644,11 +1546,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. - is role of - role_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. role of @@ -2660,10 +1559,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. - has_function has function @@ -2673,15 +1570,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. - has_quality - RO:0000086 - uberon - has_quality - has_quality - has quality has quality @@ -2692,10 +1582,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. - has_role has role @@ -2729,13 +1617,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this cell derives from this parent cell (cell division) - this nucleus derives from this parent nucleus (nuclear division) - a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. - derives_from - This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. derives from @@ -2745,12 +1628,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this parent cell derives into this cell (cell division) - this parent nucleus derives into this nucleus (nuclear division) - a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. - derives_into derives into @@ -2762,18 +1641,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - is location of - my head is the location of my brain - this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - location_of - - RO:0001015 - uberon - location_of - location_of - location of location of @@ -2789,21 +1658,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. - located in - my brain is located in my head - this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - located_in - - http://www.obofoundry.org/ro/#OBO_REL:located_in - RO:0001025 - uberon - located_in - located_in - located in located in https://wiki.geneontology.org/Located_in @@ -2827,16 +1685,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. - the surface of my skin is a 2D boundary of my body a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - 2D_boundary_of - boundary of - is 2D boundary of - is boundary of - surface of - 2D boundary of @@ -2848,19 +1699,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. - my body has 2D boundary the surface of my skin a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - - has boundary - has_2D_boundary - - RO:0002002 - uberon - has_boundary - has_boundary - has 2D boundary has 2D boundary @@ -2871,17 +1712,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - http://www.ncbi.nlm.nih.gov/pubmed/22402613 - RO:0002005 - uberon - innervated_by - innervated_by - innervated_by innervated_by @@ -2892,8 +1722,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - has synaptic terminal of @@ -2913,10 +1741,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - RO:0002007 external - uberon bounding_layer_of bounding_layer_of @@ -3095,8 +1921,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland - <= Primitive instance level timing relation between events before or simultaneous with @@ -3111,15 +1935,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time. - - David Osumi-Sutherland - RO:0002082 - uberon - simultaneous_with - simultaneous_with t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) - simultaneous with simultaneous with @@ -3130,7 +1947,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after @@ -3147,11 +1963,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland - starts_at_end_of RO:0002087 external - uberon immediately_preceded_by immediately_preceded_by X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) @@ -3169,11 +1982,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - - David Osumi-Sutherland - ends_at_start_of - meets - RO:0002090 external immediately_precedes @@ -3196,12 +2004,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between a neuron and a material anatomical entity that its soma is part of. - <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) - has soma location @@ -3213,33 +2018,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. - - fasciculates with - (forall (?x ?y) - (iff - (fasciculates_with ?x ?y) - (exists (?nps ?npbs) - (and - ("neuron ; CL_0000540" ?x) - ("neuron projection bundle ; CARO_0001001" ?y) - ("neuron projection segment ; CARO_0001502" ?nps) - ("neuron projection bundle segment ; CARO_0001500' " ?npbs) - (part_of ?npbs ?y) - (part_of ?nps ?x) - (part_of ?nps ?npbs) - (forall (?npbss) - (if - (and - ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) - (part_of ?npbss ?npbs) - ) - (overlaps ?nps ?npbss) - )))))) - - fasciculates with @@ -3254,16 +2034,11 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between a neuron and some structure its axon forms (chemical) synapses in. - - <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y))) - - axon synapses in @@ -3285,18 +2060,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. - - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) - - - RO:0002103 - uberon - synapsed_by - synapsed_by - synapsed by synapsed by @@ -3308,15 +2073,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] - Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. - - - - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) - has plasma membrane part @@ -3332,16 +2090,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. - - - synapsed in http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)) - - has postsynaptic terminal in @@ -3356,12 +2108,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. - synapses in <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) - - has presynaptic terminal in @@ -3382,14 +2130,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. - - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) - - N1 synapsed_to some N2 Expands to: N1 SubclassOf ( @@ -3411,13 +2154,8 @@ N1 SubclassOf ( - A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. - - has synapse in <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) - - has synaptic terminal in @@ -3432,10 +2170,6 @@ N1 SubclassOf ( - - - - @@ -3444,13 +2178,10 @@ N1 SubclassOf ( - x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) - RO:0002131 external - uberon overlaps @@ -3459,15 +2190,6 @@ N1 SubclassOf ( overlaps overlaps - - - - - - - - true - @@ -3486,35 +2208,7 @@ N1 SubclassOf ( - The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. - - has fasciculating component - (forall (?x ?y) - (iff - (has_fasciculating_neuron_projection ?x ?y) - (exists (?nps ?npbs) - (and - ("neuron projection bundle ; CARO_0001001" ?x) - ("neuron projection ; GO0043005" ?y) - ("neuron projection segment ; CARO_0001502" ?nps) - ("neuron projection bundle segment ; CARO_0001500" ?npbs) - (part_of ?nps ?y) - (part_of ?npbs ?x) - (part_of ?nps ?npbs) - (forall (?npbss) - (if - (and - ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) - (part_of ?npbss ?npbs) - ) - (overlaps ?nps ?npbss) - )))))) - - - - - has fasciculating neuron projection @@ -3527,19 +2221,10 @@ N1 SubclassOf ( - Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - <http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) - - - RO:0002134 - uberon - innervates - innervates - innervates innervates @@ -3552,17 +2237,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - X continuous_with Y if and only if X and Y share a fiat boundary. - - connected to - The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) - - RO:0002150 - uberon - continuous_with - continuous_with - continuous with continuous with FMA:85972 @@ -3575,13 +2250,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a. - Consider obsoleting and merging with child relation, 'in homology relationship with' - RO:0002158 - uberon - homologous_to - homologous_to VBO calls this homologous_to shares ancestor with @@ -3592,19 +2261,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - lactation SubClassOf 'only in taxon' some 'Mammalia' - x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria - - - - RO:0002160 - uberon - only_in_taxon - only_in_taxon only in taxon @@ -3623,30 +2283,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - - - - - - - - - - - - - - - - - - - - - @@ -3667,53 +2303,16 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. - - - - - RO:0002162 - uberon - in_taxon - in_taxon Connects a biological entity to its taxon of origin. in taxon @@ -3725,14 +2324,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. - - - Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) - spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern @@ -3750,14 +2344,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b - - RO:0002170 - uberon - connected_to - connected_to - connected to connected to https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern @@ -3770,15 +2357,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - The M8 connects Glasgow and Edinburgh - a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system. - - RO:0002176 - uberon - connects - connects - connects connects https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern @@ -3793,28 +2372,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. - attached to part of (anatomical structure to anatomical structure) - RO:0002177 - uberon - attaches_to_part_of - attaches_to_part_of - attached to part of attached to part of - - - - - - - - true - @@ -3824,12 +2384,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy. Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure - - RO:0002178 - uberon - supplies - supplies - supplies supplies @@ -3841,12 +2395,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure. Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure - - RO:0002179 - uberon - drains - drains - drains drains @@ -3856,14 +2404,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. - For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. - RO:0002180 external - uberon has_component has_component @@ -3883,18 +2427,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y - - - - - RO:0002202 - uberon - develops_from - develops_from This is the transitive form of the develops from relation - develops from develops from @@ -3907,17 +2441,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of develops from - - - - RO:0002203 - uberon - develops_into - develops_into - develops into develops into @@ -3934,10 +2459,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - 'neural crest cell' SubClassOf expresses some 'Wnt1 gene' - x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process - expressed in @@ -3964,19 +2486,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. - - - FBbt - - RO:0002207 has developmental precursor - uberon - directly_develops_from - directly_develops_from TODO - add child relations from DOS - directly develops from directly develops from @@ -3986,9 +2498,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of directly develops from - developmental precursor of directly develops into @@ -4016,14 +2526,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. - - - - - GO - Regulation precludes parthood; the regulatory process may not be within the regulated process. - regulates (processual) - false RO:0002211 external regulates @@ -4048,9 +2550,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. - - - negatively regulates (process to process) RO:0002212 external @@ -4081,10 +2580,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. - - - positively regulates (process to process) - RO:0002213 external positively_regulates @@ -4104,17 +2599,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) - osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. - - has function realized in - - - For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". RO:0002215 external - uberon capable_of capable_of @@ -4129,31 +2616,15 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. - - has function in RO:0002216 external - uberon capable_of_part_of capable_of_part_of capable of part of capable of part of - - - - - - - - true - @@ -4162,15 +2633,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x - - - RO:0002219 - uberon - surrounded_by - surrounded_by - surrounded by surrounded by @@ -4182,18 +2645,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. - The epidermis layer of a vertebrate is adjacent to the dermis. - The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. - The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. - x adjacent to y if and only if x and y share a boundary. This relation acts as a join point with BSPO - - RO:0002220 external - uberon adjacent_to @@ -4202,12 +2657,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.adjacent to adjacent to - - - - A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. - - @@ -4215,16 +2664,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of surrounded by - - - RO:0002221 - uberon - surrounds - surrounds - surrounds surrounds @@ -4235,11 +2676,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. - https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to @@ -4253,17 +2689,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of starts with - - Chris Mungall - Allen - RO:0002223 - uberon - starts - starts - starts starts @@ -4275,15 +2702,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor - x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - - Chris Mungall - started by RO:0002224 external - uberon starts_with starts_with @@ -4301,14 +2722,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x develops from part of y if and only if there exists some z such that x develops from z and z is part of y - - RO:0002225 - uberon - develops_from_part_of - develops_from_part_of - develops from part of develops from part of @@ -4323,16 +2737,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x develops_in y if x is located in y whilst x is developing - - EHDAA2 - Jonathan Bard, EHDAA2 - RO:0002226 - uberon - develops_in - develops_in - develops in develops in @@ -4344,16 +2749,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of ends with - - Chris Mungall - RO:0002229 - uberon - ends - ends - ends ends @@ -4365,14 +2762,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - - Chris Mungall - finished by RO:0002230 external - uberon ends_with ends_with @@ -4392,10 +2784,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y - - starts with process that occurs in RO:0002231 external has_start_location @@ -4417,10 +2806,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y - - ends with process that occurs in RO:0002232 external has_end_location @@ -4442,10 +2828,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. - - consumes RO:0002233 external has_input @@ -4470,10 +2853,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. - - produces RO:0002234 external has_output @@ -4495,13 +2875,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1. b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t. - - RO:0002252 - uberon - connecting_branch_of - connecting_branch_of connecting branch of @@ -4513,7 +2887,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of connecting branch of - has connecting branch @@ -4531,15 +2904,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] - x has developmental contribution from y iff x has some part z such that z develops from y - - RO:0002254 - uberon - has_developmental_contribution_from - has_developmental_contribution_from - has developmental contribution from has developmental contribution from @@ -4554,9 +2919,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of has developmental contribution from - developmentally contributes to @@ -4570,21 +2933,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T - - - - induced by - - Developmental Biology, Gilbert, 8th edition, figure 6.5(F) - GO:0001759 - We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm] - RO:0002256 - uberon - developmentally_induced_by - developmentally_induced_by - developmentally induced by developmentally induced by @@ -4595,9 +2944,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Inverse of developmentally induced by - developmentally induces @@ -4610,11 +2957,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false - - In general you should not use this relation to make assertions - use one of the more specific relations below this one This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from developmentally preceded by @@ -4629,7 +2973,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. acts upstream of @@ -4646,7 +2989,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects @@ -4660,16 +3002,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage - - replaces - RO:0002285 - uberon - developmentally_replaces - developmentally_replaces - developmentally replaces developmentally replaces @@ -4679,9 +3013,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Inverse of developmentally preceded by - developmentally succeeded by @@ -4695,9 +3027,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue - - part of developmental precursor of @@ -4707,9 +3036,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process. - expresses @@ -4721,10 +3048,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. - RO:0002295 external results_in_developmental_progression_of @@ -4741,11 +3066,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - every flower development (GO:0009908) results in development of some flower (PO:0009046) - p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. - - http://www.geneontology.org/GO.doc.development.shtml RO:0002296 external results_in_development_of @@ -4765,11 +3086,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. - every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) - - - GOC:mtg_berkeley_2013 RO:0002297 external results_in_formation_of @@ -4778,7 +3094,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. results_in_formation_of results in formation of - results in formation of + results in formation of anatomical entity @@ -4788,12 +3104,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. - tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) - The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. - - GOC:mtg_berkeley_2013 RO:0002298 external results_in_morphogenesis_of @@ -4812,12 +3123,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process - bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) - The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. - - GOC:mtg_berkeley_2013 RO:0002299 external results_in_maturation_of @@ -4837,8 +3143,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. - - RO:0002304 external causally_upstream_of,_positive_effect @@ -4859,7 +3163,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. - RO:0002305 external causally_upstream_of,_negative_effect @@ -4876,32 +3179,15 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of characteristic of part of - - inheres in part of - - characteristic of part of - - - - - - - - true - @@ -4911,10 +3197,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity - - GOC:mtg_berkeley_2013 RO:0002315 external results_in_acquisition_of_features_of @@ -4932,8 +3215,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A relationship that holds via some environmental process - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. evolutionarily related to @@ -4943,9 +3224,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A mereological relationship or a topological relationship - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships - mereotopologically related to @@ -4955,8 +3233,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A relationship that holds between entities participating in some developmental process (GO:0032502) - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development developmentally related to @@ -4975,15 +3251,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - a particular instances of akt-2 enables some instance of protein kinase activity c enables p iff c is capable of p and c acts to execute p. - - catalyzes - executes - has - is catalyzing - is executing - This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. enables https://wiki.geneontology.org/Enables @@ -4995,13 +3263,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. - - This is a grouping relation that collects relations used for the purpose of connecting structure and function - RO:0002328 - uberon - functionally_related_to - functionally_related_to - functionally related to functionally related to @@ -5011,24 +3272,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - this relation holds between c and p when c is part of some c', and c' is capable of p. - - false part of structure that is capable of - - - - - - - - true - @@ -5038,8 +3284,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts. - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism genomically related to @@ -5059,9 +3303,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. c involved_in p if and only if c enables some process p', and p' is part of p - - actively involved in - enables part of involved in https://wiki.geneontology.org/Involved_in @@ -5074,11 +3315,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid p regulates levels of c if p regulates some amount (PATO:0000070) of c - - - regulates levels of (process to entity) RO:0002332 external regulates_levels_of @@ -5095,7 +3332,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of enables - enabled by https://wiki.geneontology.org/Enabled_by @@ -5111,8 +3347,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of regulates - - regulated by (processual) RO:0002334 external regulated_by @@ -5129,7 +3363,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of negatively regulates - RO:0002335 external negatively_regulated_by @@ -5146,7 +3379,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of positively regulates - RO:0002336 external positively_regulated_by @@ -5164,8 +3396,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A relationship that holds via some process of localization - - Do not use this relation directly. It is a grouping relation. related via localization to @@ -5180,7 +3410,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. - RO:0002338 external has_target_start_location @@ -5203,7 +3432,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. - RO:0002339 external has_target_end_location @@ -5222,7 +3450,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l - RO:0002341 external results_in_transport_along @@ -5239,7 +3466,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. - RO:0002342 external results_in_transport_across @@ -5256,8 +3482,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - 'pollen tube growth' results_in growth_of some 'pollen tube' - RO:0002343 external results_in_growth_of @@ -5272,8 +3496,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) - RO:0002344 external results_in_transport_to_from_or_in @@ -5289,12 +3511,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - An organism that is a member of a population of organisms is member of is a mereological relation between a item and a collection. - is member of - member part of - SIO - member of @@ -5306,13 +3523,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. has member is a mereological relation between a collection and an item. - SIO - - RO:0002351 - uberon - has_member - has_member - has member has member @@ -5324,14 +3534,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of has input - - RO:0002352 - uberon - input_of - input_of - input of input of @@ -5343,10 +3547,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of has output - RO:0002353 external - uberon output_of @@ -5361,7 +3563,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - formed as result of @@ -5371,8 +3572,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - http://neurolex.org/wiki/Property:DendriteLocation has dendrite location @@ -5385,14 +3584,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a - - attached to (anatomical structure to anatomical structure) - RO:0002371 - uberon - attaches_to - attaches_to - attached to attached to @@ -5405,13 +3597,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. - - Wikipedia:Insertion_(anatomy) - RO:0002372 - uberon - has_muscle_origin - has_muscle_origin - has muscle origin has muscle origin @@ -5431,13 +3616,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. - - Wikipedia:Insertion_(anatomy) - RO:0002373 - uberon - has_muscle_insertion - has_muscle_insertion - has muscle insertion has muscle insertion @@ -5456,12 +3634,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships - This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) - in branching relationship with https://github.com/obophenotype/uberon/issues/170 @@ -5474,23 +3647,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Deschutes River tributary_of Columbia River - inferior epigastric vein tributary_of external iliac vein - x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. - - drains into - drains to - tributary channel of - http://en.wikipedia.org/wiki/Tributary - http://www.medindia.net/glossary/venous_tributary.htm - This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries) - RO:0002376 - uberon - tributary_of - tributary_of - tributary of tributary of http://en.wikipedia.org/wiki/Tributary @@ -5508,10 +3666,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location - - This relation is added for formal completeness. It is unlikely to be used in many practical scenarios spatially coextensive with @@ -5529,15 +3684,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y - - RO:0002380 - uberon - branching_part_of - branching_part_of - branching part of branching part of FMA:85994 @@ -5551,9 +3699,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). - has developmental potential involving @@ -5563,14 +3709,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y - - RO:0002385 - uberon - has_potential_to_developmentally_contribute_to - has_potential_to_developmentally_contribute_to - has potential to developmentally contribute to has potential to developmentally contribute to @@ -5580,9 +3719,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y - has potential to developmentally induce @@ -5592,14 +3729,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x has the potential to develop into y iff x develops into y or if x is capable of developing into y - - RO:0002387 - uberon - has_potential_to_develop_into - has_potential_to_develop_into - has potential to develop into has potential to develop into @@ -5609,9 +3739,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y - has potential to directly develop into @@ -5623,9 +3751,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of upstream of - RO:0002404 external causally_downstream_of @@ -5642,8 +3768,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - RO:0002405 external immediately_causally_downstream_of @@ -5677,9 +3801,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. - - indirectly activates - indirectly positively regulates https://wiki.geneontology.org/Indirectly_positively_regulates @@ -5705,9 +3826,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. - - indirectly inhibits - indirectly negatively regulates https://wiki.geneontology.org/Indirectly_negatively_regulates @@ -5733,8 +3851,6 @@ For the second, we consider a relationship to be regulatory if the system in whi For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to @@ -5753,7 +3869,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. - RO:0002411 external causally_upstream_of @@ -5772,8 +3887,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. - - RO:0002412 external immediately_causally_upstream_of @@ -5792,8 +3905,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 - - influences (processual) RO:0002418 external affects @@ -5810,8 +3921,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different inverse of causally upstream of or within - - RO:0002427 external causally_downstream_of_or_within @@ -5836,7 +3945,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' regulates some p - involved in regulation of @@ -5855,8 +3963,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' positively regulates some p - - involved in positive regulation of @@ -5875,7 +3981,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' negatively regulates some p - involved in negative regulation of @@ -5890,8 +3995,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union - - involved in or reguates involved in or involved in regulation of @@ -5902,28 +4005,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - - executes activity in enables activity in is active in https://wiki.geneontology.org/Is_active_in - - - - - - - - true - @@ -5939,11 +4026,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. - - RO:0002433 - uberon - contributes_to_morphology_of - contributes_to_morphology_of contributes to morphology of @@ -5958,13 +4040,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different A relationship that holds between two entities in which the processes executed by the two entities are causally connected. This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. Considering relabeling as 'pairwise interacts with' - - Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. in pairwise interaction with interacts with http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ - http://purl.obolibrary.org/obo/MI_0914 @@ -5975,12 +4054,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. - - binds - molecularly binds with molecularly interacts with - http://purl.obolibrary.org/obo/MI_0915 @@ -5990,8 +4065,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different Axiomatization to GO to be added later - - An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. phosphorylates @@ -6012,8 +4085,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. - - molecularly controls directly regulates activity of @@ -6033,9 +4104,6 @@ A and B can be physically interacting but not necessarily. Immediately upstream The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. - - - directly inhibits molecularly decreases activity of directly negatively regulates activity of @@ -6055,9 +4123,6 @@ For example, A and B may be gene products and binding of B by A negatively regul The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. - - - directly activates molecularly increases activity of directly positively regulates activity of @@ -6067,8 +4132,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. helper property (not for use in curation) @@ -6080,16 +4143,8 @@ For example, A and B may be gene products and binding of B by A positively regul - 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. - - - - RO:0002473 - uberon - composed_primarily_of - composed_primarily_of composed primarily of @@ -6100,24 +4155,10 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. - has part that occurs in - - - - - - - - true - @@ -6125,7 +4166,6 @@ For example, A and B may be gene products and binding of B by A positively regul - is kinase activity @@ -6137,7 +4177,6 @@ For example, A and B may be gene products and binding of B by A positively regul See notes for inverse relation - receives input from @@ -6148,7 +4187,6 @@ For example, A and B may be gene products and binding of B by A positively regul This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. - sends output to @@ -6159,8 +4197,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. relation between physical entity and a process or stage @@ -6176,11 +4212,6 @@ For example, A and B may be gene products and binding of B by A positively regul x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). - - RO:0002488 - uberon - existence_starts_during - existence_starts_during existence starts during @@ -6191,11 +4222,6 @@ For example, A and B may be gene products and binding of B by A positively regul x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). - - RO:0002489 - uberon - existence_starts_with - existence_starts_with existence starts with @@ -6206,7 +4232,6 @@ For example, A and B may be gene products and binding of B by A positively regul x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence overlaps @@ -6219,12 +4244,7 @@ For example, A and B may be gene products and binding of B by A positively regul x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) - - RO:0002491 exists during - uberon - existence_starts_and_ends_during - existence_starts_and_ends_during The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts and ends during @@ -6240,23 +4260,10 @@ For example, A and B may be gene products and binding of B by A positively regul - Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). - - RO:0002492 - ceases_to_exist_during - uberon - existence_ends_during - existence_ends_during The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during - - - - Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. - https://orcid.org/0000-0002-6601-2165 - @@ -6265,11 +4272,6 @@ For example, A and B may be gene products and binding of B by A positively regul x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). - - RO:0002493 - uberon - existence_ends_with - existence_ends_with The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends with @@ -6282,11 +4284,6 @@ For example, A and B may be gene products and binding of B by A positively regul x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships - - RO:0002494 - uberon - transformation_of - transformation_of transformation of @@ -6298,12 +4295,6 @@ For example, A and B may be gene products and binding of B by A positively regul x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t - - - RO:0002495 - uberon - immediate_transformation_of - immediate_transformation_of immediate transformation of @@ -6334,11 +4325,6 @@ For example, A and B may be gene products and binding of B by A positively regul x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). - - RO:0002496 - uberon - existence_starts_during_or_after - existence_starts_during_or_after The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts during or after @@ -6370,11 +4356,6 @@ For example, A and B may be gene products and binding of B by A positively regul x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. - - RO:0002497 - uberon - existence_ends_during_or_before - existence_ends_during_or_before The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during or before @@ -6387,7 +4368,6 @@ For example, A and B may be gene products and binding of B by A positively regul A relationship between a material entity and a process where the material entity has some causal role that influences the process - causal agent in process @@ -6400,9 +4380,6 @@ For example, A and B may be gene products and binding of B by A positively regul p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. - - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes @@ -6411,7 +4388,6 @@ For example, A and B may be gene products and binding of B by A positively regul - depends on @@ -6425,9 +4401,6 @@ For example, A and B may be gene products and binding of B by A positively regul The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch - - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between entities @@ -6441,18 +4414,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - - Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. - - has supporting framework - The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). - RO:0002551 - uberon - has_skeleton - has_skeleton has skeleton @@ -6469,9 +4432,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - causally influenced by (entity-centric) causally influenced by @@ -6481,7 +4441,6 @@ For example, A and B may be gene products and binding of B by A positively regul - interaction relation helper property http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ @@ -6493,7 +4452,6 @@ For example, A and B may be gene products and binding of B by A positively regul - molecular interaction relation helper property @@ -6504,8 +4462,6 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - - RO:0002565 external results_in_movement_of @@ -6535,10 +4491,6 @@ For example, A and B may be gene products and binding of B by A positively regul The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). - - - - causally influences (entity-centric) causally influences @@ -6551,8 +4503,6 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between elements of a musculoskeletal system or its analogs. - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. biomechanically related to @@ -6563,12 +4513,6 @@ For example, A and B may be gene products and binding of B by A positively regul m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. - - Wikipedia:Antagonist_(muscle) - RO:0002568 - uberon - has_muscle_antagonist - has_muscle_antagonist has muscle antagonist @@ -6581,13 +4525,8 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of branching part of - - RO:0002569 - uberon - has_branching_part - has_branching_part has branching part @@ -6600,14 +4539,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. - - UBERON:cjm - This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. - RO:0002570 - uberon - conduit_for - conduit_for conduit for @@ -6619,13 +4551,7 @@ For example, A and B may be gene products and binding of B by A positively regul x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - - - RO:0002571 - uberon - lumen_of - lumen_of lumen of @@ -6637,12 +4563,7 @@ For example, A and B may be gene products and binding of B by A positively regul s is luminal space of x iff s is lumen_of x and s is an immaterial entity - - RO:0002572 - uberon - luminal_space_of - luminal_space_of luminal space of @@ -6655,12 +4576,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has skeleton - - RO:0002576 - uberon - skeleton_of - skeleton_of skeleton of @@ -6672,10 +4588,6 @@ For example, A and B may be gene products and binding of B by A positively regul p directly regulates q iff p is immediately causally upstream of q and p regulates q. - - - directly regulates (processual) - RO:0002578 external directly_regulates @@ -6697,9 +4609,7 @@ For example, A and B may be gene products and binding of B by A positively regul - gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p - has part structure that is capable of @@ -6769,8 +4679,6 @@ For example, A and B may be gene products and binding of B by A positively regul A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - - causal relation between material entity and a process @@ -6784,9 +4692,7 @@ For example, A and B may be gene products and binding of B by A positively regul - pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. - capable of regulating @@ -6801,7 +4707,6 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. - capable of negatively regulating @@ -6815,9 +4720,7 @@ For example, A and B may be gene products and binding of B by A positively regul - renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. - capable of positively regulating @@ -6828,7 +4731,6 @@ For example, A and B may be gene products and binding of B by A positively regul Inverse of 'causal agent in process' - RO:0002608 external process_has_causal_agent @@ -6844,9 +4746,6 @@ For example, A and B may be gene products and binding of B by A positively regul p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. - - directly positively regulates (process to process) - RO:0002629 external directly_positively_regulates @@ -6866,8 +4765,6 @@ For example, A and B may be gene products and binding of B by A positively regul p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. - - directly negatively regulates (process to process) RO:0002630 external @@ -6894,12 +4791,9 @@ For example, A and B may be gene products and binding of B by A positively regul - a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. - RO:0003000 external - uberon produces produces @@ -6915,12 +4809,9 @@ For example, A and B may be gene products and binding of B by A positively regul - a produced_by b iff some process that occurs_in b has_output a. - RO:0003001 external - uberon produced_by produced_by @@ -7027,7 +4918,6 @@ For example, A and B may be gene products and binding of B by A positively regul - 2018-01-26T23:49:30Z @@ -7065,7 +4955,6 @@ For example, A and B may be gene products and binding of B by A positively regul c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive - 2018-01-26T23:53:14Z @@ -7112,7 +5001,6 @@ For example, A and B may be gene products and binding of B by A positively regul - 2018-03-13T23:55:19Z causally upstream of or within, positive effect @@ -7128,7 +5016,6 @@ For example, A and B may be gene products and binding of B by A positively regul The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. - regulates activity of @@ -7375,7 +5262,6 @@ For example, A and B may be gene products and binding of B by A positively regul - 'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)') A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. @@ -7395,7 +5281,6 @@ For example, A and B may be gene products and binding of B by A positively regul - 'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor') A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. @@ -7417,12 +5302,7 @@ For example, A and B may be gene products and binding of B by A positively regul - A diagnostic testing device utilizes a specimen. X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. - - - A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. - See github ticket https://github.com/oborel/obo-relations/issues/497 2021-11-08T12:00:00Z utilizes device utilizes material @@ -7548,7 +5428,6 @@ For example, A and B may be gene products and binding of B by A positively regul - x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y. @@ -7568,8 +5447,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - carries uberon channel_for @@ -7581,7 +5458,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uberon channels_from channels_from @@ -7592,7 +5468,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uberon channels_into channels_into @@ -7603,10 +5478,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y. uberon distally_connected_to @@ -7625,11 +5498,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y uberon extends_fibers_into @@ -7659,11 +5527,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - @@ -7691,7 +5554,6 @@ For example, A and B may be gene products and binding of B by A positively regul - x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y. uberon @@ -7720,7 +5582,6 @@ For example, A and B may be gene products and binding of B by A positively regul - x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y. @@ -7774,7 +5635,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uberon transitively_anteriorly_connected_to transitively anteriorly connected to @@ -7786,7 +5646,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uberon transitively_distally_connected_to transitively distally connected to @@ -7798,7 +5657,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uberon transitively_proximally_connected_to transitively proximally connected to @@ -11949,6 +9807,12 @@ For example, A and B may be gene products and binding of B by A positively regul reticulocyte + + + + + true + @@ -11958,12 +9822,6 @@ For example, A and B may be gene products and binding of B by A positively regul PMID:15946868 PMID:2037622 - - - - - true - @@ -20042,32 +17900,32 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer - + - + - + PMID:12382326 - + PMID:12382326 @@ -32168,7 +30026,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 PMID:15371245 ncbi_taxonomy @@ -32182,7 +30039,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 Mus mice @@ -32201,7 +30057,7 @@ For example, A and B may be gene products and binding of B by A positively regul mice - + @@ -32216,7 +30072,6 @@ For example, A and B may be gene products and binding of B by A positively regul - NCBITaxon:85055 GC_ID:1 house mouse @@ -32244,7 +30099,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 ncbi_taxonomy NCBITaxon:117570 @@ -32257,7 +30111,6 @@ For example, A and B may be gene products and binding of B by A positively regul - NCBITaxon:40673 GC_ID:1 bony vertebrates @@ -32297,7 +30150,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 ncbi_taxonomy NCBITaxon:1338369 @@ -32310,7 +30162,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 PMID:11743200 PMID:11791233 @@ -32332,7 +30183,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 mice and others ncbi_taxonomy @@ -32359,7 +30209,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 PMID:23020233 PMID:30257078 @@ -32423,7 +30272,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 PMID:11214319 PMID:12082125 @@ -32440,7 +30288,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 PMID:11214319 PMID:12082125 @@ -32463,7 +30310,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 tetrapods ncbi_taxonomy @@ -32483,7 +30329,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 amniotes ncbi_taxonomy @@ -32503,7 +30348,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 Theria ncbi_taxonomy @@ -32523,7 +30367,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 ncbi_taxonomy Fungi/Metazoa group @@ -32550,7 +30393,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 metazoans multicellular animals @@ -32591,7 +30433,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 ncbi_taxonomy NCBITaxon:33213 @@ -32604,7 +30445,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 deuterostomes ncbi_taxonomy @@ -32624,7 +30464,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 PMID:15019624 PMID:15371245 @@ -32639,7 +30478,6 @@ For example, A and B may be gene products and binding of B by A positively regul - NCBITaxon:109679 GC_ID:1 ncbi_taxonomy @@ -32653,7 +30491,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 mammals ncbi_taxonomy @@ -32680,7 +30517,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 ncbi_taxonomy NCBITaxon:6072 @@ -32693,7 +30529,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 chordates ncbi_taxonomy @@ -32720,7 +30555,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 Vertebrata vertebrates @@ -32754,7 +30588,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 Gnathostomata jawed vertebrates @@ -32781,7 +30614,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 ncbi_taxonomy NCBITaxon:8287 @@ -32794,7 +30626,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 Mus ncbi_taxonomy @@ -32814,7 +30645,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 Craniata ncbi_taxonomy @@ -32834,7 +30664,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 eutherian mammals placental mammals @@ -32882,7 +30711,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 rodent ncbi_taxonomy @@ -33017,7 +30845,6 @@ For example, A and B may be gene products and binding of B by A positively regul A branchiness quality inhering in a bearer by virtue of the bearer's having branches. - ramified ramiform quality @@ -33345,7 +31172,6 @@ For example, A and B may be gene products and binding of B by A positively regul A quality inhering in a bearer by virtue of the bearer's lacking complete growth, differentiation, or development. - quality underdeveloped PATO:0001501 @@ -33407,7 +31233,6 @@ For example, A and B may be gene products and binding of B by A positively regul A contractility quality inhering in a bearer by virtue of the bearer's ability of contracting or being contracted. - quality PATO:0001690 @@ -33429,7 +31254,6 @@ For example, A and B may be gene products and binding of B by A positively regul A shape quality in a bearer by virtue of the bearer's curving inward. - quality PATO:0001857 @@ -33625,7 +31449,6 @@ For example, A and B may be gene products and binding of B by A positively regul A complete three dimensional shape in which for every line connecting pair of points on the object is within the object. Or: a shape lacking cavities. Contrast: concave. - Image:http://upload.wikimedia.org/wikipedia/commons/0/06/Convex_polygon_illustration1.png quality PATO:0002007 @@ -33686,7 +31509,6 @@ For example, A and B may be gene products and binding of B by A positively regul A concave quality inhering in a bearer by virtue of the bearer's curving inward on both sides or surfaces. - quality PATO:0002039 @@ -34193,7 +32015,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001006 Category=gene. Requested by=CL. receptor-type tyrosine-protein phosphatase C - @@ -34243,7 +32064,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001012 Category=gene. Requested by=CL. integrin alpha-M - @@ -34290,7 +32110,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001013 Category=gene. Requested by=CL. integrin alpha-X - @@ -34428,7 +32247,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001024 Category=gene. Requested by=CL. neural cell adhesion molecule 1 - @@ -34513,7 +32331,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001084 Category=gene. Requested by=CL. T-cell surface glycoprotein CD8 alpha chain - @@ -34664,7 +32481,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001254 Category=gene. Requested by=CL. C-C chemokine receptor type 1 - @@ -34722,7 +32538,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001255 Category=gene. Requested by=CL. C-C chemokine receptor type 3 - @@ -34936,7 +32751,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001332 Category=gene. Requested by=CL. carcinoembryonic antigen-related cell adhesion molecule 8 - @@ -35023,7 +32837,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001344 Category=gene. Requested by=CL. ectonucleotide pyrophosphatase/phosphodiesterase family member 3 - @@ -35109,7 +32922,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001408 Category=gene. Requested by=CL. ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 - @@ -35141,7 +32953,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001444 Category=gene. Requested by=CL. cadherin-5 - @@ -35263,7 +33074,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001839 Category=gene. Requested by=CL. T-cell surface glycoprotein CD5 - @@ -35303,7 +33113,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001850 Category=gene. Requested by=CL. cathepsin K - @@ -35421,7 +33230,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001867 Category=gene. Requested by=CL. interleukin-5 receptor subunit alpha - @@ -35463,7 +33271,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001869 Category=gene. Requested by=CL. interleukin-7 receptor subunit alpha - @@ -35520,7 +33327,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001879 Category=gene. Requested by=CL. leukosialin - @@ -35597,7 +33403,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001898 Category=gene. Requested by=CL. neprilysin - @@ -35634,7 +33439,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001903 Category=gene. Requested by=CL. paired box protein PAX-5 - @@ -35677,7 +33481,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001932 Category=gene. The mouse ortholog is Cd24a. Mouse protein Cd24b likely also orthologous. Currently it is not in UniProt. Requested by=CL. signal transducer CD24 - @@ -35716,7 +33519,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001935 Category=gene. Requested by=CL. syndecan-1 - @@ -35763,7 +33565,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001937 Category=gene. Requested by=CL. tartrate-resistant acid phosphatase type 5 - @@ -35807,7 +33608,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001944 Category=gene. Requested by=CL. transcription factor PU.1 - @@ -35854,7 +33654,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001945 Category=gene. Requested by=CL. transferrin receptor protein 1 - @@ -35955,7 +33754,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001954 Category=gene. Requested by=CL. tumor necrosis factor receptor superfamily member 11A - @@ -36036,7 +33834,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001969 Category=gene. Requested by=CL. urokinase plasminogen activator surface receptor - @@ -36106,7 +33903,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000002062 Category=gene. Requested by=CL. macrophage colony-stimulating factor 1 receptor - @@ -36202,7 +33998,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000002112 Category=gene. Requested by=CL. vascular endothelial growth factor receptor 2 - @@ -36398,7 +34193,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000003457 Category=gene. Requested by=CL. V(D)J recombination-activating protein 1 - @@ -36433,7 +34227,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000003460 Category=gene. Requested by=CL. V(D)J recombination-activating protein 2 - @@ -36526,7 +34319,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000005307 Category=gene. Requested by=CL. CCAAT/enhancer-binding protein alpha - @@ -36596,7 +34388,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000006611 Category=gene. Requested by=CL. DNA nucleotidylexotransferase - @@ -36635,7 +34426,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000007431 Category=gene. Requested by=CL. high affinity immunoglobulin epsilon receptor subunit alpha - @@ -36674,7 +34464,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000007597 Category=gene. Requested by=CL. protein c-Fos - @@ -36715,7 +34504,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000007857 Category=gene. Requested by=CL. erythroid transcription factor - @@ -36756,7 +34544,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000007858 Category=gene. Requested by=CL. endothelial transcription factor GATA-2 - @@ -36788,7 +34575,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000009143 Category=gene. Requested by=CL. integrin beta-7 - @@ -36823,7 +34609,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000011178 Category=gene. Requested by=CL. nuclear factor NF-kappa-B p100 subunit - @@ -36861,7 +34646,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000014841 Category=gene. sonic hedgehog protein - @@ -36903,7 +34687,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000016043 Category=gene. Requested by=CL. T-cell acute lymphocytic leukemia protein 1 - @@ -36955,7 +34738,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000016401 Category=gene. Requested by=CL. transmembrane emp24 domain-containing protein 1 - @@ -37306,8 +35088,6 @@ For example, A and B may be gene products and binding of B by A positively regul Any hollow cylindrical anatomical structure containing a lumen through which substances are transported. - not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts) - tubular galen:Tube anatomical tube duct @@ -37369,10 +35149,8 @@ For example, A and B may be gene products and binding of B by A positively regul Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. - in FMA, serosa is a wall UBERON:0009915 wall - EMAPA:25036 FMA:82482 galen:Wall wall of organ @@ -37388,12 +35166,6 @@ For example, A and B may be gene products and binding of B by A positively regul Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. FMA:82482 - - - - in FMA, serosa is a wall - FMA - @@ -37429,7 +35201,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0000003 EHDAA2:0003003 EMAPA:0 - FBbt:00007001 FMA:305751 FMA:67135 GAID:781 @@ -37457,12 +35228,6 @@ For example, A and B may be gene products and binding of B by A positively regul Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. CARO:0000003 - - - - FBbt:00007001 - - @@ -37500,8 +35265,6 @@ For example, A and B may be gene products and binding of B by A positively regul - Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. - CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4 BIRNLEX:4 CARO:0020004 EFO:0000634 @@ -37535,12 +35298,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia - - - - Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. - GO:0048513 - @@ -37567,7 +35324,6 @@ For example, A and B may be gene products and binding of B by A positively regul A multicellular structure that is a part of an organ. - currently defined in a very broad sense, may be replaced by more specific classes in the future @@ -37724,7 +35480,6 @@ For example, A and B may be gene products and binding of B by A positively regul - ncit:Death is an outcome XAO:0000437 XtroDO:0000085 uberon @@ -37739,12 +35494,6 @@ For example, A and B may be gene products and binding of B by A positively regul End of the life of an organism. XAO:0000437 - - - - ncit:Death is an outcome - ncit - @@ -37830,7 +35579,6 @@ For example, A and B may be gene products and binding of B by A positively regul Stage succeeding embryo, including mature structure. - In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997) BilaDO:0000003 OGES:000010 OGES:000014 @@ -37916,8 +35664,6 @@ For example, A and B may be gene products and binding of B by A positively regul - the WBls class 'all stages' belongs here as it is the superclass of other WBls stages - we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage BILS:0000105 EFO:0000399 FBdv:00007012 @@ -37968,13 +35714,11 @@ For example, A and B may be gene products and binding of B by A positively regul A stage at which the organism is a single cell produced by means of sexual reproduction. - As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG] BILS:0000106 BilaDO:0000005 EFO:0001322 EHDAA:27 FBdv:00005288 - IDOMAL:0000302 NCIT:C12601 PdumDv:0000100 VHOG:0000745 @@ -38000,24 +35744,6 @@ For example, A and B may be gene products and binding of B by A positively regul A stage at which the organism is a single cell produced by means of sexual reproduction. Wikipedia:Zygote - - - - As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG] - 2012-09-17 - VHOG:0000745 - VHOG - ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107 - http://bgee.unil.ch/ - - - - - IDOMAL:0000302 - - - https://github.com/biopragmatics/biomappings - @@ -38165,7 +35891,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -38201,14 +35927,14 @@ For example, A and B may be gene products and binding of B by A positively regul gastrula stage - + - + BILS @@ -38286,8 +36012,6 @@ For example, A and B may be gene products and binding of B by A positively regul Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system. - - In zebrafish, the times of neurulation and segmentation overlap so extensively there is no distinct neurula period of development, such as occurs largely before segmentation in amphibian embryos. BILS:0000110 BilaDO:0000009 HsapDv:0000012 @@ -38358,24 +36082,7 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - @@ -38389,11 +36096,6 @@ For example, A and B may be gene products and binding of B by A positively regul The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks). - Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO] - Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG] - oral - some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives - in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips AAO:0010355 BTO:0001090 BTO:0004698 @@ -38402,7 +36104,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA2:0001326 EHDAA:542 EMAPA:16262 - FBbt:00003126 FMA:49184 GAID:75 MA:0000341 @@ -38448,12 +36149,6 @@ For example, A and B may be gene products and binding of B by A positively regul https://github.com/obophenotype/uberon/issues/661 http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg - - - - - the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts - @@ -38461,37 +36156,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Mouth https://github.com/obophenotype/uberon/wiki/The-digestive-tract - - - - Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO] - 2012-06-20 - AAO:0010355 - AAO - AAO:BJB - - - - - Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG] - 2012-09-17 - VHOG:0000812 - VHOG - DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008) - http://bgee.unil.ch/ - - - - - in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips - FMA - - - - - FBbt:00003126 - - @@ -38582,22 +36246,17 @@ For example, A and B may be gene products and binding of B by A positively regul - + - - + + A fluid that is composed of blood plasma and erythrocytes. - This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid. - A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO] - Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO] - relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] - Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG] AAO:0000046 BTO:0000089 CALOHA:TS-0079 @@ -38632,34 +36291,34 @@ For example, A and B may be gene products and binding of B by A positively regul blood - + - + - + - + CL:tm - + https://github.com/obophenotype/uberon/issues/1330 - + Bgee:AN @@ -38671,42 +36330,6 @@ For example, A and B may be gene products and binding of B by A positively regul http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/9 - - - - A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO] - 2012-08-14 - TAO:0000007 - TAO - ZFIN:curator - - - - - Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO] - 2012-06-20 - AAO:0000046 - AAO - AAO:LAP - - - - - relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] - 2012-06-20 - AAO:0000046 - AAO - - - - - Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG] - 2012-09-17 - VHOG:0000224 - VHOG - DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006) - http://bgee.unil.ch/ - @@ -38870,14 +36493,11 @@ For example, A and B may be gene products and binding of B by A positively regul consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77 - Anatomical system that consists of the muscles of the body.[VSAO] - we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA AAO:0000307 BILA:0000088 BTO:0001369 BTO:0001485 EFO:0000801 - EMAPA:35578 FMA:72954 MA:0002888 MAT:0000025 @@ -38905,21 +36525,6 @@ For example, A and B may be gene products and binding of B by A positively regul The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified]. VSAO:0000033 - - - - Anatomical system that consists of the muscles of the body.[VSAO] - 2012-08-14 - VSAO:0000033 - VSAO - VSAO:curator - - - - - we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA - MA - @@ -38963,7 +36568,12 @@ For example, A and B may be gene products and binding of B by A positively regul - + + + + + + @@ -38981,7 +36591,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0000004 EHDAA2:0003004 EMAPA:35178 - FBbt:00007019 FMA:9669 HAO:0000004 MA:0002450 @@ -39005,28 +36614,12 @@ For example, A and B may be gene products and binding of B by A positively regul organism substance - - - - - - - - - this relationship may be too strong and may be weakened in future - Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007019 - - @@ -39081,7 +36674,6 @@ For example, A and B may be gene products and binding of B by A positively regul BILA:0000005 CARO:0000005 EHDAA2:0003005 - FBbt:00007017 FMA:5897 HAO:0000005 NCIT:C94478 @@ -39105,12 +36697,6 @@ For example, A and B may be gene products and binding of B by A positively regul Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures. http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007017 - - @@ -39142,7 +36728,6 @@ For example, A and B may be gene products and binding of B by A positively regul BILA:0000006 CARO:0000006 EHDAA2:0003006 - FBbt:00007016 FMA:67165 HAO:0000006 TAO:0001836 @@ -39160,12 +36745,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical entity that has mass. http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007016 - - @@ -39183,7 +36762,6 @@ For example, A and B may be gene products and binding of B by A positively regul BILA:0000007 CARO:0000007 EHDAA2:0003007 - FBbt:00007015 FMA:67112 HAO:0000007 TAO:0001835 @@ -39202,12 +36780,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical entity that has no mass. http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007015 - - @@ -39250,10 +36822,8 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA:392 EMAPA:16103 EV:0100000 - FBbt:00004856 FMA:7149 HAO:0000011 - IDOMAL:0002460 MA:0000003 NCIT:C12919 SCTID:278195005 @@ -39293,20 +36863,6 @@ For example, A and B may be gene products and binding of B by A positively regul system GO:0048731 - - - - FBbt:00004856 - - - - - - IDOMAL:0002460 - - - https://github.com/biopragmatics/biomappings - @@ -39344,7 +36900,6 @@ For example, A and B may be gene products and binding of B by A positively regul - organismal organism AAO:0010026 AEO:0000191 @@ -39359,7 +36914,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA:1 EMAPA:25765 EV:0100016 - FBbt:00000001 FMA:256135 HAO:0000012 NCIT:C13041 @@ -39404,12 +36958,6 @@ For example, A and B may be gene products and binding of B by A positively regul VHOG:0000671 WBbt:0007833 - - - - FBbt:00000001 - - @@ -39470,7 +37018,6 @@ For example, A and B may be gene products and binding of B by A positively regul EFO:0000808 EHDAA2:0003032 EMAPA:36031 - FBbt:00007009 FMA:7153 HAO:0000032 MA:0002433 @@ -39513,12 +37060,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:DOS http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007009 - - @@ -39560,7 +37101,6 @@ For example, A and B may be gene products and binding of B by A positively regul BILA:0000040 CARO:0000040 EHDAA2:0003040 - FBbt:00007013 FMA:63863 HAO:0000040 TAO:0000382 @@ -39586,12 +37126,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue. http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007013 - - @@ -39610,7 +37144,6 @@ For example, A and B may be gene products and binding of B by A positively regul - FBbt:00007277 VHOG:0001737 uberon UBERON:0000477 @@ -39624,12 +37157,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical group whose component anatomical structures lie in close proximity to each other. FBbt:00007277 - - - - FBbt:00007277 - - @@ -39663,7 +37190,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0000043 EHDAA2:0003043 EMAPA:35868 - FBbt:00007003 FMA:9637 HAO:0000043 MA:0003002 @@ -39699,12 +37225,6 @@ For example, A and B may be gene products and binding of B by A positively regul Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. CARO:0000043 - - - - FBbt:00007003 - - @@ -39745,7 +37265,6 @@ For example, A and B may be gene products and binding of B by A positively regul BILA:0000055 CARO:0000055 EHDAA2:0003055 - FBbt:00007010 HAO:0000055 TAO:0001488 TGMA:0001847 @@ -39772,12 +37291,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0000055 http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007010 - - @@ -39816,7 +37329,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -39824,8 +37337,6 @@ For example, A and B may be gene products and binding of B by A positively regul Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]. - The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG] - epithelial AAO:0000144 AAO:0010055 AEO:0000066 @@ -39835,7 +37346,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0000066 EHDAA2:0003066 EMAPA:32738 - FBbt:00007005 FMA:9639 GAID:402 HAO:0000066 @@ -39860,14 +37370,14 @@ For example, A and B may be gene products and binding of B by A positively regul epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg - + - + http://palaeos.com/metazoa/porifera/homoscleromorpha.html @@ -39877,22 +37387,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Epithelium http://orcid.org/0000-0001-9114-8737 - - - - The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG] - 2012-09-17 - VHOG:0000387 - VHOG - ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.59 - http://bgee.unil.ch/ - - - - - FBbt:00007005 - - @@ -39925,7 +37419,6 @@ For example, A and B may be gene products and binding of B by A positively regul Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA]. - Unilaminar epithelium that consists of a single layer of squamous cells.[CARO] AAO:0010066 AEO:0000070 BILA:0000070 @@ -39957,16 +37450,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Simple_squamous_epithelium http://orcid.org/0000-0001-9114-8737 - - - - Unilaminar epithelium that consists of a single layer of squamous cells.[CARO] - 2012-06-20 - CARO:0000070 - CARO - FMA:45565 - http://orcid.org/0000-0001-9114-8737 - @@ -39989,7 +37472,6 @@ For example, A and B may be gene products and binding of B by A positively regul Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA]. consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable - Epithelium that consists of a single layer of epithelial cells.[CARO] AAO:0010062 AEO:0000073 BILA:0000073 @@ -40018,16 +37500,6 @@ For example, A and B may be gene products and binding of B by A positively regul FMA:45561 http://orcid.org/0000-0001-9114-8737 - - - - Epithelium that consists of a single layer of epithelial cells.[CARO] - 2012-06-20 - CARO:0000073 - CARO - FMA:45561 - http://orcid.org/0000-0001-9114-8737 - @@ -40073,10 +37545,6 @@ For example, A and B may be gene products and binding of B by A positively regul Subdivision of trunk that lies between the head and the abdomen. - note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest - - - EMAPA:35862 FMA:259209 MA:0000022 @@ -40150,8 +37618,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. - embryonic - Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo AAO:0011035 AEO:0000169 BILA:0000056 @@ -40163,10 +37629,8 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA2_RETIRED:0003236 EHDAA:38 EMAPA:16039 - FBbt:00000052 FMA:69068 GAID:963 - IDOMAL:0000646 MAT:0000226 MESH:D004622 MIAA:0000019 @@ -40202,26 +37666,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0009790 Wikipedia:Embryo - - - - Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo - ZFA - - - - - FBbt:00000052 - - - - - - IDOMAL:0000646 - - - https://github.com/biopragmatics/biomappings - @@ -40254,13 +37698,11 @@ For example, A and B may be gene products and binding of B by A positively regul A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm. - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] embryonic tissue AAO:0000480 BILA:0000035 BTO:0000556 EMAPA:36033 - FBbt:00000110 FMA:69069 GAID:1303 MESH:D005855 @@ -40291,28 +37733,12 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Germ_layer https://github.com/obophenotype/uberon/issues/203 - - - - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - 2012-09-17 - VHOG:0001223 - VHOG - ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 - http://bgee.unil.ch/ - embryonic tissue FMA:69069 - - - - FBbt:00000110 - - @@ -40351,11 +37777,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. - Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO] - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - ectodermal AAO:0000137 BILA:0000036 BTO:0000315 @@ -40364,7 +37787,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA2:0000428 EMAPA:16069 EV:0100003 - FBbt:00000111 FMA:69070 GAID:1304 MAT:0000155 @@ -40389,14 +37811,14 @@ For example, A and B may be gene products and binding of B by A positively regul ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -40405,31 +37827,6 @@ For example, A and B may be gene products and binding of B by A positively regul Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. Wikipedia:Ectoderm - - - - Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO] - 2012-06-20 - AAO:0000137 - AAO - AAO:EJS - - - - - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - 2012-09-17 - VHOG:0000153 - VHOG - ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 - http://bgee.unil.ch/ - - - - - FBbt:00000111 - - @@ -40455,10 +37852,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - endodermal AAO:0000139 BILA:0000038 BTO:0000800 @@ -40467,7 +37862,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA2:0000436 EMAPA:16062 EV:0100005 - FBbt:00000125 FMA:69071 GAID:1305 MAT:0000175 @@ -40492,14 +37886,14 @@ For example, A and B may be gene products and binding of B by A positively regul http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -40508,22 +37902,6 @@ For example, A and B may be gene products and binding of B by A positively regul Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. Wikipedia:Endoderm - - - - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - 2012-09-17 - VHOG:0000154 - VHOG - ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 - http://bgee.unil.ch/ - - - - - FBbt:00000125 - - @@ -40550,13 +37928,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + The middle germ layer of the embryo, between the endoderm and ectoderm. - Primary germ layer that is the middle of the embryonic germ layers.[AAO] - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - mesodermal - sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates UBERON:0003263 AAO:0000304 BILA:0000037 @@ -40569,7 +37943,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA:183 EMAPA:16083 EV:0100006 - FBbt:00000126 FMA:69072 GAID:522 MAT:0000174 @@ -40595,20 +37968,14 @@ For example, A and B may be gene products and binding of B by A positively regul mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + - - sometimes not considered primary - - - - - + Bgee:AN @@ -40617,37 +37984,6 @@ For example, A and B may be gene products and binding of B by A positively regul The middle germ layer of the embryo, between the endoderm and ectoderm. Wikipedia:Mesoderm - - - - Primary germ layer that is the middle of the embryonic germ layers.[AAO] - 2012-06-20 - AAO:0000304 - AAO - AAO:EJS - - - - - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - 2012-09-17 - VHOG:0000152 - VHOG - ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 - http://bgee.unil.ch/ - - - - - sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates - https://github.com/obophenotype/uberon/wiki/The-neural-crest - - - - - FBbt:00000126 - - @@ -40694,15 +38030,10 @@ For example, A and B may be gene products and binding of B by A positively regul Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity. consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence - Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO] - the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx - stomodeal - This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity. stomodeal-hypophyseal primordium BTO:0004224 EHDAA2:0001929 EMAPA:16263 - FBbt:00000439 FMA:295846 NCIT:C34306 TAO:0001290 @@ -40735,34 +38066,12 @@ For example, A and B may be gene products and binding of B by A positively regul http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/326 - - - - Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO] - 2012-08-14 - TAO:0001290 - TAO - ZFIN:curator - - - - - the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx - MP:0012522 - NCBITaxon:40674 - stomodeal-hypophyseal primordium XAO:0000269 - - - - FBbt:00000439 - - @@ -40827,7 +38136,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -40856,11 +38165,6 @@ For example, A and B may be gene products and binding of B by A positively regul - Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO] - Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO] - relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO] - As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG] - cardiac AAO:0010210 BILA:0000020 BTO:0000562 @@ -40904,14 +38208,14 @@ For example, A and B may be gene products and binding of B by A positively regul https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb - + - + MA @@ -40921,42 +38225,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Heart http://orcid.org/0000-0002-6601-2165 - - - - Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO] - 2012-08-14 - TAO:0000114 - TAO - ZFIN:curator - - - - - Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO] - 2012-06-20 - AAO:0010210 - AAO - AAO:BJB - - - - - relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO] - 2012-06-20 - AAO:0010210 - AAO - - - - - As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG] - 2012-09-17 - VHOG:0000276 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481 - http://bgee.unil.ch/ - @@ -41002,8 +38270,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical structure that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO]. - Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO] - Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO] articulation joint AEO:0000182 @@ -41048,24 +38314,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Joint http://dx.plos.org/10.1371/journal.pone.0051070 - - - - Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO] - 2012-08-14 - VSAO:0000101 - VSAO - PSPUB:0000170 - - - - - Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO] - 2012-08-14 - TAO:0000367 - TAO - TAO:pem - @@ -41136,16 +38384,11 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes. - An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO] - digestive - many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class AAO:0000129 BILA:0000082 BTO:0000058 CALOHA:TS-1293 EFO:0000793 - EV:0100056 - FBbt:00005055 FMA:7152 GAID:278 MA:0002431 @@ -41182,27 +38425,6 @@ For example, A and B may be gene products and binding of B by A positively regul NLM:alimentary+system Wikipedia:Digestive_system - - - - An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO] - 2012-06-20 - AAO:0000129 - AAO - AAO:BJB - - - - - many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class - MA - - - - - FBbt:00005055 - - @@ -41234,17 +38456,12 @@ For example, A and B may be gene products and binding of B by A positively regul Organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP]. - the cardiovascular system and the lymphatic system are parts of the circulatory system - - Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO] - We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG] AAO:0000959 CALOHA:TS-2103 - MESH:D002319 VHOG:0001248 Wikipedia:Circulatory_system uberon @@ -41267,38 +38484,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Acoelomorpha - - - - - WBbt coelomocyte currently classified as circulating cell - - - - - Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO] - 2012-06-20 - AAO:0000959 - AAO - AAO:BJB - - - - - We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG] - 2012-09-17 - VHOG:0001248 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.493 - http://bgee.unil.ch/ - - - - - MESH:D002319 - - https://github.com/biopragmatics/biomappings - @@ -41326,12 +38511,8 @@ For example, A and B may be gene products and binding of B by A positively regul A subdivision of the muscular system corresponding to a subdisivision of an organism. - - In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here. - AAO:0011066 BTO:0000887 EFO:0001949 - EMAPA:32715 EMAPA:35577 FMA:32558 MA:0000165 @@ -41367,12 +38548,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Muscular_system https://orcid.org/0000-0002-6601-2165 - - - - In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here. - FMA - @@ -41436,7 +38611,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -41444,11 +38619,6 @@ For example, A and B may be gene products and binding of B by A positively regul The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]. - A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO] - Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO] - Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG] - nervous - neural AAO:0000324 BILA:0000079 BIRNLEX:844 @@ -41459,7 +38629,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA:826 EMAPA:16469 EV:0100162 - FBbt:00005093 FMA:7157 GAID:466 MA:0000016 @@ -41491,14 +38660,14 @@ For example, A and B may be gene products and binding of B by A positively regul http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -41513,40 +38682,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Nervous_system ZFIN:curator - - - - A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO] - 2012-08-14 - TAO:0000396 - TAO - ZFIN:curator - - - - - Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO] - 2012-06-20 - AAO:0000324 - AAO - AAO:BJB - - - - - Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG] - 2012-09-17 - VHOG:0000402 - VHOG - ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.117 - http://bgee.unil.ch/ - - - - - FBbt:00005093 - - @@ -41592,14 +38727,10 @@ For example, A and B may be gene products and binding of B by A positively regul - + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. - Part of the nervous system which includes the brain and spinal cord.[AAO] - The brain and spinal cord. Kimmel et al, 1995.[TAO] - The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO). - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG] AAO:0000090 BAMS:CNS BILA:0000080 @@ -41612,7 +38743,6 @@ For example, A and B may be gene products and binding of B by A positively regul EMAPA:16470 EMAPA:16754 EV:0100163 - FBbt:00005094 FMA:55675 GAID:570 MA:0000167 @@ -41641,7 +38771,7 @@ For example, A and B may be gene products and binding of B by A positively regul central nervous system - + @@ -41655,7 +38785,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + Bgee:AN @@ -41672,46 +38802,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Acoelomorpha - - - - Part of the nervous system which includes the brain and spinal cord.[AAO] - 2012-06-20 - AAO:0000090 - AAO - AAO:BJB - - - - - The brain and spinal cord. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000012 - TAO - ZFIN:curator - - - - - The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO). - BIRNLEX:1099 - - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG] - 2012-09-17 - VHOG:0000293 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 (reference 1), ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 (reference 2), DOI:10.1016/j.cell.2007.02.040 Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud'homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007) (reference 3) - http://bgee.unil.ch/ - - - - - FBbt:00005094 - - @@ -41763,7 +38853,6 @@ For example, A and B may be gene products and binding of B by A positively regul BTO:0001886 EFO:0001652 EHDAA2:0003171 - FBbt:00005495 FMA:86589 MAT:0000482 NCIT:C34275 @@ -41797,12 +38886,6 @@ For example, A and B may be gene products and binding of B by A positively regul FB:FBrf0089570 http://flybase.org/reports/FBrf0178740.html - - - - FBbt:00005495 - - @@ -41839,10 +38922,6 @@ For example, A and B may be gene products and binding of B by A positively regul In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted]. - Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO] - The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG] - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] - The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium AAO:0010617 BTO:0001057 CALOHA:TS-2371 @@ -41854,7 +38933,6 @@ For example, A and B may be gene products and binding of B by A positively regul EMAPA:16757 FMA:293882 MAT:0000069 - MESH:D054259 MIAA:0000069 NCIT:C34226 SCTID:362852000 @@ -41888,49 +38966,6 @@ For example, A and B may be gene products and binding of B by A positively regul In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted]. Wikipedia:Neural_tube - - - - Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO] - 2012-06-20 - AAO:0010617 - AAO - AAO:JOR - - - - - The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG] - 2012-09-17 - VHOG:0000307 - VHOG - http://bgee.unil.ch/ - http://medical-dictionary.thefreedictionary.com/neural+tube - - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] - 2012-09-17 - VHOG:0000307 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 - http://bgee.unil.ch/ - - - - - The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium - GO:0021915 - - - - - MESH:D054259 - - - https://github.com/biopragmatics/biomappings - @@ -41961,7 +38996,6 @@ For example, A and B may be gene products and binding of B by A positively regul BIRNLEX:6 CARO:0000000 EHDAA2:0002229 - FBbt:10000000 FMA:62955 HAO:0000000 MA:0000001 @@ -41985,12 +39019,6 @@ For example, A and B may be gene products and binding of B by A positively regul FMA:62955 http://orcid.org/0000-0001-9114-8737 - - - - FBbt:10000000 - - @@ -42048,13 +39076,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system. - - Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO] - Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO] - System that provides physical support to the organism.[AAO] - By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG] - skeletal - GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates AAO:0000566 BTO:0001486 CALOHA:TS-1320 @@ -42090,50 +39111,6 @@ For example, A and B may be gene products and binding of B by A positively regul VSAO:0000027 http://dx.plos.org/10.1371/journal.pone.0051070 - - - - Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO] - 2012-08-14 - TAO:0000434 - TAO - TAO:wd - - - - - Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO] - 2012-08-14 - VSAO:0000027 - VSAO - GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 - PSPUB:0000170 - - - - - System that provides physical support to the organism.[AAO] - 2012-06-20 - AAO:0000566 - AAO - AAO:LAP - - - - - By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG] - 2012-09-17 - VHOG:0001254 - VHOG - DOI:10.1159/000324245 Donoghue PCJ, Sansom IJ, Origin and early evolution of vertebrate skeletonization. Microscopy research and technique (2002) - http://bgee.unil.ch/ - - - - - GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates - GO - @@ -42176,18 +39153,10 @@ For example, A and B may be gene products and binding of B by A positively regul - + Skeletal element that is composed of bone tissue. - - - - Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO] - Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO] - Skeletal element that is composed of bone tissue.[VSAO] - relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] - The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG] AAO:0000047 AEO:0000082 BTO:0000140 @@ -42226,14 +39195,14 @@ For example, A and B may be gene products and binding of B by A positively regul bone element - + - + VSAO-modified @@ -42246,51 +39215,6 @@ For example, A and B may be gene products and binding of B by A positively regul http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/277 - - - - Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO] - 2012-06-20 - AAO:0000047 - AAO - AAO:LAP - - - - - Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO] - 2012-08-14 - TAO:0001514 - TAO - ZFIN:curator - - - - - Skeletal element that is composed of bone tissue.[VSAO] - 2012-08-14 - VSAO:0000057 - VSAO - PSPUB:0000170 - - - - - relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] - 2012-06-20 - AAO:0000047 - AAO - - - - - The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG] - 2012-09-17 - VHOG:0001190 - VHOG - DOI:10.1159/000324245 Murdock DJ, Donoghue PC, Evolutionary Origins of Animal Skeletal Biomineralization. Cells Tissues Organs (2011) - http://bgee.unil.ch/ - @@ -42344,16 +39268,11 @@ For example, A and B may be gene products and binding of B by A positively regul - + A tube extending from the mouth to the anus. - The alimentary or digestive tract, and associated organs.[TAO] - The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] - FMA also has a term 'gastrointestinal tract', but this includes the liver. - we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509 - we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this gut AAO:0010023 BILA:0000083 @@ -42362,10 +39281,8 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA2:0000726 EHDAA:518 EMAPA:16247 - FBbt:00003125 FMA:45615 MA:0000917 - MESH:D041981 NCIT:C34082 TAO:0000112 TGMA:0001819 @@ -42387,14 +39304,14 @@ For example, A and B may be gene products and binding of B by A positively regul digestive tract - + - + NCBIBook:NBK10107 @@ -42416,50 +39333,6 @@ For example, A and B may be gene products and binding of B by A positively regul DOI:10.1371/journal.pone.0016309 - - - - The alimentary or digestive tract, and associated organs.[TAO] - 2012-08-14 - TAO:0000112 - TAO - ZFIN:curator - - - - - The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0000309 - VHOG - ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 - http://bgee.unil.ch/ - - - - - FMA also has a term 'gastrointestinal tract', but this includes the liver. - FMA - - - - - we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509 - MA - - - - - FBbt:00003125 - - - - - - MESH:D041981 - - https://github.com/biopragmatics/biomappings - @@ -42510,12 +39383,7 @@ For example, A and B may be gene products and binding of B by A positively regul Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]. - Portion of tissue composed of contractile fibers.[TAO] - It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG] - muscular muscle - AAO:0011066 - EMAPA:32715 EMAPA:37474 EV:0100146 FMA:5022 @@ -42541,25 +39409,6 @@ For example, A and B may be gene products and binding of B by A positively regul Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]. GO:0007517 - - - - Portion of tissue composed of contractile fibers.[TAO] - 2012-08-14 - TAO:0005145 - TAO - ZFIN:curator - - - - - It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG] - 2012-09-17 - VHOG:0001245 - VHOG - ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.75 - http://bgee.unil.ch/ - @@ -42678,14 +39527,15 @@ For example, A and B may be gene products and binding of B by A positively regul + - - + + @@ -42698,7 +39548,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -42714,11 +39564,6 @@ For example, A and B may be gene products and binding of B by A positively regul A vessel through which blood circulates in the body. consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus - Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG] - Any of the vessels through which blood circulates in the body.[AAO] - The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] - annelids have blood vessels, but this class is not applicable to annelids. - FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX vascular element AAO:0011004 AEO:0000207 @@ -42757,34 +39602,34 @@ For example, A and B may be gene products and binding of B by A positively regul blood vessel http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg - + - + - + - + AEO - + EHDAA2 - + GO:0072360 @@ -42794,40 +39639,6 @@ For example, A and B may be gene products and binding of B by A positively regul BTO:0001102 Wikipedia:Blood_vessel - - - - Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG] - 2012-09-17 - VHOG:0001250 - VHOG - http://bgee.unil.ch/ - - - - - Any of the vessels through which blood circulates in the body.[AAO] - 2012-06-20 - AAO:0011004 - AAO - AAO:EJS - - - - - The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] - 2012-09-17 - VHOG:0001250 - VHOG - DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006) - http://bgee.unil.ch/ - - - - - FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX - FMA - @@ -42892,7 +39703,6 @@ For example, A and B may be gene products and binding of B by A positively regul A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA]. - endothelial BTO:0000393 CALOHA:TS-0278 EFO:0002548 @@ -42960,7 +39770,6 @@ For example, A and B may be gene products and binding of B by A positively regul An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face. see also: vascular system. Consider merging? - vascular BTO:0003718 FMA:69050 TAO:0005249 @@ -43018,16 +39827,11 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical structure that is part of an embryo. - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO] - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO] - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO] - in FMA embryo is_a embryonic structure AAO:0000138 BILA:0000034 BTO:0000174 CALOHA:TS-2110 EFO:0000461 - FBbt:00004208 FMA:69067 GAID:407 MESH:D004628 @@ -43058,45 +39862,6 @@ For example, A and B may be gene products and binding of B by A positively regul BTO:0000174 ZFIN:curator - - - - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO] - 2012-06-20 - AAO:0000138 - AAO - AAO:BJB - - - - - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO] - 2012-08-14 - TAO:0001105 - TAO - ZFIN:curator - - - - - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO] - 2012-08-14 - VSAO:0000178 - VSAO - ZFIN:curator - - - - - in FMA embryo is_a embryonic structure - FMA - - - - - FBbt:00004208 - - @@ -43153,8 +39918,6 @@ For example, A and B may be gene products and binding of B by A positively regul An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen. - An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO] - general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs. AAO:0010386 BTO:0001491 EHDAA:512 @@ -43189,21 +39952,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Viscus https://github.com/obophenotype/mouse-anatomy-ontology/issues/14 - - - - An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO] - 2012-06-20 - AAO:0010386 - AAO - BTO:0001491 - - - - - general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs. - FMA - @@ -43260,21 +40008,15 @@ For example, A and B may be gene products and binding of B by A positively regul The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA]. - Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO] - The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO] - The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO] - The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG] axial skeleton AAO:0000034 EFO:0000942 EHDAA2:0000161 EHDAA:5049 - EMAPA:17214 EMAPA:37721 FMA:71221 MA:0002986 MAT:0000148 - MESH:D013131 MIAA:0000148 TAO:0000317 VHOG:0000317 @@ -43300,43 +40042,6 @@ For example, A and B may be gene products and binding of B by A positively regul https://sourceforge.net/tracker/?func=detail&aid=2983975&group_id=76834&atid=974957 https://sourceforge.net/tracker/?func=detail&atid=1205376&aid=2983977&group_id=76834 - - - - Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO] - 2012-08-14 - VSAO:0000093 - VSAO - PSPUB:0000170 - - - - - The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO] - 2012-06-20 - AAO:0000034 - AAO - AAO:LAP - - - - - The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO] - 2012-08-14 - TAO:0000317 - TAO - ZFIN:curator - - - - - The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG] - 2012-09-17 - VHOG:0000317 - VHOG - DOI:10.1186/1742-9994-8-4 Schilling N, Evolution of the axial system in craniates: morphology and function of the perivertebral musculature. Frontiers in Zoology (2011) - http://bgee.unil.ch/ - @@ -43350,13 +40055,6 @@ For example, A and B may be gene products and binding of B by A positively regul EMAPA:37721 MA:th - - - - MESH:D013131 - - https://github.com/biopragmatics/biomappings - @@ -43371,10 +40069,6 @@ For example, A and B may be gene products and binding of B by A positively regul Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present. - - - Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO] - Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO] AAO:0010339 BILA:0000116 BTO:0001493 @@ -43414,32 +40108,6 @@ For example, A and B may be gene products and binding of B by A positively regul UBERONREF:0000006 Wikipedia:Torso - - - - - ZFA - https://github.com/obophenotype/uberon/issues/378 - pending - - - - - Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO] - 2012-06-20 - AAO:0010339 - AAO - AAO:BJB - - - - - Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO] - 2012-08-14 - TAO:0001115 - TAO - ZFIN:curator - @@ -43521,7 +40189,12 @@ For example, A and B may be gene products and binding of B by A positively regul - + + + + + + @@ -43531,9 +40204,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that consists of the muscular and skeletal systems. - Anatomical system that provides locomotion and physical support to the organism.[AAO] - There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG] - musculoskeletal AAO:0010546 CALOHA:TS-1311 EMAPA:32714 @@ -43555,16 +40225,6 @@ For example, A and B may be gene products and binding of B by A positively regul musculoskeletal system - - - - - - - - - check ctenophore - @@ -43573,25 +40233,6 @@ For example, A and B may be gene products and binding of B by A positively regul VSAO:curator https://github.com/obophenotype/uberon/issues/77 - - - - Anatomical system that provides locomotion and physical support to the organism.[AAO] - 2012-06-20 - AAO:0010546 - AAO - AAO:EJS - - - - - There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG] - 2012-09-17 - VHOG:0001275 - VHOG - DOI:10.1002/jez.b.21246 Shearman RM, Burke AC, The lateral somitic frontier in ontogeny and phylogeny. Journal of Experimental Zoology (2009) - http://bgee.unil.ch/ - @@ -43633,7 +40274,6 @@ For example, A and B may be gene products and binding of B by A positively regul The part of the coelemic cavity lumen that is enclosed by the walls of the thorax. - In many species, the diaphragm separates thoracic and abdominal cavities EMAPA:36497 FMA:7565 GAID:93 @@ -43691,7 +40331,12 @@ For example, A and B may be gene products and binding of B by A positively regul - + + + + + + @@ -43699,15 +40344,11 @@ For example, A and B may be gene products and binding of B by A positively regul The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities. - Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]. - The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]. - In mammals it forms the peritoneal, pleural, and pericardial cavities UBERON:0000169 body cavity AEO:0000186 BTO:0001707 EHDAA2:0000267 - FBbt:00005060 FMA:85006 NCIT:C25444 RETIRED_EHDAA2:0003186 @@ -43732,52 +40373,18 @@ For example, A and B may be gene products and binding of B by A positively regul EDITOR_NOTE check the FMA placement here; ncit placement of body cavity here probably not correct coelemic cavity lumen - - - - - - - - - definitional - The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities. BTO:0001707 - - - - Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]. - 2012-09-12 - ZFA:0001438 - ZFA - ZFIN:curator - - - - - The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]. - 2012-09-12 - BTO:0001707 - BTO - BTO - body cavity BTO:0001707 - - - - FBbt:00005060 - - @@ -43834,6 +40441,7 @@ For example, A and B may be gene products and binding of B by A positively regul + @@ -43841,21 +40449,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - + + + @@ -43869,13 +40465,6 @@ For example, A and B may be gene products and binding of B by A positively regul A flexible rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In some chordates, it persists throughout life as the main axial support of the body, while in most vertebrates it becomes the nucleus pulposus of the intervertebral disc. The notochord is found ventral to the neural tube. - Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO] - Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO] - Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO] - relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO] - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG] - notochordal - In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord. AAO:0000327 BTO:0001768 CALOHA:TS-0690 @@ -43910,15 +40499,15 @@ For example, A and B may be gene products and binding of B by A positively regul notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + @@ -43937,19 +40526,19 @@ For example, A and B may be gene products and binding of B by A positively regul - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -43962,51 +40551,6 @@ For example, A and B may be gene products and binding of B by A positively regul https://github.com/obophenotype/uberon/issues/25 https://github.com/obophenotype/uberon/issues/271 - - - - Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO] - 2012-08-14 - VSAO:0000032 - VSAO - PSPUB:0000170 - - - - - Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000135 - TAO - ZFIN:curator - - - - - Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO] - 2012-06-20 - AAO:0000327 - AAO - AAO:LAP - - - - - relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO] - 2012-06-20 - AAO:0000327 - AAO - - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG] - 2012-09-17 - VHOG:0000199 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 - http://bgee.unil.ch/ - @@ -44034,18 +40578,10 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. - EDITOR_NOTE currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk - Post-cranial axial segments which form sclerotome and dermomyotome.[AAO] - Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO] - relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO] - relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO] - relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO] - (...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG] - somitic mesodermal cluster AAO:0010569 AEO:0001015 @@ -44081,11 +40617,11 @@ For example, A and B may be gene products and binding of B by A positively regul somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + @@ -44098,13 +40634,13 @@ For example, A and B may be gene products and binding of B by A positively regul - + GOTAX:0000352 - + ZFA @@ -44120,58 +40656,6 @@ For example, A and B may be gene products and binding of B by A positively regul PMID:17237766 - - - - Post-cranial axial segments which form sclerotome and dermomyotome.[AAO] - 2012-06-20 - AAO:0010569 - AAO - AAO:EJS - - - - - Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000155 - TAO - ZFIN:curator - - - - - relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO] - 2012-08-14 - TAO:0000155 - TAO - - - - - relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO] - 2012-08-14 - TAO:0000155 - TAO - - - - - relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO] - 2012-06-20 - AAO:0010569 - AAO - - - - - (...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0000191 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.40, DOI:10.1093/icb/43.1.137 Balavoine G, Adoutte A, The segmented urbilateria: a testable scenario. Integrative and Comparative Biology (2003) - http://bgee.unil.ch/ - @@ -44216,20 +40700,25 @@ For example, A and B may be gene products and binding of B by A positively regul + - - - - - - + + + + + + + + + + + + + + + + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. - EDITOR_NOTE consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams). - - A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO] - Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO] - A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831] - We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG] AAO:0010578 BTO:0001764 CALOHA:TS-0676 @@ -44242,7 +40731,6 @@ For example, A and B may be gene products and binding of B by A positively regul MIAA:0000066 NCIT:C34222 SCTID:361462002 - TAO:0000045 UMLS:C0027789 VHOG:0000057 Wikipedia:Neural_crest @@ -44262,66 +40750,45 @@ For example, A and B may be gene products and binding of B by A positively regul http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - - - - - + - + - - - - - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - - Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells - ISBN:0073040584 - - - - - + BTO - + PMID:11523831 - - pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest - - - - - + PMID:11523831 @@ -44330,47 +40797,6 @@ For example, A and B may be gene products and binding of B by A positively regul A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. MP:0009846 - - - - - ISBN:0073040584 - PMID:17377535 - - - - - A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000045 - TAO - ZFIN:curator - - - - - Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO] - 2012-06-20 - AAO:0010578 - AAO - AAO:EJS - - - - - A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831] - PMID:11523831 - - - - - We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG] - 2012-09-17 - VHOG:0000057 - VHOG - DOI:10.1111/j.1469-7580.2012.01495.x Hall BK, Gillis JA, Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues. J Anat (2012) - http://bgee.unil.ch/ - @@ -44412,9 +40838,6 @@ For example, A and B may be gene products and binding of B by A positively regul Embryonic ectoderm that gives rise to nervous tissue. - (...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG] - neurectodermal - we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here AAO:0011074 BILA:0000039 CALOHA:TS-1212 @@ -44423,7 +40846,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA:255 EMAPA:16073 EV:0100004 - FBbt:00001057 FMA:87657 MAT:0000176 MIAA:0000176 @@ -44452,22 +40874,6 @@ For example, A and B may be gene products and binding of B by A positively regul Embryonic ectoderm that gives rise to nervous tissue. Wikipedia:Neuroectoderm - - - - (...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG] - 2012-09-17 - VHOG:0000150 - VHOG - DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) - http://bgee.unil.ch/ - - - - - FBbt:00001057 - - @@ -44509,13 +40915,14 @@ For example, A and B may be gene products and binding of B by A positively regul + - + @@ -44538,8 +40945,6 @@ For example, A and B may be gene products and binding of B by A positively regul TODO - create superclass for bone marrow / head kidney. both are portions of tissue in the hematopoetic system. also consider adding as subclass of zone of bone organ for consistency with FMA. See also: Leydig and epigonal organs consider placement of NCIT:C53466 medullary bone - The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG] - In adults, marrow in large bones produces new blood cells[Wikipedia:Bone_marrow] AAO:0011007 BTO:0000141 BTO:0000829 @@ -44573,14 +40978,14 @@ For example, A and B may be gene products and binding of B by A positively regul bone marrow http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg - + - + FMA MA @@ -44591,16 +40996,6 @@ For example, A and B may be gene products and binding of B by A positively regul MGI:cwg MP:0002397 - - - - The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG] - 2012-09-17 - VHOG:0001218 - VHOG - DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood Cells and Blood Cell Development in the Animal Kingdom. Annual Review of Cell and Developmental Biology (2006) - http://bgee.unil.ch/ - @@ -44644,10 +41039,6 @@ For example, A and B may be gene products and binding of B by A positively regul Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance. - One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO] - Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO] - Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO] - MA also has set of connective tissues AAO:0000098 BTO:0000421 CALOHA:TS-2009 @@ -44688,40 +41079,6 @@ For example, A and B may be gene products and binding of B by A positively regul http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/23 - - - - One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO] - 2012-06-20 - AAO:0000098 - AAO - AAO:LAP - - - - - Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO] - 2012-08-14 - TAO:0001641 - TAO - TAO:wd - - - - - Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO] - 2012-08-14 - VSAO:0000017 - VSAO - GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 - PSPUB:0000170 - - - - - MA also has set of connective tissues - MA - @@ -44784,8 +41141,6 @@ For example, A and B may be gene products and binding of B by A positively regul Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]. - - One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO] AAO:0000306 AEO:0000122 CALOHA:TS-0642 @@ -44816,15 +41171,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Muscle_tissue https://sourceforge.net/tracker/index.php?func=detail&aid=2801266&group_id=36855&atid=440764 - - - - One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO] - 2012-06-20 - AAO:0000306 - AAO - AAO:LAP - @@ -44851,21 +41197,22 @@ For example, A and B may be gene products and binding of B by A positively regul - + - + + + + + + Anatomical system that is involved in the production of hematopoietic cells. - Anatomical system that consists of the blood and blood forming tissues.[AAO] - Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG] - hematopoietic - In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes AAO:0011002 BTO:0000570 CALOHA:TS-0449 @@ -44903,57 +41250,22 @@ For example, A and B may be gene products and binding of B by A positively regul hematopoietic system - + - - - - - + FMA - - - - - definitional - Anatomical system that is involved in the production of hematopoietic cells. Wikipedia:Haematopoiesis - - - - Anatomical system that consists of the blood and blood forming tissues.[AAO] - 2012-06-20 - AAO:0011002 - AAO - AAO:EJS - - - - - Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG] - 2012-09-17 - VHOG:0001624 - VHOG - DOI:10.1016/j.coph.2010.05.004 Ellett F, Lieschke GJ, Zebrafish as a model for vertebrate hematopoiesis. Current Opinion in Pharmacology (2010) - http://bgee.unil.ch/ - - - - - In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes - WP - @@ -44993,7 +41305,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies. - The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG] AAO:0011003 BILA:0000104 BTO:0005810 @@ -45023,16 +41334,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies. Wikipedia:Immune_system - - - - The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG] - 2012-09-17 - VHOG:0001247 - VHOG - PMID:21046016 Dzik JM, The ancestry and cumulative evolution of immune reactions. Acta biochimica Polonica (2010) - http://bgee.unil.ch/ - @@ -45061,7 +41362,6 @@ For example, A and B may be gene products and binding of B by A positively regul Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts. see https://github.com/obophenotype/uberon/issues/27 - Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO] CALOHA:TS-2011 EMAPA:35179 FMA:224804 @@ -45101,16 +41401,6 @@ For example, A and B may be gene products and binding of B by A positively regul VSAO:0000047 http://dx.plos.org/10.1371/journal.pone.0051070 - - - - Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO] - 2012-08-14 - VSAO:0000047 - VSAO - GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 - PSPUB:0000170 - @@ -45156,7 +41446,6 @@ For example, A and B may be gene products and binding of B by A positively regul In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA]. MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class - In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG] BTO:0004593 FMA:296704 MAT:0000067 @@ -45184,16 +41473,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Epiblast ZFIN:curator - - - - In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG] - 2012-09-17 - VHOG:0000243 - VHOG - DOI:10.1146/annurev.cellbio.042308.113344 Zorn AM, Wells JM, Vertebrate endoderm development and organ formation. Annual Review of Cell Developmental Biology (2009) - http://bgee.unil.ch/ - @@ -45291,10 +41570,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. - Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO] - It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG] AAO:0011086 EFO:0001982 EMAPA:16189 @@ -45316,14 +41593,14 @@ For example, A and B may be gene products and binding of B by A positively regul presomitic mesoderm - + - + Bgee:AN @@ -45332,25 +41609,6 @@ For example, A and B may be gene products and binding of B by A positively regul Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. ZFIN:curator - - - - Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000279 - TAO - ZFIN:curator - - - - - It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG] - 2012-09-17 - VHOG:0000559 - VHOG - DOI:10.1006/dbio.2001.0460 Schubert M, Holland LZ, Dale Stokes M and Holland ND, Three Amphoxius Wnt Genes (AmphiWnt3, AmphiWnt5, and AmphiWnt6) Associated with the Tail Bud: the Evolution of Somitogenesis in Chordates. Developmental Biology (2001) - http://bgee.unil.ch/ - @@ -45389,11 +41647,6 @@ For example, A and B may be gene products and binding of B by A positively regul Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted]. - Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO] - Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO] - relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO] - Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG] - EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac ventral lateral plate mesoderm AAO:0011006 EFO:0003489 @@ -45426,48 +41679,6 @@ For example, A and B may be gene products and binding of B by A positively regul Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted]. Wikipedia:Blood_island_of_umbilical_vesicle - - - - Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000094 - TAO - ZFIN:curator - - - - - Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO] - 2012-06-20 - AAO:0011006 - AAO - AAO:EJS - - - - - relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO] - 2012-08-14 - TAO:0000094 - TAO - - - - - Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0000085 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450, DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual Review of Cell and Developmental Biology (2006) - http://bgee.unil.ch/ - - - - - EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac - EHDAA2 - @@ -45506,7 +41717,6 @@ For example, A and B may be gene products and binding of B by A positively regul The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord. - The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] AAO:0011017 EFO:0003647 TAO:0001204 @@ -45529,15 +41739,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0048318 Wikipedia:Chordamesoderm - - - - The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] - 2012-09-17 - VHOG:0000107 - VHOG - http://bgee.unil.ch/ - @@ -45553,12 +41754,10 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. - The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO] - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] AAO:0011072 BTO:0001765 DHBA:10153 @@ -45567,7 +41766,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA:902 EMAPA:35593 FMA:293879 - MESH:D054258 NCIT:C34225 RETIRED_EHDAA2:0001252 TAO:0000132 @@ -45587,34 +41785,34 @@ For example, A and B may be gene products and binding of B by A positively regul neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -45626,33 +41824,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Neural_plate ZFIN:curator - - - - The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000132 - TAO - ZFIN:curator - - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] - 2012-09-17 - VHOG:0000068 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 - http://bgee.unil.ch/ - - - - - MESH:D054258 - - - https://github.com/biopragmatics/biomappings - @@ -45675,23 +41846,14 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. - Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO] - Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG] - note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here) AAO:0010568 EFO:0003515 EMAPA:16183 @@ -45716,7 +41878,7 @@ For example, A and B may be gene products and binding of B by A positively regul paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -45729,7 +41891,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + Bgee:AN @@ -45739,31 +41901,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0048339 https://github.com/obophenotype/uberon/issues/30 - - - - Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO] - 2012-06-20 - AAO:0010568 - AAO - AAO:EJS - - - - - Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG] - 2012-09-17 - VHOG:0000114 - VHOG - DOI:10.1002/dvdy.21177 Kusakabe R and Kuratani S. Evolutionary perspectives from development of mesodermal components in the lamprey. Developmental dynamics (2007) - http://bgee.unil.ch/ - - - - - note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here) - ZFA - @@ -45801,7 +41938,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -45815,10 +41952,6 @@ For example, A and B may be gene products and binding of B by A positively regul Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]. - Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO] - The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] - A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG] - subclass of mesoderm in ZFA. UBERON:0006258 AAO:0010574 EHDAA2:0000919 @@ -45845,7 +41978,7 @@ For example, A and B may be gene products and binding of B by A positively regul lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -45858,7 +41991,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + EHDAA2 VHOG @@ -45869,40 +42002,6 @@ For example, A and B may be gene products and binding of B by A positively regul MP:0010117 Wikipedia:Lateral_plate_mesoderm - - - - Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO] - 2012-06-20 - AAO:0010574 - AAO - AAO:EJS - - - - - The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] - 2012-09-17 - VHOG:0000118 - VHOG - http://bgee.unil.ch/ - - - - - A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG] - 2012-09-17 - VHOG:0000118 - VHOG - DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) - http://bgee.unil.ch/ - - - - - subclass of mesoderm in ZFA. - ZFA - @@ -45942,20 +42041,17 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + - + Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. should probably be merged with heart rudiment. - Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO] - The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO] - relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO] AAO:0011044 BTO:0001887 NCIT:C34276 @@ -45970,15 +42066,15 @@ For example, A and B may be gene products and binding of B by A positively regul heart primordium - + - + - + @@ -45991,19 +42087,19 @@ For example, A and B may be gene products and binding of B by A positively regul - + ZFA - + ZFA - + XAO @@ -46012,32 +42108,6 @@ For example, A and B may be gene products and binding of B by A positively regul Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. ZFIN:curator - - - - Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO] - 2012-08-14 - TAO:0000028 - TAO - ZFIN:curator - - - - - The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO] - 2012-06-20 - AAO:0011044 - AAO - XAO:curator - - - - - relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO] - 2012-08-14 - TAO:0000028 - TAO - @@ -46058,15 +42128,11 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. - Skeletogenic portion of somites.[AAO] - The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG] - part_of somite in XAO AAO:0010571 AEO:0000212 - BTO:0006255 EHDAA2:0003439 EMAPA:31159 FMA:295652 @@ -46087,11 +42153,11 @@ For example, A and B may be gene products and binding of B by A positively regul sclerotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + - + @@ -46110,13 +42176,13 @@ For example, A and B may be gene products and binding of B by A positively regul - + VHOG:0000680 - + ZFA @@ -46127,39 +42193,6 @@ For example, A and B may be gene products and binding of B by A positively regul XB:curator https://github.com/obophenotype/uberon/issues/316 - - - - Skeletogenic portion of somites.[AAO] - 2012-06-20 - AAO:0010571 - AAO - AAO:EJS - - - - - The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG] - 2012-09-17 - VHOG:0000680 - VHOG - DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) - http://bgee.unil.ch/ - - - - - part_of somite in XAO - XAO - - - - - BTO:0006255 - - - https://github.com/biopragmatics/biomappings - @@ -46188,7 +42221,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types. - this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs AAO:0010015 AEO:0000024 BILA:0000024 @@ -46252,9 +42284,6 @@ For example, A and B may be gene products and binding of B by A positively regul Portion of tissue composed of mesenchymal cells (motile cells that develop from epthelia via an epithelial to mesenchymal transition) and surrounding extracellular material. Mesenchyme has different embryological origins in different metazoan taxa - in many invertebrates it derives in whole or part from ectoderm. In vertebrates it derives largely from mesoderm, and sometimes the terms are used interchangeably, e.g. lateral plate mesoderm/mesenchyme. the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense - A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO] - Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO] - mesenchymal AAO:0010427 AEO:0000145 BTO:0001393 @@ -46289,24 +42318,6 @@ For example, A and B may be gene products and binding of B by A positively regul https://en.wikipedia.org/wiki/Mesenchyme https://github.com/obophenotype/uberon/issues/1641 - - - - A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000393 - TAO - ZFIN:curator - - - - - Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO] - 2012-06-20 - AAO:0010427 - AAO - AAO:EJS - @@ -46390,10 +42401,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults - (...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG] EHDAA:251 EMAPA:16088 NCIT:C34195 @@ -46406,14 +42416,14 @@ For example, A and B may be gene products and binding of B by A positively regul intraembryonic coelom - + - + Wikipedia @@ -46423,16 +42433,6 @@ For example, A and B may be gene products and binding of B by A positively regul MGI:anna MP:0012187 - - - - (...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG] - 2012-09-17 - VHOG:0000316 - VHOG - ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.166 - http://bgee.unil.ch/ - @@ -46465,10 +42465,8 @@ For example, A and B may be gene products and binding of B by A positively regul Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. - contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers AEO:0000114 EHDAA2:0003114 - FBbt:00007474 epithelial or endothelial tube uberon UBERON:0003914 @@ -46481,12 +42479,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0060562 PMID:12526790 - - - - FBbt:00007474 - - @@ -46532,7 +42524,6 @@ For example, A and B may be gene products and binding of B by A positively regul - FMA has both conduit and conduit space. In EHDAA2 this is a surface feature AEO:0000080 EHDAA2:0003080 FMA:242873 @@ -46554,12 +42545,6 @@ For example, A and B may be gene products and binding of B by A positively regul Any tube, opening or passage that connects two distinct anatomical spaces. http://orcid.org/0000-0002-6601-2165 - - - - FMA has both conduit and conduit space. In EHDAA2 this is a surface feature - FMA - @@ -46604,7 +42589,6 @@ For example, A and B may be gene products and binding of B by A positively regul An anatomical structure that develops (entirely or partially) from the mesoderm. - Grouping term for query purposes mesodermal derivative uberon UBERON:0004120 @@ -46648,7 +42632,6 @@ For example, A and B may be gene products and binding of B by A positively regul An anatomical structure that develops (entirely or partially) from the ectoderm. - Grouping term for query purposes ectodermal deriviative uberon UBERON:0004121 @@ -46682,7 +42665,6 @@ For example, A and B may be gene products and binding of B by A positively regul The first recognizable structure derived from the heart field. TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO - (In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG] EHDAA2:0000215 EMAPA:16106 VHOG:0000975 @@ -46701,16 +42683,6 @@ For example, A and B may be gene products and binding of B by A positively regul The first recognizable structure derived from the heart field. GO:0003142 - - - - (In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG] - 2012-09-17 - VHOG:0000975 - VHOG - PMID:15611355 Gittenberger-de Groot AC, Bartelings MM, Deruiter MC, Poelmann RE, Basics of cardiac development for the understanding of congenital heart malformations. Pediatric Research (2005) - http://bgee.unil.ch/ - @@ -46736,12 +42708,12 @@ For example, A and B may be gene products and binding of B by A positively regul + - - + + A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. - this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138] XAO:0004185 first heart field primary heart field @@ -46752,24 +42724,24 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0004140 primary heart field - + - + - + GO:0003128 - + https://orcid.org/0000-0003-3308-6245 @@ -46780,12 +42752,6 @@ For example, A and B may be gene products and binding of B by A positively regul GOC:mtg_heart GOC:rl - - - - this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138] - GO - @@ -46828,9 +42794,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + An epithelial tube that will give rise to the mature heart. - the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube. AAO:0010411 EFO:0003526 EMAPA:32685 @@ -46848,14 +42813,14 @@ For example, A and B may be gene products and binding of B by A positively regul heart tube - + - + ZFA-modified @@ -46865,12 +42830,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0003143 GOC:mtg_heart - - - - the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube. - MP:0012700 - @@ -46896,6 +42855,7 @@ For example, A and B may be gene products and binding of B by A positively regul + @@ -46939,10 +42899,7 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body. - - Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO] - skeletal AEO:0000168 EHDAA2:0001843 EHDAA:5047 @@ -46975,15 +42932,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body. VSAO:0000026 - - - - Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO] - 2012-08-14 - VSAO:0000026 - VSAO - GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 - @@ -46998,7 +42946,6 @@ For example, A and B may be gene products and binding of B by A positively regul A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube. - The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO] TAO:0000115 ZFA:0000115 heart cone @@ -47013,15 +42960,6 @@ For example, A and B may be gene products and binding of B by A positively regul A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube. GO:0003313 - - - - The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO] - 2012-08-14 - TAO:0000115 - TAO - ZFIN:curator - @@ -47080,18 +43018,14 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that has as its parts the heart and blood vessels. - we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph. - The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG] AAO:0011001 BILA:0000016 BTO:0000088 CALOHA:TS-1297 EFO:0000791 - EHDAA2:0000216 EHDAA:394 EMAPA:16104 - EMAPA:16370 EV:0100017 FMA:7161 GAID:467 @@ -47125,16 +43059,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that has as its parts the heart and blood vessels. BTO:0000088 - - - - The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG] - 2012-09-17 - VHOG:0000302 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.451 - http://bgee.unil.ch/ - @@ -47355,11 +43279,9 @@ For example, A and B may be gene products and binding of B by A positively regul Organism at the gastrula stage. - We explicitly merge the NCITA terms here UBERON:0007012 BILA:0000060 BTO:0001403 - FBbt:00005317 FMA:293108 GAID:1302 MESH:D005775 @@ -47391,18 +43313,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Gastrula Wikipedia:Trilaminar_blastocyst - - - - We explicitly merge the NCITA terms here - NCIT - - - - - FBbt:00005317 - - @@ -47482,9 +43392,13 @@ For example, A and B may be gene products and binding of B by A positively regul - + + + + + + A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]. - A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO] EMAPA:37744 MA:0003047 SCTID:309311006 @@ -47496,24 +43410,12 @@ For example, A and B may be gene products and binding of B by A positively regul Four classes of mineralized tissues are found in vertebrates: bone, cartilage, dentine, and enamel. We think of cartilage and bone as skeletal tissues and of enamel and dentine as dental tissues, but enamel and dentine arose evolutionarily together with bone as skeletal tissues in the dermal skeleton (exoskeleton) of early vertebrates. Scales and teeth of sharks are examples of dermal skeletal elements that are still composed of the three ancient components-enamel, dentine, and bone. Cartilage, on the other hand, provided the basis for the second vertebrate skeletal system, the endoskeleton (Smith and Hall, 1990; Hall, 1998a,b). some invertebrate skeletal tissues have surprisingly bone-like features. Examples include chondrocytes interconnected by cell processes in cephalopod cartilages (Cole and Hall, 2004a,b), and the calcium phosphate layer in the shells of brachiopods (Rodland et al., 2003). However, neither bone nor mineralized cartilage have been found in invertebrates. Editors notes: TODO - develops_from skeletal tissue - - - - VSAO - - - - - 2012-08-14 - VSAO:0000015 - VSAO - @@ -47524,17 +43426,6 @@ For example, A and B may be gene products and binding of B by A positively regul http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/134 - - - - A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO] - 2012-08-14 - VSAO:0000015 - taken from version of VSAO used in TAO and used directly in Uberon - VSAO - GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 - PSPUB:0000170 - @@ -47548,10 +43439,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. - Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO] - Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO] AAO:0011129 TAO:0001890 VSAO:0000128 @@ -47564,14 +43453,14 @@ For example, A and B may be gene products and binding of B by A positively regul skeletal element - + - + VSAO @@ -47580,24 +43469,6 @@ For example, A and B may be gene products and binding of B by A positively regul Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. https://orcid.org/0000-0002-6601-2165 - - - - Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO] - 2012-08-14 - VSAO:0000128 - VSAO - PSPUB:0000170 - - - - - Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO] - 2012-08-14 - TAO:0001890 - TAO - TAO:VSAO_workshop - @@ -47616,7 +43487,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -47655,14 +43526,14 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0004770 articular system - + - + FMA @@ -47715,7 +43586,6 @@ For example, A and B may be gene products and binding of B by A positively regul An endothelium that is part of the cardiovascular system. consider merging with 'endothelium' - Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] BTO:0001853 EMAPA:35201 GAID:519 @@ -47740,16 +43610,6 @@ For example, A and B may be gene products and binding of B by A positively regul An endothelium that is part of the cardiovascular system. https://orcid.org/0000-0002-6601-2165 - - - - Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] - 2012-09-17 - VHOG:0001217 - VHOG - ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207 - http://bgee.unil.ch/ - @@ -47784,7 +43644,6 @@ For example, A and B may be gene products and binding of B by A positively regul Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP]. - We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors visceral mesoderm AAO:0011102 BILA:0000044 @@ -47804,12 +43663,6 @@ For example, A and B may be gene products and binding of B by A positively regul Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP]. Wikipedia:Lateral_plate_mesoderm#Division_into_layers - - - - We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors - BILA - @@ -47844,8 +43697,6 @@ For example, A and B may be gene products and binding of B by A positively regul The central region of trunk mesoderm. This tissue forms the notochord. - Notochord rudiment[ZFIN:ZDB-PUB-961014-576]. - WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord. AAO:0000478 EFO:0003426 TAO:0000091 @@ -47866,12 +43717,6 @@ For example, A and B may be gene products and binding of B by A positively regul The central region of trunk mesoderm. This tissue forms the notochord. https://orcid.org/0000-0002-6601-2165 - - - - Notochord rudiment[ZFIN:ZDB-PUB-961014-576]. - ZFIN:ZDB-PUB-961014-576 - @@ -47904,7 +43749,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts. - FBbt:00005811 joint uberon UBERON:0004905 @@ -47917,12 +43761,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts. http://orcid.org/0000-0002-6601-2165 - - - - FBbt:00005811 - - @@ -47954,9 +43792,7 @@ For example, A and B may be gene products and binding of B by A positively regul A proximal-distal subdivision of the digestive tract. - intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct. - FBbt:00100315 FMA:71131 uberon alimentary system subdivision @@ -47975,12 +43811,6 @@ For example, A and B may be gene products and binding of B by A positively regul A proximal-distal subdivision of the digestive tract. http://orcid.org/0000-0002-6601-2165 - - - - FBbt:00100315 - - @@ -48045,7 +43875,6 @@ For example, A and B may be gene products and binding of B by A positively regul The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds. - The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]. AAO:0011071 EMAPA:35594 FMA:295624 @@ -48067,12 +43896,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Neural_groove http://orcid.org/0000-0002-6601-2165 - - - - The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]. - Wikipedia:Neural_groove - @@ -48088,6 +43911,7 @@ For example, A and B may be gene products and binding of B by A positively regul + @@ -48095,14 +43919,7 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - One of the two elevated edges of the neural groove[GO,MP]. - In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]. EHDAA2:0001249 FMA:295618 NCIT:C34223 @@ -48125,12 +43942,6 @@ For example, A and B may be gene products and binding of B by A positively regul MP:0011256 Wikipedia:Neural_fold - - - - In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]. - Wikipedia:Neural_fold - @@ -48157,7 +43968,6 @@ For example, A and B may be gene products and binding of B by A positively regul A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN]. - An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO] EFO:0003498 TAO:0000133 ZFA:0000133 @@ -48174,15 +43984,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0014024 ZFA:0000133 - - - - An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000133 - TAO - ZFIN:curator - @@ -48209,8 +44010,6 @@ For example, A and B may be gene products and binding of B by A positively regul Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO]. - in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila - EMAPA:32715 FMA:30316 musculus uberon @@ -48434,7 +44233,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -48450,14 +44249,14 @@ For example, A and B may be gene products and binding of B by A positively regul trunk mesenchyme - + - + EHDAA2 @@ -48537,7 +44336,6 @@ For example, A and B may be gene products and binding of B by A positively regul AEO:0000125 CALOHA:TS-2122 EHDAA2:0003125 - FBbt:00007006 FMA:292313 MIAA:0000019 uberon @@ -48548,12 +44346,6 @@ For example, A and B may be gene products and binding of B by A positively regul developing anatomical structure - - - - FBbt:00007006 - - @@ -48574,9 +44366,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + Multi-tissue structure that arises from the heart rudiment and will become the heart tube. - BTO:0006179 EHDAA2:0001512 EHDAA:424 EHDAA:436 @@ -48593,14 +44384,14 @@ For example, A and B may be gene products and binding of B by A positively regul primitive heart tube - + - + ZFA @@ -48609,14 +44400,6 @@ For example, A and B may be gene products and binding of B by A positively regul Multi-tissue structure that arises from the heart rudiment and will become the heart tube. ZFA:0000149 - - - - BTO:0006179 - - - https://github.com/biopragmatics/biomappings - @@ -48708,7 +44491,6 @@ For example, A and B may be gene products and binding of B by A positively regul An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina. - this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell. AAO:0010596 FMA:63872 @@ -48776,7 +44558,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 @@ -48786,7 +44568,7 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0005856 developing mesenchymal condensation - + @@ -48805,7 +44587,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + AEO-modified-relation @@ -48847,10 +44629,8 @@ For example, A and B may be gene products and binding of B by A positively regul Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified]. - Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO] AAO:0000963 EMAPA:17214 - EMAPA:18043 MA:0000308 NCIT:C32172 SCTID:361725000 @@ -48878,15 +44658,6 @@ For example, A and B may be gene products and binding of B by A positively regul https://github.com/obophenotype/uberon/issues/44 https://github.com/obophenotype/uberon/wiki/The-axial-skeleton - - - - Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO] - 2012-08-14 - VSAO:0000056 - VSAO - PSPUB:0000170 - @@ -48910,10 +44681,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB - The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG] EHDAA2:0001278 EHDAA:264 EMAPA:16101 @@ -48925,7 +44695,7 @@ For example, A and B may be gene products and binding of B by A positively regul notochordal plate - + @@ -48938,7 +44708,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + EHDAA2 @@ -48947,15 +44717,6 @@ For example, A and B may be gene products and binding of B by A positively regul The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. VHOG:0001212 - - - - The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG] - 2012-09-17 - VHOG:0001212 - VHOG - http://bgee.unil.ch/ - @@ -48975,7 +44736,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -48992,14 +44753,14 @@ For example, A and B may be gene products and binding of B by A positively regul The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -49360,7 +45121,6 @@ For example, A and B may be gene products and binding of B by A positively regul An epithelium characterised by its most superficial layer consisting of squamous epithelial cells. - FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium BTO:0002072 NCIT:C12848 SCTID:40118003 @@ -49376,12 +45136,6 @@ For example, A and B may be gene products and binding of B by A positively regul An epithelium characterised by its most superficial layer consisting of squamous epithelial cells. Wikipedia:Squamous_epithelium - - - - FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium - FBbt - @@ -49456,12 +45210,6 @@ For example, A and B may be gene products and binding of B by A positively regul Old definition: 'Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.' Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism. anatomical surface - - - - - via morphological boundary in CARO - @@ -49480,6 +45228,7 @@ For example, A and B may be gene products and binding of B by A positively regul + @@ -49654,7 +45403,6 @@ For example, A and B may be gene products and binding of B by A positively regul - The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis BILA:0000084 NCIT:C34268 SCTID:360394002 @@ -49670,12 +45418,6 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0007026 presumptive gut - - - - The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis - NCBIBook:NBK10107 - @@ -49706,10 +45448,13 @@ For example, A and B may be gene products and binding of B by A positively regul - + + + + + + A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]. - note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis - SPD:0000130 TADS:0000147 http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg dorsal tube @@ -49721,16 +45466,6 @@ For example, A and B may be gene products and binding of B by A positively regul Gene notes: Bmp, Nkx, Gata primary circulatory organ - - - - - - - - - GO uses blood circulation generically to include the haemolymphatic fluid of arthropods - @@ -49769,7 +45504,6 @@ For example, A and B may be gene products and binding of B by A positively regul An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. - An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO] EFO:0003497 TAO:0000131 ZFA:0000131 @@ -49785,15 +45519,6 @@ For example, A and B may be gene products and binding of B by A positively regul An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. ZFIN:ZDB-PUB-961014-576 - - - - An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000131 - TAO - ZFIN:curator - @@ -49818,7 +45543,12 @@ For example, A and B may be gene products and binding of B by A positively regul - + + + + + + @@ -49835,17 +45565,6 @@ For example, A and B may be gene products and binding of B by A positively regul presumptive segmental plate - - - - - - - - - https://github.com/obophenotype/uberon/wiki/The-neural-crest - EDHAA2 - @@ -49897,7 +45616,6 @@ For example, A and B may be gene products and binding of B by A positively regul A presumptive structure that has the potential to develop into a neural plate. consider merging - Region of the gastrula which gives rise to the neural plate.[TAO] EFO:0003424 TAO:0000063 ZFA:0000063 @@ -49914,15 +45632,6 @@ For example, A and B may be gene products and binding of B by A positively regul A presumptive structure that has the potential to develop into a neural plate. OBOL:automatic - - - - Region of the gastrula which gives rise to the neural plate.[TAO] - 2012-08-14 - TAO:0000063 - TAO - ZFIN:curator - @@ -49941,7 +45650,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -49967,7 +45676,7 @@ For example, A and B may be gene products and binding of B by A positively regul presumptive paraxial mesoderm - + @@ -49983,7 +45692,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + https://github.com/obophenotype/uberon/issues/1277 @@ -50059,7 +45768,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -50067,7 +45776,7 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0007524 dense mesenchyme tissue - + @@ -50080,7 +45789,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + AEO @@ -50140,7 +45849,6 @@ For example, A and B may be gene products and binding of B by A positively regul AEO:0000170 EFO:0001649 EHDAA2:0003170 - FBbt:00005426 Wikipedia:Anlage_(biology) developmental field uberon @@ -50170,12 +45878,6 @@ For example, A and B may be gene products and binding of B by A positively regul FBbt:00005426 http://flybase.org/reports/FBrf0178740.html - - - - FBbt:00005426 - - @@ -50183,12 +45885,10 @@ For example, A and B may be gene products and binding of B by A positively regul - + Anatomical system that consists of all blood and lymph vessels. consider merging with vasculature - The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]. - in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system BTO:0001085 CALOHA:TS-2053 EHDAA2:0004520 @@ -50202,14 +45902,14 @@ For example, A and B may be gene products and binding of B by A positively regul vascular system - + - + MA @@ -50218,18 +45918,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that consists of all blood and lymph vessels. http://orcid.org/0000-0002-6601-2165 - - - - The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]. - ncithesaurus:Vascular_System - - - - - in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system - MA - @@ -50249,7 +45937,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -50266,14 +45954,14 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -50329,7 +46017,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -50337,14 +46025,14 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -50365,8 +46053,9 @@ For example, A and B may be gene products and binding of B by A positively regul + - + EFO:0003704 TAO:0005041 ZFA:0005041 @@ -50376,14 +46065,14 @@ For example, A and B may be gene products and binding of B by A positively regul anterior lateral plate mesoderm - + - + ZFA @@ -50427,7 +46116,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0010000 - FBbt:00100313 multicellular structure uberon UBERON:0010000 @@ -50441,12 +46129,6 @@ For example, A and B may be gene products and binding of B by A positively regul An anatomical structure that has more than one cell as a part. CARO:0010000 - - - - FBbt:00100313 - - @@ -50523,7 +46205,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -50543,14 +46225,14 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0010210 blood clot - + - + BTO @@ -50597,7 +46279,6 @@ For example, A and B may be gene products and binding of B by A positively regul An anatomical structure that has some part that develops from the neural crest. - Grouping term for query purposes uberon UBERON:0010314 @@ -50672,10 +46353,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. - Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO] FMA:23879 SCTID:129140006 VSAO:0000042 @@ -50686,11 +46366,11 @@ For example, A and B may be gene products and binding of B by A positively regul subdivision of skeleton - + - + @@ -50703,13 +46383,13 @@ For example, A and B may be gene products and binding of B by A positively regul - + UBERONREF:0000003 - + VSAO @@ -50719,16 +46399,6 @@ For example, A and B may be gene products and binding of B by A positively regul UBERONREF:0000003 https://orcid.org/0000-0002-6601-2165 - - - - Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO] - 2012-08-14 - VSAO:0000042 - incorrect - VSAO - VSAO:curator - @@ -50780,7 +46450,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system FMA:302077 @@ -50790,7 +46460,7 @@ For example, A and B may be gene products and binding of B by A positively regul postcranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton - + @@ -50803,7 +46473,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + cjm @@ -50837,7 +46507,6 @@ For example, A and B may be gene products and binding of B by A positively regul - FBbt:00007330 FMA:67509 SCTID:91690000 uberon @@ -50859,12 +46528,6 @@ For example, A and B may be gene products and binding of B by A positively regul A subdivision of an anatomical system. http://orcid.org/0000-0002-6601-2165 - - - - FBbt:00007330 - - @@ -50981,7 +46644,6 @@ For example, A and B may be gene products and binding of B by A positively regul The aggregate of the coelemic cavity lumen plus the membranes that line the lumen. EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining. - coelomic EHDAA2:0004731 Wikipedia:Coelom enterocoelom @@ -51075,8 +46737,9 @@ For example, A and B may be gene products and binding of B by A positively regul + - + @@ -51084,7 +46747,6 @@ For example, A and B may be gene products and binding of B by A positively regul Blood-forming tissue, consisting of reticular fibers and cells. - Bone marrow in humans, kidney interstitium in Danio, within a stroma of reticuloendothelial tissue CALOHA:TS-2142 FMA:14073 NCIT:C13051 @@ -51098,7 +46760,7 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0012429 hematopoietic tissue - + @@ -51111,7 +46773,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + defitional @@ -51274,10 +46936,8 @@ For example, A and B may be gene products and binding of B by A positively regul The region of the organism associated with the visceral organs. - Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]. AEO:0000103 BTO:0001489 - EMAPA:36031 FMA:231424 uberon body @@ -51298,12 +46958,6 @@ For example, A and B may be gene products and binding of B by A positively regul The region of the organism associated with the visceral organs. AEO:0000103 - - - - Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]. - FMA:231424 - @@ -51416,7 +47070,6 @@ For example, A and B may be gene products and binding of B by A positively regul An anatomical group whose component structures share a common function. AEO:0000093 - FBbt:00007278 uberon UBERON:0015203 non-connected functional system @@ -51430,36 +47083,13 @@ For example, A and B may be gene products and binding of B by A positively regul FBC:DOS FBbt:00007278 - - - - FBbt:00007278 - - - - - - - - - - - - - - - - - - - @@ -51467,7 +47097,6 @@ For example, A and B may be gene products and binding of B by A positively regul Any structure that is placed on one side of the left-right axis of a bilaterian. - This class is primarily to implement taxon constraints. It may be removed in the future. uberon UBERON:0015212 @@ -51501,7 +47130,6 @@ For example, A and B may be gene products and binding of B by A positively regul A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile. heart - SPD:0000130 cardiac pump heart or heart like organ circulatory vessel @@ -51689,7 +47317,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -51712,7 +47340,7 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0016887 entire extraembryonic component - + @@ -51725,7 +47353,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + AEO @@ -51833,7 +47461,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0020000 - FBbt:00007276 uberon UBERON:0034923 @@ -51851,12 +47478,6 @@ For example, A and B may be gene products and binding of B by A positively regul Material anatomical entity consisting of multiple anatomical structures that are not connected to each other. CARO:0020000 - - - - FBbt:00007276 - - @@ -51970,7 +47591,6 @@ For example, A and B may be gene products and binding of B by A positively regul - example to be eventually removed example to be eventually removed @@ -51979,9 +47599,7 @@ For example, A and B may be gene products and binding of B by A positively regul - failed exploratory term The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job - Person:Alan Ruttenberg failed exploratory term @@ -51990,7 +47608,6 @@ For example, A and B may be gene products and binding of B by A positively regul - metadata complete Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. metadata complete @@ -52000,7 +47617,6 @@ For example, A and B may be gene products and binding of B by A positively regul - organizational term Term created to ease viewing/sort terms for development purpose, and will not be included in a release organizational term @@ -52010,7 +47626,6 @@ For example, A and B may be gene products and binding of B by A positively regul - ready for release Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release @@ -52020,7 +47635,6 @@ For example, A and B may be gene products and binding of B by A positively regul - metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete @@ -52030,7 +47644,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated @@ -52040,7 +47653,6 @@ For example, A and B may be gene products and binding of B by A positively regul - pending final vetting All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting @@ -52050,7 +47662,6 @@ For example, A and B may be gene products and binding of B by A positively regul - placeholder removed placeholder removed @@ -52059,7 +47670,6 @@ For example, A and B may be gene products and binding of B by A positively regul - terms merged An editor note should explain what were the merged terms and the reason for the merge. terms merged @@ -52069,7 +47679,6 @@ For example, A and B may be gene products and binding of B by A positively regul - term imported This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. term imported @@ -52079,7 +47688,6 @@ For example, A and B may be gene products and binding of B by A positively regul - term split This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. term split @@ -52089,10 +47697,7 @@ For example, A and B may be gene products and binding of B by A positively regul - universal Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. - Alan Ruttenberg - A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf universal @@ -52101,10 +47706,8 @@ For example, A and B may be gene products and binding of B by A positively regul - defined class A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. - Alan Ruttenberg defined class @@ -52113,10 +47716,8 @@ For example, A and B may be gene products and binding of B by A positively regul - named class expression A named class expression is a logical expression that is given a name. The name can be used in place of the expression. named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions - Alan Ruttenberg named class expression @@ -52125,10 +47726,7 @@ For example, A and B may be gene products and binding of B by A positively regul - to be replaced with external ontology term Terms with this status should eventually replaced with a term from another ontology. - Alan Ruttenberg - group:OBI to be replaced with external ontology term @@ -52137,10 +47735,7 @@ For example, A and B may be gene products and binding of B by A positively regul - requires discussion A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. - Alan Ruttenberg - group:OBI requires discussion @@ -52151,9 +47746,7 @@ For example, A and B may be gene products and binding of B by A positively regul The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. - https://github.com/information-artifact-ontology/ontology-metadata/issues/77 - https://orcid.org/0000-0001-5208-3432 out of scope @@ -52233,24 +47826,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - @@ -52302,69 +47877,48 @@ For example, A and B may be gene products and binding of B by A positively regul /////////////////////////////////////////////////////////////////////////////////////// --> - - - - - - - - - - - - - + - + - + - + - + - + - + - + - + - + - + - + - + - - - - - - - - - @@ -52377,8 +47931,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -52388,7 +47942,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -52398,7 +47952,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -52415,79 +47969,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - true - MF(X)-directly_regulates->MF(Y)-enabled_by->GP(Z) => MF(Y)-has_input->GP(Y) e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z - infer input from direct reg - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + @@ -52506,7 +47989,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + @@ -52516,8 +47999,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52527,8 +48010,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52545,67 +48028,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - - - - - - - - true - GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' - involved in BP - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + @@ -52623,8 +48047,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52634,8 +48058,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52645,8 +48069,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52663,8 +48087,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52681,8 +48105,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52692,8 +48116,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52703,8 +48127,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52721,8 +48145,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52739,8 +48163,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52750,8 +48174,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52761,8 +48185,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52779,8 +48203,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52797,8 +48221,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52808,8 +48232,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52824,8 +48248,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52842,8 +48266,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52853,8 +48277,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52869,8 +48293,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52887,8 +48311,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52898,8 +48322,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52914,8 +48338,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52932,8 +48356,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52943,8 +48367,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52959,8 +48383,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52977,8 +48401,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -52988,8 +48412,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -53004,8 +48428,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -53065,8 +48489,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -53076,8 +48500,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -53092,8 +48516,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -53108,9 +48532,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -53120,8 +48544,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -53135,9 +48559,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -53152,9 +48576,9 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - - + + + @@ -53164,8 +48588,8 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - - + + @@ -53179,7 +48603,7 @@ e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase - + diff --git a/subsets/blood_and_immune_upper_slim.tsv b/subsets/blood_and_immune_upper_slim.tsv index ed97b6166..19def9327 100644 --- a/subsets/blood_and_immune_upper_slim.tsv +++ b/subsets/blood_and_immune_upper_slim.tsv @@ -1,392 +1,389 @@ ?x ?label -_:Bfc26b7c9X2D6e5eX2D4e75X2D81bcX2D5596fb9a64a9genid1011 -_:Bfc26b7c9X2D6e5eX2D4e75X2D81bcX2D5596fb9a64a9genid1024 -_:Bfc26b7c9X2D6e5eX2D4e75X2D81bcX2D5596fb9a64a9genid1038 -_:Bfc26b7c9X2D6e5eX2D4e75X2D81bcX2D5596fb9a64a9genid1054 -_:Bfc26b7c9X2D6e5eX2D4e75X2D81bcX2D5596fb9a64a9genid1072 -_:Bfc26b7c9X2D6e5eX2D4e75X2D81bcX2D5596fb9a64a9genid1079 -_:Bfc26b7c9X2D6e5eX2D4e75X2D81bcX2D5596fb9a64a9genid1085 -_:Bfc26b7c9X2D6e5eX2D4e75X2D81bcX2D5596fb9a64a9genid1097 -_:Bfc26b7c9X2D6e5eX2D4e75X2D81bcX2D5596fb9a64a9genid1107 -_:Bfc26b7c9X2D6e5eX2D4e75X2D81bcX2D5596fb9a64a9genid1115 -_:Bfc26b7c9X2D6e5eX2D4e75X2D81bcX2D5596fb9a64a9genid112 -_:Bfc26b7c9X2D6e5eX2D4e75X2D81bcX2D5596fb9a64a9genid115 -_:Bfc26b7c9X2D6e5eX2D4e75X2D81bcX2D5596fb9a64a9genid1162 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+_:Bd3a92e4aX2D59e9X2D479fX2D9102X2D86cde55c1e05genid76 +_:Bd3a92e4aX2D59e9X2D479fX2D9102X2D86cde55c1e05genid772 +_:Bd3a92e4aX2D59e9X2D479fX2D9102X2D86cde55c1e05genid789 +_:Bd3a92e4aX2D59e9X2D479fX2D9102X2D86cde55c1e05genid79 +_:Bd3a92e4aX2D59e9X2D479fX2D9102X2D86cde55c1e05genid809 +_:Bd3a92e4aX2D59e9X2D479fX2D9102X2D86cde55c1e05genid824 +_:Bd3a92e4aX2D59e9X2D479fX2D9102X2D86cde55c1e05genid879 +_:Bd3a92e4aX2D59e9X2D479fX2D9102X2D86cde55c1e05genid910 +_:Bd3a92e4aX2D59e9X2D479fX2D9102X2D86cde55c1e05genid954 +_:Bd3a92e4aX2D59e9X2D479fX2D9102X2D86cde55c1e05genid967 +_:Bd3a92e4aX2D59e9X2D479fX2D9102X2D86cde55c1e05genid981 +_:Bd3a92e4aX2D59e9X2D479fX2D9102X2D86cde55c1e05genid997 "continuant" "occurrent" "independent continuant" diff --git a/subsets/eye_upper_slim.json b/subsets/eye_upper_slim.json index 8b2e399be..800e7810c 100644 --- a/subsets/eye_upper_slim.json +++ b/subsets/eye_upper_slim.json @@ -4,9 +4,9 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-02-13" + "val" : "2024-04-05" } ], - "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-02-13/subsets/eye_upper_slim.owl" + "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-04-05/subsets/eye_upper_slim.owl" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/BFO_0000002", @@ -78,18 +78,6 @@ "val" : "BFO:0000050" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "is part of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my brain is part of my body (continuant parthood, two material entities)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this day is part of this year (occurrent parthood)" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." }, { @@ -98,42 +86,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "part_of" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000002" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000003" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000004" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000017" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000019" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000020" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000031" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "part_of" @@ -164,18 +122,6 @@ "val" : "BFO:0000051" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has part" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my body has part my brain (continuant parthood, two material entities)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this year has part this day (occurrent parthood)" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." }, { @@ -184,21 +130,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has_part" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_part" @@ -217,26 +154,11 @@ "val" : "BFO:0000062" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "preceded by" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is preceded by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "preceded_by" - }, { - "pred" : "http://purl.org/dc/terms/source", - "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "preceded_by" @@ -255,14 +177,8 @@ "val" : "BFO:0000063" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "precedes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "precedes" @@ -282,26 +198,11 @@ "val" : "BFO:0000066" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "occurs in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "occurs_in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "unfolds in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "unfolds_in" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "occurs_in" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Occurs_in" @@ -315,412 +216,12 @@ "definition" : { "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" }, - "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ], - "xrefs" : [ { - "val" : "BFO:0000067" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "site of" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "contains_process" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - } ] + "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000141", "lbl" : "immaterial entity", "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000096", - "lbl" : "anterior to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000096" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "anterior_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000097", - "lbl" : "distal to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000097" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "distal_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000098", - "lbl" : "dorsal to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000098" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dorsal_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000099", - "lbl" : "posterior to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000099" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "posterior_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000100", - "lbl" : "proximal to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000100" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "proximal_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000102", - "lbl" : "ventral to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000102" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "ventral_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000107", - "lbl" : "deep to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000107" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "deep_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000108", - "lbl" : "superficial to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000108" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "superficial_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000120", - "lbl" : "in left side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000120" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_left_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000121", - "lbl" : "in right side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000121" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_right_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000122", - "lbl" : "in posterior side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000122" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_posterior_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000123", - "lbl" : "in anterior side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000123" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_anterior_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000124", - "lbl" : "in proximal side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000124" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_proximal_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "lbl" : "in lateral side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000126" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_lateral_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001100", - "lbl" : "in superficial part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001100" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_superficial_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001101", - "lbl" : "in deep part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001101" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_deep_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001106", - "lbl" : "proximalmost part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001106" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "proximalmost_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001107", - "lbl" : "immediately deep to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001107" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "immediately_deep_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001108", - "lbl" : "distalmost part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001108" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "distalmost_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001113", - "lbl" : "preaxialmost part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001113" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "preaxialmost_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001115", - "lbl" : "postaxialmost part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001115" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "postaxialmost_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0005001", - "lbl" : "intersects midsagittal plane of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0005001" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "intersects_midsagittal_plane_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0015014", - "lbl" : "immediately superficial to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0015014" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "immediately_superficial_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0015101", - "lbl" : "in dorsal side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0015101" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_dorsal_side_of" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000000", "lbl" : "cell", @@ -754,13 +255,17 @@ } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000005", - "lbl" : "fibroblast neural crest derived", + "lbl" : "neural crest derived fibroblast", "type" : "CLASS", "meta" : { "definition" : { - "val" : "Any fibroblast that is deriived from the neural crest.", + "val" : "Any fibroblast that is derived from the neural crest.", "xrefs" : [ "https://orcid.org/0000-0001-5208-3432" ] - } + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "fibroblast neural crest derived" + } ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000006", @@ -10345,13 +9850,7 @@ }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000002", "lbl" : "example to be eventually removed", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "example to be eventually removed" - } ] - } + "type" : "INDIVIDUAL" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000028", "lbl" : "symbol", @@ -10363,14 +9862,7 @@ "meta" : { "definition" : { "val" : "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "failed exploratory term" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person:Alan Ruttenberg" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000115", @@ -10381,20 +9873,8 @@ "val" : "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "definition" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2012-04-05: \nBarry Smith\n\nThe official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. \n\nOn the specifics of the proposed definition:\n\nWe don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Daniel Schober" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" } ] } }, { @@ -10404,32 +9884,7 @@ "meta" : { "definition" : { "val" : "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology." - }, - "xrefs" : [ { - "val" : "IAO:0000116" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "editor note" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Daniel Schober" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "editor_note" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000120", @@ -10438,11 +9893,7 @@ "meta" : { "definition" : { "val" : "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "metadata complete" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000121", @@ -10451,11 +9902,7 @@ "meta" : { "definition" : { "val" : "Term created to ease viewing/sort terms for development purpose, and will not be included in a release" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "organizational term" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000122", @@ -10464,11 +9911,7 @@ "meta" : { "definition" : { "val" : "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\"" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "ready for release" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000123", @@ -10477,11 +9920,7 @@ "meta" : { "definition" : { "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "metadata incomplete" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000124", @@ -10490,11 +9929,7 @@ "meta" : { "definition" : { "val" : "Nothing done yet beyond assigning a unique class ID and proposing a preferred term." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "uncurated" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000125", @@ -10503,31 +9938,18 @@ "meta" : { "definition" : { "val" : "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "pending final vetting" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000226", "lbl" : "placeholder removed", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "placeholder removed" - } ] - } + "type" : "INDIVIDUAL" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000227", "lbl" : "terms merged", "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "terms merged" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "An editor note should explain what were the merged terms and the reason for the merge." } ] @@ -10538,9 +9960,6 @@ "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "term imported" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use." } ] @@ -10551,9 +9970,6 @@ "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "term split" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created." } ] @@ -10565,17 +9981,7 @@ "meta" : { "definition" : { "val" : "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has obsolescence reason" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Melanie Courtot" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000233", @@ -10590,29 +9996,8 @@ "val" : "IAO:0000233" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "term tracker item" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_class_level", - "val" : "true" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", "val" : "true" @@ -10627,17 +10012,8 @@ "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "universal" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf" } ] } }, { @@ -10649,14 +10025,8 @@ "val" : "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "defined class" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" } ] } }, { @@ -10668,14 +10038,8 @@ "val" : "A named class expression is a logical expression that is given a name. The name can be used in place of the expression." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "named class expression" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" } ] } }, { @@ -10685,17 +10049,7 @@ "meta" : { "definition" : { "val" : "Terms with this status should eventually replaced with a term from another ontology." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "to be replaced with external ontology term" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "group:OBI" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000424", @@ -10704,17 +10058,7 @@ "meta" : { "definition" : { "val" : "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "expand expression to" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "ObjectProperty: RO_0002104\nLabel: has plasma membrane part\nAnnotations: IAO_0000424 \"http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\"\n" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000428", @@ -10723,17 +10067,7 @@ "meta" : { "definition" : { "val" : "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "requires discussion" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "group:OBI" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000700", @@ -10747,20 +10081,8 @@ "val" : "IAO:0000700" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has ontology root term" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Nicolas Matentzoglu" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_class_level", - "val" : "true" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", "val" : "true" @@ -10777,20 +10099,7 @@ "definition" : { "val" : "Use on obsolete terms, relating the term to another term that can be used as a substitute" }, - "comments" : [ "Add as annotation triples in the granting ontology" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "term replaced by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person:Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Person:Alan Ruttenberg" - } ] + "comments" : [ "Add as annotation triples in the granting ontology" ] } }, { "id" : "http://purl.obolibrary.org/obo/NCBITaxon_1", @@ -10825,9 +10134,6 @@ "val" : "PMID:15371245" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_family" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -10842,7 +10148,7 @@ "pred" : "hasExactSynonym", "val" : "Mus" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003003", + "synonymType" : "http://purl.obolibrary.org/obo/ncbitaxon#genbank_common_name", "pred" : "hasExactSynonym", "val" : "mice" }, { @@ -10854,9 +10160,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_genus" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -10879,9 +10182,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_species" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "NCBITaxon:85055" }, { @@ -10898,9 +10198,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -10919,9 +10216,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "NCBITaxon:40673" }, { @@ -10956,9 +10250,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -10981,9 +10272,6 @@ "val" : "PMID:11791233" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11006,9 +10294,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_suborder" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11055,9 +10340,6 @@ "val" : "PMID:30257078" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_superkingdom" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11079,9 +10361,6 @@ "val" : "PMID:15522813" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_superorder" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11106,9 +10385,6 @@ "val" : "PMID:15522813" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11127,9 +10403,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11148,9 +10421,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11169,9 +10439,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11194,9 +10461,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11227,9 +10491,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_kingdom" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11243,9 +10504,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11264,9 +10522,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11284,9 +10539,6 @@ "val" : "PMID:15371245" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11300,9 +10552,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_subfamily" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "NCBITaxon:109679" }, { @@ -11328,9 +10577,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_class" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11344,9 +10590,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11369,9 +10612,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_phylum" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11398,9 +10638,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11423,9 +10660,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11439,9 +10673,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_superclass" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11460,9 +10691,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_subgenus" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11481,9 +10709,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_subphylum" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11518,9 +10743,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11543,9 +10765,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_order" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11561,15 +10780,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/77" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", - "val" : "https://orcid.org/0000-0001-5208-3432" } ] } }, { @@ -11581,9 +10794,6 @@ "val" : "Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'part disjoint with' 'defined by construct' \"\"\"\n PREFIX owl: \n PREFIX : some (\n and some (\n and some (\n and some ?Y)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { @@ -14807,33 +13577,9 @@ "definition" : { "val" : "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " }, - "xrefs" : [ { - "val" : "RO:0002103" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that part_of some ( that has_part some ( that some Y?)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "synapsed_by" } ] } }, { @@ -14845,29 +13591,8 @@ "val" : "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9990-8331" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-1617-8244" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19243617" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( and some ?Y)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] } }, { @@ -14879,26 +13604,8 @@ "val" : "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. " }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "synapsed in" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (\n http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some (\n http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { @@ -14910,20 +13617,8 @@ "val" : "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "synapses in" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that some ( that some Y?)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { @@ -14936,23 +13631,8 @@ }, "comments" : [ "N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part some (\n ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( \n\t‘synapse ; GO:0045202’ that has_part some (\n\t ‘post-synaptic membrane ; GO:0045211’ that part_of some N2))))" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that part_of some ( that some ( that some Y?)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { @@ -14964,23 +13644,8 @@ "val" : "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has synapse in" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that some Y?)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { @@ -14996,20 +13661,11 @@ "val" : "RO:0002131" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "overlaps" @@ -15022,26 +13678,7 @@ "meta" : { "definition" : { "val" : "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has fasciculating component" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", - "val" : "(forall (?x ?y) \n\t(iff \n\t\t(has_fasciculating_neuron_projection ?x ?y)\n\t\t(exists (?nps ?npbs)\t\t\n\t\t\t(and \n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?x)\n\t\t\t\t(\"neuron projection ; GO0043005\" ?y)\n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n\t\t\t\t(part_of ?nps ?y)\n\t\t\t\t(part_of ?npbs ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))\n\n\n" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002134", @@ -15051,30 +13688,9 @@ "definition" : { "val" : "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." }, - "xrefs" : [ { - "val" : "RO:0002134" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that ( some ( that some Y?)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "innervates" } ] } }, { @@ -15085,31 +13701,7 @@ "definition" : { "val" : "X continuous_with Y if and only if X and Y share a fiat boundary." }, - "xrefs" : [ { - "val" : "RO:0002150" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "connected to" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "continuous_with" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "FMA:85972" } ] @@ -15122,23 +13714,7 @@ "definition" : { "val" : "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." }, - "comments" : [ "VBO calls this homologous_to" ], - "xrefs" : [ { - "val" : "RO:0002158" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Consider obsoleting and merging with child relation, 'in homology relationship with'" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "homologous_to" - } ] + "comments" : [ "VBO calls this homologous_to" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -15148,33 +13724,9 @@ "definition" : { "val" : "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." }, - "xrefs" : [ { - "val" : "RO:0002160" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "lactation SubClassOf 'only in taxon' some 'Mammalia'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "only_in_taxon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" @@ -15182,48 +13734,15 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002161", - "lbl" : "never_in_taxon", + "lbl" : "never in taxon", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL." }, - "xrefs" : [ { - "val" : "RO:0002161" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "tooth SubClassOf 'never in taxon' value 'Aves'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", - "val" : "Class: EquivalentTo: ?X and (RO_0002162 some ?Y)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", - "val" : "Class: ?X DisjointWith: RO_0002162 some ?Y " - }, { "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_class_level", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "never_in_taxon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" @@ -15239,31 +13758,7 @@ }, "comments" : [ "Connects a biological entity to its taxon of origin." ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002162" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9227-417X" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_taxon" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] @@ -15278,26 +13773,11 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" @@ -15311,22 +13791,7 @@ "definition" : { "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" }, - "xrefs" : [ { - "val" : "RO:0002170" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "connected_to" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" }, { @@ -15336,42 +13801,16 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002175", - "lbl" : "present_in_taxon", + "lbl" : "present in taxon", "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S" }, "comments" : [ "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "applicable for taxon" - } ], - "xrefs" : [ { - "val" : "RO:0002175" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_class_level", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "present_in_taxon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" @@ -15385,25 +13824,7 @@ "definition" : { "val" : "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." }, - "xrefs" : [ { - "val" : "RO:0002176" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The M8 connects Glasgow and Edinburgh" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "connects" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" }, { @@ -15418,20 +13839,7 @@ "meta" : { "definition" : { "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." - }, - "xrefs" : [ { - "val" : "RO:0002177" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "attached to part of (anatomical structure to anatomical structure)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "attaches_to_part_of" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002178", @@ -15441,21 +13849,9 @@ "definition" : { "val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." }, - "xrefs" : [ { - "val" : "RO:0002178" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "supplies" } ] } }, { @@ -15466,21 +13862,9 @@ "definition" : { "val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." }, - "xrefs" : [ { - "val" : "RO:0002179" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "drains" } ] } }, { @@ -15496,23 +13880,11 @@ "val" : "RO:0002180" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_component" @@ -15529,32 +13901,7 @@ "definition" : { "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" }, - "comments" : [ "This is the transitive form of the develops from relation" ], - "xrefs" : [ { - "val" : "RO:0002202" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9114-8737" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-1980-3228" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "develops_from" - } ] + "comments" : [ "This is the transitive form of the develops from relation" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002203", @@ -15564,29 +13911,7 @@ "definition" : { "val" : "inverse of develops from" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "xrefs" : [ { - "val" : "RO:0002203" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-1980-3228" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "develops_into" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002206", @@ -15595,17 +13920,7 @@ "meta" : { "definition" : { "val" : "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002207", @@ -15619,31 +13934,6 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "has developmental precursor" - } ], - "xrefs" : [ { - "val" : "RO:0002207" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "FBbt" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002202" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "directly_develops_from" } ] } }, { @@ -15654,14 +13944,7 @@ "definition" : { "val" : "inverse of directly develops from" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "developmental precursor of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002211", @@ -15676,30 +13959,6 @@ "val" : "RO:0002211" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-7476-6306" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-3837-8864" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GO" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Regulation precludes parthood; the regulatory process may not be within the regulated process." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "regulates (processual)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "false" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -15720,15 +13979,6 @@ "val" : "RO:0002212" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "negatively regulates (process to process)" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002211" }, { @@ -15752,18 +14002,6 @@ "val" : "RO:0002213" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "positively regulates (process to process)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002211" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -15784,32 +14022,8 @@ "val" : "RO:0002215" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "osteoclast SubClassOf 'capable of' some 'bone resorption'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has function realized in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20123131" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/21208450" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "capable_of" @@ -15827,17 +14041,8 @@ "val" : "RO:0002216" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has function in" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "capable_of_part_of" @@ -15853,26 +14058,7 @@ "meta" : { "definition" : { "val" : "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" - }, - "xrefs" : [ { - "val" : "RO:0002219" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "surrounded_by" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002220", @@ -15887,35 +14073,11 @@ "val" : "RO:0002220" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The epidermis layer of a vertebrate is adjacent to the dermis." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This relation acts as a join point with BSPO" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "adjacent_to" @@ -15929,26 +14091,7 @@ "definition" : { "val" : "inverse of surrounded by" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "xrefs" : [ { - "val" : "RO:0002221" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "surrounds" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002222", @@ -15956,23 +14099,7 @@ "type" : "PROPERTY", "meta" : { "comments" : [ "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations." ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://en.wikipedia.org/wiki/Allen%27s_interval_algebra" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." - }, { - "pred" : "http://purl.org/dc/terms/source", - "val" : "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002223", @@ -15982,29 +14109,7 @@ "definition" : { "val" : "inverse of starts with" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002223" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Allen" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "starts" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002224", @@ -16019,26 +14124,8 @@ "val" : "RO:0002224" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "started by" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "starts_with" @@ -16051,23 +14138,7 @@ "meta" : { "definition" : { "val" : "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" - }, - "xrefs" : [ { - "val" : "RO:0002225" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "develops_from_part_of" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002226", @@ -16076,29 +14147,7 @@ "meta" : { "definition" : { "val" : "x develops_in y if x is located in y whilst x is developing" - }, - "xrefs" : [ { - "val" : "RO:0002226" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "EHDAA2" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Jonathan Bard, EHDAA2" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "develops_in" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002229", @@ -16108,26 +14157,7 @@ "definition" : { "val" : "inverse of ends with" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002229" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "ends" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002230", @@ -16142,23 +14172,8 @@ "val" : "RO:0002230" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "finished by" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "ends_with" @@ -16177,15 +14192,6 @@ "val" : "RO:0002231" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "starts with process that occurs in" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16206,15 +14212,6 @@ "val" : "RO:0002232" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "ends with process that occurs in" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16235,15 +14232,6 @@ "val" : "RO:0002233" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "consumes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16267,15 +14255,6 @@ "val" : "RO:0002234" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "produces" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16294,22 +14273,7 @@ "definition" : { "val" : "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." }, - "xrefs" : [ { - "val" : "RO:0002252" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004036", - "val" : "http://purl.obolibrary.org/obo/BFO_0000050" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "connecting_branch_of" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/issues/2212" } ] @@ -16322,11 +14286,7 @@ "definition" : { "val" : "inverse of connecting branch of" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004036", - "val" : "http://purl.obolibrary.org/obo/BFO_0000051" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002254", @@ -16335,26 +14295,7 @@ "meta" : { "definition" : { "val" : "x has developmental contribution from y iff x has some part z such that z develops from y" - }, - "xrefs" : [ { - "val" : "RO:0002254" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_developmental_contribution_from" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002255", @@ -16364,14 +14305,7 @@ "definition" : { "val" : "inverse of has developmental contribution from" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002256", @@ -16380,44 +14314,7 @@ "meta" : { "definition" : { "val" : "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" - }, - "xrefs" : [ { - "val" : "RO:0002256" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9114-8737" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "induced by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GO:0001759" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "developmentally_induced_by" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002257", @@ -16426,14 +14323,7 @@ "meta" : { "definition" : { "val" : "Inverse of developmentally induced by" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002258", @@ -16445,17 +14335,8 @@ }, "comments" : [ "This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "false" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "In general you should not use this relation to make assertions - use one of the more specific relations below this one" } ] } }, { @@ -16468,9 +14349,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of" } ] @@ -16489,9 +14367,6 @@ "val" : "affects" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within" } ] @@ -16504,27 +14379,9 @@ "definition" : { "val" : "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" }, - "xrefs" : [ { - "val" : "RO:0002285" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "replaces" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "developmentally_replaces" } ] } }, { @@ -16534,31 +14391,12 @@ "meta" : { "definition" : { "val" : "Inverse of developmentally preceded by" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002287", "lbl" : "part of developmental precursor of", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002292", "lbl" : "expresses", @@ -16566,14 +14404,7 @@ "meta" : { "definition" : { "val" : "y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002295", @@ -16587,14 +14418,8 @@ "val" : "RO:0002295" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" @@ -16619,18 +14444,6 @@ "val" : "RO:0002296" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "every flower development (GO:0009908) results in development of some flower (PO:0009046)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.geneontology.org/GO.doc.development.shtml" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16640,7 +14453,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -16648,21 +14461,6 @@ "val" : "RO:0002297" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:mtg_berkeley_2013" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16683,21 +14481,6 @@ "val" : "RO:0002298" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:mtg_berkeley_2013" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16718,21 +14501,6 @@ "val" : "RO:0002299" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:mtg_berkeley_2013" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16754,12 +14522,6 @@ "val" : "RO:0002304" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002411" - }, { - "pred" : "http://purl.org/dc/terms/creator", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16785,9 +14547,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002411" - }, { - "pred" : "http://purl.org/dc/terms/creator", - "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" @@ -16810,18 +14569,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "inheres in part of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" @@ -16840,15 +14587,6 @@ "val" : "RO:0002315" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:mtg_berkeley_2013" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16863,14 +14601,7 @@ "meta" : { "definition" : { "val" : "A relationship that holds via some environmental process" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002323", @@ -16879,17 +14610,7 @@ "meta" : { "definition" : { "val" : "A mereological relationship or a topological relationship" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002324", @@ -16898,14 +14619,7 @@ "meta" : { "definition" : { "val" : "A relationship that holds between entities participating in some developmental process (GO:0032502)" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002327", @@ -16917,30 +14631,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a particular instances of akt-2 enables some instance of protein kinase activity" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "catalyzes" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "executes" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is catalyzing" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is executing" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Enables" } ] @@ -16952,23 +14642,7 @@ "meta" : { "definition" : { "val" : "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." - }, - "xrefs" : [ { - "val" : "RO:0002328" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This is a grouping relation that collects relations used for the purpose of connecting structure and function" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "functionally_related_to" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002329", @@ -16977,14 +14651,7 @@ "meta" : { "definition" : { "val" : "this relation holds between c and p when c is part of some c', and c' is capable of p." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "false" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002330", @@ -16993,14 +14660,7 @@ "meta" : { "definition" : { "val" : "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002331", @@ -17011,15 +14671,6 @@ "val" : "c involved_in p if and only if c enables some process p', and p' is part of p" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "actively involved in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "enables part of" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Involved_in" } ] @@ -17036,18 +14687,6 @@ "val" : "RO:0002332" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "regulates levels of (process to entity)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17065,9 +14704,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Enabled_by" } ] @@ -17085,12 +14721,6 @@ "val" : "RO:0002334" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "regulated by (processual)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17111,9 +14741,6 @@ "val" : "RO:0002335" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17134,9 +14761,6 @@ "val" : "RO:0002336" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17151,14 +14775,7 @@ "meta" : { "definition" : { "val" : "A relationship that holds via some process of localization" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is a grouping relation." - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002338", @@ -17173,9 +14790,6 @@ "val" : "RO:0002338" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17196,9 +14810,6 @@ "val" : "RO:0002339" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17218,9 +14829,6 @@ "val" : "RO:0002341" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17241,9 +14849,6 @@ "val" : "RO:0002342" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17260,12 +14865,6 @@ "val" : "RO:0002343" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'pollen tube growth' results_in growth_of some 'pollen tube'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17282,12 +14881,6 @@ "val" : "RO:0002344" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17302,23 +14895,7 @@ "meta" : { "definition" : { "val" : "is member of is a mereological relation between a item and a collection." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "An organism that is a member of a population of organisms" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is member of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "member part of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "SIO" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002351", @@ -17327,23 +14904,7 @@ "meta" : { "definition" : { "val" : "has member is a mereological relation between a collection and an item." - }, - "xrefs" : [ { - "val" : "RO:0002351" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "SIO" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_member" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002352", @@ -17353,20 +14914,7 @@ "definition" : { "val" : "inverse of has input" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002352" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "input_of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002353", @@ -17381,14 +14929,8 @@ "val" : "RO:0002353" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "output_of" @@ -17397,26 +14939,11 @@ }, { "id" : "http://purl.obolibrary.org/obo/RO_0002354", "lbl" : "formed as result of", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002360", "lbl" : "has dendrite location", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.org/dc/terms/source", - "val" : "http://neurolex.org/wiki/Property:DendriteLocation" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002371", "lbl" : "attached to", @@ -17425,23 +14952,7 @@ "definition" : { "val" : "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002371" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "attached to (anatomical structure to anatomical structure)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "attaches_to" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002372", @@ -17451,22 +14962,7 @@ "definition" : { "val" : "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." }, - "xrefs" : [ { - "val" : "RO:0002372" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Wikipedia:Insertion_(anatomy)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_muscle_origin" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://dbpedia.org/property/origin" } ] @@ -17479,22 +14975,7 @@ "definition" : { "val" : "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." }, - "xrefs" : [ { - "val" : "RO:0002373" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Wikipedia:Insertion_(anatomy)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_muscle_insertion" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://dbpedia.org/property/insertion" } ] @@ -17507,78 +14988,24 @@ "definition" : { "val" : "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004036", - "val" : "http://purl.obolibrary.org/obo/BFO_0000050" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "https://github.com/obophenotype/uberon/issues/170" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002376", - "lbl" : "tributary of", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." - }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002376" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Deschutes River tributary_of Columbia River" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "inferior epigastric vein tributary_of external iliac vein" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "drains into" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "drains to" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "tributary channel of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://en.wikipedia.org/wiki/Tributary" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.medindia.net/glossary/venous_tributary.htm" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "tributary_of" + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png" }, { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/uberon/issues/170" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/RO_0002376", + "lbl" : "tributary of", + "type" : "PROPERTY", + "meta" : { + "definition" : { + "val" : "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." + }, + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], + "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://dbpedia.org/ontology/drainsTo" }, { @@ -17593,17 +15020,7 @@ "meta" : { "definition" : { "val" : "x spatially_coextensive_with y if and inly if x and y have the same location" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A lump of clay and a statue" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002380", @@ -17614,22 +15031,7 @@ "val" : "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002380" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "branching_part_of" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/issues/2212" }, { @@ -17644,14 +15046,7 @@ "meta" : { "definition" : { "val" : "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002385", @@ -17660,23 +15055,7 @@ "meta" : { "definition" : { "val" : "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" - }, - "xrefs" : [ { - "val" : "RO:0002385" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_potential_to_developmentally_contribute_to" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002386", @@ -17685,14 +15064,7 @@ "meta" : { "definition" : { "val" : "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002387", @@ -17701,23 +15073,7 @@ "meta" : { "definition" : { "val" : "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" - }, - "xrefs" : [ { - "val" : "RO:0002387" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_potential_to_develop_into" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002388", @@ -17726,14 +15082,7 @@ "meta" : { "definition" : { "val" : "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002404", @@ -17747,12 +15096,6 @@ "val" : "RO:0002404" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17769,12 +15112,6 @@ "val" : "RO:0002405" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17791,15 +15128,6 @@ "val" : "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "indirectly activates" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002579", - "val" : "http://purl.obolibrary.org/obo/RO_0002213" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Indirectly_positively_regulates" } ] @@ -17813,15 +15141,6 @@ "val" : "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "indirectly inhibits" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002579", - "val" : "http://purl.obolibrary.org/obo/RO_0002212" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Indirectly_negatively_regulates" } ] @@ -17838,12 +15157,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." } ] } }, { @@ -17859,9 +15172,6 @@ "val" : "RO:0002411" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17881,12 +15191,6 @@ "val" : "RO:0002412" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002411" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17912,12 +15216,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "influences (processual)" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" @@ -17939,12 +15237,6 @@ "val" : "RO:0002427" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17959,11 +15251,7 @@ "meta" : { "definition" : { "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002429", @@ -17972,14 +15260,7 @@ "meta" : { "definition" : { "val" : "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002428" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002430", @@ -17990,9 +15271,6 @@ "val" : "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002428" } ] @@ -18008,12 +15286,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "OWL does not allow defining object properties via a Union" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "involved in or reguates" } ] } }, { @@ -18031,15 +15303,6 @@ "val" : "enables activity in" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A protein that enables activity in a cytosol." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "executes activity in" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Is_active_in" } ] @@ -18051,20 +15314,7 @@ "meta" : { "definition" : { "val" : "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." - }, - "xrefs" : [ { - "val" : "RO:0002433" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "contributes_to_morphology_of" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002434", @@ -18085,18 +15335,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Considering relabeling as 'pairwise interacts with'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" - }, { - "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", - "val" : "http://purl.obolibrary.org/obo/MI_0914" } ] } }, { @@ -18108,20 +15349,8 @@ "val" : "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "binds" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "molecularly binds with" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ECO_0000353" - }, { - "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", - "val" : "http://purl.obolibrary.org/obo/MI_0915" } ] } }, { @@ -18132,12 +15361,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Axiomatization to GO to be added later" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." } ] } }, { @@ -18151,13 +15374,6 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "molecularly controls" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" } ] } }, { @@ -18171,16 +15387,6 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "molecularly decreases activity of" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "directly inhibits" } ] } }, { @@ -18194,31 +15400,12 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "molecularly increases activity of" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "directly activates" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002464", "lbl" : "helper property (not for use in curation)", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002473", "lbl" : "composed primarily of", @@ -18227,29 +15414,7 @@ "definition" : { "val" : "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002473" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "composed_primarily_of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002479", @@ -18259,22 +15424,12 @@ "definition" : { "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002481", "lbl" : "is kinase activity", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002485", "lbl" : "receives input from", @@ -18283,9 +15438,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "See notes for inverse relation" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { @@ -18296,24 +15448,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002487", "lbl" : "relation between physical entity and a process or stage", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage." - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002488", "lbl" : "existence starts during", @@ -18321,20 +15461,7 @@ "meta" : { "definition" : { "val" : "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." - }, - "xrefs" : [ { - "val" : "RO:0002488" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_starts_during" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002489", @@ -18343,20 +15470,7 @@ "meta" : { "definition" : { "val" : "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." - }, - "xrefs" : [ { - "val" : "RO:0002489" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_starts_with" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002490", @@ -18366,11 +15480,7 @@ "definition" : { "val" : "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002491", @@ -18384,19 +15494,6 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "exists during" - } ], - "xrefs" : [ { - "val" : "RO:0002491" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_starts_and_ends_during" } ] } }, { @@ -18407,24 +15504,7 @@ "definition" : { "val" : "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "ceases_to_exist_during" - } ], - "xrefs" : [ { - "val" : "RO:0002492" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_ends_during" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002493", @@ -18434,20 +15514,7 @@ "definition" : { "val" : "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "xrefs" : [ { - "val" : "RO:0002493" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_ends_with" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002494", @@ -18456,20 +15523,7 @@ "meta" : { "definition" : { "val" : "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" - }, - "xrefs" : [ { - "val" : "RO:0002494" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "transformation_of" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002495", @@ -18478,23 +15532,7 @@ "meta" : { "definition" : { "val" : "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" - }, - "xrefs" : [ { - "val" : "RO:0002495" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002494" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "immediate_transformation_of" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002496", @@ -18504,20 +15542,7 @@ "definition" : { "val" : "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "xrefs" : [ { - "val" : "RO:0002496" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_starts_during_or_after" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002497", @@ -18527,20 +15552,7 @@ "definition" : { "val" : "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "xrefs" : [ { - "val" : "RO:0002497" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_ends_during_or_before" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002500", @@ -18549,11 +15561,7 @@ "meta" : { "definition" : { "val" : "A relationship between a material entity and a process where the material entity has some causal role that influences the process" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002501", @@ -18562,17 +15570,7 @@ "meta" : { "definition" : { "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002502", @@ -18580,9 +15578,6 @@ "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/BFO_0000169" } ] @@ -18595,15 +15590,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." } ] } }, { @@ -18613,55 +15599,18 @@ "meta" : { "definition" : { "val" : "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." - }, - "xrefs" : [ { - "val" : "RO:0002551" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has supporting framework" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_skeleton" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002559", "lbl" : "causally influenced by", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "causally influenced by (entity-centric)" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002563", "lbl" : "interaction relation helper property", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29" }, { @@ -18672,13 +15621,7 @@ }, { "id" : "http://purl.obolibrary.org/obo/RO_0002564", "lbl" : "molecular interaction relation helper property", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002565", "lbl" : "results in movement of", @@ -18692,11 +15635,6 @@ "val" : "RO:0002565" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -18711,20 +15649,7 @@ "meta" : { "definition" : { "val" : "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "causally influences (entity-centric)" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002567", @@ -18733,14 +15658,7 @@ "meta" : { "definition" : { "val" : "A relation that holds between elements of a musculoskeletal system or its analogs." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002568", @@ -18749,23 +15667,7 @@ "meta" : { "definition" : { "val" : "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." - }, - "xrefs" : [ { - "val" : "RO:0002568" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Wikipedia:Antagonist_(muscle)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_muscle_antagonist" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002569", @@ -18775,20 +15677,7 @@ "definition" : { "val" : "inverse of branching part of" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002569" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_branching_part" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002570", @@ -18798,26 +15687,7 @@ "definition" : { "val" : "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002570" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "UBERON:cjm" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "conduit_for" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002571", @@ -18827,23 +15697,7 @@ "definition" : { "val" : "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002571" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "lumen_of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002572", @@ -18853,20 +15707,7 @@ "definition" : { "val" : "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002572" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "luminal_space_of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002576", @@ -18876,20 +15717,7 @@ "definition" : { "val" : "inverse of has skeleton" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "xrefs" : [ { - "val" : "RO:0002576" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "skeleton_of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002578", @@ -18904,18 +15732,6 @@ "val" : "RO:0002578" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "directly regulates (processual)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002211" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -18923,24 +15739,6 @@ "val" : "directly_regulates" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002581", - "lbl" : "is a defining property chain axiom", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002582", - "lbl" : "is a defining property chain axiom where second argument is reflexive", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R." - } - } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002584", "lbl" : "has part structure that is capable of", @@ -18948,14 +15746,7 @@ "meta" : { "definition" : { "val" : "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002586", @@ -19029,12 +15820,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] } }, { @@ -19044,14 +15829,7 @@ "meta" : { "definition" : { "val" : "Holds between c and p if and only if c is capable of some activity a, and a regulates p." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "pyrethroid -> growth" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002597", @@ -19060,11 +15838,7 @@ "meta" : { "definition" : { "val" : "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002598", @@ -19073,14 +15847,7 @@ "meta" : { "definition" : { "val" : "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "renin -> arteriolar smooth muscle contraction" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002608", @@ -19094,9 +15861,6 @@ "val" : "RO:0002608" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -19117,15 +15881,6 @@ "val" : "RO:0002629" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "directly positively regulates (process to process)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002578" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -19149,12 +15904,6 @@ "val" : "RO:0002630" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "directly negatively regulates (process to process)" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002578" }, { @@ -19182,17 +15931,8 @@ "val" : "RO:0003000" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9114-8737" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "produces" @@ -19211,17 +15951,8 @@ "val" : "RO:0003001" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9114-8737" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "produced_by" @@ -19330,9 +16061,6 @@ "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002264" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { @@ -19373,9 +16101,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002263" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { @@ -19434,9 +16159,6 @@ "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002418" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { @@ -19467,11 +16189,7 @@ "meta" : { "definition" : { "val" : "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0012000", @@ -19733,9 +16451,6 @@ "xrefs" : [ "PMID:19243617" ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" - }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1617-8244" }, { @@ -19753,9 +16468,6 @@ "xrefs" : [ "PMID:19243617" ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" - }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1617-8244" }, { @@ -19776,21 +16488,6 @@ "val" : "utilizes" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A diagnostic testing device utilizes a specimen." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9625-1899" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-2620-0345" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "See github ticket https://github.com/oborel/obo-relations/issues/497" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-11-08T12:00:00Z" } ] @@ -19986,15 +16683,6 @@ "val" : "ZFA:0000107" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A cavitated compound organ that transduces light waves into neural signals.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "FMA distinguishes Eye (subdivision of face) which has its parts an Eyeball (organ), as well as other structures, and the orbit of skull. MA includes eyelid, conjunctiva and lacrimal apparatus as part of MA:eye - consistent with FMA - so we can infer that MA:eye is more like FMA:eye than FMA:eyeball. For other AOs this distinction is less meaningful - e.g. ZFA has no eyelid; XAO has no eyelid, but it has conjuctiva, which is considered part of the xao:eye. GO considers eyelid development part of eye development. See also notes on optic nerve - XAO, AAO and BTO consider this part of the eye. MA considers the eye muscles part of the eye, whereas FMA has a class 'orbital content' for this" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -20062,8 +16750,6 @@ "val" : "EHDAA:500" }, { "val" : "EMAPA:35955" - }, { - "val" : "FBbt:00005155" }, { "val" : "GAID:63" }, { @@ -20111,12 +16797,6 @@ "val" : "galen:Tube" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts)" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "tubular" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -20201,18 +16881,6 @@ "val" : "galen:Head" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000948" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -20261,15 +16929,6 @@ "val" : "ZFA:0005425" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -20341,16 +17000,11 @@ "xrefs" : [ "FMA:82482" ] } ], "xrefs" : [ { - "val" : "EMAPA:25036" - }, { "val" : "FMA:82482" }, { "val" : "galen:Wall" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in FMA, serosa is a wall" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0009915" }, { @@ -20388,8 +17042,6 @@ "val" : "EHDAA2:0003003" }, { "val" : "EMAPA:0" - }, { - "val" : "FBbt:00007001" }, { "val" : "FMA:305751" }, { @@ -20489,12 +17141,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -20529,12 +17175,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -20573,9 +17213,6 @@ "val" : "SCTID:91717005" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "currently defined in a very broad sense, may be replaced by more specific classes in the future" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { @@ -20706,9 +17343,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "ncit:Death is an outcome" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -20805,8 +17439,6 @@ "xrefs" : [ "MP:0012532" ] } ], "xrefs" : [ { - "val" : "BTO:0006242" - }, { "val" : "EHDAA2:0001968" }, { "val" : "EHDAA:1494" @@ -20834,12 +17466,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0002346" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "(or external ectoderm) forms the following structures: Skin Epithelium of the mouth and nasal cavity saliavary glands, and glands of mouth and nasal cavity Enamel - as a side note dentin and dental pulp are formed from ectomesenchyme which is derived from ectoderm Epithelium of pineal and pituitary glands Lens and cornea of the eye Apical ectodermal ridge inducing development of the limb buds of the embryo. Sensory receptors in epidermis" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -20883,9 +17509,6 @@ "val" : "WBls:0000103" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -21002,12 +17625,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "the WBls class 'all stages' belongs here as it is the superclass of other WBls stages" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -21060,8 +17677,6 @@ "val" : "EHDAA:27" }, { "val" : "FBdv:00005288" - }, { - "val" : "IDOMAL:0000302" }, { "val" : "NCIT:C12601" }, { @@ -21076,9 +17691,6 @@ "val" : "ZFS:0000001" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -21256,12 +17868,6 @@ "val" : "XAO:1000006" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002174", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7955" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In zebrafish, the times of neurulation and segmentation overlap so extensively there is no distinct neurula period of development, such as occurs largely before segmentation in amphibian embryos." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -21333,8 +17939,6 @@ } ], "xrefs" : [ { "val" : "CARO:0001001" - }, { - "val" : "FBbt:00005099" }, { "val" : "NLX:147821" } ], @@ -21449,8 +18053,6 @@ "val" : "EHDAA:542" }, { "val" : "EMAPA:16262" - }, { - "val" : "FBbt:00003126" }, { "val" : "FMA:49184" }, { @@ -21493,21 +18095,6 @@ "val" : "http://purl.obolibrary.org/obo/uberon/images/lamprey_sucker_rosava_3238889218.jpg" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "oral" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -21585,23 +18172,8 @@ "val" : "galen:Blood" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid." - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -21734,8 +18306,6 @@ "val" : "BTO:0001485" }, { "val" : "EFO:0000801" - }, { - "val" : "EMAPA:35578" }, { "val" : "FMA:72954" }, { @@ -21758,12 +18328,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system that consists of the muscles of the body.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -21814,8 +18378,6 @@ "val" : "EHDAA2:0003004" }, { "val" : "EMAPA:35178" - }, { - "val" : "FBbt:00007019" }, { "val" : "FMA:9669" }, { @@ -21888,8 +18450,6 @@ "val" : "CARO:0000005" }, { "val" : "EHDAA2:0003005" - }, { - "val" : "FBbt:00007017" }, { "val" : "FMA:5897" }, { @@ -21943,8 +18503,6 @@ "val" : "CARO:0000006" }, { "val" : "EHDAA2:0003006" - }, { - "val" : "FBbt:00007016" }, { "val" : "FMA:67165" }, { @@ -21995,8 +18553,6 @@ "val" : "CARO:0000007" }, { "val" : "EHDAA2:0003007" - }, { - "val" : "FBbt:00007015" }, { "val" : "FMA:67112" }, { @@ -22075,14 +18631,10 @@ "val" : "EMAPA:16103" }, { "val" : "EV:0100000" - }, { - "val" : "FBbt:00004856" }, { "val" : "FMA:7149" }, { "val" : "HAO:0000011" - }, { - "val" : "IDOMAL:0002460" }, { "val" : "MA:0000003" }, { @@ -22191,8 +18743,6 @@ "val" : "EMAPA:25765" }, { "val" : "EV:0100016" - }, { - "val" : "FBbt:00000001" }, { "val" : "FMA:256135" }, { @@ -22234,9 +18784,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "organismal" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -22286,8 +18833,6 @@ "val" : "EHDAA2:0003032" }, { "val" : "EMAPA:36031" - }, { - "val" : "FBbt:00007009" }, { "val" : "FMA:7153" }, { @@ -22362,8 +18907,6 @@ "val" : "CARO:0000040" }, { "val" : "EHDAA2:0003040" - }, { - "val" : "FBbt:00007013" }, { "val" : "FMA:63863" }, { @@ -22402,8 +18945,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "xrefs" : [ { - "val" : "FBbt:00007277" - }, { "val" : "VHOG:0001737" } ], "basicPropertyValues" : [ { @@ -22460,8 +19001,6 @@ "val" : "EHDAA2:0003043" }, { "val" : "EMAPA:35868" - }, { - "val" : "FBbt:00007003" }, { "val" : "FMA:9637" }, { @@ -22532,8 +19071,6 @@ "val" : "CARO:0000055" }, { "val" : "EHDAA2:0003055" - }, { - "val" : "FBbt:00007010" }, { "val" : "HAO:0000055" }, { @@ -22598,8 +19135,6 @@ "val" : "EHDAA2:0003066" }, { "val" : "EMAPA:32738" - }, { - "val" : "FBbt:00007005" }, { "val" : "FMA:9639" }, { @@ -22628,12 +19163,6 @@ "val" : "ZFA:0001486" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "epithelial" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -22690,9 +19219,6 @@ "val" : "ZFA:0001498" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Unilaminar epithelium that consists of a single layer of squamous cells.[CARO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -22791,9 +19317,6 @@ "val" : "ZFA:0001490" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -22850,9 +19373,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Epithelium that consists of a single layer of epithelial cells.[CARO]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -22895,18 +19415,6 @@ "val" : "Wikipedia:Thorax" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000026" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000033" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0002417" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -22955,14 +19463,10 @@ "val" : "EHDAA:38" }, { "val" : "EMAPA:16039" - }, { - "val" : "FBbt:00000052" }, { "val" : "FMA:69068" }, { "val" : "GAID:963" - }, { - "val" : "IDOMAL:0000646" }, { "val" : "MAT:0000226" }, { @@ -22989,12 +19493,6 @@ "val" : "http://neurolex.org/wiki/Category:Embryonic_organism" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "embryonic" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -23043,8 +19541,6 @@ "val" : "BTO:0000556" }, { "val" : "EMAPA:36033" - }, { - "val" : "FBbt:00000110" }, { "val" : "FMA:69069" }, { @@ -23071,9 +19567,6 @@ "val" : "ZFA:0001122" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -23109,8 +19602,6 @@ "val" : "EMAPA:16069" }, { "val" : "EV:0100003" - }, { - "val" : "FBbt:00000111" }, { "val" : "FMA:69070" }, { @@ -23141,15 +19632,6 @@ "val" : "ZFA:0000016" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "ectodermal" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -23189,8 +19671,6 @@ "val" : "EMAPA:16062" }, { "val" : "EV:0100005" - }, { - "val" : "FBbt:00000125" }, { "val" : "FMA:69071" }, { @@ -23219,12 +19699,6 @@ "val" : "ZFA:0000017" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "endodermal" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -23279,8 +19753,6 @@ "val" : "EMAPA:16083" }, { "val" : "EV:0100006" - }, { - "val" : "FBbt:00000126" }, { "val" : "FMA:69072" }, { @@ -23311,18 +19783,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Primary germ layer that is the middle of the embryonic germ layers.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "mesodermal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0003263" @@ -23382,8 +19842,6 @@ "val" : "EHDAA2:0001929" }, { "val" : "EMAPA:16263" - }, { - "val" : "FBbt:00000439" }, { "val" : "FMA:295846" }, { @@ -23404,18 +19862,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "stomodeal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -23543,18 +19989,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Do not classify under 'cranial nerve', as this is not a true nerve - should be classified as evaginated sensory afferent[ISBN:0471888893]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A collection of nerve cells that project visual information from the eyes to the brain. (Source: BioGlossary, www.Biology-Text.com)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Fibrous, somatic sensory element covered by a fibrous connective-tissue sheath and is continuous with the layer of nerve cells on the inner surface of the eye.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup (reference 1); The (optic) stalk persists as the optic nerve (reference 2).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "(relaion to eye): MA, XAO, AAO and BTO consider this part of the eye. This is in contrast to GO, FMA, EHDAA2 (FMA has a class 'intra-ocular part of optic nerve' which represents the region of overlap). Relation to brain: part of diencephalon in EHDAA2, ZFA. In NIF, has the optic nerve root as part, which is a feature part of the diencphalon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -23645,21 +20079,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "cardiac" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -23734,8 +20153,6 @@ "val" : "EMAPA:16894" }, { "val" : "EV:0100164" - }, { - "val" : "FBbt:00005095" }, { "val" : "FMA:50801" }, { @@ -23785,18 +20202,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO)" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -23828,9 +20233,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO - merge with cell layer?" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "laminar" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -23933,12 +20335,6 @@ "val" : "neuronames:459" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The point at which fibers of the optic nerves cross.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The chiasm has been studied in great detail in some animals, while in others relatively little or nothing is known. Although there are some gross architectural features that are conserved within some animals, such as birds and fish, the general picture is one of diversity. This review will attempt to consider the key features of such diversity of chiasmatic organisation in vertebrates and the mechanisms that sculpt them from the limited literature that is available. However, as so much research has been undertaken on the structure and development of the chiasm in laboratory animals, any review must consider the information that has been gleaned from them and hope that future studies will determine whether the features revealed in these animals, and the underlying mechanisms that generate them, have a common vertebrate plan.[uncertain][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -24013,12 +20409,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "corneal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals. In fish, and aquatic vertebrates in general, the cornea plays no role in focusing light, since it has virtually the same refractive index as water" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -24110,17 +20500,8 @@ "val" : "ZFA:0000035" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0002049" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "This class excludes compound eye corneal lenses." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -24220,15 +20601,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The portion of the eye developing from the optic primordium and including the neural retina and the retinal pigment layer. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "retinal" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -24265,8 +20637,6 @@ "val" : "EFO:0000827" }, { "val" : "EV:0100336" - }, { - "val" : "FBbt:00005162" }, { "val" : "GAID:69" }, { @@ -24279,20 +20649,8 @@ "val" : "Wikipedia:Eye" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This class encompasses a variety of light-detecting structures from different phyla with no implication of homology, from the compound insect eye to the vertebrate camera-type eye (distinct classes are provided for each)" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "ocular" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "optic" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000010", - "val" : "Note that whilst this is classified as an organ, it is in fact more of a unit composed of different structures: in Drosophila, it includes the interommatidial bristle as a part; we consider here the vertebrate eye to include the eyeball/eye proper as a part, with the eye having as parts (when present): eyelids, conjuctiva," }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -24372,12 +20730,6 @@ "val" : "galen:Joint" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -24415,10 +20767,6 @@ "val" : "CALOHA:TS-1293" }, { "val" : "EFO:0000793" - }, { - "val" : "EV:0100056" - }, { - "val" : "FBbt:00005055" }, { "val" : "FMA:7152" }, { @@ -24453,15 +20801,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "digestive" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -24487,17 +20826,12 @@ "val" : "AAO:0000959" }, { "val" : "CALOHA:TS-2103" - }, { - "val" : "MESH:D002319" }, { "val" : "VHOG:0001248" }, { "val" : "Wikipedia:Circulatory_system" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "the cardiovascular system and the lymphatic system are parts of the circulatory system" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_147099" }, { @@ -24506,18 +20840,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6157" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002174", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6231" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -24569,13 +20894,9 @@ "val" : "musculature system" } ], "xrefs" : [ { - "val" : "AAO:0011066" - }, { "val" : "BTO:0000887" }, { "val" : "EFO:0001949" - }, { - "val" : "EMAPA:32715" }, { "val" : "EMAPA:35577" }, { @@ -24598,12 +20919,6 @@ "val" : "ZFA:0000548" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0001474" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -24655,8 +20970,6 @@ "val" : "EMAPA:16469" }, { "val" : "EV:0100162" - }, { - "val" : "FBbt:00005093" }, { "val" : "FMA:7157" }, { @@ -24696,21 +21009,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "nervous" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "neural" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -24774,8 +21072,6 @@ "val" : "EMAPA:16754" }, { "val" : "EV:0100163" - }, { - "val" : "FBbt:00005094" }, { "val" : "FMA:55675" }, { @@ -24811,18 +21107,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Part of the nervous system which includes the brain and spinal cord.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The brain and spinal cord. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO)." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -24865,17 +21149,12 @@ "val" : "BIRNLEX:1649" }, { "val" : "EV:0100304" - }, { - "val" : "FBbt:00005100" }, { "val" : "FMA:83847" }, { "val" : "NLX:147822" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "White matter structure of CNS that contains axons that arise predominantly in one central nervous system part and terminate in another. Tracts are generally named by their region or origin followed by their region of primary termination, e.g., mammillothalamic tract contains axons that arise from neurons in the mammillary bodies and terminate in the thalamus. (CUMBO)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -24997,8 +21276,6 @@ "val" : "EHDAA2:0003094" }, { "val" : "EMAPA:16192" - }, { - "val" : "FBbt:00007692" }, { "val" : "FMA:75259" }, { @@ -25021,12 +21298,6 @@ "val" : "ZFA:0000282" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -25071,8 +21342,6 @@ "val" : "EFO:0001652" }, { "val" : "EHDAA2:0003171" - }, { - "val" : "FBbt:00005495" }, { "val" : "FMA:86589" }, { @@ -25135,8 +21404,6 @@ "val" : "FMA:293882" }, { "val" : "MAT:0000069" - }, { - "val" : "MESH:D054259" }, { "val" : "MIAA:0000069" }, { @@ -25159,18 +21426,6 @@ "val" : "neuronames:1365" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -25202,8 +21457,6 @@ "val" : "CARO:0000000" }, { "val" : "EHDAA2:0002229" - }, { - "val" : "FBbt:10000000" }, { "val" : "FMA:62955" }, { @@ -25327,18 +21580,6 @@ "val" : "galen:SmoothMuscleTissue" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) the first bilateral animals possessed only smooth muscles with the molecular repertoire necessary to build a striated muscle. (...) it is more parsimonious to regard striated muscle cells as a sister cell type to the smooth muscle cells. In this scenario, striated and smooth muscles would have arisen in the stem lineage that led to the Nephrozoa (i.e. all Bilateria exclusive the acoelomorphs) (Hejnol et al., 2009), from an 'acoel-like' smooth muscle, by segregation and divergence of functions and through differential recruitment of additional genes[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000013", - "val" : "GO uses visceral and smooth interchangeably. However visceral can also be used in the sense of the viscera. Many fly annotations to smooth muscle terms. If we want to be inclusive of insects have to have a general definition of tissue that includes cells." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -25445,12 +21686,6 @@ "val" : "galen:Back" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "dorsal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In humans, called the back, a large posterior area of the human body, rising from the top of the buttocks to the back of the neck and the shoulders. It is the surface opposite to the chest, its height being defined by the vertebral column (commonly referred to as the spine or backbone) and its breadth being supported by the ribcage and shoulders. The spinal canal runs through the spine and provides nerves to the rest of the body" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -25512,27 +21747,6 @@ "val" : "ZFA:0000434" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0001016" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "System that provides physical support to the organism.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "skeletal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -25616,18 +21830,6 @@ "val" : "galen:Face" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The area that extends from the median ocellus to the oral foramen[HAO]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "facial" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "The face develops from outward growth of tissue located rostral to the cranium & pharynx. The lower jaw and most of the upper jaw are formed by growth of the first pharyngeal (branchial) arch. The upper incisor region and the nose and forehead (frontal region) are formed from tissue located rostral to the neural tube (frontonasal prominence)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -25683,14 +21885,10 @@ "val" : "EHDAA:518" }, { "val" : "EMAPA:16247" - }, { - "val" : "FBbt:00003125" }, { "val" : "FMA:45615" }, { "val" : "MA:0000917" - }, { - "val" : "MESH:D041981" }, { "val" : "NCIT:C34082" }, { @@ -25717,21 +21915,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The alimentary or digestive tract, and associated organs.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "FMA also has a term 'gastrointestinal tract', but this includes the liver." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000013", - "val" : "we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -25809,10 +21992,6 @@ "xrefs" : [ "ZFA:0005145" ] } ], "xrefs" : [ { - "val" : "AAO:0011066" - }, { - "val" : "EMAPA:32715" - }, { "val" : "EMAPA:37474" }, { "val" : "EV:0100146" @@ -25836,15 +22015,6 @@ "val" : "galen:Muscle" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of tissue composed of contractile fibers.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "muscular" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -25907,24 +22077,6 @@ "val" : "Wikipedia:Eyelid" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "blepharic" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "palpebral" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In humans the upper and lower eyelid consists of the following layers, starting anteriorly: (1) skin, (2) a layer of subcutaneous connective tissue, (3) a layer of striated muscle fibres of the orbicularis muscle, (4) a layer of submuscular connective tissue, (5) a fibrous layer, including the tarsal plates, (6) a layer of smooth muscle, (7) the palpebral conjunctiva." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "Consider adding 'eye surface', like MA" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "FMA divides this into skin, fascia, conjunctiva" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000202", - "val" : "http://purl.obolibrary.org/obo/FMA_75178" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -25997,12 +22149,6 @@ "val" : "Wikipedia:Anterior_chamber_of_eyeball" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The part of the eyeball between the cornea and the iris, filled with aqueous humor. [TFD][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "space in EHDAA2 - consider adding Cavity of anterior chamber of eyeball" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -26077,9 +22223,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7955" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "uveal" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26151,18 +22294,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The opaque muscular contractile diaphragm suspended in the aqueous humour in front of the lens of the eye. The organ is perforated by the pupil and continues peripherally with the ciliary body. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "iridial" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "The avian iris and ciliary body undergoes a transition from smooth-to-striated muscle during embryonic development [DOI:dx.doi.org/10.1006/dbio.1998.9019]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26270,15 +22401,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of tissue comprised of four to six layers of nonkeratinized, stratified squamous cells and represents approximately 60% of the thickness of the cornea.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In Humans: It consists of several layers of cells. The cells of the deepest layer are columnar; then follow two or three layers of polyhedral cells, the majority of which are prickle cells similar to those found in the stratum mucosum of the cuticle. Lastly, there are three or four layers of squamous cells, with flattened nuclei" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In zebrafish: nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26336,27 +22458,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The sclera, also known as the white part of the eye, is the opaque (usually white, though certain animals, such as horses and lizards, can have black sclera), fibrous, protective, outer layer of the eye containing collagen and elastic fiber. It is derived from the neural crest. In children, it is thinner and shows some of the underlying pigment, appearing slightly blue. In the elderly, however, fatty deposits on the sclera can make it appear slightly yellow. The sclera forms the posterior five sixths of the connective tissue coat of the globe. It is continuous with the dura mater and the cornea, and maintains the shape of the globe, offering resistance to internal and external forces, and provides an attachment for the extraocular muscle insertions. The sclera is perforated by plenty of nerves and vessels passing through the posterior scleral foramen, the hole that is formed by the optic nerve. At the optic disk the outer two-thirds of the sclera continues with the dura mater (outer coat of the brain) via the dural sheath of the optic nerve. The inner third joins with some choroidal tissue to form a plate (lamina cribrosa) across the optic nerve with perforations through which the optic fibers (fasciculi). The thickness of the sclera varies from 1mm at the posterior pole to 0.3 mm just behind the rectus muscle insertions. The sclera's blood vessels are mainly on the surface, and together with the conjunctiva (which lies on top) This is a thin layer covering the sclera. Along with the vessels of the conjunctiva, those of the sclera renders the inflamed eye bright red. [WP,unvetted][Wikipedia:Sclera]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The tough, usually white, outer coat of the eyeball, covering all the posterior surface and continuous anteriorly with the cornea. [TFD][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "scleral" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "in fish, reptiles and monotremes the connective tissue of the sclera is skeletal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000010", - "val" : "continuous with the dura mater and the cornea; The sclera forms the posterior five-sixths of the connective tissue coat of the globe." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "Majority derives from NC that surrounds optic cup of neurectoderm; a small temporal portion develops from the mesoderm that contributes to striated extra-ocular muscles and vascular endothelia[Rada&Johnson]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "Seko et al demonstrate chondrogenic potential and identify this as connective tissue[DOI:10.1371/journal.pone.0003709]." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26428,9 +22529,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26520,12 +22618,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "choroidal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "MP treats posterior uvea and optic choroid as distinct" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26588,15 +22680,6 @@ "val" : "ZFA:0001685" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of tissue that is located basal to Bowman's layer and distal to Descemet's membrane and is comprised largely of connective tissue.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship type change: subclass tissue (CARO:0000043) CHANGED TO: develops_from tissue (UBERON:0000479)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship type change: subclass tissue (CARO:0000043) CHANGED TO: has_developmental_contribution_from tissue (UBERON:0000479)[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -26696,9 +22779,6 @@ "val" : "XAO:0000266" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "MA does not treat internal/external limiting memranes as layers - these are classified as laminae. Here we follow other ontologies in grouping with other layers. MA also treats retinal pigment epithelium and neural retina epithelium as distinct from the layers. We follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers - these are also classified as layers, giving us over the usual 10 layers" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -26812,15 +22892,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A monolayer of pigmented epithelium covering the neural retina; develops from the outer of the two layers of the optic cup. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The monolayer of pigmented epithelium covering the neural retina.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26885,12 +22956,6 @@ "val" : "ZFA:0000143" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "we follow MA and ZFA in subdividing this into inner and outer segments" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -27063,9 +23128,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27145,12 +23207,6 @@ "val" : "ZFA:0001330" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The layer within the retina where the bipolar cells synapse with the photoreceptor cells.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -27237,12 +23293,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The layer of the retina composed of the cell bodies of bipolar cells, horizontal cells, and some of the cell bodies of amacrine cells[BTO:0003176]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27333,15 +23383,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "a layer of the retina that consists of retinal ganglion cells[WP]. innermost nuclear layer of the retina, which contains neurons that project axons through the optic nerve to the brain[Wikipedia:Ganglion_cell_layer]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "NIFSTD class appears to be retired in nlx[http://neurolex.org/wiki/Nlx_anat_1005030]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27429,9 +23470,6 @@ "val" : "ZFA:0001619" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0005888" }, { @@ -27509,9 +23547,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO - check frog/fish" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Membrane on the apical surface of the retina. The retinal vasculature becomes adhered to the apical surface of the ILM by 30dpf[ZFIN:ZDB-PUB-071023-7, ZFIN:ZDB-PUB-120529-3]." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27599,18 +23634,6 @@ "val" : "ZFA:0001329" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The inner plexiform layer (IPL) is positioned between the INL and the ganglion cell layer and contains the dendrites of RGCs and processes of bipolar and amacrine cells[GO][GO:0010842]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The layer within the retina where the bipolar cells synapse with the dendrites of the ganglion cells.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "http://neurolex.org/wiki/Nlx_anat_1005032 appears to be retired" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -27671,15 +23694,6 @@ "val" : "ZFA:0005564" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The fluid produced by the ciliary process in the eye and occupying the anterior and posterior chambers. It provides nourishment for the lens and cornea and maintains the ocular pressure, and hence the optical integrity of the eyeball. [TFD][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "FMA says A+P chambers, and MA states A chamber. ZFA states A chamber and tha it is produced primarily by dorsal ciliary epithelial cells.To be investigated across taxa." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -27747,8 +23761,6 @@ "val" : "FMA:58822" }, { "val" : "MA:0001286" - }, { - "val" : "MESH:D014822" }, { "val" : "NCIT:C13323" }, { @@ -27921,9 +23933,6 @@ "val" : "ZFA:0005566" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0001802" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -28029,8 +24038,6 @@ "val" : "CALOHA:TS-2232" }, { "val" : "EFO:0000374" - }, { - "val" : "EMAPA:18233" }, { "val" : "EV:0100340" }, { @@ -28055,9 +24062,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "conjunctival" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28141,21 +24145,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Most anterior of the three regions of the brain consisting of the telencephalon and diencephalon.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The most anterior region the brain including both the telencephalon and diencephalon. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship loss: develops_from forebrain neural tube (TAO:0007041)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "In craniate embryos, neural expression of Distal-less-related genes is exclusively in the forebrain (...). Because the major neural expression domain of amphioxus AmphiDll is in the anterior three-fourths of the cerebral vesicle, we suggest that this region of the neural tube is homologous to parts of the craniate forebrain. This conclusion is strongly supported by three-dimensional, computer-assisted reconstruction of the neural tube of amphioxus based on serial transmission electron microscopy. At the neuroanatomical level, a number of detailed homologies are indicated between the anterior three-fourths of the amphioxus cerebral vesicle and the diencephalic region of the craniate forebrain. If one assumes that the amphioxus condition fairly represents the nervous system of the proximate ancestor of the craniates, one can suggest that they evolved from a creature that had the beginnings of a forebrain.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "prosencephalic" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28249,30 +24238,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "developmental relationships need revised" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0001894" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0002028" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Middle part of the brain composed of the optic tectum and penducular region.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "mesencephalic" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "part of brainstem in ABA - we reject this in favor of ISBN:0471888893 which has an implicit overlaps relationships" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28397,30 +24365,6 @@ "val" : "neuronames:288" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0001891" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0002028" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7762" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The more posterior and ventral of two forebrain neuromeres, the other being the telencephalon; major derivatives are the eye cups, the brain pretectal region, the thalamus, hypothalamus, and epithalamus (including the habenula and epiphysis). Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Unpaired part of the forebrain comprised of three major parts; the epithalamus, thalamus, and hypothalamus.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "diencephalic" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in ABA, this is part of the brain stem" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -28526,15 +24470,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Posterior portion of the hindbrain which controls respiration, heartbeat, digestion, and swallowing as well as some locomotor responses.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The posterior region of the brain that is continuous with the spinal cord. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-17, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Classical anatomical studies subdivided the vertebrate rhombencephalon into pons and medulla oblongata. (...) The medulla oblongata appears therefore as a tagma, that is, a group of segmental units (pseudorhombomeres, in this case) sharing some morphological and molecular characteristics, and in some aspects different from the segmental units present in adjoining brain regions, pons and spinal cord.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28586,8 +24521,6 @@ "val" : "DHBA:10589" }, { "val" : "DMBA:17785" - }, { - "val" : "EMAPA:16678" }, { "val" : "EMAPA:35617" }, { @@ -28701,8 +24634,6 @@ "val" : "MA:0000212" }, { "val" : "MAT:0000452" - }, { - "val" : "MESH:D013681" }, { "val" : "SCTID:362392007" }, { @@ -28723,9 +24654,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28874,21 +24802,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Any of the vessels through which blood circulates in the body.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "annelids have blood vessels, but this class is not applicable to annelids." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28992,9 +24905,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "endothelial" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -29058,8 +24968,6 @@ "val" : "HBA:4006" }, { "val" : "MA:0001112" - }, { - "val" : "MESH:D066128" }, { "val" : "NCIT:C32695" }, { @@ -29076,9 +24984,6 @@ "val" : "neuronames:2869" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Multi-tissue comprised of neurons, dendrites, axon terminals, glial cells, and capillaries.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -29158,35 +25063,11 @@ "val" : "neuronames:540" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0001891" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0001894" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7762" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Posterior part of the brain consisting of the cerebellum and medulla oblongata.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The most posterior of the three principal regions of the brain, forming the rhombencephalon and all or most of the metencephalon. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship loss: develops_from hindbrain neural tube (TAO:0007043)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "rhombencephalic" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in MA, brainstem and hindbrain and part-of siblings under brain, consistent with FMA and NIF. See also notes for cerebellum. We weaken the relation in ABA to overlaps" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -29225,9 +25106,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "vascular" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -29277,8 +25155,6 @@ "val" : "CALOHA:TS-2110" }, { "val" : "EFO:0000461" - }, { - "val" : "FBbt:00004208" }, { "val" : "FMA:69067" }, { @@ -29303,18 +25179,6 @@ "val" : "ZFA:0001105" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in FMA embryo is_a embryonic structure" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -29377,12 +25241,6 @@ "val" : "XAO:0003034" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -29414,8 +25272,6 @@ "val" : "EHDAA2:0000161" }, { "val" : "EHDAA:5049" - }, { - "val" : "EMAPA:17214" }, { "val" : "EMAPA:37721" }, { @@ -29424,8 +25280,6 @@ "val" : "MA:0002986" }, { "val" : "MAT:0000148" - }, { - "val" : "MESH:D013131" }, { "val" : "MIAA:0000148" }, { @@ -29440,18 +25294,6 @@ "val" : "ZFA:0000317" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -29524,18 +25366,6 @@ "val" : "galen:Trunk" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000026" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000033" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -29586,9 +25416,6 @@ "val" : "http://uri.neuinfo.org/nif/nifstd/FMAID_7191" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The sensory system used for sight.[AAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0007036" }, { @@ -29732,9 +25559,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "not part of the eye in ZFA. Note this changed to a blood vessel in ZFA" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -29792,15 +25616,6 @@ "val" : "XAO:0000168" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system that provides locomotion and physical support to the organism.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "musculoskeletal" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -29860,9 +25675,6 @@ "val" : "Wikipedia:Thoracic_cavity" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In many species, the diaphragm separates thoracic and abdominal cavities" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -29981,18 +25793,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO - add superclass to unify with VNC?" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000955" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Part of the central nervous system which descends from the hindbrain within the vertebral column.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -30097,24 +25900,6 @@ "val" : "neuronames:236" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0001890" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0002037" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0002314" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,adopted][ZFA:0001707]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "the stalk-like part of the brain that comprises the midbrain (aka mesencephalon), the pons (aka pons Varolii), and the medulla oblongata, and connects the cerebral hemispheres with the cervical spinal cord[MP]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -30177,8 +25962,6 @@ "val" : "HBA:9218" }, { "val" : "MA:0001135" - }, { - "val" : "MESH:D066127" }, { "val" : "NCIT:C33892" }, { @@ -30205,18 +25988,6 @@ "val" : "neuronames:2870" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Cell part cluster consisting predominantly of neurites in the brain and the spinal cord[FMA:83929]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Multi-tissue structure comprised largely of myelinated axons.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The myelination of axons by glial cells was the last major step in the evolution of cells in the vertebrate nervous system, and white-matter tracts are key to the architecture of the mammalian brain.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "nlx_anat_101177 seems to have been lost in the transition from NIFGA to Neurolex" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -30283,8 +26054,6 @@ "val" : "BTO:0001707" }, { "val" : "EHDAA2:0000267" - }, { - "val" : "FBbt:00005060" }, { "val" : "FMA:85006" }, { @@ -30303,15 +26072,6 @@ "val" : "galen:BodyCavity" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In mammals it forms the peritoneal, pleural, and pericardial cavities" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0000169" }, { @@ -30389,27 +26149,6 @@ "val" : "http://evolution.berkeley.edu/evolibrary/images/history/notochords.jpg" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "notochordal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -30496,32 +26235,8 @@ "val" : "ZFA:0000155" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "EDITOR_NOTE currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7712" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Post-cranial axial segments which form sclerotome and dermomyotome.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "somitic" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -30580,8 +26295,6 @@ "val" : "NCIT:C34222" }, { "val" : "SCTID:361462002" - }, { - "val" : "TAO:0000045" }, { "val" : "UMLS:C0027789" }, { @@ -30596,24 +26309,6 @@ "val" : "neuronames:1366" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "EDITOR_NOTE consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams)." - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002174", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_117565" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -30672,8 +26367,6 @@ "val" : "EMAPA:16073" }, { "val" : "EV:0100004" - }, { - "val" : "FBbt:00001057" }, { "val" : "FMA:87657" }, { @@ -30696,15 +26389,6 @@ "val" : "ZFA:0001120" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "neurectodermal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000013", - "val" : "we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -30773,18 +26457,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "MA also has set of connective tissues" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -30841,12 +26513,6 @@ "val" : "galen:MuscleTissue" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0003714" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -30931,18 +26597,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system that consists of the blood and blood forming tissues.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "hematopoietic" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -31054,9 +26708,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -31098,8 +26749,6 @@ "val" : "AAO:0010466" }, { "val" : "EFO:0001650" - }, { - "val" : "FMA:293966" }, { "val" : "MAT:0000369" }, { @@ -31110,12 +26759,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Do not merge with neurogenic placode" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000013", - "val" : "The term placode or placodes also applies to developing organs such as teeth, mammary glands, hair follicles, feathers and scales. We include a separate parent class for this. to avoid confusion, we include neurogenic placode as a subclass" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -31274,9 +26917,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider adding class for organizer. Consider adding separate class for isthmus as a structure" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -31307,9 +26947,6 @@ "val" : "ZFA:0007016" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -31337,9 +26974,6 @@ "val" : "ZFA:0007017" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -31397,12 +27031,6 @@ "val" : "ZFA:0000279" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -31464,21 +27092,6 @@ "val" : "ZFA:0000094" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -31514,9 +27127,6 @@ "val" : "ZFA:0001204" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -31586,9 +27196,6 @@ "val" : "ZFA:0000570" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "TODO - check that GO's optic placode is the same as ZFA's eye primordium; we may want to have separate term for ocular primordium precursor. XAO has both optic field and eye primordium." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0005060" }, { @@ -31644,9 +27251,6 @@ "val" : "ZFA:0001202" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -31700,15 +27304,6 @@ "val" : "ZFA:0000122" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Ectodermal primordium of the lens of the eye. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "Classical transplantation experiments using amphibian embryos suggested that the optic vesicle is the source of lens-inducing signals sufficient to generate lens tissues in competent ectoderm (reviewed in Grainger et al., 1996). More recent findings suggest a multistep model for lens induction. There is now good evidence that lens specification occurs at the neurula stage, before the optic vesicle contact the surface ectoderm, and that neural crest cell migration in the frontonasal region is required to restrict the position of the lens placode (Bailey et al., 2006)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -31751,8 +27346,6 @@ "val" : "EMAPA:35593" }, { "val" : "FMA:293879" - }, { - "val" : "MESH:D054258" }, { "val" : "NCIT:C34225" }, { @@ -31773,12 +27366,6 @@ "val" : "neuronames:1362" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -31803,9 +27390,6 @@ "val" : "ZFA:0007037" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -31862,15 +27446,6 @@ "val" : "ZFA:0000255" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -31897,9 +27472,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO - add grouping class for the anterior end of the neural tube at all stages" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -31965,18 +27537,6 @@ "val" : "ZFA:0000121" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "subclass of mesoderm in ZFA." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0006258" }, { @@ -32023,15 +27583,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "should probably be merged with heart rudiment." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -32062,8 +27613,6 @@ "val" : "AAO:0010571" }, { "val" : "AEO:0000212" - }, { - "val" : "BTO:0006255" }, { "val" : "EHDAA2:0003439" }, { @@ -32086,15 +27635,6 @@ "val" : "ZFA:0001080" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Skeletogenic portion of somites.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "part_of somite in XAO" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -32149,12 +27689,6 @@ "val" : "ZFA:0000137" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The evagination from the neural tube of the developing embryo which develops the optic cup at its extremity; the stalk persists as the optic nerve. [TFD][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -32219,15 +27753,6 @@ "val" : "ZFA:0001194" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anterior most portion of the neural crest. Migrates in three highly conserved streams: mandibular, hyoid and branchial.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Neural crest that is part of the head.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -32272,9 +27797,6 @@ "val" : "ZFA:0000496" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -32337,15 +27859,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "mesenchymal" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -32446,8 +27959,6 @@ } ], "xrefs" : [ { "val" : "EMAPA:35187" - }, { - "val" : "HBA:9218" }, { "val" : "MA:0000820" }, { @@ -32515,8 +28026,6 @@ "xrefs" : [ "OBOL:automatic" ] } ], "xrefs" : [ { - "val" : "EMAPA:16098" - }, { "val" : "MA:0000577" } ], "basicPropertyValues" : [ { @@ -32566,12 +28075,6 @@ "val" : "UMLS:C0027757" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "FMA definition includes vasculature" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -32628,9 +28131,6 @@ "val" : "XAO:0000252" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0005713" }, { @@ -32671,9 +28171,6 @@ "val" : "ZFA:0000935" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -32719,9 +28216,6 @@ "val" : "ZFA:0000811" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -32763,12 +28257,6 @@ "val" : "ZFA:0007063" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Cranial neural crest that is part of the hindbrain.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -32801,9 +28289,6 @@ "val" : "VHOG:0001006" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -32861,9 +28346,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -32891,9 +28373,6 @@ "val" : "UMLS:C0927195" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "stromal" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -32968,9 +28447,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -32993,13 +28469,8 @@ "val" : "AEO:0000114" }, { "val" : "EHDAA2:0003114" - }, { - "val" : "FBbt:00007474" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33073,9 +28544,6 @@ "xrefs" : [ "NCBIBook:NBK10047" ] } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "As the cells adjacent to the lumen continue to divide, the migrating cells form a second layer around the original neural tube. This layer becomes progressively thicker as more cells are added to it from the germinal neuroepithelium. This new layer is called the mantle (or intermediate) zone, and the germinal epithelium is now called the ventricular zone (and, later, the ependyma)[NCBIBook:NBK10047]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33123,9 +28591,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The layer of undifferentiated, proliferating cells that line the neural tube lumen" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -33233,9 +28698,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "note the FMA class is more narrow though, and is more like eye + muscles + vasculature. The FMA also has FMA:72951 orbital part of eye" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in HP covers eyelid, eyebrow." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -33291,9 +28753,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "FMA has both conduit and conduit space. In EHDAA2 this is a surface feature" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -33315,9 +28774,6 @@ "xrefs" : [ "FBbt:00025998" ] } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Grouping term for query purposes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33338,9 +28794,6 @@ "xrefs" : [ "FBbt:00025990" ] } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Grouping term for query purposes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33399,9 +28852,6 @@ "val" : "ZFA:0000050" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -33445,9 +28895,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -33489,9 +28936,6 @@ "val" : "XAO:0004185" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33535,9 +28979,6 @@ "val" : "ZFA:0000360" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33640,17 +29081,8 @@ "val" : "galen:Skeleton" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000383" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "skeletal" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -33683,9 +29115,6 @@ "val" : "ZFA:0000115" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33778,9 +29207,6 @@ "val" : "ZFA:0001686" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Acellular anatomical structure composed of collagen, Descemet's membrane is secreted as a basement membrane of the corneal endothelium. Located between the stroma and the corneal endothelium, it is approximately 0.15 micrometer thick at 6 months post-fertilization.[ZFIN]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -33859,12 +29285,6 @@ "val" : "ZFA:0001684" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Acellular anatomical structure that is the zone of collagen fibers adjacent the basement membrane of the corneal epithelium.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33888,9 +29308,6 @@ "val" : "FMA:78499" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33924,14 +29341,10 @@ "val" : "CALOHA:TS-1297" }, { "val" : "EFO:0000791" - }, { - "val" : "EHDAA2:0000216" }, { "val" : "EHDAA:394" }, { "val" : "EMAPA:16104" - }, { - "val" : "EMAPA:16370" }, { "val" : "EV:0100017" }, { @@ -33966,14 +29379,8 @@ "val" : "ZFA:0000010" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph." - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -34199,8 +29606,6 @@ "val" : "BILA:0000060" }, { "val" : "BTO:0001403" - }, { - "val" : "FBbt:00005317" }, { "val" : "FMA:293108" }, { @@ -34223,9 +29628,6 @@ "val" : "Wikipedia:Trilaminar_blastocyst" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "We explicitly merge the NCITA terms here" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0007012" }, { @@ -34257,12 +29659,6 @@ "val" : "galen:SkeletalStructure" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34355,9 +29751,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider merging with 'endothelium'" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -34397,9 +29790,6 @@ "val" : "XAO:0000276" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34440,12 +29830,6 @@ "val" : "ZFA:0000091" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Notochord rudiment[ZFIN:ZDB-PUB-961014-576]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34464,9 +29848,6 @@ "pred" : "hasNarrowSynonym", "val" : "joint" } ], - "xrefs" : [ { - "val" : "FBbt:00005811" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -34502,14 +29883,9 @@ "xrefs" : [ "FMA:71131" ] } ], "xrefs" : [ { - "val" : "FBbt:00100315" - }, { "val" : "FMA:71131" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct." - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { @@ -34564,9 +29940,6 @@ "val" : "neuronames:1363" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34604,9 +29977,6 @@ "val" : "neuronames:1364" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34634,9 +30004,6 @@ "val" : "ZFA:0000133" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34661,12 +30028,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consder adding placodal ectoderm as a distinct class? Also place placodal ectoderm as develops_from ectoderm; need to check taxon-appropriateness" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "With the exception of the adenohypophysis, homologues of the nonneurogenic placodes (e.g. placodes giving rise to the teeth, hair follicles and lens), appear to be lacking in invertebrate chordates." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in GO, covers optic, otic, olfactory, mammary, hair, tooth, sebaceous - and also insect structures" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -34693,14 +30054,9 @@ "val" : "muscle element" } ], "xrefs" : [ { - "val" : "EMAPA:32715" - }, { "val" : "FMA:30316" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34746,15 +30102,10 @@ "val" : "AAO:0011000" }, { "val" : "CARO:0001000" - }, { - "val" : "FBbt:00007060" }, { "val" : "FMA:83115" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "we go with the FMA classification rather than the CARO one. FMA def: 'Anatomical cluster which has as direct parts cell parts from two or more cells.'" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34906,9 +30257,6 @@ "val" : "ZFA:0000113" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Mesoderm that will give rise, along with cranial neural crest cells, to connective tissue, bone and musculature in the head. (Source: BioGlossary, www.Biology-Text.com)[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34981,26 +30329,12 @@ "val" : "HBA:9512" }, { "val" : "MA:0000205" - }, { - "val" : "MESH:D054024" }, { "val" : "VHOG:0000456" }, { "val" : "Wikipedia:Myelencephalon" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002174", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7955" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000013", - "val" : "the terms metencephalon and myelencephalon are only meaningful in mammals and birds - Neuroanatomy of the Zebrafish Brain. Note that its not clear if this refers to the developing medulla oblongata - MA (adult) has two distinct classes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -35047,9 +30381,6 @@ "pred" : "hasExactSynonym", "val" : "light-sensitive tissue" } ], - "xrefs" : [ { - "val" : "FBbt:00004200" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -35070,9 +30401,6 @@ "val" : "lens" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000009", - "val" : "directing or focusing light onto light receptors" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -35100,8 +30428,6 @@ "val" : "CALOHA:TS-2122" }, { "val" : "EHDAA2:0003125" - }, { - "val" : "FBbt:00007006" }, { "val" : "FMA:292313" }, { @@ -35179,9 +30505,6 @@ "val" : "ZFA:0000064" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -35243,9 +30566,6 @@ "val" : "ZFA:0001071" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -35298,15 +30618,6 @@ "val" : "ZFA:0001679" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A vesicle formed from the lens pit of the embryo, developing into the crystalline lens. [TFD][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "the lens of zebrafish (and other teleosts) forms from delamination of cells from the lens placode; thus, there is no formation of a hollow lens vesicle, in contrast to the situation in mammals and birds (Glass and Dahm, 2004) [PMID:16496288] The lens of the zebrafish forms by delamination of lens placodal cells and not through invagination. This results in a solid spherical mass as opposed to a hollow lens vesicle. Detachment of the solid lens vesicle of zebrafish at 24b26 hpf is accomplished in part by apoptosis, similar to mammals" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -35350,8 +30661,6 @@ "xrefs" : [ "EMAPA:16208" ] } ], "xrefs" : [ { - "val" : "BTO:0006179" - }, { "val" : "EHDAA2:0001512" }, { "val" : "EHDAA:424" @@ -35394,9 +30703,6 @@ "val" : "VHOG:0001477" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A depression in the front of the vitreous body, lodging the lens. [adapted_from_the_definition_of_the_hyaloid_fossa]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -35467,9 +30773,6 @@ "val" : "Wikipedia:Basement_membrane" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell." - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_80999" }, { @@ -35572,8 +30875,6 @@ "val" : "AAO:0000963" }, { "val" : "EMAPA:17214" - }, { - "val" : "EMAPA:18043" }, { "val" : "MA:0000308" }, { @@ -35592,9 +30893,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -35654,9 +30952,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "neurofibrous" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -35697,9 +30992,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7776" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "http://www1.pbrc.hawaii.edu/~danh/MyelinEvolution/evolution.html, http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=6134604, Wikipedia:Myelin#Invertebrate_myelin" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -35789,9 +31081,6 @@ "val" : "ZFA:0000146" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -35916,9 +31205,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO - check ordering; awaiting confirmation from JB" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -36017,9 +31303,6 @@ "val" : "MA:0001911" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000009", - "val" : "ocular refraction" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -36087,18 +31370,6 @@ "val" : "MIAA:0000049" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "currently this is an extremely generic class, encompassing both protostomes and deuterostomes." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0006012", - "val" : "2023-04-20" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "branchial" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "pharyngeal" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -36286,9 +31557,6 @@ "val" : "Wikipedia:Squamous_epithelium" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -36459,9 +31727,6 @@ "val" : "UMLS:C1514442" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -36491,16 +31756,11 @@ "xrefs" : [ "FBbt:00003154" ] } ], "xrefs" : [ { - "val" : "SPD:0000130" - }, { "val" : "TADS:0000147" }, { "val" : "http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -36528,9 +31788,6 @@ "val" : "ZFA:0000131" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -36623,9 +31880,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO - unify naming conventions" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The embryonic rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. Rhombomeres Rh7-Rh4 form the myelencephalon that will give the medulla oblongata. Rhombomeres Rh3-Rh1 form the metencephalon that will form the pons and the cerebellum[NPX:PDR]." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -36721,9 +31975,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider merging" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Region of the gastrula which gives rise to the neural plate.[TAO]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -36925,9 +32176,6 @@ "val" : "SCTID:280667001" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "MA does treat internal/external limiting membranes as layers - these are classified as laminae. We do not follow this convention. However, we do following MA is grouping these terms together" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -37022,8 +32270,6 @@ "val" : "EFO:0001649" }, { "val" : "EHDAA2:0003170" - }, { - "val" : "FBbt:00005426" }, { "val" : "Wikipedia:Anlage_(biology)" } ], @@ -37092,12 +32338,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -37418,8 +32658,6 @@ } ], "xrefs" : [ { "val" : "CARO:0010000" - }, { - "val" : "FBbt:00100313" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", @@ -37513,12 +32751,6 @@ "val" : "Wikipedia:Globe_(human_eye)" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "See notes for camera-type eye" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000202", - "val" : "http://purl.obolibrary.org/obo/FMA_264089" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -37599,9 +32831,6 @@ "val" : "ZFA:0001678" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Multi-tissue structure that consists of the structures that develop into the retina and lens.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -37617,9 +32846,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Grouping term for query purposes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -37635,9 +32861,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Grouping term for query purposes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -37794,9 +33017,6 @@ "val" : "VSAO:0000042" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -37887,8 +33107,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "xrefs" : [ { - "val" : "FBbt:00007330" - }, { "val" : "FMA:67509" }, { "val" : "SCTID:91690000" @@ -37931,9 +33149,6 @@ "val" : "FMA:49150" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Muscles within the eye (bulbus oculi).[AAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -38195,9 +33410,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_147099" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "coelomic" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -38367,15 +33579,39 @@ "val" : "AEO:0000103" }, { "val" : "BTO:0001489" - }, { - "val" : "EMAPA:36031" }, { "val" : "FMA:231424" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]." + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0014387", + "lbl" : "mesenchyme derived from neural crest", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Mesenchyme that develops_from the neural crest[Automatically generated definition].", + "xrefs" : [ "OBOL:automatic", "https://github.com/obophenotype/uberon/issues/248" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "mesenchyme from neural crest" + }, { + "pred" : "hasExactSynonym", + "val" : "neural crest derived mesenchyme" }, { + "pred" : "hasExactSynonym", + "val" : "neural crest mesenchyme" + } ], + "xrefs" : [ { + "val" : "EMAPA:32735" + }, { + "val" : "FMA:293883" + } ], + "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -38448,8 +33684,6 @@ }, "xrefs" : [ { "val" : "AEO:0000093" - }, { - "val" : "FBbt:00007278" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -38467,9 +33701,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This class is primarily to implement taxon constraints. It may be removed in the future." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -38500,9 +33731,6 @@ "pred" : "hasRelatedSynonym", "val" : "cardiac structure" } ], - "xrefs" : [ { - "val" : "SPD:0000130" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -38895,8 +34123,6 @@ "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], "xrefs" : [ { "val" : "CARO:0020000" - }, { - "val" : "FBbt:00007276" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", @@ -39427,120 +34653,6 @@ "val" : "uberon" } ] } - }, { - "id" : "http://purl.org/dc/elements/1.1/creator", - "lbl" : "creator", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/elements/1.1/creator" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-creator" - } ] - } - }, { - "id" : "http://purl.org/dc/elements/1.1/description", - "lbl" : "description", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/elements/1.1/description" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-description" - } ] - } - }, { - "id" : "http://purl.org/dc/elements/1.1/title", - "lbl" : "title", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/elements/1.1/title" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-title" - } ] - } - }, { - "id" : "http://purl.org/dc/terms/contributor", - "lbl" : "contributor", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/terms/contributor" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-contributor" - } ] - } - }, { - "id" : "http://purl.org/dc/terms/date", - "lbl" : "date", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/terms/date" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dcterms-date" - } ] - } - }, { - "id" : "http://purl.org/dc/terms/license", - "lbl" : "license", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/terms/license" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dcterms-license" - } ] - } }, { "id" : "http://www.geneontology.org/formats/oboInOwl#SubsetProperty", "lbl" : "subset_property", @@ -39574,9 +34686,6 @@ "val" : "An alternative label for a class or property which has a more general meaning than the preferred name/primary label." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/18" }, { @@ -39597,9 +34706,6 @@ "val" : "An alternative label for a class or property which has the exact same meaning than the preferred name/primary label." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/20" }, { @@ -39616,9 +34722,6 @@ "val" : "An alternative label for a class or property which has a more specific meaning than the preferred name/primary label." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/19" }, { @@ -39639,9 +34742,6 @@ "val" : "An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/21" }, { @@ -39674,35 +34774,10 @@ "val" : "http://www.w3.org/2000/01/rdf-schema#seeAlso" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "seeAlso" } ] } - }, { - "id" : "http://xmlns.com/foaf/0.1/depiction", - "lbl" : "depiction", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://xmlns.com/foaf/0.1/depiction" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "depiction" - } ] - } } ], "edges" : [ { "sub" : "http://purl.obolibrary.org/obo/BFO_0000004", @@ -41424,10 +36499,20 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0010009", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000287" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0010009", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0009004" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0010009", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000019" + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000966", + "meta" : { + "basicPropertyValues" : [ { + "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", + "val" : "https://github.com/obophenotype/cell-ontology/issues/2245" + } ] + } }, { "sub" : "http://purl.obolibrary.org/obo/CL_0010017", "pred" : "is_a", @@ -44198,20 +39283,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000019", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000966" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000019", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000033" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000019", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0003072", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "definitional" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0003072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000019", "pred" : "http://purl.obolibrary.org/obo/RO_0002492", @@ -44624,10 +39699,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000153", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000475" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000153", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000096", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000154" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000153", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -44643,17 +39714,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0004921", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts" - } ] - } - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0001106", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0001555" + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004921" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -44755,13 +39816,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000463", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000468", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "this relationship may be too strong and may be weakened in future" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000468" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000463", "pred" : "http://purl.obolibrary.org/obo/RO_0000086", @@ -44991,13 +40046,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000926", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000923", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "sometimes not considered primary" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000923" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000926", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -45028,10 +40077,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000930", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000941", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000941", "pred" : "is_a", @@ -45132,10 +40177,6 @@ "val" : "FMA" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000955", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000123", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000468" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000955", "pred" : "http://purl.obolibrary.org/obo/RO_0002433", @@ -45239,13 +40280,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000964", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0004348", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "definitional" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004348" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000964", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -45258,6 +40293,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000964", "pred" : "http://purl.obolibrary.org/obo/RO_0002433", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001801" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0000965", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000965", "pred" : "is_a", @@ -45721,6 +40760,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001711", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000064" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001711", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001711", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -45761,6 +40804,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001766", "pred" : "http://purl.obolibrary.org/obo/RO_0002433", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001801" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001768", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001768", "pred" : "is_a", @@ -45771,6 +40818,10 @@ "val" : "FMA" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001768", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010314" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001768", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -45817,6 +40868,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001769", "pred" : "http://purl.obolibrary.org/obo/RO_0002433", "obj" : "http://purl.obolibrary.org/obo/UBERON_0011892" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001772", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010313" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001772", "pred" : "is_a", @@ -45843,6 +40898,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001773", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000064" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001773", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010313" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001773", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -45877,22 +40936,6 @@ "val" : "ISBN:0781772214" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0001773", - "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0007213", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#inferred_by", - "val" : "cjm" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "ISBN:0781772214" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "Wikipedia" - } ] - } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001773", "pred" : "http://purl.obolibrary.org/obo/RO_0002433", @@ -45979,6 +41022,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001777", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0003891" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001777", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010313" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001777", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -45986,19 +41033,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001777", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0007213", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#inferred_by", - "val" : "cjm" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "ISBN:0781772214" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "Wikipedia" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0007213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001777", "pred" : "http://purl.obolibrary.org/obo/RO_0002220", @@ -46055,6 +41090,10 @@ "val" : "Wikipedia" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001781", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001781", "pred" : "is_a", @@ -46075,10 +41114,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001782", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001781" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0001782", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0010371" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001782", "pred" : "is_a", @@ -46152,16 +41187,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001789", "pred" : "http://purl.obolibrary.org/obo/RO_0002131", - "obj" : "http://purl.obolibrary.org/obo/CL_0000287", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "soma" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "ZFA" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/CL_0000287" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001789", "pred" : "http://purl.obolibrary.org/obo/RO_0002220", @@ -46286,6 +41312,10 @@ "val" : "MA" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001794", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010314" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001794", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -46345,19 +41375,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001796", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0001766", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "FMA def states A and P" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "located_in in EHDAA2" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "VHOG" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0001766" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001796", "pred" : "http://purl.obolibrary.org/obo/RO_0002433", @@ -46382,6 +41400,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001798", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0003566" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001798", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001798", "pred" : "is_a", @@ -46399,16 +41421,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001798", "pred" : "http://purl.obolibrary.org/obo/RO_0002254", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0002346", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "neural ectoderm of optic cup" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "ISBN:0781772214" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0002346" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001798", "pred" : "http://purl.obolibrary.org/obo/RO_0002473", @@ -46431,22 +41444,16 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000063" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001801", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0010230", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "FMA" - } ] - } + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001801", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000123", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0010230", "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "cjm" + "val" : "FMA" } ] } }, { @@ -46459,22 +41466,16 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000063" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001802", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0010230", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "FMA" - } ] - } + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001802", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000122", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0010230", "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "cjm" + "val" : "FMA" } ] } }, { @@ -46491,6 +41492,10 @@ "val" : "FMA" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001811", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001811", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -46537,10 +41542,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001890", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0002616" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0001890", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001890", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -46552,21 +41553,11 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001890", "pred" : "http://purl.obolibrary.org/obo/RO_0002495", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0006240", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "definitional" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0006240" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001891", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0002616" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0001891", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001891", "pred" : "is_a", @@ -46574,13 +41565,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001891", "pred" : "http://purl.obolibrary.org/obo/RO_0002254", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0003849", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "definitional" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0003849" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001891", "pred" : "http://purl.obolibrary.org/obo/RO_0002433", @@ -46599,10 +41584,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001894", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0002616" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0001894", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001894", "pred" : "is_a", @@ -46614,13 +41595,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001894", "pred" : "http://purl.obolibrary.org/obo/RO_0002254", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0003851", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "definitional" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0003851" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001894", "pred" : "http://purl.obolibrary.org/obo/RO_0002433", @@ -46628,17 +41603,15 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001894", "pred" : "http://purl.obolibrary.org/obo/RO_0002495", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0006222", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "definitional" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0006222" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001896", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000064" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001896", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001896", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -46737,6 +41710,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000055" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -46795,10 +41772,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001985", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0010313" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0001985", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0010371" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001985", "pred" : "is_a", @@ -46852,23 +41825,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002028", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0002616" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0002028", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002028", "pred" : "http://purl.obolibrary.org/obo/RO_0002131", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0002298", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "modified-source-relation" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "ABA" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0002298" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002028", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -47020,13 +41980,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002204", "pred" : "http://purl.obolibrary.org/obo/RO_0002254", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000926", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "check ctenophore" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000926" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002204", "pred" : "http://purl.obolibrary.org/obo/RO_0002492", @@ -47080,23 +42034,11 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002240", "pred" : "http://purl.obolibrary.org/obo/RO_0002254", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0003853", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "definitional" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0003853" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002240", "pred" : "http://purl.obolibrary.org/obo/RO_0002495", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0006241", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "definitional" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0006241" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002298", "pred" : "is_a", @@ -47132,13 +42074,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002323", "pred" : "http://purl.obolibrary.org/obo/RO_0002494", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0003886", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "definitional" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0003886" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002323", "pred" : "http://purl.obolibrary.org/obo/RO_0002572", @@ -47163,6 +42099,10 @@ "val" : "VSAO" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", "pred" : "is_a", @@ -47171,14 +42111,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0011137" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000098", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0001555" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000102", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0001049" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -47255,6 +42187,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010314" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "is_a", @@ -47275,16 +42211,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_89593", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "ISBN:0073040584" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_89593" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -47308,13 +42235,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "http://purl.obolibrary.org/obo/RO_0002473", - "obj" : "http://purl.obolibrary.org/obo/CL_0000333", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/CL_0000333" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "http://purl.obolibrary.org/obo/RO_0002488", @@ -47394,13 +42315,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002390", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0003061", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "definitional" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0003061" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002506", "pred" : "is_a", @@ -47486,6 +42401,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002616", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000073" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0002616", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002616", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -47501,16 +42420,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003052", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0007651", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#inconsistent_with", - "val" : "ZFA" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/106/" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0007651" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003052", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -47539,6 +42449,10 @@ "val" : "ZFA" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0003056", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003056", "pred" : "is_a", @@ -47547,10 +42461,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0003056", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0003075" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0003056", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000096", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0009615" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003057", "pred" : "is_a", @@ -47559,10 +42469,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0003057", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0003075" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0003057", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000099", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0009615" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003059", "pred" : "is_a", @@ -47635,6 +42541,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0003071", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0006598" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0003071", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010371" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003071", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -47696,6 +42606,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0003073", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0006598" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0003073", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010312" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003073", "pred" : "is_a", @@ -47796,10 +42710,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0003077", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0015212" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0003077", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000922" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003077", "pred" : "http://purl.obolibrary.org/obo/RO_0002488", @@ -47975,10 +42885,18 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0003098", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", "obj" : "http://purl.obolibrary.org/obo/UBERON_0003072" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0003099", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003099", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0005291" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0003099", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010314" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003099", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -48007,6 +42925,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0003104", "pred" : "http://purl.obolibrary.org/obo/RO_0002473", "obj" : "http://purl.obolibrary.org/obo/CL_0008019" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0003314", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0007213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003314", "pred" : "is_a", @@ -48029,6 +42951,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0003386", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001135" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0003386", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003386", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -48195,10 +43121,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0003902", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001781" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0003902", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003902", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -48237,6 +43159,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004022", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0005291" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004022", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010371" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004022", "pred" : "is_a", @@ -48299,6 +43225,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004061", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0005291" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004061", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010371" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004061", "pred" : "is_a", @@ -48316,16 +43246,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004061", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0004022", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "by division" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "NCBIBook:NBK10047" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004022" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004061", "pred" : "http://purl.obolibrary.org/obo/RO_0002220", @@ -48334,6 +43255,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004061", "pred" : "http://purl.obolibrary.org/obo/RO_0002220", "obj" : "http://purl.obolibrary.org/obo/UBERON_0004062" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004062", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004062", "pred" : "is_a", @@ -48345,13 +43270,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004062", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0004061", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "forms from axons" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004061" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004062", "pred" : "http://purl.obolibrary.org/obo/RO_0002220", @@ -48446,6 +43365,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004140", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0002050" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004140", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004140", "pred" : "is_a", @@ -48500,6 +43423,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004151", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000064" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004151", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004151", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -48508,6 +43435,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004277", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001630" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004277", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004277", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -48554,6 +43485,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004367", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0005769" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004367", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010313" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004367", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -48584,6 +43519,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004370", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0005769" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004370", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010313" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004370", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -48676,6 +43615,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004732", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001016" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004733", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004733", "pred" : "is_a", @@ -48823,14 +43766,14 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005062", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0015212" + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010371" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005062", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0005061" + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0015212" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005062", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000126", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0005061" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005068", @@ -48956,10 +43899,6 @@ "val" : "EHDAA2" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0005290", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005290", "pred" : "is_a", @@ -48967,13 +43906,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005290", "pred" : "http://purl.obolibrary.org/obo/RO_0002495", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0010096", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "definitional" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010096" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005291", "pred" : "is_a", @@ -49022,6 +43955,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0005424", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0006598" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0005424", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010312" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005424", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -49034,6 +43971,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0005425", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0006598" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0005425", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010312" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005425", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -49046,6 +43987,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0005426", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000479" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0005426", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005426", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -49070,6 +44015,10 @@ "val" : "Obol" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0005427", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010312" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005427", "pred" : "is_a", @@ -49206,6 +44155,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0005906", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/UBERON_0002553" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0005908", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005908", "pred" : "is_a", @@ -49239,13 +44192,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005908", "pred" : "http://purl.obolibrary.org/obo/RO_0002220", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0001801", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#modified_from", - "val" : "MA" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0001801" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005944", "pred" : "is_a", @@ -49408,6 +44355,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0006311", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000063" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0006311", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006311", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -49547,13 +44498,11 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006984", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0010199", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "via morphological boundary in CARO" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010199" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0007005", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007005", "pred" : "is_a", @@ -49617,13 +44566,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007100", "pred" : "http://purl.obolibrary.org/obo/RO_0002215", - "obj" : "http://purl.obolibrary.org/obo/GO_0008015", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "GO uses blood circulation generically to include the haemolymphatic fluid of arthropods" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/GO_0008015" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007135", "pred" : "is_a", @@ -49642,6 +44585,10 @@ "val" : "ZFA" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0007213", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0014387" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007213", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -49703,16 +44650,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007282", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0009618", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#consistent_with", - "val" : "https://github.com/obophenotype/uberon/wiki/The-neural-crest" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "EDHAA2" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0009618" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007282", "pred" : "http://purl.obolibrary.org/obo/RO_0002387", @@ -49993,16 +44931,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0009615", "pred" : "http://purl.obolibrary.org/obo/RO_0002495", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0007281", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "https://github.com/obophenotype/uberon/issues/438" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "Bgee:AN" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0007281" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0009616", "pred" : "is_a", @@ -50053,6 +44982,10 @@ "val" : "EHDAA2" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0009881", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0009881", "pred" : "is_a", @@ -50078,7 +45011,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0009920", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0005253" + "obj" : "http://purl.obolibrary.org/obo/UBERON_0007213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0009920", "pred" : "is_a", @@ -50137,6 +45070,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0010230", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000020" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0010230", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0010230", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -50181,6 +45118,10 @@ "val" : "ZFA" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0010286", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0010286", "pred" : "is_a", @@ -50202,13 +45143,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0010312", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0003071", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "definitional" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0003071" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0010312", "pred" : "http://purl.obolibrary.org/obo/RO_0002254", @@ -50263,16 +45198,20 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000063" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0010409", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000019" + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0010409", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000108", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0022288" + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000019" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0010427", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000481" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0010427", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0010427", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -50341,6 +45280,10 @@ "val" : "cjm" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0011215", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0011215", "pred" : "is_a", @@ -50363,6 +45306,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0011216", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000467" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0011222", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0011222", "pred" : "is_a", @@ -50451,6 +45398,10 @@ "val" : "ZFA" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0011892", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0011892", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -50503,6 +45454,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0012430", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PR_000050567" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0012430", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0012430", "pred" : "is_a", @@ -50593,6 +45548,14 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0013702", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0013701" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0014387", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0003104" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0014387", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010313" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0014477", "pred" : "is_a", @@ -50625,10 +45588,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0015212", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0015212", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000465" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0015212", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -50663,6 +45622,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0015808", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0007625" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0015808", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010371" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0015808", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -50727,6 +45690,14 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0019207", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000481" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0019207", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0019207", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010314" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0019207", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -50815,10 +45786,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0034713", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0015212" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0034713", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000033" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0034713", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -52071,10 +47038,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000057" - }, { - "sub" : "http://purl.obolibrary.org/obo/uberon/core#anteriorly_connected_to", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BSPO_0000099" }, { "sub" : "http://purl.obolibrary.org/obo/uberon/core#anteriorly_connected_to", "pred" : "subPropertyOf", @@ -52083,10 +47046,6 @@ "sub" : "http://purl.obolibrary.org/obo/uberon/core#anteriorly_connected_to", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/uberon/core#transitively_anteriorly_connected_to" - }, { - "sub" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BSPO_0000100" }, { "sub" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", "pred" : "subPropertyOf", @@ -52103,18 +47062,10 @@ "sub" : "http://purl.obolibrary.org/obo/uberon/core#layer_part_of", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000050" - }, { - "sub" : "http://purl.obolibrary.org/obo/uberon/core#posteriorly_connected_to", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BSPO_0000096" }, { "sub" : "http://purl.obolibrary.org/obo/uberon/core#posteriorly_connected_to", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002170" - }, { - "sub" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BSPO_0000097" }, { "sub" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to", "pred" : "subPropertyOf", @@ -52331,10 +47282,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012001", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012005" - }, { - "sub" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", - "pred" : "inverseOf", - "obj" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to" } ], "logicalDefinitionAxioms" : [ { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000005", @@ -53886,13 +48833,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002082", "fillerId" : "http://purl.obolibrary.org/obo/GO_0040016" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0000165", - "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0004921" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BSPO_0001106", - "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0001555" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0000179", "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000463" ], @@ -54806,6 +49746,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0000086", "fillerId" : "http://purl.obolibrary.org/obo/PATO_0000608" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0014387", + "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0003104" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002202", + "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0002342" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0014903", "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001048" ], @@ -54813,13 +49760,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002387", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0002049" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0015212", - "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0000465" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0015808", "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000483" ], @@ -55173,8 +50113,8 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002551", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061", "http://purl.obolibrary.org/obo/UBERON_0000475" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465", "http://purl.obolibrary.org/obo/UBERON_0010912" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002566", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], @@ -55235,10 +50175,6 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0019000", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/uberon/core#channel_for", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0004111" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000463" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] @@ -55270,21 +50206,12 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002287", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002210" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002329", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002215" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002496" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002497" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002479", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/BFO_0000066" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/RO_0000057" ] @@ -55303,24 +50230,12 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000066", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000066", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002314", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0000052", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0001025", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0001025", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002005", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002005", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002005", "http://purl.obolibrary.org/obo/RO_0002380" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002100", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002100", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/uberon/core#extends_fibers_into", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002100", "http://purl.obolibrary.org/obo/RO_0013001" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002102", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002102", "http://purl.obolibrary.org/obo/BFO_0000050" ] @@ -55336,24 +50251,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002131", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002131", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002134", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002134", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002150", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002170", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002176", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002178", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002202", "http://purl.obolibrary.org/obo/RO_0002162" ] @@ -55390,9 +50290,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0019002", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002213", "http://purl.obolibrary.org/obo/RO_0019002" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002216", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002215", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002215", "http://purl.obolibrary.org/obo/RO_0002162" ] @@ -55441,9 +50338,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002254", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002256", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002258", "http://purl.obolibrary.org/obo/RO_0002496" ] @@ -55465,9 +50359,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004031", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/BFO_0000051" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002432", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/BFO_0000066" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002327", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002017" ] @@ -55531,15 +50422,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002339", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002339", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002177", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002371", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002371", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002387", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002407", "http://purl.obolibrary.org/obo/RO_0002629" ] @@ -55552,15 +50434,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002488", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002488", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002488", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002492", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002492", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002492", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002496", "http://purl.obolibrary.org/obo/BFO_0000050" ] @@ -55579,9 +50455,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002497", "http://purl.obolibrary.org/obo/RO_0002082" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/uberon/core#indirectly_supplies", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002569", "http://purl.obolibrary.org/obo/RO_0002178" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/uberon/core#indirectly_supplies", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002569", "http://purl.obolibrary.org/obo/uberon/core#indirectly_supplies" ] @@ -55600,12 +50473,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002630", "http://purl.obolibrary.org/obo/RO_0002630" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0003000", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0003001", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0013001", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0013001", "http://purl.obolibrary.org/obo/BFO_0000050" ] diff --git a/subsets/eye_upper_slim.obo b/subsets/eye_upper_slim.obo index 998c256f5..d5390cbe7 100644 --- a/subsets/eye_upper_slim.obo +++ b/subsets/eye_upper_slim.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: cl/releases/2024-02-13/subsets/eye_upper_slim.owl +data-version: cl/releases/2024-04-05/subsets/eye_upper_slim.owl subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -88,7 +88,7 @@ synonymtypedef: synonym "" synonymtypedef: SYSTEMATIC "" synonymtypedef: systematic_synonym "" ontology: cl/subsets/eye_upper_slim -property_value: owl:versionInfo "2024-02-13" xsd:string +property_value: owl:versionInfo "2024-04-05" xsd:string [Term] id: BFO:0000002 @@ -159,16 +159,17 @@ is_a: UBERON:0000061 ! anatomical structure disjoint_from: GO:0031012 ! extracellular matrix disjoint_from: GO:0032991 ! protein-containing complex disjoint_from: GO:0043226 ! organelle -relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms +relationship: RO:0002160 NCBITaxon:131567 ! only in taxon cellular organisms [Term] id: CL:0000005 -name: fibroblast neural crest derived -def: "Any fibroblast that is deriived from the neural crest." [https://orcid.org/0000-0001-5208-3432] +name: neural crest derived fibroblast +def: "Any fibroblast that is derived from the neural crest." [https://orcid.org/0000-0001-5208-3432] +synonym: "fibroblast neural crest derived" EXACT [] is_a: CL:0000057 ! fibroblast intersection_of: CL:0000057 ! fibroblast -intersection_of: develops_from CL:0000333 ! migratory neural crest cell -relationship: develops_from CL:0000008 ! migratory cranial neural crest cell +intersection_of: RO:0002202 CL:0000333 ! develops from migratory neural crest cell +relationship: RO:0002202 CL:0000008 ! develops from migratory cranial neural crest cell [Term] id: CL:0000006 @@ -198,7 +199,7 @@ id: CL:0000030 name: glioblast subset: cellxgene_subset is_a: CL:0000055 ! non-terminally differentiated cell -relationship: develops_from CL:0000133 ! neurectodermal cell +relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell [Term] id: CL:0000031 @@ -210,7 +211,7 @@ xref: BTO:0000930 xref: FMA:70563 is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0000255 ! eukaryotic cell -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata [Term] id: CL:0000034 @@ -227,8 +228,8 @@ is_a: CL:0011115 ! precursor cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0017145 ! stem cell division relationship: capable_of GO:0017145 ! stem cell division -relationship: in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000037 @@ -278,8 +279,8 @@ relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surfac relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -relationship: develops_from CL:0000566 ! angioblastic mesenchymal cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000566 ! develops from angioblastic mesenchymal cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000038 @@ -296,7 +297,7 @@ synonym: "erythroid stem cell" RELATED [] xref: BTO:0004911 is_a: CL:0000764 ! erythroid lineage cell is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor cell -relationship: develops_from CL:0000050 ! megakaryocyte-erythroid progenitor cell +relationship: RO:0002202 CL:0000050 ! develops from megakaryocyte-erythroid progenitor cell [Term] id: CL:0000048 @@ -331,7 +332,7 @@ synonym: "pluripotent stem cell (bone marrow)" RELATED [ISBN:0878932437] xref: BTO:0004730 is_a: CL:0002032 {is_inferred="true"} ! hematopoietic oligopotent progenitor cell disjoint_from: CL:0000050 ! megakaryocyte-erythroid progenitor cell -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000050 @@ -355,7 +356,7 @@ intersection_of: capable_of GO:0030218 ! erythrocyte differentiation intersection_of: capable_of GO:0030219 ! megakaryocyte differentiation relationship: capable_of GO:0030218 ! erythrocyte differentiation relationship: capable_of GO:0030219 ! megakaryocyte differentiation -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000052 @@ -402,8 +403,8 @@ xref: FMA:63877 xref: NCIT:C12482 xref: VHOG:0001482 is_a: CL:0002320 ! connective tissue cell -relationship: develops_from CL:0000134 ! mesenchymal stem cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000066 @@ -421,8 +422,8 @@ xref: FMA:66768 xref: WBbt:0003672 is_a: CL:0000000 ! cell relationship: part_of UBERON:0000483 ! epithelium -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000071 @@ -435,9 +436,9 @@ is_a: CL:0000076 {is_inferred="true"} ! squamous epithelial cell is_a: CL:0002139 ! endothelial cell of vascular tree intersection_of: CL:0000076 ! squamous epithelial cell intersection_of: part_of UBERON:0004638 ! blood vessel endothelium -relationship: develops_from CL:0002546 ! embryonic blood vessel endothelial progenitor cell relationship: part_of UBERON:0004638 ! blood vessel endothelium -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0002546 ! develops from embryonic blood vessel endothelial progenitor cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000075 @@ -446,7 +447,7 @@ def: "A columnar/cuboidal epithelial cell is a cell usually found in a two dimen subset: cellxgene_subset subset: human_reference_atlas is_a: CL:0000066 ! epithelial cell -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000076 @@ -466,7 +467,7 @@ xref: FMA:66773 is_a: CL:0000076 ! squamous epithelial cell is_a: CL:0000213 ! lining cell is_a: CL:0002078 ! meso-epithelial cell -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000081 @@ -486,7 +487,7 @@ id: CL:0000095 name: neuron associated cell subset: cellxgene_subset is_a: CL:0002319 ! neural cell -relationship: develops_from CL:0000133 ! neurectodermal cell +relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell [Term] id: CL:0000099 @@ -499,7 +500,7 @@ xref: FBbt:00005125 xref: FMA:67313 xref: WBbt:0005113 is_a: CL:0000540 ! neuron -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000101 @@ -540,14 +541,14 @@ xref: CALOHA:TS-0278 xref: FMA:66772 is_a: CL:0000213 ! lining cell is_a: CL:0002078 ! meso-epithelial cell -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000117 name: CNS neuron (sensu Vertebrata) is_a: CL:0000540 ! neuron -relationship: develops_from CL:0000031 ! neuroblast (sensu Vertebrata) relationship: part_of UBERON:0001017 ! central nervous system +relationship: RO:0002202 CL:0000031 ! develops from neuroblast (sensu Vertebrata) [Term] id: CL:0000123 @@ -555,8 +556,8 @@ name: neuron associated cell (sensu Vertebrata) subset: cellxgene_subset is_a: CL:0000095 ! neuron associated cell is_a: CL:0000255 ! eukaryotic cell -relationship: develops_from CL:0000333 ! migratory neural crest cell -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell [Term] id: CL:0000125 @@ -584,7 +585,7 @@ xref: BTO:0000771 xref: CALOHA:TS-2027 xref: FMA:54538 is_a: CL:0000125 ! glial cell -relationship: develops_from CL:0000339 ! glioblast (sensu Vertebrata) +relationship: RO:0002202 CL:0000339 ! develops from glioblast (sensu Vertebrata) [Term] id: CL:0000127 @@ -598,7 +599,7 @@ xref: BTO:0000099 xref: CALOHA:TS-0060 xref: FMA:54537 is_a: CL:0000126 ! macroglial cell -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000132 @@ -611,9 +612,9 @@ xref: CALOHA:TS-0172 xref: FMA:70614 is_a: CL:0000115 ! endothelial cell is_a: CL:0000710 ! neurecto-epithelial cell -relationship: develops_from CL:0000008 ! migratory cranial neural crest cell relationship: part_of UBERON:0001985 ! corneal endothelium -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000008 ! develops from migratory cranial neural crest cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000133 @@ -671,11 +672,11 @@ xref: MESH:D008544 xref: VHOG:0001679 is_a: CL:0000147 ! pigment cell intersection_of: CL:0000147 ! pigment cell -intersection_of: develops_from CL:0000541 ! melanoblast intersection_of: has_part GO:0042470 ! melanosome -relationship: develops_from CL:0000541 ! melanoblast +intersection_of: RO:0002202 CL:0000541 ! develops from melanoblast relationship: has_part GO:0042470 ! melanosome -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000541 ! develops from melanoblast +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000149 @@ -717,8 +718,8 @@ xref: FMA:67328 xref: WBbt:0003675 is_a: CL:0000183 ! contractile cell is_a: CL:0000393 ! electrically responsive cell -relationship: develops_from CL:0000056 ! myoblast -property_value: depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI +relationship: RO:0002202 CL:0000056 ! develops from myoblast +property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI [Term] id: CL:0000192 @@ -736,8 +737,8 @@ xref: CALOHA:TS-2159 xref: FMA:14072 is_a: CL:0008000 ! non-striated muscle cell is_a: CL:0008007 ! visceral muscle cell -relationship: develops_from CL:0000514 ! smooth muscle myoblast -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000514 ! develops from smooth muscle myoblast +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000197 @@ -764,7 +765,7 @@ is_a: CL:0000006 {is_inferred="true"} ! neuronal receptor cell intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0050962 ! detection of light stimulus involved in sensory perception relationship: capable_of GO:0050962 ! detection of light stimulus involved in sensory perception -property_value: depiction "https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg" xsd:anyURI [Term] id: CL:0000211 @@ -847,8 +848,8 @@ intersection_of: CL:4030046 PR:000001945 ! lacks_plasma_membrane_part transferri relationship: bearer_of PATO:0002039 ! biconcave relationship: CL:4030045 GO:0005840 ! lacks_part ribosome relationship: CL:4030046 PR:000001945 ! lacks_plasma_membrane_part transferrin receptor protein 1 -relationship: develops_from CL:0000558 ! reticulocyte -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000558 ! develops from reticulocyte +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000255 @@ -857,8 +858,8 @@ subset: cellxgene_subset xref: MESH:D005057 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell -intersection_of: only_in_taxon NCBITaxon:2759 ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +intersection_of: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota [Term] id: CL:0000287 @@ -870,7 +871,7 @@ is_a: CL:0000210 ! photoreceptor cell intersection_of: CL:0000210 ! photoreceptor cell intersection_of: part_of UBERON:0000970 ! eye relationship: part_of UBERON:0000970 ! eye -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000293 @@ -908,7 +909,7 @@ xref: FMA:86667 is_a: CL:0000219 ! motile cell is_a: CL:0011012 ! neural crest cell is_a: CL:0011026 ! progenitor cell -relationship: develops_from CL:0007004 ! premigratory neural crest cell +relationship: RO:0002202 CL:0007004 ! develops from premigratory neural crest cell [Term] id: CL:0000335 @@ -932,7 +933,7 @@ name: pigment cell (sensu Vertebrata) def: "Any animal cell containing pigment granules." [GOC:tfm, ISBN:0721662544] is_a: CL:0000147 ! pigment cell is_a: CL:0000255 ! eukaryotic cell -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata [Term] id: CL:0000347 @@ -942,8 +943,8 @@ subset: eye_upper_slim is_a: CL:0000293 ! structural cell intersection_of: CL:0000293 ! structural cell intersection_of: part_of UBERON:0001773 ! sclera -relationship: develops_from CL:0000008 ! migratory cranial neural crest cell relationship: part_of UBERON:0001773 ! sclera +relationship: RO:0002202 CL:0000008 ! develops from migratory cranial neural crest cell [Term] id: CL:0000348 @@ -953,8 +954,8 @@ subset: eye_upper_slim is_a: CL:0000293 ! structural cell intersection_of: CL:0000293 ! structural cell intersection_of: part_of UBERON:0001776 ! optic choroid -relationship: develops_from CL:0000008 ! migratory cranial neural crest cell relationship: part_of UBERON:0001776 ! optic choroid +relationship: RO:0002202 CL:0000008 ! develops from migratory cranial neural crest cell [Term] id: CL:0000352 @@ -974,8 +975,8 @@ is_a: CL:0000007 ! early embryonic cell (metazoa) is_a: CL:0000255 ! eukaryotic cell is_a: CL:0010017 ! zygote intersection_of: CL:0010017 ! zygote -intersection_of: only_in_taxon NCBITaxon:33208 ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +intersection_of: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa [Term] id: CL:0000393 @@ -993,7 +994,7 @@ is_a: CL:0000099 ! interneuron is_a: CL:2000029 ! central nervous system neuron intersection_of: CL:0000099 ! interneuron intersection_of: RO:0002100 UBERON:0001017 ! has soma location central nervous system -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000404 @@ -1011,8 +1012,8 @@ synonym: "satellite cell" RELATED [] xref: FMA:84798 is_a: CL:0000056 ! myoblast intersection_of: CL:0000056 ! myoblast -intersection_of: develops_into CL:0000192 ! smooth muscle cell -relationship: develops_into CL:0000192 ! smooth muscle cell +intersection_of: RO:0002203 CL:0000192 ! develops into smooth muscle cell +relationship: RO:0002203 CL:0000192 ! develops into smooth muscle cell [Term] id: CL:0000526 @@ -1022,7 +1023,7 @@ subset: human_reference_atlas synonym: "input neuron" EXACT [] xref: FMA:87653 is_a: CL:0000540 ! neuron -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000529 @@ -1049,8 +1050,8 @@ is_a: CL:0000393 ! electrically responsive cell is_a: CL:0000404 ! electrically signaling cell is_a: CL:0002319 ! neural cell relationship: capable_of GO:0019226 ! transmission of nerve impulse -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://www.swissbiopics.org/api/image/Neuron_cells.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Neuron_cells.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000541 @@ -1061,7 +1062,7 @@ xref: BTO:0003217 xref: FMA:83377 is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0011026 ! progenitor cell -relationship: develops_from CL:0000333 ! migratory neural crest cell +relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell [Term] id: CL:0000547 @@ -1104,10 +1105,10 @@ relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-span relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD5 relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G -relationship: develops_from CL:0000038 ! erythroid progenitor cell relationship: has_part CL:0017503 ! basophilic cytoplasm relationship: has_part GO:0005730 ! nucleolus relationship: RO:0002104 PR:000001945 ! has plasma membrane part transferrin receptor protein 1 +relationship: RO:0002202 CL:0000038 ! develops from erythroid progenitor cell [Term] id: CL:0000549 @@ -1145,10 +1146,10 @@ intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017504 ! polychromatophilic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin intersection_of: RO:0002104 PR:000001945 ! has plasma membrane part transferrin receptor protein 1 -relationship: develops_from CL:0000549 ! basophilic erythroblast relationship: has_part CL:0017504 ! polychromatophilic cytoplasm relationship: has_part GO:0000792 ! heterochromatin relationship: RO:0002104 PR:000001945 ! has plasma membrane part transferrin receptor protein 1 +relationship: RO:0002202 CL:0000549 ! develops from basophilic erythroblast [Term] id: CL:0000552 @@ -1164,9 +1165,9 @@ is_a: CL:0000765 {is_inferred="true"} ! erythroblast intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017502 ! acidophilic cytoplasm intersection_of: participates_in GO:0030263 ! apoptotic chromosome condensation -relationship: develops_from CL:0000550 ! polychromatophilic erythroblast relationship: has_part CL:0017502 ! acidophilic cytoplasm relationship: participates_in GO:0030263 ! apoptotic chromosome condensation +relationship: RO:0002202 CL:0000550 ! develops from polychromatophilic erythroblast [Term] id: CL:0000553 @@ -1220,8 +1221,8 @@ relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surfac relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -relationship: develops_from CL:0000050 ! megakaryocyte-erythroid progenitor cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000050 ! develops from megakaryocyte-erythroid progenitor cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000556 @@ -1240,8 +1241,8 @@ xref: FMA:83555 is_a: CL:0000763 {is_inferred="true"} ! myeloid cell disjoint_from: CL:0000764 ! erythroid lineage cell relationship: bearer_of PATO:0001393 ! euploid -relationship: develops_from CL:0000553 ! megakaryocyte progenitor cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000553 ! develops from megakaryocyte progenitor cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000558 @@ -1280,8 +1281,8 @@ relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-span relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD5 relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G -relationship: develops_from CL:0000552 ! orthochromatic erythroblast relationship: RO:0002104 PR:000001945 ! has plasma membrane part transferrin receptor protein 1 +relationship: RO:0002202 CL:0000552 ! develops from orthochromatic erythroblast [Term] id: CL:0000561 @@ -1297,10 +1298,10 @@ xref: BTO:0004044 xref: FMA:67766 is_a: CL:0000099 ! interneuron is_a: CL:0009004 ! retinal cell -relationship: in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0000966 ! retina -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002120 CL:0000740 ! synapsed to retinal ganglion cell +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000566 @@ -1316,10 +1317,10 @@ intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: RO:0002104 PR:000001444 ! has plasma membrane part cadherin-5 intersection_of: RO:0002104 PR:000002112 ! has plasma membrane part vascular endothelial growth factor receptor 2 intersection_of: RO:0002104 PR:000016043 ! has plasma membrane part T-cell acute lymphocytic leukemia protein 1 -relationship: develops_from CL:0000134 ! mesenchymal stem cell relationship: RO:0002104 PR:000001444 ! has plasma membrane part cadherin-5 relationship: RO:0002104 PR:000002112 ! has plasma membrane part vascular endothelial growth factor receptor 2 relationship: RO:0002104 PR:000016043 ! has plasma membrane part T-cell acute lymphocytic leukemia protein 1 +relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell [Term] id: CL:0000573 @@ -1332,8 +1333,8 @@ xref: BTO:0001036 xref: CALOHA:TS-0866 xref: FMA:67748 is_a: CL:0010009 ! camera-type eye photoreceptor cell -relationship: develops_from CL:0002672 ! retinal progenitor cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0002672 ! develops from retinal progenitor cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000575 @@ -1351,7 +1352,7 @@ is_a: CL:0002159 ! general ecto-epithelial cell intersection_of: CL:0000076 ! squamous epithelial cell intersection_of: part_of UBERON:0001772 ! corneal epithelium relationship: part_of UBERON:0001772 ! corneal epithelium -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000604 @@ -1364,8 +1365,8 @@ xref: BTO:0001024 xref: CALOHA:TS-0870 xref: FMA:67747 is_a: CL:0010009 ! camera-type eye photoreceptor cell -relationship: develops_from CL:0002672 ! retinal progenitor cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0002672 ! develops from retinal progenitor cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000636 @@ -1381,7 +1382,7 @@ xref: BTO:0003064 is_a: CL:0000681 ! radial glial cell is_a: CL:0009004 ! retinal cell relationship: part_of UBERON:0000966 ! retina -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000679 @@ -1396,7 +1397,7 @@ is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0061535 ! glutamate secretion, neurotransmission relationship: capable_of GO:0061535 ! glutamate secretion, neurotransmission -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000680 @@ -1405,9 +1406,9 @@ def: "A non-terminally differentiated cell that is capable of developing into a subset: cellxgene_subset is_a: CL:0000055 ! non-terminally differentiated cell intersection_of: CL:0011115 ! precursor cell -intersection_of: develops_into CL:0000187 ! muscle cell -relationship: develops_from CL:0000222 ! mesodermal cell -relationship: develops_into CL:0000187 ! muscle cell +intersection_of: RO:0002203 CL:0000187 ! develops into muscle cell +relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell +relationship: RO:0002203 CL:0000187 ! develops into muscle cell [Term] id: CL:0000681 @@ -1417,7 +1418,7 @@ comment: Unlike that of mammals, the brain of adult teleost fish exhibits an int subset: cellxgene_subset synonym: "forebrain radial glial cell" NARROW [] is_a: CL:0000125 ! glial cell -relationship: develops_from CL:0000710 ! neurecto-epithelial cell +relationship: RO:0002202 CL:0000710 ! develops from neurecto-epithelial cell [Term] id: CL:0000710 @@ -1430,8 +1431,8 @@ xref: FMA:70557 is_a: CL:0000075 ! columnar/cuboidal epithelial cell is_a: CL:0002077 ! ecto-epithelial cell intersection_of: CL:0002077 ! ecto-epithelial cell -intersection_of: develops_from CL:0000133 ! neurectodermal cell -relationship: develops_from CL:0000133 ! neurectodermal cell +intersection_of: RO:0002202 CL:0000133 ! develops from neurectodermal cell +relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell [Term] id: CL:0000723 @@ -1459,8 +1460,8 @@ xref: BTO:0001800 xref: FMA:67765 xref: MESH:D012165 is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002100 UBERON:0000966 ! has soma location retina +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000745 @@ -1474,8 +1475,8 @@ synonym: "HCs" RELATED OMO:0003004 [doi:10.1038/s41598-020-66092-9] synonym: "horizontal cell" EXACT [] xref: BTO:0004120 is_a: CL:0000099 ! interneuron -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002100 UBERON:0003902 ! has soma location retinal neural layer +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000748 @@ -1493,8 +1494,8 @@ is_a: CL:0008028 ! visual system neuron is_a: CL:0009004 ! retinal cell intersection_of: CL:0000103 ! bipolar neuron intersection_of: RO:0002100 UBERON:0001791 ! has soma location inner nuclear layer of retina -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002100 UBERON:0001791 ! has soma location inner nuclear layer of retina +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000763 @@ -1506,8 +1507,8 @@ xref: CALOHA:TS-0647 xref: MESH:D022423 is_a: CL:0000988 {is_inferred="true"} ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell -intersection_of: develops_from CL:0000049 ! common myeloid progenitor -relationship: develops_from CL:0000049 ! common myeloid progenitor +intersection_of: RO:0002202 CL:0000049 ! develops from common myeloid progenitor +relationship: RO:0002202 CL:0000049 ! develops from common myeloid progenitor [Term] id: CL:0000764 @@ -1521,7 +1522,7 @@ xref: CALOHA:TS-0290 xref: FMA:62845 xref: FMA:83516 is_a: CL:0000763 ! myeloid cell -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000765 @@ -1564,8 +1565,8 @@ relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-span relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD5 relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G -relationship: develops_from CL:0000547 ! proerythroblast relationship: has_part GO:0005634 ! nucleus +relationship: RO:0002202 CL:0000547 ! develops from proerythroblast [Term] id: CL:0000837 @@ -1612,9 +1613,9 @@ relationship: CL:4030046 PR:000001869 ! lacks_plasma_membrane_part interleukin-7 relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -relationship: develops_from CL:0000037 ! hematopoietic stem cell -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule +relationship: RO:0002202 CL:0000037 ! develops from hematopoietic stem cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000839 @@ -1632,7 +1633,7 @@ is_a: CL:0011026 ! progenitor cell intersection_of: CL:0002031 ! hematopoietic lineage restricted progenitor cell intersection_of: capable_of GO:0030099 ! myeloid cell differentiation relationship: capable_of GO:0030099 ! myeloid cell differentiation -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000988 @@ -1658,8 +1659,8 @@ intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001400 ! unipotent disjoint_from: CL:0002032 ! hematopoietic oligopotent progenitor cell relationship: bearer_of PATO:0001400 ! unipotent -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002032 ! hematopoietic oligopotent progenitor cell +relationship: RO:0002202 CL:0002032 ! develops from hematopoietic oligopotent progenitor cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:20Z [Term] @@ -1672,8 +1673,8 @@ is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001401 ! oligopotent relationship: bearer_of PATO:0001401 ! oligopotent -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000837 ! hematopoietic multipotent progenitor cell +relationship: RO:0002202 CL:0000837 ! develops from hematopoietic multipotent progenitor cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:27Z [Term] @@ -1683,9 +1684,9 @@ def: "An epithelial cell derived from ectoderm." [FMA:69074, GOC:tfm] xref: FMA:69074 is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell -intersection_of: develops_from CL:0000221 ! ectodermal cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000221 ! ectodermal cell +intersection_of: RO:0002202 CL:0000221 ! develops from ectodermal cell +relationship: RO:0002202 CL:0000221 ! develops from ectodermal cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T03:38:22Z [Term] @@ -1696,9 +1697,9 @@ synonym: "epithelial mesenchymal cell" EXACT [] xref: FMA:69076 is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell -intersection_of: develops_from CL:0000222 ! mesodermal cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000222 ! mesodermal cell +intersection_of: RO:0002202 CL:0000222 ! develops from mesodermal cell +relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T03:49:14Z [Term] @@ -1713,7 +1714,7 @@ xref: BTO:0001854 xref: CALOHA:TS-1106 xref: FMA:67755 is_a: CL:0000115 ! endothelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T02:06:40Z [Term] @@ -1722,7 +1723,7 @@ name: general ecto-epithelial cell def: "Epithelial cells derived from general body ectoderm and ectoderm placodes." [GOC:tfm] xref: FMA:70556 is_a: CL:0002077 ! ecto-epithelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-26T08:31:08Z [Term] @@ -1733,8 +1734,8 @@ subset: eye_upper_slim xref: FMA:70950 is_a: CL:0000066 ! epithelial cell is_a: CL:0000306 ! crystallin accumulating cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0000965 ! lens of camera-type eye +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T10:38:03Z [Term] @@ -1746,7 +1747,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0002505 ! nucleated relationship: bearer_of PATO:0002505 ! nucleated -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T03:32:33Z [Term] @@ -1760,9 +1761,9 @@ subset: human_reference_atlas synonym: "PE cell" EXACT [https://doi.org/10.1016/j.exer.2003.09.021] xref: FMA:70606 is_a: CL:0000529 ! pigmented epithelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001778 ! ciliary epithelium -relationship: present_in_taxon NCBITaxon:9606 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-09-13T04:09:27Z [Term] @@ -1777,9 +1778,9 @@ synonym: "nonpigmented ciliary epithelial cell" EXACT [PMID:10913011] synonym: "NPE cell" EXACT [https://doi.org/10.1016/j.exer.2003.09.021] xref: FMA:70607 is_a: CL:0000710 ! neurecto-epithelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001778 ! ciliary epithelium -relationship: present_in_taxon NCBITaxon:9606 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-09-13T04:09:31Z [Term] @@ -1792,8 +1793,8 @@ xref: FMA:70333 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001016 ! nervous system -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001016 ! nervous system +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T01:34:57Z [Term] @@ -1807,8 +1808,8 @@ xref: MESH:D003239 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0002384 ! connective tissue -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002384 ! connective tissue +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T03:01:54Z [Term] @@ -1819,7 +1820,7 @@ xref: CALOHA:TS-0263 xref: FMA:82840 xref: WBbt:0007028 is_a: CL:0000000 ! cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T03:39:21Z [Term] @@ -1831,12 +1832,12 @@ subset: eye_upper_slim subset: human_reference_atlas synonym: "corneal fibroblast" EXACT [] synonym: "corneal keratocyte" EXACT [] -is_a: CL:0000005 ! fibroblast neural crest derived +is_a: CL:0000005 ! neural crest derived fibroblast intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0001777 ! substantia propria of cornea -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001777 ! substantia propria of cornea -relationship: present_in_taxon NCBITaxon:9606 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2010-09-22T01:57:40Z [Term] @@ -1848,8 +1849,8 @@ is_a: CL:0000148 ! melanocyte is_a: CL:0009004 ! retinal cell intersection_of: CL:0000148 ! melanocyte intersection_of: part_of UBERON:0000966 ! retina -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0000966 ! retina +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-03T03:25:32Z [Term] @@ -1865,8 +1866,8 @@ xref: FMA:84791 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0007100 ! primary circulatory organ -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0007100 ! primary circulatory organ +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T09:37:22Z [Term] @@ -1875,7 +1876,7 @@ name: embryonic blood vessel endothelial progenitor cell def: "An endothelial progenitor cell that participates in angiogenesis during development." [GOC:tfm] comment: See CL:0002619. is_a: CL:0000222 ! mesodermal cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T04:20:39Z [Term] @@ -1888,9 +1889,9 @@ is_a: CL:0000066 ! epithelial cell is_a: CL:0000342 {is_inferred="true"} ! pigment cell (sensu Vertebrata) intersection_of: CL:0000342 ! pigment cell (sensu Vertebrata) intersection_of: part_of UBERON:0002506 ! iris epithelium -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002506 ! iris epithelium -relationship: present_in_taxon NCBITaxon:9606 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2011-03-01T05:28:52Z [Term] @@ -1904,9 +1905,9 @@ is_a: CL:0000071 {is_inferred="true"} ! blood vessel endothelial cell is_a: CL:0009004 ! retinal cell intersection_of: CL:0000071 ! blood vessel endothelial cell intersection_of: part_of UBERON:0000966 ! retina -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0000966 ! retina -relationship: present_in_taxon NCBITaxon:9606 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2011-03-06T03:28:27Z [Term] @@ -1923,10 +1924,10 @@ is_a: CL:0000149 ! visual pigment cell is_a: CL:0009004 ! retinal cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001782 ! pigmented layer of retina -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: has_part GO:0042470 ! melanosome relationship: part_of UBERON:0001782 ! pigmented layer of retina -relationship: present_in_taxon NCBITaxon:9606 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2011-03-06T03:37:09Z [Term] @@ -1934,8 +1935,8 @@ id: CL:0002672 name: retinal progenitor cell def: "A multi-fate stem cell that can give rise to different retinal cell types including rod and cone cells." [GOC:tfm, PMID:20959166, PMID:21148186] is_a: CL:0000048 ! multi fate stem cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000133 ! neurectodermal cell +relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-08-16T02:38:01Z [Term] @@ -1953,9 +1954,9 @@ id: CL:0007004 name: premigratory neural crest cell def: "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells." [UBERONREF:0000002] is_a: CL:0011012 ! neural crest cell -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 -relationship: develops_from CL:0000133 ! neurectodermal cell relationship: part_of UBERON:0002342 ! neural crest +relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-27T08:27:35Z [Term] @@ -1991,7 +1992,7 @@ synonym: "mesenchyme cell" EXACT [] is_a: CL:0000219 ! motile cell relationship: capable_of GO:0016477 ! cell migration relationship: part_of UBERON:0003104 ! mesenchyme -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0008028 @@ -2000,7 +2001,7 @@ is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron intersection_of: capable_of_part_of GO:0007601 ! visual perception relationship: capable_of_part_of GO:0007601 ! visual perception -relationship: dc-contributor https://orcid.org/0000-0002-7073-9172 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2017-07-09T19:12:36Z [Term] @@ -2019,9 +2020,10 @@ id: CL:0010009 name: camera-type eye photoreceptor cell synonym: "camera type eye photoreceptor cell" EXACT [] is_a: CL:0000287 ! eye photoreceptor cell +is_a: CL:0009004 ! retinal cell intersection_of: CL:0000210 ! photoreceptor cell intersection_of: part_of UBERON:0000019 ! camera-type eye -relationship: part_of UBERON:0000019 ! camera-type eye +relationship: part_of UBERON:0000966 {seeAlso="https://github.com/obophenotype/cell-ontology/issues/2245"} ! retina [Term] id: CL:0010017 @@ -2029,7 +2031,7 @@ name: zygote def: "A zygote in a plant or an animal." [] xref: MESH:D015053 is_a: CL:0000000 ! cell -relationship: seeAlso https://github.com/obophenotype/cell-ontology/issues/786 +property_value: seeAlso https://github.com/obophenotype/cell-ontology/issues/786 [Term] id: CL:0011012 @@ -2046,9 +2048,9 @@ def: "A precursor cell that has a tendency to differentiate into a specific type subset: cellxgene_subset is_a: CL:0011115 ! precursor cell intersection_of: CL:0011115 ! precursor cell -intersection_of: develops_from CL:0000034 ! stem cell -relationship: dc-contributor https://orcid.org/0000-0001-5208-3432 -relationship: develops_from CL:0000034 ! stem cell +intersection_of: RO:0002202 CL:0000034 ! develops from stem cell +relationship: RO:0002202 CL:0000034 ! develops from stem cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011104 @@ -2080,7 +2082,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0002418 ! acidophilic relationship: bearer_of PATO:0002418 ! acidophilic -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-22T04:23:25Z [Term] @@ -2091,7 +2093,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0002094 ! basophilic relationship: bearer_of PATO:0002094 ! basophilic -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-22T04:24:54Z [Term] @@ -2102,7 +2104,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0070047 ! polychromatophilic relationship: bearer_of PATO:0070047 ! polychromatophilic -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-28T04:25:23Z [Term] @@ -2138,8 +2140,8 @@ def: "Any neuron that is part of a central nervous system." [GOC:TermGenie] is_a: CL:0000540 ! neuron intersection_of: CL:0000540 ! neuron intersection_of: RO:0002100 UBERON:0001017 ! has soma location central nervous system -relationship: dc-contributor https://www.wikidata.org/entity/Q35563349 relationship: RO:0002100 UBERON:0001017 ! has soma location central nervous system +property_value: http://purl.org/dc/terms/contributor https://www.wikidata.org/entity/Q35563349 creation_date: 2014-06-25T01:17:43Z [Term] @@ -2149,9 +2151,9 @@ def: "A retinal cell that is immature or undifferentiated." [PMID:17565741] subset: eye_upper_slim synonym: "retinal stem cell" EXACT [PMID:17565741] is_a: CL:0009004 ! retinal cell -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 -relationship: dc-contributor https://orcid.org/0000-0002-0819-0473 relationship: part_of UBERON:0000966 ! retina +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0819-0473 [Term] id: CL:4033015 @@ -2164,9 +2166,9 @@ is_a: CL:0000127 ! astrocyte is_a: CL:0009004 ! retinal cell intersection_of: CL:0000127 ! astrocyte intersection_of: part_of UBERON:0000966 ! retina -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 relationship: part_of UBERON:0000966 ! retina -property_value: dcterms-date "2023-03-02T14:38:32Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-03-02T14:38:32Z" xsd:dateTime [Term] id: GO:0000278 @@ -2185,8 +2187,8 @@ is_a: GO:0007049 ! cell cycle intersection_of: GO:0007049 ! cell cycle intersection_of: has_part GO:0140014 ! mitotic nuclear division relationship: has_part GO:0140014 ! mitotic nuclear division -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota [Term] id: GO:0000280 @@ -2238,7 +2240,7 @@ namespace: biological_process def: "A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities." [GOC:dph, GOC:go_curators, GOC:tb, ISBN:978-0-07-139011-8] comment: Action potentials typically propagate across excitable membranes. This class covers both action potentials that propagate and those that fail to do so. is_a: GO:0042391 ! regulation of membrane potential -relationship: never_in_taxon NCBITaxon:4895 +property_value: RO:0002161 NCBITaxon:4895 [Term] id: GO:0001677 @@ -2390,7 +2392,7 @@ subset: goslim_mouse subset: goslim_pir xref: Wikipedia:Immune_system is_a: GO:0008150 ! biological_process -relationship: never_in_taxon NCBITaxon:4895 +property_value: RO:0002161 NCBITaxon:4895 [Term] id: GO:0003008 @@ -2489,8 +2491,8 @@ namespace: cellular_component def: "A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures." [GOC:dos, GOC:mah, ISBN:0721639976, PMID:19693541, PMID:21421911] xref: Wikipedia:Collagen is_a: GO:0032991 ! protein-containing complex -relationship: in_taxon NCBITaxon:33208 {all_only="true", source="PMID:12382326"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 {source="PMID:12382326"} ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 {source="PMID:12382326"} ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true", source="PMID:12382326"} ! in taxon Metazoa [Term] id: GO:0005587 @@ -2571,8 +2573,8 @@ xref: NIF_Subcellular:sao1702920020 xref: Wikipedia:Cell_nucleus is_a: GO:0043231 ! intracellular membrane-bounded organelle disjoint_from: GO:0005737 ! cytoplasm -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota [Term] id: GO:0005694 @@ -2809,8 +2811,8 @@ def: "The directed movement of a neurotransmitter into, out of or within a cell, subset: goslim_pir synonym: "sodium:neurotransmitter transport" NARROW [] is_a: GO:0006810 ! transport -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0006865 @@ -2848,11 +2850,11 @@ synonym: "type I programmed cell death" NARROW [] xref: Wikipedia:Apoptosis is_a: GO:0012501 ! programmed cell death relationship: ends_with GO:0097194 ! execution phase of apoptosis -relationship: in_taxon NCBITaxon:33154 {all_only="true"} ! Opisthokonta -relationship: never_in_taxon NCBITaxon:2 -relationship: never_in_taxon NCBITaxon:4896 -relationship: only_in_taxon NCBITaxon:33154 ! Opisthokonta +relationship: RO:0002160 NCBITaxon:33154 ! only in taxon Opisthokonta +relationship: RO:0002162 NCBITaxon:33154 {all_only="true"} ! in taxon Opisthokonta relationship: starts_with GO:0097190 ! apoptotic signaling pathway +property_value: RO:0002161 NCBITaxon:2 +property_value: RO:0002161 NCBITaxon:4896 [Term] id: GO:0006921 @@ -3372,8 +3374,8 @@ namespace: biological_process def: "The process whose specific outcome is the progression of an embryo over time, from zygote formation until the end of the embryonic life stage. The end of the embryonic life stage is organism-specific and may be somewhat arbitrary; for mammals it is usually considered to be birth, for insects the hatching of the first instar larva from the eggshell." [GOC:go_curators, GOC:isa_complete, GOC:mtg_sensu] synonym: "embryogenesis" BROAD [] is_a: GO:0009790 ! embryo development -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0009888 @@ -3386,14 +3388,14 @@ xref: Wikipedia:Histogenesis is_a: GO:0048856 ! anatomical structure development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0000479 ! tissue -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: never_in_taxon NCBITaxon:147554 -relationship: never_in_taxon NCBITaxon:33630 -relationship: never_in_taxon NCBITaxon:33682 -relationship: never_in_taxon NCBITaxon:38254 -relationship: never_in_taxon NCBITaxon:4891 -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota relationship: results_in_development_of UBERON:0000479 ! tissue +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota +property_value: RO:0002161 NCBITaxon:147554 +property_value: RO:0002161 NCBITaxon:33630 +property_value: RO:0002161 NCBITaxon:33682 +property_value: RO:0002161 NCBITaxon:38254 +property_value: RO:0002161 NCBITaxon:4891 [Term] id: GO:0009987 @@ -3561,7 +3563,7 @@ namespace: biological_process def: "The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues." [GOC:cjm, GOC:dph, GOC:ems, GOC:pf, Wikipedia:Cell_migration] xref: Wikipedia:Cell_migration is_a: GO:0048870 ! cell motility -relationship: never_in_taxon NCBITaxon:4890 +property_value: RO:0002161 NCBITaxon:4890 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24787" xsd:anyURI [Term] @@ -3778,7 +3780,7 @@ subset: goslim_drosophila subset: goslim_flybase_ribbon xref: Wikipedia:Cell_junction is_a: GO:0110165 ! cellular anatomical entity -relationship: never_in_taxon NCBITaxon:4751 +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0030097 @@ -4021,10 +4023,10 @@ subset: goslim_pir synonym: "organismal physiological process" EXACT [] synonym: "single-multicellular organism process" RELATED [] is_a: GO:0008150 ! biological_process -relationship: never_in_taxon NCBITaxon:2 -relationship: never_in_taxon NCBITaxon:2157 -relationship: never_in_taxon NCBITaxon:4896 -relationship: never_in_taxon NCBITaxon:4932 +property_value: RO:0002161 NCBITaxon:2 +property_value: RO:0002161 NCBITaxon:2157 +property_value: RO:0002161 NCBITaxon:4896 +property_value: RO:0002161 NCBITaxon:4932 created_by: jl creation_date: 2012-09-19T16:07:47Z @@ -4190,7 +4192,7 @@ def: "Self-propelled movement of a cell or organism from one location to another subset: goslim_chembl subset: goslim_pir is_a: GO:0008150 ! biological_process -relationship: never_in_taxon NCBITaxon:451864 +property_value: RO:0002161 NCBITaxon:451864 [Term] id: GO:0040016 @@ -4215,11 +4217,11 @@ namespace: cellular_component def: "A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells." [GOC:jl, PMID:11584301] xref: Wikipedia:Melanosome is_a: GO:0048770 ! pigment granule -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: never_in_taxon NCBITaxon:4895 -relationship: never_in_taxon NCBITaxon:6237 {source="GOC:kmv"} -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa relationship: part_of CL:0000148 ! melanocyte +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa +property_value: RO:0002161 NCBITaxon:4895 +property_value: RO:0002161 NCBITaxon:6237 {source="GOC:kmv"} [Term] id: GO:0042592 @@ -4271,8 +4273,8 @@ xref: NIF_Subcellular:sao867568886 is_a: GO:0120025 ! plasma membrane bounded cell projection intersection_of: GO:0120025 ! plasma membrane bounded cell projection intersection_of: part_of CL:0000540 ! neuron -relationship: never_in_taxon NCBITaxon:4751 relationship: part_of CL:0000540 ! neuron +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0043009 @@ -4280,8 +4282,8 @@ name: chordate embryonic development namespace: biological_process def: "The process whose specific outcome is the progression of the embryo over time, from zygote formation through a stage including a notochord and neural tube until birth or egg hatching." [GOC:mtg_sensu] is_a: GO:0009792 ! embryo development ending in birth or egg hatching -relationship: in_taxon NCBITaxon:7711 {all_only="true"} ! Chordata -relationship: only_in_taxon NCBITaxon:7711 ! Chordata +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {all_only="true"} ! in taxon Chordata [Term] id: GO:0043025 @@ -4328,9 +4330,9 @@ xref: FMA:62983 xref: NIF_Subcellular:sao593830697 xref: Wikipedia:Myelin is_a: GO:0110165 ! cellular anatomical entity -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa relationship: part_of CL:0000125 ! glial cell +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0043226 @@ -4551,8 +4553,8 @@ xref: FBbt:00005107 xref: FMA:67301 xref: Wikipedia:Cell_body is_a: GO:0110165 ! cellular anatomical entity -relationship: never_in_taxon NCBITaxon:4890 relationship: part_of CL:0000000 ! cell +property_value: RO:0002161 NCBITaxon:4890 created_by: jl creation_date: 2010-02-05T10:37:16Z @@ -4573,8 +4575,8 @@ synonym: "synaptic junction" EXACT [] xref: NIF_Subcellular:sao914572699 xref: Wikipedia:Chemical_synapse is_a: GO:0030054 ! cell junction -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0046903 @@ -4809,8 +4811,8 @@ is_a: GO:0003008 ! system process intersection_of: GO:0003008 ! system process intersection_of: has_participant UBERON:0001016 ! nervous system relationship: has_participant UBERON:0001016 ! nervous system -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13824" xsd:anyURI [Term] @@ -4990,10 +4992,10 @@ synonym: "positioning within cell" NARROW [] is_a: GO:0051234 ! establishment of localization intersection_of: GO:0051234 ! establishment of localization intersection_of: occurs_in CL:0000000 ! cell -relationship: in_taxon NCBITaxon:131567 {all_only="true"} ! cellular organisms relationship: occurs_in CL:0000000 ! cell -relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms relationship: part_of GO:0051641 ! cellular localization +relationship: RO:0002160 NCBITaxon:131567 ! only in taxon cellular organisms +relationship: RO:0002162 NCBITaxon:131567 {all_only="true"} ! in taxon cellular organisms [Term] id: GO:0051716 @@ -5133,8 +5135,8 @@ name: collagen-containing extracellular matrix namespace: cellular_component def: "An extracellular matrix consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that provides not only essential physical scaffolding for the cellular constituents but can also initiate crucial biochemical and biomechanical cues required for tissue morphogenesis, differentiation and homeostasis. The components are secreted by cells in the vicinity and form a sheet underlying or overlying cells such as endothelial and epithelial cells." [GOC:BHF, GOC:rph, PMID:21123617] is_a: GO:0031012 ! extracellular matrix -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa created_by: dph creation_date: 2018-04-13T12:47:21Z @@ -5531,9 +5533,9 @@ subset: goslim_synapse is_a: GO:0007267 ! cell-cell signaling intersection_of: GO:0007267 ! cell-cell signaling intersection_of: occurs_in GO:0045202 ! synapse -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa relationship: occurs_in GO:0045202 ! synapse -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0099537 @@ -5567,10 +5569,10 @@ subset: goslim_synapse is_a: GO:0023061 ! signal release intersection_of: GO:0023061 ! signal release intersection_of: occurs_in GO:0045202 ! synapse -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa relationship: occurs_in GO:0045202 ! synapse -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa relationship: part_of GO:0099536 ! synaptic signaling +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0110165 @@ -5762,18 +5764,16 @@ namespace: ncbi_taxonomy xref: GC_ID:1 xref: PMID:15371245 is_a: NCBITaxon:337687 ! Muroidea -property_value: has_rank NCBITaxon:family [Term] id: NCBITaxon:10088 name: Mus namespace: ncbi_taxonomy -synonym: "mice" EXACT OMO:0003003 [] +synonym: "mice" EXACT genbank_common_name [] synonym: "mouse" EXACT OMO:0003003 [] synonym: "Mus" EXACT scientific_name [] xref: GC_ID:1 is_a: NCBITaxon:39107 ! Murinae -property_value: has_rank NCBITaxon:genus [Term] id: NCBITaxon:10090 @@ -5784,7 +5784,6 @@ synonym: "house mouse" EXACT genbank_common_name [] synonym: "mouse" EXACT OMO:0003003 [] xref: GC_ID:1 is_a: NCBITaxon:862507 ! Mus -property_value: has_rank NCBITaxon:species [Term] id: NCBITaxon:117570 @@ -5792,7 +5791,6 @@ name: Teleostomi namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:7776 ! Gnathostomata -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:117571 @@ -5802,7 +5800,6 @@ alt_id: NCBITaxon:40673 synonym: "bony vertebrates" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:117570 ! Teleostomi -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:131567 @@ -5818,7 +5815,6 @@ name: Dipnotetrapodomorpha namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:8287 ! Sarcopterygii -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:1437010 @@ -5829,7 +5825,6 @@ xref: GC_ID:1 xref: PMID:11743200 xref: PMID:11791233 is_a: NCBITaxon:9347 ! Eutheria -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:1963758 @@ -5839,7 +5834,6 @@ synonym: "mice and others" EXACT genbank_common_name [] synonym: "Sciurognathi" RELATED in_part [] xref: GC_ID:1 is_a: NCBITaxon:9989 ! Rodentia -property_value: has_rank NCBITaxon:suborder [Term] id: NCBITaxon:2759 @@ -5856,7 +5850,6 @@ xref: GC_ID:1 xref: PMID:23020233 xref: PMID:30257078 is_a: NCBITaxon:131567 ! cellular organisms -property_value: has_rank NCBITaxon:superkingdom [Term] id: NCBITaxon:314146 @@ -5868,7 +5861,6 @@ xref: PMID:12082125 xref: PMID:12878460 xref: PMID:15522813 is_a: NCBITaxon:1437010 ! Boreoeutheria -property_value: has_rank NCBITaxon:superorder [Term] id: NCBITaxon:314147 @@ -5880,7 +5872,6 @@ xref: PMID:11214319 xref: PMID:12082125 xref: PMID:15522813 is_a: NCBITaxon:314146 ! Euarchontoglires -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:32523 @@ -5889,7 +5880,6 @@ namespace: ncbi_taxonomy synonym: "tetrapods" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:1338369 ! Dipnotetrapodomorpha -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:32524 @@ -5898,7 +5888,6 @@ namespace: ncbi_taxonomy synonym: "amniotes" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:32523 ! Tetrapoda -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:32525 @@ -5907,7 +5896,6 @@ namespace: ncbi_taxonomy synonym: "Theria" EXACT scientific_name [] xref: GC_ID:1 is_a: NCBITaxon:40674 ! Mammalia -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:33154 @@ -5917,7 +5905,6 @@ synonym: "Fungi/Metazoa group" RELATED synonym [] synonym: "opisthokonts" RELATED synonym [] xref: GC_ID:1 is_a: NCBITaxon:2759 ! Eukaryota -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:33208 @@ -5929,7 +5916,6 @@ synonym: "metazoans" EXACT genbank_common_name [] synonym: "multicellular animals" EXACT OMO:0003003 [] xref: GC_ID:1 is_a: NCBITaxon:33154 ! Opisthokonta -property_value: has_rank NCBITaxon:kingdom [Term] id: NCBITaxon:33213 @@ -5937,7 +5923,6 @@ name: Bilateria namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:6072 ! Eumetazoa -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:33511 @@ -5946,7 +5931,6 @@ namespace: ncbi_taxonomy synonym: "deuterostomes" EXACT OMO:0003003 [] xref: GC_ID:1 is_a: NCBITaxon:33213 ! Bilateria -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:337687 @@ -5956,7 +5940,6 @@ xref: GC_ID:1 xref: PMID:15019624 xref: PMID:15371245 is_a: NCBITaxon:1963758 ! Myomorpha -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:39107 @@ -5965,7 +5948,6 @@ namespace: ncbi_taxonomy alt_id: NCBITaxon:109679 xref: GC_ID:1 is_a: NCBITaxon:10066 ! Muridae -property_value: has_rank NCBITaxon:subfamily [Term] id: NCBITaxon:40674 @@ -5975,7 +5957,6 @@ synonym: "mammals" EXACT genbank_common_name [] synonym: "mammals" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:32524 ! Amniota -property_value: has_rank NCBITaxon:class [Term] id: NCBITaxon:6072 @@ -5983,7 +5964,6 @@ name: Eumetazoa namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:33208 ! Metazoa -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:7711 @@ -5993,7 +5973,6 @@ synonym: "chordates" EXACT genbank_common_name [] synonym: "chordates" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:33511 ! Deuterostomia -property_value: has_rank NCBITaxon:phylum [Term] id: NCBITaxon:7742 @@ -6004,7 +5983,6 @@ synonym: "vertebrates" EXACT genbank_common_name [] synonym: "vertebrates" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:89593 ! Craniata -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:7776 @@ -6014,7 +5992,6 @@ synonym: "Gnathostomata" EXACT scientific_name [] synonym: "jawed vertebrates" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:7742 ! Vertebrata -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:8287 @@ -6022,7 +5999,6 @@ name: Sarcopterygii namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:117571 ! Euteleostomi -property_value: has_rank NCBITaxon:superclass [Term] id: NCBITaxon:862507 @@ -6031,7 +6007,6 @@ namespace: ncbi_taxonomy synonym: "Mus" EXACT scientific_name [] xref: GC_ID:1 is_a: NCBITaxon:10088 ! Mus -property_value: has_rank NCBITaxon:subgenus [Term] id: NCBITaxon:89593 @@ -6040,7 +6015,6 @@ namespace: ncbi_taxonomy synonym: "Craniata" EXACT scientific_name [] xref: GC_ID:1 is_a: NCBITaxon:7711 ! Chordata -property_value: has_rank NCBITaxon:subphylum [Term] id: NCBITaxon:9347 @@ -6053,7 +6027,6 @@ synonym: "placentals" EXACT genbank_common_name [] synonym: "placentals" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:32525 ! Theria -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:9989 @@ -6063,7 +6036,6 @@ synonym: "rodent" EXACT genbank_common_name [] synonym: "rodents" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:314147 ! Glires -property_value: has_rank NCBITaxon:order [Term] id: PATO:0000001 @@ -6122,7 +6094,6 @@ subset: value_slim synonym: "ramified" EXACT [] synonym: "ramiform" EXACT [] is_a: PATO:0002009 ! branchiness -property_value: RO:0002604 PATO:0000414 [Term] id: PATO:0000411 @@ -6144,7 +6115,6 @@ def: "A morphological quality inhering in a bearer by virtue of the bearer's aff subset: value_slim synonym: "blocked" RELATED [] is_a: PATO:0000136 ! closure -property_value: RO:0002604 PATO:0000610 [Term] id: PATO:0000947 @@ -6180,7 +6150,6 @@ synonym: "clouding" RELATED [] synonym: "cloudy" RELATED [] synonym: "non-transparent" EXACT [] is_a: PATO:0000957 ! opacity -property_value: RO:0002604 PATO:0000964 [Term] id: PATO:0000964 @@ -6192,7 +6161,6 @@ subset: value_slim synonym: "clear" EXACT [] synonym: "hyaline" EXACT [] is_a: PATO:0000957 ! opacity -property_value: RO:0002604 PATO:0000963 [Term] id: PATO:0001018 @@ -6333,7 +6301,6 @@ comment: This refers to the disposition of the bearer. subset: disposition_slim subset: value_slim is_a: PATO:0001579 ! contractility -property_value: RO:0002604 PATO:0001691 [Term] id: PATO:0001857 @@ -6343,7 +6310,6 @@ def: "A shape quality in a bearer by virtue of the bearer's curving inward." [Wo subset: cell_quality subset: value_slim is_a: PATO:0002005 ! concavity -property_value: RO:0002604 PATO:0001355 [Term] id: PATO:0001873 @@ -6411,7 +6377,6 @@ subset: attribute_slim xref: Image:http\://upload.wikimedia.org/wikipedia/commons/0/06/Convex_polygon_illustration1.png is_a: PATO:0002266 ! 3-D shape relationship: RO:0015011 PATO:0002006 ! has cross section 2-D shape -property_value: RO:0002604 PATO:0002008 [Term] id: PATO:0002009 @@ -6437,7 +6402,6 @@ namespace: quality def: "A concave quality inhering in a bearer by virtue of the bearer's curving inward on both sides or surfaces." [PATOC:GVG] subset: value_slim is_a: PATO:0001857 ! concave -property_value: RO:0002604 PATO:0002040 [Term] id: PATO:0002045 @@ -6449,7 +6413,7 @@ synonym: "dendriform" EXACT [] synonym: "dendroid" EXACT [] synonym: "dendroidal" EXACT [] is_a: PATO:0000402 ! branched -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-02-15T08:11:41Z [Term] @@ -6459,7 +6423,7 @@ namespace: quality def: "A quality inhering in a bearer by virtue of the bearer's having an empty space or cavity within." [url:http\://www.merriam-webster.com/dictionary/hollow] subset: value_slim is_a: PATO:0002014 ! structure, cavities -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-09-18T02:19:20Z [Term] @@ -6471,7 +6435,7 @@ subset: disposition_slim subset: mpath_slim subset: value_slim is_a: PATO:0070045 ! anatomical histological quality -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-10-05T12:05:23Z [Term] @@ -6482,7 +6446,7 @@ def: "A quality inhering in a bearer by virtue of the bearer's processing the fo subset: mpath_slim subset: value_slim is_a: PATO:0000141 ! structure -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-10-06T04:37:14Z [Term] @@ -6492,7 +6456,7 @@ namespace: quality def: "A quality inhering in a bearer by virtue of its constitution." [PATOC:GVG] subset: attribute_slim is_a: PATO:0001018 ! physical quality -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-03-15T04:35:27Z [Term] @@ -6502,7 +6466,7 @@ namespace: quality def: "A cylindrical shape quality inhering in a bearer by virtue of the bearer's being imperfectly cylindrical or approximately cylindrical." [url:http\://www.thefreedictionary.com/Subcylindrical] subset: value_slim is_a: PATO:0001873 ! cylindrical -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-07-13T04:22:30Z [Term] @@ -6511,7 +6475,7 @@ name: 3-D shape namespace: quality def: "A shape that inheres in a 3 dimensional entity." [PATOC:OREGON] is_a: PATO:0000052 ! shape -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-10-05T12:31:16Z [Term] @@ -6524,7 +6488,7 @@ synonym: "tube-shaped" EXACT [] synonym: "tubulate" EXACT [] is_a: PATO:0001873 ! cylindrical is_a: PATO:0002078 ! hollow -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-06-08T06:33:50Z [Term] @@ -6535,7 +6499,7 @@ def: "A convex 3-D shape quality inhering in a bearer by virtue of the bearer's comment: Note that a fiber shaped object may take any circuitous or straight path through space (think of a length of string or rope). subset: value_slim is_a: PATO:0002226 ! subcylindrical -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-09-09T04:50:10Z [Term] @@ -6545,7 +6509,7 @@ namespace: quality def: "A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt" [wiktionary:superellipse] synonym: "Lamé curve" EXACT [] is_a: PATO:0002006 ! 2-D shape -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-10-12T12:45:16Z [Term] @@ -6558,7 +6522,7 @@ subset: mpath_slim subset: value_slim synonym: "eosinophilic" EXACT [] is_a: PATO:0070045 ! anatomical histological quality -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2012-12-17T03:01:19Z [Term] @@ -6569,7 +6533,7 @@ def: "A nucleate quality inhering in a bearer by virtue of the bearer's having o subset: mpath_slim subset: value_slim is_a: PATO:0001404 ! nucleate quality -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2013-10-21T05:44:34Z [Term] @@ -6578,7 +6542,7 @@ name: disconnected namespace: quality def: "A structural quality inhering in the bearer by virtue of the bearer consisting of multiple structures lacking any physical connection to each other." [GOC:dos] is_a: PATO:0000141 ! structure -relationship: dc-contributor https://orcid.org/0000-0002-7073-9172 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2014-12-12T08:43:17Z [Term] @@ -6588,7 +6552,7 @@ namespace: quality def: "A quality of a single cell inhering in the bearer by virtue of the bearer's size or shape or structure." [ORCID:0000-0002-7073-9172] comment: Use this term for morphologies that can *only* inhere in a cell, e.g. morphological qualities inhering in a cell by virtue of the presence, location or shape of one or more cell parts. is_a: PATO:0000051 ! morphology -relationship: dc-contributor https://orcid.org/0000-0002-7073-9172 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2021-01-23T11:31:53Z [Term] @@ -6620,7 +6584,7 @@ xref: ILX:0101312 xref: ilxtr:BipolarPhenotype xref: nifext:2 is_a: PATO:0070027 ! bitufted dendrite cell morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070027 @@ -6629,7 +6593,7 @@ namespace: quality def: "A cell morphology that inheres in neurons with dendrites that are bidirectional, emerging from opposite ends of the soma, with the two arbors extending in radial or tangential directions." [PMID:18568015] comment: This morphology type is distinct from bitufted cell morphology in that it refers to bitufted dendrite morphology rather than bitufted cell morphology. is_a: PATO:0010006 ! cell morphology -relationship: dc-contributor https://orcid.org/0000-0001-7258-9596 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7258-9596 [Term] id: PATO:0070044 @@ -6737,7 +6701,6 @@ synonym: "leukocyte adhesion receptor MO1" EXACT [] synonym: "neutrophil adherence receptor" EXACT [] xref: IUPHARobj:2452 is_a: PR:000001005 ! integrin alpha with A domain -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P11215 [Term] id: PR:000001018 @@ -6793,7 +6756,6 @@ synonym: "NCAM-1" EXACT [] synonym: "NCAM1" EXACT PRO-short-label [PRO:DNx] xref: IUPHARobj:2769 is_a: PR:000001023 ! neural cell adhesion molecule NCAM -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P13591 [Term] id: PR:000001083 @@ -6830,7 +6792,6 @@ synonym: "MAL" RELATED Gene-based [] synonym: "T-cell surface glycoprotein Lyt-2" EXACT [] synonym: "T-lymphocyte differentiation antigen T8/Leu-2" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P01732 [Term] id: PR:000001289 @@ -6874,7 +6835,6 @@ synonym: "CDH5" EXACT PRO-short-label [PRO:DNx] synonym: "vascular endothelial cadherin" EXACT [] synonym: "VE-cadherin" EXACT [] is_a: PR:000001327 ! cadherin -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P33151 [Term] id: PR:000001839 @@ -6889,7 +6849,6 @@ synonym: "lymphocyte antigen 1" EXACT [] synonym: "lymphocyte antigen T1/Leu-1" EXACT [] synonym: "Lyt-1" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P06127 [Term] id: PR:000001869 @@ -6907,7 +6866,6 @@ synonym: "IL7R" EXACT PRO-short-label [PRO:DNx] xref: IUPHARobj:1698 xref: PIRSF:PIRSF001960 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P16871 [Term] id: PR:000001889 @@ -6936,7 +6894,6 @@ synonym: "TFRC" EXACT PRO-short-label [PRO:DNx] synonym: "TR" RELATED [] synonym: "Trfr" RELATED Gene-based [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P02786 [Term] id: PR:000001971 @@ -6965,7 +6922,6 @@ synonym: "VEGFR-2" EXACT [] synonym: "VEGFR2" RELATED Gene-based [] xref: IUPHARobj:1813 is_a: PR:000001971 ! vascular endothelial growth factor receptor -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P35968 [Term] id: PR:000002976 @@ -7010,7 +6966,6 @@ synonym: "SHH" EXACT PRO-short-label [PRO:DNx] synonym: "Shh unprocessed N-terminal signaling and C-terminal autoprocessing domains" EXACT [] synonym: "ShhNC" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q15465 [Term] id: PR:000016043 @@ -7028,7 +6983,6 @@ synonym: "TAL-1" EXACT [] synonym: "TAL1" EXACT PRO-short-label [PRO:DNx] synonym: "TCL5" RELATED Gene-based [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P17542 [Term] id: PR:000025796 @@ -7046,8 +7000,8 @@ def: "A protein that is encoded in the genome of Mus musculus." [PRO:DAN] synonym: "mouse protein" EXACT PRO-short-label [PRO:DAN] is_a: PR:000036194 ! eukaryotic protein intersection_of: PR:000000001 ! protein -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus -relationship: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus +relationship: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:000036194 @@ -7057,8 +7011,8 @@ def: "A protein that is encoded in the genome of some Eukaryota." [PRO:DAN] synonym: "Eukaryota protein" EXACT [PRO:DAN] is_a: PR:000000001 ! protein intersection_of: PR:000000001 ! protein -intersection_of: only_in_taxon NCBITaxon:2759 ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +intersection_of: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota [Term] id: PR:000050567 @@ -7084,9 +7038,9 @@ subset: common_anatomy subset: upper_level xref: BFO:0000003 disjoint_from: UBERON:0001062 ! anatomical entity -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000019 @@ -7123,15 +7077,11 @@ is_a: UBERON:0000047 ! simple eye is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0015212 ! lateral structure -relationship: develops_from UBERON:0003072 {evidence="definitional"} ! optic cup -relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: has_part UBERON:0000965 ! lens of camera-type eye relationship: has_part UBERON:0000966 ! retina -relationship: in_lateral_side_of UBERON:0000033 ! head relationship: part_of UBERON:0004088 ! orbital region -property_value: UBPROP:0000001 "A cavitated compound organ that transduces light waves into neural signals.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000107", ontology="TAO", source="TAO:wd"} -property_value: UBPROP:0000003 "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000275", ontology="VHOG", source="DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "FMA distinguishes Eye (subdivision of face) which has its parts an Eyeball (organ), as well as other structures, and the orbit of skull. MA includes eyelid, conjunctiva and lacrimal apparatus as part of MA:eye - consistent with FMA - so we can infer that MA:eye is more like FMA:eye than FMA:eyeball. For other AOs this distinction is less meaningful - e.g. ZFA has no eyelid; XAO has no eyelid, but it has conjuctiva, which is considered part of the xao:eye. GO considers eyelid development part of eye development. See also notes on optic nerve - XAO, AAO and BTO consider this part of the eye. MA considers the eye muscles part of the eye, whereas FMA has a class 'orbital content' for this" xsd:string {external_ontology="FMA"} +relationship: RO:0002202 UBERON:0003072 ! develops from optic cup +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage [Term] id: UBERON:0000020 @@ -7156,7 +7106,6 @@ xref: CALOHA:TS-2043 xref: EHDAA2:0001824 xref: EHDAA:500 xref: EMAPA:35955 -xref: FBbt:00005155 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: GAID:63 xref: HAO:0000930 xref: MA:0000017 @@ -7171,7 +7120,7 @@ intersection_of: UBERON:0000062 ! organ intersection_of: capable_of GO:0050906 ! detection of stimulus involved in sensory perception relationship: capable_of GO:0050906 ! detection of stimulus involved in sensory perception relationship: part_of UBERON:0001032 ! sensory system -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" xsd:anyURI [Term] id: UBERON:0000025 @@ -7183,11 +7132,9 @@ synonym: "duct" NARROW [] xref: galen:Tube is_a: UBERON:0004111 ! anatomical conduit intersection_of: UBERON:0004111 ! anatomical conduit -intersection_of: has_quality PATO:0002299 ! tubular +intersection_of: RO:0000086 PATO:0002299 ! has quality tubular relationship: has_part UBERON:0013522 ! subdivision of tube -relationship: has_quality PATO:0002299 ! tubular -property_value: IAO:0000232 "not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts)" xsd:string -property_value: UBPROP:0000007 "tubular" xsd:string +relationship: RO:0000086 PATO:0002299 ! has quality tubular [Term] id: UBERON:0000033 @@ -7230,12 +7177,8 @@ xref: Wikipedia:Head xref: XAO:0003024 xref: ZFA:0001114 is_a: UBERON:0011676 ! subdivision of organism along main body axis -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0007811 ! craniocervical region -property_value: RO:0002171 UBERON:0000948 -property_value: UBPROP:0000001 "Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010335", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001114", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001644", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.82", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria [Term] id: UBERON:0000042 @@ -7262,11 +7205,8 @@ is_a: UBERON:0004120 ! mesoderm-derived structure relationship: has_part UBERON:0001136 ! mesothelium relationship: has_part UBERON:0002384 ! connective tissue relationship: part_of UBERON:0000060 ! anatomical wall -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png" xsd:anyURI -property_value: UBPROP:0000001 "A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005425", ontology="TAO", source="Wikipedia:Serous_membrane"} -property_value: UBPROP:0000001 "a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP]" xsd:string {source="Wikipedia:Serous_membrane"} -property_value: UBPROP:0000012 "in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA." xsd:string {external_ontology="FMA"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png" xsd:anyURI [Term] id: UBERON:0000047 @@ -7289,7 +7229,7 @@ subset: human_reference_atlas subset: pheno_slim is_a: UBERON:0004111 ! anatomical conduit relationship: channel_for UBERON:0006314 ! bodily fluid -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000060 @@ -7301,13 +7241,11 @@ subset: upper_level synonym: "organ wall" RELATED [FMA:82482] synonym: "wall" BROAD [] synonym: "wall of organ" EXACT [FMA:82482] -xref: EMAPA:25036 xref: FMA:82482 xref: galen:Wall is_a: UBERON:0000064 ! organ part relationship: adjacent_to UBERON:0002553 ! anatomical cavity relationship: has_part UBERON:0004923 ! organ component layer -property_value: UBPROP:0000012 "in FMA, serosa is a wall" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0000061 @@ -7324,7 +7262,6 @@ xref: BILA:0000003 xref: CARO:0000003 xref: EHDAA2:0003003 xref: EMAPA:0 -xref: FBbt:00007001 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:305751 xref: FMA:67135 xref: GAID:781 @@ -7339,10 +7276,10 @@ xref: VHOG:0001759 xref: XAO:0003000 xref: ZFA:0000037 is_a: UBERON:0000465 ! material anatomical entity -relationship: existence_ends_during_or_before UBERON:0000071 ! death stage -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0002497 UBERON:0000071 ! existence ends during or before death stage +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000062 @@ -7369,14 +7306,12 @@ xref: Wikipedia:Organ_(anatomy) is_a: UBERON:0010000 ! multicellular anatomical structure disjoint_from: UBERON:0034921 ! multi organ part structure relationship: capable_of GO:0008150 ! biological_process -relationship: has_boundary UBERON:0006984 ! anatomical surface -relationship: never_in_taxon NCBITaxon:110815 {source="Wikipedia"} relationship: part_of UBERON:0000467 ! anatomical system -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: UBPROP:0000001 "Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." xsd:string {source="GO:0048513"} -property_value: UBPROP:0000012 "CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4" xsd:string +relationship: RO:0002002 UBERON:0006984 ! has 2D boundary anatomical surface +property_value: RO:0002161 NCBITaxon:110815 {source="Wikipedia"} +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000063 @@ -7389,9 +7324,7 @@ synonym: "organ segment" RELATED [FMA:86140] synonym: "segment of organ" RELATED [FMA:86140] xref: FMA:86140 is_a: UBERON:0000064 ! organ part -property_value: editor_note "FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction" xsd:string -property_value: UBPROP:0000001 "Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball." xsd:string {source="FMA:86140", version="3"} -property_value: UBPROP:0000001 "Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal." xsd:string {source="FMA:86140", version="1"} +property_value: IAO:0000116 "FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction" xsd:string [Term] id: UBERON:0000064 @@ -7412,10 +7345,9 @@ xref: SCTID:113343008 xref: SCTID:91717005 is_a: UBERON:0010000 ! multicellular anatomical structure relationship: part_of UBERON:0000062 ! organ -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: IAO:0000232 "currently defined in a very broad sense, may be replaced by more specific classes in the future" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000066 @@ -7464,7 +7396,7 @@ is_a: UBERON:0000105 ! life cycle stage disjoint_from: UBERON:0000092 ! post-embryonic stage relationship: precedes UBERON:0000066 ! fully formed stage relationship: precedes UBERON:0000092 ! post-embryonic stage -relationship: simultaneous_with GO:0009790 ! embryo development +relationship: RO:0002082 GO:0009790 ! simultaneous with embryo development [Term] id: UBERON:0000071 @@ -7477,11 +7409,10 @@ xref: XAO:0000437 xref: XtroDO:0000085 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage -relationship: ends UBERON:0000104 ! life cycle -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: UBPROP:0000012 "ncit:Death is an outcome" xsd:string {external_ontology="ncit"} +relationship: RO:0002229 UBERON:0000104 ! ends life cycle +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000073 @@ -7498,8 +7429,8 @@ xref: UMLS:C1518256 {source="ncithesaurus:Nervous_System_Part"} is_a: UBERON:0000481 ! multi-tissue structure intersection_of: UBERON:0000481 ! multi-tissue structure intersection_of: part_of UBERON:0001016 ! nervous system -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 relationship: part_of UBERON:0001016 ! nervous system +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2009-06-18T09:00:04Z [Term] @@ -7517,9 +7448,9 @@ xref: NCIT:C34076 xref: SCTID:118966000 xref: UMLS:C1519343 {source="ncithesaurus:Skeletal_System_Part"} is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision -relationship: composed_primarily_of UBERON:0004765 ! skeletal element -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0001434 ! skeletal system +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002473 UBERON:0004765 ! composed primarily of skeletal element [Term] id: UBERON:0000076 @@ -7529,7 +7460,6 @@ def: "The surface (external) layer of ectoderm which begins to proliferate short subset: pheno_slim synonym: "surface (external) ectoderm" EXACT [] synonym: "surface ectoderm" EXACT [MP:0012532] -xref: BTO:0006242 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: EHDAA2:0001968 xref: EHDAA:1494 xref: EHDAA:350 @@ -7545,10 +7475,8 @@ xref: Wikipedia:External_ectoderm is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0005291 ! embryonic tissue relationship: part_of UBERON:0000924 {source="EHDAA2"} ! ectoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1d/Ectoderm.png" xsd:anyURI -property_value: editor_note "merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube)" xsd:string -property_value: RO:0002171 UBERON:0002346 -property_value: UBPROP:0000011 "(or external ectoderm) forms the following structures: Skin Epithelium of the mouth and nasal cavity saliavary glands, and glands of mouth and nasal cavity Enamel - as a side note dentin and dental pulp are formed from ectomesenchyme which is derived from ectoderm Epithelium of pineal and pituitary glands Lens and cornea of the eye Apical ectodermal ridge inducing development of the limb buds of the embryo. Sensory receptors in epidermis" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1d/Ectoderm.png" xsd:anyURI +property_value: IAO:0000116 "merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube)" xsd:string [Term] id: UBERON:0000092 @@ -7568,9 +7496,8 @@ xref: WBls:0000103 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage relationship: preceded_by UBERON:0000068 ! embryo stage -relationship: simultaneous_with GO:0009791 ! post-embryonic development +relationship: RO:0002082 GO:0009791 ! simultaneous with post-embryonic development property_value: seeAlso "https://github.com/obophenotype/uberon/issues/344" xsd:anyURI -property_value: UBPROP:0000008 "In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)" xsd:string [Term] id: UBERON:0000104 @@ -7592,9 +7519,9 @@ is_a: BFO:0000003 ! occurrent is_a: UBERON:0000000 ! processual entity relationship: ends_with UBERON:0000071 ! death stage relationship: has_part UBERON:0000105 ! life cycle stage -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 property_value: seeAlso "https://github.com/obophenotype/uberon/issues/532" xsd:anyURI [Term] @@ -7623,12 +7550,10 @@ xref: ZFS:0000000 xref: ZFS:0100000 is_a: UBERON:0000000 ! processual entity relationship: part_of UBERON:0000104 ! life cycle -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: editor_note "this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here" xsd:string -property_value: UBPROP:0000012 "the WBls class 'all stages' belongs here as it is the superclass of other WBls stages" xsd:string -property_value: UBPROP:0000012 "we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage" xsd:string +property_value: IAO:0000116 "this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000106 @@ -7648,7 +7573,6 @@ xref: BILS:0000106 xref: EFO:0001322 xref: EHDAA:27 xref: FBdv:00005288 -xref: IDOMAL:0000302 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C12601 xref: PdumDv:0000100 xref: VHOG:0000745 @@ -7658,9 +7582,8 @@ xref: ZFS:0000001 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage -relationship: seeAlso EMAPA:16033 -relationship: starts UBERON:0000104 ! life cycle -property_value: UBPROP:0000003 "As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000745", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107", source="http://bgee.unil.ch/"} +relationship: RO:0002223 UBERON:0000104 ! starts life cycle +property_value: seeAlso EMAPA:16033 [Term] id: UBERON:0000107 @@ -7683,10 +7606,10 @@ xref: ZFS:0000046 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage intersection_of: UBERON:0000105 ! life cycle stage -intersection_of: simultaneous_with GO:0040016 ! embryonic cleavage +intersection_of: RO:0002082 GO:0040016 ! simultaneous with embryonic cleavage relationship: immediately_preceded_by UBERON:0000106 ! zygote stage relationship: part_of UBERON:0000068 ! embryo stage -relationship: simultaneous_with GO:0040016 ! embryonic cleavage +relationship: RO:0002082 GO:0040016 ! simultaneous with embryonic cleavage [Term] id: UBERON:0000108 @@ -7710,8 +7633,8 @@ is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000107 ! cleavage stage -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI -property_value: editor_note "consider adding a preceding stage 'morula stage' as part of cleavage" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI +property_value: IAO:0000116 "consider adding a preceding stage 'morula stage' as part of cleavage" xsd:string [Term] id: UBERON:0000109 @@ -7738,10 +7661,10 @@ xref: XAO:1000005 xref: ZFS:0000047 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000108 {source="BILS"} ! blastula stage -relationship: simultaneous_with GO:0007369 ! gastrulation +relationship: RO:0002082 GO:0007369 ! simultaneous with gastrulation +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0000110 @@ -7755,14 +7678,12 @@ xref: MmusDv:0000017 xref: XAO:1000006 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000109 ! gastrula stage -relationship: simultaneous_with GO:0001841 ! neural tube formation -property_value: RO:0002174 NCBITaxon:7955 +relationship: RO:0002082 GO:0001841 ! simultaneous with neural tube formation +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa property_value: seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/343" xsd:anyURI -property_value: UBPROP:0000008 "In zebrafish, the times of neurulation and segmentation overlap so extensively there is no distinct neurula period of development, such as occurs largely before segmentation in amphibian embryos." xsd:string [Term] id: UBERON:0000111 @@ -7779,9 +7700,9 @@ xref: OGES:000032 xref: Wikipedia:Organogenesis is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000068 ! embryo stage -relationship: simultaneous_with GO:0048513 ! animal organ development +relationship: RO:0002082 GO:0048513 ! simultaneous with animal organ development +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa property_value: seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/533" xsd:anyURI @@ -7795,7 +7716,6 @@ synonym: "funiculus" EXACT [] synonym: "nerve fiber bundle" EXACT [FBbt:00005099] synonym: "neural fiber bundle" EXACT [] xref: CARO:0001001 -xref: FBbt:00005099 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: NLX:147821 is_a: UBERON:0005162 ! multi cell part structure relationship: has_part GO:0043005 ! neuron projection @@ -7807,15 +7727,14 @@ name: anterior region of body namespace: uberon is_a: UBERON:0000475 ! organism subdivision disjoint_from: UBERON:0000154 {source="lexical"} ! posterior region of body -relationship: anterior_to UBERON:0000154 ! posterior region of body -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria [Term] id: UBERON:0000154 name: posterior region of body namespace: uberon is_a: UBERON:0000475 ! organism subdivision -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria [Term] id: UBERON:0000165 @@ -7849,7 +7768,6 @@ xref: EFO:0000825 xref: EHDAA2:0001326 xref: EHDAA:542 xref: EMAPA:16262 -xref: FBbt:00003126 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:49184 xref: GAID:75 xref: galen:Mouth @@ -7870,19 +7788,11 @@ xref: Wikipedia:Mouth xref: XAO:0003029 xref: ZFA:0000547 xref: ZFA:0000590 -is_a: UBERON:0004921 {notes="the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts"} ! subdivision of digestive tract -intersection_of: UBERON:0004921 ! subdivision of digestive tract -intersection_of: proximalmost_part_of UBERON:0001555 ! digestive tract -relationship: develops_from UBERON:0035804 ! future mouth -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: proximalmost_part_of UBERON:0001555 ! digestive tract -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI +is_a: UBERON:0004921 ! subdivision of digestive tract +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002202 UBERON:0035804 ! develops from future mouth +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/661" xsd:anyURI -property_value: UBPROP:0000001 "Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010355", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000812", ontology="VHOG", source="DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "oral" xsd:string -property_value: UBPROP:0000011 "some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives" xsd:string -property_value: UBPROP:0000012 "in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0000178 @@ -7923,15 +7833,10 @@ is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000179 ! haemolymphatic fluid relationship: has_part CL:0000232 {source="CL:tm"} ! erythrocyte relationship: has_part UBERON:0001969 ! blood plasma -relationship: immediate_transformation_of UBERON:0006596 {source="Bgee:AN"} ! presumptive blood -relationship: located_in UBERON:0002049 {source="https://github.com/obophenotype/uberon/issues/1330"} ! vasculature relationship: part_of UBERON:0002390 ! hematopoietic system -relationship: present_in_taxon NCBITaxon:9606 -property_value: IAO:0000232 "This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid." xsd:string -property_value: UBPROP:0000001 "A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000007", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000046", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000002 "relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000046", ontology="AAO"} -property_value: UBPROP:0000003 "Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000224", ontology="VHOG", source="DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006) ", source="http://bgee.unil.ch/"} +relationship: RO:0001025 UBERON:0002049 {source="https://github.com/obophenotype/uberon/issues/1330"} ! located in vasculature +relationship: RO:0002495 UBERON:0006596 {source="Bgee:AN"} ! immediate transformation of presumptive blood +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000179 @@ -7944,9 +7849,9 @@ xref: CARO:0000081 is_a: UBERON:0006314 ! bodily fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: part_of UBERON:0002193 ! hemolymphoid system -relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0002193 ! hemolymphoid system +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 creation_date: 2009-04-08T04:38:19Z [Term] @@ -7966,11 +7871,11 @@ xref: OGEM:000006 xref: Wikipedia:Blastula is_a: UBERON:0000922 ! embryo intersection_of: UBERON:0000468 ! multicellular organism -intersection_of: existence_starts_and_ends_during UBERON:0000108 ! blastula stage -relationship: develops_from UBERON:0007010 ! cleaving embryo -relationship: existence_starts_and_ends_during UBERON:0000108 ! blastula stage -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI -property_value: editor_note "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" xsd:string +intersection_of: RO:0002491 UBERON:0000108 ! existence starts and ends during blastula stage +relationship: RO:0002202 UBERON:0007010 ! develops from cleaving embryo +relationship: RO:0002491 UBERON:0000108 ! existence starts and ends during blastula stage +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI +property_value: IAO:0000116 "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" xsd:string [Term] id: UBERON:0000383 @@ -7993,7 +7898,6 @@ xref: BILA:0000088 xref: BTO:0001369 xref: BTO:0001485 xref: EFO:0000801 -xref: EMAPA:35578 xref: FMA:72954 xref: MA:0002888 xref: MAT:0000025 @@ -8002,15 +7906,13 @@ xref: VSAO:0000033 xref: XAO:0004042 is_a: UBERON:0011216 ! organ system subdivision intersection_of: UBERON:0011216 ! organ system subdivision -intersection_of: composed_primarily_of UBERON:0001015 ! musculature +intersection_of: RO:0002473 UBERON:0001015 ! composed primarily of musculature relationship: capable_of GO:0003012 ! muscle system process -relationship: composed_primarily_of UBERON:0001015 ! musculature -relationship: never_in_taxon NCBITaxon:6040 -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: present_in_taxon NCBITaxon:9606 -property_value: editor_note "consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77" xsd:string -property_value: UBPROP:0000001 "Anatomical system that consists of the muscles of the body.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000033", ontology="VSAO", source="VSAO:curator"} -property_value: UBPROP:0000012 "we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA" xsd:string {external_ontology="MA"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002473 UBERON:0001015 ! composed primarily of musculature +property_value: IAO:0000116 "consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77" xsd:string +property_value: RO:0002161 NCBITaxon:6040 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000463 @@ -8032,7 +7934,6 @@ xref: CALOHA:TS-2101 xref: CARO:0000004 xref: EHDAA2:0003004 xref: EMAPA:35178 -xref: FBbt:00007019 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9669 xref: galen:BodySubstance xref: HAO:0000004 @@ -8045,11 +7946,11 @@ xref: VHOG:0001726 xref: XAO:0004001 xref: ZFA:0001487 is_a: UBERON:0000465 ! material anatomical entity -relationship: has_quality PATO:0002198 ! quality of a substance -relationship: part_of UBERON:0000468 {notes="this relationship may be too strong and may be weakened in future"} ! multicellular organism -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: part_of UBERON:0000468 ! multicellular organism +relationship: RO:0000086 PATO:0002198 ! has quality quality of a substance +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000464 @@ -8067,7 +7968,6 @@ xref: AEO:0000005 xref: BILA:0000005 xref: CARO:0000005 xref: EHDAA2:0003005 -xref: FBbt:00007017 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:5897 xref: HAO:0000005 xref: NCIT:C94478 @@ -8078,10 +7978,10 @@ xref: VHOG:0001728 xref: XAO:0003190 xref: ZFA:0001643 is_a: UBERON:0000466 ! immaterial anatomical entity -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -relationship: surrounded_by UBERON:0000061 ! anatomical structure +relationship: RO:0002219 UBERON:0000061 ! surrounded by anatomical structure +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000465 @@ -8095,7 +7995,6 @@ xref: AEO:0000006 xref: BILA:0000006 xref: CARO:0000006 xref: EHDAA2:0003006 -xref: FBbt:00007016 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67165 xref: HAO:0000006 xref: TAO:0001836 @@ -8104,9 +8003,9 @@ xref: VHOG:0001721 is_a: BFO:0000040 ! material entity is_a: UBERON:0001062 ! anatomical entity disjoint_from: UBERON:0000466 ! immaterial anatomical entity -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000466 @@ -8121,7 +8020,6 @@ xref: AEO:0000007 xref: BILA:0000007 xref: CARO:0000007 xref: EHDAA2:0003007 -xref: FBbt:00007015 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67112 xref: HAO:0000007 xref: TAO:0001835 @@ -8129,9 +8027,9 @@ xref: TGMA:0001827 xref: VHOG:0001727 is_a: BFO:0000141 ! immaterial entity is_a: UBERON:0001062 ! anatomical entity -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000467 @@ -8159,11 +8057,9 @@ xref: EHDAA2:0003011 xref: EHDAA:392 xref: EMAPA:16103 xref: EV:0100000 -xref: FBbt:00004856 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7149 xref: galen:AnatomicalSystem xref: HAO:0000011 -xref: IDOMAL:0002460 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: MA:0000003 xref: NCIT:C12919 xref: SCTID:278195005 @@ -8179,11 +8075,11 @@ xref: ZFA:0001439 is_a: UBERON:0000061 ! anatomical structure relationship: has_part UBERON:0000062 ! organ relationship: part_of UBERON:0000468 ! multicellular organism -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -relationship: present_in_taxon NCBITaxon:9606 -relationship: seeAlso EHDAA2:0001330 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:9606 +property_value: seeAlso EHDAA2:0001330 [Term] id: UBERON:0000468 @@ -8214,7 +8110,6 @@ xref: EHDAA2:0003191 xref: EHDAA:1 xref: EMAPA:25765 xref: EV:0100016 -xref: FBbt:00000001 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:256135 xref: galen:Organism xref: HAO:0000012 @@ -8230,11 +8125,10 @@ xref: Wikipedia:Multi-cellular_organism xref: XAO:0003004 xref: ZFA:0001094 is_a: UBERON:0010000 ! multicellular anatomical structure -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: editor_note "TODO - split body and mc organism? body continues after death stage" xsd:string -property_value: UBPROP:0000007 "organismal" xsd:string +property_value: IAO:0000116 "TODO - split body and mc organism? body continues after death stage" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000475 @@ -8259,7 +8153,6 @@ xref: CARO:0000032 xref: EFO:0000808 xref: EHDAA2:0003032 xref: EMAPA:36031 -xref: FBbt:00007009 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7153 xref: galen:BodyPart xref: HAO:0000032 @@ -8277,10 +8170,10 @@ xref: XAO:0003013 xref: ZFA:0001308 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure relationship: part_of UBERON:0000468 ! multicellular organism -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: editor_note "Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency" xsd:string +property_value: IAO:0000116 "Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000476 @@ -8295,7 +8188,6 @@ xref: AEO:0000040 xref: BILA:0000040 xref: CARO:0000040 xref: EHDAA2:0003040 -xref: FBbt:00007013 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:63863 xref: HAO:0000040 xref: TAO:0000382 @@ -8304,9 +8196,9 @@ xref: XAO:0003162 xref: ZFA:0000382 is_a: UBERON:0000061 ! anatomical structure disjoint_from: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000477 @@ -8315,12 +8207,11 @@ namespace: uberon def: "Anatomical group whose component anatomical structures lie in close proximity to each other." [FBbt:00007277] subset: common_anatomy subset: upper_level -xref: FBbt:00007277 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: VHOG:0001737 is_a: UBERON:0034923 ! disconnected anatomical group -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000479 @@ -8342,7 +8233,6 @@ xref: CALOHA:TS-2090 xref: CARO:0000043 xref: EHDAA2:0003043 xref: EMAPA:35868 -xref: FBbt:00007003 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9637 xref: galen:Tissue xref: HAO:0000043 @@ -8359,10 +8249,10 @@ xref: ZFA:0001477 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure relationship: has_part GO:0031012 ! extracellular matrix relationship: part_of UBERON:0000468 ! multicellular organism -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: editor_note "changed label and definition to reflect CARO2" xsd:string +property_value: IAO:0000116 "changed label and definition to reflect CARO2" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000481 @@ -8377,7 +8267,6 @@ xref: AEO:0000055 xref: BILA:0000055 xref: CARO:0000055 xref: EHDAA2:0003055 -xref: FBbt:00007010 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: HAO:0000055 xref: TAO:0001488 xref: TGMA:0001847 @@ -8386,9 +8275,9 @@ xref: XAO:0003037 xref: ZFA:0001488 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure relationship: has_part UBERON:0000479 ! tissue -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000483 @@ -8410,7 +8299,6 @@ xref: CALOHA:TS-0288 xref: CARO:0000066 xref: EHDAA2:0003066 xref: EMAPA:32738 -xref: FBbt:00007005 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9639 xref: GAID:402 xref: HAO:0000066 @@ -8427,14 +8315,12 @@ xref: ZFA:0001486 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue -intersection_of: composed_primarily_of CL:0000066 ! epithelial cell -relationship: composed_primarily_of CL:0000066 ! epithelial cell +intersection_of: RO:0002473 CL:0000066 ! composed primarily of epithelial cell relationship: has_part GO:0005911 ! cell-cell junction relationship: has_part UBERON:0005769 ! basement membrane of epithelium -relationship: only_in_taxon NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! Metazoa -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI -property_value: UBPROP:0000003 "The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000387", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.59", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "epithelial" xsd:string +relationship: RO:0002160 NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! only in taxon Metazoa +relationship: RO:0002473 CL:0000066 ! composed primarily of epithelial cell +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI [Term] id: UBERON:0000487 @@ -8463,8 +8349,7 @@ is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0006914 ! squamous epithelium intersection_of: UBERON:0000490 ! unilaminar epithelium intersection_of: has_part CL:0000076 ! squamous epithelial cell -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Unilaminar epithelium that consists of a single layer of squamous cells.[CARO]" xsd:string {date_retrieved="2012-06-20", external_class="CARO:0000070", ontology="CARO", source="FMA:45565", source="http://orcid.org/0000-0001-9114-8737"} +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI [Term] id: UBERON:0000488 @@ -8511,7 +8396,6 @@ is_a: UBERON:0003103 ! compound organ intersection_of: UBERON:0003103 ! compound organ intersection_of: has_part UBERON:0002553 ! anatomical cavity relationship: has_part UBERON:0002553 ! anatomical cavity -property_value: IAO:0000232 "this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future" xsd:string [Term] id: UBERON:0000490 @@ -8536,8 +8420,7 @@ xref: UMLS:C0682574 {source="ncithesaurus:Simple_Epithelium"} xref: XAO:0004007 xref: ZFA:0001495 is_a: UBERON:0000483 ! epithelium -property_value: editor_note "consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable" xsd:string -property_value: UBPROP:0000001 "Epithelium that consists of a single layer of epithelial cells.[CARO]" xsd:string {date_retrieved="2012-06-20", external_class="CARO:0000073", ontology="CARO", source="FMA:45561", source="http://orcid.org/0000-0001-9114-8737"} +property_value: IAO:0000116 "consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable" xsd:string [Term] id: UBERON:0000915 @@ -8557,12 +8440,8 @@ xref: Wikipedia:Thorax is_a: UBERON:0009569 {source="FMA"} ! subdivision of trunk is_a: UBERON:0011676 ! subdivision of organism along main body axis intersection_of: UBERON:0011676 ! subdivision of organism along main body axis -intersection_of: has_skeleton UBERON:0014477 ! thoracic skeleton -relationship: has_skeleton UBERON:0014477 ! thoracic skeleton -property_value: IAO:0000232 "note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest" xsd:string -property_value: RO:0002171 UBERON:0000026 -property_value: RO:0002171 UBERON:0000033 -property_value: RO:0002171 UBERON:0002417 +intersection_of: RO:0002551 UBERON:0014477 ! has skeleton thoracic skeleton +relationship: RO:0002551 UBERON:0014477 ! has skeleton thoracic skeleton [Term] id: UBERON:0000922 @@ -8587,11 +8466,9 @@ xref: EHDAA2:0000002 xref: EHDAA2_RETIRED:0003236 xref: EHDAA:38 xref: EMAPA:16039 -xref: FBbt:00000052 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69068 xref: GAID:963 xref: http://neurolex.org/wiki/Category\:Embryonic_organism -xref: IDOMAL:0000646 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: MAT:0000226 xref: MESH:D004622 xref: MIAA:0000019 @@ -8605,14 +8482,12 @@ xref: XAO:0000113 xref: ZFA:0000103 is_a: UBERON:0000468 ! multicellular organism intersection_of: UBERON:0000468 ! multicellular organism -intersection_of: existence_ends_with UBERON:0000068 ! embryo stage -intersection_of: existence_starts_with UBERON:0000068 ! embryo stage -relationship: existence_ends_with UBERON:0000068 ! embryo stage -relationship: existence_starts_with UBERON:0000068 ! embryo stage -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" xsd:anyURI +intersection_of: RO:0002489 UBERON:0000068 ! existence starts with embryo stage +intersection_of: RO:0002493 UBERON:0000068 ! existence ends with embryo stage +relationship: RO:0002489 UBERON:0000068 ! existence starts with embryo stage +relationship: RO:0002493 UBERON:0000068 ! existence ends with embryo stage +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/503" xsd:anyURI -property_value: UBPROP:0000007 "embryonic" xsd:string -property_value: UBPROP:0000012 "Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo" xsd:string {external_ontology="ZFA"} [Term] id: UBERON:0000923 @@ -8631,7 +8506,6 @@ xref: AAO:0000480 xref: BILA:0000035 xref: BTO:0000556 xref: EMAPA:36033 -xref: FBbt:00000110 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69069 xref: GAID:1303 xref: MESH:D005855 @@ -8645,8 +8519,7 @@ xref: Wikipedia:Germ_layer xref: XAO:0003011 xref: ZFA:0001122 is_a: UBERON:0010316 ! germ layer / neural crest -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001223", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0000924 @@ -8666,7 +8539,6 @@ xref: EFO:0000414 xref: EHDAA2:0000428 xref: EMAPA:16069 xref: EV:0100003 -xref: FBbt:00000111 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69070 xref: GAID:1304 xref: MAT:0000155 @@ -8683,11 +8555,8 @@ xref: XAO:0000001 xref: ZFA:0000016 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000221 ! ectodermal cell -relationship: immediate_transformation_of UBERON:0006601 {source="Bgee:AN"} ! presumptive ectoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png" xsd:anyURI -property_value: UBPROP:0000001 "Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000137", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000153", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "ectodermal" xsd:string +relationship: RO:0002495 UBERON:0006601 {source="Bgee:AN"} ! immediate transformation of presumptive ectoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png" xsd:anyURI [Term] id: UBERON:0000925 @@ -8707,7 +8576,6 @@ xref: EFO:0002545 xref: EHDAA2:0000436 xref: EMAPA:16062 xref: EV:0100005 -xref: FBbt:00000125 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69071 xref: GAID:1305 xref: MAT:0000175 @@ -8723,11 +8591,9 @@ xref: XAO:0000090 xref: ZFA:0000017 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000223 ! endodermal cell -relationship: immediate_transformation_of UBERON:0006595 {source="Bgee:AN"} ! presumptive endoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png" xsd:anyURI -property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000154", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "endodermal" xsd:string +relationship: RO:0002495 UBERON:0006595 {source="Bgee:AN"} ! immediate transformation of presumptive endoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png" xsd:anyURI [Term] id: UBERON:0000926 @@ -8753,7 +8619,6 @@ xref: EHDAA:160 xref: EHDAA:183 xref: EMAPA:16083 xref: EV:0100006 -xref: FBbt:00000126 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69072 xref: GAID:522 xref: MAT:0000174 @@ -8767,15 +8632,11 @@ xref: VHOG:0000152 xref: Wikipedia:Mesoderm xref: XAO:0000050 xref: ZFA:0000041 -is_a: UBERON:0000923 {notes="sometimes not considered primary"} ! germ layer +is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000222 ! mesodermal cell -relationship: immediate_transformation_of UBERON:0006603 {source="Bgee:AN"} ! presumptive mesoderm -relationship: never_in_taxon NCBITaxon:6040 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" xsd:anyURI -property_value: UBPROP:0000001 "Primary germ layer that is the middle of the embryonic germ layers.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000304", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000152", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "mesodermal" xsd:string -property_value: UBPROP:0000008 "sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates" xsd:string {source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} +relationship: RO:0002495 UBERON:0006603 {source="Bgee:AN"} ! immediate transformation of presumptive mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" xsd:anyURI +property_value: RO:0002161 NCBITaxon:6040 [Term] id: UBERON:0000930 @@ -8797,7 +8658,6 @@ synonym: "stomodeal-hypophyseal primordium" BROAD [XAO:0000269] xref: BTO:0004224 xref: EHDAA2:0001929 xref: EMAPA:16263 -xref: FBbt:00000439 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:295846 xref: NCIT:C34306 xref: TAO:0001290 @@ -8807,15 +8667,11 @@ xref: Wikipedia:Stomodeum xref: XAO:0000269 xref: ZFA:0001290 is_a: UBERON:0013522 ! subdivision of tube -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000924 ! ectoderm relationship: part_of UBERON:0035804 ! future mouth -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI -property_value: editor_note "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" xsd:string -property_value: UBPROP:0000001 "Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001290", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx" xsd:string {source="MP:0012522", taxon="NCBITaxon:40674"} -property_value: UBPROP:0000007 "stomodeal" xsd:string -property_value: UBPROP:0000008 "This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity." xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI +property_value: IAO:0000116 "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" xsd:string [Term] id: UBERON:0000941 @@ -8865,22 +8721,17 @@ xref: VHOG:0000543 xref: Wikipedia:Optic_nerve xref: XAO:0000188 xref: ZFA:0000435 -is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0011215 ! central nervous system cell part cluster is_a: UBERON:0034713 ! cranial neuron projection bundle intersection_of: UBERON:0034713 ! cranial neuron projection bundle intersection_of: extends_fibers_into UBERON:0000959 ! optic chiasma -intersection_of: innervates UBERON:0000966 ! retina -relationship: develops_from UBERON:0003902 {source="EHDAA2"} ! retinal neural layer +intersection_of: RO:0002134 UBERON:0000966 ! innervates retina relationship: extends_fibers_into UBERON:0000959 ! optic chiasma relationship: extends_fibers_into UBERON:0003098 ! optic stalk -relationship: innervates UBERON:0000966 ! retina relationship: part_of UBERON:0002104 ! visual system -property_value: editor_note "Do not classify under 'cranial nerve', as this is not a true nerve - should be classified as evaginated sensory afferent[ISBN:0471888893]" xsd:string -property_value: UBPROP:0000001 "A collection of nerve cells that project visual information from the eyes to the brain. (Source: BioGlossary, www.Biology-Text.com)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000435", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Fibrous, somatic sensory element covered by a fibrous connective-tissue sheath and is continuous with the layer of nerve cells on the inner surface of the eye.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010345", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup (reference 1); The (optic) stalk persists as the optic nerve (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000543", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429, http://medical-dictionary.thefreedictionary.com/optic+stalk", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "(relaion to eye): MA, XAO, AAO and BTO consider this part of the eye. This is in contrast to GO, FMA, EHDAA2 (FMA has a class 'intra-ocular part of optic nerve' which represents the region of overlap). Relation to brain: part of diencephalon in EHDAA2, ZFA. In NIF, has the optic nerve root as part, which is a feature part of the diencphalon" xsd:string {external_ontology="MA"} +relationship: RO:0002134 UBERON:0000966 ! innervates retina +relationship: RO:0002202 UBERON:0003902 {source="EHDAA2"} ! develops from retinal neural layer +property_value: IAO:0000116 "Do not classify under 'cranial nerve', as this is not a true nerve - should be classified as evaginated sensory afferent[ISBN:0471888893]" xsd:string [Term] id: UBERON:0000948 @@ -8929,22 +8780,17 @@ is_a: UBERON:0007100 ! primary circulatory organ is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0007100 ! primary circulatory organ intersection_of: has_part UBERON:0004151 ! cardiac chamber -relationship: contributes_to_morphology_of UBERON:0004535 ! cardiovascular system -relationship: develops_from UBERON:0004141 ! heart tube relationship: has_part UBERON:0004151 ! cardiac chamber -relationship: never_in_taxon NCBITaxon:6239 -relationship: never_in_taxon NCBITaxon:7227 -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0015410 {source="MA"} ! heart plus pericardium -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI -property_value: UBPROP:0000001 "Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000114", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010210", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000002 "relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010210", ontology="AAO"} -property_value: UBPROP:0000003 "As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000276", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "cardiac" xsd:string +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002202 UBERON:0004141 ! develops from heart tube +relationship: RO:0002433 UBERON:0004535 ! contributes to morphology of cardiovascular system +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI +property_value: RO:0002161 NCBITaxon:6239 +property_value: RO:0002161 NCBITaxon:7227 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000955 @@ -8978,7 +8824,6 @@ xref: EHDAA:2641 xref: EHDAA:6485 xref: EMAPA:16894 xref: EV:0100164 -xref: FBbt:00005095 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:50801 xref: GAID:571 xref: galen:Brain @@ -9002,20 +8847,15 @@ xref: XAO:0000010 xref: ZFA:0000008 is_a: UBERON:0000062 {source="GO"} ! organ is_a: UBERON:0004121 ! ectoderm-derived structure -relationship: composed_primarily_of CL:0002319 ! neural cell -relationship: contributes_to_morphology_of UBERON:0001016 ! nervous system -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: immediate_transformation_of UBERON:0006238 {source="Bgee:AN"} ! future brain -relationship: in_anterior_side_of UBERON:0000468 ! multicellular organism relationship: part_of UBERON:0001017 {source="FMA"} ! central nervous system -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI -property_value: editor_note "requires review for applicability to invertebrate structures, e.g. synganglion" xsd:string -property_value: UBPROP:0000001 "Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000008", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010478", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO)" xsd:string {source="http://neurolex.org/wiki/Cumbo_terms"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000157", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165", source="http://bgee.unil.ch/"} +relationship: RO:0002433 UBERON:0001016 ! contributes to morphology of nervous system +relationship: RO:0002473 CL:0002319 ! composed primarily of neural cell +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +relationship: RO:0002495 UBERON:0006238 {source="Bgee:AN"} ! immediate transformation of future brain +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI +property_value: IAO:0000116 "requires review for applicability to invertebrate structures, e.g. synganglion" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000957 @@ -9029,11 +8869,10 @@ synonym: "laminar tissue" EXACT [] xref: Wikipedia:Lamina_of_the_vertebral_arch is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue -intersection_of: has_quality PATO:0002124 ! laminar -relationship: has_quality PATO:0002124 ! laminar -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/80/Laminaarcusvertebrae.png" xsd:anyURI -property_value: editor_note "TODO - merge with cell layer?" xsd:string -property_value: UBPROP:0000007 "laminar" xsd:string +intersection_of: RO:0000086 PATO:0002124 ! has quality laminar +relationship: RO:0000086 PATO:0002124 ! has quality laminar +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/80/Laminaarcusvertebrae.png" xsd:anyURI +property_value: IAO:0000116 "TODO - merge with cell layer?" xsd:string [Term] id: UBERON:0000959 @@ -9083,9 +8922,7 @@ intersection_of: extends_fibers_into UBERON:0001908 ! optic tract intersection_of: part_of UBERON:0001894 ! diencephalon relationship: extends_fibers_into UBERON:0000941 ! cranial nerve II relationship: extends_fibers_into UBERON:0001908 ! optic tract -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b3/1543%2CVisalius%27OpticChiasma.jpg" xsd:anyURI -property_value: UBPROP:0000001 "The point at which fibers of the optic nerves cross.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010622", ontology="AAO", source="AAO:DSM"} -property_value: UBPROP:0000003 "The chiasm has been studied in great detail in some animals, while in others relatively little or nothing is known. Although there are some gross architectural features that are conserved within some animals, such as birds and fish, the general picture is one of diversity. This review will attempt to consider the key features of such diversity of chiasmatic organisation in vertebrates and the mechanisms that sculpt them from the limited literature that is available. However, as so much research has been undertaken on the structure and development of the chiasm in laboratory animals, any review must consider the information that has been gleaned from them and hope that future studies will determine whether the features revealed in these animals, and the underlying mechanisms that generate them, have a common vertebrate plan.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000190", ontology="VHOG", source="DOI:10.1016/j.preteyeres.2005.04.005 Jeffery G, Erskine L, Variations in the architecture and development of the vertebrate optic chiasm. Progress in retinal and eye research (2005)", source="http://bgee.unil.ch/"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b3/1543%2CVisalius%27OpticChiasma.jpg" xsd:anyURI [Term] id: UBERON:0000964 @@ -9123,21 +8960,19 @@ xref: ZFA:0000640 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0010000 ! multicellular anatomical structure is_a: UBERON:0010313 ! neural crest-derived structure -relationship: continuous_with UBERON:0001773 ! sclera -relationship: contributes_to_morphology_of UBERON:0001801 ! anterior segment of eyeball -relationship: developmentally_induced_by UBERON:0005426 ! lens vesicle -relationship: develops_from UBERON:0004348 {evidence="definitional"} ! optic eminence -relationship: develops_from UBERON:0005427 ! corneal primordium relationship: has_part UBERON:0001772 ! corneal epithelium relationship: has_part UBERON:0004370 ! anterior limiting lamina of cornea -relationship: has_quality PATO:0000964 ! transparent relationship: part_of UBERON:0001801 {source="MA"} ! anterior segment of eyeball relationship: part_of UBERON:0010409 {source="MA"} ! ocular surface region relationship: part_of UBERON:0012430 {source="FMA-isa"} ! tunica fibrosa of eyeball -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI -property_value: UBPROP:0000007 "corneal" xsd:string -property_value: UBPROP:0000008 "Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals. In fish, and aquatic vertebrates in general, the cornea plays no role in focusing light, since it has virtually the same refractive index as water" xsd:string +relationship: RO:0000086 PATO:0000964 ! has quality transparent +relationship: RO:0002150 UBERON:0001773 ! continuous with sclera +relationship: RO:0002202 UBERON:0004348 ! develops from optic eminence +relationship: RO:0002202 UBERON:0005427 ! develops from corneal primordium +relationship: RO:0002256 UBERON:0005426 ! developmentally induced by lens vesicle +relationship: RO:0002433 UBERON:0001801 ! contributes to morphology of anterior segment of eyeball +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000965 @@ -9176,15 +9011,13 @@ xref: VHOG:0000169 xref: Wikipedia:Lens_(anatomy) xref: XAO:0000008 xref: ZFA:0000035 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005389 ! transparent eye structure -relationship: contributes_to_morphology_of UBERON:0001801 ! anterior segment of eyeball -relationship: developmentally_induced_by UBERON:0003902 ! retinal neural layer -relationship: develops_from UBERON:0005426 ! lens vesicle relationship: part_of UBERON:0001801 ! anterior segment of eyeball -relationship: present_in_taxon NCBITaxon:9606 -property_value: RO:0002171 UBERON:0002049 -property_value: UBPROP:0000003 "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000169", ontology="VHOG", source="DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "This class excludes compound eye corneal lenses." xsd:string +relationship: RO:0002202 UBERON:0005426 ! develops from lens vesicle +relationship: RO:0002256 UBERON:0003902 ! developmentally induced by retinal neural layer +relationship: RO:0002433 UBERON:0001801 ! contributes to morphology of anterior segment of eyeball +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000966 @@ -9232,18 +9065,15 @@ xref: XAO:0000009 xref: ZFA:0000152 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005388 ! photoreceptor array -relationship: develops_from UBERON:0003072 {source="EHDAA2"} ! optic cup relationship: has_part CL:0000573 {source="FMA"} ! retinal cone cell relationship: has_part CL:0000604 {source="FMA"} ! retinal rod cell relationship: has_part CL:0000740 {source="FMA"} ! retinal ganglion cell -relationship: never_in_taxon NCBITaxon:6656 relationship: part_of UBERON:0001802 ! posterior segment of eyeball relationship: part_of UBERON:0019207 ! chorioretinal region -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png" xsd:anyURI -property_value: UBPROP:0000001 "The portion of the eye developing from the optic primordium and including the neural retina and the retinal pigment layer. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000152", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000229", ontology="VHOG", source="DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "retinal" xsd:string +relationship: RO:0002202 UBERON:0003072 {source="EHDAA2"} ! develops from optic cup +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png" xsd:anyURI +property_value: RO:0002161 NCBITaxon:6656 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000970 @@ -9263,7 +9093,6 @@ xref: BTO:0000439 xref: CALOHA:TS-0309 xref: EFO:0000827 xref: EV:0100336 -xref: FBbt:00005162 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: GAID:69 xref: MAT:0000140 xref: MESH:D005123 @@ -9274,11 +9103,7 @@ relationship: capable_of GO:0009584 ! detection of visible light relationship: has_part CL:0000149 {source="PMID:21062451"} ! visual pigment cell relationship: has_part CL:0000210 {source="PMID:21062451"} ! photoreceptor cell relationship: part_of UBERON:0002104 ! visual system -relationship: present_in_taxon NCBITaxon:9606 -property_value: IAO:0000232 "This class encompasses a variety of light-detecting structures from different phyla with no implication of homology, from the compound insect eye to the vertebrate camera-type eye (distinct classes are provided for each)" xsd:string -property_value: UBPROP:0000007 "ocular" xsd:string -property_value: UBPROP:0000007 "optic" xsd:string -property_value: UBPROP:0000010 "Note that whilst this is classified as an organ, it is in fact more of a unit composed of different structures: in Drosophila, it includes the interommatidial bristle as a part; we consider here the vertebrate eye to include the eyeball/eye proper as a part, with the eye having as parts (when present): eyelids, conjuctiva," xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000982 @@ -9317,10 +9142,8 @@ xref: Wikipedia:Joint xref: XAO:0000171 xref: ZFA:0001596 is_a: UBERON:0004905 ! articulation -relationship: connects UBERON:0004765 ! skeletal element -relationship: contributes_to_morphology_of UBERON:0001434 ! skeletal system -property_value: UBPROP:0000001 "Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000101", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000367", ontology="TAO", source="TAO:pem"} +relationship: RO:0002176 UBERON:0004765 ! connects skeletal element +relationship: RO:0002433 UBERON:0001434 ! contributes to morphology of skeletal system [Term] id: UBERON:0001007 @@ -9341,8 +9164,6 @@ xref: BILA:0000082 xref: BTO:0000058 xref: CALOHA:TS-1293 xref: EFO:0000793 -xref: EV:0100056 -xref: FBbt:00005055 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7152 xref: GAID:278 xref: galen:DigestiveSystem @@ -9368,11 +9189,8 @@ disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0022600 ! digestive system process -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000129", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000007 "digestive" xsd:string -property_value: UBPROP:0000012 "many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class" xsd:string {external_ontology="MA"} +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001009 @@ -9384,7 +9202,6 @@ subset: uberon_slim synonym: "systema cardiovasculare" RELATED OMO:0003011 [Wikipedia:Circulatory_system] xref: AAO:0000959 xref: CALOHA:TS-2103 -xref: MESH:D002319 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: VHOG:0001248 xref: Wikipedia:Circulatory_system is_a: UBERON:0000467 ! anatomical system @@ -9394,17 +9211,13 @@ disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0003013 ! circulatory system process -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} -relationship: never_in_taxon NCBITaxon:6073 -relationship: never_in_taxon NCBITaxon:6157 -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI -property_value: IAO:0000232 "the cardiovascular system and the lymphatic system are parts of the circulatory system" xsd:string -property_value: RO:0002174 NCBITaxon:6231 {notes="WBbt coelomocyte currently classified as circulating cell"} -property_value: UBPROP:0000001 "Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000959", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001248", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.493", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} +property_value: RO:0002161 NCBITaxon:6073 +property_value: RO:0002161 NCBITaxon:6157 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001015 @@ -9424,10 +9237,8 @@ synonym: "musculature system" RELATED [] synonym: "musculi" EXACT OMO:0003011 [FMA:32558, FMA:TA] synonym: "set of muscles" EXACT [FMA:32558] synonym: "set of skeletal muscles" EXACT [MA:0000165] -xref: AAO:0011066 xref: BTO:0000887 xref: EFO:0001949 -xref: EMAPA:32715 xref: EMAPA:35577 xref: FMA:32558 xref: MA:0000165 @@ -9439,11 +9250,9 @@ xref: WBbt:0005737 xref: Wikipedia:Muscular_system xref: ZFA:0000548 is_a: UBERON:0011216 ! organ system subdivision -relationship: composed_primarily_of UBERON:0001630 ! muscle organ relationship: part_of UBERON:0000383 ! musculature of body -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png" xsd:anyURI -property_value: RO:0002171 UBERON:0001474 -property_value: UBPROP:0000012 "In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here." xsd:string {external_ontology="FMA"} +relationship: RO:0002473 UBERON:0001630 ! composed primarily of muscle organ +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png" xsd:anyURI [Term] id: UBERON:0001016 @@ -9469,7 +9278,6 @@ xref: EHDAA2:0001246 xref: EHDAA:826 xref: EMAPA:16469 xref: EV:0100162 -xref: FBbt:00005093 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7157 xref: GAID:466 xref: MA:0000016 @@ -9492,20 +9300,15 @@ disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0050877 ! nervous system process -relationship: composed_primarily_of CL:0002319 ! neural cell -relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: has_part CL:0000540 ! neuron -relationship: immediate_transformation_of UBERON:0016880 {source="Bgee:AN"} ! future nervous system -relationship: never_in_taxon NCBITaxon:6040 -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI -property_value: UBPROP:0000001 "A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000396", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000324", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000402", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.117", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "nervous" xsd:string -property_value: UBPROP:0000007 "neural" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002473 CL:0002319 ! composed primarily of neural cell +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +relationship: RO:0002495 UBERON:0016880 {source="Bgee:AN"} ! immediate transformation of future nervous system +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI +property_value: RO:0002161 NCBITaxon:6040 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001017 @@ -9534,7 +9337,6 @@ xref: EHDAA:828 xref: EMAPA:16470 xref: EMAPA:16754 xref: EV:0100163 -xref: FBbt:00005094 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:55675 xref: GAID:570 xref: MA:0000167 @@ -9551,15 +9353,11 @@ xref: XAO:0000215 xref: ZFA:0000012 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0011216 {source="FBbt", source="cjm"} ! organ system subdivision -relationship: immediate_transformation_of UBERON:0016879 {source="Bgee:AN"} ! future central nervous system -relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0001016 ! nervous system -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "Part of the nervous system which includes the brain and spinal cord.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000090", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "The brain and spinal cord. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000012", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO)." xsd:string {source="BIRNLEX:1099"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000293", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 (reference 1), ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 (reference 2), DOI:10.1016/j.cell.2007.02.040 Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud'homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007) (reference 3)", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002495 UBERON:0016879 {source="Bgee:AN"} ! immediate transformation of future central nervous system +property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001018 @@ -9577,12 +9375,10 @@ synonym: "tract" RELATED [] synonym: "tract of neuraxis" EXACT [FMA:83847] xref: BIRNLEX:1649 xref: EV:0100304 -xref: FBbt:00005100 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:83847 xref: NLX:147822 is_a: UBERON:0000122 ! neuron projection bundle is_a: UBERON:0011215 ! central nervous system cell part cluster -property_value: UBPROP:0000001 "White matter structure of CNS that contains axons that arise predominantly in one central nervous system part and terminate in another. Tracts are generally named by their region or origin followed by their region of primary termination, e.g., mammillothalamic tract contains axons that arise from neurons in the mammillary bodies and terminate in the thalamus. (CUMBO)" xsd:string {source="http://neurolex.org/wiki/Cumbo_terms"} [Term] id: UBERON:0001019 @@ -9630,7 +9426,6 @@ xref: BILA:0000099 xref: EFO:0000805 xref: EHDAA2:0003094 xref: EMAPA:16192 -xref: FBbt:00007692 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:75259 xref: MA:0002442 xref: MAT:0000031 @@ -9645,9 +9440,7 @@ is_a: UBERON:0015203 ! non-connected functional system relationship: capable_of_part_of GO:0007600 ! sensory perception relationship: overlaps UBERON:0001016 ! nervous system relationship: part_of UBERON:0004456 ! entire sense organ system -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" xsd:anyURI -property_value: UBPROP:0000003 "An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001674", ontology="VHOG", source="DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" xsd:anyURI [Term] id: UBERON:0001048 @@ -9666,7 +9459,6 @@ xref: AEO:0000171 xref: BTO:0001886 xref: EFO:0001652 xref: EHDAA2:0003171 -xref: FBbt:00005495 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:86589 xref: MAT:0000482 xref: NCIT:C34275 @@ -9698,7 +9490,6 @@ xref: EMAPA:16164 xref: EMAPA:16757 xref: FMA:293882 xref: MAT:0000069 -xref: MESH:D054259 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: MIAA:0000069 xref: NCIT:C34226 xref: neuronames:1365 @@ -9713,12 +9504,8 @@ is_a: UBERON:0003914 {source="EHDAA2"} ! epithelial tube is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0016879 ! future central nervous system -relationship: develops_from UBERON:0005068 ! neural rod -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010617", ontology="AAO", source="AAO:JOR"} -property_value: UBPROP:0000001 "The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000307", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/neural+tube"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000307", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000011 "The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium" xsd:string {source="GO:0021915"} +relationship: RO:0002202 UBERON:0005068 ! develops from neural rod +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0001062 @@ -9734,7 +9521,6 @@ xref: BILA:0000000 xref: BIRNLEX:6 xref: CARO:0000000 xref: EHDAA2:0002229 -xref: FBbt:10000000 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:62955 xref: HAO:0000000 xref: MA:0000001 @@ -9745,9 +9531,9 @@ xref: UMLS:C1515976 {source="ncithesaurus:Anatomic_Structure_System_or_Substance xref: WBbt:0000100 xref: XAO:0000000 xref: ZFA:0100000 -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0001135 @@ -9792,14 +9578,10 @@ xref: ZFA:0005274 is_a: UBERON:0002385 ! muscle tissue intersection_of: UBERON:0002385 ! muscle tissue intersection_of: has_part CL:0000192 ! smooth muscle cell -relationship: composed_primarily_of CL:0000192 ! smooth muscle cell relationship: has_part CL:0000192 ! smooth muscle cell relationship: has_part GO:0071953 ! elastic fiber -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/3/3b/Glatte_Muskelzellen.jpg" xsd:anyURI -property_value: UBPROP:0000001 "A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005274", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010244", ontology="AAO", source="AAO:CAM"} -property_value: UBPROP:0000003 "(...) the first bilateral animals possessed only smooth muscles with the molecular repertoire necessary to build a striated muscle. (...) it is more parsimonious to regard striated muscle cells as a sister cell type to the smooth muscle cells. In this scenario, striated and smooth muscles would have arisen in the stem lineage that led to the Nephrozoa (i.e. all Bilateria exclusive the acoelomorphs) (Hejnol et al., 2009), from an 'acoel-like' smooth muscle, by segregation and divergence of functions and through differential recruitment of additional genes[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001246", ontology="VHOG", source="DOI:10.1002/jez.b.21416 Chiodin M, Achatz JG, Wanninger A, Martinez P, Molecular architecture of muscles in an acoel and its evolutionary implications. Journal of Experimental Zoology (2011)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000013 "GO uses visceral and smooth interchangeably. However visceral can also be used in the sense of the viscera. Many fly annotations to smooth muscle terms. If we want to be inclusive of insects have to have a general definition of tissue that includes cells." xsd:string +relationship: RO:0002473 CL:0000192 ! composed primarily of smooth muscle cell +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/3/3b/Glatte_Muskelzellen.jpg" xsd:anyURI [Term] id: UBERON:0001136 @@ -9827,11 +9609,11 @@ xref: Wikipedia:Mesothelium is_a: UBERON:0000487 ! simple squamous epithelium is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0000487 ! simple squamous epithelium -intersection_of: develops_from UBERON:0000926 ! mesoderm intersection_of: part_of UBERON:0000042 ! serous membrane -relationship: composed_primarily_of CL:0000077 {source="FMA"} ! mesothelial cell +intersection_of: RO:0002202 UBERON:0000926 ! develops from mesoderm relationship: part_of UBERON:0000042 ! serous membrane -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/25/Mesothelium_peritoneal_wash_high_mag.jpg" xsd:anyURI +relationship: RO:0002473 CL:0000077 {source="FMA"} ! composed primarily of mesothelial cell +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/25/Mesothelium_peritoneal_wash_high_mag.jpg" xsd:anyURI [Term] id: UBERON:0001137 @@ -9855,10 +9637,8 @@ xref: SCTID:123961009 xref: UMLS:C0004600 {source="ncithesaurus:Back"} xref: Wikipedia:Dorsum_(anatomy) is_a: UBERON:0000475 ! organism subdivision -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/432px-Gray-back.PNG" xsd:anyURI -property_value: UBPROP:0000007 "dorsal" xsd:string -property_value: UBPROP:0000008 "In humans, called the back, a large posterior area of the human body, rising from the top of the buttocks to the back of the neck and the shoulders. It is the surface opposite to the chest, its height being defined by the vertebral column (commonly referred to as the spine or backbone) and its breadth being supported by the ribcage and shoulders. The spinal canal runs through the spine and provides nerves to the rest of the body" xsd:string +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/432px-Gray-back.PNG" xsd:anyURI [Term] id: UBERON:0001434 @@ -9894,18 +9674,11 @@ intersection_of: has_part UBERON:0004770 ! articular system disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0004456 ! entire sense organ system -relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: has_part UBERON:0004288 ! skeleton relationship: has_part UBERON:0004770 ! articular system relationship: part_of UBERON:0002204 ! musculoskeletal system -property_value: RO:0002171 UBERON:0001016 +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/The-skeletal-system" xsd:anyURI -property_value: UBPROP:0000001 "Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000434", ontology="TAO", source="TAO:wd"} -property_value: UBPROP:0000001 "Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000027", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "System that provides physical support to the organism.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000566", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000003 "By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001254", ontology="VHOG", source="DOI:10.1159/000324245 Donoghue PCJ, Sansom IJ, Origin and early evolution of vertebrate skeletonization. Microscopy research and technique (2002)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "skeletal" xsd:string -property_value: UBPROP:0000012 "GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates" xsd:string {external_ontology="GO"} [Term] id: UBERON:0001444 @@ -9944,13 +9717,9 @@ xref: SCTID:302549007 xref: UMLS:C0015450 {source="ncithesaurus:Face"} xref: Wikipedia:Face is_a: UBERON:0001444 ! subdivision of head -relationship: contributes_to_morphology_of UBERON:0000033 ! head relationship: has_part UBERON:0000165 ! mouth -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Mona_Lisa_headcrop.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face." xsd:string {source="FMA:24728"} -property_value: UBPROP:0000001 "The area that extends from the median ocellus to the oral foramen[HAO]." xsd:string {source="HAO:0000316", source="http://api.hymao.org/api/ref/67791", taxon="NCBITaxon:7399"} -property_value: UBPROP:0000007 "facial" xsd:string -property_value: UBPROP:0000011 "The face develops from outward growth of tissue located rostral to the cranium & pharynx. The lower jaw and most of the upper jaw are formed by growth of the first pharyngeal (branchial) arch. The upper incisor region and the nose and forehead (frontal region) are formed from tissue located rostral to the neural tube (frontonasal prominence)" xsd:string {source="vanat.cvm.umn.edu/TFFlectPDFs/LectFaceDevelop.pdf"} +relationship: RO:0002433 UBERON:0000033 ! contributes to morphology of head +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Mona_Lisa_headcrop.jpg" xsd:anyURI [Term] id: UBERON:0001555 @@ -9974,11 +9743,9 @@ xref: BTO:0000545 xref: EHDAA2:0000726 xref: EHDAA:518 xref: EMAPA:16247 -xref: FBbt:00003125 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45615 xref: galen:AlimentaryTract xref: MA:0000917 -xref: MESH:D041981 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: NCIT:C34082 xref: TAO:0000112 xref: TGMA:0001819 @@ -9987,18 +9754,13 @@ xref: VHOG:0000309 xref: WBbt:0005743 xref: ZFA:0000112 is_a: UBERON:0000025 ! tube -relationship: connects UBERON:0000165 ! mouth -relationship: immediate_transformation_of UBERON:0007026 {source="NCBIBook:NBK10107"} ! presumptive gut -relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} -relationship: never_in_taxon NCBITaxon:41324 {source="DOI:10.1371/journal.pone.0016309"} -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0001007 ! digestive system -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "The alimentary or digestive tract, and associated organs.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000112", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000309", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "FMA also has a term 'gastrointestinal tract', but this includes the liver." xsd:string {external_ontology="FMA"} -property_value: UBPROP:0000012 "we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509" xsd:string {external_ontology="MA"} -property_value: UBPROP:0000013 "we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002176 UBERON:0000165 ! connects mouth +relationship: RO:0002495 UBERON:0007026 {source="NCBIBook:NBK10107"} ! immediate transformation of presumptive gut +property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} +property_value: RO:0002161 NCBITaxon:41324 {source="DOI:10.1371/journal.pone.0016309"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001605 @@ -10024,8 +9786,8 @@ is_a: UBERON:0003386 {source="MA"} ! smooth muscle of eye is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0011222 {source="FMA"} ! intra-ocular muscle relationship: part_of UBERON:0001775 {source="FMA"} ! ciliary body -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/28/Gray872.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/28/Gray872.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001630 @@ -10037,8 +9799,6 @@ subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "muscle" BROAD [ZFA:0005145] -xref: AAO:0011066 -xref: EMAPA:32715 xref: EMAPA:37474 {source="MA:th"} xref: EV:0100146 xref: FMA:5022 @@ -10053,12 +9813,9 @@ xref: ZFA:0005145 is_a: UBERON:0000062 ! organ is_a: UBERON:0005090 ! muscle structure intersection_of: UBERON:0000062 ! organ -intersection_of: composed_primarily_of UBERON:0002385 ! muscle tissue -relationship: composed_primarily_of UBERON:0002385 ! muscle tissue +intersection_of: RO:0002473 UBERON:0002385 ! composed primarily of muscle tissue relationship: part_of UBERON:0001015 ! musculature -property_value: UBPROP:0000001 "Portion of tissue composed of contractile fibers.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005145", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001245", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.75", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "muscular" xsd:string +relationship: RO:0002473 UBERON:0002385 ! composed primarily of muscle tissue [Term] id: UBERON:0001711 @@ -10087,17 +9844,12 @@ xref: UMLS:C0015426 {source="ncithesaurus:Eyelid"} xref: VHOG:0000016 xref: Wikipedia:Eyelid is_a: UBERON:0000064 ! organ part +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: capable_of GO:0060082 ! eye blink reflex -relationship: contributes_to_morphology_of UBERON:0000019 ! camera-type eye relationship: part_of UBERON:0000019 {source="multiple"} ! camera-type eye relationship: protects UBERON:0010409 ! ocular surface region -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/84/Eye_makeup.jpg" xsd:anyURI -property_value: UBPROP:0000007 "blepharic" xsd:string -property_value: UBPROP:0000007 "palpebral" xsd:string -property_value: UBPROP:0000008 "In humans the upper and lower eyelid consists of the following layers, starting anteriorly: (1) skin, (2) a layer of subcutaneous connective tissue, (3) a layer of striated muscle fibres of the orbicularis muscle, (4) a layer of submuscular connective tissue, (5) a fibrous layer, including the tarsal plates, (6) a layer of smooth muscle, (7) the palpebral conjunctiva." xsd:string -property_value: UBPROP:0000012 "Consider adding 'eye surface', like MA" xsd:string {external_ontology="MA"} -property_value: UBPROP:0000012 "FMA divides this into skin, fascia, conjunctiva" xsd:string {external_ontology="FMA"} -property_value: UBPROP:0000202 FMA:75178 +relationship: RO:0002433 UBERON:0000019 ! contributes to morphology of camera-type eye +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/84/Eye_makeup.jpg" xsd:anyURI [Term] id: UBERON:0001766 @@ -10126,11 +9878,9 @@ xref: UMLS:C0003151 {source="ncithesaurus:Anterior_Chamber_of_the_Eye"} xref: VHOG:0001431 xref: Wikipedia:Anterior_chamber_of_eyeball is_a: UBERON:0006311 {source="FMA"} ! chamber of eyeball -relationship: contributes_to_morphology_of UBERON:0001801 ! anterior segment of eyeball relationship: part_of UBERON:0001801 ! anterior segment of eyeball -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI -property_value: UBPROP:0000001 "The part of the eyeball between the cornea and the iris, filled with aqueous humor. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001431", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/anterior+chamber"} -property_value: UBPROP:0000012 "space in EHDAA2 - consider adding Cavity of anterior chamber of eyeball" xsd:string {external_ontology="EHDAA2"} +relationship: RO:0002433 UBERON:0001801 ! contributes to morphology of anterior segment of eyeball +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI [Term] id: UBERON:0001768 @@ -10156,16 +9906,17 @@ xref: NCIT:C12811 xref: SCTID:280648000 xref: UMLS:C0042160 {source="ncithesaurus:Uvea"} xref: Wikipedia:Uvea +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004923 {source="FMA"} ! organ component layer -relationship: contributes_to_morphology_of UBERON:0000019 ! camera-type eye +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: has_part UBERON:0001769 ! iris relationship: has_part UBERON:0001775 ! ciliary body relationship: has_part UBERON:0001776 ! optic choroid relationship: part_of UBERON:0001801 ! anterior segment of eyeball -relationship: present_in_taxon NCBITaxon:7955 {source="DOI:10.1177/0192623311409597"} -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/eb/Gray869.png" xsd:anyURI -property_value: editor_note "TODO - check child terms, isa vs partof. See also MA:0001284 ! tunica vasculosa plexus" xsd:string -property_value: UBPROP:0000007 "uveal" xsd:string +relationship: RO:0002433 UBERON:0000019 ! contributes to morphology of camera-type eye +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/eb/Gray869.png" xsd:anyURI +property_value: IAO:0000116 "TODO - check child terms, isa vs partof. See also MA:0001284 ! tunica vasculosa plexus" xsd:string +property_value: RO:0002175 NCBITaxon:7955 {source="DOI:10.1177/0192623311409597"} [Term] id: UBERON:0001769 @@ -10200,14 +9951,10 @@ xref: XAO:0000185 xref: ZFA:0001238 is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004121 ! ectoderm-derived structure -relationship: contributes_to_morphology_of UBERON:0011892 ! anterior uvea -relationship: develops_from UBERON:0004128 {source="XAO"} ! optic vesicle relationship: part_of UBERON:0011892 ! anterior uvea -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "The opaque muscular contractile diaphragm suspended in the aqueous humour in front of the lens of the eye. The organ is perforated by the pupil and continues peripherally with the ciliary body. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000101", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000101", ontology="VHOG", source="DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "iridial" xsd:string -property_value: UBPROP:0000008 "The avian iris and ciliary body undergoes a transition from smooth-to-striated muscle during embryonic development [DOI:dx.doi.org/10.1006/dbio.1998.9019]" xsd:string +relationship: RO:0002202 UBERON:0004128 {source="XAO"} ! develops from optic vesicle +relationship: RO:0002433 UBERON:0011892 ! contributes to morphology of anterior uvea +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001772 @@ -10249,17 +9996,15 @@ xref: TAO:0002187 xref: UMLS:C0459875 {source="ncithesaurus:Corneal_Epithelium"} xref: Wikipedia:Corneal_epithelium xref: ZFA:0001683 +is_a: UBERON:0010313 ! neural crest-derived structure is_a: UBERON:0015808 ! eye epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: bounding_layer_of UBERON:0000964 ! cornea relationship: bounding_layer_of UBERON:0000964 ! cornea -relationship: contributes_to_morphology_of UBERON:0000964 ! cornea -relationship: develops_from UBERON:0000076 {source="ISBN:0781772214"} ! external ectoderm -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png" xsd:anyURI -property_value: UBPROP:0000001 "Portion of tissue comprised of four to six layers of nonkeratinized, stratified squamous cells and represents approximately 60% of the thickness of the cornea.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002187", ontology="TAO", source="ZFIN:ZDB-PUB-061010-3"} -property_value: UBPROP:0000008 "In Humans: It consists of several layers of cells. The cells of the deepest layer are columnar; then follow two or three layers of polyhedral cells, the majority of which are prickle cells similar to those found in the stratum mucosum of the cuticle. Lastly, there are three or four layers of squamous cells, with flattened nuclei" xsd:string -property_value: UBPROP:0000008 "In zebrafish: nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals" xsd:string +relationship: RO:0002202 UBERON:0000076 {source="ISBN:0781772214"} ! develops from external ectoderm +relationship: RO:0002433 UBERON:0000964 ! contributes to morphology of cornea +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001773 @@ -10288,21 +10033,14 @@ xref: Wikipedia:Sclera xref: XAO:0000183 xref: ZFA:0005563 is_a: UBERON:0000064 ! organ part -relationship: contributes_to_morphology_of UBERON:0000019 ! camera-type eye -relationship: develops_from UBERON:0003314 {source="ISBN:0781772214"} ! eye mesenchyme -relationship: develops_from UBERON:0007213 {inferred_by="cjm", source="ISBN:0781772214", source="Wikipedia"} ! mesenchyme derived from head neural crest +is_a: UBERON:0010313 ! neural crest-derived structure relationship: has_part CL:0000347 {source="ZFA"} ! scleral cell -relationship: has_quality PATO:0000963 ! opaque relationship: part_of UBERON:0012430 {source="FMA"} ! tunica fibrosa of eyeball -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI -property_value: UBPROP:0000001 "The sclera, also known as the white part of the eye, is the opaque (usually white, though certain animals, such as horses and lizards, can have black sclera), fibrous, protective, outer layer of the eye containing collagen and elastic fiber. It is derived from the neural crest. In children, it is thinner and shows some of the underlying pigment, appearing slightly blue. In the elderly, however, fatty deposits on the sclera can make it appear slightly yellow. The sclera forms the posterior five sixths of the connective tissue coat of the globe. It is continuous with the dura mater and the cornea, and maintains the shape of the globe, offering resistance to internal and external forces, and provides an attachment for the extraocular muscle insertions. The sclera is perforated by plenty of nerves and vessels passing through the posterior scleral foramen, the hole that is formed by the optic nerve. At the optic disk the outer two-thirds of the sclera continues with the dura mater (outer coat of the brain) via the dural sheath of the optic nerve. The inner third joins with some choroidal tissue to form a plate (lamina cribrosa) across the optic nerve with perforations through which the optic fibers (fasciculi). The thickness of the sclera varies from 1mm at the posterior pole to 0.3 mm just behind the rectus muscle insertions. The sclera's blood vessels are mainly on the surface, and together with the conjunctiva (which lies on top) This is a thin layer covering the sclera. Along with the vessels of the conjunctiva, those of the sclera renders the inflamed eye bright red. [WP,unvetted][Wikipedia:Sclera]." xsd:string {source="Wikipedia:Sclera"} -property_value: UBPROP:0000001 "The tough, usually white, outer coat of the eyeball, covering all the posterior surface and continuous anteriorly with the cornea. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001274", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/sclera"} -property_value: UBPROP:0000007 "scleral" xsd:string -property_value: UBPROP:0000008 "in fish, reptiles and monotremes the connective tissue of the sclera is skeletal" xsd:string -property_value: UBPROP:0000010 "continuous with the dura mater and the cornea; The sclera forms the posterior five-sixths of the connective tissue coat of the globe." xsd:string -property_value: UBPROP:0000011 "Majority derives from NC that surrounds optic cup of neurectoderm; a small temporal portion develops from the mesoderm that contributes to striated extra-ocular muscles and vascular endothelia[Rada&Johnson]." xsd:string -property_value: UBPROP:0000011 "Seko et al demonstrate chondrogenic potential and identify this as connective tissue[DOI:10.1371/journal.pone.0003709]." xsd:string +relationship: RO:0000086 PATO:0000963 ! has quality opaque +relationship: RO:0002202 UBERON:0003314 {source="ISBN:0781772214"} ! develops from eye mesenchyme +relationship: RO:0002433 UBERON:0000019 ! contributes to morphology of camera-type eye +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001775 @@ -10335,14 +10073,13 @@ xref: Wikipedia:Ciliary_body xref: XAO:0000186 is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004121 ! ectoderm-derived structure -relationship: contributes_to_morphology_of UBERON:0011892 ! anterior uvea -relationship: develops_from UBERON:0002346 {source="ISBN:0781772214"} ! neurectoderm relationship: has_part UBERON:0001605 ! ciliary muscle relationship: has_part UBERON:0010427 ! ciliary processes relationship: part_of UBERON:0011892 ! anterior uvea -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI -property_value: UBPROP:0000003 "The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000102", ontology="VHOG", source="DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007)", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0002346 {source="ISBN:0781772214"} ! develops from neurectoderm +relationship: RO:0002433 UBERON:0011892 ! contributes to morphology of anterior uvea +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001776 @@ -10381,15 +10118,13 @@ disjoint_from: UBERON:0011892 {source="lexical"} ! anterior uvea relationship: adjacent_to UBERON:0000966 ! retina relationship: adjacent_to UBERON:0001773 ! sclera relationship: adjacent_to UBERON:0011892 ! anterior uvea -relationship: contributes_to_morphology_of UBERON:0001768 ! uvea relationship: overlaps UBERON:0001802 {source="Wikipedia"} ! posterior segment of eyeball relationship: part_of UBERON:0001768 {source="MA"} ! uvea relationship: part_of UBERON:0019207 ! chorioretinal region -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI -property_value: editor_note "check choroid vs choroid layer; check ZFA/TAO placement - no homology assertion in VHOG. Note this is entirely in the posterior region of eyeball in ZFA" xsd:string -property_value: UBPROP:0000007 "choroidal" xsd:string -property_value: UBPROP:0000012 "MP treats posterior uvea and optic choroid as distinct" xsd:string {external_ontology="MP"} +relationship: RO:0002433 UBERON:0001768 ! contributes to morphology of uvea +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: IAO:0000116 "check choroid vs choroid layer; check ZFA/TAO placement - no homology assertion in VHOG. Note this is entirely in the posterior region of eyeball in ZFA" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001777 @@ -10418,17 +10153,15 @@ xref: UMLS:C0010040 {source="ncithesaurus:Corneal_Stroma"} xref: Wikipedia:Corneal_stroma xref: ZFA:0001685 is_a: UBERON:0003891 ! stroma +is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0003891 ! stroma intersection_of: part_of UBERON:0000964 ! cornea relationship: adjacent_to UBERON:0004367 ! Descemet's membrane relationship: adjacent_to UBERON:0004370 ! anterior limiting lamina of cornea -relationship: contributes_to_morphology_of UBERON:0000964 ! cornea -relationship: develops_from UBERON:0007213 {inferred_by="cjm", source="ISBN:0781772214", source="Wikipedia"} ! mesenchyme derived from head neural crest relationship: part_of UBERON:0000964 ! cornea -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png" xsd:anyURI -property_value: UBPROP:0000001 "Portion of tissue that is located basal to Bowman's layer and distal to Descemet's membrane and is comprised largely of connective tissue.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002189", ontology="TAO", source="ZFIN:ZDB-PUB-061010-3"} -property_value: UBPROP:0000002 "relationship type change: subclass tissue (CARO:0000043) CHANGED TO: develops_from tissue (UBERON:0000479)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002189", ontology="TAO"} -property_value: UBPROP:0000002 "relationship type change: subclass tissue (CARO:0000043) CHANGED TO: has_developmental_contribution_from tissue (UBERON:0000479)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002189", ontology="TAO"} +relationship: RO:0002202 UBERON:0007213 ! develops from mesenchyme derived from head neural crest +relationship: RO:0002433 UBERON:0000964 ! contributes to morphology of cornea +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png" xsd:anyURI [Term] id: UBERON:0001778 @@ -10454,8 +10187,8 @@ intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001775 ! ciliary body relationship: has_part GO:0048770 {source="MP"} ! pigment granule relationship: part_of UBERON:0001775 {source="MA"} ! ciliary body -relationship: present_in_taxon NCBITaxon:9606 relationship: produces UBERON:0001796 {source="Wikipedia"} ! aqueous humor of eyeball +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001781 @@ -10476,10 +10209,10 @@ xref: NCIT:C49328 xref: SCTID:280657006 xref: UMLS:C0459649 {source="ncithesaurus:Retina_Layer"} xref: XAO:0000266 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0022303 ! nervous system cell part layer -relationship: contributes_to_morphology_of UBERON:0000966 ! retina relationship: part_of UBERON:0000966 ! retina -property_value: UBPROP:0000012 "MA does not treat internal/external limiting memranes as layers - these are classified as laminae. Here we follow other ontologies in grouping with other layers. MA also treats retinal pigment epithelium and neural retina epithelium as distinct from the layers. We follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers - these are also classified as layers, giving us over the usual 10 layers" xsd:string {external_ontology="MA"} +relationship: RO:0002433 UBERON:0000966 ! contributes to morphology of retina [Term] id: UBERON:0001782 @@ -10526,19 +10259,15 @@ xref: XAO:0003217 xref: ZFA:0000144 is_a: UBERON:0000957 ! lamina is_a: UBERON:0001781 ! layer of retina -is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0015808 ! eye epithelium intersection_of: UBERON:0001781 ! layer of retina -intersection_of: immediate_transformation_of UBERON:0005424 ! presumptive retinal pigmented epithelium +intersection_of: RO:0002495 UBERON:0005424 ! immediate transformation of presumptive retinal pigmented epithelium relationship: adjacent_to UBERON:0001787 {source="Wikipedia"} ! photoreceptor layer of retina relationship: adjacent_to UBERON:0003902 ! retinal neural layer relationship: has_part GO:0048770 ! pigment granule -relationship: immediate_transformation_of UBERON:0005424 ! presumptive retinal pigmented epithelium -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI -property_value: UBPROP:0000001 "A monolayer of pigmented epithelium covering the neural retina; develops from the outer of the two layers of the optic cup. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000144", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "The monolayer of pigmented epithelium covering the neural retina.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011096", ontology="AAO", source="ZFA:0000144"} -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000536", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} +relationship: RO:0002495 UBERON:0005424 ! immediate transformation of presumptive retinal pigmented epithelium +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001787 @@ -10568,9 +10297,7 @@ is_a: UBERON:0001781 ! layer of retina relationship: adjacent_to UBERON:0001788 ! outer limiting layer of retina relationship: has_part CL:0000287 {source="ZFA"} ! eye photoreceptor cell relationship: part_of UBERON:0003902 ! retinal neural layer -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001165", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "we follow MA and ZFA in subdividing this into inner and outer segments" xsd:string {external_ontology="MA"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI [Term] id: UBERON:0001788 @@ -10638,11 +10365,10 @@ xref: XAO:0003219 xref: ZFA:0001464 is_a: UBERON:0001781 ! layer of retina relationship: adjacent_to UBERON:0001790 ! outer plexiform layer of retina -relationship: contributes_to_morphology_of UBERON:0003902 ! retinal neural layer -relationship: overlaps CL:0000287 {notes="soma", source="ZFA"} ! eye photoreceptor cell +relationship: overlaps CL:0000287 ! eye photoreceptor cell relationship: part_of UBERON:0003902 ! retinal neural layer -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001170", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} +relationship: RO:0002433 UBERON:0003902 ! contributes to morphology of retinal neural layer +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001790 @@ -10675,10 +10401,8 @@ xref: XAO:0003218 xref: ZFA:0001330 is_a: UBERON:0001781 ! layer of retina relationship: adjacent_to UBERON:0001791 ! inner nuclear layer of retina -relationship: contributes_to_morphology_of UBERON:0003902 ! retinal neural layer relationship: part_of UBERON:0003902 ! retinal neural layer -property_value: UBPROP:0000001 "The layer within the retina where the bipolar cells synapse with the photoreceptor cells.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001330", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001171", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} +relationship: RO:0002433 UBERON:0003902 ! contributes to morphology of retinal neural layer [Term] id: UBERON:0001791 @@ -10716,14 +10440,12 @@ xref: XAO:0003221 xref: ZFA:0000119 is_a: UBERON:0001781 ! layer of retina relationship: adjacent_to UBERON:0001795 ! inner plexiform layer of retina -relationship: contributes_to_morphology_of UBERON:0003902 ! retinal neural layer relationship: has_part CL:0000561 ! amacrine cell relationship: has_part CL:0000745 ! retina horizontal cell relationship: has_part CL:0000748 ! retinal bipolar neuron relationship: part_of UBERON:0003902 ! retinal neural layer -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "The layer of the retina composed of the cell bodies of bipolar cells, horizontal cells, and some of the cell bodies of amacrine cells[BTO:0003176]." xsd:string {source="BTO:0003176"} -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001167", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} +relationship: RO:0002433 UBERON:0003902 ! contributes to morphology of retinal neural layer +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001792 @@ -10762,14 +10484,11 @@ xref: XAO:0003223 xref: ZFA:0000024 is_a: UBERON:0001781 {source="FMA"} ! layer of retina relationship: adjacent_to UBERON:0001793 ! nerve fiber layer of retina -relationship: composed_primarily_of CL:0000740 ! retinal ganglion cell -relationship: contributes_to_morphology_of UBERON:0003902 ! retinal neural layer relationship: part_of UBERON:0003902 {source="FMA"} ! retinal neural layer -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI -property_value: UBPROP:0000001 "a layer of the retina that consists of retinal ganglion cells[WP]. innermost nuclear layer of the retina, which contains neurons that project axons through the optic nerve to the brain[Wikipedia:Ganglion_cell_layer]." xsd:string {source="Wikipedia:Ganglion_cell_layer"} -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001166", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "NIFSTD class appears to be retired in nlx[http://neurolex.org/wiki/Nlx_anat_1005030]" xsd:string {external_ontology="NIF"} +relationship: RO:0002433 UBERON:0003902 ! contributes to morphology of retinal neural layer +relationship: RO:0002473 CL:0000740 ! composed primarily of retinal ganglion cell +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001793 @@ -10803,11 +10522,10 @@ xref: XAO:0003220 xref: ZFA:0001619 is_a: UBERON:0001781 ! layer of retina relationship: adjacent_to UBERON:0001794 ! inner limiting layer of retina -relationship: composed_primarily_of GO:0030424 ! axon -relationship: contributes_to_morphology_of UBERON:0003902 ! retinal neural layer relationship: overlaps UBERON:0000941 ! cranial nerve II relationship: part_of UBERON:0003902 {source="FMA"} ! retinal neural layer -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001169", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} +relationship: RO:0002433 UBERON:0003902 ! contributes to morphology of retinal neural layer +relationship: RO:0002473 GO:0030424 ! composed primarily of axon [Term] id: UBERON:0001794 @@ -10836,12 +10554,12 @@ xref: Wikipedia:Inner_limiting_membrane xref: XAO:0003222 xref: ZFA:0001029 is_a: UBERON:0007619 {source="MA"} ! limiting membrane of retina +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: adjacent_to UBERON:0001797 ! vitreous humor relationship: has_part CL:0000127 ! astrocyte relationship: has_part GO:0043005 ! neuron projection relationship: overlaps CL:0000636 ! Mueller cell -property_value: editor_note "TODO - check frog/fish" xsd:string -property_value: UBPROP:0000001 "Membrane on the apical surface of the retina. The retinal vasculature becomes adhered to the apical surface of the ILM by 30dpf[ZFIN:ZDB-PUB-071023-7, ZFIN:ZDB-PUB-120529-3]." xsd:string {source="ZFIN:ZDB-PUB-071023-7, ZFIN:ZDB-PUB-120529-3"} +property_value: IAO:0000116 "TODO - check frog/fish" xsd:string [Term] id: UBERON:0001795 @@ -10881,16 +10599,12 @@ intersection_of: adjacent_to UBERON:0001791 ! inner nuclear layer of retina intersection_of: adjacent_to UBERON:0001792 ! ganglionic layer of retina relationship: adjacent_to UBERON:0001791 ! inner nuclear layer of retina relationship: adjacent_to UBERON:0001792 ! ganglionic layer of retina -relationship: contributes_to_morphology_of UBERON:0003902 ! retinal neural layer relationship: has_part GO:0030425 ! dendrite relationship: overlaps CL:0000740 ! retinal ganglion cell relationship: overlaps CL:0000748 ! retinal bipolar neuron relationship: part_of UBERON:0003902 ! retinal neural layer -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI -property_value: UBPROP:0000001 "The inner plexiform layer (IPL) is positioned between the INL and the ganglion cell layer and contains the dendrites of RGCs and processes of bipolar and amacrine cells[GO][GO:0010842]." xsd:string {source="GO:0010842"} -property_value: UBPROP:0000001 "The layer within the retina where the bipolar cells synapse with the dendrites of the ganglion cells.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001329", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001168", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "http://neurolex.org/wiki/Nlx_anat_1005032 appears to be retired" xsd:string +relationship: RO:0002433 UBERON:0003902 ! contributes to morphology of retinal neural layer +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png" xsd:anyURI [Term] id: UBERON:0001796 @@ -10919,12 +10633,9 @@ xref: Wikipedia:Aqueous_humor xref: ZFA:0005564 is_a: UBERON:0006312 ! ocular refractive media is_a: UBERON:0006314 ! bodily fluid -relationship: contributes_to_morphology_of UBERON:0001766 ! anterior chamber of eyeball -relationship: part_of UBERON:0001766 {notes="FMA def states A and P", notes="located_in in EHDAA2", source="VHOG"} ! anterior chamber of eyeball -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI -property_value: UBPROP:0000001 "The fluid produced by the ciliary process in the eye and occupying the anterior and posterior chambers. It provides nourishment for the lens and cornea and maintains the ocular pressure, and hence the optical integrity of the eyeball. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000548", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/aqueous+humour"} -property_value: UBPROP:0000003 "(...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000548", ontology="VHOG", source="DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424 and p.426 and p.429 and Figure 12-24", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "FMA says A+P chambers, and MA states A chamber. ZFA states A chamber and tha it is produced primarily by dorsal ciliary epithelial cells.To be investigated across taxa." xsd:string {external_ontology="FMA"} +relationship: part_of UBERON:0001766 ! anterior chamber of eyeball +relationship: RO:0002433 UBERON:0001766 ! contributes to morphology of anterior chamber of eyeball +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI [Term] id: UBERON:0001797 @@ -10950,17 +10661,16 @@ xref: ENVO:02000032 xref: EV:0100344 xref: FMA:58822 xref: MA:0001286 -xref: MESH:D014822 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: NCIT:C13323 xref: UMLS:C0229096 {source="ncithesaurus:Vitreous_Humor"} xref: VHOG:0000795 xref: Wikipedia:Vitreous_humour xref: ZFA:0005561 is_a: UBERON:0006312 ! ocular refractive media -relationship: has_quality PATO:0000964 ! transparent -relationship: located_in UBERON:0005606 ! hyaloid cavity relationship: part_of UBERON:0001798 ! vitreous body -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +relationship: RO:0000086 PATO:0000964 ! has quality transparent +relationship: RO:0001025 UBERON:0005606 ! located in hyaloid cavity +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI [Term] id: UBERON:0001798 @@ -10978,12 +10688,13 @@ xref: NCIT:C33884 xref: SCTID:181170006 xref: UMLS:C0042905 {source="ncithesaurus:Vitreous_Body"} is_a: UBERON:0003566 ! head connective tissue +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0011825 {source="FMA"} ! loose connective tissue -relationship: composed_primarily_of UBERON:0001797 ! vitreous humor -relationship: has_developmental_contribution_from UBERON:0002346 {notes="neural ectoderm of optic cup", source="ISBN:0781772214"} ! neurectoderm relationship: part_of UBERON:0001799 ! vitreous chamber of eyeball -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI -property_value: editor_note "distinciton between body and humor requires more work. These may be merged in future. Note that FMA includes the hyaloid canal as part of the vitreous body" xsd:string +relationship: RO:0002254 UBERON:0002346 ! has developmental contribution from neurectoderm +relationship: RO:0002473 UBERON:0001797 ! composed primarily of vitreous humor +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +property_value: IAO:0000116 "distinciton between body and humor requires more work. These may be merged in future. Note that FMA includes the hyaloid canal as part of the vitreous body" xsd:string [Term] id: UBERON:0001799 @@ -11007,9 +10718,9 @@ xref: UMLS:C0229095 {source="ncithesaurus:Vitreous_Chamber"} xref: Wikipedia:Vitreous_chamber is_a: UBERON:0006311 ! chamber of eyeball intersection_of: UBERON:0006311 ! chamber of eyeball -intersection_of: location_of UBERON:0001798 ! vitreous body -relationship: location_of UBERON:0001798 ! vitreous body +intersection_of: RO:0001015 UBERON:0001798 ! location of vitreous body relationship: part_of UBERON:0001802 ! posterior segment of eyeball +relationship: RO:0001015 UBERON:0001798 ! location of vitreous body [Term] id: UBERON:0001801 @@ -11035,12 +10746,11 @@ xref: UMLS:C0003153 {source="ncithesaurus:Anterior_Eye_Segment"} xref: Wikipedia:Anterior_segment_of_eyeball xref: ZFA:0005566 is_a: UBERON:0000063 ! organ subunit +is_a: UBERON:0004121 ! ectoderm-derived structure disjoint_from: UBERON:0001802 {source="lexical"} ! posterior segment of eyeball -relationship: contributes_to_morphology_of UBERON:0000019 ! camera-type eye -relationship: in_anterior_side_of UBERON:0010230 {source="cjm"} ! eyeball of camera-type eye relationship: part_of UBERON:0010230 {source="FMA"} ! eyeball of camera-type eye -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Cataract_in_human_eye.png" xsd:anyURI -property_value: RO:0002171 UBERON:0001802 {exceptions="ZFA", source="https://github.com/obophenotype/uberon/issues/378", status="pending"} +relationship: RO:0002433 UBERON:0000019 ! contributes to morphology of camera-type eye +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Cataract_in_human_eye.png" xsd:anyURI [Term] id: UBERON:0001802 @@ -11065,10 +10775,10 @@ xref: UMLS:C0278450 {source="ncithesaurus:Posterior_Eye_Segment"} xref: Wikipedia:Posterior_segment_of_eyeball xref: ZFA:0005567 is_a: UBERON:0000063 ! organ subunit -relationship: contributes_to_morphology_of UBERON:0000019 ! camera-type eye -relationship: in_posterior_side_of UBERON:0010230 {source="cjm"} ! eyeball of camera-type eye +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0010230 {source="FMA"} ! eyeball of camera-type eye -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI +relationship: RO:0002433 UBERON:0000019 ! contributes to morphology of camera-type eye +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI [Term] id: UBERON:0001811 @@ -11087,7 +10797,6 @@ xref: AAO:0010343 xref: BTO:0003415 xref: CALOHA:TS-2232 xref: EFO:0000374 -xref: EMAPA:18233 xref: EV:0100340 xref: FMA:59011 xref: GAID:898 @@ -11099,15 +10808,15 @@ xref: UMLS:C0009758 {source="ncithesaurus:Conjunctiva"} xref: Wikipedia:Conjunctiva xref: XAO:0000182 is_a: UBERON:0000060 {source="FMA"} ! anatomical wall +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: adjacent_to UBERON:0001711 ! eyelid relationship: adjacent_to UBERON:0001773 ! sclera -relationship: contributes_to_morphology_of UBERON:0001801 ! anterior segment of eyeball -relationship: develops_from UBERON:0000076 {source="ISBN:0781772214"} ! external ectoderm relationship: part_of UBERON:0005908 {source="cjm"} ! conjunctival sac relationship: part_of UBERON:0010409 {source="MA"} ! ocular surface region -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png" xsd:anyURI -property_value: UBPROP:0000007 "conjunctival" xsd:string +relationship: RO:0002202 UBERON:0000076 {source="ISBN:0781772214"} ! develops from external ectoderm +relationship: RO:0002433 UBERON:0001801 ! contributes to morphology of anterior segment of eyeball +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001890 @@ -11148,18 +10857,12 @@ xref: Wikipedia:Forebrain xref: XAO:0000011 xref: ZFA:0000109 is_a: UBERON:0002616 ! regional part of brain -is_a: UBERON:0004121 ! ectoderm-derived structure disjoint_from: UBERON:0002298 ! brainstem -relationship: contributes_to_morphology_of UBERON:0000955 ! brain -relationship: develops_from UBERON:0003080 ! anterior neural tube -relationship: immediate_transformation_of UBERON:0006240 {evidence="definitional"} ! future forebrain -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI -property_value: UBPROP:0000001 "Most anterior of the three regions of the brain consisting of the telencephalon and diencephalon.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010147", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "The most anterior region the brain including both the telencephalon and diencephalon. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000109", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000002 "relationship loss: develops_from forebrain neural tube (TAO:0007041)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000109", ontology="TAO"} -property_value: UBPROP:0000003 "In craniate embryos, neural expression of Distal-less-related genes is exclusively in the forebrain (...). Because the major neural expression domain of amphioxus AmphiDll is in the anterior three-fourths of the cerebral vesicle, we suggest that this region of the neural tube is homologous to parts of the craniate forebrain. This conclusion is strongly supported by three-dimensional, computer-assisted reconstruction of the neural tube of amphioxus based on serial transmission electron microscopy. At the neuroanatomical level, a number of detailed homologies are indicated between the anterior three-fourths of the amphioxus cerebral vesicle and the diencephalic region of the craniate forebrain. If one assumes that the amphioxus condition fairly represents the nervous system of the proximate ancestor of the craniates, one can suggest that they evolved from a creature that had the beginnings of a forebrain.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000383", ontology="VHOG", source="PMID:8787764 Holland ND, Panganiban G, Henyey EL, Holland LZ, Sequence and developmental expression of AmphiDll, an amphioxus Distal-less gene transcribed in the ectoderm, epidermis and nervous system: insights into evolution of craniate forebrain and neural crest. Development (1996)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "prosencephalic" xsd:string +relationship: RO:0002202 UBERON:0003080 ! develops from anterior neural tube +relationship: RO:0002433 UBERON:0000955 ! contributes to morphology of brain +relationship: RO:0002495 UBERON:0006240 ! immediate transformation of future forebrain +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001891 @@ -11204,21 +10907,13 @@ xref: Wikipedia:Midbrain xref: XAO:0000014 xref: ZFA:0000128 is_a: UBERON:0002616 ! regional part of brain -is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest -relationship: contributes_to_morphology_of UBERON:0000955 ! brain -relationship: has_developmental_contribution_from UBERON:0003849 {evidence="definitional"} ! mesencephalic neural crest -relationship: immediate_transformation_of UBERON:0009616 {source="Bgee:AN"} ! presumptive midbrain -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/f9/Human_brain_inferior_view_description.JPG" xsd:anyURI -property_value: editor_note "developmental relationships need revised" xsd:string -property_value: RO:0002171 UBERON:0001894 {exceptions="ZFA", exceptions_url="https://github.com/obophenotype/uberon/issues/378", source="ABA", status="pending"} -property_value: RO:0002171 UBERON:0002028 {exceptions="ZFA", source="ABA", status="pending"} -property_value: UBPROP:0000001 "Middle part of the brain composed of the optic tectum and penducular region.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010149", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000128", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000069", ontology="VHOG", source="DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "mesencephalic" xsd:string -property_value: UBPROP:0000012 "part of brainstem in ABA - we reject this in favor of ISBN:0471888893 which has an implicit overlaps relationships" xsd:string {external_ontology="ABA"} +relationship: RO:0002254 UBERON:0003849 ! has developmental contribution from mesencephalic neural crest +relationship: RO:0002433 UBERON:0000955 ! contributes to morphology of brain +relationship: RO:0002495 UBERON:0009616 {source="Bgee:AN"} ! immediate transformation of presumptive midbrain +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f9/Human_brain_inferior_view_description.JPG" xsd:anyURI +property_value: IAO:0000116 "developmental relationships need revised" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001894 @@ -11274,21 +10969,12 @@ xref: Wikipedia:Diencephalon xref: XAO:0000013 xref: ZFA:0000101 is_a: UBERON:0002616 ! regional part of brain -is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest -relationship: contributes_to_morphology_of UBERON:0001890 ! forebrain -relationship: has_developmental_contribution_from UBERON:0003851 {evidence="definitional"} ! diencephalon neural crest -relationship: immediate_transformation_of UBERON:0006222 {evidence="definitional"} ! future diencephalon relationship: part_of UBERON:0001890 ! forebrain -relationship: present_in_taxon NCBITaxon:7762 {notes="not well differentiated from the cerebrum. (Ariens, p. 868)", source="PMID:8932866"} -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI -property_value: RO:0002171 UBERON:0001891 {exceptions="ZFA", source="ABA", source="https://github.com/obophenotype/uberon/issues/378", status="pending"} -property_value: RO:0002171 UBERON:0002028 {source="ABA"} -property_value: UBPROP:0000001 "The more posterior and ventral of two forebrain neuromeres, the other being the telencephalon; major derivatives are the eye cups, the brain pretectal region, the thalamus, hypothalamus, and epithalamus (including the habenula and epiphysis). Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000101", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Unpaired part of the forebrain comprised of three major parts; the epithalamus, thalamus, and hypothalamus.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010481", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000318", ontology="VHOG", source="DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "diencephalic" xsd:string -property_value: UBPROP:0000012 "in ABA, this is part of the brain stem" xsd:string {external_ontology="ABA"} +relationship: RO:0002254 UBERON:0003851 ! has developmental contribution from diencephalon neural crest +relationship: RO:0002433 UBERON:0001890 ! contributes to morphology of forebrain +relationship: RO:0002495 UBERON:0006222 ! immediate transformation of future diencephalon +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI [Term] id: UBERON:0001896 @@ -11337,16 +11023,14 @@ xref: Wikipedia:Bone_marrow_of_ovary_oblongata xref: XAO:0003100 xref: ZFA:0000545 is_a: UBERON:0000064 ! organ part +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: capable_of GO:0002027 ! regulation of heart rate relationship: capable_of GO:0043576 ! regulation of respiratory gaseous exchange relationship: capable_of GO:0044058 ! regulation of digestive system process relationship: part_of UBERON:0002298 ! brainstem relationship: part_of UBERON:0005290 ! myelencephalon -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/6b/Illu_pituitary_pineal_glands.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Posterior portion of the hindbrain which controls respiration, heartbeat, digestion, and swallowing as well as some locomotor responses.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010486", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "The posterior region of the brain that is continuous with the spinal cord. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-17, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000181", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "Classical anatomical studies subdivided the vertebrate rhombencephalon into pons and medulla oblongata. (...) The medulla oblongata appears therefore as a tagma, that is, a group of segmental units (pseudorhombomeres, in this case) sharing some morphological and molecular characteristics, and in some aspects different from the segmental units present in adjoining brain regions, pons and spinal cord.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000181", ontology="VHOG", source="DOI:10.1016/j.ydbio.2008.08.017 Marin F, Aroca P, Puelles L, Hox gene colinear expression in the avian medulla oblongata is correlated with pseudorhombomeric domains. Developmental Biology (2008)", source="http://bgee.unil.ch/"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6b/Illu_pituitary_pineal_glands.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001908 @@ -11367,7 +11051,6 @@ xref: BIRNLEX:1684 xref: BM:Tel-OT xref: DHBA:10589 xref: DMBA:17785 -xref: EMAPA:16678 xref: EMAPA:35617 xref: FMA:62046 xref: GAID:735 @@ -11385,17 +11068,17 @@ xref: Wikipedia:Optic_tract xref: XAO:0004101 xref: ZFA:0000252 is_a: UBERON:0011591 ! tract of diencephalon -relationship: contributes_to_morphology_of UBERON:0003544 ! brain white matter relationship: extends_fibers_into UBERON:0000941 ! cranial nerve II relationship: extends_fibers_into UBERON:0000959 ! optic chiasma -relationship: innervates UBERON:0000966 ! retina relationship: part_of UBERON:0002104 ! visual system relationship: part_of UBERON:0003931 ! diencephalic white matter -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray773.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI -property_value: editor_note "relationships need checking by expert. NIF and ZFA both state part of diencepahalon; MA says part of optic nerve II. in uberon, CNS and PNS are spatially disjoint, and axon tracts are part of the CNS so we make the relationship to CNII 'continuous_with'" xsd:string +relationship: RO:0002134 UBERON:0000966 ! innervates retina +relationship: RO:0002433 UBERON:0003544 ! contributes to morphology of brain white matter +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f6/Gray773.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb" xsd:anyURI +property_value: IAO:0000116 "relationships need checking by expert. NIF and ZFA both state part of diencepahalon; MA says part of optic nerve II. in uberon, CNS and PNS are spatially disjoint, and axon tracts are part of the CNS so we make the relationship to CNII 'continuous_with'" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001943 @@ -11425,7 +11108,6 @@ xref: FMA:62393 xref: HBA:9002 xref: MA:0000212 xref: MAT:0000452 -xref: MESH:D013681 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: neuronames:491 {source="BIRNLEX:1200"} xref: SCTID:362392007 xref: TAO:0000160 @@ -11435,12 +11117,11 @@ xref: Wikipedia:Midbrain_tegmentum xref: XAO:0004271 xref: ZFA:0000160 is_a: UBERON:0002616 ! regional part of brain -relationship: develops_from UBERON:0010285 {source="ZFA"} ! midbrain basal plate relationship: part_of UBERON:0001891 ! midbrain relationship: part_of UBERON:0002298 ! brainstem -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray712.png" xsd:anyURI -property_value: UBPROP:0000003 "Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001367", ontology="VHOG", source="DOI:10.1016/j.brainresbull.2005.05.001 Villar-Cheda B, Abalo XM, Anadon R, Rodicio MC, The tegmental proliferation region in the sea lamprey. Brain Research Bulletin (2005)", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0010285 {source="ZFA"} ! develops from midbrain basal plate +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray712.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001969 @@ -11471,12 +11152,12 @@ is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000179 ! haemolymphatic fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: has_part GO:0005577 ! fibrinogen complex -intersection_of: has_quality PATO:0001548 ! quality of a liquid intersection_of: part_of UBERON:0000178 ! blood -intersection_of: surrounds CL:0000232 ! erythrocyte +intersection_of: RO:0000086 PATO:0001548 ! has quality quality of a liquid +intersection_of: RO:0002221 CL:0000232 ! surrounds erythrocyte relationship: has_part GO:0005577 ! fibrinogen complex relationship: part_of UBERON:0000178 ! blood -relationship: surrounds CL:0000232 ! erythrocyte +relationship: RO:0002221 CL:0000232 ! surrounds erythrocyte [Term] id: UBERON:0001981 @@ -11518,22 +11199,18 @@ xref: XAO:0001011 xref: ZFA:0005314 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000055 ! vessel +is_a: UBERON:0004120 ! mesoderm-derived structure relationship: capable_of_part_of GO:0008015 ! blood circulation relationship: channel_for UBERON:0000178 ! blood -relationship: develops_from UBERON:0004872 ! splanchnic layer of lateral plate mesoderm -relationship: develops_from UBERON:0006965 {source="GO:0072360"} ! vascular cord relationship: has_part CL:0000071 {source="AEO"} ! blood vessel endothelial cell relationship: has_part UBERON:0007500 {source="EHDAA2"} ! epithelial tube open at both ends -relationship: has_quality PATO:0002045 ! dendritic relationship: part_of UBERON:0004537 ! blood vasculature -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI -property_value: editor_note "consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus" xsd:string -property_value: UBPROP:0000001 "Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001250", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000001 "Any of the vessels through which blood circulates in the body.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011004", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001250", ontology="VHOG", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "annelids have blood vessels, but this class is not applicable to annelids." xsd:string -property_value: UBPROP:0000012 "FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX" xsd:string {external_ontology="FMA"} +relationship: RO:0000086 PATO:0002045 ! has quality dendritic +relationship: RO:0002202 UBERON:0004872 ! develops from splanchnic layer of lateral plate mesoderm +relationship: RO:0002202 UBERON:0006965 {source="GO:0072360"} ! develops from vascular cord +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: IAO:0000116 "consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001985 @@ -11561,15 +11238,14 @@ xref: Wikipedia:Corneal_endothelium xref: ZFA:0001687 is_a: UBERON:0001986 ! endothelium is_a: UBERON:0010313 ! neural crest-derived structure -is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0015808 ! eye epithelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0000964 ! cornea relationship: adjacent_to UBERON:0001766 ! anterior chamber of eyeball -relationship: contributes_to_morphology_of UBERON:0000964 ! cornea relationship: part_of UBERON:0000964 ! cornea -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png" xsd:anyURI +relationship: RO:0002433 UBERON:0000964 ! contributes to morphology of cornea +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001986 @@ -11593,11 +11269,10 @@ xref: UMLS:C0014257 {source="ncithesaurus:Endothelium"} is_a: UBERON:0000487 {source="FMA-text-def", source="https://github.com/obophenotype/uberon/issues/225"} ! simple squamous epithelium is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0000483 ! epithelium -intersection_of: composed_primarily_of CL:0000115 ! endothelial cell -relationship: composed_primarily_of CL:0000115 ! endothelial cell -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000007 "endothelial" xsd:string +intersection_of: RO:0002473 CL:0000115 ! composed primarily of endothelial cell +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002473 CL:0000115 ! composed primarily of endothelial cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002020 @@ -11623,7 +11298,6 @@ xref: EMAPA:37596 {source="MA:th"} xref: FMA:67242 xref: HBA:4006 xref: MA:0001112 -xref: MESH:D066128 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C32695 xref: neuronames:2869 xref: TAO:0002197 @@ -11632,9 +11306,8 @@ xref: VHOG:0001768 xref: Wikipedia:Gray_matter xref: ZFA:0001681 is_a: UBERON:0011215 ! central nervous system cell part cluster -relationship: composed_primarily_of GO:0043025 ! neuronal cell body -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg" xsd:anyURI -property_value: UBPROP:0000001 "Multi-tissue comprised of neurons, dendrites, axon terminals, glial cells, and capillaries.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002197", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002473 GO:0043025 ! composed primarily of neuronal cell body +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg" xsd:anyURI [Term] id: UBERON:0002028 @@ -11676,22 +11349,13 @@ xref: Wikipedia:Rhombencephalon xref: XAO:0000015 xref: ZFA:0000029 is_a: UBERON:0002616 ! regional part of brain -is_a: UBERON:0004121 ! ectoderm-derived structure -relationship: contributes_to_morphology_of UBERON:0000955 ! brain -relationship: immediate_transformation_of UBERON:0007277 {source="Bgee:AN"} ! presumptive hindbrain -relationship: only_in_taxon NCBITaxon:89593 ! Craniata -relationship: overlaps UBERON:0002298 {notes="modified-source-relation", source="ABA"} ! brainstem -relationship: present_in_taxon NCBITaxon:7762 {source="PMID:8932866"} -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI -property_value: RO:0002171 UBERON:0001891 {exceptions="ZFA", source="ABA", source="https://github.com/obophenotype/uberon/issues/378", status="pending"} -property_value: RO:0002171 UBERON:0001894 {source="ABA"} -property_value: UBPROP:0000001 "Posterior part of the brain consisting of the cerebellum and medulla oblongata.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010150", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "The most posterior of the three principal regions of the brain, forming the rhombencephalon and all or most of the metencephalon. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000029", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000002 "relationship loss: develops_from hindbrain neural tube (TAO:0007043)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000029", ontology="TAO"} -property_value: UBPROP:0000003 "Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000070", ontology="VHOG", source="DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "rhombencephalic" xsd:string -property_value: UBPROP:0000012 "in MA, brainstem and hindbrain and part-of siblings under brain, consistent with FMA and NIF. See also notes for cerebellum. We weaken the relation in ABA to overlaps" xsd:string {external_ontology="MA"} +relationship: overlaps UBERON:0002298 ! brainstem +relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata +relationship: RO:0002433 UBERON:0000955 ! contributes to morphology of brain +relationship: RO:0002495 UBERON:0007277 {source="Bgee:AN"} ! immediate transformation of presumptive hindbrain +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:7762 {source="PMID:8932866"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002049 @@ -11708,13 +11372,12 @@ xref: FMA:69050 xref: TAO:0005249 xref: ZFA:0005249 is_a: UBERON:0000477 {source="FMA"} ! anatomical cluster -relationship: composed_primarily_of UBERON:0000055 ! vessel relationship: has_part UBERON:0000179 ! haemolymphatic fluid relationship: part_of UBERON:0007798 ! vascular system -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI -property_value: editor_note "see also: vascular system. Consider merging?" xsd:string -property_value: UBPROP:0000007 "vascular" xsd:string +relationship: RO:0002473 UBERON:0000055 ! composed primarily of vessel +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: IAO:0000116 "see also: vascular system. Consider merging?" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002050 @@ -11734,7 +11397,6 @@ xref: BILA:0000034 xref: BTO:0000174 xref: CALOHA:TS-2110 xref: EFO:0000461 -xref: FBbt:00004208 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69067 xref: GAID:407 xref: MESH:D004628 @@ -11750,10 +11412,6 @@ is_a: UBERON:0005423 ! developing anatomical structure intersection_of: UBERON:0005423 ! developing anatomical structure intersection_of: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0000922 ! embryo -property_value: UBPROP:0000001 "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000138", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001105", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000178", ontology="VSAO", source="ZFIN:curator"} -property_value: UBPROP:0000012 "in FMA embryo is_a embryonic structure" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0002075 @@ -11784,10 +11442,8 @@ xref: Wikipedia:Viscus xref: XAO:0003034 is_a: UBERON:0005177 ! trunk region element intersection_of: UBERON:0000062 ! organ -intersection_of: located_in UBERON:0002323 ! coelemic cavity lumen -relationship: located_in UBERON:0002323 ! coelemic cavity lumen -property_value: UBPROP:0000001 "An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010386", ontology="AAO", source="BTO:0001491"} -property_value: UBPROP:0000012 "general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs." xsd:string {external_ontology="FMA"} +intersection_of: RO:0001025 UBERON:0002323 ! located in coelemic cavity lumen +relationship: RO:0001025 UBERON:0002323 ! located in coelemic cavity lumen [Term] id: UBERON:0002090 @@ -11805,12 +11461,10 @@ xref: AAO:0000034 xref: EFO:0000942 xref: EHDAA2:0000161 xref: EHDAA:5049 -xref: EMAPA:17214 xref: EMAPA:37721 {source="MA:th"} xref: FMA:71221 xref: MA:0002986 xref: MAT:0000148 -xref: MESH:D013131 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: MIAA:0000148 xref: TAO:0000317 xref: VHOG:0000317 @@ -11818,14 +11472,10 @@ xref: VSAO:0000093 xref: XAO:0003073 xref: ZFA:0000317 is_a: UBERON:0010912 ! subdivision of skeleton -relationship: develops_from UBERON:0003089 ! sclerotome relationship: part_of UBERON:0005944 ! axial skeleton plus cranial skeleton relationship: part_of UBERON:0011138 ! postcranial axial skeletal system +relationship: RO:0002202 UBERON:0003089 ! develops from sclerotome property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" xsd:anyURI -property_value: UBPROP:0000001 "Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000093", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000034", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000001 "The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000317", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000317", ontology="VHOG", source="DOI:10.1186/1742-9994-8-4 Schilling N, Evolution of the axial system in craniates: morphology and function of the perivertebral musculature. Frontiers in Zoology (2011)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0002100 @@ -11861,10 +11511,6 @@ xref: XAO:0003025 xref: ZFA:0001115 is_a: UBERON:0011676 ! subdivision of organism along main body axis relationship: part_of UBERON:0013702 ! body proper -property_value: RO:0002171 UBERON:0000026 {exceptions="ZFA", source="https://github.com/obophenotype/uberon/issues/378", status="pending"} -property_value: RO:0002171 UBERON:0000033 -property_value: UBPROP:0000001 "Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010339", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001115", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0002104 @@ -11892,7 +11538,6 @@ xref: XAO:0003198 xref: ZFA:0001127 is_a: UBERON:0001032 ! sensory system relationship: capable_of_part_of GO:0007601 ! visual perception -property_value: UBPROP:0000001 "The sensory system used for sight.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000632", ontology="AAO", source="AAO:EJS"} [Term] id: UBERON:0002193 @@ -11908,7 +11553,7 @@ xref: EMAPA:18765 xref: FMA:74562 xref: MA:0000013 is_a: UBERON:0000467 {source="MA"} ! anatomical system -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria [Term] id: UBERON:0002200 @@ -11957,12 +11602,11 @@ is_a: UBERON:0002200 ! vasculature of head is_a: UBERON:0006876 ! vasculature of organ intersection_of: UBERON:0002049 ! vasculature intersection_of: part_of UBERON:0000019 ! camera-type eye -relationship: develops_from UBERON:0003314 {source="ISBN:0781772214"} ! eye mesenchyme relationship: part_of UBERON:0000019 ! camera-type eye -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI -property_value: UBPROP:0000012 "not part of the eye in ZFA. Note this changed to a blood vessel in ZFA" xsd:string {external_ontology="ZFA"} +relationship: RO:0002202 UBERON:0003314 {source="ISBN:0781772214"} ! develops from eye mesenchyme +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002204 @@ -11990,13 +11634,10 @@ is_a: UBERON:0000467 ! anatomical system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of_part_of GO:0040011 ! locomotion -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: has_developmental_contribution_from UBERON:0000926 {notes="check ctenophore"} ! mesoderm relationship: has_part UBERON:0000383 ! musculature of body relationship: has_part UBERON:0001434 ! skeletal system -property_value: UBPROP:0000001 "Anatomical system that provides locomotion and physical support to the organism.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010546", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001275", ontology="VHOG", source="DOI:10.1002/jez.b.21246 Shearman RM, Burke AC, The lateral somitic frontier in ontogeny and phylogeny. Journal of Experimental Zoology (2009)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "musculoskeletal" xsd:string +relationship: RO:0002254 UBERON:0000926 ! has developmental contribution from mesoderm +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage [Term] id: UBERON:0002224 @@ -12023,13 +11664,12 @@ xref: UMLS:C0230139 {source="ncithesaurus:Thoracic_Cavity"} xref: Wikipedia:Thoracic_cavity is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0000915 ! thoracic segment of trunk intersection_of: part_of UBERON:0002323 ! coelemic cavity lumen -relationship: luminal_space_of UBERON:0000915 ! thoracic segment of trunk +intersection_of: RO:0002572 UBERON:0000915 ! luminal space of thoracic segment of trunk relationship: part_of UBERON:0002323 ! coelemic cavity lumen -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI -property_value: UBPROP:0000008 "In many species, the diaphragm separates thoracic and abdominal cavities" xsd:string +relationship: RO:0002572 UBERON:0000915 ! luminal space of thoracic segment of trunk +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI [Term] id: UBERON:0002240 @@ -12085,19 +11725,16 @@ is_a: UBERON:0000489 ! cavitated compound organ is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005174 ! dorsal region element is_a: UBERON:0010314 ! structure with developmental contribution from neural crest -relationship: develops_from UBERON:0003076 ! posterior neural tube -relationship: has_developmental_contribution_from UBERON:0003853 {evidence="definitional"} ! spinal cord neural crest relationship: has_part CL:0005000 {source="ZFA"} ! spinal cord interneuron -relationship: immediate_transformation_of UBERON:0006241 {evidence="definitional"} ! future spinal cord relationship: part_of UBERON:0001017 ! central nervous system -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/58/Spinal_cord_direv.svg" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Spinal_Cord.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Spinal_Cord.glb" xsd:anyURI -property_value: editor_note "TODO - add superclass to unify with VNC?" xsd:string -property_value: RO:0002171 UBERON:0000955 {exceptions="ZFA", source="https://github.com/obophenotype/uberon/issues/378", status="pending"} -property_value: UBPROP:0000001 "Part of the central nervous system which descends from the hindbrain within the vertebral column.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010151", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000601", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003076 ! develops from posterior neural tube +relationship: RO:0002254 UBERON:0003853 ! has developmental contribution from spinal cord neural crest +relationship: RO:0002495 UBERON:0006241 ! immediate transformation of future spinal cord +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/58/Spinal_cord_direv.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Spinal_Cord.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Spinal_Cord.glb" xsd:anyURI +property_value: IAO:0000116 "TODO - add superclass to unify with VNC?" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002298 @@ -12137,17 +11774,11 @@ xref: VHOG:0001457 xref: Wikipedia:Brainstem xref: ZFA:0001707 is_a: UBERON:0002616 ! regional part of brain -relationship: continuous_with UBERON:0002240 ! spinal cord -relationship: contributes_to_morphology_of UBERON:0000955 ! brain relationship: has_part UBERON:0001896 ! medulla oblongata relationship: has_part UBERON:0001943 ! midbrain tegmentum -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b7/Gray719.png" xsd:anyURI -property_value: RO:0002171 UBERON:0001890 {notes="we apply a strict definition"} -property_value: RO:0002171 UBERON:0002037 {exceptions="ZFA", source="ABA", source="https://github.com/obophenotype/uberon/issues/378", status="pending"} -property_value: RO:0002171 UBERON:0002314 {notes="we apply a strict definition"} -property_value: UBPROP:0000001 "Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002156", ontology="TAO", source="ISBN:3764351209"} -property_value: UBPROP:0000001 "Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,adopted][ZFA:0001707]." xsd:string {source="ZFA:0001707"} -property_value: UBPROP:0000001 "the stalk-like part of the brain that comprises the midbrain (aka mesencephalon), the pons (aka pons Varolii), and the medulla oblongata, and connects the cerebral hemispheres with the cervical spinal cord[MP]" xsd:string {source="MP:0005277"} +relationship: RO:0002150 UBERON:0002240 ! continuous with spinal cord +relationship: RO:0002433 UBERON:0000955 ! contributes to morphology of brain +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b7/Gray719.png" xsd:anyURI [Term] id: UBERON:0002316 @@ -12170,7 +11801,6 @@ xref: EMAPA:35927 xref: FMA:83929 xref: HBA:9218 xref: MA:0001135 -xref: MESH:D066127 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C33892 xref: neuronames:2870 xref: NLX:412 @@ -12184,13 +11814,9 @@ xref: VHOG:0001764 xref: Wikipedia:White_matter xref: ZFA:0001682 is_a: UBERON:0011215 ! central nervous system cell part cluster -relationship: composed_primarily_of UBERON:0006135 ! myelinated nerve fiber -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/d7/Grey_matter_and_white_matter_-_very_high_mag.jpg" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg" xsd:anyURI -property_value: UBPROP:0000001 "Cell part cluster consisting predominantly of neurites in the brain and the spinal cord[FMA:83929]." xsd:string {source="FMA:83929"} -property_value: UBPROP:0000001 "Multi-tissue structure comprised largely of myelinated axons.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002142", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "The myelination of axons by glial cells was the last major step in the evolution of cells in the vertebrate nervous system, and white-matter tracts are key to the architecture of the mammalian brain.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001764", ontology="VHOG", source="DOI:10.1038/nature09614 Nave KA, Myelination and support of axonal integrity by glia. Nature (2010)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "nlx_anat_101177 seems to have been lost in the transition from NIFGA to Neurolex" xsd:string {external_ontology="NIF", seeAlso="https://github.com/SciCrunch/NIF-Ontology/issues/83"} +relationship: RO:0002473 UBERON:0006135 ! composed primarily of myelinated nerve fiber +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d7/Grey_matter_and_white_matter_-_very_high_mag.jpg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/d2/Spinal_nerve.svg" xsd:anyURI [Term] id: UBERON:0002323 @@ -12214,7 +11840,6 @@ synonym: "ventral body cavity" NARROW [NCBITaxon:7742] xref: AEO:0000186 xref: BTO:0001707 xref: EHDAA2:0000267 -xref: FBbt:00005060 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:85006 xref: galen:BodyCavity xref: NCIT:C25444 @@ -12224,11 +11849,8 @@ xref: TAO:0001438 xref: UMLS:C0333343 {source="ncithesaurus:Cavity"} xref: ZFA:0001438 is_a: UBERON:0002553 ! anatomical cavity -relationship: luminal_space_of UBERON:0011997 ! coelom -relationship: transformation_of UBERON:0003886 {evidence="definitional"} ! future coelemic cavity lumen -property_value: UBPROP:0000001 "Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]." xsd:string {date_retrieved="2012-09-12", external_class="ZFA:0001438", ontology="ZFA", source="ZFIN:curator"} -property_value: UBPROP:0000001 "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]." xsd:string {date_retrieved="2012-09-12", external_class="BTO:0001707", ontology="BTO", source="BTO"} -property_value: UBPROP:0000008 "In mammals it forms the peritoneal, pleural, and pericardial cavities" xsd:string +relationship: RO:0002494 UBERON:0003886 ! transformation of future coelemic cavity lumen +relationship: RO:0002572 UBERON:0011997 ! luminal space of coelom [Term] id: UBERON:0002328 @@ -12266,23 +11888,15 @@ xref: XAO:0000055 xref: ZFA:0000135 is_a: UBERON:0000062 {source="PMID:15890825"} ! organ is_a: UBERON:0000481 {source="VSAO"} ! multi-tissue structure +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004121 ! ectoderm-derived structure -relationship: develops_from UBERON:0004880 {source="ZFA"} ! chordamesoderm -relationship: develops_from UBERON:0006267 {source="EHDAA2"} ! notochordal plate -relationship: dorsal_to UBERON:0001555 ! digestive tract -relationship: existence_starts_during UBERON:0000068 ! embryo stage -relationship: only_in_taxon NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! Chordata relationship: part_of UBERON:0011137 ! axial skeletal system relationship: produces PR:000014841 ! sonic hedgehog protein -relationship: ventral_to UBERON:0001049 ! neural tube -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000032", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000135", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000327", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000002 "relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000327", ontology="AAO"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000199", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "notochordal" xsd:string -property_value: UBPROP:0000011 "In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord." xsd:string +relationship: RO:0002160 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! only in taxon Chordata +relationship: RO:0002202 UBERON:0004880 {source="ZFA"} ! develops from chordamesoderm +relationship: RO:0002202 UBERON:0006267 {source="EHDAA2"} ! develops from notochordal plate +relationship: RO:0002488 UBERON:0000068 ! existence starts during embryo stage +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0002329 @@ -12321,18 +11935,10 @@ xref: XAO:0000058 xref: ZFA:0000155 is_a: UBERON:0005423 ! developing anatomical structure is_a: UBERON:0007503 {source="EHDAA2"} ! epithelial vesicle -relationship: develops_from UBERON:0003059 {source="ZFA"} ! presomitic mesoderm -relationship: never_in_taxon NCBITaxon:7712 {source="PMID:17237766"} -relationship: only_in_taxon NCBITaxon:7711 {source="GOTAX:0000352"} ! Chordata -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: IAO:0000232 "EDITOR_NOTE currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk" xsd:string -property_value: UBPROP:0000001 "Post-cranial axial segments which form sclerotome and dermomyotome.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010569", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000001 "Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000155", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000002 "relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000155", ontology="TAO"} -property_value: UBPROP:0000002 "relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000155", ontology="TAO"} -property_value: UBPROP:0000002 "relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010569", ontology="AAO"} -property_value: UBPROP:0000003 "(...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000191", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.40, DOI:10.1093/icb/43.1.137 Balavoine G, Adoutte A, The segmented urbilateria: a testable scenario. Integrative and Comparative Biology (2003)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "somitic" xsd:string +relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata +relationship: RO:0002202 UBERON:0003059 {source="ZFA"} ! develops from presomitic mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: RO:0002161 NCBITaxon:7712 {source="PMID:17237766"} [Term] id: UBERON:0002342 @@ -12359,28 +11965,22 @@ xref: MIAA:0000066 xref: NCIT:C34222 xref: neuronames:1366 xref: SCTID:361462002 -xref: TAO:0000045 xref: UMLS:C0027789 {source="ncithesaurus:Neural_Crest"} xref: VHOG:0000057 xref: Wikipedia:Neural_crest xref: XAO:0000048 xref: ZFA:0000045 is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0010316 ! germ layer / neural crest -relationship: composed_primarily_of CL:0000333 {notes="pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! migratory neural crest cell -relationship: develops_from UBERON:0003075 {source="BTO"} ! neural plate -relationship: develops_from UBERON:0005062 {source="PMID:11523831"} ! neural fold -relationship: existence_starts_during UBERON:0000110 {source="PMID:11523831"} ! neurula stage -relationship: only_in_taxon NCBITaxon:89593 {notes="Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells", source="ISBN:0073040584"} ! Craniata relationship: part_of UBERON:0002346 {source="XAO", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! neurectoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI -property_value: IAO:0000232 "EDITOR_NOTE consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams)." xsd:string -property_value: RO:0002174 NCBITaxon:117565 {source="ISBN:0073040584", source="PMID:17377535"} -property_value: UBPROP:0000001 "A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000045", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010578", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831]" xsd:string {source="PMID:11523831"} -property_value: UBPROP:0000003 "We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000057", ontology="VHOG", source="DOI:10.1111/j.1469-7580.2012.01495.x Hall BK, Gillis JA, Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues. J Anat (2012)", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata +relationship: RO:0002202 UBERON:0003075 {source="BTO"} ! develops from neural plate +relationship: RO:0002202 UBERON:0005062 {source="PMID:11523831"} ! develops from neural fold +relationship: RO:0002473 CL:0000333 ! composed primarily of migratory neural crest cell +relationship: RO:0002488 UBERON:0000110 {source="PMID:11523831"} ! existence starts during neurula stage +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI [Term] id: UBERON:0002346 @@ -12403,7 +12003,6 @@ xref: EHDAA:1498 xref: EHDAA:255 xref: EMAPA:16073 xref: EV:0100004 -xref: FBbt:00001057 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:87657 xref: MAT:0000176 xref: MIAA:0000176 @@ -12417,9 +12016,6 @@ xref: ZFA:0001120 is_a: UBERON:0000923 ! germ layer is_a: UBERON:0004121 ! ectoderm-derived structure relationship: has_part CL:0000133 ! neurectodermal cell -property_value: UBPROP:0000003 "(...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000150", ontology="VHOG", source="DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "neurectodermal" xsd:string -property_value: UBPROP:0000013 "we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here" xsd:string [Term] id: UBERON:0002384 @@ -12453,12 +12049,8 @@ xref: VSAO:0000017 xref: XAO:0001017 xref: ZFA:0001632 is_a: UBERON:0000479 ! tissue -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000098", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000001 "Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001641", ontology="TAO", source="TAO:wd"} -property_value: UBPROP:0000001 "Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000017", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} -property_value: UBPROP:0000012 "MA also has set of connective tissues" xsd:string {external_ontology="MA"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002385 @@ -12486,14 +12078,12 @@ xref: Wikipedia:Muscle_tissue is_a: UBERON:0000479 ! tissue is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000479 ! tissue -intersection_of: composed_primarily_of CL:0000187 ! muscle cell +intersection_of: RO:0002473 CL:0000187 ! composed primarily of muscle cell disjoint_from: UBERON:0003714 ! neural tissue relationship: capable_of GO:0006936 ! muscle contraction -relationship: composed_primarily_of CL:0000187 ! muscle cell -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0001015 ! musculature -property_value: RO:0002171 UBERON:0003714 -property_value: UBPROP:0000001 "One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000306", ontology="AAO", source="AAO:LAP"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002473 CL:0000187 ! composed primarily of muscle cell [Term] id: UBERON:0002390 @@ -12536,14 +12126,10 @@ xref: ZFA:0005023 is_a: UBERON:0000467 ! anatomical system is_a: UBERON:0004120 ! mesoderm-derived structure disjoint_from: UBERON:0004456 ! entire sense organ system -relationship: develops_from UBERON:0003061 {evidence="definitional"} ! blood island -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0002193 {source="FMA"} ! hemolymphoid system -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "Anatomical system that consists of the blood and blood forming tissues.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011002", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001624", ontology="VHOG", source="DOI:10.1016/j.coph.2010.05.004 Ellett F, Lieschke GJ, Zebrafish as a model for vertebrate hematopoiesis. Current Opinion in Pharmacology (2010)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "hematopoietic" xsd:string -property_value: UBPROP:0000008 "In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes" xsd:string {source="WP"} +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002202 UBERON:0003061 ! develops from blood island +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002506 @@ -12567,10 +12153,10 @@ is_a: UBERON:0000488 {source="FMA"} ! atypical epithelium is_a: UBERON:0015808 ! eye epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0001769 ! iris -relationship: contributes_to_morphology_of UBERON:0001769 ! iris relationship: has_part GO:0048770 {source="MP"} ! pigment granule relationship: part_of UBERON:0001769 {source="MA"} ! iris -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002433 UBERON:0001769 ! contributes to morphology of iris +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002532 @@ -12594,9 +12180,8 @@ xref: VHOG:0000243 xref: Wikipedia:Epiblast is_a: UBERON:0002050 ! embryonic structure relationship: has_part CL:0000352 ! epiblast cell -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" xsd:anyURI -property_value: editor_note "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" xsd:string -property_value: UBPROP:0000003 "In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000243", ontology="VHOG", source="DOI:10.1146/annurev.cellbio.042308.113344 Zorn AM, Wells JM, Vertebrate endoderm development and organ formation. Annual Review of Cell Developmental Biology (2009)", source="http://bgee.unil.ch/"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" xsd:anyURI +property_value: IAO:0000116 "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" xsd:string [Term] id: UBERON:0002546 @@ -12610,16 +12195,13 @@ synonym: "ectodermal placode" BROAD INCONSISTENT [FMA:293966, PMID:22512454] synonym: "placode" BROAD [Wikipedia:Placode] xref: AAO:0010466 xref: EFO:0001650 -xref: FMA:293966 xref: MAT:0000369 xref: MIAA:0000369 xref: XAO:0000305 is_a: UBERON:0005085 {source="cjm"} ! ectodermal placode -relationship: only_in_taxon NCBITaxon:7711 {source="PMID:11523831", source="PMID:22512454"} ! Chordata relationship: part_of UBERON:0000033 ! head -property_value: editor_note "Do not merge with neurogenic placode" xsd:string -property_value: UBPROP:0000008 "Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons" xsd:string {source="PMID:11523831"} -property_value: UBPROP:0000013 "The term placode or placodes also applies to developing organs such as teeth, mammary glands, hair follicles, feathers and scales. We include a separate parent class for this. to avoid confusion, we include neurogenic placode as a subclass" xsd:string +relationship: RO:0002160 NCBITaxon:7711 {source="PMID:11523831", source="PMID:22512454"} ! only in taxon Chordata +property_value: IAO:0000116 "Do not merge with neurogenic placode" xsd:string [Term] id: UBERON:0002553 @@ -12635,7 +12217,7 @@ xref: galen:Cavity xref: MA:0002447 xref: NCIT:C34007 is_a: UBERON:0000464 ! anatomical space -relationship: location_of UBERON:0000463 ! organism substance +relationship: RO:0001015 UBERON:0000463 ! location of organism substance [Term] id: UBERON:0002616 @@ -12657,10 +12239,11 @@ xref: NCIT:C13031 xref: SCTID:384763002 xref: UMLS:C0445620 {source="ncithesaurus:Brain_Part"} is_a: UBERON:0000073 ! regional part of nervous system +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000481 ! multi-tissue structure intersection_of: part_of UBERON:0000955 ! brain -relationship: composed_primarily_of UBERON:0003714 ! neural tissue relationship: part_of UBERON:0000955 ! brain +relationship: RO:0002473 UBERON:0003714 ! composed primarily of neural tissue [Term] id: UBERON:0003052 @@ -12690,16 +12273,15 @@ xref: VHOG:0000649 xref: XAO:0000016 xref: ZFA:0000042 is_a: UBERON:0004121 ! ectoderm-derived structure -is_a: UBERON:0007651 {inconsistent_with="ZFA", source="https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/106/"} ! anatomical junction +is_a: UBERON:0007651 ! anatomical junction intersection_of: UBERON:0007651 ! anatomical junction intersection_of: overlaps UBERON:0001891 ! midbrain intersection_of: overlaps UBERON:0002028 ! hindbrain -relationship: immediate_transformation_of UBERON:0009615 {source="ZFA"} ! midbrain hindbrain boundary neural plate relationship: overlaps UBERON:0001891 ! midbrain relationship: overlaps UBERON:0002028 ! hindbrain relationship: part_of UBERON:0000955 {source="ZFA"} ! brain -property_value: editor_note "consider adding class for organizer. Consider adding separate class for isthmus as a structure" xsd:string -property_value: UBPROP:0000003 "Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000649", ontology="VHOG", source="DOI:10.1016/j.ydbio.2005.02.008 Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005)", source="http://bgee.unil.ch/"} +relationship: RO:0002495 UBERON:0009615 {source="ZFA"} ! immediate transformation of midbrain hindbrain boundary neural plate +property_value: IAO:0000116 "consider adding class for organizer. Consider adding separate class for isthmus as a structure" xsd:string [Term] id: UBERON:0003056 @@ -12712,10 +12294,9 @@ xref: TAO:0007016 xref: VHOG:0001200 xref: XAO:0000045 xref: ZFA:0007016 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue -relationship: anterior_to UBERON:0009615 ! midbrain hindbrain boundary neural plate relationship: part_of UBERON:0003075 ! neural plate -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001200", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003057 @@ -12729,8 +12310,6 @@ xref: XAO:0000046 xref: ZFA:0007017 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0003075 ! neural plate -relationship: posterior_to UBERON:0009615 ! midbrain hindbrain boundary neural plate -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001201", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003059 @@ -12756,13 +12335,11 @@ xref: XAO:0000057 xref: ZFA:0000279 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0005423 ! developing anatomical structure -intersection_of: has_potential_to_develop_into UBERON:0002329 ! somite -intersection_of: immediate_transformation_of UBERON:0007282 ! presumptive segmental plate -relationship: has_potential_to_develop_into UBERON:0002329 ! somite -relationship: immediate_transformation_of UBERON:0007282 {source="Bgee:AN"} ! presumptive segmental plate +intersection_of: RO:0002387 UBERON:0002329 ! has potential to develop into somite +intersection_of: RO:0002495 UBERON:0007282 ! immediate transformation of presumptive segmental plate relationship: part_of UBERON:0003077 ! paraxial mesoderm -property_value: UBPROP:0000001 "Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000279", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000559", ontology="VHOG", source="DOI:10.1006/dbio.2001.0460 Schubert M, Holland LZ, Dale Stokes M and Holland ND, Three Amphoxius Wnt Genes (AmphiWnt3, AmphiWnt5, and AmphiWnt6) Associated with the Tail Bud: the Evolution of Somitogenesis in Chordates. Developmental Biology (2001)", source="http://bgee.unil.ch/"} +relationship: RO:0002387 UBERON:0002329 ! has potential to develop into somite +relationship: RO:0002495 UBERON:0007282 {source="Bgee:AN"} ! immediate transformation of presumptive segmental plate [Term] id: UBERON:0003061 @@ -12792,13 +12369,8 @@ xref: Wikipedia:Blood_island_of_umbilical_vesicle xref: XAO:0000067 xref: ZFA:0000094 is_a: UBERON:0006598 ! presumptive structure -relationship: develops_from UBERON:0003081 ! lateral plate mesoderm -relationship: has_potential_to_develop_into UBERON:0002390 ! hematopoietic system -property_value: UBPROP:0000001 "Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000094", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011006", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000002 "relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000094", ontology="TAO"} -property_value: UBPROP:0000003 "Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000085", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450, DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual Review of Cell and Developmental Biology (2006)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac" xsd:string {external_ontology="EHDAA2"} +relationship: RO:0002202 UBERON:0003081 ! develops from lateral plate mesoderm +relationship: RO:0002387 UBERON:0002390 ! has potential to develop into hematopoietic system [Term] id: UBERON:0003068 @@ -12816,11 +12388,10 @@ xref: Wikipedia:Chordamesoderm xref: XAO:0000205 xref: ZFA:0001204 is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0000926 ! mesoderm -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0000926 ! mesoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000107", ontology="VHOG", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002202 UBERON:0000926 ! develops from mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003071 @@ -12850,12 +12421,12 @@ is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0001048 ! primordium is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0006598 ! presumptive structure +is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0001048 ! primordium -intersection_of: has_potential_to_develop_into UBERON:0000019 ! camera-type eye -relationship: develops_from UBERON:0003056 ! pre-chordal neural plate -relationship: has_potential_to_develop_into UBERON:0000019 ! camera-type eye +intersection_of: RO:0002387 UBERON:0000019 ! has potential to develop into camera-type eye relationship: part_of UBERON:0003056 {source="PMID:16496288", source="XAO"} ! pre-chordal neural plate -property_value: UBPROP:0000012 "TODO - check that GO's optic placode is the same as ZFA's eye primordium; we may want to have separate term for ocular primordium precursor. XAO has both optic field and eye primordium." xsd:string {external_ontology="GO"} +relationship: RO:0002202 UBERON:0003056 ! develops from pre-chordal neural plate +relationship: RO:0002387 UBERON:0000019 ! has potential to develop into camera-type eye [Term] id: UBERON:0003072 @@ -12880,10 +12451,9 @@ xref: VHOG:0000167 xref: ZFA:0001202 is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004121 ! ectoderm-derived structure -relationship: developmentally_induced_by UBERON:0003073 ! lens placode -relationship: develops_from UBERON:0004128 {source="ZFA"} ! optic vesicle relationship: part_of UBERON:0010312 {source="ZFA"} ! immature eye -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000167", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0004128 {source="ZFA"} ! develops from optic vesicle +relationship: RO:0002256 UBERON:0003073 ! developmentally induced by lens placode [Term] id: UBERON:0003073 @@ -12911,16 +12481,14 @@ xref: XAO:0000240 xref: ZFA:0000122 is_a: UBERON:0002546 ! cranial placode is_a: UBERON:0006598 ! presumptive structure +is_a: UBERON:0010312 ! immature eye is_a: UBERON:0011814 {source="NCBIBook:NBK53175"} ! non-neurogenic ectodermal placode intersection_of: UBERON:0005085 ! ectodermal placode -intersection_of: has_potential_to_develop_into UBERON:0000965 ! lens of camera-type eye -relationship: developmentally_induced_by UBERON:0004128 ! optic vesicle -relationship: has_potential_to_develop_into UBERON:0000965 ! lens of camera-type eye +intersection_of: RO:0002387 UBERON:0000965 ! has potential to develop into lens of camera-type eye relationship: part_of UBERON:0010312 {source="ZFA"} ! immature eye -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png" xsd:anyURI -property_value: UBPROP:0000001 "Ectodermal primordium of the lens of the eye. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000122", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000166", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000011 "Classical transplantation experiments using amphibian embryos suggested that the optic vesicle is the source of lens-inducing signals sufficient to generate lens tissues in competent ectoderm (reviewed in Grainger et al., 1996). More recent findings suggest a multistep model for lens induction. There is now good evidence that lens specification occurs at the neurula stage, before the optic vesicle contact the surface ectoderm, and that neural crest cell migration in the frontonasal region is required to restrict the position of the lens placode (Bailey et al., 2006)" xsd:string {source="NCBIBook:NBK53175"} +relationship: RO:0002256 UBERON:0004128 ! developmentally induced by optic vesicle +relationship: RO:0002387 UBERON:0000965 ! has potential to develop into lens of camera-type eye +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png" xsd:anyURI [Term] id: UBERON:0003075 @@ -12940,7 +12508,6 @@ xref: EHDAA:346 xref: EHDAA:902 xref: EMAPA:35593 xref: FMA:293879 -xref: MESH:D054258 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C34225 xref: neuronames:1362 xref: RETIRED_EHDAA2:0001252 @@ -12953,12 +12520,10 @@ xref: ZFA:0000132 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0016879 ! future central nervous system -relationship: developmentally_induced_by UBERON:0002328 {source="Wikipedia"} ! notochord -relationship: immediate_transformation_of UBERON:0007284 {source="Bgee:AN"} ! presumptive neural plate -relationship: only_in_taxon NCBITaxon:7711 {source="GOTAX:0000352"} ! Chordata -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI -property_value: UBPROP:0000001 "The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000132", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000068", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata +relationship: RO:0002256 UBERON:0002328 {source="Wikipedia"} ! developmentally induced by notochord +relationship: RO:0002495 UBERON:0007284 {source="Bgee:AN"} ! immediate transformation of presumptive neural plate +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI [Term] id: UBERON:0003076 @@ -12971,9 +12536,8 @@ xref: XAO:0000250 xref: ZFA:0007037 is_a: UBERON:0002050 ! embryonic structure disjoint_from: UBERON:0003080 {source="lexical"} ! anterior neural tube -relationship: develops_from UBERON:0003057 ! chordal neural plate relationship: part_of UBERON:0001049 ! neural tube -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001383", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003057 ! develops from chordal neural plate [Term] id: UBERON:0003077 @@ -13002,13 +12566,9 @@ xref: ZFA:0000255 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue is_a: UBERON:0015212 ! lateral structure -relationship: existence_starts_during UBERON:0000109 ! gastrula stage -relationship: immediate_transformation_of UBERON:0007285 {source="Bgee:AN"} ! presumptive paraxial mesoderm -relationship: in_lateral_side_of UBERON:0000922 ! embryo -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010568", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000114", ontology="VHOG", source="DOI:10.1002/dvdy.21177 Kusakabe R and Kuratani S. Evolutionary perspectives from development of mesodermal components in the lamprey. Developmental dynamics (2007)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here)" xsd:string {external_ontology="ZFA"} +relationship: RO:0002488 UBERON:0000109 ! existence starts during gastrula stage +relationship: RO:0002495 UBERON:0007285 {source="Bgee:AN"} ! immediate transformation of presumptive paraxial mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003080 @@ -13020,10 +12580,9 @@ xref: VHOG:0001384 xref: XAO:0000307 xref: ZFA:0007038 is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0003056 ! pre-chordal neural plate relationship: part_of UBERON:0001049 ! neural tube -property_value: editor_note "TODO - add grouping class for the anterior end of the neural tube at all stages" xsd:string -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001384", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003056 ! develops from pre-chordal neural plate +property_value: IAO:0000116 "TODO - add grouping class for the anterior end of the neural tube at all stages" xsd:string [Term] id: UBERON:0003081 @@ -13055,14 +12614,10 @@ is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0000926 {source="EHDAA2", source="VHOG"} ! mesoderm -relationship: surrounds UBERON:0003887 ! intraembryonic coelom -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010574", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000001 "The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000118", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000118", ontology="VHOG", source="DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "subclass of mesoderm in ZFA." xsd:string {external_ontology="ZFA"} +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002221 UBERON:0003887 ! surrounds intraembryonic coelom +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003084 @@ -13080,14 +12635,11 @@ xref: UMLS:C1514450 {source="ncithesaurus:Primordium_of_the_Heart"} xref: XAO:0000336 xref: ZFA:0000028 is_a: UBERON:0001048 {source="Obol"} ! primordium -relationship: develops_from UBERON:0003081 {source="ZFA"} ! lateral plate mesoderm -relationship: develops_from UBERON:0004140 ! primary heart field -relationship: develops_from UBERON:0007005 {source="XAO"} ! cardiogenic splanchnic mesoderm relationship: part_of UBERON:0004535 {source="ZFA"} ! cardiovascular system -property_value: editor_note "should probably be merged with heart rudiment." xsd:string -property_value: UBPROP:0000001 "Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000028", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011044", ontology="AAO", source="XAO:curator"} -property_value: UBPROP:0000002 "relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000028", ontology="TAO"} +relationship: RO:0002202 UBERON:0003081 {source="ZFA"} ! develops from lateral plate mesoderm +relationship: RO:0002202 UBERON:0004140 ! develops from primary heart field +relationship: RO:0002202 UBERON:0007005 {source="XAO"} ! develops from cardiogenic splanchnic mesoderm +property_value: IAO:0000116 "should probably be merged with heart rudiment." xsd:string [Term] id: UBERON:0003089 @@ -13101,7 +12653,6 @@ synonym: "sclerotomes" EXACT OMO:0003004 [TAO:0001080] synonym: "sclerotomus" RELATED OMO:0003011 [Wikipedia:Sclerotome] xref: AAO:0010571 xref: AEO:0000212 -xref: BTO:0006255 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: EHDAA2:0003439 xref: EMAPA:31159 xref: FMA:295652 @@ -13114,12 +12665,9 @@ xref: XAO:0000397 xref: ZFA:0001080 is_a: UBERON:0005856 {source="EHDAA2"} ! developing mesenchymal condensation is_a: UBERON:0007530 {source="EHDAA2"} ! migrating mesenchyme population -relationship: develops_from UBERON:0002329 {source="ZFA"} ! somite -relationship: only_in_taxon NCBITaxon:7742 {source="VHOG:0000680"} ! Vertebrata -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI -property_value: UBPROP:0000001 "Skeletogenic portion of somites.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010571", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000680", ontology="VHOG", source="DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "part_of somite in XAO" xsd:string {external_ontology="XAO"} +relationship: RO:0002160 NCBITaxon:7742 {source="VHOG:0000680"} ! only in taxon Vertebrata +relationship: RO:0002202 UBERON:0002329 {source="ZFA"} ! develops from somite +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI [Term] id: UBERON:0003098 @@ -13145,11 +12693,9 @@ xref: XAO:0000475 xref: ZFA:0000137 is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0034705 {source="EHDAA2"} ! developing neuroepithelium -relationship: develops_from UBERON:0003072 ! optic cup relationship: part_of UBERON:0001894 ! diencephalon -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png" xsd:anyURI -property_value: UBPROP:0000001 "The evagination from the neural tube of the developing embryo which develops the optic cup at its extremity; the stalk persists as the optic nerve. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000223", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/optic+stalk"} -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000223", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003072 ! develops from optic cup +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png" xsd:anyURI [Term] id: UBERON:0003099 @@ -13175,12 +12721,11 @@ xref: VHOG:0000063 xref: Wikipedia:Cranial_neural_crest xref: XAO:0001001 xref: ZFA:0001194 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: has_part CL:0000008 ! migratory cranial neural crest cell relationship: part_of UBERON:0002342 ! neural crest -property_value: UBPROP:0000001 "Anterior most portion of the neural crest. Migrates in three highly conserved streams: mandibular, hyoid and branchial.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010580", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000001 "Neural crest that is part of the head.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001194", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000063", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43", source="http://bgee.unil.ch/"} [Term] id: UBERON:0003103 @@ -13203,7 +12748,6 @@ xref: VHOG:0001723 xref: XAO:0003041 xref: ZFA:0000496 is_a: UBERON:0000062 ! organ -property_value: IAO:0000232 "this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs" xsd:string [Term] id: UBERON:0003104 @@ -13233,15 +12777,12 @@ xref: XAO:0003046 xref: ZFA:0000393 is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue -intersection_of: composed_primarily_of CL:0008019 ! mesenchymal cell -relationship: composed_primarily_of CL:0008019 ! mesenchymal cell -relationship: functionally_related_to GO:0032502 ! developmental process -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI -property_value: editor_note "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" xsd:string -property_value: UBPROP:0000001 "A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000393", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010427", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000007 "mesenchymal" xsd:string +intersection_of: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002328 GO:0032502 ! functionally related to developmental process +relationship: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI +property_value: IAO:0000116 "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" xsd:string [Term] id: UBERON:0003314 @@ -13253,12 +12794,13 @@ xref: EHDAA2:0000485 xref: EHDAA:2910 xref: EMAPA:16673 xref: VHOG:0001084 +is_a: UBERON:0007213 ! mesenchyme derived from head neural crest is_a: UBERON:0009891 ! facial mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0000019 ! camera-type eye -relationship: develops_from UBERON:0009920 {source="EHDAA2"} ! optic neural crest relationship: part_of UBERON:0000019 ! camera-type eye -property_value: editor_note "TODO - change mesenchyme relationships to precursor_of" xsd:string +relationship: RO:0002202 UBERON:0009920 {source="EHDAA2"} ! develops from optic neural crest +property_value: IAO:0000116 "TODO - change mesenchyme relationships to precursor_of" xsd:string [Term] id: UBERON:0003386 @@ -13270,11 +12812,12 @@ synonym: "ocular smooth muscle" EXACT [MA:0001268] xref: EMAPA:18807 xref: MA:0001268 is_a: UBERON:0001135 ! smooth muscle tissue +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0001135 ! smooth muscle tissue intersection_of: part_of UBERON:0000019 ! camera-type eye -relationship: contributes_to_morphology_of UBERON:0001015 ! musculature relationship: part_of UBERON:0000019 ! camera-type eye -property_value: editor_note "Not clear if we need this and intra-ocular muscle. See issue #331. MA includes ciliary and iris smooth muscle" xsd:string +relationship: RO:0002433 UBERON:0001015 ! contributes to morphology of musculature +property_value: IAO:0000116 "Not clear if we need this and intra-ocular muscle. See issue #331. MA includes ciliary and iris smooth muscle" xsd:string [Term] id: UBERON:0003544 @@ -13288,15 +12831,14 @@ synonym: "white matter of brain" EXACT [OBOL:automatic] synonym: "white matter of neuraxis of brain" EXACT [OBOL:automatic] synonym: "white substance of brain" EXACT [OBOL:automatic] xref: EMAPA:35187 -xref: HBA:9218 xref: MA:0000820 xref: NCIT:C49334 xref: UMLS:C1706995 {source="ncithesaurus:Brain_White_Matter"} is_a: UBERON:0002316 ! white matter intersection_of: UBERON:0002316 ! white matter intersection_of: part_of UBERON:0000955 ! brain -relationship: contributes_to_morphology_of UBERON:0000955 ! brain relationship: part_of UBERON:0000955 ! brain +relationship: RO:0002433 UBERON:0000955 ! contributes to morphology of brain [Term] id: UBERON:0003566 @@ -13314,13 +12856,12 @@ synonym: "portion of connective tissue of adult head" EXACT [OBOL:automatic] synonym: "portion of connective tissue of head" EXACT [OBOL:automatic] synonym: "textus connectivus of adult head" EXACT [OBOL:automatic] synonym: "textus connectivus of head" EXACT [OBOL:automatic] -xref: EMAPA:16098 xref: MA:0000577 is_a: UBERON:0002384 ! connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: part_of UBERON:0000033 ! head relationship: part_of UBERON:0000033 ! head -relationship: transformation_of UBERON:0005253 ! head mesenchyme +relationship: RO:0002494 UBERON:0005253 ! transformation of head mesenchyme [Term] id: UBERON:0003714 @@ -13346,8 +12887,6 @@ intersection_of: has_part CL:0000540 ! neuron relationship: has_part CL:0000125 ! glial cell relationship: has_part CL:0000540 ! neuron relationship: part_of UBERON:0001016 ! nervous system -property_value: UBPROP:0000001 "One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000325", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000012 "FMA definition includes vasculature" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0003842 @@ -13371,10 +12910,9 @@ xref: VHOG:0001119 xref: XAO:0000252 is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0001049 ! neural tube -relationship: luminal_space_of UBERON:0001049 ! neural tube +intersection_of: RO:0002572 UBERON:0001049 ! luminal space of neural tube relationship: part_of UBERON:0001049 ! neural tube -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001119", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} +relationship: RO:0002572 UBERON:0001049 ! luminal space of neural tube [Term] id: UBERON:0003849 @@ -13394,9 +12932,8 @@ xref: ZFA:0000935 is_a: UBERON:0002342 ! neural crest is_a: UBERON:0003099 {source="ZFA"} ! cranial neural crest intersection_of: UBERON:0002342 ! neural crest -intersection_of: has_potential_to_developmentally_contribute_to UBERON:0001891 ! midbrain -relationship: has_potential_to_developmentally_contribute_to UBERON:0001891 ! midbrain -property_value: UBPROP:0000003 "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000796", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43", source="http://bgee.unil.ch/"} +intersection_of: RO:0002385 UBERON:0001891 ! has potential to developmentally contribute to midbrain +relationship: RO:0002385 UBERON:0001891 ! has potential to developmentally contribute to midbrain [Term] id: UBERON:0003851 @@ -13416,9 +12953,8 @@ xref: VHOG:0000798 xref: ZFA:0000811 is_a: UBERON:0002342 ! neural crest intersection_of: UBERON:0002342 ! neural crest -intersection_of: has_potential_to_developmentally_contribute_to UBERON:0001894 ! diencephalon -relationship: has_potential_to_developmentally_contribute_to UBERON:0001894 ! diencephalon -property_value: UBPROP:0000003 "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000798", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43", source="http://bgee.unil.ch/"} +intersection_of: RO:0002385 UBERON:0001894 ! has potential to developmentally contribute to diencephalon +relationship: RO:0002385 UBERON:0001894 ! has potential to developmentally contribute to diencephalon [Term] id: UBERON:0003852 @@ -13438,10 +12974,8 @@ xref: ZFA:0007063 is_a: UBERON:0002342 ! neural crest is_a: UBERON:0003099 {source="ZFA"} ! cranial neural crest intersection_of: UBERON:0002342 ! neural crest -intersection_of: has_potential_to_developmentally_contribute_to UBERON:0002028 ! hindbrain -relationship: has_potential_to_developmentally_contribute_to UBERON:0002028 ! hindbrain -property_value: UBPROP:0000001 "Cranial neural crest that is part of the hindbrain.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0007063", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001210", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43", source="http://bgee.unil.ch/"} +intersection_of: RO:0002385 UBERON:0002028 ! has potential to developmentally contribute to hindbrain +relationship: RO:0002385 UBERON:0002028 ! has potential to developmentally contribute to hindbrain [Term] id: UBERON:0003853 @@ -13456,9 +12990,8 @@ xref: EMAPA:16881 xref: VHOG:0001006 is_a: UBERON:0002342 ! neural crest intersection_of: UBERON:0002342 ! neural crest -intersection_of: has_potential_to_developmentally_contribute_to UBERON:0002240 ! spinal cord -relationship: has_potential_to_developmentally_contribute_to UBERON:0002240 ! spinal cord -property_value: UBPROP:0000003 "We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001006", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43", source="http://bgee.unil.ch/"} +intersection_of: RO:0002385 UBERON:0002240 ! has potential to developmentally contribute to spinal cord +relationship: RO:0002385 UBERON:0002240 ! has potential to developmentally contribute to spinal cord [Term] id: UBERON:0003886 @@ -13471,11 +13004,11 @@ synonym: "body cavity precursor" RELATED [] synonym: "future coelomic cavity lumen" EXACT [] is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: has_potential_to_develop_into UBERON:0002323 ! coelemic cavity lumen -relationship: existence_ends_during UBERON:0000111 ! organogenesis stage -relationship: existence_starts_during UBERON:0000109 ! gastrula stage -relationship: has_potential_to_develop_into UBERON:0002323 ! coelemic cavity lumen +intersection_of: RO:0002387 UBERON:0002323 ! has potential to develop into coelemic cavity lumen relationship: part_of UBERON:0000926 ! mesoderm +relationship: RO:0002387 UBERON:0002323 ! has potential to develop into coelemic cavity lumen +relationship: RO:0002488 UBERON:0000109 ! existence starts during gastrula stage +relationship: RO:0002492 UBERON:0000111 ! existence ends during organogenesis stage [Term] id: UBERON:0003887 @@ -13491,10 +13024,9 @@ xref: UMLS:C1512940 {source="ncithesaurus:Intraembryonic_Coelom"} xref: VHOG:0000316 xref: Wikipedia:Intraembryonic_coelom is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0003081 {source="Wikipedia"} ! lateral plate mesoderm relationship: part_of UBERON:0011997 ! coelom -property_value: editor_note "consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults" xsd:string -property_value: UBPROP:0000003 "(...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000316", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.166", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003081 {source="Wikipedia"} ! develops from lateral plate mesoderm +property_value: IAO:0000116 "consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults" xsd:string [Term] id: UBERON:0003891 @@ -13507,9 +13039,8 @@ xref: FMA:81494 xref: NCIT:C67387 xref: UMLS:C0927195 {source="ncithesaurus:Stroma_Connective_Tissue"} is_a: UBERON:0000064 ! organ part -relationship: composed_primarily_of UBERON:0002384 ! connective tissue -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: UBPROP:0000007 "stromal" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002473 UBERON:0002384 ! composed primarily of connective tissue [Term] id: UBERON:0003902 @@ -13541,14 +13072,12 @@ xref: VHOG:0000535 xref: XAO:0003216 xref: ZFA:0000046 is_a: UBERON:0001781 ! layer of retina -is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0001781 ! layer of retina -intersection_of: immediate_transformation_of UBERON:0005425 ! presumptive neural retina -relationship: developmentally_induced_by UBERON:0005426 ! lens vesicle +intersection_of: RO:0002495 UBERON:0005425 ! immediate transformation of presumptive neural retina relationship: has_part CL:0000210 ! photoreceptor cell -relationship: immediate_transformation_of UBERON:0005425 {source="Bgee:AN"} ! presumptive neural retina -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000535", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} +relationship: RO:0002256 UBERON:0005426 ! developmentally induced by lens vesicle +relationship: RO:0002495 UBERON:0005425 {source="Bgee:AN"} ! immediate transformation of presumptive neural retina +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003914 @@ -13558,12 +13087,10 @@ def: "Epithelial tubes transport gases, liquids and cells from one site to anoth synonym: "epithelial or endothelial tube" EXACT [] xref: AEO:0000114 xref: EHDAA2:0003114 -xref: FBbt:00007474 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000025 ! tube is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium -intersection_of: has_quality PATO:0002299 ! tubular -property_value: IAO:0000232 "contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers" xsd:string +intersection_of: RO:0000086 PATO:0002299 ! has quality tubular [Term] id: UBERON:0003931 @@ -13595,11 +13122,11 @@ synonym: "germinal neuroepithelial layer" EXACT [http://orcid.org/0000-0002-6601 synonym: "germinal neuroepithelium" EXACT [NCBIBook:NBK10047] synonym: "original neural tube" EXACT [NCBIBook:NBK10047] is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0034706 {source="NCBIBook:NBK10047"} ! proliferating neuroepithelium relationship: adjacent_to UBERON:0003842 ! neural tube lumen relationship: bounding_layer_of UBERON:0001049 ! neural tube relationship: part_of UBERON:0001049 ! neural tube -property_value: UBPROP:0000011 "As the cells adjacent to the lumen continue to divide, the migrating cells form a second layer around the original neural tube. This layer becomes progressively thicker as more cells are added to it from the germinal neuroepithelium. This new layer is called the mantle (or intermediate) zone, and the germinal epithelium is now called the ventricular zone (and, later, the ependyma)[NCBIBook:NBK10047]" xsd:string [Term] id: UBERON:0004060 @@ -13620,10 +13147,9 @@ is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0034706 {source="NCBIBook:NBK10047"} ! proliferating neuroepithelium relationship: adjacent_to UBERON:0003842 ! neural tube lumen -relationship: immediate_transformation_of UBERON:0004022 {source="NCBIBook:NBK10047"} ! germinal neuroepithelium relationship: part_of UBERON:0001049 ! neural tube -property_value: editor_note "consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure" xsd:string -property_value: UBPROP:0000001 "The layer of undifferentiated, proliferating cells that line the neural tube lumen" xsd:string {source="MP:0009689"} +relationship: RO:0002495 UBERON:0004022 {source="NCBIBook:NBK10047"} ! immediate transformation of germinal neuroepithelium +property_value: IAO:0000116 "consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure" xsd:string [Term] id: UBERON:0004061 @@ -13637,11 +13163,12 @@ xref: EMAPA:17148 xref: EMAPA:35360 xref: neuronames:1367 is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0034707 {source="NCBIBook:NBK10047"} ! differentiating neuroepithelium relationship: adjacent_to UBERON:0004060 ! neural tube ventricular layer relationship: adjacent_to UBERON:0004062 ! neural tube marginal layer -relationship: develops_from UBERON:0004022 {notes="by division", source="NCBIBook:NBK10047"} ! germinal neuroepithelium relationship: part_of UBERON:0001049 ! neural tube +relationship: RO:0002202 UBERON:0004022 ! develops from germinal neuroepithelium [Term] id: UBERON:0004062 @@ -13653,10 +13180,11 @@ synonym: "brain marginal zone" RELATED [] synonym: "neural tube marginal zone" EXACT [MP:0009691] xref: EMAPA:17151 xref: neuronames:1368 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005162 ! multi cell part structure relationship: adjacent_to UBERON:0004061 ! neural tube mantle layer -relationship: develops_from UBERON:0004061 {notes="forms from axons"} ! neural tube mantle layer relationship: part_of UBERON:0001049 ! neural tube +relationship: RO:0002202 UBERON:0004061 ! develops from neural tube mantle layer [Term] id: UBERON:0004088 @@ -13674,8 +13202,7 @@ synonym: "orbital part of face" EXACT [http://orcid.org/0000-0002-6601-2165] xref: FMA:260119 is_a: UBERON:0001444 ! subdivision of head relationship: part_of UBERON:0001456 ! face -property_value: editor_note "note the FMA class is more narrow though, and is more like eye + muscles + vasculature. The FMA also has FMA:72951 orbital part of eye" xsd:string -property_value: UBPROP:0000012 "in HP covers eyelid, eyebrow." xsd:string {external_ontology="HP:0000284"} +property_value: IAO:0000116 "note the FMA class is more narrow though, and is more like eye + muscles + vasculature. The FMA also has FMA:72951 orbital part of eye" xsd:string [Term] id: UBERON:0004111 @@ -13695,15 +13222,14 @@ xref: SCTID:346902003 xref: Wikipedia:Foramen is_a: UBERON:0010000 ! multicellular anatomical structure intersection_of: UBERON:0010000 ! multicellular anatomical structure -intersection_of: conduit_for UBERON:0000061 ! anatomical structure intersection_of: has_part UBERON:0013686 ! anatomical conduit space -relationship: conduit_for UBERON:0000061 ! anatomical structure -relationship: connects UBERON:0000464 {cardinality="2"} ! anatomical space +intersection_of: RO:0002570 UBERON:0000061 ! conduit for anatomical structure relationship: has_part UBERON:0013686 ! anatomical conduit space -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: UBPROP:0000012 "FMA has both conduit and conduit space. In EHDAA2 this is a surface feature" xsd:string {external_ontology="FMA"} +relationship: RO:0002176 UBERON:0000464 {cardinality="2"} ! connects anatomical space +relationship: RO:0002570 UBERON:0000061 ! conduit for anatomical structure +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0004120 @@ -13714,9 +13240,8 @@ subset: grouping_class synonym: "mesodermal derivative" EXACT [FBbt:00025998] is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: develops_from UBERON:0000926 ! mesoderm -relationship: develops_from UBERON:0000926 ! mesoderm -property_value: IAO:0000232 "Grouping term for query purposes" xsd:string +intersection_of: RO:0002202 UBERON:0000926 ! develops from mesoderm +relationship: RO:0002202 UBERON:0000926 ! develops from mesoderm [Term] id: UBERON:0004121 @@ -13727,9 +13252,8 @@ subset: grouping_class synonym: "ectodermal deriviative" EXACT [FBbt:00025990] is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: develops_from UBERON:0000924 ! ectoderm -relationship: develops_from UBERON:0000924 ! ectoderm -property_value: IAO:0000232 "Grouping term for query purposes" xsd:string +intersection_of: RO:0002202 UBERON:0000924 ! develops from ectoderm +relationship: RO:0002202 UBERON:0000924 ! develops from ectoderm [Term] id: UBERON:0004128 @@ -13757,12 +13281,11 @@ xref: XAO:0000228 xref: ZFA:0000050 is_a: UBERON:0000479 ! tissue is_a: UBERON:0004121 ! ectoderm-derived structure -relationship: developmentally_induced_by UBERON:0004880 ! chordamesoderm -relationship: develops_from UBERON:0002346 {source="GO-def"} ! neurectoderm -relationship: develops_from UBERON:0003071 {source="ZFA"} ! eye primordium relationship: part_of UBERON:0010312 {source="ZFA"} ! immature eye -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e0/Gray863.png" xsd:anyURI -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000165", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0002346 {source="GO-def"} ! develops from neurectoderm +relationship: RO:0002202 UBERON:0003071 {source="ZFA"} ! develops from eye primordium +relationship: RO:0002256 UBERON:0004880 ! developmentally induced by chordamesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e0/Gray863.png" xsd:anyURI [Term] id: UBERON:0004139 @@ -13778,9 +13301,8 @@ xref: EHDAA2:0000215 xref: EMAPA:16106 xref: VHOG:0000975 is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0003084 ! heart primordium -property_value: editor_note "TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO" xsd:string -property_value: UBPROP:0000003 "(In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000975", ontology="VHOG", source="PMID:15611355 Gittenberger-de Groot AC, Bartelings MM, Deruiter MC, Poelmann RE, Basics of cardiac development for the understanding of congenital heart malformations. Pediatric Research (2005)", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003084 ! develops from heart primordium +property_value: IAO:0000116 "TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO" xsd:string [Term] id: UBERON:0004140 @@ -13794,11 +13316,11 @@ synonym: "PHF" RELATED OMO:0003000 [XAO:0004185] synonym: "primary heart field" EXACT [PMID:17276708, XAO:0004185] xref: XAO:0004185 is_a: UBERON:0002050 ! embryonic structure +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007688 ! anlage relationship: part_of UBERON:0003081 {source="GO:0003128"} ! lateral plate mesoderm relationship: part_of UBERON:0036146 {source="https://orcid.org/0000-0003-3308-6245"} ! cardiopharyngeal field -property_value: UBPROP:0000012 "this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138]" xsd:string {external_ontology="GO"} [Term] id: UBERON:0004141 @@ -13821,8 +13343,7 @@ xref: ZFA:0000360 is_a: UBERON:0003914 ! epithelial tube is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0012275 ! meso-epithelium -relationship: immediate_transformation_of UBERON:0005498 {source="ZFA-modified"} ! primitive heart tube -property_value: UBPROP:0000001 "the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube." xsd:string {source="MP:0012700"} +relationship: RO:0002495 UBERON:0005498 {source="ZFA-modified"} ! immediate transformation of primitive heart tube [Term] id: UBERON:0004151 @@ -13835,6 +13356,7 @@ synonym: "heart chamber" EXACT [] xref: FMA:7095 xref: SCTID:276456008 is_a: UBERON:0000064 ! organ part +is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0000948 ! heart [Term] @@ -13847,10 +13369,11 @@ xref: AAO:0000156 xref: EMAPA:35335 xref: MA:0000271 is_a: UBERON:0001630 ! muscle organ +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0001630 ! muscle organ intersection_of: part_of UBERON:0000019 ! camera-type eye -relationship: contributes_to_morphology_of UBERON:0000019 ! camera-type eye relationship: part_of UBERON:0000019 {source="MA"} ! camera-type eye +relationship: RO:0002433 UBERON:0000019 ! contributes to morphology of camera-type eye [Term] id: UBERON:0004288 @@ -13880,13 +13403,10 @@ xref: Wikipedia:Skeleton xref: XAO:0004053 is_a: UBERON:0034925 ! anatomical collection disjoint_from: UBERON:0004770 ! articular system -relationship: has_member UBERON:0004765 ! skeletal element relationship: part_of UBERON:0001434 ! skeletal system -relationship: present_in_taxon NCBITaxon:9606 -property_value: RO:0002171 UBERON:0000383 +relationship: RO:0002351 UBERON:0004765 ! has member skeletal element +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/The-skeletal-system" xsd:anyURI -property_value: UBPROP:0000001 "Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000026", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070"} -property_value: UBPROP:0000007 "skeletal" xsd:string [Term] id: UBERON:0004291 @@ -13898,8 +13418,7 @@ synonym: "rudimentary heart" EXACT [ZFA:0000115] xref: TAO:0000115 xref: ZFA:0000115 is_a: UBERON:0012275 ! meso-epithelium -relationship: develops_from UBERON:0004139 ! cardiogenic plate -property_value: UBPROP:0000001 "The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000115", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002202 UBERON:0004139 ! develops from cardiogenic plate [Term] id: UBERON:0004348 @@ -13912,7 +13431,7 @@ xref: EMAPA:16322 xref: RETIRED_EHDAA2:0001308 xref: VHOG:0001296 is_a: UBERON:0006598 ! presumptive structure -relationship: has_potential_to_develop_into UBERON:0000964 ! cornea +relationship: RO:0002387 UBERON:0000964 ! has potential to develop into cornea [Term] id: UBERON:0004367 @@ -13941,6 +13460,7 @@ xref: UMLS:C0011665 {source="ncithesaurus:Descemet_s_Membrane"} xref: Wikipedia:Descemet%27s_membrane xref: ZFA:0001686 is_a: UBERON:0005769 ! basement membrane of epithelium +is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0005769 ! basement membrane of epithelium intersection_of: adjacent_to UBERON:0001777 ! substantia propria of cornea intersection_of: adjacent_to UBERON:0001985 ! corneal endothelium @@ -13948,11 +13468,10 @@ intersection_of: part_of UBERON:0000964 ! cornea disjoint_from: UBERON:0004370 {source="lexical"} ! anterior limiting lamina of cornea relationship: adjacent_to UBERON:0001777 ! substantia propria of cornea relationship: adjacent_to UBERON:0001985 ! corneal endothelium -relationship: has_quality PATO:0000964 ! transparent relationship: part_of UBERON:0000964 ! cornea relationship: produced_by UBERON:0001985 {source="Cline et al"} ! corneal endothelium +relationship: RO:0000086 PATO:0000964 ! has quality transparent property_value: seeAlso "https://github.com/obophenotype/uberon/issues/15" xsd:anyURI -property_value: UBPROP:0000001 "Acellular anatomical structure composed of collagen, Descemet's membrane is secreted as a basement membrane of the corneal endothelium. Located between the stroma and the corneal endothelium, it is approximately 0.15 micrometer thick at 6 months post-fertilization.[ZFIN]" xsd:string {date_retrieved="2016-05-01", external_class="TAO:0002157", ontology="ZFIN", source="ZFIN:ZDB-PUB-061010-3", source="https://orcid.org/0000-0001-9114-8737"} [Term] id: UBERON:0004370 @@ -13980,13 +13499,12 @@ xref: UMLS:C0229127 {source="ncithesaurus:Bowman_s_Membrane"} xref: Wikipedia:Bowman%27s_membrane xref: ZFA:0001684 is_a: UBERON:0005769 ! basement membrane of epithelium +is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0005769 ! basement membrane of epithelium -intersection_of: attaches_to UBERON:0001772 ! corneal epithelium intersection_of: part_of UBERON:0000964 ! cornea -relationship: attaches_to UBERON:0001772 ! corneal epithelium +intersection_of: RO:0002371 UBERON:0001772 ! attached to corneal epithelium relationship: part_of UBERON:0000964 ! cornea -property_value: UBPROP:0000001 "Acellular anatomical structure that is the zone of collagen fibers adjacent the basement membrane of the corneal epithelium.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002155", ontology="TAO", source="ZFIN:ZDB-PUB-061010-3"} -property_value: UBPROP:0000008 "Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals" xsd:string +relationship: RO:0002371 UBERON:0001772 ! attached to corneal epithelium [Term] id: UBERON:0004456 @@ -13997,9 +13515,8 @@ subset: uberon_slim synonym: "sense organ system" EXACT [FMA:78499] xref: FMA:78499 is_a: UBERON:0000467 ! anatomical system -relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: overlaps UBERON:0001016 ! nervous system -property_value: UBPROP:0000012 "note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs" xsd:string +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage [Term] id: UBERON:0004535 @@ -14018,10 +13535,8 @@ xref: BILA:0000016 xref: BTO:0000088 xref: CALOHA:TS-1297 xref: EFO:0000791 -xref: EHDAA2:0000216 xref: EHDAA:394 xref: EMAPA:16104 -xref: EMAPA:16370 xref: EV:0100017 xref: FMA:7161 xref: GAID:467 @@ -14047,9 +13562,7 @@ intersection_of: part_of UBERON:0001009 ! circulatory system relationship: has_part UBERON:0000948 ! heart relationship: has_part UBERON:0001981 ! blood vessel relationship: part_of UBERON:0001009 ! circulatory system -relationship: present_in_taxon NCBITaxon:9606 -property_value: IAO:0000232 "we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph." xsd:string -property_value: UBPROP:0000003 "The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000302", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.451", source="http://bgee.unil.ch/"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004537 @@ -14067,11 +13580,11 @@ xref: ZFA:0001079 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature -intersection_of: composed_primarily_of UBERON:0001981 ! blood vessel -relationship: composed_primarily_of UBERON:0001981 ! blood vessel -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +intersection_of: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel +relationship: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004638 @@ -14093,7 +13606,7 @@ is_a: UBERON:0004852 ! cardiovascular system endothelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0001981 ! blood vessel relationship: part_of UBERON:0001981 ! blood vessel -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004716 @@ -14110,12 +13623,12 @@ xref: NCIT:C34131 xref: UMLS:C1516779 {source="ncithesaurus:Conceptus"} xref: Wikipedia:Conceptus is_a: UBERON:0000061 ! anatomical structure -relationship: develops_from CL:0000365 ! animal zygote -relationship: existence_ends_with UBERON:0000068 ! embryo stage -relationship: existence_starts_with UBERON:0000068 ! embryo stage relationship: has_part UBERON:0002050 ! embryonic structure relationship: has_part UBERON:0016887 ! entire extraembryonic component -property_value: editor_note "EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus" xsd:string +relationship: RO:0002202 CL:0000365 ! develops from animal zygote +relationship: RO:0002489 UBERON:0000068 ! existence starts with embryo stage +relationship: RO:0002493 UBERON:0000068 ! existence ends with embryo stage +property_value: IAO:0000116 "EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus" xsd:string [Term] id: UBERON:0004732 @@ -14128,7 +13641,7 @@ is_a: UBERON:0000063 ! organ subunit intersection_of: UBERON:0000063 ! organ subunit intersection_of: part_of UBERON:0001016 ! nervous system relationship: part_of UBERON:0001016 ! nervous system -property_value: editor_note "revisit this after CARO is revised and/or we have defined metameric segment; note that with the additional of an A/P axis constraint this corresponds to what Richter at al call a neuromere (PMID:21062451)" xsd:string +property_value: IAO:0000116 "revisit this after CARO is revised and/or we have defined metameric segment; note that with the additional of an A/P axis constraint this corresponds to what Richter at al call a neuromere (PMID:21062451)" xsd:string [Term] id: UBERON:0004733 @@ -14139,6 +13652,7 @@ subset: non_informative synonym: "hindbrain segment" EXACT [FMA:61998] synonym: "segment of hindbrain" EXACT [FMA:61998] xref: FMA:61998 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004732 ! segmental subdivision of nervous system intersection_of: UBERON:0000063 ! organ subunit intersection_of: part_of UBERON:0002028 ! hindbrain @@ -14162,7 +13676,6 @@ synonym: "trilaminar disk" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "trilaminar germ" RELATED [https://orcid.org/0000-0002-6601-2165] xref: BILA:0000060 xref: BTO:0001403 -xref: FBbt:00005317 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:293108 xref: GAID:1302 xref: MESH:D005775 @@ -14175,10 +13688,9 @@ xref: Wikipedia:Gastrula xref: Wikipedia:Trilaminar_blastocyst is_a: UBERON:0000922 ! embryo intersection_of: UBERON:0000468 ! multicellular organism -intersection_of: existence_starts_and_ends_during UBERON:0000109 ! gastrula stage -relationship: develops_from UBERON:0000307 ! blastula -relationship: existence_starts_and_ends_during UBERON:0000109 ! gastrula stage -property_value: UBPROP:0000012 "We explicitly merge the NCITA terms here" xsd:string {external_ontology="NCIT"} +intersection_of: RO:0002491 UBERON:0000109 ! existence starts and ends during gastrula stage +relationship: RO:0002202 UBERON:0000307 ! develops from blastula +relationship: RO:0002491 UBERON:0000109 ! existence starts and ends during gastrula stage [Term] id: UBERON:0004765 @@ -14195,8 +13707,6 @@ xref: XAO:0004012 xref: ZFA:0005494 is_a: UBERON:0000062 ! organ relationship: part_of UBERON:0001434 {source="VSAO"} ! skeletal system -property_value: UBPROP:0000001 "Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000128", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001890", ontology="TAO", source="TAO:VSAO_workshop"} [Term] id: UBERON:0004770 @@ -14214,12 +13724,12 @@ xref: SCTID:361827000 xref: VSAO:0000181 is_a: UBERON:0034925 ! anatomical collection intersection_of: UBERON:0034925 ! anatomical collection -intersection_of: has_member UBERON:0000982 ! skeletal joint -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: functionally_related_to GO:0040011 ! locomotion -relationship: has_member UBERON:0000982 ! skeletal joint -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +intersection_of: RO:0002351 UBERON:0000982 ! has member skeletal joint relationship: part_of UBERON:0001434 {source="FMA"} ! skeletal system +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002328 GO:0040011 ! functionally related to locomotion +relationship: RO:0002351 UBERON:0000982 ! has member skeletal joint +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage [Term] id: UBERON:0004852 @@ -14244,8 +13754,7 @@ is_a: UBERON:0001986 ! endothelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0004535 ! cardiovascular system relationship: part_of UBERON:0004535 ! cardiovascular system -property_value: editor_note "consider merging with 'endothelium'" xsd:string -property_value: UBPROP:0000003 "Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001217", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207", source="http://bgee.unil.ch/"} +property_value: IAO:0000116 "consider merging with 'endothelium'" xsd:string [Term] id: UBERON:0004872 @@ -14263,7 +13772,6 @@ xref: Wikipedia:Lateral_plate_mesoderm#Division_into_layers xref: XAO:0000276 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0003081 ! lateral plate mesoderm -property_value: UBPROP:0000012 "We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors" xsd:string {external_ontology="BILA"} [Term] id: UBERON:0004880 @@ -14281,10 +13789,8 @@ xref: EFO:0003426 xref: TAO:0000091 xref: ZFA:0000091 is_a: UBERON:0002050 ! embryonic structure -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0003068 ! axial mesoderm -property_value: UBPROP:0000001 "Notochord rudiment[ZFIN:ZDB-PUB-961014-576]." xsd:string {source="ZFIN:ZDB-PUB-961014-576"} -property_value: UBPROP:0000012 "WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord." xsd:string +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata [Term] id: UBERON:0004905 @@ -14293,7 +13799,6 @@ namespace: uberon def: "Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts." [http://orcid.org/0000-0002-6601-2165] subset: grouping_class synonym: "joint" NARROW [] -xref: FBbt:00005811 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0034921 ! multi organ part structure relationship: part_of UBERON:0004770 ! articular system @@ -14309,15 +13814,13 @@ synonym: "gut section" RELATED [FBbt:00100315] synonym: "intestinal tract" RELATED [] synonym: "segment of intestinal tract" RELATED [] synonym: "subdivision of alimentary system" RELATED [FMA:71131] -xref: FBbt:00100315 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:71131 is_a: UBERON:0013522 ! subdivision of tube intersection_of: UBERON:0013522 ! subdivision of tube intersection_of: subdivision_of UBERON:0001555 ! digestive tract relationship: part_of UBERON:0001555 ! digestive tract -relationship: present_in_taxon NCBITaxon:9606 relationship: subdivision_of UBERON:0001555 ! digestive tract -property_value: IAO:0000232 "intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct." xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004923 @@ -14327,8 +13830,8 @@ def: "A part of a wall of an organ that forms a layer." [http://orcid.org/0000-0 subset: upper_level xref: FMA:82485 is_a: UBERON:0000064 ! organ part -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000060 ! anatomical wall +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0005061 @@ -14346,7 +13849,6 @@ xref: Wikipedia:Neural_groove xref: XAO:0000248 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0003075 ! neural plate -property_value: UBPROP:0000001 "The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]." xsd:string {source="Wikipedia:Neural_groove"} [Term] id: UBERON:0005062 @@ -14366,10 +13868,9 @@ xref: XAO:0004087 is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0005157 ! epithelial fold is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0015212 ! lateral structure -relationship: in_lateral_side_of UBERON:0005061 ! neural groove relationship: part_of UBERON:0005061 ! neural groove -property_value: UBPROP:0000001 "In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]." xsd:string {source="Wikipedia:Neural_fold"} [Term] id: UBERON:0005068 @@ -14382,8 +13883,7 @@ xref: EFO:0003498 xref: TAO:0000133 xref: ZFA:0000133 is_a: UBERON:0016879 ! future central nervous system -relationship: develops_from UBERON:0007135 ! neural keel -property_value: UBPROP:0000001 "An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000133", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002202 UBERON:0007135 ! develops from neural keel [Term] id: UBERON:0005085 @@ -14395,9 +13895,7 @@ xref: AEO:0000218 is_a: UBERON:0001048 ! primordium is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0000924 ! ectoderm -property_value: editor_note "consder adding placodal ectoderm as a distinct class? Also place placodal ectoderm as develops_from ectoderm; need to check taxon-appropriateness" xsd:string -property_value: UBPROP:0000008 "With the exception of the adenohypophysis, homologues of the nonneurogenic placodes (e.g. placodes giving rise to the teeth, hair follicles and lens), appear to be lacking in invertebrate chordates." xsd:string -property_value: UBPROP:0000012 "in GO, covers optic, otic, olfactory, mammary, hair, tooth, sebaceous - and also insect structures" xsd:string {external_ontology="GO", source="https://github.com/geneontology/go-ontology/issues/12223#issuecomment-215692347"} +property_value: IAO:0000116 "consder adding placodal ectoderm as a distinct class? Also place placodal ectoderm as develops_from ectoderm; need to check taxon-appropriateness" xsd:string [Term] id: UBERON:0005090 @@ -14407,12 +13905,10 @@ def: "Muscle structures are contractile cells, tissues or organs that are found synonym: "muscle" RELATED [] synonym: "muscle element" RELATED [] synonym: "musculus" EXACT [FMA:30316] -xref: EMAPA:32715 xref: FMA:30316 is_a: UBERON:0000061 ! anatomical structure relationship: has_part CL:0000187 ! muscle cell -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: IAO:0000232 "in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0005157 @@ -14432,11 +13928,9 @@ synonym: "multi-cell-component structure" EXACT [CARO:0001000] synonym: "multi-cell-part structure" EXACT [CARO:0001000] xref: AAO:0011000 xref: CARO:0001000 -xref: FBbt:00007060 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:83115 is_a: UBERON:0000061 ! anatomical structure -relationship: composed_primarily_of GO:0005575 ! cellular_component -property_value: UBPROP:0000012 "we go with the FMA classification rather than the CARO one. FMA def: 'Anatomical cluster which has as direct parts cell parts from two or more cells.'" xsd:string {external_ontology="CARO", external_ontology="FMA"} +relationship: RO:0002473 GO:0005575 ! composed primarily of cellular_component [Term] id: UBERON:0005174 @@ -14481,8 +13975,8 @@ xref: MA:0000557 is_a: UBERON:0002075 ! viscus is_a: UBERON:0005181 ! thoracic segment organ intersection_of: UBERON:0000062 ! organ -intersection_of: located_in UBERON:0002224 ! thoracic cavity -relationship: located_in UBERON:0002224 ! thoracic cavity +intersection_of: RO:0001025 UBERON:0002224 ! located in thoracic cavity +relationship: RO:0001025 UBERON:0002224 ! located in thoracic cavity [Term] id: UBERON:0005181 @@ -14524,7 +14018,6 @@ intersection_of: UBERON:0003104 ! mesenchyme intersection_of: part_of UBERON:0000033 ! head relationship: part_of UBERON:0000033 ! head relationship: part_of UBERON:0009142 {source="EHDAA2"} ! entire embryonic mesenchyme -property_value: UBPROP:0000001 "Mesoderm that will give rise, along with cranial neural crest cells, to connective tissue, bone and musculature in the head. (Source: BioGlossary, www.Biology-Text.com)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000113", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0005256 @@ -14565,17 +14058,11 @@ xref: EHDAA:5526 xref: EMAPA:17082 xref: HBA:9512 xref: MA:0000205 -xref: MESH:D054024 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: VHOG:0000456 xref: Wikipedia:Myelencephalon -is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004733 ! segmental subdivision of hindbrain -relationship: immediate_transformation_of UBERON:0010096 {evidence="definitional"} ! future myelencephalon -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI -property_value: RO:0002174 NCBITaxon:7955 -property_value: UBPROP:0000001 "The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000456", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/myelencephalon"} -property_value: UBPROP:0000003 "The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000456", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000013 "the terms metencephalon and myelencephalon are only meaningful in mammals and birds - Neuroanatomy of the Zebrafish Brain. Note that its not clear if this refers to the developing medulla oblongata - MA (adult) has two distinct classes" xsd:string +relationship: RO:0002495 UBERON:0010096 ! immediate transformation of future myelencephalon +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI [Term] id: UBERON:0005291 @@ -14598,14 +14085,13 @@ name: photoreceptor array namespace: uberon def: "An array of photoreceptors and any supporting cells found in an eye." [https://orcid.org/0000-0002-6601-2165] synonym: "light-sensitive tissue" EXACT [] -xref: FBbt:00004200 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0004923 ! organ component layer intersection_of: UBERON:0004923 ! organ component layer -intersection_of: composed_primarily_of CL:0000210 ! photoreceptor cell intersection_of: part_of UBERON:0000970 ! eye -relationship: composed_primarily_of CL:0000210 ! photoreceptor cell +intersection_of: RO:0002473 CL:0000210 ! composed primarily of photoreceptor cell relationship: part_of UBERON:0000970 ! eye relationship: part_of UBERON:0001016 ! nervous system +relationship: RO:0002473 CL:0000210 ! composed primarily of photoreceptor cell [Term] id: UBERON:0005389 @@ -14615,9 +14101,8 @@ def: "A transparent structure that is part of a visual sense organ, the function subset: grouping_class synonym: "lens" NARROW [] is_a: UBERON:0000061 ! anatomical structure -relationship: has_quality PATO:0000964 ! transparent relationship: part_of UBERON:0000970 ! eye -property_value: UBPROP:0000009 "directing or focusing light onto light receptors" xsd:string +relationship: RO:0000086 PATO:0000964 ! has quality transparent [Term] id: UBERON:0005423 @@ -14630,14 +14115,13 @@ synonym: "developmental tissue" RELATED [MIAA:0000019] xref: AEO:0000125 xref: CALOHA:TS-2122 xref: EHDAA2:0003125 -xref: FBbt:00007006 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:292313 xref: MIAA:0000019 is_a: UBERON:0000465 ! material anatomical entity relationship: capable_of GO:0032502 ! developmental process -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0005424 @@ -14660,11 +14144,11 @@ xref: TAO:0000064 xref: VHOG:0000492 xref: ZFA:0000064 is_a: UBERON:0006598 ! presumptive structure +is_a: UBERON:0010312 ! immature eye intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001782 ! pigmented layer of retina -relationship: has_potential_to_develop_into UBERON:0001782 ! pigmented layer of retina +intersection_of: RO:0002387 UBERON:0001782 ! has potential to develop into pigmented layer of retina relationship: part_of UBERON:0003072 ! optic cup -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000492", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} +relationship: RO:0002387 UBERON:0001782 ! has potential to develop into pigmented layer of retina [Term] id: UBERON:0005425 @@ -14687,11 +14171,11 @@ xref: TAO:0001071 xref: VHOG:0000490 xref: ZFA:0001071 is_a: UBERON:0006598 ! presumptive structure +is_a: UBERON:0010312 ! immature eye intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0003902 ! retinal neural layer -relationship: has_potential_to_develop_into UBERON:0003902 ! retinal neural layer +intersection_of: RO:0002387 UBERON:0003902 ! has potential to develop into retinal neural layer relationship: part_of UBERON:0003072 ! optic cup -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000490", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} +relationship: RO:0002387 UBERON:0003902 ! has potential to develop into retinal neural layer [Term] id: UBERON:0005426 @@ -14713,10 +14197,8 @@ xref: TAO:0002205 xref: VHOG:0001163 xref: ZFA:0001679 is_a: UBERON:0000479 ! tissue -relationship: develops_from UBERON:0003073 ! lens placode -property_value: UBPROP:0000001 "A vesicle formed from the lens pit of the embryo, developing into the crystalline lens. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001163", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/lens+vesicle"} -property_value: UBPROP:0000003 "(...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001163", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000011 "the lens of zebrafish (and other teleosts) forms from delamination of cells from the lens placode; thus, there is no formation of a hollow lens vesicle, in contrast to the situation in mammals and birds (Glass and Dahm, 2004) [PMID:16496288] The lens of the zebrafish forms by delamination of lens placodal cells and not through invagination. This results in a solid spherical mass as opposed to a hollow lens vesicle. Detachment of the solid lens vesicle of zebrafish at 24b26 hpf is accomplished in part by apoptosis, similar to mammals" xsd:string {source="ZFA"} +is_a: UBERON:0004121 ! ectoderm-derived structure +relationship: RO:0002202 UBERON:0003073 ! develops from lens placode [Term] id: UBERON:0005427 @@ -14727,6 +14209,7 @@ xref: TAO:0002188 xref: ZFA:0001688 is_a: UBERON:0000479 {source="ZFA"} ! tissue is_a: UBERON:0001048 {source="Obol"} ! primordium +is_a: UBERON:0010312 ! immature eye is_a: UBERON:0010313 ! neural crest-derived structure relationship: part_of UBERON:0000019 {source="ZFA"} ! camera-type eye @@ -14738,7 +14221,6 @@ def: "Multi-tissue structure that arises from the heart rudiment and will become subset: vertebrate_core synonym: "early primitive heart tube" NARROW [EMAPA:16208] synonym: "primitive heart tube" EXACT [EMAPA:16215] -xref: BTO:0006179 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: EHDAA2:0001512 xref: EHDAA:424 xref: EHDAA:436 @@ -14750,8 +14232,8 @@ xref: Wikipedia:Primitive_heart_tube xref: ZFA:0000149 is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004120 ! mesoderm-derived structure -relationship: develops_from UBERON:0004291 {source="ZFA"} ! heart rudiment relationship: part_of UBERON:0000922 ! embryo +relationship: RO:0002202 UBERON:0004291 {source="ZFA"} ! develops from heart rudiment [Term] id: UBERON:0005606 @@ -14766,7 +14248,6 @@ xref: VHOG:0001477 is_a: UBERON:0002553 ! anatomical cavity is_a: UBERON:0012467 ! enclosed anatomical space relationship: part_of UBERON:0002203 ! vasculature of eye -property_value: UBPROP:0000001 "A depression in the front of the vitreous body, lodging the lens. [adapted_from_the_definition_of_the_hyaloid_fossa]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001477", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/hyaloid+fossa"} [Term] id: UBERON:0005764 @@ -14779,9 +14260,9 @@ is_a: UBERON:0000476 ! acellular anatomical structure intersection_of: UBERON:0000476 ! acellular anatomical structure intersection_of: bounding_layer_of UBERON:0000061 ! anatomical structure relationship: bounding_layer_of UBERON:0000061 ! anatomical structure -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0005769 @@ -14801,12 +14282,11 @@ xref: Wikipedia:Basement_membrane is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005764 {source="FMA"} ! acellular membrane relationship: adjacent_to CL:0000066 ! epithelial cell -relationship: composed_primarily_of GO:0005604 ! basement membrane relationship: has_part GO:0005587 ! collagen type IV trimer -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa relationship: part_of UBERON:0000483 ! epithelium -relationship: present_in_taxon NCBITaxon:80999 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} -property_value: IAO:0000232 "this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell." xsd:string +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002473 GO:0005604 ! composed primarily of basement membrane +property_value: RO:0002175 NCBITaxon:80999 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} [Term] id: UBERON:0005856 @@ -14819,7 +14299,7 @@ xref: EHDAA2_RETIRED:0003148 xref: EHDAA:8979 is_a: UBERON:0007524 {source="AEO"} ! dense mesenchyme tissue is_a: UBERON:0011585 {source="cjm"} ! cell condensation -relationship: composed_primarily_of CL:0000335 {source="AEO-modified-relation"} ! mesenchyme condensation cell +relationship: RO:0002473 CL:0000335 {source="AEO-modified-relation"} ! composed primarily of mesenchyme condensation cell [Term] id: UBERON:0005906 @@ -14844,8 +14324,9 @@ synonym: "subbrillar sac" NARROW [NCBITaxon:8570] xref: EMAPA:18233 xref: FMA:20291 xref: SCTID:362531001 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005906 {source="FMA"} ! serous sac -relationship: adjacent_to UBERON:0001801 {modified_from="MA"} ! anterior segment of eyeball +relationship: adjacent_to UBERON:0001801 ! anterior segment of eyeball relationship: part_of UBERON:0000019 {source="FMA"} ! camera-type eye relationship: part_of UBERON:0035639 {source="HPO:pr"} ! ocular adnexa @@ -14860,7 +14341,6 @@ subset: uberon_slim synonym: "skeleton axiale" RELATED OMO:0003011 [Wikipedia:Axial_skeleton] xref: AAO:0000963 xref: EMAPA:17214 -xref: EMAPA:18043 xref: MA:0000308 xref: NCIT:C32172 xref: SCTID:361725000 @@ -14869,13 +14349,12 @@ xref: VSAO:0000056 xref: Wikipedia:Axial_skeleton xref: XAO:0004011 is_a: UBERON:0010912 ! subdivision of skeleton -relationship: contributes_to_morphology_of UBERON:0001434 ! skeletal system -relationship: develops_from UBERON:0003089 ! sclerotome relationship: part_of UBERON:0011137 ! axial skeletal system -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg" xsd:anyURI +relationship: RO:0002202 UBERON:0003089 ! develops from sclerotome +relationship: RO:0002433 UBERON:0001434 ! contributes to morphology of skeletal system +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" xsd:anyURI -property_value: UBPROP:0000001 "Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000056", ontology="VSAO", source="PSPUB:0000170"} [Term] id: UBERON:0006134 @@ -14897,8 +14376,7 @@ is_a: UBERON:0005162 ! multi cell part structure relationship: extends_fibers_into CL:0000540 ! neuron relationship: has_part GO:0030424 ! axon relationship: part_of UBERON:0001019 ! nerve fasciculus -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000007 "neurofibrous" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0006135 @@ -14916,12 +14394,11 @@ is_a: UBERON:0006134 ! nerve fiber intersection_of: UBERON:0006134 ! nerve fiber intersection_of: has_part GO:0043209 ! myelin sheath relationship: has_part GO:0043209 ! myelin sheath -relationship: never_in_taxon NCBITaxon:117569 -relationship: never_in_taxon NCBITaxon:7762 -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -relationship: present_in_taxon NCBITaxon:7776 ! Gnathostomata -property_value: editor_note "consider adding link to UBERON:0002316 ! white matter of neuraxis" xsd:string -property_value: UBPROP:0000008 "http://www1.pbrc.hawaii.edu/~danh/MyelinEvolution/evolution.html, http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=6134604, Wikipedia:Myelin#Invertebrate_myelin" xsd:string +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +property_value: IAO:0000116 "consider adding link to UBERON:0002316 ! white matter of neuraxis" xsd:string +property_value: RO:0002161 NCBITaxon:117569 +property_value: RO:0002161 NCBITaxon:7762 +property_value: RO:0002175 NCBITaxon:7776 [Term] id: UBERON:0006222 @@ -14941,9 +14418,9 @@ xref: TAO:0000574 xref: ZFA:0000574 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001894 ! diencephalon -relationship: has_potential_to_develop_into UBERON:0001894 ! diencephalon +intersection_of: RO:0002387 UBERON:0001894 ! has potential to develop into diencephalon relationship: part_of UBERON:0006240 {source="EHDAA2"} ! future forebrain +relationship: RO:0002387 UBERON:0001894 ! has potential to develop into diencephalon [Term] id: UBERON:0006238 @@ -14969,9 +14446,8 @@ xref: RETIRED_EHDAA2:0000591 xref: TAO:0000146 xref: ZFA:0000146 is_a: UBERON:0006598 ! presumptive structure -relationship: has_potential_to_develop_into UBERON:0000955 ! brain relationship: part_of UBERON:0002346 ! neurectoderm -property_value: UBPROP:0000001 "The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO)" xsd:string {source="http://neurolex.org/wiki/Cumbo_terms"} +relationship: RO:0002387 UBERON:0000955 ! has potential to develop into brain [Term] id: UBERON:0006240 @@ -14995,10 +14471,10 @@ xref: Wikipedia:Prosencephalon xref: ZFA:0000062 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001890 ! forebrain -relationship: has_potential_to_develop_into UBERON:0001890 ! forebrain +intersection_of: RO:0002387 UBERON:0001890 ! has potential to develop into forebrain relationship: part_of UBERON:0006238 ! future brain -property_value: editor_note "TODO. Add relationships to neural plate (both ZFA and EMAPA time this with the neural plate)" xsd:string +relationship: RO:0002387 UBERON:0001890 ! has potential to develop into forebrain +property_value: IAO:0000116 "TODO. Add relationships to neural plate (both ZFA and EMAPA time this with the neural plate)" xsd:string [Term] id: UBERON:0006241 @@ -15018,9 +14494,9 @@ xref: EMAPA:16755 xref: TAO:0000417 xref: ZFA:0000417 is_a: UBERON:0006598 ! presumptive structure -relationship: has_potential_to_develop_into UBERON:0001049 {source="EHDAA2"} ! neural tube -relationship: has_potential_to_develop_into UBERON:0002240 ! spinal cord relationship: part_of UBERON:0001017 ! central nervous system +relationship: RO:0002387 UBERON:0001049 {source="EHDAA2"} ! has potential to develop into neural tube +relationship: RO:0002387 UBERON:0002240 ! has potential to develop into spinal cord [Term] id: UBERON:0006267 @@ -15038,9 +14514,8 @@ is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium -relationship: develops_from UBERON:0006268 {source="EHDAA2"} ! notochordal process -property_value: editor_note "TODO - check ordering; awaiting confirmation from JB" xsd:string -property_value: UBPROP:0000001 "The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001212", ontology="VHOG", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0006268 {source="EHDAA2"} ! develops from notochordal process +property_value: IAO:0000116 "TODO - check ordering; awaiting confirmation from JB" xsd:string [Term] id: UBERON:0006268 @@ -15059,8 +14534,8 @@ xref: NCIT:C34232 xref: UMLS:C1518430 {source="ncithesaurus:Notochordal_Process"} xref: VHOG:0001213 is_a: UBERON:0005423 ! developing anatomical structure -relationship: develops_from UBERON:0000924 {source="EHDAA2"} ! ectoderm -relationship: only_in_taxon NCBITaxon:7711 ! Chordata +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002202 UBERON:0000924 {source="EHDAA2"} ! develops from ectoderm [Term] id: UBERON:0006311 @@ -15078,11 +14553,12 @@ xref: NCIT:C32301 xref: SCTID:280540004 xref: UMLS:C0459556 {source="ncithesaurus:Chamber_of_the_Eye"} is_a: UBERON:0000063 ! organ subunit +is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000063 ! organ subunit -intersection_of: location_of UBERON:0006312 ! ocular refractive media intersection_of: part_of UBERON:0000019 ! camera-type eye -relationship: location_of UBERON:0006312 ! ocular refractive media +intersection_of: RO:0001015 UBERON:0006312 ! location of ocular refractive media relationship: part_of UBERON:0000019 ! camera-type eye +relationship: RO:0001015 UBERON:0006312 ! location of ocular refractive media [Term] id: UBERON:0006312 @@ -15092,7 +14568,6 @@ def: "Body substance in a liquid or semi-solid state in the eyeball which serves xref: MA:0001911 is_a: UBERON:0000463 ! organism substance relationship: part_of UBERON:0000019 ! camera-type eye -property_value: UBPROP:0000009 "ocular refraction" xsd:string [Term] id: UBERON:0006314 @@ -15111,8 +14586,8 @@ xref: MESH:D001826 xref: Wikipedia:Body_fluid is_a: UBERON:0000463 ! organism substance intersection_of: UBERON:0000463 ! organism substance -intersection_of: has_quality PATO:0001548 ! quality of a liquid -relationship: has_quality PATO:0001548 ! quality of a liquid +intersection_of: RO:0000086 PATO:0001548 ! has quality quality of a liquid +relationship: RO:0000086 PATO:0001548 ! has quality quality of a liquid [Term] id: UBERON:0006562 @@ -15127,11 +14602,7 @@ xref: MAT:0000049 xref: MESH:D010614 xref: MIAA:0000049 is_a: UBERON:0004921 ! subdivision of digestive tract -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -property_value: IAO:0000232 "currently this is an extremely generic class, encompassing both protostomes and deuterostomes." xsd:string -property_value: IAO:0006012 "2023-04-20" xsd:string -property_value: UBPROP:0000007 "branchial" xsd:string -property_value: UBPROP:0000007 "pharyngeal" xsd:string +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria [Term] id: UBERON:0006595 @@ -15145,11 +14616,11 @@ xref: TAO:0000416 xref: ZFA:0000416 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0000925 ! endoderm intersection_of: part_of UBERON:0000307 ! blastula -relationship: has_potential_to_develop_into UBERON:0000925 ! endoderm -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +intersection_of: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm relationship: part_of UBERON:0000307 ! blastula +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm [Term] id: UBERON:0006596 @@ -15163,8 +14634,8 @@ xref: TAO:0000568 xref: ZFA:0000568 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0000178 ! blood -relationship: has_potential_to_develop_into UBERON:0000178 ! blood +intersection_of: RO:0002387 UBERON:0000178 ! has potential to develop into blood +relationship: RO:0002387 UBERON:0000178 ! has potential to develop into blood [Term] id: UBERON:0006598 @@ -15178,10 +14649,10 @@ xref: TAO:0001116 xref: ZFA:0001116 is_a: UBERON:0002050 ! embryonic structure intersection_of: UBERON:0005423 ! developing anatomical structure -intersection_of: has_potential_to_develop_into UBERON:0000061 ! anatomical structure intersection_of: part_of UBERON:0000922 ! embryo -relationship: has_potential_to_develop_into UBERON:0000061 ! anatomical structure -property_value: editor_note "Consider merging with anlage" xsd:string +intersection_of: RO:0002387 UBERON:0000061 ! has potential to develop into anatomical structure +relationship: RO:0002387 UBERON:0000061 ! has potential to develop into anatomical structure +property_value: IAO:0000116 "Consider merging with anlage" xsd:string [Term] id: UBERON:0006601 @@ -15197,11 +14668,11 @@ xref: XAO:0004132 xref: ZFA:0001376 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0000924 ! ectoderm intersection_of: part_of UBERON:0000307 ! blastula -relationship: has_potential_to_develop_into UBERON:0000924 ! ectoderm -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +intersection_of: RO:0002387 UBERON:0000924 ! has potential to develop into ectoderm relationship: part_of UBERON:0000307 ! blastula +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002387 UBERON:0000924 ! has potential to develop into ectoderm [Term] id: UBERON:0006603 @@ -15215,11 +14686,11 @@ xref: TAO:0001377 xref: ZFA:0001377 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0000926 ! mesoderm intersection_of: part_of UBERON:0000307 ! blastula -relationship: has_potential_to_develop_into UBERON:0000926 ! mesoderm -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +intersection_of: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm relationship: part_of UBERON:0000307 ! blastula +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm [Term] id: UBERON:0006876 @@ -15249,7 +14720,6 @@ is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: has_part CL:0000076 ! squamous epithelial cell relationship: has_part CL:0000076 ! squamous epithelial cell -property_value: UBPROP:0000012 "FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium" xsd:string {external_ontology="FBbt"} [Term] id: UBERON:0006965 @@ -15280,7 +14750,7 @@ xref: EHDAA2_RETIRED:0003192 xref: FMA:24137 xref: NCIT:C34022 xref: UMLS:C1515977 {source="ncithesaurus:Anatomic_Surface"} -is_a: UBERON:0010199 {notes="via morphological boundary in CARO"} ! bona-fide anatomical boundary +is_a: UBERON:0010199 ! bona-fide anatomical boundary [Term] id: UBERON:0007005 @@ -15303,13 +14773,14 @@ xref: FMA:293143 xref: SCTID:360387000 xref: VHOG:0001641 xref: XAO:0000235 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue -relationship: developmentally_induced_by UBERON:0009881 ! anterior lateral plate mesoderm -relationship: develops_from UBERON:0004872 ! splanchnic layer of lateral plate mesoderm relationship: part_of UBERON:0004140 ! primary heart field relationship: part_of UBERON:0009881 ! anterior lateral plate mesoderm -property_value: editor_note "consider FBbt:00005541 ! cardiogenic mesoderm" xsd:string -property_value: editor_note "review EHDAA2 placement" xsd:string +relationship: RO:0002202 UBERON:0004872 ! develops from splanchnic layer of lateral plate mesoderm +relationship: RO:0002256 UBERON:0009881 ! developmentally induced by anterior lateral plate mesoderm +property_value: IAO:0000116 "consider FBbt:00005541 ! cardiogenic mesoderm" xsd:string +property_value: IAO:0000116 "review EHDAA2 placement" xsd:string [Term] id: UBERON:0007010 @@ -15319,10 +14790,10 @@ def: "Organism at the cleavage stage." [OBOL:automatic] xref: BILA:0000058 is_a: UBERON:0000922 ! embryo intersection_of: UBERON:0000468 ! multicellular organism -intersection_of: existence_ends_with UBERON:0000107 ! cleavage stage -intersection_of: existence_starts_with UBERON:0000107 ! cleavage stage -relationship: existence_ends_with UBERON:0000107 ! cleavage stage -relationship: existence_starts_with UBERON:0000107 ! cleavage stage +intersection_of: RO:0002489 UBERON:0000107 ! existence starts with cleavage stage +intersection_of: RO:0002493 UBERON:0000107 ! existence ends with cleavage stage +relationship: RO:0002489 UBERON:0000107 ! existence starts with cleavage stage +relationship: RO:0002493 UBERON:0000107 ! existence ends with cleavage stage [Term] id: UBERON:0007026 @@ -15341,12 +14812,11 @@ xref: SCTID:360394002 xref: UMLS:C1514442 {source="ncithesaurus:Primordial_Gut"} is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001555 ! digestive tract -relationship: existence_starts_during UBERON:0000109 ! gastrula stage -relationship: has_developmental_contribution_from UBERON:0000925 ! endoderm -relationship: has_developmental_contribution_from UBERON:0000926 ! mesoderm -relationship: has_potential_to_develop_into UBERON:0001555 ! digestive tract -property_value: UBPROP:0000011 "The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis" xsd:string {source="NCBIBook:NBK10107"} +intersection_of: RO:0002387 UBERON:0001555 ! has potential to develop into digestive tract +relationship: RO:0002254 UBERON:0000925 ! has developmental contribution from endoderm +relationship: RO:0002254 UBERON:0000926 ! has developmental contribution from mesoderm +relationship: RO:0002387 UBERON:0001555 ! has potential to develop into digestive tract +relationship: RO:0002488 UBERON:0000109 ! existence starts during gastrula stage [Term] id: UBERON:0007100 @@ -15359,14 +14829,12 @@ synonym: "adult heart" RELATED [FBbt:00003154] synonym: "dorsal tube" NARROW [Wikipedia:Heart] synonym: "heart" NARROW [GO:0007507] xref: http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg -xref: SPD:0000130 xref: TADS:0000147 is_a: UBERON:0015228 ! circulatory organ intersection_of: UBERON:0015228 ! circulatory organ intersection_of: capable_of GO:0008015 ! blood circulation -relationship: capable_of GO:0008015 {notes="GO uses blood circulation generically to include the haemolymphatic fluid of arthropods"} ! blood circulation +relationship: capable_of GO:0008015 ! blood circulation relationship: has_part CL:0002494 ! cardiocyte -property_value: UBPROP:0000008 "note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis" xsd:string [Term] id: UBERON:0007135 @@ -15379,8 +14847,7 @@ xref: EFO:0003497 xref: TAO:0000131 xref: ZFA:0000131 is_a: UBERON:0016879 ! future central nervous system -relationship: develops_from UBERON:0003075 ! neural plate -property_value: UBPROP:0000001 "An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000131", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002202 UBERON:0003075 ! develops from neural plate [Term] id: UBERON:0007213 @@ -15400,9 +14867,10 @@ xref: EMAPA_RETIRED:16271 xref: TAO:0000787 xref: ZFA:0000787 is_a: UBERON:0005253 {source="ZFA"} ! head mesenchyme +is_a: UBERON:0014387 ! mesenchyme derived from neural crest intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: develops_from UBERON:0003099 ! cranial neural crest -relationship: develops_from UBERON:0003099 ! cranial neural crest +intersection_of: RO:0002202 UBERON:0003099 ! develops from cranial neural crest +relationship: RO:0002202 UBERON:0003099 ! develops from cranial neural crest [Term] id: UBERON:0007277 @@ -15424,13 +14892,12 @@ xref: Wikipedia:Rhombencephalon xref: ZFA:0000569 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0002028 ! hindbrain -relationship: develops_from UBERON:0003076 {source="XAO-abduced"} ! posterior neural tube -relationship: has_developmental_contribution_from UBERON:0003852 {source="cjm"} ! rhombencephalon neural crest -relationship: has_potential_to_develop_into UBERON:0002028 ! hindbrain +intersection_of: RO:0002387 UBERON:0002028 ! has potential to develop into hindbrain relationship: part_of UBERON:0006238 ! future brain -property_value: editor_note "TODO - unify naming conventions" xsd:string -property_value: UBPROP:0000001 "The embryonic rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. Rhombomeres Rh7-Rh4 form the myelencephalon that will give the medulla oblongata. Rhombomeres Rh3-Rh1 form the metencephalon that will form the pons and the cerebellum[NPX:PDR]." xsd:string {source="NPX:PDR"} +relationship: RO:0002202 UBERON:0003076 {source="XAO-abduced"} ! develops from posterior neural tube +relationship: RO:0002254 UBERON:0003852 {source="cjm"} ! has developmental contribution from rhombencephalon neural crest +relationship: RO:0002387 UBERON:0002028 ! has potential to develop into hindbrain +property_value: IAO:0000116 "TODO - unify naming conventions" xsd:string [Term] id: UBERON:0007281 @@ -15446,9 +14913,9 @@ xref: XAO:0004086 xref: ZFA:0001187 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0003052 ! midbrain-hindbrain boundary -relationship: has_potential_to_develop_into UBERON:0003052 ! midbrain-hindbrain boundary +intersection_of: RO:0002387 UBERON:0003052 ! has potential to develop into midbrain-hindbrain boundary relationship: part_of UBERON:0006238 {source="ZFA"} ! future brain +relationship: RO:0002387 UBERON:0003052 ! has potential to develop into midbrain-hindbrain boundary [Term] id: UBERON:0007282 @@ -15462,9 +14929,9 @@ xref: TAO:0000053 xref: ZFA:0000053 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0003059 ! presomitic mesoderm -relationship: develops_from UBERON:0009618 {consistent_with="https://github.com/obophenotype/uberon/wiki/The-neural-crest", source="EDHAA2"} ! trunk paraxial mesoderm -relationship: has_potential_to_develop_into UBERON:0003059 ! presomitic mesoderm +intersection_of: RO:0002387 UBERON:0003059 ! has potential to develop into presomitic mesoderm +relationship: RO:0002202 UBERON:0009618 ! develops from trunk paraxial mesoderm +relationship: RO:0002387 UBERON:0003059 ! has potential to develop into presomitic mesoderm [Term] id: UBERON:0007284 @@ -15479,12 +14946,11 @@ xref: TAO:0000063 xref: ZFA:0000063 is_a: UBERON:0016879 ! future central nervous system intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0003075 ! neural plate -relationship: develops_from UBERON:0002346 ! neurectoderm -relationship: has_potential_to_develop_into UBERON:0003075 ! neural plate +intersection_of: RO:0002387 UBERON:0003075 ! has potential to develop into neural plate relationship: part_of UBERON:0004734 ! gastrula -property_value: editor_note "consider merging" xsd:string -property_value: UBPROP:0000001 "Region of the gastrula which gives rise to the neural plate.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000063", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002202 UBERON:0002346 ! develops from neurectoderm +relationship: RO:0002387 UBERON:0003075 ! has potential to develop into neural plate +property_value: IAO:0000116 "consider merging" xsd:string [Term] id: UBERON:0007285 @@ -15500,10 +14966,10 @@ xref: XAO:0004134 xref: ZFA:0000591 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 {source="https://github.com/obophenotype/uberon/issues/1277"} ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0003077 {source="https://github.com/obophenotype/uberon/issues/1277"} ! paraxial mesoderm intersection_of: part_of UBERON:0000307 {source="https://github.com/obophenotype/uberon/issues/1277"} ! blastula -relationship: has_potential_to_develop_into UBERON:0003077 ! paraxial mesoderm +intersection_of: RO:0002387 UBERON:0003077 {source="https://github.com/obophenotype/uberon/issues/1277"} ! has potential to develop into paraxial mesoderm relationship: part_of UBERON:0000307 ! blastula +relationship: RO:0002387 UBERON:0003077 ! has potential to develop into paraxial mesoderm [Term] id: UBERON:0007418 @@ -15576,7 +15042,7 @@ is_a: UBERON:0003104 ! mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: participates_in GO:0016477 ! cell migration relationship: participates_in GO:0016477 ! cell migration -property_value: editor_note "this class will be an important part of the NC reorganization" xsd:string +property_value: IAO:0000116 "this class will be an important part of the NC reorganization" xsd:string [Term] id: UBERON:0007619 @@ -15588,7 +15054,6 @@ xref: MA:0001318 xref: SCTID:280667001 is_a: UBERON:0001781 {source="UBERON"} ! layer of retina relationship: part_of UBERON:0003902 ! retinal neural layer -property_value: UBPROP:0000012 "MA does treat internal/external limiting membranes as layers - these are classified as laminae. We do not follow this convention. However, we do following MA is grouping these terms together" xsd:string {external_ontology="MA"} [Term] id: UBERON:0007625 @@ -15616,10 +15081,10 @@ synonym: "junction" BROAD [] xref: FMA:5898 xref: SCTID:91833003 is_a: UBERON:0000061 {source="FMA"} ! anatomical structure -relationship: connects UBERON:0000061 {minCardinality="2"} ! anatomical structure -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0002176 UBERON:0000061 {minCardinality="2"} ! connects anatomical structure +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0007688 @@ -15634,7 +15099,6 @@ synonym: "organ field" RELATED [] xref: AEO:0000170 xref: EFO:0001649 xref: EHDAA2:0003170 -xref: FBbt:00005426 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: Wikipedia:Anlage_(biology) is_a: UBERON:0000479 {source="FBbt"} ! tissue is_a: UBERON:0005423 {source="AEO", source="FBbt"} ! developing anatomical structure @@ -15652,7 +15116,7 @@ intersection_of: UBERON:0001018 ! axon tract intersection_of: part_of UBERON:0000955 ! brain relationship: part_of UBERON:0000955 ! brain relationship: part_of UBERON:0002316 {source="cjm"} ! white matter -property_value: editor_note "the NIFSTD class 'nerve tract' is classified under 'regional part of brain', so it may seem like it belongs here, but actually includes spinal cord tracts" xsd:string +property_value: IAO:0000116 "the NIFSTD class 'nerve tract' is classified under 'regional part of brain', so it may seem like it belongs here, but actually includes spinal cord tracts" xsd:string [Term] id: UBERON:0007798 @@ -15670,10 +15134,8 @@ xref: NCIT:C33854 xref: UMLS:C0489903 {source="ncithesaurus:Vascular_System"} is_a: UBERON:0000467 ! anatomical system relationship: part_of UBERON:0004535 {source="MA"} ! cardiovascular system -relationship: present_in_taxon NCBITaxon:9606 -property_value: editor_note "consider merging with vasculature" xsd:string -property_value: UBPROP:0000001 "The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]." xsd:string {source="ncithesaurus:Vascular_System"} -property_value: UBPROP:0000012 "in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system" xsd:string {external_ontology="MA"} +property_value: IAO:0000116 "consider merging with vasculature" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0007811 @@ -15711,10 +15173,10 @@ xref: EHDAA2:0001113 xref: EHDAA:177 xref: EMAPA:16097 is_a: UBERON:0000477 ! anatomical cluster -relationship: composed_primarily_of UBERON:0003104 ! mesenchyme -relationship: has_developmental_contribution_from UBERON:0000926 {source="EHDAA2"} ! mesoderm relationship: part_of UBERON:0000922 ! embryo -property_value: editor_note "consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)" xsd:string +relationship: RO:0002254 UBERON:0000926 {source="EHDAA2"} ! has developmental contribution from mesoderm +relationship: RO:0002473 UBERON:0003104 ! composed primarily of mesenchyme +property_value: IAO:0000116 "consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)" xsd:string [Term] id: UBERON:0009569 @@ -15752,9 +15214,9 @@ synonym: "midbrain-hindbrain boundary neural plate" EXACT [ZFA:0007044] xref: TAO:0007044 xref: ZFA:0007044 is_a: UBERON:0006598 ! presumptive structure -relationship: immediate_transformation_of UBERON:0007281 {notes="https://github.com/obophenotype/uberon/issues/438", source="Bgee:AN"} ! presumptive midbrain hindbrain boundary relationship: part_of UBERON:0003075 {source="ZFA"} ! neural plate -property_value: editor_note "TODO - developmental relationships for lines" xsd:string +relationship: RO:0002495 UBERON:0007281 ! immediate transformation of presumptive midbrain hindbrain boundary +property_value: IAO:0000116 "TODO - developmental relationships for lines" xsd:string [Term] id: UBERON:0009616 @@ -15775,12 +15237,12 @@ xref: Wikipedia:Mesencephalon xref: ZFA:0000148 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001891 ! midbrain -relationship: develops_from UBERON:0003080 ! anterior neural tube -relationship: develops_from UBERON:0010286 {source="ZFA"} ! midbrain neural tube -relationship: has_potential_to_develop_into UBERON:0001891 ! midbrain +intersection_of: RO:0002387 UBERON:0001891 ! has potential to develop into midbrain relationship: part_of UBERON:0006238 {source="ZFA"} ! future brain -property_value: editor_note "TODO - unify naming conventions" xsd:string +relationship: RO:0002202 UBERON:0003080 ! develops from anterior neural tube +relationship: RO:0002202 UBERON:0010286 {source="ZFA"} ! develops from midbrain neural tube +relationship: RO:0002387 UBERON:0001891 ! has potential to develop into midbrain +property_value: IAO:0000116 "TODO - unify naming conventions" xsd:string [Term] id: UBERON:0009618 @@ -15802,6 +15264,7 @@ synonym: "ALPM" EXACT [ZFA:0005041] xref: EFO:0003704 xref: TAO:0005041 xref: ZFA:0005041 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue relationship: part_of UBERON:0003081 {source="ZFA"} ! lateral plate mesoderm @@ -15825,7 +15288,7 @@ name: optic neural crest namespace: uberon xref: EHDAA2:0001315 xref: EHDAA:1122 -is_a: UBERON:0005253 ! head mesenchyme +is_a: UBERON:0007213 ! mesenchyme derived from head neural crest is_a: UBERON:0007530 {source="EHDAA2"} ! migrating mesenchyme population relationship: part_of UBERON:0007213 {source="EHDAA2"} ! mesenchyme derived from head neural crest @@ -15838,15 +15301,14 @@ subset: common_anatomy subset: upper_level synonym: "multicellular structure" EXACT [FBbt:00100313] xref: CARO:0010000 -xref: FBbt:00100313 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: has_quality PATO:0001993 ! multicellular +intersection_of: RO:0000086 PATO:0001993 ! has quality multicellular relationship: has_part CL:0000000 ! cell -relationship: has_quality PATO:0001993 ! multicellular -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0000086 PATO:0001993 ! has quality multicellular +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0010096 @@ -15856,9 +15318,9 @@ def: "A developing anatomical structure that has the potential to develop into a xref: EHDAA2:0000640 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0005290 ! myelencephalon -relationship: has_potential_to_develop_into UBERON:0005290 ! myelencephalon +intersection_of: RO:0002387 UBERON:0005290 ! has potential to develop into myelencephalon relationship: part_of UBERON:0002028 ! hindbrain +relationship: RO:0002387 UBERON:0005290 ! has potential to develop into myelencephalon [Term] id: UBERON:0010199 @@ -15887,10 +15349,9 @@ xref: SCTID:244486005 xref: VHOG:0001616 xref: Wikipedia:Globe_(human_eye) is_a: UBERON:0000020 ! sense organ -relationship: contributes_to_morphology_of UBERON:0000019 ! camera-type eye +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0000019 {source="FMA"} ! camera-type eye -property_value: IAO:0000232 "See notes for camera-type eye" xsd:string -property_value: UBPROP:0000202 FMA:264089 +relationship: RO:0002433 UBERON:0000019 ! contributes to morphology of camera-type eye [Term] id: UBERON:0010285 @@ -15916,9 +15377,10 @@ namespace: uberon def: "Portion of neural tube that gives rise to the midbrain." [ZFA:0007039] xref: TAO:0007039 xref: ZFA:0007039 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue relationship: part_of UBERON:0003080 {source="ZFA"} ! anterior neural tube -property_value: editor_note "we follow ZFA in temporally dividing midbrain NT from presumptive midbrain, but in future this may be collapsed" xsd:string +property_value: IAO:0000116 "we follow ZFA in temporally dividing midbrain NT from presumptive midbrain, but in future this may be collapsed" xsd:string [Term] id: UBERON:0010312 @@ -15930,10 +15392,9 @@ xref: TAO:0002201 xref: ZFA:0001678 is_a: UBERON:0005423 ! developing anatomical structure intersection_of: UBERON:0005423 ! developing anatomical structure -intersection_of: has_developmental_contribution_from UBERON:0003071 ! eye primordium -relationship: develops_from UBERON:0003071 {evidence="definitional"} ! eye primordium -relationship: has_developmental_contribution_from UBERON:0003071 ! eye primordium -property_value: UBPROP:0000001 "Multi-tissue structure that consists of the structures that develop into the retina and lens.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002201", ontology="TAO", source="ZFIN:curator"} +intersection_of: RO:0002254 UBERON:0003071 ! has developmental contribution from eye primordium +relationship: RO:0002202 UBERON:0003071 ! develops from eye primordium +relationship: RO:0002254 UBERON:0003071 ! has developmental contribution from eye primordium [Term] id: UBERON:0010313 @@ -15944,9 +15405,8 @@ subset: grouping_class is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: develops_from UBERON:0002342 ! neural crest -relationship: develops_from UBERON:0002342 ! neural crest -property_value: IAO:0000232 "Grouping term for query purposes" xsd:string +intersection_of: RO:0002202 UBERON:0002342 ! develops from neural crest +relationship: RO:0002202 UBERON:0002342 ! develops from neural crest [Term] id: UBERON:0010314 @@ -15956,9 +15416,8 @@ def: "An anatomical structure that has some part that develops from the neural c subset: grouping_class is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: has_developmental_contribution_from UBERON:0002342 ! neural crest -relationship: has_developmental_contribution_from UBERON:0002342 ! neural crest -property_value: IAO:0000232 "Grouping term for query purposes" xsd:string +intersection_of: RO:0002254 UBERON:0002342 ! has developmental contribution from neural crest +relationship: RO:0002254 UBERON:0002342 ! has developmental contribution from neural crest [Term] id: UBERON:0010316 @@ -15966,7 +15425,7 @@ name: germ layer / neural crest namespace: uberon is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0005291 ! embryonic tissue -relationship: develops_from UBERON:0002532 ! epiblast (generic) +relationship: RO:0002202 UBERON:0002532 ! develops from epiblast (generic) [Term] id: UBERON:0010371 @@ -15978,8 +15437,8 @@ xref: FMA:69064 is_a: UBERON:0000483 ! epithelium is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000483 ! epithelium -intersection_of: develops_from UBERON:0000924 ! ectoderm -relationship: composed_primarily_of CL:0002077 ! ecto-epithelial cell +intersection_of: RO:0002202 UBERON:0000924 ! develops from ectoderm +relationship: RO:0002473 CL:0002077 ! composed primarily of ecto-epithelial cell [Term] id: UBERON:0010409 @@ -15993,8 +15452,8 @@ synonym: "ocular surface" EXACT [] xref: EMAPA:35336 xref: MA:0002486 is_a: UBERON:0000063 ! organ subunit +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0000019 ! camera-type eye -relationship: superficial_to UBERON:0022288 ! surface of eyeball [Term] id: UBERON:0010427 @@ -16011,12 +15470,13 @@ xref: FMA:76551 xref: SCTID:280860001 xref: Wikipedia:Ciliary_processes is_a: UBERON:0000481 ! multi-tissue structure +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001775 ! ciliary body -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/Gray875.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-l.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-r.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-l.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-r.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/Gray875.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-l.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-f-eye-r.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-l.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.4/3d-vh-m-eye-r.glb" xsd:anyURI [Term] id: UBERON:0010912 @@ -16032,7 +15492,6 @@ xref: VSAO:0000042 is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision relationship: part_of UBERON:0000075 {source="UBERONREF:0000003"} ! subdivision of skeletal system relationship: part_of UBERON:0004288 {source="VSAO"} ! skeleton -property_value: UBPROP:0000001 "Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000042", notes="incorrect", ontology="VSAO", source="VSAO:curator"} [Term] id: UBERON:0011137 @@ -16053,7 +15512,7 @@ synonym: "axial skeletal system" BROAD [https://github.com/obophenotype/uberon/w synonym: "post-cranial axial skeletal system" EXACT [] xref: FMA:302077 is_a: UBERON:0000075 {source="FMA"} ! subdivision of skeletal system -relationship: develops_from UBERON:0003089 {source="cjm"} ! sclerotome +relationship: RO:0002202 UBERON:0003089 {source="cjm"} ! develops from sclerotome property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" xsd:anyURI [Term] @@ -16065,6 +15524,7 @@ subset: upper_level synonym: "cell part cluster of neuraxis" EXACT [FMA:83143] synonym: "neuraxis layer" EXACT [FMA:83143] xref: FMA:83143 +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005162 ! multi cell part structure intersection_of: UBERON:0005162 ! multi cell part structure intersection_of: part_of UBERON:0001017 ! central nervous system @@ -16078,15 +15538,14 @@ def: "A subdivision of an anatomical system." [http://orcid.org/0000-0002-6601-2 subset: common_anatomy subset: human_reference_atlas subset: upper_level -xref: FBbt:00007330 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67509 xref: SCTID:91690000 is_a: UBERON:0010000 {source="FBbt"} ! multicellular anatomical structure relationship: part_of UBERON:0000467 ! anatomical system -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0011222 @@ -16097,9 +15556,9 @@ synonym: "intrinsic ocular muscle" EXACT [EMAPA:18808] xref: AAO:0010038 xref: EMAPA:18808 xref: FMA:49150 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004277 ! eye muscle relationship: part_of UBERON:0003386 {source="EMAPA"} ! smooth muscle of eye -property_value: UBPROP:0000001 "Muscles within the eye (bulbus oculi).[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010038", ontology="AAO", source="AAO:EJS"} [Term] id: UBERON:0011585 @@ -16109,7 +15568,7 @@ def: "Anatomical structure that is an aggregation of similar cells from which ca xref: VSAO:0000006 xref: XAO:0004021 is_a: UBERON:0000061 {source="VSAO"} ! anatomical structure -property_value: editor_note "consider obsoleting, coordinate with VSAO" xsd:string +property_value: IAO:0000116 "consider obsoleting, coordinate with VSAO" xsd:string [Term] id: UBERON:0011591 @@ -16134,7 +15593,7 @@ synonym: "body segment" RELATED [] synonym: "main body segment" RELATED [] is_a: UBERON:0000475 ! organism subdivision relationship: part_of UBERON:0013701 ! main body axis -property_value: editor_note "Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem" xsd:string +property_value: IAO:0000116 "Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem" xsd:string [Term] id: UBERON:0011695 @@ -16198,11 +15657,12 @@ synonym: "ventral uveal tract" EXACT [] xref: EMAPA:37417 {source="MA:th"} xref: SCTID:280656002 is_a: UBERON:0000481 {source="ZFA"} ! multi-tissue structure -relationship: contributes_to_morphology_of UBERON:0001768 ! uvea -relationship: contributes_to_morphology_of UBERON:0001801 ! anterior segment of eyeball +is_a: UBERON:0004121 ! ectoderm-derived structure relationship: has_part UBERON:0001769 ! iris relationship: has_part UBERON:0001775 ! ciliary body relationship: part_of UBERON:0001768 {source="MP"} ! uvea +relationship: RO:0002433 UBERON:0001768 ! contributes to morphology of uvea +relationship: RO:0002433 UBERON:0001801 ! contributes to morphology of anterior segment of eyeball [Term] id: UBERON:0011997 @@ -16217,10 +15677,9 @@ synonym: "schizocoelom" NARROW [] xref: EHDAA2:0004731 xref: Wikipedia:Coelom is_a: UBERON:0000481 {source="EHDAA2"} ! multi-tissue structure -relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -property_value: editor_note "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." xsd:string -property_value: UBPROP:0000007 "coelomic" xsd:string +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +property_value: IAO:0000116 "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." xsd:string +property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} [Term] id: UBERON:0012275 @@ -16233,7 +15692,7 @@ xref: FMA:86452 is_a: UBERON:0000483 ! epithelium is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000483 ! epithelium -intersection_of: develops_from UBERON:0000926 ! mesoderm +intersection_of: RO:0002202 UBERON:0000926 ! develops from mesoderm [Term] id: UBERON:0012430 @@ -16248,12 +15707,13 @@ xref: FMA:58102 xref: SCTID:361318005 xref: Wikipedia:Fibrous_tunic_of_eyeball is_a: PR:000050567 ! protein-containing material entity +is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004923 {source="FMA"} ! organ component layer is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: has_part UBERON:0000964 ! cornea relationship: has_part UBERON:0001773 ! sclera relationship: part_of UBERON:0010230 ! eyeball of camera-type eye -relationship: present_in_taxon NCBITaxon:7955 {source="DOI:10.1177/0192623311409597"} +property_value: RO:0002175 NCBITaxon:7955 {source="DOI:10.1177/0192623311409597"} [Term] id: UBERON:0012467 @@ -16264,8 +15724,8 @@ synonym: "closed anatomical space" EXACT [] xref: AEO:0000222 is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: has_quality PATO:0000608 ! closed -relationship: has_quality PATO:0000608 ! closed +intersection_of: RO:0000086 PATO:0000608 ! has quality closed +relationship: RO:0000086 PATO:0000608 ! has quality closed [Term] id: UBERON:0013522 @@ -16286,11 +15746,11 @@ subset: common_anatomy synonym: "foramen space" NARROW [] xref: FMA:9338 is_a: UBERON:0000464 {source="FMA"} ! anatomical space -relationship: connects UBERON:0000464 {cardinality="2"} ! anatomical space -relationship: luminal_space_of UBERON:0004111 ! anatomical conduit -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0002176 UBERON:0000464 {cardinality="2"} ! connects anatomical space +relationship: RO:0002572 UBERON:0004111 ! luminal space of anatomical conduit +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0013701 @@ -16299,7 +15759,7 @@ namespace: uberon def: "A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages." [https://orcid.org/0000-0002-6601-2165] subset: non_informative is_a: UBERON:0000475 ! organism subdivision -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0013702 @@ -16311,11 +15771,24 @@ synonym: "body" RELATED [AEO:0000103] synonym: "whole body" RELATED [BTO:0001489] xref: AEO:0000103 xref: BTO:0001489 -xref: EMAPA:36031 xref: FMA:231424 is_a: UBERON:0000475 {source="AEO"} ! organism subdivision relationship: part_of UBERON:0013701 ! main body axis -property_value: UBPROP:0000001 "Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]." xsd:string {source="FMA:231424"} + +[Term] +id: UBERON:0014387 +name: mesenchyme derived from neural crest +namespace: uberon +def: "Mesenchyme that develops_from the neural crest[Automatically generated definition]." [https://github.com/obophenotype/uberon/issues/248, OBOL:automatic] +synonym: "mesenchyme from neural crest" EXACT [] +synonym: "neural crest derived mesenchyme" EXACT [] +synonym: "neural crest mesenchyme" EXACT [] +xref: EMAPA:32735 +xref: FMA:293883 +is_a: UBERON:0003104 ! mesenchyme +is_a: UBERON:0010313 ! neural crest-derived structure +intersection_of: UBERON:0003104 ! mesenchyme +intersection_of: RO:0002202 UBERON:0002342 ! develops from neural crest [Term] id: UBERON:0014477 @@ -16333,7 +15806,7 @@ xref: Wikipedia:Thoracic_skeleton is_a: UBERON:0010912 ! subdivision of skeleton relationship: part_of UBERON:0000915 ! thoracic segment of trunk relationship: part_of UBERON:0002090 ! postcranial axial skeleton -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0014903 @@ -16345,9 +15818,9 @@ xref: TAO:0005076 xref: ZFA:0005076 is_a: UBERON:0001048 ! primordium intersection_of: UBERON:0001048 ! primordium -intersection_of: has_potential_to_develop_into UBERON:0002049 ! vasculature -relationship: has_potential_to_develop_into UBERON:0002049 ! vasculature +intersection_of: RO:0002387 UBERON:0002049 ! has potential to develop into vasculature relationship: part_of UBERON:0011695 ! embryonic cardiovascular system +relationship: RO:0002387 UBERON:0002049 ! has potential to develop into vasculature [Term] id: UBERON:0015203 @@ -16355,7 +15828,6 @@ name: non-connected functional system namespace: uberon def: "An anatomical group whose component structures share a common function." [AEO:0000093, AEO:JB, FBbt:00007278, FBC:DOS] xref: AEO:0000093 -xref: FBbt:00007278 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0034923 ! disconnected anatomical group [Term] @@ -16366,11 +15838,7 @@ def: "Any structure that is placed on one side of the left-right axis of a bilat subset: grouping_class subset: non_informative is_a: UBERON:0000061 ! anatomical structure -intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: in_lateral_side_of UBERON:0000465 ! material anatomical entity -relationship: in_lateral_side_of UBERON:0000465 ! material anatomical entity -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -property_value: IAO:0000232 "This class is primarily to implement taxon constraints. It may be removed in the future." xsd:string +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria [Term] id: UBERON:0015228 @@ -16383,10 +15851,9 @@ synonym: "cardiac structure" RELATED [] synonym: "circulatory vessel" NARROW [] synonym: "heart" BROAD [] synonym: "heart or heart like organ" EXACT [] -xref: SPD:0000130 is_a: UBERON:0003103 ! compound organ -relationship: has_quality PATO:0001690 ! contractile relationship: part_of UBERON:0001009 ! circulatory system +relationship: RO:0000086 PATO:0001690 ! has quality contractile [Term] id: UBERON:0015410 @@ -16398,7 +15865,7 @@ xref: EMAPA:37597 {source="MA:th"} xref: MA:0002449 is_a: UBERON:0005178 {source="MA"} ! thoracic cavity element relationship: part_of UBERON:0004535 ! cardiovascular system -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0015808 @@ -16408,6 +15875,7 @@ def: "An epithelium that is part of a camera-type eye." [OBOL:automatic] xref: EMAPA:35957 xref: MA:0003162 is_a: UBERON:0007625 ! pigment epithelium of eye +is_a: UBERON:0010371 ! ecto-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000019 ! camera-type eye relationship: part_of UBERON:0000019 ! camera-type eye @@ -16422,10 +15890,10 @@ synonym: "future CNS" EXACT [] synonym: "presumptive central nervous system" EXACT [] is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001017 ! central nervous system -relationship: develops_from UBERON:0000924 ! ectoderm -relationship: has_potential_to_develop_into UBERON:0001017 ! central nervous system +intersection_of: RO:0002387 UBERON:0001017 ! has potential to develop into central nervous system relationship: part_of UBERON:0016880 ! future nervous system +relationship: RO:0002202 UBERON:0000924 ! develops from ectoderm +relationship: RO:0002387 UBERON:0001017 ! has potential to develop into central nervous system [Term] id: UBERON:0016880 @@ -16437,9 +15905,9 @@ synonym: "presumptive nervous system" EXACT [AAO:0000477] xref: AAO:0000477 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001016 ! nervous system -relationship: existence_starts_during_or_after UBERON:0000111 ! organogenesis stage -relationship: has_potential_to_develop_into UBERON:0001016 ! nervous system +intersection_of: RO:0002387 UBERON:0001016 ! has potential to develop into nervous system +relationship: RO:0002387 UBERON:0001016 ! has potential to develop into nervous system +relationship: RO:0002496 UBERON:0000111 ! existence starts during or after organogenesis stage [Term] id: UBERON:0016887 @@ -16453,8 +15921,8 @@ xref: EHDAA2:0000003 xref: EMAPA:16042 is_a: UBERON:0000481 {source="AEO"} ! multi-tissue structure relationship: adjacent_to UBERON:0002050 ! embryonic structure -relationship: existence_starts_and_ends_during UBERON:0000068 ! embryo stage relationship: part_of UBERON:0004716 {source="AEO"} ! conceptus +relationship: RO:0002491 UBERON:0000068 ! existence starts and ends during embryo stage [Term] id: UBERON:0019207 @@ -16468,6 +15936,8 @@ synonym: "retinachoroid" EXACT [] synonym: "retinachoroidal region" EXACT [] xref: SCTID:110701000 is_a: UBERON:0000481 ! multi-tissue structure +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: has_part UBERON:0000966 ! retina relationship: has_part UBERON:0001776 ! optic choroid relationship: part_of UBERON:0010230 ! eyeball of camera-type eye @@ -16484,7 +15954,7 @@ is_a: UBERON:0003544 ! brain white matter intersection_of: UBERON:0002316 ! white matter intersection_of: part_of UBERON:0001890 ! forebrain relationship: part_of UBERON:0001890 ! forebrain -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0019304 @@ -16519,11 +15989,11 @@ synonym: "layer" BROAD [CUMBO:CUMBO] xref: NLX:149357 is_a: UBERON:0005162 ! multi cell part structure intersection_of: UBERON:0005162 ! multi cell part structure -intersection_of: has_quality PATO:0002124 ! laminar intersection_of: part_of UBERON:0001016 ! nervous system -relationship: has_quality PATO:0002124 ! laminar +intersection_of: RO:0000086 PATO:0002124 ! has quality laminar relationship: part_of UBERON:0001016 ! nervous system -property_value: editor_note "this is currently used to group some cellular layers that may not strictly conform to the CARO definition of cell-part layer. Consider genericisizing and introducing subtypes for cellular layer, fibrous layer and cell soma layer" xsd:string +relationship: RO:0000086 PATO:0002124 ! has quality laminar +property_value: IAO:0000116 "this is currently used to group some cellular layers that may not strictly conform to the CARO definition of cell-part layer. Consider genericisizing and introducing subtypes for cellular layer, fibrous layer and cell soma layer" xsd:string [Term] id: UBERON:0034705 @@ -16570,9 +16040,8 @@ synonym: "neuron projection bundle from brain" RELATED [http://orcid.org/0000-00 is_a: UBERON:0000122 ! neuron projection bundle is_a: UBERON:0015212 ! lateral structure relationship: extends_fibers_into UBERON:0000955 ! brain -relationship: in_lateral_side_of UBERON:0000033 ! head -relationship: only_in_taxon NCBITaxon:89593 ! Craniata -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0034921 @@ -16583,10 +16052,10 @@ subset: common_anatomy synonym: "anatomical cluster" RELATED [CARO:0020001] xref: CARO:0020001 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure -relationship: composed_primarily_of UBERON:0000064 ! organ part -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0002473 UBERON:0000064 ! composed primarily of organ part +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0034923 @@ -16595,14 +16064,13 @@ namespace: uberon def: "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other." [CARO:0020000] subset: common_anatomy xref: CARO:0020000 -xref: FBbt:00007276 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000465 {source="CARO"} ! material anatomical entity -relationship: composed_primarily_of UBERON:0000061 ! anatomical structure relationship: has_component UBERON:0000061 {minCardinality="2"} ! anatomical structure -relationship: has_quality PATO:0010001 ! disconnected -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0000086 PATO:0010001 ! has quality disconnected +relationship: RO:0002473 UBERON:0000061 ! composed primarily of anatomical structure +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0034925 @@ -16611,11 +16079,11 @@ namespace: uberon def: "A collection of anatomical structures that are alike in terms of their morphology or developmental origin." [http://orcid.org/0000-0002-6601-2165] subset: common_anatomy is_a: UBERON:0000465 ! material anatomical entity -relationship: has_member UBERON:0000061 ! anatomical structure -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: editor_note "resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected" xsd:string +relationship: RO:0002351 UBERON:0000061 ! has member anatomical structure +property_value: IAO:0000116 "resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0035639 @@ -16673,9 +16141,9 @@ xref: AAO:0010270 xref: ZFA:0005594 is_a: UBERON:0000465 ! material anatomical entity relationship: bounding_layer_of UBERON:0000061 ! anatomical structure -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:8600004 @@ -16685,9 +16153,15 @@ def: "A muscle tissue that is associated with soft internal organs (viscera)." [ comment: It is quite common to refer to visceral muscles as smooth muscles, by analogy with vertebrates; however, most visceral muscles in arthropods are actually striated. {xref="https://en.wikipedia.org/wiki/Smooth_muscle", xref="FBbt:00005070", comment="PMID:8720463"} synonym: "visceral muscle" EXACT [] {comment="BTO:0002780"} is_a: UBERON:0002385 ! muscle tissue -relationship: composed_primarily_of CL:0008007 ! visceral muscle cell -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -property_value: dcterms-date "2023-02-16T10:17:46Z" xsd:dateTime +relationship: RO:0002473 CL:0008007 ! composed primarily of visceral muscle cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-02-16T10:17:46Z" xsd:dateTime + +[Typedef] +id: BFO:0000067 +name: contains process +def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] +comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant [Typedef] id: CL:4030044 @@ -16708,11 +16182,6 @@ id: RO:0000052 name: characteristic of def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." [] comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. -property_value: IAO:0000111 "inheres in" xsd:string -property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string -property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string -property_value: IAO:0000118 "inheres_in" xsd:string -property_value: RO:0001900 RO:0001901 is_functional: true is_a: RO:0002314 ! characteristic of part of inverse_of: bearer_of ! bearer of @@ -16722,10 +16191,7 @@ id: RO:0000079 name: function of def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. -property_value: editor_note "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string -property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string -property_value: IAO:0000118 "function_of" xsd:string -property_value: IAO:0000118 "is function of" xsd:string +property_value: IAO:0000116 "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string is_a: RO:0000052 ! characteristic of inverse_of: RO:0000085 ! has function @@ -16734,22 +16200,16 @@ id: RO:0000080 name: quality of def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. -property_value: editor_note "A quality inheres in its bearer at all times for which the quality exists." xsd:string -property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string -property_value: IAO:0000118 "is quality of" xsd:string -property_value: IAO:0000118 "quality_of" xsd:string +property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string is_a: RO:0000052 ! characteristic of -inverse_of: has_quality ! has quality +inverse_of: RO:0000086 ! has quality [Typedef] id: RO:0000081 name: role of def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. -property_value: editor_note "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string -property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string -property_value: IAO:0000118 "is role of" xsd:string -property_value: IAO:0000118 "role_of" xsd:string +property_value: IAO:0000116 "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string is_a: RO:0000052 ! characteristic of inverse_of: RO:0000087 ! has role @@ -16757,19 +16217,22 @@ inverse_of: RO:0000087 ! has role id: RO:0000085 name: has function def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] -property_value: editor_note "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string -property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string -property_value: IAO:0000118 "has_function" xsd:string +property_value: IAO:0000116 "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string domain: BFO:0000004 ! independent continuant is_a: bearer_of ! bearer of +[Typedef] +id: RO:0000086 +name: has quality +def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] +property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string +is_a: bearer_of ! bearer of + [Typedef] id: RO:0000087 name: has role def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] -property_value: editor_note "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string -property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string -property_value: IAO:0000118 "has_role" xsd:string +property_value: IAO:0000116 "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string domain: BFO:0000004 ! independent continuant is_a: bearer_of ! bearer of @@ -16794,12 +16257,7 @@ id: RO:0001000 name: derives from def: "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" [] subset: ro-eco -property_value: editor_note "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." xsd:string -property_value: IAO:0000112 "this cell derives from this parent cell (cell division)" xsd:string -property_value: IAO:0000112 "this nucleus derives from this parent nucleus (nuclear division)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000118 "derives_from" xsd:string -property_value: IAO:0000232 "This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations." xsd:string +property_value: IAO:0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." xsd:string inverse_of: RO:0001001 ! derives into [Typedef] @@ -16807,33 +16265,58 @@ id: RO:0001001 name: derives into def: "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" [] subset: ro-eco -property_value: editor_note "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." xsd:string -property_value: IAO:0000112 "this parent cell derives into this cell (cell division)" xsd:string -property_value: IAO:0000112 "this parent nucleus derives into this nucleus (nuclear division)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000118 "derives_into" xsd:string +property_value: IAO:0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." xsd:string + +[Typedef] +id: RO:0001015 +name: location of +def: "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" [] +property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +is_transitive: true +inverse_of: RO:0001025 ! located in + +[Typedef] +id: RO:0001025 +name: located in +def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +property_value: IAO:0000116 "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" xsd:string +property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Located_in" xsd:anyURI +domain: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +range: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +is_transitive: true +transitive_over: part_of ! part of [Typedef] id: RO:0002000 name: 2D boundary of def: "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" [] -property_value: editor_note "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string -property_value: editor_note "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string -property_value: IAO:0000112 "the surface of my skin is a 2D boundary of my body" xsd:string -property_value: IAO:0000118 "2D_boundary_of" xsd:string -property_value: IAO:0000118 "boundary of" xsd:string -property_value: IAO:0000118 "is 2D boundary of" xsd:string -property_value: IAO:0000118 "is boundary of" xsd:string -property_value: IAO:0000118 "surface of" xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string +is_a: RO:0002323 ! mereotopologically related to +inverse_of: RO:0002002 ! has 2D boundary + +[Typedef] +id: RO:0002002 +name: has 2D boundary +def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000141 ! immaterial entity is_a: RO:0002323 ! mereotopologically related to -inverse_of: has_boundary ! has 2D boundary + +[Typedef] +id: RO:0002005 +name: innervated_by +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000122 ! neuron projection bundle +inverse_of: RO:0002134 ! innervates [Typedef] id: RO:0002006 name: has synaptic terminal of -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: overlaps ! overlaps inverse_of: RO:0002130 ! has synaptic terminal in @@ -16915,16 +16398,23 @@ id: RO:0002081 name: before or simultaneous with comment: Primitive instance level timing relation between events subset: ro-eco -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000118 "<=" xsd:string is_a: RO:0002222 ! temporally related to +[Typedef] +id: RO:0002082 +name: simultaneous with +def: "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." [] +comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) +subset: ro-eco +is_symmetric: true +is_transitive: true +is_a: RO:0002081 ! before or simultaneous with + [Typedef] id: RO:0002086 name: ends after comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) subset: ro-eco -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string is_transitive: true is_a: RO:0002222 ! temporally related to @@ -16932,25 +16422,16 @@ is_a: RO:0002222 ! temporally related to id: RO:0002100 name: has soma location def: "Relation between a neuron and a material anatomical entity that its soma is part of." [] -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron range: UBERON:0000465 ! material anatomical entity is_a: overlaps ! overlaps -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] [Typedef] id: RO:0002101 name: fasciculates with def: "relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.\n" [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "fasciculates with" xsd:string -property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron range: UBERON:0000122 ! neuron projection bundle is_a: overlaps ! overlaps @@ -16960,27 +16441,23 @@ inverse_of: RO:0002132 ! has fasciculating neuron projection id: RO:0002102 name: axon synapses in def: "Relation between a neuron and some structure its axon forms (chemical) synapses in." [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: RO:0002113 ! has presynaptic terminal in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "BFO_0000051 some (\n GO_0030424 and BFO_0000051 some (\n GO_0042734 and BFO_0000050 some (\n GO_0045202 and BFO_0000050 some ?Y)))" [] +[Typedef] +id: RO:0002103 +name: synapsed by +def: "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " [] +is_a: RO:0002485 ! receives input from +inverse_of: RO:0002120 ! synapsed to +expand_expression_to: "BFO_0000051 some (GO_0045211 that part_of some (GO_0045202 that has_part some (GO_0042734 that BFO_0000050 some Y?)))" [] + [Typedef] id: RO:0002104 name: has plasma membrane part def: "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part." [] -property_value: IAO:0000112 "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9990-8331 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 -property_value: RO:0001900 RO:0001901 domain: UBERON:0000465 ! material anatomical entity range: UBERON:0000465 ! material anatomical entity is_a: has_part ! has part @@ -16990,29 +16467,19 @@ expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] id: RO:0002110 name: has postsynaptic terminal in def: "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. " [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "synapsed in" xsd:string -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: RO:0002130 ! has synaptic terminal in inverse_of: RO:0002113 ! has presynaptic terminal in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (\n http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some (\n http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))" [] [Typedef] id: RO:0002113 name: has presynaptic terminal in def: "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input." [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000118 "synapses in" xsd:string -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: RO:0002130 ! has synaptic terminal in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000050 some Y?)" [] [Typedef] @@ -17020,11 +16487,6 @@ id: RO:0002120 name: synapsed to def: " Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.\n " [] comment: N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part some (\n ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( \n ‘synapse ; GO:0045202’ that has_part some (\n ‘post-synaptic membrane ; GO:0045211’ that part_of some N2)))) -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 is_a: RO:0002486 ! sends output to expand_expression_to: "BFO_0000051 some (GO_0042734 that part_of some (GO_0045202 that BFO_0000051 some (GO_0045211 that BFO_0000050 some Y?)))" [] @@ -17032,104 +16494,272 @@ expand_expression_to: "BFO_0000051 some (GO_0042734 that part_of some (GO_004520 id: RO:0002130 name: has synaptic terminal in def: "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "has synapse in" xsd:string -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: overlaps ! overlaps -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "RO_0002131 some (GO_0045202 that BFO_0000050 some Y?)" [] [Typedef] id: RO:0002132 name: has fasciculating neuron projection def: "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "has fasciculating component" xsd:string -property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string -property_value: RO:0001900 RO:0001901 domain: UBERON:0000122 ! neuron projection bundle is_a: overlaps ! overlaps +[Typedef] +id: RO:0002134 +name: innervates +def: "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." [] +domain: UBERON:0000122 ! neuron projection bundle +transitive_over: part_of ! part of +expand_expression_to: "RO_0002132 some (GO_0043005 that (RO_0002131 some (GO_0045202 that BFO_0000050 some Y?)))" [] + +[Typedef] +id: RO:0002150 +name: continuous with +def: "X continuous_with Y if and only if X and Y share a fiat boundary." [] +property_value: seeAlso "FMA:85972" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000004 ! independent continuant +is_symmetric: true +is_a: RO:0002323 ! mereotopologically related to + +[Typedef] +id: RO:0002158 +name: shares ancestor with +def: "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." [] +comment: VBO calls this homologous_to +is_symmetric: true +is_transitive: true +is_a: RO:0002320 ! evolutionarily related to + +[Typedef] +id: RO:0002160 +name: only in taxon +def: "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." [] +property_value: IAO:0000116 "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" xsd:string +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints +is_a: RO:0002162 ! in taxon + +[Typedef] +id: RO:0002162 +name: in taxon +def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." [] +comment: Connects a biological entity to its taxon of origin. +subset: ro-eco +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints +holds_over_chain: capable_of RO:0002162 +holds_over_chain: extends_fibers_into RO:0002162 +holds_over_chain: has_part RO:0002162 +holds_over_chain: part_of RO:0002162 +holds_over_chain: results_in_developmental_progression_of RO:0002162 +holds_over_chain: RO:0002202 RO:0002162 +holds_over_chain: RO:0002206 RO:0002162 +holds_over_chain: RO:0002225 RO:0002162 +holds_over_chain: RO:0002254 RO:0002162 +is_a: RO:0002320 ! evolutionarily related to + [Typedef] id: RO:0002163 name: spatially disjoint from def: "A is spatially_disjoint_from B if and only if they have no parts in common" [] subset: ro-eco -property_value: editor_note "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" xsd:anyURI is_a: RO:0002323 ! mereotopologically related to expand_expression_to: "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" [] +[Typedef] +id: RO:0002170 +name: connected to +def: "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" [] +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI +is_a: RO:0002323 ! mereotopologically related to + +[Typedef] +id: RO:0002176 +name: connects +def: "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." [] +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI +domain: BFO:0000004 ! independent continuant +is_a: RO:0002323 ! mereotopologically related to + +[Typedef] +id: RO:0002177 +name: attached to part of +def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000061 ! anatomical structure +is_a: RO:0002323 ! mereotopologically related to +is_a: RO:0002567 ! biomechanically related to + +[Typedef] +id: RO:0002178 +name: supplies +def: "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." [] +property_value: IAO:0000116 "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" xsd:string +is_a: RO:0002170 ! connected to + +[Typedef] +id: RO:0002179 +name: drains +def: "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." [] +property_value: IAO:0000116 "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" xsd:string +is_a: RO:0002170 ! connected to + +[Typedef] +id: RO:0002202 +name: develops from +def: "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" [] +comment: This is the transitive form of the develops from relation +domain: BFO:0000004 ! independent continuant +range: BFO:0000004 ! independent continuant +is_transitive: true +is_a: RO:0002254 ! has developmental contribution from +is_a: RO:0002258 ! developmentally preceded by +inverse_of: RO:0002203 ! develops into + +[Typedef] +id: RO:0002203 +name: develops into +def: "inverse of develops from" [] +subset: RO:0002259 +is_transitive: true +is_a: RO:0002286 ! developmentally succeeded by +is_a: RO:0002387 ! has potential to develop into +is_a: RO:0002388 ! has potential to directly develop into + [Typedef] id: RO:0002206 name: expressed in def: "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" [] -property_value: IAO:0000112 "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000002 ! continuant range: UBERON:0000465 ! material anatomical entity is_a: RO:0002330 ! genomically related to inverse_of: RO:0002292 ! expresses -transitive_over: part_of ! part_of +transitive_over: part_of ! part of + +[Typedef] +id: RO:0002207 +name: directly develops from +def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] +comment: TODO - add child relations from DOS +synonym: "has developmental precursor" EXACT [] +is_a: RO:0002202 ! develops from +inverse_of: RO:0002210 ! directly develops into [Typedef] id: RO:0002210 name: directly develops into def: "inverse of directly develops from" [] subset: RO:0002259 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000118 "developmental precursor of" xsd:string -is_a: develops_into ! develops into +is_a: RO:0002203 ! develops into + +[Typedef] +id: RO:0002219 +name: surrounded by +def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" [] +is_a: adjacent_to ! adjacent to +inverse_of: RO:0002221 ! surrounds + +[Typedef] +id: RO:0002221 +name: surrounds +def: "inverse of surrounded by" [] +subset: RO:0002259 +is_a: adjacent_to ! adjacent to [Typedef] id: RO:0002222 name: temporally related to comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. subset: ro-eco -property_value: http://purl.org/dc/terms/source "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" xsd:anyURI -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent [Typedef] -id: RO:0002253 -name: has connecting branch -def: "inverse of connecting branch of" [] -subset: RO:0002259 -property_value: RO:0004036 BFO:0000051 -is_a: RO:0002375 ! in branching relationship with +id: RO:0002223 +name: starts +def: "inverse of starts with" [] +subset: ro-eco +is_a: part_of ! part of +is_a: RO:0002222 ! temporally related to +inverse_of: starts_with ! starts with [Typedef] -id: RO:0002255 -name: developmentally contributes to -def: "inverse of has developmental contribution from" [] -subset: RO:0002259 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -holds_over_chain: develops_into part_of -is_a: has_potential_to_developmentally_contribute_to ! has potential to developmentally contribute to -is_a: RO:0002286 ! developmentally succeeded by +id: RO:0002225 +name: develops from part of +def: "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" [] +holds_over_chain: RO:0002207 part_of +is_a: RO:0002202 ! develops from [Typedef] -id: RO:0002257 -name: developmentally induces -def: "Inverse of developmentally induced by" [] -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +id: RO:0002226 +name: develops in +def: "x develops_in y if x is located in y whilst x is developing" [] +domain: UBERON:0001062 ! anatomical entity +holds_over_chain: RO:0002207 RO:0001025 +is_a: RO:0002258 ! developmentally preceded by + +[Typedef] +id: RO:0002229 +name: ends +def: "inverse of ends with" [] +subset: ro-eco +is_a: part_of ! part of +is_a: RO:0002222 ! temporally related to +inverse_of: ends_with ! ends with + +[Typedef] +id: RO:0002252 +name: connecting branch of +def: "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." [] +property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 +is_a: RO:0002170 ! connected to +is_a: RO:0002375 ! in branching relationship with +inverse_of: RO:0002253 ! has connecting branch + +[Typedef] +id: RO:0002253 +name: has connecting branch +def: "inverse of connecting branch of" [] +subset: RO:0002259 +is_a: RO:0002375 ! in branching relationship with + +[Typedef] +id: RO:0002254 +name: has developmental contribution from +def: "x has developmental contribution from y iff x has some part z such that z develops from y" [] +domain: UBERON:0001062 ! anatomical entity +range: UBERON:0001062 ! anatomical entity +holds_over_chain: has_part RO:0002202 +is_a: RO:0002258 ! developmentally preceded by +inverse_of: RO:0002255 ! developmentally contributes to + +[Typedef] +id: RO:0002255 +name: developmentally contributes to +def: "inverse of has developmental contribution from" [] +subset: RO:0002259 +holds_over_chain: RO:0002203 part_of +is_a: RO:0002286 ! developmentally succeeded by +is_a: RO:0002385 ! has potential to developmentally contribute to + +[Typedef] +id: RO:0002256 +name: developmentally induced by +def: "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" [] +domain: UBERON:0000465 ! material anatomical entity +range: UBERON:0000465 ! material anatomical entity +is_a: RO:0002258 ! developmentally preceded by +inverse_of: RO:0002257 ! developmentally induces + +[Typedef] +id: RO:0002257 +name: developmentally induces +def: "Inverse of developmentally induced by" [] is_a: RO:0002286 ! developmentally succeeded by is_a: RO:0002386 ! has potential to developmentally induce @@ -17138,10 +16768,7 @@ id: RO:0002258 name: developmentally preceded by def: "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p" [] comment: This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from -property_value: editor_note "false" xsd:boolean -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string +property_value: IAO:0000116 "false" xsd:boolean domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant is_a: RO:0002324 ! developmentally related to @@ -17152,7 +16779,6 @@ id: RO:0002263 name: acts upstream of def: "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: IAO:0000112 "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." xsd:string property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of holds_over_chain: RO:0002327 causally_upstream_of is_a: RO:0002264 ! acts upstream of or within @@ -17163,25 +16789,26 @@ name: acts upstream of or within def: "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term synonym: "affects" RELATED [] -property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within" xsd:anyURI holds_over_chain: RO:0002327 causally_upstream_of_or_within is_a: RO:0002500 ! causal agent in process +[Typedef] +id: RO:0002285 +name: developmentally replaces +def: "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" [] +property_value: IAO:0000116 "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" xsd:string +is_a: RO:0002258 ! developmentally preceded by + [Typedef] id: RO:0002286 name: developmentally succeeded by def: "Inverse of developmentally preceded by" [] -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002384 ! has developmental potential involving [Typedef] id: RO:0002287 name: part of developmental precursor of -property_value: IAO:0000112 "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: part_of RO:0002210 is_a: RO:0002286 ! developmentally succeeded by @@ -17189,80 +16816,58 @@ is_a: RO:0002286 ! developmentally succeeded by id: RO:0002292 name: expresses def: "y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." [] -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002330 ! genomically related to [Typedef] id: RO:0002314 name: characteristic of part of def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." [] -property_value: editor_note "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "inheres in part of" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: RO:0000052 part_of {RO:0002582="true"} is_a: RO:0002502 ! depends on -transitive_over: part_of ! part_of +transitive_over: part_of ! part of [Typedef] id: RO:0002320 name: evolutionarily related to def: "A relationship that holds via some environmental process" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." xsd:string [Typedef] id: RO:0002323 name: mereotopologically related to def: "A mereological relationship or a topological relationship" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string -property_value: RO:0001900 RO:0001901 [Typedef] id: RO:0002324 name: developmentally related to def: "A relationship that holds between entities participating in some developmental process (GO:0032502)" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" xsd:string [Typedef] id: RO:0002327 name: enables def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "catalyzes" xsd:string -property_value: IAO:0000118 "executes" xsd:string -property_value: IAO:0000118 "has" xsd:string -property_value: IAO:0000118 "is catalyzing" xsd:string -property_value: IAO:0000118 "is executing" xsd:string -property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string property_value: seeAlso "https://wiki.geneontology.org/Enables" xsd:anyURI is_a: capable_of ! capable of inverse_of: RO:0002333 ! enabled by transitive_over: has_part ! has part transitive_over: RO:0002017 ! has component activity +[Typedef] +id: RO:0002328 +name: functionally related to +def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] + [Typedef] id: RO:0002329 name: part of structure that is capable of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "false" xsd:boolean -holds_over_chain: part_of capable_of {RO:0002581="true"} -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002330 name: genomically related to def: "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant @@ -17270,31 +16875,25 @@ range: BFO:0000002 ! continuant id: RO:0002331 name: involved in def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "actively involved in" xsd:string -property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Involved_in" xsd:anyURI holds_over_chain: RO:0002327 part_of is_a: participates_in ! participates in is_a: RO:0002431 ! involved in or involved in regulation of -transitive_over: part_of ! part_of +transitive_over: part_of ! part of [Typedef] id: RO:0002333 name: enabled by def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso "https://wiki.geneontology.org/Enabled_by" xsd:anyURI -is_a: functionally_related_to ! functionally related to is_a: has_participant ! has participant +is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002337 name: related via localization to def: "A relationship that holds via some process of localization" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is a grouping relation." xsd:string domain: BFO:0000015 ! process range: BFO:0000002 ! continuant @@ -17302,84 +16901,134 @@ range: BFO:0000002 ! continuant id: RO:0002350 name: member of def: "is member of is a mereological relation between a item and a collection." [] -property_value: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string -property_value: IAO:0000118 "is member of" xsd:string -property_value: IAO:0000118 "member part of" xsd:string -property_value: IAO:0000119 "SIO" xsd:string -property_value: RO:0001900 RO:0001901 -is_a: part_of ! part_of -inverse_of: has_member ! has member +is_a: part_of ! part of +inverse_of: RO:0002351 ! has member + +[Typedef] +id: RO:0002351 +name: has member +def: "has member is a mereological relation between a collection and an item." [] +is_a: has_part ! has part + +[Typedef] +id: RO:0002352 +name: input of +def: "inverse of has input" [] +subset: ro-eco +subset: RO:0002259 +is_a: participates_in ! participates in +is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002354 name: formed as result of -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: output_of ! output of [Typedef] id: RO:0002360 name: has dendrite location -property_value: http://purl.org/dc/terms/source "http://neurolex.org/wiki/Property:DendriteLocation" xsd:anyURI -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps +[Typedef] +id: RO:0002371 +name: attached to +def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] +subset: ro-eco +is_symmetric: true +is_a: RO:0002170 ! connected to +is_a: RO:0002177 ! attached to part of + +[Typedef] +id: RO:0002372 +name: has muscle origin +def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] +property_value: seeAlso http://dbpedia.org/property/origin +domain: UBERON:0000061 {comment="We need to import uberon muscle to create a stricter domain constraint"} ! anatomical structure +is_a: RO:0002371 ! attached to +is_a: RO:0002567 ! biomechanically related to + +[Typedef] +id: RO:0002373 +name: has muscle insertion +def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] +property_value: seeAlso http://dbpedia.org/property/insertion +domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} ! anatomical structure +is_a: RO:0002371 ! attached to +is_a: RO:0002567 ! biomechanically related to + [Typedef] id: RO:0002375 name: in branching relationship with def: "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" xsd:string -property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string -property_value: RO:0004036 BFO:0000050 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png property_value: seeAlso "https://github.com/obophenotype/uberon/issues/170" xsd:anyURI domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002323 ! mereotopologically related to +[Typedef] +id: RO:0002376 +name: tributary of +def: "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." [] +subset: ro-eco +property_value: seeAlso http://dbpedia.org/ontology/drainsTo +property_value: seeAlso "http://en.wikipedia.org/wiki/Tributary" xsd:anyURI +is_a: RO:0002170 ! connected to +is_a: RO:0002375 ! in branching relationship with + [Typedef] id: RO:0002379 name: spatially coextensive with def: "x spatially_coextensive_with y if and inly if x and y have the same location" [] -property_value: IAO:0000112 "A lump of clay and a statue" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" xsd:string is_a: overlaps ! overlaps +[Typedef] +id: RO:0002380 +name: branching part of +def: "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" [] +subset: ro-eco +property_value: seeAlso "FMA:85994" xsd:string +property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 +is_a: part_of ! part of +is_a: RO:0002375 ! in branching relationship with +inverse_of: RO:0002569 ! has branching part + [Typedef] id: RO:0002384 name: has developmental potential involving def: "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: UBERON:0001062 ! anatomical entity range: UBERON:0001062 ! anatomical entity is_a: RO:0002324 ! developmentally related to +[Typedef] +id: RO:0002385 +name: has potential to developmentally contribute to +def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] +is_a: RO:0002384 ! has developmental potential involving + [Typedef] id: RO:0002386 name: has potential to developmentally induce def: "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002384 ! has developmental potential involving + +[Typedef] +id: RO:0002387 +name: has potential to develop into +def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] is_a: RO:0002384 ! has developmental potential involving [Typedef] id: RO:0002388 name: has potential to directly develop into def: "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: has_potential_to_develop_into ! has potential to develop into +is_a: RO:0002387 ! has potential to develop into [Typedef] id: RO:0002407 name: indirectly positively regulates def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "indirectly activates" xsd:string -property_value: RO:0002579 RO:0002213 property_value: seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates" xsd:anyURI holds_over_chain: directly_positively_regulates directly_positively_regulates holds_over_chain: directly_positively_regulates RO:0002407 @@ -17393,9 +17042,6 @@ transitive_over: directly_positively_regulates ! directly positively regulates id: RO:0002409 name: indirectly negatively regulates def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "indirectly inhibits" xsd:string -property_value: RO:0002579 RO:0002212 property_value: seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates" xsd:anyURI holds_over_chain: directly_negatively_regulates directly_negatively_regulates holds_over_chain: directly_negatively_regulates RO:0002409 @@ -17408,15 +17054,12 @@ transitive_over: directly_negatively_regulates ! directly negatively regulates id: RO:0002410 name: causally related to def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] -property_value: editor_note "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string [Typedef] id: RO:0002428 name: involved in regulation of def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002327 regulates holds_over_chain: RO:0002331 regulates is_a: RO:0002263 ! acts upstream of @@ -17426,8 +17069,6 @@ is_a: RO:0002431 ! involved in or involved in regulation of id: RO:0002429 name: involved in positive regulation of def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0004049 RO:0002428 holds_over_chain: RO:0002327 positively_regulates holds_over_chain: RO:0002331 positively_regulates is_a: RO:0002428 ! involved in regulation of @@ -17436,7 +17077,6 @@ is_a: RO:0002428 ! involved in regulation of id: RO:0002430 name: involved in negative regulation of def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002428 holds_over_chain: RO:0002327 negatively_regulates holds_over_chain: RO:0002331 negatively_regulates @@ -17446,11 +17086,9 @@ is_a: RO:0002428 ! involved in regulation of id: RO:0002431 name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] -property_value: editor_note "OWL does not allow defining object properties via a Union" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "involved in or reguates" xsd:string -is_a: functionally_related_to ! functionally related to +property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string is_a: RO:0002264 ! acts upstream of or within +is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process [Typedef] @@ -17458,12 +17096,14 @@ id: RO:0002432 name: is active in def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [https://orcid.org/0000-0002-6601-2165, https://orcid.org/0000-0002-7073-9172] synonym: "enables activity in" EXACT [] -property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "executes activity in" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Is_active_in" xsd:anyURI -holds_over_chain: RO:0002327 occurs_in {RO:0002581="true"} -is_a: functionally_related_to ! functionally related to +is_a: overlaps ! overlaps +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002433 +name: contributes to morphology of +def: "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." [] is_a: overlaps ! overlaps [Typedef] @@ -17472,11 +17112,8 @@ name: interacts with def: "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." [] subset: ro-eco synonym: "in pairwise interaction with" EXACT [] -property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0914" xsd:anyURI -property_value: editor_note "Considering relabeling as 'pairwise interacts with'" xsd:anyURI -property_value: editor_note "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string +property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI +property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity @@ -17486,10 +17123,6 @@ is_symmetric: true id: RO:0002436 name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] -property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0915" xsd:anyURI -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "binds" xsd:string -property_value: IAO:0000118 "molecularly binds with" xsd:string property_value: seeAlso ECO:0000353 is_symmetric: true is_a: RO:0002434 ! interacts with @@ -17497,9 +17130,7 @@ is_a: RO:0002434 ! interacts with [Typedef] id: RO:0002447 name: phosphorylates -property_value: editor_note "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string +property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string is_a: RO:0002436 ! molecularly interacts with [Typedef] @@ -17507,8 +17138,6 @@ id: RO:0002448 name: directly regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." [] synonym: "molecularly controls" EXACT [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002436 ! molecularly interacts with @@ -17519,9 +17148,6 @@ id: RO:0002449 name: directly negatively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] synonym: "molecularly decreases activity of" EXACT [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 -property_value: IAO:0000118 "directly inhibits" xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002448 ! directly regulates activity of @@ -17531,9 +17157,6 @@ id: RO:0002450 name: directly positively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] synonym: "molecularly increases activity of" EXACT [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 -property_value: IAO:0000118 "directly activates" xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002448 ! directly regulates activity of @@ -17541,61 +17164,136 @@ is_a: RO:0002448 ! directly regulates activity of [Typedef] id: RO:0002464 name: helper property (not for use in curation) -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string + +[Typedef] +id: RO:0002473 +name: composed primarily of +def: "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." [] +subset: ro-eco +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: has_part ! has part [Typedef] id: RO:0002479 name: has part that occurs in def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] subset: ro-eco -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant -holds_over_chain: has_part occurs_in {RO:0002581="true"} [Typedef] id: RO:0002481 name: is kinase activity -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002564 ! molecular interaction relation helper property [Typedef] id: RO:0002485 name: receives input from -property_value: editor_note "See notes for inverse relation" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: connected_to ! connected to +property_value: IAO:0000116 "See notes for inverse relation" xsd:string +is_a: RO:0002170 ! connected to inverse_of: RO:0002486 ! sends output to [Typedef] id: RO:0002486 name: sends output to -property_value: editor_note "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: connected_to ! connected to +property_value: IAO:0000116 "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." xsd:string +is_a: RO:0002170 ! connected to [Typedef] id: RO:0002487 name: relation between physical entity and a process or stage -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage." xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000003 ! occurrent +[Typedef] +id: RO:0002488 +name: existence starts during +def: "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." [] +is_a: RO:0002490 ! existence overlaps +is_a: RO:0002496 ! existence starts during or after +transitive_over: part_of ! part of + +[Typedef] +id: RO:0002489 +name: existence starts with +def: "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." [] +is_a: RO:0002488 ! existence starts during + [Typedef] id: RO:0002490 name: existence overlaps def: "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" [] comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002487 ! relation between physical entity and a process or stage +[Typedef] +id: RO:0002491 +name: existence starts and ends during +def: "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +synonym: "exists during" EXACT [] +is_a: RO:0002488 ! existence starts during +is_a: RO:0002492 ! existence ends during + +[Typedef] +id: RO:0002492 +name: existence ends during +def: "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +is_a: RO:0002490 ! existence overlaps +is_a: RO:0002497 ! existence ends during or before +transitive_over: part_of ! part of + +[Typedef] +id: RO:0002493 +name: existence ends with +def: "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +is_a: RO:0002492 ! existence ends during + +[Typedef] +id: RO:0002494 +name: transformation of +def: "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" [] +is_transitive: true +is_a: RO:0002202 ! develops from + +[Typedef] +id: RO:0002495 +name: immediate transformation of +def: "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" [] +is_a: RO:0002207 ! directly develops from +is_a: RO:0002494 ! transformation of + +[Typedef] +id: RO:0002496 +name: existence starts during or after +def: "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +holds_over_chain: part_of RO:0002496 +holds_over_chain: RO:0002258 RO:0002496 +is_a: RO:0002487 ! relation between physical entity and a process or stage +transitive_over: part_of ! part of +transitive_over: preceded_by ! preceded by +transitive_over: RO:0002082 ! simultaneous with + +[Typedef] +id: RO:0002497 +name: existence ends during or before +def: "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +holds_over_chain: part_of RO:0002497 +holds_over_chain: RO:0002286 RO:0002497 +is_a: RO:0002487 ! relation between physical entity and a process or stage +transitive_over: part_of ! part of +transitive_over: precedes ! precedes +transitive_over: RO:0002082 ! simultaneous with + [Typedef] id: RO:0002500 name: causal agent in process def: "A relationship between a material entity and a process where the material entity has some causal role that influences the process" [] -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_a: RO:0002595 ! causal relation between material entity and a process inverse_of: process_has_causal_agent ! process has causal agent @@ -17603,9 +17301,6 @@ inverse_of: process_has_causal_agent ! process has causal agent id: RO:0002501 name: causal relation between processes def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent is_a: RO:0002410 ! causally related to @@ -17613,33 +17308,35 @@ is_a: RO:0002410 ! causally related to [Typedef] id: RO:0002502 name: depends on -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso BFO:0000169 [Typedef] id: RO:0002506 name: causal relation between entities -property_value: editor_note "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: IAO:0000116 "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant is_a: RO:0002410 ! causally related to +[Typedef] +id: RO:0002551 +name: has skeleton +def: "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." [] +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000465 {IAO:0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} ! material anatomical entity +is_a: has_part ! has part +inverse_of: RO:0002576 ! skeleton of +is_asymmetric: true + [Typedef] id: RO:0002559 name: causally influenced by -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string is_a: RO:0002506 ! causal relation between entities inverse_of: RO:0002566 ! causally influences [Typedef] id: RO:0002563 name: interaction relation helper property -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29 property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI is_a: RO:0002464 ! helper property (not for use in curation) @@ -17647,17 +17344,12 @@ is_a: RO:0002464 ! helper property (not for use in curation) [Typedef] id: RO:0002564 name: molecular interaction relation helper property -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002563 ! interaction relation helper property [Typedef] id: RO:0002566 name: causally influences def: "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant is_a: RO:0002506 ! causal relation between entities @@ -17666,20 +17358,66 @@ is_a: RO:0002506 ! causal relation between entities id: RO:0002567 name: biomechanically related to def: "A relation that holds between elements of a musculoskeletal system or its analogs." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string domain: UBERON:0000061 ! anatomical structure range: UBERON:0000061 ! anatomical structure -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002568 +name: has muscle antagonist +def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] +is_a: RO:0002567 ! biomechanically related to + +[Typedef] +id: RO:0002569 +name: has branching part +def: "inverse of branching part of" [] +subset: ro-eco +subset: RO:0002259 +is_transitive: true +is_a: has_part ! has part +is_a: RO:0002375 ! in branching relationship with + +[Typedef] +id: RO:0002570 +name: conduit for +def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] +subset: ro-eco +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: overlaps ! overlaps + +[Typedef] +id: RO:0002571 +name: lumen of +def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] +subset: ro-eco +range: BFO:0000040 ! material entity +is_a: part_of ! part of + +[Typedef] +id: RO:0002572 +name: luminal space of +def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" [] +subset: ro-eco +domain: BFO:0000141 ! immaterial entity +is_a: RO:0002571 ! lumen of + +[Typedef] +id: RO:0002576 +name: skeleton of +def: "inverse of has skeleton" [] +subset: RO:0002259 +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000061 ! anatomical structure +is_a: part_of ! part of [Typedef] id: RO:0002584 name: has part structure that is capable of def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" [] -property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: has_part capable_of -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to is_a: RO:0002595 ! causal relation between material entity and a process [Typedef] @@ -17692,9 +17430,7 @@ is_a: has_input ! has input id: RO:0002595 name: causal relation between material entity and a process def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." [] -property_value: editor_note "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000040 ! material entity range: BFO:0000015 ! process is_a: RO:0002410 ! causally related to @@ -17703,8 +17439,6 @@ is_a: RO:0002410 ! causally related to id: RO:0002596 name: capable of regulating def: "Holds between c and p if and only if c is capable of some activity a, and a regulates p." [] -property_value: IAO:0000112 "pyrethroid -> growth" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations holds_over_chain: capable_of regulates is_a: RO:0002500 ! causal agent in process @@ -17712,7 +17446,6 @@ is_a: RO:0002500 ! causal agent in process id: RO:0002597 name: capable of negatively regulating def: "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." [] -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations holds_over_chain: capable_of negatively_regulates is_a: RO:0002596 ! capable of regulating @@ -17720,8 +17453,6 @@ is_a: RO:0002596 ! capable of regulating id: RO:0002598 name: capable of positively regulating def: "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." [] -property_value: IAO:0000112 "renin -> arteriolar smooth muscle contraction" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations holds_over_chain: capable_of positively_regulates is_a: RO:0002596 ! capable of regulating @@ -17730,7 +17461,7 @@ id: RO:0004031 name: enables subfunction def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] holds_over_chain: RO:0002327 has_part -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z @@ -17738,7 +17469,6 @@ creation_date: 2018-01-25T23:20:13Z id: RO:0004032 name: acts upstream of or within, positive effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: RO:0004049 RO:0002264 property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0004047 is_a: RO:0002264 ! acts upstream of or within @@ -17761,7 +17491,6 @@ id: RO:0004034 name: acts upstream of, positive effect def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: RO:0004049 RO:0002263 property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 causally_upstream_of,_positive_effect is_a: RO:0002263 ! acts upstream of @@ -17794,7 +17523,6 @@ creation_date: 2018-03-13T23:55:05Z [Typedef] id: RO:0004047 name: causally upstream of or within, positive effect -property_value: RO:0004049 RO:0002418 property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect is_a: causally_upstream_of_or_within ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 @@ -17804,7 +17532,6 @@ creation_date: 2018-03-13T23:55:19Z id: RO:0011002 name: regulates activity of def: "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." [] -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002566 ! causally influences @@ -17859,7 +17586,7 @@ name: has synaptic IO in region def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region." [] synonym: "has synaptic input or output in" EXACT [] is_a: RO:0002130 ! has synaptic terminal in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:26:52Z @@ -17872,7 +17599,7 @@ synonym: "has sensory terminal in" EXACT [] synonym: "has sensory terminal location" EXACT [] domain: CL:0000101 ! sensory neuron is_a: RO:0002360 ! has dendrite location -transitive_over: part_of ! part_of +transitive_over: part_of ! part of created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-20T12:10:09Z @@ -17915,9 +17642,8 @@ comment: Example: a spherical object has the quality of being spherical, and the id: RO:0015015 name: has high plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: dc-contributor https://orcid.org/0000-0003-1617-8244 -property_value: dc-contributor https://orcid.org/0000-0003-1940-6740 -property_value: IAO:0000112 "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part @@ -17925,9 +17651,8 @@ is_a: RO:0002104 ! has plasma membrane part id: RO:0015016 name: has low plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: dc-contributor https://orcid.org/0000-0003-1617-8244 -property_value: dc-contributor https://orcid.org/0000-0003-1940-6740 -property_value: IAO:0000112 "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part @@ -17936,11 +17661,6 @@ id: RO:0017001 name: device utilizes material def: "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." [] synonym: "utilizes" BROAD [] -property_value: IAO:0000112 "A diagnostic testing device utilizes a specimen." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 -property_value: IAO:0000117 https://orcid.org/0000-0003-2620-0345 -property_value: IAO:0000232 "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." xsd:string -property_value: IAO:0000232 "See github ticket https://github.com/oborel/obo-relations/issues/497" xsd:string holds_over_chain: capable_of has_input creation_date: 2021-11-08T12:00:00Z @@ -17961,65 +17681,24 @@ creation_date: 2020-06-08T17:21:33Z id: adjacent_to name: adjacent to namespace: external -namespace: uberon def: "x adjacent to y if and only if x and y share a boundary." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002220 -property_value: editor_note "This relation acts as a join point with BSPO" xsd:string -property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} -property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string -property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string -property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000004 ! independent continuant is_a: RO:0002163 ! spatially disjoint from -[Typedef] -id: anterior_to -name: anterior to -namespace: uberon -xref: BSPO:0000096 - [Typedef] id: anteriorly_connected_to name: anteriorly connected to namespace: uberon def: "x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] -is_a: connected_to ! connected to -is_a: posterior_to ! posterior to +is_a: RO:0002170 ! connected to is_a: transitively_anteriorly_connected_to ! transitively anteriorly connected to -[Typedef] -id: attaches_to -name: attached to -namespace: uberon -def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] -subset: ro-eco -xref: RO:0002371 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000589 "attached to (anatomical structure to anatomical structure)" xsd:string -is_symmetric: true -is_a: attaches_to_part_of ! attached to part of -is_a: connected_to ! connected to - -[Typedef] -id: attaches_to_part_of -name: attached to part of -namespace: uberon -def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] -xref: RO:0002177 -property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string -domain: UBERON:0000061 ! anatomical structure -range: UBERON:0000061 ! anatomical structure -holds_over_chain: attaches_to part_of {RO:0002582="true"} -is_a: RO:0002323 ! mereotopologically related to -is_a: RO:0002567 ! biomechanically related to - [Typedef] id: bearer_of name: bearer of @@ -18027,13 +17706,7 @@ name: has characteristic namespace: external def: "Inverse of characteristic_of" [] xref: RO:0000053 -property_value: editor_note "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string -property_value: IAO:0000111 "bearer of" xsd:string -property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string -property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string -property_value: IAO:0000118 "bearer_of" xsd:string -property_value: IAO:0000118 "is bearer of" xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string range: BFO:0000020 ! specifically dependent continuant is_inverse_functional: true @@ -18041,45 +17714,20 @@ is_inverse_functional: true id: bounding_layer_of name: bounding layer of namespace: external -namespace: uberon def: "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000" [] comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. subset: ro-eco xref: RO:0002007 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 range: BFO:0000040 ! material entity -is_a: part_of ! part_of - -[Typedef] -id: branching_part_of -name: branching part of -namespace: uberon -def: "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" [] -subset: ro-eco -xref: RO:0002380 -property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso "FMA:85994" xsd:string -property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 -is_a: part_of ! part_of -is_a: RO:0002375 ! in branching relationship with -inverse_of: has_branching_part ! has branching part +is_a: part_of ! part of [Typedef] id: capable_of name: capable of namespace: external -namespace: uberon def: "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " [] subset: ro-eco xref: RO:0002215 -property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string -property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "has function realized in" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 -property_value: IAO:0000232 "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000015 ! process is_a: capable_of_part_of ! capable of part of @@ -18088,14 +17736,10 @@ is_a: capable_of_part_of ! capable of part of id: capable_of_part_of name: capable of part of namespace: external -namespace: uberon def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] xref: RO:0002216 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "has function in" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: capable_of part_of {RO:0002582="true"} -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process [Typedef] @@ -18104,8 +17748,6 @@ name: causally downstream of namespace: external def: "inverse of upstream of" [] xref: RO:0002404 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of_or_within ! causally downstream of or within is_a: preceded_by ! preceded by inverse_of: causally_upstream_of ! causally upstream of @@ -18117,8 +17759,6 @@ namespace: external def: "inverse of causally upstream of or within" [] subset: RO:0002259 xref: RO:0002427 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_transitive: true is_a: RO:0002501 ! causal relation between processes @@ -18130,7 +17770,6 @@ def: "p is causally upstream of q iff p is causally related to q, the end of p p subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002411 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within is_a: precedes ! precedes @@ -18143,7 +17782,6 @@ def: "p is causally upstream of, negative effect q iff p is casually upstream of subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 -property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_negative_effect is_a: causally_upstream_of ! causally upstream of @@ -18158,8 +17796,6 @@ comment: holds between x and y if and only if x is causally upstream of y and th subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002304 -property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 -property_value: RO:0004049 RO:0002411 property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_positive_effect is_a: causally_upstream_of ! causally upstream of is_a: RO:0004047 ! causally upstream of or within, positive effect @@ -18171,9 +17807,7 @@ namespace: external def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] synonym: "affects" RELATED [] xref: RO:0002418 -property_value: editor_note "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "influences (processual)" xsd:string +property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string is_transitive: true is_a: RO:0002501 ! causal relation between processes inverse_of: causally_downstream_of_or_within ! causally downstream of or within @@ -18183,287 +17817,16 @@ id: channel_for name: channel for namespace: uberon synonym: "carries" BROAD [] -domain: UBERON:0004111 ! anatomical conduit -range: UBERON:0000463 ! organism substance [Typedef] id: channels_from name: channels_from namespace: uberon -is_transitive: true [Typedef] id: channels_into name: channels_into namespace: uberon -is_transitive: true - -[Typedef] -id: composed_primarily_of -name: composed primarily of -namespace: uberon -def: "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." [] -subset: ro-eco -xref: RO:0002473 -property_value: IAO:0000112 "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: RO:0001900 RO:0001901 -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: has_part ! has part - -[Typedef] -id: conduit_for -name: conduit for -namespace: uberon -def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] -subset: ro-eco -xref: RO:0002570 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "UBERON:cjm" xsd:string -property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: overlaps ! overlaps - -[Typedef] -id: connected_to -name: connected to -namespace: uberon -def: "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" [] -xref: RO:0002170 -property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI -property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: connecting_branch_of -name: connecting branch of -namespace: uberon -def: "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." [] -xref: RO:0002252 -property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." xsd:string -property_value: RO:0004036 BFO:0000050 -property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 -is_a: connected_to ! connected to -is_a: RO:0002375 ! in branching relationship with -inverse_of: RO:0002253 ! has connecting branch - -[Typedef] -id: connects -name: connects -namespace: uberon -def: "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." [] -xref: RO:0002176 -property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string -property_value: IAO:0000112 "The M8 connects Glasgow and Edinburgh" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI -property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI -domain: BFO:0000004 ! independent continuant -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: contains_process -name: contains process -namespace: uberon -def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] -comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant -xref: BFO:0000067 -property_value: IAO:0000111 "site of" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - -[Typedef] -id: continuous_with -name: continuous with -namespace: uberon -def: "X continuous_with Y if and only if X and Y share a fiat boundary." [] -xref: RO:0002150 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "connected to" xsd:string -property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string -property_value: RO:0001900 RO:0001901 -property_value: seeAlso "FMA:85972" xsd:string -domain: BFO:0000004 ! independent continuant -range: BFO:0000004 ! independent continuant -is_symmetric: true -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: contributes_to_morphology_of -name: contributes to morphology of -namespace: uberon -def: "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." [] -xref: RO:0002433 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: overlaps ! overlaps - -[Typedef] -id: dc-contributor -name: contributor -namespace: uberon -xref: http://purl.org/dc/terms/contributor -is_metadata_tag: true - -[Typedef] -id: dc-creator -name: creator -namespace: uberon -xref: http://purl.org/dc/elements/1.1/creator -is_metadata_tag: true - -[Typedef] -id: dc-description -name: description -namespace: uberon -xref: http://purl.org/dc/elements/1.1/description -is_metadata_tag: true - -[Typedef] -id: dc-title -name: title -namespace: uberon -xref: http://purl.org/dc/elements/1.1/title -is_metadata_tag: true - -[Typedef] -id: dcterms-date -name: date -namespace: uberon -xref: http://purl.org/dc/terms/date -is_metadata_tag: true - -[Typedef] -id: dcterms-license -name: license -namespace: uberon -xref: http://purl.org/dc/terms/license -is_metadata_tag: true - -[Typedef] -id: deep_to -name: deep to -namespace: uberon -xref: BSPO:0000107 - -[Typedef] -id: depiction -name: depiction -namespace: uberon -xref: http://xmlns.com/foaf/0.1/depiction -is_metadata_tag: true - -[Typedef] -id: developmentally_induced_by -name: developmentally induced by -namespace: uberon -def: "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" [] -xref: RO:0002256 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "induced by" xsd:string -property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string -property_value: IAO:0000119 "GO:0001759" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 -property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string -domain: UBERON:0000465 ! material anatomical entity -range: UBERON:0000465 ! material anatomical entity -is_a: RO:0002258 ! developmentally preceded by -inverse_of: RO:0002257 ! developmentally induces - -[Typedef] -id: developmentally_replaces -name: developmentally replaces -namespace: uberon -def: "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" [] -xref: RO:0002285 -property_value: editor_note "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "replaces" xsd:string -is_a: RO:0002258 ! developmentally preceded by - -[Typedef] -id: develops_from -name: develops from -namespace: uberon -def: "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" [] -comment: This is the transitive form of the develops from relation -xref: RO:0002202 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 -domain: BFO:0000004 ! independent continuant -range: BFO:0000004 ! independent continuant -is_transitive: true -is_a: has_developmental_contribution_from ! has developmental contribution from -is_a: RO:0002258 ! developmentally preceded by -inverse_of: develops_into ! develops into - -[Typedef] -id: develops_from_part_of -name: develops from part of -namespace: uberon -def: "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" [] -xref: RO:0002225 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -holds_over_chain: directly_develops_from part_of -is_a: develops_from ! develops from - -[Typedef] -id: develops_in -name: develops in -namespace: uberon -def: "x develops_in y if x is located in y whilst x is developing" [] -xref: RO:0002226 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "EHDAA2" xsd:string -property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string -domain: UBERON:0001062 ! anatomical entity -holds_over_chain: directly_develops_from located_in -is_a: RO:0002258 ! developmentally preceded by - -[Typedef] -id: develops_into -name: develops into -namespace: uberon -def: "inverse of develops from" [] -subset: RO:0002259 -xref: RO:0002203 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 -is_transitive: true -is_a: has_potential_to_develop_into ! has potential to develop into -is_a: RO:0002286 ! developmentally succeeded by -is_a: RO:0002388 ! has potential to directly develop into - -[Typedef] -id: directly_develops_from -name: directly develops from -namespace: uberon -def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] -comment: TODO - add child relations from DOS -synonym: "has developmental precursor" EXACT [] -xref: RO:0002207 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000119 "FBbt" xsd:string -property_value: RO:0002575 RO:0002202 -is_a: develops_from ! develops from -inverse_of: RO:0002210 ! directly develops into [Typedef] id: directly_negatively_regulates @@ -18474,8 +17837,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002630 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002578 property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates" xsd:anyURI is_a: directly_regulates ! directly regulates @@ -18490,9 +17851,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002629 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string -property_value: RO:0004049 RO:0002578 property_value: seeAlso "https://wiki.geneontology.org/Directly_positively_regulates" xsd:anyURI is_a: directly_regulates ! directly regulates is_a: positively_regulates ! positively regulates @@ -18506,187 +17864,34 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002578 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly regulates (processual)" xsd:string -property_value: RO:0002575 RO:0002211 is_a: immediately_causally_upstream_of ! immediately causally upstream of is_a: regulates ! regulates -[Typedef] -id: distal_to -name: distal to -namespace: uberon -xref: BSPO:0000097 - [Typedef] id: distally_connected_to name: distally connected to namespace: uberon def: "x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] -is_a: connected_to ! connected to -is_a: proximal_to ! proximal to +is_a: RO:0002170 ! connected to is_a: transitively_distally_connected_to ! transitively distally connected to -inverse_of: proximally_connected_to ! proximally connected to - -[Typedef] -id: distalmost_part_of -name: distalmost part of -namespace: uberon -xref: BSPO:0001108 - -[Typedef] -id: dorsal_to -name: dorsal to -namespace: uberon -xref: BSPO:0000098 - -[Typedef] -id: drains -name: drains -namespace: uberon -def: "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." [] -xref: RO:0002179 -property_value: editor_note "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 -is_a: connected_to ! connected to - -[Typedef] -id: editor_note -name: editor note -namespace: uberon -def: "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology." [] -xref: IAO:0000116 -property_value: IAO:0000111 "editor note" xsd:string -property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000117 "PERSON:Daniel Schober" xsd:string -property_value: IAO:0000119 "GROUP:OBI:" xsd:string -is_metadata_tag: true - -[Typedef] -id: ends -name: ends -namespace: uberon -def: "inverse of ends with" [] -subset: ro-eco -xref: RO:0002229 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: part_of ! part_of -is_a: RO:0002222 ! temporally related to -inverse_of: ends_with ! ends with [Typedef] id: ends_with name: ends with namespace: external -namespace: uberon def: "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002230 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "finished by" xsd:string is_transitive: true is_a: has_part ! has part is_a: RO:0002222 ! temporally related to -[Typedef] -id: existence_ends_during -name: existence ends during -namespace: uberon -def: "Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely." [https://orcid.org/0000-0002-6601-2165] -def: "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -synonym: "ceases_to_exist_during" EXACT [] -xref: RO:0002492 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_ends_during_or_before ! existence ends during or before -is_a: RO:0002490 ! existence overlaps -transitive_over: part_of ! part_of - -[Typedef] -id: existence_ends_during_or_before -name: existence ends during or before -namespace: uberon -def: "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -xref: RO:0002497 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -holds_over_chain: part_of existence_ends_during_or_before -holds_over_chain: RO:0002286 existence_ends_during_or_before -is_a: RO:0002487 ! relation between physical entity and a process or stage -transitive_over: part_of ! part_of -transitive_over: precedes ! precedes -transitive_over: simultaneous_with ! simultaneous with - -[Typedef] -id: existence_ends_with -name: existence ends with -namespace: uberon -def: "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -xref: RO:0002493 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_ends_during ! existence ends during - -[Typedef] -id: existence_starts_and_ends_during -name: existence starts and ends during -namespace: uberon -def: "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -synonym: "exists during" EXACT [] -xref: RO:0002491 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_ends_during ! existence ends during -is_a: existence_starts_during ! existence starts during - -[Typedef] -id: existence_starts_during -name: existence starts during -namespace: uberon -def: "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." [] -xref: RO:0002488 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_starts_during_or_after ! existence starts during or after -is_a: RO:0002490 ! existence overlaps -transitive_over: part_of ! part_of - -[Typedef] -id: existence_starts_during_or_after -name: existence starts during or after -namespace: uberon -def: "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -xref: RO:0002496 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -holds_over_chain: part_of existence_starts_during_or_after -holds_over_chain: RO:0002258 existence_starts_during_or_after -is_a: RO:0002487 ! relation between physical entity and a process or stage -transitive_over: part_of ! part_of -transitive_over: preceded_by ! preceded by -transitive_over: simultaneous_with ! simultaneous with - -[Typedef] -id: existence_starts_with -name: existence starts with -namespace: uberon -def: "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." [] -xref: RO:0002489 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_starts_during ! existence starts during - [Typedef] id: extends_fibers_into name: extends_fibers_into namespace: uberon def: "X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y" [https://orcid.org/0000-0002-7073-9172] -holds_over_chain: RO:0002100 RO:0013001 -is_symmetric: true -is_a: connected_to ! connected to +is_a: RO:0002170 ! connected to [Typedef] id: filtered_through @@ -18695,75 +17900,17 @@ namespace: uberon def: "Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity." [] comment: Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed -[Typedef] -id: functionally_related_to -name: functionally related to -namespace: uberon -def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] -xref: RO:0002328 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string - -[Typedef] -id: has_boundary -name: has 2D boundary -namespace: uberon -def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] -xref: RO:0002002 -property_value: editor_note "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string -property_value: editor_note "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string -property_value: IAO:0000112 "my body has 2D boundary the surface of my skin" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "has boundary" xsd:string -property_value: IAO:0000118 "has_2D_boundary" xsd:string -property_value: RO:0001900 RO:0001901 -domain: BFO:0000040 ! material entity -range: BFO:0000141 ! immaterial entity -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: has_branching_part -name: has branching part -namespace: uberon -def: "inverse of branching part of" [] -subset: ro-eco -subset: RO:0002259 -xref: RO:0002569 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_transitive: true -is_a: has_part ! has part -is_a: RO:0002375 ! in branching relationship with - [Typedef] id: has_component name: has component namespace: external -namespace: uberon def: "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] subset: ro-eco xref: RO:0002180 -property_value: editor_note "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency is_a: has_part ! has part -[Typedef] -id: has_developmental_contribution_from -name: has developmental contribution from -namespace: uberon -def: "x has developmental contribution from y iff x has some part z such that z develops from y" [] -xref: RO:0002254 -property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: UBERON:0001062 ! anatomical entity -range: UBERON:0001062 ! anatomical entity -holds_over_chain: has_part develops_from -is_a: RO:0002258 ! developmentally preceded by -inverse_of: RO:0002255 ! developmentally contributes to - [Typedef] id: has_end_location name: has end location @@ -18771,9 +17918,6 @@ namespace: external def: "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" [] subset: ro-eco xref: RO:0002232 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "ends with process that occurs in" xsd:string domain: BFO:0000015 ! process range: BFO:0000004 ! independent continuant holds_over_chain: ends_with occurs_in @@ -18797,14 +17941,11 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002233 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "consumes" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Has_input" xsd:anyURI domain: BFO:0000015 ! process holds_over_chain: starts_with has_input is_a: has_participant ! has participant -inverse_of: input_of ! input of +inverse_of: RO:0002352 ! input of [Typedef] id: has_low_plasma_membrane_amount @@ -18814,52 +17955,6 @@ property_value: term_tracker_item https://github.com/obophenotype/cell-ontology/ is_obsolete: true replaced_by: RO:0015016 -[Typedef] -id: has_member -name: has member -namespace: uberon -def: "has member is a mereological relation between a collection and an item." [] -xref: RO:0002351 -property_value: IAO:0000119 "SIO" xsd:string -property_value: RO:0001900 RO:0001901 -is_a: has_part ! has part - -[Typedef] -id: has_muscle_antagonist -name: has muscle antagonist -namespace: uberon -def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] -xref: RO:0002568 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "Wikipedia:Antagonist_(muscle)" xsd:string -is_a: RO:0002567 ! biomechanically related to - -[Typedef] -id: has_muscle_insertion -name: has muscle insertion -namespace: uberon -def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] -xref: RO:0002373 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string -property_value: seeAlso http://dbpedia.org/property/insertion -domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} ! anatomical structure -is_a: attaches_to ! attached to -is_a: RO:0002567 ! biomechanically related to - -[Typedef] -id: has_muscle_origin -name: has muscle origin -namespace: uberon -def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] -xref: RO:0002372 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string -property_value: seeAlso http://dbpedia.org/property/origin -domain: UBERON:0000061 {comment="We need to import uberon muscle to create a stricter domain constraint"} ! anatomical structure -is_a: attaches_to ! attached to -is_a: RO:0002567 ! biomechanically related to - [Typedef] id: has_negative_regulatory_component_activity name: has negative regulatory component activity @@ -18877,13 +17972,9 @@ id: has_ontology_root_term name: has ontology root term name: preferred_root namespace: external -namespace: uberon def: "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root." [] xref: IAO:0000700 -property_value: IAO:0000111 "has ontology root term" xsd:string -property_value: IAO:0000117 "Nicolas Matentzoglu" xsd:string is_metadata_tag: true -is_class_level: true [Typedef] id: has_output @@ -18895,9 +17986,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002234 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "produces" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Has_output" xsd:anyURI holds_over_chain: ends_with has_output is_a: has_participant ! has participant @@ -18909,60 +17997,27 @@ name: has part name: has_part namespace: external namespace: quality -namespace: uberon def: "a core relation that holds between a whole and its part" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000051 -property_value: editor_note "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string -property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string -property_value: IAO:0000111 "has part" xsd:string -property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string -property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string -property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string -property_value: IAO:0000118 "has_part" xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string is_transitive: true is_a: overlaps ! overlaps [Typedef] -id: has_participant -name: has participant -namespace: external -def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] -xref: RO:0000057 -property_value: editor_note "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string -property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string -property_value: IAO:0000111 "has participant" xsd:string -property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string -property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string -property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string -property_value: IAO:0000118 "has_participant" xsd:string -domain: BFO:0000003 ! occurrent -range: BFO:0000002 ! continuant -holds_over_chain: has_part has_participant - -[Typedef] -id: has_potential_to_develop_into -name: has potential to develop into -namespace: uberon -def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] -xref: RO:0002387 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: RO:0002384 ! has developmental potential involving - -[Typedef] -id: has_potential_to_developmentally_contribute_to -name: has potential to developmentally contribute to -namespace: uberon -def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] -xref: RO:0002385 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: RO:0002384 ! has developmental potential involving +id: has_participant +name: has participant +namespace: external +def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] +xref: RO:0000057 +property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string +domain: BFO:0000003 ! occurrent +range: BFO:0000002 ! continuant +holds_over_chain: has_part has_participant [Typedef] id: has_primary_input @@ -18999,17 +18054,6 @@ is_a: has_primary_input_or_output ! has primary input or output created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z -[Typedef] -id: has_quality -name: has quality -namespace: uberon -def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] -xref: RO:0000086 -property_value: editor_note "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string -property_value: IAO:0000112 "this apple has quality this red color" xsd:string -property_value: IAO:0000118 "has_quality" xsd:string -is_a: bearer_of ! bearer of - [Typedef] id: has_regulatory_component_activity name: has regulatory component activity @@ -19021,24 +18065,6 @@ is_a: RO:0002017 ! has component activity created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z -[Typedef] -id: has_skeleton -name: has skeleton -namespace: uberon -def: "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." [] -xref: RO:0002551 -property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "has supporting framework" xsd:string -property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string -domain: UBERON:0000061 ! anatomical structure -domain: UBERON:0000475 ! organism subdivision -range: UBERON:0000465 {IAO:0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} ! material anatomical entity -range: UBERON:0010912 ! subdivision of skeleton -is_a: has_part ! has part -inverse_of: skeleton_of ! skeleton of -is_asymmetric: true - [Typedef] id: has_small_molecule_activator name: has small molecule activator @@ -19057,9 +18083,6 @@ namespace: external def: "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y" [] subset: ro-eco xref: RO:0002231 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "starts with process that occurs in" xsd:string domain: BFO:0000015 ! process range: BFO:0000004 ! independent continuant holds_over_chain: starts_with occurs_in @@ -19074,9 +18097,8 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002339 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of [Typedef] id: has_target_start_location @@ -19087,41 +18109,14 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002338 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in -transitive_over: part_of ! part_of - -[Typedef] -id: homologous_to -name: shares ancestor with -namespace: uberon -def: "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." [] -comment: VBO calls this homologous_to -xref: RO:0002158 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000232 "Consider obsoleting and merging with child relation, 'in homology relationship with'" xsd:string -is_symmetric: true -is_transitive: true -is_a: RO:0002320 ! evolutionarily related to - -[Typedef] -id: immediate_transformation_of -name: immediate transformation of -namespace: uberon -def: "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" [] -xref: RO:0002495 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0002575 RO:0002494 -is_a: directly_develops_from ! directly develops from -is_a: transformation_of ! transformation of +transitive_over: part_of ! part of [Typedef] id: immediately_causally_downstream_of name: immediately causally downstream of namespace: external xref: RO:0002405 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of ! causally downstream of is_a: immediately_preceded_by ! immediately preceded by inverse_of: immediately_causally_upstream_of ! immediately causally upstream of @@ -19132,26 +18127,15 @@ name: immediately causally upstream of namespace: external def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] xref: RO:0002412 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: immediately_precedes ! immediately precedes -[Typedef] -id: immediately_deep_to -name: immediately deep to -namespace: uberon -xref: BSPO:0001107 - [Typedef] id: immediately_preceded_by name: immediately preceded by namespace: external -namespace: uberon comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) xref: RO:0002087 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000118 "starts_at_end_of" xsd:string holds_over_chain: starts_with ends_with is_a: preceded_by ! preceded by inverse_of: immediately_precedes ! immediately precedes @@ -19163,230 +18147,22 @@ namespace: external comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) subset: ro-eco xref: RO:0002090 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "ends_at_start_of" xsd:string -property_value: IAO:0000118 "meets" xsd:string -property_value: RO:0002575 BFO:0000063 holds_over_chain: ends_with starts_with is_a: precedes ! precedes -[Typedef] -id: immediately_superficial_to -name: immediately superficial to -namespace: uberon -xref: BSPO:0015014 - -[Typedef] -id: in_anterior_side_of -name: in anterior side of -namespace: uberon -xref: BSPO:0000123 - -[Typedef] -id: in_deep_part_of -name: in deep part of -namespace: uberon -xref: BSPO:0001101 - -[Typedef] -id: in_dorsal_side_of -name: in dorsal side of -namespace: uberon -xref: BSPO:0015101 - -[Typedef] -id: in_lateral_side_of -name: in lateral side of -namespace: uberon -xref: BSPO:0000126 - -[Typedef] -id: in_left_side_of -name: in left side of -namespace: uberon -xref: BSPO:0000120 - -[Typedef] -id: in_posterior_side_of -name: in posterior side of -namespace: uberon -xref: BSPO:0000122 - -[Typedef] -id: in_proximal_side_of -name: in proximal side of -namespace: uberon -xref: BSPO:0000124 - -[Typedef] -id: in_right_side_of -name: in right side of -namespace: uberon -xref: BSPO:0000121 - -[Typedef] -id: in_superficial_part_of -name: in superficial part of -namespace: uberon -xref: BSPO:0001100 - -[Typedef] -id: in_taxon -name: in taxon -namespace: uberon -def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." [] -comment: Connects a biological entity to its taxon of origin. -subset: ro-eco -xref: RO:0002162 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9227-417X -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -holds_over_chain: attaches_to in_taxon -holds_over_chain: capable_of in_taxon -holds_over_chain: connected_to in_taxon -holds_over_chain: connects in_taxon -holds_over_chain: continuous_with in_taxon -holds_over_chain: developmentally_induced_by in_taxon -holds_over_chain: develops_from in_taxon -holds_over_chain: develops_from_part_of in_taxon -holds_over_chain: existence_ends_during in_taxon -holds_over_chain: existence_starts_during in_taxon -holds_over_chain: extends_fibers_into in_taxon -holds_over_chain: has_developmental_contribution_from in_taxon -holds_over_chain: has_part in_taxon -holds_over_chain: has_potential_to_develop_into in_taxon -holds_over_chain: innervated_by in_taxon -holds_over_chain: overlaps in_taxon -holds_over_chain: part_of in_taxon -holds_over_chain: produced_by in_taxon -holds_over_chain: produces in_taxon -holds_over_chain: results_in_developmental_progression_of in_taxon -holds_over_chain: RO:0002206 in_taxon -holds_over_chain: supplies in_taxon -is_a: RO:0002320 ! evolutionarily related to - [Typedef] id: indirectly_supplies name: indirectly_supplies namespace: uberon def: "a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s." [] -property_value: editor_note "add to RO" xsd:string -holds_over_chain: has_branching_part indirectly_supplies -holds_over_chain: has_branching_part supplies -is_transitive: true - -[Typedef] -id: innervated_by -name: innervated_by -namespace: uberon -xref: RO:0002005 -property_value: http://purl.org/spar/cito/citesAsAuthority "http://www.ncbi.nlm.nih.gov/pubmed/22402613" xsd:anyURI -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -domain: UBERON:0000061 ! anatomical structure -range: UBERON:0000122 ! neuron projection bundle -inverse_of: innervates ! innervates -transitive_over: branching_part_of ! branching part of - -[Typedef] -id: innervates -name: innervates -namespace: uberon -def: "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." [] -xref: RO:0002134 -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 -domain: UBERON:0000122 ! neuron projection bundle -transitive_over: part_of ! part_of -expand_expression_to: "RO_0002132 some (GO_0043005 that (RO_0002131 some (GO_0045202 that BFO_0000050 some Y?)))" [] - -[Typedef] -id: input_of -name: input of -namespace: uberon -def: "inverse of has input" [] -subset: ro-eco -subset: RO:0002259 -xref: RO:0002352 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: functionally_related_to ! functionally related to -is_a: participates_in ! participates in - -[Typedef] -id: intersects_midsagittal_plane_of -name: intersects midsagittal plane of -namespace: uberon -xref: BSPO:0005001 +property_value: IAO:0000116 "add to RO" xsd:string +holds_over_chain: RO:0002569 indirectly_supplies [Typedef] id: layer_part_of name: layer part of namespace: uberon -is_a: part_of ! part_of - -[Typedef] -id: located_in -name: located in -namespace: uberon -def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -xref: RO:0001025 -property_value: editor_note "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" xsd:string -property_value: editor_note "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:located_in" xsd:string -property_value: IAO:0000111 "located in" xsd:string -property_value: IAO:0000112 "my brain is located in my head" xsd:string -property_value: IAO:0000112 "this rat is located in this cage" xsd:string -property_value: IAO:0000118 "located_in" xsd:string -property_value: RO:0001900 RO:0001901 -property_value: seeAlso "https://wiki.geneontology.org/Located_in" xsd:anyURI -domain: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant -range: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant -is_transitive: true -transitive_over: part_of ! part_of - -[Typedef] -id: location_of -name: location of -namespace: uberon -def: "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" [] -xref: RO:0001015 -property_value: editor_note "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: IAO:0000111 "is location of" xsd:string -property_value: IAO:0000112 "my head is the location of my brain" xsd:string -property_value: IAO:0000112 "this cage is the location of this rat" xsd:string -property_value: IAO:0000118 "location_of" xsd:string -property_value: RO:0001900 RO:0001901 -is_transitive: true -inverse_of: located_in ! located in - -[Typedef] -id: lumen_of -name: lumen of -namespace: uberon -def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] -subset: ro-eco -xref: RO:0002571 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 https://orcid.org/0000-0002-6601-2165 -range: BFO:0000040 ! material entity -is_a: part_of ! part_of - -[Typedef] -id: luminal_space_of -name: luminal space of -namespace: uberon -def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" [] -subset: ro-eco -xref: RO:0002572 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: BFO:0000141 ! immaterial entity -is_a: lumen_of ! lumen of +is_a: part_of ! part of [Typedef] id: negatively_regulated_by @@ -19395,7 +18171,6 @@ namespace: external def: "inverse of negatively regulates" [] subset: RO:0002259 xref: RO:0002335 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -19407,9 +18182,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002212 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002211 holds_over_chain: ends_with negatively_regulates is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect @@ -19422,30 +18194,11 @@ name: negatively regulates characteristic namespace: gene_ontology def: "A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C." [] xref: RO:0019002 -property_value: dc-contributor https://orcid.org/0000-0002-8688-6599 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 holds_over_chain: negatively_regulates positively_regulates_characteristic holds_over_chain: positively_regulates negatively_regulates_characteristic is_a: regulates_characteristic ! regulates characteristic -[Typedef] -id: never_in_taxon -name: never in taxon -name: never_in_taxon -namespace: uberon -def: "S never_in_taxon T iff: S SubClassOf in_taxon only not T." [PMID:20973947] -def: "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL." [] -xref: RO:0002161 -property_value: IAO:0000112 "tooth SubClassOf 'never in taxon' value 'Aves'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 -property_value: OMO:0002000 "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" xsd:string -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -expand_assertion_to: "Class: EquivalentTo: ?X and (RO_0002162 some ?Y)" [] -expand_assertion_to: "Class: ?X DisjointWith: RO_0002162 some ?Y " [] -is_metadata_tag: true -is_class_level: true - [Typedef] id: occurs_in name: occurs in @@ -19456,64 +18209,38 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000066 -property_value: IAO:0000111 "occurs in" xsd:string -property_value: IAO:0000118 "occurs_in" xsd:string -property_value: IAO:0000118 "unfolds in" xsd:string -property_value: IAO:0000118 "unfolds_in" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl property_value: seeAlso "https://wiki.geneontology.org/Occurs_in" xsd:anyURI domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant holds_over_chain: part_of occurs_in -inverse_of: contains_process ! contains process -transitive_over: part_of ! part_of - -[Typedef] -id: only_in_taxon -name: only in taxon -namespace: uberon -def: "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." [] -xref: RO:0002160 -property_value: editor_note "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" xsd:string -property_value: IAO:0000112 "lactation SubClassOf 'only in taxon' some 'Mammalia'" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -is_a: in_taxon ! in taxon +inverse_of: BFO:0000067 ! contains process +transitive_over: part_of ! part of [Typedef] id: output_of name: output of namespace: external -namespace: uberon def: "inverse of has output" [] subset: ro-eco subset: RO:0002259 xref: RO:0002353 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: functionally_related_to ! functionally related to is_a: participates_in ! participates in +is_a: RO:0002328 ! functionally related to [Typedef] id: overlaps name: overlaps namespace: external -namespace: uberon def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002131 -property_value: IAO:0000114 IAO:0000125 -property_value: RO:0001900 RO:0001901 holds_over_chain: has_part overlaps -holds_over_chain: has_part part_of {RO:0002582="true"} holds_over_chain: part_of part_of is_symmetric: true is_a: RO:0002323 ! mereotopologically related to -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] [Typedef] @@ -19522,29 +18249,15 @@ name: part of name: part_of namespace: external namespace: quality -namespace: uberon def: "a core relation that holds between a part and its whole" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000050 -property_value: editor_note "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string -property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string -property_value: IAO:0000111 "is part of" xsd:string -property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string -property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string -property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string -property_value: IAO:0000118 "part_of" xsd:string -property_value: RO:0001900 RO:0001901 -property_value: RO:0040042 BFO:0000002 -property_value: RO:0040042 BFO:0000003 -property_value: RO:0040042 BFO:0000004 -property_value: RO:0040042 BFO:0000017 -property_value: RO:0040042 BFO:0000019 -property_value: RO:0040042 BFO:0000020 -property_value: RO:0040042 BFO:0000031 +property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string @@ -19557,14 +18270,8 @@ inverse_of: has_part ! has part id: participates_in name: participates in namespace: external -namespace: uberon def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] xref: RO:0000056 -property_value: IAO:0000111 "participates in" xsd:string -property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string -property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string -property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string -property_value: IAO:0000118 "participates_in" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000003 ! occurrent inverse_of: has_participant ! has participant @@ -19576,7 +18283,6 @@ namespace: external def: "inverse of positively regulates" [] subset: RO:0002259 xref: RO:0002336 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -19588,10 +18294,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002213 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "positively regulates (process to process)" xsd:string -property_value: RO:0004049 RO:0002211 holds_over_chain: ends_with positively_regulates holds_over_chain: negatively_regulates negatively_regulates is_transitive: true @@ -19605,49 +18307,25 @@ name: positively regulates characteristic namespace: gene_ontology def: "A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C." [] xref: RO:0019001 -property_value: dc-contributor https://orcid.org/0000-0002-8688-6599 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 holds_over_chain: positively_regulates positively_regulates_characteristic is_a: regulates_characteristic ! regulates characteristic -[Typedef] -id: postaxialmost_part_of -name: postaxialmost part of -namespace: uberon -xref: BSPO:0001115 - -[Typedef] -id: posterior_to -name: posterior to -namespace: uberon -xref: BSPO:0000099 - [Typedef] id: posteriorly_connected_to name: posteriorly connected to namespace: uberon def: "x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] -is_a: anterior_to ! anterior to -is_a: connected_to ! connected to - -[Typedef] -id: preaxialmost_part_of -name: preaxialmost part of -namespace: uberon -xref: BSPO:0001113 +is_a: RO:0002170 ! connected to [Typedef] id: preceded_by name: preceded by namespace: external -namespace: uberon def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000062 -property_value: editor_note "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string -property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string -property_value: IAO:0000111 "preceded by" xsd:string -property_value: IAO:0000118 "is preceded by" xsd:string -property_value: IAO:0000118 "preceded_by" xsd:string +property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent holds_over_chain: part_of preceded_by @@ -19659,53 +18337,30 @@ inverse_of: precedes ! precedes id: precedes name: precedes namespace: external -namespace: uberon def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000063 -property_value: IAO:0000111 "precedes" xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent holds_over_chain: part_of precedes is_transitive: true is_a: RO:0002222 ! temporally related to -[Typedef] -id: present_in_taxon -name: present in taxon -name: present_in_taxon -namespace: uberon -def: "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S" [] -def: "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S." [https://orcid.org/0000-0002-6601-2165] -comment: The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology. -synonym: "applicable for taxon" EXACT [] -xref: RO:0002175 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: OMO:0002000 "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" xsd:string -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -is_metadata_tag: true -is_class_level: true - [Typedef] id: process_has_causal_agent name: process has causal agent namespace: external def: "Inverse of 'causal agent in process'" [] xref: RO:0002608 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_a: RO:0002410 ! causally related to [Typedef] id: produced_by name: produced by namespace: external -namespace: uberon def: "a produced_by b iff some process that occurs_in b has_output a." [] subset: ro-eco xref: RO:0003001 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity @@ -19713,13 +18368,10 @@ range: BFO:0000040 ! material entity id: produces name: produces namespace: external -namespace: uberon def: "a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix." [] comment: Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. subset: ro-eco xref: RO:0003000 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity inverse_of: produced_by ! produced by @@ -19729,27 +18381,14 @@ id: protects name: protects namespace: uberon -[Typedef] -id: proximal_to -name: proximal to -namespace: uberon -xref: BSPO:0000100 - [Typedef] id: proximally_connected_to name: proximally connected to namespace: uberon def: "x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] -is_a: connected_to ! connected to -is_a: distal_to ! distal to +is_a: RO:0002170 ! connected to is_a: transitively_proximally_connected_to ! transitively proximally connected to -[Typedef] -id: proximalmost_part_of -name: proximalmost part of -namespace: uberon -xref: BSPO:0001106 - [Typedef] id: regulated_by name: regulated by @@ -19757,8 +18396,6 @@ namespace: external def: "inverse of regulates" [] subset: RO:0002259 xref: RO:0002334 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000589 "regulated by (processual)" xsd:string domain: BFO:0000015 ! process range: BFO:0000015 ! process is_transitive: true @@ -19773,14 +18410,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 -property_value: IAO:0000117 https://orcid.org/0000-0001-7476-6306 -property_value: IAO:0000117 https://orcid.org/0000-0002-3837-8864 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GO" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string -property_value: IAO:0000589 "regulates (processual)" xsd:string -property_value: IAO:0000600 "false" xsd:boolean domain: BFO:0000015 ! process range: BFO:0000015 ! process holds_over_chain: directly_regulates directly_regulates @@ -19796,7 +18425,7 @@ name: regulates characteristic namespace: gene_ontology def: "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C." [] xref: RO:0019000 -property_value: dc-contributor https://orcid.org/0000-0002-8688-6599 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 domain: BFO:0000015 ! process range: PATO:0000001 ! quality holds_over_chain: regulates regulates_characteristic @@ -19808,13 +18437,9 @@ name: regulates levels of namespace: external def: "p regulates levels of c if p regulates some amount (PATO:0000070) of c" [] xref: RO:0002332 -property_value: IAO:0000112 "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "regulates levels of (process to entity)" xsd:string domain: BFO:0000015 ! process range: BFO:0000040 ! material entity -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to [Typedef] id: results_in_acquisition_of_features_of @@ -19825,9 +18450,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002315 -property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string range: UBERON:0000061 ! anatomical structure is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -19862,10 +18484,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002296 -property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "http://www.geneontology.org/GO.doc.development.shtml" xsd:anyURI is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -19875,9 +18493,7 @@ name: results in developmental progression of namespace: external def: "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." [] xref: RO:0002295 -property_value: editor_note "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000116 "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string property_value: seeAlso Ontology:extensions domain: GO:0008150 ! biological_process range: UBERON:0001062 ! anatomical entity @@ -19909,16 +18525,12 @@ is_a: has_participant ! has participant [Typedef] id: results_in_formation_of name: results in formation of +name: results in formation of anatomical entity namespace: external subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002297 -property_value: IAO:0000112 "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." xsd:string -property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of inverse_of: RO:0002354 ! formed as result of @@ -19940,8 +18552,6 @@ id: results_in_growth_of name: results in growth of namespace: external xref: RO:0002343 -property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -19954,11 +18564,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002299 -property_value: IAO:0000112 " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" xsd:string -property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -19971,11 +18576,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002298 -property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." xsd:string -property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -19988,8 +18588,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002565 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure [Typedef] @@ -20008,7 +18606,6 @@ namespace: external def: "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002342 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in is_a: RO:0002021 ! occurs across @@ -20018,7 +18615,6 @@ name: results in transport along namespace: external def: "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " [] xref: RO:0002341 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002337 ! related via localization to [Typedef] @@ -20026,36 +18622,13 @@ id: results_in_transport_to_from_or_in name: results in transport to from or in namespace: external xref: RO:0002344 -property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002337 ! related via localization to -[Typedef] -id: seeAlso -name: see also -namespace: uberon -xref: http://www.w3.org/2000/01/rdf-schema#seeAlso -is_metadata_tag: true - [Typedef] id: sexually_homologous_to name: sexually_homologous_to namespace: uberon -is_a: homologous_to ! shares ancestor with - -[Typedef] -id: simultaneous_with -name: simultaneous with -namespace: uberon -def: "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." [] -comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) -subset: ro-eco -xref: RO:0002082 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -is_symmetric: true -is_transitive: true -is_a: RO:0002081 ! before or simultaneous with +is_a: RO:0002158 ! shares ancestor with [Typedef] id: site_of @@ -20064,46 +18637,13 @@ namespace: uberon def: "c site_of p if c is the bearer of a disposition that is realized by a process that has p as part." [] synonym: "capable_of_has_part" RELATED [] -[Typedef] -id: skeleton_of -name: skeleton of -namespace: uberon -def: "inverse of has skeleton" [] -subset: RO:0002259 -xref: RO:0002576 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: UBERON:0000061 ! anatomical structure -range: UBERON:0000061 ! anatomical structure -is_a: part_of ! part_of - -[Typedef] -id: starts -name: starts -namespace: uberon -def: "inverse of starts with" [] -subset: ro-eco -xref: RO:0002223 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "Allen" xsd:string -is_a: part_of ! part_of -is_a: RO:0002222 ! temporally related to -inverse_of: starts_with ! starts with - [Typedef] id: starts_with name: starts with namespace: external -namespace: uberon def: "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002224 -property_value: IAO:0000112 "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "started by" xsd:string is_transitive: true is_a: has_part ! has part is_a: RO:0002222 ! temporally related to @@ -20114,139 +18654,36 @@ name: subdivision of namespace: uberon comment: placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B -[Typedef] -id: superficial_to -name: superficial to -namespace: uberon -xref: BSPO:0000108 - -[Typedef] -id: supplies -name: supplies -namespace: uberon -def: "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." [] -xref: RO:0002178 -property_value: editor_note "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 -is_a: connected_to ! connected to - -[Typedef] -id: surrounded_by -name: surrounded by -namespace: uberon -def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" [] -xref: RO:0002219 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0001900 RO:0001901 -is_a: adjacent_to ! adjacent to -inverse_of: surrounds ! surrounds - -[Typedef] -id: surrounds -name: surrounds -namespace: uberon -def: "inverse of surrounded by" [] -subset: RO:0002259 -xref: RO:0002221 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0001900 RO:0001901 -is_a: adjacent_to ! adjacent to - -[Typedef] -id: synapsed_by -name: synapsed by -namespace: uberon -def: "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " [] -xref: RO:0002103 -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 -is_a: RO:0002485 ! receives input from -inverse_of: RO:0002120 ! synapsed to -expand_expression_to: "BFO_0000051 some (GO_0045211 that part_of some (GO_0045202 that has_part some (GO_0042734 that BFO_0000050 some Y?)))" [] - [Typedef] id: term_tracker_item name: term tracker item namespace: external -namespace: uberon def: "An IRI or similar locator for a request or discussion of an ontology term." [] comment: The 'tracker item' can associate a tracker with a specific ontology term. xref: IAO:0000233 -property_value: IAO:0000111 "term tracker item" xsd:string -property_value: IAO:0000112 "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" xsd:string -property_value: IAO:0000119 "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" xsd:string is_metadata_tag: true -is_class_level: true - -[Typedef] -id: transformation_of -name: transformation of -namespace: uberon -def: "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" [] -xref: RO:0002494 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_transitive: true -is_a: develops_from ! develops from [Typedef] id: transitively_anteriorly_connected_to name: transitively anteriorly connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI -is_transitive: true [Typedef] id: transitively_distally_connected_to name: transitively distally connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI -is_transitive: true [Typedef] id: transitively_proximally_connected_to name: transitively proximally connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI -is_transitive: true - -[Typedef] -id: tributary_of -name: tributary of -namespace: uberon -def: "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." [] -subset: ro-eco -xref: RO:0002376 -property_value: IAO:0000112 "Deschutes River tributary_of Columbia River" xsd:string -property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "drains into" xsd:string -property_value: IAO:0000118 "drains to" xsd:string -property_value: IAO:0000118 "tributary channel of" xsd:string -property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Tributary" xsd:string -property_value: IAO:0000119 "http://www.medindia.net/glossary/venous_tributary.htm" xsd:string -property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" xsd:anyURI -property_value: seeAlso http://dbpedia.org/ontology/drainsTo -property_value: seeAlso "http://en.wikipedia.org/wiki/Tributary" xsd:anyURI -is_a: connected_to ! connected to -is_a: RO:0002375 ! in branching relationship with [Typedef] id: trunk_part_of name: trunk_part_of namespace: uberon -is_a: part_of ! part_of - -[Typedef] -id: ventral_to -name: ventral to -namespace: uberon -xref: BSPO:0000102 +is_a: part_of ! part of diff --git a/subsets/eye_upper_slim.owl b/subsets/eye_upper_slim.owl index 379bb2999..d878a3456 100644 --- a/subsets/eye_upper_slim.owl +++ b/subsets/eye_upper_slim.owl @@ -10,28 +10,21 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" - xmlns:cito="http://purl.org/spar/cito/" xmlns:core="http://purl.obolibrary.org/obo/uberon/core#" xmlns:foaf="http://xmlns.com/foaf/0.1/" - xmlns:obo2="http://www.geneontology.org/formats/oboInOwl#http://purl.obolibrary.org/obo/" xmlns:pato="http://purl.obolibrary.org/obo/pato#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" - xmlns:skos="http://www.w3.org/2004/02/skos/core#" xmlns:swrl="http://www.w3.org/2003/11/swrl#" - xmlns:sssom="https://w3id.org/sssom/" - xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#" xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:terms="http://purl.org/dc/terms/" - xmlns:vocab="https://w3id.org/semapv/vocab/" - xmlns:terms1="http://www.geneontology.org/formats/oboInOwl#http://purl.org/dc/terms/" xmlns:uberon="http://purl.obolibrary.org/obo/uberon#" xmlns:ubprop="http://purl.obolibrary.org/obo/ubprop#" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - 2024-02-13 + + 2024-04-05 @@ -55,29 +48,9 @@ - - - - - - - - - - - - - - - - - - - definition - The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith @@ -99,8 +72,6 @@ We don't have definitions of 'meaning' or 'expression' Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition @@ -110,72 +81,28 @@ We also have the outstanding issue of how to aim different definitions to differ - editor note - An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obofoundry.org/obo/obi> - IAO:0000116 - uberon - editor_note - true - editor_note - editor note editor note - - - - - - - - - - - - - - - - - - - has obsolescence reason Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. - PERSON:Alan Ruttenberg - PERSON:Melanie Courtot has obsolescence reason - - - - - - - term tracker item - the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ - An IRI or similar locator for a request or discussion of an ontology term. - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg IAO:0000233 external - uberon term_tracker_item - true true term_tracker_item The 'tracker item' can associate a tracker with a specific ontology term. @@ -185,63 +112,23 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - - expand expression to - ObjectProperty: RO_0002104 -Label: has plasma membrane part -Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" - A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones - Chris Mungall expand expression to expand expression to - - - - - - - - - - - - - - - - - - - - - - - - - has ontology root term Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. - Nicolas Matentzoglu IAO:0000700 external - uberon has_ontology_root_term - true true has_ontology_root_term has ontology root term @@ -251,20 +138,10 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - - - - - - - term replaced by - Use on obsolete terms, relating the term to another term that can be used as a substitute - Person:Alan Ruttenberg - Person:Alan Ruttenberg Add as annotation triples in the granting ontology term replaced by term replaced by @@ -275,24 +152,6 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - 'part disjoint with' 'defined by construct' """ - PREFIX owl: <http://www.w3.org/2002/07/owl#> - PREFIX : <http://example.org/ - CONSTRUCT { - [ - a owl:Restriction ; - owl:onProperty :part_of ; - owl:someValuesFrom ?a ; - owl:disjointWith [ - a owl:Restriction ; - owl:onProperty :part_of ; - owl:someValuesFrom ?b - ] - ] - } - WHERE { - ?a :part_disjoint_with ?b . - } Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. @@ -305,11 +164,9 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation) A synonym type for describing abbreviations or initalisms - 2023-03-03 abbreviation @@ -335,11 +192,9 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form) A synonym type for describing pluralization synonyms - 2023-03-03 plural form @@ -354,23 +209,10 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - - - - - - - tooth SubClassOf 'never in taxon' value 'Aves' - S never_in_taxon T iff: S SubClassOf in_taxon only not T. x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL. - - - - Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: ?X and (RO_0002162 some ?Y) - Class: ?X DisjointWith: RO_0002162 some ?Y PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> @@ -394,34 +236,9 @@ CONSTRUCT { WHERE { ?x never_in_taxon: ?taxon . } - RO:0002161 - uberon - never_in_taxon - true - true - never_in_taxon never in taxon - never_in_taxon - - - - S never_in_taxon T iff: S SubClassOf in_taxon only not T. - PMID:20973947 - - - - - - - - - - - - - @@ -429,9 +246,6 @@ WHERE { S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S - S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S. - - PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> @@ -456,24 +270,10 @@ WHERE { )) as ?witness) BIND(CONCAT(STR(?x), " in taxon ", STR(?taxon)) AS ?label) } - RO:0002175 - applicable for taxon - uberon - present_in_taxon - true - true - present_in_taxon The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology. present in taxon - present_in_taxon - - - - S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S. - https://orcid.org/0000-0002-6601-2165 - @@ -485,60 +285,6 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL - is a defining property chain axiom - - - - - - - - If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. - is a defining property chain axiom where second argument is reflexive - - - - - - - - - - - - - - - - - - - - - - @@ -549,126 +295,6 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -927,12 +553,6 @@ WHERE { - - - - - - @@ -1363,14 +983,7 @@ WHERE { - - http://purl.org/dc/elements/1.1/creator - uberon - dc-creator - true - dc-creator - creator - + @@ -1382,14 +995,7 @@ WHERE { - - http://purl.org/dc/elements/1.1/description - uberon - dc-description - true - dc-description - description - + @@ -1401,71 +1007,25 @@ WHERE { - - http://purl.org/dc/elements/1.1/title - uberon - dc-title - true - dc-title - title - + - - http://purl.org/dc/terms/contributor - uberon - dc-contributor - true - dc-contributor - contributor - - - - - - - - - - - - - + - - http://purl.org/dc/terms/date - uberon - dcterms-date - true - dcterms-date - date - + - - http://purl.org/dc/terms/license - uberon - dcterms-license - true - dcterms-license - license - - - - - - - + @@ -1475,18 +1035,6 @@ WHERE { - - - - - - - - - - - - @@ -1503,18 +1051,6 @@ WHERE { - - - - - - - - - - - - @@ -1523,18 +1059,6 @@ WHERE { - - - - - - - - - - - - @@ -1551,66 +1075,6 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -1623,7 +1087,6 @@ WHERE { An alternative label for a class or property which has a more general meaning than the preferred name/primary label. - https://github.com/information-artifact-ontology/ontology-metadata/issues/18 has broad synonym has_broad_synonym @@ -1644,7 +1107,6 @@ WHERE { An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. - https://github.com/information-artifact-ontology/ontology-metadata/issues/20 has exact synonym has_exact_synonym @@ -1657,7 +1119,6 @@ WHERE { An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. - https://github.com/information-artifact-ontology/ontology-metadata/issues/19 has narrow synonym has_narrow_synonym @@ -1678,7 +1139,6 @@ WHERE { An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. - https://github.com/information-artifact-ontology/ontology-metadata/issues/21 has related synonym has_related_synonym @@ -1687,12 +1147,6 @@ WHERE { - - - - - - @@ -1717,30 +1171,6 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - - - @@ -1753,72 +1183,12 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -1833,60 +1203,6 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -1903,9 +1219,6 @@ WHERE { http://www.w3.org/2000/01/rdf-schema#seeAlso - uberon - seeAlso - true seeAlso see also @@ -1918,63 +1231,9 @@ WHERE { - - - - - - - - http://xmlns.com/foaf/0.1/depiction - uberon - depiction - true - depiction - depiction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + @@ -1995,29 +1254,15 @@ WHERE { - is part of - my brain is part of my body (continuant parthood, two material entities) - my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) - this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. - part_of - - - - - - - - BFO:0000050 external quality - uberon part_of @@ -2040,22 +1285,15 @@ A continuant cannot be part of an occurrent: use 'participates in'. An - has part - my body has part my brain (continuant parthood, two material entities) - my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) - this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. - has_part - BFO:0000051 external quality - uberon has_part @@ -2080,15 +1318,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. - preceded by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. - is preceded by - preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 external - uberon preceded_by preceded_by @@ -2109,11 +1342,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. - precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. BFO:0000063 external - uberon precedes precedes @@ -2137,11 +1368,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - occurs_in - unfolds in - unfolds_in BFO:0000066 external occurs_in @@ -2150,7 +1377,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. occurs_in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant - occurs in occurs in https://wiki.geneontology.org/Occurs_in @@ -2161,308 +1387,13 @@ A continuant cannot have an occurrent as part: use 'participates in'. - site of [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - BFO:0000067 - uberon - contains_process - contains_process Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant - - contains process contains process - - - - BSPO:0000096 - uberon - anterior_to - anterior_to - anterior to - - - - - - - - BSPO:0000097 - uberon - distal_to - distal_to - distal to - - - - - - - - BSPO:0000098 - uberon - dorsal_to - dorsal_to - dorsal to - - - - - - - - BSPO:0000099 - uberon - posterior_to - posterior_to - posterior to - - - - - - - - BSPO:0000100 - uberon - proximal_to - proximal_to - proximal to - - - - - - - - BSPO:0000102 - uberon - ventral_to - ventral_to - ventral to - - - - - - - - BSPO:0000107 - uberon - deep_to - deep_to - deep to - - - - - - - - BSPO:0000108 - uberon - superficial_to - superficial_to - superficial to - - - - - - - - BSPO:0000120 - uberon - in_left_side_of - in_left_side_of - in left side of - - - - - - - - BSPO:0000121 - uberon - in_right_side_of - in_right_side_of - in right side of - - - - - - - - BSPO:0000122 - uberon - in_posterior_side_of - in_posterior_side_of - in posterior side of - - - - - - - - BSPO:0000123 - uberon - in_anterior_side_of - in_anterior_side_of - in anterior side of - - - - - - - - BSPO:0000124 - uberon - in_proximal_side_of - in_proximal_side_of - in proximal side of - - - - - - - - BSPO:0000126 - uberon - in_lateral_side_of - in_lateral_side_of - in lateral side of - - - - - - - - BSPO:0001100 - uberon - in_superficial_part_of - in_superficial_part_of - in superficial part of - - - - - - - - BSPO:0001101 - uberon - in_deep_part_of - in_deep_part_of - in deep part of - - - - - - - - BSPO:0001106 - uberon - proximalmost_part_of - proximalmost_part_of - proximalmost part of - - - - - - - - BSPO:0001107 - uberon - immediately_deep_to - immediately_deep_to - immediately deep to - - - - - - - - BSPO:0001108 - uberon - distalmost_part_of - distalmost_part_of - distalmost part of - - - - - - - - BSPO:0001113 - uberon - preaxialmost_part_of - preaxialmost_part_of - preaxialmost part of - - - - - - - - BSPO:0001115 - uberon - postaxialmost_part_of - postaxialmost_part_of - postaxialmost part of - - - - - - - - BSPO:0005001 - uberon - intersects_midsagittal_plane_of - intersects_midsagittal_plane_of - intersects midsagittal plane of - - - - - - - - BSPO:0015014 - uberon - immediately_superficial_to - immediately_superficial_to - immediately superficial to - - - - - - - - BSPO:0015101 - uberon - in_dorsal_side_of - in_dorsal_side_of - in dorsal side of - - - - @@ -2522,12 +1453,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - inheres in - this fragility is a characteristic of this vase - this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. - inheres_in - Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of @@ -2539,14 +1465,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - bearer of - this apple is bearer of this red color - this vase is bearer of this fragility Inverse of characteristic_of A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. - bearer_of - is bearer of - RO:0000053 external bearer_of @@ -2563,15 +1483,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. - participates in - this blood clot participates in this blood coagulation - this input material (or this output material) participates in this process - this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process - participates_in RO:0000056 external - uberon participates_in participates_in participates in @@ -2589,14 +1503,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - has participant - this blood coagulation has participant this blood clot - this investigation has participant this investigator - this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. - has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 external has_participant @@ -2612,11 +1520,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. - function_of - is function of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. function of @@ -2628,11 +1533,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. - is quality of - quality_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. quality of @@ -2644,11 +1546,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. - is role of - role_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. role of @@ -2660,10 +1559,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. - has_function has function @@ -2673,15 +1570,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. - has_quality - RO:0000086 - uberon - has_quality - has_quality - has quality has quality @@ -2692,10 +1582,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. - has_role has role @@ -2729,13 +1617,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this cell derives from this parent cell (cell division) - this nucleus derives from this parent nucleus (nuclear division) - a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. - derives_from - This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. derives from @@ -2745,12 +1628,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this parent cell derives into this cell (cell division) - this parent nucleus derives into this nucleus (nuclear division) - a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. - derives_into derives into @@ -2762,18 +1641,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - is location of - my head is the location of my brain - this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - location_of - - RO:0001015 - uberon - location_of - location_of - location of location of @@ -2789,21 +1658,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. - located in - my brain is located in my head - this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - located_in - - http://www.obofoundry.org/ro/#OBO_REL:located_in - RO:0001025 - uberon - located_in - located_in - located in located in https://wiki.geneontology.org/Located_in @@ -2827,16 +1685,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. - the surface of my skin is a 2D boundary of my body a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - 2D_boundary_of - boundary of - is 2D boundary of - is boundary of - surface of - 2D boundary of @@ -2848,19 +1699,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. - my body has 2D boundary the surface of my skin a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - - has boundary - has_2D_boundary - - RO:0002002 - uberon - has_boundary - has_boundary - has 2D boundary has 2D boundary @@ -2872,17 +1713,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - http://www.ncbi.nlm.nih.gov/pubmed/22402613 - RO:0002005 - uberon - innervated_by - innervated_by - innervated_by innervated_by @@ -2893,8 +1723,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - has synaptic terminal of @@ -2925,10 +1753,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - RO:0002007 external - uberon bounding_layer_of bounding_layer_of @@ -3107,8 +1933,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland - <= Primitive instance level timing relation between events before or simultaneous with @@ -3123,15 +1947,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time. - - David Osumi-Sutherland - RO:0002082 - uberon - simultaneous_with - simultaneous_with t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) - simultaneous with simultaneous with @@ -3142,7 +1959,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after @@ -3159,11 +1975,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland - starts_at_end_of RO:0002087 external - uberon immediately_preceded_by immediately_preceded_by X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) @@ -3181,11 +1994,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - - David Osumi-Sutherland - ends_at_start_of - meets - RO:0002090 external immediately_precedes @@ -3208,12 +2016,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between a neuron and a material anatomical entity that its soma is part of. - <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) - has soma location @@ -3226,33 +2031,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. - - fasciculates with - (forall (?x ?y) - (iff - (fasciculates_with ?x ?y) - (exists (?nps ?npbs) - (and - ("neuron ; CL_0000540" ?x) - ("neuron projection bundle ; CARO_0001001" ?y) - ("neuron projection segment ; CARO_0001502" ?nps) - ("neuron projection bundle segment ; CARO_0001500' " ?npbs) - (part_of ?npbs ?y) - (part_of ?nps ?x) - (part_of ?nps ?npbs) - (forall (?npbss) - (if - (and - ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) - (part_of ?npbss ?npbs) - ) - (overlaps ?nps ?npbss) - )))))) - - fasciculates with @@ -3267,16 +2047,11 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between a neuron and some structure its axon forms (chemical) synapses in. - - <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y))) - - axon synapses in @@ -3298,18 +2073,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. - - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) - - - RO:0002103 - uberon - synapsed_by - synapsed_by - synapsed by synapsed by @@ -3321,15 +2086,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] - Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. - - - - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) - has plasma membrane part @@ -3345,16 +2103,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. - - - synapsed in http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)) - - has postsynaptic terminal in @@ -3369,12 +2121,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. - synapses in <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) - - has presynaptic terminal in @@ -3395,14 +2143,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. - - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) - - N1 synapsed_to some N2 Expands to: N1 SubclassOf ( @@ -3424,13 +2167,8 @@ N1 SubclassOf ( - A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. - - has synapse in <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) - - has synaptic terminal in @@ -3445,10 +2183,6 @@ N1 SubclassOf ( - - - - @@ -3457,13 +2191,10 @@ N1 SubclassOf ( - x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) - RO:0002131 external - uberon overlaps @@ -3472,15 +2203,6 @@ N1 SubclassOf ( overlaps overlaps - - - - - - - - true - @@ -3500,35 +2222,7 @@ N1 SubclassOf ( - The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. - - has fasciculating component - (forall (?x ?y) - (iff - (has_fasciculating_neuron_projection ?x ?y) - (exists (?nps ?npbs) - (and - ("neuron projection bundle ; CARO_0001001" ?x) - ("neuron projection ; GO0043005" ?y) - ("neuron projection segment ; CARO_0001502" ?nps) - ("neuron projection bundle segment ; CARO_0001500" ?npbs) - (part_of ?nps ?y) - (part_of ?npbs ?x) - (part_of ?nps ?npbs) - (forall (?npbss) - (if - (and - ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) - (part_of ?npbss ?npbs) - ) - (overlaps ?nps ?npbss) - )))))) - - - - - has fasciculating neuron projection @@ -3542,19 +2236,10 @@ N1 SubclassOf ( - Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - <http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) - - - RO:0002134 - uberon - innervates - innervates - innervates innervates @@ -3567,17 +2252,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - X continuous_with Y if and only if X and Y share a fiat boundary. - - connected to - The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) - - RO:0002150 - uberon - continuous_with - continuous_with - continuous with continuous with FMA:85972 @@ -3590,13 +2265,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a. - Consider obsoleting and merging with child relation, 'in homology relationship with' - RO:0002158 - uberon - homologous_to - homologous_to VBO calls this homologous_to shares ancestor with @@ -3607,19 +2276,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - lactation SubClassOf 'only in taxon' some 'Mammalia' - x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria - - - - RO:0002160 - uberon - only_in_taxon - only_in_taxon only in taxon @@ -3638,30 +2298,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - - - - - - - - - - - - - - - - - - - - - @@ -3682,53 +2318,16 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. - - - - - RO:0002162 - uberon - in_taxon - in_taxon Connects a biological entity to its taxon of origin. in taxon @@ -3740,14 +2339,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. - - - Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) - spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern @@ -3765,14 +2359,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b - - RO:0002170 - uberon - connected_to - connected_to - connected to connected to https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern @@ -3785,15 +2372,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - The M8 connects Glasgow and Edinburgh - a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system. - - RO:0002176 - uberon - connects - connects - connects connects https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern @@ -3808,28 +2387,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. - attached to part of (anatomical structure to anatomical structure) - RO:0002177 - uberon - attaches_to_part_of - attaches_to_part_of - attached to part of attached to part of - - - - - - - - true - @@ -3839,12 +2399,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy. Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure - - RO:0002178 - uberon - supplies - supplies - supplies supplies @@ -3856,12 +2410,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure. Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure - - RO:0002179 - uberon - drains - drains - drains drains @@ -3871,14 +2419,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. - For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. - RO:0002180 external - uberon has_component has_component @@ -3898,18 +2442,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y - - - - - RO:0002202 - uberon - develops_from - develops_from This is the transitive form of the develops from relation - develops from develops from @@ -3922,17 +2456,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of develops from - - - - RO:0002203 - uberon - develops_into - develops_into - develops into develops into @@ -3949,10 +2474,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - 'neural crest cell' SubClassOf expresses some 'Wnt1 gene' - x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process - expressed in @@ -3979,19 +2501,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. - - - FBbt - - RO:0002207 has developmental precursor - uberon - directly_develops_from - directly_develops_from TODO - add child relations from DOS - directly develops from directly develops from @@ -4001,9 +2513,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of directly develops from - developmental precursor of directly develops into @@ -4031,14 +2541,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. - - - - - GO - Regulation precludes parthood; the regulatory process may not be within the regulated process. - regulates (processual) - false RO:0002211 external regulates @@ -4063,9 +2565,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. - - - negatively regulates (process to process) RO:0002212 external @@ -4096,10 +2595,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. - - - positively regulates (process to process) - RO:0002213 external positively_regulates @@ -4119,17 +2614,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) - osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. - - has function realized in - - - For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". RO:0002215 external - uberon capable_of capable_of @@ -4144,31 +2631,15 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. - - has function in RO:0002216 external - uberon capable_of_part_of capable_of_part_of capable of part of capable of part of - - - - - - - - true - @@ -4177,15 +2648,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x - - - RO:0002219 - uberon - surrounded_by - surrounded_by - surrounded by surrounded by @@ -4197,18 +2660,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. - The epidermis layer of a vertebrate is adjacent to the dermis. - The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. - The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. - x adjacent to y if and only if x and y share a boundary. This relation acts as a join point with BSPO - - RO:0002220 external - uberon adjacent_to @@ -4217,12 +2672,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.adjacent to adjacent to - - - - A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. - - @@ -4230,16 +2679,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of surrounded by - - - RO:0002221 - uberon - surrounds - surrounds - surrounds surrounds @@ -4250,11 +2691,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. - https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to @@ -4268,17 +2704,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of starts with - - Chris Mungall - Allen - RO:0002223 - uberon - starts - starts - starts starts @@ -4290,15 +2717,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor - x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - - Chris Mungall - started by RO:0002224 external - uberon starts_with starts_with @@ -4316,14 +2737,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x develops from part of y if and only if there exists some z such that x develops from z and z is part of y - - RO:0002225 - uberon - develops_from_part_of - develops_from_part_of - develops from part of develops from part of @@ -4338,16 +2752,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x develops_in y if x is located in y whilst x is developing - - EHDAA2 - Jonathan Bard, EHDAA2 - RO:0002226 - uberon - develops_in - develops_in - develops in develops in @@ -4359,16 +2764,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of ends with - - Chris Mungall - RO:0002229 - uberon - ends - ends - ends ends @@ -4380,14 +2777,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - - Chris Mungall - finished by RO:0002230 external - uberon ends_with ends_with @@ -4407,10 +2799,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y - - starts with process that occurs in RO:0002231 external has_start_location @@ -4432,10 +2821,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y - - ends with process that occurs in RO:0002232 external has_end_location @@ -4457,10 +2843,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. - - consumes RO:0002233 external has_input @@ -4485,10 +2868,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. - - produces RO:0002234 external has_output @@ -4510,13 +2890,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1. b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t. - - RO:0002252 - uberon - connecting_branch_of - connecting_branch_of connecting branch of @@ -4528,7 +2902,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of connecting branch of - has connecting branch @@ -4546,15 +2919,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] - x has developmental contribution from y iff x has some part z such that z develops from y - - RO:0002254 - uberon - has_developmental_contribution_from - has_developmental_contribution_from - has developmental contribution from has developmental contribution from @@ -4569,9 +2934,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of has developmental contribution from - developmentally contributes to @@ -4585,21 +2948,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T - - - - induced by - - Developmental Biology, Gilbert, 8th edition, figure 6.5(F) - GO:0001759 - We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm] - RO:0002256 - uberon - developmentally_induced_by - developmentally_induced_by - developmentally induced by developmentally induced by @@ -4610,9 +2959,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Inverse of developmentally induced by - developmentally induces @@ -4625,11 +2972,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false - - In general you should not use this relation to make assertions - use one of the more specific relations below this one This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from developmentally preceded by @@ -4644,7 +2988,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. acts upstream of @@ -4661,7 +3004,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects @@ -4675,16 +3017,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage - - replaces - RO:0002285 - uberon - developmentally_replaces - developmentally_replaces - developmentally replaces developmentally replaces @@ -4694,9 +3028,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Inverse of developmentally preceded by - developmentally succeeded by @@ -4710,9 +3042,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue - - part of developmental precursor of @@ -4722,9 +3051,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process. - expresses @@ -4736,10 +3063,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. - RO:0002295 external results_in_developmental_progression_of @@ -4756,11 +3081,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - every flower development (GO:0009908) results in development of some flower (PO:0009046) - p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. - - http://www.geneontology.org/GO.doc.development.shtml RO:0002296 external results_in_development_of @@ -4780,11 +3101,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. - every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) - - - GOC:mtg_berkeley_2013 RO:0002297 external results_in_formation_of @@ -4793,7 +3109,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. results_in_formation_of results in formation of - results in formation of + results in formation of anatomical entity @@ -4803,12 +3119,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. - tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) - The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. - - GOC:mtg_berkeley_2013 RO:0002298 external results_in_morphogenesis_of @@ -4827,12 +3138,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process - bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) - The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. - - GOC:mtg_berkeley_2013 RO:0002299 external results_in_maturation_of @@ -4852,8 +3158,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. - - RO:0002304 external causally_upstream_of,_positive_effect @@ -4874,7 +3178,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. - RO:0002305 external causally_upstream_of,_negative_effect @@ -4891,32 +3194,15 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of characteristic of part of - - inheres in part of - - characteristic of part of - - - - - - - - true - @@ -4926,10 +3212,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity - - GOC:mtg_berkeley_2013 RO:0002315 external results_in_acquisition_of_features_of @@ -4947,8 +3230,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A relationship that holds via some environmental process - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. evolutionarily related to @@ -4958,9 +3239,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A mereological relationship or a topological relationship - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships - mereotopologically related to @@ -4970,8 +3248,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A relationship that holds between entities participating in some developmental process (GO:0032502) - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development developmentally related to @@ -4990,15 +3266,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - a particular instances of akt-2 enables some instance of protein kinase activity c enables p iff c is capable of p and c acts to execute p. - - catalyzes - executes - has - is catalyzing - is executing - This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. enables https://wiki.geneontology.org/Enables @@ -5010,13 +3278,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. - - This is a grouping relation that collects relations used for the purpose of connecting structure and function - RO:0002328 - uberon - functionally_related_to - functionally_related_to - functionally related to functionally related to @@ -5026,24 +3287,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - this relation holds between c and p when c is part of some c', and c' is capable of p. - - false part of structure that is capable of - - - - - - - - true - @@ -5053,8 +3299,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts. - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism genomically related to @@ -5074,9 +3318,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. c involved_in p if and only if c enables some process p', and p' is part of p - - actively involved in - enables part of involved in https://wiki.geneontology.org/Involved_in @@ -5089,11 +3330,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid p regulates levels of c if p regulates some amount (PATO:0000070) of c - - - regulates levels of (process to entity) RO:0002332 external regulates_levels_of @@ -5110,7 +3347,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of enables - enabled by https://wiki.geneontology.org/Enabled_by @@ -5126,8 +3362,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of regulates - - regulated by (processual) RO:0002334 external regulated_by @@ -5144,7 +3378,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of negatively regulates - RO:0002335 external negatively_regulated_by @@ -5161,7 +3394,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of positively regulates - RO:0002336 external positively_regulated_by @@ -5179,8 +3411,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A relationship that holds via some process of localization - - Do not use this relation directly. It is a grouping relation. related via localization to @@ -5195,7 +3425,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. - RO:0002338 external has_target_start_location @@ -5218,7 +3447,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. - RO:0002339 external has_target_end_location @@ -5237,7 +3465,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l - RO:0002341 external results_in_transport_along @@ -5254,7 +3481,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. - RO:0002342 external results_in_transport_across @@ -5271,8 +3497,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - 'pollen tube growth' results_in growth_of some 'pollen tube' - RO:0002343 external results_in_growth_of @@ -5287,8 +3511,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) - RO:0002344 external results_in_transport_to_from_or_in @@ -5304,12 +3526,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - An organism that is a member of a population of organisms is member of is a mereological relation between a item and a collection. - is member of - member part of - SIO - member of @@ -5321,13 +3538,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. has member is a mereological relation between a collection and an item. - SIO - - RO:0002351 - uberon - has_member - has_member - has member has member @@ -5339,14 +3549,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of has input - - RO:0002352 - uberon - input_of - input_of - input of input of @@ -5358,10 +3562,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of has output - RO:0002353 external - uberon output_of @@ -5376,7 +3578,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - formed as result of @@ -5386,8 +3587,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - http://neurolex.org/wiki/Property:DendriteLocation has dendrite location @@ -5400,14 +3599,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a - - attached to (anatomical structure to anatomical structure) - RO:0002371 - uberon - attaches_to - attaches_to - attached to attached to @@ -5420,13 +3612,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. - - Wikipedia:Insertion_(anatomy) - RO:0002372 - uberon - has_muscle_origin - has_muscle_origin - has muscle origin has muscle origin @@ -5446,13 +3631,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. - - Wikipedia:Insertion_(anatomy) - RO:0002373 - uberon - has_muscle_insertion - has_muscle_insertion - has muscle insertion has muscle insertion @@ -5471,12 +3649,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships - This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) - in branching relationship with https://github.com/obophenotype/uberon/issues/170 @@ -5489,23 +3662,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Deschutes River tributary_of Columbia River - inferior epigastric vein tributary_of external iliac vein - x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. - - drains into - drains to - tributary channel of - http://en.wikipedia.org/wiki/Tributary - http://www.medindia.net/glossary/venous_tributary.htm - This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries) - RO:0002376 - uberon - tributary_of - tributary_of - tributary of tributary of http://en.wikipedia.org/wiki/Tributary @@ -5523,10 +3681,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location - - This relation is added for formal completeness. It is unlikely to be used in many practical scenarios spatially coextensive with @@ -5544,15 +3699,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y - - RO:0002380 - uberon - branching_part_of - branching_part_of - branching part of branching part of FMA:85994 @@ -5566,9 +3714,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). - has developmental potential involving @@ -5578,14 +3724,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y - - RO:0002385 - uberon - has_potential_to_developmentally_contribute_to - has_potential_to_developmentally_contribute_to - has potential to developmentally contribute to has potential to developmentally contribute to @@ -5595,9 +3734,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y - has potential to developmentally induce @@ -5607,14 +3744,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x has the potential to develop into y iff x develops into y or if x is capable of developing into y - - RO:0002387 - uberon - has_potential_to_develop_into - has_potential_to_develop_into - has potential to develop into has potential to develop into @@ -5624,9 +3754,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y - has potential to directly develop into @@ -5638,9 +3766,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of upstream of - RO:0002404 external causally_downstream_of @@ -5657,8 +3783,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - RO:0002405 external immediately_causally_downstream_of @@ -5692,9 +3816,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. - - indirectly activates - indirectly positively regulates https://wiki.geneontology.org/Indirectly_positively_regulates @@ -5720,9 +3841,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. - - indirectly inhibits - indirectly negatively regulates https://wiki.geneontology.org/Indirectly_negatively_regulates @@ -5748,8 +3866,6 @@ For the second, we consider a relationship to be regulatory if the system in whi For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to @@ -5768,7 +3884,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. - RO:0002411 external causally_upstream_of @@ -5787,8 +3902,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. - - RO:0002412 external immediately_causally_upstream_of @@ -5807,8 +3920,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 - - influences (processual) RO:0002418 external affects @@ -5825,8 +3936,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different inverse of causally upstream of or within - - RO:0002427 external causally_downstream_of_or_within @@ -5851,7 +3960,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' regulates some p - involved in regulation of @@ -5870,8 +3978,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' positively regulates some p - - involved in positive regulation of @@ -5890,7 +3996,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' negatively regulates some p - involved in negative regulation of @@ -5905,8 +4010,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union - - involved in or reguates involved in or involved in regulation of @@ -5917,28 +4020,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - - executes activity in enables activity in is active in https://wiki.geneontology.org/Is_active_in - - - - - - - - true - @@ -5954,11 +4041,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. - - RO:0002433 - uberon - contributes_to_morphology_of - contributes_to_morphology_of contributes to morphology of @@ -5973,13 +4055,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different A relationship that holds between two entities in which the processes executed by the two entities are causally connected. This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. Considering relabeling as 'pairwise interacts with' - - Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. in pairwise interaction with interacts with http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ - http://purl.obolibrary.org/obo/MI_0914 @@ -5990,12 +4069,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. - - binds - molecularly binds with molecularly interacts with - http://purl.obolibrary.org/obo/MI_0915 @@ -6005,8 +4080,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different Axiomatization to GO to be added later - - An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. phosphorylates @@ -6027,8 +4100,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. - - molecularly controls directly regulates activity of @@ -6048,9 +4119,6 @@ A and B can be physically interacting but not necessarily. Immediately upstream The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. - - - directly inhibits molecularly decreases activity of directly negatively regulates activity of @@ -6070,9 +4138,6 @@ For example, A and B may be gene products and binding of B by A negatively regul The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. - - - directly activates molecularly increases activity of directly positively regulates activity of @@ -6082,8 +4147,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. helper property (not for use in curation) @@ -6095,16 +4158,8 @@ For example, A and B may be gene products and binding of B by A positively regul - 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. - - - - RO:0002473 - uberon - composed_primarily_of - composed_primarily_of composed primarily of @@ -6115,24 +4170,10 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. - has part that occurs in - - - - - - - - true - @@ -6140,7 +4181,6 @@ For example, A and B may be gene products and binding of B by A positively regul - is kinase activity @@ -6152,7 +4192,6 @@ For example, A and B may be gene products and binding of B by A positively regul See notes for inverse relation - receives input from @@ -6163,7 +4202,6 @@ For example, A and B may be gene products and binding of B by A positively regul This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. - sends output to @@ -6174,8 +4212,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. relation between physical entity and a process or stage @@ -6191,11 +4227,6 @@ For example, A and B may be gene products and binding of B by A positively regul x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). - - RO:0002488 - uberon - existence_starts_during - existence_starts_during existence starts during @@ -6206,11 +4237,6 @@ For example, A and B may be gene products and binding of B by A positively regul x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). - - RO:0002489 - uberon - existence_starts_with - existence_starts_with existence starts with @@ -6221,7 +4247,6 @@ For example, A and B may be gene products and binding of B by A positively regul x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence overlaps @@ -6234,12 +4259,7 @@ For example, A and B may be gene products and binding of B by A positively regul x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) - - RO:0002491 exists during - uberon - existence_starts_and_ends_during - existence_starts_and_ends_during The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts and ends during @@ -6255,23 +4275,10 @@ For example, A and B may be gene products and binding of B by A positively regul - Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). - - RO:0002492 - ceases_to_exist_during - uberon - existence_ends_during - existence_ends_during The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during - - - - Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. - https://orcid.org/0000-0002-6601-2165 - @@ -6280,11 +4287,6 @@ For example, A and B may be gene products and binding of B by A positively regul x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). - - RO:0002493 - uberon - existence_ends_with - existence_ends_with The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends with @@ -6297,11 +4299,6 @@ For example, A and B may be gene products and binding of B by A positively regul x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships - - RO:0002494 - uberon - transformation_of - transformation_of transformation of @@ -6313,12 +4310,6 @@ For example, A and B may be gene products and binding of B by A positively regul x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t - - - RO:0002495 - uberon - immediate_transformation_of - immediate_transformation_of immediate transformation of @@ -6349,11 +4340,6 @@ For example, A and B may be gene products and binding of B by A positively regul x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). - - RO:0002496 - uberon - existence_starts_during_or_after - existence_starts_during_or_after The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts during or after @@ -6385,11 +4371,6 @@ For example, A and B may be gene products and binding of B by A positively regul x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. - - RO:0002497 - uberon - existence_ends_during_or_before - existence_ends_during_or_before The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during or before @@ -6402,7 +4383,6 @@ For example, A and B may be gene products and binding of B by A positively regul A relationship between a material entity and a process where the material entity has some causal role that influences the process - causal agent in process @@ -6415,9 +4395,6 @@ For example, A and B may be gene products and binding of B by A positively regul p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. - - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes @@ -6426,7 +4403,6 @@ For example, A and B may be gene products and binding of B by A positively regul - depends on @@ -6440,9 +4416,6 @@ For example, A and B may be gene products and binding of B by A positively regul The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch - - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between entities @@ -6456,18 +4429,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - - Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. - - has supporting framework - The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). - RO:0002551 - uberon - has_skeleton - has_skeleton has skeleton @@ -6484,9 +4447,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - causally influenced by (entity-centric) causally influenced by @@ -6496,7 +4456,6 @@ For example, A and B may be gene products and binding of B by A positively regul - interaction relation helper property http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ @@ -6508,7 +4467,6 @@ For example, A and B may be gene products and binding of B by A positively regul - molecular interaction relation helper property @@ -6519,8 +4477,6 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - - RO:0002565 external results_in_movement_of @@ -6550,10 +4506,6 @@ For example, A and B may be gene products and binding of B by A positively regul The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). - - - - causally influences (entity-centric) causally influences @@ -6566,8 +4518,6 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between elements of a musculoskeletal system or its analogs. - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. biomechanically related to @@ -6578,12 +4528,6 @@ For example, A and B may be gene products and binding of B by A positively regul m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. - - Wikipedia:Antagonist_(muscle) - RO:0002568 - uberon - has_muscle_antagonist - has_muscle_antagonist has muscle antagonist @@ -6596,13 +4540,8 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of branching part of - - RO:0002569 - uberon - has_branching_part - has_branching_part has branching part @@ -6615,14 +4554,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. - - UBERON:cjm - This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. - RO:0002570 - uberon - conduit_for - conduit_for conduit for @@ -6634,13 +4566,7 @@ For example, A and B may be gene products and binding of B by A positively regul x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - - - RO:0002571 - uberon - lumen_of - lumen_of lumen of @@ -6652,12 +4578,7 @@ For example, A and B may be gene products and binding of B by A positively regul s is luminal space of x iff s is lumen_of x and s is an immaterial entity - - RO:0002572 - uberon - luminal_space_of - luminal_space_of luminal space of @@ -6670,12 +4591,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has skeleton - - RO:0002576 - uberon - skeleton_of - skeleton_of skeleton of @@ -6687,10 +4603,6 @@ For example, A and B may be gene products and binding of B by A positively regul p directly regulates q iff p is immediately causally upstream of q and p regulates q. - - - directly regulates (processual) - RO:0002578 external directly_regulates @@ -6712,9 +4624,7 @@ For example, A and B may be gene products and binding of B by A positively regul - gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p - has part structure that is capable of @@ -6784,8 +4694,6 @@ For example, A and B may be gene products and binding of B by A positively regul A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - - causal relation between material entity and a process @@ -6799,9 +4707,7 @@ For example, A and B may be gene products and binding of B by A positively regul - pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. - capable of regulating @@ -6816,7 +4722,6 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. - capable of negatively regulating @@ -6830,9 +4735,7 @@ For example, A and B may be gene products and binding of B by A positively regul - renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. - capable of positively regulating @@ -6843,7 +4746,6 @@ For example, A and B may be gene products and binding of B by A positively regul Inverse of 'causal agent in process' - RO:0002608 external process_has_causal_agent @@ -6859,9 +4761,6 @@ For example, A and B may be gene products and binding of B by A positively regul p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. - - directly positively regulates (process to process) - RO:0002629 external directly_positively_regulates @@ -6881,8 +4780,6 @@ For example, A and B may be gene products and binding of B by A positively regul p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. - - directly negatively regulates (process to process) RO:0002630 external @@ -6909,12 +4806,9 @@ For example, A and B may be gene products and binding of B by A positively regul - a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. - RO:0003000 external - uberon produces produces @@ -6930,12 +4824,9 @@ For example, A and B may be gene products and binding of B by A positively regul - a produced_by b iff some process that occurs_in b has_output a. - RO:0003001 external - uberon produced_by produced_by @@ -7042,7 +4933,6 @@ For example, A and B may be gene products and binding of B by A positively regul - 2018-01-26T23:49:30Z @@ -7080,7 +4970,6 @@ For example, A and B may be gene products and binding of B by A positively regul c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive - 2018-01-26T23:53:14Z @@ -7127,7 +5016,6 @@ For example, A and B may be gene products and binding of B by A positively regul - 2018-03-13T23:55:19Z causally upstream of or within, positive effect @@ -7143,7 +5031,6 @@ For example, A and B may be gene products and binding of B by A positively regul The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. - regulates activity of @@ -7391,7 +5278,6 @@ For example, A and B may be gene products and binding of B by A positively regul - 'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)') A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. @@ -7411,7 +5297,6 @@ For example, A and B may be gene products and binding of B by A positively regul - 'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor') A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. @@ -7433,12 +5318,7 @@ For example, A and B may be gene products and binding of B by A positively regul - A diagnostic testing device utilizes a specimen. X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. - - - A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. - See github ticket https://github.com/oborel/obo-relations/issues/497 2021-11-08T12:00:00Z utilizes device utilizes material @@ -7564,7 +5444,6 @@ For example, A and B may be gene products and binding of B by A positively regul - x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y. @@ -7584,8 +5463,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - carries uberon channel_for @@ -7597,7 +5474,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uberon channels_from channels_from @@ -7608,7 +5484,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uberon channels_into channels_into @@ -7619,10 +5494,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y. uberon distally_connected_to @@ -7641,11 +5514,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y uberon extends_fibers_into @@ -7675,11 +5543,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - @@ -7707,7 +5570,6 @@ For example, A and B may be gene products and binding of B by A positively regul - x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y. uberon @@ -7736,7 +5598,6 @@ For example, A and B may be gene products and binding of B by A positively regul - x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y. @@ -7790,7 +5651,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uberon transitively_anteriorly_connected_to transitively anteriorly connected to @@ -7802,7 +5662,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uberon transitively_distally_connected_to transitively distally connected to @@ -7814,7 +5673,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uberon transitively_proximally_connected_to transitively proximally connected to @@ -8024,13 +5882,14 @@ For example, A and B may be gene products and binding of B by A positively regul - Any fibroblast that is deriived from the neural crest. - fibroblast neural crest derived + Any fibroblast that is derived from the neural crest. + fibroblast neural crest derived + neural crest derived fibroblast - Any fibroblast that is deriived from the neural crest. + Any fibroblast that is derived from the neural crest. https://orcid.org/0000-0001-5208-3432 @@ -13529,15 +11388,21 @@ radial glial cells acting as neural progenitors throughout life. - - - - - - + + camera type eye photoreceptor cell camera-type eye photoreceptor cell + + + + + + + + + https://github.com/obophenotype/cell-ontology/issues/2245 + @@ -14862,32 +12727,32 @@ plexiform layer. - - + + A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer - + - + - + PMID:12382326 - + PMID:12382326 @@ -23472,7 +21337,6 @@ plexiform layer. - GC_ID:1 PMID:15371245 ncbi_taxonomy @@ -23486,7 +21350,6 @@ plexiform layer. - GC_ID:1 Mus mice @@ -23505,7 +21368,7 @@ plexiform layer. mice - + @@ -23520,7 +21383,6 @@ plexiform layer. - NCBITaxon:85055 GC_ID:1 house mouse @@ -23548,7 +21410,6 @@ plexiform layer. - GC_ID:1 ncbi_taxonomy NCBITaxon:117570 @@ -23561,7 +21422,6 @@ plexiform layer. - NCBITaxon:40673 GC_ID:1 bony vertebrates @@ -23601,7 +21461,6 @@ plexiform layer. - GC_ID:1 ncbi_taxonomy NCBITaxon:1338369 @@ -23614,7 +21473,6 @@ plexiform layer. - GC_ID:1 PMID:11743200 PMID:11791233 @@ -23636,7 +21494,6 @@ plexiform layer. - GC_ID:1 mice and others ncbi_taxonomy @@ -23663,7 +21520,6 @@ plexiform layer. - GC_ID:1 PMID:23020233 PMID:30257078 @@ -23727,7 +21583,6 @@ plexiform layer. - GC_ID:1 PMID:11214319 PMID:12082125 @@ -23744,7 +21599,6 @@ plexiform layer. - GC_ID:1 PMID:11214319 PMID:12082125 @@ -23767,7 +21621,6 @@ plexiform layer. - GC_ID:1 tetrapods ncbi_taxonomy @@ -23787,7 +21640,6 @@ plexiform layer. - GC_ID:1 amniotes ncbi_taxonomy @@ -23807,7 +21659,6 @@ plexiform layer. - GC_ID:1 Theria ncbi_taxonomy @@ -23827,7 +21678,6 @@ plexiform layer. - GC_ID:1 ncbi_taxonomy Fungi/Metazoa group @@ -23854,7 +21704,6 @@ plexiform layer. - GC_ID:1 metazoans multicellular animals @@ -23895,7 +21744,6 @@ plexiform layer. - GC_ID:1 ncbi_taxonomy NCBITaxon:33213 @@ -23908,7 +21756,6 @@ plexiform layer. - GC_ID:1 deuterostomes ncbi_taxonomy @@ -23928,7 +21775,6 @@ plexiform layer. - GC_ID:1 PMID:15019624 PMID:15371245 @@ -23943,7 +21789,6 @@ plexiform layer. - NCBITaxon:109679 GC_ID:1 ncbi_taxonomy @@ -23957,7 +21802,6 @@ plexiform layer. - GC_ID:1 mammals ncbi_taxonomy @@ -23984,7 +21828,6 @@ plexiform layer. - GC_ID:1 ncbi_taxonomy NCBITaxon:6072 @@ -23997,7 +21840,6 @@ plexiform layer. - GC_ID:1 chordates ncbi_taxonomy @@ -24024,7 +21866,6 @@ plexiform layer. - GC_ID:1 Vertebrata vertebrates @@ -24058,7 +21899,6 @@ plexiform layer. - GC_ID:1 Gnathostomata jawed vertebrates @@ -24085,7 +21925,6 @@ plexiform layer. - GC_ID:1 ncbi_taxonomy NCBITaxon:8287 @@ -24098,7 +21937,6 @@ plexiform layer. - GC_ID:1 Mus ncbi_taxonomy @@ -24118,7 +21956,6 @@ plexiform layer. - GC_ID:1 Craniata ncbi_taxonomy @@ -24138,7 +21975,6 @@ plexiform layer. - GC_ID:1 eutherian mammals placental mammals @@ -24186,7 +22022,6 @@ plexiform layer. - GC_ID:1 rodent ncbi_taxonomy @@ -24322,7 +22157,6 @@ plexiform layer. A branchiness quality inhering in a bearer by virtue of the bearer's having branches. - ramified ramiform quality @@ -24369,7 +22203,6 @@ plexiform layer. A morphological quality inhering in a bearer by virtue of the bearer's affording blocked passage or view. - quality blocked PATO:0000608 @@ -24435,7 +22268,6 @@ plexiform layer. A optical quality inhering in a bearer by virtue of the bearer's not being clear; not transmitting or reflecting light or radiant energy. - non-transparent quality clouding @@ -24459,7 +22291,6 @@ plexiform layer. A optical quality inhering in a bearer by virtue of the bearer's lacking opacity. - clear hyaline quality @@ -24755,7 +22586,6 @@ plexiform layer. A contractility quality inhering in a bearer by virtue of the bearer's ability of contracting or being contracted. - quality PATO:0001690 @@ -24777,7 +22607,6 @@ plexiform layer. A shape quality in a bearer by virtue of the bearer's curving inward. - quality PATO:0001857 @@ -24931,7 +22760,6 @@ plexiform layer. A complete three dimensional shape in which for every line connecting pair of points on the object is within the object. Or: a shape lacking cavities. Contrast: concave. - Image:http://upload.wikimedia.org/wikipedia/commons/0/06/Convex_polygon_illustration1.png quality PATO:0002007 @@ -24992,7 +22820,6 @@ plexiform layer. A concave quality inhering in a bearer by virtue of the bearer's curving inward on both sides or surfaces. - quality PATO:0002039 @@ -25630,7 +23457,6 @@ plexiform layer. PR:000001012 Category=gene. Requested by=CL. integrin alpha-M - @@ -25774,7 +23600,6 @@ plexiform layer. PR:000001024 Category=gene. Requested by=CL. neural cell adhesion molecule 1 - @@ -25859,7 +23684,6 @@ plexiform layer. PR:000001084 Category=gene. Requested by=CL. T-cell surface glycoprotein CD8 alpha chain - @@ -25988,7 +23812,6 @@ plexiform layer. PR:000001444 Category=gene. Requested by=CL. cadherin-5 - @@ -26021,7 +23844,6 @@ plexiform layer. PR:000001839 Category=gene. Requested by=CL. T-cell surface glycoprotein CD5 - @@ -26063,7 +23885,6 @@ plexiform layer. PR:000001869 Category=gene. Requested by=CL. interleukin-7 receptor subunit alpha - @@ -26128,7 +23949,6 @@ plexiform layer. PR:000001945 Category=gene. Requested by=CL. transferrin receptor protein 1 - @@ -26198,7 +24018,6 @@ plexiform layer. PR:000002112 Category=gene. Requested by=CL. vascular endothelial growth factor receptor 2 - @@ -26321,7 +24140,6 @@ plexiform layer. PR:000014841 Category=gene. sonic hedgehog protein - @@ -26363,7 +24181,6 @@ plexiform layer. PR:000016043 Category=gene. Requested by=CL. T-cell acute lymphocytic leukemia protein 1 - @@ -26618,11 +24435,10 @@ plexiform layer. - - + + - @@ -26630,9 +24446,6 @@ plexiform layer. An organ of sight that includes the camera-type eyeball and supporting structures such as the lacrimal apparatus, the conjunctiva, the eyelid. - A cavitated compound organ that transduces light waves into neural signals.[TAO] - The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] - FMA distinguishes Eye (subdivision of face) which has its parts an Eyeball (organ), as well as other structures, and the orbit of skull. MA includes eyelid, conjunctiva and lacrimal apparatus as part of MA:eye - consistent with FMA - so we can infer that MA:eye is more like FMA:eye than FMA:eyeball. For other AOs this distinction is less meaningful - e.g. ZFA has no eyelid; XAO has no eyelid, but it has conjuctiva, which is considered part of the xao:eye. GO considers eyelid development part of eye development. See also notes on optic nerve - XAO, AAO and BTO consider this part of the eye. MA considers the eye muscles part of the eye, whereas FMA has a class 'orbital content' for this eye AAO:0010340 BIRNLEX:1169 @@ -26663,16 +24476,6 @@ plexiform layer. camera-type eye - - - - - - - - - definitional - @@ -26680,31 +24483,6 @@ plexiform layer. GO:0043010 https://orcid.org/0000-0002-6601-2165 - - - - A cavitated compound organ that transduces light waves into neural signals.[TAO] - 2012-08-14 - TAO:0000107 - TAO - TAO:wd - - - - - The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] - 2012-09-17 - VHOG:0000275 - VHOG - DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007) - http://bgee.unil.ch/ - - - - - FMA distinguishes Eye (subdivision of face) which has its parts an Eyeball (organ), as well as other structures, and the orbit of skull. MA includes eyelid, conjunctiva and lacrimal apparatus as part of MA:eye - consistent with FMA - so we can infer that MA:eye is more like FMA:eye than FMA:eyeball. For other AOs this distinction is less meaningful - e.g. ZFA has no eyelid; XAO has no eyelid, but it has conjuctiva, which is considered part of the xao:eye. GO considers eyelid development part of eye development. See also notes on optic nerve - XAO, AAO and BTO consider this part of the eye. MA considers the eye muscles part of the eye, whereas FMA has a class 'orbital content' for this - FMA - @@ -26789,7 +24567,6 @@ plexiform layer. EHDAA2:0001824 EHDAA:500 EMAPA:35955 - FBbt:00005155 GAID:63 HAO:0000930 MA:0000017 @@ -26822,12 +24599,6 @@ plexiform layer. https://github.com/obophenotype/uberon/issues/549 https://orcid.org/0000-0002-6601-2165 - - - - FBbt:00005155 - - @@ -26913,8 +24684,6 @@ plexiform layer. Any hollow cylindrical anatomical structure containing a lumen through which substances are transported. - not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts) - tubular galen:Tube anatomical tube duct @@ -26948,10 +24717,6 @@ plexiform layer. The head is the anterior-most division of the body [GO]. - - Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO] - Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO] - Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG] AAO:0010335 AEO:0000106 BILA:0000115 @@ -26998,34 +24763,6 @@ plexiform layer. GO:0060322 Wikipedia:Head - - - - Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO] - 2012-06-20 - AAO:0010335 - AAO - AAO:BJB - - - - - Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO] - 2012-08-14 - TAO:0001114 - TAO - ZFIN:curator - - - - - Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG] - 2012-09-17 - VHOG:0001644 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.82 - http://bgee.unil.ch/ - @@ -27073,9 +24810,6 @@ plexiform layer. Multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer. - A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO] - a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP] - in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA. FMA:9581 GAID:19 MESH:D012704 @@ -27103,27 +24837,6 @@ plexiform layer. Wikipedia:Serous_membrane https://github.com/obophenotype/uberon/issues/86 - - - - A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO] - 2012-08-14 - TAO:0005425 - TAO - Wikipedia:Serous_membrane - - - - - a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP] - Wikipedia:Serous_membrane - - - - - in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA. - FMA - @@ -27219,10 +24932,8 @@ plexiform layer. Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. - in FMA, serosa is a wall UBERON:0009915 wall - EMAPA:25036 FMA:82482 galen:Wall wall of organ @@ -27238,12 +24949,6 @@ plexiform layer. Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. FMA:82482 - - - - in FMA, serosa is a wall - FMA - @@ -27279,7 +24984,6 @@ plexiform layer. CARO:0000003 EHDAA2:0003003 EMAPA:0 - FBbt:00007001 FMA:305751 FMA:67135 GAID:781 @@ -27307,12 +25011,6 @@ plexiform layer. Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. CARO:0000003 - - - - FBbt:00007001 - - @@ -27350,8 +25048,6 @@ plexiform layer. - Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. - CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4 BIRNLEX:4 CARO:0020004 EFO:0000634 @@ -27385,12 +25081,6 @@ plexiform layer. Wikipedia - - - - Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. - GO:0048513 - @@ -27412,8 +25102,6 @@ plexiform layer. A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity. FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction - Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball. - Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal. FMA:86140 uberon organ region with fixed fiat boundary @@ -27429,20 +25117,6 @@ plexiform layer. A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity. http://orcid.org/0000-0002-6601-2165 - - - - Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball. - FMA:86140 - 3 - - - - - Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal. - FMA:86140 - 1 - @@ -27475,7 +25149,6 @@ plexiform layer. A multicellular structure that is a part of an organ. - currently defined in a very broad sense, may be replaced by more specific classes in the future @@ -27632,7 +25305,6 @@ plexiform layer. - ncit:Death is an outcome XAO:0000437 XtroDO:0000085 uberon @@ -27647,12 +25319,6 @@ plexiform layer. End of the life of an organism. XAO:0000437 - - - - ncit:Death is an outcome - ncit - @@ -27781,12 +25447,9 @@ plexiform layer. - + The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm. merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube) - - (or external ectoderm) forms the following structures: Skin Epithelium of the mouth and nasal cavity saliavary glands, and glands of mouth and nasal cavity Enamel - as a side note dentin and dental pulp are formed from ectomesenchyme which is derived from ectoderm Epithelium of pineal and pituitary glands Lens and cornea of the eye Apical ectodermal ridge inducing development of the limb buds of the embryo. Sensory receptors in epidermis - BTO:0006242 EHDAA2:0001968 EHDAA:1494 EHDAA:350 @@ -27807,7 +25470,7 @@ plexiform layer. external ectoderm http://upload.wikimedia.org/wikipedia/commons/1/1d/Ectoderm.png - + @@ -27820,7 +25483,7 @@ plexiform layer. - + EHDAA2 @@ -27830,14 +25493,6 @@ plexiform layer. MGI:anna MP:0012532 - - - - BTO:0006242 - - - https://github.com/biopragmatics/biomappings - @@ -27871,7 +25526,6 @@ plexiform layer. Stage succeeding embryo, including mature structure. - In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997) BilaDO:0000003 OGES:000010 OGES:000014 @@ -27957,8 +25611,6 @@ plexiform layer. - the WBls class 'all stages' belongs here as it is the superclass of other WBls stages - we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage BILS:0000105 EFO:0000399 FBdv:00007012 @@ -28009,13 +25661,11 @@ plexiform layer. A stage at which the organism is a single cell produced by means of sexual reproduction. - As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG] BILS:0000106 BilaDO:0000005 EFO:0001322 EHDAA:27 FBdv:00005288 - IDOMAL:0000302 NCIT:C12601 PdumDv:0000100 VHOG:0000745 @@ -28041,24 +25691,6 @@ plexiform layer. A stage at which the organism is a single cell produced by means of sexual reproduction. Wikipedia:Zygote - - - - As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG] - 2012-09-17 - VHOG:0000745 - VHOG - ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107 - http://bgee.unil.ch/ - - - - - IDOMAL:0000302 - - - https://github.com/biopragmatics/biomappings - @@ -28206,7 +25838,7 @@ plexiform layer. - + @@ -28242,14 +25874,14 @@ plexiform layer. gastrula stage - + - + BILS @@ -28327,8 +25959,6 @@ plexiform layer. Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system. - - In zebrafish, the times of neurulation and segmentation overlap so extensively there is no distinct neurula period of development, such as occurs largely before segmentation in amphibian embryos. BILS:0000110 BilaDO:0000009 HsapDv:0000012 @@ -28415,7 +26045,6 @@ plexiform layer. A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses. UBERON:0005163 CARO:0001001 - FBbt:00005099 NLX:147821 funiculus nerve fiber bundle @@ -28432,12 +26061,6 @@ plexiform layer. FBC:DOS FBbt:00005099 - - - - FBbt:00005099 - - @@ -28451,12 +26074,6 @@ plexiform layer. - - - - - - @@ -28497,24 +26114,7 @@ plexiform layer. - - - - - - - - - - - - - - - - - @@ -28528,11 +26128,6 @@ plexiform layer. The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks). - Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO] - Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG] - oral - some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives - in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips AAO:0010355 BTO:0001090 BTO:0004698 @@ -28541,7 +26136,6 @@ plexiform layer. EHDAA2:0001326 EHDAA:542 EMAPA:16262 - FBbt:00003126 FMA:49184 GAID:75 MA:0000341 @@ -28587,12 +26181,6 @@ plexiform layer. https://github.com/obophenotype/uberon/issues/661 http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg - - - - - the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts - @@ -28600,37 +26188,6 @@ plexiform layer. Wikipedia:Mouth https://github.com/obophenotype/uberon/wiki/The-digestive-tract - - - - Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO] - 2012-06-20 - AAO:0010355 - AAO - AAO:BJB - - - - - Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG] - 2012-09-17 - VHOG:0000812 - VHOG - DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008) - http://bgee.unil.ch/ - - - - - in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips - FMA - - - - - FBbt:00003126 - - @@ -28721,22 +26278,17 @@ plexiform layer. - + - - + + A fluid that is composed of blood plasma and erythrocytes. - This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid. - A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO] - Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO] - relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] - Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG] AAO:0000046 BTO:0000089 CALOHA:TS-0079 @@ -28771,34 +26323,34 @@ plexiform layer. blood - + - + - + - + CL:tm - + https://github.com/obophenotype/uberon/issues/1330 - + Bgee:AN @@ -28810,42 +26362,6 @@ plexiform layer. http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/9 - - - - A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO] - 2012-08-14 - TAO:0000007 - TAO - ZFIN:curator - - - - - Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO] - 2012-06-20 - AAO:0000046 - AAO - AAO:LAP - - - - - relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] - 2012-06-20 - AAO:0000046 - AAO - - - - - Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG] - 2012-09-17 - VHOG:0000224 - VHOG - DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006) - http://bgee.unil.ch/ - @@ -29009,14 +26525,11 @@ plexiform layer. consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77 - Anatomical system that consists of the muscles of the body.[VSAO] - we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA AAO:0000307 BILA:0000088 BTO:0001369 BTO:0001485 EFO:0000801 - EMAPA:35578 FMA:72954 MA:0002888 MAT:0000025 @@ -29044,21 +26557,6 @@ plexiform layer. The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified]. VSAO:0000033 - - - - Anatomical system that consists of the muscles of the body.[VSAO] - 2012-08-14 - VSAO:0000033 - VSAO - VSAO:curator - - - - - we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA - MA - @@ -29102,7 +26600,12 @@ plexiform layer. - + + + + + + @@ -29120,7 +26623,6 @@ plexiform layer. CARO:0000004 EHDAA2:0003004 EMAPA:35178 - FBbt:00007019 FMA:9669 HAO:0000004 MA:0002450 @@ -29144,28 +26646,12 @@ plexiform layer. organism substance - - - - - - - - - this relationship may be too strong and may be weakened in future - Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007019 - - @@ -29220,7 +26706,6 @@ plexiform layer. BILA:0000005 CARO:0000005 EHDAA2:0003005 - FBbt:00007017 FMA:5897 HAO:0000005 NCIT:C94478 @@ -29244,12 +26729,6 @@ plexiform layer. Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures. http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007017 - - @@ -29281,7 +26760,6 @@ plexiform layer. BILA:0000006 CARO:0000006 EHDAA2:0003006 - FBbt:00007016 FMA:67165 HAO:0000006 TAO:0001836 @@ -29299,12 +26777,6 @@ plexiform layer. Anatomical entity that has mass. http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007016 - - @@ -29322,7 +26794,6 @@ plexiform layer. BILA:0000007 CARO:0000007 EHDAA2:0003007 - FBbt:00007015 FMA:67112 HAO:0000007 TAO:0001835 @@ -29341,12 +26812,6 @@ plexiform layer. Anatomical entity that has no mass. http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007015 - - @@ -29389,10 +26854,8 @@ plexiform layer. EHDAA:392 EMAPA:16103 EV:0100000 - FBbt:00004856 FMA:7149 HAO:0000011 - IDOMAL:0002460 MA:0000003 NCIT:C12919 SCTID:278195005 @@ -29432,20 +26895,6 @@ plexiform layer. system GO:0048731 - - - - FBbt:00004856 - - - - - - IDOMAL:0002460 - - - https://github.com/biopragmatics/biomappings - @@ -29483,7 +26932,6 @@ plexiform layer. - organismal organism AAO:0010026 AEO:0000191 @@ -29498,7 +26946,6 @@ plexiform layer. EHDAA:1 EMAPA:25765 EV:0100016 - FBbt:00000001 FMA:256135 HAO:0000012 NCIT:C13041 @@ -29543,12 +26990,6 @@ plexiform layer. VHOG:0000671 WBbt:0007833 - - - - FBbt:00000001 - - @@ -29609,7 +27050,6 @@ plexiform layer. EFO:0000808 EHDAA2:0003032 EMAPA:36031 - FBbt:00007009 FMA:7153 HAO:0000032 MA:0002433 @@ -29652,12 +27092,6 @@ plexiform layer. CARO:DOS http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007009 - - @@ -29699,7 +27133,6 @@ plexiform layer. BILA:0000040 CARO:0000040 EHDAA2:0003040 - FBbt:00007013 FMA:63863 HAO:0000040 TAO:0000382 @@ -29725,12 +27158,6 @@ plexiform layer. Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue. http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007013 - - @@ -29749,7 +27176,6 @@ plexiform layer. - FBbt:00007277 VHOG:0001737 uberon UBERON:0000477 @@ -29763,12 +27189,6 @@ plexiform layer. Anatomical group whose component anatomical structures lie in close proximity to each other. FBbt:00007277 - - - - FBbt:00007277 - - @@ -29802,7 +27222,6 @@ plexiform layer. CARO:0000043 EHDAA2:0003043 EMAPA:35868 - FBbt:00007003 FMA:9637 HAO:0000043 MA:0003002 @@ -29838,12 +27257,6 @@ plexiform layer. Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. CARO:0000043 - - - - FBbt:00007003 - - @@ -29884,7 +27297,6 @@ plexiform layer. BILA:0000055 CARO:0000055 EHDAA2:0003055 - FBbt:00007010 HAO:0000055 TAO:0001488 TGMA:0001847 @@ -29911,12 +27323,6 @@ plexiform layer. CARO:0000055 http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007010 - - @@ -29955,7 +27361,7 @@ plexiform layer. - + @@ -29963,8 +27369,6 @@ plexiform layer. Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]. - The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG] - epithelial AAO:0000144 AAO:0010055 AEO:0000066 @@ -29974,7 +27378,6 @@ plexiform layer. CARO:0000066 EHDAA2:0003066 EMAPA:32738 - FBbt:00007005 FMA:9639 GAID:402 HAO:0000066 @@ -29999,14 +27402,14 @@ plexiform layer. epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg - + - + http://palaeos.com/metazoa/porifera/homoscleromorpha.html @@ -30016,22 +27419,6 @@ plexiform layer. Wikipedia:Epithelium http://orcid.org/0000-0001-9114-8737 - - - - The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG] - 2012-09-17 - VHOG:0000387 - VHOG - ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.59 - http://bgee.unil.ch/ - - - - - FBbt:00007005 - - @@ -30064,7 +27451,6 @@ plexiform layer. Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA]. - Unilaminar epithelium that consists of a single layer of squamous cells.[CARO] AAO:0010066 AEO:0000070 BILA:0000070 @@ -30096,16 +27482,6 @@ plexiform layer. Wikipedia:Simple_squamous_epithelium http://orcid.org/0000-0001-9114-8737 - - - - Unilaminar epithelium that consists of a single layer of squamous cells.[CARO] - 2012-06-20 - CARO:0000070 - CARO - FMA:45565 - http://orcid.org/0000-0001-9114-8737 - @@ -30182,7 +27558,6 @@ plexiform layer. Compound organ that contains one or more macroscopic anatomical spaces. - this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future AAO:0010016 AEO:0000072 BILA:0000072 @@ -30231,7 +27606,6 @@ plexiform layer. Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA]. consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable - Epithelium that consists of a single layer of epithelial cells.[CARO] AAO:0010062 AEO:0000073 BILA:0000073 @@ -30260,16 +27634,6 @@ plexiform layer. FMA:45561 http://orcid.org/0000-0001-9114-8737 - - - - Epithelium that consists of a single layer of epithelial cells.[CARO] - 2012-06-20 - CARO:0000073 - CARO - FMA:45561 - http://orcid.org/0000-0001-9114-8737 - @@ -30315,10 +27679,6 @@ plexiform layer. Subdivision of trunk that lies between the head and the abdomen. - note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest - - - EMAPA:35862 FMA:259209 MA:0000022 @@ -30392,8 +27752,6 @@ plexiform layer. Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. - embryonic - Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo AAO:0011035 AEO:0000169 BILA:0000056 @@ -30405,10 +27763,8 @@ plexiform layer. EHDAA2_RETIRED:0003236 EHDAA:38 EMAPA:16039 - FBbt:00000052 FMA:69068 GAID:963 - IDOMAL:0000646 MAT:0000226 MESH:D004622 MIAA:0000019 @@ -30444,26 +27800,6 @@ plexiform layer. GO:0009790 Wikipedia:Embryo - - - - Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo - ZFA - - - - - FBbt:00000052 - - - - - - IDOMAL:0000646 - - - https://github.com/biopragmatics/biomappings - @@ -30496,13 +27832,11 @@ plexiform layer. A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm. - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] embryonic tissue AAO:0000480 BILA:0000035 BTO:0000556 EMAPA:36033 - FBbt:00000110 FMA:69069 GAID:1303 MESH:D005855 @@ -30533,28 +27867,12 @@ plexiform layer. Wikipedia:Germ_layer https://github.com/obophenotype/uberon/issues/203 - - - - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - 2012-09-17 - VHOG:0001223 - VHOG - ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 - http://bgee.unil.ch/ - embryonic tissue FMA:69069 - - - - FBbt:00000110 - - @@ -30593,11 +27911,8 @@ plexiform layer. - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. - Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO] - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - ectodermal AAO:0000137 BILA:0000036 BTO:0000315 @@ -30606,7 +27921,6 @@ plexiform layer. EHDAA2:0000428 EMAPA:16069 EV:0100003 - FBbt:00000111 FMA:69070 GAID:1304 MAT:0000155 @@ -30631,14 +27945,14 @@ plexiform layer. ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -30647,31 +27961,6 @@ plexiform layer. Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. Wikipedia:Ectoderm - - - - Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO] - 2012-06-20 - AAO:0000137 - AAO - AAO:EJS - - - - - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - 2012-09-17 - VHOG:0000153 - VHOG - ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 - http://bgee.unil.ch/ - - - - - FBbt:00000111 - - @@ -30697,10 +27986,8 @@ plexiform layer. - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - endodermal AAO:0000139 BILA:0000038 BTO:0000800 @@ -30709,7 +27996,6 @@ plexiform layer. EHDAA2:0000436 EMAPA:16062 EV:0100005 - FBbt:00000125 FMA:69071 GAID:1305 MAT:0000175 @@ -30734,14 +28020,14 @@ plexiform layer. http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -30750,22 +28036,6 @@ plexiform layer. Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. Wikipedia:Endoderm - - - - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - 2012-09-17 - VHOG:0000154 - VHOG - ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 - http://bgee.unil.ch/ - - - - - FBbt:00000125 - - @@ -30792,13 +28062,9 @@ plexiform layer. - + The middle germ layer of the embryo, between the endoderm and ectoderm. - Primary germ layer that is the middle of the embryonic germ layers.[AAO] - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - mesodermal - sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates UBERON:0003263 AAO:0000304 BILA:0000037 @@ -30811,7 +28077,6 @@ plexiform layer. EHDAA:183 EMAPA:16083 EV:0100006 - FBbt:00000126 FMA:69072 GAID:522 MAT:0000174 @@ -30837,20 +28102,14 @@ plexiform layer. mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + - - sometimes not considered primary - - - - - + Bgee:AN @@ -30859,37 +28118,6 @@ plexiform layer. The middle germ layer of the embryo, between the endoderm and ectoderm. Wikipedia:Mesoderm - - - - Primary germ layer that is the middle of the embryonic germ layers.[AAO] - 2012-06-20 - AAO:0000304 - AAO - AAO:EJS - - - - - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - 2012-09-17 - VHOG:0000152 - VHOG - ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 - http://bgee.unil.ch/ - - - - - sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates - https://github.com/obophenotype/uberon/wiki/The-neural-crest - - - - - FBbt:00000126 - - @@ -30936,15 +28164,10 @@ plexiform layer. Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity. consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence - Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO] - the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx - stomodeal - This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity. stomodeal-hypophyseal primordium BTO:0004224 EHDAA2:0001929 EMAPA:16263 - FBbt:00000439 FMA:295846 NCIT:C34306 TAO:0001290 @@ -30977,34 +28200,12 @@ plexiform layer. http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/326 - - - - Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO] - 2012-08-14 - TAO:0001290 - TAO - ZFIN:curator - - - - - the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx - MP:0012522 - NCBITaxon:40674 - stomodeal-hypophyseal primordium XAO:0000269 - - - - FBbt:00000439 - - @@ -31069,7 +28270,6 @@ plexiform layer. - @@ -31084,7 +28284,7 @@ plexiform layer. - + @@ -31099,10 +28299,6 @@ plexiform layer. Cranial nerve fiber tract which is comprised of retinal ganglion cell axons running posterior medially towards the optic chiasm, at which some of the axons cross the midline and after which the structure is termed the optic tract. Transmits visual information from the retina to the brain[ZFA]. Do not classify under 'cranial nerve', as this is not a true nerve - should be classified as evaginated sensory afferent[ISBN:0471888893] - A collection of nerve cells that project visual information from the eyes to the brain. (Source: BioGlossary, www.Biology-Text.com)[TAO] - Fibrous, somatic sensory element covered by a fibrous connective-tissue sheath and is continuous with the layer of nerve cells on the inner surface of the eye.[AAO] - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup (reference 1); The (optic) stalk persists as the optic nerve (reference 2).[well established][VHOG] - (relaion to eye): MA, XAO, AAO and BTO consider this part of the eye. This is in contrast to GO, FMA, EHDAA2 (FMA has a class 'intra-ocular part of optic nerve' which represents the region of overlap). Relation to brain: part of diencephalon in EHDAA2, ZFA. In NIF, has the optic nerve root as part, which is a feature part of the diencphalon 2n optic nerve AAO:0010345 @@ -31150,14 +28346,14 @@ plexiform layer. cranial nerve II - + - + EHDAA2 @@ -31167,40 +28363,6 @@ plexiform layer. ISBN:0471209627 ISBN:0471888893 - - - - A collection of nerve cells that project visual information from the eyes to the brain. (Source: BioGlossary, www.Biology-Text.com)[TAO] - 2012-08-14 - TAO:0000435 - TAO - ZFIN:curator - - - - - Fibrous, somatic sensory element covered by a fibrous connective-tissue sheath and is continuous with the layer of nerve cells on the inner surface of the eye.[AAO] - 2012-06-20 - AAO:0010345 - AAO - AAO:EJS - - - - - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup (reference 1); The (optic) stalk persists as the optic nerve (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0000543 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429, http://medical-dictionary.thefreedictionary.com/optic+stalk - http://bgee.unil.ch/ - - - - - (relaion to eye): MA, XAO, AAO and BTO consider this part of the eye. This is in contrast to GO, FMA, EHDAA2 (FMA has a class 'intra-ocular part of optic nerve' which represents the region of overlap). Relation to brain: part of diencephalon in EHDAA2, ZFA. In NIF, has the optic nerve root as part, which is a feature part of the diencphalon - MA - @@ -31301,7 +28463,7 @@ plexiform layer. - + @@ -31330,11 +28492,6 @@ plexiform layer. - Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO] - Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO] - relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO] - As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG] - cardiac AAO:0010210 BILA:0000020 BTO:0000562 @@ -31378,14 +28535,14 @@ plexiform layer. https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb - + - + MA @@ -31395,42 +28552,6 @@ plexiform layer. Wikipedia:Heart http://orcid.org/0000-0002-6601-2165 - - - - Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO] - 2012-08-14 - TAO:0000114 - TAO - ZFIN:curator - - - - - Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO] - 2012-06-20 - AAO:0010210 - AAO - AAO:BJB - - - - - relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO] - 2012-06-20 - AAO:0010210 - AAO - - - - - As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG] - 2012-09-17 - VHOG:0000276 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481 - http://bgee.unil.ch/ - @@ -31463,13 +28584,7 @@ plexiform layer. - - - - - - - + @@ -31488,14 +28603,10 @@ plexiform layer. - + The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. requires review for applicability to invertebrate structures, e.g. synganglion - Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO] - Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO] - The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO) - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG] AAO:0010478 ABA:Brain BAMS:Br @@ -31511,7 +28622,6 @@ plexiform layer. EHDAA:6485 EMAPA:16894 EV:0100164 - FBbt:00005095 FMA:50801 GAID:571 HBA:4005 @@ -31551,11 +28661,11 @@ plexiform layer. https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_F_Brain.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/Allen_M_Brain.glb - + - + @@ -31568,13 +28678,13 @@ plexiform layer. - + FMA - + Bgee:AN @@ -31584,46 +28694,6 @@ plexiform layer. Wikipedia:Brain https://github.com/obophenotype/uberon/issues/300 - - - - Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO] - 2012-08-14 - TAO:0000008 - TAO - ZFIN:curator - - - - - Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO] - 2012-06-20 - AAO:0010478 - AAO - AAO:BJB - - - - - The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO) - http://neurolex.org/wiki/Cumbo_terms - - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0000157 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 - http://bgee.unil.ch/ - - - - - FBbt:00005095 - - @@ -31693,7 +28763,6 @@ plexiform layer. Any thin layer or plate. TODO - merge with cell layer? - laminar Wikipedia:Lamina_of_the_vertebral_arch laminar tissue uberon @@ -31749,8 +28818,6 @@ plexiform layer. A decussation of the diencephalon where the fibers of the optic nerve cross. - The point at which fibers of the optic nerves cross.[AAO] - The chiasm has been studied in great detail in some animals, while in others relatively little or nothing is known. Although there are some gross architectural features that are conserved within some animals, such as birds and fish, the general picture is one of diversity. This review will attempt to consider the key features of such diversity of chiasmatic organisation in vertebrates and the mechanisms that sculpt them from the limited literature that is available. However, as so much research has been undertaken on the structure and development of the chiasm in laboratory animals, any review must consider the information that has been gleaned from them and hope that future studies will determine whether the features revealed in these animals, and the underlying mechanisms that generate them, have a common vertebrate plan.[uncertain][VHOG] AAO:0010622 BAMS:DC BAMS:OC @@ -31801,25 +28868,6 @@ plexiform layer. Wikipedia:Optic_chiasm http://orcid.org/0000-0002-6601-2165 - - - - The point at which fibers of the optic nerves cross.[AAO] - 2012-06-20 - AAO:0010622 - AAO - AAO:DSM - - - - - The chiasm has been studied in great detail in some animals, while in others relatively little or nothing is known. Although there are some gross architectural features that are conserved within some animals, such as birds and fish, the general picture is one of diversity. This review will attempt to consider the key features of such diversity of chiasmatic organisation in vertebrates and the mechanisms that sculpt them from the limited literature that is available. However, as so much research has been undertaken on the structure and development of the chiasm in laboratory animals, any review must consider the information that has been gleaned from them and hope that future studies will determine whether the features revealed in these animals, and the underlying mechanisms that generate them, have a common vertebrate plan.[uncertain][VHOG] - 2012-09-17 - VHOG:0000190 - VHOG - DOI:10.1016/j.preteyeres.2005.04.005 Jeffery G, Erskine L, Variations in the architecture and development of the vertebrate optic chiasm. Progress in retinal and eye research (2005) - http://bgee.unil.ch/ - @@ -31881,9 +28929,9 @@ plexiform layer. - - - + + + @@ -31908,7 +28956,12 @@ plexiform layer. - + + + + + + @@ -31929,8 +28982,6 @@ plexiform layer. The transparent anterior portion of the fibrous coat of the eye that serves as the chief refractory structure. - corneal - Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals. In fish, and aquatic vertebrates in general, the cornea plays no role in focusing light, since it has virtually the same refractive index as water AAO:0010344 BTO:0000286 CALOHA:TS-0171 @@ -31964,46 +29015,36 @@ plexiform layer. cornea http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + - - - - - + MA - + MA - + FMA-isa - - - - - definitional - @@ -32037,6 +29078,7 @@ plexiform layer. + @@ -32063,10 +29105,7 @@ plexiform layer. A transparent and refractive lens located posterior to the iris. The lens of camera-type eye refracts light to be focused on the retina. - - The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] - This class excludes compound eye corneal lenses. AAO:0010348 BTO:0000723 CALOHA:TS-0545 @@ -32110,16 +29149,6 @@ plexiform layer. Wikipedia:Lens_(anatomy) http://orcid.org/0000-0002-6601-2165 - - - - The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] - 2012-09-17 - VHOG:0000169 - VHOG - DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007) - http://bgee.unil.ch/ - @@ -32190,16 +29219,13 @@ plexiform layer. - - - - + + + + The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. - The portion of the eye developing from the optic primordium and including the neural retina and the retinal pigment layer. Kimmel et al, 1995.[TAO] - The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] - retinal AAO:0010352 BAMS:R BIRNLEX:1153 @@ -32244,44 +29270,44 @@ plexiform layer. retina http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png - + - + - + - + - + FMA - + FMA - + FMA - + EHDAA2 @@ -32291,25 +29317,6 @@ plexiform layer. Wikipedia:Retina ZFIN:curator - - - - The portion of the eye developing from the optic primordium and including the neural retina and the retinal pigment layer. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000152 - TAO - ZFIN:curator - - - - - The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] - 2012-09-17 - VHOG:0000229 - VHOG - DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007) - http://bgee.unil.ch/ - @@ -32355,8 +29362,8 @@ plexiform layer. - - + + @@ -32364,17 +29371,12 @@ plexiform layer. An organ that detects light. - This class encompasses a variety of light-detecting structures from different phyla with no implication of homology, from the compound insect eye to the vertebrate camera-type eye (distinct classes are provided for each) - ocular - optic - Note that whilst this is classified as an organ, it is in fact more of a unit composed of different structures: in Drosophila, it includes the interommatidial bristle as a part; we consider here the vertebrate eye to include the eyeball/eye proper as a part, with the eye having as parts (when present): eyelids, conjuctiva, BILA:0000017 BTO:0000439 CALOHA:TS-0309 EFO:0000827 EV:0100336 - FBbt:00005162 GAID:69 MAT:0000140 MESH:D005123 @@ -32392,24 +29394,24 @@ plexiform layer. eye - + - + - + PMID:21062451 - + PMID:21062451 @@ -32418,12 +29420,6 @@ plexiform layer. An organ that detects light. https://orcid.org/0000-0002-6601-2165 - - - - FBbt:00005162 - - @@ -32450,8 +29446,6 @@ plexiform layer. Anatomical structure that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO]. - Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO] - Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO] articulation joint AEO:0000182 @@ -32496,24 +29490,6 @@ plexiform layer. Wikipedia:Joint http://dx.plos.org/10.1371/journal.pone.0051070 - - - - Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO] - 2012-08-14 - VSAO:0000101 - VSAO - PSPUB:0000170 - - - - - Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO] - 2012-08-14 - TAO:0000367 - TAO - TAO:pem - @@ -32584,16 +29560,11 @@ plexiform layer. Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes. - An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO] - digestive - many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class AAO:0000129 BILA:0000082 BTO:0000058 CALOHA:TS-1293 EFO:0000793 - EV:0100056 - FBbt:00005055 FMA:7152 GAID:278 MA:0002431 @@ -32630,27 +29601,6 @@ plexiform layer. NLM:alimentary+system Wikipedia:Digestive_system - - - - An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO] - 2012-06-20 - AAO:0000129 - AAO - AAO:BJB - - - - - many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class - MA - - - - - FBbt:00005055 - - @@ -32682,17 +29632,12 @@ plexiform layer. Organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP]. - the cardiovascular system and the lymphatic system are parts of the circulatory system - - Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO] - We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG] AAO:0000959 CALOHA:TS-2103 - MESH:D002319 VHOG:0001248 Wikipedia:Circulatory_system uberon @@ -32715,38 +29660,6 @@ plexiform layer. Wikipedia:Acoelomorpha - - - - - WBbt coelomocyte currently classified as circulating cell - - - - - Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO] - 2012-06-20 - AAO:0000959 - AAO - AAO:BJB - - - - - We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG] - 2012-09-17 - VHOG:0001248 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.493 - http://bgee.unil.ch/ - - - - - MESH:D002319 - - https://github.com/biopragmatics/biomappings - @@ -32774,12 +29687,8 @@ plexiform layer. A subdivision of the muscular system corresponding to a subdisivision of an organism. - - In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here. - AAO:0011066 BTO:0000887 EFO:0001949 - EMAPA:32715 EMAPA:35577 FMA:32558 MA:0000165 @@ -32815,12 +29724,6 @@ plexiform layer. Wikipedia:Muscular_system https://orcid.org/0000-0002-6601-2165 - - - - In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here. - FMA - @@ -32884,7 +29787,7 @@ plexiform layer. - + @@ -32892,11 +29795,6 @@ plexiform layer. The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]. - A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO] - Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO] - Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG] - nervous - neural AAO:0000324 BILA:0000079 BIRNLEX:844 @@ -32907,7 +29805,6 @@ plexiform layer. EHDAA:826 EMAPA:16469 EV:0100162 - FBbt:00005093 FMA:7157 GAID:466 MA:0000016 @@ -32939,14 +29836,14 @@ plexiform layer. http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -32961,40 +29858,6 @@ plexiform layer. Wikipedia:Nervous_system ZFIN:curator - - - - A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO] - 2012-08-14 - TAO:0000396 - TAO - ZFIN:curator - - - - - Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO] - 2012-06-20 - AAO:0000324 - AAO - AAO:BJB - - - - - Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG] - 2012-09-17 - VHOG:0000402 - VHOG - ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.117 - http://bgee.unil.ch/ - - - - - FBbt:00005093 - - @@ -33040,14 +29903,10 @@ plexiform layer. - + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. - Part of the nervous system which includes the brain and spinal cord.[AAO] - The brain and spinal cord. Kimmel et al, 1995.[TAO] - The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO). - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG] AAO:0000090 BAMS:CNS BILA:0000080 @@ -33060,7 +29919,6 @@ plexiform layer. EMAPA:16470 EMAPA:16754 EV:0100163 - FBbt:00005094 FMA:55675 GAID:570 MA:0000167 @@ -33089,7 +29947,7 @@ plexiform layer. central nervous system - + @@ -33103,7 +29961,7 @@ plexiform layer. - + Bgee:AN @@ -33120,46 +29978,6 @@ plexiform layer. Wikipedia:Acoelomorpha - - - - Part of the nervous system which includes the brain and spinal cord.[AAO] - 2012-06-20 - AAO:0000090 - AAO - AAO:BJB - - - - - The brain and spinal cord. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000012 - TAO - ZFIN:curator - - - - - The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO). - BIRNLEX:1099 - - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG] - 2012-09-17 - VHOG:0000293 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 (reference 1), ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 (reference 2), DOI:10.1016/j.cell.2007.02.040 Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud'homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007) (reference 3) - http://bgee.unil.ch/ - - - - - FBbt:00005094 - - @@ -33202,10 +30020,8 @@ plexiform layer. A group of axons linking two or more neuropils and having a common origin, termination[FBbt]. - White matter structure of CNS that contains axons that arise predominantly in one central nervous system part and terminate in another. Tracts are generally named by their region or origin followed by their region of primary termination, e.g., mammillothalamic tract contains axons that arise from neurons in the mammillary bodies and terminate in the thalamus. (CUMBO) BIRNLEX:1649 EV:0100304 - FBbt:00005100 FMA:83847 NLX:147822 axonal tract @@ -33228,18 +30044,6 @@ plexiform layer. http://flybrain.uni-freiburg.de/Flybrain/html/terms/terms.html https://github.com/obophenotype/uberon/issues/286 - - - - White matter structure of CNS that contains axons that arise predominantly in one central nervous system part and terminate in another. Tracts are generally named by their region or origin followed by their region of primary termination, e.g., mammillothalamic tract contains axons that arise from neurons in the mammillary bodies and terminate in the thalamus. (CUMBO) - http://neurolex.org/wiki/Cumbo_terms - - - - - FBbt:00005100 - - @@ -33361,15 +30165,12 @@ plexiform layer. Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information. - An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG] - note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs AAO:0000555 BAMS:SEN BILA:0000099 EFO:0000805 EHDAA2:0003094 EMAPA:16192 - FBbt:00007692 FMA:75259 MA:0002442 MAT:0000031 @@ -33403,22 +30204,6 @@ plexiform layer. Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information. Wikipedia:Sensory_system - - - - An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG] - 2012-09-17 - VHOG:0001674 - VHOG - DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) - http://bgee.unil.ch/ - - - - - FBbt:00007692 - - @@ -33477,7 +30262,6 @@ plexiform layer. BTO:0001886 EFO:0001652 EHDAA2:0003171 - FBbt:00005495 FMA:86589 MAT:0000482 NCIT:C34275 @@ -33511,12 +30295,6 @@ plexiform layer. FB:FBrf0089570 http://flybase.org/reports/FBrf0178740.html - - - - FBbt:00005495 - - @@ -33553,10 +30331,6 @@ plexiform layer. In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted]. - Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO] - The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG] - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] - The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium AAO:0010617 BTO:0001057 CALOHA:TS-2371 @@ -33568,7 +30342,6 @@ plexiform layer. EMAPA:16757 FMA:293882 MAT:0000069 - MESH:D054259 MIAA:0000069 NCIT:C34226 SCTID:362852000 @@ -33602,49 +30375,6 @@ plexiform layer. In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted]. Wikipedia:Neural_tube - - - - Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO] - 2012-06-20 - AAO:0010617 - AAO - AAO:JOR - - - - - The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG] - 2012-09-17 - VHOG:0000307 - VHOG - http://bgee.unil.ch/ - http://medical-dictionary.thefreedictionary.com/neural+tube - - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] - 2012-09-17 - VHOG:0000307 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 - http://bgee.unil.ch/ - - - - - The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium - GO:0021915 - - - - - MESH:D054259 - - - https://github.com/biopragmatics/biomappings - @@ -33675,7 +30405,6 @@ plexiform layer. BIRNLEX:6 CARO:0000000 EHDAA2:0002229 - FBbt:10000000 FMA:62955 HAO:0000000 MA:0000001 @@ -33699,12 +30428,6 @@ plexiform layer. FMA:62955 http://orcid.org/0000-0001-9114-8737 - - - - FBbt:10000000 - - @@ -33748,10 +30471,6 @@ plexiform layer. Muscle tissue which is unstriated, composed primarily of smooth muscle fibers surrounded by a reticulum of collagen and elastic fibers. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length[GO]. - A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO] - Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO] - (...) the first bilateral animals possessed only smooth muscles with the molecular repertoire necessary to build a striated muscle. (...) it is more parsimonious to regard striated muscle cells as a sister cell type to the smooth muscle cells. In this scenario, striated and smooth muscles would have arisen in the stem lineage that led to the Nephrozoa (i.e. all Bilateria exclusive the acoelomorphs) (Hejnol et al., 2009), from an 'acoel-like' smooth muscle, by segregation and divergence of functions and through differential recruitment of additional genes[well established][VHOG] - GO uses visceral and smooth interchangeably. However visceral can also be used in the sense of the viscera. Many fly annotations to smooth muscle terms. If we want to be inclusive of insects have to have a general definition of tissue that includes cells. AAO:0010244 AEO:0000141 BTO:0001260 @@ -33799,34 +30518,6 @@ plexiform layer. GO:0006939 Wikipedia:Smooth_muscle_tissue - - - - A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO] - 2012-08-14 - TAO:0005274 - TAO - ZFIN:curator - - - - - Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO] - 2012-06-20 - AAO:0010244 - AAO - AAO:CAM - - - - - (...) the first bilateral animals possessed only smooth muscles with the molecular repertoire necessary to build a striated muscle. (...) it is more parsimonious to regard striated muscle cells as a sister cell type to the smooth muscle cells. In this scenario, striated and smooth muscles would have arisen in the stem lineage that led to the Nephrozoa (i.e. all Bilateria exclusive the acoelomorphs) (Hejnol et al., 2009), from an 'acoel-like' smooth muscle, by segregation and divergence of functions and through differential recruitment of additional genes[well established][VHOG] - 2012-09-17 - VHOG:0001246 - VHOG - DOI:10.1002/jez.b.21416 Chiodin M, Achatz JG, Wanninger A, Martinez P, Molecular architecture of muscles in an acoel and its evolutionary implications. Journal of Experimental Zoology (2011) - http://bgee.unil.ch/ - @@ -33889,7 +30580,7 @@ plexiform layer. - + Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. Wikipedia: The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri). AEO:0000111 BTO:0002422 @@ -33914,14 +30605,14 @@ plexiform layer. mesothelium http://upload.wikimedia.org/wikipedia/commons/2/25/Mesothelium_peritoneal_wash_high_mag.jpg - + - + FMA @@ -33951,8 +30642,6 @@ plexiform layer. A major subdivision of an organism that is the entire part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. In vertebrares this includes the vertebral column.. - dorsal - In humans, called the back, a large posterior area of the human body, rising from the top of the buttocks to the back of the neck and the shoulders. It is the surface opposite to the chest, its height being defined by the vertebral column (commonly referred to as the spine or backbone) and its breadth being supported by the ribcage and shoulders. The spinal canal runs through the spine and provides nerves to the rest of the body BTO:0001713 CALOHA:TS-2223 EFO:0001405 @@ -34050,13 +30739,6 @@ plexiform layer. Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system. - - Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO] - Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO] - System that provides physical support to the organism.[AAO] - By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG] - skeletal - GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates AAO:0000566 BTO:0001486 CALOHA:TS-1320 @@ -34092,50 +30774,6 @@ plexiform layer. VSAO:0000027 http://dx.plos.org/10.1371/journal.pone.0051070 - - - - Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO] - 2012-08-14 - TAO:0000434 - TAO - TAO:wd - - - - - Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO] - 2012-08-14 - VSAO:0000027 - VSAO - GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 - PSPUB:0000170 - - - - - System that provides physical support to the organism.[AAO] - 2012-06-20 - AAO:0000566 - AAO - AAO:LAP - - - - - By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG] - 2012-09-17 - VHOG:0001254 - VHOG - DOI:10.1159/000324245 Donoghue PCJ, Sansom IJ, Origin and early evolution of vertebrate skeletonization. Microscopy research and technique (2002) - http://bgee.unil.ch/ - - - - - GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates - GO - @@ -34198,10 +30836,6 @@ plexiform layer. A subdivision of the head that has as parts the layers deep to the surface of the anterior surface, including the mouth, eyes, and nose (when present). In vertebrates, this includes the facial skeleton and structures superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, etc). - Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face. - The area that extends from the median ocellus to the oral foramen[HAO]. - facial - The face develops from outward growth of tissue located rostral to the cranium & pharynx. The lower jaw and most of the upper jaw are formed by growth of the first pharyngeal (branchial) arch. The upper incisor region and the nose and forehead (frontal region) are formed from tissue located rostral to the neural tube (frontonasal prominence) BTO:0003369 CALOHA:TS-2216 EMAPA:32763 @@ -34230,26 +30864,6 @@ plexiform layer. A subdivision of the head that has as parts the layers deep to the surface of the anterior surface, including the mouth, eyes, and nose (when present). In vertebrates, this includes the facial skeleton and structures superficial to the facial skeleton (cheeks, mouth, eyeballs, skin of face, etc). http://orcid.org/0000-0002-6601-2165 - - - - Subdivision of head which consists of the viscerocranium and all layers superficial to it. Examples: There is only one face. - FMA:24728 - - - - - The area that extends from the median ocellus to the oral foramen[HAO]. - HAO:0000316 - http://api.hymao.org/api/ref/67791 - NCBITaxon:7399 - - - - - The face develops from outward growth of tissue located rostral to the cranium & pharynx. The lower jaw and most of the upper jaw are formed by growth of the first pharyngeal (branchial) arch. The upper incisor region and the nose and forehead (frontal region) are formed from tissue located rostral to the neural tube (frontonasal prominence) - vanat.cvm.umn.edu/TFFlectPDFs/LectFaceDevelop.pdf - @@ -34294,16 +30908,11 @@ plexiform layer. - + A tube extending from the mouth to the anus. - The alimentary or digestive tract, and associated organs.[TAO] - The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] - FMA also has a term 'gastrointestinal tract', but this includes the liver. - we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509 - we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this gut AAO:0010023 BILA:0000083 @@ -34312,10 +30921,8 @@ plexiform layer. EHDAA2:0000726 EHDAA:518 EMAPA:16247 - FBbt:00003125 FMA:45615 MA:0000917 - MESH:D041981 NCIT:C34082 TAO:0000112 TGMA:0001819 @@ -34337,14 +30944,14 @@ plexiform layer. digestive tract - + - + NCBIBook:NBK10107 @@ -34366,50 +30973,6 @@ plexiform layer. DOI:10.1371/journal.pone.0016309 - - - - The alimentary or digestive tract, and associated organs.[TAO] - 2012-08-14 - TAO:0000112 - TAO - ZFIN:curator - - - - - The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0000309 - VHOG - ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 - http://bgee.unil.ch/ - - - - - FMA also has a term 'gastrointestinal tract', but this includes the liver. - FMA - - - - - we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509 - MA - - - - - FBbt:00003125 - - - - - - MESH:D041981 - - https://github.com/biopragmatics/biomappings - @@ -34437,7 +31000,7 @@ plexiform layer. - + The ciliary muscle is a ring of smooth muscle in the middle layer of the eye that controls the eye's accommodation for viewing objects at varying distances and regulates the flow of aqueous humour through Schlemm's canal. [WP,unvetted]. BTO:0000654 @@ -34460,7 +31023,7 @@ plexiform layer. ciliary muscle http://upload.wikimedia.org/wikipedia/commons/2/28/Gray872.png - + @@ -34479,7 +31042,7 @@ plexiform layer. - + FMA @@ -34551,12 +31114,7 @@ plexiform layer. Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]. - Portion of tissue composed of contractile fibers.[TAO] - It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG] - muscular muscle - AAO:0011066 - EMAPA:32715 EMAPA:37474 EV:0100146 FMA:5022 @@ -34582,25 +31140,6 @@ plexiform layer. Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]. GO:0007517 - - - - Portion of tissue composed of contractile fibers.[TAO] - 2012-08-14 - TAO:0005145 - TAO - ZFIN:curator - - - - - It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG] - 2012-09-17 - VHOG:0001245 - VHOG - ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.75 - http://bgee.unil.ch/ - @@ -34620,7 +31159,8 @@ plexiform layer. - + + @@ -34640,12 +31180,6 @@ plexiform layer. A fold of skin that covers and protects part of the eyeball. Examples: upper eyelid, lower eyelid, nictitating membrane. - blepharic - palpebral - In humans the upper and lower eyelid consists of the following layers, starting anteriorly: (1) skin, (2) a layer of subcutaneous connective tissue, (3) a layer of striated muscle fibres of the orbicularis muscle, (4) a layer of submuscular connective tissue, (5) a fibrous layer, including the tarsal plates, (6) a layer of smooth muscle, (7) the palpebral conjunctiva. - Consider adding 'eye surface', like MA - FMA divides this into skin, fascia, conjunctiva - BTO:0002241 EHDAA2:0000487 EHDAA:9037 @@ -34672,14 +31206,14 @@ plexiform layer. eyelid https://upload.wikimedia.org/wikipedia/commons/8/84/Eye_makeup.jpg - + - + multiple @@ -34688,18 +31222,6 @@ plexiform layer. A fold of skin that covers and protects part of the eyeball. Examples: upper eyelid, lower eyelid, nictitating membrane. http://orcid.org/0000-0002-6601-2165 - - - - Consider adding 'eye surface', like MA - MA - - - - - FMA divides this into skin, fascia, conjunctiva - FMA - @@ -34738,8 +31260,6 @@ plexiform layer. The space in the eye, filled with aqueous humor, and bounded anteriorly by the cornea and a small portion of the sclera and posteriorly by a small portion of the ciliary body, the iris, and part of the crystalline lens. - The part of the eyeball between the cornea and the iris, filled with aqueous humor. [TFD][VHOG] - space in EHDAA2 - consider adding Cavity of anterior chamber of eyeball BTO:0002084 EHDAA2:0000129 EHDAA:9033 @@ -34779,22 +31299,6 @@ plexiform layer. MESH:A09.371.060.067 MP:0005205 - - - - The part of the eyeball between the cornea and the iris, filled with aqueous humor. [TFD][VHOG] - 2012-09-17 - VHOG:0001431 - VHOG - http://bgee.unil.ch/ - http://medical-dictionary.thefreedictionary.com/anterior+chamber - - - - - space in EHDAA2 - consider adding Cavity of anterior chamber of eyeball - EHDAA2 - @@ -34833,7 +31337,9 @@ plexiform layer. + + @@ -34867,7 +31373,6 @@ plexiform layer. The pigmented middle of the three concentric layers that make up an eye, consisting of the iris, ciliary body and choroid[WP,edited]. TODO - check child terms, isa vs partof. See also MA:0001284 ! tunica vasculosa plexus - uveal CALOHA:TS-2228 EMAPA:35901 FMA:58103 @@ -34974,7 +31479,7 @@ plexiform layer. - + @@ -34983,10 +31488,6 @@ plexiform layer. The adjustable membrane, composed of the stroma and pigmented epithelium, located just in front of the crystalline lens within the eye. - The opaque muscular contractile diaphragm suspended in the aqueous humour in front of the lens of the eye. The organ is perforated by the pupil and continues peripherally with the ciliary body. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] - The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] - iridial - The avian iris and ciliary body undergoes a transition from smooth-to-striated muscle during embryonic development [DOI:dx.doi.org/10.1006/dbio.1998.9019] AAO:0010347 BTO:0000653 CALOHA:TS-0491 @@ -35017,14 +31518,14 @@ plexiform layer. iris - + - + XAO @@ -35034,25 +31535,6 @@ plexiform layer. ISBN:0-683-40008-8 MP:0001322 - - - - The opaque muscular contractile diaphragm suspended in the aqueous humour in front of the lens of the eye. The organ is perforated by the pupil and continues peripherally with the ciliary body. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] - 2012-09-17 - VHOG:0000101 - VHOG - http://bgee.unil.ch/ - - - - - The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] - 2012-09-17 - VHOG:0000101 - VHOG - DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007) - http://bgee.unil.ch/ - @@ -35089,6 +31571,7 @@ plexiform layer. + @@ -35096,7 +31579,7 @@ plexiform layer. - + @@ -35105,9 +31588,6 @@ plexiform layer. The smooth stratified squamous epithelium that covers the outer surface of the cornea. - Portion of tissue comprised of four to six layers of nonkeratinized, stratified squamous cells and represents approximately 60% of the thickness of the cornea.[TAO] - In Humans: It consists of several layers of cells. The cells of the deepest layer are columnar; then follow two or three layers of polyhedral cells, the majority of which are prickle cells similar to those found in the stratum mucosum of the cuticle. Lastly, there are three or four layers of squamous cells, with flattened nuclei - In zebrafish: nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals BTO:0000287 CALOHA:TS-0173 EFO:0001917 @@ -35148,14 +31628,14 @@ plexiform layer. corneal epithelium http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png - + - + ISBN:0781772214 @@ -35166,15 +31646,6 @@ plexiform layer. MGI:smb MP:0006000 - - - - Portion of tissue comprised of four to six layers of nonkeratinized, stratified squamous cells and represents approximately 60% of the thickness of the cornea.[TAO] - 2012-08-14 - TAO:0002187 - TAO - ZFIN:ZDB-PUB-061010-3 - @@ -35251,16 +31722,16 @@ plexiform layer. - - + + + - - + @@ -35269,13 +31740,6 @@ plexiform layer. Opaque fibrous outer layer of the eyeball[ZFA,Kardong,WP]. - The sclera, also known as the white part of the eye, is the opaque (usually white, though certain animals, such as horses and lizards, can have black sclera), fibrous, protective, outer layer of the eye containing collagen and elastic fiber. It is derived from the neural crest. In children, it is thinner and shows some of the underlying pigment, appearing slightly blue. In the elderly, however, fatty deposits on the sclera can make it appear slightly yellow. The sclera forms the posterior five sixths of the connective tissue coat of the globe. It is continuous with the dura mater and the cornea, and maintains the shape of the globe, offering resistance to internal and external forces, and provides an attachment for the extraocular muscle insertions. The sclera is perforated by plenty of nerves and vessels passing through the posterior scleral foramen, the hole that is formed by the optic nerve. At the optic disk the outer two-thirds of the sclera continues with the dura mater (outer coat of the brain) via the dural sheath of the optic nerve. The inner third joins with some choroidal tissue to form a plate (lamina cribrosa) across the optic nerve with perforations through which the optic fibers (fasciculi). The thickness of the sclera varies from 1mm at the posterior pole to 0.3 mm just behind the rectus muscle insertions. The sclera's blood vessels are mainly on the surface, and together with the conjunctiva (which lies on top) This is a thin layer covering the sclera. Along with the vessels of the conjunctiva, those of the sclera renders the inflamed eye bright red. [WP,unvetted][Wikipedia:Sclera]. - The tough, usually white, outer coat of the eyeball, covering all the posterior surface and continuous anteriorly with the cornea. [TFD][VHOG] - scleral - in fish, reptiles and monotremes the connective tissue of the sclera is skeletal - continuous with the dura mater and the cornea; The sclera forms the posterior five-sixths of the connective tissue coat of the globe. - Majority derives from NC that surrounds optic cup of neurectoderm; a small temporal portion develops from the mesoderm that contributes to striated extra-ocular muscles and vascular endothelia[Rada&Johnson]. - Seko et al demonstrate chondrogenic potential and identify this as connective tissue[DOI:10.1371/journal.pone.0003709]. AAO:0010354 BTO:0001606 EMAPA:19027 @@ -35302,48 +31766,36 @@ plexiform layer. sclera http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + - - - - - + FMA - + ZFA - + ISBN:0781772214 - - - - - cjm - ISBN:0781772214 - Wikipedia - @@ -35351,22 +31803,6 @@ plexiform layer. Wikipedia:Sclera ZFIN:ZDB-PUB-050701-15 - - - - The sclera, also known as the white part of the eye, is the opaque (usually white, though certain animals, such as horses and lizards, can have black sclera), fibrous, protective, outer layer of the eye containing collagen and elastic fiber. It is derived from the neural crest. In children, it is thinner and shows some of the underlying pigment, appearing slightly blue. In the elderly, however, fatty deposits on the sclera can make it appear slightly yellow. The sclera forms the posterior five sixths of the connective tissue coat of the globe. It is continuous with the dura mater and the cornea, and maintains the shape of the globe, offering resistance to internal and external forces, and provides an attachment for the extraocular muscle insertions. The sclera is perforated by plenty of nerves and vessels passing through the posterior scleral foramen, the hole that is formed by the optic nerve. At the optic disk the outer two-thirds of the sclera continues with the dura mater (outer coat of the brain) via the dural sheath of the optic nerve. The inner third joins with some choroidal tissue to form a plate (lamina cribrosa) across the optic nerve with perforations through which the optic fibers (fasciculi). The thickness of the sclera varies from 1mm at the posterior pole to 0.3 mm just behind the rectus muscle insertions. The sclera's blood vessels are mainly on the surface, and together with the conjunctiva (which lies on top) This is a thin layer covering the sclera. Along with the vessels of the conjunctiva, those of the sclera renders the inflamed eye bright red. [WP,unvetted][Wikipedia:Sclera]. - Wikipedia:Sclera - - - - - The tough, usually white, outer coat of the eyeball, covering all the posterior surface and continuous anteriorly with the cornea. [TFD][VHOG] - 2012-09-17 - VHOG:0001274 - VHOG - http://bgee.unil.ch/ - http://medical-dictionary.thefreedictionary.com/sclera - @@ -35399,7 +31835,7 @@ plexiform layer. - + @@ -35408,7 +31844,6 @@ plexiform layer. The thickened portion of the vascular tunic, which lies between the choroid and the iris, composed of ciliary muscle and ciliary processes. - The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] AAO:0010341 BTO:0000260 CALOHA:TS-0694 @@ -35438,14 +31873,14 @@ plexiform layer. ciliary body http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + ISBN:0781772214 @@ -35456,16 +31891,6 @@ plexiform layer. MP:0005099 Wikipedia:Ciliary_body - - - - The eye of the adult lamprey is remarkably similar to our own, and it possesses numerous features (including the expression of opsin genes) that are very similar to those of the eyes of jawed vertebrates. The lamprey's camera-like eye has a lens, an iris and extra-ocular muscles (five of them, unlike the eyes of jawed vertebrates, which have six), although it lacks intra-ocular muscles. Its retina also has a structure very similar to that of the retinas of other vertebrates, with three nuclear layers comprised of the cell bodies of photoreceptors and bipolar, horizontal, amacrine and ganglion cells. The southern hemisphere lamprey, Geotria australis, possesses five morphological classes of retinal photoreceptor and five classes of opsin, each of which is closely related to the opsins of jawed vertebrates. Given these similarities, we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya.[well established][VHOG] - 2012-09-17 - VHOG:0000102 - VHOG - DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007) - http://bgee.unil.ch/ - @@ -35493,14 +31918,14 @@ plexiform layer. - + - + @@ -35529,8 +31954,6 @@ plexiform layer. Vascular layer containing connective tissue, of the eye lying between the retina and the sclera. The choroid provides oxygen and nourishment to the outer layers of the retina. Along with the ciliary body and iris, the choroid forms the uveal tract[WP]. check choroid vs choroid layer; check ZFA/TAO placement - no homology assertion in VHOG. Note this is entirely in the posterior region of eyeball in ZFA - choroidal - MP treats posterior uvea and optic choroid as distinct BTO:0001829 CALOHA:TS-2054 EMAPA:19077 @@ -35563,24 +31986,24 @@ plexiform layer. optic choroid http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + MA - + Wikipedia @@ -35595,12 +32018,6 @@ plexiform layer. Vascular layer containing connective tissue, of the eye lying between the retina and the sclera. The choroid provides oxygen and nourishment to the outer layers of the retina. Along with the ciliary body and iris, the choroid forms the uveal tract[WP]. Wikipedia:Choroid - - - - MP treats posterior uvea and optic choroid as distinct - MP - @@ -35674,13 +32091,19 @@ plexiform layer. + - + + + + + + @@ -35700,9 +32123,6 @@ plexiform layer. The lamellated connective tissue of the cornea between the Bowman and Descemet membranes. - Portion of tissue that is located basal to Bowman's layer and distal to Descemet's membrane and is comprised largely of connective tissue.[TAO] - relationship type change: subclass tissue (CARO:0000043) CHANGED TO: develops_from tissue (UBERON:0000479)[TAO] - relationship type change: subclass tissue (CARO:0000043) CHANGED TO: has_developmental_contribution_from tissue (UBERON:0000479)[TAO] substantia propria CALOHA:TS-1138 EFO:0002514 @@ -35729,18 +32149,6 @@ plexiform layer. substantia propria of cornea http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png - - - - - - - - - cjm - ISBN:0781772214 - Wikipedia - @@ -35749,31 +32157,6 @@ plexiform layer. MESH:A09.371.060.217.228 MP:0005300 - - - - Portion of tissue that is located basal to Bowman's layer and distal to Descemet's membrane and is comprised largely of connective tissue.[TAO] - 2012-08-14 - TAO:0002189 - TAO - ZFIN:ZDB-PUB-061010-3 - - - - - relationship type change: subclass tissue (CARO:0000043) CHANGED TO: develops_from tissue (UBERON:0000479)[TAO] - 2012-08-14 - TAO:0002189 - TAO - - - - - relationship type change: subclass tissue (CARO:0000043) CHANGED TO: has_developmental_contribution_from tissue (UBERON:0000479)[TAO] - 2012-08-14 - TAO:0002189 - TAO - @@ -35813,9 +32196,9 @@ plexiform layer. - - - + + + A double layer covering the ciliary body that produces aqueous humor. BTO:0001770 @@ -35835,15 +32218,15 @@ plexiform layer. ciliary epithelium - + - + - + @@ -35856,19 +32239,19 @@ plexiform layer. - + MA - + MP - + Wikipedia @@ -35901,6 +32284,7 @@ plexiform layer. + @@ -35915,7 +32299,6 @@ plexiform layer. Any of the layers that make up the retina[MP]. - MA does not treat internal/external limiting memranes as layers - these are classified as laminae. Here we follow other ontologies in grouping with other layers. MA also treats retinal pigment epithelium and neural retina epithelium as distinct from the layers. We follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers - these are also classified as layers, giving us over the usual 10 layers AAO:0010353 EMAPA:35742 FMA:58617 @@ -35940,12 +32323,6 @@ plexiform layer. Any of the layers that make up the retina[MP]. MP:0003727 - - - - MA does not treat internal/external limiting memranes as layers - these are classified as laminae. Here we follow other ontologies in grouping with other layers. MA also treats retinal pigment epithelium and neural retina epithelium as distinct from the layers. We follow ontologies such as FMA and ZFA in first dividing into pigmented and neural layers - these are also classified as layers, giving us over the usual 10 layers - MA - @@ -35983,7 +32360,6 @@ plexiform layer. - @@ -35991,7 +32367,7 @@ plexiform layer. - + @@ -36006,9 +32382,6 @@ plexiform layer. A monolayer of pigmented epithelium covering the neural retina; develops from the outer of the two layers of the optic cup[ZFA]. the pigmented cell layer just outside the neurosensory retina that nourishes retinal visual cells, and is firmly attached to the underlying choroid and overlying retinal visual cells[WP]. - A monolayer of pigmented epithelium covering the neural retina; develops from the outer of the two layers of the optic cup. Kimmel et al, 1995.[TAO] - The monolayer of pigmented epithelium covering the neural retina.[AAO] - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] AAO:0011096 BTO:0001177 CALOHA:TS-0869 @@ -36052,14 +32425,14 @@ plexiform layer. pigmented layer of retina http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png - + - + Wikipedia @@ -36069,34 +32442,6 @@ plexiform layer. Wikipedia:Retinal_pigment_epithelium ZFIN:curator - - - - A monolayer of pigmented epithelium covering the neural retina; develops from the outer of the two layers of the optic cup. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000144 - TAO - ZFIN:curator - - - - - The monolayer of pigmented epithelium covering the neural retina.[AAO] - 2012-06-20 - AAO:0011096 - AAO - ZFA:0000144 - - - - - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] - 2012-09-17 - VHOG:0000536 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 - http://bgee.unil.ch/ - @@ -36163,7 +32508,7 @@ plexiform layer. - + @@ -36171,8 +32516,6 @@ plexiform layer. The layer within the retina where the photoreceptor cell receptor segments reside. - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] - we follow MA and ZFA in subdividing this into inner and outer segments EMAPA:35686 FMA:58680 MA:0001308 @@ -36197,14 +32540,14 @@ plexiform layer. photoreceptor layer of retina http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png - + - + ZFA @@ -36214,22 +32557,6 @@ plexiform layer. Wikipedia:Layer_of_rods_and_cones ZFA:0000143 - - - - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] - 2012-09-17 - VHOG:0001165 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 - http://bgee.unil.ch/ - - - - - we follow MA and ZFA in subdividing this into inner and outer segments - MA - @@ -36377,7 +32704,12 @@ plexiform layer. - + + + + + + @@ -36392,7 +32724,6 @@ plexiform layer. The layer within the retina where the photoreceptor cell bodies reside. - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] outer nuclear layer BAMS:Ronl BTO:0005600 @@ -36424,33 +32755,12 @@ plexiform layer. outer nuclear layer of retina - - - - - - - - - soma - ZFA - The layer within the retina where the photoreceptor cell bodies reside. ZFA:0001464 - - - - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] - 2012-09-17 - VHOG:0001170 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 - http://bgee.unil.ch/ - @@ -36522,8 +32832,6 @@ plexiform layer. The layer within the retina where the bipolar cells synapse with the photoreceptor cells[ZFA]. Between the inner and outer nuclear layers, the outer plexiform layer (OPL) contains connections between the photoreceptors and bipolar and horizontal cells[GO]. - The layer within the retina where the bipolar cells synapse with the photoreceptor cells.[TAO] - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] external plexiform layer BAMS:Ropl BTO:0003174 @@ -36558,25 +32866,6 @@ plexiform layer. The layer within the retina where the bipolar cells synapse with the photoreceptor cells[ZFA]. Between the inner and outer nuclear layers, the outer plexiform layer (OPL) contains connections between the photoreceptors and bipolar and horizontal cells[GO]. ZFA:0001330 - - - - The layer within the retina where the bipolar cells synapse with the photoreceptor cells.[TAO] - 2012-08-14 - TAO:0001330 - TAO - ZFIN:curator - - - - - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] - 2012-09-17 - VHOG:0001171 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 - http://bgee.unil.ch/ - @@ -36667,8 +32956,6 @@ plexiform layer. Cytoarchitectural layer of retina containing closely packed cell bodies, the majority of which are bipolar cells (adapted from Wikipedia). - The layer of the retina composed of the cell bodies of bipolar cells, horizontal cells, and some of the cell bodies of amacrine cells[BTO:0003176]. - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] BAMS:Rinl BTO:0003176 EMAPA:19155 @@ -36708,22 +32995,6 @@ plexiform layer. Cytoarchitectural layer of retina containing closely packed cell bodies, the majority of which are bipolar cells (adapted from Wikipedia). NLX:93816 - - - - The layer of the retina composed of the cell bodies of bipolar cells, horizontal cells, and some of the cell bodies of amacrine cells[BTO:0003176]. - BTO:0003176 - - - - - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] - 2012-09-17 - VHOG:0001167 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 - http://bgee.unil.ch/ - @@ -36769,7 +33040,7 @@ plexiform layer. - + @@ -36790,9 +33061,6 @@ plexiform layer. Cytoarchitectural layer of retina that contains somata of retinal ganglion cells, bounded by the stratum opticum and the inner plexiform layer. - a layer of the retina that consists of retinal ganglion cells[WP]. innermost nuclear layer of the retina, which contains neurons that project axons through the optic nerve to the brain[Wikipedia:Ganglion_cell_layer]. - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] - NIFSTD class appears to be retired in nlx[http://neurolex.org/wiki/Nlx_anat_1005030] ganglion cell layer BAMS:Rgcl BTO:0003398 @@ -36828,7 +33096,7 @@ plexiform layer. ganglionic layer of retina http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png - + @@ -36841,7 +33109,7 @@ plexiform layer. - + FMA @@ -36850,28 +33118,6 @@ plexiform layer. Cytoarchitectural layer of retina that contains somata of retinal ganglion cells, bounded by the stratum opticum and the inner plexiform layer. NLX:36500 - - - - a layer of the retina that consists of retinal ganglion cells[WP]. innermost nuclear layer of the retina, which contains neurons that project axons through the optic nerve to the brain[Wikipedia:Ganglion_cell_layer]. - Wikipedia:Ganglion_cell_layer - - - - - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] - 2012-09-17 - VHOG:0001166 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 - http://bgee.unil.ch/ - - - - - NIFSTD class appears to be retired in nlx[http://neurolex.org/wiki/Nlx_anat_1005030] - NIF - @@ -36917,7 +33163,7 @@ plexiform layer. - + @@ -36943,7 +33189,6 @@ plexiform layer. Layer of the retina formed by expansion of the fibers of the optic nerve. - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] UBERON:0005888 nerve fiber layer DMBA:15652 @@ -36973,14 +33218,14 @@ plexiform layer. nerve fiber layer of retina - + - + FMA @@ -36990,16 +33235,6 @@ plexiform layer. ISBN:0-914294-08-3 MGI:smb - - - - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] - 2012-09-17 - VHOG:0001169 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 - http://bgee.unil.ch/ - @@ -37053,6 +33288,7 @@ plexiform layer. + @@ -37079,7 +33315,6 @@ plexiform layer. The row of fused Muller cell processes and astrocytes that separates the retinal nerve fiber layer from the vitreous[MP]. TODO - check frog/fish - Membrane on the apical surface of the retina. The retinal vasculature becomes adhered to the apical surface of the ILM by 30dpf[ZFIN:ZDB-PUB-071023-7, ZFIN:ZDB-PUB-120529-3]. ILM EMAPA:36519 FMA:58689 @@ -37117,12 +33352,6 @@ plexiform layer. The row of fused Muller cell processes and astrocytes that separates the retinal nerve fiber layer from the vitreous[MP]. MP:0010235 - - - - Membrane on the apical surface of the retina. The retinal vasculature becomes adhered to the apical surface of the ILM by 30dpf[ZFIN:ZDB-PUB-071023-7, ZFIN:ZDB-PUB-120529-3]. - ZFIN:ZDB-PUB-071023-7, ZFIN:ZDB-PUB-120529-3 - @@ -37228,10 +33457,6 @@ plexiform layer. Cytoarchitectural layer of the retina that is made up of a dense reticulum of fibrils formed by interlaced dendrites of retinal ganglion cells and cells of the inner nuclear layer (adapted from Wikipedia). - The inner plexiform layer (IPL) is positioned between the INL and the ganglion cell layer and contains the dendrites of RGCs and processes of bipolar and amacrine cells[GO][GO:0010842]. - The layer within the retina where the bipolar cells synapse with the dendrites of the ganglion cells.[TAO] - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] - http://neurolex.org/wiki/Nlx_anat_1005032 appears to be retired BAMS:Ripl BTO:0003175 EMAPA:35741 @@ -37270,31 +33495,6 @@ plexiform layer. Cytoarchitectural layer of the retina that is made up of a dense reticulum of fibrils formed by interlaced dendrites of retinal ganglion cells and cells of the inner nuclear layer (adapted from Wikipedia). NLX:20558 - - - - The inner plexiform layer (IPL) is positioned between the INL and the ganglion cell layer and contains the dendrites of RGCs and processes of bipolar and amacrine cells[GO][GO:0010842]. - GO:0010842 - - - - - The layer within the retina where the bipolar cells synapse with the dendrites of the ganglion cells.[TAO] - 2012-08-14 - TAO:0001329 - TAO - ZFIN:curator - - - - - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] - 2012-09-17 - VHOG:0001168 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 - http://bgee.unil.ch/ - @@ -37358,7 +33558,12 @@ plexiform layer. - + + + + + + @@ -37366,9 +33571,6 @@ plexiform layer. A thick watery refractive medium that fills the space between the lens and the cornea[WP]. - The fluid produced by the ciliary process in the eye and occupying the anterior and posterior chambers. It provides nourishment for the lens and cornea and maintains the ocular pressure, and hence the optical integrity of the eyeball. [TFD][VHOG] - (...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG] - FMA says A+P chambers, and MA states A chamber. ZFA states A chamber and tha it is produced primarily by dorsal ciliary epithelial cells.To be investigated across taxa. EHDAA2:0000139 EHDAA:10196 EMAPA:18232 @@ -37394,50 +33596,12 @@ plexiform layer. aqueous humor of eyeball http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - - - - - - - - - FMA def states A and P - located_in in EHDAA2 - VHOG - A thick watery refractive medium that fills the space between the lens and the cornea[WP]. Wikipedia:Aqueous_humor - - - - The fluid produced by the ciliary process in the eye and occupying the anterior and posterior chambers. It provides nourishment for the lens and cornea and maintains the ocular pressure, and hence the optical integrity of the eyeball. [TFD][VHOG] - 2012-09-17 - VHOG:0000548 - VHOG - http://bgee.unil.ch/ - http://medical-dictionary.thefreedictionary.com/aqueous+humour - - - - - (...) we reach the inescapable conclusion that the last common ancestor of jawless and jawed vertebrates already possessed an eye that was comparable to that of extant lampreys and gnathostomes. Accordingly, a vertebrate camera-like eye must have been present by the time that lampreys and gnathostomes diverged, around 500 Mya (reference 1); Although the eye varies greatly in adaptative details among vertebrates, its basic structure is the same in all. The human eye is representative of the design typical for a tetrapod. (...) A watery aqueous humor fills the spaces in the eye in front of the lens (...) (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0000548 - VHOG - DOI:10.1038/nrn2283 Lamb TD, Collin SP and Pugh EN Jr, Evolution of the vertebrate eye: opsins, photoreceptors, retina and eye cup. Nature Reviews Neuroscience (2007), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.424 and p.426 and p.429 and Figure 12-24 - http://bgee.unil.ch/ - - - - - FMA says A+P chambers, and MA states A chamber. ZFA states A chamber and tha it is produced primarily by dorsal ciliary epithelial cells.To be investigated across taxa. - FMA - @@ -37492,7 +33656,6 @@ plexiform layer. EV:0100344 FMA:58822 MA:0001286 - MESH:D014822 NCIT:C13323 UMLS:C0229096 VHOG:0000795 @@ -37526,13 +33689,6 @@ plexiform layer. portion of vitreous humor FMA:67388 - - - - MESH:D014822 - - https://github.com/biopragmatics/biomappings - @@ -37584,6 +33740,7 @@ plexiform layer. + @@ -37591,7 +33748,12 @@ plexiform layer. - + + + + + + @@ -37615,23 +33777,12 @@ plexiform layer. vitreous body http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - - - - FMA - - - - - neural ectoderm of optic cup - ISBN:0781772214 - @@ -37763,8 +33914,8 @@ plexiform layer. - - + + @@ -37773,7 +33924,6 @@ plexiform layer. Any of the parts of the eye that lie in front of, or ventral to, the lens (inclusive). - EMAPA:36594 FMA:58865 MA:0002484 @@ -37797,26 +33947,16 @@ plexiform layer. anterior segment of eyeball http://upload.wikimedia.org/wikipedia/commons/b/ba/Cataract_in_human_eye.png - + - - - - - + FMA - - - - - cjm - @@ -37831,14 +33971,6 @@ plexiform layer. MESH:A09.371.060 MP:0005193 - - - - - ZFA - https://github.com/obophenotype/uberon/issues/378 - pending - @@ -37865,8 +33997,8 @@ plexiform layer. - - + + @@ -37896,26 +34028,16 @@ plexiform layer. posterior segment of eyeball http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - - - - - + FMA - - - - - cjm - @@ -37949,9 +34071,10 @@ plexiform layer. - - - + + + + @@ -37972,12 +34095,10 @@ plexiform layer. The mucous membrane that lines the inner surface of the eyelids and the front of the eyeball. - conjunctival AAO:0010343 BTO:0003415 CALOHA:TS-2232 EFO:0000374 - EMAPA:18233 EV:0100340 FMA:59011 GAID:898 @@ -38001,15 +34122,15 @@ plexiform layer. conjunctiva http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png - + - + - + @@ -38022,19 +34143,19 @@ plexiform layer. - + cjm - + MA - + ISBN:0781772214 @@ -38085,7 +34206,6 @@ plexiform layer. - @@ -38098,15 +34218,15 @@ plexiform layer. - + + + + + + The most anterior region of the brain including both the telencephalon and diencephalon. - Most anterior of the three regions of the brain consisting of the telencephalon and diencephalon.[AAO] - The most anterior region the brain including both the telencephalon and diencephalon. Kimmel et al, 1995.[TAO] - relationship loss: develops_from forebrain neural tube (TAO:0007041)[TAO] - In craniate embryos, neural expression of Distal-less-related genes is exclusively in the forebrain (...). Because the major neural expression domain of amphioxus AmphiDll is in the anterior three-fourths of the cerebral vesicle, we suggest that this region of the neural tube is homologous to parts of the craniate forebrain. This conclusion is strongly supported by three-dimensional, computer-assisted reconstruction of the neural tube of amphioxus based on serial transmission electron microscopy. At the neuroanatomical level, a number of detailed homologies are indicated between the anterior three-fourths of the amphioxus cerebral vesicle and the diencephalic region of the craniate forebrain. If one assumes that the amphioxus condition fairly represents the nervous system of the proximate ancestor of the craniates, one can suggest that they evolved from a creature that had the beginnings of a forebrain.[well established][VHOG] - prosencephalic FB AAO:0010147 BAMS:FB @@ -38145,16 +34265,6 @@ plexiform layer. forebrain http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg - - - - - - - - - definitional - @@ -38162,42 +34272,6 @@ plexiform layer. Wikipedia:Forebrain ZFIN:ZDB-PUB-961014-576 - - - - Most anterior of the three regions of the brain consisting of the telencephalon and diencephalon.[AAO] - 2012-06-20 - AAO:0010147 - AAO - AAO:BJB - - - - - The most anterior region the brain including both the telencephalon and diencephalon. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000109 - TAO - ZFIN:curator - - - - - relationship loss: develops_from forebrain neural tube (TAO:0007041)[TAO] - 2012-08-14 - TAO:0000109 - TAO - - - - - In craniate embryos, neural expression of Distal-less-related genes is exclusively in the forebrain (...). Because the major neural expression domain of amphioxus AmphiDll is in the anterior three-fourths of the cerebral vesicle, we suggest that this region of the neural tube is homologous to parts of the craniate forebrain. This conclusion is strongly supported by three-dimensional, computer-assisted reconstruction of the neural tube of amphioxus based on serial transmission electron microscopy. At the neuroanatomical level, a number of detailed homologies are indicated between the anterior three-fourths of the amphioxus cerebral vesicle and the diencephalic region of the craniate forebrain. If one assumes that the amphioxus condition fairly represents the nervous system of the proximate ancestor of the craniates, one can suggest that they evolved from a creature that had the beginnings of a forebrain.[well established][VHOG] - 2012-09-17 - VHOG:0000383 - VHOG - PMID:8787764 Holland ND, Panganiban G, Henyey EL, Holland LZ, Sequence and developmental expression of AmphiDll, an amphioxus Distal-less gene transcribed in the ectoderm, epidermis and nervous system: insights into evolution of craniate forebrain and neural crest. Development (1996) - http://bgee.unil.ch/ - @@ -38226,26 +34300,23 @@ plexiform layer. - - + + + + + + - + The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO]. developmental relationships need revised - - - Middle part of the brain composed of the optic tectum and penducular region.[AAO] - The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally. Kimmel et al, 1995.[TAO] - Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] - mesencephalic - part of brainstem in ABA - we reject this in favor of ISBN:0471888893 which has an implicit overlaps relationships MB AAO:0010149 BAMS:MES @@ -38288,24 +34359,14 @@ plexiform layer. midbrain http://upload.wikimedia.org/wikipedia/commons/f/f9/Human_brain_inferior_view_description.JPG - - - - - + - - definitional - - - - - + Bgee:AN @@ -38314,57 +34375,6 @@ plexiform layer. The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO]. GO:0030901 - - - - - ZFA - https://github.com/obophenotype/uberon/issues/378 - ABA - pending - - - - - - ZFA - ABA - pending - - - - - Middle part of the brain composed of the optic tectum and penducular region.[AAO] - 2012-06-20 - AAO:0010149 - AAO - AAO:BJB - - - - - The brain region between the forebrain anteriorly and the hindbrain posteriorly, including the tectum dorsally and the midbrain tegmentum ventrally. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000128 - TAO - ZFIN:curator - - - - - Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] - 2012-09-17 - VHOG:0000069 - VHOG - DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999) - http://bgee.unil.ch/ - - - - - part of brainstem in ABA - we reject this in favor of ISBN:0471888893 which has an implicit overlaps relationships - ABA - @@ -38400,7 +34410,6 @@ plexiform layer. - @@ -38408,23 +34417,25 @@ plexiform layer. - + + + + + + - + + + + + + The division of the forebrain that develops from the foremost primary cerebral vesicle. - - - - The more posterior and ventral of two forebrain neuromeres, the other being the telencephalon; major derivatives are the eye cups, the brain pretectal region, the thalamus, hypothalamus, and epithalamus (including the habenula and epiphysis). Kimmel et al, 1995.[TAO] - Unpaired part of the forebrain comprised of three major parts; the epithalamus, thalamus, and hypothalamus.[AAO] - Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] - diencephalic - in ABA, this is part of the brain stem DiE AAO:0010481 BAMS:DI @@ -38478,88 +34489,12 @@ plexiform layer. diencephalon http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg - - - - - - - - - - - - - definitional - - - - - - definitional - The division of the forebrain that develops from the foremost primary cerebral vesicle. Wikipedia:Diencephalon - - - - - ZFA - ABA - https://github.com/obophenotype/uberon/issues/378 - pending - - - - - - ABA - - - - - - not well differentiated from the cerebrum. (Ariens, p. 868) - PMID:8932866 - - - - - The more posterior and ventral of two forebrain neuromeres, the other being the telencephalon; major derivatives are the eye cups, the brain pretectal region, the thalamus, hypothalamus, and epithalamus (including the habenula and epiphysis). Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000101 - TAO - ZFIN:curator - - - - - Unpaired part of the forebrain comprised of three major parts; the epithalamus, thalamus, and hypothalamus.[AAO] - 2012-06-20 - AAO:0010481 - AAO - AAO:BJB - - - - - Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] - 2012-09-17 - VHOG:0000318 - VHOG - DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999) - http://bgee.unil.ch/ - - - - - in ABA, this is part of the brain stem - ABA - @@ -38619,6 +34554,7 @@ plexiform layer. + @@ -38651,9 +34587,6 @@ plexiform layer. Organ component of neuraxis that has as its parts the medullary reticular formation, inferior olivary complex and cochlear nuclear complex, among other structures[FMA]. The medulla oblongata lies directly above the spinal cord and controls vital autonomic functions such as digestion, breathing and the control of heart rate[GO]. - Posterior portion of the hindbrain which controls respiration, heartbeat, digestion, and swallowing as well as some locomotor responses.[AAO] - The posterior region of the brain that is continuous with the spinal cord. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-17, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] - Classical anatomical studies subdivided the vertebrate rhombencephalon into pons and medulla oblongata. (...) The medulla oblongata appears therefore as a tagma, that is, a group of segmental units (pseudorhombomeres, in this case) sharing some morphological and molecular characteristics, and in some aspects different from the segmental units present in adjoining brain regions, pons and spinal cord.[well established][VHOG] bulb medulla AAO:0010486 @@ -38708,34 +34641,6 @@ plexiform layer. GO:0021550 Wikipedia:Bone_marrow_of_ovary_oblongata - - - - Posterior portion of the hindbrain which controls respiration, heartbeat, digestion, and swallowing as well as some locomotor responses.[AAO] - 2012-06-20 - AAO:0010486 - AAO - AAO:BJB - - - - - The posterior region of the brain that is continuous with the spinal cord. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-17, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] - 2012-09-17 - VHOG:0000181 - VHOG - http://bgee.unil.ch/ - - - - - Classical anatomical studies subdivided the vertebrate rhombencephalon into pons and medulla oblongata. (...) The medulla oblongata appears therefore as a tagma, that is, a group of segmental units (pseudorhombomeres, in this case) sharing some morphological and molecular characteristics, and in some aspects different from the segmental units present in adjoining brain regions, pons and spinal cord.[well established][VHOG] - 2012-09-17 - VHOG:0000181 - VHOG - DOI:10.1016/j.ydbio.2008.08.017 Marin F, Aroca P, Puelles L, Hox gene colinear expression in the avian medulla oblongata is correlated with pseudorhombomeric domains. Developmental Biology (2008) - http://bgee.unil.ch/ - @@ -38833,7 +34738,6 @@ plexiform layer. BM:Tel-OT DHBA:10589 DMBA:17785 - EMAPA:16678 EMAPA:35617 FMA:62046 GAID:735 @@ -38933,10 +34837,9 @@ plexiform layer. - + Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP]. - Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG] MTg tegmentum BAMS:MTg @@ -38950,7 +34853,6 @@ plexiform layer. HBA:9002 MA:0000212 MAT:0000452 - MESH:D013681 SCTID:362392007 TAO:0000160 UMLS:C0039441 @@ -38974,14 +34876,14 @@ plexiform layer. midbrain tegmentum http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray712.png - + - + ZFA @@ -38992,16 +34894,6 @@ plexiform layer. ISBN:0471888893 Wikipedia:Midbrain_tegmentum - - - - Together, our results reveal a shared basic organization in the tegmental domains of the diencephalon and midbrain of developing lamprey, indicating early appearance of the domain in vertebrate phylogeny.[well established][VHOG] - 2012-09-17 - VHOG:0001367 - VHOG - DOI:10.1016/j.brainresbull.2005.05.001 Villar-Cheda B, Abalo XM, Anadon R, Rodicio MC, The tegmental proliferation region in the sea lamprey. Brain Research Bulletin (2005) - http://bgee.unil.ch/ - @@ -39016,13 +34908,6 @@ plexiform layer. tegmentum ISBN:0471888893 - - - - MESH:D013681 - - https://github.com/biopragmatics/biomappings - @@ -39161,14 +35046,15 @@ plexiform layer. + - - + + @@ -39181,7 +35067,7 @@ plexiform layer. - + @@ -39197,11 +35083,6 @@ plexiform layer. A vessel through which blood circulates in the body. consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus - Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG] - Any of the vessels through which blood circulates in the body.[AAO] - The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] - annelids have blood vessels, but this class is not applicable to annelids. - FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX vascular element AAO:0011004 AEO:0000207 @@ -39240,34 +35121,34 @@ plexiform layer. blood vessel http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg - + - + - + - + AEO - + EHDAA2 - + GO:0072360 @@ -39277,40 +35158,6 @@ plexiform layer. BTO:0001102 Wikipedia:Blood_vessel - - - - Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG] - 2012-09-17 - VHOG:0001250 - VHOG - http://bgee.unil.ch/ - - - - - Any of the vessels through which blood circulates in the body.[AAO] - 2012-06-20 - AAO:0011004 - AAO - AAO:EJS - - - - - The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] - 2012-09-17 - VHOG:0001250 - VHOG - DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006) - http://bgee.unil.ch/ - - - - - FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX - FMA - @@ -39361,7 +35208,6 @@ plexiform layer. - @@ -39471,7 +35317,6 @@ plexiform layer. A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA]. - endothelial BTO:0000393 CALOHA:TS-0278 EFO:0002548 @@ -39525,7 +35370,6 @@ plexiform layer. A nervous system structure composed primarily of nerve cell bodies (somas). May also include dendrites and the initial unmyelinated portion of axons. - Multi-tissue comprised of neurons, dendrites, axon terminals, glial cells, and capillaries.[TAO] AEO:0001012 EHDAA2:0003136 EHDAA2_RETIRED:0004658 @@ -39533,7 +35377,6 @@ plexiform layer. FMA:67242 HBA:4006 MA:0001112 - MESH:D066128 NCIT:C32695 TAO:0002197 UMLS:C0018220 @@ -39565,29 +35408,12 @@ plexiform layer. Wikipedia:Gray_matter http://orcid.org/0000-0002-6601-2165 - - - - Multi-tissue comprised of neurons, dendrites, axon terminals, glial cells, and capillaries.[TAO] - 2012-08-14 - TAO:0002197 - TAO - ZFIN:curator - EMAPA:37596 MA:th - - - - MESH:D066128 - - - https://github.com/biopragmatics/biomappings - @@ -39633,8 +35459,12 @@ plexiform layer. - - + + + + + + @@ -39647,18 +35477,10 @@ plexiform layer. - + The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA]. - - - Posterior part of the brain consisting of the cerebellum and medulla oblongata.[AAO] - The most posterior of the three principal regions of the brain, forming the rhombencephalon and all or most of the metencephalon. Kimmel et al, 1995.[TAO] - relationship loss: develops_from hindbrain neural tube (TAO:0007043)[TAO] - Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] - rhombencephalic - in MA, brainstem and hindbrain and part-of siblings under brain, consistent with FMA and NIF. See also notes for cerebellum. We weaken the relation in ABA to overlaps AAO:0010150 BAMS:HB BIRNLEX:942 @@ -39698,25 +35520,14 @@ plexiform layer. hindbrain http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg - - - - - + - - modified-source-relation - ABA - - - - - + Bgee:AN @@ -39727,69 +35538,12 @@ plexiform layer. ZFA:0000029 ZFIN:curator - - - - - ZFA - ABA - https://github.com/obophenotype/uberon/issues/378 - pending - - - - - - ABA - PMID:8932866 - - - - Posterior part of the brain consisting of the cerebellum and medulla oblongata.[AAO] - 2012-06-20 - AAO:0010150 - AAO - AAO:BJB - - - - - The most posterior of the three principal regions of the brain, forming the rhombencephalon and all or most of the metencephalon. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000029 - TAO - ZFIN:curator - - - - - relationship loss: develops_from hindbrain neural tube (TAO:0007043)[TAO] - 2012-08-14 - TAO:0000029 - TAO - - - - - Fine structural, computerized three-dimensional (3D) mapping of cell connectivity in the amphioxus nervous system and comparative molecular genetic studies of amphioxus and tunicates have provided recent insights into the phylogenetic origin of the vertebrate nervous system. The results suggest that several of the genetic mechanisms for establishing and patterning the vertebrate nervous system already operated in the ancestral chordate and that the nerve cord of the proximate invertebrate ancestor of the vertebrates included a diencephalon, midbrain, hindbrain, and spinal cord.[well established][VHOG] - 2012-09-17 - VHOG:0000070 - VHOG - DOI:10.1016/S0959-4388(99)00003-3 Holland LZ and Holland ND, Chordate origins of the vertebrate central nervous system. Current Opinion in Neurobiology (1999) - http://bgee.unil.ch/ - - - - - in MA, brainstem and hindbrain and part-of siblings under brain, consistent with FMA and NIF. See also notes for cerebellum. We weaken the relation in ABA to overlaps - MA - @@ -39837,7 +35591,6 @@ plexiform layer. An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face. see also: vascular system. Consider merging? - vascular BTO:0003718 FMA:69050 TAO:0005249 @@ -39895,16 +35648,11 @@ plexiform layer. Anatomical structure that is part of an embryo. - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO] - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO] - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO] - in FMA embryo is_a embryonic structure AAO:0000138 BILA:0000034 BTO:0000174 CALOHA:TS-2110 EFO:0000461 - FBbt:00004208 FMA:69067 GAID:407 MESH:D004628 @@ -39935,45 +35683,6 @@ plexiform layer. BTO:0000174 ZFIN:curator - - - - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO] - 2012-06-20 - AAO:0000138 - AAO - AAO:BJB - - - - - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO] - 2012-08-14 - TAO:0001105 - TAO - ZFIN:curator - - - - - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO] - 2012-08-14 - VSAO:0000178 - VSAO - ZFIN:curator - - - - - in FMA embryo is_a embryonic structure - FMA - - - - - FBbt:00004208 - - @@ -40030,8 +35739,6 @@ plexiform layer. An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen. - An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO] - general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs. AAO:0010386 BTO:0001491 EHDAA:512 @@ -40066,21 +35773,6 @@ plexiform layer. Wikipedia:Viscus https://github.com/obophenotype/mouse-anatomy-ontology/issues/14 - - - - An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO] - 2012-06-20 - AAO:0010386 - AAO - BTO:0001491 - - - - - general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs. - FMA - @@ -40137,21 +35829,15 @@ plexiform layer. The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA]. - Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO] - The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO] - The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO] - The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG] axial skeleton AAO:0000034 EFO:0000942 EHDAA2:0000161 EHDAA:5049 - EMAPA:17214 EMAPA:37721 FMA:71221 MA:0002986 MAT:0000148 - MESH:D013131 MIAA:0000148 TAO:0000317 VHOG:0000317 @@ -40177,43 +35863,6 @@ plexiform layer. https://sourceforge.net/tracker/?func=detail&aid=2983975&group_id=76834&atid=974957 https://sourceforge.net/tracker/?func=detail&atid=1205376&aid=2983977&group_id=76834 - - - - Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO] - 2012-08-14 - VSAO:0000093 - VSAO - PSPUB:0000170 - - - - - The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO] - 2012-06-20 - AAO:0000034 - AAO - AAO:LAP - - - - - The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO] - 2012-08-14 - TAO:0000317 - TAO - ZFIN:curator - - - - - The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG] - 2012-09-17 - VHOG:0000317 - VHOG - DOI:10.1186/1742-9994-8-4 Schilling N, Evolution of the axial system in craniates: morphology and function of the perivertebral musculature. Frontiers in Zoology (2011) - http://bgee.unil.ch/ - @@ -40227,13 +35876,6 @@ plexiform layer. EMAPA:37721 MA:th - - - - MESH:D013131 - - https://github.com/biopragmatics/biomappings - @@ -40248,10 +35890,6 @@ plexiform layer. Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present. - - - Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO] - Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO] AAO:0010339 BILA:0000116 BTO:0001493 @@ -40291,32 +35929,6 @@ plexiform layer. UBERONREF:0000006 Wikipedia:Torso - - - - - ZFA - https://github.com/obophenotype/uberon/issues/378 - pending - - - - - Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO] - 2012-06-20 - AAO:0010339 - AAO - AAO:BJB - - - - - Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO] - 2012-08-14 - TAO:0001115 - TAO - ZFIN:curator - @@ -40349,7 +35961,6 @@ plexiform layer. The sensory system subserving the sense of vision. - The sensory system used for sight.[AAO] UBERON:0007036 AAO:0000632 BILA:0000140 @@ -40379,15 +35990,6 @@ plexiform layer. The sensory system subserving the sense of vision. NIFSTD:FMAID_7191 - - - - The sensory system used for sight.[AAO] - 2012-06-20 - AAO:0000632 - AAO - AAO:EJS - @@ -40549,10 +36151,9 @@ plexiform layer. - + Vasculature that is part of the eye region. - not part of the eye in ZFA. Note this changed to a blood vessel in ZFA FMA:74743 SCTID:123846009 TAO:0007057 @@ -40572,14 +36173,14 @@ plexiform layer. https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb - + - + ISBN:0781772214 @@ -40589,12 +36190,6 @@ plexiform layer. OBOL:automatic https://sourceforge.net/tracker/?func=detail&aid=3489658&group_id=76834&atid=994726 - - - - not part of the eye in ZFA. Note this changed to a blood vessel in ZFA - ZFA - @@ -40638,7 +36233,12 @@ plexiform layer. - + + + + + + @@ -40648,9 +36248,6 @@ plexiform layer. Anatomical system that consists of the muscular and skeletal systems. - Anatomical system that provides locomotion and physical support to the organism.[AAO] - There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG] - musculoskeletal AAO:0010546 CALOHA:TS-1311 EMAPA:32714 @@ -40672,16 +36269,6 @@ plexiform layer. musculoskeletal system - - - - - - - - - check ctenophore - @@ -40690,25 +36277,6 @@ plexiform layer. VSAO:curator https://github.com/obophenotype/uberon/issues/77 - - - - Anatomical system that provides locomotion and physical support to the organism.[AAO] - 2012-06-20 - AAO:0010546 - AAO - AAO:EJS - - - - - There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG] - 2012-09-17 - VHOG:0001275 - VHOG - DOI:10.1002/jez.b.21246 Shearman RM, Burke AC, The lateral somitic frontier in ontogeny and phylogeny. Journal of Experimental Zoology (2009) - http://bgee.unil.ch/ - @@ -40750,7 +36318,6 @@ plexiform layer. The part of the coelemic cavity lumen that is enclosed by the walls of the thorax. - In many species, the diaphragm separates thoracic and abdominal cavities EMAPA:36497 FMA:7565 GAID:93 @@ -40817,21 +36384,28 @@ plexiform layer. - + - - + + + + + + + + + + + + Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO). TODO - add superclass to unify with VNC? - - Part of the central nervous system which descends from the hindbrain within the vertebral column.[AAO] - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG] AAO:0010151 BAMS:SP BAMS:Spinal @@ -40884,69 +36458,22 @@ plexiform layer. https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Spinal_Cord.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Spinal_Cord.glb - + - - - - - - - - - + ZFA - - - - - definitional - - - - - - definitional - Part of the central nervous system located in the vertebral canal continuous with and caudal to the brain; demarcated from brain by plane of foramen magnum. It is composed of an inner core of gray matter in which nerve cells predominate, and an outer layer of white matter in which myelinated nerve fibers predominate, and surrounds the central canal. (CUMBO). BIRNLEX:1709 - - - - - ZFA - https://github.com/obophenotype/uberon/issues/378 - pending - - - - - Part of the central nervous system which descends from the hindbrain within the vertebral column.[AAO] - 2012-06-20 - AAO:0010151 - AAO - AAO:BJB - - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0000601 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28, ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 - http://bgee.unil.ch/ - @@ -41044,12 +36571,6 @@ plexiform layer. Stalk-like part of the brain that includes amongst its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,MP,generalized]. - - - - Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain.[TAO] - Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,adopted][ZFA:0001707]. - the stalk-like part of the brain that comprises the midbrain (aka mesencephalon), the pons (aka pons Varolii), and the medulla oblongata, and connects the cerebral hemispheres with the cervical spinal cord[MP] BAMS:BS BIRNLEX:1565 BTO:0000146 @@ -41096,48 +36617,6 @@ plexiform layer. Wikipedia:Brainstem ZFA:0001707 - - - - - we apply a strict definition - - - - - - ZFA - ABA - https://github.com/obophenotype/uberon/issues/378 - pending - - - - - - we apply a strict definition - - - - - Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain.[TAO] - 2012-08-14 - TAO:0002156 - TAO - ISBN:3764351209 - - - - - Multi-tissue structure that has as its parts the medulla oblongata of the hindbrain and the tegmentum of the midbrain[ZFA,adopted][ZFA:0001707]. - ZFA:0001707 - - - - - the stalk-like part of the brain that comprises the midbrain (aka mesencephalon), the pons (aka pons Varolii), and the medulla oblongata, and connects the cerebral hemispheres with the cervical spinal cord[MP] - MP:0005277 - @@ -41219,17 +36698,12 @@ plexiform layer. Neural tissue consisting of myelinated axons connecting grey matter areas of the central nervous system. - Cell part cluster consisting predominantly of neurites in the brain and the spinal cord[FMA:83929]. - Multi-tissue structure comprised largely of myelinated axons.[TAO] - The myelination of axons by glial cells was the last major step in the evolution of cells in the vertebrate nervous system, and white-matter tracts are key to the architecture of the mammalian brain.[well established][VHOG] - nlx_anat_101177 seems to have been lost in the transition from NIFGA to Neurolex AEO:0000139 AEO:0001011 EMAPA:35927 FMA:83929 HBA:9218 MA:0001135 - MESH:D066127 NCIT:C33892 NLX:412 NLXANAT:101177 @@ -41265,46 +36739,6 @@ plexiform layer. Wikipedia:White_matter https://orcid.org/0000-0002-6601-2165 - - - - Cell part cluster consisting predominantly of neurites in the brain and the spinal cord[FMA:83929]. - FMA:83929 - - - - - Multi-tissue structure comprised largely of myelinated axons.[TAO] - 2012-08-14 - TAO:0002142 - TAO - ZFIN:curator - - - - - The myelination of axons by glial cells was the last major step in the evolution of cells in the vertebrate nervous system, and white-matter tracts are key to the architecture of the mammalian brain.[well established][VHOG] - 2012-09-17 - VHOG:0001764 - VHOG - DOI:10.1038/nature09614 Nave KA, Myelination and support of axonal integrity by glia. Nature (2010) - http://bgee.unil.ch/ - - - - - nlx_anat_101177 seems to have been lost in the transition from NIFGA to Neurolex - NIF - https://github.com/SciCrunch/NIF-Ontology/issues/83 - - - - - MESH:D066127 - - - https://github.com/biopragmatics/biomappings - @@ -41361,7 +36795,12 @@ plexiform layer. - + + + + + + @@ -41369,15 +36808,11 @@ plexiform layer. The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities. - Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]. - The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]. - In mammals it forms the peritoneal, pleural, and pericardial cavities UBERON:0000169 body cavity AEO:0000186 BTO:0001707 EHDAA2:0000267 - FBbt:00005060 FMA:85006 NCIT:C25444 RETIRED_EHDAA2:0003186 @@ -41402,52 +36837,18 @@ plexiform layer. EDITOR_NOTE check the FMA placement here; ncit placement of body cavity here probably not correct coelemic cavity lumen - - - - - - - - - definitional - The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities. BTO:0001707 - - - - Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]. - 2012-09-12 - ZFA:0001438 - ZFA - ZFIN:curator - - - - - The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]. - 2012-09-12 - BTO:0001707 - BTO - BTO - body cavity BTO:0001707 - - - - FBbt:00005060 - - @@ -41504,6 +36905,7 @@ plexiform layer. + @@ -41511,21 +36913,9 @@ plexiform layer. - - - - - - - - - - - - - - - + + + @@ -41539,13 +36929,6 @@ plexiform layer. A flexible rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In some chordates, it persists throughout life as the main axial support of the body, while in most vertebrates it becomes the nucleus pulposus of the intervertebral disc. The notochord is found ventral to the neural tube. - Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO] - Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO] - Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO] - relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO] - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG] - notochordal - In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord. AAO:0000327 BTO:0001768 CALOHA:TS-0690 @@ -41580,15 +36963,15 @@ plexiform layer. notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + @@ -41607,19 +36990,19 @@ plexiform layer. - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -41632,51 +37015,6 @@ plexiform layer. https://github.com/obophenotype/uberon/issues/25 https://github.com/obophenotype/uberon/issues/271 - - - - Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO] - 2012-08-14 - VSAO:0000032 - VSAO - PSPUB:0000170 - - - - - Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000135 - TAO - ZFIN:curator - - - - - Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO] - 2012-06-20 - AAO:0000327 - AAO - AAO:LAP - - - - - relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO] - 2012-06-20 - AAO:0000327 - AAO - - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG] - 2012-09-17 - VHOG:0000199 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 - http://bgee.unil.ch/ - @@ -41704,18 +37042,10 @@ plexiform layer. - - + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. - EDITOR_NOTE currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk - Post-cranial axial segments which form sclerotome and dermomyotome.[AAO] - Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO] - relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO] - relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO] - relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO] - (...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG] - somitic mesodermal cluster AAO:0010569 AEO:0001015 @@ -41751,11 +37081,11 @@ plexiform layer. somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + @@ -41768,13 +37098,13 @@ plexiform layer. - + GOTAX:0000352 - + ZFA @@ -41790,58 +37120,6 @@ plexiform layer. PMID:17237766 - - - - Post-cranial axial segments which form sclerotome and dermomyotome.[AAO] - 2012-06-20 - AAO:0010569 - AAO - AAO:EJS - - - - - Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000155 - TAO - ZFIN:curator - - - - - relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO] - 2012-08-14 - TAO:0000155 - TAO - - - - - relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO] - 2012-08-14 - TAO:0000155 - TAO - - - - - relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO] - 2012-06-20 - AAO:0010569 - AAO - - - - - (...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0000191 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.40, DOI:10.1093/icb/43.1.137 Balavoine G, Adoutte A, The segmented urbilateria: a testable scenario. Integrative and Comparative Biology (2003) - http://bgee.unil.ch/ - @@ -41886,20 +37164,25 @@ plexiform layer. + - - - - - - + + + + + + + + + + + + + + + + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. - EDITOR_NOTE consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams). - - A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO] - Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO] - A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831] - We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG] AAO:0010578 BTO:0001764 CALOHA:TS-0676 @@ -41912,7 +37195,6 @@ plexiform layer. MIAA:0000066 NCIT:C34222 SCTID:361462002 - TAO:0000045 UMLS:C0027789 VHOG:0000057 Wikipedia:Neural_crest @@ -41932,66 +37214,45 @@ plexiform layer. http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - - - - - + - + - - - - - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - - Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells - ISBN:0073040584 - - - - - + BTO - + PMID:11523831 - - pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest - - - - - + PMID:11523831 @@ -42000,47 +37261,6 @@ plexiform layer. A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. MP:0009846 - - - - - ISBN:0073040584 - PMID:17377535 - - - - - A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000045 - TAO - ZFIN:curator - - - - - Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO] - 2012-06-20 - AAO:0010578 - AAO - AAO:EJS - - - - - A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831] - PMID:11523831 - - - - - We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG] - 2012-09-17 - VHOG:0000057 - VHOG - DOI:10.1111/j.1469-7580.2012.01495.x Hall BK, Gillis JA, Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues. J Anat (2012) - http://bgee.unil.ch/ - @@ -42082,9 +37302,6 @@ plexiform layer. Embryonic ectoderm that gives rise to nervous tissue. - (...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG] - neurectodermal - we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here AAO:0011074 BILA:0000039 CALOHA:TS-1212 @@ -42093,7 +37310,6 @@ plexiform layer. EHDAA:255 EMAPA:16073 EV:0100004 - FBbt:00001057 FMA:87657 MAT:0000176 MIAA:0000176 @@ -42122,22 +37338,6 @@ plexiform layer. Embryonic ectoderm that gives rise to nervous tissue. Wikipedia:Neuroectoderm - - - - (...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG] - 2012-09-17 - VHOG:0000150 - VHOG - DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) - http://bgee.unil.ch/ - - - - - FBbt:00001057 - - @@ -42172,10 +37372,6 @@ plexiform layer. Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance. - One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO] - Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO] - Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO] - MA also has set of connective tissues AAO:0000098 BTO:0000421 CALOHA:TS-2009 @@ -42216,40 +37412,6 @@ plexiform layer. http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/23 - - - - One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO] - 2012-06-20 - AAO:0000098 - AAO - AAO:LAP - - - - - Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO] - 2012-08-14 - TAO:0001641 - TAO - TAO:wd - - - - - Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO] - 2012-08-14 - VSAO:0000017 - VSAO - GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 - PSPUB:0000170 - - - - - MA also has set of connective tissues - MA - @@ -42313,8 +37475,6 @@ plexiform layer. Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]. - - One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO] AAO:0000306 AEO:0000122 CALOHA:TS-0642 @@ -42345,15 +37505,6 @@ plexiform layer. Wikipedia:Muscle_tissue https://sourceforge.net/tracker/index.php?func=detail&aid=2801266&group_id=36855&atid=440764 - - - - One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO] - 2012-06-20 - AAO:0000306 - AAO - AAO:LAP - @@ -42380,21 +37531,22 @@ plexiform layer. - + - + + + + + + Anatomical system that is involved in the production of hematopoietic cells. - Anatomical system that consists of the blood and blood forming tissues.[AAO] - Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG] - hematopoietic - In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes AAO:0011002 BTO:0000570 CALOHA:TS-0449 @@ -42432,57 +37584,22 @@ plexiform layer. hematopoietic system - + - - - - - + FMA - - - - - definitional - Anatomical system that is involved in the production of hematopoietic cells. Wikipedia:Haematopoiesis - - - - Anatomical system that consists of the blood and blood forming tissues.[AAO] - 2012-06-20 - AAO:0011002 - AAO - AAO:EJS - - - - - Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG] - 2012-09-17 - VHOG:0001624 - VHOG - DOI:10.1016/j.coph.2010.05.004 Ellett F, Lieschke GJ, Zebrafish as a model for vertebrate hematopoiesis. Current Opinion in Pharmacology (2010) - http://bgee.unil.ch/ - - - - - In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes - WP - @@ -42514,8 +37631,8 @@ plexiform layer. - - + + @@ -42541,11 +37658,11 @@ plexiform layer. iris epithelium - + - + @@ -42558,13 +37675,13 @@ plexiform layer. - + MA - + MP @@ -42638,7 +37755,6 @@ plexiform layer. In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA]. MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class - In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG] BTO:0004593 FMA:296704 MAT:0000067 @@ -42666,16 +37782,6 @@ plexiform layer. Wikipedia:Epiblast ZFIN:curator - - - - In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG] - 2012-09-17 - VHOG:0000243 - VHOG - DOI:10.1146/annurev.cellbio.042308.113344 Zorn AM, Wells JM, Vertebrate endoderm development and organ formation. Annual Review of Cell Developmental Biology (2009) - http://bgee.unil.ch/ - @@ -42714,16 +37820,13 @@ plexiform layer. - + Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic. Do not merge with neurogenic placode - Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons - The term placode or placodes also applies to developing organs such as teeth, mammary glands, hair follicles, feathers and scales. We include a separate parent class for this. to avoid confusion, we include neurogenic placode as a subclass ectodermal placode placode AAO:0010466 EFO:0001650 - FMA:293966 MAT:0000369 MIAA:0000369 XAO:0000305 @@ -42734,7 +37837,7 @@ plexiform layer. cranial placode - + @@ -42747,7 +37850,7 @@ plexiform layer. - + PMID:11523831 PMID:22512454 @@ -42761,12 +37864,6 @@ plexiform layer. https://orcid.org/0000-0002-6601-2165 https://sourceforge.net/p/obo/xenopus-anatomy-xao-term-requests/11/ - - - - Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons - PMID:11523831 - @@ -42850,6 +37947,7 @@ plexiform layer. + @@ -42952,7 +38050,7 @@ plexiform layer. - + @@ -42965,10 +38063,9 @@ plexiform layer. - + The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate. consider adding class for organizer. Consider adding separate class for isthmus as a structure - Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG] AAO:0011064 DMBA:16810 EHDAA2:0004395 @@ -42995,31 +38092,24 @@ plexiform layer. midbrain-hindbrain boundary - + - + - - ZFA - https://sourceforge.net/p/obo/zebrafish-anatomy-zfa-term-requests/106/ - - - - - + ZFA - + ZFA @@ -43028,16 +38118,6 @@ plexiform layer. The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate. GO:0021555 - - - - Lampreys also have an MHB [midbrain hindbrain boundary], expressing a similar repertoire of regulatory gene cognates as in gnathostomes.[well established][VHOG] - 2012-09-17 - VHOG:0000649 - VHOG - DOI:10.1016/j.ydbio.2005.02.008 Murakami Y, Uchida K, Rijli FM and Kuratani S, Evolution of the brain developmental plan: Insights from agnathans. Developmental Biology (2005) - http://bgee.unil.ch/ - @@ -43063,6 +38143,7 @@ plexiform layer. + @@ -43070,14 +38151,7 @@ plexiform layer. - - - - - - The portion of neural plate anterior to the mid-hindbrain junction. - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] AAO:0011084 TAO:0007016 VHOG:0001200 @@ -43094,16 +38168,6 @@ plexiform layer. The portion of neural plate anterior to the mid-hindbrain junction. XB:curator - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] - 2012-09-17 - VHOG:0001200 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 - http://bgee.unil.ch/ - @@ -43117,14 +38181,7 @@ plexiform layer. - - - - - - The portion of neural plate posterior to the mid-hindbrain junction. - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] TAO:0007017 VHOG:0001201 XAO:0000046 @@ -43140,16 +38197,6 @@ plexiform layer. The portion of neural plate posterior to the mid-hindbrain junction. XB:curator - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] - 2012-09-17 - VHOG:0001201 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 - http://bgee.unil.ch/ - @@ -43184,10 +38231,8 @@ plexiform layer. - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. - Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO] - It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG] AAO:0011086 EFO:0001982 EMAPA:16189 @@ -43209,14 +38254,14 @@ plexiform layer. presomitic mesoderm - + - + Bgee:AN @@ -43225,25 +38270,6 @@ plexiform layer. Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. ZFIN:curator - - - - Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000279 - TAO - ZFIN:curator - - - - - It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG] - 2012-09-17 - VHOG:0000559 - VHOG - DOI:10.1006/dbio.2001.0460 Schubert M, Holland LZ, Dale Stokes M and Holland ND, Three Amphoxius Wnt Genes (AmphiWnt3, AmphiWnt5, and AmphiWnt6) Associated with the Tail Bud: the Evolution of Somitogenesis in Chordates. Developmental Biology (2001) - http://bgee.unil.ch/ - @@ -43282,11 +38308,6 @@ plexiform layer. Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted]. - Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO] - Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO] - relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO] - Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG] - EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac ventral lateral plate mesoderm AAO:0011006 EFO:0003489 @@ -43319,48 +38340,6 @@ plexiform layer. Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted]. Wikipedia:Blood_island_of_umbilical_vesicle - - - - Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000094 - TAO - ZFIN:curator - - - - - Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO] - 2012-06-20 - AAO:0011006 - AAO - AAO:EJS - - - - - relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO] - 2012-08-14 - TAO:0000094 - TAO - - - - - Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0000085 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450, DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual Review of Cell and Developmental Biology (2006) - http://bgee.unil.ch/ - - - - - EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac - EHDAA2 - @@ -43399,7 +38378,6 @@ plexiform layer. The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord. - The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] AAO:0011017 EFO:0003647 TAO:0001204 @@ -43422,15 +38400,6 @@ plexiform layer. GO:0048318 Wikipedia:Chordamesoderm - - - - The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] - 2012-09-17 - VHOG:0000107 - VHOG - http://bgee.unil.ch/ - @@ -43458,7 +38427,8 @@ plexiform layer. - + + @@ -43472,7 +38442,6 @@ plexiform layer. Portion of tissue that is part of the anterior neural keel and will form the optic vesicle[ZFA]. A paired ectodermal placode that becomes invaginated to form the embryonic lens vesicles. - TODO - check that GO's optic placode is the same as ZFA's eye primordium; we may want to have separate term for ocular primordium precursor. XAO has both optic field and eye primordium. UBERON:0005060 AAO:0011038 EFO:0003541 @@ -43496,7 +38465,7 @@ plexiform layer. eye primordium - + @@ -43509,7 +38478,7 @@ plexiform layer. - + PMID:16496288 XAO @@ -43520,12 +38489,6 @@ plexiform layer. GO:0046619 ZFA:0000570 - - - - TODO - check that GO's optic placode is the same as ZFA's eye primordium; we may want to have separate term for ocular primordium precursor. XAO has both optic field and eye primordium. - GO - @@ -43565,8 +38528,8 @@ plexiform layer. - - + + @@ -43574,7 +38537,6 @@ plexiform layer. Multi-tissue structure that is comprised of neural and non-neural epithelial layers which will form the retina and retinal pigmented epithelium of the mature eye[ZFA]. double walled structured formed by expansion and invagination of the distal end of the optic vesicle that develops into the pigmented and sensory layers of the retina while the mouth of the optic cup eventually forms the pupil of the eye[MP]. - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG] BTO:0005351 EHDAA2:0001303 EHDAA:2912 @@ -43595,24 +38557,24 @@ plexiform layer. optic cup - + - + - + ZFA - + ZFA @@ -43623,16 +38585,6 @@ plexiform layer. Wikipedia:Optic_cup_(embryology) ZFA:0001202 - - - - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG] - 2012-09-17 - VHOG:0000167 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 - http://bgee.unil.ch/ - @@ -43676,8 +38628,9 @@ plexiform layer. + - + @@ -43691,9 +38644,6 @@ plexiform layer. A thickened portion of ectoderm which serves as the precursor to the lens. SOX2 and Pou2f1 are involved in its development[WP]. - Ectodermal primordium of the lens of the eye. Kimmel et al, 1995.[TAO] - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG] - Classical transplantation experiments using amphibian embryos suggested that the optic vesicle is the source of lens-inducing signals sufficient to generate lens tissues in competent ectoderm (reviewed in Grainger et al., 1996). More recent findings suggest a multistep model for lens induction. There is now good evidence that lens specification occurs at the neurula stage, before the optic vesicle contact the surface ectoderm, and that neural crest cell migration in the frontonasal region is required to restrict the position of the lens placode (Bailey et al., 2006) AAO:0011055 EFO:0003494 EHDAA2:0000982 @@ -43718,7 +38668,7 @@ plexiform layer. lens placode http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png - + @@ -43731,7 +38681,7 @@ plexiform layer. - + ZFA @@ -43741,31 +38691,6 @@ plexiform layer. Wikipedia:Lens_placode ZFIN:curator - - - - Ectodermal primordium of the lens of the eye. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000122 - TAO - ZFIN:curator - - - - - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG] - 2012-09-17 - VHOG:0000166 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 - http://bgee.unil.ch/ - - - - - Classical transplantation experiments using amphibian embryos suggested that the optic vesicle is the source of lens-inducing signals sufficient to generate lens tissues in competent ectoderm (reviewed in Grainger et al., 1996). More recent findings suggest a multistep model for lens induction. There is now good evidence that lens specification occurs at the neurula stage, before the optic vesicle contact the surface ectoderm, and that neural crest cell migration in the frontonasal region is required to restrict the position of the lens placode (Bailey et al., 2006) - NCBIBook:NBK53175 - @@ -43795,12 +38720,10 @@ plexiform layer. - - - + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. - The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO] - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] AAO:0011072 BTO:0001765 DHBA:10153 @@ -43809,7 +38732,6 @@ plexiform layer. EHDAA:902 EMAPA:35593 FMA:293879 - MESH:D054258 NCIT:C34225 RETIRED_EHDAA2:0001252 TAO:0000132 @@ -43829,34 +38751,34 @@ plexiform layer. neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -43868,33 +38790,6 @@ plexiform layer. Wikipedia:Neural_plate ZFIN:curator - - - - The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000132 - TAO - ZFIN:curator - - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] - 2012-09-17 - VHOG:0000068 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 - http://bgee.unil.ch/ - - - - - MESH:D054258 - - - https://github.com/biopragmatics/biomappings - @@ -43928,7 +38823,6 @@ plexiform layer. - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] AAO:0011082 TAO:0007037 VHOG:0001383 @@ -43944,16 +38838,6 @@ plexiform layer. lexical - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] - 2012-09-17 - VHOG:0001383 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 - http://bgee.unil.ch/ - @@ -43963,23 +38847,14 @@ plexiform layer. - - - - - - - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. - Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO] - Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG] - note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here) AAO:0010568 EFO:0003515 EMAPA:16183 @@ -44004,7 +38879,7 @@ plexiform layer. paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -44017,7 +38892,7 @@ plexiform layer. - + Bgee:AN @@ -44027,31 +38902,6 @@ plexiform layer. GO:0048339 https://github.com/obophenotype/uberon/issues/30 - - - - Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO] - 2012-06-20 - AAO:0010568 - AAO - AAO:EJS - - - - - Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG] - 2012-09-17 - VHOG:0000114 - VHOG - DOI:10.1002/dvdy.21177 Kusakabe R and Kuratani S. Evolutionary perspectives from development of mesodermal components in the lamprey. Developmental dynamics (2007) - http://bgee.unil.ch/ - - - - - note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here) - ZFA - @@ -44099,7 +38949,6 @@ plexiform layer. TODO - add grouping class for the anterior end of the neural tube at all stages - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] AAO:0011012 TAO:0007038 VHOG:0001384 @@ -44109,16 +38958,6 @@ plexiform layer. UBERON:0003080 anterior neural tube - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] - 2012-09-17 - VHOG:0001384 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 - http://bgee.unil.ch/ - @@ -44129,7 +38968,7 @@ plexiform layer. - + @@ -44143,10 +38982,6 @@ plexiform layer. Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]. - Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO] - The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] - A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG] - subclass of mesoderm in ZFA. UBERON:0006258 AAO:0010574 EHDAA2:0000919 @@ -44173,7 +39008,7 @@ plexiform layer. lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -44186,7 +39021,7 @@ plexiform layer. - + EHDAA2 VHOG @@ -44197,40 +39032,6 @@ plexiform layer. MP:0010117 Wikipedia:Lateral_plate_mesoderm - - - - Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO] - 2012-06-20 - AAO:0010574 - AAO - AAO:EJS - - - - - The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] - 2012-09-17 - VHOG:0000118 - VHOG - http://bgee.unil.ch/ - - - - - A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG] - 2012-09-17 - VHOG:0000118 - VHOG - DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) - http://bgee.unil.ch/ - - - - - subclass of mesoderm in ZFA. - ZFA - @@ -44270,20 +39071,17 @@ plexiform layer. - - + + - + Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. should probably be merged with heart rudiment. - Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO] - The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO] - relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO] AAO:0011044 BTO:0001887 NCIT:C34276 @@ -44298,15 +39096,15 @@ plexiform layer. heart primordium - + - + - + @@ -44319,19 +39117,19 @@ plexiform layer. - + ZFA - + ZFA - + XAO @@ -44340,32 +39138,6 @@ plexiform layer. Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. ZFIN:curator - - - - Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO] - 2012-08-14 - TAO:0000028 - TAO - ZFIN:curator - - - - - The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO] - 2012-06-20 - AAO:0011044 - AAO - XAO:curator - - - - - relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO] - 2012-08-14 - TAO:0000028 - TAO - @@ -44386,15 +39158,11 @@ plexiform layer. - - + + Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. - Skeletogenic portion of somites.[AAO] - The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG] - part_of somite in XAO AAO:0010571 AEO:0000212 - BTO:0006255 EHDAA2:0003439 EMAPA:31159 FMA:295652 @@ -44415,11 +39183,11 @@ plexiform layer. sclerotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + - + @@ -44438,13 +39206,13 @@ plexiform layer. - + VHOG:0000680 - + ZFA @@ -44455,39 +39223,6 @@ plexiform layer. XB:curator https://github.com/obophenotype/uberon/issues/316 - - - - Skeletogenic portion of somites.[AAO] - 2012-06-20 - AAO:0010571 - AAO - AAO:EJS - - - - - The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG] - 2012-09-17 - VHOG:0000680 - VHOG - DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) - http://bgee.unil.ch/ - - - - - part_of somite in XAO - XAO - - - - - BTO:0006255 - - - https://github.com/biopragmatics/biomappings - @@ -44529,8 +39264,6 @@ plexiform layer. The narrow, proximal portion of the optic vesicle which connects the embryonic eye and forebrain. - The evagination from the neural tube of the developing embryo which develops the optic cup at its extremity; the stalk persists as the optic nerve. [TFD][VHOG] - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG] AAO:0011077 EHDAA2:0001318 EHDAA:3816 @@ -44566,26 +39299,6 @@ plexiform layer. ISBN:0-914294-08-3 MP:0004268 - - - - The evagination from the neural tube of the developing embryo which develops the optic cup at its extremity; the stalk persists as the optic nerve. [TFD][VHOG] - 2012-09-17 - VHOG:0000223 - VHOG - http://bgee.unil.ch/ - http://medical-dictionary.thefreedictionary.com/optic+stalk - - - - - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup.[well established][VHOG] - 2012-09-17 - VHOG:0000223 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 - http://bgee.unil.ch/ - @@ -44612,7 +39325,9 @@ plexiform layer. + + @@ -44626,9 +39341,6 @@ plexiform layer. Neural crest cells (NCCs) originating in the anterior part of the developing embryo and residing between the mid-diencephalon and the forming hindbrain; cranial NCCs migrate dorsolaterally to form the craniofacial mesenchyme that differentiates into various craniofacial cartilages and bones, cranial neurons, glia, and connective tissues of the face; these cells enter the pharyngeal pouches and arches where they give rise to thymic cells, bones of the middle ear and jaw (mandible), and the odontoblasts of the tooth primordia; like their counterparts in the trunk, cranial NCCs also contribute to the developing peripheral nervous system, along with the pigmented cell (i.e. melanocyte) lineage. - Anterior most portion of the neural crest. Migrates in three highly conserved streams: mandibular, hyoid and branchial.[AAO] - Neural crest that is part of the head.[TAO] - We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] AAO:0010580 EFO:0003645 EHDAA2:0004420 @@ -44658,34 +39370,6 @@ plexiform layer. Neural crest cells (NCCs) originating in the anterior part of the developing embryo and residing between the mid-diencephalon and the forming hindbrain; cranial NCCs migrate dorsolaterally to form the craniofacial mesenchyme that differentiates into various craniofacial cartilages and bones, cranial neurons, glia, and connective tissues of the face; these cells enter the pharyngeal pouches and arches where they give rise to thymic cells, bones of the middle ear and jaw (mandible), and the odontoblasts of the tooth primordia; like their counterparts in the trunk, cranial NCCs also contribute to the developing peripheral nervous system, along with the pigmented cell (i.e. melanocyte) lineage. MGI:anna - - - - Anterior most portion of the neural crest. Migrates in three highly conserved streams: mandibular, hyoid and branchial.[AAO] - 2012-06-20 - AAO:0010580 - AAO - AAO:EJS - - - - - Neural crest that is part of the head.[TAO] - 2012-08-14 - TAO:0001194 - TAO - ZFIN:curator - - - - - We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] - 2012-09-17 - VHOG:0000063 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 - http://bgee.unil.ch/ - @@ -44714,7 +39398,6 @@ plexiform layer. Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types. - this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs AAO:0010015 AEO:0000024 BILA:0000024 @@ -44778,9 +39461,6 @@ plexiform layer. Portion of tissue composed of mesenchymal cells (motile cells that develop from epthelia via an epithelial to mesenchymal transition) and surrounding extracellular material. Mesenchyme has different embryological origins in different metazoan taxa - in many invertebrates it derives in whole or part from ectoderm. In vertebrates it derives largely from mesoderm, and sometimes the terms are used interchangeably, e.g. lateral plate mesoderm/mesenchyme. the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense - A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO] - Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO] - mesenchymal AAO:0010427 AEO:0000145 BTO:0001393 @@ -44815,24 +39495,6 @@ plexiform layer. https://en.wikipedia.org/wiki/Mesenchyme https://github.com/obophenotype/uberon/issues/1641 - - - - A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000393 - TAO - ZFIN:curator - - - - - Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO] - 2012-06-20 - AAO:0010427 - AAO - AAO:EJS - @@ -44863,6 +39525,7 @@ plexiform layer. + @@ -44870,7 +39533,7 @@ plexiform layer. - + Mesenchyme that is part of a developing camera-type eye. TODO - change mesenchyme relationships to precursor_of EHDAA2:0000485 @@ -44882,14 +39545,14 @@ plexiform layer. UBERON:0003314 eye mesenchyme - + - + EHDAA2 @@ -44922,6 +39585,7 @@ plexiform layer. + @@ -44989,7 +39653,6 @@ plexiform layer. The regions of the brain that are largely or entirely composed of myelinated nerve cell axons and contain few or no neural cell bodies or dendrites. EMAPA:35187 - HBA:9218 MA:0000820 NCIT:C49334 UMLS:C1706995 @@ -45076,7 +39739,6 @@ plexiform layer. A portion of connective tissue that is part of a head [Automatically generated definition]. - EMAPA:16098 MA:0000577 adult head connective tissue adult head portion of connective tissue @@ -45206,8 +39868,6 @@ plexiform layer. Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature. - One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO] - FMA definition includes vasculature AAO:0000325 AEO:0000123 EHDAA2:0003123 @@ -45230,21 +39890,6 @@ plexiform layer. Portion of tissue in the nervous system which consists of neurons and glial cells, and may also contain parts of the vasculature. FMA:9642 - - - - One of the four types of tissue in traditional classifications. Cells forming the brain, spinal cord and peripheral nervous system.[AAO] - 2012-06-20 - AAO:0000325 - AAO - AAO:LAP - - - - - FMA definition includes vasculature - FMA - @@ -45300,7 +39945,6 @@ plexiform layer. An anatomical space that surrounded_by a neural tube. - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] UBERON:0005713 AAO:0011073 EHDAA2:0001269 @@ -45326,16 +39970,6 @@ plexiform layer. An anatomical space that surrounded_by a neural tube. OBOL:automatic - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] - 2012-09-17 - VHOG:0001119 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 - http://bgee.unil.ch/ - @@ -45392,7 +40026,6 @@ plexiform layer. A neural crest that has_potential_to_developmentally_contribute_to a midbrain. - We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] EFO:0003591 EHDAA2:0001101 EHDAA:360 @@ -45419,16 +40052,6 @@ plexiform layer. A neural crest that has_potential_to_developmentally_contribute_to a midbrain. OBOL:automatic - - - - We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] - 2012-09-17 - VHOG:0000796 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 - http://bgee.unil.ch/ - @@ -45466,7 +40089,6 @@ plexiform layer. A neural crest that has_potential_to_developmentally_contribute_to a diencephalon. - We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] EFO:0003573 EHDAA2:0000603 EMAPA:16518 @@ -45488,16 +40110,6 @@ plexiform layer. A neural crest that has_potential_to_developmentally_contribute_to a diencephalon. OBOL:automatic - - - - We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] - 2012-09-17 - VHOG:0000798 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 - http://bgee.unil.ch/ - @@ -45548,8 +40160,6 @@ plexiform layer. A neural crest that has_potential_to_developmentally_contribute_to a hindbrain. - Cranial neural crest that is part of the hindbrain.[TAO] - We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] EHDAA2:0001628 EHDAA:362 EMAPA:35747 @@ -45576,25 +40186,6 @@ plexiform layer. A neural crest that has_potential_to_developmentally_contribute_to a hindbrain. OBOL:automatic - - - - Cranial neural crest that is part of the hindbrain.[TAO] - 2012-08-14 - TAO:0007063 - TAO - ZFIN:curator - - - - - We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...).[well established][VHOG] - 2012-09-17 - VHOG:0001210 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 - http://bgee.unil.ch/ - @@ -45638,7 +40229,6 @@ plexiform layer. A neural crest that has_potential_to_developmentally_contribute_to a spinal cord. - We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)[well established][VHOG] EHDAA:696 EMAPA:16163 EMAPA:16881 @@ -45655,16 +40245,6 @@ plexiform layer. A neural crest that has_potential_to_developmentally_contribute_to a spinal cord. OBOL:automatic - - - - We conclude this section by listing some of the many synapomorphies of craniates, including (1) the neural crest (...)[well established][VHOG] - 2012-09-17 - VHOG:0001006 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.43 - http://bgee.unil.ch/ - @@ -45747,10 +40327,9 @@ plexiform layer. - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults - (...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG] EHDAA:251 EMAPA:16088 NCIT:C34195 @@ -45763,14 +40342,14 @@ plexiform layer. intraembryonic coelom - + - + Wikipedia @@ -45780,16 +40359,6 @@ plexiform layer. MGI:anna MP:0012187 - - - - (...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG] - 2012-09-17 - VHOG:0000316 - VHOG - ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.166 - http://bgee.unil.ch/ - @@ -45822,7 +40391,6 @@ plexiform layer. Connective, non-functional supportive framework of a biological cell, tissue, or organ. Contrast with parenchyma. - stromal FMA:81494 NCIT:C67387 UMLS:C0927195 @@ -45862,7 +40430,6 @@ plexiform layer. - @@ -45875,10 +40442,9 @@ plexiform layer. - + The part of the retina that contains neurons and photoreceptor cells[GO]. - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] AAO:0011095 BTO:0000929 CALOHA:TS-0685 @@ -45907,14 +40473,14 @@ plexiform layer. retinal neural layer - + - + Bgee:AN @@ -45923,16 +40489,6 @@ plexiform layer. The part of the retina that contains neurons and photoreceptor cells[GO]. GO:0003407 - - - - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] - 2012-09-17 - VHOG:0000535 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 - http://bgee.unil.ch/ - @@ -45998,10 +40554,8 @@ plexiform layer. Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. - contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers AEO:0000114 EHDAA2:0003114 - FBbt:00007474 epithelial or endothelial tube uberon UBERON:0003914 @@ -46014,12 +40568,6 @@ plexiform layer. GO:0060562 PMID:12526790 - - - - FBbt:00007474 - - @@ -46097,6 +40645,7 @@ plexiform layer. + @@ -46117,7 +40666,6 @@ plexiform layer. The single layer of epithelial cells that lines the early neural tube and develops into the nervous system and into the neural crest cells. - As the cells adjacent to the lumen continue to divide, the migrating cells form a second layer around the original neural tube. This layer becomes progressively thicker as more cells are added to it from the germinal neuroepithelium. This new layer is called the mantle (or intermediate) zone, and the germinal epithelium is now called the ventricular zone (and, later, the ependyma)[NCBIBook:NBK10047] germinal neuroepithelial layer germinal neuroepithelium original neural tube @@ -46178,10 +40726,9 @@ plexiform layer. - + The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium. consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure - The layer of undifferentiated, proliferating cells that line the neural tube lumen ependymal layer EMAPA:17152 EMAPA:35362 @@ -46196,7 +40743,7 @@ plexiform layer. neural tube ventricular layer - + @@ -46209,7 +40756,7 @@ plexiform layer. - + NCBIBook:NBK10047 @@ -46219,12 +40766,6 @@ plexiform layer. MP:0009689 http://www.ncbi.nlm.nih.gov/books/NBK10047 - - - - The layer of undifferentiated, proliferating cells that line the neural tube lumen - MP:0009689 - @@ -46262,6 +40803,7 @@ plexiform layer. + @@ -46269,7 +40811,12 @@ plexiform layer. - + + + + + + @@ -46293,23 +40840,12 @@ plexiform layer. neural tube mantle layer - - - - NCBIBook:NBK10047 - - - - - by division - NCBIBook:NBK10047 - @@ -46336,6 +40872,7 @@ plexiform layer. + @@ -46343,7 +40880,12 @@ plexiform layer. - + + + + + + @@ -46360,16 +40902,6 @@ plexiform layer. neural tube marginal layer - - - - - - - - - forms from axons - @@ -46398,7 +40930,6 @@ plexiform layer. The subdivision of the face that includes the eye (eyeball plus adnexa such as eyelids) and the orbit of the skull and associated parts of the face such as the eyebrows, if present. note the FMA class is more narrow though, and is more like eye + muscles + vasculature. The FMA also has FMA:72951 orbital part of eye - in HP covers eyelid, eyebrow. FMA:260119 content of orbital part of eye eye region @@ -46418,12 +40949,6 @@ plexiform layer. The subdivision of the face that includes the eye (eyeball plus adnexa such as eyelids) and the orbit of the skull and associated parts of the face such as the eyebrows, if present. http://orcid.org/0000-0002-6601-2165 - - - - in HP covers eyelid, eyebrow. - HP:0000284 - @@ -46499,7 +41024,6 @@ plexiform layer. - FMA has both conduit and conduit space. In EHDAA2 this is a surface feature AEO:0000080 EHDAA2:0003080 FMA:242873 @@ -46521,12 +41045,6 @@ plexiform layer. Any tube, opening or passage that connects two distinct anatomical spaces. http://orcid.org/0000-0002-6601-2165 - - - - FMA has both conduit and conduit space. In EHDAA2 this is a surface feature - FMA - @@ -46571,7 +41089,6 @@ plexiform layer. An anatomical structure that develops (entirely or partially) from the mesoderm. - Grouping term for query purposes mesodermal derivative uberon UBERON:0004120 @@ -46615,7 +41132,6 @@ plexiform layer. An anatomical structure that develops (entirely or partially) from the ectoderm. - Grouping term for query purposes ectodermal deriviative uberon UBERON:0004121 @@ -46642,9 +41158,9 @@ plexiform layer. - - - + + + @@ -46652,7 +41168,6 @@ plexiform layer. The optic vesicle is the evagination of neurectoderm that precedes formation of the optic cup[GO]. Portion of tissue that is comprised of neuroepitheium which has pinched off from the anterior neural keel and will form the optic cup[ZFA]. - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles.[well established][VHOG] AAO:0011039 EHDAA2:0001320 EMAPA:16540 @@ -46677,34 +41192,34 @@ plexiform layer. optic vesicle http://upload.wikimedia.org/wikipedia/commons/e/e0/Gray863.png - + - + - + - + ZFA - + GO-def - + ZFA @@ -46714,16 +41229,6 @@ plexiform layer. GO:0003404 Wikipedia:Optic_vesicles - - - - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles.[well established][VHOG] - 2012-09-17 - VHOG:0000165 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 - http://bgee.unil.ch/ - @@ -46764,7 +41269,6 @@ plexiform layer. The first recognizable structure derived from the heart field. TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO - (In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG] EHDAA2:0000215 EMAPA:16106 VHOG:0000975 @@ -46783,16 +41287,6 @@ plexiform layer. The first recognizable structure derived from the heart field. GO:0003142 - - - - (In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG] - 2012-09-17 - VHOG:0000975 - VHOG - PMID:15611355 Gittenberger-de Groot AC, Bartelings MM, Deruiter MC, Poelmann RE, Basics of cardiac development for the understanding of congenital heart malformations. Pediatric Research (2005) - http://bgee.unil.ch/ - @@ -46818,12 +41312,12 @@ plexiform layer. + - - + + A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. - this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138] XAO:0004185 first heart field primary heart field @@ -46834,24 +41328,24 @@ plexiform layer. UBERON:0004140 primary heart field - + - + - + GO:0003128 - + https://orcid.org/0000-0003-3308-6245 @@ -46862,12 +41356,6 @@ plexiform layer. GOC:mtg_heart GOC:rl - - - - this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138] - GO - @@ -46910,9 +41398,8 @@ plexiform layer. - + An epithelial tube that will give rise to the mature heart. - the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube. AAO:0010411 EFO:0003526 EMAPA:32685 @@ -46930,14 +41417,14 @@ plexiform layer. heart tube - + - + ZFA-modified @@ -46947,12 +41434,6 @@ plexiform layer. GO:0003143 GOC:mtg_heart - - - - the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube. - MP:0012700 - @@ -46978,6 +41459,7 @@ plexiform layer. + @@ -47018,7 +41500,8 @@ plexiform layer. - + + @@ -47034,14 +41517,14 @@ plexiform layer. eye muscle - + - + MA @@ -47071,10 +41554,7 @@ plexiform layer. Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body. - - Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO] - skeletal AEO:0000168 EHDAA2:0001843 EHDAA:5047 @@ -47107,15 +41587,6 @@ plexiform layer. Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body. VSAO:0000026 - - - - Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO] - 2012-08-14 - VSAO:0000026 - VSAO - GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 - @@ -47130,7 +41601,6 @@ plexiform layer. A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube. - The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO] TAO:0000115 ZFA:0000115 heart cone @@ -47145,15 +41615,6 @@ plexiform layer. A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube. GO:0003313 - - - - The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO] - 2012-08-14 - TAO:0000115 - TAO - ZFIN:curator - @@ -47221,6 +41682,7 @@ plexiform layer. + @@ -47245,10 +41707,9 @@ plexiform layer. - + A transparent homogeneous acellular layer found between the substantia propria and the endothelial layer of the cornea[MP]. - Acellular anatomical structure composed of collagen, Descemet's membrane is secreted as a basement membrane of the corneal endothelium. Located between the stroma and the corneal endothelium, it is approximately 0.15 micrometer thick at 6 months post-fertilization.[ZFIN] EMAPA:18804 FMA:58309 GAID:894 @@ -47275,14 +41736,14 @@ plexiform layer. Descemet's membrane https://github.com/obophenotype/uberon/issues/15 - + - + Cline et al @@ -47298,16 +41759,6 @@ plexiform layer. MP:0004285 https://github.com/obophenotype/uberon/issues/15 - - - - Acellular anatomical structure composed of collagen, Descemet's membrane is secreted as a basement membrane of the corneal endothelium. Located between the stroma and the corneal endothelium, it is approximately 0.15 micrometer thick at 6 months post-fertilization.[ZFIN] - 2016-05-01 - TAO:0002157 - ZFIN - ZFIN:ZDB-PUB-061010-3 - https://orcid.org/0000-0001-9114-8737 - @@ -47374,6 +41825,7 @@ plexiform layer. + @@ -47387,8 +41839,6 @@ plexiform layer. A transparent homogeneous acellular layer, 6 to 9 um thick, lying between the basal lamina of the outer layer of stratified epithelium and the substantia propria of the cornea; it is considered to be a basement membrane. - Acellular anatomical structure that is the zone of collagen fibers adjacent the basement membrane of the corneal epithelium.[TAO] - Compared to terrestial animals, the cornea of zebrafish is relatively flat. It consists of nonpigmented, stratified squamous nonkeratinizing epithelial cells, attached to a thick basement membrane that is considered to be analogous to the Bowman's membrane in mammals FMA:58273 MA:0001240 NCIT:C32226 @@ -47419,15 +41869,6 @@ plexiform layer. A transparent homogeneous acellular layer, 6 to 9 um thick, lying between the basal lamina of the outer layer of stratified epithelium and the substantia propria of the cornea; it is considered to be a basement membrane. ncithesaurus:Bowman_s_Membrane - - - - Acellular anatomical structure that is the zone of collagen fibers adjacent the basement membrane of the corneal epithelium.[TAO] - 2012-08-14 - TAO:0002155 - TAO - ZFIN:ZDB-PUB-061010-3 - @@ -47517,7 +41958,6 @@ plexiform layer. Sum of all sensory systems in an organism. - note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs FMA:78499 sense organ system uberon @@ -47583,18 +42023,14 @@ plexiform layer. Anatomical system that has as its parts the heart and blood vessels. - we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph. - The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG] AAO:0011001 BILA:0000016 BTO:0000088 CALOHA:TS-1297 EFO:0000791 - EHDAA2:0000216 EHDAA:394 EMAPA:16104 - EMAPA:16370 EV:0100017 FMA:7161 GAID:467 @@ -47628,16 +42064,6 @@ plexiform layer. Anatomical system that has as its parts the heart and blood vessels. BTO:0000088 - - - - The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG] - 2012-09-17 - VHOG:0000302 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.451 - http://bgee.unil.ch/ - @@ -47889,6 +42315,7 @@ plexiform layer. + @@ -47954,11 +42381,9 @@ plexiform layer. Organism at the gastrula stage. - We explicitly merge the NCITA terms here UBERON:0007012 BILA:0000060 BTO:0001403 - FBbt:00005317 FMA:293108 GAID:1302 MESH:D005775 @@ -47990,18 +42415,6 @@ plexiform layer. Wikipedia:Gastrula Wikipedia:Trilaminar_blastocyst - - - - We explicitly merge the NCITA terms here - NCIT - - - - - FBbt:00005317 - - @@ -48075,10 +42488,8 @@ plexiform layer. - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. - Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO] - Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO] AAO:0011129 TAO:0001890 VSAO:0000128 @@ -48091,14 +42502,14 @@ plexiform layer. skeletal element - + - + VSAO @@ -48107,24 +42518,6 @@ plexiform layer. Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. https://orcid.org/0000-0002-6601-2165 - - - - Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO] - 2012-08-14 - VSAO:0000128 - VSAO - PSPUB:0000170 - - - - - Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO] - 2012-08-14 - TAO:0001890 - TAO - TAO:VSAO_workshop - @@ -48143,7 +42536,7 @@ plexiform layer. - + @@ -48182,14 +42575,14 @@ plexiform layer. UBERON:0004770 articular system - + - + FMA @@ -48242,7 +42635,6 @@ plexiform layer. An endothelium that is part of the cardiovascular system. consider merging with 'endothelium' - Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] BTO:0001853 EMAPA:35201 GAID:519 @@ -48267,16 +42659,6 @@ plexiform layer. An endothelium that is part of the cardiovascular system. https://orcid.org/0000-0002-6601-2165 - - - - Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] - 2012-09-17 - VHOG:0001217 - VHOG - ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207 - http://bgee.unil.ch/ - @@ -48311,7 +42693,6 @@ plexiform layer. Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP]. - We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors visceral mesoderm AAO:0011102 BILA:0000044 @@ -48331,12 +42712,6 @@ plexiform layer. Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP]. Wikipedia:Lateral_plate_mesoderm#Division_into_layers - - - - We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors - BILA - @@ -48371,8 +42746,6 @@ plexiform layer. The central region of trunk mesoderm. This tissue forms the notochord. - Notochord rudiment[ZFIN:ZDB-PUB-961014-576]. - WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord. AAO:0000478 EFO:0003426 TAO:0000091 @@ -48393,12 +42766,6 @@ plexiform layer. The central region of trunk mesoderm. This tissue forms the notochord. https://orcid.org/0000-0002-6601-2165 - - - - Notochord rudiment[ZFIN:ZDB-PUB-961014-576]. - ZFIN:ZDB-PUB-961014-576 - @@ -48431,7 +42798,6 @@ plexiform layer. Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts. - FBbt:00005811 joint uberon UBERON:0004905 @@ -48444,12 +42810,6 @@ plexiform layer. Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts. http://orcid.org/0000-0002-6601-2165 - - - - FBbt:00005811 - - @@ -48481,9 +42841,7 @@ plexiform layer. A proximal-distal subdivision of the digestive tract. - intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct. - FBbt:00100315 FMA:71131 uberon alimentary system subdivision @@ -48502,12 +42860,6 @@ plexiform layer. A proximal-distal subdivision of the digestive tract. http://orcid.org/0000-0002-6601-2165 - - - - FBbt:00100315 - - @@ -48572,7 +42924,6 @@ plexiform layer. The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds. - The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]. AAO:0011071 EMAPA:35594 FMA:295624 @@ -48594,12 +42945,6 @@ plexiform layer. Wikipedia:Neural_groove http://orcid.org/0000-0002-6601-2165 - - - - The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]. - Wikipedia:Neural_groove - @@ -48615,6 +42960,7 @@ plexiform layer. + @@ -48622,14 +42968,7 @@ plexiform layer. - - - - - - One of the two elevated edges of the neural groove[GO,MP]. - In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]. EHDAA2:0001249 FMA:295618 NCIT:C34223 @@ -48652,12 +42991,6 @@ plexiform layer. MP:0011256 Wikipedia:Neural_fold - - - - In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]. - Wikipedia:Neural_fold - @@ -48684,7 +43017,6 @@ plexiform layer. A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN]. - An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO] EFO:0003498 TAO:0000133 ZFA:0000133 @@ -48701,15 +43033,6 @@ plexiform layer. GO:0014024 ZFA:0000133 - - - - An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000133 - TAO - ZFIN:curator - @@ -48732,8 +43055,6 @@ plexiform layer. An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm[GO]. consder adding placodal ectoderm as a distinct class? Also place placodal ectoderm as develops_from ectoderm; need to check taxon-appropriateness - With the exception of the adenohypophysis, homologues of the nonneurogenic placodes (e.g. placodes giving rise to the teeth, hair follicles and lens), appear to be lacking in invertebrate chordates. - in GO, covers optic, otic, olfactory, mammary, hair, tooth, sebaceous - and also insect structures AEO:0000218 uberon epithelial placode @@ -48746,13 +43067,6 @@ plexiform layer. An ectodermal placode is a thickening of the ectoderm that is the primordium of many structures derived from the ectoderm[GO]. GO:0060788 - - - - in GO, covers optic, otic, olfactory, mammary, hair, tooth, sebaceous - and also insect structures - GO - https://github.com/geneontology/go-ontology/issues/12223#issuecomment-215692347 - @@ -48779,8 +43093,6 @@ plexiform layer. Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO]. - in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila - EMAPA:32715 FMA:30316 musculus uberon @@ -48833,10 +43145,8 @@ plexiform layer. A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part. - we go with the FMA classification rather than the CARO one. FMA def: 'Anatomical cluster which has as direct parts cell parts from two or more cells.' AAO:0011000 CARO:0001000 - FBbt:00007060 FMA:83115 multi-cell-component structure multi-cell-part structure @@ -48852,19 +43162,6 @@ plexiform layer. A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part. CARO:0001000 - - - - we go with the FMA classification rather than the CARO one. FMA def: 'Anatomical cluster which has as direct parts cell parts from two or more cells.' - CARO - FMA - - - - - FBbt:00007060 - - @@ -49116,9 +43413,8 @@ plexiform layer. - + Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells. - Mesoderm that will give rise, along with cranial neural crest cells, to connective tissue, bone and musculature in the head. (Source: BioGlossary, www.Biology-Text.com)[TAO] EFO:0003492 EHDAA2:0000732 EHDAA:179 @@ -49138,14 +43434,14 @@ plexiform layer. head mesenchyme - + - + EHDAA2 @@ -49155,15 +43451,6 @@ plexiform layer. ISBN:0683400088 MP:0011260 - - - - Mesoderm that will give rise, along with cranial neural crest cells, to connective tissue, bone and musculature in the head. (Source: BioGlossary, www.Biology-Text.com)[TAO] - 2012-08-14 - TAO:0000113 - TAO - ZFIN:curator - @@ -49212,7 +43499,7 @@ plexiform layer. - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -49228,14 +43515,14 @@ plexiform layer. trunk mesenchyme - + - + EHDAA2 @@ -49256,14 +43543,14 @@ plexiform layer. - - + + + + + + The posterior part of the developing vertebrate hindbrain or the corresponding part of the adult brain composed of the medulla oblongata and a portion of the fourth ventricle; as well as the glossopharyngeal nerve (CN IX), vagus nerve (CN X), accessory nerve (CN XI), hypoglossal nerve (CN XII), and a portion of the vestibulocochlear nerve (CN VIII).[BTO,WP]. - - The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG] - The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] - the terms metencephalon and myelencephalon are only meaningful in mammals and birds - Neuroanatomy of the Zebrafish Brain. Note that its not clear if this refers to the developing medulla oblongata - MA (adult) has two distinct classes BTO:0000758 CALOHA:TS-0607 CALOHA:TS-2365 @@ -49273,7 +43560,6 @@ plexiform layer. EMAPA:17082 HBA:9512 MA:0000205 - MESH:D054024 VHOG:0000456 Wikipedia:Myelencephalon uberon @@ -49283,16 +43569,6 @@ plexiform layer. myelencephalon http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg - - - - - - - - - definitional - @@ -49300,34 +43576,6 @@ plexiform layer. BTO:0000758 Wikipedia:Myelencephalon - - - - The posterior of the two brain vesicles formed by specialization of the rhombencephalon in the developing embryo, it comprises the medulla oblongata. [TFD][VHOG] - 2012-09-17 - VHOG:0000456 - VHOG - http://bgee.unil.ch/ - http://medical-dictionary.thefreedictionary.com/myelencephalon - - - - - The early development of most vertebrate brains is similar (...). The zebrafish neural tube follows the same basic differentiation pattern as the mammalian neural tube (reference 1); The brain develops from three embryonic enlargements of the neural tube, which later differentiate into five regions. A forebrain differentiates into telencephalon and diencephalon. The midbrain, or mesencephalon, remains undivided. The hindbrain divides into the metencephalon and myelencephalon. Cavities within the brain enlarge to form a series of interconnected ventricles (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0000456 - VHOG - ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.381-382, ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.500 - http://bgee.unil.ch/ - - - - - MESH:D054024 - - - https://github.com/biopragmatics/biomappings - @@ -49421,7 +43669,6 @@ plexiform layer. An array of photoreceptors and any supporting cells found in an eye. - FBbt:00004200 light-sensitive tissue uberon UBERON:0005388 @@ -49433,12 +43680,6 @@ plexiform layer. An array of photoreceptors and any supporting cells found in an eye. https://orcid.org/0000-0002-6601-2165 - - - - FBbt:00004200 - - @@ -49459,7 +43700,6 @@ plexiform layer. A transparent structure that is part of a visual sense organ, the function of which is to direct or focus light onto a photoreceptor array. - directing or focusing light onto light receptors lens uberon UBERON:0005389 @@ -49491,7 +43731,6 @@ plexiform layer. AEO:0000125 CALOHA:TS-2122 EHDAA2:0003125 - FBbt:00007006 FMA:292313 MIAA:0000019 uberon @@ -49502,12 +43741,6 @@ plexiform layer. developing anatomical structure - - - - FBbt:00007006 - - @@ -49532,6 +43765,7 @@ plexiform layer. + @@ -49545,7 +43779,6 @@ plexiform layer. Portion of tissue that is the outer layer of the optic cup and will become the retinal pigmented epithelium. - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] EHDAA2:0001306 EMAPA:16677 TAO:0000064 @@ -49571,16 +43804,6 @@ plexiform layer. Portion of tissue that is the outer layer of the optic cup and will become the retinal pigmented epithelium. ZFIN:curator - - - - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] - 2012-09-17 - VHOG:0000492 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 - http://bgee.unil.ch/ - @@ -49642,6 +43865,7 @@ plexiform layer. + @@ -49655,7 +43879,6 @@ plexiform layer. Portion of tissue that is the inner layer of the optic cup and will become the neural retina. - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] EHDAA2:0001304 EMAPA:16675 TAO:0001071 @@ -49681,16 +43904,6 @@ plexiform layer. Portion of tissue that is the inner layer of the optic cup and will become the neural retina. ZFIN:curator - - - - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The outer layer of the optic cup becomes the pigment layer of the retina, whereas the inner layer differentiates into the photoreceptive cells and neuronal layers of the retina.[well established][VHOG] - 2012-09-17 - VHOG:0000490 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 - http://bgee.unil.ch/ - @@ -49735,6 +43948,7 @@ plexiform layer. + @@ -49742,9 +43956,6 @@ plexiform layer. Portion of tissue that gives rise to the lens. - A vesicle formed from the lens pit of the embryo, developing into the crystalline lens. [TFD][VHOG] - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG] - the lens of zebrafish (and other teleosts) forms from delamination of cells from the lens placode; thus, there is no formation of a hollow lens vesicle, in contrast to the situation in mammals and birds (Glass and Dahm, 2004) [PMID:16496288] The lens of the zebrafish forms by delamination of lens placodal cells and not through invagination. This results in a solid spherical mass as opposed to a hollow lens vesicle. Detachment of the solid lens vesicle of zebrafish at 24b26 hpf is accomplished in part by apoptosis, similar to mammals EHDAA2:0000983 EHDAA:4737 EMAPA:17163 @@ -49770,32 +43981,6 @@ plexiform layer. ZFIN:curator https://sourceforge.net/tracker/?func=detail&atid=994726&aid=3514998&group_id=76834 - - - - A vesicle formed from the lens pit of the embryo, developing into the crystalline lens. [TFD][VHOG] - 2012-09-17 - VHOG:0001163 - VHOG - http://bgee.unil.ch/ - http://medical-dictionary.thefreedictionary.com/lens+vesicle - - - - - (...) an essentially similar sequence of events occurs during the embryonic development of the vertebrate eye. The eye initially develops as a single median evagination of the diencephalon that soon bifurcates to form the paired optic vesicles. As each optic vesicle grows towards the body surface, its proximal part narrows as the optic stalk, and its distal part invaginates to form a two-layered optic cup. (...) The optic cup induces the overlying surface ectoderm first to thicken as a lens placode and then to invaginate and form a lens vesicle that differentiates into the lens.[well established][VHOG] - 2012-09-17 - VHOG:0001163 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.429 - http://bgee.unil.ch/ - - - - - the lens of zebrafish (and other teleosts) forms from delamination of cells from the lens placode; thus, there is no formation of a hollow lens vesicle, in contrast to the situation in mammals and birds (Glass and Dahm, 2004) [PMID:16496288] The lens of the zebrafish forms by delamination of lens placodal cells and not through invagination. This results in a solid spherical mass as opposed to a hollow lens vesicle. Detachment of the solid lens vesicle of zebrafish at 24b26 hpf is accomplished in part by apoptosis, similar to mammals - ZFA - @@ -49836,8 +44021,9 @@ plexiform layer. + - + Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea. TAO:0002188 ZFA:0001688 @@ -49845,7 +44031,7 @@ plexiform layer. UBERON:0005427 corneal primordium - + @@ -49864,7 +44050,7 @@ plexiform layer. - + ZFA @@ -49887,9 +44073,8 @@ plexiform layer. - + Multi-tissue structure that arises from the heart rudiment and will become the heart tube. - BTO:0006179 EHDAA2:0001512 EHDAA:424 EHDAA:436 @@ -49906,14 +44091,14 @@ plexiform layer. primitive heart tube - + - + ZFA @@ -49922,14 +44107,6 @@ plexiform layer. Multi-tissue structure that arises from the heart rudiment and will become the heart tube. ZFA:0000149 - - - - BTO:0006179 - - - https://github.com/biopragmatics/biomappings - @@ -49956,7 +44133,6 @@ plexiform layer. - A depression in the front of the vitreous body, lodging the lens. [adapted_from_the_definition_of_the_hyaloid_fossa] EHDAA2:0000789 EHDAA:4733 EMAPA:17302 @@ -49967,16 +44143,6 @@ plexiform layer. UBERON:0005606 hyaloid cavity - - - - A depression in the front of the vitreous body, lodging the lens. [adapted_from_the_definition_of_the_hyaloid_fossa] - 2012-09-17 - VHOG:0001477 - VHOG - http://bgee.unil.ch/ - http://medical-dictionary.thefreedictionary.com/hyaloid+fossa - @@ -50056,7 +44222,6 @@ plexiform layer. An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina. - this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell. AAO:0010596 FMA:63872 @@ -50124,7 +44289,7 @@ plexiform layer. - + A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 @@ -50134,7 +44299,7 @@ plexiform layer. UBERON:0005856 developing mesenchymal condensation - + @@ -50153,7 +44318,7 @@ plexiform layer. - + AEO-modified-relation @@ -50209,10 +44374,16 @@ plexiform layer. + - - - + + + + + + + + A serous sac which is the aggregate of the conjunctiva plus the conjunctival space. EMAPA:18233 FMA:20291 @@ -50223,18 +44394,14 @@ plexiform layer. UBERON:0005908 conjunctival sac - + - + - - - - @@ -50244,21 +44411,15 @@ plexiform layer. - + FMA - + HPO:pr - - - - - MA - @@ -50298,10 +44459,8 @@ plexiform layer. Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified]. - Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO] AAO:0000963 EMAPA:17214 - EMAPA:18043 MA:0000308 NCIT:C32172 SCTID:361725000 @@ -50329,15 +44488,6 @@ plexiform layer. https://github.com/obophenotype/uberon/issues/44 https://github.com/obophenotype/uberon/wiki/The-axial-skeleton - - - - Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO] - 2012-08-14 - VSAO:0000056 - VSAO - PSPUB:0000170 - @@ -50378,7 +44528,6 @@ plexiform layer. A threadlike extension of a nerve cell and consists of an axon and myelin sheath (if it is myelinated) in the nervous system. There are nerve fibers in the central nervous system and peripheral nervous system. A nerve fiber may be myelinated and/or unmyelinated. In the central nervous system (CNS), myelin by oligodendroglia cells is formed. Schwann cells form myelin in the peripheral nervous system (PNS). Schwann cells also make a thin covering in an axon without myelin (in the PNS). A peripheral nerve fiber contains an axon, myelin sheath, schwann cells and its endoneurium. There are no endoneurium and schwann cells in the central nervous system. - neurofibrous BAMS:nfi FMA:5914 MESH:D009412 @@ -50469,7 +44618,6 @@ plexiform layer. - http://www1.pbrc.hawaii.edu/~danh/MyelinEvolution/evolution.html, http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=6134604, Wikipedia:Myelin#Invertebrate_myelin FMA:5915 GAID:745 MESH:D009413 @@ -50511,7 +44659,7 @@ plexiform layer. - + @@ -50534,14 +44682,14 @@ plexiform layer. future diencephalon - + - + EHDAA2 @@ -50577,7 +44725,6 @@ plexiform layer. The embryonic precursor of the brain. - The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO) BAMS:Enc BTO:0004726 EFO:0003431 @@ -50606,12 +44753,6 @@ plexiform layer. The embryonic precursor of the brain. NLX:94995 - - - - The embryonic precursor of the brain and the set of mature brain structures that derive from it (CUMBO) - http://neurolex.org/wiki/Cumbo_terms - @@ -50724,7 +44865,7 @@ plexiform layer. - + @@ -50748,14 +44889,14 @@ plexiform layer. future spinal cord - + - + EHDAA2 @@ -50792,10 +44933,9 @@ plexiform layer. - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB - The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG] EHDAA2:0001278 EHDAA:264 EMAPA:16101 @@ -50807,7 +44947,7 @@ plexiform layer. notochordal plate - + @@ -50820,7 +44960,7 @@ plexiform layer. - + EHDAA2 @@ -50829,15 +44969,6 @@ plexiform layer. The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. VHOG:0001212 - - - - The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG] - 2012-09-17 - VHOG:0001212 - VHOG - http://bgee.unil.ch/ - @@ -50857,7 +44988,7 @@ plexiform layer. - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -50874,14 +45005,14 @@ plexiform layer. The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -50918,6 +45049,7 @@ plexiform layer. + @@ -50995,7 +45127,6 @@ plexiform layer. Body substance in a liquid or semi-solid state in the eyeball which serves to refract light. - ocular refraction MA:0001911 uberon UBERON:0006312 @@ -51079,10 +45210,6 @@ plexiform layer. The pharynx is the part of the digestive system immediately posterior to the mouth[GO]. - currently this is an extremely generic class, encompassing both protostomes and deuterostomes. - 2023-04-20 - branchial - pharyngeal MAT:0000049 MESH:D010614 MIAA:0000049 @@ -51439,7 +45566,6 @@ plexiform layer. An epithelium characterised by its most superficial layer consisting of squamous epithelial cells. - FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium BTO:0002072 NCIT:C12848 SCTID:40118003 @@ -51455,12 +45581,6 @@ plexiform layer. An epithelium characterised by its most superficial layer consisting of squamous epithelial cells. Wikipedia:Squamous_epithelium - - - - FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium - FBbt - @@ -51535,12 +45655,6 @@ plexiform layer. Old definition: 'Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.' Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism. anatomical surface - - - - - via morphological boundary in CARO - @@ -51559,6 +45673,7 @@ plexiform layer. + @@ -51733,7 +45848,6 @@ plexiform layer. - The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis BILA:0000084 NCIT:C34268 SCTID:360394002 @@ -51749,12 +45863,6 @@ plexiform layer. UBERON:0007026 presumptive gut - - - - The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis - NCBIBook:NBK10107 - @@ -51785,10 +45893,13 @@ plexiform layer. - + + + + + + A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]. - note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis - SPD:0000130 TADS:0000147 http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg dorsal tube @@ -51800,16 +45911,6 @@ plexiform layer. Gene notes: Bmp, Nkx, Gata primary circulatory organ - - - - - - - - - GO uses blood circulation generically to include the haemolymphatic fluid of arthropods - @@ -51848,7 +45949,6 @@ plexiform layer. An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. - An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO] EFO:0003497 TAO:0000131 ZFA:0000131 @@ -51864,15 +45964,6 @@ plexiform layer. An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. ZFIN:ZDB-PUB-961014-576 - - - - An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000131 - TAO - ZFIN:curator - @@ -51897,6 +45988,7 @@ plexiform layer. + @@ -51962,8 +46054,8 @@ plexiform layer. - - + + @@ -51972,7 +46064,6 @@ plexiform layer. The rhombencephalon (or hindbrain) is a developmental categorization of portions of the central nervous system in vertebrates. The rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. In the human embryo eight rhombomeres can be distinguished, from caudal to rostral: Rh7-Rh1 and the isthmus (the most rostral rhombomere). A rare disease of the rhombencephalon, 'rhombencephalosynapsis' is characterized by a missing vermis resulting in a fused cerebellum. Patients generally present with cerebellar ataxia. The caudal rhombencephalon has been generally considered as the initiation site for neural tube closure. TODO - unify naming conventions - The embryonic rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. Rhombomeres Rh7-Rh4 form the myelencephalon that will give the medulla oblongata. Rhombomeres Rh3-Rh1 form the metencephalon that will form the pons and the cerebellum[NPX:PDR]. BAMS:HB CALOHA:TS-2118 EFO:0003440 @@ -51990,24 +46081,24 @@ plexiform layer. presumptive hindbrain - + - + - + XAO-abduced - + cjm @@ -52016,12 +46107,6 @@ plexiform layer. The rhombencephalon (or hindbrain) is a developmental categorization of portions of the central nervous system in vertebrates. The rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. In the human embryo eight rhombomeres can be distinguished, from caudal to rostral: Rh7-Rh1 and the isthmus (the most rostral rhombomere). A rare disease of the rhombencephalon, 'rhombencephalosynapsis' is characterized by a missing vermis resulting in a fused cerebellum. Patients generally present with cerebellar ataxia. The caudal rhombencephalon has been generally considered as the initiation site for neural tube closure. Wikipedia:Rhombencephalon - - - - The embryonic rhombencephalon can be subdivided in a variable number of transversal swellings called rhombomeres. Rhombomeres Rh7-Rh4 form the myelencephalon that will give the medulla oblongata. Rhombomeres Rh3-Rh1 form the metencephalon that will form the pons and the cerebellum[NPX:PDR]. - NPX:PDR - @@ -52064,7 +46149,7 @@ plexiform layer. - + @@ -52083,14 +46168,14 @@ plexiform layer. presumptive midbrain hindbrain boundary - + - + ZFA @@ -52129,7 +46214,12 @@ plexiform layer. - + + + + + + @@ -52146,17 +46236,6 @@ plexiform layer. presumptive segmental plate - - - - - - - - - https://github.com/obophenotype/uberon/wiki/The-neural-crest - EDHAA2 - @@ -52208,7 +46287,6 @@ plexiform layer. A presumptive structure that has the potential to develop into a neural plate. consider merging - Region of the gastrula which gives rise to the neural plate.[TAO] EFO:0003424 TAO:0000063 ZFA:0000063 @@ -52225,15 +46303,6 @@ plexiform layer. A presumptive structure that has the potential to develop into a neural plate. OBOL:automatic - - - - Region of the gastrula which gives rise to the neural plate.[TAO] - 2012-08-14 - TAO:0000063 - TAO - ZFIN:curator - @@ -52252,7 +46321,7 @@ plexiform layer. - + @@ -52278,7 +46347,7 @@ plexiform layer. presumptive paraxial mesoderm - + @@ -52294,7 +46363,7 @@ plexiform layer. - + https://github.com/obophenotype/uberon/issues/1277 @@ -52376,7 +46445,7 @@ plexiform layer. - + A neural decussation that is part of a diencephalon. FMA:62446 diencephalon decussation @@ -52384,7 +46453,7 @@ plexiform layer. UBERON:0007425 decussation of diencephalon - + @@ -52397,7 +46466,7 @@ plexiform layer. - + Obol @@ -52472,7 +46541,7 @@ plexiform layer. - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -52480,7 +46549,7 @@ plexiform layer. UBERON:0007524 dense mesenchyme tissue - + @@ -52493,7 +46562,7 @@ plexiform layer. - + AEO @@ -52553,7 +46622,6 @@ plexiform layer. - MA does treat internal/external limiting membranes as layers - these are classified as laminae. We do not follow this convention. However, we do following MA is grouping these terms together MA:0001318 SCTID:280667001 retina lamina @@ -52568,12 +46636,6 @@ plexiform layer. UBERON - - - - MA does treat internal/external limiting membranes as layers - these are classified as laminae. We do not follow this convention. However, we do following MA is grouping these terms together - MA - @@ -52679,7 +46741,6 @@ plexiform layer. AEO:0000170 EFO:0001649 EHDAA2:0003170 - FBbt:00005426 Wikipedia:Anlage_(biology) developmental field uberon @@ -52709,12 +46770,6 @@ plexiform layer. FBbt:00005426 http://flybase.org/reports/FBrf0178740.html - - - - FBbt:00005426 - - @@ -52739,7 +46794,7 @@ plexiform layer. - + An axon tract that is part of a brain. the NIFSTD class 'nerve tract' is classified under 'regional part of brain', so it may seem like it belongs here, but actually includes spinal cord tracts FMA:83848 @@ -52749,14 +46804,14 @@ plexiform layer. UBERON:0007702 tract of brain - + - + cjm @@ -52784,12 +46839,10 @@ plexiform layer. - + Anatomical system that consists of all blood and lymph vessels. consider merging with vasculature - The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]. - in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system BTO:0001085 CALOHA:TS-2053 EHDAA2:0004520 @@ -52803,14 +46856,14 @@ plexiform layer. vascular system - + - + MA @@ -52819,18 +46872,6 @@ plexiform layer. Anatomical system that consists of all blood and lymph vessels. http://orcid.org/0000-0002-6601-2165 - - - - The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]. - ncithesaurus:Vascular_System - - - - - in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system - MA - @@ -52943,7 +46984,7 @@ plexiform layer. - + @@ -52960,14 +47001,14 @@ plexiform layer. UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -53063,8 +47104,13 @@ plexiform layer. - - + + + + + + + TODO - developmental relationships for lines TAO:0007044 ZFA:0007044 @@ -53074,27 +47120,16 @@ plexiform layer. UBERON:0009615 midbrain hindbrain boundary neural plate - + - - - - - + ZFA - - - - - https://github.com/obophenotype/uberon/issues/438 - Bgee:AN - @@ -53125,14 +47160,14 @@ plexiform layer. - + - + @@ -53157,24 +47192,24 @@ plexiform layer. presumptive midbrain - + - + - + ZFA - + ZFA @@ -53220,7 +47255,7 @@ plexiform layer. - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -53228,14 +47263,14 @@ plexiform layer. UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -53256,8 +47291,9 @@ plexiform layer. + - + EFO:0003704 TAO:0005041 ZFA:0005041 @@ -53267,14 +47303,14 @@ plexiform layer. anterior lateral plate mesoderm - + - + ZFA @@ -53328,16 +47364,16 @@ plexiform layer. - + - + EHDAA2:0001315 EHDAA:1122 uberon UBERON:0009920 optic neural crest - + @@ -53350,7 +47386,7 @@ plexiform layer. - + EHDAA2 @@ -53388,7 +47424,6 @@ plexiform layer. CARO:0010000 - FBbt:00100313 multicellular structure uberon UBERON:0010000 @@ -53402,12 +47437,6 @@ plexiform layer. An anatomical structure that has more than one cell as a part. CARO:0010000 - - - - FBbt:00100313 - - @@ -53490,7 +47519,8 @@ plexiform layer. - + + @@ -53498,8 +47528,6 @@ plexiform layer. The core globe-shaped component of the camera-type eye. - See notes for camera-type eye - FMA:12513 MIAA:0000283 SCTID:244486005 @@ -53515,14 +47543,14 @@ plexiform layer. eyeball of camera-type eye - + - + FMA @@ -53563,8 +47591,8 @@ plexiform layer. - - + + Portion of tissue that is dorsolateral to the floor plate and part of the midbrain. DHBA:12322 EFO:0003567 @@ -53578,11 +47606,11 @@ plexiform layer. midbrain basal plate - + - + @@ -53595,13 +47623,13 @@ plexiform layer. - + EHDAA2 - + ZFA @@ -53628,8 +47656,9 @@ plexiform layer. + - + Portion of neural tube that gives rise to the midbrain. we follow ZFA in temporally dividing midbrain NT from presumptive midbrain, but in future this may be collapsed TAO:0007039 @@ -53638,14 +47667,14 @@ plexiform layer. UBERON:0010286 midbrain neural tube - + - + ZFA @@ -53672,7 +47701,12 @@ plexiform layer. - + + + + + + @@ -53680,7 +47714,6 @@ plexiform layer. Developing anatomical structure that develops into the eyeball and associated structures. - Multi-tissue structure that consists of the structures that develop into the retina and lens.[TAO] TAO:0002201 ZFA:0001678 future eye @@ -53688,31 +47721,12 @@ plexiform layer. UBERON:0010312 immature eye - - - - - - - - - definitional - Developing anatomical structure that develops into the eyeball and associated structures. ZFA:0001678 - - - - Multi-tissue structure that consists of the structures that develop into the retina and lens.[TAO] - 2012-08-14 - TAO:0002201 - TAO - ZFIN:curator - @@ -53739,7 +47753,6 @@ plexiform layer. An anatomical structure that develops from the neural crest. - Grouping term for query purposes uberon UBERON:0010313 @@ -53776,7 +47789,6 @@ plexiform layer. An anatomical structure that has some part that develops from the neural crest. - Grouping term for query purposes uberon UBERON:0010314 @@ -53851,18 +47863,13 @@ plexiform layer. + - - - - - - The integrated unit (of the eye) that consists of the conjunctiva, the corneal surface, and the ocular mucosal adnexa including the lid margins and the meibomian gland openings, the lacrimal glands and the lacrimal drainage system, all which are critical to maintain ocular surface integrity and provide protection from external antigens and pathogenic microorganisms. EMAPA:35336 MA:0002486 @@ -53893,6 +47900,7 @@ plexiform layer. + @@ -53969,10 +47977,9 @@ plexiform layer. - - + + Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. - Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO] FMA:23879 SCTID:129140006 VSAO:0000042 @@ -53983,11 +47990,11 @@ plexiform layer. subdivision of skeleton - + - + @@ -54000,13 +48007,13 @@ plexiform layer. - + UBERONREF:0000003 - + VSAO @@ -54016,16 +48023,6 @@ plexiform layer. UBERONREF:0000003 https://orcid.org/0000-0002-6601-2165 - - - - Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO] - 2012-08-14 - VSAO:0000042 - incorrect - VSAO - VSAO:curator - @@ -54077,7 +48074,7 @@ plexiform layer. - + Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system FMA:302077 @@ -54087,7 +48084,7 @@ plexiform layer. postcranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton - + @@ -54100,7 +48097,7 @@ plexiform layer. - + cjm @@ -54133,6 +48130,7 @@ plexiform layer. + @@ -54185,7 +48183,6 @@ plexiform layer. - FBbt:00007330 FMA:67509 SCTID:91690000 uberon @@ -54207,21 +48204,15 @@ plexiform layer. A subdivision of an anatomical system. http://orcid.org/0000-0002-6601-2165 - - - - FBbt:00007330 - - + - - Muscles within the eye (bulbus oculi).[AAO] + AAO:0010038 EMAPA:18808 FMA:49150 @@ -54231,25 +48222,16 @@ plexiform layer. UBERON:0011222 intra-ocular muscle - + - + EMAPA - - - - Muscles within the eye (bulbus oculi).[AAO] - 2012-06-20 - AAO:0010038 - AAO - AAO:EJS - @@ -54508,7 +48490,8 @@ plexiform layer. - + + @@ -54550,7 +48533,7 @@ plexiform layer. anterior uvea - + @@ -54563,7 +48546,7 @@ plexiform layer. - + MP @@ -54612,7 +48595,6 @@ plexiform layer. The aggregate of the coelemic cavity lumen plus the membranes that line the lumen. EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining. - coelomic EHDAA2:0004731 Wikipedia:Coelom enterocoelom @@ -54696,6 +48678,7 @@ plexiform layer. + @@ -54920,10 +48903,8 @@ plexiform layer. The region of the organism associated with the visceral organs. - Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]. AEO:0000103 BTO:0001489 - EMAPA:36031 FMA:231424 uberon body @@ -54944,12 +48925,6 @@ plexiform layer. The region of the organism associated with the visceral organs. AEO:0000103 - - - - Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]. - FMA:231424 - @@ -54965,6 +48940,42 @@ plexiform layer. + + + + + + + + + + + + + + + + + Mesenchyme that develops_from the neural crest[Automatically generated definition]. + EMAPA:32735 + FMA:293883 + mesenchyme from neural crest + neural crest derived mesenchyme + neural crest mesenchyme + uberon + UBERON:0014387 + mesenchyme derived from neural crest + + + + + Mesenchyme that develops_from the neural crest[Automatically generated definition]. + OBOL:automatic + https://github.com/obophenotype/uberon/issues/248 + + + + @@ -55062,7 +49073,6 @@ plexiform layer. An anatomical group whose component structures share a common function. AEO:0000093 - FBbt:00007278 uberon UBERON:0015203 non-connected functional system @@ -55076,36 +49086,13 @@ plexiform layer. FBC:DOS FBbt:00007278 - - - - FBbt:00007278 - - - - - - - - - - - - - - - - - - - @@ -55113,7 +49100,6 @@ plexiform layer. Any structure that is placed on one side of the left-right axis of a bilaterian. - This class is primarily to implement taxon constraints. It may be removed in the future. uberon UBERON:0015212 @@ -55147,7 +49133,6 @@ plexiform layer. A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile. heart - SPD:0000130 cardiac pump heart or heart like organ circulatory vessel @@ -55221,6 +49206,7 @@ plexiform layer. + @@ -55347,7 +49333,7 @@ plexiform layer. - + @@ -55370,7 +49356,7 @@ plexiform layer. UBERON:0016887 entire extraembryonic component - + @@ -55383,7 +49369,7 @@ plexiform layer. - + AEO @@ -55406,6 +49392,8 @@ plexiform layer. + + @@ -55723,12 +49711,6 @@ plexiform layer. - - - - - - @@ -55856,7 +49838,6 @@ plexiform layer. CARO:0020000 - FBbt:00007276 uberon UBERON:0034923 @@ -55874,12 +49855,6 @@ plexiform layer. Material anatomical entity consisting of multiple anatomical structures that are not connected to each other. CARO:0020000 - - - - FBbt:00007276 - - @@ -56154,7 +50129,6 @@ plexiform layer. - example to be eventually removed example to be eventually removed @@ -56163,9 +50137,7 @@ plexiform layer. - failed exploratory term The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job - Person:Alan Ruttenberg failed exploratory term @@ -56174,7 +50146,6 @@ plexiform layer. - metadata complete Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. metadata complete @@ -56184,7 +50155,6 @@ plexiform layer. - organizational term Term created to ease viewing/sort terms for development purpose, and will not be included in a release organizational term @@ -56194,7 +50164,6 @@ plexiform layer. - ready for release Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release @@ -56204,7 +50173,6 @@ plexiform layer. - metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete @@ -56214,7 +50182,6 @@ plexiform layer. - uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated @@ -56224,7 +50191,6 @@ plexiform layer. - pending final vetting All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting @@ -56234,7 +50200,6 @@ plexiform layer. - placeholder removed placeholder removed @@ -56243,7 +50208,6 @@ plexiform layer. - terms merged An editor note should explain what were the merged terms and the reason for the merge. terms merged @@ -56253,7 +50217,6 @@ plexiform layer. - term imported This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. term imported @@ -56263,7 +50226,6 @@ plexiform layer. - term split This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. term split @@ -56273,10 +50235,7 @@ plexiform layer. - universal Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. - Alan Ruttenberg - A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf universal @@ -56285,10 +50244,8 @@ plexiform layer. - defined class A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. - Alan Ruttenberg defined class @@ -56297,10 +50254,8 @@ plexiform layer. - named class expression A named class expression is a logical expression that is given a name. The name can be used in place of the expression. named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions - Alan Ruttenberg named class expression @@ -56309,10 +50264,7 @@ plexiform layer. - to be replaced with external ontology term Terms with this status should eventually replaced with a term from another ontology. - Alan Ruttenberg - group:OBI to be replaced with external ontology term @@ -56321,10 +50273,7 @@ plexiform layer. - requires discussion A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. - Alan Ruttenberg - group:OBI requires discussion @@ -56335,9 +50284,7 @@ plexiform layer. The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. - https://github.com/information-artifact-ontology/ontology-metadata/issues/77 - https://orcid.org/0000-0001-5208-3432 out of scope @@ -56351,42 +50298,6 @@ plexiform layer. /////////////////////////////////////////////////////////////////////////////////////// --> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -56448,46 +50359,34 @@ plexiform layer. /////////////////////////////////////////////////////////////////////////////////////// --> - - - - - - - - - - - - - + - + - + - + - + - + - + - + - + - + @@ -56514,8 +50413,8 @@ plexiform layer. - - + + @@ -56525,7 +50424,7 @@ plexiform layer. - + @@ -56535,7 +50434,7 @@ plexiform layer. - + @@ -56552,67 +50451,8 @@ plexiform layer. - - - - - - - - - - true - GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' - involved in BP - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + @@ -56630,8 +50470,8 @@ plexiform layer. - - + + @@ -56641,8 +50481,8 @@ plexiform layer. - - + + @@ -56652,8 +50492,8 @@ plexiform layer. - - + + @@ -56670,8 +50510,8 @@ plexiform layer. - - + + @@ -56688,8 +50528,8 @@ plexiform layer. - - + + @@ -56699,8 +50539,8 @@ plexiform layer. - - + + @@ -56710,8 +50550,8 @@ plexiform layer. - - + + @@ -56728,8 +50568,8 @@ plexiform layer. - - + + @@ -56746,8 +50586,8 @@ plexiform layer. - - + + @@ -56757,8 +50597,8 @@ plexiform layer. - - + + @@ -56768,8 +50608,8 @@ plexiform layer. - - + + @@ -56786,8 +50626,8 @@ plexiform layer. - - + + @@ -56804,8 +50644,8 @@ plexiform layer. - - + + @@ -56815,8 +50655,8 @@ plexiform layer. - - + + @@ -56831,8 +50671,8 @@ plexiform layer. - - + + @@ -56849,8 +50689,8 @@ plexiform layer. - - + + @@ -56860,8 +50700,8 @@ plexiform layer. - - + + @@ -56876,8 +50716,8 @@ plexiform layer. - - + + @@ -56894,8 +50734,8 @@ plexiform layer. - - + + @@ -56905,8 +50745,8 @@ plexiform layer. - - + + @@ -56921,8 +50761,8 @@ plexiform layer. - - + + @@ -56939,8 +50779,8 @@ plexiform layer. - - + + @@ -56950,8 +50790,8 @@ plexiform layer. - - + + @@ -56966,8 +50806,8 @@ plexiform layer. - - + + @@ -56984,8 +50824,8 @@ plexiform layer. - - + + @@ -56995,8 +50835,8 @@ plexiform layer. - - + + @@ -57011,8 +50851,8 @@ plexiform layer. - - + + @@ -57072,8 +50912,8 @@ plexiform layer. - - + + @@ -57083,8 +50923,8 @@ plexiform layer. - - + + @@ -57099,8 +50939,8 @@ plexiform layer. - - + + @@ -57115,9 +50955,9 @@ plexiform layer. - - - + + + @@ -57127,8 +50967,8 @@ plexiform layer. - - + + @@ -57142,9 +50982,9 @@ plexiform layer. - - - + + + @@ -57159,9 +50999,9 @@ plexiform layer. - - - + + + @@ -57171,8 +51011,8 @@ plexiform layer. - - + + @@ -57186,7 +51026,7 @@ plexiform layer. - + diff --git 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+_:B4f14f866X2Da756X2D48e6X2D9c37X2D1d31e14ff4c3genid726 +_:B4f14f866X2Da756X2D48e6X2D9c37X2D1d31e14ff4c3genid776 +_:B4f14f866X2Da756X2D48e6X2D9c37X2D1d31e14ff4c3genid793 +_:B4f14f866X2Da756X2D48e6X2D9c37X2D1d31e14ff4c3genid80 +_:B4f14f866X2Da756X2D48e6X2D9c37X2D1d31e14ff4c3genid806 +_:B4f14f866X2Da756X2D48e6X2D9c37X2D1d31e14ff4c3genid811 +_:B4f14f866X2Da756X2D48e6X2D9c37X2D1d31e14ff4c3genid820 +_:B4f14f866X2Da756X2D48e6X2D9c37X2D1d31e14ff4c3genid826 +_:B4f14f866X2Da756X2D48e6X2D9c37X2D1d31e14ff4c3genid83 +_:B4f14f866X2Da756X2D48e6X2D9c37X2D1d31e14ff4c3genid840 +_:B4f14f866X2Da756X2D48e6X2D9c37X2D1d31e14ff4c3genid846 +_:B4f14f866X2Da756X2D48e6X2D9c37X2D1d31e14ff4c3genid854 +_:B4f14f866X2Da756X2D48e6X2D9c37X2D1d31e14ff4c3genid862 +_:B4f14f866X2Da756X2D48e6X2D9c37X2D1d31e14ff4c3genid909 +_:B4f14f866X2Da756X2D48e6X2D9c37X2D1d31e14ff4c3genid958 +_:B4f14f866X2Da756X2D48e6X2D9c37X2D1d31e14ff4c3genid966 +_:B4f14f866X2Da756X2D48e6X2D9c37X2D1d31e14ff4c3genid973 +_:B4f14f866X2Da756X2D48e6X2D9c37X2D1d31e14ff4c3genid980 +_:B4f14f866X2Da756X2D48e6X2D9c37X2D1d31e14ff4c3genid986 +_:B4f14f866X2Da756X2D48e6X2D9c37X2D1d31e14ff4c3genid996 "continuant" "occurrent" "independent continuant" @@ -323,7 +320,7 @@ _:B0eeff062X2D4c9fX2D4f5fX2D85faX2D91dcf1dacab2genid966 "material entity" "immaterial entity" "cell" - "fibroblast neural crest derived" + "neural crest derived fibroblast" "neuronal receptor cell" "early embryonic cell (metazoa)" "migratory cranial neural crest cell" @@ -1202,6 +1199,7 @@ _:B0eeff062X2D4c9fX2D4f5fX2D85faX2D91dcf1dacab2genid966 "anatomical conduit space" "main body axis" "body proper" + "mesenchyme derived from neural crest" "thoracic skeleton" "primordial vasculature" "non-connected functional system" diff --git a/subsets/general_cell_types_upper_slim.json b/subsets/general_cell_types_upper_slim.json index 423bc976d..1f330c5ba 100644 --- a/subsets/general_cell_types_upper_slim.json +++ b/subsets/general_cell_types_upper_slim.json @@ -4,9 +4,9 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-02-13" + "val" : "2024-04-05" } ], - "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-02-13/subsets/general_cell_types_upper_slim.owl" + "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-04-05/subsets/general_cell_types_upper_slim.owl" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/BFO_0000002", @@ -78,18 +78,6 @@ "val" : "BFO:0000050" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "is part of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my brain is part of my body (continuant parthood, two material entities)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this day is part of this year (occurrent parthood)" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." }, { @@ -98,42 +86,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "part_of" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000002" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000003" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000004" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000017" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000019" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000020" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000031" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "part_of" @@ -164,18 +122,6 @@ "val" : "BFO:0000051" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has part" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my body has part my brain (continuant parthood, two material entities)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this year has part this day (occurrent parthood)" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." }, { @@ -184,21 +130,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has_part" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_part" @@ -217,26 +154,11 @@ "val" : "BFO:0000062" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "preceded by" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is preceded by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "preceded_by" - }, { - "pred" : "http://purl.org/dc/terms/source", - "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "preceded_by" @@ -255,14 +177,8 @@ "val" : "BFO:0000063" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "precedes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "precedes" @@ -282,26 +198,11 @@ "val" : "BFO:0000066" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "occurs in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "occurs_in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "unfolds in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "unfolds_in" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "occurs_in" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Occurs_in" @@ -315,412 +216,12 @@ "definition" : { "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" }, - "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ], - "xrefs" : [ { - "val" : "BFO:0000067" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "site of" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "contains_process" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - } ] + "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000141", "lbl" : "immaterial entity", "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000096", - "lbl" : "anterior to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000096" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "anterior_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000097", - "lbl" : "distal to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000097" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "distal_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000098", - "lbl" : "dorsal to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000098" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dorsal_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000099", - "lbl" : "posterior to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000099" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "posterior_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000100", - "lbl" : "proximal to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000100" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "proximal_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000102", - "lbl" : "ventral to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000102" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "ventral_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000107", - "lbl" : "deep to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000107" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "deep_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000108", - "lbl" : "superficial to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000108" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "superficial_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000120", - "lbl" : "in left side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000120" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_left_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000121", - "lbl" : "in right side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000121" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_right_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000122", - "lbl" : "in posterior side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000122" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_posterior_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000123", - "lbl" : "in anterior side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000123" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_anterior_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000124", - "lbl" : "in proximal side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000124" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_proximal_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "lbl" : "in lateral side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000126" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_lateral_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001100", - "lbl" : "in superficial part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001100" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_superficial_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001101", - "lbl" : "in deep part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001101" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_deep_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001106", - "lbl" : "proximalmost part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001106" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "proximalmost_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001107", - "lbl" : "immediately deep to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001107" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "immediately_deep_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001108", - "lbl" : "distalmost part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001108" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "distalmost_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001113", - "lbl" : "preaxialmost part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001113" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "preaxialmost_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001115", - "lbl" : "postaxialmost part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001115" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "postaxialmost_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0005001", - "lbl" : "intersects midsagittal plane of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0005001" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "intersects_midsagittal_plane_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0015014", - "lbl" : "immediately superficial to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0015014" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "immediately_superficial_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0015101", - "lbl" : "in dorsal side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0015101" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_dorsal_side_of" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000000", "lbl" : "cell", @@ -10199,13 +9700,7 @@ }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000002", "lbl" : "example to be eventually removed", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "example to be eventually removed" - } ] - } + "type" : "INDIVIDUAL" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000028", "lbl" : "symbol", @@ -10217,14 +9712,7 @@ "meta" : { "definition" : { "val" : "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "failed exploratory term" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person:Alan Ruttenberg" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000115", @@ -10235,20 +9723,8 @@ "val" : "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "definition" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2012-04-05: \nBarry Smith\n\nThe official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. \n\nOn the specifics of the proposed definition:\n\nWe don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Daniel Schober" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" } ] } }, { @@ -10258,32 +9734,7 @@ "meta" : { "definition" : { "val" : "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology." - }, - "xrefs" : [ { - "val" : "IAO:0000116" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "editor note" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Daniel Schober" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "editor_note" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000120", @@ -10292,11 +9743,7 @@ "meta" : { "definition" : { "val" : "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "metadata complete" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000121", @@ -10305,11 +9752,7 @@ "meta" : { "definition" : { "val" : "Term created to ease viewing/sort terms for development purpose, and will not be included in a release" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "organizational term" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000122", @@ -10318,11 +9761,7 @@ "meta" : { "definition" : { "val" : "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\"" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "ready for release" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000123", @@ -10331,11 +9770,7 @@ "meta" : { "definition" : { "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "metadata incomplete" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000124", @@ -10344,11 +9779,7 @@ "meta" : { "definition" : { "val" : "Nothing done yet beyond assigning a unique class ID and proposing a preferred term." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "uncurated" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000125", @@ -10357,31 +9788,18 @@ "meta" : { "definition" : { "val" : "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "pending final vetting" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000226", "lbl" : "placeholder removed", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "placeholder removed" - } ] - } + "type" : "INDIVIDUAL" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000227", "lbl" : "terms merged", "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "terms merged" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "An editor note should explain what were the merged terms and the reason for the merge." } ] @@ -10392,9 +9810,6 @@ "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "term imported" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use." } ] @@ -10405,9 +9820,6 @@ "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "term split" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created." } ] @@ -10419,17 +9831,7 @@ "meta" : { "definition" : { "val" : "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has obsolescence reason" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Melanie Courtot" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000233", @@ -10444,29 +9846,8 @@ "val" : "IAO:0000233" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "term tracker item" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_class_level", - "val" : "true" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", "val" : "true" @@ -10481,17 +9862,8 @@ "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "universal" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf" } ] } }, { @@ -10503,14 +9875,8 @@ "val" : "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "defined class" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" } ] } }, { @@ -10522,14 +9888,8 @@ "val" : "A named class expression is a logical expression that is given a name. The name can be used in place of the expression." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "named class expression" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" } ] } }, { @@ -10539,17 +9899,7 @@ "meta" : { "definition" : { "val" : "Terms with this status should eventually replaced with a term from another ontology." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "to be replaced with external ontology term" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "group:OBI" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000424", @@ -10558,17 +9908,7 @@ "meta" : { "definition" : { "val" : "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "expand expression to" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "ObjectProperty: RO_0002104\nLabel: has plasma membrane part\nAnnotations: IAO_0000424 \"http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\"\n" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000428", @@ -10577,17 +9917,7 @@ "meta" : { "definition" : { "val" : "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "requires discussion" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "group:OBI" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000700", @@ -10601,20 +9931,8 @@ "val" : "IAO:0000700" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has ontology root term" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Nicolas Matentzoglu" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_class_level", - "val" : "true" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", "val" : "true" @@ -10631,20 +9949,7 @@ "definition" : { "val" : "Use on obsolete terms, relating the term to another term that can be used as a substitute" }, - "comments" : [ "Add as annotation triples in the granting ontology" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "term replaced by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person:Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Person:Alan Ruttenberg" - } ] + "comments" : [ "Add as annotation triples in the granting ontology" ] } }, { "id" : "http://purl.obolibrary.org/obo/NCBITaxon_1", @@ -10679,9 +9984,6 @@ "val" : "PMID:15371245" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_family" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -10696,7 +9998,7 @@ "pred" : "hasExactSynonym", "val" : "Mus" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003003", + "synonymType" : "http://purl.obolibrary.org/obo/ncbitaxon#genbank_common_name", "pred" : "hasExactSynonym", "val" : "mice" }, { @@ -10708,9 +10010,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_genus" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -10733,9 +10032,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_species" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "NCBITaxon:85055" }, { @@ -10752,9 +10048,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -10773,9 +10066,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "NCBITaxon:40673" }, { @@ -10810,9 +10100,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -10835,9 +10122,6 @@ "val" : "PMID:11791233" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -10860,9 +10144,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_suborder" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -10909,9 +10190,6 @@ "val" : "PMID:30257078" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_superkingdom" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -10933,9 +10211,6 @@ "val" : "PMID:15522813" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_superorder" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -10960,9 +10235,6 @@ "val" : "PMID:15522813" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -10981,9 +10253,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11002,9 +10271,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11023,9 +10289,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11048,9 +10311,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11081,9 +10341,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_kingdom" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11097,9 +10354,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11118,9 +10372,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11138,9 +10389,6 @@ "val" : "PMID:15371245" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11154,9 +10402,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_subfamily" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "NCBITaxon:109679" }, { @@ -11182,9 +10427,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_class" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11198,9 +10440,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11223,9 +10462,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_phylum" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11252,9 +10488,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11277,9 +10510,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11293,9 +10523,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_superclass" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11314,9 +10541,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_subgenus" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11335,9 +10559,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_subphylum" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11372,9 +10593,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11397,9 +10615,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_order" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11415,15 +10630,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/77" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", - "val" : "https://orcid.org/0000-0001-5208-3432" } ] } }, { @@ -11435,9 +10644,6 @@ "val" : "Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'part disjoint with' 'defined by construct' \"\"\"\n PREFIX owl: \n PREFIX : some (\n and some (\n and some (\n and some ?Y)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { @@ -15399,33 +14126,9 @@ "definition" : { "val" : "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " }, - "xrefs" : [ { - "val" : "RO:0002103" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that part_of some ( that has_part some ( that some Y?)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "synapsed_by" } ] } }, { @@ -15437,29 +14140,8 @@ "val" : "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9990-8331" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-1617-8244" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19243617" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( and some ?Y)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] } }, { @@ -15471,26 +14153,8 @@ "val" : "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. " }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "synapsed in" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (\n http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some (\n http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { @@ -15502,20 +14166,8 @@ "val" : "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "synapses in" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that some ( that some Y?)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { @@ -15528,23 +14180,8 @@ }, "comments" : [ "N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part some (\n ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( \n\t‘synapse ; GO:0045202’ that has_part some (\n\t ‘post-synaptic membrane ; GO:0045211’ that part_of some N2))))" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that part_of some ( that some ( that some Y?)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { @@ -15556,23 +14193,8 @@ "val" : "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has synapse in" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that some Y?)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { @@ -15588,20 +14210,11 @@ "val" : "RO:0002131" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "overlaps" @@ -15614,26 +14227,7 @@ "meta" : { "definition" : { "val" : "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has fasciculating component" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", - "val" : "(forall (?x ?y) \n\t(iff \n\t\t(has_fasciculating_neuron_projection ?x ?y)\n\t\t(exists (?nps ?npbs)\t\t\n\t\t\t(and \n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?x)\n\t\t\t\t(\"neuron projection ; GO0043005\" ?y)\n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n\t\t\t\t(part_of ?nps ?y)\n\t\t\t\t(part_of ?npbs ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))\n\n\n" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002134", @@ -15643,30 +14237,9 @@ "definition" : { "val" : "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." }, - "xrefs" : [ { - "val" : "RO:0002134" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that ( some ( that some Y?)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "innervates" } ] } }, { @@ -15677,31 +14250,7 @@ "definition" : { "val" : "X continuous_with Y if and only if X and Y share a fiat boundary." }, - "xrefs" : [ { - "val" : "RO:0002150" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "connected to" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "continuous_with" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "FMA:85972" } ] @@ -15714,23 +14263,7 @@ "definition" : { "val" : "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." }, - "comments" : [ "VBO calls this homologous_to" ], - "xrefs" : [ { - "val" : "RO:0002158" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Consider obsoleting and merging with child relation, 'in homology relationship with'" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "homologous_to" - } ] + "comments" : [ "VBO calls this homologous_to" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -15740,33 +14273,9 @@ "definition" : { "val" : "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." }, - "xrefs" : [ { - "val" : "RO:0002160" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "lactation SubClassOf 'only in taxon' some 'Mammalia'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "only_in_taxon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" @@ -15774,48 +14283,15 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002161", - "lbl" : "never_in_taxon", + "lbl" : "never in taxon", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL." }, - "xrefs" : [ { - "val" : "RO:0002161" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "tooth SubClassOf 'never in taxon' value 'Aves'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", - "val" : "Class: EquivalentTo: ?X and (RO_0002162 some ?Y)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", - "val" : "Class: ?X DisjointWith: RO_0002162 some ?Y " - }, { "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_class_level", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "never_in_taxon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" @@ -15831,31 +14307,7 @@ }, "comments" : [ "Connects a biological entity to its taxon of origin." ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002162" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9227-417X" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_taxon" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] @@ -15870,26 +14322,11 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" @@ -15903,22 +14340,7 @@ "definition" : { "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" }, - "xrefs" : [ { - "val" : "RO:0002170" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "connected_to" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" }, { @@ -15928,42 +14350,16 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002175", - "lbl" : "present_in_taxon", + "lbl" : "present in taxon", "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S" }, "comments" : [ "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "applicable for taxon" - } ], - "xrefs" : [ { - "val" : "RO:0002175" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_class_level", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "present_in_taxon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" @@ -15977,25 +14373,7 @@ "definition" : { "val" : "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." }, - "xrefs" : [ { - "val" : "RO:0002176" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The M8 connects Glasgow and Edinburgh" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "connects" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" }, { @@ -16010,20 +14388,7 @@ "meta" : { "definition" : { "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." - }, - "xrefs" : [ { - "val" : "RO:0002177" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "attached to part of (anatomical structure to anatomical structure)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "attaches_to_part_of" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002178", @@ -16033,21 +14398,9 @@ "definition" : { "val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." }, - "xrefs" : [ { - "val" : "RO:0002178" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "supplies" } ] } }, { @@ -16058,21 +14411,9 @@ "definition" : { "val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." }, - "xrefs" : [ { - "val" : "RO:0002179" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "drains" } ] } }, { @@ -16088,23 +14429,11 @@ "val" : "RO:0002180" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_component" @@ -16121,32 +14450,7 @@ "definition" : { "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" }, - "comments" : [ "This is the transitive form of the develops from relation" ], - "xrefs" : [ { - "val" : "RO:0002202" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9114-8737" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-1980-3228" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "develops_from" - } ] + "comments" : [ "This is the transitive form of the develops from relation" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002203", @@ -16156,29 +14460,7 @@ "definition" : { "val" : "inverse of develops from" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "xrefs" : [ { - "val" : "RO:0002203" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-1980-3228" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "develops_into" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002206", @@ -16187,17 +14469,7 @@ "meta" : { "definition" : { "val" : "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002207", @@ -16211,31 +14483,6 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "has developmental precursor" - } ], - "xrefs" : [ { - "val" : "RO:0002207" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "FBbt" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002202" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "directly_develops_from" } ] } }, { @@ -16246,14 +14493,7 @@ "definition" : { "val" : "inverse of directly develops from" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "developmental precursor of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002211", @@ -16268,30 +14508,6 @@ "val" : "RO:0002211" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-7476-6306" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-3837-8864" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GO" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Regulation precludes parthood; the regulatory process may not be within the regulated process." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "regulates (processual)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "false" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16312,15 +14528,6 @@ "val" : "RO:0002212" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "negatively regulates (process to process)" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002211" }, { @@ -16344,18 +14551,6 @@ "val" : "RO:0002213" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "positively regulates (process to process)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002211" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16376,32 +14571,8 @@ "val" : "RO:0002215" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "osteoclast SubClassOf 'capable of' some 'bone resorption'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has function realized in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20123131" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/21208450" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "capable_of" @@ -16419,17 +14590,8 @@ "val" : "RO:0002216" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has function in" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "capable_of_part_of" @@ -16445,26 +14607,7 @@ "meta" : { "definition" : { "val" : "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" - }, - "xrefs" : [ { - "val" : "RO:0002219" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "surrounded_by" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002220", @@ -16479,35 +14622,11 @@ "val" : "RO:0002220" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The epidermis layer of a vertebrate is adjacent to the dermis." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This relation acts as a join point with BSPO" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "adjacent_to" @@ -16521,26 +14640,7 @@ "definition" : { "val" : "inverse of surrounded by" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "xrefs" : [ { - "val" : "RO:0002221" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "surrounds" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002222", @@ -16548,23 +14648,7 @@ "type" : "PROPERTY", "meta" : { "comments" : [ "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations." ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://en.wikipedia.org/wiki/Allen%27s_interval_algebra" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." - }, { - "pred" : "http://purl.org/dc/terms/source", - "val" : "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002223", @@ -16574,29 +14658,7 @@ "definition" : { "val" : "inverse of starts with" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002223" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Allen" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "starts" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002224", @@ -16611,26 +14673,8 @@ "val" : "RO:0002224" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "started by" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "starts_with" @@ -16643,23 +14687,7 @@ "meta" : { "definition" : { "val" : "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" - }, - "xrefs" : [ { - "val" : "RO:0002225" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "develops_from_part_of" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002226", @@ -16668,29 +14696,7 @@ "meta" : { "definition" : { "val" : "x develops_in y if x is located in y whilst x is developing" - }, - "xrefs" : [ { - "val" : "RO:0002226" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "EHDAA2" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Jonathan Bard, EHDAA2" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "develops_in" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002229", @@ -16700,26 +14706,7 @@ "definition" : { "val" : "inverse of ends with" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002229" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "ends" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002230", @@ -16734,23 +14721,8 @@ "val" : "RO:0002230" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "finished by" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "ends_with" @@ -16769,15 +14741,6 @@ "val" : "RO:0002231" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "starts with process that occurs in" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16798,15 +14761,6 @@ "val" : "RO:0002232" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "ends with process that occurs in" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16827,15 +14781,6 @@ "val" : "RO:0002233" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "consumes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16859,15 +14804,6 @@ "val" : "RO:0002234" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "produces" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16886,22 +14822,7 @@ "definition" : { "val" : "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." }, - "xrefs" : [ { - "val" : "RO:0002252" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004036", - "val" : "http://purl.obolibrary.org/obo/BFO_0000050" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "connecting_branch_of" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/issues/2212" } ] @@ -16914,11 +14835,7 @@ "definition" : { "val" : "inverse of connecting branch of" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004036", - "val" : "http://purl.obolibrary.org/obo/BFO_0000051" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002254", @@ -16927,26 +14844,7 @@ "meta" : { "definition" : { "val" : "x has developmental contribution from y iff x has some part z such that z develops from y" - }, - "xrefs" : [ { - "val" : "RO:0002254" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_developmental_contribution_from" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002255", @@ -16956,14 +14854,7 @@ "definition" : { "val" : "inverse of has developmental contribution from" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002256", @@ -16972,44 +14863,7 @@ "meta" : { "definition" : { "val" : "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" - }, - "xrefs" : [ { - "val" : "RO:0002256" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9114-8737" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "induced by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GO:0001759" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "developmentally_induced_by" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002257", @@ -17018,14 +14872,7 @@ "meta" : { "definition" : { "val" : "Inverse of developmentally induced by" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002258", @@ -17037,17 +14884,8 @@ }, "comments" : [ "This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "false" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "In general you should not use this relation to make assertions - use one of the more specific relations below this one" } ] } }, { @@ -17060,9 +14898,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of" } ] @@ -17081,9 +14916,6 @@ "val" : "affects" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within" } ] @@ -17096,27 +14928,9 @@ "definition" : { "val" : "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" }, - "xrefs" : [ { - "val" : "RO:0002285" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "replaces" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "developmentally_replaces" } ] } }, { @@ -17126,31 +14940,12 @@ "meta" : { "definition" : { "val" : "Inverse of developmentally preceded by" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002287", "lbl" : "part of developmental precursor of", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002292", "lbl" : "expresses", @@ -17158,14 +14953,7 @@ "meta" : { "definition" : { "val" : "y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002295", @@ -17179,14 +14967,8 @@ "val" : "RO:0002295" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" @@ -17211,18 +14993,6 @@ "val" : "RO:0002296" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "every flower development (GO:0009908) results in development of some flower (PO:0009046)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.geneontology.org/GO.doc.development.shtml" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17232,7 +15002,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -17240,21 +15010,6 @@ "val" : "RO:0002297" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:mtg_berkeley_2013" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17275,21 +15030,6 @@ "val" : "RO:0002298" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:mtg_berkeley_2013" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17310,21 +15050,6 @@ "val" : "RO:0002299" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:mtg_berkeley_2013" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17346,12 +15071,6 @@ "val" : "RO:0002304" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002411" - }, { - "pred" : "http://purl.org/dc/terms/creator", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17377,9 +15096,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002411" - }, { - "pred" : "http://purl.org/dc/terms/creator", - "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" @@ -17402,18 +15118,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "inheres in part of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" @@ -17432,15 +15136,6 @@ "val" : "RO:0002315" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:mtg_berkeley_2013" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17455,14 +15150,7 @@ "meta" : { "definition" : { "val" : "A relationship that holds via some environmental process" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002323", @@ -17471,17 +15159,7 @@ "meta" : { "definition" : { "val" : "A mereological relationship or a topological relationship" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002324", @@ -17490,14 +15168,7 @@ "meta" : { "definition" : { "val" : "A relationship that holds between entities participating in some developmental process (GO:0032502)" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002327", @@ -17509,30 +15180,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a particular instances of akt-2 enables some instance of protein kinase activity" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "catalyzes" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "executes" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is catalyzing" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is executing" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Enables" } ] @@ -17544,23 +15191,7 @@ "meta" : { "definition" : { "val" : "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." - }, - "xrefs" : [ { - "val" : "RO:0002328" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This is a grouping relation that collects relations used for the purpose of connecting structure and function" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "functionally_related_to" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002329", @@ -17569,14 +15200,7 @@ "meta" : { "definition" : { "val" : "this relation holds between c and p when c is part of some c', and c' is capable of p." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "false" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002330", @@ -17585,14 +15209,7 @@ "meta" : { "definition" : { "val" : "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002331", @@ -17603,15 +15220,6 @@ "val" : "c involved_in p if and only if c enables some process p', and p' is part of p" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "actively involved in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "enables part of" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Involved_in" } ] @@ -17628,18 +15236,6 @@ "val" : "RO:0002332" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "regulates levels of (process to entity)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17657,9 +15253,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Enabled_by" } ] @@ -17677,12 +15270,6 @@ "val" : "RO:0002334" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "regulated by (processual)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17703,9 +15290,6 @@ "val" : "RO:0002335" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17726,9 +15310,6 @@ "val" : "RO:0002336" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17743,14 +15324,7 @@ "meta" : { "definition" : { "val" : "A relationship that holds via some process of localization" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is a grouping relation." - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002338", @@ -17765,9 +15339,6 @@ "val" : "RO:0002338" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17788,9 +15359,6 @@ "val" : "RO:0002339" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17810,9 +15378,6 @@ "val" : "RO:0002341" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17833,9 +15398,6 @@ "val" : "RO:0002342" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17852,12 +15414,6 @@ "val" : "RO:0002343" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'pollen tube growth' results_in growth_of some 'pollen tube'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17874,12 +15430,6 @@ "val" : "RO:0002344" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17894,23 +15444,7 @@ "meta" : { "definition" : { "val" : "is member of is a mereological relation between a item and a collection." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "An organism that is a member of a population of organisms" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is member of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "member part of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "SIO" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002351", @@ -17919,23 +15453,7 @@ "meta" : { "definition" : { "val" : "has member is a mereological relation between a collection and an item." - }, - "xrefs" : [ { - "val" : "RO:0002351" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "SIO" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_member" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002352", @@ -17945,20 +15463,7 @@ "definition" : { "val" : "inverse of has input" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002352" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "input_of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002353", @@ -17973,14 +15478,8 @@ "val" : "RO:0002353" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "output_of" @@ -17989,26 +15488,11 @@ }, { "id" : "http://purl.obolibrary.org/obo/RO_0002354", "lbl" : "formed as result of", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002360", "lbl" : "has dendrite location", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.org/dc/terms/source", - "val" : "http://neurolex.org/wiki/Property:DendriteLocation" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002371", "lbl" : "attached to", @@ -18017,23 +15501,7 @@ "definition" : { "val" : "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002371" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "attached to (anatomical structure to anatomical structure)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "attaches_to" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002372", @@ -18043,22 +15511,7 @@ "definition" : { "val" : "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." }, - "xrefs" : [ { - "val" : "RO:0002372" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Wikipedia:Insertion_(anatomy)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_muscle_origin" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://dbpedia.org/property/origin" } ] @@ -18071,22 +15524,7 @@ "definition" : { "val" : "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." }, - "xrefs" : [ { - "val" : "RO:0002373" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Wikipedia:Insertion_(anatomy)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_muscle_insertion" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://dbpedia.org/property/insertion" } ] @@ -18100,21 +15538,6 @@ "val" : "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004036", - "val" : "http://purl.obolibrary.org/obo/BFO_0000050" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png" }, { @@ -18131,46 +15554,7 @@ "val" : "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002376" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Deschutes River tributary_of Columbia River" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "inferior epigastric vein tributary_of external iliac vein" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "drains into" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "drains to" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "tributary channel of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://en.wikipedia.org/wiki/Tributary" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.medindia.net/glossary/venous_tributary.htm" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "tributary_of" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://dbpedia.org/ontology/drainsTo" }, { @@ -18185,17 +15569,7 @@ "meta" : { "definition" : { "val" : "x spatially_coextensive_with y if and inly if x and y have the same location" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A lump of clay and a statue" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002380", @@ -18206,22 +15580,7 @@ "val" : "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002380" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "branching_part_of" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/issues/2212" }, { @@ -18236,14 +15595,7 @@ "meta" : { "definition" : { "val" : "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002385", @@ -18252,23 +15604,7 @@ "meta" : { "definition" : { "val" : "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" - }, - "xrefs" : [ { - "val" : "RO:0002385" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_potential_to_developmentally_contribute_to" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002386", @@ -18277,14 +15613,7 @@ "meta" : { "definition" : { "val" : "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002387", @@ -18293,23 +15622,7 @@ "meta" : { "definition" : { "val" : "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" - }, - "xrefs" : [ { - "val" : "RO:0002387" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_potential_to_develop_into" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002388", @@ -18318,14 +15631,7 @@ "meta" : { "definition" : { "val" : "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002404", @@ -18339,12 +15645,6 @@ "val" : "RO:0002404" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -18361,12 +15661,6 @@ "val" : "RO:0002405" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -18383,15 +15677,6 @@ "val" : "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "indirectly activates" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002579", - "val" : "http://purl.obolibrary.org/obo/RO_0002213" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Indirectly_positively_regulates" } ] @@ -18405,15 +15690,6 @@ "val" : "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "indirectly inhibits" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002579", - "val" : "http://purl.obolibrary.org/obo/RO_0002212" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Indirectly_negatively_regulates" } ] @@ -18430,12 +15706,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." } ] } }, { @@ -18451,9 +15721,6 @@ "val" : "RO:0002411" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -18473,12 +15740,6 @@ "val" : "RO:0002412" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002411" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -18504,12 +15765,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "influences (processual)" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" @@ -18531,12 +15786,6 @@ "val" : "RO:0002427" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -18551,11 +15800,7 @@ "meta" : { "definition" : { "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002429", @@ -18564,14 +15809,7 @@ "meta" : { "definition" : { "val" : "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002428" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002430", @@ -18582,9 +15820,6 @@ "val" : "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002428" } ] @@ -18600,12 +15835,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "OWL does not allow defining object properties via a Union" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "involved in or reguates" } ] } }, { @@ -18623,15 +15852,6 @@ "val" : "enables activity in" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A protein that enables activity in a cytosol." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "executes activity in" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Is_active_in" } ] @@ -18643,20 +15863,7 @@ "meta" : { "definition" : { "val" : "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." - }, - "xrefs" : [ { - "val" : "RO:0002433" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "contributes_to_morphology_of" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002434", @@ -18677,18 +15884,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Considering relabeling as 'pairwise interacts with'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" - }, { - "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", - "val" : "http://purl.obolibrary.org/obo/MI_0914" } ] } }, { @@ -18700,20 +15898,8 @@ "val" : "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "binds" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "molecularly binds with" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ECO_0000353" - }, { - "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", - "val" : "http://purl.obolibrary.org/obo/MI_0915" } ] } }, { @@ -18724,12 +15910,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Axiomatization to GO to be added later" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." } ] } }, { @@ -18743,13 +15923,6 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "molecularly controls" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" } ] } }, { @@ -18763,16 +15936,6 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "molecularly decreases activity of" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "directly inhibits" } ] } }, { @@ -18786,31 +15949,12 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "molecularly increases activity of" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "directly activates" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002464", "lbl" : "helper property (not for use in curation)", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002473", "lbl" : "composed primarily of", @@ -18819,29 +15963,7 @@ "definition" : { "val" : "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002473" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "composed_primarily_of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002479", @@ -18851,22 +15973,12 @@ "definition" : { "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002481", "lbl" : "is kinase activity", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002485", "lbl" : "receives input from", @@ -18875,9 +15987,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "See notes for inverse relation" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { @@ -18888,24 +15997,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002487", "lbl" : "relation between physical entity and a process or stage", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage." - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002488", "lbl" : "existence starts during", @@ -18913,20 +16010,7 @@ "meta" : { "definition" : { "val" : "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." - }, - "xrefs" : [ { - "val" : "RO:0002488" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_starts_during" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002489", @@ -18935,20 +16019,7 @@ "meta" : { "definition" : { "val" : "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." - }, - "xrefs" : [ { - "val" : "RO:0002489" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_starts_with" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002490", @@ -18958,11 +16029,7 @@ "definition" : { "val" : "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002491", @@ -18976,19 +16043,6 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "exists during" - } ], - "xrefs" : [ { - "val" : "RO:0002491" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_starts_and_ends_during" } ] } }, { @@ -18999,24 +16053,7 @@ "definition" : { "val" : "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "ceases_to_exist_during" - } ], - "xrefs" : [ { - "val" : "RO:0002492" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_ends_during" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002493", @@ -19026,20 +16063,7 @@ "definition" : { "val" : "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "xrefs" : [ { - "val" : "RO:0002493" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_ends_with" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002494", @@ -19048,20 +16072,7 @@ "meta" : { "definition" : { "val" : "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" - }, - "xrefs" : [ { - "val" : "RO:0002494" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "transformation_of" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002495", @@ -19070,23 +16081,7 @@ "meta" : { "definition" : { "val" : "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" - }, - "xrefs" : [ { - "val" : "RO:0002495" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002494" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "immediate_transformation_of" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002496", @@ -19096,20 +16091,7 @@ "definition" : { "val" : "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "xrefs" : [ { - "val" : "RO:0002496" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_starts_during_or_after" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002497", @@ -19119,20 +16101,7 @@ "definition" : { "val" : "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "xrefs" : [ { - "val" : "RO:0002497" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_ends_during_or_before" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002500", @@ -19141,11 +16110,7 @@ "meta" : { "definition" : { "val" : "A relationship between a material entity and a process where the material entity has some causal role that influences the process" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002501", @@ -19154,17 +16119,7 @@ "meta" : { "definition" : { "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002502", @@ -19172,9 +16127,6 @@ "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/BFO_0000169" } ] @@ -19187,15 +16139,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." } ] } }, { @@ -19205,55 +16148,18 @@ "meta" : { "definition" : { "val" : "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." - }, - "xrefs" : [ { - "val" : "RO:0002551" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has supporting framework" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_skeleton" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002559", "lbl" : "causally influenced by", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "causally influenced by (entity-centric)" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002563", "lbl" : "interaction relation helper property", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29" }, { @@ -19264,13 +16170,7 @@ }, { "id" : "http://purl.obolibrary.org/obo/RO_0002564", "lbl" : "molecular interaction relation helper property", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002565", "lbl" : "results in movement of", @@ -19284,11 +16184,6 @@ "val" : "RO:0002565" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -19303,20 +16198,7 @@ "meta" : { "definition" : { "val" : "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "causally influences (entity-centric)" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002567", @@ -19325,14 +16207,7 @@ "meta" : { "definition" : { "val" : "A relation that holds between elements of a musculoskeletal system or its analogs." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002568", @@ -19341,23 +16216,7 @@ "meta" : { "definition" : { "val" : "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." - }, - "xrefs" : [ { - "val" : "RO:0002568" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Wikipedia:Antagonist_(muscle)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_muscle_antagonist" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002569", @@ -19367,20 +16226,7 @@ "definition" : { "val" : "inverse of branching part of" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002569" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_branching_part" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002570", @@ -19390,26 +16236,7 @@ "definition" : { "val" : "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002570" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "UBERON:cjm" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "conduit_for" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002571", @@ -19419,23 +16246,7 @@ "definition" : { "val" : "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002571" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "lumen_of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002572", @@ -19445,20 +16256,7 @@ "definition" : { "val" : "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002572" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "luminal_space_of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002576", @@ -19468,20 +16266,7 @@ "definition" : { "val" : "inverse of has skeleton" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "xrefs" : [ { - "val" : "RO:0002576" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "skeleton_of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002578", @@ -19496,18 +16281,6 @@ "val" : "RO:0002578" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "directly regulates (processual)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002211" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -19515,24 +16288,6 @@ "val" : "directly_regulates" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002581", - "lbl" : "is a defining property chain axiom", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002582", - "lbl" : "is a defining property chain axiom where second argument is reflexive", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R." - } - } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002584", "lbl" : "has part structure that is capable of", @@ -19540,14 +16295,7 @@ "meta" : { "definition" : { "val" : "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002586", @@ -19621,12 +16369,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] } }, { @@ -19636,14 +16378,7 @@ "meta" : { "definition" : { "val" : "Holds between c and p if and only if c is capable of some activity a, and a regulates p." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "pyrethroid -> growth" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002597", @@ -19652,11 +16387,7 @@ "meta" : { "definition" : { "val" : "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002598", @@ -19665,14 +16396,7 @@ "meta" : { "definition" : { "val" : "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "renin -> arteriolar smooth muscle contraction" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002608", @@ -19686,9 +16410,6 @@ "val" : "RO:0002608" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -19709,15 +16430,6 @@ "val" : "RO:0002629" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "directly positively regulates (process to process)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002578" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -19741,12 +16453,6 @@ "val" : "RO:0002630" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "directly negatively regulates (process to process)" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002578" }, { @@ -19774,17 +16480,8 @@ "val" : "RO:0003000" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9114-8737" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "produces" @@ -19803,17 +16500,8 @@ "val" : "RO:0003001" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9114-8737" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "produced_by" @@ -19922,9 +16610,6 @@ "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002264" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { @@ -19965,9 +16650,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002263" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { @@ -20026,9 +16708,6 @@ "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002418" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { @@ -20059,11 +16738,7 @@ "meta" : { "definition" : { "val" : "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0012000", @@ -20325,9 +17000,6 @@ "xrefs" : [ "PMID:19243617" ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" - }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1617-8244" }, { @@ -20345,9 +17017,6 @@ "xrefs" : [ "PMID:19243617" ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" - }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1617-8244" }, { @@ -20368,21 +17037,6 @@ "val" : "utilizes" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A diagnostic testing device utilizes a specimen." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9625-1899" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-2620-0345" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "See github ticket https://github.com/oborel/obo-relations/issues/497" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-11-08T12:00:00Z" } ] @@ -20568,8 +17222,6 @@ "val" : "EHDAA:500" }, { "val" : "EMAPA:35955" - }, { - "val" : "FBbt:00005155" }, { "val" : "GAID:63" }, { @@ -20617,12 +17269,6 @@ "val" : "galen:Tube" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts)" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "tubular" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -20687,15 +17333,6 @@ "val" : "galen:Tendon" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Dense regular connective tissue that connects muscle to bone.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Phylogenetically, tendinous tissue first appears in the invertebrate chordate Branchiostoma as myosepta. This two-dimensional array of collagen fibers is highly organized, with fibers running along two primary axes. In hagfish the first linear tendons appear and the myosepta have developed specialized regions with unidirectional fiber orientation - a linear tendon within the flat sheet of myoseptum.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in FMA, tendon is an organ component that with parts dense-irregular-connective-tissue of tendon and dense-irregular-connective-tissue of tendon sheath; we follow VSAO in making it a subtype of the former. In VSAO tendons connect muscle to bone; in WP the def states integument (e.g. auricular muscles) - but JB confirms this is not actually tendon but aponeurosis" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -20730,8 +17367,6 @@ } ], "xrefs" : [ { "val" : "AAO:0011123" - }, { - "val" : "FBbt:00100314" }, { "val" : "FMA:30320" }, { @@ -20752,12 +17387,6 @@ "val" : "galen:Duct" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -20785,16 +17414,11 @@ "xrefs" : [ "FMA:82482" ] } ], "xrefs" : [ { - "val" : "EMAPA:25036" - }, { "val" : "FMA:82482" }, { "val" : "galen:Wall" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in FMA, serosa is a wall" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0009915" }, { @@ -20832,8 +17456,6 @@ "val" : "EHDAA2:0003003" }, { "val" : "EMAPA:0" - }, { - "val" : "FBbt:00007001" }, { "val" : "FMA:305751" }, { @@ -20933,12 +17555,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -20973,12 +17589,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -21017,9 +17627,6 @@ "val" : "SCTID:91717005" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "currently defined in a very broad sense, may be replaced by more specific classes in the future" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { @@ -21150,9 +17757,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "ncit:Death is an outcome" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -21230,9 +17834,6 @@ "val" : "WBls:0000103" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -21349,12 +17950,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "the WBls class 'all stages' belongs here as it is the superclass of other WBls stages" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -21407,8 +18002,6 @@ "val" : "EHDAA:27" }, { "val" : "FBdv:00005288" - }, { - "val" : "IDOMAL:0000302" }, { "val" : "NCIT:C12601" }, { @@ -21423,9 +18016,6 @@ "val" : "ZFS:0000001" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -21603,12 +18193,6 @@ "val" : "XAO:1000006" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002174", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7955" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In zebrafish, the times of neurulation and segmentation overlap so extensively there is no distinct neurula period of development, such as occurs largely before segmentation in amphibian embryos." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -21741,8 +18325,6 @@ "val" : "EHDAA:542" }, { "val" : "EMAPA:16262" - }, { - "val" : "FBbt:00003126" }, { "val" : "FMA:49184" }, { @@ -21785,21 +18367,6 @@ "val" : "http://purl.obolibrary.org/obo/uberon/images/lamprey_sucker_rosava_3238889218.jpg" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "oral" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -21907,8 +18474,6 @@ "val" : "BTO:0001485" }, { "val" : "EFO:0000801" - }, { - "val" : "EMAPA:35578" }, { "val" : "FMA:72954" }, { @@ -21931,12 +18496,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system that consists of the muscles of the body.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -21987,8 +18546,6 @@ "val" : "EHDAA2:0003004" }, { "val" : "EMAPA:35178" - }, { - "val" : "FBbt:00007019" }, { "val" : "FMA:9669" }, { @@ -22061,8 +18618,6 @@ "val" : "CARO:0000005" }, { "val" : "EHDAA2:0003005" - }, { - "val" : "FBbt:00007017" }, { "val" : "FMA:5897" }, { @@ -22116,8 +18671,6 @@ "val" : "CARO:0000006" }, { "val" : "EHDAA2:0003006" - }, { - "val" : "FBbt:00007016" }, { "val" : "FMA:67165" }, { @@ -22168,8 +18721,6 @@ "val" : "CARO:0000007" }, { "val" : "EHDAA2:0003007" - }, { - "val" : "FBbt:00007015" }, { "val" : "FMA:67112" }, { @@ -22248,14 +18799,10 @@ "val" : "EMAPA:16103" }, { "val" : "EV:0100000" - }, { - "val" : "FBbt:00004856" }, { "val" : "FMA:7149" }, { "val" : "HAO:0000011" - }, { - "val" : "IDOMAL:0002460" }, { "val" : "MA:0000003" }, { @@ -22364,8 +18911,6 @@ "val" : "EMAPA:25765" }, { "val" : "EV:0100016" - }, { - "val" : "FBbt:00000001" }, { "val" : "FMA:256135" }, { @@ -22407,9 +18952,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "organismal" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -22459,8 +19001,6 @@ "val" : "EHDAA2:0003032" }, { "val" : "EMAPA:36031" - }, { - "val" : "FBbt:00007009" }, { "val" : "FMA:7153" }, { @@ -22535,8 +19075,6 @@ "val" : "CARO:0000040" }, { "val" : "EHDAA2:0003040" - }, { - "val" : "FBbt:00007013" }, { "val" : "FMA:63863" }, { @@ -22575,8 +19113,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "xrefs" : [ { - "val" : "FBbt:00007277" - }, { "val" : "VHOG:0001737" } ], "basicPropertyValues" : [ { @@ -22630,8 +19166,6 @@ "val" : "EHDAA2:0003042" }, { "val" : "EHDAA:46" - }, { - "val" : "FBbt:00005835" }, { "val" : "FMA:85537" }, { @@ -22698,8 +19232,6 @@ "val" : "EHDAA2:0003043" }, { "val" : "EMAPA:35868" - }, { - "val" : "FBbt:00007003" }, { "val" : "FMA:9637" }, { @@ -22770,8 +19302,6 @@ "val" : "CARO:0000055" }, { "val" : "EHDAA2:0003055" - }, { - "val" : "FBbt:00007010" }, { "val" : "HAO:0000055" }, { @@ -22836,8 +19366,6 @@ "val" : "EHDAA2:0003066" }, { "val" : "EMAPA:32738" - }, { - "val" : "FBbt:00007005" }, { "val" : "FMA:9639" }, { @@ -22866,12 +19394,6 @@ "val" : "ZFA:0001486" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "epithelial" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -22929,9 +19451,6 @@ "val" : "ZFA:0001494" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Epithelium that consists of more than one layer of epithelial cells.[CARO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -22988,9 +19507,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Epithelium that consists of a single layer of epithelial cells.[CARO]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -23040,14 +19556,10 @@ "val" : "EHDAA:38" }, { "val" : "EMAPA:16039" - }, { - "val" : "FBbt:00000052" }, { "val" : "FMA:69068" }, { "val" : "GAID:963" - }, { - "val" : "IDOMAL:0000646" }, { "val" : "MAT:0000226" }, { @@ -23074,12 +19586,6 @@ "val" : "http://neurolex.org/wiki/Category:Embryonic_organism" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "embryonic" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -23128,8 +19634,6 @@ "val" : "BTO:0000556" }, { "val" : "EMAPA:36033" - }, { - "val" : "FBbt:00000110" }, { "val" : "FMA:69069" }, { @@ -23156,9 +19660,6 @@ "val" : "ZFA:0001122" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -23194,8 +19695,6 @@ "val" : "EMAPA:16069" }, { "val" : "EV:0100003" - }, { - "val" : "FBbt:00000111" }, { "val" : "FMA:69070" }, { @@ -23226,15 +19725,6 @@ "val" : "ZFA:0000016" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "ectodermal" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -23274,8 +19764,6 @@ "val" : "EMAPA:16062" }, { "val" : "EV:0100005" - }, { - "val" : "FBbt:00000125" }, { "val" : "FMA:69071" }, { @@ -23304,12 +19792,6 @@ "val" : "ZFA:0000017" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "endodermal" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -23364,8 +19846,6 @@ "val" : "EMAPA:16083" }, { "val" : "EV:0100006" - }, { - "val" : "FBbt:00000126" }, { "val" : "FMA:69072" }, { @@ -23396,18 +19876,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Primary germ layer that is the middle of the embryonic germ layers.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "mesodermal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0003263" @@ -23467,8 +19935,6 @@ "val" : "EHDAA2:0001929" }, { "val" : "EMAPA:16263" - }, { - "val" : "FBbt:00000439" }, { "val" : "FMA:295846" }, { @@ -23489,18 +19955,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "stomodeal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -23542,8 +19996,6 @@ "val" : "EMAPA:35306" }, { "val" : "EV:0100128" - }, { - "val" : "FBbt:00005068" }, { "val" : "FMA:9668" }, { @@ -23570,15 +20022,6 @@ "val" : "ZFA:0001158" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "endocrine" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -23611,8 +20054,6 @@ "val" : "EFO:0000827" }, { "val" : "EV:0100336" - }, { - "val" : "FBbt:00005162" }, { "val" : "GAID:69" }, { @@ -23625,20 +20066,8 @@ "val" : "Wikipedia:Eye" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This class encompasses a variety of light-detecting structures from different phyla with no implication of homology, from the compound insect eye to the vertebrate camera-type eye (distinct classes are provided for each)" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "ocular" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "optic" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000010", - "val" : "Note that whilst this is classified as an organ, it is in fact more of a unit composed of different structures: in Drosophila, it includes the interommatidial bristle as a part; we consider here the vertebrate eye to include the eyeball/eye proper as a part, with the eye having as parts (when present): eyelids, conjuctiva," }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -23718,12 +20147,6 @@ "val" : "galen:Joint" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -23761,10 +20184,6 @@ "val" : "CALOHA:TS-1293" }, { "val" : "EFO:0000793" - }, { - "val" : "EV:0100056" - }, { - "val" : "FBbt:00005055" }, { "val" : "FMA:7152" }, { @@ -23799,15 +20218,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "digestive" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -23833,17 +20243,12 @@ "val" : "AAO:0000959" }, { "val" : "CALOHA:TS-2103" - }, { - "val" : "MESH:D002319" }, { "val" : "VHOG:0001248" }, { "val" : "Wikipedia:Circulatory_system" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "the cardiovascular system and the lymphatic system are parts of the circulatory system" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_147099" }, { @@ -23852,18 +20257,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6157" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002174", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6231" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -23915,13 +20311,9 @@ "val" : "musculature system" } ], "xrefs" : [ { - "val" : "AAO:0011066" - }, { "val" : "BTO:0000887" }, { "val" : "EFO:0001949" - }, { - "val" : "EMAPA:32715" }, { "val" : "EMAPA:35577" }, { @@ -23944,12 +20336,6 @@ "val" : "ZFA:0000548" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0001474" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -24001,8 +20387,6 @@ "val" : "EMAPA:16469" }, { "val" : "EV:0100162" - }, { - "val" : "FBbt:00005093" }, { "val" : "FMA:7157" }, { @@ -24042,21 +20426,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "nervous" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "neural" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -24120,8 +20489,6 @@ "val" : "EMAPA:16754" }, { "val" : "EV:0100163" - }, { - "val" : "FBbt:00005094" }, { "val" : "FMA:55675" }, { @@ -24157,18 +20524,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Part of the nervous system which includes the brain and spinal cord.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The brain and spinal cord. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO)." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -24233,8 +20588,6 @@ "val" : "EHDAA2:0003094" }, { "val" : "EMAPA:16192" - }, { - "val" : "FBbt:00007692" }, { "val" : "FMA:75259" }, { @@ -24257,12 +20610,6 @@ "val" : "ZFA:0000282" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -24314,8 +20661,6 @@ "val" : "FMA:293882" }, { "val" : "MAT:0000069" - }, { - "val" : "MESH:D054259" }, { "val" : "MIAA:0000069" }, { @@ -24338,18 +20683,6 @@ "val" : "neuronames:1365" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -24381,8 +20714,6 @@ "val" : "CARO:0000000" }, { "val" : "EHDAA2:0002229" - }, { - "val" : "FBbt:10000000" }, { "val" : "FMA:62955" }, { @@ -24596,15 +20927,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "This result implies the following views in terms of evolutionary differentiation: (1) Arthropod striated muscle and vertebrate skeletal and cardiac muscles share a common ancestor. In other words, they did not evolve independently (...) (5) The divergence of vertebrate skeletal and cardiac muscles/vertebrate smooth muscle and nonmuscle is at least before that of vertebrates/arthropods. In other words, emergence of skeletal and cardiac musle type tissues preceded the vertebrate/arthropod divergence (ca. 700 MYA).[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -24667,27 +20989,6 @@ "val" : "ZFA:0000434" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0001016" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "System that provides physical support to the organism.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "skeletal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -24771,30 +21072,6 @@ "val" : "galen:Bone" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0001015" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0001630" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0002385" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Skeletal element that is composed of bone tissue.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -24847,14 +21124,10 @@ "val" : "EHDAA:518" }, { "val" : "EMAPA:16247" - }, { - "val" : "FBbt:00003125" }, { "val" : "FMA:45615" }, { "val" : "MA:0000917" - }, { - "val" : "MESH:D041981" }, { "val" : "NCIT:C34082" }, { @@ -24881,21 +21154,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The alimentary or digestive tract, and associated organs.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "FMA also has a term 'gastrointestinal tract', but this includes the liver." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000013", - "val" : "we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -24917,10 +21175,6 @@ "xrefs" : [ "ZFA:0005145" ] } ], "xrefs" : [ { - "val" : "AAO:0011066" - }, { - "val" : "EMAPA:32715" - }, { "val" : "EMAPA:37474" }, { "val" : "EV:0100146" @@ -24944,15 +21198,6 @@ "val" : "galen:Muscle" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of tissue composed of contractile fibers.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "muscular" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -24997,9 +21242,6 @@ "val" : "galen:StriatedMuscle" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Voluntary muscle tissue arranged in bundles of fibers.[AAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -25045,8 +21287,6 @@ "val" : "CALOHA:TS-2110" }, { "val" : "EFO:0000461" - }, { - "val" : "FBbt:00004208" }, { "val" : "FMA:69067" }, { @@ -25071,18 +21311,6 @@ "val" : "ZFA:0001105" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in FMA embryo is_a embryonic structure" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -25152,18 +21380,6 @@ "val" : "galen:Trunk" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000026" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000033" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -25214,9 +21430,6 @@ "val" : "http://uri.neuinfo.org/nif/nifstd/FMAID_7191" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The sensory system used for sight.[AAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0007036" }, { @@ -25305,15 +21518,6 @@ "val" : "XAO:0000168" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system that provides locomotion and physical support to the organism.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "musculoskeletal" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -25388,27 +21592,6 @@ "val" : "http://evolution.berkeley.edu/evolibrary/images/history/notochords.jpg" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "notochordal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -25495,32 +21678,8 @@ "val" : "ZFA:0000155" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "EDITOR_NOTE currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7712" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Post-cranial axial segments which form sclerotome and dermomyotome.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "somitic" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -25618,8 +21777,6 @@ "val" : "NCIT:C34222" }, { "val" : "SCTID:361462002" - }, { - "val" : "TAO:0000045" }, { "val" : "UMLS:C0027789" }, { @@ -25634,24 +21791,6 @@ "val" : "neuronames:1366" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "EDITOR_NOTE consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams)." - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002174", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_117565" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -25710,8 +21849,6 @@ "val" : "EMAPA:16073" }, { "val" : "EV:0100004" - }, { - "val" : "FBbt:00001057" }, { "val" : "FMA:87657" }, { @@ -25734,15 +21871,6 @@ "val" : "ZFA:0001120" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "neurectodermal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000013", - "val" : "we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -25942,12 +22070,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000009", - "val" : "In adults, marrow in large bones produces new blood cells[Wikipedia:Bone_marrow]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26020,18 +22142,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "MA also has set of connective tissues" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26088,12 +22198,6 @@ "val" : "galen:MuscleTissue" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0003714" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -26178,18 +22282,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system that consists of the blood and blood forming tissues.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "hematopoietic" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26239,9 +22331,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26308,9 +22397,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "see https://github.com/obophenotype/uberon/issues/27" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26352,14 +22438,8 @@ "val" : "EHDAA2:0003096" }, { "val" : "EHDAA:2161" - }, { - "val" : "EHDAA:4475" - }, { - "val" : "EHDAA:6522" }, { "val" : "EMAPA:18425" - }, { - "val" : "FBbt:00100317" }, { "val" : "FMA:7146" }, { @@ -26386,12 +22466,6 @@ "val" : "galen:Gland" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0001434" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "glandular" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -26446,9 +22520,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26542,12 +22613,6 @@ "val" : "ZFA:0000279" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -26609,21 +22674,6 @@ "val" : "ZFA:0000094" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -26659,9 +22709,6 @@ "val" : "ZFA:0001204" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -26704,8 +22751,6 @@ "val" : "EMAPA:35593" }, { "val" : "FMA:293879" - }, { - "val" : "MESH:D054258" }, { "val" : "NCIT:C34225" }, { @@ -26726,12 +22771,6 @@ "val" : "neuronames:1362" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -26791,15 +22830,6 @@ "val" : "ZFA:0000255" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -26867,18 +22897,6 @@ "val" : "ZFA:0000121" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "subclass of mesoderm in ZFA." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0006258" }, { @@ -26962,12 +22980,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The term 'myotome' is also used to describe the muscles served by a single nerve root / spinal segment - consider adding new class, myomere." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of the somites giving rise to body wall muscle masses. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "In all vertebrates, the skeletal muscle of the body axis is chiefly derived from an early embryonic compartment, known as the myotome.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27016,9 +23028,6 @@ "val" : "ZFA:0000496" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -27081,15 +23090,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "mesenchymal" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27129,9 +23129,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27154,13 +23151,8 @@ "val" : "AEO:0000114" }, { "val" : "EHDAA2:0003114" - }, { - "val" : "FBbt:00007474" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -27215,9 +23207,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "FMA has both conduit and conduit space. In EHDAA2 this is a surface feature" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27239,9 +23228,6 @@ "xrefs" : [ "FBbt:00025998" ] } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Grouping term for query purposes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -27262,9 +23248,6 @@ "xrefs" : [ "FBbt:00025990" ] } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Grouping term for query purposes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -27318,17 +23301,8 @@ "val" : "galen:Skeleton" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000383" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "skeletal" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27378,21 +23352,6 @@ "val" : "ZFA:0001513" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of somites that gives rise to dermis and muscles.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "all but the sclerotome of a mesodermal somite; the primordium of skeletal muscle and, perhaps, of the dermis." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -27416,9 +23375,6 @@ "val" : "FMA:78499" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -27512,8 +23468,6 @@ "val" : "BILA:0000060" }, { "val" : "BTO:0001403" - }, { - "val" : "FBbt:00005317" }, { "val" : "FMA:293108" }, { @@ -27536,9 +23490,6 @@ "val" : "Wikipedia:Trilaminar_blastocyst" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "We explicitly merge the NCITA terms here" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0007012" }, { @@ -27570,9 +23521,6 @@ "val" : "ZFA:0005619" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -27601,12 +23549,6 @@ "val" : "galen:SkeletalStructure" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -27688,12 +23630,6 @@ "val" : "ZFA:0000091" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Notochord rudiment[ZFIN:ZDB-PUB-961014-576]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -27712,9 +23648,6 @@ "pred" : "hasNarrowSynonym", "val" : "joint" } ], - "xrefs" : [ { - "val" : "FBbt:00005811" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27750,14 +23683,9 @@ "xrefs" : [ "FMA:71131" ] } ], "xrefs" : [ { - "val" : "FBbt:00100315" - }, { "val" : "FMA:71131" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct." - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { @@ -27812,9 +23740,6 @@ "val" : "neuronames:1363" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -27852,9 +23777,6 @@ "val" : "neuronames:1364" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -27882,9 +23804,6 @@ "val" : "ZFA:0000133" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -27910,14 +23829,9 @@ "val" : "muscle element" } ], "xrefs" : [ { - "val" : "EMAPA:32715" - }, { "val" : "FMA:30316" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -28010,9 +23924,6 @@ "pred" : "hasExactSynonym", "val" : "light-sensitive tissue" } ], - "xrefs" : [ { - "val" : "FBbt:00004200" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28041,8 +23952,6 @@ "val" : "CALOHA:TS-2122" }, { "val" : "EHDAA2:0003125" - }, { - "val" : "FBbt:00007006" }, { "val" : "FMA:292313" }, { @@ -28128,9 +24037,6 @@ "val" : "Wikipedia:Basement_membrane" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell." - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_80999" }, { @@ -28164,9 +24070,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO - check ordering; awaiting confirmation from JB" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28404,9 +24307,6 @@ "val" : "UMLS:C1514442" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -28436,16 +24336,11 @@ "xrefs" : [ "FBbt:00003154" ] } ], "xrefs" : [ { - "val" : "SPD:0000130" - }, { "val" : "TADS:0000147" }, { "val" : "http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -28473,9 +24368,6 @@ "val" : "ZFA:0000131" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -28537,9 +24429,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider merging" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Region of the gastrula which gives rise to the neural plate.[TAO]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28680,12 +24569,6 @@ "val" : "XAO:0004030" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Regular connective tissue, the intercellular matrix of which consists predominantly of collagen fiber bundles arranged in parallel arrays.[FMA]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -28756,8 +24639,6 @@ } ], "xrefs" : [ { "val" : "CARO:0010000" - }, { - "val" : "FBbt:00100313" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", @@ -28792,6 +24673,21 @@ "val" : "uberon" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/UBERON_0010314", + "lbl" : "structure with developmental contribution from neural crest", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "An anatomical structure that has some part that develops from the neural crest.", + "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "uberon" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/UBERON_0010316", "lbl" : "germ layer / neural crest", @@ -28854,8 +24750,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "xrefs" : [ { - "val" : "FBbt:00007330" - }, { "val" : "FMA:67509" }, { "val" : "SCTID:91690000" @@ -28949,9 +24843,6 @@ "val" : "Wikipedia:Dense_irregular_connective_tissue" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Tissue characterized by a thick, random arrangement of collagen and elastin fibers with very few cells. The majority of the cells are fibroblasts, but mast cells and macrophages may also be seen. It is found in the dermis, periosteum, perichondrium, capsules of organs and sheaths of nerves and muscles[NCIT]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -28977,9 +24868,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "our OWL definition states that this is differentiated from other connective tissue types by virtue of the fact that the collage fiber component predominates, as opposed to cells and fluid." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -29000,9 +24888,6 @@ "val" : "NIF_Subcellular:sao7547390221" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "the FMA class specifically refers to ureter" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -29039,9 +24924,6 @@ "val" : "Wikipedia:Epimysium" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000009", - "val" : "The Epimysium also protects muscles from friction against other muscles and bones" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -29084,9 +24966,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_147099" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "coelomic" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -29132,9 +25011,6 @@ "val" : "UMLS:C0229619" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "Bone marrow in humans, kidney interstitium in Danio, within a stroma of reticuloendothelial tissue" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -29218,15 +25094,10 @@ "val" : "AEO:0000103" }, { "val" : "BTO:0001489" - }, { - "val" : "EMAPA:36031" }, { "val" : "FMA:231424" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -29303,8 +25174,6 @@ }, "xrefs" : [ { "val" : "AEO:0000093" - }, { - "val" : "FBbt:00007278" } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", @@ -29339,9 +25208,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This class is primarily to implement taxon constraints. It may be removed in the future." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -29372,9 +25238,6 @@ "pred" : "hasRelatedSynonym", "val" : "cardiac structure" } ], - "xrefs" : [ { - "val" : "SPD:0000130" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -29520,8 +25383,6 @@ "val" : "EHDAA2:0001842" }, { "val" : "EMAPA:35578" - }, { - "val" : "MA:0000165" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", @@ -29593,8 +25454,6 @@ "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], "xrefs" : [ { "val" : "CARO:0020000" - }, { - "val" : "FBbt:00007276" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", @@ -30062,120 +25921,6 @@ "val" : "uberon" } ] } - }, { - "id" : "http://purl.org/dc/elements/1.1/creator", - "lbl" : "creator", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/elements/1.1/creator" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-creator" - } ] - } - }, { - "id" : "http://purl.org/dc/elements/1.1/description", - "lbl" : "description", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/elements/1.1/description" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-description" - } ] - } - }, { - "id" : "http://purl.org/dc/elements/1.1/title", - "lbl" : "title", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/elements/1.1/title" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-title" - } ] - } - }, { - "id" : "http://purl.org/dc/terms/contributor", - "lbl" : "contributor", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/terms/contributor" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-contributor" - } ] - } - }, { - "id" : "http://purl.org/dc/terms/date", - "lbl" : "date", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/terms/date" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dcterms-date" - } ] - } - }, { - "id" : "http://purl.org/dc/terms/license", - "lbl" : "license", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/terms/license" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dcterms-license" - } ] - } }, { "id" : "http://www.geneontology.org/formats/oboInOwl#SubsetProperty", "lbl" : "subset_property", @@ -30209,9 +25954,6 @@ "val" : "An alternative label for a class or property which has a more general meaning than the preferred name/primary label." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/18" }, { @@ -30232,9 +25974,6 @@ "val" : "An alternative label for a class or property which has the exact same meaning than the preferred name/primary label." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/20" }, { @@ -30251,9 +25990,6 @@ "val" : "An alternative label for a class or property which has a more specific meaning than the preferred name/primary label." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/19" }, { @@ -30274,9 +26010,6 @@ "val" : "An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/21" }, { @@ -30309,35 +26042,10 @@ "val" : "http://www.w3.org/2000/01/rdf-schema#seeAlso" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "seeAlso" } ] } - }, { - "id" : "http://xmlns.com/foaf/0.1/depiction", - "lbl" : "depiction", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://xmlns.com/foaf/0.1/depiction" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "depiction" - } ] - } } ], "edges" : [ { "sub" : "http://purl.obolibrary.org/obo/BFO_0000004", @@ -35356,17 +31064,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0004921", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts" - } ] - } - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0001106", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0001555" + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004921" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -35410,13 +31108,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000463", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000468", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "this relationship may be too strong and may be weakened in future" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000468" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000463", "pred" : "http://purl.obolibrary.org/obo/RO_0000086", @@ -35620,13 +31312,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000926", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000923", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "sometimes not considered primary" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000923" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000926", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -36045,13 +31731,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002204", "pred" : "http://purl.obolibrary.org/obo/RO_0002254", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000926", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "check ctenophore" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000926" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002204", "pred" : "http://purl.obolibrary.org/obo/RO_0002492", @@ -36076,6 +31756,10 @@ "val" : "VSAO" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", "pred" : "is_a", @@ -36084,14 +31768,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0011137" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000098", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0001555" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000102", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0001049" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -36188,6 +31864,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010314" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "is_a", @@ -36208,16 +31888,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_89593", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "ISBN:0073040584" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_89593" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -36241,13 +31912,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "http://purl.obolibrary.org/obo/RO_0002473", - "obj" : "http://purl.obolibrary.org/obo/CL_0000333", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/CL_0000333" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "http://purl.obolibrary.org/obo/RO_0002488", @@ -36302,6 +31967,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002371", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000479" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0002371", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002371", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -36388,13 +32057,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002390", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0003061", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "definitional" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0003061" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002405", "pred" : "is_a", @@ -36571,10 +32234,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0003077", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0015212" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0003077", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000922" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003077", "pred" : "http://purl.obolibrary.org/obo/RO_0002488", @@ -36844,19 +32503,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004755", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/CL_0007001", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#date_retrieved", - "val" : "2012-08-14" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#external_class", - "val" : "VSAO:0000015" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "VSAO" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/CL_0007001" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004765", "pred" : "is_a", @@ -36968,14 +32615,14 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005062", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0015212" + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010371" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005062", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0005061" + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0015212" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005062", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000126", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0005061" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005068", @@ -37206,13 +32853,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006984", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0010199", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "via morphological boundary in CARO" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010199" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007010", "pred" : "is_a", @@ -37256,13 +32897,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007100", "pred" : "http://purl.obolibrary.org/obo/RO_0002215", - "obj" : "http://purl.obolibrary.org/obo/GO_0008015", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "GO uses blood circulation generically to include the haemolymphatic fluid of arthropods" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/GO_0008015" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007135", "pred" : "is_a", @@ -37278,16 +32913,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007282", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0009618", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#consistent_with", - "val" : "https://github.com/obophenotype/uberon/wiki/The-neural-crest" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "EDHAA2" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0009618" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007282", "pred" : "http://purl.obolibrary.org/obo/RO_0002387", @@ -37458,6 +33084,14 @@ "val" : "CARO" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0010314", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0010314", + "pred" : "http://purl.obolibrary.org/obo/RO_0002254", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0002342" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0010316", "pred" : "is_a", @@ -37580,6 +33214,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0011860", "pred" : "http://purl.obolibrary.org/obo/RO_0002473", "obj" : "http://purl.obolibrary.org/obo/GO_0098643" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0011899", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0011899", "pred" : "is_a", @@ -37622,6 +33260,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0011997", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0012429", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0012429", "pred" : "is_a", @@ -37746,10 +33388,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0015212", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0015212", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000465" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0015212", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -39106,10 +34744,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000057" - }, { - "sub" : "http://purl.obolibrary.org/obo/uberon/core#anteriorly_connected_to", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BSPO_0000099" }, { "sub" : "http://purl.obolibrary.org/obo/uberon/core#anteriorly_connected_to", "pred" : "subPropertyOf", @@ -39118,10 +34752,6 @@ "sub" : "http://purl.obolibrary.org/obo/uberon/core#anteriorly_connected_to", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/uberon/core#transitively_anteriorly_connected_to" - }, { - "sub" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BSPO_0000100" }, { "sub" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", "pred" : "subPropertyOf", @@ -39138,18 +34768,10 @@ "sub" : "http://purl.obolibrary.org/obo/uberon/core#layer_part_of", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000050" - }, { - "sub" : "http://purl.obolibrary.org/obo/uberon/core#posteriorly_connected_to", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BSPO_0000096" }, { "sub" : "http://purl.obolibrary.org/obo/uberon/core#posteriorly_connected_to", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002170" - }, { - "sub" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BSPO_0000097" }, { "sub" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to", "pred" : "subPropertyOf", @@ -39366,10 +34988,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012001", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012005" - }, { - "sub" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", - "pred" : "inverseOf", - "obj" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to" } ], "logicalDefinitionAxioms" : [ { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000006", @@ -41170,13 +36788,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002082", "fillerId" : "http://purl.obolibrary.org/obo/GO_0040016" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0000165", - "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0004921" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BSPO_0001106", - "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0001555" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0000307", "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000468" ], @@ -41513,6 +37124,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0000086", "fillerId" : "http://purl.obolibrary.org/obo/PATO_0001993" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0010314", + "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002254", + "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0002342" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0010371", "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000483" ], @@ -41567,13 +37185,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002473", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0002530" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0015212", - "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0000465" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0016879", "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0006598" ], @@ -41887,7 +37498,7 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002551", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061", "http://purl.obolibrary.org/obo/UBERON_0000475" ], + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002566", @@ -41949,10 +37560,6 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0019000", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/uberon/core#channel_for", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0004111" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000463" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] @@ -41984,21 +37591,12 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002287", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002210" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002329", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002215" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002496" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002497" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002479", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/BFO_0000066" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/RO_0000057" ] @@ -42017,24 +37615,12 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000066", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000066", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002314", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0000052", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0001025", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0001025", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002005", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002005", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002005", "http://purl.obolibrary.org/obo/RO_0002380" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002100", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002100", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/uberon/core#extends_fibers_into", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002100", "http://purl.obolibrary.org/obo/RO_0013001" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002102", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002102", "http://purl.obolibrary.org/obo/BFO_0000050" ] @@ -42050,24 +37636,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002131", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002131", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002134", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002134", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002150", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002170", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002176", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002178", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002202", "http://purl.obolibrary.org/obo/RO_0002162" ] @@ -42104,9 +37675,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0019002", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002213", "http://purl.obolibrary.org/obo/RO_0019002" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002216", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002215", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002215", "http://purl.obolibrary.org/obo/RO_0002162" ] @@ -42155,9 +37723,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002254", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002256", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002258", "http://purl.obolibrary.org/obo/RO_0002496" ] @@ -42179,9 +37744,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004031", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/BFO_0000051" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002432", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/BFO_0000066" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002327", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002017" ] @@ -42245,15 +37807,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002339", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002339", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002177", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002371", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002371", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002387", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002407", "http://purl.obolibrary.org/obo/RO_0002629" ] @@ -42266,15 +37819,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002488", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002488", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002488", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002492", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002492", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002492", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002496", "http://purl.obolibrary.org/obo/BFO_0000050" ] @@ -42293,9 +37840,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002497", "http://purl.obolibrary.org/obo/RO_0002082" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/uberon/core#indirectly_supplies", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002569", "http://purl.obolibrary.org/obo/RO_0002178" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/uberon/core#indirectly_supplies", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002569", "http://purl.obolibrary.org/obo/uberon/core#indirectly_supplies" ] @@ -42314,12 +37858,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002630", "http://purl.obolibrary.org/obo/RO_0002630" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0003000", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0003001", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0013001", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0013001", "http://purl.obolibrary.org/obo/BFO_0000050" ] diff --git a/subsets/general_cell_types_upper_slim.obo b/subsets/general_cell_types_upper_slim.obo index bf1c7bcd8..e08277a75 100644 --- a/subsets/general_cell_types_upper_slim.obo +++ b/subsets/general_cell_types_upper_slim.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: cl/releases/2024-02-13/subsets/general_cell_types_upper_slim.owl +data-version: cl/releases/2024-04-05/subsets/general_cell_types_upper_slim.owl subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -88,7 +88,7 @@ synonymtypedef: synonym "" synonymtypedef: SYSTEMATIC "" synonymtypedef: systematic_synonym "" ontology: cl/subsets/general_cell_types_upper_slim -property_value: owl:versionInfo "2024-02-13" xsd:string +property_value: owl:versionInfo "2024-04-05" xsd:string [Term] id: BFO:0000002 @@ -159,7 +159,7 @@ is_a: UBERON:0000061 ! anatomical structure disjoint_from: GO:0031012 ! extracellular matrix disjoint_from: GO:0032991 ! protein-containing complex disjoint_from: GO:0043226 ! organelle -relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms +relationship: RO:0002160 NCBITaxon:131567 ! only in taxon cellular organisms [Term] id: CL:0000006 @@ -193,8 +193,8 @@ is_a: CL:0011115 ! precursor cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0017145 ! stem cell division relationship: capable_of GO:0017145 ! stem cell division -relationship: in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000037 @@ -244,8 +244,8 @@ relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surfac relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -relationship: develops_from CL:0000566 ! angioblastic mesenchymal cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000566 ! develops from angioblastic mesenchymal cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000039 @@ -277,11 +277,11 @@ intersection_of: has_part CL:0017503 ! basophilic cytoplasm intersection_of: has_part GO:0000791 ! euchromatin intersection_of: has_part GO:0005730 ! nucleolus intersection_of: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M -relationship: develops_from CL:0002009 ! macrophage dendritic cell progenitor relationship: has_part CL:0017503 ! basophilic cytoplasm relationship: has_part GO:0000791 ! euchromatin relationship: has_part GO:0005730 ! nucleolus relationship: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M +relationship: RO:0002202 CL:0002009 ! develops from macrophage dendritic cell progenitor [Term] id: CL:0000048 @@ -317,7 +317,7 @@ xref: BTO:0004730 is_a: CL:0002032 {is_inferred="true"} ! hematopoietic oligopotent progenitor cell disjoint_from: CL:0000051 ! common lymphoid progenitor disjoint_from: CL:0000557 ! granulocyte monocyte progenitor cell -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000051 @@ -340,7 +340,7 @@ is_a: CL:0011026 ! progenitor cell intersection_of: CL:0002032 ! hematopoietic oligopotent progenitor cell intersection_of: capable_of GO:0030098 ! lymphocyte differentiation relationship: capable_of GO:0030098 ! lymphocyte differentiation -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000052 @@ -387,8 +387,8 @@ xref: FMA:63877 xref: NCIT:C12482 xref: VHOG:0001482 is_a: CL:0002320 ! connective tissue cell -relationship: develops_from CL:0000134 ! mesenchymal stem cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000066 @@ -407,8 +407,8 @@ xref: WBbt:0003672 is_a: CL:0000000 ! cell disjoint_from: CL:0000738 ! leukocyte relationship: part_of UBERON:0000483 ! epithelium -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000075 @@ -417,7 +417,7 @@ def: "A columnar/cuboidal epithelial cell is a cell usually found in a two dimen subset: cellxgene_subset subset: human_reference_atlas is_a: CL:0000066 ! epithelial cell -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000081 @@ -454,8 +454,8 @@ intersection_of: CL:0000542 ! lymphocyte intersection_of: capable_of GO:0002456 ! T cell mediated immunity disjoint_from: CL:0000945 ! lymphocyte of B lineage relationship: capable_of GO:0002456 ! T cell mediated immunity -relationship: develops_from CL:0000827 ! pro-T cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000827 ! develops from pro-T cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000092 @@ -483,7 +483,6 @@ intersection_of: part_of UBERON:0001474 ! bone element intersection_of: RO:0002104 PR:000001954 ! has plasma membrane part tumor necrosis factor receptor superfamily member 11A intersection_of: RO:0002104 PR:000002062 ! has plasma membrane part macrophage colony-stimulating factor 1 receptor relationship: capable_of GO:0045453 ! bone resorption -relationship: develops_from CL:0000576 ! monocyte relationship: has_part PR:000001850 ! cathepsin K relationship: has_part PR:000001937 ! tartrate-resistant acid phosphatase type 5 relationship: has_part PR:000001944 ! transcription factor PU.1 @@ -491,6 +490,7 @@ relationship: has_part PR:000007597 ! protein c-Fos relationship: has_part PR:000011178 ! nuclear factor NF-kappa-B p100 subunit relationship: RO:0002104 PR:000001954 ! has plasma membrane part tumor necrosis factor receptor superfamily member 11A relationship: RO:0002104 PR:000002062 ! has plasma membrane part macrophage colony-stimulating factor 1 receptor +relationship: RO:0002202 CL:0000576 ! develops from monocyte [Term] id: CL:0000094 @@ -523,17 +523,17 @@ relationship: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon relationship: CL:4030046 PR:000001024 ! lacks_plasma_membrane_part neural cell adhesion molecule 1 relationship: CL:4030046 PR:000001084 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD8 alpha chain relationship: has_part GO:0030141 ! secretory granule -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M relationship: RO:0002104 PR:000001332 ! has plasma membrane part carcinoembryonic antigen-related cell adhesion molecule 8 relationship: RO:0002104 PR:000001969 ! has plasma membrane part urokinase plasminogen activator surface receptor +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000095 name: neuron associated cell subset: cellxgene_subset is_a: CL:0002319 ! neural cell -relationship: develops_from CL:0000133 ! neurectodermal cell +relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell [Term] id: CL:0000100 @@ -547,7 +547,7 @@ xref: FBbt:00005123 xref: FMA:83617 xref: WBbt:0005409 is_a: CL:0000527 ! efferent neuron -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000101 @@ -574,7 +574,7 @@ is_a: CL:0000518 {is_inferred="true"} ! phagocyte (sensu Vertebrata) is_a: CL:0000842 ! mononuclear cell intersection_of: CL:0000518 ! phagocyte (sensu Vertebrata) intersection_of: bearer_of PATO:0001407 ! mononucleate -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000125 @@ -637,8 +637,8 @@ xref: CALOHA:TS-0012 xref: FMA:63880 is_a: CL:0000325 ! stuff accumulating cell is_a: CL:0002320 ! connective tissue cell -relationship: develops_from CL:0000134 ! mesenchymal stem cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000145 @@ -677,11 +677,11 @@ xref: MESH:D008544 xref: VHOG:0001679 is_a: CL:0000147 ! pigment cell intersection_of: CL:0000147 ! pigment cell -intersection_of: develops_from CL:0000541 ! melanoblast intersection_of: has_part GO:0042470 ! melanosome -relationship: develops_from CL:0000541 ! melanoblast +intersection_of: RO:0002202 CL:0000541 ! develops from melanoblast relationship: has_part GO:0042470 ! melanosome -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000541 ! develops from melanoblast +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000149 @@ -723,7 +723,7 @@ synonym: "endocrinocyte" EXACT [] xref: FMA:83809 is_a: CL:0000151 ! secretory cell relationship: part_of UBERON:0000949 ! endocrine system -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000183 @@ -747,8 +747,8 @@ xref: FMA:67328 xref: WBbt:0003675 is_a: CL:0000183 ! contractile cell is_a: CL:0000393 ! electrically responsive cell -relationship: develops_from CL:0000056 ! myoblast -property_value: depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI +relationship: RO:0002202 CL:0000056 ! develops from myoblast +property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI [Term] id: CL:0000188 @@ -765,7 +765,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001134 ! skeletal muscle tissue relationship: part_of UBERON:0001134 ! skeletal muscle tissue -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000192 @@ -783,8 +783,8 @@ xref: CALOHA:TS-2159 xref: FMA:14072 is_a: CL:0008000 ! non-striated muscle cell is_a: CL:0008007 ! visceral muscle cell -relationship: develops_from CL:0000514 ! smooth muscle myoblast -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000514 ! develops from smooth muscle myoblast +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000197 @@ -811,7 +811,7 @@ is_a: CL:0000006 {is_inferred="true"} ! neuronal receptor cell intersection_of: CL:0000540 ! neuron intersection_of: capable_of GO:0050962 ! detection of light stimulus involved in sensory perception relationship: capable_of GO:0050962 ! detection of light stimulus involved in sensory perception -property_value: depiction "https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg" xsd:anyURI [Term] id: CL:0000211 @@ -918,8 +918,8 @@ intersection_of: capable_of GO:0002504 ! antigen processing and presentation of intersection_of: capable_of GO:0006909 ! phagocytosis intersection_of: capable_of GO:0031268 ! pseudopodium organization relationship: capable_of GO:0031268 ! pseudopodium organization -relationship: develops_from CL:0000576 ! monocyte -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000576 ! develops from monocyte +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000236 @@ -941,7 +941,7 @@ is_a: CL:0000945 {is_inferred="true"} ! lymphocyte of B lineage intersection_of: CL:0000945 ! lymphocyte of B lineage intersection_of: capable_of GO:0019724 ! B cell mediated immunity relationship: capable_of GO:0019724 ! B cell mediated immunity -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000255 @@ -950,8 +950,8 @@ subset: cellxgene_subset xref: MESH:D005057 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell -intersection_of: only_in_taxon NCBITaxon:2759 ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +intersection_of: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota [Term] id: CL:0000325 @@ -973,7 +973,7 @@ xref: FMA:86667 is_a: CL:0000219 ! motile cell is_a: CL:0011012 ! neural crest cell is_a: CL:0011026 ! progenitor cell -relationship: develops_from CL:0007004 ! premigratory neural crest cell +relationship: RO:0002202 CL:0007004 ! develops from premigratory neural crest cell [Term] id: CL:0000349 @@ -1013,8 +1013,8 @@ is_a: CL:0000007 ! early embryonic cell (metazoa) is_a: CL:0000255 ! eukaryotic cell is_a: CL:0010017 ! zygote intersection_of: CL:0010017 ! zygote -intersection_of: only_in_taxon NCBITaxon:33208 ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +intersection_of: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa [Term] id: CL:0000393 @@ -1065,7 +1065,7 @@ relationship: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon relationship: CL:4030046 PR:000001024 ! lacks_plasma_membrane_part neural cell adhesion molecule 1 relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-spanning 4-domains subfamily A member 1 relationship: has_part GO:0042613 ! MHC class II protein complex -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000473 @@ -1083,8 +1083,8 @@ subset: human_reference_atlas xref: BTO:0002064 xref: FMA:83624 is_a: CL:0002320 ! connective tissue cell -relationship: develops_from CL:0000134 ! mesenchymal stem cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000513 @@ -1097,8 +1097,8 @@ xref: FMA:84797 is_a: CL:0002494 ! cardiocyte is_a: CL:0010021 ! cardiac myoblast intersection_of: CL:0000056 ! myoblast -intersection_of: develops_into CL:0000746 ! cardiac muscle cell intersection_of: part_of UBERON:0001133 ! cardiac muscle tissue +intersection_of: RO:0002203 CL:0000746 ! develops into cardiac muscle cell relationship: part_of UBERON:0001133 ! cardiac muscle tissue [Term] @@ -1111,8 +1111,8 @@ synonym: "satellite cell" RELATED [] xref: FMA:84798 is_a: CL:0000056 ! myoblast intersection_of: CL:0000056 ! myoblast -intersection_of: develops_into CL:0000192 ! smooth muscle cell -relationship: develops_into CL:0000192 ! smooth muscle cell +intersection_of: RO:0002203 CL:0000192 ! develops into smooth muscle cell +relationship: RO:0002203 CL:0000192 ! develops into smooth muscle cell [Term] id: CL:0000515 @@ -1123,9 +1123,9 @@ xref: FMA:84799 is_a: CL:0000056 ! myoblast is_a: CL:0011026 ! progenitor cell intersection_of: CL:0000056 ! myoblast -intersection_of: develops_into CL:0008002 ! skeletal muscle fiber -relationship: develops_from CL:0000355 ! multi-potent skeletal muscle stem cell -relationship: develops_into CL:0008002 ! skeletal muscle fiber +intersection_of: RO:0002203 CL:0008002 ! develops into skeletal muscle fiber +relationship: RO:0002202 CL:0000355 ! develops from multi-potent skeletal muscle stem cell +relationship: RO:0002203 CL:0008002 ! develops into skeletal muscle fiber [Term] id: CL:0000518 @@ -1133,7 +1133,7 @@ name: phagocyte (sensu Vertebrata) def: "A phagocyte in vertebrates that is able to phagocytosis." [GOC:tfm] is_a: CL:0000234 ! phagocyte is_a: CL:0000255 ! eukaryotic cell -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata [Term] id: CL:0000526 @@ -1143,7 +1143,7 @@ subset: human_reference_atlas synonym: "input neuron" EXACT [] xref: FMA:87653 is_a: CL:0000540 ! neuron -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000527 @@ -1171,8 +1171,8 @@ is_a: CL:0000393 ! electrically responsive cell is_a: CL:0000404 ! electrically signaling cell is_a: CL:0002319 ! neural cell relationship: capable_of GO:0019226 ! transmission of nerve impulse -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://www.swissbiopics.org/api/image/Neuron_cells.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Neuron_cells.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000541 @@ -1183,7 +1183,7 @@ xref: BTO:0003217 xref: FMA:83377 is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0011026 ! progenitor cell -relationship: develops_from CL:0000333 ! migratory neural crest cell +relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell [Term] id: CL:0000542 @@ -1206,10 +1206,10 @@ intersection_of: has_part CL:0017500 ! neutrophillic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin disjoint_from: CL:0000766 ! myeloid leukocyte relationship: bearer_of PATO:0040072 ! high nuclear/cytoplasmic ratio -relationship: develops_from CL:0000051 ! common lymphoid progenitor relationship: has_part CL:0017500 ! neutrophillic cytoplasm relationship: has_part GO:0000792 ! heterochromatin -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000051 ! develops from common lymphoid progenitor +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000557 @@ -1245,8 +1245,8 @@ relationship: CL:4030045 PR:000007857 ! lacks_part erythroid transcription facto relationship: CL:4030045 PR:000007858 ! lacks_part endothelial transcription factor GATA-2 relationship: has_part PR:000001944 ! transcription factor PU.1 relationship: has_part PR:000005307 ! CCAAT/enhancer-binding protein alpha -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002104 PR:000001865 ! has plasma membrane part interleukin-3 receptor class 2 alpha chain +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000559 @@ -1264,10 +1264,10 @@ intersection_of: CL:0002194 ! monopoietic cell intersection_of: capable_of GO:0030224 ! monocyte differentiation intersection_of: has_part GO:0042582 ! azurophil granule intersection_of: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M -relationship: develops_from CL:0000040 ! monoblast relationship: has_part GO:0042582 ! azurophil granule -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M +relationship: RO:0002202 CL:0000040 ! develops from monoblast +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000566 @@ -1283,10 +1283,10 @@ intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: RO:0002104 PR:000001444 ! has plasma membrane part cadherin-5 intersection_of: RO:0002104 PR:000002112 ! has plasma membrane part vascular endothelial growth factor receptor 2 intersection_of: RO:0002104 PR:000016043 ! has plasma membrane part T-cell acute lymphocytic leukemia protein 1 -relationship: develops_from CL:0000134 ! mesenchymal stem cell relationship: RO:0002104 PR:000001444 ! has plasma membrane part cadherin-5 relationship: RO:0002104 PR:000002112 ! has plasma membrane part vascular endothelial growth factor receptor 2 relationship: RO:0002104 PR:000016043 ! has plasma membrane part T-cell acute lymphocytic leukemia protein 1 +relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell [Term] id: CL:0000576 @@ -1311,8 +1311,8 @@ intersection_of: capable_of GO:0043011 ! myeloid dendritic cell differentiation relationship: capable_of GO:0030225 ! macrophage differentiation relationship: capable_of GO:0030316 ! osteoclast differentiation relationship: capable_of GO:0043011 ! myeloid dendritic cell differentiation -relationship: develops_from CL:0000559 ! promonocyte -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000559 ! develops from promonocyte +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000623 @@ -1343,8 +1343,8 @@ relationship: capable_of GO:0002228 ! natural killer cell mediated immunity relationship: capable_of GO:0050776 ! regulation of immune response relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-spanning 4-domains subfamily A member 1 relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule -relationship: develops_from CL:0000825 ! pro-NK cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000825 ! develops from pro-NK cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000680 @@ -1353,9 +1353,9 @@ def: "A non-terminally differentiated cell that is capable of developing into a subset: cellxgene_subset is_a: CL:0000055 ! non-terminally differentiated cell intersection_of: CL:0011115 ! precursor cell -intersection_of: develops_into CL:0000187 ! muscle cell -relationship: develops_from CL:0000222 ! mesodermal cell -relationship: develops_into CL:0000187 ! muscle cell +intersection_of: RO:0002203 CL:0000187 ! develops into muscle cell +relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell +relationship: RO:0002203 CL:0000187 ! develops into muscle cell [Term] id: CL:0000723 @@ -1405,10 +1405,10 @@ intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0002505 ! nucleated intersection_of: capable_of GO:0001667 ! ameboidal-type cell migration relationship: capable_of GO:0001667 ! ameboidal-type cell migration -relationship: develops_from CL:0000037 ! hematopoietic stem cell -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0002405 ! immune system -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002202 CL:0000037 ! develops from hematopoietic stem cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000746 @@ -1436,9 +1436,9 @@ intersection_of: has_part GO:0030017 ! sarcomere intersection_of: part_of UBERON:0007100 ! primary circulatory organ intersection_of: participates_in GO:0060047 ! heart contraction relationship: bearer_of PATO:0002478 ! transversely striated -relationship: develops_from CL:0000513 ! cardiac muscle myoblast relationship: participates_in GO:0060047 ! heart contraction -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000513 ! develops from cardiac muscle myoblast +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000763 @@ -1450,8 +1450,8 @@ xref: CALOHA:TS-0647 xref: MESH:D022423 is_a: CL:0000988 {is_inferred="true"} ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell -intersection_of: develops_from CL:0000049 ! common myeloid progenitor -relationship: develops_from CL:0000049 ! common myeloid progenitor +intersection_of: RO:0002202 CL:0000049 ! develops from common myeloid progenitor +relationship: RO:0002202 CL:0000049 ! develops from common myeloid progenitor [Term] id: CL:0000766 @@ -1461,7 +1461,7 @@ subset: cellxgene_subset is_a: CL:0000738 {is_inferred="true"} ! leukocyte is_a: CL:0000763 ! myeloid cell intersection_of: CL:0000738 ! leukocyte -intersection_of: develops_from CL:0000049 ! common myeloid progenitor +intersection_of: RO:0002202 CL:0000049 ! develops from common myeloid progenitor [Term] id: CL:0000775 @@ -1490,9 +1490,9 @@ is_a: CL:0000094 {is_inferred="true"} ! granulocyte intersection_of: CL:0000094 ! granulocyte intersection_of: RO:0002104 PR:000001479 ! has plasma membrane part low affinity immunoglobulin gamma Fc region receptor II intersection_of: RO:0002104 PR:000001879 ! has plasma membrane part leukosialin -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002104 PR:000001479 ! has plasma membrane part low affinity immunoglobulin gamma Fc region receptor II relationship: RO:0002104 PR:000001879 ! has plasma membrane part leukosialin +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000782 @@ -1509,9 +1509,9 @@ is_a: CL:0000766 ! myeloid leukocyte is_a: CL:0000990 {is_inferred="true"} ! conventional dendritic cell intersection_of: CL:0000990 ! conventional dendritic cell intersection_of: CL:4030046 PR:000001865 ! lacks_plasma_membrane_part interleukin-3 receptor class 2 alpha chain -intersection_of: develops_from CL:0000763 ! myeloid cell +intersection_of: RO:0002202 CL:0000763 ! develops from myeloid cell relationship: CL:4030046 PR:000001865 ! lacks_plasma_membrane_part interleukin-3 receptor class 2 alpha chain -relationship: develops_from CL:0000763 ! myeloid cell +relationship: RO:0002202 CL:0000763 ! develops from myeloid cell [Term] id: CL:0000825 @@ -1534,11 +1534,11 @@ intersection_of: RO:0002104 PR:000001381 ! has plasma membrane part interleukin- intersection_of: RO:0002104 PR:000001898 ! has plasma membrane part neprilysin relationship: CL:4030046 PR:000001874 ! lacks_plasma_membrane_part KLRB1-like protein relationship: CL:4030046 PR:000002065 ! lacks_plasma_membrane_part mast/stem cell growth factor receptor -relationship: develops_from CL:0000051 ! common lymphoid progenitor relationship: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule relationship: RO:0002104 PR:000001015 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RA relationship: RO:0002104 PR:000001381 ! has plasma membrane part interleukin-2 receptor subunit beta relationship: RO:0002104 PR:000001898 ! has plasma membrane part neprilysin +relationship: RO:0002202 CL:0000051 ! develops from common lymphoid progenitor [Term] id: CL:0000826 @@ -1563,11 +1563,11 @@ intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: has_part PR:000001903 ! paired box protein PAX-5 intersection_of: has_part PR:000006611 ! DNA nucleotidylexotransferase intersection_of: participates_in GO:0033152 ! immunoglobulin V(D)J recombination -relationship: develops_from CL:0000051 ! common lymphoid progenitor relationship: has_part PR:000001903 ! paired box protein PAX-5 relationship: has_part PR:000006611 ! DNA nucleotidylexotransferase relationship: participates_in GO:0033152 ! immunoglobulin V(D)J recombination -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000051 ! develops from common lymphoid progenitor +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000827 @@ -1583,7 +1583,7 @@ is_a: CL:0000838 {is_inferred="true"} ! lymphoid lineage restricted progenitor c intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: capable_of GO:0030217 ! T cell differentiation relationship: capable_of GO:0030217 ! T cell differentiation -relationship: develops_from CL:0000051 ! common lymphoid progenitor +relationship: RO:0002202 CL:0000051 ! develops from common lymphoid progenitor [Term] id: CL:0000837 @@ -1630,9 +1630,9 @@ relationship: CL:4030046 PR:000001869 ! lacks_plasma_membrane_part interleukin-7 relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -relationship: develops_from CL:0000037 ! hematopoietic stem cell -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule +relationship: RO:0002202 CL:0000037 ! develops from hematopoietic stem cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000838 @@ -1667,7 +1667,7 @@ is_a: CL:0011026 ! progenitor cell intersection_of: CL:0002031 ! hematopoietic lineage restricted progenitor cell intersection_of: capable_of GO:0030099 ! myeloid cell differentiation relationship: capable_of GO:0030099 ! myeloid cell differentiation -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000842 @@ -1692,8 +1692,8 @@ def: "A lymphocyte of B lineage with the commitment to express an immunoglobulin comment: Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells). Lymphocytes of B cell lineage can be distinguished from those of T cell lineage by their lack of CD3e (as part of the T cell receptor complex). subset: human_reference_atlas is_a: CL:0000542 {is_inferred="true"} ! lymphocyte -relationship: develops_from CL:0000826 ! pro-B cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000826 ! develops from pro-B cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000988 @@ -1727,8 +1727,8 @@ xref: FMA:84191 is_a: CL:0000451 {is_inferred="true"} ! dendritic cell intersection_of: CL:0000451 ! dendritic cell intersection_of: RO:0015015 PR:000001013 ! has high plasma membrane amount integrin alpha-X -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0015015 PR:000001013 ! has high plasma membrane amount integrin alpha-X +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0001012 @@ -1745,9 +1745,9 @@ subset: human_reference_atlas is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001474 ! bone element -relationship: dc-contributor https://orcid.org/0000-0001-9990-8331 relationship: part_of UBERON:0001474 ! bone element -relationship: present_in_taxon NCBITaxon:9606 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2011-11-16T04:28:16Z [Term] @@ -1781,7 +1781,7 @@ relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surfac relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:27Z [Term] @@ -1801,9 +1801,9 @@ relationship: capable_of GO:0001816 ! cytokine production relationship: capable_of GO:0045087 ! innate immune response relationship: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule relationship: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon -relationship: dc-contributor https://orcid.org/0000-0001-9990-8331 -relationship: present_in_taxon NCBITaxon:9606 -property_value: dcterms-date "2017-01-30T20:20:48Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 +property_value: http://purl.org/dc/terms/date "2017-01-30T20:20:48Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0001067 @@ -1814,9 +1814,9 @@ is_a: CL:0001065 ! innate lymphoid cell intersection_of: CL:0001065 ! innate lymphoid cell intersection_of: capable_of GO:0032609 ! type II interferon production relationship: capable_of GO:0032609 ! type II interferon production -relationship: dc-contributor https://orcid.org/0000-0001-9990-8331 -relationship: present_in_taxon NCBITaxon:9606 -property_value: dcterms-date "2017-01-30T20:42:44Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9990-8331 +property_value: http://purl.org/dc/terms/date "2017-01-30T20:42:44Z" xsd:dateTime +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0002009 @@ -1832,8 +1832,8 @@ intersection_of: capable_of GO:0030224 ! monocyte differentiation intersection_of: capable_of GO:0043011 ! myeloid dendritic cell differentiation relationship: capable_of GO:0030224 ! monocyte differentiation relationship: capable_of GO:0043011 ! myeloid dendritic cell differentiation -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000557 ! granulocyte monocyte progenitor cell +relationship: RO:0002202 CL:0000557 ! develops from granulocyte monocyte progenitor cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-19T02:51:58Z [Term] @@ -1846,8 +1846,8 @@ intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001400 ! unipotent disjoint_from: CL:0002032 ! hematopoietic oligopotent progenitor cell relationship: bearer_of PATO:0001400 ! unipotent -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002032 ! hematopoietic oligopotent progenitor cell +relationship: RO:0002202 CL:0002032 ! develops from hematopoietic oligopotent progenitor cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:20Z [Term] @@ -1860,8 +1860,8 @@ is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001401 ! oligopotent relationship: bearer_of PATO:0001401 ! oligopotent -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000837 ! hematopoietic multipotent progenitor cell +relationship: RO:0002202 CL:0000837 ! develops from hematopoietic multipotent progenitor cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:27Z [Term] @@ -1871,9 +1871,9 @@ def: "An epithelial cell derived from ectoderm." [FMA:69074, GOC:tfm] xref: FMA:69074 is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell -intersection_of: develops_from CL:0000221 ! ectodermal cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000221 ! ectodermal cell +intersection_of: RO:0002202 CL:0000221 ! develops from ectodermal cell +relationship: RO:0002202 CL:0000221 ! develops from ectodermal cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T03:38:22Z [Term] @@ -1888,8 +1888,8 @@ xref: MESH:D001854 is_a: CL:0001035 {is_inferred="true"} ! bone cell intersection_of: CL:0001035 ! bone cell intersection_of: part_of UBERON:0002371 ! bone marrow -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002371 ! bone marrow +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-07-22T04:48:15Z [Term] @@ -1901,7 +1901,7 @@ is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor ce intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: capable_of GO:0030224 ! monocyte differentiation relationship: capable_of GO:0030224 ! monocyte differentiation -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-30T01:27:48Z [Term] @@ -1913,7 +1913,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0002505 ! nucleated relationship: bearer_of PATO:0002505 ! nucleated -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T03:32:33Z [Term] @@ -1926,8 +1926,8 @@ xref: FMA:70333 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001016 ! nervous system -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001016 ! nervous system +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T01:34:57Z [Term] @@ -1941,8 +1941,8 @@ xref: MESH:D003239 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0002384 ! connective tissue -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002384 ! connective tissue +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T03:01:54Z [Term] @@ -1953,7 +1953,7 @@ xref: CALOHA:TS-0263 xref: FMA:82840 xref: WBbt:0007028 is_a: CL:0000000 ! cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T03:39:21Z [Term] @@ -1970,7 +1970,7 @@ intersection_of: bearer_of PATO:0001908 ! multinucleate intersection_of: bearer_of PATO:0002478 ! transversely striated intersection_of: has_part GO:0030017 ! sarcomere relationship: bearer_of PATO:0002478 ! transversely striated -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-24T01:13:01Z [Term] @@ -1986,8 +1986,8 @@ xref: FMA:84791 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0007100 ! primary circulatory organ -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0007100 ! primary circulatory organ +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T09:37:22Z [Term] @@ -1997,7 +1997,7 @@ def: "Cell that has the potential to form a skeletal cell type (e.g. cells in pe comment: Needs logical definition. Should be capable_of skeletal system morphogenesis? or skeletal tissue development? needs to be added to GO. NOTES:a cell type of the early embryo (see also: mesenchymal cells) that will give rise to mineralized connective tissue. Scleroblasts can differentiate into osteoblasts (bone-forming cells), chondroblasts (cartilage-forming cells), odontoblasts (dentin-forming cells), ameloblasts (enamel-forming cells). The mesenchymal cells developing into osteoblasts and chondroblasts are derived from the mesoderm. Those developing into odontoblasts are neural crest cells. Those developing into ameloblasts are derived from the ectoderm. (http://www.copewithcytokines.de/cope.cgi?key=scleroblasts) synonym: "scleroblast" EXACT [GO_REF:0000034] is_a: CL:0000000 ! cell -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-15T02:51:27Z [Term] @@ -2005,9 +2005,9 @@ id: CL:0007004 name: premigratory neural crest cell def: "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells." [UBERONREF:0000002] is_a: CL:0011012 ! neural crest cell -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 -relationship: develops_from CL:0000133 ! neurectodermal cell relationship: part_of UBERON:0002342 ! neural crest +relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-27T08:27:35Z [Term] @@ -2036,7 +2036,7 @@ intersection_of: bearer_of PATO:0001908 ! multinucleate intersection_of: bearer_of PATO:0002478 ! transversely striated intersection_of: has_part GO:0030017 ! sarcomere intersection_of: part_of UBERON:0001134 ! skeletal muscle tissue -relationship: develops_from CL:0000515 ! skeletal muscle myoblast +relationship: RO:0002202 CL:0000515 ! develops from skeletal muscle myoblast [Term] id: CL:0008007 @@ -2058,7 +2058,7 @@ synonym: "mesenchyme cell" EXACT [] is_a: CL:0000219 ! motile cell relationship: capable_of GO:0016477 ! cell migration relationship: part_of UBERON:0003104 ! mesenchyme -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0009004 @@ -2077,7 +2077,7 @@ name: zygote def: "A zygote in a plant or an animal." [] xref: MESH:D015053 is_a: CL:0000000 ! cell -relationship: seeAlso https://github.com/obophenotype/cell-ontology/issues/786 +property_value: seeAlso https://github.com/obophenotype/cell-ontology/issues/786 [Term] id: CL:0010021 @@ -2085,8 +2085,8 @@ name: cardiac myoblast xref: MESH:D032386 is_a: CL:0000056 ! myoblast intersection_of: CL:0000056 ! myoblast -intersection_of: develops_into CL:0000746 ! cardiac muscle cell -relationship: develops_into CL:0000746 ! cardiac muscle cell +intersection_of: RO:0002203 CL:0000746 ! develops into cardiac muscle cell +relationship: RO:0002203 CL:0000746 ! develops into cardiac muscle cell [Term] id: CL:0011012 @@ -2103,9 +2103,9 @@ def: "A precursor cell that has a tendency to differentiate into a specific type subset: cellxgene_subset is_a: CL:0011115 ! precursor cell intersection_of: CL:0011115 ! precursor cell -intersection_of: develops_from CL:0000034 ! stem cell -relationship: dc-contributor https://orcid.org/0000-0001-5208-3432 -relationship: develops_from CL:0000034 ! stem cell +intersection_of: RO:0002202 CL:0000034 ! develops from stem cell +relationship: RO:0002202 CL:0000034 ! develops from stem cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011115 @@ -2126,7 +2126,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0070046 ! neutrophillic relationship: bearer_of PATO:0070046 ! neutrophillic -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-05-25T01:36:34Z [Term] @@ -2137,7 +2137,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0002094 ! basophilic relationship: bearer_of PATO:0002094 ! basophilic -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-22T04:24:54Z [Term] @@ -2228,7 +2228,7 @@ namespace: biological_process def: "A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities." [GOC:dph, GOC:go_curators, GOC:tb, ISBN:978-0-07-139011-8] comment: Action potentials typically propagate across excitable membranes. This class covers both action potentials that propagate and those that fail to do so. is_a: GO:0042391 ! regulation of membrane potential -relationship: never_in_taxon NCBITaxon:4895 +property_value: RO:0002161 NCBITaxon:4895 [Term] id: GO:0001667 @@ -2304,8 +2304,8 @@ def: "A multicellular organismal process by which exposure to an activating fact subset: goslim_pir is_a: GO:0009987 ! cellular process is_a: GO:0032501 ! multicellular organismal process -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24416" xsd:anyURI [Term] @@ -2419,8 +2419,8 @@ synonym: "acquired immune response" EXACT [ISBN:068340007X] synonym: "immune memory response" EXACT [GOC:add] xref: Wikipedia:Adaptive_immune_system is_a: GO:0006955 ! immune response -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0002252 @@ -2455,7 +2455,7 @@ subset: goslim_mouse subset: goslim_pir xref: Wikipedia:Immune_system is_a: GO:0008150 ! biological_process -relationship: never_in_taxon NCBITaxon:4895 +property_value: RO:0002161 NCBITaxon:4895 [Term] id: GO:0002377 @@ -2499,9 +2499,9 @@ synonym: "leukocyte immune effector process" EXACT [] is_a: GO:0002252 ! immune effector process intersection_of: GO:0002376 ! immune system process intersection_of: process_has_causal_agent CL:0000738 ! leukocyte -relationship: in_taxon NCBITaxon:7742 {all_only="true"} ! Vertebrata -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: process_has_causal_agent CL:0000738 ! leukocyte +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 {all_only="true"} ! in taxon Vertebrata [Term] id: GO:0002449 @@ -2699,8 +2699,8 @@ namespace: cellular_component def: "A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures." [GOC:dos, GOC:mah, ISBN:0721639976, PMID:19693541, PMID:21421911] xref: Wikipedia:Collagen is_a: GO:0032991 ! protein-containing complex -relationship: in_taxon NCBITaxon:33208 {all_only="true", source="PMID:12382326"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 {source="PMID:12382326"} ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 {source="PMID:12382326"} ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true", source="PMID:12382326"} ! in taxon Metazoa [Term] id: GO:0005587 @@ -2766,8 +2766,8 @@ xref: NIF_Subcellular:sao1702920020 xref: Wikipedia:Cell_nucleus is_a: GO:0043231 ! intracellular membrane-bounded organelle disjoint_from: GO:0005737 ! cytoplasm -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota [Term] id: GO:0005694 @@ -2836,7 +2836,7 @@ subset: goslim_plant xref: NIF_Subcellular:sao585356902 xref: Wikipedia:Lysosome is_a: GO:0000323 ! lytic vacuole -relationship: never_in_taxon NCBITaxon:4751 +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0005766 @@ -3051,7 +3051,7 @@ namespace: biological_process def: "A vesicle-mediated transport process that results in the engulfment of external particulate material by phagocytes and their delivery to the lysosome. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles." [ISBN:0198506732] xref: Wikipedia:Phagocytosis is_a: GO:0006897 ! endocytosis -relationship: never_in_taxon NCBITaxon:4751 +property_value: RO:0002161 NCBITaxon:4751 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24907" xsd:anyURI [Term] @@ -3465,8 +3465,8 @@ namespace: biological_process def: "The process whose specific outcome is the progression of an embryo over time, from zygote formation until the end of the embryonic life stage. The end of the embryonic life stage is organism-specific and may be somewhat arbitrary; for mammals it is usually considered to be birth, for insects the hatching of the first instar larva from the eggshell." [GOC:go_curators, GOC:isa_complete, GOC:mtg_sensu] synonym: "embryogenesis" BROAD [] is_a: GO:0009790 ! embryo development -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0009888 @@ -3479,14 +3479,14 @@ xref: Wikipedia:Histogenesis is_a: GO:0048856 ! anatomical structure development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0000479 ! tissue -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: never_in_taxon NCBITaxon:147554 -relationship: never_in_taxon NCBITaxon:33630 -relationship: never_in_taxon NCBITaxon:33682 -relationship: never_in_taxon NCBITaxon:38254 -relationship: never_in_taxon NCBITaxon:4891 -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota relationship: results_in_development_of UBERON:0000479 ! tissue +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota +property_value: RO:0002161 NCBITaxon:147554 +property_value: RO:0002161 NCBITaxon:33630 +property_value: RO:0002161 NCBITaxon:33682 +property_value: RO:0002161 NCBITaxon:38254 +property_value: RO:0002161 NCBITaxon:4891 [Term] id: GO:0009914 @@ -3697,7 +3697,7 @@ namespace: biological_process def: "The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues." [GOC:cjm, GOC:dph, GOC:ems, GOC:pf, Wikipedia:Cell_migration] xref: Wikipedia:Cell_migration is_a: GO:0048870 ! cell motility -relationship: never_in_taxon NCBITaxon:4890 +property_value: RO:0002161 NCBITaxon:4890 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24787" xsd:anyURI [Term] @@ -3871,7 +3871,7 @@ subset: goslim_drosophila subset: goslim_flybase_ribbon xref: Wikipedia:Cell_junction is_a: GO:0110165 ! cellular anatomical entity -relationship: never_in_taxon NCBITaxon:4751 +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0030097 @@ -3938,8 +3938,8 @@ def: "A small subcellular vesicle, surrounded by a membrane, that is formed from comment: Note that the term 'secretory vesicle' is sometimes used in this sense, but can also mean 'transport vesicle ; GO:0030133'. synonym: "secretory vesicle" BROAD [] is_a: GO:0099503 ! secretory vesicle -relationship: never_in_taxon NCBITaxon:4890 relationship: part_of GO:0012505 ! endomembrane system +property_value: RO:0002161 NCBITaxon:4890 [Term] id: GO:0030154 @@ -4159,10 +4159,10 @@ subset: goslim_pir synonym: "organismal physiological process" EXACT [] synonym: "single-multicellular organism process" RELATED [] is_a: GO:0008150 ! biological_process -relationship: never_in_taxon NCBITaxon:2 -relationship: never_in_taxon NCBITaxon:2157 -relationship: never_in_taxon NCBITaxon:4896 -relationship: never_in_taxon NCBITaxon:4932 +property_value: RO:0002161 NCBITaxon:2 +property_value: RO:0002161 NCBITaxon:2157 +property_value: RO:0002161 NCBITaxon:4896 +property_value: RO:0002161 NCBITaxon:4932 created_by: jl creation_date: 2012-09-19T16:07:47Z @@ -4320,7 +4320,7 @@ def: "Self-propelled movement of a cell or organism from one location to another subset: goslim_chembl subset: goslim_pir is_a: GO:0008150 ! biological_process -relationship: never_in_taxon NCBITaxon:451864 +property_value: RO:0002161 NCBITaxon:451864 [Term] id: GO:0040016 @@ -4358,11 +4358,11 @@ namespace: cellular_component def: "A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells." [GOC:jl, PMID:11584301] xref: Wikipedia:Melanosome is_a: GO:0048770 ! pigment granule -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: never_in_taxon NCBITaxon:4895 -relationship: never_in_taxon NCBITaxon:6237 {source="GOC:kmv"} -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa relationship: part_of CL:0000148 ! melanocyte +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa +property_value: RO:0002161 NCBITaxon:4895 +property_value: RO:0002161 NCBITaxon:6237 {source="GOC:kmv"} [Term] id: GO:0042582 @@ -4430,8 +4430,8 @@ name: chordate embryonic development namespace: biological_process def: "The process whose specific outcome is the progression of the embryo over time, from zygote formation through a stage including a notochord and neural tube until birth or egg hatching." [GOC:mtg_sensu] is_a: GO:0009792 ! embryo development ending in birth or egg hatching -relationship: in_taxon NCBITaxon:7711 {all_only="true"} ! Chordata -relationship: only_in_taxon NCBITaxon:7711 ! Chordata +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {all_only="true"} ! in taxon Chordata [Term] id: GO:0043011 @@ -4603,7 +4603,7 @@ synonym: "interspecies interaction" EXACT [] synonym: "interspecies interaction between organisms" EXACT [] synonym: "interspecies interaction with other organisms" EXACT [] is_a: GO:0008150 ! biological_process -relationship: never_in_taxon NCBITaxon:4895 +property_value: RO:0002161 NCBITaxon:4895 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20191" xsd:anyURI [Term] @@ -4635,8 +4635,8 @@ synonym: "synaptic junction" EXACT [] xref: NIF_Subcellular:sao914572699 xref: Wikipedia:Chemical_synapse is_a: GO:0030054 ! cell junction -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0045321 @@ -4651,8 +4651,8 @@ is_a: GO:0002376 ! immune system process intersection_of: GO:0001775 ! cell activation intersection_of: has_primary_input CL:0000738 ! leukocyte relationship: has_primary_input CL:0000738 ! leukocyte -relationship: in_taxon NCBITaxon:7742 {all_only="true"} ! Vertebrata -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 {all_only="true"} ! in taxon Vertebrata [Term] id: GO:0045453 @@ -5007,8 +5007,8 @@ is_a: GO:0003008 ! system process intersection_of: GO:0003008 ! system process intersection_of: has_participant UBERON:0001016 ! nervous system relationship: has_participant UBERON:0001016 ! nervous system -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13824" xsd:anyURI [Term] @@ -5276,8 +5276,8 @@ name: collagen-containing extracellular matrix namespace: cellular_component def: "An extracellular matrix consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that provides not only essential physical scaffolding for the cellular constituents but can also initiate crucial biochemical and biomechanical cues required for tissue morphogenesis, differentiation and homeostasis. The components are secreted by cells in the vicinity and form a sheet underlying or overlying cells such as endothelial and epithelial cells." [GOC:BHF, GOC:rph, PMID:21123617] is_a: GO:0031012 ! extracellular matrix -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa created_by: dph creation_date: 2018-04-13T12:47:21Z @@ -5632,9 +5632,9 @@ subset: goslim_synapse is_a: GO:0007267 ! cell-cell signaling intersection_of: GO:0007267 ! cell-cell signaling intersection_of: occurs_in GO:0045202 ! synapse -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa relationship: occurs_in GO:0045202 ! synapse -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0099537 @@ -5816,18 +5816,16 @@ namespace: ncbi_taxonomy xref: GC_ID:1 xref: PMID:15371245 is_a: NCBITaxon:337687 ! Muroidea -property_value: has_rank NCBITaxon:family [Term] id: NCBITaxon:10088 name: Mus namespace: ncbi_taxonomy -synonym: "mice" EXACT OMO:0003003 [] +synonym: "mice" EXACT genbank_common_name [] synonym: "mouse" EXACT OMO:0003003 [] synonym: "Mus" EXACT scientific_name [] xref: GC_ID:1 is_a: NCBITaxon:39107 ! Murinae -property_value: has_rank NCBITaxon:genus [Term] id: NCBITaxon:10090 @@ -5838,7 +5836,6 @@ synonym: "house mouse" EXACT genbank_common_name [] synonym: "mouse" EXACT OMO:0003003 [] xref: GC_ID:1 is_a: NCBITaxon:862507 ! Mus -property_value: has_rank NCBITaxon:species [Term] id: NCBITaxon:117570 @@ -5846,7 +5843,6 @@ name: Teleostomi namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:7776 ! Gnathostomata -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:117571 @@ -5856,7 +5852,6 @@ alt_id: NCBITaxon:40673 synonym: "bony vertebrates" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:117570 ! Teleostomi -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:131567 @@ -5872,7 +5867,6 @@ name: Dipnotetrapodomorpha namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:8287 ! Sarcopterygii -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:1437010 @@ -5883,7 +5877,6 @@ xref: GC_ID:1 xref: PMID:11743200 xref: PMID:11791233 is_a: NCBITaxon:9347 ! Eutheria -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:1963758 @@ -5893,7 +5886,6 @@ synonym: "mice and others" EXACT genbank_common_name [] synonym: "Sciurognathi" RELATED in_part [] xref: GC_ID:1 is_a: NCBITaxon:9989 ! Rodentia -property_value: has_rank NCBITaxon:suborder [Term] id: NCBITaxon:2759 @@ -5910,7 +5902,6 @@ xref: GC_ID:1 xref: PMID:23020233 xref: PMID:30257078 is_a: NCBITaxon:131567 ! cellular organisms -property_value: has_rank NCBITaxon:superkingdom [Term] id: NCBITaxon:314146 @@ -5922,7 +5913,6 @@ xref: PMID:12082125 xref: PMID:12878460 xref: PMID:15522813 is_a: NCBITaxon:1437010 ! Boreoeutheria -property_value: has_rank NCBITaxon:superorder [Term] id: NCBITaxon:314147 @@ -5934,7 +5924,6 @@ xref: PMID:11214319 xref: PMID:12082125 xref: PMID:15522813 is_a: NCBITaxon:314146 ! Euarchontoglires -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:32523 @@ -5943,7 +5932,6 @@ namespace: ncbi_taxonomy synonym: "tetrapods" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:1338369 ! Dipnotetrapodomorpha -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:32524 @@ -5952,7 +5940,6 @@ namespace: ncbi_taxonomy synonym: "amniotes" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:32523 ! Tetrapoda -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:32525 @@ -5961,7 +5948,6 @@ namespace: ncbi_taxonomy synonym: "Theria" EXACT scientific_name [] xref: GC_ID:1 is_a: NCBITaxon:40674 ! Mammalia -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:33154 @@ -5971,7 +5957,6 @@ synonym: "Fungi/Metazoa group" RELATED synonym [] synonym: "opisthokonts" RELATED synonym [] xref: GC_ID:1 is_a: NCBITaxon:2759 ! Eukaryota -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:33208 @@ -5983,7 +5968,6 @@ synonym: "metazoans" EXACT genbank_common_name [] synonym: "multicellular animals" EXACT OMO:0003003 [] xref: GC_ID:1 is_a: NCBITaxon:33154 ! Opisthokonta -property_value: has_rank NCBITaxon:kingdom [Term] id: NCBITaxon:33213 @@ -5991,7 +5975,6 @@ name: Bilateria namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:6072 ! Eumetazoa -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:33511 @@ -6000,7 +5983,6 @@ namespace: ncbi_taxonomy synonym: "deuterostomes" EXACT OMO:0003003 [] xref: GC_ID:1 is_a: NCBITaxon:33213 ! Bilateria -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:337687 @@ -6010,7 +5992,6 @@ xref: GC_ID:1 xref: PMID:15019624 xref: PMID:15371245 is_a: NCBITaxon:1963758 ! Myomorpha -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:39107 @@ -6019,7 +6000,6 @@ namespace: ncbi_taxonomy alt_id: NCBITaxon:109679 xref: GC_ID:1 is_a: NCBITaxon:10066 ! Muridae -property_value: has_rank NCBITaxon:subfamily [Term] id: NCBITaxon:40674 @@ -6029,7 +6009,6 @@ synonym: "mammals" EXACT genbank_common_name [] synonym: "mammals" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:32524 ! Amniota -property_value: has_rank NCBITaxon:class [Term] id: NCBITaxon:6072 @@ -6037,7 +6016,6 @@ name: Eumetazoa namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:33208 ! Metazoa -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:7711 @@ -6047,7 +6025,6 @@ synonym: "chordates" EXACT genbank_common_name [] synonym: "chordates" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:33511 ! Deuterostomia -property_value: has_rank NCBITaxon:phylum [Term] id: NCBITaxon:7742 @@ -6058,7 +6035,6 @@ synonym: "vertebrates" EXACT genbank_common_name [] synonym: "vertebrates" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:89593 ! Craniata -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:7776 @@ -6068,7 +6044,6 @@ synonym: "Gnathostomata" EXACT scientific_name [] synonym: "jawed vertebrates" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:7742 ! Vertebrata -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:8287 @@ -6076,7 +6051,6 @@ name: Sarcopterygii namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:117571 ! Euteleostomi -property_value: has_rank NCBITaxon:superclass [Term] id: NCBITaxon:862507 @@ -6085,7 +6059,6 @@ namespace: ncbi_taxonomy synonym: "Mus" EXACT scientific_name [] xref: GC_ID:1 is_a: NCBITaxon:10088 ! Mus -property_value: has_rank NCBITaxon:subgenus [Term] id: NCBITaxon:89593 @@ -6094,7 +6067,6 @@ namespace: ncbi_taxonomy synonym: "Craniata" EXACT scientific_name [] xref: GC_ID:1 is_a: NCBITaxon:7711 ! Chordata -property_value: has_rank NCBITaxon:subphylum [Term] id: NCBITaxon:9347 @@ -6107,7 +6079,6 @@ synonym: "placentals" EXACT genbank_common_name [] synonym: "placentals" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:32525 ! Theria -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:9989 @@ -6117,7 +6088,6 @@ synonym: "rodent" EXACT genbank_common_name [] synonym: "rodents" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:314147 ! Glires -property_value: has_rank NCBITaxon:order [Term] id: PATO:0000001 @@ -6309,7 +6279,6 @@ comment: This refers to the disposition of the bearer. subset: disposition_slim subset: value_slim is_a: PATO:0001579 ! contractility -property_value: RO:0002604 PATO:0001691 [Term] id: PATO:0001873 @@ -6378,7 +6347,6 @@ subset: attribute_slim xref: Image:http\://upload.wikimedia.org/wikipedia/commons/0/06/Convex_polygon_illustration1.png is_a: PATO:0002266 ! 3-D shape relationship: RO:0015011 PATO:0002006 ! has cross section 2-D shape -property_value: RO:0002604 PATO:0002008 [Term] id: PATO:0002014 @@ -6395,7 +6363,7 @@ namespace: quality def: "A quality inhering in a bearer by virtue of the bearer's having an empty space or cavity within." [url:http\://www.merriam-webster.com/dictionary/hollow] subset: value_slim is_a: PATO:0002014 ! structure, cavities -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-09-18T02:19:20Z [Term] @@ -6407,7 +6375,7 @@ subset: disposition_slim subset: mpath_slim subset: value_slim is_a: PATO:0070045 ! anatomical histological quality -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-10-05T12:05:23Z [Term] @@ -6417,7 +6385,7 @@ namespace: quality def: "A quality inhering in a bearer by virtue of its constitution." [PATOC:GVG] subset: attribute_slim is_a: PATO:0001018 ! physical quality -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-03-15T04:35:27Z [Term] @@ -6427,7 +6395,7 @@ namespace: quality def: "A cylindrical shape quality inhering in a bearer by virtue of the bearer's being imperfectly cylindrical or approximately cylindrical." [url:http\://www.thefreedictionary.com/Subcylindrical] subset: value_slim is_a: PATO:0001873 ! cylindrical -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-07-13T04:22:30Z [Term] @@ -6436,7 +6404,7 @@ name: 3-D shape namespace: quality def: "A shape that inheres in a 3 dimensional entity." [PATOC:OREGON] is_a: PATO:0000052 ! shape -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-10-05T12:31:16Z [Term] @@ -6449,7 +6417,7 @@ synonym: "tube-shaped" EXACT [] synonym: "tubulate" EXACT [] is_a: PATO:0001873 ! cylindrical is_a: PATO:0002078 ! hollow -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-06-08T06:33:50Z [Term] @@ -6460,7 +6428,7 @@ def: "A convex 3-D shape quality inhering in a bearer by virtue of the bearer's comment: Note that a fiber shaped object may take any circuitous or straight path through space (think of a length of string or rope). subset: value_slim is_a: PATO:0002226 ! subcylindrical -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-09-09T04:50:10Z [Term] @@ -6470,7 +6438,7 @@ namespace: quality def: "A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt" [wiktionary:superellipse] synonym: "Lamé curve" EXACT [] is_a: PATO:0002006 ! 2-D shape -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-10-12T12:45:16Z [Term] @@ -6482,7 +6450,7 @@ subset: cell_quality subset: mpath_slim subset: value_slim is_a: PATO:0001410 ! striated -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2013-09-15T12:29:15Z [Term] @@ -6493,7 +6461,7 @@ def: "A nucleate quality inhering in a bearer by virtue of the bearer's having o subset: mpath_slim subset: value_slim is_a: PATO:0001404 ! nucleate quality -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2013-10-21T05:44:34Z [Term] @@ -6502,7 +6470,7 @@ name: disconnected namespace: quality def: "A structural quality inhering in the bearer by virtue of the bearer consisting of multiple structures lacking any physical connection to each other." [GOC:dos] is_a: PATO:0000141 ! structure -relationship: dc-contributor https://orcid.org/0000-0002-7073-9172 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2014-12-12T08:43:17Z [Term] @@ -6621,7 +6589,6 @@ synonym: "T200" BROAD [PRO:DNx] xref: IUPHARobj:1852 xref: PIRSF:PIRSF002004 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P08575 [Term] id: PR:000001012 @@ -6640,7 +6607,6 @@ synonym: "leukocyte adhesion receptor MO1" EXACT [] synonym: "neutrophil adherence receptor" EXACT [] xref: IUPHARobj:2452 is_a: PR:000001005 ! integrin alpha with A domain -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P11215 [Term] id: PR:000001013 @@ -6657,7 +6623,6 @@ synonym: "leukocyte adhesion glycoprotein p150,95 alpha chain" EXACT [] synonym: "leukocyte adhesion receptor p150,95" EXACT [] xref: IUPHARobj:2454 is_a: PR:000001005 ! integrin alpha with A domain -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P20702 [Term] id: PR:000001015 @@ -6668,7 +6633,6 @@ comment: Category=sequence. Requested by=CL. Note: This isoform includes the reg synonym: "CD45RA" EXACT [] synonym: "PTPRC/iso:CD45RA" EXACT PRO-short-label [PRO:DNx] is_a: PR:000050216 ! receptor-type tyrosine-protein phosphatase C isoform CD45R -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P08575-8 [Term] id: PR:000001018 @@ -6724,7 +6688,6 @@ synonym: "NCAM-1" EXACT [] synonym: "NCAM1" EXACT PRO-short-label [PRO:DNx] xref: IUPHARobj:2769 is_a: PR:000001023 ! neural cell adhesion molecule NCAM -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P13591 [Term] id: PR:000001083 @@ -6761,7 +6724,6 @@ synonym: "MAL" RELATED Gene-based [] synonym: "T-cell surface glycoprotein Lyt-2" EXACT [] synonym: "T-lymphocyte differentiation antigen T8/Leu-2" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P01732 [Term] id: PR:000001289 @@ -6806,7 +6768,6 @@ synonym: "CEACAM8" EXACT PRO-short-label [PRO:DNx] synonym: "CGM6" RELATED Gene-based [] synonym: "non-specific cross-reacting antigen NCA-95" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P31997 [Term] id: PR:000001355 @@ -6834,7 +6795,6 @@ synonym: "p70-75" EXACT [] synonym: "p75" BROAD [PRO:DNx] xref: IUPHARobj:1696 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P14784 [Term] id: PR:000001444 @@ -6848,7 +6808,6 @@ synonym: "CDH5" EXACT PRO-short-label [PRO:DNx] synonym: "vascular endothelial cadherin" EXACT [] synonym: "VE-cadherin" EXACT [] is_a: PR:000001327 ! cadherin -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P33151 [Term] id: PR:000001479 @@ -6900,7 +6859,6 @@ synonym: "lymphocyte antigen 1" EXACT [] synonym: "lymphocyte antigen T1/Leu-1" EXACT [] synonym: "Lyt-1" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P06127 [Term] id: PR:000001850 @@ -6916,7 +6874,6 @@ synonym: "CTSO" RELATED Gene-based [] synonym: "CTSO2" RELATED Gene-based [] xref: IUPHARobj:2350 is_a: PR:000040662 ! cathepsin-like protease -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P43235 [Term] id: PR:000001865 @@ -6952,7 +6909,6 @@ synonym: "IL7R" EXACT PRO-short-label [PRO:DNx] xref: IUPHARobj:1698 xref: PIRSF:PIRSF001960 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P16871 [Term] id: PR:000001874 @@ -6980,7 +6936,6 @@ synonym: "sialophorin" EXACT [] synonym: "SPN" EXACT PRO-short-label [PRO:DNx] xref: PIRSF:PIRSF001994 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P16150 [Term] id: PR:000001889 @@ -7015,7 +6970,6 @@ synonym: "skin fibroblast elastase" EXACT [] xref: IUPHARobj:1611 xref: PIRSF:PIRSF501074 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P08473 [Term] id: PR:000001903 @@ -7028,7 +6982,6 @@ synonym: "BSAP" EXACT [] synonym: "Pax-5" RELATED Gene-based [] synonym: "PAX5" EXACT PRO-short-label [PRO:DNx] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q02548 [Term] id: PR:000001937 @@ -7045,7 +6998,6 @@ synonym: "TrATPase" EXACT [] synonym: "type 5 acid phosphatase" EXACT [] xref: PIRSF:PIRSF000898 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P13686 [Term] id: PR:000001944 @@ -7059,7 +7011,6 @@ synonym: "Sfpi-1" RELATED Gene-based [] synonym: "Sfpi1" RELATED Gene-based [] synonym: "SPI1" EXACT PRO-short-label [PRO:DNx] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P17947 [Term] id: PR:000001954 @@ -7076,7 +7027,6 @@ synonym: "TNFRSF11A" EXACT PRO-short-label [PRO:DNx] xref: IUPHARobj:1881 xref: PIRSF:PIRSF038806 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q9Y6Q6 [Term] id: PR:000001969 @@ -7093,7 +7043,6 @@ synonym: "UPAR" RELATED Gene-based [] synonym: "uPAR" EXACT [] xref: PIRSF:PIRSF002022 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q03405 [Term] id: PR:000001971 @@ -7122,7 +7071,6 @@ synonym: "proto-oncogene c-Fms" EXACT [] xref: IUPHARobj:1806 xref: PIRSF:PIRSF500947 is_a: PR:000001810 ! CSF-1/PDGF receptor-type tyrosine-protein kinase -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P07333 [Term] id: PR:000002065 @@ -7158,7 +7106,6 @@ synonym: "VEGFR-2" EXACT [] synonym: "VEGFR2" RELATED Gene-based [] xref: IUPHARobj:1813 is_a: PR:000001971 ! vascular endothelial growth factor receptor -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P35968 [Term] id: PR:000002976 @@ -7201,7 +7148,6 @@ synonym: "C/EBP alpha" EXACT [] synonym: "CEBP" RELATED Gene-based [] synonym: "CEBPA" EXACT PRO-short-label [PRO:DNx] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P49715 [Term] id: PR:000006611 @@ -7215,7 +7161,6 @@ synonym: "terminal addition enzyme" EXACT [] synonym: "terminal deoxynucleotidyltransferase" EXACT [] synonym: "terminal transferase" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P04053 [Term] id: PR:000007597 @@ -7230,7 +7175,6 @@ synonym: "G0S7" RELATED Gene-based [] synonym: "proto-oncogene protein c-fos" EXACT [] synonym: "transcription factor AP-1 subunit c-Fos" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P01100 [Term] id: PR:000007857 @@ -7247,7 +7191,6 @@ synonym: "GF-1" RELATED [] synonym: "GF1" RELATED Gene-based [] synonym: "NF-E1 DNA-binding protein" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P15976 [Term] id: PR:000007858 @@ -7258,7 +7201,6 @@ comment: Category=gene. Requested by=CL. synonym: "GATA-binding protein 2" EXACT [] synonym: "GATA2" EXACT PRO-short-label [PRO:DNx] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P23769 [Term] id: PR:000011178 @@ -7275,7 +7217,6 @@ synonym: "NFKB2" EXACT PRO-short-label [PRO:DNx] synonym: "nuclear factor of kappa light polypeptide gene enhancer in B-cells 2" EXACT [] synonym: "oncogene Lyt-10" EXACT [] is_a: PR:000001753 ! transcription factor NF-kappa-B subunit -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q00653 [Term] id: PR:000014841 @@ -7289,7 +7230,6 @@ synonym: "SHH" EXACT PRO-short-label [PRO:DNx] synonym: "Shh unprocessed N-terminal signaling and C-terminal autoprocessing domains" EXACT [] synonym: "ShhNC" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q15465 [Term] id: PR:000016043 @@ -7307,7 +7247,6 @@ synonym: "TAL-1" EXACT [] synonym: "TAL1" EXACT PRO-short-label [PRO:DNx] synonym: "TCL5" RELATED Gene-based [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P17542 [Term] id: PR:000025796 @@ -7325,8 +7264,8 @@ def: "A protein that is encoded in the genome of Mus musculus." [PRO:DAN] synonym: "mouse protein" EXACT PRO-short-label [PRO:DAN] is_a: PR:000036194 ! eukaryotic protein intersection_of: PR:000000001 ! protein -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus -relationship: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus +relationship: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:000036194 @@ -7336,8 +7275,8 @@ def: "A protein that is encoded in the genome of some Eukaryota." [PRO:DAN] synonym: "Eukaryota protein" EXACT [PRO:DAN] is_a: PR:000000001 ! protein intersection_of: PR:000000001 ! protein -intersection_of: only_in_taxon NCBITaxon:2759 ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +intersection_of: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota [Term] id: PR:000040662 @@ -7348,7 +7287,7 @@ comment: Category=family. synonym: "cathepsin" NARROW [PRO:DAN] synonym: "fam:CTS" EXACT PRO-short-label [PRO:DNx] is_a: PR:000036194 ! eukaryotic protein -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa [Term] id: PR:000050216 @@ -7384,9 +7323,9 @@ subset: common_anatomy subset: upper_level xref: BFO:0000003 disjoint_from: UBERON:0001062 ! anatomical entity -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000020 @@ -7411,7 +7350,6 @@ xref: CALOHA:TS-2043 xref: EHDAA2:0001824 xref: EHDAA:500 xref: EMAPA:35955 -xref: FBbt:00005155 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: GAID:63 xref: HAO:0000930 xref: MA:0000017 @@ -7426,7 +7364,7 @@ intersection_of: UBERON:0000062 ! organ intersection_of: capable_of GO:0050906 ! detection of stimulus involved in sensory perception relationship: capable_of GO:0050906 ! detection of stimulus involved in sensory perception relationship: part_of UBERON:0001032 ! sensory system -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" xsd:anyURI [Term] id: UBERON:0000025 @@ -7438,11 +7376,9 @@ synonym: "duct" NARROW [] xref: galen:Tube is_a: UBERON:0004111 ! anatomical conduit intersection_of: UBERON:0004111 ! anatomical conduit -intersection_of: has_quality PATO:0002299 ! tubular +intersection_of: RO:0000086 PATO:0002299 ! has quality tubular relationship: has_part UBERON:0013522 ! subdivision of tube -relationship: has_quality PATO:0002299 ! tubular -property_value: IAO:0000232 "not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts)" xsd:string -property_value: UBPROP:0000007 "tubular" xsd:string +relationship: RO:0000086 PATO:0002299 ! has quality tubular [Term] id: UBERON:0000043 @@ -7473,15 +7409,12 @@ xref: Wikipedia:Tendon xref: XAO:0000173 xref: ZFA:0005647 is_a: UBERON:0007846 {source="VSAO"} ! dense regular connective tissue -relationship: connects UBERON:0001474 ! bone element -relationship: connects UBERON:0001630 ! muscle organ relationship: has_part CL:0000327 {source="AEO"} ! extracellular matrix secreting cell -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0002204 {source="OG"} ! musculoskeletal system -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Dense regular connective tissue that connects muscle to bone.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000073", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000003 "Phylogenetically, tendinous tissue first appears in the invertebrate chordate Branchiostoma as myosepta. This two-dimensional array of collagen fibers is highly organized, with fibers running along two primary axes. In hagfish the first linear tendons appear and the myosepta have developed specialized regions with unidirectional fiber orientation - a linear tendon within the flat sheet of myoseptum.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001286", ontology="VHOG", source="DOI:10.1016/S1095-6433(02)00241-6 Summers AP, Koob TJ, The evolution of tendon - morphology and material properties. Comparative Biochemistry and Physiology-Part A: Molecular and Integrative Physiology (2002)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "in FMA, tendon is an organ component that with parts dense-irregular-connective-tissue of tendon and dense-irregular-connective-tissue of tendon sheath; we follow VSAO in making it a subtype of the former. In VSAO tendons connect muscle to bone; in WP the def states integument (e.g. auricular muscles) - but JB confirms this is not actually tendon but aponeurosis" xsd:string {external_ontology="FMA"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002176 UBERON:0001474 ! connects bone element +relationship: RO:0002176 UBERON:0001630 ! connects muscle organ +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg" xsd:anyURI [Term] id: UBERON:0000058 @@ -7494,7 +7427,6 @@ synonym: "ducts" RELATED OMO:0003004 [XAO:0004000] synonym: "exocrine duct" NARROW [] synonym: "exocrine gland duct" NARROW [] xref: AAO:0011123 -xref: FBbt:00100314 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:30320 xref: galen:Duct xref: NCIT:C12948 @@ -7506,11 +7438,9 @@ xref: XAO:0004000 xref: ZFA:0005171 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000063 ! organ subunit -relationship: conduit_for UBERON:0000463 ! organism substance relationship: has_part UBERON:0034969 ! epithelial layer of duct -relationship: has_quality PATO:0002299 ! tubular -property_value: UBPROP:0000001 "A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171]." xsd:string {source="ZFA:0005171"} -property_value: UBPROP:0000012 "Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here." xsd:string +relationship: RO:0000086 PATO:0002299 ! has quality tubular +relationship: RO:0002570 UBERON:0000463 ! conduit for organism substance [Term] id: UBERON:0000060 @@ -7522,13 +7452,11 @@ subset: upper_level synonym: "organ wall" RELATED [FMA:82482] synonym: "wall" BROAD [] synonym: "wall of organ" EXACT [FMA:82482] -xref: EMAPA:25036 xref: FMA:82482 xref: galen:Wall is_a: UBERON:0000064 ! organ part relationship: adjacent_to UBERON:0002553 ! anatomical cavity relationship: has_part UBERON:0004923 ! organ component layer -property_value: UBPROP:0000012 "in FMA, serosa is a wall" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0000061 @@ -7545,7 +7473,6 @@ xref: BILA:0000003 xref: CARO:0000003 xref: EHDAA2:0003003 xref: EMAPA:0 -xref: FBbt:00007001 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:305751 xref: FMA:67135 xref: GAID:781 @@ -7560,10 +7487,10 @@ xref: VHOG:0001759 xref: XAO:0003000 xref: ZFA:0000037 is_a: UBERON:0000465 ! material anatomical entity -relationship: existence_ends_during_or_before UBERON:0000071 ! death stage -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0002497 UBERON:0000071 ! existence ends during or before death stage +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000062 @@ -7590,14 +7517,12 @@ xref: Wikipedia:Organ_(anatomy) is_a: UBERON:0010000 ! multicellular anatomical structure disjoint_from: UBERON:0034921 ! multi organ part structure relationship: capable_of GO:0008150 ! biological_process -relationship: has_boundary UBERON:0006984 ! anatomical surface -relationship: never_in_taxon NCBITaxon:110815 {source="Wikipedia"} relationship: part_of UBERON:0000467 ! anatomical system -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: UBPROP:0000001 "Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." xsd:string {source="GO:0048513"} -property_value: UBPROP:0000012 "CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4" xsd:string +relationship: RO:0002002 UBERON:0006984 ! has 2D boundary anatomical surface +property_value: RO:0002161 NCBITaxon:110815 {source="Wikipedia"} +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000063 @@ -7610,9 +7535,7 @@ synonym: "organ segment" RELATED [FMA:86140] synonym: "segment of organ" RELATED [FMA:86140] xref: FMA:86140 is_a: UBERON:0000064 ! organ part -property_value: editor_note "FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction" xsd:string -property_value: UBPROP:0000001 "Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball." xsd:string {source="FMA:86140", version="3"} -property_value: UBPROP:0000001 "Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal." xsd:string {source="FMA:86140", version="1"} +property_value: IAO:0000116 "FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction" xsd:string [Term] id: UBERON:0000064 @@ -7633,10 +7556,9 @@ xref: SCTID:113343008 xref: SCTID:91717005 is_a: UBERON:0010000 ! multicellular anatomical structure relationship: part_of UBERON:0000062 ! organ -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: IAO:0000232 "currently defined in a very broad sense, may be replaced by more specific classes in the future" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000066 @@ -7685,7 +7607,7 @@ is_a: UBERON:0000105 ! life cycle stage disjoint_from: UBERON:0000092 ! post-embryonic stage relationship: precedes UBERON:0000066 ! fully formed stage relationship: precedes UBERON:0000092 ! post-embryonic stage -relationship: simultaneous_with GO:0009790 ! embryo development +relationship: RO:0002082 GO:0009790 ! simultaneous with embryo development [Term] id: UBERON:0000071 @@ -7698,11 +7620,10 @@ xref: XAO:0000437 xref: XtroDO:0000085 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage -relationship: ends UBERON:0000104 ! life cycle -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: UBPROP:0000012 "ncit:Death is an outcome" xsd:string {external_ontology="ncit"} +relationship: RO:0002229 UBERON:0000104 ! ends life cycle +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000075 @@ -7719,9 +7640,9 @@ xref: NCIT:C34076 xref: SCTID:118966000 xref: UMLS:C1519343 {source="ncithesaurus:Skeletal_System_Part"} is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision -relationship: composed_primarily_of UBERON:0004765 ! skeletal element -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0001434 ! skeletal system +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002473 UBERON:0004765 ! composed primarily of skeletal element [Term] id: UBERON:0000092 @@ -7741,9 +7662,8 @@ xref: WBls:0000103 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage relationship: preceded_by UBERON:0000068 ! embryo stage -relationship: simultaneous_with GO:0009791 ! post-embryonic development +relationship: RO:0002082 GO:0009791 ! simultaneous with post-embryonic development property_value: seeAlso "https://github.com/obophenotype/uberon/issues/344" xsd:anyURI -property_value: UBPROP:0000008 "In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)" xsd:string [Term] id: UBERON:0000104 @@ -7765,9 +7685,9 @@ is_a: BFO:0000003 ! occurrent is_a: UBERON:0000000 ! processual entity relationship: ends_with UBERON:0000071 ! death stage relationship: has_part UBERON:0000105 ! life cycle stage -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 property_value: seeAlso "https://github.com/obophenotype/uberon/issues/532" xsd:anyURI [Term] @@ -7796,12 +7716,10 @@ xref: ZFS:0000000 xref: ZFS:0100000 is_a: UBERON:0000000 ! processual entity relationship: part_of UBERON:0000104 ! life cycle -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: editor_note "this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here" xsd:string -property_value: UBPROP:0000012 "the WBls class 'all stages' belongs here as it is the superclass of other WBls stages" xsd:string -property_value: UBPROP:0000012 "we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage" xsd:string +property_value: IAO:0000116 "this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000106 @@ -7821,7 +7739,6 @@ xref: BILS:0000106 xref: EFO:0001322 xref: EHDAA:27 xref: FBdv:00005288 -xref: IDOMAL:0000302 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C12601 xref: PdumDv:0000100 xref: VHOG:0000745 @@ -7831,9 +7748,8 @@ xref: ZFS:0000001 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage -relationship: seeAlso EMAPA:16033 -relationship: starts UBERON:0000104 ! life cycle -property_value: UBPROP:0000003 "As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000745", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107", source="http://bgee.unil.ch/"} +relationship: RO:0002223 UBERON:0000104 ! starts life cycle +property_value: seeAlso EMAPA:16033 [Term] id: UBERON:0000107 @@ -7856,10 +7772,10 @@ xref: ZFS:0000046 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage intersection_of: UBERON:0000105 ! life cycle stage -intersection_of: simultaneous_with GO:0040016 ! embryonic cleavage +intersection_of: RO:0002082 GO:0040016 ! simultaneous with embryonic cleavage relationship: immediately_preceded_by UBERON:0000106 ! zygote stage relationship: part_of UBERON:0000068 ! embryo stage -relationship: simultaneous_with GO:0040016 ! embryonic cleavage +relationship: RO:0002082 GO:0040016 ! simultaneous with embryonic cleavage [Term] id: UBERON:0000108 @@ -7883,8 +7799,8 @@ is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000107 ! cleavage stage -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI -property_value: editor_note "consider adding a preceding stage 'morula stage' as part of cleavage" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI +property_value: IAO:0000116 "consider adding a preceding stage 'morula stage' as part of cleavage" xsd:string [Term] id: UBERON:0000109 @@ -7911,10 +7827,10 @@ xref: XAO:1000005 xref: ZFS:0000047 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000108 {source="BILS"} ! blastula stage -relationship: simultaneous_with GO:0007369 ! gastrulation +relationship: RO:0002082 GO:0007369 ! simultaneous with gastrulation +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0000110 @@ -7928,14 +7844,12 @@ xref: MmusDv:0000017 xref: XAO:1000006 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000109 ! gastrula stage -relationship: simultaneous_with GO:0001841 ! neural tube formation -property_value: RO:0002174 NCBITaxon:7955 +relationship: RO:0002082 GO:0001841 ! simultaneous with neural tube formation +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa property_value: seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/343" xsd:anyURI -property_value: UBPROP:0000008 "In zebrafish, the times of neurulation and segmentation overlap so extensively there is no distinct neurula period of development, such as occurs largely before segmentation in amphibian embryos." xsd:string [Term] id: UBERON:0000111 @@ -7952,9 +7866,9 @@ xref: OGES:000032 xref: Wikipedia:Organogenesis is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000068 ! embryo stage -relationship: simultaneous_with GO:0048513 ! animal organ development +relationship: RO:0002082 GO:0048513 ! simultaneous with animal organ development +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa property_value: seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/533" xsd:anyURI @@ -7990,7 +7904,6 @@ xref: EFO:0000825 xref: EHDAA2:0001326 xref: EHDAA:542 xref: EMAPA:16262 -xref: FBbt:00003126 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:49184 xref: GAID:75 xref: galen:Mouth @@ -8011,19 +7924,11 @@ xref: Wikipedia:Mouth xref: XAO:0003029 xref: ZFA:0000547 xref: ZFA:0000590 -is_a: UBERON:0004921 {notes="the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts"} ! subdivision of digestive tract -intersection_of: UBERON:0004921 ! subdivision of digestive tract -intersection_of: proximalmost_part_of UBERON:0001555 ! digestive tract -relationship: develops_from UBERON:0035804 ! future mouth -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: proximalmost_part_of UBERON:0001555 ! digestive tract -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI +is_a: UBERON:0004921 ! subdivision of digestive tract +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002202 UBERON:0035804 ! develops from future mouth +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/661" xsd:anyURI -property_value: UBPROP:0000001 "Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010355", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000812", ontology="VHOG", source="DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "oral" xsd:string -property_value: UBPROP:0000011 "some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives" xsd:string -property_value: UBPROP:0000012 "in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0000307 @@ -8042,11 +7947,11 @@ xref: OGEM:000006 xref: Wikipedia:Blastula is_a: UBERON:0000922 ! embryo intersection_of: UBERON:0000468 ! multicellular organism -intersection_of: existence_starts_and_ends_during UBERON:0000108 ! blastula stage -relationship: develops_from UBERON:0007010 ! cleaving embryo -relationship: existence_starts_and_ends_during UBERON:0000108 ! blastula stage -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI -property_value: editor_note "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" xsd:string +intersection_of: RO:0002491 UBERON:0000108 ! existence starts and ends during blastula stage +relationship: RO:0002202 UBERON:0007010 ! develops from cleaving embryo +relationship: RO:0002491 UBERON:0000108 ! existence starts and ends during blastula stage +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI +property_value: IAO:0000116 "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" xsd:string [Term] id: UBERON:0000383 @@ -8069,7 +7974,6 @@ xref: BILA:0000088 xref: BTO:0001369 xref: BTO:0001485 xref: EFO:0000801 -xref: EMAPA:35578 xref: FMA:72954 xref: MA:0002888 xref: MAT:0000025 @@ -8078,15 +7982,13 @@ xref: VSAO:0000033 xref: XAO:0004042 is_a: UBERON:0011216 ! organ system subdivision intersection_of: UBERON:0011216 ! organ system subdivision -intersection_of: composed_primarily_of UBERON:0001015 ! musculature +intersection_of: RO:0002473 UBERON:0001015 ! composed primarily of musculature relationship: capable_of GO:0003012 ! muscle system process -relationship: composed_primarily_of UBERON:0001015 ! musculature -relationship: never_in_taxon NCBITaxon:6040 -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: present_in_taxon NCBITaxon:9606 -property_value: editor_note "consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77" xsd:string -property_value: UBPROP:0000001 "Anatomical system that consists of the muscles of the body.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000033", ontology="VSAO", source="VSAO:curator"} -property_value: UBPROP:0000012 "we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA" xsd:string {external_ontology="MA"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002473 UBERON:0001015 ! composed primarily of musculature +property_value: IAO:0000116 "consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77" xsd:string +property_value: RO:0002161 NCBITaxon:6040 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000463 @@ -8108,7 +8010,6 @@ xref: CALOHA:TS-2101 xref: CARO:0000004 xref: EHDAA2:0003004 xref: EMAPA:35178 -xref: FBbt:00007019 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9669 xref: galen:BodySubstance xref: HAO:0000004 @@ -8121,11 +8022,11 @@ xref: VHOG:0001726 xref: XAO:0004001 xref: ZFA:0001487 is_a: UBERON:0000465 ! material anatomical entity -relationship: has_quality PATO:0002198 ! quality of a substance -relationship: part_of UBERON:0000468 {notes="this relationship may be too strong and may be weakened in future"} ! multicellular organism -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: part_of UBERON:0000468 ! multicellular organism +relationship: RO:0000086 PATO:0002198 ! has quality quality of a substance +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000464 @@ -8143,7 +8044,6 @@ xref: AEO:0000005 xref: BILA:0000005 xref: CARO:0000005 xref: EHDAA2:0003005 -xref: FBbt:00007017 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:5897 xref: HAO:0000005 xref: NCIT:C94478 @@ -8154,10 +8054,10 @@ xref: VHOG:0001728 xref: XAO:0003190 xref: ZFA:0001643 is_a: UBERON:0000466 ! immaterial anatomical entity -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -relationship: surrounded_by UBERON:0000061 ! anatomical structure +relationship: RO:0002219 UBERON:0000061 ! surrounded by anatomical structure +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000465 @@ -8171,7 +8071,6 @@ xref: AEO:0000006 xref: BILA:0000006 xref: CARO:0000006 xref: EHDAA2:0003006 -xref: FBbt:00007016 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67165 xref: HAO:0000006 xref: TAO:0001836 @@ -8180,9 +8079,9 @@ xref: VHOG:0001721 is_a: BFO:0000040 ! material entity is_a: UBERON:0001062 ! anatomical entity disjoint_from: UBERON:0000466 ! immaterial anatomical entity -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000466 @@ -8197,7 +8096,6 @@ xref: AEO:0000007 xref: BILA:0000007 xref: CARO:0000007 xref: EHDAA2:0003007 -xref: FBbt:00007015 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67112 xref: HAO:0000007 xref: TAO:0001835 @@ -8205,9 +8103,9 @@ xref: TGMA:0001827 xref: VHOG:0001727 is_a: BFO:0000141 ! immaterial entity is_a: UBERON:0001062 ! anatomical entity -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000467 @@ -8235,11 +8133,9 @@ xref: EHDAA2:0003011 xref: EHDAA:392 xref: EMAPA:16103 xref: EV:0100000 -xref: FBbt:00004856 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7149 xref: galen:AnatomicalSystem xref: HAO:0000011 -xref: IDOMAL:0002460 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: MA:0000003 xref: NCIT:C12919 xref: SCTID:278195005 @@ -8255,11 +8151,11 @@ xref: ZFA:0001439 is_a: UBERON:0000061 ! anatomical structure relationship: has_part UBERON:0000062 ! organ relationship: part_of UBERON:0000468 ! multicellular organism -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -relationship: present_in_taxon NCBITaxon:9606 -relationship: seeAlso EHDAA2:0001330 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:9606 +property_value: seeAlso EHDAA2:0001330 [Term] id: UBERON:0000468 @@ -8290,7 +8186,6 @@ xref: EHDAA2:0003191 xref: EHDAA:1 xref: EMAPA:25765 xref: EV:0100016 -xref: FBbt:00000001 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:256135 xref: galen:Organism xref: HAO:0000012 @@ -8306,11 +8201,10 @@ xref: Wikipedia:Multi-cellular_organism xref: XAO:0003004 xref: ZFA:0001094 is_a: UBERON:0010000 ! multicellular anatomical structure -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: editor_note "TODO - split body and mc organism? body continues after death stage" xsd:string -property_value: UBPROP:0000007 "organismal" xsd:string +property_value: IAO:0000116 "TODO - split body and mc organism? body continues after death stage" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000475 @@ -8335,7 +8229,6 @@ xref: CARO:0000032 xref: EFO:0000808 xref: EHDAA2:0003032 xref: EMAPA:36031 -xref: FBbt:00007009 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7153 xref: galen:BodyPart xref: HAO:0000032 @@ -8353,10 +8246,10 @@ xref: XAO:0003013 xref: ZFA:0001308 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure relationship: part_of UBERON:0000468 ! multicellular organism -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: editor_note "Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency" xsd:string +property_value: IAO:0000116 "Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000476 @@ -8371,7 +8264,6 @@ xref: AEO:0000040 xref: BILA:0000040 xref: CARO:0000040 xref: EHDAA2:0003040 -xref: FBbt:00007013 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:63863 xref: HAO:0000040 xref: TAO:0000382 @@ -8380,9 +8272,9 @@ xref: XAO:0003162 xref: ZFA:0000382 is_a: UBERON:0000061 ! anatomical structure disjoint_from: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000477 @@ -8391,12 +8283,11 @@ namespace: uberon def: "Anatomical group whose component anatomical structures lie in close proximity to each other." [FBbt:00007277] subset: common_anatomy subset: upper_level -xref: FBbt:00007277 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: VHOG:0001737 is_a: UBERON:0034923 ! disconnected anatomical group -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000478 @@ -8417,7 +8308,6 @@ xref: CALOHA:TS-2119 xref: CARO:0000042 xref: EHDAA2:0003042 xref: EHDAA:46 -xref: FBbt:00005835 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:85537 xref: HAO:0000042 xref: NCIT:C34055 @@ -8453,7 +8343,6 @@ xref: CALOHA:TS-2090 xref: CARO:0000043 xref: EHDAA2:0003043 xref: EMAPA:35868 -xref: FBbt:00007003 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9637 xref: galen:Tissue xref: HAO:0000043 @@ -8470,10 +8359,10 @@ xref: ZFA:0001477 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure relationship: has_part GO:0031012 ! extracellular matrix relationship: part_of UBERON:0000468 ! multicellular organism -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: editor_note "changed label and definition to reflect CARO2" xsd:string +property_value: IAO:0000116 "changed label and definition to reflect CARO2" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000481 @@ -8488,7 +8377,6 @@ xref: AEO:0000055 xref: BILA:0000055 xref: CARO:0000055 xref: EHDAA2:0003055 -xref: FBbt:00007010 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: HAO:0000055 xref: TAO:0001488 xref: TGMA:0001847 @@ -8497,9 +8385,9 @@ xref: XAO:0003037 xref: ZFA:0001488 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure relationship: has_part UBERON:0000479 ! tissue -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000483 @@ -8521,7 +8409,6 @@ xref: CALOHA:TS-0288 xref: CARO:0000066 xref: EHDAA2:0003066 xref: EMAPA:32738 -xref: FBbt:00007005 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9639 xref: GAID:402 xref: HAO:0000066 @@ -8538,16 +8425,14 @@ xref: ZFA:0001486 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue -intersection_of: composed_primarily_of CL:0000066 ! epithelial cell +intersection_of: RO:0002473 CL:0000066 ! composed primarily of epithelial cell union_of: UBERON:0000486 ! multilaminar epithelium union_of: UBERON:0000490 ! unilaminar epithelium -relationship: composed_primarily_of CL:0000066 ! epithelial cell relationship: has_part GO:0005911 ! cell-cell junction relationship: has_part UBERON:0005769 ! basement membrane of epithelium -relationship: only_in_taxon NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! Metazoa -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI -property_value: UBPROP:0000003 "The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000387", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.59", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "epithelial" xsd:string +relationship: RO:0002160 NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! only in taxon Metazoa +relationship: RO:0002473 CL:0000066 ! composed primarily of epithelial cell +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI [Term] id: UBERON:0000486 @@ -8574,7 +8459,6 @@ xref: Wikipedia:Stratified_epithelium xref: XAO:0004006 xref: ZFA:0001494 is_a: UBERON:0000483 ! epithelium -property_value: UBPROP:0000001 "Epithelium that consists of more than one layer of epithelial cells.[CARO]" xsd:string {date_retrieved="2012-06-20", external_class="CARO:0000069", ontology="CARO", source="FMA:45562", source="http://orcid.org/0000-0001-9114-8737"} [Term] id: UBERON:0000490 @@ -8599,8 +8483,7 @@ xref: UMLS:C0682574 {source="ncithesaurus:Simple_Epithelium"} xref: XAO:0004007 xref: ZFA:0001495 is_a: UBERON:0000483 ! epithelium -property_value: editor_note "consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable" xsd:string -property_value: UBPROP:0000001 "Epithelium that consists of a single layer of epithelial cells.[CARO]" xsd:string {date_retrieved="2012-06-20", external_class="CARO:0000073", ontology="CARO", source="FMA:45561", source="http://orcid.org/0000-0001-9114-8737"} +property_value: IAO:0000116 "consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable" xsd:string [Term] id: UBERON:0000922 @@ -8625,11 +8508,9 @@ xref: EHDAA2:0000002 xref: EHDAA2_RETIRED:0003236 xref: EHDAA:38 xref: EMAPA:16039 -xref: FBbt:00000052 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69068 xref: GAID:963 xref: http://neurolex.org/wiki/Category\:Embryonic_organism -xref: IDOMAL:0000646 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: MAT:0000226 xref: MESH:D004622 xref: MIAA:0000019 @@ -8643,14 +8524,12 @@ xref: XAO:0000113 xref: ZFA:0000103 is_a: UBERON:0000468 ! multicellular organism intersection_of: UBERON:0000468 ! multicellular organism -intersection_of: existence_ends_with UBERON:0000068 ! embryo stage -intersection_of: existence_starts_with UBERON:0000068 ! embryo stage -relationship: existence_ends_with UBERON:0000068 ! embryo stage -relationship: existence_starts_with UBERON:0000068 ! embryo stage -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" xsd:anyURI +intersection_of: RO:0002489 UBERON:0000068 ! existence starts with embryo stage +intersection_of: RO:0002493 UBERON:0000068 ! existence ends with embryo stage +relationship: RO:0002489 UBERON:0000068 ! existence starts with embryo stage +relationship: RO:0002493 UBERON:0000068 ! existence ends with embryo stage +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/503" xsd:anyURI -property_value: UBPROP:0000007 "embryonic" xsd:string -property_value: UBPROP:0000012 "Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo" xsd:string {external_ontology="ZFA"} [Term] id: UBERON:0000923 @@ -8669,7 +8548,6 @@ xref: AAO:0000480 xref: BILA:0000035 xref: BTO:0000556 xref: EMAPA:36033 -xref: FBbt:00000110 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69069 xref: GAID:1303 xref: MESH:D005855 @@ -8683,8 +8561,7 @@ xref: Wikipedia:Germ_layer xref: XAO:0003011 xref: ZFA:0001122 is_a: UBERON:0010316 ! germ layer / neural crest -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001223", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0000924 @@ -8704,7 +8581,6 @@ xref: EFO:0000414 xref: EHDAA2:0000428 xref: EMAPA:16069 xref: EV:0100003 -xref: FBbt:00000111 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69070 xref: GAID:1304 xref: MAT:0000155 @@ -8721,11 +8597,8 @@ xref: XAO:0000001 xref: ZFA:0000016 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000221 ! ectodermal cell -relationship: immediate_transformation_of UBERON:0006601 {source="Bgee:AN"} ! presumptive ectoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png" xsd:anyURI -property_value: UBPROP:0000001 "Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000137", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000153", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "ectodermal" xsd:string +relationship: RO:0002495 UBERON:0006601 {source="Bgee:AN"} ! immediate transformation of presumptive ectoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png" xsd:anyURI [Term] id: UBERON:0000925 @@ -8745,7 +8618,6 @@ xref: EFO:0002545 xref: EHDAA2:0000436 xref: EMAPA:16062 xref: EV:0100005 -xref: FBbt:00000125 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69071 xref: GAID:1305 xref: MAT:0000175 @@ -8761,11 +8633,9 @@ xref: XAO:0000090 xref: ZFA:0000017 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000223 ! endodermal cell -relationship: immediate_transformation_of UBERON:0006595 {source="Bgee:AN"} ! presumptive endoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png" xsd:anyURI -property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000154", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "endodermal" xsd:string +relationship: RO:0002495 UBERON:0006595 {source="Bgee:AN"} ! immediate transformation of presumptive endoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png" xsd:anyURI [Term] id: UBERON:0000926 @@ -8791,7 +8661,6 @@ xref: EHDAA:160 xref: EHDAA:183 xref: EMAPA:16083 xref: EV:0100006 -xref: FBbt:00000126 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69072 xref: GAID:522 xref: MAT:0000174 @@ -8805,15 +8674,11 @@ xref: VHOG:0000152 xref: Wikipedia:Mesoderm xref: XAO:0000050 xref: ZFA:0000041 -is_a: UBERON:0000923 {notes="sometimes not considered primary"} ! germ layer +is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000222 ! mesodermal cell -relationship: immediate_transformation_of UBERON:0006603 {source="Bgee:AN"} ! presumptive mesoderm -relationship: never_in_taxon NCBITaxon:6040 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" xsd:anyURI -property_value: UBPROP:0000001 "Primary germ layer that is the middle of the embryonic germ layers.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000304", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000152", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "mesodermal" xsd:string -property_value: UBPROP:0000008 "sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates" xsd:string {source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} +relationship: RO:0002495 UBERON:0006603 {source="Bgee:AN"} ! immediate transformation of presumptive mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" xsd:anyURI +property_value: RO:0002161 NCBITaxon:6040 [Term] id: UBERON:0000930 @@ -8835,7 +8700,6 @@ synonym: "stomodeal-hypophyseal primordium" BROAD [XAO:0000269] xref: BTO:0004224 xref: EHDAA2:0001929 xref: EMAPA:16263 -xref: FBbt:00000439 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:295846 xref: NCIT:C34306 xref: TAO:0001290 @@ -8845,15 +8709,11 @@ xref: Wikipedia:Stomodeum xref: XAO:0000269 xref: ZFA:0001290 is_a: UBERON:0013522 ! subdivision of tube -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000924 ! ectoderm relationship: part_of UBERON:0035804 ! future mouth -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI -property_value: editor_note "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" xsd:string -property_value: UBPROP:0000001 "Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001290", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx" xsd:string {source="MP:0012522", taxon="NCBITaxon:40674"} -property_value: UBPROP:0000007 "stomodeal" xsd:string -property_value: UBPROP:0000008 "This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity." xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI +property_value: IAO:0000116 "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" xsd:string [Term] id: UBERON:0000949 @@ -8873,7 +8733,6 @@ xref: EFO:0002969 xref: EHDAA2:0002224 xref: EMAPA:35306 xref: EV:0100128 -xref: FBbt:00005068 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9668 xref: GAID:439 xref: MA:0000012 @@ -8896,12 +8755,9 @@ disjoint_from: UBERON:0002330 ! exocrine system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0004456 ! entire sense organ system -relationship: composed_primarily_of UBERON:0002368 ! endocrine gland -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: UBPROP:0000001 "Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010279", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000098", ontology="VHOG", source="DOI:10.1073/pnas.0812138106 Markov GV, Tavares R, Dauphin-Villemant C, Demeneix BA, Baker ME, Laudet V, Independent elaboration of steroid hormone signaling pathways in metazoans. PNAS (2009)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "endocrine" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002473 UBERON:0002368 ! composed primarily of endocrine gland +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage [Term] id: UBERON:0000970 @@ -8921,7 +8777,6 @@ xref: BTO:0000439 xref: CALOHA:TS-0309 xref: EFO:0000827 xref: EV:0100336 -xref: FBbt:00005162 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: GAID:69 xref: MAT:0000140 xref: MESH:D005123 @@ -8932,11 +8787,7 @@ relationship: capable_of GO:0009584 ! detection of visible light relationship: has_part CL:0000149 {source="PMID:21062451"} ! visual pigment cell relationship: has_part CL:0000210 {source="PMID:21062451"} ! photoreceptor cell relationship: part_of UBERON:0002104 ! visual system -relationship: present_in_taxon NCBITaxon:9606 -property_value: IAO:0000232 "This class encompasses a variety of light-detecting structures from different phyla with no implication of homology, from the compound insect eye to the vertebrate camera-type eye (distinct classes are provided for each)" xsd:string -property_value: UBPROP:0000007 "ocular" xsd:string -property_value: UBPROP:0000007 "optic" xsd:string -property_value: UBPROP:0000010 "Note that whilst this is classified as an organ, it is in fact more of a unit composed of different structures: in Drosophila, it includes the interommatidial bristle as a part; we consider here the vertebrate eye to include the eyeball/eye proper as a part, with the eye having as parts (when present): eyelids, conjuctiva," xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000982 @@ -8976,10 +8827,8 @@ xref: XAO:0000171 xref: ZFA:0001596 is_a: UBERON:0004905 ! articulation disjoint_from: UBERON:0001474 ! bone element -relationship: connects UBERON:0004765 ! skeletal element -relationship: contributes_to_morphology_of UBERON:0001434 ! skeletal system -property_value: UBPROP:0000001 "Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000101", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000367", ontology="TAO", source="TAO:pem"} +relationship: RO:0002176 UBERON:0004765 ! connects skeletal element +relationship: RO:0002433 UBERON:0001434 ! contributes to morphology of skeletal system [Term] id: UBERON:0001007 @@ -9000,8 +8849,6 @@ xref: BILA:0000082 xref: BTO:0000058 xref: CALOHA:TS-1293 xref: EFO:0000793 -xref: EV:0100056 -xref: FBbt:00005055 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7152 xref: GAID:278 xref: galen:DigestiveSystem @@ -9029,11 +8876,8 @@ disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0022600 ! digestive system process -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000129", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000007 "digestive" xsd:string -property_value: UBPROP:0000012 "many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class" xsd:string {external_ontology="MA"} +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001009 @@ -9045,7 +8889,6 @@ subset: uberon_slim synonym: "systema cardiovasculare" RELATED OMO:0003011 [Wikipedia:Circulatory_system] xref: AAO:0000959 xref: CALOHA:TS-2103 -xref: MESH:D002319 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: VHOG:0001248 xref: Wikipedia:Circulatory_system is_a: UBERON:0000467 ! anatomical system @@ -9057,17 +8900,13 @@ disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0003013 ! circulatory system process -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} -relationship: never_in_taxon NCBITaxon:6073 -relationship: never_in_taxon NCBITaxon:6157 -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI -property_value: IAO:0000232 "the cardiovascular system and the lymphatic system are parts of the circulatory system" xsd:string -property_value: RO:0002174 NCBITaxon:6231 {notes="WBbt coelomocyte currently classified as circulating cell"} -property_value: UBPROP:0000001 "Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000959", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001248", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.493", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} +property_value: RO:0002161 NCBITaxon:6073 +property_value: RO:0002161 NCBITaxon:6157 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001015 @@ -9087,10 +8926,8 @@ synonym: "musculature system" RELATED [] synonym: "musculi" EXACT OMO:0003011 [FMA:32558, FMA:TA] synonym: "set of muscles" EXACT [FMA:32558] synonym: "set of skeletal muscles" EXACT [MA:0000165] -xref: AAO:0011066 xref: BTO:0000887 xref: EFO:0001949 -xref: EMAPA:32715 xref: EMAPA:35577 xref: FMA:32558 xref: MA:0000165 @@ -9102,11 +8939,9 @@ xref: WBbt:0005737 xref: Wikipedia:Muscular_system xref: ZFA:0000548 is_a: UBERON:0011216 ! organ system subdivision -relationship: composed_primarily_of UBERON:0001630 ! muscle organ relationship: part_of UBERON:0000383 ! musculature of body -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png" xsd:anyURI -property_value: RO:0002171 UBERON:0001474 -property_value: UBPROP:0000012 "In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here." xsd:string {external_ontology="FMA"} +relationship: RO:0002473 UBERON:0001630 ! composed primarily of muscle organ +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png" xsd:anyURI [Term] id: UBERON:0001016 @@ -9132,7 +8967,6 @@ xref: EHDAA2:0001246 xref: EHDAA:826 xref: EMAPA:16469 xref: EV:0100162 -xref: FBbt:00005093 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7157 xref: GAID:466 xref: MA:0000016 @@ -9157,20 +8991,15 @@ disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0050877 ! nervous system process -relationship: composed_primarily_of CL:0002319 ! neural cell -relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: has_part CL:0000540 ! neuron -relationship: immediate_transformation_of UBERON:0016880 {source="Bgee:AN"} ! future nervous system -relationship: never_in_taxon NCBITaxon:6040 -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI -property_value: UBPROP:0000001 "A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000396", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000324", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000402", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.117", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "nervous" xsd:string -property_value: UBPROP:0000007 "neural" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002473 CL:0002319 ! composed primarily of neural cell +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +relationship: RO:0002495 UBERON:0016880 {source="Bgee:AN"} ! immediate transformation of future nervous system +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI +property_value: RO:0002161 NCBITaxon:6040 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001017 @@ -9199,7 +9028,6 @@ xref: EHDAA:828 xref: EMAPA:16470 xref: EMAPA:16754 xref: EV:0100163 -xref: FBbt:00005094 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:55675 xref: GAID:570 xref: MA:0000167 @@ -9216,15 +9044,11 @@ xref: XAO:0000215 xref: ZFA:0000012 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0011216 {source="FBbt", source="cjm"} ! organ system subdivision -relationship: immediate_transformation_of UBERON:0016879 {source="Bgee:AN"} ! future central nervous system -relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0001016 ! nervous system -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "Part of the nervous system which includes the brain and spinal cord.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000090", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "The brain and spinal cord. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000012", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO)." xsd:string {source="BIRNLEX:1099"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000293", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 (reference 1), ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 (reference 2), DOI:10.1016/j.cell.2007.02.040 Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud'homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007) (reference 3)", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002495 UBERON:0016879 {source="Bgee:AN"} ! immediate transformation of future central nervous system +property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001032 @@ -9249,7 +9073,6 @@ xref: BILA:0000099 xref: EFO:0000805 xref: EHDAA2:0003094 xref: EMAPA:16192 -xref: FBbt:00007692 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:75259 xref: MA:0002442 xref: MAT:0000031 @@ -9264,9 +9087,7 @@ is_a: UBERON:0015203 ! non-connected functional system relationship: capable_of_part_of GO:0007600 ! sensory perception relationship: overlaps UBERON:0001016 ! nervous system relationship: part_of UBERON:0004456 ! entire sense organ system -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" xsd:anyURI -property_value: UBPROP:0000003 "An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001674", ontology="VHOG", source="DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Gray722.png" xsd:anyURI [Term] id: UBERON:0001049 @@ -9290,7 +9111,6 @@ xref: EMAPA:16164 xref: EMAPA:16757 xref: FMA:293882 xref: MAT:0000069 -xref: MESH:D054259 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: MIAA:0000069 xref: NCIT:C34226 xref: neuronames:1365 @@ -9305,12 +9125,8 @@ is_a: UBERON:0003914 {source="EHDAA2"} ! epithelial tube is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0016879 ! future central nervous system -relationship: develops_from UBERON:0005068 ! neural rod -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010617", ontology="AAO", source="AAO:JOR"} -property_value: UBPROP:0000001 "The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000307", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/neural+tube"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000307", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000011 "The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium" xsd:string {source="GO:0021915"} +relationship: RO:0002202 UBERON:0005068 ! develops from neural rod +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0001062 @@ -9326,7 +9142,6 @@ xref: BILA:0000000 xref: BIRNLEX:6 xref: CARO:0000000 xref: EHDAA2:0002229 -xref: FBbt:10000000 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:62955 xref: HAO:0000000 xref: MA:0000001 @@ -9337,9 +9152,9 @@ xref: UMLS:C1515976 {source="ncithesaurus:Anatomic_Structure_System_or_Substance xref: WBbt:0000100 xref: XAO:0000000 xref: ZFA:0100000 -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0001133 @@ -9390,10 +9205,10 @@ is_a: UBERON:8600006 ! visceral striated muscle tissue intersection_of: UBERON:0002036 ! striated muscle tissue intersection_of: has_part CL:0000746 ! cardiac muscle cell disjoint_from: UBERON:0001134 ! skeletal muscle tissue -relationship: composed_primarily_of CL:0000746 ! cardiac muscle cell relationship: has_part CL:0000746 ! cardiac muscle cell relationship: part_of UBERON:0007100 ! primary circulatory organ -property_value: editor_note "check relationship with myocardium. part_of in MA - but we also have a more specific class 'cardiac muscle tissue of myocardium'. Check ncit" xsd:string +relationship: RO:0002473 CL:0000746 ! composed primarily of cardiac muscle cell +property_value: IAO:0000116 "check relationship with myocardium. part_of in MA - but we also have a more specific class 'cardiac muscle tissue of myocardium'. Check ncit" xsd:string [Term] id: UBERON:0001134 @@ -9415,15 +9230,12 @@ xref: UMLS:C0242692 {source="ncithesaurus:Skeletal_Muscle_Tissue"} xref: Wikipedia:Skeletal_striated_muscle is_a: UBERON:0002036 ! striated muscle tissue intersection_of: UBERON:0002385 ! muscle tissue -intersection_of: composed_primarily_of CL:0008002 ! skeletal muscle fiber -relationship: composed_primarily_of CL:0008002 ! skeletal muscle fiber -relationship: develops_from UBERON:0003082 ! myotome +intersection_of: RO:0002473 CL:0008002 ! composed primarily of skeletal muscle fiber relationship: part_of UBERON:0014892 ! skeletal muscle organ, vertebrate -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/c/c0/Skeletal_muscle.jpg" xsd:anyURI -property_value: editor_note "TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle." xsd:string -property_value: UBPROP:0000001 "Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005277", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA]" xsd:string {external_class="FMA:14069", ontology="FMA"} -property_value: UBPROP:0000003 "This result implies the following views in terms of evolutionary differentiation: (1) Arthropod striated muscle and vertebrate skeletal and cardiac muscles share a common ancestor. In other words, they did not evolve independently (...) (5) The divergence of vertebrate skeletal and cardiac muscles/vertebrate smooth muscle and nonmuscle is at least before that of vertebrates/arthropods. In other words, emergence of skeletal and cardiac musle type tissues preceded the vertebrate/arthropod divergence (ca. 700 MYA).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000319", ontology="VHOG", source="PMID:10368962 Oota S, Saitou N, Phylogenetic relationship of muscle tissues deduced from superimposition of gene trees. Mol Biol Evol (1999)", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003082 ! develops from myotome +relationship: RO:0002473 CL:0008002 ! composed primarily of skeletal muscle fiber +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/c/c0/Skeletal_muscle.jpg" xsd:anyURI +property_value: IAO:0000116 "TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle." xsd:string [Term] id: UBERON:0001434 @@ -9462,18 +9274,11 @@ disjoint_from: UBERON:0002330 ! exocrine system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0004456 ! entire sense organ system -relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: has_part UBERON:0004288 ! skeleton relationship: has_part UBERON:0004770 ! articular system relationship: part_of UBERON:0002204 ! musculoskeletal system -property_value: RO:0002171 UBERON:0001016 +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/The-skeletal-system" xsd:anyURI -property_value: UBPROP:0000001 "Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000434", ontology="TAO", source="TAO:wd"} -property_value: UBPROP:0000001 "Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000027", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "System that provides physical support to the organism.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000566", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000003 "By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001254", ontology="VHOG", source="DOI:10.1159/000324245 Donoghue PCJ, Sansom IJ, Origin and early evolution of vertebrate skeletonization. Microscopy research and technique (2002)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "skeletal" xsd:string -property_value: UBPROP:0000012 "GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates" xsd:string {external_ontology="GO"} [Term] id: UBERON:0001474 @@ -9516,19 +9321,11 @@ xref: XAO:0000169 xref: ZFA:0001514 is_a: UBERON:0004765 ! skeletal element intersection_of: UBERON:0004765 ! skeletal element -intersection_of: composed_primarily_of UBERON:0002481 ! bone tissue +intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue disjoint_from: UBERON:0001630 ! muscle organ disjoint_from: UBERON:0005090 ! muscle structure -relationship: composed_primarily_of UBERON:0002481 {source="VSAO-modified"} ! bone tissue -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata -property_value: RO:0002171 UBERON:0001015 -property_value: RO:0002171 UBERON:0001630 -property_value: RO:0002171 UBERON:0002385 -property_value: UBPROP:0000001 "Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000047", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000001 "Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001514", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Skeletal element that is composed of bone tissue.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000057", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000002 "relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000047", ontology="AAO"} -property_value: UBPROP:0000003 "The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001190", ontology="VHOG", source="DOI:10.1159/000324245 Murdock DJ, Donoghue PC, Evolutionary Origins of Animal Skeletal Biomineralization. Cells Tissues Organs (2011)", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002473 UBERON:0002481 {source="VSAO-modified"} ! composed primarily of bone tissue [Term] id: UBERON:0001555 @@ -9552,11 +9349,9 @@ xref: BTO:0000545 xref: EHDAA2:0000726 xref: EHDAA:518 xref: EMAPA:16247 -xref: FBbt:00003125 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45615 xref: galen:AlimentaryTract xref: MA:0000917 -xref: MESH:D041981 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: NCIT:C34082 xref: TAO:0000112 xref: TGMA:0001819 @@ -9565,18 +9360,13 @@ xref: VHOG:0000309 xref: WBbt:0005743 xref: ZFA:0000112 is_a: UBERON:0000025 ! tube -relationship: connects UBERON:0000165 ! mouth -relationship: immediate_transformation_of UBERON:0007026 {source="NCBIBook:NBK10107"} ! presumptive gut -relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} -relationship: never_in_taxon NCBITaxon:41324 {source="DOI:10.1371/journal.pone.0016309"} -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0001007 ! digestive system -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "The alimentary or digestive tract, and associated organs.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000112", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000309", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "FMA also has a term 'gastrointestinal tract', but this includes the liver." xsd:string {external_ontology="FMA"} -property_value: UBPROP:0000012 "we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509" xsd:string {external_ontology="MA"} -property_value: UBPROP:0000013 "we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002176 UBERON:0000165 ! connects mouth +relationship: RO:0002495 UBERON:0007026 {source="NCBIBook:NBK10107"} ! immediate transformation of presumptive gut +property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} +property_value: RO:0002161 NCBITaxon:41324 {source="DOI:10.1371/journal.pone.0016309"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001630 @@ -9588,8 +9378,6 @@ subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "muscle" BROAD [ZFA:0005145] -xref: AAO:0011066 -xref: EMAPA:32715 xref: EMAPA:37474 {source="MA:th"} xref: EV:0100146 xref: FMA:5022 @@ -9604,12 +9392,9 @@ xref: ZFA:0005145 is_a: UBERON:0000062 ! organ is_a: UBERON:0005090 ! muscle structure intersection_of: UBERON:0000062 ! organ -intersection_of: composed_primarily_of UBERON:0002385 ! muscle tissue -relationship: composed_primarily_of UBERON:0002385 ! muscle tissue +intersection_of: RO:0002473 UBERON:0002385 ! composed primarily of muscle tissue relationship: part_of UBERON:0001015 ! musculature -property_value: UBPROP:0000001 "Portion of tissue composed of contractile fibers.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005145", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001245", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.75", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "muscular" xsd:string +relationship: RO:0002473 UBERON:0002385 ! composed primarily of muscle tissue [Term] id: UBERON:0002036 @@ -9633,9 +9418,8 @@ xref: WBbt:0005779 xref: Wikipedia:Striated_muscle is_a: UBERON:0002385 ! muscle tissue intersection_of: UBERON:0002385 ! muscle tissue -intersection_of: composed_primarily_of CL:0000737 ! striated muscle cell -relationship: composed_primarily_of CL:0000737 ! striated muscle cell -property_value: UBPROP:0000001 "Voluntary muscle tissue arranged in bundles of fibers.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010762", ontology="AAO", source="AAO:CAM"} +intersection_of: RO:0002473 CL:0000737 ! composed primarily of striated muscle cell +relationship: RO:0002473 CL:0000737 ! composed primarily of striated muscle cell [Term] id: UBERON:0002050 @@ -9655,7 +9439,6 @@ xref: BILA:0000034 xref: BTO:0000174 xref: CALOHA:TS-2110 xref: EFO:0000461 -xref: FBbt:00004208 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69067 xref: GAID:407 xref: MESH:D004628 @@ -9671,10 +9454,6 @@ is_a: UBERON:0005423 ! developing anatomical structure intersection_of: UBERON:0005423 ! developing anatomical structure intersection_of: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0000922 ! embryo -property_value: UBPROP:0000001 "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000138", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001105", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000178", ontology="VSAO", source="ZFIN:curator"} -property_value: UBPROP:0000012 "in FMA embryo is_a embryonic structure" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0002100 @@ -9710,10 +9489,6 @@ xref: XAO:0003025 xref: ZFA:0001115 is_a: UBERON:0011676 ! subdivision of organism along main body axis relationship: part_of UBERON:0013702 ! body proper -property_value: RO:0002171 UBERON:0000026 {exceptions="ZFA", source="https://github.com/obophenotype/uberon/issues/378", status="pending"} -property_value: RO:0002171 UBERON:0000033 -property_value: UBPROP:0000001 "Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010339", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001115", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0002104 @@ -9741,7 +9516,6 @@ xref: XAO:0003198 xref: ZFA:0001127 is_a: UBERON:0001032 ! sensory system relationship: capable_of_part_of GO:0007601 ! visual perception -property_value: UBPROP:0000001 "The sensory system used for sight.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000632", ontology="AAO", source="AAO:EJS"} [Term] id: UBERON:0002193 @@ -9757,7 +9531,7 @@ xref: EMAPA:18765 xref: FMA:74562 xref: MA:0000013 is_a: UBERON:0000467 {source="MA"} ! anatomical system -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria [Term] id: UBERON:0002204 @@ -9787,13 +9561,10 @@ disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of_part_of GO:0040011 ! locomotion -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: has_developmental_contribution_from UBERON:0000926 {notes="check ctenophore"} ! mesoderm relationship: has_part UBERON:0000383 ! musculature of body relationship: has_part UBERON:0001434 ! skeletal system -property_value: UBPROP:0000001 "Anatomical system that provides locomotion and physical support to the organism.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010546", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001275", ontology="VHOG", source="DOI:10.1002/jez.b.21246 Shearman RM, Burke AC, The lateral somitic frontier in ontogeny and phylogeny. Journal of Experimental Zoology (2009)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "musculoskeletal" xsd:string +relationship: RO:0002254 UBERON:0000926 ! has developmental contribution from mesoderm +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage [Term] id: UBERON:0002328 @@ -9831,23 +9602,15 @@ xref: XAO:0000055 xref: ZFA:0000135 is_a: UBERON:0000062 {source="PMID:15890825"} ! organ is_a: UBERON:0000481 {source="VSAO"} ! multi-tissue structure +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004121 ! ectoderm-derived structure -relationship: develops_from UBERON:0004880 {source="ZFA"} ! chordamesoderm -relationship: develops_from UBERON:0006267 {source="EHDAA2"} ! notochordal plate -relationship: dorsal_to UBERON:0001555 ! digestive tract -relationship: existence_starts_during UBERON:0000068 ! embryo stage -relationship: only_in_taxon NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! Chordata relationship: part_of UBERON:0011137 ! axial skeletal system relationship: produces PR:000014841 ! sonic hedgehog protein -relationship: ventral_to UBERON:0001049 ! neural tube -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000032", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000135", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000327", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000002 "relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000327", ontology="AAO"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000199", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "notochordal" xsd:string -property_value: UBPROP:0000011 "In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord." xsd:string +relationship: RO:0002160 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! only in taxon Chordata +relationship: RO:0002202 UBERON:0004880 {source="ZFA"} ! develops from chordamesoderm +relationship: RO:0002202 UBERON:0006267 {source="EHDAA2"} ! develops from notochordal plate +relationship: RO:0002488 UBERON:0000068 ! existence starts during embryo stage +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0002329 @@ -9886,18 +9649,10 @@ xref: XAO:0000058 xref: ZFA:0000155 is_a: UBERON:0005423 ! developing anatomical structure is_a: UBERON:0007503 {source="EHDAA2"} ! epithelial vesicle -relationship: develops_from UBERON:0003059 {source="ZFA"} ! presomitic mesoderm -relationship: never_in_taxon NCBITaxon:7712 {source="PMID:17237766"} -relationship: only_in_taxon NCBITaxon:7711 {source="GOTAX:0000352"} ! Chordata -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: IAO:0000232 "EDITOR_NOTE currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk" xsd:string -property_value: UBPROP:0000001 "Post-cranial axial segments which form sclerotome and dermomyotome.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010569", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000001 "Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000155", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000002 "relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000155", ontology="TAO"} -property_value: UBPROP:0000002 "relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000155", ontology="TAO"} -property_value: UBPROP:0000002 "relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010569", ontology="AAO"} -property_value: UBPROP:0000003 "(...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000191", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.40, DOI:10.1093/icb/43.1.137 Balavoine G, Adoutte A, The segmented urbilateria: a testable scenario. Integrative and Comparative Biology (2003)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "somitic" xsd:string +relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata +relationship: RO:0002202 UBERON:0003059 {source="ZFA"} ! develops from presomitic mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: RO:0002161 NCBITaxon:7712 {source="PMID:17237766"} [Term] id: UBERON:0002330 @@ -9921,9 +9676,9 @@ is_a: UBERON:0000467 ! anatomical system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0004456 ! entire sense organ system -relationship: composed_primarily_of UBERON:0002365 ! exocrine gland -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002473 UBERON:0002365 ! composed primarily of exocrine gland +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage [Term] id: UBERON:0002342 @@ -9950,28 +9705,22 @@ xref: MIAA:0000066 xref: NCIT:C34222 xref: neuronames:1366 xref: SCTID:361462002 -xref: TAO:0000045 xref: UMLS:C0027789 {source="ncithesaurus:Neural_Crest"} xref: VHOG:0000057 xref: Wikipedia:Neural_crest xref: XAO:0000048 xref: ZFA:0000045 is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0010316 ! germ layer / neural crest -relationship: composed_primarily_of CL:0000333 {notes="pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! migratory neural crest cell -relationship: develops_from UBERON:0003075 {source="BTO"} ! neural plate -relationship: develops_from UBERON:0005062 {source="PMID:11523831"} ! neural fold -relationship: existence_starts_during UBERON:0000110 {source="PMID:11523831"} ! neurula stage -relationship: only_in_taxon NCBITaxon:89593 {notes="Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells", source="ISBN:0073040584"} ! Craniata relationship: part_of UBERON:0002346 {source="XAO", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! neurectoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI -property_value: IAO:0000232 "EDITOR_NOTE consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams)." xsd:string -property_value: RO:0002174 NCBITaxon:117565 {source="ISBN:0073040584", source="PMID:17377535"} -property_value: UBPROP:0000001 "A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000045", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010578", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831]" xsd:string {source="PMID:11523831"} -property_value: UBPROP:0000003 "We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000057", ontology="VHOG", source="DOI:10.1111/j.1469-7580.2012.01495.x Hall BK, Gillis JA, Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues. J Anat (2012)", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata +relationship: RO:0002202 UBERON:0003075 {source="BTO"} ! develops from neural plate +relationship: RO:0002202 UBERON:0005062 {source="PMID:11523831"} ! develops from neural fold +relationship: RO:0002473 CL:0000333 ! composed primarily of migratory neural crest cell +relationship: RO:0002488 UBERON:0000110 {source="PMID:11523831"} ! existence starts during neurula stage +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI [Term] id: UBERON:0002346 @@ -9994,7 +9743,6 @@ xref: EHDAA:1498 xref: EHDAA:255 xref: EMAPA:16073 xref: EV:0100004 -xref: FBbt:00001057 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:87657 xref: MAT:0000176 xref: MIAA:0000176 @@ -10008,9 +9756,6 @@ xref: ZFA:0001120 is_a: UBERON:0000923 ! germ layer is_a: UBERON:0004121 ! ectoderm-derived structure relationship: has_part CL:0000133 ! neurectodermal cell -property_value: UBPROP:0000003 "(...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000150", ontology="VHOG", source="DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "neurectodermal" xsd:string -property_value: UBPROP:0000013 "we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here" xsd:string [Term] id: UBERON:0002365 @@ -10041,7 +9786,7 @@ intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0002330 ! exocrine system relationship: has_part UBERON:0000058 ! duct relationship: part_of UBERON:0002330 ! exocrine system -property_value: editor_note "Currently this is logically defined by the system it belongs to, but a better system may be base this on presence/absence of ducts. However, the dual nature of the liver should be taken into consideration here. Consider adding subclasses" xsd:string +property_value: IAO:0000116 "Currently this is logically defined by the system it belongs to, but a better system may be base this on presence/absence of ducts. However, the dual nature of the liver should be taken into consideration here. Consider adding subclasses" xsd:string [Term] id: UBERON:0002368 @@ -10073,7 +9818,7 @@ intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0000949 ! endocrine system relationship: capable_of GO:0046879 ! hormone secretion relationship: part_of UBERON:0000949 ! endocrine system -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/da/Illu_endocrine_system.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/da/Illu_endocrine_system.png" xsd:anyURI [Term] id: UBERON:0002371 @@ -10109,6 +9854,7 @@ xref: VHOG:0001218 xref: Wikipedia:Bone_marrow xref: XAO:0000123 is_a: UBERON:0000479 ! tissue +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000479 ! tissue intersection_of: has_part UBERON:0012429 ! hematopoietic tissue intersection_of: part_of UBERON:0001474 ! bone element @@ -10117,12 +9863,10 @@ relationship: has_part UBERON:0012429 ! hematopoietic tissue relationship: part_of UBERON:0001474 ! bone element relationship: part_of UBERON:0002390 {source="FMA", source="MA"} ! hematopoietic system relationship: part_of UBERON:0002405 ! immune system -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg" xsd:anyURI -property_value: editor_note "consider placement of NCIT:C53466 medullary bone" xsd:string -property_value: editor_note "TODO - create superclass for bone marrow / head kidney. both are portions of tissue in the hematopoetic system. also consider adding as subclass of zone of bone organ for consistency with FMA. See also: Leydig and epigonal organs" xsd:string -property_value: UBPROP:0000003 "The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001218", ontology="VHOG", source="DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood Cells and Blood Cell Development in the Animal Kingdom. Annual Review of Cell and Developmental Biology (2006)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000009 "In adults, marrow in large bones produces new blood cells[Wikipedia:Bone_marrow]" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg" xsd:anyURI +property_value: IAO:0000116 "consider placement of NCIT:C53466 medullary bone" xsd:string +property_value: IAO:0000116 "TODO - create superclass for bone marrow / head kidney. both are portions of tissue in the hematopoetic system. also consider adding as subclass of zone of bone organ for consistency with FMA. See also: Leydig and epigonal organs" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002384 @@ -10156,12 +9900,8 @@ xref: VSAO:0000017 xref: XAO:0001017 xref: ZFA:0001632 is_a: UBERON:0000479 ! tissue -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000098", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000001 "Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001641", ontology="TAO", source="TAO:wd"} -property_value: UBPROP:0000001 "Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000017", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} -property_value: UBPROP:0000012 "MA also has set of connective tissues" xsd:string {external_ontology="MA"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002385 @@ -10189,13 +9929,11 @@ xref: Wikipedia:Muscle_tissue is_a: UBERON:0000479 ! tissue is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000479 ! tissue -intersection_of: composed_primarily_of CL:0000187 ! muscle cell +intersection_of: RO:0002473 CL:0000187 ! composed primarily of muscle cell relationship: capable_of GO:0006936 ! muscle contraction -relationship: composed_primarily_of CL:0000187 ! muscle cell -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0001015 ! musculature -property_value: RO:0002171 UBERON:0003714 -property_value: UBPROP:0000001 "One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000306", ontology="AAO", source="AAO:LAP"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002473 CL:0000187 ! composed primarily of muscle cell [Term] id: UBERON:0002390 @@ -10239,14 +9977,10 @@ is_a: UBERON:0000467 ! anatomical system is_a: UBERON:0004120 ! mesoderm-derived structure disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0004456 ! entire sense organ system -relationship: develops_from UBERON:0003061 {evidence="definitional"} ! blood island -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0002193 {source="FMA"} ! hemolymphoid system -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "Anatomical system that consists of the blood and blood forming tissues.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011002", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001624", ontology="VHOG", source="DOI:10.1016/j.coph.2010.05.004 Ellett F, Lieschke GJ, Zebrafish as a model for vertebrate hematopoiesis. Current Opinion in Pharmacology (2010)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "hematopoietic" xsd:string -property_value: UBPROP:0000008 "In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes" xsd:string {source="WP"} +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002202 UBERON:0003061 ! develops from blood island +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002405 @@ -10275,10 +10009,9 @@ xref: ZFA:0001159 is_a: UBERON:0015203 ! non-connected functional system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0002376 ! immune system process -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: present_in_taxon NCBITaxon:9606 relationship: protects UBERON:0000468 ! multicellular organism -property_value: UBPROP:0000003 "The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001247", ontology="VHOG", source="PMID:21046016 Dzik JM, The ancestry and cumulative evolution of immune reactions. Acta biochimica Polonica (2010)", source="http://bgee.unil.ch/"} +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002481 @@ -10307,10 +10040,9 @@ xref: XAO:0004040 xref: ZFA:0005621 is_a: UBERON:0004755 {source="VSAO"} ! skeletal tissue disjoint_from: UBERON:0005090 ! muscle structure -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0001474 ! bone element -property_value: editor_note "see https://github.com/obophenotype/uberon/issues/27" xsd:string -property_value: UBPROP:0000001 "Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000047", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +property_value: IAO:0000116 "see https://github.com/obophenotype/uberon/issues/27" xsd:string [Term] id: UBERON:0002530 @@ -10329,10 +10061,7 @@ xref: BTO:0000522 xref: EFO:0000797 xref: EHDAA2:0003096 xref: EHDAA:2161 -xref: EHDAA:4475 -xref: EHDAA:6522 xref: EMAPA:18425 -xref: FBbt:00100317 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7146 xref: FMA:86294 xref: galen:Gland @@ -10347,11 +10076,9 @@ xref: Wikipedia:Gland xref: WikipediaCategory:Glands is_a: UBERON:0000062 ! organ relationship: capable_of GO:0046903 ! secretion -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: produces UBERON:0000463 ! organism substance -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/a1/Gray1026.png" xsd:anyURI -property_value: RO:0002171 UBERON:0001434 -property_value: UBPROP:0000007 "glandular" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/a1/Gray1026.png" xsd:anyURI [Term] id: UBERON:0002532 @@ -10375,9 +10102,8 @@ xref: VHOG:0000243 xref: Wikipedia:Epiblast is_a: UBERON:0002050 ! embryonic structure relationship: has_part CL:0000352 ! epiblast cell -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" xsd:anyURI -property_value: editor_note "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" xsd:string -property_value: UBPROP:0000003 "In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000243", ontology="VHOG", source="DOI:10.1146/annurev.cellbio.042308.113344 Zorn AM, Wells JM, Vertebrate endoderm development and organ formation. Annual Review of Cell Developmental Biology (2009)", source="http://bgee.unil.ch/"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" xsd:anyURI +property_value: IAO:0000116 "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" xsd:string [Term] id: UBERON:0002553 @@ -10393,7 +10119,7 @@ xref: galen:Cavity xref: MA:0002447 xref: NCIT:C34007 is_a: UBERON:0000464 ! anatomical space -relationship: location_of UBERON:0000463 ! organism substance +relationship: RO:0001015 UBERON:0000463 ! location of organism substance [Term] id: UBERON:0003059 @@ -10419,13 +10145,11 @@ xref: XAO:0000057 xref: ZFA:0000279 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0005423 ! developing anatomical structure -intersection_of: has_potential_to_develop_into UBERON:0002329 ! somite -intersection_of: immediate_transformation_of UBERON:0007282 ! presumptive segmental plate -relationship: has_potential_to_develop_into UBERON:0002329 ! somite -relationship: immediate_transformation_of UBERON:0007282 {source="Bgee:AN"} ! presumptive segmental plate +intersection_of: RO:0002387 UBERON:0002329 ! has potential to develop into somite +intersection_of: RO:0002495 UBERON:0007282 ! immediate transformation of presumptive segmental plate relationship: part_of UBERON:0003077 ! paraxial mesoderm -property_value: UBPROP:0000001 "Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000279", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000559", ontology="VHOG", source="DOI:10.1006/dbio.2001.0460 Schubert M, Holland LZ, Dale Stokes M and Holland ND, Three Amphoxius Wnt Genes (AmphiWnt3, AmphiWnt5, and AmphiWnt6) Associated with the Tail Bud: the Evolution of Somitogenesis in Chordates. Developmental Biology (2001)", source="http://bgee.unil.ch/"} +relationship: RO:0002387 UBERON:0002329 ! has potential to develop into somite +relationship: RO:0002495 UBERON:0007282 {source="Bgee:AN"} ! immediate transformation of presumptive segmental plate [Term] id: UBERON:0003061 @@ -10455,13 +10179,8 @@ xref: Wikipedia:Blood_island_of_umbilical_vesicle xref: XAO:0000067 xref: ZFA:0000094 is_a: UBERON:0006598 ! presumptive structure -relationship: develops_from UBERON:0003081 ! lateral plate mesoderm -relationship: has_potential_to_develop_into UBERON:0002390 ! hematopoietic system -property_value: UBPROP:0000001 "Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000094", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011006", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000002 "relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000094", ontology="TAO"} -property_value: UBPROP:0000003 "Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000085", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450, DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual Review of Cell and Developmental Biology (2006)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac" xsd:string {external_ontology="EHDAA2"} +relationship: RO:0002202 UBERON:0003081 ! develops from lateral plate mesoderm +relationship: RO:0002387 UBERON:0002390 ! has potential to develop into hematopoietic system [Term] id: UBERON:0003068 @@ -10479,11 +10198,10 @@ xref: Wikipedia:Chordamesoderm xref: XAO:0000205 xref: ZFA:0001204 is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0000926 ! mesoderm -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0000926 ! mesoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000107", ontology="VHOG", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002202 UBERON:0000926 ! develops from mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003075 @@ -10503,7 +10221,6 @@ xref: EHDAA:346 xref: EHDAA:902 xref: EMAPA:35593 xref: FMA:293879 -xref: MESH:D054258 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C34225 xref: neuronames:1362 xref: RETIRED_EHDAA2:0001252 @@ -10516,12 +10233,10 @@ xref: ZFA:0000132 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0016879 ! future central nervous system -relationship: developmentally_induced_by UBERON:0002328 {source="Wikipedia"} ! notochord -relationship: immediate_transformation_of UBERON:0007284 {source="Bgee:AN"} ! presumptive neural plate -relationship: only_in_taxon NCBITaxon:7711 {source="GOTAX:0000352"} ! Chordata -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI -property_value: UBPROP:0000001 "The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000132", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000068", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata +relationship: RO:0002256 UBERON:0002328 {source="Wikipedia"} ! developmentally induced by notochord +relationship: RO:0002495 UBERON:0007284 {source="Bgee:AN"} ! immediate transformation of presumptive neural plate +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI [Term] id: UBERON:0003077 @@ -10550,13 +10265,9 @@ xref: ZFA:0000255 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue is_a: UBERON:0015212 ! lateral structure -relationship: existence_starts_during UBERON:0000109 ! gastrula stage -relationship: immediate_transformation_of UBERON:0007285 {source="Bgee:AN"} ! presumptive paraxial mesoderm -relationship: in_lateral_side_of UBERON:0000922 ! embryo -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010568", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000114", ontology="VHOG", source="DOI:10.1002/dvdy.21177 Kusakabe R and Kuratani S. Evolutionary perspectives from development of mesodermal components in the lamprey. Developmental dynamics (2007)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here)" xsd:string {external_ontology="ZFA"} +relationship: RO:0002488 UBERON:0000109 ! existence starts during gastrula stage +relationship: RO:0002495 UBERON:0007285 {source="Bgee:AN"} ! immediate transformation of presumptive paraxial mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003081 @@ -10588,14 +10299,10 @@ is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0000926 {source="EHDAA2", source="VHOG"} ! mesoderm -relationship: surrounds UBERON:0003887 ! intraembryonic coelom -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010574", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000001 "The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000118", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000118", ontology="VHOG", source="DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "subclass of mesoderm in ZFA." xsd:string {external_ontology="ZFA"} +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002221 UBERON:0003887 ! surrounds intraembryonic coelom +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003082 @@ -10630,12 +10337,10 @@ xref: Wikipedia:Myotome xref: XAO:0000315 xref: ZFA:0001056 is_a: UBERON:0017650 {source="AEO"} ! developing mesenchymal structure -relationship: contributes_to_morphology_of UBERON:0001630 ! muscle organ -relationship: develops_from UBERON:0004290 {source="EHDAA2-abduced"} ! dermomyotome -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI -property_value: editor_note "The term 'myotome' is also used to describe the muscles served by a single nerve root / spinal segment - consider adding new class, myomere." xsd:string -property_value: UBPROP:0000001 "Portion of the somites giving rise to body wall muscle masses. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001056", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "In all vertebrates, the skeletal muscle of the body axis is chiefly derived from an early embryonic compartment, known as the myotome.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001244", ontology="VHOG", source="DOI:10.1038/sj.embor.embor920 Hollway GE, Currie PD, Myotome meanderings. Cellular morphogenesis and the making of muscle. EMBO Rep.(2003)", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0004290 {source="EHDAA2-abduced"} ! develops from dermomyotome +relationship: RO:0002433 UBERON:0001630 ! contributes to morphology of muscle organ +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI +property_value: IAO:0000116 "The term 'myotome' is also used to describe the muscles served by a single nerve root / spinal segment - consider adding new class, myomere." xsd:string [Term] id: UBERON:0003103 @@ -10658,7 +10363,6 @@ xref: VHOG:0001723 xref: XAO:0003041 xref: ZFA:0000496 is_a: UBERON:0000062 ! organ -property_value: IAO:0000232 "this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs" xsd:string [Term] id: UBERON:0003104 @@ -10688,15 +10392,12 @@ xref: XAO:0003046 xref: ZFA:0000393 is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue -intersection_of: composed_primarily_of CL:0008019 ! mesenchymal cell -relationship: composed_primarily_of CL:0008019 ! mesenchymal cell -relationship: functionally_related_to GO:0032502 ! developmental process -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI -property_value: editor_note "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" xsd:string -property_value: UBPROP:0000001 "A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000393", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010427", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000007 "mesenchymal" xsd:string +intersection_of: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002328 GO:0032502 ! functionally related to developmental process +relationship: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI +property_value: IAO:0000116 "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" xsd:string [Term] id: UBERON:0003887 @@ -10712,10 +10413,9 @@ xref: UMLS:C1512940 {source="ncithesaurus:Intraembryonic_Coelom"} xref: VHOG:0000316 xref: Wikipedia:Intraembryonic_coelom is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0003081 {source="Wikipedia"} ! lateral plate mesoderm relationship: part_of UBERON:0011997 ! coelom -property_value: editor_note "consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults" xsd:string -property_value: UBPROP:0000003 "(...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000316", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.166", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003081 {source="Wikipedia"} ! develops from lateral plate mesoderm +property_value: IAO:0000116 "consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults" xsd:string [Term] id: UBERON:0003914 @@ -10725,12 +10425,10 @@ def: "Epithelial tubes transport gases, liquids and cells from one site to anoth synonym: "epithelial or endothelial tube" EXACT [] xref: AEO:0000114 xref: EHDAA2:0003114 -xref: FBbt:00007474 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000025 ! tube is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium -intersection_of: has_quality PATO:0002299 ! tubular -property_value: IAO:0000232 "contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers" xsd:string +intersection_of: RO:0000086 PATO:0002299 ! has quality tubular [Term] id: UBERON:0004111 @@ -10750,15 +10448,14 @@ xref: SCTID:346902003 xref: Wikipedia:Foramen is_a: UBERON:0010000 ! multicellular anatomical structure intersection_of: UBERON:0010000 ! multicellular anatomical structure -intersection_of: conduit_for UBERON:0000061 ! anatomical structure intersection_of: has_part UBERON:0013686 ! anatomical conduit space -relationship: conduit_for UBERON:0000061 ! anatomical structure -relationship: connects UBERON:0000464 {cardinality="2"} ! anatomical space +intersection_of: RO:0002570 UBERON:0000061 ! conduit for anatomical structure relationship: has_part UBERON:0013686 ! anatomical conduit space -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: UBPROP:0000012 "FMA has both conduit and conduit space. In EHDAA2 this is a surface feature" xsd:string {external_ontology="FMA"} +relationship: RO:0002176 UBERON:0000464 {cardinality="2"} ! connects anatomical space +relationship: RO:0002570 UBERON:0000061 ! conduit for anatomical structure +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0004120 @@ -10769,9 +10466,8 @@ subset: grouping_class synonym: "mesodermal derivative" EXACT [FBbt:00025998] is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: develops_from UBERON:0000926 ! mesoderm -relationship: develops_from UBERON:0000926 ! mesoderm -property_value: IAO:0000232 "Grouping term for query purposes" xsd:string +intersection_of: RO:0002202 UBERON:0000926 ! develops from mesoderm +relationship: RO:0002202 UBERON:0000926 ! develops from mesoderm [Term] id: UBERON:0004121 @@ -10782,9 +10478,8 @@ subset: grouping_class synonym: "ectodermal deriviative" EXACT [FBbt:00025990] is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: develops_from UBERON:0000924 ! ectoderm -relationship: develops_from UBERON:0000924 ! ectoderm -property_value: IAO:0000232 "Grouping term for query purposes" xsd:string +intersection_of: RO:0002202 UBERON:0000924 ! develops from ectoderm +relationship: RO:0002202 UBERON:0000924 ! develops from ectoderm [Term] id: UBERON:0004288 @@ -10814,13 +10509,10 @@ xref: Wikipedia:Skeleton xref: XAO:0004053 is_a: UBERON:0034925 ! anatomical collection disjoint_from: UBERON:0004770 ! articular system -relationship: has_member UBERON:0004765 ! skeletal element relationship: part_of UBERON:0001434 ! skeletal system -relationship: present_in_taxon NCBITaxon:9606 -property_value: RO:0002171 UBERON:0000383 +relationship: RO:0002351 UBERON:0004765 ! has member skeletal element +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/The-skeletal-system" xsd:anyURI -property_value: UBPROP:0000001 "Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000026", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070"} -property_value: UBPROP:0000007 "skeletal" xsd:string [Term] id: UBERON:0004290 @@ -10841,13 +10533,8 @@ xref: VHOG:0000676 xref: ZFA:0001513 is_a: UBERON:0000486 {source="AEO"} ! multilaminar epithelium is_a: UBERON:0016888 {source="AEO"} ! transitional anatomical structure -relationship: develops_from UBERON:0002329 {source="EHDAA2", source="ZFA"} ! somite relationship: has_part CL:0000075 ! columnar/cuboidal epithelial cell -property_value: UBPROP:0000001 "all but the sclerotome of a mesodermal somite; the primordium of skeletal muscle and, perhaps, of the dermis." xsd:string {source="http://medical-dictionary.thefreedictionary.com/dermomyotome"} -property_value: UBPROP:0000001 "Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768]." xsd:string {source="http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768"} -property_value: UBPROP:0000001 "Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001513", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Portion of somites that gives rise to dermis and muscles.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010572", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000676", ontology="VHOG", source="DOI:10.1111/j.1525-142X.2006.05079.x Devoto SH, Stoiber W, Hammond CL, Steinbacher P, Haslett JR, Barresi MJF, Patterson SE, Adiarte EG and Hughes SM, Generality of vertebrate developmental patterns: evidence for a dermomyotome in fish. Evolution and Development (2006)", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0002329 {source="EHDAA2", source="ZFA"} ! develops from somite [Term] id: UBERON:0004456 @@ -10858,9 +10545,8 @@ subset: uberon_slim synonym: "sense organ system" EXACT [FMA:78499] xref: FMA:78499 is_a: UBERON:0000467 ! anatomical system -relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: overlaps UBERON:0001016 ! nervous system -property_value: UBPROP:0000012 "note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs" xsd:string +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage [Term] id: UBERON:0004716 @@ -10877,12 +10563,12 @@ xref: NCIT:C34131 xref: UMLS:C1516779 {source="ncithesaurus:Conceptus"} xref: Wikipedia:Conceptus is_a: UBERON:0000061 ! anatomical structure -relationship: develops_from CL:0000365 ! animal zygote -relationship: existence_ends_with UBERON:0000068 ! embryo stage -relationship: existence_starts_with UBERON:0000068 ! embryo stage relationship: has_part UBERON:0002050 ! embryonic structure relationship: has_part UBERON:0016887 ! entire extraembryonic component -property_value: editor_note "EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus" xsd:string +relationship: RO:0002202 CL:0000365 ! develops from animal zygote +relationship: RO:0002489 UBERON:0000068 ! existence starts with embryo stage +relationship: RO:0002493 UBERON:0000068 ! existence ends with embryo stage +property_value: IAO:0000116 "EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus" xsd:string [Term] id: UBERON:0004734 @@ -10902,7 +10588,6 @@ synonym: "trilaminar disk" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "trilaminar germ" RELATED [https://orcid.org/0000-0002-6601-2165] xref: BILA:0000060 xref: BTO:0001403 -xref: FBbt:00005317 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:293108 xref: GAID:1302 xref: MESH:D005775 @@ -10915,10 +10600,9 @@ xref: Wikipedia:Gastrula xref: Wikipedia:Trilaminar_blastocyst is_a: UBERON:0000922 ! embryo intersection_of: UBERON:0000468 ! multicellular organism -intersection_of: existence_starts_and_ends_during UBERON:0000109 ! gastrula stage -relationship: develops_from UBERON:0000307 ! blastula -relationship: existence_starts_and_ends_during UBERON:0000109 ! gastrula stage -property_value: UBPROP:0000012 "We explicitly merge the NCITA terms here" xsd:string {external_ontology="NCIT"} +intersection_of: RO:0002491 UBERON:0000109 ! existence starts and ends during gastrula stage +relationship: RO:0002202 UBERON:0000307 ! develops from blastula +relationship: RO:0002491 UBERON:0000109 ! existence starts and ends during gastrula stage [Term] id: UBERON:0004755 @@ -10933,9 +10617,8 @@ xref: VSAO:0000015 xref: XAO:0004038 xref: ZFA:0005619 is_a: UBERON:0002384 {source="VSAO"} ! connective tissue -relationship: develops_from CL:0007001 {date_retrieved="2012-08-14", external_class="VSAO:0000015", source="VSAO"} ! skeletogenic cell relationship: part_of UBERON:0004765 ! skeletal element -property_value: UBPROP:0000001 "A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000015", notes="taken from version of VSAO used in TAO and used directly in Uberon", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} +relationship: RO:0002202 CL:0007001 ! develops from skeletogenic cell [Term] id: UBERON:0004765 @@ -10952,8 +10635,6 @@ xref: XAO:0004012 xref: ZFA:0005494 is_a: UBERON:0000062 ! organ relationship: part_of UBERON:0001434 {source="VSAO"} ! skeletal system -property_value: UBPROP:0000001 "Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000128", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001890", ontology="TAO", source="TAO:VSAO_workshop"} [Term] id: UBERON:0004770 @@ -10971,12 +10652,12 @@ xref: SCTID:361827000 xref: VSAO:0000181 is_a: UBERON:0034925 ! anatomical collection intersection_of: UBERON:0034925 ! anatomical collection -intersection_of: has_member UBERON:0000982 ! skeletal joint -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: functionally_related_to GO:0040011 ! locomotion -relationship: has_member UBERON:0000982 ! skeletal joint -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +intersection_of: RO:0002351 UBERON:0000982 ! has member skeletal joint relationship: part_of UBERON:0001434 {source="FMA"} ! skeletal system +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002328 GO:0040011 ! functionally related to locomotion +relationship: RO:0002351 UBERON:0000982 ! has member skeletal joint +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage [Term] id: UBERON:0004880 @@ -10994,10 +10675,8 @@ xref: EFO:0003426 xref: TAO:0000091 xref: ZFA:0000091 is_a: UBERON:0002050 ! embryonic structure -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0003068 ! axial mesoderm -property_value: UBPROP:0000001 "Notochord rudiment[ZFIN:ZDB-PUB-961014-576]." xsd:string {source="ZFIN:ZDB-PUB-961014-576"} -property_value: UBPROP:0000012 "WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord." xsd:string +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata [Term] id: UBERON:0004905 @@ -11006,7 +10685,6 @@ namespace: uberon def: "Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts." [http://orcid.org/0000-0002-6601-2165] subset: grouping_class synonym: "joint" NARROW [] -xref: FBbt:00005811 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0034921 ! multi organ part structure relationship: part_of UBERON:0004770 ! articular system @@ -11022,15 +10700,13 @@ synonym: "gut section" RELATED [FBbt:00100315] synonym: "intestinal tract" RELATED [] synonym: "segment of intestinal tract" RELATED [] synonym: "subdivision of alimentary system" RELATED [FMA:71131] -xref: FBbt:00100315 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:71131 is_a: UBERON:0013522 ! subdivision of tube intersection_of: UBERON:0013522 ! subdivision of tube intersection_of: subdivision_of UBERON:0001555 ! digestive tract relationship: part_of UBERON:0001555 ! digestive tract -relationship: present_in_taxon NCBITaxon:9606 relationship: subdivision_of UBERON:0001555 ! digestive tract -property_value: IAO:0000232 "intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct." xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004923 @@ -11040,8 +10716,8 @@ def: "A part of a wall of an organ that forms a layer." [http://orcid.org/0000-0 subset: upper_level xref: FMA:82485 is_a: UBERON:0000064 ! organ part -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000060 ! anatomical wall +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0005061 @@ -11059,7 +10735,6 @@ xref: Wikipedia:Neural_groove xref: XAO:0000248 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0003075 ! neural plate -property_value: UBPROP:0000001 "The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]." xsd:string {source="Wikipedia:Neural_groove"} [Term] id: UBERON:0005062 @@ -11079,10 +10754,9 @@ xref: XAO:0004087 is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0005157 ! epithelial fold is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0015212 ! lateral structure -relationship: in_lateral_side_of UBERON:0005061 ! neural groove relationship: part_of UBERON:0005061 ! neural groove -property_value: UBPROP:0000001 "In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]." xsd:string {source="Wikipedia:Neural_fold"} [Term] id: UBERON:0005068 @@ -11095,8 +10769,7 @@ xref: EFO:0003498 xref: TAO:0000133 xref: ZFA:0000133 is_a: UBERON:0016879 ! future central nervous system -relationship: develops_from UBERON:0007135 ! neural keel -property_value: UBPROP:0000001 "An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000133", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002202 UBERON:0007135 ! develops from neural keel [Term] id: UBERON:0005090 @@ -11106,12 +10779,10 @@ def: "Muscle structures are contractile cells, tissues or organs that are found synonym: "muscle" RELATED [] synonym: "muscle element" RELATED [] synonym: "musculus" EXACT [FMA:30316] -xref: EMAPA:32715 xref: FMA:30316 is_a: UBERON:0000061 ! anatomical structure relationship: has_part CL:0000187 ! muscle cell -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: IAO:0000232 "in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0005157 @@ -11164,14 +10835,13 @@ name: photoreceptor array namespace: uberon def: "An array of photoreceptors and any supporting cells found in an eye." [https://orcid.org/0000-0002-6601-2165] synonym: "light-sensitive tissue" EXACT [] -xref: FBbt:00004200 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0004923 ! organ component layer intersection_of: UBERON:0004923 ! organ component layer -intersection_of: composed_primarily_of CL:0000210 ! photoreceptor cell intersection_of: part_of UBERON:0000970 ! eye -relationship: composed_primarily_of CL:0000210 ! photoreceptor cell +intersection_of: RO:0002473 CL:0000210 ! composed primarily of photoreceptor cell relationship: part_of UBERON:0000970 ! eye relationship: part_of UBERON:0001016 ! nervous system +relationship: RO:0002473 CL:0000210 ! composed primarily of photoreceptor cell [Term] id: UBERON:0005423 @@ -11184,14 +10854,13 @@ synonym: "developmental tissue" RELATED [MIAA:0000019] xref: AEO:0000125 xref: CALOHA:TS-2122 xref: EHDAA2:0003125 -xref: FBbt:00007006 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:292313 xref: MIAA:0000019 is_a: UBERON:0000465 ! material anatomical entity relationship: capable_of GO:0032502 ! developmental process -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0005764 @@ -11204,9 +10873,9 @@ is_a: UBERON:0000476 ! acellular anatomical structure intersection_of: UBERON:0000476 ! acellular anatomical structure intersection_of: bounding_layer_of UBERON:0000061 ! anatomical structure relationship: bounding_layer_of UBERON:0000061 ! anatomical structure -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0005769 @@ -11226,12 +10895,11 @@ xref: Wikipedia:Basement_membrane is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005764 {source="FMA"} ! acellular membrane relationship: adjacent_to CL:0000066 ! epithelial cell -relationship: composed_primarily_of GO:0005604 ! basement membrane relationship: has_part GO:0005587 ! collagen type IV trimer -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa relationship: part_of UBERON:0000483 ! epithelium -relationship: present_in_taxon NCBITaxon:80999 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} -property_value: IAO:0000232 "this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell." xsd:string +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002473 GO:0005604 ! composed primarily of basement membrane +property_value: RO:0002175 NCBITaxon:80999 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} [Term] id: UBERON:0006267 @@ -11249,9 +10917,8 @@ is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium -relationship: develops_from UBERON:0006268 {source="EHDAA2"} ! notochordal process -property_value: editor_note "TODO - check ordering; awaiting confirmation from JB" xsd:string -property_value: UBPROP:0000001 "The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001212", ontology="VHOG", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0006268 {source="EHDAA2"} ! develops from notochordal process +property_value: IAO:0000116 "TODO - check ordering; awaiting confirmation from JB" xsd:string [Term] id: UBERON:0006268 @@ -11270,8 +10937,8 @@ xref: NCIT:C34232 xref: UMLS:C1518430 {source="ncithesaurus:Notochordal_Process"} xref: VHOG:0001213 is_a: UBERON:0005423 ! developing anatomical structure -relationship: develops_from UBERON:0000924 {source="EHDAA2"} ! ectoderm -relationship: only_in_taxon NCBITaxon:7711 ! Chordata +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002202 UBERON:0000924 {source="EHDAA2"} ! develops from ectoderm [Term] id: UBERON:0006595 @@ -11285,11 +10952,11 @@ xref: TAO:0000416 xref: ZFA:0000416 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0000925 ! endoderm intersection_of: part_of UBERON:0000307 ! blastula -relationship: has_potential_to_develop_into UBERON:0000925 ! endoderm -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +intersection_of: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm relationship: part_of UBERON:0000307 ! blastula +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm [Term] id: UBERON:0006598 @@ -11303,10 +10970,10 @@ xref: TAO:0001116 xref: ZFA:0001116 is_a: UBERON:0002050 ! embryonic structure intersection_of: UBERON:0005423 ! developing anatomical structure -intersection_of: has_potential_to_develop_into UBERON:0000061 ! anatomical structure intersection_of: part_of UBERON:0000922 ! embryo -relationship: has_potential_to_develop_into UBERON:0000061 ! anatomical structure -property_value: editor_note "Consider merging with anlage" xsd:string +intersection_of: RO:0002387 UBERON:0000061 ! has potential to develop into anatomical structure +relationship: RO:0002387 UBERON:0000061 ! has potential to develop into anatomical structure +property_value: IAO:0000116 "Consider merging with anlage" xsd:string [Term] id: UBERON:0006601 @@ -11322,11 +10989,11 @@ xref: XAO:0004132 xref: ZFA:0001376 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0000924 ! ectoderm intersection_of: part_of UBERON:0000307 ! blastula -relationship: has_potential_to_develop_into UBERON:0000924 ! ectoderm -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +intersection_of: RO:0002387 UBERON:0000924 ! has potential to develop into ectoderm relationship: part_of UBERON:0000307 ! blastula +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002387 UBERON:0000924 ! has potential to develop into ectoderm [Term] id: UBERON:0006603 @@ -11340,11 +11007,11 @@ xref: TAO:0001377 xref: ZFA:0001377 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0000926 ! mesoderm intersection_of: part_of UBERON:0000307 ! blastula -relationship: has_potential_to_develop_into UBERON:0000926 ! mesoderm -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +intersection_of: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm relationship: part_of UBERON:0000307 ! blastula +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm [Term] id: UBERON:0006984 @@ -11359,7 +11026,7 @@ xref: EHDAA2_RETIRED:0003192 xref: FMA:24137 xref: NCIT:C34022 xref: UMLS:C1515977 {source="ncithesaurus:Anatomic_Surface"} -is_a: UBERON:0010199 {notes="via morphological boundary in CARO"} ! bona-fide anatomical boundary +is_a: UBERON:0010199 ! bona-fide anatomical boundary [Term] id: UBERON:0007010 @@ -11369,10 +11036,10 @@ def: "Organism at the cleavage stage." [OBOL:automatic] xref: BILA:0000058 is_a: UBERON:0000922 ! embryo intersection_of: UBERON:0000468 ! multicellular organism -intersection_of: existence_ends_with UBERON:0000107 ! cleavage stage -intersection_of: existence_starts_with UBERON:0000107 ! cleavage stage -relationship: existence_ends_with UBERON:0000107 ! cleavage stage -relationship: existence_starts_with UBERON:0000107 ! cleavage stage +intersection_of: RO:0002489 UBERON:0000107 ! existence starts with cleavage stage +intersection_of: RO:0002493 UBERON:0000107 ! existence ends with cleavage stage +relationship: RO:0002489 UBERON:0000107 ! existence starts with cleavage stage +relationship: RO:0002493 UBERON:0000107 ! existence ends with cleavage stage [Term] id: UBERON:0007026 @@ -11391,12 +11058,11 @@ xref: SCTID:360394002 xref: UMLS:C1514442 {source="ncithesaurus:Primordial_Gut"} is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001555 ! digestive tract -relationship: existence_starts_during UBERON:0000109 ! gastrula stage -relationship: has_developmental_contribution_from UBERON:0000925 ! endoderm -relationship: has_developmental_contribution_from UBERON:0000926 ! mesoderm -relationship: has_potential_to_develop_into UBERON:0001555 ! digestive tract -property_value: UBPROP:0000011 "The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis" xsd:string {source="NCBIBook:NBK10107"} +intersection_of: RO:0002387 UBERON:0001555 ! has potential to develop into digestive tract +relationship: RO:0002254 UBERON:0000925 ! has developmental contribution from endoderm +relationship: RO:0002254 UBERON:0000926 ! has developmental contribution from mesoderm +relationship: RO:0002387 UBERON:0001555 ! has potential to develop into digestive tract +relationship: RO:0002488 UBERON:0000109 ! existence starts during gastrula stage [Term] id: UBERON:0007100 @@ -11409,14 +11075,12 @@ synonym: "adult heart" RELATED [FBbt:00003154] synonym: "dorsal tube" NARROW [Wikipedia:Heart] synonym: "heart" NARROW [GO:0007507] xref: http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg -xref: SPD:0000130 xref: TADS:0000147 is_a: UBERON:0015228 ! circulatory organ intersection_of: UBERON:0015228 ! circulatory organ intersection_of: capable_of GO:0008015 ! blood circulation -relationship: capable_of GO:0008015 {notes="GO uses blood circulation generically to include the haemolymphatic fluid of arthropods"} ! blood circulation +relationship: capable_of GO:0008015 ! blood circulation relationship: has_part CL:0002494 ! cardiocyte -property_value: UBPROP:0000008 "note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis" xsd:string [Term] id: UBERON:0007135 @@ -11429,8 +11093,7 @@ xref: EFO:0003497 xref: TAO:0000131 xref: ZFA:0000131 is_a: UBERON:0016879 ! future central nervous system -relationship: develops_from UBERON:0003075 ! neural plate -property_value: UBPROP:0000001 "An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000131", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002202 UBERON:0003075 ! develops from neural plate [Term] id: UBERON:0007282 @@ -11444,9 +11107,9 @@ xref: TAO:0000053 xref: ZFA:0000053 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0003059 ! presomitic mesoderm -relationship: develops_from UBERON:0009618 {consistent_with="https://github.com/obophenotype/uberon/wiki/The-neural-crest", source="EDHAA2"} ! trunk paraxial mesoderm -relationship: has_potential_to_develop_into UBERON:0003059 ! presomitic mesoderm +intersection_of: RO:0002387 UBERON:0003059 ! has potential to develop into presomitic mesoderm +relationship: RO:0002202 UBERON:0009618 ! develops from trunk paraxial mesoderm +relationship: RO:0002387 UBERON:0003059 ! has potential to develop into presomitic mesoderm [Term] id: UBERON:0007284 @@ -11461,12 +11124,11 @@ xref: TAO:0000063 xref: ZFA:0000063 is_a: UBERON:0016879 ! future central nervous system intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0003075 ! neural plate -relationship: develops_from UBERON:0002346 ! neurectoderm -relationship: has_potential_to_develop_into UBERON:0003075 ! neural plate +intersection_of: RO:0002387 UBERON:0003075 ! has potential to develop into neural plate relationship: part_of UBERON:0004734 ! gastrula -property_value: editor_note "consider merging" xsd:string -property_value: UBPROP:0000001 "Region of the gastrula which gives rise to the neural plate.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000063", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002202 UBERON:0002346 ! develops from neurectoderm +relationship: RO:0002387 UBERON:0003075 ! has potential to develop into neural plate +property_value: IAO:0000116 "consider merging" xsd:string [Term] id: UBERON:0007285 @@ -11482,10 +11144,10 @@ xref: XAO:0004134 xref: ZFA:0000591 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 {source="https://github.com/obophenotype/uberon/issues/1277"} ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0003077 {source="https://github.com/obophenotype/uberon/issues/1277"} ! paraxial mesoderm intersection_of: part_of UBERON:0000307 {source="https://github.com/obophenotype/uberon/issues/1277"} ! blastula -relationship: has_potential_to_develop_into UBERON:0003077 ! paraxial mesoderm +intersection_of: RO:0002387 UBERON:0003077 {source="https://github.com/obophenotype/uberon/issues/1277"} ! has potential to develop into paraxial mesoderm relationship: part_of UBERON:0000307 ! blastula +relationship: RO:0002387 UBERON:0003077 ! has potential to develop into paraxial mesoderm [Term] id: UBERON:0007503 @@ -11518,7 +11180,7 @@ disjoint_from: UBERON:0011821 ! irregular connective tissue relationship: has_part CL:0000057 ! fibroblast relationship: has_part GO:0071953 ! elastic fiber relationship: has_part UBERON:0011860 ! collection of collagen fibrils -property_value: editor_note "the connective tissue hierarchy largely follows FMA with definitions from VSAO. Note that in FMA, loose-CT is irregular-CT. This means regular-CT is necessarily equivalent to dense-regular-CT (assuming a JEPD classification)." xsd:string +property_value: IAO:0000116 "the connective tissue hierarchy largely follows FMA with definitions from VSAO. Note that in FMA, loose-CT is irregular-CT. This means regular-CT is necessarily equivalent to dense-regular-CT (assuming a JEPD classification)." xsd:string [Term] id: UBERON:0007846 @@ -11540,10 +11202,8 @@ xref: XAO:0004030 is_a: UBERON:0007845 {source="FMA"} ! regular connective tissue is_a: UBERON:0011823 {source="ncithesaurus"} ! dense connective tissue intersection_of: UBERON:0007845 ! regular connective tissue -intersection_of: composed_primarily_of UBERON:0011860 ! collection of collagen fibrils intersection_of: has_part GO:0071953 ! elastic fiber -property_value: UBPROP:0000001 "Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000050", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "Regular connective tissue, the intercellular matrix of which consists predominantly of collagen fiber bundles arranged in parallel arrays.[FMA]" xsd:string {date_retrieved="2012-08-29", external_class="FMA:64781", ontology="FMA"} +intersection_of: RO:0002473 UBERON:0011860 ! composed primarily of collection of collagen fibrils [Term] id: UBERON:0009142 @@ -11555,10 +11215,10 @@ xref: EHDAA2:0001113 xref: EHDAA:177 xref: EMAPA:16097 is_a: UBERON:0000477 ! anatomical cluster -relationship: composed_primarily_of UBERON:0003104 ! mesenchyme -relationship: has_developmental_contribution_from UBERON:0000926 {source="EHDAA2"} ! mesoderm relationship: part_of UBERON:0000922 ! embryo -property_value: editor_note "consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)" xsd:string +relationship: RO:0002254 UBERON:0000926 {source="EHDAA2"} ! has developmental contribution from mesoderm +relationship: RO:0002473 UBERON:0003104 ! composed primarily of mesenchyme +property_value: IAO:0000116 "consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)" xsd:string [Term] id: UBERON:0009618 @@ -11580,15 +11240,14 @@ subset: common_anatomy subset: upper_level synonym: "multicellular structure" EXACT [FBbt:00100313] xref: CARO:0010000 -xref: FBbt:00100313 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: has_quality PATO:0001993 ! multicellular +intersection_of: RO:0000086 PATO:0001993 ! has quality multicellular relationship: has_part CL:0000000 ! cell -relationship: has_quality PATO:0001993 ! multicellular -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0000086 PATO:0001993 ! has quality multicellular +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0010199 @@ -11600,13 +11259,24 @@ subset: upper_level xref: CARO:0001004 is_a: UBERON:0000466 {source="CARO"} ! immaterial anatomical entity +[Term] +id: UBERON:0010314 +name: structure with developmental contribution from neural crest +namespace: uberon +def: "An anatomical structure that has some part that develops from the neural crest." [https://orcid.org/0000-0002-6601-2165] +subset: grouping_class +is_a: UBERON:0000061 ! anatomical structure +intersection_of: UBERON:0000061 ! anatomical structure +intersection_of: RO:0002254 UBERON:0002342 ! has developmental contribution from neural crest +relationship: RO:0002254 UBERON:0002342 ! has developmental contribution from neural crest + [Term] id: UBERON:0010316 name: germ layer / neural crest namespace: uberon is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0005291 ! embryonic tissue -relationship: develops_from UBERON:0002532 ! epiblast (generic) +relationship: RO:0002202 UBERON:0002532 ! develops from epiblast (generic) [Term] id: UBERON:0010371 @@ -11618,8 +11288,8 @@ xref: FMA:69064 is_a: UBERON:0000483 ! epithelium is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000483 ! epithelium -intersection_of: develops_from UBERON:0000924 ! ectoderm -relationship: composed_primarily_of CL:0002077 ! ecto-epithelial cell +intersection_of: RO:0002202 UBERON:0000924 ! develops from ectoderm +relationship: RO:0002473 CL:0002077 ! composed primarily of ecto-epithelial cell [Term] id: UBERON:0011137 @@ -11639,15 +11309,14 @@ def: "A subdivision of an anatomical system." [http://orcid.org/0000-0002-6601-2 subset: common_anatomy subset: human_reference_atlas subset: upper_level -xref: FBbt:00007330 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67509 xref: SCTID:91690000 is_a: UBERON:0010000 {source="FBbt"} ! multicellular anatomical structure relationship: part_of UBERON:0000467 ! anatomical system -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0011676 @@ -11660,7 +11329,7 @@ synonym: "body segment" RELATED [] synonym: "main body segment" RELATED [] is_a: UBERON:0000475 ! organism subdivision relationship: part_of UBERON:0013701 ! main body axis -property_value: editor_note "Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem" xsd:string +property_value: IAO:0000116 "Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem" xsd:string [Term] id: UBERON:0011821 @@ -11684,10 +11353,9 @@ xref: Wikipedia:Dense_irregular_connective_tissue is_a: UBERON:0011821 {source="FMA"} ! irregular connective tissue is_a: UBERON:0011823 ! dense connective tissue intersection_of: UBERON:0011821 ! irregular connective tissue -intersection_of: composed_primarily_of UBERON:0011860 ! collection of collagen fibrils intersection_of: has_part GO:0071953 ! elastic fiber +intersection_of: RO:0002473 UBERON:0011860 ! composed primarily of collection of collagen fibrils relationship: has_part GO:0071953 ! elastic fiber -property_value: UBPROP:0000001 "Tissue characterized by a thick, random arrangement of collagen and elastin fibers with very few cells. The majority of the cells are fibroblasts, but mast cells and macrophages may also be seen. It is found in the dermis, periosteum, perichondrium, capsules of organs and sheaths of nerves and muscles[NCIT]" xsd:string {date_retrieved="2012-08-29", external_class="ncithesaurus:Irregular_Dense_Connective_Tissue", ontology="NCIT"} [Term] id: UBERON:0011823 @@ -11701,10 +11369,9 @@ xref: Wikipedia:Dense_connective_tissue is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002384 ! connective tissue intersection_of: UBERON:0002384 ! connective tissue -intersection_of: composed_primarily_of UBERON:0011860 ! collection of collagen fibrils -relationship: composed_primarily_of UBERON:0011860 ! collection of collagen fibrils -property_value: editor_note "our OWL definition states that this is differentiated from other connective tissue types by virtue of the fact that the collage fiber component predominates, as opposed to cells and fluid." xsd:string -property_value: UBPROP:0000001 "Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT]" xsd:string {date_retrieved="2012-08-29", external_class="ncithesaurus:Dense_Connective_Tissue", ontology="NCIT"} +intersection_of: RO:0002473 UBERON:0011860 ! composed primarily of collection of collagen fibrils +relationship: RO:0002473 UBERON:0011860 ! composed primarily of collection of collagen fibrils +property_value: IAO:0000116 "our OWL definition states that this is differentiated from other connective tissue types by virtue of the fact that the collage fiber component predominates, as opposed to cells and fluid." xsd:string [Term] id: UBERON:0011860 @@ -11716,10 +11383,9 @@ xref: NCIT:C32339 xref: NIF_Subcellular:sao7547390221 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000476 {source="ZFA"} ! acellular anatomical structure -relationship: composed_primarily_of GO:0005581 ! collagen trimer -relationship: composed_primarily_of GO:0098643 ! banded collagen fibril -relationship: seeAlso UBERON:0007377 -property_value: UBPROP:0000012 "the FMA class specifically refers to ureter" xsd:string {external_ontology="FMA"} +relationship: RO:0002473 GO:0005581 ! composed primarily of collagen trimer +relationship: RO:0002473 GO:0098643 ! composed primarily of banded collagen fibril +property_value: seeAlso UBERON:0007377 [Term] id: UBERON:0011899 @@ -11732,11 +11398,11 @@ xref: FMA:9726 xref: NCIT:C32527 xref: UMLS:C0504096 {source="ncithesaurus:Epimysium"} xref: Wikipedia:Epimysium +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0011822 {source="FMA"} ! dense irregular connective tissue relationship: bounding_layer_of UBERON:0014892 ! skeletal muscle organ, vertebrate -relationship: continuous_with UBERON:0000043 ! tendon relationship: part_of UBERON:0001134 {source="FMA"} ! skeletal muscle tissue -property_value: UBPROP:0000009 "The Epimysium also protects muscles from friction against other muscles and bones" xsd:string +relationship: RO:0002150 UBERON:0000043 ! continuous with tendon [Term] id: UBERON:0011997 @@ -11751,10 +11417,9 @@ synonym: "schizocoelom" NARROW [] xref: EHDAA2:0004731 xref: Wikipedia:Coelom is_a: UBERON:0000481 {source="EHDAA2"} ! multi-tissue structure -relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -property_value: editor_note "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." xsd:string -property_value: UBPROP:0000007 "coelomic" xsd:string +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +property_value: IAO:0000116 "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." xsd:string +property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} [Term] id: UBERON:0012429 @@ -11770,12 +11435,12 @@ xref: CALOHA:TS-2142 xref: FMA:14073 xref: NCIT:C13051 xref: UMLS:C0229619 {source="ncithesaurus:Hematopoietic_Tissue"} +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0034769 {source="FMA"} ! lymphomyeloid tissue intersection_of: UBERON:0000479 ! tissue intersection_of: site_of GO:0030097 ! hemopoiesis relationship: part_of UBERON:0002390 {source="defitional"} ! hematopoietic system relationship: site_of GO:0030097 ! hemopoiesis -property_value: UBPROP:0000008 "Bone marrow in humans, kidney interstitium in Danio, within a stroma of reticuloendothelial tissue" xsd:string [Term] id: UBERON:0013522 @@ -11796,11 +11461,11 @@ subset: common_anatomy synonym: "foramen space" NARROW [] xref: FMA:9338 is_a: UBERON:0000464 {source="FMA"} ! anatomical space -relationship: connects UBERON:0000464 {cardinality="2"} ! anatomical space -relationship: luminal_space_of UBERON:0004111 ! anatomical conduit -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0002176 UBERON:0000464 {cardinality="2"} ! connects anatomical space +relationship: RO:0002572 UBERON:0004111 ! luminal space of anatomical conduit +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0013701 @@ -11809,7 +11474,7 @@ namespace: uberon def: "A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages." [https://orcid.org/0000-0002-6601-2165] subset: non_informative is_a: UBERON:0000475 ! organism subdivision -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0013702 @@ -11821,11 +11486,9 @@ synonym: "body" RELATED [AEO:0000103] synonym: "whole body" RELATED [BTO:0001489] xref: AEO:0000103 xref: BTO:0001489 -xref: EMAPA:36031 xref: FMA:231424 is_a: UBERON:0000475 {source="AEO"} ! organism subdivision relationship: part_of UBERON:0013701 ! main body axis -property_value: UBPROP:0000001 "Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]." xsd:string {source="FMA:231424"} [Term] id: UBERON:0014892 @@ -11855,17 +11518,17 @@ xref: XAO:0000174 xref: ZFA:0005277 is_a: UBERON:0001630 ! muscle organ intersection_of: UBERON:0001630 ! muscle organ -intersection_of: composed_primarily_of UBERON:0001134 ! skeletal muscle tissue -intersection_of: develops_from UBERON:0003082 ! myotome -intersection_of: surrounded_by UBERON:0011899 ! epimysium -intersection_of: synapsed_by CL:0000100 ! motor neuron -relationship: composed_primarily_of UBERON:0001134 ! skeletal muscle tissue -relationship: develops_from UBERON:0003082 ! myotome -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +intersection_of: RO:0002103 CL:0000100 ! synapsed by motor neuron +intersection_of: RO:0002202 UBERON:0003082 ! develops from myotome +intersection_of: RO:0002219 UBERON:0011899 ! surrounded by epimysium +intersection_of: RO:0002473 UBERON:0001134 ! composed primarily of skeletal muscle tissue relationship: part_of UBERON:0018254 ! skeletal musculature -relationship: present_in_taxon NCBITaxon:9606 -relationship: surrounded_by UBERON:0011899 ! epimysium -relationship: synapsed_by CL:0000100 ! motor neuron +relationship: RO:0002103 CL:0000100 ! synapsed by motor neuron +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002202 UBERON:0003082 ! develops from myotome +relationship: RO:0002219 UBERON:0011899 ! surrounded by epimysium +relationship: RO:0002473 UBERON:0001134 ! composed primarily of skeletal muscle tissue +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0015203 @@ -11873,7 +11536,6 @@ name: non-connected functional system namespace: uberon def: "An anatomical group whose component structures share a common function." [AEO:0000093, AEO:JB, FBbt:00007278, FBC:DOS] xref: AEO:0000093 -xref: FBbt:00007278 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0034923 ! disconnected anatomical group [Term] @@ -11884,8 +11546,8 @@ def: "A non-connected functional system that is composed primarily of a gland." xref: EHDAA2:0002223 is_a: UBERON:0015203 ! non-connected functional system intersection_of: UBERON:0015203 ! non-connected functional system -intersection_of: composed_primarily_of UBERON:0002530 ! gland -relationship: composed_primarily_of UBERON:0002530 ! gland +intersection_of: RO:0002473 UBERON:0002530 ! composed primarily of gland +relationship: RO:0002473 UBERON:0002530 ! composed primarily of gland [Term] id: UBERON:0015212 @@ -11895,11 +11557,7 @@ def: "Any structure that is placed on one side of the left-right axis of a bilat subset: grouping_class subset: non_informative is_a: UBERON:0000061 ! anatomical structure -intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: in_lateral_side_of UBERON:0000465 ! material anatomical entity -relationship: in_lateral_side_of UBERON:0000465 ! material anatomical entity -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -property_value: IAO:0000232 "This class is primarily to implement taxon constraints. It may be removed in the future." xsd:string +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria [Term] id: UBERON:0015228 @@ -11912,10 +11570,9 @@ synonym: "cardiac structure" RELATED [] synonym: "circulatory vessel" NARROW [] synonym: "heart" BROAD [] synonym: "heart or heart like organ" EXACT [] -xref: SPD:0000130 is_a: UBERON:0003103 ! compound organ -relationship: has_quality PATO:0001690 ! contractile relationship: part_of UBERON:0001009 ! circulatory system +relationship: RO:0000086 PATO:0001690 ! has quality contractile [Term] id: UBERON:0015757 @@ -11935,10 +11592,10 @@ synonym: "future CNS" EXACT [] synonym: "presumptive central nervous system" EXACT [] is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001017 ! central nervous system -relationship: develops_from UBERON:0000924 ! ectoderm -relationship: has_potential_to_develop_into UBERON:0001017 ! central nervous system +intersection_of: RO:0002387 UBERON:0001017 ! has potential to develop into central nervous system relationship: part_of UBERON:0016880 ! future nervous system +relationship: RO:0002202 UBERON:0000924 ! develops from ectoderm +relationship: RO:0002387 UBERON:0001017 ! has potential to develop into central nervous system [Term] id: UBERON:0016880 @@ -11950,9 +11607,9 @@ synonym: "presumptive nervous system" EXACT [AAO:0000477] xref: AAO:0000477 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001016 ! nervous system -relationship: existence_starts_during_or_after UBERON:0000111 ! organogenesis stage -relationship: has_potential_to_develop_into UBERON:0001016 ! nervous system +intersection_of: RO:0002387 UBERON:0001016 ! has potential to develop into nervous system +relationship: RO:0002387 UBERON:0001016 ! has potential to develop into nervous system +relationship: RO:0002496 UBERON:0000111 ! existence starts during or after organogenesis stage [Term] id: UBERON:0016887 @@ -11966,8 +11623,8 @@ xref: EHDAA2:0000003 xref: EMAPA:16042 is_a: UBERON:0000481 {source="AEO"} ! multi-tissue structure relationship: adjacent_to UBERON:0002050 ! embryonic structure -relationship: existence_starts_and_ends_during UBERON:0000068 ! embryo stage relationship: part_of UBERON:0004716 {source="AEO"} ! conceptus +relationship: RO:0002491 UBERON:0000068 ! existence starts and ends during embryo stage [Term] id: UBERON:0016888 @@ -11985,8 +11642,8 @@ def: "A mesenchyme-derived anatomical entity undergoing a transtion to become an xref: AEO:0001016 is_a: UBERON:0005423 ! developing anatomical structure intersection_of: UBERON:0005423 ! developing anatomical structure -intersection_of: composed_primarily_of UBERON:0003104 ! mesenchyme -relationship: composed_primarily_of UBERON:0003104 ! mesenchyme +intersection_of: RO:0002473 UBERON:0003104 ! composed primarily of mesenchyme +relationship: RO:0002473 UBERON:0003104 ! composed primarily of mesenchyme [Term] id: UBERON:0018254 @@ -11996,12 +11653,11 @@ subset: grouping_class subset: human_reference_atlas xref: EHDAA2:0001842 xref: EMAPA:35578 -xref: MA:0000165 is_a: UBERON:0000061 ! anatomical structure -relationship: composed_primarily_of UBERON:0014892 ! skeletal muscle organ, vertebrate relationship: part_of UBERON:0000383 {source="MA"} ! musculature of body -relationship: present_in_taxon NCBITaxon:9606 -property_value: editor_note "Added for consistency with MA EMAPA and EHDAA2. See https://github.com/obophenotype/mouse-anatomy-ontology/issues/104" xsd:string +relationship: RO:0002473 UBERON:0014892 ! composed primarily of skeletal muscle organ, vertebrate +property_value: IAO:0000116 "Added for consistency with MA EMAPA and EHDAA2. See https://github.com/obophenotype/mouse-anatomy-ontology/issues/104" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0034769 @@ -12020,10 +11676,10 @@ subset: common_anatomy synonym: "anatomical cluster" RELATED [CARO:0020001] xref: CARO:0020001 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure -relationship: composed_primarily_of UBERON:0000064 ! organ part -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0002473 UBERON:0000064 ! composed primarily of organ part +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0034923 @@ -12032,14 +11688,13 @@ namespace: uberon def: "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other." [CARO:0020000] subset: common_anatomy xref: CARO:0020000 -xref: FBbt:00007276 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000465 {source="CARO"} ! material anatomical entity -relationship: composed_primarily_of UBERON:0000061 ! anatomical structure relationship: has_component UBERON:0000061 {minCardinality="2"} ! anatomical structure -relationship: has_quality PATO:0010001 ! disconnected -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0000086 PATO:0010001 ! has quality disconnected +relationship: RO:0002473 UBERON:0000061 ! composed primarily of anatomical structure +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0034925 @@ -12048,11 +11703,11 @@ namespace: uberon def: "A collection of anatomical structures that are alike in terms of their morphology or developmental origin." [http://orcid.org/0000-0002-6601-2165] subset: common_anatomy is_a: UBERON:0000465 ! material anatomical entity -relationship: has_member UBERON:0000061 ! anatomical structure -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: editor_note "resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected" xsd:string +relationship: RO:0002351 UBERON:0000061 ! has member anatomical structure +property_value: IAO:0000116 "resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0034969 @@ -12088,9 +11743,9 @@ def: "A muscle tissue that is associated with soft internal organs (viscera)." [ comment: It is quite common to refer to visceral muscles as smooth muscles, by analogy with vertebrates; however, most visceral muscles in arthropods are actually striated. {xref="https://en.wikipedia.org/wiki/Smooth_muscle", xref="FBbt:00005070", comment="PMID:8720463"} synonym: "visceral muscle" EXACT [] {comment="BTO:0002780"} is_a: UBERON:0002385 ! muscle tissue -relationship: composed_primarily_of CL:0008007 ! visceral muscle cell -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -property_value: dcterms-date "2023-02-16T10:17:46Z" xsd:dateTime +relationship: RO:0002473 CL:0008007 ! composed primarily of visceral muscle cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-02-16T10:17:46Z" xsd:dateTime [Term] id: UBERON:8600006 @@ -12100,8 +11755,14 @@ def: "A striated muscle tissue that is associated with soft internal organs (vis synonym: "striated visceral muscle tissue" EXACT [] is_a: UBERON:0002036 ! striated muscle tissue is_a: UBERON:8600004 ! visceral muscle tissue -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -property_value: dcterms-date "2023-02-16T10:34:43Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-02-16T10:34:43Z" xsd:dateTime + +[Typedef] +id: BFO:0000067 +name: contains process +def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] +comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant [Typedef] id: CL:4030044 @@ -12122,11 +11783,6 @@ id: RO:0000052 name: characteristic of def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." [] comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. -property_value: IAO:0000111 "inheres in" xsd:string -property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string -property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string -property_value: IAO:0000118 "inheres_in" xsd:string -property_value: RO:0001900 RO:0001901 is_functional: true is_a: RO:0002314 ! characteristic of part of inverse_of: bearer_of ! bearer of @@ -12136,10 +11792,7 @@ id: RO:0000079 name: function of def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. -property_value: editor_note "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string -property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string -property_value: IAO:0000118 "function_of" xsd:string -property_value: IAO:0000118 "is function of" xsd:string +property_value: IAO:0000116 "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string is_a: RO:0000052 ! characteristic of inverse_of: RO:0000085 ! has function @@ -12148,22 +11801,16 @@ id: RO:0000080 name: quality of def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. -property_value: editor_note "A quality inheres in its bearer at all times for which the quality exists." xsd:string -property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string -property_value: IAO:0000118 "is quality of" xsd:string -property_value: IAO:0000118 "quality_of" xsd:string +property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string is_a: RO:0000052 ! characteristic of -inverse_of: has_quality ! has quality +inverse_of: RO:0000086 ! has quality [Typedef] id: RO:0000081 name: role of def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. -property_value: editor_note "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string -property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string -property_value: IAO:0000118 "is role of" xsd:string -property_value: IAO:0000118 "role_of" xsd:string +property_value: IAO:0000116 "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string is_a: RO:0000052 ! characteristic of inverse_of: RO:0000087 ! has role @@ -12171,19 +11818,22 @@ inverse_of: RO:0000087 ! has role id: RO:0000085 name: has function def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] -property_value: editor_note "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string -property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string -property_value: IAO:0000118 "has_function" xsd:string +property_value: IAO:0000116 "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string domain: BFO:0000004 ! independent continuant is_a: bearer_of ! bearer of +[Typedef] +id: RO:0000086 +name: has quality +def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] +property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string +is_a: bearer_of ! bearer of + [Typedef] id: RO:0000087 name: has role def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] -property_value: editor_note "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string -property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string -property_value: IAO:0000118 "has_role" xsd:string +property_value: IAO:0000116 "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string domain: BFO:0000004 ! independent continuant is_a: bearer_of ! bearer of @@ -12208,12 +11858,7 @@ id: RO:0001000 name: derives from def: "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" [] subset: ro-eco -property_value: editor_note "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." xsd:string -property_value: IAO:0000112 "this cell derives from this parent cell (cell division)" xsd:string -property_value: IAO:0000112 "this nucleus derives from this parent nucleus (nuclear division)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000118 "derives_from" xsd:string -property_value: IAO:0000232 "This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations." xsd:string +property_value: IAO:0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." xsd:string inverse_of: RO:0001001 ! derives into [Typedef] @@ -12221,33 +11866,57 @@ id: RO:0001001 name: derives into def: "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" [] subset: ro-eco -property_value: editor_note "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." xsd:string -property_value: IAO:0000112 "this parent cell derives into this cell (cell division)" xsd:string -property_value: IAO:0000112 "this parent nucleus derives into this nucleus (nuclear division)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000118 "derives_into" xsd:string +property_value: IAO:0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." xsd:string + +[Typedef] +id: RO:0001015 +name: location of +def: "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" [] +property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +is_transitive: true +inverse_of: RO:0001025 ! located in + +[Typedef] +id: RO:0001025 +name: located in +def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +property_value: IAO:0000116 "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" xsd:string +property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Located_in" xsd:anyURI +domain: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +range: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +is_transitive: true +transitive_over: part_of ! part of [Typedef] id: RO:0002000 name: 2D boundary of def: "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" [] -property_value: editor_note "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string -property_value: editor_note "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string -property_value: IAO:0000112 "the surface of my skin is a 2D boundary of my body" xsd:string -property_value: IAO:0000118 "2D_boundary_of" xsd:string -property_value: IAO:0000118 "boundary of" xsd:string -property_value: IAO:0000118 "is 2D boundary of" xsd:string -property_value: IAO:0000118 "is boundary of" xsd:string -property_value: IAO:0000118 "surface of" xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string +is_a: RO:0002323 ! mereotopologically related to +inverse_of: RO:0002002 ! has 2D boundary + +[Typedef] +id: RO:0002002 +name: has 2D boundary +def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000141 ! immaterial entity is_a: RO:0002323 ! mereotopologically related to -inverse_of: has_boundary ! has 2D boundary + +[Typedef] +id: RO:0002005 +name: innervated_by +domain: UBERON:0000061 ! anatomical structure +inverse_of: RO:0002134 ! innervates [Typedef] id: RO:0002006 name: has synaptic terminal of -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: overlaps ! overlaps inverse_of: RO:0002130 ! has synaptic terminal in @@ -12329,16 +11998,23 @@ id: RO:0002081 name: before or simultaneous with comment: Primitive instance level timing relation between events subset: ro-eco -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000118 "<=" xsd:string is_a: RO:0002222 ! temporally related to +[Typedef] +id: RO:0002082 +name: simultaneous with +def: "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." [] +comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) +subset: ro-eco +is_symmetric: true +is_transitive: true +is_a: RO:0002081 ! before or simultaneous with + [Typedef] id: RO:0002086 name: ends after comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) subset: ro-eco -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string is_transitive: true is_a: RO:0002222 ! temporally related to @@ -12346,25 +12022,16 @@ is_a: RO:0002222 ! temporally related to id: RO:0002100 name: has soma location def: "Relation between a neuron and a material anatomical entity that its soma is part of." [] -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron range: UBERON:0000465 ! material anatomical entity is_a: overlaps ! overlaps -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] [Typedef] id: RO:0002101 name: fasciculates with def: "relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.\n" [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "fasciculates with" xsd:string -property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: overlaps ! overlaps inverse_of: RO:0002132 ! has fasciculating neuron projection @@ -12373,27 +12040,23 @@ inverse_of: RO:0002132 ! has fasciculating neuron projection id: RO:0002102 name: axon synapses in def: "Relation between a neuron and some structure its axon forms (chemical) synapses in." [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: RO:0002113 ! has presynaptic terminal in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "BFO_0000051 some (\n GO_0030424 and BFO_0000051 some (\n GO_0042734 and BFO_0000050 some (\n GO_0045202 and BFO_0000050 some ?Y)))" [] +[Typedef] +id: RO:0002103 +name: synapsed by +def: "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " [] +is_a: RO:0002485 ! receives input from +inverse_of: RO:0002120 ! synapsed to +expand_expression_to: "BFO_0000051 some (GO_0045211 that part_of some (GO_0045202 that has_part some (GO_0042734 that BFO_0000050 some Y?)))" [] + [Typedef] id: RO:0002104 name: has plasma membrane part def: "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part." [] -property_value: IAO:0000112 "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9990-8331 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 -property_value: RO:0001900 RO:0001901 domain: UBERON:0000465 ! material anatomical entity range: UBERON:0000465 ! material anatomical entity is_a: has_part ! has part @@ -12403,29 +12066,19 @@ expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] id: RO:0002110 name: has postsynaptic terminal in def: "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. " [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "synapsed in" xsd:string -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: RO:0002130 ! has synaptic terminal in inverse_of: RO:0002113 ! has presynaptic terminal in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (\n http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some (\n http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))" [] [Typedef] id: RO:0002113 name: has presynaptic terminal in def: "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input." [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000118 "synapses in" xsd:string -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: RO:0002130 ! has synaptic terminal in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000050 some Y?)" [] [Typedef] @@ -12433,11 +12086,6 @@ id: RO:0002120 name: synapsed to def: " Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.\n " [] comment: N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part some (\n ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( \n ‘synapse ; GO:0045202’ that has_part some (\n ‘post-synaptic membrane ; GO:0045211’ that part_of some N2)))) -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 is_a: RO:0002486 ! sends output to expand_expression_to: "BFO_0000051 some (GO_0042734 that part_of some (GO_0045202 that BFO_0000051 some (GO_0045211 that BFO_0000050 some Y?)))" [] @@ -12445,103 +12093,270 @@ expand_expression_to: "BFO_0000051 some (GO_0042734 that part_of some (GO_004520 id: RO:0002130 name: has synaptic terminal in def: "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "has synapse in" xsd:string -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: overlaps ! overlaps -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "RO_0002131 some (GO_0045202 that BFO_0000050 some Y?)" [] [Typedef] id: RO:0002132 name: has fasciculating neuron projection def: "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "has fasciculating component" xsd:string -property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string -property_value: RO:0001900 RO:0001901 is_a: overlaps ! overlaps +[Typedef] +id: RO:0002134 +name: innervates +def: "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." [] +transitive_over: part_of ! part of +expand_expression_to: "RO_0002132 some (GO_0043005 that (RO_0002131 some (GO_0045202 that BFO_0000050 some Y?)))" [] + +[Typedef] +id: RO:0002150 +name: continuous with +def: "X continuous_with Y if and only if X and Y share a fiat boundary." [] +property_value: seeAlso "FMA:85972" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000004 ! independent continuant +is_symmetric: true +is_a: RO:0002323 ! mereotopologically related to + +[Typedef] +id: RO:0002158 +name: shares ancestor with +def: "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." [] +comment: VBO calls this homologous_to +is_symmetric: true +is_transitive: true +is_a: RO:0002320 ! evolutionarily related to + +[Typedef] +id: RO:0002160 +name: only in taxon +def: "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." [] +property_value: IAO:0000116 "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" xsd:string +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints +is_a: RO:0002162 ! in taxon + +[Typedef] +id: RO:0002162 +name: in taxon +def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." [] +comment: Connects a biological entity to its taxon of origin. +subset: ro-eco +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints +holds_over_chain: capable_of RO:0002162 +holds_over_chain: extends_fibers_into RO:0002162 +holds_over_chain: has_part RO:0002162 +holds_over_chain: part_of RO:0002162 +holds_over_chain: results_in_developmental_progression_of RO:0002162 +holds_over_chain: RO:0002202 RO:0002162 +holds_over_chain: RO:0002206 RO:0002162 +holds_over_chain: RO:0002225 RO:0002162 +holds_over_chain: RO:0002254 RO:0002162 +is_a: RO:0002320 ! evolutionarily related to + [Typedef] id: RO:0002163 name: spatially disjoint from def: "A is spatially_disjoint_from B if and only if they have no parts in common" [] subset: ro-eco -property_value: editor_note "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" xsd:anyURI is_a: RO:0002323 ! mereotopologically related to expand_expression_to: "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" [] +[Typedef] +id: RO:0002170 +name: connected to +def: "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" [] +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI +is_a: RO:0002323 ! mereotopologically related to + +[Typedef] +id: RO:0002176 +name: connects +def: "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." [] +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI +domain: BFO:0000004 ! independent continuant +is_a: RO:0002323 ! mereotopologically related to + +[Typedef] +id: RO:0002177 +name: attached to part of +def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000061 ! anatomical structure +is_a: RO:0002323 ! mereotopologically related to +is_a: RO:0002567 ! biomechanically related to + +[Typedef] +id: RO:0002178 +name: supplies +def: "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." [] +property_value: IAO:0000116 "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" xsd:string +is_a: RO:0002170 ! connected to + +[Typedef] +id: RO:0002179 +name: drains +def: "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." [] +property_value: IAO:0000116 "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" xsd:string +is_a: RO:0002170 ! connected to + +[Typedef] +id: RO:0002202 +name: develops from +def: "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" [] +comment: This is the transitive form of the develops from relation +domain: BFO:0000004 ! independent continuant +range: BFO:0000004 ! independent continuant +is_transitive: true +is_a: RO:0002254 ! has developmental contribution from +is_a: RO:0002258 ! developmentally preceded by +inverse_of: RO:0002203 ! develops into + +[Typedef] +id: RO:0002203 +name: develops into +def: "inverse of develops from" [] +subset: RO:0002259 +is_transitive: true +is_a: RO:0002286 ! developmentally succeeded by +is_a: RO:0002387 ! has potential to develop into +is_a: RO:0002388 ! has potential to directly develop into + [Typedef] id: RO:0002206 name: expressed in def: "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" [] -property_value: IAO:0000112 "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000002 ! continuant range: UBERON:0000465 ! material anatomical entity is_a: RO:0002330 ! genomically related to inverse_of: RO:0002292 ! expresses -transitive_over: part_of ! part_of +transitive_over: part_of ! part of + +[Typedef] +id: RO:0002207 +name: directly develops from +def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] +comment: TODO - add child relations from DOS +synonym: "has developmental precursor" EXACT [] +is_a: RO:0002202 ! develops from +inverse_of: RO:0002210 ! directly develops into [Typedef] id: RO:0002210 name: directly develops into def: "inverse of directly develops from" [] subset: RO:0002259 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000118 "developmental precursor of" xsd:string -is_a: develops_into ! develops into +is_a: RO:0002203 ! develops into + +[Typedef] +id: RO:0002219 +name: surrounded by +def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" [] +is_a: adjacent_to ! adjacent to +inverse_of: RO:0002221 ! surrounds + +[Typedef] +id: RO:0002221 +name: surrounds +def: "inverse of surrounded by" [] +subset: RO:0002259 +is_a: adjacent_to ! adjacent to [Typedef] id: RO:0002222 name: temporally related to comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. subset: ro-eco -property_value: http://purl.org/dc/terms/source "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" xsd:anyURI -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent +[Typedef] +id: RO:0002223 +name: starts +def: "inverse of starts with" [] +subset: ro-eco +is_a: part_of ! part of +is_a: RO:0002222 ! temporally related to +inverse_of: starts_with ! starts with + +[Typedef] +id: RO:0002225 +name: develops from part of +def: "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" [] +holds_over_chain: RO:0002207 part_of +is_a: RO:0002202 ! develops from + +[Typedef] +id: RO:0002226 +name: develops in +def: "x develops_in y if x is located in y whilst x is developing" [] +domain: UBERON:0001062 ! anatomical entity +holds_over_chain: RO:0002207 RO:0001025 +is_a: RO:0002258 ! developmentally preceded by + +[Typedef] +id: RO:0002229 +name: ends +def: "inverse of ends with" [] +subset: ro-eco +is_a: part_of ! part of +is_a: RO:0002222 ! temporally related to +inverse_of: ends_with ! ends with + +[Typedef] +id: RO:0002252 +name: connecting branch of +def: "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." [] +property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 +is_a: RO:0002170 ! connected to +is_a: RO:0002375 ! in branching relationship with +inverse_of: RO:0002253 ! has connecting branch + [Typedef] id: RO:0002253 name: has connecting branch def: "inverse of connecting branch of" [] subset: RO:0002259 -property_value: RO:0004036 BFO:0000051 is_a: RO:0002375 ! in branching relationship with +[Typedef] +id: RO:0002254 +name: has developmental contribution from +def: "x has developmental contribution from y iff x has some part z such that z develops from y" [] +domain: UBERON:0001062 ! anatomical entity +range: UBERON:0001062 ! anatomical entity +holds_over_chain: has_part RO:0002202 +is_a: RO:0002258 ! developmentally preceded by +inverse_of: RO:0002255 ! developmentally contributes to + [Typedef] id: RO:0002255 name: developmentally contributes to def: "inverse of has developmental contribution from" [] subset: RO:0002259 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -holds_over_chain: develops_into part_of -is_a: has_potential_to_developmentally_contribute_to ! has potential to developmentally contribute to +holds_over_chain: RO:0002203 part_of is_a: RO:0002286 ! developmentally succeeded by +is_a: RO:0002385 ! has potential to developmentally contribute to + +[Typedef] +id: RO:0002256 +name: developmentally induced by +def: "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" [] +domain: UBERON:0000465 ! material anatomical entity +range: UBERON:0000465 ! material anatomical entity +is_a: RO:0002258 ! developmentally preceded by +inverse_of: RO:0002257 ! developmentally induces [Typedef] id: RO:0002257 name: developmentally induces def: "Inverse of developmentally induced by" [] -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002286 ! developmentally succeeded by is_a: RO:0002386 ! has potential to developmentally induce @@ -12550,10 +12365,7 @@ id: RO:0002258 name: developmentally preceded by def: "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p" [] comment: This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from -property_value: editor_note "false" xsd:boolean -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string +property_value: IAO:0000116 "false" xsd:boolean domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant is_a: RO:0002324 ! developmentally related to @@ -12564,7 +12376,6 @@ id: RO:0002263 name: acts upstream of def: "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: IAO:0000112 "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." xsd:string property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of holds_over_chain: RO:0002327 causally_upstream_of is_a: RO:0002264 ! acts upstream of or within @@ -12575,25 +12386,26 @@ name: acts upstream of or within def: "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term synonym: "affects" RELATED [] -property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within" xsd:anyURI holds_over_chain: RO:0002327 causally_upstream_of_or_within is_a: RO:0002500 ! causal agent in process +[Typedef] +id: RO:0002285 +name: developmentally replaces +def: "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" [] +property_value: IAO:0000116 "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" xsd:string +is_a: RO:0002258 ! developmentally preceded by + [Typedef] id: RO:0002286 name: developmentally succeeded by def: "Inverse of developmentally preceded by" [] -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002384 ! has developmental potential involving [Typedef] id: RO:0002287 name: part of developmental precursor of -property_value: IAO:0000112 "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: part_of RO:0002210 is_a: RO:0002286 ! developmentally succeeded by @@ -12601,80 +12413,58 @@ is_a: RO:0002286 ! developmentally succeeded by id: RO:0002292 name: expresses def: "y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." [] -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002330 ! genomically related to [Typedef] id: RO:0002314 name: characteristic of part of def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." [] -property_value: editor_note "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "inheres in part of" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: RO:0000052 part_of {RO:0002582="true"} is_a: RO:0002502 ! depends on -transitive_over: part_of ! part_of +transitive_over: part_of ! part of [Typedef] id: RO:0002320 name: evolutionarily related to def: "A relationship that holds via some environmental process" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." xsd:string [Typedef] id: RO:0002323 name: mereotopologically related to def: "A mereological relationship or a topological relationship" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string -property_value: RO:0001900 RO:0001901 [Typedef] id: RO:0002324 name: developmentally related to def: "A relationship that holds between entities participating in some developmental process (GO:0032502)" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" xsd:string [Typedef] id: RO:0002327 name: enables def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "catalyzes" xsd:string -property_value: IAO:0000118 "executes" xsd:string -property_value: IAO:0000118 "has" xsd:string -property_value: IAO:0000118 "is catalyzing" xsd:string -property_value: IAO:0000118 "is executing" xsd:string -property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string property_value: seeAlso "https://wiki.geneontology.org/Enables" xsd:anyURI is_a: capable_of ! capable of inverse_of: RO:0002333 ! enabled by transitive_over: has_part ! has part transitive_over: RO:0002017 ! has component activity +[Typedef] +id: RO:0002328 +name: functionally related to +def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] + [Typedef] id: RO:0002329 name: part of structure that is capable of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "false" xsd:boolean -holds_over_chain: part_of capable_of {RO:0002581="true"} -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002330 name: genomically related to def: "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant @@ -12682,31 +12472,25 @@ range: BFO:0000002 ! continuant id: RO:0002331 name: involved in def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "actively involved in" xsd:string -property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Involved_in" xsd:anyURI holds_over_chain: RO:0002327 part_of is_a: participates_in ! participates in is_a: RO:0002431 ! involved in or involved in regulation of -transitive_over: part_of ! part_of +transitive_over: part_of ! part of [Typedef] id: RO:0002333 name: enabled by def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso "https://wiki.geneontology.org/Enabled_by" xsd:anyURI -is_a: functionally_related_to ! functionally related to is_a: has_participant ! has participant +is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002337 name: related via localization to def: "A relationship that holds via some process of localization" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is a grouping relation." xsd:string domain: BFO:0000015 ! process range: BFO:0000002 ! continuant @@ -12714,84 +12498,134 @@ range: BFO:0000002 ! continuant id: RO:0002350 name: member of def: "is member of is a mereological relation between a item and a collection." [] -property_value: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string -property_value: IAO:0000118 "is member of" xsd:string -property_value: IAO:0000118 "member part of" xsd:string -property_value: IAO:0000119 "SIO" xsd:string -property_value: RO:0001900 RO:0001901 -is_a: part_of ! part_of -inverse_of: has_member ! has member +is_a: part_of ! part of +inverse_of: RO:0002351 ! has member + +[Typedef] +id: RO:0002351 +name: has member +def: "has member is a mereological relation between a collection and an item." [] +is_a: has_part ! has part + +[Typedef] +id: RO:0002352 +name: input of +def: "inverse of has input" [] +subset: ro-eco +subset: RO:0002259 +is_a: participates_in ! participates in +is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002354 name: formed as result of -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: output_of ! output of [Typedef] id: RO:0002360 name: has dendrite location -property_value: http://purl.org/dc/terms/source "http://neurolex.org/wiki/Property:DendriteLocation" xsd:anyURI -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps [Typedef] -id: RO:0002375 -name: in branching relationship with -def: "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" xsd:string -property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string -property_value: RO:0004036 BFO:0000050 -property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png -property_value: seeAlso "https://github.com/obophenotype/uberon/issues/170" xsd:anyURI -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: RO:0002323 ! mereotopologically related to +id: RO:0002371 +name: attached to +def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] +subset: ro-eco +is_symmetric: true +is_a: RO:0002170 ! connected to +is_a: RO:0002177 ! attached to part of [Typedef] -id: RO:0002379 -name: spatially coextensive with -def: "x spatially_coextensive_with y if and inly if x and y have the same location" [] -property_value: IAO:0000112 "A lump of clay and a statue" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" xsd:string +id: RO:0002372 +name: has muscle origin +def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] +property_value: seeAlso http://dbpedia.org/property/origin +domain: UBERON:0000061 {comment="We need to import uberon muscle to create a stricter domain constraint"} ! anatomical structure +is_a: RO:0002371 ! attached to +is_a: RO:0002567 ! biomechanically related to + +[Typedef] +id: RO:0002373 +name: has muscle insertion +def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] +property_value: seeAlso http://dbpedia.org/property/insertion +domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} ! anatomical structure +is_a: RO:0002371 ! attached to +is_a: RO:0002567 ! biomechanically related to + +[Typedef] +id: RO:0002375 +name: in branching relationship with +def: "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." [] +property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png +property_value: seeAlso "https://github.com/obophenotype/uberon/issues/170" xsd:anyURI +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: RO:0002323 ! mereotopologically related to + +[Typedef] +id: RO:0002376 +name: tributary of +def: "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." [] +subset: ro-eco +property_value: seeAlso http://dbpedia.org/ontology/drainsTo +property_value: seeAlso "http://en.wikipedia.org/wiki/Tributary" xsd:anyURI +is_a: RO:0002170 ! connected to +is_a: RO:0002375 ! in branching relationship with + +[Typedef] +id: RO:0002379 +name: spatially coextensive with +def: "x spatially_coextensive_with y if and inly if x and y have the same location" [] is_a: overlaps ! overlaps +[Typedef] +id: RO:0002380 +name: branching part of +def: "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" [] +subset: ro-eco +property_value: seeAlso "FMA:85994" xsd:string +property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 +is_a: part_of ! part of +is_a: RO:0002375 ! in branching relationship with +inverse_of: RO:0002569 ! has branching part + [Typedef] id: RO:0002384 name: has developmental potential involving def: "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: UBERON:0001062 ! anatomical entity range: UBERON:0001062 ! anatomical entity is_a: RO:0002324 ! developmentally related to +[Typedef] +id: RO:0002385 +name: has potential to developmentally contribute to +def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] +is_a: RO:0002384 ! has developmental potential involving + [Typedef] id: RO:0002386 name: has potential to developmentally induce def: "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002384 ! has developmental potential involving + +[Typedef] +id: RO:0002387 +name: has potential to develop into +def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] is_a: RO:0002384 ! has developmental potential involving [Typedef] id: RO:0002388 name: has potential to directly develop into def: "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: has_potential_to_develop_into ! has potential to develop into +is_a: RO:0002387 ! has potential to develop into [Typedef] id: RO:0002407 name: indirectly positively regulates def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "indirectly activates" xsd:string -property_value: RO:0002579 RO:0002213 property_value: seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates" xsd:anyURI holds_over_chain: directly_positively_regulates directly_positively_regulates holds_over_chain: directly_positively_regulates RO:0002407 @@ -12805,9 +12639,6 @@ transitive_over: directly_positively_regulates ! directly positively regulates id: RO:0002409 name: indirectly negatively regulates def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "indirectly inhibits" xsd:string -property_value: RO:0002579 RO:0002212 property_value: seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates" xsd:anyURI holds_over_chain: directly_negatively_regulates directly_negatively_regulates holds_over_chain: directly_negatively_regulates RO:0002409 @@ -12820,15 +12651,12 @@ transitive_over: directly_negatively_regulates ! directly negatively regulates id: RO:0002410 name: causally related to def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] -property_value: editor_note "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string [Typedef] id: RO:0002428 name: involved in regulation of def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002327 regulates holds_over_chain: RO:0002331 regulates is_a: RO:0002263 ! acts upstream of @@ -12838,8 +12666,6 @@ is_a: RO:0002431 ! involved in or involved in regulation of id: RO:0002429 name: involved in positive regulation of def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0004049 RO:0002428 holds_over_chain: RO:0002327 positively_regulates holds_over_chain: RO:0002331 positively_regulates is_a: RO:0002428 ! involved in regulation of @@ -12848,7 +12674,6 @@ is_a: RO:0002428 ! involved in regulation of id: RO:0002430 name: involved in negative regulation of def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002428 holds_over_chain: RO:0002327 negatively_regulates holds_over_chain: RO:0002331 negatively_regulates @@ -12858,11 +12683,9 @@ is_a: RO:0002428 ! involved in regulation of id: RO:0002431 name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] -property_value: editor_note "OWL does not allow defining object properties via a Union" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "involved in or reguates" xsd:string -is_a: functionally_related_to ! functionally related to +property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string is_a: RO:0002264 ! acts upstream of or within +is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process [Typedef] @@ -12870,12 +12693,14 @@ id: RO:0002432 name: is active in def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [https://orcid.org/0000-0002-6601-2165, https://orcid.org/0000-0002-7073-9172] synonym: "enables activity in" EXACT [] -property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "executes activity in" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Is_active_in" xsd:anyURI -holds_over_chain: RO:0002327 occurs_in {RO:0002581="true"} -is_a: functionally_related_to ! functionally related to +is_a: overlaps ! overlaps +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002433 +name: contributes to morphology of +def: "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." [] is_a: overlaps ! overlaps [Typedef] @@ -12884,11 +12709,8 @@ name: interacts with def: "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." [] subset: ro-eco synonym: "in pairwise interaction with" EXACT [] -property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0914" xsd:anyURI -property_value: editor_note "Considering relabeling as 'pairwise interacts with'" xsd:anyURI -property_value: editor_note "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string +property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI +property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity @@ -12898,10 +12720,6 @@ is_symmetric: true id: RO:0002436 name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] -property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0915" xsd:anyURI -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "binds" xsd:string -property_value: IAO:0000118 "molecularly binds with" xsd:string property_value: seeAlso ECO:0000353 is_symmetric: true is_a: RO:0002434 ! interacts with @@ -12909,9 +12727,7 @@ is_a: RO:0002434 ! interacts with [Typedef] id: RO:0002447 name: phosphorylates -property_value: editor_note "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string +property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string is_a: RO:0002436 ! molecularly interacts with [Typedef] @@ -12919,8 +12735,6 @@ id: RO:0002448 name: directly regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." [] synonym: "molecularly controls" EXACT [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002436 ! molecularly interacts with @@ -12931,9 +12745,6 @@ id: RO:0002449 name: directly negatively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] synonym: "molecularly decreases activity of" EXACT [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 -property_value: IAO:0000118 "directly inhibits" xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002448 ! directly regulates activity of @@ -12943,9 +12754,6 @@ id: RO:0002450 name: directly positively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] synonym: "molecularly increases activity of" EXACT [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 -property_value: IAO:0000118 "directly activates" xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002448 ! directly regulates activity of @@ -12953,61 +12761,136 @@ is_a: RO:0002448 ! directly regulates activity of [Typedef] id: RO:0002464 name: helper property (not for use in curation) -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string + +[Typedef] +id: RO:0002473 +name: composed primarily of +def: "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." [] +subset: ro-eco +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: has_part ! has part [Typedef] id: RO:0002479 name: has part that occurs in def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] subset: ro-eco -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant -holds_over_chain: has_part occurs_in {RO:0002581="true"} [Typedef] id: RO:0002481 name: is kinase activity -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002564 ! molecular interaction relation helper property [Typedef] id: RO:0002485 name: receives input from -property_value: editor_note "See notes for inverse relation" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: connected_to ! connected to +property_value: IAO:0000116 "See notes for inverse relation" xsd:string +is_a: RO:0002170 ! connected to inverse_of: RO:0002486 ! sends output to [Typedef] id: RO:0002486 name: sends output to -property_value: editor_note "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: connected_to ! connected to +property_value: IAO:0000116 "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." xsd:string +is_a: RO:0002170 ! connected to [Typedef] id: RO:0002487 name: relation between physical entity and a process or stage -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage." xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000003 ! occurrent +[Typedef] +id: RO:0002488 +name: existence starts during +def: "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." [] +is_a: RO:0002490 ! existence overlaps +is_a: RO:0002496 ! existence starts during or after +transitive_over: part_of ! part of + +[Typedef] +id: RO:0002489 +name: existence starts with +def: "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." [] +is_a: RO:0002488 ! existence starts during + [Typedef] id: RO:0002490 name: existence overlaps def: "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" [] comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002487 ! relation between physical entity and a process or stage +[Typedef] +id: RO:0002491 +name: existence starts and ends during +def: "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +synonym: "exists during" EXACT [] +is_a: RO:0002488 ! existence starts during +is_a: RO:0002492 ! existence ends during + +[Typedef] +id: RO:0002492 +name: existence ends during +def: "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +is_a: RO:0002490 ! existence overlaps +is_a: RO:0002497 ! existence ends during or before +transitive_over: part_of ! part of + +[Typedef] +id: RO:0002493 +name: existence ends with +def: "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +is_a: RO:0002492 ! existence ends during + +[Typedef] +id: RO:0002494 +name: transformation of +def: "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" [] +is_transitive: true +is_a: RO:0002202 ! develops from + +[Typedef] +id: RO:0002495 +name: immediate transformation of +def: "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" [] +is_a: RO:0002207 ! directly develops from +is_a: RO:0002494 ! transformation of + +[Typedef] +id: RO:0002496 +name: existence starts during or after +def: "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +holds_over_chain: part_of RO:0002496 +holds_over_chain: RO:0002258 RO:0002496 +is_a: RO:0002487 ! relation between physical entity and a process or stage +transitive_over: part_of ! part of +transitive_over: preceded_by ! preceded by +transitive_over: RO:0002082 ! simultaneous with + +[Typedef] +id: RO:0002497 +name: existence ends during or before +def: "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +holds_over_chain: part_of RO:0002497 +holds_over_chain: RO:0002286 RO:0002497 +is_a: RO:0002487 ! relation between physical entity and a process or stage +transitive_over: part_of ! part of +transitive_over: precedes ! precedes +transitive_over: RO:0002082 ! simultaneous with + [Typedef] id: RO:0002500 name: causal agent in process def: "A relationship between a material entity and a process where the material entity has some causal role that influences the process" [] -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_a: RO:0002595 ! causal relation between material entity and a process inverse_of: process_has_causal_agent ! process has causal agent @@ -13015,9 +12898,6 @@ inverse_of: process_has_causal_agent ! process has causal agent id: RO:0002501 name: causal relation between processes def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent is_a: RO:0002410 ! causally related to @@ -13025,33 +12905,35 @@ is_a: RO:0002410 ! causally related to [Typedef] id: RO:0002502 name: depends on -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso BFO:0000169 [Typedef] id: RO:0002506 name: causal relation between entities -property_value: editor_note "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: IAO:0000116 "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant is_a: RO:0002410 ! causally related to +[Typedef] +id: RO:0002551 +name: has skeleton +def: "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." [] +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000465 {IAO:0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} ! material anatomical entity +is_a: has_part ! has part +inverse_of: RO:0002576 ! skeleton of +is_asymmetric: true + [Typedef] id: RO:0002559 name: causally influenced by -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string is_a: RO:0002506 ! causal relation between entities inverse_of: RO:0002566 ! causally influences [Typedef] id: RO:0002563 name: interaction relation helper property -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29 property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI is_a: RO:0002464 ! helper property (not for use in curation) @@ -13059,17 +12941,12 @@ is_a: RO:0002464 ! helper property (not for use in curation) [Typedef] id: RO:0002564 name: molecular interaction relation helper property -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002563 ! interaction relation helper property [Typedef] id: RO:0002566 name: causally influences def: "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant is_a: RO:0002506 ! causal relation between entities @@ -13078,20 +12955,66 @@ is_a: RO:0002506 ! causal relation between entities id: RO:0002567 name: biomechanically related to def: "A relation that holds between elements of a musculoskeletal system or its analogs." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string domain: UBERON:0000061 ! anatomical structure range: UBERON:0000061 ! anatomical structure -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002568 +name: has muscle antagonist +def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] +is_a: RO:0002567 ! biomechanically related to + +[Typedef] +id: RO:0002569 +name: has branching part +def: "inverse of branching part of" [] +subset: ro-eco +subset: RO:0002259 +is_transitive: true +is_a: has_part ! has part +is_a: RO:0002375 ! in branching relationship with + +[Typedef] +id: RO:0002570 +name: conduit for +def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] +subset: ro-eco +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: overlaps ! overlaps + +[Typedef] +id: RO:0002571 +name: lumen of +def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] +subset: ro-eco +range: BFO:0000040 ! material entity +is_a: part_of ! part of + +[Typedef] +id: RO:0002572 +name: luminal space of +def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" [] +subset: ro-eco +domain: BFO:0000141 ! immaterial entity +is_a: RO:0002571 ! lumen of + +[Typedef] +id: RO:0002576 +name: skeleton of +def: "inverse of has skeleton" [] +subset: RO:0002259 +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000061 ! anatomical structure +is_a: part_of ! part of [Typedef] id: RO:0002584 name: has part structure that is capable of def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" [] -property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: has_part capable_of -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to is_a: RO:0002595 ! causal relation between material entity and a process [Typedef] @@ -13104,9 +13027,7 @@ is_a: has_input ! has input id: RO:0002595 name: causal relation between material entity and a process def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." [] -property_value: editor_note "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000040 ! material entity range: BFO:0000015 ! process is_a: RO:0002410 ! causally related to @@ -13115,8 +13036,6 @@ is_a: RO:0002410 ! causally related to id: RO:0002596 name: capable of regulating def: "Holds between c and p if and only if c is capable of some activity a, and a regulates p." [] -property_value: IAO:0000112 "pyrethroid -> growth" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations holds_over_chain: capable_of regulates is_a: RO:0002500 ! causal agent in process @@ -13124,7 +13043,6 @@ is_a: RO:0002500 ! causal agent in process id: RO:0002597 name: capable of negatively regulating def: "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." [] -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations holds_over_chain: capable_of negatively_regulates is_a: RO:0002596 ! capable of regulating @@ -13132,8 +13050,6 @@ is_a: RO:0002596 ! capable of regulating id: RO:0002598 name: capable of positively regulating def: "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." [] -property_value: IAO:0000112 "renin -> arteriolar smooth muscle contraction" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations holds_over_chain: capable_of positively_regulates is_a: RO:0002596 ! capable of regulating @@ -13142,7 +13058,7 @@ id: RO:0004031 name: enables subfunction def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] holds_over_chain: RO:0002327 has_part -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z @@ -13150,7 +13066,6 @@ creation_date: 2018-01-25T23:20:13Z id: RO:0004032 name: acts upstream of or within, positive effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: RO:0004049 RO:0002264 property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0004047 is_a: RO:0002264 ! acts upstream of or within @@ -13173,7 +13088,6 @@ id: RO:0004034 name: acts upstream of, positive effect def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: RO:0004049 RO:0002263 property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 causally_upstream_of,_positive_effect is_a: RO:0002263 ! acts upstream of @@ -13206,7 +13120,6 @@ creation_date: 2018-03-13T23:55:05Z [Typedef] id: RO:0004047 name: causally upstream of or within, positive effect -property_value: RO:0004049 RO:0002418 property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect is_a: causally_upstream_of_or_within ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 @@ -13216,7 +13129,6 @@ creation_date: 2018-03-13T23:55:19Z id: RO:0011002 name: regulates activity of def: "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." [] -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002566 ! causally influences @@ -13271,7 +13183,7 @@ name: has synaptic IO in region def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region." [] synonym: "has synaptic input or output in" EXACT [] is_a: RO:0002130 ! has synaptic terminal in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:26:52Z @@ -13284,7 +13196,7 @@ synonym: "has sensory terminal in" EXACT [] synonym: "has sensory terminal location" EXACT [] domain: CL:0000101 ! sensory neuron is_a: RO:0002360 ! has dendrite location -transitive_over: part_of ! part_of +transitive_over: part_of ! part of created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-20T12:10:09Z @@ -13327,9 +13239,8 @@ comment: Example: a spherical object has the quality of being spherical, and the id: RO:0015015 name: has high plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: dc-contributor https://orcid.org/0000-0003-1617-8244 -property_value: dc-contributor https://orcid.org/0000-0003-1940-6740 -property_value: IAO:0000112 "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part @@ -13337,9 +13248,8 @@ is_a: RO:0002104 ! has plasma membrane part id: RO:0015016 name: has low plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: dc-contributor https://orcid.org/0000-0003-1617-8244 -property_value: dc-contributor https://orcid.org/0000-0003-1940-6740 -property_value: IAO:0000112 "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part @@ -13348,11 +13258,6 @@ id: RO:0017001 name: device utilizes material def: "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." [] synonym: "utilizes" BROAD [] -property_value: IAO:0000112 "A diagnostic testing device utilizes a specimen." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 -property_value: IAO:0000117 https://orcid.org/0000-0003-2620-0345 -property_value: IAO:0000232 "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." xsd:string -property_value: IAO:0000232 "See github ticket https://github.com/oborel/obo-relations/issues/497" xsd:string holds_over_chain: capable_of has_input creation_date: 2021-11-08T12:00:00Z @@ -13373,65 +13278,24 @@ creation_date: 2020-06-08T17:21:33Z id: adjacent_to name: adjacent to namespace: external -namespace: uberon def: "x adjacent to y if and only if x and y share a boundary." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002220 -property_value: editor_note "This relation acts as a join point with BSPO" xsd:string -property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} -property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string -property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string -property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000004 ! independent continuant is_a: RO:0002163 ! spatially disjoint from -[Typedef] -id: anterior_to -name: anterior to -namespace: uberon -xref: BSPO:0000096 - [Typedef] id: anteriorly_connected_to name: anteriorly connected to namespace: uberon def: "x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] -is_a: connected_to ! connected to -is_a: posterior_to ! posterior to +is_a: RO:0002170 ! connected to is_a: transitively_anteriorly_connected_to ! transitively anteriorly connected to -[Typedef] -id: attaches_to -name: attached to -namespace: uberon -def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] -subset: ro-eco -xref: RO:0002371 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000589 "attached to (anatomical structure to anatomical structure)" xsd:string -is_symmetric: true -is_a: attaches_to_part_of ! attached to part of -is_a: connected_to ! connected to - -[Typedef] -id: attaches_to_part_of -name: attached to part of -namespace: uberon -def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] -xref: RO:0002177 -property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string -domain: UBERON:0000061 ! anatomical structure -range: UBERON:0000061 ! anatomical structure -holds_over_chain: attaches_to part_of {RO:0002582="true"} -is_a: RO:0002323 ! mereotopologically related to -is_a: RO:0002567 ! biomechanically related to - [Typedef] id: bearer_of name: bearer of @@ -13439,13 +13303,7 @@ name: has characteristic namespace: external def: "Inverse of characteristic_of" [] xref: RO:0000053 -property_value: editor_note "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string -property_value: IAO:0000111 "bearer of" xsd:string -property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string -property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string -property_value: IAO:0000118 "bearer_of" xsd:string -property_value: IAO:0000118 "is bearer of" xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string range: BFO:0000020 ! specifically dependent continuant is_inverse_functional: true @@ -13453,45 +13311,20 @@ is_inverse_functional: true id: bounding_layer_of name: bounding layer of namespace: external -namespace: uberon def: "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000" [] comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. subset: ro-eco xref: RO:0002007 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 range: BFO:0000040 ! material entity -is_a: part_of ! part_of - -[Typedef] -id: branching_part_of -name: branching part of -namespace: uberon -def: "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" [] -subset: ro-eco -xref: RO:0002380 -property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso "FMA:85994" xsd:string -property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 -is_a: part_of ! part_of -is_a: RO:0002375 ! in branching relationship with -inverse_of: has_branching_part ! has branching part +is_a: part_of ! part of [Typedef] id: capable_of name: capable of namespace: external -namespace: uberon def: "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " [] subset: ro-eco xref: RO:0002215 -property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string -property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "has function realized in" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 -property_value: IAO:0000232 "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000015 ! process is_a: capable_of_part_of ! capable of part of @@ -13500,14 +13333,10 @@ is_a: capable_of_part_of ! capable of part of id: capable_of_part_of name: capable of part of namespace: external -namespace: uberon def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] xref: RO:0002216 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "has function in" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: capable_of part_of {RO:0002582="true"} -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process [Typedef] @@ -13516,8 +13345,6 @@ name: causally downstream of namespace: external def: "inverse of upstream of" [] xref: RO:0002404 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of_or_within ! causally downstream of or within is_a: preceded_by ! preceded by inverse_of: causally_upstream_of ! causally upstream of @@ -13529,8 +13356,6 @@ namespace: external def: "inverse of causally upstream of or within" [] subset: RO:0002259 xref: RO:0002427 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_transitive: true is_a: RO:0002501 ! causal relation between processes @@ -13542,7 +13367,6 @@ def: "p is causally upstream of q iff p is causally related to q, the end of p p subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002411 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within is_a: precedes ! precedes @@ -13555,7 +13379,6 @@ def: "p is causally upstream of, negative effect q iff p is casually upstream of subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 -property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_negative_effect is_a: causally_upstream_of ! causally upstream of @@ -13570,8 +13393,6 @@ comment: holds between x and y if and only if x is causally upstream of y and th subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002304 -property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 -property_value: RO:0004049 RO:0002411 property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_positive_effect is_a: causally_upstream_of ! causally upstream of is_a: RO:0004047 ! causally upstream of or within, positive effect @@ -13583,9 +13404,7 @@ namespace: external def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] synonym: "affects" RELATED [] xref: RO:0002418 -property_value: editor_note "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "influences (processual)" xsd:string +property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string is_transitive: true is_a: RO:0002501 ! causal relation between processes inverse_of: causally_downstream_of_or_within ! causally downstream of or within @@ -13595,510 +13414,81 @@ id: channel_for name: channel for namespace: uberon synonym: "carries" BROAD [] -domain: UBERON:0004111 ! anatomical conduit -range: UBERON:0000463 ! organism substance [Typedef] id: channels_from name: channels_from namespace: uberon -is_transitive: true [Typedef] id: channels_into name: channels_into namespace: uberon -is_transitive: true [Typedef] -id: composed_primarily_of -name: composed primarily of -namespace: uberon -def: "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." [] -subset: ro-eco -xref: RO:0002473 -property_value: IAO:0000112 "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: RO:0001900 RO:0001901 -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: has_part ! has part +id: directly_negatively_regulates +name: directly negatively regulates +namespace: external +def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0002630 +property_value: RO:0004050 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates" xsd:anyURI +is_a: directly_regulates ! directly regulates +is_a: negatively_regulates ! negatively regulates [Typedef] -id: conduit_for -name: conduit for -namespace: uberon -def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] -subset: ro-eco -xref: RO:0002570 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "UBERON:cjm" xsd:string -property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: overlaps ! overlaps +id: directly_positively_regulates +name: directly positively regulates +namespace: external +def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0002629 +property_value: seeAlso "https://wiki.geneontology.org/Directly_positively_regulates" xsd:anyURI +is_a: directly_regulates ! directly regulates +is_a: positively_regulates ! positively regulates [Typedef] -id: connected_to -name: connected to -namespace: uberon -def: "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" [] -xref: RO:0002170 -property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI -property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI -is_a: RO:0002323 ! mereotopologically related to +id: directly_regulates +name: directly regulates +namespace: external +def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0002578 +is_a: immediately_causally_upstream_of ! immediately causally upstream of +is_a: regulates ! regulates [Typedef] -id: connecting_branch_of -name: connecting branch of -namespace: uberon -def: "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." [] -xref: RO:0002252 -property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." xsd:string -property_value: RO:0004036 BFO:0000050 -property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 -is_a: connected_to ! connected to -is_a: RO:0002375 ! in branching relationship with -inverse_of: RO:0002253 ! has connecting branch - -[Typedef] -id: connects -name: connects -namespace: uberon -def: "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." [] -xref: RO:0002176 -property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string -property_value: IAO:0000112 "The M8 connects Glasgow and Edinburgh" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI -property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI -domain: BFO:0000004 ! independent continuant -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: contains_process -name: contains process -namespace: uberon -def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] -comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant -xref: BFO:0000067 -property_value: IAO:0000111 "site of" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - -[Typedef] -id: continuous_with -name: continuous with -namespace: uberon -def: "X continuous_with Y if and only if X and Y share a fiat boundary." [] -xref: RO:0002150 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "connected to" xsd:string -property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string -property_value: RO:0001900 RO:0001901 -property_value: seeAlso "FMA:85972" xsd:string -domain: BFO:0000004 ! independent continuant -range: BFO:0000004 ! independent continuant -is_symmetric: true -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: contributes_to_morphology_of -name: contributes to morphology of -namespace: uberon -def: "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." [] -xref: RO:0002433 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: overlaps ! overlaps - -[Typedef] -id: dc-contributor -name: contributor -namespace: uberon -xref: http://purl.org/dc/terms/contributor -is_metadata_tag: true - -[Typedef] -id: dc-creator -name: creator -namespace: uberon -xref: http://purl.org/dc/elements/1.1/creator -is_metadata_tag: true - -[Typedef] -id: dc-description -name: description -namespace: uberon -xref: http://purl.org/dc/elements/1.1/description -is_metadata_tag: true - -[Typedef] -id: dc-title -name: title -namespace: uberon -xref: http://purl.org/dc/elements/1.1/title -is_metadata_tag: true - -[Typedef] -id: dcterms-date -name: date -namespace: uberon -xref: http://purl.org/dc/terms/date -is_metadata_tag: true - -[Typedef] -id: dcterms-license -name: license -namespace: uberon -xref: http://purl.org/dc/terms/license -is_metadata_tag: true - -[Typedef] -id: deep_to -name: deep to -namespace: uberon -xref: BSPO:0000107 - -[Typedef] -id: depiction -name: depiction -namespace: uberon -xref: http://xmlns.com/foaf/0.1/depiction -is_metadata_tag: true - -[Typedef] -id: developmentally_induced_by -name: developmentally induced by -namespace: uberon -def: "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" [] -xref: RO:0002256 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "induced by" xsd:string -property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string -property_value: IAO:0000119 "GO:0001759" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 -property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string -domain: UBERON:0000465 ! material anatomical entity -range: UBERON:0000465 ! material anatomical entity -is_a: RO:0002258 ! developmentally preceded by -inverse_of: RO:0002257 ! developmentally induces - -[Typedef] -id: developmentally_replaces -name: developmentally replaces -namespace: uberon -def: "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" [] -xref: RO:0002285 -property_value: editor_note "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "replaces" xsd:string -is_a: RO:0002258 ! developmentally preceded by - -[Typedef] -id: develops_from -name: develops from -namespace: uberon -def: "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" [] -comment: This is the transitive form of the develops from relation -xref: RO:0002202 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 -domain: BFO:0000004 ! independent continuant -range: BFO:0000004 ! independent continuant -is_transitive: true -is_a: has_developmental_contribution_from ! has developmental contribution from -is_a: RO:0002258 ! developmentally preceded by -inverse_of: develops_into ! develops into - -[Typedef] -id: develops_from_part_of -name: develops from part of -namespace: uberon -def: "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" [] -xref: RO:0002225 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -holds_over_chain: directly_develops_from part_of -is_a: develops_from ! develops from - -[Typedef] -id: develops_in -name: develops in -namespace: uberon -def: "x develops_in y if x is located in y whilst x is developing" [] -xref: RO:0002226 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "EHDAA2" xsd:string -property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string -domain: UBERON:0001062 ! anatomical entity -holds_over_chain: directly_develops_from located_in -is_a: RO:0002258 ! developmentally preceded by - -[Typedef] -id: develops_into -name: develops into -namespace: uberon -def: "inverse of develops from" [] -subset: RO:0002259 -xref: RO:0002203 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 -is_transitive: true -is_a: has_potential_to_develop_into ! has potential to develop into -is_a: RO:0002286 ! developmentally succeeded by -is_a: RO:0002388 ! has potential to directly develop into - -[Typedef] -id: directly_develops_from -name: directly develops from -namespace: uberon -def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] -comment: TODO - add child relations from DOS -synonym: "has developmental precursor" EXACT [] -xref: RO:0002207 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000119 "FBbt" xsd:string -property_value: RO:0002575 RO:0002202 -is_a: develops_from ! develops from -inverse_of: RO:0002210 ! directly develops into - -[Typedef] -id: directly_negatively_regulates -name: directly negatively regulates -namespace: external -def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -xref: RO:0002630 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string -property_value: RO:0004050 RO:0002578 -property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates" xsd:anyURI -is_a: directly_regulates ! directly regulates -is_a: negatively_regulates ! negatively regulates - -[Typedef] -id: directly_positively_regulates -name: directly positively regulates -namespace: external -def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -xref: RO:0002629 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string -property_value: RO:0004049 RO:0002578 -property_value: seeAlso "https://wiki.geneontology.org/Directly_positively_regulates" xsd:anyURI -is_a: directly_regulates ! directly regulates -is_a: positively_regulates ! positively regulates - -[Typedef] -id: directly_regulates -name: directly regulates -namespace: external -def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -xref: RO:0002578 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly regulates (processual)" xsd:string -property_value: RO:0002575 RO:0002211 -is_a: immediately_causally_upstream_of ! immediately causally upstream of -is_a: regulates ! regulates - -[Typedef] -id: distal_to -name: distal to -namespace: uberon -xref: BSPO:0000097 - -[Typedef] -id: distally_connected_to -name: distally connected to +id: distally_connected_to +name: distally connected to namespace: uberon def: "x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] -is_a: connected_to ! connected to -is_a: proximal_to ! proximal to +is_a: RO:0002170 ! connected to is_a: transitively_distally_connected_to ! transitively distally connected to -inverse_of: proximally_connected_to ! proximally connected to - -[Typedef] -id: distalmost_part_of -name: distalmost part of -namespace: uberon -xref: BSPO:0001108 - -[Typedef] -id: dorsal_to -name: dorsal to -namespace: uberon -xref: BSPO:0000098 - -[Typedef] -id: drains -name: drains -namespace: uberon -def: "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." [] -xref: RO:0002179 -property_value: editor_note "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 -is_a: connected_to ! connected to - -[Typedef] -id: editor_note -name: editor note -namespace: uberon -def: "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology." [] -xref: IAO:0000116 -property_value: IAO:0000111 "editor note" xsd:string -property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000117 "PERSON:Daniel Schober" xsd:string -property_value: IAO:0000119 "GROUP:OBI:" xsd:string -is_metadata_tag: true - -[Typedef] -id: ends -name: ends -namespace: uberon -def: "inverse of ends with" [] -subset: ro-eco -xref: RO:0002229 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: part_of ! part_of -is_a: RO:0002222 ! temporally related to -inverse_of: ends_with ! ends with [Typedef] id: ends_with name: ends with namespace: external -namespace: uberon def: "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002230 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "finished by" xsd:string is_transitive: true is_a: has_part ! has part is_a: RO:0002222 ! temporally related to -[Typedef] -id: existence_ends_during -name: existence ends during -namespace: uberon -def: "Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely." [https://orcid.org/0000-0002-6601-2165] -def: "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -synonym: "ceases_to_exist_during" EXACT [] -xref: RO:0002492 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_ends_during_or_before ! existence ends during or before -is_a: RO:0002490 ! existence overlaps -transitive_over: part_of ! part_of - -[Typedef] -id: existence_ends_during_or_before -name: existence ends during or before -namespace: uberon -def: "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -xref: RO:0002497 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -holds_over_chain: part_of existence_ends_during_or_before -holds_over_chain: RO:0002286 existence_ends_during_or_before -is_a: RO:0002487 ! relation between physical entity and a process or stage -transitive_over: part_of ! part_of -transitive_over: precedes ! precedes -transitive_over: simultaneous_with ! simultaneous with - -[Typedef] -id: existence_ends_with -name: existence ends with -namespace: uberon -def: "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -xref: RO:0002493 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_ends_during ! existence ends during - -[Typedef] -id: existence_starts_and_ends_during -name: existence starts and ends during -namespace: uberon -def: "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -synonym: "exists during" EXACT [] -xref: RO:0002491 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_ends_during ! existence ends during -is_a: existence_starts_during ! existence starts during - -[Typedef] -id: existence_starts_during -name: existence starts during -namespace: uberon -def: "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." [] -xref: RO:0002488 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_starts_during_or_after ! existence starts during or after -is_a: RO:0002490 ! existence overlaps -transitive_over: part_of ! part_of - -[Typedef] -id: existence_starts_during_or_after -name: existence starts during or after -namespace: uberon -def: "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -xref: RO:0002496 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -holds_over_chain: part_of existence_starts_during_or_after -holds_over_chain: RO:0002258 existence_starts_during_or_after -is_a: RO:0002487 ! relation between physical entity and a process or stage -transitive_over: part_of ! part_of -transitive_over: preceded_by ! preceded by -transitive_over: simultaneous_with ! simultaneous with - -[Typedef] -id: existence_starts_with -name: existence starts with -namespace: uberon -def: "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." [] -xref: RO:0002489 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_starts_during ! existence starts during - [Typedef] id: extends_fibers_into name: extends_fibers_into namespace: uberon def: "X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y" [https://orcid.org/0000-0002-7073-9172] -holds_over_chain: RO:0002100 RO:0013001 -is_symmetric: true -is_a: connected_to ! connected to +is_a: RO:0002170 ! connected to [Typedef] id: filtered_through @@ -14107,75 +13497,17 @@ namespace: uberon def: "Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity." [] comment: Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed -[Typedef] -id: functionally_related_to -name: functionally related to -namespace: uberon -def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] -xref: RO:0002328 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string - -[Typedef] -id: has_boundary -name: has 2D boundary -namespace: uberon -def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] -xref: RO:0002002 -property_value: editor_note "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string -property_value: editor_note "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string -property_value: IAO:0000112 "my body has 2D boundary the surface of my skin" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "has boundary" xsd:string -property_value: IAO:0000118 "has_2D_boundary" xsd:string -property_value: RO:0001900 RO:0001901 -domain: BFO:0000040 ! material entity -range: BFO:0000141 ! immaterial entity -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: has_branching_part -name: has branching part -namespace: uberon -def: "inverse of branching part of" [] -subset: ro-eco -subset: RO:0002259 -xref: RO:0002569 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_transitive: true -is_a: has_part ! has part -is_a: RO:0002375 ! in branching relationship with - [Typedef] id: has_component name: has component namespace: external -namespace: uberon def: "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] subset: ro-eco xref: RO:0002180 -property_value: editor_note "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency is_a: has_part ! has part -[Typedef] -id: has_developmental_contribution_from -name: has developmental contribution from -namespace: uberon -def: "x has developmental contribution from y iff x has some part z such that z develops from y" [] -xref: RO:0002254 -property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: UBERON:0001062 ! anatomical entity -range: UBERON:0001062 ! anatomical entity -holds_over_chain: has_part develops_from -is_a: RO:0002258 ! developmentally preceded by -inverse_of: RO:0002255 ! developmentally contributes to - [Typedef] id: has_end_location name: has end location @@ -14183,9 +13515,6 @@ namespace: external def: "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" [] subset: ro-eco xref: RO:0002232 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "ends with process that occurs in" xsd:string domain: BFO:0000015 ! process range: BFO:0000004 ! independent continuant holds_over_chain: ends_with occurs_in @@ -14209,14 +13538,11 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002233 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "consumes" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Has_input" xsd:anyURI domain: BFO:0000015 ! process holds_over_chain: starts_with has_input is_a: has_participant ! has participant -inverse_of: input_of ! input of +inverse_of: RO:0002352 ! input of [Typedef] id: has_low_plasma_membrane_amount @@ -14226,52 +13552,6 @@ property_value: term_tracker_item https://github.com/obophenotype/cell-ontology/ is_obsolete: true replaced_by: RO:0015016 -[Typedef] -id: has_member -name: has member -namespace: uberon -def: "has member is a mereological relation between a collection and an item." [] -xref: RO:0002351 -property_value: IAO:0000119 "SIO" xsd:string -property_value: RO:0001900 RO:0001901 -is_a: has_part ! has part - -[Typedef] -id: has_muscle_antagonist -name: has muscle antagonist -namespace: uberon -def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] -xref: RO:0002568 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "Wikipedia:Antagonist_(muscle)" xsd:string -is_a: RO:0002567 ! biomechanically related to - -[Typedef] -id: has_muscle_insertion -name: has muscle insertion -namespace: uberon -def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] -xref: RO:0002373 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string -property_value: seeAlso http://dbpedia.org/property/insertion -domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} ! anatomical structure -is_a: attaches_to ! attached to -is_a: RO:0002567 ! biomechanically related to - -[Typedef] -id: has_muscle_origin -name: has muscle origin -namespace: uberon -def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] -xref: RO:0002372 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string -property_value: seeAlso http://dbpedia.org/property/origin -domain: UBERON:0000061 {comment="We need to import uberon muscle to create a stricter domain constraint"} ! anatomical structure -is_a: attaches_to ! attached to -is_a: RO:0002567 ! biomechanically related to - [Typedef] id: has_negative_regulatory_component_activity name: has negative regulatory component activity @@ -14289,13 +13569,9 @@ id: has_ontology_root_term name: has ontology root term name: preferred_root namespace: external -namespace: uberon def: "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root." [] xref: IAO:0000700 -property_value: IAO:0000111 "has ontology root term" xsd:string -property_value: IAO:0000117 "Nicolas Matentzoglu" xsd:string is_metadata_tag: true -is_class_level: true [Typedef] id: has_output @@ -14307,9 +13583,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002234 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "produces" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Has_output" xsd:anyURI holds_over_chain: ends_with has_output is_a: has_participant ! has participant @@ -14321,62 +13594,29 @@ name: has part name: has_part namespace: external namespace: quality -namespace: uberon def: "a core relation that holds between a whole and its part" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000051 -property_value: editor_note "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string -property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string -property_value: IAO:0000111 "has part" xsd:string -property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string -property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string -property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string -property_value: IAO:0000118 "has_part" xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string is_transitive: true is_a: overlaps ! overlaps [Typedef] -id: has_participant -name: has participant -namespace: external -def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] -xref: RO:0000057 -property_value: editor_note "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string -property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string -property_value: IAO:0000111 "has participant" xsd:string -property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string -property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string -property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string -property_value: IAO:0000118 "has_participant" xsd:string -domain: BFO:0000003 ! occurrent -range: BFO:0000002 ! continuant -holds_over_chain: has_part has_participant - -[Typedef] -id: has_potential_to_develop_into -name: has potential to develop into -namespace: uberon -def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] -xref: RO:0002387 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: RO:0002384 ! has developmental potential involving - -[Typedef] -id: has_potential_to_developmentally_contribute_to -name: has potential to developmentally contribute to -namespace: uberon -def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] -xref: RO:0002385 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: RO:0002384 ! has developmental potential involving - -[Typedef] +id: has_participant +name: has participant +namespace: external +def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] +xref: RO:0000057 +property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string +domain: BFO:0000003 ! occurrent +range: BFO:0000002 ! continuant +holds_over_chain: has_part has_participant + +[Typedef] id: has_primary_input name: has primary input namespace: external @@ -14411,17 +13651,6 @@ is_a: has_primary_input_or_output ! has primary input or output created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z -[Typedef] -id: has_quality -name: has quality -namespace: uberon -def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] -xref: RO:0000086 -property_value: editor_note "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string -property_value: IAO:0000112 "this apple has quality this red color" xsd:string -property_value: IAO:0000118 "has_quality" xsd:string -is_a: bearer_of ! bearer of - [Typedef] id: has_regulatory_component_activity name: has regulatory component activity @@ -14433,23 +13662,6 @@ is_a: RO:0002017 ! has component activity created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z -[Typedef] -id: has_skeleton -name: has skeleton -namespace: uberon -def: "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." [] -xref: RO:0002551 -property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "has supporting framework" xsd:string -property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string -domain: UBERON:0000061 ! anatomical structure -domain: UBERON:0000475 ! organism subdivision -range: UBERON:0000465 {IAO:0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} ! material anatomical entity -is_a: has_part ! has part -inverse_of: skeleton_of ! skeleton of -is_asymmetric: true - [Typedef] id: has_small_molecule_activator name: has small molecule activator @@ -14468,9 +13680,6 @@ namespace: external def: "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y" [] subset: ro-eco xref: RO:0002231 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "starts with process that occurs in" xsd:string domain: BFO:0000015 ! process range: BFO:0000004 ! independent continuant holds_over_chain: starts_with occurs_in @@ -14485,9 +13694,8 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002339 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of [Typedef] id: has_target_start_location @@ -14498,41 +13706,14 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002338 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in -transitive_over: part_of ! part_of - -[Typedef] -id: homologous_to -name: shares ancestor with -namespace: uberon -def: "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." [] -comment: VBO calls this homologous_to -xref: RO:0002158 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000232 "Consider obsoleting and merging with child relation, 'in homology relationship with'" xsd:string -is_symmetric: true -is_transitive: true -is_a: RO:0002320 ! evolutionarily related to - -[Typedef] -id: immediate_transformation_of -name: immediate transformation of -namespace: uberon -def: "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" [] -xref: RO:0002495 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0002575 RO:0002494 -is_a: directly_develops_from ! directly develops from -is_a: transformation_of ! transformation of +transitive_over: part_of ! part of [Typedef] id: immediately_causally_downstream_of name: immediately causally downstream of namespace: external xref: RO:0002405 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of ! causally downstream of is_a: immediately_preceded_by ! immediately preceded by inverse_of: immediately_causally_upstream_of ! immediately causally upstream of @@ -14543,26 +13724,15 @@ name: immediately causally upstream of namespace: external def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] xref: RO:0002412 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: immediately_precedes ! immediately precedes -[Typedef] -id: immediately_deep_to -name: immediately deep to -namespace: uberon -xref: BSPO:0001107 - [Typedef] id: immediately_preceded_by name: immediately preceded by namespace: external -namespace: uberon comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) xref: RO:0002087 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000118 "starts_at_end_of" xsd:string holds_over_chain: starts_with ends_with is_a: preceded_by ! preceded by inverse_of: immediately_precedes ! immediately precedes @@ -14574,228 +13744,22 @@ namespace: external comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) subset: ro-eco xref: RO:0002090 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "ends_at_start_of" xsd:string -property_value: IAO:0000118 "meets" xsd:string -property_value: RO:0002575 BFO:0000063 holds_over_chain: ends_with starts_with is_a: precedes ! precedes -[Typedef] -id: immediately_superficial_to -name: immediately superficial to -namespace: uberon -xref: BSPO:0015014 - -[Typedef] -id: in_anterior_side_of -name: in anterior side of -namespace: uberon -xref: BSPO:0000123 - -[Typedef] -id: in_deep_part_of -name: in deep part of -namespace: uberon -xref: BSPO:0001101 - -[Typedef] -id: in_dorsal_side_of -name: in dorsal side of -namespace: uberon -xref: BSPO:0015101 - -[Typedef] -id: in_lateral_side_of -name: in lateral side of -namespace: uberon -xref: BSPO:0000126 - -[Typedef] -id: in_left_side_of -name: in left side of -namespace: uberon -xref: BSPO:0000120 - -[Typedef] -id: in_posterior_side_of -name: in posterior side of -namespace: uberon -xref: BSPO:0000122 - -[Typedef] -id: in_proximal_side_of -name: in proximal side of -namespace: uberon -xref: BSPO:0000124 - -[Typedef] -id: in_right_side_of -name: in right side of -namespace: uberon -xref: BSPO:0000121 - -[Typedef] -id: in_superficial_part_of -name: in superficial part of -namespace: uberon -xref: BSPO:0001100 - -[Typedef] -id: in_taxon -name: in taxon -namespace: uberon -def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." [] -comment: Connects a biological entity to its taxon of origin. -subset: ro-eco -xref: RO:0002162 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9227-417X -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -holds_over_chain: attaches_to in_taxon -holds_over_chain: capable_of in_taxon -holds_over_chain: connected_to in_taxon -holds_over_chain: connects in_taxon -holds_over_chain: continuous_with in_taxon -holds_over_chain: developmentally_induced_by in_taxon -holds_over_chain: develops_from in_taxon -holds_over_chain: develops_from_part_of in_taxon -holds_over_chain: existence_ends_during in_taxon -holds_over_chain: existence_starts_during in_taxon -holds_over_chain: extends_fibers_into in_taxon -holds_over_chain: has_developmental_contribution_from in_taxon -holds_over_chain: has_part in_taxon -holds_over_chain: has_potential_to_develop_into in_taxon -holds_over_chain: innervated_by in_taxon -holds_over_chain: overlaps in_taxon -holds_over_chain: part_of in_taxon -holds_over_chain: produced_by in_taxon -holds_over_chain: produces in_taxon -holds_over_chain: results_in_developmental_progression_of in_taxon -holds_over_chain: RO:0002206 in_taxon -holds_over_chain: supplies in_taxon -is_a: RO:0002320 ! evolutionarily related to - [Typedef] id: indirectly_supplies name: indirectly_supplies namespace: uberon def: "a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s." [] -property_value: editor_note "add to RO" xsd:string -holds_over_chain: has_branching_part indirectly_supplies -holds_over_chain: has_branching_part supplies -is_transitive: true - -[Typedef] -id: innervated_by -name: innervated_by -namespace: uberon -xref: RO:0002005 -property_value: http://purl.org/spar/cito/citesAsAuthority "http://www.ncbi.nlm.nih.gov/pubmed/22402613" xsd:anyURI -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -domain: UBERON:0000061 ! anatomical structure -inverse_of: innervates ! innervates -transitive_over: branching_part_of ! branching part of - -[Typedef] -id: innervates -name: innervates -namespace: uberon -def: "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." [] -xref: RO:0002134 -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 -transitive_over: part_of ! part_of -expand_expression_to: "RO_0002132 some (GO_0043005 that (RO_0002131 some (GO_0045202 that BFO_0000050 some Y?)))" [] - -[Typedef] -id: input_of -name: input of -namespace: uberon -def: "inverse of has input" [] -subset: ro-eco -subset: RO:0002259 -xref: RO:0002352 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: functionally_related_to ! functionally related to -is_a: participates_in ! participates in - -[Typedef] -id: intersects_midsagittal_plane_of -name: intersects midsagittal plane of -namespace: uberon -xref: BSPO:0005001 +property_value: IAO:0000116 "add to RO" xsd:string +holds_over_chain: RO:0002569 indirectly_supplies [Typedef] id: layer_part_of name: layer part of namespace: uberon -is_a: part_of ! part_of - -[Typedef] -id: located_in -name: located in -namespace: uberon -def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -xref: RO:0001025 -property_value: editor_note "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" xsd:string -property_value: editor_note "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:located_in" xsd:string -property_value: IAO:0000111 "located in" xsd:string -property_value: IAO:0000112 "my brain is located in my head" xsd:string -property_value: IAO:0000112 "this rat is located in this cage" xsd:string -property_value: IAO:0000118 "located_in" xsd:string -property_value: RO:0001900 RO:0001901 -property_value: seeAlso "https://wiki.geneontology.org/Located_in" xsd:anyURI -domain: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant -range: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant -is_transitive: true -transitive_over: part_of ! part_of - -[Typedef] -id: location_of -name: location of -namespace: uberon -def: "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" [] -xref: RO:0001015 -property_value: editor_note "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: IAO:0000111 "is location of" xsd:string -property_value: IAO:0000112 "my head is the location of my brain" xsd:string -property_value: IAO:0000112 "this cage is the location of this rat" xsd:string -property_value: IAO:0000118 "location_of" xsd:string -property_value: RO:0001900 RO:0001901 -is_transitive: true -inverse_of: located_in ! located in - -[Typedef] -id: lumen_of -name: lumen of -namespace: uberon -def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] -subset: ro-eco -xref: RO:0002571 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 https://orcid.org/0000-0002-6601-2165 -range: BFO:0000040 ! material entity -is_a: part_of ! part_of - -[Typedef] -id: luminal_space_of -name: luminal space of -namespace: uberon -def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" [] -subset: ro-eco -xref: RO:0002572 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: BFO:0000141 ! immaterial entity -is_a: lumen_of ! lumen of +is_a: part_of ! part of [Typedef] id: negatively_regulated_by @@ -14804,7 +13768,6 @@ namespace: external def: "inverse of negatively regulates" [] subset: RO:0002259 xref: RO:0002335 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -14816,9 +13779,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002212 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002211 holds_over_chain: ends_with negatively_regulates is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect @@ -14831,30 +13791,11 @@ name: negatively regulates characteristic namespace: gene_ontology def: "A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C." [] xref: RO:0019002 -property_value: dc-contributor https://orcid.org/0000-0002-8688-6599 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 holds_over_chain: negatively_regulates positively_regulates_characteristic holds_over_chain: positively_regulates negatively_regulates_characteristic is_a: regulates_characteristic ! regulates characteristic -[Typedef] -id: never_in_taxon -name: never in taxon -name: never_in_taxon -namespace: uberon -def: "S never_in_taxon T iff: S SubClassOf in_taxon only not T." [PMID:20973947] -def: "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL." [] -xref: RO:0002161 -property_value: IAO:0000112 "tooth SubClassOf 'never in taxon' value 'Aves'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 -property_value: OMO:0002000 "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" xsd:string -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -expand_assertion_to: "Class: EquivalentTo: ?X and (RO_0002162 some ?Y)" [] -expand_assertion_to: "Class: ?X DisjointWith: RO_0002162 some ?Y " [] -is_metadata_tag: true -is_class_level: true - [Typedef] id: occurs_in name: occurs in @@ -14865,64 +13806,38 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000066 -property_value: IAO:0000111 "occurs in" xsd:string -property_value: IAO:0000118 "occurs_in" xsd:string -property_value: IAO:0000118 "unfolds in" xsd:string -property_value: IAO:0000118 "unfolds_in" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl property_value: seeAlso "https://wiki.geneontology.org/Occurs_in" xsd:anyURI domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant holds_over_chain: part_of occurs_in -inverse_of: contains_process ! contains process -transitive_over: part_of ! part_of - -[Typedef] -id: only_in_taxon -name: only in taxon -namespace: uberon -def: "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." [] -xref: RO:0002160 -property_value: editor_note "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" xsd:string -property_value: IAO:0000112 "lactation SubClassOf 'only in taxon' some 'Mammalia'" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -is_a: in_taxon ! in taxon +inverse_of: BFO:0000067 ! contains process +transitive_over: part_of ! part of [Typedef] id: output_of name: output of namespace: external -namespace: uberon def: "inverse of has output" [] subset: ro-eco subset: RO:0002259 xref: RO:0002353 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: functionally_related_to ! functionally related to is_a: participates_in ! participates in +is_a: RO:0002328 ! functionally related to [Typedef] id: overlaps name: overlaps namespace: external -namespace: uberon def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002131 -property_value: IAO:0000114 IAO:0000125 -property_value: RO:0001900 RO:0001901 holds_over_chain: has_part overlaps -holds_over_chain: has_part part_of {RO:0002582="true"} holds_over_chain: part_of part_of is_symmetric: true is_a: RO:0002323 ! mereotopologically related to -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] [Typedef] @@ -14931,29 +13846,15 @@ name: part of name: part_of namespace: external namespace: quality -namespace: uberon def: "a core relation that holds between a part and its whole" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000050 -property_value: editor_note "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string -property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string -property_value: IAO:0000111 "is part of" xsd:string -property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string -property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string -property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string -property_value: IAO:0000118 "part_of" xsd:string -property_value: RO:0001900 RO:0001901 -property_value: RO:0040042 BFO:0000002 -property_value: RO:0040042 BFO:0000003 -property_value: RO:0040042 BFO:0000004 -property_value: RO:0040042 BFO:0000017 -property_value: RO:0040042 BFO:0000019 -property_value: RO:0040042 BFO:0000020 -property_value: RO:0040042 BFO:0000031 +property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string @@ -14966,14 +13867,8 @@ inverse_of: has_part ! has part id: participates_in name: participates in namespace: external -namespace: uberon def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] xref: RO:0000056 -property_value: IAO:0000111 "participates in" xsd:string -property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string -property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string -property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string -property_value: IAO:0000118 "participates_in" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000003 ! occurrent inverse_of: has_participant ! has participant @@ -14985,7 +13880,6 @@ namespace: external def: "inverse of positively regulates" [] subset: RO:0002259 xref: RO:0002336 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -14997,10 +13891,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002213 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "positively regulates (process to process)" xsd:string -property_value: RO:0004049 RO:0002211 holds_over_chain: ends_with positively_regulates holds_over_chain: negatively_regulates negatively_regulates is_transitive: true @@ -15014,49 +13904,25 @@ name: positively regulates characteristic namespace: gene_ontology def: "A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C." [] xref: RO:0019001 -property_value: dc-contributor https://orcid.org/0000-0002-8688-6599 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 holds_over_chain: positively_regulates positively_regulates_characteristic is_a: regulates_characteristic ! regulates characteristic -[Typedef] -id: postaxialmost_part_of -name: postaxialmost part of -namespace: uberon -xref: BSPO:0001115 - -[Typedef] -id: posterior_to -name: posterior to -namespace: uberon -xref: BSPO:0000099 - [Typedef] id: posteriorly_connected_to name: posteriorly connected to namespace: uberon def: "x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] -is_a: anterior_to ! anterior to -is_a: connected_to ! connected to - -[Typedef] -id: preaxialmost_part_of -name: preaxialmost part of -namespace: uberon -xref: BSPO:0001113 +is_a: RO:0002170 ! connected to [Typedef] id: preceded_by name: preceded by namespace: external -namespace: uberon def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000062 -property_value: editor_note "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string -property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string -property_value: IAO:0000111 "preceded by" xsd:string -property_value: IAO:0000118 "is preceded by" xsd:string -property_value: IAO:0000118 "preceded_by" xsd:string +property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent holds_over_chain: part_of preceded_by @@ -15068,53 +13934,30 @@ inverse_of: precedes ! precedes id: precedes name: precedes namespace: external -namespace: uberon def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000063 -property_value: IAO:0000111 "precedes" xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent holds_over_chain: part_of precedes is_transitive: true is_a: RO:0002222 ! temporally related to -[Typedef] -id: present_in_taxon -name: present in taxon -name: present_in_taxon -namespace: uberon -def: "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S" [] -def: "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S." [https://orcid.org/0000-0002-6601-2165] -comment: The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology. -synonym: "applicable for taxon" EXACT [] -xref: RO:0002175 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: OMO:0002000 "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" xsd:string -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -is_metadata_tag: true -is_class_level: true - [Typedef] id: process_has_causal_agent name: process has causal agent namespace: external def: "Inverse of 'causal agent in process'" [] xref: RO:0002608 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_a: RO:0002410 ! causally related to [Typedef] id: produced_by name: produced by namespace: external -namespace: uberon def: "a produced_by b iff some process that occurs_in b has_output a." [] subset: ro-eco xref: RO:0003001 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity @@ -15122,13 +13965,10 @@ range: BFO:0000040 ! material entity id: produces name: produces namespace: external -namespace: uberon def: "a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix." [] comment: Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. subset: ro-eco xref: RO:0003000 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity inverse_of: produced_by ! produced by @@ -15138,27 +13978,14 @@ id: protects name: protects namespace: uberon -[Typedef] -id: proximal_to -name: proximal to -namespace: uberon -xref: BSPO:0000100 - [Typedef] id: proximally_connected_to name: proximally connected to namespace: uberon def: "x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] -is_a: connected_to ! connected to -is_a: distal_to ! distal to +is_a: RO:0002170 ! connected to is_a: transitively_proximally_connected_to ! transitively proximally connected to -[Typedef] -id: proximalmost_part_of -name: proximalmost part of -namespace: uberon -xref: BSPO:0001106 - [Typedef] id: regulated_by name: regulated by @@ -15166,8 +13993,6 @@ namespace: external def: "inverse of regulates" [] subset: RO:0002259 xref: RO:0002334 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000589 "regulated by (processual)" xsd:string domain: BFO:0000015 ! process range: BFO:0000015 ! process is_transitive: true @@ -15182,14 +14007,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 -property_value: IAO:0000117 https://orcid.org/0000-0001-7476-6306 -property_value: IAO:0000117 https://orcid.org/0000-0002-3837-8864 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GO" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string -property_value: IAO:0000589 "regulates (processual)" xsd:string -property_value: IAO:0000600 "false" xsd:boolean domain: BFO:0000015 ! process range: BFO:0000015 ! process holds_over_chain: directly_regulates directly_regulates @@ -15205,7 +14022,7 @@ name: regulates characteristic namespace: gene_ontology def: "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C." [] xref: RO:0019000 -property_value: dc-contributor https://orcid.org/0000-0002-8688-6599 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 domain: BFO:0000015 ! process range: PATO:0000001 ! quality holds_over_chain: regulates regulates_characteristic @@ -15217,13 +14034,9 @@ name: regulates levels of namespace: external def: "p regulates levels of c if p regulates some amount (PATO:0000070) of c" [] xref: RO:0002332 -property_value: IAO:0000112 "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "regulates levels of (process to entity)" xsd:string domain: BFO:0000015 ! process range: BFO:0000040 ! material entity -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to [Typedef] id: results_in_acquisition_of_features_of @@ -15234,9 +14047,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002315 -property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string range: UBERON:0000061 ! anatomical structure is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -15271,10 +14081,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002296 -property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "http://www.geneontology.org/GO.doc.development.shtml" xsd:anyURI is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -15284,9 +14090,7 @@ name: results in developmental progression of namespace: external def: "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." [] xref: RO:0002295 -property_value: editor_note "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000116 "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string property_value: seeAlso Ontology:extensions domain: GO:0008150 ! biological_process range: UBERON:0001062 ! anatomical entity @@ -15318,16 +14122,12 @@ is_a: has_participant ! has participant [Typedef] id: results_in_formation_of name: results in formation of +name: results in formation of anatomical entity namespace: external subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002297 -property_value: IAO:0000112 "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." xsd:string -property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of inverse_of: RO:0002354 ! formed as result of @@ -15349,8 +14149,6 @@ id: results_in_growth_of name: results in growth of namespace: external xref: RO:0002343 -property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -15363,11 +14161,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002299 -property_value: IAO:0000112 " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" xsd:string -property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -15380,11 +14173,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002298 -property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." xsd:string -property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -15397,8 +14185,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002565 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure [Typedef] @@ -15417,7 +14203,6 @@ namespace: external def: "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002342 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in is_a: RO:0002021 ! occurs across @@ -15427,7 +14212,6 @@ name: results in transport along namespace: external def: "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " [] xref: RO:0002341 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002337 ! related via localization to [Typedef] @@ -15435,36 +14219,13 @@ id: results_in_transport_to_from_or_in name: results in transport to from or in namespace: external xref: RO:0002344 -property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002337 ! related via localization to -[Typedef] -id: seeAlso -name: see also -namespace: uberon -xref: http://www.w3.org/2000/01/rdf-schema#seeAlso -is_metadata_tag: true - [Typedef] id: sexually_homologous_to name: sexually_homologous_to namespace: uberon -is_a: homologous_to ! shares ancestor with - -[Typedef] -id: simultaneous_with -name: simultaneous with -namespace: uberon -def: "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." [] -comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) -subset: ro-eco -xref: RO:0002082 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -is_symmetric: true -is_transitive: true -is_a: RO:0002081 ! before or simultaneous with +is_a: RO:0002158 ! shares ancestor with [Typedef] id: site_of @@ -15473,46 +14234,13 @@ namespace: uberon def: "c site_of p if c is the bearer of a disposition that is realized by a process that has p as part." [] synonym: "capable_of_has_part" RELATED [] -[Typedef] -id: skeleton_of -name: skeleton of -namespace: uberon -def: "inverse of has skeleton" [] -subset: RO:0002259 -xref: RO:0002576 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: UBERON:0000061 ! anatomical structure -range: UBERON:0000061 ! anatomical structure -is_a: part_of ! part_of - -[Typedef] -id: starts -name: starts -namespace: uberon -def: "inverse of starts with" [] -subset: ro-eco -xref: RO:0002223 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "Allen" xsd:string -is_a: part_of ! part_of -is_a: RO:0002222 ! temporally related to -inverse_of: starts_with ! starts with - [Typedef] id: starts_with name: starts with namespace: external -namespace: uberon def: "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002224 -property_value: IAO:0000112 "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "started by" xsd:string is_transitive: true is_a: has_part ! has part is_a: RO:0002222 ! temporally related to @@ -15523,139 +14251,36 @@ name: subdivision of namespace: uberon comment: placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B -[Typedef] -id: superficial_to -name: superficial to -namespace: uberon -xref: BSPO:0000108 - -[Typedef] -id: supplies -name: supplies -namespace: uberon -def: "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." [] -xref: RO:0002178 -property_value: editor_note "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 -is_a: connected_to ! connected to - -[Typedef] -id: surrounded_by -name: surrounded by -namespace: uberon -def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" [] -xref: RO:0002219 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0001900 RO:0001901 -is_a: adjacent_to ! adjacent to -inverse_of: surrounds ! surrounds - -[Typedef] -id: surrounds -name: surrounds -namespace: uberon -def: "inverse of surrounded by" [] -subset: RO:0002259 -xref: RO:0002221 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0001900 RO:0001901 -is_a: adjacent_to ! adjacent to - -[Typedef] -id: synapsed_by -name: synapsed by -namespace: uberon -def: "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " [] -xref: RO:0002103 -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 -is_a: RO:0002485 ! receives input from -inverse_of: RO:0002120 ! synapsed to -expand_expression_to: "BFO_0000051 some (GO_0045211 that part_of some (GO_0045202 that has_part some (GO_0042734 that BFO_0000050 some Y?)))" [] - [Typedef] id: term_tracker_item name: term tracker item namespace: external -namespace: uberon def: "An IRI or similar locator for a request or discussion of an ontology term." [] comment: The 'tracker item' can associate a tracker with a specific ontology term. xref: IAO:0000233 -property_value: IAO:0000111 "term tracker item" xsd:string -property_value: IAO:0000112 "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" xsd:string -property_value: IAO:0000119 "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" xsd:string is_metadata_tag: true -is_class_level: true - -[Typedef] -id: transformation_of -name: transformation of -namespace: uberon -def: "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" [] -xref: RO:0002494 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_transitive: true -is_a: develops_from ! develops from [Typedef] id: transitively_anteriorly_connected_to name: transitively anteriorly connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI -is_transitive: true [Typedef] id: transitively_distally_connected_to name: transitively distally connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI -is_transitive: true [Typedef] id: transitively_proximally_connected_to name: transitively proximally connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI -is_transitive: true - -[Typedef] -id: tributary_of -name: tributary of -namespace: uberon -def: "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." [] -subset: ro-eco -xref: RO:0002376 -property_value: IAO:0000112 "Deschutes River tributary_of Columbia River" xsd:string -property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "drains into" xsd:string -property_value: IAO:0000118 "drains to" xsd:string -property_value: IAO:0000118 "tributary channel of" xsd:string -property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Tributary" xsd:string -property_value: IAO:0000119 "http://www.medindia.net/glossary/venous_tributary.htm" xsd:string -property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" xsd:anyURI -property_value: seeAlso http://dbpedia.org/ontology/drainsTo -property_value: seeAlso "http://en.wikipedia.org/wiki/Tributary" xsd:anyURI -is_a: connected_to ! connected to -is_a: RO:0002375 ! in branching relationship with [Typedef] id: trunk_part_of name: trunk_part_of namespace: uberon -is_a: part_of ! part_of - -[Typedef] -id: ventral_to -name: ventral to -namespace: uberon -xref: BSPO:0000102 +is_a: part_of ! part of diff --git a/subsets/general_cell_types_upper_slim.owl b/subsets/general_cell_types_upper_slim.owl index 48fbe975e..8532201d2 100644 --- a/subsets/general_cell_types_upper_slim.owl +++ b/subsets/general_cell_types_upper_slim.owl @@ -10,28 +10,21 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" - xmlns:cito="http://purl.org/spar/cito/" xmlns:core="http://purl.obolibrary.org/obo/uberon/core#" xmlns:foaf="http://xmlns.com/foaf/0.1/" - xmlns:obo2="http://www.geneontology.org/formats/oboInOwl#http://purl.obolibrary.org/obo/" xmlns:pato="http://purl.obolibrary.org/obo/pato#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" - xmlns:skos="http://www.w3.org/2004/02/skos/core#" xmlns:swrl="http://www.w3.org/2003/11/swrl#" - xmlns:sssom="https://w3id.org/sssom/" - xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#" xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:terms="http://purl.org/dc/terms/" - xmlns:vocab="https://w3id.org/semapv/vocab/" - xmlns:terms1="http://www.geneontology.org/formats/oboInOwl#http://purl.org/dc/terms/" xmlns:uberon="http://purl.obolibrary.org/obo/uberon#" xmlns:ubprop="http://purl.obolibrary.org/obo/ubprop#" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - 2024-02-13 + + 2024-04-05 @@ -55,29 +48,9 @@ - - - - - - - - - - - - - - - - - - - definition - The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith @@ -99,8 +72,6 @@ We don't have definitions of 'meaning' or 'expression' Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition @@ -110,72 +81,28 @@ We also have the outstanding issue of how to aim different definitions to differ - editor note - An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obofoundry.org/obo/obi> - IAO:0000116 - uberon - editor_note - true - editor_note - editor note editor note - - - - - - - - - - - - - - - - - - - has obsolescence reason Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. - PERSON:Alan Ruttenberg - PERSON:Melanie Courtot has obsolescence reason - - - - - - - term tracker item - the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ - An IRI or similar locator for a request or discussion of an ontology term. - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg IAO:0000233 external - uberon term_tracker_item - true true term_tracker_item The 'tracker item' can associate a tracker with a specific ontology term. @@ -185,63 +112,23 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - - expand expression to - ObjectProperty: RO_0002104 -Label: has plasma membrane part -Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" - A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones - Chris Mungall expand expression to expand expression to - - - - - - - - - - - - - - - - - - - - - - - - - has ontology root term Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. - Nicolas Matentzoglu IAO:0000700 external - uberon has_ontology_root_term - true true has_ontology_root_term has ontology root term @@ -251,20 +138,10 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - - - - - - - term replaced by - Use on obsolete terms, relating the term to another term that can be used as a substitute - Person:Alan Ruttenberg - Person:Alan Ruttenberg Add as annotation triples in the granting ontology term replaced by term replaced by @@ -275,24 +152,6 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - 'part disjoint with' 'defined by construct' """ - PREFIX owl: <http://www.w3.org/2002/07/owl#> - PREFIX : <http://example.org/ - CONSTRUCT { - [ - a owl:Restriction ; - owl:onProperty :part_of ; - owl:someValuesFrom ?a ; - owl:disjointWith [ - a owl:Restriction ; - owl:onProperty :part_of ; - owl:someValuesFrom ?b - ] - ] - } - WHERE { - ?a :part_disjoint_with ?b . - } Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. @@ -305,11 +164,9 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation) A synonym type for describing abbreviations or initalisms - 2023-03-03 abbreviation @@ -335,11 +192,9 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form) A synonym type for describing pluralization synonyms - 2023-03-03 plural form @@ -354,23 +209,10 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - - - - - - - tooth SubClassOf 'never in taxon' value 'Aves' - S never_in_taxon T iff: S SubClassOf in_taxon only not T. x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL. - - - - Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: ?X and (RO_0002162 some ?Y) - Class: ?X DisjointWith: RO_0002162 some ?Y PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> @@ -394,34 +236,9 @@ CONSTRUCT { WHERE { ?x never_in_taxon: ?taxon . } - RO:0002161 - uberon - never_in_taxon - true - true - never_in_taxon never in taxon - never_in_taxon - - - - S never_in_taxon T iff: S SubClassOf in_taxon only not T. - PMID:20973947 - - - - - - - - - - - - - @@ -429,9 +246,6 @@ WHERE { S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S - S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S. - - PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> @@ -456,24 +270,10 @@ WHERE { )) as ?witness) BIND(CONCAT(STR(?x), " in taxon ", STR(?taxon)) AS ?label) } - RO:0002175 - applicable for taxon - uberon - present_in_taxon - true - true - present_in_taxon The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology. present in taxon - present_in_taxon - - - - S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S. - https://orcid.org/0000-0002-6601-2165 - @@ -485,60 +285,6 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL - is a defining property chain axiom - - - - - - - - If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. - is a defining property chain axiom where second argument is reflexive - - - - - - - - - - - - - - - - - - - - - - @@ -549,126 +295,6 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -927,12 +553,6 @@ WHERE { - - - - - - @@ -1363,14 +983,7 @@ WHERE { - - http://purl.org/dc/elements/1.1/creator - uberon - dc-creator - true - dc-creator - creator - + @@ -1382,14 +995,7 @@ WHERE { - - http://purl.org/dc/elements/1.1/description - uberon - dc-description - true - dc-description - description - + @@ -1401,71 +1007,25 @@ WHERE { - - http://purl.org/dc/elements/1.1/title - uberon - dc-title - true - dc-title - title - + - - http://purl.org/dc/terms/contributor - uberon - dc-contributor - true - dc-contributor - contributor - - - - - - - - - - - - - + - - http://purl.org/dc/terms/date - uberon - dcterms-date - true - dcterms-date - date - + - - http://purl.org/dc/terms/license - uberon - dcterms-license - true - dcterms-license - license - - - - - - - + @@ -1475,18 +1035,6 @@ WHERE { - - - - - - - - - - - - @@ -1503,18 +1051,6 @@ WHERE { - - - - - - - - - - - - @@ -1523,18 +1059,6 @@ WHERE { - - - - - - - - - - - - @@ -1551,66 +1075,6 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -1623,7 +1087,6 @@ WHERE { An alternative label for a class or property which has a more general meaning than the preferred name/primary label. - https://github.com/information-artifact-ontology/ontology-metadata/issues/18 has broad synonym has_broad_synonym @@ -1644,7 +1107,6 @@ WHERE { An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. - https://github.com/information-artifact-ontology/ontology-metadata/issues/20 has exact synonym has_exact_synonym @@ -1657,7 +1119,6 @@ WHERE { An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. - https://github.com/information-artifact-ontology/ontology-metadata/issues/19 has narrow synonym has_narrow_synonym @@ -1678,7 +1139,6 @@ WHERE { An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. - https://github.com/information-artifact-ontology/ontology-metadata/issues/21 has related synonym has_related_synonym @@ -1687,12 +1147,6 @@ WHERE { - - - - - - @@ -1717,30 +1171,6 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - - - @@ -1753,72 +1183,12 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -1833,60 +1203,6 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -1903,9 +1219,6 @@ WHERE { http://www.w3.org/2000/01/rdf-schema#seeAlso - uberon - seeAlso - true seeAlso see also @@ -1918,63 +1231,9 @@ WHERE { - - - - - - - - http://xmlns.com/foaf/0.1/depiction - uberon - depiction - true - depiction - depiction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + @@ -1995,29 +1254,15 @@ WHERE { - is part of - my brain is part of my body (continuant parthood, two material entities) - my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) - this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. - part_of - - - - - - - - BFO:0000050 external quality - uberon part_of @@ -2040,22 +1285,15 @@ A continuant cannot be part of an occurrent: use 'participates in'. An - has part - my body has part my brain (continuant parthood, two material entities) - my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) - this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. - has_part - BFO:0000051 external quality - uberon has_part @@ -2080,15 +1318,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. - preceded by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. - is preceded by - preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 external - uberon preceded_by preceded_by @@ -2109,11 +1342,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. - precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. BFO:0000063 external - uberon precedes precedes @@ -2137,11 +1368,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - occurs_in - unfolds in - unfolds_in BFO:0000066 external occurs_in @@ -2150,7 +1377,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. occurs_in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant - occurs in occurs in https://wiki.geneontology.org/Occurs_in @@ -2161,308 +1387,13 @@ A continuant cannot have an occurrent as part: use 'participates in'. - site of [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - BFO:0000067 - uberon - contains_process - contains_process Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant - - contains process contains process - - - - BSPO:0000096 - uberon - anterior_to - anterior_to - anterior to - - - - - - - - BSPO:0000097 - uberon - distal_to - distal_to - distal to - - - - - - - - BSPO:0000098 - uberon - dorsal_to - dorsal_to - dorsal to - - - - - - - - BSPO:0000099 - uberon - posterior_to - posterior_to - posterior to - - - - - - - - BSPO:0000100 - uberon - proximal_to - proximal_to - proximal to - - - - - - - - BSPO:0000102 - uberon - ventral_to - ventral_to - ventral to - - - - - - - - BSPO:0000107 - uberon - deep_to - deep_to - deep to - - - - - - - - BSPO:0000108 - uberon - superficial_to - superficial_to - superficial to - - - - - - - - BSPO:0000120 - uberon - in_left_side_of - in_left_side_of - in left side of - - - - - - - - BSPO:0000121 - uberon - in_right_side_of - in_right_side_of - in right side of - - - - - - - - BSPO:0000122 - uberon - in_posterior_side_of - in_posterior_side_of - in posterior side of - - - - - - - - BSPO:0000123 - uberon - in_anterior_side_of - in_anterior_side_of - in anterior side of - - - - - - - - BSPO:0000124 - uberon - in_proximal_side_of - in_proximal_side_of - in proximal side of - - - - - - - - BSPO:0000126 - uberon - in_lateral_side_of - in_lateral_side_of - in lateral side of - - - - - - - - BSPO:0001100 - uberon - in_superficial_part_of - in_superficial_part_of - in superficial part of - - - - - - - - BSPO:0001101 - uberon - in_deep_part_of - in_deep_part_of - in deep part of - - - - - - - - BSPO:0001106 - uberon - proximalmost_part_of - proximalmost_part_of - proximalmost part of - - - - - - - - BSPO:0001107 - uberon - immediately_deep_to - immediately_deep_to - immediately deep to - - - - - - - - BSPO:0001108 - uberon - distalmost_part_of - distalmost_part_of - distalmost part of - - - - - - - - BSPO:0001113 - uberon - preaxialmost_part_of - preaxialmost_part_of - preaxialmost part of - - - - - - - - BSPO:0001115 - uberon - postaxialmost_part_of - postaxialmost_part_of - postaxialmost part of - - - - - - - - BSPO:0005001 - uberon - intersects_midsagittal_plane_of - intersects_midsagittal_plane_of - intersects midsagittal plane of - - - - - - - - BSPO:0015014 - uberon - immediately_superficial_to - immediately_superficial_to - immediately superficial to - - - - - - - - BSPO:0015101 - uberon - in_dorsal_side_of - in_dorsal_side_of - in dorsal side of - - - - @@ -2522,12 +1453,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - inheres in - this fragility is a characteristic of this vase - this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. - inheres_in - Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of @@ -2539,14 +1465,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - bearer of - this apple is bearer of this red color - this vase is bearer of this fragility Inverse of characteristic_of A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. - bearer_of - is bearer of - RO:0000053 external bearer_of @@ -2563,15 +1483,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. - participates in - this blood clot participates in this blood coagulation - this input material (or this output material) participates in this process - this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process - participates_in RO:0000056 external - uberon participates_in participates_in participates in @@ -2589,14 +1503,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - has participant - this blood coagulation has participant this blood clot - this investigation has participant this investigator - this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. - has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 external has_participant @@ -2612,11 +1520,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. - function_of - is function of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. function of @@ -2628,11 +1533,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. - is quality of - quality_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. quality of @@ -2644,11 +1546,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. - is role of - role_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. role of @@ -2660,10 +1559,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. - has_function has function @@ -2673,15 +1570,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. - has_quality - RO:0000086 - uberon - has_quality - has_quality - has quality has quality @@ -2692,10 +1582,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. - has_role has role @@ -2729,13 +1617,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this cell derives from this parent cell (cell division) - this nucleus derives from this parent nucleus (nuclear division) - a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. - derives_from - This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. derives from @@ -2745,12 +1628,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this parent cell derives into this cell (cell division) - this parent nucleus derives into this nucleus (nuclear division) - a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. - derives_into derives into @@ -2762,18 +1641,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - is location of - my head is the location of my brain - this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - location_of - - RO:0001015 - uberon - location_of - location_of - location of location of @@ -2789,21 +1658,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. - located in - my brain is located in my head - this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - located_in - - http://www.obofoundry.org/ro/#OBO_REL:located_in - RO:0001025 - uberon - located_in - located_in - located in located in https://wiki.geneontology.org/Located_in @@ -2827,16 +1685,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. - the surface of my skin is a 2D boundary of my body a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - 2D_boundary_of - boundary of - is 2D boundary of - is boundary of - surface of - 2D boundary of @@ -2848,19 +1699,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. - my body has 2D boundary the surface of my skin a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - - has boundary - has_2D_boundary - - RO:0002002 - uberon - has_boundary - has_boundary - has 2D boundary has 2D boundary @@ -2871,17 +1712,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - http://www.ncbi.nlm.nih.gov/pubmed/22402613 - RO:0002005 - uberon - innervated_by - innervated_by - innervated_by innervated_by @@ -2892,8 +1722,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - has synaptic terminal of @@ -2913,10 +1741,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - RO:0002007 external - uberon bounding_layer_of bounding_layer_of @@ -3095,8 +1921,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland - <= Primitive instance level timing relation between events before or simultaneous with @@ -3111,15 +1935,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time. - - David Osumi-Sutherland - RO:0002082 - uberon - simultaneous_with - simultaneous_with t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) - simultaneous with simultaneous with @@ -3130,7 +1947,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after @@ -3147,11 +1963,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland - starts_at_end_of RO:0002087 external - uberon immediately_preceded_by immediately_preceded_by X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) @@ -3169,11 +1982,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - - David Osumi-Sutherland - ends_at_start_of - meets - RO:0002090 external immediately_precedes @@ -3196,12 +2004,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between a neuron and a material anatomical entity that its soma is part of. - <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) - has soma location @@ -3213,33 +2018,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. - - fasciculates with - (forall (?x ?y) - (iff - (fasciculates_with ?x ?y) - (exists (?nps ?npbs) - (and - ("neuron ; CL_0000540" ?x) - ("neuron projection bundle ; CARO_0001001" ?y) - ("neuron projection segment ; CARO_0001502" ?nps) - ("neuron projection bundle segment ; CARO_0001500' " ?npbs) - (part_of ?npbs ?y) - (part_of ?nps ?x) - (part_of ?nps ?npbs) - (forall (?npbss) - (if - (and - ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) - (part_of ?npbss ?npbs) - ) - (overlaps ?nps ?npbss) - )))))) - - fasciculates with @@ -3254,16 +2034,11 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between a neuron and some structure its axon forms (chemical) synapses in. - - <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y))) - - axon synapses in @@ -3285,18 +2060,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. - - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) - - - RO:0002103 - uberon - synapsed_by - synapsed_by - synapsed by synapsed by @@ -3308,15 +2073,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] - Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. - - - - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) - has plasma membrane part @@ -3332,16 +2090,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. - - - synapsed in http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)) - - has postsynaptic terminal in @@ -3356,12 +2108,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. - synapses in <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) - - has presynaptic terminal in @@ -3382,14 +2130,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. - - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) - - N1 synapsed_to some N2 Expands to: N1 SubclassOf ( @@ -3411,13 +2154,8 @@ N1 SubclassOf ( - A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. - - has synapse in <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) - - has synaptic terminal in @@ -3432,10 +2170,6 @@ N1 SubclassOf ( - - - - @@ -3444,13 +2178,10 @@ N1 SubclassOf ( - x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) - RO:0002131 external - uberon overlaps @@ -3459,15 +2190,6 @@ N1 SubclassOf ( overlaps overlaps - - - - - - - - true - @@ -3486,35 +2208,7 @@ N1 SubclassOf ( - The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. - - has fasciculating component - (forall (?x ?y) - (iff - (has_fasciculating_neuron_projection ?x ?y) - (exists (?nps ?npbs) - (and - ("neuron projection bundle ; CARO_0001001" ?x) - ("neuron projection ; GO0043005" ?y) - ("neuron projection segment ; CARO_0001502" ?nps) - ("neuron projection bundle segment ; CARO_0001500" ?npbs) - (part_of ?nps ?y) - (part_of ?npbs ?x) - (part_of ?nps ?npbs) - (forall (?npbss) - (if - (and - ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) - (part_of ?npbss ?npbs) - ) - (overlaps ?nps ?npbss) - )))))) - - - - - has fasciculating neuron projection @@ -3527,19 +2221,10 @@ N1 SubclassOf ( - Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - <http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) - - - RO:0002134 - uberon - innervates - innervates - innervates innervates @@ -3552,17 +2237,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - X continuous_with Y if and only if X and Y share a fiat boundary. - - connected to - The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) - - RO:0002150 - uberon - continuous_with - continuous_with - continuous with continuous with FMA:85972 @@ -3575,13 +2250,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a. - Consider obsoleting and merging with child relation, 'in homology relationship with' - RO:0002158 - uberon - homologous_to - homologous_to VBO calls this homologous_to shares ancestor with @@ -3592,19 +2261,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - lactation SubClassOf 'only in taxon' some 'Mammalia' - x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria - - - - RO:0002160 - uberon - only_in_taxon - only_in_taxon only in taxon @@ -3623,30 +2283,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - - - - - - - - - - - - - - - - - - - - - @@ -3667,53 +2303,16 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. - - - - - RO:0002162 - uberon - in_taxon - in_taxon Connects a biological entity to its taxon of origin. in taxon @@ -3725,14 +2324,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. - - - Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) - spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern @@ -3750,14 +2344,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b - - RO:0002170 - uberon - connected_to - connected_to - connected to connected to https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern @@ -3770,15 +2357,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - The M8 connects Glasgow and Edinburgh - a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system. - - RO:0002176 - uberon - connects - connects - connects connects https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern @@ -3793,28 +2372,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. - attached to part of (anatomical structure to anatomical structure) - RO:0002177 - uberon - attaches_to_part_of - attaches_to_part_of - attached to part of attached to part of - - - - - - - - true - @@ -3824,12 +2384,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy. Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure - - RO:0002178 - uberon - supplies - supplies - supplies supplies @@ -3841,12 +2395,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure. Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure - - RO:0002179 - uberon - drains - drains - drains drains @@ -3856,14 +2404,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. - For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. - RO:0002180 external - uberon has_component has_component @@ -3883,18 +2427,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y - - - - - RO:0002202 - uberon - develops_from - develops_from This is the transitive form of the develops from relation - develops from develops from @@ -3907,17 +2441,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of develops from - - - - RO:0002203 - uberon - develops_into - develops_into - develops into develops into @@ -3934,10 +2459,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - 'neural crest cell' SubClassOf expresses some 'Wnt1 gene' - x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process - expressed in @@ -3964,19 +2486,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. - - - FBbt - - RO:0002207 has developmental precursor - uberon - directly_develops_from - directly_develops_from TODO - add child relations from DOS - directly develops from directly develops from @@ -3986,9 +2498,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of directly develops from - developmental precursor of directly develops into @@ -4016,14 +2526,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. - - - - - GO - Regulation precludes parthood; the regulatory process may not be within the regulated process. - regulates (processual) - false RO:0002211 external regulates @@ -4048,9 +2550,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. - - - negatively regulates (process to process) RO:0002212 external @@ -4081,10 +2580,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. - - - positively regulates (process to process) - RO:0002213 external positively_regulates @@ -4104,17 +2599,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) - osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. - - has function realized in - - - For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". RO:0002215 external - uberon capable_of capable_of @@ -4129,31 +2616,15 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. - - has function in RO:0002216 external - uberon capable_of_part_of capable_of_part_of capable of part of capable of part of - - - - - - - - true - @@ -4162,15 +2633,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x - - - RO:0002219 - uberon - surrounded_by - surrounded_by - surrounded by surrounded by @@ -4182,18 +2645,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. - The epidermis layer of a vertebrate is adjacent to the dermis. - The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. - The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. - x adjacent to y if and only if x and y share a boundary. This relation acts as a join point with BSPO - - RO:0002220 external - uberon adjacent_to @@ -4202,12 +2657,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.adjacent to adjacent to - - - - A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. - - @@ -4215,16 +2664,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of surrounded by - - - RO:0002221 - uberon - surrounds - surrounds - surrounds surrounds @@ -4235,11 +2676,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. - https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to @@ -4253,17 +2689,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of starts with - - Chris Mungall - Allen - RO:0002223 - uberon - starts - starts - starts starts @@ -4275,15 +2702,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor - x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - - Chris Mungall - started by RO:0002224 external - uberon starts_with starts_with @@ -4301,14 +2722,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x develops from part of y if and only if there exists some z such that x develops from z and z is part of y - - RO:0002225 - uberon - develops_from_part_of - develops_from_part_of - develops from part of develops from part of @@ -4323,16 +2737,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x develops_in y if x is located in y whilst x is developing - - EHDAA2 - Jonathan Bard, EHDAA2 - RO:0002226 - uberon - develops_in - develops_in - develops in develops in @@ -4344,16 +2749,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of ends with - - Chris Mungall - RO:0002229 - uberon - ends - ends - ends ends @@ -4365,14 +2762,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - - Chris Mungall - finished by RO:0002230 external - uberon ends_with ends_with @@ -4392,10 +2784,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y - - starts with process that occurs in RO:0002231 external has_start_location @@ -4417,10 +2806,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y - - ends with process that occurs in RO:0002232 external has_end_location @@ -4442,10 +2828,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. - - consumes RO:0002233 external has_input @@ -4470,10 +2853,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. - - produces RO:0002234 external has_output @@ -4495,13 +2875,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1. b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t. - - RO:0002252 - uberon - connecting_branch_of - connecting_branch_of connecting branch of @@ -4513,7 +2887,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of connecting branch of - has connecting branch @@ -4531,15 +2904,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] - x has developmental contribution from y iff x has some part z such that z develops from y - - RO:0002254 - uberon - has_developmental_contribution_from - has_developmental_contribution_from - has developmental contribution from has developmental contribution from @@ -4554,9 +2919,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of has developmental contribution from - developmentally contributes to @@ -4570,21 +2933,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T - - - - induced by - - Developmental Biology, Gilbert, 8th edition, figure 6.5(F) - GO:0001759 - We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm] - RO:0002256 - uberon - developmentally_induced_by - developmentally_induced_by - developmentally induced by developmentally induced by @@ -4595,9 +2944,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Inverse of developmentally induced by - developmentally induces @@ -4610,11 +2957,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false - - In general you should not use this relation to make assertions - use one of the more specific relations below this one This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from developmentally preceded by @@ -4629,7 +2973,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. acts upstream of @@ -4646,7 +2989,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects @@ -4660,16 +3002,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage - - replaces - RO:0002285 - uberon - developmentally_replaces - developmentally_replaces - developmentally replaces developmentally replaces @@ -4679,9 +3013,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Inverse of developmentally preceded by - developmentally succeeded by @@ -4695,9 +3027,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue - - part of developmental precursor of @@ -4707,9 +3036,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process. - expresses @@ -4721,10 +3048,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. - RO:0002295 external results_in_developmental_progression_of @@ -4741,11 +3066,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - every flower development (GO:0009908) results in development of some flower (PO:0009046) - p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. - - http://www.geneontology.org/GO.doc.development.shtml RO:0002296 external results_in_development_of @@ -4765,11 +3086,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. - every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) - - - GOC:mtg_berkeley_2013 RO:0002297 external results_in_formation_of @@ -4778,7 +3094,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. results_in_formation_of results in formation of - results in formation of + results in formation of anatomical entity @@ -4788,12 +3104,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. - tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) - The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. - - GOC:mtg_berkeley_2013 RO:0002298 external results_in_morphogenesis_of @@ -4812,12 +3123,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process - bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) - The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. - - GOC:mtg_berkeley_2013 RO:0002299 external results_in_maturation_of @@ -4837,8 +3143,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. - - RO:0002304 external causally_upstream_of,_positive_effect @@ -4859,7 +3163,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. - RO:0002305 external causally_upstream_of,_negative_effect @@ -4876,32 +3179,15 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of characteristic of part of - - inheres in part of - - characteristic of part of - - - - - - - - true - @@ -4911,10 +3197,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity - - GOC:mtg_berkeley_2013 RO:0002315 external results_in_acquisition_of_features_of @@ -4932,8 +3215,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A relationship that holds via some environmental process - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. evolutionarily related to @@ -4943,9 +3224,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A mereological relationship or a topological relationship - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships - mereotopologically related to @@ -4955,8 +3233,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A relationship that holds between entities participating in some developmental process (GO:0032502) - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development developmentally related to @@ -4975,15 +3251,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - a particular instances of akt-2 enables some instance of protein kinase activity c enables p iff c is capable of p and c acts to execute p. - - catalyzes - executes - has - is catalyzing - is executing - This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. enables https://wiki.geneontology.org/Enables @@ -4995,13 +3263,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. - - This is a grouping relation that collects relations used for the purpose of connecting structure and function - RO:0002328 - uberon - functionally_related_to - functionally_related_to - functionally related to functionally related to @@ -5011,24 +3272,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - this relation holds between c and p when c is part of some c', and c' is capable of p. - - false part of structure that is capable of - - - - - - - - true - @@ -5038,8 +3284,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts. - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism genomically related to @@ -5059,9 +3303,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. c involved_in p if and only if c enables some process p', and p' is part of p - - actively involved in - enables part of involved in https://wiki.geneontology.org/Involved_in @@ -5074,11 +3315,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid p regulates levels of c if p regulates some amount (PATO:0000070) of c - - - regulates levels of (process to entity) RO:0002332 external regulates_levels_of @@ -5095,7 +3332,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of enables - enabled by https://wiki.geneontology.org/Enabled_by @@ -5111,8 +3347,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of regulates - - regulated by (processual) RO:0002334 external regulated_by @@ -5129,7 +3363,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of negatively regulates - RO:0002335 external negatively_regulated_by @@ -5146,7 +3379,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of positively regulates - RO:0002336 external positively_regulated_by @@ -5164,8 +3396,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A relationship that holds via some process of localization - - Do not use this relation directly. It is a grouping relation. related via localization to @@ -5180,7 +3410,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. - RO:0002338 external has_target_start_location @@ -5203,7 +3432,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. - RO:0002339 external has_target_end_location @@ -5222,7 +3450,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l - RO:0002341 external results_in_transport_along @@ -5239,7 +3466,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. - RO:0002342 external results_in_transport_across @@ -5256,8 +3482,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - 'pollen tube growth' results_in growth_of some 'pollen tube' - RO:0002343 external results_in_growth_of @@ -5272,8 +3496,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) - RO:0002344 external results_in_transport_to_from_or_in @@ -5289,12 +3511,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - An organism that is a member of a population of organisms is member of is a mereological relation between a item and a collection. - is member of - member part of - SIO - member of @@ -5306,13 +3523,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. has member is a mereological relation between a collection and an item. - SIO - - RO:0002351 - uberon - has_member - has_member - has member has member @@ -5324,14 +3534,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of has input - - RO:0002352 - uberon - input_of - input_of - input of input of @@ -5343,10 +3547,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of has output - RO:0002353 external - uberon output_of @@ -5361,7 +3563,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - formed as result of @@ -5371,8 +3572,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - http://neurolex.org/wiki/Property:DendriteLocation has dendrite location @@ -5385,14 +3584,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a - - attached to (anatomical structure to anatomical structure) - RO:0002371 - uberon - attaches_to - attaches_to - attached to attached to @@ -5405,13 +3597,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. - - Wikipedia:Insertion_(anatomy) - RO:0002372 - uberon - has_muscle_origin - has_muscle_origin - has muscle origin has muscle origin @@ -5431,13 +3616,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. - - Wikipedia:Insertion_(anatomy) - RO:0002373 - uberon - has_muscle_insertion - has_muscle_insertion - has muscle insertion has muscle insertion @@ -5456,12 +3634,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships - This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) - in branching relationship with https://github.com/obophenotype/uberon/issues/170 @@ -5474,23 +3647,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Deschutes River tributary_of Columbia River - inferior epigastric vein tributary_of external iliac vein - x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. - - drains into - drains to - tributary channel of - http://en.wikipedia.org/wiki/Tributary - http://www.medindia.net/glossary/venous_tributary.htm - This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries) - RO:0002376 - uberon - tributary_of - tributary_of - tributary of tributary of http://en.wikipedia.org/wiki/Tributary @@ -5508,10 +3666,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location - - This relation is added for formal completeness. It is unlikely to be used in many practical scenarios spatially coextensive with @@ -5523,15 +3678,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y - - RO:0002380 - uberon - branching_part_of - branching_part_of - branching part of branching part of FMA:85994 @@ -5545,9 +3693,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). - has developmental potential involving @@ -5557,14 +3703,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y - - RO:0002385 - uberon - has_potential_to_developmentally_contribute_to - has_potential_to_developmentally_contribute_to - has potential to developmentally contribute to has potential to developmentally contribute to @@ -5574,9 +3713,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y - has potential to developmentally induce @@ -5586,14 +3723,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x has the potential to develop into y iff x develops into y or if x is capable of developing into y - - RO:0002387 - uberon - has_potential_to_develop_into - has_potential_to_develop_into - has potential to develop into has potential to develop into @@ -5603,9 +3733,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y - has potential to directly develop into @@ -5617,9 +3745,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of upstream of - RO:0002404 external causally_downstream_of @@ -5636,8 +3762,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - RO:0002405 external immediately_causally_downstream_of @@ -5671,9 +3795,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. - - indirectly activates - indirectly positively regulates https://wiki.geneontology.org/Indirectly_positively_regulates @@ -5699,9 +3820,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. - - indirectly inhibits - indirectly negatively regulates https://wiki.geneontology.org/Indirectly_negatively_regulates @@ -5727,8 +3845,6 @@ For the second, we consider a relationship to be regulatory if the system in whi For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to @@ -5747,7 +3863,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. - RO:0002411 external causally_upstream_of @@ -5766,8 +3881,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. - - RO:0002412 external immediately_causally_upstream_of @@ -5786,8 +3899,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 - - influences (processual) RO:0002418 external affects @@ -5804,8 +3915,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different inverse of causally upstream of or within - - RO:0002427 external causally_downstream_of_or_within @@ -5830,7 +3939,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' regulates some p - involved in regulation of @@ -5849,8 +3957,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' positively regulates some p - - involved in positive regulation of @@ -5869,7 +3975,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' negatively regulates some p - involved in negative regulation of @@ -5884,8 +3989,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union - - involved in or reguates involved in or involved in regulation of @@ -5896,28 +3999,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - - executes activity in enables activity in is active in https://wiki.geneontology.org/Is_active_in - - - - - - - - true - @@ -5933,11 +4020,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. - - RO:0002433 - uberon - contributes_to_morphology_of - contributes_to_morphology_of contributes to morphology of @@ -5952,13 +4034,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different A relationship that holds between two entities in which the processes executed by the two entities are causally connected. This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. Considering relabeling as 'pairwise interacts with' - - Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. in pairwise interaction with interacts with http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ - http://purl.obolibrary.org/obo/MI_0914 @@ -5969,12 +4048,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. - - binds - molecularly binds with molecularly interacts with - http://purl.obolibrary.org/obo/MI_0915 @@ -5984,8 +4059,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different Axiomatization to GO to be added later - - An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. phosphorylates @@ -6006,8 +4079,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. - - molecularly controls directly regulates activity of @@ -6027,9 +4098,6 @@ A and B can be physically interacting but not necessarily. Immediately upstream The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. - - - directly inhibits molecularly decreases activity of directly negatively regulates activity of @@ -6049,9 +4117,6 @@ For example, A and B may be gene products and binding of B by A negatively regul The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. - - - directly activates molecularly increases activity of directly positively regulates activity of @@ -6061,8 +4126,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. helper property (not for use in curation) @@ -6074,16 +4137,8 @@ For example, A and B may be gene products and binding of B by A positively regul - 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. - - - - RO:0002473 - uberon - composed_primarily_of - composed_primarily_of composed primarily of @@ -6094,24 +4149,10 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. - has part that occurs in - - - - - - - - true - @@ -6119,7 +4160,6 @@ For example, A and B may be gene products and binding of B by A positively regul - is kinase activity @@ -6131,7 +4171,6 @@ For example, A and B may be gene products and binding of B by A positively regul See notes for inverse relation - receives input from @@ -6142,7 +4181,6 @@ For example, A and B may be gene products and binding of B by A positively regul This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. - sends output to @@ -6153,8 +4191,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. relation between physical entity and a process or stage @@ -6170,11 +4206,6 @@ For example, A and B may be gene products and binding of B by A positively regul x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). - - RO:0002488 - uberon - existence_starts_during - existence_starts_during existence starts during @@ -6185,11 +4216,6 @@ For example, A and B may be gene products and binding of B by A positively regul x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). - - RO:0002489 - uberon - existence_starts_with - existence_starts_with existence starts with @@ -6200,7 +4226,6 @@ For example, A and B may be gene products and binding of B by A positively regul x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence overlaps @@ -6213,12 +4238,7 @@ For example, A and B may be gene products and binding of B by A positively regul x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) - - RO:0002491 exists during - uberon - existence_starts_and_ends_during - existence_starts_and_ends_during The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts and ends during @@ -6234,23 +4254,10 @@ For example, A and B may be gene products and binding of B by A positively regul - Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). - - RO:0002492 - ceases_to_exist_during - uberon - existence_ends_during - existence_ends_during The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during - - - - Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. - https://orcid.org/0000-0002-6601-2165 - @@ -6259,11 +4266,6 @@ For example, A and B may be gene products and binding of B by A positively regul x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). - - RO:0002493 - uberon - existence_ends_with - existence_ends_with The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends with @@ -6276,11 +4278,6 @@ For example, A and B may be gene products and binding of B by A positively regul x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships - - RO:0002494 - uberon - transformation_of - transformation_of transformation of @@ -6292,12 +4289,6 @@ For example, A and B may be gene products and binding of B by A positively regul x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t - - - RO:0002495 - uberon - immediate_transformation_of - immediate_transformation_of immediate transformation of @@ -6328,11 +4319,6 @@ For example, A and B may be gene products and binding of B by A positively regul x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). - - RO:0002496 - uberon - existence_starts_during_or_after - existence_starts_during_or_after The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts during or after @@ -6364,11 +4350,6 @@ For example, A and B may be gene products and binding of B by A positively regul x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. - - RO:0002497 - uberon - existence_ends_during_or_before - existence_ends_during_or_before The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during or before @@ -6381,7 +4362,6 @@ For example, A and B may be gene products and binding of B by A positively regul A relationship between a material entity and a process where the material entity has some causal role that influences the process - causal agent in process @@ -6394,9 +4374,6 @@ For example, A and B may be gene products and binding of B by A positively regul p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. - - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes @@ -6405,7 +4382,6 @@ For example, A and B may be gene products and binding of B by A positively regul - depends on @@ -6419,9 +4395,6 @@ For example, A and B may be gene products and binding of B by A positively regul The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch - - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between entities @@ -6435,17 +4408,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. - - has supporting framework - The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). - RO:0002551 - uberon - has_skeleton - has_skeleton has skeleton @@ -6462,9 +4426,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - causally influenced by (entity-centric) causally influenced by @@ -6474,7 +4435,6 @@ For example, A and B may be gene products and binding of B by A positively regul - interaction relation helper property http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ @@ -6486,7 +4446,6 @@ For example, A and B may be gene products and binding of B by A positively regul - molecular interaction relation helper property @@ -6497,8 +4456,6 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - - RO:0002565 external results_in_movement_of @@ -6528,10 +4485,6 @@ For example, A and B may be gene products and binding of B by A positively regul The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). - - - - causally influences (entity-centric) causally influences @@ -6544,8 +4497,6 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between elements of a musculoskeletal system or its analogs. - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. biomechanically related to @@ -6556,12 +4507,6 @@ For example, A and B may be gene products and binding of B by A positively regul m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. - - Wikipedia:Antagonist_(muscle) - RO:0002568 - uberon - has_muscle_antagonist - has_muscle_antagonist has muscle antagonist @@ -6574,13 +4519,8 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of branching part of - - RO:0002569 - uberon - has_branching_part - has_branching_part has branching part @@ -6593,14 +4533,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. - - UBERON:cjm - This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. - RO:0002570 - uberon - conduit_for - conduit_for conduit for @@ -6612,13 +4545,7 @@ For example, A and B may be gene products and binding of B by A positively regul x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - - - RO:0002571 - uberon - lumen_of - lumen_of lumen of @@ -6630,12 +4557,7 @@ For example, A and B may be gene products and binding of B by A positively regul s is luminal space of x iff s is lumen_of x and s is an immaterial entity - - RO:0002572 - uberon - luminal_space_of - luminal_space_of luminal space of @@ -6648,12 +4570,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has skeleton - - RO:0002576 - uberon - skeleton_of - skeleton_of skeleton of @@ -6665,10 +4582,6 @@ For example, A and B may be gene products and binding of B by A positively regul p directly regulates q iff p is immediately causally upstream of q and p regulates q. - - - directly regulates (processual) - RO:0002578 external directly_regulates @@ -6690,9 +4603,7 @@ For example, A and B may be gene products and binding of B by A positively regul - gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p - has part structure that is capable of @@ -6762,8 +4673,6 @@ For example, A and B may be gene products and binding of B by A positively regul A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - - causal relation between material entity and a process @@ -6777,9 +4686,7 @@ For example, A and B may be gene products and binding of B by A positively regul - pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. - capable of regulating @@ -6794,7 +4701,6 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. - capable of negatively regulating @@ -6808,9 +4714,7 @@ For example, A and B may be gene products and binding of B by A positively regul - renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. - capable of positively regulating @@ -6821,7 +4725,6 @@ For example, A and B may be gene products and binding of B by A positively regul Inverse of 'causal agent in process' - RO:0002608 external process_has_causal_agent @@ -6837,9 +4740,6 @@ For example, A and B may be gene products and binding of B by A positively regul p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. - - directly positively regulates (process to process) - RO:0002629 external directly_positively_regulates @@ -6859,8 +4759,6 @@ For example, A and B may be gene products and binding of B by A positively regul p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. - - directly negatively regulates (process to process) RO:0002630 external @@ -6887,12 +4785,9 @@ For example, A and B may be gene products and binding of B by A positively regul - a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. - RO:0003000 external - uberon produces produces @@ -6908,12 +4803,9 @@ For example, A and B may be gene products and binding of B by A positively regul - a produced_by b iff some process that occurs_in b has_output a. - RO:0003001 external - uberon produced_by produced_by @@ -7020,7 +4912,6 @@ For example, A and B may be gene products and binding of B by A positively regul - 2018-01-26T23:49:30Z @@ -7058,7 +4949,6 @@ For example, A and B may be gene products and binding of B by A positively regul c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive - 2018-01-26T23:53:14Z @@ -7105,7 +4995,6 @@ For example, A and B may be gene products and binding of B by A positively regul - 2018-03-13T23:55:19Z causally upstream of or within, positive effect @@ -7121,7 +5010,6 @@ For example, A and B may be gene products and binding of B by A positively regul The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. - regulates activity of @@ -7369,7 +5257,6 @@ For example, A and B may be gene products and binding of B by A positively regul - 'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)') A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. @@ -7389,7 +5276,6 @@ For example, A and B may be gene products and binding of B by A positively regul - 'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor') A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. @@ -7411,12 +5297,7 @@ For example, A and B may be gene products and binding of B by A positively regul - A diagnostic testing device utilizes a specimen. X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. - - - A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. - See github ticket https://github.com/oborel/obo-relations/issues/497 2021-11-08T12:00:00Z utilizes device utilizes material @@ -7542,7 +5423,6 @@ For example, A and B may be gene products and binding of B by A positively regul - x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y. @@ -7562,8 +5442,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - carries uberon channel_for @@ -7575,7 +5453,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uberon channels_from channels_from @@ -7586,7 +5463,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uberon channels_into channels_into @@ -7597,10 +5473,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y. uberon distally_connected_to @@ -7619,11 +5493,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y uberon extends_fibers_into @@ -7653,11 +5522,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - @@ -7685,7 +5549,6 @@ For example, A and B may be gene products and binding of B by A positively regul - x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y. uberon @@ -7714,7 +5577,6 @@ For example, A and B may be gene products and binding of B by A positively regul - x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y. @@ -7768,7 +5630,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uberon transitively_anteriorly_connected_to transitively anteriorly connected to @@ -7780,7 +5641,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uberon transitively_distally_connected_to transitively distally connected to @@ -7792,7 +5652,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uberon transitively_proximally_connected_to transitively proximally connected to @@ -15450,32 +13309,32 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer - + - + - + PMID:12382326 - + PMID:12382326 @@ -23691,7 +21550,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 PMID:15371245 ncbi_taxonomy @@ -23705,7 +21563,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 Mus mice @@ -23724,7 +21581,7 @@ For example, A and B may be gene products and binding of B by A positively regul mice - + @@ -23739,7 +21596,6 @@ For example, A and B may be gene products and binding of B by A positively regul - NCBITaxon:85055 GC_ID:1 house mouse @@ -23767,7 +21623,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 ncbi_taxonomy NCBITaxon:117570 @@ -23780,7 +21635,6 @@ For example, A and B may be gene products and binding of B by A positively regul - NCBITaxon:40673 GC_ID:1 bony vertebrates @@ -23820,7 +21674,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 ncbi_taxonomy NCBITaxon:1338369 @@ -23833,7 +21686,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 PMID:11743200 PMID:11791233 @@ -23855,7 +21707,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 mice and others ncbi_taxonomy @@ -23882,7 +21733,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 PMID:23020233 PMID:30257078 @@ -23946,7 +21796,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 PMID:11214319 PMID:12082125 @@ -23963,7 +21812,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 PMID:11214319 PMID:12082125 @@ -23986,7 +21834,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 tetrapods ncbi_taxonomy @@ -24006,7 +21853,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 amniotes ncbi_taxonomy @@ -24026,7 +21872,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 Theria ncbi_taxonomy @@ -24046,7 +21891,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 ncbi_taxonomy Fungi/Metazoa group @@ -24073,7 +21917,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 metazoans multicellular animals @@ -24114,7 +21957,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 ncbi_taxonomy NCBITaxon:33213 @@ -24127,7 +21969,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 deuterostomes ncbi_taxonomy @@ -24147,7 +21988,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 PMID:15019624 PMID:15371245 @@ -24162,7 +22002,6 @@ For example, A and B may be gene products and binding of B by A positively regul - NCBITaxon:109679 GC_ID:1 ncbi_taxonomy @@ -24176,7 +22015,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 mammals ncbi_taxonomy @@ -24203,7 +22041,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 ncbi_taxonomy NCBITaxon:6072 @@ -24216,7 +22053,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 chordates ncbi_taxonomy @@ -24243,7 +22079,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 Vertebrata vertebrates @@ -24277,7 +22112,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 Gnathostomata jawed vertebrates @@ -24304,7 +22138,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 ncbi_taxonomy NCBITaxon:8287 @@ -24317,7 +22150,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 Mus ncbi_taxonomy @@ -24337,7 +22169,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 Craniata ncbi_taxonomy @@ -24357,7 +22188,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 eutherian mammals placental mammals @@ -24405,7 +22235,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 rodent ncbi_taxonomy @@ -24807,7 +22636,6 @@ For example, A and B may be gene products and binding of B by A positively regul A contractility quality inhering in a bearer by virtue of the bearer's ability of contracting or being contracted. - quality PATO:0001690 @@ -24963,7 +22791,6 @@ For example, A and B may be gene products and binding of B by A positively regul A complete three dimensional shape in which for every line connecting pair of points on the object is within the object. Or: a shape lacking cavities. Contrast: concave. - Image:http://upload.wikimedia.org/wikipedia/commons/0/06/Convex_polygon_illustration1.png quality PATO:0002007 @@ -25490,7 +23317,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001006 Category=gene. Requested by=CL. receptor-type tyrosine-protein phosphatase C - @@ -25540,7 +23366,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001012 Category=gene. Requested by=CL. integrin alpha-M - @@ -25587,7 +23412,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001013 Category=gene. Requested by=CL. integrin alpha-X - @@ -25622,7 +23446,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001015 Category=sequence. Requested by=CL. Note: This isoform includes the region encoded by the variable exon 4(A), and lacks the region encoded by exons 5(B) and 6(C). receptor-type tyrosine-protein phosphatase C isoform CD45RA - @@ -25756,7 +23579,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001024 Category=gene. Requested by=CL. neural cell adhesion molecule 1 - @@ -25841,7 +23663,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001084 Category=gene. Requested by=CL. T-cell surface glycoprotein CD8 alpha chain - @@ -25971,7 +23792,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001332 Category=gene. Requested by=CL. carcinoembryonic antigen-related cell adhesion molecule 8 - @@ -26034,7 +23854,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001381 Category=gene. Requested by=CL. interleukin-2 receptor subunit beta - @@ -26078,7 +23897,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001444 Category=gene. Requested by=CL. cadherin-5 - @@ -26200,7 +24018,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001839 Category=gene. Requested by=CL. T-cell surface glycoprotein CD5 - @@ -26240,7 +24057,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001850 Category=gene. Requested by=CL. cathepsin K - @@ -26337,7 +24153,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001869 Category=gene. Requested by=CL. interleukin-7 receptor subunit alpha - @@ -26394,7 +24209,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001879 Category=gene. Requested by=CL. leukosialin - @@ -26471,7 +24285,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001898 Category=gene. Requested by=CL. neprilysin - @@ -26508,7 +24321,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001903 Category=gene. Requested by=CL. paired box protein PAX-5 - @@ -26549,7 +24361,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001937 Category=gene. Requested by=CL. tartrate-resistant acid phosphatase type 5 - @@ -26593,7 +24404,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001944 Category=gene. Requested by=CL. transcription factor PU.1 - @@ -26640,7 +24450,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001954 Category=gene. Requested by=CL. tumor necrosis factor receptor superfamily member 11A - @@ -26681,7 +24490,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001969 Category=gene. Requested by=CL. urokinase plasminogen activator surface receptor - @@ -26751,7 +24559,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000002062 Category=gene. Requested by=CL. macrophage colony-stimulating factor 1 receptor - @@ -26847,7 +24654,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000002112 Category=gene. Requested by=CL. vascular endothelial growth factor receptor 2 - @@ -26968,7 +24774,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000005307 Category=gene. Requested by=CL. CCAAT/enhancer-binding protein alpha - @@ -27006,7 +24811,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000006611 Category=gene. Requested by=CL. DNA nucleotidylexotransferase - @@ -27045,7 +24849,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000007597 Category=gene. Requested by=CL. protein c-Fos - @@ -27086,7 +24889,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000007857 Category=gene. Requested by=CL. erythroid transcription factor - @@ -27127,7 +24929,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000007858 Category=gene. Requested by=CL. endothelial transcription factor GATA-2 - @@ -27162,7 +24963,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000011178 Category=gene. Requested by=CL. nuclear factor NF-kappa-B p100 subunit - @@ -27200,7 +25000,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000014841 Category=gene. sonic hedgehog protein - @@ -27242,7 +25041,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000016043 Category=gene. Requested by=CL. T-cell acute lymphocytic leukemia protein 1 - @@ -27575,7 +25373,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA2:0001824 EHDAA:500 EMAPA:35955 - FBbt:00005155 GAID:63 HAO:0000930 MA:0000017 @@ -27608,12 +25405,6 @@ For example, A and B may be gene products and binding of B by A positively regul https://github.com/obophenotype/uberon/issues/549 https://orcid.org/0000-0002-6601-2165 - - - - FBbt:00005155 - - @@ -27699,8 +25490,6 @@ For example, A and B may be gene products and binding of B by A positively regul Any hollow cylindrical anatomical structure containing a lumen through which substances are transported. - not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts) - tubular galen:Tube anatomical tube duct @@ -27721,8 +25510,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -27742,9 +25531,6 @@ For example, A and B may be gene products and binding of B by A positively regul Dense regular connective tissue that connects muscle to bone[VSAO]. - Dense regular connective tissue that connects muscle to bone.[VSAO] - Phylogenetically, tendinous tissue first appears in the invertebrate chordate Branchiostoma as myosepta. This two-dimensional array of collagen fibers is highly organized, with fibers running along two primary axes. In hagfish the first linear tendons appear and the myosepta have developed specialized regions with unidirectional fiber orientation - a linear tendon within the flat sheet of myoseptum.[well established][VHOG] - in FMA, tendon is an organ component that with parts dense-irregular-connective-tissue of tendon and dense-irregular-connective-tissue of tendon sheath; we follow VSAO in making it a subtype of the former. In VSAO tendons connect muscle to bone; in WP the def states integument (e.g. auricular muscles) - but JB confirms this is not actually tendon but aponeurosis AEO:0000091 BTO:0001356 CALOHA:TS-1021 @@ -27773,11 +25559,11 @@ For example, A and B may be gene products and binding of B by A positively regul tendon http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg - + - + @@ -27790,13 +25576,13 @@ For example, A and B may be gene products and binding of B by A positively regul - + OG - + AEO @@ -27808,31 +25594,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Tendon http://dx.plos.org/10.1371/journal.pone.0051070 - - - - Dense regular connective tissue that connects muscle to bone.[VSAO] - 2012-08-14 - VSAO:0000073 - VSAO - PSPUB:0000170 - - - - - Phylogenetically, tendinous tissue first appears in the invertebrate chordate Branchiostoma as myosepta. This two-dimensional array of collagen fibers is highly organized, with fibers running along two primary axes. In hagfish the first linear tendons appear and the myosepta have developed specialized regions with unidirectional fiber orientation - a linear tendon within the flat sheet of myoseptum.[well established][VHOG] - 2012-09-17 - VHOG:0001286 - VHOG - DOI:10.1016/S1095-6433(02)00241-6 Summers AP, Koob TJ, The evolution of tendon - morphology and material properties. Comparative Biochemistry and Physiology-Part A: Molecular and Integrative Physiology (2002) - http://bgee.unil.ch/ - - - - - in FMA, tendon is an organ component that with parts dense-irregular-connective-tissue of tendon and dense-irregular-connective-tissue of tendon sheath; we follow VSAO in making it a subtype of the former. In VSAO tendons connect muscle to bone; in WP the def states integument (e.g. auricular muscles) - but JB confirms this is not actually tendon but aponeurosis - FMA - @@ -27879,10 +25640,7 @@ For example, A and B may be gene products and binding of B by A positively regul A tubular structure that transports secreted or excreted substances. - A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171]. - Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here. AAO:0011123 - FBbt:00100314 FMA:30320 NCIT:C12948 SCTID:91726008 @@ -27908,18 +25666,6 @@ For example, A and B may be gene products and binding of B by A positively regul http://orcid.org/0000-0002-6601-2165 http://www.siumed.edu/~dking2/intro/glands.htm#ducts - - - - A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171]. - ZFA:0005171 - - - - - FBbt:00100314 - - @@ -27953,10 +25699,8 @@ For example, A and B may be gene products and binding of B by A positively regul Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. - in FMA, serosa is a wall UBERON:0009915 wall - EMAPA:25036 FMA:82482 galen:Wall wall of organ @@ -27972,12 +25716,6 @@ For example, A and B may be gene products and binding of B by A positively regul Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. FMA:82482 - - - - in FMA, serosa is a wall - FMA - @@ -28013,7 +25751,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0000003 EHDAA2:0003003 EMAPA:0 - FBbt:00007001 FMA:305751 FMA:67135 GAID:781 @@ -28041,12 +25778,6 @@ For example, A and B may be gene products and binding of B by A positively regul Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. CARO:0000003 - - - - FBbt:00007001 - - @@ -28084,8 +25815,6 @@ For example, A and B may be gene products and binding of B by A positively regul - Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. - CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4 BIRNLEX:4 CARO:0020004 EFO:0000634 @@ -28119,12 +25848,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia - - - - Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. - GO:0048513 - @@ -28146,8 +25869,6 @@ For example, A and B may be gene products and binding of B by A positively regul A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity. FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction - Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball. - Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal. FMA:86140 uberon organ region with fixed fiat boundary @@ -28163,20 +25884,6 @@ For example, A and B may be gene products and binding of B by A positively regul A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity. http://orcid.org/0000-0002-6601-2165 - - - - Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball. - FMA:86140 - 3 - - - - - Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal. - FMA:86140 - 1 - @@ -28209,7 +25916,6 @@ For example, A and B may be gene products and binding of B by A positively regul A multicellular structure that is a part of an organ. - currently defined in a very broad sense, may be replaced by more specific classes in the future @@ -28366,7 +26072,6 @@ For example, A and B may be gene products and binding of B by A positively regul - ncit:Death is an outcome XAO:0000437 XtroDO:0000085 uberon @@ -28381,12 +26086,6 @@ For example, A and B may be gene products and binding of B by A positively regul End of the life of an organism. XAO:0000437 - - - - ncit:Death is an outcome - ncit - @@ -28472,7 +26171,6 @@ For example, A and B may be gene products and binding of B by A positively regul Stage succeeding embryo, including mature structure. - In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997) BilaDO:0000003 OGES:000010 OGES:000014 @@ -28558,8 +26256,6 @@ For example, A and B may be gene products and binding of B by A positively regul - the WBls class 'all stages' belongs here as it is the superclass of other WBls stages - we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage BILS:0000105 EFO:0000399 FBdv:00007012 @@ -28610,13 +26306,11 @@ For example, A and B may be gene products and binding of B by A positively regul A stage at which the organism is a single cell produced by means of sexual reproduction. - As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG] BILS:0000106 BilaDO:0000005 EFO:0001322 EHDAA:27 FBdv:00005288 - IDOMAL:0000302 NCIT:C12601 PdumDv:0000100 VHOG:0000745 @@ -28642,24 +26336,6 @@ For example, A and B may be gene products and binding of B by A positively regul A stage at which the organism is a single cell produced by means of sexual reproduction. Wikipedia:Zygote - - - - As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG] - 2012-09-17 - VHOG:0000745 - VHOG - ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107 - http://bgee.unil.ch/ - - - - - IDOMAL:0000302 - - - https://github.com/biopragmatics/biomappings - @@ -28807,7 +26483,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -28843,14 +26519,14 @@ For example, A and B may be gene products and binding of B by A positively regul gastrula stage - + - + BILS @@ -28928,8 +26604,6 @@ For example, A and B may be gene products and binding of B by A positively regul Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system. - - In zebrafish, the times of neurulation and segmentation overlap so extensively there is no distinct neurula period of development, such as occurs largely before segmentation in amphibian embryos. BILS:0000110 BilaDO:0000009 HsapDv:0000012 @@ -29000,24 +26674,7 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - @@ -29031,11 +26688,6 @@ For example, A and B may be gene products and binding of B by A positively regul The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks). - Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO] - Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG] - oral - some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives - in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips AAO:0010355 BTO:0001090 BTO:0004698 @@ -29044,7 +26696,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA2:0001326 EHDAA:542 EMAPA:16262 - FBbt:00003126 FMA:49184 GAID:75 MA:0000341 @@ -29090,12 +26741,6 @@ For example, A and B may be gene products and binding of B by A positively regul https://github.com/obophenotype/uberon/issues/661 http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg - - - - - the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts - @@ -29103,37 +26748,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Mouth https://github.com/obophenotype/uberon/wiki/The-digestive-tract - - - - Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO] - 2012-06-20 - AAO:0010355 - AAO - AAO:BJB - - - - - Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG] - 2012-09-17 - VHOG:0000812 - VHOG - DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008) - http://bgee.unil.ch/ - - - - - in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips - FMA - - - - - FBbt:00003126 - - @@ -29315,14 +26929,11 @@ For example, A and B may be gene products and binding of B by A positively regul consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77 - Anatomical system that consists of the muscles of the body.[VSAO] - we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA AAO:0000307 BILA:0000088 BTO:0001369 BTO:0001485 EFO:0000801 - EMAPA:35578 FMA:72954 MA:0002888 MAT:0000025 @@ -29350,21 +26961,6 @@ For example, A and B may be gene products and binding of B by A positively regul The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified]. VSAO:0000033 - - - - Anatomical system that consists of the muscles of the body.[VSAO] - 2012-08-14 - VSAO:0000033 - VSAO - VSAO:curator - - - - - we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA - MA - @@ -29408,7 +27004,12 @@ For example, A and B may be gene products and binding of B by A positively regul - + + + + + + @@ -29426,7 +27027,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0000004 EHDAA2:0003004 EMAPA:35178 - FBbt:00007019 FMA:9669 HAO:0000004 MA:0002450 @@ -29450,28 +27050,12 @@ For example, A and B may be gene products and binding of B by A positively regul organism substance - - - - - - - - - this relationship may be too strong and may be weakened in future - Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007019 - - @@ -29526,7 +27110,6 @@ For example, A and B may be gene products and binding of B by A positively regul BILA:0000005 CARO:0000005 EHDAA2:0003005 - FBbt:00007017 FMA:5897 HAO:0000005 NCIT:C94478 @@ -29550,12 +27133,6 @@ For example, A and B may be gene products and binding of B by A positively regul Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures. http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007017 - - @@ -29587,7 +27164,6 @@ For example, A and B may be gene products and binding of B by A positively regul BILA:0000006 CARO:0000006 EHDAA2:0003006 - FBbt:00007016 FMA:67165 HAO:0000006 TAO:0001836 @@ -29605,12 +27181,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical entity that has mass. http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007016 - - @@ -29628,7 +27198,6 @@ For example, A and B may be gene products and binding of B by A positively regul BILA:0000007 CARO:0000007 EHDAA2:0003007 - FBbt:00007015 FMA:67112 HAO:0000007 TAO:0001835 @@ -29647,12 +27216,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical entity that has no mass. http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007015 - - @@ -29695,10 +27258,8 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA:392 EMAPA:16103 EV:0100000 - FBbt:00004856 FMA:7149 HAO:0000011 - IDOMAL:0002460 MA:0000003 NCIT:C12919 SCTID:278195005 @@ -29738,20 +27299,6 @@ For example, A and B may be gene products and binding of B by A positively regul system GO:0048731 - - - - FBbt:00004856 - - - - - - IDOMAL:0002460 - - - https://github.com/biopragmatics/biomappings - @@ -29789,7 +27336,6 @@ For example, A and B may be gene products and binding of B by A positively regul - organismal organism AAO:0010026 AEO:0000191 @@ -29804,7 +27350,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA:1 EMAPA:25765 EV:0100016 - FBbt:00000001 FMA:256135 HAO:0000012 NCIT:C13041 @@ -29849,12 +27394,6 @@ For example, A and B may be gene products and binding of B by A positively regul VHOG:0000671 WBbt:0007833 - - - - FBbt:00000001 - - @@ -29915,7 +27454,6 @@ For example, A and B may be gene products and binding of B by A positively regul EFO:0000808 EHDAA2:0003032 EMAPA:36031 - FBbt:00007009 FMA:7153 HAO:0000032 MA:0002433 @@ -29958,12 +27496,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:DOS http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007009 - - @@ -30005,7 +27537,6 @@ For example, A and B may be gene products and binding of B by A positively regul BILA:0000040 CARO:0000040 EHDAA2:0003040 - FBbt:00007013 FMA:63863 HAO:0000040 TAO:0000382 @@ -30031,12 +27562,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue. http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007013 - - @@ -30055,7 +27580,6 @@ For example, A and B may be gene products and binding of B by A positively regul - FBbt:00007277 VHOG:0001737 uberon UBERON:0000477 @@ -30069,12 +27593,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical group whose component anatomical structures lie in close proximity to each other. FBbt:00007277 - - - - FBbt:00007277 - - @@ -30107,7 +27625,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0000042 EHDAA2:0003042 EHDAA:46 - FBbt:00005835 FMA:85537 HAO:0000042 NCIT:C34055 @@ -30137,12 +27654,6 @@ For example, A and B may be gene products and binding of B by A positively regul http://orcid.org/0000-0001-9114-8737 https://cedar.bio.indiana.edu/trac/env/ontologies/ticket/279 - - - - FBbt:00005835 - - @@ -30189,7 +27700,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0000043 EHDAA2:0003043 EMAPA:35868 - FBbt:00007003 FMA:9637 HAO:0000043 MA:0003002 @@ -30225,12 +27735,6 @@ For example, A and B may be gene products and binding of B by A positively regul Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. CARO:0000043 - - - - FBbt:00007003 - - @@ -30271,7 +27775,6 @@ For example, A and B may be gene products and binding of B by A positively regul BILA:0000055 CARO:0000055 EHDAA2:0003055 - FBbt:00007010 HAO:0000055 TAO:0001488 TGMA:0001847 @@ -30298,12 +27801,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0000055 http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007010 - - @@ -30350,7 +27847,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -30358,8 +27855,6 @@ For example, A and B may be gene products and binding of B by A positively regul Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]. - The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG] - epithelial AAO:0000144 AAO:0010055 AEO:0000066 @@ -30369,7 +27864,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0000066 EHDAA2:0003066 EMAPA:32738 - FBbt:00007005 FMA:9639 GAID:402 HAO:0000066 @@ -30394,14 +27888,14 @@ For example, A and B may be gene products and binding of B by A positively regul epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg - + - + http://palaeos.com/metazoa/porifera/homoscleromorpha.html @@ -30411,22 +27905,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Epithelium http://orcid.org/0000-0001-9114-8737 - - - - The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG] - 2012-09-17 - VHOG:0000387 - VHOG - ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.59 - http://bgee.unil.ch/ - - - - - FBbt:00007005 - - @@ -30447,7 +27925,6 @@ For example, A and B may be gene products and binding of B by A positively regul Epithelium which consists of more than one layer of epithelial cells that may or may not be in contact with a basement membrane. Examples: keratinized stratified squamous epithelium, ciliated stratified columnar epithelium.[FMA]. - Epithelium that consists of more than one layer of epithelial cells.[CARO] AAO:0010059 AEO:0000069 BILA:0000069 @@ -30479,16 +27956,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Stratified_epithelium http://orcid.org/0000-0001-9114-8737 - - - - Epithelium that consists of more than one layer of epithelial cells.[CARO] - 2012-06-20 - CARO:0000069 - CARO - FMA:45562 - http://orcid.org/0000-0001-9114-8737 - @@ -30510,7 +27977,6 @@ For example, A and B may be gene products and binding of B by A positively regul Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA]. consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable - Epithelium that consists of a single layer of epithelial cells.[CARO] AAO:0010062 AEO:0000073 BILA:0000073 @@ -30539,16 +28005,6 @@ For example, A and B may be gene products and binding of B by A positively regul FMA:45561 http://orcid.org/0000-0001-9114-8737 - - - - Epithelium that consists of a single layer of epithelial cells.[CARO] - 2012-06-20 - CARO:0000073 - CARO - FMA:45561 - http://orcid.org/0000-0001-9114-8737 - @@ -30603,8 +28059,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. - embryonic - Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo AAO:0011035 AEO:0000169 BILA:0000056 @@ -30616,10 +28070,8 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA2_RETIRED:0003236 EHDAA:38 EMAPA:16039 - FBbt:00000052 FMA:69068 GAID:963 - IDOMAL:0000646 MAT:0000226 MESH:D004622 MIAA:0000019 @@ -30655,26 +28107,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0009790 Wikipedia:Embryo - - - - Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo - ZFA - - - - - FBbt:00000052 - - - - - - IDOMAL:0000646 - - - https://github.com/biopragmatics/biomappings - @@ -30707,13 +28139,11 @@ For example, A and B may be gene products and binding of B by A positively regul A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm. - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] embryonic tissue AAO:0000480 BILA:0000035 BTO:0000556 EMAPA:36033 - FBbt:00000110 FMA:69069 GAID:1303 MESH:D005855 @@ -30744,28 +28174,12 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Germ_layer https://github.com/obophenotype/uberon/issues/203 - - - - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - 2012-09-17 - VHOG:0001223 - VHOG - ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 - http://bgee.unil.ch/ - embryonic tissue FMA:69069 - - - - FBbt:00000110 - - @@ -30804,11 +28218,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. - Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO] - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - ectodermal AAO:0000137 BILA:0000036 BTO:0000315 @@ -30817,7 +28228,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA2:0000428 EMAPA:16069 EV:0100003 - FBbt:00000111 FMA:69070 GAID:1304 MAT:0000155 @@ -30842,14 +28252,14 @@ For example, A and B may be gene products and binding of B by A positively regul ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -30858,31 +28268,6 @@ For example, A and B may be gene products and binding of B by A positively regul Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. Wikipedia:Ectoderm - - - - Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO] - 2012-06-20 - AAO:0000137 - AAO - AAO:EJS - - - - - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - 2012-09-17 - VHOG:0000153 - VHOG - ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 - http://bgee.unil.ch/ - - - - - FBbt:00000111 - - @@ -30908,10 +28293,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - endodermal AAO:0000139 BILA:0000038 BTO:0000800 @@ -30920,7 +28303,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA2:0000436 EMAPA:16062 EV:0100005 - FBbt:00000125 FMA:69071 GAID:1305 MAT:0000175 @@ -30945,14 +28327,14 @@ For example, A and B may be gene products and binding of B by A positively regul http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -30961,22 +28343,6 @@ For example, A and B may be gene products and binding of B by A positively regul Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. Wikipedia:Endoderm - - - - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - 2012-09-17 - VHOG:0000154 - VHOG - ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 - http://bgee.unil.ch/ - - - - - FBbt:00000125 - - @@ -31003,13 +28369,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + The middle germ layer of the embryo, between the endoderm and ectoderm. - Primary germ layer that is the middle of the embryonic germ layers.[AAO] - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - mesodermal - sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates UBERON:0003263 AAO:0000304 BILA:0000037 @@ -31022,7 +28384,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA:183 EMAPA:16083 EV:0100006 - FBbt:00000126 FMA:69072 GAID:522 MAT:0000174 @@ -31048,20 +28409,14 @@ For example, A and B may be gene products and binding of B by A positively regul mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + - - sometimes not considered primary - - - - - + Bgee:AN @@ -31070,37 +28425,6 @@ For example, A and B may be gene products and binding of B by A positively regul The middle germ layer of the embryo, between the endoderm and ectoderm. Wikipedia:Mesoderm - - - - Primary germ layer that is the middle of the embryonic germ layers.[AAO] - 2012-06-20 - AAO:0000304 - AAO - AAO:EJS - - - - - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - 2012-09-17 - VHOG:0000152 - VHOG - ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 - http://bgee.unil.ch/ - - - - - sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates - https://github.com/obophenotype/uberon/wiki/The-neural-crest - - - - - FBbt:00000126 - - @@ -31147,15 +28471,10 @@ For example, A and B may be gene products and binding of B by A positively regul Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity. consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence - Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO] - the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx - stomodeal - This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity. stomodeal-hypophyseal primordium BTO:0004224 EHDAA2:0001929 EMAPA:16263 - FBbt:00000439 FMA:295846 NCIT:C34306 TAO:0001290 @@ -31188,34 +28507,12 @@ For example, A and B may be gene products and binding of B by A positively regul http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/326 - - - - Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO] - 2012-08-14 - TAO:0001290 - TAO - ZFIN:curator - - - - - the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx - MP:0012522 - NCBITaxon:40674 - stomodeal-hypophyseal primordium XAO:0000269 - - - - FBbt:00000439 - - @@ -31294,16 +28591,12 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity. - Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO] - Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG] - endocrine AAO:0010279 CALOHA:TS-1301 EFO:0002969 EHDAA2:0002224 EMAPA:35306 EV:0100128 - FBbt:00005068 FMA:9668 GAID:439 MA:0000012 @@ -31334,31 +28627,6 @@ For example, A and B may be gene products and binding of B by A positively regul NLM:endocrine+system Wikipedia:Endocrine_system - - - - Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO] - 2012-06-20 - AAO:0010279 - AAO - AAO:BJB - - - - - Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG] - 2012-09-17 - VHOG:0000098 - VHOG - DOI:10.1073/pnas.0812138106 Markov GV, Tavares R, Dauphin-Villemant C, Demeneix BA, Baker ME, Laudet V, Independent elaboration of steroid hormone signaling pathways in metazoans. PNAS (2009) - http://bgee.unil.ch/ - - - - - FBbt:00005068 - - @@ -31384,8 +28652,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -31393,17 +28661,12 @@ For example, A and B may be gene products and binding of B by A positively regul An organ that detects light. - This class encompasses a variety of light-detecting structures from different phyla with no implication of homology, from the compound insect eye to the vertebrate camera-type eye (distinct classes are provided for each) - ocular - optic - Note that whilst this is classified as an organ, it is in fact more of a unit composed of different structures: in Drosophila, it includes the interommatidial bristle as a part; we consider here the vertebrate eye to include the eyeball/eye proper as a part, with the eye having as parts (when present): eyelids, conjuctiva, BILA:0000017 BTO:0000439 CALOHA:TS-0309 EFO:0000827 EV:0100336 - FBbt:00005162 GAID:69 MAT:0000140 MESH:D005123 @@ -31421,24 +28684,24 @@ For example, A and B may be gene products and binding of B by A positively regul eye - + - + - + PMID:21062451 - + PMID:21062451 @@ -31447,12 +28710,6 @@ For example, A and B may be gene products and binding of B by A positively regul An organ that detects light. https://orcid.org/0000-0002-6601-2165 - - - - FBbt:00005162 - - @@ -31480,8 +28737,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical structure that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO]. - Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO] - Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO] articulation joint AEO:0000182 @@ -31526,24 +28781,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Joint http://dx.plos.org/10.1371/journal.pone.0051070 - - - - Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO] - 2012-08-14 - VSAO:0000101 - VSAO - PSPUB:0000170 - - - - - Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO] - 2012-08-14 - TAO:0000367 - TAO - TAO:pem - @@ -31616,16 +28853,11 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes. - An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO] - digestive - many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class AAO:0000129 BILA:0000082 BTO:0000058 CALOHA:TS-1293 EFO:0000793 - EV:0100056 - FBbt:00005055 FMA:7152 GAID:278 MA:0002431 @@ -31662,27 +28894,6 @@ For example, A and B may be gene products and binding of B by A positively regul NLM:alimentary+system Wikipedia:Digestive_system - - - - An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO] - 2012-06-20 - AAO:0000129 - AAO - AAO:BJB - - - - - many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class - MA - - - - - FBbt:00005055 - - @@ -31716,17 +28927,12 @@ For example, A and B may be gene products and binding of B by A positively regul Organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP]. - the cardiovascular system and the lymphatic system are parts of the circulatory system - - Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO] - We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG] AAO:0000959 CALOHA:TS-2103 - MESH:D002319 VHOG:0001248 Wikipedia:Circulatory_system uberon @@ -31749,38 +28955,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Acoelomorpha - - - - - WBbt coelomocyte currently classified as circulating cell - - - - - Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO] - 2012-06-20 - AAO:0000959 - AAO - AAO:BJB - - - - - We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG] - 2012-09-17 - VHOG:0001248 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.493 - http://bgee.unil.ch/ - - - - - MESH:D002319 - - https://github.com/biopragmatics/biomappings - @@ -31808,12 +28982,8 @@ For example, A and B may be gene products and binding of B by A positively regul A subdivision of the muscular system corresponding to a subdisivision of an organism. - - In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here. - AAO:0011066 BTO:0000887 EFO:0001949 - EMAPA:32715 EMAPA:35577 FMA:32558 MA:0000165 @@ -31849,12 +29019,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Muscular_system https://orcid.org/0000-0002-6601-2165 - - - - In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here. - FMA - @@ -31918,7 +29082,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -31928,11 +29092,6 @@ For example, A and B may be gene products and binding of B by A positively regul The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]. - A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO] - Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO] - Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG] - nervous - neural AAO:0000324 BILA:0000079 BIRNLEX:844 @@ -31943,7 +29102,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA:826 EMAPA:16469 EV:0100162 - FBbt:00005093 FMA:7157 GAID:466 MA:0000016 @@ -31975,14 +29133,14 @@ For example, A and B may be gene products and binding of B by A positively regul http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -31997,40 +29155,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Nervous_system ZFIN:curator - - - - A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO] - 2012-08-14 - TAO:0000396 - TAO - ZFIN:curator - - - - - Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO] - 2012-06-20 - AAO:0000324 - AAO - AAO:BJB - - - - - Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG] - 2012-09-17 - VHOG:0000402 - VHOG - ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.117 - http://bgee.unil.ch/ - - - - - FBbt:00005093 - - @@ -32076,14 +29200,10 @@ For example, A and B may be gene products and binding of B by A positively regul - + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. - Part of the nervous system which includes the brain and spinal cord.[AAO] - The brain and spinal cord. Kimmel et al, 1995.[TAO] - The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO). - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG] AAO:0000090 BAMS:CNS BILA:0000080 @@ -32096,7 +29216,6 @@ For example, A and B may be gene products and binding of B by A positively regul EMAPA:16470 EMAPA:16754 EV:0100163 - FBbt:00005094 FMA:55675 GAID:570 MA:0000167 @@ -32125,7 +29244,7 @@ For example, A and B may be gene products and binding of B by A positively regul central nervous system - + @@ -32139,7 +29258,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + Bgee:AN @@ -32156,46 +29275,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Acoelomorpha - - - - Part of the nervous system which includes the brain and spinal cord.[AAO] - 2012-06-20 - AAO:0000090 - AAO - AAO:BJB - - - - - The brain and spinal cord. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000012 - TAO - ZFIN:curator - - - - - The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO). - BIRNLEX:1099 - - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG] - 2012-09-17 - VHOG:0000293 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 (reference 1), ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 (reference 2), DOI:10.1016/j.cell.2007.02.040 Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud'homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007) (reference 3) - http://bgee.unil.ch/ - - - - - FBbt:00005094 - - @@ -32255,15 +29334,12 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information. - An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG] - note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs AAO:0000555 BAMS:SEN BILA:0000099 EFO:0000805 EHDAA2:0003094 EMAPA:16192 - FBbt:00007692 FMA:75259 MA:0002442 MAT:0000031 @@ -32297,22 +29373,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information. Wikipedia:Sensory_system - - - - An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG] - 2012-09-17 - VHOG:0001674 - VHOG - DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) - http://bgee.unil.ch/ - - - - - FBbt:00007692 - - @@ -32370,10 +29430,6 @@ For example, A and B may be gene products and binding of B by A positively regul In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted]. - Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO] - The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG] - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] - The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium AAO:0010617 BTO:0001057 CALOHA:TS-2371 @@ -32385,7 +29441,6 @@ For example, A and B may be gene products and binding of B by A positively regul EMAPA:16757 FMA:293882 MAT:0000069 - MESH:D054259 MIAA:0000069 NCIT:C34226 SCTID:362852000 @@ -32419,49 +29474,6 @@ For example, A and B may be gene products and binding of B by A positively regul In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted]. Wikipedia:Neural_tube - - - - Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO] - 2012-06-20 - AAO:0010617 - AAO - AAO:JOR - - - - - The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG] - 2012-09-17 - VHOG:0000307 - VHOG - http://bgee.unil.ch/ - http://medical-dictionary.thefreedictionary.com/neural+tube - - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] - 2012-09-17 - VHOG:0000307 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 - http://bgee.unil.ch/ - - - - - The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium - GO:0021915 - - - - - MESH:D054259 - - - https://github.com/biopragmatics/biomappings - @@ -32492,7 +29504,6 @@ For example, A and B may be gene products and binding of B by A positively regul BIRNLEX:6 CARO:0000000 EHDAA2:0002229 - FBbt:10000000 FMA:62955 HAO:0000000 MA:0000001 @@ -32516,12 +29527,6 @@ For example, A and B may be gene products and binding of B by A positively regul FMA:62955 http://orcid.org/0000-0001-9114-8737 - - - - FBbt:10000000 - - @@ -32781,9 +29786,6 @@ For example, A and B may be gene products and binding of B by A positively regul Muscle tissue that consists primarily of skeletal muscle fibers. TODO - add skeletal muscle organ? See GO:0060538 skeletal muscle organ development. Todo - group FBbt:00005073 - somatic muscle. - Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO] - Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA] - This result implies the following views in terms of evolutionary differentiation: (1) Arthropod striated muscle and vertebrate skeletal and cardiac muscles share a common ancestor. In other words, they did not evolve independently (...) (5) The divergence of vertebrate skeletal and cardiac muscles/vertebrate smooth muscle and nonmuscle is at least before that of vertebrates/arthropods. In other words, emergence of skeletal and cardiac musle type tissues preceded the vertebrate/arthropod divergence (ca. 700 MYA).[well established][VHOG] skeletal muscle EMAPA:32716 FMA:14069 @@ -32808,32 +29810,6 @@ For example, A and B may be gene products and binding of B by A positively regul Muscle tissue that consists primarily of skeletal muscle fibers. https://github.com/obophenotype/uberon/issues/324 - - - - Muscle, composed of long cylindrical, multinucleated cells that attaches to the skeleton via tendons.[TAO] - 2012-08-14 - TAO:0005277 - TAO - ZFIN:curator - - - - - Tissue which consists of skeletal muscle fibers surrounded by endomysium. Examples: Skeletal muscle tissue of biceps, Skeletal muscle tissue of diaphragm[FMA] - FMA:14069 - FMA - - - - - This result implies the following views in terms of evolutionary differentiation: (1) Arthropod striated muscle and vertebrate skeletal and cardiac muscles share a common ancestor. In other words, they did not evolve independently (...) (5) The divergence of vertebrate skeletal and cardiac muscles/vertebrate smooth muscle and nonmuscle is at least before that of vertebrates/arthropods. In other words, emergence of skeletal and cardiac musle type tissues preceded the vertebrate/arthropod divergence (ca. 700 MYA).[well established][VHOG] - 2012-09-17 - VHOG:0000319 - VHOG - PMID:10368962 Oota S, Saitou N, Phylogenetic relationship of muscle tissues deduced from superimposition of gene trees. Mol Biol Evol (1999) - http://bgee.unil.ch/ - @@ -32905,13 +29881,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system. - - Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO] - Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO] - System that provides physical support to the organism.[AAO] - By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG] - skeletal - GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates AAO:0000566 BTO:0001486 CALOHA:TS-1320 @@ -32947,50 +29916,6 @@ For example, A and B may be gene products and binding of B by A positively regul VSAO:0000027 http://dx.plos.org/10.1371/journal.pone.0051070 - - - - Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO] - 2012-08-14 - TAO:0000434 - TAO - TAO:wd - - - - - Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO] - 2012-08-14 - VSAO:0000027 - VSAO - GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 - PSPUB:0000170 - - - - - System that provides physical support to the organism.[AAO] - 2012-06-20 - AAO:0000566 - AAO - AAO:LAP - - - - - By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG] - 2012-09-17 - VHOG:0001254 - VHOG - DOI:10.1159/000324245 Donoghue PCJ, Sansom IJ, Origin and early evolution of vertebrate skeletonization. Microscopy research and technique (2002) - http://bgee.unil.ch/ - - - - - GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates - GO - @@ -33033,18 +29958,10 @@ For example, A and B may be gene products and binding of B by A positively regul - + Skeletal element that is composed of bone tissue. - - - - Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO] - Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO] - Skeletal element that is composed of bone tissue.[VSAO] - relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] - The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG] AAO:0000047 AEO:0000082 BTO:0000140 @@ -33083,14 +30000,14 @@ For example, A and B may be gene products and binding of B by A positively regul bone element - + - + VSAO-modified @@ -33103,51 +30020,6 @@ For example, A and B may be gene products and binding of B by A positively regul http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/277 - - - - Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO] - 2012-06-20 - AAO:0000047 - AAO - AAO:LAP - - - - - Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO] - 2012-08-14 - TAO:0001514 - TAO - ZFIN:curator - - - - - Skeletal element that is composed of bone tissue.[VSAO] - 2012-08-14 - VSAO:0000057 - VSAO - PSPUB:0000170 - - - - - relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] - 2012-06-20 - AAO:0000047 - AAO - - - - - The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG] - 2012-09-17 - VHOG:0001190 - VHOG - DOI:10.1159/000324245 Murdock DJ, Donoghue PC, Evolutionary Origins of Animal Skeletal Biomineralization. Cells Tissues Organs (2011) - http://bgee.unil.ch/ - @@ -33201,16 +30073,11 @@ For example, A and B may be gene products and binding of B by A positively regul - + A tube extending from the mouth to the anus. - The alimentary or digestive tract, and associated organs.[TAO] - The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] - FMA also has a term 'gastrointestinal tract', but this includes the liver. - we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509 - we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this gut AAO:0010023 BILA:0000083 @@ -33219,10 +30086,8 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA2:0000726 EHDAA:518 EMAPA:16247 - FBbt:00003125 FMA:45615 MA:0000917 - MESH:D041981 NCIT:C34082 TAO:0000112 TGMA:0001819 @@ -33244,14 +30109,14 @@ For example, A and B may be gene products and binding of B by A positively regul digestive tract - + - + NCBIBook:NBK10107 @@ -33273,50 +30138,6 @@ For example, A and B may be gene products and binding of B by A positively regul DOI:10.1371/journal.pone.0016309 - - - - The alimentary or digestive tract, and associated organs.[TAO] - 2012-08-14 - TAO:0000112 - TAO - ZFIN:curator - - - - - The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0000309 - VHOG - ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 - http://bgee.unil.ch/ - - - - - FMA also has a term 'gastrointestinal tract', but this includes the liver. - FMA - - - - - we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509 - MA - - - - - FBbt:00003125 - - - - - - MESH:D041981 - - https://github.com/biopragmatics/biomappings - @@ -33367,12 +30188,7 @@ For example, A and B may be gene products and binding of B by A positively regul Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]. - Portion of tissue composed of contractile fibers.[TAO] - It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG] - muscular muscle - AAO:0011066 - EMAPA:32715 EMAPA:37474 EV:0100146 FMA:5022 @@ -33398,25 +30214,6 @@ For example, A and B may be gene products and binding of B by A positively regul Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]. GO:0007517 - - - - Portion of tissue composed of contractile fibers.[TAO] - 2012-08-14 - TAO:0005145 - TAO - ZFIN:curator - - - - - It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG] - 2012-09-17 - VHOG:0001245 - VHOG - ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.75 - http://bgee.unil.ch/ - @@ -33454,7 +30251,6 @@ For example, A and B may be gene products and binding of B by A positively regul Muscle tissue that contains fibers that are divided by transverse bands into striations. - Voluntary muscle tissue arranged in bundles of fibers.[AAO] AAO:0010762 AEO:0000140 CALOHA:TS-2047 @@ -33482,15 +30278,6 @@ For example, A and B may be gene products and binding of B by A positively regul GOC:dph GOC:mtg_muscle - - - - Voluntary muscle tissue arranged in bundles of fibers.[AAO] - 2012-06-20 - AAO:0010762 - AAO - AAO:CAM - @@ -33522,16 +30309,11 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical structure that is part of an embryo. - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO] - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO] - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO] - in FMA embryo is_a embryonic structure AAO:0000138 BILA:0000034 BTO:0000174 CALOHA:TS-2110 EFO:0000461 - FBbt:00004208 FMA:69067 GAID:407 MESH:D004628 @@ -33562,45 +30344,6 @@ For example, A and B may be gene products and binding of B by A positively regul BTO:0000174 ZFIN:curator - - - - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO] - 2012-06-20 - AAO:0000138 - AAO - AAO:BJB - - - - - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO] - 2012-08-14 - TAO:0001105 - TAO - ZFIN:curator - - - - - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO] - 2012-08-14 - VSAO:0000178 - VSAO - ZFIN:curator - - - - - in FMA embryo is_a embryonic structure - FMA - - - - - FBbt:00004208 - - @@ -33646,10 +30389,6 @@ For example, A and B may be gene products and binding of B by A positively regul Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present. - - - Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO] - Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO] AAO:0010339 BILA:0000116 BTO:0001493 @@ -33689,32 +30428,6 @@ For example, A and B may be gene products and binding of B by A positively regul UBERONREF:0000006 Wikipedia:Torso - - - - - ZFA - https://github.com/obophenotype/uberon/issues/378 - pending - - - - - Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO] - 2012-06-20 - AAO:0010339 - AAO - AAO:BJB - - - - - Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO] - 2012-08-14 - TAO:0001115 - TAO - ZFIN:curator - @@ -33747,7 +30460,6 @@ For example, A and B may be gene products and binding of B by A positively regul The sensory system subserving the sense of vision. - The sensory system used for sight.[AAO] UBERON:0007036 AAO:0000632 BILA:0000140 @@ -33777,15 +30489,6 @@ For example, A and B may be gene products and binding of B by A positively regul The sensory system subserving the sense of vision. NIFSTD:FMAID_7191 - - - - The sensory system used for sight.[AAO] - 2012-06-20 - AAO:0000632 - AAO - AAO:EJS - @@ -33861,7 +30564,12 @@ For example, A and B may be gene products and binding of B by A positively regul - + + + + + + @@ -33873,9 +30581,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that consists of the muscular and skeletal systems. - Anatomical system that provides locomotion and physical support to the organism.[AAO] - There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG] - musculoskeletal AAO:0010546 CALOHA:TS-1311 EMAPA:32714 @@ -33897,16 +30602,6 @@ For example, A and B may be gene products and binding of B by A positively regul musculoskeletal system - - - - - - - - - check ctenophore - @@ -33915,25 +30610,6 @@ For example, A and B may be gene products and binding of B by A positively regul VSAO:curator https://github.com/obophenotype/uberon/issues/77 - - - - Anatomical system that provides locomotion and physical support to the organism.[AAO] - 2012-06-20 - AAO:0010546 - AAO - AAO:EJS - - - - - There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG] - 2012-09-17 - VHOG:0001275 - VHOG - DOI:10.1002/jez.b.21246 Shearman RM, Burke AC, The lateral somitic frontier in ontogeny and phylogeny. Journal of Experimental Zoology (2009) - http://bgee.unil.ch/ - @@ -33948,6 +30624,7 @@ For example, A and B may be gene products and binding of B by A positively regul + @@ -33955,21 +30632,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - + + + @@ -33983,13 +30648,6 @@ For example, A and B may be gene products and binding of B by A positively regul A flexible rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In some chordates, it persists throughout life as the main axial support of the body, while in most vertebrates it becomes the nucleus pulposus of the intervertebral disc. The notochord is found ventral to the neural tube. - Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO] - Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO] - Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO] - relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO] - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG] - notochordal - In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord. AAO:0000327 BTO:0001768 CALOHA:TS-0690 @@ -34024,15 +30682,15 @@ For example, A and B may be gene products and binding of B by A positively regul notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + @@ -34051,19 +30709,19 @@ For example, A and B may be gene products and binding of B by A positively regul - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -34076,51 +30734,6 @@ For example, A and B may be gene products and binding of B by A positively regul https://github.com/obophenotype/uberon/issues/25 https://github.com/obophenotype/uberon/issues/271 - - - - Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO] - 2012-08-14 - VSAO:0000032 - VSAO - PSPUB:0000170 - - - - - Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000135 - TAO - ZFIN:curator - - - - - Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO] - 2012-06-20 - AAO:0000327 - AAO - AAO:LAP - - - - - relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO] - 2012-06-20 - AAO:0000327 - AAO - - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG] - 2012-09-17 - VHOG:0000199 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 - http://bgee.unil.ch/ - @@ -34148,18 +30761,10 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. - EDITOR_NOTE currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk - Post-cranial axial segments which form sclerotome and dermomyotome.[AAO] - Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO] - relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO] - relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO] - relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO] - (...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG] - somitic mesodermal cluster AAO:0010569 AEO:0001015 @@ -34195,11 +30800,11 @@ For example, A and B may be gene products and binding of B by A positively regul somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + @@ -34212,13 +30817,13 @@ For example, A and B may be gene products and binding of B by A positively regul - + GOTAX:0000352 - + ZFA @@ -34234,58 +30839,6 @@ For example, A and B may be gene products and binding of B by A positively regul PMID:17237766 - - - - Post-cranial axial segments which form sclerotome and dermomyotome.[AAO] - 2012-06-20 - AAO:0010569 - AAO - AAO:EJS - - - - - Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000155 - TAO - ZFIN:curator - - - - - relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO] - 2012-08-14 - TAO:0000155 - TAO - - - - - relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO] - 2012-08-14 - TAO:0000155 - TAO - - - - - relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO] - 2012-06-20 - AAO:0010569 - AAO - - - - - (...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0000191 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.40, DOI:10.1093/icb/43.1.137 Balavoine G, Adoutte A, The segmented urbilateria: a testable scenario. Integrative and Comparative Biology (2003) - http://bgee.unil.ch/ - @@ -34394,20 +30947,25 @@ For example, A and B may be gene products and binding of B by A positively regul + - - - - - - + + + + + + + + + + + + + + + + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. - EDITOR_NOTE consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams). - - A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO] - Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO] - A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831] - We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG] AAO:0010578 BTO:0001764 CALOHA:TS-0676 @@ -34420,7 +30978,6 @@ For example, A and B may be gene products and binding of B by A positively regul MIAA:0000066 NCIT:C34222 SCTID:361462002 - TAO:0000045 UMLS:C0027789 VHOG:0000057 Wikipedia:Neural_crest @@ -34440,66 +30997,45 @@ For example, A and B may be gene products and binding of B by A positively regul http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - - - - - + - + - - - - - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - - Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells - ISBN:0073040584 - - - - - + BTO - + PMID:11523831 - - pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest - - - - - + PMID:11523831 @@ -34508,47 +31044,6 @@ For example, A and B may be gene products and binding of B by A positively regul A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. MP:0009846 - - - - - ISBN:0073040584 - PMID:17377535 - - - - - A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000045 - TAO - ZFIN:curator - - - - - Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO] - 2012-06-20 - AAO:0010578 - AAO - AAO:EJS - - - - - A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831] - PMID:11523831 - - - - - We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG] - 2012-09-17 - VHOG:0000057 - VHOG - DOI:10.1111/j.1469-7580.2012.01495.x Hall BK, Gillis JA, Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues. J Anat (2012) - http://bgee.unil.ch/ - @@ -34590,9 +31085,6 @@ For example, A and B may be gene products and binding of B by A positively regul Embryonic ectoderm that gives rise to nervous tissue. - (...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG] - neurectodermal - we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here AAO:0011074 BILA:0000039 CALOHA:TS-1212 @@ -34601,7 +31093,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA:255 EMAPA:16073 EV:0100004 - FBbt:00001057 FMA:87657 MAT:0000176 MIAA:0000176 @@ -34630,22 +31121,6 @@ For example, A and B may be gene products and binding of B by A positively regul Embryonic ectoderm that gives rise to nervous tissue. Wikipedia:Neuroectoderm - - - - (...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG] - 2012-09-17 - VHOG:0000150 - VHOG - DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) - http://bgee.unil.ch/ - - - - - FBbt:00001057 - - @@ -34854,13 +31329,14 @@ For example, A and B may be gene products and binding of B by A positively regul + - + @@ -34883,8 +31359,6 @@ For example, A and B may be gene products and binding of B by A positively regul TODO - create superclass for bone marrow / head kidney. both are portions of tissue in the hematopoetic system. also consider adding as subclass of zone of bone organ for consistency with FMA. See also: Leydig and epigonal organs consider placement of NCIT:C53466 medullary bone - The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG] - In adults, marrow in large bones produces new blood cells[Wikipedia:Bone_marrow] AAO:0011007 BTO:0000141 BTO:0000829 @@ -34918,14 +31392,14 @@ For example, A and B may be gene products and binding of B by A positively regul bone marrow http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg - + - + FMA MA @@ -34936,16 +31410,6 @@ For example, A and B may be gene products and binding of B by A positively regul MGI:cwg MP:0002397 - - - - The bone marrow is the hematopoietic organ in all vertebrates but fishes, in which hematopoiesis occurs in the kidney.[well established][VHOG] - 2012-09-17 - VHOG:0001218 - VHOG - DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood Cells and Blood Cell Development in the Animal Kingdom. Annual Review of Cell and Developmental Biology (2006) - http://bgee.unil.ch/ - @@ -34989,10 +31453,6 @@ For example, A and B may be gene products and binding of B by A positively regul Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance. - One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO] - Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO] - Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO] - MA also has set of connective tissues AAO:0000098 BTO:0000421 CALOHA:TS-2009 @@ -35033,40 +31493,6 @@ For example, A and B may be gene products and binding of B by A positively regul http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/23 - - - - One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO] - 2012-06-20 - AAO:0000098 - AAO - AAO:LAP - - - - - Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO] - 2012-08-14 - TAO:0001641 - TAO - TAO:wd - - - - - Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO] - 2012-08-14 - VSAO:0000017 - VSAO - GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 - PSPUB:0000170 - - - - - MA also has set of connective tissues - MA - @@ -35129,8 +31555,6 @@ For example, A and B may be gene products and binding of B by A positively regul Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]. - - One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO] AAO:0000306 AEO:0000122 CALOHA:TS-0642 @@ -35161,15 +31585,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Muscle_tissue https://sourceforge.net/tracker/index.php?func=detail&aid=2801266&group_id=36855&atid=440764 - - - - One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO] - 2012-06-20 - AAO:0000306 - AAO - AAO:LAP - @@ -35196,22 +31611,23 @@ For example, A and B may be gene products and binding of B by A positively regul - + - + + + + + + Anatomical system that is involved in the production of hematopoietic cells. - Anatomical system that consists of the blood and blood forming tissues.[AAO] - Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG] - hematopoietic - In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes AAO:0011002 BTO:0000570 CALOHA:TS-0449 @@ -35249,57 +31665,22 @@ For example, A and B may be gene products and binding of B by A positively regul hematopoietic system - + - - - - - + FMA - - - - - definitional - Anatomical system that is involved in the production of hematopoietic cells. Wikipedia:Haematopoiesis - - - - Anatomical system that consists of the blood and blood forming tissues.[AAO] - 2012-06-20 - AAO:0011002 - AAO - AAO:EJS - - - - - Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG] - 2012-09-17 - VHOG:0001624 - VHOG - DOI:10.1016/j.coph.2010.05.004 Ellett F, Lieschke GJ, Zebrafish as a model for vertebrate hematopoiesis. Current Opinion in Pharmacology (2010) - http://bgee.unil.ch/ - - - - - In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes - WP - @@ -35340,7 +31721,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies. - The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG] AAO:0011003 BILA:0000104 BTO:0005810 @@ -35370,16 +31750,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies. Wikipedia:Immune_system - - - - The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG] - 2012-09-17 - VHOG:0001247 - VHOG - PMID:21046016 Dzik JM, The ancestry and cumulative evolution of immune reactions. Acta biochimica Polonica (2010) - http://bgee.unil.ch/ - @@ -35408,7 +31778,6 @@ For example, A and B may be gene products and binding of B by A positively regul Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts. see https://github.com/obophenotype/uberon/issues/27 - Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO] CALOHA:TS-2011 EMAPA:35179 FMA:224804 @@ -35448,16 +31817,6 @@ For example, A and B may be gene products and binding of B by A positively regul VSAO:0000047 http://dx.plos.org/10.1371/journal.pone.0051070 - - - - Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO] - 2012-08-14 - VSAO:0000047 - VSAO - GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 - PSPUB:0000170 - @@ -35514,18 +31873,13 @@ For example, A and B may be gene products and binding of B by A positively regul An organ that functions as a secretory or excretory organ. - - glandular AAO:0000212 AEO:0000096 BTO:0000522 EFO:0000797 EHDAA2:0003096 EHDAA:2161 - EHDAA:4475 - EHDAA:6522 EMAPA:18425 - FBbt:00100317 FMA:7146 FMA:86294 HAO:0000375 @@ -35556,12 +31910,6 @@ For example, A and B may be gene products and binding of B by A positively regul MGI:csmith MP:0002163 - - - - FBbt:00100317 - - @@ -35603,7 +31951,6 @@ For example, A and B may be gene products and binding of B by A positively regul In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA]. MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class - In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG] BTO:0004593 FMA:296704 MAT:0000067 @@ -35631,16 +31978,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Epiblast ZFIN:curator - - - - In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG] - 2012-09-17 - VHOG:0000243 - VHOG - DOI:10.1146/annurev.cellbio.042308.113344 Zorn AM, Wells JM, Vertebrate endoderm development and organ formation. Annual Review of Cell Developmental Biology (2009) - http://bgee.unil.ch/ - @@ -35738,10 +32075,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. - Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO] - It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG] AAO:0011086 EFO:0001982 EMAPA:16189 @@ -35763,14 +32098,14 @@ For example, A and B may be gene products and binding of B by A positively regul presomitic mesoderm - + - + Bgee:AN @@ -35779,25 +32114,6 @@ For example, A and B may be gene products and binding of B by A positively regul Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. ZFIN:curator - - - - Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000279 - TAO - ZFIN:curator - - - - - It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG] - 2012-09-17 - VHOG:0000559 - VHOG - DOI:10.1006/dbio.2001.0460 Schubert M, Holland LZ, Dale Stokes M and Holland ND, Three Amphoxius Wnt Genes (AmphiWnt3, AmphiWnt5, and AmphiWnt6) Associated with the Tail Bud: the Evolution of Somitogenesis in Chordates. Developmental Biology (2001) - http://bgee.unil.ch/ - @@ -35836,11 +32152,6 @@ For example, A and B may be gene products and binding of B by A positively regul Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted]. - Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO] - Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO] - relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO] - Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG] - EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac ventral lateral plate mesoderm AAO:0011006 EFO:0003489 @@ -35873,48 +32184,6 @@ For example, A and B may be gene products and binding of B by A positively regul Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted]. Wikipedia:Blood_island_of_umbilical_vesicle - - - - Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000094 - TAO - ZFIN:curator - - - - - Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO] - 2012-06-20 - AAO:0011006 - AAO - AAO:EJS - - - - - relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO] - 2012-08-14 - TAO:0000094 - TAO - - - - - Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0000085 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450, DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual Review of Cell and Developmental Biology (2006) - http://bgee.unil.ch/ - - - - - EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac - EHDAA2 - @@ -35953,7 +32222,6 @@ For example, A and B may be gene products and binding of B by A positively regul The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord. - The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] AAO:0011017 EFO:0003647 TAO:0001204 @@ -35976,15 +32244,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0048318 Wikipedia:Chordamesoderm - - - - The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] - 2012-09-17 - VHOG:0000107 - VHOG - http://bgee.unil.ch/ - @@ -36000,12 +32259,10 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. - The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO] - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] AAO:0011072 BTO:0001765 DHBA:10153 @@ -36014,7 +32271,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA:902 EMAPA:35593 FMA:293879 - MESH:D054258 NCIT:C34225 RETIRED_EHDAA2:0001252 TAO:0000132 @@ -36034,34 +32290,34 @@ For example, A and B may be gene products and binding of B by A positively regul neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -36073,33 +32329,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Neural_plate ZFIN:curator - - - - The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000132 - TAO - ZFIN:curator - - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] - 2012-09-17 - VHOG:0000068 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 - http://bgee.unil.ch/ - - - - - MESH:D054258 - - - https://github.com/biopragmatics/biomappings - @@ -36122,23 +32351,14 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. - Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO] - Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG] - note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here) AAO:0010568 EFO:0003515 EMAPA:16183 @@ -36163,7 +32383,7 @@ For example, A and B may be gene products and binding of B by A positively regul paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -36176,7 +32396,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + Bgee:AN @@ -36186,31 +32406,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0048339 https://github.com/obophenotype/uberon/issues/30 - - - - Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO] - 2012-06-20 - AAO:0010568 - AAO - AAO:EJS - - - - - Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG] - 2012-09-17 - VHOG:0000114 - VHOG - DOI:10.1002/dvdy.21177 Kusakabe R and Kuratani S. Evolutionary perspectives from development of mesodermal components in the lamprey. Developmental dynamics (2007) - http://bgee.unil.ch/ - - - - - note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here) - ZFA - @@ -36248,7 +32443,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -36262,10 +32457,6 @@ For example, A and B may be gene products and binding of B by A positively regul Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]. - Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO] - The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] - A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG] - subclass of mesoderm in ZFA. UBERON:0006258 AAO:0010574 EHDAA2:0000919 @@ -36292,7 +32483,7 @@ For example, A and B may be gene products and binding of B by A positively regul lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -36305,7 +32496,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + EHDAA2 VHOG @@ -36316,40 +32507,6 @@ For example, A and B may be gene products and binding of B by A positively regul MP:0010117 Wikipedia:Lateral_plate_mesoderm - - - - Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO] - 2012-06-20 - AAO:0010574 - AAO - AAO:EJS - - - - - The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] - 2012-09-17 - VHOG:0000118 - VHOG - http://bgee.unil.ch/ - - - - - A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG] - 2012-09-17 - VHOG:0000118 - VHOG - DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) - http://bgee.unil.ch/ - - - - - subclass of mesoderm in ZFA. - ZFA - @@ -36389,7 +32546,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -36398,8 +32555,6 @@ For example, A and B may be gene products and binding of B by A positively regul A transitional population of migrating mesenchymal cells that derive from somites and that will become muscle cells. The term 'myotome' is also used to describe the muscles served by a single nerve root / spinal segment - consider adding new class, myomere. - Portion of the somites giving rise to body wall muscle masses. Kimmel et al, 1995.[TAO] - In all vertebrates, the skeletal muscle of the body axis is chiefly derived from an early embryonic compartment, known as the myotome.[well established][VHOG] AAO:0011067 AEO:0001018 BTO:0000742 @@ -36432,7 +32587,7 @@ For example, A and B may be gene products and binding of B by A positively regul myotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + @@ -36445,7 +32600,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + EHDAA2-abduced @@ -36454,25 +32609,6 @@ For example, A and B may be gene products and binding of B by A positively regul A transitional population of migrating mesenchymal cells that derive from somites and that will become muscle cells. AEO:0001018 - - - - Portion of the somites giving rise to body wall muscle masses. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0001056 - TAO - ZFIN:curator - - - - - In all vertebrates, the skeletal muscle of the body axis is chiefly derived from an early embryonic compartment, known as the myotome.[well established][VHOG] - 2012-09-17 - VHOG:0001244 - VHOG - DOI:10.1038/sj.embor.embor920 Hollway GE, Currie PD, Myotome meanderings. Cellular morphogenesis and the making of muscle. EMBO Rep.(2003) - http://bgee.unil.ch/ - @@ -36501,7 +32637,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types. - this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs AAO:0010015 AEO:0000024 BILA:0000024 @@ -36565,9 +32700,6 @@ For example, A and B may be gene products and binding of B by A positively regul Portion of tissue composed of mesenchymal cells (motile cells that develop from epthelia via an epithelial to mesenchymal transition) and surrounding extracellular material. Mesenchyme has different embryological origins in different metazoan taxa - in many invertebrates it derives in whole or part from ectoderm. In vertebrates it derives largely from mesoderm, and sometimes the terms are used interchangeably, e.g. lateral plate mesoderm/mesenchyme. the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense - A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO] - Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO] - mesenchymal AAO:0010427 AEO:0000145 BTO:0001393 @@ -36602,24 +32734,6 @@ For example, A and B may be gene products and binding of B by A positively regul https://en.wikipedia.org/wiki/Mesenchyme https://github.com/obophenotype/uberon/issues/1641 - - - - A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000393 - TAO - ZFIN:curator - - - - - Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO] - 2012-06-20 - AAO:0010427 - AAO - AAO:EJS - @@ -36646,10 +32760,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults - (...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG] EHDAA:251 EMAPA:16088 NCIT:C34195 @@ -36662,14 +32775,14 @@ For example, A and B may be gene products and binding of B by A positively regul intraembryonic coelom - + - + Wikipedia @@ -36679,16 +32792,6 @@ For example, A and B may be gene products and binding of B by A positively regul MGI:anna MP:0012187 - - - - (...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG] - 2012-09-17 - VHOG:0000316 - VHOG - ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.166 - http://bgee.unil.ch/ - @@ -36721,10 +32824,8 @@ For example, A and B may be gene products and binding of B by A positively regul Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. - contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers AEO:0000114 EHDAA2:0003114 - FBbt:00007474 epithelial or endothelial tube uberon UBERON:0003914 @@ -36737,12 +32838,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0060562 PMID:12526790 - - - - FBbt:00007474 - - @@ -36788,7 +32883,6 @@ For example, A and B may be gene products and binding of B by A positively regul - FMA has both conduit and conduit space. In EHDAA2 this is a surface feature AEO:0000080 EHDAA2:0003080 FMA:242873 @@ -36810,12 +32904,6 @@ For example, A and B may be gene products and binding of B by A positively regul Any tube, opening or passage that connects two distinct anatomical spaces. http://orcid.org/0000-0002-6601-2165 - - - - FMA has both conduit and conduit space. In EHDAA2 this is a surface feature - FMA - @@ -36860,7 +32948,6 @@ For example, A and B may be gene products and binding of B by A positively regul An anatomical structure that develops (entirely or partially) from the mesoderm. - Grouping term for query purposes mesodermal derivative uberon UBERON:0004120 @@ -36904,7 +32991,6 @@ For example, A and B may be gene products and binding of B by A positively regul An anatomical structure that develops (entirely or partially) from the ectoderm. - Grouping term for query purposes ectodermal deriviative uberon UBERON:0004121 @@ -36944,10 +33030,7 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body. - - Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO] - skeletal AEO:0000168 EHDAA2:0001843 EHDAA:5047 @@ -36980,15 +33063,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body. VSAO:0000026 - - - - Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO] - 2012-08-14 - VSAO:0000026 - VSAO - GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 - @@ -37003,13 +33077,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + The bilaminar epithelium formed from the myotome and dermatome. - Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768]. - Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO] - Portion of somites that gives rise to dermis and muscles.[AAO] - all but the sclerotome of a mesodermal somite; the primordium of skeletal muscle and, perhaps, of the dermis. - Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic.[well established][VHOG] AAO:0010572 AEO:0000214 EHDAA2:0003259 @@ -37026,7 +33095,7 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0004290 dermomyotome - + @@ -37045,7 +33114,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + EHDAA2 ZFA @@ -37055,46 +33124,6 @@ For example, A and B may be gene products and binding of B by A positively regul The bilaminar epithelium formed from the myotome and dermatome. AEO:0000214 - - - - Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis. Within the dermomyotome there is also a medio-lateral difference. The central region makes dermis, the mesenchymal connective tissue of the back skin. The medial region (closest to neural tube) makes epaxial muscle, and the lateral region (furthest from neural tube) makes hypaxial muscle[http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768]. - http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=eurekah&part=A66768 - - - - - Epithelial sheet on the external surface of the somite that gives rise to trunk, muscle and dermis.[TAO] - 2012-08-14 - TAO:0001513 - TAO - ZFIN:curator - - - - - Portion of somites that gives rise to dermis and muscles.[AAO] - 2012-06-20 - AAO:0010572 - AAO - AAO:EJS - - - - - all but the sclerotome of a mesodermal somite; the primordium of skeletal muscle and, perhaps, of the dermis. - http://medical-dictionary.thefreedictionary.com/dermomyotome - - - - - Thus, representatives of the agnathan vertebrates, chondrichthyans, and sarcopterygians all have a layer of undifferentiated cells external to the embryonic myotome. In the amniotes, this external cell layer is the dermomyotome. The simplest interpretation of the similar position, morphology, and lack of myosin labeling is that a dermomyotome epithelium is a shared, ancestral vertebrate characteristic.[well established][VHOG] - 2012-09-17 - VHOG:0000676 - VHOG - DOI:10.1111/j.1525-142X.2006.05079.x Devoto SH, Stoiber W, Hammond CL, Steinbacher P, Haslett JR, Barresi MJF, Patterson SE, Adiarte EG and Hughes SM, Generality of vertebrate developmental patterns: evidence for a dermomyotome in fish. Evolution and Development (2006) - http://bgee.unil.ch/ - @@ -37134,7 +33163,6 @@ For example, A and B may be gene products and binding of B by A positively regul Sum of all sensory systems in an organism. - note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs FMA:78499 sense organ system uberon @@ -37250,11 +33278,9 @@ For example, A and B may be gene products and binding of B by A positively regul Organism at the gastrula stage. - We explicitly merge the NCITA terms here UBERON:0007012 BILA:0000060 BTO:0001403 - FBbt:00005317 FMA:293108 GAID:1302 MESH:D005775 @@ -37286,18 +33312,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Gastrula Wikipedia:Trilaminar_blastocyst - - - - We explicitly merge the NCITA terms here - NCIT - - - - - FBbt:00005317 - - @@ -37377,9 +33391,13 @@ For example, A and B may be gene products and binding of B by A positively regul - + + + + + + A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]. - A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO] EMAPA:37744 MA:0003047 SCTID:309311006 @@ -37391,24 +33409,12 @@ For example, A and B may be gene products and binding of B by A positively regul Four classes of mineralized tissues are found in vertebrates: bone, cartilage, dentine, and enamel. We think of cartilage and bone as skeletal tissues and of enamel and dentine as dental tissues, but enamel and dentine arose evolutionarily together with bone as skeletal tissues in the dermal skeleton (exoskeleton) of early vertebrates. Scales and teeth of sharks are examples of dermal skeletal elements that are still composed of the three ancient components-enamel, dentine, and bone. Cartilage, on the other hand, provided the basis for the second vertebrate skeletal system, the endoskeleton (Smith and Hall, 1990; Hall, 1998a,b). some invertebrate skeletal tissues have surprisingly bone-like features. Examples include chondrocytes interconnected by cell processes in cephalopod cartilages (Cole and Hall, 2004a,b), and the calcium phosphate layer in the shells of brachiopods (Rodland et al., 2003). However, neither bone nor mineralized cartilage have been found in invertebrates. Editors notes: TODO - develops_from skeletal tissue - - - - VSAO - - - - - 2012-08-14 - VSAO:0000015 - VSAO - @@ -37419,17 +33425,6 @@ For example, A and B may be gene products and binding of B by A positively regul http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/134 - - - - A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO] - 2012-08-14 - VSAO:0000015 - taken from version of VSAO used in TAO and used directly in Uberon - VSAO - GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 - PSPUB:0000170 - @@ -37443,10 +33438,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. - Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO] - Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO] AAO:0011129 TAO:0001890 VSAO:0000128 @@ -37459,14 +33452,14 @@ For example, A and B may be gene products and binding of B by A positively regul skeletal element - + - + VSAO @@ -37475,24 +33468,6 @@ For example, A and B may be gene products and binding of B by A positively regul Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. https://orcid.org/0000-0002-6601-2165 - - - - Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO] - 2012-08-14 - VSAO:0000128 - VSAO - PSPUB:0000170 - - - - - Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO] - 2012-08-14 - TAO:0001890 - TAO - TAO:VSAO_workshop - @@ -37511,7 +33486,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -37550,14 +33525,14 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0004770 articular system - + - + FMA @@ -37604,8 +33579,6 @@ For example, A and B may be gene products and binding of B by A positively regul The central region of trunk mesoderm. This tissue forms the notochord. - Notochord rudiment[ZFIN:ZDB-PUB-961014-576]. - WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord. AAO:0000478 EFO:0003426 TAO:0000091 @@ -37626,12 +33599,6 @@ For example, A and B may be gene products and binding of B by A positively regul The central region of trunk mesoderm. This tissue forms the notochord. https://orcid.org/0000-0002-6601-2165 - - - - Notochord rudiment[ZFIN:ZDB-PUB-961014-576]. - ZFIN:ZDB-PUB-961014-576 - @@ -37664,7 +33631,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts. - FBbt:00005811 joint uberon UBERON:0004905 @@ -37677,12 +33643,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts. http://orcid.org/0000-0002-6601-2165 - - - - FBbt:00005811 - - @@ -37714,9 +33674,7 @@ For example, A and B may be gene products and binding of B by A positively regul A proximal-distal subdivision of the digestive tract. - intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct. - FBbt:00100315 FMA:71131 uberon alimentary system subdivision @@ -37735,12 +33693,6 @@ For example, A and B may be gene products and binding of B by A positively regul A proximal-distal subdivision of the digestive tract. http://orcid.org/0000-0002-6601-2165 - - - - FBbt:00100315 - - @@ -37805,7 +33757,6 @@ For example, A and B may be gene products and binding of B by A positively regul The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds. - The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]. AAO:0011071 EMAPA:35594 FMA:295624 @@ -37827,12 +33778,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Neural_groove http://orcid.org/0000-0002-6601-2165 - - - - The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]. - Wikipedia:Neural_groove - @@ -37848,6 +33793,7 @@ For example, A and B may be gene products and binding of B by A positively regul + @@ -37855,14 +33801,7 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - One of the two elevated edges of the neural groove[GO,MP]. - In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]. EHDAA2:0001249 FMA:295618 NCIT:C34223 @@ -37885,12 +33824,6 @@ For example, A and B may be gene products and binding of B by A positively regul MP:0011256 Wikipedia:Neural_fold - - - - In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]. - Wikipedia:Neural_fold - @@ -37917,7 +33850,6 @@ For example, A and B may be gene products and binding of B by A positively regul A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN]. - An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO] EFO:0003498 TAO:0000133 ZFA:0000133 @@ -37934,15 +33866,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0014024 ZFA:0000133 - - - - An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000133 - TAO - ZFIN:curator - @@ -37969,8 +33892,6 @@ For example, A and B may be gene products and binding of B by A positively regul Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO]. - in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila - EMAPA:32715 FMA:30316 musculus uberon @@ -38038,7 +33959,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -38054,14 +33975,14 @@ For example, A and B may be gene products and binding of B by A positively regul trunk mesenchyme - + - + EHDAA2 @@ -38163,7 +34084,6 @@ For example, A and B may be gene products and binding of B by A positively regul An array of photoreceptors and any supporting cells found in an eye. - FBbt:00004200 light-sensitive tissue uberon UBERON:0005388 @@ -38175,12 +34095,6 @@ For example, A and B may be gene products and binding of B by A positively regul An array of photoreceptors and any supporting cells found in an eye. https://orcid.org/0000-0002-6601-2165 - - - - FBbt:00004200 - - @@ -38200,7 +34114,6 @@ For example, A and B may be gene products and binding of B by A positively regul AEO:0000125 CALOHA:TS-2122 EHDAA2:0003125 - FBbt:00007006 FMA:292313 MIAA:0000019 uberon @@ -38211,12 +34124,6 @@ For example, A and B may be gene products and binding of B by A positively regul developing anatomical structure - - - - FBbt:00007006 - - @@ -38302,7 +34209,6 @@ For example, A and B may be gene products and binding of B by A positively regul An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina. - this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell. AAO:0010596 FMA:63872 @@ -38372,10 +34278,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB - The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG] EHDAA2:0001278 EHDAA:264 EMAPA:16101 @@ -38387,7 +34292,7 @@ For example, A and B may be gene products and binding of B by A positively regul notochordal plate - + @@ -38400,7 +34305,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + EHDAA2 @@ -38409,15 +34314,6 @@ For example, A and B may be gene products and binding of B by A positively regul The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. VHOG:0001212 - - - - The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG] - 2012-09-17 - VHOG:0001212 - VHOG - http://bgee.unil.ch/ - @@ -38437,7 +34333,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -38454,14 +34350,14 @@ For example, A and B may be gene products and binding of B by A positively regul The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -38725,12 +34621,6 @@ For example, A and B may be gene products and binding of B by A positively regul Old definition: 'Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.' Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism. anatomical surface - - - - - via morphological boundary in CARO - @@ -38831,7 +34721,6 @@ For example, A and B may be gene products and binding of B by A positively regul - The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis BILA:0000084 NCIT:C34268 SCTID:360394002 @@ -38847,12 +34736,6 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0007026 presumptive gut - - - - The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis - NCBIBook:NBK10107 - @@ -38883,10 +34766,13 @@ For example, A and B may be gene products and binding of B by A positively regul - + + + + + + A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]. - note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis - SPD:0000130 TADS:0000147 http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg dorsal tube @@ -38898,16 +34784,6 @@ For example, A and B may be gene products and binding of B by A positively regul Gene notes: Bmp, Nkx, Gata primary circulatory organ - - - - - - - - - GO uses blood circulation generically to include the haemolymphatic fluid of arthropods - @@ -38946,7 +34822,6 @@ For example, A and B may be gene products and binding of B by A positively regul An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. - An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO] EFO:0003497 TAO:0000131 ZFA:0000131 @@ -38962,15 +34837,6 @@ For example, A and B may be gene products and binding of B by A positively regul An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. ZFIN:ZDB-PUB-961014-576 - - - - An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000131 - TAO - ZFIN:curator - @@ -38995,7 +34861,12 @@ For example, A and B may be gene products and binding of B by A positively regul - + + + + + + @@ -39012,17 +34883,6 @@ For example, A and B may be gene products and binding of B by A positively regul presumptive segmental plate - - - - - - - - - https://github.com/obophenotype/uberon/wiki/The-neural-crest - EDHAA2 - @@ -39074,7 +34934,6 @@ For example, A and B may be gene products and binding of B by A positively regul A presumptive structure that has the potential to develop into a neural plate. consider merging - Region of the gastrula which gives rise to the neural plate.[TAO] EFO:0003424 TAO:0000063 ZFA:0000063 @@ -39091,15 +34950,6 @@ For example, A and B may be gene products and binding of B by A positively regul A presumptive structure that has the potential to develop into a neural plate. OBOL:automatic - - - - Region of the gastrula which gives rise to the neural plate.[TAO] - 2012-08-14 - TAO:0000063 - TAO - ZFIN:curator - @@ -39118,7 +34968,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -39144,7 +34994,7 @@ For example, A and B may be gene products and binding of B by A positively regul presumptive paraxial mesoderm - + @@ -39160,7 +35010,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + https://github.com/obophenotype/uberon/issues/1277 @@ -39209,7 +35059,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -39217,7 +35067,7 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0007524 dense mesenchyme tissue - + @@ -39230,7 +35080,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + AEO @@ -39309,8 +35159,6 @@ For example, A and B may be gene products and binding of B by A positively regul Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts). - Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).[VSAO] - Regular connective tissue, the intercellular matrix of which consists predominantly of collagen fiber bundles arranged in parallel arrays.[FMA] FMA:64781 NCIT:C33453 SCTID:22560007 @@ -39348,24 +35196,6 @@ For example, A and B may be gene products and binding of B by A positively regul VSAO:0000050 http://dx.plos.org/10.1371/journal.pone.0051070 - - - - Connective tissue that is dominated by collagen fibres organized into a definitive pattern (e.g., parallel to one another), with comparatively fewer cells (mostly fibroblasts).[VSAO] - 2012-08-14 - VSAO:0000050 - VSAO - GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 - PSPUB:0000170 - - - - - Regular connective tissue, the intercellular matrix of which consists predominantly of collagen fiber bundles arranged in parallel arrays.[FMA] - 2012-08-29 - FMA:64781 - FMA - @@ -39409,7 +35239,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -39426,14 +35256,14 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -39455,7 +35285,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -39463,14 +35293,14 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -39520,7 +35350,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0010000 - FBbt:00100313 multicellular structure uberon UBERON:0010000 @@ -39534,12 +35363,6 @@ For example, A and B may be gene products and binding of B by A positively regul An anatomical structure that has more than one cell as a part. CARO:0010000 - - - - FBbt:00100313 - - @@ -39576,6 +35399,42 @@ For example, A and B may be gene products and binding of B by A positively regul + + + + + + + + + + + + + + + + + + + + + + An anatomical structure that has some part that develops from the neural crest. + uberon + UBERON:0010314 + + structure with developmental contribution from neural crest + + + + + An anatomical structure that has some part that develops from the neural crest. + https://orcid.org/0000-0002-6601-2165 + + + + @@ -39679,7 +35538,6 @@ For example, A and B may be gene products and binding of B by A positively regul - FBbt:00007330 FMA:67509 SCTID:91690000 uberon @@ -39701,12 +35559,6 @@ For example, A and B may be gene products and binding of B by A positively regul A subdivision of an anatomical system. http://orcid.org/0000-0002-6601-2165 - - - - FBbt:00007330 - - @@ -39791,7 +35643,6 @@ For example, A and B may be gene products and binding of B by A positively regul Irregular connective tissue is an irregular connective tissue, the intercellular matrix of which contains a dense irregular network of collagen and elastic fiber bundles. Examples: connective tissue of peritoneum, connective tissue of fibrous pericardium. - Tissue characterized by a thick, random arrangement of collagen and elastin fibers with very few cells. The majority of the cells are fibroblasts, but mast cells and macrophages may also be seen. It is found in the dermis, periosteum, perichondrium, capsules of organs and sheaths of nerves and muscles[NCIT] FMA:20109 NCIT:C32882 UMLS:C0738366 @@ -39815,14 +35666,6 @@ For example, A and B may be gene products and binding of B by A positively regul FMA:20109 Wikipedia:Dense_irregular_connective_tissue - - - - Tissue characterized by a thick, random arrangement of collagen and elastin fibers with very few cells. The majority of the cells are fibroblasts, but mast cells and macrophages may also be seen. It is found in the dermis, periosteum, perichondrium, capsules of organs and sheaths of nerves and muscles[NCIT] - 2012-08-29 - ncithesaurus:Irregular_Dense_Connective_Tissue - NCIT - @@ -39862,7 +35705,6 @@ For example, A and B may be gene products and binding of B by A positively regul Dense connective tissue is mainly composed of collagen type I. Crowded between the collagen fibers are rows of fibroblasts, fiber-forming cells, that manufacture the fibers. Dense connective tissue forms strong, rope-like structures such as tendons and ligaments. Tendons attach skeletal muscles to bones; ligaments connect bones to bones at joints. Ligaments are more stretchy and contain more elastic fibers than tendons. Dense connective tissue also make up the lower layers of the skin (dermis), where it is arranged in sheets. our OWL definition states that this is differentiated from other connective tissue types by virtue of the fact that the collage fiber component predominates, as opposed to cells and fluid. - Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT] AAO:0000121 NCIT:C32450 UMLS:C1511770 @@ -39877,14 +35719,6 @@ For example, A and B may be gene products and binding of B by A positively regul Dense connective tissue is mainly composed of collagen type I. Crowded between the collagen fibers are rows of fibroblasts, fiber-forming cells, that manufacture the fibers. Dense connective tissue forms strong, rope-like structures such as tendons and ligaments. Tendons attach skeletal muscles to bones; ligaments connect bones to bones at joints. Ligaments are more stretchy and contain more elastic fibers than tendons. Dense connective tissue also make up the lower layers of the skin (dermis), where it is arranged in sheets. Wikipedia:Dense_connective_tissue - - - - Connective tissue in which the fibrous component predominates. The cells, ground substance, and tissue fluid represent a minor component[NCIT] - 2012-08-29 - ncithesaurus:Dense_Connective_Tissue - NCIT - @@ -39911,7 +35745,6 @@ For example, A and B may be gene products and binding of B by A positively regul - the FMA class specifically refers to ureter FMA:63212 MESH:D024022 NCIT:C32339 @@ -39927,20 +35760,15 @@ For example, A and B may be gene products and binding of B by A positively regul ZFA - - - - the FMA class specifically refers to ureter - FMA - + - + @@ -39954,7 +35782,6 @@ For example, A and B may be gene products and binding of B by A positively regul Epimysium is a layer of connective tissue which ensheaths the entire muscle. It is composed of dense irregular connective tissue. It is continuous with fascia and other connective tissue wrappings of muscle including the endomysium, and perimysium. It is also continuous with tendons where it becomes thicker and collagenous. - The Epimysium also protects muscles from friction against other muscles and bones FMA:9726 NCIT:C32527 UMLS:C0504096 @@ -39965,7 +35792,7 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0011899 epimysium - + @@ -39978,7 +35805,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + FMA @@ -40022,7 +35849,6 @@ For example, A and B may be gene products and binding of B by A positively regul The aggregate of the coelemic cavity lumen plus the membranes that line the lumen. EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining. - coelomic EHDAA2:0004731 Wikipedia:Coelom enterocoelom @@ -40083,8 +35909,9 @@ For example, A and B may be gene products and binding of B by A positively regul + - + @@ -40092,7 +35919,6 @@ For example, A and B may be gene products and binding of B by A positively regul Blood-forming tissue, consisting of reticular fibers and cells. - Bone marrow in humans, kidney interstitium in Danio, within a stroma of reticuloendothelial tissue CALOHA:TS-2142 FMA:14073 NCIT:C13051 @@ -40106,7 +35932,7 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0012429 hematopoietic tissue - + @@ -40119,7 +35945,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + defitional @@ -40282,10 +36108,8 @@ For example, A and B may be gene products and binding of B by A positively regul The region of the organism associated with the visceral organs. - Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]. AEO:0000103 BTO:0001489 - EMAPA:36031 FMA:231424 uberon body @@ -40306,12 +36130,6 @@ For example, A and B may be gene products and binding of B by A positively regul The region of the organism associated with the visceral organs. AEO:0000103 - - - - Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]. - FMA:231424 - @@ -40432,7 +36250,6 @@ For example, A and B may be gene products and binding of B by A positively regul An anatomical group whose component structures share a common function. AEO:0000093 - FBbt:00007278 uberon UBERON:0015203 non-connected functional system @@ -40446,12 +36263,6 @@ For example, A and B may be gene products and binding of B by A positively regul FBC:DOS FBbt:00007278 - - - - FBbt:00007278 - - @@ -40494,24 +36305,7 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - @@ -40519,7 +36313,6 @@ For example, A and B may be gene products and binding of B by A positively regul Any structure that is placed on one side of the left-right axis of a bilaterian. - This class is primarily to implement taxon constraints. It may be removed in the future. uberon UBERON:0015212 @@ -40553,7 +36346,6 @@ For example, A and B may be gene products and binding of B by A positively regul A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile. heart - SPD:0000130 cardiac pump heart or heart like organ circulatory vessel @@ -40701,7 +36493,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -40724,7 +36516,7 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0016887 entire extraembryonic component - + @@ -40737,7 +36529,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + AEO @@ -40823,7 +36615,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -40834,21 +36626,20 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA2:0001842 EMAPA:35578 - MA:0000165 uberon UBERON:0018254 skeletal musculature - + - + MA @@ -40943,7 +36734,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0020000 - FBbt:00007276 uberon UBERON:0034923 @@ -40961,12 +36751,6 @@ For example, A and B may be gene products and binding of B by A positively regul Material anatomical entity consisting of multiple anatomical structures that are not connected to each other. CARO:0020000 - - - - FBbt:00007276 - - @@ -41156,7 +36940,6 @@ For example, A and B may be gene products and binding of B by A positively regul - example to be eventually removed example to be eventually removed @@ -41165,9 +36948,7 @@ For example, A and B may be gene products and binding of B by A positively regul - failed exploratory term The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job - Person:Alan Ruttenberg failed exploratory term @@ -41176,7 +36957,6 @@ For example, A and B may be gene products and binding of B by A positively regul - metadata complete Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. metadata complete @@ -41186,7 +36966,6 @@ For example, A and B may be gene products and binding of B by A positively regul - organizational term Term created to ease viewing/sort terms for development purpose, and will not be included in a release organizational term @@ -41196,7 +36975,6 @@ For example, A and B may be gene products and binding of B by A positively regul - ready for release Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release @@ -41206,7 +36984,6 @@ For example, A and B may be gene products and binding of B by A positively regul - metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete @@ -41216,7 +36993,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated @@ -41226,7 +37002,6 @@ For example, A and B may be gene products and binding of B by A positively regul - pending final vetting All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting @@ -41236,7 +37011,6 @@ For example, A and B may be gene products and binding of B by A positively regul - placeholder removed placeholder removed @@ -41245,7 +37019,6 @@ For example, A and B may be gene products and binding of B by A positively regul - terms merged An editor note should explain what were the merged terms and the reason for the merge. terms merged @@ -41255,7 +37028,6 @@ For example, A and B may be gene products and binding of B by A positively regul - term imported This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. term imported @@ -41265,7 +37037,6 @@ For example, A and B may be gene products and binding of B by A positively regul - term split This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. term split @@ -41275,10 +37046,7 @@ For example, A and B may be gene products and binding of B by A positively regul - universal Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. - Alan Ruttenberg - A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf universal @@ -41287,10 +37055,8 @@ For example, A and B may be gene products and binding of B by A positively regul - defined class A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. - Alan Ruttenberg defined class @@ -41299,10 +37065,8 @@ For example, A and B may be gene products and binding of B by A positively regul - named class expression A named class expression is a logical expression that is given a name. The name can be used in place of the expression. named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions - Alan Ruttenberg named class expression @@ -41311,10 +37075,7 @@ For example, A and B may be gene products and binding of B by A positively regul - to be replaced with external ontology term Terms with this status should eventually replaced with a term from another ontology. - Alan Ruttenberg - group:OBI to be replaced with external ontology term @@ -41323,10 +37084,7 @@ For example, A and B may be gene products and binding of B by A positively regul - requires discussion A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. - Alan Ruttenberg - group:OBI requires discussion @@ -41337,9 +37095,7 @@ For example, A and B may be gene products and binding of B by A positively regul The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. - https://github.com/information-artifact-ontology/ontology-metadata/issues/77 - https://orcid.org/0000-0001-5208-3432 out of scope @@ -41395,24 +37151,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - - @@ -41454,46 +37192,34 @@ For example, A and B may be gene products and binding of B by A positively regul /////////////////////////////////////////////////////////////////////////////////////// --> - - - - + - - - - - - - - - - + - + - + - + - + - + - + - + - + @@ -41520,8 +37246,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41531,7 +37257,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -41541,7 +37267,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -41558,67 +37284,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - true - GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' - involved in BP - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + @@ -41636,8 +37303,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41647,8 +37314,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41658,8 +37325,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41676,8 +37343,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41694,8 +37361,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41705,8 +37372,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41716,8 +37383,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41734,8 +37401,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41752,8 +37419,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41763,8 +37430,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41774,8 +37441,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41792,8 +37459,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41810,8 +37477,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41821,8 +37488,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41837,8 +37504,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41855,8 +37522,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41866,8 +37533,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41882,8 +37549,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41900,8 +37567,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41911,8 +37578,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41927,8 +37594,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41945,8 +37612,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41956,8 +37623,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41972,8 +37639,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -41990,8 +37657,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -42001,8 +37668,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -42017,8 +37684,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -42078,8 +37745,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -42089,8 +37756,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -42105,8 +37772,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -42121,9 +37788,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + @@ -42133,8 +37800,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -42148,9 +37815,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + @@ -42165,9 +37832,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + @@ -42177,8 +37844,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -42192,7 +37859,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + diff --git a/subsets/general_cell_types_upper_slim.tsv b/subsets/general_cell_types_upper_slim.tsv index a0a6dd677..6d53c2d02 100644 --- a/subsets/general_cell_types_upper_slim.tsv +++ b/subsets/general_cell_types_upper_slim.tsv @@ -1,275 +1,273 @@ ?x ?label -_:B9ac295d7X2Ded0bX2D4368X2D889cX2D7714613be411genid1047 -_:B9ac295d7X2Ded0bX2D4368X2D889cX2D7714613be411genid1054 -_:B9ac295d7X2Ded0bX2D4368X2D889cX2D7714613be411genid1061 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b/subsets/kidney_upper_slim.json index 84c2067cc..f32433dec 100644 --- a/subsets/kidney_upper_slim.json +++ b/subsets/kidney_upper_slim.json @@ -4,9 +4,9 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-02-13" + "val" : "2024-04-05" } ], - "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-02-13/subsets/kidney_upper_slim.owl" + "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-04-05/subsets/kidney_upper_slim.owl" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/BFO_0000002", @@ -78,18 +78,6 @@ "val" : "BFO:0000050" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "is part of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my brain is part of my body (continuant parthood, two material entities)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this day is part of this year (occurrent parthood)" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." }, { @@ -98,42 +86,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "part_of" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000002" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000003" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000004" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000017" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000019" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000020" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0040042", - "val" : "http://purl.obolibrary.org/obo/BFO_0000031" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "part_of" @@ -164,18 +122,6 @@ "val" : "BFO:0000051" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has part" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my body has part my brain (continuant parthood, two material entities)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "this year has part this day (occurrent parthood)" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." }, { @@ -184,21 +130,12 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has_part" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "quality" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_part" @@ -217,26 +154,11 @@ "val" : "BFO:0000062" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "preceded by" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is preceded by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "preceded_by" - }, { - "pred" : "http://purl.org/dc/terms/source", - "val" : "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "preceded_by" @@ -255,14 +177,8 @@ "val" : "BFO:0000063" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "precedes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "precedes" @@ -282,26 +198,11 @@ "val" : "BFO:0000066" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "occurs in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "occurs_in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "unfolds in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "unfolds_in" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "occurs_in" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Occurs_in" @@ -315,412 +216,12 @@ "definition" : { "val" : "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" }, - "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ], - "xrefs" : [ { - "val" : "BFO:0000067" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "site of" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "contains_process" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#isDefinedBy", - "val" : "http://purl.obolibrary.org/obo/bfo.owl" - } ] + "comments" : [ "Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant" ] } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000141", "lbl" : "immaterial entity", "type" : "CLASS" - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000096", - "lbl" : "anterior to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000096" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "anterior_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000097", - "lbl" : "distal to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000097" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "distal_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000098", - "lbl" : "dorsal to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000098" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dorsal_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000099", - "lbl" : "posterior to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000099" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "posterior_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000100", - "lbl" : "proximal to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000100" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "proximal_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000102", - "lbl" : "ventral to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000102" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "ventral_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000107", - "lbl" : "deep to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000107" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "deep_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000108", - "lbl" : "superficial to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000108" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "superficial_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000120", - "lbl" : "in left side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000120" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_left_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000121", - "lbl" : "in right side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000121" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_right_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000122", - "lbl" : "in posterior side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000122" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_posterior_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000123", - "lbl" : "in anterior side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000123" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_anterior_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000124", - "lbl" : "in proximal side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000124" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_proximal_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "lbl" : "in lateral side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0000126" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_lateral_side_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001100", - "lbl" : "in superficial part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001100" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_superficial_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001101", - "lbl" : "in deep part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001101" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_deep_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001106", - "lbl" : "proximalmost part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001106" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "proximalmost_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001107", - "lbl" : "immediately deep to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001107" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "immediately_deep_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001108", - "lbl" : "distalmost part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001108" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "distalmost_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001113", - "lbl" : "preaxialmost part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001113" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "preaxialmost_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0001115", - "lbl" : "postaxialmost part of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0001115" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "postaxialmost_part_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0005001", - "lbl" : "intersects midsagittal plane of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0005001" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "intersects_midsagittal_plane_of" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0015014", - "lbl" : "immediately superficial to", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0015014" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "immediately_superficial_to" - } ] - } - }, { - "id" : "http://purl.obolibrary.org/obo/BSPO_0015101", - "lbl" : "in dorsal side of", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "BSPO:0015101" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_dorsal_side_of" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000000", "lbl" : "cell", @@ -3018,7 +2519,8 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A cell that is part of a renal medulla." + "val" : "A cell that is part of a renal medulla.", + "xrefs" : [ "PMID:22343825" ] }, "xrefs" : [ { "val" : "KUPO:0001017" @@ -3123,6 +2625,10 @@ "lbl" : "kidney interstitial fibroblast", "type" : "CLASS", "meta" : { + "definition" : { + "val" : "A fibroblast that is part of an interstitial compartment of a kidney.", + "xrefs" : [ "PMID:10559635" ] + }, "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "xrefs" : [ { "val" : "KUPO:0001102" @@ -3174,6 +2680,10 @@ "lbl" : "kidney blood vessel cell", "type" : "CLASS", "meta" : { + "definition" : { + "val" : "A blood vessel cell that is part of a kidney.", + "xrefs" : [ "PMID:34843404" ] + }, "xrefs" : [ { "val" : "KUPO:0001014" } ] @@ -11124,13 +10634,7 @@ }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000002", "lbl" : "example to be eventually removed", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "example to be eventually removed" - } ] - } + "type" : "INDIVIDUAL" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000028", "lbl" : "symbol", @@ -11142,14 +10646,7 @@ "meta" : { "definition" : { "val" : "The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "failed exploratory term" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person:Alan Ruttenberg" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000115", @@ -11160,20 +10657,8 @@ "val" : "The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "definition" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "2012-04-05: \nBarry Smith\n\nThe official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible.\n\nCan you fix to something like:\n\nA statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property.\n\nAlan Ruttenberg\n\nYour proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. \n\nOn the specifics of the proposed definition:\n\nWe don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. \n\nPersonally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. \n\nWe also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Daniel Schober" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" } ] } }, { @@ -11183,32 +10668,7 @@ "meta" : { "definition" : { "val" : "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology." - }, - "xrefs" : [ { - "val" : "IAO:0000116" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "editor note" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000122" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Daniel Schober" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GROUP:OBI:" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "editor_note" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000120", @@ -11217,11 +10677,7 @@ "meta" : { "definition" : { "val" : "Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "metadata complete" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000121", @@ -11230,11 +10686,7 @@ "meta" : { "definition" : { "val" : "Term created to ease viewing/sort terms for development purpose, and will not be included in a release" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "organizational term" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000122", @@ -11243,11 +10695,7 @@ "meta" : { "definition" : { "val" : "Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking \"ready_for_release\" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed \"ready_for_release\" will also derived from a chain of ancestor classes that are also \"ready_for_release.\"" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "ready for release" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000123", @@ -11256,11 +10704,7 @@ "meta" : { "definition" : { "val" : "Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "metadata incomplete" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000124", @@ -11269,11 +10713,7 @@ "meta" : { "definition" : { "val" : "Nothing done yet beyond assigning a unique class ID and proposing a preferred term." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "uncurated" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000125", @@ -11282,31 +10722,18 @@ "meta" : { "definition" : { "val" : "All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "pending final vetting" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000226", "lbl" : "placeholder removed", - "type" : "INDIVIDUAL", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "placeholder removed" - } ] - } + "type" : "INDIVIDUAL" }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000227", "lbl" : "terms merged", "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "terms merged" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "An editor note should explain what were the merged terms and the reason for the merge." } ] @@ -11317,9 +10744,6 @@ "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "term imported" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use." } ] @@ -11330,9 +10754,6 @@ "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "term split" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created." } ] @@ -11344,17 +10765,7 @@ "meta" : { "definition" : { "val" : "Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has obsolescence reason" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "PERSON:Melanie Courtot" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000233", @@ -11369,29 +10780,8 @@ "val" : "IAO:0000233" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "term tracker item" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_class_level", - "val" : "true" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", "val" : "true" @@ -11406,17 +10796,8 @@ "type" : "INDIVIDUAL", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "universal" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Hard to give a definition for. Intuitively a \"natural kind\" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf" } ] } }, { @@ -11428,14 +10809,8 @@ "val" : "A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "defined class" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "\"definitions\", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" } ] } }, { @@ -11447,14 +10822,8 @@ "val" : "A named class expression is a logical expression that is given a name. The name can be used in place of the expression." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "named class expression" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" } ] } }, { @@ -11464,17 +10833,7 @@ "meta" : { "definition" : { "val" : "Terms with this status should eventually replaced with a term from another ontology." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "to be replaced with external ontology term" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "group:OBI" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000424", @@ -11483,17 +10842,7 @@ "meta" : { "definition" : { "val" : "A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "expand expression to" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "ObjectProperty: RO_0002104\nLabel: has plasma membrane part\nAnnotations: IAO_0000424 \"http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)\"\n" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000428", @@ -11502,17 +10851,7 @@ "meta" : { "definition" : { "val" : "A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "requires discussion" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "group:OBI" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/IAO_0000700", @@ -11526,20 +10865,8 @@ "val" : "IAO:0000700" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "has ontology root term" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Nicolas Matentzoglu" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_class_level", - "val" : "true" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", "val" : "true" @@ -11556,20 +10883,7 @@ "definition" : { "val" : "Use on obsolete terms, relating the term to another term that can be used as a substitute" }, - "comments" : [ "Add as annotation triples in the granting ontology" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000111", - "val" : "term replaced by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Person:Alan Ruttenberg" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Person:Alan Ruttenberg" - } ] + "comments" : [ "Add as annotation triples in the granting ontology" ] } }, { "id" : "http://purl.obolibrary.org/obo/NCBITaxon_1", @@ -11604,9 +10918,6 @@ "val" : "PMID:15371245" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_family" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11621,7 +10932,7 @@ "pred" : "hasExactSynonym", "val" : "Mus" }, { - "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003003", + "synonymType" : "http://purl.obolibrary.org/obo/ncbitaxon#genbank_common_name", "pred" : "hasExactSynonym", "val" : "mice" }, { @@ -11633,9 +10944,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_genus" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11658,9 +10966,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_species" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "NCBITaxon:85055" }, { @@ -11677,9 +10982,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11698,9 +11000,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "NCBITaxon:40673" }, { @@ -11735,9 +11034,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11760,9 +11056,6 @@ "val" : "PMID:11791233" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11785,9 +11078,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_suborder" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11834,9 +11124,6 @@ "val" : "PMID:30257078" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_superkingdom" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11858,9 +11145,6 @@ "val" : "PMID:15522813" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_superorder" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11885,9 +11169,6 @@ "val" : "PMID:15522813" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11906,9 +11187,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11927,9 +11205,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11948,9 +11223,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -11973,9 +11245,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -12006,9 +11275,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_kingdom" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -12022,9 +11288,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -12043,9 +11306,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -12063,9 +11323,6 @@ "val" : "PMID:15371245" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -12079,9 +11336,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_subfamily" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "NCBITaxon:109679" }, { @@ -12107,9 +11361,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_class" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -12123,9 +11374,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -12148,9 +11396,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_phylum" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -12177,9 +11422,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -12202,9 +11444,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -12218,9 +11457,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_superclass" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -12239,9 +11475,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_subgenus" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -12260,9 +11493,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_subphylum" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -12297,9 +11527,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_clade" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -12322,9 +11549,6 @@ "val" : "GC_ID:1" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/ncbitaxon#has_rank", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_order" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "ncbi_taxonomy" } ] @@ -12340,15 +11564,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/77" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000234", - "val" : "https://orcid.org/0000-0001-5208-3432" } ] } }, { @@ -12360,9 +11578,6 @@ "val" : "Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'part disjoint with' 'defined by construct' \"\"\"\n PREFIX owl: \n PREFIX : some (\n and some (\n and some (\n and some ?Y)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { @@ -15493,33 +14274,9 @@ "definition" : { "val" : "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " }, - "xrefs" : [ { - "val" : "RO:0002103" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that part_of some ( that has_part some ( that some Y?)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "synapsed_by" } ] } }, { @@ -15531,29 +14288,8 @@ "val" : "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9990-8331" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-1617-8244" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/19243617" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( and some ?Y)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" } ] } }, { @@ -15565,26 +14301,8 @@ "val" : "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. " }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "synapsed in" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (\n http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some (\n http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { @@ -15596,20 +14314,8 @@ "val" : "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "synapses in" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that some ( that some Y?)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { @@ -15622,23 +14328,8 @@ }, "comments" : [ "N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part some (\n ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( \n\t‘synapse ; GO:0045202’ that has_part some (\n\t ‘post-synaptic membrane ; GO:0045211’ that part_of some N2))))" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that part_of some ( that some ( that some Y?)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { @@ -15650,23 +14341,8 @@ "val" : "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has synapse in" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that some Y?)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" } ] } }, { @@ -15682,20 +14358,11 @@ "val" : "RO:0002131" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "overlaps" @@ -15708,26 +14375,7 @@ "meta" : { "definition" : { "val" : "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has fasciculating component" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000426", - "val" : "(forall (?x ?y) \n\t(iff \n\t\t(has_fasciculating_neuron_projection ?x ?y)\n\t\t(exists (?nps ?npbs)\t\t\n\t\t\t(and \n\t\t\t\t(\"neuron projection bundle ; CARO_0001001\" ?x)\n\t\t\t\t(\"neuron projection ; GO0043005\" ?y)\n\t\t\t\t(\"neuron projection segment ; CARO_0001502\" ?nps)\n\t\t\t\t(\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n\t\t\t\t(part_of ?nps ?y)\n\t\t\t\t(part_of ?npbs ?x)\n\t\t\t\t(part_of ?nps ?npbs)\n\t\t\t\t(forall (?npbss)\n\t\t\t\t\t(if\n\t\t\t\t\t\t(and \n\t\t\t\t\t\t\t(\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n\t\t\t\t\t\t\t(part_of ?npbss ?npbs) \n\t\t\t\t\t\t)\n\t\t\t\t\t\t(overlaps ?nps ?npbss)\n\t\t\t\t\t))))))\n\n\n" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002134", @@ -15737,30 +14385,9 @@ "definition" : { "val" : "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." }, - "xrefs" : [ { - "val" : "RO:0002134" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : " some ( that ( some ( that some Y?)))" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://purl.org/spar/cito/citesAsAuthority", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22402613" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "innervates" } ] } }, { @@ -15771,31 +14398,7 @@ "definition" : { "val" : "X continuous_with Y if and only if X and Y share a fiat boundary." }, - "xrefs" : [ { - "val" : "RO:0002150" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "connected to" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "continuous_with" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "FMA:85972" } ] @@ -15808,23 +14411,7 @@ "definition" : { "val" : "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." }, - "comments" : [ "VBO calls this homologous_to" ], - "xrefs" : [ { - "val" : "RO:0002158" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Consider obsoleting and merging with child relation, 'in homology relationship with'" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "homologous_to" - } ] + "comments" : [ "VBO calls this homologous_to" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -15834,33 +14421,9 @@ "definition" : { "val" : "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." }, - "xrefs" : [ { - "val" : "RO:0002160" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "lactation SubClassOf 'only in taxon' some 'Mammalia'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "only_in_taxon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" @@ -15868,48 +14431,15 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002161", - "lbl" : "never_in_taxon", + "lbl" : "never in taxon", "type" : "PROPERTY", "meta" : { "definition" : { "val" : "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL." }, - "xrefs" : [ { - "val" : "RO:0002161" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "tooth SubClassOf 'never in taxon' value 'Aves'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", - "val" : "Class: EquivalentTo: ?X and (RO_0002162 some ?Y)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000425", - "val" : "Class: ?X DisjointWith: RO_0002162 some ?Y " - }, { "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_class_level", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "never_in_taxon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" @@ -15925,31 +14455,7 @@ }, "comments" : [ "Connects a biological entity to its taxon of origin." ], "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002162" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9227-417X" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/17921072" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20973947" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "in_taxon" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" } ] @@ -15964,26 +14470,11 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000424", "val" : "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" @@ -15997,22 +14488,7 @@ "definition" : { "val" : "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" }, - "xrefs" : [ { - "val" : "RO:0002170" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "connected_to" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" }, { @@ -16022,42 +14498,16 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002175", - "lbl" : "present_in_taxon", + "lbl" : "present in taxon", "type" : "PROPERTY", "meta" : { "definition" : { - "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S.", - "xrefs" : [ "https://orcid.org/0000-0002-6601-2165" ] + "val" : "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S" }, "comments" : [ "The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "applicable for taxon" - } ], - "xrefs" : [ { - "val" : "RO:0002175" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { "pred" : "http://purl.obolibrary.org/obo/OMO_0002000", "val" : "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_class_level", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "present_in_taxon" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Taxon-constraints" @@ -16071,25 +14521,7 @@ "definition" : { "val" : "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." }, - "xrefs" : [ { - "val" : "RO:0002176" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The M8 connects Glasgow and Edinburgh" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "connects" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" }, { @@ -16104,20 +14536,7 @@ "meta" : { "definition" : { "val" : "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." - }, - "xrefs" : [ { - "val" : "RO:0002177" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "attached to part of (anatomical structure to anatomical structure)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "attaches_to_part_of" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002178", @@ -16127,21 +14546,9 @@ "definition" : { "val" : "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." }, - "xrefs" : [ { - "val" : "RO:0002178" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "supplies" } ] } }, { @@ -16152,21 +14559,9 @@ "definition" : { "val" : "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." }, - "xrefs" : [ { - "val" : "RO:0002179" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "drains" } ] } }, { @@ -16182,23 +14577,11 @@ "val" : "RO:0002180" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_component" @@ -16215,32 +14598,7 @@ "definition" : { "val" : "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" }, - "comments" : [ "This is the transitive form of the develops from relation" ], - "xrefs" : [ { - "val" : "RO:0002202" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9114-8737" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-1980-3228" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "develops_from" - } ] + "comments" : [ "This is the transitive form of the develops from relation" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002203", @@ -16250,29 +14608,7 @@ "definition" : { "val" : "inverse of develops from" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "xrefs" : [ { - "val" : "RO:0002203" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-1980-3228" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "develops_into" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002206", @@ -16281,17 +14617,7 @@ "meta" : { "definition" : { "val" : "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002207", @@ -16305,31 +14631,6 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "has developmental precursor" - } ], - "xrefs" : [ { - "val" : "RO:0002207" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "FBbt" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002202" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "directly_develops_from" } ] } }, { @@ -16340,14 +14641,7 @@ "definition" : { "val" : "inverse of directly develops from" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "developmental precursor of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002211", @@ -16362,30 +14656,6 @@ "val" : "RO:0002211" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-7476-6306" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-3837-8864" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GO" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Regulation precludes parthood; the regulatory process may not be within the regulated process." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "regulates (processual)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000600", - "val" : "false" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16406,15 +14676,6 @@ "val" : "RO:0002212" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "negatively regulates (process to process)" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002211" }, { @@ -16438,18 +14699,6 @@ "val" : "RO:0002213" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "positively regulates (process to process)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002211" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16470,32 +14719,8 @@ "val" : "RO:0002215" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "osteoclast SubClassOf 'capable of' some 'bone resorption'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has function realized in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20123131" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/21208450" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "capable_of" @@ -16513,17 +14738,8 @@ "val" : "RO:0002216" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has function in" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "capable_of_part_of" @@ -16539,26 +14755,7 @@ "meta" : { "definition" : { "val" : "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" - }, - "xrefs" : [ { - "val" : "RO:0002219" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "surrounded_by" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002220", @@ -16573,35 +14770,11 @@ "val" : "RO:0002220" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The epidermis layer of a vertebrate is adjacent to the dermis." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This relation acts as a join point with BSPO" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "adjacent_to" @@ -16615,26 +14788,7 @@ "definition" : { "val" : "inverse of surrounded by" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "xrefs" : [ { - "val" : "RO:0002221" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "surrounds" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002222", @@ -16642,23 +14796,7 @@ "type" : "PROPERTY", "meta" : { "comments" : [ "A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations." ], - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://en.wikipedia.org/wiki/Allen%27s_interval_algebra" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." - }, { - "pred" : "http://purl.org/dc/terms/source", - "val" : "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002223", @@ -16668,29 +14806,7 @@ "definition" : { "val" : "inverse of starts with" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002223" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Allen" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "starts" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002224", @@ -16705,26 +14821,8 @@ "val" : "RO:0002224" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "started by" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "starts_with" @@ -16737,23 +14835,7 @@ "meta" : { "definition" : { "val" : "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" - }, - "xrefs" : [ { - "val" : "RO:0002225" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "develops_from_part_of" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002226", @@ -16762,29 +14844,7 @@ "meta" : { "definition" : { "val" : "x develops_in y if x is located in y whilst x is developing" - }, - "xrefs" : [ { - "val" : "RO:0002226" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "EHDAA2" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Jonathan Bard, EHDAA2" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "develops_in" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002229", @@ -16794,26 +14854,7 @@ "definition" : { "val" : "inverse of ends with" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002229" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "ends" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002230", @@ -16828,23 +14869,8 @@ "val" : "RO:0002230" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "Chris Mungall" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "finished by" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "ends_with" @@ -16863,15 +14889,6 @@ "val" : "RO:0002231" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "starts with process that occurs in" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16892,15 +14909,6 @@ "val" : "RO:0002232" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "ends with process that occurs in" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16921,15 +14929,6 @@ "val" : "RO:0002233" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "consumes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16953,15 +14952,6 @@ "val" : "RO:0002234" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "produces" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -16980,22 +14970,7 @@ "definition" : { "val" : "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." }, - "xrefs" : [ { - "val" : "RO:0002252" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004036", - "val" : "http://purl.obolibrary.org/obo/BFO_0000050" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "connecting_branch_of" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/issues/2212" } ] @@ -17008,11 +14983,7 @@ "definition" : { "val" : "inverse of connecting branch of" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004036", - "val" : "http://purl.obolibrary.org/obo/BFO_0000051" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002254", @@ -17021,26 +14992,7 @@ "meta" : { "definition" : { "val" : "x has developmental contribution from y iff x has some part z such that z develops from y" - }, - "xrefs" : [ { - "val" : "RO:0002254" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_developmental_contribution_from" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002255", @@ -17050,14 +15002,7 @@ "definition" : { "val" : "inverse of has developmental contribution from" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002256", @@ -17066,44 +15011,7 @@ "meta" : { "definition" : { "val" : "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" - }, - "xrefs" : [ { - "val" : "RO:0002256" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9114-8737" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-7073-9172" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "induced by" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GO:0001759" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "developmentally_induced_by" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002257", @@ -17112,14 +15020,7 @@ "meta" : { "definition" : { "val" : "Inverse of developmentally induced by" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002258", @@ -17131,17 +15032,8 @@ }, "comments" : [ "This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "false" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "In general you should not use this relation to make assertions - use one of the more specific relations below this one" } ] } }, { @@ -17154,9 +15046,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://wiki.geneontology.org/index.php/Acts_upstream_of" } ] @@ -17175,9 +15064,6 @@ "val" : "affects" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Acts_upstream_of_or_within" } ] @@ -17190,27 +15076,9 @@ "definition" : { "val" : "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" }, - "xrefs" : [ { - "val" : "RO:0002285" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "replaces" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "developmentally_replaces" } ] } }, { @@ -17220,31 +15088,12 @@ "meta" : { "definition" : { "val" : "Inverse of developmentally preceded by" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002287", "lbl" : "part of developmental precursor of", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002292", "lbl" : "expresses", @@ -17252,14 +15101,7 @@ "meta" : { "definition" : { "val" : "y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002295", @@ -17273,14 +15115,8 @@ "val" : "RO:0002295" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" @@ -17305,18 +15141,6 @@ "val" : "RO:0002296" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "every flower development (GO:0009908) results in development of some flower (PO:0009046)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.geneontology.org/GO.doc.development.shtml" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17326,7 +15150,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002297", - "lbl" : "results in formation of", + "lbl" : "results in formation of anatomical entity", "type" : "PROPERTY", "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_annotation_extension", "http://purl.obolibrary.org/obo/valid_for_go_ontology", "http://purl.obolibrary.org/obo/valid_for_gocam" ], @@ -17334,21 +15158,6 @@ "val" : "RO:0002297" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:mtg_berkeley_2013" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17369,21 +15178,6 @@ "val" : "RO:0002298" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:mtg_berkeley_2013" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17404,21 +15198,6 @@ "val" : "RO:0002299" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:mtg_berkeley_2013" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17440,12 +15219,6 @@ "val" : "RO:0002304" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002411" - }, { - "pred" : "http://purl.org/dc/terms/creator", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17471,9 +15244,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002411" - }, { - "pred" : "http://purl.org/dc/terms/creator", - "val" : "https://orcid.org/0000-0002-6601-2165" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" @@ -17496,18 +15266,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "inheres in part of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/20064205" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/reflexivity/" @@ -17526,15 +15284,6 @@ "val" : "RO:0002315" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "GOC:mtg_berkeley_2013" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17549,14 +15298,7 @@ "meta" : { "definition" : { "val" : "A relationship that holds via some environmental process" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002323", @@ -17565,17 +15307,7 @@ "meta" : { "definition" : { "val" : "A mereological relationship or a topological relationship" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002324", @@ -17584,14 +15316,7 @@ "meta" : { "definition" : { "val" : "A relationship that holds between entities participating in some developmental process (GO:0032502)" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002327", @@ -17603,30 +15328,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "a particular instances of akt-2 enables some instance of protein kinase activity" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "catalyzes" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "executes" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is catalyzing" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is executing" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Enables" } ] @@ -17638,23 +15339,7 @@ "meta" : { "definition" : { "val" : "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." - }, - "xrefs" : [ { - "val" : "RO:0002328" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This is a grouping relation that collects relations used for the purpose of connecting structure and function" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "functionally_related_to" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002329", @@ -17663,14 +15348,7 @@ "meta" : { "definition" : { "val" : "this relation holds between c and p when c is part of some c', and c' is capable of p." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "false" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002330", @@ -17679,14 +15357,7 @@ "meta" : { "definition" : { "val" : "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002331", @@ -17697,15 +15368,6 @@ "val" : "c involved_in p if and only if c enables some process p', and p' is part of p" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "actively involved in" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "enables part of" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Involved_in" } ] @@ -17722,18 +15384,6 @@ "val" : "RO:0002332" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "regulates levels of (process to entity)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17751,9 +15401,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_gocam" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Enabled_by" } ] @@ -17771,12 +15418,6 @@ "val" : "RO:0002334" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "regulated by (processual)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17797,9 +15438,6 @@ "val" : "RO:0002335" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17820,9 +15458,6 @@ "val" : "RO:0002336" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17837,14 +15472,7 @@ "meta" : { "definition" : { "val" : "A relationship that holds via some process of localization" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is a grouping relation." - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002338", @@ -17859,9 +15487,6 @@ "val" : "RO:0002338" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17882,9 +15507,6 @@ "val" : "RO:0002339" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17904,9 +15526,6 @@ "val" : "RO:0002341" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17927,9 +15546,6 @@ "val" : "RO:0002342" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17946,12 +15562,6 @@ "val" : "RO:0002343" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'pollen tube growth' results_in growth_of some 'pollen tube'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17968,12 +15578,6 @@ "val" : "RO:0002344" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -17988,23 +15592,7 @@ "meta" : { "definition" : { "val" : "is member of is a mereological relation between a item and a collection." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "An organism that is a member of a population of organisms" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "is member of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "member part of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "SIO" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002351", @@ -18013,23 +15601,7 @@ "meta" : { "definition" : { "val" : "has member is a mereological relation between a collection and an item." - }, - "xrefs" : [ { - "val" : "RO:0002351" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "SIO" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_member" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002352", @@ -18039,20 +15611,7 @@ "definition" : { "val" : "inverse of has input" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002352" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "input_of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002353", @@ -18067,14 +15626,8 @@ "val" : "RO:0002353" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "output_of" @@ -18083,26 +15636,11 @@ }, { "id" : "http://purl.obolibrary.org/obo/RO_0002354", "lbl" : "formed as result of", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002360", "lbl" : "has dendrite location", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.org/dc/terms/source", - "val" : "http://neurolex.org/wiki/Property:DendriteLocation" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002371", "lbl" : "attached to", @@ -18111,23 +15649,7 @@ "definition" : { "val" : "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002371" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "attached to (anatomical structure to anatomical structure)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "attaches_to" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002372", @@ -18137,22 +15659,7 @@ "definition" : { "val" : "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." }, - "xrefs" : [ { - "val" : "RO:0002372" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Wikipedia:Insertion_(anatomy)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_muscle_origin" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://dbpedia.org/property/origin" } ] @@ -18165,22 +15672,7 @@ "definition" : { "val" : "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." }, - "xrefs" : [ { - "val" : "RO:0002373" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Wikipedia:Insertion_(anatomy)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_muscle_insertion" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://dbpedia.org/property/insertion" } ] @@ -18194,21 +15686,6 @@ "val" : "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004036", - "val" : "http://purl.obolibrary.org/obo/BFO_0000050" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png" }, { @@ -18225,46 +15702,7 @@ "val" : "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002376" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Deschutes River tributary_of Columbia River" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "inferior epigastric vein tributary_of external iliac vein" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "drains into" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "drains to" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "tributary channel of" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://en.wikipedia.org/wiki/Tributary" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.medindia.net/glossary/venous_tributary.htm" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "tributary_of" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://dbpedia.org/ontology/drainsTo" }, { @@ -18279,17 +15717,7 @@ "meta" : { "definition" : { "val" : "x spatially_coextensive_with y if and inly if x and y have the same location" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A lump of clay and a statue" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002380", @@ -18300,22 +15728,7 @@ "val" : "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" }, "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002380" - } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "branching_part_of" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://github.com/obophenotype/uberon/issues/2212" }, { @@ -18330,14 +15743,7 @@ "meta" : { "definition" : { "val" : "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002385", @@ -18346,23 +15752,7 @@ "meta" : { "definition" : { "val" : "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" - }, - "xrefs" : [ { - "val" : "RO:0002385" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_potential_to_developmentally_contribute_to" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002386", @@ -18371,14 +15761,7 @@ "meta" : { "definition" : { "val" : "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002387", @@ -18387,23 +15770,7 @@ "meta" : { "definition" : { "val" : "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" - }, - "xrefs" : [ { - "val" : "RO:0002387" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_potential_to_develop_into" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002388", @@ -18412,14 +15779,7 @@ "meta" : { "definition" : { "val" : "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002404", @@ -18433,12 +15793,6 @@ "val" : "RO:0002404" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -18455,12 +15809,6 @@ "val" : "RO:0002405" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000428" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -18477,15 +15825,6 @@ "val" : "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "indirectly activates" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002579", - "val" : "http://purl.obolibrary.org/obo/RO_0002213" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Indirectly_positively_regulates" } ] @@ -18499,15 +15838,6 @@ "val" : "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "indirectly inhibits" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002579", - "val" : "http://purl.obolibrary.org/obo/RO_0002212" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Indirectly_negatively_regulates" } ] @@ -18524,12 +15854,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." } ] } }, { @@ -18545,9 +15869,6 @@ "val" : "RO:0002411" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -18567,12 +15888,6 @@ "val" : "RO:0002412" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002411" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -18598,12 +15913,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "influences (processual)" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" @@ -18625,12 +15934,6 @@ "val" : "RO:0002427" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -18645,11 +15948,7 @@ "meta" : { "definition" : { "val" : "c involved in regulation of p if c is involved in some p' and p' regulates some p" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002429", @@ -18658,14 +15957,7 @@ "meta" : { "definition" : { "val" : "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002428" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002430", @@ -18676,9 +15968,6 @@ "val" : "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002428" } ] @@ -18694,12 +15983,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "OWL does not allow defining object properties via a Union" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "involved in or reguates" } ] } }, { @@ -18717,15 +16000,6 @@ "val" : "enables activity in" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A protein that enables activity in a cytosol." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "executes activity in" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "https://wiki.geneontology.org/Is_active_in" } ] @@ -18737,20 +16011,7 @@ "meta" : { "definition" : { "val" : "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." - }, - "xrefs" : [ { - "val" : "RO:0002433" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "contributes_to_morphology_of" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002434", @@ -18771,18 +16032,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Considering relabeling as 'pairwise interacts with'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" - }, { - "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", - "val" : "http://purl.obolibrary.org/obo/MI_0914" } ] } }, { @@ -18794,20 +16046,8 @@ "val" : "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "binds" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "molecularly binds with" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/ECO_0000353" - }, { - "pred" : "http://www.w3.org/2004/02/skos/core#closeMatch", - "val" : "http://purl.obolibrary.org/obo/MI_0915" } ] } }, { @@ -18818,12 +16058,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Axiomatization to GO to be added later" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." } ] } }, { @@ -18837,13 +16071,6 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "molecularly controls" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" } ] } }, { @@ -18857,16 +16084,6 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "molecularly decreases activity of" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "directly inhibits" } ] } }, { @@ -18880,31 +16097,12 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "molecularly increases activity of" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "directly activates" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002464", "lbl" : "helper property (not for use in curation)", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002473", "lbl" : "composed primarily of", @@ -18913,29 +16111,7 @@ "definition" : { "val" : "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002473" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://www.ncbi.nlm.nih.gov/pubmed/22293552" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0001900", - "val" : "http://purl.obolibrary.org/obo/RO_0001901" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "composed_primarily_of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002479", @@ -18945,22 +16121,12 @@ "definition" : { "val" : "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002481", "lbl" : "is kinase activity", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002485", "lbl" : "receives input from", @@ -18969,9 +16135,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "See notes for inverse relation" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { @@ -18982,24 +16145,12 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" } ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002487", "lbl" : "relation between physical entity and a process or stage", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage." - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002488", "lbl" : "existence starts during", @@ -19007,20 +16158,7 @@ "meta" : { "definition" : { "val" : "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." - }, - "xrefs" : [ { - "val" : "RO:0002488" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_starts_during" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002489", @@ -19029,20 +16167,7 @@ "meta" : { "definition" : { "val" : "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." - }, - "xrefs" : [ { - "val" : "RO:0002489" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_starts_with" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002490", @@ -19052,11 +16177,7 @@ "definition" : { "val" : "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002491", @@ -19070,19 +16191,6 @@ "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "exists during" - } ], - "xrefs" : [ { - "val" : "RO:0002491" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_starts_and_ends_during" } ] } }, { @@ -19093,24 +16201,7 @@ "definition" : { "val" : "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "ceases_to_exist_during" - } ], - "xrefs" : [ { - "val" : "RO:0002492" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_ends_during" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002493", @@ -19120,20 +16211,7 @@ "definition" : { "val" : "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "xrefs" : [ { - "val" : "RO:0002493" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_ends_with" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002494", @@ -19142,20 +16220,7 @@ "meta" : { "definition" : { "val" : "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" - }, - "xrefs" : [ { - "val" : "RO:0002494" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "transformation_of" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002495", @@ -19164,23 +16229,7 @@ "meta" : { "definition" : { "val" : "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" - }, - "xrefs" : [ { - "val" : "RO:0002495" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002494" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "immediate_transformation_of" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002496", @@ -19190,20 +16239,7 @@ "definition" : { "val" : "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "xrefs" : [ { - "val" : "RO:0002496" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_starts_during_or_after" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002497", @@ -19213,20 +16249,7 @@ "definition" : { "val" : "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." }, - "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ], - "xrefs" : [ { - "val" : "RO:0002497" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "existence_ends_during_or_before" - } ] + "comments" : [ "The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription." ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002500", @@ -19235,11 +16258,7 @@ "meta" : { "definition" : { "val" : "A relationship between a material entity and a process where the material entity has some causal role that influences the process" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002501", @@ -19248,17 +16267,7 @@ "meta" : { "definition" : { "val" : "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002502", @@ -19266,9 +16275,6 @@ "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://purl.obolibrary.org/obo/BFO_0000169" } ] @@ -19281,15 +16287,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." } ] } }, { @@ -19299,55 +16296,18 @@ "meta" : { "definition" : { "val" : "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." - }, - "xrefs" : [ { - "val" : "RO:0002551" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000118", - "val" : "has supporting framework" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_skeleton" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002559", "lbl" : "causally influenced by", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "causally influenced by (entity-centric)" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002563", "lbl" : "interaction relation helper property", "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", "val" : "http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29" }, { @@ -19358,13 +16318,7 @@ }, { "id" : "http://purl.obolibrary.org/obo/RO_0002564", "lbl" : "molecular interaction relation helper property", - "type" : "PROPERTY", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] - } + "type" : "PROPERTY" }, { "id" : "http://purl.obolibrary.org/obo/RO_0002565", "lbl" : "results in movement of", @@ -19378,11 +16332,6 @@ "val" : "RO:0002565" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -19397,20 +16346,7 @@ "meta" : { "definition" : { "val" : "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "causally influences (entity-centric)" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002567", @@ -19419,14 +16355,7 @@ "meta" : { "definition" : { "val" : "A relation that holds between elements of a musculoskeletal system or its analogs." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002568", @@ -19435,23 +16364,7 @@ "meta" : { "definition" : { "val" : "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." - }, - "xrefs" : [ { - "val" : "RO:0002568" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "Wikipedia:Antagonist_(muscle)" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_muscle_antagonist" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002569", @@ -19461,20 +16374,7 @@ "definition" : { "val" : "inverse of branching part of" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002569" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "has_branching_part" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259", "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002570", @@ -19484,26 +16384,7 @@ "definition" : { "val" : "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002570" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "UBERON:cjm" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "conduit_for" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002571", @@ -19513,23 +16394,7 @@ "definition" : { "val" : "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002571" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "lumen_of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002572", @@ -19539,20 +16404,7 @@ "definition" : { "val" : "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" }, - "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ], - "xrefs" : [ { - "val" : "RO:0002572" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "luminal_space_of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/ro/subsets#ro-eco" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002576", @@ -19562,20 +16414,7 @@ "definition" : { "val" : "inverse of has skeleton" }, - "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ], - "xrefs" : [ { - "val" : "RO:0002576" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "skeleton_of" - } ] + "subsets" : [ "http://purl.obolibrary.org/obo/RO_0002259" ] } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002578", @@ -19590,18 +16429,6 @@ "val" : "RO:0002578" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "directly regulates (processual)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002575", - "val" : "http://purl.obolibrary.org/obo/RO_0002211" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -19609,24 +16436,6 @@ "val" : "directly_regulates" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002581", - "lbl" : "is a defining property chain axiom", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL" - } - } - }, { - "id" : "http://purl.obolibrary.org/obo/RO_0002582", - "lbl" : "is a defining property chain axiom where second argument is reflexive", - "type" : "PROPERTY", - "meta" : { - "definition" : { - "val" : "If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R." - } - } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002584", "lbl" : "has part structure that is capable of", @@ -19634,14 +16443,7 @@ "meta" : { "definition" : { "val" : "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002586", @@ -19715,12 +16517,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0002-6601-2165" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" } ] } }, { @@ -19730,14 +16526,7 @@ "meta" : { "definition" : { "val" : "Holds between c and p if and only if c is capable of some activity a, and a regulates p." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "pyrethroid -> growth" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002597", @@ -19746,11 +16535,7 @@ "meta" : { "definition" : { "val" : "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002598", @@ -19759,14 +16544,7 @@ "meta" : { "definition" : { "val" : "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "renin -> arteriolar smooth muscle contraction" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0002608", @@ -19780,9 +16558,6 @@ "val" : "RO:0002608" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -19803,15 +16578,6 @@ "val" : "RO:0002629" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "directly positively regulates (process to process)" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002578" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" }, { @@ -19835,12 +16601,6 @@ "val" : "RO:0002630" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000119", - "val" : "http://purl.obolibrary.org/obo/ro/docs/causal-relations" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000589", - "val" : "directly negatively regulates (process to process)" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0004050", "val" : "http://purl.obolibrary.org/obo/RO_0002578" }, { @@ -19868,17 +16628,8 @@ "val" : "RO:0003000" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9114-8737" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "produces" @@ -19897,17 +16648,8 @@ "val" : "RO:0003001" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000114", - "val" : "http://purl.obolibrary.org/obo/IAO_0000125" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9114-8737" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "produced_by" @@ -20016,9 +16758,6 @@ "meta" : { "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002264" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { @@ -20059,9 +16798,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/valid_for_go_gp2term" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002263" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { @@ -20120,9 +16856,6 @@ "type" : "PROPERTY", "meta" : { "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0004049", - "val" : "http://purl.obolibrary.org/obo/RO_0002418" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "https://orcid.org/0000-0002-6601-2165" }, { @@ -20153,11 +16886,7 @@ "meta" : { "definition" : { "val" : "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." - }, - "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-4639-4431" - } ] + } } }, { "id" : "http://purl.obolibrary.org/obo/RO_0012000", @@ -20419,9 +17148,6 @@ "xrefs" : [ "PMID:19243617" ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" - }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1617-8244" }, { @@ -20439,9 +17165,6 @@ "xrefs" : [ "PMID:19243617" ] }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" - }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1617-8244" }, { @@ -20462,21 +17185,6 @@ "val" : "utilizes" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000112", - "val" : "A diagnostic testing device utilizes a specimen." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0001-9625-1899" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "https://orcid.org/0000-0003-2620-0345" - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." - }, { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "See github ticket https://github.com/oborel/obo-relations/issues/497" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2021-11-08T12:00:00Z" } ] @@ -20619,12 +17327,6 @@ "val" : "galen:Tube" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts)" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "tubular" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -20672,8 +17374,6 @@ "val" : "EMAPA:37283" }, { "val" : "EV:0100155" - }, { - "val" : "FBbt:00007000" }, { "val" : "HAO:0000144" }, { @@ -20694,18 +17394,6 @@ "val" : "XAO:0000218" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "An appendage is an external body part, or natural prolongation, that protrudes from an organism's body, such as a vertebrate's limbs[BILA][BILA:0000018]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organ or organ part that is attached to the body of an organism. For example a limb[GO, modified][GO:0048736]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "appendicular" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "this is currently a subtype of organism subdivision - which would exclude feathers" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -20789,24 +17477,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical structure consisting of long narrow duct which carries urine from the kidney to the urinary bladder.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The duct of amniotes that carries urine from a metanephric kidney to the urinary bladder. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "ureteral" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "ureteric" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000010", - "val" : "in humans, consists of adventitial, muscular and mucoa layers" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -20863,12 +17533,6 @@ "val" : "galen:Urethra" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "urethral" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In human males, the urethra travels through the penis, and carries semen as well as urine. In females, the urethra is shorter and emerges above the vaginal opening." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -20903,8 +17567,6 @@ } ], "xrefs" : [ { "val" : "AAO:0011123" - }, { - "val" : "FBbt:00100314" }, { "val" : "FMA:30320" }, { @@ -20925,12 +17587,6 @@ "val" : "galen:Duct" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -20958,16 +17614,11 @@ "xrefs" : [ "FMA:82482" ] } ], "xrefs" : [ { - "val" : "EMAPA:25036" - }, { "val" : "FMA:82482" }, { "val" : "galen:Wall" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in FMA, serosa is a wall" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0009915" }, { @@ -21005,8 +17656,6 @@ "val" : "EHDAA2:0003003" }, { "val" : "EMAPA:0" - }, { - "val" : "FBbt:00007001" }, { "val" : "FMA:305751" }, { @@ -21106,12 +17755,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -21146,12 +17789,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -21190,9 +17827,6 @@ "val" : "SCTID:91717005" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "currently defined in a very broad sense, may be replaced by more specific classes in the future" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_33090" }, { @@ -21323,9 +17957,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "ncit:Death is an outcome" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -21411,9 +18042,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "ZFA - The multi-tissue structure where the glomerular basement membrane supported by mesonephric podocytes filters blood from the glomerular capillaries. GUDMAP: 'Together, the Bowman's capsule and the glomerulus comprise the definitive renal corpuscle.' - here the glomerulus is part of the capsule?" }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0001-9114-8737" @@ -21555,24 +18183,6 @@ "val" : "ZFA:0000529" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A kidney formed of nephric tubules arising in the middle region of the nephric ridge; a transient embryonic stage that replaces the pronephros, but is itself replaced by the adult metanephros [in mammals; in fishes and amphibians it is the adult kidney]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organ that is the definitive adult kidney. It replaces the earlier pronephros, which degenerates as the mesonephros becomes functional in feeding stage tadpoles.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates. (...) In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "mesonephric" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In mammals, the mesonephros is the second of the three embryonic kidneys to be established and exists only transiently. In fish and amphibians, the mesonephros will form the mature kidney" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000009", - "val" : "By contrast to the pronephros, the histological features of the mammalian mesonephros, with its primitive glomeruli, suggest that it probably functions as a primitive kidney, and is involved in the production of much of the amniotic fluid. Within the two mesonephroi, one located on either side of the dorsal mesentery of the hindgut, a substantial number (in the region of about 40 or more) of cranio-caudally segmented mesonephric tubules are formed. It has, however, been suggested that only the most rostrally located 4-6 pairs of mesonephric tubules drain into the mesonephric portion of the nephric duct. This is now seen to extend along the length of the mesonephroi, being located towards their lateral sides. The mesonephros is also retained over a considerably longer period than the pronephros, but gradually undergoes regression in a cranio-caudal direction. While the rostral part displays clear evidence of regression its more caudal part appears to display evidence of functional activity. Within the medial part of the mesonephros, vesicles are formed, although no glomeruli are formed there in this species. It is, however, difficult to believe that the relatively enormous mesonephroi do not have an excretory role in the mouse, only serving as a base for gonadal differentiation. In the human embryo, the medial part of the mesonephric tubules enlarges, become invaginated by capillaries, and form glomeruli. These then take on an excretory role. In the mouse, the mesonephric ducts appear to be patent throughout their length[GUDMAP, modified]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -21639,18 +18249,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO check developmental relationships" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A kidney formed of nephric tubules arising in the posterior region of the nephric ridge and drained by a ureter; replaces the embryonic pronephros and mesonephros [in mammals]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "metanephric" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "During the fifth week of gestation, the mesonephric duct develops an outpouching, the ureteric bud, near its attachment to the cloaca. This bud, also called the metanephrogenic diverticulum, grows posteriorly and towards the head of the embryo. The elongated stalk of the ureteric bud, the metanephric duct, later forms the ureter. As the cranial end of the bud extends into the intermediate mesoderm, it undergoes a series of branchings to form the collecting duct system of the kidney. It also forms the major and minor calyces and the renal pelvis" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -21692,12 +18290,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO check" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Any of the renal tubules composing the mesonephros. In mammals they function as excretory structures during the early embryonic development but are later incorporated into the reproductive system. [TFD][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -21765,15 +18357,6 @@ "val" : "Wikipedia:Ureteric_bud" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts. [Embryology, See_Dudek_RW_and_Fix_JD, Third_Edition_(2004)_Philadelphia:_Lippincott_William_and_Wilkins, p.137][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts[VHOG:0000541]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -21813,9 +18396,6 @@ "val" : "WBls:0000103" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -21932,12 +18512,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "the WBls class 'all stages' belongs here as it is the superclass of other WBls stages" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -21990,8 +18564,6 @@ "val" : "EHDAA:27" }, { "val" : "FBdv:00005288" - }, { - "val" : "IDOMAL:0000302" }, { "val" : "NCIT:C12601" }, { @@ -22006,9 +18578,6 @@ "val" : "ZFS:0000001" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -22186,12 +18755,6 @@ "val" : "XAO:1000006" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002174", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7955" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In zebrafish, the times of neurulation and segmentation overlap so extensively there is no distinct neurula period of development, such as occurs largely before segmentation in amphibian embryos." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -22309,9 +18872,6 @@ "val" : "NCIT:C12749" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A thin sheet or layer of pliable tissue, serving as a covering or envelope of a part, as the lining of a cavity, as a partition or septum, or to connect two structures." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -22346,9 +18906,6 @@ "val" : "SCTID:91837002" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in FMA, this is an anatomical conduit *space*, rather than anatomical conduit" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -22397,27 +18954,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "adding df link to embryonic cloaca leads to a cycle in uberon-simple, as cloaca is a suberclass of embryonic cloaca" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9369" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A common passage for fecal, urinary, and reproductive discharge in most lower vertebrates as well as the terminal end of the hindgut before division into rectum, bladder, and genital primordia in mammalian embryos. [TFD][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical structure which is the common receptacle for the alimentary canal, Wolffian ducts, oviducts, and the bladder.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "A cloaca is apparently a primitive vertebrate feature because it occurs in most primitive gnathostomes and persists in the embryos of almost all vertebrates.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "cloacal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "Human beings only have an embryonic cloaca, which is split up into separate tracts during the development of the urinary and reproductive organs" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "hindgut endoderm and proctodeal ectoderm." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -22448,9 +18984,6 @@ "val" : "Wikipedia:Cloaca_(embryology)" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "this class represents the embryonic form of the cloaca, as found in both mammals and non-mammals." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -22502,15 +19035,6 @@ "val" : "Wikipedia:Definitive_urogenital_sinus" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The ventral part of the cloaca after its separation from the rectum, giving rise to the lower part of the bladder in both sexes, to the prostatic portion of the male urethra, and to the urethra and vestibule in the female. [TFD][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "In mammals the lowly monotremes still have a cloaca. Higher types have done away with this structure and have a separate anal outlet for the rectum. The monotreme cloaca shows the initiation of this subdivision. The cloaca has such includes only the distal part, roughly comparable to the proctodeum. The more proximal part is divided into (1) a large dorsal passage into which the intestine opens, the coprodeum, and (2) a ventral portion, the urodeum with which the bladder connects. (...) the development of the placental mammals recapitulates in many respects the phylogenetic story. In the sexually indifferent stage of placental mammal there is a cloaca. While the indifferent stage still persists, a septum develops, and extends out to the closing membrane. This divides the cloaca into two chambers: a coprodeum continuous with the gut above, and a urodeum or urogenital sinus below.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000013", - "val" : "the term 'urogenital sinus' may refer to the primitive urogenital sinus present as a transient developmental structure in most mammals or it may refer to a condition in which an unseptated cloaca persists in animals longer than normal" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -22601,8 +19125,6 @@ "val" : "EHDAA:542" }, { "val" : "EMAPA:16262" - }, { - "val" : "FBbt:00003126" }, { "val" : "FMA:49184" }, { @@ -22645,21 +19167,6 @@ "val" : "http://purl.obolibrary.org/obo/uberon/images/lamprey_sucker_rosava_3238889218.jpg" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "oral" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -22786,23 +19293,8 @@ "val" : "galen:Blood" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid." - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -22894,10 +19386,6 @@ "xrefs" : [ "Wikipedia:Parenchyma" ] }, "xrefs" : [ { - "val" : "BTO:0000999" - }, { - "val" : "BTO:0001539" - }, { "val" : "EHDAA:3015" }, { "val" : "EHDAA:3905" @@ -22931,15 +19419,6 @@ "val" : "Wikipedia:Parenchyma" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "parenchymal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "Early in development the mammalian embryo has three distinct layers: ectoderm (external layer), endoderm (internal layer) and in between those two layers the middle layer or mesoderm. The parenchyma of most organs is of ectodermal (brain, skin) or endodermal origin (lungs, gastrointestinal tract, liver, pancreas). The parenchyma of a few organs (spleen, kidneys, heart) is of mesodermal origin. The stroma of all organs is of mesodermal origin" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "the FMA definition is more restrictive, and limits this to solid organs. This would seem to cause problems for the lung parenchyma, except FMA classifies Lung as solid rather than cavitated" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -23029,9 +19508,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000010", - "val" : "The renal medulla is split up into a number of sections, known as the renal pyramids. Blood enters into the kidney via the renal artery, which then splits up to form the arcuate arterioles. The arcuate arterioles each in turn branch into interlobular arterioles, which finally reach the glomeruli. At the glomerulus the blood reaches a highly disfavourable pressure gradient and a large exchange surface area, which forces the serum portion of the blood out of the vessel into the renal tubules. Flow continues through the renal tubules, including the proximal tubule, the Loop of Henle, and finally leaves the kidney by means of the collecting duct, leading to the renal ureter. The renal medulla contains the structures of the nephrons responsible for maintaining the salt and water balance of the blood. The renal medulla is hypertonic to the filtrate in the nephron and aids in the reabsorption of water" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -23103,8 +19579,6 @@ "val" : "BTO:0001485" }, { "val" : "EFO:0000801" - }, { - "val" : "EMAPA:35578" }, { "val" : "FMA:72954" }, { @@ -23127,12 +19601,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system that consists of the muscles of the body.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -23183,8 +19651,6 @@ "val" : "EHDAA2:0003004" }, { "val" : "EMAPA:35178" - }, { - "val" : "FBbt:00007019" }, { "val" : "FMA:9669" }, { @@ -23257,8 +19723,6 @@ "val" : "CARO:0000005" }, { "val" : "EHDAA2:0003005" - }, { - "val" : "FBbt:00007017" }, { "val" : "FMA:5897" }, { @@ -23312,8 +19776,6 @@ "val" : "CARO:0000006" }, { "val" : "EHDAA2:0003006" - }, { - "val" : "FBbt:00007016" }, { "val" : "FMA:67165" }, { @@ -23364,8 +19826,6 @@ "val" : "CARO:0000007" }, { "val" : "EHDAA2:0003007" - }, { - "val" : "FBbt:00007015" }, { "val" : "FMA:67112" }, { @@ -23444,14 +19904,10 @@ "val" : "EMAPA:16103" }, { "val" : "EV:0100000" - }, { - "val" : "FBbt:00004856" }, { "val" : "FMA:7149" }, { "val" : "HAO:0000011" - }, { - "val" : "IDOMAL:0002460" }, { "val" : "MA:0000003" }, { @@ -23560,8 +20016,6 @@ "val" : "EMAPA:25765" }, { "val" : "EV:0100016" - }, { - "val" : "FBbt:00000001" }, { "val" : "FMA:256135" }, { @@ -23603,9 +20057,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "organismal" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -23649,9 +20100,6 @@ "val" : "ZFA:0001489" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -23700,8 +20148,6 @@ "val" : "EHDAA2:0003032" }, { "val" : "EMAPA:36031" - }, { - "val" : "FBbt:00007009" }, { "val" : "FMA:7153" }, { @@ -23776,8 +20222,6 @@ "val" : "CARO:0000040" }, { "val" : "EHDAA2:0003040" - }, { - "val" : "FBbt:00007013" }, { "val" : "FMA:63863" }, { @@ -23816,8 +20260,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "xrefs" : [ { - "val" : "FBbt:00007277" - }, { "val" : "VHOG:0001737" } ], "basicPropertyValues" : [ { @@ -23874,8 +20316,6 @@ "val" : "EHDAA2:0003043" }, { "val" : "EMAPA:35868" - }, { - "val" : "FBbt:00007003" }, { "val" : "FMA:9637" }, { @@ -23946,8 +20386,6 @@ "val" : "CARO:0000055" }, { "val" : "EHDAA2:0003055" - }, { - "val" : "FBbt:00007010" }, { "val" : "HAO:0000055" }, { @@ -24012,8 +20450,6 @@ "val" : "EHDAA2:0003066" }, { "val" : "EMAPA:32738" - }, { - "val" : "FBbt:00007005" }, { "val" : "FMA:9639" }, { @@ -24042,12 +20478,6 @@ "val" : "ZFA:0001486" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "epithelial" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -24095,8 +20525,6 @@ "val" : "CARO:0000068" }, { "val" : "EHDAA2_RETIRED:0003068" - }, { - "val" : "FBbt:00007027" }, { "val" : "FMA:45567" }, { @@ -24173,9 +20601,6 @@ "val" : "ZFA:0001498" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Unilaminar epithelium that consists of a single layer of squamous cells.[CARO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -24229,9 +20654,6 @@ "val" : "ZFA:0001490" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -24288,9 +20710,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Epithelium that consists of a single layer of epithelial cells.[CARO]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -24333,18 +20752,6 @@ "val" : "Wikipedia:Thorax" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000026" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000033" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0002417" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -24409,12 +20816,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "abdominal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "celiac" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -24464,14 +20865,10 @@ "val" : "EHDAA:38" }, { "val" : "EMAPA:16039" - }, { - "val" : "FBbt:00000052" }, { "val" : "FMA:69068" }, { "val" : "GAID:963" - }, { - "val" : "IDOMAL:0000646" }, { "val" : "MAT:0000226" }, { @@ -24498,12 +20895,6 @@ "val" : "http://neurolex.org/wiki/Category:Embryonic_organism" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "embryonic" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -24552,8 +20943,6 @@ "val" : "BTO:0000556" }, { "val" : "EMAPA:36033" - }, { - "val" : "FBbt:00000110" }, { "val" : "FMA:69069" }, { @@ -24580,9 +20969,6 @@ "val" : "ZFA:0001122" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -24618,8 +21004,6 @@ "val" : "EMAPA:16069" }, { "val" : "EV:0100003" - }, { - "val" : "FBbt:00000111" }, { "val" : "FMA:69070" }, { @@ -24650,15 +21034,6 @@ "val" : "ZFA:0000016" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "ectodermal" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -24698,8 +21073,6 @@ "val" : "EMAPA:16062" }, { "val" : "EV:0100005" - }, { - "val" : "FBbt:00000125" }, { "val" : "FMA:69071" }, { @@ -24728,12 +21101,6 @@ "val" : "ZFA:0000017" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "endodermal" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -24788,8 +21155,6 @@ "val" : "EMAPA:16083" }, { "val" : "EV:0100006" - }, { - "val" : "FBbt:00000126" }, { "val" : "FMA:69072" }, { @@ -24820,18 +21185,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Primary germ layer that is the middle of the embryonic germ layers.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "mesodermal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0003263" @@ -24891,8 +21244,6 @@ "val" : "EHDAA2:0001929" }, { "val" : "EMAPA:16263" - }, { - "val" : "FBbt:00000439" }, { "val" : "FMA:295846" }, { @@ -24913,18 +21264,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "stomodeal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -24968,8 +21307,6 @@ "val" : "EHDAA2:0000121" }, { "val" : "EMAPA:25038" - }, { - "val" : "FBbt:00000123" }, { "val" : "NCIT:C34278" }, { @@ -24988,15 +21325,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "removed WBbt:0006795 'proctodeum' - junction between the alimentary and genital tracts in the male." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "An inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "proctodeal" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -25090,21 +21418,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "cardiac" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -25139,9 +21452,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO - merge with cell layer?" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "laminar" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -25171,12 +21481,6 @@ "val" : "galen:Medulla" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "this class is used in a very general sense" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "medullary" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -25255,12 +21559,6 @@ "val" : "galen:Joint" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -25328,8 +21626,6 @@ "val" : "EMAPA:17381" }, { "val" : "EV:0100100" - }, { - "val" : "FBbt:00004857" }, { "val" : "FMA:7160" }, { @@ -25340,8 +21636,6 @@ "val" : "HAO:0000895" }, { "val" : "MA:0000326" - }, { - "val" : "MESH:D005835" }, { "val" : "MIAA:0000305" }, { @@ -25369,15 +21663,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system which consists of organs and tissues associated with sexual reproduction of the organism.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Arguably, one of the most important aspects of urbilaterian organogenesis would have been gonadogenesis, since Urbilateria must have successfully generated gametes and developed a strategy for extrusion and fertilization, in order to be the ancestor of all living Bilateria.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000202", - "val" : "http://purl.obolibrary.org/obo/FMA_75572" }, { "pred" : "http://purl.org/dc/terms/date", "val" : "2022-06-10T18:22:34Z" @@ -25418,8 +21703,6 @@ "val" : "BTO:0000534" }, { "val" : "EMAPA:17383" - }, { - "val" : "FBbt:00004858" }, { "val" : "FMA:18250" }, { @@ -25450,21 +21733,6 @@ "val" : "ZFA:0000413" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "gonadal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "FMA xref is a 'general anatomical term'" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -25502,10 +21770,6 @@ "val" : "CALOHA:TS-1293" }, { "val" : "EFO:0000793" - }, { - "val" : "EV:0100056" - }, { - "val" : "FBbt:00005055" }, { "val" : "FMA:7152" }, { @@ -25540,15 +21804,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "digestive" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -25610,8 +21865,6 @@ "val" : "EMAPA:17366" }, { "val" : "EV:0100095" - }, { - "val" : "FBbt:00005056" }, { "val" : "FMA:7159" }, { @@ -25656,18 +21909,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Evolution of vertebrate renal anatomy appears quite conservative when compared, for example, to evolution of respiratory and cardiovascular systems in vertebrates. Major anatomical changes in vertebrates kidneys separate those of birds and mammals from kidneys of lower vertebrates. General increase in animal size from fish to mammals is reflected by an increase in total number of nephrons per kidney, rather than by constant change in tubular dimensions.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "This definition is inclusive of the organs of the vertebrate renal system, as well as the Malpighian tubules of insects, and allows for future incorporation of structures such as the antennal glands of crustaceans" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -25693,17 +21934,12 @@ "val" : "AAO:0000959" }, { "val" : "CALOHA:TS-2103" - }, { - "val" : "MESH:D002319" }, { "val" : "VHOG:0001248" }, { "val" : "Wikipedia:Circulatory_system" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "the cardiovascular system and the lymphatic system are parts of the circulatory system" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_147099" }, { @@ -25712,18 +21948,9 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6157" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002174", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6231" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -25775,13 +22002,9 @@ "val" : "musculature system" } ], "xrefs" : [ { - "val" : "AAO:0011066" - }, { "val" : "BTO:0000887" }, { "val" : "EFO:0001949" - }, { - "val" : "EMAPA:32715" }, { "val" : "EMAPA:35577" }, { @@ -25804,12 +22027,6 @@ "val" : "ZFA:0000548" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0001474" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -25861,8 +22078,6 @@ "val" : "EMAPA:16469" }, { "val" : "EV:0100162" - }, { - "val" : "FBbt:00005093" }, { "val" : "FMA:7157" }, { @@ -25902,21 +22117,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "nervous" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "neural" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -25980,8 +22180,6 @@ "val" : "EMAPA:16754" }, { "val" : "EV:0100163" - }, { - "val" : "FBbt:00005094" }, { "val" : "FMA:55675" }, { @@ -26017,18 +22215,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Part of the nervous system which includes the brain and spinal cord.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The brain and spinal cord. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO)." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26067,8 +22253,6 @@ "val" : "EHDAA:520" }, { "val" : "EMAPA:16548" - }, { - "val" : "FBbt:00005379" }, { "val" : "FMA:45616" }, { @@ -26091,12 +22275,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. In vertebrates the term may refer to a developmental structure" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The anterior portion of the primitive digestive tube of the embryo that lies cephalic to the junction of the yolk stalk, consists of endodermal tissue, and gives rise to the the pharynx, lower respiratory system, esophagus, stomach, duodenum proximal to the biliary tract, liver, pancreas, biliary tract, and gall bladder." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26133,8 +22311,6 @@ "val" : "EHDAA:983" }, { "val" : "EMAPA:16255" - }, { - "val" : "FBbt:00005383" }, { "val" : "FMA:45617" }, { @@ -26157,15 +22333,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. We may explicitly make this a developmental class" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In humans: originates from the foregut at the opening of the bile duct into the duodenum and continues through the small intestine and much of the large intestine until the transition to the hindgut about two-thirds of the way through the transverse colon" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in FMA this represents an embryonic region." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26202,8 +22369,6 @@ "val" : "EHDAA:975" }, { "val" : "EMAPA:16715" - }, { - "val" : "FBbt:00005384" }, { "val" : "FMA:45618" }, { @@ -26226,15 +22391,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future (vertebrates have some contribution from NC - https://github.com/obophenotype/uberon/wiki/The-neural-crest). We may explicitly make this a developmental class" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "the caudal portion of the primitive digestive tube of the embryo" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in FMA this class has no children. In MA it has a single child hindgut epithelium" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26280,8 +22436,6 @@ "val" : "EFO:0001652" }, { "val" : "EHDAA2:0003171" - }, { - "val" : "FBbt:00005495" }, { "val" : "FMA:86589" }, { @@ -26344,8 +22498,6 @@ "val" : "FMA:293882" }, { "val" : "MAT:0000069" - }, { - "val" : "MESH:D054259" }, { "val" : "MIAA:0000069" }, { @@ -26368,18 +22520,6 @@ "val" : "neuronames:1365" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -26411,8 +22551,6 @@ "val" : "CARO:0000000" }, { "val" : "EHDAA2:0002229" - }, { - "val" : "FBbt:10000000" }, { "val" : "FMA:62955" }, { @@ -26517,12 +22655,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Trunk of systemic vein which is formed by the union of the right common iliac vein and the left common iliac vein and terminates in the right atrium[FMA]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Phylogenetic modifications within this basic pattern of arteries and veins are largely correlated with functional changes. In the transition from water to land, gills gave way to lungs, accompanied by the establishment of a pulmonary circulation. In some fishes and certainly in tetrapods, the cardinal veins become less involved in blood return. Instead, the composite, prominent postcava (posterior vena cava) arose to drain the posterior part of the body and the precava (anterior vena cava) developed to drain the anterior part of the body.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26573,9 +22705,6 @@ "val" : "galen:Urine" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "kidney excreta from some taxa (e.g. in aves) may not be liquid" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -26637,12 +22766,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The renal veins are veins that drain the kidney. They connect the kidney to the inferior vena cava. It is usually singular to each kidney, except in the condition 'multiple renal veins'. It also divides into 2 divisions upon entering the kidney: the anterior branch which receives blood from the anterior portion of the kidney and, the posterior branch which receives blood from the posterior portion. Often, each renal vein will have a branch that receives blood from the ureter. [WP,unvetted][Wikipedia:Renal_vein]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in EHDAA2, the renal vein is part of the kidney" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26768,9 +22891,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000010", - "val" : "In the adult metanephros, it forms a continuous smooth outer zone with a number of projections that extend down between the pyramids. It contains the renal corpuscles and the renal tubules except for parts of the loop of Henle which descend into the renal medulla. It also contains blood vessels and cortical collecting ducts. The renal cortex is the part of the kidney where ultrafiltration occurs.[WP]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26861,15 +22981,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A mass of arterial capillaries enveloped in a capsule and attached to a tubule in the kidney[BTO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A tuft of capillaries found in a Bowman's capsule in which waste products are filtered from the blood and urine formation is initiated. Paired highly vascularized structures of the pronephros, responsible for blood filtration.[XAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The part of the nephron that filters blood.[TAO]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -26966,15 +23077,6 @@ "val" : "ZFA:0005310" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical structure found in the kidney consisting of an expanded end of a kidney tubule surrounding a glomerulus and is the major site of filtration.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000009", - "val" : "Fluids from blood in the glomerulus are collected in the Bowman's capsule and further processed along the nephron to form urine. This process is known as ultrafiltration[WP]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "One fold of the S-shaped body gives rise to Bowman's capsule[GUDMAP]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -27041,9 +23143,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "note that in ISBN:0073040584 (Vertebrates, Kardong), the uriniferous tubule contains the nephron, so we have a separate class, rather than using a synonym, as in MA" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0004210" @@ -27132,12 +23231,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Renal duct that collects the output from renal tubules.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in ISBN:0073040584 (Vertebrates, Kardong), the nephron is adjacent to the collecting tubule, consistent with FMA, but not GO. Wikipedia says: Many sources include the connecting tubule as part of the collecting duct system. However, the embryological origin is more similar to the nephron than it is to the rest of the collecting duct (which derives from the ureteric bud), and other sources therefore classify the connecting tubule with the nephron" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27172,8 +23265,6 @@ "val" : "CALOHA:TS-2005" }, { "val" : "EV:0100082" - }, { - "val" : "FBbt:00047153" }, { "val" : "FMA:15711" }, { @@ -27200,12 +23291,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "anal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27289,26 +23374,8 @@ "val" : "galen:UrinaryBladder" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002161", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_8782" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A saccular organ in which urine accumulates before discharge from the body. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical structure which consists of a membranous sac used to temporarily store urine until it is excreted from the body.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "In tetrapods, the urinary bladder arises as an outpocketing of the cloaca. (...) The tetrapod urinary bladder appears first among amphibians and is present in Sphenodon, turtles, most lizards, ostriches among birds, and all mammals.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "vesical" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "The urinary bladder evolved in tetrapods. Birds to not possess a true urinary bladder, although Palaeognathae have an undifferentiated cloacal outpocketing that serves a similar function[https://github.com/obophenotype/uberon/issues/454]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27355,12 +23422,6 @@ "val" : "VSAO:0000304" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "this class describes the subdivision of the limb/fin, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831). See also comments on obo-anatomy mail list. Note that even though the class includes soft tissue it is more restrictive than 'pelvis' which also includes structures in cavities etc. TODO this needs to be better documented" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Subdivision of lower limb or fin which links the limb/fin to the body[FMA,modified]. There is only one instance of the pelvic girdle region per organism.[VSAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -27427,12 +23488,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Functional unit of the kidney that filters waste.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In the avian kidney, three types of nephron are identified: mammalian-type nephrons with long and short loops of Henle, and reptilian type nephrons (Gambaryan, 1992)" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27508,9 +23563,6 @@ "val" : "ZFA:0005290" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Renal tubule that connects to the renal corpuscle.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -27568,21 +23620,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "the definitions of some kidney parts (e.g. proximal straight tubule) refer to Henle's loop, even in species where this may not be present. Requires review." - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002174", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_8353" }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_8782" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A highly specialized segment of the mammalian kidney tubules, that dips into the medulla. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, p.648, see_Liem_KF][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "The structure differs considerably between species; there is a definite physical loop of Henle in the mammalian and avian renal systems but this seems to be absent in Xenopus. However, homologs of some, but not all, molecular markers (e.g. cldn8 and clcnk) of the mammalian loop of Henle were found to be present in the pronephros of the frog larva ." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000009", - "val" : "The loop of Henle plays an important role in creating a concentration gradient in the medulla of the kidney. It is involved in reabsorption of filtered water and ions including sodium, potassium and calcium, and independently regulates both the volume and osmolarity of body fluids." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27696,9 +23736,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of the renal tubule which is just posterior to the proximal convoluted tubule.[TAO]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0005166" @@ -27756,12 +23793,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "a portion of kidney nephron between the loop of Henle and the collecting duct system[Wikipedia:Distal_convoluted_tubule]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000009", - "val" : "in humans it is responsible for the reabsorption of about 5% of filtered sodium via the thiazide-sensitive Na-Cl symporter." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -27871,9 +23902,6 @@ "val" : "WBbt:0006919" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -27938,27 +23966,6 @@ "val" : "ZFA:0000434" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0001016" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "System that provides physical support to the organism.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "skeletal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -28052,14 +24059,10 @@ "val" : "EHDAA:518" }, { "val" : "EMAPA:16247" - }, { - "val" : "FBbt:00003125" }, { "val" : "FMA:45615" }, { "val" : "MA:0000917" - }, { - "val" : "MESH:D041981" }, { "val" : "NCIT:C34082" }, { @@ -28086,21 +24089,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The alimentary or digestive tract, and associated organs.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "FMA also has a term 'gastrointestinal tract', but this includes the liver." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000013", - "val" : "we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28149,10 +24137,6 @@ "xrefs" : [ "ZFA:0005145" ] } ], "xrefs" : [ { - "val" : "AAO:0011066" - }, { - "val" : "EMAPA:32715" - }, { "val" : "EMAPA:37474" }, { "val" : "EV:0100146" @@ -28176,15 +24160,6 @@ "val" : "galen:Muscle" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of tissue composed of contractile fibers.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "muscular" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -28227,8 +24202,6 @@ "val" : "CALOHA:TS-0054" }, { "val" : "EFO:0000814" - }, { - "val" : "EHDAA2:0000143" }, { "val" : "EHDAA2:0003253" }, { @@ -28269,21 +24242,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "Note that in FMA an artery is a tree, whereas AEO/JB defines it as a tube; FMA includes a separate class for what it calls the trunk. Classification in this ontology may currently (Jan 2012) represent a mix of both schemes, although we are gradually revising in the direction of the AEO scheme." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Part of the circulatory system composed of blood vessels which carry oxygenated blood away from the heart to the rest of the body.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "arterial" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "Some arthropods have primitive arterial systems but this term refers to arteries in a true closed circulatory system." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000202", - "val" : "http://purl.obolibrary.org/obo/FMA_63812" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28373,18 +24331,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO - check with MA - vein vs venous blood vessel" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Part of the circulatory system composed of blood vessels which carry blood from other organs, tissues, and cells to the heart.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "venous" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000202", - "val" : "http://purl.obolibrary.org/obo/FMA_63814" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28423,12 +24369,6 @@ "val" : "galen:Cortex" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "cortical" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "this class is used more generically than in FMA, and includes e.g. cortex of hair" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -28534,9 +24474,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Multi-tissue structure part of the blood vasculature formed by the anastomosis of capillaries. Venules carry blood toward the heart.[TAO]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28589,12 +24526,6 @@ "val" : "ZFA:0005255" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Multi-tissue structure part of the blood vasculature, feeds into capillaries. Arterioles carry blood away from the heart.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Small, terminal branch of an artery which generally connects to capillaries.[AAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -28685,21 +24616,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Any of the vessels through which blood circulates in the body.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "annelids have blood vessels, but this class is not applicable to annelids." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28766,15 +24682,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Any of the tiny blood vessels connecting the arterioles to the venules.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000010", - "val" : "capillaries lack tunica media and tunica adventitia; only the endothelial wall of the tunica intima belongs" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28821,9 +24728,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "endothelial" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28859,9 +24763,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "vascular" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28911,8 +24812,6 @@ "val" : "CALOHA:TS-2110" }, { "val" : "EFO:0000461" - }, { - "val" : "FBbt:00004208" }, { "val" : "FMA:69067" }, { @@ -28937,18 +24836,6 @@ "val" : "ZFA:0001105" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in FMA embryo is_a embryonic structure" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -29011,12 +24898,6 @@ "val" : "XAO:0003034" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -29084,15 +24965,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Right cardiac chamber which is continuous with the superior vena cava and inferior vena cava.[FMA]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000006", - "val" : "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -29184,15 +25056,6 @@ "val" : "galen:Atrium" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "One of four heart chambers.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "One of two chambers of the heart which receive blood from the veins and forces it by muscular contration to the ventricle.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -29224,8 +25087,6 @@ "val" : "EHDAA2:0000161" }, { "val" : "EHDAA:5049" - }, { - "val" : "EMAPA:17214" }, { "val" : "EMAPA:37721" }, { @@ -29234,8 +25095,6 @@ "val" : "MA:0002986" }, { "val" : "MAT:0000148" - }, { - "val" : "MESH:D013131" }, { "val" : "MIAA:0000148" }, { @@ -29250,18 +25109,6 @@ "val" : "ZFA:0000317" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -29316,8 +25163,6 @@ "val" : "SCTID:322050006" }, { "val" : "UMLS:C0222646" - }, { - "val" : "VHOG:0001666" }, { "val" : "VSAO:0000076" }, { @@ -29328,18 +25173,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Skeletal subdivision consisting of all the skeletal elements in the pectoral and pelvic appendage complexes.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Skeletal system that consists of the paired fins (pectoral or pelvic fins).[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The pectoral and pelvic girdles, which articulate with the axial skeleton, together with their associated limbs, the forelimbs and hind limbs, form the appendicular skeleton.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "ontologies differ in whether they treat the term appendicular skeleton as being the entire set of bones in the limbs, or whether the fore and hind limbs/fins are treated as seperate appendicular skeletons. Here we follow FMA, and treat the appendicular skeleton as the sum total of skeletal elements in the organism (this is evidenced by the fact that in FMA, skeleton of left/right upper/lower limb is part_of a appendicular skeleton, and subtypes of 'subdivision of appendicular skeleton'). We have separate classes such as 'skeleton of limb', and 'skeleton of hindlimb' for the 4 parts of the appendicular skeleton. In future the ZFA/TAO classes may be moved." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -29416,18 +25249,6 @@ "val" : "galen:Trunk" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000026" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000033" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -29438,8 +25259,8 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A paired organ of the urinary tract which has the production of urine as its primary function.", - "xrefs" : [ "Wikipedia:Kidney", "http://anatomy.uams.edu/anatomyhtml/kidney.html" ] + "val" : "A paired organ of the urinary tract that produces urine and maintains bodily fluid homeostasis, blood pressure, pH levels, red blood cell production and skeleton mineralization.", + "xrefs" : [ "PMID:25140012", "PMID:35003210", "Wikipedia:Kidney", "http://anatomy.uams.edu/anatomyhtml/kidney.html", "https://www.kidney.org/kidneydisease/top-5-jobs-kidneys-do" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#major_organ", "http://purl.obolibrary.org/obo/uberon/core#organ_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { @@ -29454,28 +25275,14 @@ "val" : "BTO:0000671" }, { "val" : "CALOHA:TS-0510" - }, { - "val" : "EFO:0000929" - }, { - "val" : "EMAPA:17373" - }, { - "val" : "EV:0100096" - }, { - "val" : "FMA:7203" }, { "val" : "GAID:423" - }, { - "val" : "MA:0000368" }, { "val" : "MAT:0000119" }, { "val" : "MESH:D007668" }, { "val" : "MIAA:0000119" - }, { - "val" : "NCIT:C12415" - }, { - "val" : "SCTID:181414000" }, { "val" : "UMLS:C0022646" }, { @@ -29486,20 +25293,14 @@ "val" : "galen:Kidney" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000160" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "One of either of a pair of structures lying on either side of the dorsal aorta in which fluid balance is regulated and waste is excreted out in the form of urine.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "renal" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0001-7655-4833" }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000202", - "val" : "http://purl.obolibrary.org/obo/FMA_264815" + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0003-2804-127X" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -29549,8 +25350,6 @@ "val" : "FMA:72170" }, { "val" : "MAT:0000117" - }, { - "val" : "MESH:D060910" }, { "val" : "MIAA:0000117" }, { @@ -29571,21 +25370,6 @@ "val" : "ZFA:0000151" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A kidney formed of nephric tubules arising in the anterior region of the nephric ridge; forms only as a transient embryonic structure. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.748][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organ that serves as a transient kidney, providing osmoregulation during early developmental stages and then degenerating during metamorphosis.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The embryonic kidney, present at the level of the third somite, is composed of two glomeruli fused at the midline, two pronephric tubules, and paired bilateral pronephric ducts that modify the composition of the blood filtrate before delivering it to the cloaca for excretion.Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "pronephric" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0005794" }, { @@ -29724,15 +25508,6 @@ "val" : "XAO:0000168" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system that provides locomotion and physical support to the organism.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "musculoskeletal" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -29792,9 +25567,6 @@ "val" : "Wikipedia:Thoracic_cavity" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In many species, the diaphragm separates thoracic and abdominal cavities" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -29865,8 +25637,6 @@ "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim" ], "xrefs" : [ { "val" : "BTO:0002494" - }, { - "val" : "EMAPA:28248" }, { "val" : "EMAPA:36561" }, { @@ -29883,12 +25653,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "mesangial" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "WP considers this the same as glomerular mesangium. In MA, glomerular and extraglomerular are distingsuished. FMA class has no definition and is a type of stroma, which is inconsistent with our classification of this here." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -29973,8 +25737,6 @@ "val" : "BTO:0001707" }, { "val" : "EHDAA2:0000267" - }, { - "val" : "FBbt:00005060" }, { "val" : "FMA:85006" }, { @@ -29993,15 +25755,6 @@ "val" : "galen:BodyCavity" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In mammals it forms the peritoneal, pleural, and pericardial cavities" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0000169" }, { @@ -30079,27 +25832,6 @@ "val" : "http://evolution.berkeley.edu/evolibrary/images/history/notochords.jpg" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "notochordal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -30186,32 +25918,8 @@ "val" : "ZFA:0000155" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "EDITOR_NOTE currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_7712" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Post-cranial axial segments which form sclerotome and dermomyotome.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "somitic" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -30250,9 +25958,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "not part of a nephron or distal tubule in MA and FMA" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -30308,8 +26013,6 @@ "val" : "NCIT:C34222" }, { "val" : "SCTID:361462002" - }, { - "val" : "TAO:0000045" }, { "val" : "UMLS:C0027789" }, { @@ -30324,24 +26027,6 @@ "val" : "neuronames:1366" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "EDITOR_NOTE consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams)." - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002174", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_117565" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -30400,8 +26085,6 @@ "val" : "EMAPA:16073" }, { "val" : "EV:0100004" - }, { - "val" : "FBbt:00001057" }, { "val" : "FMA:87657" }, { @@ -30424,15 +26107,6 @@ "val" : "ZFA:0001120" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "neurectodermal" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000013", - "val" : "we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -30496,12 +26170,6 @@ "val" : "galen:Pelvis" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "pelvic" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "MA and FMA differ in what they consider to be parts of the pelvis. MA includes ureter, urethra, urinary bladder, reproductive organs" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -30570,18 +26238,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "MA also has set of connective tissues" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -30638,12 +26294,6 @@ "val" : "galen:MuscleTissue" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0003714" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -30728,18 +26378,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system that consists of the blood and blood forming tissues.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "hematopoietic" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -30834,9 +26472,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -30930,12 +26565,6 @@ "val" : "ZFA:0000279" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -30968,8 +26597,6 @@ } ], "xrefs" : [ { "val" : "AAO:0011088" - }, { - "val" : "BTO:0005991" }, { "val" : "NCIT:C34279" }, { @@ -30978,8 +26605,6 @@ "val" : "TAO:0000150" }, { "val" : "UMLS:C1283945" - }, { - "val" : "VHOG:0000082" }, { "val" : "Wikipedia:Pronephric_duct" }, { @@ -30988,15 +26613,6 @@ "val" : "ZFA:0000150" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Duct of the embryonic kidney, present bilaterally ventral to the somites and leading to the anal region where it empties separately from, and just posterior to the anus. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -31058,21 +26674,6 @@ "val" : "ZFA:0000094" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -31134,15 +26735,6 @@ "val" : "ZFA:0001206" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Mesoderm between somite and lateral plate. Traditionally thought to give rise to the urogenital system.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...)the mesoderm of a developing vertebrate transitionally differentiates into the following sub-types: Chordamesoderm (also known as axial mesoderm) which later on gives rise to notochord in all chordates, Paraxial mesoderm, Intermediate mesoderm, Lateral plate mesoderm (reference 1); The mesoderm is present in Bilateria, therefore they are sometimes called triploblasts. Ectoderm and endoderm are usually organized as epithelial layers, while mesoderm can be epithelial or a compact, three-dimensional tissue.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm')." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -31181,9 +26773,6 @@ "val" : "ZFA:0001204" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -31224,14 +26813,10 @@ } ], "xrefs" : [ { "val" : "AAO:0000637" - }, { - "val" : "BTO:0005990" }, { "val" : "EHDAA2:0001243" }, { "val" : "EHDAA:1590" - }, { - "val" : "EMAPA:16577" }, { "val" : "GAID:1315" }, { @@ -31244,8 +26829,6 @@ "val" : "TAO:0000546" }, { "val" : "UMLS:C0043204" - }, { - "val" : "VHOG:0000082" }, { "val" : "Wikipedia:Mesonephric_duct" }, { @@ -31259,18 +26842,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO - mesonephric portion of the nephric duct" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical structure consisting of either of a pair of longitudinal ducts which carry urine and in males, sperm, to the cloaca.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "In the male the Wolffian duct persists, and forms for example the epididymis, the ductus deferens, the ejaculatory duct, seminal vesicle and efferent ducts." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -31314,8 +26885,6 @@ "val" : "EMAPA:35593" }, { "val" : "FMA:293879" - }, { - "val" : "MESH:D054258" }, { "val" : "NCIT:C34225" }, { @@ -31336,12 +26905,6 @@ "val" : "neuronames:1362" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -31401,15 +26964,6 @@ "val" : "ZFA:0000255" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here)" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -31477,18 +27031,6 @@ "val" : "ZFA:0000121" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "subclass of mesoderm in ZFA." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0006258" }, { @@ -31535,15 +27077,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "should probably be merged with heart rudiment." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -31574,8 +27107,6 @@ "val" : "AAO:0010571" }, { "val" : "AEO:0000212" - }, { - "val" : "BTO:0006255" }, { "val" : "EHDAA2:0003439" }, { @@ -31598,15 +27129,6 @@ "val" : "ZFA:0001080" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Skeletogenic portion of somites.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "part_of somite in XAO" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -31654,9 +27176,6 @@ "val" : "ZFA:0000496" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -31719,15 +27238,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "mesenchymal" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -31761,8 +27271,6 @@ "val" : "genitalia" } ], "xrefs" : [ { - "val" : "EMAPA:17381" - }, { "val" : "EMAPA:37731" }, { "val" : "MA:0001752" @@ -31780,9 +27288,6 @@ "val" : "WBbt:0008422" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "GO uses genitalia for the singular organ" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -31833,12 +27338,6 @@ "val" : "Wikipedia:Metanephric_blastema" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A mass of intermediate mesodermal cells around the distal end of the ureteric bud that gives rise to nephrons in the metanephric kidney. [TFD][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "When the ureteric buds emerge from the nephric duct, they enter the metanephrogenic mesenchyme. The ureteric buds induce this mesenchymal tissue to condense around them and differentiate into the nephrons of the mammalian kidney. As this mesenchyme differentiates, it tells the ureteric bud to branch and grow.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -31919,9 +27418,6 @@ "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" - }, { - "pred" : "http://www.w3.org/2000/01/rdf-schema#seeAlso", - "val" : "UBERON:0012254" } ] } }, { @@ -31997,8 +27493,6 @@ "xrefs" : [ "OBOL:automatic" ] } ], "xrefs" : [ { - "val" : "EMAPA:28457" - }, { "val" : "MA:0001682" }, { "val" : "TAO:0005306" @@ -32225,9 +27719,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -32255,9 +27746,6 @@ "val" : "UMLS:C0927195" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "stromal" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -32279,13 +27767,8 @@ "val" : "AEO:0000114" }, { "val" : "EHDAA2:0003114" - }, { - "val" : "FBbt:00007474" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -32498,9 +27981,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "FMA has both conduit and conduit space. In EHDAA2 this is a surface feature" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -32522,9 +28002,6 @@ "xrefs" : [ "FBbt:00025998" ] } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Grouping term for query purposes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -32545,9 +28022,6 @@ "xrefs" : [ "FBbt:00025990" ] } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Grouping term for query purposes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -32621,21 +28095,6 @@ "val" : "galen:GenitoUrinarySystem" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship type change: differentiates_from intermediate mesoderm (AAO:0010575) CHANGED TO: develops_from intermediate mesoderm (UBERON:0003064)[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Kidneys and gonads (of vertebrates) develop from adjacent tissues, and after the excretory or urinary ducts have developed, the reproductive system usually taps into them or their derivatives.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "genitourinary" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "urogenital" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -32713,9 +28172,6 @@ "val" : "MESH:D007686" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0012424" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -32784,9 +28240,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -32828,9 +28281,6 @@ "val" : "XAO:0004185" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -32874,9 +28324,6 @@ "val" : "ZFA:0000360" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33070,8 +28517,6 @@ } ], "xrefs" : [ { "val" : "EMAPA:27756" - }, { - "val" : "VO:0010896" }, { "val" : "ZFA:0005589" } ], @@ -33161,12 +28606,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "not the same as FMA:50609 Pyramid (which is a volume / dimensional entity)" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000202", - "val" : "http://purl.obolibrary.org/obo/FMA_74268" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0002449" @@ -33380,9 +28819,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Capillary that is part of the renal glomerulus. Glomerular capillary endothelial membranes in zebrafish normally have a fenestrated morphology that is visible at the ultrastructural level.[TAO]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -33437,17 +28873,8 @@ "val" : "galen:Skeleton" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0000383" - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "skeletal" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -33480,9 +28907,6 @@ "val" : "ZFA:0000115" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -33510,8 +28934,6 @@ "val" : "EMAPA:16072" }, { "val" : "FMA:293110" - }, { - "val" : "MESH:D054240" }, { "val" : "NCIT:C28402" }, { @@ -33524,15 +28946,6 @@ "val" : "Wikipedia:Primitive_streak" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002174", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_32443" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "(...) the blastopore equivalent of chordates (germ ring in fish, marginal zone/blastopore lip in frog and node/primitive streak in chick and mouse) (...) (reference 1); Indeed, the primitive streak has been considered the homologue of the blastopore since the 1870s (reference 2).[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "VHOG includes a very broad grouping here based on http://www.ncbi.nlm.nih.gov/pubmed/9609826" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -33569,14 +28982,10 @@ "val" : "CALOHA:TS-1297" }, { "val" : "EFO:0000791" - }, { - "val" : "EHDAA2:0000216" }, { "val" : "EHDAA:394" }, { "val" : "EMAPA:16104" - }, { - "val" : "EMAPA:16370" }, { "val" : "EV:0100017" }, { @@ -33611,14 +29020,8 @@ "val" : "ZFA:0000010" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph." - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -33700,9 +29103,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -33744,9 +29144,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -34008,8 +29405,6 @@ "val" : "BILA:0000060" }, { "val" : "BTO:0001403" - }, { - "val" : "FBbt:00005317" }, { "val" : "FMA:293108" }, { @@ -34032,9 +29427,6 @@ "val" : "Wikipedia:Trilaminar_blastocyst" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "We explicitly merge the NCITA terms here" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0007012" }, { @@ -34066,12 +29458,6 @@ "val" : "galen:SkeletalStructure" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34239,9 +29625,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider merging with 'endothelium'" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -34281,9 +29664,6 @@ "val" : "XAO:0000276" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34315,12 +29695,6 @@ "val" : "Wikipedia:Somatopleure" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "Gives rise to the paired appendages in jawed vertebrates. a persistent somatopleure through the redistribution and expansion of the lateral plate mesoderm is a synapomorphy for gnathostomes and a critical step in generating a novel developmental module with dramatic evolutionary potentia (Tulenko et al. 2012) http://burkelab.research.wesleyan.edu/current-projects/lamprey/" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "sources differ as to whether this is part-of or develops-from the LPM" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -34394,9 +29768,6 @@ "val" : "Wikipedia:Urogenital_folds" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000013", - "val" : "Less commonly, urogenital fold refers to the fold in the mesonephros which is the precursor of e.g. the suspensory ligament of the ovary. This is the case in older versions of Gray's anatomy[WP]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34437,12 +29808,6 @@ "val" : "ZFA:0000091" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Notochord rudiment[ZFIN:ZDB-PUB-961014-576]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34461,9 +29826,6 @@ "pred" : "hasNarrowSynonym", "val" : "joint" } ], - "xrefs" : [ { - "val" : "FBbt:00005811" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -34499,14 +29861,9 @@ "xrefs" : [ "FMA:71131" ] } ], "xrefs" : [ { - "val" : "FBbt:00100315" - }, { "val" : "FMA:71131" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct." - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { @@ -34561,9 +29918,6 @@ "val" : "neuronames:1363" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34601,9 +29955,6 @@ "val" : "neuronames:1364" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34631,9 +29982,6 @@ "val" : "ZFA:0000133" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -34687,14 +30035,9 @@ "val" : "muscle element" } ], "xrefs" : [ { - "val" : "EMAPA:32715" - }, { "val" : "FMA:30316" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -35008,9 +30351,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "interstital" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -35254,12 +30594,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000009", - "val" : "The interstitium is necessarily involved in all intrarenal exchange processes since the reabsorption and secretion of fluid and solutes implicates a transit across the interstitial compartment." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000010", - "val" : "The fibroblasts in the interstitium provide the 'skeleton' of the tissue and maintain the three-dimensional architecture of the tissue." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -35349,8 +30683,6 @@ "val" : "CALOHA:TS-2122" }, { "val" : "EHDAA2:0003125" - }, { - "val" : "FBbt:00007006" }, { "val" : "FMA:292313" }, { @@ -35390,8 +30722,6 @@ "xrefs" : [ "EMAPA:16208" ] } ], "xrefs" : [ { - "val" : "BTO:0006179" - }, { "val" : "EHDAA2:0001512" }, { "val" : "EHDAA:424" @@ -35462,12 +30792,6 @@ "val" : "ZFA:0001262" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Immature reproductive tissue that has not undergone final maturation into either testis or ovary.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "this is a very broad grouping class" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -35514,9 +30838,6 @@ "val" : "ZFA:0000067" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Portion of tissue that consists of the mesenchymal precursor to the pronephric kidney and that begins to separate from the intermediate mesoderm at NF stage 21 and epithelializes by NF stage 30.[AAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -35542,15 +30863,10 @@ } ], "xrefs" : [ { "val" : "EMAPA:28239" - }, { - "val" : "SCTID:362217000" }, { "val" : "Wikipedia:Glomerulus" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "...Soon afterwards, endothelial cells invade to make a capillary knot-like outgrowth, the glomerular tuft, which goes on to form the glomerulus" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -35666,9 +30982,6 @@ "val" : "Wikipedia:Basement_membrane" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell." - }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_80999" }, { @@ -35707,8 +31020,6 @@ "val" : "FMA:74274" }, { "val" : "MA:0001659" - }, { - "val" : "MESH:D050533" }, { "val" : "NCIT:C32683" }, { @@ -35723,9 +31034,6 @@ "val" : "ZFA:0005285" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Membrane between the mesonephric podocytes and the renal glomerular capillaries. It is a trilaminar structure composed of the fused basement membranes of the glomerular capillaries and basement membrane of the podocytes. The capillary membranes touch the GBM at contact points that are separated by pores. The membrane is semi-permeable allowing water and small molecules to pass into the renal capsular space.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -35810,8 +31118,6 @@ "val" : "AAO:0000963" }, { "val" : "EMAPA:17214" - }, { - "val" : "EMAPA:18043" }, { "val" : "MA:0000308" }, { @@ -35830,9 +31136,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -35885,12 +31188,6 @@ "val" : "Wikipedia:Cloacal_membrane" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "A membrane that separates the proctodeum and the hindgut in the early embryo. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.497, see_Kardong_KV][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "In mammals, the cloaca exists as an embryonic structure that undergoes septation to become distinct urethral, anal, and genital orifices.[well established][VHOG]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -35924,9 +31221,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "TODO - check ordering; awaiting confirmation from JB" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -36103,9 +31397,6 @@ "val" : "ZFA:0005289" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in ZFA this is defined as part of mesonephros" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -36308,14 +31599,9 @@ "val" : "terminal section of digestive tract" } ], "xrefs" : [ { - "val" : "FBbt:00005756" - }, { "val" : "WBbt:0005773" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "this class is the superclass of 'rectum', which is currently reserved for the vertebrate structure. May be merged in future." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -36368,9 +31654,6 @@ "val" : "Wikipedia:Squamous_epithelium" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -36541,9 +31824,6 @@ "val" : "UMLS:C1514442" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000011", - "val" : "The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -36573,16 +31853,11 @@ "xrefs" : [ "FBbt:00003154" ] } ], "xrefs" : [ { - "val" : "SPD:0000130" - }, { "val" : "TADS:0000147" }, { "val" : "http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -36610,9 +31885,6 @@ "val" : "ZFA:0000131" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -36674,9 +31946,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "consider merging" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Region of the gastrula which gives rise to the neural plate.[TAO]" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -36874,9 +32143,6 @@ "val" : "FMA:17692" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "consider moving MA:0000377 renal tubule here, as it includes the various segments (proximal etc) as subclasses, not parts" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -36929,8 +32195,6 @@ "val" : "EFO:0001649" }, { "val" : "EHDAA2:0003170" - }, { - "val" : "FBbt:00005426" }, { "val" : "Wikipedia:Anlage_(biology)" } ], @@ -36970,12 +32234,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -37021,12 +32279,6 @@ "val" : "VSAO:0000303" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "this encompasses non-skeletal tissue" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There are only two instances of appendage girdle regions per organism.[VSAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "UBERON:0007824" }, { @@ -37102,21 +32354,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "need to resolve whether this is a paired structure or a single belt (Paired in FMA - implicitly paired in VSAO)" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical cluster by which the hind limbs are supported and attached to the vertebral column.[AAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical cluster that consists of the paired basipterygia which support the pelvic fin.[TAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Girdle skeleton consisting of a set of bones linking the axial series to the hindlimb/fin skeleton and offering anchoring areas for hindlimb/fin and caudal musculature.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000003", - "val" : "The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin.[well established][VHOG]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "Note that the VSAO and many ontologies use the label 'pelvic girdle' to denote the skeletal region specifically. We place the EHDAA2 class here, note that this includes the pre-cartilage condensation as parts" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -37314,9 +32551,6 @@ "xrefs" : [ "OBOL:automatic", "https://orcid.org/0000-0002-6601-2165" ] } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "this class groups vertebrate nephron tubules with analagous structures such as insect Malpighian tubules" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -37416,9 +32650,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "FMA only has the set term" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -37496,9 +32727,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "todo - add has_part relationships." - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "human kidneys have multilobar (multipyramidal) architecture while mice and rats have unilobar (unipyramidal) kidneys" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -37524,8 +32752,6 @@ } ], "xrefs" : [ { "val" : "CARO:0010000" - }, { - "val" : "FBbt:00100313" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", @@ -37605,9 +32831,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "Grouping term for query purposes" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -37713,9 +32936,6 @@ "val" : "presumptive nephron" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "EHDAA2 treats this as already having a tubular structure, but in the ZFA representation this is a cluster of cells" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -37772,15 +32992,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000116", "val" : "It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical group that consists of the soft and skeletal tissues of the appendicular region of the body and the appendage proper.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000005", - "val" : "It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "note that the FMA uses the term 'limb' to refer to the entire appendage complex (free limb plus girdle region)" }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0001-9114-8737" @@ -37839,15 +33050,6 @@ "val" : "VSAO:0000215" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/RO_0002171", - "val" : "http://purl.obolibrary.org/obo/UBERON_0010708" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Appendage girdle complex that when present, encompasses the pelvic appendage and the pelvic girdle.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000012", - "val" : "note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region). Note the MA class 'hindlimb' may also belong here" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -37871,15 +33073,6 @@ "val" : "VSAO:0000302" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Skeletal subdivision that is part of the appendage girdle region.[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: part_of subdivision of skeleton (UBERON:0010912)[VSAO]" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000002", - "val" : "relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: proximally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -37911,9 +33104,6 @@ "val" : "VSAO:0000042" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -38004,8 +33194,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#upper_level" ], "xrefs" : [ { - "val" : "FBbt:00007330" - }, { "val" : "FMA:67509" }, { "val" : "SCTID:91690000" @@ -38038,15 +33226,10 @@ }, "xrefs" : [ { "val" : "FMA:7484" - }, { - "val" : "VHOG:0001666" }, { "val" : "VSAO:0000306" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Skeletal system which consists of the appendicular skeleton plus associated joints.[VSAO]" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" }, { @@ -38173,9 +33356,6 @@ }, { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_147099" - }, { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "coelomic" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -38341,9 +33521,6 @@ "val" : "Wikipedia:Urethral_groove" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000008", - "val" : "In humans, the urethral groove is a temporary linear indentation on the underside (ventral side) of the male penis during embryonic development. It typically appears around 8 weeks of gestation and becomes closed into a normal male urethra by the 12th week" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -38427,15 +33604,10 @@ "val" : "AEO:0000103" }, { "val" : "BTO:0001489" - }, { - "val" : "EMAPA:36031" }, { "val" : "FMA:231424" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000001", - "val" : "Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -38463,8 +33635,6 @@ "xrefs" : [ "FMA:83067" ] } ], "xrefs" : [ { - "val" : "BTO:0006187" - }, { "val" : "FMA:83067" } ], "basicPropertyValues" : [ { @@ -38570,9 +33740,6 @@ }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#grouping_class", "http://purl.obolibrary.org/obo/uberon/core#non_informative" ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000232", - "val" : "This class is primarily to implement taxon constraints. It may be removed in the future." - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" } ] @@ -38603,9 +33770,6 @@ "pred" : "hasRelatedSynonym", "val" : "cardiac structure" } ], - "xrefs" : [ { - "val" : "SPD:0000130" - } ], "basicPropertyValues" : [ { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -38797,8 +33961,6 @@ "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#common_anatomy" ], "xrefs" : [ { "val" : "CARO:0020000" - }, { - "val" : "FBbt:00007276" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", @@ -39034,9 +34196,6 @@ "val" : "microvessel" } ], "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/UBPROP_0000007", - "val" : "microvascular" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "http://orcid.org/0000-0002-2825-0621" }, { @@ -39057,9 +34216,6 @@ "xrefs" : [ "GO:0007588" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], - "xrefs" : [ { - "val" : "BTO:0006338" - } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" @@ -39428,120 +34584,6 @@ "val" : "uberon" } ] } - }, { - "id" : "http://purl.org/dc/elements/1.1/creator", - "lbl" : "creator", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/elements/1.1/creator" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-creator" - } ] - } - }, { - "id" : "http://purl.org/dc/elements/1.1/description", - "lbl" : "description", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/elements/1.1/description" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-description" - } ] - } - }, { - "id" : "http://purl.org/dc/elements/1.1/title", - "lbl" : "title", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/elements/1.1/title" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-title" - } ] - } - }, { - "id" : "http://purl.org/dc/terms/contributor", - "lbl" : "contributor", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/terms/contributor" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dc-contributor" - } ] - } - }, { - "id" : "http://purl.org/dc/terms/date", - "lbl" : "date", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/terms/date" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dcterms-date" - } ] - } - }, { - "id" : "http://purl.org/dc/terms/license", - "lbl" : "license", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://purl.org/dc/terms/license" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "dcterms-license" - } ] - } }, { "id" : "http://www.geneontology.org/formats/oboInOwl#SubsetProperty", "lbl" : "subset_property", @@ -39575,9 +34617,6 @@ "val" : "An alternative label for a class or property which has a more general meaning than the preferred name/primary label." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/18" }, { @@ -39598,9 +34637,6 @@ "val" : "An alternative label for a class or property which has the exact same meaning than the preferred name/primary label." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/20" }, { @@ -39617,9 +34653,6 @@ "val" : "An alternative label for a class or property which has a more specific meaning than the preferred name/primary label." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/19" }, { @@ -39640,9 +34673,6 @@ "val" : "An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct." }, "basicPropertyValues" : [ { - "pred" : "http://purl.obolibrary.org/obo/IAO_0000117", - "val" : "http://orcid.org/0000-0001-5208-3432" - }, { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/information-artifact-ontology/ontology-metadata/issues/21" }, { @@ -39675,35 +34705,10 @@ "val" : "http://www.w3.org/2000/01/rdf-schema#seeAlso" } ], "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "seeAlso" } ] } - }, { - "id" : "http://xmlns.com/foaf/0.1/depiction", - "lbl" : "depiction", - "type" : "PROPERTY", - "meta" : { - "xrefs" : [ { - "val" : "http://xmlns.com/foaf/0.1/depiction" - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "uberon" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_metadata_tag", - "val" : "true" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", - "val" : "depiction" - } ] - } } ], "edges" : [ { "sub" : "http://purl.obolibrary.org/obo/BFO_0000004", @@ -44677,10 +39682,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000056", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0036295" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000056", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000468" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000056", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -44726,16 +39727,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000057", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000164", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "pelvic part of UG sinus gives rise to prostatic and membranous parts of urethra" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "Wikipedia" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000164" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000057", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -44952,13 +39944,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000081", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0003220", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "definitional" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0003220" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000081", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -45013,10 +39999,6 @@ "val" : "EHDAA2" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000084", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0012275" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000084", "pred" : "is_a", @@ -45324,17 +40306,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0004921", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts" - } ] - } - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0001106", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0001555" + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004921" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -45476,13 +40448,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000463", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000468", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "this relationship may be too strong and may be weakened in future" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000468" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000463", "pred" : "http://purl.obolibrary.org/obo/RO_0000086", @@ -45742,13 +40708,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000926", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000923", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "sometimes not considered primary" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000923" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000926", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -46296,13 +41256,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001231", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0003918", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "checkme" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0003918" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001231", "pred" : "http://purl.obolibrary.org/obo/RO_0002433", @@ -46314,16 +41268,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001232", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0001285", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "checkme" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "GO" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0001285" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001232", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -46344,10 +41289,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001245", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001555" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0001245", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0001108", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0001555" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001245", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -46383,13 +41324,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001255", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000164", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "upper part of UG sinus" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000164" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001271", "pred" : "is_a", @@ -46406,10 +41341,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001271", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0010709" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0001271", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0002355" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001271", "pred" : "http://purl.obolibrary.org/obo/RO_0002551", @@ -46431,13 +41362,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001285", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0004208", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "definitional" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004208" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001285", "pred" : "http://purl.obolibrary.org/obo/RO_0002433", @@ -46473,16 +41398,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001287", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0004134", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "MA uses subclass" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "GOC:mtg_kidney_jan10" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004134" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001287", "pred" : "http://purl.obolibrary.org/obo/RO_0002150", @@ -46578,16 +41494,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001290", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0004134", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "MA uses subclass" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "GOC:mtg_kidney_jan10" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004134" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001290", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -46671,13 +41578,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001353", "pred" : "http://purl.obolibrary.org/obo/RO_0002254", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000931", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "cjm" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000931" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001434", "pred" : "is_a", @@ -46876,6 +41777,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000055" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -47013,10 +41918,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002078", "pred" : "http://purl.obolibrary.org/obo/RO_0002170", "obj" : "http://purl.obolibrary.org/obo/UBERON_0004537" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0002081", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002081", "pred" : "is_a", @@ -47095,10 +41996,6 @@ "val" : "FMA" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0002113", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000468" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002113", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -47106,13 +42003,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002113", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0003918", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "definitional" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0003918" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002113", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -47204,13 +42095,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002204", "pred" : "http://purl.obolibrary.org/obo/RO_0002254", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000926", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "check ctenophore" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0000926" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002204", "pred" : "http://purl.obolibrary.org/obo/RO_0002492", @@ -47271,6 +42156,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002319", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000119" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0002319", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002319", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -47295,6 +42184,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002321", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0003891" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0002321", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002321", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -47326,13 +42219,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002323", "pred" : "http://purl.obolibrary.org/obo/RO_0002494", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0003886", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "definitional" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0003886" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002323", "pred" : "http://purl.obolibrary.org/obo/RO_0002572", @@ -47357,6 +42244,10 @@ "val" : "VSAO" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", "pred" : "is_a", @@ -47365,14 +42256,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0011137" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000098", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0001555" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000102", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0001049" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -47473,6 +42356,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0004121" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010314" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "is_a", @@ -47493,16 +42380,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", - "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_89593", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "ISBN:0073040584" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_89593" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -47526,13 +42404,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "http://purl.obolibrary.org/obo/RO_0002473", - "obj" : "http://purl.obolibrary.org/obo/CL_0000333", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/CL_0000333" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", "pred" : "http://purl.obolibrary.org/obo/RO_0002488", @@ -47624,13 +42496,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002390", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0003061", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#evidence", - "val" : "definitional" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0003061" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002417", "pred" : "is_a", @@ -47805,10 +42671,6 @@ "val" : "GO" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0003074", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0012275" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003074", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -47883,10 +42745,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0003077", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0015212" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0003077", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000922" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003077", "pred" : "http://purl.obolibrary.org/obo/RO_0002488", @@ -48354,6 +43212,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004140", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0002050" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004140", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004140", "pred" : "is_a", @@ -48408,6 +43270,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004151", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000064" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004151", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004151", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -48420,6 +43286,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004188", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0004211" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004188", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0012275" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004188", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -48987,14 +43857,14 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005062", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0015212" + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010371" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005062", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0005061" + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0015212" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005062", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000126", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0005061" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005068", @@ -49080,6 +43950,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0005103", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0004819" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0005103", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0012275" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005103", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -49290,6 +44164,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0005721", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000926" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0005721", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005721", "pred" : "is_a", @@ -49402,6 +44280,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", "pred" : "http://purl.obolibrary.org/obo/RO_0002473", "obj" : "http://purl.obolibrary.org/obo/GO_0005604" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0005777", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005777", "pred" : "is_a", @@ -49742,13 +44624,11 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006984", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0010199", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "via morphological boundary in CARO" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0010199" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0007005", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007005", "pred" : "is_a", @@ -49812,13 +44692,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007100", "pred" : "http://purl.obolibrary.org/obo/RO_0002215", - "obj" : "http://purl.obolibrary.org/obo/GO_0008015", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#notes", - "val" : "GO uses blood circulation generically to include the haemolymphatic fluid of arthropods" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/GO_0008015" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007135", "pred" : "is_a", @@ -49834,16 +44708,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007282", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0009618", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#consistent_with", - "val" : "https://github.com/obophenotype/uberon/wiki/The-neural-crest" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "EDHAA2" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/UBERON_0009618" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007282", "pred" : "http://purl.obolibrary.org/obo/RO_0002387", @@ -50043,6 +44908,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0007823", "pred" : "http://purl.obolibrary.org/obo/RO_0002551", "obj" : "http://purl.obolibrary.org/obo/UBERON_0010719" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0007832", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007832", "pred" : "is_a", @@ -50197,6 +45066,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0009856", "pred" : "http://purl.obolibrary.org/obo/RO_0000086", "obj" : "http://purl.obolibrary.org/obo/PATO_0001987" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0009881", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0009881", "pred" : "is_a", @@ -50313,6 +45186,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0010371", "pred" : "http://purl.obolibrary.org/obo/RO_0002473", "obj" : "http://purl.obolibrary.org/obo/CL_0002077" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0010377", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0010377", "pred" : "is_a", @@ -50423,10 +45300,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0010707", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0015212" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0010707", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000468" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0010707", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -50557,16 +45430,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0011143", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/UBERON_0002113" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0011143", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0001008", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#source", - "val" : "FMA-abduced-lr" - } ] - } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0011216", "pred" : "is_a", @@ -50831,10 +45694,6 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0015212", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" - }, { - "sub" : "http://purl.obolibrary.org/obo/UBERON_0015212", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000465" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0015212", "pred" : "http://purl.obolibrary.org/obo/RO_0002160", @@ -51011,8 +45870,8 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0004151" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0035554", - "pred" : "http://purl.obolibrary.org/obo/BSPO_0000121", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0000948" + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0015212" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0035804", "pred" : "is_a", @@ -52239,10 +47098,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0040036", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0000057" - }, { - "sub" : "http://purl.obolibrary.org/obo/uberon/core#anteriorly_connected_to", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BSPO_0000099" }, { "sub" : "http://purl.obolibrary.org/obo/uberon/core#anteriorly_connected_to", "pred" : "subPropertyOf", @@ -52251,10 +47106,6 @@ "sub" : "http://purl.obolibrary.org/obo/uberon/core#anteriorly_connected_to", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/uberon/core#transitively_anteriorly_connected_to" - }, { - "sub" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BSPO_0000100" }, { "sub" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", "pred" : "subPropertyOf", @@ -52271,18 +47122,10 @@ "sub" : "http://purl.obolibrary.org/obo/uberon/core#layer_part_of", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/BFO_0000050" - }, { - "sub" : "http://purl.obolibrary.org/obo/uberon/core#posteriorly_connected_to", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BSPO_0000096" }, { "sub" : "http://purl.obolibrary.org/obo/uberon/core#posteriorly_connected_to", "pred" : "subPropertyOf", "obj" : "http://purl.obolibrary.org/obo/RO_0002170" - }, { - "sub" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to", - "pred" : "subPropertyOf", - "obj" : "http://purl.obolibrary.org/obo/BSPO_0000097" }, { "sub" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to", "pred" : "subPropertyOf", @@ -52499,10 +47342,6 @@ "sub" : "http://purl.obolibrary.org/obo/RO_0012001", "pred" : "inverseOf", "obj" : "http://purl.obolibrary.org/obo/RO_0012005" - }, { - "sub" : "http://purl.obolibrary.org/obo/uberon/core#distally_connected_to", - "pred" : "inverseOf", - "obj" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to" } ], "logicalDefinitionAxioms" : [ { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000034", @@ -53285,7 +48124,7 @@ } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_1000854", - "genusIds" : [ "http://purl.obolibrary.org/obo/CL_1000504" ], + "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0003517" @@ -54364,13 +49203,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002082", "fillerId" : "http://purl.obolibrary.org/obo/GO_0040016" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0000165", - "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0004921" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BSPO_0001106", - "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0001555" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0000174", "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000463" ], @@ -54521,13 +49353,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0001285" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0001245", - "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000161" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BSPO_0001108", - "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0001555" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0001271", "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0007823" ], @@ -54626,13 +49451,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0001025", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0002323" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0002078", - "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0002081" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BSPO_0000121", - "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0000948" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0002201", "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0002049" ], @@ -55359,13 +50177,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002387", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0002049" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0015212", - "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BSPO_0000126", - "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0000465" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0016879", "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0006598" ], @@ -55401,13 +50212,6 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0000362" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_0035554", - "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0004151" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BSPO_0000121", - "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0000948" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/UBERON_8450002", "genusIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000467" ], @@ -55598,12 +50402,6 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0002177", "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002178", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001637" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002179", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0001638" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002202", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000004" ], @@ -55726,8 +50524,8 @@ "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002551", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061", "http://purl.obolibrary.org/obo/UBERON_0000475" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465", "http://purl.obolibrary.org/obo/UBERON_0010912" ] + "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000061" ], + "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000465" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002566", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000002" ], @@ -55785,10 +50583,6 @@ "predicateId" : "http://purl.obolibrary.org/obo/RO_0019000", "domainClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000015" ], "rangeClassIds" : [ "http://purl.obolibrary.org/obo/PATO_0000001" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/uberon/core#channel_for", - "domainClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0004111" ], - "rangeClassIds" : [ "http://purl.obolibrary.org/obo/UBERON_0000463" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000053", "rangeClassIds" : [ "http://purl.obolibrary.org/obo/BFO_0000020" ] @@ -55820,21 +50614,12 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002287", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002210" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002329", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002215" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002496" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000050", "http://purl.obolibrary.org/obo/RO_0002497" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002479", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/BFO_0000066" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0000057", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000051", "http://purl.obolibrary.org/obo/RO_0000057" ] @@ -55853,24 +50638,12 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/BFO_0000066", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/BFO_0000066", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002314", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0000052", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0001025", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0001025", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002005", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002005", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002005", "http://purl.obolibrary.org/obo/RO_0002380" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002100", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002100", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/uberon/core#extends_fibers_into", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002100", "http://purl.obolibrary.org/obo/RO_0013001" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002102", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002102", "http://purl.obolibrary.org/obo/BFO_0000050" ] @@ -55886,24 +50659,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002131", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002131", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002131", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002134", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002134", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002150", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002170", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002176", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002178", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002202", "http://purl.obolibrary.org/obo/RO_0002162" ] @@ -55940,9 +50698,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0019002", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002213", "http://purl.obolibrary.org/obo/RO_0019002" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002216", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002215", "http://purl.obolibrary.org/obo/BFO_0000050" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002215", "http://purl.obolibrary.org/obo/RO_0002162" ] @@ -55991,9 +50746,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002254", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002256", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002258", "http://purl.obolibrary.org/obo/RO_0002496" ] @@ -56015,9 +50767,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0004031", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/BFO_0000051" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002432", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/BFO_0000066" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002327", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002327", "http://purl.obolibrary.org/obo/RO_0002017" ] @@ -56081,15 +50830,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002339", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002339", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002177", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002371", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002371", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002387", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002407", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002407", "http://purl.obolibrary.org/obo/RO_0002629" ] @@ -56102,15 +50842,9 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002488", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002488", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002488", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002492", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002492", "http://purl.obolibrary.org/obo/BFO_0000050" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002492", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002496", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002496", "http://purl.obolibrary.org/obo/BFO_0000050" ] @@ -56129,9 +50863,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002497", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002497", "http://purl.obolibrary.org/obo/RO_0002082" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/uberon/core#indirectly_supplies", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002569", "http://purl.obolibrary.org/obo/RO_0002178" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/uberon/core#indirectly_supplies", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002569", "http://purl.obolibrary.org/obo/uberon/core#indirectly_supplies" ] @@ -56150,12 +50881,6 @@ }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0002409", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0002630", "http://purl.obolibrary.org/obo/RO_0002630" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0003000", "http://purl.obolibrary.org/obo/RO_0002162" ] - }, { - "predicateId" : "http://purl.obolibrary.org/obo/RO_0002162", - "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0003001", "http://purl.obolibrary.org/obo/RO_0002162" ] }, { "predicateId" : "http://purl.obolibrary.org/obo/RO_0013001", "chainPredicateIds" : [ "http://purl.obolibrary.org/obo/RO_0013001", "http://purl.obolibrary.org/obo/BFO_0000050" ] diff --git a/subsets/kidney_upper_slim.obo b/subsets/kidney_upper_slim.obo index 161bb5549..39727a2fa 100644 --- a/subsets/kidney_upper_slim.obo +++ b/subsets/kidney_upper_slim.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: cl/releases/2024-02-13/subsets/kidney_upper_slim.owl +data-version: cl/releases/2024-04-05/subsets/kidney_upper_slim.owl subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -88,7 +88,7 @@ synonymtypedef: synonym "" synonymtypedef: SYSTEMATIC "" synonymtypedef: systematic_synonym "" ontology: cl/subsets/kidney_upper_slim -property_value: owl:versionInfo "2024-02-13" xsd:string +property_value: owl:versionInfo "2024-04-05" xsd:string [Term] id: BFO:0000002 @@ -159,7 +159,7 @@ is_a: UBERON:0000061 ! anatomical structure disjoint_from: GO:0031012 ! extracellular matrix disjoint_from: GO:0032991 ! protein-containing complex disjoint_from: GO:0043226 ! organelle -relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms +relationship: RO:0002160 NCBITaxon:131567 ! only in taxon cellular organisms [Term] id: CL:0000007 @@ -182,8 +182,8 @@ is_a: CL:0011115 ! precursor cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0017145 ! stem cell division relationship: capable_of GO:0017145 ! stem cell division -relationship: in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000037 @@ -233,8 +233,8 @@ relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surfac relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -relationship: develops_from CL:0000566 ! angioblastic mesenchymal cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000566 ! develops from angioblastic mesenchymal cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000038 @@ -251,7 +251,7 @@ synonym: "erythroid stem cell" RELATED [] xref: BTO:0004911 is_a: CL:0000764 ! erythroid lineage cell is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor cell -relationship: develops_from CL:0000050 ! megakaryocyte-erythroid progenitor cell +relationship: RO:0002202 CL:0000050 ! develops from megakaryocyte-erythroid progenitor cell [Term] id: CL:0000039 @@ -296,7 +296,7 @@ synonym: "pluripotent stem cell (bone marrow)" RELATED [ISBN:0878932437] xref: BTO:0004730 is_a: CL:0002032 {is_inferred="true"} ! hematopoietic oligopotent progenitor cell disjoint_from: CL:0000050 ! megakaryocyte-erythroid progenitor cell -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000050 @@ -320,7 +320,7 @@ intersection_of: capable_of GO:0030218 ! erythrocyte differentiation intersection_of: capable_of GO:0030219 ! megakaryocyte differentiation relationship: capable_of GO:0030218 ! erythrocyte differentiation relationship: capable_of GO:0030219 ! megakaryocyte differentiation -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000052 @@ -367,8 +367,8 @@ xref: FMA:63877 xref: NCIT:C12482 xref: VHOG:0001482 is_a: CL:0002320 ! connective tissue cell -relationship: develops_from CL:0000134 ! mesenchymal stem cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000064 @@ -399,8 +399,8 @@ xref: FMA:66768 xref: WBbt:0003672 is_a: CL:0000000 ! cell relationship: part_of UBERON:0000483 ! epithelium -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000067 @@ -434,9 +434,9 @@ is_a: CL:0000076 {is_inferred="true"} ! squamous epithelial cell is_a: CL:0002139 ! endothelial cell of vascular tree intersection_of: CL:0000076 ! squamous epithelial cell intersection_of: part_of UBERON:0004638 ! blood vessel endothelium -relationship: develops_from CL:0002546 ! embryonic blood vessel endothelial progenitor cell relationship: part_of UBERON:0004638 ! blood vessel endothelium -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0002546 ! develops from embryonic blood vessel endothelial progenitor cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000072 @@ -451,7 +451,7 @@ def: "A columnar/cuboidal epithelial cell is a cell usually found in a two dimen subset: cellxgene_subset subset: human_reference_atlas is_a: CL:0000066 ! epithelial cell -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000076 @@ -486,7 +486,7 @@ xref: CALOHA:TS-0278 xref: FMA:66772 is_a: CL:0000213 ! lining cell is_a: CL:0002078 ! meso-epithelial cell -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000133 @@ -562,8 +562,8 @@ xref: FMA:67328 xref: WBbt:0003675 is_a: CL:0000183 ! contractile cell is_a: CL:0000393 ! electrically responsive cell -relationship: develops_from CL:0000056 ! myoblast -property_value: depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI +relationship: RO:0002202 CL:0000056 ! develops from myoblast +property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI [Term] id: CL:0000192 @@ -581,8 +581,8 @@ xref: CALOHA:TS-2159 xref: FMA:14072 is_a: CL:0008000 ! non-striated muscle cell is_a: CL:0008007 ! visceral muscle cell -relationship: develops_from CL:0000514 ! smooth muscle myoblast -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000514 ! develops from smooth muscle myoblast +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000211 @@ -665,8 +665,8 @@ intersection_of: CL:4030046 PR:000001945 ! lacks_plasma_membrane_part transferri relationship: bearer_of PATO:0002039 ! biconcave relationship: CL:4030045 GO:0005840 ! lacks_part ribosome relationship: CL:4030046 PR:000001945 ! lacks_plasma_membrane_part transferrin receptor protein 1 -relationship: develops_from CL:0000558 ! reticulocyte -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000558 ! develops from reticulocyte +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000239 @@ -681,8 +681,8 @@ subset: cellxgene_subset xref: MESH:D005057 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell -intersection_of: only_in_taxon NCBITaxon:2759 ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +intersection_of: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota [Term] id: CL:0000329 @@ -700,7 +700,7 @@ xref: FMA:86667 is_a: CL:0000219 ! motile cell is_a: CL:0011012 ! neural crest cell is_a: CL:0011026 ! progenitor cell -relationship: develops_from CL:0007004 ! premigratory neural crest cell +relationship: RO:0002202 CL:0007004 ! develops from premigratory neural crest cell [Term] id: CL:0000335 @@ -726,8 +726,8 @@ is_a: CL:0000007 ! early embryonic cell (metazoa) is_a: CL:0000255 ! eukaryotic cell is_a: CL:0010017 ! zygote intersection_of: CL:0010017 ! zygote -intersection_of: only_in_taxon NCBITaxon:33208 ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +intersection_of: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa [Term] id: CL:0000393 @@ -751,8 +751,8 @@ synonym: "satellite cell" RELATED [] xref: FMA:84798 is_a: CL:0000056 ! myoblast intersection_of: CL:0000056 ! myoblast -intersection_of: develops_into CL:0000192 ! smooth muscle cell -relationship: develops_into CL:0000192 ! smooth muscle cell +intersection_of: RO:0002203 CL:0000192 ! develops into smooth muscle cell +relationship: RO:0002203 CL:0000192 ! develops into smooth muscle cell [Term] id: CL:0000540 @@ -773,8 +773,8 @@ is_a: CL:0000393 ! electrically responsive cell is_a: CL:0000404 ! electrically signaling cell is_a: CL:0002319 ! neural cell relationship: capable_of GO:0019226 ! transmission of nerve impulse -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://www.swissbiopics.org/api/image/Neuron_cells.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://www.swissbiopics.org/api/image/Neuron_cells.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000547 @@ -817,10 +817,10 @@ relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-span relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD5 relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G -relationship: develops_from CL:0000038 ! erythroid progenitor cell relationship: has_part CL:0017503 ! basophilic cytoplasm relationship: has_part GO:0005730 ! nucleolus relationship: RO:0002104 PR:000001945 ! has plasma membrane part transferrin receptor protein 1 +relationship: RO:0002202 CL:0000038 ! develops from erythroid progenitor cell [Term] id: CL:0000549 @@ -858,10 +858,10 @@ intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017504 ! polychromatophilic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin intersection_of: RO:0002104 PR:000001945 ! has plasma membrane part transferrin receptor protein 1 -relationship: develops_from CL:0000549 ! basophilic erythroblast relationship: has_part CL:0017504 ! polychromatophilic cytoplasm relationship: has_part GO:0000792 ! heterochromatin relationship: RO:0002104 PR:000001945 ! has plasma membrane part transferrin receptor protein 1 +relationship: RO:0002202 CL:0000549 ! develops from basophilic erythroblast [Term] id: CL:0000552 @@ -877,9 +877,9 @@ is_a: CL:0000765 {is_inferred="true"} ! erythroblast intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017502 ! acidophilic cytoplasm intersection_of: participates_in GO:0030263 ! apoptotic chromosome condensation -relationship: develops_from CL:0000550 ! polychromatophilic erythroblast relationship: has_part CL:0017502 ! acidophilic cytoplasm relationship: participates_in GO:0030263 ! apoptotic chromosome condensation +relationship: RO:0002202 CL:0000550 ! develops from polychromatophilic erythroblast [Term] id: CL:0000553 @@ -933,8 +933,8 @@ relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surfac relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -relationship: develops_from CL:0000050 ! megakaryocyte-erythroid progenitor cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000050 ! develops from megakaryocyte-erythroid progenitor cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000556 @@ -953,8 +953,8 @@ xref: FMA:83555 is_a: CL:0000763 {is_inferred="true"} ! myeloid cell disjoint_from: CL:0000764 ! erythroid lineage cell relationship: bearer_of PATO:0001393 ! euploid -relationship: develops_from CL:0000553 ! megakaryocyte progenitor cell -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002202 CL:0000553 ! develops from megakaryocyte progenitor cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000558 @@ -993,8 +993,8 @@ relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-span relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD5 relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G -relationship: develops_from CL:0000552 ! orthochromatic erythroblast relationship: RO:0002104 PR:000001945 ! has plasma membrane part transferrin receptor protein 1 +relationship: RO:0002202 CL:0000552 ! develops from orthochromatic erythroblast [Term] id: CL:0000566 @@ -1010,10 +1010,10 @@ intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: RO:0002104 PR:000001444 ! has plasma membrane part cadherin-5 intersection_of: RO:0002104 PR:000002112 ! has plasma membrane part vascular endothelial growth factor receptor 2 intersection_of: RO:0002104 PR:000016043 ! has plasma membrane part T-cell acute lymphocytic leukemia protein 1 -relationship: develops_from CL:0000134 ! mesenchymal stem cell relationship: RO:0002104 PR:000001444 ! has plasma membrane part cadherin-5 relationship: RO:0002104 PR:000002112 ! has plasma membrane part vascular endothelial growth factor receptor 2 relationship: RO:0002104 PR:000016043 ! has plasma membrane part T-cell acute lymphocytic leukemia protein 1 +relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell [Term] id: CL:0000586 @@ -1052,7 +1052,7 @@ intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0002001 ! renin secretion into blood stream intersection_of: part_of UBERON:0002113 ! kidney relationship: capable_of GO:0002001 ! renin secretion into blood stream -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000650 @@ -1066,7 +1066,7 @@ xref: CALOHA:TS-0617 xref: FMA:70972 xref: MESH:D050527 is_a: CL:0000669 ! pericyte -relationship: develops_from CL:0000134 ! mesenchymal stem cell +relationship: RO:0002202 CL:0000134 ! develops from mesenchymal stem cell [Term] id: CL:0000666 @@ -1094,7 +1094,7 @@ is_a: CL:0000183 ! contractile cell is_a: CL:0000630 ! supporting cell is_a: CL:0002320 ! connective tissue cell is_a: CL:0008034 ! mural cell -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000680 @@ -1103,9 +1103,9 @@ def: "A non-terminally differentiated cell that is capable of developing into a subset: cellxgene_subset is_a: CL:0000055 ! non-terminally differentiated cell intersection_of: CL:0011115 ! precursor cell -intersection_of: develops_into CL:0000187 ! muscle cell -relationship: develops_from CL:0000222 ! mesodermal cell -relationship: develops_into CL:0000187 ! muscle cell +intersection_of: RO:0002203 CL:0000187 ! develops into muscle cell +relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell +relationship: RO:0002203 CL:0000187 ! develops into muscle cell [Term] id: CL:0000723 @@ -1128,8 +1128,8 @@ xref: CALOHA:TS-0647 xref: MESH:D022423 is_a: CL:0000988 {is_inferred="true"} ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell -intersection_of: develops_from CL:0000049 ! common myeloid progenitor -relationship: develops_from CL:0000049 ! common myeloid progenitor +intersection_of: RO:0002202 CL:0000049 ! develops from common myeloid progenitor +relationship: RO:0002202 CL:0000049 ! develops from common myeloid progenitor [Term] id: CL:0000764 @@ -1143,7 +1143,7 @@ xref: CALOHA:TS-0290 xref: FMA:62845 xref: FMA:83516 is_a: CL:0000763 ! myeloid cell -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000765 @@ -1186,8 +1186,8 @@ relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-span relationship: CL:4030046 PR:000001839 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD5 relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G -relationship: develops_from CL:0000547 ! proerythroblast relationship: has_part GO:0005634 ! nucleus +relationship: RO:0002202 CL:0000547 ! develops from proerythroblast [Term] id: CL:0000837 @@ -1234,9 +1234,9 @@ relationship: CL:4030046 PR:000001869 ! lacks_plasma_membrane_part interleukin-7 relationship: CL:4030046 PR:000001889 ! lacks_plasma_membrane_part CD14 molecule relationship: CL:4030046 PR:000002978 ! lacks_plasma_membrane_part lymphocyte antigen 6G relationship: CL:4030046 PR:000002981 ! lacks_plasma_membrane_part lymphocyte antigen 76 (mouse) -relationship: develops_from CL:0000037 ! hematopoietic stem cell -relationship: present_in_taxon NCBITaxon:9606 relationship: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule +relationship: RO:0002202 CL:0000037 ! develops from hematopoietic stem cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000839 @@ -1254,7 +1254,7 @@ is_a: CL:0011026 ! progenitor cell intersection_of: CL:0002031 ! hematopoietic lineage restricted progenitor cell intersection_of: capable_of GO:0030099 ! myeloid cell differentiation relationship: capable_of GO:0030099 ! myeloid cell differentiation -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000988 @@ -1280,8 +1280,8 @@ intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001400 ! unipotent disjoint_from: CL:0002032 ! hematopoietic oligopotent progenitor cell relationship: bearer_of PATO:0001400 ! unipotent -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0002032 ! hematopoietic oligopotent progenitor cell +relationship: RO:0002202 CL:0002032 ! develops from hematopoietic oligopotent progenitor cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:20Z [Term] @@ -1294,8 +1294,8 @@ is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001401 ! oligopotent relationship: bearer_of PATO:0001401 ! oligopotent -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000837 ! hematopoietic multipotent progenitor cell +relationship: RO:0002202 CL:0000837 ! develops from hematopoietic multipotent progenitor cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-01-06T03:43:27Z [Term] @@ -1305,9 +1305,9 @@ def: "An epithelial cell derived from ectoderm." [FMA:69074, GOC:tfm] xref: FMA:69074 is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell -intersection_of: develops_from CL:0000221 ! ectodermal cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000221 ! ectodermal cell +intersection_of: RO:0002202 CL:0000221 ! develops from ectodermal cell +relationship: RO:0002202 CL:0000221 ! develops from ectodermal cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T03:38:22Z [Term] @@ -1318,9 +1318,9 @@ synonym: "epithelial mesenchymal cell" EXACT [] xref: FMA:69076 is_a: CL:0000066 ! epithelial cell intersection_of: CL:0000066 ! epithelial cell -intersection_of: develops_from CL:0000222 ! mesodermal cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 -relationship: develops_from CL:0000222 ! mesodermal cell +intersection_of: RO:0002202 CL:0000222 ! develops from mesodermal cell +relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-06-29T03:49:14Z [Term] @@ -1335,7 +1335,7 @@ xref: BTO:0001854 xref: CALOHA:TS-1106 xref: FMA:67755 is_a: CL:0000115 ! endothelial cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-24T02:06:40Z [Term] @@ -1352,8 +1352,8 @@ is_a: CL:1000618 {is_inferred="true"} ! juxtaglomerular complex cell is_a: CL:1001318 ! renal interstitial pericyte intersection_of: CL:0002320 ! connective tissue cell intersection_of: part_of UBERON:0002321 ! extraglomerular mesangium -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002321 ! extraglomerular mesangium +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T02:20:55Z [Term] @@ -1369,7 +1369,7 @@ is_a: CL:0000666 ! fenestrated cell is_a: CL:1000746 ! glomerular cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0000074 ! renal glomerulus -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-26T10:59:44Z [Term] @@ -1381,7 +1381,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0002505 ! nucleated relationship: bearer_of PATO:0002505 ! nucleated -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-07T03:32:33Z [Term] @@ -1416,7 +1416,7 @@ is_a: CL:1000615 ! kidney cortex tubule cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0004134 ! proximal tubule relationship: part_of UBERON:0004134 ! proximal tubule -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0002319 @@ -1428,8 +1428,8 @@ xref: FMA:70333 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001016 ! nervous system -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0001016 ! nervous system +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T01:34:57Z [Term] @@ -1443,8 +1443,8 @@ xref: MESH:D003239 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0002384 ! connective tissue -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0002384 ! connective tissue +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T03:01:54Z [Term] @@ -1455,7 +1455,7 @@ xref: CALOHA:TS-0263 xref: FMA:82840 xref: WBbt:0007028 is_a: CL:0000000 ! cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T03:39:21Z [Term] @@ -1471,8 +1471,8 @@ xref: FMA:84791 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0007100 ! primary circulatory organ -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 relationship: part_of UBERON:0007100 ! primary circulatory organ +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T09:37:22Z [Term] @@ -1485,7 +1485,7 @@ is_a: CL:0000066 ! epithelial cell is_a: CL:1000497 {is_inferred="true"} ! kidney cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0002113 ! kidney -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-08T10:46:34Z [Term] @@ -1494,7 +1494,7 @@ name: embryonic blood vessel endothelial progenitor cell def: "An endothelial progenitor cell that participates in angiogenesis during development." [GOC:tfm] comment: See CL:0002619. is_a: CL:0000222 ! mesodermal cell -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-28T04:20:39Z [Term] @@ -1514,8 +1514,8 @@ def: "A cell that is part of a cortex of kidney." [] is_a: CL:1000497 ! kidney cell intersection_of: CL:1000497 ! kidney cell intersection_of: part_of UBERON:0001225 ! cortex of kidney -relationship: dc-contributor https://orcid.org/0000-0002-0956-8634 relationship: part_of UBERON:0001225 ! cortex of kidney +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-0956-8634 creation_date: 2011-10-25T03:49:41Z [Term] @@ -1531,9 +1531,9 @@ id: CL:0007004 name: premigratory neural crest cell def: "Cell that is part of the neural crest region of the neuroepithelium, prior to migration. Note that not all premigratory neural crest cells may become migratory neural crest cells." [UBERONREF:0000002] is_a: CL:0011012 ! neural crest cell -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 -relationship: develops_from CL:0000133 ! neurectodermal cell relationship: part_of UBERON:0002342 ! neural crest +relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-27T08:27:35Z [Term] @@ -1569,7 +1569,7 @@ synonym: "mesenchyme cell" EXACT [] is_a: CL:0000219 ! motile cell relationship: capable_of GO:0016477 ! cell migration relationship: part_of UBERON:0003104 ! mesenchyme -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0008034 @@ -1579,8 +1579,8 @@ subset: added_for_HCA subset: cellxgene_subset subset: human_reference_atlas is_a: CL:4033054 ! perivascular cell -relationship: dc-contributor https://orcid.org/0000-0002-7073-9172 -relationship: present_in_taxon NCBITaxon:9606 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2020-02-29T17:33:55Z [Term] @@ -1589,7 +1589,7 @@ name: zygote def: "A zygote in a plant or an animal." [] xref: MESH:D015053 is_a: CL:0000000 ! cell -relationship: seeAlso https://github.com/obophenotype/cell-ontology/issues/786 +property_value: seeAlso https://github.com/obophenotype/cell-ontology/issues/786 [Term] id: CL:0011012 @@ -1606,9 +1606,9 @@ def: "A precursor cell that has a tendency to differentiate into a specific type subset: cellxgene_subset is_a: CL:0011115 ! precursor cell intersection_of: CL:0011115 ! precursor cell -intersection_of: develops_from CL:0000034 ! stem cell -relationship: dc-contributor https://orcid.org/0000-0001-5208-3432 -relationship: develops_from CL:0000034 ! stem cell +intersection_of: RO:0002202 CL:0000034 ! develops from stem cell +relationship: RO:0002202 CL:0000034 ! develops from stem cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-5208-3432 [Term] id: CL:0011115 @@ -1630,7 +1630,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0002418 ! acidophilic relationship: bearer_of PATO:0002418 ! acidophilic -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-22T04:23:25Z [Term] @@ -1641,7 +1641,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0002094 ! basophilic relationship: bearer_of PATO:0002094 ! basophilic -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-22T04:24:54Z [Term] @@ -1652,7 +1652,7 @@ is_a: GO:0005737 ! cytoplasm intersection_of: GO:0005737 ! cytoplasm intersection_of: bearer_of PATO:0070047 ! polychromatophilic relationship: bearer_of PATO:0070047 ! polychromatophilic -relationship: dc-contributor https://orcid.org/0000-0003-1980-3228 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2009-12-28T04:25:23Z [Term] @@ -1696,7 +1696,7 @@ is_a: CL:1000449 ! epithelial cell of nephron is_a: CL:1001225 {is_inferred="true"} ! kidney collecting duct cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001232 ! collecting duct of renal tubule -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000494 @@ -1740,7 +1740,7 @@ relationship: part_of UBERON:0005215 ! kidney interstitium [Term] id: CL:1000504 name: kidney medulla cell -def: "A cell that is part of a renal medulla." [] +def: "A cell that is part of a renal medulla." [PMID:22343825] xref: KUPO:0001017 is_a: CL:1000497 ! kidney cell intersection_of: CL:1000497 ! kidney cell @@ -1838,6 +1838,7 @@ relationship: part_of UBERON:0002303 ! juxtaglomerular apparatus [Term] id: CL:1000692 name: kidney interstitial fibroblast +def: "A fibroblast that is part of an interstitial compartment of a kidney." [PMID:10559635] subset: cellxgene_subset subset: human_reference_atlas xref: KUPO:0001102 @@ -1845,7 +1846,7 @@ is_a: CL:0000057 ! fibroblast is_a: CL:1000500 ! kidney interstitial cell intersection_of: CL:0000057 ! fibroblast intersection_of: part_of UBERON:0005215 ! kidney interstitium -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000746 @@ -1868,7 +1869,7 @@ is_a: CL:1000615 ! kidney cortex tubule cell intersection_of: CL:1000494 ! nephron tubule epithelial cell intersection_of: part_of UBERON:0005097 ! renal connecting tubule relationship: part_of UBERON:0005097 ! renal connecting tubule -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000849 @@ -1881,15 +1882,16 @@ is_a: CL:0002305 {is_inferred="true"} ! epithelial cell of distal tubule intersection_of: CL:0002305 ! epithelial cell of distal tubule intersection_of: part_of UBERON:0001292 ! distal convoluted tubule relationship: part_of UBERON:0001292 ! distal convoluted tubule -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:1000854 name: kidney blood vessel cell +def: "A blood vessel cell that is part of a kidney." [PMID:34843404] xref: KUPO:0001014 is_a: CL:0002584 ! renal cortical epithelial cell is_a: CL:1000504 {is_inferred="true"} ! kidney medulla cell -intersection_of: CL:1000504 ! kidney medulla cell +intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0003517 ! kidney blood vessel relationship: part_of UBERON:0003517 ! kidney blood vessel relationship: participates_in GO:0008015 ! blood circulation @@ -1981,7 +1983,7 @@ is_a: CL:0000669 {is_inferred="true"} ! pericyte is_a: CL:1000500 ! kidney interstitial cell intersection_of: CL:0000669 ! pericyte intersection_of: part_of UBERON:0005215 ! kidney interstitium -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:4030031 @@ -1991,7 +1993,7 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0005169 ! interstitial tissue relationship: part_of UBERON:0005169 ! interstitial tissue -property_value: dcterms-date "2022-11-30T14:35:08Z" xsd:dateTime +property_value: http://purl.org/dc/terms/date "2022-11-30T14:35:08Z" xsd:dateTime [Term] id: CL:4033054 @@ -2001,8 +2003,8 @@ is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell intersection_of: adjacent_to UBERON:0002049 ! vasculature relationship: adjacent_to UBERON:0002049 ! vasculature -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -property_value: dcterms-date "2023-08-22T13:40:28Z" xsd:dateTime +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-08-22T13:40:28Z" xsd:dateTime [Term] id: GO:0000003 @@ -2053,8 +2055,8 @@ is_a: GO:0007049 ! cell cycle intersection_of: GO:0007049 ! cell cycle intersection_of: has_part GO:0140014 ! mitotic nuclear division relationship: has_part GO:0140014 ! mitotic nuclear division -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota [Term] id: GO:0000280 @@ -2106,7 +2108,7 @@ namespace: biological_process def: "A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities." [GOC:dph, GOC:go_curators, GOC:tb, ISBN:978-0-07-139011-8] comment: Action potentials typically propagate across excitable membranes. This class covers both action potentials that propagate and those that fail to do so. is_a: GO:0042391 ! regulation of membrane potential -relationship: never_in_taxon NCBITaxon:4895 +property_value: RO:0002161 NCBITaxon:4895 [Term] id: GO:0001578 @@ -2314,7 +2316,7 @@ subset: goslim_mouse subset: goslim_pir xref: Wikipedia:Immune_system is_a: GO:0008150 ! biological_process -relationship: never_in_taxon NCBITaxon:4895 +property_value: RO:0002161 NCBITaxon:4895 [Term] id: GO:0003008 @@ -2492,8 +2494,8 @@ namespace: cellular_component def: "A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures." [GOC:dos, GOC:mah, ISBN:0721639976, PMID:19693541, PMID:21421911] xref: Wikipedia:Collagen is_a: GO:0032991 ! protein-containing complex -relationship: in_taxon NCBITaxon:33208 {all_only="true", source="PMID:12382326"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 {source="PMID:12382326"} ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 {source="PMID:12382326"} ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true", source="PMID:12382326"} ! in taxon Metazoa [Term] id: GO:0005587 @@ -2574,8 +2576,8 @@ xref: NIF_Subcellular:sao1702920020 xref: Wikipedia:Cell_nucleus is_a: GO:0043231 ! intracellular membrane-bounded organelle disjoint_from: GO:0005737 ! cytoplasm -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota [Term] id: GO:0005694 @@ -2674,10 +2676,10 @@ synonym: "Golgi ribbon" NARROW [] xref: NIF_Subcellular:sao451912436 xref: Wikipedia:Golgi_apparatus is_a: GO:0043231 ! intracellular membrane-bounded organelle -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota relationship: part_of GO:0005737 ! cytoplasm relationship: part_of GO:0012505 ! endomembrane system +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota [Term] id: GO:0005798 @@ -2812,14 +2814,14 @@ is_a: GO:0043227 ! membrane-bounded organelle is_a: GO:0120025 ! plasma membrane bounded cell projection is_a: PR:000050567 ! protein-containing material entity relationship: has_part GO:0030990 ! intraciliary transport particle -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: never_in_taxon NCBITaxon:3176 -relationship: never_in_taxon NCBITaxon:3312 -relationship: never_in_taxon NCBITaxon:3378 -relationship: never_in_taxon NCBITaxon:3398 -relationship: never_in_taxon NCBITaxon:4890 -relationship: never_in_taxon NCBITaxon:5782 -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota +property_value: RO:0002161 NCBITaxon:3176 +property_value: RO:0002161 NCBITaxon:3312 +property_value: RO:0002161 NCBITaxon:3378 +property_value: RO:0002161 NCBITaxon:3398 +property_value: RO:0002161 NCBITaxon:4890 +property_value: RO:0002161 NCBITaxon:5782 [Term] id: GO:0005930 @@ -2986,11 +2988,11 @@ synonym: "type I programmed cell death" NARROW [] xref: Wikipedia:Apoptosis is_a: GO:0012501 ! programmed cell death relationship: ends_with GO:0097194 ! execution phase of apoptosis -relationship: in_taxon NCBITaxon:33154 {all_only="true"} ! Opisthokonta -relationship: never_in_taxon NCBITaxon:2 -relationship: never_in_taxon NCBITaxon:4896 -relationship: only_in_taxon NCBITaxon:33154 ! Opisthokonta +relationship: RO:0002160 NCBITaxon:33154 ! only in taxon Opisthokonta +relationship: RO:0002162 NCBITaxon:33154 {all_only="true"} ! in taxon Opisthokonta relationship: starts_with GO:0097190 ! apoptotic signaling pathway +property_value: RO:0002161 NCBITaxon:2 +property_value: RO:0002161 NCBITaxon:4896 [Term] id: GO:0006921 @@ -3492,8 +3494,8 @@ namespace: biological_process def: "The process whose specific outcome is the progression of an embryo over time, from zygote formation until the end of the embryonic life stage. The end of the embryonic life stage is organism-specific and may be somewhat arbitrary; for mammals it is usually considered to be birth, for insects the hatching of the first instar larva from the eggshell." [GOC:go_curators, GOC:isa_complete, GOC:mtg_sensu] synonym: "embryogenesis" BROAD [] is_a: GO:0009790 ! embryo development -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0009888 @@ -3506,14 +3508,14 @@ xref: Wikipedia:Histogenesis is_a: GO:0048856 ! anatomical structure development intersection_of: GO:0048856 ! anatomical structure development intersection_of: results_in_development_of UBERON:0000479 ! tissue -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: never_in_taxon NCBITaxon:147554 -relationship: never_in_taxon NCBITaxon:33630 -relationship: never_in_taxon NCBITaxon:33682 -relationship: never_in_taxon NCBITaxon:38254 -relationship: never_in_taxon NCBITaxon:4891 -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota relationship: results_in_development_of UBERON:0000479 ! tissue +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota +property_value: RO:0002161 NCBITaxon:147554 +property_value: RO:0002161 NCBITaxon:33630 +property_value: RO:0002161 NCBITaxon:33682 +property_value: RO:0002161 NCBITaxon:38254 +property_value: RO:0002161 NCBITaxon:4891 [Term] id: GO:0009987 @@ -3743,7 +3745,7 @@ namespace: biological_process def: "The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues." [GOC:cjm, GOC:dph, GOC:ems, GOC:pf, Wikipedia:Cell_migration] xref: Wikipedia:Cell_migration is_a: GO:0048870 ! cell motility -relationship: never_in_taxon NCBITaxon:4890 +property_value: RO:0002161 NCBITaxon:4890 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24787" xsd:anyURI [Term] @@ -3993,7 +3995,7 @@ subset: goslim_drosophila subset: goslim_flybase_ribbon xref: Wikipedia:Cell_junction is_a: GO:0110165 ! cellular anatomical entity -relationship: never_in_taxon NCBITaxon:4751 +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0030097 @@ -4261,10 +4263,10 @@ subset: goslim_pir synonym: "organismal physiological process" EXACT [] synonym: "single-multicellular organism process" RELATED [] is_a: GO:0008150 ! biological_process -relationship: never_in_taxon NCBITaxon:2 -relationship: never_in_taxon NCBITaxon:2157 -relationship: never_in_taxon NCBITaxon:4896 -relationship: never_in_taxon NCBITaxon:4932 +property_value: RO:0002161 NCBITaxon:2 +property_value: RO:0002161 NCBITaxon:2157 +property_value: RO:0002161 NCBITaxon:4896 +property_value: RO:0002161 NCBITaxon:4932 created_by: jl creation_date: 2012-09-19T16:07:47Z @@ -4517,7 +4519,7 @@ def: "Self-propelled movement of a cell or organism from one location to another subset: goslim_chembl subset: goslim_pir is_a: GO:0008150 ! biological_process -relationship: never_in_taxon NCBITaxon:451864 +property_value: RO:0002161 NCBITaxon:451864 [Term] id: GO:0040016 @@ -4553,16 +4555,16 @@ intersection_of: GO:0006810 ! transport intersection_of: has_primary_input GO:0032991 ! protein-containing complex intersection_of: occurs_in GO:0005929 ! cilium intersection_of: results_in_transport_along GO:0005874 ! microtubule -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: never_in_taxon NCBITaxon:3176 -relationship: never_in_taxon NCBITaxon:3312 -relationship: never_in_taxon NCBITaxon:3378 -relationship: never_in_taxon NCBITaxon:3398 -relationship: never_in_taxon NCBITaxon:4890 -relationship: never_in_taxon NCBITaxon:5782 relationship: occurs_in GO:0005929 ! cilium -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota relationship: part_of GO:0044782 ! cilium organization +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota +property_value: RO:0002161 NCBITaxon:3176 +property_value: RO:0002161 NCBITaxon:3312 +property_value: RO:0002161 NCBITaxon:3378 +property_value: RO:0002161 NCBITaxon:3398 +property_value: RO:0002161 NCBITaxon:4890 +property_value: RO:0002161 NCBITaxon:5782 [Term] id: GO:0042391 @@ -4613,8 +4615,8 @@ name: chordate embryonic development namespace: biological_process def: "The process whose specific outcome is the progression of the embryo over time, from zygote formation through a stage including a notochord and neural tube until birth or egg hatching." [GOC:mtg_sensu] is_a: GO:0009792 ! embryo development ending in birth or egg hatching -relationship: in_taxon NCBITaxon:7711 {all_only="true"} ! Chordata -relationship: only_in_taxon NCBITaxon:7711 ! Chordata +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {all_only="true"} ! in taxon Chordata [Term] id: GO:0043073 @@ -4845,9 +4847,9 @@ is_a: GO:0006996 ! organelle organization is_a: GO:0120036 ! plasma membrane bounded cell projection organization intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0005929 ! cilium -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota relationship: results_in_organization_of GO:0005929 ! cilium +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota created_by: jl creation_date: 2013-03-27T15:09:58Z @@ -4879,8 +4881,8 @@ synonym: "synaptic junction" EXACT [] xref: NIF_Subcellular:sao914572699 xref: Wikipedia:Chemical_synapse is_a: GO:0030054 ! cell junction -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0046903 @@ -5163,8 +5165,8 @@ is_a: GO:0003008 ! system process intersection_of: GO:0003008 ! system process intersection_of: has_participant UBERON:0001016 ! nervous system relationship: has_participant UBERON:0001016 ! nervous system -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/13824" xsd:anyURI [Term] @@ -5303,8 +5305,8 @@ is_a: GO:0051179 ! localization intersection_of: GO:0051179 ! localization intersection_of: has_primary_input GO:0043226 ! organelle relationship: has_primary_input GO:0043226 ! organelle -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/19809" xsd:anyURI [Term] @@ -5352,10 +5354,10 @@ synonym: "positioning within cell" NARROW [] is_a: GO:0051234 ! establishment of localization intersection_of: GO:0051234 ! establishment of localization intersection_of: occurs_in CL:0000000 ! cell -relationship: in_taxon NCBITaxon:131567 {all_only="true"} ! cellular organisms relationship: occurs_in CL:0000000 ! cell -relationship: only_in_taxon NCBITaxon:131567 ! cellular organisms relationship: part_of GO:0051641 ! cellular localization +relationship: RO:0002160 NCBITaxon:131567 ! only in taxon cellular organisms +relationship: RO:0002162 NCBITaxon:131567 {all_only="true"} ! in taxon cellular organisms [Term] id: GO:0051650 @@ -5447,15 +5449,15 @@ relationship: has_part GO:0035735 ! intraciliary transport involved in cilium as relationship: has_part GO:0061512 ! protein localization to cilium relationship: has_part GO:0097712 ! vesicle targeting, trans-Golgi to periciliary membrane compartment relationship: has_part GO:1905349 ! ciliary transition zone assembly -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: never_in_taxon NCBITaxon:3176 -relationship: never_in_taxon NCBITaxon:3312 -relationship: never_in_taxon NCBITaxon:3378 -relationship: never_in_taxon NCBITaxon:3398 -relationship: never_in_taxon NCBITaxon:4890 -relationship: never_in_taxon NCBITaxon:5782 relationship: results_in_assembly_of GO:0005929 ! cilium +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota relationship: starts_with GO:0097711 ! ciliary basal body-plasma membrane docking +property_value: RO:0002161 NCBITaxon:3176 +property_value: RO:0002161 NCBITaxon:3312 +property_value: RO:0002161 NCBITaxon:3378 +property_value: RO:0002161 NCBITaxon:3398 +property_value: RO:0002161 NCBITaxon:4890 +property_value: RO:0002161 NCBITaxon:5782 [Term] id: GO:0060429 @@ -5500,14 +5502,14 @@ is_a: GO:0033365 ! protein localization to organelle intersection_of: GO:0008104 ! protein localization intersection_of: has_target_end_location GO:0005929 ! cilium relationship: has_target_end_location GO:0005929 ! cilium -relationship: in_taxon NCBITaxon:2759 {all_only="true"} ! Eukaryota -relationship: never_in_taxon NCBITaxon:3176 -relationship: never_in_taxon NCBITaxon:3312 -relationship: never_in_taxon NCBITaxon:3378 -relationship: never_in_taxon NCBITaxon:3398 -relationship: never_in_taxon NCBITaxon:4890 -relationship: never_in_taxon NCBITaxon:5782 -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota +property_value: RO:0002161 NCBITaxon:3176 +property_value: RO:0002161 NCBITaxon:3312 +property_value: RO:0002161 NCBITaxon:3378 +property_value: RO:0002161 NCBITaxon:3398 +property_value: RO:0002161 NCBITaxon:4890 +property_value: RO:0002161 NCBITaxon:5782 created_by: dph creation_date: 2013-03-22T15:41:44Z @@ -5517,8 +5519,8 @@ name: collagen-containing extracellular matrix namespace: cellular_component def: "An extracellular matrix consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that provides not only essential physical scaffolding for the cellular constituents but can also initiate crucial biochemical and biomechanical cues required for tissue morphogenesis, differentiation and homeostasis. The components are secreted by cells in the vicinity and form a sheet underlying or overlying cells such as endothelial and epithelial cells." [GOC:BHF, GOC:rph, PMID:21123617] is_a: GO:0031012 ! extracellular matrix -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa created_by: dph creation_date: 2018-04-13T12:47:21Z @@ -6053,9 +6055,9 @@ subset: goslim_synapse is_a: GO:0007267 ! cell-cell signaling intersection_of: GO:0007267 ! cell-cell signaling intersection_of: occurs_in GO:0045202 ! synapse -relationship: in_taxon NCBITaxon:33208 {all_only="true"} ! Metazoa relationship: occurs_in GO:0045202 ! synapse -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0099537 @@ -6282,18 +6284,16 @@ namespace: ncbi_taxonomy xref: GC_ID:1 xref: PMID:15371245 is_a: NCBITaxon:337687 ! Muroidea -property_value: has_rank NCBITaxon:family [Term] id: NCBITaxon:10088 name: Mus namespace: ncbi_taxonomy -synonym: "mice" EXACT OMO:0003003 [] +synonym: "mice" EXACT genbank_common_name [] synonym: "mouse" EXACT OMO:0003003 [] synonym: "Mus" EXACT scientific_name [] xref: GC_ID:1 is_a: NCBITaxon:39107 ! Murinae -property_value: has_rank NCBITaxon:genus [Term] id: NCBITaxon:10090 @@ -6304,7 +6304,6 @@ synonym: "house mouse" EXACT genbank_common_name [] synonym: "mouse" EXACT OMO:0003003 [] xref: GC_ID:1 is_a: NCBITaxon:862507 ! Mus -property_value: has_rank NCBITaxon:species [Term] id: NCBITaxon:117570 @@ -6312,7 +6311,6 @@ name: Teleostomi namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:7776 ! Gnathostomata -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:117571 @@ -6322,7 +6320,6 @@ alt_id: NCBITaxon:40673 synonym: "bony vertebrates" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:117570 ! Teleostomi -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:131567 @@ -6338,7 +6335,6 @@ name: Dipnotetrapodomorpha namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:8287 ! Sarcopterygii -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:1437010 @@ -6349,7 +6345,6 @@ xref: GC_ID:1 xref: PMID:11743200 xref: PMID:11791233 is_a: NCBITaxon:9347 ! Eutheria -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:1963758 @@ -6359,7 +6354,6 @@ synonym: "mice and others" EXACT genbank_common_name [] synonym: "Sciurognathi" RELATED in_part [] xref: GC_ID:1 is_a: NCBITaxon:9989 ! Rodentia -property_value: has_rank NCBITaxon:suborder [Term] id: NCBITaxon:2759 @@ -6376,7 +6370,6 @@ xref: GC_ID:1 xref: PMID:23020233 xref: PMID:30257078 is_a: NCBITaxon:131567 ! cellular organisms -property_value: has_rank NCBITaxon:superkingdom [Term] id: NCBITaxon:314146 @@ -6388,7 +6381,6 @@ xref: PMID:12082125 xref: PMID:12878460 xref: PMID:15522813 is_a: NCBITaxon:1437010 ! Boreoeutheria -property_value: has_rank NCBITaxon:superorder [Term] id: NCBITaxon:314147 @@ -6400,7 +6392,6 @@ xref: PMID:11214319 xref: PMID:12082125 xref: PMID:15522813 is_a: NCBITaxon:314146 ! Euarchontoglires -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:32523 @@ -6409,7 +6400,6 @@ namespace: ncbi_taxonomy synonym: "tetrapods" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:1338369 ! Dipnotetrapodomorpha -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:32524 @@ -6418,7 +6408,6 @@ namespace: ncbi_taxonomy synonym: "amniotes" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:32523 ! Tetrapoda -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:32525 @@ -6427,7 +6416,6 @@ namespace: ncbi_taxonomy synonym: "Theria" EXACT scientific_name [] xref: GC_ID:1 is_a: NCBITaxon:40674 ! Mammalia -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:33154 @@ -6437,7 +6425,6 @@ synonym: "Fungi/Metazoa group" RELATED synonym [] synonym: "opisthokonts" RELATED synonym [] xref: GC_ID:1 is_a: NCBITaxon:2759 ! Eukaryota -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:33208 @@ -6449,7 +6436,6 @@ synonym: "metazoans" EXACT genbank_common_name [] synonym: "multicellular animals" EXACT OMO:0003003 [] xref: GC_ID:1 is_a: NCBITaxon:33154 ! Opisthokonta -property_value: has_rank NCBITaxon:kingdom [Term] id: NCBITaxon:33213 @@ -6457,7 +6443,6 @@ name: Bilateria namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:6072 ! Eumetazoa -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:33511 @@ -6466,7 +6451,6 @@ namespace: ncbi_taxonomy synonym: "deuterostomes" EXACT OMO:0003003 [] xref: GC_ID:1 is_a: NCBITaxon:33213 ! Bilateria -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:337687 @@ -6476,7 +6460,6 @@ xref: GC_ID:1 xref: PMID:15019624 xref: PMID:15371245 is_a: NCBITaxon:1963758 ! Myomorpha -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:39107 @@ -6485,7 +6468,6 @@ namespace: ncbi_taxonomy alt_id: NCBITaxon:109679 xref: GC_ID:1 is_a: NCBITaxon:10066 ! Muridae -property_value: has_rank NCBITaxon:subfamily [Term] id: NCBITaxon:40674 @@ -6495,7 +6477,6 @@ synonym: "mammals" EXACT genbank_common_name [] synonym: "mammals" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:32524 ! Amniota -property_value: has_rank NCBITaxon:class [Term] id: NCBITaxon:6072 @@ -6503,7 +6484,6 @@ name: Eumetazoa namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:33208 ! Metazoa -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:7711 @@ -6513,7 +6493,6 @@ synonym: "chordates" EXACT genbank_common_name [] synonym: "chordates" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:33511 ! Deuterostomia -property_value: has_rank NCBITaxon:phylum [Term] id: NCBITaxon:7742 @@ -6524,7 +6503,6 @@ synonym: "vertebrates" EXACT genbank_common_name [] synonym: "vertebrates" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:89593 ! Craniata -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:7776 @@ -6534,7 +6512,6 @@ synonym: "Gnathostomata" EXACT scientific_name [] synonym: "jawed vertebrates" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:7742 ! Vertebrata -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:8287 @@ -6542,7 +6519,6 @@ name: Sarcopterygii namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:117571 ! Euteleostomi -property_value: has_rank NCBITaxon:superclass [Term] id: NCBITaxon:862507 @@ -6551,7 +6527,6 @@ namespace: ncbi_taxonomy synonym: "Mus" EXACT scientific_name [] xref: GC_ID:1 is_a: NCBITaxon:10088 ! Mus -property_value: has_rank NCBITaxon:subgenus [Term] id: NCBITaxon:89593 @@ -6560,7 +6535,6 @@ namespace: ncbi_taxonomy synonym: "Craniata" EXACT scientific_name [] xref: GC_ID:1 is_a: NCBITaxon:7711 ! Chordata -property_value: has_rank NCBITaxon:subphylum [Term] id: NCBITaxon:9347 @@ -6573,7 +6547,6 @@ synonym: "placentals" EXACT genbank_common_name [] synonym: "placentals" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:32525 ! Theria -property_value: has_rank NCBITaxon:clade [Term] id: NCBITaxon:9989 @@ -6583,7 +6556,6 @@ synonym: "rodent" EXACT genbank_common_name [] synonym: "rodents" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:314147 ! Glires -property_value: has_rank NCBITaxon:order [Term] id: PATO:0000001 @@ -6634,7 +6606,6 @@ subset: value_slim synonym: "ramified" EXACT [] synonym: "ramiform" EXACT [] is_a: PATO:0002009 ! branchiness -property_value: RO:0002604 PATO:0000414 [Term] id: PATO:0000411 @@ -6794,7 +6765,6 @@ comment: This refers to the disposition of the bearer. subset: disposition_slim subset: value_slim is_a: PATO:0001579 ! contractility -property_value: RO:0002604 PATO:0001691 [Term] id: PATO:0001857 @@ -6804,7 +6774,6 @@ def: "A shape quality in a bearer by virtue of the bearer's curving inward." [Wo subset: cell_quality subset: value_slim is_a: PATO:0002005 ! concavity -property_value: RO:0002604 PATO:0001355 [Term] id: PATO:0001873 @@ -6881,7 +6850,6 @@ subset: attribute_slim xref: Image:http\://upload.wikimedia.org/wikipedia/commons/0/06/Convex_polygon_illustration1.png is_a: PATO:0002266 ! 3-D shape relationship: RO:0015011 PATO:0002006 ! has cross section 2-D shape -property_value: RO:0002604 PATO:0002008 [Term] id: PATO:0002009 @@ -6907,7 +6875,6 @@ namespace: quality def: "A concave quality inhering in a bearer by virtue of the bearer's curving inward on both sides or surfaces." [PATOC:GVG] subset: value_slim is_a: PATO:0001857 ! concave -property_value: RO:0002604 PATO:0002040 [Term] id: PATO:0002045 @@ -6919,7 +6886,7 @@ synonym: "dendriform" EXACT [] synonym: "dendroid" EXACT [] synonym: "dendroidal" EXACT [] is_a: PATO:0000402 ! branched -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-02-15T08:11:41Z [Term] @@ -6929,7 +6896,7 @@ namespace: quality def: "A quality inhering in a bearer by virtue of the bearer's having an empty space or cavity within." [url:http\://www.merriam-webster.com/dictionary/hollow] subset: value_slim is_a: PATO:0002014 ! structure, cavities -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-09-18T02:19:20Z [Term] @@ -6941,7 +6908,7 @@ subset: disposition_slim subset: mpath_slim subset: value_slim is_a: PATO:0070045 ! anatomical histological quality -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-10-05T12:05:23Z [Term] @@ -6952,7 +6919,7 @@ def: "A quality inhering in a bearer by virtue of the bearer's processing the fo subset: mpath_slim subset: value_slim is_a: PATO:0000141 ! structure -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2009-10-06T04:37:14Z [Term] @@ -6962,7 +6929,7 @@ namespace: quality def: "A quality inhering in a bearer by virtue of its constitution." [PATOC:GVG] subset: attribute_slim is_a: PATO:0001018 ! physical quality -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-03-15T04:35:27Z [Term] @@ -6972,7 +6939,7 @@ namespace: quality def: "A cylindrical shape quality inhering in a bearer by virtue of the bearer's being imperfectly cylindrical or approximately cylindrical." [url:http\://www.thefreedictionary.com/Subcylindrical] subset: value_slim is_a: PATO:0001873 ! cylindrical -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-07-13T04:22:30Z [Term] @@ -6981,7 +6948,7 @@ name: 3-D shape namespace: quality def: "A shape that inheres in a 3 dimensional entity." [PATOC:OREGON] is_a: PATO:0000052 ! shape -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2010-10-05T12:31:16Z [Term] @@ -6994,7 +6961,7 @@ synonym: "tube-shaped" EXACT [] synonym: "tubulate" EXACT [] is_a: PATO:0001873 ! cylindrical is_a: PATO:0002078 ! hollow -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-06-08T06:33:50Z [Term] @@ -7005,7 +6972,7 @@ def: "A convex 3-D shape quality inhering in a bearer by virtue of the bearer's comment: Note that a fiber shaped object may take any circuitous or straight path through space (think of a length of string or rope). subset: value_slim is_a: PATO:0002226 ! subcylindrical -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-09-09T04:50:10Z [Term] @@ -7015,7 +6982,7 @@ namespace: quality def: "A shape constituting a transition between a rectangle and a circle; a closed curve, of which the circle and ellipse are special cases, whose parametric equation is x = a.cos2/rt, y = b.cos2/rt" [wiktionary:superellipse] synonym: "Lamé curve" EXACT [] is_a: PATO:0002006 ! 2-D shape -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2011-10-12T12:45:16Z [Term] @@ -7028,7 +6995,7 @@ subset: mpath_slim subset: value_slim synonym: "eosinophilic" EXACT [] is_a: PATO:0070045 ! anatomical histological quality -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2012-12-17T03:01:19Z [Term] @@ -7038,7 +7005,7 @@ namespace: quality def: "A structure quality inhering in a bearer by virtue of the bearer's being capable of swelling or stretching." [PATOC:WD] subset: value_slim is_a: PATO:0015008 ! distensibility -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2013-09-15T11:48:26Z [Term] @@ -7049,7 +7016,7 @@ def: "A nucleate quality inhering in a bearer by virtue of the bearer's having o subset: mpath_slim subset: value_slim is_a: PATO:0001404 ! nucleate quality -relationship: dc-contributor https://orcid.org/0000-0002-2061-091X +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-2061-091X creation_date: 2013-10-21T05:44:34Z [Term] @@ -7058,7 +7025,7 @@ name: disconnected namespace: quality def: "A structural quality inhering in the bearer by virtue of the bearer consisting of multiple structures lacking any physical connection to each other." [GOC:dos] is_a: PATO:0000141 ! structure -relationship: dc-contributor https://orcid.org/0000-0002-7073-9172 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2014-12-12T08:43:17Z [Term] @@ -7186,7 +7153,6 @@ synonym: "leukocyte adhesion receptor MO1" EXACT [] synonym: "neutrophil adherence receptor" EXACT [] xref: IUPHARobj:2452 is_a: PR:000001005 ! integrin alpha with A domain -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P11215 [Term] id: PR:000001018 @@ -7242,7 +7208,6 @@ synonym: "NCAM-1" EXACT [] synonym: "NCAM1" EXACT PRO-short-label [PRO:DNx] xref: IUPHARobj:2769 is_a: PR:000001023 ! neural cell adhesion molecule NCAM -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P13591 [Term] id: PR:000001083 @@ -7279,7 +7244,6 @@ synonym: "MAL" RELATED Gene-based [] synonym: "T-cell surface glycoprotein Lyt-2" EXACT [] synonym: "T-lymphocyte differentiation antigen T8/Leu-2" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P01732 [Term] id: PR:000001289 @@ -7323,7 +7287,6 @@ synonym: "CDH5" EXACT PRO-short-label [PRO:DNx] synonym: "vascular endothelial cadherin" EXACT [] synonym: "VE-cadherin" EXACT [] is_a: PR:000001327 ! cadherin -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P33151 [Term] id: PR:000001839 @@ -7338,7 +7301,6 @@ synonym: "lymphocyte antigen 1" EXACT [] synonym: "lymphocyte antigen T1/Leu-1" EXACT [] synonym: "Lyt-1" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P06127 [Term] id: PR:000001869 @@ -7356,7 +7318,6 @@ synonym: "IL7R" EXACT PRO-short-label [PRO:DNx] xref: IUPHARobj:1698 xref: PIRSF:PIRSF001960 is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P16871 [Term] id: PR:000001889 @@ -7385,7 +7346,6 @@ synonym: "TFRC" EXACT PRO-short-label [PRO:DNx] synonym: "TR" RELATED [] synonym: "Trfr" RELATED Gene-based [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P02786 [Term] id: PR:000001971 @@ -7414,7 +7374,6 @@ synonym: "VEGFR-2" EXACT [] synonym: "VEGFR2" RELATED Gene-based [] xref: IUPHARobj:1813 is_a: PR:000001971 ! vascular endothelial growth factor receptor -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P35968 [Term] id: PR:000002976 @@ -7457,7 +7416,6 @@ synonym: "angiotensinogenase" RELATED [] synonym: "REN" EXACT PRO-short-label [PRO:DNx] xref: IUPHARobj:2413 is_a: PR:000050025 ! angiotensinogenase -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P00797 [Term] id: PR:000014841 @@ -7471,7 +7429,6 @@ synonym: "SHH" EXACT PRO-short-label [PRO:DNx] synonym: "Shh unprocessed N-terminal signaling and C-terminal autoprocessing domains" EXACT [] synonym: "ShhNC" EXACT [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:Q15465 [Term] id: PR:000016043 @@ -7489,7 +7446,6 @@ synonym: "TAL-1" EXACT [] synonym: "TAL1" EXACT PRO-short-label [PRO:DNx] synonym: "TCL5" RELATED Gene-based [] is_a: PR:000000001 ! protein -property_value: https://w3id.org/semapv/vocab/crossSpeciesExactMatch PR:P17542 [Term] id: PR:000025796 @@ -7507,8 +7463,8 @@ def: "A protein that is encoded in the genome of Mus musculus." [PRO:DAN] synonym: "mouse protein" EXACT PRO-short-label [PRO:DAN] is_a: PR:000036194 ! eukaryotic protein intersection_of: PR:000000001 ! protein -intersection_of: only_in_taxon NCBITaxon:10090 ! Mus musculus -relationship: only_in_taxon NCBITaxon:10090 ! Mus musculus +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus +relationship: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus [Term] id: PR:000036194 @@ -7518,8 +7474,8 @@ def: "A protein that is encoded in the genome of some Eukaryota." [PRO:DAN] synonym: "Eukaryota protein" EXACT [PRO:DAN] is_a: PR:000000001 ! protein intersection_of: PR:000000001 ! protein -intersection_of: only_in_taxon NCBITaxon:2759 ! Eukaryota -relationship: only_in_taxon NCBITaxon:2759 ! Eukaryota +intersection_of: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota [Term] id: PR:000050025 @@ -7554,9 +7510,9 @@ subset: common_anatomy subset: upper_level xref: BFO:0000003 disjoint_from: UBERON:0001062 ! anatomical entity -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000025 @@ -7568,11 +7524,9 @@ synonym: "duct" NARROW [] xref: galen:Tube is_a: UBERON:0004111 ! anatomical conduit intersection_of: UBERON:0004111 ! anatomical conduit -intersection_of: has_quality PATO:0002299 ! tubular +intersection_of: RO:0000086 PATO:0002299 ! has quality tubular relationship: has_part UBERON:0013522 ! subdivision of tube -relationship: has_quality PATO:0002299 ! tubular -property_value: IAO:0000232 "not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts)" xsd:string -property_value: UBPROP:0000007 "tubular" xsd:string +relationship: RO:0000086 PATO:0002299 ! has quality tubular [Term] id: UBERON:0000026 @@ -7594,7 +7548,6 @@ xref: EFO:0000799 xref: EHDAA2:0003193 xref: EMAPA:37283 {source="MA:th"} xref: EV:0100155 -xref: FBbt:00007000 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: HAO:0000144 xref: MAT:0000023 xref: MESH:D005121 @@ -7605,11 +7558,7 @@ xref: VSAO:0000075 xref: Wikipedia:Appendage xref: XAO:0000218 is_a: UBERON:0000475 ! organism subdivision -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: UBPROP:0000001 "An appendage is an external body part, or natural prolongation, that protrudes from an organism's body, such as a vertebrate's limbs[BILA][BILA:0000018]." xsd:string {source="BILA:0000018"} -property_value: UBPROP:0000001 "Organ or organ part that is attached to the body of an organism. For example a limb[GO, modified][GO:0048736]." xsd:string {source="GO:0048736"} -property_value: UBPROP:0000007 "appendicular" xsd:string -property_value: UBPROP:0000008 "this is currently a subtype of organism subdivision - which would exclude feathers" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0000055 @@ -7621,7 +7570,7 @@ subset: human_reference_atlas subset: pheno_slim is_a: UBERON:0004111 ! anatomical conduit relationship: channel_for UBERON:0006314 ! bodily fluid -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000056 @@ -7663,17 +7612,10 @@ is_a: UBERON:0015212 ! lateral structure relationship: channel_for UBERON:0001088 ! urine relationship: channels_from UBERON:0001224 ! renal pelvis relationship: channels_into UBERON:0001255 ! urinary bladder -relationship: develops_from UBERON:0005081 {source="GO"} ! ureter ureteric bud -relationship: in_lateral_side_of UBERON:0000468 ! multicellular organism relationship: part_of UBERON:0036295 ! renal pelvis/ureter -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg" xsd:anyURI -property_value: UBPROP:0000001 "Anatomical structure consisting of long narrow duct which carries urine from the kidney to the urinary bladder.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010254", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "The duct of amniotes that carries urine from a metanephric kidney to the urinary bladder. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000605", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000605", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "ureteral" xsd:string -property_value: UBPROP:0000007 "ureteric" xsd:string -property_value: UBPROP:0000010 "in humans, consists of adventitial, muscular and mucoa layers" xsd:string +relationship: RO:0002202 UBERON:0005081 {source="GO"} ! develops from ureter ureteric bud +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000057 @@ -7709,13 +7651,11 @@ is_a: UBERON:0004120 ! mesoderm-derived structure relationship: capable_of_part_of GO:0060073 ! micturition relationship: channel_for UBERON:0001088 ! urine relationship: channels_from UBERON:0001255 ! urinary bladder -relationship: continuous_with UBERON:0001255 ! urinary bladder -relationship: develops_from UBERON:0000164 {notes="pelvic part of UG sinus gives rise to prostatic and membranous parts of urethra", source="Wikipedia"} ! primitive urogenital sinus -relationship: develops_from UBERON:0013241 {source="Wikipedia"} ! embryonic urethral groove relationship: part_of UBERON:0001556 ! lower urinary tract -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png" xsd:anyURI -property_value: UBPROP:0000007 "urethral" xsd:string -property_value: UBPROP:0000008 "In human males, the urethra travels through the penis, and carries semen as well as urine. In females, the urethra is shorter and emerges above the vaginal opening." xsd:string +relationship: RO:0002150 UBERON:0001255 ! continuous with urinary bladder +relationship: RO:0002202 UBERON:0000164 ! develops from primitive urogenital sinus +relationship: RO:0002202 UBERON:0013241 {source="Wikipedia"} ! develops from embryonic urethral groove +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png" xsd:anyURI [Term] id: UBERON:0000058 @@ -7728,7 +7668,6 @@ synonym: "ducts" RELATED OMO:0003004 [XAO:0004000] synonym: "exocrine duct" NARROW [] synonym: "exocrine gland duct" NARROW [] xref: AAO:0011123 -xref: FBbt:00100314 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:30320 xref: galen:Duct xref: NCIT:C12948 @@ -7740,11 +7679,9 @@ xref: XAO:0004000 xref: ZFA:0005171 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000063 ! organ subunit -relationship: conduit_for UBERON:0000463 ! organism substance relationship: has_part UBERON:0034969 ! epithelial layer of duct -relationship: has_quality PATO:0002299 ! tubular -property_value: UBPROP:0000001 "A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171]." xsd:string {source="ZFA:0005171"} -property_value: UBPROP:0000012 "Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here." xsd:string +relationship: RO:0000086 PATO:0002299 ! has quality tubular +relationship: RO:0002570 UBERON:0000463 ! conduit for organism substance [Term] id: UBERON:0000060 @@ -7756,13 +7693,11 @@ subset: upper_level synonym: "organ wall" RELATED [FMA:82482] synonym: "wall" BROAD [] synonym: "wall of organ" EXACT [FMA:82482] -xref: EMAPA:25036 xref: FMA:82482 xref: galen:Wall is_a: UBERON:0000064 ! organ part relationship: adjacent_to UBERON:0002553 ! anatomical cavity relationship: has_part UBERON:0004923 ! organ component layer -property_value: UBPROP:0000012 "in FMA, serosa is a wall" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0000061 @@ -7779,7 +7714,6 @@ xref: BILA:0000003 xref: CARO:0000003 xref: EHDAA2:0003003 xref: EMAPA:0 -xref: FBbt:00007001 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:305751 xref: FMA:67135 xref: GAID:781 @@ -7794,10 +7728,10 @@ xref: VHOG:0001759 xref: XAO:0003000 xref: ZFA:0000037 is_a: UBERON:0000465 ! material anatomical entity -relationship: existence_ends_during_or_before UBERON:0000071 ! death stage -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0002497 UBERON:0000071 ! existence ends during or before death stage +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000062 @@ -7824,14 +7758,12 @@ xref: Wikipedia:Organ_(anatomy) is_a: UBERON:0010000 ! multicellular anatomical structure disjoint_from: UBERON:0034921 ! multi organ part structure relationship: capable_of GO:0008150 ! biological_process -relationship: has_boundary UBERON:0006984 ! anatomical surface -relationship: never_in_taxon NCBITaxon:110815 {source="Wikipedia"} relationship: part_of UBERON:0000467 ! anatomical system -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: UBPROP:0000001 "Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions." xsd:string {source="GO:0048513"} -property_value: UBPROP:0000012 "CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4" xsd:string +relationship: RO:0002002 UBERON:0006984 ! has 2D boundary anatomical surface +property_value: RO:0002161 NCBITaxon:110815 {source="Wikipedia"} +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000063 @@ -7844,9 +7776,7 @@ synonym: "organ segment" RELATED [FMA:86140] synonym: "segment of organ" RELATED [FMA:86140] xref: FMA:86140 is_a: UBERON:0000064 ! organ part -property_value: editor_note "FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction" xsd:string -property_value: UBPROP:0000001 "Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball." xsd:string {source="FMA:86140", version="3"} -property_value: UBPROP:0000001 "Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal." xsd:string {source="FMA:86140", version="1"} +property_value: IAO:0000116 "FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction" xsd:string [Term] id: UBERON:0000064 @@ -7867,10 +7797,9 @@ xref: SCTID:113343008 xref: SCTID:91717005 is_a: UBERON:0010000 ! multicellular anatomical structure relationship: part_of UBERON:0000062 ! organ -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: IAO:0000232 "currently defined in a very broad sense, may be replaced by more specific classes in the future" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000066 @@ -7919,7 +7848,7 @@ is_a: UBERON:0000105 ! life cycle stage disjoint_from: UBERON:0000092 ! post-embryonic stage relationship: precedes UBERON:0000066 ! fully formed stage relationship: precedes UBERON:0000092 ! post-embryonic stage -relationship: simultaneous_with GO:0009790 ! embryo development +relationship: RO:0002082 GO:0009790 ! simultaneous with embryo development [Term] id: UBERON:0000071 @@ -7932,11 +7861,10 @@ xref: XAO:0000437 xref: XtroDO:0000085 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage -relationship: ends UBERON:0000104 ! life cycle -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: UBPROP:0000012 "ncit:Death is an outcome" xsd:string {external_ontology="ncit"} +relationship: RO:0002229 UBERON:0000104 ! ends life cycle +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000074 @@ -7972,14 +7900,13 @@ xref: Wikipedia:Glomerulus xref: ZFA:0001288 is_a: UBERON:0000064 ! organ part is_a: UBERON:0004120 ! mesoderm-derived structure -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 -relationship: develops_from UBERON:0005749 ! glomerular tuft relationship: part_of UBERON:0001229 {source="FMA", source="MA"} ! renal corpuscle -relationship: present_in_taxon NCBITaxon:9606 -relationship: surrounded_by UBERON:0001230 ! glomerular capsule -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg" xsd:anyURI -property_value: UBPROP:0000012 "ZFA - The multi-tissue structure where the glomerular basement membrane supported by mesonephric podocytes filters blood from the glomerular capillaries. GUDMAP: 'Together, the Bowman's capsule and the glomerulus comprise the definitive renal corpuscle.' - here the glomerulus is part of the capsule?" xsd:string {external_ontology="ZFA"} +relationship: RO:0002202 UBERON:0005749 ! develops from glomerular tuft +relationship: RO:0002219 UBERON:0001230 ! surrounded by glomerular capsule +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 creation_date: 2009-06-18T09:26:37Z [Term] @@ -7997,9 +7924,9 @@ xref: NCIT:C34076 xref: SCTID:118966000 xref: UMLS:C1519343 {source="ncithesaurus:Skeletal_System_Part"} is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision -relationship: composed_primarily_of UBERON:0004765 ! skeletal element -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0001434 ! skeletal system +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002473 UBERON:0004765 ! composed primarily of skeletal element [Term] id: UBERON:0000080 @@ -8040,14 +7967,8 @@ xref: XAO:0000141 xref: ZFA:0000529 is_a: UBERON:0002113 ! kidney is_a: UBERON:0004120 ! mesoderm-derived structure -relationship: develops_from UBERON:0002120 ! pronephros -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray986.png" xsd:anyURI -property_value: UBPROP:0000001 "A kidney formed of nephric tubules arising in the middle region of the nephric ridge; a transient embryonic stage that replaces the pronephros, but is itself replaced by the adult metanephros [in mammals; in fishes and amphibians it is the adult kidney]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000038", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000001 "Organ that is the definitive adult kidney. It replaces the earlier pronephros, which degenerates as the mesonephros becomes functional in feeding stage tadpoles.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010384", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates. (...) In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000038", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "mesonephric" xsd:string -property_value: UBPROP:0000008 "In mammals, the mesonephros is the second of the three embryonic kidneys to be established and exists only transiently. In fish and amphibians, the mesonephros will form the mature kidney" xsd:string -property_value: UBPROP:0000009 "By contrast to the pronephros, the histological features of the mammalian mesonephros, with its primitive glomeruli, suggest that it probably functions as a primitive kidney, and is involved in the production of much of the amniotic fluid. Within the two mesonephroi, one located on either side of the dorsal mesentery of the hindgut, a substantial number (in the region of about 40 or more) of cranio-caudally segmented mesonephric tubules are formed. It has, however, been suggested that only the most rostrally located 4-6 pairs of mesonephric tubules drain into the mesonephric portion of the nephric duct. This is now seen to extend along the length of the mesonephroi, being located towards their lateral sides. The mesonephros is also retained over a considerably longer period than the pronephros, but gradually undergoes regression in a cranio-caudal direction. While the rostral part displays clear evidence of regression its more caudal part appears to display evidence of functional activity. Within the medial part of the mesonephros, vesicles are formed, although no glomeruli are formed there in this species. It is, however, difficult to believe that the relatively enormous mesonephroi do not have an excretory role in the mouse, only serving as a base for gonadal differentiation. In the human embryo, the medial part of the mesonephric tubules enlarges, become invaginated by capillaries, and form glomeruli. These then take on an excretory role. In the mouse, the mesonephric ducts appear to be patent throughout their length[GUDMAP, modified]" xsd:string +relationship: RO:0002202 UBERON:0002120 ! develops from pronephros +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/a/ad/Gray986.png" xsd:anyURI [Term] id: UBERON:0000081 @@ -8075,16 +7996,12 @@ xref: VHOG:0000039 xref: Wikipedia:Metanephros#Metanephros is_a: UBERON:0002113 ! kidney is_a: UBERON:0004120 ! mesoderm-derived structure -relationship: developmentally_replaces UBERON:0000080 {source="ISBN:9780878932504"} ! mesonephros -relationship: develops_from UBERON:0003220 {evidence="definitional"} ! metanephric mesenchyme -relationship: develops_from UBERON:0005080 {source="GO"} ! metanephric ureteric bud -relationship: develops_from UBERON:0005753 ! caudal part of nephrogenic cord -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -property_value: editor_note "TODO check developmental relationships" xsd:string -property_value: UBPROP:0000001 "A kidney formed of nephric tubules arising in the posterior region of the nephric ridge and drained by a ureter; replaces the embryonic pronephros and mesonephros [in mammals]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000039", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000039", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "metanephric" xsd:string -property_value: UBPROP:0000011 "During the fifth week of gestation, the mesonephric duct develops an outpouching, the ureteric bud, near its attachment to the cloaca. This bud, also called the metanephrogenic diverticulum, grows posteriorly and towards the head of the embryo. The elongated stalk of the ureteric bud, the metanephric duct, later forms the ureter. As the cranial end of the bud extends into the intermediate mesoderm, it undergoes a series of branchings to form the collecting duct system of the kidney. It also forms the major and minor calyces and the renal pelvis" xsd:string +relationship: RO:0002202 UBERON:0003220 ! develops from metanephric mesenchyme +relationship: RO:0002202 UBERON:0005080 {source="GO"} ! develops from metanephric ureteric bud +relationship: RO:0002202 UBERON:0005753 ! develops from caudal part of nephrogenic cord +relationship: RO:0002285 UBERON:0000080 {source="ISBN:9780878932504"} ! developmentally replaces mesonephros +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +property_value: IAO:0000116 "TODO check developmental relationships" xsd:string [Term] id: UBERON:0000083 @@ -8104,9 +8021,7 @@ is_a: UBERON:0005103 ! mesonephric epithelium is_a: UBERON:0006555 ! excretory tube intersection_of: UBERON:0003914 ! epithelial tube intersection_of: part_of UBERON:0000080 ! mesonephros -property_value: editor_note "TODO check" xsd:string -property_value: UBPROP:0000001 "Any of the renal tubules composing the mesonephros. In mammals they function as excretory structures during the early embryonic development but are later incorporated into the reproductive system. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000500", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/mesonephric+tubule"} -property_value: UBPROP:0000003 "As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000500", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639", source="http://bgee.unil.ch/"} +property_value: IAO:0000116 "TODO check" xsd:string [Term] id: UBERON:0000084 @@ -8133,14 +8048,10 @@ xref: VHOG:0000541 xref: Wikipedia:Ureteric_bud is_a: UBERON:0000083 ! mesonephric tubule is_a: UBERON:0007499 {source="EHDAA2"} ! epithelial sac -is_a: UBERON:0012275 ! meso-epithelium is_a: UBERON:0034969 ! epithelial layer of duct -relationship: developmentally_induced_by UBERON:0003220 {source="ISBN:9780878932504"} ! metanephric mesenchyme -relationship: develops_from UBERON:0003074 {source="EHDAA2"} ! mesonephric duct relationship: part_of UBERON:0003074 ! mesonephric duct -property_value: UBPROP:0000001 "Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts. [Embryology, See_Dudek_RW_and_Fix_JD, Third_Edition_(2004)_Philadelphia:_Lippincott_William_and_Wilkins, p.137][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000541", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000001 "Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts[VHOG:0000541]." xsd:string {source="VHOG:0000541"} -property_value: UBPROP:0000003 "The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000541", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003074 {source="EHDAA2"} ! develops from mesonephric duct +relationship: RO:0002256 UBERON:0003220 {source="ISBN:9780878932504"} ! developmentally induced by metanephric mesenchyme [Term] id: UBERON:0000092 @@ -8160,9 +8071,8 @@ xref: WBls:0000103 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage relationship: preceded_by UBERON:0000068 ! embryo stage -relationship: simultaneous_with GO:0009791 ! post-embryonic development +relationship: RO:0002082 GO:0009791 ! simultaneous with post-embryonic development property_value: seeAlso "https://github.com/obophenotype/uberon/issues/344" xsd:anyURI -property_value: UBPROP:0000008 "In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997)" xsd:string [Term] id: UBERON:0000104 @@ -8184,9 +8094,9 @@ is_a: BFO:0000003 ! occurrent is_a: UBERON:0000000 ! processual entity relationship: ends_with UBERON:0000071 ! death stage relationship: has_part UBERON:0000105 ! life cycle stage -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 property_value: seeAlso "https://github.com/obophenotype/uberon/issues/532" xsd:anyURI [Term] @@ -8215,12 +8125,10 @@ xref: ZFS:0000000 xref: ZFS:0100000 is_a: UBERON:0000000 ! processual entity relationship: part_of UBERON:0000104 ! life cycle -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: editor_note "this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here" xsd:string -property_value: UBPROP:0000012 "the WBls class 'all stages' belongs here as it is the superclass of other WBls stages" xsd:string -property_value: UBPROP:0000012 "we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage" xsd:string +property_value: IAO:0000116 "this class represents a proper part of the life cycle of an organism. The class 'life cycle' should not be placed here" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000106 @@ -8240,7 +8148,6 @@ xref: BILS:0000106 xref: EFO:0001322 xref: EHDAA:27 xref: FBdv:00005288 -xref: IDOMAL:0000302 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C12601 xref: PdumDv:0000100 xref: VHOG:0000745 @@ -8250,9 +8157,8 @@ xref: ZFS:0000001 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage -relationship: seeAlso EMAPA:16033 -relationship: starts UBERON:0000104 ! life cycle -property_value: UBPROP:0000003 "As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000745", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107", source="http://bgee.unil.ch/"} +relationship: RO:0002223 UBERON:0000104 ! starts life cycle +property_value: seeAlso EMAPA:16033 [Term] id: UBERON:0000107 @@ -8275,10 +8181,10 @@ xref: ZFS:0000046 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage intersection_of: UBERON:0000105 ! life cycle stage -intersection_of: simultaneous_with GO:0040016 ! embryonic cleavage +intersection_of: RO:0002082 GO:0040016 ! simultaneous with embryonic cleavage relationship: immediately_preceded_by UBERON:0000106 ! zygote stage relationship: part_of UBERON:0000068 ! embryo stage -relationship: simultaneous_with GO:0040016 ! embryonic cleavage +relationship: RO:0002082 GO:0040016 ! simultaneous with embryonic cleavage [Term] id: UBERON:0000108 @@ -8302,8 +8208,8 @@ is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000107 ! cleavage stage -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI -property_value: editor_note "consider adding a preceding stage 'morula stage' as part of cleavage" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI +property_value: IAO:0000116 "consider adding a preceding stage 'morula stage' as part of cleavage" xsd:string [Term] id: UBERON:0000109 @@ -8330,10 +8236,10 @@ xref: XAO:1000005 xref: ZFS:0000047 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000108 {source="BILS"} ! blastula stage -relationship: simultaneous_with GO:0007369 ! gastrulation +relationship: RO:0002082 GO:0007369 ! simultaneous with gastrulation +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0000110 @@ -8347,14 +8253,12 @@ xref: MmusDv:0000017 xref: XAO:1000006 is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000109 ! gastrula stage -relationship: simultaneous_with GO:0001841 ! neural tube formation -property_value: RO:0002174 NCBITaxon:7955 +relationship: RO:0002082 GO:0001841 ! simultaneous with neural tube formation +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa property_value: seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/343" xsd:anyURI -property_value: UBPROP:0000008 "In zebrafish, the times of neurulation and segmentation overlap so extensively there is no distinct neurula period of development, such as occurs largely before segmentation in amphibian embryos." xsd:string [Term] id: UBERON:0000111 @@ -8371,9 +8275,9 @@ xref: OGES:000032 xref: Wikipedia:Organogenesis is_a: BFO:0000003 ! occurrent is_a: UBERON:0000105 ! life cycle stage -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000068 ! embryo stage -relationship: simultaneous_with GO:0048513 ! animal organ development +relationship: RO:0002082 GO:0048513 ! simultaneous with animal organ development +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa property_value: seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/533" xsd:anyURI @@ -8389,14 +8293,14 @@ synonym: "layer of cells" EXACT [] synonym: "sheath of cells" RELATED [] xref: NCIT:C66831 is_a: UBERON:0000957 ! lamina -property_value: editor_note "consider adding to caro" xsd:string +property_value: IAO:0000116 "consider adding to caro" xsd:string [Term] id: UBERON:0000154 name: posterior region of body namespace: uberon is_a: UBERON:0000475 ! organism subdivision -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria [Term] id: UBERON:0000158 @@ -8410,7 +8314,6 @@ xref: MESH:D008566 xref: NCIT:C12749 is_a: UBERON:0004923 ! organ component layer relationship: bounding_layer_of UBERON:0000064 ! organ part -property_value: UBPROP:0000001 "A thin sheet or layer of pliable tissue, serving as a covering or envelope of a part, as the lining of a cavity, as a partition or septum, or to connect two structures." xsd:string {source="ncithesaurus:Membrane"} [Term] id: UBERON:0000161 @@ -8424,7 +8327,6 @@ synonym: "ostium" BROAD [] xref: FMA:3724 xref: SCTID:91837002 is_a: UBERON:0004111 ! anatomical conduit -property_value: UBPROP:0000012 "in FMA, this is an anatomical conduit *space*, rather than anatomical conduit" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0000162 @@ -8445,17 +8347,10 @@ xref: Wikipedia:Cloaca xref: XAO:0000244 xref: ZFA:0005781 is_a: UBERON:0013522 ! subdivision of tube -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0001555 {source="ZFA"} ! digestive tract relationship: part_of UBERON:0004122 {source="AAO"} ! genitourinary system -relationship: present_in_taxon NCBITaxon:9369 {notes="most adult placentals have no trace of a cloaca. However, the tenrecs and golden moles, small placental mammals native to Africa, retain a cloaca as adults."} -property_value: editor_note "adding df link to embryonic cloaca leads to a cycle in uberon-simple, as cloaca is a suberclass of embryonic cloaca" xsd:string -property_value: UBPROP:0000001 "A common passage for fecal, urinary, and reproductive discharge in most lower vertebrates as well as the terminal end of the hindgut before division into rectum, bladder, and genital primordia in mammalian embryos. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001186", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/cloaca"} -property_value: UBPROP:0000001 "Anatomical structure which is the common receptacle for the alimentary canal, Wolffian ducts, oviducts, and the bladder.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000095", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "A cloaca is apparently a primitive vertebrate feature because it occurs in most primitive gnathostomes and persists in the embryos of almost all vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001186", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.572", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "cloacal" xsd:string -property_value: UBPROP:0000008 "Human beings only have an embryonic cloaca, which is split up into separate tracts during the development of the urinary and reproductive organs" xsd:string -property_value: UBPROP:0000011 "hindgut endoderm and proctodeal ectoderm." xsd:string {source="WP"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +property_value: IAO:0000116 "adding df link to embryonic cloaca leads to a cycle in uberon-simple, as cloaca is a suberclass of embryonic cloaca" xsd:string [Term] id: UBERON:0000163 @@ -8469,11 +8364,10 @@ xref: EHDAA:4895 xref: EMAPA:27573 xref: Wikipedia:Cloaca_(embryology) is_a: UBERON:0000162 ! cloaca -relationship: has_developmental_contribution_from UBERON:0003064 ! intermediate mesoderm relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0001008 {source="EHDAA2"} ! renal system relationship: part_of UBERON:0012361 {source="EHDAA2"} ! internal anal region -property_value: IAO:0000232 "this class represents the embryonic form of the cloaca, as found in both mammals and non-mammals." xsd:string +relationship: RO:0002254 UBERON:0003064 ! has developmental contribution from intermediate mesoderm [Term] id: UBERON:0000164 @@ -8495,14 +8389,11 @@ xref: UMLS:C0231057 {source="ncithesaurus:Urogenital_Sinus"} xref: VHOG:0000414 xref: Wikipedia:Definitive_urogenital_sinus is_a: UBERON:0002050 ! embryonic structure -relationship: contributes_to_morphology_of UBERON:0000163 ! embryonic cloaca -relationship: develops_from UBERON:0003064 ! intermediate mesoderm -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0000163 {source="MP-def"} ! embryonic cloaca -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png" xsd:anyURI -property_value: UBPROP:0000001 "The ventral part of the cloaca after its separation from the rectum, giving rise to the lower part of the bladder in both sexes, to the prostatic portion of the male urethra, and to the urethra and vestibule in the female. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000414", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/urogenital+sinus"} -property_value: UBPROP:0000003 "In mammals the lowly monotremes still have a cloaca. Higher types have done away with this structure and have a separate anal outlet for the rectum. The monotreme cloaca shows the initiation of this subdivision. The cloaca has such includes only the distal part, roughly comparable to the proctodeum. The more proximal part is divided into (1) a large dorsal passage into which the intestine opens, the coprodeum, and (2) a ventral portion, the urodeum with which the bladder connects. (...) the development of the placental mammals recapitulates in many respects the phylogenetic story. In the sexually indifferent stage of placental mammal there is a cloaca. While the indifferent stage still persists, a septum develops, and extends out to the closing membrane. This divides the cloaca into two chambers: a coprodeum continuous with the gut above, and a urodeum or urogenital sinus below.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000414", ontology="VHOG", source="ISBN:978-0721676678 Romer AS, Vertebrate body (1970)p.388-89 and Figure 300", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000013 "the term 'urogenital sinus' may refer to the primitive urogenital sinus present as a transient developmental structure in most mammals or it may refer to a condition in which an unseptated cloaca persists in animals longer than normal" xsd:string {source="MP"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002202 UBERON:0003064 ! develops from intermediate mesoderm +relationship: RO:0002433 UBERON:0000163 ! contributes to morphology of embryonic cloaca +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png" xsd:anyURI [Term] id: UBERON:0000165 @@ -8536,7 +8427,6 @@ xref: EFO:0000825 xref: EHDAA2:0001326 xref: EHDAA:542 xref: EMAPA:16262 -xref: FBbt:00003126 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:49184 xref: GAID:75 xref: galen:Mouth @@ -8557,19 +8447,11 @@ xref: Wikipedia:Mouth xref: XAO:0003029 xref: ZFA:0000547 xref: ZFA:0000590 -is_a: UBERON:0004921 {notes="the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts"} ! subdivision of digestive tract -intersection_of: UBERON:0004921 ! subdivision of digestive tract -intersection_of: proximalmost_part_of UBERON:0001555 ! digestive tract -relationship: develops_from UBERON:0035804 ! future mouth -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: proximalmost_part_of UBERON:0001555 ! digestive tract -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI +is_a: UBERON:0004921 ! subdivision of digestive tract +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002202 UBERON:0035804 ! develops from future mouth +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/661" xsd:anyURI -property_value: UBPROP:0000001 "Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010355", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000812", ontology="VHOG", source="DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "oral" xsd:string -property_value: UBPROP:0000011 "some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives" xsd:string -property_value: UBPROP:0000012 "in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0000174 @@ -8632,15 +8514,10 @@ is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000179 ! haemolymphatic fluid relationship: has_part CL:0000232 {source="CL:tm"} ! erythrocyte relationship: has_part UBERON:0001969 ! blood plasma -relationship: immediate_transformation_of UBERON:0006596 {source="Bgee:AN"} ! presumptive blood -relationship: located_in UBERON:0002049 {source="https://github.com/obophenotype/uberon/issues/1330"} ! vasculature relationship: part_of UBERON:0002390 ! hematopoietic system -relationship: present_in_taxon NCBITaxon:9606 -property_value: IAO:0000232 "This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid." xsd:string -property_value: UBPROP:0000001 "A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000007", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000046", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000002 "relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000046", ontology="AAO"} -property_value: UBPROP:0000003 "Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000224", ontology="VHOG", source="DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006) ", source="http://bgee.unil.ch/"} +relationship: RO:0001025 UBERON:0002049 {source="https://github.com/obophenotype/uberon/issues/1330"} ! located in vasculature +relationship: RO:0002495 UBERON:0006596 {source="Bgee:AN"} ! immediate transformation of presumptive blood +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000179 @@ -8653,9 +8530,9 @@ xref: CARO:0000081 is_a: UBERON:0006314 ! bodily fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: part_of UBERON:0002193 ! hemolymphoid system -relationship: dc-contributor https://orcid.org/0000-0002-6601-2165 -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0002193 ! hemolymphoid system +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-6601-2165 creation_date: 2009-04-08T04:38:19Z [Term] @@ -8675,19 +8552,17 @@ xref: OGEM:000006 xref: Wikipedia:Blastula is_a: UBERON:0000922 ! embryo intersection_of: UBERON:0000468 ! multicellular organism -intersection_of: existence_starts_and_ends_during UBERON:0000108 ! blastula stage -relationship: develops_from UBERON:0007010 ! cleaving embryo -relationship: existence_starts_and_ends_during UBERON:0000108 ! blastula stage -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI -property_value: editor_note "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" xsd:string +intersection_of: RO:0002491 UBERON:0000108 ! existence starts and ends during blastula stage +relationship: RO:0002202 UBERON:0007010 ! develops from cleaving embryo +relationship: RO:0002491 UBERON:0000108 ! existence starts and ends during blastula stage +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Blastulation.png" xsd:anyURI +property_value: IAO:0000116 "TODO - check relationship with epiblast. Note in FMA this is not a subclass of embryo, but in uberon embryo is the whole organism from zygote onwards and thus includes the blastula" xsd:string [Term] id: UBERON:0000353 name: parenchyma namespace: uberon def: "Functional part of an organ in the body. This is in contrast to the stroma, which refers to the structural tissue of organs, being exactly, connective tissues." [Wikipedia:Parenchyma] -xref: BTO:0000999 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} -xref: BTO:0001539 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: EHDAA:3015 xref: EHDAA:3905 xref: EHDAA:3999 @@ -8707,10 +8582,7 @@ xref: Wikipedia:Parenchyma is_a: UBERON:0000064 ! organ part disjoint_from: UBERON:0003891 ! stroma relationship: capable_of GO:0032501 ! multicellular organismal process -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: UBPROP:0000007 "parenchymal" xsd:string -property_value: UBPROP:0000011 "Early in development the mammalian embryo has three distinct layers: ectoderm (external layer), endoderm (internal layer) and in between those two layers the middle layer or mesoderm. The parenchyma of most organs is of ectodermal (brain, skin) or endodermal origin (lungs, gastrointestinal tract, liver, pancreas). The parenchyma of a few organs (spleen, kidneys, heart) is of mesodermal origin. The stroma of all organs is of mesodermal origin" xsd:string {source="WP"} -property_value: UBPROP:0000012 "the FMA definition is more restrictive, and limits this to solid organs. This would seem to cause problems for the lung parenchyma, except FMA classifies Lung as solid rather than cavitated" xsd:string {external_ontology="FMA"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0000362 @@ -8745,16 +8617,15 @@ is_a: UBERON:0000958 ! medulla of organ intersection_of: UBERON:0000958 ! medulla of organ intersection_of: part_of UBERON:0002113 ! kidney relationship: capable_of_part_of GO:0070295 ! renal water absorption -relationship: contributes_to_morphology_of UBERON:0002113 ! kidney relationship: has_part UBERON:0004200 ! kidney pyramid relationship: part_of UBERON:0002113 ! kidney -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" xsd:anyURI -property_value: UBPROP:0000010 "The renal medulla is split up into a number of sections, known as the renal pyramids. Blood enters into the kidney via the renal artery, which then splits up to form the arcuate arterioles. The arcuate arterioles each in turn branch into interlobular arterioles, which finally reach the glomeruli. At the glomerulus the blood reaches a highly disfavourable pressure gradient and a large exchange surface area, which forces the serum portion of the blood out of the vessel into the renal tubules. Flow continues through the renal tubules, including the proximal tubule, the Loop of Henle, and finally leaves the kidney by means of the collecting duct, leading to the renal ureter. The renal medulla contains the structures of the nephrons responsible for maintaining the salt and water balance of the blood. The renal medulla is hypertonic to the filtrate in the nephron and aids in the reabsorption of water" xsd:string +relationship: RO:0002433 UBERON:0002113 ! contributes to morphology of kidney +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000383 @@ -8777,7 +8648,6 @@ xref: BILA:0000088 xref: BTO:0001369 xref: BTO:0001485 xref: EFO:0000801 -xref: EMAPA:35578 xref: FMA:72954 xref: MA:0002888 xref: MAT:0000025 @@ -8786,15 +8656,13 @@ xref: VSAO:0000033 xref: XAO:0004042 is_a: UBERON:0011216 ! organ system subdivision intersection_of: UBERON:0011216 ! organ system subdivision -intersection_of: composed_primarily_of UBERON:0001015 ! musculature +intersection_of: RO:0002473 UBERON:0001015 ! composed primarily of musculature relationship: capable_of GO:0003012 ! muscle system process -relationship: composed_primarily_of UBERON:0001015 ! musculature -relationship: never_in_taxon NCBITaxon:6040 -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: present_in_taxon NCBITaxon:9606 -property_value: editor_note "consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77" xsd:string -property_value: UBPROP:0000001 "Anatomical system that consists of the muscles of the body.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000033", ontology="VSAO", source="VSAO:curator"} -property_value: UBPROP:0000012 "we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA" xsd:string {external_ontology="MA"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002473 UBERON:0001015 ! composed primarily of musculature +property_value: IAO:0000116 "consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77" xsd:string +property_value: RO:0002161 NCBITaxon:6040 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000463 @@ -8816,7 +8684,6 @@ xref: CALOHA:TS-2101 xref: CARO:0000004 xref: EHDAA2:0003004 xref: EMAPA:35178 -xref: FBbt:00007019 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9669 xref: galen:BodySubstance xref: HAO:0000004 @@ -8829,11 +8696,11 @@ xref: VHOG:0001726 xref: XAO:0004001 xref: ZFA:0001487 is_a: UBERON:0000465 ! material anatomical entity -relationship: has_quality PATO:0002198 ! quality of a substance -relationship: part_of UBERON:0000468 {notes="this relationship may be too strong and may be weakened in future"} ! multicellular organism -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: part_of UBERON:0000468 ! multicellular organism +relationship: RO:0000086 PATO:0002198 ! has quality quality of a substance +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000464 @@ -8851,7 +8718,6 @@ xref: AEO:0000005 xref: BILA:0000005 xref: CARO:0000005 xref: EHDAA2:0003005 -xref: FBbt:00007017 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:5897 xref: HAO:0000005 xref: NCIT:C94478 @@ -8862,10 +8728,10 @@ xref: VHOG:0001728 xref: XAO:0003190 xref: ZFA:0001643 is_a: UBERON:0000466 ! immaterial anatomical entity -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -relationship: surrounded_by UBERON:0000061 ! anatomical structure +relationship: RO:0002219 UBERON:0000061 ! surrounded by anatomical structure +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000465 @@ -8879,7 +8745,6 @@ xref: AEO:0000006 xref: BILA:0000006 xref: CARO:0000006 xref: EHDAA2:0003006 -xref: FBbt:00007016 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67165 xref: HAO:0000006 xref: TAO:0001836 @@ -8888,9 +8753,9 @@ xref: VHOG:0001721 is_a: BFO:0000040 ! material entity is_a: UBERON:0001062 ! anatomical entity disjoint_from: UBERON:0000466 ! immaterial anatomical entity -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000466 @@ -8905,7 +8770,6 @@ xref: AEO:0000007 xref: BILA:0000007 xref: CARO:0000007 xref: EHDAA2:0003007 -xref: FBbt:00007015 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67112 xref: HAO:0000007 xref: TAO:0001835 @@ -8913,9 +8777,9 @@ xref: TGMA:0001827 xref: VHOG:0001727 is_a: BFO:0000141 ! immaterial entity is_a: UBERON:0001062 ! anatomical entity -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000467 @@ -8943,11 +8807,9 @@ xref: EHDAA2:0003011 xref: EHDAA:392 xref: EMAPA:16103 xref: EV:0100000 -xref: FBbt:00004856 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7149 xref: galen:AnatomicalSystem xref: HAO:0000011 -xref: IDOMAL:0002460 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: MA:0000003 xref: NCIT:C12919 xref: SCTID:278195005 @@ -8963,11 +8825,11 @@ xref: ZFA:0001439 is_a: UBERON:0000061 ! anatomical structure relationship: has_part UBERON:0000062 ! organ relationship: part_of UBERON:0000468 ! multicellular organism -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -relationship: present_in_taxon NCBITaxon:9606 -relationship: seeAlso EHDAA2:0001330 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:9606 +property_value: seeAlso EHDAA2:0001330 [Term] id: UBERON:0000468 @@ -8998,7 +8860,6 @@ xref: EHDAA2:0003191 xref: EHDAA:1 xref: EMAPA:25765 xref: EV:0100016 -xref: FBbt:00000001 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:256135 xref: galen:Organism xref: HAO:0000012 @@ -9014,11 +8875,10 @@ xref: Wikipedia:Multi-cellular_organism xref: XAO:0003004 xref: ZFA:0001094 is_a: UBERON:0010000 ! multicellular anatomical structure -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: editor_note "TODO - split body and mc organism? body continues after death stage" xsd:string -property_value: UBPROP:0000007 "organismal" xsd:string +property_value: IAO:0000116 "TODO - split body and mc organism? body continues after death stage" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000471 @@ -9039,7 +8899,6 @@ xref: XAO:0003039 xref: ZFA:0001489 is_a: UBERON:0000481 ! multi-tissue structure relationship: part_of UBERON:0003103 ! compound organ -property_value: IAO:0000232 "this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future" xsd:string [Term] id: UBERON:0000475 @@ -9064,7 +8923,6 @@ xref: CARO:0000032 xref: EFO:0000808 xref: EHDAA2:0003032 xref: EMAPA:36031 -xref: FBbt:00007009 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7153 xref: galen:BodyPart xref: HAO:0000032 @@ -9082,10 +8940,10 @@ xref: XAO:0003013 xref: ZFA:0001308 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure relationship: part_of UBERON:0000468 ! multicellular organism -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: editor_note "Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency" xsd:string +property_value: IAO:0000116 "Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000476 @@ -9100,7 +8958,6 @@ xref: AEO:0000040 xref: BILA:0000040 xref: CARO:0000040 xref: EHDAA2:0003040 -xref: FBbt:00007013 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:63863 xref: HAO:0000040 xref: TAO:0000382 @@ -9109,9 +8966,9 @@ xref: XAO:0003162 xref: ZFA:0000382 is_a: UBERON:0000061 ! anatomical structure disjoint_from: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000477 @@ -9120,12 +8977,11 @@ namespace: uberon def: "Anatomical group whose component anatomical structures lie in close proximity to each other." [FBbt:00007277] subset: common_anatomy subset: upper_level -xref: FBbt:00007277 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: VHOG:0001737 is_a: UBERON:0034923 ! disconnected anatomical group -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000479 @@ -9147,7 +9003,6 @@ xref: CALOHA:TS-2090 xref: CARO:0000043 xref: EHDAA2:0003043 xref: EMAPA:35868 -xref: FBbt:00007003 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9637 xref: galen:Tissue xref: HAO:0000043 @@ -9164,10 +9019,10 @@ xref: ZFA:0001477 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure relationship: has_part GO:0031012 ! extracellular matrix relationship: part_of UBERON:0000468 ! multicellular organism -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: editor_note "changed label and definition to reflect CARO2" xsd:string +property_value: IAO:0000116 "changed label and definition to reflect CARO2" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000481 @@ -9182,7 +9037,6 @@ xref: AEO:0000055 xref: BILA:0000055 xref: CARO:0000055 xref: EHDAA2:0003055 -xref: FBbt:00007010 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: HAO:0000055 xref: TAO:0001488 xref: TGMA:0001847 @@ -9191,9 +9045,9 @@ xref: XAO:0003037 xref: ZFA:0001488 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure relationship: has_part UBERON:0000479 ! tissue -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0000483 @@ -9215,7 +9069,6 @@ xref: CALOHA:TS-0288 xref: CARO:0000066 xref: EHDAA2:0003066 xref: EMAPA:32738 -xref: FBbt:00007005 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:9639 xref: GAID:402 xref: HAO:0000066 @@ -9232,14 +9085,12 @@ xref: ZFA:0001486 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue -intersection_of: composed_primarily_of CL:0000066 ! epithelial cell -relationship: composed_primarily_of CL:0000066 ! epithelial cell +intersection_of: RO:0002473 CL:0000066 ! composed primarily of epithelial cell relationship: has_part GO:0005911 ! cell-cell junction relationship: has_part UBERON:0005769 ! basement membrane of epithelium -relationship: only_in_taxon NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! Metazoa -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI -property_value: UBPROP:0000003 "The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000387", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.59", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "epithelial" xsd:string +relationship: RO:0002160 NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! only in taxon Metazoa +relationship: RO:0002473 CL:0000066 ! composed primarily of epithelial cell +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI [Term] id: UBERON:0000485 @@ -9258,7 +9109,6 @@ xref: AEO:0000068 xref: BILA:0000068 xref: CARO:0000068 xref: EHDAA2_RETIRED:0003068 -xref: FBbt:00007027 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45567 xref: HAO:0000068 xref: NCIT:C33552 @@ -9270,7 +9120,7 @@ xref: XAO:0004008 xref: ZFA:0001496 is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0012274 ! columnar epithelium -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray1059.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray1059.png" xsd:anyURI [Term] id: UBERON:0000487 @@ -9299,8 +9149,7 @@ is_a: UBERON:0000490 ! unilaminar epithelium is_a: UBERON:0006914 ! squamous epithelium intersection_of: UBERON:0000490 ! unilaminar epithelium intersection_of: has_part CL:0000076 ! squamous epithelial cell -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Unilaminar epithelium that consists of a single layer of squamous cells.[CARO]" xsd:string {date_retrieved="2012-06-20", external_class="CARO:0000070", ontology="CARO", source="FMA:45565", source="http://orcid.org/0000-0001-9114-8737"} +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI [Term] id: UBERON:0000489 @@ -9327,7 +9176,6 @@ is_a: UBERON:0003103 ! compound organ intersection_of: UBERON:0003103 ! compound organ intersection_of: has_part UBERON:0002553 ! anatomical cavity relationship: has_part UBERON:0002553 ! anatomical cavity -property_value: IAO:0000232 "this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future" xsd:string [Term] id: UBERON:0000490 @@ -9352,8 +9200,7 @@ xref: UMLS:C0682574 {source="ncithesaurus:Simple_Epithelium"} xref: XAO:0004007 xref: ZFA:0001495 is_a: UBERON:0000483 ! epithelium -property_value: editor_note "consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable" xsd:string -property_value: UBPROP:0000001 "Epithelium that consists of a single layer of epithelial cells.[CARO]" xsd:string {date_retrieved="2012-06-20", external_class="CARO:0000073", ontology="CARO", source="FMA:45561", source="http://orcid.org/0000-0001-9114-8737"} +property_value: IAO:0000116 "consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable" xsd:string [Term] id: UBERON:0000915 @@ -9373,12 +9220,8 @@ xref: Wikipedia:Thorax is_a: UBERON:0009569 {source="FMA"} ! subdivision of trunk is_a: UBERON:0011676 ! subdivision of organism along main body axis intersection_of: UBERON:0011676 ! subdivision of organism along main body axis -intersection_of: has_skeleton UBERON:0014477 ! thoracic skeleton -relationship: has_skeleton UBERON:0014477 ! thoracic skeleton -property_value: IAO:0000232 "note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest" xsd:string -property_value: RO:0002171 UBERON:0000026 -property_value: RO:0002171 UBERON:0000033 -property_value: RO:0002171 UBERON:0002417 +intersection_of: RO:0002551 UBERON:0014477 ! has skeleton thoracic skeleton +relationship: RO:0002551 UBERON:0014477 ! has skeleton thoracic skeleton [Term] id: UBERON:0000916 @@ -9408,11 +9251,9 @@ xref: MIAA:0000298 xref: SCTID:302553009 xref: Wikipedia:Abdomen is_a: UBERON:0009569 ! subdivision of trunk -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0002417 {source="MA"} ! abdominal segment of trunk -property_value: editor_note "Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class" xsd:string -property_value: UBPROP:0000007 "abdominal" xsd:string -property_value: UBPROP:0000007 "celiac" xsd:string +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +property_value: IAO:0000116 "Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class" xsd:string [Term] id: UBERON:0000922 @@ -9437,11 +9278,9 @@ xref: EHDAA2:0000002 xref: EHDAA2_RETIRED:0003236 xref: EHDAA:38 xref: EMAPA:16039 -xref: FBbt:00000052 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69068 xref: GAID:963 xref: http://neurolex.org/wiki/Category\:Embryonic_organism -xref: IDOMAL:0000646 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: MAT:0000226 xref: MESH:D004622 xref: MIAA:0000019 @@ -9455,14 +9294,12 @@ xref: XAO:0000113 xref: ZFA:0000103 is_a: UBERON:0000468 ! multicellular organism intersection_of: UBERON:0000468 ! multicellular organism -intersection_of: existence_ends_with UBERON:0000068 ! embryo stage -intersection_of: existence_starts_with UBERON:0000068 ! embryo stage -relationship: existence_ends_with UBERON:0000068 ! embryo stage -relationship: existence_starts_with UBERON:0000068 ! embryo stage -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" xsd:anyURI +intersection_of: RO:0002489 UBERON:0000068 ! existence starts with embryo stage +intersection_of: RO:0002493 UBERON:0000068 ! existence ends with embryo stage +relationship: RO:0002489 UBERON:0000068 ! existence starts with embryo stage +relationship: RO:0002493 UBERON:0000068 ! existence ends with embryo stage +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/2d/Wrinkledfrog_embryos.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/503" xsd:anyURI -property_value: UBPROP:0000007 "embryonic" xsd:string -property_value: UBPROP:0000012 "Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo" xsd:string {external_ontology="ZFA"} [Term] id: UBERON:0000923 @@ -9481,7 +9318,6 @@ xref: AAO:0000480 xref: BILA:0000035 xref: BTO:0000556 xref: EMAPA:36033 -xref: FBbt:00000110 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69069 xref: GAID:1303 xref: MESH:D005855 @@ -9495,8 +9331,7 @@ xref: Wikipedia:Germ_layer xref: XAO:0003011 xref: ZFA:0001122 is_a: UBERON:0010316 ! germ layer / neural crest -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001223", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0000924 @@ -9516,7 +9351,6 @@ xref: EFO:0000414 xref: EHDAA2:0000428 xref: EMAPA:16069 xref: EV:0100003 -xref: FBbt:00000111 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69070 xref: GAID:1304 xref: MAT:0000155 @@ -9533,11 +9367,8 @@ xref: XAO:0000001 xref: ZFA:0000016 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000221 ! ectodermal cell -relationship: immediate_transformation_of UBERON:0006601 {source="Bgee:AN"} ! presumptive ectoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png" xsd:anyURI -property_value: UBPROP:0000001 "Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000137", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000153", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "ectodermal" xsd:string +relationship: RO:0002495 UBERON:0006601 {source="Bgee:AN"} ! immediate transformation of presumptive ectoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png" xsd:anyURI [Term] id: UBERON:0000925 @@ -9557,7 +9388,6 @@ xref: EFO:0002545 xref: EHDAA2:0000436 xref: EMAPA:16062 xref: EV:0100005 -xref: FBbt:00000125 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69071 xref: GAID:1305 xref: MAT:0000175 @@ -9573,11 +9403,9 @@ xref: XAO:0000090 xref: ZFA:0000017 is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000223 ! endodermal cell -relationship: immediate_transformation_of UBERON:0006595 {source="Bgee:AN"} ! presumptive endoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png" xsd:anyURI -property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000154", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "endodermal" xsd:string +relationship: RO:0002495 UBERON:0006595 {source="Bgee:AN"} ! immediate transformation of presumptive endoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png" xsd:anyURI [Term] id: UBERON:0000926 @@ -9603,7 +9431,6 @@ xref: EHDAA:160 xref: EHDAA:183 xref: EMAPA:16083 xref: EV:0100006 -xref: FBbt:00000126 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69072 xref: GAID:522 xref: MAT:0000174 @@ -9617,15 +9444,11 @@ xref: VHOG:0000152 xref: Wikipedia:Mesoderm xref: XAO:0000050 xref: ZFA:0000041 -is_a: UBERON:0000923 {notes="sometimes not considered primary"} ! germ layer +is_a: UBERON:0000923 ! germ layer relationship: has_part CL:0000222 ! mesodermal cell -relationship: immediate_transformation_of UBERON:0006603 {source="Bgee:AN"} ! presumptive mesoderm -relationship: never_in_taxon NCBITaxon:6040 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" xsd:anyURI -property_value: UBPROP:0000001 "Primary germ layer that is the middle of the embryonic germ layers.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000304", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000152", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "mesodermal" xsd:string -property_value: UBPROP:0000008 "sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates" xsd:string {source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} +relationship: RO:0002495 UBERON:0006603 {source="Bgee:AN"} ! immediate transformation of presumptive mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png" xsd:anyURI +property_value: RO:0002161 NCBITaxon:6040 [Term] id: UBERON:0000930 @@ -9647,7 +9470,6 @@ synonym: "stomodeal-hypophyseal primordium" BROAD [XAO:0000269] xref: BTO:0004224 xref: EHDAA2:0001929 xref: EMAPA:16263 -xref: FBbt:00000439 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:295846 xref: NCIT:C34306 xref: TAO:0001290 @@ -9657,15 +9479,11 @@ xref: Wikipedia:Stomodeum xref: XAO:0000269 xref: ZFA:0001290 is_a: UBERON:0013522 ! subdivision of tube -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000924 ! ectoderm relationship: part_of UBERON:0035804 ! future mouth -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI -property_value: editor_note "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" xsd:string -property_value: UBPROP:0000001 "Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001290", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx" xsd:string {source="MP:0012522", taxon="NCBITaxon:40674"} -property_value: UBPROP:0000007 "stomodeal" xsd:string -property_value: UBPROP:0000008 "This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity." xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI +property_value: IAO:0000116 "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" xsd:string [Term] id: UBERON:0000931 @@ -9681,7 +9499,6 @@ synonym: "proctodaeum" EXACT [] xref: AAO:0011087 xref: EHDAA2:0000121 xref: EMAPA:25038 -xref: FBbt:00000123 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: NCIT:C34278 xref: TAO:0000066 xref: UMLS:C0231054 {source="ncithesaurus:Proctodeum"} @@ -9690,16 +9507,13 @@ xref: Wikipedia:Proctodeum xref: XAO:0001019 xref: ZFA:0000066 is_a: UBERON:0016566 {source="EHDAA2"} ! pit -relationship: develops_from UBERON:0000924 ! ectoderm -relationship: has_potential_to_develop_into UBERON:0001353 ! anal region -relationship: located_in UBERON:0012469 {source="EHDAA2"} ! external anal region -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0007026 ! presumptive gut -property_value: editor_note "removed WBbt:0006795 'proctodeum' - junction between the alimentary and genital tracts in the male." xsd:string +relationship: RO:0001025 UBERON:0012469 {source="EHDAA2"} ! located in external anal region +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002202 UBERON:0000924 ! develops from ectoderm +relationship: RO:0002387 UBERON:0001353 ! has potential to develop into anal region +property_value: IAO:0000116 "removed WBbt:0006795 'proctodeum' - junction between the alimentary and genital tracts in the male." xsd:string property_value: seeAlso "https://github.com/obophenotype/uberon/issues/685" xsd:anyURI -property_value: UBPROP:0000001 "An inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000066", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011087", ontology="AAO", source="ZFA:0000066"} -property_value: UBPROP:0000007 "proctodeal" xsd:string [Term] id: UBERON:0000948 @@ -9748,22 +9562,17 @@ is_a: UBERON:0007100 ! primary circulatory organ is_a: UBERON:0010314 ! structure with developmental contribution from neural crest intersection_of: UBERON:0007100 ! primary circulatory organ intersection_of: has_part UBERON:0004151 ! cardiac chamber -relationship: contributes_to_morphology_of UBERON:0004535 ! cardiovascular system -relationship: develops_from UBERON:0004141 ! heart tube relationship: has_part UBERON:0004151 ! cardiac chamber -relationship: never_in_taxon NCBITaxon:6239 -relationship: never_in_taxon NCBITaxon:7227 -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0015410 {source="MA"} ! heart plus pericardium -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI -property_value: UBPROP:0000001 "Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000114", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010210", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000002 "relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010210", ontology="AAO"} -property_value: UBPROP:0000003 "As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000276", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "cardiac" xsd:string +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002202 UBERON:0004141 ! develops from heart tube +relationship: RO:0002433 UBERON:0004535 ! contributes to morphology of cardiovascular system +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.0/VH_F_Heart.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI +property_value: RO:0002161 NCBITaxon:6239 +property_value: RO:0002161 NCBITaxon:7227 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000957 @@ -9777,11 +9586,10 @@ synonym: "laminar tissue" EXACT [] xref: Wikipedia:Lamina_of_the_vertebral_arch is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue -intersection_of: has_quality PATO:0002124 ! laminar -relationship: has_quality PATO:0002124 ! laminar -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/80/Laminaarcusvertebrae.png" xsd:anyURI -property_value: editor_note "TODO - merge with cell layer?" xsd:string -property_value: UBPROP:0000007 "laminar" xsd:string +intersection_of: RO:0000086 PATO:0002124 ! has quality laminar +relationship: RO:0000086 PATO:0002124 ! has quality laminar +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/80/Laminaarcusvertebrae.png" xsd:anyURI +property_value: IAO:0000116 "TODO - merge with cell layer?" xsd:string [Term] id: UBERON:0000958 @@ -9793,10 +9601,8 @@ synonym: "medulla" EXACT [FMA:61108] xref: FMA:61108 xref: galen:Medulla is_a: UBERON:0000471 ! compound organ component -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: surrounded_by UBERON:0001851 ! cortex -property_value: IAO:0000232 "this class is used in a very general sense" xsd:string -property_value: UBPROP:0000007 "medullary" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002219 UBERON:0001851 ! surrounded by cortex [Term] id: UBERON:0000982 @@ -9835,10 +9641,8 @@ xref: Wikipedia:Joint xref: XAO:0000171 xref: ZFA:0001596 is_a: UBERON:0004905 ! articulation -relationship: connects UBERON:0004765 ! skeletal element -relationship: contributes_to_morphology_of UBERON:0001434 ! skeletal system -property_value: UBPROP:0000001 "Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000101", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000367", ontology="TAO", source="TAO:pem"} +relationship: RO:0002176 UBERON:0004765 ! connects skeletal element +relationship: RO:0002433 UBERON:0001434 ! contributes to morphology of skeletal system [Term] id: UBERON:0000990 @@ -9869,13 +9673,11 @@ xref: EHDAA2:0001603 xref: EHDAA:5923 xref: EMAPA:17381 xref: EV:0100100 -xref: FBbt:00004857 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7160 xref: GAID:363 xref: HAO:0000374 xref: HAO:0000895 xref: MA:0000326 -xref: MESH:D005835 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: MIAA:0000305 xref: NCIT:C12841 xref: SCTID:278875001 @@ -9897,15 +9699,12 @@ disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:8450002 ! excretory system relationship: capable_of_part_of GO:0000003 ! reproduction -relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: has_part UBERON:0000991 ! gonad -relationship: present_in_taxon NCBITaxon:9606 -property_value: dcterms-date "2022-06-10T18:22:34Z" xsd:dateTime -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/52/Penis.svg" xsd:anyURI -property_value: editor_note "consider splitting genitalia from reproductive system" xsd:string -property_value: UBPROP:0000001 "Anatomical system which consists of organs and tissues associated with sexual reproduction of the organism.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010258", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "Arguably, one of the most important aspects of urbilaterian organogenesis would have been gonadogenesis, since Urbilateria must have successfully generated gametes and developed a strategy for extrusion and fertilization, in order to be the ancestor of all living Bilateria.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000182", ontology="VHOG", source="PMID:21672850 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across Bilateria. Integrative and Comparative Biology (2007)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000202 FMA:75572 +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +property_value: http://purl.org/dc/terms/date "2022-06-10T18:22:34Z" xsd:dateTime +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/52/Penis.svg" xsd:anyURI +property_value: IAO:0000116 "consider splitting genitalia from reproductive system" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000991 @@ -9924,7 +9723,6 @@ xref: BILA:0000123 xref: BSA:0000079 xref: BTO:0000534 xref: EMAPA:17383 -xref: FBbt:00004858 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:18250 xref: GAID:368 xref: HAO:0000379 @@ -9942,14 +9740,9 @@ xref: ZFA:0000413 is_a: UBERON:0003133 ! reproductive organ intersection_of: UBERON:0003133 ! reproductive organ intersection_of: has_part CL:0000586 ! germ cell -relationship: contains_process GO:0007276 ! gamete generation -relationship: develops_from UBERON:0005564 ! gonad primordium +relationship: BFO:0000067 GO:0007276 ! contains process gamete generation relationship: has_part CL:0000586 ! germ cell -property_value: UBPROP:0000001 "Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000213", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000413", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000397", ontology="VHOG", source="DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T, Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "gonadal" xsd:string -property_value: UBPROP:0000012 "FMA xref is a 'general anatomical term'" xsd:string {external_ontology="FMA"} +relationship: RO:0002202 UBERON:0005564 ! develops from gonad primordium [Term] id: UBERON:0001007 @@ -9970,8 +9763,6 @@ xref: BILA:0000082 xref: BTO:0000058 xref: CALOHA:TS-1293 xref: EFO:0000793 -xref: EV:0100056 -xref: FBbt:00005055 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7152 xref: GAID:278 xref: galen:DigestiveSystem @@ -9997,11 +9788,8 @@ disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:8450002 ! excretory system relationship: capable_of GO:0022600 ! digestive system process -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000129", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000007 "digestive" xsd:string -property_value: UBPROP:0000012 "many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class" xsd:string {external_ontology="MA"} +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001008 @@ -10031,7 +9819,6 @@ xref: EHDAA2:0001601 xref: EHDAA:5901 xref: EMAPA:17366 xref: EV:0100095 -xref: FBbt:00005056 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7159 xref: GAID:391 xref: galen:UrinaryTract @@ -10053,15 +9840,11 @@ is_a: UBERON:8450002 ! excretory system intersection_of: UBERON:8450002 ! excretory system intersection_of: capable_of GO:0097254 ! renal tubular secretion relationship: capable_of GO:0097254 ! renal tubular secretion -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: never_in_taxon NCBITaxon:110815 {source="Wikipedia"} -relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010257", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "Evolution of vertebrate renal anatomy appears quite conservative when compared, for example, to evolution of respiratory and cardiovascular systems in vertebrates. Major anatomical changes in vertebrates kidneys separate those of birds and mammals from kidneys of lower vertebrates. General increase in animal size from fish to mammals is reflected by an increase in total number of nephrons per kidney, rather than by constant change in tubular dimensions.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000723", ontology="VHOG", source="ISBN:978-3540428541 Kapoor BG, Bhavna Khanna, Ichthyology Handbook (2004) p.406", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels" xsd:string {source="GO"} -property_value: UBPROP:0000008 "This definition is inclusive of the organs of the vertebrate renal system, as well as the Malpighian tubules of insects, and allows for future incorporation of structures such as the antennal glands of crustaceans" xsd:string {source="DOI:10.1371/journal.pone.0099864"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +property_value: RO:0002161 NCBITaxon:110815 {source="Wikipedia"} +property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001009 @@ -10073,7 +9856,6 @@ subset: uberon_slim synonym: "systema cardiovasculare" RELATED OMO:0003011 [Wikipedia:Circulatory_system] xref: AAO:0000959 xref: CALOHA:TS-2103 -xref: MESH:D002319 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: VHOG:0001248 xref: Wikipedia:Circulatory_system is_a: UBERON:0000467 ! anatomical system @@ -10083,17 +9865,13 @@ disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:8450002 ! excretory system relationship: capable_of GO:0003013 ! circulatory system process -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} -relationship: never_in_taxon NCBITaxon:6073 -relationship: never_in_taxon NCBITaxon:6157 -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI -property_value: IAO:0000232 "the cardiovascular system and the lymphatic system are parts of the circulatory system" xsd:string -property_value: RO:0002174 NCBITaxon:6231 {notes="WBbt coelomocyte currently classified as circulating cell"} -property_value: UBPROP:0000001 "Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000959", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001248", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.493", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} +property_value: RO:0002161 NCBITaxon:6073 +property_value: RO:0002161 NCBITaxon:6157 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001015 @@ -10113,10 +9891,8 @@ synonym: "musculature system" RELATED [] synonym: "musculi" EXACT OMO:0003011 [FMA:32558, FMA:TA] synonym: "set of muscles" EXACT [FMA:32558] synonym: "set of skeletal muscles" EXACT [MA:0000165] -xref: AAO:0011066 xref: BTO:0000887 xref: EFO:0001949 -xref: EMAPA:32715 xref: EMAPA:35577 xref: FMA:32558 xref: MA:0000165 @@ -10128,11 +9904,9 @@ xref: WBbt:0005737 xref: Wikipedia:Muscular_system xref: ZFA:0000548 is_a: UBERON:0011216 ! organ system subdivision -relationship: composed_primarily_of UBERON:0001630 ! muscle organ relationship: part_of UBERON:0000383 ! musculature of body -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png" xsd:anyURI -property_value: RO:0002171 UBERON:0001474 -property_value: UBPROP:0000012 "In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here." xsd:string {external_ontology="FMA"} +relationship: RO:0002473 UBERON:0001630 ! composed primarily of muscle organ +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e5/Muscles_anterior_labeled.png" xsd:anyURI [Term] id: UBERON:0001016 @@ -10158,7 +9932,6 @@ xref: EHDAA2:0001246 xref: EHDAA:826 xref: EMAPA:16469 xref: EV:0100162 -xref: FBbt:00005093 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:7157 xref: GAID:466 xref: MA:0000016 @@ -10181,20 +9954,15 @@ disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:8450002 ! excretory system relationship: capable_of GO:0050877 ! nervous system process -relationship: composed_primarily_of CL:0002319 ! neural cell -relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: has_part CL:0000540 ! neuron -relationship: immediate_transformation_of UBERON:0016880 {source="Bgee:AN"} ! future nervous system -relationship: never_in_taxon NCBITaxon:6040 -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI -property_value: UBPROP:0000001 "A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000396", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000324", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000402", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.117", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "nervous" xsd:string -property_value: UBPROP:0000007 "neural" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002473 CL:0002319 ! composed primarily of neural cell +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage +relationship: RO:0002495 UBERON:0016880 {source="Bgee:AN"} ! immediate transformation of future nervous system +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI +property_value: RO:0002161 NCBITaxon:6040 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001017 @@ -10223,7 +9991,6 @@ xref: EHDAA:828 xref: EMAPA:16470 xref: EMAPA:16754 xref: EV:0100163 -xref: FBbt:00005094 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:55675 xref: GAID:570 xref: MA:0000167 @@ -10240,15 +10007,11 @@ xref: XAO:0000215 xref: ZFA:0000012 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0011216 {source="FBbt", source="cjm"} ! organ system subdivision -relationship: immediate_transformation_of UBERON:0016879 {source="Bgee:AN"} ! future central nervous system -relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0001016 ! nervous system -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "Part of the nervous system which includes the brain and spinal cord.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000090", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "The brain and spinal cord. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000012", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO)." xsd:string {source="BIRNLEX:1099"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000293", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 (reference 1), ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 (reference 2), DOI:10.1016/j.cell.2007.02.040 Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud'homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007) (reference 3)", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002495 UBERON:0016879 {source="Bgee:AN"} ! immediate transformation of future central nervous system +property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001041 @@ -10266,7 +10029,6 @@ xref: BTO:0000507 xref: EHDAA2:0000557 xref: EHDAA:520 xref: EMAPA:16548 -xref: FBbt:00005379 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45616 xref: MA:0001526 xref: NCIT:C34180 @@ -10277,10 +10039,8 @@ xref: VHOG:0000285 xref: Wikipedia:Foregut xref: XAO:0000232 is_a: UBERON:0004921 ! subdivision of digestive tract -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/9a/Gray27.png" xsd:anyURI -property_value: editor_note "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. In vertebrates the term may refer to a developmental structure" xsd:string -property_value: UBPROP:0000001 "The anterior portion of the primitive digestive tube of the embryo that lies cephalic to the junction of the yolk stalk, consists of endodermal tissue, and gives rise to the the pharynx, lower respiratory system, esophagus, stomach, duodenum proximal to the biliary tract, liver, pancreas, biliary tract, and gall bladder." xsd:string {source="MP:0000474"} -property_value: UBPROP:0000003 "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000285", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11", source="http://bgee.unil.ch/"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/9a/Gray27.png" xsd:anyURI +property_value: IAO:0000116 "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. In vertebrates the term may refer to a developmental structure" xsd:string [Term] id: UBERON:0001045 @@ -10298,7 +10058,6 @@ xref: EFO:0001950 xref: EHDAA2:0001185 xref: EHDAA:983 xref: EMAPA:16255 -xref: FBbt:00005383 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45617 xref: MA:0001564 xref: NCIT:C34210 @@ -10310,11 +10069,8 @@ xref: Wikipedia:Midgut xref: XAO:0000103 is_a: UBERON:0004921 ! subdivision of digestive tract relationship: proximally_connected_to UBERON:0001041 ! foregut -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/3d/Illu_small_intestine.jpg" xsd:anyURI -property_value: editor_note "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. We may explicitly make this a developmental class" xsd:string -property_value: UBPROP:0000003 "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000290", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "In humans: originates from the foregut at the opening of the bile duct into the duodenum and continues through the small intestine and much of the large intestine until the transition to the hindgut about two-thirds of the way through the transverse colon" xsd:string {source="WP"} -property_value: UBPROP:0000012 "in FMA this represents an embryonic region." xsd:string {external_ontology="FMA"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/3d/Illu_small_intestine.jpg" xsd:anyURI +property_value: IAO:0000116 "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. We may explicitly make this a developmental class" xsd:string [Term] id: UBERON:0001046 @@ -10331,7 +10087,6 @@ xref: BTO:0000510 xref: EHDAA2:0000779 xref: EHDAA:975 xref: EMAPA:16715 -xref: FBbt:00005384 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45618 xref: MA:0001527 xref: NCIT:C34188 @@ -10342,13 +10097,10 @@ xref: VHOG:0000459 xref: Wikipedia:Hindgut xref: XAO:0000104 is_a: UBERON:0004921 ! subdivision of digestive tract -relationship: develops_from UBERON:0003104 {source="Wikipedia"} ! mesenchyme relationship: proximally_connected_to UBERON:0001045 ! midgut -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray472.png" xsd:anyURI -property_value: editor_note "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future (vertebrates have some contribution from NC - https://github.com/obophenotype/uberon/wiki/The-neural-crest). We may explicitly make this a developmental class" xsd:string -property_value: UBPROP:0000001 "the caudal portion of the primitive digestive tube of the embryo" xsd:string {source="MP:0008786"} -property_value: UBPROP:0000003 "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000459", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "in FMA this class has no children. In MA it has a single child hindgut epithelium" xsd:string {external_ontology="FMA"} +relationship: RO:0002202 UBERON:0003104 {source="Wikipedia"} ! develops from mesenchyme +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray472.png" xsd:anyURI +property_value: IAO:0000116 "Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future (vertebrates have some contribution from NC - https://github.com/obophenotype/uberon/wiki/The-neural-crest). We may explicitly make this a developmental class" xsd:string [Term] id: UBERON:0001048 @@ -10367,7 +10119,6 @@ xref: AEO:0000171 xref: BTO:0001886 xref: EFO:0001652 xref: EHDAA2:0003171 -xref: FBbt:00005495 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:86589 xref: MAT:0000482 xref: NCIT:C34275 @@ -10399,7 +10150,6 @@ xref: EMAPA:16164 xref: EMAPA:16757 xref: FMA:293882 xref: MAT:0000069 -xref: MESH:D054259 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: MIAA:0000069 xref: NCIT:C34226 xref: neuronames:1365 @@ -10414,12 +10164,8 @@ is_a: UBERON:0003914 {source="EHDAA2"} ! epithelial tube is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0016879 ! future central nervous system -relationship: develops_from UBERON:0005068 ! neural rod -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010617", ontology="AAO", source="AAO:JOR"} -property_value: UBPROP:0000001 "The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000307", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/neural+tube"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000307", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000011 "The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium" xsd:string {source="GO:0021915"} +relationship: RO:0002202 UBERON:0005068 ! develops from neural rod +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0001062 @@ -10435,7 +10181,6 @@ xref: BILA:0000000 xref: BIRNLEX:6 xref: CARO:0000000 xref: EHDAA2:0002229 -xref: FBbt:10000000 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:62955 xref: HAO:0000000 xref: MA:0000001 @@ -10446,9 +10191,9 @@ xref: UMLS:C1515976 {source="ncithesaurus:Anatomic_Structure_System_or_Substance xref: WBbt:0000100 xref: XAO:0000000 xref: ZFA:0100000 -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0001072 @@ -10481,13 +10226,11 @@ xref: Wikipedia:Inferior_vena_cava xref: XAO:0000388 is_a: UBERON:0004087 ! vena cava intersection_of: UBERON:0004087 ! vena cava -intersection_of: drains UBERON:0000154 ! posterior region of body -relationship: connected_to UBERON:0002078 ! right cardiac atrium -relationship: drains UBERON:0000154 ! posterior region of body -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray577.png" xsd:anyURI -property_value: UBPROP:0000001 "Trunk of systemic vein which is formed by the union of the right common iliac vein and the left common iliac vein and terminates in the right atrium[FMA]." xsd:string {source="FMA:10951"} -property_value: UBPROP:0000003 "Phylogenetic modifications within this basic pattern of arteries and veins are largely correlated with functional changes. In the transition from water to land, gills gave way to lungs, accompanied by the establishment of a pulmonary circulation. In some fishes and certainly in tetrapods, the cardinal veins become less involved in blood return. Instead, the composite, prominent postcava (posterior vena cava) arose to drain the posterior part of the body and the precava (anterior vena cava) developed to drain the anterior part of the body.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001194", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.454-455", source="http://bgee.unil.ch/"} +intersection_of: RO:0002179 UBERON:0000154 ! drains posterior region of body +relationship: RO:0002170 UBERON:0002078 ! connected to right cardiac atrium +relationship: RO:0002179 UBERON:0000154 ! drains posterior region of body +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/4/4d/Gray577.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001088 @@ -10516,7 +10259,6 @@ is_a: UBERON:0000174 ! excreta intersection_of: UBERON:0000174 ! excreta intersection_of: produced_by UBERON:0002113 ! kidney relationship: produced_by UBERON:0002113 ! kidney -property_value: UBPROP:0000008 "kidney excreta from some taxa (e.g. in aves) may not be liquid" xsd:string [Term] id: UBERON:0001140 @@ -10545,15 +10287,13 @@ xref: UMLS:C0035092 {source="ncithesaurus:Renal_Vein"} xref: Wikipedia:Renal_vein is_a: UBERON:0001638 ! vein intersection_of: UBERON:0001638 ! vein -intersection_of: drains UBERON:0002113 ! kidney -relationship: drains UBERON:0002113 ! kidney -relationship: present_in_taxon NCBITaxon:9606 -relationship: tributary_of UBERON:0001072 ! posterior vena cava -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI -property_value: UBPROP:0000001 "The renal veins are veins that drain the kidney. They connect the kidney to the inferior vena cava. It is usually singular to each kidney, except in the condition 'multiple renal veins'. It also divides into 2 divisions upon entering the kidney: the anterior branch which receives blood from the anterior portion of the kidney and, the posterior branch which receives blood from the posterior portion. Often, each renal vein will have a branch that receives blood from the ureter. [WP,unvetted][Wikipedia:Renal_vein]." xsd:string {source="Wikipedia:Renal_vein"} -property_value: UBPROP:0000012 "in EHDAA2, the renal vein is part of the kidney" xsd:string {external_ontology="EHDAA2"} +intersection_of: RO:0002179 UBERON:0002113 ! drains kidney +relationship: RO:0002179 UBERON:0002113 ! drains kidney +relationship: RO:0002376 UBERON:0001072 ! tributary of posterior vena cava +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/76/Gray1122.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001224 @@ -10585,12 +10325,12 @@ disjoint_from: UBERON:0002355 ! pelvic region of trunk relationship: channel_for UBERON:0001088 ! urine relationship: channels_from UBERON:0002113 ! kidney relationship: channels_into UBERON:0000056 ! ureter -relationship: continuous_with UBERON:0000056 {source="FMA"} ! ureter -relationship: contributes_to_morphology_of UBERON:0000056 ! ureter relationship: part_of UBERON:0002113 {source="MA"} ! kidney relationship: part_of UBERON:0036295 ! renal pelvis/ureter -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/c/c0/Illu_kidney2.jpg" xsd:anyURI +relationship: RO:0002150 UBERON:0000056 {source="FMA"} ! continuous with ureter +relationship: RO:0002433 UBERON:0000056 ! contributes to morphology of ureter +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/c/c0/Illu_kidney2.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001225 @@ -10618,15 +10358,14 @@ xref: Wikipedia:Renal_cortex is_a: UBERON:0001851 ! cortex intersection_of: UBERON:0001851 ! cortex intersection_of: part_of UBERON:0002113 ! kidney -relationship: contributes_to_morphology_of UBERON:0002113 ! kidney relationship: part_of UBERON:0008987 {source="FMA"} ! renal parenchyma -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" xsd:anyURI -property_value: UBPROP:0000010 "In the adult metanephros, it forms a continuous smooth outer zone with a number of projections that extend down between the pyramids. It contains the renal corpuscles and the renal tubules except for parts of the loop of Henle which descend into the renal medulla. It also contains blood vessels and cortical collecting ducts. The renal cortex is the part of the kidney where ultrafiltration occurs.[WP]" xsd:string +relationship: RO:0002433 UBERON:0002113 ! contributes to morphology of kidney +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001229 @@ -10659,15 +10398,12 @@ xref: VHOG:0001262 xref: Wikipedia:Renal_corpuscle xref: ZFA:0005281 is_a: UBERON:0000063 ! organ subunit -relationship: contributes_to_morphology_of UBERON:0001225 ! cortex of kidney -relationship: contributes_to_morphology_of UBERON:0001285 ! nephron relationship: part_of UBERON:0001225 ! cortex of kidney relationship: part_of UBERON:0001285 {source="MA", source="ZFA"} ! nephron -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg" xsd:anyURI -property_value: UBPROP:0000001 "A mass of arterial capillaries enveloped in a capsule and attached to a tubule in the kidney[BTO]" xsd:string {date_retrieved="2012-11-28", external_class="BTO:0000333", ontology="BTO", source="BTO:curator"} -property_value: UBPROP:0000001 "A tuft of capillaries found in a Bowman's capsule in which waste products are filtered from the blood and urine formation is initiated. Paired highly vascularized structures of the pronephros, responsible for blood filtration.[XAO]" xsd:string {date_retrieved="2012-11-28", external_class="XAO:0000146", ontology="XAO", source="XAO:curator"} -property_value: UBPROP:0000001 "The part of the nephron that filters blood.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005281", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002433 UBERON:0001225 ! contributes to morphology of cortex of kidney +relationship: RO:0002433 UBERON:0001285 ! contributes to morphology of nephron +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001230 @@ -10705,13 +10441,10 @@ xref: ZFA:0005254 xref: ZFA:0005310 is_a: UBERON:0000064 ! organ part relationship: capable_of_part_of GO:0003094 {source="Wikipedia"} ! glomerular filtration -relationship: contributes_to_morphology_of UBERON:0001229 ! renal corpuscle -relationship: develops_from UBERON:0004199 ! S-shaped body relationship: part_of UBERON:0001229 ! renal corpuscle -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg" xsd:anyURI -property_value: UBPROP:0000001 "Anatomical structure found in the kidney consisting of an expanded end of a kidney tubule surrounding a glomerulus and is the major site of filtration.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010526", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000009 "Fluids from blood in the glomerulus are collected in the Bowman's capsule and further processed along the nephron to form urine. This process is known as ultrafiltration[WP]." xsd:string -property_value: UBPROP:0000011 "One fold of the S-shaped body gives rise to Bowman's capsule[GUDMAP]" xsd:string +relationship: RO:0002202 UBERON:0004199 ! develops from S-shaped body +relationship: RO:0002433 UBERON:0001229 ! contributes to morphology of renal corpuscle +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg" xsd:anyURI [Term] id: UBERON:0001231 @@ -10747,11 +10480,10 @@ is_a: UBERON:0004211 ! nephron epithelium is_a: UBERON:0009773 {source="GO"} ! renal tubule intersection_of: UBERON:0003914 {source="GO", source="MA", source="ZFA"} ! epithelial tube intersection_of: part_of UBERON:0001285 {source="GO", source="MA", source="ZFA"} ! nephron -relationship: contributes_to_morphology_of UBERON:0001285 ! nephron -relationship: develops_from UBERON:0003918 {notes="checkme"} ! kidney mesenchyme relationship: has_part CL:0005009 {source="ZFA"} ! renal principal cell -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000012 "note that in ISBN:0073040584 (Vertebrates, Kardong), the uriniferous tubule contains the nephron, so we have a separate class, rather than using a synonym, as in MA" xsd:string {external_ontology="MA"} +relationship: RO:0002202 UBERON:0003918 ! develops from kidney mesenchyme +relationship: RO:0002433 UBERON:0001285 ! contributes to morphology of nephron +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001232 @@ -10786,12 +10518,10 @@ xref: TAO:0005294 xref: Wikipedia:Collecting_tubule xref: ZFA:0005294 is_a: UBERON:0006555 ! excretory tube -relationship: contributes_to_morphology_of UBERON:0002113 ! kidney -relationship: part_of UBERON:0001285 {notes="checkme", source="GO"} ! nephron +relationship: part_of UBERON:0001285 ! nephron relationship: part_of UBERON:0004100 ! renal collecting system -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "Renal duct that collects the output from renal tubules.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005294", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000012 "in ISBN:0073040584 (Vertebrates, Kardong), the nephron is adjacent to the collecting tubule, consistent with FMA, but not GO. Wikipedia says: Many sources include the connecting tubule as part of the collecting duct system. However, the embryological origin is more similar to the nephron than it is to the rest of the collecting duct (which derives from the ureteric bud), and other sources therefore classify the connecting tubule with the nephron" xsd:string {external_ontology="FMA"} +relationship: RO:0002433 UBERON:0002113 ! contributes to morphology of kidney +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001245 @@ -10808,7 +10538,6 @@ synonym: "proctodeum" RELATED [] xref: BTO:0001680 xref: CALOHA:TS-2005 xref: EV:0100082 -xref: FBbt:00047153 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:15711 xref: GAID:312 xref: galen:Anus @@ -10822,16 +10551,11 @@ xref: WBbt:0005364 xref: Wikipedia:Anus is_a: UBERON:0000161 ! orifice is_a: UBERON:0004121 ! ectoderm-derived structure -intersection_of: UBERON:0000161 ! orifice -intersection_of: distalmost_part_of UBERON:0001555 ! digestive tract -relationship: develops_from UBERON:0000931 ! proctodeum -relationship: distalmost_part_of UBERON:0001555 ! digestive tract relationship: part_of UBERON:0001555 ! digestive tract -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/65/Protovsdeuterostomes.svg" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/75/Anorectum.gif" xsd:anyURI -property_value: UBPROP:0000007 "anal" xsd:string -property_value: UBPROP:0000008 "In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html" xsd:string +relationship: RO:0002202 UBERON:0000931 ! develops from proctodeum +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/65/Protovsdeuterostomes.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/75/Anorectum.gif" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001255 @@ -10872,18 +10596,12 @@ xref: XAO:0000154 is_a: UBERON:0002075 ! viscus is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0018707 {source="BTO"} ! bladder organ -relationship: develops_from UBERON:0000164 {notes="upper part of UG sinus"} ! primitive urogenital sinus -relationship: never_in_taxon NCBITaxon:8782 {editor="https://orcid.org/0000-0003-3308-6245", id="GOTAX:0010073", source="https://github.com/obophenotype/uberon/issues/454"} relationship: part_of UBERON:0001556 {source="FMA"} ! lower urinary tract -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Urinary_Bladder.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urinary_Bladder.glb" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg" xsd:anyURI -property_value: UBPROP:0000001 "A saccular organ in which urine accumulates before discharge from the body. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000740", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000001 "Anatomical structure which consists of a membranous sac used to temporarily store urine until it is excreted from the body.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000623", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "In tetrapods, the urinary bladder arises as an outpocketing of the cloaca. (...) The tetrapod urinary bladder appears first among amphibians and is present in Sphenodon, turtles, most lizards, ostriches among birds, and all mammals.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000740", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.577-78", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "vesical" xsd:string -property_value: UBPROP:0000008 "The urinary bladder evolved in tetrapods. Birds to not possess a true urinary bladder, although Palaeognathae have an undifferentiated cloacal outpocketing that serves a similar function[https://github.com/obophenotype/uberon/issues/454]" xsd:string +relationship: RO:0002202 UBERON:0000164 ! develops from primitive urogenital sinus +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Urinary_Bladder.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urinary_Bladder.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001271 @@ -10905,12 +10623,9 @@ is_a: UBERON:0015212 ! lateral structure intersection_of: UBERON:0007823 ! appendage girdle region intersection_of: part_of UBERON:0010709 ! pelvic complex disjoint_from: UBERON:0007832 ! pelvic girdle skeleton -relationship: has_skeleton UBERON:0007832 ! pelvic girdle skeleton -relationship: in_lateral_side_of UBERON:0002355 ! pelvic region of trunk relationship: part_of UBERON:0002355 ! pelvic region of trunk relationship: part_of UBERON:0010709 ! pelvic complex -property_value: IAO:0000232 "this class describes the subdivision of the limb/fin, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831). See also comments on obo-anatomy mail list. Note that even though the class includes soft tissue it is more restrictive than 'pelvis' which also includes structures in cavities etc. TODO this needs to be better documented" xsd:string -property_value: UBPROP:0000001 "Subdivision of lower limb or fin which links the limb/fin to the body[FMA,modified]. There is only one instance of the pelvic girdle region per organism.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000304", ontology="VSAO", source="https://orcid.org/0000-0002-6601-2165"} +relationship: RO:0002551 UBERON:0007832 ! has skeleton pelvic girdle skeleton [Term] id: UBERON:0001285 @@ -10940,15 +10655,13 @@ xref: UMLS:C0027713 {source="ncithesaurus:Nephron"} xref: Wikipedia:Nephron xref: ZFA:0005282 is_a: UBERON:0000064 ! organ part -relationship: contributes_to_morphology_of UBERON:0002113 ! kidney -relationship: develops_from UBERON:0004208 {evidence="definitional"} ! nephrogenic mesenchyme -relationship: immediate_transformation_of UBERON:0010532 {source="Bgee:AN"} ! primitive nephron relationship: part_of UBERON:0007684 {source="FMA"} ! uriniferous tubule -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI -property_value: editor_note "kidney terms require review for cross-vertebrate compatibility and developmental relationships." xsd:string -property_value: UBPROP:0000001 "Functional unit of the kidney that filters waste.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002153", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000008 "In the avian kidney, three types of nephron are identified: mammalian-type nephrons with long and short loops of Henle, and reptilian type nephrons (Gambaryan, 1992)" xsd:string {source="GO"} +relationship: RO:0002202 UBERON:0004208 ! develops from nephrogenic mesenchyme +relationship: RO:0002433 UBERON:0002113 ! contributes to morphology of kidney +relationship: RO:0002495 UBERON:0010532 {source="Bgee:AN"} ! immediate transformation of primitive nephron +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: IAO:0000116 "kidney terms require review for cross-vertebrate compatibility and developmental relationships." xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001287 @@ -10981,13 +10694,12 @@ xref: ZFA:0005290 is_a: UBERON:0006534 {source="MA"} ! renal convoluted tubule is_a: UBERON:0006853 ! renal cortex tubule is_a: UBERON:0012275 ! meso-epithelium -relationship: continuous_with UBERON:0001230 {source="GO"} ! glomerular capsule -relationship: continuous_with UBERON:0001290 ! proximal straight tubule -relationship: contributes_to_morphology_of UBERON:0001231 ! nephron tubule -relationship: develops_from UBERON:0003220 {source="Wikipedia"} ! metanephric mesenchyme -relationship: part_of UBERON:0004134 {notes="MA uses subclass", source="GOC:mtg_kidney_jan10"} ! proximal tubule -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI -property_value: UBPROP:0000001 "Renal tubule that connects to the renal corpuscle.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005290", ontology="TAO", source="ZFIN:curator"} +relationship: part_of UBERON:0004134 ! proximal tubule +relationship: RO:0002150 UBERON:0001230 {source="GO"} ! continuous with glomerular capsule +relationship: RO:0002150 UBERON:0001290 ! continuous with proximal straight tubule +relationship: RO:0002202 UBERON:0003220 {source="Wikipedia"} ! develops from metanephric mesenchyme +relationship: RO:0002433 UBERON:0001231 ! contributes to morphology of nephron tubule +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI [Term] id: UBERON:0001288 @@ -11013,18 +10725,14 @@ xref: VHOG:0001270 xref: Wikipedia:Loop_of_Henle is_a: UBERON:0007685 ! region of nephron tubule intersection_of: UBERON:0007685 ! region of nephron tubule -intersection_of: continuous_with UBERON:0001287 ! proximal convoluted tubule -intersection_of: continuous_with UBERON:0001292 ! distal convoluted tubule -relationship: continuous_with UBERON:0001287 ! proximal convoluted tubule -relationship: continuous_with UBERON:0001292 ! distal convoluted tubule -relationship: contributes_to_morphology_of UBERON:0001231 ! nephron tubule -relationship: present_in_taxon NCBITaxon:8782 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI -property_value: editor_note "the definitions of some kidney parts (e.g. proximal straight tubule) refer to Henle's loop, even in species where this may not be present. Requires review." xsd:string -property_value: RO:0002174 NCBITaxon:8353 -property_value: UBPROP:0000001 "A highly specialized segment of the mammalian kidney tubules, that dips into the medulla. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, p.648, see_Liem_KF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001270", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "The structure differs considerably between species; there is a definite physical loop of Henle in the mammalian and avian renal systems but this seems to be absent in Xenopus. However, homologs of some, but not all, molecular markers (e.g. cldn8 and clcnk) of the mammalian loop of Henle were found to be present in the pronephros of the frog larva ." xsd:string {source="DOI:10.1371/journal.pone.0099864"} -property_value: UBPROP:0000009 "The loop of Henle plays an important role in creating a concentration gradient in the medulla of the kidney. It is involved in reabsorption of filtered water and ions including sodium, potassium and calcium, and independently regulates both the volume and osmolarity of body fluids." xsd:string {source="DOI:10.1371/journal.pone.0099864"} +intersection_of: RO:0002150 UBERON:0001287 ! continuous with proximal convoluted tubule +intersection_of: RO:0002150 UBERON:0001292 ! continuous with distal convoluted tubule +relationship: RO:0002150 UBERON:0001287 ! continuous with proximal convoluted tubule +relationship: RO:0002150 UBERON:0001292 ! continuous with distal convoluted tubule +relationship: RO:0002433 UBERON:0001231 ! contributes to morphology of nephron tubule +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: IAO:0000116 "the definitions of some kidney parts (e.g. proximal straight tubule) refer to Henle's loop, even in species where this may not be present. Requires review." xsd:string +property_value: RO:0002175 NCBITaxon:8782 [Term] id: UBERON:0001289 @@ -11045,10 +10753,10 @@ xref: SCTID:245350001 xref: UMLS:C0227657 {source="ncithesaurus:Descending_Limb_of_the_Henle_s_Loop"} xref: Wikipedia:Descending_limb_of_loop_of_henle is_a: UBERON:0007685 {source="FMA"} ! region of nephron tubule -relationship: contributes_to_morphology_of UBERON:0001288 ! loop of Henle relationship: part_of UBERON:0001288 {source="FMA"} ! loop of Henle -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +relationship: RO:0002433 UBERON:0001288 ! contributes to morphology of loop of Henle +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001290 @@ -11076,14 +10784,13 @@ xref: Wikipedia:Proximal_straight_tubule xref: ZFA:0005291 is_a: UBERON:0006853 ! renal cortex tubule is_a: UBERON:0009035 {source="MA"} ! renal straight tubule -relationship: continuous_with UBERON:0001287 ! proximal convoluted tubule -relationship: continuous_with UBERON:0005096 ! descending thin limb relationship: part_of UBERON:0001289 {source="MA"} ! descending limb of loop of Henle -relationship: part_of UBERON:0004134 {notes="MA uses subclass", source="GOC:mtg_kidney_jan10"} ! proximal tubule +relationship: part_of UBERON:0004134 ! proximal tubule relationship: part_of UBERON:0006542 {source="MA"} ! outer medulla outer stripe loop of Henle -relationship: present_in_taxon NCBITaxon:9606 -property_value: editor_note "TODO - is S3 exactly coincident with PST? todo - ensure relationships work across species (loop of Henle)" xsd:string -property_value: UBPROP:0000001 "Portion of the renal tubule which is just posterior to the proximal convoluted tubule.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005291", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002150 UBERON:0001287 ! continuous with proximal convoluted tubule +relationship: RO:0002150 UBERON:0005096 ! continuous with descending thin limb +property_value: IAO:0000116 "TODO - is S3 exactly coincident with PST? todo - ensure relationships work across species (loop of Henle)" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001292 @@ -11109,13 +10816,11 @@ xref: Wikipedia:Distal_convoluted_tubule is_a: UBERON:0006534 {source="MA"} ! renal convoluted tubule is_a: UBERON:0006853 ! renal cortex tubule is_a: UBERON:0012275 ! meso-epithelium -relationship: contributes_to_morphology_of UBERON:0001231 ! nephron tubule -relationship: develops_from UBERON:0003220 ! metanephric mesenchyme relationship: part_of UBERON:0004135 {source="EMAPA", source="GO", source="MA-modified-from-isa"} ! distal tubule -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/2/21/Kidney_nephron.png" xsd:anyURI -property_value: UBPROP:0000001 "a portion of kidney nephron between the loop of Henle and the collecting duct system[Wikipedia:Distal_convoluted_tubule]." xsd:string {source="Wikipedia:Distal_convoluted_tubule"} -property_value: UBPROP:0000009 "in humans it is responsible for the reabsorption of about 5% of filtered sodium via the thiazide-sensitive Na-Cl symporter." xsd:string +relationship: RO:0002202 UBERON:0003220 ! develops from metanephric mesenchyme +relationship: RO:0002433 UBERON:0001231 ! contributes to morphology of nephron tubule +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/2/21/Kidney_nephron.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001293 @@ -11137,8 +10842,8 @@ xref: EMAPA:28310 xref: FMA:17733 xref: MA:0001653 is_a: UBERON:0000064 ! organ part -relationship: contributes_to_morphology_of UBERON:0000362 ! renal medulla relationship: part_of UBERON:0000362 ! renal medulla +relationship: RO:0002433 UBERON:0000362 ! contributes to morphology of renal medulla [Term] id: UBERON:0001353 @@ -11163,11 +10868,10 @@ xref: UMLS:C0230120 {source="ncithesaurus:Anal_Region"} xref: VHOG:0000395 xref: WBbt:0006919 is_a: UBERON:0000475 ! organism subdivision -relationship: has_developmental_contribution_from UBERON:0000931 {evidence="cjm"} ! proctodeum relationship: overlaps UBERON:0006866 ! terminal part of digestive tract -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray408.png" xsd:anyURI +relationship: RO:0002254 UBERON:0000931 ! has developmental contribution from proctodeum +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray408.png" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/507" xsd:anyURI -property_value: UBPROP:0000003 "Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000395", ontology="VHOG", source="ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11", source="http://bgee.unil.ch/"} [Term] id: UBERON:0001434 @@ -11203,18 +10907,11 @@ intersection_of: has_part UBERON:0004770 ! articular system disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:8450002 ! excretory system -relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: has_part UBERON:0004288 ! skeleton relationship: has_part UBERON:0004770 ! articular system relationship: part_of UBERON:0002204 ! musculoskeletal system -property_value: RO:0002171 UBERON:0001016 +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/The-skeletal-system" xsd:anyURI -property_value: UBPROP:0000001 "Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000434", ontology="TAO", source="TAO:wd"} -property_value: UBPROP:0000001 "Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000027", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "System that provides physical support to the organism.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000566", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000003 "By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001254", ontology="VHOG", source="DOI:10.1159/000324245 Donoghue PCJ, Sansom IJ, Origin and early evolution of vertebrate skeletonization. Microscopy research and technique (2002)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "skeletal" xsd:string -property_value: UBPROP:0000012 "GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates" xsd:string {external_ontology="GO"} [Term] id: UBERON:0001552 @@ -11232,10 +10929,10 @@ xref: MA:0002583 xref: Wikipedia:Arcuate_arteries_of_the_kidney is_a: UBERON:0001637 ! artery is_a: UBERON:0003644 ! kidney arterial blood vessel -relationship: connecting_branch_of UBERON:0009885 ! interlobar artery relationship: part_of UBERON:0001225 {source="MA"} ! cortex of kidney -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/87/2610_The_Kidney.jpg" xsd:anyURI +relationship: RO:0002252 UBERON:0009885 ! connecting branch of interlobar artery +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/87/2610_The_Kidney.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001555 @@ -11259,11 +10956,9 @@ xref: BTO:0000545 xref: EHDAA2:0000726 xref: EHDAA:518 xref: EMAPA:16247 -xref: FBbt:00003125 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:45615 xref: galen:AlimentaryTract xref: MA:0000917 -xref: MESH:D041981 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: NCIT:C34082 xref: TAO:0000112 xref: TGMA:0001819 @@ -11272,18 +10967,13 @@ xref: VHOG:0000309 xref: WBbt:0005743 xref: ZFA:0000112 is_a: UBERON:0000025 ! tube -relationship: connects UBERON:0000165 ! mouth -relationship: immediate_transformation_of UBERON:0007026 {source="NCBIBook:NBK10107"} ! presumptive gut -relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} -relationship: never_in_taxon NCBITaxon:41324 {source="DOI:10.1371/journal.pone.0016309"} -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0001007 ! digestive system -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "The alimentary or digestive tract, and associated organs.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000112", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000309", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "FMA also has a term 'gastrointestinal tract', but this includes the liver." xsd:string {external_ontology="FMA"} -property_value: UBPROP:0000012 "we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509" xsd:string {external_ontology="MA"} -property_value: UBPROP:0000013 "we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002176 UBERON:0000165 ! connects mouth +relationship: RO:0002495 UBERON:0007026 {source="NCBIBook:NBK10107"} ! immediate transformation of presumptive gut +property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} +property_value: RO:0002161 NCBITaxon:41324 {source="DOI:10.1371/journal.pone.0016309"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001556 @@ -11301,7 +10991,7 @@ is_a: UBERON:0011216 ! organ system subdivision relationship: has_part UBERON:0000057 ! urethra relationship: has_part UBERON:0001255 ! urinary bladder relationship: part_of UBERON:0001008 ! renal system -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001630 @@ -11313,8 +11003,6 @@ subset: pheno_slim subset: uberon_slim subset: vertebrate_core synonym: "muscle" BROAD [ZFA:0005145] -xref: AAO:0011066 -xref: EMAPA:32715 xref: EMAPA:37474 {source="MA:th"} xref: EV:0100146 xref: FMA:5022 @@ -11329,12 +11017,9 @@ xref: ZFA:0005145 is_a: UBERON:0000062 ! organ is_a: UBERON:0005090 ! muscle structure intersection_of: UBERON:0000062 ! organ -intersection_of: composed_primarily_of UBERON:0002385 ! muscle tissue -relationship: composed_primarily_of UBERON:0002385 ! muscle tissue +intersection_of: RO:0002473 UBERON:0002385 ! composed primarily of muscle tissue relationship: part_of UBERON:0001015 ! musculature -property_value: UBPROP:0000001 "Portion of tissue composed of contractile fibers.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005145", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001245", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.75", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "muscular" xsd:string +relationship: RO:0002473 UBERON:0002385 ! composed primarily of muscle tissue [Term] id: UBERON:0001637 @@ -11355,7 +11040,6 @@ xref: AEO:0000208 xref: BTO:0000573 xref: CALOHA:TS-0054 xref: EFO:0000814 -xref: EHDAA2:0000143 xref: EHDAA2:0003253 xref: EMAPA:35147 xref: EV:0100026 @@ -11376,12 +11060,7 @@ xref: XAO:0000114 xref: ZFA:0000005 is_a: UBERON:0003509 ! arterial blood vessel relationship: channels_from UBERON:0000948 ! heart -property_value: editor_note "Note that in FMA an artery is a tree, whereas AEO/JB defines it as a tube; FMA includes a separate class for what it calls the trunk. Classification in this ontology may currently (Jan 2012) represent a mix of both schemes, although we are gradually revising in the direction of the AEO scheme." xsd:string -property_value: UBPROP:0000001 "Part of the circulatory system composed of blood vessels which carry oxygenated blood away from the heart to the rest of the body.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010211", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001251", ontology="VHOG", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "arterial" xsd:string -property_value: UBPROP:0000012 "Some arthropods have primitive arterial systems but this term refers to arteries in a true closed circulatory system." xsd:string -property_value: UBPROP:0000202 FMA:63812 +property_value: IAO:0000116 "Note that in FMA an artery is a tree, whereas AEO/JB defines it as a tube; FMA includes a separate class for what it calls the trunk. Classification in this ontology may currently (Jan 2012) represent a mix of both schemes, although we are gradually revising in the direction of the AEO scheme." xsd:string [Term] id: UBERON:0001638 @@ -11426,12 +11105,8 @@ intersection_of: UBERON:0003920 ! venous blood vessel intersection_of: channel_for UBERON:0013756 ! venous blood relationship: channel_for UBERON:0013756 ! venous blood relationship: channels_from UBERON:0001982 ! capillary -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/c2/Venous_system_en.svg" xsd:anyURI -property_value: editor_note "TODO - check with MA - vein vs venous blood vessel" xsd:string -property_value: UBPROP:0000001 "Part of the circulatory system composed of blood vessels which carry blood from other organs, tissues, and cells to the heart.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010212", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001743", ontology="VHOG", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "venous" xsd:string -property_value: UBPROP:0000202 FMA:63814 +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/c2/Venous_system_en.svg" xsd:anyURI +property_value: IAO:0000116 "TODO - check with MA - vein vs venous blood vessel" xsd:string [Term] id: UBERON:0001851 @@ -11450,8 +11125,6 @@ xref: galen:Cortex xref: Wikipedia:Cortex_(anatomy) is_a: UBERON:0000064 ! organ part relationship: bounding_layer_of UBERON:0000062 ! organ -property_value: UBPROP:0000007 "cortical" xsd:string -property_value: UBPROP:0000012 "this class is used more generically than in FMA, and includes e.g. cortex of hair" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0001969 @@ -11482,12 +11155,12 @@ is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000179 ! haemolymphatic fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: has_part GO:0005577 ! fibrinogen complex -intersection_of: has_quality PATO:0001548 ! quality of a liquid intersection_of: part_of UBERON:0000178 ! blood -intersection_of: surrounds CL:0000232 ! erythrocyte +intersection_of: RO:0000086 PATO:0001548 ! has quality quality of a liquid +intersection_of: RO:0002221 CL:0000232 ! surrounds erythrocyte relationship: has_part GO:0005577 ! fibrinogen complex relationship: part_of UBERON:0000178 ! blood -relationship: surrounds CL:0000232 ! erythrocyte +relationship: RO:0002221 CL:0000232 ! surrounds erythrocyte [Term] id: UBERON:0001979 @@ -11513,11 +11186,10 @@ xref: Wikipedia:Venule xref: ZFA:0005315 is_a: UBERON:0003920 ! venous blood vessel is_a: UBERON:8410081 ! blood microvessel -relationship: connects UBERON:0001638 ! vein -relationship: connects UBERON:0001982 ! capillary -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/d/da/Illu_capillary.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Multi-tissue structure part of the blood vasculature formed by the anastomosis of capillaries. Venules carry blood toward the heart.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005315", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002176 UBERON:0001638 ! connects vein +relationship: RO:0002176 UBERON:0001982 ! connects capillary +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/da/Illu_capillary.jpg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001980 @@ -11544,14 +11216,12 @@ xref: ZFA:0005255 is_a: UBERON:0003509 {source="MA"} ! arterial blood vessel is_a: UBERON:8410081 ! blood microvessel intersection_of: UBERON:0001981 ! blood vessel -intersection_of: connects UBERON:0001637 ! artery -intersection_of: connects UBERON:0001982 ! capillary -relationship: connects UBERON:0001637 ! artery -relationship: connects UBERON:0001982 ! capillary -relationship: contributes_to_morphology_of UBERON:0001637 ! artery -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/d/da/Illu_capillary.jpg" xsd:anyURI -property_value: UBPROP:0000001 "Multi-tissue structure part of the blood vasculature, feeds into capillaries. Arterioles carry blood away from the heart.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0002138", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Small, terminal branch of an artery which generally connects to capillaries.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010253", ontology="AAO", source="AAO:BJB"} +intersection_of: RO:0002176 UBERON:0001637 ! connects artery +intersection_of: RO:0002176 UBERON:0001982 ! connects capillary +relationship: RO:0002176 UBERON:0001637 ! connects artery +relationship: RO:0002176 UBERON:0001982 ! connects capillary +relationship: RO:0002433 UBERON:0001637 ! contributes to morphology of artery +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/d/da/Illu_capillary.jpg" xsd:anyURI [Term] id: UBERON:0001981 @@ -11593,22 +11263,18 @@ xref: XAO:0001011 xref: ZFA:0005314 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000055 ! vessel +is_a: UBERON:0004120 ! mesoderm-derived structure relationship: capable_of_part_of GO:0008015 ! blood circulation relationship: channel_for UBERON:0000178 ! blood -relationship: develops_from UBERON:0004872 ! splanchnic layer of lateral plate mesoderm -relationship: develops_from UBERON:0006965 {source="GO:0072360"} ! vascular cord relationship: has_part CL:0000071 {source="AEO"} ! blood vessel endothelial cell relationship: has_part UBERON:0007500 {source="EHDAA2"} ! epithelial tube open at both ends -relationship: has_quality PATO:0002045 ! dendritic relationship: part_of UBERON:0004537 ! blood vasculature -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI -property_value: editor_note "consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus" xsd:string -property_value: UBPROP:0000001 "Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001250", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000001 "Any of the vessels through which blood circulates in the body.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011004", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001250", ontology="VHOG", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000008 "annelids have blood vessels, but this class is not applicable to annelids." xsd:string -property_value: UBPROP:0000012 "FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX" xsd:string {external_ontology="FMA"} +relationship: RO:0000086 PATO:0002045 ! has quality dendritic +relationship: RO:0002202 UBERON:0004872 ! develops from splanchnic layer of lateral plate mesoderm +relationship: RO:0002202 UBERON:0006965 {source="GO:0072360"} ! develops from vascular cord +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: IAO:0000116 "consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001982 @@ -11641,17 +11307,14 @@ xref: XAO:0000116 xref: ZFA:0005250 is_a: UBERON:8410081 ! blood microvessel intersection_of: UBERON:8410081 ! blood microvessel -intersection_of: connects UBERON:0001979 ! venule -intersection_of: connects UBERON:0001980 ! arteriole -relationship: connects UBERON:0001979 ! venule -relationship: connects UBERON:0001980 ! arteriole -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/A_red_blood_cell_in_a_capillary,_pancreatic_tissue_-_TEM.jpg" xsd:anyURI -property_value: editor_note "not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element" xsd:string +intersection_of: RO:0002176 UBERON:0001979 ! connects venule +intersection_of: RO:0002176 UBERON:0001980 ! connects arteriole +relationship: RO:0002176 UBERON:0001979 ! connects venule +relationship: RO:0002176 UBERON:0001980 ! connects arteriole +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/2f/A_red_blood_cell_in_a_capillary,_pancreatic_tissue_-_TEM.jpg" xsd:anyURI +property_value: IAO:0000116 "not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element" xsd:string +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/uberon/issues/2186" xsd:string -property_value: UBPROP:0000001 "Any of the tiny blood vessels connecting the arterioles to the venules.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010252", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001253", ontology="VHOG", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000010 "capillaries lack tunica media and tunica adventitia; only the endothelial wall of the tunica intima belongs" xsd:string [Term] id: UBERON:0001986 @@ -11675,11 +11338,10 @@ xref: UMLS:C0014257 {source="ncithesaurus:Endothelium"} is_a: UBERON:0000487 {source="FMA-text-def", source="https://github.com/obophenotype/uberon/issues/225"} ! simple squamous epithelium is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0000483 ! epithelium -intersection_of: composed_primarily_of CL:0000115 ! endothelial cell -relationship: composed_primarily_of CL:0000115 ! endothelial cell -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000007 "endothelial" xsd:string +intersection_of: RO:0002473 CL:0000115 ! composed primarily of endothelial cell +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002473 CL:0000115 ! composed primarily of endothelial cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002049 @@ -11696,13 +11358,12 @@ xref: FMA:69050 xref: TAO:0005249 xref: ZFA:0005249 is_a: UBERON:0000477 {source="FMA"} ! anatomical cluster -relationship: composed_primarily_of UBERON:0000055 ! vessel relationship: has_part UBERON:0000179 ! haemolymphatic fluid relationship: part_of UBERON:0007798 ! vascular system -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI -property_value: editor_note "see also: vascular system. Consider merging?" xsd:string -property_value: UBPROP:0000007 "vascular" xsd:string +relationship: RO:0002473 UBERON:0000055 ! composed primarily of vessel +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI +property_value: IAO:0000116 "see also: vascular system. Consider merging?" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002050 @@ -11722,7 +11383,6 @@ xref: BILA:0000034 xref: BTO:0000174 xref: CALOHA:TS-2110 xref: EFO:0000461 -xref: FBbt:00004208 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:69067 xref: GAID:407 xref: MESH:D004628 @@ -11738,10 +11398,6 @@ is_a: UBERON:0005423 ! developing anatomical structure intersection_of: UBERON:0005423 ! developing anatomical structure intersection_of: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0000922 ! embryo -property_value: UBPROP:0000001 "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000138", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001105", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000178", ontology="VSAO", source="ZFIN:curator"} -property_value: UBPROP:0000012 "in FMA embryo is_a embryonic structure" xsd:string {external_ontology="FMA"} [Term] id: UBERON:0002075 @@ -11772,10 +11428,8 @@ xref: Wikipedia:Viscus xref: XAO:0003034 is_a: UBERON:0005177 ! trunk region element intersection_of: UBERON:0000062 ! organ -intersection_of: located_in UBERON:0002323 ! coelemic cavity lumen -relationship: located_in UBERON:0002323 ! coelemic cavity lumen -property_value: UBPROP:0000001 "An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010386", ontology="AAO", source="BTO:0001491"} -property_value: UBPROP:0000012 "general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs." xsd:string {external_ontology="FMA"} +intersection_of: RO:0001025 UBERON:0002323 ! located in coelemic cavity lumen +relationship: RO:0001025 UBERON:0002323 ! located in coelemic cavity lumen [Term] id: UBERON:0002078 @@ -11806,16 +11460,11 @@ xref: Wikipedia:Right_atrium xref: XAO:0003192 is_a: UBERON:0002081 ! cardiac atrium is_a: UBERON:0035554 ! right cardiac chamber -intersection_of: UBERON:0002081 ! cardiac atrium -intersection_of: in_right_side_of UBERON:0000948 ! heart -relationship: connected_to UBERON:0004537 ! blood vasculature -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI -property_value: UBPROP:0000001 "Right cardiac chamber which is continuous with the superior vena cava and inferior vena cava.[FMA]" xsd:string {source="FMA:7096"} -property_value: UBPROP:0000003 "The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000328", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000006 "https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern" xsd:anyURI +relationship: RO:0002170 UBERON:0004537 ! connected to blood vasculature +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/20/Diagram_of_the_human_heart_%28cropped%29.svg" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002081 @@ -11853,13 +11502,9 @@ xref: UMLS:C0018792 {source="ncithesaurus:Cardiac_Atrium"} xref: VHOG:0000175 xref: Wikipedia:Heart_atrium xref: ZFA:0000471 -is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004151 ! cardiac chamber -relationship: contributes_to_morphology_of UBERON:0000948 ! heart -relationship: immediate_transformation_of UBERON:0010227 ! future cardiac atrium -property_value: UBPROP:0000001 "One of four heart chambers.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000471", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "One of two chambers of the heart which receive blood from the veins and forces it by muscular contration to the ventricle.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010246", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000003 "In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000175", ontology="VHOG", source="ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.428", source="http://bgee.unil.ch/"} +relationship: RO:0002433 UBERON:0000948 ! contributes to morphology of heart +relationship: RO:0002495 UBERON:0010227 ! immediate transformation of future cardiac atrium [Term] id: UBERON:0002090 @@ -11877,12 +11522,10 @@ xref: AAO:0000034 xref: EFO:0000942 xref: EHDAA2:0000161 xref: EHDAA:5049 -xref: EMAPA:17214 xref: EMAPA:37721 {source="MA:th"} xref: FMA:71221 xref: MA:0002986 xref: MAT:0000148 -xref: MESH:D013131 {mapping:provider="https://github.com/biopragmatics/biomappings", mapping:justification="https://w3id.org/semapv/vocab/LexicalMatching"} xref: MIAA:0000148 xref: TAO:0000317 xref: VHOG:0000317 @@ -11890,14 +11533,10 @@ xref: VSAO:0000093 xref: XAO:0003073 xref: ZFA:0000317 is_a: UBERON:0010912 ! subdivision of skeleton -relationship: develops_from UBERON:0003089 ! sclerotome relationship: part_of UBERON:0005944 ! axial skeleton plus cranial skeleton relationship: part_of UBERON:0011138 ! postcranial axial skeletal system +relationship: RO:0002202 UBERON:0003089 ! develops from sclerotome property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" xsd:anyURI -property_value: UBPROP:0000001 "Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000093", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000034", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000001 "The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000317", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000317", ontology="VHOG", source="DOI:10.1186/1742-9994-8-4 Schilling N, Evolution of the axial system in craniates: morphology and function of the perivertebral musculature. Frontiers in Zoology (2011)", source="http://bgee.unil.ch/"} [Term] id: UBERON:0002091 @@ -11923,22 +11562,17 @@ xref: MIAA:0000278 xref: NCIT:C49477 xref: SCTID:322050006 xref: UMLS:C0222646 {source="ncithesaurus:Appendicular_Skeleton"} -xref: VHOG:0001666 xref: VSAO:0000076 xref: Wikipedia:Appendicular_skeleton xref: XAO:0003166 is_a: UBERON:0010912 ! subdivision of skeleton -relationship: contributes_to_morphology_of UBERON:0001434 ! skeletal system -relationship: only_in_taxon NCBITaxon:7776 ! Gnathostomata relationship: overlaps UBERON:0000026 ! appendage relationship: part_of UBERON:0011249 ! appendicular skeletal system -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/7/7c/Appendicular_skeleton_diagram.svg" xsd:anyURI +relationship: RO:0002160 NCBITaxon:7776 ! only in taxon Gnathostomata +relationship: RO:0002433 UBERON:0001434 ! contributes to morphology of skeletal system +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/7/7c/Appendicular_skeleton_diagram.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton" xsd:anyURI -property_value: UBPROP:0000001 "Skeletal subdivision consisting of all the skeletal elements in the pectoral and pelvic appendage complexes.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000076", ontology="VSAO", source="PSPUB:0000170", source="https://orcid.org/0000-0002-6601-2165"} -property_value: UBPROP:0000001 "Skeletal system that consists of the paired fins (pectoral or pelvic fins).[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000027", ontology="TAO", source="TAO:wd"} -property_value: UBPROP:0000001 "The pectoral and pelvic girdles, which articulate with the axial skeleton, together with their associated limbs, the forelimbs and hind limbs, form the appendicular skeleton.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000747", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000012 "ontologies differ in whether they treat the term appendicular skeleton as being the entire set of bones in the limbs, or whether the fore and hind limbs/fins are treated as seperate appendicular skeletons. Here we follow FMA, and treat the appendicular skeleton as the sum total of skeletal elements in the organism (this is evidenced by the fact that in FMA, skeleton of left/right upper/lower limb is part_of a appendicular skeleton, and subtypes of 'subdivision of appendicular skeleton'). We have separate classes such as 'skeleton of limb', and 'skeleton of hindlimb' for the 4 parts of the appendicular skeleton. In future the ZFA/TAO classes may be moved." xsd:string {external_ontology="FMA"} [Term] id: UBERON:0002100 @@ -11974,16 +11608,12 @@ xref: XAO:0003025 xref: ZFA:0001115 is_a: UBERON:0011676 ! subdivision of organism along main body axis relationship: part_of UBERON:0013702 ! body proper -property_value: RO:0002171 UBERON:0000026 {exceptions="ZFA", source="https://github.com/obophenotype/uberon/issues/378", status="pending"} -property_value: RO:0002171 UBERON:0000033 -property_value: UBPROP:0000001 "Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010339", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001115", ontology="TAO", source="ZFIN:curator"} [Term] id: UBERON:0002113 name: kidney namespace: uberon -def: "A paired organ of the urinary tract which has the production of urine as its primary function." [http://anatomy.uams.edu/anatomyhtml/kidney.html, Wikipedia:Kidney] +def: "A paired organ of the urinary tract that produces urine and maintains bodily fluid homeostasis, blood pressure, pH levels, red blood cell production and skeleton mineralization." [http://anatomy.uams.edu/anatomyhtml/kidney.html, https://www.kidney.org/kidneydisease/top-5-jobs-kidneys-do, PMID:25140012, PMID:35003210, Wikipedia:Kidney] subset: efo_slim subset: human_reference_atlas subset: major_organ @@ -11995,35 +11625,25 @@ synonym: "reniculate kidney" NARROW SENSU [Wikipedia:Reniculate_kidney] xref: AAO:0000250 xref: BTO:0000671 xref: CALOHA:TS-0510 -xref: EFO:0000929 -xref: EMAPA:17373 -xref: EV:0100096 -xref: FMA:7203 xref: GAID:423 xref: galen:Kidney -xref: MA:0000368 xref: MAT:0000119 xref: MESH:D007668 xref: MIAA:0000119 -xref: NCIT:C12415 -xref: SCTID:181414000 xref: UMLS:C0022646 {source="ncithesaurus:Kidney"} xref: Wikipedia:Kidney xref: XAO:0003267 is_a: UBERON:0000489 ! cavitated compound organ is_a: UBERON:0005172 ! abdomen element is_a: UBERON:0015212 ! lateral structure -relationship: contributes_to_morphology_of UBERON:0001008 ! renal system -relationship: develops_from UBERON:0003918 {evidence="definitional"} ! kidney mesenchyme -relationship: develops_from UBERON:0005095 ! kidney rudiment -relationship: in_lateral_side_of UBERON:0000468 ! multicellular organism -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata relationship: part_of UBERON:0011143 {source="FMA"} ! upper urinary tract -relationship: present_in_taxon NCBITaxon:9606 -property_value: RO:0002171 UBERON:0000160 -property_value: UBPROP:0000001 "One of either of a pair of structures lying on either side of the dorsal aorta in which fluid balance is regulated and waste is excreted out in the form of urine.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000250", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000007 "renal" xsd:string -property_value: UBPROP:0000202 FMA:264815 +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002202 UBERON:0003918 ! develops from kidney mesenchyme +relationship: RO:0002202 UBERON:0005095 ! develops from kidney rudiment +relationship: RO:0002433 UBERON:0001008 ! contributes to morphology of renal system +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-7655-4833 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-2804-127X +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002120 @@ -12047,7 +11667,6 @@ xref: EHDAA:1017 xref: EMAPA:16579 xref: FMA:72170 xref: MAT:0000117 -xref: MESH:D060910 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: MIAA:0000117 xref: NCIT:C34280 xref: SCTID:308804007 @@ -12060,14 +11679,9 @@ xref: ZFA:0000151 is_a: UBERON:0002113 {source="GO"} ! kidney is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005423 ! developing anatomical structure -relationship: develops_from UBERON:0005721 {source="ZFA"} ! pronephric mesoderm -relationship: develops_from UBERON:0005754 ! rostral part of nephrogenic cord -relationship: located_in UBERON:0003887 {source="OG"} ! intraembryonic coelom -property_value: UBPROP:0000001 "A kidney formed of nephric tubules arising in the anterior region of the nephric ridge; forms only as a transient embryonic structure. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.748][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000037", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000001 "Organ that serves as a transient kidney, providing osmoregulation during early developmental stages and then degenerating during metamorphosis.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011089", ontology="AAO", source="XAO:curator"} -property_value: UBPROP:0000001 "The embryonic kidney, present at the level of the third somite, is composed of two glomeruli fused at the midline, two pronephric tubules, and paired bilateral pronephric ducts that modify the composition of the blood filtrate before delivering it to the cloaca for excretion.Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000151", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000037", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.637", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "pronephric" xsd:string +relationship: RO:0001025 UBERON:0003887 {source="OG"} ! located in intraembryonic coelom +relationship: RO:0002202 UBERON:0005721 {source="ZFA"} ! develops from pronephric mesoderm +relationship: RO:0002202 UBERON:0005754 ! develops from rostral part of nephrogenic cord [Term] id: UBERON:0002193 @@ -12083,7 +11697,7 @@ xref: EMAPA:18765 xref: FMA:74562 xref: MA:0000013 is_a: UBERON:0000467 {source="MA"} ! anatomical system -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria [Term] id: UBERON:0002201 @@ -12132,13 +11746,10 @@ is_a: UBERON:0000467 ! anatomical system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:8450002 ! excretory system relationship: capable_of_part_of GO:0040011 ! locomotion -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: has_developmental_contribution_from UBERON:0000926 {notes="check ctenophore"} ! mesoderm relationship: has_part UBERON:0000383 ! musculature of body relationship: has_part UBERON:0001434 ! skeletal system -property_value: UBPROP:0000001 "Anatomical system that provides locomotion and physical support to the organism.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010546", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001275", ontology="VHOG", source="DOI:10.1002/jez.b.21246 Shearman RM, Burke AC, The lateral somitic frontier in ontogeny and phylogeny. Journal of Experimental Zoology (2009)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "musculoskeletal" xsd:string +relationship: RO:0002254 UBERON:0000926 ! has developmental contribution from mesoderm +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage [Term] id: UBERON:0002224 @@ -12165,13 +11776,12 @@ xref: UMLS:C0230139 {source="ncithesaurus:Thoracic_Cavity"} xref: Wikipedia:Thoracic_cavity is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: luminal_space_of UBERON:0000915 ! thoracic segment of trunk intersection_of: part_of UBERON:0002323 ! coelemic cavity lumen -relationship: luminal_space_of UBERON:0000915 ! thoracic segment of trunk +intersection_of: RO:0002572 UBERON:0000915 ! luminal space of thoracic segment of trunk relationship: part_of UBERON:0002323 ! coelemic cavity lumen -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png" xsd:anyURI -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI -property_value: UBPROP:0000008 "In many species, the diaphragm separates thoracic and abdominal cavities" xsd:string +relationship: RO:0002572 UBERON:0000915 ! luminal space of thoracic segment of trunk +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/c/ce/Gray846.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Scheme_body_cavities-en.svg" xsd:anyURI [Term] id: UBERON:0002303 @@ -12200,7 +11810,7 @@ relationship: has_part CL:0000648 ! kidney granular cell relationship: has_part CL:0002173 ! extraglomerular mesangial cell relationship: has_part UBERON:0002335 ! macula densa relationship: part_of UBERON:0001225 {source="MA"} ! cortex of kidney -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002319 @@ -12211,7 +11821,6 @@ subset: human_reference_atlas subset: pheno_slim subset: uberon_slim xref: BTO:0002494 -xref: EMAPA:28248 xref: EMAPA:36561 {source="MA:th"} xref: FMA:84139 xref: MA:0002617 @@ -12219,17 +11828,16 @@ xref: NCIT:C33101 xref: UMLS:C0017655 {source="ncithesaurus:Mesangium"} xref: Wikipedia:Mesangium is_a: UBERON:0000119 ! cell layer +is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000119 ! cell layer -intersection_of: composed_primarily_of CL:0000650 ! mesangial cell -intersection_of: located_in UBERON:0005777 ! glomerular basement membrane -relationship: composed_primarily_of CL:0000650 ! mesangial cell -relationship: located_in UBERON:0005777 ! glomerular basement membrane +intersection_of: RO:0001025 UBERON:0005777 ! located in glomerular basement membrane +intersection_of: RO:0002473 CL:0000650 ! composed primarily of mesangial cell relationship: part_of UBERON:0000074 ! renal glomerulus relationship: part_of UBERON:0005215 ! kidney interstitium -relationship: present_in_taxon NCBITaxon:9606 -relationship: surrounds UBERON:0004212 ! glomerular capillary -property_value: UBPROP:0000007 "mesangial" xsd:string -property_value: UBPROP:0000012 "WP considers this the same as glomerular mesangium. In MA, glomerular and extraglomerular are distingsuished. FMA class has no definition and is a type of stroma, which is inconsistent with our classification of this here." xsd:string {external_ontology="MA"} +relationship: RO:0001025 UBERON:0005777 ! located in glomerular basement membrane +relationship: RO:0002221 UBERON:0004212 ! surrounds glomerular capillary +relationship: RO:0002473 CL:0000650 ! composed primarily of mesangial cell +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002321 @@ -12242,6 +11850,7 @@ xref: EMAPA:28278 xref: FMA:84141 xref: MA:0002602 is_a: UBERON:0003891 ! stroma +is_a: UBERON:0004120 ! mesoderm-derived structure relationship: overlaps UBERON:0000074 ! renal glomerulus relationship: part_of UBERON:0002303 {source="MA"} ! juxtaglomerular apparatus relationship: part_of UBERON:0002319 {source="MA"} ! mesangium @@ -12268,7 +11877,6 @@ synonym: "ventral body cavity" NARROW [NCBITaxon:7742] xref: AEO:0000186 xref: BTO:0001707 xref: EHDAA2:0000267 -xref: FBbt:00005060 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:85006 xref: galen:BodyCavity xref: NCIT:C25444 @@ -12278,11 +11886,8 @@ xref: TAO:0001438 xref: UMLS:C0333343 {source="ncithesaurus:Cavity"} xref: ZFA:0001438 is_a: UBERON:0002553 ! anatomical cavity -relationship: luminal_space_of UBERON:0011997 ! coelom -relationship: transformation_of UBERON:0003886 {evidence="definitional"} ! future coelemic cavity lumen -property_value: UBPROP:0000001 "Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]." xsd:string {date_retrieved="2012-09-12", external_class="ZFA:0001438", ontology="ZFA", source="ZFIN:curator"} -property_value: UBPROP:0000001 "The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]." xsd:string {date_retrieved="2012-09-12", external_class="BTO:0001707", ontology="BTO", source="BTO"} -property_value: UBPROP:0000008 "In mammals it forms the peritoneal, pleural, and pericardial cavities" xsd:string +relationship: RO:0002494 UBERON:0003886 ! transformation of future coelemic cavity lumen +relationship: RO:0002572 UBERON:0011997 ! luminal space of coelom [Term] id: UBERON:0002328 @@ -12320,23 +11925,15 @@ xref: XAO:0000055 xref: ZFA:0000135 is_a: UBERON:0000062 {source="PMID:15890825"} ! organ is_a: UBERON:0000481 {source="VSAO"} ! multi-tissue structure +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004121 ! ectoderm-derived structure -relationship: develops_from UBERON:0004880 {source="ZFA"} ! chordamesoderm -relationship: develops_from UBERON:0006267 {source="EHDAA2"} ! notochordal plate -relationship: dorsal_to UBERON:0001555 ! digestive tract -relationship: existence_starts_during UBERON:0000068 ! embryo stage -relationship: only_in_taxon NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! Chordata relationship: part_of UBERON:0011137 ! axial skeletal system relationship: produces PR:000014841 ! sonic hedgehog protein -relationship: ventral_to UBERON:0001049 ! neural tube -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000032", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000135", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000327", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000002 "relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000327", ontology="AAO"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000199", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "notochordal" xsd:string -property_value: UBPROP:0000011 "In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord." xsd:string +relationship: RO:0002160 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! only in taxon Chordata +relationship: RO:0002202 UBERON:0004880 {source="ZFA"} ! develops from chordamesoderm +relationship: RO:0002202 UBERON:0006267 {source="EHDAA2"} ! develops from notochordal plate +relationship: RO:0002488 UBERON:0000068 ! existence starts during embryo stage +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0002329 @@ -12375,18 +11972,10 @@ xref: XAO:0000058 xref: ZFA:0000155 is_a: UBERON:0005423 ! developing anatomical structure is_a: UBERON:0007503 {source="EHDAA2"} ! epithelial vesicle -relationship: develops_from UBERON:0003059 {source="ZFA"} ! presomitic mesoderm -relationship: never_in_taxon NCBITaxon:7712 {source="PMID:17237766"} -relationship: only_in_taxon NCBITaxon:7711 {source="GOTAX:0000352"} ! Chordata -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: IAO:0000232 "EDITOR_NOTE currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk" xsd:string -property_value: UBPROP:0000001 "Post-cranial axial segments which form sclerotome and dermomyotome.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010569", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000001 "Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000155", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000002 "relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000155", ontology="TAO"} -property_value: UBPROP:0000002 "relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000155", ontology="TAO"} -property_value: UBPROP:0000002 "relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010569", ontology="AAO"} -property_value: UBPROP:0000003 "(...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000191", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.40, DOI:10.1093/icb/43.1.137 Balavoine G, Adoutte A, The segmented urbilateria: a testable scenario. Integrative and Comparative Biology (2003)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "somitic" xsd:string +relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata +relationship: RO:0002202 UBERON:0003059 {source="ZFA"} ! develops from presomitic mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI +property_value: RO:0002161 NCBITaxon:7712 {source="PMID:17237766"} [Term] id: UBERON:0002335 @@ -12407,8 +11996,7 @@ xref: Wikipedia:Macula_densa is_a: UBERON:0004211 ! nephron epithelium relationship: part_of UBERON:0002303 {source="MA"} ! juxtaglomerular apparatus relationship: part_of UBERON:0004135 {source="GO"} ! distal tubule -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000012 "not part of a nephron or distal tubule in MA and FMA" xsd:string {external_ontology="MA"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002342 @@ -12435,28 +12023,22 @@ xref: MIAA:0000066 xref: NCIT:C34222 xref: neuronames:1366 xref: SCTID:361462002 -xref: TAO:0000045 xref: UMLS:C0027789 {source="ncithesaurus:Neural_Crest"} xref: VHOG:0000057 xref: Wikipedia:Neural_crest xref: XAO:0000048 xref: ZFA:0000045 is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0010316 ! germ layer / neural crest -relationship: composed_primarily_of CL:0000333 {notes="pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! migratory neural crest cell -relationship: develops_from UBERON:0003075 {source="BTO"} ! neural plate -relationship: develops_from UBERON:0005062 {source="PMID:11523831"} ! neural fold -relationship: existence_starts_during UBERON:0000110 {source="PMID:11523831"} ! neurula stage -relationship: only_in_taxon NCBITaxon:89593 {notes="Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells", source="ISBN:0073040584"} ! Craniata relationship: part_of UBERON:0002346 {source="XAO", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! neurectoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI -property_value: IAO:0000232 "EDITOR_NOTE consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams)." xsd:string -property_value: RO:0002174 NCBITaxon:117565 {source="ISBN:0073040584", source="PMID:17377535"} -property_value: UBPROP:0000001 "A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000045", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010578", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831]" xsd:string {source="PMID:11523831"} -property_value: UBPROP:0000003 "We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000057", ontology="VHOG", source="DOI:10.1111/j.1469-7580.2012.01495.x Hall BK, Gillis JA, Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues. J Anat (2012)", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata +relationship: RO:0002202 UBERON:0003075 {source="BTO"} ! develops from neural plate +relationship: RO:0002202 UBERON:0005062 {source="PMID:11523831"} ! develops from neural fold +relationship: RO:0002473 CL:0000333 ! composed primarily of migratory neural crest cell +relationship: RO:0002488 UBERON:0000110 {source="PMID:11523831"} ! existence starts during neurula stage +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI [Term] id: UBERON:0002346 @@ -12479,7 +12061,6 @@ xref: EHDAA:1498 xref: EHDAA:255 xref: EMAPA:16073 xref: EV:0100004 -xref: FBbt:00001057 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:87657 xref: MAT:0000176 xref: MIAA:0000176 @@ -12493,9 +12074,6 @@ xref: ZFA:0001120 is_a: UBERON:0000923 ! germ layer is_a: UBERON:0004121 ! ectoderm-derived structure relationship: has_part CL:0000133 ! neurectodermal cell -property_value: UBPROP:0000003 "(...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000150", ontology="VHOG", source="DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "neurectodermal" xsd:string -property_value: UBPROP:0000013 "we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here" xsd:string [Term] id: UBERON:0002355 @@ -12527,8 +12105,6 @@ xref: Wikipedia:Pelvis is_a: UBERON:0000475 ! organism subdivision relationship: has_part UBERON:0007832 ! pelvic girdle skeleton relationship: part_of UBERON:0002417 ! abdominal segment of trunk -property_value: UBPROP:0000007 "pelvic" xsd:string -property_value: UBPROP:0000012 "MA and FMA differ in what they consider to be parts of the pelvis. MA includes ureter, urethra, urinary bladder, reproductive organs" xsd:string {external_ontology="MA"} [Term] id: UBERON:0002384 @@ -12562,12 +12138,8 @@ xref: VSAO:0000017 xref: XAO:0001017 xref: ZFA:0001632 is_a: UBERON:0000479 ! tissue -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000098", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000001 "Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001641", ontology="TAO", source="TAO:wd"} -property_value: UBPROP:0000001 "Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000017", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070", source="PSPUB:0000170"} -property_value: UBPROP:0000012 "MA also has set of connective tissues" xsd:string {external_ontology="MA"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002385 @@ -12595,13 +12167,11 @@ xref: Wikipedia:Muscle_tissue is_a: UBERON:0000479 ! tissue is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000479 ! tissue -intersection_of: composed_primarily_of CL:0000187 ! muscle cell +intersection_of: RO:0002473 CL:0000187 ! composed primarily of muscle cell relationship: capable_of GO:0006936 ! muscle contraction -relationship: composed_primarily_of CL:0000187 ! muscle cell -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0001015 ! musculature -property_value: RO:0002171 UBERON:0003714 -property_value: UBPROP:0000001 "One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000306", ontology="AAO", source="AAO:LAP"} +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002473 CL:0000187 ! composed primarily of muscle cell [Term] id: UBERON:0002390 @@ -12644,14 +12214,10 @@ xref: ZFA:0005023 is_a: UBERON:0000467 ! anatomical system is_a: UBERON:0004120 ! mesoderm-derived structure disjoint_from: UBERON:8450002 ! excretory system -relationship: develops_from UBERON:0003061 {evidence="definitional"} ! blood island -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0002193 {source="FMA"} ! hemolymphoid system -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "Anatomical system that consists of the blood and blood forming tissues.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011002", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001624", ontology="VHOG", source="DOI:10.1016/j.coph.2010.05.004 Ellett F, Lieschke GJ, Zebrafish as a model for vertebrate hematopoiesis. Current Opinion in Pharmacology (2010)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "hematopoietic" xsd:string -property_value: UBPROP:0000008 "In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes" xsd:string {source="WP"} +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002202 UBERON:0003061 ! develops from blood island +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002417 @@ -12692,9 +12258,8 @@ xref: VHOG:0000243 xref: Wikipedia:Epiblast is_a: UBERON:0002050 ! embryonic structure relationship: has_part CL:0000352 ! epiblast cell -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" xsd:anyURI -property_value: editor_note "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" xsd:string -property_value: UBPROP:0000003 "In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000243", ontology="VHOG", source="DOI:10.1146/annurev.cellbio.042308.113344 Zorn AM, Wells JM, Vertebrate endoderm development and organ formation. Annual Review of Cell Developmental Biology (2009)", source="http://bgee.unil.ch/"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/e/e3/Gray21.png" xsd:anyURI +property_value: IAO:0000116 "MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class" xsd:string [Term] id: UBERON:0002553 @@ -12710,7 +12275,7 @@ xref: galen:Cavity xref: MA:0002447 xref: NCIT:C34007 is_a: UBERON:0000464 ! anatomical space -relationship: location_of UBERON:0000463 ! organism substance +relationship: RO:0001015 UBERON:0000463 ! location of organism substance [Term] id: UBERON:0003059 @@ -12736,13 +12301,11 @@ xref: XAO:0000057 xref: ZFA:0000279 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0005423 ! developing anatomical structure -intersection_of: has_potential_to_develop_into UBERON:0002329 ! somite -intersection_of: immediate_transformation_of UBERON:0007282 ! presumptive segmental plate -relationship: has_potential_to_develop_into UBERON:0002329 ! somite -relationship: immediate_transformation_of UBERON:0007282 {source="Bgee:AN"} ! presumptive segmental plate +intersection_of: RO:0002387 UBERON:0002329 ! has potential to develop into somite +intersection_of: RO:0002495 UBERON:0007282 ! immediate transformation of presumptive segmental plate relationship: part_of UBERON:0003077 ! paraxial mesoderm -property_value: UBPROP:0000001 "Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000279", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000559", ontology="VHOG", source="DOI:10.1006/dbio.2001.0460 Schubert M, Holland LZ, Dale Stokes M and Holland ND, Three Amphoxius Wnt Genes (AmphiWnt3, AmphiWnt5, and AmphiWnt6) Associated with the Tail Bud: the Evolution of Somitogenesis in Chordates. Developmental Biology (2001)", source="http://bgee.unil.ch/"} +relationship: RO:0002387 UBERON:0002329 ! has potential to develop into somite +relationship: RO:0002495 UBERON:0007282 {source="Bgee:AN"} ! immediate transformation of presumptive segmental plate [Term] id: UBERON:0003060 @@ -12755,23 +12318,18 @@ synonym: "archinephric duct" RELATED [VHOG:0000082] synonym: "ductus pronephricus" RELATED OMO:0003011 [Wikipedia:Pronephric_duct] synonym: "pronephric ducts" RELATED OMO:0003004 [ZFA:0000150] xref: AAO:0011088 -xref: BTO:0005991 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C34279 xref: SCTID:361406002 xref: TAO:0000150 xref: UMLS:C1283945 {source="ncithesaurus:Pronephric_Duct"} -xref: VHOG:0000082 xref: Wikipedia:Pronephric_duct xref: XAO:0000063 xref: ZFA:0000150 is_a: UBERON:0009201 {source="GO"} ! nephric duct is_a: UBERON:0012275 ! meso-epithelium -relationship: develops_from UBERON:0003064 {source="Wikipedia"} ! intermediate mesoderm -relationship: develops_from UBERON:0005721 {source="XAO"} ! pronephric mesoderm relationship: part_of UBERON:0002120 ! pronephros -property_value: UBPROP:0000001 "Duct of the embryonic kidney, present bilaterally ventral to the somites and leading to the anal region where it empties separately from, and just posterior to the anus. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000150", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000082", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "(...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000082", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.686", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003064 {source="Wikipedia"} ! develops from intermediate mesoderm +relationship: RO:0002202 UBERON:0005721 {source="XAO"} ! develops from pronephric mesoderm [Term] id: UBERON:0003061 @@ -12801,13 +12359,8 @@ xref: Wikipedia:Blood_island_of_umbilical_vesicle xref: XAO:0000067 xref: ZFA:0000094 is_a: UBERON:0006598 ! presumptive structure -relationship: develops_from UBERON:0003081 ! lateral plate mesoderm -relationship: has_potential_to_develop_into UBERON:0002390 ! hematopoietic system -property_value: UBPROP:0000001 "Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000094", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011006", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000002 "relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000094", ontology="TAO"} -property_value: UBPROP:0000003 "Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000085", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450, DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual Review of Cell and Developmental Biology (2006)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac" xsd:string {external_ontology="EHDAA2"} +relationship: RO:0002202 UBERON:0003081 ! develops from lateral plate mesoderm +relationship: RO:0002387 UBERON:0002390 ! has potential to develop into hematopoietic system [Term] id: UBERON:0003064 @@ -12837,13 +12390,10 @@ xref: ZFA:0001206 is_a: UBERON:0002050 ! embryonic structure relationship: adjacent_to UBERON:0003077 ! paraxial mesoderm relationship: adjacent_to UBERON:0003081 ! lateral plate mesoderm -relationship: develops_from UBERON:0000926 {source="XAO"} ! mesoderm relationship: part_of UBERON:0000926 {source="AAO"} ! mesoderm relationship: part_of UBERON:0005256 {source="EMAPA"} ! trunk mesenchyme -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "Mesoderm between somite and lateral plate. Traditionally thought to give rise to the urogenital system.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010575", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "(...)the mesoderm of a developing vertebrate transitionally differentiates into the following sub-types: Chordamesoderm (also known as axial mesoderm) which later on gives rise to notochord in all chordates, Paraxial mesoderm, Intermediate mesoderm, Lateral plate mesoderm (reference 1); The mesoderm is present in Bilateria, therefore they are sometimes called triploblasts. Ectoderm and endoderm are usually organized as epithelial layers, while mesoderm can be epithelial or a compact, three-dimensional tissue.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000087", ontology="VHOG", source="Wikipedia:Mesoderm, ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.43", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm')." xsd:string {external_ontology="ZFA"} +relationship: RO:0002202 UBERON:0000926 {source="XAO"} ! develops from mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003068 @@ -12861,11 +12411,10 @@ xref: Wikipedia:Chordamesoderm xref: XAO:0000205 xref: ZFA:0001204 is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0000926 ! mesoderm -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0000926 ! mesoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000107", ontology="VHOG", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002202 UBERON:0000926 ! develops from mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003074 @@ -12881,32 +12430,24 @@ synonym: "Leydig's duct" RELATED [Wikipedia:Wolffian_duct] synonym: "renal duct" RELATED [] synonym: "Wolffian duct" EXACT [GOC:yaf, Wikipedia:Wolffian_duct, ZFA:0000546] xref: AAO:0000637 -xref: BTO:0005990 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: EHDAA2:0001243 xref: EHDAA:1590 -xref: EMAPA:16577 xref: GAID:1315 xref: MESH:D014928 xref: NCIT:C26469 xref: SCTID:308800003 xref: TAO:0000546 xref: UMLS:C0043204 {source="ncithesaurus:Mesonephric_Duct"} -xref: VHOG:0000082 xref: Wikipedia:Mesonephric_duct xref: XAO:0000242 xref: ZFA:0000546 is_a: UBERON:0000083 ! mesonephric tubule is_a: UBERON:0009201 {source="GO"} ! nephric duct -is_a: UBERON:0012275 ! meso-epithelium -relationship: develops_from UBERON:0003060 ! pronephric duct -relationship: develops_from UBERON:0005792 {source="EHDAA2"} ! nephric ridge -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png" xsd:anyURI -property_value: editor_note "Consider adding subclasses for male and female specific variants" xsd:string -property_value: editor_note "TODO - mesonephric portion of the nephric duct" xsd:string -property_value: UBPROP:0000001 "Anatomical structure consisting of either of a pair of longitudinal ducts which carry urine and in males, sperm, to the cloaca.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000637", ontology="AAO", source="AAO:BJB"} -property_value: UBPROP:0000001 "The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000082", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "(...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000082", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.686", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000011 "In the male the Wolffian duct persists, and forms for example the epididymis, the ductus deferens, the ejaculatory duct, seminal vesicle and efferent ducts." xsd:string +relationship: RO:0002202 UBERON:0003060 ! develops from pronephric duct +relationship: RO:0002202 UBERON:0005792 {source="EHDAA2"} ! develops from nephric ridge +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png" xsd:anyURI +property_value: IAO:0000116 "Consider adding subclasses for male and female specific variants" xsd:string +property_value: IAO:0000116 "TODO - mesonephric portion of the nephric duct" xsd:string [Term] id: UBERON:0003075 @@ -12926,7 +12467,6 @@ xref: EHDAA:346 xref: EHDAA:902 xref: EMAPA:35593 xref: FMA:293879 -xref: MESH:D054258 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C34225 xref: neuronames:1362 xref: RETIRED_EHDAA2:0001252 @@ -12939,12 +12479,10 @@ xref: ZFA:0000132 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0016879 ! future central nervous system -relationship: developmentally_induced_by UBERON:0002328 {source="Wikipedia"} ! notochord -relationship: immediate_transformation_of UBERON:0007284 {source="Bgee:AN"} ! presumptive neural plate -relationship: only_in_taxon NCBITaxon:7711 {source="GOTAX:0000352"} ! Chordata -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI -property_value: UBPROP:0000001 "The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000132", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000003 "(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000068", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28", source="http://bgee.unil.ch/"} +relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata +relationship: RO:0002256 UBERON:0002328 {source="Wikipedia"} ! developmentally induced by notochord +relationship: RO:0002495 UBERON:0007284 {source="Bgee:AN"} ! immediate transformation of presumptive neural plate +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI [Term] id: UBERON:0003077 @@ -12973,13 +12511,9 @@ xref: ZFA:0000255 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue is_a: UBERON:0015212 ! lateral structure -relationship: existence_starts_during UBERON:0000109 ! gastrula stage -relationship: immediate_transformation_of UBERON:0007285 {source="Bgee:AN"} ! presumptive paraxial mesoderm -relationship: in_lateral_side_of UBERON:0000922 ! embryo -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010568", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000114", ontology="VHOG", source="DOI:10.1002/dvdy.21177 Kusakabe R and Kuratani S. Evolutionary perspectives from development of mesodermal components in the lamprey. Developmental dynamics (2007)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here)" xsd:string {external_ontology="ZFA"} +relationship: RO:0002488 UBERON:0000109 ! existence starts during gastrula stage +relationship: RO:0002495 UBERON:0007285 {source="Bgee:AN"} ! immediate transformation of presumptive paraxial mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003081 @@ -13011,14 +12545,10 @@ is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria relationship: part_of UBERON:0000926 {source="EHDAA2", source="VHOG"} ! mesoderm -relationship: surrounds UBERON:0003887 ! intraembryonic coelom -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI -property_value: UBPROP:0000001 "Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010574", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000001 "The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000118", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000118", ontology="VHOG", source="DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "subclass of mesoderm in ZFA." xsd:string {external_ontology="ZFA"} +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002221 UBERON:0003887 ! surrounds intraembryonic coelom +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI [Term] id: UBERON:0003084 @@ -13036,14 +12566,11 @@ xref: UMLS:C1514450 {source="ncithesaurus:Primordium_of_the_Heart"} xref: XAO:0000336 xref: ZFA:0000028 is_a: UBERON:0001048 {source="Obol"} ! primordium -relationship: develops_from UBERON:0003081 {source="ZFA"} ! lateral plate mesoderm -relationship: develops_from UBERON:0004140 ! primary heart field -relationship: develops_from UBERON:0007005 {source="XAO"} ! cardiogenic splanchnic mesoderm relationship: part_of UBERON:0004535 {source="ZFA"} ! cardiovascular system -property_value: editor_note "should probably be merged with heart rudiment." xsd:string -property_value: UBPROP:0000001 "Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000028", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011044", ontology="AAO", source="XAO:curator"} -property_value: UBPROP:0000002 "relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000028", ontology="TAO"} +relationship: RO:0002202 UBERON:0003081 {source="ZFA"} ! develops from lateral plate mesoderm +relationship: RO:0002202 UBERON:0004140 ! develops from primary heart field +relationship: RO:0002202 UBERON:0007005 {source="XAO"} ! develops from cardiogenic splanchnic mesoderm +property_value: IAO:0000116 "should probably be merged with heart rudiment." xsd:string [Term] id: UBERON:0003089 @@ -13057,7 +12584,6 @@ synonym: "sclerotomes" EXACT OMO:0003004 [TAO:0001080] synonym: "sclerotomus" RELATED OMO:0003011 [Wikipedia:Sclerotome] xref: AAO:0010571 xref: AEO:0000212 -xref: BTO:0006255 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: EHDAA2:0003439 xref: EMAPA:31159 xref: FMA:295652 @@ -13070,12 +12596,9 @@ xref: XAO:0000397 xref: ZFA:0001080 is_a: UBERON:0005856 {source="EHDAA2"} ! developing mesenchymal condensation is_a: UBERON:0007530 {source="EHDAA2"} ! migrating mesenchyme population -relationship: develops_from UBERON:0002329 {source="ZFA"} ! somite -relationship: only_in_taxon NCBITaxon:7742 {source="VHOG:0000680"} ! Vertebrata -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI -property_value: UBPROP:0000001 "Skeletogenic portion of somites.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010571", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000003 "The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000680", ontology="VHOG", source="DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000)", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "part_of somite in XAO" xsd:string {external_ontology="XAO"} +relationship: RO:0002160 NCBITaxon:7742 {source="VHOG:0000680"} ! only in taxon Vertebrata +relationship: RO:0002202 UBERON:0002329 {source="ZFA"} ! develops from somite +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI [Term] id: UBERON:0003103 @@ -13098,7 +12621,6 @@ xref: VHOG:0001723 xref: XAO:0003041 xref: ZFA:0000496 is_a: UBERON:0000062 ! organ -property_value: IAO:0000232 "this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs" xsd:string [Term] id: UBERON:0003104 @@ -13128,15 +12650,12 @@ xref: XAO:0003046 xref: ZFA:0000393 is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue -intersection_of: composed_primarily_of CL:0008019 ! mesenchymal cell -relationship: composed_primarily_of CL:0008019 ! mesenchymal cell -relationship: functionally_related_to GO:0032502 ! developmental process -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI -property_value: editor_note "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" xsd:string -property_value: UBPROP:0000001 "A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000393", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000001 "Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0010427", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000007 "mesenchymal" xsd:string +intersection_of: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002328 GO:0032502 ! functionally related to developmental process +relationship: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI +property_value: IAO:0000116 "the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense" xsd:string [Term] id: UBERON:0003133 @@ -13150,7 +12669,6 @@ synonym: "genital organ" EXACT [] synonym: "genitalia" RELATED OMO:0003004 [] synonym: "reproductive system organ" EXACT [] synonym: "sex organ" EXACT [] -xref: EMAPA:17381 xref: EMAPA:37731 {source="MA:th"} xref: MA:0001752 xref: MESH:D005835 @@ -13164,7 +12682,6 @@ is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0000062 ! organ intersection_of: capable_of_part_of GO:0000003 ! reproduction relationship: capable_of_part_of GO:0000003 ! reproduction -property_value: UBPROP:0000012 "GO uses genitalia for the singular organ" xsd:string {external_ontology="GO"} [Term] id: UBERON:0003220 @@ -13190,12 +12707,10 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: has_potential_to_develop_into UBERON:0000081 ! metanephros -relationship: developmentally_induced_by UBERON:0000084 {source="ISBN:9780878932504"} ! ureteric bud -relationship: develops_from UBERON:0003074 ! mesonephric duct -relationship: has_potential_to_develop_into UBERON:0000081 ! metanephros -property_value: UBPROP:0000001 "A mass of intermediate mesodermal cells around the distal end of the ureteric bud that gives rise to nephrons in the metanephric kidney. [TFD][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000540", ontology="VHOG", source="http://bgee.unil.ch/", source="http://medical-dictionary.thefreedictionary.com/metanephric+mesenchyme"} -property_value: UBPROP:0000003 "When the ureteric buds emerge from the nephric duct, they enter the metanephrogenic mesenchyme. The ureteric buds induce this mesenchymal tissue to condense around them and differentiate into the nephrons of the mammalian kidney. As this mesenchyme differentiates, it tells the ureteric bud to branch and grow.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000540", ontology="VHOG", source="ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.462", source="http://bgee.unil.ch/"} +intersection_of: RO:0002387 UBERON:0000081 ! has potential to develop into metanephros +relationship: RO:0002202 UBERON:0003074 ! develops from mesonephric duct +relationship: RO:0002256 UBERON:0000084 {source="ISBN:9780878932504"} ! developmentally induced by ureteric bud +relationship: RO:0002387 UBERON:0000081 ! has potential to develop into metanephros [Term] id: UBERON:0003479 @@ -13216,7 +12731,7 @@ xref: MA:0001903 is_a: UBERON:0001638 ! vein is_a: UBERON:0003519 ! thoracic cavity blood vessel intersection_of: UBERON:0001638 ! vein -intersection_of: located_in UBERON:0002224 ! thoracic cavity +intersection_of: RO:0001025 UBERON:0002224 ! located in thoracic cavity [Term] id: UBERON:0003497 @@ -13229,7 +12744,6 @@ is_a: UBERON:0003835 ! abdominal segment blood vessel intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0000916 ! abdomen relationship: part_of UBERON:0000916 ! abdomen -property_value: seeAlso "UBERON:0012254" xsd:string {notes="abdominal aorta artery"} [Term] id: UBERON:0003509 @@ -13270,7 +12784,6 @@ subset: pheno_slim subset: vertebrate_core synonym: "blood vessel of kidney" EXACT [OBOL:automatic] synonym: "renal blood vessel" EXACT [OBOL:automatic] -xref: EMAPA:28457 xref: MA:0001682 xref: TAO:0005306 xref: ZFA:0005306 @@ -13278,7 +12791,7 @@ is_a: UBERON:0003497 ! abdomen blood vessel intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0002113 ! kidney relationship: part_of UBERON:0006544 ! kidney vasculature -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003519 @@ -13298,8 +12811,8 @@ xref: EMAPA:37240 {source="MA:th"} xref: MA:0000554 is_a: UBERON:0001981 ! blood vessel intersection_of: UBERON:0001981 ! blood vessel -intersection_of: located_in UBERON:0002224 ! thoracic cavity -relationship: located_in UBERON:0002224 ! thoracic cavity +intersection_of: RO:0001025 UBERON:0002224 ! located in thoracic cavity +relationship: RO:0001025 UBERON:0002224 ! located in thoracic cavity [Term] id: UBERON:0003527 @@ -13321,7 +12834,7 @@ is_a: UBERON:0001982 ! capillary is_a: UBERON:0003517 ! kidney blood vessel intersection_of: UBERON:0001982 ! capillary intersection_of: part_of UBERON:0002113 ! kidney -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0003644 @@ -13362,11 +12875,11 @@ synonym: "body cavity precursor" RELATED [] synonym: "future coelomic cavity lumen" EXACT [] is_a: UBERON:0000464 ! anatomical space intersection_of: UBERON:0000464 ! anatomical space -intersection_of: has_potential_to_develop_into UBERON:0002323 ! coelemic cavity lumen -relationship: existence_ends_during UBERON:0000111 ! organogenesis stage -relationship: existence_starts_during UBERON:0000109 ! gastrula stage -relationship: has_potential_to_develop_into UBERON:0002323 ! coelemic cavity lumen +intersection_of: RO:0002387 UBERON:0002323 ! has potential to develop into coelemic cavity lumen relationship: part_of UBERON:0000926 ! mesoderm +relationship: RO:0002387 UBERON:0002323 ! has potential to develop into coelemic cavity lumen +relationship: RO:0002488 UBERON:0000109 ! existence starts during gastrula stage +relationship: RO:0002492 UBERON:0000111 ! existence ends during organogenesis stage [Term] id: UBERON:0003887 @@ -13382,10 +12895,9 @@ xref: UMLS:C1512940 {source="ncithesaurus:Intraembryonic_Coelom"} xref: VHOG:0000316 xref: Wikipedia:Intraembryonic_coelom is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0003081 {source="Wikipedia"} ! lateral plate mesoderm relationship: part_of UBERON:0011997 ! coelom -property_value: editor_note "consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults" xsd:string -property_value: UBPROP:0000003 "(...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000316", ontology="VHOG", source="ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.166", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003081 {source="Wikipedia"} ! develops from lateral plate mesoderm +property_value: IAO:0000116 "consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults" xsd:string [Term] id: UBERON:0003891 @@ -13398,9 +12910,8 @@ xref: FMA:81494 xref: NCIT:C67387 xref: UMLS:C0927195 {source="ncithesaurus:Stroma_Connective_Tissue"} is_a: UBERON:0000064 ! organ part -relationship: composed_primarily_of UBERON:0002384 ! connective tissue -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: UBPROP:0000007 "stromal" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002473 UBERON:0002384 ! composed primarily of connective tissue [Term] id: UBERON:0003914 @@ -13410,12 +12921,10 @@ def: "Epithelial tubes transport gases, liquids and cells from one site to anoth synonym: "epithelial or endothelial tube" EXACT [] xref: AEO:0000114 xref: EHDAA2:0003114 -xref: FBbt:00007474 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000025 ! tube is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium -intersection_of: has_quality PATO:0002299 ! tubular -property_value: IAO:0000232 "contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers" xsd:string +intersection_of: RO:0000086 PATO:0002299 ! has quality tubular [Term] id: UBERON:0003918 @@ -13426,9 +12935,9 @@ subset: pheno_slim synonym: "mesenchyme of kidney" EXACT [] is_a: UBERON:0003104 ! mesenchyme intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: has_potential_to_develop_into UBERON:0002113 ! kidney -relationship: has_potential_to_develop_into UBERON:0002113 ! kidney -property_value: editor_note "check this" xsd:string +intersection_of: RO:0002387 UBERON:0002113 ! has potential to develop into kidney +relationship: RO:0002387 UBERON:0002113 ! has potential to develop into kidney +property_value: IAO:0000116 "check this" xsd:string [Term] id: UBERON:0003920 @@ -13446,7 +12955,7 @@ is_a: UBERON:0001981 ! blood vessel intersection_of: UBERON:0001981 ! blood vessel intersection_of: part_of UBERON:0004582 ! venous system relationship: part_of UBERON:0004582 ! venous system -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004087 @@ -13469,10 +12978,10 @@ xref: UMLS:C0042460 {source="ncithesaurus:Vena_Cava"} xref: Wikipedia:Venae_cavae is_a: UBERON:0003479 ! thoracic cavity vein is_a: UBERON:0013768 ! great vessel of heart -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/3/35/Relations_of_the_aorta,_trachea,_esophagus_and_other_heart_structures.png" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/7/7c/Heart_numlabels.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/3/35/Relations_of_the_aorta,_trachea,_esophagus_and_other_heart_structures.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/7c/Heart_numlabels.png" xsd:anyURI [Term] id: UBERON:0004100 @@ -13489,8 +12998,8 @@ xref: SCTID:279371005 xref: Wikipedia:Collecting_duct_system is_a: UBERON:0000467 ! anatomical system relationship: part_of UBERON:0002113 ! kidney -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004111 @@ -13510,15 +13019,14 @@ xref: SCTID:346902003 xref: Wikipedia:Foramen is_a: UBERON:0010000 ! multicellular anatomical structure intersection_of: UBERON:0010000 ! multicellular anatomical structure -intersection_of: conduit_for UBERON:0000061 ! anatomical structure intersection_of: has_part UBERON:0013686 ! anatomical conduit space -relationship: conduit_for UBERON:0000061 ! anatomical structure -relationship: connects UBERON:0000464 {cardinality="2"} ! anatomical space +intersection_of: RO:0002570 UBERON:0000061 ! conduit for anatomical structure relationship: has_part UBERON:0013686 ! anatomical conduit space -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: UBPROP:0000012 "FMA has both conduit and conduit space. In EHDAA2 this is a surface feature" xsd:string {external_ontology="FMA"} +relationship: RO:0002176 UBERON:0000464 {cardinality="2"} ! connects anatomical space +relationship: RO:0002570 UBERON:0000061 ! conduit for anatomical structure +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0004120 @@ -13529,9 +13037,8 @@ subset: grouping_class synonym: "mesodermal derivative" EXACT [FBbt:00025998] is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: develops_from UBERON:0000926 ! mesoderm -relationship: develops_from UBERON:0000926 ! mesoderm -property_value: IAO:0000232 "Grouping term for query purposes" xsd:string +intersection_of: RO:0002202 UBERON:0000926 ! develops from mesoderm +relationship: RO:0002202 UBERON:0000926 ! develops from mesoderm [Term] id: UBERON:0004121 @@ -13542,9 +13049,8 @@ subset: grouping_class synonym: "ectodermal deriviative" EXACT [FBbt:00025990] is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: develops_from UBERON:0000924 ! ectoderm -relationship: develops_from UBERON:0000924 ! ectoderm -property_value: IAO:0000232 "Grouping term for query purposes" xsd:string +intersection_of: RO:0002202 UBERON:0000924 ! develops from ectoderm +relationship: RO:0002202 UBERON:0000924 ! develops from ectoderm [Term] id: UBERON:0004122 @@ -13580,14 +13086,9 @@ is_a: UBERON:0000467 ! anatomical system intersection_of: UBERON:0000467 ! anatomical system intersection_of: has_part UBERON:0000990 ! reproductive system intersection_of: has_part UBERON:0001008 ! renal system -relationship: existence_ends_during UBERON:0000066 ! fully formed stage relationship: has_part UBERON:0000990 ! reproductive system relationship: has_part UBERON:0001008 ! renal system -property_value: UBPROP:0000001 "Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000624", ontology="AAO", source="AAO:EJS"} -property_value: UBPROP:0000002 "relationship type change: differentiates_from intermediate mesoderm (AAO:0010575) CHANGED TO: develops_from intermediate mesoderm (UBERON:0003064)[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000624", ontology="AAO"} -property_value: UBPROP:0000003 "Kidneys and gonads (of vertebrates) develop from adjacent tissues, and after the excretory or urinary ducts have developed, the reproductive system usually taps into them or their derivatives.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000286", ontology="VHOG", source="ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.633", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000007 "genitourinary" xsd:string -property_value: UBPROP:0000007 "urogenital" xsd:string +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage [Term] id: UBERON:0004134 @@ -13604,10 +13105,10 @@ xref: EMAPA:28281 xref: MA:0002611 xref: MESH:D007687 is_a: UBERON:0006853 ! renal cortex tubule -relationship: continuous_with UBERON:0001230 {source="GO"} ! glomerular capsule -relationship: continuous_with UBERON:0001289 {source="GO"} ! descending limb of loop of Henle -relationship: present_in_taxon NCBITaxon:9606 -property_value: editor_note "TODO - ensure definition works across species." xsd:string +relationship: RO:0002150 UBERON:0001230 {source="GO"} ! continuous with glomerular capsule +relationship: RO:0002150 UBERON:0001289 {source="GO"} ! continuous with descending limb of loop of Henle +property_value: IAO:0000116 "TODO - ensure definition works across species." xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004135 @@ -13622,7 +13123,6 @@ xref: EMAPA:28387 xref: MA:0002633 xref: MESH:D007686 is_a: UBERON:0007685 ! region of nephron tubule -property_value: RO:0002171 UBERON:0012424 [Term] id: UBERON:0004136 @@ -13634,7 +13134,7 @@ synonym: "tubulus attenuatus" EXACT [FMA:17718] xref: FMA:17718 is_a: UBERON:0007685 ! region of nephron tubule relationship: part_of UBERON:0001288 {source="FMA"} ! loop of Henle -property_value: editor_note "TODO - check for applicability across species" xsd:string +property_value: IAO:0000116 "TODO - check for applicability across species" xsd:string [Term] id: UBERON:0004139 @@ -13650,9 +13150,8 @@ xref: EHDAA2:0000215 xref: EMAPA:16106 xref: VHOG:0000975 is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0003084 ! heart primordium -property_value: editor_note "TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO" xsd:string -property_value: UBPROP:0000003 "(In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000975", ontology="VHOG", source="PMID:15611355 Gittenberger-de Groot AC, Bartelings MM, Deruiter MC, Poelmann RE, Basics of cardiac development for the understanding of congenital heart malformations. Pediatric Research (2005)", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0003084 ! develops from heart primordium +property_value: IAO:0000116 "TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO" xsd:string [Term] id: UBERON:0004140 @@ -13666,11 +13165,11 @@ synonym: "PHF" RELATED OMO:0003000 [XAO:0004185] synonym: "primary heart field" EXACT [PMID:17276708, XAO:0004185] xref: XAO:0004185 is_a: UBERON:0002050 ! embryonic structure +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007688 ! anlage relationship: part_of UBERON:0003081 {source="GO:0003128"} ! lateral plate mesoderm relationship: part_of UBERON:0036146 {source="https://orcid.org/0000-0003-3308-6245"} ! cardiopharyngeal field -property_value: UBPROP:0000012 "this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138]" xsd:string {external_ontology="GO"} [Term] id: UBERON:0004141 @@ -13693,8 +13192,7 @@ xref: ZFA:0000360 is_a: UBERON:0003914 ! epithelial tube is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0012275 ! meso-epithelium -relationship: immediate_transformation_of UBERON:0005498 {source="ZFA-modified"} ! primitive heart tube -property_value: UBPROP:0000001 "the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube." xsd:string {source="MP:0012700"} +relationship: RO:0002495 UBERON:0005498 {source="ZFA-modified"} ! immediate transformation of primitive heart tube [Term] id: UBERON:0004151 @@ -13707,6 +13205,7 @@ synonym: "heart chamber" EXACT [] xref: FMA:7095 xref: SCTID:276456008 is_a: UBERON:0000064 ! organ part +is_a: UBERON:0004120 ! mesoderm-derived structure relationship: part_of UBERON:0000948 ! heart [Term] @@ -13739,11 +13238,12 @@ xref: BTO:0001515 xref: EMAPA:35458 xref: MA:0002847 is_a: UBERON:0004211 ! nephron epithelium +is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000074 ! renal glomerulus relationship: part_of UBERON:0000074 ! renal glomerulus -relationship: present_in_taxon NCBITaxon:9606 -property_value: editor_note "TODO - check - GO says outer, BTO says inner. Make this a superclass" xsd:string +property_value: IAO:0000116 "TODO - check - GO says outer, BTO says inner. Make this a superclass" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004190 @@ -13760,7 +13260,7 @@ is_a: UBERON:0006544 ! kidney vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: part_of UBERON:0000074 ! renal glomerulus relationship: part_of UBERON:0000074 ! renal glomerulus -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004198 @@ -13772,8 +13272,8 @@ synonym: "CSB" EXACT OMO:0003000 [] xref: EMAPA:27681 xref: ZFA:0005588 is_a: UBERON:0005423 ! developing anatomical structure -relationship: develops_from UBERON:0004209 {source="ZFA"} ! renal vesicle relationship: part_of UBERON:0010532 {source="cjm"} ! primitive nephron +relationship: RO:0002202 UBERON:0004209 {source="ZFA"} ! develops from renal vesicle [Term] id: UBERON:0004199 @@ -13784,12 +13284,11 @@ subset: pheno_slim synonym: "SSB" EXACT OMO:0003000 [] synonym: "stage II nephron" EXACT [http://www.gudmap.org/Organ_Summaries/Metanephros/Renal_vesicle.html] xref: EMAPA:27756 -xref: VO:0010896 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: ZFA:0005589 is_a: UBERON:0005423 ! developing anatomical structure -relationship: develops_from UBERON:0004198 {source="GO"} ! comma-shaped body relationship: part_of UBERON:0010532 {source="cjm"} ! primitive nephron -property_value: editor_note "TODO" xsd:string +relationship: RO:0002202 UBERON:0004198 {source="GO"} ! develops from comma-shaped body +property_value: IAO:0000116 "TODO" xsd:string [Term] id: UBERON:0004200 @@ -13821,16 +13320,14 @@ xref: UMLS:C0227629 {source="ncithesaurus:Renal_Pyramid"} xref: UMLS:C1514613 {source="ncithesaurus:Pyramid_of_Malpighi"} xref: Wikipedia:Renal_pyramids is_a: UBERON:0000064 ! organ part -relationship: contributes_to_morphology_of UBERON:0000362 ! renal medulla relationship: part_of UBERON:0000362 ! renal medulla -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI -property_value: UBPROP:0000012 "not the same as FMA:50609 Pyramid (which is a volume / dimensional entity)" xsd:string {external_ontology="FMA"} -property_value: UBPROP:0000202 FMA:74268 +relationship: RO:0002433 UBERON:0000362 ! contributes to morphology of renal medulla +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_L.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Kidney_R.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_L.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004202 @@ -13849,9 +13346,9 @@ xref: EMAPA:29663 xref: FMA:76662 xref: MA:0002629 is_a: UBERON:0010000 ! multicellular anatomical structure -relationship: contributes_to_morphology_of UBERON:0001293 ! outer medulla of kidney relationship: part_of UBERON:0001293 ! outer medulla of kidney -relationship: present_in_taxon NCBITaxon:9606 +relationship: RO:0002433 UBERON:0001293 ! contributes to morphology of outer medulla of kidney +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004208 @@ -13863,8 +13360,8 @@ synonym: "mesenchyme of nephron" EXACT [OBOL:automatic] synonym: "nephron mesenchyme" EXACT [OBOL:automatic] is_a: UBERON:0003104 ! mesenchyme intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: has_potential_to_develop_into UBERON:0001285 ! nephron -relationship: has_potential_to_develop_into UBERON:0001285 ! nephron +intersection_of: RO:0002387 UBERON:0001285 ! has potential to develop into nephron +relationship: RO:0002387 UBERON:0001285 ! has potential to develop into nephron [Term] id: UBERON:0004209 @@ -13873,11 +13370,11 @@ namespace: uberon def: "The renal vesicle is the primordial structure of the nephron epithelium, and is formed by the condensation of mesenchymal cells." [GO:0072077] synonym: "stage I nephron" EXACT [http://www.gudmap.org/Organ_Summaries/Metanephros/Renal_vesicle.html, ZFA:0005586] is_a: UBERON:0007503 {source="EHDAA2"} ! epithelial vesicle -relationship: developmentally_induced_by UBERON:0000084 ! ureteric bud -relationship: develops_from UBERON:0004208 ! nephrogenic mesenchyme -relationship: has_potential_to_develop_into UBERON:0004211 ! nephron epithelium relationship: part_of UBERON:0010536 ! nephron progenitor -property_value: editor_note "note that this class includes both metanephric and mesonephric vesicles - ZFA and EHDAA2 associations are placed with these classes. TODO - make a more specific develops_from relationship - see UBERON:0005107 ! metanephric cap" xsd:string +relationship: RO:0002202 UBERON:0004208 ! develops from nephrogenic mesenchyme +relationship: RO:0002256 UBERON:0000084 ! developmentally induced by ureteric bud +relationship: RO:0002387 UBERON:0004211 ! has potential to develop into nephron epithelium +property_value: IAO:0000116 "note that this class includes both metanephric and mesonephric vesicles - ZFA and EHDAA2 associations are placed with these classes. TODO - make a more specific develops_from relationship - see UBERON:0005107 ! metanephric cap" xsd:string [Term] id: UBERON:0004211 @@ -13919,11 +13416,10 @@ xref: ZFA:0005284 is_a: UBERON:0003527 ! kidney capillary intersection_of: UBERON:0001982 ! capillary intersection_of: part_of UBERON:0000074 ! renal glomerulus -relationship: connected_to UBERON:0004639 ! renal afferent arteriole -relationship: contributes_to_morphology_of UBERON:0000074 ! renal glomerulus relationship: part_of UBERON:0004190 {source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! renal glomerulus vasculature -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000001 "Capillary that is part of the renal glomerulus. Glomerular capillary endothelial membranes in zebrafish normally have a fenestrated morphology that is visible at the ultrastructural level.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005284", ontology="TAO", source="ZFIN:ZDB-PUB-000824-1", source="ZFIN:curator"} +relationship: RO:0002170 UBERON:0004639 ! connected to renal afferent arteriole +relationship: RO:0002433 UBERON:0000074 ! contributes to morphology of renal glomerulus +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004288 @@ -13953,13 +13449,10 @@ xref: Wikipedia:Skeleton xref: XAO:0004053 is_a: UBERON:0034925 ! anatomical collection disjoint_from: UBERON:0004770 ! articular system -relationship: has_member UBERON:0004765 ! skeletal element relationship: part_of UBERON:0001434 ! skeletal system -relationship: present_in_taxon NCBITaxon:9606 -property_value: RO:0002171 UBERON:0000383 +relationship: RO:0002351 UBERON:0004765 ! has member skeletal element +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/The-skeletal-system" xsd:anyURI -property_value: UBPROP:0000001 "Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000026", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070"} -property_value: UBPROP:0000007 "skeletal" xsd:string [Term] id: UBERON:0004291 @@ -13971,8 +13464,7 @@ synonym: "rudimentary heart" EXACT [ZFA:0000115] xref: TAO:0000115 xref: ZFA:0000115 is_a: UBERON:0012275 ! meso-epithelium -relationship: develops_from UBERON:0004139 ! cardiogenic plate -property_value: UBPROP:0000001 "The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000115", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002202 UBERON:0004139 ! develops from cardiogenic plate [Term] id: UBERON:0004341 @@ -13986,7 +13478,6 @@ xref: EHDAA2:0001525 xref: EHDAA:185 xref: EMAPA:16072 xref: FMA:293110 -xref: MESH:D054240 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C28402 xref: SCTID:361438007 xref: UMLS:C0033153 {source="ncithesaurus:Primitive_Streak"} @@ -13994,12 +13485,9 @@ xref: VHOG:0001202 xref: Wikipedia:Primitive_streak is_a: UBERON:0000485 {source="EHDAA2"} ! simple columnar epithelium is_a: UBERON:0005291 ! embryonic tissue -relationship: has_potential_to_develop_into UBERON:0000925 ! endoderm -relationship: has_potential_to_develop_into UBERON:0000926 ! mesoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Gray13.png" xsd:anyURI -property_value: RO:0002174 NCBITaxon:32443 -property_value: UBPROP:0000003 "(...) the blastopore equivalent of chordates (germ ring in fish, marginal zone/blastopore lip in frog and node/primitive streak in chick and mouse) (...) (reference 1); Indeed, the primitive streak has been considered the homologue of the blastopore since the 1870s (reference 2).[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001202", ontology="VHOG", source="PMID:9609826 Wu LH, Lengyel JA, Role of caudal in hindgut specification and gastrulation suggests homology between Drosophila amnioproctodeal invagination and vertebrate blastopore. Development (1998), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.139", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "VHOG includes a very broad grouping here based on http://www.ncbi.nlm.nih.gov/pubmed/9609826" xsd:string {external_ontology="VHOG"} +relationship: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm +relationship: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Gray13.png" xsd:anyURI [Term] id: UBERON:0004535 @@ -14018,10 +13506,8 @@ xref: BILA:0000016 xref: BTO:0000088 xref: CALOHA:TS-1297 xref: EFO:0000791 -xref: EHDAA2:0000216 xref: EHDAA:394 xref: EMAPA:16104 -xref: EMAPA:16370 xref: EV:0100017 xref: FMA:7161 xref: GAID:467 @@ -14047,9 +13533,7 @@ intersection_of: part_of UBERON:0001009 ! circulatory system relationship: has_part UBERON:0000948 ! heart relationship: has_part UBERON:0001981 ! blood vessel relationship: part_of UBERON:0001009 ! circulatory system -relationship: present_in_taxon NCBITaxon:9606 -property_value: IAO:0000232 "we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph." xsd:string -property_value: UBPROP:0000003 "The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000302", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.451", source="http://bgee.unil.ch/"} +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004537 @@ -14067,11 +13551,11 @@ xref: ZFA:0001079 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature -intersection_of: composed_primarily_of UBERON:0001981 ! blood vessel -relationship: composed_primarily_of UBERON:0001981 ! blood vessel -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI -property_value: depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +intersection_of: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel +relationship: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Blood_Vasculature.glb" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Blood_Vasculature.glb" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004572 @@ -14090,9 +13574,8 @@ xref: SCTID:362030008 xref: VHOG:0000273 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0007798 {source="MA"} ! vascular system -relationship: has_member UBERON:0001637 ! artery -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000003 "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000273", ontology="VHOG", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005)", source="http://bgee.unil.ch/"} +relationship: RO:0002351 UBERON:0001637 ! has member artery +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004582 @@ -14112,9 +13595,8 @@ xref: UMLS:C1267406 {source="ncithesaurus:Venous_System"} xref: VHOG:0000277 is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0007798 {source="MA"} ! vascular system -relationship: composed_primarily_of UBERON:0001638 ! vein -relationship: present_in_taxon NCBITaxon:9606 -property_value: UBPROP:0000003 "The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000277", ontology="VHOG", source="DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005)", source="http://bgee.unil.ch/"} +relationship: RO:0002473 UBERON:0001638 ! composed primarily of vein +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004638 @@ -14136,7 +13618,7 @@ is_a: UBERON:0004852 ! cardiovascular system endothelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0001981 ! blood vessel relationship: part_of UBERON:0001981 ! blood vessel -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004639 @@ -14164,12 +13646,12 @@ is_a: UBERON:0001637 ! artery is_a: UBERON:0001980 ! arteriole is_a: UBERON:0003644 ! kidney arterial blood vessel relationship: capable_of GO:0003093 {source="Wikipedia"} ! regulation of glomerular filtration -relationship: connecting_branch_of UBERON:0004723 ! interlobular artery -relationship: contributes_to_morphology_of UBERON:0001229 ! renal corpuscle relationship: part_of UBERON:0001229 ! renal corpuscle -relationship: present_in_taxon NCBITaxon:9606 -relationship: supplies UBERON:0001285 ! nephron -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +relationship: RO:0002178 UBERON:0001285 ! supplies nephron +relationship: RO:0002252 UBERON:0004723 ! connecting branch of interlobular artery +relationship: RO:0002433 UBERON:0001229 ! contributes to morphology of renal corpuscle +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004716 @@ -14186,12 +13668,12 @@ xref: NCIT:C34131 xref: UMLS:C1516779 {source="ncithesaurus:Conceptus"} xref: Wikipedia:Conceptus is_a: UBERON:0000061 ! anatomical structure -relationship: develops_from CL:0000365 ! animal zygote -relationship: existence_ends_with UBERON:0000068 ! embryo stage -relationship: existence_starts_with UBERON:0000068 ! embryo stage relationship: has_part UBERON:0002050 ! embryonic structure relationship: has_part UBERON:0016887 ! entire extraembryonic component -property_value: editor_note "EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus" xsd:string +relationship: RO:0002202 CL:0000365 ! develops from animal zygote +relationship: RO:0002489 UBERON:0000068 ! existence starts with embryo stage +relationship: RO:0002493 UBERON:0000068 ! existence ends with embryo stage +property_value: IAO:0000116 "EHDAA2 places this as a subtype of organism. This leads to the inference that a conceptus is an embryo (if an embryo is defined as an organism at embryo stage), which eliminates the embryonic + extra-embryonic = conceptus" xsd:string [Term] id: UBERON:0004723 @@ -14216,9 +13698,9 @@ xref: UMLS:C1512856 {source="ncithesaurus:Interlobular_Artery"} xref: Wikipedia:Interlobular_arteries is_a: UBERON:0003644 ! kidney arterial blood vessel disjoint_from: UBERON:0009885 {source="Wikipedia:Renal_circulation"} ! interlobar artery -relationship: connected_to UBERON:0001552 ! kidney arcuate artery -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +relationship: RO:0002170 UBERON:0001552 ! connected to kidney arcuate artery +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004734 @@ -14238,7 +13720,6 @@ synonym: "trilaminar disk" RELATED [https://orcid.org/0000-0002-6601-2165] synonym: "trilaminar germ" RELATED [https://orcid.org/0000-0002-6601-2165] xref: BILA:0000060 xref: BTO:0001403 -xref: FBbt:00005317 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:293108 xref: GAID:1302 xref: MESH:D005775 @@ -14251,10 +13732,9 @@ xref: Wikipedia:Gastrula xref: Wikipedia:Trilaminar_blastocyst is_a: UBERON:0000922 ! embryo intersection_of: UBERON:0000468 ! multicellular organism -intersection_of: existence_starts_and_ends_during UBERON:0000109 ! gastrula stage -relationship: develops_from UBERON:0000307 ! blastula -relationship: existence_starts_and_ends_during UBERON:0000109 ! gastrula stage -property_value: UBPROP:0000012 "We explicitly merge the NCITA terms here" xsd:string {external_ontology="NCIT"} +intersection_of: RO:0002491 UBERON:0000109 ! existence starts and ends during gastrula stage +relationship: RO:0002202 UBERON:0000307 ! develops from blastula +relationship: RO:0002491 UBERON:0000109 ! existence starts and ends during gastrula stage [Term] id: UBERON:0004765 @@ -14271,8 +13751,6 @@ xref: XAO:0004012 xref: ZFA:0005494 is_a: UBERON:0000062 ! organ relationship: part_of UBERON:0001434 {source="VSAO"} ! skeletal system -property_value: UBPROP:0000001 "Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000128", ontology="VSAO", source="PSPUB:0000170"} -property_value: UBPROP:0000001 "Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001890", ontology="TAO", source="TAO:VSAO_workshop"} [Term] id: UBERON:0004770 @@ -14290,12 +13768,12 @@ xref: SCTID:361827000 xref: VSAO:0000181 is_a: UBERON:0034925 ! anatomical collection intersection_of: UBERON:0034925 ! anatomical collection -intersection_of: has_member UBERON:0000982 ! skeletal joint -relationship: existence_ends_during UBERON:0000066 ! fully formed stage -relationship: functionally_related_to GO:0040011 ! locomotion -relationship: has_member UBERON:0000982 ! skeletal joint -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria +intersection_of: RO:0002351 UBERON:0000982 ! has member skeletal joint relationship: part_of UBERON:0001434 {source="FMA"} ! skeletal system +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002328 GO:0040011 ! functionally related to locomotion +relationship: RO:0002351 UBERON:0000982 ! has member skeletal joint +relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage [Term] id: UBERON:0004810 @@ -14314,9 +13792,9 @@ intersection_of: UBERON:0000483 ! epithelium intersection_of: adjacent_to UBERON:0000464 ! anatomical space intersection_of: part_of UBERON:0001231 ! nephron tubule relationship: adjacent_to UBERON:0000464 ! anatomical space -relationship: contributes_to_morphology_of UBERON:0001231 ! nephron tubule relationship: part_of UBERON:0001231 ! nephron tubule -property_value: editor_note "See https://github.com/obophenotype/uberon/issues/1305" xsd:string +relationship: RO:0002433 UBERON:0001231 ! contributes to morphology of nephron tubule +property_value: IAO:0000116 "See https://github.com/obophenotype/uberon/issues/1305" xsd:string [Term] id: UBERON:0004819 @@ -14335,8 +13813,8 @@ xref: MA:0002846 is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002113 ! kidney -relationship: contributes_to_morphology_of UBERON:0002113 ! kidney relationship: part_of UBERON:0002113 ! kidney +relationship: RO:0002433 UBERON:0002113 ! contributes to morphology of kidney [Term] id: UBERON:0004852 @@ -14361,8 +13839,7 @@ is_a: UBERON:0001986 ! endothelium intersection_of: UBERON:0001986 ! endothelium intersection_of: part_of UBERON:0004535 ! cardiovascular system relationship: part_of UBERON:0004535 ! cardiovascular system -property_value: editor_note "consider merging with 'endothelium'" xsd:string -property_value: UBPROP:0000003 "Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001217", ontology="VHOG", source="ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207", source="http://bgee.unil.ch/"} +property_value: IAO:0000116 "consider merging with 'endothelium'" xsd:string [Term] id: UBERON:0004872 @@ -14380,7 +13857,6 @@ xref: Wikipedia:Lateral_plate_mesoderm#Division_into_layers xref: XAO:0000276 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0003081 ! lateral plate mesoderm -property_value: UBPROP:0000012 "We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors" xsd:string {external_ontology="BILA"} [Term] id: UBERON:0004874 @@ -14398,9 +13874,7 @@ xref: Wikipedia:Somatopleure is_a: UBERON:0002050 ! embryonic structure relationship: overlaps UBERON:0000924 ! ectoderm relationship: part_of UBERON:0003081 {source="EHDAA2"} ! lateral plate mesoderm -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png" xsd:anyURI -property_value: UBPROP:0000011 "Gives rise to the paired appendages in jawed vertebrates. a persistent somatopleure through the redistribution and expansion of the lateral plate mesoderm is a synapomorphy for gnathostomes and a critical step in generating a novel developmental module with dramatic evolutionary potentia (Tulenko et al. 2012) http://burkelab.research.wesleyan.edu/current-projects/lamprey/" xsd:string -property_value: UBPROP:0000012 "sources differ as to whether this is part-of or develops-from the LPM" xsd:string +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png" xsd:anyURI [Term] id: UBERON:0004875 @@ -14415,7 +13889,7 @@ xref: SCTID:361405003 xref: UMLS:C1283944 {source="ncithesaurus:Nephrogenic_Cord"} xref: Wikipedia:Nephrogenic_cord is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0004876 ! urogenital fold +relationship: RO:0002202 UBERON:0004876 ! develops from urogenital fold [Term] id: UBERON:0004876 @@ -14431,11 +13905,10 @@ xref: EMAPA:30888 xref: FMA:321919 xref: Wikipedia:Urogenital_folds is_a: UBERON:0006598 ! presumptive structure -relationship: develops_from UBERON:0003064 {source="Wikipedia"} ! intermediate mesoderm -relationship: develops_from UBERON:0012292 {source="EHDAA2"} ! embryonic cloacal fold -relationship: has_potential_to_develop_into UBERON:0004176 ! external genitalia relationship: part_of UBERON:0009196 {source="EHDAA2"} ! indifferent external genitalia -property_value: UBPROP:0000013 "Less commonly, urogenital fold refers to the fold in the mesonephros which is the precursor of e.g. the suspensory ligament of the ovary. This is the case in older versions of Gray's anatomy[WP]" xsd:string +relationship: RO:0002202 UBERON:0003064 {source="Wikipedia"} ! develops from intermediate mesoderm +relationship: RO:0002202 UBERON:0012292 {source="EHDAA2"} ! develops from embryonic cloacal fold +relationship: RO:0002387 UBERON:0004176 ! has potential to develop into external genitalia [Term] id: UBERON:0004880 @@ -14453,10 +13926,8 @@ xref: EFO:0003426 xref: TAO:0000091 xref: ZFA:0000091 is_a: UBERON:0002050 ! embryonic structure -relationship: only_in_taxon NCBITaxon:7711 ! Chordata relationship: part_of UBERON:0003068 ! axial mesoderm -property_value: UBPROP:0000001 "Notochord rudiment[ZFIN:ZDB-PUB-961014-576]." xsd:string {source="ZFIN:ZDB-PUB-961014-576"} -property_value: UBPROP:0000012 "WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord." xsd:string +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata [Term] id: UBERON:0004905 @@ -14465,7 +13936,6 @@ namespace: uberon def: "Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts." [http://orcid.org/0000-0002-6601-2165] subset: grouping_class synonym: "joint" NARROW [] -xref: FBbt:00005811 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0034921 ! multi organ part structure relationship: part_of UBERON:0004770 ! articular system @@ -14481,15 +13951,13 @@ synonym: "gut section" RELATED [FBbt:00100315] synonym: "intestinal tract" RELATED [] synonym: "segment of intestinal tract" RELATED [] synonym: "subdivision of alimentary system" RELATED [FMA:71131] -xref: FBbt:00100315 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:71131 is_a: UBERON:0013522 ! subdivision of tube intersection_of: UBERON:0013522 ! subdivision of tube intersection_of: subdivision_of UBERON:0001555 ! digestive tract relationship: part_of UBERON:0001555 ! digestive tract -relationship: present_in_taxon NCBITaxon:9606 relationship: subdivision_of UBERON:0001555 ! digestive tract -property_value: IAO:0000232 "intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct." xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0004923 @@ -14499,8 +13967,8 @@ def: "A part of a wall of an organ that forms a layer." [http://orcid.org/0000-0 subset: upper_level xref: FMA:82485 is_a: UBERON:0000064 ! organ part -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa relationship: part_of UBERON:0000060 ! anatomical wall +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0005061 @@ -14518,7 +13986,6 @@ xref: Wikipedia:Neural_groove xref: XAO:0000248 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0003075 ! neural plate -property_value: UBPROP:0000001 "The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]." xsd:string {source="Wikipedia:Neural_groove"} [Term] id: UBERON:0005062 @@ -14538,10 +14005,9 @@ xref: XAO:0004087 is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0005157 ! epithelial fold is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0015212 ! lateral structure -relationship: in_lateral_side_of UBERON:0005061 ! neural groove relationship: part_of UBERON:0005061 ! neural groove -property_value: UBPROP:0000001 "In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]." xsd:string {source="Wikipedia:Neural_fold"} [Term] id: UBERON:0005068 @@ -14554,8 +14020,7 @@ xref: EFO:0003498 xref: TAO:0000133 xref: ZFA:0000133 is_a: UBERON:0016879 ! future central nervous system -relationship: develops_from UBERON:0007135 ! neural keel -property_value: UBPROP:0000001 "An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000133", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002202 UBERON:0007135 ! develops from neural keel [Term] id: UBERON:0005080 @@ -14564,8 +14029,8 @@ namespace: uberon def: "The portion of the ureteric bud tube that contributes to the morphogenesis of the metanephros[GO]." [GO:0035502] is_a: UBERON:0000084 ! ureteric bud intersection_of: UBERON:0000084 ! ureteric bud -intersection_of: has_potential_to_develop_into UBERON:0000081 ! metanephros -relationship: has_potential_to_develop_into UBERON:0000081 ! metanephros +intersection_of: RO:0002387 UBERON:0000081 ! has potential to develop into metanephros +relationship: RO:0002387 UBERON:0000081 ! has potential to develop into metanephros [Term] id: UBERON:0005081 @@ -14574,8 +14039,8 @@ namespace: uberon def: "The portion of the ureteric bud that contributes to the morphogenesis of the ureter. The ureter ureteric bud is the initial structure that forms the ureter[GO]." [GO:0035503] is_a: UBERON:0000084 ! ureteric bud intersection_of: UBERON:0000084 ! ureteric bud -intersection_of: has_potential_to_develop_into UBERON:0000056 ! ureter -relationship: has_potential_to_develop_into UBERON:0000056 ! ureter +intersection_of: RO:0002387 UBERON:0000056 ! has potential to develop into ureter +relationship: RO:0002387 UBERON:0000056 ! has potential to develop into ureter [Term] id: UBERON:0005090 @@ -14585,12 +14050,10 @@ def: "Muscle structures are contractile cells, tissues or organs that are found synonym: "muscle" RELATED [] synonym: "muscle element" RELATED [] synonym: "musculus" EXACT [FMA:30316] -xref: EMAPA:32715 xref: FMA:30316 is_a: UBERON:0000061 ! anatomical structure relationship: has_part CL:0000187 ! muscle cell -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa -property_value: IAO:0000232 "in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila" xsd:string +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0005095 @@ -14599,8 +14062,8 @@ namespace: uberon def: "Missing definition for term UBERON:0005095. Please replace it using linked reference." [GO:0072003] synonym: "kidney anlage" RELATED [GOC:mtg_kidney_jan10] is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0007687 {source="GO"} ! kidney field -property_value: editor_note "class added for consistency with GO - consider merging with kidney mesenchyme." xsd:string +relationship: RO:0002202 UBERON:0007687 {source="GO"} ! develops from kidney field +property_value: IAO:0000116 "class added for consistency with GO - consider merging with kidney mesenchyme." xsd:string [Term] id: UBERON:0005096 @@ -14627,8 +14090,8 @@ xref: Wikipedia:Descending_limb_of_loop_of_Henle is_a: UBERON:0000064 ! organ part relationship: part_of UBERON:0001289 ! descending limb of loop of Henle relationship: part_of UBERON:0004136 ! intermediate tubule -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/uberon/issues/2276" xsd:string [Term] @@ -14648,9 +14111,9 @@ xref: MA:0002610 xref: Wikipedia:Connecting_tubule is_a: UBERON:0007685 ! region of nephron tubule is_a: UBERON:0012275 ! meso-epithelium -relationship: develops_from UBERON:0003220 {source="Wikipedia"} ! metanephric mesenchyme -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +relationship: RO:0002202 UBERON:0003220 {source="Wikipedia"} ! develops from metanephric mesenchyme +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0005103 @@ -14658,6 +14121,7 @@ name: mesonephric epithelium namespace: uberon def: "An epithelium that is part of a mesonephros [Automatically generated definition]." [OBOL:automatic] is_a: UBERON:0004819 ! kidney epithelium +is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0000080 ! mesonephros relationship: part_of UBERON:0000080 ! mesonephros @@ -14701,9 +14165,9 @@ xref: SCTID:245434005 xref: UMLS:C0227658 {source="ncithesaurus:Ascending_Limb_of_the_Henle_s_Loop"} xref: Wikipedia:Ascending_limb_of_loop_of_Henle is_a: UBERON:0004135 ! distal tubule -relationship: contributes_to_morphology_of UBERON:0001288 ! loop of Henle relationship: part_of UBERON:0001288 ! loop of Henle -property_value: editor_note "TODO - thick/thin check. Also relationship to distal tubule. We need a home for MA:0002634-renal straight tubule" xsd:string +relationship: RO:0002433 UBERON:0001288 ! contributes to morphology of loop of Henle +property_value: IAO:0000116 "TODO - thick/thin check. Also relationship to distal tubule. We need a home for MA:0002634-renal straight tubule" xsd:string [Term] id: UBERON:0005167 @@ -14734,9 +14198,8 @@ synonym: "interstitium" EXACT [] xref: FMA:86301 xref: SCTID:85293002 is_a: UBERON:0003891 {source="FMA"} ! stroma -relationship: present_in_taxon NCBITaxon:9606 -property_value: editor_note "specify differentia from stroma" xsd:string -property_value: UBPROP:0000007 "interstital" xsd:string +property_value: IAO:0000116 "specify differentia from stroma" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0005172 @@ -14794,8 +14257,8 @@ xref: MA:0000557 is_a: UBERON:0002075 ! viscus is_a: UBERON:0005181 ! thoracic segment organ intersection_of: UBERON:0000062 ! organ -intersection_of: located_in UBERON:0002224 ! thoracic cavity -relationship: located_in UBERON:0002224 ! thoracic cavity +intersection_of: RO:0001025 UBERON:0002224 ! located in thoracic cavity +relationship: RO:0001025 UBERON:0002224 ! located in thoracic cavity [Term] id: UBERON:0005179 @@ -14868,13 +14331,11 @@ xref: SCTID:362210003 is_a: UBERON:0005169 ! interstitial tissue intersection_of: UBERON:0005169 ! interstitial tissue intersection_of: part_of UBERON:0002113 ! kidney -relationship: composed_primarily_of CL:1000692 ! kidney interstitial fibroblast -relationship: contributes_to_morphology_of UBERON:0002113 ! kidney relationship: part_of UBERON:0002113 ! kidney -relationship: present_in_taxon NCBITaxon:9606 -property_value: editor_note "See https://sourceforge.net/p/geneontology/ontology-requests/10941/" xsd:string -property_value: UBPROP:0000009 "The interstitium is necessarily involved in all intrarenal exchange processes since the reabsorption and secretion of fluid and solutes implicates a transit across the interstitial compartment." xsd:string -property_value: UBPROP:0000010 "The fibroblasts in the interstitium provide the 'skeleton' of the tissue and maintain the three-dimensional architecture of the tissue." xsd:string +relationship: RO:0002433 UBERON:0002113 ! contributes to morphology of kidney +relationship: RO:0002473 CL:1000692 ! composed primarily of kidney interstitial fibroblast +property_value: IAO:0000116 "See https://sourceforge.net/p/geneontology/ontology-requests/10941/" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0005256 @@ -14925,14 +14386,13 @@ synonym: "developmental tissue" RELATED [MIAA:0000019] xref: AEO:0000125 xref: CALOHA:TS-2122 xref: EHDAA2:0003125 -xref: FBbt:00007006 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:292313 xref: MIAA:0000019 is_a: UBERON:0000465 ! material anatomical entity relationship: capable_of GO:0032502 ! developmental process -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0005498 @@ -14942,7 +14402,6 @@ def: "Multi-tissue structure that arises from the heart rudiment and will become subset: vertebrate_core synonym: "early primitive heart tube" NARROW [EMAPA:16208] synonym: "primitive heart tube" EXACT [EMAPA:16215] -xref: BTO:0006179 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: EHDAA2:0001512 xref: EHDAA:424 xref: EHDAA:436 @@ -14954,8 +14413,8 @@ xref: Wikipedia:Primitive_heart_tube xref: ZFA:0000149 is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004120 ! mesoderm-derived structure -relationship: develops_from UBERON:0004291 {source="ZFA"} ! heart rudiment relationship: part_of UBERON:0000922 ! embryo +relationship: RO:0002202 UBERON:0004291 {source="ZFA"} ! develops from heart rudiment [Term] id: UBERON:0005564 @@ -14978,10 +14437,8 @@ xref: TAO:0001262 xref: WBbt:0008366 xref: ZFA:0001262 is_a: UBERON:0001048 {source="Obol"} ! primordium -relationship: has_potential_to_develop_into UBERON:0000991 ! gonad relationship: part_of UBERON:0000990 {source="ZFA"} ! reproductive system -property_value: UBPROP:0000001 "Immature reproductive tissue that has not undergone final maturation into either testis or ovary.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0001262", ontology="TAO", source="ZFIN:curator"} -property_value: UBPROP:0000008 "this is a very broad grouping class" xsd:string +relationship: RO:0002387 UBERON:0000991 ! has potential to develop into gonad [Term] id: UBERON:0005721 @@ -15001,13 +14458,13 @@ xref: VHOG:0001239 xref: XAO:0000264 xref: ZFA:0000067 is_a: UBERON:0000926 ! mesoderm +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0000926 ! mesoderm -intersection_of: has_potential_to_develop_into UBERON:0002120 ! pronephros -relationship: has_potential_to_develop_into UBERON:0002120 ! pronephros -relationship: immediate_transformation_of UBERON:0007297 {source="Bgee:AN"} ! presumptive pronephric mesoderm +intersection_of: RO:0002387 UBERON:0002120 ! has potential to develop into pronephros relationship: part_of UBERON:0003064 {source="ZFA"} ! intermediate mesoderm -property_value: UBPROP:0000001 "Portion of tissue that consists of the mesenchymal precursor to the pronephric kidney and that begins to separate from the intermediate mesoderm at NF stage 21 and epithelializes by NF stage 30.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0011090", ontology="AAO", source="XAO:curator"} +relationship: RO:0002387 UBERON:0002120 ! has potential to develop into pronephros +relationship: RO:0002495 UBERON:0007297 {source="Bgee:AN"} ! immediate transformation of presumptive pronephric mesoderm [Term] id: UBERON:0005749 @@ -15018,14 +14475,12 @@ subset: pheno_slim synonym: "glomerular capillary tuft" RELATED [] synonym: "glomerulus" RELATED INCONSISTENT [EMAPA:28239] xref: EMAPA:28239 -xref: SCTID:362217000 xref: Wikipedia:Glomerulus is_a: UBERON:0000064 ! organ part is_a: UBERON:0004120 ! mesoderm-derived structure relationship: capable_of_part_of GO:0003094 ! glomerular filtration -relationship: develops_from UBERON:0003220 {source="Wikipedia"} ! metanephric mesenchyme relationship: part_of UBERON:0001230 ! glomerular capsule -property_value: UBPROP:0000011 "...Soon afterwards, endothelial cells invade to make a capillary knot-like outgrowth, the glomerular tuft, which goes on to form the glomerulus" xsd:string {source="GudMap"} +relationship: RO:0002202 UBERON:0003220 {source="Wikipedia"} ! develops from metanephric mesenchyme [Term] id: UBERON:0005753 @@ -15058,9 +14513,9 @@ is_a: UBERON:0000476 ! acellular anatomical structure intersection_of: UBERON:0000476 ! acellular anatomical structure intersection_of: bounding_layer_of UBERON:0000061 ! anatomical structure relationship: bounding_layer_of UBERON:0000061 ! anatomical structure -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0005769 @@ -15080,12 +14535,11 @@ xref: Wikipedia:Basement_membrane is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005764 {source="FMA"} ! acellular membrane relationship: adjacent_to CL:0000066 ! epithelial cell -relationship: composed_primarily_of GO:0005604 ! basement membrane relationship: has_part GO:0005587 ! collagen type IV trimer -relationship: only_in_taxon NCBITaxon:33208 ! Metazoa relationship: part_of UBERON:0000483 ! epithelium -relationship: present_in_taxon NCBITaxon:80999 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} -property_value: IAO:0000232 "this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell." xsd:string +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002473 GO:0005604 ! composed primarily of basement membrane +property_value: RO:0002175 NCBITaxon:80999 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} [Term] id: UBERON:0005777 @@ -15101,20 +14555,19 @@ xref: EMAPA:28251 xref: EMAPA:30965 xref: FMA:74274 xref: MA:0001659 -xref: MESH:D050533 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0001-9439-5346", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: NCIT:C32683 xref: SCTID:243897006 xref: TAO:0005285 xref: UMLS:C0599297 {source="ncithesaurus:Glomerular_Basement_Membrane"} xref: Wikipedia:Glomerular_basement_membrane xref: ZFA:0005285 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005769 ! basement membrane of epithelium intersection_of: UBERON:0005769 ! basement membrane of epithelium intersection_of: part_of UBERON:0000074 ! renal glomerulus relationship: capable_of GO:0003094 ! glomerular filtration relationship: part_of UBERON:0004188 {is_inferred="true", source="https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships"} ! glomerular epithelium -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/de/PhysiologieGlom%C3%A9rulaire.png" xsd:anyURI -property_value: UBPROP:0000001 "Membrane between the mesonephric podocytes and the renal glomerular capillaries. It is a trilaminar structure composed of the fused basement membranes of the glomerular capillaries and basement membrane of the podocytes. The capillary membranes touch the GBM at contact points that are separated by pores. The membrane is semi-permeable allowing water and small molecules to pass into the renal capsular space.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0005285", ontology="TAO", source="ZFIN:ZDB-PUB-000824-1"} +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/de/PhysiologieGlom%C3%A9rulaire.png" xsd:anyURI [Term] id: UBERON:0005792 @@ -15129,7 +14582,7 @@ xref: VHOG:0001240 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0001008 ! renal system relationship: part_of UBERON:0004122 ! genitourinary system -property_value: editor_note "TODO - check ridge vs cord vs nephrogenic cord vs blastema" xsd:string +property_value: IAO:0000116 "TODO - check ridge vs cord vs nephrogenic cord vs blastema" xsd:string [Term] id: UBERON:0005856 @@ -15142,7 +14595,7 @@ xref: EHDAA2_RETIRED:0003148 xref: EHDAA:8979 is_a: UBERON:0007524 {source="AEO"} ! dense mesenchyme tissue is_a: UBERON:0011585 {source="cjm"} ! cell condensation -relationship: composed_primarily_of CL:0000335 {source="AEO-modified-relation"} ! mesenchyme condensation cell +relationship: RO:0002473 CL:0000335 {source="AEO-modified-relation"} ! composed primarily of mesenchyme condensation cell [Term] id: UBERON:0005944 @@ -15155,7 +14608,6 @@ subset: uberon_slim synonym: "skeleton axiale" RELATED OMO:0003011 [Wikipedia:Axial_skeleton] xref: AAO:0000963 xref: EMAPA:17214 -xref: EMAPA:18043 xref: MA:0000308 xref: NCIT:C32172 xref: SCTID:361725000 @@ -15164,13 +14616,12 @@ xref: VSAO:0000056 xref: Wikipedia:Axial_skeleton xref: XAO:0004011 is_a: UBERON:0010912 ! subdivision of skeleton -relationship: contributes_to_morphology_of UBERON:0001434 ! skeletal system -relationship: develops_from UBERON:0003089 ! sclerotome relationship: part_of UBERON:0011137 ! axial skeletal system -relationship: present_in_taxon NCBITaxon:9606 -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg" xsd:anyURI +relationship: RO:0002202 UBERON:0003089 ! develops from sclerotome +relationship: RO:0002433 UBERON:0001434 ! contributes to morphology of skeletal system +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Axial_skeleton_diagram.svg" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" xsd:anyURI -property_value: UBPROP:0000001 "Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000056", ontology="VSAO", source="PSPUB:0000170"} [Term] id: UBERON:0006217 @@ -15192,14 +14643,12 @@ xref: UMLS:C0231056 {source="ncithesaurus:Cloacal_Membrane"} xref: VHOG:0001198 xref: Wikipedia:Cloacal_membrane is_a: UBERON:0000158 ! membranous layer -relationship: contributes_to_morphology_of UBERON:0000163 ! embryonic cloaca -relationship: develops_from UBERON:0004341 {source="Wikipedia"} ! primitive streak -relationship: has_developmental_contribution_from UBERON:0000924 ! ectoderm -relationship: has_developmental_contribution_from UBERON:0000925 ! endoderm relationship: part_of UBERON:0000163 ! embryonic cloaca -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray991.png" xsd:anyURI -property_value: UBPROP:0000001 "A membrane that separates the proctodeum and the hindgut in the early embryo. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.497, see_Kardong_KV][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001198", ontology="VHOG", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000003 "In mammals, the cloaca exists as an embryonic structure that undergoes septation to become distinct urethral, anal, and genital orifices.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001198", ontology="VHOG", source="PMID:11830557 De Santa Barbara P, Roberts DJ, Tail gut endoderm and gut/genitourinary/tail development: a new tissue-specific role for Hoxa13. Development (2002)", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0004341 {source="Wikipedia"} ! develops from primitive streak +relationship: RO:0002254 UBERON:0000924 ! has developmental contribution from ectoderm +relationship: RO:0002254 UBERON:0000925 ! has developmental contribution from endoderm +relationship: RO:0002433 UBERON:0000163 ! contributes to morphology of embryonic cloaca +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray991.png" xsd:anyURI [Term] id: UBERON:0006267 @@ -15217,9 +14666,8 @@ is_a: UBERON:0000490 {source="EHDAA2"} ! unilaminar epithelium is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium -relationship: develops_from UBERON:0006268 {source="EHDAA2"} ! notochordal process -property_value: editor_note "TODO - check ordering; awaiting confirmation from JB" xsd:string -property_value: UBPROP:0000001 "The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0001212", ontology="VHOG", source="http://bgee.unil.ch/"} +relationship: RO:0002202 UBERON:0006268 {source="EHDAA2"} ! develops from notochordal process +property_value: IAO:0000116 "TODO - check ordering; awaiting confirmation from JB" xsd:string [Term] id: UBERON:0006268 @@ -15238,8 +14686,8 @@ xref: NCIT:C34232 xref: UMLS:C1518430 {source="ncithesaurus:Notochordal_Process"} xref: VHOG:0001213 is_a: UBERON:0005423 ! developing anatomical structure -relationship: develops_from UBERON:0000924 {source="EHDAA2"} ! ectoderm -relationship: only_in_taxon NCBITaxon:7711 ! Chordata +relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002202 UBERON:0000924 {source="EHDAA2"} ! develops from ectoderm [Term] id: UBERON:0006314 @@ -15258,8 +14706,8 @@ xref: MESH:D001826 xref: Wikipedia:Body_fluid is_a: UBERON:0000463 ! organism substance intersection_of: UBERON:0000463 ! organism substance -intersection_of: has_quality PATO:0001548 ! quality of a liquid -relationship: has_quality PATO:0001548 ! quality of a liquid +intersection_of: RO:0000086 PATO:0001548 ! has quality quality of a liquid +relationship: RO:0000086 PATO:0001548 ! has quality quality of a liquid [Term] id: UBERON:0006534 @@ -15304,7 +14752,7 @@ is_a: UBERON:0006876 ! vasculature of organ intersection_of: UBERON:0002049 ! vasculature intersection_of: part_of UBERON:0002113 ! kidney relationship: part_of UBERON:0002113 ! kidney -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0006553 @@ -15317,7 +14765,6 @@ is_a: UBERON:0000058 ! duct intersection_of: UBERON:0000058 ! duct intersection_of: part_of UBERON:0002113 ! kidney relationship: part_of UBERON:0002113 ! kidney -property_value: UBPROP:0000012 "in ZFA this is defined as part of mesonephros" xsd:string {external_ontology="ZFA"} [Term] id: UBERON:0006555 @@ -15341,11 +14788,11 @@ xref: TAO:0000416 xref: ZFA:0000416 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0000925 ! endoderm intersection_of: part_of UBERON:0000307 ! blastula -relationship: has_potential_to_develop_into UBERON:0000925 ! endoderm -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +intersection_of: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm relationship: part_of UBERON:0000307 ! blastula +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm [Term] id: UBERON:0006596 @@ -15359,8 +14806,8 @@ xref: TAO:0000568 xref: ZFA:0000568 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0000178 ! blood -relationship: has_potential_to_develop_into UBERON:0000178 ! blood +intersection_of: RO:0002387 UBERON:0000178 ! has potential to develop into blood +relationship: RO:0002387 UBERON:0000178 ! has potential to develop into blood [Term] id: UBERON:0006598 @@ -15374,10 +14821,10 @@ xref: TAO:0001116 xref: ZFA:0001116 is_a: UBERON:0002050 ! embryonic structure intersection_of: UBERON:0005423 ! developing anatomical structure -intersection_of: has_potential_to_develop_into UBERON:0000061 ! anatomical structure intersection_of: part_of UBERON:0000922 ! embryo -relationship: has_potential_to_develop_into UBERON:0000061 ! anatomical structure -property_value: editor_note "Consider merging with anlage" xsd:string +intersection_of: RO:0002387 UBERON:0000061 ! has potential to develop into anatomical structure +relationship: RO:0002387 UBERON:0000061 ! has potential to develop into anatomical structure +property_value: IAO:0000116 "Consider merging with anlage" xsd:string [Term] id: UBERON:0006601 @@ -15393,11 +14840,11 @@ xref: XAO:0004132 xref: ZFA:0001376 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0000924 ! ectoderm intersection_of: part_of UBERON:0000307 ! blastula -relationship: has_potential_to_develop_into UBERON:0000924 ! ectoderm -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +intersection_of: RO:0002387 UBERON:0000924 ! has potential to develop into ectoderm relationship: part_of UBERON:0000307 ! blastula +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002387 UBERON:0000924 ! has potential to develop into ectoderm [Term] id: UBERON:0006603 @@ -15411,11 +14858,11 @@ xref: TAO:0001377 xref: ZFA:0001377 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0000926 ! mesoderm intersection_of: part_of UBERON:0000307 ! blastula -relationship: has_potential_to_develop_into UBERON:0000926 ! mesoderm -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +intersection_of: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm relationship: part_of UBERON:0000307 ! blastula +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm [Term] id: UBERON:0006853 @@ -15439,12 +14886,10 @@ def: "The distalmost portion of the digestive tract, derived from the hindgut, a synonym: "rectal part of digestive tract" RELATED [] synonym: "rectum" NARROW [FBbt:00005756] synonym: "terminal section of digestive tract" RELATED [] -xref: FBbt:00005756 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: WBbt:0005773 is_a: UBERON:0004921 ! subdivision of digestive tract -relationship: continuous_with UBERON:0001245 ! anus -relationship: develops_from UBERON:0001046 ! hindgut -property_value: IAO:0000232 "this class is the superclass of 'rectum', which is currently reserved for the vertebrate structure. May be merged in future." xsd:string +relationship: RO:0002150 UBERON:0001245 ! continuous with anus +relationship: RO:0002202 UBERON:0001046 ! develops from hindgut [Term] id: UBERON:0006876 @@ -15474,7 +14919,6 @@ is_a: UBERON:0000483 ! epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: has_part CL:0000076 ! squamous epithelial cell relationship: has_part CL:0000076 ! squamous epithelial cell -property_value: UBPROP:0000012 "FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium" xsd:string {external_ontology="FBbt"} [Term] id: UBERON:0006965 @@ -15505,7 +14949,7 @@ xref: EHDAA2_RETIRED:0003192 xref: FMA:24137 xref: NCIT:C34022 xref: UMLS:C1515977 {source="ncithesaurus:Anatomic_Surface"} -is_a: UBERON:0010199 {notes="via morphological boundary in CARO"} ! bona-fide anatomical boundary +is_a: UBERON:0010199 ! bona-fide anatomical boundary [Term] id: UBERON:0007005 @@ -15528,13 +14972,14 @@ xref: FMA:293143 xref: SCTID:360387000 xref: VHOG:0001641 xref: XAO:0000235 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue -relationship: developmentally_induced_by UBERON:0009881 ! anterior lateral plate mesoderm -relationship: develops_from UBERON:0004872 ! splanchnic layer of lateral plate mesoderm relationship: part_of UBERON:0004140 ! primary heart field relationship: part_of UBERON:0009881 ! anterior lateral plate mesoderm -property_value: editor_note "consider FBbt:00005541 ! cardiogenic mesoderm" xsd:string -property_value: editor_note "review EHDAA2 placement" xsd:string +relationship: RO:0002202 UBERON:0004872 ! develops from splanchnic layer of lateral plate mesoderm +relationship: RO:0002256 UBERON:0009881 ! developmentally induced by anterior lateral plate mesoderm +property_value: IAO:0000116 "consider FBbt:00005541 ! cardiogenic mesoderm" xsd:string +property_value: IAO:0000116 "review EHDAA2 placement" xsd:string [Term] id: UBERON:0007010 @@ -15544,10 +14989,10 @@ def: "Organism at the cleavage stage." [OBOL:automatic] xref: BILA:0000058 is_a: UBERON:0000922 ! embryo intersection_of: UBERON:0000468 ! multicellular organism -intersection_of: existence_ends_with UBERON:0000107 ! cleavage stage -intersection_of: existence_starts_with UBERON:0000107 ! cleavage stage -relationship: existence_ends_with UBERON:0000107 ! cleavage stage -relationship: existence_starts_with UBERON:0000107 ! cleavage stage +intersection_of: RO:0002489 UBERON:0000107 ! existence starts with cleavage stage +intersection_of: RO:0002493 UBERON:0000107 ! existence ends with cleavage stage +relationship: RO:0002489 UBERON:0000107 ! existence starts with cleavage stage +relationship: RO:0002493 UBERON:0000107 ! existence ends with cleavage stage [Term] id: UBERON:0007026 @@ -15566,12 +15011,11 @@ xref: SCTID:360394002 xref: UMLS:C1514442 {source="ncithesaurus:Primordial_Gut"} is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001555 ! digestive tract -relationship: existence_starts_during UBERON:0000109 ! gastrula stage -relationship: has_developmental_contribution_from UBERON:0000925 ! endoderm -relationship: has_developmental_contribution_from UBERON:0000926 ! mesoderm -relationship: has_potential_to_develop_into UBERON:0001555 ! digestive tract -property_value: UBPROP:0000011 "The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis" xsd:string {source="NCBIBook:NBK10107"} +intersection_of: RO:0002387 UBERON:0001555 ! has potential to develop into digestive tract +relationship: RO:0002254 UBERON:0000925 ! has developmental contribution from endoderm +relationship: RO:0002254 UBERON:0000926 ! has developmental contribution from mesoderm +relationship: RO:0002387 UBERON:0001555 ! has potential to develop into digestive tract +relationship: RO:0002488 UBERON:0000109 ! existence starts during gastrula stage [Term] id: UBERON:0007100 @@ -15584,14 +15028,12 @@ synonym: "adult heart" RELATED [FBbt:00003154] synonym: "dorsal tube" NARROW [Wikipedia:Heart] synonym: "heart" NARROW [GO:0007507] xref: http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg -xref: SPD:0000130 xref: TADS:0000147 is_a: UBERON:0015228 ! circulatory organ intersection_of: UBERON:0015228 ! circulatory organ intersection_of: capable_of GO:0008015 ! blood circulation -relationship: capable_of GO:0008015 {notes="GO uses blood circulation generically to include the haemolymphatic fluid of arthropods"} ! blood circulation +relationship: capable_of GO:0008015 ! blood circulation relationship: has_part CL:0002494 ! cardiocyte -property_value: UBPROP:0000008 "note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis" xsd:string [Term] id: UBERON:0007135 @@ -15604,8 +15046,7 @@ xref: EFO:0003497 xref: TAO:0000131 xref: ZFA:0000131 is_a: UBERON:0016879 ! future central nervous system -relationship: develops_from UBERON:0003075 ! neural plate -property_value: UBPROP:0000001 "An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000131", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002202 UBERON:0003075 ! develops from neural plate [Term] id: UBERON:0007282 @@ -15619,9 +15060,9 @@ xref: TAO:0000053 xref: ZFA:0000053 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0003059 ! presomitic mesoderm -relationship: develops_from UBERON:0009618 {consistent_with="https://github.com/obophenotype/uberon/wiki/The-neural-crest", source="EDHAA2"} ! trunk paraxial mesoderm -relationship: has_potential_to_develop_into UBERON:0003059 ! presomitic mesoderm +intersection_of: RO:0002387 UBERON:0003059 ! has potential to develop into presomitic mesoderm +relationship: RO:0002202 UBERON:0009618 ! develops from trunk paraxial mesoderm +relationship: RO:0002387 UBERON:0003059 ! has potential to develop into presomitic mesoderm [Term] id: UBERON:0007284 @@ -15636,12 +15077,11 @@ xref: TAO:0000063 xref: ZFA:0000063 is_a: UBERON:0016879 ! future central nervous system intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0003075 ! neural plate -relationship: develops_from UBERON:0002346 ! neurectoderm -relationship: has_potential_to_develop_into UBERON:0003075 ! neural plate +intersection_of: RO:0002387 UBERON:0003075 ! has potential to develop into neural plate relationship: part_of UBERON:0004734 ! gastrula -property_value: editor_note "consider merging" xsd:string -property_value: UBPROP:0000001 "Region of the gastrula which gives rise to the neural plate.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000063", ontology="TAO", source="ZFIN:curator"} +relationship: RO:0002202 UBERON:0002346 ! develops from neurectoderm +relationship: RO:0002387 UBERON:0003075 ! has potential to develop into neural plate +property_value: IAO:0000116 "consider merging" xsd:string [Term] id: UBERON:0007285 @@ -15657,10 +15097,10 @@ xref: XAO:0004134 xref: ZFA:0000591 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 {source="https://github.com/obophenotype/uberon/issues/1277"} ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0003077 {source="https://github.com/obophenotype/uberon/issues/1277"} ! paraxial mesoderm intersection_of: part_of UBERON:0000307 {source="https://github.com/obophenotype/uberon/issues/1277"} ! blastula -relationship: has_potential_to_develop_into UBERON:0003077 ! paraxial mesoderm +intersection_of: RO:0002387 UBERON:0003077 {source="https://github.com/obophenotype/uberon/issues/1277"} ! has potential to develop into paraxial mesoderm relationship: part_of UBERON:0000307 ! blastula +relationship: RO:0002387 UBERON:0003077 ! has potential to develop into paraxial mesoderm [Term] id: UBERON:0007297 @@ -15674,8 +15114,8 @@ xref: TAO:0001070 xref: ZFA:0001070 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0005721 ! pronephric mesoderm -relationship: has_potential_to_develop_into UBERON:0005721 ! pronephric mesoderm +intersection_of: RO:0002387 UBERON:0005721 ! has potential to develop into pronephric mesoderm +relationship: RO:0002387 UBERON:0005721 ! has potential to develop into pronephric mesoderm [Term] id: UBERON:0007499 @@ -15687,7 +15127,7 @@ xref: EHDAA2:0003115 is_a: UBERON:0003914 {source="AEO"} ! epithelial tube is_a: UBERON:0009856 ! sac intersection_of: UBERON:0000483 ! epithelium -intersection_of: has_quality PATO:0001987 ! saccular +intersection_of: RO:0000086 PATO:0001987 ! has quality saccular [Term] id: UBERON:0007500 @@ -15728,7 +15168,7 @@ is_a: UBERON:0003104 ! mesenchyme intersection_of: UBERON:0003104 ! mesenchyme intersection_of: participates_in GO:0016477 ! cell migration relationship: participates_in GO:0016477 ! cell migration -property_value: editor_note "this class will be an important part of the NC reorganization" xsd:string +property_value: IAO:0000116 "this class will be an important part of the NC reorganization" xsd:string [Term] id: UBERON:0007684 @@ -15751,7 +15191,6 @@ synonym: "renal tubule region" EXACT [FMA:17692] xref: FMA:17692 is_a: UBERON:0001231 ! nephron tubule relationship: part_of UBERON:0001231 ! nephron tubule -property_value: UBPROP:0000012 "consider moving MA:0000377 renal tubule here, as it includes the various segments (proximal etc) as subclasses, not parts" xsd:string {external_ontology="MA"} [Term] id: UBERON:0007687 @@ -15763,8 +15202,8 @@ is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0006598 ! presumptive structure is_a: UBERON:0007688 ! anlage intersection_of: UBERON:0007688 ! anlage -intersection_of: has_potential_to_develop_into UBERON:0002113 ! kidney -relationship: has_potential_to_develop_into UBERON:0002113 ! kidney +intersection_of: RO:0002387 UBERON:0002113 ! has potential to develop into kidney +relationship: RO:0002387 UBERON:0002113 ! has potential to develop into kidney [Term] id: UBERON:0007688 @@ -15779,7 +15218,6 @@ synonym: "organ field" RELATED [] xref: AEO:0000170 xref: EFO:0001649 xref: EHDAA2:0003170 -xref: FBbt:00005426 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: Wikipedia:Anlage_(biology) is_a: UBERON:0000479 {source="FBbt"} ! tissue is_a: UBERON:0005423 {source="AEO", source="FBbt"} ! developing anatomical structure @@ -15800,10 +15238,8 @@ xref: NCIT:C33854 xref: UMLS:C0489903 {source="ncithesaurus:Vascular_System"} is_a: UBERON:0000467 ! anatomical system relationship: part_of UBERON:0004535 {source="MA"} ! cardiovascular system -relationship: present_in_taxon NCBITaxon:9606 -property_value: editor_note "consider merging with vasculature" xsd:string -property_value: UBPROP:0000001 "The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]." xsd:string {source="ncithesaurus:Vascular_System"} -property_value: UBPROP:0000012 "in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system" xsd:string {external_ontology="MA"} +property_value: IAO:0000116 "consider merging with vasculature" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0007823 @@ -15822,12 +15258,10 @@ xref: FMA:24874 xref: VSAO:0000303 is_a: UBERON:0000475 ! organism subdivision intersection_of: UBERON:0000475 ! organism subdivision -intersection_of: has_skeleton UBERON:0010719 ! girdle skeleton -relationship: has_skeleton UBERON:0010719 ! girdle skeleton -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata +intersection_of: RO:0002551 UBERON:0010719 ! has skeleton girdle skeleton relationship: part_of UBERON:0010707 ! appendage girdle complex -property_value: IAO:0000232 "this encompasses non-skeletal tissue" xsd:string -property_value: UBPROP:0000001 "An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There are only two instances of appendage girdle regions per organism.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000303", ontology="VSAO", source="https://orcid.org/0000-0002-6601-2165"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002551 UBERON:0010719 ! has skeleton girdle skeleton [Term] id: UBERON:0007832 @@ -15858,21 +15292,17 @@ xref: VSAO:0000155 xref: Wikipedia:Pelvis xref: XAO:0003064 xref: ZFA:0000565 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010719 ! girdle skeleton intersection_of: UBERON:0010912 ! subdivision of skeleton intersection_of: part_of UBERON:0001271 ! pelvic girdle region -intersection_of: skeleton_of UBERON:0001271 ! pelvic girdle region -relationship: develops_from UBERON:0010377 {source="PMID:21455939"} ! mesenchyme from somatopleure +intersection_of: RO:0002576 UBERON:0001271 ! skeleton of pelvic girdle region relationship: part_of UBERON:0001271 ! pelvic girdle region relationship: part_of UBERON:0012476 ! skeleton of pelvic complex -relationship: skeleton_of UBERON:0001271 ! pelvic girdle region -property_value: depiction "http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png" xsd:anyURI -property_value: editor_note "need to resolve whether this is a paired structure or a single belt (Paired in FMA - implicitly paired in VSAO)" xsd:string -property_value: UBPROP:0000001 "Anatomical cluster by which the hind limbs are supported and attached to the vertebral column.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000426", ontology="AAO", source="AAO:LAP"} -property_value: UBPROP:0000001 "Anatomical cluster that consists of the paired basipterygia which support the pelvic fin.[TAO]" xsd:string {date_retrieved="2012-08-14", external_class="TAO:0000565", ontology="TAO", source="TAO:wd"} -property_value: UBPROP:0000001 "Girdle skeleton consisting of a set of bones linking the axial series to the hindlimb/fin skeleton and offering anchoring areas for hindlimb/fin and caudal musculature.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000155", ontology="VSAO", source="https://orcid.org/0000-0002-6601-2165"} -property_value: UBPROP:0000003 "The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin.[well established][VHOG]" xsd:string {date_retrieved="2012-09-17", external_class="VHOG:0000305", ontology="VHOG", source="ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.333", source="http://bgee.unil.ch/"} -property_value: UBPROP:0000012 "Note that the VSAO and many ontologies use the label 'pelvic girdle' to denote the skeletal region specifically. We place the EHDAA2 class here, note that this includes the pre-cartilage condensation as parts" xsd:string {external_ontology="VSAO"} +relationship: RO:0002202 UBERON:0010377 {source="PMID:21455939"} ! develops from mesenchyme from somatopleure +relationship: RO:0002576 UBERON:0001271 ! skeleton of pelvic girdle region +property_value: http://xmlns.com/foaf/0.1/depiction "http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png" xsd:anyURI +property_value: IAO:0000116 "need to resolve whether this is a paired structure or a single belt (Paired in FMA - implicitly paired in VSAO)" xsd:string [Term] id: UBERON:0008987 @@ -15912,10 +15342,10 @@ xref: EHDAA2:0001113 xref: EHDAA:177 xref: EMAPA:16097 is_a: UBERON:0000477 ! anatomical cluster -relationship: composed_primarily_of UBERON:0003104 ! mesenchyme -relationship: has_developmental_contribution_from UBERON:0000926 {source="EHDAA2"} ! mesoderm relationship: part_of UBERON:0000922 ! embryo -property_value: editor_note "consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)" xsd:string +relationship: RO:0002254 UBERON:0000926 {source="EHDAA2"} ! has developmental contribution from mesoderm +relationship: RO:0002473 UBERON:0003104 ! composed primarily of mesenchyme +property_value: IAO:0000116 "consider adding new class (EMAPA:16097) for mesenchyme of embryo (some mesenchyme is extraembryonic - e.g. amnion mesoderm)" xsd:string [Term] id: UBERON:0009196 @@ -15975,8 +15405,7 @@ synonym: "renal tubule (generic)" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "tubule of excretory system" EXACT [https://orcid.org/0000-0002-6601-2165, OBOL:automatic] is_a: UBERON:0003914 ! epithelial tube is_a: UBERON:0006555 ! excretory tube -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -property_value: IAO:0000232 "this class groups vertebrate nephron tubules with analagous structures such as insect Malpighian tubules" xsd:string +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria [Term] id: UBERON:0009856 @@ -15987,8 +15416,8 @@ synonym: "pouch" EXACT [] xref: galen:Diverticulum is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: has_quality PATO:0001987 ! saccular -relationship: has_quality PATO:0001987 ! saccular +intersection_of: RO:0000086 PATO:0001987 ! has quality saccular +relationship: RO:0000086 PATO:0001987 ! has quality saccular [Term] id: UBERON:0009881 @@ -15999,6 +15428,7 @@ synonym: "ALPM" EXACT [ZFA:0005041] xref: EFO:0003704 xref: TAO:0005041 xref: ZFA:0005041 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue relationship: part_of UBERON:0003081 {source="ZFA"} ! lateral plate mesoderm @@ -16022,11 +15452,10 @@ xref: SCTID:62802007 xref: Wikipedia:Interlobar_arteries is_a: UBERON:0001637 ! artery intersection_of: UBERON:0001637 ! artery -intersection_of: supplies UBERON:0009913 ! renal lobe -relationship: present_in_taxon NCBITaxon:9606 -relationship: supplies UBERON:0009913 ! renal lobe -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI -property_value: UBPROP:0000012 "FMA only has the set term" xsd:string {external_ontology="FMA"} +intersection_of: RO:0002178 UBERON:0009913 ! supplies renal lobe +relationship: RO:0002178 UBERON:0009913 ! supplies renal lobe +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0009912 @@ -16057,11 +15486,10 @@ xref: Wikipedia:Renal_lobe is_a: UBERON:0009912 ! anatomical lobe intersection_of: UBERON:0009912 ! anatomical lobe intersection_of: part_of UBERON:0002113 ! kidney -relationship: contributes_to_morphology_of UBERON:0002113 ! kidney relationship: part_of UBERON:0002113 ! kidney -property_value: depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI -property_value: editor_note "todo - add has_part relationships." xsd:string -property_value: UBPROP:0000008 "human kidneys have multilobar (multipyramidal) architecture while mice and rats have unilobar (unipyramidal) kidneys" xsd:string {source="MP"} +relationship: RO:0002433 UBERON:0002113 ! contributes to morphology of kidney +property_value: http://xmlns.com/foaf/0.1/depiction "https://upload.wikimedia.org/wikipedia/commons/7/7e/Kidney_PioM.png" xsd:anyURI +property_value: IAO:0000116 "todo - add has_part relationships." xsd:string [Term] id: UBERON:0010000 @@ -16072,15 +15500,14 @@ subset: common_anatomy subset: upper_level synonym: "multicellular structure" EXACT [FBbt:00100313] xref: CARO:0010000 -xref: FBbt:00100313 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: has_quality PATO:0001993 ! multicellular +intersection_of: RO:0000086 PATO:0001993 ! has quality multicellular relationship: has_part CL:0000000 ! cell -relationship: has_quality PATO:0001993 ! multicellular -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0000086 PATO:0001993 ! has quality multicellular +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0010199 @@ -16104,8 +15531,8 @@ xref: FMA:71005 xref: TAO:0002228 xref: ZFA:0001718 is_a: UBERON:0006598 ! presumptive structure -relationship: has_potential_to_develop_into UBERON:0002081 ! cardiac atrium relationship: part_of UBERON:0004141 {source="ZFA"} ! heart tube +relationship: RO:0002387 UBERON:0002081 ! has potential to develop into cardiac atrium [Term] id: UBERON:0010314 @@ -16115,9 +15542,8 @@ def: "An anatomical structure that has some part that develops from the neural c subset: grouping_class is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: has_developmental_contribution_from UBERON:0002342 ! neural crest -relationship: has_developmental_contribution_from UBERON:0002342 ! neural crest -property_value: IAO:0000232 "Grouping term for query purposes" xsd:string +intersection_of: RO:0002254 UBERON:0002342 ! has developmental contribution from neural crest +relationship: RO:0002254 UBERON:0002342 ! has developmental contribution from neural crest [Term] id: UBERON:0010316 @@ -16125,7 +15551,7 @@ name: germ layer / neural crest namespace: uberon is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0005291 ! embryonic tissue -relationship: develops_from UBERON:0002532 ! epiblast (generic) +relationship: RO:0002202 UBERON:0002532 ! develops from epiblast (generic) [Term] id: UBERON:0010371 @@ -16137,8 +15563,8 @@ xref: FMA:69064 is_a: UBERON:0000483 ! epithelium is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000483 ! epithelium -intersection_of: develops_from UBERON:0000924 ! ectoderm -relationship: composed_primarily_of CL:0002077 ! ecto-epithelial cell +intersection_of: RO:0002202 UBERON:0000924 ! develops from ectoderm +relationship: RO:0002473 CL:0002077 ! composed primarily of ecto-epithelial cell [Term] id: UBERON:0010377 @@ -16146,14 +15572,15 @@ name: mesenchyme from somatopleure namespace: uberon def: "Mesenchyme that develops_from a somatopleure." [OBOL:automatic] xref: EHDAA2:0001120 +is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue intersection_of: UBERON:0003104 ! mesenchyme -intersection_of: develops_from UBERON:0004874 ! somatopleure intersection_of: part_of UBERON:0000922 ! embryo -relationship: develops_from UBERON:0004874 ! somatopleure +intersection_of: RO:0002202 UBERON:0004874 ! develops from somatopleure relationship: part_of UBERON:0009142 {source="EHDAA2"} ! entire embryonic mesenchyme -property_value: editor_note "the way this class is defined also includes extraembryonic mesenchyme such as the amniotic mesenchyme; in future this may be restricted to embryonic derivatives" xsd:string +relationship: RO:0002202 UBERON:0004874 ! develops from somatopleure +property_value: IAO:0000116 "the way this class is defined also includes extraembryonic mesenchyme such as the amniotic mesenchyme; in future this may be restricted to embryonic derivatives" xsd:string [Term] id: UBERON:0010523 @@ -16179,18 +15606,17 @@ synonym: "primitive nephron" BROAD [] is_a: UBERON:0003914 {source="EHDAA2-inferred"} ! epithelial tube is_a: UBERON:0004819 ! kidney epithelium is_a: UBERON:0006555 ! excretory tube -relationship: develops_from UBERON:0004209 {source="EHDAA2"} ! renal vesicle -relationship: has_potential_to_develop_into UBERON:0001285 ! nephron -relationship: located_in UBERON:0003918 ! kidney mesenchyme -property_value: UBPROP:0000012 "EHDAA2 treats this as already having a tubular structure, but in the ZFA representation this is a cluster of cells" xsd:string {external_ontology="EHDAA2"} +relationship: RO:0001025 UBERON:0003918 ! located in kidney mesenchyme +relationship: RO:0002202 UBERON:0004209 {source="EHDAA2"} ! develops from renal vesicle +relationship: RO:0002387 UBERON:0001285 ! has potential to develop into nephron [Term] id: UBERON:0010536 name: nephron progenitor namespace: uberon is_a: UBERON:0000479 {source="ZFA"} ! tissue -relationship: has_potential_to_develop_into UBERON:0001285 ! nephron relationship: part_of UBERON:0003918 {source="cjm"} ! kidney mesenchyme +relationship: RO:0002387 UBERON:0001285 ! has potential to develop into nephron [Term] id: UBERON:0010707 @@ -16208,14 +15634,10 @@ xref: FMA:7182 xref: VSAO:0000214 is_a: UBERON:0000475 ! organism subdivision is_a: UBERON:0015212 ! lateral structure -relationship: dc-contributor https://orcid.org/0000-0001-9114-8737 -relationship: functionally_related_to GO:0040011 ! locomotion -relationship: in_lateral_side_of UBERON:0000468 ! multicellular organism -relationship: only_in_taxon NCBITaxon:7742 ! Vertebrata -property_value: editor_note "It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO]" xsd:string -property_value: UBPROP:0000001 "Anatomical group that consists of the soft and skeletal tissues of the appendicular region of the body and the appendage proper.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000214", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070"} -property_value: UBPROP:0000005 "It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO]" xsd:string {date_retrieved="2012-09-06", external_class="VSAO:0000214", ontology="VSAO", source="Curator"} -property_value: UBPROP:0000012 "note that the FMA uses the term 'limb' to refer to the entire appendage complex (free limb plus girdle region)" xsd:string {external_ontology="FMA"} +relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002328 GO:0040011 ! functionally related to locomotion +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-9114-8737 +property_value: IAO:0000116 "It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO]" xsd:string creation_date: 2012-04-23T10:46:51Z [Term] @@ -16238,10 +15660,7 @@ is_a: UBERON:0010707 ! appendage girdle complex intersection_of: UBERON:0010707 ! appendage girdle complex intersection_of: has_part UBERON:0001271 ! pelvic girdle region relationship: has_part UBERON:0001271 ! pelvic girdle region -relationship: has_skeleton UBERON:0012476 ! skeleton of pelvic complex -property_value: RO:0002171 UBERON:0010708 -property_value: UBPROP:0000001 "Appendage girdle complex that when present, encompasses the pelvic appendage and the pelvic girdle.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000215", ontology="VSAO", source="VSAO:MAH"} -property_value: UBPROP:0000012 "note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region). Note the MA class 'hindlimb' may also belong here" xsd:string {external_ontology="FMA"} +relationship: RO:0002551 UBERON:0012476 ! has skeleton skeleton of pelvic complex [Term] id: UBERON:0010719 @@ -16253,14 +15672,11 @@ xref: AAO:0010686 xref: VSAO:0000302 is_a: UBERON:0010912 ! subdivision of skeleton intersection_of: UBERON:0010912 ! subdivision of skeleton -intersection_of: skeleton_of UBERON:0007823 ! appendage girdle region +intersection_of: RO:0002576 UBERON:0007823 ! skeleton of appendage girdle region relationship: part_of UBERON:0002091 ! appendicular skeleton relationship: part_of UBERON:0007823 ! appendage girdle region relationship: proximally_connected_to UBERON:0002090 ! postcranial axial skeleton -relationship: skeleton_of UBERON:0007823 ! appendage girdle region -property_value: UBPROP:0000001 "Skeletal subdivision that is part of the appendage girdle region.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000302", ontology="VSAO", source="GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070"} -property_value: UBPROP:0000002 "relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: part_of subdivision of skeleton (UBERON:0010912)[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000302", ontology="VSAO"} -property_value: UBPROP:0000002 "relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: proximally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000302", ontology="VSAO"} +relationship: RO:0002576 UBERON:0007823 ! skeleton of appendage girdle region [Term] id: UBERON:0010912 @@ -16276,7 +15692,6 @@ xref: VSAO:0000042 is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision relationship: part_of UBERON:0000075 {source="UBERONREF:0000003"} ! subdivision of skeletal system relationship: part_of UBERON:0004288 {source="VSAO"} ! skeleton -property_value: UBPROP:0000001 "Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000042", notes="incorrect", ontology="VSAO", source="VSAO:curator"} [Term] id: UBERON:0011137 @@ -16297,7 +15712,7 @@ synonym: "axial skeletal system" BROAD [https://github.com/obophenotype/uberon/w synonym: "post-cranial axial skeletal system" EXACT [] xref: FMA:302077 is_a: UBERON:0000075 {source="FMA"} ! subdivision of skeletal system -relationship: develops_from UBERON:0003089 {source="cjm"} ! sclerotome +relationship: RO:0002202 UBERON:0003089 {source="cjm"} ! develops from sclerotome property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton" xsd:anyURI [Term] @@ -16315,9 +15730,8 @@ is_a: UBERON:0011216 ! organ system subdivision is_a: UBERON:0015212 ! lateral structure relationship: has_part UBERON:0000056 ! ureter relationship: has_part UBERON:0002113 ! kidney -relationship: in_lateral_side_of UBERON:0001008 {source="FMA-abduced-lr"} ! renal system relationship: part_of UBERON:0001008 {source="FMA"} ! renal system -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0011216 @@ -16327,15 +15741,14 @@ def: "A subdivision of an anatomical system." [http://orcid.org/0000-0002-6601-2 subset: common_anatomy subset: human_reference_atlas subset: upper_level -xref: FBbt:00007330 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:67509 xref: SCTID:91690000 is_a: UBERON:0010000 {source="FBbt"} ! multicellular anatomical structure relationship: part_of UBERON:0000467 ! anatomical system -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0011249 @@ -16343,13 +15756,11 @@ name: appendicular skeletal system namespace: uberon def: "Subdivision of the skeletal system which consists of the appendicular skeleton plus associated joints." [https://orcid.org/0000-0002-6601-2165] xref: FMA:7484 -xref: VHOG:0001666 xref: VSAO:0000306 is_a: UBERON:0000075 ! subdivision of skeletal system relationship: has_part UBERON:0000982 ! skeletal joint relationship: has_part UBERON:0002091 ! appendicular skeleton property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton" xsd:anyURI -property_value: UBPROP:0000001 "Skeletal system which consists of the appendicular skeleton plus associated joints.[VSAO]" xsd:string {date_retrieved="2012-08-14", external_class="VSAO:0000306", ontology="VSAO", source="https://orcid.org/0000-0002-6601-2165"} [Term] id: UBERON:0011585 @@ -16359,7 +15770,7 @@ def: "Anatomical structure that is an aggregation of similar cells from which ca xref: VSAO:0000006 xref: XAO:0004021 is_a: UBERON:0000061 {source="VSAO"} ! anatomical structure -property_value: editor_note "consider obsoleting, coordinate with VSAO" xsd:string +property_value: IAO:0000116 "consider obsoleting, coordinate with VSAO" xsd:string [Term] id: UBERON:0011676 @@ -16372,7 +15783,7 @@ synonym: "body segment" RELATED [] synonym: "main body segment" RELATED [] is_a: UBERON:0000475 ! organism subdivision relationship: part_of UBERON:0013701 ! main body axis -property_value: editor_note "Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem" xsd:string +property_value: IAO:0000116 "Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem" xsd:string [Term] id: UBERON:0011695 @@ -16403,10 +15814,9 @@ synonym: "schizocoelom" NARROW [] xref: EHDAA2:0004731 xref: Wikipedia:Coelom is_a: UBERON:0000481 {source="EHDAA2"} ! multi-tissue structure -relationship: never_in_taxon NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -property_value: editor_note "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." xsd:string -property_value: UBPROP:0000007 "coelomic" xsd:string +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +property_value: IAO:0000116 "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." xsd:string +property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} [Term] id: UBERON:0012274 @@ -16428,7 +15838,7 @@ xref: FMA:86452 is_a: UBERON:0000483 ! epithelium is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0000483 ! epithelium -intersection_of: develops_from UBERON:0000926 ! mesoderm +intersection_of: RO:0002202 UBERON:0000926 ! develops from mesoderm [Term] id: UBERON:0012292 @@ -16474,10 +15884,10 @@ synonym: "skeleton of posterior limb/fin and girdle" RELATED [https://orcid.org/ xref: FMA:24140 is_a: UBERON:0010912 ! subdivision of skeleton intersection_of: UBERON:0010912 ! subdivision of skeleton -intersection_of: skeleton_of UBERON:0010709 ! pelvic complex +intersection_of: RO:0002576 UBERON:0010709 ! skeleton of pelvic complex relationship: part_of UBERON:0002091 ! appendicular skeleton relationship: part_of UBERON:0010709 {source="FMA"} ! pelvic complex -relationship: skeleton_of UBERON:0010709 ! pelvic complex +relationship: RO:0002576 UBERON:0010709 ! skeleton of pelvic complex [Term] id: UBERON:0013241 @@ -16490,8 +15900,7 @@ synonym: "urethral sulcus" EXACT [] xref: SCTID:361531004 xref: Wikipedia:Urethral_groove is_a: UBERON:0002050 ! embryonic structure -relationship: develops_from UBERON:0004876 {source="Wikipedia"} ! urogenital fold -property_value: UBPROP:0000008 "In humans, the urethral groove is a temporary linear indentation on the underside (ventral side) of the male penis during embryonic development. It typically appears around 8 weeks of gestation and becomes closed into a normal male urethra by the 12th week" xsd:string {source="Wikipedia:Urethral_groove"} +relationship: RO:0002202 UBERON:0004876 {source="Wikipedia"} ! develops from urogenital fold [Term] id: UBERON:0013522 @@ -16512,11 +15921,11 @@ subset: common_anatomy synonym: "foramen space" NARROW [] xref: FMA:9338 is_a: UBERON:0000464 {source="FMA"} ! anatomical space -relationship: connects UBERON:0000464 {cardinality="2"} ! anatomical space -relationship: luminal_space_of UBERON:0004111 ! anatomical conduit -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0002176 UBERON:0000464 {cardinality="2"} ! connects anatomical space +relationship: RO:0002572 UBERON:0004111 ! luminal space of anatomical conduit +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0013701 @@ -16525,7 +15934,7 @@ namespace: uberon def: "A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages." [https://orcid.org/0000-0002-6601-2165] subset: non_informative is_a: UBERON:0000475 ! organism subdivision -relationship: only_in_taxon NCBITaxon:6072 ! Eumetazoa +relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa [Term] id: UBERON:0013702 @@ -16537,11 +15946,9 @@ synonym: "body" RELATED [AEO:0000103] synonym: "whole body" RELATED [BTO:0001489] xref: AEO:0000103 xref: BTO:0001489 -xref: EMAPA:36031 xref: FMA:231424 is_a: UBERON:0000475 {source="AEO"} ! organism subdivision relationship: part_of UBERON:0013701 ! main body axis -property_value: UBPROP:0000001 "Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]." xsd:string {source="FMA:231424"} [Term] id: UBERON:0013756 @@ -16551,12 +15958,11 @@ def: "A blood that is part of a vein." [OBOL:automatic] synonym: "blood in vein" EXACT [FMA:83067] synonym: "portion of venous blood" EXACT [FMA:83067] synonym: "venous blood" EXACT [FMA:83067] -xref: BTO:0006187 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} xref: FMA:83067 is_a: UBERON:0000178 ! blood intersection_of: UBERON:0000178 ! blood -intersection_of: located_in UBERON:0001638 ! vein -relationship: located_in UBERON:0001638 ! vein +intersection_of: RO:0001025 UBERON:0001638 ! located in vein +relationship: RO:0001025 UBERON:0001638 ! located in vein [Term] id: UBERON:0013768 @@ -16588,7 +15994,7 @@ xref: Wikipedia:Thoracic_skeleton is_a: UBERON:0010912 ! subdivision of skeleton relationship: part_of UBERON:0000915 ! thoracic segment of trunk relationship: part_of UBERON:0002090 ! postcranial axial skeleton -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0014903 @@ -16600,9 +16006,9 @@ xref: TAO:0005076 xref: ZFA:0005076 is_a: UBERON:0001048 ! primordium intersection_of: UBERON:0001048 ! primordium -intersection_of: has_potential_to_develop_into UBERON:0002049 ! vasculature -relationship: has_potential_to_develop_into UBERON:0002049 ! vasculature +intersection_of: RO:0002387 UBERON:0002049 ! has potential to develop into vasculature relationship: part_of UBERON:0011695 ! embryonic cardiovascular system +relationship: RO:0002387 UBERON:0002049 ! has potential to develop into vasculature [Term] id: UBERON:0015212 @@ -16612,11 +16018,7 @@ def: "Any structure that is placed on one side of the left-right axis of a bilat subset: grouping_class subset: non_informative is_a: UBERON:0000061 ! anatomical structure -intersection_of: UBERON:0000061 ! anatomical structure -intersection_of: in_lateral_side_of UBERON:0000465 ! material anatomical entity -relationship: in_lateral_side_of UBERON:0000465 ! material anatomical entity -relationship: only_in_taxon NCBITaxon:33213 ! Bilateria -property_value: IAO:0000232 "This class is primarily to implement taxon constraints. It may be removed in the future." xsd:string +relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria [Term] id: UBERON:0015228 @@ -16629,10 +16031,9 @@ synonym: "cardiac structure" RELATED [] synonym: "circulatory vessel" NARROW [] synonym: "heart" BROAD [] synonym: "heart or heart like organ" EXACT [] -xref: SPD:0000130 is_a: UBERON:0003103 ! compound organ -relationship: has_quality PATO:0001690 ! contractile relationship: part_of UBERON:0001009 ! circulatory system +relationship: RO:0000086 PATO:0001690 ! has quality contractile [Term] id: UBERON:0015410 @@ -16644,7 +16045,7 @@ xref: EMAPA:37597 {source="MA:th"} xref: MA:0002449 is_a: UBERON:0005178 {source="MA"} ! thoracic cavity element relationship: part_of UBERON:0004535 ! cardiovascular system -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0016566 @@ -16665,10 +16066,10 @@ synonym: "future CNS" EXACT [] synonym: "presumptive central nervous system" EXACT [] is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001017 ! central nervous system -relationship: develops_from UBERON:0000924 ! ectoderm -relationship: has_potential_to_develop_into UBERON:0001017 ! central nervous system +intersection_of: RO:0002387 UBERON:0001017 ! has potential to develop into central nervous system relationship: part_of UBERON:0016880 ! future nervous system +relationship: RO:0002202 UBERON:0000924 ! develops from ectoderm +relationship: RO:0002387 UBERON:0001017 ! has potential to develop into central nervous system [Term] id: UBERON:0016880 @@ -16680,9 +16081,9 @@ synonym: "presumptive nervous system" EXACT [AAO:0000477] xref: AAO:0000477 is_a: UBERON:0006598 ! presumptive structure intersection_of: UBERON:0006598 ! presumptive structure -intersection_of: has_potential_to_develop_into UBERON:0001016 ! nervous system -relationship: existence_starts_during_or_after UBERON:0000111 ! organogenesis stage -relationship: has_potential_to_develop_into UBERON:0001016 ! nervous system +intersection_of: RO:0002387 UBERON:0001016 ! has potential to develop into nervous system +relationship: RO:0002387 UBERON:0001016 ! has potential to develop into nervous system +relationship: RO:0002496 UBERON:0000111 ! existence starts during or after organogenesis stage [Term] id: UBERON:0016887 @@ -16696,8 +16097,8 @@ xref: EHDAA2:0000003 xref: EMAPA:16042 is_a: UBERON:0000481 {source="AEO"} ! multi-tissue structure relationship: adjacent_to UBERON:0002050 ! embryonic structure -relationship: existence_starts_and_ends_during UBERON:0000068 ! embryo stage relationship: part_of UBERON:0004716 {source="AEO"} ! conceptus +relationship: RO:0002491 UBERON:0000068 ! existence starts and ends during embryo stage [Term] id: UBERON:0018707 @@ -16708,8 +16109,8 @@ synonym: "bladder" NARROW [BTO:0000123] xref: BTO:0000123 is_a: UBERON:0000489 ! cavitated compound organ is_a: UBERON:0009856 ! sac -relationship: has_quality PATO:0002468 ! distensible -relationship: location_of UBERON:0000463 ! organism substance +relationship: RO:0000086 PATO:0002468 ! has quality distensible +relationship: RO:0001015 UBERON:0000463 ! location of organism substance [Term] id: UBERON:0034921 @@ -16720,10 +16121,10 @@ subset: common_anatomy synonym: "anatomical cluster" RELATED [CARO:0020001] xref: CARO:0020001 is_a: UBERON:0010000 {source="CARO"} ! multicellular anatomical structure -relationship: composed_primarily_of UBERON:0000064 ! organ part -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0002473 UBERON:0000064 ! composed primarily of organ part +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0034923 @@ -16732,14 +16133,13 @@ namespace: uberon def: "Material anatomical entity consisting of multiple anatomical structures that are not connected to each other." [CARO:0020000] subset: common_anatomy xref: CARO:0020000 -xref: FBbt:00007276 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0000465 {source="CARO"} ! material anatomical entity -relationship: composed_primarily_of UBERON:0000061 ! anatomical structure relationship: has_component UBERON:0000061 {minCardinality="2"} ! anatomical structure -relationship: has_quality PATO:0010001 ! disconnected -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +relationship: RO:0000086 PATO:0010001 ! has quality disconnected +relationship: RO:0002473 UBERON:0000061 ! composed primarily of anatomical structure +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0034925 @@ -16748,11 +16148,11 @@ namespace: uberon def: "A collection of anatomical structures that are alike in terms of their morphology or developmental origin." [http://orcid.org/0000-0002-6601-2165] subset: common_anatomy is_a: UBERON:0000465 ! material anatomical entity -relationship: has_member UBERON:0000061 ! anatomical structure -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 -property_value: editor_note "resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected" xsd:string +relationship: RO:0002351 UBERON:0000061 ! has member anatomical structure +property_value: IAO:0000116 "resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected" xsd:string +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0034969 @@ -16798,9 +16198,7 @@ def: "Any chamber of the right side of the heart." [http://orcid.org/0000-0002-6 xref: FMA:7165 xref: SCTID:362007002 is_a: UBERON:0004151 ! cardiac chamber -intersection_of: UBERON:0004151 ! cardiac chamber -intersection_of: in_right_side_of UBERON:0000948 ! heart -relationship: in_right_side_of UBERON:0000948 ! heart +is_a: UBERON:0015212 ! lateral structure [Term] id: UBERON:0035804 @@ -16835,9 +16233,9 @@ xref: AAO:0010270 xref: ZFA:0005594 is_a: UBERON:0000465 ! material anatomical entity relationship: bounding_layer_of UBERON:0000061 ! anatomical structure -relationship: present_in_taxon NCBITaxon:33090 -relationship: present_in_taxon NCBITaxon:33208 ! Metazoa -relationship: present_in_taxon NCBITaxon:4751 +property_value: RO:0002175 NCBITaxon:33090 +property_value: RO:0002175 NCBITaxon:33208 +property_value: RO:0002175 NCBITaxon:4751 [Term] id: UBERON:0036295 @@ -16850,7 +16248,7 @@ synonym: "renal pelvis plus ureter" EXACT [] xref: NCIT:C54419 is_a: UBERON:0000477 ! anatomical cluster relationship: part_of UBERON:0011143 {source="NCIT"} ! upper urinary tract -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:8410081 @@ -16862,7 +16260,6 @@ synonym: "microvessel" BROAD [] is_a: UBERON:0001981 ! blood vessel is_a: UBERON:0010523 ! microcirculatory vessel property_value: seeAlso "https://github.com/obophenotype/uberon/issues/2186" xsd:string -property_value: UBPROP:0000007 "microvascular" xsd:string created_by: http://orcid.org/0000-0002-2825-0621 [Term] @@ -16871,12 +16268,11 @@ name: excretory system namespace: uberon def: "An anatomical system that eliminates waste products that arise as a result of metabolic activity." [GO:0007588] subset: human_reference_atlas -xref: BTO:0006338 {mapping:justification="https://w3id.org/semapv/vocab/ManualMappingCuration", author:id="https://orcid.org/0000-0003-4423-4370", mapping:provider="https://github.com/biopragmatics/biomappings"} is_a: UBERON:0000467 ! anatomical system intersection_of: UBERON:0000467 ! anatomical system intersection_of: capable_of GO:0046903 ! secretion relationship: capable_of GO:0046903 ! secretion -relationship: present_in_taxon NCBITaxon:9606 +property_value: RO:0002175 NCBITaxon:9606 created_by: http://orcid.org/0000-0002-6095-8718 creation_date: 2022-05-25T18:21:29Z @@ -16888,9 +16284,15 @@ def: "A muscle tissue that is associated with soft internal organs (viscera)." [ comment: It is quite common to refer to visceral muscles as smooth muscles, by analogy with vertebrates; however, most visceral muscles in arthropods are actually striated. {xref="https://en.wikipedia.org/wiki/Smooth_muscle", xref="FBbt:00005070", comment="PMID:8720463"} synonym: "visceral muscle" EXACT [] {comment="BTO:0002780"} is_a: UBERON:0002385 ! muscle tissue -relationship: composed_primarily_of CL:0008007 ! visceral muscle cell -relationship: dc-contributor https://orcid.org/0000-0001-6677-8489 -property_value: dcterms-date "2023-02-16T10:17:46Z" xsd:dateTime +relationship: RO:0002473 CL:0008007 ! composed primarily of visceral muscle cell +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0001-6677-8489 +property_value: http://purl.org/dc/terms/date "2023-02-16T10:17:46Z" xsd:dateTime + +[Typedef] +id: BFO:0000067 +name: contains process +def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] +comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant [Typedef] id: CL:4030044 @@ -16911,11 +16313,6 @@ id: RO:0000052 name: characteristic of def: "a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence." [] comment: Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. -property_value: IAO:0000111 "inheres in" xsd:string -property_value: IAO:0000112 "this fragility is a characteristic of this vase" xsd:string -property_value: IAO:0000112 "this red color is a characteristic of this apple" xsd:string -property_value: IAO:0000118 "inheres_in" xsd:string -property_value: RO:0001900 RO:0001901 is_functional: true is_a: RO:0002314 ! characteristic of part of inverse_of: bearer_of ! bearer of @@ -16925,10 +16322,7 @@ id: RO:0000079 name: function of def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. -property_value: editor_note "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string -property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string -property_value: IAO:0000118 "function_of" xsd:string -property_value: IAO:0000118 "is function of" xsd:string +property_value: IAO:0000116 "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string is_a: RO:0000052 ! characteristic of inverse_of: RO:0000085 ! has function @@ -16937,22 +16331,16 @@ id: RO:0000080 name: quality of def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. -property_value: editor_note "A quality inheres in its bearer at all times for which the quality exists." xsd:string -property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string -property_value: IAO:0000118 "is quality of" xsd:string -property_value: IAO:0000118 "quality_of" xsd:string +property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string is_a: RO:0000052 ! characteristic of -inverse_of: has_quality ! has quality +inverse_of: RO:0000086 ! has quality [Typedef] id: RO:0000081 name: role of def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] comment: This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. -property_value: editor_note "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string -property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string -property_value: IAO:0000118 "is role of" xsd:string -property_value: IAO:0000118 "role_of" xsd:string +property_value: IAO:0000116 "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string is_a: RO:0000052 ! characteristic of inverse_of: RO:0000087 ! has role @@ -16960,19 +16348,22 @@ inverse_of: RO:0000087 ! has role id: RO:0000085 name: has function def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] -property_value: editor_note "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string -property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string -property_value: IAO:0000118 "has_function" xsd:string +property_value: IAO:0000116 "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string domain: BFO:0000004 ! independent continuant is_a: bearer_of ! bearer of +[Typedef] +id: RO:0000086 +name: has quality +def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] +property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string +is_a: bearer_of ! bearer of + [Typedef] id: RO:0000087 name: has role def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] -property_value: editor_note "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string -property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string -property_value: IAO:0000118 "has_role" xsd:string +property_value: IAO:0000116 "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string domain: BFO:0000004 ! independent continuant is_a: bearer_of ! bearer of @@ -16997,12 +16388,7 @@ id: RO:0001000 name: derives from def: "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" [] subset: ro-eco -property_value: editor_note "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." xsd:string -property_value: IAO:0000112 "this cell derives from this parent cell (cell division)" xsd:string -property_value: IAO:0000112 "this nucleus derives from this parent nucleus (nuclear division)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000118 "derives_from" xsd:string -property_value: IAO:0000232 "This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations." xsd:string +property_value: IAO:0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." xsd:string inverse_of: RO:0001001 ! derives into [Typedef] @@ -17010,33 +16396,57 @@ id: RO:0001001 name: derives into def: "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" [] subset: ro-eco -property_value: editor_note "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." xsd:string -property_value: IAO:0000112 "this parent cell derives into this cell (cell division)" xsd:string -property_value: IAO:0000112 "this parent nucleus derives into this nucleus (nuclear division)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000118 "derives_into" xsd:string +property_value: IAO:0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." xsd:string + +[Typedef] +id: RO:0001015 +name: location of +def: "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" [] +property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +is_transitive: true +inverse_of: RO:0001025 ! located in + +[Typedef] +id: RO:0001025 +name: located in +def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] +subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term +property_value: IAO:0000116 "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" xsd:string +property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: seeAlso "https://wiki.geneontology.org/Located_in" xsd:anyURI +domain: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +range: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant +is_transitive: true +transitive_over: part_of ! part of [Typedef] id: RO:0002000 name: 2D boundary of def: "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" [] -property_value: editor_note "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string -property_value: editor_note "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string -property_value: IAO:0000112 "the surface of my skin is a 2D boundary of my body" xsd:string -property_value: IAO:0000118 "2D_boundary_of" xsd:string -property_value: IAO:0000118 "boundary of" xsd:string -property_value: IAO:0000118 "is 2D boundary of" xsd:string -property_value: IAO:0000118 "is boundary of" xsd:string -property_value: IAO:0000118 "surface of" xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string +is_a: RO:0002323 ! mereotopologically related to +inverse_of: RO:0002002 ! has 2D boundary + +[Typedef] +id: RO:0002002 +name: has 2D boundary +def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] +property_value: IAO:0000116 "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string +property_value: IAO:0000116 "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string +domain: BFO:0000040 ! material entity +range: BFO:0000141 ! immaterial entity is_a: RO:0002323 ! mereotopologically related to -inverse_of: has_boundary ! has 2D boundary + +[Typedef] +id: RO:0002005 +name: innervated_by +domain: UBERON:0000061 ! anatomical structure +inverse_of: RO:0002134 ! innervates [Typedef] id: RO:0002006 name: has synaptic terminal of -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 is_a: overlaps ! overlaps inverse_of: RO:0002130 ! has synaptic terminal in @@ -17118,16 +16528,23 @@ id: RO:0002081 name: before or simultaneous with comment: Primitive instance level timing relation between events subset: ro-eco -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000118 "<=" xsd:string is_a: RO:0002222 ! temporally related to +[Typedef] +id: RO:0002082 +name: simultaneous with +def: "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." [] +comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) +subset: ro-eco +is_symmetric: true +is_transitive: true +is_a: RO:0002081 ! before or simultaneous with + [Typedef] id: RO:0002086 name: ends after comment: X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) subset: ro-eco -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string is_transitive: true is_a: RO:0002222 ! temporally related to @@ -17135,25 +16552,16 @@ is_a: RO:0002222 ! temporally related to id: RO:0002100 name: has soma location def: "Relation between a neuron and a material anatomical entity that its soma is part of." [] -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron range: UBERON:0000465 ! material anatomical entity is_a: overlaps ! overlaps -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "BFO_0000051 some (\n GO_0043025 and BFO_0000050 some ?Y)" [] [Typedef] id: RO:0002101 name: fasciculates with def: "relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through.\n" [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "fasciculates with" xsd:string -property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (fasciculates_with ?x ?y)\n (exists (?nps ?npbs)\n (and \n (\"neuron ; CL_0000540\" ?x)\n (\"neuron projection bundle ; CARO_0001001\" ?y) \n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500' \" ?npbs)\n (part_of ?npbs ?y) \n (part_of ?nps ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))" xsd:string -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: overlaps ! overlaps inverse_of: RO:0002132 ! has fasciculating neuron projection @@ -17162,27 +16570,23 @@ inverse_of: RO:0002132 ! has fasciculating neuron projection id: RO:0002102 name: axon synapses in def: "Relation between a neuron and some structure its axon forms (chemical) synapses in." [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: RO:0002113 ! has presynaptic terminal in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "BFO_0000051 some (\n GO_0030424 and BFO_0000051 some (\n GO_0042734 and BFO_0000050 some (\n GO_0045202 and BFO_0000050 some ?Y)))" [] +[Typedef] +id: RO:0002103 +name: synapsed by +def: "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " [] +is_a: RO:0002485 ! receives input from +inverse_of: RO:0002120 ! synapsed to +expand_expression_to: "BFO_0000051 some (GO_0045211 that part_of some (GO_0045202 that has_part some (GO_0042734 that BFO_0000050 some Y?)))" [] + [Typedef] id: RO:0002104 name: has plasma membrane part def: "Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part." [] -property_value: IAO:0000112 "Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814]" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9990-8331 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-1617-8244 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/19243617 -property_value: RO:0001900 RO:0001901 domain: UBERON:0000465 ! material anatomical entity range: UBERON:0000465 ! material anatomical entity is_a: has_part ! has part @@ -17192,29 +16596,19 @@ expand_expression_to: "BFO_0000051 some (GO_0005886 and BFO_0000051 some ?Y)" [] id: RO:0002110 name: has postsynaptic terminal in def: "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. " [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "synapsed in" xsd:string -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: RO:0002130 ! has synaptic terminal in inverse_of: RO:0002113 ! has presynaptic terminal in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (\n http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some (\n http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y))" [] [Typedef] id: RO:0002113 name: has presynaptic terminal in def: "Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input." [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000118 "synapses in" xsd:string -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: RO:0002130 ! has synaptic terminal in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "BFO_0000051 some (GO_0042734 that BFO_0000050 some (GO_0045202 that BFO_0000050 some Y?)" [] [Typedef] @@ -17222,11 +16616,6 @@ id: RO:0002120 name: synapsed to def: " Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to.\n " [] comment: N1 synapsed_to some N2 \nExpands to:\nN1 SubclassOf ( \n has_part some (\n ‘pre-synaptic membrane ; GO:0042734’ that part_of some ( \n ‘synapse ; GO:0045202’ that has_part some (\n ‘post-synaptic membrane ; GO:0045211’ that part_of some N2)))) -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 is_a: RO:0002486 ! sends output to expand_expression_to: "BFO_0000051 some (GO_0042734 that part_of some (GO_0045202 that BFO_0000051 some (GO_0045211 that BFO_0000050 some Y?)))" [] @@ -17234,103 +16623,270 @@ expand_expression_to: "BFO_0000051 some (GO_0042734 that part_of some (GO_004520 id: RO:0002130 name: has synaptic terminal in def: "A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input." [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "has synapse in" xsd:string -property_value: RO:0001900 RO:0001901 domain: CL:0000540 ! neuron is_a: overlaps ! overlaps -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "RO_0002131 some (GO_0045202 that BFO_0000050 some Y?)" [] [Typedef] id: RO:0002132 name: has fasciculating neuron projection def: "The relation between a neuron projection bundle and a neuron projection that is fasciculated with it." [] -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "has fasciculating component" xsd:string -property_value: IAO:0000426 "(forall (?x ?y) \n (iff \n (has_fasciculating_neuron_projection ?x ?y)\n (exists (?nps ?npbs) \n (and \n (\"neuron projection bundle ; CARO_0001001\" ?x)\n (\"neuron projection ; GO0043005\" ?y)\n (\"neuron projection segment ; CARO_0001502\" ?nps)\n (\"neuron projection bundle segment ; CARO_0001500\" ?npbs)\n (part_of ?nps ?y)\n (part_of ?npbs ?x)\n (part_of ?nps ?npbs)\n (forall (?npbss)\n (if\n (and \n (\"neuron projection bundle subsegment ; CARO_0001501\" ?npbss)\n (part_of ?npbss ?npbs) \n )\n (overlaps ?nps ?npbss)\n ))))))\n\n\n" xsd:string -property_value: RO:0001900 RO:0001901 is_a: overlaps ! overlaps +[Typedef] +id: RO:0002134 +name: innervates +def: "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." [] +transitive_over: part_of ! part of +expand_expression_to: "RO_0002132 some (GO_0043005 that (RO_0002131 some (GO_0045202 that BFO_0000050 some Y?)))" [] + +[Typedef] +id: RO:0002150 +name: continuous with +def: "X continuous_with Y if and only if X and Y share a fiat boundary." [] +property_value: seeAlso "FMA:85972" xsd:string +domain: BFO:0000004 ! independent continuant +range: BFO:0000004 ! independent continuant +is_symmetric: true +is_a: RO:0002323 ! mereotopologically related to + +[Typedef] +id: RO:0002158 +name: shares ancestor with +def: "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." [] +comment: VBO calls this homologous_to +is_symmetric: true +is_transitive: true +is_a: RO:0002320 ! evolutionarily related to + +[Typedef] +id: RO:0002160 +name: only in taxon +def: "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." [] +property_value: IAO:0000116 "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" xsd:string +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints +is_a: RO:0002162 ! in taxon + +[Typedef] +id: RO:0002162 +name: in taxon +def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." [] +comment: Connects a biological entity to its taxon of origin. +subset: ro-eco +property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints +holds_over_chain: capable_of RO:0002162 +holds_over_chain: extends_fibers_into RO:0002162 +holds_over_chain: has_part RO:0002162 +holds_over_chain: part_of RO:0002162 +holds_over_chain: results_in_developmental_progression_of RO:0002162 +holds_over_chain: RO:0002202 RO:0002162 +holds_over_chain: RO:0002206 RO:0002162 +holds_over_chain: RO:0002225 RO:0002162 +holds_over_chain: RO:0002254 RO:0002162 +is_a: RO:0002320 ! evolutionarily related to + [Typedef] id: RO:0002163 name: spatially disjoint from def: "A is spatially_disjoint_from B if and only if they have no parts in common" [] subset: ro-eco -property_value: editor_note "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: IAO:0000232 "Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy" xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. " xsd:string property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern" xsd:anyURI is_a: RO:0002323 ! mereotopologically related to expand_expression_to: "BFO_0000051 exactly 0 (BFO_0000050 some ?Y)" [] +[Typedef] +id: RO:0002170 +name: connected to +def: "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" [] +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI +is_a: RO:0002323 ! mereotopologically related to + +[Typedef] +id: RO:0002176 +name: connects +def: "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." [] +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI +property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI +domain: BFO:0000004 ! independent continuant +is_a: RO:0002323 ! mereotopologically related to + +[Typedef] +id: RO:0002177 +name: attached to part of +def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000061 ! anatomical structure +is_a: RO:0002323 ! mereotopologically related to +is_a: RO:0002567 ! biomechanically related to + +[Typedef] +id: RO:0002178 +name: supplies +def: "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." [] +property_value: IAO:0000116 "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" xsd:string +is_a: RO:0002170 ! connected to + +[Typedef] +id: RO:0002179 +name: drains +def: "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." [] +property_value: IAO:0000116 "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" xsd:string +is_a: RO:0002170 ! connected to + +[Typedef] +id: RO:0002202 +name: develops from +def: "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" [] +comment: This is the transitive form of the develops from relation +domain: BFO:0000004 ! independent continuant +range: BFO:0000004 ! independent continuant +is_transitive: true +is_a: RO:0002254 ! has developmental contribution from +is_a: RO:0002258 ! developmentally preceded by +inverse_of: RO:0002203 ! develops into + +[Typedef] +id: RO:0002203 +name: develops into +def: "inverse of develops from" [] +subset: RO:0002259 +is_transitive: true +is_a: RO:0002286 ! developmentally succeeded by +is_a: RO:0002387 ! has potential to develop into +is_a: RO:0002388 ! has potential to directly develop into + [Typedef] id: RO:0002206 name: expressed in def: "x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process" [] -property_value: IAO:0000112 "'neural crest cell' SubClassOf expresses some 'Wnt1 gene'" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000002 ! continuant range: UBERON:0000465 ! material anatomical entity is_a: RO:0002330 ! genomically related to inverse_of: RO:0002292 ! expresses -transitive_over: part_of ! part_of +transitive_over: part_of ! part of + +[Typedef] +id: RO:0002207 +name: directly develops from +def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] +comment: TODO - add child relations from DOS +synonym: "has developmental precursor" EXACT [] +is_a: RO:0002202 ! develops from +inverse_of: RO:0002210 ! directly develops into [Typedef] id: RO:0002210 name: directly develops into def: "inverse of directly develops from" [] subset: RO:0002259 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000118 "developmental precursor of" xsd:string -is_a: develops_into ! develops into +is_a: RO:0002203 ! develops into + +[Typedef] +id: RO:0002219 +name: surrounded by +def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" [] +is_a: adjacent_to ! adjacent to +inverse_of: RO:0002221 ! surrounds + +[Typedef] +id: RO:0002221 +name: surrounds +def: "inverse of surrounded by" [] +subset: RO:0002259 +is_a: adjacent_to ! adjacent to [Typedef] id: RO:0002222 name: temporally related to comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. subset: ro-eco -property_value: http://purl.org/dc/terms/source "https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1" xsd:anyURI -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 https://en.wikipedia.org/wiki/Allen%27s_interval_algebra -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends." xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent +[Typedef] +id: RO:0002223 +name: starts +def: "inverse of starts with" [] +subset: ro-eco +is_a: part_of ! part of +is_a: RO:0002222 ! temporally related to +inverse_of: starts_with ! starts with + +[Typedef] +id: RO:0002225 +name: develops from part of +def: "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" [] +holds_over_chain: RO:0002207 part_of +is_a: RO:0002202 ! develops from + +[Typedef] +id: RO:0002226 +name: develops in +def: "x develops_in y if x is located in y whilst x is developing" [] +domain: UBERON:0001062 ! anatomical entity +holds_over_chain: RO:0002207 RO:0001025 +is_a: RO:0002258 ! developmentally preceded by + +[Typedef] +id: RO:0002229 +name: ends +def: "inverse of ends with" [] +subset: ro-eco +is_a: part_of ! part of +is_a: RO:0002222 ! temporally related to +inverse_of: ends_with ! ends with + +[Typedef] +id: RO:0002252 +name: connecting branch of +def: "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." [] +property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 +is_a: RO:0002170 ! connected to +is_a: RO:0002375 ! in branching relationship with +inverse_of: RO:0002253 ! has connecting branch + [Typedef] id: RO:0002253 name: has connecting branch def: "inverse of connecting branch of" [] subset: RO:0002259 -property_value: RO:0004036 BFO:0000051 is_a: RO:0002375 ! in branching relationship with +[Typedef] +id: RO:0002254 +name: has developmental contribution from +def: "x has developmental contribution from y iff x has some part z such that z develops from y" [] +domain: UBERON:0001062 ! anatomical entity +range: UBERON:0001062 ! anatomical entity +holds_over_chain: has_part RO:0002202 +is_a: RO:0002258 ! developmentally preceded by +inverse_of: RO:0002255 ! developmentally contributes to + [Typedef] id: RO:0002255 name: developmentally contributes to def: "inverse of has developmental contribution from" [] subset: RO:0002259 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -holds_over_chain: develops_into part_of -is_a: has_potential_to_developmentally_contribute_to ! has potential to developmentally contribute to +holds_over_chain: RO:0002203 part_of is_a: RO:0002286 ! developmentally succeeded by +is_a: RO:0002385 ! has potential to developmentally contribute to + +[Typedef] +id: RO:0002256 +name: developmentally induced by +def: "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" [] +domain: UBERON:0000465 ! material anatomical entity +range: UBERON:0000465 ! material anatomical entity +is_a: RO:0002258 ! developmentally preceded by +inverse_of: RO:0002257 ! developmentally induces [Typedef] id: RO:0002257 name: developmentally induces def: "Inverse of developmentally induced by" [] -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002286 ! developmentally succeeded by is_a: RO:0002386 ! has potential to developmentally induce @@ -17339,10 +16895,7 @@ id: RO:0002258 name: developmentally preceded by def: "Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p" [] comment: This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from -property_value: editor_note "false" xsd:boolean -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "In general you should not use this relation to make assertions - use one of the more specific relations below this one" xsd:string +property_value: IAO:0000116 "false" xsd:boolean domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant is_a: RO:0002324 ! developmentally related to @@ -17353,7 +16906,6 @@ id: RO:0002263 name: acts upstream of def: "c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: IAO:0000112 "A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision." xsd:string property_value: seeAlso http://wiki.geneontology.org/index.php/Acts_upstream_of holds_over_chain: RO:0002327 causally_upstream_of is_a: RO:0002264 ! acts upstream of or within @@ -17364,25 +16916,26 @@ name: acts upstream of or within def: "c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term synonym: "affects" RELATED [] -property_value: IAO:0000112 "A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway." xsd:string property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within" xsd:anyURI holds_over_chain: RO:0002327 causally_upstream_of_or_within is_a: RO:0002500 ! causal agent in process +[Typedef] +id: RO:0002285 +name: developmentally replaces +def: "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" [] +property_value: IAO:0000116 "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" xsd:string +is_a: RO:0002258 ! developmentally preceded by + [Typedef] id: RO:0002286 name: developmentally succeeded by def: "Inverse of developmentally preceded by" [] -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002384 ! has developmental potential involving [Typedef] id: RO:0002287 name: part of developmental precursor of -property_value: IAO:0000112 "'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: part_of RO:0002210 is_a: RO:0002286 ! developmentally succeeded by @@ -17390,80 +16943,58 @@ is_a: RO:0002286 ! developmentally succeeded by id: RO:0002292 name: expresses def: "y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process." [] -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002330 ! genomically related to [Typedef] id: RO:0002314 name: characteristic of part of def: "q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w." [] -property_value: editor_note "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "inheres in part of" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "Because part_of is transitive, inheres in is a sub-relation of characteristic of part of" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: RO:0000052 part_of {RO:0002582="true"} is_a: RO:0002502 ! depends on -transitive_over: part_of ! part_of +transitive_over: part_of ! part of [Typedef] id: RO:0002320 name: evolutionarily related to def: "A relationship that holds via some environmental process" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution." xsd:string [Typedef] id: RO:0002323 name: mereotopologically related to def: "A mereological relationship or a topological relationship" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships" xsd:string -property_value: RO:0001900 RO:0001901 [Typedef] id: RO:0002324 name: developmentally related to def: "A relationship that holds between entities participating in some developmental process (GO:0032502)" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development" xsd:string [Typedef] id: RO:0002327 name: enables def: "c enables p iff c is capable of p and c acts to execute p." [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: IAO:0000112 "a particular instances of akt-2 enables some instance of protein kinase activity" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "catalyzes" xsd:string -property_value: IAO:0000118 "executes" xsd:string -property_value: IAO:0000118 "has" xsd:string -property_value: IAO:0000118 "is catalyzing" xsd:string -property_value: IAO:0000118 "is executing" xsd:string -property_value: IAO:0000232 "This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized." xsd:string property_value: seeAlso "https://wiki.geneontology.org/Enables" xsd:anyURI is_a: capable_of ! capable of inverse_of: RO:0002333 ! enabled by transitive_over: has_part ! has part transitive_over: RO:0002017 ! has component activity +[Typedef] +id: RO:0002328 +name: functionally related to +def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] + [Typedef] id: RO:0002329 name: part of structure that is capable of def: "this relation holds between c and p when c is part of some c', and c' is capable of p." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "false" xsd:boolean -holds_over_chain: part_of capable_of {RO:0002581="true"} -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002330 name: genomically related to def: "holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant @@ -17471,31 +17002,25 @@ range: BFO:0000002 ! continuant id: RO:0002331 name: involved in def: "c involved_in p if and only if c enables some process p', and p' is part of p" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "actively involved in" xsd:string -property_value: IAO:0000118 "enables part of" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Involved_in" xsd:anyURI holds_over_chain: RO:0002327 part_of is_a: participates_in ! participates in is_a: RO:0002431 ! involved in or involved in regulation of -transitive_over: part_of ! part_of +transitive_over: part_of ! part of [Typedef] id: RO:0002333 name: enabled by def: "inverse of enables" [] subset: http://purl.obolibrary.org/obo/valid_for_gocam -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso "https://wiki.geneontology.org/Enabled_by" xsd:anyURI -is_a: functionally_related_to ! functionally related to is_a: has_participant ! has participant +is_a: RO:0002328 ! functionally related to [Typedef] id: RO:0002337 name: related via localization to def: "A relationship that holds via some process of localization" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is a grouping relation." xsd:string domain: BFO:0000015 ! process range: BFO:0000002 ! continuant @@ -17503,84 +17028,134 @@ range: BFO:0000002 ! continuant id: RO:0002350 name: member of def: "is member of is a mereological relation between a item and a collection." [] -property_value: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string -property_value: IAO:0000118 "is member of" xsd:string -property_value: IAO:0000118 "member part of" xsd:string -property_value: IAO:0000119 "SIO" xsd:string -property_value: RO:0001900 RO:0001901 -is_a: part_of ! part_of -inverse_of: has_member ! has member +is_a: part_of ! part of +inverse_of: RO:0002351 ! has member [Typedef] -id: RO:0002354 -name: formed as result of -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: output_of ! output of +id: RO:0002351 +name: has member +def: "has member is a mereological relation between a collection and an item." [] +is_a: has_part ! has part [Typedef] -id: RO:0002360 +id: RO:0002352 +name: input of +def: "inverse of has input" [] +subset: ro-eco +subset: RO:0002259 +is_a: participates_in ! participates in +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002354 +name: formed as result of +is_a: output_of ! output of + +[Typedef] +id: RO:0002360 name: has dendrite location -property_value: http://purl.org/dc/terms/source "http://neurolex.org/wiki/Property:DendriteLocation" xsd:anyURI -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: overlaps ! overlaps +[Typedef] +id: RO:0002371 +name: attached to +def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] +subset: ro-eco +is_symmetric: true +is_a: RO:0002170 ! connected to +is_a: RO:0002177 ! attached to part of + +[Typedef] +id: RO:0002372 +name: has muscle origin +def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] +property_value: seeAlso http://dbpedia.org/property/origin +domain: UBERON:0000061 {comment="We need to import uberon muscle to create a stricter domain constraint"} ! anatomical structure +is_a: RO:0002371 ! attached to +is_a: RO:0002567 ! biomechanically related to + +[Typedef] +id: RO:0002373 +name: has muscle insertion +def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] +property_value: seeAlso http://dbpedia.org/property/insertion +domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} ! anatomical structure +is_a: RO:0002371 ! attached to +is_a: RO:0002567 ! biomechanically related to + [Typedef] id: RO:0002375 name: in branching relationship with def: "A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network." [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships" xsd:string -property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves)" xsd:string -property_value: RO:0004036 BFO:0000050 property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/branching_part_of.png property_value: seeAlso "https://github.com/obophenotype/uberon/issues/170" xsd:anyURI domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002323 ! mereotopologically related to +[Typedef] +id: RO:0002376 +name: tributary of +def: "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." [] +subset: ro-eco +property_value: seeAlso http://dbpedia.org/ontology/drainsTo +property_value: seeAlso "http://en.wikipedia.org/wiki/Tributary" xsd:anyURI +is_a: RO:0002170 ! connected to +is_a: RO:0002375 ! in branching relationship with + [Typedef] id: RO:0002379 name: spatially coextensive with def: "x spatially_coextensive_with y if and inly if x and y have the same location" [] -property_value: IAO:0000112 "A lump of clay and a statue" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "This relation is added for formal completeness. It is unlikely to be used in many practical scenarios" xsd:string is_a: overlaps ! overlaps +[Typedef] +id: RO:0002380 +name: branching part of +def: "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" [] +subset: ro-eco +property_value: seeAlso "FMA:85994" xsd:string +property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 +is_a: part_of ! part of +is_a: RO:0002375 ! in branching relationship with +inverse_of: RO:0002569 ! has branching part + [Typedef] id: RO:0002384 name: has developmental potential involving def: "x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction)." [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: UBERON:0001062 ! anatomical entity range: UBERON:0001062 ! anatomical entity is_a: RO:0002324 ! developmentally related to +[Typedef] +id: RO:0002385 +name: has potential to developmentally contribute to +def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] +is_a: RO:0002384 ! has developmental potential involving + [Typedef] id: RO:0002386 name: has potential to developmentally induce def: "x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y" [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +is_a: RO:0002384 ! has developmental potential involving + +[Typedef] +id: RO:0002387 +name: has potential to develop into +def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] is_a: RO:0002384 ! has developmental potential involving [Typedef] id: RO:0002388 name: has potential to directly develop into def: "x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y" [] -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: has_potential_to_develop_into ! has potential to develop into +is_a: RO:0002387 ! has potential to develop into [Typedef] id: RO:0002407 name: indirectly positively regulates def: "p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "indirectly activates" xsd:string -property_value: RO:0002579 RO:0002213 property_value: seeAlso "https://wiki.geneontology.org/Indirectly_positively_regulates" xsd:anyURI holds_over_chain: directly_positively_regulates directly_positively_regulates holds_over_chain: directly_positively_regulates RO:0002407 @@ -17594,9 +17169,6 @@ transitive_over: directly_positively_regulates ! directly positively regulates id: RO:0002409 name: indirectly negatively regulates def: "p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "indirectly inhibits" xsd:string -property_value: RO:0002579 RO:0002212 property_value: seeAlso "https://wiki.geneontology.org/Indirectly_negatively_regulates" xsd:anyURI holds_over_chain: directly_negatively_regulates directly_negatively_regulates holds_over_chain: directly_negatively_regulates RO:0002409 @@ -17609,15 +17181,12 @@ transitive_over: directly_negatively_regulates ! directly negatively regulates id: RO:0002410 name: causally related to def: "relation that links two events, processes, states, or objects such that one event, process, state, or object (a cause) contributes to the production of another event, process, state, or object (an effect) where the cause is partly or wholly responsible for the effect, and the effect is partly or wholly dependent on the cause." [https://en.wikipedia.org/wiki/Causality] -property_value: editor_note "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: IAO:0000116 "This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents.\n\nTo define causal relations in an activity-flow type network, we make use of 3 primitives:\n\n * Temporal: how do the intervals of the two occurrents relate? \n * Is the causal relation regulatory?\n * Is the influence positive or negative?\n\nThe first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified.\n\nFor the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule.\n\nFor the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral.\n\nEach of these 3 primitives can be composed to yield a cross-product of different relation types." xsd:string [Typedef] id: RO:0002428 name: involved in regulation of def: "c involved in regulation of p if c is involved in some p' and p' regulates some p" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: RO:0002327 regulates holds_over_chain: RO:0002331 regulates is_a: RO:0002263 ! acts upstream of @@ -17627,8 +17196,6 @@ is_a: RO:0002431 ! involved in or involved in regulation of id: RO:0002429 name: involved in positive regulation of def: "c involved in regulation of p if c is involved in some p' and p' positively regulates some p" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0004049 RO:0002428 holds_over_chain: RO:0002327 positively_regulates holds_over_chain: RO:0002331 positively_regulates is_a: RO:0002428 ! involved in regulation of @@ -17637,7 +17204,6 @@ is_a: RO:0002428 ! involved in regulation of id: RO:0002430 name: involved in negative regulation of def: "c involved in regulation of p if c is involved in some p' and p' negatively regulates some p" [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002428 holds_over_chain: RO:0002327 negatively_regulates holds_over_chain: RO:0002331 negatively_regulates @@ -17647,11 +17213,9 @@ is_a: RO:0002428 ! involved in regulation of id: RO:0002431 name: involved in or involved in regulation of def: "c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p" [] -property_value: editor_note "OWL does not allow defining object properties via a Union" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "involved in or reguates" xsd:string -is_a: functionally_related_to ! functionally related to +property_value: IAO:0000116 "OWL does not allow defining object properties via a Union" xsd:string is_a: RO:0002264 ! acts upstream of or within +is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process [Typedef] @@ -17659,12 +17223,14 @@ id: RO:0002432 name: is active in def: "c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure." [https://orcid.org/0000-0002-6601-2165, https://orcid.org/0000-0002-7073-9172] synonym: "enables activity in" EXACT [] -property_value: IAO:0000112 "A protein that enables activity in a cytosol." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "executes activity in" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Is_active_in" xsd:anyURI -holds_over_chain: RO:0002327 occurs_in {RO:0002581="true"} -is_a: functionally_related_to ! functionally related to +is_a: overlaps ! overlaps +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002433 +name: contributes to morphology of +def: "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." [] is_a: overlaps ! overlaps [Typedef] @@ -17673,11 +17239,8 @@ name: interacts with def: "A relationship that holds between two entities in which the processes executed by the two entities are causally connected." [] subset: ro-eco synonym: "in pairwise interaction with" EXACT [] -property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0914" xsd:anyURI -property_value: editor_note "Considering relabeling as 'pairwise interacts with'" xsd:anyURI -property_value: editor_note "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules." xsd:string +property_value: IAO:0000116 "Considering relabeling as 'pairwise interacts with'" xsd:anyURI +property_value: IAO:0000116 "This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact." xsd:string property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity @@ -17687,10 +17250,6 @@ is_symmetric: true id: RO:0002436 name: molecularly interacts with def: "An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other." [] -property_value: closeMatch "http://purl.obolibrary.org/obo/MI_0915" xsd:anyURI -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "binds" xsd:string -property_value: IAO:0000118 "molecularly binds with" xsd:string property_value: seeAlso ECO:0000353 is_symmetric: true is_a: RO:0002434 ! interacts with @@ -17698,9 +17257,7 @@ is_a: RO:0002434 ! interacts with [Typedef] id: RO:0002447 name: phosphorylates -property_value: editor_note "Axiomatization to GO to be added later" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y." xsd:string +property_value: IAO:0000116 "Axiomatization to GO to be added later" xsd:string is_a: RO:0002436 ! molecularly interacts with [Typedef] @@ -17708,8 +17265,6 @@ id: RO:0002448 name: directly regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B.\n\nA and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B." [] synonym: "molecularly controls" EXACT [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002436 ! molecularly interacts with @@ -17720,9 +17275,6 @@ id: RO:0002449 name: directly negatively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B." [] synonym: "molecularly decreases activity of" EXACT [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 -property_value: IAO:0000118 "directly inhibits" xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002448 ! directly regulates activity of @@ -17732,9 +17284,6 @@ id: RO:0002450 name: directly positively regulates activity of def: "The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. \nFor example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B." [] synonym: "molecularly increases activity of" EXACT [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 -property_value: IAO:0000118 "directly activates" xsd:string domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002448 ! directly regulates activity of @@ -17742,61 +17291,136 @@ is_a: RO:0002448 ! directly regulates activity of [Typedef] id: RO:0002464 name: helper property (not for use in curation) -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning." xsd:string + +[Typedef] +id: RO:0002473 +name: composed primarily of +def: "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." [] +subset: ro-eco +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: has_part ! has part [Typedef] id: RO:0002479 name: has part that occurs in def: "p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c." [] subset: ro-eco -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant -holds_over_chain: has_part occurs_in {RO:0002581="true"} [Typedef] id: RO:0002481 name: is kinase activity -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002564 ! molecular interaction relation helper property [Typedef] id: RO:0002485 name: receives input from -property_value: editor_note "See notes for inverse relation" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: connected_to ! connected to +property_value: IAO:0000116 "See notes for inverse relation" xsd:string +is_a: RO:0002170 ! connected to inverse_of: RO:0002486 ! sends output to [Typedef] id: RO:0002486 name: sends output to -property_value: editor_note "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: connected_to ! connected to +property_value: IAO:0000116 "This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in." xsd:string +is_a: RO:0002170 ! connected to [Typedef] id: RO:0002487 name: relation between physical entity and a process or stage -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage." xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000003 ! occurrent +[Typedef] +id: RO:0002488 +name: existence starts during +def: "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." [] +is_a: RO:0002490 ! existence overlaps +is_a: RO:0002496 ! existence starts during or after +transitive_over: part_of ! part of + +[Typedef] +id: RO:0002489 +name: existence starts with +def: "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." [] +is_a: RO:0002488 ! existence starts during + [Typedef] id: RO:0002490 name: existence overlaps def: "x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y))" [] comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002487 ! relation between physical entity and a process or stage +[Typedef] +id: RO:0002491 +name: existence starts and ends during +def: "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +synonym: "exists during" EXACT [] +is_a: RO:0002488 ! existence starts during +is_a: RO:0002492 ! existence ends during + +[Typedef] +id: RO:0002492 +name: existence ends during +def: "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +is_a: RO:0002490 ! existence overlaps +is_a: RO:0002497 ! existence ends during or before +transitive_over: part_of ! part of + +[Typedef] +id: RO:0002493 +name: existence ends with +def: "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +is_a: RO:0002492 ! existence ends during + +[Typedef] +id: RO:0002494 +name: transformation of +def: "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" [] +is_transitive: true +is_a: RO:0002202 ! develops from + +[Typedef] +id: RO:0002495 +name: immediate transformation of +def: "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" [] +is_a: RO:0002207 ! directly develops from +is_a: RO:0002494 ! transformation of + +[Typedef] +id: RO:0002496 +name: existence starts during or after +def: "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +holds_over_chain: part_of RO:0002496 +holds_over_chain: RO:0002258 RO:0002496 +is_a: RO:0002487 ! relation between physical entity and a process or stage +transitive_over: part_of ! part of +transitive_over: preceded_by ! preceded by +transitive_over: RO:0002082 ! simultaneous with + +[Typedef] +id: RO:0002497 +name: existence ends during or before +def: "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." [] +comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. +holds_over_chain: part_of RO:0002497 +holds_over_chain: RO:0002286 RO:0002497 +is_a: RO:0002487 ! relation between physical entity and a process or stage +transitive_over: part_of ! part of +transitive_over: precedes ! precedes +transitive_over: RO:0002082 ! simultaneous with + [Typedef] id: RO:0002500 name: causal agent in process def: "A relationship between a material entity and a process where the material entity has some causal role that influences the process" [] -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_a: RO:0002595 ! causal relation between material entity and a process inverse_of: process_has_causal_agent ! process has causal agent @@ -17804,9 +17428,6 @@ inverse_of: process_has_causal_agent ! process has causal agent id: RO:0002501 name: causal relation between processes def: "p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent is_a: RO:0002410 ! causally related to @@ -17814,33 +17435,35 @@ is_a: RO:0002410 ! causally related to [Typedef] id: RO:0002502 name: depends on -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso BFO:0000169 [Typedef] id: RO:0002506 name: causal relation between entities -property_value: editor_note "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string +property_value: IAO:0000116 "The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant is_a: RO:0002410 ! causally related to +[Typedef] +id: RO:0002551 +name: has skeleton +def: "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." [] +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000465 {IAO:0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} ! material anatomical entity +is_a: has_part ! has part +inverse_of: RO:0002576 ! skeleton of +is_asymmetric: true + [Typedef] id: RO:0002559 name: causally influenced by -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "causally influenced by (entity-centric)" xsd:string is_a: RO:0002506 ! causal relation between entities inverse_of: RO:0002566 ! causally influences [Typedef] id: RO:0002563 name: interaction relation helper property -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:N-Ary_Relation_Pattern_%28OWL_2%29 property_value: seeAlso "http://purl.obolibrary.org/obo/ro/docs/interaction-relations/" xsd:anyURI is_a: RO:0002464 ! helper property (not for use in curation) @@ -17848,17 +17471,12 @@ is_a: RO:0002464 ! helper property (not for use in curation) [Typedef] id: RO:0002564 name: molecular interaction relation helper property -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002563 ! interaction relation helper property [Typedef] id: RO:0002566 name: causally influences def: "The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size)." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "causally influences (entity-centric)" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant is_a: RO:0002506 ! causal relation between entities @@ -17867,20 +17485,66 @@ is_a: RO:0002506 ! causal relation between entities id: RO:0002567 name: biomechanically related to def: "A relation that holds between elements of a musculoskeletal system or its analogs." [] -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes." xsd:string domain: UBERON:0000061 ! anatomical structure range: UBERON:0000061 ! anatomical structure -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to + +[Typedef] +id: RO:0002568 +name: has muscle antagonist +def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] +is_a: RO:0002567 ! biomechanically related to + +[Typedef] +id: RO:0002569 +name: has branching part +def: "inverse of branching part of" [] +subset: ro-eco +subset: RO:0002259 +is_transitive: true +is_a: has_part ! has part +is_a: RO:0002375 ! in branching relationship with + +[Typedef] +id: RO:0002570 +name: conduit for +def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] +subset: ro-eco +domain: BFO:0000040 ! material entity +range: BFO:0000040 ! material entity +is_a: overlaps ! overlaps + +[Typedef] +id: RO:0002571 +name: lumen of +def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] +subset: ro-eco +range: BFO:0000040 ! material entity +is_a: part_of ! part of + +[Typedef] +id: RO:0002572 +name: luminal space of +def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" [] +subset: ro-eco +domain: BFO:0000141 ! immaterial entity +is_a: RO:0002571 ! lumen of + +[Typedef] +id: RO:0002576 +name: skeleton of +def: "inverse of has skeleton" [] +subset: RO:0002259 +domain: UBERON:0000061 ! anatomical structure +range: UBERON:0000061 ! anatomical structure +is_a: part_of ! part of [Typedef] id: RO:0002584 name: has part structure that is capable of def: "s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p" [] -property_value: IAO:0000112 "gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 holds_over_chain: has_part capable_of -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to is_a: RO:0002595 ! causal relation between material entity and a process [Typedef] @@ -17893,9 +17557,7 @@ is_a: has_input ! has input id: RO:0002595 name: causal relation between material entity and a process def: "A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity." [] -property_value: editor_note "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations +property_value: IAO:0000116 "Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect." xsd:string domain: BFO:0000040 ! material entity range: BFO:0000015 ! process is_a: RO:0002410 ! causally related to @@ -17904,8 +17566,6 @@ is_a: RO:0002410 ! causally related to id: RO:0002596 name: capable of regulating def: "Holds between c and p if and only if c is capable of some activity a, and a regulates p." [] -property_value: IAO:0000112 "pyrethroid -> growth" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations holds_over_chain: capable_of regulates is_a: RO:0002500 ! causal agent in process @@ -17913,7 +17573,6 @@ is_a: RO:0002500 ! causal agent in process id: RO:0002597 name: capable of negatively regulating def: "Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p." [] -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations holds_over_chain: capable_of negatively_regulates is_a: RO:0002596 ! capable of regulating @@ -17921,8 +17580,6 @@ is_a: RO:0002596 ! capable of regulating id: RO:0002598 name: capable of positively regulating def: "Holds between c and p if and only if c is capable of some activity a, and a positively regulates p." [] -property_value: IAO:0000112 "renin -> arteriolar smooth muscle contraction" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations holds_over_chain: capable_of positively_regulates is_a: RO:0002596 ! capable of regulating @@ -17931,7 +17588,7 @@ id: RO:0004031 name: enables subfunction def: "Holds between an entity and an process P where the entity enables some larger compound process, and that larger process has-part P." [] holds_over_chain: RO:0002327 has_part -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-01-25T23:20:13Z @@ -17939,7 +17596,6 @@ creation_date: 2018-01-25T23:20:13Z id: RO:0004032 name: acts upstream of or within, positive effect subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: RO:0004049 RO:0002264 property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 RO:0004047 is_a: RO:0002264 ! acts upstream of or within @@ -17962,7 +17618,6 @@ id: RO:0004034 name: acts upstream of, positive effect def: "c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive" [] subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -property_value: RO:0004049 RO:0002263 property_value: seeAlso "https://wiki.geneontology.org/Acts_upstream_of,_positive_effect" xsd:anyURI holds_over_chain: RO:0002327 causally_upstream_of,_positive_effect is_a: RO:0002263 ! acts upstream of @@ -17995,7 +17650,6 @@ creation_date: 2018-03-13T23:55:05Z [Typedef] id: RO:0004047 name: causally upstream of or within, positive effect -property_value: RO:0004049 RO:0002418 property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of_or_within,_positive_effect is_a: causally_upstream_of_or_within ! causally upstream of or within created_by: https://orcid.org/0000-0002-6601-2165 @@ -18005,7 +17659,6 @@ creation_date: 2018-03-13T23:55:19Z id: RO:0011002 name: regulates activity of def: "The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B." [] -property_value: IAO:0000117 https://orcid.org/0000-0003-4639-4431 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_a: RO:0002566 ! causally influences @@ -18060,7 +17713,7 @@ name: has synaptic IO in region def: "A relationship between a neuron and a region, where the neuron has a functionally relevant number of input and/or output synapses in that region." [] synonym: "has synaptic input or output in" EXACT [] is_a: RO:0002130 ! has synaptic terminal in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-17T09:26:52Z @@ -18072,7 +17725,7 @@ synonym: "has sensory dendrite location" EXACT [] synonym: "has sensory terminal in" EXACT [] synonym: "has sensory terminal location" EXACT [] is_a: RO:0002360 ! has dendrite location -transitive_over: part_of ! part_of +transitive_over: part_of ! part of created_by: https://orcid.org/0000-0002-1373-1705 creation_date: 2020-07-20T12:10:09Z @@ -18115,9 +17768,8 @@ comment: Example: a spherical object has the quality of being spherical, and the id: RO:0015015 name: has high plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: dc-contributor https://orcid.org/0000-0003-1617-8244 -property_value: dc-contributor https://orcid.org/0000-0003-1940-6740 -property_value: IAO:0000112 "'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)')" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part @@ -18125,9 +17777,8 @@ is_a: RO:0002104 ! has plasma membrane part id: RO:0015016 name: has low plasma membrane amount def: "A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface." [PMID:19243617] -property_value: dc-contributor https://orcid.org/0000-0003-1617-8244 -property_value: dc-contributor https://orcid.org/0000-0003-1940-6740 -property_value: IAO:0000112 "'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor')" xsd:string +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1617-8244 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0003-1940-6740 domain: CL:0000000 ! cell is_a: RO:0002104 ! has plasma membrane part @@ -18136,11 +17787,6 @@ id: RO:0017001 name: device utilizes material def: "X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y." [] synonym: "utilizes" BROAD [] -property_value: IAO:0000112 "A diagnostic testing device utilizes a specimen." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0001-9625-1899 -property_value: IAO:0000117 https://orcid.org/0000-0003-2620-0345 -property_value: IAO:0000232 "A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input." xsd:string -property_value: IAO:0000232 "See github ticket https://github.com/oborel/obo-relations/issues/497" xsd:string holds_over_chain: capable_of has_input creation_date: 2021-11-08T12:00:00Z @@ -18161,65 +17807,24 @@ creation_date: 2020-06-08T17:21:33Z id: adjacent_to name: adjacent to namespace: external -namespace: uberon def: "x adjacent to y if and only if x and y share a boundary." [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002220 -property_value: editor_note "This relation acts as a join point with BSPO" xsd:string -property_value: IAO:0000112 "A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts." xsd:string {seeAlso="issuecomment-218584934"} -property_value: IAO:0000112 "The epidermis layer of a vertebrate is adjacent to the dermis." xsd:string -property_value: IAO:0000112 "The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies." xsd:string -property_value: IAO:0000112 "The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "This relation acts as a join point with BSPO" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000004 ! independent continuant is_a: RO:0002163 ! spatially disjoint from -[Typedef] -id: anterior_to -name: anterior to -namespace: uberon -xref: BSPO:0000096 - [Typedef] id: anteriorly_connected_to name: anteriorly connected to namespace: uberon def: "x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] -is_a: connected_to ! connected to -is_a: posterior_to ! posterior to +is_a: RO:0002170 ! connected to is_a: transitively_anteriorly_connected_to ! transitively anteriorly connected to -[Typedef] -id: attaches_to -name: attached to -namespace: uberon -def: "a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a" [] -subset: ro-eco -xref: RO:0002371 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000589 "attached to (anatomical structure to anatomical structure)" xsd:string -is_symmetric: true -is_a: attaches_to_part_of ! attached to part of -is_a: connected_to ! connected to - -[Typedef] -id: attaches_to_part_of -name: attached to part of -namespace: uberon -def: "a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b." [] -xref: RO:0002177 -property_value: IAO:0000589 "attached to part of (anatomical structure to anatomical structure)" xsd:string -domain: UBERON:0000061 ! anatomical structure -range: UBERON:0000061 ! anatomical structure -holds_over_chain: attaches_to part_of {RO:0002582="true"} -is_a: RO:0002323 ! mereotopologically related to -is_a: RO:0002567 ! biomechanically related to - [Typedef] id: bearer_of name: bearer of @@ -18227,13 +17832,7 @@ name: has characteristic namespace: external def: "Inverse of characteristic_of" [] xref: RO:0000053 -property_value: editor_note "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string -property_value: IAO:0000111 "bearer of" xsd:string -property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string -property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string -property_value: IAO:0000118 "bearer_of" xsd:string -property_value: IAO:0000118 "is bearer of" xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string range: BFO:0000020 ! specifically dependent continuant is_inverse_functional: true @@ -18241,45 +17840,20 @@ is_inverse_functional: true id: bounding_layer_of name: bounding layer of namespace: external -namespace: uberon def: "X outer_layer_of Y iff:\n. X :continuant that bearer_of some PATO:laminar\n. X part_of Y\n. exists Z :surface\n. X has_boundary Z\n. Z boundary_of Y\n\nhas_boundary: http://purl.obolibrary.org/obo/RO_0002002\nboundary_of: http://purl.obolibrary.org/obo/RO_0002000" [] comment: A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. subset: ro-eco xref: RO:0002007 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 range: BFO:0000040 ! material entity -is_a: part_of ! part_of - -[Typedef] -id: branching_part_of -name: branching part of -namespace: uberon -def: "x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y" [] -subset: ro-eco -xref: RO:0002380 -property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: seeAlso "FMA:85994" xsd:string -property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 -is_a: part_of ! part_of -is_a: RO:0002375 ! in branching relationship with -inverse_of: has_branching_part ! has branching part +is_a: part_of ! part of [Typedef] id: capable_of name: capable of namespace: external -namespace: uberon def: "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. " [] subset: ro-eco xref: RO:0002215 -property_value: IAO:0000112 "mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)" xsd:string -property_value: IAO:0000112 "osteoclast SubClassOf 'capable of' some 'bone resorption'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "has function realized in" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20123131 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21208450 -property_value: IAO:0000232 "For compatibility with BFO, this relation has a shortcut definition in which the expression \"capable of some P\" expands to \"bearer_of (some realized_by only P)\"." xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000015 ! process is_a: capable_of_part_of ! capable of part of @@ -18288,14 +17862,10 @@ is_a: capable_of_part_of ! capable of part of id: capable_of_part_of name: capable of part of namespace: external -namespace: uberon def: "c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p." [] xref: RO:0002216 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "has function in" xsd:string property_value: seeAlso http://purl.obolibrary.org/obo/ro/docs/reflexivity/ -holds_over_chain: capable_of part_of {RO:0002582="true"} -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to is_a: RO:0002500 ! causal agent in process [Typedef] @@ -18304,8 +17874,6 @@ name: causally downstream of namespace: external def: "inverse of upstream of" [] xref: RO:0002404 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of_or_within ! causally downstream of or within is_a: preceded_by ! preceded by inverse_of: causally_upstream_of ! causally upstream of @@ -18317,8 +17885,6 @@ namespace: external def: "inverse of causally upstream of or within" [] subset: RO:0002259 xref: RO:0002427 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_transitive: true is_a: RO:0002501 ! causal relation between processes @@ -18330,7 +17896,6 @@ def: "p is causally upstream of q iff p is causally related to q, the end of p p subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002411 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_transitive: true is_a: causally_upstream_of_or_within ! causally upstream of or within is_a: precedes ! precedes @@ -18343,7 +17908,6 @@ def: "p is causally upstream of, negative effect q iff p is casually upstream of subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002305 -property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 property_value: RO:0004050 RO:0002411 property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_negative_effect is_a: causally_upstream_of ! causally upstream of @@ -18358,8 +17922,6 @@ comment: holds between x and y if and only if x is causally upstream of y and th subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002304 -property_value: http://purl.org/dc/terms/creator https://orcid.org/0000-0002-6601-2165 -property_value: RO:0004049 RO:0002411 property_value: seeAlso https://wiki.geneontology.org/Causally_upstream_of,_positive_effect is_a: causally_upstream_of ! causally upstream of is_a: RO:0004047 ! causally upstream of or within, positive effect @@ -18371,9 +17933,7 @@ namespace: external def: "p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q." [] synonym: "affects" RELATED [] xref: RO:0002418 -property_value: editor_note "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "influences (processual)" xsd:string +property_value: IAO:0000116 "We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2" xsd:string is_transitive: true is_a: RO:0002501 ! causal relation between processes inverse_of: causally_downstream_of_or_within ! causally downstream of or within @@ -18383,511 +17943,81 @@ id: channel_for name: channel for namespace: uberon synonym: "carries" BROAD [] -domain: UBERON:0004111 ! anatomical conduit -range: UBERON:0000463 ! organism substance [Typedef] id: channels_from name: channels_from namespace: uberon -is_transitive: true [Typedef] id: channels_into name: channels_into namespace: uberon -is_transitive: true [Typedef] -id: composed_primarily_of -name: composed primarily of -namespace: uberon -def: "x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y." [] -subset: ro-eco -xref: RO:0002473 -property_value: IAO:0000112 "'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: RO:0001900 RO:0001901 -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: has_part ! has part +id: directly_negatively_regulates +name: directly negatively regulates +namespace: external +def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0002630 +property_value: RO:0004050 RO:0002578 +property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates" xsd:anyURI +is_a: directly_regulates ! directly regulates +is_a: negatively_regulates ! negatively regulates [Typedef] -id: conduit_for -name: conduit for -namespace: uberon -def: "x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x." [] -subset: ro-eco -xref: RO:0002570 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "UBERON:cjm" xsd:string -property_value: IAO:0000232 "This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through." xsd:string -domain: BFO:0000040 ! material entity -range: BFO:0000040 ! material entity -is_a: overlaps ! overlaps +id: directly_positively_regulates +name: directly positively regulates +namespace: external +def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0002629 +property_value: seeAlso "https://wiki.geneontology.org/Directly_positively_regulates" xsd:anyURI +is_a: directly_regulates ! directly regulates +is_a: positively_regulates ! positively regulates [Typedef] -id: connected_to -name: connected to -namespace: uberon -def: "a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b" [] -xref: RO:0002170 -property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI -property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: connecting_branch_of -name: connecting branch of -namespace: uberon -def: "b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t." [] -xref: RO:0002252 -property_value: IAO:0000112 "In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1." xsd:string -property_value: RO:0004036 BFO:0000050 -property_value: seeAlso https://github.com/obophenotype/uberon/issues/2212 -is_a: connected_to ! connected to -is_a: RO:0002375 ! in branching relationship with -inverse_of: RO:0002253 ! has connecting branch - -[Typedef] -id: connects -name: connects -namespace: uberon -def: "c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system." [] -xref: RO:0002176 -property_value: IAO:0000112 "a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones)." xsd:string -property_value: IAO:0000112 "The M8 connects Glasgow and Edinburgh" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern" xsd:anyURI -property_value: seeAlso "https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern" xsd:anyURI -domain: BFO:0000004 ! independent continuant -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: contains_process -name: contains process -namespace: uberon -def: "[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t" [] -comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant -xref: BFO:0000067 -property_value: IAO:0000111 "site of" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl - -[Typedef] -id: continuous_with -name: continuous with -namespace: uberon -def: "X continuous_with Y if and only if X and Y share a fiat boundary." [] -xref: RO:0002150 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "connected to" xsd:string -property_value: IAO:0000232 "The label for this relation was previously connected to. I relabeled this to \"continuous with\". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint)" xsd:string -property_value: RO:0001900 RO:0001901 -property_value: seeAlso "FMA:85972" xsd:string -domain: BFO:0000004 ! independent continuant -range: BFO:0000004 ! independent continuant -is_symmetric: true -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: contributes_to_morphology_of -name: contributes to morphology of -namespace: uberon -def: "p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm." [] -xref: RO:0002433 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: overlaps ! overlaps - -[Typedef] -id: dc-contributor -name: contributor -namespace: uberon -xref: http://purl.org/dc/terms/contributor -is_metadata_tag: true - -[Typedef] -id: dc-creator -name: creator -namespace: uberon -xref: http://purl.org/dc/elements/1.1/creator -is_metadata_tag: true - -[Typedef] -id: dc-description -name: description -namespace: uberon -xref: http://purl.org/dc/elements/1.1/description -is_metadata_tag: true - -[Typedef] -id: dc-title -name: title -namespace: uberon -xref: http://purl.org/dc/elements/1.1/title -is_metadata_tag: true - -[Typedef] -id: dcterms-date -name: date -namespace: uberon -xref: http://purl.org/dc/terms/date -is_metadata_tag: true - -[Typedef] -id: dcterms-license -name: license -namespace: uberon -xref: http://purl.org/dc/terms/license -is_metadata_tag: true - -[Typedef] -id: deep_to -name: deep to -namespace: uberon -xref: BSPO:0000107 - -[Typedef] -id: depiction -name: depiction -namespace: uberon -xref: http://xmlns.com/foaf/0.1/depiction -is_metadata_tag: true - -[Typedef] -id: developmentally_induced_by -name: developmentally induced by -namespace: uberon -def: "t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T" [] -xref: RO:0002256 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "induced by" xsd:string -property_value: IAO:0000119 " Developmental Biology, Gilbert, 8th edition, figure 6.5(F)" xsd:string -property_value: IAO:0000119 "GO:0001759" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 -property_value: IAO:0000232 "We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm]" xsd:string -domain: UBERON:0000465 ! material anatomical entity -range: UBERON:0000465 ! material anatomical entity -is_a: RO:0002258 ! developmentally preceded by -inverse_of: RO:0002257 ! developmentally induces - -[Typedef] -id: developmentally_replaces -name: developmentally replaces -namespace: uberon -def: "x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else" [] -xref: RO:0002285 -property_value: editor_note "This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "replaces" xsd:string -is_a: RO:0002258 ! developmentally preceded by - -[Typedef] -id: develops_from -name: develops from -namespace: uberon -def: "x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y" [] -comment: This is the transitive form of the develops from relation -xref: RO:0002202 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 -domain: BFO:0000004 ! independent continuant -range: BFO:0000004 ! independent continuant -is_transitive: true -is_a: has_developmental_contribution_from ! has developmental contribution from -is_a: RO:0002258 ! developmentally preceded by -inverse_of: develops_into ! develops into - -[Typedef] -id: develops_from_part_of -name: develops from part of -namespace: uberon -def: "x develops from part of y if and only if there exists some z such that x develops from z and z is part of y" [] -xref: RO:0002225 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -holds_over_chain: directly_develops_from part_of -is_a: develops_from ! develops from - -[Typedef] -id: develops_in -name: develops in -namespace: uberon -def: "x develops_in y if x is located in y whilst x is developing" [] -xref: RO:0002226 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "EHDAA2" xsd:string -property_value: IAO:0000119 "Jonathan Bard, EHDAA2" xsd:string -domain: UBERON:0001062 ! anatomical entity -holds_over_chain: directly_develops_from located_in -is_a: RO:0002258 ! developmentally preceded by - -[Typedef] -id: develops_into -name: develops into -namespace: uberon -def: "inverse of develops from" [] -subset: RO:0002259 -xref: RO:0002203 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000117 https://orcid.org/0000-0003-1980-3228 -is_transitive: true -is_a: has_potential_to_develop_into ! has potential to develop into -is_a: RO:0002286 ! developmentally succeeded by -is_a: RO:0002388 ! has potential to directly develop into - -[Typedef] -id: directly_develops_from -name: directly develops from -namespace: uberon -def: "Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y." [] -comment: TODO - add child relations from DOS -synonym: "has developmental precursor" EXACT [] -xref: RO:0002207 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000119 "FBbt" xsd:string -property_value: RO:0002575 RO:0002202 -is_a: develops_from ! develops from -inverse_of: RO:0002210 ! directly develops into - -[Typedef] -id: directly_negatively_regulates -name: directly negatively regulates -namespace: external -def: "p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -xref: RO:0002630 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly negatively regulates (process to process)" xsd:string -property_value: RO:0004050 RO:0002578 -property_value: seeAlso "https://wiki.geneontology.org/Directly_negatively_regulates" xsd:anyURI -is_a: directly_regulates ! directly regulates -is_a: negatively_regulates ! negatively regulates - -[Typedef] -id: directly_positively_regulates -name: directly positively regulates -namespace: external -def: "p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -xref: RO:0002629 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly positively regulates (process to process)" xsd:string -property_value: RO:0004049 RO:0002578 -property_value: seeAlso "https://wiki.geneontology.org/Directly_positively_regulates" xsd:anyURI -is_a: directly_regulates ! directly regulates -is_a: positively_regulates ! positively regulates - -[Typedef] -id: directly_regulates -name: directly regulates -namespace: external -def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] -subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension -subset: http://purl.obolibrary.org/obo/valid_for_go_ontology -subset: http://purl.obolibrary.org/obo/valid_for_gocam -xref: RO:0002578 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "directly regulates (processual)" xsd:string -property_value: RO:0002575 RO:0002211 -is_a: immediately_causally_upstream_of ! immediately causally upstream of -is_a: regulates ! regulates - -[Typedef] -id: distal_to -name: distal to -namespace: uberon -xref: BSPO:0000097 - -[Typedef] -id: distally_connected_to -name: distally connected to +id: directly_regulates +name: directly regulates +namespace: external +def: "p directly regulates q iff p is immediately causally upstream of q and p regulates q." [] +subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension +subset: http://purl.obolibrary.org/obo/valid_for_go_ontology +subset: http://purl.obolibrary.org/obo/valid_for_gocam +xref: RO:0002578 +is_a: immediately_causally_upstream_of ! immediately causally upstream of +is_a: regulates ! regulates + +[Typedef] +id: distally_connected_to +name: distally connected to namespace: uberon def: "x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] -is_a: connected_to ! connected to -is_a: proximal_to ! proximal to +is_a: RO:0002170 ! connected to is_a: transitively_distally_connected_to ! transitively distally connected to -inverse_of: proximally_connected_to ! proximally connected to - -[Typedef] -id: distalmost_part_of -name: distalmost part of -namespace: uberon -xref: BSPO:0001108 - -[Typedef] -id: dorsal_to -name: dorsal to -namespace: uberon -xref: BSPO:0000098 - -[Typedef] -id: drains -name: drains -namespace: uberon -def: "Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure." [] -xref: RO:0002179 -property_value: editor_note "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 -domain: UBERON:0001638 ! vein -is_a: connected_to ! connected to - -[Typedef] -id: editor_note -name: editor note -namespace: uberon -def: "An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology." [] -xref: IAO:0000116 -property_value: IAO:0000111 "editor note" xsd:string -property_value: IAO:0000114 IAO:0000122 -property_value: IAO:0000117 "PERSON:Daniel Schober" xsd:string -property_value: IAO:0000119 "GROUP:OBI:" xsd:string -is_metadata_tag: true - -[Typedef] -id: ends -name: ends -namespace: uberon -def: "inverse of ends with" [] -subset: ro-eco -xref: RO:0002229 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: part_of ! part_of -is_a: RO:0002222 ! temporally related to -inverse_of: ends_with ! ends with [Typedef] id: ends_with name: ends with namespace: external -namespace: uberon def: "x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002230 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "finished by" xsd:string is_transitive: true is_a: has_part ! has part is_a: RO:0002222 ! temporally related to -[Typedef] -id: existence_ends_during -name: existence ends during -namespace: uberon -def: "Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely." [https://orcid.org/0000-0002-6601-2165] -def: "x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y)." [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -synonym: "ceases_to_exist_during" EXACT [] -xref: RO:0002492 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_ends_during_or_before ! existence ends during or before -is_a: RO:0002490 ! existence overlaps -transitive_over: part_of ! part_of - -[Typedef] -id: existence_ends_during_or_before -name: existence ends during or before -namespace: uberon -def: "x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends." [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -xref: RO:0002497 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -holds_over_chain: part_of existence_ends_during_or_before -holds_over_chain: RO:0002286 existence_ends_during_or_before -is_a: RO:0002487 ! relation between physical entity and a process or stage -transitive_over: part_of ! part_of -transitive_over: precedes ! precedes -transitive_over: simultaneous_with ! simultaneous with - -[Typedef] -id: existence_ends_with -name: existence ends with -namespace: uberon -def: "x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y)." [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -xref: RO:0002493 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_ends_during ! existence ends during - -[Typedef] -id: existence_starts_and_ends_during -name: existence starts and ends during -namespace: uberon -def: "x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y)" [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -synonym: "exists during" EXACT [] -xref: RO:0002491 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_ends_during ! existence ends during -is_a: existence_starts_during ! existence starts during - -[Typedef] -id: existence_starts_during -name: existence starts during -namespace: uberon -def: "x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y)." [] -xref: RO:0002488 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_starts_during_or_after ! existence starts during or after -is_a: RO:0002490 ! existence overlaps -transitive_over: part_of ! part_of - -[Typedef] -id: existence_starts_during_or_after -name: existence starts during or after -namespace: uberon -def: "x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y)." [] -comment: The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. -xref: RO:0002496 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -holds_over_chain: part_of existence_starts_during_or_after -holds_over_chain: RO:0002258 existence_starts_during_or_after -is_a: RO:0002487 ! relation between physical entity and a process or stage -transitive_over: part_of ! part_of -transitive_over: preceded_by ! preceded by -transitive_over: simultaneous_with ! simultaneous with - -[Typedef] -id: existence_starts_with -name: existence starts with -namespace: uberon -def: "x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y)." [] -xref: RO:0002489 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: existence_starts_during ! existence starts during - [Typedef] id: extends_fibers_into name: extends_fibers_into namespace: uberon def: "X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y" [https://orcid.org/0000-0002-7073-9172] -holds_over_chain: RO:0002100 RO:0013001 -is_symmetric: true -is_a: connected_to ! connected to +is_a: RO:0002170 ! connected to [Typedef] id: filtered_through @@ -18896,75 +18026,17 @@ namespace: uberon def: "Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity." [] comment: Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed -[Typedef] -id: functionally_related_to -name: functionally related to -namespace: uberon -def: "A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities." [] -xref: RO:0002328 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "This is a grouping relation that collects relations used for the purpose of connecting structure and function" xsd:string - -[Typedef] -id: has_boundary -name: has 2D boundary -namespace: uberon -def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] -xref: RO:0002002 -property_value: editor_note "A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts." xsd:string -property_value: editor_note "Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape." xsd:string -property_value: IAO:0000112 "my body has 2D boundary the surface of my skin" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "has boundary" xsd:string -property_value: IAO:0000118 "has_2D_boundary" xsd:string -property_value: RO:0001900 RO:0001901 -domain: BFO:0000040 ! material entity -range: BFO:0000141 ! immaterial entity -is_a: RO:0002323 ! mereotopologically related to - -[Typedef] -id: has_branching_part -name: has branching part -namespace: uberon -def: "inverse of branching part of" [] -subset: ro-eco -subset: RO:0002259 -xref: RO:0002569 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_transitive: true -is_a: has_part ! has part -is_a: RO:0002375 ! in branching relationship with - [Typedef] id: has_component name: has component namespace: external -namespace: uberon def: "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] subset: ro-eco xref: RO:0002180 -property_value: editor_note "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000232 "For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit." xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity." xsd:string property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:Componency is_a: has_part ! has part -[Typedef] -id: has_developmental_contribution_from -name: has developmental contribution from -namespace: uberon -def: "x has developmental contribution from y iff x has some part z such that z develops from y" [] -xref: RO:0002254 -property_value: IAO:0000112 "Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong]" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: UBERON:0001062 ! anatomical entity -range: UBERON:0001062 ! anatomical entity -holds_over_chain: has_part develops_from -is_a: RO:0002258 ! developmentally preceded by -inverse_of: RO:0002255 ! developmentally contributes to - [Typedef] id: has_end_location name: has end location @@ -18972,9 +18044,6 @@ namespace: external def: "x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y" [] subset: ro-eco xref: RO:0002232 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "ends with process that occurs in" xsd:string domain: BFO:0000015 ! process range: BFO:0000004 ! independent continuant holds_over_chain: ends_with occurs_in @@ -18998,14 +18067,11 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002233 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "consumes" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Has_input" xsd:anyURI domain: BFO:0000015 ! process holds_over_chain: starts_with has_input is_a: has_participant ! has participant -inverse_of: input_of ! input of +inverse_of: RO:0002352 ! input of [Typedef] id: has_low_plasma_membrane_amount @@ -19015,52 +18081,6 @@ property_value: term_tracker_item https://github.com/obophenotype/cell-ontology/ is_obsolete: true replaced_by: RO:0015016 -[Typedef] -id: has_member -name: has member -namespace: uberon -def: "has member is a mereological relation between a collection and an item." [] -xref: RO:0002351 -property_value: IAO:0000119 "SIO" xsd:string -property_value: RO:0001900 RO:0001901 -is_a: has_part ! has part - -[Typedef] -id: has_muscle_antagonist -name: has muscle antagonist -namespace: uberon -def: "m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position." [] -xref: RO:0002568 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "Wikipedia:Antagonist_(muscle)" xsd:string -is_a: RO:0002567 ! biomechanically related to - -[Typedef] -id: has_muscle_insertion -name: has muscle insertion -namespace: uberon -def: "m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone." [] -xref: RO:0002373 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string -property_value: seeAlso http://dbpedia.org/property/insertion -domain: UBERON:0000061 {IAO:0000116="We need to import uberon muscle into RO to use as a stricter domain constraint"} ! anatomical structure -is_a: attaches_to ! attached to -is_a: RO:0002567 ! biomechanically related to - -[Typedef] -id: has_muscle_origin -name: has muscle origin -namespace: uberon -def: "m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to." [] -xref: RO:0002372 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "Wikipedia:Insertion_(anatomy)" xsd:string -property_value: seeAlso http://dbpedia.org/property/origin -domain: UBERON:0000061 {comment="We need to import uberon muscle to create a stricter domain constraint"} ! anatomical structure -is_a: attaches_to ! attached to -is_a: RO:0002567 ! biomechanically related to - [Typedef] id: has_negative_regulatory_component_activity name: has negative regulatory component activity @@ -19078,13 +18098,9 @@ id: has_ontology_root_term name: has ontology root term name: preferred_root namespace: external -namespace: uberon def: "Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root." [] xref: IAO:0000700 -property_value: IAO:0000111 "has ontology root term" xsd:string -property_value: IAO:0000117 "Nicolas Matentzoglu" xsd:string is_metadata_tag: true -is_class_level: true [Typedef] id: has_output @@ -19096,9 +18112,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002234 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "produces" xsd:string property_value: seeAlso "https://wiki.geneontology.org/Has_output" xsd:anyURI holds_over_chain: ends_with has_output is_a: has_participant ! has participant @@ -19110,62 +18123,29 @@ name: has part name: has_part namespace: external namespace: quality -namespace: uberon def: "a core relation that holds between a whole and its part" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000051 -property_value: editor_note "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string -property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string -property_value: IAO:0000111 "has part" xsd:string -property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string -property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string -property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string -property_value: IAO:0000118 "has_part" xsd:string -property_value: RO:0001900 RO:0001901 +property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string is_transitive: true is_a: overlaps ! overlaps [Typedef] -id: has_participant -name: has participant -namespace: external -def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] -xref: RO:0000057 -property_value: editor_note "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string -property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:has_participant" xsd:string -property_value: IAO:0000111 "has participant" xsd:string -property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string -property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string -property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string -property_value: IAO:0000118 "has_participant" xsd:string -domain: BFO:0000003 ! occurrent -range: BFO:0000002 ! continuant -holds_over_chain: has_part has_participant - -[Typedef] -id: has_potential_to_develop_into -name: has potential to develop into -namespace: uberon -def: "x has the potential to develop into y iff x develops into y or if x is capable of developing into y" [] -xref: RO:0002387 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: RO:0002384 ! has developmental potential involving - -[Typedef] -id: has_potential_to_developmentally_contribute_to -name: has potential to developmentally contribute to -namespace: uberon -def: "x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y" [] -xref: RO:0002385 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: RO:0002384 ! has developmental potential involving - -[Typedef] +id: has_participant +name: has participant +namespace: external +def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] +xref: RO:0000057 +property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string +domain: BFO:0000003 ! occurrent +range: BFO:0000002 ! continuant +holds_over_chain: has_part has_participant + +[Typedef] id: has_primary_input name: has primary input namespace: external @@ -19200,17 +18180,6 @@ is_a: has_primary_input_or_output ! has primary input or output created_by: https://orcid.org/0000-0002-6601-2165 creation_date: 2018-12-13T11:26:32Z -[Typedef] -id: has_quality -name: has quality -namespace: uberon -def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] -xref: RO:0000086 -property_value: editor_note "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string -property_value: IAO:0000112 "this apple has quality this red color" xsd:string -property_value: IAO:0000118 "has_quality" xsd:string -is_a: bearer_of ! bearer of - [Typedef] id: has_regulatory_component_activity name: has regulatory component activity @@ -19222,24 +18191,6 @@ is_a: RO:0002017 ! has component activity created_by: https://orcid.org/0000-0002-7073-9172 creation_date: 2017-05-24T09:30:46Z -[Typedef] -id: has_skeleton -name: has skeleton -namespace: uberon -def: "A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision." [] -xref: RO:0002551 -property_value: IAO:0000112 "Forelimb SubClassOf has_skeleton some 'Forelimb skeleton'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "has supporting framework" xsd:string -property_value: IAO:0000232 "The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell)." xsd:string -domain: UBERON:0000061 ! anatomical structure -domain: UBERON:0000475 ! organism subdivision -range: UBERON:0000465 {IAO:0000116="This should be to a more restricted class, but not the Uberon class may be too restricted since it is a composition-based definition of skeleton rather than functional."} ! material anatomical entity -range: UBERON:0010912 ! subdivision of skeleton -is_a: has_part ! has part -inverse_of: skeleton_of ! skeleton of -is_asymmetric: true - [Typedef] id: has_small_molecule_activator name: has small molecule activator @@ -19258,9 +18209,6 @@ namespace: external def: "x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y" [] subset: ro-eco xref: RO:0002231 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "starts with process that occurs in" xsd:string domain: BFO:0000015 ! process range: BFO:0000004 ! independent continuant holds_over_chain: starts_with occurs_in @@ -19275,9 +18223,8 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002339 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in -transitive_over: part_of ! part_of +transitive_over: part_of ! part of [Typedef] id: has_target_start_location @@ -19288,41 +18235,14 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002338 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in -transitive_over: part_of ! part_of - -[Typedef] -id: homologous_to -name: shares ancestor with -namespace: uberon -def: "two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a." [] -comment: VBO calls this homologous_to -xref: RO:0002158 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000232 "Consider obsoleting and merging with child relation, 'in homology relationship with'" xsd:string -is_symmetric: true -is_transitive: true -is_a: RO:0002320 ! evolutionarily related to - -[Typedef] -id: immediate_transformation_of -name: immediate transformation of -namespace: uberon -def: "x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t" [] -xref: RO:0002495 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0002575 RO:0002494 -is_a: directly_develops_from ! directly develops from -is_a: transformation_of ! transformation of +transitive_over: part_of ! part of [Typedef] id: immediately_causally_downstream_of name: immediately causally downstream of namespace: external xref: RO:0002405 -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: causally_downstream_of ! causally downstream of is_a: immediately_preceded_by ! immediately preceded by inverse_of: immediately_causally_upstream_of ! immediately causally upstream of @@ -19333,26 +18253,15 @@ name: immediately causally upstream of namespace: external def: "p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q." [] xref: RO:0002412 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0002575 RO:0002411 is_a: causally_upstream_of ! causally upstream of is_a: immediately_precedes ! immediately precedes -[Typedef] -id: immediately_deep_to -name: immediately deep to -namespace: uberon -xref: BSPO:0001107 - [Typedef] id: immediately_preceded_by name: immediately preceded by namespace: external -namespace: uberon comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) xref: RO:0002087 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000118 "starts_at_end_of" xsd:string holds_over_chain: starts_with ends_with is_a: preceded_by ! preceded by inverse_of: immediately_precedes ! immediately precedes @@ -19364,228 +18273,22 @@ namespace: external comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) subset: ro-eco xref: RO:0002090 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: IAO:0000118 "ends_at_start_of" xsd:string -property_value: IAO:0000118 "meets" xsd:string -property_value: RO:0002575 BFO:0000063 holds_over_chain: ends_with starts_with is_a: precedes ! precedes -[Typedef] -id: immediately_superficial_to -name: immediately superficial to -namespace: uberon -xref: BSPO:0015014 - -[Typedef] -id: in_anterior_side_of -name: in anterior side of -namespace: uberon -xref: BSPO:0000123 - -[Typedef] -id: in_deep_part_of -name: in deep part of -namespace: uberon -xref: BSPO:0001101 - -[Typedef] -id: in_dorsal_side_of -name: in dorsal side of -namespace: uberon -xref: BSPO:0015101 - -[Typedef] -id: in_lateral_side_of -name: in lateral side of -namespace: uberon -xref: BSPO:0000126 - -[Typedef] -id: in_left_side_of -name: in left side of -namespace: uberon -xref: BSPO:0000120 - -[Typedef] -id: in_posterior_side_of -name: in posterior side of -namespace: uberon -xref: BSPO:0000122 - -[Typedef] -id: in_proximal_side_of -name: in proximal side of -namespace: uberon -xref: BSPO:0000124 - -[Typedef] -id: in_right_side_of -name: in right side of -namespace: uberon -xref: BSPO:0000121 - -[Typedef] -id: in_superficial_part_of -name: in superficial part of -namespace: uberon -xref: BSPO:0001100 - -[Typedef] -id: in_taxon -name: in taxon -namespace: uberon -def: "x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." [] -comment: Connects a biological entity to its taxon of origin. -subset: ro-eco -xref: RO:0002162 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9227-417X -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -holds_over_chain: attaches_to in_taxon -holds_over_chain: capable_of in_taxon -holds_over_chain: connected_to in_taxon -holds_over_chain: connects in_taxon -holds_over_chain: continuous_with in_taxon -holds_over_chain: developmentally_induced_by in_taxon -holds_over_chain: develops_from in_taxon -holds_over_chain: develops_from_part_of in_taxon -holds_over_chain: existence_ends_during in_taxon -holds_over_chain: existence_starts_during in_taxon -holds_over_chain: extends_fibers_into in_taxon -holds_over_chain: has_developmental_contribution_from in_taxon -holds_over_chain: has_part in_taxon -holds_over_chain: has_potential_to_develop_into in_taxon -holds_over_chain: innervated_by in_taxon -holds_over_chain: overlaps in_taxon -holds_over_chain: part_of in_taxon -holds_over_chain: produced_by in_taxon -holds_over_chain: produces in_taxon -holds_over_chain: results_in_developmental_progression_of in_taxon -holds_over_chain: RO:0002206 in_taxon -holds_over_chain: supplies in_taxon -is_a: RO:0002320 ! evolutionarily related to - [Typedef] id: indirectly_supplies name: indirectly_supplies namespace: uberon def: "a indirectly_supplies s iff a has a branch and the branch supplies or indirectly supplies s." [] -property_value: editor_note "add to RO" xsd:string -holds_over_chain: has_branching_part indirectly_supplies -holds_over_chain: has_branching_part supplies -is_transitive: true - -[Typedef] -id: innervated_by -name: innervated_by -namespace: uberon -xref: RO:0002005 -property_value: http://purl.org/spar/cito/citesAsAuthority "http://www.ncbi.nlm.nih.gov/pubmed/22402613" xsd:anyURI -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -domain: UBERON:0000061 ! anatomical structure -inverse_of: innervates ! innervates -transitive_over: branching_part_of ! branching part of - -[Typedef] -id: innervates -name: innervates -namespace: uberon -def: "Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input.\nT innervates some R\nExpands_to: T has_fasciculating_neuron_projection that synapse_in some R." [] -xref: RO:0002134 -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 -transitive_over: part_of ! part_of -expand_expression_to: "RO_0002132 some (GO_0043005 that (RO_0002131 some (GO_0045202 that BFO_0000050 some Y?)))" [] - -[Typedef] -id: input_of -name: input of -namespace: uberon -def: "inverse of has input" [] -subset: ro-eco -subset: RO:0002259 -xref: RO:0002352 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: functionally_related_to ! functionally related to -is_a: participates_in ! participates in - -[Typedef] -id: intersects_midsagittal_plane_of -name: intersects midsagittal plane of -namespace: uberon -xref: BSPO:0005001 +property_value: IAO:0000116 "add to RO" xsd:string +holds_over_chain: RO:0002569 indirectly_supplies [Typedef] id: layer_part_of name: layer part of namespace: uberon -is_a: part_of ! part_of - -[Typedef] -id: located_in -name: located in -namespace: uberon -def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] -subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term -xref: RO:0001025 -property_value: editor_note "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" xsd:string -property_value: editor_note "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:located_in" xsd:string -property_value: IAO:0000111 "located in" xsd:string -property_value: IAO:0000112 "my brain is located in my head" xsd:string -property_value: IAO:0000112 "this rat is located in this cage" xsd:string -property_value: IAO:0000118 "located_in" xsd:string -property_value: RO:0001900 RO:0001901 -property_value: seeAlso "https://wiki.geneontology.org/Located_in" xsd:anyURI -domain: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant -range: BFO:0000004 {IAO:0000116="This is redundant with the more specific 'independent and not spatial region' constraint. We leave in the redundant axiom for use with reasoners that do not use negation."} ! independent continuant -is_transitive: true -transitive_over: part_of ! part_of - -[Typedef] -id: location_of -name: location of -namespace: uberon -def: "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" [] -xref: RO:0001015 -property_value: editor_note "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: IAO:0000111 "is location of" xsd:string -property_value: IAO:0000112 "my head is the location of my brain" xsd:string -property_value: IAO:0000112 "this cage is the location of this rat" xsd:string -property_value: IAO:0000118 "location_of" xsd:string -property_value: RO:0001900 RO:0001901 -is_transitive: true -inverse_of: located_in ! located in - -[Typedef] -id: lumen_of -name: lumen of -namespace: uberon -def: "x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull." [] -subset: ro-eco -xref: RO:0002571 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 https://orcid.org/0000-0002-6601-2165 -range: BFO:0000040 ! material entity -is_a: part_of ! part_of - -[Typedef] -id: luminal_space_of -name: luminal space of -namespace: uberon -def: "s is luminal space of x iff s is lumen_of x and s is an immaterial entity" [] -subset: ro-eco -xref: RO:0002572 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: BFO:0000141 ! immaterial entity -is_a: lumen_of ! lumen of +is_a: part_of ! part of [Typedef] id: negatively_regulated_by @@ -19594,7 +18297,6 @@ namespace: external def: "inverse of negatively regulates" [] subset: RO:0002259 xref: RO:0002335 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -19606,9 +18308,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002212 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "negatively regulates (process to process)" xsd:string property_value: RO:0004050 RO:0002211 holds_over_chain: ends_with negatively_regulates is_a: causally_upstream_of,_negative_effect ! causally upstream of, negative effect @@ -19621,30 +18320,11 @@ name: negatively regulates characteristic namespace: gene_ontology def: "A relationship that holds between a process and a characteristic in which process (P) negatively regulates characteristic (C) iff: P results in a decrease in the intensity or magnitude of C." [] xref: RO:0019002 -property_value: dc-contributor https://orcid.org/0000-0002-8688-6599 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 holds_over_chain: negatively_regulates positively_regulates_characteristic holds_over_chain: positively_regulates negatively_regulates_characteristic is_a: regulates_characteristic ! regulates characteristic -[Typedef] -id: never_in_taxon -name: never in taxon -name: never_in_taxon -namespace: uberon -def: "S never_in_taxon T iff: S SubClassOf in_taxon only not T." [PMID:20973947] -def: "x never in taxon T if and only if T is a class, and x does not instantiate the class expression \"in taxon some T\". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL." [] -xref: RO:0002161 -property_value: IAO:0000112 "tooth SubClassOf 'never in taxon' value 'Aves'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 -property_value: OMO:0002000 "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX never_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?x owl:disjointWith [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n ?x rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom [\n a owl:Class ;\n owl:complementOf ?taxon\n ]\n ] .\n}\nWHERE {\n ?x never_in_taxon: ?taxon .\n}" xsd:string -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -expand_assertion_to: "Class: EquivalentTo: ?X and (RO_0002162 some ?Y)" [] -expand_assertion_to: "Class: ?X DisjointWith: RO_0002162 some ?Y " [] -is_metadata_tag: true -is_class_level: true - [Typedef] id: occurs_in name: occurs in @@ -19655,64 +18335,38 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000066 -property_value: IAO:0000111 "occurs in" xsd:string -property_value: IAO:0000118 "occurs_in" xsd:string -property_value: IAO:0000118 "unfolds in" xsd:string -property_value: IAO:0000118 "unfolds_in" xsd:string -property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl property_value: seeAlso "https://wiki.geneontology.org/Occurs_in" xsd:anyURI domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant holds_over_chain: part_of occurs_in -inverse_of: contains_process ! contains process -transitive_over: part_of ! part_of - -[Typedef] -id: only_in_taxon -name: only in taxon -namespace: uberon -def: "x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z." [] -xref: RO:0002160 -property_value: editor_note "The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g.\n\n 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria" xsd:string -property_value: IAO:0000112 "lactation SubClassOf 'only in taxon' some 'Mammalia'" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/17921072 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20973947 -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -is_a: in_taxon ! in taxon +inverse_of: BFO:0000067 ! contains process +transitive_over: part_of ! part of [Typedef] id: output_of name: output of namespace: external -namespace: uberon def: "inverse of has output" [] subset: ro-eco subset: RO:0002259 xref: RO:0002353 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_a: functionally_related_to ! functionally related to is_a: participates_in ! participates in +is_a: RO:0002328 ! functionally related to [Typedef] id: overlaps name: overlaps namespace: external -namespace: uberon def: "x overlaps y if and only if there exists some z such that x has part z and z part of y" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_gocam subset: ro-eco xref: RO:0002131 -property_value: IAO:0000114 IAO:0000125 -property_value: RO:0001900 RO:0001901 holds_over_chain: has_part overlaps -holds_over_chain: has_part part_of {RO:0002582="true"} holds_over_chain: part_of part_of is_symmetric: true is_a: RO:0002323 ! mereotopologically related to -transitive_over: part_of ! part_of +transitive_over: part_of ! part of expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)" [] [Typedef] @@ -19721,29 +18375,15 @@ name: part of name: part_of namespace: external namespace: quality -namespace: uberon def: "a core relation that holds between a part and its whole" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: BFO:0000050 -property_value: editor_note "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string -property_value: editor_note "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string -property_value: editor_note "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string -property_value: IAO:0000111 "is part of" xsd:string -property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string -property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string -property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string -property_value: IAO:0000118 "part_of" xsd:string -property_value: RO:0001900 RO:0001901 -property_value: RO:0040042 BFO:0000002 -property_value: RO:0040042 BFO:0000003 -property_value: RO:0040042 BFO:0000004 -property_value: RO:0040042 BFO:0000017 -property_value: RO:0040042 BFO:0000019 -property_value: RO:0040042 BFO:0000020 -property_value: RO:0040042 BFO:0000031 +property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string +property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/" xsd:string +property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string property_value: seeAlso http://ontologydesignpatterns.org/wiki/Community:Parts_and_Collections property_value: seeAlso http://ontologydesignpatterns.org/wiki/Submissions:PartOf property_value: seeAlso "http://www.obofoundry.org/ro/#OBO_REL:part_of" xsd:string @@ -19756,14 +18396,8 @@ inverse_of: has_part ! has part id: participates_in name: participates in namespace: external -namespace: uberon def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] xref: RO:0000056 -property_value: IAO:0000111 "participates in" xsd:string -property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string -property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string -property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string -property_value: IAO:0000118 "participates_in" xsd:string domain: BFO:0000002 ! continuant range: BFO:0000003 ! occurrent inverse_of: has_participant ! has participant @@ -19775,7 +18409,6 @@ namespace: external def: "inverse of positively regulates" [] subset: RO:0002259 xref: RO:0002336 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: regulated_by ! regulated by [Typedef] @@ -19787,10 +18420,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002213 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "positively regulates (process to process)" xsd:string -property_value: RO:0004049 RO:0002211 holds_over_chain: ends_with positively_regulates holds_over_chain: negatively_regulates negatively_regulates is_transitive: true @@ -19804,49 +18433,25 @@ name: positively regulates characteristic namespace: gene_ontology def: "A relationship that holds between a process and a characteristic in which process (P) positively regulates characteristic (C) iff: P results in an increase in the intensity or magnitude of C." [] xref: RO:0019001 -property_value: dc-contributor https://orcid.org/0000-0002-8688-6599 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 holds_over_chain: positively_regulates positively_regulates_characteristic is_a: regulates_characteristic ! regulates characteristic -[Typedef] -id: postaxialmost_part_of -name: postaxialmost part of -namespace: uberon -xref: BSPO:0001115 - -[Typedef] -id: posterior_to -name: posterior to -namespace: uberon -xref: BSPO:0000099 - [Typedef] id: posteriorly_connected_to name: posteriorly connected to namespace: uberon def: "x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] -is_a: anterior_to ! anterior to -is_a: connected_to ! connected to - -[Typedef] -id: preaxialmost_part_of -name: preaxialmost part of -namespace: uberon -xref: BSPO:0001113 +is_a: RO:0002170 ! connected to [Typedef] id: preceded_by name: preceded by namespace: external -namespace: uberon def: "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000062 -property_value: editor_note "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string -property_value: http://purl.org/dc/terms/source "http://www.obofoundry.org/ro/#OBO_REL:preceded_by" xsd:string -property_value: IAO:0000111 "preceded by" xsd:string -property_value: IAO:0000118 "is preceded by" xsd:string -property_value: IAO:0000118 "preceded_by" xsd:string +property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent holds_over_chain: part_of preceded_by @@ -19858,53 +18463,30 @@ inverse_of: precedes ! precedes id: precedes name: precedes namespace: external -namespace: uberon def: "x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: BFO:0000063 -property_value: IAO:0000111 "precedes" xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent holds_over_chain: part_of precedes is_transitive: true is_a: RO:0002222 ! temporally related to -[Typedef] -id: present_in_taxon -name: present in taxon -name: present_in_taxon -namespace: uberon -def: "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S" [] -def: "S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S." [https://orcid.org/0000-0002-6601-2165] -comment: The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology. -synonym: "applicable for taxon" EXACT [] -xref: RO:0002175 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/22293552 -property_value: OMO:0002000 "PREFIX rdfs: \nPREFIX owl: \nPREFIX in_taxon: \nPREFIX present_in_taxon: \nCONSTRUCT {\n in_taxon: a owl:ObjectProperty .\n ?witness rdfs:label ?label .\n ?witness rdfs:subClassOf ?x .\n ?witness rdfs:subClassOf [\n a owl:Restriction ;\n owl:onProperty in_taxon: ;\n owl:someValuesFrom ?taxon\n ] .\n}\nWHERE {\n ?x present_in_taxon: ?taxon .\n BIND(IRI(CONCAT(\n \"http://purl.obolibrary.org/obo/RO_0002175#\",\n MD5(STR(?x)),\n \"-\",\n MD5(STR(?taxon))\n )) as ?witness)\n BIND(CONCAT(STR(?x), \" in taxon \", STR(?taxon)) AS ?label)\n}" xsd:string -property_value: seeAlso https://github.com/obophenotype/uberon/wiki/Taxon-constraints -is_metadata_tag: true -is_class_level: true - [Typedef] id: process_has_causal_agent name: process has causal agent namespace: external def: "Inverse of 'causal agent in process'" [] xref: RO:0002608 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations is_a: RO:0002410 ! causally related to [Typedef] id: produced_by name: produced by namespace: external -namespace: uberon def: "a produced_by b iff some process that occurs_in b has_output a." [] subset: ro-eco xref: RO:0003001 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity @@ -19912,13 +18494,10 @@ range: BFO:0000040 ! material entity id: produces name: produces namespace: external -namespace: uberon def: "a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix." [] comment: Note that this definition doesn't quite distinguish the output of a transformation process from a production process, which is related to the identity/granularity issue. subset: ro-eco xref: RO:0003000 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0001-9114-8737 domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity inverse_of: produced_by ! produced by @@ -19928,27 +18507,14 @@ id: protects name: protects namespace: uberon -[Typedef] -id: proximal_to -name: proximal to -namespace: uberon -xref: BSPO:0000100 - [Typedef] id: proximally_connected_to name: proximally connected to namespace: uberon def: "x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y." [http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern] -is_a: connected_to ! connected to -is_a: distal_to ! distal to +is_a: RO:0002170 ! connected to is_a: transitively_proximally_connected_to ! transitively proximally connected to -[Typedef] -id: proximalmost_part_of -name: proximalmost part of -namespace: uberon -xref: BSPO:0001106 - [Typedef] id: regulated_by name: regulated by @@ -19956,8 +18522,6 @@ namespace: external def: "inverse of regulates" [] subset: RO:0002259 xref: RO:0002334 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000589 "regulated by (processual)" xsd:string domain: BFO:0000015 ! process range: BFO:0000015 ! process is_transitive: true @@ -19972,14 +18536,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002211 -property_value: IAO:0000117 https://orcid.org/0000-0001-7476-6306 -property_value: IAO:0000117 https://orcid.org/0000-0002-3837-8864 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GO" xsd:string -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000232 "Regulation precludes parthood; the regulatory process may not be within the regulated process." xsd:string -property_value: IAO:0000589 "regulates (processual)" xsd:string -property_value: IAO:0000600 "false" xsd:boolean domain: BFO:0000015 ! process range: BFO:0000015 ! process holds_over_chain: directly_regulates directly_regulates @@ -19995,7 +18551,7 @@ name: regulates characteristic namespace: gene_ontology def: "A relationship that holds between a process and a characteristic in which process (P) regulates characteristic (C) iff: P results in the existence of C OR affects the intensity or magnitude of C." [] xref: RO:0019000 -property_value: dc-contributor https://orcid.org/0000-0002-8688-6599 +property_value: http://purl.org/dc/terms/contributor https://orcid.org/0000-0002-8688-6599 domain: BFO:0000015 ! process range: PATO:0000001 ! quality holds_over_chain: regulates regulates_characteristic @@ -20007,13 +18563,9 @@ name: regulates levels of namespace: external def: "p regulates levels of c if p regulates some amount (PATO:0000070) of c" [] xref: RO:0002332 -property_value: IAO:0000112 "every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 http://purl.obolibrary.org/obo/ro/docs/causal-relations -property_value: IAO:0000589 "regulates levels of (process to entity)" xsd:string domain: BFO:0000015 ! process range: BFO:0000040 ! material entity -is_a: functionally_related_to ! functionally related to +is_a: RO:0002328 ! functionally related to [Typedef] id: results_in_acquisition_of_features_of @@ -20024,9 +18576,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002315 -property_value: IAO:0000112 "an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast." xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string range: UBERON:0000061 ! anatomical structure is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -20061,10 +18610,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002296 -property_value: IAO:0000112 "every flower development (GO:0009908) results in development of some flower (PO:0009046)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "http://www.geneontology.org/GO.doc.development.shtml" xsd:anyURI is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -20074,9 +18619,7 @@ name: results in developmental progression of namespace: external def: "p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss)." [] xref: RO:0002295 -property_value: editor_note "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 +property_value: IAO:0000116 "This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint." xsd:string property_value: seeAlso Ontology:extensions domain: GO:0008150 ! biological_process range: UBERON:0001062 ! anatomical entity @@ -20108,16 +18651,12 @@ is_a: has_participant ! has participant [Typedef] id: results_in_formation_of name: results in formation of +name: results in formation of anatomical entity namespace: external subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002297 -property_value: IAO:0000112 "an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists." xsd:string -property_value: IAO:0000112 "every \"endocardial cushion formation\" (GO:0003272) results_in_formation_of some \"endocardial cushion\" (UBERON:0002062)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: has_output ! has output is_a: results_in_developmental_progression_of ! results in developmental progression of inverse_of: RO:0002354 ! formed as result of @@ -20139,8 +18678,6 @@ id: results_in_growth_of name: results in growth of namespace: external xref: RO:0002343 -property_value: IAO:0000112 "'pollen tube growth' results_in growth_of some 'pollen tube'" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -20153,11 +18690,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002299 -property_value: IAO:0000112 " an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process" xsd:string -property_value: IAO:0000112 "bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -20170,11 +18702,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002298 -property_value: IAO:0000112 "an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape." xsd:string -property_value: IAO:0000112 "tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "GOC:mtg_berkeley_2013" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure is_a: results_in_developmental_progression_of ! results in developmental progression of @@ -20187,8 +18714,6 @@ subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology subset: http://purl.obolibrary.org/obo/valid_for_gocam xref: RO:0002565 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000232 "" xsd:string is_a: results_in_changes_to_anatomical_or_cellular_structure ! results in changes to anatomical or cellular structure [Typedef] @@ -20207,7 +18732,6 @@ namespace: external def: "Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m." [] subset: http://purl.obolibrary.org/obo/valid_for_go_ontology xref: RO:0002342 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: results_in_transport_to_from_or_in ! results in transport to from or in is_a: RO:0002021 ! occurs across @@ -20217,7 +18741,6 @@ name: results in transport along namespace: external def: "Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l " [] xref: RO:0002341 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002337 ! related via localization to [Typedef] @@ -20225,36 +18748,13 @@ id: results_in_transport_to_from_or_in name: results in transport to from or in namespace: external xref: RO:0002344 -property_value: IAO:0000112 "'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739)" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 is_a: RO:0002337 ! related via localization to -[Typedef] -id: seeAlso -name: see also -namespace: uberon -xref: http://www.w3.org/2000/01/rdf-schema#seeAlso -is_metadata_tag: true - [Typedef] id: sexually_homologous_to name: sexually_homologous_to namespace: uberon -is_a: homologous_to ! shares ancestor with - -[Typedef] -id: simultaneous_with -name: simultaneous with -namespace: uberon -def: "x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time." [] -comment: t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) -subset: ro-eco -xref: RO:0002082 -property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -is_symmetric: true -is_transitive: true -is_a: RO:0002081 ! before or simultaneous with +is_a: RO:0002158 ! shares ancestor with [Typedef] id: site_of @@ -20263,46 +18763,13 @@ namespace: uberon def: "c site_of p if c is the bearer of a disposition that is realized by a process that has p as part." [] synonym: "capable_of_has_part" RELATED [] -[Typedef] -id: skeleton_of -name: skeleton of -namespace: uberon -def: "inverse of has skeleton" [] -subset: RO:0002259 -xref: RO:0002576 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -domain: UBERON:0000061 ! anatomical structure -range: UBERON:0000061 ! anatomical structure -is_a: part_of ! part_of - -[Typedef] -id: starts -name: starts -namespace: uberon -def: "inverse of starts with" [] -subset: ro-eco -xref: RO:0002223 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000119 "Allen" xsd:string -is_a: part_of ! part_of -is_a: RO:0002222 ! temporally related to -inverse_of: starts_with ! starts with - [Typedef] id: starts_with name: starts with namespace: external -namespace: uberon def: "x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point." [] subset: ro-eco xref: RO:0002224 -property_value: IAO:0000112 "Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Chris Mungall" xsd:string -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "started by" xsd:string is_transitive: true is_a: has_part ! has part is_a: RO:0002222 ! temporally related to @@ -20313,140 +18780,36 @@ name: subdivision of namespace: uberon comment: placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B -[Typedef] -id: superficial_to -name: superficial to -namespace: uberon -xref: BSPO:0000108 - -[Typedef] -id: supplies -name: supplies -namespace: uberon -def: "Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy." [] -xref: RO:0002178 -property_value: editor_note "Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure" xsd:string -property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/20064205 -domain: UBERON:0001637 ! artery -is_a: connected_to ! connected to - -[Typedef] -id: surrounded_by -name: surrounded by -namespace: uberon -def: "x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x" [] -xref: RO:0002219 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0001900 RO:0001901 -is_a: adjacent_to ! adjacent to -inverse_of: surrounds ! surrounds - -[Typedef] -id: surrounds -name: surrounds -namespace: uberon -def: "inverse of surrounded by" [] -subset: RO:0002259 -xref: RO:0002221 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: RO:0001900 RO:0001901 -is_a: adjacent_to ! adjacent to - -[Typedef] -id: synapsed_by -name: synapsed by -namespace: uberon -def: "Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. " [] -xref: RO:0002103 -property_value: http://purl.org/spar/cito/citesAsAuthority http://www.ncbi.nlm.nih.gov/pubmed/22402613 -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000117 https://orcid.org/0000-0002-7073-9172 -property_value: RO:0001900 RO:0001901 -is_a: RO:0002485 ! receives input from -inverse_of: RO:0002120 ! synapsed to -expand_expression_to: "BFO_0000051 some (GO_0045211 that part_of some (GO_0045202 that has_part some (GO_0042734 that BFO_0000050 some Y?)))" [] - [Typedef] id: term_tracker_item name: term tracker item namespace: external -namespace: uberon def: "An IRI or similar locator for a request or discussion of an ontology term." [] comment: The 'tracker item' can associate a tracker with a specific ontology term. xref: IAO:0000233 -property_value: IAO:0000111 "term tracker item" xsd:string -property_value: IAO:0000112 "the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/" xsd:string -property_value: IAO:0000114 IAO:0000125 -property_value: IAO:0000117 "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" xsd:string -property_value: IAO:0000119 "Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg" xsd:string is_metadata_tag: true -is_class_level: true - -[Typedef] -id: transformation_of -name: transformation of -namespace: uberon -def: "x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships" [] -xref: RO:0002494 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -is_transitive: true -is_a: develops_from ! develops from [Typedef] id: transitively_anteriorly_connected_to name: transitively anteriorly connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI -is_transitive: true [Typedef] id: transitively_distally_connected_to name: transitively distally connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI -is_transitive: true [Typedef] id: transitively_proximally_connected_to name: transitively proximally connected to namespace: uberon property_value: seeAlso "http://purl.obolibrary.org/obo/uberon/docs/Connectivity-Design-Pattern" xsd:anyURI -is_transitive: true - -[Typedef] -id: tributary_of -name: tributary of -namespace: uberon -def: "x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein." [] -subset: ro-eco -xref: RO:0002376 -property_value: IAO:0000112 "Deschutes River tributary_of Columbia River" xsd:string -property_value: IAO:0000112 "inferior epigastric vein tributary_of external iliac vein" xsd:string -property_value: IAO:0000114 IAO:0000428 -property_value: IAO:0000117 https://orcid.org/0000-0002-6601-2165 -property_value: IAO:0000118 "drains into" xsd:string -property_value: IAO:0000118 "drains to" xsd:string -property_value: IAO:0000118 "tributary channel of" xsd:string -property_value: IAO:0000119 "http://en.wikipedia.org/wiki/Tributary" xsd:string -property_value: IAO:0000119 "http://www.medindia.net/glossary/venous_tributary.htm" xsd:string -property_value: IAO:0000232 "This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries)" xsd:anyURI -property_value: seeAlso http://dbpedia.org/ontology/drainsTo -property_value: seeAlso "http://en.wikipedia.org/wiki/Tributary" xsd:anyURI -is_a: connected_to ! connected to -is_a: RO:0002375 ! in branching relationship with [Typedef] id: trunk_part_of name: trunk_part_of namespace: uberon -is_a: part_of ! part_of - -[Typedef] -id: ventral_to -name: ventral to -namespace: uberon -xref: BSPO:0000102 +is_a: part_of ! part of diff --git a/subsets/kidney_upper_slim.owl b/subsets/kidney_upper_slim.owl index a3abeb5aa..4dc7611c9 100644 --- a/subsets/kidney_upper_slim.owl +++ b/subsets/kidney_upper_slim.owl @@ -10,28 +10,21 @@ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:xml="http://www.w3.org/XML/1998/namespace" xmlns:xsd="http://www.w3.org/2001/XMLSchema#" - xmlns:cito="http://purl.org/spar/cito/" xmlns:core="http://purl.obolibrary.org/obo/uberon/core#" xmlns:foaf="http://xmlns.com/foaf/0.1/" - xmlns:obo2="http://www.geneontology.org/formats/oboInOwl#http://purl.obolibrary.org/obo/" xmlns:pato="http://purl.obolibrary.org/obo/pato#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" - xmlns:skos="http://www.w3.org/2004/02/skos/core#" xmlns:swrl="http://www.w3.org/2003/11/swrl#" - xmlns:sssom="https://w3id.org/sssom/" - xmlns:swrla="http://swrl.stanford.edu/ontologies/3.3/swrla.owl#" xmlns:swrlb="http://www.w3.org/2003/11/swrlb#" xmlns:terms="http://purl.org/dc/terms/" - xmlns:vocab="https://w3id.org/semapv/vocab/" - xmlns:terms1="http://www.geneontology.org/formats/oboInOwl#http://purl.org/dc/terms/" xmlns:uberon="http://purl.obolibrary.org/obo/uberon#" xmlns:ubprop="http://purl.obolibrary.org/obo/ubprop#" xmlns:subsets="http://purl.obolibrary.org/obo/ro/subsets#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - 2024-02-13 + + 2024-04-05 @@ -55,29 +48,9 @@ - - - - - - - - - - - - - - - - - - - definition - The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. 2012-04-05: Barry Smith @@ -99,8 +72,6 @@ We don't have definitions of 'meaning' or 'expression' Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition @@ -110,72 +81,28 @@ We also have the outstanding issue of how to aim different definitions to differ - editor note - An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. - PERSON:Daniel Schober - GROUP:OBI:<http://purl.obofoundry.org/obo/obi> - IAO:0000116 - uberon - editor_note - true - editor_note - editor note editor note - - - - - - - - - - - - - - - - - - - has obsolescence reason Relates an annotation property to an obsolescence reason. The values of obsolescence reasons come from a list of predefined terms, instances of the class obsolescence reason specification. - PERSON:Alan Ruttenberg - PERSON:Melanie Courtot has obsolescence reason - - - - - - - term tracker item - the URI for an OBI Terms ticket at sourceforge, such as https://sourceforge.net/p/obi/obi-terms/772/ - An IRI or similar locator for a request or discussion of an ontology term. - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg - Person: Jie Zheng, Chris Stoeckert, Alan Ruttenberg IAO:0000233 external - uberon term_tracker_item - true true term_tracker_item The 'tracker item' can associate a tracker with a specific ontology term. @@ -185,63 +112,23 @@ We also have the outstanding issue of how to aim different definitions to differ - - - - - - - expand expression to - ObjectProperty: RO_0002104 -Label: has plasma membrane part -Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.org/obo/owl/GO#GO_0005886 and http://purl.obolibrary.org/obo/BFO_0000051 some ?Y)" - A macro expansion tag applied to an object property (or possibly a data property) which can be used by a macro-expansion engine to generate more complex expressions from simpler ones - Chris Mungall expand expression to expand expression to - - - - - - - - - - - - - - - - - - - - - - - - - has ontology root term Ontology annotation property. Relates an ontology to a term that is a designated root term of the ontology. Display tools like OLS can use terms annotated with this property as the starting point for rendering the ontology class hierarchy. There can be more than one root. - Nicolas Matentzoglu IAO:0000700 external - uberon has_ontology_root_term - true true has_ontology_root_term has ontology root term @@ -251,20 +138,10 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - - - - - - - term replaced by - Use on obsolete terms, relating the term to another term that can be used as a substitute - Person:Alan Ruttenberg - Person:Alan Ruttenberg Add as annotation triples in the granting ontology term replaced by term replaced by @@ -275,24 +152,6 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - 'part disjoint with' 'defined by construct' """ - PREFIX owl: <http://www.w3.org/2002/07/owl#> - PREFIX : <http://example.org/ - CONSTRUCT { - [ - a owl:Restriction ; - owl:onProperty :part_of ; - owl:someValuesFrom ?a ; - owl:disjointWith [ - a owl:Restriction ; - owl:onProperty :part_of ; - owl:someValuesFrom ?b - ] - ] - } - WHERE { - ?a :part_disjoint_with ?b . - } Links an annotation property to a SPARQL CONSTRUCT query which is meant to provide semantics for a shortcut relation. @@ -305,11 +164,9 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - CHEBI:26523 (reactive oxygen species) has an exact synonym (ROS), which is of type OMO:0003000 (abbreviation) A synonym type for describing abbreviations or initalisms - 2023-03-03 abbreviation @@ -335,11 +192,9 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - CHEBI:23367 (molecular entity) has an exact synonym (molecular entities), which is of the type OMO:0003004 (plural form) A synonym type for describing pluralization synonyms - 2023-03-03 plural form @@ -354,23 +209,10 @@ Annotations: IAO_0000424 "http://purl.obolibrary.org/obo/BFO_0000051 some ( - - - - - - - tooth SubClassOf 'never in taxon' value 'Aves' - S never_in_taxon T iff: S SubClassOf in_taxon only not T. x never in taxon T if and only if T is a class, and x does not instantiate the class expression "in taxon some T". Note that this is a shortcut relation, and should be used as a hasValue restriction in OWL. - - - - Class: <http://www.w3.org/2002/07/owl#Nothing> EquivalentTo: ?X and (RO_0002162 some ?Y) - Class: ?X DisjointWith: RO_0002162 some ?Y PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> @@ -394,34 +236,9 @@ CONSTRUCT { WHERE { ?x never_in_taxon: ?taxon . } - RO:0002161 - uberon - never_in_taxon - true - true - never_in_taxon never in taxon - never_in_taxon - - - - S never_in_taxon T iff: S SubClassOf in_taxon only not T. - PMID:20973947 - - - - - - - - - - - - - @@ -429,9 +246,6 @@ WHERE { S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S - S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S. - - PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX owl: <http://www.w3.org/2002/07/owl#> PREFIX in_taxon: <http://purl.obolibrary.org/obo/RO_0002162> @@ -456,24 +270,10 @@ WHERE { )) as ?witness) BIND(CONCAT(STR(?x), " in taxon ", STR(?taxon)) AS ?label) } - RO:0002175 - applicable for taxon - uberon - present_in_taxon - true - true - present_in_taxon The SPARQL expansion for this relation introduces new named classes into the ontology. For this reason it is likely that the expansion should only be performed during a QC pipeline; the expanded output should usually not be included in a published version of the ontology. present in taxon - present_in_taxon - - - - S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S. - https://orcid.org/0000-0002-6601-2165 - @@ -485,60 +285,6 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - If R <- P o Q is a defining property chain axiom, then it also holds that R -> P o Q. Note that this cannot be expressed directly in OWL - is a defining property chain axiom - - - - - - - - If R <- P o Q is a defining property chain axiom, then (1) R -> P o Q holds and (2) Q is either reflexive or locally reflexive. A corollary of this is that P SubPropertyOf R. - is a defining property chain axiom where second argument is reflexive - - - - - - - - - - - - - - - - - - - - - - @@ -549,126 +295,6 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -927,12 +553,6 @@ WHERE { - - - - - - @@ -1363,14 +983,7 @@ WHERE { - - http://purl.org/dc/elements/1.1/creator - uberon - dc-creator - true - dc-creator - creator - + @@ -1382,14 +995,7 @@ WHERE { - - http://purl.org/dc/elements/1.1/description - uberon - dc-description - true - dc-description - description - + @@ -1401,71 +1007,25 @@ WHERE { - - http://purl.org/dc/elements/1.1/title - uberon - dc-title - true - dc-title - title - + - - http://purl.org/dc/terms/contributor - uberon - dc-contributor - true - dc-contributor - contributor - - - - - - - - - - - - - + - - http://purl.org/dc/terms/date - uberon - dcterms-date - true - dcterms-date - date - + - - http://purl.org/dc/terms/license - uberon - dcterms-license - true - dcterms-license - license - - - - - - - + @@ -1475,18 +1035,6 @@ WHERE { - - - - - - - - - - - - @@ -1503,18 +1051,6 @@ WHERE { - - - - - - - - - - - - @@ -1523,18 +1059,6 @@ WHERE { - - - - - - - - - - - - @@ -1551,66 +1075,6 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -1623,7 +1087,6 @@ WHERE { An alternative label for a class or property which has a more general meaning than the preferred name/primary label. - https://github.com/information-artifact-ontology/ontology-metadata/issues/18 has broad synonym has_broad_synonym @@ -1644,7 +1107,6 @@ WHERE { An alternative label for a class or property which has the exact same meaning than the preferred name/primary label. - https://github.com/information-artifact-ontology/ontology-metadata/issues/20 has exact synonym has_exact_synonym @@ -1657,7 +1119,6 @@ WHERE { An alternative label for a class or property which has a more specific meaning than the preferred name/primary label. - https://github.com/information-artifact-ontology/ontology-metadata/issues/19 has narrow synonym has_narrow_synonym @@ -1678,7 +1139,6 @@ WHERE { An alternative label for a class or property that has been used synonymously with the primary term name, but the usage is not strictly correct. - https://github.com/information-artifact-ontology/ontology-metadata/issues/21 has related synonym has_related_synonym @@ -1687,12 +1147,6 @@ WHERE { - - - - - - @@ -1717,30 +1171,6 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - - - @@ -1753,72 +1183,12 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -1833,60 +1203,6 @@ WHERE { - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - @@ -1903,9 +1219,6 @@ WHERE { http://www.w3.org/2000/01/rdf-schema#seeAlso - uberon - seeAlso - true seeAlso see also @@ -1918,63 +1231,9 @@ WHERE { - - - - - - - - http://xmlns.com/foaf/0.1/depiction - uberon - depiction - true - depiction - depiction - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + @@ -1995,29 +1254,15 @@ WHERE { - is part of - my brain is part of my body (continuant parthood, two material entities) - my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) - this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. - part_of - - - - - - - - BFO:0000050 external quality - uberon part_of @@ -2040,22 +1285,15 @@ A continuant cannot be part of an occurrent: use 'participates in'. An - has part - my body has part my brain (continuant parthood, two material entities) - my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) - this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. - has_part - BFO:0000051 external quality - uberon has_part @@ -2080,15 +1318,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. - preceded by x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. - is preceded by - preceded_by - http://www.obofoundry.org/ro/#OBO_REL:preceded_by BFO:0000062 external - uberon preceded_by preceded_by @@ -2109,11 +1342,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. - precedes x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. BFO:0000063 external - uberon precedes precedes @@ -2137,11 +1368,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - occurs in b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - occurs_in - unfolds in - unfolds_in BFO:0000066 external occurs_in @@ -2150,7 +1377,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. occurs_in Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant - occurs in occurs in https://wiki.geneontology.org/Occurs_in @@ -2161,308 +1387,13 @@ A continuant cannot have an occurrent as part: use 'participates in'. - site of [copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t - BFO:0000067 - uberon - contains_process - contains_process Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant - - contains process contains process - - - - BSPO:0000096 - uberon - anterior_to - anterior_to - anterior to - - - - - - - - BSPO:0000097 - uberon - distal_to - distal_to - distal to - - - - - - - - BSPO:0000098 - uberon - dorsal_to - dorsal_to - dorsal to - - - - - - - - BSPO:0000099 - uberon - posterior_to - posterior_to - posterior to - - - - - - - - BSPO:0000100 - uberon - proximal_to - proximal_to - proximal to - - - - - - - - BSPO:0000102 - uberon - ventral_to - ventral_to - ventral to - - - - - - - - BSPO:0000107 - uberon - deep_to - deep_to - deep to - - - - - - - - BSPO:0000108 - uberon - superficial_to - superficial_to - superficial to - - - - - - - - BSPO:0000120 - uberon - in_left_side_of - in_left_side_of - in left side of - - - - - - - - BSPO:0000121 - uberon - in_right_side_of - in_right_side_of - in right side of - - - - - - - - BSPO:0000122 - uberon - in_posterior_side_of - in_posterior_side_of - in posterior side of - - - - - - - - BSPO:0000123 - uberon - in_anterior_side_of - in_anterior_side_of - in anterior side of - - - - - - - - BSPO:0000124 - uberon - in_proximal_side_of - in_proximal_side_of - in proximal side of - - - - - - - - BSPO:0000126 - uberon - in_lateral_side_of - in_lateral_side_of - in lateral side of - - - - - - - - BSPO:0001100 - uberon - in_superficial_part_of - in_superficial_part_of - in superficial part of - - - - - - - - BSPO:0001101 - uberon - in_deep_part_of - in_deep_part_of - in deep part of - - - - - - - - BSPO:0001106 - uberon - proximalmost_part_of - proximalmost_part_of - proximalmost part of - - - - - - - - BSPO:0001107 - uberon - immediately_deep_to - immediately_deep_to - immediately deep to - - - - - - - - BSPO:0001108 - uberon - distalmost_part_of - distalmost_part_of - distalmost part of - - - - - - - - BSPO:0001113 - uberon - preaxialmost_part_of - preaxialmost_part_of - preaxialmost part of - - - - - - - - BSPO:0001115 - uberon - postaxialmost_part_of - postaxialmost_part_of - postaxialmost part of - - - - - - - - BSPO:0005001 - uberon - intersects_midsagittal_plane_of - intersects_midsagittal_plane_of - intersects midsagittal plane of - - - - - - - - BSPO:0015014 - uberon - immediately_superficial_to - immediately_superficial_to - immediately superficial to - - - - - - - - BSPO:0015101 - uberon - in_dorsal_side_of - in_dorsal_side_of - in dorsal side of - - - - @@ -2522,12 +1453,7 @@ A continuant cannot have an occurrent as part: use 'participates in'. - inheres in - this fragility is a characteristic of this vase - this red color is a characteristic of this apple a relation between a specifically dependent continuant (the characteristic) and any other entity (the bearer), in which the characteristic depends on the bearer for its existence. - inheres_in - Note that this relation was previously called "inheres in", but was changed to be called "characteristic of" because BFO2 uses "inheres in" in a more restricted fashion. This relation differs from BFO2:inheres_in in two respects: (1) it does not impose a range constraint, and thus it allows qualities of processes, as well as of information entities, whereas BFO2 restricts inheres_in to only apply to independent continuants (2) it is declared functional, i.e. something can only be a characteristic of one thing. characteristic of @@ -2539,14 +1465,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - bearer of - this apple is bearer of this red color - this vase is bearer of this fragility Inverse of characteristic_of A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. - bearer_of - is bearer of - RO:0000053 external bearer_of @@ -2563,15 +1483,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. - participates in - this blood clot participates in this blood coagulation - this input material (or this output material) participates in this process - this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process - participates_in RO:0000056 external - uberon participates_in participates_in participates in @@ -2589,14 +1503,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - has participant - this blood coagulation has participant this blood clot - this investigation has participant this investigator - this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. - has_participant - http://www.obofoundry.org/ro/#OBO_REL:has_participant RO:0000057 external has_participant @@ -2612,11 +1520,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. - function_of - is function of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. function of @@ -2628,11 +1533,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. - is quality of - quality_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. quality of @@ -2644,11 +1546,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. - is role of - role_of This relation is modeled after the BFO relation of the same name which was in BFO2, but is used in a more restricted sense - specifically, we model this relation as functional (inherited from characteristic-of). Note that this relation is now removed from BFO2020. role of @@ -2660,10 +1559,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function) a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists. - has_function has function @@ -2673,15 +1570,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this apple has quality this red color a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist. - has_quality - RO:0000086 - uberon - has_quality - has_quality - has quality has quality @@ -2692,10 +1582,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. - has_role has role @@ -2729,13 +1617,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this cell derives from this parent cell (cell division) - this nucleus derives from this parent nucleus (nuclear division) - a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. - derives_from - This relation is taken from the RO2005 version of RO. It may be obsoleted and replaced by relations with different definitions. See also the 'develops from' family of relations. derives from @@ -2745,12 +1628,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - this parent cell derives into this cell (cell division) - this parent nucleus derives into this nucleus (nuclear division) - a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'. - derives_into derives into @@ -2762,18 +1641,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. - is location of - my head is the location of my brain - this cage is the location of this rat a relation between two independent continuants, the location and the target, in which the target is entirely within the location Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - location_of - - RO:0001015 - uberon - location_of - location_of - location of location of @@ -2789,21 +1658,10 @@ A continuant cannot have an occurrent as part: use 'participates in'. - located in - my brain is located in my head - this rat is located in this cage a relation between two independent continuants, the target and the location, in which the target is entirely within the location Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus Most location relations will only hold at certain times, but this is difficult to specify in OWL. See http://purl.obolibrary.org/obo/ro/docs/temporal-semantics/ - located_in - - http://www.obofoundry.org/ro/#OBO_REL:located_in - RO:0001025 - uberon - located_in - located_in - located in located in https://wiki.geneontology.org/Located_in @@ -2827,16 +1685,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. - the surface of my skin is a 2D boundary of my body a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - 2D_boundary_of - boundary of - is 2D boundary of - is boundary of - surface of - 2D boundary of @@ -2848,19 +1699,9 @@ A continuant cannot have an occurrent as part: use 'participates in'. - my body has 2D boundary the surface of my skin a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity A 2D boundary may have holes and gaps, but it must be a single connected entity, not an aggregate of several disconnected parts. Although the boundary is two-dimensional, it exists in three-dimensional space and thus has a 3D shape. - - has boundary - has_2D_boundary - - RO:0002002 - uberon - has_boundary - has_boundary - has 2D boundary has 2D boundary @@ -2871,17 +1712,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - - - - - http://www.ncbi.nlm.nih.gov/pubmed/22402613 - RO:0002005 - uberon - innervated_by - innervated_by - innervated_by innervated_by @@ -2892,8 +1722,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. - - has synaptic terminal of @@ -2924,10 +1752,8 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_boundary: http://purl.obolibrary.org/obo/RO_0002002 boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - RO:0002007 external - uberon bounding_layer_of bounding_layer_of @@ -3106,8 +1932,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland - <= Primitive instance level timing relation between events before or simultaneous with @@ -3122,15 +1946,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 x simultaneous with y iff ω(x) = ω(y) and ω(α ) = ω(α), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point and '=' indicates the same instance in time. - - David Osumi-Sutherland - RO:0002082 - uberon - simultaneous_with - simultaneous_with t1 simultaneous_with t2 iff:= t1 before_or_simultaneous_with t2 and not (t1 before t2) - simultaneous with simultaneous with @@ -3141,7 +1958,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland X ends_after Y iff: end(Y) before_or_simultaneous_with end(X) ends after @@ -3158,11 +1974,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - David Osumi-Sutherland - starts_at_end_of RO:0002087 external - uberon immediately_preceded_by immediately_preceded_by X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) @@ -3180,11 +1993,6 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - - David Osumi-Sutherland - ends_at_start_of - meets - RO:0002090 external immediately_precedes @@ -3207,12 +2015,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between a neuron and a material anatomical entity that its soma is part of. - <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0043025> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y) - has soma location @@ -3224,33 +2029,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - relationship between a neuron and a neuron projection bundle (e.g.- tract or nerve bundle) that one or more of its projections travels through. - - fasciculates with - (forall (?x ?y) - (iff - (fasciculates_with ?x ?y) - (exists (?nps ?npbs) - (and - ("neuron ; CL_0000540" ?x) - ("neuron projection bundle ; CARO_0001001" ?y) - ("neuron projection segment ; CARO_0001502" ?nps) - ("neuron projection bundle segment ; CARO_0001500' " ?npbs) - (part_of ?npbs ?y) - (part_of ?nps ?x) - (part_of ?nps ?npbs) - (forall (?npbss) - (if - (and - ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) - (part_of ?npbss ?npbs) - ) - (overlaps ?nps ?npbss) - )))))) - - fasciculates with @@ -3265,16 +2045,11 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between a neuron and some structure its axon forms (chemical) synapses in. - - <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0030424> and <http://purl.obolibrary.org/obo/BFO_0000051> some ( <http://purl.obolibrary.org/obo/GO_0042734> and <http://purl.obolibrary.org/obo/BFO_0000050> some ( <http://purl.obolibrary.org/obo/GO_0045202> and <http://purl.obolibrary.org/obo/BFO_0000050> some ?Y))) - - axon synapses in @@ -3296,18 +2071,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between an anatomical structure (including cells) and a neuron that chemically synapses to it. - - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that has_part some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) - - - RO:0002103 - uberon - synapsed_by - synapsed_by - synapsed by synapsed by @@ -3319,15 +2084,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Every B cell[CL_0000236] has plasma membrane part some immunoglobulin complex[GO_0019814] - Holds between a cell c and a protein complex or protein p if and only if that cell has as part a plasma_membrane[GO:0005886], and that plasma membrane has p as part. - - - - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0005886> and <http://purl.obolibrary.org/obo/BFO_0000051> some ?Y) - has plasma membrane part @@ -3343,16 +2101,10 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. - - - synapsed in http://purl.obolibrary.org/obo/BFO_0000051 some ( http://purl.org/obo/owl/GO#GO_0045211 and http://purl.obolibrary.org/obo/BFO_0000050 some ( http://purl.org/obo/owl/GO#GO_0045202 and http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)) - - has postsynaptic terminal in @@ -3367,12 +2119,8 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between a neuron and some structure (e.g.- a brain region) in which it receives (chemical) synaptic input. - synapses in <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that <http://purl.obolibrary.org/obo/BFO_0000050> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) - - has presynaptic terminal in @@ -3393,14 +2141,9 @@ boundary_of: http://purl.obolibrary.org/obo/RO_0002000 - Relation between a neuron and an anatomical structure (including cells) that it chemically synapses to. - - <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0042734> that part_of some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000051> some (<http://purl.obolibrary.org/obo/GO_0045211> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) - - N1 synapsed_to some N2 Expands to: N1 SubclassOf ( @@ -3422,13 +2165,8 @@ N1 SubclassOf ( - A general relation between a neuron and some structure in which it either chemically synapses to some target or in which it receives (chemical) synaptic input. - - has synapse in <http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?) - - has synaptic terminal in @@ -3443,10 +2181,6 @@ N1 SubclassOf ( - - - - @@ -3455,13 +2189,10 @@ N1 SubclassOf ( - x overlaps y if and only if there exists some z such that x has part z and z part of y http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y) - RO:0002131 external - uberon overlaps @@ -3470,15 +2201,6 @@ N1 SubclassOf ( overlaps overlaps - - - - - - - - true - @@ -3497,35 +2219,7 @@ N1 SubclassOf ( - The relation between a neuron projection bundle and a neuron projection that is fasciculated with it. - - has fasciculating component - (forall (?x ?y) - (iff - (has_fasciculating_neuron_projection ?x ?y) - (exists (?nps ?npbs) - (and - ("neuron projection bundle ; CARO_0001001" ?x) - ("neuron projection ; GO0043005" ?y) - ("neuron projection segment ; CARO_0001502" ?nps) - ("neuron projection bundle segment ; CARO_0001500" ?npbs) - (part_of ?nps ?y) - (part_of ?npbs ?x) - (part_of ?nps ?npbs) - (forall (?npbss) - (if - (and - ("neuron projection bundle subsegment ; CARO_0001501" ?npbss) - (part_of ?npbss ?npbs) - ) - (overlaps ?nps ?npbss) - )))))) - - - - - has fasciculating neuron projection @@ -3538,19 +2232,10 @@ N1 SubclassOf ( - Relation between a 'neuron projection bundle' and a region in which one or more of its component neuron projections either synapses to targets or receives synaptic input. T innervates some R Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - <http://purl.obolibrary.org/obo/RO_0002132> some (<http://purl.obolibrary.org/obo/GO_0043005> that (<http://purl.obolibrary.org/obo/RO_0002131> some (<http://purl.obolibrary.org/obo/GO_0045202> that <http://purl.obolibrary.org/obo/BFO_0000050> some Y?))) - - - RO:0002134 - uberon - innervates - innervates - innervates innervates @@ -3563,17 +2248,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - X continuous_with Y if and only if X and Y share a fiat boundary. - - connected to - The label for this relation was previously connected to. I relabeled this to "continuous with". The standard notion of connectedness does not imply shared boundaries - e.g. Glasgow connected_to Edinburgh via M8; my patella connected_to my femur (via patellar-femoral joint) - - RO:0002150 - uberon - continuous_with - continuous_with - continuous with continuous with FMA:85972 @@ -3586,13 +2261,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - two individual entities d1 and d2 stand in a shares_ancestor_with relation if and only if there exists some a such that d1 derived_by_descent_from a and d2 derived_by_descent_from a. - Consider obsoleting and merging with child relation, 'in homology relationship with' - RO:0002158 - uberon - homologous_to - homologous_to VBO calls this homologous_to shares ancestor with @@ -3603,19 +2272,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - lactation SubClassOf 'only in taxon' some 'Mammalia' - x only in taxon y if and only if x is in taxon y, and there is no other organism z such that y!=z a and x is in taxon z. The original intent was to treat this as a macro that expands to 'in taxon' only ?Y - however, this is not necessary if we instead have supplemental axioms that state that each pair of sibling tax have a disjointness axiom using the 'in taxon' property - e.g. 'in taxon' some Eukaryota DisjointWith 'in taxon' some Eubacteria - - - - RO:0002160 - uberon - only_in_taxon - only_in_taxon only in taxon @@ -3634,30 +2294,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - - - - - - - - - - - - - - - - - - - - - @@ -3678,53 +2314,16 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed. - - - - - RO:0002162 - uberon - in_taxon - in_taxon Connects a biological entity to its taxon of origin. in taxon @@ -3736,14 +2335,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A is spatially_disjoint_from B if and only if they have no parts in common There are two ways to encode this as a shortcut relation. The other possibility to use an annotation assertion between two classes, and expand this to a disjointness axiom. - - - Note that it would be possible to use the relation to label the relationship between a near infinite number of structures - between the rings of saturn and my left earlobe. The intent is that this is used for parsiomoniously for disambiguation purposes - for example, between siblings in a jointly exhaustive pairwise disjointness hierarchy BFO_0000051 exactly 0 (BFO_0000050 some ?Y) - spatially disjoint from https://github.com/obophenotype/uberon/wiki/Part-disjointness-Design-Pattern @@ -3761,14 +2355,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b - - RO:0002170 - uberon - connected_to - connected_to - connected to connected to https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern @@ -3781,15 +2368,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - The M8 connects Glasgow and Edinburgh - a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones). c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system. - - RO:0002176 - uberon - connects - connects - connects connects https://github.com/obophenotype/uberon/wiki/Connectivity-Design-Pattern https://github.com/obophenotype/uberon/wiki/Modeling-articulations-Design-Pattern @@ -3804,28 +2383,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - a is attached to part of b if a is attached to b, or a is attached to some p, where p is part of b. - attached to part of (anatomical structure to anatomical structure) - RO:0002177 - uberon - attaches_to_part_of - attaches_to_part_of - attached to part of attached to part of - - - - - - - - true - @@ -3833,15 +2393,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Relation between an arterial structure and another structure, where the arterial structure acts as a conduit channeling fluid, substance or energy. Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between an artery and an anatomical structure - - RO:0002178 - uberon - supplies - supplies - supplies supplies @@ -3851,15 +2404,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure. Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure - - RO:0002179 - uberon - drains - drains - drains drains @@ -3869,14 +2415,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type. The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity. - For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit. - RO:0002180 external - uberon has_component has_component @@ -3896,18 +2438,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x develops from y if and only if either (a) x directly develops from y or (b) there exists some z such that x directly develops from z and z develops from y - - - - - RO:0002202 - uberon - develops_from - develops_from This is the transitive form of the develops from relation - develops from develops from @@ -3920,17 +2452,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of develops from - - - - RO:0002203 - uberon - develops_into - develops_into - develops into develops into @@ -3947,10 +2470,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - 'neural crest cell' SubClassOf expresses some 'Wnt1 gene' - x expressed in y if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and the transcription of x is part of the gene expression process (iii) x is a mature gene product such as a protein, and x was translated or otherwise processes from a transcript that was transcribed as part of this gene expression process - expressed in @@ -3977,19 +2497,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Candidate definition: x directly_develops from y if and only if there exists some developmental process (GO:0032502) p such that x and y both participate in p, and x is the output of p and y is the input of p, and a substantial portion of the matter of x comes from y, and the start of x is coincident with or after the end of y. - - - FBbt - - RO:0002207 has developmental precursor - uberon - directly_develops_from - directly_develops_from TODO - add child relations from DOS - directly develops from directly develops from @@ -3999,9 +2509,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of directly develops from - developmental precursor of directly develops into @@ -4029,14 +2537,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p regulates q iff p is causally upstream of q, the execution of p is not constant and varies according to specific conditions, and p influences the rate or magnitude of execution of q due to an effect either on some enabler of q or some enabler of a part of q. - - - - - GO - Regulation precludes parthood; the regulatory process may not be within the regulated process. - regulates (processual) - false RO:0002211 external regulates @@ -4061,9 +2561,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p negatively regulates q iff p regulates q, and p decreases the rate or magnitude of execution of q. - - - negatively regulates (process to process) RO:0002212 external @@ -4094,10 +2591,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p positively regulates q iff p regulates q, and p increases the rate or magnitude of execution of q. - - - positively regulates (process to process) - RO:0002213 external positively_regulates @@ -4117,17 +2610,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974) - osteoclast SubClassOf 'capable of' some 'bone resorption' A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process. - - has function realized in - - - For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)". RO:0002215 external - uberon capable_of capable_of @@ -4142,31 +2627,15 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p. - - has function in RO:0002216 external - uberon capable_of_part_of capable_of_part_of capable of part of capable of part of - - - - - - - - true - @@ -4175,15 +2644,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x surrounded_by y if and only if (1) x is adjacent to y and for every region r that is adjacent to x, r overlaps y (2) the shared boundary between x and y occupies the majority of the outermost boundary of x - - - RO:0002219 - uberon - surrounded_by - surrounded_by - surrounded by surrounded by @@ -4195,18 +2656,10 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. - The epidermis layer of a vertebrate is adjacent to the dermis. - The plasma membrane of a cell is adjacent to the cytoplasm, and also to the cell lumen which the cytoplasm occupies. - The skin of the forelimb is adjacent to the skin of the torso if these are considered anatomical subdivisions with a defined border. Otherwise a relation such as continuous_with would be used. - x adjacent to y if and only if x and y share a boundary. This relation acts as a join point with BSPO - - RO:0002220 external - uberon adjacent_to @@ -4215,12 +2668,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R.adjacent to adjacent to - - - - A caterpillar walking on the surface of a leaf is adjacent_to the leaf, if one of the caterpillar appendages is touching the leaf. In contrast, a butterfly flying close to a flower is not considered adjacent, unless there are any touching parts. - - @@ -4228,16 +2675,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of surrounded by - - - RO:0002221 - uberon - surrounds - surrounds - surrounds surrounds @@ -4248,11 +2687,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends. - https://docs.google.com/document/d/1kBv1ep_9g3sTR-SD3jqzFqhuwo9TPNF-l-9fUDbO6rM/edit?pli=1 A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. temporally related to @@ -4266,17 +2700,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of starts with - - Chris Mungall - Allen - RO:0002223 - uberon - starts - starts - starts starts @@ -4288,15 +2713,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor - x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - - Chris Mungall - started by RO:0002224 external - uberon starts_with starts_with @@ -4314,14 +2733,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x develops from part of y if and only if there exists some z such that x develops from z and z is part of y - - RO:0002225 - uberon - develops_from_part_of - develops_from_part_of - develops from part of develops from part of @@ -4336,16 +2748,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x develops_in y if x is located in y whilst x is developing - - EHDAA2 - Jonathan Bard, EHDAA2 - RO:0002226 - uberon - develops_in - develops_in - develops in develops in @@ -4357,16 +2760,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of ends with - - Chris Mungall - RO:0002229 - uberon - ends - ends - ends ends @@ -4378,14 +2773,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point. - - Chris Mungall - finished by RO:0002230 external - uberon ends_with ends_with @@ -4405,10 +2795,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x 'has starts location' y if and only if there exists some process z such that x 'starts with' z and z 'occurs in' y - - starts with process that occurs in RO:0002231 external has_start_location @@ -4430,10 +2817,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x 'has end location' y if and only if there exists some process z such that x 'ends with' z and z 'occurs in' y - - ends with process that occurs in RO:0002232 external has_end_location @@ -4455,10 +2839,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p. - - consumes RO:0002233 external has_input @@ -4483,10 +2864,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - p has output c iff c is a participant in p, c is present at the end of p, and c is not present in the same state at the beginning of p. - - produces RO:0002234 external has_output @@ -4508,13 +2886,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is connecting branch of S, and B1-1 as a connecting branch of B1. b connecting-branch-of s iff b is connected to s, and there exists some tree-like structure t such that the mereological sum of b plus s is either the same as t or a branching-part-of t. - - RO:0002252 - uberon - connecting_branch_of - connecting_branch_of connecting branch of @@ -4526,7 +2898,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of connecting branch of - has connecting branch @@ -4544,15 +2915,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Mammalian thymus has developmental contribution from some pharyngeal pouch 3; Mammalian thymus has developmental contribution from some pharyngeal pouch 4 [Kardong] - x has developmental contribution from y iff x has some part z such that z develops from y - - RO:0002254 - uberon - has_developmental_contribution_from - has_developmental_contribution_from - has developmental contribution from has developmental contribution from @@ -4567,9 +2930,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of has developmental contribution from - developmentally contributes to @@ -4583,21 +2944,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - t1 induced_by t2 if there is a process of developmental induction (GO:0031128) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor material anatomical entity type T to T', where T' develops_from T - - - - induced by - - Developmental Biology, Gilbert, 8th edition, figure 6.5(F) - GO:0001759 - We place this under 'developmentally preceded by'. This placement should be examined in the context of reciprocal inductions[cjm] - RO:0002256 - uberon - developmentally_induced_by - developmentally_induced_by - developmentally induced by developmentally induced by @@ -4608,9 +2955,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Inverse of developmentally induced by - developmentally induces @@ -4623,11 +2968,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Candidate definition: x developmentally related to y if and only if there exists some developmental process (GO:0032502) p such that x and y both participates in p, and x is the output of p and y is the input of p false - - In general you should not use this relation to make assertions - use one of the more specific relations below this one This relation groups together various other developmental relations. It is fairly generic, encompassing induction, developmental contribution and direct and transitive develops from developmentally preceded by @@ -4642,7 +2984,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision. c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes. acts upstream of @@ -4659,7 +3000,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway. c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process. affects @@ -4673,16 +3013,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x developmentally replaces y if and only if there is some developmental process that causes x to move or to cease to exist, and for the site that was occupied by x to become occupied by y, where y either comes into existence in this site or moves to this site from somewhere else This relation is intended for cases such as when we have a bone element replacing its cartilage element precursor. Currently most AOs represent this using 'develops from'. We need to decide whether 'develops from' will be generic and encompass replacement, or whether we need a new name for a generic relation that encompasses replacement and development-via-cell-lineage - - replaces - RO:0002285 - uberon - developmentally_replaces - developmentally_replaces - developmentally replaces developmentally replaces @@ -4692,9 +3024,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Inverse of developmentally preceded by - developmentally succeeded by @@ -4708,9 +3038,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - 'hypopharyngeal eminence' SubClassOf 'part of precursor of' some tongue - - part of developmental precursor of @@ -4720,9 +3047,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - y expresses x if and only if there is a gene expression process (GO:0010467) that occurs in y, and one of the following holds: (i) x is a gene, and x is transcribed into a transcript as part of the gene expression process (ii) x is a transcript, and x was transcribed from a gene as part of the gene expression process (iii) x is a mature gene product (protein or RNA), and x was translated or otherwise processed from a transcript that was transcribed as part of the gene expression process. - expresses @@ -4734,10 +3059,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - p results in the developmental progression of s iff p is a developmental process and s is an anatomical entity and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss). This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint. - RO:0002295 external results_in_developmental_progression_of @@ -4754,11 +3077,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - every flower development (GO:0009908) results in development of some flower (PO:0009046) - p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state. - - http://www.geneontology.org/GO.doc.development.shtml RO:0002296 external results_in_development_of @@ -4778,11 +3097,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists. - every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062) - - - GOC:mtg_berkeley_2013 RO:0002297 external results_in_formation_of @@ -4791,7 +3105,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. results_in_formation_of results in formation of - results in formation of + results in formation of anatomical entity @@ -4801,12 +3115,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape. - tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723) - The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state. - - GOC:mtg_berkeley_2013 RO:0002298 external results_in_morphogenesis_of @@ -4825,12 +3134,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process - bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474) - The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity. - - GOC:mtg_berkeley_2013 RO:0002299 external results_in_maturation_of @@ -4850,8 +3154,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p is causally upstream of, positive effect q iff p is casually upstream of q, and the execution of p is required for the execution of q. - - RO:0002304 external causally_upstream_of,_positive_effect @@ -4872,7 +3174,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p is causally upstream of, negative effect q iff p is casually upstream of q, and the execution of p decreases the execution of q. - RO:0002305 external causally_upstream_of,_negative_effect @@ -4889,32 +3190,15 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - q characteristic of part of w if and only if there exists some p such that q inheres in p and p part of w. Because part_of is transitive, inheres in is a sub-relation of characteristic of part of - - inheres in part of - - characteristic of part of - - - - - - - - true - @@ -4924,10 +3208,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast. The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity - - GOC:mtg_berkeley_2013 RO:0002315 external results_in_acquisition_of_features_of @@ -4945,8 +3226,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A relationship that holds via some environmental process - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the process of evolution. evolutionarily related to @@ -4956,9 +3235,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A mereological relationship or a topological relationship - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships - mereotopologically related to @@ -4968,8 +3244,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A relationship that holds between entities participating in some developmental process (GO:0032502) - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development developmentally related to @@ -4988,15 +3262,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - a particular instances of akt-2 enables some instance of protein kinase activity c enables p iff c is capable of p and c acts to execute p. - - catalyzes - executes - has - is catalyzing - is executing - This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized. enables https://wiki.geneontology.org/Enables @@ -5008,13 +3274,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities. - - This is a grouping relation that collects relations used for the purpose of connecting structure and function - RO:0002328 - uberon - functionally_related_to - functionally_related_to - functionally related to functionally related to @@ -5024,24 +3283,9 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - - - this relation holds between c and p when c is part of some c', and c' is capable of p. - - false part of structure that is capable of - - - - - - - - true - @@ -5051,8 +3295,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. holds between two entities when some genome-level process such as gene expression is involved. This includes transcriptional, spliceosomal events. These relations can be used between either macromolecule entities (such as regions of nucleic acid) or between their abstract informational counterparts. - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving the genome of an organism genomically related to @@ -5072,9 +3314,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. c involved_in p if and only if c enables some process p', and p' is part of p - - actively involved in - enables part of involved in https://wiki.geneontology.org/Involved_in @@ -5087,11 +3326,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - every cellular sphingolipid homeostasis process regulates_level_of some sphingolipid p regulates levels of c if p regulates some amount (PATO:0000070) of c - - - regulates levels of (process to entity) RO:0002332 external regulates_levels_of @@ -5108,7 +3343,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of enables - enabled by https://wiki.geneontology.org/Enabled_by @@ -5124,8 +3358,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of regulates - - regulated by (processual) RO:0002334 external regulated_by @@ -5142,7 +3374,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of negatively regulates - RO:0002335 external negatively_regulated_by @@ -5159,7 +3390,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of positively regulates - RO:0002336 external positively_regulated_by @@ -5177,8 +3407,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. A relationship that holds via some process of localization - - Do not use this relation directly. It is a grouping relation. related via localization to @@ -5193,7 +3421,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from some initial location l to some destination. - RO:0002338 external has_target_start_location @@ -5216,7 +3443,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. This relationship holds between p and l when p is a transport or localization process in which the outcome is to move some cargo c from a an initial location to some destination l. - RO:0002339 external has_target_end_location @@ -5235,7 +3461,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. Holds between p and l when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that is aligned_with l - RO:0002341 external results_in_transport_along @@ -5252,7 +3477,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. Holds between p and m when p is a transportation or localization process and the outcome of this process is to move c from one location to another, and the route taken by c follows a path that crosses m. - RO:0002342 external results_in_transport_across @@ -5269,8 +3493,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - 'pollen tube growth' results_in growth_of some 'pollen tube' - RO:0002343 external results_in_growth_of @@ -5285,8 +3507,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - 'mitochondrial transport' results_in_transport_to_from_or_in some mitochondrion (GO:0005739) - RO:0002344 external results_in_transport_to_from_or_in @@ -5302,12 +3522,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - An organism that is a member of a population of organisms is member of is a mereological relation between a item and a collection. - is member of - member part of - SIO - member of @@ -5319,13 +3534,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. has member is a mereological relation between a collection and an item. - SIO - - RO:0002351 - uberon - has_member - has_member - has member has member @@ -5337,14 +3545,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of has input - - RO:0002352 - uberon - input_of - input_of - input of input of @@ -5356,10 +3558,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. inverse of has output - RO:0002353 external - uberon output_of @@ -5374,7 +3574,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - formed as result of @@ -5384,8 +3583,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - http://neurolex.org/wiki/Property:DendriteLocation has dendrite location @@ -5398,14 +3595,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. a is attached to b if and only if a and b are discrete objects or object parts, and there are physical connections between a and b such that a force pulling a will move b, or a force pulling b will move a - - attached to (anatomical structure to anatomical structure) - RO:0002371 - uberon - attaches_to - attaches_to - attached to attached to @@ -5418,13 +3608,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. m has_muscle_origin s iff m is attached_to s, and it is the case that when m contracts, s does not move. The site of the origin tends to be more proximal and have greater mass than what the other end attaches to. - - Wikipedia:Insertion_(anatomy) - RO:0002372 - uberon - has_muscle_origin - has_muscle_origin - has muscle origin has muscle origin @@ -5444,13 +3627,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. m has_muscle_insertion s iff m is attaches_to s, and it is the case that when m contracts, s moves. Insertions are usually connections of muscle via tendon to bone. - - Wikipedia:Insertion_(anatomy) - RO:0002373 - uberon - has_muscle_insertion - has_muscle_insertion - has muscle insertion has muscle insertion @@ -5469,12 +3645,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A relationship that holds between two material entities in a system of connected structures, where the branching relationship holds based on properties of the connecting network. - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving branching relationships - This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (plant branches and roots, leaf veins, animal veins, arteries, nerves) - in branching relationship with https://github.com/obophenotype/uberon/issues/170 @@ -5487,23 +3658,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - Deschutes River tributary_of Columbia River - inferior epigastric vein tributary_of external iliac vein - x tributary_of y if and only if x a channel for the flow of a substance into y, where y is larger than x. If x and y are hydrographic features, then y is the main stem of a river, or a lake or bay, but not the sea or ocean. If x and y are anatomical, then y is a vein. - - drains into - drains to - tributary channel of - http://en.wikipedia.org/wiki/Tributary - http://www.medindia.net/glossary/venous_tributary.htm - This relation can be used for geographic features (e.g. rivers) as well as anatomical structures (veins, arteries) - RO:0002376 - uberon - tributary_of - tributary_of - tributary of tributary of http://en.wikipedia.org/wiki/Tributary @@ -5521,10 +3677,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - A lump of clay and a statue x spatially_coextensive_with y if and inly if x and y have the same location - - This relation is added for formal completeness. It is unlikely to be used in many practical scenarios spatially coextensive with @@ -5542,15 +3695,8 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - In the tree T depicted in https://oborel.github.io/obo-relations/branching_part_of.png, B1 is a (direct) branching part of T. B1-1, B1-2, and B1-3 are also branching parts of T, but these are considered indirect branching parts as they do not directly connect to the main stem S x is a branching part of y if and only if x is part of y and x is connected directly or indirectly to the main stem of y - - RO:0002380 - uberon - branching_part_of - branching_part_of - branching part of branching part of FMA:85994 @@ -5564,9 +3710,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x has developmental potential involving y iff x is capable of a developmental process with output y. y may be the successor of x, or may be a different structure in the vicinity (as for example in the case of developmental induction). - has developmental potential involving @@ -5576,14 +3720,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y - - RO:0002385 - uberon - has_potential_to_developmentally_contribute_to - has_potential_to_developmentally_contribute_to - has potential to developmentally contribute to has potential to developmentally contribute to @@ -5593,9 +3730,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x has potential to developmentally induce y iff x developmentally induces y or x is capable of developmentally inducing y - has potential to developmentally induce @@ -5605,14 +3740,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x has the potential to develop into y iff x develops into y or if x is capable of developing into y - - RO:0002387 - uberon - has_potential_to_develop_into - has_potential_to_develop_into - has potential to develop into has potential to develop into @@ -5622,9 +3750,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - x has potential to directly develop into y iff x directly develops into y or x is capable of directly developing into y - has potential to directly develop into @@ -5636,9 +3762,7 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - inverse of upstream of - RO:0002404 external causally_downstream_of @@ -5655,8 +3779,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. - - RO:0002405 external immediately_causally_downstream_of @@ -5690,9 +3812,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p indirectly positively regulates q iff p is indirectly causally upstream of q and p positively regulates q. - - indirectly activates - indirectly positively regulates https://wiki.geneontology.org/Indirectly_positively_regulates @@ -5718,9 +3837,6 @@ Expands_to: T has_fasciculating_neuron_projection that synapse_in some R. p indirectly negatively regulates q iff p is indirectly causally upstream of q and p negatively regulates q. - - indirectly inhibits - indirectly negatively regulates https://wiki.geneontology.org/Indirectly_negatively_regulates @@ -5746,8 +3862,6 @@ For the second, we consider a relationship to be regulatory if the system in whi For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types. - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causally related to @@ -5766,7 +3880,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is causally upstream of q iff p is causally related to q, the end of p precedes the end of q, and p is not an occurrent part of q. - RO:0002411 external causally_upstream_of @@ -5785,8 +3898,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is immediately causally upstream of q iff p is causally upstream of q, and the end of p is coincident with the beginning of q. - - RO:0002412 external immediately_causally_upstream_of @@ -5805,8 +3916,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p is 'causally upstream or within' q iff p is causally related to q, and the end of p precedes, or is coincident with, the end of q. We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 - - influences (processual) RO:0002418 external affects @@ -5823,8 +3932,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different inverse of causally upstream of or within - - RO:0002427 external causally_downstream_of_or_within @@ -5849,7 +3956,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' regulates some p - involved in regulation of @@ -5868,8 +3974,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' positively regulates some p - - involved in positive regulation of @@ -5888,7 +3992,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in regulation of p if c is involved in some p' and p' negatively regulates some p - involved in negative regulation of @@ -5903,8 +4006,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p OWL does not allow defining object properties via a Union - - involved in or reguates involved in or involved in regulation of @@ -5915,28 +4016,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - A protein that enables activity in a cytosol. c executes activity in d if and only if c enables p and p occurs_in d. Assuming no action at a distance by gene products, if a gene product enables (is capable of) a process that occurs in some structure, it must have at least some part in that structure. - - executes activity in enables activity in is active in https://wiki.geneontology.org/Is_active_in - - - - - - - - true - @@ -5952,11 +4037,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different p contributes to morphology of w if and only if a change in the morphology of p entails a change in the morphology of w. Examples: every skull contributes to morphology of the head which it is a part of. Counter-example: nuclei do not generally contribute to the morphology of the cell they are part of, as they are buffered by cytoplasm. - - RO:0002433 - uberon - contributes_to_morphology_of - contributes_to_morphology_of contributes to morphology of @@ -5971,13 +4051,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different A relationship that holds between two entities in which the processes executed by the two entities are causally connected. This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact. Considering relabeling as 'pairwise interacts with' - - Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules. in pairwise interaction with interacts with http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ - http://purl.obolibrary.org/obo/MI_0914 @@ -5988,12 +4065,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other. - - binds - molecularly binds with molecularly interacts with - http://purl.obolibrary.org/obo/MI_0915 @@ -6003,8 +4076,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different Axiomatization to GO to be added later - - An interaction relation between x and y in which x catalyzes a reaction in which a phosphate group is added to y. phosphorylates @@ -6025,8 +4096,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B. - - molecularly controls directly regulates activity of @@ -6046,9 +4115,6 @@ A and B can be physically interacting but not necessarily. Immediately upstream The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B. - - - directly inhibits molecularly decreases activity of directly negatively regulates activity of @@ -6068,9 +4134,6 @@ For example, A and B may be gene products and binding of B by A negatively regul The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B. - - - directly activates molecularly increases activity of directly positively regulates activity of @@ -6080,8 +4143,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - This property or its subproperties is not to be used directly. These properties exist as helper properties that are used to support OWL reasoning. helper property (not for use in curation) @@ -6093,16 +4154,8 @@ For example, A and B may be gene products and binding of B by A positively regul - 'otolith organ' SubClassOf 'composed primarily of' some 'calcium carbonate' x composed_primarily_of y if and only if more than half of the mass of x is made from y or units of the same type as y. - - - - RO:0002473 - uberon - composed_primarily_of - composed_primarily_of composed primarily of @@ -6113,24 +4166,10 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - p has part that occurs in c if and only if there exists some p1, such that p has_part p1, and p1 occurs in c. - has part that occurs in - - - - - - - - true - @@ -6138,7 +4177,6 @@ For example, A and B may be gene products and binding of B by A positively regul - is kinase activity @@ -6150,7 +4188,6 @@ For example, A and B may be gene products and binding of B by A positively regul See notes for inverse relation - receives input from @@ -6161,7 +4198,6 @@ For example, A and B may be gene products and binding of B by A positively regul This is an exploratory relation. The label is taken from the FMA. It needs aligned with the neuron-specific relations such as has postsynaptic terminal in. - sends output to @@ -6172,8 +4208,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, typically connecting an anatomical entity to a biological process or developmental stage. relation between physical entity and a process or stage @@ -6189,11 +4223,6 @@ For example, A and B may be gene products and binding of B by A positively regul x existence starts during y if and only if the time point at which x starts is after or equivalent to the time point at which y starts and before or equivalent to the time point at which y ends. Formally: x existence starts during y iff α(x) >= α(y) & α(x) <= ω(y). - - RO:0002488 - uberon - existence_starts_during - existence_starts_during existence starts during @@ -6204,11 +4233,6 @@ For example, A and B may be gene products and binding of B by A positively regul x starts ends with y if and only if the time point at which x starts is equivalent to the time point at which y starts. Formally: x existence starts with y iff α(x) = α(y). - - RO:0002489 - uberon - existence_starts_with - existence_starts_with existence starts with @@ -6219,7 +4243,6 @@ For example, A and B may be gene products and binding of B by A positively regul x existence overlaps y if and only if either (a) the start of x is part of y or (b) the end of x is part of y. Formally: x existence starts and ends during y iff (α(x) >= α(y) & α(x) <= ω(y)) OR (ω(x) <= ω(y) & ω(x) >= α(y)) - The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence overlaps @@ -6232,12 +4255,7 @@ For example, A and B may be gene products and binding of B by A positively regul x exists during y if and only if: 1) the time point at which x begins to exist is after or equal to the time point at which y begins and 2) the time point at which x ceases to exist is before or equal to the point at which y ends. Formally: x existence starts and ends during y iff α(x) >= α(y) & α(x) <= ω(y) & ω(x) <= ω(y) & ω(x) >= α(y) - - RO:0002491 exists during - uberon - existence_starts_and_ends_during - existence_starts_and_ends_during The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts and ends during @@ -6253,23 +4271,10 @@ For example, A and B may be gene products and binding of B by A positively regul - Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. x existence ends during y if and only if the time point at which x ends is before or equivalent to the time point at which y ends and after or equivalent to the point at which y starts. Formally: x existence ends during y iff ω(x) <= ω(y) and ω(x) >= α(y). - - RO:0002492 - ceases_to_exist_during - uberon - existence_ends_during - existence_ends_during The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during - - - - Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. - https://orcid.org/0000-0002-6601-2165 - @@ -6278,11 +4283,6 @@ For example, A and B may be gene products and binding of B by A positively regul x existence ends with y if and only if the time point at which x ends is equivalent to the time point at which y ends. Formally: x existence ends with y iff ω(x) = ω(y). - - RO:0002493 - uberon - existence_ends_with - existence_ends_with The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends with @@ -6295,11 +4295,6 @@ For example, A and B may be gene products and binding of B by A positively regul x transformation of y if x is the immediate transformation of y, or is linked to y through a chain of transformation relationships - - RO:0002494 - uberon - transformation_of - transformation_of transformation of @@ -6311,12 +4306,6 @@ For example, A and B may be gene products and binding of B by A positively regul x immediate transformation of y iff x immediately succeeds y temporally at a time boundary t, and all of the matter present in x at t is present in y at t, and all the matter in y at t is present in x at t - - - RO:0002495 - uberon - immediate_transformation_of - immediate_transformation_of immediate transformation of @@ -6347,11 +4336,6 @@ For example, A and B may be gene products and binding of B by A positively regul x existence starts during or after y if and only if the time point at which x starts is after or equivalent to the time point at which y starts. Formally: x existence starts during or after y iff α (x) >= α (y). - - RO:0002496 - uberon - existence_starts_during_or_after - existence_starts_during_or_after The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence starts during or after @@ -6383,11 +4367,6 @@ For example, A and B may be gene products and binding of B by A positively regul x existence ends during or before y if and only if the time point at which x ends is before or equivalent to the time point at which y ends. - - RO:0002497 - uberon - existence_ends_during_or_before - existence_ends_during_or_before The relations here were created based on work originally by Fabian Neuhaus and David Osumi-Sutherland. The work has not yet been vetted and errors in definitions may have occurred during transcription. existence ends during or before @@ -6400,7 +4379,6 @@ For example, A and B may be gene products and binding of B by A positively regul A relationship between a material entity and a process where the material entity has some causal role that influences the process - causal agent in process @@ -6413,9 +4391,6 @@ For example, A and B may be gene products and binding of B by A positively regul p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one where the execution of p influences the execution of q. p may be upstream, downstream, part of, or a container of q. - - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between processes @@ -6424,7 +4399,6 @@ For example, A and B may be gene products and binding of B by A positively regul - depends on @@ -6438,9 +4412,6 @@ For example, A and B may be gene products and binding of B by A positively regul The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch - - - Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. causal relation between entities @@ -6454,18 +4425,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - - Forelimb SubClassOf has_skeleton some 'Forelimb skeleton' A relation between a segment or subdivision of an organism and the maximal subdivision of material entities that provides structural support for that segment or subdivision. - - has supporting framework - The skeleton of a structure may be a true skeleton (for example, the bony skeleton of a hand) or any kind of support framework (the hydrostatic skeleton of a sea star, the exoskeleton of an insect, the cytoskeleton of a cell). - RO:0002551 - uberon - has_skeleton - has_skeleton has skeleton @@ -6482,9 +4443,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - causally influenced by (entity-centric) causally influenced by @@ -6494,7 +4452,6 @@ For example, A and B may be gene products and binding of B by A positively regul - interaction relation helper property http://purl.obolibrary.org/obo/ro/docs/interaction-relations/ @@ -6506,7 +4463,6 @@ For example, A and B may be gene products and binding of B by A positively regul - molecular interaction relation helper property @@ -6517,8 +4473,6 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c - - RO:0002565 external results_in_movement_of @@ -6548,10 +4502,6 @@ For example, A and B may be gene products and binding of B by A positively regul The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size). - - - - causally influences (entity-centric) causally influences @@ -6564,8 +4514,6 @@ For example, A and B may be gene products and binding of B by A positively regul A relation that holds between elements of a musculoskeletal system or its analogs. - - Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving the biomechanical processes. biomechanically related to @@ -6576,12 +4524,6 @@ For example, A and B may be gene products and binding of B by A positively regul m1 has_muscle_antagonist m2 iff m1 has_muscle_insertion s, m2 has_muscle_insection s, m1 acts in opposition to m2, and m2 is responsible for returning the structure to its initial position. - - Wikipedia:Antagonist_(muscle) - RO:0002568 - uberon - has_muscle_antagonist - has_muscle_antagonist has muscle antagonist @@ -6594,13 +4536,8 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of branching part of - - RO:0002569 - uberon - has_branching_part - has_branching_part has branching part @@ -6613,14 +4550,7 @@ For example, A and B may be gene products and binding of B by A positively regul x is a conduit for y iff y overlaps through the lumen_of of x, and y has parts on either side of the lumen of x. - - UBERON:cjm - This relation holds between a thing with a 'conduit' (e.g. a bone foramen) and a 'conduee' (for example, a nerve) such that at the time the relationship holds, the conduee has two ends sticking out either end of the conduit. It should therefore note be used for objects that move through the conduit but whose spatial extent does not span the passage. For example, it would not be used for a mountain that contains a long tunnel through which trains pass. Nor would we use it for a digestive tract and objects such as food that pass through. - RO:0002570 - uberon - conduit_for - conduit_for conduit for @@ -6632,13 +4562,7 @@ For example, A and B may be gene products and binding of B by A positively regul x lumen_of y iff x is the space or substance that is part of y and does not cross any of the inner membranes or boundaries of y that is maximal with respect to the volume of the convex hull. - - - RO:0002571 - uberon - lumen_of - lumen_of lumen of @@ -6650,12 +4574,7 @@ For example, A and B may be gene products and binding of B by A positively regul s is luminal space of x iff s is lumen_of x and s is an immaterial entity - - RO:0002572 - uberon - luminal_space_of - luminal_space_of luminal space of @@ -6668,12 +4587,7 @@ For example, A and B may be gene products and binding of B by A positively regul inverse of has skeleton - - RO:0002576 - uberon - skeleton_of - skeleton_of skeleton of @@ -6685,10 +4599,6 @@ For example, A and B may be gene products and binding of B by A positively regul p directly regulates q iff p is immediately causally upstream of q and p regulates q. - - - directly regulates (processual) - RO:0002578 external directly_regulates @@ -6710,9 +4620,7 @@ For example, A and B may be gene products and binding of B by A positively regul - gland SubClassOf 'has part structure that is capable of' some 'secretion by cell' s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p - has part structure that is capable of @@ -6782,8 +4690,6 @@ For example, A and B may be gene products and binding of B by A positively regul A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity. Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect. - - causal relation between material entity and a process @@ -6797,9 +4703,7 @@ For example, A and B may be gene products and binding of B by A positively regul - pyrethroid -> growth Holds between c and p if and only if c is capable of some activity a, and a regulates p. - capable of regulating @@ -6814,7 +4718,6 @@ For example, A and B may be gene products and binding of B by A positively regul Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p. - capable of negatively regulating @@ -6828,9 +4731,7 @@ For example, A and B may be gene products and binding of B by A positively regul - renin -> arteriolar smooth muscle contraction Holds between c and p if and only if c is capable of some activity a, and a positively regulates p. - capable of positively regulating @@ -6841,7 +4742,6 @@ For example, A and B may be gene products and binding of B by A positively regul Inverse of 'causal agent in process' - RO:0002608 external process_has_causal_agent @@ -6857,9 +4757,6 @@ For example, A and B may be gene products and binding of B by A positively regul p directly positively regulates q iff p is immediately causally upstream of q, and p positively regulates q. - - directly positively regulates (process to process) - RO:0002629 external directly_positively_regulates @@ -6879,8 +4776,6 @@ For example, A and B may be gene products and binding of B by A positively regul p directly negatively regulates q iff p is immediately causally upstream of q, and p negatively regulates q. - - directly negatively regulates (process to process) RO:0002630 external @@ -6907,12 +4802,9 @@ For example, A and B may be gene products and binding of B by A positively regul - a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix. - RO:0003000 external - uberon produces produces @@ -6928,12 +4820,9 @@ For example, A and B may be gene products and binding of B by A positively regul - a produced_by b iff some process that occurs_in b has_output a. - RO:0003001 external - uberon produced_by produced_by @@ -7040,7 +4929,6 @@ For example, A and B may be gene products and binding of B by A positively regul - 2018-01-26T23:49:30Z @@ -7078,7 +4966,6 @@ For example, A and B may be gene products and binding of B by A positively regul c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive - 2018-01-26T23:53:14Z @@ -7125,7 +5012,6 @@ For example, A and B may be gene products and binding of B by A positively regul - 2018-03-13T23:55:19Z causally upstream of or within, positive effect @@ -7141,7 +5027,6 @@ For example, A and B may be gene products and binding of B by A positively regul The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B. - regulates activity of @@ -7388,7 +5273,6 @@ For example, A and B may be gene products and binding of B by A positively regul - 'Ly-76 high positive erythrocyte' equivalent to 'enucleate erythrocyte' and (has_high_plasma_membrane_amount some 'lymphocyte antigen 76 (mouse)') A relation between a cell and molecule or complex such that every instance of the cell has a high number of instances of that molecule expressed on the cell surface. @@ -7408,7 +5292,6 @@ For example, A and B may be gene products and binding of B by A positively regul - 'DN2b thymocyte' equivalent to 'DN2 thymocyte' and (has_low_plasma_membrane_amount some 'mast/stem cell growth factor receptor') A relation between a cell and molecule or complex such that every instance of the cell has a low number of instances of that molecule expressed on the cell surface. @@ -7430,12 +5313,7 @@ For example, A and B may be gene products and binding of B by A positively regul - A diagnostic testing device utilizes a specimen. X device utilizes material Y means X and Y are material entities, and X is capable of some process P that has input Y. - - - A diagnostic testing device utilizes a specimen means that the diagnostic testing device is capable of an assay, and this assay a specimen as its input. - See github ticket https://github.com/oborel/obo-relations/issues/497 2021-11-08T12:00:00Z utilizes device utilizes material @@ -7561,7 +5439,6 @@ For example, A and B may be gene products and binding of B by A positively regul - x anteriorly_connected_to y iff the anterior part of x is connected to y. i.e. x connected_to y and x posterior_to y. @@ -7581,8 +5458,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - carries uberon channel_for @@ -7594,7 +5469,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uberon channels_from channels_from @@ -7605,7 +5479,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uberon channels_into channels_into @@ -7616,10 +5489,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - x distally_connected_to y iff the distal part of x is connected to y. i.e. x connected_to y and x proximal_to y. uberon distally_connected_to @@ -7638,11 +5509,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - X extends_fibers into Y iff there exists some neuron (N) and N has_soma_location X and N 'has synaptic IO in region' some Y uberon extends_fibers_into @@ -7672,11 +5538,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - @@ -7704,7 +5565,6 @@ For example, A and B may be gene products and binding of B by A positively regul - x posteriorly_connected_to y iff the posterior part of x is connected to y. i.e. x connected_to y and x anterior_to y. uberon @@ -7733,7 +5593,6 @@ For example, A and B may be gene products and binding of B by A positively regul - x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y. @@ -7787,7 +5646,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uberon transitively_anteriorly_connected_to transitively anteriorly connected to @@ -7799,7 +5657,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uberon transitively_distally_connected_to transitively distally connected to @@ -7811,7 +5668,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uberon transitively_proximally_connected_to transitively proximally connected to @@ -12806,6 +10662,12 @@ For example, A and B may be gene products and binding of B by A positively regul KUPO:0001017 kidney medulla cell + + + + A cell that is part of a renal medulla. + PMID:22343825 + @@ -13081,12 +10943,19 @@ For example, A and B may be gene products and binding of B by A positively regul + A fibroblast that is part of an interstitial compartment of a kidney. KUPO:0001102 kidney interstitial fibroblast + + + + A fibroblast that is part of an interstitial compartment of a kidney. + PMID:10559635 + @@ -13204,7 +11073,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -13226,6 +11095,7 @@ For example, A and B may be gene products and binding of B by A positively regul + A blood vessel cell that is part of a kidney. KUPO:0001014 kidney blood vessel cell @@ -13235,6 +11105,12 @@ For example, A and B may be gene products and binding of B by A positively regul true + + + + A blood vessel cell that is part of a kidney. + PMID:34843404 + @@ -14910,32 +12786,32 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer - + - + - + PMID:12382326 - + PMID:12382326 @@ -25001,7 +22877,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 PMID:15371245 ncbi_taxonomy @@ -25015,7 +22890,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 Mus mice @@ -25034,7 +22908,7 @@ For example, A and B may be gene products and binding of B by A positively regul mice - + @@ -25049,7 +22923,6 @@ For example, A and B may be gene products and binding of B by A positively regul - NCBITaxon:85055 GC_ID:1 house mouse @@ -25077,7 +22950,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 ncbi_taxonomy NCBITaxon:117570 @@ -25090,7 +22962,6 @@ For example, A and B may be gene products and binding of B by A positively regul - NCBITaxon:40673 GC_ID:1 bony vertebrates @@ -25130,7 +23001,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 ncbi_taxonomy NCBITaxon:1338369 @@ -25143,7 +23013,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 PMID:11743200 PMID:11791233 @@ -25165,7 +23034,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 mice and others ncbi_taxonomy @@ -25192,7 +23060,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 PMID:23020233 PMID:30257078 @@ -25256,7 +23123,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 PMID:11214319 PMID:12082125 @@ -25273,7 +23139,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 PMID:11214319 PMID:12082125 @@ -25296,7 +23161,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 tetrapods ncbi_taxonomy @@ -25316,7 +23180,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 amniotes ncbi_taxonomy @@ -25336,7 +23199,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 Theria ncbi_taxonomy @@ -25356,7 +23218,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 ncbi_taxonomy Fungi/Metazoa group @@ -25383,7 +23244,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 metazoans multicellular animals @@ -25424,7 +23284,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 ncbi_taxonomy NCBITaxon:33213 @@ -25437,7 +23296,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 deuterostomes ncbi_taxonomy @@ -25457,7 +23315,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 PMID:15019624 PMID:15371245 @@ -25472,7 +23329,6 @@ For example, A and B may be gene products and binding of B by A positively regul - NCBITaxon:109679 GC_ID:1 ncbi_taxonomy @@ -25486,7 +23342,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 mammals ncbi_taxonomy @@ -25513,7 +23368,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 ncbi_taxonomy NCBITaxon:6072 @@ -25526,7 +23380,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 chordates ncbi_taxonomy @@ -25553,7 +23406,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 Vertebrata vertebrates @@ -25587,7 +23439,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 Gnathostomata jawed vertebrates @@ -25614,7 +23465,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 ncbi_taxonomy NCBITaxon:8287 @@ -25627,7 +23477,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 Mus ncbi_taxonomy @@ -25647,7 +23496,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 Craniata ncbi_taxonomy @@ -25667,7 +23515,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 eutherian mammals placental mammals @@ -25715,7 +23562,6 @@ For example, A and B may be gene products and binding of B by A positively regul - GC_ID:1 rodent ncbi_taxonomy @@ -25831,7 +23677,6 @@ For example, A and B may be gene products and binding of B by A positively regul A branchiness quality inhering in a bearer by virtue of the bearer's having branches. - ramified ramiform quality @@ -26158,7 +24003,6 @@ For example, A and B may be gene products and binding of B by A positively regul A contractility quality inhering in a bearer by virtue of the bearer's ability of contracting or being contracted. - quality PATO:0001690 @@ -26180,7 +24024,6 @@ For example, A and B may be gene products and binding of B by A positively regul A shape quality in a bearer by virtue of the bearer's curving inward. - quality PATO:0001857 @@ -26354,7 +24197,6 @@ For example, A and B may be gene products and binding of B by A positively regul A complete three dimensional shape in which for every line connecting pair of points on the object is within the object. Or: a shape lacking cavities. Contrast: concave. - Image:http://upload.wikimedia.org/wikipedia/commons/0/06/Convex_polygon_illustration1.png quality PATO:0002007 @@ -26415,7 +24257,6 @@ For example, A and B may be gene products and binding of B by A positively regul A concave quality inhering in a bearer by virtue of the bearer's curving inward on both sides or surfaces. - quality PATO:0002039 @@ -27009,7 +24850,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001012 Category=gene. Requested by=CL. integrin alpha-M - @@ -27153,7 +24993,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001024 Category=gene. Requested by=CL. neural cell adhesion molecule 1 - @@ -27238,7 +25077,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001084 Category=gene. Requested by=CL. T-cell surface glycoprotein CD8 alpha chain - @@ -27367,7 +25205,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001444 Category=gene. Requested by=CL. cadherin-5 - @@ -27400,7 +25237,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001839 Category=gene. Requested by=CL. T-cell surface glycoprotein CD5 - @@ -27442,7 +25278,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001869 Category=gene. Requested by=CL. interleukin-7 receptor subunit alpha - @@ -27507,7 +25342,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000001945 Category=gene. Requested by=CL. transferrin receptor protein 1 - @@ -27577,7 +25411,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000002112 Category=gene. Requested by=CL. vascular endothelial growth factor receptor 2 - @@ -27698,7 +25531,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000013883 Category=gene. renin - @@ -27730,7 +25562,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000014841 Category=gene. sonic hedgehog protein - @@ -27772,7 +25603,6 @@ For example, A and B may be gene products and binding of B by A positively regul PR:000016043 Category=gene. Requested by=CL. T-cell acute lymphocytic leukemia protein 1 - @@ -28055,8 +25885,6 @@ For example, A and B may be gene products and binding of B by A positively regul Any hollow cylindrical anatomical structure containing a lumen through which substances are transported. - not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts) - tubular galen:Tube anatomical tube duct @@ -28084,10 +25912,6 @@ For example, A and B may be gene products and binding of B by A positively regul Major subdivision of an organism that protrudes from the body[DOS, CARO]. - An appendage is an external body part, or natural prolongation, that protrudes from an organism's body, such as a vertebrate's limbs[BILA][BILA:0000018]. - Organ or organ part that is attached to the body of an organism. For example a limb[GO, modified][GO:0048736]. - appendicular - this is currently a subtype of organism subdivision - which would exclude feathers AEO:0000193 BILA:0000018 BTO:0001492 @@ -28096,7 +25920,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA2:0003193 EMAPA:37283 EV:0100155 - FBbt:00007000 HAO:0000144 MAT:0000023 MESH:D005121 @@ -28123,30 +25946,12 @@ For example, A and B may be gene products and binding of B by A positively regul Major subdivision of an organism that protrudes from the body[DOS, CARO]. CARO:DOS - - - - An appendage is an external body part, or natural prolongation, that protrudes from an organism's body, such as a vertebrate's limbs[BILA][BILA:0000018]. - BILA:0000018 - - - - - Organ or organ part that is attached to the body of an organism. For example a limb[GO, modified][GO:0048736]. - GO:0048736 - EMAPA:37283 MA:th - - - - FBbt:00007000 - - @@ -28216,13 +26021,7 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - + @@ -28243,12 +26042,6 @@ For example, A and B may be gene products and binding of B by A positively regul Muscular duct that propels urine from the kidneys to the urinary bladder, or related organs. - Anatomical structure consisting of long narrow duct which carries urine from the kidney to the urinary bladder.[AAO] - The duct of amniotes that carries urine from a metanephric kidney to the urinary bladder. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] - The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG] - ureteral - ureteric - in humans, consists of adventitial, muscular and mucoa layers AAO:0010254 BTO:0001409 CALOHA:TS-1084 @@ -28282,14 +26075,14 @@ For example, A and B may be gene products and binding of B by A positively regul ureter https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg - + - + GO @@ -28299,34 +26092,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0090189 Wikipedia:Ureter - - - - Anatomical structure consisting of long narrow duct which carries urine from the kidney to the urinary bladder.[AAO] - 2012-06-20 - AAO:0010254 - AAO - AAO:BJB - - - - - The duct of amniotes that carries urine from a metanephric kidney to the urinary bladder. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] - 2012-09-17 - VHOG:0000605 - VHOG - http://bgee.unil.ch/ - - - - - The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG] - 2012-09-17 - VHOG:0000605 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543 - http://bgee.unil.ch/ - @@ -28361,8 +26126,13 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + + + + + + @@ -28382,8 +26152,6 @@ For example, A and B may be gene products and binding of B by A positively regul The fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening. - urethral - In human males, the urethra travels through the penis, and carries semen as well as urine. In females, the urethra is shorter and emerges above the vaginal opening. BTO:0001426 CALOHA:TS-1132 EFO:0000931 @@ -28412,25 +26180,14 @@ For example, A and B may be gene products and binding of B by A positively regul urethra https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png - - - - - + - - pelvic part of UG sinus gives rise to prostatic and membranous parts of urethra - Wikipedia - - - - - + Wikipedia @@ -28473,10 +26230,7 @@ For example, A and B may be gene products and binding of B by A positively regul A tubular structure that transports secreted or excreted substances. - A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171]. - Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here. AAO:0011123 - FBbt:00100314 FMA:30320 NCIT:C12948 SCTID:91726008 @@ -28502,18 +26256,6 @@ For example, A and B may be gene products and binding of B by A positively regul http://orcid.org/0000-0002-6601-2165 http://www.siumed.edu/~dking2/intro/glands.htm#ducts - - - - A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171]. - ZFA:0005171 - - - - - FBbt:00100314 - - @@ -28547,10 +26289,8 @@ For example, A and B may be gene products and binding of B by A positively regul Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. - in FMA, serosa is a wall UBERON:0009915 wall - EMAPA:25036 FMA:82482 galen:Wall wall of organ @@ -28566,12 +26306,6 @@ For example, A and B may be gene products and binding of B by A positively regul Organ component adjacent to an organ cavity and which consists of a maximal aggregate of organ component layers. FMA:82482 - - - - in FMA, serosa is a wall - FMA - @@ -28607,7 +26341,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0000003 EHDAA2:0003003 EMAPA:0 - FBbt:00007001 FMA:305751 FMA:67135 GAID:781 @@ -28635,12 +26368,6 @@ For example, A and B may be gene products and binding of B by A positively regul Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. CARO:0000003 - - - - FBbt:00007001 - - @@ -28678,8 +26405,6 @@ For example, A and B may be gene products and binding of B by A positively regul - Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. - CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4 BIRNLEX:4 CARO:0020004 EFO:0000634 @@ -28713,12 +26438,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia - - - - Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. - GO:0048513 - @@ -28740,8 +26459,6 @@ For example, A and B may be gene products and binding of B by A positively regul A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity. FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction - Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball. - Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal. FMA:86140 uberon organ region with fixed fiat boundary @@ -28757,20 +26474,6 @@ For example, A and B may be gene products and binding of B by A positively regul A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity. http://orcid.org/0000-0002-6601-2165 - - - - Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball. - FMA:86140 - 3 - - - - - Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal. - FMA:86140 - 1 - @@ -28803,7 +26506,6 @@ For example, A and B may be gene products and binding of B by A positively regul A multicellular structure that is a part of an organ. - currently defined in a very broad sense, may be replaced by more specific classes in the future @@ -28960,7 +26662,6 @@ For example, A and B may be gene products and binding of B by A positively regul - ncit:Death is an outcome XAO:0000437 XtroDO:0000085 uberon @@ -28975,12 +26676,6 @@ For example, A and B may be gene products and binding of B by A positively regul End of the life of an organism. XAO:0000437 - - - - ncit:Death is an outcome - ncit - @@ -28989,7 +26684,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -29004,7 +26699,6 @@ For example, A and B may be gene products and binding of B by A positively regul A capillary tuft which forms a close network with the visceral epithelium (podocytes) and the mesangium to form the filtration barrier and is surrounded by Bowman's capsule in nephrons of the vertebrate kidney[GO]. - ZFA - The multi-tissue structure where the glomerular basement membrane supported by mesonephric podocytes filters blood from the glomerular capillaries. GUDMAP: 'Together, the Bowman's capsule and the glomerulus comprise the definitive renal corpuscle.' - here the glomerulus is part of the capsule? 2009-06-18T09:26:37Z glomerulus @@ -29040,14 +26734,14 @@ For example, A and B may be gene products and binding of B by A positively regul http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg - + - + FMA MA @@ -29058,12 +26752,6 @@ For example, A and B may be gene products and binding of B by A positively regul MP:0005325 Wikipedia:Glomerulus - - - - ZFA - The multi-tissue structure where the glomerular basement membrane supported by mesonephric podocytes filters blood from the glomerular capillaries. GUDMAP: 'Together, the Bowman's capsule and the glomerulus comprise the definitive renal corpuscle.' - here the glomerulus is part of the capsule? - ZFA - @@ -29199,12 +26887,6 @@ For example, A and B may be gene products and binding of B by A positively regul The second stage of the kidney. It serves as the main excretory organ of aquatic vertebrates and as a temporary embryonic kidney in higher vertebrates. It is composed of the mesonephric duct (also called the Wolffian duct), mesonephric tubules, and associated capillary tufts. A single tubule and its associated capillary tuft is called a mesonephric excretory unit; these units are similar in structure and function to nephrons of the adult kidney. The mesonephros is derived from intermediate mesoderm in the vertebrate embryo. - A kidney formed of nephric tubules arising in the middle region of the nephric ridge; a transient embryonic stage that replaces the pronephros, but is itself replaced by the adult metanephros [in mammals; in fishes and amphibians it is the adult kidney]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG] - Organ that is the definitive adult kidney. It replaces the earlier pronephros, which degenerates as the mesonephros becomes functional in feeding stage tadpoles.[AAO] - As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates. (...) In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG] - mesonephric - In mammals, the mesonephros is the second of the three embryonic kidneys to be established and exists only transiently. In fish and amphibians, the mesonephros will form the mature kidney - By contrast to the pronephros, the histological features of the mammalian mesonephros, with its primitive glomeruli, suggest that it probably functions as a primitive kidney, and is involved in the production of much of the amniotic fluid. Within the two mesonephroi, one located on either side of the dorsal mesentery of the hindgut, a substantial number (in the region of about 40 or more) of cranio-caudally segmented mesonephric tubules are formed. It has, however, been suggested that only the most rostrally located 4-6 pairs of mesonephric tubules drain into the mesonephric portion of the nephric duct. This is now seen to extend along the length of the mesonephroi, being located towards their lateral sides. The mesonephros is also retained over a considerably longer period than the pronephros, but gradually undergoes regression in a cranio-caudal direction. While the rostral part displays clear evidence of regression its more caudal part appears to display evidence of functional activity. Within the medial part of the mesonephros, vesicles are formed, although no glomeruli are formed there in this species. It is, however, difficult to believe that the relatively enormous mesonephroi do not have an excretory role in the mouse, only serving as a base for gonadal differentiation. In the human embryo, the medial part of the mesonephric tubules enlarges, become invaginated by capillaries, and form glomeruli. These then take on an excretory role. In the mouse, the mesonephric ducts appear to be patent throughout their length[GUDMAP, modified] AAO:0010384 BTO:0001542 CALOHA:TS-0624 @@ -29249,34 +26931,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0001823 Wikipedia:Mesonephros - - - - A kidney formed of nephric tubules arising in the middle region of the nephric ridge; a transient embryonic stage that replaces the pronephros, but is itself replaced by the adult metanephros [in mammals; in fishes and amphibians it is the adult kidney]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG] - 2012-09-17 - VHOG:0000038 - VHOG - http://bgee.unil.ch/ - - - - - Organ that is the definitive adult kidney. It replaces the earlier pronephros, which degenerates as the mesonephros becomes functional in feeding stage tadpoles.[AAO] - 2012-06-20 - AAO:0010384 - AAO - AAO:BJB - - - - - As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates. (...) In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG] - 2012-09-17 - VHOG:0000038 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639 - http://bgee.unil.ch/ - @@ -29344,15 +26998,20 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + + + + + + - + @@ -29361,10 +27020,6 @@ For example, A and B may be gene products and binding of B by A positively regul In mammals, the metanephros is the excretory organ of the fetus, which develops into the mature kidney and is formed from the rear portion of the nephrogenic cord. The metanephros is an endocrine and metabolic organ that filters the blood and excretes the end products of body metabolism in the form of urine[GO]. TODO check developmental relationships - A kidney formed of nephric tubules arising in the posterior region of the nephric ridge and drained by a ureter; replaces the embryonic pronephros and mesonephros [in mammals]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG] - The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes.[well established][VHOG] - metanephric - During the fifth week of gestation, the mesonephric duct develops an outpouching, the ureteric bud, near its attachment to the cloaca. This bud, also called the metanephrogenic diverticulum, grows posteriorly and towards the head of the embryo. The elongated stalk of the ureteric bud, the metanephric duct, later forms the ureter. As the cranial end of the bud extends into the intermediate mesoderm, it undergoes a series of branchings to form the collecting duct system of the kidney. It also forms the major and minor calyces and the renal pelvis BTO:0001543 EHDAA2:0001137 EHDAA:3089 @@ -29388,34 +27043,24 @@ For example, A and B may be gene products and binding of B by A positively regul metanephros - - - - - + - + - - definitional - - - - - + GO - + ISBN:9780878932504 @@ -29425,25 +27070,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0001656 Wikipedia:Metanephros#Metanephros - - - - A kidney formed of nephric tubules arising in the posterior region of the nephric ridge and drained by a ureter; replaces the embryonic pronephros and mesonephros [in mammals]. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.745][VHOG] - 2012-09-17 - VHOG:0000039 - VHOG - http://bgee.unil.ch/ - - - - - The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes.[well established][VHOG] - 2012-09-17 - VHOG:0000039 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543 - http://bgee.unil.ch/ - @@ -29502,8 +27128,6 @@ For example, A and B may be gene products and binding of B by A positively regul A mesonephric tubule is an epithelial tube that is part of the mesonephros[GO]. Genital ridge that is next to the mesonephros[WP]. TODO check - Any of the renal tubules composing the mesonephros. In mammals they function as excretory structures during the early embryonic development but are later incorporated into the reproductive system. [TFD][VHOG] - As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates.[well established][VHOG] AAO:0010389 EHDAA2:0001134 EMAPA:16747 @@ -29522,26 +27146,6 @@ For example, A and B may be gene products and binding of B by A positively regul A mesonephric tubule is an epithelial tube that is part of the mesonephros[GO]. Genital ridge that is next to the mesonephros[WP]. Wikipedia:Mesonephric_tubules - - - - Any of the renal tubules composing the mesonephros. In mammals they function as excretory structures during the early embryonic development but are later incorporated into the reproductive system. [TFD][VHOG] - 2012-09-17 - VHOG:0000500 - VHOG - http://bgee.unil.ch/ - http://medical-dictionary.thefreedictionary.com/mesonephric+tubule - - - - - As the pronephros regresses, the archinephric duct induces the sequential differentiation of tubules in the more caudal parts of the nephric ridge. (...) Tubules that differentiate in the middle part of the nephric ridge form a kidney called the mesonephros. This kidney functions in the embryos and larvae of all vertebrates.[well established][VHOG] - 2012-09-17 - VHOG:0000500 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.639 - http://bgee.unil.ch/ - @@ -29564,7 +27168,6 @@ For example, A and B may be gene products and binding of B by A positively regul - @@ -29572,12 +27175,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + An epithelial swelling on the Wolffian duct that elongates to invade the adjacent metanephric mesenchyme[MP]. - Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts. [Embryology, See_Dudek_RW_and_Fix_JD, Third_Edition_(2004)_Philadelphia:_Lippincott_William_and_Wilkins, p.137][VHOG] - Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts[VHOG:0000541]. - The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG] BTO:0001646 EHDAA2:0002140 EHDAA:3091 @@ -29600,11 +27200,11 @@ For example, A and B may be gene products and binding of B by A positively regul ureteric bud - + - + @@ -29617,13 +27217,13 @@ For example, A and B may be gene products and binding of B by A positively regul - + EHDAA2 - + ISBN:9780878932504 @@ -29633,31 +27233,6 @@ For example, A and B may be gene products and binding of B by A positively regul MP:0010979 PMID:19828308 - - - - Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts. [Embryology, See_Dudek_RW_and_Fix_JD, Third_Edition_(2004)_Philadelphia:_Lippincott_William_and_Wilkins, p.137][VHOG] - 2012-09-17 - VHOG:0000541 - VHOG - http://bgee.unil.ch/ - - - - - Outgrowth of the mesonephric duct that penetrates the metanephric mesoderm and forms the ureter, renal pelvis, major and minor calyces and collecting ducts[VHOG:0000541]. - VHOG:0000541 - - - - - The first embryonic hint of a metanephros is the formation of the metanephric duct that appears as a ureteric diverticulum arising at the base of preexisting mesonephric duct. The ureteric diverticulum grows dorsally into the posterior region of the nephric ridge. Here it enlarges and stimulates the growth of metanephric tubules that come to make up the metanephric kidney. The metanephros becomes the adult kidney of amniotes, and the metanephric duct is usually called the ureter.[well established][VHOG] - 2012-09-17 - VHOG:0000541 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.543 - http://bgee.unil.ch/ - @@ -29723,7 +27298,6 @@ For example, A and B may be gene products and binding of B by A positively regul Stage succeeding embryo, including mature structure. - In birds, the postnatal stage begins when the beak penetrates the shell (i.e., external pipping) (Brown et al. 1997) BilaDO:0000003 OGES:000010 OGES:000014 @@ -29809,8 +27383,6 @@ For example, A and B may be gene products and binding of B by A positively regul - the WBls class 'all stages' belongs here as it is the superclass of other WBls stages - we map the ZFS unknown stage here as it is logically equivalent to saying *some* life cycle stage BILS:0000105 EFO:0000399 FBdv:00007012 @@ -29861,13 +27433,11 @@ For example, A and B may be gene products and binding of B by A positively regul A stage at which the organism is a single cell produced by means of sexual reproduction. - As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG] BILS:0000106 BilaDO:0000005 EFO:0001322 EHDAA:27 FBdv:00005288 - IDOMAL:0000302 NCIT:C12601 PdumDv:0000100 VHOG:0000745 @@ -29893,24 +27463,6 @@ For example, A and B may be gene products and binding of B by A positively regul A stage at which the organism is a single cell produced by means of sexual reproduction. Wikipedia:Zygote - - - - As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote.[well established][VHOG] - 2012-09-17 - VHOG:0000745 - VHOG - ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107 - http://bgee.unil.ch/ - - - - - IDOMAL:0000302 - - - https://github.com/biopragmatics/biomappings - @@ -30058,7 +27610,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -30094,14 +27646,14 @@ For example, A and B may be gene products and binding of B by A positively regul gastrula stage - + - + BILS @@ -30179,8 +27731,6 @@ For example, A and B may be gene products and binding of B by A positively regul Staged defined by the formation of a tube from the flat layer of ectodermal cells known as the neural plate. This will give rise to the central nervous system. - - In zebrafish, the times of neurulation and segmentation overlap so extensively there is no distinct neurula period of development, such as occurs largely before segmentation in amphibian embryos. BILS:0000110 BilaDO:0000009 HsapDv:0000012 @@ -30306,7 +27856,6 @@ For example, A and B may be gene products and binding of B by A positively regul - A thin sheet or layer of pliable tissue, serving as a covering or envelope of a part, as the lining of a cavity, as a partition or septum, or to connect two structures. membrane FMA:30322 FMA:82500 @@ -30317,12 +27866,6 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0000158 membranous layer - - - - A thin sheet or layer of pliable tissue, serving as a covering or envelope of a part, as the lining of a cavity, as a partition or septum, or to connect two structures. - ncithesaurus:Membrane - @@ -30337,7 +27880,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical conduit that connects two adjacent body spaces (or a body space with the space surrounding the organism)[FMA,modified]. - in FMA, this is an anatomical conduit *space*, rather than anatomical conduit anatomical ostium ostium FMA:3724 @@ -30354,12 +27896,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical conduit that connects two adjacent body spaces (or a body space with the space surrounding the organism)[FMA,modified]. FMA:3724 - - - - in FMA, this is an anatomical conduit *space*, rather than anatomical conduit - FMA - @@ -30379,8 +27915,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -30389,13 +27925,6 @@ For example, A and B may be gene products and binding of B by A positively regul Common chamber into which the intestines and excretory system opens. Arises during development in all vertebrates, but in many it becomes subdivided, lost or incorporated into other structures. adding df link to embryonic cloaca leads to a cycle in uberon-simple, as cloaca is a suberclass of embryonic cloaca - - A common passage for fecal, urinary, and reproductive discharge in most lower vertebrates as well as the terminal end of the hindgut before division into rectum, bladder, and genital primordia in mammalian embryos. [TFD][VHOG] - Anatomical structure which is the common receptacle for the alimentary canal, Wolffian ducts, oviducts, and the bladder.[AAO] - A cloaca is apparently a primitive vertebrate feature because it occurs in most primitive gnathostomes and persists in the embryos of almost all vertebrates.[well established][VHOG] - cloacal - Human beings only have an embryonic cloaca, which is split up into separate tracts during the development of the urinary and reproductive organs - hindgut endoderm and proctodeal ectoderm. AAO:0000095 GAID:1206 MESH:D002988 @@ -30413,24 +27942,24 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0000162 cloaca - + - + - + ZFA - + AAO @@ -30440,47 +27969,6 @@ For example, A and B may be gene products and binding of B by A positively regul ISBN:0073040584 Wikipedia:Cloaca - - - - - most adult placentals have no trace of a cloaca. However, the tenrecs and golden moles, small placental mammals native to Africa, retain a cloaca as adults. - - - - - A common passage for fecal, urinary, and reproductive discharge in most lower vertebrates as well as the terminal end of the hindgut before division into rectum, bladder, and genital primordia in mammalian embryos. [TFD][VHOG] - 2012-09-17 - VHOG:0001186 - VHOG - http://bgee.unil.ch/ - http://medical-dictionary.thefreedictionary.com/cloaca - - - - - Anatomical structure which is the common receptacle for the alimentary canal, Wolffian ducts, oviducts, and the bladder.[AAO] - 2012-06-20 - AAO:0000095 - AAO - AAO:BJB - - - - - A cloaca is apparently a primitive vertebrate feature because it occurs in most primitive gnathostomes and persists in the embryos of almost all vertebrates.[well established][VHOG] - 2012-09-17 - VHOG:0001186 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.572 - http://bgee.unil.ch/ - - - - - hindgut endoderm and proctodeal ectoderm. - WP - @@ -30512,8 +28000,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -30521,7 +28009,6 @@ For example, A and B may be gene products and binding of B by A positively regul Endoderm-lined chamber that develops as pouch-like dilation of the caudal end of the hindgut and receives the allantois ventrally and two mesonephric ducts laterally; caudally it ends blindly at the cloacal membrane formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm[MP]. - this class represents the embryonic form of the cloaca, as found in both mammals and non-mammals. EHDAA2:0000256 EHDAA:4895 EMAPA:27573 @@ -30532,24 +28019,24 @@ For example, A and B may be gene products and binding of B by A positively regul embryonic cloaca - + - + - + EHDAA2 - + EHDAA2 @@ -30572,7 +28059,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -30592,9 +28079,6 @@ For example, A and B may be gene products and binding of B by A positively regul The ventral part of the cloaca remaining after septation of the rectum, which further develops into part of the bladder, part of the prostatic part of the male urethra and the urethra and vestibule in females. - The ventral part of the cloaca after its separation from the rectum, giving rise to the lower part of the bladder in both sexes, to the prostatic portion of the male urethra, and to the urethra and vestibule in the female. [TFD][VHOG] - In mammals the lowly monotremes still have a cloaca. Higher types have done away with this structure and have a separate anal outlet for the rectum. The monotreme cloaca shows the initiation of this subdivision. The cloaca has such includes only the distal part, roughly comparable to the proctodeum. The more proximal part is divided into (1) a large dorsal passage into which the intestine opens, the coprodeum, and (2) a ventral portion, the urodeum with which the bladder connects. (...) the development of the placental mammals recapitulates in many respects the phylogenetic story. In the sexually indifferent stage of placental mammal there is a cloaca. While the indifferent stage still persists, a septum develops, and extends out to the closing membrane. This divides the cloaca into two chambers: a coprodeum continuous with the gut above, and a urodeum or urogenital sinus below.[well established][VHOG] - the term 'urogenital sinus' may refer to the primitive urogenital sinus present as a transient developmental structure in most mammals or it may refer to a condition in which an unseptated cloaca persists in animals longer than normal urogenital sinus EHDAA2:0004060 EHDAA:5029 @@ -30614,14 +28098,14 @@ For example, A and B may be gene products and binding of B by A positively regul primitive urogenital sinus http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png - + - + MP-def @@ -30631,32 +28115,6 @@ For example, A and B may be gene products and binding of B by A positively regul ISBN:0-683-40008-8 MP:0010116 - - - - The ventral part of the cloaca after its separation from the rectum, giving rise to the lower part of the bladder in both sexes, to the prostatic portion of the male urethra, and to the urethra and vestibule in the female. [TFD][VHOG] - 2012-09-17 - VHOG:0000414 - VHOG - http://bgee.unil.ch/ - http://medical-dictionary.thefreedictionary.com/urogenital+sinus - - - - - In mammals the lowly monotremes still have a cloaca. Higher types have done away with this structure and have a separate anal outlet for the rectum. The monotreme cloaca shows the initiation of this subdivision. The cloaca has such includes only the distal part, roughly comparable to the proctodeum. The more proximal part is divided into (1) a large dorsal passage into which the intestine opens, the coprodeum, and (2) a ventral portion, the urodeum with which the bladder connects. (...) the development of the placental mammals recapitulates in many respects the phylogenetic story. In the sexually indifferent stage of placental mammal there is a cloaca. While the indifferent stage still persists, a septum develops, and extends out to the closing membrane. This divides the cloaca into two chambers: a coprodeum continuous with the gut above, and a urodeum or urogenital sinus below.[well established][VHOG] - 2012-09-17 - VHOG:0000414 - VHOG - ISBN:978-0721676678 Romer AS, Vertebrate body (1970)p.388-89 and Figure 300 - http://bgee.unil.ch/ - - - - - the term 'urogenital sinus' may refer to the primitive urogenital sinus present as a transient developmental structure in most mammals or it may refer to a condition in which an unseptated cloaca persists in animals longer than normal - MP - @@ -30693,24 +28151,7 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - @@ -30724,11 +28165,6 @@ For example, A and B may be gene products and binding of B by A positively regul The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks). - Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO] - Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG] - oral - some AOs place this as developing from the stomodeum but we weaken this to developmental contribution, as the mouth includes non-ectodermal derivatives - in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips AAO:0010355 BTO:0001090 BTO:0004698 @@ -30737,7 +28173,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA2:0001326 EHDAA:542 EMAPA:16262 - FBbt:00003126 FMA:49184 GAID:75 MA:0000341 @@ -30783,12 +28218,6 @@ For example, A and B may be gene products and binding of B by A positively regul https://github.com/obophenotype/uberon/issues/661 http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg - - - - - the mouth contains structures such as jaw skeleton that may not strictly be considered tract parts - @@ -30796,37 +28225,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Mouth https://github.com/obophenotype/uberon/wiki/The-digestive-tract - - - - Cavity in which food is initially ingested and generally contains teeth, tongue and glands.[AAO] - 2012-06-20 - AAO:0010355 - AAO - AAO:BJB - - - - - Molecular and developmental cell lineage data suggest that the acoel mouth opening is homologous to the mouth of protostomes and deuterostomes and that the last common ancestor of the Bilateria (the 'urbilaterian') had only this single digestive opening.[well established][VHOG] - 2012-09-17 - VHOG:0000812 - VHOG - DOI:10.1038/nature07309 Hejnol A, Martindale MQ, Acoel development indicates the independent evolution of the bilaterian mouth and anus. Nature (2008) - http://bgee.unil.ch/ - - - - - in FMA, the tongue, palate etc are part of the mouth which is itself a subdivision of the face. ZFA includes a separate class 'oral region' which is part of the mouth, but excludes tongue and lips - FMA - - - - - FBbt:00003126 - - @@ -30983,22 +28381,17 @@ For example, A and B may be gene products and binding of B by A positively regul - + - - + + A fluid that is composed of blood plasma and erythrocytes. - This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid. - A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO] - Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO] - relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] - Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG] AAO:0000046 BTO:0000089 CALOHA:TS-0079 @@ -31033,34 +28426,34 @@ For example, A and B may be gene products and binding of B by A positively regul blood - + - + - + - + CL:tm - + https://github.com/obophenotype/uberon/issues/1330 - + Bgee:AN @@ -31072,42 +28465,6 @@ For example, A and B may be gene products and binding of B by A positively regul http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/9 - - - - A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO] - 2012-08-14 - TAO:0000007 - TAO - ZFIN:curator - - - - - Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO] - 2012-06-20 - AAO:0000046 - AAO - AAO:LAP - - - - - relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] - 2012-06-20 - AAO:0000046 - AAO - - - - - Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG] - 2012-09-17 - VHOG:0000224 - VHOG - DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual review of cell and developmental biology (2006) - http://bgee.unil.ch/ - @@ -31252,11 +28609,6 @@ For example, A and B may be gene products and binding of B by A positively regul Functional part of an organ in the body. This is in contrast to the stroma, which refers to the structural tissue of organs, being exactly, connective tissues. - parenchymal - Early in development the mammalian embryo has three distinct layers: ectoderm (external layer), endoderm (internal layer) and in between those two layers the middle layer or mesoderm. The parenchyma of most organs is of ectodermal (brain, skin) or endodermal origin (lungs, gastrointestinal tract, liver, pancreas). The parenchyma of a few organs (spleen, kidneys, heart) is of mesodermal origin. The stroma of all organs is of mesodermal origin - the FMA definition is more restrictive, and limits this to solid organs. This would seem to cause problems for the lung parenchyma, except FMA classifies Lung as solid rather than cavitated - BTO:0000999 - BTO:0001539 EHDAA:3015 EHDAA:3905 EHDAA:3999 @@ -31283,34 +28635,6 @@ For example, A and B may be gene products and binding of B by A positively regul Functional part of an organ in the body. This is in contrast to the stroma, which refers to the structural tissue of organs, being exactly, connective tissues. Wikipedia:Parenchyma - - - - Early in development the mammalian embryo has three distinct layers: ectoderm (external layer), endoderm (internal layer) and in between those two layers the middle layer or mesoderm. The parenchyma of most organs is of ectodermal (brain, skin) or endodermal origin (lungs, gastrointestinal tract, liver, pancreas). The parenchyma of a few organs (spleen, kidneys, heart) is of mesodermal origin. The stroma of all organs is of mesodermal origin - WP - - - - - the FMA definition is more restrictive, and limits this to solid organs. This would seem to cause problems for the lung parenchyma, except FMA classifies Lung as solid rather than cavitated - FMA - - - - - BTO:0000999 - - - https://github.com/biopragmatics/biomappings - - - - - BTO:0001539 - - - https://github.com/biopragmatics/biomappings - @@ -31361,7 +28685,6 @@ For example, A and B may be gene products and binding of B by A positively regul The inner portion of the kidney consisting of the renal pyramids. - The renal medulla is split up into a number of sections, known as the renal pyramids. Blood enters into the kidney via the renal artery, which then splits up to form the arcuate arterioles. The arcuate arterioles each in turn branch into interlobular arterioles, which finally reach the glomeruli. At the glomerulus the blood reaches a highly disfavourable pressure gradient and a large exchange surface area, which forces the serum portion of the blood out of the vessel into the renal tubules. Flow continues through the renal tubules, including the proximal tubule, the Loop of Henle, and finally leaves the kidney by means of the collecting duct, leading to the renal ureter. The renal medulla contains the structures of the nephrons responsible for maintaining the salt and water balance of the blood. The renal medulla is hypertonic to the filtrate in the nephron and aids in the reabsorption of water BTO:0001167 CALOHA:TS-1157 EMAPA:19279 @@ -31518,14 +28841,11 @@ For example, A and B may be gene products and binding of B by A positively regul consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77 - Anatomical system that consists of the muscles of the body.[VSAO] - we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA AAO:0000307 BILA:0000088 BTO:0001369 BTO:0001485 EFO:0000801 - EMAPA:35578 FMA:72954 MA:0002888 MAT:0000025 @@ -31553,21 +28873,6 @@ For example, A and B may be gene products and binding of B by A positively regul The subdivision of the musculoskeletal system that consists of all the muscles of the body[VSAO, modified]. VSAO:0000033 - - - - Anatomical system that consists of the muscles of the body.[VSAO] - 2012-08-14 - VSAO:0000033 - VSAO - VSAO:curator - - - - - we place the MA term musculature here, rather than under uberon:musculature, as this seems more appropriate given the structure of MA - MA - @@ -31611,7 +28916,12 @@ For example, A and B may be gene products and binding of B by A positively regul - + + + + + + @@ -31629,7 +28939,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0000004 EHDAA2:0003004 EMAPA:35178 - FBbt:00007019 FMA:9669 HAO:0000004 MA:0002450 @@ -31653,28 +28962,12 @@ For example, A and B may be gene products and binding of B by A positively regul organism substance - - - - - - - - - this relationship may be too strong and may be weakened in future - Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007019 - - @@ -31729,7 +29022,6 @@ For example, A and B may be gene products and binding of B by A positively regul BILA:0000005 CARO:0000005 EHDAA2:0003005 - FBbt:00007017 FMA:5897 HAO:0000005 NCIT:C94478 @@ -31753,12 +29045,6 @@ For example, A and B may be gene products and binding of B by A positively regul Non-material anatomical entity of three dimensions, that is generated by morphogenetic or other physiologic processes; is surrounded by one or more anatomical structures; contains one or more organism substances or anatomical structures. http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007017 - - @@ -31790,7 +29076,6 @@ For example, A and B may be gene products and binding of B by A positively regul BILA:0000006 CARO:0000006 EHDAA2:0003006 - FBbt:00007016 FMA:67165 HAO:0000006 TAO:0001836 @@ -31808,12 +29093,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical entity that has mass. http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007016 - - @@ -31831,7 +29110,6 @@ For example, A and B may be gene products and binding of B by A positively regul BILA:0000007 CARO:0000007 EHDAA2:0003007 - FBbt:00007015 FMA:67112 HAO:0000007 TAO:0001835 @@ -31850,12 +29128,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical entity that has no mass. http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007015 - - @@ -31898,10 +29170,8 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA:392 EMAPA:16103 EV:0100000 - FBbt:00004856 FMA:7149 HAO:0000011 - IDOMAL:0002460 MA:0000003 NCIT:C12919 SCTID:278195005 @@ -31941,20 +29211,6 @@ For example, A and B may be gene products and binding of B by A positively regul system GO:0048731 - - - - FBbt:00004856 - - - - - - IDOMAL:0002460 - - - https://github.com/biopragmatics/biomappings - @@ -31992,7 +29248,6 @@ For example, A and B may be gene products and binding of B by A positively regul - organismal organism AAO:0010026 AEO:0000191 @@ -32007,7 +29262,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA:1 EMAPA:25765 EV:0100016 - FBbt:00000001 FMA:256135 HAO:0000012 NCIT:C13041 @@ -32052,12 +29306,6 @@ For example, A and B may be gene products and binding of B by A positively regul VHOG:0000671 WBbt:0007833 - - - - FBbt:00000001 - - @@ -32105,7 +29353,6 @@ For example, A and B may be gene products and binding of B by A positively regul Multi-tissue structure that is part of a compound organ. - this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future AAO:0010017 AEO:0000019 BILA:0000019 @@ -32163,7 +29410,6 @@ For example, A and B may be gene products and binding of B by A positively regul EFO:0000808 EHDAA2:0003032 EMAPA:36031 - FBbt:00007009 FMA:7153 HAO:0000032 MA:0002433 @@ -32206,12 +29452,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:DOS http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007009 - - @@ -32253,7 +29493,6 @@ For example, A and B may be gene products and binding of B by A positively regul BILA:0000040 CARO:0000040 EHDAA2:0003040 - FBbt:00007013 FMA:63863 HAO:0000040 TAO:0000382 @@ -32279,12 +29518,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue. http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007013 - - @@ -32303,7 +29536,6 @@ For example, A and B may be gene products and binding of B by A positively regul - FBbt:00007277 VHOG:0001737 uberon UBERON:0000477 @@ -32317,12 +29549,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical group whose component anatomical structures lie in close proximity to each other. FBbt:00007277 - - - - FBbt:00007277 - - @@ -32356,7 +29582,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0000043 EHDAA2:0003043 EMAPA:35868 - FBbt:00007003 FMA:9637 HAO:0000043 MA:0003002 @@ -32392,12 +29617,6 @@ For example, A and B may be gene products and binding of B by A positively regul Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. CARO:0000043 - - - - FBbt:00007003 - - @@ -32438,7 +29657,6 @@ For example, A and B may be gene products and binding of B by A positively regul BILA:0000055 CARO:0000055 EHDAA2:0003055 - FBbt:00007010 HAO:0000055 TAO:0001488 TGMA:0001847 @@ -32465,12 +29683,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0000055 http://orcid.org/0000-0001-9114-8737 - - - - FBbt:00007010 - - @@ -32509,7 +29721,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -32517,8 +29729,6 @@ For example, A and B may be gene products and binding of B by A positively regul Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]. - The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG] - epithelial AAO:0000144 AAO:0010055 AEO:0000066 @@ -32528,7 +29738,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0000066 EHDAA2:0003066 EMAPA:32738 - FBbt:00007005 FMA:9639 GAID:402 HAO:0000066 @@ -32553,14 +29762,14 @@ For example, A and B may be gene products and binding of B by A positively regul epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg - + - + http://palaeos.com/metazoa/porifera/homoscleromorpha.html @@ -32570,22 +29779,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Epithelium http://orcid.org/0000-0001-9114-8737 - - - - The two basic types of metazoan tissue are epithelial and connective. The simplest metazoans, and developmental stages of many primitive invertebrates, consist solely of these two layers. Thus, epithelial and connective tissues may be the primary (original) tissues of metazoans, and both are important in the functional organization of animals.[well established][VHOG] - 2012-09-17 - VHOG:0000387 - VHOG - ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.59 - http://bgee.unil.ch/ - - - - - FBbt:00007005 - - @@ -32614,7 +29807,6 @@ For example, A and B may be gene products and binding of B by A positively regul BILA:0000068 CARO:0000068 EHDAA2_RETIRED:0003068 - FBbt:00007027 FMA:45567 HAO:0000068 NCIT:C33552 @@ -32654,12 +29846,6 @@ For example, A and B may be gene products and binding of B by A positively regul columnar epithlium AEO:0000068 - - - - FBbt:00007027 - - @@ -32693,7 +29879,6 @@ For example, A and B may be gene products and binding of B by A positively regul Unilaminar epithelium which consists of a single layer of squamous cells. Examples: pulmonary alveolar epithelium, endothelium.[FMA]. - Unilaminar epithelium that consists of a single layer of squamous cells.[CARO] AAO:0010066 AEO:0000070 BILA:0000070 @@ -32725,16 +29910,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Simple_squamous_epithelium http://orcid.org/0000-0001-9114-8737 - - - - Unilaminar epithelium that consists of a single layer of squamous cells.[CARO] - 2012-06-20 - CARO:0000070 - CARO - FMA:45565 - http://orcid.org/0000-0001-9114-8737 - @@ -32773,7 +29948,6 @@ For example, A and B may be gene products and binding of B by A positively regul Compound organ that contains one or more macroscopic anatomical spaces. - this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future AAO:0010016 AEO:0000072 BILA:0000072 @@ -32822,7 +29996,6 @@ For example, A and B may be gene products and binding of B by A positively regul Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.[FMA]. consider adding disjointness axiom between unilaminar and multilaminar - but note that this will render EHDAA2:0003244 (chorionic trophoblast) unsatisfiable - Epithelium that consists of a single layer of epithelial cells.[CARO] AAO:0010062 AEO:0000073 BILA:0000073 @@ -32851,16 +30024,6 @@ For example, A and B may be gene products and binding of B by A positively regul FMA:45561 http://orcid.org/0000-0001-9114-8737 - - - - Epithelium that consists of a single layer of epithelial cells.[CARO] - 2012-06-20 - CARO:0000073 - CARO - FMA:45561 - http://orcid.org/0000-0001-9114-8737 - @@ -32906,10 +30069,6 @@ For example, A and B may be gene products and binding of B by A positively regul Subdivision of trunk that lies between the head and the abdomen. - note that we use the slightly verbose term 'thoracic segment of trunk' to avoid confusuon with insect thorax. todo - taxonomic constraints. Also, in FMA 'thorax' is a synonym for chest - - - EMAPA:35862 FMA:259209 MA:0000022 @@ -32955,7 +30114,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -32964,8 +30123,6 @@ For example, A and B may be gene products and binding of B by A positively regul The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column. Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class - abdominal - celiac BTO:0000020 CALOHA:TS-0001 EFO:0000968 @@ -32992,14 +30149,14 @@ For example, A and B may be gene products and binding of B by A positively regul abdomen - + - + MA @@ -33055,8 +30212,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. - embryonic - Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo AAO:0011035 AEO:0000169 BILA:0000056 @@ -33068,10 +30223,8 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA2_RETIRED:0003236 EHDAA:38 EMAPA:16039 - FBbt:00000052 FMA:69068 GAID:963 - IDOMAL:0000646 MAT:0000226 MESH:D004622 MIAA:0000019 @@ -33107,26 +30260,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0009790 Wikipedia:Embryo - - - - Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo - ZFA - - - - - FBbt:00000052 - - - - - - IDOMAL:0000646 - - - https://github.com/biopragmatics/biomappings - @@ -33159,13 +30292,11 @@ For example, A and B may be gene products and binding of B by A positively regul A layer of cells produced during the process of gastrulation during the early development of the animal embryo, which is distinct from other such layers of cells, as an early step of cell differentiation. The three types of germ layers are the endoderm, ectoderm, and mesoderm. - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] embryonic tissue AAO:0000480 BILA:0000035 BTO:0000556 EMAPA:36033 - FBbt:00000110 FMA:69069 GAID:1303 MESH:D005855 @@ -33196,28 +30327,12 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Germ_layer https://github.com/obophenotype/uberon/issues/203 - - - - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - 2012-09-17 - VHOG:0001223 - VHOG - ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 - http://bgee.unil.ch/ - embryonic tissue FMA:69069 - - - - FBbt:00000110 - - @@ -33256,11 +30371,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. - Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO] - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - ectodermal AAO:0000137 BILA:0000036 BTO:0000315 @@ -33269,7 +30381,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA2:0000428 EMAPA:16069 EV:0100003 - FBbt:00000111 FMA:69070 GAID:1304 MAT:0000155 @@ -33294,14 +30405,14 @@ For example, A and B may be gene products and binding of B by A positively regul ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -33310,31 +30421,6 @@ For example, A and B may be gene products and binding of B by A positively regul Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. Wikipedia:Ectoderm - - - - Primary germ layer that is the outer of the embryonic germ layers and gives rise to epidermis and neural tissue.[AAO] - 2012-06-20 - AAO:0000137 - AAO - AAO:EJS - - - - - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - 2012-09-17 - VHOG:0000153 - VHOG - ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 - http://bgee.unil.ch/ - - - - - FBbt:00000111 - - @@ -33360,10 +30446,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - endodermal AAO:0000139 BILA:0000038 BTO:0000800 @@ -33372,7 +30456,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA2:0000436 EMAPA:16062 EV:0100005 - FBbt:00000125 FMA:69071 GAID:1305 MAT:0000175 @@ -33397,14 +30480,14 @@ For example, A and B may be gene products and binding of B by A positively regul http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -33413,22 +30496,6 @@ For example, A and B may be gene products and binding of B by A positively regul Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. Wikipedia:Endoderm - - - - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - 2012-09-17 - VHOG:0000154 - VHOG - ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 - http://bgee.unil.ch/ - - - - - FBbt:00000125 - - @@ -33455,13 +30522,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + The middle germ layer of the embryo, between the endoderm and ectoderm. - Primary germ layer that is the middle of the embryonic germ layers.[AAO] - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - mesodermal - sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates UBERON:0003263 AAO:0000304 BILA:0000037 @@ -33474,7 +30537,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA:183 EMAPA:16083 EV:0100006 - FBbt:00000126 FMA:69072 GAID:522 MAT:0000174 @@ -33500,20 +30562,14 @@ For example, A and B may be gene products and binding of B by A positively regul mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + - - sometimes not considered primary - - - - - + Bgee:AN @@ -33522,37 +30578,6 @@ For example, A and B may be gene products and binding of B by A positively regul The middle germ layer of the embryo, between the endoderm and ectoderm. Wikipedia:Mesoderm - - - - Primary germ layer that is the middle of the embryonic germ layers.[AAO] - 2012-06-20 - AAO:0000304 - AAO - AAO:EJS - - - - - The Bilateria are triploblastic (with true endoderm, mesoderm, and ectoderm) (...).[well established][VHOG] - 2012-09-17 - VHOG:0000152 - VHOG - ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) Limb development and evolution, p.722 - http://bgee.unil.ch/ - - - - - sponges do not seem to have a mesoderm and accordingly Amphimedon lacks transcription factors involved in mesoderm development (Fkh, Gsc, Twist, Snail)[http://www.nature.com/nature/journal/v466/n7307/full/nature09201.html]. Mesoderm may not be homologous across verteberates - https://github.com/obophenotype/uberon/wiki/The-neural-crest - - - - - FBbt:00000126 - - @@ -33599,15 +30624,10 @@ For example, A and B may be gene products and binding of B by A positively regul Anterior part of the embryonic digestive tract that develops into a mouth. The stomodeum includes as parts an invagination of the ectoderm and the stomodeal cavity. consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence - Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO] - the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx - stomodeal - This class groups together disparate structures as all being the anterior part of the early metazoan digestive tract and precursor of the mouth. However, the developmental processes vary, so this class may be split in future. E.g. in mammals it is a rostral depression surrounded by prominences. Outgrowth of the prominences produces a stomodeal cavity. stomodeal-hypophyseal primordium BTO:0004224 EHDAA2:0001929 EMAPA:16263 - FBbt:00000439 FMA:295846 NCIT:C34306 TAO:0001290 @@ -33640,34 +30660,12 @@ For example, A and B may be gene products and binding of B by A positively regul http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/326 - - - - Anterior part of the embryonic alimentary canal formed as an invagination of the ectoderm; the future mouth.[TAO] - 2012-08-14 - TAO:0001290 - TAO - ZFIN:curator - - - - - the primordial mouth region of the developing head, initially a midline ectodermal depression between the forebrain bulge (cranially) and the heart bulge (caudally) and between the maxillary and mandibular components of the first pharyngeal arch; the stomodeum is separated from the anterior end of the foregut by the buccopharyngeal membrane; the mouth is developed partly from the stomodeum, and partly from the floor of the anterior portion of the foregut; the lips, teeth, and gums are formed from the walls of the stomodeum, but the tongue is developed in the floor of the pharynx - MP:0012522 - NCBITaxon:40674 - stomodeal-hypophyseal primordium XAO:0000269 - - - - FBbt:00000439 - - @@ -33724,7 +30722,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -33745,13 +30743,9 @@ For example, A and B may be gene products and binding of B by A positively regul Inward fold on the surface of the embryonic ectoderm that develops into an ectodermal terminal part of the digestive tract. removed WBbt:0006795 'proctodeum' - junction between the alimentary and genital tracts in the male. - An inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[TAO] - Inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[AAO] - proctodeal AAO:0011087 EHDAA2:0000121 EMAPA:25038 - FBbt:00000123 NCIT:C34278 TAO:0000066 UMLS:C0231054 @@ -33770,7 +30764,7 @@ For example, A and B may be gene products and binding of B by A positively regul proctodeum https://github.com/obophenotype/uberon/issues/685 - + @@ -33783,7 +30777,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + EHDAA2 @@ -33794,30 +30788,6 @@ For example, A and B may be gene products and binding of B by A positively regul https://github.com/obophenotype/uberon/issues/685 https://sourceforge.net/p/fbbtdv/tickets/52 - - - - An inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[TAO] - 2012-08-14 - TAO:0000066 - TAO - ZFIN:curator - - - - - Inward fold on the surface of the embryonic ectoderm that develops into part of the anal passage.[AAO] - 2012-06-20 - AAO:0011087 - AAO - ZFA:0000066 - - - - - FBbt:00000123 - - @@ -33863,7 +30833,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -33892,11 +30862,6 @@ For example, A and B may be gene products and binding of B by A positively regul - Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO] - Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO] - relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO] - As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG] - cardiac AAO:0010210 BILA:0000020 BTO:0000562 @@ -33940,14 +30905,14 @@ For example, A and B may be gene products and binding of B by A positively regul https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_F_Heart.glb https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Heart.glb - + - + MA @@ -33957,42 +30922,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Heart http://orcid.org/0000-0002-6601-2165 - - - - Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO] - 2012-08-14 - TAO:0000114 - TAO - ZFIN:curator - - - - - Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO] - 2012-06-20 - AAO:0010210 - AAO - AAO:BJB - - - - - relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO] - 2012-06-20 - AAO:0010210 - AAO - - - - - As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG] - 2012-09-17 - VHOG:0000276 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.481 - http://bgee.unil.ch/ - @@ -34043,7 +30972,6 @@ For example, A and B may be gene products and binding of B by A positively regul Any thin layer or plate. TODO - merge with cell layer? - laminar Wikipedia:Lamina_of_the_vertebral_arch laminar tissue uberon @@ -34080,8 +31008,6 @@ For example, A and B may be gene products and binding of B by A positively regul Middle part of an organ, surrounded by the cortex. - this class is used in a very general sense - medullary FMA:61108 galen:Medulla medulla @@ -34122,8 +31048,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical structure that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO]. - Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO] - Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO] articulation joint AEO:0000182 @@ -34168,24 +31092,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Joint http://dx.plos.org/10.1371/journal.pone.0051070 - - - - Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO] - 2012-08-14 - VSAO:0000101 - VSAO - PSPUB:0000170 - - - - - Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO] - 2012-08-14 - TAO:0000367 - TAO - TAO:pem - @@ -34264,9 +31170,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that has as its parts the organs concerned with reproduction. consider splitting genitalia from reproductive system - Anatomical system which consists of organs and tissues associated with sexual reproduction of the organism.[AAO] - Arguably, one of the most important aspects of urbilaterian organogenesis would have been gonadogenesis, since Urbilateria must have successfully generated gametes and developed a strategy for extrusion and fertilization, in order to be the ancestor of all living Bilateria.[well established][VHOG] - 2022-06-10T18:22:34Z AAO:0010258 BILA:0000103 @@ -34277,13 +31180,11 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA:5923 EMAPA:17381 EV:0100100 - FBbt:00004857 FMA:7160 GAID:363 HAO:0000374 HAO:0000895 MA:0000326 - MESH:D005835 MIAA:0000305 NCIT:C12841 SCTID:278875001 @@ -34320,38 +31221,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that has as its parts the organs concerned with reproduction. Wikipedia:Reproductive_system - - - - Anatomical system which consists of organs and tissues associated with sexual reproduction of the organism.[AAO] - 2012-06-20 - AAO:0010258 - AAO - AAO:BJB - - - - - Arguably, one of the most important aspects of urbilaterian organogenesis would have been gonadogenesis, since Urbilateria must have successfully generated gametes and developed a strategy for extrusion and fertilization, in order to be the ancestor of all living Bilateria.[well established][VHOG] - 2012-09-17 - VHOG:0000182 - VHOG - PMID:21672850 Extavour CGM, Gray anatomy: phylogenetic patterns of somatic gonad structures and reproductive strategies across Bilateria. Integrative and Comparative Biology (2007) - http://bgee.unil.ch/ - - - - - FBbt:00004857 - - - - - - MESH:D005835 - - https://github.com/biopragmatics/biomappings - @@ -34432,17 +31301,11 @@ For example, A and B may be gene products and binding of B by A positively regul Reproductive organ that produces and releases eggs (ovary) or sperm (testis). - Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO] - The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO] - Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG] - gonadal - FMA xref is a 'general anatomical term' AAO:0000213 BILA:0000123 BSA:0000079 BTO:0000534 EMAPA:17383 - FBbt:00004858 FMA:18250 GAID:368 HAO:0000379 @@ -34477,46 +31340,6 @@ For example, A and B may be gene products and binding of B by A positively regul ZFA:0000413 ZFIN:curator - - - - Anatomical structure which produces gametes as well as certain sex hormones controlled by the pituitary gonadotropins.[AAO] - 2012-06-20 - AAO:0000213 - AAO - AAO:BJB - - - - - The part of the reproductive system that produces and releases eggs (ovary) or sperm (testis).[TAO] - 2012-08-14 - TAO:0000413 - TAO - ZFIN:curator - - - - - Examination of different vertebrate species shows that the adult gonad is remarkably similar in its morphology across different phylogenetic classes. Surprisingly, however, the cellular and molecular programs employed to create similar organs are not evolutionarily conserved.[uncertain][VHOG] - 2012-09-17 - VHOG:0000397 - VHOG - DOI:10.1146/annurev.cellbio.042308.13350 DeFalco T, Capel B, Gonad morphogenesis in vertebrates: divergent means to a convergent end. Annual review of cell and developmental biology (2009) - http://bgee.unil.ch/ - - - - - FMA xref is a 'general anatomical term' - FMA - - - - - FBbt:00004858 - - @@ -34568,16 +31391,11 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes. - An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO] - digestive - many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class AAO:0000129 BILA:0000082 BTO:0000058 CALOHA:TS-1293 EFO:0000793 - EV:0100056 - FBbt:00005055 FMA:7152 GAID:278 MA:0002431 @@ -34614,27 +31432,6 @@ For example, A and B may be gene products and binding of B by A positively regul NLM:alimentary+system Wikipedia:Digestive_system - - - - An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO] - 2012-06-20 - AAO:0000129 - AAO - AAO:BJB - - - - - many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class - MA - - - - - FBbt:00005055 - - @@ -34675,10 +31472,6 @@ For example, A and B may be gene products and binding of B by A positively regul - An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO] - Evolution of vertebrate renal anatomy appears quite conservative when compared, for example, to evolution of respiratory and cardiovascular systems in vertebrates. Major anatomical changes in vertebrates kidneys separate those of birds and mammals from kidneys of lower vertebrates. General increase in animal size from fish to mammals is reflected by an increase in total number of nephrons per kidney, rather than by constant change in tubular dimensions.[well established][VHOG] - In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels - This definition is inclusive of the organs of the vertebrate renal system, as well as the Malpighian tubules of insects, and allows for future incorporation of structures such as the antennal glands of crustaceans excretory system AAO:0010257 BILA:0000015 @@ -34690,7 +31483,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA:5901 EMAPA:17366 EV:0100095 - FBbt:00005056 FMA:7159 GAID:391 MA:0000325 @@ -34743,43 +31535,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Acoelomorpha - - - - An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO] - 2012-06-20 - AAO:0010257 - AAO - AAO:BJB - - - - - Evolution of vertebrate renal anatomy appears quite conservative when compared, for example, to evolution of respiratory and cardiovascular systems in vertebrates. Major anatomical changes in vertebrates kidneys separate those of birds and mammals from kidneys of lower vertebrates. General increase in animal size from fish to mammals is reflected by an increase in total number of nephrons per kidney, rather than by constant change in tubular dimensions.[well established][VHOG] - 2012-09-17 - VHOG:0000723 - VHOG - ISBN:978-3540428541 Kapoor BG, Bhavna Khanna, Ichthyology Handbook (2004) p.406 - http://bgee.unil.ch/ - - - - - In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels - GO - - - - - This definition is inclusive of the organs of the vertebrate renal system, as well as the Malpighian tubules of insects, and allows for future incorporation of structures such as the antennal glands of crustaceans - DOI:10.1371/journal.pone.0099864 - - - - - FBbt:00005056 - - @@ -34835,17 +31590,12 @@ For example, A and B may be gene products and binding of B by A positively regul Organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP]. - the cardiovascular system and the lymphatic system are parts of the circulatory system - - Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO] - We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG] AAO:0000959 CALOHA:TS-2103 - MESH:D002319 VHOG:0001248 Wikipedia:Circulatory_system uberon @@ -34868,38 +31618,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Acoelomorpha - - - - - WBbt coelomocyte currently classified as circulating cell - - - - - Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO] - 2012-06-20 - AAO:0000959 - AAO - AAO:BJB - - - - - We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG] - 2012-09-17 - VHOG:0001248 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.493 - http://bgee.unil.ch/ - - - - - MESH:D002319 - - https://github.com/biopragmatics/biomappings - @@ -34927,12 +31645,8 @@ For example, A and B may be gene products and binding of B by A positively regul A subdivision of the muscular system corresponding to a subdisivision of an organism. - - In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here. - AAO:0011066 BTO:0000887 EFO:0001949 - EMAPA:32715 EMAPA:35577 FMA:32558 MA:0000165 @@ -34968,12 +31682,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Muscular_system https://orcid.org/0000-0002-6601-2165 - - - - In FMA this is classified as a set of organs. ZFA musculature system has subtypes, so it is classified here. WBbt muscular system has subtypes so it goes here. Note that we use the MA term set of skeletal muscles here as it seems most appropriate (*not* MA:musculature). AAO is generally confused here. - FMA - @@ -35037,7 +31745,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -35045,11 +31753,6 @@ For example, A and B may be gene products and binding of B by A positively regul The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]. - A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO] - Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO] - Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG] - nervous - neural AAO:0000324 BILA:0000079 BIRNLEX:844 @@ -35060,7 +31763,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA:826 EMAPA:16469 EV:0100162 - FBbt:00005093 FMA:7157 GAID:466 MA:0000016 @@ -35092,14 +31794,14 @@ For example, A and B may be gene products and binding of B by A positively regul http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -35114,40 +31816,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Nervous_system ZFIN:curator - - - - A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO] - 2012-08-14 - TAO:0000396 - TAO - ZFIN:curator - - - - - Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO] - 2012-06-20 - AAO:0000324 - AAO - AAO:BJB - - - - - Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG] - 2012-09-17 - VHOG:0000402 - VHOG - ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.117 - http://bgee.unil.ch/ - - - - - FBbt:00005093 - - @@ -35193,14 +31861,10 @@ For example, A and B may be gene products and binding of B by A positively regul - + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. - Part of the nervous system which includes the brain and spinal cord.[AAO] - The brain and spinal cord. Kimmel et al, 1995.[TAO] - The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO). - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG] AAO:0000090 BAMS:CNS BILA:0000080 @@ -35213,7 +31877,6 @@ For example, A and B may be gene products and binding of B by A positively regul EMAPA:16470 EMAPA:16754 EV:0100163 - FBbt:00005094 FMA:55675 GAID:570 MA:0000167 @@ -35242,7 +31905,7 @@ For example, A and B may be gene products and binding of B by A positively regul central nervous system - + @@ -35256,7 +31919,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + Bgee:AN @@ -35273,46 +31936,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Acoelomorpha - - - - Part of the nervous system which includes the brain and spinal cord.[AAO] - 2012-06-20 - AAO:0000090 - AAO - AAO:BJB - - - - - The brain and spinal cord. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000012 - TAO - ZFIN:curator - - - - - The central nervous system (CNS) is the part of the nervous system which includes the brain, spinal cord, and nerve cell layer of the retina (CUMBO). - BIRNLEX:1099 - - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2); Taken together, our data make a very strong case that the complex molecular mediolateral architecture of the developing trunk CNS (central nervous system), as shared between Platynereis and vertebrates, was already present in their last common ancestor, Urbilateria. The concept of bilaterian nervous system centralization implies that neuron types concentrate on one side of the trunk, as is the case in vertebrates and many invertebrates including Platynereis, where they segregate and become spatially organized (as opposed to a diffuse nerve net). Our data reveal that a large part of the spatial organization of the annelid and vertebrate CNS was already present in their last common ancestor, which implies that Urbilateria had already possessed a CNS (reference 3).[well established][VHOG] - 2012-09-17 - VHOG:0000293 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 (reference 1), ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.165 (reference 2), DOI:10.1016/j.cell.2007.02.040 Denes AS, Jekely G, Steinmetz PRH, Raible F, Snyman H, Prud'homme B, Ferrier DEK, Balavoine G and Arendt D, Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in Bilateria. Cell (2007) (reference 3) - http://bgee.unil.ch/ - - - - - FBbt:00005094 - - @@ -35355,15 +31978,12 @@ For example, A and B may be gene products and binding of B by A positively regul Anterior subdivision of a digestive tract. Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. In vertebrates the term may refer to a developmental structure - The anterior portion of the primitive digestive tube of the embryo that lies cephalic to the junction of the yolk stalk, consists of endodermal tissue, and gives rise to the the pharynx, lower respiratory system, esophagus, stomach, duodenum proximal to the biliary tract, liver, pancreas, biliary tract, and gall bladder. - The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] AAO:0011042 BILA:0000085 BTO:0000507 EHDAA2:0000557 EHDAA:520 EMAPA:16548 - FBbt:00005379 FMA:45616 MA:0001526 NCIT:C34180 @@ -35389,28 +32009,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anterior subdivision of a digestive tract. http://orcid.org/0000-0002-6601-2165 - - - - The anterior portion of the primitive digestive tube of the embryo that lies cephalic to the junction of the yolk stalk, consists of endodermal tissue, and gives rise to the the pharynx, lower respiratory system, esophagus, stomach, duodenum proximal to the biliary tract, liver, pancreas, biliary tract, and gall bladder. - MP:0000474 - - - - - The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0000285 - VHOG - ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 - http://bgee.unil.ch/ - - - - - FBbt:00005379 - - @@ -35446,16 +32044,12 @@ For example, A and B may be gene products and binding of B by A positively regul Middle subdivision of a digestive tract[CJM]. In vertebrates: The middle part of the alimentary canal from the stomach, or entrance of the bile duct, to, or including, the large intestine[GO]. Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future. We may explicitly make this a developmental class - The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] - In humans: originates from the foregut at the opening of the bile duct into the duodenum and continues through the small intestine and much of the large intestine until the transition to the hindgut about two-thirds of the way through the transverse colon - in FMA this represents an embryonic region. BILA:0000086 BTO:0000863 EFO:0001950 EHDAA2:0001185 EHDAA:983 EMAPA:16255 - FBbt:00005383 FMA:45617 MA:0001564 NCIT:C34210 @@ -35482,34 +32076,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0007494 Wikipedia:Midgut - - - - The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0000290 - VHOG - ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 - http://bgee.unil.ch/ - - - - - In humans: originates from the foregut at the opening of the bile duct into the duodenum and continues through the small intestine and much of the large intestine until the transition to the hindgut about two-thirds of the way through the transverse colon - WP - - - - - in FMA this represents an embryonic region. - FMA - - - - - FBbt:00005383 - - @@ -35530,7 +32096,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -35539,16 +32105,12 @@ For example, A and B may be gene products and binding of B by A positively regul The caudalmost subdivision of a digestive tract. Note we define this generically to include invertebrates (partly for consistency with GO), but the class may be split in future (vertebrates have some contribution from NC - https://github.com/obophenotype/uberon/wiki/The-neural-crest). We may explicitly make this a developmental class - the caudal portion of the primitive digestive tube of the embryo - The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] - in FMA this class has no children. In MA it has a single child hindgut epithelium AAO:0011052 BILA:0000087 BTO:0000510 EHDAA2:0000779 EHDAA:975 EMAPA:16715 - FBbt:00005384 FMA:45618 MA:0001527 NCIT:C34188 @@ -35567,14 +32129,14 @@ For example, A and B may be gene products and binding of B by A positively regul hindgut http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray472.png - + - + Wikipedia @@ -35583,34 +32145,6 @@ For example, A and B may be gene products and binding of B by A positively regul The caudalmost subdivision of a digestive tract. http://orcid.org/0000-0002-6601-2165 - - - - the caudal portion of the primitive digestive tube of the embryo - MP:0008786 - - - - - The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0000459 - VHOG - ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 - http://bgee.unil.ch/ - - - - - in FMA this class has no children. In MA it has a single child hindgut epithelium - FMA - - - - - FBbt:00005384 - - @@ -35642,7 +32176,6 @@ For example, A and B may be gene products and binding of B by A positively regul BTO:0001886 EFO:0001652 EHDAA2:0003171 - FBbt:00005495 FMA:86589 MAT:0000482 NCIT:C34275 @@ -35676,12 +32209,6 @@ For example, A and B may be gene products and binding of B by A positively regul FB:FBrf0089570 http://flybase.org/reports/FBrf0178740.html - - - - FBbt:00005495 - - @@ -35718,10 +32245,6 @@ For example, A and B may be gene products and binding of B by A positively regul In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted]. - Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO] - The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG] - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] - The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium AAO:0010617 BTO:0001057 CALOHA:TS-2371 @@ -35733,7 +32256,6 @@ For example, A and B may be gene products and binding of B by A positively regul EMAPA:16757 FMA:293882 MAT:0000069 - MESH:D054259 MIAA:0000069 NCIT:C34226 SCTID:362852000 @@ -35767,49 +32289,6 @@ For example, A and B may be gene products and binding of B by A positively regul In the developing vertebrate, the neural tube is the embryo's precursor to the central nervous system, which comprises the brain and spinal cord. The neural groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or neural canal (which strictly speaking is the center of the neural tube), the ectodermal wall of which forms the rudiment of the nervous system. [WP,unvetted]. Wikipedia:Neural_tube - - - - Hollow epithelial tube on dorsal side of the embryo that develops into the central nervous system.[AAO] - 2012-06-20 - AAO:0010617 - AAO - AAO:JOR - - - - - The dorsal tubular structure in the vertebrate embryo that develops into the brain and spinal cord. [TFD][VHOG] - 2012-09-17 - VHOG:0000307 - VHOG - http://bgee.unil.ch/ - http://medical-dictionary.thefreedictionary.com/neural+tube - - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] - 2012-09-17 - VHOG:0000307 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 - http://bgee.unil.ch/ - - - - - The mature structure of the neural tube exists when the tube has been segmented into the forebrain, midbrain, hindbrain and spinal cord regions. In addition neural crest has budded away from the epithelium - GO:0021915 - - - - - MESH:D054259 - - - https://github.com/biopragmatics/biomappings - @@ -35840,7 +32319,6 @@ For example, A and B may be gene products and binding of B by A positively regul BIRNLEX:6 CARO:0000000 EHDAA2:0002229 - FBbt:10000000 FMA:62955 HAO:0000000 MA:0000001 @@ -35864,12 +32342,6 @@ For example, A and B may be gene products and binding of B by A positively regul FMA:62955 http://orcid.org/0000-0001-9114-8737 - - - - FBbt:10000000 - - @@ -35908,8 +32380,6 @@ For example, A and B may be gene products and binding of B by A positively regul A vein that carries deoxygenated blood from the lower half of the body into the right atrium of the heart. - Trunk of systemic vein which is formed by the union of the right common iliac vein and the left common iliac vein and terminates in the right atrium[FMA]. - Phylogenetic modifications within this basic pattern of arteries and veins are largely correlated with functional changes. In the transition from water to land, gills gave way to lungs, accompanied by the establishment of a pulmonary circulation. In some fishes and certainly in tetrapods, the cardinal veins become less involved in blood return. Instead, the composite, prominent postcava (posterior vena cava) arose to drain the posterior part of the body and the precava (anterior vena cava) developed to drain the anterior part of the body.[well established][VHOG] AAO:0011083 BTO:0002682 EHDAA2:0000611 @@ -35946,22 +32416,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Inferior_vena_cava http://orcid.org/0000-0002-6601-2165 - - - - Trunk of systemic vein which is formed by the union of the right common iliac vein and the left common iliac vein and terminates in the right atrium[FMA]. - FMA:10951 - - - - - Phylogenetic modifications within this basic pattern of arteries and veins are largely correlated with functional changes. In the transition from water to land, gills gave way to lungs, accompanied by the establishment of a pulmonary circulation. In some fishes and certainly in tetrapods, the cardinal veins become less involved in blood return. Instead, the composite, prominent postcava (posterior vena cava) arose to drain the posterior part of the body and the precava (anterior vena cava) developed to drain the anterior part of the body.[well established][VHOG] - 2012-09-17 - VHOG:0001194 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.454-455 - http://bgee.unil.ch/ - @@ -36025,7 +32479,6 @@ For example, A and B may be gene products and binding of B by A positively regul Excretion that is the output of a kidney. - kidney excreta from some taxa (e.g. in aves) may not be liquid BTO:0001419 CALOHA:TS-1092 EFO:0001939 @@ -36093,8 +32546,6 @@ For example, A and B may be gene products and binding of B by A positively regul Either of the pair of major vessels which arise from the renal hilus and return blood from the kidneys, suprarenal gland and the ureter to the inferior vena cava. - The renal veins are veins that drain the kidney. They connect the kidney to the inferior vena cava. It is usually singular to each kidney, except in the condition 'multiple renal veins'. It also divides into 2 divisions upon entering the kidney: the anterior branch which receives blood from the anterior portion of the kidney and, the posterior branch which receives blood from the posterior portion. Often, each renal vein will have a branch that receives blood from the ureter. [WP,unvetted][Wikipedia:Renal_vein]. - in EHDAA2, the renal vein is part of the kidney BTO:0002681 EHDAA2:0001602 EHDAA:8722 @@ -36130,18 +32581,6 @@ For example, A and B may be gene products and binding of B by A positively regul MGI:csmith MP:0011323 - - - - The renal veins are veins that drain the kidney. They connect the kidney to the inferior vena cava. It is usually singular to each kidney, except in the condition 'multiple renal veins'. It also divides into 2 divisions upon entering the kidney: the anterior branch which receives blood from the anterior portion of the kidney and, the posterior branch which receives blood from the posterior portion. Often, each renal vein will have a branch that receives blood from the ureter. [WP,unvetted][Wikipedia:Renal_vein]. - Wikipedia:Renal_vein - - - - - in EHDAA2, the renal vein is part of the kidney - EHDAA2 - @@ -36175,14 +32614,14 @@ For example, A and B may be gene products and binding of B by A positively regul - + - + @@ -36234,24 +32673,24 @@ For example, A and B may be gene products and binding of B by A positively regul renal pelvis https://upload.wikimedia.org/wikipedia/commons/c/c0/Illu_kidney2.jpg - + - + - + MA - + FMA @@ -36297,7 +32736,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -36306,7 +32745,6 @@ For example, A and B may be gene products and binding of B by A positively regul Outer cortical portion of the kidney, between the renal capsule and the renal medulla. - In the adult metanephros, it forms a continuous smooth outer zone with a number of projections that extend down between the pyramids. It contains the renal corpuscles and the renal tubules except for parts of the loop of Henle which descend into the renal medulla. It also contains blood vessels and cortical collecting ducts. The renal cortex is the part of the kidney where ultrafiltration occurs.[WP] BTO:0001166 CALOHA:TS-0503 EMAPA:17952 @@ -36334,14 +32772,14 @@ For example, A and B may be gene products and binding of B by A positively regul https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Kidney_R.glb https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg - + - + FMA @@ -36377,7 +32815,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -36392,9 +32830,6 @@ For example, A and B may be gene products and binding of B by A positively regul The structure containing the glomerular capsule and the glomerulus that serves as the initial blood-filtering component of a nephron. - A mass of arterial capillaries enveloped in a capsule and attached to a tubule in the kidney[BTO] - A tuft of capillaries found in a Bowman's capsule in which waste products are filtered from the blood and urine formation is initiated. Paired highly vascularized structures of the pronephros, responsible for blood filtration.[XAO] - The part of the nephron that filters blood.[TAO] BTO:0000333 CALOHA:TS-1317 EMAPA:28236 @@ -36425,14 +32860,14 @@ For example, A and B may be gene products and binding of B by A positively regul renal corpuscle https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg - + - + MA ZFA @@ -36443,33 +32878,6 @@ For example, A and B may be gene products and binding of B by A positively regul ISBN:0-683-40008-8 MP:0002827 - - - - A mass of arterial capillaries enveloped in a capsule and attached to a tubule in the kidney[BTO] - 2012-11-28 - BTO:0000333 - BTO - BTO:curator - - - - - A tuft of capillaries found in a Bowman's capsule in which waste products are filtered from the blood and urine formation is initiated. Paired highly vascularized structures of the pronephros, responsible for blood filtration.[XAO] - 2012-11-28 - XAO:0000146 - XAO - XAO:curator - - - - - The part of the nephron that filters blood.[TAO] - 2012-08-14 - TAO:0005281 - TAO - ZFIN:curator - @@ -36533,7 +32941,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -36541,9 +32949,6 @@ For example, A and B may be gene products and binding of B by A positively regul A cup-like sac at the expanded beginning of a tubular component of a nephron that contains the glomerulus. - Anatomical structure found in the kidney consisting of an expanded end of a kidney tubule surrounding a glomerulus and is the major site of filtration.[AAO] - Fluids from blood in the glomerulus are collected in the Bowman's capsule and further processed along the nephron to form urine. This process is known as ultrafiltration[WP]. - One fold of the S-shaped body gives rise to Bowman's capsule[GUDMAP] AAO:0010526 BTO:0002297 EMAPA:27973 @@ -36578,14 +32983,14 @@ For example, A and B may be gene products and binding of B by A positively regul glomerular capsule http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg - + - + Wikipedia @@ -36596,15 +33001,6 @@ For example, A and B may be gene products and binding of B by A positively regul MP:0002828 Wikipedia:Bowman%27s_capsule - - - - Anatomical structure found in the kidney consisting of an expanded end of a kidney tubule surrounding a glomerulus and is the major site of filtration.[AAO] - 2012-06-20 - AAO:0010526 - AAO - AAO:BJB - @@ -36684,11 +33080,16 @@ For example, A and B may be gene products and binding of B by A positively regul - + - - + + + + + + + @@ -36697,7 +33098,6 @@ For example, A and B may be gene products and binding of B by A positively regul An epithelial tube that is part of the nephron, the functional part of the kidney. - note that in ISBN:0073040584 (Vertebrates, Kardong), the uriniferous tubule contains the nephron, so we have a separate class, rather than using a synonym, as in MA UBERON:0004210 renal tubule BTO:0000343 @@ -36727,7 +33127,7 @@ For example, A and B may be gene products and binding of B by A positively regul nephron tubule - + @@ -36736,18 +33136,14 @@ For example, A and B may be gene products and binding of B by A positively regul - + - - - - - + GO MA ZFA @@ -36761,15 +33157,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + ZFA - - - - - checkme - @@ -36777,12 +33167,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0072078 Wikipedia:Renal_tubule - - - - note that in ISBN:0073040584 (Vertebrates, Kardong), the uriniferous tubule contains the nephron, so we have a separate class, rather than using a synonym, as in MA - MA - @@ -36808,7 +33192,12 @@ For example, A and B may be gene products and binding of B by A positively regul - + + + + + + @@ -36823,8 +33212,6 @@ For example, A and B may be gene products and binding of B by A positively regul The collecting duct is a portion of the nephron through which water flows, moving passively down its concentration gradient. - Renal duct that collects the output from renal tubules.[TAO] - in ISBN:0073040584 (Vertebrates, Kardong), the nephron is adjacent to the collecting tubule, consistent with FMA, but not GO. Wikipedia says: Many sources include the connecting tubule as part of the collecting duct system. However, the embryological origin is more similar to the nephron than it is to the rest of the collecting duct (which derives from the ureteric bud), and other sources therefore classify the connecting tubule with the nephron BTO:0000761 CALOHA:TS-0860 EMAPA:28407 @@ -36856,17 +33243,6 @@ For example, A and B may be gene products and binding of B by A positively regul collecting duct of renal tubule - - - - - - - - - checkme - GO - @@ -36874,21 +33250,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0072044 Wikipedia:Collecting_tubule - - - - Renal duct that collects the output from renal tubules.[TAO] - 2012-08-14 - TAO:0005294 - TAO - ZFIN:curator - - - - - in ISBN:0073040584 (Vertebrates, Kardong), the nephron is adjacent to the collecting tubule, consistent with FMA, but not GO. Wikipedia says: Many sources include the connecting tubule as part of the collecting duct system. However, the embryological origin is more similar to the nephron than it is to the rest of the collecting duct (which derives from the ureteric bud), and other sources therefore classify the connecting tubule with the nephron - FMA - @@ -36938,17 +33299,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - @@ -36957,12 +33307,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - @@ -36971,12 +33315,9 @@ For example, A and B may be gene products and binding of B by A positively regul Orifice at the opposite end of an animal's digestive tract from the mouth. Its function is to expel feces, unwanted semi-solid matter produced during digestion, which, depending on the type of animal, may be one or more of: matter which the animal cannot digest, such as bones; food material after all the nutrients have been extracted, for example cellulose or lignin; ingested matter which would be toxic if it remained in the digestive tract; and dead or excess gut bacteria and other endosymbionts. - anal - In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html BTO:0001680 CALOHA:TS-2005 EV:0100082 - FBbt:00047153 FMA:15711 GAID:312 MA:0000331 @@ -37008,12 +33349,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Anus ZFIN:curator - - - - FBbt:00047153 - - @@ -37029,16 +33364,15 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + + + + + + Distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP]. - - A saccular organ in which urine accumulates before discharge from the body. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] - Anatomical structure which consists of a membranous sac used to temporarily store urine until it is excreted from the body.[AAO] - In tetrapods, the urinary bladder arises as an outpocketing of the cloaca. (...) The tetrapod urinary bladder appears first among amphibians and is present in Sphenodon, turtles, most lizards, ostriches among birds, and all mammals.[well established][VHOG] - vesical - The urinary bladder evolved in tetrapods. Birds to not possess a true urinary bladder, although Palaeognathae have an undifferentiated cloacal outpocketing that serves a similar function[https://github.com/obophenotype/uberon/issues/454] bladder AAO:0000623 BTO:0001418 @@ -37077,14 +33411,10 @@ For example, A and B may be gene products and binding of B by A positively regul https://ccf-ontology.hubmapconsortium.org/objects/v1.2/VH_M_Urinary_Bladder.glb https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg - + - - - - @@ -37094,15 +33424,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + FMA - - - - - upper part of UG sinus - @@ -37110,42 +33434,6 @@ For example, A and B may be gene products and binding of B by A positively regul MGI:anna Wikipedia:Urinary_bladder - - - - - https://orcid.org/0000-0003-3308-6245 - GOTAX:0010073 - https://github.com/obophenotype/uberon/issues/454 - - - - - A saccular organ in which urine accumulates before discharge from the body. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] - 2012-09-17 - VHOG:0000740 - VHOG - http://bgee.unil.ch/ - - - - - Anatomical structure which consists of a membranous sac used to temporarily store urine until it is excreted from the body.[AAO] - 2012-06-20 - AAO:0000623 - AAO - AAO:BJB - - - - - In tetrapods, the urinary bladder arises as an outpocketing of the cloaca. (...) The tetrapod urinary bladder appears first among amphibians and is present in Sphenodon, turtles, most lizards, ostriches among birds, and all mammals.[well established][VHOG] - 2012-09-17 - VHOG:0000740 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.577-78 - http://bgee.unil.ch/ - @@ -37208,12 +33496,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - @@ -37222,8 +33504,6 @@ For example, A and B may be gene products and binding of B by A positively regul The organism subdivision that includes the pelvic girdle skeleton and associated soft tissue. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). Examples: There are only two instances in an organism, right and left pelvic girdle regions. - this class describes the subdivision of the limb/fin, NOT the skeleton within. See also: skeleton of pectoral girdle (UBERON:0007831). See also comments on obo-anatomy mail list. Note that even though the class includes soft tissue it is more restrictive than 'pelvis' which also includes structures in cavities etc. TODO this needs to be better documented - Subdivision of lower limb or fin which links the limb/fin to the body[FMA,modified]. There is only one instance of the pelvic girdle region per organism.[VSAO] EMAPA:37862 FMA:16581 NCIT:C33291 @@ -37249,15 +33529,6 @@ For example, A and B may be gene products and binding of B by A positively regul https://groups.google.com/d/topic/obo-anatomy/h4R4xKmINrw/discussion https://orcid.org/0000-0002-6601-2165 - - - - Subdivision of lower limb or fin which links the limb/fin to the body[FMA,modified]. There is only one instance of the pelvic girdle region per organism.[VSAO] - 2012-08-14 - VSAO:0000304 - VSAO - https://orcid.org/0000-0002-6601-2165 - @@ -37283,20 +33554,23 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + + + + + + - + The basic functional unit of the kidney. its chief function is to regulate the concentration of water and soluble substances like sodium salts by filtering the blood, reabsorbing what is needed and excreting the rest as urine. A nephron eliminates wastes from the body, regulates blood volume and blood pressure, controls levels of electrolytes and metabolites, and regulates blood pH. Its functions are vital to life and are regulated by the endocrine system by hormones such as antidiuretic hormone, aldosterone, and parathyroid hormone.[WP]. kidney terms require review for cross-vertebrate compatibility and developmental relationships. - Functional unit of the kidney that filters waste.[TAO] - In the avian kidney, three types of nephron are identified: mammalian-type nephrons with long and short loops of Henle, and reptilian type nephrons (Gambaryan, 1992) BTO:0000924 CALOHA:TS-1312 EMAPA:28491 @@ -37324,34 +33598,24 @@ For example, A and B may be gene products and binding of B by A positively regul nephron http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + - - - - - + - + FMA - - definitional - - - - - + Bgee:AN @@ -37361,21 +33625,6 @@ For example, A and B may be gene products and binding of B by A positively regul PMID:9268568 Wikipedia:Nephron - - - - Functional unit of the kidney that filters waste.[TAO] - 2012-08-14 - TAO:0002153 - TAO - ZFIN:curator - - - - - In the avian kidney, three types of nephron are identified: mammalian-type nephrons with long and short loops of Henle, and reptilian type nephrons (Gambaryan, 1992) - GO - @@ -37411,15 +33660,20 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + + + + + + - + @@ -37427,7 +33681,6 @@ For example, A and B may be gene products and binding of B by A positively regul The proximal convoluted tubule is the most proximal portion of the proximal tubule and extends from the glomerular capsule to the proximal straight tubule. - Renal tubule that connects to the renal corpuscle.[TAO] CALOHA:TS-2198 EMAPA:28287 EV:0100388 @@ -37456,15 +33709,11 @@ For example, A and B may be gene products and binding of B by A positively regul proximal convoluted tubule http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - - - - - + - + @@ -37477,20 +33726,13 @@ For example, A and B may be gene products and binding of B by A positively regul - - MA uses subclass - GOC:mtg_kidney_jan10 - - - - - + GO - + Wikipedia @@ -37499,15 +33741,6 @@ For example, A and B may be gene products and binding of B by A positively regul The proximal convoluted tubule is the most proximal portion of the proximal tubule and extends from the glomerular capsule to the proximal straight tubule. GO:0072019 - - - - Renal tubule that connects to the renal corpuscle.[TAO] - 2012-08-14 - TAO:0005290 - TAO - ZFIN:curator - @@ -37581,11 +33814,7 @@ For example, A and B may be gene products and binding of B by A positively regul The section of the renal tubule in the kidney medulla with a hairpin bend; consists of a descending limb and an ascending limb, and is situated between the proximal convoluted tubule to the distal convoluted tubule; it functions to reabsorb water and ions from the urine. the definitions of some kidney parts (e.g. proximal straight tubule) refer to Henle's loop, even in species where this may not be present. Requires review. - - A highly specialized segment of the mammalian kidney tubules, that dips into the medulla. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, p.648, see_Liem_KF][VHOG] - The structure differs considerably between species; there is a definite physical loop of Henle in the mammalian and avian renal systems but this seems to be absent in Xenopus. However, homologs of some, but not all, molecular markers (e.g. cldn8 and clcnk) of the mammalian loop of Henle were found to be present in the pronephros of the frog larva . - The loop of Henle plays an important role in creating a concentration gradient in the medulla of the kidney. It is involved in reabsorption of filtered water and ions including sodium, potassium and calcium, and independently regulates both the volume and osmolarity of body fluids. BTO:0004608 EMAPA:19280 EV:0100390 @@ -37615,27 +33844,6 @@ For example, A and B may be gene products and binding of B by A positively regul MGI:csmith MP:0004755 - - - - A highly specialized segment of the mammalian kidney tubules, that dips into the medulla. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Grande_L, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF, p.648, see_Liem_KF][VHOG] - 2012-09-17 - VHOG:0001270 - VHOG - http://bgee.unil.ch/ - - - - - The structure differs considerably between species; there is a definite physical loop of Henle in the mammalian and avian renal systems but this seems to be absent in Xenopus. However, homologs of some, but not all, molecular markers (e.g. cldn8 and clcnk) of the mammalian loop of Henle were found to be present in the pronephros of the frog larva . - DOI:10.1371/journal.pone.0099864 - - - - - The loop of Henle plays an important role in creating a concentration gradient in the medulla of the kidney. It is involved in reabsorption of filtered water and ions including sodium, potassium and calcium, and independently regulates both the volume and osmolarity of body fluids. - DOI:10.1371/journal.pone.0099864 - @@ -37656,7 +33864,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -37683,7 +33891,7 @@ For example, A and B may be gene products and binding of B by A positively regul descending limb of loop of Henle http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + @@ -37696,7 +33904,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + FMA @@ -37720,9 +33928,14 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + + + + + + @@ -37738,7 +33951,6 @@ For example, A and B may be gene products and binding of B by A positively regul The proximal straight tubule is the part of the descending limb that extends from the proximal convoluted tubule to the descending thin tubule. TODO - is S3 exactly coincident with PST? todo - ensure relationships work across species (loop of Henle) - Portion of the renal tubule which is just posterior to the proximal convoluted tubule.[TAO] UBERON:0005166 BTO:0000055 EMAPA:29661 @@ -37762,15 +33974,11 @@ For example, A and B may be gene products and binding of B by A positively regul proximal straight tubule - + - - - - - + @@ -37783,20 +33991,13 @@ For example, A and B may be gene products and binding of B by A positively regul - + MA - - MA uses subclass - GOC:mtg_kidney_jan10 - - - - - + MA @@ -37805,15 +34006,6 @@ For example, A and B may be gene products and binding of B by A positively regul The proximal straight tubule is the part of the descending limb that extends from the proximal convoluted tubule to the descending thin tubule. GO:0072020 - - - - Portion of the renal tubule which is just posterior to the proximal convoluted tubule.[TAO] - 2012-08-14 - TAO:0005291 - TAO - ZFIN:curator - @@ -37847,7 +34039,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -37862,8 +34054,6 @@ For example, A and B may be gene products and binding of B by A positively regul The first segment of the nephron lying just downstream from the loop of Henle, immediately after the macula densa. - a portion of kidney nephron between the loop of Henle and the collecting duct system[Wikipedia:Distal_convoluted_tubule]. - in humans it is responsible for the reabsorption of about 5% of filtered sodium via the thiazide-sensitive Na-Cl symporter. EMAPA:28393 EV:0100389 FMA:17721 @@ -37885,7 +34075,7 @@ For example, A and B may be gene products and binding of B by A positively regul distal convoluted tubule https://upload.wikimedia.org/wikipedia/commons/2/21/Kidney_nephron.png - + @@ -37898,7 +34088,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + EMAPA GO MA-modified-from-isa @@ -37909,12 +34099,6 @@ For example, A and B may be gene products and binding of B by A positively regul The first segment of the nephron lying just downstream from the loop of Henle, immediately after the macula densa. GO:0072025 - - - - a portion of kidney nephron between the loop of Henle and the collecting duct system[Wikipedia:Distal_convoluted_tubule]. - Wikipedia:Distal_convoluted_tubule - @@ -38026,9 +34210,13 @@ For example, A and B may be gene products and binding of B by A positively regul - + + + + + + The anus and surrounding regions. Encompasses both internal and external regions, where present. - Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] EFO:0000847 EHDAA2:0000122 EHDAA:2931 @@ -38052,32 +34240,12 @@ For example, A and B may be gene products and binding of B by A positively regul https://github.com/obophenotype/uberon/issues/507 http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray408.png - - - - - - - - - cjm - The anus and surrounding regions. Encompasses both internal and external regions, where present. https://orcid.org/0000-0002-6601-2165 - - - - Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] - 2012-09-17 - VHOG:0000395 - VHOG - ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 - http://bgee.unil.ch/ - @@ -38134,13 +34302,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system. - - Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO] - Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO] - System that provides physical support to the organism.[AAO] - By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG] - skeletal - GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates AAO:0000566 BTO:0001486 CALOHA:TS-1320 @@ -38176,50 +34337,6 @@ For example, A and B may be gene products and binding of B by A positively regul VSAO:0000027 http://dx.plos.org/10.1371/journal.pone.0051070 - - - - Anatomical system consisting of multiple elements and tissues that provides physical support.[TAO] - 2012-08-14 - TAO:0000434 - TAO - TAO:wd - - - - - Anatomical system that is a multi-element, multi-tissue anatomical cluster that consists of the skeleton and the articular system.[VSAO] - 2012-08-14 - VSAO:0000027 - VSAO - GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 - PSPUB:0000170 - - - - - System that provides physical support to the organism.[AAO] - 2012-06-20 - AAO:0000566 - AAO - AAO:LAP - - - - - By taking a holistic approach, integration of the evidence from molecular and developmental features of model organisms, the phylogenetic distribution in the 'new animal phylogeny' and the earliest fossilized remains of mineralized animal skeletons suggests independent origins of the skeleton at the phylum level.[debated][VHOG] - 2012-09-17 - VHOG:0001254 - VHOG - DOI:10.1159/000324245 Donoghue PCJ, Sansom IJ, Origin and early evolution of vertebrate skeletonization. Microscopy research and technique (2002) - http://bgee.unil.ch/ - - - - - GO defines skeletal system very generically: The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton) GO:0001501; however, all annotations are to vertebrates - GO - @@ -38246,7 +34363,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -38269,14 +34386,14 @@ For example, A and B may be gene products and binding of B by A positively regul kidney arcuate artery https://upload.wikimedia.org/wikipedia/commons/8/87/2610_The_Kidney.jpg - + - + MA @@ -38317,16 +34434,11 @@ For example, A and B may be gene products and binding of B by A positively regul - + A tube extending from the mouth to the anus. - The alimentary or digestive tract, and associated organs.[TAO] - The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] - FMA also has a term 'gastrointestinal tract', but this includes the liver. - we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509 - we following Kardong in naming the entire tube from mouth to anus the alimentary canal. Kardong calls the portion of this tract that excludes buccal cavity and pharynx the 'alimentary canal', consider adding an extra class for this gut AAO:0010023 BILA:0000083 @@ -38335,10 +34447,8 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA2:0000726 EHDAA:518 EMAPA:16247 - FBbt:00003125 FMA:45615 MA:0000917 - MESH:D041981 NCIT:C34082 TAO:0000112 TGMA:0001819 @@ -38360,14 +34470,14 @@ For example, A and B may be gene products and binding of B by A positively regul digestive tract - + - + NCBIBook:NBK10107 @@ -38389,50 +34499,6 @@ For example, A and B may be gene products and binding of B by A positively regul DOI:10.1371/journal.pone.0016309 - - - - The alimentary or digestive tract, and associated organs.[TAO] - 2012-08-14 - TAO:0000112 - TAO - ZFIN:curator - - - - - The bilaterian gut is typically a complete tube that opens to the exterior at both ends. It consists of mouth, foregut, midgut, hindgut, and anus (reference 1); Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0000309 - VHOG - ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.203, ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 - http://bgee.unil.ch/ - - - - - FMA also has a term 'gastrointestinal tract', but this includes the liver. - FMA - - - - - we place the MA and EMAPA class here, although the intent is probably a smaller region. See https://github.com/obophenotype/uberon/issues/509 - MA - - - - - FBbt:00003125 - - - - - - MESH:D041981 - - https://github.com/biopragmatics/biomappings - @@ -38527,12 +34593,7 @@ For example, A and B may be gene products and binding of B by A positively regul Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]. - Portion of tissue composed of contractile fibers.[TAO] - It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG] - muscular muscle - AAO:0011066 - EMAPA:32715 EMAPA:37474 EV:0100146 FMA:5022 @@ -38558,25 +34619,6 @@ For example, A and B may be gene products and binding of B by A positively regul Organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work[GO]. GO:0007517 - - - - Portion of tissue composed of contractile fibers.[TAO] - 2012-08-14 - TAO:0005145 - TAO - ZFIN:curator - - - - - It seems clear that the metazoan ancestor inherited from its unicellular descendants an actin cytoskeleton and motor-proteins of the myosin superfamily. Within metazoans, these two molecules were arranged into effective contractile units, the muscles. The basic trends for muscle evolution are already expressed in the diploblastic taxa.[well established][VHOG] - 2012-09-17 - VHOG:0001245 - VHOG - ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.75 - http://bgee.unil.ch/ - @@ -38604,17 +34646,11 @@ For example, A and B may be gene products and binding of B by A positively regul An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition]. Note that in FMA an artery is a tree, whereas AEO/JB defines it as a tube; FMA includes a separate class for what it calls the trunk. Classification in this ontology may currently (Jan 2012) represent a mix of both schemes, although we are gradually revising in the direction of the AEO scheme. - Part of the circulatory system composed of blood vessels which carry oxygenated blood away from the heart to the rest of the body.[AAO] - The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] - arterial - Some arthropods have primitive arterial systems but this term refers to arteries in a true closed circulatory system. - AAO:0010211 AEO:0000208 BTO:0000573 CALOHA:TS-0054 EFO:0000814 - EHDAA2:0000143 EHDAA2:0003253 EMAPA:35147 EV:0100026 @@ -38652,25 +34688,6 @@ For example, A and B may be gene products and binding of B by A positively regul An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition]. AEO:JB - - - - Part of the circulatory system composed of blood vessels which carry oxygenated blood away from the heart to the rest of the body.[AAO] - 2012-06-20 - AAO:0010211 - AAO - AAO:BJB - - - - - The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] - 2012-09-17 - VHOG:0001251 - VHOG - DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006) - http://bgee.unil.ch/ - @@ -38716,10 +34733,6 @@ For example, A and B may be gene products and binding of B by A positively regul Any of the tubular branching vessels that carry blood from the capillaries toward the heart. TODO - check with MA - vein vs venous blood vessel - Part of the circulatory system composed of blood vessels which carry blood from other organs, tissues, and cells to the heart.[AAO] - The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] - venous - venous subtree venous vessel AAO:0010212 @@ -38764,25 +34777,6 @@ For example, A and B may be gene products and binding of B by A positively regul Any of the tubular branching vessels that carry blood from the capillaries toward the heart. Wikipedia:Vein - - - - Part of the circulatory system composed of blood vessels which carry blood from other organs, tissues, and cells to the heart.[AAO] - 2012-06-20 - AAO:0010212 - AAO - AAO:BJB - - - - - The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] - 2012-09-17 - VHOG:0001743 - VHOG - DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006) - http://bgee.unil.ch/ - @@ -38823,8 +34817,6 @@ For example, A and B may be gene products and binding of B by A positively regul Outermost layer of an organ[WP]. - cortical - this class is used more generically than in FMA, and includes e.g. cortex of hair EFO:0000383 EHDAA:9344 FMA:61109 @@ -38845,12 +34837,6 @@ For example, A and B may be gene products and binding of B by A positively regul Outermost layer of an organ[WP]. Wikipedia:Cortex_(anatomy) - - - - this class is used more generically than in FMA, and includes e.g. cortex of hair - FMA - @@ -38977,7 +34963,6 @@ For example, A and B may be gene products and binding of B by A positively regul One of the minute vessels that collect deoxygenated blood from the capillary plexuses returns it to the veins. - Multi-tissue structure part of the blood vasculature formed by the anastomosis of capillaries. Venules carry blood toward the heart.[TAO] BTO:0002626 EMAPA:35917 FMA:63130 @@ -39007,15 +34992,6 @@ For example, A and B may be gene products and binding of B by A positively regul MESH:A07.231.432.952 MP:0004125 - - - - Multi-tissue structure part of the blood vasculature formed by the anastomosis of capillaries. Venules carry blood toward the heart.[TAO] - 2012-08-14 - TAO:0005315 - TAO - ZFIN:curator - @@ -39071,8 +35047,6 @@ For example, A and B may be gene products and binding of B by A positively regul The smallest division of the artery located between the muscular arteries and the capillaries[GO]. - Multi-tissue structure part of the blood vasculature, feeds into capillaries. Arterioles carry blood away from the heart.[TAO] - Small, terminal branch of an artery which generally connects to capillaries.[AAO] AAO:0010253 BTO:0001997 EMAPA:35146 @@ -39107,24 +35081,6 @@ For example, A and B may be gene products and binding of B by A positively regul The smallest division of the artery located between the muscular arteries and the capillaries[GO]. GO:0014830 - - - - Multi-tissue structure part of the blood vasculature, feeds into capillaries. Arterioles carry blood away from the heart.[TAO] - 2012-08-14 - TAO:0002138 - TAO - ZFIN:curator - - - - - Small, terminal branch of an artery which generally connects to capillaries.[AAO] - 2012-06-20 - AAO:0010253 - AAO - AAO:BJB - @@ -39146,14 +35102,15 @@ For example, A and B may be gene products and binding of B by A positively regul + - - + + @@ -39166,7 +35123,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -39182,11 +35139,6 @@ For example, A and B may be gene products and binding of B by A positively regul A vessel through which blood circulates in the body. consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus - Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG] - Any of the vessels through which blood circulates in the body.[AAO] - The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] - annelids have blood vessels, but this class is not applicable to annelids. - FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX vascular element AAO:0011004 AEO:0000207 @@ -39225,34 +35177,34 @@ For example, A and B may be gene products and binding of B by A positively regul blood vessel http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg - + - + - + - + AEO - + EHDAA2 - + GO:0072360 @@ -39262,40 +35214,6 @@ For example, A and B may be gene products and binding of B by A positively regul BTO:0001102 Wikipedia:Blood_vessel - - - - Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG] - 2012-09-17 - VHOG:0001250 - VHOG - http://bgee.unil.ch/ - - - - - Any of the vessels through which blood circulates in the body.[AAO] - 2012-06-20 - AAO:0011004 - AAO - AAO:EJS - - - - - The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] - 2012-09-17 - VHOG:0001250 - VHOG - DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006) - http://bgee.unil.ch/ - - - - - FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX - FMA - @@ -39364,9 +35282,6 @@ For example, A and B may be gene products and binding of B by A positively regul Any of the smallest blood vessels connecting arterioles with venules. not all sources agree capillary is a blood vessel - consider adopting EMAPA superclass of vascular element - Any of the tiny blood vessels connecting the arterioles to the venules.[AAO] - The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] - capillaries lack tunica media and tunica adventitia; only the endothelial wall of the tunica intima belongs AAO:0010252 BTO:0002045 CALOHA:TS-2006 @@ -39405,25 +35320,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Capillary https://github.com/obophenotype/uberon/issues/137 - - - - Any of the tiny blood vessels connecting the arterioles to the venules.[AAO] - 2012-06-20 - AAO:0010252 - AAO - AAO:BJB - - - - - The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] - 2012-09-17 - VHOG:0001253 - VHOG - DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2006) - http://bgee.unil.ch/ - @@ -39463,7 +35359,6 @@ For example, A and B may be gene products and binding of B by A positively regul A layer of epithelium that lines the heart, blood vessels (endothelium, vascular), lymph vessels (endothelium, lymphatic), and the serous cavities of the body[MESH]. Simple squamous epithelium which lines blood and lymphatic vessels and the heart[FMA]. - endothelial BTO:0000393 CALOHA:TS-0278 EFO:0002548 @@ -39531,7 +35426,6 @@ For example, A and B may be gene products and binding of B by A positively regul An interconnected tubular multi-tissue structure contains fluid that is actively transported around the organism[ZFA]. Examples: vasculature of lung, vasculature of face. see also: vascular system. Consider merging? - vascular BTO:0003718 FMA:69050 TAO:0005249 @@ -39589,16 +35483,11 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical structure that is part of an embryo. - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO] - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO] - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO] - in FMA embryo is_a embryonic structure AAO:0000138 BILA:0000034 BTO:0000174 CALOHA:TS-2110 EFO:0000461 - FBbt:00004208 FMA:69067 GAID:407 MESH:D004628 @@ -39629,45 +35518,6 @@ For example, A and B may be gene products and binding of B by A positively regul BTO:0000174 ZFIN:curator - - - - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO] - 2012-06-20 - AAO:0000138 - AAO - AAO:BJB - - - - - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO] - 2012-08-14 - TAO:0001105 - TAO - ZFIN:curator - - - - - Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO] - 2012-08-14 - VSAO:0000178 - VSAO - ZFIN:curator - - - - - in FMA embryo is_a embryonic structure - FMA - - - - - FBbt:00004208 - - @@ -39724,8 +35574,6 @@ For example, A and B may be gene products and binding of B by A positively regul An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen. - An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO] - general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs. AAO:0010386 BTO:0001491 EHDAA:512 @@ -39760,21 +35608,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Viscus https://github.com/obophenotype/mouse-anatomy-ontology/issues/14 - - - - An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO] - 2012-06-20 - AAO:0010386 - AAO - BTO:0001491 - - - - - general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs. - FMA - @@ -39811,17 +35644,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - @@ -39832,9 +35654,6 @@ For example, A and B may be gene products and binding of B by A positively regul A cardiac atrium that is in the right side of the heart. It receives deoxygenated blood. In mammals, this comes from the superior and inferior vena cava and the coronary sinus, and pumps it into the right ventricle through the tricuspid valve. - Right cardiac chamber which is continuous with the superior vena cava and inferior vena cava.[FMA] - The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG] - https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern AAO:0010248 BTO:0001703 EHDAA2:0000290 @@ -39871,22 +35690,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Right_atrium http://orcid.org/0000-0002-6601-2165 - - - - Right cardiac chamber which is continuous with the superior vena cava and inferior vena cava.[FMA] - FMA:7096 - - - - - The tetrapod clade develops a complete atrial septum and loses the fifth aortic arch altogether.[well established][VHOG] - 2012-09-17 - VHOG:0000328 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.620 - http://bgee.unil.ch/ - @@ -39918,7 +35721,6 @@ For example, A and B may be gene products and binding of B by A positively regul - @@ -39933,9 +35735,6 @@ For example, A and B may be gene products and binding of B by A positively regul Cardiac chamber in which blood enters the heart. - One of four heart chambers.[TAO] - One of two chambers of the heart which receive blood from the veins and forces it by muscular contration to the ventricle.[AAO] - In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG] AAO:0010246 BTO:0000903 CALOHA:TS-0437 @@ -39978,34 +35777,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Heart_atrium http://orcid.org/0000-0002-6601-2165 - - - - One of four heart chambers.[TAO] - 2012-08-14 - TAO:0000471 - TAO - ZFIN:curator - - - - - One of two chambers of the heart which receive blood from the veins and forces it by muscular contration to the ventricle.[AAO] - 2012-06-20 - AAO:0010246 - AAO - AAO:BJB - - - - - In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG] - 2012-09-17 - VHOG:0000175 - VHOG - ISBN:978-0721676678 Romer AS, Vertebrate body (1970) p.428 - http://bgee.unil.ch/ - @@ -40062,21 +35833,15 @@ For example, A and B may be gene products and binding of B by A positively regul The postcranial subdivision of skeleton structural components forming the long axis of the vertebrate body; in Danio, consisting of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins; in human consists of the bones of the vertebral column, the thoracic cage and the pelvis[ZFA+FMA]. - Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO] - The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO] - The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO] - The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG] axial skeleton AAO:0000034 EFO:0000942 EHDAA2:0000161 EHDAA:5049 - EMAPA:17214 EMAPA:37721 FMA:71221 MA:0002986 MAT:0000148 - MESH:D013131 MIAA:0000148 TAO:0000317 VHOG:0000317 @@ -40102,43 +35867,6 @@ For example, A and B may be gene products and binding of B by A positively regul https://sourceforge.net/tracker/?func=detail&aid=2983975&group_id=76834&atid=974957 https://sourceforge.net/tracker/?func=detail&atid=1205376&aid=2983977&group_id=76834 - - - - Skeletal subdivision of the central body axis including vertebrae, notochord, ribs, and sternum.[VSAO] - 2012-08-14 - VSAO:0000093 - VSAO - PSPUB:0000170 - - - - - The axial skeleton is formed by the vertebral column, a metameric, semi-flexible, arched bar located in the dorsal part of the trunk, and is formed by a series of cartilaginous or bony vertebrae. It provides suspension for the appendicular skeleton and protection for the spinal nerve cord.[AAO] - 2012-06-20 - AAO:0000034 - AAO - AAO:LAP - - - - - The post-cranial structural components forming the long axis of the vertebrate body; usually consists of the notochord, vertebrae, ribs, supraneurals, intermuscular bones, and unpaired median fins.[TAO] - 2012-08-14 - TAO:0000317 - TAO - ZFIN:curator - - - - - The axial musculoskeletal system represents the plesiomorphic locomotor engine of the vertebrate body, playing a central role in locomotion. In craniates, the evolution of the postcranial skeleton is characterized by two major transformations. First, the axial skeleton became increasingly functionally and morphologically regionalized. Second, the axial-based locomotion plesiomorphic for craniates became progressively appendage-based with the evolution of extremities in tetrapods.[well established][VHOG] - 2012-09-17 - VHOG:0000317 - VHOG - DOI:10.1186/1742-9994-8-4 Schilling N, Evolution of the axial system in craniates: morphology and function of the perivertebral musculature. Frontiers in Zoology (2011) - http://bgee.unil.ch/ - @@ -40152,13 +35880,6 @@ For example, A and B may be gene products and binding of B by A positively regul EMAPA:37721 MA:th - - - - MESH:D013131 - - https://github.com/biopragmatics/biomappings - @@ -40192,10 +35913,6 @@ For example, A and B may be gene products and binding of B by A positively regul Subdivision of skeleton which which consists of all the skeletal elements in in the pectoral and pelvic appendage complexes[cjm]. - Skeletal subdivision consisting of all the skeletal elements in the pectoral and pelvic appendage complexes.[VSAO] - Skeletal system that consists of the paired fins (pectoral or pelvic fins).[TAO] - The pectoral and pelvic girdles, which articulate with the axial skeleton, together with their associated limbs, the forelimbs and hind limbs, form the appendicular skeleton.[AAO] - ontologies differ in whether they treat the term appendicular skeleton as being the entire set of bones in the limbs, or whether the fore and hind limbs/fins are treated as seperate appendicular skeletons. Here we follow FMA, and treat the appendicular skeleton as the sum total of skeletal elements in the organism (this is evidenced by the fact that in FMA, skeleton of left/right upper/lower limb is part_of a appendicular skeleton, and subtypes of 'subdivision of appendicular skeleton'). We have separate classes such as 'skeleton of limb', and 'skeleton of hindlimb' for the 4 parts of the appendicular skeleton. In future the ZFA/TAO classes may be moved. AAO:0000747 EFO:0000951 EMAPA:32729 @@ -40206,7 +35923,6 @@ For example, A and B may be gene products and binding of B by A positively regul NCIT:C49477 SCTID:322050006 UMLS:C0222646 - VHOG:0001666 VSAO:0000076 Wikipedia:Appendicular_skeleton XAO:0003166 @@ -40233,40 +35949,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Appendicular_skeleton https://orcid.org/0000-0002-6601-2165 - - - - Skeletal subdivision consisting of all the skeletal elements in the pectoral and pelvic appendage complexes.[VSAO] - 2012-08-14 - VSAO:0000076 - VSAO - PSPUB:0000170 - https://orcid.org/0000-0002-6601-2165 - - - - - Skeletal system that consists of the paired fins (pectoral or pelvic fins).[TAO] - 2012-08-14 - TAO:0000027 - TAO - TAO:wd - - - - - The pectoral and pelvic girdles, which articulate with the axial skeleton, together with their associated limbs, the forelimbs and hind limbs, form the appendicular skeleton.[AAO] - 2012-06-20 - AAO:0000747 - AAO - AAO:LAP - - - - - ontologies differ in whether they treat the term appendicular skeleton as being the entire set of bones in the limbs, or whether the fore and hind limbs/fins are treated as seperate appendicular skeletons. Here we follow FMA, and treat the appendicular skeleton as the sum total of skeletal elements in the organism (this is evidenced by the fact that in FMA, skeleton of left/right upper/lower limb is part_of a appendicular skeleton, and subtypes of 'subdivision of appendicular skeleton'). We have separate classes such as 'skeleton of limb', and 'skeleton of hindlimb' for the 4 parts of the appendicular skeleton. In future the ZFA/TAO classes may be moved. - FMA - @@ -40306,10 +35988,6 @@ For example, A and B may be gene products and binding of B by A positively regul Organism subdivision which is the part of the body posterior to the cervical region (or head, when cervical region not present) and anterior to the caudal region. Includes the sacrum when present. - - - Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO] - Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO] AAO:0010339 BILA:0000116 BTO:0001493 @@ -40349,32 +36027,6 @@ For example, A and B may be gene products and binding of B by A positively regul UBERONREF:0000006 Wikipedia:Torso - - - - - ZFA - https://github.com/obophenotype/uberon/issues/378 - pending - - - - - Organism subdivision that is the part of the body posterior to the head and anterior to the tail.[AAO] - 2012-06-20 - AAO:0010339 - AAO - AAO:BJB - - - - - Organism subdivision which is the part of the body posterior to the head and anterior to the tail.[TAO] - 2012-08-14 - TAO:0001115 - TAO - ZFIN:curator - @@ -40402,20 +36054,19 @@ For example, A and B may be gene products and binding of B by A positively regul - + - - + + - - + + - @@ -40428,26 +36079,17 @@ For example, A and B may be gene products and binding of B by A positively regul - A paired organ of the urinary tract which has the production of urine as its primary function. - + A paired organ of the urinary tract that produces urine and maintains bodily fluid homeostasis, blood pressure, pH levels, red blood cell production and skeleton mineralization. - One of either of a pair of structures lying on either side of the dorsal aorta in which fluid balance is regulated and waste is excreted out in the form of urine.[AAO] - renal - + + AAO:0000250 BTO:0000671 CALOHA:TS-0510 - EFO:0000929 - EMAPA:17373 - EV:0100096 - FMA:7203 GAID:423 - MA:0000368 MAT:0000119 MESH:D007668 MIAA:0000119 - NCIT:C12415 - SCTID:181414000 UMLS:C0022646 Wikipedia:Kidney XAO:0003267 @@ -40464,41 +36106,25 @@ For example, A and B may be gene products and binding of B by A positively regul kidney - + - - - - - + FMA - - - - - definitional - - A paired organ of the urinary tract which has the production of urine as its primary function. + A paired organ of the urinary tract that produces urine and maintains bodily fluid homeostasis, blood pressure, pH levels, red blood cell production and skeleton mineralization. + PMID:25140012 + PMID:35003210 Wikipedia:Kidney http://anatomy.uams.edu/anatomyhtml/kidney.html - - - - - One of either of a pair of structures lying on either side of the dorsal aorta in which fluid balance is regulated and waste is excreted out in the form of urine.[AAO] - 2012-06-20 - AAO:0000250 - AAO - AAO:BJB + https://www.kidney.org/kidneydisease/top-5-jobs-kidneys-do @@ -40522,8 +36148,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -40531,11 +36157,6 @@ For example, A and B may be gene products and binding of B by A positively regul In mammals, the pronephros is the first of the three embryonic kidneys to be established and exists only transiently. In lower vertebrates such as fish and amphibia, the pronephros is the fully functional embryonic kidney and is indispensible for larval life[GO]. - A kidney formed of nephric tubules arising in the anterior region of the nephric ridge; forms only as a transient embryonic structure. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.748][VHOG] - Organ that serves as a transient kidney, providing osmoregulation during early developmental stages and then degenerating during metamorphosis.[AAO] - The embryonic kidney, present at the level of the third somite, is composed of two glomeruli fused at the midline, two pronephric tubules, and paired bilateral pronephric ducts that modify the composition of the blood filtrate before delivering it to the cloaca for excretion.Kimmel et al, 1995.[TAO] - In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG] - pronephric UBERON:0005794 AAO:0011089 BTO:0001541 @@ -40545,7 +36166,6 @@ For example, A and B may be gene products and binding of B by A positively regul EMAPA:16579 FMA:72170 MAT:0000117 - MESH:D060910 MIAA:0000117 NCIT:C34280 SCTID:308804007 @@ -40567,11 +36187,11 @@ For example, A and B may be gene products and binding of B by A positively regul Once the more complex mesonephros forms the pronephros undergoes apoptosis in amphibians. In fishes the nephron degenerates but the organ remains and becomes a component of the immune system[Wikipedia:Pronephros]. // TODO - check developmental relationships. Note that we previously include the ZFA/XAO terms under the more specific 'pronephric kidney', but these are now merged. TODO GCI: relationship: capable_of GO:0030104 pronephros - + - + @@ -40584,13 +36204,13 @@ For example, A and B may be gene products and binding of B by A positively regul - + OG - + ZFA @@ -40600,51 +36220,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0048793 Wikipedia:Pronephros - - - - A kidney formed of nephric tubules arising in the anterior region of the nephric ridge; forms only as a transient embryonic structure. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Kardong_KV, Vertebrates:_Comparative_Anatomy, p.748][VHOG] - 2012-09-17 - VHOG:0000037 - VHOG - http://bgee.unil.ch/ - - - - - Organ that serves as a transient kidney, providing osmoregulation during early developmental stages and then degenerating during metamorphosis.[AAO] - 2012-06-20 - AAO:0011089 - AAO - XAO:curator - - - - - The embryonic kidney, present at the level of the third somite, is composed of two glomeruli fused at the midline, two pronephric tubules, and paired bilateral pronephric ducts that modify the composition of the blood filtrate before delivering it to the cloaca for excretion.Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000151 - TAO - ZFIN:curator - - - - - In all vertebrate embryos, the kidney begins with the differentiation of a few renal tubules from the anterior end of the nephric ridge overlying the pericardial cavity. (...) This early-developing embryonic kidney is called the pronephros.[well established][VHOG] - 2012-09-17 - VHOG:0000037 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.637 - http://bgee.unil.ch/ - - - - - MESH:D060910 - - - https://github.com/biopragmatics/biomappings - @@ -40820,7 +36395,12 @@ For example, A and B may be gene products and binding of B by A positively regul - + + + + + + @@ -40830,9 +36410,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that consists of the muscular and skeletal systems. - Anatomical system that provides locomotion and physical support to the organism.[AAO] - There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG] - musculoskeletal AAO:0010546 CALOHA:TS-1311 EMAPA:32714 @@ -40854,16 +36431,6 @@ For example, A and B may be gene products and binding of B by A positively regul musculoskeletal system - - - - - - - - - check ctenophore - @@ -40872,25 +36439,6 @@ For example, A and B may be gene products and binding of B by A positively regul VSAO:curator https://github.com/obophenotype/uberon/issues/77 - - - - Anatomical system that provides locomotion and physical support to the organism.[AAO] - 2012-06-20 - AAO:0010546 - AAO - AAO:EJS - - - - - There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG] - 2012-09-17 - VHOG:0001275 - VHOG - DOI:10.1002/jez.b.21246 Shearman RM, Burke AC, The lateral somitic frontier in ontogeny and phylogeny. Journal of Experimental Zoology (2009) - http://bgee.unil.ch/ - @@ -40932,7 +36480,6 @@ For example, A and B may be gene products and binding of B by A positively regul The part of the coelemic cavity lumen that is enclosed by the walls of the thorax. - In many species, the diaphragm separates thoracic and abdominal cavities EMAPA:36497 FMA:7565 GAID:93 @@ -40991,7 +36538,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -41010,7 +36557,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + An anatomical structure which consists of juxtaglomerular cells, extraglomerular mesangial cells and the macula densa. The juxtaglomerular apparatus lies adjacent to the glomerulus and regulates kidney function by maintaining the blood flow to the kidney and the filtration rate[GO]. a microscopic structure in the kidney, which regulates the function of each nephron. The juxtaglomerular apparatus is named for its proximity to the glomerulus: it is found between the vascular pole of the renal corpuscle and the returning distal convoluted tubule of the same nephron. This location is critical to its function in regulating renal blood flow and glomerular filtration rate. The three cellular components of the apparatus are the macula densa, extraglomerular mesangial cells, and juxtaglomerular cells (also known as granular cells)[WP]. BTO:0005157 @@ -41032,24 +36579,24 @@ For example, A and B may be gene products and binding of B by A positively regul juxtaglomerular apparatus - + - + - + MA - + GO @@ -41099,6 +36646,7 @@ For example, A and B may be gene products and binding of B by A positively regul + @@ -41131,10 +36679,7 @@ For example, A and B may be gene products and binding of B by A positively regul The inner layer of the glomerulus, within the basement membrane surrounding the glomerular capillaries. - mesangial - WP considers this the same as glomerular mesangium. In MA, glomerular and extraglomerular are distingsuished. FMA class has no definition and is a type of stroma, which is inconsistent with our classification of this here. BTO:0002494 - EMAPA:28248 EMAPA:36561 FMA:84139 MA:0002617 @@ -41155,12 +36700,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Mesangium https://sourceforge.net/p/obo/foundational-model-of-anatomy-fma-requests/13/ - - - - WP considers this the same as glomerular mesangium. In MA, glomerular and extraglomerular are distingsuished. FMA class has no definition and is a type of stroma, which is inconsistent with our classification of this here. - MA - @@ -41180,8 +36719,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + + @@ -41198,24 +36738,24 @@ For example, A and B may be gene products and binding of B by A positively regul EDITOR_NOTE check MA part_ofs - should be spatially disjoint from renal glomerulus? extraglomerular mesangium - + - + - + MA - + MA @@ -41232,7 +36772,12 @@ For example, A and B may be gene products and binding of B by A positively regul - + + + + + + @@ -41240,15 +36785,11 @@ For example, A and B may be gene products and binding of B by A positively regul The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities. - Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]. - The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]. - In mammals it forms the peritoneal, pleural, and pericardial cavities UBERON:0000169 body cavity AEO:0000186 BTO:0001707 EHDAA2:0000267 - FBbt:00005060 FMA:85006 NCIT:C25444 RETIRED_EHDAA2:0003186 @@ -41273,52 +36814,18 @@ For example, A and B may be gene products and binding of B by A positively regul EDITOR_NOTE check the FMA placement here; ncit placement of body cavity here probably not correct coelemic cavity lumen - - - - - - - - - definitional - The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities. BTO:0001707 - - - - Anatomical space, part of the trunk that contains the pericardial and pleuroperitoneal cavities[ZFA]. - 2012-09-12 - ZFA:0001438 - ZFA - ZFIN:curator - - - - - The cavity within the body of all animals higher than the coelenterates and certain primitive worms, formed by the splitting of the embryonic mesoderm into two layers. In mammals it forms the peritoneal, pleural, and pericardial cavities[BTO]. - 2012-09-12 - BTO:0001707 - BTO - BTO - body cavity BTO:0001707 - - - - FBbt:00005060 - - @@ -41375,6 +36882,7 @@ For example, A and B may be gene products and binding of B by A positively regul + @@ -41382,21 +36890,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - + + + @@ -41410,13 +36906,6 @@ For example, A and B may be gene products and binding of B by A positively regul A flexible rod-shaped body found in embryos of all chordates. It is composed of cells derived from the mesoderm and defines the primitive axis of the embryo. In some chordates, it persists throughout life as the main axial support of the body, while in most vertebrates it becomes the nucleus pulposus of the intervertebral disc. The notochord is found ventral to the neural tube. - Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO] - Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO] - Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO] - relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO] - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG] - notochordal - In between vertebra the notochord becomes the nucleus pulposus, under it degenerates, and at anterior end in some species its tissue merges with some of the cranial bones.. Some organisms retain a post-embryonic notochord. AAO:0000327 BTO:0001768 CALOHA:TS-0690 @@ -41451,15 +36940,15 @@ For example, A and B may be gene products and binding of B by A positively regul notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + @@ -41478,19 +36967,19 @@ For example, A and B may be gene products and binding of B by A positively regul - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -41503,51 +36992,6 @@ For example, A and B may be gene products and binding of B by A positively regul https://github.com/obophenotype/uberon/issues/25 https://github.com/obophenotype/uberon/issues/271 - - - - Avascular multi-tissue structure composed of large vacuolated epithelial cells (chordablasts) and perichordal fibrous tissue.[VSAO] - 2012-08-14 - VSAO:0000032 - VSAO - PSPUB:0000170 - - - - - Rod-like principal supportive element of the embryo and larva, present in the midline just ventral to the neural tube, and differentiating during the segmentation period to form large vacuolated epithelial cells and a surrounding a sheath of fibrous and elastic layers. Layering of the sheath may differ in structure, thickness and development among groups; in cypriniforms there are actually three very thin layers to the sheath. A functional, well developed notochord is present throughout life in certain basal fish groups but not in cypriniforms. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000135 - TAO - ZFIN:curator - - - - - Slender rod of fibrous connective tissue surrounding a core of fluid-filled cells of mesodermal origin; it lies above the gut and directly beneath the spinal cord. The notochord is present during early development and in a few cases it is retained through life; however, usually the notochord is replaced by the vertebral column.[AAO] - 2012-06-20 - AAO:0000327 - AAO - AAO:LAP - - - - - relationship type change: differentiates_from mesoderm (AAO:0000304) CHANGED TO: develops_from mesoderm (UBERON:0000926)[AAO] - 2012-06-20 - AAO:0000327 - AAO - - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (3) a stiff, longitudinal rod of turgid cells along the dorsal part of the body that is called a notochord (...).[well established][VHOG] - 2012-09-17 - VHOG:0000199 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 - http://bgee.unil.ch/ - @@ -41575,18 +37019,10 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. - EDITOR_NOTE currently classified as an epithelial vesicle, consistent with EHDAA2 and https://github.com/obophenotype/uberon/wiki/The-neural-crest. Consider making 'somitic mesoderm' a separate term and correlate with regionalization processes. Consider moving ZFA term to 'trunk somite' as it is part of the trunk - Post-cranial axial segments which form sclerotome and dermomyotome.[AAO] - Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO] - relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO] - relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO] - relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO] - (...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG] - somitic mesodermal cluster AAO:0010569 AEO:0001015 @@ -41622,11 +37058,11 @@ For example, A and B may be gene products and binding of B by A positively regul somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + @@ -41639,13 +37075,13 @@ For example, A and B may be gene products and binding of B by A positively regul - + GOTAX:0000352 - + ZFA @@ -41661,58 +37097,6 @@ For example, A and B may be gene products and binding of B by A positively regul PMID:17237766 - - - - Post-cranial axial segments which form sclerotome and dermomyotome.[AAO] - 2012-06-20 - AAO:0010569 - AAO - AAO:EJS - - - - - Undifferentiated mesodermal components of early trunk or tail segments or metameres, derived from paraxial mesoderm; forms myotomes, sclerotomes and perhaps dermatomes. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000155 - TAO - ZFIN:curator - - - - - relationship loss: develops_from paraxial mesenchyme (TAO:0000942)[TAO] - 2012-08-14 - TAO:0000155 - TAO - - - - - relationship type change: OBO_REL:part_of trunk (TAO:0001115) CHANGED TO: develops_from trunk (UBERON:0002100)[TAO] - 2012-08-14 - TAO:0000155 - TAO - - - - - relationship type change: part_of paraxial mesoderm (AAO:0010568) CHANGED TO: develops_from paraxial mesoderm (UBERON:0003077)[AAO] - 2012-06-20 - AAO:0010569 - AAO - - - - - (...) cephalocordates and craniates belong to a group known as Somitichordata. Somitichordate synapomorphies include (1) somites (...) (reference 1); The idea that the last common ancestor of bilaterian animals (Urbilateria) was segmented has been raised recently on evidence coming from comparative molecular embryology (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0000191 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.40, DOI:10.1093/icb/43.1.137 Balavoine G, Adoutte A, The segmented urbilateria: a testable scenario. Integrative and Comparative Biology (2003) - http://bgee.unil.ch/ - @@ -41757,11 +37141,10 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + The macula densa is an area of specialized cells in the distal tubule that makes contact with the vascular pole of the glomerulus[GO]. - not part of a nephron or distal tubule in MA and FMA BTO:0003940 EMAPA:28399 FMA:86333 @@ -41777,24 +37160,24 @@ For example, A and B may be gene products and binding of B by A positively regul macula densa - + - + - + MA - + GO @@ -41804,12 +37187,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0072024 Wikipedia:Macula_densa - - - - not part of a nephron or distal tubule in MA and FMA - MA - @@ -41823,20 +37200,25 @@ For example, A and B may be gene products and binding of B by A positively regul + - - - - - - + + + + + + + + + + + + + + + + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. - EDITOR_NOTE consider including subclasses for pre- and post- migratory (e.g. sheets/paths/streams). - - A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO] - Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO] - A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831] - We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG] AAO:0010578 BTO:0001764 CALOHA:TS-0676 @@ -41849,7 +37231,6 @@ For example, A and B may be gene products and binding of B by A positively regul MIAA:0000066 NCIT:C34222 SCTID:361462002 - TAO:0000045 UMLS:C0027789 VHOG:0000057 Wikipedia:Neural_crest @@ -41869,66 +37250,45 @@ For example, A and B may be gene products and binding of B by A positively regul http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - - - - - + - + - - - - - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - - Hall and others restrict NC to vertebrates but we opt for a less restrictive constraint to avoid inconsistencies when areas such as P1 area of pallium in hagfishes inherit cell lineage from telecephalon-contributing NC cells - ISBN:0073040584 - - - - - + BTO - + PMID:11523831 - - pre migratory https://github.com/obophenotype/uberon/wiki/The-neural-crest - - - - - + PMID:11523831 @@ -41937,47 +37297,6 @@ For example, A and B may be gene products and binding of B by A positively regul A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. MP:0009846 - - - - - ISBN:0073040584 - PMID:17377535 - - - - - A cell population arising from the dorsolateral aspect of the central nervous system primordium during the segmentation period, and later migrating along stereotyped pathways to give rise to a diverse and well-defined set of cell types including pigment cells, peripheral neurons and glia, and head cartilage. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000045 - TAO - ZFIN:curator - - - - - Migratory cell population which delaminates from neural tube, borders surface ectoderm and neural ectoderm, and gives rise to many different tissue types.[AAO] - 2012-06-20 - AAO:0010578 - AAO - AAO:EJS - - - - - A well developed neural crest population is present in lampreys (Horigome et al. 1999 ; Tomsa & Langeland, 1999) and gnathostomes. chordate fossils from the early Cambrian (Yunnanozoan and Haikouella) with apparent neural-crest derived structures (pharyngeal denticles and pharyngeal skeletons resembling the striped mucocartilage of the branchial bars in lamprey ammocoete larvae), suggests that neural crest arose very early in vertebrate evolution (Chen et al. 1999; Holland & Chen, 2001). The invertebrate chordates apparently lack defini- tive neural crest. One marker of migrating neural crest in some vertebrates, the antibody HNK1, does not recognize any cells in amphioxus embryos (Holland, unpublished). Even so, in both amphioxus and tunicates, cells at the edges of the neural plate and adjacent nonneural ectoderm share some properties of neural crest[PMID:11523831] - PMID:11523831 - - - - - We conclude that the neural crest is a vertebrate novelty, but that neural crest cells and their derivatives evolved and diversified in a step-wise fashion - first by elaboration of neural plate border cells, then by the innovation or co-option of new or ancient metazoan cell fates.[well established][VHOG] - 2012-09-17 - VHOG:0000057 - VHOG - DOI:10.1111/j.1469-7580.2012.01495.x Hall BK, Gillis JA, Incremental evolution of the neural crest, neural crest cells and neural crest-derived skeletal tissues. J Anat (2012) - http://bgee.unil.ch/ - @@ -42019,9 +37338,6 @@ For example, A and B may be gene products and binding of B by A positively regul Embryonic ectoderm that gives rise to nervous tissue. - (...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG] - neurectodermal - we prefer neurectoderm to neural ectoderm since placodal ectoderm is not classified here AAO:0011074 BILA:0000039 CALOHA:TS-1212 @@ -42030,7 +37346,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA:255 EMAPA:16073 EV:0100004 - FBbt:00001057 FMA:87657 MAT:0000176 MIAA:0000176 @@ -42059,22 +37374,6 @@ For example, A and B may be gene products and binding of B by A positively regul Embryonic ectoderm that gives rise to nervous tissue. Wikipedia:Neuroectoderm - - - - (...) the ability of ectoderm to produce neuronal cells is a general metazoan feature.[well established][VHOG] - 2012-09-17 - VHOG:0000150 - VHOG - DOI:10.1046/j.1469-7580.2001.19910133.x Graham A. The development and evolution of the pharyngeal arches. J Anat (2001) - http://bgee.unil.ch/ - - - - - FBbt:00001057 - - @@ -42114,8 +37413,6 @@ For example, A and B may be gene products and binding of B by A positively regul The lower segment of the trunk, inferioposterior to the abdomen proper, in the transition area between the trunk and the lower limbs. - pelvic - MA and FMA differ in what they consider to be parts of the pelvis. MA includes ureter, urethra, urinary bladder, reproductive organs BTO:0001006 CALOHA:TS-2227 EFO:0002805 @@ -42150,12 +37447,6 @@ For example, A and B may be gene products and binding of B by A positively regul http://orcid.org/0000-0002-6601-2165 https://github.com/obophenotype/uberon/issues/720 - - - - MA and FMA differ in what they consider to be parts of the pelvis. MA includes ureter, urethra, urinary bladder, reproductive organs - MA - @@ -42196,10 +37487,6 @@ For example, A and B may be gene products and binding of B by A positively regul Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance. - One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO] - Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO] - Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO] - MA also has set of connective tissues AAO:0000098 BTO:0000421 CALOHA:TS-2009 @@ -42240,40 +37527,6 @@ For example, A and B may be gene products and binding of B by A positively regul http://dx.plos.org/10.1371/journal.pone.0051070 https://github.com/obophenotype/uberon/issues/23 - - - - One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO] - 2012-06-20 - AAO:0000098 - AAO - AAO:LAP - - - - - Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO] - 2012-08-14 - TAO:0001641 - TAO - TAO:wd - - - - - Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO] - 2012-08-14 - VSAO:0000017 - VSAO - GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 - PSPUB:0000170 - - - - - MA also has set of connective tissues - MA - @@ -42336,8 +37589,6 @@ For example, A and B may be gene products and binding of B by A positively regul Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO]. - - One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO] AAO:0000306 AEO:0000122 CALOHA:TS-0642 @@ -42368,15 +37619,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Muscle_tissue https://sourceforge.net/tracker/index.php?func=detail&aid=2801266&group_id=36855&atid=440764 - - - - One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO] - 2012-06-20 - AAO:0000306 - AAO - AAO:LAP - @@ -42403,21 +37645,22 @@ For example, A and B may be gene products and binding of B by A positively regul - + - + + + + + + Anatomical system that is involved in the production of hematopoietic cells. - Anatomical system that consists of the blood and blood forming tissues.[AAO] - Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG] - hematopoietic - In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes AAO:0011002 BTO:0000570 CALOHA:TS-0449 @@ -42455,57 +37698,22 @@ For example, A and B may be gene products and binding of B by A positively regul hematopoietic system - + - - - - - + FMA - - - - - definitional - Anatomical system that is involved in the production of hematopoietic cells. Wikipedia:Haematopoiesis - - - - Anatomical system that consists of the blood and blood forming tissues.[AAO] - 2012-06-20 - AAO:0011002 - AAO - AAO:EJS - - - - - Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG] - 2012-09-17 - VHOG:0001624 - VHOG - DOI:10.1016/j.coph.2010.05.004 Ellett F, Lieschke GJ, Zebrafish as a model for vertebrate hematopoiesis. Current Opinion in Pharmacology (2010) - http://bgee.unil.ch/ - - - - - In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes - WP - @@ -42591,7 +37799,6 @@ For example, A and B may be gene products and binding of B by A positively regul In amniote animal embryology, the epiblast is a tissue type derived either from the inner cell mass in mammals or the blastodisc in birds and reptiles. It lies above the hypoblast. In mammalian embryogenesis, the columnar cells of the epiblast are adjacent to the trophoblast, while the cuboidal cells of the hypoblast are closer to the blastocoele. The epiblast, whilst referred to as the primary ectoderm, differentiates to form all three layers of the trilaminar germ disc in a process called gastrulation[WP]. The outer of the two layers of the blastoderm that form during gastrulation, corresponding to primitive ectoderm during gastrulation and to the definitive ectoderm after gastrulation[ZFA]. MP says - tissue that gives rise to the ectoderm, endoderm and mesoderm of the embryo proper. In HOG, epiblast is part of primitive streak/blastpore, which is inconsistent with the MP definition of primitive streak as a ridge of the epiblast. Note that these terms, epiblast and hypoblast, are also used to describe layers of the avian embryonic blastoderm, but the layers so-named seem to be altogether different in these two kinds of vertebrate embryos(CVS). Consider obsoleting this as a grouping class - In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG] BTO:0004593 FMA:296704 MAT:0000067 @@ -42619,16 +37826,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Epiblast ZFIN:curator - - - - In pregastrula zebrafish embryos, the epiblast is an inverted cup of cells that sits on top of a large yolk cell. (...) In amniote embryos (mammals and birds), gastrulation initiates in an epithelial layer called the epiblast. Cells in the epiblast undergo an epithelial to mesenchymal transition (EMT), migrate through the primitive streak (PS), and incorporate in the middle (mesoderm) or outer (endoderm) layer. The presumptive definitive endoderm (DE) cells invade and displace an outer layer of extraembryonic tissue cells, the hypoblast in chick and the visceral endoderm (VE) in mouse, which form supporting structures such as the yolk sac.[uncertain][VHOG] - 2012-09-17 - VHOG:0000243 - VHOG - DOI:10.1146/annurev.cellbio.042308.113344 Zorn AM, Wells JM, Vertebrate endoderm development and organ formation. Annual Review of Cell Developmental Biology (2009) - http://bgee.unil.ch/ - @@ -42726,10 +37923,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. - Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO] - It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG] AAO:0011086 EFO:0001982 EMAPA:16189 @@ -42751,14 +37946,14 @@ For example, A and B may be gene products and binding of B by A positively regul presomitic mesoderm - + - + Bgee:AN @@ -42767,25 +37962,6 @@ For example, A and B may be gene products and binding of B by A positively regul Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. ZFIN:curator - - - - Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000279 - TAO - ZFIN:curator - - - - - It is reasonable to assume that the proximate invertebrate ancestor of the vertebrates had an amphioxus-like tail bud in its larval stage. This archetypal tail bud would have (...) (3) lacked any component of mesenchyme cells, (4) budded off new mesodermal segments directly, without any intervening zone of presomitic mesoderm (...). Then, early in vertebrate evolution, epithelium-to-mesenchyme interconversions (and the gene networks for effecting them) became prominent features of development. (...) In any case, conspicuous mesenchymal components tended to be added to the vertebrate tail bud itself. In addition, a mesenchymatous presomitic mesoderm (not a part of the tail bud proper) came to intervene between the tail bud and the forming somites.[well established][VHOG] - 2012-09-17 - VHOG:0000559 - VHOG - DOI:10.1006/dbio.2001.0460 Schubert M, Holland LZ, Dale Stokes M and Holland ND, Three Amphoxius Wnt Genes (AmphiWnt3, AmphiWnt5, and AmphiWnt6) Associated with the Tail Bud: the Evolution of Somitogenesis in Chordates. Developmental Biology (2001) - http://bgee.unil.ch/ - @@ -42818,19 +37994,14 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + In mammals, the pronephric duct is the predecessor of the Wolffian duct[WP]. - Duct of the embryonic kidney, present bilaterally ventral to the somites and leading to the anal region where it empties separately from, and just posterior to the anus. Kimmel et al, 1995.[TAO] - The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] - (...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG] AAO:0011088 - BTO:0005991 NCIT:C34279 SCTID:361406002 TAO:0000150 UMLS:C1283945 - VHOG:0000082 Wikipedia:Pronephric_duct XAO:0000063 ZFA:0000150 @@ -42843,11 +38014,11 @@ For example, A and B may be gene products and binding of B by A positively regul The pronephric duct collects the filtrate from the pronephric tubules and opens to the exterior of the pronephric kidney[GOC:mtg_kidney_jan10, PMID:15647339, XAO:0000063, ZFA:0000150] pronephric duct - + - + @@ -42860,13 +38031,13 @@ For example, A and B may be gene products and binding of B by A positively regul - + Wikipedia - + XAO @@ -42875,42 +38046,6 @@ For example, A and B may be gene products and binding of B by A positively regul In mammals, the pronephric duct is the predecessor of the Wolffian duct[WP]. Wikipedia:Pronephric_duct - - - - Duct of the embryonic kidney, present bilaterally ventral to the somites and leading to the anal region where it empties separately from, and just posterior to the anus. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000150 - TAO - ZFIN:curator - - - - - The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] - 2012-09-17 - VHOG:0000082 - VHOG - http://bgee.unil.ch/ - - - - - (...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG] - 2012-09-17 - VHOG:0000082 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.686 - http://bgee.unil.ch/ - - - - - BTO:0005991 - - - https://github.com/biopragmatics/biomappings - @@ -42957,11 +38092,6 @@ For example, A and B may be gene products and binding of B by A positively regul Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted]. - Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO] - Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO] - relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO] - Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG] - EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac ventral lateral plate mesoderm AAO:0011006 EFO:0003489 @@ -42994,48 +38124,6 @@ For example, A and B may be gene products and binding of B by A positively regul Blood islands are structures in the developing embryo which lead to many different parts of the circulatory system. They primarily derive from plexuses formed from angioblasts. Within them, vacuoles appear through liquefaction of the central part of the syncytium into plasma. The lumen of the blood vessels thus formed is probably intracellular. The flattened cells at the periphery form the endothelium. The nucleated red blood corpuscles develop either from small masses of the original angioblast left attached to the inner wall of the lumen or directly from the flat endothelial cells. In either case the syncytial mass thus formed projects from and is attached to the wall of the vessel. Such a mass is known as a blood island and hemoglobin gradually accumulates within it. Later the cells on the surface round up, giving the mass a mulberry-like appearance. Then the red blood cells break loose and are carried away in the plasma. Such free blood cells continue to divide. Blood islands have been seen in the area vasculosa in the omphalomesenteric vein and arteries, and in the dorsal aorta[WP, unvetted]. Wikipedia:Blood_island_of_umbilical_vesicle - - - - Nests of developing blood cells arising late in the segmentation period from the intermediate mass, and located in the anterior-ventral tail, just posterior to the yolk extension. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000094 - TAO - ZFIN:curator - - - - - Region located on the ventral surface of the developing embryo that is a site of hematopoiesis and that is analogous to the yolk sac blood islands of higher vertebrates.[AAO] - 2012-06-20 - AAO:0011006 - AAO - AAO:EJS - - - - - relationship loss: part_of intermediate cell mass of mesoderm (TAO:0000033)[TAO] - 2012-08-14 - TAO:0000094 - TAO - - - - - Small clusters of mesodermal cells called blood islands mark the embryonic debut of the cardiovascular system (in vertebrates) (reference 1); In birds and mammals, primitive hemangioblasts are extraembryonic, populating the yolk sac as the so-called blood islands (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0000085 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.450, DOI:10.1146/annurev.cellbio.22.010605.093317 Hartenstein V, Blood cells and blood cell development in the animal kingdom. Annual Review of Cell and Developmental Biology (2006) - http://bgee.unil.ch/ - - - - - EHDAA2 distinguishes 3 types, but does not have a superclass. The VHOG class may refer to yolk sac - EHDAA2 - @@ -43055,9 +38143,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + @@ -43071,9 +38159,6 @@ For example, A and B may be gene products and binding of B by A positively regul The intermediate mesoderm is located between the lateral mesoderm and the paraxial mesoderm. It develops into the kidney and gonads. - Mesoderm between somite and lateral plate. Traditionally thought to give rise to the urogenital system.[AAO] - (...)the mesoderm of a developing vertebrate transitionally differentiates into the following sub-types: Chordamesoderm (also known as axial mesoderm) which later on gives rise to notochord in all chordates, Paraxial mesoderm, Intermediate mesoderm, Lateral plate mesoderm (reference 1); The mesoderm is present in Bilateria, therefore they are sometimes called triploblasts. Ectoderm and endoderm are usually organized as epithelial layers, while mesoderm can be epithelial or a compact, three-dimensional tissue.[well established][VHOG] - all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). AAO:0010575 EMAPA:16056 EMAPA:16178 @@ -43099,34 +38184,34 @@ For example, A and B may be gene products and binding of B by A positively regul intermediate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + - + AAO - + EMAPA - + XAO @@ -43136,31 +38221,6 @@ For example, A and B may be gene products and binding of B by A positively regul GOC:curators Wikipedia:Intermediate_mesoderm - - - - Mesoderm between somite and lateral plate. Traditionally thought to give rise to the urogenital system.[AAO] - 2012-06-20 - AAO:0010575 - AAO - AAO:EJS - - - - - (...)the mesoderm of a developing vertebrate transitionally differentiates into the following sub-types: Chordamesoderm (also known as axial mesoderm) which later on gives rise to notochord in all chordates, Paraxial mesoderm, Intermediate mesoderm, Lateral plate mesoderm (reference 1); The mesoderm is present in Bilateria, therefore they are sometimes called triploblasts. Ectoderm and endoderm are usually organized as epithelial layers, while mesoderm can be epithelial or a compact, three-dimensional tissue.[well established][VHOG] - 2012-09-17 - VHOG:0000087 - VHOG - Wikipedia:Mesoderm, ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.43 - http://bgee.unil.ch/ - - - - - all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). - ZFA - @@ -43218,7 +38278,6 @@ For example, A and B may be gene products and binding of B by A positively regul The axial mesoderm includes the prechordal mesoderm and the chordamesoderm. It gives rise to the prechordal plate and to the notochord. - The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] AAO:0011017 EFO:0003647 TAO:0001204 @@ -43241,15 +38300,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0048318 Wikipedia:Chordamesoderm - - - - The portion of the mesoderm underlying the midline of the embryo. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] - 2012-09-17 - VHOG:0000107 - VHOG - http://bgee.unil.ch/ - @@ -43264,33 +38314,25 @@ For example, A and B may be gene products and binding of B by A positively regul - - + Paired organ that connects the primitive kidney Wolffian body (or mesonephros) to the cloaca and serves as the anlage for certain male reproductive organs. the Wolffian duct is what remains of the pronephric duct after the atrophy of the pronephros[WP]. In Zebrafish: Duct of the adult kidney (mesonephros), present bilaterally ventral to the somites and leading to the cloacal chamber[ZFA]. Consider adding subclasses for male and female specific variants TODO - mesonephric portion of the nephric duct - Anatomical structure consisting of either of a pair of longitudinal ducts which carry urine and in males, sperm, to the cloaca.[AAO] - The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] - (...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG] - In the male the Wolffian duct persists, and forms for example the epididymis, the ductus deferens, the ejaculatory duct, seminal vesicle and efferent ducts. AAO:0000637 - BTO:0005990 EHDAA2:0001243 EHDAA:1590 - EMAPA:16577 GAID:1315 MESH:D014928 NCIT:C26469 SCTID:308800003 TAO:0000546 UMLS:C0043204 - VHOG:0000082 Wikipedia:Mesonephric_duct XAO:0000242 ZFA:0000546 @@ -43307,7 +38349,7 @@ For example, A and B may be gene products and binding of B by A positively regul mesonephric duct http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png - + @@ -43320,7 +38362,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + EHDAA2 @@ -43331,42 +38373,6 @@ For example, A and B may be gene products and binding of B by A positively regul ZFIN:curator https://github.com/obophenotype/uberon/issues/28 - - - - Anatomical structure consisting of either of a pair of longitudinal ducts which carry urine and in males, sperm, to the cloaca.[AAO] - 2012-06-20 - AAO:0000637 - AAO - AAO:BJB - - - - - The first-formed kidney duct, which drains the kidney of most anamniotes and becomes the ductus deferens of male amniotes. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-3, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG] - 2012-09-17 - VHOG:0000082 - VHOG - http://bgee.unil.ch/ - - - - - (...) in all craniates, the archinephric duct develops in embryogeny.[well established][VHOG] - 2012-09-17 - VHOG:0000082 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.686 - http://bgee.unil.ch/ - - - - - BTO:0005990 - - - https://github.com/biopragmatics/biomappings - @@ -43410,12 +38416,10 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. - The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO] - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] AAO:0011072 BTO:0001765 DHBA:10153 @@ -43424,7 +38428,6 @@ For example, A and B may be gene products and binding of B by A positively regul EHDAA:902 EMAPA:35593 FMA:293879 - MESH:D054258 NCIT:C34225 RETIRED_EHDAA2:0001252 TAO:0000132 @@ -43444,34 +38447,34 @@ For example, A and B may be gene products and binding of B by A positively regul neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -43483,33 +38486,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Neural_plate ZFIN:curator - - - - The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000132 - TAO - ZFIN:curator - - - - - (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...).[well established][VHOG] - 2012-09-17 - VHOG:0000068 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.28 - http://bgee.unil.ch/ - - - - - MESH:D054258 - - - https://github.com/biopragmatics/biomappings - @@ -43532,23 +38508,14 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. - Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO] - Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG] - note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here) AAO:0010568 EFO:0003515 EMAPA:16183 @@ -43573,7 +38540,7 @@ For example, A and B may be gene products and binding of B by A positively regul paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -43586,7 +38553,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + Bgee:AN @@ -43596,31 +38563,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0048339 https://github.com/obophenotype/uberon/issues/30 - - - - Mesoderm lateral to the neural tube and notochord that is divided into cranial and post-cranial portions. The trunk portions further segment into somites.[AAO] - 2012-06-20 - AAO:0010568 - AAO - AAO:EJS - - - - - Presently, Cephalochordata, Urochordata, and Vertebrata are placed as subphyla of the phylum Chordata, in which the overall organization of embryonic tissues (dorsal hollow nerve cord, ventral digestive tract, axial notochord, and bilateral paraxial mesoderm) is largely conserved. In contrast, the echinoderms and hemichordates are sister groups of the chordates and they lack the notochord and paraxial mesoderm. Thus, the basic mesodermal organization of vertebrates must have appeared first in the common ancestor of the chordates.[well established][VHOG] - 2012-09-17 - VHOG:0000114 - VHOG - DOI:10.1002/dvdy.21177 Kusakabe R and Kuratani S. Evolutionary perspectives from development of mesodermal components in the lamprey. Developmental dynamics (2007) - http://bgee.unil.ch/ - - - - - note that all AOs differ in the relationship between this structure and the mesoderm; in ZFA it is a subclass (and this is implied by the GO definition and GO relationships), in AAO it is part of, and in EHDAA2 it develops from the mesoderm (but in EHDAA2 the naming convention is to use 'paraxial mesenchyme', rather than 'paraxial mesoderm'). Also in ZFA it is part of the trunk whereas this conflicts with the division into head and trunk in ehdaa2 (which we follow here) - ZFA - @@ -43658,7 +38600,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -43672,10 +38614,6 @@ For example, A and B may be gene products and binding of B by A positively regul Portion of the middle of the three primary germ layers of the embryo that resides on the periphery of the embryo, is continuous with the extra-embryonic mesoderm, splits into two layers enclosing the intra-embryonic coelom, and gives rise to body wall structures[MP]. - Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO] - The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] - A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG] - subclass of mesoderm in ZFA. UBERON:0006258 AAO:0010574 EHDAA2:0000919 @@ -43702,7 +38640,7 @@ For example, A and B may be gene products and binding of B by A positively regul lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -43715,7 +38653,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + EHDAA2 VHOG @@ -43726,40 +38664,6 @@ For example, A and B may be gene products and binding of B by A positively regul MP:0010117 Wikipedia:Lateral_plate_mesoderm - - - - Portion of mesoderm traditionally thought to give rise to limb bones and parts of the girdles.[AAO] - 2012-06-20 - AAO:0010574 - AAO - AAO:EJS - - - - - The portion of the mesoderm of the trunk of vertebrate embryos lying lateral to the intermediate mesoderm. [...] [It] subdivides into two plates: one dorsal, called the somatopleure, and one ventral, called the splanchnopleure. [Gastrulation:_From_cells_to_embryo_(2004)_Cold_Spring_Harbor, Glossary_XV, New_York:_Cold_Spring_Harbor_Laboratory_Press, Stern_CD][VHOG] - 2012-09-17 - VHOG:0000118 - VHOG - http://bgee.unil.ch/ - - - - - A ventrolateral zone of amphioxus mesoderm grows down to surround the gut. Homology of this zone to the lateral plate mesoderm of vertebrates is supported by site of origin and fate.[well established][VHOG] - 2012-09-17 - VHOG:0000118 - VHOG - DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) - http://bgee.unil.ch/ - - - - - subclass of mesoderm in ZFA. - ZFA - @@ -43799,20 +38703,17 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + - + Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. should probably be merged with heart rudiment. - Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO] - The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO] - relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO] AAO:0011044 BTO:0001887 NCIT:C34276 @@ -43827,15 +38728,15 @@ For example, A and B may be gene products and binding of B by A positively regul heart primordium - + - + - + @@ -43848,19 +38749,19 @@ For example, A and B may be gene products and binding of B by A positively regul - + ZFA - + ZFA - + XAO @@ -43869,32 +38770,6 @@ For example, A and B may be gene products and binding of B by A positively regul Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. ZFIN:curator - - - - Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline between 21 and 26 somites to form the heart rudiment or cone. Stainier 2001.[TAO] - 2012-08-14 - TAO:0000028 - TAO - ZFIN:curator - - - - - The fused aspects of ventral mesoderm, which have migrated from either side of the prechordal plate, and fused ventrally, just behind the cement gland. They will give rise to the endocardium at NF stage 27&28.[AAO] - 2012-06-20 - AAO:0011044 - AAO - XAO:curator - - - - - relationship loss: develops_from lateral mesoderm (TAO:0001065)[TAO] - 2012-08-14 - TAO:0000028 - TAO - @@ -43915,15 +38790,11 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. - Skeletogenic portion of somites.[AAO] - The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG] - part_of somite in XAO AAO:0010571 AEO:0000212 - BTO:0006255 EHDAA2:0003439 EMAPA:31159 FMA:295652 @@ -43944,11 +38815,11 @@ For example, A and B may be gene products and binding of B by A positively regul sclerotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + - + @@ -43967,13 +38838,13 @@ For example, A and B may be gene products and binding of B by A positively regul - + VHOG:0000680 - + ZFA @@ -43984,39 +38855,6 @@ For example, A and B may be gene products and binding of B by A positively regul XB:curator https://github.com/obophenotype/uberon/issues/316 - - - - Skeletogenic portion of somites.[AAO] - 2012-06-20 - AAO:0010571 - AAO - AAO:EJS - - - - - The vertebrate sclerotome has no equivalent in amphioxus and is a novelty linked with the evolution of the axial skeleton.[well established][VHOG] - 2012-09-17 - VHOG:0000680 - VHOG - DOI:10.1073/pnas.97.9.4449 Shimeld SM and Holland PW. Vertebrate innovations. PNAS (2000) - http://bgee.unil.ch/ - - - - - part_of somite in XAO - XAO - - - - - BTO:0006255 - - - https://github.com/biopragmatics/biomappings - @@ -44045,7 +38883,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types. - this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs AAO:0010015 AEO:0000024 BILA:0000024 @@ -44109,9 +38946,6 @@ For example, A and B may be gene products and binding of B by A positively regul Portion of tissue composed of mesenchymal cells (motile cells that develop from epthelia via an epithelial to mesenchymal transition) and surrounding extracellular material. Mesenchyme has different embryological origins in different metazoan taxa - in many invertebrates it derives in whole or part from ectoderm. In vertebrates it derives largely from mesoderm, and sometimes the terms are used interchangeably, e.g. lateral plate mesoderm/mesenchyme. the relationship to mesoderm is weaker than develops_from in order to have classes such as 'head mesenchyme from mesoderm' make sense - A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO] - Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO] - mesenchymal AAO:0010427 AEO:0000145 BTO:0001393 @@ -44146,24 +38980,6 @@ For example, A and B may be gene products and binding of B by A positively regul https://en.wikipedia.org/wiki/Mesenchyme https://github.com/obophenotype/uberon/issues/1641 - - - - A mesh-like cell arrangement, less compact than an epithelium. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000393 - TAO - ZFIN:curator - - - - - Portion of tissue consisting of loosely organized undifferentiated mesodermal cells that give rise to such structures as connective tissues, blood, lymphatics, bone, and cartilage.[AAO] - 2012-06-20 - AAO:0010427 - AAO - AAO:EJS - @@ -44203,8 +39019,6 @@ For example, A and B may be gene products and binding of B by A positively regul An organ involved in reproduction. - GO uses genitalia for the singular organ - EMAPA:17381 EMAPA:37731 MA:0001752 MESH:D005835 @@ -44230,12 +39044,6 @@ For example, A and B may be gene products and binding of B by A positively regul An organ involved in reproduction. UBERON:xp - - - - GO uses genitalia for the singular organ - GO - @@ -44281,7 +39089,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -44289,8 +39097,6 @@ For example, A and B may be gene products and binding of B by A positively regul One of the two embryological structures that give rise to the kidney (the other is the ureteric bud). The metanephric blastema mostly develops into nephrons, but can also form parts of the collecting duct system.[WP]. Metanephric mesenchyme is the tissue made up of loosely connected mesenchymal cells in the metanephros[GO]. - A mass of intermediate mesodermal cells around the distal end of the ureteric bud that gives rise to nephrons in the metanephric kidney. [TFD][VHOG] - When the ureteric buds emerge from the nephric duct, they enter the metanephrogenic mesenchyme. The ureteric buds induce this mesenchymal tissue to condense around them and differentiate into the nephrons of the mammalian kidney. As this mesenchyme differentiates, it tells the ureteric bud to branch and grow.[well established][VHOG] EHDAA2:0004062 EHDAA:4041 EHDAA:5021 @@ -44309,14 +39115,14 @@ For example, A and B may be gene products and binding of B by A positively regul Genes: The positional specification of the metanephrogenic mesenchyme is negatively regulated by Foxc1 and Foxc2. Next the permanent kidney forming metanephrogenic mesenchyme is specified by Hox11 genes. The competence to respond to ureteric bud inducers is regulated by WT1. GDNF secretion restricted to posterior region by Robo2 and Sprouty1. The receptors for GDNF are synthesized in the nephric ducts and later in ureteric buds [ISBN:9780878932504 "Developmental Biology"] metanephric mesenchyme - + - + ISBN:9780878932504 @@ -44326,26 +39132,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0072075 Wikipedia:Metanephric_blastema - - - - A mass of intermediate mesodermal cells around the distal end of the ureteric bud that gives rise to nephrons in the metanephric kidney. [TFD][VHOG] - 2012-09-17 - VHOG:0000540 - VHOG - http://bgee.unil.ch/ - http://medical-dictionary.thefreedictionary.com/metanephric+mesenchyme - - - - - When the ureteric buds emerge from the nephric duct, they enter the metanephrogenic mesenchyme. The ureteric buds induce this mesenchymal tissue to condense around them and differentiate into the nephrons of the mammalian kidney. As this mesenchyme differentiates, it tells the ureteric bud to branch and grow.[well established][VHOG] - 2012-09-17 - VHOG:0000540 - VHOG - ISBN:978-0878932504 Gilbert SF, Developmental Biology (2006) p.462 - http://bgee.unil.ch/ - @@ -44501,7 +39287,6 @@ For example, A and B may be gene products and binding of B by A positively regul uberon UBERON:0003497 abdomen blood vessel - UBERON:0012254 @@ -44515,12 +39300,6 @@ For example, A and B may be gene products and binding of B by A positively regul blood vessel of abdomen OBOL:automatic - - - - UBERON:0012254 - abdominal aorta artery - @@ -44650,7 +39429,6 @@ For example, A and B may be gene products and binding of B by A positively regul A blood vessel that is part of a kidney [Automatically generated definition]. - EMAPA:28457 MA:0001682 TAO:0005306 ZFA:0005306 @@ -45032,10 +39810,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults - (...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG] EHDAA:251 EMAPA:16088 NCIT:C34195 @@ -45048,14 +39825,14 @@ For example, A and B may be gene products and binding of B by A positively regul intraembryonic coelom - + - + Wikipedia @@ -45065,16 +39842,6 @@ For example, A and B may be gene products and binding of B by A positively regul MGI:anna MP:0012187 - - - - (...) I regard it unlikely that coeloms of all bilaterian animals are comparable and evolved very early. Considering all these questions, few convincing characters concerning the evolution of body cavities remain to be named. (...) A segmental coelom appears to have evolved at least two times, in Annelida and in Myomerata (Acrania and Craniota).[well established][VHOG] - 2012-09-17 - VHOG:0000316 - VHOG - ISBN:978-0198566694 Schmidt-Rhaesa A, The evolution of organ systems (2007) p.166 - http://bgee.unil.ch/ - @@ -45107,7 +39874,6 @@ For example, A and B may be gene products and binding of B by A positively regul Connective, non-functional supportive framework of a biological cell, tissue, or organ. Contrast with parenchyma. - stromal FMA:81494 NCIT:C67387 UMLS:C0927195 @@ -45149,10 +39915,8 @@ For example, A and B may be gene products and binding of B by A positively regul Epithelial tubes transport gases, liquids and cells from one site to another and form the basic structure of many organs and tissues, with tube shape and organization varying from the single-celled excretory organ in Caenorhabditis elegans to the branching trees of the mammalian kidney and insect tracheal system. - contrast with a multi-tissue tube, which has as parts both epithelium, connective tissue, possibly muscle layers AEO:0000114 EHDAA2:0003114 - FBbt:00007474 epithelial or endothelial tube uberon UBERON:0003914 @@ -45165,12 +39929,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0060562 PMID:12526790 - - - - FBbt:00007474 - - @@ -45414,7 +40172,6 @@ For example, A and B may be gene products and binding of B by A positively regul - FMA has both conduit and conduit space. In EHDAA2 this is a surface feature AEO:0000080 EHDAA2:0003080 FMA:242873 @@ -45436,12 +40193,6 @@ For example, A and B may be gene products and binding of B by A positively regul Any tube, opening or passage that connects two distinct anatomical spaces. http://orcid.org/0000-0002-6601-2165 - - - - FMA has both conduit and conduit space. In EHDAA2 this is a surface feature - FMA - @@ -45486,7 +40237,6 @@ For example, A and B may be gene products and binding of B by A positively regul An anatomical structure that develops (entirely or partially) from the mesoderm. - Grouping term for query purposes mesodermal derivative uberon UBERON:0004120 @@ -45530,7 +40280,6 @@ For example, A and B may be gene products and binding of B by A positively regul An anatomical structure that develops (entirely or partially) from the ectoderm. - Grouping term for query purposes ectodermal deriviative uberon UBERON:0004121 @@ -45590,11 +40339,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction. - Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.[AAO] - relationship type change: differentiates_from intermediate mesoderm (AAO:0010575) CHANGED TO: develops_from intermediate mesoderm (UBERON:0003064)[AAO] - Kidneys and gonads (of vertebrates) develop from adjacent tissues, and after the excretory or urinary ducts have developed, the reproductive system usually taps into them or their derivatives.[well established][VHOG] - genitourinary - urogenital AAO:0000624 BILA:0000122 BTO:0003091 @@ -45630,33 +40374,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction. VHOG:0000286 - - - - Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.[AAO] - 2012-06-20 - AAO:0000624 - AAO - AAO:EJS - - - - - relationship type change: differentiates_from intermediate mesoderm (AAO:0010575) CHANGED TO: develops_from intermediate mesoderm (UBERON:0003064)[AAO] - 2012-06-20 - AAO:0000624 - AAO - - - - - Kidneys and gonads (of vertebrates) develop from adjacent tissues, and after the excretory or urinary ducts have developed, the reproductive system usually taps into them or their derivatives.[well established][VHOG] - 2012-09-17 - VHOG:0000286 - VHOG - ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.633 - http://bgee.unil.ch/ - @@ -45688,8 +40405,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + In mammals, the proximal tubule is a nephron tubule that connects Bowman's capsule to the loop of Henle. It has a brush border epithelial morphology[GO]. TODO - ensure definition works across species. @@ -45706,24 +40423,24 @@ For example, A and B may be gene products and binding of B by A positively regul proximal tubule - + - + - + GO - + GO @@ -45752,7 +40469,6 @@ For example, A and B may be gene products and binding of B by A positively regul The distal tubule is a nephron tubule that consists of the distal convoluted tubule and distal straight tubule segments. - BTO:0000482 CALOHA:TS-0504 EMAPA:28387 @@ -45783,7 +40499,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + The intermediate tubule is a nephron tubule that lies between the proximal and distal tubules. TODO - check for applicability across species FMA:17718 @@ -45793,14 +40509,14 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0004136 intermediate tubule - + - + FMA @@ -45830,7 +40546,6 @@ For example, A and B may be gene products and binding of B by A positively regul The first recognizable structure derived from the heart field. TODO - check plate vs rudiment vs primordium vs endocardial tube. See XAO - (In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG] EHDAA2:0000215 EMAPA:16106 VHOG:0000975 @@ -45849,16 +40564,6 @@ For example, A and B may be gene products and binding of B by A positively regul The first recognizable structure derived from the heart field. GO:0003142 - - - - (In vertebrates) The embryonic mesoderm is the source of both the cardiogenic plate, giving rise to the future myocardium as well as the endocardium that will line the system on the inner side.[well established][VHOG] - 2012-09-17 - VHOG:0000975 - VHOG - PMID:15611355 Gittenberger-de Groot AC, Bartelings MM, Deruiter MC, Poelmann RE, Basics of cardiac development for the understanding of congenital heart malformations. Pediatric Research (2005) - http://bgee.unil.ch/ - @@ -45884,12 +40589,12 @@ For example, A and B may be gene products and binding of B by A positively regul + - - + + A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. - this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138] XAO:0004185 first heart field primary heart field @@ -45900,24 +40605,24 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0004140 primary heart field - + - + - + GO:0003128 - + https://orcid.org/0000-0003-3308-6245 @@ -45928,12 +40633,6 @@ For example, A and B may be gene products and binding of B by A positively regul GOC:mtg_heart GOC:rl - - - - this term denotes the primary heart field; GO:0003128 denotes the superclass of primary and secondary: specific region of the lateral mesoderm into the area which will form the primary beating heart tube[GO:0003138] - GO - @@ -45976,9 +40675,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + An epithelial tube that will give rise to the mature heart. - the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube. AAO:0010411 EFO:0003526 EMAPA:32685 @@ -45996,14 +40694,14 @@ For example, A and B may be gene products and binding of B by A positively regul heart tube - + - + ZFA-modified @@ -46013,12 +40711,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0003143 GOC:mtg_heart - - - - the paired, longitudinal, endothelial-lined channels formed from the cardiogenic mesoderm in embryonic development; angiogenic cell clusters (aka angioblastic cords) located in a horse-shoe shape configuration in the cardiogenic plate coalesce to form the right and left endocardial heart tubes which then fuse in cephalo-caudal direction to form a single primitive heart tube. - MP:0012700 - @@ -46044,6 +40736,7 @@ For example, A and B may be gene products and binding of B by A positively regul + @@ -46110,6 +40803,7 @@ For example, A and B may be gene products and binding of B by A positively regul + @@ -46229,8 +40923,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + The comma-shaped body is the precursor structure to the S-shaped body that contributes to the morphogenesis of the nephron. EMAPA:27681 ZFA:0005588 @@ -46240,24 +40934,24 @@ For example, A and B may be gene products and binding of B by A positively regul comma-shaped body - + - + - + cjm - + ZFA @@ -46279,12 +40973,11 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + The S-shaped body is the successor of the comma-shaped body that contributes to the morphogenesis of the nephron. TODO EMAPA:27756 - VO:0010896 ZFA:0005589 SSB stage II nephron @@ -46293,24 +40986,24 @@ For example, A and B may be gene products and binding of B by A positively regul S-shaped body - + - + - + cjm - + GO @@ -46319,14 +41012,6 @@ For example, A and B may be gene products and binding of B by A positively regul The S-shaped body is the successor of the comma-shaped body that contributes to the morphogenesis of the nephron. GO:0072050 - - - - VO:0010896 - - - https://github.com/biopragmatics/biomappings - @@ -46360,8 +41045,6 @@ For example, A and B may be gene products and binding of B by A positively regul Kidney pyramids are the conical arrangements of tubules that constitute the renal medulla in a multi-lobed mammalian kidney; they contain the loops of Henle and the medullary collecting ducts. - not the same as FMA:50609 Pyramid (which is a volume / dimensional entity) - UBERON:0002449 UBERON:0005098 pyramid @@ -46402,12 +41085,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0072056 http://anatomy.uams.edu/anatomyhtml/kidney.html - - - - not the same as FMA:50609 Pyramid (which is a volume / dimensional entity) - FMA - @@ -46738,7 +41415,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -46753,7 +41430,6 @@ For example, A and B may be gene products and binding of B by A positively regul The small branching blood vessels in the kidney glomerulus that receives blood from the kidney afferent arterioles; these capillaries are under high pressure for filtering within the glomerulus. - Capillary that is part of the renal glomerulus. Glomerular capillary endothelial membranes in zebrafish normally have a fenestrated morphology that is visible at the ultrastructural level.[TAO] EMAPA:28245 FMA:274259 MA:0002587 @@ -46777,14 +41453,14 @@ For example, A and B may be gene products and binding of B by A positively regul glomerular capillary - + - + https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -46794,16 +41470,6 @@ For example, A and B may be gene products and binding of B by A positively regul MGI:csmith MP:0011320 - - - - Capillary that is part of the renal glomerulus. Glomerular capillary endothelial membranes in zebrafish normally have a fenestrated morphology that is visible at the ultrastructural level.[TAO] - 2012-08-14 - TAO:0005284 - TAO - ZFIN:ZDB-PUB-000824-1 - ZFIN:curator - @@ -46879,10 +41545,7 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body. - - Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO] - skeletal AEO:0000168 EHDAA2:0001843 EHDAA:5047 @@ -46915,15 +41578,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body. VSAO:0000026 - - - - Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO] - 2012-08-14 - VSAO:0000026 - VSAO - GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 - @@ -46938,7 +41592,6 @@ For example, A and B may be gene products and binding of B by A positively regul A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube. - The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO] TAO:0000115 ZFA:0000115 heart cone @@ -46953,15 +41606,6 @@ For example, A and B may be gene products and binding of B by A positively regul A cone-like structure that is formed when myocardial progenitor cells of the heart field fuse at the midline. The heart rudiment is the first structure of the heart tube. GO:0003313 - - - - The migrating myocardial precursors of the heart rudiment form a cone like structure between 19.5hpf and 22hpf, and eventually telescope out into the primitive heart tube at 24hpf. Stainier 2001.[TAO] - 2012-08-14 - TAO:0000115 - TAO - ZFIN:curator - @@ -46995,14 +41639,10 @@ For example, A and B may be gene products and binding of B by A positively regul The primitive streak is a structure that forms during the early stages of avian, reptilian and mammalian embryonic development[WP]. the midline ridge of the embryonic epiblast that later develops into mesoderm and endoderm[MP]. - - (...) the blastopore equivalent of chordates (germ ring in fish, marginal zone/blastopore lip in frog and node/primitive streak in chick and mouse) (...) (reference 1); Indeed, the primitive streak has been considered the homologue of the blastopore since the 1870s (reference 2).[well established][VHOG] - VHOG includes a very broad grouping here based on http://www.ncbi.nlm.nih.gov/pubmed/9609826 EHDAA2:0001525 EHDAA:185 EMAPA:16072 FMA:293110 - MESH:D054240 NCIT:C28402 SCTID:361438007 UMLS:C0033153 @@ -47029,30 +41669,6 @@ For example, A and B may be gene products and binding of B by A positively regul MP:0002231 Wikipedia:Primitive_streak - - - - (...) the blastopore equivalent of chordates (germ ring in fish, marginal zone/blastopore lip in frog and node/primitive streak in chick and mouse) (...) (reference 1); Indeed, the primitive streak has been considered the homologue of the blastopore since the 1870s (reference 2).[well established][VHOG] - 2012-09-17 - VHOG:0001202 - VHOG - PMID:9609826 Wu LH, Lengyel JA, Role of caudal in hindgut specification and gastrulation suggests homology between Drosophila amnioproctodeal invagination and vertebrate blastopore. Development (1998), ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.139 - http://bgee.unil.ch/ - - - - - VHOG includes a very broad grouping here based on http://www.ncbi.nlm.nih.gov/pubmed/9609826 - VHOG - - - - - MESH:D054240 - - - https://github.com/biopragmatics/biomappings - @@ -47111,18 +41727,14 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that has as its parts the heart and blood vessels. - we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph. - The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG] AAO:0011001 BILA:0000016 BTO:0000088 CALOHA:TS-1297 EFO:0000791 - EHDAA2:0000216 EHDAA:394 EMAPA:16104 - EMAPA:16370 EV:0100017 FMA:7161 GAID:467 @@ -47156,16 +41768,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that has as its parts the heart and blood vessels. BTO:0000088 - - - - The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG] - 2012-09-17 - VHOG:0000302 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.451 - http://bgee.unil.ch/ - @@ -47253,7 +41855,6 @@ For example, A and B may be gene products and binding of B by A positively regul The part of the cardiovascular system consisting of all arteries. - The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] BTO:0004690 EHDAA2:0000143 EHDAA:396 @@ -47280,16 +41881,6 @@ For example, A and B may be gene products and binding of B by A positively regul The part of the cardiovascular system consisting of all arteries. https://orcid.org/0000-0002-6601-2165 - - - - The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] - 2012-09-17 - VHOG:0000273 - VHOG - DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005) - http://bgee.unil.ch/ - @@ -47306,7 +41897,6 @@ For example, A and B may be gene products and binding of B by A positively regul The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions. - The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] BTO:0004692 EHDAA2:0002171 EHDAA:486 @@ -47334,16 +41924,6 @@ For example, A and B may be gene products and binding of B by A positively regul The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions. https://orcid.org/0000-0002-6601-2165 - - - - The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] - 2012-09-17 - VHOG:0000277 - VHOG - DOI:10.1196/annals.1341.002 Bishopric NH, Evolution of the heart from bacteria to man. Annals of the New York Academy of Sciences (2005) - http://bgee.unil.ch/ - @@ -47424,7 +42004,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -47461,14 +42041,14 @@ For example, A and B may be gene products and binding of B by A positively regul renal afferent arteriole http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + - + Wikipedia @@ -47714,11 +42294,9 @@ For example, A and B may be gene products and binding of B by A positively regul Organism at the gastrula stage. - We explicitly merge the NCITA terms here UBERON:0007012 BILA:0000060 BTO:0001403 - FBbt:00005317 FMA:293108 GAID:1302 MESH:D005775 @@ -47750,18 +42328,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Gastrula Wikipedia:Trilaminar_blastocyst - - - - We explicitly merge the NCITA terms here - NCIT - - - - - FBbt:00005317 - - @@ -47835,10 +42401,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. - Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO] - Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO] AAO:0011129 TAO:0001890 VSAO:0000128 @@ -47851,14 +42415,14 @@ For example, A and B may be gene products and binding of B by A positively regul skeletal element - + - + VSAO @@ -47867,24 +42431,6 @@ For example, A and B may be gene products and binding of B by A positively regul Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. https://orcid.org/0000-0002-6601-2165 - - - - Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO] - 2012-08-14 - VSAO:0000128 - VSAO - PSPUB:0000170 - - - - - Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO] - 2012-08-14 - TAO:0001890 - TAO - TAO:VSAO_workshop - @@ -47903,7 +42449,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -47942,14 +42488,14 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0004770 articular system - + - + FMA @@ -48149,7 +42695,6 @@ For example, A and B may be gene products and binding of B by A positively regul An endothelium that is part of the cardiovascular system. consider merging with 'endothelium' - Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] BTO:0001853 EMAPA:35201 GAID:519 @@ -48174,16 +42719,6 @@ For example, A and B may be gene products and binding of B by A positively regul An endothelium that is part of the cardiovascular system. https://orcid.org/0000-0002-6601-2165 - - - - Vertebrates and a very few invertebrates such as squids have evolved a secondary epithelium, the endothelium, that lines their blood vessels.[well established][VHOG] - 2012-09-17 - VHOG:0001217 - VHOG - ISBN:978-0030259821 Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.207 - http://bgee.unil.ch/ - @@ -48218,7 +42753,6 @@ For example, A and B may be gene products and binding of B by A positively regul Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP]. - We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors visceral mesoderm AAO:0011102 BILA:0000044 @@ -48238,12 +42772,6 @@ For example, A and B may be gene products and binding of B by A positively regul Layer of lateral plate mesoderm that forms the circulatory system and future gut wall - overlies endoderm[WP]. Wikipedia:Lateral_plate_mesoderm#Division_into_layers - - - - We group the BILA class here. Considering adding more general class for metazoa grouping cardiogenic successors - BILA - @@ -48265,7 +42793,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -48273,8 +42801,6 @@ For example, A and B may be gene products and binding of B by A positively regul A structure created during embryogenesis when the lateral mesoderm splits into two layers - the outer (or somatic) layer becomes applied to the inner surface of the ectoderm, and with it forms the somatopleure.[WP]. - Gives rise to the paired appendages in jawed vertebrates. a persistent somatopleure through the redistribution and expansion of the lateral plate mesoderm is a synapomorphy for gnathostomes and a critical step in generating a novel developmental module with dramatic evolutionary potentia (Tulenko et al. 2012) http://burkelab.research.wesleyan.edu/current-projects/lamprey/ - sources differ as to whether this is part-of or develops-from the LPM EHDAA2:0001847 EHDAA:381 EMAPA:16180 @@ -48288,14 +42814,14 @@ For example, A and B may be gene products and binding of B by A positively regul somatopleure http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png - + - + EHDAA2 @@ -48361,9 +42887,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + @@ -48371,7 +42897,6 @@ For example, A and B may be gene products and binding of B by A positively regul One of of the pair of folds derived from the cloacal folds which give rise to a portion of the external genitalia; in male embryos they close over the urethral plate and fuse to form the spongy (penile) urethra and ventral aspect of the penis, not including the glans; failure of fusion of the urethral folds leads to hypospadias; in female embryos they fuse only anterior to the anus and form the labia minora[MP]. - Less commonly, urogenital fold refers to the fold in the mesonephros which is the precursor of e.g. the suspensory ligament of the ovary. This is the case in older versions of Gray's anatomy[WP] EHDAA2:0004022 EMAPA:30888 FMA:321919 @@ -48384,34 +42909,34 @@ For example, A and B may be gene products and binding of B by A positively regul urogenital fold - + - + - + - + EHDAA2 - + Wikipedia - + EHDAA2 @@ -48462,8 +42987,6 @@ For example, A and B may be gene products and binding of B by A positively regul The central region of trunk mesoderm. This tissue forms the notochord. - Notochord rudiment[ZFIN:ZDB-PUB-961014-576]. - WP treats this as synonym of axial mesoderm. Induces neural tube. Gilbert: contains an anterior head process and the notochord. AAO:0000478 EFO:0003426 TAO:0000091 @@ -48484,12 +43007,6 @@ For example, A and B may be gene products and binding of B by A positively regul The central region of trunk mesoderm. This tissue forms the notochord. https://orcid.org/0000-0002-6601-2165 - - - - Notochord rudiment[ZFIN:ZDB-PUB-961014-576]. - ZFIN:ZDB-PUB-961014-576 - @@ -48522,7 +43039,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts. - FBbt:00005811 joint uberon UBERON:0004905 @@ -48535,12 +43051,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical structure that connects two or more adjacent skeletal elements or hardened body parts. http://orcid.org/0000-0002-6601-2165 - - - - FBbt:00005811 - - @@ -48572,9 +43082,7 @@ For example, A and B may be gene products and binding of B by A positively regul A proximal-distal subdivision of the digestive tract. - intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct. - FBbt:00100315 FMA:71131 uberon alimentary system subdivision @@ -48593,12 +43101,6 @@ For example, A and B may be gene products and binding of B by A positively regul A proximal-distal subdivision of the digestive tract. http://orcid.org/0000-0002-6601-2165 - - - - FBbt:00100315 - - @@ -48663,7 +43165,6 @@ For example, A and B may be gene products and binding of B by A positively regul The median dorsal longitudinal groove formed in the embryo by the neural plate after the appearance of the neural folds. - The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]. AAO:0011071 EMAPA:35594 FMA:295624 @@ -48685,12 +43186,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Neural_groove http://orcid.org/0000-0002-6601-2165 - - - - The neural groove is a shallow median groove between the neural folds of an embryo. The neural folds are two longitudinal ridges that are caused by a folding up of the ectoderm in front of the primitive streak of the developing embryo. The groove gradually deepens as the neural folds become elevated, and ultimately the folds meet and coalesce in the middle line and convert the groove into a closed tube, the neural tube or canal, the ectodermal wall of which forms the rudiment of the nervous system. After the coalescence of the neural folds over the anterior end of the primitive streak, the blastopore no longer opens on the surface but into the closed canal of the neural tube, and thus a transitory communication, the neurenteric canal, is established between the neural tube and the primitive digestive tube. The coalescence of the neural folds occurs first in the region of the hind-brain, and from there extends forward and backward; toward the end of the third week the front opening (anterior neuropore) of the tube finally closes at the anterior end of the future brain, and forms a recess which is in contact, for a time, with the overlying ectoderm; the hinder part of the neural groove presents for a time a rhomboidal shape, and to this expanded portion the term sinus rhomboidalis has been applied. Before the neural groove is closed a ridge of ectodermal cells appears along the prominent margin of each neural fold; this is termed the neural crest or ganglion ridge, and from it the spinal and cranial nerve ganglia and the ganglia of the sympathetic nervous system are developed. By the upward growth of the mesoderm the neural tube is ultimately separated from the overlying ectoderm. The cephalic end of the neural groove exhibits several dilatations, which, when the tube is closed, assume the form of three vesicles; these constitute the three primary cerebral vesicles, and correspond respectively to the future fore-brain (prosencephalon), mid-brain (mesencephalon), and hind-brain (rhombencephalon). The walls of the vesicles are developed into the nervous tissue and neuroglia of the brain, and their cavities are modified to form its ventricles. The remainder of the tube forms the medulla spinalis or spinal cord; from its ectodermal wall the nervous and neuroglial elements of the medulla spinalis are developed while the cavity persists as the central canal[Wikipedia:Neural_groove]. - Wikipedia:Neural_groove - @@ -48706,6 +43201,7 @@ For example, A and B may be gene products and binding of B by A positively regul + @@ -48713,14 +43209,7 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - One of the two elevated edges of the neural groove[GO,MP]. - In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]. EHDAA2:0001249 FMA:295618 NCIT:C34223 @@ -48743,12 +43232,6 @@ For example, A and B may be gene products and binding of B by A positively regul MP:0011256 Wikipedia:Neural_fold - - - - In front of the primitive streak two longitudinal ridges, caused by a folding up of the ectoderm, make their appearance, one on either side of the middle line. These are named the neural folds; they commence some little distance behind the anterior end of the embryonic disk, where they are continuous with each other, and from there gradually extend backward, one on either side of the anterior end of the primitive streak. Also, after differentiation it turns into the neural tubes[Wikipedia:Neural_fold]. - Wikipedia:Neural_fold - @@ -48775,7 +43258,6 @@ For example, A and B may be gene products and binding of B by A positively regul A solid rod of neurectoderm derived from the neural keel. The neural rod is roughly circular in cross section. Neural rod formation occurs during primary neurulation in teleosts[GO]. An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube[ZFIN]. - An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO] EFO:0003498 TAO:0000133 ZFA:0000133 @@ -48792,15 +43274,6 @@ For example, A and B may be gene products and binding of B by A positively regul GO:0014024 ZFA:0000133 - - - - An intermediate stage in the development of the central nervous system present during the segmentation period; the neural rod is roughly cylindrical in shape, forms from the neural keel, and is not yet hollowed out into the neural tube. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000133 - TAO - ZFIN:curator - @@ -48897,8 +43370,6 @@ For example, A and B may be gene products and binding of B by A positively regul Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO]. - in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila - EMAPA:32715 FMA:30316 musculus uberon @@ -48926,7 +43397,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + Missing definition for term UBERON:0005095. Please replace it using linked reference. class added for consistency with GO - consider merging with kidney mesenchyme. uberon @@ -48934,14 +43405,14 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0005095 kidney rudiment - + - + GO @@ -49057,7 +43528,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + The connecting tubule is a tubular segment of the nephron; it connects the distal convoluted tubule to the collecting duct[GO]. BTO:0004539 @@ -49075,14 +43546,14 @@ For example, A and B may be gene products and binding of B by A positively regul renal connecting tubule http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + - + Wikipedia @@ -49129,6 +43600,7 @@ For example, A and B may be gene products and binding of B by A positively regul + @@ -49304,7 +43776,6 @@ For example, A and B may be gene products and binding of B by A positively regul Connective tissue between the cellular elements of a structure. specify differentia from stroma - interstital FMA:86301 SCTID:85293002 interstitium @@ -49735,8 +44206,6 @@ For example, A and B may be gene products and binding of B by A positively regul The interstitial compartment of the kidney, comprising the extravascular intertubular spaces of the renal parenchyma, with their attendant cellular elements and extracellular substances, bounded on all sides by epithelial and vascular basement membranes. See https://sourceforge.net/p/geneontology/ontology-requests/10941/ - The interstitium is necessarily involved in all intrarenal exchange processes since the reabsorption and secretion of fluid and solutes implicates a transit across the interstitial compartment. - The fibroblasts in the interstitium provide the 'skeleton' of the tissue and maintain the three-dimensional architecture of the tissue. EMAPA:28518 FMA:70983 MA:0002616 @@ -49815,7 +44284,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -49831,14 +44300,14 @@ For example, A and B may be gene products and binding of B by A positively regul trunk mesenchyme - + - + EHDAA2 @@ -49918,7 +44387,6 @@ For example, A and B may be gene products and binding of B by A positively regul AEO:0000125 CALOHA:TS-2122 EHDAA2:0003125 - FBbt:00007006 FMA:292313 MIAA:0000019 uberon @@ -49929,12 +44397,6 @@ For example, A and B may be gene products and binding of B by A positively regul developing anatomical structure - - - - FBbt:00007006 - - @@ -49955,9 +44417,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + Multi-tissue structure that arises from the heart rudiment and will become the heart tube. - BTO:0006179 EHDAA2:0001512 EHDAA:424 EHDAA:436 @@ -49974,14 +44435,14 @@ For example, A and B may be gene products and binding of B by A positively regul primitive heart tube - + - + ZFA @@ -49990,14 +44451,6 @@ For example, A and B may be gene products and binding of B by A positively regul Multi-tissue structure that arises from the heart rudiment and will become the heart tube. ZFA:0000149 - - - - BTO:0006179 - - - https://github.com/biopragmatics/biomappings - @@ -50017,7 +44470,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -50025,8 +44478,6 @@ For example, A and B may be gene products and binding of B by A positively regul Portion of tissue that gives rise to the immature gonad. - Immature reproductive tissue that has not undergone final maturation into either testis or ovary.[TAO] - this is a very broad grouping class EFO:0003651 EHDAA:5927 EMAPA:17204 @@ -50046,7 +44497,7 @@ For example, A and B may be gene products and binding of B by A positively regul gonad primordium - + @@ -50059,7 +44510,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + ZFA @@ -50068,15 +44519,6 @@ For example, A and B may be gene products and binding of B by A positively regul Portion of tissue that gives rise to the immature gonad. ZFA:0001262 - - - - Immature reproductive tissue that has not undergone final maturation into either testis or ovary.[TAO] - 2012-08-14 - TAO:0001262 - TAO - ZFIN:curator - @@ -50125,17 +44567,17 @@ For example, A and B may be gene products and binding of B by A positively regul + - + - + A mesoderm that has the potential to develop into a pronephros. - Portion of tissue that consists of the mesenchymal precursor to the pronephric kidney and that begins to separate from the intermediate mesoderm at NF stage 21 and epithelializes by NF stage 30.[AAO] AAO:0011090 EFO:0003479 TAO:0000067 @@ -50152,24 +44594,24 @@ For example, A and B may be gene products and binding of B by A positively regul the intermediate mesoderm of the chick embryo acquires its ability to form kidneys through its interactions with the paraxial mesoderm [ISBN:9780878932504 "Developmental Biology", PMID:10720431 "Signals from trunk paraxial mesoderm induce pronephros formation in chick intermediate mesoderm"]. These interactions induce the expression of TFs including Lim1, Pax2 and Pax6 that cause the intermediate mesoderm to form the kidney pronephric mesoderm - + - + - + ZFA - + Bgee:AN @@ -50178,15 +44620,6 @@ For example, A and B may be gene products and binding of B by A positively regul A mesoderm that has the potential to develop into a pronephros. OBOL:automatic - - - - Portion of tissue that consists of the mesenchymal precursor to the pronephric kidney and that begins to separate from the intermediate mesoderm at NF stage 21 and epithelializes by NF stage 30.[AAO] - 2012-06-20 - AAO:0011090 - AAO - XAO:curator - @@ -50225,7 +44658,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -50233,9 +44666,7 @@ For example, A and B may be gene products and binding of B by A positively regul The capillary loops of the kidney that normally function as a filtration unit[MP]. - ...Soon afterwards, endothelial cells invade to make a capillary knot-like outgrowth, the glomerular tuft, which goes on to form the glomerulus EMAPA:28239 - SCTID:362217000 Wikipedia:Glomerulus uberon glomerular capillary tuft @@ -50244,14 +44675,14 @@ For example, A and B may be gene products and binding of B by A positively regul glomerular tuft - + - + Wikipedia @@ -50262,12 +44693,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Glomerulus http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron - - - - ...Soon afterwards, endothelial cells invade to make a capillary knot-like outgrowth, the glomerular tuft, which goes on to form the glomerulus - GudMap - @@ -50430,7 +44855,6 @@ For example, A and B may be gene products and binding of B by A positively regul An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina. - this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell. AAO:0010596 FMA:63872 @@ -50507,8 +44931,9 @@ For example, A and B may be gene products and binding of B by A positively regul + - + @@ -50516,13 +44941,11 @@ For example, A and B may be gene products and binding of B by A positively regul The layer of extracellular matrix that lies between the endothelium of the glomerular capillaries and the podocytes of the inner or visceral layer of the Bowman capsule; it is a fusion of the endothelial cell and podocyte basal laminas and acts as a physical barrier and an ion-selective filter. - Membrane between the mesonephric podocytes and the renal glomerular capillaries. It is a trilaminar structure composed of the fused basement membranes of the glomerular capillaries and basement membrane of the podocytes. The capillary membranes touch the GBM at contact points that are separated by pores. The membrane is semi-permeable allowing water and small molecules to pass into the renal capsular space.[TAO] GBM EMAPA:28251 EMAPA:30965 FMA:74274 MA:0001659 - MESH:D050533 NCIT:C32683 SCTID:243897006 TAO:0005285 @@ -50538,14 +44961,14 @@ For example, A and B may be gene products and binding of B by A positively regul glomerular basement membrane http://upload.wikimedia.org/wikipedia/commons/d/de/PhysiologieGlom%C3%A9rulaire.png - + - + true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -50556,29 +44979,12 @@ For example, A and B may be gene products and binding of B by A positively regul MGI:anna MP:0011348 - - - - Membrane between the mesonephric podocytes and the renal glomerular capillaries. It is a trilaminar structure composed of the fused basement membranes of the glomerular capillaries and basement membrane of the podocytes. The capillary membranes touch the GBM at contact points that are separated by pores. The membrane is semi-permeable allowing water and small molecules to pass into the renal capsular space.[TAO] - 2012-08-14 - TAO:0005285 - TAO - ZFIN:ZDB-PUB-000824-1 - GBM - - - - MESH:D050533 - - - https://github.com/biopragmatics/biomappings - @@ -50647,7 +45053,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 @@ -50657,7 +45063,7 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0005856 developing mesenchymal condensation - + @@ -50676,7 +45082,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + AEO-modified-relation @@ -50718,10 +45124,8 @@ For example, A and B may be gene products and binding of B by A positively regul Subdivision of skeleton which consists of cranial skeleton, set of all vertebrae, set of all ribs and sternum[FMA, modified]. - Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO] AAO:0000963 EMAPA:17214 - EMAPA:18043 MA:0000308 NCIT:C32172 SCTID:361725000 @@ -50749,15 +45153,6 @@ For example, A and B may be gene products and binding of B by A positively regul https://github.com/obophenotype/uberon/issues/44 https://github.com/obophenotype/uberon/wiki/The-axial-skeleton - - - - Skeletal subdivision of the central body axis including the cranium, vertebrae, notochord, ribs, and sternum.[VSAO] - 2012-08-14 - VSAO:0000056 - VSAO - PSPUB:0000170 - @@ -50784,7 +45179,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -50804,8 +45199,6 @@ For example, A and B may be gene products and binding of B by A positively regul The membrane that covers the embryonic cloaca, formed by the union of proctodeal (anal pit) ectoderm and cloacal endoderm, with no intervening mesoderm; the urorectal septum joins the cloacal membrane and divides it into an anal membrane and a urogenital membrane; the point where the urorectal septum intersects the cloacal membrane is the future site of the perineal body; proliferation of mesoderm and ectoderm around the cloacal membrane produces primordial tissues of the external genitalia in both sexes: the genital tubercle, genital folds, and genital swellings. - A membrane that separates the proctodeum and the hindgut in the early embryo. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.497, see_Kardong_KV][VHOG] - In mammals, the cloaca exists as an embryonic structure that undergoes septation to become distinct urethral, anal, and genital orifices.[well established][VHOG] EHDAA2:0000257 EHDAA:214 EHDAA:2933 @@ -50825,14 +45218,14 @@ For example, A and B may be gene products and binding of B by A positively regul cloacal membrane http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray991.png - + - + Wikipedia @@ -50843,25 +45236,6 @@ For example, A and B may be gene products and binding of B by A positively regul MP:anna Wikipedia:Cloacal_membrane - - - - A membrane that separates the proctodeum and the hindgut in the early embryo. [Evolution, Fourth_Edition_(2006)_McGraw-Hill, Function, Vertebrates:_Comparative_Anatomy, p.497, see_Kardong_KV][VHOG] - 2012-09-17 - VHOG:0001198 - VHOG - http://bgee.unil.ch/ - - - - - In mammals, the cloaca exists as an embryonic structure that undergoes septation to become distinct urethral, anal, and genital orifices.[well established][VHOG] - 2012-09-17 - VHOG:0001198 - VHOG - PMID:11830557 De Santa Barbara P, Roberts DJ, Tail gut endoderm and gut/genitourinary/tail development: a new tissue-specific role for Hoxa13. Development (2002) - http://bgee.unil.ch/ - @@ -50885,10 +45259,9 @@ For example, A and B may be gene products and binding of B by A positively regul - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB - The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG] EHDAA2:0001278 EHDAA:264 EMAPA:16101 @@ -50900,7 +45273,7 @@ For example, A and B may be gene products and binding of B by A positively regul notochordal plate - + @@ -50913,7 +45286,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + EHDAA2 @@ -50922,15 +45295,6 @@ For example, A and B may be gene products and binding of B by A positively regul The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. VHOG:0001212 - - - - The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. [Carson_JL, Dehart_DB, Developmental_Dynamics_(1994)_201:_260-278, Gesteland_K_and_Schoenwolf_GC, Inagaki_T, Morphogenesis_of_the_murine_node_and_notochordal_plate, The_prechordal_plate, Vrablic_T, see_Mueller_F_and_O'Rahilly_R, the_rostral_end_of_the_notochord_and_nearby_median_features_in_staged_human_embryos._Cells_Tissues_Organs_(2003)_173:_1-20_and_Sulik_K][VHOG] - 2012-09-17 - VHOG:0001212 - VHOG - http://bgee.unil.ch/ - @@ -50950,7 +45314,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -50967,14 +45331,14 @@ For example, A and B may be gene products and binding of B by A positively regul The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -51190,7 +45554,6 @@ For example, A and B may be gene products and binding of B by A positively regul A tube in the kidney that collect and transport urine. - in ZFA this is defined as part of mesonephros TAO:0005289 ZFA:0005289 uberon @@ -51203,12 +45566,6 @@ For example, A and B may be gene products and binding of B by A positively regul A tube in the kidney that collect and transport urine. ZFIN:ZDB-PUB-071029-9 - - - - in ZFA this is defined as part of mesonephros - ZFA - @@ -51525,7 +45882,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + A region of nephron tubule that is part of a cortex of kidney. EMAPA:18976 MA:0002609 @@ -51535,14 +45892,14 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0006853 renal cortex tubule - + - + MA @@ -51583,8 +45940,6 @@ For example, A and B may be gene products and binding of B by A positively regul The distalmost portion of the digestive tract, derived from the hindgut, and terminating with the anus. - this class is the superclass of 'rectum', which is currently reserved for the vertebrate structure. May be merged in future. - FBbt:00005756 WBbt:0005773 rectum uberon @@ -51599,12 +45954,6 @@ For example, A and B may be gene products and binding of B by A positively regul The distalmost portion of the digestive tract, derived from the hindgut, and terminating with the anus. http://orcid.org/0000-0002-6601-2165 - - - - FBbt:00005756 - - @@ -51687,7 +46036,6 @@ For example, A and B may be gene products and binding of B by A positively regul An epithelium characterised by its most superficial layer consisting of squamous epithelial cells. - FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium BTO:0002072 NCIT:C12848 SCTID:40118003 @@ -51703,12 +46051,6 @@ For example, A and B may be gene products and binding of B by A positively regul An epithelium characterised by its most superficial layer consisting of squamous epithelial cells. Wikipedia:Squamous_epithelium - - - - FBbt:00007028 (squamous epithelium) A type of epithelium that is made up of flattened cells which are arranged with their long axes in the plane of the epithelium - FBbt - @@ -51783,12 +46125,6 @@ For example, A and B may be gene products and binding of B by A positively regul Old definition: 'Non-material anatomical entity of two dimensions, that is demarcated by anatomical lines or points on the external or internal surfaces of anatomical structures.' Note, in the new definition, the space referred to is not necessarily an anatomical space. It may be the outside of an organism. anatomical surface - - - - - via morphological boundary in CARO - @@ -51807,6 +46143,7 @@ For example, A and B may be gene products and binding of B by A positively regul + @@ -51981,7 +46318,6 @@ For example, A and B may be gene products and binding of B by A positively regul - The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis BILA:0000084 NCIT:C34268 SCTID:360394002 @@ -51997,12 +46333,6 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0007026 presumptive gut - - - - The endodermal cells generate only the lining of the digestive tube and its glands; mesodermal mesenchyme cells will surround this tube to provide the muscles for peristalsis - NCBIBook:NBK10107 - @@ -52033,10 +46363,13 @@ For example, A and B may be gene products and binding of B by A positively regul - + + + + + + A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]. - note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis - SPD:0000130 TADS:0000147 http://www.sciencemag.org/content/313/5795/1922/F1.large.jpg dorsal tube @@ -52048,16 +46381,6 @@ For example, A and B may be gene products and binding of B by A positively regul Gene notes: Bmp, Nkx, Gata primary circulatory organ - - - - - - - - - GO uses blood circulation generically to include the haemolymphatic fluid of arthropods - @@ -52096,7 +46419,6 @@ For example, A and B may be gene products and binding of B by A positively regul An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. - An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO] EFO:0003497 TAO:0000131 ZFA:0000131 @@ -52112,15 +46434,6 @@ For example, A and B may be gene products and binding of B by A positively regul An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. ZFIN:ZDB-PUB-961014-576 - - - - An intermediate stage (between the neural plate and neural rod) during the early segmentation period in the morphogenesis of the central nervous system primordium; the keel is roughly triangular shaped in cross section. Kimmel et al, 1995.[TAO] - 2012-08-14 - TAO:0000131 - TAO - ZFIN:curator - @@ -52145,7 +46458,12 @@ For example, A and B may be gene products and binding of B by A positively regul - + + + + + + @@ -52162,17 +46480,6 @@ For example, A and B may be gene products and binding of B by A positively regul presumptive segmental plate - - - - - - - - - https://github.com/obophenotype/uberon/wiki/The-neural-crest - EDHAA2 - @@ -52224,7 +46531,6 @@ For example, A and B may be gene products and binding of B by A positively regul A presumptive structure that has the potential to develop into a neural plate. consider merging - Region of the gastrula which gives rise to the neural plate.[TAO] EFO:0003424 TAO:0000063 ZFA:0000063 @@ -52241,15 +46547,6 @@ For example, A and B may be gene products and binding of B by A positively regul A presumptive structure that has the potential to develop into a neural plate. OBOL:automatic - - - - Region of the gastrula which gives rise to the neural plate.[TAO] - 2012-08-14 - TAO:0000063 - TAO - ZFIN:curator - @@ -52268,7 +46565,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -52294,7 +46591,7 @@ For example, A and B may be gene products and binding of B by A positively regul presumptive paraxial mesoderm - + @@ -52310,7 +46607,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + https://github.com/obophenotype/uberon/issues/1277 @@ -52471,7 +46768,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -52479,7 +46776,7 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0007524 dense mesenchyme tissue - + @@ -52492,7 +46789,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + AEO @@ -52585,7 +46882,6 @@ For example, A and B may be gene products and binding of B by A positively regul - consider moving MA:0000377 renal tubule here, as it includes the various segments (proximal etc) as subclasses, not parts FMA:17692 renal tubule region uberon @@ -52593,12 +46889,6 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0007685 region of nephron tubule - - - - consider moving MA:0000377 renal tubule here, as it includes the various segments (proximal etc) as subclasses, not parts - MA - @@ -52670,7 +46960,6 @@ For example, A and B may be gene products and binding of B by A positively regul AEO:0000170 EFO:0001649 EHDAA2:0003170 - FBbt:00005426 Wikipedia:Anlage_(biology) developmental field uberon @@ -52700,12 +46989,6 @@ For example, A and B may be gene products and binding of B by A positively regul FBbt:00005426 http://flybase.org/reports/FBrf0178740.html - - - - FBbt:00005426 - - @@ -52713,12 +46996,10 @@ For example, A and B may be gene products and binding of B by A positively regul - + Anatomical system that consists of all blood and lymph vessels. consider merging with vasculature - The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]. - in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system BTO:0001085 CALOHA:TS-2053 EHDAA2:0004520 @@ -52732,14 +47013,14 @@ For example, A and B may be gene products and binding of B by A positively regul vascular system - + - + MA @@ -52748,18 +47029,6 @@ For example, A and B may be gene products and binding of B by A positively regul Anatomical system that consists of all blood and lymph vessels. http://orcid.org/0000-0002-6601-2165 - - - - The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]. - ncithesaurus:Vascular_System - - - - - in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system - MA - @@ -52803,8 +47072,6 @@ For example, A and B may be gene products and binding of B by A positively regul An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). - this encompasses non-skeletal tissue - An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There are only two instances of appendage girdle regions per organism.[VSAO] UBERON:0007824 girdle girdle region @@ -52826,15 +47093,6 @@ For example, A and B may be gene products and binding of B by A positively regul UBERONREF:0000003 https://orcid.org/0000-0002-6601-2165 - - - - An organism subdivision that encompasses the region containing the pectoral or pelvic girdle. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). There are only two instances of appendage girdle regions per organism.[VSAO] - 2012-08-14 - VSAO:0000303 - VSAO - https://orcid.org/0000-0002-6601-2165 - @@ -52886,6 +47144,7 @@ For example, A and B may be gene products and binding of B by A positively regul + @@ -52899,7 +47158,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -52908,11 +47167,6 @@ For example, A and B may be gene products and binding of B by A positively regul Skeletal subdivision consisting of a set of bones linking the axial series to the hindlimb zeugopodium and offering anchoring areas for hindlimb and caudal musculature. need to resolve whether this is a paired structure or a single belt (Paired in FMA - implicitly paired in VSAO) - Anatomical cluster by which the hind limbs are supported and attached to the vertebral column.[AAO] - Anatomical cluster that consists of the paired basipterygia which support the pelvic fin.[TAO] - Girdle skeleton consisting of a set of bones linking the axial series to the hindlimb/fin skeleton and offering anchoring areas for hindlimb/fin and caudal musculature.[VSAO] - The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin.[well established][VHOG] - Note that the VSAO and many ontologies use the label 'pelvic girdle' to denote the skeletal region specifically. We place the EHDAA2 class here, note that this includes the pre-cartilage condensation as parts AAO:0000426 AAO:0000768 EFO:0000947 @@ -52942,14 +47196,14 @@ For example, A and B may be gene products and binding of B by A positively regul pelvic girdle skeleton http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png - + - + PMID:21455939 @@ -52959,49 +47213,6 @@ For example, A and B may be gene products and binding of B by A positively regul VSAO:0000155 Wikipedia:Pelvis - - - - Anatomical cluster by which the hind limbs are supported and attached to the vertebral column.[AAO] - 2012-06-20 - AAO:0000426 - AAO - AAO:LAP - - - - - Anatomical cluster that consists of the paired basipterygia which support the pelvic fin.[TAO] - 2012-08-14 - TAO:0000565 - TAO - TAO:wd - - - - - Girdle skeleton consisting of a set of bones linking the axial series to the hindlimb/fin skeleton and offering anchoring areas for hindlimb/fin and caudal musculature.[VSAO] - 2012-08-14 - VSAO:0000155 - VSAO - https://orcid.org/0000-0002-6601-2165 - - - - - The pelvic girdle is never joined by contributions of dermal bone. From its first appearance in placoderms, the pelvic girdle is exclusively endoskeletal. It arose from pterygiophores, perhaps several times, in support of the fin.[well established][VHOG] - 2012-09-17 - VHOG:0000305 - VHOG - ISBN:978-0072528305 Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) p.333 - http://bgee.unil.ch/ - - - - - Note that the VSAO and many ontologies use the label 'pelvic girdle' to denote the skeletal region specifically. We place the EHDAA2 class here, note that this includes the pre-cartilage condensation as parts - VSAO - @@ -53045,7 +47256,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + The functional tissue of the kidney, consisting of the nephrons. BTO:0003604 FMA:15574 @@ -53056,7 +47267,7 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0008987 renal parenchyma - + @@ -53069,7 +47280,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + FMA @@ -53139,7 +47350,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -53156,14 +47367,14 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -53282,7 +47493,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -53290,14 +47501,14 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -53327,7 +47538,6 @@ For example, A and B may be gene products and binding of B by A positively regul A renal tubule is a tube that filters, re-absorbs and secretes substances to rid an organism of waste and to play a role in fluid homeostasis. - this class groups vertebrate nephron tubules with analagous structures such as insect Malpighian tubules renal tubule (generic) tubule of excretory system uberon @@ -53395,8 +47605,9 @@ For example, A and B may be gene products and binding of B by A positively regul + - + EFO:0003704 TAO:0005041 ZFA:0005041 @@ -53406,14 +47617,14 @@ For example, A and B may be gene products and binding of B by A positively regul anterior lateral plate mesoderm - + - + ZFA @@ -53448,7 +47659,6 @@ For example, A and B may be gene products and binding of B by A positively regul An artery that supplies a renal lobe. - FMA only has the set term EMAPA:37091 FMA:71637 SCTID:62802007 @@ -53474,12 +47684,6 @@ For example, A and B may be gene products and binding of B by A positively regul Wikipedia:Interlobar_arteries http://orcid.org/0000-0002-6601-2165 - - - - FMA only has the set term - FMA - @@ -53593,7 +47797,6 @@ For example, A and B may be gene products and binding of B by A positively regul The portion of a kidney consisting of a renal medullary pyramid and the renal cortex above it[MP]. It is composed of many renal lobules[WP]. todo - add has_part relationships. - human kidneys have multilobar (multipyramidal) architecture while mice and rats have unilobar (unipyramidal) kidneys FMA:17881 NCIT:C32894 UMLS:C0736382 @@ -53615,12 +47818,6 @@ For example, A and B may be gene products and binding of B by A positively regul MP:0011381 Wikipedia:Renal_lobe - - - - human kidneys have multilobar (multipyramidal) architecture while mice and rats have unilobar (unipyramidal) kidneys - MP - @@ -53688,7 +47885,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0010000 - FBbt:00100313 multicellular structure uberon UBERON:0010000 @@ -53702,12 +47898,6 @@ For example, A and B may be gene products and binding of B by A positively regul An anatomical structure that has more than one cell as a part. CARO:0010000 - - - - FBbt:00100313 - - @@ -53748,7 +47938,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -53766,14 +47956,14 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0010227 future cardiac atrium - + - + ZFA @@ -53825,7 +48015,6 @@ For example, A and B may be gene products and binding of B by A positively regul An anatomical structure that has some part that develops from the neural crest. - Grouping term for query purposes uberon UBERON:0010314 @@ -53914,9 +48103,10 @@ For example, A and B may be gene products and binding of B by A positively regul + - + @@ -53930,7 +48120,7 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0010377 mesenchyme from somatopleure - + @@ -53943,7 +48133,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + EHDAA2 @@ -53959,7 +48149,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses. MESH:D055806 TAO:0005251 @@ -53969,14 +48159,14 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0010523 microcirculatory vessel - + - + ZFA @@ -54009,7 +48199,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -54017,7 +48207,6 @@ For example, A and B may be gene products and binding of B by A positively regul An epithelial tube that is fated to become a nephron. - EHDAA2 treats this as already having a tubular structure, but in the ZFA representation this is a cluster of cells developing nephron primitive nephron future nephron @@ -54026,7 +48215,7 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0010532 primitive nephron - + @@ -54039,7 +48228,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + EHDAA2 @@ -54048,12 +48237,6 @@ For example, A and B may be gene products and binding of B by A positively regul An epithelial tube that is fated to become a nephron. http://orcid.org/0000-0002-6601-2165 - - - - EHDAA2 treats this as already having a tubular structure, but in the ZFA representation this is a cluster of cells - EHDAA2 - @@ -54061,7 +48244,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -54072,7 +48255,7 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0010536 nephron progenitor - + @@ -54085,7 +48268,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + cjm @@ -54096,12 +48279,6 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - @@ -54116,9 +48293,6 @@ For example, A and B may be gene products and binding of B by A positively regul An organism subdivision that includes both an appendage and its associated girdle region. Note that this includes both the skeletal elements and associated tissues (integument, muscle, etc). It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO] - Anatomical group that consists of the soft and skeletal tissues of the appendicular region of the body and the appendage proper.[VSAO] - It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO] - note that the FMA uses the term 'limb' to refer to the entire appendage complex (free limb plus girdle region) 2012-04-23T10:46:51Z EMAPA:37858 @@ -54141,30 +48315,6 @@ For example, A and B may be gene products and binding of B by A positively regul https://github.com/obophenotype/uberon/wiki/Appendages-and-the-appendicular-skeleton https://orcid.org/0000-0002-6601-2165 - - - - Anatomical group that consists of the soft and skeletal tissues of the appendicular region of the body and the appendage proper.[VSAO] - 2012-08-14 - VSAO:0000214 - VSAO - GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 - - - - - It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO] - 2012-09-06 - VSAO:0000214 - VSAO - Curator - - - - - note that the FMA uses the term 'limb' to refer to the entire appendage complex (free limb plus girdle region) - FMA - @@ -54233,9 +48383,6 @@ For example, A and B may be gene products and binding of B by A positively regul Appendage girdle complex that when present, encompasses the pelvic appendicular skeleton and the pelvic girdle. - - Appendage girdle complex that when present, encompasses the pelvic appendage and the pelvic girdle.[VSAO] - note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region). Note the MA class 'hindlimb' may also belong here EMAPA:37863 FMA:7184 SCTID:416631005 @@ -54257,21 +48404,6 @@ For example, A and B may be gene products and binding of B by A positively regul Appendage girdle complex that when present, encompasses the pelvic appendicular skeleton and the pelvic girdle. VSAO:0000215 - - - - Appendage girdle complex that when present, encompasses the pelvic appendage and the pelvic girdle.[VSAO] - 2012-08-14 - VSAO:0000215 - VSAO - VSAO:MAH - - - - - note that the FMA uses the terms 'upper limb' and 'lower limb' to refer to the entire appendage complex (free limb plus girdle region). Note the MA class 'hindlimb' may also belong here - FMA - @@ -54359,9 +48491,6 @@ For example, A and B may be gene products and binding of B by A positively regul The subdivision of the skeleton of either the pectoral or pelvic girdle. - Skeletal subdivision that is part of the appendage girdle region.[VSAO] - relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: part_of subdivision of skeleton (UBERON:0010912)[VSAO] - relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: proximally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO] AAO:0010686 VSAO:0000302 skeleton of girdle @@ -54375,31 +48504,6 @@ For example, A and B may be gene products and binding of B by A positively regul The subdivision of the skeleton of either the pectoral or pelvic girdle. https://orcid.org/0000-0002-6601-2165 - - - - Skeletal subdivision that is part of the appendage girdle region.[VSAO] - 2012-08-14 - VSAO:0000302 - VSAO - GO_REF:0000034, http://dx.plos.org/10.1371/journal.pone.0051070 - - - - - relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: part_of subdivision of skeleton (UBERON:0010912)[VSAO] - 2012-08-14 - VSAO:0000302 - VSAO - - - - - relationship type change: subclass skeletal subdivision (VSAO:0000042) CHANGED TO: proximally_connected_to subdivision of skeleton (UBERON:0010912)[VSAO] - 2012-08-14 - VSAO:0000302 - VSAO - @@ -54407,10 +48511,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. - Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO] FMA:23879 SCTID:129140006 VSAO:0000042 @@ -54421,11 +48524,11 @@ For example, A and B may be gene products and binding of B by A positively regul subdivision of skeleton - + - + @@ -54438,13 +48541,13 @@ For example, A and B may be gene products and binding of B by A positively regul - + UBERONREF:0000003 - + VSAO @@ -54454,16 +48557,6 @@ For example, A and B may be gene products and binding of B by A positively regul UBERONREF:0000003 https://orcid.org/0000-0002-6601-2165 - - - - Anatomical cluster consisting of the skeletal elements that are part of the skeleton.[VSAO] - 2012-08-14 - VSAO:0000042 - incorrect - VSAO - VSAO:curator - @@ -54515,7 +48608,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system FMA:302077 @@ -54525,7 +48618,7 @@ For example, A and B may be gene products and binding of B by A positively regul postcranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton - + @@ -54538,7 +48631,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + cjm @@ -54562,7 +48655,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -54575,7 +48668,6 @@ For example, A and B may be gene products and binding of B by A positively regul - Subdivision of urinary system which consists of the kidney and the ureters. FMA:45658 @@ -54588,26 +48680,16 @@ For example, A and B may be gene products and binding of B by A positively regul upper urinary tract - + - - - - - + FMA - - - - - FMA-abduced-lr - @@ -54632,7 +48714,6 @@ For example, A and B may be gene products and binding of B by A positively regul - FBbt:00007330 FMA:67509 SCTID:91690000 uberon @@ -54654,12 +48735,6 @@ For example, A and B may be gene products and binding of B by A positively regul A subdivision of an anatomical system. http://orcid.org/0000-0002-6601-2165 - - - - FBbt:00007330 - - @@ -54680,9 +48755,7 @@ For example, A and B may be gene products and binding of B by A positively regul Subdivision of the skeletal system which consists of the appendicular skeleton plus associated joints. - Skeletal system which consists of the appendicular skeleton plus associated joints.[VSAO] FMA:7484 - VHOG:0001666 VSAO:0000306 uberon UBERON:0011249 @@ -54695,15 +48768,6 @@ For example, A and B may be gene products and binding of B by A positively regul Subdivision of the skeletal system which consists of the appendicular skeleton plus associated joints. https://orcid.org/0000-0002-6601-2165 - - - - Skeletal system which consists of the appendicular skeleton plus associated joints.[VSAO] - 2012-08-14 - VSAO:0000306 - VSAO - https://orcid.org/0000-0002-6601-2165 - @@ -54820,7 +48884,6 @@ For example, A and B may be gene products and binding of B by A positively regul The aggregate of the coelemic cavity lumen plus the membranes that line the lumen. EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining. - coelomic EHDAA2:0004731 Wikipedia:Coelom enterocoelom @@ -54935,7 +48998,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -54950,14 +49013,14 @@ For example, A and B may be gene products and binding of B by A positively regul We presume this is distinct from AAO:0001003, an external integumentary structure - check with amphibian anatomy ontology developers. AO notes: the text def states mesenchymal swelling, EHDAA2 splits into mesenchymal and epithelial parts embryonic cloacal fold - + - + EHDAA2 @@ -54980,20 +49043,20 @@ For example, A and B may be gene products and binding of B by A positively regul - + EHDAA2:0004588 uberon UBERON:0012361 internal anal region - + - + EHDAA2 @@ -55003,20 +49066,20 @@ For example, A and B may be gene products and binding of B by A positively regul - + EHDAA2:0004589 uberon UBERON:0012469 external anal region - + - + EHDAA2 @@ -55043,7 +49106,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -55063,14 +49126,14 @@ For example, A and B may be gene products and binding of B by A positively regul skeleton of pelvic complex - + - + FMA @@ -55122,9 +49185,8 @@ For example, A and B may be gene products and binding of B by A positively regul - + The precursor of the urethra. - In humans, the urethral groove is a temporary linear indentation on the underside (ventral side) of the male penis during embryonic development. It typically appears around 8 weeks of gestation and becomes closed into a normal male urethra by the 12th week SCTID:361531004 Wikipedia:Urethral_groove sulcus urethralis primarius @@ -55134,14 +49196,14 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0013241 embryonic urethral groove - + - + Wikipedia @@ -55150,12 +49212,6 @@ For example, A and B may be gene products and binding of B by A positively regul The precursor of the urethra. http://orcid.org/0000-0002-6601-2165 - - - - In humans, the urethral groove is a temporary linear indentation on the underside (ventral side) of the male penis during embryonic development. It typically appears around 8 weeks of gestation and becomes closed into a normal male urethra by the 12th week - Wikipedia:Urethral_groove - @@ -55281,10 +49337,8 @@ For example, A and B may be gene products and binding of B by A positively regul The region of the organism associated with the visceral organs. - Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]. AEO:0000103 BTO:0001489 - EMAPA:36031 FMA:231424 uberon body @@ -55305,12 +49359,6 @@ For example, A and B may be gene products and binding of B by A positively regul The region of the organism associated with the visceral organs. AEO:0000103 - - - - Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424]. - FMA:231424 - @@ -55348,7 +49396,6 @@ For example, A and B may be gene products and binding of B by A positively regul A blood that is part of a vein. - BTO:0006187 FMA:83067 blood in vein portion of venous blood @@ -55363,14 +49410,6 @@ For example, A and B may be gene products and binding of B by A positively regul A blood that is part of a vein. OBOL:automatic - - - - BTO:0006187 - - - https://github.com/biopragmatics/biomappings - @@ -55511,24 +49550,7 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - @@ -55536,7 +49558,6 @@ For example, A and B may be gene products and binding of B by A positively regul Any structure that is placed on one side of the left-right axis of a bilaterian. - This class is primarily to implement taxon constraints. It may be removed in the future. uberon UBERON:0015212 @@ -55570,7 +49591,6 @@ For example, A and B may be gene products and binding of B by A positively regul A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile. heart - SPD:0000130 cardiac pump heart or heart like organ circulatory vessel @@ -55754,7 +49774,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -55777,7 +49797,7 @@ For example, A and B may be gene products and binding of B by A positively regul UBERON:0016887 entire extraembryonic component - + @@ -55790,7 +49810,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + AEO @@ -55918,7 +49938,6 @@ For example, A and B may be gene products and binding of B by A positively regul CARO:0020000 - FBbt:00007276 uberon UBERON:0034923 @@ -55936,12 +49955,6 @@ For example, A and B may be gene products and binding of B by A positively regul Material anatomical entity consisting of multiple anatomical structures that are not connected to each other. CARO:0020000 - - - - FBbt:00007276 - - @@ -56082,24 +50095,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - - - - - - - - + Any chamber of the right side of the heart. FMA:7165 SCTID:362007002 @@ -56217,7 +50214,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + The upper tract of the renal system. The renal pelvis is the large cavity in the middle of each kidney. Urine drains from each kidney through a long tube called the ureter, into the bladder, where it is stored until it is passed from the body through the urethra. NCIT:C54419 @@ -56228,14 +50225,14 @@ For example, A and B may be gene products and binding of B by A positively regul renal pelvis/ureter - + - + NCIT @@ -56253,7 +50250,6 @@ For example, A and B may be gene products and binding of B by A positively regul Any of the smallest blood vessels where blood circulates within organ tissues. Microvessels include terminal arterioles, metarterioles, capillaries, and venules (but exclude lymphatic capillaries). Arterioles carry oxygenated blood to the capillaries, and blood flows out of the capillaries through venules into veins. - microvascular http://orcid.org/0000-0002-2825-0621 microvasculature microvessel @@ -56297,7 +50293,6 @@ For example, A and B may be gene products and binding of B by A positively regul http://orcid.org/0000-0002-6095-8718 2022-05-25T18:21:29Z - BTO:0006338 uberon UBERON:8450002 @@ -56309,14 +50304,6 @@ For example, A and B may be gene products and binding of B by A positively regul An anatomical system that eliminates waste products that arise as a result of metabolic activity. GO:0007588 - - - - BTO:0006338 - - - https://github.com/biopragmatics/biomappings - @@ -56377,7 +50364,6 @@ For example, A and B may be gene products and binding of B by A positively regul - example to be eventually removed example to be eventually removed @@ -56386,9 +50372,7 @@ For example, A and B may be gene products and binding of B by A positively regul - failed exploratory term The term was used in an attempt to structure part of the ontology but in retrospect failed to do a good job - Person:Alan Ruttenberg failed exploratory term @@ -56397,7 +50381,6 @@ For example, A and B may be gene products and binding of B by A positively regul - metadata complete Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. metadata complete @@ -56407,7 +50390,6 @@ For example, A and B may be gene products and binding of B by A positively regul - organizational term Term created to ease viewing/sort terms for development purpose, and will not be included in a release organizational term @@ -56417,7 +50399,6 @@ For example, A and B may be gene products and binding of B by A positively regul - ready for release Class has undergone final review, is ready for use, and will be included in the next release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release @@ -56427,7 +50408,6 @@ For example, A and B may be gene products and binding of B by A positively regul - metadata incomplete Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete @@ -56437,7 +50417,6 @@ For example, A and B may be gene products and binding of B by A positively regul - uncurated Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated @@ -56447,7 +50426,6 @@ For example, A and B may be gene products and binding of B by A positively regul - pending final vetting All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the term editor. pending final vetting @@ -56457,7 +50435,6 @@ For example, A and B may be gene products and binding of B by A positively regul - placeholder removed placeholder removed @@ -56466,7 +50443,6 @@ For example, A and B may be gene products and binding of B by A positively regul - terms merged An editor note should explain what were the merged terms and the reason for the merge. terms merged @@ -56476,7 +50452,6 @@ For example, A and B may be gene products and binding of B by A positively regul - term imported This is to be used when the original term has been replaced by a term imported from an other ontology. An editor note should indicate what is the URI of the new term to use. term imported @@ -56486,7 +50461,6 @@ For example, A and B may be gene products and binding of B by A positively regul - term split This is to be used when a term has been split in two or more new terms. An editor note should indicate the reason for the split and indicate the URIs of the new terms created. term split @@ -56496,10 +50470,7 @@ For example, A and B may be gene products and binding of B by A positively regul - universal Hard to give a definition for. Intuitively a "natural kind" rather than a collection of any old things, which a class is able to be, formally. At the meta level, universals are defined as positives, are disjoint with their siblings, have single asserted parents. - Alan Ruttenberg - A Formal Theory of Substances, Qualities, and Universals, http://ontology.buffalo.edu/bfo/SQU.pdf universal @@ -56508,10 +50479,8 @@ For example, A and B may be gene products and binding of B by A positively regul - defined class A defined class is a class that is defined by a set of logically necessary and sufficient conditions but is not a universal "definitions", in some readings, always are given by necessary and sufficient conditions. So one must be careful (and this is difficult sometimes) to distinguish between defined classes and universal. - Alan Ruttenberg defined class @@ -56520,10 +50489,8 @@ For example, A and B may be gene products and binding of B by A positively regul - named class expression A named class expression is a logical expression that is given a name. The name can be used in place of the expression. named class expressions are used in order to have more concise logical definition but their extensions may not be interesting classes on their own. In languages such as OWL, with no provisions for macros, these show up as actuall classes. Tools may with to not show them as such, and to replace uses of the macros with their expansions - Alan Ruttenberg named class expression @@ -56532,10 +50499,7 @@ For example, A and B may be gene products and binding of B by A positively regul - to be replaced with external ontology term Terms with this status should eventually replaced with a term from another ontology. - Alan Ruttenberg - group:OBI to be replaced with external ontology term @@ -56544,10 +50508,7 @@ For example, A and B may be gene products and binding of B by A positively regul - requires discussion A term that is metadata complete, has been reviewed, and problems have been identified that require discussion before release. Such a term requires editor note(s) to identify the outstanding issues. - Alan Ruttenberg - group:OBI requires discussion @@ -56558,9 +50519,7 @@ For example, A and B may be gene products and binding of B by A positively regul The term was added to the ontology on the assumption it was in scope, but it turned out later that it was not. This obsolesence reason should be used conservatively. Typical valid examples are: un-necessary grouping classes in disease ontologies, a phenotype term added on the assumption it was a disease. - https://github.com/information-artifact-ontology/ontology-metadata/issues/77 - https://orcid.org/0000-0001-5208-3432 out of scope @@ -56574,24 +50533,6 @@ For example, A and B may be gene products and binding of B by A positively regul /////////////////////////////////////////////////////////////////////////////////////// --> - - - - - - - - - - - - - - - - - - @@ -56643,46 +50584,34 @@ For example, A and B may be gene products and binding of B by A positively regul /////////////////////////////////////////////////////////////////////////////////////// --> - - - - - - - - - - - - - + - + - + - + - + - + - + - + - + - + @@ -56709,8 +50638,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -56720,7 +50649,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -56730,7 +50659,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + @@ -56747,67 +50676,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - - - - - - - - - true - GP(X)-enables->MF(Y)-part_of->BP(Z) => GP(X) involved_in BP(Z) e.g. if X enables 'protein kinase activity' and Y 'part of' 'signal tranduction' then X involved in 'signal transduction' - involved in BP - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + @@ -56825,8 +50695,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -56836,8 +50706,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -56847,8 +50717,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -56865,8 +50735,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -56883,8 +50753,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -56894,8 +50764,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -56905,8 +50775,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -56923,8 +50793,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -56941,8 +50811,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -56952,8 +50822,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -56963,8 +50833,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -56981,8 +50851,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -56999,8 +50869,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -57010,8 +50880,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -57026,8 +50896,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -57044,8 +50914,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -57055,8 +50925,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -57071,8 +50941,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -57089,8 +50959,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -57100,8 +50970,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -57116,8 +50986,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -57134,8 +51004,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -57145,8 +51015,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -57161,8 +51031,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -57179,8 +51049,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -57190,8 +51060,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -57206,8 +51076,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -57267,8 +51137,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -57278,8 +51148,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -57294,8 +51164,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -57310,9 +51180,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + @@ -57322,8 +51192,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -57337,9 +51207,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + @@ -57354,9 +51224,9 @@ For example, A and B may be gene products and binding of B by A positively regul - - - + + + @@ -57366,8 +51236,8 @@ For example, A and B may be gene products and binding of B by A positively regul - - + + @@ -57381,7 +51251,7 @@ For example, A and B may be gene products and binding of B by A positively regul - + diff --git a/subsets/kidney_upper_slim.tsv b/subsets/kidney_upper_slim.tsv index 134b85af5..b82848970 100644 --- a/subsets/kidney_upper_slim.tsv +++ b/subsets/kidney_upper_slim.tsv @@ -1,373 +1,367 @@ ?x ?label -_:Be350484aX2D0263X2D4acdX2Da142X2D4091eb1e8e26genid1000 -_:Be350484aX2D0263X2D4acdX2Da142X2D4091eb1e8e26genid1011 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